diff --git a/src/ASPHERE/compute_erotate_asphere.cpp b/src/ASPHERE/compute_erotate_asphere.cpp
index a18b62c1f142b813fb7af82658434ee13452bebd..5a8538567510d5d6b72d4e7ec0ec0770dc9c763a 100644
--- a/src/ASPHERE/compute_erotate_asphere.cpp
+++ b/src/ASPHERE/compute_erotate_asphere.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -41,9 +41,9 @@ ComputeERotateAsphere(LAMMPS *lmp, int narg, char **arg) :
avec_ellipsoid = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
avec_line = (AtomVecLine *) atom->style_match("line");
avec_tri = (AtomVecTri *) atom->style_match("tri");
- if (!avec_ellipsoid && !avec_line && !avec_tri)
+ if (!avec_ellipsoid && !avec_line && !avec_tri)
error->all(FLERR,"Compute erotate/asphere requires "
- "atom style ellipsoid or line or tri");
+ "atom style ellipsoid or line or tri");
}
/* ---------------------------------------------------------------------- */
@@ -67,7 +67,7 @@ void ComputeERotateAsphere::init()
if (line && line[i] >= 0) flag = 1;
if (tri && tri[i] >= 0) flag = 1;
if (!flag)
- error->one(FLERR,"Compute erotate/asphere requires extended particles");
+ error->one(FLERR,"Compute erotate/asphere requires extended particles");
}
pfactor = 0.5 * force->mvv2e;
@@ -106,53 +106,53 @@ double ComputeERotateAsphere::compute_scalar()
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (ellipsoid && ellipsoid[i] >= 0) {
- shape = ebonus[ellipsoid[i]].shape;
- quat = ebonus[ellipsoid[i]].quat;
-
- // principal moments of inertia
-
- inertia[0] = rmass[i] * (shape[1]*shape[1]+shape[2]*shape[2]) / 5.0;
- inertia[1] = rmass[i] * (shape[0]*shape[0]+shape[2]*shape[2]) / 5.0;
- inertia[2] = rmass[i] * (shape[0]*shape[0]+shape[1]*shape[1]) / 5.0;
-
- // wbody = angular velocity in body frame
-
- MathExtra::quat_to_mat(quat,rot);
- MathExtra::transpose_matvec(rot,angmom[i],wbody);
- wbody[0] /= inertia[0];
- wbody[1] /= inertia[1];
- wbody[2] /= inertia[2];
-
- erotate += inertia[0]*wbody[0]*wbody[0] +
- inertia[1]*wbody[1]*wbody[1] + inertia[2]*wbody[2]*wbody[2];
+ shape = ebonus[ellipsoid[i]].shape;
+ quat = ebonus[ellipsoid[i]].quat;
+
+ // principal moments of inertia
+
+ inertia[0] = rmass[i] * (shape[1]*shape[1]+shape[2]*shape[2]) / 5.0;
+ inertia[1] = rmass[i] * (shape[0]*shape[0]+shape[2]*shape[2]) / 5.0;
+ inertia[2] = rmass[i] * (shape[0]*shape[0]+shape[1]*shape[1]) / 5.0;
+
+ // wbody = angular velocity in body frame
+
+ MathExtra::quat_to_mat(quat,rot);
+ MathExtra::transpose_matvec(rot,angmom[i],wbody);
+ wbody[0] /= inertia[0];
+ wbody[1] /= inertia[1];
+ wbody[2] /= inertia[2];
+
+ erotate += inertia[0]*wbody[0]*wbody[0] +
+ inertia[1]*wbody[1]*wbody[1] + inertia[2]*wbody[2]*wbody[2];
} else if (line && line[i] >= 0) {
- length = lbonus[line[i]].length;
+ length = lbonus[line[i]].length;
- erotate += (omega[i][0]*omega[i][0] + omega[i][1]*omega[i][1] +
- omega[i][2]*omega[i][2]) * length*length*rmass[i] / 12.0;
+ erotate += (omega[i][0]*omega[i][0] + omega[i][1]*omega[i][1] +
+ omega[i][2]*omega[i][2]) * length*length*rmass[i] / 12.0;
} else if (tri && tri[i] >= 0) {
- // principal moments of inertia
-
- inertia[0] = tbonus[tri[i]].inertia[0];
- inertia[1] = tbonus[tri[i]].inertia[1];
- inertia[2] = tbonus[tri[i]].inertia[2];
-
- // wbody = angular velocity in body frame
-
- MathExtra::quat_to_mat(tbonus[tri[i]].quat,rot);
- MathExtra::transpose_matvec(rot,angmom[i],wbody);
- wbody[0] /= inertia[0];
- wbody[1] /= inertia[1];
- wbody[2] /= inertia[2];
-
- erotate += inertia[0]*wbody[0]*wbody[0] +
- inertia[1]*wbody[1]*wbody[1] + inertia[2]*wbody[2]*wbody[2];
+ // principal moments of inertia
+
+ inertia[0] = tbonus[tri[i]].inertia[0];
+ inertia[1] = tbonus[tri[i]].inertia[1];
+ inertia[2] = tbonus[tri[i]].inertia[2];
+
+ // wbody = angular velocity in body frame
+
+ MathExtra::quat_to_mat(tbonus[tri[i]].quat,rot);
+ MathExtra::transpose_matvec(rot,angmom[i],wbody);
+ wbody[0] /= inertia[0];
+ wbody[1] /= inertia[1];
+ wbody[2] /= inertia[2];
+
+ erotate += inertia[0]*wbody[0]*wbody[0] +
+ inertia[1]*wbody[1]*wbody[1] + inertia[2]*wbody[2]*wbody[2];
}
}
-
+
MPI_Allreduce(&erotate,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
scalar *= pfactor;
return scalar;
diff --git a/src/ASPHERE/compute_erotate_asphere.h b/src/ASPHERE/compute_erotate_asphere.h
index e29d15ec244d7b8f09077a03f605f95fc2389729..9318c46323f959e886b726e379d5795062731c6e 100644
--- a/src/ASPHERE/compute_erotate_asphere.h
+++ b/src/ASPHERE/compute_erotate_asphere.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/ASPHERE/compute_temp_asphere.cpp b/src/ASPHERE/compute_temp_asphere.cpp
index 69139369cf2a7e62e45ac403705f8216e8b0ad82..1df8fef86766d68e23d2f58a03b3c62e78568706 100755
--- a/src/ASPHERE/compute_temp_asphere.cpp
+++ b/src/ASPHERE/compute_temp_asphere.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -76,7 +76,7 @@ ComputeTempAsphere::ComputeTempAsphere(LAMMPS *lmp, int narg, char **arg) :
// error check
avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
- if (!avec)
+ if (!avec)
error->all(FLERR,"Compute temp/asphere requires atom style ellipsoid");
}
@@ -101,7 +101,7 @@ void ComputeTempAsphere::init()
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (ellipsoid[i] < 0)
- error->one(FLERR,"Compute temp/asphere requires extended particles");
+ error->one(FLERR,"Compute temp/asphere requires extended particles");
if (tempbias) {
int i = modify->find_compute(id_bias);
@@ -154,7 +154,7 @@ void ComputeTempAsphere::dof_compute()
int count = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
- if (tbias->dof_remove(i)) count++;
+ if (tbias->dof_remove(i)) count++;
int count_all;
MPI_Allreduce(&count,&count_all,1,MPI_INT,MPI_SUM,world);
dof -= nper*count_all;
@@ -187,7 +187,7 @@ double ComputeTempAsphere::compute_scalar()
double *shape,*quat;
double wbody[3],inertia[3];
double rot[3][3];
-
+
// sum translational and rotational energy for each particle
// no point particles since divide by inertia
@@ -196,52 +196,52 @@ double ComputeTempAsphere::compute_scalar()
if (mode == ALL) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) * rmass[i];
-
- // principal moments of inertia
-
- shape = bonus[ellipsoid[i]].shape;
- quat = bonus[ellipsoid[i]].quat;
-
- inertia[0] = INERTIA*rmass[i] * (shape[1]*shape[1]+shape[2]*shape[2]);
- inertia[1] = INERTIA*rmass[i] * (shape[0]*shape[0]+shape[2]*shape[2]);
- inertia[2] = INERTIA*rmass[i] * (shape[0]*shape[0]+shape[1]*shape[1]);
-
- // wbody = angular velocity in body frame
-
- MathExtra::quat_to_mat(quat,rot);
- MathExtra::transpose_matvec(rot,angmom[i],wbody);
- wbody[0] /= inertia[0];
- wbody[1] /= inertia[1];
- wbody[2] /= inertia[2];
-
- t += inertia[0]*wbody[0]*wbody[0] +
- inertia[1]*wbody[1]*wbody[1] + inertia[2]*wbody[2]*wbody[2];
+ t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) * rmass[i];
+
+ // principal moments of inertia
+
+ shape = bonus[ellipsoid[i]].shape;
+ quat = bonus[ellipsoid[i]].quat;
+
+ inertia[0] = INERTIA*rmass[i] * (shape[1]*shape[1]+shape[2]*shape[2]);
+ inertia[1] = INERTIA*rmass[i] * (shape[0]*shape[0]+shape[2]*shape[2]);
+ inertia[2] = INERTIA*rmass[i] * (shape[0]*shape[0]+shape[1]*shape[1]);
+
+ // wbody = angular velocity in body frame
+
+ MathExtra::quat_to_mat(quat,rot);
+ MathExtra::transpose_matvec(rot,angmom[i],wbody);
+ wbody[0] /= inertia[0];
+ wbody[1] /= inertia[1];
+ wbody[2] /= inertia[2];
+
+ t += inertia[0]*wbody[0]*wbody[0] +
+ inertia[1]*wbody[1]*wbody[1] + inertia[2]*wbody[2]*wbody[2];
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- // principal moments of inertia
-
- shape = bonus[ellipsoid[i]].shape;
- quat = bonus[ellipsoid[i]].quat;
-
- inertia[0] = INERTIA*rmass[i] * (shape[1]*shape[1]+shape[2]*shape[2]);
- inertia[1] = INERTIA*rmass[i] * (shape[0]*shape[0]+shape[2]*shape[2]);
- inertia[2] = INERTIA*rmass[i] * (shape[0]*shape[0]+shape[1]*shape[1]);
-
- // wbody = angular velocity in body frame
-
- MathExtra::quat_to_mat(quat,rot);
- MathExtra::transpose_matvec(rot,angmom[i],wbody);
- wbody[0] /= inertia[0];
- wbody[1] /= inertia[1];
- wbody[2] /= inertia[2];
-
- t += inertia[0]*wbody[0]*wbody[0] +
- inertia[1]*wbody[1]*wbody[1] + inertia[2]*wbody[2]*wbody[2];
+ // principal moments of inertia
+
+ shape = bonus[ellipsoid[i]].shape;
+ quat = bonus[ellipsoid[i]].quat;
+
+ inertia[0] = INERTIA*rmass[i] * (shape[1]*shape[1]+shape[2]*shape[2]);
+ inertia[1] = INERTIA*rmass[i] * (shape[0]*shape[0]+shape[2]*shape[2]);
+ inertia[2] = INERTIA*rmass[i] * (shape[0]*shape[0]+shape[1]*shape[1]);
+
+ // wbody = angular velocity in body frame
+
+ MathExtra::quat_to_mat(quat,rot);
+ MathExtra::transpose_matvec(rot,angmom[i],wbody);
+ wbody[0] /= inertia[0];
+ wbody[1] /= inertia[1];
+ wbody[2] /= inertia[2];
+
+ t += inertia[0]*wbody[0]*wbody[0] +
+ inertia[1]*wbody[1]*wbody[1] + inertia[2]*wbody[2]*wbody[2];
}
}
@@ -287,71 +287,71 @@ void ComputeTempAsphere::compute_vector()
if (mode == ALL) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- massone = rmass[i];
- t[0] += massone * v[i][0]*v[i][0];
- t[1] += massone * v[i][1]*v[i][1];
- t[2] += massone * v[i][2]*v[i][2];
- t[3] += massone * v[i][0]*v[i][1];
- t[4] += massone * v[i][0]*v[i][2];
- t[5] += massone * v[i][1]*v[i][2];
-
- // principal moments of inertia
-
- shape = bonus[ellipsoid[i]].shape;
- quat = bonus[ellipsoid[i]].quat;
-
- inertia[0] = INERTIA*massone * (shape[1]*shape[1]+shape[2]*shape[2]);
- inertia[1] = INERTIA*massone * (shape[0]*shape[0]+shape[2]*shape[2]);
- inertia[2] = INERTIA*massone * (shape[0]*shape[0]+shape[1]*shape[1]);
-
- // wbody = angular velocity in body frame
-
- MathExtra::quat_to_mat(quat,rot);
- MathExtra::transpose_matvec(rot,angmom[i],wbody);
- wbody[0] /= inertia[0];
- wbody[1] /= inertia[1];
- wbody[2] /= inertia[2];
-
- // rotational kinetic energy
-
- t[0] += inertia[0]*wbody[0]*wbody[0];
- t[1] += inertia[1]*wbody[1]*wbody[1];
- t[2] += inertia[2]*wbody[2]*wbody[2];
- t[3] += inertia[0]*wbody[0]*wbody[1];
- t[4] += inertia[1]*wbody[0]*wbody[2];
- t[5] += inertia[2]*wbody[1]*wbody[2];
+ massone = rmass[i];
+ t[0] += massone * v[i][0]*v[i][0];
+ t[1] += massone * v[i][1]*v[i][1];
+ t[2] += massone * v[i][2]*v[i][2];
+ t[3] += massone * v[i][0]*v[i][1];
+ t[4] += massone * v[i][0]*v[i][2];
+ t[5] += massone * v[i][1]*v[i][2];
+
+ // principal moments of inertia
+
+ shape = bonus[ellipsoid[i]].shape;
+ quat = bonus[ellipsoid[i]].quat;
+
+ inertia[0] = INERTIA*massone * (shape[1]*shape[1]+shape[2]*shape[2]);
+ inertia[1] = INERTIA*massone * (shape[0]*shape[0]+shape[2]*shape[2]);
+ inertia[2] = INERTIA*massone * (shape[0]*shape[0]+shape[1]*shape[1]);
+
+ // wbody = angular velocity in body frame
+
+ MathExtra::quat_to_mat(quat,rot);
+ MathExtra::transpose_matvec(rot,angmom[i],wbody);
+ wbody[0] /= inertia[0];
+ wbody[1] /= inertia[1];
+ wbody[2] /= inertia[2];
+
+ // rotational kinetic energy
+
+ t[0] += inertia[0]*wbody[0]*wbody[0];
+ t[1] += inertia[1]*wbody[1]*wbody[1];
+ t[2] += inertia[2]*wbody[2]*wbody[2];
+ t[3] += inertia[0]*wbody[0]*wbody[1];
+ t[4] += inertia[1]*wbody[0]*wbody[2];
+ t[5] += inertia[2]*wbody[1]*wbody[2];
}
} else {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
-
- // principal moments of inertia
-
- shape = bonus[ellipsoid[i]].shape;
- quat = bonus[ellipsoid[i]].quat;
- massone = rmass[i];
-
- inertia[0] = INERTIA*massone * (shape[1]*shape[1]+shape[2]*shape[2]);
- inertia[1] = INERTIA*massone * (shape[0]*shape[0]+shape[2]*shape[2]);
- inertia[2] = INERTIA*massone * (shape[0]*shape[0]+shape[1]*shape[1]);
-
- // wbody = angular velocity in body frame
-
- MathExtra::quat_to_mat(quat,rot);
- MathExtra::transpose_matvec(rot,angmom[i],wbody);
- wbody[0] /= inertia[0];
- wbody[1] /= inertia[1];
- wbody[2] /= inertia[2];
-
- // rotational kinetic energy
-
- t[0] += inertia[0]*wbody[0]*wbody[0];
- t[1] += inertia[1]*wbody[1]*wbody[1];
- t[2] += inertia[2]*wbody[2]*wbody[2];
- t[3] += inertia[0]*wbody[0]*wbody[1];
- t[4] += inertia[1]*wbody[0]*wbody[2];
- t[5] += inertia[2]*wbody[1]*wbody[2];
+
+ // principal moments of inertia
+
+ shape = bonus[ellipsoid[i]].shape;
+ quat = bonus[ellipsoid[i]].quat;
+ massone = rmass[i];
+
+ inertia[0] = INERTIA*massone * (shape[1]*shape[1]+shape[2]*shape[2]);
+ inertia[1] = INERTIA*massone * (shape[0]*shape[0]+shape[2]*shape[2]);
+ inertia[2] = INERTIA*massone * (shape[0]*shape[0]+shape[1]*shape[1]);
+
+ // wbody = angular velocity in body frame
+
+ MathExtra::quat_to_mat(quat,rot);
+ MathExtra::transpose_matvec(rot,angmom[i],wbody);
+ wbody[0] /= inertia[0];
+ wbody[1] /= inertia[1];
+ wbody[2] /= inertia[2];
+
+ // rotational kinetic energy
+
+ t[0] += inertia[0]*wbody[0]*wbody[0];
+ t[1] += inertia[1]*wbody[1]*wbody[1];
+ t[2] += inertia[2]*wbody[2]*wbody[2];
+ t[3] += inertia[0]*wbody[0]*wbody[1];
+ t[4] += inertia[1]*wbody[0]*wbody[2];
+ t[5] += inertia[2]*wbody[1]*wbody[2];
}
}
diff --git a/src/ASPHERE/compute_temp_asphere.h b/src/ASPHERE/compute_temp_asphere.h
index 715150f5e423faa70fbfc8c82cd4284db0eb981d..ee7e73b435fc7795f27221155ab3806c0fd2041c 100755
--- a/src/ASPHERE/compute_temp_asphere.h
+++ b/src/ASPHERE/compute_temp_asphere.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/ASPHERE/fix_nh_asphere.cpp b/src/ASPHERE/fix_nh_asphere.cpp
index a8290924da543cf015fc5d3a60358abf8fbe9281..476d4a6e5c2c501f5306badacc814de814032eac 100644
--- a/src/ASPHERE/fix_nh_asphere.cpp
+++ b/src/ASPHERE/fix_nh_asphere.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -35,7 +35,7 @@ FixNHAsphere::FixNHAsphere(LAMMPS *lmp, int narg, char **arg) :
FixNH(lmp, narg, arg)
{
avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
- if (!avec)
+ if (!avec)
error->all(FLERR,"Compute nvt/nph/npt asphere requires atom style ellipsoid");
}
@@ -53,7 +53,7 @@ void FixNHAsphere::init()
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (ellipsoid[i] < 0)
- error->one(FLERR,"Fix nvt/nph/npt asphere requires extended particles");
+ error->one(FLERR,"Fix nvt/nph/npt asphere requires extended particles");
FixNH::init();
}
@@ -76,7 +76,7 @@ void FixNHAsphere::nve_v()
// update angular momentum by 1/2 step for all particles
- for (int i = 0; i < nlocal; i++) {
+ for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
angmom[i][0] += dtf*torque[i][0];
angmom[i][1] += dtf*torque[i][1];
@@ -127,7 +127,7 @@ void FixNHAsphere::nve_x()
inertia[0] = rmass[i] * (shape[1]*shape[1]+shape[2]*shape[2]) / 5.0;
inertia[1] = rmass[i] * (shape[0]*shape[0]+shape[2]*shape[2]) / 5.0;
inertia[2] = rmass[i] * (shape[0]*shape[0]+shape[1]*shape[1]) / 5.0;
-
+
// compute omega at 1/2 step from angmom at 1/2 step and current q
// update quaternion a full step via Richardson iteration
// returns new normalized quaternion
@@ -152,7 +152,7 @@ void FixNHAsphere::nh_v_temp()
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
- for (int i = 0; i < nlocal; i++) {
+ for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
angmom[i][0] *= factor_eta;
angmom[i][1] *= factor_eta;
diff --git a/src/ASPHERE/fix_nh_asphere.h b/src/ASPHERE/fix_nh_asphere.h
index 5c98e412ce8df0e27fb396e840e0cf4de22c597d..8f01b2538f5287fb7e1a3b98e89f2271b9ab06a0 100644
--- a/src/ASPHERE/fix_nh_asphere.h
+++ b/src/ASPHERE/fix_nh_asphere.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/ASPHERE/fix_nph_asphere.cpp b/src/ASPHERE/fix_nph_asphere.cpp
index 76a3495693feb804a408f8fffaa5cb11bfc7ee06..a1a113a33713a58c32a99afce3a28d606eef918d 100644
--- a/src/ASPHERE/fix_nph_asphere.cpp
+++ b/src/ASPHERE/fix_nph_asphere.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -38,7 +38,7 @@ FixNPHAsphere::FixNPHAsphere(LAMMPS *lmp, int narg, char **arg) :
id_temp = new char[n];
strcpy(id_temp,id);
strcat(id_temp,"_temp");
-
+
char **newarg = new char*[3];
newarg[0] = id_temp;
newarg[1] = (char *) "all";
@@ -56,7 +56,7 @@ FixNPHAsphere::FixNPHAsphere(LAMMPS *lmp, int narg, char **arg) :
id_press = new char[n];
strcpy(id_press,id);
strcat(id_press,"_press");
-
+
newarg = new char*[4];
newarg[0] = id_press;
newarg[1] = (char *) "all";
diff --git a/src/ASPHERE/fix_nph_asphere.h b/src/ASPHERE/fix_nph_asphere.h
index 7dfd992269cfd9393ed4506acf8adf349c9490fc..91f36b45c3a2a281a7b80f5cb3fc69476b0a843b 100644
--- a/src/ASPHERE/fix_nph_asphere.h
+++ b/src/ASPHERE/fix_nph_asphere.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/ASPHERE/fix_npt_asphere.cpp b/src/ASPHERE/fix_npt_asphere.cpp
index 6296302e677b9b38810f8f08630539cbeca99e06..dab72dc29fe3767ee8022ff11c363f496a93c682 100755
--- a/src/ASPHERE/fix_npt_asphere.cpp
+++ b/src/ASPHERE/fix_npt_asphere.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -38,7 +38,7 @@ FixNPTAsphere::FixNPTAsphere(LAMMPS *lmp, int narg, char **arg) :
id_temp = new char[n];
strcpy(id_temp,id);
strcat(id_temp,"_temp");
-
+
char **newarg = new char*[3];
newarg[0] = id_temp;
newarg[1] = (char *) "all";
@@ -56,7 +56,7 @@ FixNPTAsphere::FixNPTAsphere(LAMMPS *lmp, int narg, char **arg) :
id_press = new char[n];
strcpy(id_press,id);
strcat(id_press,"_press");
-
+
newarg = new char*[4];
newarg[0] = id_press;
newarg[1] = (char *) "all";
diff --git a/src/ASPHERE/fix_npt_asphere.h b/src/ASPHERE/fix_npt_asphere.h
index 1b874928e6b0bb4d169fb2b4f0955850f263fc21..b6e93993f254b43bea5b1e408d637d1b2b86723e 100755
--- a/src/ASPHERE/fix_npt_asphere.h
+++ b/src/ASPHERE/fix_npt_asphere.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/ASPHERE/fix_nve_asphere.cpp b/src/ASPHERE/fix_nve_asphere.cpp
index 6504219245ff38bf10d2af4aa42bafca2c2aaf75..1590e1f20e59ede790dd1e0bd67d0766bd328dce 100755
--- a/src/ASPHERE/fix_nve_asphere.cpp
+++ b/src/ASPHERE/fix_nve_asphere.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -34,11 +34,11 @@ using namespace FixConst;
/* ---------------------------------------------------------------------- */
-FixNVEAsphere::FixNVEAsphere(LAMMPS *lmp, int narg, char **arg) :
+FixNVEAsphere::FixNVEAsphere(LAMMPS *lmp, int narg, char **arg) :
FixNVE(lmp, narg, arg)
{
avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
- if (!avec)
+ if (!avec)
error->all(FLERR,"Compute nve/asphere requires atom style ellipsoid");
}
@@ -56,7 +56,7 @@ void FixNVEAsphere::init()
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (ellipsoid[i] < 0)
- error->one(FLERR,"Fix nve/asphere requires extended particles");
+ error->one(FLERR,"Fix nve/asphere requires extended particles");
FixNVE::init();
}
@@ -96,7 +96,7 @@ void FixNVEAsphere::initial_integrate(int vflag)
x[i][2] += dtv * v[i][2];
// update angular momentum by 1/2 step
-
+
angmom[i][0] += dtf * torque[i][0];
angmom[i][1] += dtf * torque[i][1];
angmom[i][2] += dtf * torque[i][2];
@@ -140,7 +140,7 @@ void FixNVEAsphere::final_integrate()
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
-
+
angmom[i][0] += dtf * torque[i][0];
angmom[i][1] += dtf * torque[i][1];
angmom[i][2] += dtf * torque[i][2];
diff --git a/src/ASPHERE/fix_nve_asphere.h b/src/ASPHERE/fix_nve_asphere.h
index fe6334fd1f1383904e536c5dc3d517df46cb0514..1af989520707ba400709b3ea38bcba96aafdaba6 100755
--- a/src/ASPHERE/fix_nve_asphere.h
+++ b/src/ASPHERE/fix_nve_asphere.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/ASPHERE/fix_nve_asphere_noforce.cpp b/src/ASPHERE/fix_nve_asphere_noforce.cpp
index 2fb8bd98ef4711dedc27d2f94e14641f9ffc625e..8ce195f12041d634345dbf1888054e10fb98f861 100644
--- a/src/ASPHERE/fix_nve_asphere_noforce.cpp
+++ b/src/ASPHERE/fix_nve_asphere_noforce.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -38,7 +38,7 @@ FixNVEAsphereNoforce::FixNVEAsphereNoforce(LAMMPS *lmp, int narg, char **arg) :
// error check
avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
- if (!atom->ellipsoid_flag)
+ if (!atom->ellipsoid_flag)
error->all(FLERR,"Fix nve/asphere/noforce requires atom style ellipsoid");
}
@@ -59,7 +59,7 @@ void FixNVEAsphereNoforce::init()
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (ellipsoid[i] < 0)
- error->one(FLERR,"Fix nve/asphere/noforce requires extended particles");
+ error->one(FLERR,"Fix nve/asphere/noforce requires extended particles");
}
/* ---------------------------------------------------------------------- */
@@ -94,15 +94,15 @@ void FixNVEAsphereNoforce::initial_integrate(int vflag)
shape = bonus[ellipsoid[i]].shape;
quat = bonus[ellipsoid[i]].quat;
-
+
inertia[0] = rmass[i] * (shape[1]*shape[1]+shape[2]*shape[2]) / 5.0;
inertia[1] = rmass[i] * (shape[0]*shape[0]+shape[2]*shape[2]) / 5.0;
inertia[2] = rmass[i] * (shape[0]*shape[0]+shape[1]*shape[1]) / 5.0;
-
+
// compute omega at 1/2 step from angmom at 1/2 step and current q
// update quaternion a full step via Richardson iteration
// returns new normalized quaternion
-
+
MathExtra::mq_to_omega(angmom[i],quat,inertia,omega);
MathExtra::richardson(quat,angmom[i],omega,inertia,dtq);
}
diff --git a/src/ASPHERE/fix_nve_asphere_noforce.h b/src/ASPHERE/fix_nve_asphere_noforce.h
index 6e0209d722f77fb6f11a28664e1056bf8a0efe99..b3d306b1ec03ec2489a393cc92b9e664dde3f021 100755
--- a/src/ASPHERE/fix_nve_asphere_noforce.h
+++ b/src/ASPHERE/fix_nve_asphere_noforce.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -29,7 +29,7 @@ class FixNVEAsphereNoforce : public FixNVENoforce {
FixNVEAsphereNoforce(class LAMMPS *, int, char **);
void initial_integrate(int);
void init();
-
+
private:
double dtq;
class AtomVecEllipsoid *avec;
diff --git a/src/ASPHERE/fix_nve_line.cpp b/src/ASPHERE/fix_nve_line.cpp
index 5f022db24ab29301e75ed68e396cb331d4210d44..1350713acf8dcd749f181d2a94134864c9bb34e0 100644
--- a/src/ASPHERE/fix_nve_line.cpp
+++ b/src/ASPHERE/fix_nve_line.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -155,7 +155,7 @@ void FixNVELine::final_integrate()
dtfm = dtf / rmass[i];
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
-
+
length = bonus[line[i]].length;
dtirotate = dtfrotate / (length*length*rmass[i]);
omega[i][2] += dtirotate * torque[i][2];
diff --git a/src/ASPHERE/fix_nve_line.h b/src/ASPHERE/fix_nve_line.h
index 2a2e957be2acb3cfef0639d7c3691c8dee5cf2c5..00b3f57f9e8ed804f2592630d4fc88d106e52c9b 100644
--- a/src/ASPHERE/fix_nve_line.h
+++ b/src/ASPHERE/fix_nve_line.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/ASPHERE/fix_nve_tri.cpp b/src/ASPHERE/fix_nve_tri.cpp
index 9048f89269eaf32635298fac33514856d92d2785..eb901273464b2917a3b3f555845bd82e6b892fd1 100644
--- a/src/ASPHERE/fix_nve_tri.cpp
+++ b/src/ASPHERE/fix_nve_tri.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -109,7 +109,7 @@ void FixNVETri::initial_integrate(int vflag)
x[i][2] += dtv * v[i][2];
// update angular momentum by 1/2 step
-
+
angmom[i][0] += dtf * torque[i][0];
angmom[i][1] += dtf * torque[i][1];
angmom[i][2] += dtf * torque[i][2];
@@ -119,9 +119,9 @@ void FixNVETri::initial_integrate(int vflag)
// returns new normalized quaternion
MathExtra::mq_to_omega(angmom[i],bonus[tri[i]].quat,
- bonus[tri[i]].inertia,omega);
+ bonus[tri[i]].inertia,omega);
MathExtra::richardson(bonus[tri[i]].quat,angmom[i],omega,
- bonus[tri[i]].inertia,dtq);
+ bonus[tri[i]].inertia,dtq);
}
}
@@ -149,7 +149,7 @@ void FixNVETri::final_integrate()
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
-
+
angmom[i][0] += dtf * torque[i][0];
angmom[i][1] += dtf * torque[i][1];
angmom[i][2] += dtf * torque[i][2];
diff --git a/src/ASPHERE/fix_nve_tri.h b/src/ASPHERE/fix_nve_tri.h
index a3877a938fcfef9b8199f2fdd49fb0f74ad12e5d..bf533662e093a33d3882fd8b97c90730adf24f07 100644
--- a/src/ASPHERE/fix_nve_tri.h
+++ b/src/ASPHERE/fix_nve_tri.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/ASPHERE/fix_nvt_asphere.cpp b/src/ASPHERE/fix_nvt_asphere.cpp
index 4ec80141c0b7f73274ff61e48d6090d172015fb3..796bbdf40cafd60a3640bd57b25e19e92315fda0 100755
--- a/src/ASPHERE/fix_nvt_asphere.cpp
+++ b/src/ASPHERE/fix_nvt_asphere.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -37,7 +37,7 @@ FixNVTAsphere::FixNVTAsphere(LAMMPS *lmp, int narg, char **arg) :
id_temp = new char[n];
strcpy(id_temp,id);
strcat(id_temp,"_temp");
-
+
char **newarg = new char*[3];
newarg[0] = id_temp;
newarg[1] = group->names[igroup];
diff --git a/src/ASPHERE/fix_nvt_asphere.h b/src/ASPHERE/fix_nvt_asphere.h
index 223c073ec10dc0707477a4530de688d1174960ff..e12f596413fc90106e0beceda1a4d9cde54f5966 100755
--- a/src/ASPHERE/fix_nvt_asphere.h
+++ b/src/ASPHERE/fix_nvt_asphere.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/ASPHERE/pair_gayberne.cpp b/src/ASPHERE/pair_gayberne.cpp
index e3ad48491bd98c082a8e04aca0d6d9776033c296..3af5e5994d0fea670c2c889430071ecd34293cbc 100755
--- a/src/ASPHERE/pair_gayberne.cpp
+++ b/src/ASPHERE/pair_gayberne.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -99,7 +99,7 @@ void PairGayBerne::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@@ -135,81 +135,81 @@ void PairGayBerne::compute(int eflag, int vflag)
if (rsq < cutsq[itype][jtype]) {
- switch (form[itype][jtype]) {
- case SPHERE_SPHERE:
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- forcelj *= -r2inv;
- if (eflag) one_eng =
- r6inv*(r6inv*lj3[itype][jtype]-lj4[itype][jtype]) -
- offset[itype][jtype];
- fforce[0] = r12[0]*forcelj;
- fforce[1] = r12[1]*forcelj;
- fforce[2] = r12[2]*forcelj;
- ttor[0] = ttor[1] = ttor[2] = 0.0;
- rtor[0] = rtor[1] = rtor[2] = 0.0;
- break;
+ switch (form[itype][jtype]) {
+ case SPHERE_SPHERE:
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ forcelj *= -r2inv;
+ if (eflag) one_eng =
+ r6inv*(r6inv*lj3[itype][jtype]-lj4[itype][jtype]) -
+ offset[itype][jtype];
+ fforce[0] = r12[0]*forcelj;
+ fforce[1] = r12[1]*forcelj;
+ fforce[2] = r12[2]*forcelj;
+ ttor[0] = ttor[1] = ttor[2] = 0.0;
+ rtor[0] = rtor[1] = rtor[2] = 0.0;
+ break;
case SPHERE_ELLIPSE:
- jquat = bonus[ellipsoid[j]].quat;
- MathExtra::quat_to_mat_trans(jquat,a2);
- MathExtra::diag_times3(well[jtype],a2,temp);
- MathExtra::transpose_times3(a2,temp,b2);
- MathExtra::diag_times3(shape2[jtype],a2,temp);
- MathExtra::transpose_times3(a2,temp,g2);
- one_eng = gayberne_lj(j,i,a2,b2,g2,r12,rsq,fforce,rtor);
- ttor[0] = ttor[1] = ttor[2] = 0.0;
- break;
+ jquat = bonus[ellipsoid[j]].quat;
+ MathExtra::quat_to_mat_trans(jquat,a2);
+ MathExtra::diag_times3(well[jtype],a2,temp);
+ MathExtra::transpose_times3(a2,temp,b2);
+ MathExtra::diag_times3(shape2[jtype],a2,temp);
+ MathExtra::transpose_times3(a2,temp,g2);
+ one_eng = gayberne_lj(j,i,a2,b2,g2,r12,rsq,fforce,rtor);
+ ttor[0] = ttor[1] = ttor[2] = 0.0;
+ break;
case ELLIPSE_SPHERE:
- one_eng = gayberne_lj(i,j,a1,b1,g1,r12,rsq,fforce,ttor);
- rtor[0] = rtor[1] = rtor[2] = 0.0;
- break;
-
- default:
- jquat = bonus[ellipsoid[j]].quat;
- MathExtra::quat_to_mat_trans(jquat,a2);
- MathExtra::diag_times3(well[jtype],a2,temp);
- MathExtra::transpose_times3(a2,temp,b2);
- MathExtra::diag_times3(shape2[jtype],a2,temp);
- MathExtra::transpose_times3(a2,temp,g2);
- one_eng = gayberne_analytic(i,j,a1,a2,b1,b2,g1,g2,r12,rsq,
- fforce,ttor,rtor);
- break;
- }
+ one_eng = gayberne_lj(i,j,a1,b1,g1,r12,rsq,fforce,ttor);
+ rtor[0] = rtor[1] = rtor[2] = 0.0;
+ break;
+
+ default:
+ jquat = bonus[ellipsoid[j]].quat;
+ MathExtra::quat_to_mat_trans(jquat,a2);
+ MathExtra::diag_times3(well[jtype],a2,temp);
+ MathExtra::transpose_times3(a2,temp,b2);
+ MathExtra::diag_times3(shape2[jtype],a2,temp);
+ MathExtra::transpose_times3(a2,temp,g2);
+ one_eng = gayberne_analytic(i,j,a1,a2,b1,b2,g1,g2,r12,rsq,
+ fforce,ttor,rtor);
+ break;
+ }
fforce[0] *= factor_lj;
- fforce[1] *= factor_lj;
- fforce[2] *= factor_lj;
+ fforce[1] *= factor_lj;
+ fforce[2] *= factor_lj;
ttor[0] *= factor_lj;
- ttor[1] *= factor_lj;
- ttor[2] *= factor_lj;
+ ttor[1] *= factor_lj;
+ ttor[2] *= factor_lj;
f[i][0] += fforce[0];
- f[i][1] += fforce[1];
- f[i][2] += fforce[2];
+ f[i][1] += fforce[1];
+ f[i][2] += fforce[2];
tor[i][0] += ttor[0];
- tor[i][1] += ttor[1];
- tor[i][2] += ttor[2];
+ tor[i][1] += ttor[1];
+ tor[i][2] += ttor[2];
if (newton_pair || j < nlocal) {
rtor[0] *= factor_lj;
- rtor[1] *= factor_lj;
- rtor[2] *= factor_lj;
+ rtor[1] *= factor_lj;
+ rtor[2] *= factor_lj;
f[j][0] -= fforce[0];
- f[j][1] -= fforce[1];
- f[j][2] -= fforce[2];
+ f[j][1] -= fforce[1];
+ f[j][2] -= fforce[2];
tor[j][0] += rtor[0];
- tor[j][1] += rtor[1];
- tor[j][2] += rtor[2];
+ tor[j][1] += rtor[1];
+ tor[j][2] += rtor[2];
}
if (eflag) evdwl = factor_lj*one_eng;
- if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,
- evdwl,0.0,fforce[0],fforce[1],fforce[2],
- -r12[0],-r12[1],-r12[2]);
+ if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,
+ evdwl,0.0,fforce[0],fforce[1],fforce[2],
+ -r12[0],-r12[1],-r12[2]);
}
}
}
@@ -263,14 +263,14 @@ void PairGayBerne::settings(int narg, char **arg)
upsilon = force->numeric(arg[1])/2.0;
mu = force->numeric(arg[2]);
cut_global = force->numeric(arg[3]);
-
+
// reset cutoffs that have been explicitly set
if (allocated) {
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
- if (setflag[i][j]) cut[i][j] = cut_global;
+ if (setflag[i][j]) cut[i][j] = cut_global;
}
}
@@ -296,7 +296,7 @@ void PairGayBerne::coeff(int narg, char **arg)
double eja_one = force->numeric(arg[7]);
double ejb_one = force->numeric(arg[8]);
double ejc_one = force->numeric(arg[9]);
-
+
double cut_one = cut_global;
if (narg == 11) cut_one = force->numeric(arg[10]);
@@ -307,18 +307,18 @@ void PairGayBerne::coeff(int narg, char **arg)
sigma[i][j] = sigma_one;
cut[i][j] = cut_one;
if (eia_one != 0.0 || eib_one != 0.0 || eic_one != 0.0) {
- well[i][0] = pow(eia_one,-1.0/mu);
+ well[i][0] = pow(eia_one,-1.0/mu);
well[i][1] = pow(eib_one,-1.0/mu);
- well[i][2] = pow(eic_one,-1.0/mu);
- if (eia_one == eib_one && eib_one == eic_one) setwell[i] = 2;
- else setwell[i] = 1;
+ well[i][2] = pow(eic_one,-1.0/mu);
+ if (eia_one == eib_one && eib_one == eic_one) setwell[i] = 2;
+ else setwell[i] = 1;
}
if (eja_one != 0.0 || ejb_one != 0.0 || ejc_one != 0.0) {
- well[j][0] = pow(eja_one,-1.0/mu);
+ well[j][0] = pow(eja_one,-1.0/mu);
well[j][1] = pow(ejb_one,-1.0/mu);
- well[j][2] = pow(ejc_one,-1.0/mu);
- if (eja_one == ejb_one && ejb_one == ejc_one) setwell[j] = 2;
- else setwell[j] = 1;
+ well[j][2] = pow(ejc_one,-1.0/mu);
+ if (eja_one == ejb_one && ejb_one == ejc_one) setwell[j] = 2;
+ else setwell[j] = 1;
}
setflag[i][j] = 1;
count++;
@@ -349,7 +349,7 @@ void PairGayBerne::init_style()
shape2[i][0] = shape1[i][0]*shape1[i][0];
shape2[i][1] = shape1[i][1]*shape1[i][1];
shape2[i][2] = shape1[i][2]*shape1[i][2];
- lshape[i] = (shape1[i][0]*shape1[i][1]+shape1[i][2]*shape1[i][2]) *
+ lshape[i] = (shape1[i][0]*shape1[i][1]+shape1[i][2]*shape1[i][2]) *
sqrt(shape1[i][0]*shape1[i][1]);
}
}
@@ -365,41 +365,41 @@ double PairGayBerne::init_one(int i, int j)
if (setflag[i][j] == 0) {
epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j],
- sigma[i][i],sigma[j][j]);
+ sigma[i][i],sigma[j][j]);
sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]);
cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
}
-
+
lj1[i][j] = 48.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
lj2[i][j] = 24.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
-
+
if (offset_flag) {
double ratio = sigma[i][j] / cut[i][j];
offset[i][j] = 4.0 * epsilon[i][j] * (pow(ratio,12.0) - pow(ratio,6.0));
} else offset[i][j] = 0.0;
int ishape = 0;
- if (shape1[i][0] != shape1[i][1] ||
- shape1[i][0] != shape1[i][2] ||
+ if (shape1[i][0] != shape1[i][1] ||
+ shape1[i][0] != shape1[i][2] ||
shape1[i][1] != shape1[i][2]) ishape = 1;
if (setwell[i] == 1) ishape = 1;
int jshape = 0;
- if (shape1[j][0] != shape1[j][1] ||
- shape1[j][0] != shape1[j][2] ||
+ if (shape1[j][0] != shape1[j][1] ||
+ shape1[j][0] != shape1[j][2] ||
shape1[j][1] != shape1[j][2]) jshape = 1;
if (setwell[j] == 1) jshape = 1;
-
+
if (ishape == 0 && jshape == 0)
form[i][i] = form[j][j] = form[i][j] = form[j][i] = SPHERE_SPHERE;
else if (ishape == 0) {
form[i][i] = SPHERE_SPHERE; form[j][j] = ELLIPSE_ELLIPSE;
- form[i][j] = SPHERE_ELLIPSE; form[j][i] = ELLIPSE_SPHERE;
+ form[i][j] = SPHERE_ELLIPSE; form[j][i] = ELLIPSE_SPHERE;
} else if (jshape == 0) {
form[j][j] = SPHERE_SPHERE; form[i][i] = ELLIPSE_ELLIPSE;
- form[j][i] = SPHERE_ELLIPSE; form[i][j] = ELLIPSE_SPHERE;
- } else
+ form[j][i] = SPHERE_ELLIPSE; form[i][j] = ELLIPSE_SPHERE;
+ } else
form[i][i] = form[j][j] = form[i][j] = form[j][i] = ELLIPSE_ELLIPSE;
epsilon[j][i] = epsilon[i][j];
@@ -696,9 +696,9 @@ double PairGayBerne::gayberne_analytic(const int i,const int j,double a1[3][3],
------------------------------------------------------------------------- */
double PairGayBerne::gayberne_lj(const int i,const int j,double a1[3][3],
- double b1[3][3],double g1[3][3],
+ double b1[3][3],double g1[3][3],
double *r12,const double rsq,double *fforce,
- double *ttor)
+ double *ttor)
{
double tempv[3], tempv2[3];
double temp[3][3];
@@ -713,9 +713,9 @@ double PairGayBerne::gayberne_lj(const int i,const int j,double a1[3][3],
// compute distance of closest approach
double g12[3][3];
- g12[0][0] = g1[0][0]+shape2[type[j]][0];
- g12[1][1] = g1[1][1]+shape2[type[j]][0];
- g12[2][2] = g1[2][2]+shape2[type[j]][0];
+ g12[0][0] = g1[0][0]+shape2[type[j]][0];
+ g12[1][1] = g1[1][1]+shape2[type[j]][0];
+ g12[2][2] = g1[2][2]+shape2[type[j]][0];
g12[0][1] = g1[0][1]; g12[1][0] = g1[1][0];
g12[0][2] = g1[0][2]; g12[2][0] = g1[2][0];
g12[1][2] = g1[1][2]; g12[2][1] = g1[2][1];
@@ -750,9 +750,9 @@ double PairGayBerne::gayberne_lj(const int i,const int j,double a1[3][3],
double b12[3][3];
double iota[3];
- b12[0][0] = b1[0][0] + well[type[j]][0];
- b12[1][1] = b1[1][1] + well[type[j]][0];
- b12[2][2] = b1[2][2] + well[type[j]][0];
+ b12[0][0] = b1[0][0] + well[type[j]][0];
+ b12[1][1] = b1[1][1] + well[type[j]][0];
+ b12[2][2] = b1[2][2] + well[type[j]][0];
b12[0][1] = b1[0][1]; b12[1][0] = b1[1][0];
b12[0][2] = b1[0][2]; b12[2][0] = b1[2][0];
b12[1][2] = b1[1][2]; b12[2][1] = b1[2][1];
@@ -853,58 +853,58 @@ void PairGayBerne::compute_eta_torque(double m[3][3], double m2[3][3],
double den = m[1][0]*m[0][2]*m[2][1]-m[0][0]*m[1][2]*m[2][1]-
m[0][2]*m[2][0]*m[1][1]+m[0][1]*m[2][0]*m[1][2]-
m[1][0]*m[0][1]*m[2][2]+m[0][0]*m[1][1]*m[2][2];
-
+
ans[0][0] = s[0]*(m[1][2]*m[0][1]*m2[0][2]+2.0*m[1][1]*m[2][2]*m2[0][0]-
- m[1][1]*m2[0][2]*m[0][2]-2.0*m[1][2]*m2[0][0]*m[2][1]+
- m2[0][1]*m[0][2]*m[2][1]-m2[0][1]*m[0][1]*m[2][2]-
- m[1][0]*m[2][2]*m2[0][1]+m[2][0]*m[1][2]*m2[0][1]+
- m[1][0]*m2[0][2]*m[2][1]-m2[0][2]*m[2][0]*m[1][1])/den;
-
+ m[1][1]*m2[0][2]*m[0][2]-2.0*m[1][2]*m2[0][0]*m[2][1]+
+ m2[0][1]*m[0][2]*m[2][1]-m2[0][1]*m[0][1]*m[2][2]-
+ m[1][0]*m[2][2]*m2[0][1]+m[2][0]*m[1][2]*m2[0][1]+
+ m[1][0]*m2[0][2]*m[2][1]-m2[0][2]*m[2][0]*m[1][1])/den;
+
ans[0][1] = s[0]*(m[0][2]*m2[0][0]*m[2][1]-m[2][2]*m2[0][0]*m[0][1]+
- 2.0*m[0][0]*m[2][2]*m2[0][1]-m[0][0]*m2[0][2]*m[1][2]-
- 2.0*m[2][0]*m[0][2]*m2[0][1]+m2[0][2]*m[1][0]*m[0][2]-
- m[2][2]*m[1][0]*m2[0][0]+m[2][0]*m2[0][0]*m[1][2]+
- m[2][0]*m2[0][2]*m[0][1]-m2[0][2]*m[0][0]*m[2][1])/den;
-
+ 2.0*m[0][0]*m[2][2]*m2[0][1]-m[0][0]*m2[0][2]*m[1][2]-
+ 2.0*m[2][0]*m[0][2]*m2[0][1]+m2[0][2]*m[1][0]*m[0][2]-
+ m[2][2]*m[1][0]*m2[0][0]+m[2][0]*m2[0][0]*m[1][2]+
+ m[2][0]*m2[0][2]*m[0][1]-m2[0][2]*m[0][0]*m[2][1])/den;
+
ans[0][2] = s[0]*(m[0][1]*m[1][2]*m2[0][0]-m[0][2]*m2[0][0]*m[1][1]-
- m[0][0]*m[1][2]*m2[0][1]+m[1][0]*m[0][2]*m2[0][1]-
- m2[0][1]*m[0][0]*m[2][1]-m[2][0]*m[1][1]*m2[0][0]+
- 2.0*m[1][1]*m[0][0]*m2[0][2]-2.0*m[1][0]*m2[0][2]*m[0][1]+
- m[1][0]*m[2][1]*m2[0][0]+m[2][0]*m2[0][1]*m[0][1])/den;
-
+ m[0][0]*m[1][2]*m2[0][1]+m[1][0]*m[0][2]*m2[0][1]-
+ m2[0][1]*m[0][0]*m[2][1]-m[2][0]*m[1][1]*m2[0][0]+
+ 2.0*m[1][1]*m[0][0]*m2[0][2]-2.0*m[1][0]*m2[0][2]*m[0][1]+
+ m[1][0]*m[2][1]*m2[0][0]+m[2][0]*m2[0][1]*m[0][1])/den;
+
ans[1][0] = s[1]*(-m[1][1]*m2[1][2]*m[0][2]+2.0*m[1][1]*m[2][2]*m2[1][0]+
- m[1][2]*m[0][1]*m2[1][2]-2.0*m[1][2]*m2[1][0]*m[2][1]+
- m2[1][1]*m[0][2]*m[2][1]-m2[1][1]*m[0][1]*m[2][2]-
- m[1][0]*m[2][2]*m2[1][1]+m[2][0]*m[1][2]*m2[1][1]-
- m2[1][2]*m[2][0]*m[1][1]+m[1][0]*m2[1][2]*m[2][1])/den;
-
+ m[1][2]*m[0][1]*m2[1][2]-2.0*m[1][2]*m2[1][0]*m[2][1]+
+ m2[1][1]*m[0][2]*m[2][1]-m2[1][1]*m[0][1]*m[2][2]-
+ m[1][0]*m[2][2]*m2[1][1]+m[2][0]*m[1][2]*m2[1][1]-
+ m2[1][2]*m[2][0]*m[1][1]+m[1][0]*m2[1][2]*m[2][1])/den;
+
ans[1][1] = s[1]*(m[0][2]*m2[1][0]*m[2][1]-m[0][1]*m[2][2]*m2[1][0]+
- 2.0*m[2][2]*m[0][0]*m2[1][1]-m2[1][2]*m[0][0]*m[1][2]-
- 2.0*m[2][0]*m2[1][1]*m[0][2]-m[1][0]*m[2][2]*m2[1][0]+
- m[2][0]*m[1][2]*m2[1][0]+m[1][0]*m2[1][2]*m[0][2]-
- m[0][0]*m2[1][2]*m[2][1]+m2[1][2]*m[0][1]*m[2][0])/den;
-
+ 2.0*m[2][2]*m[0][0]*m2[1][1]-m2[1][2]*m[0][0]*m[1][2]-
+ 2.0*m[2][0]*m2[1][1]*m[0][2]-m[1][0]*m[2][2]*m2[1][0]+
+ m[2][0]*m[1][2]*m2[1][0]+m[1][0]*m2[1][2]*m[0][2]-
+ m[0][0]*m2[1][2]*m[2][1]+m2[1][2]*m[0][1]*m[2][0])/den;
+
ans[1][2] = s[1]*(m[0][1]*m[1][2]*m2[1][0]-m[0][2]*m2[1][0]*m[1][1]-
- m[0][0]*m[1][2]*m2[1][1]+m[1][0]*m[0][2]*m2[1][1]+
- 2.0*m[1][1]*m[0][0]*m2[1][2]-m[0][0]*m2[1][1]*m[2][1]+
- m[0][1]*m[2][0]*m2[1][1]-m2[1][0]*m[2][0]*m[1][1]-
- 2.0*m[1][0]*m[0][1]*m2[1][2]+m[1][0]*m2[1][0]*m[2][1])/den;
-
+ m[0][0]*m[1][2]*m2[1][1]+m[1][0]*m[0][2]*m2[1][1]+
+ 2.0*m[1][1]*m[0][0]*m2[1][2]-m[0][0]*m2[1][1]*m[2][1]+
+ m[0][1]*m[2][0]*m2[1][1]-m2[1][0]*m[2][0]*m[1][1]-
+ 2.0*m[1][0]*m[0][1]*m2[1][2]+m[1][0]*m2[1][0]*m[2][1])/den;
+
ans[2][0] = s[2]*(-m[1][1]*m[0][2]*m2[2][2]+m[0][1]*m[1][2]*m2[2][2]+
- 2.0*m[1][1]*m2[2][0]*m[2][2]-m[0][1]*m2[2][1]*m[2][2]+
- m[0][2]*m[2][1]*m2[2][1]-2.0*m2[2][0]*m[2][1]*m[1][2]-
- m[1][0]*m2[2][1]*m[2][2]+m[1][2]*m[2][0]*m2[2][1]-
- m[1][1]*m[2][0]*m2[2][2]+m[2][1]*m[1][0]*m2[2][2])/den;
-
+ 2.0*m[1][1]*m2[2][0]*m[2][2]-m[0][1]*m2[2][1]*m[2][2]+
+ m[0][2]*m[2][1]*m2[2][1]-2.0*m2[2][0]*m[2][1]*m[1][2]-
+ m[1][0]*m2[2][1]*m[2][2]+m[1][2]*m[2][0]*m2[2][1]-
+ m[1][1]*m[2][0]*m2[2][2]+m[2][1]*m[1][0]*m2[2][2])/den;
+
ans[2][1] = s[2]*-(m[0][1]*m[2][2]*m2[2][0]-m[0][2]*m2[2][0]*m[2][1]-
- 2.0*m2[2][1]*m[0][0]*m[2][2]+m[1][2]*m2[2][2]*m[0][0]+
- 2.0*m2[2][1]*m[0][2]*m[2][0]+m[1][0]*m2[2][0]*m[2][2]-
- m[1][0]*m[0][2]*m2[2][2]-m[1][2]*m[2][0]*m2[2][0]+
- m[0][0]*m2[2][2]*m[2][1]-m2[2][2]*m[0][1]*m[2][0])/den;
-
+ 2.0*m2[2][1]*m[0][0]*m[2][2]+m[1][2]*m2[2][2]*m[0][0]+
+ 2.0*m2[2][1]*m[0][2]*m[2][0]+m[1][0]*m2[2][0]*m[2][2]-
+ m[1][0]*m[0][2]*m2[2][2]-m[1][2]*m[2][0]*m2[2][0]+
+ m[0][0]*m2[2][2]*m[2][1]-m2[2][2]*m[0][1]*m[2][0])/den;
+
ans[2][2] = s[2]*(m[0][1]*m[1][2]*m2[2][0]-m[0][2]*m2[2][0]*m[1][1]-
- m[0][0]*m[1][2]*m2[2][1]+m[1][0]*m[0][2]*m2[2][1]-
- m[1][1]*m[2][0]*m2[2][0]-m[2][1]*m2[2][1]*m[0][0]+
- 2.0*m[1][1]*m2[2][2]*m[0][0]+m[2][1]*m[1][0]*m2[2][0]+
- m[2][0]*m[0][1]*m2[2][1]-2.0*m2[2][2]*m[1][0]*m[0][1])/den;
+ m[0][0]*m[1][2]*m2[2][1]+m[1][0]*m[0][2]*m2[2][1]-
+ m[1][1]*m[2][0]*m2[2][0]-m[2][1]*m2[2][1]*m[0][0]+
+ 2.0*m[1][1]*m2[2][2]*m[0][0]+m[2][1]*m[1][0]*m2[2][0]+
+ m[2][0]*m[0][1]*m2[2][1]-2.0*m2[2][2]*m[1][0]*m[0][1])/den;
}
diff --git a/src/ASPHERE/pair_gayberne.h b/src/ASPHERE/pair_gayberne.h
index 1fa0a8a0e7790028034f4ab4b9ef1a8d05f30202..450f8f3a9580174de67762ca3d94a6d76d10b720 100755
--- a/src/ASPHERE/pair_gayberne.h
+++ b/src/ASPHERE/pair_gayberne.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -60,12 +60,12 @@ class PairGayBerne : public Pair {
void allocate();
double gayberne_analytic(const int i, const int j, double a1[3][3],
double a2[3][3], double b1[3][3], double b2[3][3],
- double g1[3][3], double g2[3][3], double *r12,
- const double rsq, double *fforce, double *ttor,
+ double g1[3][3], double g2[3][3], double *r12,
+ const double rsq, double *fforce, double *ttor,
double *rtor);
double gayberne_lj(const int i, const int j, double a1[3][3],
- double b1[3][3],double g1[3][3],double *r12,
- const double rsq, double *fforce, double *ttor);
+ double b1[3][3],double g1[3][3],double *r12,
+ const double rsq, double *fforce, double *ttor);
void compute_eta_torque(double m[3][3], double m2[3][3],
double *s, double ans[3][3]);
};
diff --git a/src/ASPHERE/pair_line_lj.cpp b/src/ASPHERE/pair_line_lj.cpp
index f875158e6e27912c7d96b747bb8fc0fe24e6a0d7..2088ca20f2c42103f708dc61db098f1e8dc4a944 100644
--- a/src/ASPHERE/pair_line_lj.cpp
+++ b/src/ASPHERE/pair_line_lj.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -88,12 +88,12 @@ void PairLineLJ::compute(int eflag, int vflag)
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int newton_pair = force->newton_pair;
-
+
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// grow discrete list if necessary and initialize
if (nall > nmax) {
@@ -116,7 +116,7 @@ void PairLineLJ::compute(int eflag, int vflag)
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
-
+
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
@@ -126,179 +126,179 @@ void PairLineLJ::compute(int eflag, int vflag)
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
-
+
if (rsq >= cutsq[itype][jtype]) continue;
-
+
// line/line interactions = NxN particles
-
+
evdwl = 0.0;
if (line[i] >= 0 && line[j] >= 0) {
- if (dnum[i] == 0) discretize(i,sigma[itype][itype]);
- npi = dnum[i];
- ifirst = dfirst[i];
- if (dnum[j] == 0) discretize(j,sigma[jtype][jtype]);
- npj = dnum[j];
- jfirst = dfirst[j];
-
- for (ni = 0; ni < npi; ni++) {
- dxi = discrete[ifirst+ni].dx;
- dyi = discrete[ifirst+ni].dy;
-
- for (nj = 0; nj < npj; nj++) {
- dxj = discrete[jfirst+nj].dx;
- dyj = discrete[jfirst+nj].dy;
-
- xi[0] = x[i][0] + dxi;
- xi[1] = x[i][1] + dyi;
- xj[0] = x[j][0] + dxj;
- xj[1] = x[j][1] + dyj;
-
- delx = xi[0] - xj[0];
- dely = xi[1] - xj[1];
- rsq = delx*delx + dely*dely;
-
- sig = 0.5 * (discrete[ifirst+ni].sigma+discrete[jfirst+nj].sigma);
- sig3 = sig*sig*sig;
- term2 = 24.0*epsilon[itype][jtype] * sig3*sig3;
- term1 = 2.0 * term2 * sig3*sig3;
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (term1*r6inv - term2);
- fpair = forcelj*r2inv;
-
- if (eflag) evdwl += r6inv*(term1/12.0*r6inv-term2/6.0);
-
- fi[0] = delx*fpair;
- fi[1] = dely*fpair;
- f[i][0] += fi[0];
- f[i][1] += fi[1];
- torque[i][2] += dxi*fi[1] - dyi*fi[0];
-
- if (newton_pair || j < nlocal) {
- fj[0] = -delx*fpair;
- fj[1] = -dely*fpair;
- f[j][0] += fj[0];
- f[j][1] += fj[1];
- torque[j][2] += dxj*fj[1] - dyj*fj[0];
- }
- }
- }
+ if (dnum[i] == 0) discretize(i,sigma[itype][itype]);
+ npi = dnum[i];
+ ifirst = dfirst[i];
+ if (dnum[j] == 0) discretize(j,sigma[jtype][jtype]);
+ npj = dnum[j];
+ jfirst = dfirst[j];
+
+ for (ni = 0; ni < npi; ni++) {
+ dxi = discrete[ifirst+ni].dx;
+ dyi = discrete[ifirst+ni].dy;
+
+ for (nj = 0; nj < npj; nj++) {
+ dxj = discrete[jfirst+nj].dx;
+ dyj = discrete[jfirst+nj].dy;
+
+ xi[0] = x[i][0] + dxi;
+ xi[1] = x[i][1] + dyi;
+ xj[0] = x[j][0] + dxj;
+ xj[1] = x[j][1] + dyj;
+
+ delx = xi[0] - xj[0];
+ dely = xi[1] - xj[1];
+ rsq = delx*delx + dely*dely;
+
+ sig = 0.5 * (discrete[ifirst+ni].sigma+discrete[jfirst+nj].sigma);
+ sig3 = sig*sig*sig;
+ term2 = 24.0*epsilon[itype][jtype] * sig3*sig3;
+ term1 = 2.0 * term2 * sig3*sig3;
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (term1*r6inv - term2);
+ fpair = forcelj*r2inv;
+
+ if (eflag) evdwl += r6inv*(term1/12.0*r6inv-term2/6.0);
+
+ fi[0] = delx*fpair;
+ fi[1] = dely*fpair;
+ f[i][0] += fi[0];
+ f[i][1] += fi[1];
+ torque[i][2] += dxi*fi[1] - dyi*fi[0];
+
+ if (newton_pair || j < nlocal) {
+ fj[0] = -delx*fpair;
+ fj[1] = -dely*fpair;
+ f[j][0] += fj[0];
+ f[j][1] += fj[1];
+ torque[j][2] += dxj*fj[1] - dyj*fj[0];
+ }
+ }
+ }
// line/particle interaction = Nx1 particles
// convert line into Np particles based on sigma and line length
} else if (line[i] >= 0) {
- if (dnum[i] == 0) discretize(i,sigma[itype][itype]);
- npi = dnum[i];
- ifirst = dfirst[i];
-
- for (ni = 0; ni < npi; ni++) {
- dxi = discrete[ifirst+ni].dx;
- dyi = discrete[ifirst+ni].dy;
-
- xi[0] = x[i][0] + dxi;
- xi[1] = x[i][1] + dyi;
- xj[0] = x[j][0];
- xj[1] = x[j][1];
-
- delx = xi[0] - xj[0];
- dely = xi[1] - xj[1];
- rsq = delx*delx + dely*dely;
-
- sig = 0.5 * (discrete[ifirst+ni].sigma+sigma[jtype][jtype]);
- sig3 = sig*sig*sig;
- term2 = 24.0*epsilon[itype][jtype] * sig3*sig3;
- term1 = 2.0 * term2 * sig3*sig3;
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (term1*r6inv - term2);
- fpair = forcelj*r2inv;
-
- if (eflag) evdwl += r6inv*(term1/12.0*r6inv-term2/6.0);
-
- fi[0] = delx*fpair;
- fi[1] = dely*fpair;
- f[i][0] += fi[0];
- f[i][1] += fi[1];
- torque[i][2] += dxi*fi[1] - dyi*fi[0];
-
- if (newton_pair || j < nlocal) {
- fj[0] = -delx*fpair;
- fj[1] = -dely*fpair;
- f[j][0] += fj[0];
- f[j][1] += fj[1];
- }
- }
+ if (dnum[i] == 0) discretize(i,sigma[itype][itype]);
+ npi = dnum[i];
+ ifirst = dfirst[i];
+
+ for (ni = 0; ni < npi; ni++) {
+ dxi = discrete[ifirst+ni].dx;
+ dyi = discrete[ifirst+ni].dy;
+
+ xi[0] = x[i][0] + dxi;
+ xi[1] = x[i][1] + dyi;
+ xj[0] = x[j][0];
+ xj[1] = x[j][1];
+
+ delx = xi[0] - xj[0];
+ dely = xi[1] - xj[1];
+ rsq = delx*delx + dely*dely;
+
+ sig = 0.5 * (discrete[ifirst+ni].sigma+sigma[jtype][jtype]);
+ sig3 = sig*sig*sig;
+ term2 = 24.0*epsilon[itype][jtype] * sig3*sig3;
+ term1 = 2.0 * term2 * sig3*sig3;
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (term1*r6inv - term2);
+ fpair = forcelj*r2inv;
+
+ if (eflag) evdwl += r6inv*(term1/12.0*r6inv-term2/6.0);
+
+ fi[0] = delx*fpair;
+ fi[1] = dely*fpair;
+ f[i][0] += fi[0];
+ f[i][1] += fi[1];
+ torque[i][2] += dxi*fi[1] - dyi*fi[0];
+
+ if (newton_pair || j < nlocal) {
+ fj[0] = -delx*fpair;
+ fj[1] = -dely*fpair;
+ f[j][0] += fj[0];
+ f[j][1] += fj[1];
+ }
+ }
// particle/line interaction = Nx1 particles
// convert line into Np particles based on sigma and line length
} else if (line[j] >= 0) {
- if (dnum[j] == 0) discretize(j,sigma[jtype][jtype]);
- npj = dnum[j];
- jfirst = dfirst[j];
-
- for (nj = 0; nj < npj; nj++) {
- dxj = discrete[jfirst+nj].dx;
- dyj = discrete[jfirst+nj].dy;
-
- xi[0] = x[i][0];
- xi[1] = x[i][1];
- xj[0] = x[j][0] + dxj;
- xj[1] = x[j][1] + dyj;
-
- delx = xi[0] - xj[0];
- dely = xi[1] - xj[1];
- rsq = delx*delx + dely*dely;
-
- sig = 0.5 * (sigma[itype][itype]+discrete[jfirst+nj].sigma);
- sig3 = sig*sig*sig;
- term2 = 24.0*epsilon[itype][jtype] * sig3*sig3;
- term1 = 2.0 * term2 * sig3*sig3;
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (term1*r6inv - term2);
- fpair = forcelj*r2inv;
-
- if (eflag) evdwl += r6inv*(term1/12.0*r6inv-term2/6.0);
-
- fi[0] = delx*fpair;
- fi[1] = dely*fpair;
- f[i][0] += fi[0];
- f[i][1] += fi[1];
-
- if (newton_pair || j < nlocal) {
- f[j][0] += fj[0];
- f[j][1] += fj[1];
- fj[0] = -delx*fpair;
- fj[1] = -dely*fpair;
- torque[j][2] += dxj*fj[1] - dyj*fj[0];
- }
- }
-
+ if (dnum[j] == 0) discretize(j,sigma[jtype][jtype]);
+ npj = dnum[j];
+ jfirst = dfirst[j];
+
+ for (nj = 0; nj < npj; nj++) {
+ dxj = discrete[jfirst+nj].dx;
+ dyj = discrete[jfirst+nj].dy;
+
+ xi[0] = x[i][0];
+ xi[1] = x[i][1];
+ xj[0] = x[j][0] + dxj;
+ xj[1] = x[j][1] + dyj;
+
+ delx = xi[0] - xj[0];
+ dely = xi[1] - xj[1];
+ rsq = delx*delx + dely*dely;
+
+ sig = 0.5 * (sigma[itype][itype]+discrete[jfirst+nj].sigma);
+ sig3 = sig*sig*sig;
+ term2 = 24.0*epsilon[itype][jtype] * sig3*sig3;
+ term1 = 2.0 * term2 * sig3*sig3;
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (term1*r6inv - term2);
+ fpair = forcelj*r2inv;
+
+ if (eflag) evdwl += r6inv*(term1/12.0*r6inv-term2/6.0);
+
+ fi[0] = delx*fpair;
+ fi[1] = dely*fpair;
+ f[i][0] += fi[0];
+ f[i][1] += fi[1];
+
+ if (newton_pair || j < nlocal) {
+ f[j][0] += fj[0];
+ f[j][1] += fj[1];
+ fj[0] = -delx*fpair;
+ fj[1] = -dely*fpair;
+ torque[j][2] += dxj*fj[1] - dyj*fj[0];
+ }
+ }
+
// particle/particle interaction = 1x1 particles
} else {
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- fpair = forcelj*r2inv;
-
- if (eflag)
- evdwl += r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ fpair = forcelj*r2inv;
+
+ if (eflag)
+ evdwl += r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
- evdwl,0.0,fpair,delx,dely,delz);
+ evdwl,0.0,fpair,delx,dely,delz);
}
}
@@ -306,7 +306,7 @@ void PairLineLJ::compute(int eflag, int vflag)
}
/* ----------------------------------------------------------------------
- allocate all arrays
+ allocate all arrays
------------------------------------------------------------------------- */
void PairLineLJ::allocate()
@@ -331,7 +331,7 @@ void PairLineLJ::allocate()
}
/* ----------------------------------------------------------------------
- global settings
+ global settings
------------------------------------------------------------------------- */
void PairLineLJ::settings(int narg, char **arg)
@@ -346,7 +346,7 @@ void PairLineLJ::settings(int narg, char **arg)
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
- if (setflag[i][j]) cut[i][j] = cut_global;
+ if (setflag[i][j]) cut[i][j] = cut_global;
}
}
@@ -356,7 +356,7 @@ void PairLineLJ::settings(int narg, char **arg)
void PairLineLJ::coeff(int narg, char **arg)
{
- if (narg < 4 || narg > 5)
+ if (narg < 4 || narg > 5)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
@@ -392,7 +392,7 @@ double PairLineLJ::init_one(int i, int j)
{
if (setflag[i][j] == 0) {
epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j],
- sigma[i][i],sigma[j][j]);
+ sigma[i][i],sigma[j][j]);
sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]);
cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
}
diff --git a/src/ASPHERE/pair_line_lj.h b/src/ASPHERE/pair_line_lj.h
index b6c2d3bc0b3dbb66c662396ed1d1cf408ee029e7..8a802ad295875ec62e5b4d769da8b0f522bb2acc 100644
--- a/src/ASPHERE/pair_line_lj.h
+++ b/src/ASPHERE/pair_line_lj.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/ASPHERE/pair_resquared.cpp b/src/ASPHERE/pair_resquared.cpp
index c2654ca7fd7689edb685e3fb421820a2918f63d1..a1684afe227025e150a30112ea4b746ffbcae12f 100755
--- a/src/ASPHERE/pair_resquared.cpp
+++ b/src/ASPHERE/pair_resquared.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -35,8 +35,8 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-PairRESquared::PairRESquared(LAMMPS *lmp) : Pair(lmp),
- b_alpha(45.0/56.0),
+PairRESquared::PairRESquared(LAMMPS *lmp) : Pair(lmp),
+ b_alpha(45.0/56.0),
cr60(pow(60.0,1.0/3.0))
{
avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
@@ -103,7 +103,7 @@ void PairRESquared::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@@ -133,7 +133,7 @@ void PairRESquared::compute(int eflag, int vflag)
// compute if less than cutoff
if (rsq < cutsq[itype][jtype]) {
- fforce[0] = fforce[1] = fforce[2] = 0.0;
+ fforce[0] = fforce[1] = fforce[2] = 0.0;
switch (form[itype][jtype]) {
@@ -197,9 +197,9 @@ void PairRESquared::compute(int eflag, int vflag)
if (eflag) evdwl = factor_lj*one_eng;
- if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,
- evdwl,0.0,fforce[0],fforce[1],fforce[2],
- -r12[0],-r12[1],-r12[2]);
+ if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,
+ evdwl,0.0,fforce[0],fforce[1],fforce[2],
+ -r12[0],-r12[1],-r12[2]);
}
}
}
@@ -250,7 +250,7 @@ void PairRESquared::settings(int narg, char **arg)
if (narg != 1) error->all(FLERR,"Illegal pair_style command");
cut_global = force->numeric(arg[0]);
-
+
// reset cutoffs that have been explicitly set
if (allocated) {
@@ -283,7 +283,7 @@ void PairRESquared::coeff(int narg, char **arg)
double eja_one = force->numeric(arg[7]);
double ejb_one = force->numeric(arg[8]);
double ejc_one = force->numeric(arg[9]);
-
+
double cut_one = cut_global;
if (narg == 11) cut_one = force->numeric(arg[10]);
@@ -348,12 +348,12 @@ double PairRESquared::init_one(int i, int j)
error->all(FLERR,"Pair resquared epsilon a,b,c coeffs are not all set");
int ishape = 0;
- if (shape1[i][0] != 0.0 && shape1[i][1] != 0.0 && shape1[i][2] != 0.0)
+ if (shape1[i][0] != 0.0 && shape1[i][1] != 0.0 && shape1[i][2] != 0.0)
ishape = 1;
int jshape = 0;
- if (shape1[j][0] != 0.0 && shape1[j][1] != 0.0 && shape1[j][2] != 0.0)
+ if (shape1[j][0] != 0.0 && shape1[j][1] != 0.0 && shape1[j][2] != 0.0)
jshape = 1;
-
+
if (ishape == 0 && jshape == 0) {
form[i][j] = SPHERE_SPHERE;
form[j][i] = SPHERE_SPHERE;
@@ -384,12 +384,12 @@ double PairRESquared::init_one(int i, int j)
sigma[i][j] = sigma[j][i];
cut[i][j] = cut[j][i];
}
-
+
lj1[i][j] = 48.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
lj2[i][j] = 24.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
-
+
if (offset_flag) {
double ratio = sigma[i][j] / cut[i][j];
offset[i][j] = 4.0 * epsilon[i][j] * (pow(ratio,12.0) - pow(ratio,6.0));
@@ -513,7 +513,7 @@ void PairRESquared::precompute_i(const int i,RE2Vars &ws)
MathExtra::plus3(ws.lAsa[i],ws.lAtwo[i],ws.lAsa[i]);
}
}
-
+
/* ----------------------------------------------------------------------
Compute the derivative of the determinant of m, using m and the
derivative of m (m2)
@@ -545,7 +545,7 @@ double PairRESquared::resquared_analytic(const int i, const int j,
double *rtor)
{
int *type = atom->type;
-
+
// pair computations for energy, force, torque
double z1[3],z2[3]; // A1*rhat # don't need to store
@@ -568,7 +568,7 @@ double PairRESquared::resquared_analytic(const int i, const int j,
double sigh; // sigma/h12
double tprod; // eta*chi*sigh
double Ua,Ur; // attractive/repulsive parts of potential
-
+
// pair computations for force, torque
double sec; // sigma*eta*chi
@@ -593,7 +593,7 @@ double PairRESquared::resquared_analytic(const int i, const int j,
double ddH; // derivative of det(H12)
double deta,dchi,dh12; // derivatives of eta,chi,h12
double dUr,dUa; // derivatives of Ua,Ur
-
+
// pair computations for torque
double fwae[3]; // -fourw'*aTe
@@ -715,7 +715,7 @@ double PairRESquared::resquared_analytic(const int i, const int j,
hsec = h12+3.0*sec;
dspu = 1.0/h12-1.0/hsec+stemp;
pbsu = 3.0*sigma[type[i]][type[j]]/hsec;
-
+
stemp = 1.0/(shape1[type[i]][0]*cr60+h12)+
1.0/(shape1[type[i]][1]*cr60+h12)+
1.0/(shape1[type[i]][2]*cr60+h12)+
@@ -725,7 +725,7 @@ double PairRESquared::resquared_analytic(const int i, const int j,
hsec = h12+b_alpha*sec;
dspr = 7.0/h12-1.0/hsec+stemp;
pbsr = b_alpha*sigma[type[i]][type[j]]/hsec;
-
+
for (int i=0; i<3; i++) {
u[0] = -rhat[i]*rhat[0];
u[1] = -rhat[i]*rhat[1];
@@ -757,7 +757,7 @@ double PairRESquared::resquared_analytic(const int i, const int j,
dUr = pbsr*(eta*dchi+deta*chi)-dh12*dspr;
fforce[i]=dUr*Ur+dUa*Ua;
}
-
+
// torque on i
MathExtra::vecmat(fourw,wi.aTe,fwae);
@@ -787,7 +787,7 @@ double PairRESquared::resquared_analytic(const int i, const int j,
dUr = pbsr*(eta*dchi + deta*chi)-dh12*dspr;
ttor[i] = -(dUa*Ua+dUr*Ur);
}
-
+
// torque on j
if (!(force->newton_pair || j < atom->nlocal))
@@ -829,12 +829,12 @@ double PairRESquared::resquared_analytic(const int i, const int j,
------------------------------------------------------------------------- */
double PairRESquared::resquared_lj(const int i, const int j,
- const RE2Vars &wi, const double *r,
- const double rsq, double *fforce,
+ const RE2Vars &wi, const double *r,
+ const double rsq, double *fforce,
double *ttor, bool calc_torque)
{
int *type = atom->type;
-
+
// pair computations for energy, force, torque
double rnorm; // L2 norm of r
@@ -847,7 +847,7 @@ double PairRESquared::resquared_lj(const int i, const int j,
double sigh; // sigma/h12
double tprod; // chi*sigh
double Ua,Ur; // attractive/repulsive parts of potential
-
+
// pair computations for force, torque
double sec; // sigma*chi
@@ -863,7 +863,7 @@ double PairRESquared::resquared_lj(const int i, const int j,
double dchi,dh12; // derivatives of chi,h12
double dUr,dUa; // derivatives of Ua,Ur
double h12p3; // h12^3
-
+
// pair computations for torque
double fwae[3]; // -fourw'*aTe
@@ -943,7 +943,7 @@ double PairRESquared::resquared_lj(const int i, const int j,
hsec = h12+3.0*sec;
dspu = 1.0/h12-1.0/hsec+stemp;
pbsu = 3.0*sigma[type[i]][type[j]]/hsec;
-
+
stemp = 1.0/(shape1[type[i]][0]*cr60+h12)+
1.0/(shape1[type[i]][1]*cr60+h12)+
1.0/(shape1[type[i]][2]*cr60+h12)+
@@ -951,7 +951,7 @@ double PairRESquared::resquared_lj(const int i, const int j,
hsec = h12+b_alpha*sec;
dspr = 7.0/h12-1.0/hsec+stemp;
pbsr = b_alpha*sigma[type[i]][type[j]]/hsec;
-
+
for (int i=0; i<3; i++) {
u[0] = -rhat[i]*rhat[0];
u[1] = -rhat[i]*rhat[1];
@@ -966,7 +966,7 @@ double PairRESquared::resquared_lj(const int i, const int j,
dUr = pbsr*dchi-dh12*dspr;
fforce[i]=dUr*Ur+dUa*Ua;
}
-
+
// torque on i
if (calc_torque) {
diff --git a/src/ASPHERE/pair_resquared.h b/src/ASPHERE/pair_resquared.h
index da0b24a8b8e6eb9d0b366bd5ec2bf6a9378fa7fa..f2c2b0106a3e1e0b53dbe0a86b06282ffae149d7 100755
--- a/src/ASPHERE/pair_resquared.h
+++ b/src/ASPHERE/pair_resquared.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -64,7 +64,7 @@ class PairRESquared : public Pair {
double A[3][3]; // Rotation matrix (lab->body)
double aTe[3][3]; // A'*E
double gamma[3][3]; // A'*S^2*A
-
+
// per particle precomputations for torque
double sa[3][3]; // S^2*A;
@@ -72,7 +72,7 @@ class PairRESquared : public Pair {
double lAtwo[3][3][3]; // A'*S^2*lA
double lAsa[3][3][3]; // lAtwo+lA'*sa
};
-
+
void allocate();
void precompute_i(const int i,RE2Vars &ws);
@@ -82,8 +82,8 @@ class PairRESquared : public Pair {
const double *r, const double rsq,
double *fforce, double *ttor,
double *rtor);
- double resquared_lj(const int i, const int j, const RE2Vars &wi,
- const double *r, const double rsq, double *fforce,
+ double resquared_lj(const int i, const int j, const RE2Vars &wi,
+ const double *r, const double rsq, double *fforce,
double *ttor, bool calc_torque);
double cr60; // 60^1/3
diff --git a/src/ASPHERE/pair_tri_lj.cpp b/src/ASPHERE/pair_tri_lj.cpp
index 13650bb611bcc23c1b364554192e027014ccd8be..ec0a07abeef4c31cce33a2e5657bbe3972b6483c 100644
--- a/src/ASPHERE/pair_tri_lj.cpp
+++ b/src/ASPHERE/pair_tri_lj.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -92,12 +92,12 @@ void PairTriLJ::compute(int eflag, int vflag)
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int newton_pair = force->newton_pair;
-
+
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// grow discrete list if necessary and initialize
if (nall > nmax) {
@@ -130,259 +130,259 @@ void PairTriLJ::compute(int eflag, int vflag)
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
-
+
if (rsq >= cutsq[itype][jtype]) continue;
-
+
// tri/tri interactions = NxN particles
// c1,c2,c3 = corner pts of triangle I or J
-
+
evdwl = 0.0;
if (tri[i] >= 0 && tri[j] >= 0) {
- if (dnum[i] == 0) {
- MathExtra::quat_to_mat(bonus[tri[i]].quat,p);
- MathExtra::matvec(p,bonus[tri[i]].c1,dc1);
- MathExtra::matvec(p,bonus[tri[i]].c2,dc2);
- MathExtra::matvec(p,bonus[tri[i]].c3,dc3);
- dfirst[i] = ndiscrete;
- discretize(i,sigma[itype][itype],dc1,dc2,dc3);
- dnum[i] = ndiscrete - dfirst[i];
- }
- npi = dnum[i];
- ifirst = dfirst[i];
-
- if (dnum[j] == 0) {
- MathExtra::quat_to_mat(bonus[tri[j]].quat,p);
- MathExtra::matvec(p,bonus[tri[j]].c1,dc1);
- MathExtra::matvec(p,bonus[tri[j]].c2,dc2);
- MathExtra::matvec(p,bonus[tri[j]].c3,dc3);
- dfirst[j] = ndiscrete;
- discretize(j,sigma[jtype][jtype],dc1,dc2,dc3);
- dnum[j] = ndiscrete - dfirst[j];
- }
- npj = dnum[j];
- jfirst = dfirst[j];
-
- for (ni = 0; ni < npi; ni++) {
- dxi = discrete[ifirst+ni].dx;
- dyi = discrete[ifirst+ni].dy;
- dzi = discrete[ifirst+ni].dz;
-
- for (nj = 0; nj < npj; nj++) {
- dxj = discrete[jfirst+nj].dx;
- dyj = discrete[jfirst+nj].dy;
- dzj = discrete[jfirst+nj].dz;
-
- xi[0] = x[i][0] + dxi;
- xi[1] = x[i][1] + dyi;
- xi[2] = x[i][2] + dzi;
- xj[0] = x[j][0] + dxj;
- xj[1] = x[j][1] + dyj;
- xj[2] = x[j][2] + dzj;
-
- delx = xi[0] - xj[0];
- dely = xi[1] - xj[1];
- delz = xi[2] - xj[2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- sig = 0.5 * (discrete[ifirst+ni].sigma+discrete[jfirst+nj].sigma);
- sig3 = sig*sig*sig;
- term2 = 24.0*epsilon[itype][jtype] * sig3*sig3;
- term1 = 2.0 * term2 * sig3*sig3;
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (term1*r6inv - term2);
- fpair = forcelj*r2inv;
-
- if (eflag) evdwl += r6inv*(term1/12.0*r6inv-term2/6.0);
-
- fi[0] = delx*fpair;
- fi[1] = dely*fpair;
- fi[2] = delz*fpair;
- f[i][0] += fi[0];
- f[i][1] += fi[1];
- f[i][2] += fi[2];
- ti[0] = dyi*fi[2] - dzi*fi[1];
- ti[1] = dzi*fi[0] - dxi*fi[2];
- ti[2] = dxi*fi[1] - dyi*fi[0];
- torque[i][0] += ti[0];
- torque[i][1] += ti[1];
- torque[i][2] += ti[2];
-
- if (newton_pair || j < nlocal) {
- fj[0] = -delx*fpair;
- fj[1] = -dely*fpair;
- fj[2] = -delz*fpair;
- f[j][0] += fj[0];
- f[j][1] += fj[1];
- f[j][2] += fj[2];
- tj[0] = dyj*fj[2] - dzj*fj[1];
- tj[1] = dzj*fj[0] - dxj*fj[2];
- tj[2] = dxj*fj[1] - dyj*fj[0];
- torque[j][0] += tj[0];
- torque[j][1] += tj[1];
- torque[j][2] += tj[2];
- }
- }
- }
+ if (dnum[i] == 0) {
+ MathExtra::quat_to_mat(bonus[tri[i]].quat,p);
+ MathExtra::matvec(p,bonus[tri[i]].c1,dc1);
+ MathExtra::matvec(p,bonus[tri[i]].c2,dc2);
+ MathExtra::matvec(p,bonus[tri[i]].c3,dc3);
+ dfirst[i] = ndiscrete;
+ discretize(i,sigma[itype][itype],dc1,dc2,dc3);
+ dnum[i] = ndiscrete - dfirst[i];
+ }
+ npi = dnum[i];
+ ifirst = dfirst[i];
+
+ if (dnum[j] == 0) {
+ MathExtra::quat_to_mat(bonus[tri[j]].quat,p);
+ MathExtra::matvec(p,bonus[tri[j]].c1,dc1);
+ MathExtra::matvec(p,bonus[tri[j]].c2,dc2);
+ MathExtra::matvec(p,bonus[tri[j]].c3,dc3);
+ dfirst[j] = ndiscrete;
+ discretize(j,sigma[jtype][jtype],dc1,dc2,dc3);
+ dnum[j] = ndiscrete - dfirst[j];
+ }
+ npj = dnum[j];
+ jfirst = dfirst[j];
+
+ for (ni = 0; ni < npi; ni++) {
+ dxi = discrete[ifirst+ni].dx;
+ dyi = discrete[ifirst+ni].dy;
+ dzi = discrete[ifirst+ni].dz;
+
+ for (nj = 0; nj < npj; nj++) {
+ dxj = discrete[jfirst+nj].dx;
+ dyj = discrete[jfirst+nj].dy;
+ dzj = discrete[jfirst+nj].dz;
+
+ xi[0] = x[i][0] + dxi;
+ xi[1] = x[i][1] + dyi;
+ xi[2] = x[i][2] + dzi;
+ xj[0] = x[j][0] + dxj;
+ xj[1] = x[j][1] + dyj;
+ xj[2] = x[j][2] + dzj;
+
+ delx = xi[0] - xj[0];
+ dely = xi[1] - xj[1];
+ delz = xi[2] - xj[2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ sig = 0.5 * (discrete[ifirst+ni].sigma+discrete[jfirst+nj].sigma);
+ sig3 = sig*sig*sig;
+ term2 = 24.0*epsilon[itype][jtype] * sig3*sig3;
+ term1 = 2.0 * term2 * sig3*sig3;
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (term1*r6inv - term2);
+ fpair = forcelj*r2inv;
+
+ if (eflag) evdwl += r6inv*(term1/12.0*r6inv-term2/6.0);
+
+ fi[0] = delx*fpair;
+ fi[1] = dely*fpair;
+ fi[2] = delz*fpair;
+ f[i][0] += fi[0];
+ f[i][1] += fi[1];
+ f[i][2] += fi[2];
+ ti[0] = dyi*fi[2] - dzi*fi[1];
+ ti[1] = dzi*fi[0] - dxi*fi[2];
+ ti[2] = dxi*fi[1] - dyi*fi[0];
+ torque[i][0] += ti[0];
+ torque[i][1] += ti[1];
+ torque[i][2] += ti[2];
+
+ if (newton_pair || j < nlocal) {
+ fj[0] = -delx*fpair;
+ fj[1] = -dely*fpair;
+ fj[2] = -delz*fpair;
+ f[j][0] += fj[0];
+ f[j][1] += fj[1];
+ f[j][2] += fj[2];
+ tj[0] = dyj*fj[2] - dzj*fj[1];
+ tj[1] = dzj*fj[0] - dxj*fj[2];
+ tj[2] = dxj*fj[1] - dyj*fj[0];
+ torque[j][0] += tj[0];
+ torque[j][1] += tj[1];
+ torque[j][2] += tj[2];
+ }
+ }
+ }
// tri/particle interaction = Nx1 particles
// c1,c2,c3 = corner pts of triangle I
} else if (tri[i] >= 0) {
- if (dnum[i] == 0) {
- MathExtra::quat_to_mat(bonus[tri[i]].quat,p);
- MathExtra::matvec(p,bonus[tri[i]].c1,dc1);
- MathExtra::matvec(p,bonus[tri[i]].c2,dc2);
- MathExtra::matvec(p,bonus[tri[i]].c3,dc3);
- dfirst[i] = ndiscrete;
- discretize(i,sigma[itype][itype],dc1,dc2,dc3);
- dnum[i] = ndiscrete - dfirst[i];
- }
- npi = dnum[i];
- ifirst = dfirst[i];
-
- for (ni = 0; ni < npi; ni++) {
- dxi = discrete[ifirst+ni].dx;
- dyi = discrete[ifirst+ni].dy;
- dzi = discrete[ifirst+ni].dz;
-
- xi[0] = x[i][0] + dxi;
- xi[1] = x[i][1] + dyi;
- xi[2] = x[i][2] + dzi;
- xj[0] = x[j][0];
- xj[1] = x[j][1];
- xj[2] = x[j][2];
-
- delx = xi[0] - xj[0];
- dely = xi[1] - xj[1];
- delz = xi[2] - xj[2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- sig = 0.5 * (discrete[ifirst+ni].sigma+sigma[jtype][jtype]);
- sig3 = sig*sig*sig;
- term2 = 24.0*epsilon[itype][jtype] * sig3*sig3;
- term1 = 2.0 * term2 * sig3*sig3;
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (term1*r6inv - term2);
- fpair = forcelj*r2inv;
-
- if (eflag) evdwl += r6inv*(term1/12.0*r6inv-term2/6.0);
-
- fi[0] = delx*fpair;
- fi[1] = dely*fpair;
- fi[2] = delz*fpair;
- f[i][0] += fi[0];
- f[i][1] += fi[1];
- f[i][2] += fi[2];
- ti[0] = dyi*fi[2] - dzi*fi[1];
- ti[1] = dzi*fi[0] - dxi*fi[2];
- ti[2] = dxi*fi[1] - dyi*fi[0];
- torque[i][2] += ti[0];
- torque[i][1] += ti[1];
- torque[i][2] += ti[2];
-
- if (newton_pair || j < nlocal) {
- fj[0] = -delx*fpair;
- fj[1] = -dely*fpair;
- fj[2] = -delz*fpair;
- f[j][0] += fj[0];
- f[j][1] += fj[1];
- f[j][2] += fj[2];
- }
- }
+ if (dnum[i] == 0) {
+ MathExtra::quat_to_mat(bonus[tri[i]].quat,p);
+ MathExtra::matvec(p,bonus[tri[i]].c1,dc1);
+ MathExtra::matvec(p,bonus[tri[i]].c2,dc2);
+ MathExtra::matvec(p,bonus[tri[i]].c3,dc3);
+ dfirst[i] = ndiscrete;
+ discretize(i,sigma[itype][itype],dc1,dc2,dc3);
+ dnum[i] = ndiscrete - dfirst[i];
+ }
+ npi = dnum[i];
+ ifirst = dfirst[i];
+
+ for (ni = 0; ni < npi; ni++) {
+ dxi = discrete[ifirst+ni].dx;
+ dyi = discrete[ifirst+ni].dy;
+ dzi = discrete[ifirst+ni].dz;
+
+ xi[0] = x[i][0] + dxi;
+ xi[1] = x[i][1] + dyi;
+ xi[2] = x[i][2] + dzi;
+ xj[0] = x[j][0];
+ xj[1] = x[j][1];
+ xj[2] = x[j][2];
+
+ delx = xi[0] - xj[0];
+ dely = xi[1] - xj[1];
+ delz = xi[2] - xj[2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ sig = 0.5 * (discrete[ifirst+ni].sigma+sigma[jtype][jtype]);
+ sig3 = sig*sig*sig;
+ term2 = 24.0*epsilon[itype][jtype] * sig3*sig3;
+ term1 = 2.0 * term2 * sig3*sig3;
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (term1*r6inv - term2);
+ fpair = forcelj*r2inv;
+
+ if (eflag) evdwl += r6inv*(term1/12.0*r6inv-term2/6.0);
+
+ fi[0] = delx*fpair;
+ fi[1] = dely*fpair;
+ fi[2] = delz*fpair;
+ f[i][0] += fi[0];
+ f[i][1] += fi[1];
+ f[i][2] += fi[2];
+ ti[0] = dyi*fi[2] - dzi*fi[1];
+ ti[1] = dzi*fi[0] - dxi*fi[2];
+ ti[2] = dxi*fi[1] - dyi*fi[0];
+ torque[i][2] += ti[0];
+ torque[i][1] += ti[1];
+ torque[i][2] += ti[2];
+
+ if (newton_pair || j < nlocal) {
+ fj[0] = -delx*fpair;
+ fj[1] = -dely*fpair;
+ fj[2] = -delz*fpair;
+ f[j][0] += fj[0];
+ f[j][1] += fj[1];
+ f[j][2] += fj[2];
+ }
+ }
// particle/tri interaction = Nx1 particles
// c1,c2,c3 = corner pts of triangle J
} else if (tri[j] >= 0) {
- if (dnum[j] == 0) {
- MathExtra::quat_to_mat(bonus[tri[j]].quat,p);
- MathExtra::matvec(p,bonus[tri[j]].c1,dc1);
- MathExtra::matvec(p,bonus[tri[j]].c2,dc2);
- MathExtra::matvec(p,bonus[tri[j]].c3,dc3);
- dfirst[j] = ndiscrete;
- discretize(j,sigma[jtype][jtype],dc1,dc2,dc3);
- dnum[j] = ndiscrete - dfirst[j];
- }
- npj = dnum[j];
- jfirst = dfirst[j];
-
- for (nj = 0; nj < npj; nj++) {
- dxj = discrete[jfirst+nj].dx;
- dyj = discrete[jfirst+nj].dy;
- dzj = discrete[jfirst+nj].dz;
-
- xi[0] = x[i][0];
- xi[1] = x[i][1];
- xi[2] = x[i][2];
- xj[0] = x[j][0] + dxj;
- xj[1] = x[j][1] + dyj;
- xj[2] = x[j][2] + dzj;
-
- delx = xi[0] - xj[0];
- dely = xi[1] - xj[1];
- delz = xi[2] - xj[2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- sig = 0.5 * (sigma[itype][itype]+discrete[jfirst+nj].sigma);
- sig3 = sig*sig*sig;
- term2 = 24.0*epsilon[itype][jtype] * sig3*sig3;
- term1 = 2.0 * term2 * sig3*sig3;
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (term1*r6inv - term2);
- fpair = forcelj*r2inv;
-
- if (eflag) evdwl += r6inv*(term1/12.0*r6inv-term2/6.0);
-
- fi[0] = delx*fpair;
- fi[1] = dely*fpair;
- fi[2] = delz*fpair;
- f[i][0] += fi[0];
- f[i][1] += fi[1];
- f[i][2] += fi[2];
-
- if (newton_pair || j < nlocal) {
- fj[0] = -delx*fpair;
- fj[1] = -dely*fpair;
- fj[2] = -delz*fpair;
- f[j][0] += fj[0];
- f[j][1] += fj[1];
- f[j][2] += fj[2];
- tj[0] = dyj*fj[2] - dzj*fj[1];
- tj[1] = dzj*fj[0] - dxj*fj[2];
- tj[2] = dxj*fj[1] - dyj*fj[0];
- torque[j][0] += tj[0];
- torque[j][1] += tj[1];
- torque[j][2] += tj[2];
- }
- }
+ if (dnum[j] == 0) {
+ MathExtra::quat_to_mat(bonus[tri[j]].quat,p);
+ MathExtra::matvec(p,bonus[tri[j]].c1,dc1);
+ MathExtra::matvec(p,bonus[tri[j]].c2,dc2);
+ MathExtra::matvec(p,bonus[tri[j]].c3,dc3);
+ dfirst[j] = ndiscrete;
+ discretize(j,sigma[jtype][jtype],dc1,dc2,dc3);
+ dnum[j] = ndiscrete - dfirst[j];
+ }
+ npj = dnum[j];
+ jfirst = dfirst[j];
+
+ for (nj = 0; nj < npj; nj++) {
+ dxj = discrete[jfirst+nj].dx;
+ dyj = discrete[jfirst+nj].dy;
+ dzj = discrete[jfirst+nj].dz;
+
+ xi[0] = x[i][0];
+ xi[1] = x[i][1];
+ xi[2] = x[i][2];
+ xj[0] = x[j][0] + dxj;
+ xj[1] = x[j][1] + dyj;
+ xj[2] = x[j][2] + dzj;
+
+ delx = xi[0] - xj[0];
+ dely = xi[1] - xj[1];
+ delz = xi[2] - xj[2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ sig = 0.5 * (sigma[itype][itype]+discrete[jfirst+nj].sigma);
+ sig3 = sig*sig*sig;
+ term2 = 24.0*epsilon[itype][jtype] * sig3*sig3;
+ term1 = 2.0 * term2 * sig3*sig3;
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (term1*r6inv - term2);
+ fpair = forcelj*r2inv;
+
+ if (eflag) evdwl += r6inv*(term1/12.0*r6inv-term2/6.0);
+
+ fi[0] = delx*fpair;
+ fi[1] = dely*fpair;
+ fi[2] = delz*fpair;
+ f[i][0] += fi[0];
+ f[i][1] += fi[1];
+ f[i][2] += fi[2];
+
+ if (newton_pair || j < nlocal) {
+ fj[0] = -delx*fpair;
+ fj[1] = -dely*fpair;
+ fj[2] = -delz*fpair;
+ f[j][0] += fj[0];
+ f[j][1] += fj[1];
+ f[j][2] += fj[2];
+ tj[0] = dyj*fj[2] - dzj*fj[1];
+ tj[1] = dzj*fj[0] - dxj*fj[2];
+ tj[2] = dxj*fj[1] - dyj*fj[0];
+ torque[j][0] += tj[0];
+ torque[j][1] += tj[1];
+ torque[j][2] += tj[2];
+ }
+ }
// particle/particle interaction = 1x1 particles
} else {
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- fpair = forcelj*r2inv;
-
- if (eflag)
- evdwl += r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ fpair = forcelj*r2inv;
+
+ if (eflag)
+ evdwl += r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
- evdwl,0.0,fpair,delx,dely,delz);
+ evdwl,0.0,fpair,delx,dely,delz);
}
}
@@ -390,7 +390,7 @@ void PairTriLJ::compute(int eflag, int vflag)
}
/* ----------------------------------------------------------------------
- allocate all arrays
+ allocate all arrays
------------------------------------------------------------------------- */
void PairTriLJ::allocate()
@@ -415,7 +415,7 @@ void PairTriLJ::allocate()
}
/* ----------------------------------------------------------------------
- global settings
+ global settings
------------------------------------------------------------------------- */
void PairTriLJ::settings(int narg, char **arg)
@@ -430,7 +430,7 @@ void PairTriLJ::settings(int narg, char **arg)
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
- if (setflag[i][j]) cut[i][j] = cut_global;
+ if (setflag[i][j]) cut[i][j] = cut_global;
}
}
@@ -440,7 +440,7 @@ void PairTriLJ::settings(int narg, char **arg)
void PairTriLJ::coeff(int narg, char **arg)
{
- if (narg < 4 || narg > 5)
+ if (narg < 4 || narg > 5)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
@@ -476,7 +476,7 @@ double PairTriLJ::init_one(int i, int j)
{
if (setflag[i][j] == 0) {
epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j],
- sigma[i][i],sigma[j][j]);
+ sigma[i][i],sigma[j][j]);
sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]);
cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
}
@@ -504,7 +504,7 @@ double PairTriLJ::init_one(int i, int j)
------------------------------------------------------------------------- */
void PairTriLJ::discretize(int i, double sigma,
- double *c1, double *c2, double *c3)
+ double *c1, double *c2, double *c3)
{
double c1c2[3],c2c3[3],c1c3[3];
@@ -529,7 +529,7 @@ void PairTriLJ::discretize(int i, double sigma,
if (ndiscrete == dmax) {
dmax += DELTA;
discrete = (Discrete *)
- memory->srealloc(discrete,dmax*sizeof(Discrete),"pair:discrete");
+ memory->srealloc(discrete,dmax*sizeof(Discrete),"pair:discrete");
}
discrete[ndiscrete].dx = centroid[0];
discrete[ndiscrete].dy = centroid[1];
@@ -582,7 +582,7 @@ void PairTriLJ::discretize(int i, double sigma,
/*
void PairTriLJ::discretize(int i, double sigma,
- double *c1, double *c2, double *c3)
+ double *c1, double *c2, double *c3)
{
double centroid[3],dc1[3],dc2[3],dc3[3];
@@ -605,7 +605,7 @@ void PairTriLJ::discretize(int i, double sigma,
if (ndiscrete == dmax) {
dmax += DELTA;
discrete = (Discrete *)
- memory->srealloc(discrete,dmax*sizeof(Discrete),"pair:discrete");
+ memory->srealloc(discrete,dmax*sizeof(Discrete),"pair:discrete");
}
discrete[ndiscrete].dx = centroid[0];
discrete[ndiscrete].dy = centroid[1];
diff --git a/src/ASPHERE/pair_tri_lj.h b/src/ASPHERE/pair_tri_lj.h
index df65b0fd1000e5ed83880274666ff542896e3ddf..f37903055b312a5f3ab357973f77a74a60049701 100644
--- a/src/ASPHERE/pair_tri_lj.h
+++ b/src/ASPHERE/pair_tri_lj.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/CLASS2/angle_class2.cpp b/src/CLASS2/angle_class2.cpp
index ac74f441f75addecc36e258d9b584bc168993d9a..4129216ed31530292b22a68afaf60c40f6f69b63 100644
--- a/src/CLASS2/angle_class2.cpp
+++ b/src/CLASS2/angle_class2.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -116,10 +116,10 @@ void AngleClass2::compute(int eflag, int vflag)
c = delx1*delx2 + dely1*dely2 + delz1*delz2;
c /= r1*r2;
-
+
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
-
+
s = sqrt(1.0 - c*c);
if (s < SMALL) s = SMALL;
s = 1.0/s;
@@ -131,14 +131,14 @@ void AngleClass2::compute(int eflag, int vflag)
dtheta3 = dtheta2*dtheta;
dtheta4 = dtheta3*dtheta;
- de_angle = 2.0*k2[type]*dtheta + 3.0*k3[type]*dtheta2 +
+ de_angle = 2.0*k2[type]*dtheta + 3.0*k3[type]*dtheta2 +
4.0*k4[type]*dtheta3;
a = -de_angle*s;
a11 = a*c / rsq1;
a12 = -a / (r1*r2);
a22 = a*c / rsq2;
-
+
f1[0] = a11*delx1 + a12*delx2;
f1[1] = a11*dely1 + a12*dely2;
f1[2] = a11*delz1 + a12*delz2;
@@ -227,7 +227,7 @@ void AngleClass2::compute(int eflag, int vflag)
}
if (evflag) ev_tally(i1,i2,i3,nlocal,newton_bond,eangle,f1,f3,
- delx1,dely1,delz1,delx2,dely2,delz2);
+ delx1,dely1,delz1,delx2,dely2,delz2);
}
}
@@ -283,7 +283,7 @@ void AngleClass2::coeff(int narg, char **arg)
double bb_k_one = force->numeric(arg[2]);
double bb_r1_one = force->numeric(arg[3]);
double bb_r2_one = force->numeric(arg[4]);
-
+
for (int i = ilo; i <= ihi; i++) {
bb_k[i] = bb_k_one;
bb_r1[i] = bb_r1_one;
@@ -299,7 +299,7 @@ void AngleClass2::coeff(int narg, char **arg)
double ba_k2_one = force->numeric(arg[3]);
double ba_r1_one = force->numeric(arg[4]);
double ba_r2_one = force->numeric(arg[5]);
-
+
for (int i = ilo; i <= ihi; i++) {
ba_k1[i] = ba_k1_one;
ba_k2[i] = ba_k2_one;
@@ -316,7 +316,7 @@ void AngleClass2::coeff(int narg, char **arg)
double k2_one = force->numeric(arg[2]);
double k3_one = force->numeric(arg[3]);
double k4_one = force->numeric(arg[4]);
-
+
// convert theta0 from degrees to radians
for (int i = ilo; i <= ihi; i++) {
@@ -365,7 +365,7 @@ void AngleClass2::write_restart(FILE *fp)
}
/* ----------------------------------------------------------------------
- proc 0 reads coeffs from restart file, bcasts them
+ proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void AngleClass2::read_restart(FILE *fp)
@@ -381,7 +381,7 @@ void AngleClass2::read_restart(FILE *fp)
fread(&bb_k[1],sizeof(double),atom->nangletypes,fp);
fread(&bb_r1[1],sizeof(double),atom->nangletypes,fp);
fread(&bb_r2[1],sizeof(double),atom->nangletypes,fp);
-
+
fread(&ba_k1[1],sizeof(double),atom->nangletypes,fp);
fread(&ba_k2[1],sizeof(double),atom->nangletypes,fp);
fread(&ba_r1[1],sizeof(double),atom->nangletypes,fp);
@@ -427,7 +427,7 @@ double AngleClass2::single(int type, int i1, int i2, int i3)
c /= r1*r2;
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
-
+
double s = sqrt(1.0 - c*c);
if (s < SMALL) s = SMALL;
s = 1.0/s;
@@ -436,9 +436,9 @@ double AngleClass2::single(int type, int i1, int i2, int i3)
double dtheta2 = dtheta*dtheta;
double dtheta3 = dtheta2*dtheta;
double dtheta4 = dtheta3*dtheta;
-
+
double energy = k2[type]*dtheta2 + k3[type]*dtheta3 + k4[type]*dtheta4;
-
+
double dr1 = r1 - bb_r1[type];
double dr2 = r2 - bb_r2[type];
energy += bb_k[type]*dr1*dr2;
diff --git a/src/CLASS2/angle_class2.h b/src/CLASS2/angle_class2.h
index 7db51c2e0bb403e5d378793821f1ddbfbfa87bcf..7f862f628d7c560fd9759727798b15154117574a 100644
--- a/src/CLASS2/angle_class2.h
+++ b/src/CLASS2/angle_class2.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/CLASS2/bond_class2.cpp b/src/CLASS2/bond_class2.cpp
index f18d687fe7e044a1bf6814690ace3ab7c209a3bd..2234227abe7c8f1ed2eb523a25cc8931cbabd8e3 100644
--- a/src/CLASS2/bond_class2.cpp
+++ b/src/CLASS2/bond_class2.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -124,7 +124,7 @@ void BondClass2::allocate()
}
/* ----------------------------------------------------------------------
- set coeffs from one line in input script or data file
+ set coeffs from one line in input script or data file
------------------------------------------------------------------------- */
void BondClass2::coeff(int narg, char **arg)
@@ -154,7 +154,7 @@ void BondClass2::coeff(int narg, char **arg)
}
/* ----------------------------------------------------------------------
- return an equilbrium bond length
+ return an equilbrium bond length
------------------------------------------------------------------------- */
double BondClass2::equilibrium_distance(int i)
@@ -163,7 +163,7 @@ double BondClass2::equilibrium_distance(int i)
}
/* ----------------------------------------------------------------------
- proc 0 writes out coeffs to restart file
+ proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void BondClass2::write_restart(FILE *fp)
@@ -175,7 +175,7 @@ void BondClass2::write_restart(FILE *fp)
}
/* ----------------------------------------------------------------------
- proc 0 reads coeffs from restart file, bcasts them
+ proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void BondClass2::read_restart(FILE *fp)
diff --git a/src/CLASS2/bond_class2.h b/src/CLASS2/bond_class2.h
index 233117bbb83ccf3b47257a2c217b0f44e71b5d14..52c2a0689581783db30a041e17cfd80480e71099 100644
--- a/src/CLASS2/bond_class2.h
+++ b/src/CLASS2/bond_class2.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/CLASS2/dihedral_class2.cpp b/src/CLASS2/dihedral_class2.cpp
index 07dd32442f20014bdafbdd3b349ba0ab64bab92a..dcf204a37d598caf930f92f1313ba1458c6a7756 100644
--- a/src/CLASS2/dihedral_class2.cpp
+++ b/src/CLASS2/dihedral_class2.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -181,19 +181,19 @@ void DihedralClass2::compute(int eflag, int vflag)
costh12 = (vb1x*vb2x + vb1y*vb2y + vb1z*vb2z) * r12c1;
costh13 = c0;
costh23 = (vb2xm*vb3x + vb2ym*vb3y + vb2zm*vb3z) * r12c2;
-
+
// cos and sin of 2 angles and final c
sin2 = MAX(1.0 - costh12*costh12,0.0);
sc1 = sqrt(sin2);
if (sc1 < SMALL) sc1 = SMALL;
sc1 = 1.0/sc1;
-
+
sin2 = MAX(1.0 - costh23*costh23,0.0);
sc2 = sqrt(sin2);
if (sc2 < SMALL) sc2 = SMALL;
sc2 = 1.0/sc2;
-
+
s1 = sc1 * sc1;
s2 = sc2 * sc2;
s12 = sc1 * sc2;
@@ -205,19 +205,19 @@ void DihedralClass2::compute(int eflag, int vflag)
int me;
MPI_Comm_rank(world,&me);
if (screen) {
- char str[128];
- sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " %d %d %d %d",
- me,update->ntimestep,
- atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
- error->warning(FLERR,str,0);
- fprintf(screen," 1st atom: %d %g %g %g\n",
- me,x[i1][0],x[i1][1],x[i1][2]);
- fprintf(screen," 2nd atom: %d %g %g %g\n",
- me,x[i2][0],x[i2][1],x[i2][2]);
- fprintf(screen," 3rd atom: %d %g %g %g\n",
- me,x[i3][0],x[i3][1],x[i3][2]);
- fprintf(screen," 4th atom: %d %g %g %g\n",
- me,x[i4][0],x[i4][1],x[i4][2]);
+ char str[128];
+ sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " %d %d %d %d",
+ me,update->ntimestep,
+ atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
+ error->warning(FLERR,str,0);
+ fprintf(screen," 1st atom: %d %g %g %g\n",
+ me,x[i1][0],x[i1][1],x[i1][2]);
+ fprintf(screen," 2nd atom: %d %g %g %g\n",
+ me,x[i2][0],x[i2][1],x[i2][2]);
+ fprintf(screen," 3rd atom: %d %g %g %g\n",
+ me,x[i3][0],x[i3][1],x[i3][2]);
+ fprintf(screen," 4th atom: %d %g %g %g\n",
+ me,x[i4][0],x[i4][1],x[i4][2]);
}
}
@@ -235,7 +235,7 @@ void DihedralClass2::compute(int eflag, int vflag)
a12 = r12c1 * (costh12*c*s1 + costh23*s12);
a13 = rb1*rb3*s12;
a23 = r12c2 * (-costh23*c*s2 - costh12*s12);
-
+
sx1 = a11*vb1x + a12*vb2x + a13*vb3x;
sx2 = a12*vb1x + a22*vb2x + a23*vb3x;
sx12 = a13*vb1x + a23*vb2x + a33*vb3x;
@@ -263,18 +263,18 @@ void DihedralClass2::compute(int eflag, int vflag)
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
- dphidr[i][j] = -dcosphidr[i][j] / sinphi;
+ dphidr[i][j] = -dcosphidr[i][j] / sinphi;
// energy
dphi1 = phi - phi1[type];
dphi2 = 2.0*phi - phi2[type];
dphi3 = 3.0*phi - phi3[type];
-
+
if (eflag) edihedral = k1[type]*(1.0 - cos(dphi1)) +
- k2[type]*(1.0 - cos(dphi2)) +
- k3[type]*(1.0 - cos(dphi3));
-
+ k2[type]*(1.0 - cos(dphi2)) +
+ k3[type]*(1.0 - cos(dphi3));
+
de_dihedral = k1[type]*sin(dphi1) + 2.0*k2[type]*sin(dphi2) +
3.0*k3[type]*sin(dphi3);
@@ -282,18 +282,18 @@ void DihedralClass2::compute(int eflag, int vflag)
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
- fabcd[i][j] = de_dihedral*dphidr[i][j];
+ fabcd[i][j] = de_dihedral*dphidr[i][j];
// set up d(bond)/d(r) array
// dbonddr(i,j,k) = bond i, atom j, coordinate k
for (i = 0; i < 3; i++)
for (j = 0; j < 4; j++)
- for (k = 0; k < 3; k++)
- dbonddr[i][j][k] = 0.0;
-
+ for (k = 0; k < 3; k++)
+ dbonddr[i][j][k] = 0.0;
+
// bond1
-
+
dbonddr[0][0][0] = vb1x / r1;
dbonddr[0][0][1] = vb1y / r1;
dbonddr[0][0][2] = vb1z / r1;
@@ -311,7 +311,7 @@ void DihedralClass2::compute(int eflag, int vflag)
dbonddr[1][2][2] = -vb2z / r2;
// bond3
-
+
dbonddr[2][2][0] = vb3x / r3;
dbonddr[2][2][1] = vb3y / r3;
dbonddr[2][2][2] = vb3z / r3;
@@ -324,71 +324,71 @@ void DihedralClass2::compute(int eflag, int vflag)
for (i = 0; i < 2; i++)
for (j = 0; j < 4; j++)
- for (k = 0; k < 3; k++)
- dthetadr[i][j][k] = 0.0;
-
+ for (k = 0; k < 3; k++)
+ dthetadr[i][j][k] = 0.0;
+
t1 = costh12 / r1mag2;
t2 = costh23 / r2mag2;
t3 = costh12 / r2mag2;
t4 = costh23 / r3mag2;
-
+
// angle12
-
+
dthetadr[0][0][0] = sc1 * ((t1 * vb1x) - (vb2x * r12c1));
dthetadr[0][0][1] = sc1 * ((t1 * vb1y) - (vb2y * r12c1));
dthetadr[0][0][2] = sc1 * ((t1 * vb1z) - (vb2z * r12c1));
-
+
dthetadr[0][1][0] = sc1 * ((-t1 * vb1x) + (vb2x * r12c1) +
- (-t3 * vb2x) + (vb1x * r12c1));
+ (-t3 * vb2x) + (vb1x * r12c1));
dthetadr[0][1][1] = sc1 * ((-t1 * vb1y) + (vb2y * r12c1) +
- (-t3 * vb2y) + (vb1y * r12c1));
+ (-t3 * vb2y) + (vb1y * r12c1));
dthetadr[0][1][2] = sc1 * ((-t1 * vb1z) + (vb2z * r12c1) +
- (-t3 * vb2z) + (vb1z * r12c1));
-
- dthetadr[0][2][0] = sc1 * ((t3 * vb2x) - (vb1x * r12c1));
+ (-t3 * vb2z) + (vb1z * r12c1));
+
+ dthetadr[0][2][0] = sc1 * ((t3 * vb2x) - (vb1x * r12c1));
dthetadr[0][2][1] = sc1 * ((t3 * vb2y) - (vb1y * r12c1));
dthetadr[0][2][2] = sc1 * ((t3 * vb2z) - (vb1z * r12c1));
-
+
// angle23
-
+
dthetadr[1][1][0] = sc2 * ((t2 * vb2x) + (vb3x * r12c2));
dthetadr[1][1][1] = sc2 * ((t2 * vb2y) + (vb3y * r12c2));
dthetadr[1][1][2] = sc2 * ((t2 * vb2z) + (vb3z * r12c2));
-
+
dthetadr[1][2][0] = sc2 * ((-t2 * vb2x) - (vb3x * r12c2) +
- (t4 * vb3x) + (vb2x * r12c2));
+ (t4 * vb3x) + (vb2x * r12c2));
dthetadr[1][2][1] = sc2 * ((-t2 * vb2y) - (vb3y * r12c2) +
- (t4 * vb3y) + (vb2y * r12c2));
+ (t4 * vb3y) + (vb2y * r12c2));
dthetadr[1][2][2] = sc2 * ((-t2 * vb2z) - (vb3z * r12c2) +
- (t4 * vb3z) + (vb2z * r12c2));
-
+ (t4 * vb3z) + (vb2z * r12c2));
+
dthetadr[1][3][0] = -sc2 * ((t4 * vb3x) + (vb2x * r12c2));
dthetadr[1][3][1] = -sc2 * ((t4 * vb3y) + (vb2y * r12c2));
dthetadr[1][3][2] = -sc2 * ((t4 * vb3z) + (vb2z * r12c2));
-
+
// mid-bond/torsion coupling
// energy on bond2 (middle bond)
-
+
cos2phi = cos(2.0*phi);
cos3phi = cos(3.0*phi);
-
+
bt1 = mbt_f1[type] * cosphi;
bt2 = mbt_f2[type] * cos2phi;
bt3 = mbt_f3[type] * cos3phi;
sumbte = bt1 + bt2 + bt3;
db = r2 - mbt_r0[type];
if (eflag) edihedral += db * sumbte;
-
+
// force on bond2
-
+
bt1 = -mbt_f1[type] * sinphi;
bt2 = -2.0 * mbt_f2[type] * sin(2.0*phi);
bt3 = -3.0 * mbt_f3[type] * sin(3.0*phi);
sumbtf = bt1 + bt2 + bt3;
-
+
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
- fabcd[i][j] += db*sumbtf*dphidr[i][j] + sumbte*dbonddr[1][i][j];
+ fabcd[i][j] += db*sumbtf*dphidr[i][j] + sumbte*dbonddr[1][i][j];
// end-bond/torsion coupling
// energy on bond1 (first bond)
@@ -410,7 +410,7 @@ void DihedralClass2::compute(int eflag, int vflag)
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
- fabcd[i][j] -= db*sumbtf*dphidr[i][j] + sumbte*dbonddr[0][i][j];
+ fabcd[i][j] -= db*sumbtf*dphidr[i][j] + sumbte*dbonddr[0][i][j];
// end-bond/torsion coupling
// energy on bond3 (last bond)
@@ -432,7 +432,7 @@ void DihedralClass2::compute(int eflag, int vflag)
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
- fabcd[i][j] += db*sumbtf*dphidr[i][j] + sumbte*dbonddr[2][i][j];
+ fabcd[i][j] += db*sumbtf*dphidr[i][j] + sumbte*dbonddr[2][i][j];
// angle/torsion coupling
// energy on angle1
@@ -454,7 +454,7 @@ void DihedralClass2::compute(int eflag, int vflag)
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
- fabcd[i][j] -= da*sumbtf*dphidr[i][j] + sumbte*dthetadr[0][i][j];
+ fabcd[i][j] -= da*sumbtf*dphidr[i][j] + sumbte*dthetadr[0][i][j];
// energy on angle2
@@ -475,20 +475,20 @@ void DihedralClass2::compute(int eflag, int vflag)
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
- fabcd[i][j] += da*sumbtf*dphidr[i][j] + sumbte*dthetadr[1][i][j];
+ fabcd[i][j] += da*sumbtf*dphidr[i][j] + sumbte*dthetadr[1][i][j];
// angle/angle/torsion coupling
da1 = acos(costh12) - aat_theta0_1[type];
da2 = acos(costh23) - aat_theta0_2[type];
-
+
if (eflag) edihedral += aat_k[type]*da1*da2*cosphi;
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
- fabcd[i][j] -= aat_k[type] *
- (cosphi * (da2*dthetadr[0][i][j] - da1*dthetadr[1][i][j]) +
- sinphi * da1*da2*dphidr[i][j]);
+ fabcd[i][j] -= aat_k[type] *
+ (cosphi * (da2*dthetadr[0][i][j] - da1*dthetadr[1][i][j]) +
+ sinphi * da1*da2*dphidr[i][j]);
// bond1/bond3 coupling
@@ -502,7 +502,7 @@ void DihedralClass2::compute(int eflag, int vflag)
tk2 = -bb13t_k[type] * dr2 / r1;
if (eflag) edihedral += bb13t_k[type]*dr1*dr2;
-
+
fabcd[0][0] += tk2 * vb1x;
fabcd[0][1] += tk2 * vb1y;
fabcd[0][2] += tk2 * vb1z;
@@ -510,7 +510,7 @@ void DihedralClass2::compute(int eflag, int vflag)
fabcd[1][0] -= tk2 * vb1x;
fabcd[1][1] -= tk2 * vb1y;
fabcd[1][2] -= tk2 * vb1z;
-
+
fabcd[2][0] -= tk1 * vb3x;
fabcd[2][1] -= tk1 * vb3y;
fabcd[2][2] -= tk1 * vb3z;
@@ -548,8 +548,8 @@ void DihedralClass2::compute(int eflag, int vflag)
if (evflag)
ev_tally(i1,i2,i3,i4,nlocal,newton_bond,edihedral,
- fabcd[0],fabcd[2],fabcd[3],
- vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
+ fabcd[0],fabcd[2],fabcd[3],
+ vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
}
}
@@ -608,7 +608,7 @@ void DihedralClass2::allocate()
memory->create(setflag_aat,n+1,"dihedral:setflag_aat");
memory->create(setflag_bb13t,n+1,"dihedral:setflag_bb13t");
for (int i = 1; i <= n; i++)
- setflag[i] = setflag_d[i] = setflag_mbt[i] = setflag_ebt[i] =
+ setflag[i] = setflag_d[i] = setflag_mbt[i] = setflag_ebt[i] =
setflag_at[i] = setflag_aat[i] = setflag_bb13t[i] = 0;
}
@@ -639,7 +639,7 @@ void DihedralClass2::coeff(int narg, char **arg)
double f2_one = force->numeric(arg[3]);
double f3_one = force->numeric(arg[4]);
double r0_one = force->numeric(arg[5]);
-
+
for (int i = ilo; i <= ihi; i++) {
mbt_f1[i] = f1_one;
mbt_f2[i] = f2_one;
@@ -660,7 +660,7 @@ void DihedralClass2::coeff(int narg, char **arg)
double f3_2_one = force->numeric(arg[7]);
double r0_1_one = force->numeric(arg[8]);
double r0_2_one = force->numeric(arg[9]);
-
+
for (int i = ilo; i <= ihi; i++) {
ebt_f1_1[i] = f1_1_one;
ebt_f2_1[i] = f2_1_one;
@@ -687,7 +687,7 @@ void DihedralClass2::coeff(int narg, char **arg)
double theta0_2_one = force->numeric(arg[9]);
// convert theta0's from degrees to radians
-
+
for (int i = ilo; i <= ihi; i++) {
at_f1_1[i] = f1_1_one;
at_f2_1[i] = f2_1_one;
@@ -709,7 +709,7 @@ void DihedralClass2::coeff(int narg, char **arg)
double theta0_2_one = force->numeric(arg[4]);
// convert theta0's from degrees to radians
-
+
for (int i = ilo; i <= ihi; i++) {
aat_k[i] = k_one;
aat_theta0_1[i] = theta0_1_one/180.0 * MY_PI;
@@ -724,7 +724,7 @@ void DihedralClass2::coeff(int narg, char **arg)
double k_one = force->numeric(arg[2]);
double r10_one = force->numeric(arg[3]);
double r30_one = force->numeric(arg[4]);
-
+
for (int i = ilo; i <= ihi; i++) {
bb13t_k[i] = k_one;
bb13t_r10[i] = r10_one;
@@ -742,7 +742,7 @@ void DihedralClass2::coeff(int narg, char **arg)
double phi2_one = force->numeric(arg[4]);
double k3_one = force->numeric(arg[5]);
double phi3_one = force->numeric(arg[6]);
-
+
// convert phi's from degrees to radians
for (int i = ilo; i <= ihi; i++) {
@@ -761,12 +761,12 @@ void DihedralClass2::coeff(int narg, char **arg)
for (int i = ilo; i <= ihi; i++)
if (setflag_d[i] == 1 && setflag_mbt[i] == 1 && setflag_ebt[i] == 1 &&
- setflag_at[i] == 1 && setflag_aat[i] == 1 && setflag_bb13t[i] == 1)
+ setflag_at[i] == 1 && setflag_aat[i] == 1 && setflag_bb13t[i] == 1)
setflag[i] = 1;
}
/* ----------------------------------------------------------------------
- proc 0 writes out coeffs to restart file
+ proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void DihedralClass2::write_restart(FILE *fp)
@@ -813,7 +813,7 @@ void DihedralClass2::write_restart(FILE *fp)
}
/* ----------------------------------------------------------------------
- proc 0 reads coeffs from restart file, bcasts them
+ proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void DihedralClass2::read_restart(FILE *fp)
diff --git a/src/CLASS2/dihedral_class2.h b/src/CLASS2/dihedral_class2.h
index 66173efaea8b88fdf72858a52419356f45e9b328..c84ab1d5e9f7bb35d69c82580e3e12d096aa8319 100644
--- a/src/CLASS2/dihedral_class2.h
+++ b/src/CLASS2/dihedral_class2.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/CLASS2/improper_class2.cpp b/src/CLASS2/improper_class2.cpp
index 8a77a16d54cf76b8e74deb59a56b87ee64c8eaed..5c05493840531ad58fb26788a2c916b04ff81018 100644
--- a/src/CLASS2/improper_class2.cpp
+++ b/src/CLASS2/improper_class2.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -91,10 +91,10 @@ void ImproperClass2::compute(int eflag, int vflag)
for (i = 0; i < 3; i++)
for (j = 0; j < 4; j++)
for (k = 0; k < 3; k++) {
- dthetadr[i][j][k] = 0.0;
- drAB[i][j][k] = 0.0;
- drCB[i][j][k] = 0.0;
- drDB[i][j][k] = 0.0;
+ dthetadr[i][j][k] = 0.0;
+ drAB[i][j][k] = 0.0;
+ drCB[i][j][k] = 0.0;
+ drDB[i][j][k] = 0.0;
}
double **x = atom->x;
@@ -133,43 +133,43 @@ void ImproperClass2::compute(int eflag, int vflag)
// bond lengths and associated values
for (i = 0; i < 3; i++) {
- rmag2[i] = delr[i][0]*delr[i][0] + delr[i][1]*delr[i][1] +
- delr[i][2]*delr[i][2];
+ rmag2[i] = delr[i][0]*delr[i][0] + delr[i][1]*delr[i][1] +
+ delr[i][2]*delr[i][2];
rmag[i] = sqrt(rmag2[i]);
rinvmag[i] = 1.0/rmag[i];
}
// angle ABC, CBD, ABD
- costheta[0] = (delr[0][0]*delr[1][0] + delr[0][1]*delr[1][1] +
- delr[0][2]*delr[1][2]) / (rmag[0]*rmag[1]);
- costheta[1] = (delr[1][0]*delr[2][0] + delr[1][1]*delr[2][1] +
- delr[1][2]*delr[2][2]) / (rmag[1]*rmag[2]);
- costheta[2] = (delr[0][0]*delr[2][0] + delr[0][1]*delr[2][1] +
- delr[0][2]*delr[2][2]) / (rmag[0]*rmag[2]);
+ costheta[0] = (delr[0][0]*delr[1][0] + delr[0][1]*delr[1][1] +
+ delr[0][2]*delr[1][2]) / (rmag[0]*rmag[1]);
+ costheta[1] = (delr[1][0]*delr[2][0] + delr[1][1]*delr[2][1] +
+ delr[1][2]*delr[2][2]) / (rmag[1]*rmag[2]);
+ costheta[2] = (delr[0][0]*delr[2][0] + delr[0][1]*delr[2][1] +
+ delr[0][2]*delr[2][2]) / (rmag[0]*rmag[2]);
// angle error check
for (i = 0; i < 3; i++) {
if (costheta[i] == -1.0) {
- int me;
- MPI_Comm_rank(world,&me);
- if (screen) {
- char str[128];
- sprintf(str,
- "Improper problem: %d " BIGINT_FORMAT " %d %d %d %d",
- me,update->ntimestep,
- atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
- error->warning(FLERR,str,0);
- fprintf(screen," 1st atom: %d %g %g %g\n",
- me,x[i1][0],x[i1][1],x[i1][2]);
- fprintf(screen," 2nd atom: %d %g %g %g\n",
- me,x[i2][0],x[i2][1],x[i2][2]);
- fprintf(screen," 3rd atom: %d %g %g %g\n",
- me,x[i3][0],x[i3][1],x[i3][2]);
- fprintf(screen," 4th atom: %d %g %g %g\n",
- me,x[i4][0],x[i4][1],x[i4][2]);
- }
+ int me;
+ MPI_Comm_rank(world,&me);
+ if (screen) {
+ char str[128];
+ sprintf(str,
+ "Improper problem: %d " BIGINT_FORMAT " %d %d %d %d",
+ me,update->ntimestep,
+ atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
+ error->warning(FLERR,str,0);
+ fprintf(screen," 1st atom: %d %g %g %g\n",
+ me,x[i1][0],x[i1][1],x[i1][2]);
+ fprintf(screen," 2nd atom: %d %g %g %g\n",
+ me,x[i2][0],x[i2][1],x[i2][2]);
+ fprintf(screen," 3rd atom: %d %g %g %g\n",
+ me,x[i3][0],x[i3][1],x[i3][2]);
+ fprintf(screen," 4th atom: %d %g %g %g\n",
+ me,x[i4][0],x[i4][1],x[i4][2]);
+ }
}
}
@@ -223,7 +223,7 @@ void ImproperClass2::compute(int eflag, int vflag)
for (i = 0; i < 3; i++)
for (j = 0; j < 4; j++)
- ddelr[i][j] = 0.0;
+ ddelr[i][j] = 0.0;
ddelr[0][0] = 1.0;
ddelr[0][1] = -1.0;
@@ -238,19 +238,19 @@ void ImproperClass2::compute(int eflag, int vflag)
for (i = 0; i < 3; i++)
for (j = 0; j < 4; j++)
- for (k = 0; k < 3; k++) {
- dr[i][j][k] = delr[i][k] * ddelr[i][j] / rmag[i];
- dinvr[i][j][k] = -dr[i][j][k] / rmag2[i];
- }
+ for (k = 0; k < 3; k++) {
+ dr[i][j][k] = delr[i][k] * ddelr[i][j] / rmag[i];
+ dinvr[i][j][k] = -dr[i][j][k] / rmag2[i];
+ }
// compute d(1 / (|r_AB| * |r_CB| * |r_DB|) / dr
// i = atom A/B/C/D, j = X/Y/Z
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
- dinv3r[i][j] = rinvmag[1] * (rinvmag[2] * dinvr[0][i][j] +
- rinvmag[0] * dinvr[2][i][j]) +
- rinvmag[2] * rinvmag[0] * dinvr[1][i][j];
+ dinv3r[i][j] = rinvmag[1] * (rinvmag[2] * dinvr[0][i][j] +
+ rinvmag[0] * dinvr[2][i][j]) +
+ rinvmag[2] * rinvmag[0] * dinvr[1][i][j];
// compute d(theta)/d(r) for 3 angles
// angleABC
@@ -259,30 +259,30 @@ void ImproperClass2::compute(int eflag, int vflag)
tt3 = costheta[0] / rmag2[1];
sc1 = 1.0 / sqrt(1.0 - cossqtheta[0]);
- dthetadr[0][0][0] = sc1 * ((tt1 * delr[0][0]) -
- (delr[1][0] * rinvmag[0] * rinvmag[1]));
- dthetadr[0][0][1] = sc1 * ((tt1 * delr[0][1]) -
- (delr[1][1] * rinvmag[0] * rinvmag[1]));
- dthetadr[0][0][2] = sc1 * ((tt1 * delr[0][2]) -
- (delr[1][2] * rinvmag[0] * rinvmag[1]));
- dthetadr[0][1][0] = -sc1 * ((tt1 * delr[0][0]) -
- (delr[1][0] * rinvmag[0] * rinvmag[1]) +
- (tt3 * delr[1][0]) -
- (delr[0][0] * rinvmag[0] * rinvmag[1]));
- dthetadr[0][1][1] = -sc1 * ((tt1 * delr[0][1]) -
- (delr[1][1] * rinvmag[0] * rinvmag[1]) +
- (tt3 * delr[1][1]) -
- (delr[0][1] * rinvmag[0] * rinvmag[1]));
- dthetadr[0][1][2] = -sc1 * ((tt1 * delr[0][2]) -
- (delr[1][2] * rinvmag[0] * rinvmag[1]) +
- (tt3 * delr[1][2]) -
- (delr[0][2] * rinvmag[0] * rinvmag[1]));
- dthetadr[0][2][0] = sc1 * ((tt3 * delr[1][0]) -
- (delr[0][0] * rinvmag[0] * rinvmag[1]));
- dthetadr[0][2][1] = sc1 * ((tt3 * delr[1][1]) -
- (delr[0][1] * rinvmag[0] * rinvmag[1]));
- dthetadr[0][2][2] = sc1 * ((tt3 * delr[1][2]) -
- (delr[0][2] * rinvmag[0] * rinvmag[1]));
+ dthetadr[0][0][0] = sc1 * ((tt1 * delr[0][0]) -
+ (delr[1][0] * rinvmag[0] * rinvmag[1]));
+ dthetadr[0][0][1] = sc1 * ((tt1 * delr[0][1]) -
+ (delr[1][1] * rinvmag[0] * rinvmag[1]));
+ dthetadr[0][0][2] = sc1 * ((tt1 * delr[0][2]) -
+ (delr[1][2] * rinvmag[0] * rinvmag[1]));
+ dthetadr[0][1][0] = -sc1 * ((tt1 * delr[0][0]) -
+ (delr[1][0] * rinvmag[0] * rinvmag[1]) +
+ (tt3 * delr[1][0]) -
+ (delr[0][0] * rinvmag[0] * rinvmag[1]));
+ dthetadr[0][1][1] = -sc1 * ((tt1 * delr[0][1]) -
+ (delr[1][1] * rinvmag[0] * rinvmag[1]) +
+ (tt3 * delr[1][1]) -
+ (delr[0][1] * rinvmag[0] * rinvmag[1]));
+ dthetadr[0][1][2] = -sc1 * ((tt1 * delr[0][2]) -
+ (delr[1][2] * rinvmag[0] * rinvmag[1]) +
+ (tt3 * delr[1][2]) -
+ (delr[0][2] * rinvmag[0] * rinvmag[1]));
+ dthetadr[0][2][0] = sc1 * ((tt3 * delr[1][0]) -
+ (delr[0][0] * rinvmag[0] * rinvmag[1]));
+ dthetadr[0][2][1] = sc1 * ((tt3 * delr[1][1]) -
+ (delr[0][1] * rinvmag[0] * rinvmag[1]));
+ dthetadr[0][2][2] = sc1 * ((tt3 * delr[1][2]) -
+ (delr[0][2] * rinvmag[0] * rinvmag[1]));
// angleCBD
@@ -290,30 +290,30 @@ void ImproperClass2::compute(int eflag, int vflag)
tt3 = costheta[1] / rmag2[2];
sc1 = 1.0 / sqrt(1.0 - cossqtheta[1]);
- dthetadr[1][2][0] = sc1 * ((tt1 * delr[1][0]) -
- (delr[2][0] * rinvmag[1] * rinvmag[2]));
- dthetadr[1][2][1] = sc1 * ((tt1 * delr[1][1]) -
- (delr[2][1] * rinvmag[1] * rinvmag[2]));
- dthetadr[1][2][2] = sc1 * ((tt1 * delr[1][2]) -
- (delr[2][2] * rinvmag[1] * rinvmag[2]));
- dthetadr[1][1][0] = -sc1 * ((tt1 * delr[1][0]) -
- (delr[2][0] * rinvmag[1] * rinvmag[2]) +
- (tt3 * delr[2][0]) -
- (delr[1][0] * rinvmag[2] * rinvmag[1]));
- dthetadr[1][1][1] = -sc1 * ((tt1 * delr[1][1]) -
- (delr[2][1] * rinvmag[1] * rinvmag[2]) +
- (tt3 * delr[2][1]) -
- (delr[1][1] * rinvmag[2] * rinvmag[1]));
- dthetadr[1][1][2] = -sc1 * ((tt1 * delr[1][2]) -
- (delr[2][2] * rinvmag[1] * rinvmag[2]) +
- (tt3 * delr[2][2]) -
- (delr[1][2] * rinvmag[2] * rinvmag[1]));
- dthetadr[1][3][0] = sc1 * ((tt3 * delr[2][0]) -
- (delr[1][0] * rinvmag[2] * rinvmag[1]));
- dthetadr[1][3][1] = sc1 * ((tt3 * delr[2][1]) -
- (delr[1][1] * rinvmag[2] * rinvmag[1]));
- dthetadr[1][3][2] = sc1 * ((tt3 * delr[2][2]) -
- (delr[1][2] * rinvmag[2] * rinvmag[1]));
+ dthetadr[1][2][0] = sc1 * ((tt1 * delr[1][0]) -
+ (delr[2][0] * rinvmag[1] * rinvmag[2]));
+ dthetadr[1][2][1] = sc1 * ((tt1 * delr[1][1]) -
+ (delr[2][1] * rinvmag[1] * rinvmag[2]));
+ dthetadr[1][2][2] = sc1 * ((tt1 * delr[1][2]) -
+ (delr[2][2] * rinvmag[1] * rinvmag[2]));
+ dthetadr[1][1][0] = -sc1 * ((tt1 * delr[1][0]) -
+ (delr[2][0] * rinvmag[1] * rinvmag[2]) +
+ (tt3 * delr[2][0]) -
+ (delr[1][0] * rinvmag[2] * rinvmag[1]));
+ dthetadr[1][1][1] = -sc1 * ((tt1 * delr[1][1]) -
+ (delr[2][1] * rinvmag[1] * rinvmag[2]) +
+ (tt3 * delr[2][1]) -
+ (delr[1][1] * rinvmag[2] * rinvmag[1]));
+ dthetadr[1][1][2] = -sc1 * ((tt1 * delr[1][2]) -
+ (delr[2][2] * rinvmag[1] * rinvmag[2]) +
+ (tt3 * delr[2][2]) -
+ (delr[1][2] * rinvmag[2] * rinvmag[1]));
+ dthetadr[1][3][0] = sc1 * ((tt3 * delr[2][0]) -
+ (delr[1][0] * rinvmag[2] * rinvmag[1]));
+ dthetadr[1][3][1] = sc1 * ((tt3 * delr[2][1]) -
+ (delr[1][1] * rinvmag[2] * rinvmag[1]));
+ dthetadr[1][3][2] = sc1 * ((tt3 * delr[2][2]) -
+ (delr[1][2] * rinvmag[2] * rinvmag[1]));
// angleABD
@@ -321,30 +321,30 @@ void ImproperClass2::compute(int eflag, int vflag)
tt3 = costheta[2] / rmag2[2];
sc1 = 1.0 / sqrt(1.0 - cossqtheta[2]);
- dthetadr[2][0][0] = sc1 * ((tt1 * delr[0][0]) -
- (delr[2][0] * rinvmag[0] * rinvmag[2]));
- dthetadr[2][0][1] = sc1 * ((tt1 * delr[0][1]) -
- (delr[2][1] * rinvmag[0] * rinvmag[2]));
- dthetadr[2][0][2] = sc1 * ((tt1 * delr[0][2]) -
- (delr[2][2] * rinvmag[0] * rinvmag[2]));
- dthetadr[2][1][0] = -sc1 * ((tt1 * delr[0][0]) -
- (delr[2][0] * rinvmag[0] * rinvmag[2]) +
- (tt3 * delr[2][0]) -
- (delr[0][0] * rinvmag[2] * rinvmag[0]));
- dthetadr[2][1][1] = -sc1 * ((tt1 * delr[0][1]) -
- (delr[2][1] * rinvmag[0] * rinvmag[2]) +
- (tt3 * delr[2][1]) -
- (delr[0][1] * rinvmag[2] * rinvmag[0]));
- dthetadr[2][1][2] = -sc1 * ((tt1 * delr[0][2]) -
- (delr[2][2] * rinvmag[0] * rinvmag[2]) +
- (tt3 * delr[2][2]) -
- (delr[0][2] * rinvmag[2] * rinvmag[0]));
- dthetadr[2][3][0] = sc1 * ((tt3 * delr[2][0]) -
- (delr[0][0] * rinvmag[2] * rinvmag[0]));
- dthetadr[2][3][1] = sc1 * ((tt3 * delr[2][1]) -
- (delr[0][1] * rinvmag[2] * rinvmag[0]));
- dthetadr[2][3][2] = sc1 * ((tt3 * delr[2][2]) -
- (delr[0][2] * rinvmag[2] * rinvmag[0]));
+ dthetadr[2][0][0] = sc1 * ((tt1 * delr[0][0]) -
+ (delr[2][0] * rinvmag[0] * rinvmag[2]));
+ dthetadr[2][0][1] = sc1 * ((tt1 * delr[0][1]) -
+ (delr[2][1] * rinvmag[0] * rinvmag[2]));
+ dthetadr[2][0][2] = sc1 * ((tt1 * delr[0][2]) -
+ (delr[2][2] * rinvmag[0] * rinvmag[2]));
+ dthetadr[2][1][0] = -sc1 * ((tt1 * delr[0][0]) -
+ (delr[2][0] * rinvmag[0] * rinvmag[2]) +
+ (tt3 * delr[2][0]) -
+ (delr[0][0] * rinvmag[2] * rinvmag[0]));
+ dthetadr[2][1][1] = -sc1 * ((tt1 * delr[0][1]) -
+ (delr[2][1] * rinvmag[0] * rinvmag[2]) +
+ (tt3 * delr[2][1]) -
+ (delr[0][1] * rinvmag[2] * rinvmag[0]));
+ dthetadr[2][1][2] = -sc1 * ((tt1 * delr[0][2]) -
+ (delr[2][2] * rinvmag[0] * rinvmag[2]) +
+ (tt3 * delr[2][2]) -
+ (delr[0][2] * rinvmag[2] * rinvmag[0]));
+ dthetadr[2][3][0] = sc1 * ((tt3 * delr[2][0]) -
+ (delr[0][0] * rinvmag[2] * rinvmag[0]));
+ dthetadr[2][3][1] = sc1 * ((tt3 * delr[2][1]) -
+ (delr[0][1] * rinvmag[2] * rinvmag[0]));
+ dthetadr[2][3][2] = sc1 * ((tt3 * delr[2][2]) -
+ (delr[0][2] * rinvmag[2] * rinvmag[0]));
// compute d( 1 / sin(theta))/dr
// i = angle, j = atom, k = direction
@@ -352,8 +352,8 @@ void ImproperClass2::compute(int eflag, int vflag)
for (i = 0; i < 3; i++) {
cossin2 = -costheta[i] / sinsqtheta[i];
for (j = 0; j < 4; j++)
- for (k = 0; k < 3; k++)
- dinvsth[i][j][k] = cossin2 * dthetadr[i][j][k];
+ for (k = 0; k < 3; k++)
+ dinvsth[i][j][k] = cossin2 * dthetadr[i][j][k];
}
// compute d(1 / sin(theta) * |r_AB| * |r_CB| * |r_DB|)/dr
@@ -361,12 +361,12 @@ void ImproperClass2::compute(int eflag, int vflag)
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++) {
- dinvs3r[0][i][j] = (invstheta[1] * dinv3r[i][j]) +
- (inv3r * dinvsth[1][i][j]);
- dinvs3r[1][i][j] = (invstheta[2] * dinv3r[i][j]) +
- (inv3r * dinvsth[2][i][j]);
- dinvs3r[2][i][j] = (invstheta[0] * dinv3r[i][j]) +
- (inv3r * dinvsth[0][i][j]);
+ dinvs3r[0][i][j] = (invstheta[1] * dinv3r[i][j]) +
+ (inv3r * dinvsth[1][i][j]);
+ dinvs3r[1][i][j] = (invstheta[2] * dinv3r[i][j]) +
+ (inv3r * dinvsth[2][i][j]);
+ dinvs3r[2][i][j] = (invstheta[0] * dinv3r[i][j]) +
+ (inv3r * dinvsth[0][i][j]);
}
// drCB(i,j,k), etc
@@ -390,12 +390,12 @@ void ImproperClass2::compute(int eflag, int vflag)
for (i = 0; i < 3; i++)
for (j = 0; j < 4; j++) {
- cross(delr[1],drDB[i][j],rCBxdrDB);
- cross(drCB[i][j],delr[2],drCBxrDB);
- for (k = 0; k < 3; k++) dd[k] = rCBxdrDB[k] + drCBxrDB[k];
- dot1 = dot(dd,delr[0]);
- dot2 = dot(rCBxrDB,drAB[i][j]);
- fdot[0][j][i] = dot1 + dot2;
+ cross(delr[1],drDB[i][j],rCBxdrDB);
+ cross(drCB[i][j],delr[2],drCBxrDB);
+ for (k = 0; k < 3; k++) dd[k] = rCBxdrDB[k] + drCBxrDB[k];
+ dot1 = dot(dd,delr[0]);
+ dot2 = dot(rCBxrDB,drAB[i][j]);
+ fdot[0][j][i] = dot1 + dot2;
}
// d((r_DB x r_AB) dot r_CB)
@@ -407,12 +407,12 @@ void ImproperClass2::compute(int eflag, int vflag)
for (i = 0; i < 3; i++)
for (j = 0; j < 4; j++) {
- cross(delr[2],drAB[i][j],rDBxdrAB);
- cross(drDB[i][j],delr[0],drDBxrAB);
- for (k = 0; k < 3; k++) dd[k] = rDBxdrAB[k] + drDBxrAB[k];
- dot1 = dot(dd,delr[1]);
- dot2 = dot(rDBxrAB,drCB[i][j]);
- fdot[1][j][i] = dot1 + dot2;
+ cross(delr[2],drAB[i][j],rDBxdrAB);
+ cross(drDB[i][j],delr[0],drDBxrAB);
+ for (k = 0; k < 3; k++) dd[k] = rDBxdrAB[k] + drDBxrAB[k];
+ dot1 = dot(dd,delr[1]);
+ dot2 = dot(rDBxrAB,drCB[i][j]);
+ fdot[1][j][i] = dot1 + dot2;
}
// d((r_AB x r_CB) dot r_DB)
@@ -424,33 +424,33 @@ void ImproperClass2::compute(int eflag, int vflag)
for (i = 0; i < 3; i++)
for (j = 0; j < 4; j++) {
- cross(delr[0],drCB[i][j],rABxdrCB);
- cross(drAB[i][j],delr[1],drABxrCB);
- for (k = 0; k < 3; k++) dd[k] = rABxdrCB[k] + drABxrCB[k];
- dot1 = dot(dd,delr[2]);
- dot2 = dot(rABxrCB,drDB[i][j]);
- fdot[2][j][i] = dot1 + dot2;
+ cross(delr[0],drCB[i][j],rABxdrCB);
+ cross(drAB[i][j],delr[1],drABxrCB);
+ for (k = 0; k < 3; k++) dd[k] = rABxdrCB[k] + drABxrCB[k];
+ dot1 = dot(dd,delr[2]);
+ dot2 = dot(rABxrCB,drDB[i][j]);
+ fdot[2][j][i] = dot1 + dot2;
}
// force on each atom
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++) {
- ftmp = (fdot[0][i][j] * invs3r[0]) +
- (dinvs3r[0][i][j] * dotCBDBAB);
- dchi[0][i][j] = ftmp / cos(chiABCD);
- ftmp = (fdot[1][i][j] * invs3r[1]) +
- (dinvs3r[1][i][j] * dotDBABCB);
- dchi[1][i][j] = ftmp / cos(chiCBDA);
- ftmp = (fdot[2][i][j] * invs3r[2]) +
- (dinvs3r[2][i][j] * dotABCBDB);
- dchi[2][i][j] = ftmp / cos(chiDBAC);
- dtotalchi[i][j] = (dchi[0][i][j]+dchi[1][i][j]+dchi[2][i][j]) / 3.0;
+ ftmp = (fdot[0][i][j] * invs3r[0]) +
+ (dinvs3r[0][i][j] * dotCBDBAB);
+ dchi[0][i][j] = ftmp / cos(chiABCD);
+ ftmp = (fdot[1][i][j] * invs3r[1]) +
+ (dinvs3r[1][i][j] * dotDBABCB);
+ dchi[1][i][j] = ftmp / cos(chiCBDA);
+ ftmp = (fdot[2][i][j] * invs3r[2]) +
+ (dinvs3r[2][i][j] * dotABCBDB);
+ dchi[2][i][j] = ftmp / cos(chiDBAC);
+ dtotalchi[i][j] = (dchi[0][i][j]+dchi[1][i][j]+dchi[2][i][j]) / 3.0;
}
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
- fabcd[i][j] = -2.0*k0[type] * deltachi*dtotalchi[i][j];
+ fabcd[i][j] = -2.0*k0[type] * deltachi*dtotalchi[i][j];
// apply force to each of 4 atoms
@@ -480,11 +480,11 @@ void ImproperClass2::compute(int eflag, int vflag)
if (evflag)
ev_tally(i1,i2,i3,i4,nlocal,newton_bond,eimproper,
- fabcd[0],fabcd[2],fabcd[3],
- delr[0][0],delr[0][1],delr[0][2],
- delr[1][0],delr[1][1],delr[1][2],
- delr[2][0]-delr[1][0],delr[2][1]-delr[1][1],
- delr[2][2]-delr[1][2]);
+ fabcd[0],fabcd[2],fabcd[3],
+ delr[0][0],delr[0][1],delr[0][2],
+ delr[1][0],delr[1][1],delr[1][2],
+ delr[2][0]-delr[1][0],delr[2][1]-delr[1][1],
+ delr[2][2]-delr[1][2]);
}
// compute angle-angle interactions
@@ -541,7 +541,7 @@ void ImproperClass2::coeff(int narg, char **arg)
double theta0_1_one = force->numeric(arg[5]);
double theta0_2_one = force->numeric(arg[6]);
double theta0_3_one = force->numeric(arg[7]);
-
+
// convert theta0's from degrees to radians
for (int i = ilo; i <= ihi; i++) {
@@ -578,7 +578,7 @@ void ImproperClass2::coeff(int narg, char **arg)
}
/* ----------------------------------------------------------------------
- proc 0 writes out coeffs to restart file
+ proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void ImproperClass2::write_restart(FILE *fp)
@@ -595,7 +595,7 @@ void ImproperClass2::write_restart(FILE *fp)
}
/* ----------------------------------------------------------------------
- proc 0 reads coeffs from restart file, bcasts them
+ proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void ImproperClass2::read_restart(FILE *fp)
@@ -681,7 +681,7 @@ void ImproperClass2::angleangle(int eflag, int vflag)
rBC = sqrt(rBCmag2);
rBDmag2 = delxBD*delxBD + delyBD*delyBD + delzBD*delzBD;
rBD = sqrt(rBDmag2);
-
+
// angle ABC, ABD, CBD
costhABC = (delxAB*delxBC + delyAB*delyBC + delzAB*delzBC) / (rAB * rBC);
@@ -705,17 +705,17 @@ void ImproperClass2::angleangle(int eflag, int vflag)
// energy
- if (eflag) eimproper = aa_k2[type] * dthABC * dthABD +
- aa_k1[type] * dthABC * dthCBD +
- aa_k3[type] * dthABD * dthCBD;
+ if (eflag) eimproper = aa_k2[type] * dthABC * dthABD +
+ aa_k1[type] * dthABC * dthCBD +
+ aa_k3[type] * dthABD * dthCBD;
// d(theta)/d(r) array
// angle i, atom j, coordinate k
for (i = 0; i < 3; i++)
for (j = 0; j < 4; j++)
- for (k = 0; k < 3; k++)
- dthetadr[i][j][k] = 0.0;
+ for (k = 0; k < 3; k++)
+ dthetadr[i][j][k] = 0.0;
// angle ABC
@@ -728,11 +728,11 @@ void ImproperClass2::angleangle(int eflag, int vflag)
dthetadr[0][0][1] = sc1 * ((t1 * delyAB) - (delyBC * r12));
dthetadr[0][0][2] = sc1 * ((t1 * delzAB) - (delzBC * r12));
dthetadr[0][1][0] = sc1 * ((-t1 * delxAB) + (delxBC * r12) +
- (-t3 * delxBC) + (delxAB * r12));
+ (-t3 * delxBC) + (delxAB * r12));
dthetadr[0][1][1] = sc1 * ((-t1 * delyAB) + (delyBC * r12) +
- (-t3 * delyBC) + (delyAB * r12));
+ (-t3 * delyBC) + (delyAB * r12));
dthetadr[0][1][2] = sc1 * ((-t1 * delzAB) + (delzBC * r12) +
- (-t3 * delzBC) + (delzAB * r12));
+ (-t3 * delzBC) + (delzAB * r12));
dthetadr[0][2][0] = sc1 * ((t3 * delxBC) - (delxAB * r12));
dthetadr[0][2][1] = sc1 * ((t3 * delyBC) - (delyAB * r12));
dthetadr[0][2][2] = sc1 * ((t3 * delzBC) - (delzAB * r12));
@@ -748,11 +748,11 @@ void ImproperClass2::angleangle(int eflag, int vflag)
dthetadr[1][2][1] = sc1 * ((t1 * delyBC) - (delyBD * r12));
dthetadr[1][2][2] = sc1 * ((t1 * delzBC) - (delzBD * r12));
dthetadr[1][1][0] = sc1 * ((-t1 * delxBC) + (delxBD * r12) +
- (-t3 * delxBD) + (delxBC * r12));
+ (-t3 * delxBD) + (delxBC * r12));
dthetadr[1][1][1] = sc1 * ((-t1 * delyBC) + (delyBD * r12) +
- (-t3 * delyBD) + (delyBC * r12));
+ (-t3 * delyBD) + (delyBC * r12));
dthetadr[1][1][2] = sc1 * ((-t1 * delzBC) + (delzBD * r12) +
- (-t3 * delzBD) + (delzBC * r12));
+ (-t3 * delzBD) + (delzBC * r12));
dthetadr[1][3][0] = sc1 * ((t3 * delxBD) - (delxBC * r12));
dthetadr[1][3][1] = sc1 * ((t3 * delyBD) - (delyBC * r12));
dthetadr[1][3][2] = sc1 * ((t3 * delzBD) - (delzBC * r12));
@@ -768,11 +768,11 @@ void ImproperClass2::angleangle(int eflag, int vflag)
dthetadr[2][0][1] = sc1 * ((t1 * delyAB) - (delyBD * r12));
dthetadr[2][0][2] = sc1 * ((t1 * delzAB) - (delzBD * r12));
dthetadr[2][1][0] = sc1 * ((-t1 * delxAB) + (delxBD * r12) +
- (-t3 * delxBD) + (delxAB * r12));
+ (-t3 * delxBD) + (delxAB * r12));
dthetadr[2][1][1] = sc1 * ((-t1 * delyAB) + (delyBD * r12) +
- (-t3 * delyBD) + (delyAB * r12));
+ (-t3 * delyBD) + (delyAB * r12));
dthetadr[2][1][2] = sc1 * ((-t1 * delzAB) + (delzBD * r12) +
- (-t3 * delzBD) + (delzAB * r12));
+ (-t3 * delzBD) + (delzAB * r12));
dthetadr[2][3][0] = sc1 * ((t3 * delxBD) - (delxAB * r12));
dthetadr[2][3][1] = sc1 * ((t3 * delyBD) - (delyAB * r12));
dthetadr[2][3][2] = sc1 * ((t3 * delzBD) - (delzAB * r12));
@@ -781,13 +781,13 @@ void ImproperClass2::angleangle(int eflag, int vflag)
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
- fabcd[i][j] = -
- ((aa_k1[type] *
- (dthABC*dthetadr[1][i][j] + dthCBD*dthetadr[0][i][j])) +
- (aa_k2[type] *
- (dthABC*dthetadr[2][i][j] + dthABD*dthetadr[0][i][j])) +
- (aa_k3[type] *
- (dthABD*dthetadr[1][i][j] + dthCBD*dthetadr[2][i][j])));
+ fabcd[i][j] = -
+ ((aa_k1[type] *
+ (dthABC*dthetadr[1][i][j] + dthCBD*dthetadr[0][i][j])) +
+ (aa_k2[type] *
+ (dthABC*dthetadr[2][i][j] + dthABD*dthetadr[0][i][j])) +
+ (aa_k3[type] *
+ (dthABD*dthetadr[1][i][j] + dthCBD*dthetadr[2][i][j])));
// apply force to each of 4 atoms
@@ -817,8 +817,8 @@ void ImproperClass2::angleangle(int eflag, int vflag)
if (evflag)
ev_tally(i1,i2,i3,i4,nlocal,newton_bond,eimproper,
- fabcd[0],fabcd[2],fabcd[3],
- delxAB,delyAB,delzAB,delxBC,delyBC,delzBC,delxBD,delyBD,delzBD);
+ fabcd[0],fabcd[2],fabcd[3],
+ delxAB,delyAB,delzAB,delxBC,delyBC,delzBC,delxBD,delyBD,delzBD);
}
}
diff --git a/src/CLASS2/improper_class2.h b/src/CLASS2/improper_class2.h
index 1e47b407c4a66b9ffca9ebaa396c137093878f5a..b6e40aad3e575d825adef7585a51ad0d1c08e5e0 100644
--- a/src/CLASS2/improper_class2.h
+++ b/src/CLASS2/improper_class2.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/CLASS2/pair_lj_class2.cpp b/src/CLASS2/pair_lj_class2.cpp
index ee5d7d3e322b46fe1ea4ac71f84f8e56e556bccb..5c8b419b197a4f415c9d64d18a2a7f057a40fa65 100644
--- a/src/CLASS2/pair_lj_class2.cpp
+++ b/src/CLASS2/pair_lj_class2.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -73,7 +73,7 @@ void PairLJClass2::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@@ -97,30 +97,30 @@ void PairLJClass2::compute(int eflag, int vflag)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- rinv = sqrt(r2inv);
- r3inv = r2inv*rinv;
- r6inv = r3inv*r3inv;
- forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
- fpair = factor_lj*forcelj*r2inv;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (eflag) {
- evdwl = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) -
- offset[itype][jtype];
- evdwl *= factor_lj;
- }
-
- if (evflag) ev_tally(i,j,nlocal,newton_pair,
- evdwl,0.0,fpair,delx,dely,delz);
+ r2inv = 1.0/rsq;
+ rinv = sqrt(r2inv);
+ r3inv = r2inv*rinv;
+ r6inv = r3inv*r3inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
+ fpair = factor_lj*forcelj*r2inv;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (eflag) {
+ evdwl = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) -
+ offset[itype][jtype];
+ evdwl *= factor_lj;
+ }
+
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ evdwl,0.0,fpair,delx,dely,delz);
}
}
}
@@ -129,7 +129,7 @@ void PairLJClass2::compute(int eflag, int vflag)
}
/* ----------------------------------------------------------------------
- allocate all arrays
+ allocate all arrays
------------------------------------------------------------------------- */
void PairLJClass2::allocate()
@@ -155,7 +155,7 @@ void PairLJClass2::allocate()
}
/* ----------------------------------------------------------------------
- global settings
+ global settings
------------------------------------------------------------------------- */
void PairLJClass2::settings(int narg, char **arg)
@@ -170,7 +170,7 @@ void PairLJClass2::settings(int narg, char **arg)
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
- if (setflag[i][j]) cut[i][j] = cut_global;
+ if (setflag[i][j]) cut[i][j] = cut_global;
}
}
@@ -218,9 +218,9 @@ double PairLJClass2::init_one(int i, int j)
if (setflag[i][j] == 0) {
epsilon[i][j] = 2.0 * sqrt(epsilon[i][i]*epsilon[j][j]) *
- pow(sigma[i][i],3.0) * pow(sigma[j][j],3.0) /
+ pow(sigma[i][i],3.0) * pow(sigma[j][j],3.0) /
(pow(sigma[i][i],6.0) + pow(sigma[j][j],6.0));
- sigma[i][j] =
+ sigma[i][j] =
pow((0.5 * (pow(sigma[i][i],6.0) + pow(sigma[j][j],6.0))),1.0/6.0);
cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
}
@@ -255,22 +255,22 @@ double PairLJClass2::init_one(int i, int j)
if (type[k] == j) count[1] += 1.0;
}
MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world);
-
+
double sig3 = sigma[i][j]*sigma[i][j]*sigma[i][j];
double sig6 = sig3*sig3;
double rc3 = cut[i][j]*cut[i][j]*cut[i][j];
double rc6 = rc3*rc3;
etail_ij = 2.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
sig6 * (sig3 - 3.0*rc3) / (3.0*rc6);
- ptail_ij = 2.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
+ ptail_ij = 2.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
sig6 * (sig3 - 2.0*rc3) / rc6;
- }
+ }
return cut[i][j];
}
/* ----------------------------------------------------------------------
- proc 0 writes to restart file
+ proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairLJClass2::write_restart(FILE *fp)
@@ -282,9 +282,9 @@ void PairLJClass2::write_restart(FILE *fp)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
- fwrite(&epsilon[i][j],sizeof(double),1,fp);
- fwrite(&sigma[i][j],sizeof(double),1,fp);
- fwrite(&cut[i][j],sizeof(double),1,fp);
+ fwrite(&epsilon[i][j],sizeof(double),1,fp);
+ fwrite(&sigma[i][j],sizeof(double),1,fp);
+ fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
@@ -305,14 +305,14 @@ void PairLJClass2::read_restart(FILE *fp)
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
- if (me == 0) {
- fread(&epsilon[i][j],sizeof(double),1,fp);
- fread(&sigma[i][j],sizeof(double),1,fp);
- fread(&cut[i][j],sizeof(double),1,fp);
- }
- MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
+ if (me == 0) {
+ fread(&epsilon[i][j],sizeof(double),1,fp);
+ fread(&sigma[i][j],sizeof(double),1,fp);
+ fread(&cut[i][j],sizeof(double),1,fp);
+ }
+ MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
@@ -348,8 +348,8 @@ void PairLJClass2::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairLJClass2::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
- double &fforce)
+ double factor_coul, double factor_lj,
+ double &fforce)
{
double r2inv,rinv,r3inv,r6inv,forcelj,philj;
diff --git a/src/CLASS2/pair_lj_class2.h b/src/CLASS2/pair_lj_class2.h
index 766f5787b91b05a1c2a560b6fec410b978a9c2b3..674599d52332763005a4001cbdfdbc84940b9f50 100644
--- a/src/CLASS2/pair_lj_class2.h
+++ b/src/CLASS2/pair_lj_class2.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/CLASS2/pair_lj_class2_coul_cut.cpp b/src/CLASS2/pair_lj_class2_coul_cut.cpp
index 9cd784ff581fb4e0772053311c18c25b0268c65e..5e5671c76fe079cd640f13daf167056a3f1f51be 100644
--- a/src/CLASS2/pair_lj_class2_coul_cut.cpp
+++ b/src/CLASS2/pair_lj_class2_coul_cut.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -81,7 +81,7 @@ void PairLJClass2CoulCut::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@@ -107,43 +107,43 @@ void PairLJClass2CoulCut::compute(int eflag, int vflag)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
-
- if (rsq < cut_coulsq[itype][jtype])
- forcecoul = qqrd2e * qtmp*q[j]*sqrt(r2inv);
- else forcecoul = 0.0;
-
- if (rsq < cut_ljsq[itype][jtype]) {
- rinv = sqrt(r2inv);
- r3inv = r2inv*rinv;
- r6inv = r3inv*r3inv;
- forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
- } else forcelj = 0.0;
-
- fpair = (factor_coul*forcecoul + factor_lj*forcelj) * r2inv;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (eflag) {
- if (rsq < cut_coulsq[itype][jtype])
- ecoul = factor_coul * qqrd2e * qtmp*q[j]*sqrt(r2inv);
- else ecoul = 0.0;
- if (rsq < cut_ljsq[itype][jtype]) {
- evdwl = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) -
- offset[itype][jtype];
- evdwl *= factor_lj;
- } else evdwl = 0.0;
- }
-
- if (evflag) ev_tally(i,j,nlocal,newton_pair,
- evdwl,ecoul,fpair,delx,dely,delz);
+ r2inv = 1.0/rsq;
+
+ if (rsq < cut_coulsq[itype][jtype])
+ forcecoul = qqrd2e * qtmp*q[j]*sqrt(r2inv);
+ else forcecoul = 0.0;
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ rinv = sqrt(r2inv);
+ r3inv = r2inv*rinv;
+ r6inv = r3inv*r3inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
+ } else forcelj = 0.0;
+
+ fpair = (factor_coul*forcecoul + factor_lj*forcelj) * r2inv;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (eflag) {
+ if (rsq < cut_coulsq[itype][jtype])
+ ecoul = factor_coul * qqrd2e * qtmp*q[j]*sqrt(r2inv);
+ else ecoul = 0.0;
+ if (rsq < cut_ljsq[itype][jtype]) {
+ evdwl = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) -
+ offset[itype][jtype];
+ evdwl *= factor_lj;
+ } else evdwl = 0.0;
+ }
+
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
@@ -152,7 +152,7 @@ void PairLJClass2CoulCut::compute(int eflag, int vflag)
}
/* ----------------------------------------------------------------------
- allocate all arrays
+ allocate all arrays
------------------------------------------------------------------------- */
void PairLJClass2CoulCut::allocate()
@@ -181,7 +181,7 @@ void PairLJClass2CoulCut::allocate()
}
/* ----------------------------------------------------------------------
- global settings
+ global settings
------------------------------------------------------------------------- */
void PairLJClass2CoulCut::settings(int narg, char **arg)
@@ -198,10 +198,10 @@ void PairLJClass2CoulCut::settings(int narg, char **arg)
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
- if (setflag[i][j]) {
- cut_lj[i][j] = cut_lj_global;
- cut_coul[i][j] = cut_coul_global;
- }
+ if (setflag[i][j]) {
+ cut_lj[i][j] = cut_lj_global;
+ cut_coul[i][j] = cut_coul_global;
+ }
}
}
@@ -264,9 +264,9 @@ double PairLJClass2CoulCut::init_one(int i, int j)
if (setflag[i][j] == 0) {
epsilon[i][j] = 2.0 * sqrt(epsilon[i][i]*epsilon[j][j]) *
- pow(sigma[i][i],3.0) * pow(sigma[j][j],3.0) /
+ pow(sigma[i][i],3.0) * pow(sigma[j][j],3.0) /
(pow(sigma[i][i],6.0) + pow(sigma[j][j],6.0));
- sigma[i][j] =
+ sigma[i][j] =
pow((0.5 * (pow(sigma[i][i],6.0) + pow(sigma[j][j],6.0))),1.0/6.0);
cut_lj[i][j] = mix_distance(cut_lj[i][i],cut_lj[j][j]);
cut_coul[i][j] = mix_distance(cut_coul[i][i],cut_coul[j][j]);
@@ -308,22 +308,22 @@ double PairLJClass2CoulCut::init_one(int i, int j)
if (type[k] == j) count[1] += 1.0;
}
MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world);
-
+
double sig3 = sigma[i][j]*sigma[i][j]*sigma[i][j];
double sig6 = sig3*sig3;
double rc3 = cut_lj[i][j]*cut_lj[i][j]*cut_lj[i][j];
double rc6 = rc3*rc3;
etail_ij = 2.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
sig6 * (sig3 - 3.0*rc3) / (3.0*rc6);
- ptail_ij = 2.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
+ ptail_ij = 2.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
sig6 * (sig3 - 2.0*rc3) / rc6;
- }
+ }
return cut;
}
/* ----------------------------------------------------------------------
- proc 0 writes to restart file
+ proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairLJClass2CoulCut::write_restart(FILE *fp)
@@ -335,10 +335,10 @@ void PairLJClass2CoulCut::write_restart(FILE *fp)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
- fwrite(&epsilon[i][j],sizeof(double),1,fp);
- fwrite(&sigma[i][j],sizeof(double),1,fp);
- fwrite(&cut_lj[i][j],sizeof(double),1,fp);
- fwrite(&cut_coul[i][j],sizeof(double),1,fp);
+ fwrite(&epsilon[i][j],sizeof(double),1,fp);
+ fwrite(&sigma[i][j],sizeof(double),1,fp);
+ fwrite(&cut_lj[i][j],sizeof(double),1,fp);
+ fwrite(&cut_coul[i][j],sizeof(double),1,fp);
}
}
}
@@ -359,16 +359,16 @@ void PairLJClass2CoulCut::read_restart(FILE *fp)
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
- if (me == 0) {
- fread(&epsilon[i][j],sizeof(double),1,fp);
- fread(&sigma[i][j],sizeof(double),1,fp);
- fread(&cut_lj[i][j],sizeof(double),1,fp);
- fread(&cut_coul[i][j],sizeof(double),1,fp);
- }
- MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&cut_coul[i][j],1,MPI_DOUBLE,0,world);
+ if (me == 0) {
+ fread(&epsilon[i][j],sizeof(double),1,fp);
+ fread(&sigma[i][j],sizeof(double),1,fp);
+ fread(&cut_lj[i][j],sizeof(double),1,fp);
+ fread(&cut_coul[i][j],sizeof(double),1,fp);
+ }
+ MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut_coul[i][j],1,MPI_DOUBLE,0,world);
}
}
}
@@ -406,9 +406,9 @@ void PairLJClass2CoulCut::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairLJClass2CoulCut::single(int i, int j, int itype, int jtype,
- double rsq,
- double factor_coul, double factor_lj,
- double &fforce)
+ double rsq,
+ double factor_coul, double factor_lj,
+ double &fforce)
{
double r2inv,rinv,r3inv,r6inv,forcecoul,forcelj,phicoul,philj;
diff --git a/src/CLASS2/pair_lj_class2_coul_cut.h b/src/CLASS2/pair_lj_class2_coul_cut.h
index 823bfe6c17a832db87f615bbfd8f2dde46f64c61..4f754406dc9fff9637ab1dcba528ac8e2b7d45b1 100644
--- a/src/CLASS2/pair_lj_class2_coul_cut.h
+++ b/src/CLASS2/pair_lj_class2_coul_cut.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/CLASS2/pair_lj_class2_coul_long.cpp b/src/CLASS2/pair_lj_class2_coul_long.cpp
index 3dbf8e2ec33954e7dec65e41a0a8de73ba1469f7..76feaea620a75d2abb727223c7bf4edfae3dfa2d 100644
--- a/src/CLASS2/pair_lj_class2_coul_long.cpp
+++ b/src/CLASS2/pair_lj_class2_coul_long.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -90,7 +90,7 @@ void PairLJClass2CoulLong::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@@ -116,51 +116,51 @@ void PairLJClass2CoulLong::compute(int eflag, int vflag)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
-
- if (rsq < cut_coulsq) {
- r = sqrt(rsq);
- grij = g_ewald * r;
- expm2 = exp(-grij*grij);
- t = 1.0 / (1.0 + EWALD_P*grij);
- erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
- prefactor = qqrd2e * qtmp*q[j]/r;
- forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
- if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
- } else forcecoul = 0.0;
-
- if (rsq < cut_ljsq[itype][jtype]) {
- rinv = sqrt(r2inv);
- r3inv = r2inv*rinv;
- r6inv = r3inv*r3inv;
- forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
- } else forcelj = 0.0;
-
- fpair = (forcecoul + factor_lj*forcelj) * r2inv;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (eflag) {
- if (rsq < cut_coulsq) {
- ecoul = prefactor*erfc;
- if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
- } else ecoul = 0.0;
- if (rsq < cut_ljsq[itype][jtype]) {
- evdwl = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) -
- offset[itype][jtype];
- evdwl *= factor_lj;
- } else evdwl = 0.0;
- }
-
- if (evflag) ev_tally(i,j,nlocal,newton_pair,
- evdwl,ecoul,fpair,delx,dely,delz);
+ r2inv = 1.0/rsq;
+
+ if (rsq < cut_coulsq) {
+ r = sqrt(rsq);
+ grij = g_ewald * r;
+ expm2 = exp(-grij*grij);
+ t = 1.0 / (1.0 + EWALD_P*grij);
+ erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
+ prefactor = qqrd2e * qtmp*q[j]/r;
+ forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
+ if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
+ } else forcecoul = 0.0;
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ rinv = sqrt(r2inv);
+ r3inv = r2inv*rinv;
+ r6inv = r3inv*r3inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
+ } else forcelj = 0.0;
+
+ fpair = (forcecoul + factor_lj*forcelj) * r2inv;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (eflag) {
+ if (rsq < cut_coulsq) {
+ ecoul = prefactor*erfc;
+ if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
+ } else ecoul = 0.0;
+ if (rsq < cut_ljsq[itype][jtype]) {
+ evdwl = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) -
+ offset[itype][jtype];
+ evdwl *= factor_lj;
+ } else evdwl = 0.0;
+ }
+
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
@@ -169,7 +169,7 @@ void PairLJClass2CoulLong::compute(int eflag, int vflag)
}
/* ----------------------------------------------------------------------
- allocate all arrays
+ allocate all arrays
------------------------------------------------------------------------- */
void PairLJClass2CoulLong::allocate()
@@ -196,7 +196,7 @@ void PairLJClass2CoulLong::allocate()
}
/* ----------------------------------------------------------------------
- global settings
+ global settings
------------------------------------------------------------------------- */
void PairLJClass2CoulLong::settings(int narg, char **arg)
@@ -213,7 +213,7 @@ void PairLJClass2CoulLong::settings(int narg, char **arg)
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
- if (setflag[i][j]) cut_lj[i][j] = cut_lj_global;
+ if (setflag[i][j]) cut_lj[i][j] = cut_lj_global;
}
}
@@ -265,7 +265,7 @@ void PairLJClass2CoulLong::init_style()
// insure use of KSpace long-range solver, set g_ewald
- if (force->kspace == NULL)
+ if (force->kspace == NULL)
error->all(FLERR,"Pair style is incompatible with KSpace style");
g_ewald = force->kspace->g_ewald;
}
@@ -281,9 +281,9 @@ double PairLJClass2CoulLong::init_one(int i, int j)
if (setflag[i][j] == 0) {
epsilon[i][j] = 2.0 * sqrt(epsilon[i][i]*epsilon[j][j]) *
- pow(sigma[i][i],3.0) * pow(sigma[j][j],3.0) /
+ pow(sigma[i][i],3.0) * pow(sigma[j][j],3.0) /
(pow(sigma[i][i],6.0) + pow(sigma[j][j],6.0));
- sigma[i][j] =
+ sigma[i][j] =
pow((0.5 * (pow(sigma[i][i],6.0) + pow(sigma[j][j],6.0))),1.0/6.0);
cut_lj[i][j] = mix_distance(cut_lj[i][i],cut_lj[j][j]);
}
@@ -322,22 +322,22 @@ double PairLJClass2CoulLong::init_one(int i, int j)
if (type[k] == j) count[1] += 1.0;
}
MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world);
-
+
double sig3 = sigma[i][j]*sigma[i][j]*sigma[i][j];
double sig6 = sig3*sig3;
double rc3 = cut_lj[i][j]*cut_lj[i][j]*cut_lj[i][j];
double rc6 = rc3*rc3;
etail_ij = 2.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
sig6 * (sig3 - 3.0*rc3) / (3.0*rc6);
- ptail_ij = 2.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
+ ptail_ij = 2.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
sig6 * (sig3 - 2.0*rc3) / rc6;
- }
+ }
return cut;
}
/* ----------------------------------------------------------------------
- proc 0 writes to restart file
+ proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairLJClass2CoulLong::write_restart(FILE *fp)
@@ -349,9 +349,9 @@ void PairLJClass2CoulLong::write_restart(FILE *fp)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
- fwrite(&epsilon[i][j],sizeof(double),1,fp);
- fwrite(&sigma[i][j],sizeof(double),1,fp);
- fwrite(&cut_lj[i][j],sizeof(double),1,fp);
+ fwrite(&epsilon[i][j],sizeof(double),1,fp);
+ fwrite(&sigma[i][j],sizeof(double),1,fp);
+ fwrite(&cut_lj[i][j],sizeof(double),1,fp);
}
}
}
@@ -372,14 +372,14 @@ void PairLJClass2CoulLong::read_restart(FILE *fp)
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
- if (me == 0) {
- fread(&epsilon[i][j],sizeof(double),1,fp);
- fread(&sigma[i][j],sizeof(double),1,fp);
- fread(&cut_lj[i][j],sizeof(double),1,fp);
- }
- MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world);
+ if (me == 0) {
+ fread(&epsilon[i][j],sizeof(double),1,fp);
+ fread(&sigma[i][j],sizeof(double),1,fp);
+ fread(&cut_lj[i][j],sizeof(double),1,fp);
+ }
+ MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world);
}
}
}
@@ -417,9 +417,9 @@ void PairLJClass2CoulLong::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairLJClass2CoulLong::single(int i, int j, int itype, int jtype,
- double rsq,
- double factor_coul, double factor_lj,
- double &fforce)
+ double rsq,
+ double factor_coul, double factor_lj,
+ double &fforce)
{
double r2inv,r,rinv,r3inv,r6inv,grij,expm2,t,erfc,prefactor;
double forcecoul,forcelj,phicoul,philj;
diff --git a/src/CLASS2/pair_lj_class2_coul_long.h b/src/CLASS2/pair_lj_class2_coul_long.h
index 0e5ebd6a1a332c2d8f57d709f8f695eae91fa0bb..148633cd4a7036af541550542257c041bf6c8b4b 100644
--- a/src/CLASS2/pair_lj_class2_coul_long.h
+++ b/src/CLASS2/pair_lj_class2_coul_long.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/COLLOID/fix_wall_colloid.cpp b/src/COLLOID/fix_wall_colloid.cpp
index 33717104c2520ca6e6abdc3a67529056cb8603e8..1ce2cbabd809da6d36dfd07eddd481cd4d960353 100644
--- a/src/COLLOID/fix_wall_colloid.cpp
+++ b/src/COLLOID/fix_wall_colloid.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -29,14 +29,14 @@ using namespace FixConst;
/* ---------------------------------------------------------------------- */
-FixWallColloid::FixWallColloid(LAMMPS *lmp, int narg, char **arg) :
+FixWallColloid::FixWallColloid(LAMMPS *lmp, int narg, char **arg) :
FixWall(lmp, narg, arg) {}
/* ---------------------------------------------------------------------- */
void FixWallColloid::init()
{
- if (!atom->sphere_flag)
+ if (!atom->sphere_flag)
error->all(FLERR,"Fix wall/colloid requires atom style sphere");
// insure all particles in group are extended particles
@@ -101,8 +101,8 @@ void FixWallColloid::wall_particle(int m, int which, double coord)
if (delta >= cutoff[m]) continue;
rad = radius[i];
if (rad >= delta) {
- onflag = 1;
- continue;
+ onflag = 1;
+ continue;
}
new_coeff2 = coeff2[m]*rad*rad*rad;
@@ -116,9 +116,9 @@ void FixWallColloid::wall_particle(int m, int which, double coord)
r4inv = r2inv*r2inv;
r8inv = r4inv*r4inv;
fwall = side * (coeff1[m]*(rad8*rad + 27.0*rad4*rad2*rad*pow(delta,2.0)
- + 63.0*rad4*rad*pow(delta,4.0)
- + 21.0*rad2*rad*pow(delta,6.0))*r8inv -
- new_coeff2*r2inv);
+ + 63.0*rad4*rad*pow(delta,4.0)
+ + 21.0*rad2*rad*pow(delta,6.0))*r8inv -
+ new_coeff2*r2inv);
f[i][dim] -= fwall;
r2 = rad - delta;
@@ -131,9 +131,9 @@ void FixWallColloid::wall_particle(int m, int which, double coord)
r4inv3 = r2inv3*r2inv3;
r6inv3 = r4inv3*r2inv3;
ewall[0] += coeff3[m]*((-3.5*diam+delta)*r4inv2*r2inv2*rinv2
- + (3.5*diam+delta)*r4inv3*r2inv3*rinv3) -
- coeff4[m]*((diam*delta-r2*r3*(log(-r2)-log(r3)))*
- (-rinv2)*rinv3);
+ + (3.5*diam+delta)*r4inv3*r2inv3*rinv3) -
+ coeff4[m]*((diam*delta-r2*r3*(log(-r2)-log(r3)))*
+ (-rinv2)*rinv3);
// offset depends on particle size
@@ -147,9 +147,9 @@ void FixWallColloid::wall_particle(int m, int which, double coord)
r4inv3 = r2inv3*r2inv3;
r6inv3 = r4inv3*r2inv3;
eoffset = coeff3[m]*((-3.5*diam+cutoff[m])*r4inv2*r2inv2*rinv2
- + (3.5*diam+cutoff[m])*r4inv3*r2inv3*rinv3) -
- coeff4[m]*((diam*cutoff[m]-r2*r3*(log(-r2)-log(r3)))*
- (-rinv2)*rinv3);
+ + (3.5*diam+cutoff[m])*r4inv3*r2inv3*rinv3) -
+ coeff4[m]*((diam*cutoff[m]-r2*r3*(log(-r2)-log(r3)))*
+ (-rinv2)*rinv3);
ewall[0] -= eoffset;
ewall[m+1] += fwall;
diff --git a/src/COLLOID/fix_wall_colloid.h b/src/COLLOID/fix_wall_colloid.h
index 03e3b9e88f2eb0311ef217e2d04cf29d99dfc2b0..61aa4078f9416703c0d36e7afefdee08c58e7a3a 100644
--- a/src/COLLOID/fix_wall_colloid.h
+++ b/src/COLLOID/fix_wall_colloid.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/COLLOID/pair_colloid.cpp b/src/COLLOID/pair_colloid.cpp
index 04211a3509b16e7d1cef6f5fe1fa94baabe0ddfc..b1111119eacb71c934c1bbef6bf4cc54dc9f1cbb 100644
--- a/src/COLLOID/pair_colloid.cpp
+++ b/src/COLLOID/pair_colloid.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -50,7 +50,7 @@ PairColloid::~PairColloid()
memory->destroy(a1);
memory->destroy(a2);
memory->destroy(diameter);
- memory->destroy(cut);
+ memory->destroy(cut);
memory->destroy(offset);
memory->destroy(sigma3);
memory->destroy(sigma6);
@@ -87,7 +87,7 @@ void PairColloid::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@@ -103,7 +103,7 @@ void PairColloid::compute(int eflag, int vflag)
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
-
+
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
@@ -113,87 +113,87 @@ void PairColloid::compute(int eflag, int vflag)
if (rsq >= cutsq[itype][jtype]) continue;
switch (form[itype][jtype]) {
- case SMALL_SMALL:
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- fpair = factor_lj*forcelj*r2inv;
- if (eflag) evdwl = r6inv*(r6inv*lj3[itype][jtype]-lj4[itype][jtype]) -
- offset[itype][jtype];
- break;
-
+ case SMALL_SMALL:
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ fpair = factor_lj*forcelj*r2inv;
+ if (eflag) evdwl = r6inv*(r6inv*lj3[itype][jtype]-lj4[itype][jtype]) -
+ offset[itype][jtype];
+ break;
+
case SMALL_LARGE:
- c2 = a2[itype][jtype];
- K[1] = c2*c2;
- K[2] = rsq;
- K[0] = K[1] - rsq;
- K[4] = rsq*rsq;
- K[3] = K[1] - K[2];
- K[3] *= K[3]*K[3];
- K[6] = K[3]*K[3];
- fR = sigma3[itype][jtype]*a12[itype][jtype]*c2*K[1]/K[3];
- fpair = 4.0/15.0*fR*factor_lj *
- (2.0*(K[1]+K[2]) * (K[1]*(5.0*K[1]+22.0*K[2])+5.0*K[4]) *
- sigma6[itype][jtype]/K[6]-5.0) / K[0];
- if (eflag)
- evdwl = 2.0/9.0*fR *
- (1.0-(K[1]*(K[1]*(K[1]/3.0+3.0*K[2])+4.2*K[4])+K[2]*K[4]) *
- sigma6[itype][jtype]/K[6]) - offset[itype][jtype];
- if (rsq <= K[1]) error->one(FLERR,"Overlapping small/large in pair colloid");
- break;
+ c2 = a2[itype][jtype];
+ K[1] = c2*c2;
+ K[2] = rsq;
+ K[0] = K[1] - rsq;
+ K[4] = rsq*rsq;
+ K[3] = K[1] - K[2];
+ K[3] *= K[3]*K[3];
+ K[6] = K[3]*K[3];
+ fR = sigma3[itype][jtype]*a12[itype][jtype]*c2*K[1]/K[3];
+ fpair = 4.0/15.0*fR*factor_lj *
+ (2.0*(K[1]+K[2]) * (K[1]*(5.0*K[1]+22.0*K[2])+5.0*K[4]) *
+ sigma6[itype][jtype]/K[6]-5.0) / K[0];
+ if (eflag)
+ evdwl = 2.0/9.0*fR *
+ (1.0-(K[1]*(K[1]*(K[1]/3.0+3.0*K[2])+4.2*K[4])+K[2]*K[4]) *
+ sigma6[itype][jtype]/K[6]) - offset[itype][jtype];
+ if (rsq <= K[1]) error->one(FLERR,"Overlapping small/large in pair colloid");
+ break;
case LARGE_LARGE:
- r = sqrt(rsq);
- c1 = a1[itype][jtype];
- c2 = a2[itype][jtype];
- K[0] = c1*c2;
- K[1] = c1+c2;
- K[2] = c1-c2;
- K[3] = K[1]+r;
- K[4] = K[1]-r;
- K[5] = K[2]+r;
- K[6] = K[2]-r;
- K[7] = 1.0/(K[3]*K[4]);
- K[8] = 1.0/(K[5]*K[6]);
- g[0] = pow(K[3],-7.0);
- g[1] = pow(K[4],-7.0);
- g[2] = pow(K[5],-7.0);
- g[3] = pow(K[6],-7.0);
- h[0] = ((K[3]+5.0*K[1])*K[3]+30.0*K[0])*g[0];
- h[1] = ((K[4]+5.0*K[1])*K[4]+30.0*K[0])*g[1];
- h[2] = ((K[5]+5.0*K[2])*K[5]-30.0*K[0])*g[2];
- h[3] = ((K[6]+5.0*K[2])*K[6]-30.0*K[0])*g[3];
- g[0] *= 42.0*K[0]/K[3]+6.0*K[1]+K[3];
- g[1] *= 42.0*K[0]/K[4]+6.0*K[1]+K[4];
- g[2] *= -42.0*K[0]/K[5]+6.0*K[2]+K[5];
- g[3] *= -42.0*K[0]/K[6]+6.0*K[2]+K[6];
-
- fR = a12[itype][jtype]*sigma6[itype][jtype]/r/37800.0;
- evdwl = fR * (h[0]-h[1]-h[2]+h[3]);
- dUR = evdwl/r + 5.0*fR*(g[0]+g[1]-g[2]-g[3]);
- dUA = -a12[itype][jtype]/3.0*r*((2.0*K[0]*K[7]+1.0)*K[7] +
- (2.0*K[0]*K[8]-1.0)*K[8]);
- fpair = factor_lj * (dUR+dUA)/r;
- if (eflag)
- evdwl += a12[itype][jtype]/6.0 *
- (2.0*K[0]*(K[7]+K[8])-log(K[8]/K[7])) - offset[itype][jtype];
- if (r <= K[1]) error->one(FLERR,"Overlapping large/large in pair colloid");
- break;
+ r = sqrt(rsq);
+ c1 = a1[itype][jtype];
+ c2 = a2[itype][jtype];
+ K[0] = c1*c2;
+ K[1] = c1+c2;
+ K[2] = c1-c2;
+ K[3] = K[1]+r;
+ K[4] = K[1]-r;
+ K[5] = K[2]+r;
+ K[6] = K[2]-r;
+ K[7] = 1.0/(K[3]*K[4]);
+ K[8] = 1.0/(K[5]*K[6]);
+ g[0] = pow(K[3],-7.0);
+ g[1] = pow(K[4],-7.0);
+ g[2] = pow(K[5],-7.0);
+ g[3] = pow(K[6],-7.0);
+ h[0] = ((K[3]+5.0*K[1])*K[3]+30.0*K[0])*g[0];
+ h[1] = ((K[4]+5.0*K[1])*K[4]+30.0*K[0])*g[1];
+ h[2] = ((K[5]+5.0*K[2])*K[5]-30.0*K[0])*g[2];
+ h[3] = ((K[6]+5.0*K[2])*K[6]-30.0*K[0])*g[3];
+ g[0] *= 42.0*K[0]/K[3]+6.0*K[1]+K[3];
+ g[1] *= 42.0*K[0]/K[4]+6.0*K[1]+K[4];
+ g[2] *= -42.0*K[0]/K[5]+6.0*K[2]+K[5];
+ g[3] *= -42.0*K[0]/K[6]+6.0*K[2]+K[6];
+
+ fR = a12[itype][jtype]*sigma6[itype][jtype]/r/37800.0;
+ evdwl = fR * (h[0]-h[1]-h[2]+h[3]);
+ dUR = evdwl/r + 5.0*fR*(g[0]+g[1]-g[2]-g[3]);
+ dUA = -a12[itype][jtype]/3.0*r*((2.0*K[0]*K[7]+1.0)*K[7] +
+ (2.0*K[0]*K[8]-1.0)*K[8]);
+ fpair = factor_lj * (dUR+dUA)/r;
+ if (eflag)
+ evdwl += a12[itype][jtype]/6.0 *
+ (2.0*K[0]*(K[7]+K[8])-log(K[8]/K[7])) - offset[itype][jtype];
+ if (r <= K[1]) error->one(FLERR,"Overlapping large/large in pair colloid");
+ break;
}
-
+
if (eflag) evdwl *= factor_lj;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
- evdwl,0.0,fpair,delx,dely,delz);
+ evdwl,0.0,fpair,delx,dely,delz);
}
}
@@ -201,7 +201,7 @@ void PairColloid::compute(int eflag, int vflag)
}
/* ----------------------------------------------------------------------
- allocate all arrays
+ allocate all arrays
------------------------------------------------------------------------- */
void PairColloid::allocate()
@@ -235,7 +235,7 @@ void PairColloid::allocate()
}
/* ----------------------------------------------------------------------
- global settings
+ global settings
------------------------------------------------------------------------- */
void PairColloid::settings(int narg, char **arg)
@@ -250,7 +250,7 @@ void PairColloid::settings(int narg, char **arg)
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
- if (setflag[i][j]) cut[i][j] = cut_global;
+ if (setflag[i][j]) cut[i][j] = cut_global;
}
}
@@ -275,7 +275,7 @@ void PairColloid::coeff(int narg, char **arg)
double cut_one = cut_global;
if (narg == 7) cut_one = force->numeric(arg[6]);
- if (d1_one < 0.0 || d2_one < 0.0)
+ if (d1_one < 0.0 || d2_one < 0.0)
error->all(FLERR,"Invalid d1 or d2 value for pair colloid coeff");
int count = 0;
@@ -284,7 +284,7 @@ void PairColloid::coeff(int narg, char **arg)
a12[i][j] = a12_one;
sigma[i][j] = sigma_one;
if (i == j && d1_one != d2_one)
- error->all(FLERR,"Invalid d1 or d2 value for pair colloid coeff");
+ error->all(FLERR,"Invalid d1 or d2 value for pair colloid coeff");
d1[i][j] = d1_one;
d2[i][j] = d2_one;
diameter[i][j] = 0.5*(d1_one+d2_one);
@@ -349,7 +349,7 @@ double PairColloid::init_one(int i, int j)
offset[j][i] = offset[i][j] = 0.0;
if (offset_flag) {
double tmp;
- offset[j][i] = offset[i][j] =
+ offset[j][i] = offset[i][j] =
single(0,0,i,j,cut[i][j]*cut[i][j],0.0,1.0,tmp);
}
@@ -357,7 +357,7 @@ double PairColloid::init_one(int i, int j)
}
/* ----------------------------------------------------------------------
- proc 0 writes to restart file
+ proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairColloid::write_restart(FILE *fp)
@@ -369,11 +369,11 @@ void PairColloid::write_restart(FILE *fp)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
- fwrite(&a12[i][j],sizeof(double),1,fp);
- fwrite(&sigma[i][j],sizeof(double),1,fp);
- fwrite(&d1[i][j],sizeof(double),1,fp);
- fwrite(&d2[i][j],sizeof(double),1,fp);
- fwrite(&cut[i][j],sizeof(double),1,fp);
+ fwrite(&a12[i][j],sizeof(double),1,fp);
+ fwrite(&sigma[i][j],sizeof(double),1,fp);
+ fwrite(&d1[i][j],sizeof(double),1,fp);
+ fwrite(&d2[i][j],sizeof(double),1,fp);
+ fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
@@ -394,18 +394,18 @@ void PairColloid::read_restart(FILE *fp)
if (comm->me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
- if (comm->me == 0) {
- fread(&a12[i][j],sizeof(double),1,fp);
- fread(&sigma[i][j],sizeof(double),1,fp);
- fread(&d1[i][j],sizeof(double),1,fp);
- fread(&d2[i][j],sizeof(double),1,fp);
- fread(&cut[i][j],sizeof(double),1,fp);
- }
- MPI_Bcast(&a12[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&d1[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&d2[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
+ if (comm->me == 0) {
+ fread(&a12[i][j],sizeof(double),1,fp);
+ fread(&sigma[i][j],sizeof(double),1,fp);
+ fread(&d1[i][j],sizeof(double),1,fp);
+ fread(&d2[i][j],sizeof(double),1,fp);
+ fread(&cut[i][j],sizeof(double),1,fp);
+ }
+ MPI_Bcast(&a12[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&d1[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&d2[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
@@ -441,8 +441,8 @@ void PairColloid::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairColloid::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
- double &fforce)
+ double factor_coul, double factor_lj,
+ double &fforce)
{
double K[9],h[4],g[4];
double r,r2inv,r6inv,forcelj,c1,c2,phi,fR,dUR,dUA;
@@ -467,11 +467,11 @@ double PairColloid::single(int i, int j, int itype, int jtype, double rsq,
K[3] *= K[3]*K[3];
K[6] = K[3]*K[3];
fR = sigma3[itype][jtype]*a12[itype][jtype]*c2*K[1]/K[3];
- fforce = 4.0/15.0*fR*factor_lj *
- (2.0*(K[1]+K[2])*(K[1]*(5.0*K[1]+22.0*K[2])+5.0*K[4]) *
+ fforce = 4.0/15.0*fR*factor_lj *
+ (2.0*(K[1]+K[2])*(K[1]*(5.0*K[1]+22.0*K[2])+5.0*K[4]) *
sigma6[itype][jtype]/K[6] - 5.0)/K[0];
- phi = 2.0/9.0*fR *
- (1.0-(K[1]*(K[1]*(K[1]/3.0+3.0*K[2])+4.2*K[4])+K[2]*K[4]) *
+ phi = 2.0/9.0*fR *
+ (1.0-(K[1]*(K[1]*(K[1]/3.0+3.0*K[2])+4.2*K[4])+K[2]*K[4]) *
sigma6[itype][jtype]/K[6]) - offset[itype][jtype];
break;
@@ -500,14 +500,14 @@ double PairColloid::single(int i, int j, int itype, int jtype, double rsq,
g[1] *= 42.0*K[0]/K[4]+6.0*K[1]+K[4];
g[2] *= -42.0*K[0]/K[5]+6.0*K[2]+K[5];
g[3] *= -42.0*K[0]/K[6]+6.0*K[2]+K[6];
-
+
fR = a12[itype][jtype]*sigma6[itype][jtype]/r/37800.0;
phi = fR * (h[0]-h[1]-h[2]+h[3]);
dUR = phi/r + 5.0*fR*(g[0]+g[1]-g[2]-g[3]);
- dUA = -a12[itype][jtype]/3.0*r*((2.0*K[0]*K[7]+1.0)*K[7] +
- (2.0*K[0]*K[8]-1.0)*K[8]);
+ dUA = -a12[itype][jtype]/3.0*r*((2.0*K[0]*K[7]+1.0)*K[7] +
+ (2.0*K[0]*K[8]-1.0)*K[8]);
fforce = factor_lj*(dUR+dUA)/r;
- phi += a12[itype][jtype]/6.0*(2.0*K[0]*(K[7]+K[8])-log(K[8]/K[7])) -
+ phi += a12[itype][jtype]/6.0*(2.0*K[0]*(K[7]+K[8])-log(K[8]/K[7])) -
offset[itype][jtype];
break;
}
diff --git a/src/COLLOID/pair_colloid.h b/src/COLLOID/pair_colloid.h
index a9b720330a03a8d7e6480cf71bd31adc4e3b886c..18eec2290c7815d024a0daf84fb6ac7bd08722aa 100644
--- a/src/COLLOID/pair_colloid.h
+++ b/src/COLLOID/pair_colloid.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/COLLOID/pair_yukawa_colloid.cpp b/src/COLLOID/pair_yukawa_colloid.cpp
index ca68a56c9c9621bdc1f01b5a25e320fdc52babb5..d311e44a48aeacd5413b60a8ecffc9e31266ed85 100644
--- a/src/COLLOID/pair_yukawa_colloid.cpp
+++ b/src/COLLOID/pair_yukawa_colloid.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -58,7 +58,7 @@ void PairYukawaColloid::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@@ -82,32 +82,32 @@ void PairYukawaColloid::compute(int eflag, int vflag)
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
radj = radius[j];
-
+
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- r = sqrt(rsq);
- rinv = 1.0/r;
- screening = exp(-kappa*(r-(radi+radj)));
- forceyukawa = a[itype][jtype] * screening;
-
- fpair = factor*forceyukawa * rinv;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (eflag) {
- evdwl = a[itype][jtype]/kappa * screening - offset[itype][jtype];
- evdwl *= factor;
- }
-
- if (evflag) ev_tally(i,j,nlocal,newton_pair,
- evdwl,0.0,fpair,delx,dely,delz);
+ r2inv = 1.0/rsq;
+ r = sqrt(rsq);
+ rinv = 1.0/r;
+ screening = exp(-kappa*(r-(radi+radj)));
+ forceyukawa = a[itype][jtype] * screening;
+
+ fpair = factor*forceyukawa * rinv;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (eflag) {
+ evdwl = a[itype][jtype]/kappa * screening - offset[itype][jtype];
+ evdwl *= factor;
+ }
+
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ evdwl,0.0,fpair,delx,dely,delz);
}
}
}
@@ -123,7 +123,7 @@ void PairYukawaColloid::init_style()
{
if (!atom->sphere_flag)
error->all(FLERR,"Pair yukawa/colloid requires atom style sphere");
-
+
neighbor->request(this);
// require that atom radii are identical within each type
@@ -131,7 +131,7 @@ void PairYukawaColloid::init_style()
for (int i = 1; i <= atom->ntypes; i++)
if (!atom->radius_consistency(i,rad[i]))
error->all(FLERR,"Pair yukawa/colloid requires atoms with same type "
- "have same radius");
+ "have same radius");
}
/* ----------------------------------------------------------------------
@@ -159,12 +159,12 @@ double PairYukawaColloid::init_one(int i, int j)
/* ---------------------------------------------------------------------- */
double PairYukawaColloid::single(int i, int j, int itype, int jtype,
- double rsq,
- double factor_coul, double factor_lj,
- double &fforce)
+ double rsq,
+ double factor_coul, double factor_lj,
+ double &fforce)
{
double r2inv,r,rinv,screening,forceyukawa,phi;
-
+
r2inv = 1.0/rsq;
r = sqrt(rsq);
rinv = 1.0/r;
@@ -172,6 +172,6 @@ double PairYukawaColloid::single(int i, int j, int itype, int jtype,
forceyukawa = a[itype][jtype] * screening;
fforce = factor_lj*forceyukawa * rinv;
- phi = a[itype][jtype]/kappa * screening - offset[itype][jtype];
+ phi = a[itype][jtype]/kappa * screening - offset[itype][jtype];
return factor_lj*phi;
}
diff --git a/src/COLLOID/pair_yukawa_colloid.h b/src/COLLOID/pair_yukawa_colloid.h
index 29d5b6521f55b8bac7a8c180123859b2166d0968..be04d790a2ba4583f9c1de0ff6a1767bf1958c94 100644
--- a/src/COLLOID/pair_yukawa_colloid.h
+++ b/src/COLLOID/pair_yukawa_colloid.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/DIPOLE/atom_vec_dipole.cpp b/src/DIPOLE/atom_vec_dipole.cpp
index 86d0119eaad9962a6c4816edcb14e695ba191c96..02f048e3d8f7029a27ff38a5de1904a4811f377b 100644
--- a/src/DIPOLE/atom_vec_dipole.cpp
+++ b/src/DIPOLE/atom_vec_dipole.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -50,7 +50,7 @@ AtomVecDipole::AtomVecDipole(LAMMPS *lmp, int narg, char **arg) :
/* ----------------------------------------------------------------------
grow atom arrays
n = 0 grows arrays by DELTA
- n > 0 allocates arrays to size n
+ n > 0 allocates arrays to size n
------------------------------------------------------------------------- */
void AtomVecDipole::grow(int n)
@@ -73,7 +73,7 @@ void AtomVecDipole::grow(int n)
mu = memory->grow(atom->mu,nmax,4,"atom:mu");
if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
}
@@ -113,14 +113,14 @@ void AtomVecDipole::copy(int i, int j, int delflag)
mu[j][3] = mu[i][3];
if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j);
}
/* ---------------------------------------------------------------------- */
int AtomVecDipole::pack_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
@@ -162,7 +162,7 @@ int AtomVecDipole::pack_comm(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
int AtomVecDipole::pack_comm_vel(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz,dvx,dvy,dvz;
@@ -193,38 +193,38 @@ int AtomVecDipole::pack_comm_vel(int n, int *list, double *buf,
}
if (!deform_vremap) {
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = mu[j][0];
- buf[m++] = mu[j][1];
- buf[m++] = mu[j][2];
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = mu[j][0];
+ buf[m++] = mu[j][1];
+ buf[m++] = mu[j][2];
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
}
} else {
dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
dvz = pbc[2]*h_rate[2];
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = mu[j][0];
- buf[m++] = mu[j][1];
- buf[m++] = mu[j][2];
- if (mask[i] & deform_groupbit) {
- buf[m++] = v[j][0] + dvx;
- buf[m++] = v[j][1] + dvy;
- buf[m++] = v[j][2] + dvz;
- } else {
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
- }
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = mu[j][0];
+ buf[m++] = mu[j][1];
+ buf[m++] = mu[j][2];
+ if (mask[i] & deform_groupbit) {
+ buf[m++] = v[j][0] + dvx;
+ buf[m++] = v[j][1] + dvy;
+ buf[m++] = v[j][2] + dvz;
+ } else {
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
+ }
}
}
}
@@ -336,7 +336,7 @@ void AtomVecDipole::unpack_reverse(int n, int *list, double *buf)
/* ---------------------------------------------------------------------- */
int AtomVecDipole::pack_border(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
@@ -388,7 +388,7 @@ int AtomVecDipole::pack_border(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
int AtomVecDipole::pack_border_vel(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz,dvx,dvy,dvz;
@@ -424,48 +424,48 @@ int AtomVecDipole::pack_border_vel(int n, int *list, double *buf,
}
if (!deform_vremap) {
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = tag[j];
- buf[m++] = type[j];
- buf[m++] = mask[j];
- buf[m++] = q[j];
- buf[m++] = mu[j][0];
- buf[m++] = mu[j][1];
- buf[m++] = mu[j][2];
- buf[m++] = mu[j][3];
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = tag[j];
+ buf[m++] = type[j];
+ buf[m++] = mask[j];
+ buf[m++] = q[j];
+ buf[m++] = mu[j][0];
+ buf[m++] = mu[j][1];
+ buf[m++] = mu[j][2];
+ buf[m++] = mu[j][3];
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
}
} else {
dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
dvz = pbc[2]*h_rate[2];
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = tag[j];
- buf[m++] = type[j];
- buf[m++] = mask[j];
- buf[m++] = q[j];
- buf[m++] = mu[j][0];
- buf[m++] = mu[j][1];
- buf[m++] = mu[j][2];
- buf[m++] = mu[j][3];
- if (mask[i] & deform_groupbit) {
- buf[m++] = v[j][0] + dvx;
- buf[m++] = v[j][1] + dvy;
- buf[m++] = v[j][2] + dvz;
- } else {
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
- }
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = tag[j];
+ buf[m++] = type[j];
+ buf[m++] = mask[j];
+ buf[m++] = q[j];
+ buf[m++] = mu[j][0];
+ buf[m++] = mu[j][1];
+ buf[m++] = mu[j][2];
+ buf[m++] = mu[j][3];
+ if (mask[i] & deform_groupbit) {
+ buf[m++] = v[j][0] + dvx;
+ buf[m++] = v[j][1] + dvy;
+ buf[m++] = v[j][2] + dvz;
+ } else {
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
+ }
}
}
}
@@ -585,7 +585,7 @@ int AtomVecDipole::pack_exchange(int i, double *buf)
buf[m++] = mu[i][3];
if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]);
buf[0] = m;
@@ -618,9 +618,9 @@ int AtomVecDipole::unpack_exchange(double *buf)
mu[nlocal][3] = buf[m++];
if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->
- unpack_exchange(nlocal,&buf[m]);
+ unpack_exchange(nlocal,&buf[m]);
atom->nlocal++;
return m;
@@ -639,9 +639,9 @@ int AtomVecDipole::size_restart()
int n = 16 * nlocal;
if (atom->nextra_restart)
- for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
for (i = 0; i < nlocal; i++)
- n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
+ n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
return n;
}
@@ -649,7 +649,7 @@ int AtomVecDipole::size_restart()
/* ----------------------------------------------------------------------
pack atom I's data for restart file including extra quantities
xyz must be 1st 3 values, so that read_restart can test on them
- molecular types may be negative, but write as positive
+ molecular types may be negative, but write as positive
------------------------------------------------------------------------- */
int AtomVecDipole::pack_restart(int i, double *buf)
@@ -673,7 +673,7 @@ int AtomVecDipole::pack_restart(int i, double *buf)
buf[m++] = mu[i][3];
if (atom->nextra_restart)
- for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]);
buf[0] = m;
@@ -778,9 +778,9 @@ void AtomVecDipole::data_atom(double *coord, int imagetmp, char **values)
mu[nlocal][0] = atof(values[6]);
mu[nlocal][1] = atof(values[7]);
mu[nlocal][2] = atof(values[8]);
- mu[nlocal][3] = sqrt(mu[nlocal][0]*mu[nlocal][0] +
- mu[nlocal][1]*mu[nlocal][1] +
- mu[nlocal][2]*mu[nlocal][2]);
+ mu[nlocal][3] = sqrt(mu[nlocal][0]*mu[nlocal][0] +
+ mu[nlocal][1]*mu[nlocal][1] +
+ mu[nlocal][2]*mu[nlocal][2]);
image[nlocal] = imagetmp;
@@ -803,14 +803,14 @@ int AtomVecDipole::data_atom_hybrid(int nlocal, char **values)
mu[nlocal][0] = atof(values[1]);
mu[nlocal][1] = atof(values[2]);
mu[nlocal][2] = atof(values[3]);
- mu[nlocal][3] = sqrt(mu[nlocal][0]*mu[nlocal][0] +
- mu[nlocal][1]*mu[nlocal][1] +
- mu[nlocal][2]*mu[nlocal][2]);
+ mu[nlocal][3] = sqrt(mu[nlocal][0]*mu[nlocal][0] +
+ mu[nlocal][1]*mu[nlocal][1] +
+ mu[nlocal][2]*mu[nlocal][2]);
return 4;
}
/* ----------------------------------------------------------------------
- return # of bytes of allocated memory
+ return # of bytes of allocated memory
------------------------------------------------------------------------- */
bigint AtomVecDipole::memory_usage()
diff --git a/src/DIPOLE/atom_vec_dipole.h b/src/DIPOLE/atom_vec_dipole.h
index 6aa17157bccc2ad570b1348dc9a13677fd60c6fd..52b751f10d5cb3f5abb355289c02904f2909d440 100644
--- a/src/DIPOLE/atom_vec_dipole.h
+++ b/src/DIPOLE/atom_vec_dipole.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/DIPOLE/pair_dipole_cut.cpp b/src/DIPOLE/pair_dipole_cut.cpp
index f443854b9032923bc863ad66b836ad84398599c3..e95955062b6104a0c5f5eff5f1db8c8d3478f5df 100644
--- a/src/DIPOLE/pair_dipole_cut.cpp
+++ b/src/DIPOLE/pair_dipole_cut.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -86,7 +86,7 @@ void PairDipoleCut::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@@ -112,142 +112,142 @@ void PairDipoleCut::compute(int eflag, int vflag)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- rinv = sqrt(r2inv);
+ r2inv = 1.0/rsq;
+ rinv = sqrt(r2inv);
+
+ // atom can have both a charge and dipole
+ // i,j = charge-charge, dipole-dipole, dipole-charge, or charge-dipole
- // atom can have both a charge and dipole
- // i,j = charge-charge, dipole-dipole, dipole-charge, or charge-dipole
+ forcecoulx = forcecouly = forcecoulz = 0.0;
+ tixcoul = tiycoul = tizcoul = 0.0;
+ tjxcoul = tjycoul = tjzcoul = 0.0;
- forcecoulx = forcecouly = forcecoulz = 0.0;
- tixcoul = tiycoul = tizcoul = 0.0;
- tjxcoul = tjycoul = tjzcoul = 0.0;
-
- if (rsq < cut_coulsq[itype][jtype]) {
+ if (rsq < cut_coulsq[itype][jtype]) {
- if (qtmp != 0.0 && q[j] != 0.0) {
+ if (qtmp != 0.0 && q[j] != 0.0) {
r3inv = r2inv*rinv;
- pre1 = qtmp*q[j]*r3inv;
+ pre1 = qtmp*q[j]*r3inv;
- forcecoulx += pre1*delx;
- forcecouly += pre1*dely;
- forcecoulz += pre1*delz;
- }
+ forcecoulx += pre1*delx;
+ forcecouly += pre1*dely;
+ forcecoulz += pre1*delz;
+ }
- if (mu[i][3] > 0.0 && mu[j][3] > 0.0) {
+ if (mu[i][3] > 0.0 && mu[j][3] > 0.0) {
r3inv = r2inv*rinv;
r5inv = r3inv*r2inv;
- r7inv = r5inv*r2inv;
+ r7inv = r5inv*r2inv;
pdotp = mu[i][0]*mu[j][0] + mu[i][1]*mu[j][1] + mu[i][2]*mu[j][2];
pidotr = mu[i][0]*delx + mu[i][1]*dely + mu[i][2]*delz;
pjdotr = mu[j][0]*delx + mu[j][1]*dely + mu[j][2]*delz;
- pre1 = 3.0*r5inv*pdotp - 15.0*r7inv*pidotr*pjdotr;
- pre2 = 3.0*r5inv*pjdotr;
- pre3 = 3.0*r5inv*pidotr;
- pre4 = -1.0*r3inv;
-
- forcecoulx += pre1*delx + pre2*mu[i][0] + pre3*mu[j][0];
- forcecouly += pre1*dely + pre2*mu[i][1] + pre3*mu[j][1];
- forcecoulz += pre1*delz + pre2*mu[i][2] + pre3*mu[j][2];
-
- crossx = pre4 * (mu[i][1]*mu[j][2] - mu[i][2]*mu[j][1]);
- crossy = pre4 * (mu[i][2]*mu[j][0] - mu[i][0]*mu[j][2]);
- crossz = pre4 * (mu[i][0]*mu[j][1] - mu[i][1]*mu[j][0]);
-
- tixcoul += crossx + pre2 * (mu[i][1]*delz - mu[i][2]*dely);
- tiycoul += crossy + pre2 * (mu[i][2]*delx - mu[i][0]*delz);
- tizcoul += crossz + pre2 * (mu[i][0]*dely - mu[i][1]*delx);
- tjxcoul += -crossx + pre3 * (mu[j][1]*delz - mu[j][2]*dely);
- tjycoul += -crossy + pre3 * (mu[j][2]*delx - mu[j][0]*delz);
- tjzcoul += -crossz + pre3 * (mu[j][0]*dely - mu[j][1]*delx);
- }
-
- if (mu[i][3] > 0.0 && q[j] != 0.0) {
+ pre1 = 3.0*r5inv*pdotp - 15.0*r7inv*pidotr*pjdotr;
+ pre2 = 3.0*r5inv*pjdotr;
+ pre3 = 3.0*r5inv*pidotr;
+ pre4 = -1.0*r3inv;
+
+ forcecoulx += pre1*delx + pre2*mu[i][0] + pre3*mu[j][0];
+ forcecouly += pre1*dely + pre2*mu[i][1] + pre3*mu[j][1];
+ forcecoulz += pre1*delz + pre2*mu[i][2] + pre3*mu[j][2];
+
+ crossx = pre4 * (mu[i][1]*mu[j][2] - mu[i][2]*mu[j][1]);
+ crossy = pre4 * (mu[i][2]*mu[j][0] - mu[i][0]*mu[j][2]);
+ crossz = pre4 * (mu[i][0]*mu[j][1] - mu[i][1]*mu[j][0]);
+
+ tixcoul += crossx + pre2 * (mu[i][1]*delz - mu[i][2]*dely);
+ tiycoul += crossy + pre2 * (mu[i][2]*delx - mu[i][0]*delz);
+ tizcoul += crossz + pre2 * (mu[i][0]*dely - mu[i][1]*delx);
+ tjxcoul += -crossx + pre3 * (mu[j][1]*delz - mu[j][2]*dely);
+ tjycoul += -crossy + pre3 * (mu[j][2]*delx - mu[j][0]*delz);
+ tjzcoul += -crossz + pre3 * (mu[j][0]*dely - mu[j][1]*delx);
+ }
+
+ if (mu[i][3] > 0.0 && q[j] != 0.0) {
r3inv = r2inv*rinv;
r5inv = r3inv*r2inv;
pidotr = mu[i][0]*delx + mu[i][1]*dely + mu[i][2]*delz;
- pre1 = 3.0*q[j]*r5inv * pidotr;
- pre2 = q[j]*r3inv;
+ pre1 = 3.0*q[j]*r5inv * pidotr;
+ pre2 = q[j]*r3inv;
- forcecoulx += pre2*mu[i][0] - pre1*delx;
+ forcecoulx += pre2*mu[i][0] - pre1*delx;
forcecouly += pre2*mu[i][1] - pre1*dely;
forcecoulz += pre2*mu[i][2] - pre1*delz;
- tixcoul += pre2 * (mu[i][1]*delz - mu[i][2]*dely);
- tiycoul += pre2 * (mu[i][2]*delx - mu[i][0]*delz);
- tizcoul += pre2 * (mu[i][0]*dely - mu[i][1]*delx);
- }
+ tixcoul += pre2 * (mu[i][1]*delz - mu[i][2]*dely);
+ tiycoul += pre2 * (mu[i][2]*delx - mu[i][0]*delz);
+ tizcoul += pre2 * (mu[i][0]*dely - mu[i][1]*delx);
+ }
- if (mu[j][3] > 0.0 && qtmp != 0.0) {
+ if (mu[j][3] > 0.0 && qtmp != 0.0) {
r3inv = r2inv*rinv;
r5inv = r3inv*r2inv;
pjdotr = mu[j][0]*delx + mu[j][1]*dely + mu[j][2]*delz;
- pre1 = 3.0*qtmp*r5inv * pjdotr;
- pre2 = qtmp*r3inv;
+ pre1 = 3.0*qtmp*r5inv * pjdotr;
+ pre2 = qtmp*r3inv;
- forcecoulx += pre1*delx - pre2*mu[j][0];
+ forcecoulx += pre1*delx - pre2*mu[j][0];
forcecouly += pre1*dely - pre2*mu[j][1];
forcecoulz += pre1*delz - pre2*mu[j][2];
- tjxcoul += -pre2 * (mu[j][1]*delz - mu[j][2]*dely);
- tjycoul += -pre2 * (mu[j][2]*delx - mu[j][0]*delz);
- tjzcoul += -pre2 * (mu[j][0]*dely - mu[j][1]*delx);
- }
- }
-
- // LJ interaction
-
- if (rsq < cut_ljsq[itype][jtype]) {
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- forcelj *= factor_lj * r2inv;
- } else forcelj = 0.0;
-
- // total force
-
- fq = factor_coul*qqrd2e;
- fx = fq*forcecoulx + delx*forcelj;
- fy = fq*forcecouly + dely*forcelj;
- fz = fq*forcecoulz + delz*forcelj;
-
- // force & torque accumulation
-
- f[i][0] += fx;
- f[i][1] += fy;
- f[i][2] += fz;
- torque[i][0] += fq*tixcoul;
- torque[i][1] += fq*tiycoul;
- torque[i][2] += fq*tizcoul;
-
- if (newton_pair || j < nlocal) {
- f[j][0] -= fx;
- f[j][1] -= fy;
- f[j][2] -= fz;
- torque[j][0] += fq*tjxcoul;
- torque[j][1] += fq*tjycoul;
- torque[j][2] += fq*tjzcoul;
- }
-
- if (eflag) {
- if (rsq < cut_coulsq[itype][jtype]) {
- ecoul = qtmp*q[j]*rinv;
- if (mu[i][3] > 0.0 && mu[j][3] > 0.0)
- ecoul += r3inv*pdotp - 3.0*r5inv*pidotr*pjdotr;
- if (mu[i][3] > 0.0 && q[j] != 0.0)
- ecoul += -q[j]*r3inv*pidotr;
- if (mu[j][3] > 0.0 && qtmp != 0.0)
- ecoul += qtmp*r3inv*pjdotr;
- ecoul *= factor_coul*qqrd2e;
- } else ecoul = 0.0;
-
- if (rsq < cut_ljsq[itype][jtype]) {
- evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
- offset[itype][jtype];
- evdwl *= factor_lj;
- } else evdwl = 0.0;
- }
-
- if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,
- evdwl,ecoul,fx,fy,fz,delx,dely,delz);
+ tjxcoul += -pre2 * (mu[j][1]*delz - mu[j][2]*dely);
+ tjycoul += -pre2 * (mu[j][2]*delx - mu[j][0]*delz);
+ tjzcoul += -pre2 * (mu[j][0]*dely - mu[j][1]*delx);
+ }
+ }
+
+ // LJ interaction
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ forcelj *= factor_lj * r2inv;
+ } else forcelj = 0.0;
+
+ // total force
+
+ fq = factor_coul*qqrd2e;
+ fx = fq*forcecoulx + delx*forcelj;
+ fy = fq*forcecouly + dely*forcelj;
+ fz = fq*forcecoulz + delz*forcelj;
+
+ // force & torque accumulation
+
+ f[i][0] += fx;
+ f[i][1] += fy;
+ f[i][2] += fz;
+ torque[i][0] += fq*tixcoul;
+ torque[i][1] += fq*tiycoul;
+ torque[i][2] += fq*tizcoul;
+
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= fx;
+ f[j][1] -= fy;
+ f[j][2] -= fz;
+ torque[j][0] += fq*tjxcoul;
+ torque[j][1] += fq*tjycoul;
+ torque[j][2] += fq*tjzcoul;
+ }
+
+ if (eflag) {
+ if (rsq < cut_coulsq[itype][jtype]) {
+ ecoul = qtmp*q[j]*rinv;
+ if (mu[i][3] > 0.0 && mu[j][3] > 0.0)
+ ecoul += r3inv*pdotp - 3.0*r5inv*pidotr*pjdotr;
+ if (mu[i][3] > 0.0 && q[j] != 0.0)
+ ecoul += -q[j]*r3inv*pidotr;
+ if (mu[j][3] > 0.0 && qtmp != 0.0)
+ ecoul += qtmp*r3inv*pjdotr;
+ ecoul *= factor_coul*qqrd2e;
+ } else ecoul = 0.0;
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
+ offset[itype][jtype];
+ evdwl *= factor_lj;
+ } else evdwl = 0.0;
+ }
+
+ if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,
+ evdwl,ecoul,fx,fy,fz,delx,dely,delz);
}
}
}
@@ -256,7 +256,7 @@ void PairDipoleCut::compute(int eflag, int vflag)
}
/* ----------------------------------------------------------------------
- allocate all arrays
+ allocate all arrays
------------------------------------------------------------------------- */
void PairDipoleCut::allocate()
@@ -285,7 +285,7 @@ void PairDipoleCut::allocate()
}
/* ----------------------------------------------------------------------
- global settings
+ global settings
------------------------------------------------------------------------- */
void PairDipoleCut::settings(int narg, char **arg)
@@ -303,10 +303,10 @@ void PairDipoleCut::settings(int narg, char **arg)
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
- if (setflag[i][j]) {
- cut_lj[i][j] = cut_lj_global;
- cut_coul[i][j] = cut_coul_global;
- }
+ if (setflag[i][j]) {
+ cut_lj[i][j] = cut_lj_global;
+ cut_coul[i][j] = cut_coul_global;
+ }
}
}
@@ -316,7 +316,7 @@ void PairDipoleCut::settings(int narg, char **arg)
void PairDipoleCut::coeff(int narg, char **arg)
{
- if (narg < 4 || narg > 6)
+ if (narg < 4 || narg > 6)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
@@ -367,7 +367,7 @@ double PairDipoleCut::init_one(int i, int j)
{
if (setflag[i][j] == 0) {
epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j],
- sigma[i][i],sigma[j][j]);
+ sigma[i][i],sigma[j][j]);
sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]);
cut_lj[i][j] = mix_distance(cut_lj[i][i],cut_lj[j][j]);
cut_coul[i][j] = mix_distance(cut_coul[i][i],cut_coul[j][j]);
@@ -381,12 +381,12 @@ double PairDipoleCut::init_one(int i, int j)
lj2[i][j] = 24.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
-
+
if (offset_flag) {
double ratio = sigma[i][j] / cut_lj[i][j];
offset[i][j] = 4.0 * epsilon[i][j] * (pow(ratio,12.0) - pow(ratio,6.0));
} else offset[i][j] = 0.0;
-
+
cut_ljsq[j][i] = cut_ljsq[i][j];
cut_coulsq[j][i] = cut_coulsq[i][j];
lj1[j][i] = lj1[i][j];
@@ -411,10 +411,10 @@ void PairDipoleCut::write_restart(FILE *fp)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
- fwrite(&epsilon[i][j],sizeof(double),1,fp);
- fwrite(&sigma[i][j],sizeof(double),1,fp);
- fwrite(&cut_lj[i][j],sizeof(double),1,fp);
- fwrite(&cut_coul[i][j],sizeof(double),1,fp);
+ fwrite(&epsilon[i][j],sizeof(double),1,fp);
+ fwrite(&sigma[i][j],sizeof(double),1,fp);
+ fwrite(&cut_lj[i][j],sizeof(double),1,fp);
+ fwrite(&cut_coul[i][j],sizeof(double),1,fp);
}
}
}
@@ -436,16 +436,16 @@ void PairDipoleCut::read_restart(FILE *fp)
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
- if (me == 0) {
- fread(&epsilon[i][j],sizeof(double),1,fp);
- fread(&sigma[i][j],sizeof(double),1,fp);
- fread(&cut_lj[i][j],sizeof(double),1,fp);
- fread(&cut_coul[i][j],sizeof(double),1,fp);
- }
- MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&cut_coul[i][j],1,MPI_DOUBLE,0,world);
+ if (me == 0) {
+ fread(&epsilon[i][j],sizeof(double),1,fp);
+ fread(&sigma[i][j],sizeof(double),1,fp);
+ fread(&cut_lj[i][j],sizeof(double),1,fp);
+ fread(&cut_coul[i][j],sizeof(double),1,fp);
+ }
+ MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut_coul[i][j],1,MPI_DOUBLE,0,world);
}
}
}
diff --git a/src/DIPOLE/pair_dipole_cut.h b/src/DIPOLE/pair_dipole_cut.h
index f787dda55d4a57e17f5da2250f21ca5739909e5e..212e5f8a2be51af15816bd4ee372ee7c010b8059 100644
--- a/src/DIPOLE/pair_dipole_cut.h
+++ b/src/DIPOLE/pair_dipole_cut.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/FLD/pair_brownian.cpp b/src/FLD/pair_brownian.cpp
index 586c83cd0a311b16ed7264a4a0e24c8ec855f668..b4966dca52f16f249648a78c2894d7bce666a38d 100755
--- a/src/FLD/pair_brownian.cpp
+++ b/src/FLD/pair_brownian.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -104,37 +104,37 @@ void PairBrownian::compute(int eflag, int vflag)
if (flagVF) // Flag for volume fraction corrections
if (flagdeform || flagwall == 2){ // Possible changes in volume fraction
if (flagdeform && !flagwall)
- for (j = 0; j < 3; j++)
- dims[j] = domain->prd[j];
+ for (j = 0; j < 3; j++)
+ dims[j] = domain->prd[j];
else if (flagwall == 2 || (flagdeform && flagwall == 1)){
- double wallhi[3], walllo[3];
- for (int j = 0; j < 3; j++){
- wallhi[j] = domain->prd[j];
- walllo[j] = 0;
- }
- for (int m = 0; m < wallfix->nwall; m++){
- int dim = wallfix->wallwhich[m] / 2;
- int side = wallfix->wallwhich[m] % 2;
- if (wallfix->wallstyle[m] == VARIABLE){
- wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
- }
- else wallcoord = wallfix->coord0[m];
- if (side == 0) walllo[dim] = wallcoord;
- else wallhi[dim] = wallcoord;
- }
- for (int j = 0; j < 3; j++)
- dims[j] = wallhi[j] - walllo[j];
+ double wallhi[3], walllo[3];
+ for (int j = 0; j < 3; j++){
+ wallhi[j] = domain->prd[j];
+ walllo[j] = 0;
+ }
+ for (int m = 0; m < wallfix->nwall; m++){
+ int dim = wallfix->wallwhich[m] / 2;
+ int side = wallfix->wallwhich[m] % 2;
+ if (wallfix->wallstyle[m] == VARIABLE){
+ wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
+ }
+ else wallcoord = wallfix->coord0[m];
+ if (side == 0) walllo[dim] = wallcoord;
+ else wallhi[dim] = wallcoord;
+ }
+ for (int j = 0; j < 3; j++)
+ dims[j] = wallhi[j] - walllo[j];
}
double vol_T = dims[0]*dims[1]*dims[2];
double vol_f = vol_P/vol_T;
if (flaglog == 0) {
- R0 = 6*MY_PI*mu*rad*(1.0 + 2.16*vol_f);
- RT0 = 8*MY_PI*mu*pow(rad,3.0);
- //RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3)*(1.0 + 3.33*vol_f + 2.80*vol_f*vol_f);
+ R0 = 6*MY_PI*mu*rad*(1.0 + 2.16*vol_f);
+ RT0 = 8*MY_PI*mu*pow(rad,3.0);
+ //RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3)*(1.0 + 3.33*vol_f + 2.80*vol_f*vol_f);
} else {
- R0 = 6*MY_PI*mu*rad*(1.0 + 2.725*vol_f - 6.583*vol_f*vol_f);
- RT0 = 8*MY_PI*mu*pow(rad,3.0)*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
- //RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3)*(1.0 + 3.64*vol_f - 6.95*vol_f*vol_f);
+ R0 = 6*MY_PI*mu*rad*(1.0 + 2.725*vol_f - 6.583*vol_f*vol_f);
+ RT0 = 8*MY_PI*mu*pow(rad,3.0)*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
+ //RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3)*(1.0 + 3.64*vol_f - 6.95*vol_f*vol_f);
}
}
@@ -156,8 +156,8 @@ void PairBrownian::compute(int eflag, int vflag)
itype = type[i];
radi = radius[i];
jlist = firstneigh[i];
- jnum = numneigh[i];
-
+ jnum = numneigh[i];
+
// FLD contribution to force and torque due to isotropic terms
if (flagfld) {
@@ -165,12 +165,12 @@ void PairBrownian::compute(int eflag, int vflag)
f[i][1] += prethermostat*sqrt(R0)*(random->uniform()-0.5);
f[i][2] += prethermostat*sqrt(R0)*(random->uniform()-0.5);
if (flaglog) {
- torque[i][0] += prethermostat*sqrt(RT0)*(random->uniform()-0.5);
- torque[i][1] += prethermostat*sqrt(RT0)*(random->uniform()-0.5);
- torque[i][2] += prethermostat*sqrt(RT0)*(random->uniform()-0.5);
+ torque[i][0] += prethermostat*sqrt(RT0)*(random->uniform()-0.5);
+ torque[i][1] += prethermostat*sqrt(RT0)*(random->uniform()-0.5);
+ torque[i][2] += prethermostat*sqrt(RT0)*(random->uniform()-0.5);
}
}
-
+
if (!flagHI) continue;
for (jj = 0; jj < jnum; jj++) {
@@ -184,25 +184,25 @@ void PairBrownian::compute(int eflag, int vflag)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r = sqrt(rsq);
-
+ r = sqrt(rsq);
+
// scalar resistances a_sq and a_sh
h_sep = r - 2.0*radi;
-
+
// check for overlaps
if (h_sep < 0.0) overlaps++;
-
+
// if less than minimum gap, use minimum gap instead
if (r < cut_inner[itype][jtype])
- h_sep = cut_inner[itype][jtype] - 2.0*radi;
-
+ h_sep = cut_inner[itype][jtype] - 2.0*radi;
+
// scale h_sep by radi
h_sep = h_sep/radi;
-
+
// scalar resistances
if (flaglog) {
@@ -211,70 +211,70 @@ void PairBrownian::compute(int eflag, int vflag)
a_pu = 8.0*MY_PI*mu*pow(radi,3.0)*(3.0/160.0*log(1.0/h_sep));
} else
a_sq = 6.0*MY_PI*mu*radi*(1.0/4.0/h_sep);
-
+
// generate the Pairwise Brownian Force: a_sq
Fbmag = prethermostat*sqrt(a_sq);
-
+
// generate a random number
randr = random->uniform()-0.5;
-
+
// contribution due to Brownian motion
fx = Fbmag*randr*delx/r;
fy = Fbmag*randr*dely/r;
fz = Fbmag*randr*delz/r;
-
+
// add terms due to a_sh
if (flaglog) {
// generate two orthogonal vectors to the line of centers
- p1[0] = delx/r; p1[1] = dely/r; p1[2] = delz/r;
+ p1[0] = delx/r; p1[1] = dely/r; p1[2] = delz/r;
set_3_orthogonal_vectors(p1,p2,p3);
-
+
// magnitude
- Fbmag = prethermostat*sqrt(a_sh);
-
+ Fbmag = prethermostat*sqrt(a_sh);
+
// force in each of the two directions
randr = random->uniform()-0.5;
fx += Fbmag*randr*p2[0];
fy += Fbmag*randr*p2[1];
fz += Fbmag*randr*p2[2];
-
+
randr = random->uniform()-0.5;
fx += Fbmag*randr*p3[0];
fy += Fbmag*randr*p3[1];
- fz += Fbmag*randr*p3[2];
- }
-
+ fz += Fbmag*randr*p3[2];
+ }
+
// scale forces to appropriate units
fx = vxmu2f*fx;
fy = vxmu2f*fy;
fz = vxmu2f*fz;
-
+
// sum to total force
f[i][0] -= fx;
f[i][1] -= fy;
- f[i][2] -= fz;
-
- if (newton_pair || j < nlocal) {
- //randr = random->uniform()-0.5;
- //fx = Fbmag*randr*delx/r;
- //fy = Fbmag*randr*dely/r;
- //fz = Fbmag*randr*delz/r;
-
- f[j][0] += fx;
- f[j][1] += fy;
- f[j][2] += fz;
- }
-
+ f[i][2] -= fz;
+
+ if (newton_pair || j < nlocal) {
+ //randr = random->uniform()-0.5;
+ //fx = Fbmag*randr*delx/r;
+ //fy = Fbmag*randr*dely/r;
+ //fz = Fbmag*randr*delz/r;
+
+ f[j][0] += fx;
+ f[j][1] += fy;
+ f[j][2] += fz;
+ }
+
// torque due to the Brownian Force
if (flaglog) {
@@ -284,56 +284,56 @@ void PairBrownian::compute(int eflag, int vflag)
xl[0] = -delx/r*radi;
xl[1] = -dely/r*radi;
xl[2] = -delz/r*radi;
-
+
// torque = xl_cross_F
tx = xl[1]*fz - xl[2]*fy;
ty = xl[2]*fx - xl[0]*fz;
- tz = xl[0]*fy - xl[1]*fx;
-
+ tz = xl[0]*fy - xl[1]*fx;
+
// torque is same on both particles
torque[i][0] -= tx;
torque[i][1] -= ty;
- torque[i][2] -= tz;
-
- if (newton_pair || j < nlocal) {
- torque[j][0] -= tx;
- torque[j][1] -= ty;
- torque[j][2] -= tz;
- }
+ torque[i][2] -= tz;
+
+ if (newton_pair || j < nlocal) {
+ torque[j][0] -= tx;
+ torque[j][1] -= ty;
+ torque[j][2] -= tz;
+ }
// torque due to a_pu
- Fbmag = prethermostat*sqrt(a_pu);
-
+ Fbmag = prethermostat*sqrt(a_pu);
+
// force in each direction
randr = random->uniform()-0.5;
tx = Fbmag*randr*p2[0];
ty = Fbmag*randr*p2[1];
tz = Fbmag*randr*p2[2];
-
+
randr = random->uniform()-0.5;
tx += Fbmag*randr*p3[0];
ty += Fbmag*randr*p3[1];
- tz += Fbmag*randr*p3[2];
-
+ tz += Fbmag*randr*p3[2];
+
// torque has opposite sign on two particles
torque[i][0] -= tx;
torque[i][1] -= ty;
- torque[i][2] -= tz;
-
- if (newton_pair || j < nlocal) {
- torque[j][0] += tx;
- torque[j][1] += ty;
- torque[j][2] += tz;
- }
+ torque[i][2] -= tz;
+
+ if (newton_pair || j < nlocal) {
+ torque[j][0] += tx;
+ torque[j][1] += ty;
+ torque[j][2] += tz;
+ }
}
if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,
- 0.0,0.0,-fx,-fy,-fz,delx,dely,delz);
+ 0.0,0.0,-fx,-fy,-fz,delx,dely,delz);
}
}
}
@@ -346,7 +346,7 @@ void PairBrownian::compute(int eflag, int vflag)
}
/* ----------------------------------------------------------------------
- allocate all arrays
+ allocate all arrays
------------------------------------------------------------------------- */
void PairBrownian::allocate()
@@ -366,7 +366,7 @@ void PairBrownian::allocate()
}
/* ----------------------------------------------------------------------
- global settings
+ global settings
------------------------------------------------------------------------- */
void PairBrownian::settings(int narg, char **arg)
@@ -374,12 +374,12 @@ void PairBrownian::settings(int narg, char **arg)
if (narg != 7 && narg != 9) error->all(FLERR,"Illegal pair_style command");
mu = atof(arg[0]);
- flaglog = atoi(arg[1]);
- flagfld = atoi(arg[2]);
- cut_inner_global = atof(arg[3]);
- cut_global = atof(arg[4]);
- t_target = atof(arg[5]);
- seed = atoi(arg[6]);
+ flaglog = atoi(arg[1]);
+ flagfld = atoi(arg[2]);
+ cut_inner_global = atof(arg[3]);
+ cut_global = atof(arg[4]);
+ t_target = atof(arg[5]);
+ seed = atoi(arg[6]);
flagHI = flagVF = 1;
if (narg == 9) {
@@ -389,9 +389,9 @@ void PairBrownian::settings(int narg, char **arg)
if (flaglog == 1 && flagHI == 0) {
error->warning(FLERR,"Cannot include log terms without 1/r terms; "
- "setting flagHI to 1");
+ "setting flagHI to 1");
flagHI = 1;
- }
+ }
// initialize Marsaglia RNG with processor-unique seed
@@ -427,7 +427,7 @@ void PairBrownian::coeff(int narg, char **arg)
double cut_inner_one = cut_inner_global;
double cut_one = cut_global;
-
+
if (narg == 4) {
cut_inner_one = atof(arg[2]);
cut_one = atof(arg[3]);
@@ -459,8 +459,8 @@ void PairBrownian::init_style()
if (force->newton_pair == 0 && comm->me == 0)
error->warning(FLERR,
- "Pair brownian needs newton pair on for "
- "momentum conservation");
+ "Pair brownian needs newton pair on for "
+ "momentum conservation");
int irequest = neighbor->request(this);
@@ -472,7 +472,7 @@ void PairBrownian::init_style()
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
- if (radius[i] == 0.0)
+ if (radius[i] == 0.0)
error->one(FLERR,"Pair brownian requires extended particles");
// require monodisperse system with same radii for all types
@@ -485,7 +485,7 @@ void PairBrownian::init_style()
error->all(FLERR,"Pair brownian requires monodisperse particles");
rad = radtype;
}
-
+
// set the isotropic constants that depend on the volume fraction
// vol_T = total volume
// check for fix deform, if exists it must use "remap v"
@@ -499,52 +499,52 @@ void PairBrownian::init_style()
flagdeform = flagwall = 0;
for (int i = 0; i < modify->nfix; i++){
- if (strcmp(modify->fix[i]->style,"deform") == 0)
+ if (strcmp(modify->fix[i]->style,"deform") == 0)
flagdeform = 1;
else if (strstr(modify->fix[i]->style,"wall") != NULL){
flagwall = 1; // Walls exist
if (((FixWall *) modify->fix[i])->varflag ) {
- flagwall = 2; // Moving walls exist
- wallfix = (FixWall *) modify->fix[i];
+ flagwall = 2; // Moving walls exist
+ wallfix = (FixWall *) modify->fix[i];
}
}
}
-
+
// set the isotropic constants depending on the volume fraction
- // vol_T = total volumeshearing = flagdeform = flagwall = 0;
+ // vol_T = total volumeshearing = flagdeform = flagwall = 0;
double vol_T, wallcoord;
if (!flagwall) vol_T = domain->xprd*domain->yprd*domain->zprd;
- else {
+ else {
double wallhi[3], walllo[3];
for (int j = 0; j < 3; j++){
wallhi[j] = domain->prd[j];
walllo[j] = 0;
- }
+ }
for (int m = 0; m < wallfix->nwall; m++){
int dim = wallfix->wallwhich[m] / 2;
int side = wallfix->wallwhich[m] % 2;
if (wallfix->wallstyle[m] == VARIABLE){
- wallfix->varindex[m] = input->variable->find(wallfix->varstr[m]);
- // Since fix->wall->init happens after pair->init_style
- wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
+ wallfix->varindex[m] = input->variable->find(wallfix->varstr[m]);
+ // Since fix->wall->init happens after pair->init_style
+ wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
}
-
+
else wallcoord = wallfix->coord0[m];
-
+
if (side == 0) walllo[dim] = wallcoord;
else wallhi[dim] = wallcoord;
}
- vol_T = (wallhi[0] - walllo[0]) * (wallhi[1] - walllo[1]) *
+ vol_T = (wallhi[0] - walllo[0]) * (wallhi[1] - walllo[1]) *
(wallhi[2] - walllo[2]);
}
-
+
// vol_P = volume of particles, assuming mono-dispersity
// vol_f = volume fraction
vol_P = atom->natoms*(4.0/3.0)*MY_PI*pow(rad,3.0);
-
+
double vol_f = vol_P/vol_T;
-
+
// set isotropic constants
if (!flagVF) vol_f = 0;
@@ -553,7 +553,7 @@ void PairBrownian::init_style()
RT0 = 8*MY_PI*mu*pow(rad,3.0); // not actually needed
} else {
R0 = 6*MY_PI*mu*rad*(1.0 + 2.725*vol_f - 6.583*vol_f*vol_f);
- RT0 = 8*MY_PI*mu*pow(rad,3.0)*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
+ RT0 = 8*MY_PI*mu*pow(rad,3.0)*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
}
}
@@ -574,7 +574,7 @@ double PairBrownian::init_one(int i, int j)
}
/* ----------------------------------------------------------------------
- proc 0 writes to restart file
+ proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairBrownian::write_restart(FILE *fp)
@@ -586,8 +586,8 @@ void PairBrownian::write_restart(FILE *fp)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
- fwrite(&cut_inner[i][j],sizeof(double),1,fp);
- fwrite(&cut[i][j],sizeof(double),1,fp);
+ fwrite(&cut_inner[i][j],sizeof(double),1,fp);
+ fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
@@ -608,12 +608,12 @@ void PairBrownian::read_restart(FILE *fp)
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
- if (me == 0) {
- fread(&cut_inner[i][j],sizeof(double),1,fp);
- fread(&cut[i][j],sizeof(double),1,fp);
- }
- MPI_Bcast(&cut_inner[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
+ if (me == 0) {
+ fread(&cut_inner[i][j],sizeof(double),1,fp);
+ fread(&cut[i][j],sizeof(double),1,fp);
+ }
+ MPI_Bcast(&cut_inner[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
@@ -678,11 +678,11 @@ void PairBrownian::read_restart_settings(FILE *fp)
/* ----------------------------------------------------------------------*/
void PairBrownian::set_3_orthogonal_vectors(double p1[3],
- double p2[3], double p3[3])
+ double p2[3], double p3[3])
{
double norm;
int ix,iy,iz;
-
+
// find the index of maximum magnitude and store it in iz
if (fabs(p1[0]) > fabs(p1[1])) {
@@ -694,7 +694,7 @@ void PairBrownian::set_3_orthogonal_vectors(double p1[3],
ix=2;
iy=0;
}
-
+
if (iz==0) {
if (fabs(p1[0]) < fabs(p1[2])) {
iz = 2;
@@ -708,24 +708,24 @@ void PairBrownian::set_3_orthogonal_vectors(double p1[3],
iy = 1;
}
}
-
+
// set p2 arbitrarily such that it's orthogonal to p1
p2[ix]=1.0;
- p2[iy]=1.0;
+ p2[iy]=1.0;
p2[iz] = -(p1[ix]*p2[ix] + p1[iy]*p2[iy])/p1[iz];
-
+
// normalize p2
norm = sqrt(p2[0]*p2[0] + p2[1]*p2[1] + p2[2]*p2[2]);
-
+
p2[0] = p2[0]/norm;
p2[1] = p2[1]/norm;
p2[2] = p2[2]/norm;
-
+
// Set p3 by taking the cross product p3=p2xp1
p3[0] = p1[1]*p2[2] - p1[2]*p2[1];
p3[1] = p1[2]*p2[0] - p1[0]*p2[2];
- p3[2] = p1[0]*p2[1] - p1[1]*p2[0];
+ p3[2] = p1[0]*p2[1] - p1[1]*p2[0];
}
diff --git a/src/FLD/pair_brownian.h b/src/FLD/pair_brownian.h
index 97b7b8cb7b0358d665562ea369d18eb56ea20f89..99fad06a1422097ebbf6def76ce63417ef74cf34 100644
--- a/src/FLD/pair_brownian.h
+++ b/src/FLD/pair_brownian.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -28,7 +28,7 @@ class PairBrownian : public Pair {
public:
PairBrownian(class LAMMPS *);
virtual ~PairBrownian();
- virtual void compute(int, int);
+ virtual void compute(int, int);
void settings(int, char **);
void coeff(int, char **);
virtual double init_one(int, int);
@@ -36,7 +36,7 @@ class PairBrownian : public Pair {
void write_restart(FILE *);
void read_restart(FILE *);
void write_restart_settings(FILE *);
- void read_restart_settings(FILE *);
+ void read_restart_settings(FILE *);
protected:
double cut_inner_global,cut_global;
diff --git a/src/FLD/pair_brownian_poly.cpp b/src/FLD/pair_brownian_poly.cpp
index eeec6e33fcc053efa7e14bcdc8d8f8cfe3fb7a53..379f2a7ce936f10cf416a6208c2a4c9c87e671f8 100644
--- a/src/FLD/pair_brownian_poly.cpp
+++ b/src/FLD/pair_brownian_poly.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -81,7 +81,7 @@ void PairBrownianPoly::compute(int eflag, int vflag)
double prethermostat;
double xl[3],a_sq,a_sh,a_pu,Fbmag;
double p1[3],p2[3],p3[3];
-
+
// This section of code adjusts R0/RT0/RS0 if necessary due to changes
// in the volume fraction as a result of fix deform or moving walls
@@ -90,37 +90,37 @@ void PairBrownianPoly::compute(int eflag, int vflag)
if (flagVF) // Flag for volume fraction corrections
if (flagdeform || flagwall == 2){ // Possible changes in volume fraction
if (flagdeform && !flagwall)
- for (j = 0; j < 3; j++)
- dims[j] = domain->prd[j];
+ for (j = 0; j < 3; j++)
+ dims[j] = domain->prd[j];
else if (flagwall == 2 || (flagdeform && flagwall == 1)){
- double wallhi[3], walllo[3];
- for (j = 0; j < 3; j++){
- wallhi[j] = domain->prd[j];
- walllo[j] = 0;
- }
- for (int m = 0; m < wallfix->nwall; m++){
- int dim = wallfix->wallwhich[m] / 2;
- int side = wallfix->wallwhich[m] % 2;
- if (wallfix->wallstyle[m] == VARIABLE){
- wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
- }
- else wallcoord = wallfix->coord0[m];
- if (side == 0) walllo[dim] = wallcoord;
- else wallhi[dim] = wallcoord;
- }
- for (j = 0; j < 3; j++)
- dims[j] = wallhi[j] - walllo[j];
+ double wallhi[3], walllo[3];
+ for (j = 0; j < 3; j++){
+ wallhi[j] = domain->prd[j];
+ walllo[j] = 0;
+ }
+ for (int m = 0; m < wallfix->nwall; m++){
+ int dim = wallfix->wallwhich[m] / 2;
+ int side = wallfix->wallwhich[m] % 2;
+ if (wallfix->wallstyle[m] == VARIABLE){
+ wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
+ }
+ else wallcoord = wallfix->coord0[m];
+ if (side == 0) walllo[dim] = wallcoord;
+ else wallhi[dim] = wallcoord;
+ }
+ for (j = 0; j < 3; j++)
+ dims[j] = wallhi[j] - walllo[j];
}
double vol_T = dims[0]*dims[1]*dims[2];
double vol_f = vol_P/vol_T;
if (flaglog == 0) {
- R0 = 6*MY_PI*mu*rad*(1.0 + 2.16*vol_f);
- RT0 = 8*MY_PI*mu*pow(rad,3.0);
- //RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3)*(1.0 + 3.33*vol_f + 2.80*vol_f*vol_f);
+ R0 = 6*MY_PI*mu*rad*(1.0 + 2.16*vol_f);
+ RT0 = 8*MY_PI*mu*pow(rad,3.0);
+ //RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3)*(1.0 + 3.33*vol_f + 2.80*vol_f*vol_f);
} else {
- R0 = 6*MY_PI*mu*rad*(1.0 + 2.725*vol_f - 6.583*vol_f*vol_f);
- RT0 = 8*MY_PI*mu*pow(rad,3.0)*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
- //RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3)*(1.0 + 3.64*vol_f - 6.95*vol_f*vol_f);
+ R0 = 6*MY_PI*mu*rad*(1.0 + 2.725*vol_f - 6.583*vol_f*vol_f);
+ RT0 = 8*MY_PI*mu*pow(rad,3.0)*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
+ //RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3)*(1.0 + 3.64*vol_f - 6.95*vol_f*vol_f);
}
}
// scale factor for Brownian moments
@@ -142,8 +142,8 @@ void PairBrownianPoly::compute(int eflag, int vflag)
itype = type[i];
radi = radius[i];
jlist = firstneigh[i];
- jnum = numneigh[i];
-
+ jnum = numneigh[i];
+
// FLD contribution to force and torque due to isotropic terms
if (flagfld) {
@@ -151,16 +151,16 @@ void PairBrownianPoly::compute(int eflag, int vflag)
f[i][1] += prethermostat*sqrt(R0*radi)*(random->uniform()-0.5);
f[i][2] += prethermostat*sqrt(R0*radi)*(random->uniform()-0.5);
if (flaglog) {
- const double radi3 = radi*radi*radi;
- torque[i][0] += prethermostat*sqrt(RT0*radi3) *
- (random->uniform()-0.5);
- torque[i][1] += prethermostat*sqrt(RT0*radi3) *
- (random->uniform()-0.5);
- torque[i][2] += prethermostat*sqrt(RT0*radi3) *
- (random->uniform()-0.5);
+ const double radi3 = radi*radi*radi;
+ torque[i][0] += prethermostat*sqrt(RT0*radi3) *
+ (random->uniform()-0.5);
+ torque[i][1] += prethermostat*sqrt(RT0*radi3) *
+ (random->uniform()-0.5);
+ torque[i][2] += prethermostat*sqrt(RT0*radi3) *
+ (random->uniform()-0.5);
}
}
-
+
if (!flagHI) continue;
for (jj = 0; jj < jnum; jj++) {
@@ -175,99 +175,99 @@ void PairBrownianPoly::compute(int eflag, int vflag)
radj = radius[j];
if (rsq < cutsq[itype][jtype]) {
- r = sqrt(rsq);
-
+ r = sqrt(rsq);
+
// scalar resistances a_sq and a_sh
h_sep = r - radi-radj;
-
+
// check for overlaps
if (h_sep < 0.0) overlaps++;
-
+
// if less than minimum gap, use minimum gap instead
if (r < cut_inner[itype][jtype])
h_sep = cut_inner[itype][jtype] - radi-radj;
-
+
// scale h_sep by radi
h_sep = h_sep/radi;
beta0 = radj/radi;
beta1 = 1.0 + beta0;
-
+
// scalar resistances
if (flaglog) {
- a_sq = beta0*beta0/beta1/beta1/h_sep +
- (1.0+7.0*beta0+beta0*beta0)/5.0/pow(beta1,3.0)*log(1.0/h_sep);
- a_sq += (1.0+18.0*beta0-29.0*beta0*beta0+18.0*pow(beta0,3.0) +
- pow(beta0,4.0))/21.0/pow(beta1,4.0)*h_sep*log(1.0/h_sep);
+ a_sq = beta0*beta0/beta1/beta1/h_sep +
+ (1.0+7.0*beta0+beta0*beta0)/5.0/pow(beta1,3.0)*log(1.0/h_sep);
+ a_sq += (1.0+18.0*beta0-29.0*beta0*beta0+18.0*pow(beta0,3.0) +
+ pow(beta0,4.0))/21.0/pow(beta1,4.0)*h_sep*log(1.0/h_sep);
a_sq *= 6.0*MY_PI*mu*radi;
- a_sh = 4.0*beta0*(2.0+beta0+2.0*beta0*beta0)/15.0/pow(beta1,3.0) *
- log(1.0/h_sep);
- a_sh += 4.0*(16.0-45.0*beta0+58.0*beta0*beta0-45.0*pow(beta0,3.0) +
- 16.0*pow(beta0,4.0))/375.0/pow(beta1,4.0) *
- h_sep*log(1.0/h_sep);
+ a_sh = 4.0*beta0*(2.0+beta0+2.0*beta0*beta0)/15.0/pow(beta1,3.0) *
+ log(1.0/h_sep);
+ a_sh += 4.0*(16.0-45.0*beta0+58.0*beta0*beta0-45.0*pow(beta0,3.0) +
+ 16.0*pow(beta0,4.0))/375.0/pow(beta1,4.0) *
+ h_sep*log(1.0/h_sep);
a_sh *= 6.0*MY_PI*mu*radi;
a_pu = beta0*(4.0+beta0)/10.0/beta1/beta1*log(1.0/h_sep);
- a_pu += (32.0-33.0*beta0+83.0*beta0*beta0+43.0 *
- pow(beta0,3.0))/250.0/pow(beta1,3.0)*h_sep*log(1.0/h_sep);
+ a_pu += (32.0-33.0*beta0+83.0*beta0*beta0+43.0 *
+ pow(beta0,3.0))/250.0/pow(beta1,3.0)*h_sep*log(1.0/h_sep);
a_pu *= 8.0*MY_PI*mu*pow(radi,3.0);
} else a_sq = 6.0*MY_PI*mu*radi*(beta0*beta0/beta1/beta1/h_sep);
-
+
// generate the Pairwise Brownian Force: a_sq
Fbmag = prethermostat*sqrt(a_sq);
-
+
// generate a random number
randr = random->uniform()-0.5;
-
+
// contribution due to Brownian motion
fx = Fbmag*randr*delx/r;
fy = Fbmag*randr*dely/r;
fz = Fbmag*randr*delz/r;
-
+
// add terms due to a_sh
if (flaglog) {
// generate two orthogonal vectors to the line of centers
- p1[0] = delx/r; p1[1] = dely/r; p1[2] = delz/r;
+ p1[0] = delx/r; p1[1] = dely/r; p1[2] = delz/r;
set_3_orthogonal_vectors(p1,p2,p3);
-
+
// magnitude
- Fbmag = prethermostat*sqrt(a_sh);
-
+ Fbmag = prethermostat*sqrt(a_sh);
+
// force in each of the two directions
randr = random->uniform()-0.5;
fx += Fbmag*randr*p2[0];
fy += Fbmag*randr*p2[1];
fz += Fbmag*randr*p2[2];
-
+
randr = random->uniform()-0.5;
fx += Fbmag*randr*p3[0];
fy += Fbmag*randr*p3[1];
- fz += Fbmag*randr*p3[2];
- }
-
+ fz += Fbmag*randr*p3[2];
+ }
+
// scale forces to appropriate units
fx = vxmu2f*fx;
fy = vxmu2f*fy;
fz = vxmu2f*fz;
-
+
// sum to total Force
f[i][0] -= fx;
f[i][1] -= fy;
- f[i][2] -= fz;
+ f[i][2] -= fz;
// torque due to the Brownian Force
@@ -278,47 +278,47 @@ void PairBrownianPoly::compute(int eflag, int vflag)
xl[0] = -delx/r*radi;
xl[1] = -dely/r*radi;
xl[2] = -delz/r*radi;
-
+
// torque = xl_cross_F
tx = xl[1]*fz - xl[2]*fy;
ty = xl[2]*fx - xl[0]*fz;
- tz = xl[0]*fy - xl[1]*fx;
-
+ tz = xl[0]*fy - xl[1]*fx;
+
// torque is same on both particles
torque[i][0] -= tx;
torque[i][1] -= ty;
- torque[i][2] -= tz;
-
+ torque[i][2] -= tz;
+
// torque due to a_pu
- Fbmag = prethermostat*sqrt(a_pu);
-
+ Fbmag = prethermostat*sqrt(a_pu);
+
// force in each direction
randr = random->uniform()-0.5;
tx = Fbmag*randr*p2[0];
ty = Fbmag*randr*p2[1];
tz = Fbmag*randr*p2[2];
-
+
randr = random->uniform()-0.5;
tx += Fbmag*randr*p3[0];
ty += Fbmag*randr*p3[1];
- tz += Fbmag*randr*p3[2];
-
+ tz += Fbmag*randr*p3[2];
+
// torque has opposite sign on two particles
torque[i][0] -= tx;
torque[i][1] -= ty;
- torque[i][2] -= tz;
-
+ torque[i][2] -= tz;
+
}
- // set j = nlocal so that only I gets tallied
+ // set j = nlocal so that only I gets tallied
if (evflag) ev_tally_xyz(i,nlocal,nlocal,0,
- 0.0,0.0,-fx,-fy,-fz,delx,dely,delz);
+ 0.0,0.0,-fx,-fy,-fz,delx,dely,delz);
}
}
}
@@ -343,61 +343,61 @@ void PairBrownianPoly::init_style()
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
- if (radius[i] == 0.0)
+ if (radius[i] == 0.0)
error->one(FLERR,"Pair brownian/poly requires extended particles");
int irequest = neighbor->request(this);
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
-
+
// set the isotropic constants that depend on the volume fraction
// vol_T = total volume
double vol_T, wallcoord;
if (!flagwall) vol_T = domain->xprd*domain->yprd*domain->zprd;
- else {
+ else {
double wallhi[3], walllo[3];
for (int j = 0; j < 3; j++){
wallhi[j] = domain->prd[j];
walllo[j] = 0;
- }
+ }
for (int m = 0; m < wallfix->nwall; m++){
int dim = wallfix->wallwhich[m] / 2;
int side = wallfix->wallwhich[m] % 2;
if (wallfix->wallstyle[m] == VARIABLE){
- wallfix->varindex[m] = input->variable->find(wallfix->varstr[m]);
- // Since fix->wall->init happens after pair->init_style
- wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
+ wallfix->varindex[m] = input->variable->find(wallfix->varstr[m]);
+ // Since fix->wall->init happens after pair->init_style
+ wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
}
-
+
else wallcoord = wallfix->coord0[m];
-
+
if (side == 0) walllo[dim] = wallcoord;
else wallhi[dim] = wallcoord;
}
- vol_T = (wallhi[0] - walllo[0]) * (wallhi[1] - walllo[1]) *
+ vol_T = (wallhi[0] - walllo[0]) * (wallhi[1] - walllo[1]) *
(wallhi[2] - walllo[2]);
}
-
+
// vol_P = volume of particles, assuming mono-dispersity
// vol_f = volume fraction
double volP = 0.0;
for (int i = 0; i < nlocal; i++)
- volP += (4.0/3.0)*MY_PI*pow(atom->radius[i],3.0);
+ volP += (4.0/3.0)*MY_PI*pow(atom->radius[i],3.0);
MPI_Allreduce(&volP,&vol_P,1,MPI_DOUBLE,MPI_SUM,world);
double vol_f = vol_P/vol_T;
if (!flagVF) vol_f = 0;
// set isotropic constants
-
+
if (flaglog == 0) {
R0 = 6*MY_PI*mu*(1.0 + 2.16*vol_f);
RT0 = 8*MY_PI*mu;
} else {
R0 = 6*MY_PI*mu*(1.0 + 2.725*vol_f - 6.583*vol_f*vol_f);
- RT0 = 8*MY_PI*mu*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
+ RT0 = 8*MY_PI*mu*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
}
}
@@ -412,6 +412,6 @@ double PairBrownianPoly::init_one(int i, int j)
cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
}
- cut_inner[j][i] = cut_inner[i][j];
+ cut_inner[j][i] = cut_inner[i][j];
return cut[i][j];
}
diff --git a/src/FLD/pair_brownian_poly.h b/src/FLD/pair_brownian_poly.h
index 98dd18ce5cb6bc9dd18a6b39076c01a45eb73409..f4bbb2ea56b15e08f23f249fd401eb389d34da88 100644
--- a/src/FLD/pair_brownian_poly.h
+++ b/src/FLD/pair_brownian_poly.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -28,7 +28,7 @@ class PairBrownianPoly : public PairBrownian {
public:
PairBrownianPoly(class LAMMPS *);
~PairBrownianPoly() {}
- void compute(int, int);
+ void compute(int, int);
double init_one(int, int);
void init_style();
};
diff --git a/src/FLD/pair_lubricate.cpp b/src/FLD/pair_lubricate.cpp
index 53f348b8b96f256dcf5c6ba74625959355913d94..4da0b28dc5bb2aa63601e6aa4c299e06ecdc8e42 100755
--- a/src/FLD/pair_lubricate.cpp
+++ b/src/FLD/pair_lubricate.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -84,7 +84,7 @@ void PairLubricate::compute(int eflag, int vflag)
double xtmp,ytmp,ztmp,delx,dely,delz,fpair,fx,fy,fz,tx,ty,tz;
double rsq,r,h_sep,radi,tfmag;
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3;
- double vt1,vt2,vt3,wt1,wt2,wt3,wdotn;
+ double vt1,vt2,vt3,wt1,wt2,wt3,wdotn;
double inertia,inv_inertia,vRS0;
double vi[3],vj[3],wi[3],wj[3],xl[3];
double a_sq,a_sh,a_pu,Fbmag,del,delmin,eta;
@@ -110,7 +110,7 @@ void PairLubricate::compute(int eflag, int vflag)
int newton_pair = force->newton_pair;
int overlaps = 0;
-
+
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
@@ -134,10 +134,10 @@ void PairLubricate::compute(int eflag, int vflag)
i = ilist[ii];
itype = type[i];
radi = radius[i];
-
+
domain->x2lamda(x[i],lamda);
- vstream[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
- h_rate[4]*lamda[2] + h_ratelo[0];
+ vstream[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
+ h_rate[4]*lamda[2] + h_ratelo[0];
vstream[1] = h_rate[1]*lamda[1] + h_rate[3]*lamda[2] + h_ratelo[1];
vstream[2] = h_rate[2]*lamda[2] + h_ratelo[2];
v[i][0] -= vstream[0];
@@ -153,7 +153,7 @@ void PairLubricate::compute(int eflag, int vflag)
Ef[0][0] = h_rate[0]/domain->xprd;
Ef[1][1] = h_rate[1]/domain->yprd;
- Ef[2][2] = h_rate[2]/domain->zprd;
+ Ef[2][2] = h_rate[2]/domain->zprd;
Ef[0][1] = Ef[1][0] = 0.5 * h_rate[5]/domain->yprd;
Ef[0][2] = Ef[2][0] = 0.5 * h_rate[4]/domain->zprd;
Ef[1][2] = Ef[2][1] = 0.5 * h_rate[3]/domain->zprd;
@@ -163,7 +163,7 @@ void PairLubricate::compute(int eflag, int vflag)
comm->forward_comm_pair(this);
}
-
+
// This section of code adjusts R0/RT0/RS0 if necessary due to changes
// in the volume fraction as a result of fix deform or moving walls
@@ -171,45 +171,45 @@ void PairLubricate::compute(int eflag, int vflag)
if (flagVF) // Flag for volume fraction corrections
if (flagdeform || flagwall == 2){ // Possible changes in volume fraction
if (flagdeform && !flagwall)
- for (j = 0; j < 3; j++)
- dims[j] = domain->prd[j];
+ for (j = 0; j < 3; j++)
+ dims[j] = domain->prd[j];
else if (flagwall == 2 || (flagdeform && flagwall == 1)){
- double wallhi[3], walllo[3];
- for (int j = 0; j < 3; j++){
- wallhi[j] = domain->prd[j];
- walllo[j] = 0;
- }
- for (int m = 0; m < wallfix->nwall; m++){
- int dim = wallfix->wallwhich[m] / 2;
- int side = wallfix->wallwhich[m] % 2;
- if (wallfix->wallstyle[m] == VARIABLE){
- wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
- }
- else wallcoord = wallfix->coord0[m];
- if (side == 0) walllo[dim] = wallcoord;
- else wallhi[dim] = wallcoord;
- }
- for (int j = 0; j < 3; j++)
- dims[j] = wallhi[j] - walllo[j];
+ double wallhi[3], walllo[3];
+ for (int j = 0; j < 3; j++){
+ wallhi[j] = domain->prd[j];
+ walllo[j] = 0;
+ }
+ for (int m = 0; m < wallfix->nwall; m++){
+ int dim = wallfix->wallwhich[m] / 2;
+ int side = wallfix->wallwhich[m] % 2;
+ if (wallfix->wallstyle[m] == VARIABLE){
+ wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
+ }
+ else wallcoord = wallfix->coord0[m];
+ if (side == 0) walllo[dim] = wallcoord;
+ else wallhi[dim] = wallcoord;
+ }
+ for (int j = 0; j < 3; j++)
+ dims[j] = wallhi[j] - walllo[j];
}
double vol_T = dims[0]*dims[1]*dims[2];
double vol_f = vol_P/vol_T;
if (flaglog == 0) {
- R0 = 6*MY_PI*mu*rad*(1.0 + 2.16*vol_f);
- RT0 = 8*MY_PI*mu*pow(rad,3.0);
- RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3.0)*
- (1.0 + 3.33*vol_f + 2.80*vol_f*vol_f);
+ R0 = 6*MY_PI*mu*rad*(1.0 + 2.16*vol_f);
+ RT0 = 8*MY_PI*mu*pow(rad,3.0);
+ RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3.0)*
+ (1.0 + 3.33*vol_f + 2.80*vol_f*vol_f);
} else {
- R0 = 6*MY_PI*mu*rad*(1.0 + 2.725*vol_f - 6.583*vol_f*vol_f);
- RT0 = 8*MY_PI*mu*pow(rad,3.0)*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
- RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3.0)*
- (1.0 + 3.64*vol_f - 6.95*vol_f*vol_f);
+ R0 = 6*MY_PI*mu*rad*(1.0 + 2.725*vol_f - 6.583*vol_f*vol_f);
+ RT0 = 8*MY_PI*mu*pow(rad,3.0)*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
+ RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3.0)*
+ (1.0 + 3.64*vol_f - 6.95*vol_f*vol_f);
}
}
-
+
// end of R0 adjustment code
-
+
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
@@ -219,30 +219,30 @@ void PairLubricate::compute(int eflag, int vflag)
itype = type[i];
radi = radius[i];
jlist = firstneigh[i];
- jnum = numneigh[i];
+ jnum = numneigh[i];
// angular velocity
wi[0] = omega[i][0];
wi[1] = omega[i][1];
- wi[2] = omega[i][2];
-
+ wi[2] = omega[i][2];
+
// FLD contribution to force and torque due to isotropic terms
// FLD contribution to stress from isotropic RS0
if (flagfld) {
f[i][0] -= vxmu2f*R0*v[i][0];
f[i][1] -= vxmu2f*R0*v[i][1];
- f[i][2] -= vxmu2f*R0*v[i][2];
+ f[i][2] -= vxmu2f*R0*v[i][2];
torque[i][0] -= vxmu2f*RT0*wi[0];
torque[i][1] -= vxmu2f*RT0*wi[1];
- torque[i][2] -= vxmu2f*RT0*wi[2];
+ torque[i][2] -= vxmu2f*RT0*wi[2];
if (shearing && vflag_either) {
- vRS0 = -vxmu2f * RS0;
- v_tally_tensor(i,i,nlocal,newton_pair,
- vRS0*Ef[0][0],vRS0*Ef[1][1],vRS0*Ef[2][2],
- vRS0*Ef[0][1],vRS0*Ef[0][2],vRS0*Ef[1][2]);
+ vRS0 = -vxmu2f * RS0;
+ v_tally_tensor(i,i,nlocal,newton_pair,
+ vRS0*Ef[0][0],vRS0*Ef[1][1],vRS0*Ef[2][2],
+ vRS0*Ef[0][1],vRS0*Ef[0][2],vRS0*Ef[1][2]);
}
}
@@ -259,20 +259,20 @@ void PairLubricate::compute(int eflag, int vflag)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r = sqrt(rsq);
-
+ r = sqrt(rsq);
+
// angular momentum = I*omega = 2/5 * M*R^2 * omega
-
- wj[0] = omega[j][0];
- wj[1] = omega[j][1];
- wj[2] = omega[j][2];
+
+ wj[0] = omega[j][0];
+ wj[1] = omega[j][1];
+ wj[2] = omega[j][2];
// xl = point of closest approach on particle i from its center
xl[0] = -delx/r*radi;
xl[1] = -dely/r*radi;
xl[2] = -delz/r*radi;
-
+
// velocity at the point of closest approach on both particles
// v = v + omega_cross_xl - Ef.xl
@@ -280,41 +280,41 @@ void PairLubricate::compute(int eflag, int vflag)
vi[0] = v[i][0] + (wi[1]*xl[2] - wi[2]*xl[1])
- (Ef[0][0]*xl[0] + Ef[0][1]*xl[1] + Ef[0][2]*xl[2]);
-
+
vi[1] = v[i][1] + (wi[2]*xl[0] - wi[0]*xl[2])
- (Ef[1][0]*xl[0] + Ef[1][1]*xl[1] + Ef[1][2]*xl[2]);
-
+
vi[2] = v[i][2] + (wi[0]*xl[1] - wi[1]*xl[0])
- (Ef[2][0]*xl[0] + Ef[2][1]*xl[1] + Ef[2][2]*xl[2]);
-
+
// particle j
vj[0] = v[j][0] - (wj[1]*xl[2] - wj[2]*xl[1])
+ (Ef[0][0]*xl[0] + Ef[0][1]*xl[1] + Ef[0][2]*xl[2]);
-
+
vj[1] = v[j][1] - (wj[2]*xl[0] - wj[0]*xl[2])
+ (Ef[1][0]*xl[0] + Ef[1][1]*xl[1] + Ef[1][2]*xl[2]);
-
+
vj[2] = v[j][2] - (wj[0]*xl[1] - wj[1]*xl[0])
+ (Ef[2][0]*xl[0] + Ef[2][1]*xl[1] + Ef[2][2]*xl[2]);
-
+
// scalar resistances XA and YA
h_sep = r - 2.0*radi;
-
+
// check for overlaps
if (h_sep < 0.0) overlaps++;
-
+
// if less than the minimum gap use the minimum gap instead
if (r < cut_inner[itype][jtype])
- h_sep = cut_inner[itype][jtype] - 2.0*radi;
-
+ h_sep = cut_inner[itype][jtype] - 2.0*radi;
+
// scale h_sep by radi
h_sep = h_sep/radi;
-
+
// scalar resistances
if (flaglog) {
@@ -323,14 +323,14 @@ void PairLubricate::compute(int eflag, int vflag)
a_pu = 8.0*MY_PI*mu*pow(radi,3.0)*(3.0/160.0*log(1.0/h_sep));
} else
a_sq = 6.0*MY_PI*mu*radi*(1.0/4.0/h_sep);
-
+
// relative velocity at the point of closest approach
- // includes fluid velocity
+ // includes fluid velocity
vr1 = vi[0] - vj[0];
vr2 = vi[1] - vj[1];
vr3 = vi[2] - vj[2];
-
+
// normal component (vr.n)n
vnnr = (vr1*delx + vr2*dely + vr3*delz)/r;
@@ -355,7 +355,7 @@ void PairLubricate::compute(int eflag, int vflag)
if (flaglog) {
fx = fx + a_sh*vt1;
fy = fy + a_sh*vt2;
- fz = fz + a_sh*vt3;
+ fz = fz + a_sh*vt3;
}
// scale forces for appropriate units
@@ -363,65 +363,65 @@ void PairLubricate::compute(int eflag, int vflag)
fx *= vxmu2f;
fy *= vxmu2f;
fz *= vxmu2f;
-
+
// add to total force
f[i][0] -= fx;
f[i][1] -= fy;
- f[i][2] -= fz;
-
+ f[i][2] -= fz;
+
if (newton_pair || j < nlocal) {
f[j][0] += fx;
f[j][1] += fy;
- f[j][2] += fz;
+ f[j][2] += fz;
}
-
+
// torque due to this force
if (flaglog) {
tx = xl[1]*fz - xl[2]*fy;
ty = xl[2]*fx - xl[0]*fz;
- tz = xl[0]*fy - xl[1]*fx;
-
+ tz = xl[0]*fy - xl[1]*fx;
+
torque[i][0] -= vxmu2f*tx;
torque[i][1] -= vxmu2f*ty;
- torque[i][2] -= vxmu2f*tz;
-
+ torque[i][2] -= vxmu2f*tz;
+
if (newton_pair || j < nlocal) {
torque[j][0] -= vxmu2f*tx;
torque[j][1] -= vxmu2f*ty;
torque[j][2] -= vxmu2f*tz;
}
-
+
// torque due to a_pu
- wdotn = ((wi[0]-wj[0])*delx + (wi[1]-wj[1])*dely +
- (wi[2]-wj[2])*delz)/r;
+ wdotn = ((wi[0]-wj[0])*delx + (wi[1]-wj[1])*dely +
+ (wi[2]-wj[2])*delz)/r;
wt1 = (wi[0]-wj[0]) - wdotn*delx/r;
wt2 = (wi[1]-wj[1]) - wdotn*dely/r;
wt3 = (wi[2]-wj[2]) - wdotn*delz/r;
-
+
tx = a_pu*wt1;
ty = a_pu*wt2;
tz = a_pu*wt3;
-
+
torque[i][0] -= vxmu2f*tx;
torque[i][1] -= vxmu2f*ty;
- torque[i][2] -= vxmu2f*tz;
-
+ torque[i][2] -= vxmu2f*tz;
+
if (newton_pair || j < nlocal) {
torque[j][0] += vxmu2f*tx;
torque[j][1] += vxmu2f*ty;
torque[j][2] += vxmu2f*tz;
}
- }
+ }
if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,
- 0.0,0.0,-fx,-fy,-fz,delx,dely,delz);
+ 0.0,0.0,-fx,-fy,-fz,delx,dely,delz);
}
}
}
-
+
// restore streaming component of velocity, omega, angmom
if (shearing) {
@@ -432,10 +432,10 @@ void PairLubricate::compute(int eflag, int vflag)
i = ilist[ii];
itype = type[i];
radi = radius[i];
-
+
domain->x2lamda(x[i],lamda);
- vstream[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
- h_rate[4]*lamda[2] + h_ratelo[0];
+ vstream[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
+ h_rate[4]*lamda[2] + h_ratelo[0];
vstream[1] = h_rate[1]*lamda[1] + h_rate[3]*lamda[2] + h_ratelo[1];
vstream[2] = h_rate[2]*lamda[2] + h_ratelo[2];
v[i][0] += vstream[0];
@@ -457,12 +457,12 @@ void PairLubricate::compute(int eflag, int vflag)
if (overlaps_all && comm->me == 0)
printf("Number of overlaps = %d\n",overlaps);
}
-
+
if (vflag_fdotr) virial_fdotr_compute();
}
/* ----------------------------------------------------------------------
- allocate all arrays
+ allocate all arrays
------------------------------------------------------------------------- */
void PairLubricate::allocate()
@@ -482,7 +482,7 @@ void PairLubricate::allocate()
}
/* ----------------------------------------------------------------------
- global settings
+ global settings
------------------------------------------------------------------------- */
void PairLubricate::settings(int narg, char **arg)
@@ -503,9 +503,9 @@ void PairLubricate::settings(int narg, char **arg)
if (flaglog == 1 && flagHI == 0) {
error->warning(FLERR,"Cannot include log terms without 1/r terms; "
- "setting flagHI to 1");
+ "setting flagHI to 1");
flagHI = 1;
- }
+ }
// reset cutoffs that have been explicitly set
@@ -587,51 +587,51 @@ void PairLubricate::init_style()
// due to walls, set volume appropriately; if walls will
// move, set appropriate flag so that volume and v.f. corrections
// are re-calculated at every step.
-
+
shearing = flagdeform = flagwall = 0;
for (int i = 0; i < modify->nfix; i++){
if (strcmp(modify->fix[i]->style,"deform") == 0) {
shearing = flagdeform = 1;
- if (((FixDeform *) modify->fix[i])->remapflag != V_REMAP)
- error->all(FLERR,"Using pair lubricate with inconsistent "
- "fix deform remap option");
+ if (((FixDeform *) modify->fix[i])->remapflag != V_REMAP)
+ error->all(FLERR,"Using pair lubricate with inconsistent "
+ "fix deform remap option");
}
if (strstr(modify->fix[i]->style,"wall") != NULL){
flagwall = 1; // Walls exist
if (((FixWall *) modify->fix[i])->varflag ) {
- flagwall = 2; // Moving walls exist
- wallfix = (FixWall *) modify->fix[i];
+ flagwall = 2; // Moving walls exist
+ wallfix = (FixWall *) modify->fix[i];
}
}
}
-
+
// set the isotropic constants that depend on the volume fraction
// vol_T = total volume
double vol_T;
double wallcoord;
if (!flagwall) vol_T = domain->xprd*domain->yprd*domain->zprd;
- else {
+ else {
double wallhi[3], walllo[3];
for (int j = 0; j < 3; j++){
wallhi[j] = domain->prd[j];
walllo[j] = 0;
- }
+ }
for (int m = 0; m < wallfix->nwall; m++){
int dim = wallfix->wallwhich[m] / 2;
int side = wallfix->wallwhich[m] % 2;
if (wallfix->wallstyle[m] == VARIABLE){
- wallfix->varindex[m] = input->variable->find(wallfix->varstr[m]);
- //Since fix->wall->init happens after pair->init_style
- wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
+ wallfix->varindex[m] = input->variable->find(wallfix->varstr[m]);
+ //Since fix->wall->init happens after pair->init_style
+ wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
}
else wallcoord = wallfix->coord0[m];
-
+
if (side == 0) walllo[dim] = wallcoord;
else wallhi[dim] = wallcoord;
}
- vol_T = (wallhi[0] - walllo[0]) * (wallhi[1] - walllo[1]) *
+ vol_T = (wallhi[0] - walllo[0]) * (wallhi[1] - walllo[1]) *
(wallhi[2] - walllo[2]);
}
@@ -642,16 +642,16 @@ void PairLubricate::init_style()
double vol_f = vol_P/vol_T;
if (!flagVF) vol_f = 0;
-
+
// set isotropic constants for FLD
-
+
if (flaglog == 0) {
R0 = 6*MY_PI*mu*rad*(1.0 + 2.16*vol_f);
RT0 = 8*MY_PI*mu*pow(rad,3.0);
RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3.0)*(1.0 + 3.33*vol_f + 2.80*vol_f*vol_f);
} else {
R0 = 6*MY_PI*mu*rad*(1.0 + 2.725*vol_f - 6.583*vol_f*vol_f);
- RT0 = 8*MY_PI*mu*pow(rad,3.0)*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
+ RT0 = 8*MY_PI*mu*pow(rad,3.0)*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3.0)*(1.0 + 3.64*vol_f - 6.95*vol_f*vol_f);
}
@@ -680,7 +680,7 @@ double PairLubricate::init_one(int i, int j)
}
/* ----------------------------------------------------------------------
- proc 0 writes to restart file
+ proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairLubricate::write_restart(FILE *fp)
@@ -692,8 +692,8 @@ void PairLubricate::write_restart(FILE *fp)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
- fwrite(&cut_inner[i][j],sizeof(double),1,fp);
- fwrite(&cut[i][j],sizeof(double),1,fp);
+ fwrite(&cut_inner[i][j],sizeof(double),1,fp);
+ fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
@@ -714,12 +714,12 @@ void PairLubricate::read_restart(FILE *fp)
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
- if (me == 0) {
- fread(&cut_inner[i][j],sizeof(double),1,fp);
- fread(&cut[i][j],sizeof(double),1,fp);
- }
- MPI_Bcast(&cut_inner[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
+ if (me == 0) {
+ fread(&cut_inner[i][j],sizeof(double),1,fp);
+ fread(&cut[i][j],sizeof(double),1,fp);
+ }
+ MPI_Bcast(&cut_inner[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
@@ -757,7 +757,7 @@ void PairLubricate::read_restart_settings(FILE *fp)
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
fread(&flagHI,sizeof(int),1,fp);
- fread(&flagVF,sizeof(int),1,fp);
+ fread(&flagVF,sizeof(int),1,fp);
}
MPI_Bcast(&mu,1,MPI_DOUBLE,0,world);
MPI_Bcast(&flaglog,1,MPI_INT,0,world);
@@ -773,7 +773,7 @@ void PairLubricate::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
int PairLubricate::pack_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
@@ -834,7 +834,7 @@ int PairLubricate::pre_adapt(char *name, int ilo, int ihi, int jlo, int jhi)
------------------------------------------------------------------------- */
void PairLubricate::adapt(int which, int ilo, int ihi, int jlo, int jhi,
- double value)
+ double value)
{
mu = value;
}
diff --git a/src/FLD/pair_lubricate.h b/src/FLD/pair_lubricate.h
index 3db8e92b386d923db9ff97733efecb44805865d5..eb2d3ee22807a7d10aa250883c20a817568d7c5b 100644
--- a/src/FLD/pair_lubricate.h
+++ b/src/FLD/pair_lubricate.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/FLD/pair_lubricateU.cpp b/src/FLD/pair_lubricateU.cpp
index 419ac3fcbec995d93c5dbb4ab677e76f975aae8d..bbb89b3f0249600c6adbc64c9d212752caa54277 100644
--- a/src/FLD/pair_lubricateU.cpp
+++ b/src/FLD/pair_lubricateU.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -108,7 +108,7 @@ PairLubricateU::~PairLubricateU()
void PairLubricateU::compute(int eflag, int vflag)
{
- int i,j,ii,jj,inum,jnum,itype,jtype;
+ int i,j,ii,jj,inum,jnum,itype,jtype;
double **x = atom->x;
double **v = atom->v;
@@ -122,7 +122,7 @@ void PairLubricateU::compute(int eflag, int vflag)
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
-
+
// skip compute() if called from integrate::setup()
// this is b/c do not want compute() to update velocities twice on a restart
// when restarting, call compute on step N (last step of prev run),
@@ -155,16 +155,16 @@ void PairLubricateU::compute(int eflag, int vflag)
xl[i][j] = x[i][j];
}
}
-
+
// Stage one of Midpoint method
// Solve for velocities based on intial positions
stage_one();
-
+
// find positions at half the timestep and store in xl
intermediates(nall,xl);
-
+
// store back the saved forces and torques in original arrays
for(i=0;i<nlocal+nghost;i++) {
@@ -173,10 +173,10 @@ void PairLubricateU::compute(int eflag, int vflag)
torque[i][j] = Tl[i][j];
}
}
-
+
// stage two: this will give the final velocities
- stage_two(xl);
+ stage_two(xl);
}
/* ------------------------------------------------------------------------
@@ -185,8 +185,8 @@ void PairLubricateU::compute(int eflag, int vflag)
void PairLubricateU::stage_one()
{
- int i,j,ii,jj,inum,jnum,itype,jtype;
-
+ int i,j,ii,jj,inum,jnum,itype,jtype;
+
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
@@ -201,13 +201,13 @@ void PairLubricateU::stage_one()
double vxmu2f = force->vxmu2f;
double inv_inertia,mo_inertia;
int *ilist;
-
+
double radi;
int nprocs = comm->nprocs;
-
+
inum = list->inum;
ilist = list->ilist;
-
+
if (6*inum > cgmax) {
memory->destroy(bcg);
memory->destroy(xcg);
@@ -227,149 +227,149 @@ void PairLubricateU::stage_one()
double alpha,beta;
double normi,error,normig;
double send[2],recv[2],rcg_dot_rcg;
-
- // First compute R_FE*E
+
+ // First compute R_FE*E
compute_RE();
-
- // Reverse communication of forces and torques to
+
+ // Reverse communication of forces and torques to
// accumulate the net force on each of the particles
-
+
if (newton_pair) comm->reverse_comm();
-
+
// CONJUGATE GRADIENT
// Find the right hand side= -ve of all forces/torques
// b = 6*Npart in overall size
-
+
for(ii = 0; ii < inum; ii++) {
- i = ilist[ii];
+ i = ilist[ii];
for (j = 0; j < 3; j++) {
bcg[6*ii+j] = -f[i][j];
- bcg[6*ii+j+3] = -torque[i][j];
+ bcg[6*ii+j+3] = -torque[i][j];
}
- }
-
- // Start solving the equation : F^H = -F^P -F^B - F^H_{Ef}
+ }
+
+ // Start solving the equation : F^H = -F^P -F^B - F^H_{Ef}
// Store initial guess for velocity and angular-velocities/angular momentum
// NOTE velocities and angular velocities are assumed relative to the fluid
-
+
for (ii=0;ii<inum;ii++)
- for (j=0;j<3;j++) {
+ for (j=0;j<3;j++) {
xcg[6*ii+j] = 0.0;
- xcg[6*ii+j+3] = 0.0;
+ xcg[6*ii+j+3] = 0.0;
}
-
+
// Copy initial guess to the global arrays to be acted upon by R_{FU}
// and returned by f and torque arrays
-
+
copy_vec_uo(inum,xcg,v,omega);
-
+
// set velocities for ghost particles
-
+
comm->forward_comm_pair(this);
-
+
// Find initial residual
-
+
compute_RU();
-
+
// reverse communication of forces and torques
-
+
if (newton_pair) comm->reverse_comm();
-
+
copy_uo_vec(inum,f,torque,RU);
-
+
for (i=0;i<6*inum;i++)
rcg[i] = bcg[i] - RU[i];
-
+
// Set initial conjugate direction
-
+
for (i=0;i<6*inum;i++)
pcg[i] = rcg[i];
-
+
// Find initial norm of the residual or norm of the RHS (either is fine)
-
+
normi = dot_vec_vec(6*inum,bcg,bcg);
-
+
MPI_Allreduce(&normi,&normig,1,MPI_DOUBLE,MPI_SUM,world);
-
+
// Loop until convergence
-
- do {
+
+ do {
// find R*p
-
+
copy_vec_uo(inum,pcg,v,omega);
-
- // set velocities for ghost particles
-
+
+ // set velocities for ghost particles
+
comm->forward_comm_pair(this);
-
+
compute_RU();
-
+
// reverse communication of forces and torques
-
+
if (newton_pair) comm->reverse_comm();
-
-
- copy_uo_vec(inum,f,torque,RU);
-
+
+
+ copy_uo_vec(inum,f,torque,RU);
+
// Find alpha
-
+
send[0] = dot_vec_vec(6*inum,rcg,rcg);
send[1] = dot_vec_vec(6*inum,RU,pcg);
-
+
MPI_Allreduce(send,recv,2,MPI_DOUBLE,MPI_SUM,world);
-
+
alpha = recv[0]/recv[1];
rcg_dot_rcg = recv[0];
-
+
// Find new x
-
+
for (i=0;i<6*inum;i++)
xcg[i] = xcg[i] + alpha*pcg[i];
-
+
// find new residual
-
+
for (i=0;i<6*inum;i++)
rcg1[i] = rcg[i] - alpha*RU[i];
-
+
// find beta
-
+
send[0] = dot_vec_vec(6*inum,rcg1,rcg1);
-
+
MPI_Allreduce(send,recv,1,MPI_DOUBLE,MPI_SUM,world);
-
+
beta = recv[0]/rcg_dot_rcg;
-
+
// Find new conjugate direction
-
+
for (i=0;i<6*inum;i++)
pcg[i] = rcg1[i] + beta*pcg[i];
-
+
for (i=0;i<6*inum;i++)
rcg[i] = rcg1[i];
-
+
// Find relative error
-
- error = sqrt(recv[0]/normig);
-
- } while (error > TOL);
-
+
+ error = sqrt(recv[0]/normig);
+
+ } while (error > TOL);
+
// update the final converged velocities in respective arrays
-
+
copy_vec_uo(inum,xcg,v,omega);
- // set velocities for ghost particles
+ // set velocities for ghost particles
comm->forward_comm_pair(this);
-
- // Find actual particle's velocities from relative velocities
- // Only non-zero component of fluid's vel : vx=gdot*y and wz=-gdot/2
+
+ // Find actual particle's velocities from relative velocities
+ // Only non-zero component of fluid's vel : vx=gdot*y and wz=-gdot/2
for (ii=0;ii<inum;ii++) {
i = ilist[ii];
itype = type[i];
radi = radius[i];
-
+
v[i][0] = v[i][0] + gdot*x[i][1];
omega[i][2] = omega[i][2] - gdot/2.0;
}
@@ -385,7 +385,7 @@ void PairLubricateU::intermediates(int nall, double **xl)
double **x = atom->x;
double **v = atom->v;
double dtv = update->dt;
-
+
for (i=0;i<nall;i++) {
xl[i][0] = x[i][0] + 0.5*dtv*v[i][0];
xl[i][1] = x[i][1] + 0.5*dtv*v[i][1];
@@ -399,7 +399,7 @@ void PairLubricateU::intermediates(int nall, double **xl)
void PairLubricateU::stage_two(double **x)
{
- int i,j,ii,jj,inum,jnum,itype,jtype;
+ int i,j,ii,jj,inum,jnum,itype,jtype;
double **v = atom->v;
double **f = atom->f;
double **omega = atom->omega;
@@ -413,163 +413,163 @@ void PairLubricateU::stage_two(double **x)
double vxmu2f = force->vxmu2f;
double inv_inertia,mo_inertia;
int *ilist;
-
+
double radi;
int nprocs = comm->nprocs;
-
+
inum = list->inum;
ilist = list->ilist;
-
+
double alpha,beta;
double normi,error,normig;
double send[2],recv[2],rcg_dot_rcg;
-
- // First compute R_FE*E
+
+ // First compute R_FE*E
compute_RE(x);
-
- // Reverse communication of forces and torques to
+
+ // Reverse communication of forces and torques to
// accumulate the net force on each of the particles
-
+
if (newton_pair) comm->reverse_comm();
-
+
// CONJUGATE GRADIENT
// Find the right hand side= -ve of all forces/torques
// b = 6*Npart in overall size
-
+
for(ii = 0; ii < inum; ii++) {
- i = ilist[ii];
+ i = ilist[ii];
for (j = 0; j < 3; j++) {
bcg[6*ii+j] = -f[i][j];
- bcg[6*ii+j+3] = -torque[i][j];
+ bcg[6*ii+j+3] = -torque[i][j];
}
- }
-
- // Start solving the equation : F^H = -F^P -F^B - F^H_{Ef}
+ }
+
+ // Start solving the equation : F^H = -F^P -F^B - F^H_{Ef}
// Store initial guess for velocity and angular-velocities/angular momentum
// NOTE velocities and angular velocities are assumed relative to the fluid
-
+
for (ii=0;ii<inum;ii++)
- for (j=0;j<3;j++) {
+ for (j=0;j<3;j++) {
xcg[6*ii+j] = 0.0;
- xcg[6*ii+j+3] = 0.0;
+ xcg[6*ii+j+3] = 0.0;
}
-
+
// Copy initial guess to the global arrays to be acted upon by R_{FU}
// and returned by f and torque arrays
-
+
copy_vec_uo(inum,xcg,v,omega);
-
+
// set velocities for ghost particles
-
+
comm->forward_comm_pair(this);
-
+
// Find initial residual
-
+
compute_RU(x);
-
+
// reverse communication of forces and torques
-
+
if (newton_pair) comm->reverse_comm();
-
+
copy_uo_vec(inum,f,torque,RU);
-
+
for (i=0;i<6*inum;i++)
rcg[i] = bcg[i] - RU[i];
-
+
// Set initial conjugate direction
-
+
for (i=0;i<6*inum;i++)
pcg[i] = rcg[i];
-
+
// Find initial norm of the residual or norm of the RHS (either is fine)
-
+
normi = dot_vec_vec(6*inum,bcg,bcg);
-
+
MPI_Allreduce(&normi,&normig,1,MPI_DOUBLE,MPI_SUM,world);
-
+
// Loop until convergence
-
- do {
+
+ do {
// find R*p
-
+
copy_vec_uo(inum,pcg,v,omega);
-
- // set velocities for ghost particles
-
+
+ // set velocities for ghost particles
+
comm->forward_comm_pair(this);
-
+
compute_RU(x);
-
+
// reverse communication of forces and torques
-
+
if (newton_pair) comm->reverse_comm();
-
- copy_uo_vec(inum,f,torque,RU);
-
+
+ copy_uo_vec(inum,f,torque,RU);
+
// Find alpha
-
+
send[0] = dot_vec_vec(6*inum,rcg,rcg);
send[1] = dot_vec_vec(6*inum,RU,pcg);
-
+
MPI_Allreduce(send,recv,2,MPI_DOUBLE,MPI_SUM,world);
-
+
alpha = recv[0]/recv[1];
rcg_dot_rcg = recv[0];
-
+
// Find new x
-
+
for (i=0;i<6*inum;i++)
xcg[i] = xcg[i] + alpha*pcg[i];
-
+
// find new residual
-
+
for (i=0;i<6*inum;i++)
rcg1[i] = rcg[i] - alpha*RU[i];
-
+
// find beta
-
+
send[0] = dot_vec_vec(6*inum,rcg1,rcg1);
-
+
MPI_Allreduce(send,recv,1,MPI_DOUBLE,MPI_SUM,world);
-
+
beta = recv[0]/rcg_dot_rcg;
-
+
// Find new conjugate direction
-
+
for (i=0;i<6*inum;i++)
pcg[i] = rcg1[i] + beta*pcg[i];
-
+
for (i=0;i<6*inum;i++)
rcg[i] = rcg1[i];
-
+
// Find relative error
-
- error = sqrt(recv[0]/normig);
-
- } while (error > TOL);
-
-
+
+ error = sqrt(recv[0]/normig);
+
+ } while (error > TOL);
+
+
// update the final converged velocities in respective arrays
-
+
copy_vec_uo(inum,xcg,v,omega);
-
+
// set velocities for ghost particles
-
+
comm->forward_comm_pair(this);
-
+
// Compute the viscosity/pressure
-
+
if (evflag) compute_Fh(x);
-
- // Find actual particle's velocities from relative velocities
+
+ // Find actual particle's velocities from relative velocities
// Only non-zero component of fluid's vel : vx=gdot*y and wz=-gdot/2
-
+
for (ii=0;ii<inum;ii++) {
i = ilist[ii];
itype = type[i];
radi = radius[i];
-
+
v[i][0] = v[i][0] + gdot*x[i][1];
omega[i][2] = omega[i][2] - gdot/2.0;
}
@@ -586,10 +586,10 @@ void PairLubricateU::compute_Fh(double **x)
double xtmp,ytmp,ztmp,delx,dely,delz,fpair,fx,fy,fz,tx,ty,tz;
double rsq,r,h_sep,radi,tfmag;
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3;
- double vt1,vt2,vt3,wdotn,wt1,wt2,wt3;
+ double vt1,vt2,vt3,wdotn,wt1,wt2,wt3;
double inv_inertia;
int *ilist,*jlist,*numneigh,**firstneigh;
-
+
double **v = atom->v;
double **f = atom->f;
double **omega = atom->omega;
@@ -603,12 +603,12 @@ void PairLubricateU::compute_Fh(double **x)
double vxmu2f = force->vxmu2f;
int overlaps = 0;
double vi[3],vj[3],wi[3],wj[3],xl[3],a_sq,a_sh,a_pu,Fbmag,del,delmin,eta;
-
+
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// This section of code adjusts R0/RT0/RS0 if necessary due to changes
// in the volume fraction as a result of fix deform or moving walls
@@ -616,43 +616,43 @@ void PairLubricateU::compute_Fh(double **x)
if (flagVF) // Flag for volume fraction corrections
if (flagdeform || flagwall == 2){ // Possible changes in volume fraction
if (flagdeform && !flagwall)
- for (j = 0; j < 3; j++)
- dims[j] = domain->prd[j];
+ for (j = 0; j < 3; j++)
+ dims[j] = domain->prd[j];
else if (flagwall == 2 || (flagdeform && flagwall == 1)){
- double wallhi[3], walllo[3];
- for (int j = 0; j < 3; j++){
- wallhi[j] = domain->prd[j];
- walllo[j] = 0;
- }
- for (int m = 0; m < wallfix->nwall; m++){
- int dim = wallfix->wallwhich[m] / 2;
- int side = wallfix->wallwhich[m] % 2;
- if (wallfix->wallstyle[m] == VARIABLE){
- wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
- }
- else wallcoord = wallfix->coord0[m];
- if (side == 0) walllo[dim] = wallcoord;
- else wallhi[dim] = wallcoord;
- }
- for (int j = 0; j < 3; j++)
- dims[j] = wallhi[j] - walllo[j];
+ double wallhi[3], walllo[3];
+ for (int j = 0; j < 3; j++){
+ wallhi[j] = domain->prd[j];
+ walllo[j] = 0;
+ }
+ for (int m = 0; m < wallfix->nwall; m++){
+ int dim = wallfix->wallwhich[m] / 2;
+ int side = wallfix->wallwhich[m] % 2;
+ if (wallfix->wallstyle[m] == VARIABLE){
+ wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
+ }
+ else wallcoord = wallfix->coord0[m];
+ if (side == 0) walllo[dim] = wallcoord;
+ else wallhi[dim] = wallcoord;
+ }
+ for (int j = 0; j < 3; j++)
+ dims[j] = wallhi[j] - walllo[j];
}
double vol_T = dims[0]*dims[1]*dims[2];
double vol_f = vol_P/vol_T;
if (flaglog == 0) {
- // R0 = 6*MY_PI*mu*rad*(1.0 + 2.16*vol_f);
- // RT0 = 8*MY_PI*mu*pow(rad,3);
- RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3.0)*
- (1.0 + 3.33*vol_f + 2.80*vol_f*vol_f);
+ // R0 = 6*MY_PI*mu*rad*(1.0 + 2.16*vol_f);
+ // RT0 = 8*MY_PI*mu*pow(rad,3);
+ RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3.0)*
+ (1.0 + 3.33*vol_f + 2.80*vol_f*vol_f);
} else {
- // R0 = 6*MY_PI*mu*rad*(1.0 + 2.725*vol_f - 6.583*vol_f*vol_f);
- // RT0 = 8*MY_PI*mu*pow(rad,3)*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
- RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3.0)*
- (1.0 + 3.64*vol_f - 6.95*vol_f*vol_f);
+ // R0 = 6*MY_PI*mu*rad*(1.0 + 2.725*vol_f - 6.583*vol_f*vol_f);
+ // RT0 = 8*MY_PI*mu*pow(rad,3)*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
+ RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3.0)*
+ (1.0 + 3.64*vol_f - 6.95*vol_f*vol_f);
}
}
-
+
// end of R0 adjustment code
// Set force to zero which is the final value after this pair interaction
@@ -661,11 +661,11 @@ void PairLubricateU::compute_Fh(double **x)
f[i][j] = 0.0;
torque[i][j] = 0.0;
}
-
+
// reverse communication of forces and torques
if (newton_pair) comm->reverse_comm(); // not really needed
-
+
// Find additional contribution from the stresslets
for (ii = 0; ii < inum; ii++) {
@@ -676,8 +676,8 @@ void PairLubricateU::compute_Fh(double **x)
itype = type[i];
radi = radius[i];
jlist = firstneigh[i];
- jnum = numneigh[i];
-
+ jnum = numneigh[i];
+
// Find the contribution to stress from isotropic RS0
// Set psuedo force to obtain the required contribution
// need to set delx and fy only
@@ -687,15 +687,15 @@ void PairLubricateU::compute_Fh(double **x)
fz = 0.0; delz = 0.0;
if (evflag)
ev_tally_xyz(i,i,nlocal,newton_pair,0.0,0.0,-fx,-fy,-fz,delx,dely,delz);
-
+
// Find angular velocity
wi[0] = omega[i][0];
wi[1] = omega[i][1];
- wi[2] = omega[i][2];
-
+ wi[2] = omega[i][2];
+
if (!flagHI) continue;
-
+
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
@@ -705,23 +705,23 @@ void PairLubricateU::compute_Fh(double **x)
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
-
+
if (rsq < cutsq[itype][jtype]) {
- r = sqrt(rsq);
-
+ r = sqrt(rsq);
+
// Use omega directly if it exists, else angmom
// angular momentum = I*omega = 2/5 * M*R^2 * omega
-
- wj[0] = omega[j][0];
- wj[1] = omega[j][1];
- wj[2] = omega[j][2];
-
+
+ wj[0] = omega[j][0];
+ wj[1] = omega[j][1];
+ wj[2] = omega[j][2];
+
// loc of the point of closest approach on particle i from its cente
xl[0] = -delx/r*radi;
xl[1] = -dely/r*radi;
xl[2] = -delz/r*radi;
-
+
// velocity at the point of closest approach on both particles
// v = v + omega_cross_xl
@@ -730,54 +730,54 @@ void PairLubricateU::compute_Fh(double **x)
vi[0] = v[i][0] + (wi[1]*xl[2] - wi[2]*xl[1]);
vi[1] = v[i][1] + (wi[2]*xl[0] - wi[0]*xl[2]);
vi[2] = v[i][2] + (wi[0]*xl[1] - wi[1]*xl[0]);
-
+
// particle j
vj[0] = v[j][0] - (wj[1]*xl[2] - wj[2]*xl[1]);
vj[1] = v[j][1] - (wj[2]*xl[0] - wj[0]*xl[2]);
vj[2] = v[j][2] - (wj[0]*xl[1] - wj[1]*xl[0]);
-
-
+
+
// Relative velocity at the point of closest approach
- // include contribution from Einf of the fluid
-
- vr1 = vi[0] - vj[0] -
- 2.0*(Ef[0][0]*xl[0] + Ef[0][1]*xl[1] + Ef[0][2]*xl[2]);
- vr2 = vi[1] - vj[1] -
- 2.0*(Ef[1][0]*xl[0] + Ef[1][1]*xl[1] + Ef[1][2]*xl[2]);
- vr3 = vi[2] - vj[2] -
- 2.0*(Ef[2][0]*xl[0] + Ef[2][1]*xl[1] + Ef[2][2]*xl[2]);
-
+ // include contribution from Einf of the fluid
+
+ vr1 = vi[0] - vj[0] -
+ 2.0*(Ef[0][0]*xl[0] + Ef[0][1]*xl[1] + Ef[0][2]*xl[2]);
+ vr2 = vi[1] - vj[1] -
+ 2.0*(Ef[1][0]*xl[0] + Ef[1][1]*xl[1] + Ef[1][2]*xl[2]);
+ vr3 = vi[2] - vj[2] -
+ 2.0*(Ef[2][0]*xl[0] + Ef[2][1]*xl[1] + Ef[2][2]*xl[2]);
+
// Normal component (vr.n)n
vnnr = (vr1*delx + vr2*dely + vr3*delz)/r;
vn1 = vnnr*delx/r;
vn2 = vnnr*dely/r;
vn3 = vnnr*delz/r;
-
+
// Tangential component vr - (vr.n)n
vt1 = vr1 - vn1;
vt2 = vr2 - vn2;
vt3 = vr3 - vn3;
-
+
// Find the scalar resistances a_sq, a_sh and a_pu
h_sep = r - 2.0*radi;
-
+
// check for overlaps
if (h_sep < 0.0) overlaps++;
-
+
// If less than the minimum gap use the minimum gap instead
if (r < cut_inner[itype][jtype])
- h_sep = cut_inner[itype][jtype] - 2.0*radi;
-
+ h_sep = cut_inner[itype][jtype] - 2.0*radi;
+
// Scale h_sep by radi
h_sep = h_sep/radi;
-
+
// Scalar resistances
if (flaglog) {
@@ -785,45 +785,45 @@ void PairLubricateU::compute_Fh(double **x)
a_sh = 6.0*MY_PI*mu*radi*(1.0/6.0*log(1.0/h_sep));
} else
a_sq = 6.0*MY_PI*mu*radi*(1.0/4.0/h_sep);
-
+
// Find force due to squeeze type motion
fx = a_sq*vn1;
fy = a_sq*vn2;
fz = a_sq*vn3;
-
+
// Find force due to all shear kind of motions
if (flaglog) {
fx = fx + a_sh*vt1;
fy = fy + a_sh*vt2;
- fz = fz + a_sh*vt3;
+ fz = fz + a_sh*vt3;
}
-
+
// Scale forces to obtain in appropriate units
fx = vxmu2f*fx;
fy = vxmu2f*fy;
fz = vxmu2f*fz;
-
+
if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,
- 0.0,0.0,-fx,-fy,-fz,delx,dely,delz);
+ 0.0,0.0,-fx,-fy,-fz,delx,dely,delz);
}
}
}
}
-/* ----------------------------------------------------------------------
- computes R_FU * U
+/* ----------------------------------------------------------------------
+ computes R_FU * U
---------------------------------------------------------------------- */
-
+
void PairLubricateU::compute_RU()
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,fpair,fx,fy,fz,tx,ty,tz;
double rsq,r,h_sep,radi,tfmag;
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3;
- double vt1,vt2,vt3,wdotn,wt1,wt2,wt3;
+ double vt1,vt2,vt3,wdotn,wt1,wt2,wt3;
double inv_inertia;
int *ilist,*jlist,*numneigh,**firstneigh;
@@ -842,7 +842,7 @@ void PairLubricateU::compute_RU()
double vxmu2f = force->vxmu2f;
int overlaps = 0;
double vi[3],vj[3],wi[3],wj[3],xl[3],a_sq,a_sh,a_pu,Fbmag,del,delmin,eta;
-
+
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
@@ -855,37 +855,37 @@ void PairLubricateU::compute_RU()
if (flagVF) // Flag for volume fraction corrections
if (flagdeform || flagwall == 2){ // Possible changes in volume fraction
if (flagdeform && !flagwall)
- for (j = 0; j < 3; j++)
- dims[j] = domain->prd[j];
+ for (j = 0; j < 3; j++)
+ dims[j] = domain->prd[j];
else if (flagwall == 2 || (flagdeform && flagwall == 1)){
- double wallhi[3], walllo[3];
- for (int j = 0; j < 3; j++){
- wallhi[j] = domain->prd[j];
- walllo[j] = 0;
- }
- for (int m = 0; m < wallfix->nwall; m++){
- int dim = wallfix->wallwhich[m] / 2;
- int side = wallfix->wallwhich[m] % 2;
- if (wallfix->wallstyle[m] == VARIABLE){
- wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
- }
- else wallcoord = wallfix->coord0[m];
- if (side == 0) walllo[dim] = wallcoord;
- else wallhi[dim] = wallcoord;
- }
- for (int j = 0; j < 3; j++)
- dims[j] = wallhi[j] - walllo[j];
+ double wallhi[3], walllo[3];
+ for (int j = 0; j < 3; j++){
+ wallhi[j] = domain->prd[j];
+ walllo[j] = 0;
+ }
+ for (int m = 0; m < wallfix->nwall; m++){
+ int dim = wallfix->wallwhich[m] / 2;
+ int side = wallfix->wallwhich[m] % 2;
+ if (wallfix->wallstyle[m] == VARIABLE){
+ wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
+ }
+ else wallcoord = wallfix->coord0[m];
+ if (side == 0) walllo[dim] = wallcoord;
+ else wallhi[dim] = wallcoord;
+ }
+ for (int j = 0; j < 3; j++)
+ dims[j] = wallhi[j] - walllo[j];
}
double vol_T = dims[0]*dims[1]*dims[2];
double vol_f = vol_P/vol_T;
if (flaglog == 0) {
- R0 = 6*MY_PI*mu*rad*(1.0 + 2.16*vol_f);
- RT0 = 8*MY_PI*mu*pow(rad,3.0);
- // RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3)*(1.0 + 3.33*vol_f + 2.80*vol_f*vol_f);
+ R0 = 6*MY_PI*mu*rad*(1.0 + 2.16*vol_f);
+ RT0 = 8*MY_PI*mu*pow(rad,3.0);
+ // RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3)*(1.0 + 3.33*vol_f + 2.80*vol_f*vol_f);
} else {
- R0 = 6*MY_PI*mu*rad*(1.0 + 2.725*vol_f - 6.583*vol_f*vol_f);
- RT0 = 8*MY_PI*mu*pow(rad,3.0)*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
- // RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3)*(1.0 + 3.64*vol_f - 6.95*vol_f*vol_f);
+ R0 = 6*MY_PI*mu*rad*(1.0 + 2.725*vol_f - 6.583*vol_f*vol_f);
+ RT0 = 8*MY_PI*mu*pow(rad,3.0)*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
+ // RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3)*(1.0 + 3.64*vol_f - 6.95*vol_f*vol_f);
}
}
@@ -897,7 +897,7 @@ void PairLubricateU::compute_RU()
f[i][j] = 0.0;
torque[i][j] = 0.0;
}
-
+
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
@@ -906,25 +906,25 @@ void PairLubricateU::compute_RU()
itype = type[i];
radi = radius[i];
jlist = firstneigh[i];
- jnum = numneigh[i];
-
+ jnum = numneigh[i];
+
// Find angular velocity
wi[0] = omega[i][0];
wi[1] = omega[i][1];
- wi[2] = omega[i][2];
-
+ wi[2] = omega[i][2];
+
// Contribution due to the isotropic terms
f[i][0] += -vxmu2f*R0*v[i][0];
f[i][1] += -vxmu2f*R0*v[i][1];
- f[i][2] += -vxmu2f*R0*v[i][2];
-
+ f[i][2] += -vxmu2f*R0*v[i][2];
+
torque[i][0] += -vxmu2f*RT0*wi[0];
torque[i][1] += -vxmu2f*RT0*wi[1];
- torque[i][2] += -vxmu2f*RT0*wi[2];
-
- if (!flagHI) continue;
+ torque[i][2] += -vxmu2f*RT0*wi[2];
+
+ if (!flagHI) continue;
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
@@ -937,21 +937,21 @@ void PairLubricateU::compute_RU()
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r = sqrt(rsq);
-
+ r = sqrt(rsq);
+
// Use omega directly if it exists, else angmom
// angular momentum = I*omega = 2/5 * M*R^2 * omega
- wj[0] = omega[j][0];
- wj[1] = omega[j][1];
- wj[2] = omega[j][2];
+ wj[0] = omega[j][0];
+ wj[1] = omega[j][1];
+ wj[2] = omega[j][2];
// loc of the point of closest approach on particle i from its center
xl[0] = -delx/r*radi;
xl[1] = -dely/r*radi;
xl[2] = -delz/r*radi;
-
+
// velocity at the point of closest approach on both particles
// v = v + omega_cross_xl
@@ -960,30 +960,30 @@ void PairLubricateU::compute_RU()
vi[0] = v[i][0] + (wi[1]*xl[2] - wi[2]*xl[1]);
vi[1] = v[i][1] + (wi[2]*xl[0] - wi[0]*xl[2]);
vi[2] = v[i][2] + (wi[0]*xl[1] - wi[1]*xl[0]);
-
+
// particle j
vj[0] = v[j][0] - (wj[1]*xl[2] - wj[2]*xl[1]);
vj[1] = v[j][1] - (wj[2]*xl[0] - wj[0]*xl[2]);
vj[2] = v[j][2] - (wj[0]*xl[1] - wj[1]*xl[0]);
-
+
// Find the scalar resistances a_sq and a_sh
h_sep = r - 2.0*radi;
-
+
// check for overlaps
if(h_sep < 0.0) overlaps++;
-
+
// If less than the minimum gap use the minimum gap instead
if (r < cut_inner[itype][jtype])
- h_sep = cut_inner[itype][jtype] - 2.0*radi;
-
+ h_sep = cut_inner[itype][jtype] - 2.0*radi;
+
// Scale h_sep by radi
h_sep = h_sep/radi;
-
+
// Scalar resistances
if (flaglog) {
@@ -992,7 +992,7 @@ void PairLubricateU::compute_RU()
a_pu = 8.0*MY_PI*mu*pow(radi,3.0)*(3.0/160.0*log(1.0/h_sep));
} else
a_sq = 6.0*MY_PI*mu*radi*(1.0/4.0/h_sep);
-
+
// Relative velocity at the point of closest approach
vr1 = vi[0] - vj[0];
@@ -1017,83 +1017,83 @@ void PairLubricateU::compute_RU()
fx = a_sq*vn1;
fy = a_sq*vn2;
fz = a_sq*vn3;
-
+
// Find force due to all shear kind of motions
if (flaglog) {
fx = fx + a_sh*vt1;
fy = fy + a_sh*vt2;
- fz = fz + a_sh*vt3;
+ fz = fz + a_sh*vt3;
}
-
+
// Scale forces to obtain in appropriate units
fx = vxmu2f*fx;
fy = vxmu2f*fy;
fz = vxmu2f*fz;
-
+
// Add to the total forc
f[i][0] -= fx;
f[i][1] -= fy;
- f[i][2] -= fz;
-
+ f[i][2] -= fz;
+
if (newton_pair || j < nlocal) {
f[j][0] += fx;
f[j][1] += fy;
- f[j][2] += fz;
+ f[j][2] += fz;
}
-
+
// Find torque due to this force
if (flaglog) {
tx = xl[1]*fz - xl[2]*fy;
ty = xl[2]*fx - xl[0]*fz;
- tz = xl[0]*fy - xl[1]*fx;
-
+ tz = xl[0]*fy - xl[1]*fx;
+
// Why a scale factor ?
torque[i][0] -= vxmu2f*tx;
torque[i][1] -= vxmu2f*ty;
- torque[i][2] -= vxmu2f*tz;
-
+ torque[i][2] -= vxmu2f*tz;
+
if(newton_pair || j < nlocal) {
torque[j][0] -= vxmu2f*tx;
torque[j][1] -= vxmu2f*ty;
torque[j][2] -= vxmu2f*tz;
}
-
+
// Torque due to a_pu
- wdotn = ((wi[0]-wj[0])*delx +
- (wi[1]-wj[1])*dely + (wi[2]-wj[2])*delz)/r;
+ wdotn = ((wi[0]-wj[0])*delx +
+ (wi[1]-wj[1])*dely + (wi[2]-wj[2])*delz)/r;
wt1 = (wi[0]-wj[0]) - wdotn*delx/r;
wt2 = (wi[1]-wj[1]) - wdotn*dely/r;
wt3 = (wi[2]-wj[2]) - wdotn*delz/r;
-
+
tx = a_pu*wt1;
ty = a_pu*wt2;
tz = a_pu*wt3;
-
+
// add to total
torque[i][0] -= vxmu2f*tx;
torque[i][1] -= vxmu2f*ty;
- torque[i][2] -= vxmu2f*tz;
-
+ torque[i][2] -= vxmu2f*tz;
+
if (newton_pair || j < nlocal) {
torque[j][0] += vxmu2f*tx;
torque[j][1] += vxmu2f*ty;
torque[j][2] += vxmu2f*tz;
}
- }
+ }
}
}
}
}
-/* ----------------------------------------------------------------------
- computes R_FU * U
+/* ----------------------------------------------------------------------
+ computes R_FU * U
---------------------------------------------------------------------- */
void PairLubricateU::compute_RU(double **x)
@@ -1102,10 +1102,10 @@ void PairLubricateU::compute_RU(double **x)
double xtmp,ytmp,ztmp,delx,dely,delz,fpair,fx,fy,fz,tx,ty,tz;
double rsq,r,h_sep,radi,tfmag;
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3;
- double vt1,vt2,vt3,wdotn,wt1,wt2,wt3;
+ double vt1,vt2,vt3,wdotn,wt1,wt2,wt3;
double inv_inertia;
int *ilist,*jlist,*numneigh,**firstneigh;
-
+
double **v = atom->v;
double **f = atom->f;
double **omega = atom->omega;
@@ -1119,12 +1119,12 @@ void PairLubricateU::compute_RU(double **x)
double vxmu2f = force->vxmu2f;
int overlaps = 0;
double vi[3],vj[3],wi[3],wj[3],xl[3],a_sq,a_sh,a_pu,Fbmag,del,delmin,eta;
-
+
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// This section of code adjusts R0/RT0/RS0 if necessary due to changes
// in the volume fraction as a result of fix deform or moving walls
@@ -1132,37 +1132,37 @@ void PairLubricateU::compute_RU(double **x)
if (flagVF) // Flag for volume fraction corrections
if (flagdeform || flagwall == 2){ // Possible changes in volume fraction
if (flagdeform && !flagwall)
- for (j = 0; j < 3; j++)
- dims[j] = domain->prd[j];
+ for (j = 0; j < 3; j++)
+ dims[j] = domain->prd[j];
else if (flagwall == 2 || (flagdeform && flagwall == 1)){
- double wallhi[3], walllo[3];
- for (int j = 0; j < 3; j++){
- wallhi[j] = domain->prd[j];
- walllo[j] = 0;
- }
- for (int m = 0; m < wallfix->nwall; m++){
- int dim = wallfix->wallwhich[m] / 2;
- int side = wallfix->wallwhich[m] % 2;
- if (wallfix->wallstyle[m] == VARIABLE){
- wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
- }
- else wallcoord = wallfix->coord0[m];
- if (side == 0) walllo[dim] = wallcoord;
- else wallhi[dim] = wallcoord;
- }
- for (int j = 0; j < 3; j++)
- dims[j] = wallhi[j] - walllo[j];
+ double wallhi[3], walllo[3];
+ for (int j = 0; j < 3; j++){
+ wallhi[j] = domain->prd[j];
+ walllo[j] = 0;
+ }
+ for (int m = 0; m < wallfix->nwall; m++){
+ int dim = wallfix->wallwhich[m] / 2;
+ int side = wallfix->wallwhich[m] % 2;
+ if (wallfix->wallstyle[m] == VARIABLE){
+ wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
+ }
+ else wallcoord = wallfix->coord0[m];
+ if (side == 0) walllo[dim] = wallcoord;
+ else wallhi[dim] = wallcoord;
+ }
+ for (int j = 0; j < 3; j++)
+ dims[j] = wallhi[j] - walllo[j];
}
double vol_T = dims[0]*dims[1]*dims[2];
double vol_f = vol_P/vol_T;
if (flaglog == 0) {
- R0 = 6*MY_PI*mu*rad*(1.0 + 2.16*vol_f);
- RT0 = 8*MY_PI*mu*pow(rad,3.0);
- // RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3)*(1.0 + 3.33*vol_f + 2.80*vol_f*vol_f);
+ R0 = 6*MY_PI*mu*rad*(1.0 + 2.16*vol_f);
+ RT0 = 8*MY_PI*mu*pow(rad,3.0);
+ // RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3)*(1.0 + 3.33*vol_f + 2.80*vol_f*vol_f);
} else {
- R0 = 6*MY_PI*mu*rad*(1.0 + 2.725*vol_f - 6.583*vol_f*vol_f);
- RT0 = 8*MY_PI*mu*pow(rad,3.0)*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
- // RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3)*(1.0 + 3.64*vol_f - 6.95*vol_f*vol_f);
+ R0 = 6*MY_PI*mu*rad*(1.0 + 2.725*vol_f - 6.583*vol_f*vol_f);
+ RT0 = 8*MY_PI*mu*pow(rad,3.0)*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
+ // RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3)*(1.0 + 3.64*vol_f - 6.95*vol_f*vol_f);
}
}
@@ -1174,7 +1174,7 @@ void PairLubricateU::compute_RU(double **x)
f[i][j] = 0.0;
torque[i][j] = 0.0;
}
-
+
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
@@ -1183,24 +1183,24 @@ void PairLubricateU::compute_RU(double **x)
itype = type[i];
radi = radius[i];
jlist = firstneigh[i];
- jnum = numneigh[i];
-
+ jnum = numneigh[i];
+
// Find angular velocity
-
+
wi[0] = omega[i][0];
wi[1] = omega[i][1];
wi[2] = omega[i][2];
-
+
// Contribution due to the isotropic terms
-
+
f[i][0] += -vxmu2f*R0*v[i][0];
f[i][1] += -vxmu2f*R0*v[i][1];
- f[i][2] += -vxmu2f*R0*v[i][2];
-
+ f[i][2] += -vxmu2f*R0*v[i][2];
+
torque[i][0] += -vxmu2f*RT0*wi[0];
torque[i][1] += -vxmu2f*RT0*wi[1];
- torque[i][2] += -vxmu2f*RT0*wi[2];
-
+ torque[i][2] += -vxmu2f*RT0*wi[2];
+
if (!flagHI) continue;
for (jj = 0; jj < jnum; jj++) {
@@ -1212,177 +1212,177 @@ void PairLubricateU::compute_RU(double **x)
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
-
+
if (rsq < cutsq[itype][jtype]) {
- r = sqrt(rsq);
-
+ r = sqrt(rsq);
+
// Use omega directly if it exists, else angmom
// angular momentum = I*omega = 2/5 * M*R^2 * omega
-
- wj[0] = omega[j][0];
- wj[1] = omega[j][1];
- wj[2] = omega[j][2];
-
+
+ wj[0] = omega[j][0];
+ wj[1] = omega[j][1];
+ wj[2] = omega[j][2];
+
// loc of the point of closest approach on particle i from its center
-
+
xl[0] = -delx/r*radi;
xl[1] = -dely/r*radi;
xl[2] = -delz/r*radi;
-
+
// velocity at the point of closest approach on both particles
// v = v + omega_cross_xl
-
+
// particle i
-
+
vi[0] = v[i][0] + (wi[1]*xl[2] - wi[2]*xl[1]);
vi[1] = v[i][1] + (wi[2]*xl[0] - wi[0]*xl[2]);
vi[2] = v[i][2] + (wi[0]*xl[1] - wi[1]*xl[0]);
-
+
// particle j
-
+
vj[0] = v[j][0] - (wj[1]*xl[2] - wj[2]*xl[1]);
vj[1] = v[j][1] - (wj[2]*xl[0] - wj[0]*xl[2]);
vj[2] = v[j][2] - (wj[0]*xl[1] - wj[1]*xl[0]);
-
+
// Find the scalar resistances a_sq and a_sh
-
+
h_sep = r - 2.0*radi;
-
+
// check for overlaps
-
+
if(h_sep < 0.0) overlaps++;
-
+
// If less than the minimum gap use the minimum gap instead
-
+
if (r < cut_inner[itype][jtype])
- h_sep = cut_inner[itype][jtype] - 2.0*radi;
-
+ h_sep = cut_inner[itype][jtype] - 2.0*radi;
+
// Scale h_sep by radi
-
+
h_sep = h_sep/radi;
-
+
// Scalar resistances
-
+
if (flaglog) {
a_sq = 6.0*MY_PI*mu*radi*(1.0/4.0/h_sep + 9.0/40.0*log(1.0/h_sep));
a_sh = 6.0*MY_PI*mu*radi*(1.0/6.0*log(1.0/h_sep));
a_pu = 8.0*MY_PI*mu*pow(radi,3.0)*(3.0/160.0*log(1.0/h_sep));
} else
a_sq = 6.0*MY_PI*mu*radi*(1.0/4.0/h_sep);
-
+
// Relative velocity at the point of closest approach
-
+
vr1 = vi[0] - vj[0];
vr2 = vi[1] - vj[1];
vr3 = vi[2] - vj[2];
-
+
// Normal component (vr.n)n
-
+
vnnr = (vr1*delx + vr2*dely + vr3*delz)/r;
vn1 = vnnr*delx/r;
vn2 = vnnr*dely/r;
vn3 = vnnr*delz/r;
-
+
// Tangential component vr - (vr.n)n
-
+
vt1 = vr1 - vn1;
vt2 = vr2 - vn2;
vt3 = vr3 - vn3;
-
+
// Find force due to squeeze type motion
-
+
fx = a_sq*vn1;
fy = a_sq*vn2;
fz = a_sq*vn3;
-
+
// Find force due to all shear kind of motions
-
+
if (flaglog) {
fx = fx + a_sh*vt1;
fy = fy + a_sh*vt2;
- fz = fz + a_sh*vt3;
+ fz = fz + a_sh*vt3;
}
-
+
// Scale forces to obtain in appropriate units
-
+
fx = vxmu2f*fx;
fy = vxmu2f*fy;
fz = vxmu2f*fz;
-
+
// Add to the total force
-
+
f[i][0] -= fx;
f[i][1] -= fy;
- f[i][2] -= fz;
-
+ f[i][2] -= fz;
+
if (newton_pair || j < nlocal) {
f[j][0] += fx;
f[j][1] += fy;
- f[j][2] += fz;
+ f[j][2] += fz;
}
-
+
// Find torque due to this force
-
+
if (flaglog) {
tx = xl[1]*fz - xl[2]*fy;
ty = xl[2]*fx - xl[0]*fz;
- tz = xl[0]*fy - xl[1]*fx;
-
+ tz = xl[0]*fy - xl[1]*fx;
+
// Why a scale factor ?
-
+
torque[i][0] -= vxmu2f*tx;
torque[i][1] -= vxmu2f*ty;
- torque[i][2] -= vxmu2f*tz;
-
+ torque[i][2] -= vxmu2f*tz;
+
if(newton_pair || j < nlocal) {
torque[j][0] -= vxmu2f*tx;
torque[j][1] -= vxmu2f*ty;
torque[j][2] -= vxmu2f*tz;
}
-
+
// Torque due to a_pu
-
- wdotn = ((wi[0]-wj[0])*delx +
+
+ wdotn = ((wi[0]-wj[0])*delx +
(wi[1]-wj[1])*dely + (wi[2]-wj[2])*delz)/r;
wt1 = (wi[0]-wj[0]) - wdotn*delx/r;
wt2 = (wi[1]-wj[1]) - wdotn*dely/r;
wt3 = (wi[2]-wj[2]) - wdotn*delz/r;
-
+
tx = a_pu*wt1;
ty = a_pu*wt2;
tz = a_pu*wt3;
-
+
// add to total
-
+
torque[i][0] -= vxmu2f*tx;
torque[i][1] -= vxmu2f*ty;
- torque[i][2] -= vxmu2f*tz;
-
+ torque[i][2] -= vxmu2f*tz;
+
if (newton_pair || j < nlocal) {
torque[j][0] += vxmu2f*tx;
torque[j][1] += vxmu2f*ty;
torque[j][2] += vxmu2f*tz;
}
- }
+ }
}
}
}
}
/* ----------------------------------------------------------------------
- This computes R_{FE}*E , where E is the rate of strain of tensor which is
+ This computes R_{FE}*E , where E is the rate of strain of tensor which is
known apriori, as it depends only on the known fluid velocity.
So, this part of the hydrodynamic interaction can be pre computed and
transferred to the RHS
---------------------------------------------------------------------- */
-
+
void PairLubricateU::compute_RE()
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,fpair,fx,fy,fz,tx,ty,tz;
double rsq,r,h_sep,radi,tfmag;
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3;
- double vt1,vt2,vt3;
+ double vt1,vt2,vt3;
double inv_inertia;
int *ilist,*jlist,*numneigh,**firstneigh;
@@ -1400,7 +1400,7 @@ void PairLubricateU::compute_RE()
double vxmu2f = force->vxmu2f;
int overlaps = 0;
double vi[3],vj[3],wi[3],wj[3],xl[3],a_sq,a_sh,a_pu,Fbmag,del,delmin,eta;
-
+
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
@@ -1416,10 +1416,10 @@ void PairLubricateU::compute_RE()
itype = type[i];
radi = radius[i];
jlist = firstneigh[i];
- jnum = numneigh[i];
-
- // No contribution from isotropic terms due to E
-
+ jnum = numneigh[i];
+
+ // No contribution from isotropic terms due to E
+
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
@@ -1431,51 +1431,51 @@ void PairLubricateU::compute_RE()
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r = sqrt(rsq);
-
+ r = sqrt(rsq);
+
// loc of the point of closest approach on particle i from its center
xl[0] = -delx/r*radi;
xl[1] = -dely/r*radi;
xl[2] = -delz/r*radi;
-
+
// Find the scalar resistances a_sq and a_sh
h_sep = r - 2.0*radi;
-
+
// check for overlaps
if(h_sep < 0.0) overlaps++;
-
+
// If less than the minimum gap use the minimum gap instead
if (r < cut_inner[itype][jtype])
- h_sep = cut_inner[itype][jtype] - 2.0*radi;
-
+ h_sep = cut_inner[itype][jtype] - 2.0*radi;
+
// Scale h_sep by radi
h_sep = h_sep/radi;
-
+
// Scalar resistance for Squeeze type motions
if (flaglog)
a_sq = 6*MY_PI*mu*radi*(1.0/4.0/h_sep + 9.0/40.0*log(1/h_sep));
else
a_sq = 6*MY_PI*mu*radi*(1.0/4.0/h_sep);
-
+
// Scalar resistance for Shear type motions
if (flaglog) {
a_sh = 6*MY_PI*mu*radi*(1.0/6.0*log(1/h_sep));
a_pu = 8.0*MY_PI*mu*pow(radi,3.0)*(3.0/160.0*log(1.0/h_sep));
}
-
+
// Relative velocity at the point of closest approach due to Ef only
vr1 = -2.0*(Ef[0][0]*xl[0] + Ef[0][1]*xl[1] + Ef[0][2]*xl[2]);
vr2 = -2.0*(Ef[1][0]*xl[0] + Ef[1][1]*xl[1] + Ef[1][2]*xl[2]);
- vr3 = -2.0*(Ef[2][0]*xl[0] + Ef[2][1]*xl[1] + Ef[2][2]*xl[2]);
-
+ vr3 = -2.0*(Ef[2][0]*xl[0] + Ef[2][1]*xl[1] + Ef[2][2]*xl[2]);
+
// Normal component (vr.n)n
vnnr = (vr1*delx + vr2*dely + vr3*delz)/r;
@@ -1494,54 +1494,54 @@ void PairLubricateU::compute_RE()
fx = a_sq*vn1;
fy = a_sq*vn2;
fz = a_sq*vn3;
-
+
// Find force due to all shear kind of motions
if (flaglog) {
fx = fx + a_sh*vt1;
fy = fy + a_sh*vt2;
- fz = fz + a_sh*vt3;
+ fz = fz + a_sh*vt3;
}
-
+
// Scale forces to obtain in appropriate units
fx = vxmu2f*fx;
fy = vxmu2f*fy;
fz = vxmu2f*fz;
-
+
// Add to the total forc
f[i][0] -= fx;
f[i][1] -= fy;
- f[i][2] -= fz;
-
+ f[i][2] -= fz;
+
if (newton_pair || j < nlocal) {
f[j][0] += fx;
f[j][1] += fy;
- f[j][2] += fz;
+ f[j][2] += fz;
}
-
+
// Find torque due to this force
if (flaglog) {
tx = xl[1]*fz - xl[2]*fy;
ty = xl[2]*fx - xl[0]*fz;
- tz = xl[0]*fy - xl[1]*fx;
-
+ tz = xl[0]*fy - xl[1]*fx;
+
// Why a scale factor ?
torque[i][0] -= vxmu2f*tx;
torque[i][1] -= vxmu2f*ty;
- torque[i][2] -= vxmu2f*tz;
-
+ torque[i][2] -= vxmu2f*tz;
+
if (newton_pair || j < nlocal) {
torque[j][0] -= vxmu2f*tx;
torque[j][1] -= vxmu2f*ty;
torque[j][2] -= vxmu2f*tz;
}
-
+
// NOTE No a_pu term needed as they add up to zero
- }
+ }
}
}
}
@@ -1552,7 +1552,7 @@ void PairLubricateU::compute_RE()
}
/* ----------------------------------------------------------------------
- This computes R_{FE}*E , where E is the rate of strain of tensor which is
+ This computes R_{FE}*E , where E is the rate of strain of tensor which is
known apriori, as it depends only on the known fluid velocity.
So, this part of the hydrodynamic interaction can be pre computed and
transferred to the RHS
@@ -1564,10 +1564,10 @@ void PairLubricateU::compute_RE(double **x)
double xtmp,ytmp,ztmp,delx,dely,delz,fpair,fx,fy,fz,tx,ty,tz;
double rsq,r,h_sep,radi,tfmag;
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3;
- double vt1,vt2,vt3;
+ double vt1,vt2,vt3;
double inv_inertia;
int *ilist,*jlist,*numneigh,**firstneigh;
-
+
double **v = atom->v;
double **f = atom->f;
double **omega = atom->omega;
@@ -1581,14 +1581,14 @@ void PairLubricateU::compute_RE(double **x)
double vxmu2f = force->vxmu2f;
int overlaps = 0;
double vi[3],vj[3],wi[3],wj[3],xl[3],a_sq,a_sh,a_pu,Fbmag,del,delmin,eta;
-
+
if (!flagHI) return;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
@@ -1597,10 +1597,10 @@ void PairLubricateU::compute_RE(double **x)
itype = type[i];
radi = radius[i];
jlist = firstneigh[i];
- jnum = numneigh[i];
-
- // No contribution from isotropic terms due to E
-
+ jnum = numneigh[i];
+
+ // No contribution from isotropic terms due to E
+
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
@@ -1610,123 +1610,123 @@ void PairLubricateU::compute_RE(double **x)
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
-
+
if (rsq < cutsq[itype][jtype]) {
- r = sqrt(rsq);
-
+ r = sqrt(rsq);
+
// loc of the point of closest approach on particle i from its center
-
+
xl[0] = -delx/r*radi;
xl[1] = -dely/r*radi;
xl[2] = -delz/r*radi;
-
+
// Find the scalar resistances a_sq and a_sh
-
+
h_sep = r - 2.0*radi;
-
+
// check for overlaps
-
+
if(h_sep < 0.0) overlaps++;
-
+
// If less than the minimum gap use the minimum gap instead
-
+
if (r < cut_inner[itype][jtype])
- h_sep = cut_inner[itype][jtype] - 2.0*radi;
-
+ h_sep = cut_inner[itype][jtype] - 2.0*radi;
+
// Scale h_sep by radi
-
+
h_sep = h_sep/radi;
-
+
// Scalar resistance for Squeeze type motions
-
+
if (flaglog)
a_sq = 6*MY_PI*mu*radi*(1.0/4.0/h_sep + 9.0/40.0*log(1/h_sep));
else
a_sq = 6*MY_PI*mu*radi*(1.0/4.0/h_sep);
-
+
// Scalar resistance for Shear type motions
-
+
if (flaglog) {
a_sh = 6*MY_PI*mu*radi*(1.0/6.0*log(1/h_sep));
a_pu = 8.0*MY_PI*mu*pow(radi,3.0)*(3.0/160.0*log(1.0/h_sep));
}
-
+
// Relative velocity at the point of closest approach due to Ef only
-
+
vr1 = -2.0*(Ef[0][0]*xl[0] + Ef[0][1]*xl[1] + Ef[0][2]*xl[2]);
vr2 = -2.0*(Ef[1][0]*xl[0] + Ef[1][1]*xl[1] + Ef[1][2]*xl[2]);
- vr3 = -2.0*(Ef[2][0]*xl[0] + Ef[2][1]*xl[1] + Ef[2][2]*xl[2]);
-
+ vr3 = -2.0*(Ef[2][0]*xl[0] + Ef[2][1]*xl[1] + Ef[2][2]*xl[2]);
+
// Normal component (vr.n)n
-
+
vnnr = (vr1*delx + vr2*dely + vr3*delz)/r;
vn1 = vnnr*delx/r;
vn2 = vnnr*dely/r;
vn3 = vnnr*delz/r;
-
+
// Tangential component vr - (vr.n)n
-
+
vt1 = vr1 - vn1;
vt2 = vr2 - vn2;
vt3 = vr3 - vn3;
-
+
// Find force due to squeeze type motion
-
+
fx = a_sq*vn1;
fy = a_sq*vn2;
fz = a_sq*vn3;
-
+
// Find force due to all shear kind of motions
-
+
if (flaglog) {
fx = fx + a_sh*vt1;
fy = fy + a_sh*vt2;
- fz = fz + a_sh*vt3;
+ fz = fz + a_sh*vt3;
}
-
+
// Scale forces to obtain in appropriate units
-
+
fx = vxmu2f*fx;
fy = vxmu2f*fy;
fz = vxmu2f*fz;
-
+
// Add to the total forc
-
+
f[i][0] -= fx;
f[i][1] -= fy;
- f[i][2] -= fz;
-
+ f[i][2] -= fz;
+
if (newton_pair || j < nlocal) {
f[j][0] += fx;
f[j][1] += fy;
- f[j][2] += fz;
+ f[j][2] += fz;
}
-
+
// Find torque due to this force
-
+
if (flaglog) {
tx = xl[1]*fz - xl[2]*fy;
ty = xl[2]*fx - xl[0]*fz;
- tz = xl[0]*fy - xl[1]*fx;
-
+ tz = xl[0]*fy - xl[1]*fx;
+
// Why a scale factor ?
-
+
torque[i][0] -= vxmu2f*tx;
torque[i][1] -= vxmu2f*ty;
- torque[i][2] -= vxmu2f*tz;
-
+ torque[i][2] -= vxmu2f*tz;
+
if (newton_pair || j < nlocal) {
torque[j][0] -= vxmu2f*tx;
torque[j][1] -= vxmu2f*ty;
torque[j][2] -= vxmu2f*tz;
}
-
+
// NOTE No a_pu term needed as they add up to zero
- }
+ }
}
}
}
-
+
int print_overlaps = 0;
if (print_overlaps && overlaps)
printf("Number of overlaps=%d\n",overlaps);
@@ -1734,7 +1734,7 @@ void PairLubricateU::compute_RE(double **x)
/* ----------------------------------------------------------------------
- allocate all arrays
+ allocate all arrays
------------------------------------------------------------------------- */
void PairLubricateU::allocate()
@@ -1754,7 +1754,7 @@ void PairLubricateU::allocate()
}
/*-----------------------------------------------------------------------
- global settings
+ global settings
------------------------------------------------------------------------- */
void PairLubricateU::settings(int narg, char **arg)
@@ -1766,7 +1766,7 @@ void PairLubricateU::settings(int narg, char **arg)
cut_inner_global = atof(arg[2]);
cut_global = atof(arg[3]);
gdot = atof(arg[4]);
-
+
flagHI = flagVF = 1;
if (narg == 7) {
flagHI = atoi(arg[5]);
@@ -1775,9 +1775,9 @@ void PairLubricateU::settings(int narg, char **arg)
if (flaglog == 1 && flagHI == 0) {
error->warning(FLERR,"Cannot include log terms without 1/r terms; "
- "setting flagHI to 1.");
+ "setting flagHI to 1.");
flagHI = 1;
- }
+ }
// reset cutoffs that have been explicitly set
@@ -1790,7 +1790,7 @@ void PairLubricateU::settings(int narg, char **arg)
cut[i][j] = cut_global;
}
}
-
+
// store the rate of strain tensor
Ef[0][0] = 0.0;
@@ -1801,7 +1801,7 @@ void PairLubricateU::settings(int narg, char **arg)
Ef[1][2] = 0.0;
Ef[2][0] = 0.0;
Ef[2][1] = 0.0;
- Ef[2][2] = 0.0;
+ Ef[2][2] = 0.0;
}
/*-----------------------------------------------------------------------
@@ -1863,7 +1863,7 @@ void PairLubricateU::init_style()
error->all(FLERR,"Pair lubricateU requires monodisperse particles");
radi = radtype;
}
-
+
// check for fix deform, if exists it must use "remap v"
// If box will change volume, set appropriate flag so that volume
// and v.f. corrections are re-calculated at every step.
@@ -1875,46 +1875,46 @@ void PairLubricateU::init_style()
flagdeform = flagwall = 0;
for (int i = 0; i < modify->nfix; i++){
- if (strcmp(modify->fix[i]->style,"deform") == 0)
+ if (strcmp(modify->fix[i]->style,"deform") == 0)
flagdeform = 1;
else if (strstr(modify->fix[i]->style,"wall") != NULL){
flagwall = 1; // Walls exist
if (((FixWall *) modify->fix[i])->varflag ) {
- flagwall = 2; // Moving walls exist
- wallfix = (FixWall *) modify->fix[i];
+ flagwall = 2; // Moving walls exist
+ wallfix = (FixWall *) modify->fix[i];
}
}
}
-
+
// set the isotropic constants depending on the volume fraction
- // vol_T = total volumeshearing = flagdeform = flagwall = 0;
+ // vol_T = total volumeshearing = flagdeform = flagwall = 0;
double vol_T, wallcoord;
if (!flagwall) vol_T = domain->xprd*domain->yprd*domain->zprd;
- else {
+ else {
double wallhi[3], walllo[3];
for (int j = 0; j < 3; j++){
wallhi[j] = domain->prd[j];
walllo[j] = 0;
- }
+ }
for (int m = 0; m < wallfix->nwall; m++){
int dim = wallfix->wallwhich[m] / 2;
int side = wallfix->wallwhich[m] % 2;
if (wallfix->wallstyle[m] == VARIABLE){
- wallfix->varindex[m] = input->variable->find(wallfix->varstr[m]);
- //Since fix->wall->init happens after pair->init_style
- wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
+ wallfix->varindex[m] = input->variable->find(wallfix->varstr[m]);
+ //Since fix->wall->init happens after pair->init_style
+ wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
}
else wallcoord = wallfix->coord0[m];
-
+
if (side == 0) walllo[dim] = wallcoord;
else wallhi[dim] = wallcoord;
}
- vol_T = (wallhi[0] - walllo[0]) * (wallhi[1] - walllo[1]) *
+ vol_T = (wallhi[0] - walllo[0]) * (wallhi[1] - walllo[1]) *
(wallhi[2] - walllo[2]);
}
-
-
+
+
// assuming monodisperse spheres, vol_P = volume of the particles
double tmp = 0.0;
@@ -1922,11 +1922,11 @@ void PairLubricateU::init_style()
MPI_Allreduce(&tmp,&rad,1,MPI_DOUBLE,MPI_MAX,world);
vol_P = atom->natoms * (4.0/3.0)*MY_PI*pow(rad,3.0);
-
+
// vol_f = volume fraction
double vol_f = vol_P/vol_T;
-
+
if (!flagVF) vol_f = 0;
// set the isotropic constant
@@ -1959,7 +1959,7 @@ double PairLubricateU::init_one(int i, int j)
}
/* ----------------------------------------------------------------------
- proc 0 writes to restart file
+ proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairLubricateU::write_restart(FILE *fp)
@@ -1971,8 +1971,8 @@ void PairLubricateU::write_restart(FILE *fp)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
- fwrite(&cut_inner[i][j],sizeof(double),1,fp);
- fwrite(&cut[i][j],sizeof(double),1,fp);
+ fwrite(&cut_inner[i][j],sizeof(double),1,fp);
+ fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
@@ -1993,12 +1993,12 @@ void PairLubricateU::read_restart(FILE *fp)
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
- if (me == 0) {
- fread(&cut_inner[i][j],sizeof(double),1,fp);
- fread(&cut[i][j],sizeof(double),1,fp);
- }
- MPI_Bcast(&cut_inner[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
+ if (me == 0) {
+ fread(&cut_inner[i][j],sizeof(double),1,fp);
+ fread(&cut[i][j],sizeof(double),1,fp);
+ }
+ MPI_Bcast(&cut_inner[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
@@ -2048,8 +2048,8 @@ void PairLubricateU::read_restart_settings(FILE *fp)
/*---------------------------------------------------------------------------*/
-void PairLubricateU::copy_vec_uo(int inum, double *xcg,
- double **v, double **omega)
+void PairLubricateU::copy_vec_uo(int inum, double *xcg,
+ double **v, double **omega)
{
int i,j,ii;
int *ilist;
@@ -2059,16 +2059,16 @@ void PairLubricateU::copy_vec_uo(int inum, double *xcg,
double *rmass = atom->rmass;
int *type = atom->type;
-
+
ilist = list->ilist;
-
+
for (ii=0;ii<inum;ii++) {
i = ilist[ii];
itype = type[i];
radi = atom->radius[i];
- inertia = 0.4*rmass[i]*radi*radi;
-
- for (j=0;j<3;j++) {
+ inertia = 0.4*rmass[i]*radi*radi;
+
+ for (j=0;j<3;j++) {
v[i][j] = xcg[6*ii+j];
omega[i][j] = xcg[6*ii+j+3];
}
@@ -2077,17 +2077,17 @@ void PairLubricateU::copy_vec_uo(int inum, double *xcg,
/*---------------------------------------------------------------------------*/
-void PairLubricateU::copy_uo_vec(int inum, double **f, double **torque,
- double *RU)
+void PairLubricateU::copy_uo_vec(int inum, double **f, double **torque,
+ double *RU)
{
int i,j,ii;
int *ilist;
-
+
ilist = list->ilist;
-
+
for (ii=0;ii<inum;ii++) {
i = ilist[ii];
- for (j=0;j<3;j++) {
+ for (j=0;j<3;j++) {
RU[6*ii+j] = f[i][j];
RU[6*ii+j+3] = torque[i][j];
}
@@ -2097,7 +2097,7 @@ void PairLubricateU::copy_uo_vec(int inum, double **f, double **torque,
/* ---------------------------------------------------------------------- */
int PairLubricateU::pack_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
diff --git a/src/FLD/pair_lubricateU.h b/src/FLD/pair_lubricateU.h
index a4b18d038286616f7382edc7395bf613cc0de913..ca8f15a2320ffb7523d19a899a89a901a745287d 100644
--- a/src/FLD/pair_lubricateU.h
+++ b/src/FLD/pair_lubricateU.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/FLD/pair_lubricateU_poly.cpp b/src/FLD/pair_lubricateU_poly.cpp
index 4662910241e33b47c0081d79d0b946e42cd54337..19b4ae818cb388fd43ec686f98dc0deeef5cc3cf 100644
--- a/src/FLD/pair_lubricateU_poly.cpp
+++ b/src/FLD/pair_lubricateU_poly.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -54,7 +54,7 @@ enum{EDGE,CONSTANT,VARIABLE};
/* ---------------------------------------------------------------------- */
-PairLubricateUPoly::PairLubricateUPoly(LAMMPS *lmp) :
+PairLubricateUPoly::PairLubricateUPoly(LAMMPS *lmp) :
PairLubricateU(lmp) {}
/* ----------------------------------------------------------------------
@@ -80,7 +80,7 @@ void PairLubricateUPoly::compute(int eflag, int vflag)
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
-
+
// grow per-atom arrays if necessary
// need to be atom->nmax in length
@@ -120,16 +120,16 @@ void PairLubricateUPoly::compute(int eflag, int vflag)
xl[i][j] = x[i][j];
}
}
-
+
// Stage one of Midpoint method
// Solve for velocities based on intial positions
iterate(atom->x,1);
-
+
// Find positions at half the timestep and store in xl
intermediates(nall,xl);
-
+
// Store back the saved forces and torques in original arrays
for(i=0;i<nlocal+nghost;i++) {
@@ -138,7 +138,7 @@ void PairLubricateUPoly::compute(int eflag, int vflag)
torque[i][j] = Tl[i][j];
}
}
-
+
// Stage two: This will give the final velocities
iterate(xl,2);
@@ -150,7 +150,7 @@ void PairLubricateUPoly::compute(int eflag, int vflag)
void PairLubricateUPoly::iterate(double **x, int stage)
{
- int i,j,ii,itype;
+ int i,j,ii,itype;
int inum = list->inum;
int *ilist = list->ilist;
@@ -161,155 +161,155 @@ void PairLubricateUPoly::iterate(double **x, int stage)
double normi,error,normig;
double send[2],recv[2],rcg_dot_rcg;
double mo_inertia,radi;
-
+
double **v = atom->v;
double **f = atom->f;
double **omega = atom->omega;
double **angmom = atom->angmom;
double **torque = atom->torque;
double *radius = atom->radius;
-
- // First compute R_FE*E
+
+ // First compute R_FE*E
compute_RE(x);
-
- // Reverse communication of forces and torques to
+
+ // Reverse communication of forces and torques to
// accumulate the net force on each of the particles
-
+
if (newton_pair) comm->reverse_comm();
-
+
// CONJUGATE GRADIENT
// Find the right hand side= -ve of all forces/torques
// b = 6*Npart in overall size
-
+
for(ii = 0; ii < inum; ii++) {
- i = ilist[ii];
+ i = ilist[ii];
for (j = 0; j < 3; j++) {
bcg[6*ii+j] = -f[i][j];
- bcg[6*ii+j+3] = -torque[i][j];
+ bcg[6*ii+j+3] = -torque[i][j];
}
- }
-
- // Start solving the equation : F^H = -F^P -F^B - F^H_{Ef}
+ }
+
+ // Start solving the equation : F^H = -F^P -F^B - F^H_{Ef}
// Store initial guess for velocity and angular-velocities/angular momentum
// NOTE velocities and angular velocities are assumed relative to the fluid
-
+
for (ii=0;ii<inum;ii++)
- for (j=0;j<3;j++) {
+ for (j=0;j<3;j++) {
xcg[6*ii+j] = 0.0;
- xcg[6*ii+j+3] = 0.0;
+ xcg[6*ii+j+3] = 0.0;
}
-
+
// Copy initial guess to the global arrays to be acted upon by R_{FU}
// and returned by f and torque arrays
-
+
copy_vec_uo(inum,xcg,v,omega);
-
+
// set velocities for ghost particles
-
+
comm->forward_comm_pair(this);
-
+
// Find initial residual
-
+
compute_RU(x);
-
+
// reverse communication of forces and torques
-
+
if (newton_pair) comm->reverse_comm();
-
+
copy_uo_vec(inum,f,torque,RU);
-
+
for (i=0;i<6*inum;i++)
rcg[i] = bcg[i] - RU[i];
-
+
// Set initial conjugate direction
-
+
for (i=0;i<6*inum;i++)
pcg[i] = rcg[i];
-
+
// Find initial norm of the residual or norm of the RHS (either is fine)
-
+
normi = dot_vec_vec(6*inum,bcg,bcg);
-
+
MPI_Allreduce(&normi,&normig,1,MPI_DOUBLE,MPI_SUM,world);
-
+
// Loop until convergence
-
- do {
+
+ do {
// find R*p
-
+
copy_vec_uo(inum,pcg,v,omega);
-
- // set velocities for ghost particles
-
+
+ // set velocities for ghost particles
+
comm->forward_comm_pair(this);
-
+
compute_RU(x);
-
+
// reverse communication of forces and torques
-
+
if (newton_pair) comm->reverse_comm();
-
- copy_uo_vec(inum,f,torque,RU);
-
+
+ copy_uo_vec(inum,f,torque,RU);
+
// Find alpha
-
+
send[0] = dot_vec_vec(6*inum,rcg,rcg);
send[1] = dot_vec_vec(6*inum,RU,pcg);
-
+
MPI_Allreduce(send,recv,2,MPI_DOUBLE,MPI_SUM,world);
-
+
alpha = recv[0]/recv[1];
rcg_dot_rcg = recv[0];
-
+
// Find new x
-
+
for (i=0;i<6*inum;i++)
xcg[i] = xcg[i] + alpha*pcg[i];
-
+
// find new residual
-
+
for (i=0;i<6*inum;i++)
rcg1[i] = rcg[i] - alpha*RU[i];
-
+
// find beta
-
+
send[0] = dot_vec_vec(6*inum,rcg1,rcg1);
-
+
MPI_Allreduce(send,recv,1,MPI_DOUBLE,MPI_SUM,world);
-
+
beta = recv[0]/rcg_dot_rcg;
-
+
// Find new conjugate direction
-
+
for (i=0;i<6*inum;i++)
pcg[i] = rcg1[i] + beta*pcg[i];
-
+
for (i=0;i<6*inum;i++)
rcg[i] = rcg1[i];
-
+
// Find relative error
-
- error = sqrt(recv[0]/normig);
-
- } while (error > TOL);
-
-
+
+ error = sqrt(recv[0]/normig);
+
+ } while (error > TOL);
+
+
// update the final converged velocities in respective arrays
-
+
copy_vec_uo(inum,xcg,v,omega);
-
+
// set velocities for ghost particles
-
+
comm->forward_comm_pair(this);
-
+
// compute the viscosity/pressure
-
+
if (evflag && stage == 2) compute_Fh(x);
-
- // find actual particle's velocities from relative velocities
+
+ // find actual particle's velocities from relative velocities
// only non-zero component of fluid's vel : vx=gdot*y and wz=-gdot/2
-
+
for (ii=0;ii<inum;ii++) {
i = ilist[ii];
itype = type[i];
@@ -338,10 +338,10 @@ void PairLubricateUPoly::compute_Fh(double **x)
double xtmp,ytmp,ztmp,delx,dely,delz,fx,fy,fz;
double rsq,r,h_sep,radi,radj;
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3;
- double vt1,vt2,vt3;
+ double vt1,vt2,vt3;
double inv_inertia;
double vi[3],vj[3],wi[3],wj[3],xl[3],jl[3],pre[2];
-
+
double **v = atom->v;
double **f = atom->f;
double **omega = atom->omega;
@@ -353,12 +353,12 @@ void PairLubricateUPoly::compute_Fh(double **x)
double vxmu2f = force->vxmu2f;
double a_sq = 0.0;
double a_sh = 0.0;
-
+
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
beta[0][0] = beta[1][0] = beta[1][4] = 0.0;
// This section of code adjusts R0/RT0/RS0 if necessary due to changes
@@ -368,37 +368,37 @@ void PairLubricateUPoly::compute_Fh(double **x)
if (flagVF) // Flag for volume fraction corrections
if (flagdeform || flagwall == 2){ // Possible changes in volume fraction
if (flagdeform && !flagwall)
- for (j = 0; j < 3; j++)
- dims[j] = domain->prd[j];
+ for (j = 0; j < 3; j++)
+ dims[j] = domain->prd[j];
else if (flagwall == 2 || (flagdeform && flagwall == 1)){
- double wallhi[3], walllo[3];
- for (int j = 0; j < 3; j++){
- wallhi[j] = domain->prd[j];
- walllo[j] = 0;
- }
- for (int m = 0; m < wallfix->nwall; m++){
- int dim = wallfix->wallwhich[m] / 2;
- int side = wallfix->wallwhich[m] % 2;
- if (wallfix->wallstyle[m] == VARIABLE){
- wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
- }
- else wallcoord = wallfix->coord0[m];
- if (side == 0) walllo[dim] = wallcoord;
- else wallhi[dim] = wallcoord;
- }
- for (int j = 0; j < 3; j++)
- dims[j] = wallhi[j] - walllo[j];
+ double wallhi[3], walllo[3];
+ for (int j = 0; j < 3; j++){
+ wallhi[j] = domain->prd[j];
+ walllo[j] = 0;
+ }
+ for (int m = 0; m < wallfix->nwall; m++){
+ int dim = wallfix->wallwhich[m] / 2;
+ int side = wallfix->wallwhich[m] % 2;
+ if (wallfix->wallstyle[m] == VARIABLE){
+ wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
+ }
+ else wallcoord = wallfix->coord0[m];
+ if (side == 0) walllo[dim] = wallcoord;
+ else wallhi[dim] = wallcoord;
+ }
+ for (int j = 0; j < 3; j++)
+ dims[j] = wallhi[j] - walllo[j];
}
double vol_T = dims[0]*dims[1]*dims[2];
double vol_f = vol_P/vol_T;
if (flaglog == 0) {
- //R0 = 6*MY_PI*mu*(1.0 + 2.16*vol_f);
- //RT0 = 8*MY_PI*mu;
- RS0 = 20.0/3.0*MY_PI*mu*(1.0 + 3.33*vol_f + 2.80*vol_f*vol_f);
+ //R0 = 6*MY_PI*mu*(1.0 + 2.16*vol_f);
+ //RT0 = 8*MY_PI*mu;
+ RS0 = 20.0/3.0*MY_PI*mu*(1.0 + 3.33*vol_f + 2.80*vol_f*vol_f);
} else {
- //R0 = 6*MY_PI*mu*(1.0 + 2.725*vol_f - 6.583*vol_f*vol_f);
- //RT0 = 8*MY_PI*mu*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
- RS0 = 20.0/3.0*MY_PI*mu*(1.0 + 3.64*vol_f - 6.95*vol_f*vol_f);
+ //R0 = 6*MY_PI*mu*(1.0 + 2.725*vol_f - 6.583*vol_f*vol_f);
+ //RT0 = 8*MY_PI*mu*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
+ RS0 = 20.0/3.0*MY_PI*mu*(1.0 + 3.64*vol_f - 6.95*vol_f*vol_f);
}
}
@@ -410,11 +410,11 @@ void PairLubricateUPoly::compute_Fh(double **x)
f[i][j] = 0.0;
torque[i][j] = 0.0;
}
-
+
// reverse communication of forces and torques
if (newton_pair) comm->reverse_comm(); // not really needed
-
+
// Find additional contribution from the stresslets
for (ii = 0; ii < inum; ii++) {
@@ -425,10 +425,10 @@ void PairLubricateUPoly::compute_Fh(double **x)
itype = type[i];
radi = radius[i];
jlist = firstneigh[i];
- jnum = numneigh[i];
+ jnum = numneigh[i];
pre[1] = 8.0*(pre[0] = MY_PI*mu*radi)*radi*radi; // BROKEN?? Should be "+"??
pre[0] *= 6.0;
-
+
// Find the contribution to stress from isotropic RS0
// Set psuedo force to obtain the required contribution
// need to set delx and fy only
@@ -438,13 +438,13 @@ void PairLubricateUPoly::compute_Fh(double **x)
fz = 0.0; delz = 0.0;
if (evflag)
ev_tally_xyz(i,i,nlocal,newton_pair,0.0,0.0,-fx,-fy,-fz,delx,dely,delz);
-
+
// Find angular velocity
wi[0] = omega[i][0];
wi[1] = omega[i][1];
- wi[2] = omega[i][2];
-
+ wi[2] = omega[i][2];
+
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
delx = xtmp - x[j][0];
@@ -453,19 +453,19 @@ void PairLubricateUPoly::compute_Fh(double **x)
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
radj = radius[j];
-
+
if (rsq < cutsq[itype][jtype]) {
- r = sqrt(rsq);
-
+ r = sqrt(rsq);
+
// Use omega directly if it exists, else angmom
// angular momentum = I*omega = 2/5 * M*R^2 * omega
-
- wj[0] = omega[j][0];
- wj[1] = omega[j][1];
- wj[2] = omega[j][2];
-
+
+ wj[0] = omega[j][0];
+ wj[1] = omega[j][1];
+ wj[2] = omega[j][2];
+
// loc of the point of closest approach on particle i from its cente
- // POC for j is in opposite direction as for i
+ // POC for j is in opposite direction as for i
xl[0] = -delx/r*radi;
xl[1] = -dely/r*radi;
@@ -473,7 +473,7 @@ void PairLubricateUPoly::compute_Fh(double **x)
jl[0] = delx/r*radj;
jl[1] = dely/r*radj;
jl[2] = delz/r*radj;
-
+
h_sep = r - radi-radj;
// velocity at the point of closest approach on both particles
@@ -484,53 +484,53 @@ void PairLubricateUPoly::compute_Fh(double **x)
vi[0] = v[i][0] + (wi[1]*xl[2] - wi[2]*xl[1]);
vi[1] = v[i][1] + (wi[2]*xl[0] - wi[0]*xl[2]);
vi[2] = v[i][2] + (wi[0]*xl[1] - wi[1]*xl[0]);
-
+
// particle j
vj[0] = v[j][0] + (wj[1]*jl[2] - wj[2]*jl[1]);
vj[1] = v[j][1] + (wj[2]*jl[0] - wj[0]*jl[2]);
vj[2] = v[j][2] + (wj[0]*jl[1] - wj[1]*jl[0]);
-
-
+
+
// Relative velocity at the point of closest approach
- // include contribution from Einf of the fluid
-
- vr1 = vi[0] - vj[0] -
- 2.0*(Ef[0][0]*xl[0] + Ef[0][1]*xl[1] + Ef[0][2]*xl[2]);
- vr2 = vi[1] - vj[1] -
- 2.0*(Ef[1][0]*xl[0] + Ef[1][1]*xl[1] + Ef[1][2]*xl[2]);
- vr3 = vi[2] - vj[2] -
- 2.0*(Ef[2][0]*xl[0] + Ef[2][1]*xl[1] + Ef[2][2]*xl[2]);
-
+ // include contribution from Einf of the fluid
+
+ vr1 = vi[0] - vj[0] -
+ 2.0*(Ef[0][0]*xl[0] + Ef[0][1]*xl[1] + Ef[0][2]*xl[2]);
+ vr2 = vi[1] - vj[1] -
+ 2.0*(Ef[1][0]*xl[0] + Ef[1][1]*xl[1] + Ef[1][2]*xl[2]);
+ vr3 = vi[2] - vj[2] -
+ 2.0*(Ef[2][0]*xl[0] + Ef[2][1]*xl[1] + Ef[2][2]*xl[2]);
+
// Normal component (vr.n)n
vnnr = (vr1*delx + vr2*dely + vr3*delz)/r;
vn1 = vnnr*delx/r;
vn2 = vnnr*dely/r;
vn3 = vnnr*delz/r;
-
+
// Tangential component vr - (vr.n)n
vt1 = vr1 - vn1;
vt2 = vr2 - vn2;
vt3 = vr3 - vn3;
-
+
// Find the scalar resistances a_sq, a_sh and a_pu
-
+
// check for overlaps
if (h_sep < 0.0) overlaps++;
-
+
// If less than the minimum gap use the minimum gap instead
if (r < cut_inner[itype][jtype])
- h_sep = cut_inner[itype][jtype] - radi-radj;
-
+ h_sep = cut_inner[itype][jtype] - radi-radj;
+
// Scale h_sep by radi
h_sep = h_sep/radi;
- beta[0][1] = radj/radi;
- beta[1][1] = 1.0 + beta[0][1];
+ beta[0][1] = radj/radi;
+ beta[1][1] = 1.0 + beta[0][1];
/*beta0 = radj/radi;
beta1 = 1.0 + beta0;*/
@@ -538,33 +538,33 @@ void PairLubricateUPoly::compute_Fh(double **x)
// Scalar resistances
if (flaglog) {
- beta[0][2] = beta[0][1]*beta[0][1];
- beta[0][3] = beta[0][2]*beta[0][1];
- beta[0][4] = beta[0][3]*beta[0][1];
- beta[1][2] = beta[1][1]*beta[1][1];
- beta[1][3] = beta[1][2]*beta[1][1];
- double log_h_sep_beta13 = log(1.0/h_sep)/beta[1][3];
- double h_sep_beta11 = h_sep/beta[1][1];
-
- a_sq = pre[0]*(beta[0][2]/beta[1][2]/h_sep
- +((0.2+1.4*beta[0][1]+0.2*beta[0][2])
- +(1.0+18.0*(beta[0][1]+beta[0][3])-29.0*beta[0][2]
- +beta[0][4])*h_sep_beta11/21.0)*log_h_sep_beta13);
-
- a_sh = pre[0]*((8.0*(beta[0][1]+beta[0][3])+4.0*beta[0][2])/15.0
- +(64.0-180.0*(beta[0][1]+beta[0][3])+232.0*beta[0][2]
- +64.0*beta[0][4])*h_sep_beta11/375.0)*log_h_sep_beta13;
-
- /*a_sq = beta0*beta0/beta1/beta1/h_sep
- +(1.0+7.0*beta0+beta0*beta0)/5.0/pow(beta1,3)*log(1.0/h_sep);
+ beta[0][2] = beta[0][1]*beta[0][1];
+ beta[0][3] = beta[0][2]*beta[0][1];
+ beta[0][4] = beta[0][3]*beta[0][1];
+ beta[1][2] = beta[1][1]*beta[1][1];
+ beta[1][3] = beta[1][2]*beta[1][1];
+ double log_h_sep_beta13 = log(1.0/h_sep)/beta[1][3];
+ double h_sep_beta11 = h_sep/beta[1][1];
+
+ a_sq = pre[0]*(beta[0][2]/beta[1][2]/h_sep
+ +((0.2+1.4*beta[0][1]+0.2*beta[0][2])
+ +(1.0+18.0*(beta[0][1]+beta[0][3])-29.0*beta[0][2]
+ +beta[0][4])*h_sep_beta11/21.0)*log_h_sep_beta13);
+
+ a_sh = pre[0]*((8.0*(beta[0][1]+beta[0][3])+4.0*beta[0][2])/15.0
+ +(64.0-180.0*(beta[0][1]+beta[0][3])+232.0*beta[0][2]
+ +64.0*beta[0][4])*h_sep_beta11/375.0)*log_h_sep_beta13;
+
+ /*a_sq = beta0*beta0/beta1/beta1/h_sep
+ +(1.0+7.0*beta0+beta0*beta0)/5.0/pow(beta1,3)*log(1.0/h_sep);
a_sq += (1.0+18.0*beta0-29.0*beta0*beta0+18.0*pow(beta0,3)
- +pow(beta0,4))/21.0/pow(beta1,4)*h_sep*log(1.0/h_sep);
+ +pow(beta0,4))/21.0/pow(beta1,4)*h_sep*log(1.0/h_sep);
a_sq *= 6.0*MY_PI*mu*radi;
a_sh = 4.0*beta0*(2.0+beta0
- +2.0*beta0*beta0)/15.0/pow(beta1,3)*log(1.0/h_sep);
+ +2.0*beta0*beta0)/15.0/pow(beta1,3)*log(1.0/h_sep);
a_sh += 4.0*(16.0-45.0*beta0+58.0*beta0*beta0-45.0*pow(beta0,3)
- +16.0*pow(beta0,4))/375.0/pow(beta1,4)*h_sep*log(1.0/h_sep);
+ +16.0*pow(beta0,4))/375.0/pow(beta1,4)*h_sep*log(1.0/h_sep);
a_sh *= 6.0*MY_PI*mu*radi;*/
} else {
//a_sq = 6.0*MY_PI*mu*radi*(beta0*beta0/beta1/beta1/h_sep);
@@ -576,34 +576,34 @@ void PairLubricateUPoly::compute_Fh(double **x)
fx = a_sq*vn1;
fy = a_sq*vn2;
fz = a_sq*vn3;
-
+
// Find force due to all shear kind of motions
if (flaglog) {
fx = fx + a_sh*vt1;
fy = fy + a_sh*vt2;
- fz = fz + a_sh*vt3;
+ fz = fz + a_sh*vt3;
}
-
+
// Scale forces to obtain in appropriate units
fx = vxmu2f*fx;
fy = vxmu2f*fy;
fz = vxmu2f*fz;
-
- // set j = nlocal so that only I gets tallied
+
+ // set j = nlocal so that only I gets tallied
if (evflag) ev_tally_xyz(i,nlocal,nlocal,0,
- 0.0,0.0,-fx,-fy,-fz,delx,dely,delz);
+ 0.0,0.0,-fx,-fy,-fz,delx,dely,delz);
}
}
}
}
-/* ----------------------------------------------------------------------
- computes R_FU * U
+/* ----------------------------------------------------------------------
+ computes R_FU * U
---------------------------------------------------------------------- */
-
+
void PairLubricateUPoly::compute_RU(double **x)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
@@ -618,10 +618,10 @@ void PairLubricateUPoly::compute_RU(double **x)
double rsq,r,radi,radj,h_sep;
//double beta0,beta1;
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3;
- double vt1,vt2,vt3,wdotn,wt1,wt2,wt3;
+ double vt1,vt2,vt3,wdotn,wt1,wt2,wt3;
double inv_inertia;
double vi[3],vj[3],wi[3],wj[3],xl[3],jl[3],pre[2];
-
+
double **v = atom->v;
double **f = atom->f;
double **omega = atom->omega;
@@ -634,14 +634,14 @@ void PairLubricateUPoly::compute_RU(double **x)
double a_sq = 0.0;
double a_sh = 0.0;
double a_pu = 0.0;
-
+
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
beta[0][0] = beta[1][0] = beta[1][4] = 0.0;
-
+
// This section of code adjusts R0/RT0/RS0 if necessary due to changes
// in the volume fraction as a result of fix deform or moving walls
@@ -649,50 +649,50 @@ void PairLubricateUPoly::compute_RU(double **x)
if (flagVF) // Flag for volume fraction corrections
if (flagdeform || flagwall == 2){ // Possible changes in volume fraction
if (flagdeform && !flagwall)
- for (j = 0; j < 3; j++)
- dims[j] = domain->prd[j];
+ for (j = 0; j < 3; j++)
+ dims[j] = domain->prd[j];
else if (flagwall == 2 || (flagdeform && flagwall == 1)){
- double wallhi[3], walllo[3];
- for (j = 0; j < 3; j++){
- wallhi[j] = domain->prd[j];
- walllo[j] = 0;
- }
- for (int m = 0; m < wallfix->nwall; m++){
- int dim = wallfix->wallwhich[m] / 2;
- int side = wallfix->wallwhich[m] % 2;
- if (wallfix->wallstyle[m] == VARIABLE){
- wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
- }
- else wallcoord = wallfix->coord0[m];
- if (side == 0) walllo[dim] = wallcoord;
- else wallhi[dim] = wallcoord;
- }
- for (j = 0; j < 3; j++)
- dims[j] = wallhi[j] - walllo[j];
+ double wallhi[3], walllo[3];
+ for (j = 0; j < 3; j++){
+ wallhi[j] = domain->prd[j];
+ walllo[j] = 0;
+ }
+ for (int m = 0; m < wallfix->nwall; m++){
+ int dim = wallfix->wallwhich[m] / 2;
+ int side = wallfix->wallwhich[m] % 2;
+ if (wallfix->wallstyle[m] == VARIABLE){
+ wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
+ }
+ else wallcoord = wallfix->coord0[m];
+ if (side == 0) walllo[dim] = wallcoord;
+ else wallhi[dim] = wallcoord;
+ }
+ for (j = 0; j < 3; j++)
+ dims[j] = wallhi[j] - walllo[j];
}
double vol_T = dims[0]*dims[1]*dims[2];
double vol_f = vol_P/vol_T;
if (flaglog == 0) {
- R0 = 6*MY_PI*mu*(1.0 + 2.16*vol_f);
- RT0 = 8*MY_PI*mu;
- // RS0 = 20.0/3.0*MY_PI*mu*(1.0 + 3.33*vol_f + 2.80*vol_f*vol_f);
+ R0 = 6*MY_PI*mu*(1.0 + 2.16*vol_f);
+ RT0 = 8*MY_PI*mu;
+ // RS0 = 20.0/3.0*MY_PI*mu*(1.0 + 3.33*vol_f + 2.80*vol_f*vol_f);
} else {
- R0 = 6*MY_PI*mu*(1.0 + 2.725*vol_f - 6.583*vol_f*vol_f);
- RT0 = 8*MY_PI*mu*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
- // RS0 = 20.0/3.0*MY_PI*mu*(1.0 + 3.64*vol_f - 6.95*vol_f*vol_f);
+ R0 = 6*MY_PI*mu*(1.0 + 2.725*vol_f - 6.583*vol_f*vol_f);
+ RT0 = 8*MY_PI*mu*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
+ // RS0 = 20.0/3.0*MY_PI*mu*(1.0 + 3.64*vol_f - 6.95*vol_f*vol_f);
}
}
// end of R0 adjustment code
// Initialize f to zero
-
+
for (i=0;i<nlocal+nghost;i++)
for (j=0;j<3;j++) {
f[i][j] = 0.0;
torque[i][j] = 0.0;
}
-
+
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
@@ -701,26 +701,26 @@ void PairLubricateUPoly::compute_RU(double **x)
itype = type[i];
radi = radius[i];
jlist = firstneigh[i];
- jnum = numneigh[i];
+ jnum = numneigh[i];
pre[1] = 8.0*(pre[0] = MY_PI*mu*radi)*radi*radi;
pre[0] *= 6.0;
-
+
// Find angular velocity
-
+
wi[0] = omega[i][0];
wi[1] = omega[i][1];
- wi[2] = omega[i][2];
-
+ wi[2] = omega[i][2];
+
// Contribution due to the isotropic terms
f[i][0] += -vxmu2f*R0*radi*v[i][0];
f[i][1] += -vxmu2f*R0*radi*v[i][1];
- f[i][2] += -vxmu2f*R0*radi*v[i][2];
-
+ f[i][2] += -vxmu2f*R0*radi*v[i][2];
+
const double radi3 = radi*radi*radi;
torque[i][0] += -vxmu2f*RT0*radi3*wi[0];
torque[i][1] += -vxmu2f*RT0*radi3*wi[1];
- torque[i][2] += -vxmu2f*RT0*radi3*wi[2];
+ torque[i][2] += -vxmu2f*RT0*radi3*wi[2];
if (!flagHI) continue;
@@ -732,184 +732,184 @@ void PairLubricateUPoly::compute_RU(double **x)
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
radj = radius[j];
-
+
if (rsq < cutsq[itype][jtype]) {
- r = sqrt(rsq);
-
- wj[0] = omega[j][0];
- wj[1] = omega[j][1];
- wj[2] = omega[j][2];
-
+ r = sqrt(rsq);
+
+ wj[0] = omega[j][0];
+ wj[1] = omega[j][1];
+ wj[2] = omega[j][2];
+
// loc of the point of closest approach on particle i from its center
-
+
xl[0] = -delx/r*radi;
xl[1] = -dely/r*radi;
xl[2] = -delz/r*radi;
jl[0] = delx/r*radj;
jl[1] = dely/r*radj;
jl[2] = delz/r*radj;
-
+
// velocity at the point of closest approach on both particles
// v = v + omega_cross_xl
-
+
// particle i
-
+
vi[0] = v[i][0] + (wi[1]*xl[2] - wi[2]*xl[1]);
vi[1] = v[i][1] + (wi[2]*xl[0] - wi[0]*xl[2]);
vi[2] = v[i][2] + (wi[0]*xl[1] - wi[1]*xl[0]);
-
+
// particle j
-
+
vj[0] = v[j][0] + (wj[1]*jl[2] - wj[2]*jl[1]);
vj[1] = v[j][1] + (wj[2]*jl[0] - wj[0]*jl[2]);
vj[2] = v[j][2] + (wj[0]*jl[1] - wj[1]*jl[0]);
-
+
// Find the scalar resistances a_sq and a_sh
-
+
h_sep = r - radi-radj;
-
+
// check for overlaps
-
+
if(h_sep < 0.0) overlaps++;
-
+
// If less than the minimum gap use the minimum gap instead
-
+
if (r < cut_inner[itype][jtype])
- h_sep = cut_inner[itype][jtype] - radi-radj;
-
+ h_sep = cut_inner[itype][jtype] - radi-radj;
+
// Scale h_sep by radi
-
+
h_sep = h_sep/radi;
- beta[0][1] = radj/radi;
- beta[1][1] = 1.0 + beta[0][1];
+ beta[0][1] = radj/radi;
+ beta[1][1] = 1.0 + beta[0][1];
// Scalar resistances
-
+
if (flaglog) {
- beta[0][2] = beta[0][1]*beta[0][1];
- beta[0][3] = beta[0][2]*beta[0][1];
- beta[0][4] = beta[0][3]*beta[0][1];
- beta[1][2] = beta[1][1]*beta[1][1];
- beta[1][3] = beta[1][2]*beta[1][1];
- double log_h_sep_beta13 = log(1.0/h_sep)/beta[1][3];
- double h_sep_beta11 = h_sep/beta[1][1];
-
- a_sq = pre[0]*(beta[0][2]/beta[1][2]/h_sep
- +((0.2+1.4*beta[0][1]+0.2*beta[0][2])
- +(1.0+18.0*(beta[0][1]+beta[0][3])-29.0*beta[0][2]
- +beta[0][4])*h_sep_beta11/21.0)*log_h_sep_beta13);
-
- a_sh = pre[0]*((8.0*(beta[0][1]+beta[0][3])+4.0*beta[0][2])/15.0
- +(64.0-180.0*(beta[0][1]+beta[0][3])+232.0*beta[0][2]
- +64.0*beta[0][4])*h_sep_beta11/375.0)*log_h_sep_beta13;
-
- a_pu = pre[1]*((0.4*beta[0][1]+0.1*beta[0][2])*beta[1][1]
- +(0.128-0.132*beta[0][1]+0.332*beta[0][2]
- +0.172*beta[0][3])*h_sep)*log_h_sep_beta13;
-
- /*//a_sq = 6*MY_PI*mu*radi*(1.0/4.0/h_sep + 9.0/40.0*log(1/h_sep));
+ beta[0][2] = beta[0][1]*beta[0][1];
+ beta[0][3] = beta[0][2]*beta[0][1];
+ beta[0][4] = beta[0][3]*beta[0][1];
+ beta[1][2] = beta[1][1]*beta[1][1];
+ beta[1][3] = beta[1][2]*beta[1][1];
+ double log_h_sep_beta13 = log(1.0/h_sep)/beta[1][3];
+ double h_sep_beta11 = h_sep/beta[1][1];
+
+ a_sq = pre[0]*(beta[0][2]/beta[1][2]/h_sep
+ +((0.2+1.4*beta[0][1]+0.2*beta[0][2])
+ +(1.0+18.0*(beta[0][1]+beta[0][3])-29.0*beta[0][2]
+ +beta[0][4])*h_sep_beta11/21.0)*log_h_sep_beta13);
+
+ a_sh = pre[0]*((8.0*(beta[0][1]+beta[0][3])+4.0*beta[0][2])/15.0
+ +(64.0-180.0*(beta[0][1]+beta[0][3])+232.0*beta[0][2]
+ +64.0*beta[0][4])*h_sep_beta11/375.0)*log_h_sep_beta13;
+
+ a_pu = pre[1]*((0.4*beta[0][1]+0.1*beta[0][2])*beta[1][1]
+ +(0.128-0.132*beta[0][1]+0.332*beta[0][2]
+ +0.172*beta[0][3])*h_sep)*log_h_sep_beta13;
+
+ /*//a_sq = 6*MY_PI*mu*radi*(1.0/4.0/h_sep + 9.0/40.0*log(1/h_sep));
a_sq = beta0*beta0/beta1/beta1/h_sep
- +(1.0+7.0*beta0+beta0*beta0)/5.0/pow(beta1,3)*log(1.0/h_sep);
+ +(1.0+7.0*beta0+beta0*beta0)/5.0/pow(beta1,3)*log(1.0/h_sep);
a_sq += (1.0+18.0*beta0-29.0*beta0*beta0+18.0*pow(beta0,3)
- +pow(beta0,4))/21.0/pow(beta1,4)*h_sep*log(1.0/h_sep);
+ +pow(beta0,4))/21.0/pow(beta1,4)*h_sep*log(1.0/h_sep);
a_sq *= 6.0*MY_PI*mu*radi;
a_sh = 4.0*beta0*(2.0+beta0
- +2.0*beta0*beta0)/15.0/pow(beta1,3)*log(1.0/h_sep);
+ +2.0*beta0*beta0)/15.0/pow(beta1,3)*log(1.0/h_sep);
a_sh += 4.0*(16.0-45.0*beta0+58.0*beta0*beta0-45.0*pow(beta0,3)
- +16.0*pow(beta0,4))/375.0/pow(beta1,4)*h_sep*log(1.0/h_sep);
+ +16.0*pow(beta0,4))/375.0/pow(beta1,4)*h_sep*log(1.0/h_sep);
a_sh *= 6.0*MY_PI*mu*radi;
-
- a_pu = beta0*(4.0+beta0)/10.0/beta1/beta1*log(1.0/h_sep);
+
+ a_pu = beta0*(4.0+beta0)/10.0/beta1/beta1*log(1.0/h_sep);
a_pu += (32.0-33.0*beta0+83.0*beta0*beta0
- +43.0*pow(beta0,3))/250.0/pow(beta1,3)*h_sep*log(1.0/h_sep);
+ +43.0*pow(beta0,3))/250.0/pow(beta1,3)*h_sep*log(1.0/h_sep);
a_pu *= 8.0*MY_PI*mu*pow(radi,3);*/
- } else
- a_sq = pre[0]*(beta[0][1]*beta[0][1]/(beta[1][1]*beta[1][1]*h_sep));
+ } else
+ a_sq = pre[0]*(beta[0][1]*beta[0][1]/(beta[1][1]*beta[1][1]*h_sep));
// Relative velocity at the point of closest approach
-
+
vr1 = vi[0] - vj[0];
vr2 = vi[1] - vj[1];
vr3 = vi[2] - vj[2];
-
+
// Normal component (vr.n)n
-
+
vnnr = (vr1*delx + vr2*dely + vr3*delz)/r;
vn1 = vnnr*delx/r;
vn2 = vnnr*dely/r;
vn3 = vnnr*delz/r;
-
+
// Tangential component vr - (vr.n)n
-
+
vt1 = vr1 - vn1;
vt2 = vr2 - vn2;
vt3 = vr3 - vn3;
-
+
// Find force due to squeeze type motion
-
+
fx = a_sq*vn1;
fy = a_sq*vn2;
fz = a_sq*vn3;
-
+
// Find force due to all shear kind of motions
-
+
if (flaglog) {
fx = fx + a_sh*vt1;
fy = fy + a_sh*vt2;
- fz = fz + a_sh*vt3;
+ fz = fz + a_sh*vt3;
}
-
+
// Scale forces to obtain in appropriate units
-
+
fx = vxmu2f*fx;
fy = vxmu2f*fy;
fz = vxmu2f*fz;
-
+
// Add to the total forc
-
+
f[i][0] -= fx;
f[i][1] -= fy;
- f[i][2] -= fz;
-
+ f[i][2] -= fz;
+
// Find torque due to this force
-
+
if (flaglog) {
tx = xl[1]*fz - xl[2]*fy;
ty = xl[2]*fx - xl[0]*fz;
- tz = xl[0]*fy - xl[1]*fx;
-
+ tz = xl[0]*fy - xl[1]*fx;
+
// Why a scale factor ?
-
+
torque[i][0] -= vxmu2f*tx;
torque[i][1] -= vxmu2f*ty;
- torque[i][2] -= vxmu2f*tz;
-
+ torque[i][2] -= vxmu2f*tz;
+
// Torque due to a_pu
-
- wdotn = ((wi[0]-wj[0])*delx +
+
+ wdotn = ((wi[0]-wj[0])*delx +
(wi[1]-wj[1])*dely + (wi[2]-wj[2])*delz)/r;
wt1 = (wi[0]-wj[0]) - wdotn*delx/r;
wt2 = (wi[1]-wj[1]) - wdotn*dely/r;
wt3 = (wi[2]-wj[2]) - wdotn*delz/r;
-
+
tx = a_pu*wt1;
ty = a_pu*wt2;
tz = a_pu*wt3;
-
+
// add to total
-
+
torque[i][0] -= vxmu2f*tx;
torque[i][1] -= vxmu2f*ty;
- torque[i][2] -= vxmu2f*tz;
- }
+ torque[i][2] -= vxmu2f*tz;
+ }
}
}
}
}
/* ----------------------------------------------------------------------
- This computes R_{FE}*E , where E is the rate of strain of tensor which is
+ This computes R_{FE}*E , where E is the rate of strain of tensor which is
known apriori, as it depends only on the known fluid velocity.
So, this part of the hydrodynamic interaction can be pre computed and
transferred to the RHS
@@ -919,17 +919,17 @@ void PairLubricateUPoly::compute_RE(double **x)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
int *ilist,*jlist,*numneigh,**firstneigh;
-
+
int *type = atom->type;
int overlaps = 0;
-
+
double xtmp,ytmp,ztmp,delx,dely,delz,fx,fy,fz,tx,ty,tz;
double rsq,r,h_sep,radi,radj;
//double beta0,beta1,lhsep;
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3;
- double vt1,vt2,vt3;
+ double vt1,vt2,vt3;
double xl[3],pre[2];
-
+
double **f = atom->f;
double **torque = atom->torque;
double *radius = atom->radius;
@@ -946,7 +946,7 @@ void PairLubricateUPoly::compute_RE(double **x)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
beta[0][0] = beta[1][0] = beta[1][4] = 0.0;
for (ii = 0; ii < inum; ii++) {
@@ -960,8 +960,8 @@ void PairLubricateUPoly::compute_RE(double **x)
jnum = numneigh[i];
pre[1] = 8.0*(pre[0] = MY_PI*mu*radi)*radi*radi;
pre[0] *= 6.0;
-
- // No contribution from isotropic terms due to E
+
+ // No contribution from isotropic terms due to E
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
delx = xtmp - x[j][0];
@@ -970,161 +970,161 @@ void PairLubricateUPoly::compute_RE(double **x)
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
radj = radius[j];
-
+
if (rsq < cutsq[itype][jtype]) {
- r = sqrt(rsq);
-
+ r = sqrt(rsq);
+
// loc of the point of closest approach on particle i from its center
-
+
xl[0] = -delx/r*radi;
xl[1] = -dely/r*radi;
xl[2] = -delz/r*radi;
-
+
// Find the scalar resistances a_sq and a_sh
-
+
h_sep = r - radi-radj;
// check for overlaps
-
+
if (h_sep < 0.0) overlaps++;
-
+
// If less than the minimum gap use the minimum gap instead
-
+
if (r < cut_inner[itype][jtype])
h_sep = cut_inner[itype][jtype] - radi-radj;
-
+
// Scale h_sep by radi
-
+
h_sep = h_sep/radi;
- beta[0][1] = radj/radi;
- beta[1][1] = 1.0 + beta[0][1];
+ beta[0][1] = radj/radi;
+ beta[1][1] = 1.0 + beta[0][1];
/*beta0 = radj/radi;
beta1 = 1.0 + beta0;
- lhsep = log(1.0/h_sep);*/
-
+ lhsep = log(1.0/h_sep);*/
+
// Scalar resistance for Squeeze type motions
-
+
if (flaglog) {
- beta[0][2] = beta[0][1]*beta[0][1];
- beta[0][3] = beta[0][2]*beta[0][1];
- beta[0][4] = beta[0][3]*beta[0][1];
- beta[1][2] = beta[1][1]*beta[1][1];
- beta[1][3] = beta[1][2]*beta[1][1];
- double log_h_sep_beta13 = log(1.0/h_sep)/beta[1][3];
- double h_sep_beta11 = h_sep/beta[1][1];
-
- a_sq = pre[0]*(beta[0][2]/beta[1][2]/h_sep
- +((0.2+1.4*beta[0][1]+0.2*beta[0][2])
- +(1.0+18.0*(beta[0][1]+beta[0][3])-29.0*beta[0][2]
- +beta[0][4])*h_sep_beta11/21.0)*log_h_sep_beta13);
-
- a_sh = pre[0]*((8.0*(beta[0][1]+beta[0][3])+4.0*beta[0][2])/15.0
- +(64.0-180.0*(beta[0][1]+beta[0][3])+232.0*beta[0][2]
- +64.0*beta[0][4])*h_sep_beta11/375.0)*log_h_sep_beta13;
-
- a_pu = pre[1]*((0.4*beta[0][1]+0.1*beta[0][2])*beta[1][1]
- +(0.128-0.132*beta[0][1]+0.332*beta[0][2]
- +0.172*beta[0][3])*h_sep)*log_h_sep_beta13;
-
- /*//a_sq = 6*MY_PI*mu*radi*(1.0/4.0/h_sep + 9.0/40.0*log(1/h_sep));
+ beta[0][2] = beta[0][1]*beta[0][1];
+ beta[0][3] = beta[0][2]*beta[0][1];
+ beta[0][4] = beta[0][3]*beta[0][1];
+ beta[1][2] = beta[1][1]*beta[1][1];
+ beta[1][3] = beta[1][2]*beta[1][1];
+ double log_h_sep_beta13 = log(1.0/h_sep)/beta[1][3];
+ double h_sep_beta11 = h_sep/beta[1][1];
+
+ a_sq = pre[0]*(beta[0][2]/beta[1][2]/h_sep
+ +((0.2+1.4*beta[0][1]+0.2*beta[0][2])
+ +(1.0+18.0*(beta[0][1]+beta[0][3])-29.0*beta[0][2]
+ +beta[0][4])*h_sep_beta11/21.0)*log_h_sep_beta13);
+
+ a_sh = pre[0]*((8.0*(beta[0][1]+beta[0][3])+4.0*beta[0][2])/15.0
+ +(64.0-180.0*(beta[0][1]+beta[0][3])+232.0*beta[0][2]
+ +64.0*beta[0][4])*h_sep_beta11/375.0)*log_h_sep_beta13;
+
+ a_pu = pre[1]*((0.4*beta[0][1]+0.1*beta[0][2])*beta[1][1]
+ +(0.128-0.132*beta[0][1]+0.332*beta[0][2]
+ +0.172*beta[0][3])*h_sep)*log_h_sep_beta13;
+
+ /*//a_sq = 6*MY_PI*mu*radi*(1.0/4.0/h_sep + 9.0/40.0*log(1/h_sep));
a_sq = beta0*beta0/beta1/beta1/h_sep
- +(1.0+7.0*beta0+beta0*beta0)/5.0/pow(beta1,3)*lhsep;
+ +(1.0+7.0*beta0+beta0*beta0)/5.0/pow(beta1,3)*lhsep;
a_sq += (1.0+18.0*beta0-29.0*beta0*beta0+18.0*pow(beta0,3)
- +pow(beta0,4))/21.0/pow(beta1,4)*h_sep*lhsep;
+ +pow(beta0,4))/21.0/pow(beta1,4)*h_sep*lhsep;
a_sq *= 6.0*MY_PI*mu*radi;
a_sh = 4.0*beta0*(2.0+beta0
- +2.0*beta0*beta0)/15.0/pow(beta1,3)*log(1.0/h_sep);
+ +2.0*beta0*beta0)/15.0/pow(beta1,3)*log(1.0/h_sep);
a_sh += 4.0*(16.0-45.0*beta0+58.0*beta0*beta0-45.0*pow(beta0,3)
- +16.0*pow(beta0,4))/375.0/pow(beta1,4)*h_sep*log(1.0/h_sep);
+ +16.0*pow(beta0,4))/375.0/pow(beta1,4)*h_sep*log(1.0/h_sep);
a_sh *= 6.0*MY_PI*mu*radi;
-
- a_pu = beta0*(4.0+beta0)/10.0/beta1/beta1*log(1.0/h_sep);
+
+ a_pu = beta0*(4.0+beta0)/10.0/beta1/beta1*log(1.0/h_sep);
a_pu += (32.0-33.0*beta0+83.0*beta0*beta0
- +43.0*pow(beta0,3))/250.0/pow(beta1,3)*h_sep*log(1.0/h_sep);
+ +43.0*pow(beta0,3))/250.0/pow(beta1,3)*h_sep*log(1.0/h_sep);
a_pu *= 8.0*MY_PI*mu*pow(radi,3);*/
- } else
+ } else
a_sq = pre[0]*(beta[0][1]*beta[0][1]/(beta[1][1]*beta[1][1]*h_sep));
// Relative velocity at the point of closest approach due to Ef only
vr1 = -2.0*(Ef[0][0]*xl[0] + Ef[0][1]*xl[1] + Ef[0][2]*xl[2]);
vr2 = -2.0*(Ef[1][0]*xl[0] + Ef[1][1]*xl[1] + Ef[1][2]*xl[2]);
- vr3 = -2.0*(Ef[2][0]*xl[0] + Ef[2][1]*xl[1] + Ef[2][2]*xl[2]);
-
+ vr3 = -2.0*(Ef[2][0]*xl[0] + Ef[2][1]*xl[1] + Ef[2][2]*xl[2]);
+
// Normal component (vr.n)n
-
+
vnnr = (vr1*delx + vr2*dely + vr3*delz)/r;
vn1 = vnnr*delx/r;
vn2 = vnnr*dely/r;
vn3 = vnnr*delz/r;
-
+
// Tangential component vr - (vr.n)n
-
+
vt1 = vr1 - vn1;
vt2 = vr2 - vn2;
vt3 = vr3 - vn3;
-
+
// Find force due to squeeze type motion
-
+
fx = a_sq*vn1;
fy = a_sq*vn2;
fz = a_sq*vn3;
-
+
// Find force due to all shear kind of motions
-
+
if (flaglog) {
fx = fx + a_sh*vt1;
fy = fy + a_sh*vt2;
- fz = fz + a_sh*vt3;
+ fz = fz + a_sh*vt3;
}
-
+
// Scale forces to obtain in appropriate units
-
+
fx = vxmu2f*fx;
fy = vxmu2f*fy;
fz = vxmu2f*fz;
-
+
// Add to the total forc
-
+
f[i][0] -= fx;
f[i][1] -= fy;
- f[i][2] -= fz;
-
+ f[i][2] -= fz;
+
// Find torque due to this force
-
+
if (flaglog) {
tx = xl[1]*fz - xl[2]*fy;
ty = xl[2]*fx - xl[0]*fz;
- tz = xl[0]*fy - xl[1]*fx;
-
+ tz = xl[0]*fy - xl[1]*fx;
+
// Why a scale factor ?
-
+
torque[i][0] -= vxmu2f*tx;
torque[i][1] -= vxmu2f*ty;
- torque[i][2] -= vxmu2f*tz;
-
+ torque[i][2] -= vxmu2f*tz;
+
// NOTE No a_pu term needed as they add up to zero
- }
+ }
}
}
}
-
+
int print_overlaps = 0;
if (print_overlaps && overlaps)
printf("Number of overlaps=%d\n",overlaps);
}
/*-----------------------------------------------------------------------
- global settings
+ global settings
------------------------------------------------------------------------- */
void PairLubricateUPoly::settings(int narg, char **arg)
{
int itype;
-
+
if (narg < 5 || narg > 7) error->all(FLERR,"Illegal pair_style command");
mu = atof(arg[0]);
@@ -1139,9 +1139,9 @@ void PairLubricateUPoly::settings(int narg, char **arg)
if (flaglog == 1 && flagHI == 0) {
error->warning(FLERR,"Cannot include log terms without 1/r terms; "
- "setting flagHI to 1");
+ "setting flagHI to 1");
flagHI = 1;
- }
+ }
// reset cutoffs that have been explicitly set
@@ -1154,7 +1154,7 @@ void PairLubricateUPoly::settings(int narg, char **arg)
cut[i][j] = cut_global;
}
}
-
+
// Store the rate of strain tensor
Ef[0][0] = 0.0;
@@ -1165,8 +1165,8 @@ void PairLubricateUPoly::settings(int narg, char **arg)
Ef[1][2] = 0.0;
Ef[2][0] = 0.0;
Ef[2][1] = 0.0;
- Ef[2][2] = 0.0;
-
+ Ef[2][2] = 0.0;
+
}
@@ -1180,7 +1180,7 @@ void PairLubricateUPoly::init_style()
error->all(FLERR,"Pair lubricateU/poly requires newton pair off");
if (comm->ghost_velocity == 0)
error->all(FLERR,
- "Pair lubricateU/poly requires ghost atoms store velocity");
+ "Pair lubricateU/poly requires ghost atoms store velocity");
if (!atom->sphere_flag)
error->all(FLERR,"Pair lubricate/poly requires atom style sphere");
@@ -1192,10 +1192,10 @@ void PairLubricateUPoly::init_style()
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
- if (radius[i] == 0.0)
+ if (radius[i] == 0.0)
error->one(FLERR,"Pair lubricate/poly requires extended particles");
// Set the isotropic constants depending on the volume fraction
-
+
// Find the total volume
// check for fix deform, if exists it must use "remap v"
// If box will change volume, set appropriate flag so that volume
@@ -1208,46 +1208,46 @@ void PairLubricateUPoly::init_style()
flagdeform = flagwall = 0;
for (int i = 0; i < modify->nfix; i++){
- if (strcmp(modify->fix[i]->style,"deform") == 0)
+ if (strcmp(modify->fix[i]->style,"deform") == 0)
flagdeform = 1;
else if (strstr(modify->fix[i]->style,"wall") != NULL){
flagwall = 1; // Walls exist
if (((FixWall *) modify->fix[i])->varflag ) {
- flagwall = 2; // Moving walls exist
- wallfix = (FixWall *) modify->fix[i];
+ flagwall = 2; // Moving walls exist
+ wallfix = (FixWall *) modify->fix[i];
}
}
}
-
+
// set the isotropic constants depending on the volume fraction
- // vol_T = total volumeshearing = flagdeform = flagwall = 0;
+ // vol_T = total volumeshearing = flagdeform = flagwall = 0;
double vol_T, wallcoord;
if (!flagwall) vol_T = domain->xprd*domain->yprd*domain->zprd;
- else {
+ else {
double wallhi[3], walllo[3];
for (int j = 0; j < 3; j++){
wallhi[j] = domain->prd[j];
walllo[j] = 0;
- }
+ }
for (int m = 0; m < wallfix->nwall; m++){
int dim = wallfix->wallwhich[m] / 2;
int side = wallfix->wallwhich[m] % 2;
if (wallfix->wallstyle[m] == VARIABLE){
- wallfix->varindex[m] = input->variable->find(wallfix->varstr[m]);
- //Since fix->wall->init happens after pair->init_style
- wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
+ wallfix->varindex[m] = input->variable->find(wallfix->varstr[m]);
+ //Since fix->wall->init happens after pair->init_style
+ wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
}
else wallcoord = wallfix->coord0[m];
-
+
if (side == 0) walllo[dim] = wallcoord;
else wallhi[dim] = wallcoord;
}
- vol_T = (wallhi[0] - walllo[0]) * (wallhi[1] - walllo[1]) *
+ vol_T = (wallhi[0] - walllo[0]) * (wallhi[1] - walllo[1]) *
(wallhi[2] - walllo[2]);
}
-
+
// Assuming monodisperse spheres, find the volume of the particles
double volP = 0.0;
@@ -1266,14 +1266,14 @@ void PairLubricateUPoly::init_style()
if (!comm->me) {
if(logfile)
fprintf(logfile, "lubricateU: vol_f = %g, vol_p = %g, vol_T = %g\n",
- vol_f,vol_P,vol_T);
+ vol_f,vol_P,vol_T);
if (screen)
fprintf(screen, "lubricateU: vol_f = %g, vol_p = %g, vol_T = %g\n",
- vol_f,vol_P,vol_T);
+ vol_f,vol_P,vol_T);
}
// Set the isotropic constant
-
+
if (flaglog == 0) {
R0 = 6*MY_PI*mu*(1.0 + 2.16*vol_f);
RT0 = 8*MY_PI*mu; // Not needed actually
diff --git a/src/FLD/pair_lubricateU_poly.h b/src/FLD/pair_lubricateU_poly.h
index 7faf0b2bcfaadef6ea4da4e4580dede01720b228..755788b718688c5598ce79e13df3cde05524860c 100644
--- a/src/FLD/pair_lubricateU_poly.h
+++ b/src/FLD/pair_lubricateU_poly.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/FLD/pair_lubricate_poly.cpp b/src/FLD/pair_lubricate_poly.cpp
index f03fae3dfa9ecb444a538ae01c7ac132b8c19566..168b6e82853e3d8308048120ed9be0029a1a54d0 100644
--- a/src/FLD/pair_lubricate_poly.cpp
+++ b/src/FLD/pair_lubricate_poly.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -69,7 +69,7 @@ void PairLubricatePoly::compute(int eflag, int vflag)
double xtmp,ytmp,ztmp,delx,dely,delz,fpair,fx,fy,fz,tx,ty,tz;
double rsq,r,h_sep,h_sepj,beta0,beta1,betaj,betaj1,radi,radj,tfmag;
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3;
- double vt1,vt2,vt3,wt1,wt2,wt3,wdotn;
+ double vt1,vt2,vt3,wt1,wt2,wt3,wdotn;
double inertia,inv_inertia,vRS0;
double vi[3],vj[3],wi[3],wj[3],xl[3],jl[3];
double a_sq,a_sh,a_pu,Fbmag,del,delmin,eta;
@@ -95,7 +95,7 @@ void PairLubricatePoly::compute(int eflag, int vflag)
int newton_pair = force->newton_pair;
int overlaps = 0;
-
+
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
@@ -120,8 +120,8 @@ void PairLubricatePoly::compute(int eflag, int vflag)
itype = type[i];
radi = radius[i];
domain->x2lamda(x[i],lamda);
- vstream[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
- h_rate[4]*lamda[2] + h_ratelo[0];
+ vstream[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
+ h_rate[4]*lamda[2] + h_ratelo[0];
vstream[1] = h_rate[1]*lamda[1] + h_rate[3]*lamda[2] + h_ratelo[1];
vstream[2] = h_rate[2]*lamda[2] + h_ratelo[2];
v[i][0] -= vstream[0];
@@ -137,7 +137,7 @@ void PairLubricatePoly::compute(int eflag, int vflag)
Ef[0][0] = h_rate[0]/domain->xprd;
Ef[1][1] = h_rate[1]/domain->yprd;
- Ef[2][2] = h_rate[2]/domain->zprd;
+ Ef[2][2] = h_rate[2]/domain->zprd;
Ef[0][1] = Ef[1][0] = 0.5 * h_rate[5]/domain->yprd;
Ef[0][2] = Ef[2][0] = 0.5 * h_rate[4]/domain->zprd;
Ef[1][2] = Ef[2][1] = 0.5 * h_rate[3]/domain->zprd;
@@ -147,7 +147,7 @@ void PairLubricatePoly::compute(int eflag, int vflag)
comm->forward_comm_pair(this);
}
-
+
// This section of code adjusts R0/RT0/RS0 if necessary due to changes
// in the volume fraction as a result of fix deform or moving walls
@@ -155,43 +155,43 @@ void PairLubricatePoly::compute(int eflag, int vflag)
if (flagVF) // Flag for volume fraction corrections
if (flagdeform || flagwall == 2){ // Possible changes in volume fraction
if (flagdeform && !flagwall)
- for (j = 0; j < 3; j++)
- dims[j] = domain->prd[j];
+ for (j = 0; j < 3; j++)
+ dims[j] = domain->prd[j];
else if (flagwall == 2 || (flagdeform && flagwall == 1)){
- double wallhi[3], walllo[3];
- for (int j = 0; j < 3; j++){
- wallhi[j] = domain->prd[j];
- walllo[j] = 0;
- }
- for (int m = 0; m < wallfix->nwall; m++){
- int dim = wallfix->wallwhich[m] / 2;
- int side = wallfix->wallwhich[m] % 2;
- if (wallfix->wallstyle[m] == VARIABLE){
- wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
- }
- else wallcoord = wallfix->coord0[m];
- if (side == 0) walllo[dim] = wallcoord;
- else wallhi[dim] = wallcoord;
- }
- for (int j = 0; j < 3; j++)
- dims[j] = wallhi[j] - walllo[j];
+ double wallhi[3], walllo[3];
+ for (int j = 0; j < 3; j++){
+ wallhi[j] = domain->prd[j];
+ walllo[j] = 0;
+ }
+ for (int m = 0; m < wallfix->nwall; m++){
+ int dim = wallfix->wallwhich[m] / 2;
+ int side = wallfix->wallwhich[m] % 2;
+ if (wallfix->wallstyle[m] == VARIABLE){
+ wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
+ }
+ else wallcoord = wallfix->coord0[m];
+ if (side == 0) walllo[dim] = wallcoord;
+ else wallhi[dim] = wallcoord;
+ }
+ for (int j = 0; j < 3; j++)
+ dims[j] = wallhi[j] - walllo[j];
}
double vol_T = dims[0]*dims[1]*dims[2];
double vol_f = vol_P/vol_T;
if (flaglog == 0) {
- R0 = 6*MY_PI*mu*(1.0 + 2.16*vol_f);
- RT0 = 8*MY_PI*mu;
- RS0 = 20.0/3.0*MY_PI*mu*(1.0 + 3.33*vol_f + 2.80*vol_f*vol_f);
+ R0 = 6*MY_PI*mu*(1.0 + 2.16*vol_f);
+ RT0 = 8*MY_PI*mu;
+ RS0 = 20.0/3.0*MY_PI*mu*(1.0 + 3.33*vol_f + 2.80*vol_f*vol_f);
} else {
- R0 = 6*MY_PI*mu*(1.0 + 2.725*vol_f - 6.583*vol_f*vol_f);
- RT0 = 8*MY_PI*mu*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
- RS0 = 20.0/3.0*MY_PI*mu*(1.0 + 3.64*vol_f - 6.95*vol_f*vol_f);
+ R0 = 6*MY_PI*mu*(1.0 + 2.725*vol_f - 6.583*vol_f*vol_f);
+ RT0 = 8*MY_PI*mu*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
+ RS0 = 20.0/3.0*MY_PI*mu*(1.0 + 3.64*vol_f - 6.95*vol_f*vol_f);
}
}
- // end of R0 adjustment code
-
+ // end of R0 adjustment code
+
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
@@ -199,15 +199,15 @@ void PairLubricatePoly::compute(int eflag, int vflag)
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
- jnum = numneigh[i];
+ jnum = numneigh[i];
radi = radius[i];
// angular velocity
wi[0] = omega[i][0];
wi[1] = omega[i][1];
- wi[2] = omega[i][2];
-
+ wi[2] = omega[i][2];
+
// FLD contribution to force and torque due to isotropic terms
// FLD contribution to stress from isotropic RS0
@@ -215,21 +215,21 @@ void PairLubricatePoly::compute(int eflag, int vflag)
f[i][0] -= vxmu2f*R0*radi*v[i][0];
f[i][1] -= vxmu2f*R0*radi*v[i][1];
f[i][2] -= vxmu2f*R0*radi*v[i][2];
- const double radi3 = radi*radi*radi;
+ const double radi3 = radi*radi*radi;
torque[i][0] -= vxmu2f*RT0*radi3*wi[0];
torque[i][1] -= vxmu2f*RT0*radi3*wi[1];
- torque[i][2] -= vxmu2f*RT0*radi3*wi[2];
-
+ torque[i][2] -= vxmu2f*RT0*radi3*wi[2];
+
if (shearing && vflag_either) {
- vRS0 = -vxmu2f * RS0*radi3;
- v_tally_tensor(i,i,nlocal,newton_pair,
- vRS0*Ef[0][0],vRS0*Ef[1][1],vRS0*Ef[2][2],
- vRS0*Ef[0][1],vRS0*Ef[0][2],vRS0*Ef[1][2]);
+ vRS0 = -vxmu2f * RS0*radi3;
+ v_tally_tensor(i,i,nlocal,newton_pair,
+ vRS0*Ef[0][0],vRS0*Ef[1][1],vRS0*Ef[2][2],
+ vRS0*Ef[0][1],vRS0*Ef[0][2],vRS0*Ef[1][2]);
}
}
if (!flagHI) continue;
-
+
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
delx = xtmp - x[j][0];
@@ -240,13 +240,13 @@ void PairLubricatePoly::compute(int eflag, int vflag)
radj = atom->radius[j];
if (rsq < cutsq[itype][jtype]) {
- r = sqrt(rsq);
-
+ r = sqrt(rsq);
+
// angular momentum = I*omega = 2/5 * M*R^2 * omega
- wj[0] = omega[j][0];
- wj[1] = omega[j][1];
- wj[2] = omega[j][2];
+ wj[0] = omega[j][0];
+ wj[1] = omega[j][1];
+ wj[2] = omega[j][2];
// xl = point of closest approach on particle i from its center
@@ -256,7 +256,7 @@ void PairLubricatePoly::compute(int eflag, int vflag)
jl[0] = -delx/r*radj;
jl[1] = -dely/r*radj;
jl[2] = -delz/r*radj;
-
+
// velocity at the point of closest approach on both particles
// v = v + omega_cross_xl - Ef.xl
@@ -264,71 +264,71 @@ void PairLubricatePoly::compute(int eflag, int vflag)
vi[0] = v[i][0] + (wi[1]*xl[2] - wi[2]*xl[1])
- (Ef[0][0]*xl[0] + Ef[0][1]*xl[1] + Ef[0][2]*xl[2]);
-
+
vi[1] = v[i][1] + (wi[2]*xl[0] - wi[0]*xl[2])
- (Ef[1][0]*xl[0] + Ef[1][1]*xl[1] + Ef[1][2]*xl[2]);
-
+
vi[2] = v[i][2] + (wi[0]*xl[1] - wi[1]*xl[0])
- (Ef[2][0]*xl[0] + Ef[2][1]*xl[1] + Ef[2][2]*xl[2]);
-
+
// particle j
vj[0] = v[j][0] - (wj[1]*jl[2] - wj[2]*jl[1])
+ (Ef[0][0]*jl[0] + Ef[0][1]*jl[1] + Ef[0][2]*jl[2]);
-
+
vj[1] = v[j][1] - (wj[2]*jl[0] - wj[0]*jl[2])
+ (Ef[1][0]*jl[0] + Ef[1][1]*jl[1] + Ef[1][2]*jl[2]);
-
+
vj[2] = v[j][2] - (wj[0]*jl[1] - wj[1]*jl[0])
+ (Ef[2][0]*jl[0] + Ef[2][1]*jl[1] + Ef[2][2]*jl[2]);
-
+
// scalar resistances XA and YA
h_sep = r - radi-radj;
-
+
// check for overlaps
if (h_sep < 0.0) overlaps++;
-
+
// if less than the minimum gap use the minimum gap instead
if (r < cut_inner[itype][jtype])
- h_sep = cut_inner[itype][jtype] - radi-radj;
-
+ h_sep = cut_inner[itype][jtype] - radi-radj;
+
// scale h_sep by radi
h_sep = h_sep/radi;
beta0 = radj/radi;
beta1 = 1.0 + beta0;
-
+
// scalar resistances
if (flaglog) {
- a_sq = beta0*beta0/beta1/beta1/h_sep +
- (1.0+7.0*beta0+beta0*beta0)/5.0/pow(beta1,3.0)*log(1.0/h_sep);
- a_sq += (1.0+18.0*beta0-29.0*beta0*beta0+18.0 *
- pow(beta0,3.0)+pow(beta0,4.0))/21.0/pow(beta1,4.0) *
- h_sep*log(1.0/h_sep);
+ a_sq = beta0*beta0/beta1/beta1/h_sep +
+ (1.0+7.0*beta0+beta0*beta0)/5.0/pow(beta1,3.0)*log(1.0/h_sep);
+ a_sq += (1.0+18.0*beta0-29.0*beta0*beta0+18.0 *
+ pow(beta0,3.0)+pow(beta0,4.0))/21.0/pow(beta1,4.0) *
+ h_sep*log(1.0/h_sep);
a_sq *= 6.0*MY_PI*mu*radi;
- a_sh = 4.0*beta0*(2.0+beta0+2.0*beta0*beta0)/15.0/pow(beta1,3.0) *
- log(1.0/h_sep);
- a_sh += 4.0*(16.0-45.0*beta0+58.0*beta0*beta0-45.0*pow(beta0,3.0) +
- 16.0*pow(beta0,4.0))/375.0/pow(beta1,4.0) *
- h_sep*log(1.0/h_sep);
+ a_sh = 4.0*beta0*(2.0+beta0+2.0*beta0*beta0)/15.0/pow(beta1,3.0) *
+ log(1.0/h_sep);
+ a_sh += 4.0*(16.0-45.0*beta0+58.0*beta0*beta0-45.0*pow(beta0,3.0) +
+ 16.0*pow(beta0,4.0))/375.0/pow(beta1,4.0) *
+ h_sep*log(1.0/h_sep);
a_sh *= 6.0*MY_PI*mu*radi;
a_pu = beta0*(4.0+beta0)/10.0/beta1/beta1*log(1.0/h_sep);
- a_pu += (32.0-33.0*beta0+83.0*beta0*beta0+43.0 *
- pow(beta0,3.0))/250.0/pow(beta1,3.0)*h_sep*log(1.0/h_sep);
+ a_pu += (32.0-33.0*beta0+83.0*beta0*beta0+43.0 *
+ pow(beta0,3.0))/250.0/pow(beta1,3.0)*h_sep*log(1.0/h_sep);
a_pu *= 8.0*MY_PI*mu*pow(radi,3.0);
} else a_sq = 6.0*MY_PI*mu*radi*(beta0*beta0/beta1/beta1/h_sep);
-
+
// relative velocity at the point of closest approach
- // includes fluid velocity
+ // includes fluid velocity
vr1 = vi[0] - vj[0];
vr2 = vi[1] - vj[1];
vr3 = vi[2] - vj[2];
-
+
// normal component (vr.n)n
vnnr = (vr1*delx + vr2*dely + vr3*delz)/r;
@@ -353,7 +353,7 @@ void PairLubricatePoly::compute(int eflag, int vflag)
if (flaglog) {
fx = fx + a_sh*vt1;
fy = fy + a_sh*vt2;
- fz = fz + a_sh*vt3;
+ fz = fz + a_sh*vt3;
}
// scale forces for appropriate units
@@ -361,50 +361,50 @@ void PairLubricatePoly::compute(int eflag, int vflag)
fx *= vxmu2f;
fy *= vxmu2f;
fz *= vxmu2f;
-
+
// add to total force
f[i][0] -= fx;
f[i][1] -= fy;
- f[i][2] -= fz;
-
+ f[i][2] -= fz;
+
// torque due to this force
if (flaglog) {
tx = xl[1]*fz - xl[2]*fy;
ty = xl[2]*fx - xl[0]*fz;
- tz = xl[0]*fy - xl[1]*fx;
-
+ tz = xl[0]*fy - xl[1]*fx;
+
torque[i][0] -= vxmu2f*tx;
torque[i][1] -= vxmu2f*ty;
- torque[i][2] -= vxmu2f*tz;
+ torque[i][2] -= vxmu2f*tz;
// torque due to a_pu
- wdotn = ((wi[0]-wj[0])*delx + (wi[1]-wj[1])*dely +
- (wi[2]-wj[2])*delz)/r;
+ wdotn = ((wi[0]-wj[0])*delx + (wi[1]-wj[1])*dely +
+ (wi[2]-wj[2])*delz)/r;
wt1 = (wi[0]-wj[0]) - wdotn*delx/r;
wt2 = (wi[1]-wj[1]) - wdotn*dely/r;
wt3 = (wi[2]-wj[2]) - wdotn*delz/r;
-
+
tx = a_pu*wt1;
ty = a_pu*wt2;
tz = a_pu*wt3;
-
+
torque[i][0] -= vxmu2f*tx;
torque[i][1] -= vxmu2f*ty;
- torque[i][2] -= vxmu2f*tz;
+ torque[i][2] -= vxmu2f*tz;
- }
+ }
- // set j = nlocal so that only I gets tallied
+ // set j = nlocal so that only I gets tallied
if (evflag) ev_tally_xyz(i,nlocal,nlocal,0,
- 0.0,0.0,-fx,-fy,-fz,delx,dely,delz);
+ 0.0,0.0,-fx,-fy,-fz,delx,dely,delz);
}
}
}
-
+
// restore streaming component of velocity, omega, angmom
if (shearing) {
@@ -415,10 +415,10 @@ void PairLubricatePoly::compute(int eflag, int vflag)
i = ilist[ii];
itype = type[i];
radi = atom->radius[i];
-
+
domain->x2lamda(x[i],lamda);
- vstream[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
- h_rate[4]*lamda[2] + h_ratelo[0];
+ vstream[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
+ h_rate[4]*lamda[2] + h_ratelo[0];
vstream[1] = h_rate[1]*lamda[1] + h_rate[3]*lamda[2] + h_ratelo[1];
vstream[2] = h_rate[2]*lamda[2] + h_ratelo[2];
v[i][0] += vstream[0];
@@ -452,7 +452,7 @@ void PairLubricatePoly::init_style()
error->all(FLERR,"Pair lubricate/poly requires newton pair off");
if (comm->ghost_velocity == 0)
error->all(FLERR,
- "Pair lubricate/poly requires ghost atoms store velocity");
+ "Pair lubricate/poly requires ghost atoms store velocity");
if (!atom->sphere_flag)
error->all(FLERR,"Pair lubricate/poly requires atom style sphere");
@@ -464,7 +464,7 @@ void PairLubricatePoly::init_style()
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
- if (radius[i] == 0.0)
+ if (radius[i] == 0.0)
error->one(FLERR,"Pair lubricate/poly requires extended particles");
int irequest = neighbor->request(this);
@@ -482,20 +482,20 @@ void PairLubricatePoly::init_style()
// due to walls, set volume appropriately; if walls will
// move, set appropriate flag so that volume and v.f. corrections
// are re-calculated at every step.
-
+
shearing = flagdeform = flagwall = 0;
for (int i = 0; i < modify->nfix; i++){
if (strcmp(modify->fix[i]->style,"deform") == 0) {
shearing = flagdeform = 1;
- if (((FixDeform *) modify->fix[i])->remapflag != V_REMAP)
- error->all(FLERR,"Using pair lubricate with inconsistent "
- "fix deform remap option");
+ if (((FixDeform *) modify->fix[i])->remapflag != V_REMAP)
+ error->all(FLERR,"Using pair lubricate with inconsistent "
+ "fix deform remap option");
}
if (strstr(modify->fix[i]->style,"wall") != NULL){
flagwall = 1; // Walls exist
if (((FixWall *) modify->fix[i])->varflag ) {
- flagwall = 2; // Moving walls exist
- wallfix = (FixWall *) modify->fix[i];
+ flagwall = 2; // Moving walls exist
+ wallfix = (FixWall *) modify->fix[i];
}
}
}
@@ -503,26 +503,26 @@ void PairLubricatePoly::init_style()
double vol_T;
double wallcoord;
if (!flagwall) vol_T = domain->xprd*domain->yprd*domain->zprd;
- else {
+ else {
double wallhi[3], walllo[3];
for (int j = 0; j < 3; j++){
wallhi[j] = domain->prd[j];
walllo[j] = 0;
- }
+ }
for (int m = 0; m < wallfix->nwall; m++){
int dim = wallfix->wallwhich[m] / 2;
int side = wallfix->wallwhich[m] % 2;
if (wallfix->wallstyle[m] == VARIABLE){
- wallfix->varindex[m] = input->variable->find(wallfix->varstr[m]);
- //Since fix->wall->init happens after pair->init_style
- wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
+ wallfix->varindex[m] = input->variable->find(wallfix->varstr[m]);
+ //Since fix->wall->init happens after pair->init_style
+ wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
}
else wallcoord = wallfix->coord0[m];
-
+
if (side == 0) walllo[dim] = wallcoord;
else wallhi[dim] = wallcoord;
}
- vol_T = (wallhi[0] - walllo[0]) * (wallhi[1] - walllo[1]) *
+ vol_T = (wallhi[0] - walllo[0]) * (wallhi[1] - walllo[1]) *
(wallhi[2] - walllo[2]);
}
@@ -534,16 +534,16 @@ void PairLubricatePoly::init_style()
double vol_f = vol_P/vol_T;
if (!flagVF) vol_f = 0;
-
+
// set isotropic constants
-
+
if (flaglog == 0) {
R0 = 6*MY_PI*mu*(1.0 + 2.16*vol_f);
RT0 = 8*MY_PI*mu;
RS0 = 20.0/3.0*MY_PI*mu*(1.0 + 3.33*vol_f + 2.80*vol_f*vol_f);
} else {
R0 = 6*MY_PI*mu*(1.0 + 2.725*vol_f - 6.583*vol_f*vol_f);
- RT0 = 8*MY_PI*mu*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
+ RT0 = 8*MY_PI*mu*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
RS0 = 20.0/3.0*MY_PI*mu*(1.0 + 3.64*vol_f - 6.95*vol_f*vol_f);
}
@@ -553,9 +553,9 @@ void PairLubricatePoly::init_style()
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"deform") == 0) {
shearing = 1;
- if (((FixDeform *) modify->fix[i])->remapflag != V_REMAP)
- error->all(FLERR,"Using pair lubricate/poly with inconsistent "
- "fix deform remap option");
+ if (((FixDeform *) modify->fix[i])->remapflag != V_REMAP)
+ error->all(FLERR,"Using pair lubricate/poly with inconsistent "
+ "fix deform remap option");
}
// set Ef = 0 since used whether shearing or not
diff --git a/src/FLD/pair_lubricate_poly.h b/src/FLD/pair_lubricate_poly.h
index 0a31137dd35b3ef40678665cb1dd114c985e5161..28103b9f6435d1f5acbf49ba5baddb3bea23871e 100644
--- a/src/FLD/pair_lubricate_poly.h
+++ b/src/FLD/pair_lubricate_poly.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/GPU/fix_gpu.cpp b/src/GPU/fix_gpu.cpp
index c7a468cf459fb1091e01a186fecf23ac35564c71..190ee86dd97bd1c2b8339ce6c7ddd0d2e81296d8 100644
--- a/src/GPU/fix_gpu.cpp
+++ b/src/GPU/fix_gpu.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -45,7 +45,7 @@ extern double lmp_gpu_forces(double **f, double **tor, double *eatom,
FixGPU::FixGPU(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
- if (lmp->cuda)
+ if (lmp->cuda)
error->all(FLERR,"Cannot use fix GPU with USER-CUDA mode enabled");
if (narg < 7) error->all(FLERR,"Illegal fix GPU command");
@@ -73,7 +73,7 @@ FixGPU::FixGPU(LAMMPS *lmp, int narg, char **arg) :
_particle_split = force->numeric(arg[6]);
if (_particle_split==0 || _particle_split>1)
error->all(FLERR,"Illegal fix GPU command");
-
+
int nthreads = 1;
int threads_per_atom = -1;
if (narg == 9) {
@@ -88,15 +88,15 @@ FixGPU::FixGPU(LAMMPS *lmp, int narg, char **arg) :
if (nthreads < 1)
error->all(FLERR,"Illegal fix GPU command");
-
+
#ifndef _OPENMP
if (nthreads > 1)
error->all(FLERR,"No OpenMP support compiled in");
#endif
int gpu_flag = lmp_init_device(universe->uworld, world, first_gpu, last_gpu,
- _gpu_mode, _particle_split, nthreads,
- threads_per_atom);
+ _gpu_mode, _particle_split, nthreads,
+ threads_per_atom);
GPU_EXTRA::check_flag(gpu_flag,error,world);
}
@@ -125,11 +125,11 @@ void FixGPU::init()
if (_gpu_mode == GPU_NEIGH || _gpu_mode == GPU_HYB_NEIGH)
if (force->pair_match("hybrid",1) != NULL ||
- force->pair_match("hybrid/overlay",1) != NULL)
+ force->pair_match("hybrid/overlay",1) != NULL)
error->all(FLERR,"Cannot use pair hybrid with GPU neighbor builds");
if (_particle_split < 0)
if (force->pair_match("hybrid",1) != NULL ||
- force->pair_match("hybrid/overlay",1) != NULL)
+ force->pair_match("hybrid/overlay",1) != NULL)
error->all(FLERR,"Fix GPU split must be positive for hybrid pair styles");
}
@@ -140,7 +140,7 @@ void FixGPU::setup(int vflag)
if (_gpu_mode == GPU_NEIGH || _gpu_mode == GPU_HYB_NEIGH)
if (neighbor->exclude_setting()!=0)
error->all(FLERR,
- "Cannot use neigh_modify exclude with GPU neighbor builds");
+ "Cannot use neigh_modify exclude with GPU neighbor builds");
post_force(vflag);
}
diff --git a/src/GPU/fix_gpu.h b/src/GPU/fix_gpu.h
index d9856102f7620e59d41b562387b2d50352e957a8..88e8d3088911248a358b450138ce2f4725f3ff7f 100644
--- a/src/GPU/fix_gpu.h
+++ b/src/GPU/fix_gpu.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/GPU/gpu_extra.h b/src/GPU/gpu_extra.h
index 9299d3b571a06e9c8957d24f896369482dc54943..2c83806c003a2bc20875d69744c06410805afb94 100644
--- a/src/GPU/gpu_extra.h
+++ b/src/GPU/gpu_extra.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -24,33 +24,33 @@
namespace GPU_EXTRA {
inline void check_flag(int error_flag, LAMMPS_NS::Error *error,
- MPI_Comm &world) {
+ MPI_Comm &world) {
int all_success;
MPI_Allreduce(&error_flag, &all_success, 1, MPI_INT, MPI_MIN, world);
if (all_success != 0) {
if (all_success == -1)
- error->all(FLERR,
- "The package gpu command is required for gpu styles");
+ error->all(FLERR,
+ "The package gpu command is required for gpu styles");
else if (all_success == -2)
- error->all(FLERR,
- "Could not find/initialize a specified accelerator device");
+ error->all(FLERR,
+ "Could not find/initialize a specified accelerator device");
else if (all_success == -3)
- error->all(FLERR,"Insufficient memory on accelerator");
+ error->all(FLERR,"Insufficient memory on accelerator");
else if (all_success == -4)
- error->all(FLERR,"GPU library not compiled for this accelerator");
+ error->all(FLERR,"GPU library not compiled for this accelerator");
else if (all_success == -5)
- error->all(FLERR,
- "Double precision is not supported on this accelerator");
+ error->all(FLERR,
+ "Double precision is not supported on this accelerator");
else if (all_success == -6)
- error->all(FLERR,"Unable to initialize accelerator for use");
+ error->all(FLERR,"Unable to initialize accelerator for use");
else if (all_success == -7)
- error->all(FLERR,
+ error->all(FLERR,
"Accelerator sharing is not currently supported on system");
else if (all_success == -8)
- error->all(FLERR,
+ error->all(FLERR,
"GPU particle split must be set to 1 for this pair style.");
else
- error->all(FLERR,"Unknown error in GPU library");
+ error->all(FLERR,"Unknown error in GPU library");
}
};
diff --git a/src/GPU/pair_buck_coul_cut_gpu.cpp b/src/GPU/pair_buck_coul_cut_gpu.cpp
index a3db1e0dd302b4c0154169b58e103008135c55ca..9a7485713bab6645df9c7ccabc0dbf1ee2761cb9 100644
--- a/src/GPU/pair_buck_coul_cut_gpu.cpp
+++ b/src/GPU/pair_buck_coul_cut_gpu.cpp
@@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
-
+
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
-
+
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@@ -38,40 +38,40 @@
// External functions from cuda library for atom decomposition
int buckc_gpu_init(const int ntypes, double **cutsq, double **host_rhoinv,
- double **host_buck1, double **host_buck2, double **host_a,
- double **host_c, double **offset, double *special_lj,
- const int inum, const int nall, const int max_nbors,
- const int maxspecial, const double cell_size,
- int &gpu_mode, FILE *screen, double **host_cut_ljsq,
- double **host_cut_coulsq, double *host_special_coul,
- const double qqrd2e);
+ double **host_buck1, double **host_buck2, double **host_a,
+ double **host_c, double **offset, double *special_lj,
+ const int inum, const int nall, const int max_nbors,
+ const int maxspecial, const double cell_size,
+ int &gpu_mode, FILE *screen, double **host_cut_ljsq,
+ double **host_cut_coulsq, double *host_special_coul,
+ const double qqrd2e);
void buckc_gpu_clear();
int ** buckc_gpu_compute_n(const int ago, const int inum_full, const int nall,
- double **host_x, int *host_type, double *sublo,
- double *subhi, int *tag, int **nspecial,
- int **special, const bool eflag, const bool vflag,
- const bool eatom, const bool vatom, int &host_start,
- int **ilist, int **jnum, const double cpu_time,
- bool &success, double *host_q, double *boxlo,
- double *prd);
+ double **host_x, int *host_type, double *sublo,
+ double *subhi, int *tag, int **nspecial,
+ int **special, const bool eflag, const bool vflag,
+ const bool eatom, const bool vatom, int &host_start,
+ int **ilist, int **jnum, const double cpu_time,
+ bool &success, double *host_q, double *boxlo,
+ double *prd);
void buckc_gpu_compute(const int ago, const int inum_full, const int nall,
- double **host_x, int *host_type, int *ilist, int *numj,
- int **firstneigh, const bool eflag, const bool vflag,
- const bool eatom, const bool vatom, int &host_start,
- const double cpu_time, bool &success, double *host_q,
- const int nlocal, double *boxlo, double *prd);
+ double **host_x, int *host_type, int *ilist, int *numj,
+ int **firstneigh, const bool eflag, const bool vflag,
+ const bool eatom, const bool vatom, int &host_start,
+ const double cpu_time, bool &success, double *host_q,
+ const int nlocal, double *boxlo, double *prd);
double buckc_gpu_bytes();
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-PairBuckCoulCutGPU::PairBuckCoulCutGPU(LAMMPS *lmp) : PairBuckCoulCut(lmp),
- gpu_mode(GPU_FORCE)
+PairBuckCoulCutGPU::PairBuckCoulCutGPU(LAMMPS *lmp) : PairBuckCoulCut(lmp),
+ gpu_mode(GPU_FORCE)
{
respa_enable = 0;
cpu_time = 0.0;
- GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
+ GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
@@ -89,30 +89,30 @@ void PairBuckCoulCutGPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
-
+
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
-
+
bool success = true;
int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = buckc_gpu_compute_n(neighbor->ago, inum, nall,
- atom->x, atom->type, domain->sublo,
- domain->subhi, atom->tag, atom->nspecial,
- atom->special, eflag, vflag, eflag_atom,
- vflag_atom, host_start,
- &ilist, &numneigh, cpu_time, success,
- atom->q, domain->boxlo, domain->prd);
+ atom->x, atom->type, domain->sublo,
+ domain->subhi, atom->tag, atom->nspecial,
+ atom->special, eflag, vflag, eflag_atom,
+ vflag_atom, host_start,
+ &ilist, &numneigh, cpu_time, success,
+ atom->q, domain->boxlo, domain->prd);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
buckc_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
- ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
- vflag_atom, host_start, cpu_time, success, atom->q,
- atom->nlocal, domain->boxlo, domain->prd);
+ ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
+ vflag_atom, host_start, cpu_time, success, atom->q,
+ atom->nlocal, domain->boxlo, domain->prd);
}
if (!success)
error->one(FLERR,"Insufficient memory on accelerator");
@@ -130,9 +130,9 @@ void PairBuckCoulCutGPU::compute(int eflag, int vflag)
void PairBuckCoulCutGPU::init_style()
{
- if (force->newton_pair)
+ if (force->newton_pair)
error->all(FLERR,
- "Cannot use newton pair with buck/coul/cut/gpu pair style");
+ "Cannot use newton pair with buck/coul/cut/gpu pair style");
// Repeat cutsq calculation because done after call to init_style
double maxcut = -1.0;
@@ -154,18 +154,18 @@ void PairBuckCoulCutGPU::init_style()
int maxspecial=0;
if (atom->molecular)
maxspecial=atom->maxspecial;
- int success = buckc_gpu_init(atom->ntypes+1, cutsq, rhoinv, buck1, buck2,
- a, c, offset, force->special_lj, atom->nlocal,
- atom->nlocal+atom->nghost, 300, maxspecial,
- cell_size, gpu_mode, screen, cut_ljsq,
- cut_coulsq, force->special_coul, force->qqrd2e);
+ int success = buckc_gpu_init(atom->ntypes+1, cutsq, rhoinv, buck1, buck2,
+ a, c, offset, force->special_lj, atom->nlocal,
+ atom->nlocal+atom->nghost, 300, maxspecial,
+ cell_size, gpu_mode, screen, cut_ljsq,
+ cut_coulsq, force->special_coul, force->qqrd2e);
GPU_EXTRA::check_flag(success,error,world);
if (gpu_mode == GPU_FORCE) {
int irequest = neighbor->request(this);
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
- }
+ }
}
/* ---------------------------------------------------------------------- */
@@ -179,8 +179,8 @@ double PairBuckCoulCutGPU::memory_usage()
/* ---------------------------------------------------------------------- */
void PairBuckCoulCutGPU::cpu_compute(int start, int inum, int eflag, int vflag,
- int *ilist, int *numneigh,
- int **firstneigh) {
+ int *ilist, int *numneigh,
+ int **firstneigh) {
int i,j,ii,jj,jnum,itype,jtype;
double xtmp,ytmp,ztmp,qtmp,delx,dely,delz,evdwl,ecoul,fpair;
double rsq,r2inv,r6inv,forcecoul,forcebuck,factor_coul,factor_lj;
@@ -188,7 +188,7 @@ void PairBuckCoulCutGPU::cpu_compute(int start, int inum, int eflag, int vflag,
int *jlist;
evdwl = ecoul = 0.0;
-
+
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
@@ -196,7 +196,7 @@ void PairBuckCoulCutGPU::cpu_compute(int start, int inum, int eflag, int vflag,
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
double qqrd2e = force->qqrd2e;
-
+
// loop over neighbors of my atoms
for (ii = start; ii < inum; ii++) {
@@ -222,37 +222,37 @@ void PairBuckCoulCutGPU::cpu_compute(int start, int inum, int eflag, int vflag,
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- r = sqrt(rsq);
-
- if (rsq < cut_coulsq[itype][jtype])
- forcecoul = qqrd2e * qtmp*q[j]/r;
- else forcecoul = 0.0;
-
- if (rsq < cut_ljsq[itype][jtype]) {
- r6inv = r2inv*r2inv*r2inv;
- rexp = exp(-r*rhoinv[itype][jtype]);
- forcebuck = buck1[itype][jtype]*r*rexp - buck2[itype][jtype]*r6inv;
- } else forcebuck = 0.0;
-
- fpair = (factor_coul*forcecoul + factor_lj*forcebuck) * r2inv;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
-
- if (eflag) {
- if (rsq < cut_coulsq[itype][jtype])
- ecoul = factor_coul * qqrd2e * qtmp*q[j]/r;
- else ecoul = 0.0;
- if (rsq < cut_ljsq[itype][jtype]) {
- evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv -
- offset[itype][jtype];
- evdwl *= factor_lj;
- } else evdwl = 0.0;
- }
-
- if (evflag) ev_tally_full(i,evdwl,ecoul,fpair,delx,dely,delz);
+ r2inv = 1.0/rsq;
+ r = sqrt(rsq);
+
+ if (rsq < cut_coulsq[itype][jtype])
+ forcecoul = qqrd2e * qtmp*q[j]/r;
+ else forcecoul = 0.0;
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ r6inv = r2inv*r2inv*r2inv;
+ rexp = exp(-r*rhoinv[itype][jtype]);
+ forcebuck = buck1[itype][jtype]*r*rexp - buck2[itype][jtype]*r6inv;
+ } else forcebuck = 0.0;
+
+ fpair = (factor_coul*forcecoul + factor_lj*forcebuck) * r2inv;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+
+ if (eflag) {
+ if (rsq < cut_coulsq[itype][jtype])
+ ecoul = factor_coul * qqrd2e * qtmp*q[j]/r;
+ else ecoul = 0.0;
+ if (rsq < cut_ljsq[itype][jtype]) {
+ evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv -
+ offset[itype][jtype];
+ evdwl *= factor_lj;
+ } else evdwl = 0.0;
+ }
+
+ if (evflag) ev_tally_full(i,evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
diff --git a/src/GPU/pair_buck_coul_cut_gpu.h b/src/GPU/pair_buck_coul_cut_gpu.h
index 85a4fafa5610278d1b0faee65762239a36bfe405..e4535a197ba653622973dc5a3ffdbe80a2e89546 100644
--- a/src/GPU/pair_buck_coul_cut_gpu.h
+++ b/src/GPU/pair_buck_coul_cut_gpu.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/GPU/pair_buck_coul_long_gpu.cpp b/src/GPU/pair_buck_coul_long_gpu.cpp
index 724f7846f2de13cdc024039a2c636c9a0ccdfc9c..6787062a09e70aa6134ff7da3391dd21cf8c4d14 100644
--- a/src/GPU/pair_buck_coul_long_gpu.cpp
+++ b/src/GPU/pair_buck_coul_long_gpu.cpp
@@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
-
+
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
-
+
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@@ -47,40 +47,40 @@
// External functions from cuda library for atom decomposition
int buckcl_gpu_init(const int ntypes, double **cutsq, double **host_rhoinv,
- double **host_buck1, double **host_buck2, double **host_a,
- double **host_c, double **offset, double *special_lj,
- const int inum, const int nall, const int max_nbors,
- const int maxspecial, const double cell_size,
- int &gpu_mode, FILE *screen, double **host_cut_ljsq,
- double host_cut_coulsq, double *host_special_coul,
- const double qqrd2e, const double g_ewald);
+ double **host_buck1, double **host_buck2, double **host_a,
+ double **host_c, double **offset, double *special_lj,
+ const int inum, const int nall, const int max_nbors,
+ const int maxspecial, const double cell_size,
+ int &gpu_mode, FILE *screen, double **host_cut_ljsq,
+ double host_cut_coulsq, double *host_special_coul,
+ const double qqrd2e, const double g_ewald);
void buckcl_gpu_clear();
int** buckcl_gpu_compute_n(const int ago, const int inum_full, const int nall,
- double **host_x, int *host_type, double *sublo,
- double *subhi, int *tag, int **nspecial,
- int **special, const bool eflag, const bool vflag,
- const bool eatom, const bool vatom, int &host_start,
- int **ilist, int **jnum, const double cpu_time,
- bool &success, double *host_q, double *boxlo,
- double *prd);
+ double **host_x, int *host_type, double *sublo,
+ double *subhi, int *tag, int **nspecial,
+ int **special, const bool eflag, const bool vflag,
+ const bool eatom, const bool vatom, int &host_start,
+ int **ilist, int **jnum, const double cpu_time,
+ bool &success, double *host_q, double *boxlo,
+ double *prd);
void buckcl_gpu_compute(const int ago, const int inum_full, const int nall,
- double **host_x, int *host_type, int *ilist, int *numj,
- int **firstneigh, const bool eflag, const bool vflag,
- const bool eatom, const bool vatom, int &host_start,
- const double cpu_time, bool &success, double *host_q,
- const int nlocal, double *boxlo, double *prd);
+ double **host_x, int *host_type, int *ilist, int *numj,
+ int **firstneigh, const bool eflag, const bool vflag,
+ const bool eatom, const bool vatom, int &host_start,
+ const double cpu_time, bool &success, double *host_q,
+ const int nlocal, double *boxlo, double *prd);
double buckcl_gpu_bytes();
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-PairBuckCoulLongGPU::PairBuckCoulLongGPU(LAMMPS *lmp) :
+PairBuckCoulLongGPU::PairBuckCoulLongGPU(LAMMPS *lmp) :
PairBuckCoulLong(lmp), gpu_mode(GPU_FORCE)
{
respa_enable = 0;
cpu_time = 0.0;
- GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
+ GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
@@ -98,30 +98,30 @@ void PairBuckCoulLongGPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
-
+
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
-
+
bool success = true;
- int *ilist, *numneigh, **firstneigh;
+ int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = buckcl_gpu_compute_n(neighbor->ago, inum, nall, atom->x,
- atom->type, domain->sublo, domain->subhi,
- atom->tag, atom->nspecial, atom->special,
- eflag, vflag, eflag_atom, vflag_atom,
- host_start, &ilist, &numneigh, cpu_time,
- success, atom->q, domain->boxlo,
- domain->prd);
+ atom->type, domain->sublo, domain->subhi,
+ atom->tag, atom->nspecial, atom->special,
+ eflag, vflag, eflag_atom, vflag_atom,
+ host_start, &ilist, &numneigh, cpu_time,
+ success, atom->q, domain->boxlo,
+ domain->prd);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
buckcl_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
- ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
- vflag_atom, host_start, cpu_time, success, atom->q,
- atom->nlocal, domain->boxlo, domain->prd);
+ ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
+ vflag_atom, host_start, cpu_time, success, atom->q,
+ atom->nlocal, domain->boxlo, domain->prd);
}
if (!success)
error->one(FLERR,"Insufficient memory on accelerator");
@@ -141,10 +141,10 @@ void PairBuckCoulLongGPU::init_style()
{
if (!atom->q_flag)
error->all(FLERR,
- "Pair style buck/coul/long/gpu requires atom attribute q");
- if (force->newton_pair)
+ "Pair style buck/coul/long/gpu requires atom attribute q");
+ if (force->newton_pair)
error->all(FLERR,
- "Cannot use newton pair with buck/coul/long/gpu pair style");
+ "Cannot use newton pair with buck/coul/long/gpu pair style");
// Repeat cutsq calculation because done after call to init_style
double maxcut = -1.0;
@@ -174,12 +174,12 @@ void PairBuckCoulLongGPU::init_style()
int maxspecial=0;
if (atom->molecular)
maxspecial=atom->maxspecial;
- int success = buckcl_gpu_init(atom->ntypes+1, cutsq, rhoinv, buck1, buck2,
- a, c, offset, force->special_lj, atom->nlocal,
- atom->nlocal+atom->nghost, 300, maxspecial,
- cell_size, gpu_mode, screen, cut_ljsq,
- cut_coulsq, force->special_coul, force->qqrd2e,
- g_ewald);
+ int success = buckcl_gpu_init(atom->ntypes+1, cutsq, rhoinv, buck1, buck2,
+ a, c, offset, force->special_lj, atom->nlocal,
+ atom->nlocal+atom->nghost, 300, maxspecial,
+ cell_size, gpu_mode, screen, cut_ljsq,
+ cut_coulsq, force->special_coul, force->qqrd2e,
+ g_ewald);
GPU_EXTRA::check_flag(success,error,world);
if (gpu_mode == GPU_FORCE) {
@@ -200,8 +200,8 @@ double PairBuckCoulLongGPU::memory_usage()
/* ---------------------------------------------------------------------- */
void PairBuckCoulLongGPU::cpu_compute(int start, int inum, int eflag,
- int vflag, int *ilist, int *numneigh,
- int **firstneigh)
+ int vflag, int *ilist, int *numneigh,
+ int **firstneigh)
{
int i,j,ii,jj,jnum,itype,jtype,itable;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
@@ -246,44 +246,44 @@ void PairBuckCoulLongGPU::cpu_compute(int start, int inum, int eflag,
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- r = sqrt(rsq);
- if (rsq < cut_coulsq) {
- grij = g_ewald * r;
- expm2 = exp(-grij*grij);
- t = 1.0 / (1.0 + EWALD_P*grij);
- erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
- prefactor = qqrd2e * qtmp*q[j]/r;
- forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
- if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
- } else forcecoul = 0.0;
-
- if (rsq < cut_ljsq[itype][jtype]) {
- r6inv = r2inv*r2inv*r2inv;
- rexp = exp(-r*rhoinv[itype][jtype]);
- forcebuck = buck1[itype][jtype]*r*rexp - buck2[itype][jtype]*r6inv;
- } else forcebuck = 0.0;
-
- fpair = (forcecoul + factor_lj*forcebuck) * r2inv;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
-
- if (eflag) {
- if (rsq < cut_coulsq) {
- ecoul = prefactor*erfc;
- if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
- } else ecoul = 0.0;
-
- if (rsq < cut_ljsq[itype][jtype]) {
- evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv -
- offset[itype][jtype];
- evdwl *= factor_lj;
- } else evdwl = 0.0;
- }
-
- if (evflag) ev_tally_full(i,evdwl,ecoul,fpair,delx,dely,delz);
+ r2inv = 1.0/rsq;
+ r = sqrt(rsq);
+ if (rsq < cut_coulsq) {
+ grij = g_ewald * r;
+ expm2 = exp(-grij*grij);
+ t = 1.0 / (1.0 + EWALD_P*grij);
+ erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
+ prefactor = qqrd2e * qtmp*q[j]/r;
+ forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
+ if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
+ } else forcecoul = 0.0;
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ r6inv = r2inv*r2inv*r2inv;
+ rexp = exp(-r*rhoinv[itype][jtype]);
+ forcebuck = buck1[itype][jtype]*r*rexp - buck2[itype][jtype]*r6inv;
+ } else forcebuck = 0.0;
+
+ fpair = (forcecoul + factor_lj*forcebuck) * r2inv;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+
+ if (eflag) {
+ if (rsq < cut_coulsq) {
+ ecoul = prefactor*erfc;
+ if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
+ } else ecoul = 0.0;
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv -
+ offset[itype][jtype];
+ evdwl *= factor_lj;
+ } else evdwl = 0.0;
+ }
+
+ if (evflag) ev_tally_full(i,evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
diff --git a/src/GPU/pair_buck_coul_long_gpu.h b/src/GPU/pair_buck_coul_long_gpu.h
index 28b44b1094a870b2bbbed365b55334ee895aaf58..8c8315b1c9e0c44b00ca4d006e16b038b2a342cf 100644
--- a/src/GPU/pair_buck_coul_long_gpu.h
+++ b/src/GPU/pair_buck_coul_long_gpu.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/GPU/pair_buck_gpu.cpp b/src/GPU/pair_buck_gpu.cpp
index d297a212ab9aaab834616566773e049e69360017..56443acff298543ec2f8f320acd1ab13fa6c822c 100644
--- a/src/GPU/pair_buck_gpu.cpp
+++ b/src/GPU/pair_buck_gpu.cpp
@@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
-
+
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
-
+
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@@ -38,24 +38,24 @@
// External functions from cuda library for atom decomposition
int buck_gpu_init(const int ntypes, double **cutsq, double **host_rhoinv,
- double **host_buck1, double **host_buck2,
- double **host_a, double **host_c,
- double **offset, double *special_lj, const int inum,
- const int nall, const int max_nbors, const int maxspecial,
- const double cell_size, int &gpu_mode, FILE *screen);
+ double **host_buck1, double **host_buck2,
+ double **host_a, double **host_c,
+ double **offset, double *special_lj, const int inum,
+ const int nall, const int max_nbors, const int maxspecial,
+ const double cell_size, int &gpu_mode, FILE *screen);
void buck_gpu_clear();
int ** buck_gpu_compute_n(const int ago, const int inum_full, const int nall,
- double **host_x, int *host_type, double *sublo,
- double *subhi, int *tag, int **nspecial,
- int **special, const bool eflag, const bool vflag,
- const bool eatom, const bool vatom, int &host_start,
- int **ilist, int **jnum, const double cpu_time,
- bool &success);
+ double **host_x, int *host_type, double *sublo,
+ double *subhi, int *tag, int **nspecial,
+ int **special, const bool eflag, const bool vflag,
+ const bool eatom, const bool vatom, int &host_start,
+ int **ilist, int **jnum, const double cpu_time,
+ bool &success);
void buck_gpu_compute(const int ago, const int inum_full, const int nall,
- double **host_x, int *host_type, int *ilist, int *numj,
- int **firstneigh, const bool eflag, const bool vflag,
- const bool eatom, const bool vatom, int &host_start,
- const double cpu_time, bool &success);
+ double **host_x, int *host_type, int *ilist, int *numj,
+ int **firstneigh, const bool eflag, const bool vflag,
+ const bool eatom, const bool vatom, int &host_start,
+ const double cpu_time, bool &success);
double buck_gpu_bytes();
using namespace LAMMPS_NS;
@@ -66,7 +66,7 @@ PairBuckGPU::PairBuckGPU(LAMMPS *lmp) : PairBuck(lmp), gpu_mode(GPU_FORCE)
{
respa_enable = 0;
cpu_time = 0.0;
- GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
+ GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
@@ -84,28 +84,28 @@ void PairBuckGPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
-
+
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
-
+
bool success = true;
int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = buck_gpu_compute_n(neighbor->ago, inum, nall,
- atom->x, atom->type, domain->sublo,
- domain->subhi, atom->tag, atom->nspecial,
- atom->special, eflag, vflag, eflag_atom,
- vflag_atom, host_start,
- &ilist, &numneigh, cpu_time, success);
+ atom->x, atom->type, domain->sublo,
+ domain->subhi, atom->tag, atom->nspecial,
+ atom->special, eflag, vflag, eflag_atom,
+ vflag_atom, host_start,
+ &ilist, &numneigh, cpu_time, success);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
buck_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
- ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
- vflag_atom, host_start, cpu_time, success);
+ ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
+ vflag_atom, host_start, cpu_time, success);
}
if (!success)
error->one(FLERR,"Insufficient memory on accelerator");
@@ -123,7 +123,7 @@ void PairBuckGPU::compute(int eflag, int vflag)
void PairBuckGPU::init_style()
{
- if (force->newton_pair)
+ if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with buck/gpu pair style");
// Repeat cutsq calculation because done after call to init_style
@@ -146,10 +146,10 @@ void PairBuckGPU::init_style()
int maxspecial=0;
if (atom->molecular)
maxspecial=atom->maxspecial;
- int success = buck_gpu_init(atom->ntypes+1, cutsq, rhoinv, buck1, buck2,
- a, c, offset, force->special_lj, atom->nlocal,
- atom->nlocal+atom->nghost, 300, maxspecial,
- cell_size, gpu_mode, screen);
+ int success = buck_gpu_init(atom->ntypes+1, cutsq, rhoinv, buck1, buck2,
+ a, c, offset, force->special_lj, atom->nlocal,
+ atom->nlocal+atom->nghost, 300, maxspecial,
+ cell_size, gpu_mode, screen);
GPU_EXTRA::check_flag(success,error,world);
if (gpu_mode == GPU_FORCE) {
@@ -169,8 +169,8 @@ double PairBuckGPU::memory_usage()
/* ---------------------------------------------------------------------- */
-void PairBuckGPU::cpu_compute(int start, int inum, int eflag, int vflag,
- int *ilist, int *numneigh, int **firstneigh) {
+void PairBuckGPU::cpu_compute(int start, int inum, int eflag, int vflag,
+ int *ilist, int *numneigh, int **firstneigh) {
int i,j,ii,jj,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,r2inv,r6inv,forcebuck,factor_lj;
@@ -205,24 +205,24 @@ void PairBuckGPU::cpu_compute(int start, int inum, int eflag, int vflag,
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
- r = sqrt(rsq);
- rexp = exp(-r*rhoinv[itype][jtype]);
- forcebuck = buck1[itype][jtype]*r*rexp - buck2[itype][jtype]*r6inv;
- fpair = factor_lj*forcebuck*r2inv;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
-
- if (eflag) {
- evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv -
- offset[itype][jtype];
- evdwl *= factor_lj;
- }
-
- if (evflag) ev_tally_full(i,evdwl,0.0,fpair,delx,dely,delz);
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
+ r = sqrt(rsq);
+ rexp = exp(-r*rhoinv[itype][jtype]);
+ forcebuck = buck1[itype][jtype]*r*rexp - buck2[itype][jtype]*r6inv;
+ fpair = factor_lj*forcebuck*r2inv;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+
+ if (eflag) {
+ evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv -
+ offset[itype][jtype];
+ evdwl *= factor_lj;
+ }
+
+ if (evflag) ev_tally_full(i,evdwl,0.0,fpair,delx,dely,delz);
}
}
}
diff --git a/src/GPU/pair_buck_gpu.h b/src/GPU/pair_buck_gpu.h
index 3969ca1b909387ba762635e013777545fcd913e7..8f8daab983e3d2fb9c7a064de24b7f031c462331 100644
--- a/src/GPU/pair_buck_gpu.h
+++ b/src/GPU/pair_buck_gpu.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/GPU/pair_coul_long_gpu.cpp b/src/GPU/pair_coul_long_gpu.cpp
index 349bb4a83789a2fe7119fb415854d3c438572dd1..3b8b522f9dc75aa8f099fe7991cfb2213964ab5b 100644
--- a/src/GPU/pair_coul_long_gpu.cpp
+++ b/src/GPU/pair_coul_long_gpu.cpp
@@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
-
+
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
-
+
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@@ -47,36 +47,36 @@
// External functions from cuda library for atom decomposition
int cl_gpu_init(const int nlocal, const int nall, const int max_nbors,
- const int maxspecial, const double cell_size, int &gpu_mode,
- FILE *screen, double host_cut_coulsq, double *host_special_coul,
- const double qqrd2e, const double g_ewald);
+ const int maxspecial, const double cell_size, int &gpu_mode,
+ FILE *screen, double host_cut_coulsq, double *host_special_coul,
+ const double qqrd2e, const double g_ewald);
void cl_gpu_clear();
int ** cl_gpu_compute_n(const int ago, const int inum,
- const int nall, double **host_x, int *host_type,
- double *sublo, double *subhi, int *tag,
- int **nspecial, int **special, const bool eflag,
- const bool vflag, const bool eatom, const bool vatom,
- int &host_start, int **ilist, int **jnum,
- const double cpu_time, bool &success, double *host_q,
- double *boxlo, double *prd);
+ const int nall, double **host_x, int *host_type,
+ double *sublo, double *subhi, int *tag,
+ int **nspecial, int **special, const bool eflag,
+ const bool vflag, const bool eatom, const bool vatom,
+ int &host_start, int **ilist, int **jnum,
+ const double cpu_time, bool &success, double *host_q,
+ double *boxlo, double *prd);
void cl_gpu_compute(const int ago, const int inum, const int nall,
- double **host_x, int *host_type, int *ilist, int *numj,
- int **firstneigh, const bool eflag, const bool vflag,
- const bool eatom, const bool vatom, int &host_start,
- const double cpu_time, bool &success, double *host_q,
- const int nlocal, double *boxlo, double *prd);
+ double **host_x, int *host_type, int *ilist, int *numj,
+ int **firstneigh, const bool eflag, const bool vflag,
+ const bool eatom, const bool vatom, int &host_start,
+ const double cpu_time, bool &success, double *host_q,
+ const int nlocal, double *boxlo, double *prd);
double cl_gpu_bytes();
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-PairCoulLongGPU::PairCoulLongGPU(LAMMPS *lmp) :
+PairCoulLongGPU::PairCoulLongGPU(LAMMPS *lmp) :
PairCoulLong(lmp), gpu_mode(GPU_FORCE)
{
respa_enable = 0;
cpu_time = 0.0;
- GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
+ GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
@@ -94,30 +94,30 @@ void PairCoulLongGPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
-
+
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
-
+
bool success = true;
- int *ilist, *numneigh, **firstneigh;
+ int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = cl_gpu_compute_n(neighbor->ago, inum, nall, atom->x,
- atom->type, domain->sublo, domain->subhi,
- atom->tag, atom->nspecial, atom->special,
- eflag, vflag, eflag_atom, vflag_atom,
- host_start, &ilist, &numneigh, cpu_time,
- success, atom->q, domain->boxlo,
- domain->prd);
+ atom->type, domain->sublo, domain->subhi,
+ atom->tag, atom->nspecial, atom->special,
+ eflag, vflag, eflag_atom, vflag_atom,
+ host_start, &ilist, &numneigh, cpu_time,
+ success, atom->q, domain->boxlo,
+ domain->prd);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
cl_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
- ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
- vflag_atom, host_start, cpu_time, success, atom->q,
- atom->nlocal, domain->boxlo, domain->prd);
+ ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
+ vflag_atom, host_start, cpu_time, success, atom->q,
+ atom->nlocal, domain->boxlo, domain->prd);
}
if (!success)
error->one(FLERR,"Insufficient memory on accelerator");
@@ -139,7 +139,7 @@ void PairCoulLongGPU::init_style()
if (!atom->q_flag)
error->all(FLERR,"Pair style coul/long/gpu requires atom attribute q");
- if (force->newton_pair)
+ if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with coul/long/gpu pair style");
// Repeat cutsq calculation because done after call to init_style
@@ -160,9 +160,9 @@ void PairCoulLongGPU::init_style()
int maxspecial=0;
if (atom->molecular)
maxspecial=atom->maxspecial;
- int success = cl_gpu_init(atom->nlocal, atom->nlocal+atom->nghost, 300,
- maxspecial, cell_size, gpu_mode, screen, cut_coulsq,
- force->special_coul, force->qqrd2e, g_ewald);
+ int success = cl_gpu_init(atom->nlocal, atom->nlocal+atom->nghost, 300,
+ maxspecial, cell_size, gpu_mode, screen, cut_coulsq,
+ force->special_coul, force->qqrd2e, g_ewald);
GPU_EXTRA::check_flag(success,error,world);
@@ -184,8 +184,8 @@ double PairCoulLongGPU::memory_usage()
/* ---------------------------------------------------------------------- */
void PairCoulLongGPU::cpu_compute(int start, int inum, int eflag,
- int vflag, int *ilist, int *numneigh,
- int **firstneigh)
+ int vflag, int *ilist, int *numneigh,
+ int **firstneigh)
{
int i,j,ii,jj,jnum,itype,jtype,itable;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
@@ -230,49 +230,49 @@ void PairCoulLongGPU::cpu_compute(int start, int inum, int eflag,
r2inv = 1.0/rsq;
if (rsq < cut_coulsq) {
- if (!ncoultablebits || rsq <= tabinnersq) {
- r = sqrt(rsq);
- grij = g_ewald * r;
- expm2 = exp(-grij*grij);
- t = 1.0 / (1.0 + EWALD_P*grij);
- erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
- prefactor = qqrd2e * qtmp*q[j]/r;
- forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
- if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
- } else {
- union_int_float_t rsq_lookup;
- rsq_lookup.f = rsq;
- itable = rsq_lookup.i & ncoulmask;
- itable >>= ncoulshiftbits;
- fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
- table = ftable[itable] + fraction*dftable[itable];
- forcecoul = qtmp*q[j] * table;
- if (factor_coul < 1.0) {
- table = ctable[itable] + fraction*dctable[itable];
- prefactor = qtmp*q[j] * table;
- forcecoul -= (1.0-factor_coul)*prefactor;
- }
- }
-
- fpair = forcecoul * r2inv;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
-
- if (eflag) {
- if (rsq < cut_coulsq) {
- if (!ncoultablebits || rsq <= tabinnersq)
- ecoul = prefactor*erfc;
- else {
- table = etable[itable] + fraction*detable[itable];
- ecoul = qtmp*q[j] * table;
- }
- if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
- } else ecoul = 0.0;
- }
-
- if (evflag) ev_tally_full(i,0.0,ecoul,fpair,delx,dely,delz);
+ if (!ncoultablebits || rsq <= tabinnersq) {
+ r = sqrt(rsq);
+ grij = g_ewald * r;
+ expm2 = exp(-grij*grij);
+ t = 1.0 / (1.0 + EWALD_P*grij);
+ erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
+ prefactor = qqrd2e * qtmp*q[j]/r;
+ forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
+ if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
+ } else {
+ union_int_float_t rsq_lookup;
+ rsq_lookup.f = rsq;
+ itable = rsq_lookup.i & ncoulmask;
+ itable >>= ncoulshiftbits;
+ fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
+ table = ftable[itable] + fraction*dftable[itable];
+ forcecoul = qtmp*q[j] * table;
+ if (factor_coul < 1.0) {
+ table = ctable[itable] + fraction*dctable[itable];
+ prefactor = qtmp*q[j] * table;
+ forcecoul -= (1.0-factor_coul)*prefactor;
+ }
+ }
+
+ fpair = forcecoul * r2inv;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+
+ if (eflag) {
+ if (rsq < cut_coulsq) {
+ if (!ncoultablebits || rsq <= tabinnersq)
+ ecoul = prefactor*erfc;
+ else {
+ table = etable[itable] + fraction*detable[itable];
+ ecoul = qtmp*q[j] * table;
+ }
+ if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
+ } else ecoul = 0.0;
+ }
+
+ if (evflag) ev_tally_full(i,0.0,ecoul,fpair,delx,dely,delz);
}
}
}
diff --git a/src/GPU/pair_coul_long_gpu.h b/src/GPU/pair_coul_long_gpu.h
index e4f2b1c89909c037c7e4fac31927e5284c27d577..42285481ab88ee929f3c6349339529a0cb422924 100644
--- a/src/GPU/pair_coul_long_gpu.h
+++ b/src/GPU/pair_coul_long_gpu.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/GPU/pair_eam_alloy_gpu.cpp b/src/GPU/pair_eam_alloy_gpu.cpp
index 2cb80a34d770dcea18b0ab5d814bea58fa5950ad..2bf370e36fc97a520420aed0d6e2e6ac4aa9ddec 100644
--- a/src/GPU/pair_eam_alloy_gpu.cpp
+++ b/src/GPU/pair_eam_alloy_gpu.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -96,9 +96,9 @@ void PairEAMAlloyGPU::coeff(int narg, char **arg)
for (i = 1; i <= n; i++) {
for (j = i; j <= n; j++) {
if (map[i] >= 0 && map[j] >= 0) {
- setflag[i][j] = 1;
- if (i == j) atom->set_mass(i,setfl->mass[map[i]]);
- count++;
+ setflag[i][j] = 1;
+ if (i == j) atom->set_mass(i,setfl->mass[map[i]]);
+ count++;
}
}
}
@@ -147,7 +147,7 @@ void PairEAMAlloyGPU::read_file(char *filename)
int nwords = atom->count_words(line);
if (nwords != file->nelements + 1)
error->all(FLERR,"Incorrect element names in EAM potential file");
-
+
char **words = new char*[file->nelements+1];
nwords = 0;
strtok(line," \t\n\r\f");
@@ -164,7 +164,7 @@ void PairEAMAlloyGPU::read_file(char *filename)
if (me == 0) {
fgets(line,MAXLINE,fptr);
sscanf(line,"%d %lg %d %lg %lg",
- &file->nrho,&file->drho,&file->nr,&file->dr,&file->cut);
+ &file->nrho,&file->drho,&file->nr,&file->dr,&file->cut);
}
MPI_Bcast(&file->nrho,1,MPI_INT,0,world);
@@ -177,7 +177,7 @@ void PairEAMAlloyGPU::read_file(char *filename)
memory->create(file->frho,file->nelements,file->nrho+1,"pair:frho");
memory->create(file->rhor,file->nelements,file->nr+1,"pair:rhor");
memory->create(file->z2r,file->nelements,file->nelements,file->nr+1,
- "pair:z2r");
+ "pair:z2r");
int i,j,tmp;
for (i = 0; i < file->nelements; i++) {
@@ -226,7 +226,7 @@ void PairEAMAlloyGPU::file2array()
// allocate frho arrays
// nfrho = # of setfl elements + 1 for zero array
-
+
nfrho = setfl->nelements + 1;
memory->destroy(frho);
memory->create(frho,nfrho,nrho+1,"pair:frho");
@@ -307,12 +307,12 @@ void PairEAMAlloyGPU::file2array()
irow = map[i];
icol = map[j];
if (irow == -1 || icol == -1) {
- type2z2r[i][j] = 0;
- continue;
+ type2z2r[i][j] = 0;
+ continue;
}
if (irow < icol) {
- irow = map[j];
- icol = map[i];
+ irow = map[j];
+ icol = map[i];
}
n = 0;
for (m = 0; m < irow; m++) n += m + 1;
diff --git a/src/GPU/pair_eam_alloy_gpu.h b/src/GPU/pair_eam_alloy_gpu.h
index 3305a4ea2433710cf4b2b9041ba1969c6f97e787..6c3263173894a967340c97e93b9a05c8e2ee2ccc 100644
--- a/src/GPU/pair_eam_alloy_gpu.h
+++ b/src/GPU/pair_eam_alloy_gpu.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/GPU/pair_eam_fs_gpu.cpp b/src/GPU/pair_eam_fs_gpu.cpp
index 1b52920e3072acbdf5b7f8c5659125b02e6f42f5..efb5716088454a4864de3a020523a28ee50a3e2f 100644
--- a/src/GPU/pair_eam_fs_gpu.cpp
+++ b/src/GPU/pair_eam_fs_gpu.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -96,9 +96,9 @@ void PairEAMFSGPU::coeff(int narg, char **arg)
for (i = 1; i <= n; i++) {
for (j = i; j <= n; j++) {
if (map[i] >= 0 && map[j] >= 0) {
- setflag[i][j] = 1;
- if (i == j) atom->set_mass(i,fs->mass[map[i]]);
- count++;
+ setflag[i][j] = 1;
+ if (i == j) atom->set_mass(i,fs->mass[map[i]]);
+ count++;
}
}
}
@@ -147,7 +147,7 @@ void PairEAMFSGPU::read_file(char *filename)
int nwords = atom->count_words(line);
if (nwords != file->nelements + 1)
error->all(FLERR,"Incorrect element names in EAM potential file");
-
+
char **words = new char*[file->nelements+1];
nwords = 0;
strtok(line," \t\n\r\f");
@@ -164,7 +164,7 @@ void PairEAMFSGPU::read_file(char *filename)
if (me == 0) {
fgets(line,MAXLINE,fptr);
sscanf(line,"%d %lg %d %lg %lg",
- &file->nrho,&file->drho,&file->nr,&file->dr,&file->cut);
+ &file->nrho,&file->drho,&file->nr,&file->dr,&file->cut);
}
MPI_Bcast(&file->nrho,1,MPI_INT,0,world);
@@ -175,11 +175,11 @@ void PairEAMFSGPU::read_file(char *filename)
file->mass = new double[file->nelements];
memory->create(file->frho,file->nelements,file->nrho+1,
- "pair:frho");
+ "pair:frho");
memory->create(file->rhor,file->nelements,file->nelements,
- file->nr+1,"pair:rhor");
+ file->nr+1,"pair:rhor");
memory->create(file->z2r,file->nelements,file->nelements,
- file->nr+1,"pair:z2r");
+ file->nr+1,"pair:z2r");
int i,j,tmp;
for (i = 0; i < file->nelements; i++) {
@@ -231,7 +231,7 @@ void PairEAMFSGPU::file2array()
// allocate frho arrays
// nfrho = # of fs elements + 1 for zero array
-
+
nfrho = fs->nelements + 1;
memory->destroy(frho);
memory->create(frho,nfrho,nrho+1,"pair:frho");
@@ -316,12 +316,12 @@ void PairEAMFSGPU::file2array()
irow = map[i];
icol = map[j];
if (irow == -1 || icol == -1) {
- type2z2r[i][j] = 0;
- continue;
+ type2z2r[i][j] = 0;
+ continue;
}
if (irow < icol) {
- irow = map[j];
- icol = map[i];
+ irow = map[j];
+ icol = map[i];
}
n = 0;
for (m = 0; m < irow; m++) n += m + 1;
diff --git a/src/GPU/pair_eam_fs_gpu.h b/src/GPU/pair_eam_fs_gpu.h
index 49733e57396fd3fb557083bfc0164fb685688aed..06aaa2c645569f8b1fb655d6d63113ce0428349f 100644
--- a/src/GPU/pair_eam_fs_gpu.h
+++ b/src/GPU/pair_eam_fs_gpu.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/GPU/pair_eam_gpu.cpp b/src/GPU/pair_eam_gpu.cpp
index 8342d8a620bde15d64c4bc87ec3733d836ac997a..344409cd349f1de1472e4476c95e110dc5419173 100644
--- a/src/GPU/pair_eam_gpu.cpp
+++ b/src/GPU/pair_eam_gpu.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -38,30 +38,30 @@ using namespace LAMMPS_NS;
// External functions from cuda library for atom decomposition
int eam_gpu_init(const int ntypes, double host_cutforcesq,
- int **host_type2rhor, int **host_type2z2r,
+ int **host_type2rhor, int **host_type2z2r,
int *host_type2frho, double ***host_rhor_spline,
- double ***host_z2r_spline, double ***host_frho_spline,
+ double ***host_z2r_spline, double ***host_frho_spline,
double rdr, double rdrho, int nrhor, int nrho, int nz2r,
- int nfrho, int nr, const int nlocal, const int nall,
- const int max_nbors, const int maxspecial,
- const double cell_size, int &gpu_mode, FILE *screen,
- int &fp_size);
+ int nfrho, int nr, const int nlocal, const int nall,
+ const int max_nbors, const int maxspecial,
+ const double cell_size, int &gpu_mode, FILE *screen,
+ int &fp_size);
void eam_gpu_clear();
int** eam_gpu_compute_n(const int ago, const int inum_full, const int nall,
- double **host_x, int *host_type, double *sublo,
- double *subhi, int *tag, int **nspecial, int **special,
- const bool eflag, const bool vflag, const bool eatom,
- const bool vatom, int &host_start, int **ilist,
- int **jnum, const double cpu_time, bool &success,
- int &inum, void **fp_ptr);
-void eam_gpu_compute(const int ago, const int inum_full, const int nlocal,
- const int nall,double **host_x, int *host_type,
- int *ilist, int *numj, int **firstneigh,
- const bool eflag, const bool vflag,
- const bool eatom, const bool vatom, int &host_start,
- const double cpu_time, bool &success, void **fp_ptr);
+ double **host_x, int *host_type, double *sublo,
+ double *subhi, int *tag, int **nspecial, int **special,
+ const bool eflag, const bool vflag, const bool eatom,
+ const bool vatom, int &host_start, int **ilist,
+ int **jnum, const double cpu_time, bool &success,
+ int &inum, void **fp_ptr);
+void eam_gpu_compute(const int ago, const int inum_full, const int nlocal,
+ const int nall,double **host_x, int *host_type,
+ int *ilist, int *numj, int **firstneigh,
+ const bool eflag, const bool vflag,
+ const bool eatom, const bool vatom, int &host_start,
+ const double cpu_time, bool &success, void **fp_ptr);
void eam_gpu_compute_force(int *ilist, const bool eflag, const bool vflag,
- const bool eatom, const bool vatom);
+ const bool eatom, const bool vatom);
double eam_gpu_bytes();
/* ---------------------------------------------------------------------- */
@@ -70,7 +70,7 @@ PairEAMGPU::PairEAMGPU(LAMMPS *lmp) : PairEAM(lmp), gpu_mode(GPU_FORCE)
{
respa_enable = 0;
cpu_time = 0.0;
- GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
+ GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
@@ -100,44 +100,44 @@ void PairEAMGPU::compute(int eflag, int vflag)
evdwl = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = eflag_global = eflag_atom = 0;
-
+
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
// compute density on each atom on GPU
- int nall = atom->nlocal + atom->nghost;
+ int nall = atom->nlocal + atom->nghost;
int inum, host_start, inum_dev;
-
+
bool success = true;
- int *ilist, *numneigh, **firstneigh;
- if (gpu_mode != GPU_FORCE) {
+ int *ilist, *numneigh, **firstneigh;
+ if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = eam_gpu_compute_n(neighbor->ago, inum, nall, atom->x,
- atom->type, domain->sublo, domain->subhi,
- atom->tag, atom->nspecial, atom->special,
- eflag, vflag, eflag_atom, vflag_atom,
- host_start, &ilist, &numneigh, cpu_time,
- success, inum_dev, &fp_pinned);
+ atom->type, domain->sublo, domain->subhi,
+ atom->tag, atom->nspecial, atom->special,
+ eflag, vflag, eflag_atom, vflag_atom,
+ host_start, &ilist, &numneigh, cpu_time,
+ success, inum_dev, &fp_pinned);
} else { // gpu_mode == GPU_FORCE
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
eam_gpu_compute(neighbor->ago, inum, nlocal, nall, atom->x, atom->type,
- ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
- vflag_atom, host_start, cpu_time, success, &fp_pinned);
+ ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
+ vflag_atom, host_start, cpu_time, success, &fp_pinned);
}
-
+
if (!success)
error->one(FLERR,"Insufficient memory on accelerator");
// communicate derivative of embedding function
comm->forward_comm_pair(this);
-
+
// compute forces on each atom on GPU
- if (gpu_mode != GPU_FORCE)
+ if (gpu_mode != GPU_FORCE)
eam_gpu_compute_force(NULL, eflag, vflag, eflag_atom, vflag_atom);
else
eam_gpu_compute_force(ilist, eflag, vflag, eflag_atom, vflag_atom);
@@ -149,14 +149,14 @@ void PairEAMGPU::compute(int eflag, int vflag)
void PairEAMGPU::init_style()
{
- if (force->newton_pair)
+ if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with eam/gpu pair style");
-
+
// convert read-in file(s) to arrays and spline them
file2array();
array2spline();
-
+
// Repeat cutsq calculation because done after call to init_style
double maxcut = -1.0;
double cut;
@@ -173,18 +173,18 @@ void PairEAMGPU::init_style()
}
}
double cell_size = sqrt(maxcut) + neighbor->skin;
-
+
int maxspecial=0;
if (atom->molecular)
maxspecial=atom->maxspecial;
int fp_size;
int success = eam_gpu_init(atom->ntypes+1, cutforcesq, type2rhor, type2z2r,
- type2frho, rhor_spline, z2r_spline, frho_spline,
- rdr, rdrho, nrhor, nrho, nz2r, nfrho, nr,
- atom->nlocal, atom->nlocal+atom->nghost, 300,
- maxspecial, cell_size, gpu_mode, screen, fp_size);
+ type2frho, rhor_spline, z2r_spline, frho_spline,
+ rdr, rdrho, nrhor, nrho, nz2r, nfrho, nr,
+ atom->nlocal, atom->nlocal+atom->nghost, 300,
+ maxspecial, cell_size, gpu_mode, screen, fp_size);
GPU_EXTRA::check_flag(success,error,world);
-
+
if (gpu_mode == GPU_FORCE) {
int irequest = neighbor->request(this);
neighbor->requests[irequest]->half = 0;
@@ -199,8 +199,8 @@ void PairEAMGPU::init_style()
/* ---------------------------------------------------------------------- */
-int PairEAMGPU::pack_comm(int n, int *list, double *buf, int pbc_flag,
- int *pbc)
+int PairEAMGPU::pack_comm(int n, int *list, double *buf, int pbc_flag,
+ int *pbc)
{
int i,j,m;
diff --git a/src/GPU/pair_eam_gpu.h b/src/GPU/pair_eam_gpu.h
index 24c9e22f324aab6579d1aab46e8278a09d5f0d00..08a2013efeb8224ba8a1ec044c92eb970dc982ba 100644
--- a/src/GPU/pair_eam_gpu.h
+++ b/src/GPU/pair_eam_gpu.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -44,7 +44,7 @@ class PairEAMGPU : public PairEAM {
double cpu_time;
int *gpulist;
void *fp_pinned;
- bool fp_single;
+ bool fp_single;
};
}
diff --git a/src/GPU/pair_gayberne_gpu.cpp b/src/GPU/pair_gayberne_gpu.cpp
index f4a094b7aba3bf7bb8f6cc63ae6799291fc9fbb8..c4ddc17e383c31326442f6020249e1a96b3d2315 100644
--- a/src/GPU/pair_gayberne_gpu.cpp
+++ b/src/GPU/pair_gayberne_gpu.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -40,26 +40,26 @@
// External functions from cuda library for atom decomposition
int gb_gpu_init(const int ntypes, const double gamma, const double upsilon,
- const double mu, double **shape, double **well, double **cutsq,
- double **sigma, double **epsilon, double *host_lshape,
- int **form, double **host_lj1, double **host_lj2,
- double **host_lj3, double **host_lj4, double **offset,
- double *special_lj, const int nlocal, const int nall,
- const int max_nbors, const int maxspecial,
- const double cell_size, int &gpu_mode, FILE *screen);
+ const double mu, double **shape, double **well, double **cutsq,
+ double **sigma, double **epsilon, double *host_lshape,
+ int **form, double **host_lj1, double **host_lj2,
+ double **host_lj3, double **host_lj4, double **offset,
+ double *special_lj, const int nlocal, const int nall,
+ const int max_nbors, const int maxspecial,
+ const double cell_size, int &gpu_mode, FILE *screen);
void gb_gpu_clear();
int ** gb_gpu_compute_n(const int ago, const int inum, const int nall,
- double **host_x, int *host_type, double *sublo,
- double *subhi, int *tag, int **nspecial, int **special,
- const bool eflag, const bool vflag,
- const bool eatom, const bool vatom, int &host_start,
- int **ilist, int **jnum, const double cpu_time,
- bool &success, double **host_quat);
+ double **host_x, int *host_type, double *sublo,
+ double *subhi, int *tag, int **nspecial, int **special,
+ const bool eflag, const bool vflag,
+ const bool eatom, const bool vatom, int &host_start,
+ int **ilist, int **jnum, const double cpu_time,
+ bool &success, double **host_quat);
int * gb_gpu_compute(const int ago, const int inum, const int nall,
- double **host_x, int *host_type, int *ilist, int *numj,
- int **firstneigh, const bool eflag, const bool vflag,
- const bool eatom, const bool vatom, int &host_start,
- const double cpu_time, bool &success, double **host_quat);
+ double **host_x, int *host_type, int *ilist, int *numj,
+ int **firstneigh, const bool eflag, const bool vflag,
+ const bool eatom, const bool vatom, int &host_start,
+ const double cpu_time, bool &success, double **host_quat);
double gb_gpu_bytes();
using namespace LAMMPS_NS;
@@ -72,11 +72,11 @@ PairGayBerneGPU::PairGayBerneGPU(LAMMPS *lmp) : PairGayBerne(lmp),
gpu_mode(GPU_FORCE)
{
avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
- if (!avec)
+ if (!avec)
error->all(FLERR,"Pair gayberne/gpu requires atom style ellipsoid");
quat_nmax = 0;
quat = NULL;
- GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
+ GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
@@ -101,7 +101,7 @@ void PairGayBerneGPU::compute(int eflag, int vflag)
int inum, host_start;
bool success = true;
- int *ilist, *numneigh, **firstneigh;
+ int *ilist, *numneigh, **firstneigh;
if (nall > quat_nmax) {
quat_nmax = static_cast<int>(1.1 * nall);
@@ -122,19 +122,19 @@ void PairGayBerneGPU::compute(int eflag, int vflag)
if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = gb_gpu_compute_n(neighbor->ago, inum, nall, atom->x,
- atom->type, domain->sublo, domain->subhi,
- atom->tag, atom->nspecial, atom->special,
- eflag, vflag, eflag_atom, vflag_atom,
- host_start, &ilist, &numneigh, cpu_time,
- success, quat);
+ atom->type, domain->sublo, domain->subhi,
+ atom->tag, atom->nspecial, atom->special,
+ eflag, vflag, eflag_atom, vflag_atom,
+ host_start, &ilist, &numneigh, cpu_time,
+ success, quat);
} else {
inum = list->inum;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
ilist = gb_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
- list->ilist, numneigh, firstneigh, eflag, vflag,
- eflag_atom, vflag_atom, host_start,
- cpu_time, success, quat);
+ list->ilist, numneigh, firstneigh, eflag, vflag,
+ eflag_atom, vflag_atom, host_start,
+ cpu_time, success, quat);
}
if (!success)
error->one(FLERR,"Insufficient memory on accelerator");
@@ -152,7 +152,7 @@ void PairGayBerneGPU::compute(int eflag, int vflag)
void PairGayBerneGPU::init_style()
{
- if (force->newton_pair)
+ if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with gayberne/gpu pair style");
if (!atom->ellipsoid_flag)
error->all(FLERR,"Pair gayberne/gpu requires atom style ellipsoid");
@@ -169,7 +169,7 @@ void PairGayBerneGPU::init_style()
shape2[i][0] = shape1[i][0]*shape1[i][0];
shape2[i][1] = shape1[i][1]*shape1[i][1];
shape2[i][2] = shape1[i][2]*shape1[i][2];
- lshape[i] = (shape1[i][0]*shape1[i][1]+shape1[i][2]*shape1[i][2]) *
+ lshape[i] = (shape1[i][0]*shape1[i][1]+shape1[i][2]*shape1[i][2]) *
sqrt(shape1[i][0]*shape1[i][1]);
}
@@ -194,11 +194,11 @@ void PairGayBerneGPU::init_style()
int maxspecial=0;
if (atom->molecular)
maxspecial=atom->maxspecial;
- int success = gb_gpu_init(atom->ntypes+1, gamma, upsilon, mu,
- shape2, well, cutsq, sigma, epsilon, lshape, form,
- lj1, lj2, lj3, lj4, offset, force->special_lj,
- atom->nlocal, atom->nlocal+atom->nghost, 300,
- maxspecial, cell_size, gpu_mode, screen);
+ int success = gb_gpu_init(atom->ntypes+1, gamma, upsilon, mu,
+ shape2, well, cutsq, sigma, epsilon, lshape, form,
+ lj1, lj2, lj3, lj4, offset, force->special_lj,
+ atom->nlocal, atom->nlocal+atom->nghost, 300,
+ maxspecial, cell_size, gpu_mode, screen);
GPU_EXTRA::check_flag(success,error,world);
if (gpu_mode == GPU_FORCE) {
@@ -221,7 +221,7 @@ double PairGayBerneGPU::memory_usage()
/* ---------------------------------------------------------------------- */
void PairGayBerneGPU::cpu_compute(int start, int inum, int eflag, int vflag,
- int *ilist, int *numneigh, int **firstneigh)
+ int *ilist, int *numneigh, int **firstneigh)
{
int i,j,ii,jj,jnum,itype,jtype;
double evdwl,one_eng,rsq,r2inv,r6inv,forcelj,factor_lj;
@@ -273,68 +273,68 @@ void PairGayBerneGPU::cpu_compute(int start, int inum, int eflag, int vflag,
if (rsq < cutsq[itype][jtype]) {
- switch (form[itype][jtype]) {
- case SPHERE_SPHERE:
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- forcelj *= -r2inv;
- if (eflag) one_eng =
- r6inv*(r6inv*lj3[itype][jtype]-lj4[itype][jtype]) -
- offset[itype][jtype];
- fforce[0] = r12[0]*forcelj;
- fforce[1] = r12[1]*forcelj;
- fforce[2] = r12[2]*forcelj;
- ttor[0] = ttor[1] = ttor[2] = 0.0;
- rtor[0] = rtor[1] = rtor[2] = 0.0;
- break;
+ switch (form[itype][jtype]) {
+ case SPHERE_SPHERE:
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ forcelj *= -r2inv;
+ if (eflag) one_eng =
+ r6inv*(r6inv*lj3[itype][jtype]-lj4[itype][jtype]) -
+ offset[itype][jtype];
+ fforce[0] = r12[0]*forcelj;
+ fforce[1] = r12[1]*forcelj;
+ fforce[2] = r12[2]*forcelj;
+ ttor[0] = ttor[1] = ttor[2] = 0.0;
+ rtor[0] = rtor[1] = rtor[2] = 0.0;
+ break;
case SPHERE_ELLIPSE:
- jquat = bonus[ellipsoid[j]].quat;
- MathExtra::quat_to_mat_trans(jquat,a2);
- MathExtra::diag_times3(well[jtype],a2,temp);
- MathExtra::transpose_times3(a2,temp,b2);
- MathExtra::diag_times3(shape2[jtype],a2,temp);
- MathExtra::transpose_times3(a2,temp,g2);
- one_eng = gayberne_lj(j,i,a2,b2,g2,r12,rsq,fforce,rtor);
- ttor[0] = ttor[1] = ttor[2] = 0.0;
- break;
+ jquat = bonus[ellipsoid[j]].quat;
+ MathExtra::quat_to_mat_trans(jquat,a2);
+ MathExtra::diag_times3(well[jtype],a2,temp);
+ MathExtra::transpose_times3(a2,temp,b2);
+ MathExtra::diag_times3(shape2[jtype],a2,temp);
+ MathExtra::transpose_times3(a2,temp,g2);
+ one_eng = gayberne_lj(j,i,a2,b2,g2,r12,rsq,fforce,rtor);
+ ttor[0] = ttor[1] = ttor[2] = 0.0;
+ break;
case ELLIPSE_SPHERE:
- one_eng = gayberne_lj(i,j,a1,b1,g1,r12,rsq,fforce,ttor);
- rtor[0] = rtor[1] = rtor[2] = 0.0;
- break;
-
- default:
- jquat = bonus[ellipsoid[j]].quat;
- MathExtra::quat_to_mat_trans(jquat,a2);
- MathExtra::diag_times3(well[jtype],a2,temp);
- MathExtra::transpose_times3(a2,temp,b2);
- MathExtra::diag_times3(shape2[jtype],a2,temp);
- MathExtra::transpose_times3(a2,temp,g2);
- one_eng = gayberne_analytic(i,j,a1,a2,b1,b2,g1,g2,r12,rsq,
- fforce,ttor,rtor);
- break;
- }
+ one_eng = gayberne_lj(i,j,a1,b1,g1,r12,rsq,fforce,ttor);
+ rtor[0] = rtor[1] = rtor[2] = 0.0;
+ break;
+
+ default:
+ jquat = bonus[ellipsoid[j]].quat;
+ MathExtra::quat_to_mat_trans(jquat,a2);
+ MathExtra::diag_times3(well[jtype],a2,temp);
+ MathExtra::transpose_times3(a2,temp,b2);
+ MathExtra::diag_times3(shape2[jtype],a2,temp);
+ MathExtra::transpose_times3(a2,temp,g2);
+ one_eng = gayberne_analytic(i,j,a1,a2,b1,b2,g1,g2,r12,rsq,
+ fforce,ttor,rtor);
+ break;
+ }
fforce[0] *= factor_lj;
- fforce[1] *= factor_lj;
- fforce[2] *= factor_lj;
+ fforce[1] *= factor_lj;
+ fforce[2] *= factor_lj;
ttor[0] *= factor_lj;
- ttor[1] *= factor_lj;
- ttor[2] *= factor_lj;
+ ttor[1] *= factor_lj;
+ ttor[2] *= factor_lj;
f[i][0] += fforce[0];
- f[i][1] += fforce[1];
- f[i][2] += fforce[2];
+ f[i][1] += fforce[1];
+ f[i][2] += fforce[2];
tor[i][0] += ttor[0];
- tor[i][1] += ttor[1];
- tor[i][2] += ttor[2];
+ tor[i][1] += ttor[1];
+ tor[i][2] += ttor[2];
if (eflag) evdwl = factor_lj*one_eng;
- if (evflag) ev_tally_xyz_full(i,evdwl,0.0,fforce[0],fforce[1],fforce[2],
- -r12[0],-r12[1],-r12[2]);
+ if (evflag) ev_tally_xyz_full(i,evdwl,0.0,fforce[0],fforce[1],fforce[2],
+ -r12[0],-r12[1],-r12[2]);
}
}
}
diff --git a/src/GPU/pair_gayberne_gpu.h b/src/GPU/pair_gayberne_gpu.h
index 00e80a965b65c18d63598dca79990e0e60838f8f..cdfdeb8932d0a44a17a92968f8f05730f8bffd20 100644
--- a/src/GPU/pair_gayberne_gpu.h
+++ b/src/GPU/pair_gayberne_gpu.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/GPU/pair_lj96_cut_gpu.cpp b/src/GPU/pair_lj96_cut_gpu.cpp
index b9c70b80afa61205b3f199defbdcfa05097eeebd..cd61efe8ed7d6c9a41619f654991868c924869d4 100644
--- a/src/GPU/pair_lj96_cut_gpu.cpp
+++ b/src/GPU/pair_lj96_cut_gpu.cpp
@@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
-
+
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
-
+
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@@ -38,23 +38,23 @@
// External functions from cuda library for atom decomposition
int lj96_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
- double **host_lj2, double **host_lj3, double **host_lj4,
- double **offset, double *special_lj, const int nlocal,
- const int nall, const int max_nbors, const int maxspecial,
- const double cell_size, int &gpu_mode, FILE *screen);
+ double **host_lj2, double **host_lj3, double **host_lj4,
+ double **offset, double *special_lj, const int nlocal,
+ const int nall, const int max_nbors, const int maxspecial,
+ const double cell_size, int &gpu_mode, FILE *screen);
void lj96_gpu_clear();
int ** lj96_gpu_compute_n(const int ago, const int inum, const int nall,
- double **host_x, int *host_type, double *sublo,
- double *subhi, int *tag, int **nspecial,
- int **special, const bool eflag, const bool vflag,
- const bool eatom, const bool vatom, int &host_start,
- int **ilist, int **jnum,
- const double cpu_time, bool &success);
+ double **host_x, int *host_type, double *sublo,
+ double *subhi, int *tag, int **nspecial,
+ int **special, const bool eflag, const bool vflag,
+ const bool eatom, const bool vatom, int &host_start,
+ int **ilist, int **jnum,
+ const double cpu_time, bool &success);
void lj96_gpu_compute(const int ago, const int inum, const int nall,
double **host_x, int *host_type, int *ilist, int *numj,
- int **firstneigh, const bool eflag, const bool vflag,
- const bool eatom, const bool vatom, int &host_start,
- const double cpu_time, bool &success);
+ int **firstneigh, const bool eflag, const bool vflag,
+ const bool eatom, const bool vatom, int &host_start,
+ const double cpu_time, bool &success);
double lj96_gpu_bytes();
using namespace LAMMPS_NS;
@@ -65,7 +65,7 @@ PairLJ96CutGPU::PairLJ96CutGPU(LAMMPS *lmp) : PairLJ96Cut(lmp), gpu_mode(GPU_FOR
{
respa_enable = 0;
cpu_time = 0.0;
- GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
+ GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
@@ -83,28 +83,28 @@ void PairLJ96CutGPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
-
+
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
-
+
bool success = true;
- int *ilist, *numneigh, **firstneigh;
+ int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = lj96_gpu_compute_n(neighbor->ago, inum, nall, atom->x,
- atom->type, domain->sublo, domain->subhi,
- atom->tag, atom->nspecial, atom->special,
- eflag, vflag, eflag_atom, vflag_atom,
- host_start, &ilist, &numneigh, cpu_time,
- success);
+ atom->type, domain->sublo, domain->subhi,
+ atom->tag, atom->nspecial, atom->special,
+ eflag, vflag, eflag_atom, vflag_atom,
+ host_start, &ilist, &numneigh, cpu_time,
+ success);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
lj96_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
- ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
- vflag_atom, host_start, cpu_time, success);
+ ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
+ vflag_atom, host_start, cpu_time, success);
}
if (!success)
error->one(FLERR,"Insufficient memory on accelerator");
@@ -124,7 +124,7 @@ void PairLJ96CutGPU::init_style()
{
cut_respa = NULL;
- if (force->newton_pair)
+ if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with lj96/cut/gpu pair style");
// Repeat cutsq calculation because done after call to init_style
@@ -148,9 +148,9 @@ void PairLJ96CutGPU::init_style()
if (atom->molecular)
maxspecial=atom->maxspecial;
int success = lj96_gpu_init(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4,
- offset, force->special_lj, atom->nlocal,
- atom->nlocal+atom->nghost, 300, maxspecial,
- cell_size, gpu_mode, screen);
+ offset, force->special_lj, atom->nlocal,
+ atom->nlocal+atom->nghost, 300, maxspecial,
+ cell_size, gpu_mode, screen);
GPU_EXTRA::check_flag(success,error,world);
if (gpu_mode == GPU_FORCE) {
@@ -171,7 +171,7 @@ double PairLJ96CutGPU::memory_usage()
/* ---------------------------------------------------------------------- */
void PairLJ96CutGPU::cpu_compute(int start, int inum, int eflag, int vflag,
- int *ilist, int *numneigh, int **firstneigh)
+ int *ilist, int *numneigh, int **firstneigh)
{
int i,j,ii,jj,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
@@ -206,23 +206,23 @@ void PairLJ96CutGPU::cpu_compute(int start, int inum, int eflag, int vflag,
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
- r3inv = sqrt(r6inv);
- forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
- fpair = factor_lj*forcelj*r2inv;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
-
- if (eflag) {
- evdwl = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) -
- offset[itype][jtype];
- evdwl *= factor_lj;
- }
-
- if (evflag) ev_tally_full(i,evdwl,0.0,fpair,delx,dely,delz);
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
+ r3inv = sqrt(r6inv);
+ forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
+ fpair = factor_lj*forcelj*r2inv;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+
+ if (eflag) {
+ evdwl = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) -
+ offset[itype][jtype];
+ evdwl *= factor_lj;
+ }
+
+ if (evflag) ev_tally_full(i,evdwl,0.0,fpair,delx,dely,delz);
}
}
}
diff --git a/src/GPU/pair_lj96_cut_gpu.h b/src/GPU/pair_lj96_cut_gpu.h
index a83b7d53689cb8031c54b372d84ab857d306b8d3..43c63354dccb4c2cb713cd786f5bded0799eeb50 100644
--- a/src/GPU/pair_lj96_cut_gpu.h
+++ b/src/GPU/pair_lj96_cut_gpu.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/GPU/pair_lj_charmm_coul_long_gpu.cpp b/src/GPU/pair_lj_charmm_coul_long_gpu.cpp
index 17db620b8361dcb9f9559c778d0e5f882c8db3f6..c750f4aeae84840f35a0523a9d2bc1a79e6e83ac 100644
--- a/src/GPU/pair_lj_charmm_coul_long_gpu.cpp
+++ b/src/GPU/pair_lj_charmm_coul_long_gpu.cpp
@@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
-
+
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
-
+
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@@ -47,42 +47,42 @@
// External functions from cuda library for atom decomposition
int crml_gpu_init(const int ntypes, double cut_bothsq, double **host_lj1,
- double **host_lj2, double **host_lj3, double **host_lj4,
- double **offset, double *special_lj, const int nlocal,
- const int nall, const int max_nbors, const int maxspecial,
- const double cell_size, int &gpu_mode, FILE *screen,
- double host_cut_ljsq, double host_cut_coulsq,
- double *host_special_coul, const double qqrd2e,
- const double g_ewald, const double cut_lj_innersq,
- const double denom_lj, double **epsilon, double **sigma,
- const bool mix_arithmetic);
+ double **host_lj2, double **host_lj3, double **host_lj4,
+ double **offset, double *special_lj, const int nlocal,
+ const int nall, const int max_nbors, const int maxspecial,
+ const double cell_size, int &gpu_mode, FILE *screen,
+ double host_cut_ljsq, double host_cut_coulsq,
+ double *host_special_coul, const double qqrd2e,
+ const double g_ewald, const double cut_lj_innersq,
+ const double denom_lj, double **epsilon, double **sigma,
+ const bool mix_arithmetic);
void crml_gpu_clear();
int ** crml_gpu_compute_n(const int ago, const int inum,
- const int nall, double **host_x, int *host_type,
- double *sublo, double *subhi, int *tag,
- int **nspecial, int **special, const bool eflag,
- const bool vflag, const bool eatom, const bool vatom,
- int &host_start, int **ilist, int **jnum,
- const double cpu_time, bool &success, double *host_q,
- double *boxlo, double *prd);
+ const int nall, double **host_x, int *host_type,
+ double *sublo, double *subhi, int *tag,
+ int **nspecial, int **special, const bool eflag,
+ const bool vflag, const bool eatom, const bool vatom,
+ int &host_start, int **ilist, int **jnum,
+ const double cpu_time, bool &success, double *host_q,
+ double *boxlo, double *prd);
void crml_gpu_compute(const int ago, const int inum, const int nall,
- double **host_x, int *host_type, int *ilist, int *numj,
- int **firstneigh, const bool eflag, const bool vflag,
- const bool eatom, const bool vatom, int &host_start,
- const double cpu_time, bool &success, double *host_q,
- const int nlocal, double *boxlo, double *prd);
+ double **host_x, int *host_type, int *ilist, int *numj,
+ int **firstneigh, const bool eflag, const bool vflag,
+ const bool eatom, const bool vatom, int &host_start,
+ const double cpu_time, bool &success, double *host_q,
+ const int nlocal, double *boxlo, double *prd);
double crml_gpu_bytes();
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-PairLJCharmmCoulLongGPU::PairLJCharmmCoulLongGPU(LAMMPS *lmp) :
+PairLJCharmmCoulLongGPU::PairLJCharmmCoulLongGPU(LAMMPS *lmp) :
PairLJCharmmCoulLong(lmp), gpu_mode(GPU_FORCE)
{
respa_enable = 0;
cpu_time = 0.0;
- GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
+ GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
@@ -100,30 +100,30 @@ void PairLJCharmmCoulLongGPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
-
+
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
-
+
bool success = true;
- int *ilist, *numneigh, **firstneigh;
+ int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = crml_gpu_compute_n(neighbor->ago, inum, nall, atom->x,
- atom->type, domain->sublo, domain->subhi,
- atom->tag, atom->nspecial, atom->special,
- eflag, vflag, eflag_atom, vflag_atom,
- host_start, &ilist, &numneigh, cpu_time,
- success, atom->q, domain->boxlo,
- domain->prd);
+ atom->type, domain->sublo, domain->subhi,
+ atom->tag, atom->nspecial, atom->special,
+ eflag, vflag, eflag_atom, vflag_atom,
+ host_start, &ilist, &numneigh, cpu_time,
+ success, atom->q, domain->boxlo,
+ domain->prd);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
crml_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
- ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
- vflag_atom, host_start, cpu_time, success, atom->q,
- atom->nlocal, domain->boxlo, domain->prd);
+ ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
+ vflag_atom, host_start, cpu_time, success, atom->q,
+ atom->nlocal, domain->boxlo, domain->prd);
}
if (!success)
error->one(FLERR,"Insufficient memory on accelerator");
@@ -145,7 +145,7 @@ void PairLJCharmmCoulLongGPU::init_style()
if (!atom->q_flag)
error->all(FLERR,"Pair style lj/charmm/coul/long/gpu requires atom attribute q");
- if (force->newton_pair)
+ if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with lj/charmm/coul/long/gpu pair style");
// Repeat cutsq calculation because done after call to init_style
@@ -162,7 +162,7 @@ void PairLJCharmmCoulLongGPU::init_style()
cut_coulsq = cut_coul * cut_coul;
cut_bothsq = MAX(cut_ljsq,cut_coulsq);
- denom_lj = (cut_ljsq-cut_lj_innersq) * (cut_ljsq-cut_lj_innersq) *
+ denom_lj = (cut_ljsq-cut_lj_innersq) * (cut_ljsq-cut_lj_innersq) *
(cut_ljsq-cut_lj_innersq);
double cell_size = sqrt(cut_bothsq) + neighbor->skin;
@@ -185,18 +185,18 @@ void PairLJCharmmCoulLongGPU::init_style()
for (int i = 1; i < atom->ntypes + 1; i++)
for (int j = i + 1; j < atom->ntypes + 1; j++) {
if (epsilon[i][j] != sqrt(epsilon[i][i] * epsilon[j][j]))
- arithmetic = false;
+ arithmetic = false;
if (sigma[i][j] != 0.5 * (sigma[i][i] + sigma[j][j]))
- arithmetic = false;
+ arithmetic = false;
}
int success = crml_gpu_init(atom->ntypes+1, cut_bothsq, lj1, lj2, lj3, lj4,
- offset, force->special_lj, atom->nlocal,
- atom->nlocal+atom->nghost, 300, maxspecial,
- cell_size, gpu_mode, screen, cut_ljsq,
- cut_coulsq, force->special_coul, force->qqrd2e,
- g_ewald, cut_lj_innersq,denom_lj,epsilon,sigma,
- arithmetic);
+ offset, force->special_lj, atom->nlocal,
+ atom->nlocal+atom->nghost, 300, maxspecial,
+ cell_size, gpu_mode, screen, cut_ljsq,
+ cut_coulsq, force->special_coul, force->qqrd2e,
+ g_ewald, cut_lj_innersq,denom_lj,epsilon,sigma,
+ arithmetic);
GPU_EXTRA::check_flag(success,error,world);
if (gpu_mode == GPU_FORCE) {
@@ -217,8 +217,8 @@ double PairLJCharmmCoulLongGPU::memory_usage()
/* ---------------------------------------------------------------------- */
void PairLJCharmmCoulLongGPU::cpu_compute(int start, int inum, int eflag,
- int vflag, int *ilist,
- int *numneigh, int **firstneigh)
+ int vflag, int *ilist,
+ int *numneigh, int **firstneigh)
{
int i,j,ii,jj,jnum,itype,jtype,itable;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
@@ -263,77 +263,77 @@ void PairLJCharmmCoulLongGPU::cpu_compute(int start, int inum, int eflag,
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cut_bothsq) {
- r2inv = 1.0/rsq;
-
- if (rsq < cut_coulsq) {
- if (!ncoultablebits || rsq <= tabinnersq) {
- r = sqrt(rsq);
- grij = g_ewald * r;
- expm2 = exp(-grij*grij);
- t = 1.0 / (1.0 + EWALD_P*grij);
- erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
- prefactor = qqrd2e * qtmp*q[j]/r;
- forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
- if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
- } else {
- union_int_float_t rsq_lookup;
- rsq_lookup.f = rsq;
- itable = rsq_lookup.i & ncoulmask;
- itable >>= ncoulshiftbits;
- fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
- table = ftable[itable] + fraction*dftable[itable];
- forcecoul = qtmp*q[j] * table;
- if (factor_coul < 1.0) {
- table = ctable[itable] + fraction*dctable[itable];
- prefactor = qtmp*q[j] * table;
- forcecoul -= (1.0-factor_coul)*prefactor;
- }
- }
- } else forcecoul = 0.0;
-
- if (rsq < cut_ljsq) {
- r6inv = r2inv*r2inv*r2inv;
- jtype = type[j];
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- if (rsq > cut_lj_innersq) {
- switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
- (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
- switch2 = 12.0*rsq * (cut_ljsq-rsq) *
- (rsq-cut_lj_innersq) / denom_lj;
- philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
- forcelj = forcelj*switch1 + philj*switch2;
- }
- } else forcelj = 0.0;
-
- fpair = (forcecoul + factor_lj*forcelj) * r2inv;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
-
- if (eflag) {
- if (rsq < cut_coulsq) {
- if (!ncoultablebits || rsq <= tabinnersq)
- ecoul = prefactor*erfc;
- else {
- table = etable[itable] + fraction*detable[itable];
- ecoul = qtmp*q[j] * table;
- }
- if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
- } else ecoul = 0.0;
-
- if (rsq < cut_ljsq) {
- evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
- if (rsq > cut_lj_innersq) {
- switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
- (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
- evdwl *= switch1;
- }
- evdwl *= factor_lj;
- } else evdwl = 0.0;
- }
-
- if (evflag) ev_tally_full(i,evdwl,ecoul,fpair,delx,dely,delz);
+ r2inv = 1.0/rsq;
+
+ if (rsq < cut_coulsq) {
+ if (!ncoultablebits || rsq <= tabinnersq) {
+ r = sqrt(rsq);
+ grij = g_ewald * r;
+ expm2 = exp(-grij*grij);
+ t = 1.0 / (1.0 + EWALD_P*grij);
+ erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
+ prefactor = qqrd2e * qtmp*q[j]/r;
+ forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
+ if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
+ } else {
+ union_int_float_t rsq_lookup;
+ rsq_lookup.f = rsq;
+ itable = rsq_lookup.i & ncoulmask;
+ itable >>= ncoulshiftbits;
+ fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
+ table = ftable[itable] + fraction*dftable[itable];
+ forcecoul = qtmp*q[j] * table;
+ if (factor_coul < 1.0) {
+ table = ctable[itable] + fraction*dctable[itable];
+ prefactor = qtmp*q[j] * table;
+ forcecoul -= (1.0-factor_coul)*prefactor;
+ }
+ }
+ } else forcecoul = 0.0;
+
+ if (rsq < cut_ljsq) {
+ r6inv = r2inv*r2inv*r2inv;
+ jtype = type[j];
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ if (rsq > cut_lj_innersq) {
+ switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
+ (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
+ switch2 = 12.0*rsq * (cut_ljsq-rsq) *
+ (rsq-cut_lj_innersq) / denom_lj;
+ philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
+ forcelj = forcelj*switch1 + philj*switch2;
+ }
+ } else forcelj = 0.0;
+
+ fpair = (forcecoul + factor_lj*forcelj) * r2inv;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+
+ if (eflag) {
+ if (rsq < cut_coulsq) {
+ if (!ncoultablebits || rsq <= tabinnersq)
+ ecoul = prefactor*erfc;
+ else {
+ table = etable[itable] + fraction*detable[itable];
+ ecoul = qtmp*q[j] * table;
+ }
+ if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
+ } else ecoul = 0.0;
+
+ if (rsq < cut_ljsq) {
+ evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
+ if (rsq > cut_lj_innersq) {
+ switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
+ (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
+ evdwl *= switch1;
+ }
+ evdwl *= factor_lj;
+ } else evdwl = 0.0;
+ }
+
+ if (evflag) ev_tally_full(i,evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
diff --git a/src/GPU/pair_lj_charmm_coul_long_gpu.h b/src/GPU/pair_lj_charmm_coul_long_gpu.h
index b445f0bc63de981fc893c23e1877618f5504f281..a4a27995211734f795408a671f94384af06d7aaf 100644
--- a/src/GPU/pair_lj_charmm_coul_long_gpu.h
+++ b/src/GPU/pair_lj_charmm_coul_long_gpu.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/GPU/pair_lj_class2_coul_long_gpu.cpp b/src/GPU/pair_lj_class2_coul_long_gpu.cpp
index f2f677a7261a5fbe466b735d9dc4826a0451340e..9c02f93c18299a698481ec8008ba7f5254fe402f 100644
--- a/src/GPU/pair_lj_class2_coul_long_gpu.cpp
+++ b/src/GPU/pair_lj_class2_coul_long_gpu.cpp
@@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
-
+
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
-
+
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@@ -47,39 +47,39 @@
// External functions from cuda library for atom decomposition
int c2cl_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
- double **host_lj2, double **host_lj3, double **host_lj4,
- double **offset, double *special_lj, const int nlocal,
- const int nall, const int max_nbors, const int maxspecial,
- const double cell_size, int &gpu_mode, FILE *screen,
- double **host_cut_ljsq, double host_cut_coulsq,
- double *host_special_coul, const double qqrd2e,
- const double g_ewald);
+ double **host_lj2, double **host_lj3, double **host_lj4,
+ double **offset, double *special_lj, const int nlocal,
+ const int nall, const int max_nbors, const int maxspecial,
+ const double cell_size, int &gpu_mode, FILE *screen,
+ double **host_cut_ljsq, double host_cut_coulsq,
+ double *host_special_coul, const double qqrd2e,
+ const double g_ewald);
void c2cl_gpu_clear();
int ** c2cl_gpu_compute_n(const int ago, const int inum,
- const int nall, double **host_x, int *host_type,
- double *sublo, double *subhi, int *tag,
- int **nspecial, int **special, const bool eflag,
- const bool vflag, const bool eatom, const bool vatom,
- int &host_start, int **ilist, int **jnum,
- const double cpu_time, bool &success, double *host_q,
- double *boxlo, double *prd);
+ const int nall, double **host_x, int *host_type,
+ double *sublo, double *subhi, int *tag,
+ int **nspecial, int **special, const bool eflag,
+ const bool vflag, const bool eatom, const bool vatom,
+ int &host_start, int **ilist, int **jnum,
+ const double cpu_time, bool &success, double *host_q,
+ double *boxlo, double *prd);
void c2cl_gpu_compute(const int ago, const int inum, const int nall,
- double **host_x, int *host_type, int *ilist, int *numj,
- int **firstneigh, const bool eflag, const bool vflag,
- const bool eatom, const bool vatom, int &host_start,
- const double cpu_time, bool &success, double *host_q,
- const int nlocal, double *boxlo, double *prd);
+ double **host_x, int *host_type, int *ilist, int *numj,
+ int **firstneigh, const bool eflag, const bool vflag,
+ const bool eatom, const bool vatom, int &host_start,
+ const double cpu_time, bool &success, double *host_q,
+ const int nlocal, double *boxlo, double *prd);
double c2cl_gpu_bytes();
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-PairLJClass2CoulLongGPU::PairLJClass2CoulLongGPU(LAMMPS *lmp) :
+PairLJClass2CoulLongGPU::PairLJClass2CoulLongGPU(LAMMPS *lmp) :
PairLJClass2CoulLong(lmp), gpu_mode(GPU_FORCE)
{
cpu_time = 0.0;
- GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
+ GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
@@ -97,30 +97,30 @@ void PairLJClass2CoulLongGPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
-
+
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
-
+
bool success = true;
- int *ilist, *numneigh, **firstneigh;
+ int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = c2cl_gpu_compute_n(neighbor->ago, inum, nall, atom->x,
- atom->type, domain->sublo, domain->subhi,
- atom->tag, atom->nspecial, atom->special,
- eflag, vflag, eflag_atom, vflag_atom,
- host_start, &ilist, &numneigh, cpu_time,
- success, atom->q, domain->boxlo,
- domain->prd);
+ atom->type, domain->sublo, domain->subhi,
+ atom->tag, atom->nspecial, atom->special,
+ eflag, vflag, eflag_atom, vflag_atom,
+ host_start, &ilist, &numneigh, cpu_time,
+ success, atom->q, domain->boxlo,
+ domain->prd);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
c2cl_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
- ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
- vflag_atom, host_start, cpu_time, success, atom->q,
- atom->nlocal, domain->boxlo, domain->prd);
+ ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
+ vflag_atom, host_start, cpu_time, success, atom->q,
+ atom->nlocal, domain->boxlo, domain->prd);
}
if (!success)
error->one(FLERR,"Insufficient memory on accelerator");
@@ -140,7 +140,7 @@ void PairLJClass2CoulLongGPU::init_style()
{
if (!atom->q_flag)
error->all(FLERR,"Pair style lj/class2/coul/long/gpu requires atom attribute q");
- if (force->newton_pair)
+ if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with lj/class2/coul/long/gpu pair style");
// Repeat cutsq calculation because done after call to init_style
@@ -196,8 +196,8 @@ double PairLJClass2CoulLongGPU::memory_usage()
/* ---------------------------------------------------------------------- */
void PairLJClass2CoulLongGPU::cpu_compute(int start, int inum, int eflag,
- int vflag, int *ilist, int *numneigh,
- int **firstneigh)
+ int vflag, int *ilist, int *numneigh,
+ int **firstneigh)
{
int i,j,ii,jj,jnum,itype,jtype;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
@@ -241,45 +241,45 @@ void PairLJClass2CoulLongGPU::cpu_compute(int start, int inum, int eflag,
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
-
- if (rsq < cut_coulsq) {
- r = sqrt(rsq);
- grij = g_ewald * r;
- expm2 = exp(-grij*grij);
- t = 1.0 / (1.0 + EWALD_P*grij);
- erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
- prefactor = qqrd2e * qtmp*q[j]/r;
- forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
- if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
- } else forcecoul = 0.0;
-
- if (rsq < cut_ljsq[itype][jtype]) {
- rinv = sqrt(r2inv);
- r3inv = r2inv*rinv;
- r6inv = r3inv*r3inv;
- forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
- } else forcelj = 0.0;
-
- fpair = (forcecoul + factor_lj*forcelj) * r2inv;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
-
- if (eflag) {
- if (rsq < cut_coulsq) {
- ecoul = prefactor*erfc;
- if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
- } else ecoul = 0.0;
- if (rsq < cut_ljsq[itype][jtype]) {
- evdwl = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) -
- offset[itype][jtype];
- evdwl *= factor_lj;
- } else evdwl = 0.0;
- }
-
- if (evflag) ev_tally_full(i,evdwl,ecoul,fpair,delx,dely,delz);
+ r2inv = 1.0/rsq;
+
+ if (rsq < cut_coulsq) {
+ r = sqrt(rsq);
+ grij = g_ewald * r;
+ expm2 = exp(-grij*grij);
+ t = 1.0 / (1.0 + EWALD_P*grij);
+ erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
+ prefactor = qqrd2e * qtmp*q[j]/r;
+ forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
+ if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
+ } else forcecoul = 0.0;
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ rinv = sqrt(r2inv);
+ r3inv = r2inv*rinv;
+ r6inv = r3inv*r3inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
+ } else forcelj = 0.0;
+
+ fpair = (forcecoul + factor_lj*forcelj) * r2inv;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+
+ if (eflag) {
+ if (rsq < cut_coulsq) {
+ ecoul = prefactor*erfc;
+ if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
+ } else ecoul = 0.0;
+ if (rsq < cut_ljsq[itype][jtype]) {
+ evdwl = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) -
+ offset[itype][jtype];
+ evdwl *= factor_lj;
+ } else evdwl = 0.0;
+ }
+
+ if (evflag) ev_tally_full(i,evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
diff --git a/src/GPU/pair_lj_class2_coul_long_gpu.h b/src/GPU/pair_lj_class2_coul_long_gpu.h
index 5cc5276f97da38fe4ccbe70ecb1a0b42c6829785..096ae4186014bb8dc5fe761579924836ff4dfa74 100644
--- a/src/GPU/pair_lj_class2_coul_long_gpu.h
+++ b/src/GPU/pair_lj_class2_coul_long_gpu.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/GPU/pair_lj_class2_gpu.cpp b/src/GPU/pair_lj_class2_gpu.cpp
index 9a1019d58ada8cc661502f5a45b0f18ee96ee66c..8e1100b09757182cbd3079908193f5439040064c 100644
--- a/src/GPU/pair_lj_class2_gpu.cpp
+++ b/src/GPU/pair_lj_class2_gpu.cpp
@@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
-
+
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
-
+
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@@ -38,23 +38,23 @@
// External functions from cuda library for atom decomposition
int lj96_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
- double **host_lj2, double **host_lj3, double **host_lj4,
- double **offset, double *special_lj, const int nlocal,
- const int nall, const int max_nbors, const int maxspecial,
- const double cell_size, int &gpu_mode, FILE *screen);
+ double **host_lj2, double **host_lj3, double **host_lj4,
+ double **offset, double *special_lj, const int nlocal,
+ const int nall, const int max_nbors, const int maxspecial,
+ const double cell_size, int &gpu_mode, FILE *screen);
void lj96_gpu_clear();
int ** lj96_gpu_compute_n(const int ago, const int inum, const int nall,
- double **host_x, int *host_type, double *sublo,
- double *subhi, int *tag, int **nspecial,
- int **special, const bool eflag, const bool vflag,
- const bool eatom, const bool vatom, int &host_start,
- int **ilist, int **jnum,
- const double cpu_time, bool &success);
+ double **host_x, int *host_type, double *sublo,
+ double *subhi, int *tag, int **nspecial,
+ int **special, const bool eflag, const bool vflag,
+ const bool eatom, const bool vatom, int &host_start,
+ int **ilist, int **jnum,
+ const double cpu_time, bool &success);
void lj96_gpu_compute(const int ago, const int inum, const int nall,
double **host_x, int *host_type, int *ilist, int *numj,
- int **firstneigh, const bool eflag, const bool vflag,
- const bool eatom, const bool vatom, int &host_start,
- const double cpu_time, bool &success);
+ int **firstneigh, const bool eflag, const bool vflag,
+ const bool eatom, const bool vatom, int &host_start,
+ const double cpu_time, bool &success);
double lj96_gpu_bytes();
using namespace LAMMPS_NS;
@@ -64,7 +64,7 @@ using namespace LAMMPS_NS;
PairLJClass2GPU::PairLJClass2GPU(LAMMPS *lmp) : PairLJClass2(lmp), gpu_mode(GPU_FORCE)
{
cpu_time = 0.0;
- GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
+ GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
@@ -82,28 +82,28 @@ void PairLJClass2GPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
-
+
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
-
+
bool success = true;
- int *ilist, *numneigh, **firstneigh;
+ int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = lj96_gpu_compute_n(neighbor->ago, inum, nall, atom->x,
- atom->type, domain->sublo, domain->subhi,
- atom->tag, atom->nspecial, atom->special,
- eflag, vflag, eflag_atom, vflag_atom,
- host_start, &ilist, &numneigh, cpu_time,
- success);
+ atom->type, domain->sublo, domain->subhi,
+ atom->tag, atom->nspecial, atom->special,
+ eflag, vflag, eflag_atom, vflag_atom,
+ host_start, &ilist, &numneigh, cpu_time,
+ success);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
lj96_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
- ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
- vflag_atom, host_start, cpu_time, success);
+ ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
+ vflag_atom, host_start, cpu_time, success);
}
if (!success)
error->one(FLERR,"Insufficient memory on accelerator");
@@ -121,7 +121,7 @@ void PairLJClass2GPU::compute(int eflag, int vflag)
void PairLJClass2GPU::init_style()
{
- if (force->newton_pair)
+ if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with lj/class2/gpu pair style");
// Repeat cutsq calculation because done after call to init_style
@@ -145,9 +145,9 @@ void PairLJClass2GPU::init_style()
if (atom->molecular)
maxspecial=atom->maxspecial;
int success = lj96_gpu_init(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4,
- offset, force->special_lj, atom->nlocal,
- atom->nlocal+atom->nghost, 300, maxspecial,
- cell_size, gpu_mode, screen);
+ offset, force->special_lj, atom->nlocal,
+ atom->nlocal+atom->nghost, 300, maxspecial,
+ cell_size, gpu_mode, screen);
GPU_EXTRA::check_flag(success,error,world);
if (gpu_mode == GPU_FORCE) {
@@ -168,7 +168,7 @@ double PairLJClass2GPU::memory_usage()
/* ---------------------------------------------------------------------- */
void PairLJClass2GPU::cpu_compute(int start, int inum, int eflag, int vflag,
- int *ilist, int *numneigh, int **firstneigh)
+ int *ilist, int *numneigh, int **firstneigh)
{
int i,j,ii,jj,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
@@ -203,23 +203,23 @@ void PairLJClass2GPU::cpu_compute(int start, int inum, int eflag, int vflag,
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
- r3inv = sqrt(r6inv);
- forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
- fpair = factor_lj*forcelj*r2inv;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
-
- if (eflag) {
- evdwl = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) -
- offset[itype][jtype];
- evdwl *= factor_lj;
- }
-
- if (evflag) ev_tally_full(i,evdwl,0.0,fpair,delx,dely,delz);
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
+ r3inv = sqrt(r6inv);
+ forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
+ fpair = factor_lj*forcelj*r2inv;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+
+ if (eflag) {
+ evdwl = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) -
+ offset[itype][jtype];
+ evdwl *= factor_lj;
+ }
+
+ if (evflag) ev_tally_full(i,evdwl,0.0,fpair,delx,dely,delz);
}
}
}
diff --git a/src/GPU/pair_lj_class2_gpu.h b/src/GPU/pair_lj_class2_gpu.h
index 21c893b04af7910a694de7242545974bdc2cc882..2512a6cdbad6ef6a8dcdc3f711803c2fb1658258 100644
--- a/src/GPU/pair_lj_class2_gpu.h
+++ b/src/GPU/pair_lj_class2_gpu.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/GPU/pair_lj_cut_coul_cut_gpu.cpp b/src/GPU/pair_lj_cut_coul_cut_gpu.cpp
index 53f6fd94b3498d50247ac0c1fa5e21bf42bc34c3..8d83ceb2555e6676b20fc69325076ab1b5d8ac56 100644
--- a/src/GPU/pair_lj_cut_coul_cut_gpu.cpp
+++ b/src/GPU/pair_lj_cut_coul_cut_gpu.cpp
@@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
-
+
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
-
+
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@@ -38,28 +38,28 @@
// External functions from cuda library for atom decomposition
int ljc_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
- double **host_lj2, double **host_lj3, double **host_lj4,
- double **offset, double *special_lj, const int nlocal,
+ double **host_lj2, double **host_lj3, double **host_lj4,
+ double **offset, double *special_lj, const int nlocal,
const int nall, const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen,
double **host_cut_ljsq, double **host_cut_coulsq,
double *host_special_coul, const double qqrd2e);
void ljc_gpu_clear();
int ** ljc_gpu_compute_n(const int ago, const int inum,
- const int nall, double **host_x, int *host_type,
- double *sublo, double *subhi, int *tag, int **nspecial,
- int **special, const bool eflag, const bool vflag,
- const bool eatom, const bool vatom, int &host_start,
- int **ilist, int **jnum, const double cpu_time,
- bool &success, double *host_q, double *boxlo,
- double *prd);
+ const int nall, double **host_x, int *host_type,
+ double *sublo, double *subhi, int *tag, int **nspecial,
+ int **special, const bool eflag, const bool vflag,
+ const bool eatom, const bool vatom, int &host_start,
+ int **ilist, int **jnum, const double cpu_time,
+ bool &success, double *host_q, double *boxlo,
+ double *prd);
void ljc_gpu_compute(const int ago, const int inum,
- const int nall, double **host_x, int *host_type,
+ const int nall, double **host_x, int *host_type,
int *ilist, int *numj, int **firstneigh,
- const bool eflag, const bool vflag, const bool eatom,
+ const bool eflag, const bool vflag, const bool eatom,
const bool vatom, int &host_start, const double cpu_time,
bool &success, double *host_q, const int nlocal,
- double *boxlo, double *prd);
+ double *boxlo, double *prd);
double ljc_gpu_bytes();
using namespace LAMMPS_NS;
@@ -70,7 +70,7 @@ PairLJCutCoulCutGPU::PairLJCutCoulCutGPU(LAMMPS *lmp) : PairLJCutCoulCut(lmp), g
{
respa_enable = 0;
cpu_time = 0.0;
- GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
+ GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
@@ -88,30 +88,30 @@ void PairLJCutCoulCutGPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
-
+
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
-
+
bool success = true;
- int *ilist, *numneigh, **firstneigh;
+ int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = ljc_gpu_compute_n(neighbor->ago, inum, nall, atom->x,
- atom->type, domain->sublo, domain->subhi,
- atom->tag, atom->nspecial, atom->special,
- eflag, vflag, eflag_atom, vflag_atom,
- host_start, &ilist, &numneigh, cpu_time,
- success, atom->q, domain->boxlo,
- domain->prd);
+ atom->type, domain->sublo, domain->subhi,
+ atom->tag, atom->nspecial, atom->special,
+ eflag, vflag, eflag_atom, vflag_atom,
+ host_start, &ilist, &numneigh, cpu_time,
+ success, atom->q, domain->boxlo,
+ domain->prd);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
ljc_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
- ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
- vflag_atom, host_start, cpu_time, success, atom->q,
- atom->nlocal, domain->boxlo, domain->prd);
+ ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
+ vflag_atom, host_start, cpu_time, success, atom->q,
+ atom->nlocal, domain->boxlo, domain->prd);
}
if (!success)
error->one(FLERR,"Insufficient memory on accelerator");
@@ -132,7 +132,7 @@ void PairLJCutCoulCutGPU::init_style()
if (!atom->q_flag)
error->all(FLERR,"Pair style lj/cut/coul/cut/gpu requires atom attribute q");
- if (force->newton_pair)
+ if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with lj/cut/coul/cut/gpu pair style");
// Repeat cutsq calculation because done after call to init_style
@@ -156,10 +156,10 @@ void PairLJCutCoulCutGPU::init_style()
if (atom->molecular)
maxspecial=atom->maxspecial;
int success = ljc_gpu_init(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4,
- offset, force->special_lj, atom->nlocal,
- atom->nlocal+atom->nghost, 300, maxspecial,
- cell_size, gpu_mode, screen, cut_ljsq, cut_coulsq,
- force->special_coul, force->qqrd2e);
+ offset, force->special_lj, atom->nlocal,
+ atom->nlocal+atom->nghost, 300, maxspecial,
+ cell_size, gpu_mode, screen, cut_ljsq, cut_coulsq,
+ force->special_coul, force->qqrd2e);
GPU_EXTRA::check_flag(success,error,world);
if (gpu_mode == GPU_FORCE) {
@@ -180,8 +180,8 @@ double PairLJCutCoulCutGPU::memory_usage()
/* ---------------------------------------------------------------------- */
void PairLJCutCoulCutGPU::cpu_compute(int start, int inum, int eflag, int vflag,
- int *ilist, int *numneigh,
- int **firstneigh)
+ int *ilist, int *numneigh,
+ int **firstneigh)
{
int i,j,ii,jj,jnum,itype,jtype;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
@@ -223,35 +223,35 @@ void PairLJCutCoulCutGPU::cpu_compute(int start, int inum, int eflag, int vflag,
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
-
- if (rsq < cut_coulsq[itype][jtype])
- forcecoul = qqrd2e * qtmp*q[j]*sqrt(r2inv);
- else forcecoul = 0.0;
-
- if (rsq < cut_ljsq[itype][jtype]) {
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- } else forcelj = 0.0;
-
- fpair = (factor_coul*forcecoul + factor_lj*forcelj) * r2inv;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
-
- if (eflag) {
- if (rsq < cut_coulsq[itype][jtype])
- ecoul = factor_coul * qqrd2e * qtmp*q[j]*sqrt(r2inv);
- else ecoul = 0.0;
- if (rsq < cut_ljsq[itype][jtype]) {
- evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
- offset[itype][jtype];
- evdwl *= factor_lj;
- } else evdwl = 0.0;
- }
-
- if (evflag) ev_tally_full(i,evdwl,ecoul,fpair,delx,dely,delz);
+ r2inv = 1.0/rsq;
+
+ if (rsq < cut_coulsq[itype][jtype])
+ forcecoul = qqrd2e * qtmp*q[j]*sqrt(r2inv);
+ else forcecoul = 0.0;
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ } else forcelj = 0.0;
+
+ fpair = (factor_coul*forcecoul + factor_lj*forcelj) * r2inv;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+
+ if (eflag) {
+ if (rsq < cut_coulsq[itype][jtype])
+ ecoul = factor_coul * qqrd2e * qtmp*q[j]*sqrt(r2inv);
+ else ecoul = 0.0;
+ if (rsq < cut_ljsq[itype][jtype]) {
+ evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
+ offset[itype][jtype];
+ evdwl *= factor_lj;
+ } else evdwl = 0.0;
+ }
+
+ if (evflag) ev_tally_full(i,evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
diff --git a/src/GPU/pair_lj_cut_coul_cut_gpu.h b/src/GPU/pair_lj_cut_coul_cut_gpu.h
index f03b16325c313f7886827a7746a83b6aa376e219..036b0845493cbf7482ff8a4dc149cb0274ea788c 100644
--- a/src/GPU/pair_lj_cut_coul_cut_gpu.h
+++ b/src/GPU/pair_lj_cut_coul_cut_gpu.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/GPU/pair_lj_cut_coul_long_gpu.cpp b/src/GPU/pair_lj_cut_coul_long_gpu.cpp
index 00b8ef38972115703a553ad336c02a1798e7efb2..1e96fe65723648c8e6eaa596eb28560590a2ec19 100644
--- a/src/GPU/pair_lj_cut_coul_long_gpu.cpp
+++ b/src/GPU/pair_lj_cut_coul_long_gpu.cpp
@@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
-
+
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
-
+
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@@ -47,28 +47,28 @@
// External functions from cuda library for atom decomposition
int ljcl_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
- double **host_lj2, double **host_lj3, double **host_lj4,
- double **offset, double *special_lj, const int nlocal,
- const int nall, const int max_nbors, const int maxspecial,
- const double cell_size, int &gpu_mode, FILE *screen,
- double **host_cut_ljsq, double host_cut_coulsq,
- double *host_special_coul, const double qqrd2e,
- const double g_ewald);
+ double **host_lj2, double **host_lj3, double **host_lj4,
+ double **offset, double *special_lj, const int nlocal,
+ const int nall, const int max_nbors, const int maxspecial,
+ const double cell_size, int &gpu_mode, FILE *screen,
+ double **host_cut_ljsq, double host_cut_coulsq,
+ double *host_special_coul, const double qqrd2e,
+ const double g_ewald);
void ljcl_gpu_clear();
int ** ljcl_gpu_compute_n(const int ago, const int inum,
- const int nall, double **host_x, int *host_type,
- double *sublo, double *subhi, int *tag,
- int **nspecial, int **special, const bool eflag,
- const bool vflag, const bool eatom, const bool vatom,
- int &host_start, int **ilist, int **jnum,
- const double cpu_time, bool &success, double *host_q,
- double *boxlo, double *prd);
+ const int nall, double **host_x, int *host_type,
+ double *sublo, double *subhi, int *tag,
+ int **nspecial, int **special, const bool eflag,
+ const bool vflag, const bool eatom, const bool vatom,
+ int &host_start, int **ilist, int **jnum,
+ const double cpu_time, bool &success, double *host_q,
+ double *boxlo, double *prd);
void ljcl_gpu_compute(const int ago, const int inum, const int nall,
- double **host_x, int *host_type, int *ilist, int *numj,
- int **firstneigh, const bool eflag, const bool vflag,
- const bool eatom, const bool vatom, int &host_start,
- const double cpu_time, bool &success, double *host_q,
- const int nlocal, double *boxlo, double *prd);
+ double **host_x, int *host_type, int *ilist, int *numj,
+ int **firstneigh, const bool eflag, const bool vflag,
+ const bool eatom, const bool vatom, int &host_start,
+ const double cpu_time, bool &success, double *host_q,
+ const int nlocal, double *boxlo, double *prd);
double ljcl_gpu_bytes();
using namespace LAMMPS_NS;
@@ -80,7 +80,7 @@ PairLJCutCoulLongGPU::PairLJCutCoulLongGPU(LAMMPS *lmp) :
{
respa_enable = 0;
cpu_time = 0.0;
- GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
+ GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
@@ -98,30 +98,30 @@ void PairLJCutCoulLongGPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
-
+
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
-
+
bool success = true;
- int *ilist, *numneigh, **firstneigh;
+ int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = ljcl_gpu_compute_n(neighbor->ago, inum, nall, atom->x,
- atom->type, domain->sublo, domain->subhi,
- atom->tag, atom->nspecial, atom->special,
- eflag, vflag, eflag_atom, vflag_atom,
- host_start, &ilist, &numneigh, cpu_time,
- success, atom->q, domain->boxlo,
- domain->prd);
+ atom->type, domain->sublo, domain->subhi,
+ atom->tag, atom->nspecial, atom->special,
+ eflag, vflag, eflag_atom, vflag_atom,
+ host_start, &ilist, &numneigh, cpu_time,
+ success, atom->q, domain->boxlo,
+ domain->prd);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
ljcl_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
- ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
- vflag_atom, host_start, cpu_time, success, atom->q,
- atom->nlocal, domain->boxlo, domain->prd);
+ ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
+ vflag_atom, host_start, cpu_time, success, atom->q,
+ atom->nlocal, domain->boxlo, domain->prd);
}
if (!success)
error->one(FLERR,"Insufficient memory on accelerator");
@@ -143,7 +143,7 @@ void PairLJCutCoulLongGPU::init_style()
if (!atom->q_flag)
error->all(FLERR,"Pair style lj/cut/coul/long/gpu requires atom attribute q");
- if (force->newton_pair)
+ if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with lj/cut/coul/long/gpu pair style");
// Repeat cutsq calculation because done after call to init_style
@@ -203,8 +203,8 @@ double PairLJCutCoulLongGPU::memory_usage()
/* ---------------------------------------------------------------------- */
void PairLJCutCoulLongGPU::cpu_compute(int start, int inum, int eflag,
- int vflag, int *ilist, int *numneigh,
- int **firstneigh)
+ int vflag, int *ilist, int *numneigh,
+ int **firstneigh)
{
int i,j,ii,jj,jnum,itype,jtype,itable;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
@@ -249,64 +249,64 @@ void PairLJCutCoulLongGPU::cpu_compute(int start, int inum, int eflag,
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
-
- if (rsq < cut_coulsq) {
- if (!ncoultablebits || rsq <= tabinnersq) {
- r = sqrt(rsq);
- grij = g_ewald * r;
- expm2 = exp(-grij*grij);
- t = 1.0 / (1.0 + EWALD_P*grij);
- erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
- prefactor = qqrd2e * qtmp*q[j]/r;
- forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
- if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
- } else {
- union_int_float_t rsq_lookup;
- rsq_lookup.f = rsq;
- itable = rsq_lookup.i & ncoulmask;
- itable >>= ncoulshiftbits;
- fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
- table = ftable[itable] + fraction*dftable[itable];
- forcecoul = qtmp*q[j] * table;
- if (factor_coul < 1.0) {
- table = ctable[itable] + fraction*dctable[itable];
- prefactor = qtmp*q[j] * table;
- forcecoul -= (1.0-factor_coul)*prefactor;
- }
- }
- } else forcecoul = 0.0;
-
- if (rsq < cut_ljsq[itype][jtype]) {
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- } else forcelj = 0.0;
-
- fpair = (forcecoul + factor_lj*forcelj) * r2inv;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
-
- if (eflag) {
- if (rsq < cut_coulsq) {
- if (!ncoultablebits || rsq <= tabinnersq)
- ecoul = prefactor*erfc;
- else {
- table = etable[itable] + fraction*detable[itable];
- ecoul = qtmp*q[j] * table;
- }
- if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
- } else ecoul = 0.0;
-
- if (rsq < cut_ljsq[itype][jtype]) {
- evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
- offset[itype][jtype];
- evdwl *= factor_lj;
- } else evdwl = 0.0;
- }
-
- if (evflag) ev_tally_full(i,evdwl,ecoul,fpair,delx,dely,delz);
+ r2inv = 1.0/rsq;
+
+ if (rsq < cut_coulsq) {
+ if (!ncoultablebits || rsq <= tabinnersq) {
+ r = sqrt(rsq);
+ grij = g_ewald * r;
+ expm2 = exp(-grij*grij);
+ t = 1.0 / (1.0 + EWALD_P*grij);
+ erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
+ prefactor = qqrd2e * qtmp*q[j]/r;
+ forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
+ if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
+ } else {
+ union_int_float_t rsq_lookup;
+ rsq_lookup.f = rsq;
+ itable = rsq_lookup.i & ncoulmask;
+ itable >>= ncoulshiftbits;
+ fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
+ table = ftable[itable] + fraction*dftable[itable];
+ forcecoul = qtmp*q[j] * table;
+ if (factor_coul < 1.0) {
+ table = ctable[itable] + fraction*dctable[itable];
+ prefactor = qtmp*q[j] * table;
+ forcecoul -= (1.0-factor_coul)*prefactor;
+ }
+ }
+ } else forcecoul = 0.0;
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ } else forcelj = 0.0;
+
+ fpair = (forcecoul + factor_lj*forcelj) * r2inv;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+
+ if (eflag) {
+ if (rsq < cut_coulsq) {
+ if (!ncoultablebits || rsq <= tabinnersq)
+ ecoul = prefactor*erfc;
+ else {
+ table = etable[itable] + fraction*detable[itable];
+ ecoul = qtmp*q[j] * table;
+ }
+ if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
+ } else ecoul = 0.0;
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
+ offset[itype][jtype];
+ evdwl *= factor_lj;
+ } else evdwl = 0.0;
+ }
+
+ if (evflag) ev_tally_full(i,evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
diff --git a/src/GPU/pair_lj_cut_coul_long_gpu.h b/src/GPU/pair_lj_cut_coul_long_gpu.h
index 9ff26f483e214fbcd09ce674d78b84eb3c537e14..1904203925d413e1691898a9ac31ee55ce701321 100644
--- a/src/GPU/pair_lj_cut_coul_long_gpu.h
+++ b/src/GPU/pair_lj_cut_coul_long_gpu.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/GPU/pair_lj_cut_gpu.cpp b/src/GPU/pair_lj_cut_gpu.cpp
index 6e954d7ad1cec24e3cdf5d29a2c63dfece8d3836..3d4db278c639d3e5d7c65b0234707297dafdf01c 100644
--- a/src/GPU/pair_lj_cut_gpu.cpp
+++ b/src/GPU/pair_lj_cut_gpu.cpp
@@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
-
+
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
-
+
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@@ -38,23 +38,23 @@
// External functions from cuda library for atom decomposition
int ljl_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
- double **host_lj2, double **host_lj3, double **host_lj4,
- double **offset, double *special_lj, const int nlocal,
- const int nall, const int max_nbors, const int maxspecial,
- const double cell_size, int &gpu_mode, FILE *screen);
+ double **host_lj2, double **host_lj3, double **host_lj4,
+ double **offset, double *special_lj, const int nlocal,
+ const int nall, const int max_nbors, const int maxspecial,
+ const double cell_size, int &gpu_mode, FILE *screen);
void ljl_gpu_clear();
int ** ljl_gpu_compute_n(const int ago, const int inum,
- const int nall, double **host_x, int *host_type,
- double *sublo, double *subhi, int *tag, int **nspecial,
- int **special, const bool eflag, const bool vflag,
- const bool eatom, const bool vatom, int &host_start,
- int **ilist, int **jnum,
- const double cpu_time, bool &success);
-void ljl_gpu_compute(const int ago, const int inum, const int nall,
- double **host_x, int *host_type, int *ilist, int *numj,
- int **firstneigh, const bool eflag, const bool vflag,
- const bool eatom, const bool vatom, int &host_start,
- const double cpu_time, bool &success);
+ const int nall, double **host_x, int *host_type,
+ double *sublo, double *subhi, int *tag, int **nspecial,
+ int **special, const bool eflag, const bool vflag,
+ const bool eatom, const bool vatom, int &host_start,
+ int **ilist, int **jnum,
+ const double cpu_time, bool &success);
+void ljl_gpu_compute(const int ago, const int inum, const int nall,
+ double **host_x, int *host_type, int *ilist, int *numj,
+ int **firstneigh, const bool eflag, const bool vflag,
+ const bool eatom, const bool vatom, int &host_start,
+ const double cpu_time, bool &success);
double ljl_gpu_bytes();
using namespace LAMMPS_NS;
@@ -65,7 +65,7 @@ PairLJCutGPU::PairLJCutGPU(LAMMPS *lmp) : PairLJCut(lmp), gpu_mode(GPU_FORCE)
{
respa_enable = 0;
cpu_time = 0.0;
- GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
+ GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
@@ -83,28 +83,28 @@ void PairLJCutGPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
-
+
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
-
+
bool success = true;
int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = ljl_gpu_compute_n(neighbor->ago, inum, nall,
- atom->x, atom->type, domain->sublo,
- domain->subhi, atom->tag, atom->nspecial,
- atom->special, eflag, vflag, eflag_atom,
- vflag_atom, host_start,
- &ilist, &numneigh, cpu_time, success);
+ atom->x, atom->type, domain->sublo,
+ domain->subhi, atom->tag, atom->nspecial,
+ atom->special, eflag, vflag, eflag_atom,
+ vflag_atom, host_start,
+ &ilist, &numneigh, cpu_time, success);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
ljl_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
- ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
- vflag_atom, host_start, cpu_time, success);
+ ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
+ vflag_atom, host_start, cpu_time, success);
}
if (!success)
error->one(FLERR,"Insufficient memory on accelerator");
@@ -124,7 +124,7 @@ void PairLJCutGPU::init_style()
{
cut_respa = NULL;
- if (force->newton_pair)
+ if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with lj/cut/gpu pair style");
// Repeat cutsq calculation because done after call to init_style
@@ -148,9 +148,9 @@ void PairLJCutGPU::init_style()
if (atom->molecular)
maxspecial=atom->maxspecial;
int success = ljl_gpu_init(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4,
- offset, force->special_lj, atom->nlocal,
- atom->nlocal+atom->nghost, 300, maxspecial,
- cell_size, gpu_mode, screen);
+ offset, force->special_lj, atom->nlocal,
+ atom->nlocal+atom->nghost, 300, maxspecial,
+ cell_size, gpu_mode, screen);
GPU_EXTRA::check_flag(success,error,world);
if (gpu_mode == GPU_FORCE) {
@@ -170,8 +170,8 @@ double PairLJCutGPU::memory_usage()
/* ---------------------------------------------------------------------- */
-void PairLJCutGPU::cpu_compute(int start, int inum, int eflag, int vflag,
- int *ilist, int *numneigh, int **firstneigh) {
+void PairLJCutGPU::cpu_compute(int start, int inum, int eflag, int vflag,
+ int *ilist, int *numneigh, int **firstneigh) {
int i,j,ii,jj,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,r2inv,r6inv,forcelj,factor_lj;
@@ -205,22 +205,22 @@ void PairLJCutGPU::cpu_compute(int start, int inum, int eflag, int vflag,
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- fpair = factor_lj*forcelj*r2inv;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
-
- if (eflag) {
- evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
- offset[itype][jtype];
- evdwl *= factor_lj;
- }
-
- if (evflag) ev_tally_full(i,evdwl,0.0,fpair,delx,dely,delz);
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ fpair = factor_lj*forcelj*r2inv;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+
+ if (eflag) {
+ evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
+ offset[itype][jtype];
+ evdwl *= factor_lj;
+ }
+
+ if (evflag) ev_tally_full(i,evdwl,0.0,fpair,delx,dely,delz);
}
}
}
diff --git a/src/GPU/pair_lj_cut_gpu.h b/src/GPU/pair_lj_cut_gpu.h
index d748651276673bbefe0adb404ec68f93406f5338..0229adc62b4d1fb33d0add44dac69750d5b2e17c 100644
--- a/src/GPU/pair_lj_cut_gpu.h
+++ b/src/GPU/pair_lj_cut_gpu.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/GPU/pair_lj_expand_gpu.cpp b/src/GPU/pair_lj_expand_gpu.cpp
index 5bce6dba7c0de10d752bd01e25e252a2886c3701..11f5495b8eeb71b70ee761398db9b1eb062cd992 100644
--- a/src/GPU/pair_lj_expand_gpu.cpp
+++ b/src/GPU/pair_lj_expand_gpu.cpp
@@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
-
+
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
-
+
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@@ -38,24 +38,24 @@
// External functions from cuda library for atom decomposition
int lje_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
- double **host_lj2, double **host_lj3, double **host_lj4,
- double **offset, double **shift, double *special_lj,
- const int nlocal, const int nall, const int max_nbors,
- const int maxspecial, const double cell_size, int &gpu_mode,
- FILE *screen);
+ double **host_lj2, double **host_lj3, double **host_lj4,
+ double **offset, double **shift, double *special_lj,
+ const int nlocal, const int nall, const int max_nbors,
+ const int maxspecial, const double cell_size, int &gpu_mode,
+ FILE *screen);
void lje_gpu_clear();
int ** lje_gpu_compute_n(const int ago, const int inum, const int nall,
- double **host_x, int *host_type, double *sublo,
- double *subhi, int *tag, int **nspecial,
- int **special, const bool eflag, const bool vflag,
- const bool eatom, const bool vatom, int &host_start,
- int **ilist, int **jnum,
- const double cpu_time, bool &success);
+ double **host_x, int *host_type, double *sublo,
+ double *subhi, int *tag, int **nspecial,
+ int **special, const bool eflag, const bool vflag,
+ const bool eatom, const bool vatom, int &host_start,
+ int **ilist, int **jnum,
+ const double cpu_time, bool &success);
void lje_gpu_compute(const int ago, const int inum, const int nall,
- double **host_x, int *host_type, int *ilist, int *numj,
- int **firstneigh, const bool eflag, const bool vflag,
- const bool eatom, const bool vatom, int &host_start,
- const double cpu_time, bool &success);
+ double **host_x, int *host_type, int *ilist, int *numj,
+ int **firstneigh, const bool eflag, const bool vflag,
+ const bool eatom, const bool vatom, int &host_start,
+ const double cpu_time, bool &success);
double lje_gpu_bytes();
using namespace LAMMPS_NS;
@@ -66,7 +66,7 @@ PairLJExpandGPU::PairLJExpandGPU(LAMMPS *lmp) : PairLJExpand(lmp), gpu_mode(GPU_
{
respa_enable = 0;
cpu_time = 0.0;
- GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
+ GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
@@ -84,28 +84,28 @@ void PairLJExpandGPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
-
+
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
-
+
bool success = true;
- int *ilist, *numneigh, **firstneigh;
+ int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = lje_gpu_compute_n(neighbor->ago, inum, nall, atom->x,
- atom->type, domain->sublo, domain->subhi,
- atom->tag, atom->nspecial, atom->special,
- eflag, vflag, eflag_atom, vflag_atom,
- host_start, &ilist, &numneigh, cpu_time,
- success);
+ atom->type, domain->sublo, domain->subhi,
+ atom->tag, atom->nspecial, atom->special,
+ eflag, vflag, eflag_atom, vflag_atom,
+ host_start, &ilist, &numneigh, cpu_time,
+ success);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
lje_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
- ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
- vflag_atom, host_start, cpu_time, success);
+ ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
+ vflag_atom, host_start, cpu_time, success);
}
if (!success)
error->one(FLERR,"Insufficient memory on accelerator");
@@ -123,7 +123,7 @@ void PairLJExpandGPU::compute(int eflag, int vflag)
void PairLJExpandGPU::init_style()
{
- if (force->newton_pair)
+ if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with lj/expand/gpu pair style");
// Repeat cutsq calculation because done after call to init_style
@@ -147,9 +147,9 @@ void PairLJExpandGPU::init_style()
if (atom->molecular)
maxspecial=atom->maxspecial;
int success = lje_gpu_init(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4,
- offset, shift, force->special_lj, atom->nlocal,
- atom->nlocal+atom->nghost, 300, maxspecial,
- cell_size, gpu_mode, screen);
+ offset, shift, force->special_lj, atom->nlocal,
+ atom->nlocal+atom->nghost, 300, maxspecial,
+ cell_size, gpu_mode, screen);
GPU_EXTRA::check_flag(success,error,world);
if (gpu_mode == GPU_FORCE) {
@@ -170,7 +170,7 @@ double PairLJExpandGPU::memory_usage()
/* ---------------------------------------------------------------------- */
void PairLJExpandGPU::cpu_compute(int start, int inum, int eflag, int vflag,
- int *ilist, int *numneigh, int **firstneigh)
+ int *ilist, int *numneigh, int **firstneigh)
{
int i,j,ii,jj,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
@@ -206,25 +206,25 @@ void PairLJExpandGPU::cpu_compute(int start, int inum, int eflag, int vflag,
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r = sqrt(rsq);
- rshift = r - shift[itype][jtype];
- rshiftsq = rshift*rshift;
- r2inv = 1.0/rshiftsq;
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- fpair = factor_lj*forcelj/rshift/r;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
-
- if (eflag) {
- evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
- offset[itype][jtype];
- evdwl *= factor_lj;
- }
-
- if (evflag) ev_tally_full(i,evdwl,0.0,fpair,delx,dely,delz);
+ r = sqrt(rsq);
+ rshift = r - shift[itype][jtype];
+ rshiftsq = rshift*rshift;
+ r2inv = 1.0/rshiftsq;
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ fpair = factor_lj*forcelj/rshift/r;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+
+ if (eflag) {
+ evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
+ offset[itype][jtype];
+ evdwl *= factor_lj;
+ }
+
+ if (evflag) ev_tally_full(i,evdwl,0.0,fpair,delx,dely,delz);
}
}
}
diff --git a/src/GPU/pair_lj_expand_gpu.h b/src/GPU/pair_lj_expand_gpu.h
index 15a82640d35ba60432d88d7984e76063dee04e05..2187ab254f2476f5bc620a72d7bc62d70bf46cbd 100644
--- a/src/GPU/pair_lj_expand_gpu.h
+++ b/src/GPU/pair_lj_expand_gpu.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/GPU/pair_lj_sdk_coul_long_gpu.cpp b/src/GPU/pair_lj_sdk_coul_long_gpu.cpp
index 98656e50fd22a01733d94117f79ebdb32c27ab68..2103295037e666ecfd2d02c9eb1a7a934583e90b 100644
--- a/src/GPU/pair_lj_sdk_coul_long_gpu.cpp
+++ b/src/GPU/pair_lj_sdk_coul_long_gpu.cpp
@@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
-
+
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
-
+
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@@ -47,28 +47,28 @@
// External functions from cuda library for atom decomposition
int cmml_gpu_init(const int ntypes, double **cutsq, int **lj_type,
- double **host_lj1, double **host_lj2, double **host_lj3,
- double **host_lj4, double **offset, double *special_lj,
- const int nlocal, const int nall, const int max_nbors,
- const int maxspecial, const double cell_size, int &gpu_mode,
- FILE *screen, double **host_cut_ljsq, double host_cut_coulsq,
- double *host_special_coul, const double qqrd2e,
- const double g_ewald);
+ double **host_lj1, double **host_lj2, double **host_lj3,
+ double **host_lj4, double **offset, double *special_lj,
+ const int nlocal, const int nall, const int max_nbors,
+ const int maxspecial, const double cell_size, int &gpu_mode,
+ FILE *screen, double **host_cut_ljsq, double host_cut_coulsq,
+ double *host_special_coul, const double qqrd2e,
+ const double g_ewald);
void cmml_gpu_clear();
int ** cmml_gpu_compute_n(const int ago, const int inum, const int nall,
- double **host_x, int *host_type, double *sublo,
- double *subhi, int *tag, int **nspecial,
- int **special, const bool eflag, const bool vflag,
- const bool eatom, const bool vatom, int &host_start,
- int **ilist, int **jnum, const double cpu_time,
- bool &success, double *host_q, double *boxlo,
- double *prd);
+ double **host_x, int *host_type, double *sublo,
+ double *subhi, int *tag, int **nspecial,
+ int **special, const bool eflag, const bool vflag,
+ const bool eatom, const bool vatom, int &host_start,
+ int **ilist, int **jnum, const double cpu_time,
+ bool &success, double *host_q, double *boxlo,
+ double *prd);
void cmml_gpu_compute(const int ago, const int inum, const int nall,
- double **host_x, int *host_type, int *ilist, int *numj,
- int **firstneigh, const bool eflag, const bool vflag,
- const bool eatom, const bool vatom, int &host_start,
- const double cpu_time, bool &success, double *host_q,
- const int nlocal, double *boxlo, double *prd);
+ double **host_x, int *host_type, int *ilist, int *numj,
+ int **firstneigh, const bool eflag, const bool vflag,
+ const bool eatom, const bool vatom, int &host_start,
+ const double cpu_time, bool &success, double *host_q,
+ const int nlocal, double *boxlo, double *prd);
double cmml_gpu_bytes();
#include "lj_sdk_common.h"
@@ -83,7 +83,7 @@ PairLJSDKCoulLongGPU::PairLJSDKCoulLongGPU(LAMMPS *lmp) :
{
respa_enable = 0;
cpu_time = 0.0;
- GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
+ GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
@@ -101,30 +101,30 @@ void PairLJSDKCoulLongGPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
-
+
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
-
+
bool success = true;
- int *ilist, *numneigh, **firstneigh;
+ int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = cmml_gpu_compute_n(neighbor->ago, inum, nall, atom->x,
- atom->type, domain->sublo, domain->subhi,
- atom->tag, atom->nspecial, atom->special,
- eflag, vflag, eflag_atom, vflag_atom,
- host_start, &ilist, &numneigh, cpu_time,
- success, atom->q, domain->boxlo,
- domain->prd);
+ atom->type, domain->sublo, domain->subhi,
+ atom->tag, atom->nspecial, atom->special,
+ eflag, vflag, eflag_atom, vflag_atom,
+ host_start, &ilist, &numneigh, cpu_time,
+ success, atom->q, domain->boxlo,
+ domain->prd);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
cmml_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
- ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
- vflag_atom, host_start, cpu_time, success, atom->q,
- atom->nlocal, domain->boxlo, domain->prd);
+ ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
+ vflag_atom, host_start, cpu_time, success, atom->q,
+ atom->nlocal, domain->boxlo, domain->prd);
}
if (!success)
error->one(FLERR,"Insufficient memory on accelerator");
@@ -147,7 +147,7 @@ void PairLJSDKCoulLongGPU::init_style()
{
if (!atom->q_flag)
error->all(FLERR,"Pair style lj/sdk/coul/long/gpu requires atom attribute q");
- if (force->newton_pair)
+ if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with lj/sdk/coul/long/gpu pair style");
// Repeat cutsq calculation because done after call to init_style
@@ -183,11 +183,11 @@ void PairLJSDKCoulLongGPU::init_style()
if (atom->molecular)
maxspecial=atom->maxspecial;
int success = cmml_gpu_init(atom->ntypes+1, cutsq, lj_type, lj1, lj2, lj3,
- lj4, offset, force->special_lj, atom->nlocal,
- atom->nlocal+atom->nghost, 300, maxspecial,
- cell_size, gpu_mode, screen, cut_ljsq,
- cut_coulsq, force->special_coul,
- force->qqrd2e, g_ewald);
+ lj4, offset, force->special_lj, atom->nlocal,
+ atom->nlocal+atom->nghost, 300, maxspecial,
+ cell_size, gpu_mode, screen, cut_ljsq,
+ cut_coulsq, force->special_coul,
+ force->qqrd2e, g_ewald);
GPU_EXTRA::check_flag(success,error,world);
if (gpu_mode == GPU_FORCE) {
@@ -208,7 +208,7 @@ double PairLJSDKCoulLongGPU::memory_usage()
/* ---------------------------------------------------------------------- */
template <int EVFLAG, int EFLAG>
void PairLJSDKCoulLongGPU::cpu_compute(int start, int inum, int *ilist,
- int *numneigh, int **firstneigh)
+ int *numneigh, int **firstneigh)
{
int i,j,ii,jj;
double qtmp,xtmp,ytmp,ztmp;
@@ -255,11 +255,11 @@ void PairLJSDKCoulLongGPU::cpu_compute(int start, int inum, int *ilist,
double fpair = 0.0;
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- const int ljt = lj_type[itype][jtype];
+ r2inv = 1.0/rsq;
+ const int ljt = lj_type[itype][jtype];
- if (rsq < cut_coulsq) {
- if (!ncoultablebits || rsq <= tabinnersq) {
+ if (rsq < cut_coulsq) {
+ if (!ncoultablebits || rsq <= tabinnersq) {
const double r = sqrt(rsq);
const double grij = g_ewald * r;
const double expm2 = exp(-grij*grij);
@@ -272,7 +272,7 @@ void PairLJSDKCoulLongGPU::cpu_compute(int start, int inum, int *ilist,
forcecoul -= (1.0-factor_coul)*prefactor;
if (EFLAG) ecoul -= (1.0-factor_coul)*prefactor;
}
- } else {
+ } else {
union_int_float_t rsq_lookup;
rsq_lookup.f = rsq;
int itable = rsq_lookup.i & ncoulmask;
@@ -291,56 +291,56 @@ void PairLJSDKCoulLongGPU::cpu_compute(int start, int inum, int *ilist,
forcecoul -= (1.0-factor_coul)*prefactor;
if (EFLAG) ecoul -= (1.0-factor_coul)*prefactor;
}
- }
- } else {
- forcecoul = 0.0;
- ecoul = 0.0;
- }
-
-
- if (rsq < cut_ljsq[itype][jtype]) {
-
- if (ljt == LJ12_4) {
- const double r4inv=r2inv*r2inv;
- forcelj = r4inv*(lj1[itype][jtype]*r4inv*r4inv
- - lj2[itype][jtype]);
-
- if (EFLAG)
- evdwl = r4inv*(lj3[itype][jtype]*r4inv*r4inv
- - lj4[itype][jtype]) - offset[itype][jtype];
-
- } else if (ljt == LJ9_6) {
- const double r3inv = r2inv*sqrt(r2inv);
- const double r6inv = r3inv*r3inv;
- forcelj = r6inv*(lj1[itype][jtype]*r3inv
- - lj2[itype][jtype]);
- if (EFLAG)
- evdwl = r6inv*(lj3[itype][jtype]*r3inv
- - lj4[itype][jtype]) - offset[itype][jtype];
-
- } else if (ljt == LJ12_6) {
- const double r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv*(lj1[itype][jtype]*r6inv
- - lj2[itype][jtype]);
- if (EFLAG)
- evdwl = r6inv*(lj3[itype][jtype]*r6inv
- - lj4[itype][jtype]) - offset[itype][jtype];
- }
-
- if (EFLAG) evdwl *= factor_lj;
-
- } else {
- forcelj=0.0;
- evdwl = 0.0;
- }
-
- fpair = (forcecoul + factor_lj*forcelj) * r2inv;
-
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
-
- if (EVFLAG) ev_tally_full(i,evdwl,ecoul,fpair,delx,dely,delz);
+ }
+ } else {
+ forcecoul = 0.0;
+ ecoul = 0.0;
+ }
+
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+
+ if (ljt == LJ12_4) {
+ const double r4inv=r2inv*r2inv;
+ forcelj = r4inv*(lj1[itype][jtype]*r4inv*r4inv
+ - lj2[itype][jtype]);
+
+ if (EFLAG)
+ evdwl = r4inv*(lj3[itype][jtype]*r4inv*r4inv
+ - lj4[itype][jtype]) - offset[itype][jtype];
+
+ } else if (ljt == LJ9_6) {
+ const double r3inv = r2inv*sqrt(r2inv);
+ const double r6inv = r3inv*r3inv;
+ forcelj = r6inv*(lj1[itype][jtype]*r3inv
+ - lj2[itype][jtype]);
+ if (EFLAG)
+ evdwl = r6inv*(lj3[itype][jtype]*r3inv
+ - lj4[itype][jtype]) - offset[itype][jtype];
+
+ } else if (ljt == LJ12_6) {
+ const double r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv*(lj1[itype][jtype]*r6inv
+ - lj2[itype][jtype]);
+ if (EFLAG)
+ evdwl = r6inv*(lj3[itype][jtype]*r6inv
+ - lj4[itype][jtype]) - offset[itype][jtype];
+ }
+
+ if (EFLAG) evdwl *= factor_lj;
+
+ } else {
+ forcelj=0.0;
+ evdwl = 0.0;
+ }
+
+ fpair = (forcecoul + factor_lj*forcelj) * r2inv;
+
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+
+ if (EVFLAG) ev_tally_full(i,evdwl,ecoul,fpair,delx,dely,delz);
}
}
f[i][0] += fxtmp;
diff --git a/src/GPU/pair_lj_sdk_coul_long_gpu.h b/src/GPU/pair_lj_sdk_coul_long_gpu.h
index 595c05c1186fa3086193baa17f193f64ef1d26f0..f8530bf35264fe748067b4d391957f35f9be78d6 100644
--- a/src/GPU/pair_lj_sdk_coul_long_gpu.h
+++ b/src/GPU/pair_lj_sdk_coul_long_gpu.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/GPU/pair_lj_sdk_gpu.cpp b/src/GPU/pair_lj_sdk_gpu.cpp
index 6d610e9f97e66acc644cb38aa991007f180052a5..745433458bea46beabd1402bdd0741db8145f3f8 100644
--- a/src/GPU/pair_lj_sdk_gpu.cpp
+++ b/src/GPU/pair_lj_sdk_gpu.cpp
@@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
-
+
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
-
+
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@@ -37,25 +37,25 @@
// External functions from cuda library for atom decomposition
-int cmm_gpu_init(const int ntypes, double **cutsq, int **cg_types,
- double **host_lj1, double **host_lj2, double **host_lj3,
- double **host_lj4, double **offset, double *special_lj,
- const int nlocal, const int nall, const int max_nbors,
- const int maxspecial, const double cell_size, int &gpu_mode,
- FILE *screen);
+int cmm_gpu_init(const int ntypes, double **cutsq, int **cg_types,
+ double **host_lj1, double **host_lj2, double **host_lj3,
+ double **host_lj4, double **offset, double *special_lj,
+ const int nlocal, const int nall, const int max_nbors,
+ const int maxspecial, const double cell_size, int &gpu_mode,
+ FILE *screen);
void cmm_gpu_clear();
int ** cmm_gpu_compute_n(const int ago, const int inum, const int nall,
- double **host_x, int *host_type, double *sublo,
- double *subhi, int *tag, int **nspecial,
- int **special, const bool eflag, const bool vflag,
- const bool eatom, const bool vatom, int &host_start,
- int **ilist, int **jnum,
- const double cpu_time, bool &success);
+ double **host_x, int *host_type, double *sublo,
+ double *subhi, int *tag, int **nspecial,
+ int **special, const bool eflag, const bool vflag,
+ const bool eatom, const bool vatom, int &host_start,
+ int **ilist, int **jnum,
+ const double cpu_time, bool &success);
void cmm_gpu_compute(const int ago, const int inum, const int nall,
- double **host_x, int *host_type, int *ilist, int *numj,
- int **firstneigh, const bool eflag, const bool vflag,
- const bool eatom, const bool vatom, int &host_start,
- const double cpu_time, bool &success);
+ double **host_x, int *host_type, int *ilist, int *numj,
+ int **firstneigh, const bool eflag, const bool vflag,
+ const bool eatom, const bool vatom, int &host_start,
+ const double cpu_time, bool &success);
double cmm_gpu_bytes();
#include "lj_sdk_common.h"
@@ -69,7 +69,7 @@ PairLJSDKGPU::PairLJSDKGPU(LAMMPS *lmp) : PairLJSDK(lmp), gpu_mode(GPU_FORCE)
{
respa_enable = 0;
cpu_time = 0.0;
- GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
+ GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
@@ -87,28 +87,28 @@ void PairLJSDKGPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
-
+
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
-
+
bool success = true;
- int *ilist, *numneigh, **firstneigh;
+ int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = cmm_gpu_compute_n(neighbor->ago, inum, nall, atom->x,
- atom->type, domain->sublo, domain->subhi,
- atom->tag, atom->nspecial, atom->special,
- eflag, vflag, eflag_atom, vflag_atom,
- host_start, &ilist, &numneigh, cpu_time,
- success);
+ atom->type, domain->sublo, domain->subhi,
+ atom->tag, atom->nspecial, atom->special,
+ eflag, vflag, eflag_atom, vflag_atom,
+ host_start, &ilist, &numneigh, cpu_time,
+ success);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
cmm_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
- ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
- vflag_atom, host_start, cpu_time, success);
+ ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
+ vflag_atom, host_start, cpu_time, success);
}
if (!success)
error->one(FLERR,"Insufficient memory on accelerator");
@@ -129,7 +129,7 @@ void PairLJSDKGPU::compute(int eflag, int vflag)
void PairLJSDKGPU::init_style()
{
- if (force->newton_pair)
+ if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with lj/sdk/gpu pair style");
// Repeat cutsq calculation because done after call to init_style
@@ -153,9 +153,9 @@ void PairLJSDKGPU::init_style()
if (atom->molecular)
maxspecial=atom->maxspecial;
int success = cmm_gpu_init(atom->ntypes+1,cutsq,lj_type,lj1,lj2,lj3,lj4,
- offset, force->special_lj, atom->nlocal,
- atom->nlocal+atom->nghost, 300, maxspecial,
- cell_size, gpu_mode, screen);
+ offset, force->special_lj, atom->nlocal,
+ atom->nlocal+atom->nghost, 300, maxspecial,
+ cell_size, gpu_mode, screen);
GPU_EXTRA::check_flag(success,error,world);
if (gpu_mode == GPU_FORCE) {
@@ -176,7 +176,7 @@ double PairLJSDKGPU::memory_usage()
/* ---------------------------------------------------------------------- */
template <int EVFLAG, int EFLAG>
void PairLJSDKGPU::cpu_compute(int start, int inum, int *ilist,
- int *numneigh, int **firstneigh)
+ int *numneigh, int **firstneigh)
{
int i,j,ii,jj,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
@@ -214,43 +214,43 @@ void PairLJSDKGPU::cpu_compute(int start, int inum, int *ilist,
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- const int ljt = lj_type[itype][jtype];
-
- if (ljt == LJ12_4) {
- const double r4inv=r2inv*r2inv;
- forcelj = r4inv*(lj1[itype][jtype]*r4inv*r4inv
- - lj2[itype][jtype]);
-
- if (EFLAG)
- evdwl = r4inv*(lj3[itype][jtype]*r4inv*r4inv
- - lj4[itype][jtype]) - offset[itype][jtype];
-
- } else if (ljt == LJ9_6) {
- const double r3inv = r2inv*sqrt(r2inv);
- const double r6inv = r3inv*r3inv;
- forcelj = r6inv*(lj1[itype][jtype]*r3inv
- - lj2[itype][jtype]);
- if (EFLAG)
- evdwl = r6inv*(lj3[itype][jtype]*r3inv
- - lj4[itype][jtype]) - offset[itype][jtype];
-
- } else if (ljt == LJ12_6) {
- const double r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv*(lj1[itype][jtype]*r6inv
- - lj2[itype][jtype]);
- if (EFLAG)
- evdwl = r6inv*(lj3[itype][jtype]*r6inv
- - lj4[itype][jtype]) - offset[itype][jtype];
- } else continue;
-
- fpair = factor_lj*forcelj*r2inv;
-
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
-
- if (EVFLAG) ev_tally_full(i,evdwl,0.0,fpair,delx,dely,delz);
+ r2inv = 1.0/rsq;
+ const int ljt = lj_type[itype][jtype];
+
+ if (ljt == LJ12_4) {
+ const double r4inv=r2inv*r2inv;
+ forcelj = r4inv*(lj1[itype][jtype]*r4inv*r4inv
+ - lj2[itype][jtype]);
+
+ if (EFLAG)
+ evdwl = r4inv*(lj3[itype][jtype]*r4inv*r4inv
+ - lj4[itype][jtype]) - offset[itype][jtype];
+
+ } else if (ljt == LJ9_6) {
+ const double r3inv = r2inv*sqrt(r2inv);
+ const double r6inv = r3inv*r3inv;
+ forcelj = r6inv*(lj1[itype][jtype]*r3inv
+ - lj2[itype][jtype]);
+ if (EFLAG)
+ evdwl = r6inv*(lj3[itype][jtype]*r3inv
+ - lj4[itype][jtype]) - offset[itype][jtype];
+
+ } else if (ljt == LJ12_6) {
+ const double r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv*(lj1[itype][jtype]*r6inv
+ - lj2[itype][jtype]);
+ if (EFLAG)
+ evdwl = r6inv*(lj3[itype][jtype]*r6inv
+ - lj4[itype][jtype]) - offset[itype][jtype];
+ } else continue;
+
+ fpair = factor_lj*forcelj*r2inv;
+
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+
+ if (EVFLAG) ev_tally_full(i,evdwl,0.0,fpair,delx,dely,delz);
}
}
f[i][0] += fxtmp;
diff --git a/src/GPU/pair_lj_sdk_gpu.h b/src/GPU/pair_lj_sdk_gpu.h
index a800ece1d763bf03a651abe064b2d14e88ec79a2..c99ea363bc9c27f9db7cb071ff907baca9ff971d 100644
--- a/src/GPU/pair_lj_sdk_gpu.h
+++ b/src/GPU/pair_lj_sdk_gpu.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/GPU/pair_morse_gpu.cpp b/src/GPU/pair_morse_gpu.cpp
index 41f420f6210103fc8a97999e7d76d148e2be0072..0deae8ef12482c01dfb67cc4f8a74095e6cd0e93 100644
--- a/src/GPU/pair_morse_gpu.cpp
+++ b/src/GPU/pair_morse_gpu.cpp
@@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
-
+
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
-
+
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@@ -38,23 +38,23 @@
// External functions from cuda library for atom decomposition
int mor_gpu_init(const int ntypes, double **cutsq, double **host_morse1,
- double **host_r0, double **host_alpha, double **host_d0,
- double **offset, double *special_lj, const int nlocal,
- const int nall, const int max_nbors, const int maxspecial,
- const double cell_size, int &gpu_mode, FILE *screen);
+ double **host_r0, double **host_alpha, double **host_d0,
+ double **offset, double *special_lj, const int nlocal,
+ const int nall, const int max_nbors, const int maxspecial,
+ const double cell_size, int &gpu_mode, FILE *screen);
void mor_gpu_clear();
int ** mor_gpu_compute_n(const int ago, const int inum,
- const int nall, double **host_x, int *host_type,
- double *sublo, double *subhi, int *tag, int **nspecial,
- int **special, const bool eflag, const bool vflag,
- const bool eatom, const bool vatom, int &host_start,
- int **ilist, int **jnum,
- const double cpu_time, bool &success);
-void mor_gpu_compute(const int ago, const int inum, const int nall,
- double **host_x, int *host_type, int *ilist, int *numj,
- int **firstneigh, const bool eflag, const bool vflag,
- const bool eatom, const bool vatom, int &host_start,
- const double cpu_time, bool &success);
+ const int nall, double **host_x, int *host_type,
+ double *sublo, double *subhi, int *tag, int **nspecial,
+ int **special, const bool eflag, const bool vflag,
+ const bool eatom, const bool vatom, int &host_start,
+ int **ilist, int **jnum,
+ const double cpu_time, bool &success);
+void mor_gpu_compute(const int ago, const int inum, const int nall,
+ double **host_x, int *host_type, int *ilist, int *numj,
+ int **firstneigh, const bool eflag, const bool vflag,
+ const bool eatom, const bool vatom, int &host_start,
+ const double cpu_time, bool &success);
double mor_gpu_bytes();
using namespace LAMMPS_NS;
@@ -64,7 +64,7 @@ using namespace LAMMPS_NS;
PairMorseGPU::PairMorseGPU(LAMMPS *lmp) : PairMorse(lmp), gpu_mode(GPU_FORCE)
{
cpu_time = 0.0;
- GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
+ GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
@@ -82,28 +82,28 @@ void PairMorseGPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
-
+
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
-
+
bool success = true;
- int *ilist, *numneigh, **firstneigh;
+ int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = mor_gpu_compute_n(neighbor->ago, inum, nall,
- atom->x, atom->type, domain->sublo,
- domain->subhi, atom->tag, atom->nspecial,
- atom->special, eflag, vflag, eflag_atom,
- vflag_atom, host_start, &ilist, &numneigh,
- cpu_time, success);
+ atom->x, atom->type, domain->sublo,
+ domain->subhi, atom->tag, atom->nspecial,
+ atom->special, eflag, vflag, eflag_atom,
+ vflag_atom, host_start, &ilist, &numneigh,
+ cpu_time, success);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
mor_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
- ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
- vflag_atom, host_start, cpu_time, success);
+ ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
+ vflag_atom, host_start, cpu_time, success);
}
if (!success)
error->one(FLERR,"Insufficient memory on accelerator");
@@ -121,7 +121,7 @@ void PairMorseGPU::compute(int eflag, int vflag)
void PairMorseGPU::init_style()
{
- if (force->newton_pair)
+ if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with morse/gpu pair style");
// Repeat cutsq calculation because done after call to init_style
@@ -145,9 +145,9 @@ void PairMorseGPU::init_style()
if (atom->molecular)
maxspecial=atom->maxspecial;
int success = mor_gpu_init(atom->ntypes+1, cutsq, morse1, r0, alpha, d0,
- offset, force->special_lj, atom->nlocal,
- atom->nlocal+atom->nghost, 300, maxspecial,
- cell_size, gpu_mode, screen);
+ offset, force->special_lj, atom->nlocal,
+ atom->nlocal+atom->nghost, 300, maxspecial,
+ cell_size, gpu_mode, screen);
GPU_EXTRA::check_flag(success,error,world);
if (gpu_mode == GPU_FORCE) {
@@ -168,7 +168,7 @@ double PairMorseGPU::memory_usage()
/* ---------------------------------------------------------------------- */
void PairMorseGPU::cpu_compute(int start, int inum, int eflag, int vflag,
- int *ilist, int *numneigh, int **firstneigh)
+ int *ilist, int *numneigh, int **firstneigh)
{
int i,j,ii,jj,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
@@ -203,22 +203,22 @@ void PairMorseGPU::cpu_compute(int start, int inum, int eflag, int vflag,
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r = sqrt(rsq);
- dr = r - r0[itype][jtype];
- dexp = exp(-alpha[itype][jtype] * dr);
- fpair = factor_lj * morse1[itype][jtype] * (dexp*dexp - dexp) / r;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
-
- if (eflag) {
- evdwl = d0[itype][jtype] * (dexp*dexp - 2.0*dexp) -
- offset[itype][jtype];
- evdwl *= factor_lj;
- }
-
- if (evflag) ev_tally_full(i,evdwl,0.0,fpair,delx,dely,delz);
+ r = sqrt(rsq);
+ dr = r - r0[itype][jtype];
+ dexp = exp(-alpha[itype][jtype] * dr);
+ fpair = factor_lj * morse1[itype][jtype] * (dexp*dexp - dexp) / r;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+
+ if (eflag) {
+ evdwl = d0[itype][jtype] * (dexp*dexp - 2.0*dexp) -
+ offset[itype][jtype];
+ evdwl *= factor_lj;
+ }
+
+ if (evflag) ev_tally_full(i,evdwl,0.0,fpair,delx,dely,delz);
}
}
}
diff --git a/src/GPU/pair_morse_gpu.h b/src/GPU/pair_morse_gpu.h
index 4cc3fe264986f7af9206c9d7189da0a50ffeed88..13dd0ab7960f0b6ef7129032925f9dc5d9bc1a91 100644
--- a/src/GPU/pair_morse_gpu.h
+++ b/src/GPU/pair_morse_gpu.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/GPU/pair_resquared_gpu.cpp b/src/GPU/pair_resquared_gpu.cpp
index 8c9939f49b7848054e9f5788a43d4cac37bb7e8e..07cf75906e1296257c4e13691821d9b99721df79 100644
--- a/src/GPU/pair_resquared_gpu.cpp
+++ b/src/GPU/pair_resquared_gpu.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -40,25 +40,25 @@
// External functions from cuda library for atom decomposition
int re_gpu_init(const int ntypes, double **shape, double **well,
- double **cutsq, double **sigma, double **epsilon,
- int **form, double **host_lj1,
- double **host_lj2, double **host_lj3, double **host_lj4,
- double **offset, double *special_lj, const int nlocal,
- const int nall, const int max_nbors, const int maxspecial,
- const double cell_size, int &gpu_mode, FILE *screen);
+ double **cutsq, double **sigma, double **epsilon,
+ int **form, double **host_lj1,
+ double **host_lj2, double **host_lj3, double **host_lj4,
+ double **offset, double *special_lj, const int nlocal,
+ const int nall, const int max_nbors, const int maxspecial,
+ const double cell_size, int &gpu_mode, FILE *screen);
void re_gpu_clear();
int ** re_gpu_compute_n(const int ago, const int inum, const int nall,
- double **host_x, int *host_type, double *sublo,
- double *subhi, int *tag, int **nspecial, int **special,
- const bool eflag, const bool vflag,
- const bool eatom, const bool vatom, int &host_start,
- int **ilist, int **jnum, const double cpu_time,
- bool &success, double **host_quat);
+ double **host_x, int *host_type, double *sublo,
+ double *subhi, int *tag, int **nspecial, int **special,
+ const bool eflag, const bool vflag,
+ const bool eatom, const bool vatom, int &host_start,
+ int **ilist, int **jnum, const double cpu_time,
+ bool &success, double **host_quat);
int * re_gpu_compute(const int ago, const int inum, const int nall,
- double **host_x, int *host_type, int *ilist, int *numj,
- int **firstneigh, const bool eflag, const bool vflag,
- const bool eatom, const bool vatom, int &host_start,
- const double cpu_time, bool &success, double **host_quat);
+ double **host_x, int *host_type, int *ilist, int *numj,
+ int **firstneigh, const bool eflag, const bool vflag,
+ const bool eatom, const bool vatom, int &host_start,
+ const double cpu_time, bool &success, double **host_quat);
double re_gpu_bytes();
using namespace LAMMPS_NS;
@@ -71,11 +71,11 @@ PairRESquaredGPU::PairRESquaredGPU(LAMMPS *lmp) : PairRESquared(lmp),
gpu_mode(GPU_FORCE)
{
avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
- if (!avec)
+ if (!avec)
error->all(FLERR,"Pair resquared/gpu requires atom style ellipsoid");
quat_nmax = 0;
quat = NULL;
- GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
+ GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
@@ -100,7 +100,7 @@ void PairRESquaredGPU::compute(int eflag, int vflag)
int inum, host_start;
bool success = true;
- int *ilist, *numneigh, **firstneigh;
+ int *ilist, *numneigh, **firstneigh;
if (nall > quat_nmax) {
quat_nmax = static_cast<int>(1.1 * nall);
@@ -121,19 +121,19 @@ void PairRESquaredGPU::compute(int eflag, int vflag)
if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = re_gpu_compute_n(neighbor->ago, inum, nall, atom->x,
- atom->type, domain->sublo, domain->subhi,
- atom->tag, atom->nspecial, atom->special,
- eflag, vflag, eflag_atom, vflag_atom,
- host_start, &ilist, &numneigh, cpu_time,
- success, quat);
+ atom->type, domain->sublo, domain->subhi,
+ atom->tag, atom->nspecial, atom->special,
+ eflag, vflag, eflag_atom, vflag_atom,
+ host_start, &ilist, &numneigh, cpu_time,
+ success, quat);
} else {
inum = list->inum;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
ilist = re_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
- list->ilist, numneigh, firstneigh, eflag, vflag,
- eflag_atom, vflag_atom, host_start,
- cpu_time, success, quat);
+ list->ilist, numneigh, firstneigh, eflag, vflag,
+ eflag_atom, vflag_atom, host_start,
+ cpu_time, success, quat);
}
if (!success)
error->one(FLERR,"Insufficient memory on accelerator");
@@ -151,7 +151,7 @@ void PairRESquaredGPU::compute(int eflag, int vflag)
void PairRESquaredGPU::init_style()
{
- if (force->newton_pair)
+ if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with resquared/gpu pair style");
if (!atom->ellipsoid_flag)
error->all(FLERR,"Pair resquared/gpu requires atom style ellipsoid");
@@ -193,10 +193,10 @@ void PairRESquaredGPU::init_style()
if (atom->molecular)
maxspecial=atom->maxspecial;
int success = re_gpu_init(atom->ntypes+1, shape1, well, cutsq, sigma,
- epsilon, form, lj1, lj2, lj3, lj4, offset,
- force->special_lj, atom->nlocal,
- atom->nlocal+atom->nghost, 300, maxspecial,
- cell_size, gpu_mode, screen);
+ epsilon, form, lj1, lj2, lj3, lj4, offset,
+ force->special_lj, atom->nlocal,
+ atom->nlocal+atom->nghost, 300, maxspecial,
+ cell_size, gpu_mode, screen);
GPU_EXTRA::check_flag(success,error,world);
if (gpu_mode == GPU_FORCE) {
@@ -219,7 +219,7 @@ double PairRESquaredGPU::memory_usage()
/* ---------------------------------------------------------------------- */
void PairRESquaredGPU::cpu_compute(int start, int inum, int eflag, int vflag,
- int *ilist, int *numneigh, int **firstneigh)
+ int *ilist, int *numneigh, int **firstneigh)
{
int i,j,ii,jj,jnum,itype,jtype;
double evdwl,one_eng,rsq,r2inv,r6inv,forcelj,factor_lj;
@@ -308,8 +308,8 @@ void PairRESquaredGPU::cpu_compute(int start, int inum, int eflag, int vflag,
if (eflag) evdwl = factor_lj*one_eng;
- if (evflag) ev_tally_xyz_full(i,evdwl,0.0,fforce[0],fforce[1],
- fforce[2],-r12[0],-r12[1],-r12[2]);
+ if (evflag) ev_tally_xyz_full(i,evdwl,0.0,fforce[0],fforce[1],
+ fforce[2],-r12[0],-r12[1],-r12[2]);
}
}
}
diff --git a/src/GPU/pair_resquared_gpu.h b/src/GPU/pair_resquared_gpu.h
index 6f95a8b17de52db3567e0be75e614d98024e9799..725088616744be9990d933b32845cbca3558656f 100644
--- a/src/GPU/pair_resquared_gpu.h
+++ b/src/GPU/pair_resquared_gpu.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/GPU/pair_table_gpu.cpp b/src/GPU/pair_table_gpu.cpp
index fcd7e7edf852d52c8c02ed7aeb80d9f405ce31e4..797ac8268dd60f965f027a41f808beb8031d0b94 100644
--- a/src/GPU/pair_table_gpu.cpp
+++ b/src/GPU/pair_table_gpu.cpp
@@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
-
+
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
-
+
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@@ -42,37 +42,37 @@
// External functions from cuda library for atom decomposition
-int table_gpu_init(const int ntypes, double **cutsq,
- double ***host_table_coeffs, double **host_table_data,
- double *special_lj, const int nlocal, const int nall,
- const int max_nbors, const int maxspecial,
- const double cell_size, int &gpu_mode, FILE *screen,
- int tabstyle, int ntables, int tablength);
+int table_gpu_init(const int ntypes, double **cutsq,
+ double ***host_table_coeffs, double **host_table_data,
+ double *special_lj, const int nlocal, const int nall,
+ const int max_nbors, const int maxspecial,
+ const double cell_size, int &gpu_mode, FILE *screen,
+ int tabstyle, int ntables, int tablength);
void table_gpu_clear();
int ** table_gpu_compute_n(const int ago, const int inum, const int nall,
- double **host_x, int *host_type, double *sublo,
- double *subhi, int *tag, int **nspecial,
- int **special, const bool eflag, const bool vflag,
- const bool eatom, const bool vatom, int &host_start,
- int **ilist, int **jnum, const double cpu_time,
- bool &success);
-void table_gpu_compute(const int ago, const int inum, const int nall,
- double **host_x, int *host_type, int *ilist, int *numj,
- int **firstneigh, const bool eflag, const bool vflag,
- const bool eatom, const bool vatom, int &host_start,
- const double cpu_time, bool &success);
+ double **host_x, int *host_type, double *sublo,
+ double *subhi, int *tag, int **nspecial,
+ int **special, const bool eflag, const bool vflag,
+ const bool eatom, const bool vatom, int &host_start,
+ int **ilist, int **jnum, const double cpu_time,
+ bool &success);
+void table_gpu_compute(const int ago, const int inum, const int nall,
+ double **host_x, int *host_type, int *ilist, int *numj,
+ int **firstneigh, const bool eflag, const bool vflag,
+ const bool eatom, const bool vatom, int &host_start,
+ const double cpu_time, bool &success);
double table_gpu_bytes();
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-PairTableGPU::PairTableGPU(LAMMPS *lmp) : PairTable(lmp),
- gpu_mode(GPU_FORCE)
+PairTableGPU::PairTableGPU(LAMMPS *lmp) : PairTable(lmp),
+ gpu_mode(GPU_FORCE)
{
respa_enable = 0;
cpu_time = 0.0;
- GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
+ GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
@@ -90,28 +90,28 @@ void PairTableGPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
-
+
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
-
+
bool success = true;
int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = table_gpu_compute_n(neighbor->ago, inum, nall, atom->x,
- atom->type, domain->sublo, domain->subhi,
- atom->tag, atom->nspecial, atom->special,
- eflag, vflag, eflag_atom, vflag_atom,
- host_start, &ilist, &numneigh, cpu_time,
- success);
+ atom->type, domain->sublo, domain->subhi,
+ atom->tag, atom->nspecial, atom->special,
+ eflag, vflag, eflag_atom, vflag_atom,
+ host_start, &ilist, &numneigh, cpu_time,
+ success);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
table_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
- ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
- vflag_atom, host_start, cpu_time, success);
+ ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
+ vflag_atom, host_start, cpu_time, success);
}
if (!success)
error->one(FLERR,"Insufficient memory on accelerator");
@@ -129,11 +129,11 @@ void PairTableGPU::compute(int eflag, int vflag)
void PairTableGPU::init_style()
{
- if (force->newton_pair)
+ if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with table/gpu pair style");
int ntypes = atom->ntypes;
-
+
// Repeat cutsq calculation because done after call to init_style
double maxcut = -1.0;
double cut;
@@ -150,12 +150,12 @@ void PairTableGPU::init_style()
}
}
double cell_size = sqrt(maxcut) + neighbor->skin;
-
+
// pack tables and send them to device
double ***table_coeffs = NULL;
double **table_data = NULL;
memory->create(table_coeffs, ntypes+1, ntypes+1, 6, "table:coeffs");
-
+
Table *tb;
for (int i = 1; i <= atom->ntypes; i++)
for (int j = 1; j <= atom->ntypes; j++) {
@@ -168,7 +168,7 @@ void PairTableGPU::init_style()
table_coeffs[i][j][4] = tb->invdelta;
table_coeffs[i][j][5] = tb->deltasq6;
}
-
+
if (tabstyle != BITMAP) {
memory->create(table_data, ntables, 6*tablength, "table:data");
for (int n = 0; n < ntables; n++) {
@@ -196,7 +196,7 @@ void PairTableGPU::init_style()
table_data[n][6*k+3] = tb->e2[k];
table_data[n][6*k+4] = tb->f2[k];
}
- }
+ }
}
} else {
int ntable = 1 << tablength;
@@ -212,17 +212,17 @@ void PairTableGPU::init_style()
table_data[n][6*k+4] = tb->df[k];
table_data[n][6*k+5] = tb->drsq[k];
}
- }
+ }
}
-
+
int maxspecial=0;
if (atom->molecular)
maxspecial=atom->maxspecial;
int success = table_gpu_init(atom->ntypes+1, cutsq, table_coeffs, table_data,
- force->special_lj, atom->nlocal,
- atom->nlocal+atom->nghost, 300, maxspecial,
- cell_size, gpu_mode, screen, tabstyle, ntables,
- tablength);
+ force->special_lj, atom->nlocal,
+ atom->nlocal+atom->nghost, 300, maxspecial,
+ cell_size, gpu_mode, screen, tabstyle, ntables,
+ tablength);
GPU_EXTRA::check_flag(success,error,world);
if (gpu_mode == GPU_FORCE) {
@@ -230,7 +230,7 @@ void PairTableGPU::init_style()
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
}
-
+
memory->destroy(table_coeffs);
memory->destroy(table_data);
}
@@ -245,17 +245,17 @@ double PairTableGPU::memory_usage()
/* ---------------------------------------------------------------------- */
-void PairTableGPU::cpu_compute(int start, int inum, int eflag, int vflag,
- int *ilist, int *numneigh, int **firstneigh) {
+void PairTableGPU::cpu_compute(int start, int inum, int eflag, int vflag,
+ int *ilist, int *numneigh, int **firstneigh) {
int i,j,ii,jj,jnum,itype,jtype,itable;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,factor_lj,fraction,value,a,b;
int *jlist;
Table *tb;
-
+
union_int_float_t rsq_lookup;
int tlm1 = tablength - 1;
-
+
double **x = atom->x;
double **f = atom->f;
int *type = atom->type;
@@ -284,58 +284,58 @@ void PairTableGPU::cpu_compute(int start, int inum, int eflag, int vflag,
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- tb = &tables[tabindex[itype][jtype]];
- if (rsq < tb->innersq)
- error->one(FLERR,"Pair distance < table inner cutoff");
-
- if (tabstyle == LOOKUP) {
- itable = static_cast<int> ((rsq - tb->innersq) * tb->invdelta);
- if (itable >= tlm1)
- error->one(FLERR,"Pair distance > table outer cutoff");
- fpair = factor_lj * tb->f[itable];
- } else if (tabstyle == LINEAR) {
- itable = static_cast<int> ((rsq - tb->innersq) * tb->invdelta);
- if (itable >= tlm1)
- error->one(FLERR,"Pair distance > table outer cutoff");
- fraction = (rsq - tb->rsq[itable]) * tb->invdelta;
- value = tb->f[itable] + fraction*tb->df[itable];
- fpair = factor_lj * value;
- } else if (tabstyle == SPLINE) {
- itable = static_cast<int> ((rsq - tb->innersq) * tb->invdelta);
- if (itable >= tlm1)
- error->one(FLERR,"Pair distance > table outer cutoff");
- b = (rsq - tb->rsq[itable]) * tb->invdelta;
- a = 1.0 - b;
- value = a * tb->f[itable] + b * tb->f[itable+1] +
- ((a*a*a-a)*tb->f2[itable] + (b*b*b-b)*tb->f2[itable+1]) *
+ tb = &tables[tabindex[itype][jtype]];
+ if (rsq < tb->innersq)
+ error->one(FLERR,"Pair distance < table inner cutoff");
+
+ if (tabstyle == LOOKUP) {
+ itable = static_cast<int> ((rsq - tb->innersq) * tb->invdelta);
+ if (itable >= tlm1)
+ error->one(FLERR,"Pair distance > table outer cutoff");
+ fpair = factor_lj * tb->f[itable];
+ } else if (tabstyle == LINEAR) {
+ itable = static_cast<int> ((rsq - tb->innersq) * tb->invdelta);
+ if (itable >= tlm1)
+ error->one(FLERR,"Pair distance > table outer cutoff");
+ fraction = (rsq - tb->rsq[itable]) * tb->invdelta;
+ value = tb->f[itable] + fraction*tb->df[itable];
+ fpair = factor_lj * value;
+ } else if (tabstyle == SPLINE) {
+ itable = static_cast<int> ((rsq - tb->innersq) * tb->invdelta);
+ if (itable >= tlm1)
+ error->one(FLERR,"Pair distance > table outer cutoff");
+ b = (rsq - tb->rsq[itable]) * tb->invdelta;
+ a = 1.0 - b;
+ value = a * tb->f[itable] + b * tb->f[itable+1] +
+ ((a*a*a-a)*tb->f2[itable] + (b*b*b-b)*tb->f2[itable+1]) *
tb->deltasq6;
- fpair = factor_lj * value;
- } else {
- rsq_lookup.f = rsq;
- itable = rsq_lookup.i & tb->nmask;
- itable >>= tb->nshiftbits;
- fraction = (rsq_lookup.f - tb->rsq[itable]) * tb->drsq[itable];
- value = tb->f[itable] + fraction*tb->df[itable];
- fpair = factor_lj * value;
- }
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
-
- if (eflag) {
- if (tabstyle == LOOKUP)
- evdwl = tb->e[itable];
- else if (tabstyle == LINEAR || tabstyle == BITMAP)
- evdwl = tb->e[itable] + fraction*tb->de[itable];
- else
- evdwl = a * tb->e[itable] + b * tb->e[itable+1] +
- ((a*a*a-a)*tb->e2[itable] + (b*b*b-b)*tb->e2[itable+1]) *
- tb->deltasq6;
- evdwl *= factor_lj;
- }
-
- if (evflag) ev_tally_full(i,evdwl,0.0,fpair,delx,dely,delz);
+ fpair = factor_lj * value;
+ } else {
+ rsq_lookup.f = rsq;
+ itable = rsq_lookup.i & tb->nmask;
+ itable >>= tb->nshiftbits;
+ fraction = (rsq_lookup.f - tb->rsq[itable]) * tb->drsq[itable];
+ value = tb->f[itable] + fraction*tb->df[itable];
+ fpair = factor_lj * value;
+ }
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+
+ if (eflag) {
+ if (tabstyle == LOOKUP)
+ evdwl = tb->e[itable];
+ else if (tabstyle == LINEAR || tabstyle == BITMAP)
+ evdwl = tb->e[itable] + fraction*tb->de[itable];
+ else
+ evdwl = a * tb->e[itable] + b * tb->e[itable+1] +
+ ((a*a*a-a)*tb->e2[itable] + (b*b*b-b)*tb->e2[itable+1]) *
+ tb->deltasq6;
+ evdwl *= factor_lj;
+ }
+
+ if (evflag) ev_tally_full(i,evdwl,0.0,fpair,delx,dely,delz);
}
}
}
diff --git a/src/GPU/pair_table_gpu.h b/src/GPU/pair_table_gpu.h
index fd7c65144d8ca549ba47a6c2eea3739c657a41aa..4e6640abd3b5c1b108decf2f4a2df1a2e1027749 100644
--- a/src/GPU/pair_table_gpu.h
+++ b/src/GPU/pair_table_gpu.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/GPU/pair_yukawa_gpu.cpp b/src/GPU/pair_yukawa_gpu.cpp
index d76dc837df7377c3cd015c9e106d9bf4c2694555..49554e54693a1ebefb57fe180bacd6505a3a15e2 100644
--- a/src/GPU/pair_yukawa_gpu.cpp
+++ b/src/GPU/pair_yukawa_gpu.cpp
@@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
-
+
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
-
+
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@@ -38,35 +38,35 @@
// External functions from cuda library for atom decomposition
int yukawa_gpu_init(const int ntypes, double **cutsq, double kappa,
- double **host_a, double **offset, double *special_lj,
- const int inum, const int nall, const int max_nbors,
- const int maxspecial, const double cell_size,
- int &gpu_mode, FILE *screen);
+ double **host_a, double **offset, double *special_lj,
+ const int inum, const int nall, const int max_nbors,
+ const int maxspecial, const double cell_size,
+ int &gpu_mode, FILE *screen);
void yukawa_gpu_clear();
int ** yukawa_gpu_compute_n(const int ago, const int inum_full, const int nall,
- double **host_x, int *host_type, double *sublo,
- double *subhi, int *tag, int **nspecial,
- int **special, const bool eflag, const bool vflag,
- const bool eatom, const bool vatom,
- int &host_start, int **ilist, int **jnum,
- const double cpu_time, bool &success);
+ double **host_x, int *host_type, double *sublo,
+ double *subhi, int *tag, int **nspecial,
+ int **special, const bool eflag, const bool vflag,
+ const bool eatom, const bool vatom,
+ int &host_start, int **ilist, int **jnum,
+ const double cpu_time, bool &success);
void yukawa_gpu_compute(const int ago, const int inum_full, const int nall,
- double **host_x, int *host_type, int *ilist, int *numj,
- int **firstneigh, const bool eflag, const bool vflag,
- const bool eatom, const bool vatom, int &host_start,
- const double cpu_time, bool &success);
+ double **host_x, int *host_type, int *ilist, int *numj,
+ int **firstneigh, const bool eflag, const bool vflag,
+ const bool eatom, const bool vatom, int &host_start,
+ const double cpu_time, bool &success);
double yukawa_gpu_bytes();
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-PairYukawaGPU::PairYukawaGPU(LAMMPS *lmp) : PairYukawa(lmp),
- gpu_mode(GPU_FORCE)
+PairYukawaGPU::PairYukawaGPU(LAMMPS *lmp) : PairYukawa(lmp),
+ gpu_mode(GPU_FORCE)
{
respa_enable = 0;
cpu_time = 0.0;
- GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
+ GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
@@ -84,28 +84,28 @@ void PairYukawaGPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
-
+
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
-
+
bool success = true;
int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = yukawa_gpu_compute_n(neighbor->ago, inum, nall,
- atom->x, atom->type, domain->sublo,
- domain->subhi, atom->tag, atom->nspecial,
- atom->special, eflag, vflag, eflag_atom,
- vflag_atom, host_start,
- &ilist, &numneigh, cpu_time, success);
+ atom->x, atom->type, domain->sublo,
+ domain->subhi, atom->tag, atom->nspecial,
+ atom->special, eflag, vflag, eflag_atom,
+ vflag_atom, host_start,
+ &ilist, &numneigh, cpu_time, success);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
yukawa_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
- ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
- vflag_atom, host_start, cpu_time, success);
+ ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
+ vflag_atom, host_start, cpu_time, success);
}
if (!success)
error->one(FLERR,"Insufficient memory on accelerator");
@@ -123,7 +123,7 @@ void PairYukawaGPU::compute(int eflag, int vflag)
void PairYukawaGPU::init_style()
{
- if (force->newton_pair)
+ if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with yukawa/gpu pair style");
// Repeat cutsq calculation because done after call to init_style
@@ -147,9 +147,9 @@ void PairYukawaGPU::init_style()
if (atom->molecular)
maxspecial=atom->maxspecial;
int success = yukawa_gpu_init(atom->ntypes+1, cutsq, kappa, a,
- offset, force->special_lj, atom->nlocal,
- atom->nlocal+atom->nghost, 300, maxspecial,
- cell_size, gpu_mode, screen);
+ offset, force->special_lj, atom->nlocal,
+ atom->nlocal+atom->nghost, 300, maxspecial,
+ cell_size, gpu_mode, screen);
GPU_EXTRA::check_flag(success,error,world);
if (gpu_mode == GPU_FORCE) {
@@ -169,8 +169,8 @@ double PairYukawaGPU::memory_usage()
/* ---------------------------------------------------------------------- */
-void PairYukawaGPU::cpu_compute(int start, int inum, int eflag, int vflag,
- int *ilist, int *numneigh, int **firstneigh) {
+void PairYukawaGPU::cpu_compute(int start, int inum, int eflag, int vflag,
+ int *ilist, int *numneigh, int **firstneigh) {
int i,j,ii,jj,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,r2inv,r,rinv,screening,forceyukawa,factor;
@@ -204,24 +204,24 @@ void PairYukawaGPU::cpu_compute(int start, int inum, int eflag, int vflag,
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- r = sqrt(rsq);
- rinv = 1.0/r;
- screening = exp(-kappa*r);
- forceyukawa = a[itype][jtype] * screening * (kappa + rinv);
+ r2inv = 1.0/rsq;
+ r = sqrt(rsq);
+ rinv = 1.0/r;
+ screening = exp(-kappa*r);
+ forceyukawa = a[itype][jtype] * screening * (kappa + rinv);
- fpair = factor*forceyukawa * r2inv;
+ fpair = factor*forceyukawa * r2inv;
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
- if (eflag) {
- evdwl = a[itype][jtype] * screening * rinv - offset[itype][jtype];
- evdwl *= factor;
- }
+ if (eflag) {
+ evdwl = a[itype][jtype] * screening * rinv - offset[itype][jtype];
+ evdwl *= factor;
+ }
- if (evflag) ev_tally_full(i,evdwl,0.0,fpair,delx,dely,delz);
+ if (evflag) ev_tally_full(i,evdwl,0.0,fpair,delx,dely,delz);
}
}
}
diff --git a/src/GPU/pair_yukawa_gpu.h b/src/GPU/pair_yukawa_gpu.h
index f5a54e6e7571e3f772699a0064a0f48b7c52e802..85bc3d0b700c71f73983d0cd7a7b5378d7a9e168 100644
--- a/src/GPU/pair_yukawa_gpu.h
+++ b/src/GPU/pair_yukawa_gpu.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/GPU/pppm_gpu.cpp b/src/GPU/pppm_gpu.cpp
index 50e55329dc73f4dd40fa2ae6e8e68f4f0b390ee5..5cdbb75e8420fda084bc9cb1d6c8a0372ee5cf54 100644
--- a/src/GPU/pppm_gpu.cpp
+++ b/src/GPU/pppm_gpu.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -65,15 +65,15 @@ using namespace MathConst;
#endif
FFT_SCALAR* PPPM_GPU_API(init)(const int nlocal, const int nall, FILE *screen,
- const int order, const int nxlo_out,
- const int nylo_out, const int nzlo_out,
- const int nxhi_out, const int nyhi_out,
- const int nzhi_out, FFT_SCALAR **rho_coeff,
- FFT_SCALAR **_vd_brick,
- const double slab_volfactor,
- const int nx_pppm, const int ny_pppm,
- const int nz_pppm, const bool split,
- int &success);
+ const int order, const int nxlo_out,
+ const int nylo_out, const int nzlo_out,
+ const int nxhi_out, const int nyhi_out,
+ const int nzhi_out, FFT_SCALAR **rho_coeff,
+ FFT_SCALAR **_vd_brick,
+ const double slab_volfactor,
+ const int nx_pppm, const int ny_pppm,
+ const int nz_pppm, const bool split,
+ int &success);
void PPPM_GPU_API(clear)(const double poisson_time);
int PPPM_GPU_API(spread)(const int ago, const int nlocal, const int nall,
double **host_x, int *host_type, bool &success,
@@ -93,11 +93,11 @@ PPPMGPU::PPPMGPU(LAMMPS *lmp, int narg, char **arg) : PPPM(lmp, narg, arg)
kspace_split = false;
im_real_space = false;
- GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
+ GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
- free all memory
+ free all memory
------------------------------------------------------------------------- */
PPPMGPU::~PPPMGPU()
@@ -106,13 +106,13 @@ PPPMGPU::~PPPMGPU()
}
/* ----------------------------------------------------------------------
- called once before run
+ called once before run
------------------------------------------------------------------------- */
void PPPMGPU::init()
{
PPPM::init();
-
+
if (strcmp(update->integrate_style,"verlet/split") == 0)
kspace_split=true;
@@ -130,25 +130,25 @@ void PPPMGPU::init()
int success;
FFT_SCALAR *data, *h_brick;
h_brick = PPPM_GPU_API(init)(atom->nlocal, atom->nlocal+atom->nghost, screen,
- order, nxlo_out, nylo_out, nzlo_out, nxhi_out,
- nyhi_out, nzhi_out, rho_coeff, &data,
- slab_volfactor,nx_pppm,ny_pppm,nz_pppm,
- kspace_split,success);
+ order, nxlo_out, nylo_out, nzlo_out, nxhi_out,
+ nyhi_out, nzhi_out, rho_coeff, &data,
+ slab_volfactor,nx_pppm,ny_pppm,nz_pppm,
+ kspace_split,success);
GPU_EXTRA::check_flag(success,error,world);
density_brick_gpu =
create_3d_offset(nzlo_out,nzhi_out,nylo_out,nyhi_out,
- nxlo_out,nxhi_out,"pppm:density_brick_gpu",h_brick,1);
+ nxlo_out,nxhi_out,"pppm:density_brick_gpu",h_brick,1);
vd_brick =
create_3d_offset(nzlo_out,nzhi_out,nylo_out,nyhi_out,
- nxlo_out,nxhi_out,"pppm:vd_brick",data,4);
+ nxlo_out,nxhi_out,"pppm:vd_brick",data,4);
poisson_time=0;
}
/* ----------------------------------------------------------------------
- compute the PPPMGPU long-range force, energy, virial
+ compute the PPPMGPU long-range force, energy, virial
------------------------------------------------------------------------- */
void PPPMGPU::compute(int eflag, int vflag)
@@ -167,10 +167,10 @@ void PPPMGPU::compute(int eflag, int vflag)
}
bool success = true;
- int flag=PPPM_GPU_API(spread)(neighbor->ago, atom->nlocal, atom->nlocal +
- atom->nghost, atom->x, atom->type, success,
- atom->q, domain->boxlo, delxinv, delyinv,
- delzinv);
+ int flag=PPPM_GPU_API(spread)(neighbor->ago, atom->nlocal, atom->nlocal +
+ atom->nghost, atom->x, atom->type, success,
+ atom->q, domain->boxlo, delxinv, delyinv,
+ delzinv);
if (!success)
error->one(FLERR,"Insufficient memory on accelerator");
if (flag != 0)
@@ -189,7 +189,7 @@ void PPPMGPU::compute(int eflag, int vflag)
int i,j;
// convert atoms from box to lamda coords
-
+
if (triclinic == 0) boxlo = domain->boxlo;
else {
boxlo = domain->boxlo_lamda;
@@ -207,7 +207,7 @@ void PPPMGPU::compute(int eflag, int vflag)
// compute potential gradient on my FFT grid and
// portion of e_long on this proc's FFT grid
// return gradients (electric fields) in 3d brick decomposition
-
+
poisson();
// all procs communicate E-field values to fill ghost cells
@@ -232,9 +232,9 @@ void PPPMGPU::compute(int eflag, int vflag)
if (eflag_atom) {
for (i = 0; i < nlocal; i++) {
- eatom[i] *= 0.5;
- eatom[i] -= g_ewald*q[i]*q[i]/MY_PIS + MY_PI2*q[i]*qsum /
- (g_ewald*g_ewald*volume);
+ eatom[i] *= 0.5;
+ eatom[i] -= g_ewald*q[i]*q[i]/MY_PIS + MY_PI2*q[i]*qsum /
+ (g_ewald*g_ewald*volume);
eatom[i] *= qscale;
}
}
@@ -251,7 +251,7 @@ void PPPMGPU::compute(int eflag, int vflag)
double energy_all;
MPI_Allreduce(&energy,&energy_all,1,MPI_DOUBLE,MPI_SUM,world);
energy = energy_all;
-
+
energy *= 0.5*volume;
energy -= g_ewald*qsqsum/1.772453851 +
MY_PI2*qsum*qsum / (g_ewald*g_ewald*volume);
@@ -271,14 +271,14 @@ void PPPMGPU::compute(int eflag, int vflag)
if (slabflag) slabcorr();
// convert atoms back from lamda to box coords
-
+
if (triclinic) domain->lamda2x(atom->nlocal);
if (kspace_split) PPPM_GPU_API(forces)(atom->f);
}
/* ----------------------------------------------------------------------
- allocate memory that depends on # of K-vectors and order
+ allocate memory that depends on # of K-vectors and order
------------------------------------------------------------------------- */
void PPPMGPU::allocate()
@@ -310,23 +310,23 @@ void PPPMGPU::allocate()
int tmp;
fft1 = new FFT3d(lmp,world,nx_pppm,ny_pppm,nz_pppm,
- nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
- nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
- 0,0,&tmp);
+ nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
+ nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
+ 0,0,&tmp);
fft2 = new FFT3d(lmp,world,nx_pppm,ny_pppm,nz_pppm,
- nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
- nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in,
- 0,0,&tmp);
+ nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
+ nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in,
+ 0,0,&tmp);
remap = new Remap(lmp,world,
- nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in,
- nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
- 1,0,0,FFT_PRECISION);
+ nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in,
+ nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
+ 1,0,0,FFT_PRECISION);
}
/* ----------------------------------------------------------------------
- deallocate memory that depends on # of K-vectors and order
+ deallocate memory that depends on # of K-vectors and order
------------------------------------------------------------------------- */
void PPPMGPU::deallocate()
@@ -358,7 +358,7 @@ void PPPMGPU::deallocate()
/* ----------------------------------------------------------------------
- ghost-swap to accumulate full density in brick decomposition
+ ghost-swap to accumulate full density in brick decomposition
remap density from 3d brick decomposition to FFT decomposition
------------------------------------------------------------------------- */
@@ -376,7 +376,7 @@ void PPPMGPU::brick2fft()
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_out; iy <= nyhi_out; iy++)
for (ix = nxhi_in+1; ix <= nxhi_out; ix++)
- buf1[n++] = density_brick_gpu[iz][iy][ix];
+ buf1[n++] = density_brick_gpu[iz][iy][ix];
if (comm->procneigh[0][1] == me)
for (i = 0; i < n; i++) buf2[i] = buf1[i];
@@ -390,7 +390,7 @@ void PPPMGPU::brick2fft()
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_out; iy <= nyhi_out; iy++)
for (ix = nxlo_in; ix < nxlo_in+nxlo_ghost; ix++)
- density_brick_gpu[iz][iy][ix] += buf2[n++];
+ density_brick_gpu[iz][iy][ix] += buf2[n++];
// pack my ghosts for -x processor
// pass data to self or -x processor
@@ -400,7 +400,7 @@ void PPPMGPU::brick2fft()
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_out; iy <= nyhi_out; iy++)
for (ix = nxlo_out; ix < nxlo_in; ix++)
- buf1[n++] = density_brick_gpu[iz][iy][ix];
+ buf1[n++] = density_brick_gpu[iz][iy][ix];
if (comm->procneigh[0][0] == me)
for (i = 0; i < n; i++) buf2[i] = buf1[i];
@@ -414,7 +414,7 @@ void PPPMGPU::brick2fft()
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_out; iy <= nyhi_out; iy++)
for (ix = nxhi_in-nxhi_ghost+1; ix <= nxhi_in; ix++)
- density_brick_gpu[iz][iy][ix] += buf2[n++];
+ density_brick_gpu[iz][iy][ix] += buf2[n++];
// pack my ghosts for +y processor
// pass data to self or +y processor
@@ -424,7 +424,7 @@ void PPPMGPU::brick2fft()
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nyhi_in+1; iy <= nyhi_out; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++)
- buf1[n++] = density_brick_gpu[iz][iy][ix];
+ buf1[n++] = density_brick_gpu[iz][iy][ix];
if (comm->procneigh[1][1] == me)
for (i = 0; i < n; i++) buf2[i] = buf1[i];
@@ -438,7 +438,7 @@ void PPPMGPU::brick2fft()
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_in; iy < nylo_in+nylo_ghost; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++)
- density_brick_gpu[iz][iy][ix] += buf2[n++];
+ density_brick_gpu[iz][iy][ix] += buf2[n++];
// pack my ghosts for -y processor
// pass data to self or -y processor
@@ -448,7 +448,7 @@ void PPPMGPU::brick2fft()
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_out; iy < nylo_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++)
- buf1[n++] = density_brick_gpu[iz][iy][ix];
+ buf1[n++] = density_brick_gpu[iz][iy][ix];
if (comm->procneigh[1][0] == me)
for (i = 0; i < n; i++) buf2[i] = buf1[i];
@@ -462,7 +462,7 @@ void PPPMGPU::brick2fft()
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nyhi_in-nyhi_ghost+1; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++)
- density_brick_gpu[iz][iy][ix] += buf2[n++];
+ density_brick_gpu[iz][iy][ix] += buf2[n++];
// pack my ghosts for +z processor
// pass data to self or +z processor
@@ -472,7 +472,7 @@ void PPPMGPU::brick2fft()
for (iz = nzhi_in+1; iz <= nzhi_out; iz++)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++)
- buf1[n++] = density_brick_gpu[iz][iy][ix];
+ buf1[n++] = density_brick_gpu[iz][iy][ix];
if (comm->procneigh[2][1] == me)
for (i = 0; i < n; i++) buf2[i] = buf1[i];
@@ -486,7 +486,7 @@ void PPPMGPU::brick2fft()
for (iz = nzlo_in; iz < nzlo_in+nzlo_ghost; iz++)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++)
- density_brick_gpu[iz][iy][ix] += buf2[n++];
+ density_brick_gpu[iz][iy][ix] += buf2[n++];
// pack my ghosts for -z processor
// pass data to self or -z processor
@@ -496,7 +496,7 @@ void PPPMGPU::brick2fft()
for (iz = nzlo_out; iz < nzlo_in; iz++)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++)
- buf1[n++] = density_brick_gpu[iz][iy][ix];
+ buf1[n++] = density_brick_gpu[iz][iy][ix];
if (comm->procneigh[2][0] == me)
for (i = 0; i < n; i++) buf2[i] = buf1[i];
@@ -510,7 +510,7 @@ void PPPMGPU::brick2fft()
for (iz = nzhi_in-nzhi_ghost+1; iz <= nzhi_in; iz++)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++)
- density_brick_gpu[iz][iy][ix] += buf2[n++];
+ density_brick_gpu[iz][iy][ix] += buf2[n++];
// remap from 3d brick decomposition to FFT decomposition
// copy grabs inner portion of density from 3d brick
@@ -521,7 +521,7 @@ void PPPMGPU::brick2fft()
for (iz = nzlo_in; iz <= nzhi_in; iz++)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++)
- density_fft[n++] = density_brick_gpu[iz][iy][ix];
+ density_fft[n++] = density_brick_gpu[iz][iy][ix];
remap->perform(density_fft,density_fft,work1);
}
@@ -546,9 +546,9 @@ void PPPMGPU::fillbrick()
for (iz = nzhi_in-nzhi_ghost+1; iz <= nzhi_in; iz++)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = x_lo; ix < x_hi; ix+=4) {
- buf1[n++] = vd_brick[iz][iy][ix];
- buf1[n++] = vd_brick[iz][iy][ix+1];
- buf1[n++] = vd_brick[iz][iy][ix+2];
+ buf1[n++] = vd_brick[iz][iy][ix];
+ buf1[n++] = vd_brick[iz][iy][ix+1];
+ buf1[n++] = vd_brick[iz][iy][ix+2];
}
if (comm->procneigh[2][1] == me)
@@ -563,9 +563,9 @@ void PPPMGPU::fillbrick()
for (iz = nzlo_out; iz < nzlo_in; iz++)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = x_lo; ix < x_hi; ix+=4) {
- vd_brick[iz][iy][ix] = buf2[n++];
- vd_brick[iz][iy][ix+1] = buf2[n++];
- vd_brick[iz][iy][ix+2] = buf2[n++];
+ vd_brick[iz][iy][ix] = buf2[n++];
+ vd_brick[iz][iy][ix+1] = buf2[n++];
+ vd_brick[iz][iy][ix+2] = buf2[n++];
}
// pack my real cells for -z processor
@@ -576,9 +576,9 @@ void PPPMGPU::fillbrick()
for (iz = nzlo_in; iz < nzlo_in+nzlo_ghost; iz++)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = x_lo; ix < x_hi; ix+=4) {
- buf1[n++] = vd_brick[iz][iy][ix];
- buf1[n++] = vd_brick[iz][iy][ix+1];
- buf1[n++] = vd_brick[iz][iy][ix+2];
+ buf1[n++] = vd_brick[iz][iy][ix];
+ buf1[n++] = vd_brick[iz][iy][ix+1];
+ buf1[n++] = vd_brick[iz][iy][ix+2];
}
if (comm->procneigh[2][0] == me)
@@ -593,9 +593,9 @@ void PPPMGPU::fillbrick()
for (iz = nzhi_in+1; iz <= nzhi_out; iz++)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = x_lo; ix < x_hi; ix+=4) {
- vd_brick[iz][iy][ix] = buf2[n++];
- vd_brick[iz][iy][ix+1] = buf2[n++];
- vd_brick[iz][iy][ix+2] = buf2[n++];
+ vd_brick[iz][iy][ix] = buf2[n++];
+ vd_brick[iz][iy][ix+1] = buf2[n++];
+ vd_brick[iz][iy][ix+2] = buf2[n++];
}
// pack my real cells for +y processor
@@ -606,9 +606,9 @@ void PPPMGPU::fillbrick()
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nyhi_in-nyhi_ghost+1; iy <= nyhi_in; iy++)
for (ix = x_lo; ix < x_hi; ix+=4) {
- buf1[n++] = vd_brick[iz][iy][ix];
- buf1[n++] = vd_brick[iz][iy][ix+1];
- buf1[n++] = vd_brick[iz][iy][ix+2];
+ buf1[n++] = vd_brick[iz][iy][ix];
+ buf1[n++] = vd_brick[iz][iy][ix+1];
+ buf1[n++] = vd_brick[iz][iy][ix+2];
}
if (comm->procneigh[1][1] == me)
@@ -623,9 +623,9 @@ void PPPMGPU::fillbrick()
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_out; iy < nylo_in; iy++)
for (ix = x_lo; ix < x_hi; ix+=4) {
- vd_brick[iz][iy][ix] = buf2[n++];
- vd_brick[iz][iy][ix+1] = buf2[n++];
- vd_brick[iz][iy][ix+2] = buf2[n++];
+ vd_brick[iz][iy][ix] = buf2[n++];
+ vd_brick[iz][iy][ix+1] = buf2[n++];
+ vd_brick[iz][iy][ix+2] = buf2[n++];
}
// pack my real cells for -y processor
@@ -636,9 +636,9 @@ void PPPMGPU::fillbrick()
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_in; iy < nylo_in+nylo_ghost; iy++)
for (ix = x_lo; ix < x_hi; ix+=4) {
- buf1[n++] = vd_brick[iz][iy][ix];
- buf1[n++] = vd_brick[iz][iy][ix+1];
- buf1[n++] = vd_brick[iz][iy][ix+2];
+ buf1[n++] = vd_brick[iz][iy][ix];
+ buf1[n++] = vd_brick[iz][iy][ix+1];
+ buf1[n++] = vd_brick[iz][iy][ix+2];
}
if (comm->procneigh[1][0] == me)
@@ -653,9 +653,9 @@ void PPPMGPU::fillbrick()
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nyhi_in+1; iy <= nyhi_out; iy++)
for (ix = x_lo; ix < x_hi; ix+=4) {
- vd_brick[iz][iy][ix] = buf2[n++];
- vd_brick[iz][iy][ix+1] = buf2[n++];
- vd_brick[iz][iy][ix+2] = buf2[n++];
+ vd_brick[iz][iy][ix] = buf2[n++];
+ vd_brick[iz][iy][ix+1] = buf2[n++];
+ vd_brick[iz][iy][ix+2] = buf2[n++];
}
// pack my real cells for +x processor
@@ -667,9 +667,9 @@ void PPPMGPU::fillbrick()
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_out; iy <= nyhi_out; iy++)
for (ix = x_lo; ix < x_hi; ix+=4) {
- buf1[n++] = vd_brick[iz][iy][ix];
- buf1[n++] = vd_brick[iz][iy][ix+1];
- buf1[n++] = vd_brick[iz][iy][ix+2];
+ buf1[n++] = vd_brick[iz][iy][ix];
+ buf1[n++] = vd_brick[iz][iy][ix+1];
+ buf1[n++] = vd_brick[iz][iy][ix+2];
}
if (comm->procneigh[0][1] == me)
@@ -686,9 +686,9 @@ void PPPMGPU::fillbrick()
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_out; iy <= nyhi_out; iy++)
for (ix = x_lo; ix < x_hi; ix+=4) {
- vd_brick[iz][iy][ix] = buf2[n++];
- vd_brick[iz][iy][ix+1] = buf2[n++];
- vd_brick[iz][iy][ix+2] = buf2[n++];
+ vd_brick[iz][iy][ix] = buf2[n++];
+ vd_brick[iz][iy][ix+1] = buf2[n++];
+ vd_brick[iz][iy][ix+2] = buf2[n++];
}
// pack my real cells for -x processor
@@ -701,9 +701,9 @@ void PPPMGPU::fillbrick()
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_out; iy <= nyhi_out; iy++)
for (ix = x_lo; ix < x_hi; ix+=4) {
- buf1[n++] = vd_brick[iz][iy][ix];
- buf1[n++] = vd_brick[iz][iy][ix+1];
- buf1[n++] = vd_brick[iz][iy][ix+2];
+ buf1[n++] = vd_brick[iz][iy][ix];
+ buf1[n++] = vd_brick[iz][iy][ix+1];
+ buf1[n++] = vd_brick[iz][iy][ix+2];
}
if (comm->procneigh[0][0] == me)
@@ -720,14 +720,14 @@ void PPPMGPU::fillbrick()
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_out; iy <= nyhi_out; iy++)
for (ix = x_lo; ix < x_hi; ix+=4) {
- vd_brick[iz][iy][ix] = buf2[n++];
- vd_brick[iz][iy][ix+1] = buf2[n++];
- vd_brick[iz][iy][ix+2] = buf2[n++];
+ vd_brick[iz][iy][ix] = buf2[n++];
+ vd_brick[iz][iy][ix+1] = buf2[n++];
+ vd_brick[iz][iy][ix+2] = buf2[n++];
}
}
/* ----------------------------------------------------------------------
- FFT-based Poisson solver
+ FFT-based Poisson solver
------------------------------------------------------------------------- */
void PPPMGPU::poisson()
@@ -735,14 +735,14 @@ void PPPMGPU::poisson()
int i,j,k,n;
double eng;
- // transform charge density (r -> k)
+ // transform charge density (r -> k)
n = 0;
for (i = 0; i < nfft; i++) {
work1[n++] = density_fft[i];
work1[n++] = ZEROF;
}
-
+
fft1->compute(work1,work1,1);
// if requested, compute energy and virial contribution
@@ -754,17 +754,17 @@ void PPPMGPU::poisson()
if (vflag_global) {
n = 0;
for (i = 0; i < nfft; i++) {
- eng = s2 * greensfn[i] * (work1[n]*work1[n] + work1[n+1]*work1[n+1]);
- for (j = 0; j < 6; j++) virial[j] += eng*vg[i][j];
- if (eflag_global) energy += eng;
- n += 2;
+ eng = s2 * greensfn[i] * (work1[n]*work1[n] + work1[n+1]*work1[n+1]);
+ for (j = 0; j < 6; j++) virial[j] += eng*vg[i][j];
+ if (eflag_global) energy += eng;
+ n += 2;
}
} else {
n = 0;
for (i = 0; i < nfft; i++) {
- energy +=
- s2 * greensfn[i] * (work1[n]*work1[n] + work1[n+1]*work1[n+1]);
- n += 2;
+ energy +=
+ s2 * greensfn[i] * (work1[n]*work1[n] + work1[n+1]*work1[n+1]);
+ n += 2;
}
}
}
@@ -792,9 +792,9 @@ void PPPMGPU::poisson()
for (k = nzlo_fft; k <= nzhi_fft; k++)
for (j = nylo_fft; j <= nyhi_fft; j++)
for (i = nxlo_fft; i <= nxhi_fft; i++) {
- work2[n] = fkx[i]*work1[n+1];
- work2[n+1] = -fkx[i]*work1[n];
- n += 2;
+ work2[n] = fkx[i]*work1[n+1];
+ work2[n+1] = -fkx[i]*work1[n];
+ n += 2;
}
fft2->compute(work2,work2,-1);
@@ -804,8 +804,8 @@ void PPPMGPU::poisson()
for (k = nzlo_in; k <= nzhi_in; k++)
for (j = nylo_in; j <= nyhi_in; j++)
for (i = nxlo_in * 4; i < x_hi; i+=4) {
- vd_brick[k][j][i] = work2[n];
- n += 2;
+ vd_brick[k][j][i] = work2[n];
+ n += 2;
}
// y direction gradient
@@ -814,9 +814,9 @@ void PPPMGPU::poisson()
for (k = nzlo_fft; k <= nzhi_fft; k++)
for (j = nylo_fft; j <= nyhi_fft; j++)
for (i = nxlo_fft; i <= nxhi_fft; i++) {
- work2[n] = fky[j]*work1[n+1];
- work2[n+1] = -fky[j]*work1[n];
- n += 2;
+ work2[n] = fky[j]*work1[n+1];
+ work2[n+1] = -fky[j]*work1[n];
+ n += 2;
}
fft2->compute(work2,work2,-1);
@@ -825,8 +825,8 @@ void PPPMGPU::poisson()
for (k = nzlo_in; k <= nzhi_in; k++)
for (j = nylo_in; j <= nyhi_in; j++)
for (i = nxlo_in * 4 + 1; i < x_hi; i+=4) {
- vd_brick[k][j][i] = work2[n];
- n += 2;
+ vd_brick[k][j][i] = work2[n];
+ n += 2;
}
// z direction gradient
@@ -835,9 +835,9 @@ void PPPMGPU::poisson()
for (k = nzlo_fft; k <= nzhi_fft; k++)
for (j = nylo_fft; j <= nyhi_fft; j++)
for (i = nxlo_fft; i <= nxhi_fft; i++) {
- work2[n] = fkz[k]*work1[n+1];
- work2[n+1] = -fkz[k]*work1[n];
- n += 2;
+ work2[n] = fkz[k]*work1[n+1];
+ work2[n+1] = -fkz[k]*work1[n];
+ n += 2;
}
fft2->compute(work2,work2,-1);
@@ -846,8 +846,8 @@ void PPPMGPU::poisson()
for (k = nzlo_in; k <= nzhi_in; k++)
for (j = nylo_in; j <= nyhi_in; j++)
for (i = nxlo_in * 4 + 2; i < x_hi; i+=4) {
- vd_brick[k][j][i] = work2[n];
- n += 2;
+ vd_brick[k][j][i] = work2[n];
+ n += 2;
}
}
@@ -856,8 +856,8 @@ void PPPMGPU::poisson()
------------------------------------------------------------------------- */
FFT_SCALAR ***PPPMGPU::create_3d_offset(int n1lo, int n1hi, int n2lo, int n2hi,
- int n3lo, int n3hi, const char *name,
- FFT_SCALAR *data, int vec_length)
+ int n3lo, int n3hi, const char *name,
+ FFT_SCALAR *data, int vec_length)
{
int i,j;
int n1 = n1hi - n1lo + 1;
@@ -888,7 +888,7 @@ FFT_SCALAR ***PPPMGPU::create_3d_offset(int n1lo, int n1hi, int n2lo, int n2hi,
------------------------------------------------------------------------- */
void PPPMGPU::destroy_3d_offset(FFT_SCALAR ***array, int n1_offset,
- int n2_offset)
+ int n2_offset)
{
if (array == NULL) return;
memory->sfree(&array[n1_offset][n2_offset]);
@@ -897,13 +897,13 @@ void PPPMGPU::destroy_3d_offset(FFT_SCALAR ***array, int n1_offset,
/* ----------------------------------------------------------------------
- memory usage of local arrays
+ memory usage of local arrays
------------------------------------------------------------------------- */
double PPPMGPU::memory_usage()
{
double bytes = nmax*3 * sizeof(double);
- int nbrick = (nxhi_out-nxlo_out+1) * (nyhi_out-nylo_out+1) *
+ int nbrick = (nxhi_out-nxlo_out+1) * (nyhi_out-nylo_out+1) *
(nzhi_out-nzlo_out+1);
bytes += 4 * nbrick * sizeof(FFT_SCALAR);
bytes += 6 * nfft_both * sizeof(double);
@@ -933,11 +933,11 @@ void PPPMGPU::timing(int n, double &time3d, double &time1d) {
}
/* ----------------------------------------------------------------------
- adjust PPPM coeffs, called initially and whenever volume has changed
+ adjust PPPM coeffs, called initially and whenever volume has changed
------------------------------------------------------------------------- */
void PPPMGPU::setup()
{
if (im_real_space) return;
PPPM::setup();
-}
+}
diff --git a/src/GPU/pppm_gpu.h b/src/GPU/pppm_gpu.h
index 8fb8a5f5d2d2e38676e10868ff772fb45ede69aa..0acc5a0060070ee7572a69b480b7bb6ba256cedc 100644
--- a/src/GPU/pppm_gpu.h
+++ b/src/GPU/pppm_gpu.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -45,10 +45,10 @@ class PPPMGPU : public PPPM {
virtual void fillbrick();
virtual void poisson();
- double poisson_time;
+ double poisson_time;
FFT_SCALAR ***create_3d_offset(int, int, int, int, int, int, const char *,
- FFT_SCALAR *, int);
+ FFT_SCALAR *, int);
void destroy_3d_offset(FFT_SCALAR ***, int, int);
};
diff --git a/src/GRANULAR/fix_freeze.cpp b/src/GRANULAR/fix_freeze.cpp
index 40672035e9de016e97dd96896183647c97df3228..655edd844b8cd8bb23ca874c7f8ed6058218f034 100644
--- a/src/GRANULAR/fix_freeze.cpp
+++ b/src/GRANULAR/fix_freeze.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/GRANULAR/fix_freeze.h b/src/GRANULAR/fix_freeze.h
index 67832532118ab6d177f4b1b5fd3a2bda4d7c1c8c..f6667632ddaa14796c79fbdd330d2270079c1708 100644
--- a/src/GRANULAR/fix_freeze.h
+++ b/src/GRANULAR/fix_freeze.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/GRANULAR/fix_pour.cpp b/src/GRANULAR/fix_pour.cpp
index c775b1603401d501543f7cd0fce77e79a88c7aab..f42b0518d130cbf2dcf2973a12746d55d8ac1688 100644
--- a/src/GRANULAR/fix_pour.cpp
+++ b/src/GRANULAR/fix_pour.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -97,20 +97,20 @@ FixPour::FixPour(LAMMPS *lmp, int narg, char **arg) :
iarg += 2;
} else if (strcmp(arg[iarg],"vel") == 0) {
if (domain->dimension == 3) {
- if (iarg+6 > narg) error->all(FLERR,"Illegal fix pour command");
- vxlo = atof(arg[iarg+1]);
- vxhi = atof(arg[iarg+2]);
- vylo = atof(arg[iarg+3]);
- vyhi = atof(arg[iarg+4]);
- vz = atof(arg[iarg+5]);
- iarg += 6;
+ if (iarg+6 > narg) error->all(FLERR,"Illegal fix pour command");
+ vxlo = atof(arg[iarg+1]);
+ vxhi = atof(arg[iarg+2]);
+ vylo = atof(arg[iarg+3]);
+ vyhi = atof(arg[iarg+4]);
+ vz = atof(arg[iarg+5]);
+ iarg += 6;
} else {
- if (iarg+4 > narg) error->all(FLERR,"Illegal fix pour command");
- vxlo = atof(arg[iarg+1]);
- vxhi = atof(arg[iarg+2]);
- vy = atof(arg[iarg+3]);
- vz = 0.0;
- iarg += 4;
+ if (iarg+4 > narg) error->all(FLERR,"Illegal fix pour command");
+ vxlo = atof(arg[iarg+1]);
+ vxhi = atof(arg[iarg+2]);
+ vy = atof(arg[iarg+3]);
+ vz = 0.0;
+ iarg += 4;
}
} else error->all(FLERR,"Illegal fix pour command");
}
@@ -131,9 +131,9 @@ FixPour::FixPour(LAMMPS *lmp, int narg, char **arg) :
yhi = ((RegBlock *) domain->regions[iregion])->yhi;
zlo = ((RegBlock *) domain->regions[iregion])->zlo;
zhi = ((RegBlock *) domain->regions[iregion])->zhi;
- if (xlo < domain->boxlo[0] || xhi > domain->boxhi[0] ||
- ylo < domain->boxlo[1] || yhi > domain->boxhi[1] ||
- zlo < domain->boxlo[2] || zhi > domain->boxhi[2])
+ if (xlo < domain->boxlo[0] || xhi > domain->boxhi[0] ||
+ ylo < domain->boxlo[1] || yhi > domain->boxhi[1] ||
+ zlo < domain->boxlo[2] || zhi > domain->boxhi[2])
error->all(FLERR,"Insertion region extends outside simulation box");
} else if (strcmp(domain->regions[iregion]->style,"cylinder") == 0) {
region_style = 2;
@@ -145,9 +145,9 @@ FixPour::FixPour(LAMMPS *lmp, int narg, char **arg) :
zhi = ((RegCylinder *) domain->regions[iregion])->hi;
if (axis != 'z')
error->all(FLERR,"Must use a z-axis cylinder with fix pour");
- if (xc-rc < domain->boxlo[0] || xc+rc > domain->boxhi[0] ||
- yc-rc < domain->boxlo[1] || yc+rc > domain->boxhi[1] ||
- zlo < domain->boxlo[2] || zhi > domain->boxhi[2])
+ if (xc-rc < domain->boxlo[0] || xc+rc > domain->boxhi[0] ||
+ yc-rc < domain->boxlo[1] || yc+rc > domain->boxhi[1] ||
+ zlo < domain->boxlo[2] || zhi > domain->boxhi[2])
error->all(FLERR,"Insertion region extends outside simulation box");
} else error->all(FLERR,"Must use a block or cylinder region with fix pour");
@@ -173,7 +173,7 @@ FixPour::FixPour(LAMMPS *lmp, int narg, char **arg) :
if (strcmp(modify->fix[ifix]->style,"gravity") == 0) break;
if (strcmp(modify->fix[ifix]->style,"gravity/omp") == 0) break;
}
- if (ifix == modify->nfix)
+ if (ifix == modify->nfix)
error->all(FLERR,"No fix gravity defined for fix pour");
grav = - ((FixGravity *) modify->fix[ifix])->magnitude * force->ftm2v;
@@ -194,7 +194,7 @@ FixPour::FixPour(LAMMPS *lmp, int narg, char **arg) :
v_relative = vy - rate;
delta = yhi - ylo;
}
- double t =
+ double t =
(-v_relative - sqrt(v_relative*v_relative - 2.0*grav*delta)) / grav;
nfreq = static_cast<int> (t/update->dt + 0.5);
@@ -232,12 +232,12 @@ FixPour::FixPour(LAMMPS *lmp, int narg, char **arg) :
if (me == 0) {
if (screen)
fprintf(screen,
- "Particle insertion: %d every %d steps, %d by step %d\n",
- nper,nfreq,ninsert,nfinal);
+ "Particle insertion: %d every %d steps, %d by step %d\n",
+ nper,nfreq,ninsert,nfinal);
if (logfile)
fprintf(logfile,
- "Particle insertion: %d every %d steps, %d by step %d\n",
- nper,nfreq,ninsert,nfinal);
+ "Particle insertion: %d every %d steps, %d by step %d\n",
+ nper,nfreq,ninsert,nfinal);
}
}
@@ -274,7 +274,7 @@ void FixPour::init()
if (strcmp(modify->fix[ifix]->style,"gravity") == 0) break;
if (strcmp(modify->fix[ifix]->style,"gravity/omp") == 0) break;
}
- if (ifix == modify->nfix)
+ if (ifix == modify->nfix)
error->all(FLERR,"No fix gravity defined for fix pour");
double xgrav = ((FixGravity *) modify->fix[ifix])->xgrav;
@@ -283,11 +283,11 @@ void FixPour::init()
if (domain->dimension == 3) {
if (fabs(xgrav) > EPSILON || fabs(ygrav) > EPSILON ||
- fabs(zgrav+1.0) > EPSILON)
+ fabs(zgrav+1.0) > EPSILON)
error->all(FLERR,"Gravity must point in -z to use with fix pour in 3d");
} else {
if (fabs(xgrav) > EPSILON || fabs(ygrav+1.0) > EPSILON ||
- fabs(zgrav) > EPSILON)
+ fabs(zgrav) > EPSILON)
error->all(FLERR,"Gravity must point in -y to use with fix pour in 2d");
}
@@ -325,7 +325,7 @@ void FixPour::pre_exchange()
// ncount = # of my atoms that overlap the insertion region
// nprevious = total of ncount across all procs
-
+
int ncount = 0;
for (i = 0; i < atom->nlocal; i++)
if (overlap(i)) ncount++;
@@ -351,7 +351,7 @@ void FixPour::pre_exchange()
displs[iproc] = displs[iproc-1] + recvcounts[iproc-1];
// load up xmine array
-
+
double **x = atom->x;
double *radius = atom->radius;
@@ -370,7 +370,7 @@ void FixPour::pre_exchange()
double *ptr = NULL;
if (ncount) ptr = xmine[0];
MPI_Allgatherv(ptr,4*ncount,MPI_DOUBLE,
- xnear[0],recvcounts,displs,MPI_DOUBLE,world);
+ xnear[0],recvcounts,displs,MPI_DOUBLE,world);
// insert new atoms into xnear list, one by one
// check against all nearby atoms and previously inserted ones
@@ -395,16 +395,16 @@ void FixPour::pre_exchange()
attempt++;
xyz_random(h,coord);
for (i = 0; i < nnear; i++) {
- delx = coord[0] - xnear[i][0];
- dely = coord[1] - xnear[i][1];
- delz = coord[2] - xnear[i][2];
- rsq = delx*delx + dely*dely + delz*delz;
- radsum = radtmp + xnear[i][3];
- if (rsq <= radsum*radsum) break;
+ delx = coord[0] - xnear[i][0];
+ dely = coord[1] - xnear[i][1];
+ delz = coord[2] - xnear[i][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+ radsum = radtmp + xnear[i][3];
+ if (rsq <= radsum*radsum) break;
}
if (i == nnear) {
- success = 1;
- break;
+ success = 1;
+ break;
}
}
if (success) {
@@ -462,15 +462,15 @@ void FixPour::pre_exchange()
flag = 0;
if (coord[0] >= sublo[0] && coord[0] < subhi[0] &&
- coord[1] >= sublo[1] && coord[1] < subhi[1] &&
- coord[2] >= sublo[2] && coord[2] < subhi[2]) flag = 1;
+ coord[1] >= sublo[1] && coord[1] < subhi[1] &&
+ coord[2] >= sublo[2] && coord[2] < subhi[2]) flag = 1;
else if (domain->dimension == 3 && coord[2] >= domain->boxhi[2] &&
- comm->myloc[2] == comm->procgrid[2]-1 &&
- coord[0] >= sublo[0] && coord[0] < subhi[0] &&
- coord[1] >= sublo[1] && coord[1] < subhi[1]) flag = 1;
+ comm->myloc[2] == comm->procgrid[2]-1 &&
+ coord[0] >= sublo[0] && coord[0] < subhi[0] &&
+ coord[1] >= sublo[1] && coord[1] < subhi[1]) flag = 1;
else if (domain->dimension == 2 && coord[1] >= domain->boxhi[1] &&
- comm->myloc[1] == comm->procgrid[1]-1 &&
- coord[0] >= sublo[0] && coord[0] < subhi[0]) flag = 1;
+ comm->myloc[1] == comm->procgrid[1]-1 &&
+ coord[0] >= sublo[0] && coord[0] < subhi[0]) flag = 1;
if (flag) {
avec->create_atom(ntype,coord);
@@ -483,7 +483,7 @@ void FixPour::pre_exchange()
atom->v[m][1] = vytmp;
atom->v[m][2] = vztmp;
for (j = 0; j < nfix; j++)
- if (fix[j]->create_attribute) fix[j]->set_arrays(m);
+ if (fix[j]->create_attribute) fix[j]->set_arrays(m);
}
}
@@ -497,9 +497,9 @@ void FixPour::pre_exchange()
if (atom->tag_enable) {
atom->tag_extend();
if (atom->map_style) {
- atom->nghost = 0;
- atom->map_init();
- atom->map_set();
+ atom->nghost = 0;
+ atom->map_init();
+ atom->map_set();
}
}
}
@@ -529,8 +529,8 @@ int FixPour::overlap(int i)
if (domain->dimension == 3) {
if (region_style == 1) {
if (x[i][0] < xlo-delta || x[i][0] > xhi+delta ||
- x[i][1] < ylo-delta || x[i][1] > yhi+delta ||
- x[i][2] < lo_current-delta || x[i][2] > hi_current+delta) return 0;
+ x[i][1] < ylo-delta || x[i][1] > yhi+delta ||
+ x[i][2] < lo_current-delta || x[i][2] > hi_current+delta) return 0;
} else {
if (x[i][2] < lo_current-delta || x[i][2] > hi_current+delta) return 0;
double delx = x[i][0] - xc;
@@ -541,7 +541,7 @@ int FixPour::overlap(int i)
}
} else {
if (x[i][0] < xlo-delta || x[i][0] > xhi+delta ||
- x[i][1] < lo_current-delta || x[i][1] > hi_current+delta) return 0;
+ x[i][1] < lo_current-delta || x[i][1] > hi_current+delta) return 0;
}
return 1;
@@ -559,9 +559,9 @@ void FixPour::xyz_random(double h, double *coord)
} else {
double r1,r2;
while (1) {
- r1 = random->uniform() - 0.5;
- r2 = random->uniform() - 0.5;
- if (r1*r1 + r2*r2 < 0.25) break;
+ r1 = random->uniform() - 0.5;
+ r2 = random->uniform() - 0.5;
+ if (r1*r1 + r2*r2 < 0.25) break;
}
coord[0] = xc + 2.0*r1*rc;
coord[1] = yc + 2.0*r2*rc;
diff --git a/src/GRANULAR/fix_pour.h b/src/GRANULAR/fix_pour.h
index 58575c6aeda734c64270c7138a365bd28a722c75..322cb30b8a295bfe5e33c180cf76b0e074e627f0 100644
--- a/src/GRANULAR/fix_pour.h
+++ b/src/GRANULAR/fix_pour.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/GRANULAR/fix_wall_gran.cpp b/src/GRANULAR/fix_wall_gran.cpp
index 8b0503656039516b8ea9c666d57b53e95385ba2d..6557a7ebf15b7727c84dd8a1b2b3ce790a08c433 100644
--- a/src/GRANULAR/fix_wall_gran.cpp
+++ b/src/GRANULAR/fix_wall_gran.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -71,7 +71,7 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) :
int dampflag = atoi(arg[8]);
if (dampflag == 0) gammat = 0.0;
- if (kn < 0.0 || kt < 0.0 || gamman < 0.0 || gammat < 0.0 ||
+ if (kn < 0.0 || kt < 0.0 || gamman < 0.0 || gammat < 0.0 ||
xmu < 0.0 || xmu > 1.0 || dampflag < 0 || dampflag > 1)
error->all(FLERR,"Illegal fix wall/gran command");
@@ -116,7 +116,7 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) :
cylradius = atof(arg[iarg+1]);
iarg += 2;
}
-
+
// check for trailing keyword/values
wiggle = 0;
@@ -154,7 +154,7 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) :
if (wallstyle == ZCYLINDER && (domain->xperiodic || domain->yperiodic))
error->all(FLERR,"Cannot use wall in periodic dimension");
- if (wiggle && wshear)
+ if (wiggle && wshear)
error->all(FLERR,"Cannot wiggle and shear fix wall/gran");
if (wiggle && wallstyle == ZCYLINDER && axis != 2)
error->all(FLERR,"Invalid wiggle direction for fix wall/gran");
@@ -298,53 +298,53 @@ void FixWallGran::post_force(int vflag)
dx = dy = dz = 0.0;
if (wallstyle == XPLANE) {
- del1 = x[i][0] - wlo;
- del2 = whi - x[i][0];
- if (del1 < del2) dx = del1;
- else dx = -del2;
+ del1 = x[i][0] - wlo;
+ del2 = whi - x[i][0];
+ if (del1 < del2) dx = del1;
+ else dx = -del2;
} else if (wallstyle == YPLANE) {
- del1 = x[i][1] - wlo;
- del2 = whi - x[i][1];
- if (del1 < del2) dy = del1;
- else dy = -del2;
+ del1 = x[i][1] - wlo;
+ del2 = whi - x[i][1];
+ if (del1 < del2) dy = del1;
+ else dy = -del2;
} else if (wallstyle == ZPLANE) {
- del1 = x[i][2] - wlo;
- del2 = whi - x[i][2];
- if (del1 < del2) dz = del1;
- else dz = -del2;
+ del1 = x[i][2] - wlo;
+ del2 = whi - x[i][2];
+ if (del1 < del2) dz = del1;
+ else dz = -del2;
} else if (wallstyle == ZCYLINDER) {
delxy = sqrt(x[i][0]*x[i][0] + x[i][1]*x[i][1]);
- delr = cylradius - delxy;
- if (delr > radius[i]) dz = cylradius;
- else {
- dx = -delr/delxy * x[i][0];
- dy = -delr/delxy * x[i][1];
- if (wshear && axis != 2) {
- vwall[0] = vshear * x[i][1]/delxy;
- vwall[1] = -vshear * x[i][0]/delxy;
- vwall[2] = 0.0;
- }
- }
+ delr = cylradius - delxy;
+ if (delr > radius[i]) dz = cylradius;
+ else {
+ dx = -delr/delxy * x[i][0];
+ dy = -delr/delxy * x[i][1];
+ if (wshear && axis != 2) {
+ vwall[0] = vshear * x[i][1]/delxy;
+ vwall[1] = -vshear * x[i][0]/delxy;
+ vwall[2] = 0.0;
+ }
+ }
}
rsq = dx*dx + dy*dy + dz*dz;
if (rsq > radius[i]*radius[i]) {
- if (pairstyle != HOOKE) {
- shear[i][0] = 0.0;
- shear[i][1] = 0.0;
- shear[i][2] = 0.0;
- }
+ if (pairstyle != HOOKE) {
+ shear[i][0] = 0.0;
+ shear[i][1] = 0.0;
+ shear[i][2] = 0.0;
+ }
} else {
- if (pairstyle == HOOKE)
- hooke(rsq,dx,dy,dz,vwall,v[i],f[i],omega[i],torque[i],
- radius[i],rmass[i]);
- else if (pairstyle == HOOKE_HISTORY)
- hooke_history(rsq,dx,dy,dz,vwall,v[i],f[i],omega[i],torque[i],
- radius[i],rmass[i],shear[i]);
- else if (pairstyle == HERTZ_HISTORY)
- hertz_history(rsq,dx,dy,dz,vwall,v[i],f[i],omega[i],torque[i],
- radius[i],rmass[i],shear[i]);
+ if (pairstyle == HOOKE)
+ hooke(rsq,dx,dy,dz,vwall,v[i],f[i],omega[i],torque[i],
+ radius[i],rmass[i]);
+ else if (pairstyle == HOOKE_HISTORY)
+ hooke_history(rsq,dx,dy,dz,vwall,v[i],f[i],omega[i],torque[i],
+ radius[i],rmass[i],shear[i]);
+ else if (pairstyle == HERTZ_HISTORY)
+ hertz_history(rsq,dx,dy,dz,vwall,v[i],f[i],omega[i],torque[i],
+ radius[i],rmass[i],shear[i]);
}
}
}
@@ -362,9 +362,9 @@ void FixWallGran::post_force_respa(int vflag, int ilevel, int iloop)
/* ---------------------------------------------------------------------- */
void FixWallGran::hooke(double rsq, double dx, double dy, double dz,
- double *vwall, double *v,
- double *f, double *omega, double *torque,
- double radius, double mass)
+ double *vwall, double *v,
+ double *f, double *omega, double *torque,
+ double radius, double mass)
{
double r,vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3;
double wr1,wr2,wr3,meff,damp,ccel,vtr1,vtr2,vtr3,vrel;
@@ -447,9 +447,9 @@ void FixWallGran::hooke(double rsq, double dx, double dy, double dz,
/* ---------------------------------------------------------------------- */
void FixWallGran::hooke_history(double rsq, double dx, double dy, double dz,
- double *vwall, double *v,
- double *f, double *omega, double *torque,
- double radius, double mass, double *shear)
+ double *vwall, double *v,
+ double *f, double *omega, double *torque,
+ double radius, double mass, double *shear)
{
double r,vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3;
double wr1,wr2,wr3,meff,damp,ccel,vtr1,vtr2,vtr3,vrel;
@@ -531,12 +531,12 @@ void FixWallGran::hooke_history(double rsq, double dx, double dy, double dz,
if (fs > fn) {
if (shrmag != 0.0) {
- shear[0] = (fn/fs) * (shear[0] + meff*gammat*vtr1/kt) -
- meff*gammat*vtr1/kt;
+ shear[0] = (fn/fs) * (shear[0] + meff*gammat*vtr1/kt) -
+ meff*gammat*vtr1/kt;
shear[1] = (fn/fs) * (shear[1] + meff*gammat*vtr2/kt) -
- meff*gammat*vtr2/kt;
+ meff*gammat*vtr2/kt;
shear[2] = (fn/fs) * (shear[2] + meff*gammat*vtr3/kt) -
- meff*gammat*vtr3/kt;
+ meff*gammat*vtr3/kt;
fs1 *= fn/fs ;
fs2 *= fn/fs;
fs3 *= fn/fs;
@@ -564,9 +564,9 @@ void FixWallGran::hooke_history(double rsq, double dx, double dy, double dz,
/* ---------------------------------------------------------------------- */
void FixWallGran::hertz_history(double rsq, double dx, double dy, double dz,
- double *vwall, double *v,
- double *f, double *omega, double *torque,
- double radius, double mass, double *shear)
+ double *vwall, double *v,
+ double *f, double *omega, double *torque,
+ double radius, double mass, double *shear)
{
double r,vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3;
double wr1,wr2,wr3,meff,damp,ccel,vtr1,vtr2,vtr3,vrel;
@@ -650,12 +650,12 @@ void FixWallGran::hertz_history(double rsq, double dx, double dy, double dz,
if (fs > fn) {
if (shrmag != 0.0) {
- shear[0] = (fn/fs) * (shear[0] + meff*gammat*vtr1/kt) -
- meff*gammat*vtr1/kt;
+ shear[0] = (fn/fs) * (shear[0] + meff*gammat*vtr1/kt) -
+ meff*gammat*vtr1/kt;
shear[1] = (fn/fs) * (shear[1] + meff*gammat*vtr2/kt) -
- meff*gammat*vtr2/kt;
+ meff*gammat*vtr2/kt;
shear[2] = (fn/fs) * (shear[2] + meff*gammat*vtr3/kt) -
- meff*gammat*vtr3/kt;
+ meff*gammat*vtr3/kt;
fs1 *= fn/fs ;
fs2 *= fn/fs;
fs3 *= fn/fs;
@@ -681,7 +681,7 @@ void FixWallGran::hertz_history(double rsq, double dx, double dy, double dz,
}
/* ----------------------------------------------------------------------
- memory usage of local atom-based arrays
+ memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double FixWallGran::memory_usage()
@@ -693,7 +693,7 @@ double FixWallGran::memory_usage()
}
/* ----------------------------------------------------------------------
- allocate local atom-based arrays
+ allocate local atom-based arrays
------------------------------------------------------------------------- */
void FixWallGran::grow_arrays(int nmax)
@@ -702,7 +702,7 @@ void FixWallGran::grow_arrays(int nmax)
}
/* ----------------------------------------------------------------------
- copy values within local atom-based arrays
+ copy values within local atom-based arrays
------------------------------------------------------------------------- */
void FixWallGran::copy_arrays(int i, int j)
@@ -722,7 +722,7 @@ void FixWallGran::set_arrays(int i)
}
/* ----------------------------------------------------------------------
- pack values in local atom-based arrays for exchange with another proc
+ pack values in local atom-based arrays for exchange with another proc
------------------------------------------------------------------------- */
int FixWallGran::pack_exchange(int i, double *buf)
@@ -734,7 +734,7 @@ int FixWallGran::pack_exchange(int i, double *buf)
}
/* ----------------------------------------------------------------------
- unpack values into local atom-based arrays after exchange
+ unpack values into local atom-based arrays after exchange
------------------------------------------------------------------------- */
int FixWallGran::unpack_exchange(int nlocal, double *buf)
@@ -746,7 +746,7 @@ int FixWallGran::unpack_exchange(int nlocal, double *buf)
}
/* ----------------------------------------------------------------------
- pack values in local atom-based arrays for restart file
+ pack values in local atom-based arrays for restart file
------------------------------------------------------------------------- */
int FixWallGran::pack_restart(int i, double *buf)
@@ -760,7 +760,7 @@ int FixWallGran::pack_restart(int i, double *buf)
}
/* ----------------------------------------------------------------------
- unpack values from atom->extra array to restart the fix
+ unpack values from atom->extra array to restart the fix
------------------------------------------------------------------------- */
void FixWallGran::unpack_restart(int nlocal, int nth)
@@ -779,7 +779,7 @@ void FixWallGran::unpack_restart(int nlocal, int nth)
}
/* ----------------------------------------------------------------------
- maxsize of any atom's restart data
+ maxsize of any atom's restart data
------------------------------------------------------------------------- */
int FixWallGran::maxsize_restart()
@@ -788,7 +788,7 @@ int FixWallGran::maxsize_restart()
}
/* ----------------------------------------------------------------------
- size of atom nlocal's restart data
+ size of atom nlocal's restart data
------------------------------------------------------------------------- */
int FixWallGran::size_restart(int nlocal)
diff --git a/src/GRANULAR/fix_wall_gran.h b/src/GRANULAR/fix_wall_gran.h
index e240f33ba0195134731a7973b75329f05042851d..4f296750577f8baaab2df74499561e08cfe1ae54 100644
--- a/src/GRANULAR/fix_wall_gran.h
+++ b/src/GRANULAR/fix_wall_gran.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -61,13 +61,13 @@ class FixWallGran : public Fix {
int shearupdate;
void hooke(double, double, double, double, double *,
- double *, double *, double *, double *, double, double);
+ double *, double *, double *, double *, double, double);
void hooke_history(double, double, double, double, double *,
- double *, double *, double *, double *, double, double,
- double *);
+ double *, double *, double *, double *, double, double,
+ double *);
void hertz_history(double, double, double, double, double *,
- double *, double *, double *, double *, double, double,
- double *);
+ double *, double *, double *, double *, double, double,
+ double *);
};
}
diff --git a/src/GRANULAR/pair_gran_hertz_history.cpp b/src/GRANULAR/pair_gran_hertz_history.cpp
index 1afecdf94d5a32a2646551e798d9b0c8ae687163..19d302a1fb6f825f264970c12f97d282b8a74a7c 100644
--- a/src/GRANULAR/pair_gran_hertz_history.cpp
+++ b/src/GRANULAR/pair_gran_hertz_history.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -101,145 +101,145 @@ void PairGranHertzHistory::compute(int eflag, int vflag)
if (rsq >= radsum*radsum) {
- // unset non-touching neighbors
+ // unset non-touching neighbors
touch[jj] = 0;
- shear = &allshear[3*jj];
+ shear = &allshear[3*jj];
shear[0] = 0.0;
shear[1] = 0.0;
shear[2] = 0.0;
} else {
- r = sqrt(rsq);
- rinv = 1.0/r;
- rsqinv = 1.0/rsq;
-
- // relative translational velocity
-
- vr1 = v[i][0] - v[j][0];
- vr2 = v[i][1] - v[j][1];
- vr3 = v[i][2] - v[j][2];
-
- // normal component
-
- vnnr = vr1*delx + vr2*dely + vr3*delz;
- vn1 = delx*vnnr * rsqinv;
- vn2 = dely*vnnr * rsqinv;
- vn3 = delz*vnnr * rsqinv;
-
- // tangential component
-
- vt1 = vr1 - vn1;
- vt2 = vr2 - vn2;
- vt3 = vr3 - vn3;
-
- // relative rotational velocity
-
- wr1 = (radi*omega[i][0] + radj*omega[j][0]) * rinv;
- wr2 = (radi*omega[i][1] + radj*omega[j][1]) * rinv;
- wr3 = (radi*omega[i][2] + radj*omega[j][2]) * rinv;
-
- // normal force = Hertzian contact + normal velocity damping
-
- if (rmass) {
- meff = rmass[i]*rmass[j] / (rmass[i]+rmass[j]);
- if (mask[i] & freeze_group_bit) meff = rmass[j];
- if (mask[j] & freeze_group_bit) meff = rmass[i];
- } else {
- itype = type[i];
- jtype = type[j];
- meff = mass[itype]*mass[jtype] / (mass[itype]+mass[jtype]);
- if (mask[i] & freeze_group_bit) meff = mass[jtype];
- if (mask[j] & freeze_group_bit) meff = mass[itype];
- }
-
- damp = meff*gamman*vnnr*rsqinv;
- ccel = kn*(radsum-r)*rinv - damp;
- polyhertz = sqrt((radsum-r)*radi*radj / radsum);
- ccel *= polyhertz;
-
- // relative velocities
-
- vtr1 = vt1 - (delz*wr2-dely*wr3);
- vtr2 = vt2 - (delx*wr3-delz*wr1);
- vtr3 = vt3 - (dely*wr1-delx*wr2);
- vrel = vtr1*vtr1 + vtr2*vtr2 + vtr3*vtr3;
- vrel = sqrt(vrel);
-
- // shear history effects
-
- touch[jj] = 1;
- shear = &allshear[3*jj];
- if (shearupdate) {
- shear[0] += vtr1*dt;
- shear[1] += vtr2*dt;
- shear[2] += vtr3*dt;
- }
- shrmag = sqrt(shear[0]*shear[0] + shear[1]*shear[1] +
- shear[2]*shear[2]);
-
- // rotate shear displacements
-
- rsht = shear[0]*delx + shear[1]*dely + shear[2]*delz;
- rsht *= rsqinv;
- if (shearupdate) {
- shear[0] -= rsht*delx;
- shear[1] -= rsht*dely;
- shear[2] -= rsht*delz;
- }
-
- // tangential forces = shear + tangential velocity damping
+ r = sqrt(rsq);
+ rinv = 1.0/r;
+ rsqinv = 1.0/rsq;
+
+ // relative translational velocity
+
+ vr1 = v[i][0] - v[j][0];
+ vr2 = v[i][1] - v[j][1];
+ vr3 = v[i][2] - v[j][2];
+
+ // normal component
+
+ vnnr = vr1*delx + vr2*dely + vr3*delz;
+ vn1 = delx*vnnr * rsqinv;
+ vn2 = dely*vnnr * rsqinv;
+ vn3 = delz*vnnr * rsqinv;
+
+ // tangential component
+
+ vt1 = vr1 - vn1;
+ vt2 = vr2 - vn2;
+ vt3 = vr3 - vn3;
+
+ // relative rotational velocity
+
+ wr1 = (radi*omega[i][0] + radj*omega[j][0]) * rinv;
+ wr2 = (radi*omega[i][1] + radj*omega[j][1]) * rinv;
+ wr3 = (radi*omega[i][2] + radj*omega[j][2]) * rinv;
+
+ // normal force = Hertzian contact + normal velocity damping
+
+ if (rmass) {
+ meff = rmass[i]*rmass[j] / (rmass[i]+rmass[j]);
+ if (mask[i] & freeze_group_bit) meff = rmass[j];
+ if (mask[j] & freeze_group_bit) meff = rmass[i];
+ } else {
+ itype = type[i];
+ jtype = type[j];
+ meff = mass[itype]*mass[jtype] / (mass[itype]+mass[jtype]);
+ if (mask[i] & freeze_group_bit) meff = mass[jtype];
+ if (mask[j] & freeze_group_bit) meff = mass[itype];
+ }
+
+ damp = meff*gamman*vnnr*rsqinv;
+ ccel = kn*(radsum-r)*rinv - damp;
+ polyhertz = sqrt((radsum-r)*radi*radj / radsum);
+ ccel *= polyhertz;
+
+ // relative velocities
+
+ vtr1 = vt1 - (delz*wr2-dely*wr3);
+ vtr2 = vt2 - (delx*wr3-delz*wr1);
+ vtr3 = vt3 - (dely*wr1-delx*wr2);
+ vrel = vtr1*vtr1 + vtr2*vtr2 + vtr3*vtr3;
+ vrel = sqrt(vrel);
+
+ // shear history effects
+
+ touch[jj] = 1;
+ shear = &allshear[3*jj];
+ if (shearupdate) {
+ shear[0] += vtr1*dt;
+ shear[1] += vtr2*dt;
+ shear[2] += vtr3*dt;
+ }
+ shrmag = sqrt(shear[0]*shear[0] + shear[1]*shear[1] +
+ shear[2]*shear[2]);
+
+ // rotate shear displacements
+
+ rsht = shear[0]*delx + shear[1]*dely + shear[2]*delz;
+ rsht *= rsqinv;
+ if (shearupdate) {
+ shear[0] -= rsht*delx;
+ shear[1] -= rsht*dely;
+ shear[2] -= rsht*delz;
+ }
+
+ // tangential forces = shear + tangential velocity damping
fs1 = -polyhertz * (kt*shear[0] + meff*gammat*vtr1);
fs2 = -polyhertz * (kt*shear[1] + meff*gammat*vtr2);
fs3 = -polyhertz * (kt*shear[2] + meff*gammat*vtr3);
- // rescale frictional displacements and forces if needed
-
- fs = sqrt(fs1*fs1 + fs2*fs2 + fs3*fs3);
- fn = xmu * fabs(ccel*r);
-
- if (fs > fn) {
- if (shrmag != 0.0) {
- shear[0] = (fn/fs) * (shear[0] + meff*gammat*vtr1/kt) -
- meff*gammat*vtr1/kt;
- shear[1] = (fn/fs) * (shear[1] + meff*gammat*vtr2/kt) -
- meff*gammat*vtr2/kt;
- shear[2] = (fn/fs) * (shear[2] + meff*gammat*vtr3/kt) -
- meff*gammat*vtr3/kt;
- fs1 *= fn/fs;
- fs2 *= fn/fs;
- fs3 *= fn/fs;
- } else fs1 = fs2 = fs3 = 0.0;
- }
-
- // forces & torques
-
- fx = delx*ccel + fs1;
- fy = dely*ccel + fs2;
- fz = delz*ccel + fs3;
- f[i][0] += fx;
- f[i][1] += fy;
- f[i][2] += fz;
-
- tor1 = rinv * (dely*fs3 - delz*fs2);
- tor2 = rinv * (delz*fs1 - delx*fs3);
- tor3 = rinv * (delx*fs2 - dely*fs1);
- torque[i][0] -= radi*tor1;
- torque[i][1] -= radi*tor2;
- torque[i][2] -= radi*tor3;
-
- if (j < nlocal) {
- f[j][0] -= fx;
- f[j][1] -= fy;
- f[j][2] -= fz;
- torque[j][0] -= radj*tor1;
- torque[j][1] -= radj*tor2;
- torque[j][2] -= radj*tor3;
- }
-
- if (evflag) ev_tally_xyz(i,j,nlocal,0,
- 0.0,0.0,fx,fy,fz,delx,dely,delz);
+ // rescale frictional displacements and forces if needed
+
+ fs = sqrt(fs1*fs1 + fs2*fs2 + fs3*fs3);
+ fn = xmu * fabs(ccel*r);
+
+ if (fs > fn) {
+ if (shrmag != 0.0) {
+ shear[0] = (fn/fs) * (shear[0] + meff*gammat*vtr1/kt) -
+ meff*gammat*vtr1/kt;
+ shear[1] = (fn/fs) * (shear[1] + meff*gammat*vtr2/kt) -
+ meff*gammat*vtr2/kt;
+ shear[2] = (fn/fs) * (shear[2] + meff*gammat*vtr3/kt) -
+ meff*gammat*vtr3/kt;
+ fs1 *= fn/fs;
+ fs2 *= fn/fs;
+ fs3 *= fn/fs;
+ } else fs1 = fs2 = fs3 = 0.0;
+ }
+
+ // forces & torques
+
+ fx = delx*ccel + fs1;
+ fy = dely*ccel + fs2;
+ fz = delz*ccel + fs3;
+ f[i][0] += fx;
+ f[i][1] += fy;
+ f[i][2] += fz;
+
+ tor1 = rinv * (dely*fs3 - delz*fs2);
+ tor2 = rinv * (delz*fs1 - delx*fs3);
+ tor3 = rinv * (delx*fs2 - dely*fs1);
+ torque[i][0] -= radi*tor1;
+ torque[i][1] -= radi*tor2;
+ torque[i][2] -= radi*tor3;
+
+ if (j < nlocal) {
+ f[j][0] -= fx;
+ f[j][1] -= fy;
+ f[j][2] -= fz;
+ torque[j][0] -= radj*tor1;
+ torque[j][1] -= radj*tor2;
+ torque[j][2] -= radj*tor3;
+ }
+
+ if (evflag) ev_tally_xyz(i,j,nlocal,0,
+ 0.0,0.0,fx,fy,fz,delx,dely,delz);
}
}
}
@@ -267,7 +267,7 @@ void PairGranHertzHistory::settings(int narg, char **arg)
dampflag = force->inumeric(arg[5]);
if (dampflag == 0) gammat = 0.0;
- if (kn < 0.0 || kt < 0.0 || gamman < 0.0 || gammat < 0.0 ||
+ if (kn < 0.0 || kt < 0.0 || gamman < 0.0 || gammat < 0.0 ||
xmu < 0.0 || xmu > 1.0 || dampflag < 0 || dampflag > 1)
error->all(FLERR,"Illegal pair_style command");
@@ -280,9 +280,9 @@ void PairGranHertzHistory::settings(int narg, char **arg)
/* ---------------------------------------------------------------------- */
double PairGranHertzHistory::single(int i, int j, int itype, int jtype,
- double rsq,
- double factor_coul, double factor_lj,
- double &fforce)
+ double rsq,
+ double factor_coul, double factor_lj,
+ double &fforce)
{
double radi,radj,radsum;
double r,rinv,rsqinv,delx,dely,delz;
@@ -314,7 +314,7 @@ double PairGranHertzHistory::single(int i, int j, int itype, int jtype,
vr3 = v[i][2] - v[j][2];
// normal component
-
+
double **x = atom->x;
delx = x[i][0] - x[j][0];
dely = x[i][1] - x[j][1];
@@ -324,7 +324,7 @@ double PairGranHertzHistory::single(int i, int j, int itype, int jtype,
vn1 = delx*vnnr * rsqinv;
vn2 = dely*vnnr * rsqinv;
vn3 = delz*vnnr * rsqinv;
-
+
// tangential component
vt1 = vr1 - vn1;
@@ -337,7 +337,7 @@ double PairGranHertzHistory::single(int i, int j, int itype, int jtype,
wr1 = (radi*omega[i][0] + radj*omega[j][0]) * rinv;
wr2 = (radi*omega[i][1] + radj*omega[j][1]) * rinv;
wr3 = (radi*omega[i][2] + radj*omega[j][2]) * rinv;
-
+
// normal force = Hertzian contact + normal velocity damping
double *rmass = atom->rmass;
@@ -353,7 +353,7 @@ double PairGranHertzHistory::single(int i, int j, int itype, int jtype,
if (mask[i] & freeze_group_bit) meff = mass[jtype];
if (mask[j] & freeze_group_bit) meff = mass[itype];
}
-
+
damp = meff*gamman*vnnr*rsqinv;
ccel = kn*(radsum-r)*rinv - damp;
polyhertz = sqrt((radsum-r)*radi*radj / radsum);
@@ -366,7 +366,7 @@ double PairGranHertzHistory::single(int i, int j, int itype, int jtype,
vtr3 = vt3 - (dely*wr1-delx*wr2);
vrel = vtr1*vtr1 + vtr2*vtr2 + vtr3*vtr3;
vrel = sqrt(vrel);
-
+
// shear history effects
// neighprev = index of found neigh on previous call
// search entire jnum list of neighbors of I for neighbor J
@@ -385,25 +385,25 @@ double PairGranHertzHistory::single(int i, int j, int itype, int jtype,
}
double *shear = &allshear[3*neighprev];
- shrmag = sqrt(shear[0]*shear[0] + shear[1]*shear[1] +
- shear[2]*shear[2]);
-
+ shrmag = sqrt(shear[0]*shear[0] + shear[1]*shear[1] +
+ shear[2]*shear[2]);
+
// rotate shear displacements
-
+
rsht = shear[0]*delx + shear[1]*dely + shear[2]*delz;
rsht *= rsqinv;
-
+
// tangential forces = shear + tangential velocity damping
-
+
fs1 = -polyhertz * (kt*shear[0] + meff*gammat*vtr1);
fs2 = -polyhertz * (kt*shear[1] + meff*gammat*vtr2);
fs3 = -polyhertz * (kt*shear[2] + meff*gammat*vtr3);
-
+
// rescale frictional displacements and forces if needed
-
+
fs = sqrt(fs1*fs1 + fs2*fs2 + fs3*fs3);
fn = xmu * fabs(ccel*r);
-
+
if (fs > fn) {
if (shrmag != 0.0) {
fs1 *= fn/fs;
@@ -412,9 +412,9 @@ double PairGranHertzHistory::single(int i, int j, int itype, int jtype,
fs *= fn/fs;
} else fs1 = fs2 = fs3 = fs = 0.0;
}
-
+
// set all forces and return no energy
-
+
fforce = ccel;
svector[0] = fs1;
svector[1] = fs2;
diff --git a/src/GRANULAR/pair_gran_hertz_history.h b/src/GRANULAR/pair_gran_hertz_history.h
index 0cb762c4f9c30da510cbd3adb6cf5d218236a3f1..b5eacb6430557587f03970d3979371a855bc47b8 100644
--- a/src/GRANULAR/pair_gran_hertz_history.h
+++ b/src/GRANULAR/pair_gran_hertz_history.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/GRANULAR/pair_gran_hooke.cpp b/src/GRANULAR/pair_gran_hooke.cpp
index 4f2c00e270d6b0f2f5975e224fb038ea28b29e25..befc20ce248a6c26a240bcbc6bf1882f09be7da1 100644
--- a/src/GRANULAR/pair_gran_hooke.cpp
+++ b/src/GRANULAR/pair_gran_hooke.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -91,100 +91,100 @@ void PairGranHooke::compute(int eflag, int vflag)
radsum = radi + radj;
if (rsq < radsum*radsum) {
- r = sqrt(rsq);
- rinv = 1.0/r;
- rsqinv = 1.0/rsq;
-
- // relative translational velocity
-
- vr1 = v[i][0] - v[j][0];
- vr2 = v[i][1] - v[j][1];
- vr3 = v[i][2] - v[j][2];
-
- // normal component
-
- vnnr = vr1*delx + vr2*dely + vr3*delz;
- vn1 = delx*vnnr * rsqinv;
- vn2 = dely*vnnr * rsqinv;
- vn3 = delz*vnnr * rsqinv;
-
- // tangential component
-
- vt1 = vr1 - vn1;
- vt2 = vr2 - vn2;
- vt3 = vr3 - vn3;
-
- // relative rotational velocity
-
- wr1 = (radi*omega[i][0] + radj*omega[j][0]) * rinv;
- wr2 = (radi*omega[i][1] + radj*omega[j][1]) * rinv;
- wr3 = (radi*omega[i][2] + radj*omega[j][2]) * rinv;
-
- // normal forces = Hookian contact + normal velocity damping
-
- if (rmass) {
- meff = rmass[i]*rmass[j] / (rmass[i]+rmass[j]);
- if (mask[i] & freeze_group_bit) meff = rmass[j];
- if (mask[j] & freeze_group_bit) meff = rmass[i];
- } else {
- itype = type[i];
- jtype = type[j];
- meff = mass[itype]*mass[jtype] / (mass[itype]+mass[jtype]);
- if (mask[i] & freeze_group_bit) meff = mass[jtype];
- if (mask[j] & freeze_group_bit) meff = mass[itype];
- }
-
- damp = meff*gamman*vnnr*rsqinv;
- ccel = kn*(radsum-r)*rinv - damp;
-
- // relative velocities
-
- vtr1 = vt1 - (delz*wr2-dely*wr3);
- vtr2 = vt2 - (delx*wr3-delz*wr1);
- vtr3 = vt3 - (dely*wr1-delx*wr2);
- vrel = vtr1*vtr1 + vtr2*vtr2 + vtr3*vtr3;
- vrel = sqrt(vrel);
-
- // force normalization
-
- fn = xmu * fabs(ccel*r);
- fs = meff*gammat*vrel;
- if (vrel != 0.0) ft = MIN(fn,fs) / vrel;
- else ft = 0.0;
-
- // tangential force due to tangential velocity damping
-
- fs1 = -ft*vtr1;
- fs2 = -ft*vtr2;
- fs3 = -ft*vtr3;
-
- // forces & torques
-
- fx = delx*ccel + fs1;
- fy = dely*ccel + fs2;
- fz = delz*ccel + fs3;
- f[i][0] += fx;
- f[i][1] += fy;
- f[i][2] += fz;
-
- tor1 = rinv * (dely*fs3 - delz*fs2);
- tor2 = rinv * (delz*fs1 - delx*fs3);
- tor3 = rinv * (delx*fs2 - dely*fs1);
- torque[i][0] -= radi*tor1;
- torque[i][1] -= radi*tor2;
- torque[i][2] -= radi*tor3;
-
- if (newton_pair || j < nlocal) {
- f[j][0] -= fx;
- f[j][1] -= fy;
- f[j][2] -= fz;
- torque[j][0] -= radj*tor1;
- torque[j][1] -= radj*tor2;
- torque[j][2] -= radj*tor3;
- }
-
- if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,
- 0.0,0.0,fx,fy,fz,delx,dely,delz);
+ r = sqrt(rsq);
+ rinv = 1.0/r;
+ rsqinv = 1.0/rsq;
+
+ // relative translational velocity
+
+ vr1 = v[i][0] - v[j][0];
+ vr2 = v[i][1] - v[j][1];
+ vr3 = v[i][2] - v[j][2];
+
+ // normal component
+
+ vnnr = vr1*delx + vr2*dely + vr3*delz;
+ vn1 = delx*vnnr * rsqinv;
+ vn2 = dely*vnnr * rsqinv;
+ vn3 = delz*vnnr * rsqinv;
+
+ // tangential component
+
+ vt1 = vr1 - vn1;
+ vt2 = vr2 - vn2;
+ vt3 = vr3 - vn3;
+
+ // relative rotational velocity
+
+ wr1 = (radi*omega[i][0] + radj*omega[j][0]) * rinv;
+ wr2 = (radi*omega[i][1] + radj*omega[j][1]) * rinv;
+ wr3 = (radi*omega[i][2] + radj*omega[j][2]) * rinv;
+
+ // normal forces = Hookian contact + normal velocity damping
+
+ if (rmass) {
+ meff = rmass[i]*rmass[j] / (rmass[i]+rmass[j]);
+ if (mask[i] & freeze_group_bit) meff = rmass[j];
+ if (mask[j] & freeze_group_bit) meff = rmass[i];
+ } else {
+ itype = type[i];
+ jtype = type[j];
+ meff = mass[itype]*mass[jtype] / (mass[itype]+mass[jtype]);
+ if (mask[i] & freeze_group_bit) meff = mass[jtype];
+ if (mask[j] & freeze_group_bit) meff = mass[itype];
+ }
+
+ damp = meff*gamman*vnnr*rsqinv;
+ ccel = kn*(radsum-r)*rinv - damp;
+
+ // relative velocities
+
+ vtr1 = vt1 - (delz*wr2-dely*wr3);
+ vtr2 = vt2 - (delx*wr3-delz*wr1);
+ vtr3 = vt3 - (dely*wr1-delx*wr2);
+ vrel = vtr1*vtr1 + vtr2*vtr2 + vtr3*vtr3;
+ vrel = sqrt(vrel);
+
+ // force normalization
+
+ fn = xmu * fabs(ccel*r);
+ fs = meff*gammat*vrel;
+ if (vrel != 0.0) ft = MIN(fn,fs) / vrel;
+ else ft = 0.0;
+
+ // tangential force due to tangential velocity damping
+
+ fs1 = -ft*vtr1;
+ fs2 = -ft*vtr2;
+ fs3 = -ft*vtr3;
+
+ // forces & torques
+
+ fx = delx*ccel + fs1;
+ fy = dely*ccel + fs2;
+ fz = delz*ccel + fs3;
+ f[i][0] += fx;
+ f[i][1] += fy;
+ f[i][2] += fz;
+
+ tor1 = rinv * (dely*fs3 - delz*fs2);
+ tor2 = rinv * (delz*fs1 - delx*fs3);
+ tor3 = rinv * (delx*fs2 - dely*fs1);
+ torque[i][0] -= radi*tor1;
+ torque[i][1] -= radi*tor2;
+ torque[i][2] -= radi*tor3;
+
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= fx;
+ f[j][1] -= fy;
+ f[j][2] -= fz;
+ torque[j][0] -= radj*tor1;
+ torque[j][1] -= radj*tor2;
+ torque[j][2] -= radj*tor3;
+ }
+
+ if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,
+ 0.0,0.0,fx,fy,fz,delx,dely,delz);
}
}
}
@@ -195,8 +195,8 @@ void PairGranHooke::compute(int eflag, int vflag)
/* ---------------------------------------------------------------------- */
double PairGranHooke::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
- double &fforce)
+ double factor_coul, double factor_lj,
+ double &fforce)
{
double radi,radj,radsum,r,rinv,rsqinv;
double delx,dely,delz;
@@ -228,7 +228,7 @@ double PairGranHooke::single(int i, int j, int itype, int jtype, double rsq,
vr1 = v[i][0] - v[j][0];
vr2 = v[i][1] - v[j][1];
vr3 = v[i][2] - v[j][2];
-
+
// normal component
double **x = atom->x;
@@ -287,15 +287,15 @@ double PairGranHooke::single(int i, int j, int itype, int jtype, double rsq,
fs = meff*gammat*vrel;
if (vrel != 0.0) ft = MIN(fn,fs) / vrel;
else ft = 0.0;
-
+
// set all forces and return no energy
-
+
fforce = ccel;
svector[0] = -ft*vtr1;
svector[1] = -ft*vtr2;
svector[2] = -ft*vtr3;
- svector[3] = sqrt(svector[0]*svector[0] +
- svector[1]*svector[1] +
- svector[2]*svector[2]);
+ svector[3] = sqrt(svector[0]*svector[0] +
+ svector[1]*svector[1] +
+ svector[2]*svector[2]);
return 0.0;
}
diff --git a/src/GRANULAR/pair_gran_hooke.h b/src/GRANULAR/pair_gran_hooke.h
index 20c2c3c1bdf61e300957290164c833262f523366..d8a63b98058320d112c8eb17224939eb45717442 100644
--- a/src/GRANULAR/pair_gran_hooke.h
+++ b/src/GRANULAR/pair_gran_hooke.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/GRANULAR/pair_gran_hooke_history.cpp b/src/GRANULAR/pair_gran_hooke_history.cpp
index 7e8cbc22fc101a3b3817ab67f9dd8fa54c8a9ce7..268b1966442315fc7fec3ca547b29ca53510e8de 100644
--- a/src/GRANULAR/pair_gran_hooke_history.cpp
+++ b/src/GRANULAR/pair_gran_hooke_history.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -115,7 +115,7 @@ void PairGranHookeHistory::compute(int eflag, int vflag)
firstneigh = list->firstneigh;
firsttouch = listgranhistory->firstneigh;
firstshear = listgranhistory->firstdouble;
-
+
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@@ -142,144 +142,144 @@ void PairGranHookeHistory::compute(int eflag, int vflag)
if (rsq >= radsum*radsum) {
- // unset non-touching neighbors
+ // unset non-touching neighbors
touch[jj] = 0;
- shear = &allshear[3*jj];
+ shear = &allshear[3*jj];
shear[0] = 0.0;
shear[1] = 0.0;
shear[2] = 0.0;
} else {
- r = sqrt(rsq);
- rinv = 1.0/r;
- rsqinv = 1.0/rsq;
+ r = sqrt(rsq);
+ rinv = 1.0/r;
+ rsqinv = 1.0/rsq;
- // relative translational velocity
+ // relative translational velocity
- vr1 = v[i][0] - v[j][0];
- vr2 = v[i][1] - v[j][1];
- vr3 = v[i][2] - v[j][2];
+ vr1 = v[i][0] - v[j][0];
+ vr2 = v[i][1] - v[j][1];
+ vr3 = v[i][2] - v[j][2];
- // normal component
+ // normal component
- vnnr = vr1*delx + vr2*dely + vr3*delz;
- vn1 = delx*vnnr * rsqinv;
- vn2 = dely*vnnr * rsqinv;
- vn3 = delz*vnnr * rsqinv;
+ vnnr = vr1*delx + vr2*dely + vr3*delz;
+ vn1 = delx*vnnr * rsqinv;
+ vn2 = dely*vnnr * rsqinv;
+ vn3 = delz*vnnr * rsqinv;
- // tangential component
+ // tangential component
- vt1 = vr1 - vn1;
- vt2 = vr2 - vn2;
- vt3 = vr3 - vn3;
+ vt1 = vr1 - vn1;
+ vt2 = vr2 - vn2;
+ vt3 = vr3 - vn3;
- // relative rotational velocity
+ // relative rotational velocity
- wr1 = (radi*omega[i][0] + radj*omega[j][0]) * rinv;
- wr2 = (radi*omega[i][1] + radj*omega[j][1]) * rinv;
- wr3 = (radi*omega[i][2] + radj*omega[j][2]) * rinv;
+ wr1 = (radi*omega[i][0] + radj*omega[j][0]) * rinv;
+ wr2 = (radi*omega[i][1] + radj*omega[j][1]) * rinv;
+ wr3 = (radi*omega[i][2] + radj*omega[j][2]) * rinv;
- // normal forces = Hookian contact + normal velocity damping
+ // normal forces = Hookian contact + normal velocity damping
- if (rmass) {
- meff = rmass[i]*rmass[j] / (rmass[i]+rmass[j]);
- if (mask[i] & freeze_group_bit) meff = rmass[j];
- if (mask[j] & freeze_group_bit) meff = rmass[i];
- } else {
- itype = type[i];
- jtype = type[j];
- meff = mass[itype]*mass[jtype] / (mass[itype]+mass[jtype]);
- if (mask[i] & freeze_group_bit) meff = mass[jtype];
- if (mask[j] & freeze_group_bit) meff = mass[itype];
- }
+ if (rmass) {
+ meff = rmass[i]*rmass[j] / (rmass[i]+rmass[j]);
+ if (mask[i] & freeze_group_bit) meff = rmass[j];
+ if (mask[j] & freeze_group_bit) meff = rmass[i];
+ } else {
+ itype = type[i];
+ jtype = type[j];
+ meff = mass[itype]*mass[jtype] / (mass[itype]+mass[jtype]);
+ if (mask[i] & freeze_group_bit) meff = mass[jtype];
+ if (mask[j] & freeze_group_bit) meff = mass[itype];
+ }
- damp = meff*gamman*vnnr*rsqinv;
- ccel = kn*(radsum-r)*rinv - damp;
+ damp = meff*gamman*vnnr*rsqinv;
+ ccel = kn*(radsum-r)*rinv - damp;
- // relative velocities
+ // relative velocities
- vtr1 = vt1 - (delz*wr2-dely*wr3);
- vtr2 = vt2 - (delx*wr3-delz*wr1);
- vtr3 = vt3 - (dely*wr1-delx*wr2);
- vrel = vtr1*vtr1 + vtr2*vtr2 + vtr3*vtr3;
- vrel = sqrt(vrel);
+ vtr1 = vt1 - (delz*wr2-dely*wr3);
+ vtr2 = vt2 - (delx*wr3-delz*wr1);
+ vtr3 = vt3 - (dely*wr1-delx*wr2);
+ vrel = vtr1*vtr1 + vtr2*vtr2 + vtr3*vtr3;
+ vrel = sqrt(vrel);
- // shear history effects
+ // shear history effects
- touch[jj] = 1;
- shear = &allshear[3*jj];
+ touch[jj] = 1;
+ shear = &allshear[3*jj];
- if (shearupdate) {
- shear[0] += vtr1*dt;
- shear[1] += vtr2*dt;
- shear[2] += vtr3*dt;
- }
+ if (shearupdate) {
+ shear[0] += vtr1*dt;
+ shear[1] += vtr2*dt;
+ shear[2] += vtr3*dt;
+ }
shrmag = sqrt(shear[0]*shear[0] + shear[1]*shear[1] +
- shear[2]*shear[2]);
-
- // rotate shear displacements
-
- rsht = shear[0]*delx + shear[1]*dely + shear[2]*delz;
- rsht *= rsqinv;
- if (shearupdate) {
- shear[0] -= rsht*delx;
- shear[1] -= rsht*dely;
- shear[2] -= rsht*delz;
- }
-
- // tangential forces = shear + tangential velocity damping
-
- fs1 = - (kt*shear[0] + meff*gammat*vtr1);
- fs2 = - (kt*shear[1] + meff*gammat*vtr2);
- fs3 = - (kt*shear[2] + meff*gammat*vtr3);
-
- // rescale frictional displacements and forces if needed
-
- fs = sqrt(fs1*fs1 + fs2*fs2 + fs3*fs3);
- fn = xmu * fabs(ccel*r);
-
- if (fs > fn) {
- if (shrmag != 0.0) {
- shear[0] = (fn/fs) * (shear[0] + meff*gammat*vtr1/kt) -
- meff*gammat*vtr1/kt;
- shear[1] = (fn/fs) * (shear[1] + meff*gammat*vtr2/kt) -
- meff*gammat*vtr2/kt;
- shear[2] = (fn/fs) * (shear[2] + meff*gammat*vtr3/kt) -
- meff*gammat*vtr3/kt;
- fs1 *= fn/fs;
- fs2 *= fn/fs;
- fs3 *= fn/fs;
- } else fs1 = fs2 = fs3 = 0.0;
- }
-
- // forces & torques
-
- fx = delx*ccel + fs1;
- fy = dely*ccel + fs2;
- fz = delz*ccel + fs3;
- f[i][0] += fx;
- f[i][1] += fy;
- f[i][2] += fz;
-
- tor1 = rinv * (dely*fs3 - delz*fs2);
- tor2 = rinv * (delz*fs1 - delx*fs3);
- tor3 = rinv * (delx*fs2 - dely*fs1);
- torque[i][0] -= radi*tor1;
- torque[i][1] -= radi*tor2;
- torque[i][2] -= radi*tor3;
-
- if (j < nlocal) {
- f[j][0] -= fx;
- f[j][1] -= fy;
- f[j][2] -= fz;
- torque[j][0] -= radj*tor1;
- torque[j][1] -= radj*tor2;
- torque[j][2] -= radj*tor3;
- }
-
- if (evflag) ev_tally_xyz(i,j,nlocal,0,
- 0.0,0.0,fx,fy,fz,delx,dely,delz);
+ shear[2]*shear[2]);
+
+ // rotate shear displacements
+
+ rsht = shear[0]*delx + shear[1]*dely + shear[2]*delz;
+ rsht *= rsqinv;
+ if (shearupdate) {
+ shear[0] -= rsht*delx;
+ shear[1] -= rsht*dely;
+ shear[2] -= rsht*delz;
+ }
+
+ // tangential forces = shear + tangential velocity damping
+
+ fs1 = - (kt*shear[0] + meff*gammat*vtr1);
+ fs2 = - (kt*shear[1] + meff*gammat*vtr2);
+ fs3 = - (kt*shear[2] + meff*gammat*vtr3);
+
+ // rescale frictional displacements and forces if needed
+
+ fs = sqrt(fs1*fs1 + fs2*fs2 + fs3*fs3);
+ fn = xmu * fabs(ccel*r);
+
+ if (fs > fn) {
+ if (shrmag != 0.0) {
+ shear[0] = (fn/fs) * (shear[0] + meff*gammat*vtr1/kt) -
+ meff*gammat*vtr1/kt;
+ shear[1] = (fn/fs) * (shear[1] + meff*gammat*vtr2/kt) -
+ meff*gammat*vtr2/kt;
+ shear[2] = (fn/fs) * (shear[2] + meff*gammat*vtr3/kt) -
+ meff*gammat*vtr3/kt;
+ fs1 *= fn/fs;
+ fs2 *= fn/fs;
+ fs3 *= fn/fs;
+ } else fs1 = fs2 = fs3 = 0.0;
+ }
+
+ // forces & torques
+
+ fx = delx*ccel + fs1;
+ fy = dely*ccel + fs2;
+ fz = delz*ccel + fs3;
+ f[i][0] += fx;
+ f[i][1] += fy;
+ f[i][2] += fz;
+
+ tor1 = rinv * (dely*fs3 - delz*fs2);
+ tor2 = rinv * (delz*fs1 - delx*fs3);
+ tor3 = rinv * (delx*fs2 - dely*fs1);
+ torque[i][0] -= radi*tor1;
+ torque[i][1] -= radi*tor2;
+ torque[i][2] -= radi*tor3;
+
+ if (j < nlocal) {
+ f[j][0] -= fx;
+ f[j][1] -= fy;
+ f[j][2] -= fz;
+ torque[j][0] -= radj*tor1;
+ torque[j][1] -= radj*tor2;
+ torque[j][2] -= radj*tor3;
+ }
+
+ if (evflag) ev_tally_xyz(i,j,nlocal,0,
+ 0.0,0.0,fx,fy,fz,delx,dely,delz);
}
}
}
@@ -329,7 +329,7 @@ void PairGranHookeHistory::settings(int narg, char **arg)
dampflag = force->inumeric(arg[5]);
if (dampflag == 0) gammat = 0.0;
- if (kn < 0.0 || kt < 0.0 || gamman < 0.0 || gammat < 0.0 ||
+ if (kn < 0.0 || kt < 0.0 || gamman < 0.0 || gammat < 0.0 ||
xmu < 0.0 || xmu > 1.0 || dampflag < 0 || dampflag > 1)
error->all(FLERR,"Illegal pair_style command");
}
@@ -441,11 +441,11 @@ void PairGranHookeHistory::init_style()
onerad_frozen[type[i]] = MAX(onerad_frozen[type[i]],radius[i]);
else
onerad_dynamic[type[i]] = MAX(onerad_dynamic[type[i]],radius[i]);
-
+
MPI_Allreduce(&onerad_dynamic[1],&maxrad_dynamic[1],atom->ntypes,
- MPI_DOUBLE,MPI_MAX,world);
+ MPI_DOUBLE,MPI_MAX,world);
MPI_Allreduce(&onerad_frozen[1],&maxrad_frozen[1],atom->ntypes,
- MPI_DOUBLE,MPI_MAX,world);
+ MPI_DOUBLE,MPI_MAX,world);
}
/* ----------------------------------------------------------------------
@@ -554,9 +554,9 @@ void PairGranHookeHistory::reset_dt()
/* ---------------------------------------------------------------------- */
double PairGranHookeHistory::single(int i, int j, int itype, int jtype,
- double rsq,
- double factor_coul, double factor_lj,
- double &fforce)
+ double rsq,
+ double factor_coul, double factor_lj,
+ double &fforce)
{
double radi,radj,radsum;
double r,rinv,rsqinv,delx,dely,delz;
@@ -588,7 +588,7 @@ double PairGranHookeHistory::single(int i, int j, int itype, int jtype,
vr3 = v[i][2] - v[j][2];
// normal component
-
+
double **x = atom->x;
delx = x[i][0] - x[j][0];
dely = x[i][1] - x[j][1];
@@ -598,7 +598,7 @@ double PairGranHookeHistory::single(int i, int j, int itype, int jtype,
vn1 = delx*vnnr * rsqinv;
vn2 = dely*vnnr * rsqinv;
vn3 = delz*vnnr * rsqinv;
-
+
// tangential component
vt1 = vr1 - vn1;
@@ -611,7 +611,7 @@ double PairGranHookeHistory::single(int i, int j, int itype, int jtype,
wr1 = (radi*omega[i][0] + radj*omega[j][0]) * rinv;
wr2 = (radi*omega[i][1] + radj*omega[j][1]) * rinv;
wr3 = (radi*omega[i][2] + radj*omega[j][2]) * rinv;
-
+
// normal force = Hertzian contact + normal velocity damping
double *rmass = atom->rmass;
@@ -627,7 +627,7 @@ double PairGranHookeHistory::single(int i, int j, int itype, int jtype,
if (mask[i] & freeze_group_bit) meff = mass[jtype];
if (mask[j] & freeze_group_bit) meff = mass[itype];
}
-
+
damp = meff*gamman*vnnr*rsqinv;
ccel = kn*(radsum-r)*rinv - damp;
@@ -638,7 +638,7 @@ double PairGranHookeHistory::single(int i, int j, int itype, int jtype,
vtr3 = vt3 - (dely*wr1-delx*wr2);
vrel = vtr1*vtr1 + vtr2*vtr2 + vtr3*vtr3;
vrel = sqrt(vrel);
-
+
// shear history effects
// neighprev = index of found neigh on previous call
// search entire jnum list of neighbors of I for neighbor J
@@ -657,25 +657,25 @@ double PairGranHookeHistory::single(int i, int j, int itype, int jtype,
}
double *shear = &allshear[3*neighprev];
- shrmag = sqrt(shear[0]*shear[0] + shear[1]*shear[1] +
- shear[2]*shear[2]);
-
+ shrmag = sqrt(shear[0]*shear[0] + shear[1]*shear[1] +
+ shear[2]*shear[2]);
+
// rotate shear displacements
-
+
rsht = shear[0]*delx + shear[1]*dely + shear[2]*delz;
rsht *= rsqinv;
-
+
// tangential forces = shear + tangential velocity damping
-
+
fs1 = - (kt*shear[0] + meff*gammat*vtr1);
fs2 = - (kt*shear[1] + meff*gammat*vtr2);
fs3 = - (kt*shear[2] + meff*gammat*vtr3);
-
+
// rescale frictional displacements and forces if needed
-
+
fs = sqrt(fs1*fs1 + fs2*fs2 + fs3*fs3);
fn = xmu * fabs(ccel*r);
-
+
if (fs > fn) {
if (shrmag != 0.0) {
fs1 *= fn/fs;
@@ -684,9 +684,9 @@ double PairGranHookeHistory::single(int i, int j, int itype, int jtype,
fs *= fn/fs;
} else fs1 = fs2 = fs3 = fs = 0.0;
}
-
+
// set all forces and return no energy
-
+
fforce = ccel;
svector[0] = fs1;
svector[1] = fs2;
diff --git a/src/GRANULAR/pair_gran_hooke_history.h b/src/GRANULAR/pair_gran_hooke_history.h
index 593143205c7dc3e76402b5e8fec23e527f3d33ae..ec111a957d41d9cb501027974057935959bdc406 100644
--- a/src/GRANULAR/pair_gran_hooke_history.h
+++ b/src/GRANULAR/pair_gran_hooke_history.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/KIM/pair_kim.cpp b/src/KIM/pair_kim.cpp
index 071248402520e8444cd6807b79f555d34f4e2b83..e86caa9e111f8e836606cf5c63c419a728e78ed0 100644
--- a/src/KIM/pair_kim.cpp
+++ b/src/KIM/pair_kim.cpp
@@ -5,14 +5,14 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
- Contributing authors: Valeriu Smirichinski, Ryan Elliott,
+ Contributing authors: Valeriu Smirichinski, Ryan Elliott,
Ellad Tadmor (U Minn)
------------------------------------------------------------------------- */
@@ -24,7 +24,7 @@
#include "atom.h"
#include "comm.h"
#include "force.h"
-#include "neighbor.h"
+#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "update.h"
@@ -132,15 +132,15 @@ void PairKIM::compute(int eflag , int vflag)
// set callback for virial tallying if necessary
- int process_dEdr_flag = 0;
+ int process_dEdr_flag = 0;
if (process_dEdr_ind >= 0 && (vflag_atom || vflag_global))
process_dEdr_flag = 1;
pkim->setm_compute_by_index(&kimerr,12, particleEnergy_ind,
- eflag_atom,1,
- particleVirial_ind,vflag_atom,1,
- virialGlobal_ind,vflag_global,1,
- process_dEdr_ind,process_dEdr_flag,1);
+ eflag_atom,1,
+ particleVirial_ind,vflag_atom,1,
+ virialGlobal_ind,vflag_global,1,
+ process_dEdr_ind,process_dEdr_flag,1);
kim_error(__LINE__,"setm_compute_by_index",kimerr);
// KIM initialization
@@ -169,18 +169,18 @@ void PairKIM::compute(int eflag , int vflag)
f[i][2] += fcopy[i][2];
}
}
-
+
// flip sign of virial
if (vflag_global && !pkim->virial_need2add)
for (int i = 0; i < 6; i++) virial[i] = -1.0*virial[i];
if (vflag_atom && !pkim->particleVirial_need2add)
- for (int i = 0; i < atom->nlocal; i++)
+ for (int i = 0; i < atom->nlocal; i++)
for (int j = 0; j < 6; j++) vatom[i][j] = -1.0*vatom[i][j];
}
-
+
/* ----------------------------------------------------------------------
- allocate all arrays
+ allocate all arrays
------------------------------------------------------------------------- */
void PairKIM::allocate()
@@ -195,7 +195,7 @@ void PairKIM::allocate()
}
/* ----------------------------------------------------------------------
- global settings
+ global settings
------------------------------------------------------------------------- */
void PairKIM::settings(int narg, char **arg)
@@ -282,8 +282,8 @@ void PairKIM::coeff(int narg, char **arg)
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
if (map[i] >= 0 && map[j] >= 0) {
- setflag[i][j] = 1;
- count++;
+ setflag[i][j] = 1;
+ count++;
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
@@ -376,7 +376,7 @@ void PairKIM::unpack_reverse_comm(int n, int *list, double *buf)
double *fp;
if (hybrid) fp = &(fcopy[0][0]);
else fp = &(atom->f[0][0]);
-
+
double *va=&(vatom[0][0]);
m = 0;
if (vflag_atom == 1) {
@@ -404,7 +404,7 @@ void PairKIM::unpack_reverse_comm(int n, int *list, double *buf)
}
/* ----------------------------------------------------------------------
- memory usage of local atom-based arrays
+ memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double PairKIM::memory_usage()
@@ -421,17 +421,17 @@ void PairKIM::kim_error(int ln, const char* msg, int errcode)
{
if (errcode == 1) return;
KIM_API_model::report_error(ln,(char *) __FILE__,
- (char *) msg,errcode);
+ (char *) msg,errcode);
error->all(__FILE__,ln,"Internal KIM error");
}
/* ---------------------------------------------------------------------- */
int PairKIM::get_neigh(void **kimmdl,int *mode,int *request,
- int *atom, int *numnei, int **nei1atom, double **pRij)
+ int *atom, int *numnei, int **nei1atom, double **pRij)
{
double * x;
-
+
KIM_API_model *pkim = (KIM_API_model *) *kimmdl;
// get neighObj from KIM API obj
@@ -439,11 +439,11 @@ int PairKIM::get_neigh(void **kimmdl,int *mode,int *request,
int kimerr;
PairKIM *self = (PairKIM *) pkim->get_test_buffer(&kimerr);
-
+
*pRij = &(self->Rij[0]);
-
+
NeighList * neiobj = (NeighList * ) (*pkim)[self->neighObject_ind].data;
-
+
int * pnAtoms = (int *)(*pkim)[self->numberOfParticles_ind].data;
if(pkim->support_Rij) x = (double *)(*pkim)[self->coordinates_ind].data;
int nAtoms = *pnAtoms;
@@ -460,39 +460,39 @@ int PairKIM::get_neigh(void **kimmdl,int *mode,int *request,
return KIM_STATUS_NEIGH_ITER_INIT_OK; //succsesful restart
} else if (*request==1) { //increment iterator
if (self->pointsto > inum || inum <0){
- self->error->one(FLERR,"KIM neighbor iterator exceeded range");
+ self->error->one(FLERR,"KIM neighbor iterator exceeded range");
} else if (self->pointsto == inum) {
- self->pointsto = 0;
- *numnei = 0;
- return KIM_STATUS_NEIGH_ITER_PAST_END; //reached end by iterator
+ self->pointsto = 0;
+ *numnei = 0;
+ return KIM_STATUS_NEIGH_ITER_PAST_END; //reached end by iterator
} else {
- *atom = ilist[self->pointsto];
- *numnei = numneigh[*atom];
-
- // strip off neighbor mask for molecular systems
-
- if (self->molecular) {
- int n = *numnei;
- int *ptr = firstneigh[*atom];
- int *onebuf = self->onebuf;
- for (int i = 0; i < n; i++)
- onebuf[i] = *(ptr++) & NEIGHMASK;
- *nei1atom = onebuf;
- } else *nei1atom = firstneigh[*atom];
-
- self->pointsto++;
- if (*numnei > KIM_API_MAX_NEIGHBORS)
- return KIM_STATUS_NEIGH_TOO_MANY_NEIGHBORS;
- if (pkim->support_Rij) {
- for (jj=0; jj < *numnei; jj++) {
- int i = *atom;
- j = (*nei1atom)[jj];
- self->Rij[jj*3 +0] = -x[i*3+0] + x[j*3+0];
- self->Rij[jj*3 +1] = -x[i*3+1] + x[j*3+1];
- self->Rij[jj*3 +2] = -x[i*3+2] + x[j*3+2];
- }
- }
- return KIM_STATUS_OK;//successful increment
+ *atom = ilist[self->pointsto];
+ *numnei = numneigh[*atom];
+
+ // strip off neighbor mask for molecular systems
+
+ if (self->molecular) {
+ int n = *numnei;
+ int *ptr = firstneigh[*atom];
+ int *onebuf = self->onebuf;
+ for (int i = 0; i < n; i++)
+ onebuf[i] = *(ptr++) & NEIGHMASK;
+ *nei1atom = onebuf;
+ } else *nei1atom = firstneigh[*atom];
+
+ self->pointsto++;
+ if (*numnei > KIM_API_MAX_NEIGHBORS)
+ return KIM_STATUS_NEIGH_TOO_MANY_NEIGHBORS;
+ if (pkim->support_Rij) {
+ for (jj=0; jj < *numnei; jj++) {
+ int i = *atom;
+ j = (*nei1atom)[jj];
+ self->Rij[jj*3 +0] = -x[i*3+0] + x[j*3+0];
+ self->Rij[jj*3 +1] = -x[i*3+1] + x[j*3+1];
+ self->Rij[jj*3 +2] = -x[i*3+2] + x[j*3+2];
+ }
+ }
+ return KIM_STATUS_OK;//successful increment
}
}
}else if (*mode ==1){//locator mode
@@ -505,7 +505,7 @@ int PairKIM::get_neigh(void **kimmdl,int *mode,int *request,
}
*atom = *request;
*numnei = numneigh[*atom];
-
+
// strip off neighbor mask for molecular systems
if (self->molecular) {
@@ -513,19 +513,19 @@ int PairKIM::get_neigh(void **kimmdl,int *mode,int *request,
int *ptr = firstneigh[*atom];
int *onebuf = self->onebuf;
for (int i = 0; i < n; i++)
- onebuf[i] = *(ptr++) & NEIGHMASK;
+ onebuf[i] = *(ptr++) & NEIGHMASK;
*nei1atom = onebuf;
} else *nei1atom = firstneigh[*atom];
- if (*numnei > KIM_API_MAX_NEIGHBORS)
+ if (*numnei > KIM_API_MAX_NEIGHBORS)
return KIM_STATUS_NEIGH_TOO_MANY_NEIGHBORS;
if (pkim->support_Rij){
for(int jj=0; jj < *numnei; jj++){
- int i = *atom;
- int j = (*nei1atom)[jj];
- self->Rij[jj*3 +0]=-x[i*3+0] + x[j*3+0];
- self->Rij[jj*3 +1]=-x[i*3+1] + x[j*3+1];
- self->Rij[jj*3 +2]=-x[i*3+2] + x[j*3+2];
+ int i = *atom;
+ int j = (*nei1atom)[jj];
+ self->Rij[jj*3 +0]=-x[i*3+0] + x[j*3+0];
+ self->Rij[jj*3 +1]=-x[i*3+1] + x[j*3+1];
+ self->Rij[jj*3 +2]=-x[i*3+2] + x[j*3+2];
}
}
return KIM_STATUS_OK;//successful end
@@ -579,22 +579,22 @@ void PairKIM::kim_init()
if (!(strcmp(update->unit_style,"metal")==0))
this->kim_error(__LINE__,
- "LAMMPS unit_style must be metal to "
- "work with KIM models",-12);
-
+ "LAMMPS unit_style must be metal to "
+ "work with KIM models",-12);
+
// create temporary kim file
test_descriptor_string = new char[80*60];
for (int i=50;i<80*60;i++) test_descriptor_string[i]='\0';
-
+
// 1. write atomic header and atomic type spec
-
+
int i_s;
sprintf(test_descriptor_string,
- "# This file is automatically generated from LAMMPS "
- "pair_style PairKIM command\n");
+ "# This file is automatically generated from LAMMPS "
+ "pair_style PairKIM command\n");
i_s=strlen(test_descriptor_string);
-
+
sprintf(&test_descriptor_string[i_s],"TEST_NAME :=%s\n" ,testname);
i_s=strlen(test_descriptor_string);
sprintf(&test_descriptor_string[i_s],"#Unit_Handling := flexible\n\n");
@@ -611,35 +611,35 @@ void PairKIM::kim_init()
i_s=strlen(test_descriptor_string);
sprintf(&test_descriptor_string[i_s],"SUPPORTED_ATOM/PARTICLES_TYPES:\n");
i_s=strlen(test_descriptor_string);
- sprintf(&test_descriptor_string[i_s],
- "# Simbol/name Type code\n");
+ sprintf(&test_descriptor_string[i_s],
+ "# Simbol/name Type code\n");
int code=1;
for (int i=0; i < nelements; i++){
i_s=strlen(test_descriptor_string);
sprintf(&test_descriptor_string[i_s],"%s\t\t\tspec\t\t%d\n",
- elements[i],code++);
+ elements[i],code++);
}
i_s=strlen(test_descriptor_string);
sprintf(&test_descriptor_string[i_s],"\n");
-
+
// 2. conventions
-
+
i_s=strlen(test_descriptor_string);
- sprintf(&test_descriptor_string[i_s], \
- "CONVENTIONS:\n# Name Type\n\n");
+ sprintf(&test_descriptor_string[i_s], \
+ "CONVENTIONS:\n# Name Type\n\n");
i_s=strlen(test_descriptor_string);
sprintf(&test_descriptor_string[i_s], "ZeroBasedLists flag\n\n");
i_s=strlen(test_descriptor_string);
-
+
// can use iterator or locator neighbor mode, unless hybrid
-
+
int iterator_only = 0;
if (force->pair_match("hybrid",0)) iterator_only = 1;
if (iterator_only)
sprintf(&test_descriptor_string[i_s],"Neigh_IterAccess flag\n\n");
else
sprintf(&test_descriptor_string[i_s],"Neigh_BothAccess flag\n\n");
-
+
i_s=strlen(test_descriptor_string);
sprintf(&test_descriptor_string[i_s],"NEIGH_PURE_H flag\n\n");
i_s=strlen(test_descriptor_string);
@@ -648,107 +648,107 @@ void PairKIM::kim_init()
sprintf(&test_descriptor_string[i_s],"NEIGH_RVEC_F flag\n\n");
i_s=strlen(test_descriptor_string);
sprintf(&test_descriptor_string[i_s],"CLUSTER flag\n\n");
-
+
// 3. input-output
-
+
i_s=strlen(test_descriptor_string);
sprintf(&test_descriptor_string[i_s],"MODEL_INPUT:\n");
i_s=strlen(test_descriptor_string);
sprintf(&test_descriptor_string[i_s],
- "# Name Type Unit Shape\n\n");
+ "# Name Type Unit Shape\n\n");
i_s=strlen(test_descriptor_string);
sprintf(&test_descriptor_string[i_s],
- "numberOfParticles integer none []\n\n");
+ "numberOfParticles integer none []\n\n");
i_s=strlen(test_descriptor_string);
sprintf(&test_descriptor_string[i_s],
- "numberContributingParticles integer none []\n\n");
-
+ "numberContributingParticles integer none []\n\n");
+
if (support_atypes){
i_s=strlen(test_descriptor_string);
sprintf(&test_descriptor_string[i_s],
- "numberParticleTypes integer none []\n\n");
+ "numberParticleTypes integer none []\n\n");
i_s=strlen(test_descriptor_string);
sprintf(&test_descriptor_string[i_s],
- "particleTypes integer none [numberOfParticles]\n\n");
+ "particleTypes integer none [numberOfParticles]\n\n");
}
i_s=strlen(test_descriptor_string);
sprintf(&test_descriptor_string[i_s],
- "coordinates real*8 length "
- "[numberOfParticles,3]\n\n");
+ "coordinates real*8 length "
+ "[numberOfParticles,3]\n\n");
i_s=strlen(test_descriptor_string);
sprintf(&test_descriptor_string[i_s],
- "neighObject pointer none []\n\n");
+ "neighObject pointer none []\n\n");
i_s=strlen(test_descriptor_string);
sprintf(&test_descriptor_string[i_s],
- "get_neigh method none []\n\n");
+ "get_neigh method none []\n\n");
i_s=strlen(test_descriptor_string);
sprintf(&test_descriptor_string[i_s], "MODEL_OUPUT:\n");
i_s=strlen(test_descriptor_string);
sprintf(&test_descriptor_string[i_s],
- "# Name Type Unit Shape\n\n");
+ "# Name Type Unit Shape\n\n");
i_s=strlen(test_descriptor_string);
sprintf(&test_descriptor_string[i_s],
- "compute method none []\n\n");
+ "compute method none []\n\n");
i_s=strlen(test_descriptor_string);
sprintf(&test_descriptor_string[i_s],
- "destroy method none []\n\n");
+ "destroy method none []\n\n");
i_s=strlen(test_descriptor_string);
sprintf(&test_descriptor_string[i_s],
- "cutoff real*8 length []\n\n");
+ "cutoff real*8 length []\n\n");
i_s=strlen(test_descriptor_string);
sprintf(&test_descriptor_string[i_s],
- "energy real*8 energy []\n\n");
+ "energy real*8 energy []\n\n");
i_s=strlen(test_descriptor_string);
sprintf(&test_descriptor_string[i_s],
- "forces real*8 force "
- "[numberOfParticles,3]\n\n");
+ "forces real*8 force "
+ "[numberOfParticles,3]\n\n");
i_s=strlen(test_descriptor_string);
sprintf(&test_descriptor_string[i_s],
- "particleEnergy real*8 energy "
- "[numberOfParticles]\n\n");
+ "particleEnergy real*8 energy "
+ "[numberOfParticles]\n\n");
//virial and virial per atom will be added here
// i_s=strlen(test_descriptor_string);
- sprintf(&test_descriptor_string[i_s],
- "virial real*8 energy [6] \n\n\0");
+ sprintf(&test_descriptor_string[i_s],
+ "virial real*8 energy [6] \n\n\0");
i_s=strlen(test_descriptor_string);
sprintf(&test_descriptor_string[i_s],
- "process_dEdr method none [] \n\n");
+ "process_dEdr method none [] \n\n");
i_s=strlen(test_descriptor_string);
sprintf(&test_descriptor_string[i_s],
- "particleVirial real*8 energy "
- "[numberOfParticles,6] \n\n\0");
-
+ "particleVirial real*8 energy "
+ "[numberOfParticles,6] \n\n\0");
+
// kim file created now init and maptypes
pkim = new KIM_API_model();
if (!pkim->init_str_testname(test_descriptor_string,modelname))
error->all(FLERR,"KIM initialization failed");
-
+
delete [] test_descriptor_string;
-
+
// get correct index of each variable in kim_api object
-
+
pkim->getm_index(&kimerr,33,
- "coordinates", &coordinates_ind,1,
- "cutoff", &cutoff_ind,1,
- "particleEnergy",&particleEnergy_ind,1,
- "energy", &energy_ind,1,
- "forces", &forces_ind,1,
- "neighObject", &neighObject_ind,1,
- "numberOfParticles",&numberOfParticles_ind,1,
- "get_neigh", &get_neigh_ind,1,
- "particleVirial", &particleVirial_ind,1,
- "virial", &virialGlobal_ind,1,
- "process_dEdr",&process_dEdr_ind,1 );
+ "coordinates", &coordinates_ind,1,
+ "cutoff", &cutoff_ind,1,
+ "particleEnergy",&particleEnergy_ind,1,
+ "energy", &energy_ind,1,
+ "forces", &forces_ind,1,
+ "neighObject", &neighObject_ind,1,
+ "numberOfParticles",&numberOfParticles_ind,1,
+ "get_neigh", &get_neigh_ind,1,
+ "particleVirial", &particleVirial_ind,1,
+ "virial", &virialGlobal_ind,1,
+ "process_dEdr",&process_dEdr_ind,1 );
this->kim_error(__LINE__,"getm_index",kimerr);
-
+
if(support_atypes){
numberParticleTypes_ind = pkim->get_index((char *) "numberParticleTypes",&kimerr);
this->kim_error(__LINE__,"numberParticleTypes",kimerr);
particleTypes_ind = pkim->get_index((char *) "particleTypes",&kimerr);
this->kim_error(__LINE__,"particleTypes",kimerr);
}
-
+
set_statics();
// setup mapping between LAMMPS and KIM atom types
@@ -762,7 +762,7 @@ void PairKIM::kim_init()
}
// check if Rij needed for get_neigh
-
+
char * NBC_method =(char *) pkim->get_NBC_method(&kimerr);
this->kim_error(__LINE__,"NBC method not set",kimerr);
support_Rij=false;
@@ -773,7 +773,7 @@ void PairKIM::kim_init()
/* ---------------------------------------------------------------------- */
void PairKIM::set_statics()
-{
+{
if(support_atypes)
pkim->set_data_by_index(numberParticleTypes_ind,1,(void *) &(atom->ntypes )) ;
if ( process_dEdr_ind >= 0 )
@@ -781,19 +781,19 @@ void PairKIM::set_statics()
localnall = (int) (atom->nghost + atom->nlocal);
int kimerr;
pkim->setm_data_by_index(&kimerr,20,
- energy_ind,1, (void *)&(this->eng_vdwl),1,
- cutoff_ind,1, (void *)&(this->cut_global),1,
- get_neigh_ind,1,(void *) &get_neigh,1,
- numberOfParticles_ind,1, (void *) &localnall,1,
- virialGlobal_ind,1,(void *)&(virial[0]),1);
+ energy_ind,1, (void *)&(this->eng_vdwl),1,
+ cutoff_ind,1, (void *)&(this->cut_global),1,
+ get_neigh_ind,1,(void *) &get_neigh,1,
+ numberOfParticles_ind,1, (void *) &localnall,1,
+ virialGlobal_ind,1,(void *)&(virial[0]),1);
this->kim_error(__LINE__,"setm_data_by_index",kimerr);
-
+
pkim->set_data((char *) "numberContributingParticles",1,(void *)&(atom->nlocal));
pkim->set_test_buffer( (void *)this, &kimerr);
this->kim_error(__LINE__,"set_test_buffer",kimerr);
-
+
}
/* ---------------------------------------------------------------------- */
@@ -802,7 +802,7 @@ void PairKIM::set_volatiles()
{
localnall = (int) (atom->nghost + atom->nlocal);
bigint nall = (bigint) localnall;
-
+
pkim->set_data_by_index(coordinates_ind,nall*3,(void *) &(atom->x[0][0]) );
if (hybrid)
pkim->set_data_by_index(forces_ind,nall*3,(void *) &(fcopy[0][0]) ) ;
@@ -810,16 +810,16 @@ void PairKIM::set_volatiles()
pkim->set_data_by_index(forces_ind,nall*3,(void *) &(atom->f[0][0]) ) ;
pkim->set_data_by_index(particleEnergy_ind,nall, (void *)this->eatom) ;
pkim->set_data_by_index(neighObject_ind,1, (void *)this->list) ;
-
+
if (support_atypes)
pkim->set_data_by_index(particleTypes_ind,nall, (void *) kimtype) ;
-
+
if(vflag_atom != 1) {
(*pkim)[particleVirial_ind].flag->calculate = 0;
} else {
(*pkim)[particleVirial_ind].flag->calculate = 1;
pkim->set_data_by_index(particleVirial_ind,(intptr_t)nall,
- (void *)&vatom[0][0]) ;
+ (void *)&vatom[0][0]) ;
}
if (vflag_global != 1) {
(*pkim)[virialGlobal_ind].flag->calculate = 0;
@@ -838,8 +838,8 @@ void PairKIM::init2zero(KIM_API_model *pkim, int *kimerr)
PairKIM *self = (PairKIM *) pkim->get_test_buffer(kimerr);
if (*kimerr < 1)
KIM_API_model::report_error(__LINE__,(char *) __FILE__,
- (char *) "Self ptr to PairKIM is invalid",
- *kimerr);
+ (char *) "Self ptr to PairKIM is invalid",
+ *kimerr);
int p1_ind=-1;bool process_d1=false;
self->process_dE.virialGlobal_flag = 0;
@@ -847,7 +847,7 @@ void PairKIM::init2zero(KIM_API_model *pkim, int *kimerr)
int ierGlobal,ierPerAtom;
self->process_dE.virialGlobal = (double *) pkim->get_data((char *) "virial",&ierGlobal);
self->process_dE.particleVirial = (double *) pkim->get_data((char *) "particleVirial",
- &ierPerAtom);
+ &ierPerAtom);
self->process_dE.numberOfParticles = (int *) pkim->get_data((char *) "numberOfParticles",kimerr);
//halfNeighbors = !pkim->requiresFullNeighbors();
p1_ind = pkim->get_index((char *) "process_dEdr");
@@ -861,7 +861,7 @@ void PairKIM::init2zero(KIM_API_model *pkim, int *kimerr)
process_d1=true;
}
}
-
+
if (ierPerAtom == KIM_STATUS_OK && self->process_dE.particleVirial != NULL) {
self->process_dE.particleVirial_flag = pkim->get_compute((char *) "particleVirial");
if (self->process_dE.particleVirial_flag==1 && pkim->particleVirial_need2add) {
@@ -878,8 +878,8 @@ void PairKIM::init2zero(KIM_API_model *pkim, int *kimerr)
/* ---------------------------------------------------------------------- */
void PairKIM::process_dEdr(KIM_API_model **ppkim,
- double *de,double *r,double ** pdx,
- int *i,int *j,int *ier)
+ double *de,double *r,double ** pdx,
+ int *i,int *j,int *ier)
{
KIM_API_model *pkim = *ppkim;
PairKIM *self = (PairKIM *) pkim->get_test_buffer(ier);
@@ -889,9 +889,9 @@ void PairKIM::process_dEdr(KIM_API_model **ppkim,
double *dx = *pdx;
//v=(*de)/((*r)*(*r))/3.0;
//v=(*de)/((*r)*(*r));
-
+
v=-(*de)/(*r);
-
+
if (self->process_dE.virialGlobal_flag ==1 && pkim->virial_need2add) {
vir[0] = v * dx[0] * dx[0];
vir[1] = v * dx[1] * dx[1];
@@ -920,7 +920,7 @@ void PairKIM::process_dEdr(KIM_API_model **ppkim,
self->process_dE.particleVirial[(*i)*6 + 3] += vir[3];
self->process_dE.particleVirial[(*i)*6 + 4] += vir[4];
self->process_dE.particleVirial[(*i)*6 + 5] += vir[5];
-
+
self->process_dE.particleVirial[(*j)*6 + 0] += vir[0];
self->process_dE.particleVirial[(*j)*6 + 1] += vir[1];
self->process_dE.particleVirial[(*j)*6 + 2] += vir[2];
@@ -928,6 +928,6 @@ void PairKIM::process_dEdr(KIM_API_model **ppkim,
self->process_dE.particleVirial[(*j)*6 + 4] += vir[4];
self->process_dE.particleVirial[(*j)*6 + 5] += vir[5];
}
-
+
*ier = KIM_STATUS_OK;
}
diff --git a/src/KIM/pair_kim.h b/src/KIM/pair_kim.h
index 4c3b41022d79ee5e4330c345893c887d4f8db0ea..8f11d52604b08ce34db331e21571c21583c2bdb3 100644
--- a/src/KIM/pair_kim.h
+++ b/src/KIM/pair_kim.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -78,7 +78,7 @@ class PairKIM : public Pair {
bool halfNeighbors;
};
process_fij_4_pair_KIM process_dE;
-
+
bool support_atypes;
bool support_Rij;
@@ -103,7 +103,7 @@ class PairKIM : public Pair {
static int get_neigh(void **,int *, int *, int *, int *, int **, double **);
static void process_dEdr(KIM_API_model **, double *, double *,
- double **, int *, int *, int *);
+ double **, int *, int *, int *);
};
}
diff --git a/src/KSPACE/ewald.cpp b/src/KSPACE/ewald.cpp
index 52a16826a18209c9e69c34d8308c5b69b716513a..8bdf47d5f50f2de7edaa58c73ac3866bb39afc60 100644
--- a/src/KSPACE/ewald.cpp
+++ b/src/KSPACE/ewald.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -61,7 +61,7 @@ Ewald::Ewald(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg)
}
/* ----------------------------------------------------------------------
- free all memory
+ free all memory
------------------------------------------------------------------------- */
Ewald::~Ewald()
@@ -84,9 +84,9 @@ void Ewald::init()
// error check
- if (domain->triclinic)
+ if (domain->triclinic)
error->all(FLERR,"Cannot use Ewald with triclinic box");
- if (domain->dimension == 2)
+ if (domain->dimension == 2)
error->all(FLERR,"Cannot use Ewald with 2d simulation");
if (!atom->q_flag) error->all(FLERR,"Kspace style requires atom attribute q");
@@ -94,8 +94,8 @@ void Ewald::init()
if (slabflag == 0 && domain->nonperiodic > 0)
error->all(FLERR,"Cannot use nonperiodic boundaries with Ewald");
if (slabflag == 1) {
- if (domain->xperiodic != 1 || domain->yperiodic != 1 ||
- domain->boundary[2][0] != 1 || domain->boundary[2][1] != 1)
+ if (domain->xperiodic != 1 || domain->yperiodic != 1 ||
+ domain->boundary[2][0] != 1 || domain->boundary[2][1] != 1)
error->all(FLERR,"Incorrect boundaries with slab Ewald");
}
@@ -132,10 +132,10 @@ void Ewald::init()
}
// set accuracy (force units) from accuracy_relative or accuracy_absolute
-
+
if (accuracy_absolute >= 0.0) accuracy = accuracy_absolute;
else accuracy = accuracy_relative * two_charge_force;
-
+
// setup K-space resolution
q2 = qsqsum * force->qqrd2e / force->dielectric;
@@ -149,7 +149,7 @@ void Ewald::init()
double yprd = domain->yprd;
double zprd = domain->zprd;
double zprd_slab = zprd*slab_volfactor;
-
+
// make initial g_ewald estimate
// based on desired accuracy and real space cutoff
// fluid-occupied volume used to estimate real-space error
@@ -172,35 +172,35 @@ void Ewald::init()
double lpry = rms(kymax,yprd,natoms,q2);
double lprz = rms(kzmax,zprd_slab,natoms,q2);
double lpr = sqrt(lprx*lprx + lpry*lpry + lprz*lprz) / sqrt(3.0);
- double spr = 2.0*q2 * exp(-g_ewald*g_ewald*cutoff*cutoff) /
+ double spr = 2.0*q2 * exp(-g_ewald*g_ewald*cutoff*cutoff) /
sqrt(natoms*cutoff*xprd*yprd*zprd_slab);
-
+
// stats
if (comm->me == 0) {
if (screen) {
fprintf(screen," G vector (1/distance) = %g\n",g_ewald);
fprintf(screen," estimated absolute RMS force accuracy = %g\n",
- MAX(lpr,spr));
+ MAX(lpr,spr));
fprintf(screen," estimated relative force accuracy = %g\n",
- MAX(lpr,spr)/two_charge_force);
+ MAX(lpr,spr)/two_charge_force);
fprintf(screen," KSpace vectors: actual max1d max3d = %d %d %d\n",
- kcount,kmax,kmax3d);
+ kcount,kmax,kmax3d);
}
if (logfile) {
fprintf(logfile," G vector (1/distnace) = %g\n",g_ewald);
fprintf(logfile," estimated absolute RMS force accuracy = %g\n",
- MAX(lpr,spr));
+ MAX(lpr,spr));
fprintf(logfile," estimated relative force accuracy = %g\n",
- MAX(lpr,spr)/two_charge_force);
+ MAX(lpr,spr)/two_charge_force);
fprintf(logfile," KSpace vectors: actual max1d max3d = %d %d %d\n",
- kcount,kmax,kmax3d);
+ kcount,kmax,kmax3d);
}
}
}
/* ----------------------------------------------------------------------
- adjust Ewald coeffs, called initially and whenever volume has changed
+ adjust Ewald coeffs, called initially and whenever volume has changed
------------------------------------------------------------------------- */
void Ewald::setup()
@@ -210,7 +210,7 @@ void Ewald::setup()
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
-
+
// adjustment of z dimension for 2d slab Ewald
// 3d Ewald just uses zprd since slab_volfactor = 1.0
@@ -229,7 +229,7 @@ void Ewald::setup()
kxmax = 1;
kymax = 1;
kzmax = 1;
-
+
err = rms(kxmax,xprd,natoms,q2);
while (err > accuracy) {
kxmax++;
@@ -246,7 +246,7 @@ void Ewald::setup()
while (err > accuracy) {
kzmax++;
err = rms(kzmax,zprd_slab,natoms,q2);
- }
+ }
int kmax_old = kmax;
kmax = MAX(kxmax,kymax);
@@ -259,7 +259,7 @@ void Ewald::setup()
gsqmx = MAX(gsqxmx,gsqymx);
gsqmx = MAX(gsqmx,gsqzmx);
gsqmx *= 1.00001;
-
+
// if size has grown, reallocate k-dependent and nlocal-dependent arrays
if (kmax > kmax_old) {
@@ -288,15 +288,15 @@ void Ewald::setup()
double Ewald::rms(int km, double prd, bigint natoms, double q2)
{
- double value = 2.0*q2*g_ewald/prd *
- sqrt(1.0/(MY_PI*km*natoms)) *
+ double value = 2.0*q2*g_ewald/prd *
+ sqrt(1.0/(MY_PI*km*natoms)) *
exp(-MY_PI*MY_PI*km*km/(g_ewald*g_ewald*prd*prd));
return value;
}
/* ----------------------------------------------------------------------
- compute the Ewald long-range force, energy, virial
+ compute the Ewald long-range force, energy, virial
------------------------------------------------------------------------- */
void Ewald::compute(int eflag, int vflag)
@@ -306,8 +306,8 @@ void Ewald::compute(int eflag, int vflag)
// set energy/virial flags
if (eflag || vflag) ev_setup(eflag,vflag);
- else evflag = evflag_atom = eflag_global = vflag_global =
- eflag_atom = vflag_atom = 0;
+ else evflag = evflag_atom = eflag_global = vflag_global =
+ eflag_atom = vflag_atom = 0;
// extend size of per-atom arrays if necessary
@@ -362,11 +362,11 @@ void Ewald::compute(int eflag, int vflag)
ek[i][2] += partial*eg[k][2];
if (evflag_atom) {
- partial_peratom = exprl*sfacrl_all[k] + expim*sfacim_all[k];
- if (eflag_atom) eatom[i] += q[i]*ug[k]*partial_peratom;
+ partial_peratom = exprl*sfacrl_all[k] + expim*sfacim_all[k];
+ if (eflag_atom) eatom[i] += q[i]*ug[k]*partial_peratom;
if (vflag_atom)
- for (j = 0; j < 6; j++)
- vatom[i][j] += ug[k]*vg[k][j]*partial_peratom;
+ for (j = 0; j < 6; j++)
+ vatom[i][j] += ug[k]*vg[k][j]*partial_peratom;
}
}
}
@@ -380,13 +380,13 @@ void Ewald::compute(int eflag, int vflag)
f[i][1] += qscale * q[i]*ek[i][1];
f[i][2] += qscale * q[i]*ek[i][2];
}
-
+
// global energy
if (eflag_global) {
for (k = 0; k < kcount; k++)
- energy += ug[k] * (sfacrl_all[k]*sfacrl_all[k] +
- sfacim_all[k]*sfacim_all[k]);
+ energy += ug[k] * (sfacrl_all[k]*sfacrl_all[k] +
+ sfacim_all[k]*sfacim_all[k]);
energy -= g_ewald*qsqsum/MY_PIS +
MY_PI2*qsum*qsum / (g_ewald*g_ewald*volume);
energy *= qscale;
@@ -409,15 +409,15 @@ void Ewald::compute(int eflag, int vflag)
if (evflag_atom) {
if (eflag_atom) {
for (i = 0; i < nlocal; i++) {
- eatom[i] -= g_ewald*q[i]*q[i]/MY_PIS + MY_PI2*q[i]*qsum /
- (g_ewald*g_ewald*volume);
+ eatom[i] -= g_ewald*q[i]*q[i]/MY_PIS + MY_PI2*q[i]*qsum /
+ (g_ewald*g_ewald*volume);
eatom[i] *= qscale;
}
}
-
+
if (vflag_atom)
for (i = 0; i < nlocal; i++)
- for (j = 0; j < 6; j++) vatom[i][j] *= q[i]*qscale;
+ for (j = 0; j < 6; j++) vatom[i][j] *= q[i]*qscale;
}
// 2d slab correction
@@ -447,14 +447,14 @@ void Ewald::eik_dot_r()
cstr1 = 0.0;
sstr1 = 0.0;
for (i = 0; i < nlocal; i++) {
- cs[0][ic][i] = 1.0;
- sn[0][ic][i] = 0.0;
- cs[1][ic][i] = cos(unitk[ic]*x[i][ic]);
- sn[1][ic][i] = sin(unitk[ic]*x[i][ic]);
- cs[-1][ic][i] = cs[1][ic][i];
- sn[-1][ic][i] = -sn[1][ic][i];
- cstr1 += q[i]*cs[1][ic][i];
- sstr1 += q[i]*sn[1][ic][i];
+ cs[0][ic][i] = 1.0;
+ sn[0][ic][i] = 0.0;
+ cs[1][ic][i] = cos(unitk[ic]*x[i][ic]);
+ sn[1][ic][i] = sin(unitk[ic]*x[i][ic]);
+ cs[-1][ic][i] = cs[1][ic][i];
+ sn[-1][ic][i] = -sn[1][ic][i];
+ cstr1 += q[i]*cs[1][ic][i];
+ sstr1 += q[i]*sn[1][ic][i];
}
sfacrl[n] = cstr1;
sfacim[n++] = sstr1;
@@ -465,20 +465,20 @@ void Ewald::eik_dot_r()
for (ic = 0; ic < 3; ic++) {
sqk = m*unitk[ic] * m*unitk[ic];
if (sqk <= gsqmx) {
- cstr1 = 0.0;
- sstr1 = 0.0;
- for (i = 0; i < nlocal; i++) {
- cs[m][ic][i] = cs[m-1][ic][i]*cs[1][ic][i] -
- sn[m-1][ic][i]*sn[1][ic][i];
- sn[m][ic][i] = sn[m-1][ic][i]*cs[1][ic][i] +
- cs[m-1][ic][i]*sn[1][ic][i];
- cs[-m][ic][i] = cs[m][ic][i];
- sn[-m][ic][i] = -sn[m][ic][i];
- cstr1 += q[i]*cs[m][ic][i];
- sstr1 += q[i]*sn[m][ic][i];
- }
- sfacrl[n] = cstr1;
- sfacim[n++] = sstr1;
+ cstr1 = 0.0;
+ sstr1 = 0.0;
+ for (i = 0; i < nlocal; i++) {
+ cs[m][ic][i] = cs[m-1][ic][i]*cs[1][ic][i] -
+ sn[m-1][ic][i]*sn[1][ic][i];
+ sn[m][ic][i] = sn[m-1][ic][i]*cs[1][ic][i] +
+ cs[m-1][ic][i]*sn[1][ic][i];
+ cs[-m][ic][i] = cs[m][ic][i];
+ sn[-m][ic][i] = -sn[m][ic][i];
+ cstr1 += q[i]*cs[m][ic][i];
+ sstr1 += q[i]*sn[m][ic][i];
+ }
+ sfacrl[n] = cstr1;
+ sfacim[n++] = sstr1;
}
}
}
@@ -489,20 +489,20 @@ void Ewald::eik_dot_r()
for (l = 1; l <= kymax; l++) {
sqk = (k*unitk[0] * k*unitk[0]) + (l*unitk[1] * l*unitk[1]);
if (sqk <= gsqmx) {
- cstr1 = 0.0;
- sstr1 = 0.0;
- cstr2 = 0.0;
- sstr2 = 0.0;
- for (i = 0; i < nlocal; i++) {
- cstr1 += q[i]*(cs[k][0][i]*cs[l][1][i] - sn[k][0][i]*sn[l][1][i]);
- sstr1 += q[i]*(sn[k][0][i]*cs[l][1][i] + cs[k][0][i]*sn[l][1][i]);
- cstr2 += q[i]*(cs[k][0][i]*cs[l][1][i] + sn[k][0][i]*sn[l][1][i]);
- sstr2 += q[i]*(sn[k][0][i]*cs[l][1][i] - cs[k][0][i]*sn[l][1][i]);
- }
- sfacrl[n] = cstr1;
- sfacim[n++] = sstr1;
- sfacrl[n] = cstr2;
- sfacim[n++] = sstr2;
+ cstr1 = 0.0;
+ sstr1 = 0.0;
+ cstr2 = 0.0;
+ sstr2 = 0.0;
+ for (i = 0; i < nlocal; i++) {
+ cstr1 += q[i]*(cs[k][0][i]*cs[l][1][i] - sn[k][0][i]*sn[l][1][i]);
+ sstr1 += q[i]*(sn[k][0][i]*cs[l][1][i] + cs[k][0][i]*sn[l][1][i]);
+ cstr2 += q[i]*(cs[k][0][i]*cs[l][1][i] + sn[k][0][i]*sn[l][1][i]);
+ sstr2 += q[i]*(sn[k][0][i]*cs[l][1][i] - cs[k][0][i]*sn[l][1][i]);
+ }
+ sfacrl[n] = cstr1;
+ sfacim[n++] = sstr1;
+ sfacrl[n] = cstr2;
+ sfacim[n++] = sstr2;
}
}
}
@@ -513,20 +513,20 @@ void Ewald::eik_dot_r()
for (m = 1; m <= kzmax; m++) {
sqk = (l*unitk[1] * l*unitk[1]) + (m*unitk[2] * m*unitk[2]);
if (sqk <= gsqmx) {
- cstr1 = 0.0;
- sstr1 = 0.0;
- cstr2 = 0.0;
- sstr2 = 0.0;
- for (i = 0; i < nlocal; i++) {
- cstr1 += q[i]*(cs[l][1][i]*cs[m][2][i] - sn[l][1][i]*sn[m][2][i]);
- sstr1 += q[i]*(sn[l][1][i]*cs[m][2][i] + cs[l][1][i]*sn[m][2][i]);
- cstr2 += q[i]*(cs[l][1][i]*cs[m][2][i] + sn[l][1][i]*sn[m][2][i]);
- sstr2 += q[i]*(sn[l][1][i]*cs[m][2][i] - cs[l][1][i]*sn[m][2][i]);
- }
- sfacrl[n] = cstr1;
- sfacim[n++] = sstr1;
- sfacrl[n] = cstr2;
- sfacim[n++] = sstr2;
+ cstr1 = 0.0;
+ sstr1 = 0.0;
+ cstr2 = 0.0;
+ sstr2 = 0.0;
+ for (i = 0; i < nlocal; i++) {
+ cstr1 += q[i]*(cs[l][1][i]*cs[m][2][i] - sn[l][1][i]*sn[m][2][i]);
+ sstr1 += q[i]*(sn[l][1][i]*cs[m][2][i] + cs[l][1][i]*sn[m][2][i]);
+ cstr2 += q[i]*(cs[l][1][i]*cs[m][2][i] + sn[l][1][i]*sn[m][2][i]);
+ sstr2 += q[i]*(sn[l][1][i]*cs[m][2][i] - cs[l][1][i]*sn[m][2][i]);
+ }
+ sfacrl[n] = cstr1;
+ sfacim[n++] = sstr1;
+ sfacrl[n] = cstr2;
+ sfacim[n++] = sstr2;
}
}
}
@@ -537,20 +537,20 @@ void Ewald::eik_dot_r()
for (m = 1; m <= kzmax; m++) {
sqk = (k*unitk[0] * k*unitk[0]) + (m*unitk[2] * m*unitk[2]);
if (sqk <= gsqmx) {
- cstr1 = 0.0;
- sstr1 = 0.0;
- cstr2 = 0.0;
- sstr2 = 0.0;
- for (i = 0; i < nlocal; i++) {
- cstr1 += q[i]*(cs[k][0][i]*cs[m][2][i] - sn[k][0][i]*sn[m][2][i]);
- sstr1 += q[i]*(sn[k][0][i]*cs[m][2][i] + cs[k][0][i]*sn[m][2][i]);
- cstr2 += q[i]*(cs[k][0][i]*cs[m][2][i] + sn[k][0][i]*sn[m][2][i]);
- sstr2 += q[i]*(sn[k][0][i]*cs[m][2][i] - cs[k][0][i]*sn[m][2][i]);
- }
- sfacrl[n] = cstr1;
- sfacim[n++] = sstr1;
- sfacrl[n] = cstr2;
- sfacim[n++] = sstr2;
+ cstr1 = 0.0;
+ sstr1 = 0.0;
+ cstr2 = 0.0;
+ sstr2 = 0.0;
+ for (i = 0; i < nlocal; i++) {
+ cstr1 += q[i]*(cs[k][0][i]*cs[m][2][i] - sn[k][0][i]*sn[m][2][i]);
+ sstr1 += q[i]*(sn[k][0][i]*cs[m][2][i] + cs[k][0][i]*sn[m][2][i]);
+ cstr2 += q[i]*(cs[k][0][i]*cs[m][2][i] + sn[k][0][i]*sn[m][2][i]);
+ sstr2 += q[i]*(sn[k][0][i]*cs[m][2][i] - cs[k][0][i]*sn[m][2][i]);
+ }
+ sfacrl[n] = cstr1;
+ sfacim[n++] = sstr1;
+ sfacrl[n] = cstr2;
+ sfacim[n++] = sstr2;
}
}
}
@@ -560,54 +560,54 @@ void Ewald::eik_dot_r()
for (k = 1; k <= kxmax; k++) {
for (l = 1; l <= kymax; l++) {
for (m = 1; m <= kzmax; m++) {
- sqk = (k*unitk[0] * k*unitk[0]) + (l*unitk[1] * l*unitk[1]) +
- (m*unitk[2] * m*unitk[2]);
- if (sqk <= gsqmx) {
- cstr1 = 0.0;
- sstr1 = 0.0;
- cstr2 = 0.0;
- sstr2 = 0.0;
- cstr3 = 0.0;
- sstr3 = 0.0;
- cstr4 = 0.0;
- sstr4 = 0.0;
- for (i = 0; i < nlocal; i++) {
- clpm = cs[l][1][i]*cs[m][2][i] - sn[l][1][i]*sn[m][2][i];
- slpm = sn[l][1][i]*cs[m][2][i] + cs[l][1][i]*sn[m][2][i];
- cstr1 += q[i]*(cs[k][0][i]*clpm - sn[k][0][i]*slpm);
- sstr1 += q[i]*(sn[k][0][i]*clpm + cs[k][0][i]*slpm);
-
- clpm = cs[l][1][i]*cs[m][2][i] + sn[l][1][i]*sn[m][2][i];
- slpm = -sn[l][1][i]*cs[m][2][i] + cs[l][1][i]*sn[m][2][i];
- cstr2 += q[i]*(cs[k][0][i]*clpm - sn[k][0][i]*slpm);
- sstr2 += q[i]*(sn[k][0][i]*clpm + cs[k][0][i]*slpm);
-
- clpm = cs[l][1][i]*cs[m][2][i] + sn[l][1][i]*sn[m][2][i];
- slpm = sn[l][1][i]*cs[m][2][i] - cs[l][1][i]*sn[m][2][i];
- cstr3 += q[i]*(cs[k][0][i]*clpm - sn[k][0][i]*slpm);
- sstr3 += q[i]*(sn[k][0][i]*clpm + cs[k][0][i]*slpm);
-
- clpm = cs[l][1][i]*cs[m][2][i] - sn[l][1][i]*sn[m][2][i];
- slpm = -sn[l][1][i]*cs[m][2][i] - cs[l][1][i]*sn[m][2][i];
- cstr4 += q[i]*(cs[k][0][i]*clpm - sn[k][0][i]*slpm);
- sstr4 += q[i]*(sn[k][0][i]*clpm + cs[k][0][i]*slpm);
- }
- sfacrl[n] = cstr1;
- sfacim[n++] = sstr1;
- sfacrl[n] = cstr2;
- sfacim[n++] = sstr2;
- sfacrl[n] = cstr3;
- sfacim[n++] = sstr3;
- sfacrl[n] = cstr4;
- sfacim[n++] = sstr4;
- }
+ sqk = (k*unitk[0] * k*unitk[0]) + (l*unitk[1] * l*unitk[1]) +
+ (m*unitk[2] * m*unitk[2]);
+ if (sqk <= gsqmx) {
+ cstr1 = 0.0;
+ sstr1 = 0.0;
+ cstr2 = 0.0;
+ sstr2 = 0.0;
+ cstr3 = 0.0;
+ sstr3 = 0.0;
+ cstr4 = 0.0;
+ sstr4 = 0.0;
+ for (i = 0; i < nlocal; i++) {
+ clpm = cs[l][1][i]*cs[m][2][i] - sn[l][1][i]*sn[m][2][i];
+ slpm = sn[l][1][i]*cs[m][2][i] + cs[l][1][i]*sn[m][2][i];
+ cstr1 += q[i]*(cs[k][0][i]*clpm - sn[k][0][i]*slpm);
+ sstr1 += q[i]*(sn[k][0][i]*clpm + cs[k][0][i]*slpm);
+
+ clpm = cs[l][1][i]*cs[m][2][i] + sn[l][1][i]*sn[m][2][i];
+ slpm = -sn[l][1][i]*cs[m][2][i] + cs[l][1][i]*sn[m][2][i];
+ cstr2 += q[i]*(cs[k][0][i]*clpm - sn[k][0][i]*slpm);
+ sstr2 += q[i]*(sn[k][0][i]*clpm + cs[k][0][i]*slpm);
+
+ clpm = cs[l][1][i]*cs[m][2][i] + sn[l][1][i]*sn[m][2][i];
+ slpm = sn[l][1][i]*cs[m][2][i] - cs[l][1][i]*sn[m][2][i];
+ cstr3 += q[i]*(cs[k][0][i]*clpm - sn[k][0][i]*slpm);
+ sstr3 += q[i]*(sn[k][0][i]*clpm + cs[k][0][i]*slpm);
+
+ clpm = cs[l][1][i]*cs[m][2][i] - sn[l][1][i]*sn[m][2][i];
+ slpm = -sn[l][1][i]*cs[m][2][i] - cs[l][1][i]*sn[m][2][i];
+ cstr4 += q[i]*(cs[k][0][i]*clpm - sn[k][0][i]*slpm);
+ sstr4 += q[i]*(sn[k][0][i]*clpm + cs[k][0][i]*slpm);
+ }
+ sfacrl[n] = cstr1;
+ sfacim[n++] = sstr1;
+ sfacrl[n] = cstr2;
+ sfacim[n++] = sstr2;
+ sfacrl[n] = cstr3;
+ sfacim[n++] = sstr3;
+ sfacrl[n] = cstr4;
+ sfacim[n++] = sstr4;
+ }
}
}
}
}
/* ----------------------------------------------------------------------
- pre-compute coefficients for each Ewald K-vector
+ pre-compute coefficients for each Ewald K-vector
------------------------------------------------------------------------- */
void Ewald::coeffs()
@@ -685,36 +685,36 @@ void Ewald::coeffs()
for (l = 1; l <= kymax; l++) {
sqk = (unitk[0]*k) * (unitk[0]*k) + (unitk[1]*l) * (unitk[1]*l);
if (sqk <= gsqmx) {
- kxvecs[kcount] = k;
- kyvecs[kcount] = l;
- kzvecs[kcount] = 0;
- ug[kcount] = preu*exp(-0.25*sqk*g_ewald_sq_inv)/sqk;
- eg[kcount][0] = 2.0*unitk[0]*k*ug[kcount];
- eg[kcount][1] = 2.0*unitk[1]*l*ug[kcount];
- eg[kcount][2] = 0.0;
- vterm = -2.0*(1.0/sqk + 0.25*g_ewald_sq_inv);
- vg[kcount][0] = 1.0 + vterm*(unitk[0]*k)*(unitk[0]*k);
- vg[kcount][1] = 1.0 + vterm*(unitk[1]*l)*(unitk[1]*l);
- vg[kcount][2] = 1.0;
- vg[kcount][3] = vterm*unitk[0]*k*unitk[1]*l;
- vg[kcount][4] = 0.0;
- vg[kcount][5] = 0.0;
- kcount++;
-
- kxvecs[kcount] = k;
- kyvecs[kcount] = -l;
- kzvecs[kcount] = 0;
- ug[kcount] = preu*exp(-0.25*sqk*g_ewald_sq_inv)/sqk;
- eg[kcount][0] = 2.0*unitk[0]*k*ug[kcount];
- eg[kcount][1] = -2.0*unitk[1]*l*ug[kcount];
- eg[kcount][2] = 0.0;
- vg[kcount][0] = 1.0 + vterm*(unitk[0]*k)*(unitk[0]*k);
- vg[kcount][1] = 1.0 + vterm*(unitk[1]*l)*(unitk[1]*l);
- vg[kcount][2] = 1.0;
- vg[kcount][3] = -vterm*unitk[0]*k*unitk[1]*l;
- vg[kcount][4] = 0.0;
- vg[kcount][5] = 0.0;
- kcount++;;
+ kxvecs[kcount] = k;
+ kyvecs[kcount] = l;
+ kzvecs[kcount] = 0;
+ ug[kcount] = preu*exp(-0.25*sqk*g_ewald_sq_inv)/sqk;
+ eg[kcount][0] = 2.0*unitk[0]*k*ug[kcount];
+ eg[kcount][1] = 2.0*unitk[1]*l*ug[kcount];
+ eg[kcount][2] = 0.0;
+ vterm = -2.0*(1.0/sqk + 0.25*g_ewald_sq_inv);
+ vg[kcount][0] = 1.0 + vterm*(unitk[0]*k)*(unitk[0]*k);
+ vg[kcount][1] = 1.0 + vterm*(unitk[1]*l)*(unitk[1]*l);
+ vg[kcount][2] = 1.0;
+ vg[kcount][3] = vterm*unitk[0]*k*unitk[1]*l;
+ vg[kcount][4] = 0.0;
+ vg[kcount][5] = 0.0;
+ kcount++;
+
+ kxvecs[kcount] = k;
+ kyvecs[kcount] = -l;
+ kzvecs[kcount] = 0;
+ ug[kcount] = preu*exp(-0.25*sqk*g_ewald_sq_inv)/sqk;
+ eg[kcount][0] = 2.0*unitk[0]*k*ug[kcount];
+ eg[kcount][1] = -2.0*unitk[1]*l*ug[kcount];
+ eg[kcount][2] = 0.0;
+ vg[kcount][0] = 1.0 + vterm*(unitk[0]*k)*(unitk[0]*k);
+ vg[kcount][1] = 1.0 + vterm*(unitk[1]*l)*(unitk[1]*l);
+ vg[kcount][2] = 1.0;
+ vg[kcount][3] = -vterm*unitk[0]*k*unitk[1]*l;
+ vg[kcount][4] = 0.0;
+ vg[kcount][5] = 0.0;
+ kcount++;;
}
}
}
@@ -725,36 +725,36 @@ void Ewald::coeffs()
for (m = 1; m <= kzmax; m++) {
sqk = (unitk[1]*l) * (unitk[1]*l) + (unitk[2]*m) * (unitk[2]*m);
if (sqk <= gsqmx) {
- kxvecs[kcount] = 0;
- kyvecs[kcount] = l;
- kzvecs[kcount] = m;
- ug[kcount] = preu*exp(-0.25*sqk*g_ewald_sq_inv)/sqk;
- eg[kcount][0] = 0.0;
- eg[kcount][1] = 2.0*unitk[1]*l*ug[kcount];
- eg[kcount][2] = 2.0*unitk[2]*m*ug[kcount];
- vterm = -2.0*(1.0/sqk + 0.25*g_ewald_sq_inv);
- vg[kcount][0] = 1.0;
- vg[kcount][1] = 1.0 + vterm*(unitk[1]*l)*(unitk[1]*l);
- vg[kcount][2] = 1.0 + vterm*(unitk[2]*m)*(unitk[2]*m);
- vg[kcount][3] = 0.0;
- vg[kcount][4] = 0.0;
- vg[kcount][5] = vterm*unitk[1]*l*unitk[2]*m;
- kcount++;
-
- kxvecs[kcount] = 0;
- kyvecs[kcount] = l;
- kzvecs[kcount] = -m;
- ug[kcount] = preu*exp(-0.25*sqk*g_ewald_sq_inv)/sqk;
- eg[kcount][0] = 0.0;
- eg[kcount][1] = 2.0*unitk[1]*l*ug[kcount];
- eg[kcount][2] = -2.0*unitk[2]*m*ug[kcount];
- vg[kcount][0] = 1.0;
- vg[kcount][1] = 1.0 + vterm*(unitk[1]*l)*(unitk[1]*l);
- vg[kcount][2] = 1.0 + vterm*(unitk[2]*m)*(unitk[2]*m);
- vg[kcount][3] = 0.0;
- vg[kcount][4] = 0.0;
- vg[kcount][5] = -vterm*unitk[1]*l*unitk[2]*m;
- kcount++;
+ kxvecs[kcount] = 0;
+ kyvecs[kcount] = l;
+ kzvecs[kcount] = m;
+ ug[kcount] = preu*exp(-0.25*sqk*g_ewald_sq_inv)/sqk;
+ eg[kcount][0] = 0.0;
+ eg[kcount][1] = 2.0*unitk[1]*l*ug[kcount];
+ eg[kcount][2] = 2.0*unitk[2]*m*ug[kcount];
+ vterm = -2.0*(1.0/sqk + 0.25*g_ewald_sq_inv);
+ vg[kcount][0] = 1.0;
+ vg[kcount][1] = 1.0 + vterm*(unitk[1]*l)*(unitk[1]*l);
+ vg[kcount][2] = 1.0 + vterm*(unitk[2]*m)*(unitk[2]*m);
+ vg[kcount][3] = 0.0;
+ vg[kcount][4] = 0.0;
+ vg[kcount][5] = vterm*unitk[1]*l*unitk[2]*m;
+ kcount++;
+
+ kxvecs[kcount] = 0;
+ kyvecs[kcount] = l;
+ kzvecs[kcount] = -m;
+ ug[kcount] = preu*exp(-0.25*sqk*g_ewald_sq_inv)/sqk;
+ eg[kcount][0] = 0.0;
+ eg[kcount][1] = 2.0*unitk[1]*l*ug[kcount];
+ eg[kcount][2] = -2.0*unitk[2]*m*ug[kcount];
+ vg[kcount][0] = 1.0;
+ vg[kcount][1] = 1.0 + vterm*(unitk[1]*l)*(unitk[1]*l);
+ vg[kcount][2] = 1.0 + vterm*(unitk[2]*m)*(unitk[2]*m);
+ vg[kcount][3] = 0.0;
+ vg[kcount][4] = 0.0;
+ vg[kcount][5] = -vterm*unitk[1]*l*unitk[2]*m;
+ kcount++;
}
}
}
@@ -765,36 +765,36 @@ void Ewald::coeffs()
for (m = 1; m <= kzmax; m++) {
sqk = (unitk[0]*k) * (unitk[0]*k) + (unitk[2]*m) * (unitk[2]*m);
if (sqk <= gsqmx) {
- kxvecs[kcount] = k;
- kyvecs[kcount] = 0;
- kzvecs[kcount] = m;
- ug[kcount] = preu*exp(-0.25*sqk*g_ewald_sq_inv)/sqk;
- eg[kcount][0] = 2.0*unitk[0]*k*ug[kcount];
- eg[kcount][1] = 0.0;
- eg[kcount][2] = 2.0*unitk[2]*m*ug[kcount];
- vterm = -2.0*(1.0/sqk + 0.25*g_ewald_sq_inv);
- vg[kcount][0] = 1.0 + vterm*(unitk[0]*k)*(unitk[0]*k);
- vg[kcount][1] = 1.0;
- vg[kcount][2] = 1.0 + vterm*(unitk[2]*m)*(unitk[2]*m);
- vg[kcount][3] = 0.0;
- vg[kcount][4] = vterm*unitk[0]*k*unitk[2]*m;
- vg[kcount][5] = 0.0;
- kcount++;
-
- kxvecs[kcount] = k;
- kyvecs[kcount] = 0;
- kzvecs[kcount] = -m;
- ug[kcount] = preu*exp(-0.25*sqk*g_ewald_sq_inv)/sqk;
- eg[kcount][0] = 2.0*unitk[0]*k*ug[kcount];
- eg[kcount][1] = 0.0;
- eg[kcount][2] = -2.0*unitk[2]*m*ug[kcount];
- vg[kcount][0] = 1.0 + vterm*(unitk[0]*k)*(unitk[0]*k);
- vg[kcount][1] = 1.0;
- vg[kcount][2] = 1.0 + vterm*(unitk[2]*m)*(unitk[2]*m);
- vg[kcount][3] = 0.0;
- vg[kcount][4] = -vterm*unitk[0]*k*unitk[2]*m;
- vg[kcount][5] = 0.0;
- kcount++;
+ kxvecs[kcount] = k;
+ kyvecs[kcount] = 0;
+ kzvecs[kcount] = m;
+ ug[kcount] = preu*exp(-0.25*sqk*g_ewald_sq_inv)/sqk;
+ eg[kcount][0] = 2.0*unitk[0]*k*ug[kcount];
+ eg[kcount][1] = 0.0;
+ eg[kcount][2] = 2.0*unitk[2]*m*ug[kcount];
+ vterm = -2.0*(1.0/sqk + 0.25*g_ewald_sq_inv);
+ vg[kcount][0] = 1.0 + vterm*(unitk[0]*k)*(unitk[0]*k);
+ vg[kcount][1] = 1.0;
+ vg[kcount][2] = 1.0 + vterm*(unitk[2]*m)*(unitk[2]*m);
+ vg[kcount][3] = 0.0;
+ vg[kcount][4] = vterm*unitk[0]*k*unitk[2]*m;
+ vg[kcount][5] = 0.0;
+ kcount++;
+
+ kxvecs[kcount] = k;
+ kyvecs[kcount] = 0;
+ kzvecs[kcount] = -m;
+ ug[kcount] = preu*exp(-0.25*sqk*g_ewald_sq_inv)/sqk;
+ eg[kcount][0] = 2.0*unitk[0]*k*ug[kcount];
+ eg[kcount][1] = 0.0;
+ eg[kcount][2] = -2.0*unitk[2]*m*ug[kcount];
+ vg[kcount][0] = 1.0 + vterm*(unitk[0]*k)*(unitk[0]*k);
+ vg[kcount][1] = 1.0;
+ vg[kcount][2] = 1.0 + vterm*(unitk[2]*m)*(unitk[2]*m);
+ vg[kcount][3] = 0.0;
+ vg[kcount][4] = -vterm*unitk[0]*k*unitk[2]*m;
+ vg[kcount][5] = 0.0;
+ kcount++;
}
}
}
@@ -804,77 +804,77 @@ void Ewald::coeffs()
for (k = 1; k <= kxmax; k++) {
for (l = 1; l <= kymax; l++) {
for (m = 1; m <= kzmax; m++) {
- sqk = (unitk[0]*k) * (unitk[0]*k) + (unitk[1]*l) * (unitk[1]*l) +
- (unitk[2]*m) * (unitk[2]*m);
- if (sqk <= gsqmx) {
- kxvecs[kcount] = k;
- kyvecs[kcount] = l;
- kzvecs[kcount] = m;
- ug[kcount] = preu*exp(-0.25*sqk*g_ewald_sq_inv)/sqk;
- eg[kcount][0] = 2.0*unitk[0]*k*ug[kcount];
- eg[kcount][1] = 2.0*unitk[1]*l*ug[kcount];
- eg[kcount][2] = 2.0*unitk[2]*m*ug[kcount];
- vterm = -2.0*(1.0/sqk + 0.25*g_ewald_sq_inv);
- vg[kcount][0] = 1.0 + vterm*(unitk[0]*k)*(unitk[0]*k);
- vg[kcount][1] = 1.0 + vterm*(unitk[1]*l)*(unitk[1]*l);
- vg[kcount][2] = 1.0 + vterm*(unitk[2]*m)*(unitk[2]*m);
- vg[kcount][3] = vterm*unitk[0]*k*unitk[1]*l;
- vg[kcount][4] = vterm*unitk[0]*k*unitk[2]*m;
- vg[kcount][5] = vterm*unitk[1]*l*unitk[2]*m;
- kcount++;
-
- kxvecs[kcount] = k;
- kyvecs[kcount] = -l;
- kzvecs[kcount] = m;
- ug[kcount] = preu*exp(-0.25*sqk*g_ewald_sq_inv)/sqk;
- eg[kcount][0] = 2.0*unitk[0]*k*ug[kcount];
- eg[kcount][1] = -2.0*unitk[1]*l*ug[kcount];
- eg[kcount][2] = 2.0*unitk[2]*m*ug[kcount];
- vg[kcount][0] = 1.0 + vterm*(unitk[0]*k)*(unitk[0]*k);
- vg[kcount][1] = 1.0 + vterm*(unitk[1]*l)*(unitk[1]*l);
- vg[kcount][2] = 1.0 + vterm*(unitk[2]*m)*(unitk[2]*m);
- vg[kcount][3] = -vterm*unitk[0]*k*unitk[1]*l;
- vg[kcount][4] = vterm*unitk[0]*k*unitk[2]*m;
- vg[kcount][5] = -vterm*unitk[1]*l*unitk[2]*m;
- kcount++;
-
- kxvecs[kcount] = k;
- kyvecs[kcount] = l;
- kzvecs[kcount] = -m;
- ug[kcount] = preu*exp(-0.25*sqk*g_ewald_sq_inv)/sqk;
- eg[kcount][0] = 2.0*unitk[0]*k*ug[kcount];
- eg[kcount][1] = 2.0*unitk[1]*l*ug[kcount];
- eg[kcount][2] = -2.0*unitk[2]*m*ug[kcount];
- vg[kcount][0] = 1.0 + vterm*(unitk[0]*k)*(unitk[0]*k);
- vg[kcount][1] = 1.0 + vterm*(unitk[1]*l)*(unitk[1]*l);
- vg[kcount][2] = 1.0 + vterm*(unitk[2]*m)*(unitk[2]*m);
- vg[kcount][3] = vterm*unitk[0]*k*unitk[1]*l;
- vg[kcount][4] = -vterm*unitk[0]*k*unitk[2]*m;
- vg[kcount][5] = -vterm*unitk[1]*l*unitk[2]*m;
- kcount++;
-
- kxvecs[kcount] = k;
- kyvecs[kcount] = -l;
- kzvecs[kcount] = -m;
- ug[kcount] = preu*exp(-0.25*sqk*g_ewald_sq_inv)/sqk;
- eg[kcount][0] = 2.0*unitk[0]*k*ug[kcount];
- eg[kcount][1] = -2.0*unitk[1]*l*ug[kcount];
- eg[kcount][2] = -2.0*unitk[2]*m*ug[kcount];
- vg[kcount][0] = 1.0 + vterm*(unitk[0]*k)*(unitk[0]*k);
- vg[kcount][1] = 1.0 + vterm*(unitk[1]*l)*(unitk[1]*l);
- vg[kcount][2] = 1.0 + vterm*(unitk[2]*m)*(unitk[2]*m);
- vg[kcount][3] = -vterm*unitk[0]*k*unitk[1]*l;
- vg[kcount][4] = -vterm*unitk[0]*k*unitk[2]*m;
- vg[kcount][5] = vterm*unitk[1]*l*unitk[2]*m;
- kcount++;
- }
+ sqk = (unitk[0]*k) * (unitk[0]*k) + (unitk[1]*l) * (unitk[1]*l) +
+ (unitk[2]*m) * (unitk[2]*m);
+ if (sqk <= gsqmx) {
+ kxvecs[kcount] = k;
+ kyvecs[kcount] = l;
+ kzvecs[kcount] = m;
+ ug[kcount] = preu*exp(-0.25*sqk*g_ewald_sq_inv)/sqk;
+ eg[kcount][0] = 2.0*unitk[0]*k*ug[kcount];
+ eg[kcount][1] = 2.0*unitk[1]*l*ug[kcount];
+ eg[kcount][2] = 2.0*unitk[2]*m*ug[kcount];
+ vterm = -2.0*(1.0/sqk + 0.25*g_ewald_sq_inv);
+ vg[kcount][0] = 1.0 + vterm*(unitk[0]*k)*(unitk[0]*k);
+ vg[kcount][1] = 1.0 + vterm*(unitk[1]*l)*(unitk[1]*l);
+ vg[kcount][2] = 1.0 + vterm*(unitk[2]*m)*(unitk[2]*m);
+ vg[kcount][3] = vterm*unitk[0]*k*unitk[1]*l;
+ vg[kcount][4] = vterm*unitk[0]*k*unitk[2]*m;
+ vg[kcount][5] = vterm*unitk[1]*l*unitk[2]*m;
+ kcount++;
+
+ kxvecs[kcount] = k;
+ kyvecs[kcount] = -l;
+ kzvecs[kcount] = m;
+ ug[kcount] = preu*exp(-0.25*sqk*g_ewald_sq_inv)/sqk;
+ eg[kcount][0] = 2.0*unitk[0]*k*ug[kcount];
+ eg[kcount][1] = -2.0*unitk[1]*l*ug[kcount];
+ eg[kcount][2] = 2.0*unitk[2]*m*ug[kcount];
+ vg[kcount][0] = 1.0 + vterm*(unitk[0]*k)*(unitk[0]*k);
+ vg[kcount][1] = 1.0 + vterm*(unitk[1]*l)*(unitk[1]*l);
+ vg[kcount][2] = 1.0 + vterm*(unitk[2]*m)*(unitk[2]*m);
+ vg[kcount][3] = -vterm*unitk[0]*k*unitk[1]*l;
+ vg[kcount][4] = vterm*unitk[0]*k*unitk[2]*m;
+ vg[kcount][5] = -vterm*unitk[1]*l*unitk[2]*m;
+ kcount++;
+
+ kxvecs[kcount] = k;
+ kyvecs[kcount] = l;
+ kzvecs[kcount] = -m;
+ ug[kcount] = preu*exp(-0.25*sqk*g_ewald_sq_inv)/sqk;
+ eg[kcount][0] = 2.0*unitk[0]*k*ug[kcount];
+ eg[kcount][1] = 2.0*unitk[1]*l*ug[kcount];
+ eg[kcount][2] = -2.0*unitk[2]*m*ug[kcount];
+ vg[kcount][0] = 1.0 + vterm*(unitk[0]*k)*(unitk[0]*k);
+ vg[kcount][1] = 1.0 + vterm*(unitk[1]*l)*(unitk[1]*l);
+ vg[kcount][2] = 1.0 + vterm*(unitk[2]*m)*(unitk[2]*m);
+ vg[kcount][3] = vterm*unitk[0]*k*unitk[1]*l;
+ vg[kcount][4] = -vterm*unitk[0]*k*unitk[2]*m;
+ vg[kcount][5] = -vterm*unitk[1]*l*unitk[2]*m;
+ kcount++;
+
+ kxvecs[kcount] = k;
+ kyvecs[kcount] = -l;
+ kzvecs[kcount] = -m;
+ ug[kcount] = preu*exp(-0.25*sqk*g_ewald_sq_inv)/sqk;
+ eg[kcount][0] = 2.0*unitk[0]*k*ug[kcount];
+ eg[kcount][1] = -2.0*unitk[1]*l*ug[kcount];
+ eg[kcount][2] = -2.0*unitk[2]*m*ug[kcount];
+ vg[kcount][0] = 1.0 + vterm*(unitk[0]*k)*(unitk[0]*k);
+ vg[kcount][1] = 1.0 + vterm*(unitk[1]*l)*(unitk[1]*l);
+ vg[kcount][2] = 1.0 + vterm*(unitk[2]*m)*(unitk[2]*m);
+ vg[kcount][3] = -vterm*unitk[0]*k*unitk[1]*l;
+ vg[kcount][4] = -vterm*unitk[0]*k*unitk[2]*m;
+ vg[kcount][5] = vterm*unitk[1]*l*unitk[2]*m;
+ kcount++;
+ }
}
}
}
}
/* ----------------------------------------------------------------------
- allocate memory that depends on # of K-vectors
+ allocate memory that depends on # of K-vectors
------------------------------------------------------------------------- */
void Ewald::allocate()
@@ -894,7 +894,7 @@ void Ewald::allocate()
}
/* ----------------------------------------------------------------------
- deallocate memory that depends on # of K-vectors
+ deallocate memory that depends on # of K-vectors
------------------------------------------------------------------------- */
void Ewald::deallocate()
@@ -902,7 +902,7 @@ void Ewald::deallocate()
delete [] kxvecs;
delete [] kyvecs;
delete [] kzvecs;
-
+
delete [] ug;
memory->destroy(eg);
memory->destroy(vg);
@@ -915,51 +915,51 @@ void Ewald::deallocate()
/* ----------------------------------------------------------------------
Slab-geometry correction term to dampen inter-slab interactions between
- periodically repeating slabs. Yields good approximation to 2-D Ewald if
- adequate empty space is left between repeating slabs (J. Chem. Phys.
- 111, 3155). Slabs defined here to be parallel to the xy plane.
+ periodically repeating slabs. Yields good approximation to 2-D Ewald if
+ adequate empty space is left between repeating slabs (J. Chem. Phys.
+ 111, 3155). Slabs defined here to be parallel to the xy plane.
------------------------------------------------------------------------- */
void Ewald::slabcorr()
{
// compute local contribution to global dipole moment
-
+
double *q = atom->q;
double **x = atom->x;
int nlocal = atom->nlocal;
double dipole = 0.0;
for (int i = 0; i < nlocal; i++) dipole += q[i]*x[i][2];
-
+
// sum local contributions to get global dipole moment
double dipole_all;
MPI_Allreduce(&dipole,&dipole_all,1,MPI_DOUBLE,MPI_SUM,world);
// compute corrections
-
+
const double e_slabcorr = 2.0*MY_PI*dipole_all*dipole_all/volume;
const double qscale = force->qqrd2e * scale;
-
+
if (eflag_global) energy += qscale * e_slabcorr;
-
+
// per-atom energy
-
+
if (eflag_atom) {
- double efact = 2.0*MY_PI*dipole_all/volume;
+ double efact = 2.0*MY_PI*dipole_all/volume;
for (int i = 0; i < nlocal; i++) eatom[i] += qscale * q[i]*x[i][2]*efact;
}
// add on force corrections
- double ffact = -4.0*MY_PI*dipole_all/volume;
+ double ffact = -4.0*MY_PI*dipole_all/volume;
double **f = atom->f;
for (int i = 0; i < nlocal; i++) f[i][2] += qscale * q[i]*ffact;
}
/* ----------------------------------------------------------------------
- memory usage of local arrays
+ memory usage of local arrays
------------------------------------------------------------------------- */
double Ewald::memory_usage()
@@ -982,76 +982,76 @@ double Ewald::memory_usage()
void Ewald::compute_group_group(int groupbit_A, int groupbit_B, int BA_flag)
{
- if (slabflag)
+ if (slabflag)
error->all(FLERR,"Cannot (yet) use Kspace slab correction "
- "with compute group/group");
-
+ "with compute group/group");
+
int i,k;
if (!group_allocate_flag) {
allocate_groups();
group_allocate_flag = 1;
- }
-
+ }
+
e2group = 0; //energy
f2group[0] = 0; //force in x-direction
f2group[1] = 0; //force in y-direction
f2group[2] = 0; //force in z-direction
-
- // partial and total structure factors for groups A and B
-
+
+ // partial and total structure factors for groups A and B
+
for (k = 0; k < kcount; k++) {
-
+
// group A
-
+
sfacrl_A[k] = 0;
sfacim_A[k] = 0;
sfacrl_A_all[k] = 0;
sfacim_A_all[k] = 0;
-
- // group B
-
+
+ // group B
+
sfacrl_B[k] = 0;
sfacim_B[k] = 0;
sfacrl_B_all[k] = 0;
sfacim_B_all[k] = 0;
}
-
+
double *q = atom->q;
int nlocal = atom->nlocal;
int *mask = atom->mask;
-
+
int kx,ky,kz;
double cypz,sypz,exprl,expim;
-
+
// partial structure factors for groups A and B on each processor
-
+
for (k = 0; k < kcount; k++) {
kx = kxvecs[k];
ky = kyvecs[k];
kz = kzvecs[k];
-
+
for (i = 0; i < nlocal; i++) {
-
+
if ((mask[i] & groupbit_A) && (mask[i] & groupbit_B))
if (BA_flag) continue;
-
- if ((mask[i] & groupbit_A) || (mask[i] & groupbit_B)) {
-
+
+ if ((mask[i] & groupbit_A) || (mask[i] & groupbit_B)) {
+
cypz = cs[ky][1][i]*cs[kz][2][i] - sn[ky][1][i]*sn[kz][2][i];
sypz = sn[ky][1][i]*cs[kz][2][i] + cs[ky][1][i]*sn[kz][2][i];
exprl = cs[kx][0][i]*cypz - sn[kx][0][i]*sypz;
expim = sn[kx][0][i]*cypz + cs[kx][0][i]*sypz;
-
+
// group A
-
+
if (mask[i] & groupbit_A) {
sfacrl_A[k] += q[i]*exprl;
sfacim_A[k] += q[i]*expim;
- }
-
+ }
+
// group B
-
+
if (mask[i] & groupbit_B) {
sfacrl_B[k] += q[i]*exprl;
sfacim_B[k] += q[i]*expim;
@@ -1059,39 +1059,39 @@ void Ewald::compute_group_group(int groupbit_A, int groupbit_B, int BA_flag)
}
}
}
-
- // total structure factor by summing over procs
-
+
+ // total structure factor by summing over procs
+
MPI_Allreduce(sfacrl_A,sfacrl_A_all,kcount,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(sfacim_A,sfacim_A_all,kcount,MPI_DOUBLE,MPI_SUM,world);
-
+
MPI_Allreduce(sfacrl_B,sfacrl_B_all,kcount,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(sfacim_B,sfacim_B_all,kcount,MPI_DOUBLE,MPI_SUM,world);
-
- const double qscale = force->qqrd2e * scale;
+
+ const double qscale = force->qqrd2e * scale;
double partial_group;
-
+
// total group A <--> group B energy
// self and boundary correction terms are in compute_group_group.cpp
-
+
for (k = 0; k < kcount; k++) {
- partial_group = sfacrl_A_all[k]*sfacrl_B_all[k] +
+ partial_group = sfacrl_A_all[k]*sfacrl_B_all[k] +
sfacim_A_all[k]*sfacim_B_all[k];
e2group += ug[k]*partial_group;
- }
-
+ }
+
e2group *= qscale;
-
+
// total group A <--> group B force
-
+
for (k = 0; k < kcount; k++) {
- partial_group = sfacim_A_all[k]*sfacrl_B_all[k] -
+ partial_group = sfacim_A_all[k]*sfacrl_B_all[k] -
sfacrl_A_all[k]*sfacim_B_all[k];
f2group[0] += eg[k][0]*partial_group;
f2group[1] += eg[k][1]*partial_group;
f2group[2] += eg[k][2]*partial_group;
}
-
+
f2group[0] *= qscale;
f2group[1] *= qscale;
f2group[2] *= qscale;
@@ -1102,16 +1102,16 @@ void Ewald::compute_group_group(int groupbit_A, int groupbit_B, int BA_flag)
------------------------------------------------------------------------- */
void Ewald::allocate_groups()
-{
+{
// group A
-
+
sfacrl_A = new double[kmax3d];
sfacim_A = new double[kmax3d];
sfacrl_A_all = new double[kmax3d];
sfacim_A_all = new double[kmax3d];
-
+
// group B
-
+
sfacrl_B = new double[kmax3d];
sfacim_B = new double[kmax3d];
sfacrl_B_all = new double[kmax3d];
@@ -1125,14 +1125,14 @@ void Ewald::allocate_groups()
void Ewald::deallocate_groups()
{
// group A
-
+
delete [] sfacrl_A;
delete [] sfacim_A;
delete [] sfacrl_A_all;
delete [] sfacim_A_all;
-
+
// group B
-
+
delete [] sfacrl_B;
delete [] sfacim_B;
delete [] sfacrl_B_all;
diff --git a/src/KSPACE/ewald.h b/src/KSPACE/ewald.h
index e8cbdecf15b159b46536052bcd2563b81d84b166..fbeb812cb89839cbd56a0a53ad77de7102e455a2 100644
--- a/src/KSPACE/ewald.h
+++ b/src/KSPACE/ewald.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/KSPACE/fft3d.cpp b/src/KSPACE/fft3d.cpp
index e3dbc63b1ef5c336e516d82bdb5167d05ba67e68..084c524f0b236fcae1c8d009fc9c983f4ab8c7a4 100644
--- a/src/KSPACE/fft3d.cpp
+++ b/src/KSPACE/fft3d.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -14,8 +14,8 @@
/* ----------------------------------------------------------------------
Contributing authors: Jim Shepherd (GA Tech) added SGI SCSL support
Axel Kohlmeyer (Temple U) added support for
- FFTW3, KISSFFT, Dfti/MKL, and ACML.
- Phil Blood (PSC) added single precision FFT.
+ FFTW3, KISSFFT, Dfti/MKL, and ACML.
+ Phil Blood (PSC) added single precision FFT.
------------------------------------------------------------------------- */
#include "mpi.h"
@@ -42,9 +42,9 @@
my subsection must not overlap with any other proc's subsection,
i.e. the union of all proc's input (or output) subsections must
exactly tile the global Nfast x Nmid x Nslow data set
- when called from C, all subsection indices are
+ when called from C, all subsection indices are
C-style from 0 to N-1 where N = Nfast or Nmid or Nslow
- when called from F77, all subsection indices are
+ when called from F77, all subsection indices are
F77-style from 1 to N where N = Nfast or Nmid or Nslow
a proc can own 0 elements on input or output
by specifying hi index < lo index
@@ -53,7 +53,7 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
- Perform 3d FFT
+ Perform 3d FFT
Arguments:
in starting address of input data on this proc
@@ -69,7 +69,7 @@ void fft_3d(FFT_DATA *in, FFT_DATA *out, int flag, struct fft_plan_3d *plan)
FFT_SCALAR norm, *out_ptr;
FFT_DATA *data,*copy;
- // system specific constants
+ // system specific constants
#if defined(FFT_SCSL)
int isys = 0;
@@ -91,19 +91,19 @@ void fft_3d(FFT_DATA *in, FFT_DATA *out, int flag, struct fft_plan_3d *plan)
#endif
// pre-remap to prepare for 1st FFTs if needed
- // copy = loc for remap result
+ // copy = loc for remap result
if (plan->pre_plan) {
if (plan->pre_target == 0) copy = out;
else copy = plan->copy;
remap_3d((FFT_SCALAR *) in, (FFT_SCALAR *) copy, (FFT_SCALAR *) plan->scratch,
- plan->pre_plan);
+ plan->pre_plan);
data = copy;
}
else
data = in;
- // 1d FFTs along fast axis
+ // 1d FFTs along fast axis
total = plan->total1;
length = plan->length1;
@@ -114,7 +114,7 @@ void fft_3d(FFT_DATA *in, FFT_DATA *out, int flag, struct fft_plan_3d *plan)
#elif defined(FFT_SCSL)
for (offset = 0; offset < total; offset += length)
FFT_1D(flag,length,scalef,&data[offset],&data[offset],plan->coeff1,
- plan->work1,&isys);
+ plan->work1,&isys);
#elif defined(FFT_ACML)
num=total/length;
FFT_1D(&flag,&num,&length,data,plan->coeff1,&info);
@@ -136,7 +136,7 @@ void fft_3d(FFT_DATA *in, FFT_DATA *out, int flag, struct fft_plan_3d *plan)
#elif defined(FFT_T3E)
for (offset = 0; offset < total; offset += length)
FFT_1D(&flag,&length,&scalef,&data[offset],&data[offset],plan->coeff1,
- plan->work1,&isys);
+ plan->work1,&isys);
#elif defined(FFT_FFTW2)
if (flag == -1)
fftw(plan->plan_fast_forward,total/length,data,1,length,NULL,0,0);
@@ -158,15 +158,15 @@ void fft_3d(FFT_DATA *in, FFT_DATA *out, int flag, struct fft_plan_3d *plan)
#endif
// 1st mid-remap to prepare for 2nd FFTs
- // copy = loc for remap result
+ // copy = loc for remap result
if (plan->mid1_target == 0) copy = out;
else copy = plan->copy;
remap_3d((FFT_SCALAR *) data, (FFT_SCALAR *) copy, (FFT_SCALAR *) plan->scratch,
- plan->mid1_plan);
+ plan->mid1_plan);
data = copy;
- // 1d FFTs along mid axis
+ // 1d FFTs along mid axis
total = plan->total2;
length = plan->length2;
@@ -177,7 +177,7 @@ void fft_3d(FFT_DATA *in, FFT_DATA *out, int flag, struct fft_plan_3d *plan)
#elif defined(FFT_SCSL)
for (offset = 0; offset < total; offset += length)
FFT_1D(flag,length,scalef,&data[offset],&data[offset],plan->coeff2,
- plan->work2,&isys);
+ plan->work2,&isys);
#elif defined(FFT_ACML)
num=total/length;
FFT_1D(&flag,&num,&length,data,plan->coeff2,&info);
@@ -199,7 +199,7 @@ void fft_3d(FFT_DATA *in, FFT_DATA *out, int flag, struct fft_plan_3d *plan)
#elif defined(FFT_T3E)
for (offset = 0; offset < total; offset += length)
FFT_1D(&flag,&length,&scalef,&data[offset],&data[offset],plan->coeff2,
- plan->work2,&isys);
+ plan->work2,&isys);
#elif defined(FFT_FFTW2)
if (flag == -1)
fftw(plan->plan_mid_forward,total/length,data,1,length,NULL,0,0);
@@ -221,15 +221,15 @@ void fft_3d(FFT_DATA *in, FFT_DATA *out, int flag, struct fft_plan_3d *plan)
#endif
// 2nd mid-remap to prepare for 3rd FFTs
- // copy = loc for remap result
+ // copy = loc for remap result
if (plan->mid2_target == 0) copy = out;
else copy = plan->copy;
remap_3d((FFT_SCALAR *) data, (FFT_SCALAR *) copy, (FFT_SCALAR *) plan->scratch,
- plan->mid2_plan);
+ plan->mid2_plan);
data = copy;
- // 1d FFTs along slow axis
+ // 1d FFTs along slow axis
total = plan->total3;
length = plan->length3;
@@ -240,7 +240,7 @@ void fft_3d(FFT_DATA *in, FFT_DATA *out, int flag, struct fft_plan_3d *plan)
#elif defined(FFT_SCSL)
for (offset = 0; offset < total; offset += length)
FFT_1D(flag,length,scalef,&data[offset],&data[offset],plan->coeff3,
- plan->work3,&isys);
+ plan->work3,&isys);
#elif defined(FFT_ACML)
num=total/length;
FFT_1D(&flag,&num,&length,data,plan->coeff3,&info);
@@ -262,7 +262,7 @@ void fft_3d(FFT_DATA *in, FFT_DATA *out, int flag, struct fft_plan_3d *plan)
#elif defined(FFT_T3E)
for (offset = 0; offset < total; offset += length)
FFT_1D(&flag,&length,&scalef,&data[offset],&data[offset],plan->coeff3,
- plan->work3,&isys);
+ plan->work3,&isys);
#elif defined(FFT_FFTW2)
if (flag == -1)
fftw(plan->plan_slow_forward,total/length,data,1,length,NULL,0,0);
@@ -284,13 +284,13 @@ void fft_3d(FFT_DATA *in, FFT_DATA *out, int flag, struct fft_plan_3d *plan)
#endif
// post-remap to put data in output format if needed
- // destination is always out
+ // destination is always out
if (plan->post_plan)
remap_3d((FFT_SCALAR *) data, (FFT_SCALAR *) out, (FFT_SCALAR *) plan->scratch,
- plan->post_plan);
+ plan->post_plan);
- // scaling if required
+ // scaling if required
#if !defined(FFT_T3E) && !defined(FFT_ACML)
if (flag == 1 && plan->scaled) {
norm = plan->norm;
@@ -330,7 +330,7 @@ void fft_3d(FFT_DATA *in, FFT_DATA *out, int flag, struct fft_plan_3d *plan)
}
/* ----------------------------------------------------------------------
- Create plan for performing a 3d FFT
+ Create plan for performing a 3d FFT
Arguments:
comm MPI communicator for the P procs which own the data
@@ -344,8 +344,8 @@ void fft_3d(FFT_DATA *in, FFT_DATA *out, int flag, struct fft_plan_3d *plan)
scaled 0 = no scaling of result, 1 = scaling
permute permutation in storage order of indices on output
0 = no permutation
- 1 = permute once = mid->fast, slow->mid, fast->slow
- 2 = permute twice = slow->fast, fast->mid, mid->slow
+ 1 = permute once = mid->fast, slow->mid, fast->slow
+ 2 = permute twice = slow->fast, fast->mid, mid->slow
nbuf returns size of internal storage buffers used by FFT
------------------------------------------------------------------------- */
@@ -367,7 +367,7 @@ struct fft_plan_3d *fft_3d_create_plan(
int np1,np2,ip1,ip2;
int list[50];
- // system specific variables
+ // system specific variables
#ifdef FFT_SCSL
FFT_DATA dummy_d[5];
@@ -384,25 +384,25 @@ struct fft_plan_3d *fft_3d_create_plan(
double scalef;
#endif
- // query MPI info
+ // query MPI info
MPI_Comm_rank(comm,&me);
MPI_Comm_size(comm,&nprocs);
- // compute division of procs in 2 dimensions not on-processor
+ // compute division of procs in 2 dimensions not on-processor
bifactor(nprocs,&np1,&np2);
ip1 = me % np1;
ip2 = me/np1;
- // allocate memory for plan data struct
+ // allocate memory for plan data struct
plan = (struct fft_plan_3d *) malloc(sizeof(struct fft_plan_3d));
if (plan == NULL) return NULL;
// remap from initial distribution to layout needed for 1st set of 1d FFTs
// not needed if all procs own entire fast axis initially
- // first indices = distribution after 1st set of FFTs
+ // first indices = distribution after 1st set of FFTs
if (in_ilo == 0 && in_ihi == nfast-1)
flag = 0;
@@ -429,19 +429,19 @@ struct fft_plan_3d *fft_3d_create_plan(
first_khi = (ip2+1)*nslow/np2 - 1;
plan->pre_plan =
remap_3d_create_plan(comm,in_ilo,in_ihi,in_jlo,in_jhi,in_klo,in_khi,
- first_ilo,first_ihi,first_jlo,first_jhi,
- first_klo,first_khi,2,0,0,FFT_PRECISION);
+ first_ilo,first_ihi,first_jlo,first_jhi,
+ first_klo,first_khi,2,0,0,FFT_PRECISION);
if (plan->pre_plan == NULL) return NULL;
}
- // 1d FFTs along fast axis
+ // 1d FFTs along fast axis
plan->length1 = nfast;
plan->total1 = nfast * (first_jhi-first_jlo+1) * (first_khi-first_klo+1);
// remap from 1st to 2nd FFT
// choose which axis is split over np1 vs np2 to minimize communication
- // second indices = distribution after 2nd set of FFTs
+ // second indices = distribution after 2nd set of FFTs
second_ilo = ip1*nfast/np1;
second_ihi = (ip1+1)*nfast/np1 - 1;
@@ -451,13 +451,13 @@ struct fft_plan_3d *fft_3d_create_plan(
second_khi = (ip2+1)*nslow/np2 - 1;
plan->mid1_plan =
remap_3d_create_plan(comm,
- first_ilo,first_ihi,first_jlo,first_jhi,
- first_klo,first_khi,
- second_ilo,second_ihi,second_jlo,second_jhi,
- second_klo,second_khi,2,1,0,FFT_PRECISION);
+ first_ilo,first_ihi,first_jlo,first_jhi,
+ first_klo,first_khi,
+ second_ilo,second_ihi,second_jlo,second_jhi,
+ second_klo,second_khi,2,1,0,FFT_PRECISION);
if (plan->mid1_plan == NULL) return NULL;
- // 1d FFTs along mid axis
+ // 1d FFTs along mid axis
plan->length2 = nmid;
plan->total2 = (second_ihi-second_ilo+1) * nmid * (second_khi-second_klo+1);
@@ -465,7 +465,7 @@ struct fft_plan_3d *fft_3d_create_plan(
// remap from 2nd to 3rd FFT
// if final distribution is permute=2 with all procs owning entire slow axis
// then this remapping goes directly to final distribution
- // third indices = distribution after 3rd set of FFTs
+ // third indices = distribution after 3rd set of FFTs
if (permute == 2 && out_klo == 0 && out_khi == nslow-1)
flag = 0;
@@ -490,22 +490,22 @@ struct fft_plan_3d *fft_3d_create_plan(
third_klo = 0;
third_khi = nslow - 1;
}
-
+
plan->mid2_plan =
remap_3d_create_plan(comm,
- second_jlo,second_jhi,second_klo,second_khi,
- second_ilo,second_ihi,
- third_jlo,third_jhi,third_klo,third_khi,
- third_ilo,third_ihi,2,1,0,FFT_PRECISION);
+ second_jlo,second_jhi,second_klo,second_khi,
+ second_ilo,second_ihi,
+ third_jlo,third_jhi,third_klo,third_khi,
+ third_ilo,third_ihi,2,1,0,FFT_PRECISION);
if (plan->mid2_plan == NULL) return NULL;
- // 1d FFTs along slow axis
+ // 1d FFTs along slow axis
plan->length3 = nslow;
plan->total3 = (third_ihi-third_ilo+1) * (third_jhi-third_jlo+1) * nslow;
// remap from 3rd FFT to final distribution
- // not needed if permute = 2 and third indices = out indices on all procs
+ // not needed if permute = 2 and third indices = out indices on all procs
if (permute == 2 &&
out_ilo == third_ilo && out_ihi == third_ihi &&
@@ -522,10 +522,10 @@ struct fft_plan_3d *fft_3d_create_plan(
else {
plan->post_plan =
remap_3d_create_plan(comm,
- third_klo,third_khi,third_ilo,third_ihi,
- third_jlo,third_jhi,
- out_klo,out_khi,out_ilo,out_ihi,
- out_jlo,out_jhi,2,(permute+1)%3,0,FFT_PRECISION);
+ third_klo,third_khi,third_ilo,third_ihi,
+ third_jlo,third_jhi,
+ out_klo,out_khi,out_ilo,out_ihi,
+ out_jlo,out_jhi,2,(permute+1)%3,0,FFT_PRECISION);
if (plan->post_plan == NULL) return NULL;
}
@@ -536,14 +536,14 @@ struct fft_plan_3d *fft_3d_create_plan(
// scratch_size = amount needed internally for remap scratch space
// for each remap:
// out space used for result if big enough, else require copy buffer
- // accumulate largest required remap scratch space
+ // accumulate largest required remap scratch space
out_size = (out_ihi-out_ilo+1) * (out_jhi-out_jlo+1) * (out_khi-out_klo+1);
- first_size = (first_ihi-first_ilo+1) * (first_jhi-first_jlo+1) *
+ first_size = (first_ihi-first_ilo+1) * (first_jhi-first_jlo+1) *
(first_khi-first_klo+1);
- second_size = (second_ihi-second_ilo+1) * (second_jhi-second_jlo+1) *
+ second_size = (second_ihi-second_ilo+1) * (second_jhi-second_jlo+1) *
(second_khi-second_klo+1);
- third_size = (third_ihi-third_ilo+1) * (third_jhi-third_jlo+1) *
+ third_size = (third_ihi-third_ilo+1) * (third_jhi-third_jlo+1) *
(third_khi-third_klo+1);
copy_size = 0;
@@ -596,8 +596,8 @@ struct fft_plan_3d *fft_3d_create_plan(
}
else plan->scratch = NULL;
- // system specific pre-computation of 1d FFT coeffs
- // and scaling normalization
+ // system specific pre-computation of 1d FFT coeffs
+ // and scaling normalization
#if defined(FFT_SGI)
@@ -612,7 +612,7 @@ struct fft_plan_3d *fft_3d_create_plan(
FFT_1D_INIT(nmid,plan->coeff2);
FFT_1D_INIT(nslow,plan->coeff3);
- if (scaled == 0)
+ if (scaled == 0)
plan->scaled = 0;
else {
plan->scaled = 1;
@@ -627,14 +627,14 @@ struct fft_plan_3d *fft_3d_create_plan(
plan->coeff2 = (FFT_PREC *) malloc((2*nmid+30)*sizeof(FFT_PREC));
plan->coeff3 = (FFT_PREC *) malloc((2*nslow+30)*sizeof(FFT_PREC));
- if (plan->coeff1 == NULL || plan->coeff2 == NULL ||
+ if (plan->coeff1 == NULL || plan->coeff2 == NULL ||
plan->coeff3 == NULL) return NULL;
plan->work1 = (FFT_PREC *) malloc((2*nfast)*sizeof(FFT_PREC));
plan->work2 = (FFT_PREC *) malloc((2*nmid)*sizeof(FFT_PREC));
plan->work3 = (FFT_PREC *) malloc((2*nslow)*sizeof(FFT_PREC));
- if (plan->work1 == NULL || plan->work2 == NULL ||
+ if (plan->work1 == NULL || plan->work2 == NULL ||
plan->work3 == NULL) return NULL;
isign = 0;
@@ -645,7 +645,7 @@ struct fft_plan_3d *fft_3d_create_plan(
FFT_1D_INIT(isign,nmid,scalef,dummy_d,dummy_d,plan->coeff2,dummy_p,&isys);
FFT_1D_INIT(isign,nslow,scalef,dummy_d,dummy_d,plan->coeff3,dummy_p,&isys);
- if (scaled == 0)
+ if (scaled == 0)
plan->scaled = 0;
else {
plan->scaled = 1;
@@ -711,7 +711,7 @@ struct fft_plan_3d *fft_3d_create_plan(
plan->coeff2 = (FFT_DATA *) malloc((3*nmid/2+1)*sizeof(FFT_DATA));
plan->coeff3 = (FFT_DATA *) malloc((3*nslow/2+1)*sizeof(FFT_DATA));
- if (plan->coeff1 == NULL || plan->coeff2 == NULL ||
+ if (plan->coeff1 == NULL || plan->coeff2 == NULL ||
plan->coeff3 == NULL) return NULL;
flag = 0;
@@ -776,14 +776,14 @@ struct fft_plan_3d *fft_3d_create_plan(
plan->coeff2 = (double *) malloc((12*nmid)*sizeof(double));
plan->coeff3 = (double *) malloc((12*nslow)*sizeof(double));
- if (plan->coeff1 == NULL || plan->coeff2 == NULL ||
+ if (plan->coeff1 == NULL || plan->coeff2 == NULL ||
plan->coeff3 == NULL) return NULL;
plan->work1 = (double *) malloc((8*nfast)*sizeof(double));
plan->work2 = (double *) malloc((8*nmid)*sizeof(double));
plan->work3 = (double *) malloc((8*nslow)*sizeof(double));
- if (plan->work1 == NULL || plan->work2 == NULL ||
+ if (plan->work1 == NULL || plan->work2 == NULL ||
plan->work3 == NULL) return NULL;
isign = 0;
@@ -794,7 +794,7 @@ struct fft_plan_3d *fft_3d_create_plan(
FFT_1D_INIT(&isign,&nmid,&scalef,dummy,dummy,plan->coeff2,dummy,&isys);
FFT_1D_INIT(&isign,&nslow,&scalef,dummy,dummy,plan->coeff3,dummy,&isys);
- if (scaled == 0)
+ if (scaled == 0)
plan->scaled = 0;
else {
plan->scaled = 1;
@@ -805,9 +805,9 @@ struct fft_plan_3d *fft_3d_create_plan(
#elif defined(FFT_FFTW2)
- plan->plan_fast_forward =
+ plan->plan_fast_forward =
fftw_create_plan(nfast,FFTW_FORWARD,FFTW_ESTIMATE | FFTW_IN_PLACE);
- plan->plan_fast_backward =
+ plan->plan_fast_backward =
fftw_create_plan(nfast,FFTW_BACKWARD,FFTW_ESTIMATE | FFTW_IN_PLACE);
if (nmid == nfast) {
@@ -815,9 +815,9 @@ struct fft_plan_3d *fft_3d_create_plan(
plan->plan_mid_backward = plan->plan_fast_backward;
}
else {
- plan->plan_mid_forward =
+ plan->plan_mid_forward =
fftw_create_plan(nmid,FFTW_FORWARD,FFTW_ESTIMATE | FFTW_IN_PLACE);
- plan->plan_mid_backward =
+ plan->plan_mid_backward =
fftw_create_plan(nmid,FFTW_BACKWARD,FFTW_ESTIMATE | FFTW_IN_PLACE);
}
@@ -830,9 +830,9 @@ struct fft_plan_3d *fft_3d_create_plan(
plan->plan_slow_backward = plan->plan_mid_backward;
}
else {
- plan->plan_slow_forward =
+ plan->plan_slow_forward =
fftw_create_plan(nslow,FFTW_FORWARD,FFTW_ESTIMATE | FFTW_IN_PLACE);
- plan->plan_slow_backward =
+ plan->plan_slow_backward =
fftw_create_plan(nslow,FFTW_BACKWARD,FFTW_ESTIMATE | FFTW_IN_PLACE);
}
@@ -846,36 +846,36 @@ struct fft_plan_3d *fft_3d_create_plan(
}
#elif defined(FFT_FFTW3)
- plan->plan_fast_forward =
+ plan->plan_fast_forward =
FFTW_API(plan_many_dft)(1, &nfast,plan->total1/plan->length1,
- NULL,&nfast,1,plan->length1,
- NULL,&nfast,1,plan->length1,
- FFTW_FORWARD,FFTW_ESTIMATE);
- plan->plan_fast_backward =
+ NULL,&nfast,1,plan->length1,
+ NULL,&nfast,1,plan->length1,
+ FFTW_FORWARD,FFTW_ESTIMATE);
+ plan->plan_fast_backward =
FFTW_API(plan_many_dft)(1, &nfast,plan->total1/plan->length1,
- NULL,&nfast,1,plan->length1,
- NULL,&nfast,1,plan->length1,
- FFTW_BACKWARD,FFTW_ESTIMATE);
- plan->plan_mid_forward =
+ NULL,&nfast,1,plan->length1,
+ NULL,&nfast,1,plan->length1,
+ FFTW_BACKWARD,FFTW_ESTIMATE);
+ plan->plan_mid_forward =
FFTW_API(plan_many_dft)(1, &nmid,plan->total2/plan->length2,
- NULL,&nmid,1,plan->length2,
- NULL,&nmid,1,plan->length2,
- FFTW_FORWARD,FFTW_ESTIMATE);
- plan->plan_mid_backward =
+ NULL,&nmid,1,plan->length2,
+ NULL,&nmid,1,plan->length2,
+ FFTW_FORWARD,FFTW_ESTIMATE);
+ plan->plan_mid_backward =
FFTW_API(plan_many_dft)(1, &nmid,plan->total2/plan->length2,
- NULL,&nmid,1,plan->length2,
- NULL,&nmid,1,plan->length2,
- FFTW_BACKWARD,FFTW_ESTIMATE);
- plan->plan_slow_forward =
+ NULL,&nmid,1,plan->length2,
+ NULL,&nmid,1,plan->length2,
+ FFTW_BACKWARD,FFTW_ESTIMATE);
+ plan->plan_slow_forward =
FFTW_API(plan_many_dft)(1, &nslow,plan->total3/plan->length3,
- NULL,&nslow,1,plan->length3,
- NULL,&nslow,1,plan->length3,
- FFTW_FORWARD,FFTW_ESTIMATE);
- plan->plan_slow_backward =
+ NULL,&nslow,1,plan->length3,
+ NULL,&nslow,1,plan->length3,
+ FFTW_FORWARD,FFTW_ESTIMATE);
+ plan->plan_slow_backward =
FFTW_API(plan_many_dft)(1, &nslow,plan->total3/plan->length3,
- NULL,&nslow,1,plan->length3,
- NULL,&nslow,1,plan->length3,
- FFTW_BACKWARD,FFTW_ESTIMATE);
+ NULL,&nslow,1,plan->length3,
+ NULL,&nslow,1,plan->length3,
+ FFTW_BACKWARD,FFTW_ESTIMATE);
if (scaled == 0)
plan->scaled = 0;
@@ -926,7 +926,7 @@ struct fft_plan_3d *fft_3d_create_plan(
}
/* ----------------------------------------------------------------------
- Destroy a 3d fft plan
+ Destroy a 3d fft plan
------------------------------------------------------------------------- */
void fft_3d_destroy_plan(struct fft_plan_3d *plan)
@@ -1052,7 +1052,7 @@ void factor(int n, int *num, int *list)
}
/* ----------------------------------------------------------------------
- divide n into 2 factors of as equal size as possible
+ divide n into 2 factors of as equal size as possible
------------------------------------------------------------------------- */
void bifactor(int n, int *factor1, int *factor2)
@@ -1087,7 +1087,7 @@ void fft_1d_only(FFT_DATA *data, int nsize, int flag, struct fft_plan_3d *plan)
int i,total,length,offset,num;
FFT_SCALAR norm, *data_ptr;
- // system specific constants
+ // system specific constants
#ifdef FFT_SCSL
int isys = 0;
@@ -1139,13 +1139,13 @@ void fft_1d_only(FFT_DATA *data, int nsize, int flag, struct fft_plan_3d *plan)
#elif defined(FFT_SCSL)
for (offset = 0; offset < total1; offset += length1)
FFT_1D(flag,length1,scalef,&data[offset],&data[offset],plan->coeff1,
- plan->work1,&isys);
+ plan->work1,&isys);
for (offset = 0; offset < total2; offset += length2)
FFT_1D(flag,length2,scalef,&data[offset],&data[offset],plan->coeff2,
- plan->work2,&isys);
+ plan->work2,&isys);
for (offset = 0; offset < total3; offset += length3)
FFT_1D(flag,length3,scalef,&data[offset],&data[offset],plan->coeff3,
- plan->work3,&isys);
+ plan->work3,&isys);
#elif defined(FFT_ACML)
int info=0;
num=total1/length1;
@@ -1190,13 +1190,13 @@ void fft_1d_only(FFT_DATA *data, int nsize, int flag, struct fft_plan_3d *plan)
#elif defined(FFT_T3E)
for (offset = 0; offset < total1; offset += length1)
FFT_1D(&flag,&length1,&scalef,&data[offset],&data[offset],plan->coeff1,
- plan->work1,&isys);
+ plan->work1,&isys);
for (offset = 0; offset < total2; offset += length2)
FFT_1D(&flag,&length2,&scalef,&data[offset],&data[offset],plan->coeff2,
- plan->work2,&isys);
+ plan->work2,&isys);
for (offset = 0; offset < total3; offset += length3)
FFT_1D(&flag,&length3,&scalef,&data[offset],&data[offset],plan->coeff3,
- plan->work3,&isys);
+ plan->work3,&isys);
#elif defined(FFT_FFTW2)
if (flag == -1) {
fftw(plan->plan_fast_forward,total1/length1,data,1,0,NULL,0,0);
@@ -1242,7 +1242,7 @@ void fft_1d_only(FFT_DATA *data, int nsize, int flag, struct fft_plan_3d *plan)
}
#endif
- // scaling if required
+ // scaling if required
// limit num to size of data
#ifndef FFT_T3E
diff --git a/src/KSPACE/fft3d.h b/src/KSPACE/fft3d.h
index 6bef24037145da15c8f7ebb2c0d9c7dea04a2d04..506d98fc9e829d7efa3ca890ef955d818b8a9e5f 100644
--- a/src/KSPACE/fft3d.h
+++ b/src/KSPACE/fft3d.h
@@ -5,16 +5,16 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-// User-settable FFT precision
+// User-settable FFT precision
-// FFT_PRECISION = 1 is single-precision complex (4-byte real, 4-byte imag)
-// FFT_PRECISION = 2 is double-precision complex (8-byte real, 8-byte imag)
+// FFT_PRECISION = 1 is single-precision complex (4-byte real, 4-byte imag)
+// FFT_PRECISION = 2 is double-precision complex (8-byte real, 8-byte imag)
#ifdef FFT_SINGLE
#define FFT_PRECISION 1
@@ -30,9 +30,9 @@ typedef double FFT_SCALAR;
#define FFT_FFTW2
#endif
-// -------------------------------------------------------------------------
+// -------------------------------------------------------------------------
-// Data types for single-precision complex
+// Data types for single-precision complex
#if FFT_PRECISION == 1
@@ -100,7 +100,7 @@ typedef complex single FFT_DATA;
#define FFT_1D_INIT GGFFT
extern "C" {
void GGFFT(int *, int *, double *, FFT_DATA *, FFT_DATA *,
- double *, double *, int *);
+ double *, double *, int *);
}
#elif defined(FFT_FFTW2)
@@ -132,9 +132,9 @@ struct kiss_fft_state;
typedef struct kiss_fft_state* kiss_fft_cfg;
#endif
-// -------------------------------------------------------------------------
+// -------------------------------------------------------------------------
-// Data types for double-precision complex
+// Data types for double-precision complex
#elif FFT_PRECISION == 2
@@ -202,7 +202,7 @@ typedef complex double FFT_DATA;
#define FFT_1D_INIT CCFFT
extern "C" {
void CCFFT(int *, int *, double *, FFT_DATA *, FFT_DATA *,
- double *, double *, int *);
+ double *, double *, int *);
}
#elif defined(FFT_FFTW2)
@@ -238,26 +238,26 @@ typedef struct kiss_fft_state* kiss_fft_cfg;
#error "FFT_PRECISION needs to be either 1 (=single) or 2 (=double)"
#endif
-// -------------------------------------------------------------------------
+// -------------------------------------------------------------------------
-// details of how to do a 3d FFT
+// details of how to do a 3d FFT
struct fft_plan_3d {
- struct remap_plan_3d *pre_plan; // remap from input -> 1st FFTs
- struct remap_plan_3d *mid1_plan; // remap from 1st -> 2nd FFTs
- struct remap_plan_3d *mid2_plan; // remap from 2nd -> 3rd FFTs
- struct remap_plan_3d *post_plan; // remap from 3rd FFTs -> output
- FFT_DATA *copy; // memory for remap results (if needed)
- FFT_DATA *scratch; // scratch space for remaps
- int total1,total2,total3; // # of 1st,2nd,3rd FFTs (times length)
- int length1,length2,length3; // length of 1st,2nd,3rd FFTs
- int pre_target; // where to put remap results
+ struct remap_plan_3d *pre_plan; // remap from input -> 1st FFTs
+ struct remap_plan_3d *mid1_plan; // remap from 1st -> 2nd FFTs
+ struct remap_plan_3d *mid2_plan; // remap from 2nd -> 3rd FFTs
+ struct remap_plan_3d *post_plan; // remap from 3rd FFTs -> output
+ FFT_DATA *copy; // memory for remap results (if needed)
+ FFT_DATA *scratch; // scratch space for remaps
+ int total1,total2,total3; // # of 1st,2nd,3rd FFTs (times length)
+ int length1,length2,length3; // length of 1st,2nd,3rd FFTs
+ int pre_target; // where to put remap results
int mid1_target,mid2_target;
- int scaled; // whether to scale FFT results
- int normnum; // # of values to rescale
- double norm; // normalization factor for rescaling
+ int scaled; // whether to scale FFT results
+ int normnum; // # of values to rescale
+ double norm; // normalization factor for rescaling
- // system specific 1d FFT info
+ // system specific 1d FFT info
#if defined(FFT_SGI)
FFT_DATA *coeff1;
FFT_DATA *coeff2;
@@ -312,7 +312,7 @@ struct fft_plan_3d {
#endif
};
-// function prototypes
+// function prototypes
void fft_3d(FFT_DATA *, FFT_DATA *, int, struct fft_plan_3d *);
struct fft_plan_3d *fft_3d_create_plan(MPI_Comm, int, int, int,
diff --git a/src/KSPACE/fft3d_wrap.cpp b/src/KSPACE/fft3d_wrap.cpp
index ef1298de40aa30888cc6665cd3db751289205f9a..da8445e2b5cae9815b3a7d6d8ba70addc88dc349 100644
--- a/src/KSPACE/fft3d_wrap.cpp
+++ b/src/KSPACE/fft3d_wrap.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -20,16 +20,16 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
FFT3d::FFT3d(LAMMPS *lmp, MPI_Comm comm, int nfast, int nmid, int nslow,
- int in_ilo, int in_ihi, int in_jlo, int in_jhi,
- int in_klo, int in_khi,
- int out_ilo, int out_ihi, int out_jlo, int out_jhi,
- int out_klo, int out_khi,
- int scaled, int permute, int *nbuf) : Pointers(lmp)
+ int in_ilo, int in_ihi, int in_jlo, int in_jhi,
+ int in_klo, int in_khi,
+ int out_ilo, int out_ihi, int out_jlo, int out_jhi,
+ int out_klo, int out_khi,
+ int scaled, int permute, int *nbuf) : Pointers(lmp)
{
plan = fft_3d_create_plan(comm,nfast,nmid,nslow,
- in_ilo,in_ihi,in_jlo,in_jhi,in_klo,in_khi,
- out_ilo,out_ihi,out_jlo,out_jhi,out_klo,out_khi,
- scaled,permute,nbuf);
+ in_ilo,in_ihi,in_jlo,in_jhi,in_klo,in_khi,
+ out_ilo,out_ihi,out_jlo,out_jhi,out_klo,out_khi,
+ scaled,permute,nbuf);
if (plan == NULL) error->one(FLERR,"Could not create 3d FFT plan");
}
diff --git a/src/KSPACE/fft3d_wrap.h b/src/KSPACE/fft3d_wrap.h
index 6b73207be74854bdba0de83c7387e3fea3b386fb..bf1cdca8e99e11cddbf215493cb7ac127aa3dcb8 100644
--- a/src/KSPACE/fft3d_wrap.h
+++ b/src/KSPACE/fft3d_wrap.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -22,7 +22,7 @@ namespace LAMMPS_NS {
class FFT3d : protected Pointers {
public:
FFT3d(class LAMMPS *, MPI_Comm,int,int,int,int,int,int,int,int,int,
- int,int,int,int,int,int,int,int,int *);
+ int,int,int,int,int,int,int,int,int *);
~FFT3d();
void compute(FFT_SCALAR *, FFT_SCALAR *, int);
void timing1d(FFT_SCALAR *, int, int);
diff --git a/src/KSPACE/kissfft.h b/src/KSPACE/kissfft.h
index 426f30c30461e7ea3c70c214e8b728fffb89a131..ec6ef97feab0eb3017fa15eae33c0a4d5a58a49d 100644
--- a/src/KSPACE/kissfft.h
+++ b/src/KSPACE/kissfft.h
@@ -6,11 +6,11 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-/*
+/*
we use a stripped down KISS FFT as default FFT for LAMMPS
this code is adapted from kiss_fft_v1_2_9
- homepage: http://kissfft.sf.net/
-
+ homepage: http://kissfft.sf.net/
+
changes 2008-2011 by Axel Kohlmeyer <akohlmey@gmail.com>
*/
#ifndef LMP_FFT_KISSFFT
@@ -23,7 +23,7 @@
#if defined(_OPENMP)
#include <omp.h>
#endif
-
+
#ifndef M_PI
#define M_PI 3.141592653589793238462643383279502884197169399375105820974944
#endif
@@ -65,7 +65,7 @@
#define KISS_FFT_MALLOC malloc
#define KISS_FFT_FREE free
#define MAXFACTORS 32
-/* e.g. an fft of length 128 has 4 factors
+/* e.g. an fft of length 128 has 4 factors
as far as kissfft is concerned: 4*4*4*2 */
struct kiss_fft_state {
int nfft;
@@ -76,18 +76,18 @@ struct kiss_fft_state {
#ifdef KISS_FFT_USE_ALLOCA
// define this to allow use of alloca instead of malloc for temporary buffers
-// Temporary buffers are used in two case:
+// Temporary buffers are used in two case:
// 1. FFT sizes that have "bad" factors. i.e. not 2,3 and 5
// 2. "in-place" FFTs. Notice the quotes, since kissfft does not really do an in-place transform.
#include <alloca.h>
#define KISS_FFT_TMP_ALLOC(nbytes) alloca(nbytes)
-#define KISS_FFT_TMP_FREE(ptr)
+#define KISS_FFT_TMP_FREE(ptr)
#else
#define KISS_FFT_TMP_ALLOC(nbytes) KISS_FFT_MALLOC(nbytes)
#define KISS_FFT_TMP_FREE(ptr) KISS_FFT_FREE(ptr)
#endif
-static kiss_fft_cfg kiss_fft_alloc(int,int,void *,size_t *);
+static kiss_fft_cfg kiss_fft_alloc(int,int,void *,size_t *);
static void kiss_fft(kiss_fft_cfg,const FFT_DATA *,FFT_DATA *);
/*
@@ -115,28 +115,28 @@ static void kiss_fft(kiss_fft_cfg,const FFT_DATA *,FFT_DATA *);
#define C_ADD( res, a,b)\
do { \
- CHECK_OVERFLOW_OP((a).re,+,(b).re)\
- CHECK_OVERFLOW_OP((a).im,+,(b).im)\
- (res).re=(a).re+(b).re; (res).im=(a).im+(b).im; \
+ CHECK_OVERFLOW_OP((a).re,+,(b).re)\
+ CHECK_OVERFLOW_OP((a).im,+,(b).im)\
+ (res).re=(a).re+(b).re; (res).im=(a).im+(b).im; \
}while(0)
#define C_SUB( res, a,b)\
do { \
- CHECK_OVERFLOW_OP((a).re,-,(b).re)\
- CHECK_OVERFLOW_OP((a).im,-,(b).im)\
- (res).re=(a).re-(b).re; (res).im=(a).im-(b).im; \
+ CHECK_OVERFLOW_OP((a).re,-,(b).re)\
+ CHECK_OVERFLOW_OP((a).im,-,(b).im)\
+ (res).re=(a).re-(b).re; (res).im=(a).im-(b).im; \
}while(0)
#define C_ADDTO( res , a)\
do { \
- CHECK_OVERFLOW_OP((res).re,+,(a).re)\
- CHECK_OVERFLOW_OP((res).im,+,(a).im)\
- (res).re += (a).re; (res).im += (a).im;\
+ CHECK_OVERFLOW_OP((res).re,+,(a).re)\
+ CHECK_OVERFLOW_OP((res).im,+,(a).im)\
+ (res).re += (a).re; (res).im += (a).im;\
}while(0)
#define C_SUBFROM( res , a)\
do {\
- CHECK_OVERFLOW_OP((res).re,-,(a).re)\
- CHECK_OVERFLOW_OP((res).im,-,(a).im)\
- (res).re -= (a).re; (res).im -= (a).im; \
+ CHECK_OVERFLOW_OP((res).re,-,(a).re)\
+ CHECK_OVERFLOW_OP((res).im,-,(a).im)\
+ (res).re -= (a).re; (res).im -= (a).im; \
}while(0)
@@ -145,10 +145,10 @@ static void kiss_fft(kiss_fft_cfg,const FFT_DATA *,FFT_DATA *);
#define HALF_OF(x) ((x)*.5)
#define kf_cexp(x,phase) \
- do{ \
- (x)->re = KISS_FFT_COS(phase);\
- (x)->im = KISS_FFT_SIN(phase);\
- }while(0)
+ do{ \
+ (x)->re = KISS_FFT_COS(phase);\
+ (x)->im = KISS_FFT_SIN(phase);\
+ }while(0)
static void kf_bfly2(FFT_DATA *Fout, const size_t fstride,
const kiss_fft_cfg st, int m)
@@ -362,7 +362,7 @@ static void kf_work(FFT_DATA * Fout, const FFT_DATA *f,
do {
/* recursive call:
DFT of size m*p performed by doing
- p instances of smaller DFTs of size m,
+ p instances of smaller DFTs of size m,
each one takes a decimated version of the input */
kf_work( Fout , f, fstride*p, in_stride, factors,st);
f += fstride*in_stride;
@@ -374,15 +374,15 @@ static void kf_work(FFT_DATA * Fout, const FFT_DATA *f,
/* recombine the p smaller DFTs */
switch (p) {
case 2: kf_bfly2(Fout,fstride,st,m); break;
- case 3: kf_bfly3(Fout,fstride,st,m); break;
+ case 3: kf_bfly3(Fout,fstride,st,m); break;
case 4: kf_bfly4(Fout,fstride,st,m); break;
- case 5: kf_bfly5(Fout,fstride,st,m); break;
+ case 5: kf_bfly5(Fout,fstride,st,m); break;
default: kf_bfly_generic(Fout,fstride,st,m,p); break;
}
}
/* facbuf is populated by p1,m1,p2,m2, ...
- where
+ where
p[i] * m[i] = m[i-1]
m0 = n */
static void kf_factor(int n, int *facbuf)
@@ -391,7 +391,7 @@ static void kf_factor(int n, int *facbuf)
double floor_sqrt;
floor_sqrt = floor( sqrt((double)n) );
- /* factor out the remaining powers of 4, powers of 2,
+ /* factor out the remaining powers of 4, powers of 2,
and then any other remaining primes */
do {
if (nf == MAXFACTORS) p = n; /* make certain that we don't run out of space */
@@ -445,7 +445,7 @@ static kiss_fft_cfg kiss_fft_alloc(int nfft, int inverse_fft, void *mem, size_t
}
return st;
}
-
+
static void kiss_fft_stride(kiss_fft_cfg st, const FFT_DATA *fin, FFT_DATA *fout, int in_stride)
{
if (fin == fout) {
@@ -454,7 +454,7 @@ static void kiss_fft_stride(kiss_fft_cfg st, const FFT_DATA *fin, FFT_DATA *fout
FFT_DATA * tmpbuf = (FFT_DATA*)KISS_FFT_TMP_ALLOC( sizeof(FFT_DATA)*st->nfft);
kf_work(tmpbuf,fin,1,in_stride, st->factors,st);
memcpy(fout,tmpbuf,sizeof(FFT_DATA)*st->nfft);
- KISS_FFT_TMP_FREE(tmpbuf);
+ KISS_FFT_TMP_FREE(tmpbuf);
}else{
kf_work( fout, fin, 1,in_stride, st->factors,st );
}
diff --git a/src/KSPACE/pair_born_coul_long.cpp b/src/KSPACE/pair_born_coul_long.cpp
index 88112d5496dd9d9643e182c3b811765196e2e587..3c5bdba2265b55af0052399f4599fe235b55bcba 100644
--- a/src/KSPACE/pair_born_coul_long.cpp
+++ b/src/KSPACE/pair_born_coul_long.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -97,7 +97,7 @@ void PairBornCoulLong::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@@ -123,51 +123,51 @@ void PairBornCoulLong::compute(int eflag, int vflag)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- r = sqrt(rsq);
-
- if (rsq < cut_coulsq) {
- grij = g_ewald * r;
- expm2 = exp(-grij*grij);
- t = 1.0 / (1.0 + EWALD_P*grij);
- erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
- prefactor = qqrd2e * qtmp*q[j]/r;
- forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
- if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
- } else forcecoul = 0.0;
-
- if (rsq < cut_ljsq[itype][jtype]) {
- r6inv = r2inv*r2inv*r2inv;
- rexp = exp((sigma[itype][jtype]-r)*rhoinv[itype][jtype]);
- forceborn = born1[itype][jtype]*r*rexp - born2[itype][jtype]*r6inv
- + born3[itype][jtype]*r2inv*r6inv;
- } else forceborn = 0.0;
-
- fpair = (forcecoul + factor_lj*forceborn) * r2inv;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (eflag) {
- if (rsq < cut_coulsq) {
- ecoul = prefactor*erfc;
- if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
- } else ecoul = 0.0;
- if (rsq < cut_ljsq[itype][jtype]) {
- evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv
- + d[itype][jtype]*r6inv*r2inv - offset[itype][jtype];
- evdwl *= factor_lj;
- } else evdwl = 0.0;
- }
-
- if (evflag) ev_tally(i,j,nlocal,newton_pair,
- evdwl,ecoul,fpair,delx,dely,delz);
+ r2inv = 1.0/rsq;
+ r = sqrt(rsq);
+
+ if (rsq < cut_coulsq) {
+ grij = g_ewald * r;
+ expm2 = exp(-grij*grij);
+ t = 1.0 / (1.0 + EWALD_P*grij);
+ erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
+ prefactor = qqrd2e * qtmp*q[j]/r;
+ forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
+ if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
+ } else forcecoul = 0.0;
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ r6inv = r2inv*r2inv*r2inv;
+ rexp = exp((sigma[itype][jtype]-r)*rhoinv[itype][jtype]);
+ forceborn = born1[itype][jtype]*r*rexp - born2[itype][jtype]*r6inv
+ + born3[itype][jtype]*r2inv*r6inv;
+ } else forceborn = 0.0;
+
+ fpair = (forcecoul + factor_lj*forceborn) * r2inv;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (eflag) {
+ if (rsq < cut_coulsq) {
+ ecoul = prefactor*erfc;
+ if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
+ } else ecoul = 0.0;
+ if (rsq < cut_ljsq[itype][jtype]) {
+ evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv
+ + d[itype][jtype]*r6inv*r2inv - offset[itype][jtype];
+ evdwl *= factor_lj;
+ } else evdwl = 0.0;
+ }
+
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
@@ -223,7 +223,7 @@ void PairBornCoulLong::settings(int narg, char **arg)
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
- if (setflag[i][j]) cut_lj[i][j] = cut_lj_global;
+ if (setflag[i][j]) cut_lj[i][j] = cut_lj_global;
}
}
@@ -282,7 +282,7 @@ double PairBornCoulLong::init_one(int i, int j)
born1[i][j] = a[i][j]/rho[i][j];
born2[i][j] = 6.0*c[i][j];
born3[i][j] = 8.0*d[i][j];
-
+
if (offset_flag) {
double rexp = exp(-cut_lj[i][j]*rhoinv[i][j]);
offset[i][j] = a[i][j]*rexp - c[i][j]/pow(cut_lj[i][j],6.0) +
@@ -300,19 +300,19 @@ double PairBornCoulLong::init_one(int i, int j)
born3[j][i] = born3[i][j];
offset[j][i] = offset[i][j];
- // compute I,J contribution to long-range tail correction
- // count total # of atoms of type I and J via Allreduce
+ // compute I,J contribution to long-range tail correction
+ // count total # of atoms of type I and J via Allreduce
- if (tail_flag) {
- int *type = atom->type;
- int nlocal = atom->nlocal;
+ if (tail_flag) {
+ int *type = atom->type;
+ int nlocal = atom->nlocal;
- double count[2],all[2];
- count[0] = count[1] = 0.0;
- for (int k = 0; k < nlocal; k++) {
- if (type[k] == i) count[0] += 1.0;
- if (type[k] == j) count[1] += 1.0;
- }
+ double count[2],all[2];
+ count[0] = count[1] = 0.0;
+ for (int k = 0; k < nlocal; k++) {
+ if (type[k] == i) count[0] += 1.0;
+ if (type[k] == j) count[1] += 1.0;
+ }
MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world);
double rho1 = rho[i][j];
@@ -322,15 +322,15 @@ double PairBornCoulLong::init_one(int i, int j)
double rc2 = rc*rc;
double rc3 = rc2*rc;
double rc5 = rc3*rc2;
- etail_ij = 2.0*MY_PI*all[0]*all[1] *
- (a[i][j]*exp((sigma[i][j]-rc)/rho1)*rho1*
- (rc2 + 2.0*rho1*rc + 2.0*rho2) -
- c[i][j]/(3.0*rc3) + d[i][j]/(5.0*rc5));
- ptail_ij = (-1/3.0)*2.0*MY_PI*all[0]*all[1] *
- (-a[i][j]*exp((sigma[i][j]-rc)/rho1) *
- (rc3 + 3.0*rho1*rc2 + 6.0*rho2*rc + 6.0*rho3) +
- 2.0*c[i][j]/rc3 - 8.0*d[i][j]/(5.0*rc5));
- }
+ etail_ij = 2.0*MY_PI*all[0]*all[1] *
+ (a[i][j]*exp((sigma[i][j]-rc)/rho1)*rho1*
+ (rc2 + 2.0*rho1*rc + 2.0*rho2) -
+ c[i][j]/(3.0*rc3) + d[i][j]/(5.0*rc5));
+ ptail_ij = (-1/3.0)*2.0*MY_PI*all[0]*all[1] *
+ (-a[i][j]*exp((sigma[i][j]-rc)/rho1) *
+ (rc3 + 3.0*rho1*rc2 + 6.0*rho2*rc + 6.0*rho3) +
+ 2.0*c[i][j]/rc3 - 8.0*d[i][j]/(5.0*rc5));
+ }
return cut;
}
@@ -368,12 +368,12 @@ void PairBornCoulLong::write_restart(FILE *fp)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
- fwrite(&a[i][j],sizeof(double),1,fp);
- fwrite(&rho[i][j],sizeof(double),1,fp);
- fwrite(&sigma[i][j],sizeof(double),1,fp);
- fwrite(&c[i][j],sizeof(double),1,fp);
- fwrite(&d[i][j],sizeof(double),1,fp);
- fwrite(&cut_lj[i][j],sizeof(double),1,fp);
+ fwrite(&a[i][j],sizeof(double),1,fp);
+ fwrite(&rho[i][j],sizeof(double),1,fp);
+ fwrite(&sigma[i][j],sizeof(double),1,fp);
+ fwrite(&c[i][j],sizeof(double),1,fp);
+ fwrite(&d[i][j],sizeof(double),1,fp);
+ fwrite(&cut_lj[i][j],sizeof(double),1,fp);
}
}
}
@@ -395,20 +395,20 @@ void PairBornCoulLong::read_restart(FILE *fp)
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
- if (me == 0) {
- fread(&a[i][j],sizeof(double),1,fp);
- fread(&rho[i][j],sizeof(double),1,fp);
- fread(&sigma[i][j],sizeof(double),1,fp);
- fread(&c[i][j],sizeof(double),1,fp);
- fread(&d[i][j],sizeof(double),1,fp);
- fread(&cut_lj[i][j],sizeof(double),1,fp);
- }
- MPI_Bcast(&a[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&rho[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&c[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&d[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world);
+ if (me == 0) {
+ fread(&a[i][j],sizeof(double),1,fp);
+ fread(&rho[i][j],sizeof(double),1,fp);
+ fread(&sigma[i][j],sizeof(double),1,fp);
+ fread(&c[i][j],sizeof(double),1,fp);
+ fread(&d[i][j],sizeof(double),1,fp);
+ fread(&cut_lj[i][j],sizeof(double),1,fp);
+ }
+ MPI_Bcast(&a[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&rho[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&c[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&d[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world);
}
}
}
@@ -446,9 +446,9 @@ void PairBornCoulLong::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairBornCoulLong::single(int i, int j, int itype, int jtype,
- double rsq,
- double factor_coul, double factor_lj,
- double &fforce)
+ double rsq,
+ double factor_coul, double factor_lj,
+ double &fforce)
{
double r2inv,r6inv,r,rexp,grij,expm2,t,erfc,prefactor;
double forcecoul,forceborn,phicoul,phiborn;
@@ -472,7 +472,7 @@ double PairBornCoulLong::single(int i, int j, int itype, int jtype,
born3[itype][jtype]*r2inv*r6inv;
} else forceborn = 0.0;
fforce = (forcecoul + factor_lj*forceborn) * r2inv;
-
+
double eng = 0.0;
if (rsq < cut_coulsq) {
phicoul = prefactor*erfc;
diff --git a/src/KSPACE/pair_born_coul_long.h b/src/KSPACE/pair_born_coul_long.h
index 5debacd85d89896de6714aa0b3b43ae0b53217e6..5f06a43c979e1712c846aa60b8be3b85f6284921 100644
--- a/src/KSPACE/pair_born_coul_long.h
+++ b/src/KSPACE/pair_born_coul_long.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/KSPACE/pair_buck_coul_long.cpp b/src/KSPACE/pair_buck_coul_long.cpp
index f3fa4d50d86888586d59d8594ea890c13d8e3ee2..393cfc1b9b3c2cc4fb7a82e38a502ffe8f538fd8 100644
--- a/src/KSPACE/pair_buck_coul_long.cpp
+++ b/src/KSPACE/pair_buck_coul_long.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -90,7 +90,7 @@ void PairBuckCoulLong::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@@ -116,50 +116,50 @@ void PairBuckCoulLong::compute(int eflag, int vflag)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- r = sqrt(rsq);
-
- if (rsq < cut_coulsq) {
- grij = g_ewald * r;
- expm2 = exp(-grij*grij);
- t = 1.0 / (1.0 + EWALD_P*grij);
- erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
- prefactor = qqrd2e * qtmp*q[j]/r;
- forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
- if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
- } else forcecoul = 0.0;
-
- if (rsq < cut_ljsq[itype][jtype]) {
- r6inv = r2inv*r2inv*r2inv;
- rexp = exp(-r*rhoinv[itype][jtype]);
- forcebuck = buck1[itype][jtype]*r*rexp - buck2[itype][jtype]*r6inv;
- } else forcebuck = 0.0;
-
- fpair = (forcecoul + factor_lj*forcebuck) * r2inv;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (eflag) {
- if (rsq < cut_coulsq) {
- ecoul = prefactor*erfc;
- if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
- } else ecoul = 0.0;
- if (rsq < cut_ljsq[itype][jtype]) {
- evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv -
- offset[itype][jtype];
- evdwl *= factor_lj;
- } else evdwl = 0.0;
- }
-
- if (evflag) ev_tally(i,j,nlocal,newton_pair,
- evdwl,ecoul,fpair,delx,dely,delz);
+ r2inv = 1.0/rsq;
+ r = sqrt(rsq);
+
+ if (rsq < cut_coulsq) {
+ grij = g_ewald * r;
+ expm2 = exp(-grij*grij);
+ t = 1.0 / (1.0 + EWALD_P*grij);
+ erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
+ prefactor = qqrd2e * qtmp*q[j]/r;
+ forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
+ if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
+ } else forcecoul = 0.0;
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ r6inv = r2inv*r2inv*r2inv;
+ rexp = exp(-r*rhoinv[itype][jtype]);
+ forcebuck = buck1[itype][jtype]*r*rexp - buck2[itype][jtype]*r6inv;
+ } else forcebuck = 0.0;
+
+ fpair = (forcecoul + factor_lj*forcebuck) * r2inv;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (eflag) {
+ if (rsq < cut_coulsq) {
+ ecoul = prefactor*erfc;
+ if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
+ } else ecoul = 0.0;
+ if (rsq < cut_ljsq[itype][jtype]) {
+ evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv -
+ offset[itype][jtype];
+ evdwl *= factor_lj;
+ } else evdwl = 0.0;
+ }
+
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
@@ -212,7 +212,7 @@ void PairBuckCoulLong::settings(int narg, char **arg)
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
- if (setflag[i][j]) cut_lj[i][j] = cut_lj_global;
+ if (setflag[i][j]) cut_lj[i][j] = cut_lj_global;
}
}
@@ -266,7 +266,7 @@ double PairBuckCoulLong::init_one(int i, int j)
rhoinv[i][j] = 1.0/rho[i][j];
buck1[i][j] = a[i][j]/rho[i][j];
buck2[i][j] = 6.0*c[i][j];
-
+
if (offset_flag) {
double rexp = exp(-cut_lj[i][j]/rho[i][j]);
offset[i][j] = a[i][j]*rexp - c[i][j]/pow(cut_lj[i][j],6.0);
@@ -280,8 +280,8 @@ double PairBuckCoulLong::init_one(int i, int j)
buck2[j][i] = buck2[i][j];
offset[j][i] = offset[i][j];
- // compute I,J contribution to long-range tail correction
- // count total # of atoms of type I and J via Allreduce
+ // compute I,J contribution to long-range tail correction
+ // count total # of atoms of type I and J via Allreduce
if (tail_flag) {
int *type = atom->type;
@@ -302,13 +302,13 @@ double PairBuckCoulLong::init_one(int i, int j)
double rc2 = rc*rc;
double rc3 = rc2*rc;
etail_ij = 2.0*MY_PI*all[0]*all[1]*
- (a[i][j]*exp(-rc/rho1)*rho1*(rc2 + 2.0*rho1*rc + 2.0*rho2) -
+ (a[i][j]*exp(-rc/rho1)*rho1*(rc2 + 2.0*rho1*rc + 2.0*rho2) -
c[i][j]/(3.0*rc3));
ptail_ij = (-1/3.0)*2.0*MY_PI*all[0]*all[1]*
(-a[i][j]*exp(-rc/rho1)*
(rc3 + 3.0*rho1*rc2 + 6.0*rho2*rc + 6.0*rho3) + 2.0*c[i][j]/rc3);
}
-
+
return cut;
}
@@ -345,10 +345,10 @@ void PairBuckCoulLong::write_restart(FILE *fp)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
- fwrite(&a[i][j],sizeof(double),1,fp);
- fwrite(&rho[i][j],sizeof(double),1,fp);
- fwrite(&c[i][j],sizeof(double),1,fp);
- fwrite(&cut_lj[i][j],sizeof(double),1,fp);
+ fwrite(&a[i][j],sizeof(double),1,fp);
+ fwrite(&rho[i][j],sizeof(double),1,fp);
+ fwrite(&c[i][j],sizeof(double),1,fp);
+ fwrite(&cut_lj[i][j],sizeof(double),1,fp);
}
}
}
@@ -370,16 +370,16 @@ void PairBuckCoulLong::read_restart(FILE *fp)
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
- if (me == 0) {
- fread(&a[i][j],sizeof(double),1,fp);
- fread(&rho[i][j],sizeof(double),1,fp);
- fread(&c[i][j],sizeof(double),1,fp);
- fread(&cut_lj[i][j],sizeof(double),1,fp);
- }
- MPI_Bcast(&a[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&rho[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&c[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world);
+ if (me == 0) {
+ fread(&a[i][j],sizeof(double),1,fp);
+ fread(&rho[i][j],sizeof(double),1,fp);
+ fread(&c[i][j],sizeof(double),1,fp);
+ fread(&cut_lj[i][j],sizeof(double),1,fp);
+ }
+ MPI_Bcast(&a[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&rho[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&c[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world);
}
}
}
@@ -417,9 +417,9 @@ void PairBuckCoulLong::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairBuckCoulLong::single(int i, int j, int itype, int jtype,
- double rsq,
- double factor_coul, double factor_lj,
- double &fforce)
+ double rsq,
+ double factor_coul, double factor_lj,
+ double &fforce)
{
double r2inv,r6inv,r,rexp,grij,expm2,t,erfc,prefactor;
double forcecoul,forcebuck,phicoul,phibuck;
@@ -442,7 +442,7 @@ double PairBuckCoulLong::single(int i, int j, int itype, int jtype,
forcebuck = buck1[itype][jtype]*r*rexp - buck2[itype][jtype]*r6inv;
} else forcebuck = 0.0;
fforce = (forcecoul + factor_lj*forcebuck) * r2inv;
-
+
double eng = 0.0;
if (rsq < cut_coulsq) {
phicoul = prefactor*erfc;
diff --git a/src/KSPACE/pair_buck_coul_long.h b/src/KSPACE/pair_buck_coul_long.h
index 96de53c26bfc6f3c87814ac22d730ff0084ed0c0..17cd53056ede86d16c03c9decb6b1ab4bc02b280 100644
--- a/src/KSPACE/pair_buck_coul_long.h
+++ b/src/KSPACE/pair_buck_coul_long.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/KSPACE/pair_coul_long.cpp b/src/KSPACE/pair_coul_long.cpp
index 0ec33fb7118f30ae2a6ffd9869aba39df4eb6bb5..a9267cf48a0c4d64604f11ff367102cbc45644d5 100644
--- a/src/KSPACE/pair_coul_long.cpp
+++ b/src/KSPACE/pair_coul_long.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -91,7 +91,7 @@ void PairCoulLong::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@@ -116,54 +116,54 @@ void PairCoulLong::compute(int eflag, int vflag)
jtype = type[j];
if (rsq < cut_coulsq) {
- r2inv = 1.0/rsq;
- if (!ncoultablebits || rsq <= tabinnersq) {
- r = sqrt(rsq);
- grij = g_ewald * r;
- expm2 = exp(-grij*grij);
- t = 1.0 / (1.0 + EWALD_P*grij);
- erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
- prefactor = qqrd2e * scale[itype][jtype] * qtmp*q[j]/r;
- forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
- if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
- } else {
- union_int_float_t rsq_lookup;
- rsq_lookup.f = rsq;
- itable = rsq_lookup.i & ncoulmask;
- itable >>= ncoulshiftbits;
- fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
- table = ftable[itable] + fraction*dftable[itable];
- forcecoul = scale[itype][jtype] * qtmp*q[j] * table;
- if (factor_coul < 1.0) {
- table = ctable[itable] + fraction*dctable[itable];
- prefactor = scale[itype][jtype] * qtmp*q[j] * table;
- forcecoul -= (1.0-factor_coul)*prefactor;
- }
- }
-
- fpair = forcecoul * r2inv;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (eflag) {
- if (!ncoultablebits || rsq <= tabinnersq)
- ecoul = prefactor*erfc;
- else {
- table = etable[itable] + fraction*detable[itable];
- ecoul = scale[itype][jtype] * qtmp*q[j] * table;
- }
- if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
- }
-
- if (evflag) ev_tally(i,j,nlocal,newton_pair,
- 0.0,ecoul,fpair,delx,dely,delz);
+ r2inv = 1.0/rsq;
+ if (!ncoultablebits || rsq <= tabinnersq) {
+ r = sqrt(rsq);
+ grij = g_ewald * r;
+ expm2 = exp(-grij*grij);
+ t = 1.0 / (1.0 + EWALD_P*grij);
+ erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
+ prefactor = qqrd2e * scale[itype][jtype] * qtmp*q[j]/r;
+ forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
+ if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
+ } else {
+ union_int_float_t rsq_lookup;
+ rsq_lookup.f = rsq;
+ itable = rsq_lookup.i & ncoulmask;
+ itable >>= ncoulshiftbits;
+ fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
+ table = ftable[itable] + fraction*dftable[itable];
+ forcecoul = scale[itype][jtype] * qtmp*q[j] * table;
+ if (factor_coul < 1.0) {
+ table = ctable[itable] + fraction*dctable[itable];
+ prefactor = scale[itype][jtype] * qtmp*q[j] * table;
+ forcecoul -= (1.0-factor_coul)*prefactor;
+ }
+ }
+
+ fpair = forcecoul * r2inv;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (eflag) {
+ if (!ncoultablebits || rsq <= tabinnersq)
+ ecoul = prefactor*erfc;
+ else {
+ table = etable[itable] + fraction*detable[itable];
+ ecoul = scale[itype][jtype] * qtmp*q[j] * table;
+ }
+ if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
+ }
+
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ 0.0,ecoul,fpair,delx,dely,delz);
}
}
}
@@ -250,7 +250,7 @@ void PairCoulLong::init_style()
// insure use of KSpace long-range solver, set g_ewald
- if (force->kspace == NULL)
+ if (force->kspace == NULL)
error->all(FLERR,"Pair style is incompatible with KSpace style");
g_ewald = force->kspace->g_ewald;
@@ -282,17 +282,17 @@ void PairCoulLong::init_tables()
tabinnersq = tabinner*tabinner;
init_bitmap(tabinner,cut_coul,ncoultablebits,
- masklo,maskhi,ncoulmask,ncoulshiftbits);
-
+ masklo,maskhi,ncoulmask,ncoulshiftbits);
+
int ntable = 1;
for (int i = 0; i < ncoultablebits; i++) ntable *= 2;
-
+
// linear lookup tables of length N = 2^ncoultablebits
// stored value = value at lower edge of bin
// d values = delta from lower edge to upper edge of bin
if (ftable) free_tables();
-
+
memory->create(rtable,ntable,"pair:rtable");
memory->create(ftable,ntable,"pair:ftable");
memory->create(ctable,ntable,"pair:ctable");
@@ -316,7 +316,7 @@ void PairCoulLong::init_tables()
int itablemin;
minrsq_lookup.i = 0 << ncoulshiftbits;
minrsq_lookup.i |= maskhi;
-
+
for (int i = 0; i < ntable; i++) {
rsq_lookup.i = i << ncoulshiftbits;
rsq_lookup.i |= masklo;
@@ -341,23 +341,23 @@ void PairCoulLong::init_tables()
ptable[i] = qqrd2e/r;
vtable[i] = qqrd2e/r * (derfc + EWALD_F*grij*expm2);
if (rsq_lookup.f > cut_respa[2]*cut_respa[2]) {
- if (rsq_lookup.f < cut_respa[3]*cut_respa[3]) {
- rsw = (r - cut_respa[2])/(cut_respa[3] - cut_respa[2]);
- ftable[i] += qqrd2e/r * rsw*rsw*(3.0 - 2.0*rsw);
- ctable[i] = qqrd2e/r * rsw*rsw*(3.0 - 2.0*rsw);
- } else {
- ftable[i] = qqrd2e/r * (derfc + EWALD_F*grij*expm2);
- ctable[i] = qqrd2e/r;
- }
+ if (rsq_lookup.f < cut_respa[3]*cut_respa[3]) {
+ rsw = (r - cut_respa[2])/(cut_respa[3] - cut_respa[2]);
+ ftable[i] += qqrd2e/r * rsw*rsw*(3.0 - 2.0*rsw);
+ ctable[i] = qqrd2e/r * rsw*rsw*(3.0 - 2.0*rsw);
+ } else {
+ ftable[i] = qqrd2e/r * (derfc + EWALD_F*grij*expm2);
+ ctable[i] = qqrd2e/r;
+ }
}
}
minrsq_lookup.f = MIN(minrsq_lookup.f,rsq_lookup.f);
}
tabinnersq = minrsq_lookup.f;
-
+
int ntablem1 = ntable - 1;
-
+
for (int i = 0; i < ntablem1; i++) {
drtable[i] = 1.0/(rtable[i+1] - rtable[i]);
dftable[i] = ftable[i+1] - ftable[i];
@@ -371,10 +371,10 @@ void PairCoulLong::init_tables()
dptable[i] = ptable[i+1] - ptable[i];
}
}
-
- // get the delta values for the last table entries
+
+ // get the delta values for the last table entries
// tables are connected periodically between 0 and ntablem1
-
+
drtable[ntablem1] = 1.0/(rtable[0] - rtable[ntablem1]);
dftable[ntablem1] = ftable[0] - ftable[ntablem1];
dctable[ntablem1] = ctable[0] - ctable[ntablem1];
@@ -384,23 +384,23 @@ void PairCoulLong::init_tables()
dptable[ntablem1] = ptable[0] - ptable[ntablem1];
}
- // get the correct delta values at itablemax
+ // get the correct delta values at itablemax
// smallest r is in bin itablemin
// largest r is in bin itablemax, which is itablemin-1,
// or ntablem1 if itablemin=0
// deltas at itablemax only needed if corresponding rsq < cut*cut
- // if so, compute deltas between rsq and cut*cut
+ // if so, compute deltas between rsq and cut*cut
double f_tmp,c_tmp,e_tmp,p_tmp,v_tmp;
itablemin = minrsq_lookup.i & ncoulmask;
- itablemin >>= ncoulshiftbits;
- int itablemax = itablemin - 1;
- if (itablemin == 0) itablemax = ntablem1;
+ itablemin >>= ncoulshiftbits;
+ int itablemax = itablemin - 1;
+ if (itablemin == 0) itablemax = ntablem1;
rsq_lookup.i = itablemax << ncoulshiftbits;
rsq_lookup.i |= maskhi;
if (rsq_lookup.f < cut_coulsq) {
- rsq_lookup.f = cut_coulsq;
+ rsq_lookup.f = cut_coulsq;
r = sqrtf(rsq_lookup.f);
grij = g_ewald * r;
expm2 = exp(-grij*grij);
@@ -418,7 +418,7 @@ void PairCoulLong::init_tables()
v_tmp = qqrd2e/r * (derfc + EWALD_F*grij*expm2);
if (rsq_lookup.f > cut_respa[2]*cut_respa[2]) {
if (rsq_lookup.f < cut_respa[3]*cut_respa[3]) {
- rsw = (r - cut_respa[2])/(cut_respa[3] - cut_respa[2]);
+ rsw = (r - cut_respa[2])/(cut_respa[3] - cut_respa[2]);
f_tmp += qqrd2e/r * rsw*rsw*(3.0 - 2.0*rsw);
c_tmp = qqrd2e/r * rsw*rsw*(3.0 - 2.0*rsw);
} else {
@@ -428,14 +428,14 @@ void PairCoulLong::init_tables()
}
}
- drtable[itablemax] = 1.0/(rsq_lookup.f - rtable[itablemax]);
+ drtable[itablemax] = 1.0/(rsq_lookup.f - rtable[itablemax]);
dftable[itablemax] = f_tmp - ftable[itablemax];
dctable[itablemax] = c_tmp - ctable[itablemax];
detable[itablemax] = e_tmp - etable[itablemax];
if (cut_respa) {
dvtable[itablemax] = v_tmp - vtable[itablemax];
dptable[itablemax] = p_tmp - ptable[itablemax];
- }
+ }
}
}
@@ -509,9 +509,9 @@ void PairCoulLong::free_tables()
/* ---------------------------------------------------------------------- */
double PairCoulLong::single(int i, int j, int itype, int jtype,
- double rsq,
- double factor_coul, double factor_lj,
- double &fforce)
+ double rsq,
+ double factor_coul, double factor_lj,
+ double &fforce)
{
double r2inv,r,grij,expm2,t,erfc,prefactor;
double fraction,table,forcecoul,phicoul;
@@ -542,7 +542,7 @@ double PairCoulLong::single(int i, int j, int itype, int jtype,
}
}
fforce = forcecoul * r2inv;
-
+
if (!ncoultablebits || rsq <= tabinnersq)
phicoul = prefactor*erfc;
else {
diff --git a/src/KSPACE/pair_coul_long.h b/src/KSPACE/pair_coul_long.h
index d67aea8141ea6108241802b6399f3ccd36bca53a..ec7398f5a0447607986e06131ab7581ca2bbc7a3 100644
--- a/src/KSPACE/pair_coul_long.h
+++ b/src/KSPACE/pair_coul_long.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/KSPACE/pair_lj_charmm_coul_long.cpp b/src/KSPACE/pair_lj_charmm_coul_long.cpp
index 8c92048d3dda6e7bccf55c791bd9c17d39f55cf2..6f5b589d71b1f8413c9e315292279d69473f13ce 100644
--- a/src/KSPACE/pair_lj_charmm_coul_long.cpp
+++ b/src/KSPACE/pair_lj_charmm_coul_long.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -108,7 +108,7 @@ void PairLJCharmmCoulLong::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@@ -133,83 +133,83 @@ void PairLJCharmmCoulLong::compute(int eflag, int vflag)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cut_bothsq) {
- r2inv = 1.0/rsq;
-
- if (rsq < cut_coulsq) {
- if (!ncoultablebits || rsq <= tabinnersq) {
- r = sqrt(rsq);
- grij = g_ewald * r;
- expm2 = exp(-grij*grij);
- t = 1.0 / (1.0 + EWALD_P*grij);
- erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
- prefactor = qqrd2e * qtmp*q[j]/r;
- forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
- if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
- } else {
- union_int_float_t rsq_lookup;
- rsq_lookup.f = rsq;
- itable = rsq_lookup.i & ncoulmask;
- itable >>= ncoulshiftbits;
- fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
- table = ftable[itable] + fraction*dftable[itable];
- forcecoul = qtmp*q[j] * table;
- if (factor_coul < 1.0) {
- table = ctable[itable] + fraction*dctable[itable];
- prefactor = qtmp*q[j] * table;
- forcecoul -= (1.0-factor_coul)*prefactor;
- }
- }
- } else forcecoul = 0.0;
-
- if (rsq < cut_ljsq) {
- r6inv = r2inv*r2inv*r2inv;
- jtype = type[j];
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- if (rsq > cut_lj_innersq) {
- switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
- (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
- switch2 = 12.0*rsq * (cut_ljsq-rsq) *
- (rsq-cut_lj_innersq) / denom_lj;
- philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
- forcelj = forcelj*switch1 + philj*switch2;
- }
- } else forcelj = 0.0;
-
- fpair = (forcecoul + factor_lj*forcelj) * r2inv;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (eflag) {
- if (rsq < cut_coulsq) {
- if (!ncoultablebits || rsq <= tabinnersq)
- ecoul = prefactor*erfc;
- else {
- table = etable[itable] + fraction*detable[itable];
- ecoul = qtmp*q[j] * table;
- }
- if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
- } else ecoul = 0.0;
-
- if (rsq < cut_ljsq) {
- evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
- if (rsq > cut_lj_innersq) {
- switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
- (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
- evdwl *= switch1;
- }
- evdwl *= factor_lj;
- } else evdwl = 0.0;
- }
-
- if (evflag) ev_tally(i,j,nlocal,newton_pair,
- evdwl,ecoul,fpair,delx,dely,delz);
+ r2inv = 1.0/rsq;
+
+ if (rsq < cut_coulsq) {
+ if (!ncoultablebits || rsq <= tabinnersq) {
+ r = sqrt(rsq);
+ grij = g_ewald * r;
+ expm2 = exp(-grij*grij);
+ t = 1.0 / (1.0 + EWALD_P*grij);
+ erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
+ prefactor = qqrd2e * qtmp*q[j]/r;
+ forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
+ if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
+ } else {
+ union_int_float_t rsq_lookup;
+ rsq_lookup.f = rsq;
+ itable = rsq_lookup.i & ncoulmask;
+ itable >>= ncoulshiftbits;
+ fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
+ table = ftable[itable] + fraction*dftable[itable];
+ forcecoul = qtmp*q[j] * table;
+ if (factor_coul < 1.0) {
+ table = ctable[itable] + fraction*dctable[itable];
+ prefactor = qtmp*q[j] * table;
+ forcecoul -= (1.0-factor_coul)*prefactor;
+ }
+ }
+ } else forcecoul = 0.0;
+
+ if (rsq < cut_ljsq) {
+ r6inv = r2inv*r2inv*r2inv;
+ jtype = type[j];
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ if (rsq > cut_lj_innersq) {
+ switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
+ (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
+ switch2 = 12.0*rsq * (cut_ljsq-rsq) *
+ (rsq-cut_lj_innersq) / denom_lj;
+ philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
+ forcelj = forcelj*switch1 + philj*switch2;
+ }
+ } else forcelj = 0.0;
+
+ fpair = (forcecoul + factor_lj*forcelj) * r2inv;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (eflag) {
+ if (rsq < cut_coulsq) {
+ if (!ncoultablebits || rsq <= tabinnersq)
+ ecoul = prefactor*erfc;
+ else {
+ table = etable[itable] + fraction*detable[itable];
+ ecoul = qtmp*q[j] * table;
+ }
+ if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
+ } else ecoul = 0.0;
+
+ if (rsq < cut_ljsq) {
+ evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
+ if (rsq > cut_lj_innersq) {
+ switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
+ (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
+ evdwl *= switch1;
+ }
+ evdwl *= factor_lj;
+ } else evdwl = 0.0;
+ }
+
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
@@ -244,7 +244,7 @@ void PairLJCharmmCoulLong::compute_inner()
double cut_out_on = cut_respa[0];
double cut_out_off = cut_respa[1];
-
+
double cut_out_diff = cut_out_off - cut_out_on;
double cut_out_on_sq = cut_out_on*cut_out_on;
double cut_out_off_sq = cut_out_off*cut_out_off;
@@ -277,15 +277,15 @@ void PairLJCharmmCoulLong::compute_inner()
forcecoul = qqrd2e * qtmp*q[j]*sqrt(r2inv);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*forcecoul;
- r6inv = r2inv*r2inv*r2inv;
- jtype = type[j];
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ r6inv = r2inv*r2inv*r2inv;
+ jtype = type[j];
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- fpair = (forcecoul + factor_lj*forcelj) * r2inv;
+ fpair = (forcecoul + factor_lj*forcelj) * r2inv;
if (rsq > cut_out_on_sq) {
- rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
- fpair *= 1.0 + rsw*rsw*(2.0*rsw-3.0);
+ rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
+ fpair *= 1.0 + rsw*rsw*(2.0*rsw-3.0);
}
f[i][0] += delx*fpair;
@@ -364,40 +364,40 @@ void PairLJCharmmCoulLong::compute_middle()
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cut_out_off_sq && rsq > cut_in_off_sq) {
- r2inv = 1.0/rsq;
+ r2inv = 1.0/rsq;
forcecoul = qqrd2e * qtmp*q[j]*sqrt(r2inv);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*forcecoul;
- r6inv = r2inv*r2inv*r2inv;
- jtype = type[j];
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- if (rsq > cut_lj_innersq) {
- switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
- (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
- switch2 = 12.0*rsq * (cut_ljsq-rsq) *
- (rsq-cut_lj_innersq) / denom_lj;
- philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
- forcelj = forcelj*switch1 + philj*switch2;
- }
-
- fpair = (forcecoul + factor_lj*forcelj) * r2inv;
+ r6inv = r2inv*r2inv*r2inv;
+ jtype = type[j];
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ if (rsq > cut_lj_innersq) {
+ switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
+ (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
+ switch2 = 12.0*rsq * (cut_ljsq-rsq) *
+ (rsq-cut_lj_innersq) / denom_lj;
+ philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
+ forcelj = forcelj*switch1 + philj*switch2;
+ }
+
+ fpair = (forcecoul + factor_lj*forcelj) * r2inv;
if (rsq < cut_in_on_sq) {
- rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff;
- fpair *= rsw*rsw*(3.0 - 2.0*rsw);
- }
+ rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff;
+ fpair *= rsw*rsw*(3.0 - 2.0*rsw);
+ }
if (rsq > cut_out_on_sq) {
- rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
- fpair *= 1.0 + rsw*rsw*(2.0*rsw - 3.0);
- }
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
+ rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
+ fpair *= 1.0 + rsw*rsw*(2.0*rsw - 3.0);
+ }
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
}
}
}
@@ -430,7 +430,7 @@ void PairLJCharmmCoulLong::compute_outer(int eflag, int vflag)
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
double qqrd2e = force->qqrd2e;
-
+
inum = listouter->inum;
ilist = listouter->ilist;
numneigh = listouter->numneigh;
@@ -460,154 +460,154 @@ void PairLJCharmmCoulLong::compute_outer(int eflag, int vflag)
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
-
+
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
-
+
if (rsq < cut_bothsq) {
- r2inv = 1.0/rsq;
-
- if (rsq < cut_coulsq) {
- if (!ncoultablebits || rsq <= tabinnersq) {
- r = sqrt(rsq);
- grij = g_ewald * r;
- expm2 = exp(-grij*grij);
- t = 1.0 / (1.0 + EWALD_P*grij);
- erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
- prefactor = qqrd2e * qtmp*q[j]/r;
- forcecoul = prefactor * (erfc + EWALD_F*grij*expm2 - 1.0);
- if (rsq > cut_in_off_sq) {
- if (rsq < cut_in_on_sq) {
- rsw = (r - cut_in_off)/cut_in_diff;
- forcecoul += prefactor*rsw*rsw*(3.0 - 2.0*rsw);
- if (factor_coul < 1.0)
- forcecoul -=
- (1.0-factor_coul)*prefactor*rsw*rsw*(3.0 - 2.0*rsw);
- } else {
- forcecoul += prefactor;
- if (factor_coul < 1.0)
- forcecoul -= (1.0-factor_coul)*prefactor;
- }
- }
- } else {
- union_int_float_t rsq_lookup;
- rsq_lookup.f = rsq;
- itable = rsq_lookup.i & ncoulmask;
- itable >>= ncoulshiftbits;
- fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
- table = ftable[itable] + fraction*dftable[itable];
- forcecoul = qtmp*q[j] * table;
- if (factor_coul < 1.0) {
- table = ctable[itable] + fraction*dctable[itable];
- prefactor = qtmp*q[j] * table;
- forcecoul -= (1.0-factor_coul)*prefactor;
- }
- }
- } else forcecoul = 0.0;
-
- if (rsq < cut_ljsq && rsq > cut_in_off_sq) {
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- if (rsq > cut_lj_innersq) {
- switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
- (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
- switch2 = 12.0*rsq * (cut_ljsq-rsq) *
- (rsq-cut_lj_innersq) / denom_lj;
- philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
- forcelj = forcelj*switch1 + philj*switch2;
- }
- if (rsq < cut_in_on_sq) {
- rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff;
- forcelj *= rsw*rsw*(3.0 - 2.0*rsw);
- }
- } else forcelj = 0.0;
-
- fpair = (forcecoul + forcelj) * r2inv;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (eflag) {
- if (rsq < cut_coulsq) {
- if (!ncoultablebits || rsq <= tabinnersq) {
- ecoul = prefactor*erfc;
- if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
- } else {
- table = etable[itable] + fraction*detable[itable];
- ecoul = qtmp*q[j] * table;
- if (factor_coul < 1.0) {
- table = ptable[itable] + fraction*dptable[itable];
- prefactor = qtmp*q[j] * table;
- ecoul -= (1.0-factor_coul)*prefactor;
- }
- }
- } else ecoul = 0.0;
-
- if (rsq < cut_ljsq) {
- r6inv = r2inv*r2inv*r2inv;
- evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
- if (rsq > cut_lj_innersq) {
- switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
- (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
- evdwl *= switch1;
- }
- evdwl *= factor_lj;
- } else evdwl = 0.0;
- }
-
- if (vflag) {
- if (rsq < cut_coulsq) {
- if (!ncoultablebits || rsq <= tabinnersq) {
- forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
- if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
- } else {
- table = vtable[itable] + fraction*dvtable[itable];
- forcecoul = qtmp*q[j] * table;
- if (factor_coul < 1.0) {
- table = ptable[itable] + fraction*dptable[itable];
- prefactor = qtmp*q[j] * table;
- forcecoul -= (1.0-factor_coul)*prefactor;
- }
- }
- } else forcecoul = 0.0;
-
- if (rsq <= cut_in_off_sq) {
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- if (rsq > cut_lj_innersq) {
- switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
- (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
- switch2 = 12.0*rsq * (cut_ljsq-rsq) *
- (rsq-cut_lj_innersq) / denom_lj;
- philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
- forcelj = forcelj*switch1 + philj*switch2;
- }
- } else if (rsq <= cut_in_on_sq) {
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- if (rsq > cut_lj_innersq) {
- switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
- (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
- switch2 = 12.0*rsq * (cut_ljsq-rsq) *
- (rsq-cut_lj_innersq) / denom_lj;
- philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
- forcelj = forcelj*switch1 + philj*switch2;
- }
- }
-
- fpair = (forcecoul + factor_lj*forcelj) * r2inv;
- }
-
- if (evflag) ev_tally(i,j,nlocal,newton_pair,
- evdwl,ecoul,fpair,delx,dely,delz);
+ r2inv = 1.0/rsq;
+
+ if (rsq < cut_coulsq) {
+ if (!ncoultablebits || rsq <= tabinnersq) {
+ r = sqrt(rsq);
+ grij = g_ewald * r;
+ expm2 = exp(-grij*grij);
+ t = 1.0 / (1.0 + EWALD_P*grij);
+ erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
+ prefactor = qqrd2e * qtmp*q[j]/r;
+ forcecoul = prefactor * (erfc + EWALD_F*grij*expm2 - 1.0);
+ if (rsq > cut_in_off_sq) {
+ if (rsq < cut_in_on_sq) {
+ rsw = (r - cut_in_off)/cut_in_diff;
+ forcecoul += prefactor*rsw*rsw*(3.0 - 2.0*rsw);
+ if (factor_coul < 1.0)
+ forcecoul -=
+ (1.0-factor_coul)*prefactor*rsw*rsw*(3.0 - 2.0*rsw);
+ } else {
+ forcecoul += prefactor;
+ if (factor_coul < 1.0)
+ forcecoul -= (1.0-factor_coul)*prefactor;
+ }
+ }
+ } else {
+ union_int_float_t rsq_lookup;
+ rsq_lookup.f = rsq;
+ itable = rsq_lookup.i & ncoulmask;
+ itable >>= ncoulshiftbits;
+ fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
+ table = ftable[itable] + fraction*dftable[itable];
+ forcecoul = qtmp*q[j] * table;
+ if (factor_coul < 1.0) {
+ table = ctable[itable] + fraction*dctable[itable];
+ prefactor = qtmp*q[j] * table;
+ forcecoul -= (1.0-factor_coul)*prefactor;
+ }
+ }
+ } else forcecoul = 0.0;
+
+ if (rsq < cut_ljsq && rsq > cut_in_off_sq) {
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ if (rsq > cut_lj_innersq) {
+ switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
+ (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
+ switch2 = 12.0*rsq * (cut_ljsq-rsq) *
+ (rsq-cut_lj_innersq) / denom_lj;
+ philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
+ forcelj = forcelj*switch1 + philj*switch2;
+ }
+ if (rsq < cut_in_on_sq) {
+ rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff;
+ forcelj *= rsw*rsw*(3.0 - 2.0*rsw);
+ }
+ } else forcelj = 0.0;
+
+ fpair = (forcecoul + forcelj) * r2inv;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (eflag) {
+ if (rsq < cut_coulsq) {
+ if (!ncoultablebits || rsq <= tabinnersq) {
+ ecoul = prefactor*erfc;
+ if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
+ } else {
+ table = etable[itable] + fraction*detable[itable];
+ ecoul = qtmp*q[j] * table;
+ if (factor_coul < 1.0) {
+ table = ptable[itable] + fraction*dptable[itable];
+ prefactor = qtmp*q[j] * table;
+ ecoul -= (1.0-factor_coul)*prefactor;
+ }
+ }
+ } else ecoul = 0.0;
+
+ if (rsq < cut_ljsq) {
+ r6inv = r2inv*r2inv*r2inv;
+ evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
+ if (rsq > cut_lj_innersq) {
+ switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
+ (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
+ evdwl *= switch1;
+ }
+ evdwl *= factor_lj;
+ } else evdwl = 0.0;
+ }
+
+ if (vflag) {
+ if (rsq < cut_coulsq) {
+ if (!ncoultablebits || rsq <= tabinnersq) {
+ forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
+ if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
+ } else {
+ table = vtable[itable] + fraction*dvtable[itable];
+ forcecoul = qtmp*q[j] * table;
+ if (factor_coul < 1.0) {
+ table = ptable[itable] + fraction*dptable[itable];
+ prefactor = qtmp*q[j] * table;
+ forcecoul -= (1.0-factor_coul)*prefactor;
+ }
+ }
+ } else forcecoul = 0.0;
+
+ if (rsq <= cut_in_off_sq) {
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ if (rsq > cut_lj_innersq) {
+ switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
+ (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
+ switch2 = 12.0*rsq * (cut_ljsq-rsq) *
+ (rsq-cut_lj_innersq) / denom_lj;
+ philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
+ forcelj = forcelj*switch1 + philj*switch2;
+ }
+ } else if (rsq <= cut_in_on_sq) {
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ if (rsq > cut_lj_innersq) {
+ switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
+ (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
+ switch2 = 12.0*rsq * (cut_ljsq-rsq) *
+ (rsq-cut_lj_innersq) / denom_lj;
+ philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
+ forcelj = forcelj*switch1 + philj*switch2;
+ }
+ }
+
+ fpair = (forcecoul + factor_lj*forcelj) * r2inv;
+ }
+
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
@@ -743,7 +743,7 @@ void PairLJCharmmCoulLong::init_style()
// require cut_lj_inner < cut_lj
- if (cut_lj_inner >= cut_lj)
+ if (cut_lj_inner >= cut_lj)
error->all(FLERR,"Pair inner cutoff >= Pair outer cutoff");
cut_lj_innersq = cut_lj_inner * cut_lj_inner;
@@ -751,7 +751,7 @@ void PairLJCharmmCoulLong::init_style()
cut_coulsq = cut_coul * cut_coul;
cut_bothsq = MAX(cut_ljsq,cut_coulsq);
- denom_lj = (cut_ljsq-cut_lj_innersq) * (cut_ljsq-cut_lj_innersq) *
+ denom_lj = (cut_ljsq-cut_lj_innersq) * (cut_ljsq-cut_lj_innersq) *
(cut_ljsq-cut_lj_innersq);
// set & error check interior rRESPA cutoffs
@@ -770,7 +770,7 @@ void PairLJCharmmCoulLong::init_style()
if (force->kspace == NULL)
error->all(FLERR,"Pair style is incompatible with KSpace style");
g_ewald = force->kspace->g_ewald;
-
+
// setup force tables
if (ncoultablebits) init_tables();
@@ -797,10 +797,10 @@ double PairLJCharmmCoulLong::init_one(int i, int j)
{
if (setflag[i][j] == 0) {
epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j],
- sigma[i][i],sigma[j][j]);
+ sigma[i][i],sigma[j][j]);
sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]);
eps14[i][j] = mix_energy(eps14[i][i],eps14[j][j],
- sigma14[i][i],sigma14[j][j]);
+ sigma14[i][i],sigma14[j][j]);
sigma14[i][j] = mix_distance(sigma14[i][i],sigma14[j][j]);
}
@@ -814,7 +814,7 @@ double PairLJCharmmCoulLong::init_one(int i, int j)
lj14_2[i][j] = 24.0 * eps14[i][j] * pow(sigma14[i][j],6.0);
lj14_3[i][j] = 4.0 * eps14[i][j] * pow(sigma14[i][j],12.0);
lj14_4[i][j] = 4.0 * eps14[i][j] * pow(sigma14[i][j],6.0);
-
+
lj1[j][i] = lj1[i][j];
lj2[j][i] = lj2[i][j];
lj3[j][i] = lj3[i][j];
@@ -839,17 +839,17 @@ void PairLJCharmmCoulLong::init_tables()
tabinnersq = tabinner*tabinner;
init_bitmap(tabinner,cut_coul,ncoultablebits,
- masklo,maskhi,ncoulmask,ncoulshiftbits);
-
+ masklo,maskhi,ncoulmask,ncoulshiftbits);
+
int ntable = 1;
for (int i = 0; i < ncoultablebits; i++) ntable *= 2;
-
+
// linear lookup tables of length N = 2^ncoultablebits
// stored value = value at lower edge of bin
// d values = delta from lower edge to upper edge of bin
if (ftable) free_tables();
-
+
memory->create(rtable,ntable,"pair:rtable");
memory->create(ftable,ntable,"pair:ftable");
memory->create(ctable,ntable,"pair:ctable");
@@ -873,7 +873,7 @@ void PairLJCharmmCoulLong::init_tables()
int itablemin;
minrsq_lookup.i = 0 << ncoulshiftbits;
minrsq_lookup.i |= maskhi;
-
+
for (int i = 0; i < ntable; i++) {
rsq_lookup.i = i << ncoulshiftbits;
rsq_lookup.i |= masklo;
@@ -898,23 +898,23 @@ void PairLJCharmmCoulLong::init_tables()
ptable[i] = qqrd2e/r;
vtable[i] = qqrd2e/r * (derfc + EWALD_F*grij*expm2);
if (rsq_lookup.f > cut_respa[2]*cut_respa[2]) {
- if (rsq_lookup.f < cut_respa[3]*cut_respa[3]) {
- rsw = (r - cut_respa[2])/(cut_respa[3] - cut_respa[2]);
- ftable[i] += qqrd2e/r * rsw*rsw*(3.0 - 2.0*rsw);
- ctable[i] = qqrd2e/r * rsw*rsw*(3.0 - 2.0*rsw);
- } else {
- ftable[i] = qqrd2e/r * (derfc + EWALD_F*grij*expm2);
- ctable[i] = qqrd2e/r;
- }
+ if (rsq_lookup.f < cut_respa[3]*cut_respa[3]) {
+ rsw = (r - cut_respa[2])/(cut_respa[3] - cut_respa[2]);
+ ftable[i] += qqrd2e/r * rsw*rsw*(3.0 - 2.0*rsw);
+ ctable[i] = qqrd2e/r * rsw*rsw*(3.0 - 2.0*rsw);
+ } else {
+ ftable[i] = qqrd2e/r * (derfc + EWALD_F*grij*expm2);
+ ctable[i] = qqrd2e/r;
+ }
}
}
minrsq_lookup.f = MIN(minrsq_lookup.f,rsq_lookup.f);
}
tabinnersq = minrsq_lookup.f;
-
+
int ntablem1 = ntable - 1;
-
+
for (int i = 0; i < ntablem1; i++) {
drtable[i] = 1.0/(rtable[i+1] - rtable[i]);
dftable[i] = ftable[i+1] - ftable[i];
@@ -928,10 +928,10 @@ void PairLJCharmmCoulLong::init_tables()
dptable[i] = ptable[i+1] - ptable[i];
}
}
-
- // get the delta values for the last table entries
+
+ // get the delta values for the last table entries
// tables are connected periodically between 0 and ntablem1
-
+
drtable[ntablem1] = 1.0/(rtable[0] - rtable[ntablem1]);
dftable[ntablem1] = ftable[0] - ftable[ntablem1];
dctable[ntablem1] = ctable[0] - ctable[ntablem1];
@@ -941,23 +941,23 @@ void PairLJCharmmCoulLong::init_tables()
dptable[ntablem1] = ptable[0] - ptable[ntablem1];
}
- // get the correct delta values at itablemax
+ // get the correct delta values at itablemax
// smallest r is in bin itablemin
// largest r is in bin itablemax, which is itablemin-1,
// or ntablem1 if itablemin=0
// deltas at itablemax only needed if corresponding rsq < cut*cut
- // if so, compute deltas between rsq and cut*cut
-
+ // if so, compute deltas between rsq and cut*cut
+
double f_tmp,c_tmp,e_tmp,p_tmp,v_tmp;
itablemin = minrsq_lookup.i & ncoulmask;
- itablemin >>= ncoulshiftbits;
- int itablemax = itablemin - 1;
- if (itablemin == 0) itablemax = ntablem1;
+ itablemin >>= ncoulshiftbits;
+ int itablemax = itablemin - 1;
+ if (itablemin == 0) itablemax = ntablem1;
rsq_lookup.i = itablemax << ncoulshiftbits;
rsq_lookup.i |= maskhi;
if (rsq_lookup.f < cut_coulsq) {
- rsq_lookup.f = cut_coulsq;
+ rsq_lookup.f = cut_coulsq;
r = sqrtf(rsq_lookup.f);
grij = g_ewald * r;
expm2 = exp(-grij*grij);
@@ -975,7 +975,7 @@ void PairLJCharmmCoulLong::init_tables()
v_tmp = qqrd2e/r * (derfc + EWALD_F*grij*expm2);
if (rsq_lookup.f > cut_respa[2]*cut_respa[2]) {
if (rsq_lookup.f < cut_respa[3]*cut_respa[3]) {
- rsw = (r - cut_respa[2])/(cut_respa[3] - cut_respa[2]);
+ rsw = (r - cut_respa[2])/(cut_respa[3] - cut_respa[2]);
f_tmp += qqrd2e/r * rsw*rsw*(3.0 - 2.0*rsw);
c_tmp = qqrd2e/r * rsw*rsw*(3.0 - 2.0*rsw);
} else {
@@ -985,14 +985,14 @@ void PairLJCharmmCoulLong::init_tables()
}
}
- drtable[itablemax] = 1.0/(rsq_lookup.f - rtable[itablemax]);
+ drtable[itablemax] = 1.0/(rsq_lookup.f - rtable[itablemax]);
dftable[itablemax] = f_tmp - ftable[itablemax];
dctable[itablemax] = c_tmp - ctable[itablemax];
detable[itablemax] = e_tmp - etable[itablemax];
if (cut_respa) {
dvtable[itablemax] = v_tmp - vtable[itablemax];
dptable[itablemax] = p_tmp - ptable[itablemax];
- }
+ }
}
}
@@ -1009,10 +1009,10 @@ void PairLJCharmmCoulLong::write_restart(FILE *fp)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
- fwrite(&epsilon[i][j],sizeof(double),1,fp);
- fwrite(&sigma[i][j],sizeof(double),1,fp);
- fwrite(&eps14[i][j],sizeof(double),1,fp);
- fwrite(&sigma14[i][j],sizeof(double),1,fp);
+ fwrite(&epsilon[i][j],sizeof(double),1,fp);
+ fwrite(&sigma[i][j],sizeof(double),1,fp);
+ fwrite(&eps14[i][j],sizeof(double),1,fp);
+ fwrite(&sigma14[i][j],sizeof(double),1,fp);
}
}
}
@@ -1034,16 +1034,16 @@ void PairLJCharmmCoulLong::read_restart(FILE *fp)
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
- if (me == 0) {
- fread(&epsilon[i][j],sizeof(double),1,fp);
- fread(&sigma[i][j],sizeof(double),1,fp);
- fread(&eps14[i][j],sizeof(double),1,fp);
- fread(&sigma14[i][j],sizeof(double),1,fp);
- }
- MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&eps14[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&sigma14[i][j],1,MPI_DOUBLE,0,world);
+ if (me == 0) {
+ fread(&epsilon[i][j],sizeof(double),1,fp);
+ fread(&sigma[i][j],sizeof(double),1,fp);
+ fread(&eps14[i][j],sizeof(double),1,fp);
+ fread(&sigma14[i][j],sizeof(double),1,fp);
+ }
+ MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&eps14[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&sigma14[i][j],1,MPI_DOUBLE,0,world);
}
}
}
@@ -1104,9 +1104,9 @@ void PairLJCharmmCoulLong::free_tables()
/* ---------------------------------------------------------------------- */
double PairLJCharmmCoulLong::single(int i, int j, int itype, int jtype,
- double rsq,
- double factor_coul, double factor_lj,
- double &fforce)
+ double rsq,
+ double factor_coul, double factor_lj,
+ double &fforce)
{
double r2inv,r6inv,r,grij,expm2,t,erfc,prefactor;
double switch1,switch2,fraction,table,forcecoul,forcelj,phicoul,philj;
@@ -1132,9 +1132,9 @@ double PairLJCharmmCoulLong::single(int i, int j, int itype, int jtype,
table = ftable[itable] + fraction*dftable[itable];
forcecoul = atom->q[i]*atom->q[j] * table;
if (factor_coul < 1.0) {
- table = ctable[itable] + fraction*dctable[itable];
- prefactor = atom->q[i]*atom->q[j] * table;
- forcecoul -= (1.0-factor_coul)*prefactor;
+ table = ctable[itable] + fraction*dctable[itable];
+ prefactor = atom->q[i]*atom->q[j] * table;
+ forcecoul -= (1.0-factor_coul)*prefactor;
}
}
} else forcecoul = 0.0;
@@ -1143,15 +1143,15 @@ double PairLJCharmmCoulLong::single(int i, int j, int itype, int jtype,
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
- (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
- switch2 = 12.0*rsq * (cut_ljsq-rsq) *
- (rsq-cut_lj_innersq) / denom_lj;
+ (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
+ switch2 = 12.0*rsq * (cut_ljsq-rsq) *
+ (rsq-cut_lj_innersq) / denom_lj;
philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
forcelj = forcelj*switch1 + philj*switch2;
}
} else forcelj = 0.0;
fforce = (forcecoul + factor_lj*forcelj) * r2inv;
-
+
double eng = 0.0;
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq)
@@ -1168,7 +1168,7 @@ double PairLJCharmmCoulLong::single(int i, int j, int itype, int jtype,
philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
- (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
+ (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
philj *= switch1;
}
eng += factor_lj*philj;
diff --git a/src/KSPACE/pair_lj_charmm_coul_long.h b/src/KSPACE/pair_lj_charmm_coul_long.h
index 47cf005d769f72aa2f4efab02e09381301099756..76c022651c34d03364a05c9bcda84af5c76e3f18 100644
--- a/src/KSPACE/pair_lj_charmm_coul_long.h
+++ b/src/KSPACE/pair_lj_charmm_coul_long.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/KSPACE/pair_lj_cut_coul_long.cpp b/src/KSPACE/pair_lj_cut_coul_long.cpp
index 52284ed31943bb14c0644dd45127aba76472546a..1ebc6d6824d02dfb1b26c5f14d2151ed6cce7315 100644
--- a/src/KSPACE/pair_lj_cut_coul_long.cpp
+++ b/src/KSPACE/pair_lj_cut_coul_long.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -105,7 +105,7 @@ void PairLJCutCoulLong::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@@ -131,70 +131,70 @@ void PairLJCutCoulLong::compute(int eflag, int vflag)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
-
- if (rsq < cut_coulsq) {
- if (!ncoultablebits || rsq <= tabinnersq) {
- r = sqrt(rsq);
- grij = g_ewald * r;
- expm2 = exp(-grij*grij);
- t = 1.0 / (1.0 + EWALD_P*grij);
- erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
- prefactor = qqrd2e * qtmp*q[j]/r;
- forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
- if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
- } else {
- union_int_float_t rsq_lookup;
- rsq_lookup.f = rsq;
- itable = rsq_lookup.i & ncoulmask;
- itable >>= ncoulshiftbits;
- fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
- table = ftable[itable] + fraction*dftable[itable];
- forcecoul = qtmp*q[j] * table;
- if (factor_coul < 1.0) {
- table = ctable[itable] + fraction*dctable[itable];
- prefactor = qtmp*q[j] * table;
- forcecoul -= (1.0-factor_coul)*prefactor;
- }
- }
- } else forcecoul = 0.0;
-
- if (rsq < cut_ljsq[itype][jtype]) {
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- } else forcelj = 0.0;
-
- fpair = (forcecoul + factor_lj*forcelj) * r2inv;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (eflag) {
- if (rsq < cut_coulsq) {
- if (!ncoultablebits || rsq <= tabinnersq)
- ecoul = prefactor*erfc;
- else {
- table = etable[itable] + fraction*detable[itable];
- ecoul = qtmp*q[j] * table;
- }
- if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
- } else ecoul = 0.0;
-
- if (rsq < cut_ljsq[itype][jtype]) {
- evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
- offset[itype][jtype];
- evdwl *= factor_lj;
- } else evdwl = 0.0;
- }
-
- if (evflag) ev_tally(i,j,nlocal,newton_pair,
- evdwl,ecoul,fpair,delx,dely,delz);
+ r2inv = 1.0/rsq;
+
+ if (rsq < cut_coulsq) {
+ if (!ncoultablebits || rsq <= tabinnersq) {
+ r = sqrt(rsq);
+ grij = g_ewald * r;
+ expm2 = exp(-grij*grij);
+ t = 1.0 / (1.0 + EWALD_P*grij);
+ erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
+ prefactor = qqrd2e * qtmp*q[j]/r;
+ forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
+ if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
+ } else {
+ union_int_float_t rsq_lookup;
+ rsq_lookup.f = rsq;
+ itable = rsq_lookup.i & ncoulmask;
+ itable >>= ncoulshiftbits;
+ fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
+ table = ftable[itable] + fraction*dftable[itable];
+ forcecoul = qtmp*q[j] * table;
+ if (factor_coul < 1.0) {
+ table = ctable[itable] + fraction*dctable[itable];
+ prefactor = qtmp*q[j] * table;
+ forcecoul -= (1.0-factor_coul)*prefactor;
+ }
+ }
+ } else forcecoul = 0.0;
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ } else forcelj = 0.0;
+
+ fpair = (forcecoul + factor_lj*forcelj) * r2inv;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (eflag) {
+ if (rsq < cut_coulsq) {
+ if (!ncoultablebits || rsq <= tabinnersq)
+ ecoul = prefactor*erfc;
+ else {
+ table = etable[itable] + fraction*detable[itable];
+ ecoul = qtmp*q[j] * table;
+ }
+ if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
+ } else ecoul = 0.0;
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
+ offset[itype][jtype];
+ evdwl *= factor_lj;
+ } else evdwl = 0.0;
+ }
+
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
@@ -229,7 +229,7 @@ void PairLJCutCoulLong::compute_inner()
double cut_out_on = cut_respa[0];
double cut_out_off = cut_respa[1];
-
+
double cut_out_diff = cut_out_off - cut_out_on;
double cut_out_on_sq = cut_out_on*cut_out_on;
double cut_out_off_sq = cut_out_off*cut_out_off;
@@ -258,30 +258,30 @@ void PairLJCutCoulLong::compute_inner()
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cut_out_off_sq) {
- r2inv = 1.0/rsq;
+ r2inv = 1.0/rsq;
forcecoul = qqrd2e * qtmp*q[j]*sqrt(r2inv);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*forcecoul;
- jtype = type[j];
- if (rsq < cut_ljsq[itype][jtype]) {
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- } else forcelj = 0.0;
+ jtype = type[j];
+ if (rsq < cut_ljsq[itype][jtype]) {
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ } else forcelj = 0.0;
- fpair = (forcecoul + factor_lj*forcelj) * r2inv;
+ fpair = (forcecoul + factor_lj*forcelj) * r2inv;
if (rsq > cut_out_on_sq) {
- rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
- fpair *= 1.0 + rsw*rsw*(2.0*rsw-3.0);
+ rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
+ fpair *= 1.0 + rsw*rsw*(2.0*rsw-3.0);
}
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
}
}
}
@@ -348,34 +348,34 @@ void PairLJCutCoulLong::compute_middle()
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cut_out_off_sq && rsq > cut_in_off_sq) {
- r2inv = 1.0/rsq;
+ r2inv = 1.0/rsq;
forcecoul = qqrd2e * qtmp*q[j]*sqrt(r2inv);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*forcecoul;
- jtype = type[j];
- if (rsq < cut_ljsq[itype][jtype]) {
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- } else forcelj = 0.0;
+ jtype = type[j];
+ if (rsq < cut_ljsq[itype][jtype]) {
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ } else forcelj = 0.0;
- fpair = (forcecoul + factor_lj*forcelj) * r2inv;
+ fpair = (forcecoul + factor_lj*forcelj) * r2inv;
if (rsq < cut_in_on_sq) {
- rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff;
- fpair *= rsw*rsw*(3.0 - 2.0*rsw);
- }
+ rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff;
+ fpair *= rsw*rsw*(3.0 - 2.0*rsw);
+ }
if (rsq > cut_out_on_sq) {
- rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
- fpair *= 1.0 + rsw*rsw*(2.0*rsw - 3.0);
- }
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
+ rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
+ fpair *= 1.0 + rsw*rsw*(2.0*rsw - 3.0);
+ }
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
}
}
}
@@ -445,117 +445,117 @@ void PairLJCutCoulLong::compute_outer(int eflag, int vflag)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
-
- if (rsq < cut_coulsq) {
- if (!ncoultablebits || rsq <= tabinnersq) {
- r = sqrt(rsq);
- grij = g_ewald * r;
- expm2 = exp(-grij*grij);
- t = 1.0 / (1.0 + EWALD_P*grij);
- erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
- prefactor = qqrd2e * qtmp*q[j]/r;
- forcecoul = prefactor * (erfc + EWALD_F*grij*expm2 - 1.0);
- if (rsq > cut_in_off_sq) {
- if (rsq < cut_in_on_sq) {
- rsw = (r - cut_in_off)/cut_in_diff;
- forcecoul += prefactor*rsw*rsw*(3.0 - 2.0*rsw);
- if (factor_coul < 1.0)
- forcecoul -=
- (1.0-factor_coul)*prefactor*rsw*rsw*(3.0 - 2.0*rsw);
- } else {
- forcecoul += prefactor;
- if (factor_coul < 1.0)
- forcecoul -= (1.0-factor_coul)*prefactor;
- }
- }
- } else {
- union_int_float_t rsq_lookup;
- rsq_lookup.f = rsq;
- itable = rsq_lookup.i & ncoulmask;
- itable >>= ncoulshiftbits;
- fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
- table = ftable[itable] + fraction*dftable[itable];
- forcecoul = qtmp*q[j] * table;
- if (factor_coul < 1.0) {
- table = ctable[itable] + fraction*dctable[itable];
- prefactor = qtmp*q[j] * table;
- forcecoul -= (1.0-factor_coul)*prefactor;
- }
- }
- } else forcecoul = 0.0;
-
- if (rsq < cut_ljsq[itype][jtype] && rsq > cut_in_off_sq) {
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- if (rsq < cut_in_on_sq) {
- rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff;
- forcelj *= rsw*rsw*(3.0 - 2.0*rsw);
- }
- } else forcelj = 0.0;
-
- fpair = (forcecoul + forcelj) * r2inv;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (eflag) {
- if (rsq < cut_coulsq) {
- if (!ncoultablebits || rsq <= tabinnersq) {
- ecoul = prefactor*erfc;
- if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
- } else {
- table = etable[itable] + fraction*detable[itable];
- ecoul = qtmp*q[j] * table;
- if (factor_coul < 1.0) {
- table = ptable[itable] + fraction*dptable[itable];
- prefactor = qtmp*q[j] * table;
- ecoul -= (1.0-factor_coul)*prefactor;
- }
- }
- } else ecoul = 0.0;
-
- if (rsq < cut_ljsq[itype][jtype]) {
- r6inv = r2inv*r2inv*r2inv;
- evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
- offset[itype][jtype];
- evdwl *= factor_lj;
- } else evdwl = 0.0;
- }
-
- if (vflag) {
- if (rsq < cut_coulsq) {
- if (!ncoultablebits || rsq <= tabinnersq) {
- forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
- if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
- } else {
- table = vtable[itable] + fraction*dvtable[itable];
- forcecoul = qtmp*q[j] * table;
- if (factor_coul < 1.0) {
- table = ptable[itable] + fraction*dptable[itable];
- prefactor = qtmp*q[j] * table;
- forcecoul -= (1.0-factor_coul)*prefactor;
- }
- }
- } else forcecoul = 0.0;
-
- if (rsq <= cut_in_off_sq) {
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- } else if (rsq <= cut_in_on_sq)
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ r2inv = 1.0/rsq;
+
+ if (rsq < cut_coulsq) {
+ if (!ncoultablebits || rsq <= tabinnersq) {
+ r = sqrt(rsq);
+ grij = g_ewald * r;
+ expm2 = exp(-grij*grij);
+ t = 1.0 / (1.0 + EWALD_P*grij);
+ erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
+ prefactor = qqrd2e * qtmp*q[j]/r;
+ forcecoul = prefactor * (erfc + EWALD_F*grij*expm2 - 1.0);
+ if (rsq > cut_in_off_sq) {
+ if (rsq < cut_in_on_sq) {
+ rsw = (r - cut_in_off)/cut_in_diff;
+ forcecoul += prefactor*rsw*rsw*(3.0 - 2.0*rsw);
+ if (factor_coul < 1.0)
+ forcecoul -=
+ (1.0-factor_coul)*prefactor*rsw*rsw*(3.0 - 2.0*rsw);
+ } else {
+ forcecoul += prefactor;
+ if (factor_coul < 1.0)
+ forcecoul -= (1.0-factor_coul)*prefactor;
+ }
+ }
+ } else {
+ union_int_float_t rsq_lookup;
+ rsq_lookup.f = rsq;
+ itable = rsq_lookup.i & ncoulmask;
+ itable >>= ncoulshiftbits;
+ fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
+ table = ftable[itable] + fraction*dftable[itable];
+ forcecoul = qtmp*q[j] * table;
+ if (factor_coul < 1.0) {
+ table = ctable[itable] + fraction*dctable[itable];
+ prefactor = qtmp*q[j] * table;
+ forcecoul -= (1.0-factor_coul)*prefactor;
+ }
+ }
+ } else forcecoul = 0.0;
+
+ if (rsq < cut_ljsq[itype][jtype] && rsq > cut_in_off_sq) {
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ if (rsq < cut_in_on_sq) {
+ rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff;
+ forcelj *= rsw*rsw*(3.0 - 2.0*rsw);
+ }
+ } else forcelj = 0.0;
+
+ fpair = (forcecoul + forcelj) * r2inv;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (eflag) {
+ if (rsq < cut_coulsq) {
+ if (!ncoultablebits || rsq <= tabinnersq) {
+ ecoul = prefactor*erfc;
+ if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
+ } else {
+ table = etable[itable] + fraction*detable[itable];
+ ecoul = qtmp*q[j] * table;
+ if (factor_coul < 1.0) {
+ table = ptable[itable] + fraction*dptable[itable];
+ prefactor = qtmp*q[j] * table;
+ ecoul -= (1.0-factor_coul)*prefactor;
+ }
+ }
+ } else ecoul = 0.0;
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ r6inv = r2inv*r2inv*r2inv;
+ evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
+ offset[itype][jtype];
+ evdwl *= factor_lj;
+ } else evdwl = 0.0;
+ }
+
+ if (vflag) {
+ if (rsq < cut_coulsq) {
+ if (!ncoultablebits || rsq <= tabinnersq) {
+ forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
+ if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
+ } else {
+ table = vtable[itable] + fraction*dvtable[itable];
+ forcecoul = qtmp*q[j] * table;
+ if (factor_coul < 1.0) {
+ table = ptable[itable] + fraction*dptable[itable];
+ prefactor = qtmp*q[j] * table;
+ forcecoul -= (1.0-factor_coul)*prefactor;
+ }
+ }
+ } else forcecoul = 0.0;
+
+ if (rsq <= cut_in_off_sq) {
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ } else if (rsq <= cut_in_on_sq)
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
fpair = (forcecoul + factor_lj*forcelj) * r2inv;
- }
+ }
- if (evflag) ev_tally(i,j,nlocal,newton_pair,
- evdwl,ecoul,fpair,delx,dely,delz);
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
@@ -606,7 +606,7 @@ void PairLJCutCoulLong::settings(int narg, char **arg)
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
- if (setflag[i][j]) cut_lj[i][j] = cut_lj_global;
+ if (setflag[i][j]) cut_lj[i][j] = cut_lj_global;
}
}
@@ -616,7 +616,7 @@ void PairLJCutCoulLong::settings(int narg, char **arg)
void PairLJCutCoulLong::coeff(int narg, char **arg)
{
- if (narg < 4 || narg > 5)
+ if (narg < 4 || narg > 5)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
@@ -730,7 +730,7 @@ double PairLJCutCoulLong::init_one(int i, int j)
{
if (setflag[i][j] == 0) {
epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j],
- sigma[i][i],sigma[j][j]);
+ sigma[i][i],sigma[j][j]);
sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]);
cut_lj[i][j] = mix_distance(cut_lj[i][i],cut_lj[j][j]);
}
@@ -776,17 +776,17 @@ double PairLJCutCoulLong::init_one(int i, int j)
if (type[k] == j) count[1] += 1.0;
}
MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world);
-
+
double sig2 = sigma[i][j]*sigma[i][j];
double sig6 = sig2*sig2*sig2;
double rc3 = cut_lj[i][j]*cut_lj[i][j]*cut_lj[i][j];
double rc6 = rc3*rc3;
double rc9 = rc3*rc6;
- etail_ij = 8.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
- sig6 * (sig6 - 3.0*rc6) / (9.0*rc9);
- ptail_ij = 16.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
- sig6 * (2.0*sig6 - 3.0*rc6) / (9.0*rc9);
- }
+ etail_ij = 8.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
+ sig6 * (sig6 - 3.0*rc6) / (9.0*rc9);
+ ptail_ij = 16.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
+ sig6 * (2.0*sig6 - 3.0*rc6) / (9.0*rc9);
+ }
return cut;
}
@@ -803,17 +803,17 @@ void PairLJCutCoulLong::init_tables()
tabinnersq = tabinner*tabinner;
init_bitmap(tabinner,cut_coul,ncoultablebits,
- masklo,maskhi,ncoulmask,ncoulshiftbits);
-
+ masklo,maskhi,ncoulmask,ncoulshiftbits);
+
int ntable = 1;
for (int i = 0; i < ncoultablebits; i++) ntable *= 2;
-
+
// linear lookup tables of length N = 2^ncoultablebits
// stored value = value at lower edge of bin
// d values = delta from lower edge to upper edge of bin
if (ftable) free_tables();
-
+
memory->create(rtable,ntable,"pair:rtable");
memory->create(ftable,ntable,"pair:ftable");
memory->create(ctable,ntable,"pair:ctable");
@@ -837,7 +837,7 @@ void PairLJCutCoulLong::init_tables()
int itablemin;
minrsq_lookup.i = 0 << ncoulshiftbits;
minrsq_lookup.i |= maskhi;
-
+
for (int i = 0; i < ntable; i++) {
rsq_lookup.i = i << ncoulshiftbits;
rsq_lookup.i |= masklo;
@@ -862,23 +862,23 @@ void PairLJCutCoulLong::init_tables()
ptable[i] = qqrd2e/r;
vtable[i] = qqrd2e/r * (derfc + EWALD_F*grij*expm2);
if (rsq_lookup.f > cut_respa[2]*cut_respa[2]) {
- if (rsq_lookup.f < cut_respa[3]*cut_respa[3]) {
- rsw = (r - cut_respa[2])/(cut_respa[3] - cut_respa[2]);
- ftable[i] += qqrd2e/r * rsw*rsw*(3.0 - 2.0*rsw);
- ctable[i] = qqrd2e/r * rsw*rsw*(3.0 - 2.0*rsw);
- } else {
- ftable[i] = qqrd2e/r * (derfc + EWALD_F*grij*expm2);
- ctable[i] = qqrd2e/r;
- }
+ if (rsq_lookup.f < cut_respa[3]*cut_respa[3]) {
+ rsw = (r - cut_respa[2])/(cut_respa[3] - cut_respa[2]);
+ ftable[i] += qqrd2e/r * rsw*rsw*(3.0 - 2.0*rsw);
+ ctable[i] = qqrd2e/r * rsw*rsw*(3.0 - 2.0*rsw);
+ } else {
+ ftable[i] = qqrd2e/r * (derfc + EWALD_F*grij*expm2);
+ ctable[i] = qqrd2e/r;
+ }
}
}
minrsq_lookup.f = MIN(minrsq_lookup.f,rsq_lookup.f);
}
tabinnersq = minrsq_lookup.f;
-
+
int ntablem1 = ntable - 1;
-
+
for (int i = 0; i < ntablem1; i++) {
drtable[i] = 1.0/(rtable[i+1] - rtable[i]);
dftable[i] = ftable[i+1] - ftable[i];
@@ -892,10 +892,10 @@ void PairLJCutCoulLong::init_tables()
dptable[i] = ptable[i+1] - ptable[i];
}
}
-
- // get the delta values for the last table entries
+
+ // get the delta values for the last table entries
// tables are connected periodically between 0 and ntablem1
-
+
drtable[ntablem1] = 1.0/(rtable[0] - rtable[ntablem1]);
dftable[ntablem1] = ftable[0] - ftable[ntablem1];
dctable[ntablem1] = ctable[0] - ctable[ntablem1];
@@ -905,23 +905,23 @@ void PairLJCutCoulLong::init_tables()
dptable[ntablem1] = ptable[0] - ptable[ntablem1];
}
- // get the correct delta values at itablemax
+ // get the correct delta values at itablemax
// smallest r is in bin itablemin
// largest r is in bin itablemax, which is itablemin-1,
// or ntablem1 if itablemin=0
// deltas at itablemax only needed if corresponding rsq < cut*cut
- // if so, compute deltas between rsq and cut*cut
+ // if so, compute deltas between rsq and cut*cut
double f_tmp,c_tmp,e_tmp,p_tmp,v_tmp;
itablemin = minrsq_lookup.i & ncoulmask;
- itablemin >>= ncoulshiftbits;
- int itablemax = itablemin - 1;
- if (itablemin == 0) itablemax = ntablem1;
+ itablemin >>= ncoulshiftbits;
+ int itablemax = itablemin - 1;
+ if (itablemin == 0) itablemax = ntablem1;
rsq_lookup.i = itablemax << ncoulshiftbits;
rsq_lookup.i |= maskhi;
if (rsq_lookup.f < cut_coulsq) {
- rsq_lookup.f = cut_coulsq;
+ rsq_lookup.f = cut_coulsq;
r = sqrtf(rsq_lookup.f);
grij = g_ewald * r;
expm2 = exp(-grij*grij);
@@ -939,7 +939,7 @@ void PairLJCutCoulLong::init_tables()
v_tmp = qqrd2e/r * (derfc + EWALD_F*grij*expm2);
if (rsq_lookup.f > cut_respa[2]*cut_respa[2]) {
if (rsq_lookup.f < cut_respa[3]*cut_respa[3]) {
- rsw = (r - cut_respa[2])/(cut_respa[3] - cut_respa[2]);
+ rsw = (r - cut_respa[2])/(cut_respa[3] - cut_respa[2]);
f_tmp += qqrd2e/r * rsw*rsw*(3.0 - 2.0*rsw);
c_tmp = qqrd2e/r * rsw*rsw*(3.0 - 2.0*rsw);
} else {
@@ -949,14 +949,14 @@ void PairLJCutCoulLong::init_tables()
}
}
- drtable[itablemax] = 1.0/(rsq_lookup.f - rtable[itablemax]);
+ drtable[itablemax] = 1.0/(rsq_lookup.f - rtable[itablemax]);
dftable[itablemax] = f_tmp - ftable[itablemax];
dctable[itablemax] = c_tmp - ctable[itablemax];
detable[itablemax] = e_tmp - etable[itablemax];
if (cut_respa) {
dvtable[itablemax] = v_tmp - vtable[itablemax];
dptable[itablemax] = p_tmp - ptable[itablemax];
- }
+ }
}
}
@@ -973,9 +973,9 @@ void PairLJCutCoulLong::write_restart(FILE *fp)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
- fwrite(&epsilon[i][j],sizeof(double),1,fp);
- fwrite(&sigma[i][j],sizeof(double),1,fp);
- fwrite(&cut_lj[i][j],sizeof(double),1,fp);
+ fwrite(&epsilon[i][j],sizeof(double),1,fp);
+ fwrite(&sigma[i][j],sizeof(double),1,fp);
+ fwrite(&cut_lj[i][j],sizeof(double),1,fp);
}
}
}
@@ -997,14 +997,14 @@ void PairLJCutCoulLong::read_restart(FILE *fp)
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
- if (me == 0) {
- fread(&epsilon[i][j],sizeof(double),1,fp);
- fread(&sigma[i][j],sizeof(double),1,fp);
- fread(&cut_lj[i][j],sizeof(double),1,fp);
- }
- MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world);
+ if (me == 0) {
+ fread(&epsilon[i][j],sizeof(double),1,fp);
+ fread(&sigma[i][j],sizeof(double),1,fp);
+ fread(&cut_lj[i][j],sizeof(double),1,fp);
+ }
+ MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world);
}
}
}
@@ -1062,9 +1062,9 @@ void PairLJCutCoulLong::free_tables()
/* ---------------------------------------------------------------------- */
double PairLJCutCoulLong::single(int i, int j, int itype, int jtype,
- double rsq,
- double factor_coul, double factor_lj,
- double &fforce)
+ double rsq,
+ double factor_coul, double factor_lj,
+ double &fforce)
{
double r2inv,r6inv,r,grij,expm2,t,erfc,prefactor;
double fraction,table,forcecoul,forcelj,phicoul,philj;
@@ -1090,9 +1090,9 @@ double PairLJCutCoulLong::single(int i, int j, int itype, int jtype,
table = ftable[itable] + fraction*dftable[itable];
forcecoul = atom->q[i]*atom->q[j] * table;
if (factor_coul < 1.0) {
- table = ctable[itable] + fraction*dctable[itable];
- prefactor = atom->q[i]*atom->q[j] * table;
- forcecoul -= (1.0-factor_coul)*prefactor;
+ table = ctable[itable] + fraction*dctable[itable];
+ prefactor = atom->q[i]*atom->q[j] * table;
+ forcecoul -= (1.0-factor_coul)*prefactor;
}
}
} else forcecoul = 0.0;
diff --git a/src/KSPACE/pair_lj_cut_coul_long.h b/src/KSPACE/pair_lj_cut_coul_long.h
index 0e9c571424829940ef08e09e4bff3d2a8c2bb496..fa8acedcdab0ae10a1117599c10b87aafcf3b300 100644
--- a/src/KSPACE/pair_lj_cut_coul_long.h
+++ b/src/KSPACE/pair_lj_cut_coul_long.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/KSPACE/pair_lj_cut_coul_long_tip4p.cpp b/src/KSPACE/pair_lj_cut_coul_long_tip4p.cpp
index bf9cc5c207c4f358b40cab6d74fba812d1089228..87a52444c3ca02717a00068dbb4df69cf104c32c 100644
--- a/src/KSPACE/pair_lj_cut_coul_long_tip4p.cpp
+++ b/src/KSPACE/pair_lj_cut_coul_long_tip4p.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -47,7 +47,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-PairLJCutCoulLongTIP4P::PairLJCutCoulLongTIP4P(LAMMPS *lmp) :
+PairLJCutCoulLongTIP4P::PairLJCutCoulLongTIP4P(LAMMPS *lmp) :
PairLJCutCoulLong(lmp)
{
single_enable = 0;
@@ -96,7 +96,7 @@ void PairLJCutCoulLongTIP4P::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@@ -128,26 +128,26 @@ void PairLJCutCoulLongTIP4P::compute(int eflag, int vflag)
// LJ interaction based on true rsq
if (rsq < cut_ljsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- forcelj *= factor_lj * r2inv;
-
- f[i][0] += delx*forcelj;
- f[i][1] += dely*forcelj;
- f[i][2] += delz*forcelj;
- f[j][0] -= delx*forcelj;
- f[j][1] -= dely*forcelj;
- f[j][2] -= delz*forcelj;
-
- if (eflag) {
- evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
- offset[itype][jtype];
- evdwl *= factor_lj;
- } else evdwl = 0.0;
-
- if (evflag) ev_tally(i,j,nlocal,newton_pair,
- evdwl,0.0,forcelj,delx,dely,delz);
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ forcelj *= factor_lj * r2inv;
+
+ f[i][0] += delx*forcelj;
+ f[i][1] += dely*forcelj;
+ f[i][2] += delz*forcelj;
+ f[j][0] -= delx*forcelj;
+ f[j][1] -= dely*forcelj;
+ f[j][2] -= delz*forcelj;
+
+ if (eflag) {
+ evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
+ offset[itype][jtype];
+ evdwl *= factor_lj;
+ } else evdwl = 0.0;
+
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ evdwl,0.0,forcelj,delx,dely,delz);
}
// adjust rsq and delxyz for off-site O charge(s) if necessary
@@ -155,214 +155,214 @@ void PairLJCutCoulLongTIP4P::compute(int eflag, int vflag)
if (rsq < cut_coulsqplus) {
- if (itype == typeO || jtype == typeO) {
- if (jtype == typeO) {
- find_M(j,jH1,jH2,xjM);
- x2 = xjM;
- } else x2 = x[j];
- delx = x1[0] - x2[0];
- dely = x1[1] - x2[1];
- delz = x1[2] - x2[2];
- rsq = delx*delx + dely*dely + delz*delz;
- }
-
- // Coulombic interaction based on modified rsq
-
- if (rsq < cut_coulsq) {
- r2inv = 1 / rsq;
- if (!ncoultablebits || rsq <= tabinnersq) {
- r = sqrt(rsq);
- grij = g_ewald * r;
- expm2 = exp(-grij*grij);
- t = 1.0 / (1.0 + EWALD_P*grij);
- erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
- prefactor = qqrd2e * qtmp*q[j]/r;
- forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
- if (factor_coul < 1.0) {
- forcecoul -= (1.0-factor_coul)*prefactor;
- }
- } else {
- union_int_float_t rsq_lookup;
- rsq_lookup.f = rsq;
- itable = rsq_lookup.i & ncoulmask;
- itable >>= ncoulshiftbits;
- fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
- table = ftable[itable] + fraction*dftable[itable];
- forcecoul = qtmp*q[j] * table;
- if (factor_coul < 1.0) {
- table = ctable[itable] + fraction*dctable[itable];
- prefactor = qtmp*q[j] * table;
- forcecoul -= (1.0-factor_coul)*prefactor;
- }
- }
-
- cforce = forcecoul * r2inv;
-
- // if i,j are not O atoms, force is applied directly
- // if i or j are O atoms, force is on fictitious atom & partitioned
- // force partitioning due to Feenstra, J Comp Chem, 20, 786 (1999)
- // f_f = fictitious force, fO = f_f (1 - 2 alpha), fH = alpha f_f
- // preserves total force and torque on water molecule
- // virial = sum(r x F) where each water's atoms are near xi and xj
- // vlist stores 2,4,6 atoms whose forces contribute to virial
-
- n = 0;
-
- if (itype != typeO) {
- f[i][0] += delx * cforce;
- f[i][1] += dely * cforce;
- f[i][2] += delz * cforce;
-
- if (vflag) {
- v[0] = x[i][0] * delx * cforce;
- v[1] = x[i][1] * dely * cforce;
- v[2] = x[i][2] * delz * cforce;
- v[3] = x[i][0] * dely * cforce;
- v[4] = x[i][0] * delz * cforce;
- v[5] = x[i][1] * delz * cforce;
- vlist[n++] = i;
- }
-
- } else {
-
- fd[0] = delx*cforce;
- fd[1] = dely*cforce;
- fd[2] = delz*cforce;
-
- delxOM = x[i][0] - x1[0];
- delyOM = x[i][1] - x1[1];
- delzOM = x[i][2] - x1[2];
-
- ddotf = (delxOM * fd[0] + delyOM * fd[1] + delzOM * fd[2]) /
- (qdist*qdist);
-
- f1[0] = ddotf * delxOM;
- f1[1] = ddotf * delyOM;
- f1[2] = ddotf * delzOM;
-
- fO[0] = fd[0] - alpha * (fd[0] - f1[0]);
- fO[1] = fd[1] - alpha * (fd[1] - f1[1]);
- fO[2] = fd[2] - alpha * (fd[2] - f1[2]);
-
- fH[0] = 0.5 * alpha * (fd[0] - f1[0]);
- fH[1] = 0.5 * alpha * (fd[1] - f1[1]);
- fH[2] = 0.5 * alpha * (fd[2] - f1[2]);
-
- f[i][0] += fO[0];
- f[i][1] += fO[1];
- f[i][2] += fO[2];
-
- f[iH1][0] += fH[0];
- f[iH1][1] += fH[1];
- f[iH1][2] += fH[2];
-
- f[iH2][0] += fH[0];
- f[iH2][1] += fH[1];
- f[iH2][2] += fH[2];
-
- if (vflag) {
- domain->closest_image(x[i],x[iH1],xH1);
- domain->closest_image(x[i],x[iH2],xH2);
-
- v[0] = x[i][0]*fO[0] + xH1[0]*fH[0] + xH2[0]*fH[0];
- v[1] = x[i][1]*fO[1] + xH1[1]*fH[1] + xH2[1]*fH[1];
- v[2] = x[i][2]*fO[2] + xH1[2]*fH[2] + xH2[2]*fH[2];
- v[3] = x[i][0]*fO[1] + xH1[0]*fH[1] + xH2[0]*fH[1];
- v[4] = x[i][0]*fO[2] + xH1[0]*fH[2] + xH2[0]*fH[2];
- v[5] = x[i][1]*fO[2] + xH1[1]*fH[2] + xH2[1]*fH[2];
-
- vlist[n++] = i;
- vlist[n++] = iH1;
- vlist[n++] = iH2;
- }
- }
-
- if (jtype != typeO) {
- f[j][0] -= delx * cforce;
- f[j][1] -= dely * cforce;
- f[j][2] -= delz * cforce;
-
- if (vflag) {
- v[0] -= x[j][0] * delx * cforce;
- v[1] -= x[j][1] * dely * cforce;
- v[2] -= x[j][2] * delz * cforce;
- v[3] -= x[j][0] * dely * cforce;
- v[4] -= x[j][0] * delz * cforce;
- v[5] -= x[j][1] * delz * cforce;
- vlist[n++] = j;
- }
-
- } else {
-
- fd[0] = -delx*cforce;
- fd[1] = -dely*cforce;
- fd[2] = -delz*cforce;
-
- delxOM = x[j][0] - x2[0];
- delyOM = x[j][1] - x2[1];
- delzOM = x[j][2] - x2[2];
-
- ddotf = (delxOM * fd[0] + delyOM * fd[1] + delzOM * fd[2]) /
- (qdist*qdist);
-
- f1[0] = ddotf * delxOM;
- f1[1] = ddotf * delyOM;
- f1[2] = ddotf * delzOM;
-
- fO[0] = fd[0] - alpha * (fd[0] - f1[0]);
- fO[1] = fd[1] - alpha * (fd[1] - f1[1]);
- fO[2] = fd[2] - alpha * (fd[2] - f1[2]);
-
- fH[0] = 0.5 * alpha * (fd[0] - f1[0]);
- fH[1] = 0.5 * alpha * (fd[1] - f1[1]);
- fH[2] = 0.5 * alpha * (fd[2] - f1[2]);
-
- f[j][0] += fO[0];
- f[j][1] += fO[1];
- f[j][2] += fO[2];
-
- f[jH1][0] += fH[0];
- f[jH1][1] += fH[1];
- f[jH1][2] += fH[2];
-
- f[jH2][0] += fH[0];
- f[jH2][1] += fH[1];
- f[jH2][2] += fH[2];
-
- if (vflag) {
- domain->closest_image(x[j],x[jH1],xH1);
- domain->closest_image(x[j],x[jH2],xH2);
-
- v[0] += x[j][0]*fO[0] + xH1[0]*fH[0] + xH2[0]*fH[0];
- v[1] += x[j][1]*fO[1] + xH1[1]*fH[1] + xH2[1]*fH[1];
- v[2] += x[j][2]*fO[2] + xH1[2]*fH[2] + xH2[2]*fH[2];
- v[3] += x[j][0]*fO[1] + xH1[0]*fH[1] + xH2[0]*fH[1];
- v[4] += x[j][0]*fO[2] + xH1[0]*fH[2] + xH2[0]*fH[2];
- v[5] += x[j][1]*fO[2] + xH1[1]*fH[2] + xH2[1]*fH[2];
-
- vlist[n++] = j;
- vlist[n++] = jH1;
- vlist[n++] = jH2;
- }
- }
-
- if (eflag) {
- if (!ncoultablebits || rsq <= tabinnersq)
- ecoul = prefactor*erfc;
- else {
- table = etable[itable] + fraction*detable[itable];
- ecoul = qtmp*q[j] * table;
- }
- if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
- } else ecoul = 0.0;
-
- if (evflag) ev_tally_list(n,vlist,ecoul,v);
- }
+ if (itype == typeO || jtype == typeO) {
+ if (jtype == typeO) {
+ find_M(j,jH1,jH2,xjM);
+ x2 = xjM;
+ } else x2 = x[j];
+ delx = x1[0] - x2[0];
+ dely = x1[1] - x2[1];
+ delz = x1[2] - x2[2];
+ rsq = delx*delx + dely*dely + delz*delz;
+ }
+
+ // Coulombic interaction based on modified rsq
+
+ if (rsq < cut_coulsq) {
+ r2inv = 1 / rsq;
+ if (!ncoultablebits || rsq <= tabinnersq) {
+ r = sqrt(rsq);
+ grij = g_ewald * r;
+ expm2 = exp(-grij*grij);
+ t = 1.0 / (1.0 + EWALD_P*grij);
+ erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
+ prefactor = qqrd2e * qtmp*q[j]/r;
+ forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
+ if (factor_coul < 1.0) {
+ forcecoul -= (1.0-factor_coul)*prefactor;
+ }
+ } else {
+ union_int_float_t rsq_lookup;
+ rsq_lookup.f = rsq;
+ itable = rsq_lookup.i & ncoulmask;
+ itable >>= ncoulshiftbits;
+ fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
+ table = ftable[itable] + fraction*dftable[itable];
+ forcecoul = qtmp*q[j] * table;
+ if (factor_coul < 1.0) {
+ table = ctable[itable] + fraction*dctable[itable];
+ prefactor = qtmp*q[j] * table;
+ forcecoul -= (1.0-factor_coul)*prefactor;
+ }
+ }
+
+ cforce = forcecoul * r2inv;
+
+ // if i,j are not O atoms, force is applied directly
+ // if i or j are O atoms, force is on fictitious atom & partitioned
+ // force partitioning due to Feenstra, J Comp Chem, 20, 786 (1999)
+ // f_f = fictitious force, fO = f_f (1 - 2 alpha), fH = alpha f_f
+ // preserves total force and torque on water molecule
+ // virial = sum(r x F) where each water's atoms are near xi and xj
+ // vlist stores 2,4,6 atoms whose forces contribute to virial
+
+ n = 0;
+
+ if (itype != typeO) {
+ f[i][0] += delx * cforce;
+ f[i][1] += dely * cforce;
+ f[i][2] += delz * cforce;
+
+ if (vflag) {
+ v[0] = x[i][0] * delx * cforce;
+ v[1] = x[i][1] * dely * cforce;
+ v[2] = x[i][2] * delz * cforce;
+ v[3] = x[i][0] * dely * cforce;
+ v[4] = x[i][0] * delz * cforce;
+ v[5] = x[i][1] * delz * cforce;
+ vlist[n++] = i;
+ }
+
+ } else {
+
+ fd[0] = delx*cforce;
+ fd[1] = dely*cforce;
+ fd[2] = delz*cforce;
+
+ delxOM = x[i][0] - x1[0];
+ delyOM = x[i][1] - x1[1];
+ delzOM = x[i][2] - x1[2];
+
+ ddotf = (delxOM * fd[0] + delyOM * fd[1] + delzOM * fd[2]) /
+ (qdist*qdist);
+
+ f1[0] = ddotf * delxOM;
+ f1[1] = ddotf * delyOM;
+ f1[2] = ddotf * delzOM;
+
+ fO[0] = fd[0] - alpha * (fd[0] - f1[0]);
+ fO[1] = fd[1] - alpha * (fd[1] - f1[1]);
+ fO[2] = fd[2] - alpha * (fd[2] - f1[2]);
+
+ fH[0] = 0.5 * alpha * (fd[0] - f1[0]);
+ fH[1] = 0.5 * alpha * (fd[1] - f1[1]);
+ fH[2] = 0.5 * alpha * (fd[2] - f1[2]);
+
+ f[i][0] += fO[0];
+ f[i][1] += fO[1];
+ f[i][2] += fO[2];
+
+ f[iH1][0] += fH[0];
+ f[iH1][1] += fH[1];
+ f[iH1][2] += fH[2];
+
+ f[iH2][0] += fH[0];
+ f[iH2][1] += fH[1];
+ f[iH2][2] += fH[2];
+
+ if (vflag) {
+ domain->closest_image(x[i],x[iH1],xH1);
+ domain->closest_image(x[i],x[iH2],xH2);
+
+ v[0] = x[i][0]*fO[0] + xH1[0]*fH[0] + xH2[0]*fH[0];
+ v[1] = x[i][1]*fO[1] + xH1[1]*fH[1] + xH2[1]*fH[1];
+ v[2] = x[i][2]*fO[2] + xH1[2]*fH[2] + xH2[2]*fH[2];
+ v[3] = x[i][0]*fO[1] + xH1[0]*fH[1] + xH2[0]*fH[1];
+ v[4] = x[i][0]*fO[2] + xH1[0]*fH[2] + xH2[0]*fH[2];
+ v[5] = x[i][1]*fO[2] + xH1[1]*fH[2] + xH2[1]*fH[2];
+
+ vlist[n++] = i;
+ vlist[n++] = iH1;
+ vlist[n++] = iH2;
+ }
+ }
+
+ if (jtype != typeO) {
+ f[j][0] -= delx * cforce;
+ f[j][1] -= dely * cforce;
+ f[j][2] -= delz * cforce;
+
+ if (vflag) {
+ v[0] -= x[j][0] * delx * cforce;
+ v[1] -= x[j][1] * dely * cforce;
+ v[2] -= x[j][2] * delz * cforce;
+ v[3] -= x[j][0] * dely * cforce;
+ v[4] -= x[j][0] * delz * cforce;
+ v[5] -= x[j][1] * delz * cforce;
+ vlist[n++] = j;
+ }
+
+ } else {
+
+ fd[0] = -delx*cforce;
+ fd[1] = -dely*cforce;
+ fd[2] = -delz*cforce;
+
+ delxOM = x[j][0] - x2[0];
+ delyOM = x[j][1] - x2[1];
+ delzOM = x[j][2] - x2[2];
+
+ ddotf = (delxOM * fd[0] + delyOM * fd[1] + delzOM * fd[2]) /
+ (qdist*qdist);
+
+ f1[0] = ddotf * delxOM;
+ f1[1] = ddotf * delyOM;
+ f1[2] = ddotf * delzOM;
+
+ fO[0] = fd[0] - alpha * (fd[0] - f1[0]);
+ fO[1] = fd[1] - alpha * (fd[1] - f1[1]);
+ fO[2] = fd[2] - alpha * (fd[2] - f1[2]);
+
+ fH[0] = 0.5 * alpha * (fd[0] - f1[0]);
+ fH[1] = 0.5 * alpha * (fd[1] - f1[1]);
+ fH[2] = 0.5 * alpha * (fd[2] - f1[2]);
+
+ f[j][0] += fO[0];
+ f[j][1] += fO[1];
+ f[j][2] += fO[2];
+
+ f[jH1][0] += fH[0];
+ f[jH1][1] += fH[1];
+ f[jH1][2] += fH[2];
+
+ f[jH2][0] += fH[0];
+ f[jH2][1] += fH[1];
+ f[jH2][2] += fH[2];
+
+ if (vflag) {
+ domain->closest_image(x[j],x[jH1],xH1);
+ domain->closest_image(x[j],x[jH2],xH2);
+
+ v[0] += x[j][0]*fO[0] + xH1[0]*fH[0] + xH2[0]*fH[0];
+ v[1] += x[j][1]*fO[1] + xH1[1]*fH[1] + xH2[1]*fH[1];
+ v[2] += x[j][2]*fO[2] + xH1[2]*fH[2] + xH2[2]*fH[2];
+ v[3] += x[j][0]*fO[1] + xH1[0]*fH[1] + xH2[0]*fH[1];
+ v[4] += x[j][0]*fO[2] + xH1[0]*fH[2] + xH2[0]*fH[2];
+ v[5] += x[j][1]*fO[2] + xH1[1]*fH[2] + xH2[1]*fH[2];
+
+ vlist[n++] = j;
+ vlist[n++] = jH1;
+ vlist[n++] = jH2;
+ }
+ }
+
+ if (eflag) {
+ if (!ncoultablebits || rsq <= tabinnersq)
+ ecoul = prefactor*erfc;
+ else {
+ table = etable[itable] + fraction*detable[itable];
+ ecoul = qtmp*q[j] * table;
+ }
+ if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
+ } else ecoul = 0.0;
+
+ if (evflag) ev_tally_list(n,vlist,ecoul,v);
+ }
}
}
}
- //if (comm->me == 0 && update->ntimestep == update->laststep)
+ //if (comm->me == 0 && update->ntimestep == update->laststep)
// printf("Count %ld %d\n",update->ntimestep,count);
}
@@ -383,14 +383,14 @@ void PairLJCutCoulLongTIP4P::settings(int narg, char **arg)
cut_lj_global = force->numeric(arg[5]);
if (narg == 6) cut_coul = cut_lj_global;
else cut_coul = force->numeric(arg[6]);
-
+
// reset cutoffs that have been explicitly set
if (allocated) {
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
- if (setflag[i][j]) cut_lj[i][j] = cut_lj_global;
+ if (setflag[i][j]) cut_lj[i][j] = cut_lj_global;
}
}
@@ -404,12 +404,12 @@ void PairLJCutCoulLongTIP4P::init_style()
if (atom->tag_enable == 0)
error->all(FLERR,"Pair style lj/cut/coul/long/tip4p requires atom IDs");
- if (!force->newton_pair)
+ if (!force->newton_pair)
error->all(FLERR,
- "Pair style lj/cut/coul/long/tip4p requires newton pair on");
+ "Pair style lj/cut/coul/long/tip4p requires newton pair on");
if (!atom->q_flag)
error->all(FLERR,
- "Pair style lj/cut/coul/long/tip4p requires atom attribute q");
+ "Pair style lj/cut/coul/long/tip4p requires atom attribute q");
if ( (strcmp(force->kspace_style,"pppm/tip4p") != 0) &&
(strcmp(force->kspace_style,"pppm/tip4p/omp") != 0) &&
(strcmp(force->kspace_style,"pppm/tip4p/proxy") != 0) )
@@ -495,7 +495,7 @@ void PairLJCutCoulLongTIP4P::find_M(int i, int &iH1, int &iH2, double *xM)
if (atom->type[iH1] != typeH || atom->type[iH2] != typeH)
error->one(FLERR,"TIP4P hydrogen has incorrect atom type");
- double **x = atom->x;
+ double **x = atom->x;
double delx1 = x[iH1][0] - x[i][0];
double dely1 = x[iH1][1] - x[i][1];
diff --git a/src/KSPACE/pair_lj_cut_coul_long_tip4p.h b/src/KSPACE/pair_lj_cut_coul_long_tip4p.h
index 674f66361c8a2605fbbc79901d6b769d4183368e..4d61be8d228b774365665b1a64f8245af19e1f14 100644
--- a/src/KSPACE/pair_lj_cut_coul_long_tip4p.h
+++ b/src/KSPACE/pair_lj_cut_coul_long_tip4p.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/KSPACE/pppm.cpp b/src/KSPACE/pppm.cpp
index 8c70c87775034d50d789f1edbc5dfe2311904c8a..560389b1fa7edb3de1ee65ca5863ac0e63a3eb40 100644
--- a/src/KSPACE/pppm.cpp
+++ b/src/KSPACE/pppm.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -97,7 +97,7 @@ PPPM::PPPM(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg)
}
/* ----------------------------------------------------------------------
- free all memory
+ free all memory
------------------------------------------------------------------------- */
PPPM::~PPPM()
@@ -110,7 +110,7 @@ PPPM::~PPPM()
}
/* ----------------------------------------------------------------------
- called once before run
+ called once before run
------------------------------------------------------------------------- */
void PPPM::init()
@@ -125,15 +125,15 @@ void PPPM::init()
if (domain->triclinic)
error->all(FLERR,"Cannot (yet) use PPPM with triclinic box");
if (domain->dimension == 2) error->all(FLERR,
- "Cannot use PPPM with 2d simulation");
+ "Cannot use PPPM with 2d simulation");
if (!atom->q_flag) error->all(FLERR,"Kspace style requires atom attribute q");
if (slabflag == 0 && domain->nonperiodic > 0)
error->all(FLERR,"Cannot use nonperiodic boundaries with PPPM");
if (slabflag == 1) {
- if (domain->xperiodic != 1 || domain->yperiodic != 1 ||
- domain->boundary[2][0] != 1 || domain->boundary[2][1] != 1)
+ if (domain->xperiodic != 1 || domain->yperiodic != 1 ||
+ domain->boundary[2][0] != 1 || domain->boundary[2][1] != 1)
error->all(FLERR,"Incorrect boundaries with slab PPPM");
}
@@ -187,11 +187,11 @@ void PPPM::init()
if (force->angle == NULL || force->bond == NULL)
error->all(FLERR,"Bond and angle potentials must be defined for TIP4P");
- if (typeA < 1 || typeA > atom->nangletypes ||
- force->angle->setflag[typeA] == 0)
+ if (typeA < 1 || typeA > atom->nangletypes ||
+ force->angle->setflag[typeA] == 0)
error->all(FLERR,"Bad TIP4P angle type for PPPM/TIP4P");
- if (typeB < 1 || typeB > atom->nbondtypes ||
- force->bond->setflag[typeB] == 0)
+ if (typeB < 1 || typeB > atom->nbondtypes ||
+ force->bond->setflag[typeB] == 0)
error->all(FLERR,"Bad TIP4P bond type for PPPM/TIP4P");
double theta = force->angle->equilibrium_angle(typeA);
double blen = force->bond->equilibrium_distance(typeB);
@@ -231,10 +231,10 @@ void PPPM::init()
}
// set accuracy (force units) from accuracy_relative or accuracy_absolute
-
+
if (accuracy_absolute >= 0.0) accuracy = accuracy_absolute;
else accuracy = accuracy_relative * two_charge_force;
-
+
// setup FFT grid resolution and g_ewald
// normally one iteration thru while loop is all that is required
// if grid stencil extends beyond neighbor proc, reduce order and try again
@@ -244,7 +244,7 @@ void PPPM::init()
while (order > 1) {
if (iteration && me == 0)
error->warning(FLERR,"Reducing PPPM order b/c stencil extends "
- "beyond neighbor processor");
+ "beyond neighbor processor");
iteration++;
set_grid();
@@ -263,9 +263,9 @@ void PPPM::init()
nylo_in = static_cast<int> (comm->ysplit[comm->myloc[1]] * ny_pppm);
nyhi_in = static_cast<int> (comm->ysplit[comm->myloc[1]+1] * ny_pppm) - 1;
- nzlo_in = static_cast<int>
+ nzlo_in = static_cast<int>
(comm->zsplit[comm->myloc[2]] * nz_pppm/slab_volfactor);
- nzhi_in = static_cast<int>
+ nzhi_in = static_cast<int>
(comm->zsplit[comm->myloc[2]+1] * nz_pppm/slab_volfactor) - 1;
// nlower,nupper = stencil size for mapping particles to PPPM grid
@@ -320,27 +320,27 @@ void PPPM::init()
dist[1] = cuthalf/domain->prd[1];
dist[2] = cuthalf/domain->prd[2];
}
-
+
int nlo,nhi;
-
- nlo = static_cast<int> ((sublo[0]-dist[0]-boxlo[0]) *
- nx_pppm/xprd + shift) - OFFSET;
- nhi = static_cast<int> ((subhi[0]+dist[0]-boxlo[0]) *
- nx_pppm/xprd + shift) - OFFSET;
+
+ nlo = static_cast<int> ((sublo[0]-dist[0]-boxlo[0]) *
+ nx_pppm/xprd + shift) - OFFSET;
+ nhi = static_cast<int> ((subhi[0]+dist[0]-boxlo[0]) *
+ nx_pppm/xprd + shift) - OFFSET;
nxlo_out = nlo + nlower;
nxhi_out = nhi + nupper;
- nlo = static_cast<int> ((sublo[1]-dist[1]-boxlo[1]) *
- ny_pppm/yprd + shift) - OFFSET;
- nhi = static_cast<int> ((subhi[1]+dist[1]-boxlo[1]) *
- ny_pppm/yprd + shift) - OFFSET;
+ nlo = static_cast<int> ((sublo[1]-dist[1]-boxlo[1]) *
+ ny_pppm/yprd + shift) - OFFSET;
+ nhi = static_cast<int> ((subhi[1]+dist[1]-boxlo[1]) *
+ ny_pppm/yprd + shift) - OFFSET;
nylo_out = nlo + nlower;
nyhi_out = nhi + nupper;
- nlo = static_cast<int> ((sublo[2]-dist[2]-boxlo[2]) *
- nz_pppm/zprd_slab + shift) - OFFSET;
- nhi = static_cast<int> ((subhi[2]+dist[2]-boxlo[2]) *
- nz_pppm/zprd_slab + shift) - OFFSET;
+ nlo = static_cast<int> ((sublo[2]-dist[2]-boxlo[2]) *
+ nz_pppm/zprd_slab + shift) - OFFSET;
+ nhi = static_cast<int> ((subhi[2]+dist[2]-boxlo[2]) *
+ nz_pppm/zprd_slab + shift) - OFFSET;
nzlo_out = nlo + nlower;
nzhi_out = nhi + nupper;
@@ -355,7 +355,7 @@ void PPPM::init()
nzhi_in = nz_pppm - 1;
nzhi_out = nz_pppm - 1;
}
-
+
// nlo_ghost,nhi_ghost = # of planes I will recv from 6 directions
// that overlay domain I own
// proc in that direction tells me via sendrecv()
@@ -367,43 +367,43 @@ void PPPM::init()
nplanes = nxlo_in - nxlo_out;
if (comm->procneigh[0][0] != me)
MPI_Sendrecv(&nplanes,1,MPI_INT,comm->procneigh[0][0],0,
- &nxhi_ghost,1,MPI_INT,comm->procneigh[0][1],0,
- world,&status);
+ &nxhi_ghost,1,MPI_INT,comm->procneigh[0][1],0,
+ world,&status);
else nxhi_ghost = nplanes;
nplanes = nxhi_out - nxhi_in;
if (comm->procneigh[0][1] != me)
MPI_Sendrecv(&nplanes,1,MPI_INT,comm->procneigh[0][1],0,
- &nxlo_ghost,1,MPI_INT,comm->procneigh[0][0],
- 0,world,&status);
+ &nxlo_ghost,1,MPI_INT,comm->procneigh[0][0],
+ 0,world,&status);
else nxlo_ghost = nplanes;
nplanes = nylo_in - nylo_out;
if (comm->procneigh[1][0] != me)
MPI_Sendrecv(&nplanes,1,MPI_INT,comm->procneigh[1][0],0,
- &nyhi_ghost,1,MPI_INT,comm->procneigh[1][1],0,
- world,&status);
+ &nyhi_ghost,1,MPI_INT,comm->procneigh[1][1],0,
+ world,&status);
else nyhi_ghost = nplanes;
nplanes = nyhi_out - nyhi_in;
if (comm->procneigh[1][1] != me)
MPI_Sendrecv(&nplanes,1,MPI_INT,comm->procneigh[1][1],0,
- &nylo_ghost,1,MPI_INT,comm->procneigh[1][0],0,
- world,&status);
+ &nylo_ghost,1,MPI_INT,comm->procneigh[1][0],0,
+ world,&status);
else nylo_ghost = nplanes;
nplanes = nzlo_in - nzlo_out;
if (comm->procneigh[2][0] != me)
MPI_Sendrecv(&nplanes,1,MPI_INT,comm->procneigh[2][0],0,
- &nzhi_ghost,1,MPI_INT,comm->procneigh[2][1],0,
- world,&status);
+ &nzhi_ghost,1,MPI_INT,comm->procneigh[2][1],0,
+ world,&status);
else nzhi_ghost = nplanes;
nplanes = nzhi_out - nzhi_in;
if (comm->procneigh[2][1] != me)
MPI_Sendrecv(&nplanes,1,MPI_INT,comm->procneigh[2][1],0,
- &nzlo_ghost,1,MPI_INT,comm->procneigh[2][0],0,
- world,&status);
+ &nzlo_ghost,1,MPI_INT,comm->procneigh[2][0],0,
+ world,&status);
else nzlo_ghost = nplanes;
// test that ghost overlap is not bigger than my sub-domain
@@ -510,9 +510,9 @@ void PPPM::init()
if (me == 0) {
if (screen) fprintf(screen," brick FFT buffer size/proc = %d %d %d\n",
- ngrid_max,nfft_both_max,nbuf_max);
+ ngrid_max,nfft_both_max,nbuf_max);
if (logfile) fprintf(logfile," brick FFT buffer size/proc = %d %d %d\n",
- ngrid_max,nfft_both_max,nbuf_max);
+ ngrid_max,nfft_both_max,nbuf_max);
}
// allocate K-space dependent memory
@@ -528,7 +528,7 @@ void PPPM::init()
}
/* ----------------------------------------------------------------------
- adjust PPPM coeffs, called initially and whenever volume has changed
+ adjust PPPM coeffs, called initially and whenever volume has changed
------------------------------------------------------------------------- */
void PPPM::setup()
@@ -548,7 +548,7 @@ void PPPM::setup()
double zprd = prd[2];
double zprd_slab = zprd*slab_volfactor;
volume = xprd * yprd * zprd_slab;
-
+
delxinv = nx_pppm/xprd;
delyinv = ny_pppm/yprd;
delzinv = nz_pppm/zprd_slab;
@@ -586,24 +586,24 @@ void PPPM::setup()
for (k = nzlo_fft; k <= nzhi_fft; k++) {
for (j = nylo_fft; j <= nyhi_fft; j++) {
for (i = nxlo_fft; i <= nxhi_fft; i++) {
- sqk = fkx[i]*fkx[i] + fky[j]*fky[j] + fkz[k]*fkz[k];
- if (sqk == 0.0) {
- vg[n][0] = 0.0;
- vg[n][1] = 0.0;
- vg[n][2] = 0.0;
- vg[n][3] = 0.0;
- vg[n][4] = 0.0;
- vg[n][5] = 0.0;
- } else {
- vterm = -2.0 * (1.0/sqk + 0.25/(g_ewald*g_ewald));
- vg[n][0] = 1.0 + vterm*fkx[i]*fkx[i];
- vg[n][1] = 1.0 + vterm*fky[j]*fky[j];
- vg[n][2] = 1.0 + vterm*fkz[k]*fkz[k];
- vg[n][3] = vterm*fkx[i]*fky[j];
- vg[n][4] = vterm*fkx[i]*fkz[k];
- vg[n][5] = vterm*fky[j]*fkz[k];
- }
- n++;
+ sqk = fkx[i]*fkx[i] + fky[j]*fky[j] + fkz[k]*fkz[k];
+ if (sqk == 0.0) {
+ vg[n][0] = 0.0;
+ vg[n][1] = 0.0;
+ vg[n][2] = 0.0;
+ vg[n][3] = 0.0;
+ vg[n][4] = 0.0;
+ vg[n][5] = 0.0;
+ } else {
+ vterm = -2.0 * (1.0/sqk + 0.25/(g_ewald*g_ewald));
+ vg[n][0] = 1.0 + vterm*fkx[i]*fkx[i];
+ vg[n][1] = 1.0 + vterm*fky[j]*fky[j];
+ vg[n][2] = 1.0 + vterm*fkz[k]*fkz[k];
+ vg[n][3] = vterm*fkx[i]*fky[j];
+ vg[n][4] = vterm*fkx[i]*fkz[k];
+ vg[n][5] = vterm*fky[j]*fkz[k];
+ }
+ n++;
}
}
}
@@ -616,12 +616,12 @@ void PPPM::setup()
double sum1,dot1,dot2;
double numerator,denominator;
- int nbx = static_cast<int> ((g_ewald*xprd/(MY_PI*nx_pppm)) *
- pow(-log(EPS_HOC),0.25));
- int nby = static_cast<int> ((g_ewald*yprd/(MY_PI*ny_pppm)) *
- pow(-log(EPS_HOC),0.25));
- int nbz = static_cast<int> ((g_ewald*zprd_slab/(MY_PI*nz_pppm)) *
- pow(-log(EPS_HOC),0.25));
+ int nbx = static_cast<int> ((g_ewald*xprd/(MY_PI*nx_pppm)) *
+ pow(-log(EPS_HOC),0.25));
+ int nby = static_cast<int> ((g_ewald*yprd/(MY_PI*ny_pppm)) *
+ pow(-log(EPS_HOC),0.25));
+ int nbz = static_cast<int> ((g_ewald*zprd_slab/(MY_PI*nz_pppm)) *
+ pow(-log(EPS_HOC),0.25));
double form = 1.0;
@@ -637,52 +637,52 @@ void PPPM::setup()
sny2 = sny*sny;
for (k = nxlo_fft; k <= nxhi_fft; k++) {
- kper = k - nx_pppm*(2*k/nx_pppm);
- snx = sin(0.5*unitkx*kper*xprd/nx_pppm);
- snx2 = snx*snx;
-
- sqk = pow(unitkx*kper,2.0) + pow(unitky*lper,2.0) +
- pow(unitkz*mper,2.0);
-
- if (sqk != 0.0) {
- numerator = form*12.5663706/sqk;
- denominator = gf_denom(snx2,sny2,snz2);
- sum1 = 0.0;
+ kper = k - nx_pppm*(2*k/nx_pppm);
+ snx = sin(0.5*unitkx*kper*xprd/nx_pppm);
+ snx2 = snx*snx;
+
+ sqk = pow(unitkx*kper,2.0) + pow(unitky*lper,2.0) +
+ pow(unitkz*mper,2.0);
+
+ if (sqk != 0.0) {
+ numerator = form*12.5663706/sqk;
+ denominator = gf_denom(snx2,sny2,snz2);
+ sum1 = 0.0;
const double dorder = static_cast<double>(order);
- for (nx = -nbx; nx <= nbx; nx++) {
- qx = unitkx*(kper+nx_pppm*nx);
- sx = exp(-0.25*pow(qx/g_ewald,2.0));
- wx = 1.0;
- argx = 0.5*qx*xprd/nx_pppm;
- if (argx != 0.0) wx = pow(sin(argx)/argx,dorder);
- for (ny = -nby; ny <= nby; ny++) {
- qy = unitky*(lper+ny_pppm*ny);
- sy = exp(-0.25*pow(qy/g_ewald,2.0));
- wy = 1.0;
- argy = 0.5*qy*yprd/ny_pppm;
- if (argy != 0.0) wy = pow(sin(argy)/argy,dorder);
- for (nz = -nbz; nz <= nbz; nz++) {
- qz = unitkz*(mper+nz_pppm*nz);
- sz = exp(-0.25*pow(qz/g_ewald,2.0));
- wz = 1.0;
- argz = 0.5*qz*zprd_slab/nz_pppm;
- if (argz != 0.0) wz = pow(sin(argz)/argz,dorder);
-
- dot1 = unitkx*kper*qx + unitky*lper*qy + unitkz*mper*qz;
- dot2 = qx*qx+qy*qy+qz*qz;
- sum1 += (dot1/dot2) * sx*sy*sz * pow(wx*wy*wz,2.0);
- }
- }
- }
- greensfn[n++] = numerator*sum1/denominator;
- } else greensfn[n++] = 0.0;
+ for (nx = -nbx; nx <= nbx; nx++) {
+ qx = unitkx*(kper+nx_pppm*nx);
+ sx = exp(-0.25*pow(qx/g_ewald,2.0));
+ wx = 1.0;
+ argx = 0.5*qx*xprd/nx_pppm;
+ if (argx != 0.0) wx = pow(sin(argx)/argx,dorder);
+ for (ny = -nby; ny <= nby; ny++) {
+ qy = unitky*(lper+ny_pppm*ny);
+ sy = exp(-0.25*pow(qy/g_ewald,2.0));
+ wy = 1.0;
+ argy = 0.5*qy*yprd/ny_pppm;
+ if (argy != 0.0) wy = pow(sin(argy)/argy,dorder);
+ for (nz = -nbz; nz <= nbz; nz++) {
+ qz = unitkz*(mper+nz_pppm*nz);
+ sz = exp(-0.25*pow(qz/g_ewald,2.0));
+ wz = 1.0;
+ argz = 0.5*qz*zprd_slab/nz_pppm;
+ if (argz != 0.0) wz = pow(sin(argz)/argz,dorder);
+
+ dot1 = unitkx*kper*qx + unitky*lper*qy + unitkz*mper*qz;
+ dot2 = qx*qx+qy*qy+qz*qz;
+ sum1 += (dot1/dot2) * sx*sy*sz * pow(wx*wy*wz,2.0);
+ }
+ }
+ }
+ greensfn[n++] = numerator*sum1/denominator;
+ } else greensfn[n++] = 0.0;
}
}
}
}
/* ----------------------------------------------------------------------
- compute the PPPM long-range force, energy, virial
+ compute the PPPM long-range force, energy, virial
------------------------------------------------------------------------- */
void PPPM::compute(int eflag, int vflag)
@@ -693,8 +693,8 @@ void PPPM::compute(int eflag, int vflag)
// invoke allocate_peratom() if needed for first time
if (eflag || vflag) ev_setup(eflag,vflag);
- else evflag = evflag_atom = eflag_global = vflag_global =
- eflag_atom = vflag_atom = 0;
+ else evflag = evflag_atom = eflag_global = vflag_global =
+ eflag_atom = vflag_atom = 0;
if (evflag_atom && !peratom_allocate_flag) {
allocate_peratom();
@@ -702,7 +702,7 @@ void PPPM::compute(int eflag, int vflag)
}
// convert atoms from box to lamda coords
-
+
if (triclinic == 0) boxlo = domain->boxlo;
else {
boxlo = domain->boxlo_lamda;
@@ -761,7 +761,7 @@ void PPPM::compute(int eflag, int vflag)
double energy_all;
MPI_Allreduce(&energy,&energy_all,1,MPI_DOUBLE,MPI_SUM,world);
energy = energy_all;
-
+
energy *= 0.5*volume;
energy -= g_ewald*qsqsum/MY_PIS +
MY_PI2*qsum*qsum / (g_ewald*g_ewald*volume);
@@ -785,9 +785,9 @@ void PPPM::compute(int eflag, int vflag)
if (eflag_atom) {
for (i = 0; i < nlocal; i++) {
- eatom[i] *= 0.5;
- eatom[i] -= g_ewald*q[i]*q[i]/MY_PIS + MY_PI2*q[i]*qsum /
- (g_ewald*g_ewald*volume);
+ eatom[i] *= 0.5;
+ eatom[i] -= g_ewald*q[i]*q[i]/MY_PIS + MY_PI2*q[i]*qsum /
+ (g_ewald*g_ewald*volume);
eatom[i] *= qscale;
}
}
@@ -803,24 +803,24 @@ void PPPM::compute(int eflag, int vflag)
if (slabflag) slabcorr();
// convert atoms back from lamda to box coords
-
+
if (triclinic) domain->lamda2x(atom->nlocal);
}
/* ----------------------------------------------------------------------
- allocate memory that depends on # of K-vectors and order
+ allocate memory that depends on # of K-vectors and order
------------------------------------------------------------------------- */
void PPPM::allocate()
{
memory->create3d_offset(density_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
- nxlo_out,nxhi_out,"pppm:density_brick");
+ nxlo_out,nxhi_out,"pppm:density_brick");
memory->create3d_offset(vdx_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
- nxlo_out,nxhi_out,"pppm:vdx_brick");
+ nxlo_out,nxhi_out,"pppm:vdx_brick");
memory->create3d_offset(vdy_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
- nxlo_out,nxhi_out,"pppm:vdy_brick");
+ nxlo_out,nxhi_out,"pppm:vdy_brick");
memory->create3d_offset(vdz_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
- nxlo_out,nxhi_out,"pppm:vdz_brick");
+ nxlo_out,nxhi_out,"pppm:vdz_brick");
memory->create(density_fft,nfft_both,"pppm:density_fft");
memory->create(greensfn,nfft_both,"pppm:greensfn");
@@ -849,49 +849,49 @@ void PPPM::allocate()
int tmp;
fft1 = new FFT3d(lmp,world,nx_pppm,ny_pppm,nz_pppm,
- nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
- nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
- 0,0,&tmp);
+ nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
+ nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
+ 0,0,&tmp);
fft2 = new FFT3d(lmp,world,nx_pppm,ny_pppm,nz_pppm,
- nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
- nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in,
- 0,0,&tmp);
+ nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
+ nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in,
+ 0,0,&tmp);
remap = new Remap(lmp,world,
- nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in,
- nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
- 1,0,0,FFT_PRECISION);
+ nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in,
+ nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
+ 1,0,0,FFT_PRECISION);
}
/* ----------------------------------------------------------------------
- allocate per-atom memory that depends on # of K-vectors and order
+ allocate per-atom memory that depends on # of K-vectors and order
------------------------------------------------------------------------- */
void PPPM::allocate_peratom()
-{
+{
memory->create3d_offset(u_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
- nxlo_out,nxhi_out,"pppm:u_brick");
-
+ nxlo_out,nxhi_out,"pppm:u_brick");
+
memory->create3d_offset(v0_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
- nxlo_out,nxhi_out,"pppm:v0_brick");
+ nxlo_out,nxhi_out,"pppm:v0_brick");
memory->create3d_offset(v1_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
- nxlo_out,nxhi_out,"pppm:v1_brick");
+ nxlo_out,nxhi_out,"pppm:v1_brick");
memory->create3d_offset(v2_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
- nxlo_out,nxhi_out,"pppm:v2_brick");
+ nxlo_out,nxhi_out,"pppm:v2_brick");
memory->create3d_offset(v3_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
- nxlo_out,nxhi_out,"pppm:v3_brick");
+ nxlo_out,nxhi_out,"pppm:v3_brick");
memory->create3d_offset(v4_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
- nxlo_out,nxhi_out,"pppm:v4_brick");
+ nxlo_out,nxhi_out,"pppm:v4_brick");
memory->create3d_offset(v5_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
- nxlo_out,nxhi_out,"pppm:v5_brick");
+ nxlo_out,nxhi_out,"pppm:v5_brick");
memory->create(buf3,nbuf_peratom,"pppm:buf3");
memory->create(buf4,nbuf_peratom,"pppm:buf4");
}
/* ----------------------------------------------------------------------
- deallocate memory that depends on # of K-vectors and order
+ deallocate memory that depends on # of K-vectors and order
------------------------------------------------------------------------- */
void PPPM::deallocate()
@@ -924,13 +924,13 @@ void PPPM::deallocate()
}
/* ----------------------------------------------------------------------
- deallocate per-atom memory that depends on # of K-vectors and order
+ deallocate per-atom memory that depends on # of K-vectors and order
------------------------------------------------------------------------- */
void PPPM::deallocate_peratom()
{
memory->destroy3d_offset(u_brick,nzlo_out,nylo_out,nxlo_out);
-
+
memory->destroy3d_offset(v0_brick,nzlo_out,nylo_out,nxlo_out);
memory->destroy3d_offset(v1_brick,nzlo_out,nylo_out,nxlo_out);
memory->destroy3d_offset(v2_brick,nzlo_out,nylo_out,nxlo_out);
@@ -939,11 +939,11 @@ void PPPM::deallocate_peratom()
memory->destroy3d_offset(v5_brick,nzlo_out,nylo_out,nxlo_out);
memory->destroy(buf3);
- memory->destroy(buf4);
+ memory->destroy(buf4);
}
/* ----------------------------------------------------------------------
- set size of FFT grid (nx,ny,nz_pppm) and g_ewald
+ set size of FFT grid (nx,ny,nz_pppm) and g_ewald
------------------------------------------------------------------------- */
void PPPM::set_grid()
@@ -993,7 +993,7 @@ void PPPM::set_grid()
double yprd = domain->yprd;
double zprd = domain->zprd;
double zprd_slab = zprd*slab_volfactor;
-
+
// make initial g_ewald estimate
// based on desired accuracy and real space cutoff
// fluid-occupied volume used to estimate real-space error
@@ -1007,7 +1007,7 @@ void PPPM::set_grid()
if (g_ewald >= 1.0)
error->all(FLERR,"KSpace accuracy too large to estimate G vector");
g_ewald = sqrt(-log(g_ewald)) / cutoff;
- }
+ }
// set optimal nx_pppm,ny_pppm,nz_pppm based on order and accuracy
// nz_pppm uses extended zprd_slab instead of zprd
@@ -1016,7 +1016,7 @@ void PPPM::set_grid()
if (!gridflag) {
double err;
- h_x = h_y = h_z = 1.0/g_ewald;
+ h_x = h_y = h_z = 1.0/g_ewald;
nx_pppm = static_cast<int> (xprd/h_x) + 1;
ny_pppm = static_cast<int> (yprd/h_y) + 1;
@@ -1075,7 +1075,7 @@ void PPPM::set_grid()
while (fabs(dgew) > SMALL && fmid != 0.0) {
dgew *= 0.5;
g_ewald = rtb + dgew;
- fmid = diffpr(h_x,h_y,h_z,q2,acons);
+ fmid = diffpr(h_x,h_y,h_z,q2,acons);
if (fmid <= 0.0) rtb = g_ewald;
ncount++;
if (ncount > LARGE) error->all(FLERR,"Cannot compute PPPM G");
@@ -1088,7 +1088,7 @@ void PPPM::set_grid()
double lpry = rms(h_y,yprd,natoms,q2,acons);
double lprz = rms(h_z,zprd_slab,natoms,q2,acons);
double lpr = sqrt(lprx*lprx + lpry*lpry + lprz*lprz) / sqrt(3.0);
- double spr = 2.0*q2 * exp(-g_ewald*g_ewald*cutoff*cutoff) /
+ double spr = 2.0*q2 * exp(-g_ewald*g_ewald*cutoff*cutoff) /
sqrt(natoms*cutoff*xprd*yprd*zprd_slab);
// free local memory
@@ -1108,9 +1108,9 @@ void PPPM::set_grid()
fprintf(screen," grid = %d %d %d\n",nx_pppm,ny_pppm,nz_pppm);
fprintf(screen," stencil order = %d\n",order);
fprintf(screen," estimated absolute RMS force accuracy = %g\n",
- MAX(lpr,spr));
+ MAX(lpr,spr));
fprintf(screen," estimated relative force accuracy = %g\n",
- MAX(lpr,spr)/two_charge_force);
+ MAX(lpr,spr)/two_charge_force);
fprintf(screen," using %s precision FFTs\n",fft_prec);
}
if (logfile) {
@@ -1118,9 +1118,9 @@ void PPPM::set_grid()
fprintf(logfile," grid = %d %d %d\n",nx_pppm,ny_pppm,nz_pppm);
fprintf(logfile," stencil order = %d\n",order);
fprintf(logfile," estimated absolute RMS force accuracy = %g\n",
- MAX(lpr,spr));
+ MAX(lpr,spr));
fprintf(logfile," estimated relative force accuracy = %g\n",
- MAX(lpr,spr)/two_charge_force);
+ MAX(lpr,spr)/two_charge_force);
fprintf(logfile," using %s precision FFTs\n",fft_prec);
}
}
@@ -1128,7 +1128,7 @@ void PPPM::set_grid()
/* ----------------------------------------------------------------------
check if all factors of n are in list of factors
- return 1 if yes, 0 if no
+ return 1 if yes, 0 if no
------------------------------------------------------------------------- */
int PPPM::factorable(int n)
@@ -1138,8 +1138,8 @@ int PPPM::factorable(int n)
while (n > 1) {
for (i = 0; i < nfactors; i++) {
if (n % factors[i] == 0) {
- n /= factors[i];
- break;
+ n /= factors[i];
+ break;
}
}
if (i == nfactors) return 0;
@@ -1153,10 +1153,10 @@ int PPPM::factorable(int n)
------------------------------------------------------------------------- */
double PPPM::rms(double h, double prd, bigint natoms,
- double q2, double **acons)
+ double q2, double **acons)
{
double sum = 0.0;
- for (int m = 0; m < order; m++)
+ for (int m = 0; m < order; m++)
sum += acons[order][m] * pow(h*g_ewald,2.0*m);
double value = q2 * pow(h*g_ewald,(double)order) *
sqrt(g_ewald*prd*sqrt(2.0*MY_PI)*sum/natoms) / (prd*prd);
@@ -1167,8 +1167,8 @@ double PPPM::rms(double h, double prd, bigint natoms,
compute difference in real-space and KSpace RMS accuracy
------------------------------------------------------------------------- */
-double PPPM::diffpr(double h_x, double h_y, double h_z, double q2,
- double **acons)
+double PPPM::diffpr(double h_x, double h_y, double h_z, double q2,
+ double **acons)
{
double lprx,lpry,lprz,kspace_prec,real_prec;
double xprd = domain->xprd;
@@ -1180,25 +1180,25 @@ double PPPM::diffpr(double h_x, double h_y, double h_z, double q2,
lpry = rms(h_y,yprd,natoms,q2,acons);
lprz = rms(h_z,zprd*slab_volfactor,natoms,q2,acons);
kspace_prec = sqrt(lprx*lprx + lpry*lpry + lprz*lprz) / sqrt(3.0);
- real_prec = 2.0*q2 * exp(-g_ewald*g_ewald*cutoff*cutoff) /
+ real_prec = 2.0*q2 * exp(-g_ewald*g_ewald*cutoff*cutoff) /
sqrt(static_cast<double>(natoms)*cutoff*xprd*yprd*zprd);
double value = kspace_prec - real_prec;
return value;
}
/* ----------------------------------------------------------------------
- pre-compute Green's function denominator expansion coeffs, Gamma(2n)
+ pre-compute Green's function denominator expansion coeffs, Gamma(2n)
------------------------------------------------------------------------- */
void PPPM::compute_gf_denom()
{
int k,l,m;
-
+
for (l = 1; l < order; l++) gf_b[l] = 0.0;
gf_b[0] = 1.0;
-
+
for (m = 1; m < order; m++) {
- for (l = m; l > 0; l--)
+ for (l = m; l > 0; l--)
gf_b[l] = 4.0 * (gf_b[l]*(l-m)*(l-m-0.5)-gf_b[l-1]*(l-m-1)*(l-m-1));
gf_b[0] = 4.0 * (gf_b[0]*(l-m)*(l-m-0.5));
}
@@ -1210,7 +1210,7 @@ void PPPM::compute_gf_denom()
}
/* ----------------------------------------------------------------------
- ghost-swap to accumulate full density in brick decomposition
+ ghost-swap to accumulate full density in brick decomposition
remap density from 3d brick decomposition to FFT decomposition
------------------------------------------------------------------------- */
@@ -1228,7 +1228,7 @@ void PPPM::brick2fft()
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_out; iy <= nyhi_out; iy++)
for (ix = nxhi_in+1; ix <= nxhi_out; ix++)
- buf1[n++] = density_brick[iz][iy][ix];
+ buf1[n++] = density_brick[iz][iy][ix];
if (comm->procneigh[0][1] == me)
for (i = 0; i < n; i++) buf2[i] = buf1[i];
@@ -1242,7 +1242,7 @@ void PPPM::brick2fft()
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_out; iy <= nyhi_out; iy++)
for (ix = nxlo_in; ix < nxlo_in+nxlo_ghost; ix++)
- density_brick[iz][iy][ix] += buf2[n++];
+ density_brick[iz][iy][ix] += buf2[n++];
// pack my ghosts for -x processor
// pass data to self or -x processor
@@ -1252,7 +1252,7 @@ void PPPM::brick2fft()
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_out; iy <= nyhi_out; iy++)
for (ix = nxlo_out; ix < nxlo_in; ix++)
- buf1[n++] = density_brick[iz][iy][ix];
+ buf1[n++] = density_brick[iz][iy][ix];
if (comm->procneigh[0][0] == me)
for (i = 0; i < n; i++) buf2[i] = buf1[i];
@@ -1266,7 +1266,7 @@ void PPPM::brick2fft()
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_out; iy <= nyhi_out; iy++)
for (ix = nxhi_in-nxhi_ghost+1; ix <= nxhi_in; ix++)
- density_brick[iz][iy][ix] += buf2[n++];
+ density_brick[iz][iy][ix] += buf2[n++];
// pack my ghosts for +y processor
// pass data to self or +y processor
@@ -1276,7 +1276,7 @@ void PPPM::brick2fft()
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nyhi_in+1; iy <= nyhi_out; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++)
- buf1[n++] = density_brick[iz][iy][ix];
+ buf1[n++] = density_brick[iz][iy][ix];
if (comm->procneigh[1][1] == me)
for (i = 0; i < n; i++) buf2[i] = buf1[i];
@@ -1290,7 +1290,7 @@ void PPPM::brick2fft()
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_in; iy < nylo_in+nylo_ghost; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++)
- density_brick[iz][iy][ix] += buf2[n++];
+ density_brick[iz][iy][ix] += buf2[n++];
// pack my ghosts for -y processor
// pass data to self or -y processor
@@ -1300,7 +1300,7 @@ void PPPM::brick2fft()
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_out; iy < nylo_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++)
- buf1[n++] = density_brick[iz][iy][ix];
+ buf1[n++] = density_brick[iz][iy][ix];
if (comm->procneigh[1][0] == me)
for (i = 0; i < n; i++) buf2[i] = buf1[i];
@@ -1314,7 +1314,7 @@ void PPPM::brick2fft()
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nyhi_in-nyhi_ghost+1; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++)
- density_brick[iz][iy][ix] += buf2[n++];
+ density_brick[iz][iy][ix] += buf2[n++];
// pack my ghosts for +z processor
// pass data to self or +z processor
@@ -1324,7 +1324,7 @@ void PPPM::brick2fft()
for (iz = nzhi_in+1; iz <= nzhi_out; iz++)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++)
- buf1[n++] = density_brick[iz][iy][ix];
+ buf1[n++] = density_brick[iz][iy][ix];
if (comm->procneigh[2][1] == me)
for (i = 0; i < n; i++) buf2[i] = buf1[i];
@@ -1338,7 +1338,7 @@ void PPPM::brick2fft()
for (iz = nzlo_in; iz < nzlo_in+nzlo_ghost; iz++)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++)
- density_brick[iz][iy][ix] += buf2[n++];
+ density_brick[iz][iy][ix] += buf2[n++];
// pack my ghosts for -z processor
// pass data to self or -z processor
@@ -1348,7 +1348,7 @@ void PPPM::brick2fft()
for (iz = nzlo_out; iz < nzlo_in; iz++)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++)
- buf1[n++] = density_brick[iz][iy][ix];
+ buf1[n++] = density_brick[iz][iy][ix];
if (comm->procneigh[2][0] == me)
for (i = 0; i < n; i++) buf2[i] = buf1[i];
@@ -1362,7 +1362,7 @@ void PPPM::brick2fft()
for (iz = nzhi_in-nzhi_ghost+1; iz <= nzhi_in; iz++)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++)
- density_brick[iz][iy][ix] += buf2[n++];
+ density_brick[iz][iy][ix] += buf2[n++];
// remap from 3d brick decomposition to FFT decomposition
// copy grabs inner portion of density from 3d brick
@@ -1373,7 +1373,7 @@ void PPPM::brick2fft()
for (iz = nzlo_in; iz <= nzhi_in; iz++)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++)
- density_fft[n++] = density_brick[iz][iy][ix];
+ density_fft[n++] = density_brick[iz][iy][ix];
remap->perform(density_fft,density_fft,work1);
}
@@ -1396,9 +1396,9 @@ void PPPM::fillbrick()
for (iz = nzhi_in-nzhi_ghost+1; iz <= nzhi_in; iz++)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++) {
- buf1[n++] = vdx_brick[iz][iy][ix];
- buf1[n++] = vdy_brick[iz][iy][ix];
- buf1[n++] = vdz_brick[iz][iy][ix];
+ buf1[n++] = vdx_brick[iz][iy][ix];
+ buf1[n++] = vdy_brick[iz][iy][ix];
+ buf1[n++] = vdz_brick[iz][iy][ix];
}
if (comm->procneigh[2][1] == me)
@@ -1413,9 +1413,9 @@ void PPPM::fillbrick()
for (iz = nzlo_out; iz < nzlo_in; iz++)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++) {
- vdx_brick[iz][iy][ix] = buf2[n++];
- vdy_brick[iz][iy][ix] = buf2[n++];
- vdz_brick[iz][iy][ix] = buf2[n++];
+ vdx_brick[iz][iy][ix] = buf2[n++];
+ vdy_brick[iz][iy][ix] = buf2[n++];
+ vdz_brick[iz][iy][ix] = buf2[n++];
}
// pack my real cells for -z processor
@@ -1426,9 +1426,9 @@ void PPPM::fillbrick()
for (iz = nzlo_in; iz < nzlo_in+nzlo_ghost; iz++)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++) {
- buf1[n++] = vdx_brick[iz][iy][ix];
- buf1[n++] = vdy_brick[iz][iy][ix];
- buf1[n++] = vdz_brick[iz][iy][ix];
+ buf1[n++] = vdx_brick[iz][iy][ix];
+ buf1[n++] = vdy_brick[iz][iy][ix];
+ buf1[n++] = vdz_brick[iz][iy][ix];
}
if (comm->procneigh[2][0] == me)
@@ -1443,9 +1443,9 @@ void PPPM::fillbrick()
for (iz = nzhi_in+1; iz <= nzhi_out; iz++)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++) {
- vdx_brick[iz][iy][ix] = buf2[n++];
- vdy_brick[iz][iy][ix] = buf2[n++];
- vdz_brick[iz][iy][ix] = buf2[n++];
+ vdx_brick[iz][iy][ix] = buf2[n++];
+ vdy_brick[iz][iy][ix] = buf2[n++];
+ vdz_brick[iz][iy][ix] = buf2[n++];
}
// pack my real cells for +y processor
@@ -1456,9 +1456,9 @@ void PPPM::fillbrick()
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nyhi_in-nyhi_ghost+1; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++) {
- buf1[n++] = vdx_brick[iz][iy][ix];
- buf1[n++] = vdy_brick[iz][iy][ix];
- buf1[n++] = vdz_brick[iz][iy][ix];
+ buf1[n++] = vdx_brick[iz][iy][ix];
+ buf1[n++] = vdy_brick[iz][iy][ix];
+ buf1[n++] = vdz_brick[iz][iy][ix];
}
if (comm->procneigh[1][1] == me)
@@ -1473,9 +1473,9 @@ void PPPM::fillbrick()
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_out; iy < nylo_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++) {
- vdx_brick[iz][iy][ix] = buf2[n++];
- vdy_brick[iz][iy][ix] = buf2[n++];
- vdz_brick[iz][iy][ix] = buf2[n++];
+ vdx_brick[iz][iy][ix] = buf2[n++];
+ vdy_brick[iz][iy][ix] = buf2[n++];
+ vdz_brick[iz][iy][ix] = buf2[n++];
}
// pack my real cells for -y processor
@@ -1486,9 +1486,9 @@ void PPPM::fillbrick()
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_in; iy < nylo_in+nylo_ghost; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++) {
- buf1[n++] = vdx_brick[iz][iy][ix];
- buf1[n++] = vdy_brick[iz][iy][ix];
- buf1[n++] = vdz_brick[iz][iy][ix];
+ buf1[n++] = vdx_brick[iz][iy][ix];
+ buf1[n++] = vdy_brick[iz][iy][ix];
+ buf1[n++] = vdz_brick[iz][iy][ix];
}
if (comm->procneigh[1][0] == me)
@@ -1503,9 +1503,9 @@ void PPPM::fillbrick()
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nyhi_in+1; iy <= nyhi_out; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++) {
- vdx_brick[iz][iy][ix] = buf2[n++];
- vdy_brick[iz][iy][ix] = buf2[n++];
- vdz_brick[iz][iy][ix] = buf2[n++];
+ vdx_brick[iz][iy][ix] = buf2[n++];
+ vdy_brick[iz][iy][ix] = buf2[n++];
+ vdz_brick[iz][iy][ix] = buf2[n++];
}
// pack my real cells for +x processor
@@ -1516,9 +1516,9 @@ void PPPM::fillbrick()
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_out; iy <= nyhi_out; iy++)
for (ix = nxhi_in-nxhi_ghost+1; ix <= nxhi_in; ix++) {
- buf1[n++] = vdx_brick[iz][iy][ix];
- buf1[n++] = vdy_brick[iz][iy][ix];
- buf1[n++] = vdz_brick[iz][iy][ix];
+ buf1[n++] = vdx_brick[iz][iy][ix];
+ buf1[n++] = vdy_brick[iz][iy][ix];
+ buf1[n++] = vdz_brick[iz][iy][ix];
}
if (comm->procneigh[0][1] == me)
@@ -1533,9 +1533,9 @@ void PPPM::fillbrick()
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_out; iy <= nyhi_out; iy++)
for (ix = nxlo_out; ix < nxlo_in; ix++) {
- vdx_brick[iz][iy][ix] = buf2[n++];
- vdy_brick[iz][iy][ix] = buf2[n++];
- vdz_brick[iz][iy][ix] = buf2[n++];
+ vdx_brick[iz][iy][ix] = buf2[n++];
+ vdy_brick[iz][iy][ix] = buf2[n++];
+ vdz_brick[iz][iy][ix] = buf2[n++];
}
// pack my real cells for -x processor
@@ -1546,9 +1546,9 @@ void PPPM::fillbrick()
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_out; iy <= nyhi_out; iy++)
for (ix = nxlo_in; ix < nxlo_in+nxlo_ghost; ix++) {
- buf1[n++] = vdx_brick[iz][iy][ix];
- buf1[n++] = vdy_brick[iz][iy][ix];
- buf1[n++] = vdz_brick[iz][iy][ix];
+ buf1[n++] = vdx_brick[iz][iy][ix];
+ buf1[n++] = vdy_brick[iz][iy][ix];
+ buf1[n++] = vdz_brick[iz][iy][ix];
}
if (comm->procneigh[0][0] == me)
@@ -1563,9 +1563,9 @@ void PPPM::fillbrick()
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_out; iy <= nyhi_out; iy++)
for (ix = nxhi_in+1; ix <= nxhi_out; ix++) {
- vdx_brick[iz][iy][ix] = buf2[n++];
- vdy_brick[iz][iy][ix] = buf2[n++];
- vdz_brick[iz][iy][ix] = buf2[n++];
+ vdx_brick[iz][iy][ix] = buf2[n++];
+ vdy_brick[iz][iy][ix] = buf2[n++];
+ vdz_brick[iz][iy][ix] = buf2[n++];
}
}
@@ -1587,22 +1587,22 @@ void PPPM::fillbrick_peratom()
for (iz = nzhi_in-nzhi_ghost+1; iz <= nzhi_in; iz++)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++) {
- if (eflag_atom) buf3[n++] = u_brick[iz][iy][ix];
- if (vflag_atom) {
- buf3[n++] = v0_brick[iz][iy][ix];
- buf3[n++] = v1_brick[iz][iy][ix];
- buf3[n++] = v2_brick[iz][iy][ix];
- buf3[n++] = v3_brick[iz][iy][ix];
- buf3[n++] = v4_brick[iz][iy][ix];
- buf3[n++] = v5_brick[iz][iy][ix];
- }
+ if (eflag_atom) buf3[n++] = u_brick[iz][iy][ix];
+ if (vflag_atom) {
+ buf3[n++] = v0_brick[iz][iy][ix];
+ buf3[n++] = v1_brick[iz][iy][ix];
+ buf3[n++] = v2_brick[iz][iy][ix];
+ buf3[n++] = v3_brick[iz][iy][ix];
+ buf3[n++] = v4_brick[iz][iy][ix];
+ buf3[n++] = v5_brick[iz][iy][ix];
+ }
}
if (comm->procneigh[2][1] == me)
for (i = 0; i < n; i++) buf4[i] = buf3[i];
else {
MPI_Irecv(buf4,nbuf_peratom,MPI_FFT_SCALAR,
- comm->procneigh[2][0],0,world,&request);
+ comm->procneigh[2][0],0,world,&request);
MPI_Send(buf3,n,MPI_FFT_SCALAR,comm->procneigh[2][1],0,world);
MPI_Wait(&request,&status);
}
@@ -1611,15 +1611,15 @@ void PPPM::fillbrick_peratom()
for (iz = nzlo_out; iz < nzlo_in; iz++)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++) {
- if (eflag_atom) u_brick[iz][iy][ix] = buf4[n++];
- if (vflag_atom) {
- v0_brick[iz][iy][ix] = buf4[n++];
- v1_brick[iz][iy][ix] = buf4[n++];
- v2_brick[iz][iy][ix] = buf4[n++];
- v3_brick[iz][iy][ix] = buf4[n++];
- v4_brick[iz][iy][ix] = buf4[n++];
- v5_brick[iz][iy][ix] = buf4[n++];
- }
+ if (eflag_atom) u_brick[iz][iy][ix] = buf4[n++];
+ if (vflag_atom) {
+ v0_brick[iz][iy][ix] = buf4[n++];
+ v1_brick[iz][iy][ix] = buf4[n++];
+ v2_brick[iz][iy][ix] = buf4[n++];
+ v3_brick[iz][iy][ix] = buf4[n++];
+ v4_brick[iz][iy][ix] = buf4[n++];
+ v5_brick[iz][iy][ix] = buf4[n++];
+ }
}
// pack my real cells for -z processor
@@ -1630,22 +1630,22 @@ void PPPM::fillbrick_peratom()
for (iz = nzlo_in; iz < nzlo_in+nzlo_ghost; iz++)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++) {
- if (eflag_atom) buf3[n++] = u_brick[iz][iy][ix];
- if (vflag_atom) {
- buf3[n++] = v0_brick[iz][iy][ix];
- buf3[n++] = v1_brick[iz][iy][ix];
- buf3[n++] = v2_brick[iz][iy][ix];
- buf3[n++] = v3_brick[iz][iy][ix];
- buf3[n++] = v4_brick[iz][iy][ix];
- buf3[n++] = v5_brick[iz][iy][ix];
- }
+ if (eflag_atom) buf3[n++] = u_brick[iz][iy][ix];
+ if (vflag_atom) {
+ buf3[n++] = v0_brick[iz][iy][ix];
+ buf3[n++] = v1_brick[iz][iy][ix];
+ buf3[n++] = v2_brick[iz][iy][ix];
+ buf3[n++] = v3_brick[iz][iy][ix];
+ buf3[n++] = v4_brick[iz][iy][ix];
+ buf3[n++] = v5_brick[iz][iy][ix];
+ }
}
if (comm->procneigh[2][0] == me)
for (i = 0; i < n; i++) buf4[i] = buf3[i];
else {
MPI_Irecv(buf4,nbuf_peratom,MPI_FFT_SCALAR,
- comm->procneigh[2][1],0,world,&request);
+ comm->procneigh[2][1],0,world,&request);
MPI_Send(buf3,n,MPI_FFT_SCALAR,comm->procneigh[2][0],0,world);
MPI_Wait(&request,&status);
}
@@ -1654,15 +1654,15 @@ void PPPM::fillbrick_peratom()
for (iz = nzhi_in+1; iz <= nzhi_out; iz++)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++) {
- if (eflag_atom) u_brick[iz][iy][ix] = buf4[n++];
- if (vflag_atom) {
- v0_brick[iz][iy][ix] = buf4[n++];
- v1_brick[iz][iy][ix] = buf4[n++];
- v2_brick[iz][iy][ix] = buf4[n++];
- v3_brick[iz][iy][ix] = buf4[n++];
- v4_brick[iz][iy][ix] = buf4[n++];
- v5_brick[iz][iy][ix] = buf4[n++];
- }
+ if (eflag_atom) u_brick[iz][iy][ix] = buf4[n++];
+ if (vflag_atom) {
+ v0_brick[iz][iy][ix] = buf4[n++];
+ v1_brick[iz][iy][ix] = buf4[n++];
+ v2_brick[iz][iy][ix] = buf4[n++];
+ v3_brick[iz][iy][ix] = buf4[n++];
+ v4_brick[iz][iy][ix] = buf4[n++];
+ v5_brick[iz][iy][ix] = buf4[n++];
+ }
}
// pack my real cells for +y processor
@@ -1673,22 +1673,22 @@ void PPPM::fillbrick_peratom()
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nyhi_in-nyhi_ghost+1; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++) {
- if (eflag_atom) buf3[n++] = u_brick[iz][iy][ix];
- if (vflag_atom) {
- buf3[n++] = v0_brick[iz][iy][ix];
- buf3[n++] = v1_brick[iz][iy][ix];
- buf3[n++] = v2_brick[iz][iy][ix];
- buf3[n++] = v3_brick[iz][iy][ix];
- buf3[n++] = v4_brick[iz][iy][ix];
- buf3[n++] = v5_brick[iz][iy][ix];
- }
+ if (eflag_atom) buf3[n++] = u_brick[iz][iy][ix];
+ if (vflag_atom) {
+ buf3[n++] = v0_brick[iz][iy][ix];
+ buf3[n++] = v1_brick[iz][iy][ix];
+ buf3[n++] = v2_brick[iz][iy][ix];
+ buf3[n++] = v3_brick[iz][iy][ix];
+ buf3[n++] = v4_brick[iz][iy][ix];
+ buf3[n++] = v5_brick[iz][iy][ix];
+ }
}
if (comm->procneigh[1][1] == me)
for (i = 0; i < n; i++) buf4[i] = buf3[i];
else {
MPI_Irecv(buf4,nbuf_peratom,MPI_FFT_SCALAR,
- comm->procneigh[1][0],0,world,&request);
+ comm->procneigh[1][0],0,world,&request);
MPI_Send(buf3,n,MPI_FFT_SCALAR,comm->procneigh[1][1],0,world);
MPI_Wait(&request,&status);
}
@@ -1697,15 +1697,15 @@ void PPPM::fillbrick_peratom()
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_out; iy < nylo_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++) {
- if (eflag_atom) u_brick[iz][iy][ix] = buf4[n++];
- if (vflag_atom) {
- v0_brick[iz][iy][ix] = buf4[n++];
- v1_brick[iz][iy][ix] = buf4[n++];
- v2_brick[iz][iy][ix] = buf4[n++];
- v3_brick[iz][iy][ix] = buf4[n++];
- v4_brick[iz][iy][ix] = buf4[n++];
- v5_brick[iz][iy][ix] = buf4[n++];
- }
+ if (eflag_atom) u_brick[iz][iy][ix] = buf4[n++];
+ if (vflag_atom) {
+ v0_brick[iz][iy][ix] = buf4[n++];
+ v1_brick[iz][iy][ix] = buf4[n++];
+ v2_brick[iz][iy][ix] = buf4[n++];
+ v3_brick[iz][iy][ix] = buf4[n++];
+ v4_brick[iz][iy][ix] = buf4[n++];
+ v5_brick[iz][iy][ix] = buf4[n++];
+ }
}
// pack my real cells for -y processor
@@ -1716,22 +1716,22 @@ void PPPM::fillbrick_peratom()
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_in; iy < nylo_in+nylo_ghost; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++) {
- if (eflag_atom) buf3[n++] = u_brick[iz][iy][ix];
- if (vflag_atom) {
- buf3[n++] = v0_brick[iz][iy][ix];
- buf3[n++] = v1_brick[iz][iy][ix];
- buf3[n++] = v2_brick[iz][iy][ix];
- buf3[n++] = v3_brick[iz][iy][ix];
- buf3[n++] = v4_brick[iz][iy][ix];
- buf3[n++] = v5_brick[iz][iy][ix];
- }
+ if (eflag_atom) buf3[n++] = u_brick[iz][iy][ix];
+ if (vflag_atom) {
+ buf3[n++] = v0_brick[iz][iy][ix];
+ buf3[n++] = v1_brick[iz][iy][ix];
+ buf3[n++] = v2_brick[iz][iy][ix];
+ buf3[n++] = v3_brick[iz][iy][ix];
+ buf3[n++] = v4_brick[iz][iy][ix];
+ buf3[n++] = v5_brick[iz][iy][ix];
+ }
}
if (comm->procneigh[1][0] == me)
for (i = 0; i < n; i++) buf4[i] = buf3[i];
else {
MPI_Irecv(buf4,nbuf_peratom,MPI_FFT_SCALAR,
- comm->procneigh[1][1],0,world,&request);
+ comm->procneigh[1][1],0,world,&request);
MPI_Send(buf3,n,MPI_FFT_SCALAR,comm->procneigh[1][0],0,world);
MPI_Wait(&request,&status);
}
@@ -1740,15 +1740,15 @@ void PPPM::fillbrick_peratom()
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nyhi_in+1; iy <= nyhi_out; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++) {
- if (eflag_atom) u_brick[iz][iy][ix] = buf4[n++];
- if (vflag_atom) {
- v0_brick[iz][iy][ix] = buf4[n++];
- v1_brick[iz][iy][ix] = buf4[n++];
- v2_brick[iz][iy][ix] = buf4[n++];
- v3_brick[iz][iy][ix] = buf4[n++];
- v4_brick[iz][iy][ix] = buf4[n++];
- v5_brick[iz][iy][ix] = buf4[n++];
- }
+ if (eflag_atom) u_brick[iz][iy][ix] = buf4[n++];
+ if (vflag_atom) {
+ v0_brick[iz][iy][ix] = buf4[n++];
+ v1_brick[iz][iy][ix] = buf4[n++];
+ v2_brick[iz][iy][ix] = buf4[n++];
+ v3_brick[iz][iy][ix] = buf4[n++];
+ v4_brick[iz][iy][ix] = buf4[n++];
+ v5_brick[iz][iy][ix] = buf4[n++];
+ }
}
// pack my real cells for +x processor
@@ -1759,22 +1759,22 @@ void PPPM::fillbrick_peratom()
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_out; iy <= nyhi_out; iy++)
for (ix = nxhi_in-nxhi_ghost+1; ix <= nxhi_in; ix++) {
- if (eflag_atom) buf3[n++] = u_brick[iz][iy][ix];
- if (vflag_atom) {
- buf3[n++] = v0_brick[iz][iy][ix];
- buf3[n++] = v1_brick[iz][iy][ix];
- buf3[n++] = v2_brick[iz][iy][ix];
- buf3[n++] = v3_brick[iz][iy][ix];
- buf3[n++] = v4_brick[iz][iy][ix];
- buf3[n++] = v5_brick[iz][iy][ix];
- }
+ if (eflag_atom) buf3[n++] = u_brick[iz][iy][ix];
+ if (vflag_atom) {
+ buf3[n++] = v0_brick[iz][iy][ix];
+ buf3[n++] = v1_brick[iz][iy][ix];
+ buf3[n++] = v2_brick[iz][iy][ix];
+ buf3[n++] = v3_brick[iz][iy][ix];
+ buf3[n++] = v4_brick[iz][iy][ix];
+ buf3[n++] = v5_brick[iz][iy][ix];
+ }
}
if (comm->procneigh[0][1] == me)
for (i = 0; i < n; i++) buf4[i] = buf3[i];
else {
MPI_Irecv(buf4,nbuf_peratom,MPI_FFT_SCALAR,
- comm->procneigh[0][0],0,world,&request);
+ comm->procneigh[0][0],0,world,&request);
MPI_Send(buf3,n,MPI_FFT_SCALAR,comm->procneigh[0][1],0,world);
MPI_Wait(&request,&status);
}
@@ -1783,15 +1783,15 @@ void PPPM::fillbrick_peratom()
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_out; iy <= nyhi_out; iy++)
for (ix = nxlo_out; ix < nxlo_in; ix++) {
- if (eflag_atom) u_brick[iz][iy][ix] = buf4[n++];
- if (vflag_atom) {
- v0_brick[iz][iy][ix] = buf4[n++];
- v1_brick[iz][iy][ix] = buf4[n++];
- v2_brick[iz][iy][ix] = buf4[n++];
- v3_brick[iz][iy][ix] = buf4[n++];
- v4_brick[iz][iy][ix] = buf4[n++];
- v5_brick[iz][iy][ix] = buf4[n++];
- }
+ if (eflag_atom) u_brick[iz][iy][ix] = buf4[n++];
+ if (vflag_atom) {
+ v0_brick[iz][iy][ix] = buf4[n++];
+ v1_brick[iz][iy][ix] = buf4[n++];
+ v2_brick[iz][iy][ix] = buf4[n++];
+ v3_brick[iz][iy][ix] = buf4[n++];
+ v4_brick[iz][iy][ix] = buf4[n++];
+ v5_brick[iz][iy][ix] = buf4[n++];
+ }
}
// pack my real cells for -x processor
@@ -1802,22 +1802,22 @@ void PPPM::fillbrick_peratom()
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_out; iy <= nyhi_out; iy++)
for (ix = nxlo_in; ix < nxlo_in+nxlo_ghost; ix++) {
- if (eflag_atom) buf3[n++] = u_brick[iz][iy][ix];
- if (vflag_atom) {
- buf3[n++] = v0_brick[iz][iy][ix];
- buf3[n++] = v1_brick[iz][iy][ix];
- buf3[n++] = v2_brick[iz][iy][ix];
- buf3[n++] = v3_brick[iz][iy][ix];
- buf3[n++] = v4_brick[iz][iy][ix];
- buf3[n++] = v5_brick[iz][iy][ix];
- }
+ if (eflag_atom) buf3[n++] = u_brick[iz][iy][ix];
+ if (vflag_atom) {
+ buf3[n++] = v0_brick[iz][iy][ix];
+ buf3[n++] = v1_brick[iz][iy][ix];
+ buf3[n++] = v2_brick[iz][iy][ix];
+ buf3[n++] = v3_brick[iz][iy][ix];
+ buf3[n++] = v4_brick[iz][iy][ix];
+ buf3[n++] = v5_brick[iz][iy][ix];
+ }
}
if (comm->procneigh[0][0] == me)
for (i = 0; i < n; i++) buf4[i] = buf3[i];
else {
MPI_Irecv(buf4,nbuf_peratom,MPI_FFT_SCALAR,
- comm->procneigh[0][1],0,world,&request);
+ comm->procneigh[0][1],0,world,&request);
MPI_Send(buf3,n,MPI_FFT_SCALAR,comm->procneigh[0][0],0,world);
MPI_Wait(&request,&status);
}
@@ -1826,22 +1826,22 @@ void PPPM::fillbrick_peratom()
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_out; iy <= nyhi_out; iy++)
for (ix = nxhi_in+1; ix <= nxhi_out; ix++) {
- if (eflag_atom) u_brick[iz][iy][ix] = buf4[n++];
- if (vflag_atom) {
- v0_brick[iz][iy][ix] = buf4[n++];
- v1_brick[iz][iy][ix] = buf4[n++];
- v2_brick[iz][iy][ix] = buf4[n++];
- v3_brick[iz][iy][ix] = buf4[n++];
- v4_brick[iz][iy][ix] = buf4[n++];
- v5_brick[iz][iy][ix] = buf4[n++];
- }
+ if (eflag_atom) u_brick[iz][iy][ix] = buf4[n++];
+ if (vflag_atom) {
+ v0_brick[iz][iy][ix] = buf4[n++];
+ v1_brick[iz][iy][ix] = buf4[n++];
+ v2_brick[iz][iy][ix] = buf4[n++];
+ v3_brick[iz][iy][ix] = buf4[n++];
+ v4_brick[iz][iy][ix] = buf4[n++];
+ v5_brick[iz][iy][ix] = buf4[n++];
+ }
}
}
/* ----------------------------------------------------------------------
find center grid pt for each of my particles
check that full stencil for the particle will fit in my 3d brick
- store central grid pt indices in part2grid array
+ store central grid pt indices in part2grid array
------------------------------------------------------------------------- */
void PPPM::particle_map()
@@ -1853,7 +1853,7 @@ void PPPM::particle_map()
int flag = 0;
for (int i = 0; i < nlocal; i++) {
-
+
// (nx,ny,nz) = global coords of grid pt to "lower left" of charge
// current particle coord can be outside global and local box
// add/subtract OFFSET to avoid int(-0.75) = 0 when want it to be -1
@@ -1869,8 +1869,8 @@ void PPPM::particle_map()
// check that entire stencil around nx,ny,nz will fit in my 3d brick
if (nx+nlower < nxlo_out || nx+nupper > nxhi_out ||
- ny+nlower < nylo_out || ny+nupper > nyhi_out ||
- nz+nlower < nzlo_out || nz+nupper > nzhi_out)
+ ny+nlower < nylo_out || ny+nupper > nyhi_out ||
+ nz+nlower < nzlo_out || nz+nupper > nzhi_out)
flag = 1;
}
@@ -1881,7 +1881,7 @@ void PPPM::particle_map()
create discretized "density" on section of global grid due to my particles
density(x,y,z) = charge "density" at grid points of my 3d brick
(nxlo:nxhi,nylo:nyhi,nzlo:nzhi) is extent of my brick (including ghosts)
- in global grid
+ in global grid
------------------------------------------------------------------------- */
void PPPM::make_rho()
@@ -1892,7 +1892,7 @@ void PPPM::make_rho()
// clear 3d density array
memset(&(density_brick[nzlo_out][nylo_out][nxlo_out]),0,
- ngrid*sizeof(FFT_SCALAR));
+ ngrid*sizeof(FFT_SCALAR));
// loop over my charges, add their contribution to nearby grid points
// (nx,ny,nz) = global coords of grid pt to "lower left" of charge
@@ -1919,19 +1919,19 @@ void PPPM::make_rho()
mz = n+nz;
y0 = z0*rho1d[2][n];
for (m = nlower; m <= nupper; m++) {
- my = m+ny;
- x0 = y0*rho1d[1][m];
- for (l = nlower; l <= nupper; l++) {
- mx = l+nx;
- density_brick[mz][my][mx] += x0*rho1d[0][l];
- }
+ my = m+ny;
+ x0 = y0*rho1d[1][m];
+ for (l = nlower; l <= nupper; l++) {
+ mx = l+nx;
+ density_brick[mz][my][mx] += x0*rho1d[0][l];
+ }
}
}
}
}
/* ----------------------------------------------------------------------
- FFT-based Poisson solver
+ FFT-based Poisson solver
------------------------------------------------------------------------- */
void PPPM::poisson()
@@ -1939,14 +1939,14 @@ void PPPM::poisson()
int i,j,k,n;
double eng;
- // transform charge density (r -> k)
+ // transform charge density (r -> k)
n = 0;
for (i = 0; i < nfft; i++) {
work1[n++] = density_fft[i];
work1[n++] = ZEROF;
}
-
+
fft1->compute(work1,work1,1);
// global energy and virial contribution
@@ -1958,17 +1958,17 @@ void PPPM::poisson()
if (vflag_global) {
n = 0;
for (i = 0; i < nfft; i++) {
- eng = s2 * greensfn[i] * (work1[n]*work1[n] + work1[n+1]*work1[n+1]);
- for (j = 0; j < 6; j++) virial[j] += eng*vg[i][j];
- if (eflag_global) energy += eng;
- n += 2;
+ eng = s2 * greensfn[i] * (work1[n]*work1[n] + work1[n+1]*work1[n+1]);
+ for (j = 0; j < 6; j++) virial[j] += eng*vg[i][j];
+ if (eflag_global) energy += eng;
+ n += 2;
}
} else {
n = 0;
for (i = 0; i < nfft; i++) {
- energy +=
- s2 * greensfn[i] * (work1[n]*work1[n] + work1[n+1]*work1[n+1]);
- n += 2;
+ energy +=
+ s2 * greensfn[i] * (work1[n]*work1[n] + work1[n+1]*work1[n+1]);
+ n += 2;
}
}
}
@@ -1996,9 +1996,9 @@ void PPPM::poisson()
for (k = nzlo_fft; k <= nzhi_fft; k++)
for (j = nylo_fft; j <= nyhi_fft; j++)
for (i = nxlo_fft; i <= nxhi_fft; i++) {
- work2[n] = fkx[i]*work1[n+1];
- work2[n+1] = -fkx[i]*work1[n];
- n += 2;
+ work2[n] = fkx[i]*work1[n+1];
+ work2[n+1] = -fkx[i]*work1[n];
+ n += 2;
}
fft2->compute(work2,work2,-1);
@@ -2007,8 +2007,8 @@ void PPPM::poisson()
for (k = nzlo_in; k <= nzhi_in; k++)
for (j = nylo_in; j <= nyhi_in; j++)
for (i = nxlo_in; i <= nxhi_in; i++) {
- vdx_brick[k][j][i] = work2[n];
- n += 2;
+ vdx_brick[k][j][i] = work2[n];
+ n += 2;
}
// y direction gradient
@@ -2017,9 +2017,9 @@ void PPPM::poisson()
for (k = nzlo_fft; k <= nzhi_fft; k++)
for (j = nylo_fft; j <= nyhi_fft; j++)
for (i = nxlo_fft; i <= nxhi_fft; i++) {
- work2[n] = fky[j]*work1[n+1];
- work2[n+1] = -fky[j]*work1[n];
- n += 2;
+ work2[n] = fky[j]*work1[n+1];
+ work2[n+1] = -fky[j]*work1[n];
+ n += 2;
}
fft2->compute(work2,work2,-1);
@@ -2028,8 +2028,8 @@ void PPPM::poisson()
for (k = nzlo_in; k <= nzhi_in; k++)
for (j = nylo_in; j <= nyhi_in; j++)
for (i = nxlo_in; i <= nxhi_in; i++) {
- vdy_brick[k][j][i] = work2[n];
- n += 2;
+ vdy_brick[k][j][i] = work2[n];
+ n += 2;
}
// z direction gradient
@@ -2038,9 +2038,9 @@ void PPPM::poisson()
for (k = nzlo_fft; k <= nzhi_fft; k++)
for (j = nylo_fft; j <= nyhi_fft; j++)
for (i = nxlo_fft; i <= nxhi_fft; i++) {
- work2[n] = fkz[k]*work1[n+1];
- work2[n+1] = -fkz[k]*work1[n];
- n += 2;
+ work2[n] = fkz[k]*work1[n+1];
+ work2[n+1] = -fkz[k]*work1[n];
+ n += 2;
}
fft2->compute(work2,work2,-1);
@@ -2049,8 +2049,8 @@ void PPPM::poisson()
for (k = nzlo_in; k <= nzhi_in; k++)
for (j = nylo_in; j <= nyhi_in; j++)
for (i = nxlo_in; i <= nxhi_in; i++) {
- vdz_brick[k][j][i] = work2[n];
- n += 2;
+ vdz_brick[k][j][i] = work2[n];
+ n += 2;
}
}
@@ -2063,7 +2063,7 @@ void PPPM::poisson_peratom()
int i,j,k,n;
// energy
-
+
if (eflag_atom) {
n = 0;
for (i = 0; i < nfft; i++) {
@@ -2071,127 +2071,127 @@ void PPPM::poisson_peratom()
work2[n+1] = work1[n+1];
n += 2;
}
-
- fft2->compute(work2,work2,-1);
-
+
+ fft2->compute(work2,work2,-1);
+
n = 0;
for (k = nzlo_in; k <= nzhi_in; k++)
for (j = nylo_in; j <= nyhi_in; j++)
for (i = nxlo_in; i <= nxhi_in; i++) {
- u_brick[k][j][i] = work2[n];
- n += 2;
+ u_brick[k][j][i] = work2[n];
+ n += 2;
}
}
-
+
// 6 components of virial in v0 thru v5
if (!vflag_atom) return;
-
+
n = 0;
for (i = 0; i < nfft; i++) {
work2[n] = work1[n]*vg[i][0];
work2[n+1] = work1[n+1]*vg[i][0];
n += 2;
}
-
- fft2->compute(work2,work2,-1);
-
+
+ fft2->compute(work2,work2,-1);
+
n = 0;
for (k = nzlo_in; k <= nzhi_in; k++)
for (j = nylo_in; j <= nyhi_in; j++)
for (i = nxlo_in; i <= nxhi_in; i++) {
- v0_brick[k][j][i] = work2[n];
- n += 2;
+ v0_brick[k][j][i] = work2[n];
+ n += 2;
}
-
+
n = 0;
for (i = 0; i < nfft; i++) {
work2[n] = work1[n]*vg[i][1];
work2[n+1] = work1[n+1]*vg[i][1];
n += 2;
}
-
- fft2->compute(work2,work2,-1);
-
+
+ fft2->compute(work2,work2,-1);
+
n = 0;
for (k = nzlo_in; k <= nzhi_in; k++)
for (j = nylo_in; j <= nyhi_in; j++)
for (i = nxlo_in; i <= nxhi_in; i++) {
- v1_brick[k][j][i] = work2[n];
- n += 2;
+ v1_brick[k][j][i] = work2[n];
+ n += 2;
}
-
+
n = 0;
for (i = 0; i < nfft; i++) {
work2[n] = work1[n]*vg[i][2];
work2[n+1] = work1[n+1]*vg[i][2];
n += 2;
}
-
- fft2->compute(work2,work2,-1);
-
+
+ fft2->compute(work2,work2,-1);
+
n = 0;
for (k = nzlo_in; k <= nzhi_in; k++)
for (j = nylo_in; j <= nyhi_in; j++)
for (i = nxlo_in; i <= nxhi_in; i++) {
- v2_brick[k][j][i] = work2[n];
- n += 2;
+ v2_brick[k][j][i] = work2[n];
+ n += 2;
}
-
+
n = 0;
for (i = 0; i < nfft; i++) {
work2[n] = work1[n]*vg[i][3];
work2[n+1] = work1[n+1]*vg[i][3];
n += 2;
}
-
- fft2->compute(work2,work2,-1);
-
+
+ fft2->compute(work2,work2,-1);
+
n = 0;
for (k = nzlo_in; k <= nzhi_in; k++)
for (j = nylo_in; j <= nyhi_in; j++)
for (i = nxlo_in; i <= nxhi_in; i++) {
- v3_brick[k][j][i] = work2[n];
- n += 2;
+ v3_brick[k][j][i] = work2[n];
+ n += 2;
}
-
+
n = 0;
for (i = 0; i < nfft; i++) {
work2[n] = work1[n]*vg[i][4];
work2[n+1] = work1[n+1]*vg[i][4];
n += 2;
}
-
- fft2->compute(work2,work2,-1);
-
+
+ fft2->compute(work2,work2,-1);
+
n = 0;
for (k = nzlo_in; k <= nzhi_in; k++)
for (j = nylo_in; j <= nyhi_in; j++)
for (i = nxlo_in; i <= nxhi_in; i++) {
- v4_brick[k][j][i] = work2[n];
- n += 2;
+ v4_brick[k][j][i] = work2[n];
+ n += 2;
}
-
+
n = 0;
for (i = 0; i < nfft; i++) {
work2[n] = work1[n]*vg[i][5];
work2[n+1] = work1[n+1]*vg[i][5];
n += 2;
}
-
- fft2->compute(work2,work2,-1);
-
+
+ fft2->compute(work2,work2,-1);
+
n = 0;
for (k = nzlo_in; k <= nzhi_in; k++)
for (j = nylo_in; j <= nyhi_in; j++)
for (i = nxlo_in; i <= nxhi_in; i++) {
- v5_brick[k][j][i] = work2[n];
- n += 2;
+ v5_brick[k][j][i] = work2[n];
+ n += 2;
}
}
/* ----------------------------------------------------------------------
- interpolate from grid to get electric field & force on my particles
+ interpolate from grid to get electric field & force on my particles
------------------------------------------------------------------------- */
void PPPM::fieldforce()
@@ -2227,15 +2227,15 @@ void PPPM::fieldforce()
mz = n+nz;
z0 = rho1d[2][n];
for (m = nlower; m <= nupper; m++) {
- my = m+ny;
- y0 = z0*rho1d[1][m];
- for (l = nlower; l <= nupper; l++) {
- mx = l+nx;
- x0 = y0*rho1d[0][l];
- ekx -= x0*vdx_brick[mz][my][mx];
- eky -= x0*vdy_brick[mz][my][mx];
- ekz -= x0*vdz_brick[mz][my][mx];
- }
+ my = m+ny;
+ y0 = z0*rho1d[1][m];
+ for (l = nlower; l <= nupper; l++) {
+ mx = l+nx;
+ x0 = y0*rho1d[0][l];
+ ekx -= x0*vdx_brick[mz][my][mx];
+ eky -= x0*vdy_brick[mz][my][mx];
+ ekz -= x0*vdz_brick[mz][my][mx];
+ }
}
}
@@ -2284,21 +2284,21 @@ void PPPM::fieldforce_peratom()
mz = n+nz;
z0 = rho1d[2][n];
for (m = nlower; m <= nupper; m++) {
- my = m+ny;
- y0 = z0*rho1d[1][m];
- for (l = nlower; l <= nupper; l++) {
- mx = l+nx;
- x0 = y0*rho1d[0][l];
- if (eflag_atom) u += x0*u_brick[mz][my][mx];
- if (vflag_atom) {
- v0 += x0*v0_brick[mz][my][mx];
- v1 += x0*v1_brick[mz][my][mx];
- v2 += x0*v2_brick[mz][my][mx];
- v3 += x0*v3_brick[mz][my][mx];
- v4 += x0*v4_brick[mz][my][mx];
- v5 += x0*v5_brick[mz][my][mx];
- }
- }
+ my = m+ny;
+ y0 = z0*rho1d[1][m];
+ for (l = nlower; l <= nupper; l++) {
+ mx = l+nx;
+ x0 = y0*rho1d[0][l];
+ if (eflag_atom) u += x0*u_brick[mz][my][mx];
+ if (vflag_atom) {
+ v0 += x0*v0_brick[mz][my][mx];
+ v1 += x0*v1_brick[mz][my][mx];
+ v2 += x0*v2_brick[mz][my][mx];
+ v3 += x0*v3_brick[mz][my][mx];
+ v4 += x0*v4_brick[mz][my][mx];
+ v5 += x0*v5_brick[mz][my][mx];
+ }
+ }
}
}
@@ -2315,7 +2315,7 @@ void PPPM::fieldforce_peratom()
}
/* ----------------------------------------------------------------------
- map nprocs to NX by NY grid as PX by PY procs - return optimal px,py
+ map nprocs to NX by NY grid as PX by PY procs - return optimal px,py
------------------------------------------------------------------------- */
void PPPM::procs2grid2d(int nprocs, int nx, int ny, int *px, int *py)
@@ -2339,13 +2339,13 @@ void PPPM::procs2grid2d(int nprocs, int nx, int ny, int *px, int *py)
boxy = ny/ipy;
if (ny % ipy) boxy++;
surf = boxx + boxy;
- if (surf < bestsurf ||
- (surf == bestsurf && boxx*boxy > bestboxx*bestboxy)) {
- bestsurf = surf;
- bestboxx = boxx;
- bestboxy = boxy;
- *px = ipx;
- *py = ipy;
+ if (surf < bestsurf ||
+ (surf == bestsurf && boxx*boxy > bestboxx*bestboxy)) {
+ bestsurf = surf;
+ bestboxx = boxx;
+ bestboxy = boxy;
+ *px = ipx;
+ *py = ipy;
}
}
ipx++;
@@ -2354,11 +2354,11 @@ void PPPM::procs2grid2d(int nprocs, int nx, int ny, int *px, int *py)
/* ----------------------------------------------------------------------
charge assignment into rho1d
- dx,dy,dz = distance of particle from "lower left" grid point
+ dx,dy,dz = distance of particle from "lower left" grid point
------------------------------------------------------------------------- */
void PPPM::compute_rho1d(const FFT_SCALAR &dx, const FFT_SCALAR &dy,
- const FFT_SCALAR &dz)
+ const FFT_SCALAR &dz)
{
int k,l;
FFT_SCALAR r1,r2,r3;
@@ -2393,7 +2393,7 @@ void PPPM::compute_rho1d(const FFT_SCALAR &dx, const FFT_SCALAR &dy,
| 0 otherwise
---
a coeffients are packed into the array rho_coeff to eliminate zeros
- rho_coeff(l,((k+mod(n+1,2))/2) = a(l,k)
+ rho_coeff(l,((k+mod(n+1,2))/2) = a(l,k)
------------------------------------------------------------------------- */
void PPPM::compute_rho_coeff()
@@ -2404,22 +2404,22 @@ void PPPM::compute_rho_coeff()
FFT_SCALAR **a;
memory->create2d_offset(a,order,-order,order,"pppm:a");
- for (k = -order; k <= order; k++)
+ for (k = -order; k <= order; k++)
for (l = 0; l < order; l++)
a[l][k] = 0.0;
-
+
a[0][0] = 1.0;
for (j = 1; j < order; j++) {
for (k = -j; k <= j; k += 2) {
s = 0.0;
for (l = 0; l < j; l++) {
- a[l+1][k] = (a[l][k+1]-a[l][k-1]) / (l+1);
+ a[l+1][k] = (a[l][k+1]-a[l][k-1]) / (l+1);
#ifdef FFT_SINGLE
- s += powf(0.5,(float) l+1) *
- (a[l][k-1] + powf(-1.0,(float) l) * a[l][k+1]) / (l+1);
+ s += powf(0.5,(float) l+1) *
+ (a[l][k-1] + powf(-1.0,(float) l) * a[l][k+1]) / (l+1);
#else
- s += pow(0.5,(double) l+1) *
- (a[l][k-1] + pow(-1.0,(double) l) * a[l][k+1]) / (l+1);
+ s += pow(0.5,(double) l+1) *
+ (a[l][k-1] + pow(-1.0,(double) l) * a[l][k+1]) / (l+1);
#endif
}
a[0][k] = s;
@@ -2438,9 +2438,9 @@ void PPPM::compute_rho_coeff()
/* ----------------------------------------------------------------------
Slab-geometry correction term to dampen inter-slab interactions between
- periodically repeating slabs. Yields good approximation to 2D Ewald if
- adequate empty space is left between repeating slabs (J. Chem. Phys.
- 111, 3155). Slabs defined here to be parallel to the xy plane.
+ periodically repeating slabs. Yields good approximation to 2D Ewald if
+ adequate empty space is left between repeating slabs (J. Chem. Phys.
+ 111, 3155). Slabs defined here to be parallel to the xy plane.
------------------------------------------------------------------------- */
void PPPM::slabcorr()
@@ -2453,29 +2453,29 @@ void PPPM::slabcorr()
double dipole = 0.0;
for (int i = 0; i < nlocal; i++) dipole += q[i]*x[i][2];
-
+
// sum local contributions to get global dipole moment
double dipole_all;
MPI_Allreduce(&dipole,&dipole_all,1,MPI_DOUBLE,MPI_SUM,world);
// compute corrections
-
+
const double e_slabcorr = 2.0*MY_PI*dipole_all*dipole_all/volume;
const double qscale = force->qqrd2e * scale;
-
+
if (eflag_global) energy += qscale * e_slabcorr;
// per-atom energy
-
+
if (eflag_atom) {
- double efact = 2.0*MY_PI*dipole_all/volume;
+ double efact = 2.0*MY_PI*dipole_all/volume;
for (int i = 0; i < nlocal; i++) eatom[i] += qscale * q[i]*x[i][2]*efact;
}
// add on force corrections
- double ffact = -4.0*MY_PI*dipole_all/volume;
+ double ffact = -4.0*MY_PI*dipole_all/volume;
double **f = atom->f;
for (int i = 0; i < nlocal; i++) f[i][2] += qscale * q[i]*ffact;
@@ -2521,13 +2521,13 @@ void PPPM::timing(int n, double &time3d, double &time1d)
}
/* ----------------------------------------------------------------------
- memory usage of local arrays
+ memory usage of local arrays
------------------------------------------------------------------------- */
double PPPM::memory_usage()
{
double bytes = nmax*3 * sizeof(double);
- int nbrick = (nxhi_out-nxlo_out+1) * (nyhi_out-nylo_out+1) *
+ int nbrick = (nxhi_out-nxlo_out+1) * (nyhi_out-nylo_out+1) *
(nzhi_out-nzlo_out+1);
bytes += 4 * nbrick * sizeof(FFT_SCALAR);
bytes += 6 * nfft_both * sizeof(double);
@@ -2558,101 +2558,101 @@ double PPPM::memory_usage()
void PPPM::compute_group_group(int groupbit_A, int groupbit_B, int BA_flag)
{
- if (slabflag)
+ if (slabflag)
error->all(FLERR,"Cannot (yet) use K-space slab "
- "correction with compute group/group");
-
+ "correction with compute group/group");
+
int i,j;
-
+
if (!group_allocate_flag) {
allocate_groups();
group_allocate_flag = 1;
- }
-
+ }
+
e2group = 0; //energy
f2group[0] = 0; //force in x-direction
f2group[1] = 0; //force in y-direction
f2group[2] = 0; //force in z-direction
-
+
double *q = atom->q;
int nlocal = atom->nlocal;
int *mask = atom->mask;
-
-
+
+
// map my particle charge onto my local 3d density grid
-
+
make_rho_groups(groupbit_A,groupbit_B,BA_flag);
-
+
// all procs communicate density values from their ghost cells
// to fully sum contribution in their 3d bricks
// remap from 3d decomposition to FFT decomposition
-
+
// temporarily store and switch pointers so we can
- // use brick2fft() for groups A and B (without
+ // use brick2fft() for groups A and B (without
// writing an additional function)
-
+
FFT_SCALAR ***density_brick_real = density_brick;
- FFT_SCALAR *density_fft_real = density_fft;
-
+ FFT_SCALAR *density_fft_real = density_fft;
+
// group A
-
- density_brick = density_A_brick;
+
+ density_brick = density_A_brick;
density_fft = density_A_fft;
-
+
brick2fft();
-
+
// group B
-
- density_brick = density_B_brick;
+
+ density_brick = density_B_brick;
density_fft = density_B_fft;
-
+
brick2fft();
// switch back pointers
-
+
density_brick = density_brick_real;
- density_fft = density_fft_real;
-
+ density_fft = density_fft_real;
+
// compute potential gradient on my FFT grid and
// portion of group-group energy/force on this proc's FFT grid
-
+
poisson_groups(BA_flag);
-
+
const double qscale = force->qqrd2e * scale;
-
+
// total group A <--> group B energy
// self and boundary correction terms are in compute_group_group.cpp
-
+
double e2group_all;
MPI_Allreduce(&e2group,&e2group_all,1,MPI_DOUBLE,MPI_SUM,world);
e2group = e2group_all;
-
+
e2group *= qscale*0.5*volume;
-
+
// total group A <--> group B force
-
+
double f2group_all[3];
MPI_Allreduce(f2group,f2group_all,3,MPI_DOUBLE,MPI_SUM,world);
-
- for (i = 0; i < 3; i++) f2group[i] = qscale*volume*f2group_all[i];
+
+ for (i = 0; i < 3; i++) f2group[i] = qscale*volume*f2group_all[i];
}
/* ----------------------------------------------------------------------
- allocate group-group memory that depends on # of K-vectors and order
+ allocate group-group memory that depends on # of K-vectors and order
------------------------------------------------------------------------- */
void PPPM::allocate_groups()
-{
+{
memory->create3d_offset(density_A_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
- nxlo_out,nxhi_out,"pppm:density_A_brick");
+ nxlo_out,nxhi_out,"pppm:density_A_brick");
memory->create3d_offset(density_B_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
- nxlo_out,nxhi_out,"pppm:density_B_brick");
+ nxlo_out,nxhi_out,"pppm:density_B_brick");
memory->create(density_A_fft,nfft_both,"pppm:density_A_fft");
memory->create(density_B_fft,nfft_both,"pppm:density_B_fft");
}
/* ----------------------------------------------------------------------
- deallocate group-group memory that depends on # of K-vectors and order
+ deallocate group-group memory that depends on # of K-vectors and order
------------------------------------------------------------------------- */
void PPPM::deallocate_groups()
@@ -2674,41 +2674,41 @@ void PPPM::make_rho_groups(int groupbit_A, int groupbit_B, int BA_flag)
{
int l,m,n,nx,ny,nz,mx,my,mz;
FFT_SCALAR dx,dy,dz,x0,y0,z0;
-
+
// clear 3d density arrays
-
+
memset(&(density_A_brick[nzlo_out][nylo_out][nxlo_out]),0,
ngrid*sizeof(FFT_SCALAR));
-
+
memset(&(density_B_brick[nzlo_out][nylo_out][nxlo_out]),0,
ngrid*sizeof(FFT_SCALAR));
-
+
// loop over my charges, add their contribution to nearby grid points
// (nx,ny,nz) = global coords of grid pt to "lower left" of charge
// (dx,dy,dz) = distance to "lower left" grid pt
// (mx,my,mz) = global coords of moving stencil pt
-
+
double *q = atom->q;
double **x = atom->x;
int nlocal = atom->nlocal;
int *mask = atom->mask;
-
+
for (int i = 0; i < nlocal; i++) {
-
+
if ((mask[i] & groupbit_A) && (mask[i] & groupbit_B))
- if (BA_flag) continue;
-
- if ((mask[i] & groupbit_A) || (mask[i] & groupbit_B)) {
-
+ if (BA_flag) continue;
+
+ if ((mask[i] & groupbit_A) || (mask[i] & groupbit_B)) {
+
nx = part2grid[i][0];
ny = part2grid[i][1];
nz = part2grid[i][2];
dx = nx+shiftone - (x[i][0]-boxlo[0])*delxinv;
dy = ny+shiftone - (x[i][1]-boxlo[1])*delyinv;
dz = nz+shiftone - (x[i][2]-boxlo[2])*delzinv;
-
+
compute_rho1d(dx,dy,dz);
-
+
z0 = delvolinv * q[i];
for (n = nlower; n <= nupper; n++) {
mz = n+nz;
@@ -2718,14 +2718,14 @@ void PPPM::make_rho_groups(int groupbit_A, int groupbit_B, int BA_flag)
x0 = y0*rho1d[1][m];
for (l = nlower; l <= nupper; l++) {
mx = l+nx;
-
+
// group A
-
+
if (mask[i] & groupbit_A)
density_A_brick[mz][my][mx] += x0*rho1d[0][l];
-
+
// group B
-
+
if (mask[i] & groupbit_B)
density_B_brick[mz][my][mx] += x0*rho1d[0][l];
}
@@ -2743,66 +2743,66 @@ void PPPM::poisson_groups(int BA_flag)
{
int i,j,k,n;
double eng;
-
- // reuse memory (already declared)
-
+
+ // reuse memory (already declared)
+
FFT_SCALAR *work_A = work1;
FFT_SCALAR *work_B = work2;
-
- // transform charge density (r -> k)
-
- // group A
-
+
+ // transform charge density (r -> k)
+
+ // group A
+
n = 0;
for (i = 0; i < nfft; i++) {
work_A[n++] = density_A_fft[i];
work_A[n++] = ZEROF;
}
-
+
fft1->compute(work_A,work_A,1);
- // group B
-
+ // group B
+
n = 0;
for (i = 0; i < nfft; i++) {
work_B[n++] = density_B_fft[i];
work_B[n++] = ZEROF;
}
-
+
fft1->compute(work_B,work_B,1);
-
+
// group-group energy and force contribution,
- // keep everything in reciprocal space so
+ // keep everything in reciprocal space so
// no inverse FFTs needed
-
+
double scaleinv = 1.0/(nx_pppm*ny_pppm*nz_pppm);
double s2 = scaleinv*scaleinv;
-
+
// energy
-
+
n = 0;
for (i = 0; i < nfft; i++) {
- e2group += s2 * greensfn[i] *
- (work_A[n]*work_B[n] + work_A[n+1]*work_B[n+1]);
+ e2group += s2 * greensfn[i] *
+ (work_A[n]*work_B[n] + work_A[n+1]*work_B[n+1]);
n += 2;
}
-
+
if (BA_flag) return;
-
-
- // multiply by Green's function and s2
+
+
+ // multiply by Green's function and s2
// (only for work_A so it is not squared below)
-
+
n = 0;
for (i = 0; i < nfft; i++) {
work_A[n++] *= s2 * greensfn[i];
work_A[n++] *= s2 * greensfn[i];
- }
-
+ }
+
double partial_group;
-
+
// force, x direction
-
+
n = 0;
for (k = nzlo_fft; k <= nzhi_fft; k++)
for (j = nylo_fft; j <= nyhi_fft; j++)
@@ -2811,9 +2811,9 @@ void PPPM::poisson_groups(int BA_flag)
f2group[0] += fkx[i] * partial_group;
n += 2;
}
-
+
// force, y direction
-
+
n = 0;
for (k = nzlo_fft; k <= nzhi_fft; k++)
for (j = nylo_fft; j <= nyhi_fft; j++)
@@ -2822,9 +2822,9 @@ void PPPM::poisson_groups(int BA_flag)
f2group[1] += fky[j] * partial_group;
n += 2;
}
-
+
// force, z direction
-
+
n = 0;
for (k = nzlo_fft; k <= nzhi_fft; k++)
for (j = nylo_fft; j <= nyhi_fft; j++)
@@ -2832,5 +2832,5 @@ void PPPM::poisson_groups(int BA_flag)
partial_group = work_A[n+1]*work_B[n] - work_A[n]*work_B[n+1];
f2group[2] += fkz[k] * partial_group;
n += 2;
- }
+ }
}
diff --git a/src/KSPACE/pppm.h b/src/KSPACE/pppm.h
index 356cda773506e87933f5e563f518e904fa708690..6a51d682380d7ce88923520e7b0c647c197596c8 100644
--- a/src/KSPACE/pppm.h
+++ b/src/KSPACE/pppm.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -121,8 +121,8 @@ class PPPM : public KSpace {
virtual void fieldforce();
virtual void fieldforce_peratom();
void procs2grid2d(int,int,int,int *, int*);
- void compute_rho1d(const FFT_SCALAR &, const FFT_SCALAR &,
- const FFT_SCALAR &);
+ void compute_rho1d(const FFT_SCALAR &, const FFT_SCALAR &,
+ const FFT_SCALAR &);
void compute_rho_coeff();
void slabcorr();
@@ -132,7 +132,7 @@ class PPPM : public KSpace {
virtual void deallocate_groups();
virtual void make_rho_groups(int, int, int);
virtual void poisson_groups(int);
-
+
/* ----------------------------------------------------------------------
denominator for Hockney-Eastwood Green's function
of x,y,z = sin(kx*deltax/2), etc
@@ -142,11 +142,11 @@ class PPPM : public KSpace {
j=-inf l=0
= -(z*z)**n /(2n-1)! * (d/dx)**(2n-1) cot(x) at z = sin(x)
- gf_b = denominator expansion coeffs
+ gf_b = denominator expansion coeffs
------------------------------------------------------------------------- */
- inline double gf_denom(const double &x, const double &y,
- const double &z) const {
+ inline double gf_denom(const double &x, const double &y,
+ const double &z) const {
double sx,sy,sz;
sz = sy = sx = 0.0;
for (int l = order-1; l >= 0; l--) {
@@ -242,7 +242,7 @@ E: PPPM order has been reduced to 0
LAMMPS has attempted to reduce the PPPM order to enable the simulation
to run, but can reduce the order no further. Try increasing the
-accuracy of PPPM by reducing the tolerance size, thus inducing a
+accuracy of PPPM by reducing the tolerance size, thus inducing a
larger PPPM grid.
E: Cannot compute PPPM G
diff --git a/src/KSPACE/pppm_cg.cpp b/src/KSPACE/pppm_cg.cpp
index fa4ece88ed990ba9f85a30b587ce46e2cad90927..f98584426b8c65a582e1fd8d6f0063c69786461c 100644
--- a/src/KSPACE/pppm_cg.cpp
+++ b/src/KSPACE/pppm_cg.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -44,7 +44,7 @@ using namespace MathConst;
PPPMCG::PPPMCG(LAMMPS *lmp, int narg, char **arg) : PPPM(lmp, narg, arg)
{
- if ((narg < 1) || (narg > 2))
+ if ((narg < 1) || (narg > 2))
error->all(FLERR,"Illegal kspace_style pppm/cg command");
if (narg == 2)
@@ -57,7 +57,7 @@ PPPMCG::PPPMCG(LAMMPS *lmp, int narg, char **arg) : PPPM(lmp, narg, arg)
}
/* ----------------------------------------------------------------------
- free all memory
+ free all memory
------------------------------------------------------------------------- */
PPPMCG::~PPPMCG()
@@ -66,7 +66,7 @@ PPPMCG::~PPPMCG()
}
/* ----------------------------------------------------------------------
- compute the PPPM long-range force, energy, virial
+ compute the PPPM long-range force, energy, virial
------------------------------------------------------------------------- */
void PPPMCG::compute(int eflag, int vflag)
@@ -77,8 +77,8 @@ void PPPMCG::compute(int eflag, int vflag)
// invoke allocate_peratom() if needed for first time
if (eflag || vflag) ev_setup(eflag,vflag);
- else evflag = evflag_atom = eflag_global = vflag_global =
- eflag_atom = vflag_atom = 0;
+ else evflag = evflag_atom = eflag_global = vflag_global =
+ eflag_atom = vflag_atom = 0;
if (evflag_atom && !peratom_allocate_flag) {
allocate_peratom();
@@ -86,7 +86,7 @@ void PPPMCG::compute(int eflag, int vflag)
}
// convert atoms from box to lamda coords
-
+
if (triclinic == 0) boxlo = domain->boxlo;
else {
boxlo = domain->boxlo_lamda;
@@ -117,7 +117,7 @@ void PPPMCG::compute(int eflag, int vflag)
// get fraction of charged particles per domain
if (atom->nlocal > 0)
- charged_frac = static_cast<double>(num_charged) * 100.0
+ charged_frac = static_cast<double>(num_charged) * 100.0
/ static_cast<double>(atom->nlocal);
else
charged_frac = 0.0;
@@ -128,22 +128,22 @@ void PPPMCG::compute(int eflag, int vflag)
charged_num = num_charged;
MPI_Reduce(&charged_num,&charged_all,1,MPI_LMP_BIGINT,MPI_SUM,0,world);
- charged_frac = static_cast<double>(charged_all) * 100.0
+ charged_frac = static_cast<double>(charged_all) * 100.0
/ static_cast<double>(atom->natoms);
if (me == 0) {
- if (screen)
- fprintf(screen,
- " PPPM/cg optimization cutoff: %g\n"
- " Total charged atoms: %.1f%%\n"
- " Min/max charged atoms/proc: %.1f%% %.1f%%\n",
- smallq,charged_frac,charged_fmin,charged_fmax);
+ if (screen)
+ fprintf(screen,
+ " PPPM/cg optimization cutoff: %g\n"
+ " Total charged atoms: %.1f%%\n"
+ " Min/max charged atoms/proc: %.1f%% %.1f%%\n",
+ smallq,charged_frac,charged_fmin,charged_fmax);
if (logfile)
- fprintf(logfile,
- " PPPM/cg optimization cutoff: %g\n"
- " Total charged atoms: %.1f%%\n"
- " Min/max charged atoms/proc: %.1f%% %.1f%%\n",
- smallq,charged_frac,charged_fmin,charged_fmax);
+ fprintf(logfile,
+ " PPPM/cg optimization cutoff: %g\n"
+ " Total charged atoms: %.1f%%\n"
+ " Min/max charged atoms/proc: %.1f%% %.1f%%\n",
+ smallq,charged_frac,charged_fmin,charged_fmax);
}
}
@@ -198,7 +198,7 @@ void PPPMCG::compute(int eflag, int vflag)
double energy_all;
MPI_Allreduce(&energy,&energy_all,1,MPI_DOUBLE,MPI_SUM,world);
energy = energy_all;
-
+
energy *= 0.5*volume;
energy -= g_ewald*qsqsum/MY_PIS +
MY_PI2*qsum*qsum / (g_ewald*g_ewald*volume);
@@ -223,9 +223,9 @@ void PPPMCG::compute(int eflag, int vflag)
if (eflag_atom) {
for (int j = 0; j < num_charged; j++) {
int i = is_charged[j];
- eatom[i] *= 0.5;
- eatom[i] -= g_ewald*q[i]*q[i]/MY_PIS + MY_PI2*q[i]*qsum /
- (g_ewald*g_ewald*volume);
+ eatom[i] *= 0.5;
+ eatom[i] -= g_ewald*q[i]*q[i]/MY_PIS + MY_PI2*q[i]*qsum /
+ (g_ewald*g_ewald*volume);
eatom[i] *= qscale;
}
}
@@ -243,14 +243,14 @@ void PPPMCG::compute(int eflag, int vflag)
if (slabflag) slabcorr();
// convert atoms back from lamda to box coords
-
+
if (triclinic) domain->lamda2x(atom->nlocal);
}
/* ----------------------------------------------------------------------
find center grid pt for each of my particles
check that full stencil for the particle will fit in my 3d brick
- store central grid pt indices in part2grid array
+ store central grid pt indices in part2grid array
------------------------------------------------------------------------- */
void PPPMCG::particle_map()
@@ -262,7 +262,7 @@ void PPPMCG::particle_map()
int flag = 0;
for (int j = 0; j < num_charged; j++) {
int i = is_charged[j];
-
+
// (nx,ny,nz) = global coords of grid pt to "lower left" of charge
// current particle coord can be outside global and local box
// add/subtract OFFSET to avoid int(-0.75) = 0 when want it to be -1
@@ -278,8 +278,8 @@ void PPPMCG::particle_map()
// check that entire stencil around nx,ny,nz will fit in my 3d brick
if (nx+nlower < nxlo_out || nx+nupper > nxhi_out ||
- ny+nlower < nylo_out || ny+nupper > nyhi_out ||
- nz+nlower < nzlo_out || nz+nupper > nzhi_out) flag = 1;
+ ny+nlower < nylo_out || ny+nupper > nyhi_out ||
+ nz+nlower < nzlo_out || nz+nupper > nzhi_out) flag = 1;
}
if (flag) error->one(FLERR,"Out of range atoms - cannot compute PPPM");
@@ -289,7 +289,7 @@ void PPPMCG::particle_map()
create discretized "density" on section of global grid due to my particles
density(x,y,z) = charge "density" at grid points of my 3d brick
(nxlo:nxhi,nylo:nyhi,nzlo:nzhi) is extent of my brick (including ghosts)
- in global grid
+ in global grid
------------------------------------------------------------------------- */
void PPPMCG::make_rho()
@@ -327,19 +327,19 @@ void PPPMCG::make_rho()
mz = n+nz;
y0 = z0*rho1d[2][n];
for (m = nlower; m <= nupper; m++) {
- my = m+ny;
- x0 = y0*rho1d[1][m];
- for (l = nlower; l <= nupper; l++) {
- mx = l+nx;
- density_brick[mz][my][mx] += x0*rho1d[0][l];
- }
+ my = m+ny;
+ x0 = y0*rho1d[1][m];
+ for (l = nlower; l <= nupper; l++) {
+ mx = l+nx;
+ density_brick[mz][my][mx] += x0*rho1d[0][l];
+ }
}
}
}
}
/* ----------------------------------------------------------------------
- interpolate from grid to get electric field & force on my particles
+ interpolate from grid to get electric field & force on my particles
------------------------------------------------------------------------- */
void PPPMCG::fieldforce()
@@ -375,15 +375,15 @@ void PPPMCG::fieldforce()
mz = n+nz;
z0 = rho1d[2][n];
for (m = nlower; m <= nupper; m++) {
- my = m+ny;
- y0 = z0*rho1d[1][m];
- for (l = nlower; l <= nupper; l++) {
- mx = l+nx;
- x0 = y0*rho1d[0][l];
- ekx -= x0*vdx_brick[mz][my][mx];
- eky -= x0*vdy_brick[mz][my][mx];
- ekz -= x0*vdz_brick[mz][my][mx];
- }
+ my = m+ny;
+ y0 = z0*rho1d[1][m];
+ for (l = nlower; l <= nupper; l++) {
+ mx = l+nx;
+ x0 = y0*rho1d[0][l];
+ ekx -= x0*vdx_brick[mz][my][mx];
+ eky -= x0*vdy_brick[mz][my][mx];
+ ekz -= x0*vdz_brick[mz][my][mx];
+ }
}
}
@@ -464,9 +464,9 @@ void PPPMCG::fieldforce_peratom()
/* ----------------------------------------------------------------------
Slab-geometry correction term to dampen inter-slab interactions between
- periodically repeating slabs. Yields good approximation to 2D Ewald if
- adequate empty space is left between repeating slabs (J. Chem. Phys.
- 111, 3155). Slabs defined here to be parallel to the xy plane.
+ periodically repeating slabs. Yields good approximation to 2D Ewald if
+ adequate empty space is left between repeating slabs (J. Chem. Phys.
+ 111, 3155). Slabs defined here to be parallel to the xy plane.
------------------------------------------------------------------------- */
void PPPMCG::slabcorr()
@@ -488,10 +488,10 @@ void PPPMCG::slabcorr()
MPI_Allreduce(&dipole,&dipole_all,1,MPI_DOUBLE,MPI_SUM,world);
// compute corrections
-
+
const double e_slabcorr = 2.0*MY_PI*dipole_all*dipole_all/volume;
const double qscale = force->qqrd2e * scale;
-
+
if (eflag_global) energy += qscale * e_slabcorr;
//per-atom energy
@@ -506,7 +506,7 @@ void PPPMCG::slabcorr()
// add on force corrections
- const double ffact = -4.0*MY_PI*dipole_all/volume * qscale;
+ const double ffact = -4.0*MY_PI*dipole_all/volume * qscale;
double **f = atom->f;
for (int j = 0; j < num_charged; j++) {
@@ -516,7 +516,7 @@ void PPPMCG::slabcorr()
}
/* ----------------------------------------------------------------------
- memory usage of local arrays
+ memory usage of local arrays
------------------------------------------------------------------------- */
double PPPMCG::memory_usage()
diff --git a/src/KSPACE/pppm_cg.h b/src/KSPACE/pppm_cg.h
index 4c0c1baa277061bd0be2b612c95ffcc032c12da6..4ab1918b3730318e1cbe2bfa00f7d5481a7df67e 100644
--- a/src/KSPACE/pppm_cg.h
+++ b/src/KSPACE/pppm_cg.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/KSPACE/pppm_tip4p.cpp b/src/KSPACE/pppm_tip4p.cpp
index bd6e880a3b084801f162f87c7ca83708b89e6cad..c9dabf94cd85491b4a7316e45212f626bba3e4cc 100644
--- a/src/KSPACE/pppm_tip4p.cpp
+++ b/src/KSPACE/pppm_tip4p.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -55,7 +55,7 @@ void PPPMTIP4P::init()
/* ----------------------------------------------------------------------
find center grid pt for each of my particles
check that full stencil for the particle will fit in my 3d brick
- store central grid pt indices in part2grid array
+ store central grid pt indices in part2grid array
------------------------------------------------------------------------- */
void PPPMTIP4P::particle_map()
@@ -70,7 +70,7 @@ void PPPMTIP4P::particle_map()
int flag = 0;
for (int i = 0; i < nlocal; i++) {
if (type[i] == typeO) {
- find_M(i,iH1,iH2,xM);
+ find_M(i,iH1,iH2,xM);
xi = xM;
} else xi = x[i];
@@ -89,8 +89,8 @@ void PPPMTIP4P::particle_map()
// check that entire stencil around nx,ny,nz will fit in my 3d brick
if (nx+nlower < nxlo_out || nx+nupper > nxhi_out ||
- ny+nlower < nylo_out || ny+nupper > nyhi_out ||
- nz+nlower < nzlo_out || nz+nupper > nzhi_out) flag++;
+ ny+nlower < nylo_out || ny+nupper > nyhi_out ||
+ nz+nlower < nzlo_out || nz+nupper > nzhi_out) flag++;
}
int flag_all;
@@ -102,7 +102,7 @@ void PPPMTIP4P::particle_map()
create discretized "density" on section of global grid due to my particles
density(x,y,z) = charge "density" at grid points of my 3d brick
(nxlo:nxhi,nylo:nyhi,nzlo:nzhi) is extent of my brick (including ghosts)
- in global grid
+ in global grid
------------------------------------------------------------------------- */
void PPPMTIP4P::make_rho()
@@ -121,14 +121,14 @@ void PPPMTIP4P::make_rho()
// (dx,dy,dz) = distance to "lower left" grid pt
// (mx,my,mz) = global coords of moving stencil pt
- int *type = atom->type;
+ int *type = atom->type;
double *q = atom->q;
double **x = atom->x;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (type[i] == typeO) {
- find_M(i,iH1,iH2,xM);
+ find_M(i,iH1,iH2,xM);
xi = xM;
} else xi = x[i];
@@ -146,19 +146,19 @@ void PPPMTIP4P::make_rho()
mz = n+nz;
y0 = z0*rho1d[2][n];
for (m = nlower; m <= nupper; m++) {
- my = m+ny;
- x0 = y0*rho1d[1][m];
- for (l = nlower; l <= nupper; l++) {
- mx = l+nx;
- density_brick[mz][my][mx] += x0*rho1d[0][l];
- }
+ my = m+ny;
+ x0 = y0*rho1d[1][m];
+ for (l = nlower; l <= nupper; l++) {
+ mx = l+nx;
+ density_brick[mz][my][mx] += x0*rho1d[0][l];
+ }
}
}
}
}
/* ----------------------------------------------------------------------
- interpolate from grid to get electric field & force on my particles
+ interpolate from grid to get electric field & force on my particles
------------------------------------------------------------------------- */
void PPPMTIP4P::fieldforce()
@@ -187,7 +187,7 @@ void PPPMTIP4P::fieldforce()
for (i = 0; i < nlocal; i++) {
if (type[i] == typeO) {
- find_M(i,iH1,iH2,xM);
+ find_M(i,iH1,iH2,xM);
xi = xM;
} else xi = x[i];
@@ -205,15 +205,15 @@ void PPPMTIP4P::fieldforce()
mz = n+nz;
z0 = rho1d[2][n];
for (m = nlower; m <= nupper; m++) {
- my = m+ny;
- y0 = z0*rho1d[1][m];
- for (l = nlower; l <= nupper; l++) {
- mx = l+nx;
- x0 = y0*rho1d[0][l];
- ekx -= x0*vdx_brick[mz][my][mx];
- eky -= x0*vdy_brick[mz][my][mx];
- ekz -= x0*vdz_brick[mz][my][mx];
- }
+ my = m+ny;
+ y0 = z0*rho1d[1][m];
+ for (l = nlower; l <= nupper; l++) {
+ mx = l+nx;
+ x0 = y0*rho1d[0][l];
+ ekx -= x0*vdx_brick[mz][my][mx];
+ eky -= x0*vdy_brick[mz][my][mx];
+ ekz -= x0*vdz_brick[mz][my][mx];
+ }
}
}
@@ -234,7 +234,7 @@ void PPPMTIP4P::fieldforce()
rOMx = xM[0] - x[i][0];
rOMy = xM[1] - x[i][1];
rOMz = xM[2] - x[i][2];
-
+
ddotf = (rOMx * fx + rOMy * fy + rOMz * fz) / (qdist * qdist);
f1x = ddotf * rOMx;
@@ -271,7 +271,7 @@ void PPPMTIP4P::find_M(int i, int &iH1, int &iH2, double *xM)
if (atom->type[iH1] != typeH || atom->type[iH2] != typeH)
error->one(FLERR,"TIP4P hydrogen has incorrect atom type");
- double **x = atom->x;
+ double **x = atom->x;
double delx1 = x[iH1][0] - x[i][0];
double dely1 = x[iH1][1] - x[i][1];
diff --git a/src/KSPACE/pppm_tip4p.h b/src/KSPACE/pppm_tip4p.h
index 8031b706b615abd93c9a9d06909d823a91b31f00..32d45f92290fc5dd8fc21a02dde06ae4958e83db 100644
--- a/src/KSPACE/pppm_tip4p.h
+++ b/src/KSPACE/pppm_tip4p.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -36,7 +36,7 @@ class PPPMTIP4P : public PPPM {
virtual void fieldforce();
private:
- void find_M(int, int &, int &, double *);
+ void find_M(int, int &, int &, double *);
};
}
diff --git a/src/KSPACE/remap.cpp b/src/KSPACE/remap.cpp
index f702cf9e9e0784251358e131aa0ebdfc4c0f0108..a43bb2294d2f962e5d179912213074d29c320def 100644
--- a/src/KSPACE/remap.cpp
+++ b/src/KSPACE/remap.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -32,9 +32,9 @@
my subsection must not overlap with any other proc's subsection,
i.e. the union of all proc's input (or output) subsections must
exactly tile the global Nfast x Nmid x Nslow data set
- when called from C, all subsection indices are
+ when called from C, all subsection indices are
C-style from 0 to N-1 where N = Nfast or Nmid or Nslow
- when called from F77, all subsection indices are
+ when called from F77, all subsection indices are
F77-style from 1 to N where N = Nfast or Nmid or Nslow
a proc can own 0 elements on input or output
by specifying hi index < lo index
@@ -43,7 +43,7 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
- Perform 3d remap
+ Perform 3d remap
Arguments:
in starting address of input data on this proc
@@ -51,16 +51,16 @@
will be placed (can be same as in)
buf extra memory required for remap
if memory=0 was used in call to remap_3d_create_plan
- then buf must be big enough to hold output result
- i.e. nqty * (out_ihi-out_ilo+1) * (out_jhi-out_jlo+1) *
- (out_khi-out_klo+1)
- if memory=1 was used in call to remap_3d_create_plan
- then buf is not used, can just be a dummy pointer
+ then buf must be big enough to hold output result
+ i.e. nqty * (out_ihi-out_ilo+1) * (out_jhi-out_jlo+1) *
+ (out_khi-out_klo+1)
+ if memory=1 was used in call to remap_3d_create_plan
+ then buf is not used, can just be a dummy pointer
plan plan returned by previous call to remap_3d_create_plan
------------------------------------------------------------------------- */
void remap_3d(FFT_SCALAR *in, FFT_SCALAR *out, FFT_SCALAR *buf,
- struct remap_plan_3d *plan)
+ struct remap_plan_3d *plan)
{
MPI_Status status;
@@ -72,45 +72,45 @@ void remap_3d(FFT_SCALAR *in, FFT_SCALAR *out, FFT_SCALAR *buf,
else
scratch = plan->scratch;
- // post all recvs into scratch space
+ // post all recvs into scratch space
for (irecv = 0; irecv < plan->nrecv; irecv++)
MPI_Irecv(&scratch[plan->recv_bufloc[irecv]],plan->recv_size[irecv],
- MPI_FFT_SCALAR,plan->recv_proc[irecv],0,
- plan->comm,&plan->request[irecv]);
+ MPI_FFT_SCALAR,plan->recv_proc[irecv],0,
+ plan->comm,&plan->request[irecv]);
- // send all messages to other procs
+ // send all messages to other procs
for (isend = 0; isend < plan->nsend; isend++) {
plan->pack(&in[plan->send_offset[isend]],
- plan->sendbuf,&plan->packplan[isend]);
+ plan->sendbuf,&plan->packplan[isend]);
MPI_Send(plan->sendbuf,plan->send_size[isend],MPI_FFT_SCALAR,
- plan->send_proc[isend],0,plan->comm);
- }
+ plan->send_proc[isend],0,plan->comm);
+ }
- // copy in -> scratch -> out for self data
+ // copy in -> scratch -> out for self data
if (plan->self) {
isend = plan->nsend;
irecv = plan->nrecv;
plan->pack(&in[plan->send_offset[isend]],
- &scratch[plan->recv_bufloc[irecv]],
- &plan->packplan[isend]);
+ &scratch[plan->recv_bufloc[irecv]],
+ &plan->packplan[isend]);
plan->unpack(&scratch[plan->recv_bufloc[irecv]],
- &out[plan->recv_offset[irecv]],&plan->unpackplan[irecv]);
+ &out[plan->recv_offset[irecv]],&plan->unpackplan[irecv]);
}
- // unpack all messages from scratch -> out
+ // unpack all messages from scratch -> out
for (i = 0; i < plan->nrecv; i++) {
MPI_Waitany(plan->nrecv,plan->request,&irecv,&status);
plan->unpack(&scratch[plan->recv_bufloc[irecv]],
- &out[plan->recv_offset[irecv]],&plan->unpackplan[irecv]);
+ &out[plan->recv_offset[irecv]],&plan->unpackplan[irecv]);
}
}
/* ----------------------------------------------------------------------
- Create plan for performing a 3d remap
+ Create plan for performing a 3d remap
Arguments:
comm MPI communicator for the P procs which own the data
@@ -123,14 +123,14 @@ void remap_3d(FFT_SCALAR *in, FFT_SCALAR *out, FFT_SCALAR *buf,
nqty # of datums per element
permute permutation in storage order of indices on output
0 = no permutation
- 1 = permute once = mid->fast, slow->mid, fast->slow
- 2 = permute twice = slow->fast, fast->mid, mid->slow
+ 1 = permute once = mid->fast, slow->mid, fast->slow
+ 2 = permute twice = slow->fast, fast->mid, mid->slow
memory user provides buffer memory for remap or system does
0 = user provides memory
- 1 = system provides memory
+ 1 = system provides memory
precision precision of data
1 = single precision (4 bytes per datum)
- 2 = double precision (8 bytes per datum)
+ 2 = double precision (8 bytes per datum)
------------------------------------------------------------------------- */
struct remap_plan_3d *remap_3d_create_plan(
@@ -147,17 +147,17 @@ struct remap_plan_3d *remap_3d_create_plan(
struct extent_3d in,out,overlap;
int i,iproc,nsend,nrecv,ibuf,size,me,nprocs;
- // query MPI info
+ // query MPI info
MPI_Comm_rank(comm,&me);
MPI_Comm_size(comm,&nprocs);
- // allocate memory for plan data struct
+ // allocate memory for plan data struct
plan = (struct remap_plan_3d *) malloc(sizeof(struct remap_plan_3d));
if (plan == NULL) return NULL;
- // store parameters in local data structs
+ // store parameters in local data structs
in.ilo = in_ilo;
in.ihi = in_ihi;
@@ -183,15 +183,15 @@ struct remap_plan_3d *remap_3d_create_plan(
out.khi = out_khi;
out.ksize = out.khi - out.klo + 1;
- // combine output extents across all procs
+ // combine output extents across all procs
array = (struct extent_3d *) malloc(nprocs*sizeof(struct extent_3d));
if (array == NULL) return NULL;
MPI_Allgather(&out,sizeof(struct extent_3d),MPI_BYTE,
- array,sizeof(struct extent_3d),MPI_BYTE,comm);
+ array,sizeof(struct extent_3d),MPI_BYTE,comm);
- // count send collides, including self
+ // count send collides, including self
nsend = 0;
iproc = me;
@@ -201,7 +201,7 @@ struct remap_plan_3d *remap_3d_create_plan(
nsend += remap_3d_collide(&in,&array[iproc],&overlap);
}
- // malloc space for send info
+ // malloc space for send info
if (nsend) {
plan->pack = pack_3d;
@@ -209,14 +209,14 @@ struct remap_plan_3d *remap_3d_create_plan(
plan->send_offset = (int *) malloc(nsend*sizeof(int));
plan->send_size = (int *) malloc(nsend*sizeof(int));
plan->send_proc = (int *) malloc(nsend*sizeof(int));
- plan->packplan = (struct pack_plan_3d *)
+ plan->packplan = (struct pack_plan_3d *)
malloc(nsend*sizeof(struct pack_plan_3d));
- if (plan->send_offset == NULL || plan->send_size == NULL ||
- plan->send_proc == NULL || plan->packplan == NULL) return NULL;
+ if (plan->send_offset == NULL || plan->send_size == NULL ||
+ plan->send_proc == NULL || plan->packplan == NULL) return NULL;
}
- // store send info, with self as last entry
+ // store send info, with self as last entry
nsend = 0;
iproc = me;
@@ -225,9 +225,9 @@ struct remap_plan_3d *remap_3d_create_plan(
if (iproc == nprocs) iproc = 0;
if (remap_3d_collide(&in,&array[iproc],&overlap)) {
plan->send_proc[nsend] = iproc;
- plan->send_offset[nsend] = nqty *
- ((overlap.klo-in.klo)*in.jsize*in.isize +
- ((overlap.jlo-in.jlo)*in.isize + overlap.ilo-in.ilo));
+ plan->send_offset[nsend] = nqty *
+ ((overlap.klo-in.klo)*in.jsize*in.isize +
+ ((overlap.jlo-in.jlo)*in.isize + overlap.ilo-in.ilo));
plan->packplan[nsend].nfast = nqty*overlap.isize;
plan->packplan[nsend].nmid = overlap.jsize;
plan->packplan[nsend].nslow = overlap.ksize;
@@ -239,19 +239,19 @@ struct remap_plan_3d *remap_3d_create_plan(
}
}
- // plan->nsend = # of sends not including self
+ // plan->nsend = # of sends not including self
if (nsend && plan->send_proc[nsend-1] == me)
plan->nsend = nsend - 1;
else
plan->nsend = nsend;
- // combine input extents across all procs
+ // combine input extents across all procs
MPI_Allgather(&in,sizeof(struct extent_3d),MPI_BYTE,
- array,sizeof(struct extent_3d),MPI_BYTE,comm);
+ array,sizeof(struct extent_3d),MPI_BYTE,comm);
- // count recv collides, including self
+ // count recv collides, including self
nrecv = 0;
iproc = me;
@@ -260,27 +260,27 @@ struct remap_plan_3d *remap_3d_create_plan(
if (iproc == nprocs) iproc = 0;
nrecv += remap_3d_collide(&out,&array[iproc],&overlap);
}
-
- // malloc space for recv info
+
+ // malloc space for recv info
if (nrecv) {
if (permute == 0)
plan->unpack = unpack_3d;
else if (permute == 1) {
if (nqty == 1)
- plan->unpack = unpack_3d_permute1_1;
+ plan->unpack = unpack_3d_permute1_1;
else if (nqty == 2)
- plan->unpack = unpack_3d_permute1_2;
+ plan->unpack = unpack_3d_permute1_2;
else
- plan->unpack = unpack_3d_permute1_n;
+ plan->unpack = unpack_3d_permute1_n;
}
else if (permute == 2) {
if (nqty == 1)
- plan->unpack = unpack_3d_permute2_1;
+ plan->unpack = unpack_3d_permute2_1;
else if (nqty == 2)
- plan->unpack = unpack_3d_permute2_2;
+ plan->unpack = unpack_3d_permute2_2;
else
- plan->unpack = unpack_3d_permute2_n;
+ plan->unpack = unpack_3d_permute2_n;
}
plan->recv_offset = (int *) malloc(nrecv*sizeof(int));
@@ -288,15 +288,15 @@ struct remap_plan_3d *remap_3d_create_plan(
plan->recv_proc = (int *) malloc(nrecv*sizeof(int));
plan->recv_bufloc = (int *) malloc(nrecv*sizeof(int));
plan->request = (MPI_Request *) malloc(nrecv*sizeof(MPI_Request));
- plan->unpackplan = (struct pack_plan_3d *)
+ plan->unpackplan = (struct pack_plan_3d *)
malloc(nrecv*sizeof(struct pack_plan_3d));
- if (plan->recv_offset == NULL || plan->recv_size == NULL ||
- plan->recv_proc == NULL || plan->recv_bufloc == NULL ||
- plan->request == NULL || plan->unpackplan == NULL) return NULL;
+ if (plan->recv_offset == NULL || plan->recv_size == NULL ||
+ plan->recv_proc == NULL || plan->recv_bufloc == NULL ||
+ plan->request == NULL || plan->unpackplan == NULL) return NULL;
}
- // store recv info, with self as last entry
+ // store recv info, with self as last entry
ibuf = 0;
nrecv = 0;
@@ -310,37 +310,37 @@ struct remap_plan_3d *remap_3d_create_plan(
plan->recv_bufloc[nrecv] = ibuf;
if (permute == 0) {
- plan->recv_offset[nrecv] = nqty *
- ((overlap.klo-out.klo)*out.jsize*out.isize +
- (overlap.jlo-out.jlo)*out.isize + (overlap.ilo-out.ilo));
- plan->unpackplan[nrecv].nfast = nqty*overlap.isize;
- plan->unpackplan[nrecv].nmid = overlap.jsize;
- plan->unpackplan[nrecv].nslow = overlap.ksize;
- plan->unpackplan[nrecv].nstride_line = nqty*out.isize;
- plan->unpackplan[nrecv].nstride_plane = nqty*out.jsize*out.isize;
- plan->unpackplan[nrecv].nqty = nqty;
+ plan->recv_offset[nrecv] = nqty *
+ ((overlap.klo-out.klo)*out.jsize*out.isize +
+ (overlap.jlo-out.jlo)*out.isize + (overlap.ilo-out.ilo));
+ plan->unpackplan[nrecv].nfast = nqty*overlap.isize;
+ plan->unpackplan[nrecv].nmid = overlap.jsize;
+ plan->unpackplan[nrecv].nslow = overlap.ksize;
+ plan->unpackplan[nrecv].nstride_line = nqty*out.isize;
+ plan->unpackplan[nrecv].nstride_plane = nqty*out.jsize*out.isize;
+ plan->unpackplan[nrecv].nqty = nqty;
}
else if (permute == 1) {
- plan->recv_offset[nrecv] = nqty *
- ((overlap.ilo-out.ilo)*out.ksize*out.jsize +
- (overlap.klo-out.klo)*out.jsize + (overlap.jlo-out.jlo));
- plan->unpackplan[nrecv].nfast = overlap.isize;
- plan->unpackplan[nrecv].nmid = overlap.jsize;
- plan->unpackplan[nrecv].nslow = overlap.ksize;
- plan->unpackplan[nrecv].nstride_line = nqty*out.jsize;
- plan->unpackplan[nrecv].nstride_plane = nqty*out.ksize*out.jsize;
- plan->unpackplan[nrecv].nqty = nqty;
+ plan->recv_offset[nrecv] = nqty *
+ ((overlap.ilo-out.ilo)*out.ksize*out.jsize +
+ (overlap.klo-out.klo)*out.jsize + (overlap.jlo-out.jlo));
+ plan->unpackplan[nrecv].nfast = overlap.isize;
+ plan->unpackplan[nrecv].nmid = overlap.jsize;
+ plan->unpackplan[nrecv].nslow = overlap.ksize;
+ plan->unpackplan[nrecv].nstride_line = nqty*out.jsize;
+ plan->unpackplan[nrecv].nstride_plane = nqty*out.ksize*out.jsize;
+ plan->unpackplan[nrecv].nqty = nqty;
}
else {
- plan->recv_offset[nrecv] = nqty *
- ((overlap.jlo-out.jlo)*out.isize*out.ksize +
- (overlap.ilo-out.ilo)*out.ksize + (overlap.klo-out.klo));
- plan->unpackplan[nrecv].nfast = overlap.isize;
- plan->unpackplan[nrecv].nmid = overlap.jsize;
- plan->unpackplan[nrecv].nslow = overlap.ksize;
- plan->unpackplan[nrecv].nstride_line = nqty*out.ksize;
- plan->unpackplan[nrecv].nstride_plane = nqty*out.isize*out.ksize;
- plan->unpackplan[nrecv].nqty = nqty;
+ plan->recv_offset[nrecv] = nqty *
+ ((overlap.jlo-out.jlo)*out.isize*out.ksize +
+ (overlap.ilo-out.ilo)*out.ksize + (overlap.klo-out.klo));
+ plan->unpackplan[nrecv].nfast = overlap.isize;
+ plan->unpackplan[nrecv].nmid = overlap.jsize;
+ plan->unpackplan[nrecv].nslow = overlap.ksize;
+ plan->unpackplan[nrecv].nstride_line = nqty*out.ksize;
+ plan->unpackplan[nrecv].nstride_plane = nqty*out.isize*out.ksize;
+ plan->unpackplan[nrecv].nqty = nqty;
}
plan->recv_size[nrecv] = nqty*overlap.isize*overlap.jsize*overlap.ksize;
@@ -349,14 +349,14 @@ struct remap_plan_3d *remap_3d_create_plan(
}
}
- // plan->nrecv = # of recvs not including self
+ // plan->nrecv = # of recvs not including self
if (nrecv && plan->recv_proc[nrecv-1] == me)
plan->nrecv = nrecv - 1;
else
plan->nrecv = nrecv;
- // init remaining fields in remap plan
+ // init remaining fields in remap plan
plan->memory = memory;
@@ -365,11 +365,11 @@ struct remap_plan_3d *remap_3d_create_plan(
else
plan->self = 1;
- // free locally malloced space
+ // free locally malloced space
free(array);
- // find biggest send message (not including self) and malloc space for it
+ // find biggest send message (not including self) and malloc space for it
plan->sendbuf = NULL;
@@ -383,39 +383,39 @@ struct remap_plan_3d *remap_3d_create_plan(
}
// if requested, allocate internal scratch space for recvs,
- // only need it if I will receive any data (including self)
+ // only need it if I will receive any data (including self)
plan->scratch = NULL;
if (memory == 1) {
if (nrecv > 0) {
plan->scratch =
- (FFT_SCALAR *) malloc(nqty*out.isize*out.jsize*out.ksize*sizeof(FFT_SCALAR));
+ (FFT_SCALAR *) malloc(nqty*out.isize*out.jsize*out.ksize*sizeof(FFT_SCALAR));
if (plan->scratch == NULL) return NULL;
}
}
- // create new MPI communicator for remap
+ // create new MPI communicator for remap
MPI_Comm_dup(comm,&plan->comm);
- // return pointer to plan
+ // return pointer to plan
return plan;
}
/* ----------------------------------------------------------------------
- Destroy a 3d remap plan
+ Destroy a 3d remap plan
------------------------------------------------------------------------- */
void remap_3d_destroy_plan(struct remap_plan_3d *plan)
{
- // free MPI communicator
+ // free MPI communicator
MPI_Comm_free(&plan->comm);
- // free internal arrays
+ // free internal arrays
if (plan->nsend || plan->self) {
free(plan->send_offset);
@@ -435,20 +435,20 @@ void remap_3d_destroy_plan(struct remap_plan_3d *plan)
if (plan->scratch) free(plan->scratch);
}
- // free plan itself
+ // free plan itself
free(plan);
}
/* ----------------------------------------------------------------------
- collide 2 sets of indices to determine overlap
+ collide 2 sets of indices to determine overlap
compare bounds of block1 with block2 to see if they overlap
return 1 if they do and put bounds of overlapping section in overlap
- return 0 if they do not overlap
+ return 0 if they do not overlap
------------------------------------------------------------------------- */
int remap_3d_collide(struct extent_3d *block1, struct extent_3d *block2,
- struct extent_3d *overlap)
+ struct extent_3d *overlap)
{
overlap->ilo = MAX(block1->ilo,block2->ilo);
@@ -457,8 +457,8 @@ int remap_3d_collide(struct extent_3d *block1, struct extent_3d *block2,
overlap->jhi = MIN(block1->jhi,block2->jhi);
overlap->klo = MAX(block1->klo,block2->klo);
overlap->khi = MIN(block1->khi,block2->khi);
-
- if (overlap->ilo > overlap->ihi ||
+
+ if (overlap->ilo > overlap->ihi ||
overlap->jlo > overlap->jhi ||
overlap->klo > overlap->khi) return 0;
diff --git a/src/KSPACE/remap.h b/src/KSPACE/remap.h
index 648b3a0d163405c81cb6e25080c1a6a75bda06b0..617569068663cbf8b8c4e8723003e0c1ace1eb12 100644
--- a/src/KSPACE/remap.h
+++ b/src/KSPACE/remap.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -21,33 +21,33 @@ typedef double FFT_SCALAR;
#define MPI_FFT_SCALAR MPI_DOUBLE
#endif
-// details of how to do a 3d remap
+// details of how to do a 3d remap
struct remap_plan_3d {
- FFT_SCALAR *sendbuf; // buffer for MPI sends
- FFT_SCALAR *scratch; // scratch buffer for MPI recvs
+ FFT_SCALAR *sendbuf; // buffer for MPI sends
+ FFT_SCALAR *scratch; // scratch buffer for MPI recvs
void (*pack)(FFT_SCALAR *, FFT_SCALAR *, struct pack_plan_3d *);
- // which pack function to use
+ // which pack function to use
void (*unpack)(FFT_SCALAR *, FFT_SCALAR *, struct pack_plan_3d *);
- // which unpack function to use
- int *send_offset; // extraction loc for each send
- int *send_size; // size of each send message
- int *send_proc; // proc to send each message to
- struct pack_plan_3d *packplan; // pack plan for each send message
- int *recv_offset; // insertion loc for each recv
- int *recv_size; // size of each recv message
- int *recv_proc; // proc to recv each message from
- int *recv_bufloc; // offset in scratch buf for each recv
- MPI_Request *request; // MPI request for each posted recv
- struct pack_plan_3d *unpackplan; // unpack plan for each recv message
- int nrecv; // # of recvs from other procs
- int nsend; // # of sends to other procs
- int self; // whether I send/recv with myself
- int memory; // user provides scratch space or not
- MPI_Comm comm; // group of procs performing remap
+ // which unpack function to use
+ int *send_offset; // extraction loc for each send
+ int *send_size; // size of each send message
+ int *send_proc; // proc to send each message to
+ struct pack_plan_3d *packplan; // pack plan for each send message
+ int *recv_offset; // insertion loc for each recv
+ int *recv_size; // size of each recv message
+ int *recv_proc; // proc to recv each message from
+ int *recv_bufloc; // offset in scratch buf for each recv
+ MPI_Request *request; // MPI request for each posted recv
+ struct pack_plan_3d *unpackplan; // unpack plan for each recv message
+ int nrecv; // # of recvs from other procs
+ int nsend; // # of sends to other procs
+ int self; // whether I send/recv with myself
+ int memory; // user provides scratch space or not
+ MPI_Comm comm; // group of procs performing remap
};
-// collision between 2 regions
+// collision between 2 regions
struct extent_3d {
int ilo,ihi,isize;
@@ -55,12 +55,12 @@ struct extent_3d {
int klo,khi,ksize;
};
-// function prototypes
+// function prototypes
void remap_3d(FFT_SCALAR *, FFT_SCALAR *, FFT_SCALAR *, struct remap_plan_3d *);
-struct remap_plan_3d *remap_3d_create_plan(MPI_Comm,
- int, int, int, int, int, int, int, int, int, int, int, int,
+struct remap_plan_3d *remap_3d_create_plan(MPI_Comm,
+ int, int, int, int, int, int, int, int, int, int, int, int,
int, int, int, int);
void remap_3d_destroy_plan(struct remap_plan_3d *);
-int remap_3d_collide(struct extent_3d *,
- struct extent_3d *, struct extent_3d *);
+int remap_3d_collide(struct extent_3d *,
+ struct extent_3d *, struct extent_3d *);
diff --git a/src/KSPACE/remap_wrap.cpp b/src/KSPACE/remap_wrap.cpp
index 679c2a8365aeb6de4af220f5c9a58485a1e9f496..dc159cc8f8240da450052e1f2b2091d757a33900 100644
--- a/src/KSPACE/remap_wrap.cpp
+++ b/src/KSPACE/remap_wrap.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -20,16 +20,16 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
Remap::Remap(LAMMPS *lmp, MPI_Comm comm,
- int in_ilo, int in_ihi, int in_jlo, int in_jhi,
- int in_klo, int in_khi,
- int out_ilo, int out_ihi, int out_jlo, int out_jhi,
- int out_klo, int out_khi,
- int nqty, int permute, int memory, int precision) : Pointers(lmp)
+ int in_ilo, int in_ihi, int in_jlo, int in_jhi,
+ int in_klo, int in_khi,
+ int out_ilo, int out_ihi, int out_jlo, int out_jhi,
+ int out_klo, int out_khi,
+ int nqty, int permute, int memory, int precision) : Pointers(lmp)
{
plan = remap_3d_create_plan(comm,
- in_ilo,in_ihi,in_jlo,in_jhi,in_klo,in_khi,
- out_ilo,out_ihi,out_jlo,out_jhi,out_klo,out_khi,
- nqty,permute,memory,precision);
+ in_ilo,in_ihi,in_jlo,in_jhi,in_klo,in_khi,
+ out_ilo,out_ihi,out_jlo,out_jhi,out_klo,out_khi,
+ nqty,permute,memory,precision);
if (plan == NULL) error->one(FLERR,"Could not create 3d remap plan");
}
diff --git a/src/KSPACE/remap_wrap.h b/src/KSPACE/remap_wrap.h
index 60ba810bd736c4ae389f14a01bb126e5d9163259..d9f817ed42ee745bbb00d880e29389a56b907f54 100644
--- a/src/KSPACE/remap_wrap.h
+++ b/src/KSPACE/remap_wrap.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -22,7 +22,7 @@ namespace LAMMPS_NS {
class Remap : protected Pointers {
public:
Remap(class LAMMPS *, MPI_Comm,int,int,int,int,int,int,
- int,int,int,int,int,int,int,int,int,int);
+ int,int,int,int,int,int,int,int,int,int);
~Remap();
void perform(FFT_SCALAR *, FFT_SCALAR *, FFT_SCALAR *);
diff --git a/src/MANYBODY/fix_qeq_comb.cpp b/src/MANYBODY/fix_qeq_comb.cpp
index f04a93bd1f5a7c97560f57c4cd4900eb865ffe9b..26d91e83aa1013bf464b2c77642372fe9023831d 100644
--- a/src/MANYBODY/fix_qeq_comb.cpp
+++ b/src/MANYBODY/fix_qeq_comb.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -60,17 +60,17 @@ FixQEQComb::FixQEQComb(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
if (strcmp(arg[iarg],"file") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix qeq/comb command");
if (me == 0) {
- fp = fopen(arg[iarg+1],"w");
- if (fp == NULL) {
- char str[128];
- sprintf(str,"Cannot open fix qeq/comb file %s",arg[iarg+1]);
- error->one(FLERR,str);
- }
+ fp = fopen(arg[iarg+1],"w");
+ if (fp == NULL) {
+ char str[128];
+ sprintf(str,"Cannot open fix qeq/comb file %s",arg[iarg+1]);
+ error->one(FLERR,str);
+ }
}
iarg += 2;
} else error->all(FLERR,"Illegal fix qeq/comb command");
}
-
+
nmax = atom->nmax;
memory->create(qf,nmax,"qeq:qf");
memory->create(q1,nmax,"qeq:q1");
@@ -161,10 +161,10 @@ void FixQEQComb::post_force(int vflag)
memory->create(q2,nmax,"qeq:q2");
vector_atom = qf;
}
-
+
// more loops for first-time charge equilibrium
- iloop = 0;
+ iloop = 0;
if (firstflag) loopmax = 5000;
else loopmax = 2000;
@@ -172,15 +172,15 @@ void FixQEQComb::post_force(int vflag)
if (me == 0 && fp)
fprintf(fp,"Charge equilibration on step " BIGINT_FORMAT "\n",
- update->ntimestep);
-
+ update->ntimestep);
+
heatpq = 0.05;
qmass = 0.000548580;
dtq = 0.0006;
dtq2 = 0.5*dtq*dtq/qmass;
double enegchk = 0.0;
- double enegtot = 0.0;
+ double enegtot = 0.0;
double enegmax = 0.0;
double *q = atom->q;
@@ -193,8 +193,8 @@ void FixQEQComb::post_force(int vflag)
for (iloop = 0; iloop < loopmax; iloop ++ ) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- q1[i] += qf[i]*dtq2 - heatpq*q1[i];
- q[i] += q1[i];
+ q1[i] += qf[i]*dtq2 - heatpq*q1[i];
+ q[i] += q1[i];
}
enegtot = comb->yasu_char(qf,igroup);
@@ -203,35 +203,35 @@ void FixQEQComb::post_force(int vflag)
for (i = 0; i < nlocal ; i++)
if (mask[i] & groupbit) {
- q2[i] = enegtot-qf[i];
- enegmax = MAX(enegmax,fabs(q2[i]));
- enegchk += fabs(q2[i]);
- qf[i] = q2[i];
+ q2[i] = enegtot-qf[i];
+ enegmax = MAX(enegmax,fabs(q2[i]));
+ enegchk += fabs(q2[i]);
+ qf[i] = q2[i];
}
MPI_Allreduce(&enegchk,&enegchkall,1,MPI_DOUBLE,MPI_SUM,world);
enegchk = enegchkall/ngroup;
MPI_Allreduce(&enegmax,&enegmaxall,1,MPI_DOUBLE,MPI_MAX,world);
enegmax = enegmaxall;
-
+
if (enegchk <= precision && enegmax <= 100.0*precision) break;
if (me == 0 && fp)
fprintf(fp," iteration: %d, enegtot %.6g, "
- "enegmax %.6g, fq deviation: %.6g\n",
- iloop,enegtot,enegmax,enegchk);
-
+ "enegmax %.6g, fq deviation: %.6g\n",
+ iloop,enegtot,enegmax,enegchk);
+
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
- q1[i] += qf[i]*dtq2 - heatpq*q1[i];
- }
+ q1[i] += qf[i]*dtq2 - heatpq*q1[i];
+ }
if (me == 0 && fp) {
if (iloop == loopmax)
fprintf(fp,"Charges did not converge in %d iterations\n",iloop);
else
fprintf(fp,"Charges converged in %d iterations to %.10f tolerance\n",
- iloop,enegchk);
+ iloop,enegchk);
}
}
diff --git a/src/MANYBODY/fix_qeq_comb.h b/src/MANYBODY/fix_qeq_comb.h
index df48bb98a3898a170c0ab308a3d98bbffcaa22bc..7452fcfa0eaaf7a4975af787ae62aa1aa00142ee 100644
--- a/src/MANYBODY/fix_qeq_comb.h
+++ b/src/MANYBODY/fix_qeq_comb.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/MANYBODY/pair_adp.cpp b/src/MANYBODY/pair_adp.cpp
index 8ce9b57732364f3414c0f9a08e6cbf7d90029b16..90d6eab223838a7f288bd6d282dcfc232deb29ae 100644
--- a/src/MANYBODY/pair_adp.cpp
+++ b/src/MANYBODY/pair_adp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -158,22 +158,22 @@ void PairADP::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// zero out density
if (newton_pair) {
m = nlocal + atom->nghost;
for (i = 0; i < m; i++) {
- rho[i] = 0.0;
+ rho[i] = 0.0;
mu[i][0] = 0.0; mu[i][1] = 0.0; mu[i][2] = 0.0;
- lambda[i][0] = 0.0; lambda[i][1] = 0.0; lambda[i][2] = 0.0;
+ lambda[i][0] = 0.0; lambda[i][1] = 0.0; lambda[i][2] = 0.0;
lambda[i][3] = 0.0; lambda[i][4] = 0.0; lambda[i][5] = 0.0;
}
} else {
for (i = 0; i < nlocal; i++) {
rho[i] = 0.0;
mu[i][0] = 0.0; mu[i][1] = 0.0; mu[i][2] = 0.0;
- lambda[i][0] = 0.0; lambda[i][1] = 0.0; lambda[i][2] = 0.0;
+ lambda[i][0] = 0.0; lambda[i][1] = 0.0; lambda[i][2] = 0.0;
lambda[i][3] = 0.0; lambda[i][4] = 0.0; lambda[i][5] = 0.0;
}
}
@@ -199,21 +199,21 @@ void PairADP::compute(int eflag, int vflag)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cutforcesq) {
- jtype = type[j];
- p = sqrt(rsq)*rdr + 1.0;
- m = static_cast<int> (p);
- m = MIN(m,nr-1);
- p -= m;
- p = MIN(p,1.0);
- coeff = rhor_spline[type2rhor[jtype][itype]][m];
- rho[i] += ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
+ jtype = type[j];
+ p = sqrt(rsq)*rdr + 1.0;
+ m = static_cast<int> (p);
+ m = MIN(m,nr-1);
+ p -= m;
+ p = MIN(p,1.0);
+ coeff = rhor_spline[type2rhor[jtype][itype]][m];
+ rho[i] += ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
coeff = u2r_spline[type2u2r[jtype][itype]][m];
- u2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
+ u2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
mu[i][0] += u2*delx;
mu[i][1] += u2*dely;
mu[i][2] += u2*delz;
coeff = w2r_spline[type2w2r[jtype][itype]][m];
- w2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
+ w2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
lambda[i][0] += w2*delx*delx;
lambda[i][1] += w2*dely*dely;
lambda[i][2] += w2*delz*delz;
@@ -221,24 +221,24 @@ void PairADP::compute(int eflag, int vflag)
lambda[i][4] += w2*delx*delz;
lambda[i][5] += w2*delx*dely;
- if (newton_pair || j < nlocal) {
+ if (newton_pair || j < nlocal) {
// verify sign difference for mu and lambda
- coeff = rhor_spline[type2rhor[itype][jtype]][m];
- rho[j] += ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
+ coeff = rhor_spline[type2rhor[itype][jtype]][m];
+ rho[j] += ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
coeff = u2r_spline[type2u2r[itype][jtype]][m];
u2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
mu[j][0] -= u2*delx;
mu[j][1] -= u2*dely;
mu[j][2] -= u2*delz;
coeff = w2r_spline[type2w2r[itype][jtype]][m];
- w2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
+ w2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
lambda[j][0] += w2*delx*delx;
lambda[j][1] += w2*dely*dely;
lambda[j][2] += w2*delz*delz;
lambda[j][3] += w2*dely*delz;
lambda[j][4] += w2*delx*delz;
lambda[j][5] += w2*delx*dely;
- }
+ }
}
}
}
@@ -263,11 +263,11 @@ void PairADP::compute(int eflag, int vflag)
phi = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
phi += 0.5*(mu[i][0]*mu[i][0]+mu[i][1]*mu[i][1]+mu[i][2]*mu[i][2]);
phi += 0.5*(lambda[i][0]*lambda[i][0]+lambda[i][1]*
- lambda[i][1]+lambda[i][2]*lambda[i][2]);
+ lambda[i][1]+lambda[i][2]*lambda[i][2]);
phi += 1.0*(lambda[i][3]*lambda[i][3]+lambda[i][4]*
- lambda[i][4]+lambda[i][5]*lambda[i][5]);
+ lambda[i][4]+lambda[i][5]*lambda[i][5]);
phi -= 1.0/6.0*(lambda[i][0]+lambda[i][1]+lambda[i][2])*
- (lambda[i][0]+lambda[i][1]+lambda[i][2]);
+ (lambda[i][0]+lambda[i][1]+lambda[i][2]);
if (eflag_global) eng_vdwl += phi;
if (eflag_atom) eatom[i] += phi;
}
@@ -299,51 +299,51 @@ void PairADP::compute(int eflag, int vflag)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cutforcesq) {
- jtype = type[j];
- r = sqrt(rsq);
- p = r*rdr + 1.0;
- m = static_cast<int> (p);
- m = MIN(m,nr-1);
- p -= m;
- p = MIN(p,1.0);
-
- // rhoip = derivative of (density at atom j due to atom i)
- // rhojp = derivative of (density at atom i due to atom j)
- // phi = pair potential energy
- // phip = phi'
- // z2 = phi * r
- // z2p = (phi * r)' = (phi' r) + phi
+ jtype = type[j];
+ r = sqrt(rsq);
+ p = r*rdr + 1.0;
+ m = static_cast<int> (p);
+ m = MIN(m,nr-1);
+ p -= m;
+ p = MIN(p,1.0);
+
+ // rhoip = derivative of (density at atom j due to atom i)
+ // rhojp = derivative of (density at atom i due to atom j)
+ // phi = pair potential energy
+ // phip = phi'
+ // z2 = phi * r
+ // z2p = (phi * r)' = (phi' r) + phi
// u2 = u
// u2p = u'
// w2 = w
// w2p = w'
- // psip needs both fp[i] and fp[j] terms since r_ij appears in two
- // terms of embed eng: Fi(sum rho_ij) and Fj(sum rho_ji)
- // hence embed' = Fi(sum rho_ij) rhojp + Fj(sum rho_ji) rhoip
-
- coeff = rhor_spline[type2rhor[itype][jtype]][m];
- rhoip = (coeff[0]*p + coeff[1])*p + coeff[2];
- coeff = rhor_spline[type2rhor[jtype][itype]][m];
- rhojp = (coeff[0]*p + coeff[1])*p + coeff[2];
- coeff = z2r_spline[type2z2r[itype][jtype]][m];
- z2p = (coeff[0]*p + coeff[1])*p + coeff[2];
- z2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
+ // psip needs both fp[i] and fp[j] terms since r_ij appears in two
+ // terms of embed eng: Fi(sum rho_ij) and Fj(sum rho_ji)
+ // hence embed' = Fi(sum rho_ij) rhojp + Fj(sum rho_ji) rhoip
+
+ coeff = rhor_spline[type2rhor[itype][jtype]][m];
+ rhoip = (coeff[0]*p + coeff[1])*p + coeff[2];
+ coeff = rhor_spline[type2rhor[jtype][itype]][m];
+ rhojp = (coeff[0]*p + coeff[1])*p + coeff[2];
+ coeff = z2r_spline[type2z2r[itype][jtype]][m];
+ z2p = (coeff[0]*p + coeff[1])*p + coeff[2];
+ z2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
coeff = u2r_spline[type2u2r[itype][jtype]][m];
- u2p = (coeff[0]*p + coeff[1])*p + coeff[2];
- u2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
+ u2p = (coeff[0]*p + coeff[1])*p + coeff[2];
+ u2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
coeff = w2r_spline[type2w2r[itype][jtype]][m];
- w2p = (coeff[0]*p + coeff[1])*p + coeff[2];
- w2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
+ w2p = (coeff[0]*p + coeff[1])*p + coeff[2];
+ w2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
- recip = 1.0/r;
- phi = z2*recip;
- phip = z2p*recip - phi*recip;
- psip = fp[i]*rhojp + fp[j]*rhoip + phip;
- fpair = -psip*recip;
+ recip = 1.0/r;
+ phi = z2*recip;
+ phip = z2p*recip - phi*recip;
+ psip = fp[i]*rhojp + fp[j]*rhoip + phip;
+ fpair = -psip*recip;
delmux = mu[i][0]-mu[j][0];
- delmuy = mu[i][1]-mu[j][1];
- delmuz = mu[i][2]-mu[j][2];
+ delmuy = mu[i][1]-mu[j][1];
+ delmuz = mu[i][2]-mu[j][2];
trdelmu = delmux*delx+delmuy*dely+delmuz*delz;
sumlamxx = lambda[i][0]+lambda[j][0];
sumlamyy = lambda[i][1]+lambda[j][1];
@@ -352,37 +352,37 @@ void PairADP::compute(int eflag, int vflag)
sumlamxz = lambda[i][4]+lambda[j][4];
sumlamxy = lambda[i][5]+lambda[j][5];
tradellam = sumlamxx*delx*delx+sumlamyy*dely*dely+
- sumlamzz*delz*delz+2.0*sumlamxy*delx*dely+
- 2.0*sumlamxz*delx*delz+2.0*sumlamyz*dely*delz;
+ sumlamzz*delz*delz+2.0*sumlamxy*delx*dely+
+ 2.0*sumlamxz*delx*delz+2.0*sumlamyz*dely*delz;
nu = sumlamxx+sumlamyy+sumlamzz;
- adpx = delmux*u2 + trdelmu*u2p*delx*recip +
- 2.0*w2*(sumlamxx*delx+sumlamxy*dely+sumlamxz*delz) +
- w2p*delx*recip*tradellam - 1.0/3.0*nu*(w2p*r+2.0*w2)*delx;
- adpy = delmuy*u2 + trdelmu*u2p*dely*recip +
- 2.0*w2*(sumlamxy*delx+sumlamyy*dely+sumlamyz*delz) +
- w2p*dely*recip*tradellam - 1.0/3.0*nu*(w2p*r+2.0*w2)*dely;
- adpz = delmuz*u2 + trdelmu*u2p*delz*recip +
- 2.0*w2*(sumlamxz*delx+sumlamyz*dely+sumlamzz*delz) +
- w2p*delz*recip*tradellam - 1.0/3.0*nu*(w2p*r+2.0*w2)*delz;
+ adpx = delmux*u2 + trdelmu*u2p*delx*recip +
+ 2.0*w2*(sumlamxx*delx+sumlamxy*dely+sumlamxz*delz) +
+ w2p*delx*recip*tradellam - 1.0/3.0*nu*(w2p*r+2.0*w2)*delx;
+ adpy = delmuy*u2 + trdelmu*u2p*dely*recip +
+ 2.0*w2*(sumlamxy*delx+sumlamyy*dely+sumlamyz*delz) +
+ w2p*dely*recip*tradellam - 1.0/3.0*nu*(w2p*r+2.0*w2)*dely;
+ adpz = delmuz*u2 + trdelmu*u2p*delz*recip +
+ 2.0*w2*(sumlamxz*delx+sumlamyz*dely+sumlamzz*delz) +
+ w2p*delz*recip*tradellam - 1.0/3.0*nu*(w2p*r+2.0*w2)*delz;
adpx*=-1.0; adpy*=-1.0; adpz*=-1.0;
fx = delx*fpair+adpx;
- fy = dely*fpair+adpy;
- fz = delz*fpair+adpz;
-
- f[i][0] += fx;
- f[i][1] += fy;
- f[i][2] += fz;
- if (newton_pair || j < nlocal) {
- f[j][0] -= fx;
- f[j][1] -= fy;
- f[j][2] -= fz;
- }
-
- if (eflag) evdwl = phi;
+ fy = dely*fpair+adpy;
+ fz = delz*fpair+adpz;
+
+ f[i][0] += fx;
+ f[i][1] += fy;
+ f[i][2] += fz;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= fx;
+ f[j][1] -= fy;
+ f[j][2] -= fz;
+ }
+
+ if (eflag) evdwl = phi;
if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,evdwl,0.0,
- fx,fy,fz,delx,dely,delz);
+ fx,fy,fz,delx,dely,delz);
}
}
}
@@ -488,9 +488,9 @@ void PairADP::coeff(int narg, char **arg)
for (i = 1; i <= n; i++) {
for (j = i; j <= n; j++) {
if (map[i] >= 0 && map[j] >= 0) {
- setflag[i][j] = 1;
- if (i == j) atom->set_mass(i,setfl->mass[map[i]]);
- count++;
+ setflag[i][j] = 1;
+ if (i == j) atom->set_mass(i,setfl->mass[map[i]]);
+ count++;
}
}
}
@@ -570,7 +570,7 @@ void PairADP::read_file(char *filename)
int nwords = atom->count_words(line);
if (nwords != file->nelements + 1)
error->all(FLERR,"Incorrect element names in ADP potential file");
-
+
char **words = new char*[file->nelements+1];
nwords = 0;
strtok(line," \t\n\r\f");
@@ -587,7 +587,7 @@ void PairADP::read_file(char *filename)
if (me == 0) {
fgets(line,MAXLINE,fp);
sscanf(line,"%d %lg %d %lg %lg",
- &file->nrho,&file->drho,&file->nr,&file->dr,&file->cut);
+ &file->nrho,&file->drho,&file->nr,&file->dr,&file->cut);
}
MPI_Bcast(&file->nrho,1,MPI_INT,0,world);
@@ -600,11 +600,11 @@ void PairADP::read_file(char *filename)
memory->create(file->frho,file->nelements,file->nrho+1,"pair:frho");
memory->create(file->rhor,file->nelements,file->nr+1,"pair:rhor");
memory->create(file->z2r,file->nelements,file->nelements,file->nr+1,
- "pair:z2r");
+ "pair:z2r");
memory->create(file->u2r,file->nelements,file->nelements,file->nr+1,
- "pair:u2r");
+ "pair:u2r");
memory->create(file->w2r,file->nelements,file->nelements,file->nr+1,
- "pair:w2r");
+ "pair:w2r");
int i,j,tmp;
for (i = 0; i < file->nelements; i++) {
@@ -666,7 +666,7 @@ void PairADP::file2array()
// allocate frho arrays
// nfrho = # of setfl elements + 1 for zero array
-
+
nfrho = setfl->nelements + 1;
memory->destroy(frho);
memory->create(frho,nfrho,nrho+1,"pair:frho");
@@ -746,8 +746,8 @@ void PairADP::file2array()
icol = map[j];
if (irow == -1 || icol == -1) continue;
if (irow < icol) {
- irow = map[j];
- icol = map[i];
+ irow = map[j];
+ icol = map[i];
}
n = 0;
for (m = 0; m < irow; m++) n += m + 1;
@@ -788,8 +788,8 @@ void PairADP::file2array()
icol = map[j];
if (irow == -1 || icol == -1) continue;
if (irow < icol) {
- irow = map[j];
- icol = map[i];
+ irow = map[j];
+ icol = map[i];
}
n = 0;
for (m = 0; m < irow; m++) n += m + 1;
@@ -830,8 +830,8 @@ void PairADP::file2array()
icol = map[j];
if (irow == -1 || icol == -1) continue;
if (irow < icol) {
- irow = map[j];
- icol = map[i];
+ irow = map[j];
+ icol = map[i];
}
n = 0;
for (m = 0; m < irow; m++) n += m + 1;
@@ -886,21 +886,21 @@ void PairADP::interpolate(int n, double delta, double *f, double **spline)
spline[2][5] = 0.5 * (spline[3][6]-spline[1][6]);
spline[n-1][5] = 0.5 * (spline[n][6]-spline[n-2][6]);
spline[n][5] = spline[n][6] - spline[n-1][6];
-
+
for (int m = 3; m <= n-2; m++)
- spline[m][5] = ((spline[m-2][6]-spline[m+2][6]) +
- 8.0*(spline[m+1][6]-spline[m-1][6])) / 12.0;
-
+ spline[m][5] = ((spline[m-2][6]-spline[m+2][6]) +
+ 8.0*(spline[m+1][6]-spline[m-1][6])) / 12.0;
+
for (int m = 1; m <= n-1; m++) {
- spline[m][4] = 3.0*(spline[m+1][6]-spline[m][6]) -
+ spline[m][4] = 3.0*(spline[m+1][6]-spline[m][6]) -
2.0*spline[m][5] - spline[m+1][5];
- spline[m][3] = spline[m][5] + spline[m+1][5] -
+ spline[m][3] = spline[m][5] + spline[m+1][5] -
2.0*(spline[m+1][6]-spline[m][6]);
}
-
+
spline[n][4] = 0.0;
spline[n][3] = 0.0;
-
+
for (int m = 1; m <= n; m++) {
spline[m][2] = spline[m][5]/delta;
spline[m][1] = 2.0*spline[m][4]/delta;
@@ -1019,7 +1019,7 @@ void PairADP::unpack_reverse_comm(int n, int *list, double *buf)
}
/* ----------------------------------------------------------------------
- memory usage of local atom-based arrays
+ memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double PairADP::memory_usage()
diff --git a/src/MANYBODY/pair_adp.h b/src/MANYBODY/pair_adp.h
index 6bd52e6d7d6144ff71e426431499765df93f7da1..1c15abe9c12ce2a5ab981d01b677d66c086d07da 100644
--- a/src/MANYBODY/pair_adp.h
+++ b/src/MANYBODY/pair_adp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -39,7 +39,7 @@ class PairADP : public Pair {
int pack_reverse_comm(int, int, double *);
void unpack_reverse_comm(int, int *, double *);
double memory_usage();
-
+
protected:
int nmax; // allocated size of per-atom arrays
double cutforcesq,cutmax;
@@ -58,7 +58,7 @@ class PairADP : public Pair {
double **u2r, **w2r;
int *type2frho,**type2rhor,**type2z2r;
int **type2u2r,**type2w2r;
-
+
// potentials in spline form used for force computation
double dr,rdr,drho,rdrho;
diff --git a/src/MANYBODY/pair_airebo.cpp b/src/MANYBODY/pair_airebo.cpp
index 07d5d8bf909257999a2b6bf284470269d01b60b2..a39d2484c4f6044876f59ee6abe9f8b05b1fceab 100644
--- a/src/MANYBODY/pair_airebo.cpp
+++ b/src/MANYBODY/pair_airebo.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -96,7 +96,7 @@ void PairAIREBO::compute(int eflag, int vflag)
FREBO(eflag,vflag);
if (ljflag) FLJ(eflag,vflag);
if (torflag) TORSION(eflag,vflag);
-
+
if (vflag_fdotr) virial_fdotr_compute();
}
@@ -193,8 +193,8 @@ void PairAIREBO::coeff(int narg, char **arg)
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
if (map[i] >= 0 && map[j] >= 0) {
- setflag[i][j] = 1;
- count++;
+ setflag[i][j] = 1;
+ count++;
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
@@ -313,11 +313,11 @@ void PairAIREBO::REBO_neigh()
memory->destroy(nH);
memory->create(REBO_numneigh,maxlocal,"AIREBO:numneigh");
REBO_firstneigh = (int **) memory->smalloc(maxlocal*sizeof(int *),
- "AIREBO:firstneigh");
+ "AIREBO:firstneigh");
memory->create(nC,maxlocal,"AIREBO:nC");
memory->create(nH,maxlocal,"AIREBO:nH");
}
-
+
allnum = list->inum + list->gnum;
ilist = list->ilist;
numneigh = list->numneigh;
@@ -358,11 +358,11 @@ void PairAIREBO::REBO_neigh()
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < rcmaxsq[itype][jtype]) {
- neighptr[n++] = j;
- if (jtype == 0)
- nC[i] += Sp(sqrt(rsq),rcmin[itype][jtype],rcmax[itype][jtype],dS);
- else
- nH[i] += Sp(sqrt(rsq),rcmin[itype][jtype],rcmax[itype][jtype],dS);
+ neighptr[n++] = j;
+ if (jtype == 0)
+ nC[i] += Sp(sqrt(rsq),rcmin[itype][jtype],rcmax[itype][jtype],dS);
+ else
+ nH[i] += Sp(sqrt(rsq),rcmin[itype][jtype],rcmax[itype][jtype],dS);
}
}
@@ -371,7 +371,7 @@ void PairAIREBO::REBO_neigh()
npnt += n;
if (npnt >= pgsize)
error->one(FLERR,
- "Neighbor list overflow, boost neigh_modify one or page");
+ "Neighbor list overflow, boost neigh_modify one or page");
}
}
@@ -416,13 +416,13 @@ void PairAIREBO::FREBO(int eflag, int vflag)
jtag = tag[j];
if (itag > jtag) {
- if ((itag+jtag) % 2 == 0) continue;
+ if ((itag+jtag) % 2 == 0) continue;
} else if (itag < jtag) {
- if ((itag+jtag) % 2 == 1) continue;
+ if ((itag+jtag) % 2 == 1) continue;
} else {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
- if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
+ if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
}
jtype = map[type[j]];
@@ -434,7 +434,7 @@ void PairAIREBO::FREBO(int eflag, int vflag)
rij = sqrt(rsq);
wij = Sp(rij,rcmin[itype][jtype],rcmax[itype][jtype],dwij);
if (wij <= TOL) continue;
-
+
Qij = Q[itype][jtype];
Aij = A[itype][jtype];
alphaij = alpha[itype][jtype];
@@ -446,9 +446,9 @@ void PairAIREBO::FREBO(int eflag, int vflag)
VA = dVA = 0.0;
for (m = 0; m < 3; m++) {
- term = -wij * BIJc[itype][jtype][m] * exp(-Beta[itype][jtype][m]*rij);
- VA += term;
- dVA += -Beta[itype][jtype][m] * term;
+ term = -wij * BIJc[itype][jtype][m] * exp(-Beta[itype][jtype][m]*rij);
+ VA += term;
+ dVA += -Beta[itype][jtype][m] * term;
}
dVA += VA/wij * dwij;
del[0] = delx;
@@ -467,7 +467,7 @@ void PairAIREBO::FREBO(int eflag, int vflag)
if (eflag) evdwl = VR + bij*VA;
if (evflag) ev_tally(i,j,nlocal,newton_pair,
- evdwl,0.0,fpair,delx,dely,delz);
+ evdwl,0.0,fpair,delx,dely,delz);
}
}
}
@@ -539,13 +539,13 @@ void PairAIREBO::FLJ(int eflag, int vflag)
jtag = tag[j];
if (itag > jtag) {
- if ((itag+jtag) % 2 == 0) continue;
+ if ((itag+jtag) % 2 == 0) continue;
} else if (itag < jtag) {
- if ((itag+jtag) % 2 == 1) continue;
+ if ((itag+jtag) % 2 == 1) continue;
} else {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
- if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
+ if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
}
jtype = map[type[j]];
@@ -561,139 +561,139 @@ void PairAIREBO::FLJ(int eflag, int vflag)
// if outside of 2-path cutoff but inside 4-path cutoff,
// best = 0.0, test 3-,4-paths
// if inside 2-path cutoff, best = wij, only test 3-,4-paths if best < 1
-
+
if (rijsq >= cutljsq[itype][jtype]) continue;
rij = sqrt(rijsq);
if (rij >= cut3rebo) {
- best = 0.0;
- testpath = 0;
+ best = 0.0;
+ testpath = 0;
} else if (rij >= rcmax[itype][jtype]) {
- best = 0.0;
- testpath = 1;
+ best = 0.0;
+ testpath = 1;
} else {
- best = Sp(rij,rcmin[itype][jtype],rcmax[itype][jtype],dwij);
- npath = 2;
- if (best < 1.0) testpath = 1;
- else testpath = 0;
+ best = Sp(rij,rcmin[itype][jtype],rcmax[itype][jtype],dwij);
+ npath = 2;
+ if (best < 1.0) testpath = 1;
+ else testpath = 0;
}
done = 0;
if (testpath) {
- // test all 3-body paths = I-K-J
- // I-K interactions come from atom I's REBO neighbors
- // if wik > current best, compute wkj
- // if best = 1.0, done
-
- REBO_neighs_i = REBO_firstneigh[i];
- for (kk = 0; kk < REBO_numneigh[i] && done==0; kk++) {
- k = REBO_neighs_i[kk];
- if (k == j) continue;
- ktype = map[type[k]];
-
- delik[0] = x[i][0] - x[k][0];
- delik[1] = x[i][1] - x[k][1];
- delik[2] = x[i][2] - x[k][2];
- rsq = delik[0]*delik[0] + delik[1]*delik[1] + delik[2]*delik[2];
- if (rsq < rcmaxsq[itype][ktype]) {
- rik = sqrt(rsq);
- wik = Sp(rik,rcmin[itype][ktype],rcmax[itype][ktype],dwik);
- } else wik = 0.0;
-
- if (wik > best) {
- deljk[0] = x[j][0] - x[k][0];
- deljk[1] = x[j][1] - x[k][1];
- deljk[2] = x[j][2] - x[k][2];
- rsq = deljk[0]*deljk[0] + deljk[1]*deljk[1] + deljk[2]*deljk[2];
- if (rsq < rcmaxsq[ktype][jtype]) {
- rkj = sqrt(rsq);
- wkj = Sp(rkj,rcmin[ktype][jtype],rcmax[ktype][jtype],dwkj);
- if (wik*wkj > best) {
- best = wik*wkj;
- npath = 3;
- atomk = k;
- delikS[0] = delik[0];
- delikS[1] = delik[1];
- delikS[2] = delik[2];
- rikS = rik;
- wikS = wik;
- dwikS = dwik;
- deljkS[0] = deljk[0];
- deljkS[1] = deljk[1];
- deljkS[2] = deljk[2];
- rkjS = rkj;
- wkjS = wkj;
- dwkjS = dwkj;
- if (best == 1.0) {
- done = 1;
- break;
- }
- }
- }
-
- // test all 4-body paths = I-K-M-J
- // K-M interactions come from atom K's REBO neighbors
- // if wik*wkm > current best, compute wmj
- // if best = 1.0, done
-
- REBO_neighs_k = REBO_firstneigh[k];
- for (mm = 0; mm < REBO_numneigh[k] && done==0; mm++) {
- m = REBO_neighs_k[mm];
- if (m == i || m == j) continue;
- mtype = map[type[m]];
- delkm[0] = x[k][0] - x[m][0];
- delkm[1] = x[k][1] - x[m][1];
- delkm[2] = x[k][2] - x[m][2];
- rsq = delkm[0]*delkm[0] + delkm[1]*delkm[1] + delkm[2]*delkm[2];
- if (rsq < rcmaxsq[ktype][mtype]) {
- rkm = sqrt(rsq);
- wkm = Sp(rkm,rcmin[ktype][mtype],rcmax[ktype][mtype],dwkm);
- } else wkm = 0.0;
-
- if (wik*wkm > best) {
- deljm[0] = x[j][0] - x[m][0];
- deljm[1] = x[j][1] - x[m][1];
- deljm[2] = x[j][2] - x[m][2];
- rsq = deljm[0]*deljm[0] + deljm[1]*deljm[1] +
- deljm[2]*deljm[2];
- if (rsq < rcmaxsq[mtype][jtype]) {
- rmj = sqrt(rsq);
- wmj = Sp(rmj,rcmin[mtype][jtype],rcmax[mtype][jtype],dwmj);
- if (wik*wkm*wmj > best) {
- best = wik*wkm*wmj;
- npath = 4;
- atomk = k;
- delikS[0] = delik[0];
- delikS[1] = delik[1];
- delikS[2] = delik[2];
- rikS = rik;
- wikS = wik;
- dwikS = dwik;
- atomm = m;
- delkmS[0] = delkm[0];
- delkmS[1] = delkm[1];
- delkmS[2] = delkm[2];
- rkmS = rkm;
- wkmS = wkm;
- dwkmS = dwkm;
- deljmS[0] = deljm[0];
- deljmS[1] = deljm[1];
- deljmS[2] = deljm[2];
- rmjS = rmj;
- wmjS = wmj;
- dwmjS = dwmj;
- if (best == 1.0) {
- done = 1;
- break;
- }
- }
- }
- }
- }
- }
- }
+ // test all 3-body paths = I-K-J
+ // I-K interactions come from atom I's REBO neighbors
+ // if wik > current best, compute wkj
+ // if best = 1.0, done
+
+ REBO_neighs_i = REBO_firstneigh[i];
+ for (kk = 0; kk < REBO_numneigh[i] && done==0; kk++) {
+ k = REBO_neighs_i[kk];
+ if (k == j) continue;
+ ktype = map[type[k]];
+
+ delik[0] = x[i][0] - x[k][0];
+ delik[1] = x[i][1] - x[k][1];
+ delik[2] = x[i][2] - x[k][2];
+ rsq = delik[0]*delik[0] + delik[1]*delik[1] + delik[2]*delik[2];
+ if (rsq < rcmaxsq[itype][ktype]) {
+ rik = sqrt(rsq);
+ wik = Sp(rik,rcmin[itype][ktype],rcmax[itype][ktype],dwik);
+ } else wik = 0.0;
+
+ if (wik > best) {
+ deljk[0] = x[j][0] - x[k][0];
+ deljk[1] = x[j][1] - x[k][1];
+ deljk[2] = x[j][2] - x[k][2];
+ rsq = deljk[0]*deljk[0] + deljk[1]*deljk[1] + deljk[2]*deljk[2];
+ if (rsq < rcmaxsq[ktype][jtype]) {
+ rkj = sqrt(rsq);
+ wkj = Sp(rkj,rcmin[ktype][jtype],rcmax[ktype][jtype],dwkj);
+ if (wik*wkj > best) {
+ best = wik*wkj;
+ npath = 3;
+ atomk = k;
+ delikS[0] = delik[0];
+ delikS[1] = delik[1];
+ delikS[2] = delik[2];
+ rikS = rik;
+ wikS = wik;
+ dwikS = dwik;
+ deljkS[0] = deljk[0];
+ deljkS[1] = deljk[1];
+ deljkS[2] = deljk[2];
+ rkjS = rkj;
+ wkjS = wkj;
+ dwkjS = dwkj;
+ if (best == 1.0) {
+ done = 1;
+ break;
+ }
+ }
+ }
+
+ // test all 4-body paths = I-K-M-J
+ // K-M interactions come from atom K's REBO neighbors
+ // if wik*wkm > current best, compute wmj
+ // if best = 1.0, done
+
+ REBO_neighs_k = REBO_firstneigh[k];
+ for (mm = 0; mm < REBO_numneigh[k] && done==0; mm++) {
+ m = REBO_neighs_k[mm];
+ if (m == i || m == j) continue;
+ mtype = map[type[m]];
+ delkm[0] = x[k][0] - x[m][0];
+ delkm[1] = x[k][1] - x[m][1];
+ delkm[2] = x[k][2] - x[m][2];
+ rsq = delkm[0]*delkm[0] + delkm[1]*delkm[1] + delkm[2]*delkm[2];
+ if (rsq < rcmaxsq[ktype][mtype]) {
+ rkm = sqrt(rsq);
+ wkm = Sp(rkm,rcmin[ktype][mtype],rcmax[ktype][mtype],dwkm);
+ } else wkm = 0.0;
+
+ if (wik*wkm > best) {
+ deljm[0] = x[j][0] - x[m][0];
+ deljm[1] = x[j][1] - x[m][1];
+ deljm[2] = x[j][2] - x[m][2];
+ rsq = deljm[0]*deljm[0] + deljm[1]*deljm[1] +
+ deljm[2]*deljm[2];
+ if (rsq < rcmaxsq[mtype][jtype]) {
+ rmj = sqrt(rsq);
+ wmj = Sp(rmj,rcmin[mtype][jtype],rcmax[mtype][jtype],dwmj);
+ if (wik*wkm*wmj > best) {
+ best = wik*wkm*wmj;
+ npath = 4;
+ atomk = k;
+ delikS[0] = delik[0];
+ delikS[1] = delik[1];
+ delikS[2] = delik[2];
+ rikS = rik;
+ wikS = wik;
+ dwikS = dwik;
+ atomm = m;
+ delkmS[0] = delkm[0];
+ delkmS[1] = delkm[1];
+ delkmS[2] = delkm[2];
+ rkmS = rkm;
+ wkmS = wkm;
+ dwkmS = dwkm;
+ deljmS[0] = deljm[0];
+ deljmS[1] = deljm[1];
+ deljmS[2] = deljm[2];
+ rmjS = rmj;
+ wmjS = wmj;
+ dwmjS = dwmj;
+ if (best == 1.0) {
+ done = 1;
+ break;
+ }
+ }
+ }
+ }
+ }
+ }
+ }
}
-
+
cij = 1.0 - best;
if (cij == 0.0) continue;
@@ -702,24 +702,24 @@ void PairAIREBO::FLJ(int eflag, int vflag)
sigwid = 0.84;
sigcut = 3.0;
sigmin = sigcut - sigwid;
-
+
rljmin = sigma[itype][jtype];
rljmax = sigcut * rljmin;
rljmin = sigmin * rljmin;
-
+
if (rij > rljmax) {
- slw = 0.0;
- dslw = 0.0;
+ slw = 0.0;
+ dslw = 0.0;
} else if (rij > rljmin) {
- drij = rij - rljmin;
- swidth = rljmax - rljmin;
- tee = drij / swidth;
- tee2 = tee*tee;
- slw = 1.0 - tee2 * (3.0 - 2.0 * tee);
- dslw = 6.0 * tee * (1.0 - tee) / rij / swidth;
+ drij = rij - rljmin;
+ swidth = rljmax - rljmin;
+ tee = drij / swidth;
+ tee2 = tee*tee;
+ slw = 1.0 - tee2 * (3.0 - 2.0 * tee);
+ dslw = 6.0 * tee * (1.0 - tee) / rij / swidth;
} else {
- slw = 1.0;
- dslw = 0.0;
+ slw = 1.0;
+ dslw = 0.0;
}
r2inv = 1.0/rijsq;
@@ -729,112 +729,112 @@ void PairAIREBO::FLJ(int eflag, int vflag)
dvdw = -r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]) / rij;
// VLJ now becomes vdw * slw, derivaties, etc.
-
+
VLJ = vdw * slw;
dVLJ = dvdw * slw + vdw * dslw;
Str = Sp2(rij,rcLJmin[itype][jtype],rcLJmax[itype][jtype],dStr);
VA = Str*cij*VLJ;
if (Str > 0.0) {
- scale = rcmin[itype][jtype] / rij;
- delscale[0] = scale * delij[0];
- delscale[1] = scale * delij[1];
- delscale[2] = scale * delij[2];
- Stb = bondorderLJ(i,j,delscale,rcmin[itype][jtype],VA,
- delij,rij,f,vflag_atom);
+ scale = rcmin[itype][jtype] / rij;
+ delscale[0] = scale * delij[0];
+ delscale[1] = scale * delij[1];
+ delscale[2] = scale * delij[2];
+ Stb = bondorderLJ(i,j,delscale,rcmin[itype][jtype],VA,
+ delij,rij,f,vflag_atom);
} else Stb = 0.0;
fpair = -(dStr * (Stb*cij*VLJ - cij*VLJ) +
- dVLJ * (Str*Stb*cij + cij - Str*cij)) / rij;
-
+ dVLJ * (Str*Stb*cij + cij - Str*cij)) / rij;
+
f[i][0] += delij[0]*fpair;
f[i][1] += delij[1]*fpair;
f[i][2] += delij[2]*fpair;
f[j][0] -= delij[0]*fpair;
f[j][1] -= delij[1]*fpair;
f[j][2] -= delij[2]*fpair;
-
+
if (eflag) evdwl = VA*Stb + (1.0-Str)*cij*VLJ;
if (evflag) ev_tally(i,j,nlocal,newton_pair,
- evdwl,0.0,fpair,delij[0],delij[1],delij[2]);
+ evdwl,0.0,fpair,delij[0],delij[1],delij[2]);
if (cij < 1.0) {
- dC = Str*Stb*VLJ + (1.0-Str)*VLJ;
- if (npath == 2) {
- fpair = dC*dwij / rij;
- f[atomi][0] += delij[0]*fpair;
- f[atomi][1] += delij[1]*fpair;
- f[atomi][2] += delij[2]*fpair;
- f[atomj][0] -= delij[0]*fpair;
- f[atomj][1] -= delij[1]*fpair;
- f[atomj][2] -= delij[2]*fpair;
-
- if (vflag_atom) v_tally2(atomi,atomj,fpair,delij);
-
- } else if (npath == 3) {
- fpair1 = dC*dwikS*wkjS / rikS;
- fi[0] = delikS[0]*fpair1;
- fi[1] = delikS[1]*fpair1;
- fi[2] = delikS[2]*fpair1;
- fpair2 = dC*wikS*dwkjS / rkjS;
- fj[0] = deljkS[0]*fpair2;
- fj[1] = deljkS[1]*fpair2;
- fj[2] = deljkS[2]*fpair2;
-
- f[atomi][0] += fi[0];
- f[atomi][1] += fi[1];
- f[atomi][2] += fi[2];
- f[atomj][0] += fj[0];
- f[atomj][1] += fj[1];
- f[atomj][2] += fj[2];
- f[atomk][0] -= fi[0] + fj[0];
- f[atomk][1] -= fi[1] + fj[1];
- f[atomk][2] -= fi[2] + fj[2];
-
- if (vflag_atom)
- v_tally3(atomi,atomj,atomk,fi,fj,delikS,deljkS);
-
- } else {
- fpair1 = dC*dwikS*wkmS*wmjS / rikS;
- fi[0] = delikS[0]*fpair1;
- fi[1] = delikS[1]*fpair1;
- fi[2] = delikS[2]*fpair1;
-
- fpair2 = dC*wikS*dwkmS*wmjS / rkmS;
- fk[0] = delkmS[0]*fpair2 - fi[0];
- fk[1] = delkmS[1]*fpair2 - fi[1];
- fk[2] = delkmS[2]*fpair2 - fi[2];
-
- fpair3 = dC*wikS*wkmS*dwmjS / rmjS;
- fj[0] = deljmS[0]*fpair3;
- fj[1] = deljmS[1]*fpair3;
- fj[2] = deljmS[2]*fpair3;
-
- fm[0] = -delkmS[0]*fpair2 - fj[0];
- fm[1] = -delkmS[1]*fpair2 - fj[1];
- fm[2] = -delkmS[2]*fpair2 - fj[2];
-
- f[atomi][0] += fi[0];
- f[atomi][1] += fi[1];
- f[atomi][2] += fi[2];
- f[atomj][0] += fj[0];
- f[atomj][1] += fj[1];
- f[atomj][2] += fj[2];
- f[atomk][0] += fk[0];
- f[atomk][1] += fk[1];
- f[atomk][2] += fk[2];
- f[atomm][0] += fm[0];
- f[atomm][1] += fm[1];
- f[atomm][2] += fm[2];
-
- if (vflag_atom) {
- delimS[0] = delikS[0] + delkmS[0];
- delimS[1] = delikS[1] + delkmS[1];
- delimS[2] = delikS[2] + delkmS[2];
- v_tally4(atomi,atomj,atomk,atomm,fi,fj,fk,delimS,deljmS,delkmS);
- }
- }
- }
+ dC = Str*Stb*VLJ + (1.0-Str)*VLJ;
+ if (npath == 2) {
+ fpair = dC*dwij / rij;
+ f[atomi][0] += delij[0]*fpair;
+ f[atomi][1] += delij[1]*fpair;
+ f[atomi][2] += delij[2]*fpair;
+ f[atomj][0] -= delij[0]*fpair;
+ f[atomj][1] -= delij[1]*fpair;
+ f[atomj][2] -= delij[2]*fpair;
+
+ if (vflag_atom) v_tally2(atomi,atomj,fpair,delij);
+
+ } else if (npath == 3) {
+ fpair1 = dC*dwikS*wkjS / rikS;
+ fi[0] = delikS[0]*fpair1;
+ fi[1] = delikS[1]*fpair1;
+ fi[2] = delikS[2]*fpair1;
+ fpair2 = dC*wikS*dwkjS / rkjS;
+ fj[0] = deljkS[0]*fpair2;
+ fj[1] = deljkS[1]*fpair2;
+ fj[2] = deljkS[2]*fpair2;
+
+ f[atomi][0] += fi[0];
+ f[atomi][1] += fi[1];
+ f[atomi][2] += fi[2];
+ f[atomj][0] += fj[0];
+ f[atomj][1] += fj[1];
+ f[atomj][2] += fj[2];
+ f[atomk][0] -= fi[0] + fj[0];
+ f[atomk][1] -= fi[1] + fj[1];
+ f[atomk][2] -= fi[2] + fj[2];
+
+ if (vflag_atom)
+ v_tally3(atomi,atomj,atomk,fi,fj,delikS,deljkS);
+
+ } else {
+ fpair1 = dC*dwikS*wkmS*wmjS / rikS;
+ fi[0] = delikS[0]*fpair1;
+ fi[1] = delikS[1]*fpair1;
+ fi[2] = delikS[2]*fpair1;
+
+ fpair2 = dC*wikS*dwkmS*wmjS / rkmS;
+ fk[0] = delkmS[0]*fpair2 - fi[0];
+ fk[1] = delkmS[1]*fpair2 - fi[1];
+ fk[2] = delkmS[2]*fpair2 - fi[2];
+
+ fpair3 = dC*wikS*wkmS*dwmjS / rmjS;
+ fj[0] = deljmS[0]*fpair3;
+ fj[1] = deljmS[1]*fpair3;
+ fj[2] = deljmS[2]*fpair3;
+
+ fm[0] = -delkmS[0]*fpair2 - fj[0];
+ fm[1] = -delkmS[1]*fpair2 - fj[1];
+ fm[2] = -delkmS[2]*fpair2 - fj[2];
+
+ f[atomi][0] += fi[0];
+ f[atomi][1] += fi[1];
+ f[atomi][2] += fi[2];
+ f[atomj][0] += fj[0];
+ f[atomj][1] += fj[1];
+ f[atomj][2] += fj[2];
+ f[atomk][0] += fk[0];
+ f[atomk][1] += fk[1];
+ f[atomk][2] += fk[2];
+ f[atomm][0] += fm[0];
+ f[atomm][1] += fm[1];
+ f[atomm][2] += fm[2];
+
+ if (vflag_atom) {
+ delimS[0] = delikS[0] + delkmS[0];
+ delimS[1] = delikS[1] + delkmS[1];
+ delimS[2] = delikS[2] + delkmS[2];
+ v_tally4(atomi,atomj,atomk,atomm,fi,fj,fk,delimS,deljmS,delkmS);
+ }
+ }
+ }
}
}
}
@@ -890,13 +890,13 @@ void PairAIREBO::TORSION(int eflag, int vflag)
jtag = tag[j];
if (itag > jtag) {
- if ((itag+jtag) % 2 == 0) continue;
+ if ((itag+jtag) % 2 == 0) continue;
} else if (itag < jtag) {
- if ((itag+jtag) % 2 == 1) continue;
+ if ((itag+jtag) % 2 == 1) continue;
} else {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
- if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
+ if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
}
jtype = map[type[j]];
@@ -914,285 +914,285 @@ void PairAIREBO::TORSION(int eflag, int vflag)
w23 = Sp(r23,rcmin[itype][jtype],rcmax[itype][jtype],dw23);
for (kk = 0; kk < REBO_numneigh[i]; kk++) {
- k = REBO_neighs_i[kk];
- ktype = map[type[k]];
- if (k == j) continue;
- del21[0] = x[i][0]-x[k][0];
- del21[1] = x[i][1]-x[k][1];
- del21[2] = x[i][2]-x[k][2];
- rsq = del21[0]*del21[0] + del21[1]*del21[1] + del21[2]*del21[2];
- r21 = sqrt(rsq);
- cos321 = - ((del21[0]*del32[0]) + (del21[1]*del32[1]) +
- (del21[2]*del32[2])) / (r21*r32);
- cos321 = MIN(cos321,1.0);
- cos321 = MAX(cos321,-1.0);
- sin321 = sqrt(1.0 - cos321*cos321);
- if (sin321 < TOL) continue;
-
- deljk[0] = del21[0]-del23[0];
- deljk[1] = del21[1]-del23[1];
- deljk[2] = del21[2]-del23[2];
- rjk2 = deljk[0]*deljk[0] + deljk[1]*deljk[1] + deljk[2]*deljk[2];
- rjk=sqrt(rjk2);
- rik2 = r21*r21;
- w21 = Sp(r21,rcmin[itype][ktype],rcmax[itype][ktype],dw21);
-
- rij = r32;
- rik = r21;
- rij2 = r32*r32;
- rik2 = r21*r21;
- costmp = 0.5*(rij2+rik2-rjk2)/rij/rik;
- tspjik = Sp2(costmp,thmin,thmax,dtsjik);
- dtsjik = -dtsjik;
-
- REBO_neighs_j = REBO_firstneigh[j];
- for (ll = 0; ll < REBO_numneigh[j]; ll++) {
- l = REBO_neighs_j[ll];
- ltype = map[type[l]];
- if (l == i || l == k) continue;
- del34[0] = x[j][0]-x[l][0];
- del34[1] = x[j][1]-x[l][1];
- del34[2] = x[j][2]-x[l][2];
- rsq = del34[0]*del34[0] + del34[1]*del34[1] + del34[2]*del34[2];
- r34 = sqrt(rsq);
- cos234 = (del32[0]*del34[0] + del32[1]*del34[1] +
- del32[2]*del34[2]) / (r32*r34);
- cos234 = MIN(cos234,1.0);
- cos234 = MAX(cos234,-1.0);
- sin234 = sqrt(1.0 - cos234*cos234);
- if (sin234 < TOL) continue;
- w34 = Sp(r34,rcmin[jtype][ltype],rcmax[jtype][ltype],dw34);
- delil[0] = del23[0] + del34[0];
- delil[1] = del23[1] + del34[1];
- delil[2] = del23[2] + del34[2];
- ril2 = delil[0]*delil[0] + delil[1]*delil[1] + delil[2]*delil[2];
- ril=sqrt(ril2);
- rjl2 = r34*r34;
-
- rjl = r34;
- rjl2 = r34*r34;
- costmp = 0.5*(rij2+rjl2-ril2)/rij/rjl;
- tspijl = Sp2(costmp,thmin,thmax,dtsijl);
- dtsijl = -dtsijl; //need minus sign
- cross321[0] = (del32[1]*del21[2])-(del32[2]*del21[1]);
- cross321[1] = (del32[2]*del21[0])-(del32[0]*del21[2]);
- cross321[2] = (del32[0]*del21[1])-(del32[1]*del21[0]);
- cross321mag = sqrt(cross321[0]*cross321[0]+
- cross321[1]*cross321[1]+
- cross321[2]*cross321[2]);
- cross234[0] = (del23[1]*del34[2])-(del23[2]*del34[1]);
- cross234[1] = (del23[2]*del34[0])-(del23[0]*del34[2]);
- cross234[2] = (del23[0]*del34[1])-(del23[1]*del34[0]);
- cross234mag = sqrt(cross234[0]*cross234[0]+
- cross234[1]*cross234[1]+
- cross234[2]*cross234[2]);
- cwnum = (cross321[0]*cross234[0]) +
- (cross321[1]*cross234[1])+(cross321[2]*cross234[2]);
- cwnom = r21*r34*r32*r32*sin321*sin234;
- cw = cwnum/cwnom;
-
- cw2 = (.5*(1.0-cw));
- ekijl = epsilonT[ktype][ltype];
- Ec = 256.0*ekijl/405.0;
- Vtors = (Ec*(pow(cw2,5.0)))-(ekijl/10.0);
-
- if (eflag) evdwl = Vtors*w21*w23*w34*(1.0-tspjik)*(1.0-tspijl);
-
- dndij[0] = (cross234[1]*del21[2])-(cross234[2]*del21[1]);
- dndij[1] = (cross234[2]*del21[0])-(cross234[0]*del21[2]);
- dndij[2] = (cross234[0]*del21[1])-(cross234[1]*del21[0]);
-
- tmpvec[0] = (del34[1]*cross321[2])-(del34[2]*cross321[1]);
- tmpvec[1] = (del34[2]*cross321[0])-(del34[0]*cross321[2]);
- tmpvec[2] = (del34[0]*cross321[1])-(del34[1]*cross321[0]);
-
- dndij[0] = dndij[0]+tmpvec[0];
- dndij[1] = dndij[1]+tmpvec[1];
- dndij[2] = dndij[2]+tmpvec[2];
-
- dndik[0] = (del23[1]*cross234[2])-(del23[2]*cross234[1]);
- dndik[1] = (del23[2]*cross234[0])-(del23[0]*cross234[2]);
- dndik[2] = (del23[0]*cross234[1])-(del23[1]*cross234[0]);
-
- dndjl[0] = (cross321[1]*del23[2])-(cross321[2]*del23[1]);
- dndjl[1] = (cross321[2]*del23[0])-(cross321[0]*del23[2]);
- dndjl[2] = (cross321[0]*del23[1])-(cross321[1]*del23[0]);
-
- dcidij = ((r23*r23)-(r21*r21)+(rjk*rjk))/(2.0*r23*r23*r21);
- dcidik = ((r21*r21)-(r23*r23)+(rjk*rjk))/(2.0*r23*r21*r21);
- dcidjk = (-rjk)/(r23*r21);
- dcjdji = ((r23*r23)-(r34*r34)+(ril*ril))/(2.0*r23*r23*r34);
- dcjdjl = ((r34*r34)-(r23*r23)+(ril*ril))/(2.0*r23*r34*r34);
- dcjdil = (-ril)/(r23*r34);
-
- dsidij = (-cos321/sin321)*dcidij;
- dsidik = (-cos321/sin321)*dcidik;
- dsidjk = (-cos321/sin321)*dcidjk;
-
- dsjdji = (-cos234/sin234)*dcjdji;
- dsjdjl = (-cos234/sin234)*dcjdjl;
- dsjdil = (-cos234/sin234)*dcjdil;
-
- dxidij = (r21*sin321)+(r23*r21*dsidij);
- dxidik = (r23*sin321)+(r23*r21*dsidik);
- dxidjk = (r23*r21*dsidjk);
-
- dxjdji = (r34*sin234)+(r23*r34*dsjdji);
- dxjdjl = (r23*sin234)+(r23*r34*dsjdjl);
- dxjdil = (r23*r34*dsjdil);
-
- ddndij = (dxidij*cross234mag)+(cross321mag*dxjdji);
- ddndik = dxidik*cross234mag;
- ddndjk = dxidjk*cross234mag;
- ddndjl = cross321mag*dxjdjl;
- ddndil = cross321mag*dxjdil;
- dcwddn = -cwnum/(cwnom*cwnom);
- dcwdn = 1.0/cwnom;
- dvpdcw = (-1.0)*Ec*(-.5)*5.0*pow(cw2,4.0) *
- w23*w21*w34*(1.0-tspjik)*(1.0-tspijl);
-
- Ftmp[0] = dvpdcw*((dcwdn*dndij[0])+(dcwddn*ddndij*del23[0]/r23));
- Ftmp[1] = dvpdcw*((dcwdn*dndij[1])+(dcwddn*ddndij*del23[1]/r23));
- Ftmp[2] = dvpdcw*((dcwdn*dndij[2])+(dcwddn*ddndij*del23[2]/r23));
- fi[0] = Ftmp[0];
- fi[1] = Ftmp[1];
- fi[2] = Ftmp[2];
- fj[0] = -Ftmp[0];
- fj[1] = -Ftmp[1];
- fj[2] = -Ftmp[2];
-
- Ftmp[0] = dvpdcw*((dcwdn*dndik[0])+(dcwddn*ddndik*del21[0]/r21));
- Ftmp[1] = dvpdcw*((dcwdn*dndik[1])+(dcwddn*ddndik*del21[1]/r21));
- Ftmp[2] = dvpdcw*((dcwdn*dndik[2])+(dcwddn*ddndik*del21[2]/r21));
- fi[0] += Ftmp[0];
- fi[1] += Ftmp[1];
- fi[2] += Ftmp[2];
- fk[0] = -Ftmp[0];
- fk[1] = -Ftmp[1];
- fk[2] = -Ftmp[2];
-
- Ftmp[0] = (dvpdcw*dcwddn*ddndjk*deljk[0])/rjk;
- Ftmp[1] = (dvpdcw*dcwddn*ddndjk*deljk[1])/rjk;
- Ftmp[2] = (dvpdcw*dcwddn*ddndjk*deljk[2])/rjk;
- fj[0] += Ftmp[0];
- fj[1] += Ftmp[1];
- fj[2] += Ftmp[2];
- fk[0] -= Ftmp[0];
- fk[1] -= Ftmp[1];
- fk[2] -= Ftmp[2];
-
- Ftmp[0] = dvpdcw*((dcwdn*dndjl[0])+(dcwddn*ddndjl*del34[0]/r34));
- Ftmp[1] = dvpdcw*((dcwdn*dndjl[1])+(dcwddn*ddndjl*del34[1]/r34));
- Ftmp[2] = dvpdcw*((dcwdn*dndjl[2])+(dcwddn*ddndjl*del34[2]/r34));
- fj[0] += Ftmp[0];
- fj[1] += Ftmp[1];
- fj[2] += Ftmp[2];
- fl[0] = -Ftmp[0];
- fl[1] = -Ftmp[1];
- fl[2] = -Ftmp[2];
-
- Ftmp[0] = (dvpdcw*dcwddn*ddndil*delil[0])/ril;
- Ftmp[1] = (dvpdcw*dcwddn*ddndil*delil[1])/ril;
- Ftmp[2] = (dvpdcw*dcwddn*ddndil*delil[2])/ril;
- fi[0] += Ftmp[0];
- fi[1] += Ftmp[1];
- fi[2] += Ftmp[2];
- fl[0] -= Ftmp[0];
- fl[1] -= Ftmp[1];
- fl[2] -= Ftmp[2];
-
- // coordination forces
-
- fpair = Vtors*dw21*w23*w34*(1.0-tspjik)*(1.0-tspijl) / r21;
- fi[0] -= del21[0]*fpair;
- fi[1] -= del21[1]*fpair;
- fi[2] -= del21[2]*fpair;
- fk[0] += del21[0]*fpair;
- fk[1] += del21[1]*fpair;
- fk[2] += del21[2]*fpair;
-
- fpair = Vtors*w21*dw23*w34*(1.0-tspjik)*(1.0-tspijl) / r23;
- fi[0] -= del23[0]*fpair;
- fi[1] -= del23[1]*fpair;
- fi[2] -= del23[2]*fpair;
- fj[0] += del23[0]*fpair;
- fj[1] += del23[1]*fpair;
- fj[2] += del23[2]*fpair;
-
- fpair = Vtors*w21*w23*dw34*(1.0-tspjik)*(1.0-tspijl) / r34;
- fj[0] -= del34[0]*fpair;
- fj[1] -= del34[1]*fpair;
- fj[2] -= del34[2]*fpair;
- fl[0] += del34[0]*fpair;
- fl[1] += del34[1]*fpair;
- fl[2] += del34[2]*fpair;
-
- // additional cut off function forces
-
- fcpc = -Vtors*w21*w23*w34*dtsjik*(1.0-tspijl);
- fpair = fcpc*dcidij/rij;
- fi[0] += fpair*del23[0];
- fi[1] += fpair*del23[1];
- fi[2] += fpair*del23[2];
- fj[0] -= fpair*del23[0];
- fj[1] -= fpair*del23[1];
- fj[2] -= fpair*del23[2];
-
- fpair = fcpc*dcidik/rik;
- fi[0] += fpair*del21[0];
- fi[1] += fpair*del21[1];
- fi[2] += fpair*del21[2];
- fk[0] -= fpair*del21[0];
- fk[1] -= fpair*del21[1];
- fk[2] -= fpair*del21[2];
-
- fpair = fcpc*dcidjk/rjk;
- fj[0] += fpair*deljk[0];
- fj[1] += fpair*deljk[1];
- fj[2] += fpair*deljk[2];
- fk[0] -= fpair*deljk[0];
- fk[1] -= fpair*deljk[1];
- fk[2] -= fpair*deljk[2];
-
- fcpc = -Vtors*w21*w23*w34*(1.0-tspjik)*dtsijl;
- fpair = fcpc*dcjdji/rij;
- fi[0] += fpair*del23[0];
- fi[1] += fpair*del23[1];
- fi[2] += fpair*del23[2];
- fj[0] -= fpair*del23[0];
- fj[1] -= fpair*del23[1];
- fj[2] -= fpair*del23[2];
-
- fpair = fcpc*dcjdjl/rjl;
- fj[0] += fpair*del34[0];
- fj[1] += fpair*del34[1];
- fj[2] += fpair*del34[2];
- fl[0] -= fpair*del34[0];
- fl[1] -= fpair*del34[1];
- fl[2] -= fpair*del34[2];
-
- fpair = fcpc*dcjdil/ril;
- fi[0] += fpair*delil[0];
- fi[1] += fpair*delil[1];
- fi[2] += fpair*delil[2];
- fl[0] -= fpair*delil[0];
- fl[1] -= fpair*delil[1];
- fl[2] -= fpair*delil[2];
-
- // sum per-atom forces into atom force array
-
- f[i][0] += fi[0]; f[i][1] += fi[1]; f[i][2] += fi[2];
- f[j][0] += fj[0]; f[j][1] += fj[1]; f[j][2] += fj[2];
- f[k][0] += fk[0]; f[k][1] += fk[1]; f[k][2] += fk[2];
- f[l][0] += fl[0]; f[l][1] += fl[1]; f[l][2] += fl[2];
-
- if (evflag) {
- delkl[0] = delil[0] - del21[0];
- delkl[1] = delil[1] - del21[1];
- delkl[2] = delil[2] - del21[2];
- ev_tally4(i,j,k,l,evdwl,fi,fj,fk,delil,del34,delkl);
- }
- }
+ k = REBO_neighs_i[kk];
+ ktype = map[type[k]];
+ if (k == j) continue;
+ del21[0] = x[i][0]-x[k][0];
+ del21[1] = x[i][1]-x[k][1];
+ del21[2] = x[i][2]-x[k][2];
+ rsq = del21[0]*del21[0] + del21[1]*del21[1] + del21[2]*del21[2];
+ r21 = sqrt(rsq);
+ cos321 = - ((del21[0]*del32[0]) + (del21[1]*del32[1]) +
+ (del21[2]*del32[2])) / (r21*r32);
+ cos321 = MIN(cos321,1.0);
+ cos321 = MAX(cos321,-1.0);
+ sin321 = sqrt(1.0 - cos321*cos321);
+ if (sin321 < TOL) continue;
+
+ deljk[0] = del21[0]-del23[0];
+ deljk[1] = del21[1]-del23[1];
+ deljk[2] = del21[2]-del23[2];
+ rjk2 = deljk[0]*deljk[0] + deljk[1]*deljk[1] + deljk[2]*deljk[2];
+ rjk=sqrt(rjk2);
+ rik2 = r21*r21;
+ w21 = Sp(r21,rcmin[itype][ktype],rcmax[itype][ktype],dw21);
+
+ rij = r32;
+ rik = r21;
+ rij2 = r32*r32;
+ rik2 = r21*r21;
+ costmp = 0.5*(rij2+rik2-rjk2)/rij/rik;
+ tspjik = Sp2(costmp,thmin,thmax,dtsjik);
+ dtsjik = -dtsjik;
+
+ REBO_neighs_j = REBO_firstneigh[j];
+ for (ll = 0; ll < REBO_numneigh[j]; ll++) {
+ l = REBO_neighs_j[ll];
+ ltype = map[type[l]];
+ if (l == i || l == k) continue;
+ del34[0] = x[j][0]-x[l][0];
+ del34[1] = x[j][1]-x[l][1];
+ del34[2] = x[j][2]-x[l][2];
+ rsq = del34[0]*del34[0] + del34[1]*del34[1] + del34[2]*del34[2];
+ r34 = sqrt(rsq);
+ cos234 = (del32[0]*del34[0] + del32[1]*del34[1] +
+ del32[2]*del34[2]) / (r32*r34);
+ cos234 = MIN(cos234,1.0);
+ cos234 = MAX(cos234,-1.0);
+ sin234 = sqrt(1.0 - cos234*cos234);
+ if (sin234 < TOL) continue;
+ w34 = Sp(r34,rcmin[jtype][ltype],rcmax[jtype][ltype],dw34);
+ delil[0] = del23[0] + del34[0];
+ delil[1] = del23[1] + del34[1];
+ delil[2] = del23[2] + del34[2];
+ ril2 = delil[0]*delil[0] + delil[1]*delil[1] + delil[2]*delil[2];
+ ril=sqrt(ril2);
+ rjl2 = r34*r34;
+
+ rjl = r34;
+ rjl2 = r34*r34;
+ costmp = 0.5*(rij2+rjl2-ril2)/rij/rjl;
+ tspijl = Sp2(costmp,thmin,thmax,dtsijl);
+ dtsijl = -dtsijl; //need minus sign
+ cross321[0] = (del32[1]*del21[2])-(del32[2]*del21[1]);
+ cross321[1] = (del32[2]*del21[0])-(del32[0]*del21[2]);
+ cross321[2] = (del32[0]*del21[1])-(del32[1]*del21[0]);
+ cross321mag = sqrt(cross321[0]*cross321[0]+
+ cross321[1]*cross321[1]+
+ cross321[2]*cross321[2]);
+ cross234[0] = (del23[1]*del34[2])-(del23[2]*del34[1]);
+ cross234[1] = (del23[2]*del34[0])-(del23[0]*del34[2]);
+ cross234[2] = (del23[0]*del34[1])-(del23[1]*del34[0]);
+ cross234mag = sqrt(cross234[0]*cross234[0]+
+ cross234[1]*cross234[1]+
+ cross234[2]*cross234[2]);
+ cwnum = (cross321[0]*cross234[0]) +
+ (cross321[1]*cross234[1])+(cross321[2]*cross234[2]);
+ cwnom = r21*r34*r32*r32*sin321*sin234;
+ cw = cwnum/cwnom;
+
+ cw2 = (.5*(1.0-cw));
+ ekijl = epsilonT[ktype][ltype];
+ Ec = 256.0*ekijl/405.0;
+ Vtors = (Ec*(pow(cw2,5.0)))-(ekijl/10.0);
+
+ if (eflag) evdwl = Vtors*w21*w23*w34*(1.0-tspjik)*(1.0-tspijl);
+
+ dndij[0] = (cross234[1]*del21[2])-(cross234[2]*del21[1]);
+ dndij[1] = (cross234[2]*del21[0])-(cross234[0]*del21[2]);
+ dndij[2] = (cross234[0]*del21[1])-(cross234[1]*del21[0]);
+
+ tmpvec[0] = (del34[1]*cross321[2])-(del34[2]*cross321[1]);
+ tmpvec[1] = (del34[2]*cross321[0])-(del34[0]*cross321[2]);
+ tmpvec[2] = (del34[0]*cross321[1])-(del34[1]*cross321[0]);
+
+ dndij[0] = dndij[0]+tmpvec[0];
+ dndij[1] = dndij[1]+tmpvec[1];
+ dndij[2] = dndij[2]+tmpvec[2];
+
+ dndik[0] = (del23[1]*cross234[2])-(del23[2]*cross234[1]);
+ dndik[1] = (del23[2]*cross234[0])-(del23[0]*cross234[2]);
+ dndik[2] = (del23[0]*cross234[1])-(del23[1]*cross234[0]);
+
+ dndjl[0] = (cross321[1]*del23[2])-(cross321[2]*del23[1]);
+ dndjl[1] = (cross321[2]*del23[0])-(cross321[0]*del23[2]);
+ dndjl[2] = (cross321[0]*del23[1])-(cross321[1]*del23[0]);
+
+ dcidij = ((r23*r23)-(r21*r21)+(rjk*rjk))/(2.0*r23*r23*r21);
+ dcidik = ((r21*r21)-(r23*r23)+(rjk*rjk))/(2.0*r23*r21*r21);
+ dcidjk = (-rjk)/(r23*r21);
+ dcjdji = ((r23*r23)-(r34*r34)+(ril*ril))/(2.0*r23*r23*r34);
+ dcjdjl = ((r34*r34)-(r23*r23)+(ril*ril))/(2.0*r23*r34*r34);
+ dcjdil = (-ril)/(r23*r34);
+
+ dsidij = (-cos321/sin321)*dcidij;
+ dsidik = (-cos321/sin321)*dcidik;
+ dsidjk = (-cos321/sin321)*dcidjk;
+
+ dsjdji = (-cos234/sin234)*dcjdji;
+ dsjdjl = (-cos234/sin234)*dcjdjl;
+ dsjdil = (-cos234/sin234)*dcjdil;
+
+ dxidij = (r21*sin321)+(r23*r21*dsidij);
+ dxidik = (r23*sin321)+(r23*r21*dsidik);
+ dxidjk = (r23*r21*dsidjk);
+
+ dxjdji = (r34*sin234)+(r23*r34*dsjdji);
+ dxjdjl = (r23*sin234)+(r23*r34*dsjdjl);
+ dxjdil = (r23*r34*dsjdil);
+
+ ddndij = (dxidij*cross234mag)+(cross321mag*dxjdji);
+ ddndik = dxidik*cross234mag;
+ ddndjk = dxidjk*cross234mag;
+ ddndjl = cross321mag*dxjdjl;
+ ddndil = cross321mag*dxjdil;
+ dcwddn = -cwnum/(cwnom*cwnom);
+ dcwdn = 1.0/cwnom;
+ dvpdcw = (-1.0)*Ec*(-.5)*5.0*pow(cw2,4.0) *
+ w23*w21*w34*(1.0-tspjik)*(1.0-tspijl);
+
+ Ftmp[0] = dvpdcw*((dcwdn*dndij[0])+(dcwddn*ddndij*del23[0]/r23));
+ Ftmp[1] = dvpdcw*((dcwdn*dndij[1])+(dcwddn*ddndij*del23[1]/r23));
+ Ftmp[2] = dvpdcw*((dcwdn*dndij[2])+(dcwddn*ddndij*del23[2]/r23));
+ fi[0] = Ftmp[0];
+ fi[1] = Ftmp[1];
+ fi[2] = Ftmp[2];
+ fj[0] = -Ftmp[0];
+ fj[1] = -Ftmp[1];
+ fj[2] = -Ftmp[2];
+
+ Ftmp[0] = dvpdcw*((dcwdn*dndik[0])+(dcwddn*ddndik*del21[0]/r21));
+ Ftmp[1] = dvpdcw*((dcwdn*dndik[1])+(dcwddn*ddndik*del21[1]/r21));
+ Ftmp[2] = dvpdcw*((dcwdn*dndik[2])+(dcwddn*ddndik*del21[2]/r21));
+ fi[0] += Ftmp[0];
+ fi[1] += Ftmp[1];
+ fi[2] += Ftmp[2];
+ fk[0] = -Ftmp[0];
+ fk[1] = -Ftmp[1];
+ fk[2] = -Ftmp[2];
+
+ Ftmp[0] = (dvpdcw*dcwddn*ddndjk*deljk[0])/rjk;
+ Ftmp[1] = (dvpdcw*dcwddn*ddndjk*deljk[1])/rjk;
+ Ftmp[2] = (dvpdcw*dcwddn*ddndjk*deljk[2])/rjk;
+ fj[0] += Ftmp[0];
+ fj[1] += Ftmp[1];
+ fj[2] += Ftmp[2];
+ fk[0] -= Ftmp[0];
+ fk[1] -= Ftmp[1];
+ fk[2] -= Ftmp[2];
+
+ Ftmp[0] = dvpdcw*((dcwdn*dndjl[0])+(dcwddn*ddndjl*del34[0]/r34));
+ Ftmp[1] = dvpdcw*((dcwdn*dndjl[1])+(dcwddn*ddndjl*del34[1]/r34));
+ Ftmp[2] = dvpdcw*((dcwdn*dndjl[2])+(dcwddn*ddndjl*del34[2]/r34));
+ fj[0] += Ftmp[0];
+ fj[1] += Ftmp[1];
+ fj[2] += Ftmp[2];
+ fl[0] = -Ftmp[0];
+ fl[1] = -Ftmp[1];
+ fl[2] = -Ftmp[2];
+
+ Ftmp[0] = (dvpdcw*dcwddn*ddndil*delil[0])/ril;
+ Ftmp[1] = (dvpdcw*dcwddn*ddndil*delil[1])/ril;
+ Ftmp[2] = (dvpdcw*dcwddn*ddndil*delil[2])/ril;
+ fi[0] += Ftmp[0];
+ fi[1] += Ftmp[1];
+ fi[2] += Ftmp[2];
+ fl[0] -= Ftmp[0];
+ fl[1] -= Ftmp[1];
+ fl[2] -= Ftmp[2];
+
+ // coordination forces
+
+ fpair = Vtors*dw21*w23*w34*(1.0-tspjik)*(1.0-tspijl) / r21;
+ fi[0] -= del21[0]*fpair;
+ fi[1] -= del21[1]*fpair;
+ fi[2] -= del21[2]*fpair;
+ fk[0] += del21[0]*fpair;
+ fk[1] += del21[1]*fpair;
+ fk[2] += del21[2]*fpair;
+
+ fpair = Vtors*w21*dw23*w34*(1.0-tspjik)*(1.0-tspijl) / r23;
+ fi[0] -= del23[0]*fpair;
+ fi[1] -= del23[1]*fpair;
+ fi[2] -= del23[2]*fpair;
+ fj[0] += del23[0]*fpair;
+ fj[1] += del23[1]*fpair;
+ fj[2] += del23[2]*fpair;
+
+ fpair = Vtors*w21*w23*dw34*(1.0-tspjik)*(1.0-tspijl) / r34;
+ fj[0] -= del34[0]*fpair;
+ fj[1] -= del34[1]*fpair;
+ fj[2] -= del34[2]*fpair;
+ fl[0] += del34[0]*fpair;
+ fl[1] += del34[1]*fpair;
+ fl[2] += del34[2]*fpair;
+
+ // additional cut off function forces
+
+ fcpc = -Vtors*w21*w23*w34*dtsjik*(1.0-tspijl);
+ fpair = fcpc*dcidij/rij;
+ fi[0] += fpair*del23[0];
+ fi[1] += fpair*del23[1];
+ fi[2] += fpair*del23[2];
+ fj[0] -= fpair*del23[0];
+ fj[1] -= fpair*del23[1];
+ fj[2] -= fpair*del23[2];
+
+ fpair = fcpc*dcidik/rik;
+ fi[0] += fpair*del21[0];
+ fi[1] += fpair*del21[1];
+ fi[2] += fpair*del21[2];
+ fk[0] -= fpair*del21[0];
+ fk[1] -= fpair*del21[1];
+ fk[2] -= fpair*del21[2];
+
+ fpair = fcpc*dcidjk/rjk;
+ fj[0] += fpair*deljk[0];
+ fj[1] += fpair*deljk[1];
+ fj[2] += fpair*deljk[2];
+ fk[0] -= fpair*deljk[0];
+ fk[1] -= fpair*deljk[1];
+ fk[2] -= fpair*deljk[2];
+
+ fcpc = -Vtors*w21*w23*w34*(1.0-tspjik)*dtsijl;
+ fpair = fcpc*dcjdji/rij;
+ fi[0] += fpair*del23[0];
+ fi[1] += fpair*del23[1];
+ fi[2] += fpair*del23[2];
+ fj[0] -= fpair*del23[0];
+ fj[1] -= fpair*del23[1];
+ fj[2] -= fpair*del23[2];
+
+ fpair = fcpc*dcjdjl/rjl;
+ fj[0] += fpair*del34[0];
+ fj[1] += fpair*del34[1];
+ fj[2] += fpair*del34[2];
+ fl[0] -= fpair*del34[0];
+ fl[1] -= fpair*del34[1];
+ fl[2] -= fpair*del34[2];
+
+ fpair = fcpc*dcjdil/ril;
+ fi[0] += fpair*delil[0];
+ fi[1] += fpair*delil[1];
+ fi[2] += fpair*delil[2];
+ fl[0] -= fpair*delil[0];
+ fl[1] -= fpair*delil[1];
+ fl[2] -= fpair*delil[2];
+
+ // sum per-atom forces into atom force array
+
+ f[i][0] += fi[0]; f[i][1] += fi[1]; f[i][2] += fi[2];
+ f[j][0] += fj[0]; f[j][1] += fj[1]; f[j][2] += fj[2];
+ f[k][0] += fk[0]; f[k][1] += fk[1]; f[k][2] += fk[2];
+ f[l][0] += fl[0]; f[l][1] += fl[1]; f[l][2] += fl[2];
+
+ if (evflag) {
+ delkl[0] = delil[0] - del21[0];
+ delkl[1] = delil[1] - del21[1];
+ delkl[2] = delil[2] - del21[2];
+ ev_tally4(i,j,k,l,evdwl,fi,fj,fk,delil,del34,delkl);
+ }
+ }
}
}
}
@@ -1203,8 +1203,8 @@ void PairAIREBO::TORSION(int eflag, int vflag)
------------------------------------------------------------------------- */
double PairAIREBO::bondorder(int i, int j, double rij[3],
- double rijmag, double VA,
- double **f, int vflag_atom)
+ double rijmag, double VA,
+ double **f, int vflag_atom)
{
int atomi,atomj,k,n,l,atomk,atoml,atomn,atom1,atom2,atom3,atom4;
int itype,jtype,ktype,ltype,ntype;
@@ -1236,7 +1236,7 @@ double PairAIREBO::bondorder(int i, int j, double rij[3],
double **x = atom->x;
int *type = atom->type;
-
+
atomi = i;
atomj = j;
itype = map[type[i]];
@@ -1255,7 +1255,7 @@ double PairAIREBO::bondorder(int i, int j, double rij[3],
NconjtmpI = 0.0;
NconjtmpJ = 0.0;
Etmp = 0.0;
-
+
REBO_neighs = REBO_firstneigh[i];
for (k = 0; k < REBO_numneigh[i]; k++) {
atomk = REBO_neighs[k];
@@ -1265,20 +1265,20 @@ double PairAIREBO::bondorder(int i, int j, double rij[3],
rik[1] = x[atomi][1]-x[atomk][1];
rik[2] = x[atomi][2]-x[atomk][2];
rikmag = sqrt((rik[0]*rik[0])+(rik[1]*rik[1])+(rik[2]*rik[2]));
- lamdajik = 4.0*kronecker(itype,1) *
- ((rho[ktype][1]-rikmag)-(rho[jtype][1]-rijmag));
+ lamdajik = 4.0*kronecker(itype,1) *
+ ((rho[ktype][1]-rikmag)-(rho[jtype][1]-rijmag));
wik = Sp(rikmag,rcmin[itype][ktype],rcmax[itype][ktype],dS);
Nki = nC[atomk]-(wik*kronecker(itype,0))+nH[atomk] -
- (wik*kronecker(itype,1));
- cosjik = ((rij[0]*rik[0])+(rij[1]*rik[1])+(rij[2]*rik[2])) /
- (rijmag*rikmag);
+ (wik*kronecker(itype,1));
+ cosjik = ((rij[0]*rik[0])+(rij[1]*rik[1])+(rij[2]*rik[2])) /
+ (rijmag*rikmag);
cosjik = MIN(cosjik,1.0);
cosjik = MAX(cosjik,-1.0);
// evaluate splines g and derivatives dg
g = gSpline(cosjik,(NijC+NijH),itype,&dgdc,&dgdN);
- Etmp = Etmp+(wik*g*exp(lamdajik));
+ Etmp = Etmp+(wik*g*exp(lamdajik));
tmp3 = tmp3+(wik*dgdN*exp(lamdajik));
NconjtmpI = NconjtmpI+(kronecker(ktype,0)*wik*Sp(Nki,Nmin,Nmax,dS));
}
@@ -1288,7 +1288,7 @@ double PairAIREBO::bondorder(int i, int j, double rij[3],
dN2[0] = 0.0;
dN2[1] = 0.0;
PijS = PijSpline(NijC,NijH,itype,jtype,dN2);
- pij = pow(1.0+Etmp+PijS,-0.5);
+ pij = pow(1.0+Etmp+PijS,-0.5);
tmp = -0.5*pow(pij,3.0);
// pij forces
@@ -1302,32 +1302,32 @@ double PairAIREBO::bondorder(int i, int j, double rij[3],
rik[1] = x[atomi][1]-x[atomk][1];
rik[2] = x[atomi][2]-x[atomk][2];
rikmag = sqrt((rik[0]*rik[0])+(rik[1]*rik[1])+(rik[2]*rik[2]));
- lamdajik = 4.0*kronecker(itype,1) *
- ((rho[ktype][1]-rikmag)-(rho[jtype][1]-rijmag));
+ lamdajik = 4.0*kronecker(itype,1) *
+ ((rho[ktype][1]-rikmag)-(rho[jtype][1]-rijmag));
wik = Sp(rikmag,rcmin[itype][ktype],rcmax[itype][ktype],dwik);
- cosjik = (rij[0]*rik[0] + rij[1]*rik[1] + rij[2]*rik[2]) /
- (rijmag*rikmag);
+ cosjik = (rij[0]*rik[0] + rij[1]*rik[1] + rij[2]*rik[2]) /
+ (rijmag*rikmag);
cosjik = MIN(cosjik,1.0);
cosjik = MAX(cosjik,-1.0);
- dcosjikdri[0] = ((rij[0]+rik[0])/(rijmag*rikmag)) -
- (cosjik*((rij[0]/(rijmag*rijmag))+(rik[0]/(rikmag*rikmag))));
- dcosjikdri[1] = ((rij[1]+rik[1])/(rijmag*rikmag)) -
- (cosjik*((rij[1]/(rijmag*rijmag))+(rik[1]/(rikmag*rikmag))));
- dcosjikdri[2] = ((rij[2]+rik[2])/(rijmag*rikmag)) -
- (cosjik*((rij[2]/(rijmag*rijmag))+(rik[2]/(rikmag*rikmag))));
- dcosjikdrk[0] = (-rij[0]/(rijmag*rikmag)) +
- (cosjik*(rik[0]/(rikmag*rikmag)));
- dcosjikdrk[1] = (-rij[1]/(rijmag*rikmag)) +
- (cosjik*(rik[1]/(rikmag*rikmag)));
- dcosjikdrk[2] = (-rij[2]/(rijmag*rikmag)) +
- (cosjik*(rik[2]/(rikmag*rikmag)));
- dcosjikdrj[0] = (-rik[0]/(rijmag*rikmag)) +
- (cosjik*(rij[0]/(rijmag*rijmag)));
- dcosjikdrj[1] = (-rik[1]/(rijmag*rikmag)) +
- (cosjik*(rij[1]/(rijmag*rijmag)));
- dcosjikdrj[2] = (-rik[2]/(rijmag*rikmag)) +
- (cosjik*(rij[2]/(rijmag*rijmag)));
+ dcosjikdri[0] = ((rij[0]+rik[0])/(rijmag*rikmag)) -
+ (cosjik*((rij[0]/(rijmag*rijmag))+(rik[0]/(rikmag*rikmag))));
+ dcosjikdri[1] = ((rij[1]+rik[1])/(rijmag*rikmag)) -
+ (cosjik*((rij[1]/(rijmag*rijmag))+(rik[1]/(rikmag*rikmag))));
+ dcosjikdri[2] = ((rij[2]+rik[2])/(rijmag*rikmag)) -
+ (cosjik*((rij[2]/(rijmag*rijmag))+(rik[2]/(rikmag*rikmag))));
+ dcosjikdrk[0] = (-rij[0]/(rijmag*rikmag)) +
+ (cosjik*(rik[0]/(rikmag*rikmag)));
+ dcosjikdrk[1] = (-rij[1]/(rijmag*rikmag)) +
+ (cosjik*(rik[1]/(rikmag*rikmag)));
+ dcosjikdrk[2] = (-rij[2]/(rijmag*rikmag)) +
+ (cosjik*(rik[2]/(rikmag*rikmag)));
+ dcosjikdrj[0] = (-rik[0]/(rijmag*rikmag)) +
+ (cosjik*(rij[0]/(rijmag*rijmag)));
+ dcosjikdrj[1] = (-rik[1]/(rijmag*rikmag)) +
+ (cosjik*(rij[1]/(rijmag*rijmag)));
+ dcosjikdrj[2] = (-rik[2]/(rijmag*rikmag)) +
+ (cosjik*(rij[2]/(rijmag*rijmag)));
g = gSpline(cosjik,(NijC+NijH),itype,&dgdc,&dgdN);
tmp2 = VA*.5*(tmp*wik*dgdc*exp(lamdajik));
@@ -1382,16 +1382,16 @@ double PairAIREBO::bondorder(int i, int j, double rij[3],
fi[2] -= tmp2*rik[2];
fk[0] += tmp2*rik[0];
fk[1] += tmp2*rik[1];
- fk[2] += tmp2*rik[2];
+ fk[2] += tmp2*rik[2];
f[atomi][0] += fi[0]; f[atomi][1] += fi[1]; f[atomi][2] += fi[2];
f[atomj][0] += fj[0]; f[atomj][1] += fj[1]; f[atomj][2] += fj[2];
f[atomk][0] += fk[0]; f[atomk][1] += fk[1]; f[atomk][2] += fk[2];
if (vflag_atom) {
- rji[0] = -rij[0]; rji[1] = -rij[1]; rji[2] = -rij[2];
- rki[0] = -rik[0]; rki[1] = -rik[1]; rki[2] = -rik[2];
- v_tally3(atomi,atomj,atomk,fj,fk,rji,rki);
+ rji[0] = -rij[0]; rji[1] = -rij[1]; rji[2] = -rij[2];
+ rki[0] = -rik[0]; rki[1] = -rik[1]; rki[2] = -rik[2];
+ v_tally3(atomi,atomj,atomk,fj,fk,rji,rki);
}
}
}
@@ -1410,21 +1410,21 @@ double PairAIREBO::bondorder(int i, int j, double rij[3],
rjl[1] = x[atomj][1]-x[atoml][1];
rjl[2] = x[atomj][2]-x[atoml][2];
rjlmag = sqrt((rjl[0]*rjl[0])+(rjl[1]*rjl[1])+(rjl[2]*rjl[2]));
- lamdaijl = 4.0*kronecker(jtype,1) *
- ((rho[ltype][1]-rjlmag)-(rho[itype][1]-rijmag));
+ lamdaijl = 4.0*kronecker(jtype,1) *
+ ((rho[ltype][1]-rjlmag)-(rho[itype][1]-rijmag));
wjl = Sp(rjlmag,rcmin[jtype][ltype],rcmax[jtype][ltype],dS);
- Nlj = nC[atoml]-(wjl*kronecker(jtype,0)) +
- nH[atoml]-(wjl*kronecker(jtype,1));
- cosijl = -1.0*((rij[0]*rjl[0])+(rij[1]*rjl[1])+(rij[2]*rjl[2])) /
- (rijmag*rjlmag);
+ Nlj = nC[atoml]-(wjl*kronecker(jtype,0)) +
+ nH[atoml]-(wjl*kronecker(jtype,1));
+ cosijl = -1.0*((rij[0]*rjl[0])+(rij[1]*rjl[1])+(rij[2]*rjl[2])) /
+ (rijmag*rjlmag);
cosijl = MIN(cosijl,1.0);
cosijl = MAX(cosijl,-1.0);
// evaluate splines g and derivatives dg
g = gSpline(cosijl,NjiC+NjiH,jtype,&dgdc,&dgdN);
- Etmp = Etmp+(wjl*g*exp(lamdaijl));
- tmp3 = tmp3+(wjl*dgdN*exp(lamdaijl));
+ Etmp = Etmp+(wjl*g*exp(lamdaijl));
+ tmp3 = tmp3+(wjl*dgdN*exp(lamdaijl));
NconjtmpJ = NconjtmpJ+(kronecker(ltype,0)*wjl*Sp(Nlj,Nmin,Nmax,dS));
}
}
@@ -1432,7 +1432,7 @@ double PairAIREBO::bondorder(int i, int j, double rij[3],
PjiS = 0.0;
dN2[0] = 0.0;
dN2[1] = 0.0;
- PjiS = PijSpline(NjiC,NjiH,jtype,itype,dN2);
+ PjiS = PijSpline(NjiC,NjiH,jtype,itype,dN2);
pji = pow(1.0+Etmp+PjiS,-0.5);
tmp = -0.5*pow(pji,3.0);
@@ -1445,26 +1445,26 @@ double PairAIREBO::bondorder(int i, int j, double rij[3],
rjl[1] = x[atomj][1]-x[atoml][1];
rjl[2] = x[atomj][2]-x[atoml][2];
rjlmag = sqrt((rjl[0]*rjl[0])+(rjl[1]*rjl[1])+(rjl[2]*rjl[2]));
- lamdaijl = 4.0*kronecker(jtype,1) *
- ((rho[ltype][1]-rjlmag)-(rho[itype][1]-rijmag));
+ lamdaijl = 4.0*kronecker(jtype,1) *
+ ((rho[ltype][1]-rjlmag)-(rho[itype][1]-rijmag));
wjl = Sp(rjlmag,rcmin[jtype][ltype],rcmax[jtype][ltype],dwjl);
- cosijl = (-1.0*((rij[0]*rjl[0])+(rij[1]*rjl[1])+(rij[2]*rjl[2]))) /
- (rijmag*rjlmag);
+ cosijl = (-1.0*((rij[0]*rjl[0])+(rij[1]*rjl[1])+(rij[2]*rjl[2]))) /
+ (rijmag*rjlmag);
cosijl = MIN(cosijl,1.0);
cosijl = MAX(cosijl,-1.0);
- dcosijldri[0] = (-rjl[0]/(rijmag*rjlmag)) -
- (cosijl*rij[0]/(rijmag*rijmag));
- dcosijldri[1] = (-rjl[1]/(rijmag*rjlmag)) -
- (cosijl*rij[1]/(rijmag*rijmag));
- dcosijldri[2] = (-rjl[2]/(rijmag*rjlmag)) -
- (cosijl*rij[2]/(rijmag*rijmag));
- dcosijldrj[0] = ((-rij[0]+rjl[0])/(rijmag*rjlmag)) +
- (cosijl*((rij[0]/pow(rijmag,2.0))-(rjl[0]/(rjlmag*rjlmag))));
- dcosijldrj[1] = ((-rij[1]+rjl[1])/(rijmag*rjlmag)) +
- (cosijl*((rij[1]/pow(rijmag,2.0))-(rjl[1]/(rjlmag*rjlmag))));
- dcosijldrj[2] = ((-rij[2]+rjl[2])/(rijmag*rjlmag)) +
- (cosijl*((rij[2]/pow(rijmag,2.0))-(rjl[2]/(rjlmag*rjlmag))));
+ dcosijldri[0] = (-rjl[0]/(rijmag*rjlmag)) -
+ (cosijl*rij[0]/(rijmag*rijmag));
+ dcosijldri[1] = (-rjl[1]/(rijmag*rjlmag)) -
+ (cosijl*rij[1]/(rijmag*rijmag));
+ dcosijldri[2] = (-rjl[2]/(rijmag*rjlmag)) -
+ (cosijl*rij[2]/(rijmag*rijmag));
+ dcosijldrj[0] = ((-rij[0]+rjl[0])/(rijmag*rjlmag)) +
+ (cosijl*((rij[0]/pow(rijmag,2.0))-(rjl[0]/(rjlmag*rjlmag))));
+ dcosijldrj[1] = ((-rij[1]+rjl[1])/(rijmag*rjlmag)) +
+ (cosijl*((rij[1]/pow(rijmag,2.0))-(rjl[1]/(rjlmag*rjlmag))));
+ dcosijldrj[2] = ((-rij[2]+rjl[2])/(rijmag*rjlmag)) +
+ (cosijl*((rij[2]/pow(rijmag,2.0))-(rjl[2]/(rjlmag*rjlmag))));
dcosijldrl[0] = (rij[0]/(rijmag*rjlmag))+(cosijl*rjl[0]/(rjlmag*rjlmag));
dcosijldrl[1] = (rij[1]/(rijmag*rjlmag))+(cosijl*rjl[1]/(rjlmag*rjlmag));
dcosijldrl[2] = (rij[2]/(rijmag*rjlmag))+(cosijl*rjl[2]/(rjlmag*rjlmag));
@@ -1473,15 +1473,15 @@ double PairAIREBO::bondorder(int i, int j, double rij[3],
g = gSpline(cosijl,NjiC+NjiH,jtype,&dgdc,&dgdN);
tmp2 = VA*.5*(tmp*wjl*dgdc*exp(lamdaijl));
- fi[0] = -tmp2*dcosijldri[0];
- fi[1] = -tmp2*dcosijldri[1];
- fi[2] = -tmp2*dcosijldri[2];
- fj[0] = -tmp2*dcosijldrj[0];
- fj[1] = -tmp2*dcosijldrj[1];
- fj[2] = -tmp2*dcosijldrj[2];
- fl[0] = -tmp2*dcosijldrl[0];
- fl[1] = -tmp2*dcosijldrl[1];
- fl[2] = -tmp2*dcosijldrl[2];
+ fi[0] = -tmp2*dcosijldri[0];
+ fi[1] = -tmp2*dcosijldri[1];
+ fi[2] = -tmp2*dcosijldri[2];
+ fj[0] = -tmp2*dcosijldrj[0];
+ fj[1] = -tmp2*dcosijldrj[1];
+ fj[2] = -tmp2*dcosijldrj[2];
+ fl[0] = -tmp2*dcosijldrl[0];
+ fl[1] = -tmp2*dcosijldrl[1];
+ fl[2] = -tmp2*dcosijldrl[2];
tmp2 = VA*.5*(tmp*wjl*g*exp(lamdaijl)*4.0*kronecker(jtype,1));
fi[0] -= tmp2*(rij[0]/rijmag);
@@ -1495,7 +1495,7 @@ double PairAIREBO::bondorder(int i, int j, double rij[3],
fl[2] -= tmp2*(rjl[2]/rjlmag);
// coordination forces
-
+
// dwik forces
tmp2 = VA*.5*(tmp*dwjl*g*exp(lamdaijl))/rjlmag;
@@ -1506,7 +1506,7 @@ double PairAIREBO::bondorder(int i, int j, double rij[3],
fl[1] += tmp2*rjl[1];
fl[2] += tmp2*rjl[2];
- // PIJ forces
+ // PIJ forces
tmp2 = VA*.5*(tmp*dN2[ltype]*dwjl)/rjlmag;
fj[0] -= tmp2*rjl[0];
@@ -1524,24 +1524,24 @@ double PairAIREBO::bondorder(int i, int j, double rij[3],
fj[2] -= tmp2*rjl[2];
fl[0] += tmp2*rjl[0];
fl[1] += tmp2*rjl[1];
- fl[2] += tmp2*rjl[2];
+ fl[2] += tmp2*rjl[2];
f[atomi][0] += fi[0]; f[atomi][1] += fi[1]; f[atomi][2] += fi[2];
f[atomj][0] += fj[0]; f[atomj][1] += fj[1]; f[atomj][2] += fj[2];
f[atoml][0] += fl[0]; f[atoml][1] += fl[1]; f[atoml][2] += fl[2];
if (vflag_atom) {
- rlj[0] = -rjl[0]; rlj[1] = -rjl[1]; rlj[2] = -rjl[2];
- v_tally3(atomi,atomj,atoml,fi,fl,rij,rlj);
+ rlj[0] = -rjl[0]; rlj[1] = -rjl[1]; rlj[2] = -rjl[2];
+ v_tally3(atomi,atomj,atoml,fi,fl,rij,rlj);
}
}
- }
-
+ }
+
// evaluate Nij conj
Nijconj = 1.0+(NconjtmpI*NconjtmpI)+(NconjtmpJ*NconjtmpJ);
piRC = piRCSpline(NijC+NijH,NjiC+NjiH,Nijconj,itype,jtype,dN3);
-
+
// piRC forces
REBO_neighs_i = REBO_firstneigh[i];
@@ -1554,57 +1554,57 @@ double PairAIREBO::bondorder(int i, int j, double rij[3],
rik[2] = x[atomi][2]-x[atomk][2];
rikmag = sqrt((rik[0]*rik[0])+(rik[1]*rik[1])+(rik[2]*rik[2]));
wik = Sp(rikmag,rcmin[itype][ktype],rcmax[itype][ktype],dwik);
- Nki = nC[atomk]-(wik*kronecker(itype,0))+nH[atomk] -
- (wik*kronecker(itype,1));
+ Nki = nC[atomk]-(wik*kronecker(itype,0))+nH[atomk] -
+ (wik*kronecker(itype,1));
SpN = Sp(Nki,Nmin,Nmax,dNki);
tmp2 = VA*dN3[0]*dwik/rikmag;
- f[atomi][0] -= tmp2*rik[0];
- f[atomi][1] -= tmp2*rik[1];
- f[atomi][2] -= tmp2*rik[2];
- f[atomk][0] += tmp2*rik[0];
- f[atomk][1] += tmp2*rik[1];
- f[atomk][2] += tmp2*rik[2];
+ f[atomi][0] -= tmp2*rik[0];
+ f[atomi][1] -= tmp2*rik[1];
+ f[atomi][2] -= tmp2*rik[2];
+ f[atomk][0] += tmp2*rik[0];
+ f[atomk][1] += tmp2*rik[1];
+ f[atomk][2] += tmp2*rik[2];
if (vflag_atom) v_tally2(atomi,atomk,-tmp2,rik);
tmp2 = VA*dN3[2]*(2.0*NconjtmpI*dwik*SpN)/rikmag;
- f[atomi][0] -= tmp2*rik[0];
- f[atomi][1] -= tmp2*rik[1];
- f[atomi][2] -= tmp2*rik[2];
- f[atomk][0] += tmp2*rik[0];
- f[atomk][1] += tmp2*rik[1];
+ f[atomi][0] -= tmp2*rik[0];
+ f[atomi][1] -= tmp2*rik[1];
+ f[atomi][2] -= tmp2*rik[2];
+ f[atomk][0] += tmp2*rik[0];
+ f[atomk][1] += tmp2*rik[1];
f[atomk][2] += tmp2*rik[2];
if (vflag_atom) v_tally2(atomi,atomk,-tmp2,rik);
if (fabs(dNki) > TOL) {
- REBO_neighs_k = REBO_firstneigh[atomk];
- for (n = 0; n < REBO_numneigh[atomk]; n++) {
- atomn = REBO_neighs_k[n];
- if (atomn != atomi) {
- ntype = map[type[atomn]];
- rkn[0] = x[atomk][0]-x[atomn][0];
- rkn[1] = x[atomk][1]-x[atomn][1];
- rkn[2] = x[atomk][2]-x[atomn][2];
- rknmag = sqrt((rkn[0]*rkn[0])+(rkn[1]*rkn[1])+(rkn[2]*rkn[2]));
- Sp(rknmag,rcmin[ktype][ntype],rcmax[ktype][ntype],dwkn);
-
- tmp2 = VA*dN3[2]*(2.0*NconjtmpI*wik*dNki*dwkn)/rknmag;
- f[atomk][0] -= tmp2*rkn[0];
- f[atomk][1] -= tmp2*rkn[1];
- f[atomk][2] -= tmp2*rkn[2];
- f[atomn][0] += tmp2*rkn[0];
- f[atomn][1] += tmp2*rkn[1];
- f[atomn][2] += tmp2*rkn[2];
-
- if (vflag_atom) v_tally2(atomk,atomn,-tmp2,rkn);
- }
- }
- }
+ REBO_neighs_k = REBO_firstneigh[atomk];
+ for (n = 0; n < REBO_numneigh[atomk]; n++) {
+ atomn = REBO_neighs_k[n];
+ if (atomn != atomi) {
+ ntype = map[type[atomn]];
+ rkn[0] = x[atomk][0]-x[atomn][0];
+ rkn[1] = x[atomk][1]-x[atomn][1];
+ rkn[2] = x[atomk][2]-x[atomn][2];
+ rknmag = sqrt((rkn[0]*rkn[0])+(rkn[1]*rkn[1])+(rkn[2]*rkn[2]));
+ Sp(rknmag,rcmin[ktype][ntype],rcmax[ktype][ntype],dwkn);
+
+ tmp2 = VA*dN3[2]*(2.0*NconjtmpI*wik*dNki*dwkn)/rknmag;
+ f[atomk][0] -= tmp2*rkn[0];
+ f[atomk][1] -= tmp2*rkn[1];
+ f[atomk][2] -= tmp2*rkn[2];
+ f[atomn][0] += tmp2*rkn[0];
+ f[atomn][1] += tmp2*rkn[1];
+ f[atomn][2] += tmp2*rkn[2];
+
+ if (vflag_atom) v_tally2(atomk,atomn,-tmp2,rkn);
+ }
+ }
+ }
}
- }
-
+ }
+
// piRC forces
REBO_neighs = REBO_firstneigh[atomj];
@@ -1617,57 +1617,57 @@ double PairAIREBO::bondorder(int i, int j, double rij[3],
rjl[2] = x[atomj][2]-x[atoml][2];
rjlmag = sqrt((rjl[0]*rjl[0])+(rjl[1]*rjl[1])+(rjl[2]*rjl[2]));
wjl = Sp(rjlmag,rcmin[jtype][ltype],rcmax[jtype][ltype],dwjl);
- Nlj = nC[atoml]-(wjl*kronecker(jtype,0))+nH[atoml] -
- (wjl*kronecker(jtype,1));
+ Nlj = nC[atoml]-(wjl*kronecker(jtype,0))+nH[atoml] -
+ (wjl*kronecker(jtype,1));
SpN = Sp(Nlj,Nmin,Nmax,dNlj);
tmp2 = VA*dN3[1]*dwjl/rjlmag;
- f[atomj][0] -= tmp2*rjl[0];
- f[atomj][1] -= tmp2*rjl[1];
+ f[atomj][0] -= tmp2*rjl[0];
+ f[atomj][1] -= tmp2*rjl[1];
f[atomj][2] -= tmp2*rjl[2];
- f[atoml][0] += tmp2*rjl[0];
- f[atoml][1] += tmp2*rjl[1];
+ f[atoml][0] += tmp2*rjl[0];
+ f[atoml][1] += tmp2*rjl[1];
f[atoml][2] += tmp2*rjl[2];
if (vflag_atom) v_tally2(atomj,atoml,-tmp2,rjl);
tmp2 = VA*dN3[2]*(2.0*NconjtmpJ*dwjl*SpN)/rjlmag;
- f[atomj][0] -= tmp2*rjl[0];
- f[atomj][1] -= tmp2*rjl[1];
+ f[atomj][0] -= tmp2*rjl[0];
+ f[atomj][1] -= tmp2*rjl[1];
f[atomj][2] -= tmp2*rjl[2];
- f[atoml][0] += tmp2*rjl[0];
- f[atoml][1] += tmp2*rjl[1];
+ f[atoml][0] += tmp2*rjl[0];
+ f[atoml][1] += tmp2*rjl[1];
f[atoml][2] += tmp2*rjl[2];
if (vflag_atom) v_tally2(atomj,atoml,-tmp2,rjl);
if (fabs(dNlj) > TOL) {
- REBO_neighs_l = REBO_firstneigh[atoml];
- for (n = 0; n < REBO_numneigh[atoml]; n++) {
- atomn = REBO_neighs_l[n];
- if (atomn != atomj) {
- ntype = map[type[atomn]];
- rln[0] = x[atoml][0]-x[atomn][0];
- rln[1] = x[atoml][1]-x[atomn][1];
- rln[2] = x[atoml][2]-x[atomn][2];
- rlnmag = sqrt((rln[0]*rln[0])+(rln[1]*rln[1])+(rln[2]*rln[2]));
- Sp(rlnmag,rcmin[ltype][ntype],rcmax[ltype][ntype],dwln);
-
- tmp2 = VA*dN3[2]*(2.0*NconjtmpJ*wjl*dNlj*dwln)/rlnmag;
- f[atoml][0] -= tmp2*rln[0];
- f[atoml][1] -= tmp2*rln[1];
- f[atoml][2] -= tmp2*rln[2];
- f[atomn][0] += tmp2*rln[0];
- f[atomn][1] += tmp2*rln[1];
- f[atomn][2] += tmp2*rln[2];
-
- if (vflag_atom) v_tally2(atoml,atomn,-tmp2,rln);
- }
- }
- }
+ REBO_neighs_l = REBO_firstneigh[atoml];
+ for (n = 0; n < REBO_numneigh[atoml]; n++) {
+ atomn = REBO_neighs_l[n];
+ if (atomn != atomj) {
+ ntype = map[type[atomn]];
+ rln[0] = x[atoml][0]-x[atomn][0];
+ rln[1] = x[atoml][1]-x[atomn][1];
+ rln[2] = x[atoml][2]-x[atomn][2];
+ rlnmag = sqrt((rln[0]*rln[0])+(rln[1]*rln[1])+(rln[2]*rln[2]));
+ Sp(rlnmag,rcmin[ltype][ntype],rcmax[ltype][ntype],dwln);
+
+ tmp2 = VA*dN3[2]*(2.0*NconjtmpJ*wjl*dNlj*dwln)/rlnmag;
+ f[atoml][0] -= tmp2*rln[0];
+ f[atoml][1] -= tmp2*rln[1];
+ f[atoml][2] -= tmp2*rln[2];
+ f[atomn][0] += tmp2*rln[0];
+ f[atomn][1] += tmp2*rln[1];
+ f[atomn][2] += tmp2*rln[2];
+
+ if (vflag_atom) v_tally2(atoml,atomn,-tmp2,rln);
+ }
+ }
+ }
}
- }
-
+ }
+
Tij = 0.0;
dN3[0] = 0.0;
dN3[1] = 0.0;
@@ -1693,260 +1693,260 @@ double PairAIREBO::bondorder(int i, int j, double rij[3],
atom1 = atomk;
ktype = map[type[atomk]];
if (atomk != atomj) {
- r21[0] = x[atom2][0]-x[atom1][0];
- r21[1] = x[atom2][1]-x[atom1][1];
- r21[2] = x[atom2][2]-x[atom1][2];
- r21mag = sqrt(r21[0]*r21[0] + r21[1]*r21[1] + r21[2]*r21[2]);
- cos321 = -1.0*((r21[0]*r32[0])+(r21[1]*r32[1])+(r21[2]*r32[2])) /
- (r21mag*r32mag);
- cos321 = MIN(cos321,1.0);
- cos321 = MAX(cos321,-1.0);
- Sp2(cos321,thmin,thmax,dcut321);
- sin321 = sqrt(1.0 - cos321*cos321);
- sink2i = 1.0/(sin321*sin321);
- rik2i = 1.0/(r21mag*r21mag);
- if (sin321 != 0.0) {
- rr = (r23mag*r23mag)-(r21mag*r21mag);
- rjk[0] = r21[0]-r23[0];
- rjk[1] = r21[1]-r23[1];
- rjk[2] = r21[2]-r23[2];
- rjk2 = (rjk[0]*rjk[0])+(rjk[1]*rjk[1])+(rjk[2]*rjk[2]);
- rijrik = 2.0*r23mag*r21mag;
- rik2 = r21mag*r21mag;
- dctik = (-rr+rjk2)/(rijrik*rik2);
- dctij = (rr+rjk2)/(rijrik*r23mag*r23mag);
- dctjk = -2.0/rijrik;
- w21 = Sp(r21mag,rcmin[itype][ktype],rcmaxp[itype][ktype],dw21);
- rijmag = r32mag;
- rikmag = r21mag;
- rij2 = r32mag*r32mag;
- rik2 = r21mag*r21mag;
- costmp = 0.5*(rij2+rik2-rjk2)/rijmag/rikmag;
- tspjik = Sp2(costmp,thmin,thmax,dtsjik);
- dtsjik = -dtsjik;
-
- REBO_neighs_j = REBO_firstneigh[j];
- for (l = 0; l < REBO_numneigh[j]; l++) {
- atoml = REBO_neighs_j[l];
- atom4 = atoml;
- ltype = map[type[atoml]];
- if (!(atoml == atomi || atoml == atomk)) {
- r34[0] = x[atom3][0]-x[atom4][0];
- r34[1] = x[atom3][1]-x[atom4][1];
- r34[2] = x[atom3][2]-x[atom4][2];
- r34mag = sqrt((r34[0]*r34[0])+(r34[1]*r34[1])+(r34[2]*r34[2]));
- cos234 = (r32[0]*r34[0] + r32[1]*r34[1] + r32[2]*r34[2]) /
- (r32mag*r34mag);
- cos234 = MIN(cos234,1.0);
- cos234 = MAX(cos234,-1.0);
- sin234 = sqrt(1.0 - cos234*cos234);
- sinl2i = 1.0/(sin234*sin234);
- rjl2i = 1.0/(r34mag*r34mag);
-
- if (sin234 != 0.0) {
- w34 = Sp(r34mag,rcmin[jtype][ltype],rcmaxp[jtype][ltype],dw34);
- rr = (r23mag*r23mag)-(r34mag*r34mag);
- ril[0] = r23[0]+r34[0];
- ril[1] = r23[1]+r34[1];
- ril[2] = r23[2]+r34[2];
- ril2 = (ril[0]*ril[0])+(ril[1]*ril[1])+(ril[2]*ril[2]);
- rijrjl = 2.0*r23mag*r34mag;
- rjl2 = r34mag*r34mag;
- dctjl = (-rr+ril2)/(rijrjl*rjl2);
- dctji = (rr+ril2)/(rijrjl*r23mag*r23mag);
- dctil = -2.0/rijrjl;
- rjlmag = r34mag;
- rjl2 = r34mag*r34mag;
- costmp = 0.5*(rij2+rjl2-ril2)/rijmag/rjlmag;
- tspijl = Sp2(costmp,thmin,thmax,dtsijl);
- dtsijl = -dtsijl;
- prefactor = VA*Tij;
-
- cross321[0] = (r32[1]*r21[2])-(r32[2]*r21[1]);
- cross321[1] = (r32[2]*r21[0])-(r32[0]*r21[2]);
- cross321[2] = (r32[0]*r21[1])-(r32[1]*r21[0]);
- cross234[0] = (r23[1]*r34[2])-(r23[2]*r34[1]);
- cross234[1] = (r23[2]*r34[0])-(r23[0]*r34[2]);
- cross234[2] = (r23[0]*r34[1])-(r23[1]*r34[0]);
-
- cwnum = (cross321[0]*cross234[0]) +
- (cross321[1]*cross234[1]) + (cross321[2]*cross234[2]);
- cwnom = r21mag*r34mag*r23mag*r23mag*sin321*sin234;
- om1234 = cwnum/cwnom;
- cw = om1234;
- Etmp += ((1.0-pow(om1234,2.0))*w21*w34) *
- (1.0-tspjik)*(1.0-tspijl);
-
- dt1dik = (rik2i)-(dctik*sink2i*cos321);
- dt1djk = (-dctjk*sink2i*cos321);
- dt1djl = (rjl2i)-(dctjl*sinl2i*cos234);
- dt1dil = (-dctil*sinl2i*cos234);
- dt1dij = (2.0/(r23mag*r23mag))-(dctij*sink2i*cos321) -
- (dctji*sinl2i*cos234);
-
- dt2dik[0] = (-r23[2]*cross234[1])+(r23[1]*cross234[2]);
- dt2dik[1] = (-r23[0]*cross234[2])+(r23[2]*cross234[0]);
- dt2dik[2] = (-r23[1]*cross234[0])+(r23[0]*cross234[1]);
-
- dt2djl[0] = (-r23[1]*cross321[2])+(r23[2]*cross321[1]);
- dt2djl[1] = (-r23[2]*cross321[0])+(r23[0]*cross321[2]);
- dt2djl[2] = (-r23[0]*cross321[1])+(r23[1]*cross321[0]);
-
- dt2dij[0] = (r21[2]*cross234[1])-(r34[2]*cross321[1]) -
- (r21[1]*cross234[2])+(r34[1]*cross321[2]);
- dt2dij[1] = (r21[0]*cross234[2])-(r34[0]*cross321[2]) -
- (r21[2]*cross234[0])+(r34[2]*cross321[0]);
- dt2dij[2] = (r21[1]*cross234[0])-(r34[1]*cross321[0]) -
- (r21[0]*cross234[1])+(r34[0]*cross321[1]);
-
- aa = (prefactor*2.0*cw/cwnom)*w21*w34 *
- (1.0-tspjik)*(1.0-tspijl);
- aaa1 = -prefactor*(1.0-pow(om1234,2.0)) *
- (1.0-tspjik)*(1.0-tspijl);
- aaa2 = aaa1*w21*w34;
- at2 = aa*cwnum;
-
- fcijpc = (-dt1dij*at2)+(aaa2*dtsjik*dctij*(1.0-tspijl)) +
- (aaa2*dtsijl*dctji*(1.0-tspjik));
- fcikpc = (-dt1dik*at2)+(aaa2*dtsjik*dctik*(1.0-tspijl));
- fcjlpc = (-dt1djl*at2)+(aaa2*dtsijl*dctjl*(1.0-tspjik));
- fcjkpc = (-dt1djk*at2)+(aaa2*dtsjik*dctjk*(1.0-tspijl));
- fcilpc = (-dt1dil*at2)+(aaa2*dtsijl*dctil*(1.0-tspjik));
-
- F23[0] = (fcijpc*r23[0])+(aa*dt2dij[0]);
- F23[1] = (fcijpc*r23[1])+(aa*dt2dij[1]);
- F23[2] = (fcijpc*r23[2])+(aa*dt2dij[2]);
-
- F12[0] = (fcikpc*r21[0])+(aa*dt2dik[0]);
- F12[1] = (fcikpc*r21[1])+(aa*dt2dik[1]);
- F12[2] = (fcikpc*r21[2])+(aa*dt2dik[2]);
-
- F34[0] = (fcjlpc*r34[0])+(aa*dt2djl[0]);
- F34[1] = (fcjlpc*r34[1])+(aa*dt2djl[1]);
- F34[2] = (fcjlpc*r34[2])+(aa*dt2djl[2]);
-
- F31[0] = (fcjkpc*rjk[0]);
- F31[1] = (fcjkpc*rjk[1]);
- F31[2] = (fcjkpc*rjk[2]);
-
- F24[0] = (fcilpc*ril[0]);
- F24[1] = (fcilpc*ril[1]);
- F24[2] = (fcilpc*ril[2]);
-
- f1[0] = -F12[0]-F31[0];
- f1[1] = -F12[1]-F31[1];
- f1[2] = -F12[2]-F31[2];
- f2[0] = F23[0]+F12[0]+F24[0];
- f2[1] = F23[1]+F12[1]+F24[1];
- f2[2] = F23[2]+F12[2]+F24[2];
- f3[0] = -F23[0]+F34[0]+F31[0];
- f3[1] = -F23[1]+F34[1]+F31[1];
- f3[2] = -F23[2]+F34[2]+F31[2];
- f4[0] = -F34[0]-F24[0];
- f4[1] = -F34[1]-F24[1];
- f4[2] = -F34[2]-F24[2];
-
- // coordination forces
-
- tmp2 = VA*Tij*((1.0-(om1234*om1234))) *
- (1.0-tspjik)*(1.0-tspijl)*dw21*w34/r21mag;
- f2[0] -= tmp2*r21[0];
- f2[1] -= tmp2*r21[1];
- f2[2] -= tmp2*r21[2];
- f1[0] += tmp2*r21[0];
- f1[1] += tmp2*r21[1];
- f1[2] += tmp2*r21[2];
-
- tmp2 = VA*Tij*((1.0-(om1234*om1234))) *
- (1.0-tspjik)*(1.0-tspijl)*w21*dw34/r34mag;
- f3[0] -= tmp2*r34[0];
- f3[1] -= tmp2*r34[1];
- f3[2] -= tmp2*r34[2];
- f4[0] += tmp2*r34[0];
- f4[1] += tmp2*r34[1];
- f4[2] += tmp2*r34[2];
-
- f[atom1][0] += f1[0]; f[atom1][1] += f1[1];
- f[atom1][2] += f1[2];
- f[atom2][0] += f2[0]; f[atom2][1] += f2[1];
- f[atom2][2] += f2[2];
- f[atom3][0] += f3[0]; f[atom3][1] += f3[1];
- f[atom3][2] += f3[2];
- f[atom4][0] += f4[0]; f[atom4][1] += f4[1];
- f[atom4][2] += f4[2];
-
- if (vflag_atom) {
- r13[0] = -rjk[0]; r13[1] = -rjk[1]; r13[2] = -rjk[2];
- r43[0] = -r34[0]; r43[1] = -r34[1]; r43[2] = -r34[2];
- v_tally4(atom1,atom2,atom3,atom4,f1,f2,f4,r13,r23,r43);
- }
- }
- }
- }
- }
+ r21[0] = x[atom2][0]-x[atom1][0];
+ r21[1] = x[atom2][1]-x[atom1][1];
+ r21[2] = x[atom2][2]-x[atom1][2];
+ r21mag = sqrt(r21[0]*r21[0] + r21[1]*r21[1] + r21[2]*r21[2]);
+ cos321 = -1.0*((r21[0]*r32[0])+(r21[1]*r32[1])+(r21[2]*r32[2])) /
+ (r21mag*r32mag);
+ cos321 = MIN(cos321,1.0);
+ cos321 = MAX(cos321,-1.0);
+ Sp2(cos321,thmin,thmax,dcut321);
+ sin321 = sqrt(1.0 - cos321*cos321);
+ sink2i = 1.0/(sin321*sin321);
+ rik2i = 1.0/(r21mag*r21mag);
+ if (sin321 != 0.0) {
+ rr = (r23mag*r23mag)-(r21mag*r21mag);
+ rjk[0] = r21[0]-r23[0];
+ rjk[1] = r21[1]-r23[1];
+ rjk[2] = r21[2]-r23[2];
+ rjk2 = (rjk[0]*rjk[0])+(rjk[1]*rjk[1])+(rjk[2]*rjk[2]);
+ rijrik = 2.0*r23mag*r21mag;
+ rik2 = r21mag*r21mag;
+ dctik = (-rr+rjk2)/(rijrik*rik2);
+ dctij = (rr+rjk2)/(rijrik*r23mag*r23mag);
+ dctjk = -2.0/rijrik;
+ w21 = Sp(r21mag,rcmin[itype][ktype],rcmaxp[itype][ktype],dw21);
+ rijmag = r32mag;
+ rikmag = r21mag;
+ rij2 = r32mag*r32mag;
+ rik2 = r21mag*r21mag;
+ costmp = 0.5*(rij2+rik2-rjk2)/rijmag/rikmag;
+ tspjik = Sp2(costmp,thmin,thmax,dtsjik);
+ dtsjik = -dtsjik;
+
+ REBO_neighs_j = REBO_firstneigh[j];
+ for (l = 0; l < REBO_numneigh[j]; l++) {
+ atoml = REBO_neighs_j[l];
+ atom4 = atoml;
+ ltype = map[type[atoml]];
+ if (!(atoml == atomi || atoml == atomk)) {
+ r34[0] = x[atom3][0]-x[atom4][0];
+ r34[1] = x[atom3][1]-x[atom4][1];
+ r34[2] = x[atom3][2]-x[atom4][2];
+ r34mag = sqrt((r34[0]*r34[0])+(r34[1]*r34[1])+(r34[2]*r34[2]));
+ cos234 = (r32[0]*r34[0] + r32[1]*r34[1] + r32[2]*r34[2]) /
+ (r32mag*r34mag);
+ cos234 = MIN(cos234,1.0);
+ cos234 = MAX(cos234,-1.0);
+ sin234 = sqrt(1.0 - cos234*cos234);
+ sinl2i = 1.0/(sin234*sin234);
+ rjl2i = 1.0/(r34mag*r34mag);
+
+ if (sin234 != 0.0) {
+ w34 = Sp(r34mag,rcmin[jtype][ltype],rcmaxp[jtype][ltype],dw34);
+ rr = (r23mag*r23mag)-(r34mag*r34mag);
+ ril[0] = r23[0]+r34[0];
+ ril[1] = r23[1]+r34[1];
+ ril[2] = r23[2]+r34[2];
+ ril2 = (ril[0]*ril[0])+(ril[1]*ril[1])+(ril[2]*ril[2]);
+ rijrjl = 2.0*r23mag*r34mag;
+ rjl2 = r34mag*r34mag;
+ dctjl = (-rr+ril2)/(rijrjl*rjl2);
+ dctji = (rr+ril2)/(rijrjl*r23mag*r23mag);
+ dctil = -2.0/rijrjl;
+ rjlmag = r34mag;
+ rjl2 = r34mag*r34mag;
+ costmp = 0.5*(rij2+rjl2-ril2)/rijmag/rjlmag;
+ tspijl = Sp2(costmp,thmin,thmax,dtsijl);
+ dtsijl = -dtsijl;
+ prefactor = VA*Tij;
+
+ cross321[0] = (r32[1]*r21[2])-(r32[2]*r21[1]);
+ cross321[1] = (r32[2]*r21[0])-(r32[0]*r21[2]);
+ cross321[2] = (r32[0]*r21[1])-(r32[1]*r21[0]);
+ cross234[0] = (r23[1]*r34[2])-(r23[2]*r34[1]);
+ cross234[1] = (r23[2]*r34[0])-(r23[0]*r34[2]);
+ cross234[2] = (r23[0]*r34[1])-(r23[1]*r34[0]);
+
+ cwnum = (cross321[0]*cross234[0]) +
+ (cross321[1]*cross234[1]) + (cross321[2]*cross234[2]);
+ cwnom = r21mag*r34mag*r23mag*r23mag*sin321*sin234;
+ om1234 = cwnum/cwnom;
+ cw = om1234;
+ Etmp += ((1.0-pow(om1234,2.0))*w21*w34) *
+ (1.0-tspjik)*(1.0-tspijl);
+
+ dt1dik = (rik2i)-(dctik*sink2i*cos321);
+ dt1djk = (-dctjk*sink2i*cos321);
+ dt1djl = (rjl2i)-(dctjl*sinl2i*cos234);
+ dt1dil = (-dctil*sinl2i*cos234);
+ dt1dij = (2.0/(r23mag*r23mag))-(dctij*sink2i*cos321) -
+ (dctji*sinl2i*cos234);
+
+ dt2dik[0] = (-r23[2]*cross234[1])+(r23[1]*cross234[2]);
+ dt2dik[1] = (-r23[0]*cross234[2])+(r23[2]*cross234[0]);
+ dt2dik[2] = (-r23[1]*cross234[0])+(r23[0]*cross234[1]);
+
+ dt2djl[0] = (-r23[1]*cross321[2])+(r23[2]*cross321[1]);
+ dt2djl[1] = (-r23[2]*cross321[0])+(r23[0]*cross321[2]);
+ dt2djl[2] = (-r23[0]*cross321[1])+(r23[1]*cross321[0]);
+
+ dt2dij[0] = (r21[2]*cross234[1])-(r34[2]*cross321[1]) -
+ (r21[1]*cross234[2])+(r34[1]*cross321[2]);
+ dt2dij[1] = (r21[0]*cross234[2])-(r34[0]*cross321[2]) -
+ (r21[2]*cross234[0])+(r34[2]*cross321[0]);
+ dt2dij[2] = (r21[1]*cross234[0])-(r34[1]*cross321[0]) -
+ (r21[0]*cross234[1])+(r34[0]*cross321[1]);
+
+ aa = (prefactor*2.0*cw/cwnom)*w21*w34 *
+ (1.0-tspjik)*(1.0-tspijl);
+ aaa1 = -prefactor*(1.0-pow(om1234,2.0)) *
+ (1.0-tspjik)*(1.0-tspijl);
+ aaa2 = aaa1*w21*w34;
+ at2 = aa*cwnum;
+
+ fcijpc = (-dt1dij*at2)+(aaa2*dtsjik*dctij*(1.0-tspijl)) +
+ (aaa2*dtsijl*dctji*(1.0-tspjik));
+ fcikpc = (-dt1dik*at2)+(aaa2*dtsjik*dctik*(1.0-tspijl));
+ fcjlpc = (-dt1djl*at2)+(aaa2*dtsijl*dctjl*(1.0-tspjik));
+ fcjkpc = (-dt1djk*at2)+(aaa2*dtsjik*dctjk*(1.0-tspijl));
+ fcilpc = (-dt1dil*at2)+(aaa2*dtsijl*dctil*(1.0-tspjik));
+
+ F23[0] = (fcijpc*r23[0])+(aa*dt2dij[0]);
+ F23[1] = (fcijpc*r23[1])+(aa*dt2dij[1]);
+ F23[2] = (fcijpc*r23[2])+(aa*dt2dij[2]);
+
+ F12[0] = (fcikpc*r21[0])+(aa*dt2dik[0]);
+ F12[1] = (fcikpc*r21[1])+(aa*dt2dik[1]);
+ F12[2] = (fcikpc*r21[2])+(aa*dt2dik[2]);
+
+ F34[0] = (fcjlpc*r34[0])+(aa*dt2djl[0]);
+ F34[1] = (fcjlpc*r34[1])+(aa*dt2djl[1]);
+ F34[2] = (fcjlpc*r34[2])+(aa*dt2djl[2]);
+
+ F31[0] = (fcjkpc*rjk[0]);
+ F31[1] = (fcjkpc*rjk[1]);
+ F31[2] = (fcjkpc*rjk[2]);
+
+ F24[0] = (fcilpc*ril[0]);
+ F24[1] = (fcilpc*ril[1]);
+ F24[2] = (fcilpc*ril[2]);
+
+ f1[0] = -F12[0]-F31[0];
+ f1[1] = -F12[1]-F31[1];
+ f1[2] = -F12[2]-F31[2];
+ f2[0] = F23[0]+F12[0]+F24[0];
+ f2[1] = F23[1]+F12[1]+F24[1];
+ f2[2] = F23[2]+F12[2]+F24[2];
+ f3[0] = -F23[0]+F34[0]+F31[0];
+ f3[1] = -F23[1]+F34[1]+F31[1];
+ f3[2] = -F23[2]+F34[2]+F31[2];
+ f4[0] = -F34[0]-F24[0];
+ f4[1] = -F34[1]-F24[1];
+ f4[2] = -F34[2]-F24[2];
+
+ // coordination forces
+
+ tmp2 = VA*Tij*((1.0-(om1234*om1234))) *
+ (1.0-tspjik)*(1.0-tspijl)*dw21*w34/r21mag;
+ f2[0] -= tmp2*r21[0];
+ f2[1] -= tmp2*r21[1];
+ f2[2] -= tmp2*r21[2];
+ f1[0] += tmp2*r21[0];
+ f1[1] += tmp2*r21[1];
+ f1[2] += tmp2*r21[2];
+
+ tmp2 = VA*Tij*((1.0-(om1234*om1234))) *
+ (1.0-tspjik)*(1.0-tspijl)*w21*dw34/r34mag;
+ f3[0] -= tmp2*r34[0];
+ f3[1] -= tmp2*r34[1];
+ f3[2] -= tmp2*r34[2];
+ f4[0] += tmp2*r34[0];
+ f4[1] += tmp2*r34[1];
+ f4[2] += tmp2*r34[2];
+
+ f[atom1][0] += f1[0]; f[atom1][1] += f1[1];
+ f[atom1][2] += f1[2];
+ f[atom2][0] += f2[0]; f[atom2][1] += f2[1];
+ f[atom2][2] += f2[2];
+ f[atom3][0] += f3[0]; f[atom3][1] += f3[1];
+ f[atom3][2] += f3[2];
+ f[atom4][0] += f4[0]; f[atom4][1] += f4[1];
+ f[atom4][2] += f4[2];
+
+ if (vflag_atom) {
+ r13[0] = -rjk[0]; r13[1] = -rjk[1]; r13[2] = -rjk[2];
+ r43[0] = -r34[0]; r43[1] = -r34[1]; r43[2] = -r34[2];
+ v_tally4(atom1,atom2,atom3,atom4,f1,f2,f4,r13,r23,r43);
+ }
+ }
+ }
+ }
+ }
}
}
-
+
// Tij forces now that we have Etmp
REBO_neighs = REBO_firstneigh[i];
for (k = 0; k < REBO_numneigh[i]; k++) {
atomk = REBO_neighs[k];
if (atomk != atomj) {
- ktype = map[type[atomk]];
- rik[0] = x[atomi][0]-x[atomk][0];
- rik[1] = x[atomi][1]-x[atomk][1];
- rik[2] = x[atomi][2]-x[atomk][2];
- rikmag = sqrt((rik[0]*rik[0])+(rik[1]*rik[1])+(rik[2]*rik[2]));
- wik = Sp(rikmag,rcmin[itype][ktype],rcmax[itype][ktype],dwik);
- Nki = nC[atomk]-(wik*kronecker(itype,0))+nH[atomk] -
- (wik*kronecker(itype,1));
- SpN = Sp(Nki,Nmin,Nmax,dNki);
-
- tmp2 = VA*dN3[0]*dwik*Etmp/rikmag;
- f[atomi][0] -= tmp2*rik[0];
- f[atomi][1] -= tmp2*rik[1];
- f[atomi][2] -= tmp2*rik[2];
- f[atomk][0] += tmp2*rik[0];
- f[atomk][1] += tmp2*rik[1];
- f[atomk][2] += tmp2*rik[2];
-
- if (vflag_atom) v_tally2(atomi,atomk,-tmp2,rik);
-
- tmp2 = VA*dN3[2]*(2.0*NconjtmpI*dwik*SpN)*Etmp/rikmag;
- f[atomi][0] -= tmp2*rik[0];
- f[atomi][1] -= tmp2*rik[1];
- f[atomi][2] -= tmp2*rik[2];
- f[atomk][0] += tmp2*rik[0];
- f[atomk][1] += tmp2*rik[1];
- f[atomk][2] += tmp2*rik[2];
-
- if (vflag_atom) v_tally2(atomi,atomk,-tmp2,rik);
-
- if (fabs(dNki) > TOL) {
- REBO_neighs_k = REBO_firstneigh[atomk];
- for (n = 0; n < REBO_numneigh[atomk]; n++) {
- atomn = REBO_neighs_k[n];
- ntype = map[type[atomn]];
- if (atomn != atomi) {
- rkn[0] = x[atomk][0]-x[atomn][0];
- rkn[1] = x[atomk][1]-x[atomn][1];
- rkn[2] = x[atomk][2]-x[atomn][2];
- rknmag = sqrt((rkn[0]*rkn[0])+(rkn[1]*rkn[1])+(rkn[2]*rkn[2]));
- Sp(rknmag,rcmin[ktype][ntype],rcmax[ktype][ntype],dwkn);
-
- tmp2 = VA*dN3[2]*(2.0*NconjtmpI*wik*dNki*dwkn)*Etmp/rknmag;
- f[atomk][0] -= tmp2*rkn[0];
- f[atomk][1] -= tmp2*rkn[1];
- f[atomk][2] -= tmp2*rkn[2];
- f[atomn][0] += tmp2*rkn[0];
- f[atomn][1] += tmp2*rkn[1];
- f[atomn][2] += tmp2*rkn[2];
-
- if (vflag_atom) v_tally2(atomk,atomn,-tmp2,rkn);
- }
- }
- }
+ ktype = map[type[atomk]];
+ rik[0] = x[atomi][0]-x[atomk][0];
+ rik[1] = x[atomi][1]-x[atomk][1];
+ rik[2] = x[atomi][2]-x[atomk][2];
+ rikmag = sqrt((rik[0]*rik[0])+(rik[1]*rik[1])+(rik[2]*rik[2]));
+ wik = Sp(rikmag,rcmin[itype][ktype],rcmax[itype][ktype],dwik);
+ Nki = nC[atomk]-(wik*kronecker(itype,0))+nH[atomk] -
+ (wik*kronecker(itype,1));
+ SpN = Sp(Nki,Nmin,Nmax,dNki);
+
+ tmp2 = VA*dN3[0]*dwik*Etmp/rikmag;
+ f[atomi][0] -= tmp2*rik[0];
+ f[atomi][1] -= tmp2*rik[1];
+ f[atomi][2] -= tmp2*rik[2];
+ f[atomk][0] += tmp2*rik[0];
+ f[atomk][1] += tmp2*rik[1];
+ f[atomk][2] += tmp2*rik[2];
+
+ if (vflag_atom) v_tally2(atomi,atomk,-tmp2,rik);
+
+ tmp2 = VA*dN3[2]*(2.0*NconjtmpI*dwik*SpN)*Etmp/rikmag;
+ f[atomi][0] -= tmp2*rik[0];
+ f[atomi][1] -= tmp2*rik[1];
+ f[atomi][2] -= tmp2*rik[2];
+ f[atomk][0] += tmp2*rik[0];
+ f[atomk][1] += tmp2*rik[1];
+ f[atomk][2] += tmp2*rik[2];
+
+ if (vflag_atom) v_tally2(atomi,atomk,-tmp2,rik);
+
+ if (fabs(dNki) > TOL) {
+ REBO_neighs_k = REBO_firstneigh[atomk];
+ for (n = 0; n < REBO_numneigh[atomk]; n++) {
+ atomn = REBO_neighs_k[n];
+ ntype = map[type[atomn]];
+ if (atomn != atomi) {
+ rkn[0] = x[atomk][0]-x[atomn][0];
+ rkn[1] = x[atomk][1]-x[atomn][1];
+ rkn[2] = x[atomk][2]-x[atomn][2];
+ rknmag = sqrt((rkn[0]*rkn[0])+(rkn[1]*rkn[1])+(rkn[2]*rkn[2]));
+ Sp(rknmag,rcmin[ktype][ntype],rcmax[ktype][ntype],dwkn);
+
+ tmp2 = VA*dN3[2]*(2.0*NconjtmpI*wik*dNki*dwkn)*Etmp/rknmag;
+ f[atomk][0] -= tmp2*rkn[0];
+ f[atomk][1] -= tmp2*rkn[1];
+ f[atomk][2] -= tmp2*rkn[2];
+ f[atomn][0] += tmp2*rkn[0];
+ f[atomn][1] += tmp2*rkn[1];
+ f[atomn][2] += tmp2*rkn[2];
+
+ if (vflag_atom) v_tally2(atomk,atomn,-tmp2,rkn);
+ }
+ }
+ }
}
}
@@ -1956,60 +1956,60 @@ double PairAIREBO::bondorder(int i, int j, double rij[3],
for (l = 0; l < REBO_numneigh[j]; l++) {
atoml = REBO_neighs[l];
if (atoml != atomi) {
- ltype = map[type[atoml]];
- rjl[0] = x[atomj][0]-x[atoml][0];
- rjl[1] = x[atomj][1]-x[atoml][1];
- rjl[2] = x[atomj][2]-x[atoml][2];
- rjlmag = sqrt((rjl[0]*rjl[0])+(rjl[1]*rjl[1])+(rjl[2]*rjl[2]));
- wjl = Sp(rjlmag,rcmin[jtype][ltype],rcmax[jtype][ltype],dwjl);
- Nlj = nC[atoml]-(wjl*kronecker(jtype,0))+nH[atoml] -
- (wjl*kronecker(jtype,1));
- SpN = Sp(Nlj,Nmin,Nmax,dNlj);
-
- tmp2 = VA*dN3[1]*dwjl*Etmp/rjlmag;
- f[atomj][0] -= tmp2*rjl[0];
- f[atomj][1] -= tmp2*rjl[1];
- f[atomj][2] -= tmp2*rjl[2];
- f[atoml][0] += tmp2*rjl[0];
- f[atoml][1] += tmp2*rjl[1];
- f[atoml][2] += tmp2*rjl[2];
-
- if (vflag_atom) v_tally2(atomj,atoml,-tmp2,rjl);
-
- tmp2 = VA*dN3[2]*(2.0*NconjtmpJ*dwjl*SpN)*Etmp/rjlmag;
- f[atomj][0] -= tmp2*rjl[0];
- f[atomj][1] -= tmp2*rjl[1];
- f[atomj][2] -= tmp2*rjl[2];
- f[atoml][0] += tmp2*rjl[0];
- f[atoml][1] += tmp2*rjl[1];
- f[atoml][2] += tmp2*rjl[2];
-
- if (vflag_atom) v_tally2(atomj,atoml,-tmp2,rjl);
-
- if (fabs(dNlj) > TOL) {
- REBO_neighs_l = REBO_firstneigh[atoml];
- for (n = 0; n < REBO_numneigh[atoml]; n++) {
- atomn = REBO_neighs_l[n];
- ntype = map[type[atomn]];
- if (atomn !=atomj) {
- rln[0] = x[atoml][0]-x[atomn][0];
- rln[1] = x[atoml][1]-x[atomn][1];
- rln[2] = x[atoml][2]-x[atomn][2];
- rlnmag = sqrt((rln[0]*rln[0])+(rln[1]*rln[1])+(rln[2]*rln[2]));
- Sp(rlnmag,rcmin[ltype][ntype],rcmax[ltype][ntype],dwln);
-
- tmp2 = VA*dN3[2]*(2.0*NconjtmpJ*wjl*dNlj*dwln)*Etmp/rlnmag;
- f[atoml][0] -= tmp2*rln[0];
- f[atoml][1] -= tmp2*rln[1];
- f[atoml][2] -= tmp2*rln[2];
- f[atomn][0] += tmp2*rln[0];
- f[atomn][1] += tmp2*rln[1];
- f[atomn][2] += tmp2*rln[2];
-
- if (vflag_atom) v_tally2(atoml,atomn,-tmp2,rln);
- }
- }
- }
+ ltype = map[type[atoml]];
+ rjl[0] = x[atomj][0]-x[atoml][0];
+ rjl[1] = x[atomj][1]-x[atoml][1];
+ rjl[2] = x[atomj][2]-x[atoml][2];
+ rjlmag = sqrt((rjl[0]*rjl[0])+(rjl[1]*rjl[1])+(rjl[2]*rjl[2]));
+ wjl = Sp(rjlmag,rcmin[jtype][ltype],rcmax[jtype][ltype],dwjl);
+ Nlj = nC[atoml]-(wjl*kronecker(jtype,0))+nH[atoml] -
+ (wjl*kronecker(jtype,1));
+ SpN = Sp(Nlj,Nmin,Nmax,dNlj);
+
+ tmp2 = VA*dN3[1]*dwjl*Etmp/rjlmag;
+ f[atomj][0] -= tmp2*rjl[0];
+ f[atomj][1] -= tmp2*rjl[1];
+ f[atomj][2] -= tmp2*rjl[2];
+ f[atoml][0] += tmp2*rjl[0];
+ f[atoml][1] += tmp2*rjl[1];
+ f[atoml][2] += tmp2*rjl[2];
+
+ if (vflag_atom) v_tally2(atomj,atoml,-tmp2,rjl);
+
+ tmp2 = VA*dN3[2]*(2.0*NconjtmpJ*dwjl*SpN)*Etmp/rjlmag;
+ f[atomj][0] -= tmp2*rjl[0];
+ f[atomj][1] -= tmp2*rjl[1];
+ f[atomj][2] -= tmp2*rjl[2];
+ f[atoml][0] += tmp2*rjl[0];
+ f[atoml][1] += tmp2*rjl[1];
+ f[atoml][2] += tmp2*rjl[2];
+
+ if (vflag_atom) v_tally2(atomj,atoml,-tmp2,rjl);
+
+ if (fabs(dNlj) > TOL) {
+ REBO_neighs_l = REBO_firstneigh[atoml];
+ for (n = 0; n < REBO_numneigh[atoml]; n++) {
+ atomn = REBO_neighs_l[n];
+ ntype = map[type[atomn]];
+ if (atomn !=atomj) {
+ rln[0] = x[atoml][0]-x[atomn][0];
+ rln[1] = x[atoml][1]-x[atomn][1];
+ rln[2] = x[atoml][2]-x[atomn][2];
+ rlnmag = sqrt((rln[0]*rln[0])+(rln[1]*rln[1])+(rln[2]*rln[2]));
+ Sp(rlnmag,rcmin[ltype][ntype],rcmax[ltype][ntype],dwln);
+
+ tmp2 = VA*dN3[2]*(2.0*NconjtmpJ*wjl*dNlj*dwln)*Etmp/rlnmag;
+ f[atoml][0] -= tmp2*rln[0];
+ f[atoml][1] -= tmp2*rln[1];
+ f[atoml][2] -= tmp2*rln[2];
+ f[atomn][0] += tmp2*rln[0];
+ f[atomn][1] += tmp2*rln[1];
+ f[atomn][2] += tmp2*rln[2];
+
+ if (vflag_atom) v_tally2(atoml,atomn,-tmp2,rln);
+ }
+ }
+ }
}
}
}
@@ -2023,8 +2023,8 @@ double PairAIREBO::bondorder(int i, int j, double rij[3],
------------------------------------------------------------------------- */
double PairAIREBO::bondorderLJ(int i, int j, double rij[3], double rijmag,
- double VA, double rij0[3], double rij0mag,
- double **f, int vflag_atom)
+ double VA, double rij0[3], double rij0mag,
+ double **f, int vflag_atom)
{
int k,n,l,atomk,atoml,atomn,atom1,atom2,atom3,atom4;
int atomi,atomj,itype,jtype,ktype,ltype,ntype;
@@ -2052,7 +2052,7 @@ double PairAIREBO::bondorderLJ(int i, int j, double rij[3], double rijmag,
double rjk[3],ril[3],dt1dik,dt1djk,dt1djl,dt1dil,dt1dij;
double dNlj;
double PijS,PjiS;
- double rij2,tspjik,dtsjik,tspijl,dtsijl,costmp;
+ double rij2,tspjik,dtsjik,tspijl,dtsijl,costmp;
int *REBO_neighs,*REBO_neighs_i,*REBO_neighs_j,*REBO_neighs_k,*REBO_neighs_l;
double F12[3],F23[3],F34[3],F31[3],F24[3];
double fi[3],fj[3],fk[3],fl[3],f1[3],f2[3],f3[3],f4[4];
@@ -2060,7 +2060,7 @@ double PairAIREBO::bondorderLJ(int i, int j, double rij[3], double rijmag,
double **x = atom->x;
int *type = atom->type;
-
+
atomi = i;
atomj = j;
itype = map[type[atomi]];
@@ -2070,7 +2070,7 @@ double PairAIREBO::bondorderLJ(int i, int j, double rij[3], double rijmag,
NijH = nH[atomi]-(wij*kronecker(jtype,1));
NjiC = nC[atomj]-(wij*kronecker(itype,0));
NjiH = nH[atomj]-(wij*kronecker(itype,1));
-
+
bij = 0.0;
tmp = 0.0;
tmp2 = 0.0;
@@ -2092,13 +2092,13 @@ double PairAIREBO::bondorderLJ(int i, int j, double rij[3], double rijmag,
rik[1] = x[atomi][1]-x[atomk][1];
rik[2] = x[atomi][2]-x[atomk][2];
rikmag = sqrt((rik[0]*rik[0])+(rik[1]*rik[1])+(rik[2]*rik[2]));
- lamdajik = 4.0*kronecker(itype,1) *
- ((rho[ktype][1]-rikmag)-(rho[jtype][1]-rijmag));
+ lamdajik = 4.0*kronecker(itype,1) *
+ ((rho[ktype][1]-rikmag)-(rho[jtype][1]-rijmag));
wik = Sp(rikmag,rcmin[itype][ktype],rcmax[itype][ktype],dS);
- Nki = nC[atomk]-(wik*kronecker(itype,0)) +
- nH[atomk]-(wik*kronecker(itype,1));
- cosjik = ((rij[0]*rik[0])+(rij[1]*rik[1])+(rij[2]*rik[2])) /
- (rijmag*rikmag);
+ Nki = nC[atomk]-(wik*kronecker(itype,0)) +
+ nH[atomk]-(wik*kronecker(itype,1));
+ cosjik = ((rij[0]*rik[0])+(rij[1]*rik[1])+(rij[2]*rik[2])) /
+ (rijmag*rikmag);
cosjik = MIN(cosjik,1.0);
cosjik = MAX(cosjik,-1.0);
@@ -2115,7 +2115,7 @@ double PairAIREBO::bondorderLJ(int i, int j, double rij[3], double rijmag,
dN2PIJ[0] = 0.0;
dN2PIJ[1] = 0.0;
PijS = PijSpline(NijC,NijH,itype,jtype,dN2PIJ);
- pij = pow(1.0+Etmp+PijS,-0.5);
+ pij = pow(1.0+Etmp+PijS,-0.5);
tmppij = -.5*pow(pij,3.0);
tmp3pij = tmp3;
tmp = 0.0;
@@ -2132,13 +2132,13 @@ double PairAIREBO::bondorderLJ(int i, int j, double rij[3], double rijmag,
rjl[1] = x[atomj][1]-x[atoml][1];
rjl[2] = x[atomj][2]-x[atoml][2];
rjlmag = sqrt((rjl[0]*rjl[0])+(rjl[1]*rjl[1])+(rjl[2]*rjl[2]));
- lamdaijl = 4.0*kronecker(jtype,1) *
- ((rho[ltype][1]-rjlmag)-(rho[itype][1]-rijmag));
+ lamdaijl = 4.0*kronecker(jtype,1) *
+ ((rho[ltype][1]-rjlmag)-(rho[itype][1]-rijmag));
wjl = Sp(rjlmag,rcmin[jtype][ltype],rcmax[jtype][ltype],dS);
- Nlj = nC[atoml]-(wjl*kronecker(jtype,0))+nH[atoml] -
- (wjl*kronecker(jtype,1));
- cosijl = -1.0*((rij[0]*rjl[0])+(rij[1]*rjl[1])+(rij[2]*rjl[2])) /
- (rijmag*rjlmag);
+ Nlj = nC[atoml]-(wjl*kronecker(jtype,0))+nH[atoml] -
+ (wjl*kronecker(jtype,1));
+ cosijl = -1.0*((rij[0]*rjl[0])+(rij[1]*rjl[1])+(rij[2]*rjl[2])) /
+ (rijmag*rjlmag);
cosijl = MIN(cosijl,1.0);
cosijl = MAX(cosijl,-1.0);
@@ -2177,77 +2177,77 @@ double PairAIREBO::bondorderLJ(int i, int j, double rij[3], double rijmag,
atomk = REBO_neighs_i[k];
ktype = map[type[atomk]];
if (atomk != atomj) {
- rik[0] = x[atomi][0]-x[atomk][0];
- rik[1] = x[atomi][1]-x[atomk][1];
- rik[2] = x[atomi][2]-x[atomk][2];
- rikmag = sqrt((rik[0]*rik[0])+(rik[1]*rik[1])+(rik[2]*rik[2]));
- cos321 = ((rij[0]*rik[0])+(rij[1]*rik[1])+(rij[2]*rik[2])) /
- (rijmag*rikmag);
- cos321 = MIN(cos321,1.0);
- cos321 = MAX(cos321,-1.0);
-
- rjk[0] = rik[0]-rij[0];
- rjk[1] = rik[1]-rij[1];
- rjk[2] = rik[2]-rij[2];
- rjk2 = (rjk[0]*rjk[0])+(rjk[1]*rjk[1])+(rjk[2]*rjk[2]);
- rij2 = rijmag*rijmag;
- rik2 = rikmag*rikmag;
- costmp = 0.5*(rij2+rik2-rjk2)/rijmag/rikmag;
- tspjik = Sp2(costmp,thmin,thmax,dtsjik);
-
- if (sqrt(1.0 - cos321*cos321) > sqrt(TOL)) {
- wik = Sp(rikmag,rcmin[itype][ktype],rcmaxp[itype][ktype],dwik);
- REBO_neighs_j = REBO_firstneigh[j];
- for (l = 0; l < REBO_numneigh[j]; l++) {
- atoml = REBO_neighs_j[l];
- ltype = map[type[atoml]];
- if (!(atoml == atomi || atoml == atomk)) {
- rjl[0] = x[atomj][0]-x[atoml][0];
- rjl[1] = x[atomj][1]-x[atoml][1];
- rjl[2] = x[atomj][2]-x[atoml][2];
- rjlmag = sqrt(rjl[0]*rjl[0] + rjl[1]*rjl[1] + rjl[2]*rjl[2]);
- cos234 = -((rij[0]*rjl[0])+(rij[1]*rjl[1])+(rij[2]*rjl[2])) /
- (rijmag*rjlmag);
- cos234 = MIN(cos234,1.0);
- cos234 = MAX(cos234,-1.0);
-
- ril[0] = rij[0]+rjl[0];
- ril[1] = rij[1]+rjl[1];
- ril[2] = rij[2]+rjl[2];
- ril2 = (ril[0]*ril[0])+(ril[1]*ril[1])+(ril[2]*ril[2]);
- rijrjl = 2.0*rijmag*rjlmag;
- rjl2 = rjlmag*rjlmag;
- costmp = 0.5*(rij2+rjl2-ril2)/rijmag/rjlmag;
- tspijl = Sp2(costmp,thmin,thmax,dtsijl);
-
- if (sqrt(1.0 - cos234*cos234) > sqrt(TOL)) {
- wjl = Sp(rjlmag,rcmin[jtype][ltype],rcmaxp[jtype][ltype],dS);
- crosskij[0] = (rij[1]*rik[2]-rij[2]*rik[1]);
- crosskij[1] = (rij[2]*rik[0]-rij[0]*rik[2]);
- crosskij[2] = (rij[0]*rik[1]-rij[1]*rik[0]);
- crosskijmag = sqrt(crosskij[0]*crosskij[0] +
- crosskij[1]*crosskij[1] +
- crosskij[2]*crosskij[2]);
- crossijl[0] = (rij[1]*rjl[2]-rij[2]*rjl[1]);
- crossijl[1] = (rij[2]*rjl[0]-rij[0]*rjl[2]);
- crossijl[2] = (rij[0]*rjl[1]-rij[1]*rjl[0]);
- crossijlmag = sqrt(crossijl[0]*crossijl[0] +
- crossijl[1]*crossijl[1] +
- crossijl[2]*crossijl[2]);
- omkijl = -1.0*(((crosskij[0]*crossijl[0]) +
- (crosskij[1]*crossijl[1]) +
- (crosskij[2]*crossijl[2])) /
- (crosskijmag*crossijlmag));
- Etmp += ((1.0-pow(omkijl,2.0))*wik*wjl) *
- (1.0-tspjik)*(1.0-tspijl);
- }
- }
- }
- }
+ rik[0] = x[atomi][0]-x[atomk][0];
+ rik[1] = x[atomi][1]-x[atomk][1];
+ rik[2] = x[atomi][2]-x[atomk][2];
+ rikmag = sqrt((rik[0]*rik[0])+(rik[1]*rik[1])+(rik[2]*rik[2]));
+ cos321 = ((rij[0]*rik[0])+(rij[1]*rik[1])+(rij[2]*rik[2])) /
+ (rijmag*rikmag);
+ cos321 = MIN(cos321,1.0);
+ cos321 = MAX(cos321,-1.0);
+
+ rjk[0] = rik[0]-rij[0];
+ rjk[1] = rik[1]-rij[1];
+ rjk[2] = rik[2]-rij[2];
+ rjk2 = (rjk[0]*rjk[0])+(rjk[1]*rjk[1])+(rjk[2]*rjk[2]);
+ rij2 = rijmag*rijmag;
+ rik2 = rikmag*rikmag;
+ costmp = 0.5*(rij2+rik2-rjk2)/rijmag/rikmag;
+ tspjik = Sp2(costmp,thmin,thmax,dtsjik);
+
+ if (sqrt(1.0 - cos321*cos321) > sqrt(TOL)) {
+ wik = Sp(rikmag,rcmin[itype][ktype],rcmaxp[itype][ktype],dwik);
+ REBO_neighs_j = REBO_firstneigh[j];
+ for (l = 0; l < REBO_numneigh[j]; l++) {
+ atoml = REBO_neighs_j[l];
+ ltype = map[type[atoml]];
+ if (!(atoml == atomi || atoml == atomk)) {
+ rjl[0] = x[atomj][0]-x[atoml][0];
+ rjl[1] = x[atomj][1]-x[atoml][1];
+ rjl[2] = x[atomj][2]-x[atoml][2];
+ rjlmag = sqrt(rjl[0]*rjl[0] + rjl[1]*rjl[1] + rjl[2]*rjl[2]);
+ cos234 = -((rij[0]*rjl[0])+(rij[1]*rjl[1])+(rij[2]*rjl[2])) /
+ (rijmag*rjlmag);
+ cos234 = MIN(cos234,1.0);
+ cos234 = MAX(cos234,-1.0);
+
+ ril[0] = rij[0]+rjl[0];
+ ril[1] = rij[1]+rjl[1];
+ ril[2] = rij[2]+rjl[2];
+ ril2 = (ril[0]*ril[0])+(ril[1]*ril[1])+(ril[2]*ril[2]);
+ rijrjl = 2.0*rijmag*rjlmag;
+ rjl2 = rjlmag*rjlmag;
+ costmp = 0.5*(rij2+rjl2-ril2)/rijmag/rjlmag;
+ tspijl = Sp2(costmp,thmin,thmax,dtsijl);
+
+ if (sqrt(1.0 - cos234*cos234) > sqrt(TOL)) {
+ wjl = Sp(rjlmag,rcmin[jtype][ltype],rcmaxp[jtype][ltype],dS);
+ crosskij[0] = (rij[1]*rik[2]-rij[2]*rik[1]);
+ crosskij[1] = (rij[2]*rik[0]-rij[0]*rik[2]);
+ crosskij[2] = (rij[0]*rik[1]-rij[1]*rik[0]);
+ crosskijmag = sqrt(crosskij[0]*crosskij[0] +
+ crosskij[1]*crosskij[1] +
+ crosskij[2]*crosskij[2]);
+ crossijl[0] = (rij[1]*rjl[2]-rij[2]*rjl[1]);
+ crossijl[1] = (rij[2]*rjl[0]-rij[0]*rjl[2]);
+ crossijl[2] = (rij[0]*rjl[1]-rij[1]*rjl[0]);
+ crossijlmag = sqrt(crossijl[0]*crossijl[0] +
+ crossijl[1]*crossijl[1] +
+ crossijl[2]*crossijl[2]);
+ omkijl = -1.0*(((crosskij[0]*crossijl[0]) +
+ (crosskij[1]*crossijl[1]) +
+ (crosskij[2]*crossijl[2])) /
+ (crosskijmag*crossijlmag));
+ Etmp += ((1.0-pow(omkijl,2.0))*wik*wjl) *
+ (1.0-tspjik)*(1.0-tspijl);
+ }
+ }
+ }
+ }
}
}
}
-
+
bij = (.5*(pij+pji))+piRC+(Tij*Etmp);
Stb = Sp2(bij,bLJmin[itype][jtype],bLJmax[itype][jtype],dStb);
VA = VA*dStb;
@@ -2264,103 +2264,103 @@ double PairAIREBO::bondorderLJ(int i, int j, double rij[3], double rijmag,
for (k = 0; k < REBO_numneigh[i]; k++) {
atomk = REBO_neighs_i[k];
if (atomk != atomj) {
- lamdajik = 0.0;
- rik[0] = x[atomi][0]-x[atomk][0];
- rik[1] = x[atomi][1]-x[atomk][1];
- rik[2] = x[atomi][2]-x[atomk][2];
- rikmag = sqrt(rik[0]*rik[0] + rik[1]*rik[1] + rik[2]*rik[2]);
- lamdajik = 4.0*kronecker(itype,1) *
- ((rho[ktype][1]-rikmag)-(rho[jtype][1]-rijmag));
- wik = Sp(rikmag,rcmin[itype][ktype],rcmax[itype][ktype],dwik);
- cosjik = ((rij[0]*rik[0])+(rij[1]*rik[1])+(rij[2]*rik[2])) /
- (rijmag*rikmag);
- cosjik = MIN(cosjik,1.0);
- cosjik = MAX(cosjik,-1.0);
-
- dcosjikdri[0] = ((rij[0]+rik[0])/(rijmag*rikmag)) -
- (cosjik*((rij[0]/(rijmag*rijmag))+(rik[0]/(rikmag*rikmag))));
- dcosjikdri[1] = ((rij[1]+rik[1])/(rijmag*rikmag)) -
- (cosjik*((rij[1]/(rijmag*rijmag))+(rik[1]/(rikmag*rikmag))));
- dcosjikdri[2] = ((rij[2]+rik[2])/(rijmag*rikmag)) -
- (cosjik*((rij[2]/(rijmag*rijmag))+(rik[2]/(rikmag*rikmag))));
- dcosjikdrk[0] = (-rij[0]/(rijmag*rikmag)) +
- (cosjik*(rik[0]/(rikmag*rikmag)));
- dcosjikdrk[1] = (-rij[1]/(rijmag*rikmag)) +
- (cosjik*(rik[1]/(rikmag*rikmag)));
- dcosjikdrk[2] = (-rij[2]/(rijmag*rikmag)) +
- (cosjik*(rik[2]/(rikmag*rikmag)));
- dcosjikdrj[0] = (-rik[0]/(rijmag*rikmag)) +
- (cosjik*(rij[0]/(rijmag*rijmag)));
- dcosjikdrj[1] = (-rik[1]/(rijmag*rikmag)) +
- (cosjik*(rij[1]/(rijmag*rijmag)));
- dcosjikdrj[2] = (-rik[2]/(rijmag*rikmag)) +
- (cosjik*(rij[2]/(rijmag*rijmag)));
-
- g = gSpline(cosjik,(NijC+NijH),itype,&dgdc,&dgdN);
-
- tmp2 = VA*.5*(tmp*wik*dgdc*exp(lamdajik));
- fj[0] = -tmp2*dcosjikdrj[0];
- fj[1] = -tmp2*dcosjikdrj[1];
- fj[2] = -tmp2*dcosjikdrj[2];
- fi[0] = -tmp2*dcosjikdri[0];
- fi[1] = -tmp2*dcosjikdri[1];
- fi[2] = -tmp2*dcosjikdri[2];
- fk[0] = -tmp2*dcosjikdrk[0];
- fk[1] = -tmp2*dcosjikdrk[1];
- fk[2] = -tmp2*dcosjikdrk[2];
-
- tmp2 = VA*.5*(tmp*wik*g*exp(lamdajik)*4.0*kronecker(itype,1));
- fj[0] -= tmp2*(-rij[0]/rijmag);
- fj[1] -= tmp2*(-rij[1]/rijmag);
- fj[2] -= tmp2*(-rij[2]/rijmag);
- fi[0] -= tmp2*((-rik[0]/rikmag)+(rij[0]/rijmag));
- fi[1] -= tmp2*((-rik[1]/rikmag)+(rij[1]/rijmag));
- fi[2] -= tmp2*((-rik[2]/rikmag)+(rij[2]/rijmag));
- fk[0] -= tmp2*(rik[0]/rikmag);
- fk[1] -= tmp2*(rik[1]/rikmag);
- fk[2] -= tmp2*(rik[2]/rikmag);
-
- // coordination forces
-
- // dwik forces
-
- tmp2 = VA*.5*(tmp*dwik*g*exp(lamdajik))/rikmag;
- fi[0] -= tmp2*rik[0];
- fi[1] -= tmp2*rik[1];
- fi[2] -= tmp2*rik[2];
- fk[0] += tmp2*rik[0];
- fk[1] += tmp2*rik[1];
- fk[2] += tmp2*rik[2];
-
- // PIJ forces
-
- tmp2 = VA*.5*(tmp*dN2[ktype]*dwik)/rikmag;
- fi[0] -= tmp2*rik[0];
- fi[1] -= tmp2*rik[1];
- fi[2] -= tmp2*rik[2];
- fk[0] += tmp2*rik[0];
- fk[1] += tmp2*rik[1];
- fk[2] += tmp2*rik[2];
-
- // dgdN forces
-
- tmp2 = VA*.5*(tmp*tmp3*dwik)/rikmag;
- fi[0] -= tmp2*rik[0];
- fi[1] -= tmp2*rik[1];
- fi[2] -= tmp2*rik[2];
- fk[0] += tmp2*rik[0];
- fk[1] += tmp2*rik[1];
- fk[2] += tmp2*rik[2];
-
- f[atomi][0] += fi[0]; f[atomi][1] += fi[1]; f[atomi][2] += fi[2];
- f[atomj][0] += fj[0]; f[atomj][1] += fj[1]; f[atomj][2] += fj[2];
- f[atomk][0] += fk[0]; f[atomk][1] += fk[1]; f[atomk][2] += fk[2];
-
- if (vflag_atom) {
- rji[0] = -rij[0]; rji[1] = -rij[1]; rji[2] = -rij[2];
- rki[0] = -rik[0]; rki[1] = -rik[1]; rki[2] = -rik[2];
- v_tally3(atomi,atomj,atomk,fj,fk,rji,rki);
- }
+ lamdajik = 0.0;
+ rik[0] = x[atomi][0]-x[atomk][0];
+ rik[1] = x[atomi][1]-x[atomk][1];
+ rik[2] = x[atomi][2]-x[atomk][2];
+ rikmag = sqrt(rik[0]*rik[0] + rik[1]*rik[1] + rik[2]*rik[2]);
+ lamdajik = 4.0*kronecker(itype,1) *
+ ((rho[ktype][1]-rikmag)-(rho[jtype][1]-rijmag));
+ wik = Sp(rikmag,rcmin[itype][ktype],rcmax[itype][ktype],dwik);
+ cosjik = ((rij[0]*rik[0])+(rij[1]*rik[1])+(rij[2]*rik[2])) /
+ (rijmag*rikmag);
+ cosjik = MIN(cosjik,1.0);
+ cosjik = MAX(cosjik,-1.0);
+
+ dcosjikdri[0] = ((rij[0]+rik[0])/(rijmag*rikmag)) -
+ (cosjik*((rij[0]/(rijmag*rijmag))+(rik[0]/(rikmag*rikmag))));
+ dcosjikdri[1] = ((rij[1]+rik[1])/(rijmag*rikmag)) -
+ (cosjik*((rij[1]/(rijmag*rijmag))+(rik[1]/(rikmag*rikmag))));
+ dcosjikdri[2] = ((rij[2]+rik[2])/(rijmag*rikmag)) -
+ (cosjik*((rij[2]/(rijmag*rijmag))+(rik[2]/(rikmag*rikmag))));
+ dcosjikdrk[0] = (-rij[0]/(rijmag*rikmag)) +
+ (cosjik*(rik[0]/(rikmag*rikmag)));
+ dcosjikdrk[1] = (-rij[1]/(rijmag*rikmag)) +
+ (cosjik*(rik[1]/(rikmag*rikmag)));
+ dcosjikdrk[2] = (-rij[2]/(rijmag*rikmag)) +
+ (cosjik*(rik[2]/(rikmag*rikmag)));
+ dcosjikdrj[0] = (-rik[0]/(rijmag*rikmag)) +
+ (cosjik*(rij[0]/(rijmag*rijmag)));
+ dcosjikdrj[1] = (-rik[1]/(rijmag*rikmag)) +
+ (cosjik*(rij[1]/(rijmag*rijmag)));
+ dcosjikdrj[2] = (-rik[2]/(rijmag*rikmag)) +
+ (cosjik*(rij[2]/(rijmag*rijmag)));
+
+ g = gSpline(cosjik,(NijC+NijH),itype,&dgdc,&dgdN);
+
+ tmp2 = VA*.5*(tmp*wik*dgdc*exp(lamdajik));
+ fj[0] = -tmp2*dcosjikdrj[0];
+ fj[1] = -tmp2*dcosjikdrj[1];
+ fj[2] = -tmp2*dcosjikdrj[2];
+ fi[0] = -tmp2*dcosjikdri[0];
+ fi[1] = -tmp2*dcosjikdri[1];
+ fi[2] = -tmp2*dcosjikdri[2];
+ fk[0] = -tmp2*dcosjikdrk[0];
+ fk[1] = -tmp2*dcosjikdrk[1];
+ fk[2] = -tmp2*dcosjikdrk[2];
+
+ tmp2 = VA*.5*(tmp*wik*g*exp(lamdajik)*4.0*kronecker(itype,1));
+ fj[0] -= tmp2*(-rij[0]/rijmag);
+ fj[1] -= tmp2*(-rij[1]/rijmag);
+ fj[2] -= tmp2*(-rij[2]/rijmag);
+ fi[0] -= tmp2*((-rik[0]/rikmag)+(rij[0]/rijmag));
+ fi[1] -= tmp2*((-rik[1]/rikmag)+(rij[1]/rijmag));
+ fi[2] -= tmp2*((-rik[2]/rikmag)+(rij[2]/rijmag));
+ fk[0] -= tmp2*(rik[0]/rikmag);
+ fk[1] -= tmp2*(rik[1]/rikmag);
+ fk[2] -= tmp2*(rik[2]/rikmag);
+
+ // coordination forces
+
+ // dwik forces
+
+ tmp2 = VA*.5*(tmp*dwik*g*exp(lamdajik))/rikmag;
+ fi[0] -= tmp2*rik[0];
+ fi[1] -= tmp2*rik[1];
+ fi[2] -= tmp2*rik[2];
+ fk[0] += tmp2*rik[0];
+ fk[1] += tmp2*rik[1];
+ fk[2] += tmp2*rik[2];
+
+ // PIJ forces
+
+ tmp2 = VA*.5*(tmp*dN2[ktype]*dwik)/rikmag;
+ fi[0] -= tmp2*rik[0];
+ fi[1] -= tmp2*rik[1];
+ fi[2] -= tmp2*rik[2];
+ fk[0] += tmp2*rik[0];
+ fk[1] += tmp2*rik[1];
+ fk[2] += tmp2*rik[2];
+
+ // dgdN forces
+
+ tmp2 = VA*.5*(tmp*tmp3*dwik)/rikmag;
+ fi[0] -= tmp2*rik[0];
+ fi[1] -= tmp2*rik[1];
+ fi[2] -= tmp2*rik[2];
+ fk[0] += tmp2*rik[0];
+ fk[1] += tmp2*rik[1];
+ fk[2] += tmp2*rik[2];
+
+ f[atomi][0] += fi[0]; f[atomi][1] += fi[1]; f[atomi][2] += fi[2];
+ f[atomj][0] += fj[0]; f[atomj][1] += fj[1]; f[atomj][2] += fj[2];
+ f[atomk][0] += fk[0]; f[atomk][1] += fk[1]; f[atomk][2] += fk[2];
+
+ if (vflag_atom) {
+ rji[0] = -rij[0]; rji[1] = -rij[1]; rji[2] = -rij[2];
+ rki[0] = -rik[0]; rki[1] = -rik[1]; rki[2] = -rik[2];
+ v_tally3(atomi,atomj,atomk,fj,fk,rji,rki);
+ }
}
}
@@ -2372,105 +2372,105 @@ double PairAIREBO::bondorderLJ(int i, int j, double rij[3], double rijmag,
for (l = 0; l < REBO_numneigh[j]; l++) {
atoml = REBO_neighs[l];
if (atoml !=atomi) {
- ltype = map[type[atoml]];
- rjl[0] = x[atomj][0]-x[atoml][0];
- rjl[1] = x[atomj][1]-x[atoml][1];
- rjl[2] = x[atomj][2]-x[atoml][2];
- rjlmag = sqrt((rjl[0]*rjl[0])+(rjl[1]*rjl[1])+(rjl[2]*rjl[2]));
- lamdaijl = 4.0*kronecker(jtype,1) *
- ((rho[ltype][1]-rjlmag)-(rho[itype][1]-rijmag));
- wjl = Sp(rjlmag,rcmin[jtype][ltype],rcmax[jtype][ltype],dwjl);
- cosijl = (-1.0*((rij[0]*rjl[0])+(rij[1]*rjl[1])+(rij[2]*rjl[2]))) /
- (rijmag*rjlmag);
- cosijl = MIN(cosijl,1.0);
- cosijl = MAX(cosijl,-1.0);
-
- dcosijldri[0] = (-rjl[0]/(rijmag*rjlmag)) -
- (cosijl*rij[0]/(rijmag*rijmag));
- dcosijldri[1] = (-rjl[1]/(rijmag*rjlmag)) -
- (cosijl*rij[1]/(rijmag*rijmag));
- dcosijldri[2] = (-rjl[2]/(rijmag*rjlmag)) -
- (cosijl*rij[2]/(rijmag*rijmag));
- dcosijldrj[0] = ((-rij[0]+rjl[0])/(rijmag*rjlmag)) +
- (cosijl*((rij[0]/pow(rijmag,2.0))-(rjl[0]/(rjlmag*rjlmag))));
- dcosijldrj[1] = ((-rij[1]+rjl[1])/(rijmag*rjlmag)) +
- (cosijl*((rij[1]/pow(rijmag,2.0))-(rjl[1]/(rjlmag*rjlmag))));
- dcosijldrj[2] = ((-rij[2]+rjl[2])/(rijmag*rjlmag)) +
- (cosijl*((rij[2]/pow(rijmag,2.0))-(rjl[2]/(rjlmag*rjlmag))));
- dcosijldrl[0] = (rij[0]/(rijmag*rjlmag)) +
- (cosijl*rjl[0]/(rjlmag*rjlmag));
- dcosijldrl[1] = (rij[1]/(rijmag*rjlmag)) +
- (cosijl*rjl[1]/(rjlmag*rjlmag));
- dcosijldrl[2] = (rij[2]/(rijmag*rjlmag)) +
- (cosijl*rjl[2]/(rjlmag*rjlmag));
-
- // evaluate splines g and derivatives dg
-
- g = gSpline(cosijl,NjiC+NjiH,jtype,&dgdc,&dgdN);
- tmp2 = VA*.5*(tmp*wjl*dgdc*exp(lamdaijl));
- fi[0] = -tmp2*dcosijldri[0];
- fi[1] = -tmp2*dcosijldri[1];
- fi[2] = -tmp2*dcosijldri[2];
- fj[0] = -tmp2*dcosijldrj[0];
- fj[1] = -tmp2*dcosijldrj[1];
- fj[2] = -tmp2*dcosijldrj[2];
- fl[0] = -tmp2*dcosijldrl[0];
- fl[1] = -tmp2*dcosijldrl[1];
- fl[2] = -tmp2*dcosijldrl[2];
-
- tmp2 = VA*.5*(tmp*wjl*g*exp(lamdaijl)*4.0*kronecker(jtype,1));
- fi[0] -= tmp2*(rij[0]/rijmag);
- fi[1] -= tmp2*(rij[1]/rijmag);
- fi[2] -= tmp2*(rij[2]/rijmag);
- fj[0] -= tmp2*((-rjl[0]/rjlmag)-(rij[0]/rijmag));
- fj[1] -= tmp2*((-rjl[1]/rjlmag)-(rij[1]/rijmag));
- fj[2] -= tmp2*((-rjl[2]/rjlmag)-(rij[2]/rijmag));
- fl[0] -= tmp2*(rjl[0]/rjlmag);
- fl[1] -= tmp2*(rjl[1]/rjlmag);
- fl[2] -= tmp2*(rjl[2]/rjlmag);
-
- // coordination forces
- // dwik forces
-
- tmp2 = VA*.5*(tmp*dwjl*g*exp(lamdaijl))/rjlmag;
- fj[0] -= tmp2*rjl[0];
- fj[1] -= tmp2*rjl[1];
- fj[2] -= tmp2*rjl[2];
- fl[0] += tmp2*rjl[0];
- fl[1] += tmp2*rjl[1];
- fl[2] += tmp2*rjl[2];
-
- // PIJ forces
-
- tmp2 = VA*.5*(tmp*dN2[ltype]*dwjl)/rjlmag;
- fj[0] -= tmp2*rjl[0];
- fj[1] -= tmp2*rjl[1];
- fj[2] -= tmp2*rjl[2];
- fl[0] += tmp2*rjl[0];
- fl[1] += tmp2*rjl[1];
- fl[2] += tmp2*rjl[2];
-
- // dgdN forces
-
- tmp2=VA*.5*(tmp*tmp3*dwjl)/rjlmag;
- fj[0] -= tmp2*rjl[0];
- fj[1] -= tmp2*rjl[1];
- fj[2] -= tmp2*rjl[2];
- fl[0] += tmp2*rjl[0];
- fl[1] += tmp2*rjl[1];
- fl[2] += tmp2*rjl[2];
-
- f[atomi][0] += fi[0]; f[atomi][1] += fi[1]; f[atomi][2] += fi[2];
- f[atomj][0] += fj[0]; f[atomj][1] += fj[1]; f[atomj][2] += fj[2];
- f[atoml][0] += fl[0]; f[atoml][1] += fl[1]; f[atoml][2] += fl[2];
-
- if (vflag_atom) {
- rlj[0] = -rjl[0]; rlj[1] = -rjl[1]; rlj[2] = -rjl[2];
- v_tally3(atomi,atomj,atoml,fi,fl,rij,rlj);
- }
+ ltype = map[type[atoml]];
+ rjl[0] = x[atomj][0]-x[atoml][0];
+ rjl[1] = x[atomj][1]-x[atoml][1];
+ rjl[2] = x[atomj][2]-x[atoml][2];
+ rjlmag = sqrt((rjl[0]*rjl[0])+(rjl[1]*rjl[1])+(rjl[2]*rjl[2]));
+ lamdaijl = 4.0*kronecker(jtype,1) *
+ ((rho[ltype][1]-rjlmag)-(rho[itype][1]-rijmag));
+ wjl = Sp(rjlmag,rcmin[jtype][ltype],rcmax[jtype][ltype],dwjl);
+ cosijl = (-1.0*((rij[0]*rjl[0])+(rij[1]*rjl[1])+(rij[2]*rjl[2]))) /
+ (rijmag*rjlmag);
+ cosijl = MIN(cosijl,1.0);
+ cosijl = MAX(cosijl,-1.0);
+
+ dcosijldri[0] = (-rjl[0]/(rijmag*rjlmag)) -
+ (cosijl*rij[0]/(rijmag*rijmag));
+ dcosijldri[1] = (-rjl[1]/(rijmag*rjlmag)) -
+ (cosijl*rij[1]/(rijmag*rijmag));
+ dcosijldri[2] = (-rjl[2]/(rijmag*rjlmag)) -
+ (cosijl*rij[2]/(rijmag*rijmag));
+ dcosijldrj[0] = ((-rij[0]+rjl[0])/(rijmag*rjlmag)) +
+ (cosijl*((rij[0]/pow(rijmag,2.0))-(rjl[0]/(rjlmag*rjlmag))));
+ dcosijldrj[1] = ((-rij[1]+rjl[1])/(rijmag*rjlmag)) +
+ (cosijl*((rij[1]/pow(rijmag,2.0))-(rjl[1]/(rjlmag*rjlmag))));
+ dcosijldrj[2] = ((-rij[2]+rjl[2])/(rijmag*rjlmag)) +
+ (cosijl*((rij[2]/pow(rijmag,2.0))-(rjl[2]/(rjlmag*rjlmag))));
+ dcosijldrl[0] = (rij[0]/(rijmag*rjlmag)) +
+ (cosijl*rjl[0]/(rjlmag*rjlmag));
+ dcosijldrl[1] = (rij[1]/(rijmag*rjlmag)) +
+ (cosijl*rjl[1]/(rjlmag*rjlmag));
+ dcosijldrl[2] = (rij[2]/(rijmag*rjlmag)) +
+ (cosijl*rjl[2]/(rjlmag*rjlmag));
+
+ // evaluate splines g and derivatives dg
+
+ g = gSpline(cosijl,NjiC+NjiH,jtype,&dgdc,&dgdN);
+ tmp2 = VA*.5*(tmp*wjl*dgdc*exp(lamdaijl));
+ fi[0] = -tmp2*dcosijldri[0];
+ fi[1] = -tmp2*dcosijldri[1];
+ fi[2] = -tmp2*dcosijldri[2];
+ fj[0] = -tmp2*dcosijldrj[0];
+ fj[1] = -tmp2*dcosijldrj[1];
+ fj[2] = -tmp2*dcosijldrj[2];
+ fl[0] = -tmp2*dcosijldrl[0];
+ fl[1] = -tmp2*dcosijldrl[1];
+ fl[2] = -tmp2*dcosijldrl[2];
+
+ tmp2 = VA*.5*(tmp*wjl*g*exp(lamdaijl)*4.0*kronecker(jtype,1));
+ fi[0] -= tmp2*(rij[0]/rijmag);
+ fi[1] -= tmp2*(rij[1]/rijmag);
+ fi[2] -= tmp2*(rij[2]/rijmag);
+ fj[0] -= tmp2*((-rjl[0]/rjlmag)-(rij[0]/rijmag));
+ fj[1] -= tmp2*((-rjl[1]/rjlmag)-(rij[1]/rijmag));
+ fj[2] -= tmp2*((-rjl[2]/rjlmag)-(rij[2]/rijmag));
+ fl[0] -= tmp2*(rjl[0]/rjlmag);
+ fl[1] -= tmp2*(rjl[1]/rjlmag);
+ fl[2] -= tmp2*(rjl[2]/rjlmag);
+
+ // coordination forces
+ // dwik forces
+
+ tmp2 = VA*.5*(tmp*dwjl*g*exp(lamdaijl))/rjlmag;
+ fj[0] -= tmp2*rjl[0];
+ fj[1] -= tmp2*rjl[1];
+ fj[2] -= tmp2*rjl[2];
+ fl[0] += tmp2*rjl[0];
+ fl[1] += tmp2*rjl[1];
+ fl[2] += tmp2*rjl[2];
+
+ // PIJ forces
+
+ tmp2 = VA*.5*(tmp*dN2[ltype]*dwjl)/rjlmag;
+ fj[0] -= tmp2*rjl[0];
+ fj[1] -= tmp2*rjl[1];
+ fj[2] -= tmp2*rjl[2];
+ fl[0] += tmp2*rjl[0];
+ fl[1] += tmp2*rjl[1];
+ fl[2] += tmp2*rjl[2];
+
+ // dgdN forces
+
+ tmp2=VA*.5*(tmp*tmp3*dwjl)/rjlmag;
+ fj[0] -= tmp2*rjl[0];
+ fj[1] -= tmp2*rjl[1];
+ fj[2] -= tmp2*rjl[2];
+ fl[0] += tmp2*rjl[0];
+ fl[1] += tmp2*rjl[1];
+ fl[2] += tmp2*rjl[2];
+
+ f[atomi][0] += fi[0]; f[atomi][1] += fi[1]; f[atomi][2] += fi[2];
+ f[atomj][0] += fj[0]; f[atomj][1] += fj[1]; f[atomj][2] += fj[2];
+ f[atoml][0] += fl[0]; f[atoml][1] += fl[1]; f[atoml][2] += fl[2];
+
+ if (vflag_atom) {
+ rlj[0] = -rjl[0]; rlj[1] = -rjl[1]; rlj[2] = -rjl[2];
+ v_tally3(atomi,atomj,atoml,fi,fl,rij,rlj);
+ }
}
- }
-
+ }
+
// piRC forces
dN3[0] = dN3piRC[0];
@@ -2481,60 +2481,60 @@ double PairAIREBO::bondorderLJ(int i, int j, double rij[3], double rijmag,
for (k = 0; k < REBO_numneigh[i]; k++) {
atomk = REBO_neighs_i[k];
if (atomk != atomj) {
- ktype = map[type[atomk]];
- rik[0] = x[atomi][0]-x[atomk][0];
- rik[1] = x[atomi][1]-x[atomk][1];
- rik[2] = x[atomi][2]-x[atomk][2];
- rikmag = sqrt((rik[0]*rik[0])+(rik[1]*rik[1])+(rik[2]*rik[2]));
- wik = Sp(rikmag,rcmin[itype][ktype],rcmax[itype][ktype],dwik);
- Nki = nC[atomk]-(wik*kronecker(itype,0))+nH[atomk] -
- (wik*kronecker(itype,1));
- SpN = Sp(Nki,Nmin,Nmax,dNki);
-
- tmp2 = VA*dN3[0]*dwik/rikmag;
- f[atomi][0] -= tmp2*rik[0];
- f[atomi][1] -= tmp2*rik[1];
- f[atomi][2] -= tmp2*rik[2];
- f[atomk][0] += tmp2*rik[0];
- f[atomk][1] += tmp2*rik[1];
- f[atomk][2] += tmp2*rik[2];
-
- if (vflag_atom) v_tally2(atomi,atomk,-tmp2,rik);
-
- tmp2 = VA*dN3[2]*(2.0*NconjtmpI*dwik*SpN)/rikmag;
- f[atomi][0] -= tmp2*rik[0];
- f[atomi][1] -= tmp2*rik[1];
- f[atomi][2] -= tmp2*rik[2];
- f[atomk][0] += tmp2*rik[0];
- f[atomk][1] += tmp2*rik[1];
- f[atomk][2] += tmp2*rik[2];
-
- if (vflag_atom) v_tally2(atomi,atomk,-tmp2,rik);
-
- if (fabs(dNki) > TOL) {
- REBO_neighs_k = REBO_firstneigh[atomk];
- for (n = 0; n < REBO_numneigh[atomk]; n++) {
- atomn = REBO_neighs_k[n];
- if (atomn != atomi) {
- ntype = map[type[atomn]];
- rkn[0] = x[atomk][0]-x[atomn][0];
- rkn[1] = x[atomk][1]-x[atomn][1];
- rkn[2] = x[atomk][2]-x[atomn][2];
- rknmag = sqrt((rkn[0]*rkn[0])+(rkn[1]*rkn[1])+(rkn[2]*rkn[2]));
- Sp(rknmag,rcmin[ktype][ntype],rcmax[ktype][ntype],dwkn);
-
- tmp2 = VA*dN3[2]*(2.0*NconjtmpI*wik*dNki*dwkn)/rknmag;
- f[atomk][0] -= tmp2*rkn[0];
- f[atomk][1] -= tmp2*rkn[1];
- f[atomk][2] -= tmp2*rkn[2];
- f[atomn][0] += tmp2*rkn[0];
- f[atomn][1] += tmp2*rkn[1];
- f[atomn][2] += tmp2*rkn[2];
-
- if (vflag_atom) v_tally2(atomk,atomn,-tmp2,rkn);
- }
- }
- }
+ ktype = map[type[atomk]];
+ rik[0] = x[atomi][0]-x[atomk][0];
+ rik[1] = x[atomi][1]-x[atomk][1];
+ rik[2] = x[atomi][2]-x[atomk][2];
+ rikmag = sqrt((rik[0]*rik[0])+(rik[1]*rik[1])+(rik[2]*rik[2]));
+ wik = Sp(rikmag,rcmin[itype][ktype],rcmax[itype][ktype],dwik);
+ Nki = nC[atomk]-(wik*kronecker(itype,0))+nH[atomk] -
+ (wik*kronecker(itype,1));
+ SpN = Sp(Nki,Nmin,Nmax,dNki);
+
+ tmp2 = VA*dN3[0]*dwik/rikmag;
+ f[atomi][0] -= tmp2*rik[0];
+ f[atomi][1] -= tmp2*rik[1];
+ f[atomi][2] -= tmp2*rik[2];
+ f[atomk][0] += tmp2*rik[0];
+ f[atomk][1] += tmp2*rik[1];
+ f[atomk][2] += tmp2*rik[2];
+
+ if (vflag_atom) v_tally2(atomi,atomk,-tmp2,rik);
+
+ tmp2 = VA*dN3[2]*(2.0*NconjtmpI*dwik*SpN)/rikmag;
+ f[atomi][0] -= tmp2*rik[0];
+ f[atomi][1] -= tmp2*rik[1];
+ f[atomi][2] -= tmp2*rik[2];
+ f[atomk][0] += tmp2*rik[0];
+ f[atomk][1] += tmp2*rik[1];
+ f[atomk][2] += tmp2*rik[2];
+
+ if (vflag_atom) v_tally2(atomi,atomk,-tmp2,rik);
+
+ if (fabs(dNki) > TOL) {
+ REBO_neighs_k = REBO_firstneigh[atomk];
+ for (n = 0; n < REBO_numneigh[atomk]; n++) {
+ atomn = REBO_neighs_k[n];
+ if (atomn != atomi) {
+ ntype = map[type[atomn]];
+ rkn[0] = x[atomk][0]-x[atomn][0];
+ rkn[1] = x[atomk][1]-x[atomn][1];
+ rkn[2] = x[atomk][2]-x[atomn][2];
+ rknmag = sqrt((rkn[0]*rkn[0])+(rkn[1]*rkn[1])+(rkn[2]*rkn[2]));
+ Sp(rknmag,rcmin[ktype][ntype],rcmax[ktype][ntype],dwkn);
+
+ tmp2 = VA*dN3[2]*(2.0*NconjtmpI*wik*dNki*dwkn)/rknmag;
+ f[atomk][0] -= tmp2*rkn[0];
+ f[atomk][1] -= tmp2*rkn[1];
+ f[atomk][2] -= tmp2*rkn[2];
+ f[atomn][0] += tmp2*rkn[0];
+ f[atomn][1] += tmp2*rkn[1];
+ f[atomn][2] += tmp2*rkn[2];
+
+ if (vflag_atom) v_tally2(atomk,atomn,-tmp2,rkn);
+ }
+ }
+ }
}
}
@@ -2544,60 +2544,60 @@ double PairAIREBO::bondorderLJ(int i, int j, double rij[3], double rijmag,
for (l = 0; l < REBO_numneigh[j]; l++) {
atoml = REBO_neighs[l];
if (atoml != atomi) {
- ltype = map[type[atoml]];
- rjl[0] = x[atomj][0]-x[atoml][0];
- rjl[1] = x[atomj][1]-x[atoml][1];
- rjl[2] = x[atomj][2]-x[atoml][2];
- rjlmag = sqrt((rjl[0]*rjl[0])+(rjl[1]*rjl[1])+(rjl[2]*rjl[2]));
- wjl = Sp(rjlmag,rcmin[jtype][ltype],rcmax[jtype][ltype],dwjl);
- Nlj = nC[atoml]-(wjl*kronecker(jtype,0))+nH[atoml] -
- (wjl*kronecker(jtype,1));
- SpN = Sp(Nlj,Nmin,Nmax,dNlj);
-
- tmp2 = VA*dN3[1]*dwjl/rjlmag;
- f[atomj][0] -= tmp2*rjl[0];
- f[atomj][1] -= tmp2*rjl[1];
- f[atomj][2] -= tmp2*rjl[2];
- f[atoml][0] += tmp2*rjl[0];
- f[atoml][1] += tmp2*rjl[1];
- f[atoml][2] += tmp2*rjl[2];
-
- if (vflag_atom) v_tally2(atomj,atoml,-tmp2,rjl);
-
- tmp2 = VA*dN3[2]*(2.0*NconjtmpJ*dwjl*SpN)/rjlmag;
- f[atomj][0] -= tmp2*rjl[0];
- f[atomj][1] -= tmp2*rjl[1];
- f[atomj][2] -= tmp2*rjl[2];
- f[atoml][0] += tmp2*rjl[0];
- f[atoml][1] += tmp2*rjl[1];
- f[atoml][2] += tmp2*rjl[2];
-
- if (vflag_atom) v_tally2(atomj,atoml,-tmp2,rjl);
-
- if (fabs(dNlj) > TOL) {
- REBO_neighs_l = REBO_firstneigh[atoml];
- for (n = 0; n < REBO_numneigh[atoml]; n++) {
- atomn = REBO_neighs_l[n];
- if (atomn != atomj) {
- ntype = map[type[atomn]];
- rln[0] = x[atoml][0]-x[atomn][0];
- rln[1] = x[atoml][1]-x[atomn][1];
- rln[2] = x[atoml][2]-x[atomn][2];
- rlnmag = sqrt((rln[0]*rln[0])+(rln[1]*rln[1])+(rln[2]*rln[2]));
- Sp(rlnmag,rcmin[ltype][ntype],rcmax[ltype][ntype],dwln);
-
- tmp2 = VA*dN3[2]*(2.0*NconjtmpJ*wjl*dNlj*dwln)/rlnmag;
- f[atoml][0] -= tmp2*rln[0];
- f[atoml][1] -= tmp2*rln[1];
- f[atoml][2] -= tmp2*rln[2];
- f[atomn][0] += tmp2*rln[0];
- f[atomn][1] += tmp2*rln[1];
- f[atomn][2] += tmp2*rln[2];
-
- if (vflag_atom) v_tally2(atoml,atomn,-tmp2,rln);
- }
- }
- }
+ ltype = map[type[atoml]];
+ rjl[0] = x[atomj][0]-x[atoml][0];
+ rjl[1] = x[atomj][1]-x[atoml][1];
+ rjl[2] = x[atomj][2]-x[atoml][2];
+ rjlmag = sqrt((rjl[0]*rjl[0])+(rjl[1]*rjl[1])+(rjl[2]*rjl[2]));
+ wjl = Sp(rjlmag,rcmin[jtype][ltype],rcmax[jtype][ltype],dwjl);
+ Nlj = nC[atoml]-(wjl*kronecker(jtype,0))+nH[atoml] -
+ (wjl*kronecker(jtype,1));
+ SpN = Sp(Nlj,Nmin,Nmax,dNlj);
+
+ tmp2 = VA*dN3[1]*dwjl/rjlmag;
+ f[atomj][0] -= tmp2*rjl[0];
+ f[atomj][1] -= tmp2*rjl[1];
+ f[atomj][2] -= tmp2*rjl[2];
+ f[atoml][0] += tmp2*rjl[0];
+ f[atoml][1] += tmp2*rjl[1];
+ f[atoml][2] += tmp2*rjl[2];
+
+ if (vflag_atom) v_tally2(atomj,atoml,-tmp2,rjl);
+
+ tmp2 = VA*dN3[2]*(2.0*NconjtmpJ*dwjl*SpN)/rjlmag;
+ f[atomj][0] -= tmp2*rjl[0];
+ f[atomj][1] -= tmp2*rjl[1];
+ f[atomj][2] -= tmp2*rjl[2];
+ f[atoml][0] += tmp2*rjl[0];
+ f[atoml][1] += tmp2*rjl[1];
+ f[atoml][2] += tmp2*rjl[2];
+
+ if (vflag_atom) v_tally2(atomj,atoml,-tmp2,rjl);
+
+ if (fabs(dNlj) > TOL) {
+ REBO_neighs_l = REBO_firstneigh[atoml];
+ for (n = 0; n < REBO_numneigh[atoml]; n++) {
+ atomn = REBO_neighs_l[n];
+ if (atomn != atomj) {
+ ntype = map[type[atomn]];
+ rln[0] = x[atoml][0]-x[atomn][0];
+ rln[1] = x[atoml][1]-x[atomn][1];
+ rln[2] = x[atoml][2]-x[atomn][2];
+ rlnmag = sqrt((rln[0]*rln[0])+(rln[1]*rln[1])+(rln[2]*rln[2]));
+ Sp(rlnmag,rcmin[ltype][ntype],rcmax[ltype][ntype],dwln);
+
+ tmp2 = VA*dN3[2]*(2.0*NconjtmpJ*wjl*dNlj*dwln)/rlnmag;
+ f[atoml][0] -= tmp2*rln[0];
+ f[atoml][1] -= tmp2*rln[1];
+ f[atoml][2] -= tmp2*rln[2];
+ f[atomn][0] += tmp2*rln[0];
+ f[atomn][1] += tmp2*rln[1];
+ f[atomn][2] += tmp2*rln[2];
+
+ if (vflag_atom) v_tally2(atoml,atomn,-tmp2,rln);
+ }
+ }
+ }
}
}
@@ -2618,329 +2618,329 @@ double PairAIREBO::bondorderLJ(int i, int j, double rij[3], double rijmag,
REBO_neighs_i = REBO_firstneigh[i];
for (k = 0; k < REBO_numneigh[i]; k++) {
- atomk = REBO_neighs_i[k];
- atom1 = atomk;
- ktype = map[type[atomk]];
- if (atomk != atomj) {
- r21[0] = x[atom2][0]-x[atom1][0];
- r21[1] = x[atom2][1]-x[atom1][1];
- r21[2] = x[atom2][2]-x[atom1][2];
- r21mag = sqrt(r21[0]*r21[0] + r21[1]*r21[1] + r21[2]*r21[2]);
- cos321 = ((r21[0]*rij[0])+(r21[1]*rij[1])+(r21[2]*rij[2])) /
- (r21mag*rijmag);
- cos321 = MIN(cos321,1.0);
- cos321 = MAX(cos321,-1.0);
- sin321 = sqrt(1.0 - cos321*cos321);
- sink2i = 1.0/(sin321*sin321);
- rik2i = 1.0/(r21mag*r21mag);
-
- if (sin321 != 0.0) {
- rr = (rijmag*rijmag)-(r21mag*r21mag);
- rjk[0] = r21[0]-rij[0];
- rjk[1] = r21[1]-rij[1];
- rjk[2] = r21[2]-rij[2];
- rjk2 = (rjk[0]*rjk[0])+(rjk[1]*rjk[1])+(rjk[2]*rjk[2]);
- rijrik = 2.0*rijmag*r21mag;
- rik2 = r21mag*r21mag;
- dctik = (-rr+rjk2)/(rijrik*rik2);
- dctij = (rr+rjk2)/(rijrik*rijmag*rijmag);
- dctjk = -2.0/rijrik;
- w21 = Sp(r21mag,rcmin[itype][ktype],rcmaxp[itype][ktype],dw21);
- rikmag = r21mag;
- rij2 = r32mag*r32mag;
- rik2 = r21mag*r21mag;
- costmp = 0.5*(rij2+rik2-rjk2)/rijmag/rikmag;
- tspjik = Sp2(costmp,thmin,thmax,dtsjik);
- dtsjik = -dtsjik;
-
- REBO_neighs_j = REBO_firstneigh[j];
- for (l = 0; l < REBO_numneigh[j]; l++) {
- atoml = REBO_neighs_j[l];
- atom4 = atoml;
- ltype = map[type[atoml]];
- if (!(atoml == atomi || atoml == atomk)) {
- r34[0] = x[atom3][0]-x[atom4][0];
- r34[1] = x[atom3][1]-x[atom4][1];
- r34[2] = x[atom3][2]-x[atom4][2];
- r34mag = sqrt(r34[0]*r34[0] + r34[1]*r34[1] + r34[2]*r34[2]);
- cos234 = -1.0*((rij[0]*r34[0])+(rij[1]*r34[1]) +
- (rij[2]*r34[2]))/(rijmag*r34mag);
- cos234 = MIN(cos234,1.0);
- cos234 = MAX(cos234,-1.0);
- sin234 = sqrt(1.0 - cos234*cos234);
- sinl2i = 1.0/(sin234*sin234);
- rjl2i = 1.0/(r34mag*r34mag);
-
- if (sin234 != 0.0) {
- w34 = Sp(r34mag,rcmin[jtype][ltype],
- rcmaxp[jtype][ltype],dw34);
- rr = (r23mag*r23mag)-(r34mag*r34mag);
- ril[0] = r23[0]+r34[0];
- ril[1] = r23[1]+r34[1];
- ril[2] = r23[2]+r34[2];
- ril2 = (ril[0]*ril[0])+(ril[1]*ril[1])+(ril[2]*ril[2]);
- rijrjl = 2.0*r23mag*r34mag;
- rjl2 = r34mag*r34mag;
- dctjl = (-rr+ril2)/(rijrjl*rjl2);
- dctji = (rr+ril2)/(rijrjl*r23mag*r23mag);
- dctil = -2.0/rijrjl;
- rjlmag = r34mag;
- rjl2 = r34mag*r34mag;
- costmp = 0.5*(rij2+rjl2-ril2)/rijmag/rjlmag;
- tspijl = Sp2(costmp,thmin,thmax,dtsijl);
- dtsijl = -dtsijl; //need minus sign
- prefactor = VA*Tij;
-
- cross321[0] = (r32[1]*r21[2])-(r32[2]*r21[1]);
- cross321[1] = (r32[2]*r21[0])-(r32[0]*r21[2]);
- cross321[2] = (r32[0]*r21[1])-(r32[1]*r21[0]);
- cross234[0] = (r23[1]*r34[2])-(r23[2]*r34[1]);
- cross234[1] = (r23[2]*r34[0])-(r23[0]*r34[2]);
- cross234[2] = (r23[0]*r34[1])-(r23[1]*r34[0]);
-
- cwnum = (cross321[0]*cross234[0]) +
- (cross321[1]*cross234[1])+(cross321[2]*cross234[2]);
- cwnom = r21mag*r34mag*r23mag*r23mag*sin321*sin234;
- om1234 = cwnum/cwnom;
- cw = om1234;
- Etmp += ((1.0-pow(om1234,2.0))*w21*w34) *
- (1.0-tspjik)*(1.0-tspijl);
-
- dt1dik = (rik2i)-(dctik*sink2i*cos321);
- dt1djk = (-dctjk*sink2i*cos321);
- dt1djl = (rjl2i)-(dctjl*sinl2i*cos234);
- dt1dil = (-dctil*sinl2i*cos234);
- dt1dij = (2.0/(r23mag*r23mag)) -
- (dctij*sink2i*cos321)-(dctji*sinl2i*cos234);
-
- dt2dik[0] = (-r23[2]*cross234[1])+(r23[1]*cross234[2]);
- dt2dik[1] = (-r23[0]*cross234[2])+(r23[2]*cross234[0]);
- dt2dik[2] = (-r23[1]*cross234[0])+(r23[0]*cross234[1]);
-
- dt2djl[0] = (-r23[1]*cross321[2])+(r23[2]*cross321[1]);
- dt2djl[1] = (-r23[2]*cross321[0])+(r23[0]*cross321[2]);
- dt2djl[2] = (-r23[0]*cross321[1])+(r23[1]*cross321[0]);
-
- dt2dij[0] = (r21[2]*cross234[1]) -
- (r34[2]*cross321[1])-(r21[1]*cross234[2]) +
- (r34[1]*cross321[2]);
- dt2dij[1] = (r21[0]*cross234[2]) -
- (r34[0]*cross321[2])-(r21[2]*cross234[0]) +
- (r34[2]*cross321[0]);
- dt2dij[2] = (r21[1]*cross234[0]) -
- (r34[1]*cross321[0])-(r21[0]*cross234[1]) +
- (r34[0]*cross321[1]);
-
- aa = (prefactor*2.0*cw/cwnom)*w21*w34 *
- (1.0-tspjik)*(1.0-tspijl);
- aaa1 = -prefactor*(1.0-pow(om1234,2.0)) *
- (1.0-tspjik)*(1.0-tspijl);
- aaa2 = aaa1*w21*w34;
- at2 = aa*cwnum;
-
- fcijpc = (-dt1dij*at2)+(aaa2*dtsjik*dctij*(1.0-tspijl)) +
- (aaa2*dtsijl*dctji*(1.0-tspjik));
- fcikpc = (-dt1dik*at2)+(aaa2*dtsjik*dctik*(1.0-tspijl));
- fcjlpc = (-dt1djl*at2)+(aaa2*dtsijl*dctjl*(1.0-tspjik));
- fcjkpc = (-dt1djk*at2)+(aaa2*dtsjik*dctjk*(1.0-tspijl));
- fcilpc = (-dt1dil*at2)+(aaa2*dtsijl*dctil*(1.0-tspjik));
-
- F23[0] = (fcijpc*r23[0])+(aa*dt2dij[0]);
- F23[1] = (fcijpc*r23[1])+(aa*dt2dij[1]);
- F23[2] = (fcijpc*r23[2])+(aa*dt2dij[2]);
-
- F12[0] = (fcikpc*r21[0])+(aa*dt2dik[0]);
- F12[1] = (fcikpc*r21[1])+(aa*dt2dik[1]);
- F12[2] = (fcikpc*r21[2])+(aa*dt2dik[2]);
-
- F34[0] = (fcjlpc*r34[0])+(aa*dt2djl[0]);
- F34[1] = (fcjlpc*r34[1])+(aa*dt2djl[1]);
- F34[2] = (fcjlpc*r34[2])+(aa*dt2djl[2]);
-
- F31[0] = (fcjkpc*rjk[0]);
- F31[1] = (fcjkpc*rjk[1]);
- F31[2] = (fcjkpc*rjk[2]);
-
- F24[0] = (fcilpc*ril[0]);
- F24[1] = (fcilpc*ril[1]);
- F24[2] = (fcilpc*ril[2]);
-
- f1[0] = -F12[0]-F31[0];
- f1[1] = -F12[1]-F31[1];
- f1[2] = -F12[2]-F31[2];
- f2[0] = F23[0]+F12[0]+F24[0];
- f2[1] = F23[1]+F12[1]+F24[1];
- f2[2] = F23[2]+F12[2]+F24[2];
- f3[0] = -F23[0]+F34[0]+F31[0];
- f3[1] = -F23[1]+F34[1]+F31[1];
- f3[2] = -F23[2]+F34[2]+F31[2];
- f4[0] = -F34[0]-F24[0];
- f4[1] = -F34[1]-F24[1];
- f4[2] = -F34[2]-F24[2];
-
- // coordination forces
-
- tmp2 = VA*Tij*((1.0-(om1234*om1234))) *
- (1.0-tspjik)*(1.0-tspijl)*dw21*w34/r21mag;
- f2[0] -= tmp2*r21[0];
- f2[1] -= tmp2*r21[1];
- f2[2] -= tmp2*r21[2];
- f1[0] += tmp2*r21[0];
- f1[1] += tmp2*r21[1];
- f1[2] += tmp2*r21[2];
-
- tmp2 = VA*Tij*((1.0-(om1234*om1234))) *
- (1.0-tspjik)*(1.0-tspijl)*w21*dw34/r34mag;
- f3[0] -= tmp2*r34[0];
- f3[1] -= tmp2*r34[1];
- f3[2] -= tmp2*r34[2];
- f4[0] += tmp2*r34[0];
- f4[1] += tmp2*r34[1];
- f4[2] += tmp2*r34[2];
-
- f[atom1][0] += f1[0]; f[atom1][1] += f1[1];
- f[atom1][2] += f1[2];
- f[atom2][0] += f2[0]; f[atom2][1] += f2[1];
- f[atom2][2] += f2[2];
- f[atom3][0] += f3[0]; f[atom3][1] += f3[1];
- f[atom3][2] += f3[2];
- f[atom4][0] += f4[0]; f[atom4][1] += f4[1];
- f[atom4][2] += f4[2];
-
- if (vflag_atom) {
- r13[0] = -rjk[0]; r13[1] = -rjk[1]; r13[2] = -rjk[2];
- r43[0] = -r34[0]; r43[1] = -r34[1]; r43[2] = -r34[2];
- v_tally4(atom1,atom2,atom3,atom4,f1,f2,f4,r13,r23,r43);
- }
- }
- }
- }
- }
- }
+ atomk = REBO_neighs_i[k];
+ atom1 = atomk;
+ ktype = map[type[atomk]];
+ if (atomk != atomj) {
+ r21[0] = x[atom2][0]-x[atom1][0];
+ r21[1] = x[atom2][1]-x[atom1][1];
+ r21[2] = x[atom2][2]-x[atom1][2];
+ r21mag = sqrt(r21[0]*r21[0] + r21[1]*r21[1] + r21[2]*r21[2]);
+ cos321 = ((r21[0]*rij[0])+(r21[1]*rij[1])+(r21[2]*rij[2])) /
+ (r21mag*rijmag);
+ cos321 = MIN(cos321,1.0);
+ cos321 = MAX(cos321,-1.0);
+ sin321 = sqrt(1.0 - cos321*cos321);
+ sink2i = 1.0/(sin321*sin321);
+ rik2i = 1.0/(r21mag*r21mag);
+
+ if (sin321 != 0.0) {
+ rr = (rijmag*rijmag)-(r21mag*r21mag);
+ rjk[0] = r21[0]-rij[0];
+ rjk[1] = r21[1]-rij[1];
+ rjk[2] = r21[2]-rij[2];
+ rjk2 = (rjk[0]*rjk[0])+(rjk[1]*rjk[1])+(rjk[2]*rjk[2]);
+ rijrik = 2.0*rijmag*r21mag;
+ rik2 = r21mag*r21mag;
+ dctik = (-rr+rjk2)/(rijrik*rik2);
+ dctij = (rr+rjk2)/(rijrik*rijmag*rijmag);
+ dctjk = -2.0/rijrik;
+ w21 = Sp(r21mag,rcmin[itype][ktype],rcmaxp[itype][ktype],dw21);
+ rikmag = r21mag;
+ rij2 = r32mag*r32mag;
+ rik2 = r21mag*r21mag;
+ costmp = 0.5*(rij2+rik2-rjk2)/rijmag/rikmag;
+ tspjik = Sp2(costmp,thmin,thmax,dtsjik);
+ dtsjik = -dtsjik;
+
+ REBO_neighs_j = REBO_firstneigh[j];
+ for (l = 0; l < REBO_numneigh[j]; l++) {
+ atoml = REBO_neighs_j[l];
+ atom4 = atoml;
+ ltype = map[type[atoml]];
+ if (!(atoml == atomi || atoml == atomk)) {
+ r34[0] = x[atom3][0]-x[atom4][0];
+ r34[1] = x[atom3][1]-x[atom4][1];
+ r34[2] = x[atom3][2]-x[atom4][2];
+ r34mag = sqrt(r34[0]*r34[0] + r34[1]*r34[1] + r34[2]*r34[2]);
+ cos234 = -1.0*((rij[0]*r34[0])+(rij[1]*r34[1]) +
+ (rij[2]*r34[2]))/(rijmag*r34mag);
+ cos234 = MIN(cos234,1.0);
+ cos234 = MAX(cos234,-1.0);
+ sin234 = sqrt(1.0 - cos234*cos234);
+ sinl2i = 1.0/(sin234*sin234);
+ rjl2i = 1.0/(r34mag*r34mag);
+
+ if (sin234 != 0.0) {
+ w34 = Sp(r34mag,rcmin[jtype][ltype],
+ rcmaxp[jtype][ltype],dw34);
+ rr = (r23mag*r23mag)-(r34mag*r34mag);
+ ril[0] = r23[0]+r34[0];
+ ril[1] = r23[1]+r34[1];
+ ril[2] = r23[2]+r34[2];
+ ril2 = (ril[0]*ril[0])+(ril[1]*ril[1])+(ril[2]*ril[2]);
+ rijrjl = 2.0*r23mag*r34mag;
+ rjl2 = r34mag*r34mag;
+ dctjl = (-rr+ril2)/(rijrjl*rjl2);
+ dctji = (rr+ril2)/(rijrjl*r23mag*r23mag);
+ dctil = -2.0/rijrjl;
+ rjlmag = r34mag;
+ rjl2 = r34mag*r34mag;
+ costmp = 0.5*(rij2+rjl2-ril2)/rijmag/rjlmag;
+ tspijl = Sp2(costmp,thmin,thmax,dtsijl);
+ dtsijl = -dtsijl; //need minus sign
+ prefactor = VA*Tij;
+
+ cross321[0] = (r32[1]*r21[2])-(r32[2]*r21[1]);
+ cross321[1] = (r32[2]*r21[0])-(r32[0]*r21[2]);
+ cross321[2] = (r32[0]*r21[1])-(r32[1]*r21[0]);
+ cross234[0] = (r23[1]*r34[2])-(r23[2]*r34[1]);
+ cross234[1] = (r23[2]*r34[0])-(r23[0]*r34[2]);
+ cross234[2] = (r23[0]*r34[1])-(r23[1]*r34[0]);
+
+ cwnum = (cross321[0]*cross234[0]) +
+ (cross321[1]*cross234[1])+(cross321[2]*cross234[2]);
+ cwnom = r21mag*r34mag*r23mag*r23mag*sin321*sin234;
+ om1234 = cwnum/cwnom;
+ cw = om1234;
+ Etmp += ((1.0-pow(om1234,2.0))*w21*w34) *
+ (1.0-tspjik)*(1.0-tspijl);
+
+ dt1dik = (rik2i)-(dctik*sink2i*cos321);
+ dt1djk = (-dctjk*sink2i*cos321);
+ dt1djl = (rjl2i)-(dctjl*sinl2i*cos234);
+ dt1dil = (-dctil*sinl2i*cos234);
+ dt1dij = (2.0/(r23mag*r23mag)) -
+ (dctij*sink2i*cos321)-(dctji*sinl2i*cos234);
+
+ dt2dik[0] = (-r23[2]*cross234[1])+(r23[1]*cross234[2]);
+ dt2dik[1] = (-r23[0]*cross234[2])+(r23[2]*cross234[0]);
+ dt2dik[2] = (-r23[1]*cross234[0])+(r23[0]*cross234[1]);
+
+ dt2djl[0] = (-r23[1]*cross321[2])+(r23[2]*cross321[1]);
+ dt2djl[1] = (-r23[2]*cross321[0])+(r23[0]*cross321[2]);
+ dt2djl[2] = (-r23[0]*cross321[1])+(r23[1]*cross321[0]);
+
+ dt2dij[0] = (r21[2]*cross234[1]) -
+ (r34[2]*cross321[1])-(r21[1]*cross234[2]) +
+ (r34[1]*cross321[2]);
+ dt2dij[1] = (r21[0]*cross234[2]) -
+ (r34[0]*cross321[2])-(r21[2]*cross234[0]) +
+ (r34[2]*cross321[0]);
+ dt2dij[2] = (r21[1]*cross234[0]) -
+ (r34[1]*cross321[0])-(r21[0]*cross234[1]) +
+ (r34[0]*cross321[1]);
+
+ aa = (prefactor*2.0*cw/cwnom)*w21*w34 *
+ (1.0-tspjik)*(1.0-tspijl);
+ aaa1 = -prefactor*(1.0-pow(om1234,2.0)) *
+ (1.0-tspjik)*(1.0-tspijl);
+ aaa2 = aaa1*w21*w34;
+ at2 = aa*cwnum;
+
+ fcijpc = (-dt1dij*at2)+(aaa2*dtsjik*dctij*(1.0-tspijl)) +
+ (aaa2*dtsijl*dctji*(1.0-tspjik));
+ fcikpc = (-dt1dik*at2)+(aaa2*dtsjik*dctik*(1.0-tspijl));
+ fcjlpc = (-dt1djl*at2)+(aaa2*dtsijl*dctjl*(1.0-tspjik));
+ fcjkpc = (-dt1djk*at2)+(aaa2*dtsjik*dctjk*(1.0-tspijl));
+ fcilpc = (-dt1dil*at2)+(aaa2*dtsijl*dctil*(1.0-tspjik));
+
+ F23[0] = (fcijpc*r23[0])+(aa*dt2dij[0]);
+ F23[1] = (fcijpc*r23[1])+(aa*dt2dij[1]);
+ F23[2] = (fcijpc*r23[2])+(aa*dt2dij[2]);
+
+ F12[0] = (fcikpc*r21[0])+(aa*dt2dik[0]);
+ F12[1] = (fcikpc*r21[1])+(aa*dt2dik[1]);
+ F12[2] = (fcikpc*r21[2])+(aa*dt2dik[2]);
+
+ F34[0] = (fcjlpc*r34[0])+(aa*dt2djl[0]);
+ F34[1] = (fcjlpc*r34[1])+(aa*dt2djl[1]);
+ F34[2] = (fcjlpc*r34[2])+(aa*dt2djl[2]);
+
+ F31[0] = (fcjkpc*rjk[0]);
+ F31[1] = (fcjkpc*rjk[1]);
+ F31[2] = (fcjkpc*rjk[2]);
+
+ F24[0] = (fcilpc*ril[0]);
+ F24[1] = (fcilpc*ril[1]);
+ F24[2] = (fcilpc*ril[2]);
+
+ f1[0] = -F12[0]-F31[0];
+ f1[1] = -F12[1]-F31[1];
+ f1[2] = -F12[2]-F31[2];
+ f2[0] = F23[0]+F12[0]+F24[0];
+ f2[1] = F23[1]+F12[1]+F24[1];
+ f2[2] = F23[2]+F12[2]+F24[2];
+ f3[0] = -F23[0]+F34[0]+F31[0];
+ f3[1] = -F23[1]+F34[1]+F31[1];
+ f3[2] = -F23[2]+F34[2]+F31[2];
+ f4[0] = -F34[0]-F24[0];
+ f4[1] = -F34[1]-F24[1];
+ f4[2] = -F34[2]-F24[2];
+
+ // coordination forces
+
+ tmp2 = VA*Tij*((1.0-(om1234*om1234))) *
+ (1.0-tspjik)*(1.0-tspijl)*dw21*w34/r21mag;
+ f2[0] -= tmp2*r21[0];
+ f2[1] -= tmp2*r21[1];
+ f2[2] -= tmp2*r21[2];
+ f1[0] += tmp2*r21[0];
+ f1[1] += tmp2*r21[1];
+ f1[2] += tmp2*r21[2];
+
+ tmp2 = VA*Tij*((1.0-(om1234*om1234))) *
+ (1.0-tspjik)*(1.0-tspijl)*w21*dw34/r34mag;
+ f3[0] -= tmp2*r34[0];
+ f3[1] -= tmp2*r34[1];
+ f3[2] -= tmp2*r34[2];
+ f4[0] += tmp2*r34[0];
+ f4[1] += tmp2*r34[1];
+ f4[2] += tmp2*r34[2];
+
+ f[atom1][0] += f1[0]; f[atom1][1] += f1[1];
+ f[atom1][2] += f1[2];
+ f[atom2][0] += f2[0]; f[atom2][1] += f2[1];
+ f[atom2][2] += f2[2];
+ f[atom3][0] += f3[0]; f[atom3][1] += f3[1];
+ f[atom3][2] += f3[2];
+ f[atom4][0] += f4[0]; f[atom4][1] += f4[1];
+ f[atom4][2] += f4[2];
+
+ if (vflag_atom) {
+ r13[0] = -rjk[0]; r13[1] = -rjk[1]; r13[2] = -rjk[2];
+ r43[0] = -r34[0]; r43[1] = -r34[1]; r43[2] = -r34[2];
+ v_tally4(atom1,atom2,atom3,atom4,f1,f2,f4,r13,r23,r43);
+ }
+ }
+ }
+ }
+ }
+ }
}
-
+
REBO_neighs = REBO_firstneigh[i];
for (k = 0; k < REBO_numneigh[i]; k++) {
- atomk = REBO_neighs[k];
- if (atomk != atomj) {
- ktype = map[type[atomk]];
- rik[0] = x[atomi][0]-x[atomk][0];
- rik[1] = x[atomi][1]-x[atomk][1];
- rik[2] = x[atomi][2]-x[atomk][2];
- rikmag = sqrt((rik[0]*rik[0])+(rik[1]*rik[1])+(rik[2]*rik[2]));
- wik = Sp(rikmag,rcmin[itype][ktype],rcmax[itype][ktype],dwik);
- Nki = nC[atomk]-(wik*kronecker(itype,0))+nH[atomk] -
- (wik*kronecker(itype,1));
- SpN = Sp(Nki,Nmin,Nmax,dNki);
-
- tmp2 = VA*dN3[0]*dwik*Etmp/rikmag;
- f[atomi][0] -= tmp2*rik[0];
- f[atomi][1] -= tmp2*rik[1];
- f[atomi][2] -= tmp2*rik[2];
- f[atomk][0] += tmp2*rik[0];
- f[atomk][1] += tmp2*rik[1];
- f[atomk][2] += tmp2*rik[2];
-
- if (vflag_atom) v_tally2(atomi,atomk,-tmp2,rik);
-
- tmp2 = VA*dN3[2]*(2.0*NconjtmpI*dwik*SpN)*Etmp/rikmag;
- f[atomi][0] -= tmp2*rik[0];
- f[atomi][1] -= tmp2*rik[1];
- f[atomi][2] -= tmp2*rik[2];
- f[atomk][0] += tmp2*rik[0];
- f[atomk][1] += tmp2*rik[1];
- f[atomk][2] += tmp2*rik[2];
-
- if (vflag_atom) v_tally2(atomi,atomk,-tmp2,rik);
-
- if (fabs(dNki) > TOL) {
- REBO_neighs_k = REBO_firstneigh[atomk];
- for (n = 0; n < REBO_numneigh[atomk]; n++) {
- atomn = REBO_neighs_k[n];
- ntype = map[type[atomn]];
- if (atomn !=atomi) {
- rkn[0] = x[atomk][0]-x[atomn][0];
- rkn[1] = x[atomk][1]-x[atomn][1];
- rkn[2] = x[atomk][2]-x[atomn][2];
- rknmag = sqrt((rkn[0]*rkn[0])+(rkn[1]*rkn[1])+(rkn[2]*rkn[2]));
- Sp(rknmag,rcmin[ktype][ntype],rcmax[ktype][ntype],dwkn);
-
- tmp2 = VA*dN3[2]*(2.0*NconjtmpI*wik*dNki*dwkn)*Etmp/rknmag;
- f[atomk][0] -= tmp2*rkn[0];
- f[atomk][1] -= tmp2*rkn[1];
- f[atomk][2] -= tmp2*rkn[2];
- f[atomn][0] += tmp2*rkn[0];
- f[atomn][1] += tmp2*rkn[1];
- f[atomn][2] += tmp2*rkn[2];
-
- if (vflag_atom) v_tally2(atomk,atomn,-tmp2,rkn);
- }
- }
- }
- }
+ atomk = REBO_neighs[k];
+ if (atomk != atomj) {
+ ktype = map[type[atomk]];
+ rik[0] = x[atomi][0]-x[atomk][0];
+ rik[1] = x[atomi][1]-x[atomk][1];
+ rik[2] = x[atomi][2]-x[atomk][2];
+ rikmag = sqrt((rik[0]*rik[0])+(rik[1]*rik[1])+(rik[2]*rik[2]));
+ wik = Sp(rikmag,rcmin[itype][ktype],rcmax[itype][ktype],dwik);
+ Nki = nC[atomk]-(wik*kronecker(itype,0))+nH[atomk] -
+ (wik*kronecker(itype,1));
+ SpN = Sp(Nki,Nmin,Nmax,dNki);
+
+ tmp2 = VA*dN3[0]*dwik*Etmp/rikmag;
+ f[atomi][0] -= tmp2*rik[0];
+ f[atomi][1] -= tmp2*rik[1];
+ f[atomi][2] -= tmp2*rik[2];
+ f[atomk][0] += tmp2*rik[0];
+ f[atomk][1] += tmp2*rik[1];
+ f[atomk][2] += tmp2*rik[2];
+
+ if (vflag_atom) v_tally2(atomi,atomk,-tmp2,rik);
+
+ tmp2 = VA*dN3[2]*(2.0*NconjtmpI*dwik*SpN)*Etmp/rikmag;
+ f[atomi][0] -= tmp2*rik[0];
+ f[atomi][1] -= tmp2*rik[1];
+ f[atomi][2] -= tmp2*rik[2];
+ f[atomk][0] += tmp2*rik[0];
+ f[atomk][1] += tmp2*rik[1];
+ f[atomk][2] += tmp2*rik[2];
+
+ if (vflag_atom) v_tally2(atomi,atomk,-tmp2,rik);
+
+ if (fabs(dNki) > TOL) {
+ REBO_neighs_k = REBO_firstneigh[atomk];
+ for (n = 0; n < REBO_numneigh[atomk]; n++) {
+ atomn = REBO_neighs_k[n];
+ ntype = map[type[atomn]];
+ if (atomn !=atomi) {
+ rkn[0] = x[atomk][0]-x[atomn][0];
+ rkn[1] = x[atomk][1]-x[atomn][1];
+ rkn[2] = x[atomk][2]-x[atomn][2];
+ rknmag = sqrt((rkn[0]*rkn[0])+(rkn[1]*rkn[1])+(rkn[2]*rkn[2]));
+ Sp(rknmag,rcmin[ktype][ntype],rcmax[ktype][ntype],dwkn);
+
+ tmp2 = VA*dN3[2]*(2.0*NconjtmpI*wik*dNki*dwkn)*Etmp/rknmag;
+ f[atomk][0] -= tmp2*rkn[0];
+ f[atomk][1] -= tmp2*rkn[1];
+ f[atomk][2] -= tmp2*rkn[2];
+ f[atomn][0] += tmp2*rkn[0];
+ f[atomn][1] += tmp2*rkn[1];
+ f[atomn][2] += tmp2*rkn[2];
+
+ if (vflag_atom) v_tally2(atomk,atomn,-tmp2,rkn);
+ }
+ }
+ }
+ }
}
// Tij forces
REBO_neighs = REBO_firstneigh[j];
for (l = 0; l < REBO_numneigh[j]; l++) {
- atoml = REBO_neighs[l];
- if (atoml != atomi) {
- ltype = map[type[atoml]];
- rjl[0] = x[atomj][0]-x[atoml][0];
- rjl[1] = x[atomj][1]-x[atoml][1];
- rjl[2] = x[atomj][2]-x[atoml][2];
- rjlmag = sqrt((rjl[0]*rjl[0])+(rjl[1]*rjl[1])+(rjl[2]*rjl[2]));
- wjl = Sp(rjlmag,rcmin[jtype][ltype],rcmax[jtype][ltype],dwjl);
- Nlj = nC[atoml]-(wjl*kronecker(jtype,0))+nH[atoml] -
- (wjl*kronecker(jtype,1));
- SpN = Sp(Nlj,Nmin,Nmax,dNlj);
-
- tmp2 = VA*dN3[1]*dwjl*Etmp/rjlmag;
- f[atomj][0] -= tmp2*rjl[0];
- f[atomj][1] -= tmp2*rjl[1];
- f[atomj][2] -= tmp2*rjl[2];
- f[atoml][0] += tmp2*rjl[0];
- f[atoml][1] += tmp2*rjl[1];
- f[atoml][2] += tmp2*rjl[2];
-
- if (vflag_atom) v_tally2(atomj,atoml,-tmp2,rjl);
-
- tmp2 = VA*dN3[2]*(2.0*NconjtmpJ*dwjl*SpN)*Etmp/rjlmag;
- f[atomj][0] -= tmp2*rjl[0];
- f[atomj][1] -= tmp2*rjl[1];
- f[atomj][2] -= tmp2*rjl[2];
- f[atoml][0] += tmp2*rjl[0];
- f[atoml][1] += tmp2*rjl[1];
- f[atoml][2] += tmp2*rjl[2];
-
- if (vflag_atom) v_tally2(atomj,atoml,-tmp2,rjl);
-
- if (fabs(dNlj) > TOL) {
- REBO_neighs_l = REBO_firstneigh[atoml];
- for (n = 0; n < REBO_numneigh[atoml]; n++) {
- atomn = REBO_neighs_l[n];
- ntype = map[type[atomn]];
- if (atomn != atomj) {
- rln[0] = x[atoml][0]-x[atomn][0];
- rln[1] = x[atoml][1]-x[atomn][1];
- rln[2] = x[atoml][2]-x[atomn][2];
- rlnmag = sqrt((rln[0]*rln[0])+(rln[1]*rln[1])+(rln[2]*rln[2]));
- Sp(rlnmag,rcmin[ltype][ntype],rcmax[ltype][ntype],dwln);
-
- tmp2 = VA*dN3[2]*(2.0*NconjtmpJ*wjl*dNlj*dwln)*Etmp/rlnmag;
- f[atoml][0] -= tmp2*rln[0];
- f[atoml][1] -= tmp2*rln[1];
- f[atoml][2] -= tmp2*rln[2];
- f[atomn][0] += tmp2*rln[0];
- f[atomn][1] += tmp2*rln[1];
- f[atomn][2] += tmp2*rln[2];
-
- if (vflag_atom) v_tally2(atoml,atomn,-tmp2,rln);
- }
- }
- }
- }
+ atoml = REBO_neighs[l];
+ if (atoml != atomi) {
+ ltype = map[type[atoml]];
+ rjl[0] = x[atomj][0]-x[atoml][0];
+ rjl[1] = x[atomj][1]-x[atoml][1];
+ rjl[2] = x[atomj][2]-x[atoml][2];
+ rjlmag = sqrt((rjl[0]*rjl[0])+(rjl[1]*rjl[1])+(rjl[2]*rjl[2]));
+ wjl = Sp(rjlmag,rcmin[jtype][ltype],rcmax[jtype][ltype],dwjl);
+ Nlj = nC[atoml]-(wjl*kronecker(jtype,0))+nH[atoml] -
+ (wjl*kronecker(jtype,1));
+ SpN = Sp(Nlj,Nmin,Nmax,dNlj);
+
+ tmp2 = VA*dN3[1]*dwjl*Etmp/rjlmag;
+ f[atomj][0] -= tmp2*rjl[0];
+ f[atomj][1] -= tmp2*rjl[1];
+ f[atomj][2] -= tmp2*rjl[2];
+ f[atoml][0] += tmp2*rjl[0];
+ f[atoml][1] += tmp2*rjl[1];
+ f[atoml][2] += tmp2*rjl[2];
+
+ if (vflag_atom) v_tally2(atomj,atoml,-tmp2,rjl);
+
+ tmp2 = VA*dN3[2]*(2.0*NconjtmpJ*dwjl*SpN)*Etmp/rjlmag;
+ f[atomj][0] -= tmp2*rjl[0];
+ f[atomj][1] -= tmp2*rjl[1];
+ f[atomj][2] -= tmp2*rjl[2];
+ f[atoml][0] += tmp2*rjl[0];
+ f[atoml][1] += tmp2*rjl[1];
+ f[atoml][2] += tmp2*rjl[2];
+
+ if (vflag_atom) v_tally2(atomj,atoml,-tmp2,rjl);
+
+ if (fabs(dNlj) > TOL) {
+ REBO_neighs_l = REBO_firstneigh[atoml];
+ for (n = 0; n < REBO_numneigh[atoml]; n++) {
+ atomn = REBO_neighs_l[n];
+ ntype = map[type[atomn]];
+ if (atomn != atomj) {
+ rln[0] = x[atoml][0]-x[atomn][0];
+ rln[1] = x[atoml][1]-x[atomn][1];
+ rln[2] = x[atoml][2]-x[atomn][2];
+ rlnmag = sqrt((rln[0]*rln[0])+(rln[1]*rln[1])+(rln[2]*rln[2]));
+ Sp(rlnmag,rcmin[ltype][ntype],rcmax[ltype][ntype],dwln);
+
+ tmp2 = VA*dN3[2]*(2.0*NconjtmpJ*wjl*dNlj*dwln)*Etmp/rlnmag;
+ f[atoml][0] -= tmp2*rln[0];
+ f[atoml][1] -= tmp2*rln[1];
+ f[atoml][2] -= tmp2*rln[2];
+ f[atomn][0] += tmp2*rln[0];
+ f[atomn][1] += tmp2*rln[1];
+ f[atomn][2] += tmp2*rln[2];
+
+ if (vflag_atom) v_tally2(atoml,atomn,-tmp2,rln);
+ }
+ }
+ }
+ }
}
}
}
@@ -2953,7 +2953,7 @@ double PairAIREBO::bondorderLJ(int i, int j, double rij[3], double rijmag,
------------------------------------------------------------------------- */
double PairAIREBO::gSpline(double costh, double Nij, int typei,
- double *dgdc, double *dgdN)
+ double *dgdc, double *dgdN)
{
double coeffs[6],dS,g1,g2,dg1,dg2,cut,g;
int i,j;
@@ -2975,9 +2975,9 @@ double PairAIREBO::gSpline(double costh, double Nij, int typei,
if (costh > gCdom[4]) costh = gCdom[4];
if (Nij >= NCmax) {
for (i = 0; i < 4; i++) {
- if (costh >= gCdom[i] && costh <= gCdom[i+1]) {
- for (j = 0; j < 6; j++) coeffs[j] = gC2[i][j];
- }
+ if (costh >= gCdom[i] && costh <= gCdom[i+1]) {
+ for (j = 0; j < 6; j++) coeffs[j] = gC2[i][j];
+ }
}
g2 = Sp5th(costh,coeffs,&dg2);
g = g2;
@@ -2986,9 +2986,9 @@ double PairAIREBO::gSpline(double costh, double Nij, int typei,
}
if (Nij <= NCmin) {
for (i = 0; i < 4; i++) {
- if (costh >= gCdom[i] && costh <= gCdom[i+1]) {
- for (j = 0; j < 6; j++) coeffs[j] = gC1[i][j];
- }
+ if (costh >= gCdom[i] && costh <= gCdom[i+1]) {
+ for (j = 0; j < 6; j++) coeffs[j] = gC1[i][j];
+ }
}
g1 = Sp5th(costh,coeffs,&dg1);
g = g1;
@@ -2997,15 +2997,15 @@ double PairAIREBO::gSpline(double costh, double Nij, int typei,
}
if (Nij > NCmin && Nij < NCmax) {
for (i = 0; i < 4; i++) {
- if (costh >= gCdom[i] && costh <= gCdom[i+1]) {
- for (j = 0; j < 6; j++) coeffs[j] = gC1[i][j];
- }
+ if (costh >= gCdom[i] && costh <= gCdom[i+1]) {
+ for (j = 0; j < 6; j++) coeffs[j] = gC1[i][j];
+ }
}
g1 = Sp5th(costh,coeffs,&dg1);
for (i = 0; i < 4; i++) {
- if (costh >= gCdom[i] && costh <= gCdom[i+1]) {
- for (j = 0; j < 6; j++) coeffs[j] = gC2[i][j];
- }
+ if (costh >= gCdom[i] && costh <= gCdom[i+1]) {
+ for (j = 0; j < 6; j++) coeffs[j] = gC2[i][j];
+ }
}
g2 = Sp5th(costh,coeffs,&dg2);
cut = Sp(Nij,NCmin,NCmax,dS);
@@ -3014,7 +3014,7 @@ double PairAIREBO::gSpline(double costh, double Nij, int typei,
*dgdN = dS*(g1-g2);
}
}
-
+
// central atom is Hydrogen
if (typei == 1) {
@@ -3022,7 +3022,7 @@ double PairAIREBO::gSpline(double costh, double Nij, int typei,
if (costh > gHdom[3]) costh = gHdom[3];
for (i = 0; i < 3; i++) {
if (costh >= gHdom[i] && costh <= gHdom[i+1]) {
- for (j = 0; j < 6; j++) coeffs[j] = gH[i][j];
+ for (j = 0; j < 6; j++) coeffs[j] = gH[i][j];
}
}
g = Sp5th(costh,coeffs,&dg1);
@@ -3038,11 +3038,11 @@ double PairAIREBO::gSpline(double costh, double Nij, int typei,
------------------------------------------------------------------------- */
double PairAIREBO::PijSpline(double NijC, double NijH, int typei, int typej,
- double dN2[2])
+ double dN2[2])
{
int x,y,i,done;
double Pij,coeffs[16];
-
+
for (i = 0; i < 16; i++) coeffs[i]=0.0;
x = 0;
@@ -3074,13 +3074,13 @@ double PairAIREBO::PijSpline(double NijC, double NijH, int typei, int typej,
}
// if inputs are out of bounds set them back to a point in bounds
-
+
if (typei == 0 && typej == 1){
if (NijC < pCHdom[0][0]) NijC=pCHdom[0][0];
if (NijC > pCHdom[0][1]) NijC=pCHdom[0][1];
if (NijH < pCHdom[1][0]) NijH=pCHdom[1][0];
if (NijH > pCHdom[1][1]) NijH=pCHdom[1][1];
-
+
if (fabs(NijC-floor(NijC)) < TOL && fabs(NijH-floor(NijH)) < TOL) {
Pij = PCHf[(int) NijC][(int) NijH];
dN2[0] = PCHdfdx[(int) NijC][(int) NijH];
@@ -3094,7 +3094,7 @@ double PairAIREBO::PijSpline(double NijC, double NijH, int typei, int typej,
Pij = Spbicubic(NijC,NijH,coeffs,dN2);
}
}
-
+
if (typei == 1 && typej == 0) {
Pij = 0.0;
dN2[0] = 0.0;
@@ -3115,7 +3115,7 @@ double PairAIREBO::PijSpline(double NijC, double NijH, int typei, int typej,
------------------------------------------------------------------------- */
double PairAIREBO::piRCSpline(double Nij, double Nji, double Nijconj,
- int typei, int typej, double dN3[3])
+ int typei, int typej, double dN3[3])
{
int x,y,z,i,done;
double piRC,coeffs[64];
@@ -3137,8 +3137,8 @@ double PairAIREBO::piRCSpline(double Nij, double Nji, double Nijconj,
if (Nijconj<piCCdom[2][0]) Nijconj=piCCdom[2][0];
if (Nijconj>piCCdom[2][1]) Nijconj=piCCdom[2][1];
- if (fabs(Nij-floor(Nij))<TOL && fabs(Nji-floor(Nji))<TOL &&
- fabs(Nijconj-floor(Nijconj))<TOL) {
+ if (fabs(Nij-floor(Nij))<TOL && fabs(Nji-floor(Nji))<TOL &&
+ fabs(Nijconj-floor(Nijconj))<TOL) {
piRC=piCCf[(int) Nij][(int) Nji][(int) Nijconj];
dN3[0]=piCCdfdx[(int) Nij][(int) Nji][(int) Nijconj];
dN3[1]=piCCdfdy[(int) Nij][(int) Nji][(int) Nijconj];
@@ -3148,27 +3148,27 @@ double PairAIREBO::piRCSpline(double Nij, double Nji, double Nijconj,
if (done==0) {
for (i=0; i<piCCdom[0][1]; i++)
- if (Nij>=(double) i && Nij<=(double) i+1 || Nij==(double) i) x=i;
+ if (Nij>=(double) i && Nij<=(double) i+1 || Nij==(double) i) x=i;
for (i=0; i<piCCdom[1][1]; i++)
- if (Nji>=(double) i && Nji<=(double) i+1 || Nji==(double) i) y=i;
+ if (Nji>=(double) i && Nji<=(double) i+1 || Nji==(double) i) y=i;
for (i=0; i<piCCdom[2][1]; i++)
- if (Nijconj>=(double) i && Nijconj<=(double) i+1 ||
- Nijconj==(double) i) z=i;
+ if (Nijconj>=(double) i && Nijconj<=(double) i+1 ||
+ Nijconj==(double) i) z=i;
for (i=0; i<64; i++) coeffs[i]=piCC[x][y][z][i];
piRC=Sptricubic(Nij,Nji,Nijconj,coeffs,dN3);
}
}
-
-
+
+
// CH interaction
if (typei==0 && typej==1 || typei==1 && typej==0) {
// if the inputs are out of bounds set them back to a point in bounds
- if (Nij<piCHdom[0][0] || Nij>piCHdom[0][1] ||
- Nji<piCHdom[1][0] || Nji>piCHdom[1][1] ||
- Nijconj<piCHdom[2][0] || Nijconj>piCHdom[2][1]) {
+ if (Nij<piCHdom[0][0] || Nij>piCHdom[0][1] ||
+ Nji<piCHdom[1][0] || Nji>piCHdom[1][1] ||
+ Nijconj<piCHdom[2][0] || Nijconj>piCHdom[2][1]) {
if (Nij<piCHdom[0][0]) Nij=piCHdom[0][0];
if (Nij>piCHdom[0][1]) Nij=piCHdom[0][1];
if (Nji<piCHdom[1][0]) Nji=piCHdom[1][0];
@@ -3177,8 +3177,8 @@ double PairAIREBO::piRCSpline(double Nij, double Nji, double Nijconj,
if (Nijconj>piCHdom[2][1]) Nijconj=piCHdom[2][1];
}
- if (fabs(Nij-floor(Nij))<TOL && fabs(Nji-floor(Nji))<TOL &&
- fabs(Nijconj-floor(Nijconj))<TOL) {
+ if (fabs(Nij-floor(Nij))<TOL && fabs(Nji-floor(Nji))<TOL &&
+ fabs(Nijconj-floor(Nijconj))<TOL) {
piRC=piCHf[(int) Nij][(int) Nji][(int) Nijconj];
dN3[0]=piCHdfdx[(int) Nij][(int) Nji][(int) Nijconj];
dN3[1]=piCHdfdy[(int) Nij][(int) Nji][(int) Nijconj];
@@ -3188,40 +3188,40 @@ double PairAIREBO::piRCSpline(double Nij, double Nji, double Nijconj,
if (done==0) {
for (i=0; i<piCHdom[0][1]; i++)
- if (Nij>=i && Nij<=i+1) x=i;
+ if (Nij>=i && Nij<=i+1) x=i;
for (i=0; i<piCHdom[1][1]; i++)
- if (Nji>=i && Nji<=i+1) y=i;
+ if (Nji>=i && Nji<=i+1) y=i;
for (i=0; i<piCHdom[2][1]; i++)
- if (Nijconj>=i && Nijconj<=i+1) z=i;
+ if (Nijconj>=i && Nijconj<=i+1) z=i;
for (i=0; i<64; i++) coeffs[i]=piCH[x][y][z][i];
piRC=Sptricubic(Nij,Nji,Nijconj,coeffs,dN3);
}
}
-
+
if (typei==1 && typej==1) {
- if (Nij<piHHdom[0][0] || Nij>piHHdom[0][1] ||
- Nji<piHHdom[1][0] || Nji>piHHdom[1][1] ||
- Nijconj<piHHdom[2][0] || Nijconj>piHHdom[2][1]) {
+ if (Nij<piHHdom[0][0] || Nij>piHHdom[0][1] ||
+ Nji<piHHdom[1][0] || Nji>piHHdom[1][1] ||
+ Nijconj<piHHdom[2][0] || Nijconj>piHHdom[2][1]) {
Nij=0.0;
Nji=0.0;
Nijconj=0.0;
}
- if (fabs(Nij-floor(Nij))<TOL && fabs(Nji-floor(Nji))<TOL &&
- fabs(Nijconj-floor(Nijconj))<TOL) {
+ if (fabs(Nij-floor(Nij))<TOL && fabs(Nji-floor(Nji))<TOL &&
+ fabs(Nijconj-floor(Nijconj))<TOL) {
piRC=piHHf[(int) Nij][(int) Nji][(int) Nijconj];
dN3[0]=piHHdfdx[(int) Nij][(int) Nji][(int) Nijconj];
dN3[1]=piHHdfdy[(int) Nij][(int) Nji][(int) Nijconj];
dN3[2]=piHHdfdz[(int) Nij][(int) Nji][(int) Nijconj];
done=1;
- }
+ }
if (done==0) {
for (i=0; i<piHHdom[0][1]; i++)
- if (Nij>=i && Nij<=i+1) x=i;
+ if (Nij>=i && Nij<=i+1) x=i;
for (i=0; i<piHHdom[1][1]; i++)
- if (Nji>=i && Nji<=i+1) y=i;
+ if (Nji>=i && Nji<=i+1) y=i;
for (i=0; i<piHHdom[2][1]; i++)
- if (Nijconj>=i && Nijconj<=i+1) z=i;
+ if (Nijconj>=i && Nijconj<=i+1) z=i;
for (i=0; i<64; i++) coeffs[i]=piHH[x][y][z][i];
piRC=Sptricubic(Nij,Nji,Nijconj,coeffs,dN3);
@@ -3236,7 +3236,7 @@ double PairAIREBO::piRCSpline(double Nij, double Nji, double Nijconj,
------------------------------------------------------------------------- */
double PairAIREBO::TijSpline(double Nij, double Nji,
- double Nijconj, double dN3[3])
+ double Nijconj, double dN3[3])
{
int x,y,z,i,done;
double Tijf,coeffs[64];
@@ -3258,7 +3258,7 @@ double PairAIREBO::TijSpline(double Nij, double Nji,
if (Nijconj<Tijdom[2][0]) Nijconj=Tijdom[2][0];
if (Nijconj>Tijdom[2][1]) Nijconj=Tijdom[2][1];
- if (fabs(Nij-floor(Nij))<TOL && fabs(Nji-floor(Nji))<TOL &&
+ if (fabs(Nij-floor(Nij))<TOL && fabs(Nji-floor(Nji))<TOL &&
fabs(Nijconj-floor(Nijconj))<TOL) {
Tijf=Tf[(int) Nij][(int) Nji][(int) Nijconj];
dN3[0]=Tdfdx[(int) Nij][(int) Nji][(int) Nijconj];
@@ -3268,11 +3268,11 @@ double PairAIREBO::TijSpline(double Nij, double Nji,
}
if (done==0) {
- for (i=0; i<Tijdom[0][1]; i++)
+ for (i=0; i<Tijdom[0][1]; i++)
if (Nij>=i && Nij<=i+1) x=i;
for (i=0; i<Tijdom[1][1]; i++)
if (Nji>=i && Nji<=i+1) y=i;
- for (i=0; i<Tijdom[2][1]; i++)
+ for (i=0; i<Tijdom[2][1]; i++)
if (Nijconj>=i && Nijconj<=i+1) z=i;
for (i=0; i<64; i++) coeffs[i]=Tijc[x][y][z][i];
@@ -3291,7 +3291,7 @@ void PairAIREBO::add_pages(int howmany)
int toppage = maxpage;
maxpage += howmany*PGDELTA;
- pages = (int **)
+ pages = (int **)
memory->srealloc(pages,maxpage*sizeof(int *),"AIREBO:pages");
for (int i = toppage; i < maxpage; i++)
memory->create(pages[i],pgsize,"AIREBO:pages[i]");
@@ -3305,9 +3305,9 @@ void PairAIREBO::read_file(char *filename)
{
int i,j,k,l,limit;
char s[MAXLINE];
-
+
// REBO Parameters (AIREBO)
-
+
double rcmin_CC,rcmin_CH,rcmin_HH,rcmax_CC,rcmax_CH,
rcmax_HH,rcmaxp_CC,rcmaxp_CH,rcmaxp_HH;
double Q_CC,Q_CH,Q_HH,alpha_CC,alpha_CH,alpha_HH,A_CC,A_CH,A_HH;
@@ -3316,19 +3316,19 @@ void PairAIREBO::read_file(char *filename)
double Beta_CC1,Beta_CC2,Beta_CC3,Beta_CH1,Beta_CH2,Beta_CH3,
Beta_HH1,Beta_HH2,Beta_HH3;
double rho_CC,rho_CH,rho_HH;
-
+
// LJ Parameters (AIREBO)
-
+
double rcLJmin_CC,rcLJmin_CH,rcLJmin_HH,rcLJmax_CC,rcLJmax_CH,
rcLJmax_HH,bLJmin_CC;
double bLJmin_CH,bLJmin_HH,bLJmax_CC,bLJmax_CH,bLJmax_HH,
epsilon_CC,epsilon_CH,epsilon_HH;
double sigma_CC,sigma_CH,sigma_HH,epsilonT_CCCC,epsilonT_CCCH,epsilonT_HCCH;
-
+
MPI_Comm_rank(world,&me);
-
+
// read file on proc 0
-
+
if (me == 0) {
FILE *fp = fopen(filename,"r");
if (fp == NULL) {
@@ -3343,9 +3343,9 @@ void PairAIREBO::read_file(char *filename)
fgets(s,MAXLINE,fp);
if (s[0] != '#') break;
}
-
+
// read parameters
-
+
fgets(s,MAXLINE,fp);
sscanf(s,"%lg",&rcmin_CC);
fgets(s,MAXLINE,fp);
@@ -3434,9 +3434,9 @@ void PairAIREBO::read_file(char *filename)
sscanf(s,"%lg",&rho_CH);
fgets(s,MAXLINE,fp);
sscanf(s,"%lg",&rho_HH);
-
+
// LJ parameters
-
+
fgets(s,MAXLINE,fp);
sscanf(s,"%lg",&rcLJmin_CC);
fgets(s,MAXLINE,fp);
@@ -3479,18 +3479,18 @@ void PairAIREBO::read_file(char *filename)
sscanf(s,"%lg",&epsilonT_CCCH);
fgets(s,MAXLINE,fp);
sscanf(s,"%lg",&epsilonT_HCCH);
-
+
// gC spline
-
+
fgets(s,MAXLINE,fp);
fgets(s,MAXLINE,fp);
fgets(s,MAXLINE,fp);
-
- // number-1 = # of domains for the spline
-
+
+ // number-1 = # of domains for the spline
+
fgets(s,MAXLINE,fp);
sscanf(s,"%d",&limit);
-
+
for (i = 0; i < limit; i++) {
fgets(s,MAXLINE,fp);
sscanf(s,"%lg",&gCdom[i]);
@@ -3498,253 +3498,253 @@ void PairAIREBO::read_file(char *filename)
fgets(s,MAXLINE,fp);
for (i = 0; i < limit-1; i++) {
for (j = 0; j < 6; j++) {
- fgets(s,MAXLINE,fp);
- sscanf(s,"%lg",&gC1[i][j]);
+ fgets(s,MAXLINE,fp);
+ sscanf(s,"%lg",&gC1[i][j]);
}
}
fgets(s,MAXLINE,fp);
for (i = 0; i < limit-1; i++) {
for (j = 0; j < 6; j++) {
- fgets(s,MAXLINE,fp);
- sscanf(s,"%lg",&gC2[i][j]);
+ fgets(s,MAXLINE,fp);
+ sscanf(s,"%lg",&gC2[i][j]);
}
}
-
+
// gH spline
-
+
fgets(s,MAXLINE,fp);
fgets(s,MAXLINE,fp);
fgets(s,MAXLINE,fp);
-
+
fgets(s,MAXLINE,fp);
- sscanf(s,"%d",&limit);
-
+ sscanf(s,"%d",&limit);
+
for (i = 0; i < limit; i++) {
fgets(s,MAXLINE,fp);
sscanf(s,"%lg",&gHdom[i]);
}
-
+
fgets(s,MAXLINE,fp);
-
+
for (i = 0; i < limit-1; i++) {
for (j = 0; j < 6; j++) {
- fgets(s,MAXLINE,fp);
- sscanf(s,"%lg",&gH[i][j]);
+ fgets(s,MAXLINE,fp);
+ sscanf(s,"%lg",&gH[i][j]);
}
}
-
+
// pCC spline
-
+
fgets(s,MAXLINE,fp);
fgets(s,MAXLINE,fp);
fgets(s,MAXLINE,fp);
-
+
fgets(s,MAXLINE,fp);
- sscanf(s,"%d",&limit);
-
+ sscanf(s,"%d",&limit);
+
for (i = 0; i < limit/2; i++) {
for (j = 0; j < limit/2; j++) {
- fgets(s,MAXLINE,fp);
- sscanf(s,"%lg",&pCCdom[i][j]);
+ fgets(s,MAXLINE,fp);
+ sscanf(s,"%lg",&pCCdom[i][j]);
}
}
fgets(s,MAXLINE,fp);
-
+
for (i = 0; i < (int) pCCdom[0][1]; i++) {
for (j = 0; j < (int) pCCdom[1][1]; j++) {
- for (k = 0; k < 16; k++) {
- fgets(s,MAXLINE,fp);
- sscanf(s,"%lg",&pCC[i][j][k]);
- }
+ for (k = 0; k < 16; k++) {
+ fgets(s,MAXLINE,fp);
+ sscanf(s,"%lg",&pCC[i][j][k]);
+ }
}
}
-
+
// pCH spline
-
+
fgets(s,MAXLINE,fp);
fgets(s,MAXLINE,fp);
fgets(s,MAXLINE,fp);
fgets(s,MAXLINE,fp);
- sscanf(s,"%d",&limit);
-
+ sscanf(s,"%d",&limit);
+
for (i = 0; i < limit/2; i++) {
for (j = 0; j < limit/2; j++) {
- fgets(s,MAXLINE,fp);
- sscanf(s,"%lg",&pCHdom[i][j]);
+ fgets(s,MAXLINE,fp);
+ sscanf(s,"%lg",&pCHdom[i][j]);
}
}
fgets(s,MAXLINE,fp);
-
+
for (i = 0; i < (int) pCHdom[0][1]; i++) {
for (j = 0; j < (int) pCHdom[1][1]; j++) {
- for (k = 0; k < 16; k++) {
- fgets(s,MAXLINE,fp);
- sscanf(s,"%lg",&pCH[i][j][k]);
- }
+ for (k = 0; k < 16; k++) {
+ fgets(s,MAXLINE,fp);
+ sscanf(s,"%lg",&pCH[i][j][k]);
+ }
}
}
-
+
// piCC cpline
-
+
fgets(s,MAXLINE,fp);
fgets(s,MAXLINE,fp);
fgets(s,MAXLINE,fp);
-
+
fgets(s,MAXLINE,fp);
sscanf(s,"%d",&limit);
-
+
for (i = 0; i < limit/2; i++) {
for (j = 0; j < limit/3; j++) {
- fgets(s,MAXLINE,fp);
- sscanf(s,"%lg",&piCCdom[i][j]);
+ fgets(s,MAXLINE,fp);
+ sscanf(s,"%lg",&piCCdom[i][j]);
}
}
fgets(s,MAXLINE,fp);
-
+
for (i = 0; i < (int) piCCdom[0][1]; i++) {
for (j = 0; j < (int) piCCdom[1][1]; j++) {
- for (k = 0; k < (int) piCCdom[2][1]; k++) {
- for (l = 0; l < 64; l = l+1) {
- fgets(s,MAXLINE,fp);
- sscanf(s,"%lg",&piCC[i][j][k][l]);
- }
- }
+ for (k = 0; k < (int) piCCdom[2][1]; k++) {
+ for (l = 0; l < 64; l = l+1) {
+ fgets(s,MAXLINE,fp);
+ sscanf(s,"%lg",&piCC[i][j][k][l]);
+ }
+ }
}
}
-
+
// piCH spline
-
+
fgets(s,MAXLINE,fp);
fgets(s,MAXLINE,fp);
fgets(s,MAXLINE,fp);
-
+
fgets(s,MAXLINE,fp);
sscanf(s,"%d",&limit);
-
+
for (i = 0; i < limit/2; i++) {
for (j = 0; j < limit/3; j++) {
- fgets(s,MAXLINE,fp);
- sscanf(s,"%lg",&piCHdom[i][j]);
+ fgets(s,MAXLINE,fp);
+ sscanf(s,"%lg",&piCHdom[i][j]);
}
}
fgets(s,MAXLINE,fp);
-
+
for (i = 0; i < (int) piCHdom[0][1]; i++) {
for (j = 0; j < (int) piCHdom[1][1]; j++) {
- for (k = 0; k < (int) piCHdom[2][1]; k++) {
- for (l = 0; l < 64; l = l+1) {
- fgets(s,MAXLINE,fp);
- sscanf(s,"%lg",&piCH[i][j][k][l]);
- }
- }
+ for (k = 0; k < (int) piCHdom[2][1]; k++) {
+ for (l = 0; l < 64; l = l+1) {
+ fgets(s,MAXLINE,fp);
+ sscanf(s,"%lg",&piCH[i][j][k][l]);
+ }
+ }
}
}
-
+
// piHH spline
-
+
fgets(s,MAXLINE,fp);
fgets(s,MAXLINE,fp);
fgets(s,MAXLINE,fp);
-
+
fgets(s,MAXLINE,fp);
sscanf(s,"%d",&limit);
-
+
for (i = 0; i < limit/2; i++) {
for (j = 0; j < limit/3; j++) {
- fgets(s,MAXLINE,fp);
- sscanf(s,"%lg",&piHHdom[i][j]);
+ fgets(s,MAXLINE,fp);
+ sscanf(s,"%lg",&piHHdom[i][j]);
}
}
fgets(s,MAXLINE,fp);
-
+
for (i = 0; i < (int) piHHdom[0][1]; i++) {
for (j = 0; j < (int) piHHdom[1][1]; j++) {
- for (k = 0; k < (int) piHHdom[2][1]; k++) {
- for (l = 0; l < 64; l = l+1) {
- fgets(s,MAXLINE,fp);
- sscanf(s,"%lg",&piHH[i][j][k][l]);
- }
- }
+ for (k = 0; k < (int) piHHdom[2][1]; k++) {
+ for (l = 0; l < 64; l = l+1) {
+ fgets(s,MAXLINE,fp);
+ sscanf(s,"%lg",&piHH[i][j][k][l]);
+ }
+ }
}
}
-
+
// Tij spline
-
+
fgets(s,MAXLINE,fp);
fgets(s,MAXLINE,fp);
fgets(s,MAXLINE,fp);
-
+
fgets(s,MAXLINE,fp);
sscanf(s,"%d",&limit);
-
+
for (i = 0; i < limit/2; i++) {
for (j = 0; j < limit/3; j++) {
- fgets(s,MAXLINE,fp);
- sscanf(s,"%lg",&Tijdom[i][j]);
+ fgets(s,MAXLINE,fp);
+ sscanf(s,"%lg",&Tijdom[i][j]);
}
}
fgets(s,MAXLINE,fp);
-
+
for (i = 0; i < (int) Tijdom[0][1]; i++) {
for (j = 0; j < (int) Tijdom[1][1]; j++) {
- for (k = 0; k < (int) Tijdom[2][1]; k++) {
- for (l = 0; l < 64; l = l+1) {
- fgets(s,MAXLINE,fp);
- sscanf(s,"%lg",&Tijc[i][j][k][l]);
- }
- }
+ for (k = 0; k < (int) Tijdom[2][1]; k++) {
+ for (l = 0; l < 64; l = l+1) {
+ fgets(s,MAXLINE,fp);
+ sscanf(s,"%lg",&Tijc[i][j][k][l]);
+ }
+ }
}
}
-
+
fclose(fp);
}
-
+
// store read-in values in arrays
-
+
if (me == 0) {
-
+
// REBO
-
+
rcmin[0][0] = rcmin_CC;
rcmin[0][1] = rcmin_CH;
rcmin[1][0] = rcmin[0][1];
rcmin[1][1] = rcmin_HH;
-
+
rcmax[0][0] = rcmax_CC;
rcmax[0][1] = rcmax_CH;
rcmax[1][0] = rcmax[0][1];
rcmax[1][1] = rcmax_HH;
-
+
rcmaxsq[0][0] = rcmax[0][0]*rcmax[0][0];
rcmaxsq[1][0] = rcmax[1][0]*rcmax[1][0];
rcmaxsq[0][1] = rcmax[0][1]*rcmax[0][1];
rcmaxsq[1][1] = rcmax[1][1]*rcmax[1][1];
-
+
rcmaxp[0][0] = rcmaxp_CC;
rcmaxp[0][1] = rcmaxp_CH;
rcmaxp[1][0] = rcmaxp[0][1];
rcmaxp[1][1] = rcmaxp_HH;
-
+
Q[0][0] = Q_CC;
Q[0][1] = Q_CH;
Q[1][0] = Q[0][1];
Q[1][1] = Q_HH;
-
+
alpha[0][0] = alpha_CC;
alpha[0][1] = alpha_CH;
alpha[1][0] = alpha[0][1];
alpha[1][1] = alpha_HH;
-
+
A[0][0] = A_CC;
A[0][1] = A_CH;
A[1][0] = A[0][1];
A[1][1] = A_HH;
-
+
rho[0][0] = rho_CC;
rho[0][1] = rho_CH;
rho[1][0] = rho[0][1];
rho[1][1] = rho_HH;
-
+
BIJc[0][0][0] = BIJc_CC1;
BIJc[0][0][1] = BIJc_CC2;
BIJc[0][0][2] = BIJc_CC3;
@@ -3757,7 +3757,7 @@ void PairAIREBO::read_file(char *filename)
BIJc[1][1][0] = BIJc_HH1;
BIJc[1][1][1] = BIJc_HH2;
BIJc[1][1][2] = BIJc_HH3;
-
+
Beta[0][0][0] = Beta_CC1;
Beta[0][0][1] = Beta_CC2;
Beta[0][0][2] = Beta_CC3;
@@ -3770,19 +3770,19 @@ void PairAIREBO::read_file(char *filename)
Beta[1][1][0] = Beta_HH1;
Beta[1][1][1] = Beta_HH2;
Beta[1][1][2] = Beta_HH3;
-
+
// LJ
-
+
rcLJmin[0][0] = rcLJmin_CC;
rcLJmin[0][1] = rcLJmin_CH;
rcLJmin[1][0] = rcLJmin[0][1];
rcLJmin[1][1] = rcLJmin_HH;
-
+
rcLJmax[0][0] = rcLJmax_CC;
rcLJmax[0][1] = rcLJmax_CH;
rcLJmax[1][0] = rcLJmax[0][1];
rcLJmax[1][1] = rcLJmax_HH;
-
+
rcLJmaxsq[0][0] = rcLJmax[0][0]*rcLJmax[0][0];
rcLJmaxsq[1][0] = rcLJmax[1][0]*rcLJmax[1][0];
rcLJmaxsq[0][1] = rcLJmax[0][1]*rcLJmax[0][1];
@@ -3792,89 +3792,89 @@ void PairAIREBO::read_file(char *filename)
bLJmin[0][1] = bLJmin_CH;
bLJmin[1][0] = bLJmin[0][1];
bLJmin[1][1] = bLJmin_HH;
-
+
bLJmax[0][0] = bLJmax_CC;
bLJmax[0][1] = bLJmax_CH;
bLJmax[1][0] = bLJmax[0][1];
bLJmax[1][1] = bLJmax_HH;
-
+
epsilon[0][0] = epsilon_CC;
epsilon[0][1] = epsilon_CH;
epsilon[1][0] = epsilon[0][1];
epsilon[1][1] = epsilon_HH;
-
+
sigma[0][0] = sigma_CC;
sigma[0][1] = sigma_CH;
sigma[1][0] = sigma[0][1];
sigma[1][1] = sigma_HH;
-
+
// torsional
thmin = -1.0;
- thmax = -0.995;
+ thmax = -0.995;
epsilonT[0][0] = epsilonT_CCCC;
epsilonT[0][1] = epsilonT_CCCH;
epsilonT[1][0] = epsilonT[0][1];
epsilonT[1][1] = epsilonT_HCCH;
}
-
+
// broadcast read-in and setup values
MPI_Bcast(&thmin,1,MPI_DOUBLE,0,world);
MPI_Bcast(&thmax,1,MPI_DOUBLE,0,world);
-
+
MPI_Bcast(&smin,1,MPI_DOUBLE,0,world);
MPI_Bcast(&Nmin,1,MPI_DOUBLE,0,world);
MPI_Bcast(&Nmax,1,MPI_DOUBLE,0,world);
MPI_Bcast(&NCmin,1,MPI_DOUBLE,0,world);
MPI_Bcast(&NCmax,1,MPI_DOUBLE,0,world);
-
-
+
+
MPI_Bcast(&rcmin[0][0],4,MPI_DOUBLE,0,world);
MPI_Bcast(&rcmax[0][0],4,MPI_DOUBLE,0,world);
MPI_Bcast(&rcmaxsq[0][0],4,MPI_DOUBLE,0,world);
MPI_Bcast(&rcmaxp[0][0],4,MPI_DOUBLE,0,world);
-
+
MPI_Bcast(&Q[0][0],4,MPI_DOUBLE,0,world);
MPI_Bcast(&alpha[0][0],4,MPI_DOUBLE,0,world);
MPI_Bcast(&A[0][0],4,MPI_DOUBLE,0,world);
MPI_Bcast(&rho[0][0],4,MPI_DOUBLE,0,world);
MPI_Bcast(&BIJc[0][0][0],12,MPI_DOUBLE,0,world);
MPI_Bcast(&Beta[0][0][0],12,MPI_DOUBLE,0,world);
-
+
MPI_Bcast(&rcLJmin[0][0],4,MPI_DOUBLE,0,world);
MPI_Bcast(&rcLJmax[0][0],4,MPI_DOUBLE,0,world);
MPI_Bcast(&rcLJmaxsq[0][0],4,MPI_DOUBLE,0,world);
MPI_Bcast(&rcLJmin[0][0],4,MPI_DOUBLE,0,world);
MPI_Bcast(&rcLJmin[0][0],4,MPI_DOUBLE,0,world);
-
+
MPI_Bcast(&rcLJmin[0][0],4,MPI_DOUBLE,0,world);
MPI_Bcast(&rcLJmax[0][0],4,MPI_DOUBLE,0,world);
MPI_Bcast(&bLJmin[0][0],4,MPI_DOUBLE,0,world);
MPI_Bcast(&bLJmax[0][0],4,MPI_DOUBLE,0,world);
-
+
MPI_Bcast(&epsilon[0][0],4,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma[0][0],4,MPI_DOUBLE,0,world);
MPI_Bcast(&epsilonT[0][0],4,MPI_DOUBLE,0,world);
-
+
MPI_Bcast(&gCdom[0],5,MPI_DOUBLE,0,world);
MPI_Bcast(&gC1[0][0],24,MPI_DOUBLE,0,world);
MPI_Bcast(&gC2[0][0],24,MPI_DOUBLE,0,world);
MPI_Bcast(&gHdom[0],4,MPI_DOUBLE,0,world);
MPI_Bcast(&gH[0][0],18,MPI_DOUBLE,0,world);
-
+
MPI_Bcast(&pCCdom[0][0],4,MPI_DOUBLE,0,world);
MPI_Bcast(&pCHdom[0][0],4,MPI_DOUBLE,0,world);
MPI_Bcast(&pCC[0][0][0],256,MPI_DOUBLE,0,world);
MPI_Bcast(&pCH[0][0][0],256,MPI_DOUBLE,0,world);
-
+
MPI_Bcast(&piCCdom[0][0],6,MPI_DOUBLE,0,world);
MPI_Bcast(&piCHdom[0][0],6,MPI_DOUBLE,0,world);
MPI_Bcast(&piHHdom[0][0],6,MPI_DOUBLE,0,world);
MPI_Bcast(&piCC[0][0][0][0],9216,MPI_DOUBLE,0,world);
MPI_Bcast(&piCH[0][0][0][0],9216,MPI_DOUBLE,0,world);
MPI_Bcast(&piHH[0][0][0][0],9216,MPI_DOUBLE,0,world);
-
+
MPI_Bcast(&Tijdom[0][0],6,MPI_DOUBLE,0,world);
MPI_Bcast(&Tijc[0][0][0][0],9216,MPI_DOUBLE,0,world);
}
@@ -3914,11 +3914,11 @@ double PairAIREBO::Sp5th(double x, double coeffs[6], double *df)
------------------------------------------------------------------------- */
double PairAIREBO::Spbicubic(double x, double y,
- double coeffs[16], double df[2])
+ double coeffs[16], double df[2])
{
double f,xn,yn,xn1,yn1,c;
int i,j;
-
+
f = 0.0;
df[0] = 0.0;
df[1] = 0.0;
@@ -3930,7 +3930,7 @@ double PairAIREBO::Spbicubic(double x, double y,
c = coeffs[i*4+j];
f += c*xn*yn;
- if (i > 0) df[0] += c * ((double) i) * xn1 * yn;
+ if (i > 0) df[0] += c * ((double) i) * xn1 * yn;
if (j > 0) df[1] += c * ((double) j) * xn * yn1;
yn1 = yn;
@@ -3948,7 +3948,7 @@ double PairAIREBO::Spbicubic(double x, double y,
------------------------------------------------------------------------- */
double PairAIREBO::Sptricubic(double x, double y, double z,
- double coeffs[64], double df[3])
+ double coeffs[64], double df[3])
{
double f,ir,jr,kr,xn,yn,zn,xn1,yn1,zn1,c;
int i,j,k;
@@ -3966,14 +3966,14 @@ double PairAIREBO::Sptricubic(double x, double y, double z,
jr = (double) j;
zn = 1.0;
for (k = 0; k < 4; k++) {
- kr = (double) k;
- c = coeffs[16*i+4*j+k];
- f += c*xn*yn*zn;
- if (i > 0) df[0] += c * ir * xn1 * yn * zn;
- if (j > 0) df[1] += c * jr * xn * yn1 * zn;
- if (k > 0) df[2] += c * kr * xn * yn * zn1;
- zn1 = zn;
- zn *= z;
+ kr = (double) k;
+ c = coeffs[16*i+4*j+k];
+ f += c*xn*yn*zn;
+ if (i > 0) df[0] += c * ir * xn1 * yn * zn;
+ if (j > 0) df[1] += c * jr * xn * yn1 * zn;
+ if (k > 0) df[2] += c * kr * xn * yn * zn1;
+ zn1 = zn;
+ zn *= z;
}
yn1 = yn;
yn *= y;
@@ -3992,7 +3992,7 @@ double PairAIREBO::Sptricubic(double x, double y, double z,
void PairAIREBO::spline_init()
{
int i,j,k;
-
+
for (i = 0; i < 5; i++) {
for (j = 0; j < 5; j++) {
PCCf[i][j] = 0.0;
@@ -4003,7 +4003,7 @@ void PairAIREBO::spline_init()
PCHdfdy[i][j] = 0.0;
}
}
-
+
PCCf[0][2] = -0.00050;
PCCf[0][3] = 0.0161253646;
PCCf[1][1] = -0.010960;
@@ -4020,26 +4020,26 @@ void PairAIREBO::spline_init()
PCHf[2][0] = -0.122042146;
PCHf[2][1] = -0.300529172;
PCHf[3][0] = -0.307584705;
-
+
for (i = 0; i < 5; i++) {
for (j = 0; j < 5; j++) {
for (k = 0; k < 10; k++) {
- piCCf[i][j][k] = 0.0;
- piCCdfdx[i][j][k] = 0.0;
- piCCdfdy[i][j][k] = 0.0;
- piCCdfdz[i][j][k] = 0.0;
- piCHf[i][j][k] = 0.0;
- piCHdfdx[i][j][k] = 0.0;
- piCHdfdy[i][j][k] = 0.0;
- piCHdfdz[i][j][k] = 0.0;
- piHHf[i][j][k] = 0.0;
- piHHdfdx[i][j][k] = 0.0;
- piHHdfdy[i][j][k] = 0.0;
- piHHdfdz[i][j][k] = 0.0;
- Tf[i][j][k] = 0.0;
- Tdfdx[i][j][k] = 0.0;
- Tdfdy[i][j][k] = 0.0;
- Tdfdz[i][j][k] = 0.0;
+ piCCf[i][j][k] = 0.0;
+ piCCdfdx[i][j][k] = 0.0;
+ piCCdfdy[i][j][k] = 0.0;
+ piCCdfdz[i][j][k] = 0.0;
+ piCHf[i][j][k] = 0.0;
+ piCHdfdx[i][j][k] = 0.0;
+ piCHdfdy[i][j][k] = 0.0;
+ piCHdfdz[i][j][k] = 0.0;
+ piHHf[i][j][k] = 0.0;
+ piHHdfdx[i][j][k] = 0.0;
+ piHHdfdy[i][j][k] = 0.0;
+ piHHdfdz[i][j][k] = 0.0;
+ Tf[i][j][k] = 0.0;
+ Tdfdx[i][j][k] = 0.0;
+ Tdfdy[i][j][k] = 0.0;
+ Tdfdz[i][j][k] = 0.0;
}
}
}
@@ -4188,7 +4188,7 @@ void PairAIREBO::spline_init()
}
/* ----------------------------------------------------------------------
- memory usage of local atom-based arrays
+ memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double PairAIREBO::memory_usage()
diff --git a/src/MANYBODY/pair_airebo.h b/src/MANYBODY/pair_airebo.h
index 9d3f69b2584eb4a83cb9d66783754747011a2ea7..7ff0a5a970d728a814c00a1b575b4f0b9b930b27 100644
--- a/src/MANYBODY/pair_airebo.h
+++ b/src/MANYBODY/pair_airebo.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -94,7 +94,7 @@ class PairAIREBO : public Pair {
double bondorder(int, int, double *, double, double, double **, int);
double bondorderLJ(int, int, double *, double, double,
- double *, double, double **, int);
+ double *, double, double **, int);
double gSpline(double, double, int, double *, double *);
double PijSpline(double, double, int, int, double *);
diff --git a/src/MANYBODY/pair_comb.cpp b/src/MANYBODY/pair_comb.cpp
index 004c96ce3fd003245b4401ec2d8122455f65a8f7..f6170bdf6cdbe07c2bcdfecd6c1a55251ea768ba 100644
--- a/src/MANYBODY/pair_comb.cpp
+++ b/src/MANYBODY/pair_comb.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -13,7 +13,7 @@
/* ----------------------------------------------------------------------
Contributing author: Tzu-Ray Shan (U Florida, present: tnshan@sandia.gov)
- LAMMPS implementation of the Charge-optimized many-body (COMB) potential
+ LAMMPS implementation of the Charge-optimized many-body (COMB) potential
based on the HELL MD program (Prof Simon Phillpot, UF, sphil@mse.ufl.edu)
and Aidan Thompson's Tersoff code in LAMMPS
------------------------------------------------------------------------- */
@@ -106,7 +106,7 @@ PairComb::~PairComb()
memory->destroy(bbij);
memory->destroy(sht_num);
memory->destroy(sht_first);
-
+
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
@@ -129,7 +129,7 @@ void PairComb::compute(int eflag, int vflag)
int mr1,mr2,mr3;
int rsc,inty;
double elp_ij,filp[3],fjlp[3],fklp[3];
- double iq,jq;
+ double iq,jq;
double yaself;
double potal,fac11,fac11e;
double vionij,fvionij,sr1,sr2,sr3,Eov,Fov;
@@ -145,7 +145,7 @@ void PairComb::compute(int eflag, int vflag)
double **x = atom->x;
double **f = atom->f;
- double *q = atom->q;
+ double *q = atom->q;
int *tag = atom->tag;
int *type = atom->type;
int nlocal = atom->nlocal;
@@ -156,12 +156,12 @@ void PairComb::compute(int eflag, int vflag)
numneigh = list->numneigh;
firstneigh = list->firstneigh;
- yaself = vionij = fvionij = Eov = Fov = 0.0;
+ yaself = vionij = fvionij = Eov = Fov = 0.0;
// self energy correction term: potal
potal_calc(potal,fac11,fac11e);
-
+
// loop over full neighbor list of my atoms
for (ii = 0; ii < inum; ii++) {
@@ -172,7 +172,7 @@ void PairComb::compute(int eflag, int vflag)
ytmp = x[i][1];
ztmp = x[i][2];
iq = q[i];
- NCo[i] = 0;
+ NCo[i] = 0;
nj = 0;
iparam_i = elem2param[itype][itype][itype];
@@ -181,7 +181,7 @@ void PairComb::compute(int eflag, int vflag)
yaself = self(¶ms[iparam_i],iq,potal);
if (evflag) ev_tally(i,i,nlocal,0,yaself,0.0,0.0,0.0,0.0,0.0);
-
+
// two-body interactions (long and short repulsive)
jlist = firstneigh[i];
@@ -202,9 +202,9 @@ void PairComb::compute(int eflag, int vflag)
if (x[j][2] < x[i][2]) continue;
if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
- }
+ }
- // Qj calculates 2-body Coulombic
+ // Qj calculates 2-body Coulombic
jtype = map[type[j]];
jq = q[j];
@@ -226,35 +226,35 @@ void PairComb::compute(int eflag, int vflag)
tri_point(rsq, mr1, mr2, mr3, sr1, sr2, sr3, itype);
// 1/r energy and forces
-
+
direct(inty,mr1,mr2,mr3,rsq,sr1,sr2,sr3,iq,jq,
- potal,fac11,fac11e,vionij,fvionij);
+ potal,fac11,fac11e,vionij,fvionij);
// field correction to self energy
-
+
field(¶ms[iparam_ij],rsq,iq,jq,vionij,fvionij);
-
+
// polarization field
// sums up long range forces
-
+
f[i][0] += delx*fvionij;
f[i][1] += dely*fvionij;
f[i][2] += delz*fvionij;
f[j][0] -= delx*fvionij;
f[j][1] -= dely*fvionij;
f[j][2] -= delz*fvionij;
-
- if (evflag)
- ev_tally(i,j,nlocal,newton_pair,0.0,vionij,fvionij,delx,dely,delz);
-
+
+ if (evflag)
+ ev_tally(i,j,nlocal,newton_pair,0.0,vionij,fvionij,delx,dely,delz);
+
// short range q-independent
-
+
if (rsq > params[iparam_ij].cutsq) continue;
-
+
repulsive(¶ms[iparam_ij],rsq,fpair,eflag,evdwl,iq,jq);
-
+
// repulsion is pure two-body, sums up pair repulsive forces
-
+
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
@@ -263,30 +263,30 @@ void PairComb::compute(int eflag, int vflag)
f[j][2] -= delz*fpair;
if (evflag)
- ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz);
+ ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz);
}
// accumulate coordination number information
if (cor_flag) {
for (jj = 0; jj < sht_jnum; jj++) {
- j = sht_jlist[jj];
- jtype = map[type[j]];
- iparam_ij = elem2param[itype][jtype][jtype];
-
- if(params[iparam_ij].hfocor > 0.0 ) {
- delr1[0] = x[j][0] - xtmp;
- delr1[1] = x[j][1] - ytmp;
- delr1[2] = x[j][2] - ztmp;
- rsq1 = vec3_dot(delr1,delr1);
-
- if (rsq1 > params[iparam_ij].cutsq) continue;
- NCo[i] += 1;
- }
+ j = sht_jlist[jj];
+ jtype = map[type[j]];
+ iparam_ij = elem2param[itype][jtype][jtype];
+
+ if(params[iparam_ij].hfocor > 0.0 ) {
+ delr1[0] = x[j][0] - xtmp;
+ delr1[1] = x[j][1] - ytmp;
+ delr1[2] = x[j][2] - ztmp;
+ rsq1 = vec3_dot(delr1,delr1);
+
+ if (rsq1 > params[iparam_ij].cutsq) continue;
+ NCo[i] += 1;
+ }
}
}
- // three-body interactions
+ // three-body interactions
// half i-j loop
for (jj = 0; jj < sht_jnum; jj++) {
@@ -309,38 +309,38 @@ void PairComb::compute(int eflag, int vflag)
// accumulate bondorder zeta for each i-j interaction via loop over k
- zeta_ij = 0.0;
+ zeta_ij = 0.0;
cuo_flag1 = 0; cuo_flag2 = 0;
for (kk = 0; kk < sht_jnum; kk++) {
- k = sht_jlist[kk];
- if (j == k) continue;
- ktype = map[type[k]];
- iparam_ijk = elem2param[itype][jtype][ktype];
+ k = sht_jlist[kk];
+ if (j == k) continue;
+ ktype = map[type[k]];
+ iparam_ijk = elem2param[itype][jtype][ktype];
- delr2[0] = x[k][0] - xtmp;
- delr2[1] = x[k][1] - ytmp;
- delr2[2] = x[k][2] - ztmp;
- rsq2 = vec3_dot(delr2,delr2);
+ delr2[0] = x[k][0] - xtmp;
+ delr2[1] = x[k][1] - ytmp;
+ delr2[2] = x[k][2] - ztmp;
+ rsq2 = vec3_dot(delr2,delr2);
- if (rsq2 > params[iparam_ijk].cutsq) continue;
+ if (rsq2 > params[iparam_ijk].cutsq) continue;
- zeta_ij += zeta(¶ms[iparam_ijk],rsq1,rsq2,delr1,delr2);
+ zeta_ij += zeta(¶ms[iparam_ijk],rsq1,rsq2,delr1,delr2);
- if (params[iparam_ijk].hfocor == -2.0) cuo_flag1 = 1;
- if (params[iparam_ijk].hfocor == -1.0) cuo_flag2 = 1;
+ if (params[iparam_ijk].hfocor == -2.0) cuo_flag1 = 1;
+ if (params[iparam_ijk].hfocor == -1.0) cuo_flag2 = 1;
}
if (cuo_flag1 && cuo_flag2) cuo_flag = 1;
else cuo_flag = 0;
force_zeta(¶ms[iparam_ij],eflag,i,nj,rsq1,zeta_ij,
- iq,jq,fpair,prefactor,evdwl);
+ iq,jq,fpair,prefactor,evdwl);
// over-coordination correction for HfO2
if (cor_flag && NCo[i] != 0)
- Over_cor(¶ms[iparam_ij],rsq1,NCo[i],Eov, Fov);
+ Over_cor(¶ms[iparam_ij],rsq1,NCo[i],Eov, Fov);
evdwl += Eov;
fpair += Fov;
@@ -352,48 +352,48 @@ void PairComb::compute(int eflag, int vflag)
f[j][2] -= delr1[2]*fpair;
if (evflag) ev_tally(i,j,nlocal,newton_pair,
- evdwl,0.0,-fpair,-delr1[0],-delr1[1],-delr1[2]);
+ evdwl,0.0,-fpair,-delr1[0],-delr1[1],-delr1[2]);
// attractive term via loop over k (3-body forces)
for (kk = 0; kk < sht_jnum; kk++) {
- k = sht_jlist[kk];
- if (j == k) continue;
- ktype = map[type[k]];
- iparam_ijk = elem2param[itype][jtype][ktype];
+ k = sht_jlist[kk];
+ if (j == k) continue;
+ ktype = map[type[k]];
+ iparam_ijk = elem2param[itype][jtype][ktype];
- delr2[0] = x[k][0] - xtmp;
- delr2[1] = x[k][1] - ytmp;
- delr2[2] = x[k][2] - ztmp;
- rsq2 = vec3_dot(delr2,delr2);
- if (rsq2 > params[iparam_ijk].cutsq) continue;
+ delr2[0] = x[k][0] - xtmp;
+ delr2[1] = x[k][1] - ytmp;
+ delr2[2] = x[k][2] - ztmp;
+ rsq2 = vec3_dot(delr2,delr2);
+ if (rsq2 > params[iparam_ijk].cutsq) continue;
- for (rsc = 0; rsc < 3; rsc++)
- fi[rsc] = fj[rsc] = fk[rsc] = 0.0;
+ for (rsc = 0; rsc < 3; rsc++)
+ fi[rsc] = fj[rsc] = fk[rsc] = 0.0;
- attractive(¶ms[iparam_ijk],prefactor,
- rsq1,rsq2,delr1,delr2,fi,fj,fk);
+ attractive(¶ms[iparam_ijk],prefactor,
+ rsq1,rsq2,delr1,delr2,fi,fj,fk);
- // 3-body LP and BB correction and forces
+ // 3-body LP and BB correction and forces
- elp_ij = elp(¶ms[iparam_ijk],rsq1,rsq2,delr1,delr2);
- flp(¶ms[iparam_ijk],rsq1,rsq2,delr1,delr2,filp,fjlp,fklp);
+ elp_ij = elp(¶ms[iparam_ijk],rsq1,rsq2,delr1,delr2);
+ flp(¶ms[iparam_ijk],rsq1,rsq2,delr1,delr2,filp,fjlp,fklp);
- for (rsc = 0; rsc < 3; rsc++) {
- fi[rsc] += filp[rsc];
- fj[rsc] += fjlp[rsc];
- fk[rsc] += fklp[rsc];
- }
+ for (rsc = 0; rsc < 3; rsc++) {
+ fi[rsc] += filp[rsc];
+ fj[rsc] += fjlp[rsc];
+ fk[rsc] += fklp[rsc];
+ }
- for (rsc = 0; rsc < 3; rsc++) {
- f[i][rsc] += fi[rsc];
- f[j][rsc] += fj[rsc];
- f[k][rsc] += fk[rsc];
- }
+ for (rsc = 0; rsc < 3; rsc++) {
+ f[i][rsc] += fi[rsc];
+ f[j][rsc] += fj[rsc];
+ f[k][rsc] += fk[rsc];
+ }
- if (evflag)
- ev_tally(i,j,nlocal,newton_pair,elp_ij,0.0,0.0,0.0,0.0,0.0);
- if (vflag_atom) v_tally3(i,j,k,fj,fk,delr1,delr2);
+ if (evflag)
+ ev_tally(i,j,nlocal,newton_pair,elp_ij,0.0,0.0,0.0,0.0,0.0);
+ if (vflag_atom) v_tally3(i,j,k,fj,fk,delr1,delr2);
}
}
@@ -417,11 +417,11 @@ void PairComb::allocate()
memory->create(cutsq,n+1,n+1,"pair:cutsq");
map = new int[n+1];
- esm = new double[n];
+ esm = new double[n];
}
/* ----------------------------------------------------------------------
- global settings
+ global settings
------------------------------------------------------------------------- */
void PairComb::settings(int narg, char **arg)
@@ -477,7 +477,7 @@ void PairComb::coeff(int narg, char **arg)
}
// read potential file and initialize potential parameters
-
+
read_file(arg[2]);
setup();
@@ -486,7 +486,7 @@ void PairComb::coeff(int narg, char **arg)
// generate streitz-mintmire direct 1/r energy look-up table
if (comm->me == 0 && screen) fprintf(screen,"Pair COMB:\n");
- if (comm->me == 0 && screen)
+ if (comm->me == 0 && screen)
fprintf(screen," generating Coulomb integral lookup table ...\n");
sm_table();
@@ -507,8 +507,8 @@ void PairComb::coeff(int narg, char **arg)
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
if (map[i] >= 0 && map[j] >= 0) {
- setflag[i][j] = 1;
- count++;
+ setflag[i][j] = 1;
+ count++;
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
@@ -590,8 +590,8 @@ void PairComb::read_file(char *file)
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fp);
if (ptr == NULL) {
- eof = 1;
- fclose(fp);
+ eof = 1;
+ fclose(fp);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
@@ -612,8 +612,8 @@ void PairComb::read_file(char *file)
if (comm->me == 0) {
ptr = fgets(&line[n],MAXLINE-n,fp);
if (ptr == NULL) {
- eof = 1;
- fclose(fp);
+ eof = 1;
+ fclose(fp);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
@@ -652,7 +652,7 @@ void PairComb::read_file(char *file)
if (nparams == maxparam) {
maxparam += DELTA;
params = (Param *) memory->srealloc(params,maxparam*sizeof(Param),
- "pair:params");
+ "pair:params");
}
params[nparams].ielement = ielement;
@@ -709,36 +709,36 @@ void PairComb::read_file(char *file)
// parameter sanity checks
- if (params[nparams].lam11 < 0.0 || params[nparams].lam12 < 0.0 ||
- params[nparams].c < 0.0 || params[nparams].d < 0.0 ||
- params[nparams].powern < 0.0 || params[nparams].beta < 0.0 ||
- params[nparams].lam21 < 0.0 || params[nparams].lam22 < 0.0 ||
- params[nparams].bigb1< 0.0 || params[nparams].bigb2< 0.0 ||
- params[nparams].biga1< 0.0 || params[nparams].biga2< 0.0 ||
- params[nparams].bigr < 0.0 || params[nparams].bigd < 0.0 ||
- params[nparams].bigd > params[nparams].bigr ||
- params[nparams].powerm - params[nparams].powermint != 0.0 ||
- (params[nparams].powermint != 3 && params[nparams].powermint != 1) ||
- params[nparams].plp1 < 0.0 || params[nparams].plp3 < 0.0 ||
- params[nparams].plp6 < 0.0 ||
- params[nparams].a123 > 360.0 || params[nparams].aconf < 0.0 ||
- params[nparams].addrep < 0.0 || params[nparams].romigb < 0.0 ||
- params[nparams].romigc < 0.0 || params[nparams].romigd < 0.0 ||
- params[nparams].romiga < 0.0 ||
- params[nparams].QL1 > 0.0 || params[nparams].QU1 < 0.0 ||
- params[nparams].DL1 < 0.0 || params[nparams].DU1 > 0.0 ||
- params[nparams].QL2 > 0.0 || params[nparams].QU2 < 0.0 ||
- params[nparams].DL2 < 0.0 || params[nparams].DU2 > 0.0 ||
- params[nparams].chi < 0.0 ||
-// params[nparams].dj < 0.0 || params[nparams].dk < 0.0 ||
-// params[nparams].dl < 0.0 || params[nparams].dm < 0.0 ||
- params[nparams].esm1 < 0.0)
+ if (params[nparams].lam11 < 0.0 || params[nparams].lam12 < 0.0 ||
+ params[nparams].c < 0.0 || params[nparams].d < 0.0 ||
+ params[nparams].powern < 0.0 || params[nparams].beta < 0.0 ||
+ params[nparams].lam21 < 0.0 || params[nparams].lam22 < 0.0 ||
+ params[nparams].bigb1< 0.0 || params[nparams].bigb2< 0.0 ||
+ params[nparams].biga1< 0.0 || params[nparams].biga2< 0.0 ||
+ params[nparams].bigr < 0.0 || params[nparams].bigd < 0.0 ||
+ params[nparams].bigd > params[nparams].bigr ||
+ params[nparams].powerm - params[nparams].powermint != 0.0 ||
+ (params[nparams].powermint != 3 && params[nparams].powermint != 1) ||
+ params[nparams].plp1 < 0.0 || params[nparams].plp3 < 0.0 ||
+ params[nparams].plp6 < 0.0 ||
+ params[nparams].a123 > 360.0 || params[nparams].aconf < 0.0 ||
+ params[nparams].addrep < 0.0 || params[nparams].romigb < 0.0 ||
+ params[nparams].romigc < 0.0 || params[nparams].romigd < 0.0 ||
+ params[nparams].romiga < 0.0 ||
+ params[nparams].QL1 > 0.0 || params[nparams].QU1 < 0.0 ||
+ params[nparams].DL1 < 0.0 || params[nparams].DU1 > 0.0 ||
+ params[nparams].QL2 > 0.0 || params[nparams].QU2 < 0.0 ||
+ params[nparams].DL2 < 0.0 || params[nparams].DU2 > 0.0 ||
+ params[nparams].chi < 0.0 ||
+// params[nparams].dj < 0.0 || params[nparams].dk < 0.0 ||
+// params[nparams].dl < 0.0 || params[nparams].dm < 0.0 ||
+ params[nparams].esm1 < 0.0)
error->all(FLERR,"Illegal COMB parameter");
- if (params[nparams].lam11 < params[nparams].lam21 ||
- params[nparams].lam12 < params[nparams].lam22 ||
- params[nparams].biga1< params[nparams].bigb1 ||
- params[nparams].biga2< params[nparams].bigb2)
+ if (params[nparams].lam11 < params[nparams].lam21 ||
+ params[nparams].lam12 < params[nparams].lam22 ||
+ params[nparams].biga1< params[nparams].bigb1 ||
+ params[nparams].biga2< params[nparams].bigb2)
error->all(FLERR,"Illegal COMB parameter");
nparams++;
@@ -763,16 +763,16 @@ void PairComb::setup()
for (i = 0; i < nelements; i++)
for (j = 0; j < nelements; j++)
for (k = 0; k < nelements; k++) {
- n = -1;
- for (m = 0; m < nparams; m++) {
- if (i == params[m].ielement && j == params[m].jelement &&
- k == params[m].kelement) {
- if (n >= 0) error->all(FLERR,"Potential file has duplicate entry");
- n = m;
- }
- }
- if (n < 0) error->all(FLERR,"Potential file is missing an entry");
- elem2param[i][j][k] = n;
+ n = -1;
+ for (m = 0; m < nparams; m++) {
+ if (i == params[m].ielement && j == params[m].jelement &&
+ k == params[m].kelement) {
+ if (n >= 0) error->all(FLERR,"Potential file has duplicate entry");
+ n = m;
+ }
+ }
+ if (n < 0) error->all(FLERR,"Potential file is missing an entry");
+ elem2param[i][j][k] = n;
}
// compute parameter values derived from inputs
@@ -789,46 +789,46 @@ void PairComb::setup()
params[m].Qo1 = (params[m].QU1+params[m].QL1)/2.0; // (A22)
params[m].dQ1 = (params[m].QU1-params[m].QL1)/2.0; // (A21)
- params[m].aB1 = 1.0 /
+ params[m].aB1 = 1.0 /
(1.0-pow(fabs(params[m].Qo1/params[m].dQ1),10.0)); // (A20)
params[m].bB1 = pow(fabs(params[m].aB1),0.1)/params[m].dQ1; // (A19)
params[m].nD1 = log(params[m].DU1/(params[m].DU1-params[m].DL1))/
- log(params[m].QU1/(params[m].QU1-params[m].QL1));
+ log(params[m].QU1/(params[m].QU1-params[m].QL1));
params[m].bD1 = (pow((params[m].DL1-params[m].DU1),(1.0/params[m].nD1)))/
- (params[m].QU1-params[m].QL1);
-
+ (params[m].QU1-params[m].QL1);
+
params[m].Qo2 = (params[m].QU2+params[m].QL2)/2.0; // (A22)
params[m].dQ2 = (params[m].QU2-params[m].QL2)/2.0; // (A21)
- params[m].aB2 = 1.0 /
+ params[m].aB2 = 1.0 /
(1.0-pow(fabs(params[m].Qo2/params[m].dQ2),10.0)); // (A20)
params[m].bB2 = pow(fabs(params[m].aB2),0.1)/params[m].dQ2; // (A19)
params[m].nD2 = log(params[m].DU2/(params[m].DU2-params[m].DL2))/
- log(params[m].QU2/(params[m].QU2-params[m].QL2));
+ log(params[m].QU2/(params[m].QU2-params[m].QL2));
params[m].bD2 = (pow((params[m].DL2-params[m].DU2),(1.0/params[m].nD2)))/
- (params[m].QU2-params[m].QL2);
+ (params[m].QU2-params[m].QL2);
params[m].lcut = params[m].coulcut;
params[m].lcutsq = params[m].lcut*params[m].lcut;
- params[m].gamma = 1.0; // for the change in pair_comb.h
+ params[m].gamma = 1.0; // for the change in pair_comb.h
}
// set cutmax to max of all params
cutmax = cutmin = 0.0;
- cor_flag = 0;
+ cor_flag = 0;
for (m = 0; m < nparams; m++) {
if (params[m].cut > cutmax) cutmax = params[m].cut;
if (params[m].lcut > cutmax) cutmax = params[m].lcut;
if (params[m].cutsq > cutmin) cutmin = params[m].cutsq+0.2;
if (params[m].hfocor > 0.0001) cor_flag = 1;
}
-}
+}
/* ---------------------------------------------------------------------- */
void PairComb::repulsive(Param *param, double rsq, double &fforce,
- int eflag, double &eng, double iq, double jq)
+ int eflag, double &eng, double iq, double jq)
{
double r,tmp_fc,tmp_fc_d,tmp_exp,Di,Dj;
double bigA,Asi,Asj,vrcs,fvrcs,fforce_tmp;
@@ -865,7 +865,7 @@ void PairComb::repulsive(Param *param, double rsq, double &fforce,
// additional repulsion for TiO2 and HfO2 (switch by cor_flag)
vrcs = 0.0; fvrcs = 0.0;
- if (romi > 0.0) {
+ if (romi > 0.0) {
if (!cor_flag) {
vrcs = romi * pow((1.0-r/rrcs),2.0);
fvrcs= romi * 2.0 * (r/rrcs-1.0)/rrcs; }
@@ -887,7 +887,7 @@ void PairComb::repulsive(Param *param, double rsq, double &fforce,
/* ---------------------------------------------------------------------- */
double PairComb::zeta(Param *param, double rsqij, double rsqik,
- double *delrij, double *delrik)
+ double *delrij, double *delrik)
{
double rij,rik,costheta,arg,ex_delr;
@@ -907,49 +907,49 @@ double PairComb::zeta(Param *param, double rsqij, double rsqik,
}
/* ----------------------------------------------------------------------
- Legendre polynomial bond angle correction to energy
+ Legendre polynomial bond angle correction to energy
------------------------------------------------------------------------- */
double PairComb::elp(Param *param, double rsqij, double rsqik,
- double *delrij, double *delrik)
+ double *delrij, double *delrik)
{
- if (param->aconf > 1.0e-6 || param->plp1 > 1.0e-6 ||
+ if (param->aconf > 1.0e-6 || param->plp1 > 1.0e-6 ||
param->plp3 > 1.0e-6 || param->plp6 > 1.0e-6) {
double rij,rik,costheta,lp1,lp3,lp6;
double rmu,rmu2,comtt,fck;
double pplp1 = param->plp1, pplp3 = param->plp3, pplp6 = param->plp6;
double c123 = cos(param->a123*MY_PI/180.0);
-
+
// cos(theta) of the i-j-k
// cutoff function of rik
-
+
rij = sqrt(rsqij);
rik = sqrt(rsqik);
costheta = vec3_dot(delrij,delrik) / (rij*rik);
fck = comb_fc(rik,param);
- rmu = costheta;
-
+ rmu = costheta;
+
// Legendre Polynomial functions
-
+
if (param->plp1 > 1.0e-6 || param->plp3 > 1.0e-6 || param->plp6 > 1.0e-6) {
rmu2 = rmu*rmu;
lp1 = rmu; lp3 = 0.5*(5.0*rmu2*rmu-3.0*rmu);
lp6 = (231.0*rmu2*rmu2*rmu2-315.0*rmu2*rmu2+105.0*rmu2-5.0)/16.0;
comtt = pplp1*lp1 + pplp3*lp3 + pplp6*lp6;
} else comtt = 0.0;
-
+
// bond-bending terms
-
+
if (param->aconf>1e-4) {
if (param->hfocor >= 0.0)
- comtt += param->aconf *(rmu-c123)*(rmu-c123);
+ comtt += param->aconf *(rmu-c123)*(rmu-c123);
else if (param->hfocor < 0.0)
- comtt += param->aconf *(4.0-(rmu-c123)*(rmu-c123));
+ comtt += param->aconf *(4.0-(rmu-c123)*(rmu-c123));
}
-
+
return 0.5 * fck * comtt;
}
-
+
return 0.0;
}
@@ -958,92 +958,92 @@ double PairComb::elp(Param *param, double rsqij, double rsqik,
------------------------------------------------------------------------- */
void PairComb::flp(Param *param, double rsqij, double rsqik,
- double *delrij, double *delrik, double *drilp,
- double *drjlp, double *drklp)
+ double *delrij, double *delrik, double *drilp,
+ double *drjlp, double *drklp)
{
- double ffj1,ffj2,ffk1,ffk2;
+ double ffj1,ffj2,ffk1,ffk2;
ffj1 = 0.0; ffj2 = 0.0; ffk1 = 0.0; ffk2 = 0.0;
- if (param->aconf > 1.0e-4 || param->plp1 > 1.0e-6 ||
+ if (param->aconf > 1.0e-4 || param->plp1 > 1.0e-6 ||
param->plp3 > 1.0e-6 || param->plp6 > 1.0e-6) {
double rij,rik,costheta,lp1,lp1_d,lp3,lp3_d,lp6,lp6_d;
double rmu,rmu2,comtt,comtt_d,com4k,com5,fcj,fck,fck_d;
-
+
double pplp1 = param->plp1;
double pplp3 = param->plp3;
double pplp6 = param->plp6;
double c123 = cos(param->a123*MY_PI/180.0);
-
+
// fck_d = derivative of cutoff function
-
+
rij = sqrt(rsqij); rik = sqrt(rsqik);
- costheta = vec3_dot(delrij,delrik) / (rij*rik);
+ costheta = vec3_dot(delrij,delrik) / (rij*rik);
fcj = comb_fc(rij,param);
fck = comb_fc(rik,param);
fck_d = comb_fc_d(rik,param);
- rmu = costheta;
-
+ rmu = costheta;
+
// Legendre Polynomial functions and derivatives
-
+
if (param->plp1 > 1.0e-6 || param->plp3 > 1.0e-6 || param->plp6 > 1.0e-6) {
- rmu2 = rmu*rmu;
+ rmu2 = rmu*rmu;
lp1 = rmu; lp3 = (2.5*rmu2*rmu-1.5*rmu);
lp6 = (231.0*rmu2*rmu2*rmu2-315.0*rmu2*rmu2+105.0*rmu2-5.0)/16.0;
lp1_d = 1.0;lp3_d = (7.5*rmu2-1.5);
lp6_d = (1386.0*rmu2*rmu2*rmu-1260.0*rmu2*rmu+210.0)/16.0;
- comtt = pplp1*lp1 + pplp3*lp3 + pplp6*lp6;
+ comtt = pplp1*lp1 + pplp3*lp3 + pplp6*lp6;
comtt_d = pplp1*lp1_d + pplp3*lp3_d + pplp6*lp6_d;
} else {
comtt = 0.0;
comtt_d = 0.0;
}
-
+
// bond-bending terms derivatives
-
+
if (param->aconf > 1.0e-4) {
if (param->hfocor >= 0.0) {
- comtt += param->aconf *(rmu-c123)*(rmu-c123);
- comtt_d += 2.0*param->aconf*(rmu-c123);
+ comtt += param->aconf *(rmu-c123)*(rmu-c123);
+ comtt_d += 2.0*param->aconf*(rmu-c123);
} else if (param->hfocor < 0.0) {
- comtt += param->aconf *(4.0-(rmu-c123)*(rmu-c123));
- comtt_d += -2.0*param->aconf*(rmu-c123);
+ comtt += param->aconf *(4.0-(rmu-c123)*(rmu-c123));
+ comtt_d += -2.0*param->aconf*(rmu-c123);
}
}
-
+
com4k = fcj * fck_d * comtt;
com5 = fcj * fck * comtt_d;
-
- ffj1 =-0.5*(com5/(rij*rik));
+
+ ffj1 =-0.5*(com5/(rij*rik));
ffj2 = 0.5*(com5*rmu/rsqij);
ffk1 = ffj1;
ffk2 = 0.5*(-com4k/rik+com5*rmu/rsqik);
-
+
} else {
ffj1 = 0.0; ffj2 = 0.0;
ffk1 = 0.0; ffk2 = 0.0;
}
-
+
// j-atom
-
- vec3_scale(ffj1,delrik,drjlp); // (k,x[],y[]), y[]=k*x[]
+
+ vec3_scale(ffj1,delrik,drjlp); // (k,x[],y[]), y[]=k*x[]
vec3_scaleadd(ffj2,delrij,drjlp,drjlp); // (k,x[],y[],z[]), z[]=k*x[]+y[]
-
+
// k-atom
-
+
vec3_scale(ffk1,delrij,drklp);
vec3_scaleadd(ffk2,delrik,drklp,drklp);
-
- // i-atom
-
- vec3_add(drjlp,drklp,drilp); // (x[],y[],z[]), z[]=x[]+y[]
+
+ // i-atom
+
+ vec3_add(drjlp,drklp,drilp); // (x[],y[],z[]), z[]=x[]+y[]
vec3_scale(-1.0,drilp,drilp);
}
/* ---------------------------------------------------------------------- */
-void PairComb::force_zeta(Param *param, int eflag, int i, int j, double rsq,
- double zeta_ij, double iq, double jq, double &fforce,
- double &prefactor, double &eng)
+void PairComb::force_zeta(Param *param, int eflag, int i, int j, double rsq,
+ double zeta_ij, double iq, double jq, double &fforce,
+ double &prefactor, double &eng)
{
double r,fa,fa_d,bij;
@@ -1057,7 +1057,7 @@ void PairComb::force_zeta(Param *param, int eflag, int i, int j, double rsq,
// force
fforce = 0.5*bij*fa_d / r;
prefactor = -0.5*fa * comb_bij_d(zeta_ij,param);
-
+
// eng = attractive energy
if (eflag) eng = 0.5*bij*fa;
}
@@ -1068,7 +1068,7 @@ double PairComb::comb_fc(double r, Param *param)
{
double comb_R = param->bigr;
double comb_D = param->bigd;
-
+
if (r < comb_R-comb_D) return 1.0;
if (r > comb_R+comb_D) return 0.0;
return 0.5*(1.0 + cos(MY_PI*(r - comb_R)/comb_D));
@@ -1080,7 +1080,7 @@ double PairComb::comb_fc_d(double r, Param *param)
{
double comb_R = param->bigr;
double comb_D = param->bigd;
-
+
if (r < comb_R-comb_D) return 0.0;
if (r > comb_R+comb_D) return 0.0;
return -(MY_PI2/comb_D) * sin(MY_PI*(r - comb_R)/comb_D);
@@ -1092,7 +1092,7 @@ double PairComb::comb_fc2(double r)
{
double comb_R = 1.89350;
double comb_D = comb_R + 0.050;
-
+
if (r < comb_R) return 0.0;
if (r > comb_D) return 1.0;
return 0.5*(1.0 + cos(MY_PI*(r - comb_R)/(comb_D-comb_R)));
@@ -1104,7 +1104,7 @@ double PairComb::comb_fc2_d(double r)
{
double comb_R = 1.89350;
double comb_D = comb_R + 0.050;
-
+
if (r < comb_R) return 0.0;
if (r > comb_D) return 0.0;
return -(MY_PI2/(comb_D-comb_R)) * sin(MY_PI*(r - comb_R)/(comb_D-comb_R));
@@ -1116,7 +1116,7 @@ double PairComb::comb_fc3(double r)
{
double comb_R = 2.51350;
double comb_D = comb_R + 0.050;
-
+
if (r < comb_R) return 1.0;
if (r > comb_D) return 0.0;
return 0.5*(1.0 + cos(MY_PI*(r - comb_R)/(comb_D-comb_R)));
@@ -1128,7 +1128,7 @@ double PairComb::comb_fc3_d(double r)
{
double comb_R = 2.51350;
double comb_D = comb_R + 0.050;
-
+
if (r < comb_R) return 0.0;
if (r > comb_D) return 0.0;
return -(MY_PI2/(comb_D-comb_R)) * sin(MY_PI*(r - comb_R)/(comb_D-comb_R));
@@ -1141,8 +1141,8 @@ double PairComb::self(Param *param, double qi, double selfpot)
double self_tmp, cmin, cmax, qmin, qmax;
double s1=param->chi, s2=param->dj, s3=param->dk, s4=param->dl, s5=param->dm;
- self_tmp = 0.0;
- qmin = param->QL1*0.90;
+ self_tmp = 0.0;
+ qmin = param->QL1*0.90;
qmax = param->QU1*0.90;
cmin = cmax = 1000.0;
@@ -1150,7 +1150,7 @@ double PairComb::self(Param *param, double qi, double selfpot)
if (qi < qmin) self_tmp += cmin * pow((qi-qmin),4.0);
if (qi > qmax) self_tmp += cmax * pow((qi-qmax),4.0);
-
+
return self_tmp;
}
@@ -1170,11 +1170,11 @@ double PairComb::comb_fa(double r, Param *param, double iq, double jq)
(param->aB1-fabs(pow(param->bB1*(qi-param->Qo1),10.0)));
Bsj = param->bigb2 * exp(param->lam22*Dj)*
(param->aB2-fabs(pow(param->bB2*(qj-param->Qo2),10.0)));
- if (Bsi > 0.0 && Bsj > 0.0) bigB = sqrt(Bsi*Bsj)*param->romigb;
+ if (Bsi > 0.0 && Bsj > 0.0) bigB = sqrt(Bsi*Bsj)*param->romigb;
else bigB = 0.0;
return -bigB * exp(-param->rlm2 * r) * comb_fc(r,param);
-}
+}
/* ---------------------------------------------------------------------- */
@@ -1220,13 +1220,13 @@ double PairComb::comb_bij_d(double zeta, Param *param)
double tmp = param->beta * zeta;
if (tmp > param->c1) return param->beta * -0.5*pow(tmp,-1.5);
if (tmp > param->c2)
- return param->beta * (-0.5*pow(tmp,-1.5) *
- (1.0 - 0.5*(1.0 + 1.0/(2.0*param->powern)) *
- pow(tmp,-param->powern)));
+ return param->beta * (-0.5*pow(tmp,-1.5) *
+ (1.0 - 0.5*(1.0 + 1.0/(2.0*param->powern)) *
+ pow(tmp,-param->powern)));
if (tmp < param->c4) return 0.0;
if (tmp < param->c3)
return -0.5*param->beta * pow(tmp,param->powern-1.0);
-
+
double tmp_n = pow(tmp,param->powern);
return -0.5 * pow(1.0+tmp_n, -1.0-(1.0/(2.0*param->powern)))*tmp_n / zeta;
}
@@ -1234,9 +1234,9 @@ double PairComb::comb_bij_d(double zeta, Param *param)
/* ---------------------------------------------------------------------- */
void PairComb::attractive(Param *param, double prefactor,
- double rsqij, double rsqik,
- double *delrij, double *delrik,
- double *fi, double *fj, double *fk)
+ double rsqij, double rsqik,
+ double *delrij, double *delrik,
+ double *fi, double *fj, double *fk)
{
double rij_hat[3],rik_hat[3];
double rij,rijinv,rik,rikinv;
@@ -1244,7 +1244,7 @@ void PairComb::attractive(Param *param, double prefactor,
rij = sqrt(rsqij);
rijinv = 1.0/rij;
vec3_scale(rijinv,delrij,rij_hat);
-
+
rik = sqrt(rsqik);
rikinv = 1.0/rik;
vec3_scale(rikinv,delrik,rik_hat);
@@ -1255,8 +1255,8 @@ void PairComb::attractive(Param *param, double prefactor,
/* ---------------------------------------------------------------------- */
void PairComb::comb_zetaterm_d(double prefactor, double *rij_hat, double rij,
- double *rik_hat, double rik, double *dri,
- double *drj, double *drk, Param *param)
+ double *rik_hat, double rik, double *dri,
+ double *drj, double *drk, Param *param)
{
double gijk,gijk_d,ex_delr,ex_delr_d,fc,dfc,cos_theta,tmp;
double dcosdri[3],dcosdrj[3],dcosdrk[3];
@@ -1273,12 +1273,12 @@ void PairComb::comb_zetaterm_d(double prefactor, double *rij_hat, double rij,
if (param->powermint == 3)
ex_delr_d = 3.0*pow(param->rlm2,3.0) * pow(rij-rik,2.0)*ex_delr; // com3
else ex_delr_d = param->rlm2 * ex_delr; // com3
-
+
cos_theta = vec3_dot(rij_hat,rik_hat);
gijk = comb_gijk(cos_theta,param);
gijk_d = comb_gijk_d(cos_theta,param);
costheta_d(rij_hat,rij,rik_hat,rik,dcosdri,dcosdrj,dcosdrk);
-
+
// compute the derivative wrt Ri
// dri = -dfc*gijk*ex_delr*rik_hat;
// dri += fc*gijk_d*ex_delr*dcosdri;
@@ -1314,8 +1314,8 @@ void PairComb::comb_zetaterm_d(double prefactor, double *rij_hat, double rij,
/* ---------------------------------------------------------------------- */
void PairComb::costheta_d(double *rij_hat, double rij,
- double *rik_hat, double rik,
- double *dri, double *drj, double *drk)
+ double *rik_hat, double rik,
+ double *dri, double *drj, double *drk)
{
// first element is devative wrt Ri, second wrt Rj, third wrt Rk
@@ -1342,17 +1342,17 @@ void PairComb::sm_table()
int n = atom->ntypes;
int nmax = atom->nmax;
-
+
dra = 0.001; // lookup table step size
- drin = 0.1; // starting distance of 1/r
+ drin = 0.1; // starting distance of 1/r
rc = cutmax;
alf = 0.20;
-
+
nntypes = int((n+1)*n/2); // interaction types
ncoul = int((rc-drin)/dra)+1;
// allocate arrays
-
+
memory->create(intype,n,n,"pair:intype");
memory->create(fafb,ncoul,nntypes,"pair:fafb");
memory->create(dfafb,ncoul,nntypes,"pair:dfafb");
@@ -1364,39 +1364,39 @@ void PairComb::sm_table()
memory->create(bbij,nmax,MAXNEIGH,"pair:bbij");
memory->create(sht_num,nmax,"pair:sht_num");
sht_first = (int **) memory->smalloc(nmax*sizeof(int *),
- "pair:sht_first");
-
+ "pair:sht_first");
+
// set interaction number: 0-0=0, 1-1=1, 0-1=1-0=2
-
+
m = 0; k = n;
for (i = 0; i < n; i++) {
for (j = 0; j < n; j++) {
- if (j == i) {
- intype[i][j] = m;
- m += 1;
+ if (j == i) {
+ intype[i][j] = m;
+ m += 1;
} else if (j != i && j > i) {
- intype[i][j] = k;
- k += 1;
+ intype[i][j] = k;
+ k += 1;
} else if (j != i && j < i) {
- intype[i][j] = intype[j][i];
+ intype[i][j] = intype[j][i];
}
}
}
-
+
// default arrays to zero
-
+
for (i = 0; i < ncoul; i ++) {
for (j = 0; j < nntypes; j ++) {
- fafb[i][j] = 0.0;
- dfafb[i][j] = 0.0;
- ddfafb[i][j] = 0.0;
- phin[i][j] = 0.0;
+ fafb[i][j] = 0.0;
+ dfafb[i][j] = 0.0;
+ ddfafb[i][j] = 0.0;
+ phin[i][j] = 0.0;
dphin[i][j] = 0.0;
}
}
-
+
// direct 1/r energy with Slater 1S orbital overlap
-
+
for (i = 0; i < n; i++) {
r = drin;
itype = params[i].ielement;
@@ -1415,70 +1415,70 @@ void PairComb::sm_table()
r = drin;
if (j == i) {
itype = params[i].ielement;
- inty = intype[itype][itype];
+ inty = intype[itype][itype];
iparam_i = elem2param[itype][itype][itype];
z = params[iparam_i].esm1;
- zrc = z * rc;
- exp2ersh = exp(-2.0 * zrc);
- fafash = -exp2ersh * (1.0 / rc +
- z * (11.0/8.0 + 3.0/4.0*zrc + zrc*zrc/6.0));
- dfafash = exp2ersh * (1.0/(rc*rc) + 2.0*z/rc +
- z*z*(2.0 + 7.0/6.0*zrc + zrc*zrc/3.0));
- for (k = 0; k < ncoul; k ++) {
- zr = z * r;
- exp2er = exp(-2.0*zr);
- F1 = -exp2er * (1.0 / r +
- z * (11.0/8.0 + 3.0/4.0*zr + zr*zr/6.0));
- dF1 = exp2er * (1.0/(r*r) + 2.0*z/r +
- z*z*(2.0 + 7.0/6.0*zr + zr*zr/3.0));
- ddF1 = -exp2er * (2.0/(r*r*r) + 4.0*z/(r*r) -
- z*z*z/3.0*(17.0/2.0 + 5.0*zr + 2.0*zr*zr));
- fafb[k][inty] = F1-fafash-(r-rc)*dfafash;
- dfafb[k][inty] = (dF1 - dfafash);
- ddfafb[k][inty] = ddF1;
- r += dra;
- }
+ zrc = z * rc;
+ exp2ersh = exp(-2.0 * zrc);
+ fafash = -exp2ersh * (1.0 / rc +
+ z * (11.0/8.0 + 3.0/4.0*zrc + zrc*zrc/6.0));
+ dfafash = exp2ersh * (1.0/(rc*rc) + 2.0*z/rc +
+ z*z*(2.0 + 7.0/6.0*zrc + zrc*zrc/3.0));
+ for (k = 0; k < ncoul; k ++) {
+ zr = z * r;
+ exp2er = exp(-2.0*zr);
+ F1 = -exp2er * (1.0 / r +
+ z * (11.0/8.0 + 3.0/4.0*zr + zr*zr/6.0));
+ dF1 = exp2er * (1.0/(r*r) + 2.0*z/r +
+ z*z*(2.0 + 7.0/6.0*zr + zr*zr/3.0));
+ ddF1 = -exp2er * (2.0/(r*r*r) + 4.0*z/(r*r) -
+ z*z*z/3.0*(17.0/2.0 + 5.0*zr + 2.0*zr*zr));
+ fafb[k][inty] = F1-fafash-(r-rc)*dfafash;
+ dfafb[k][inty] = (dF1 - dfafash);
+ ddfafb[k][inty] = ddF1;
+ r += dra;
+ }
} else if (j != i) {
itype = params[i].ielement;
jtype = params[j].ielement;
- inty = intype[itype][jtype];
+ inty = intype[itype][jtype];
iparam_ij = elem2param[itype][jtype][jtype];
ea = params[iparam_ij].esm1;
- ea3 = ea*ea*ea;
- iparam_ji = elem2param[jtype][itype][itype];
+ ea3 = ea*ea*ea;
+ iparam_ji = elem2param[jtype][itype][itype];
eb = params[iparam_ji].esm1;
- eb3 = eb*eb*eb;
- E1 = ea*eb3*eb/((ea+eb)*(ea+eb)*(ea-eb)*(ea-eb));
- E2 = eb*ea3*ea/((ea+eb)*(ea+eb)*(eb-ea)*(eb-ea));
- E3 = (3.0*ea*ea*eb3*eb-eb3*eb3) /
- ((ea+eb)*(ea+eb)*(ea+eb)*(ea-eb)*(ea-eb)*(ea-eb));
- E4 = (3.0*eb*eb*ea3*ea-ea3*ea3) /
- ((ea+eb)*(ea+eb)*(ea+eb)*(eb-ea)*(eb-ea)*(eb-ea));
- exp2earsh = exp(-2.0*ea*rc);
- exp2ebrsh = exp(-2.0*eb*rc);
- fafbsh = -exp2earsh*(E1 + E3/rc)-exp2ebrsh*(E2 + E4/rc);
- dfafbsh =
- exp2earsh*(2.0*ea*(E1+E3/rc)+E3/(rc*rc)) +
- exp2ebrsh*(2.0*eb*(E2+E4/rc)+E4/(rc*rc));
- for (k = 0; k < ncoul; k ++) {
- exp2ear = exp(-2.0*ea*r);
- exp2ebr = exp(-2.0*eb*r);
- fafb[k][inty] =
- - exp2ear*(E1+E3/r) - exp2ebr*(E2+E4/r)
- - fafbsh - (r-rc) * dfafbsh;
- dfafb[k][inty] = (exp2ear*(2.0*ea*(E1+E3/r) + E3/(r*r))
- + exp2ebr*(2.0*eb*(E2+E4/r) + E4/(r*r))- dfafbsh);
- ddfafb[k][inty] = (- exp2ear*(E3/(r*r)*(1.0/r+2.0*ea/r+2.0/(r*r))
- + 2.0*ea*(E1+E3/r))-
- exp2ebr*(E4/(r*r)
- *(1.0/r+2.0*eb/r+2.0/(r*r)) +
- 2.0*eb*(E2+E4/r)));
- r += dra;
- }
- }
+ eb3 = eb*eb*eb;
+ E1 = ea*eb3*eb/((ea+eb)*(ea+eb)*(ea-eb)*(ea-eb));
+ E2 = eb*ea3*ea/((ea+eb)*(ea+eb)*(eb-ea)*(eb-ea));
+ E3 = (3.0*ea*ea*eb3*eb-eb3*eb3) /
+ ((ea+eb)*(ea+eb)*(ea+eb)*(ea-eb)*(ea-eb)*(ea-eb));
+ E4 = (3.0*eb*eb*ea3*ea-ea3*ea3) /
+ ((ea+eb)*(ea+eb)*(ea+eb)*(eb-ea)*(eb-ea)*(eb-ea));
+ exp2earsh = exp(-2.0*ea*rc);
+ exp2ebrsh = exp(-2.0*eb*rc);
+ fafbsh = -exp2earsh*(E1 + E3/rc)-exp2ebrsh*(E2 + E4/rc);
+ dfafbsh =
+ exp2earsh*(2.0*ea*(E1+E3/rc)+E3/(rc*rc)) +
+ exp2ebrsh*(2.0*eb*(E2+E4/rc)+E4/(rc*rc));
+ for (k = 0; k < ncoul; k ++) {
+ exp2ear = exp(-2.0*ea*r);
+ exp2ebr = exp(-2.0*eb*r);
+ fafb[k][inty] =
+ - exp2ear*(E1+E3/r) - exp2ebr*(E2+E4/r)
+ - fafbsh - (r-rc) * dfafbsh;
+ dfafb[k][inty] = (exp2ear*(2.0*ea*(E1+E3/r) + E3/(r*r))
+ + exp2ebr*(2.0*eb*(E2+E4/r) + E4/(r*r))- dfafbsh);
+ ddfafb[k][inty] = (- exp2ear*(E3/(r*r)*(1.0/r+2.0*ea/r+2.0/(r*r))
+ + 2.0*ea*(E1+E3/r))-
+ exp2ebr*(E4/(r*r)
+ *(1.0/r+2.0*eb/r+2.0/(r*r)) +
+ 2.0*eb*(E2+E4/r)));
+ r += dra;
+ }
+ }
}
}
-
+
for (i = 0; i < 25000; i ++) {
r = dra * i + drin;
erpaw[i][0] = erfc(r*alf);
@@ -1492,25 +1492,25 @@ void PairComb::potal_calc(double &calc1, double &calc2, double &calc3)
{
double alf,rcoul,esucon;
int m;
-
+
rcoul = 0.0;
for (m = 0; m < nparams; m++)
if (params[m].lcut > rcoul) rcoul = params[m].lcut;
-
+
alf = 0.20;
esucon = force->qqr2e;
calc2 = (erfc(rcoul*alf)/rcoul/rcoul+2.0*alf/MY_PIS*
- exp(-alf*alf*rcoul*rcoul)/rcoul)*esucon/rcoul;
+ exp(-alf*alf*rcoul*rcoul)/rcoul)*esucon/rcoul;
calc3 = (erfc(rcoul*alf)/rcoul)*esucon;
calc1 = -(alf/MY_PIS*esucon+calc3*0.5);
}
/* ---------------------------------------------------------------------- */
-void PairComb::tri_point(double rsq, int &mr1, int &mr2,
- int &mr3, double &sr1, double &sr2,
- double &sr3, int &itype)
+void PairComb::tri_point(double rsq, int &mr1, int &mr2,
+ int &mr3, double &sr1, double &sr2,
+ double &sr3, int &itype)
{
double r, rin, dr, dd, rr1, rridr, rridr2;
@@ -1538,10 +1538,10 @@ void PairComb::tri_point(double rsq, int &mr1, int &mr2,
/* ---------------------------------------------------------------------- */
void PairComb::direct(int inty, int mr1, int mr2, int mr3, double rsq,
- double sr1, double sr2, double sr3,
- double iq, double jq,
- double potal, double fac11, double fac11e,
- double &pot_tmp, double &pot_d)
+ double sr1, double sr2, double sr3,
+ double iq, double jq,
+ double potal, double fac11, double fac11e,
+ double &pot_tmp, double &pot_d)
{
double r,erfcc,fafbn1,potij,sme2,esucon;
double r3,erfcd,dfafbn1,smf2,dvdrr,alf,alfdpi;
@@ -1560,7 +1560,7 @@ void PairComb::direct(int inty, int mr1, int mr2, int mr3, double rsq,
fafbn1= sr1*fafb[mr1][inty] + sr2*fafb[mr2][inty] + sr3*fafb[mr3][inty];
potij = (erfcc/r * esucon - fac11e);
sme2 = potij + fafbn1 * esucon;
- pot_tmp = 1.0 * iq * jq *sme2;
+ pot_tmp = 1.0 * iq * jq *sme2;
// 1/r force (wrt r)
@@ -1575,7 +1575,7 @@ void PairComb::direct(int inty, int mr1, int mr2, int mr3, double rsq,
/* ---------------------------------------------------------------------- */
void PairComb::field(Param *param, double rsq, double iq,double jq,
- double &vionij,double &fvionij)
+ double &vionij,double &fvionij)
{
double r,r5,r6,rc,rc5,rc6,rf5,drf6,smpn,smpl,rfx1,rfx2;
double cmi1,cmi2,cmj1,cmj2;
@@ -1583,12 +1583,12 @@ void PairComb::field(Param *param, double rsq, double iq,double jq,
r = sqrt(rsq);
r5 = r*r*r*r*r;
r6 = r5 * r;
- rc = param->lcut;
- rc5 = rc*rc*rc*rc*rc;
+ rc = param->lcut;
+ rc5 = rc*rc*rc*rc*rc;
rc6 = rc5 * rc;
- cmi1 = param->cmn1;
+ cmi1 = param->cmn1;
cmi2 = param->cmn2;
- cmj1 = param->cml1;
+ cmj1 = param->cml1;
cmj2 = param->cml2;
rf5 = 1.0/r5 - 1.0/rc5 + 5.0*(r-rc)/rc6;
drf6 = 5.0/rc6 - 5.0/r6;
@@ -1619,12 +1619,12 @@ double PairComb::yasu_char(double *qf_fix, int &igroup)
double potal,fac11,fac11e,sr1,sr2,sr3;
int mr1,mr2,mr3,inty,nj;
-
+
double **x = atom->x;
double *q = atom->q;
int *type = atom->type;
int *tag = atom->tag;
-
+
int inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
@@ -1675,7 +1675,7 @@ double PairComb::yasu_char(double *qf_fix, int &igroup)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
- j &= NEIGHMASK;
+ j &= NEIGHMASK;
jtag = tag[j];
if (itag > jtag) {
@@ -1686,7 +1686,7 @@ double PairComb::yasu_char(double *qf_fix, int &igroup)
if (x[j][2] < x[i][2]) continue;
if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
- }
+ }
jtype = map[type[j]];
jq = q[j];
@@ -1701,11 +1701,11 @@ double PairComb::yasu_char(double *qf_fix, int &igroup)
// long range q-dependent
if (rsq1 > params[iparam_ij].lcutsq) continue;
-
+
inty = intype[itype][jtype];
-
+
// polynomial three-point interpolation
-
+
tri_point(rsq1,mr1,mr2,mr3,sr1,sr2,sr3,itype);
// 1/r charge forces
@@ -1714,17 +1714,17 @@ double PairComb::yasu_char(double *qf_fix, int &igroup)
fqi += jq * fqij; qf[j] += iq * fqij;
// field correction to self energy and charge force
-
+
qfo_field(¶ms[iparam_ij],rsq1,iq,jq,fqij,fqjj);
fqi += fqij;
qf[j] += fqjj;
}
-
+
// three-body interactions
-
+
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
- j &= NEIGHMASK;
+ j &= NEIGHMASK;
jtype = map[type[j]];
jq = q[j];
@@ -1736,21 +1736,21 @@ double PairComb::yasu_char(double *qf_fix, int &igroup)
iparam_ij = elem2param[itype][jtype][jtype];
if (rsq1 > params[iparam_ij].cutsq) continue;
- nj ++;
+ nj ++;
// charge force in Aij and Bij
-
+
qfo_short(¶ms[iparam_ij],i,nj,rsq1,iq,jq,fqij,fqjj);
fqi += fqij; qf[j] += fqjj;
}
qf[i] += fqi;
}
}
-
+
comm->reverse_comm_pair(this);
-
+
// sum charge force on each node and return it
-
+
double eneg = 0.0;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
@@ -1773,14 +1773,14 @@ double PairComb::qfo_self(Param *param, double qi, double selfpot)
double s4 = param->dl;
double s5 = param->dm;
- self_d = 0.0;
- qmin = param->QL1*0.90;
+ self_d = 0.0;
+ qmin = param->QL1*0.90;
qmax = param->QU1*0.90;
if (qmax > 4.50 ) qmax = -0.70;
cmin = cmax = 1000.0;
-
+
self_d = s1+qi*(2.0*(s2+selfpot)+qi*(3.0*s3+qi*(4.0*s4+qi*qi*6.0*s5)));
-
+
if (qi < qmin) {
// char str[128];
// sprintf(str,"Pair COMB charge %.10f with force %.10f hit min barrier",
@@ -1791,7 +1791,7 @@ double PairComb::qfo_self(Param *param, double qi, double selfpot)
if (qi > qmax) {
// char str[128];
// sprintf(str,"Pair COMB charge %.10f with force %.10f hit max barrier",
- // qi,self_d);
+ // qi,self_d);
// error->warning(FLERR,str,0);
self_d += 4.0 * cmax * pow((qi-qmax),3.0);
}
@@ -1802,14 +1802,14 @@ double PairComb::qfo_self(Param *param, double qi, double selfpot)
/* ---------------------------------------------------------------------- */
void PairComb::qfo_direct(int inty, int mr1, int mr2, int mr3,
- double rsq, double sr1, double sr2,
- double sr3, double fac11e, double &fqij)
+ double rsq, double sr1, double sr2,
+ double sr3, double fac11e, double &fqij)
{
double r, erfcc, fafbn1, vm, esucon;
r = sqrt(rsq);
esucon=force->qqr2e;
-
+
// 1/r force (wrt q)
erfcc = sr1*erpaw[mr1][0] + sr2*erpaw[mr2][0] + sr3*erpaw[mr3][0];
@@ -1821,7 +1821,7 @@ void PairComb::qfo_direct(int inty, int mr1, int mr2, int mr3,
/* ---------------------------------------------------------------------- */
void PairComb::qfo_field(Param *param, double rsq,double iq,double jq,
- double &fqij, double &fqjj)
+ double &fqij, double &fqjj)
{
double r,r5,r6,rc,rc5,rc6;
double cmi1,cmi2,cmj1,cmj2,rf5;
@@ -1848,7 +1848,7 @@ void PairComb::qfo_field(Param *param, double rsq,double iq,double jq,
/* ---------------------------------------------------------------------- */
void PairComb::qfo_short(Param *param, int i, int j, double rsq,
- double iq, double jq, double &fqij, double &fqjj)
+ double iq, double jq, double &fqij, double &fqjj)
{
double r,tmp_fc,tmp_fc_d,tmp_exp1,tmp_exp2;
double bigA,Asi,Asj,vrcs;
@@ -1886,32 +1886,32 @@ void PairComb::qfo_short(Param *param, int i, int j, double rsq,
else if (cor_flag) {
rslp = ((arr1-r)/(arr1-arr2));
rslp2 = rslp * rslp; rslp4 = rslp2 * rslp2;
- vrcs = fc2j * fc3j * romi * ((50.0*rslp4-30.0*rslp2+4.50))/8.0;
+ vrcs = fc2j * fc3j * romi * ((50.0*rslp4-30.0*rslp2+4.50))/8.0;
}
}
-
+
Di = param->DU1 + pow(fabs(param->bD1*(param->QU1-qi)),param->nD1);
Dj = param->DU2 + pow(fabs(param->bD2*(param->QU2-qj)),param->nD2);
-
+
Asi = param->biga1 * exp(param->lam11*Di);
Asj = param->biga2 * exp(param->lam12*Dj);
Bsi = param->bigb1 * exp(param->lam21*Di)*
(param->aB1-fabs(pow(param->bB1*(qi-param->Qo1),10.0)));
Bsj = param->bigb2 * exp(param->lam22*Dj)*
(param->aB2-fabs(pow(param->bB2*(qj-param->Qo2),10.0)));
-
+
QUchi = (param->QU1-qi)*param->bD1;
QUchj = (param->QU2-qj)*param->bD2;
QOchi = (qi-param->Qo1)*param->bB1;
QOchj = (qj-param->Qo2)*param->bB2;
-
+
if (QUchi == 0.0) YYDiqp = 0.0;
- else YYDiqp = -param->nD1 * QUchi * param->bD1 *
- pow(fabs(QUchi),(param->nD1-2.0));
+ else YYDiqp = -param->nD1 * QUchi * param->bD1 *
+ pow(fabs(QUchi),(param->nD1-2.0));
if (QUchj == 0.0) YYDjqp = 0.0;
- else YYDjqp = -param->nD2 * QUchj * param->bD2 *
- pow(fabs(QUchj),(param->nD2-2.0));
+ else YYDjqp = -param->nD2 * QUchj * param->bD2 *
+ pow(fabs(QUchj),(param->nD2-2.0));
YYAsiqp = Asi * param->lam11 * YYDiqp;
YYAsjqp = Asj * param->lam12 * YYDjqp;
@@ -1933,10 +1933,10 @@ void PairComb::qfo_short(Param *param, int i, int j, double rsq,
if (Bsi > 0.0 && Bsj > 0.0) cbj = 1.0/(2.0*sqrt(Bsi*Bsj)) * romib ;
else cbj = 0.0;
-
+
cfqr = 0.50 * tmp_fc * (1.0 + vrcs); // 0.5 b/c full atom loop
cfqs = -0.50 * tmp_fc * bij;
-
+
ca1 = Asj * caj * YYAsiqp;
ca2 = Bsj * cbj * YYBsiqp;
ca3 = Asi * caj * YYAsjqp;
@@ -1951,7 +1951,7 @@ void PairComb::qfo_short(Param *param, int i, int j, double rsq,
/* ---------------------------------------------------------------------- */
void PairComb::Over_cor(Param *param, double rsq1, int NCoi,
- double &Eov, double &Fov)
+ double &Eov, double &Fov)
{
double ECo,BCo,tmp_fc,tmp_fc_d;
double r = sqrt(rsq1);
@@ -1962,12 +1962,12 @@ void PairComb::Over_cor(Param *param, double rsq1, int NCoi,
Eov = 0.0; Fov = 0.0;
ECo = param->hfocor;
BCo = 0.1;
-
+
if (NCon >= 0.20) {
Eov = tmp_fc * ECo * NCon/(1.0+exp(BCo*NCon));
Fov = -(tmp_fc_d*Eov + tmp_fc*ECo/(1.0+exp(BCo*NCon)) -
- (tmp_fc*ECo*NCon*BCo*exp(BCo*NCon)) /
- ((1.0+exp(BCo*NCon))*(1.0+exp(BCo*NCon))));
+ (tmp_fc*ECo*NCon*BCo*exp(BCo*NCon)) /
+ ((1.0+exp(BCo*NCon))*(1.0+exp(BCo*NCon))));
Fov /= r;
}
}
@@ -1984,46 +1984,46 @@ int PairComb::pack_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
buf[m++] = qf[j];
}
return 1;
-}
-
+}
+
/* ---------------------------------------------------------------------- */
-
+
void PairComb::unpack_comm(int n, int first, double *buf)
-{
+{
int i,m,last;
-
- m = 0;
+
+ m = 0;
last = first + n ;
for (i = first; i < last; i++) qf[i] = buf[m++];
-}
+}
/* ---------------------------------------------------------------------- */
int PairComb::pack_reverse_comm(int n, int first, double *buf)
{
int i,m,last;
-
+
m = 0;
- last = first + n;
+ last = first + n;
for (i = first; i < last; i++) buf[m++] = qf[i];
return 1;
-}
-
+}
+
/* ---------------------------------------------------------------------- */
-
+
void PairComb::unpack_reverse_comm(int n, int *list, double *buf)
-{
+{
int i,j,m;
- m = 0;
+ m = 0;
for (i = 0; i < n; i++) {
j = list[i];
qf[j] += buf[m++];
}
-}
+}
/* ----------------------------------------------------------------------
- memory usage of local atom-based arrays
+ memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double PairComb::memory_usage()
@@ -2053,7 +2053,7 @@ void PairComb::Short_neigh()
memory->sfree(sht_first);
nmax = atom->nmax;
sht_first = (int **) memory->smalloc(nmax*sizeof(int *),
- "pair:sht_first");
+ "pair:sht_first");
memory->grow(sht_num,nmax,"pair:sht_num");
memory->grow(NCo,nmax,"pair:NCo");
memory->grow(bbij,nmax,MAXNEIGH,"pair:bbij");
@@ -2075,7 +2075,7 @@ void PairComb::Short_neigh()
npage++;
if (npage == maxpage) add_pages();
}
-
+
nj = 0;
neighptrj = &pages[npage][npntj];
@@ -2095,7 +2095,7 @@ void PairComb::Short_neigh()
delrj[1] = ytmp - x[j][1];
delrj[2] = ztmp - x[j][2];
rsq = vec3_dot(delrj,delrj);
-
+
if (rsq > cutmin) continue;
neighptrj[nj++] = j;
}
diff --git a/src/MANYBODY/pair_comb.h b/src/MANYBODY/pair_comb.h
index 3e05ba9b9c0aae879f1fb4caa98220b97328aafb..3a073d45889a794e5cbc3d149471e21f30c7b267 100644
--- a/src/MANYBODY/pair_comb.h
+++ b/src/MANYBODY/pair_comb.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -57,7 +57,7 @@ class PairComb : public Pair {
int ielement,jelement,kelement;
int powermint;
};
-
+
double cutmax; // max cutoff for all elements
int nelements; // # of unique elements
char **elements; // names of unique elements
@@ -80,16 +80,16 @@ class PairComb : public Pair {
void allocate();
virtual void read_file(char *);
void setup();
- virtual void repulsive(Param *, double, double &, int,
- double &, double, double);
+ virtual void repulsive(Param *, double, double &, int,
+ double &, double, double);
double zeta(Param *, double, double, double *, double *);
- void force_zeta(Param *, int, int, int, double, double, double, double,
- double &, double &, double &);
+ void force_zeta(Param *, int, int, int, double, double, double, double,
+ double &, double &, double &);
void attractive(Param *, double, double, double, double *, double *,
- double *, double *, double *);
+ double *, double *, double *);
double elp(Param *, double, double, double *, double *);
- void flp(Param *, double, double, double *, double *, double *,
- double *, double *);
+ void flp(Param *, double, double, double *, double *, double *,
+ double *, double *);
double comb_fc(double, Param *);
double comb_fc_d(double, Param *);
double comb_fc2(double);
@@ -101,8 +101,8 @@ class PairComb : public Pair {
double comb_bij(double, Param *);
double comb_bij_d(double, Param *);
- inline double comb_gijk(const double costheta,
- const Param * const param) const {
+ inline double comb_gijk(const double costheta,
+ const Param * const param) const {
const double comb_c = param->c * param->c;
const double comb_d = param->d * param->d;
const double hcth = param->h - costheta;
@@ -110,8 +110,8 @@ class PairComb : public Pair {
return param->gamma*(1.0 + comb_c/comb_d - comb_c / (comb_d + hcth*hcth));
}
- inline double comb_gijk_d(const double costheta,
- const Param * const param) const {
+ inline double comb_gijk_d(const double costheta,
+ const Param * const param) const {
const double comb_c = param->c * param->c;
const double comb_d = param->d * param->d;
const double hcth = param->h - costheta;
@@ -121,22 +121,22 @@ class PairComb : public Pair {
}
void comb_zetaterm_d(double, double *, double, double *, double,
- double *, double *, double *, Param *);
+ double *, double *, double *, Param *);
void costheta_d(double *, double, double *, double,
- double *, double *, double *);
+ double *, double *, double *);
double self(Param *, double, double);
void sm_table();
void potal_calc(double &, double &, double &);
- void tri_point(double, int &, int &, int &, double &, double &,
- double &, int &);
+ void tri_point(double, int &, int &, int &, double &, double &,
+ double &, int &);
void direct(int,int,int,int,double,double,double,double,double,double,
- double,double,double,double &,double &);
+ double,double,double,double &,double &);
void field(Param *,double,double,double,double &,double &);
double qfo_self(Param *, double, double);
void qfo_short(Param *, int, int, double, double, double,
- double &, double &);
- void qfo_direct (int, int, int, int, double, double, double, double,
- double, double &);
+ double &, double &);
+ void qfo_direct (int, int, int, int, double, double, double, double,
+ double, double &);
void qfo_field(Param *, double,double ,double ,double &, double &);
void qsolve(double *);
void Over_cor(Param *, double, int, double &, double &);
@@ -150,7 +150,7 @@ class PairComb : public Pair {
void add_pages(int howmany=1);
void Short_neigh();
int maxpage, pgsize, oneatom, **pages;
- int *sht_num, **sht_first; // short-range neighbor list
+ int *sht_num, **sht_first; // short-range neighbor list
double cutmin;
// vector functions, inline for efficiency
@@ -159,18 +159,18 @@ class PairComb : public Pair {
return x[0]*y[0] + x[1]*y[1] + x[2]*y[2];
}
- inline void vec3_add(const double x[3], const double y[3],
- double * const z) const {
+ inline void vec3_add(const double x[3], const double y[3],
+ double * const z) const {
z[0] = x[0]+y[0]; z[1] = x[1]+y[1]; z[2] = x[2]+y[2];
}
inline void vec3_scale(const double k, const double x[3],
- double y[3]) const {
+ double y[3]) const {
y[0] = k*x[0]; y[1] = k*x[1]; y[2] = k*x[2];
}
- inline void vec3_scaleadd(const double k, const double x[3],
- const double y[3], double * const z) const {
+ inline void vec3_scaleadd(const double k, const double x[3],
+ const double y[3], double * const z) const {
z[0] = k*x[0]+y[0];
z[1] = k*x[1]+y[1];
z[2] = k*x[2]+y[2];
diff --git a/src/MANYBODY/pair_eam.cpp b/src/MANYBODY/pair_eam.cpp
index 7ccb61c776b4f49ccfb7e9508d8643d9cf165f6f..3f6972bc5e6662e942dabc1ca77689415168b907 100644
--- a/src/MANYBODY/pair_eam.cpp
+++ b/src/MANYBODY/pair_eam.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -154,7 +154,7 @@ void PairEAM::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// zero out density
if (newton_pair) {
@@ -184,18 +184,18 @@ void PairEAM::compute(int eflag, int vflag)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cutforcesq) {
- jtype = type[j];
- p = sqrt(rsq)*rdr + 1.0;
- m = static_cast<int> (p);
- m = MIN(m,nr-1);
- p -= m;
- p = MIN(p,1.0);
- coeff = rhor_spline[type2rhor[jtype][itype]][m];
- rho[i] += ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
- if (newton_pair || j < nlocal) {
- coeff = rhor_spline[type2rhor[itype][jtype]][m];
- rho[j] += ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
- }
+ jtype = type[j];
+ p = sqrt(rsq)*rdr + 1.0;
+ m = static_cast<int> (p);
+ m = MIN(m,nr-1);
+ p -= m;
+ p = MIN(p,1.0);
+ coeff = rhor_spline[type2rhor[jtype][itype]][m];
+ rho[i] += ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
+ if (newton_pair || j < nlocal) {
+ coeff = rhor_spline[type2rhor[itype][jtype]][m];
+ rho[j] += ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
+ }
}
}
}
@@ -250,50 +250,50 @@ void PairEAM::compute(int eflag, int vflag)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cutforcesq) {
- jtype = type[j];
- r = sqrt(rsq);
- p = r*rdr + 1.0;
- m = static_cast<int> (p);
- m = MIN(m,nr-1);
- p -= m;
- p = MIN(p,1.0);
-
- // rhoip = derivative of (density at atom j due to atom i)
- // rhojp = derivative of (density at atom i due to atom j)
- // phi = pair potential energy
- // phip = phi'
- // z2 = phi * r
- // z2p = (phi * r)' = (phi' r) + phi
- // psip needs both fp[i] and fp[j] terms since r_ij appears in two
- // terms of embed eng: Fi(sum rho_ij) and Fj(sum rho_ji)
- // hence embed' = Fi(sum rho_ij) rhojp + Fj(sum rho_ji) rhoip
-
- coeff = rhor_spline[type2rhor[itype][jtype]][m];
- rhoip = (coeff[0]*p + coeff[1])*p + coeff[2];
- coeff = rhor_spline[type2rhor[jtype][itype]][m];
- rhojp = (coeff[0]*p + coeff[1])*p + coeff[2];
- coeff = z2r_spline[type2z2r[itype][jtype]][m];
- z2p = (coeff[0]*p + coeff[1])*p + coeff[2];
- z2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
-
- recip = 1.0/r;
- phi = z2*recip;
- phip = z2p*recip - phi*recip;
- psip = fp[i]*rhojp + fp[j]*rhoip + phip;
- fpair = -psip*recip;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (eflag) evdwl = phi;
- if (evflag) ev_tally(i,j,nlocal,newton_pair,
- evdwl,0.0,fpair,delx,dely,delz);
+ jtype = type[j];
+ r = sqrt(rsq);
+ p = r*rdr + 1.0;
+ m = static_cast<int> (p);
+ m = MIN(m,nr-1);
+ p -= m;
+ p = MIN(p,1.0);
+
+ // rhoip = derivative of (density at atom j due to atom i)
+ // rhojp = derivative of (density at atom i due to atom j)
+ // phi = pair potential energy
+ // phip = phi'
+ // z2 = phi * r
+ // z2p = (phi * r)' = (phi' r) + phi
+ // psip needs both fp[i] and fp[j] terms since r_ij appears in two
+ // terms of embed eng: Fi(sum rho_ij) and Fj(sum rho_ji)
+ // hence embed' = Fi(sum rho_ij) rhojp + Fj(sum rho_ji) rhoip
+
+ coeff = rhor_spline[type2rhor[itype][jtype]][m];
+ rhoip = (coeff[0]*p + coeff[1])*p + coeff[2];
+ coeff = rhor_spline[type2rhor[jtype][itype]][m];
+ rhojp = (coeff[0]*p + coeff[1])*p + coeff[2];
+ coeff = z2r_spline[type2z2r[itype][jtype]][m];
+ z2p = (coeff[0]*p + coeff[1])*p + coeff[2];
+ z2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
+
+ recip = 1.0/r;
+ phi = z2*recip;
+ phip = z2p*recip - phi*recip;
+ psip = fp[i]*rhojp + fp[j]*rhoip + phip;
+ fpair = -psip*recip;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (eflag) evdwl = phi;
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ evdwl,0.0,fpair,delx,dely,delz);
}
}
}
@@ -360,7 +360,7 @@ void PairEAM::coeff(int narg, char **arg)
if (ifuncfl == nfuncfl) {
nfuncfl++;
- funcfl = (Funcfl *)
+ funcfl = (Funcfl *)
memory->srealloc(funcfl,nfuncfl*sizeof(Funcfl),"pair:funcfl");
read_file(arg[2]);
int n = strlen(arg[2]) + 1;
@@ -375,10 +375,10 @@ void PairEAM::coeff(int narg, char **arg)
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
if (i == j) {
- setflag[i][i] = 1;
- map[i] = ifuncfl;
- atom->set_mass(i,funcfl[ifuncfl].mass);
- count++;
+ setflag[i][i] = 1;
+ map[i] = ifuncfl;
+ atom->set_mass(i,funcfl[ifuncfl].mass);
+ count++;
}
}
}
@@ -450,7 +450,7 @@ void PairEAM::read_file(char *filename)
sscanf(line,"%d %lg",&tmp,&file->mass);
fgets(line,MAXLINE,fptr);
sscanf(line,"%d %lg %d %lg %lg",
- &file->nrho,&file->drho,&file->nr,&file->dr,&file->cut);
+ &file->nrho,&file->drho,&file->nr,&file->dr,&file->cut);
}
MPI_Bcast(&file->mass,1,MPI_DOUBLE,0,world);
@@ -518,7 +518,7 @@ void PairEAM::file2array()
// allocate frho arrays
// nfrho = # of funcfl files + 1 for zero array
-
+
nfrho = nfuncfl + 1;
memory->destroy(frho);
memory->create(frho,nfrho,nrho+1,"pair:frho");
@@ -526,7 +526,7 @@ void PairEAM::file2array()
// interpolate each file's frho to a single grid and cutoff
double r,p,cof1,cof2,cof3,cof4;
-
+
n = 0;
for (i = 0; i < nfuncfl; i++) {
Funcfl *file = &funcfl[i];
@@ -542,8 +542,8 @@ void PairEAM::file2array()
cof2 = 0.5*(p*p-1.0)*(p-2.0);
cof3 = -0.5*p*(p+1.0)*(p-2.0);
cof4 = sixth*p*(p*p-1.0);
- frho[n][m] = cof1*file->frho[k-1] + cof2*file->frho[k] +
- cof3*file->frho[k+1] + cof4*file->frho[k+2];
+ frho[n][m] = cof1*file->frho[k-1] + cof2*file->frho[k] +
+ cof3*file->frho[k+1] + cof4*file->frho[k+2];
}
n++;
}
@@ -590,7 +590,7 @@ void PairEAM::file2array()
cof3 = -0.5*p*(p+1.0)*(p-2.0);
cof4 = sixth*p*(p*p-1.0);
rhor[n][m] = cof1*file->rhor[k-1] + cof2*file->rhor[k] +
- cof3*file->rhor[k+1] + cof4*file->rhor[k+2];
+ cof3*file->rhor[k+1] + cof4*file->rhor[k+2];
}
n++;
}
@@ -626,35 +626,35 @@ void PairEAM::file2array()
Funcfl *jfile = &funcfl[j];
for (m = 1; m <= nr; m++) {
- r = (m-1)*dr;
-
- p = r/ifile->dr + 1.0;
- k = static_cast<int> (p);
- k = MIN(k,ifile->nr-2);
- k = MAX(k,2);
- p -= k;
- p = MIN(p,2.0);
- cof1 = -sixth*p*(p-1.0)*(p-2.0);
- cof2 = 0.5*(p*p-1.0)*(p-2.0);
- cof3 = -0.5*p*(p+1.0)*(p-2.0);
- cof4 = sixth*p*(p*p-1.0);
- zri = cof1*ifile->zr[k-1] + cof2*ifile->zr[k] +
- cof3*ifile->zr[k+1] + cof4*ifile->zr[k+2];
-
- p = r/jfile->dr + 1.0;
- k = static_cast<int> (p);
- k = MIN(k,jfile->nr-2);
- k = MAX(k,2);
- p -= k;
- p = MIN(p,2.0);
- cof1 = -sixth*p*(p-1.0)*(p-2.0);
- cof2 = 0.5*(p*p-1.0)*(p-2.0);
- cof3 = -0.5*p*(p+1.0)*(p-2.0);
- cof4 = sixth*p*(p*p-1.0);
- zrj = cof1*jfile->zr[k-1] + cof2*jfile->zr[k] +
- cof3*jfile->zr[k+1] + cof4*jfile->zr[k+2];
-
- z2r[n][m] = 27.2*0.529 * zri*zrj;
+ r = (m-1)*dr;
+
+ p = r/ifile->dr + 1.0;
+ k = static_cast<int> (p);
+ k = MIN(k,ifile->nr-2);
+ k = MAX(k,2);
+ p -= k;
+ p = MIN(p,2.0);
+ cof1 = -sixth*p*(p-1.0)*(p-2.0);
+ cof2 = 0.5*(p*p-1.0)*(p-2.0);
+ cof3 = -0.5*p*(p+1.0)*(p-2.0);
+ cof4 = sixth*p*(p*p-1.0);
+ zri = cof1*ifile->zr[k-1] + cof2*ifile->zr[k] +
+ cof3*ifile->zr[k+1] + cof4*ifile->zr[k+2];
+
+ p = r/jfile->dr + 1.0;
+ k = static_cast<int> (p);
+ k = MIN(k,jfile->nr-2);
+ k = MAX(k,2);
+ p -= k;
+ p = MIN(p,2.0);
+ cof1 = -sixth*p*(p-1.0)*(p-2.0);
+ cof2 = 0.5*(p*p-1.0)*(p-2.0);
+ cof3 = -0.5*p*(p+1.0)*(p-2.0);
+ cof4 = sixth*p*(p*p-1.0);
+ zrj = cof1*jfile->zr[k-1] + cof2*jfile->zr[k] +
+ cof3*jfile->zr[k+1] + cof4*jfile->zr[k+2];
+
+ z2r[n][m] = 27.2*0.529 * zri*zrj;
}
n++;
}
@@ -674,12 +674,12 @@ void PairEAM::file2array()
irow = map[i];
icol = map[j];
if (irow == -1 || icol == -1) {
- type2z2r[i][j] = 0;
- continue;
+ type2z2r[i][j] = 0;
+ continue;
}
if (irow < icol) {
- irow = map[j];
- icol = map[i];
+ irow = map[j];
+ icol = map[i];
}
n = 0;
for (m = 0; m < irow; m++) n += m + 1;
@@ -724,21 +724,21 @@ void PairEAM::interpolate(int n, double delta, double *f, double **spline)
spline[2][5] = 0.5 * (spline[3][6]-spline[1][6]);
spline[n-1][5] = 0.5 * (spline[n][6]-spline[n-2][6]);
spline[n][5] = spline[n][6] - spline[n-1][6];
-
+
for (int m = 3; m <= n-2; m++)
- spline[m][5] = ((spline[m-2][6]-spline[m+2][6]) +
- 8.0*(spline[m+1][6]-spline[m-1][6])) / 12.0;
-
+ spline[m][5] = ((spline[m-2][6]-spline[m+2][6]) +
+ 8.0*(spline[m+1][6]-spline[m-1][6])) / 12.0;
+
for (int m = 1; m <= n-1; m++) {
- spline[m][4] = 3.0*(spline[m+1][6]-spline[m][6]) -
+ spline[m][4] = 3.0*(spline[m+1][6]-spline[m][6]) -
2.0*spline[m][5] - spline[m+1][5];
- spline[m][3] = spline[m][5] + spline[m+1][5] -
+ spline[m][3] = spline[m][5] + spline[m+1][5] -
2.0*(spline[m+1][6]-spline[m][6]);
}
-
+
spline[n][4] = 0.0;
spline[n][3] = 0.0;
-
+
for (int m = 1; m <= n; m++) {
spline[m][2] = spline[m][5]/delta;
spline[m][1] = 2.0*spline[m][4]/delta;
@@ -769,8 +769,8 @@ void PairEAM::grab(FILE *fptr, int n, double *list)
/* ---------------------------------------------------------------------- */
double PairEAM::single(int i, int j, int itype, int jtype,
- double rsq, double factor_coul, double factor_lj,
- double &fforce)
+ double rsq, double factor_coul, double factor_lj,
+ double &fforce)
{
int m;
double r,p,rhoip,rhojp,z2,z2p,recip,phi,phip,psip;
@@ -782,7 +782,7 @@ double PairEAM::single(int i, int j, int itype, int jtype,
m = MIN(m,nr-1);
p -= m;
p = MIN(p,1.0);
-
+
coeff = rhor_spline[type2rhor[itype][jtype]][m];
rhoip = (coeff[0]*p + coeff[1])*p + coeff[2];
coeff = rhor_spline[type2rhor[jtype][itype]][m];
@@ -851,7 +851,7 @@ void PairEAM::unpack_reverse_comm(int n, int *list, double *buf)
}
/* ----------------------------------------------------------------------
- memory usage of local atom-based arrays
+ memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double PairEAM::memory_usage()
diff --git a/src/MANYBODY/pair_eam.h b/src/MANYBODY/pair_eam.h
index 8c4bec4e0386e67122438f5028884f4dc4baccb6..e91e73b5d54d67d6d63c98535dfd6048eb16785f 100644
--- a/src/MANYBODY/pair_eam.h
+++ b/src/MANYBODY/pair_eam.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/MANYBODY/pair_eam_alloy.cpp b/src/MANYBODY/pair_eam_alloy.cpp
index 5b6cd72f51420ff506d5c373cee867a19209df38..0f926a8cb70200ddde3cce6f52764d0164def179 100644
--- a/src/MANYBODY/pair_eam_alloy.cpp
+++ b/src/MANYBODY/pair_eam_alloy.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -96,9 +96,9 @@ void PairEAMAlloy::coeff(int narg, char **arg)
for (i = 1; i <= n; i++) {
for (j = i; j <= n; j++) {
if (map[i] >= 0 && map[j] >= 0) {
- setflag[i][j] = 1;
- if (i == j) atom->set_mass(i,setfl->mass[map[i]]);
- count++;
+ setflag[i][j] = 1;
+ if (i == j) atom->set_mass(i,setfl->mass[map[i]]);
+ count++;
}
}
}
@@ -147,7 +147,7 @@ void PairEAMAlloy::read_file(char *filename)
int nwords = atom->count_words(line);
if (nwords != file->nelements + 1)
error->all(FLERR,"Incorrect element names in EAM potential file");
-
+
char **words = new char*[file->nelements+1];
nwords = 0;
strtok(line," \t\n\r\f");
@@ -164,7 +164,7 @@ void PairEAMAlloy::read_file(char *filename)
if (me == 0) {
fgets(line,MAXLINE,fptr);
sscanf(line,"%d %lg %d %lg %lg",
- &file->nrho,&file->drho,&file->nr,&file->dr,&file->cut);
+ &file->nrho,&file->drho,&file->nr,&file->dr,&file->cut);
}
MPI_Bcast(&file->nrho,1,MPI_INT,0,world);
@@ -177,7 +177,7 @@ void PairEAMAlloy::read_file(char *filename)
memory->create(file->frho,file->nelements,file->nrho+1,"pair:frho");
memory->create(file->rhor,file->nelements,file->nr+1,"pair:rhor");
memory->create(file->z2r,file->nelements,file->nelements,file->nr+1,
- "pair:z2r");
+ "pair:z2r");
int i,j,tmp;
for (i = 0; i < file->nelements; i++) {
@@ -226,7 +226,7 @@ void PairEAMAlloy::file2array()
// allocate frho arrays
// nfrho = # of setfl elements + 1 for zero array
-
+
nfrho = setfl->nelements + 1;
memory->destroy(frho);
memory->create(frho,nfrho,nrho+1,"pair:frho");
@@ -307,12 +307,12 @@ void PairEAMAlloy::file2array()
irow = map[i];
icol = map[j];
if (irow == -1 || icol == -1) {
- type2z2r[i][j] = 0;
- continue;
+ type2z2r[i][j] = 0;
+ continue;
}
if (irow < icol) {
- irow = map[j];
- icol = map[i];
+ irow = map[j];
+ icol = map[i];
}
n = 0;
for (m = 0; m < irow; m++) n += m + 1;
diff --git a/src/MANYBODY/pair_eam_alloy.h b/src/MANYBODY/pair_eam_alloy.h
index 96abbf2efe0c94fdc7f12dee142a6f25e2ce3de6..986f4bbb305f97b7c4f1a094f6b816934bbe0855 100644
--- a/src/MANYBODY/pair_eam_alloy.h
+++ b/src/MANYBODY/pair_eam_alloy.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/MANYBODY/pair_eam_fs.cpp b/src/MANYBODY/pair_eam_fs.cpp
index 0ac0768b9801b9f08ff07e49dfaf258e168402e6..29f787b2965878fb5fbb6af96f64bfed48e35bde 100644
--- a/src/MANYBODY/pair_eam_fs.cpp
+++ b/src/MANYBODY/pair_eam_fs.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -96,9 +96,9 @@ void PairEAMFS::coeff(int narg, char **arg)
for (i = 1; i <= n; i++) {
for (j = i; j <= n; j++) {
if (map[i] >= 0 && map[j] >= 0) {
- setflag[i][j] = 1;
- if (i == j) atom->set_mass(i,fs->mass[map[i]]);
- count++;
+ setflag[i][j] = 1;
+ if (i == j) atom->set_mass(i,fs->mass[map[i]]);
+ count++;
}
}
}
@@ -147,7 +147,7 @@ void PairEAMFS::read_file(char *filename)
int nwords = atom->count_words(line);
if (nwords != file->nelements + 1)
error->all(FLERR,"Incorrect element names in EAM potential file");
-
+
char **words = new char*[file->nelements+1];
nwords = 0;
strtok(line," \t\n\r\f");
@@ -164,7 +164,7 @@ void PairEAMFS::read_file(char *filename)
if (me == 0) {
fgets(line,MAXLINE,fptr);
sscanf(line,"%d %lg %d %lg %lg",
- &file->nrho,&file->drho,&file->nr,&file->dr,&file->cut);
+ &file->nrho,&file->drho,&file->nr,&file->dr,&file->cut);
}
MPI_Bcast(&file->nrho,1,MPI_INT,0,world);
@@ -175,11 +175,11 @@ void PairEAMFS::read_file(char *filename)
file->mass = new double[file->nelements];
memory->create(file->frho,file->nelements,file->nrho+1,
- "pair:frho");
+ "pair:frho");
memory->create(file->rhor,file->nelements,file->nelements,
- file->nr+1,"pair:rhor");
+ file->nr+1,"pair:rhor");
memory->create(file->z2r,file->nelements,file->nelements,
- file->nr+1,"pair:z2r");
+ file->nr+1,"pair:z2r");
int i,j,tmp;
for (i = 0; i < file->nelements; i++) {
@@ -231,7 +231,7 @@ void PairEAMFS::file2array()
// allocate frho arrays
// nfrho = # of fs elements + 1 for zero array
-
+
nfrho = fs->nelements + 1;
memory->destroy(frho);
memory->create(frho,nfrho,nrho+1,"pair:frho");
@@ -316,12 +316,12 @@ void PairEAMFS::file2array()
irow = map[i];
icol = map[j];
if (irow == -1 || icol == -1) {
- type2z2r[i][j] = 0;
- continue;
+ type2z2r[i][j] = 0;
+ continue;
}
if (irow < icol) {
- irow = map[j];
- icol = map[i];
+ irow = map[j];
+ icol = map[i];
}
n = 0;
for (m = 0; m < irow; m++) n += m + 1;
diff --git a/src/MANYBODY/pair_eam_fs.h b/src/MANYBODY/pair_eam_fs.h
index b482e843e32564eb7b4b478a9ce198d62de2dd15..08cc07200d2ed48a582007fe772bc40696a384a1 100644
--- a/src/MANYBODY/pair_eam_fs.h
+++ b/src/MANYBODY/pair_eam_fs.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/MANYBODY/pair_eim.cpp b/src/MANYBODY/pair_eim.cpp
index a86fa2557c4ee3eb3ebdbfc0866e743b1ad07da5..f4418a25d24f29f65f0edf8e1e3a13fef5c5432a 100644
--- a/src/MANYBODY/pair_eim.cpp
+++ b/src/MANYBODY/pair_eim.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -85,7 +85,7 @@ PairEIM::~PairEIM()
for (int i = 0; i < nelements; i++) delete [] elements[i];
delete [] elements;
-
+
deallocate_setfl();
delete [] negativity;
@@ -134,7 +134,7 @@ void PairEIM::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// zero out density
if (newton_pair) {
@@ -172,17 +172,17 @@ void PairEIM::compute(int eflag, int vflag)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cutforcesq[itype][jtype]) {
- p = sqrt(rsq)*rdr + 1.0;
- m = static_cast<int> (p);
- m = MIN(m,nr-1);
- p -= m;
- p = MIN(p,1.0);
- coeff = Fij_spline[type2Fij[itype][jtype]][m];
- rho[i] += ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
- if (newton_pair || j < nlocal) {
- coeff = Fij_spline[type2Fij[jtype][itype]][m];
- rho[j] += ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
- }
+ p = sqrt(rsq)*rdr + 1.0;
+ m = static_cast<int> (p);
+ m = MIN(m,nr-1);
+ p -= m;
+ p = MIN(p,1.0);
+ coeff = Fij_spline[type2Fij[itype][jtype]][m];
+ rho[i] += ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
+ if (newton_pair || j < nlocal) {
+ coeff = Fij_spline[type2Fij[jtype][itype]][m];
+ rho[j] += ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
+ }
}
}
}
@@ -201,17 +201,17 @@ void PairEIM::compute(int eflag, int vflag)
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
-
+
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
jtype = type[j];
-
+
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
-
+
if (rsq < cutforcesq[itype][jtype]) {
p = sqrt(rsq)*rdr + 1.0;
m = static_cast<int> (p);
@@ -221,8 +221,8 @@ void PairEIM::compute(int eflag, int vflag)
coeff = Gij_spline[type2Gij[itype][jtype]][m];
fp[i] += rho[j]*(((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6]);
if (newton_pair || j < nlocal) {
- fp[j] += rho[i]*(((coeff[3]*p + coeff[4])*p + coeff[5])*p +
- coeff[6]);
+ fp[j] += rho[i]*(((coeff[3]*p + coeff[4])*p + coeff[5])*p +
+ coeff[6]);
}
}
}
@@ -373,7 +373,7 @@ void PairEIM::coeff(int narg, char **arg)
nelements = narg - 3 - atom->ntypes;
if (nelements < 1) error->all(FLERR,"Incorrect args for pair coefficients");
elements = new char*[nelements];
-
+
for (i = 0; i < nelements; i++) {
n = strlen(arg[i+2]) + 1;
elements[i] = new char[n];
@@ -412,9 +412,9 @@ void PairEIM::coeff(int narg, char **arg)
for (i = 1; i <= n; i++)
for (j = i; j <= n; j++)
if (map[i] >= 0 && map[j] >= 0) {
- setflag[i][j] = 1;
- if (i == j) atom->set_mass(i,setfl->mass[map[i]]);
- count++;
+ setflag[i][j] = 1;
+ if (i == j) atom->set_mass(i,setfl->mass[map[i]]);
+ count++;
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
@@ -497,7 +497,7 @@ void PairEIM::read_file(char *filename)
for (int i = 0; i < nelements; i++) {
if (me == 0)
if (!grabsingle(fptr,i))
- error->one(FLERR,"Could not grab element entry from EIM potential file");
+ error->one(FLERR,"Could not grab element entry from EIM potential file");
MPI_Bcast(&setfl->ielement[i],1,MPI_INT,0,world);
MPI_Bcast(&setfl->mass[i],1,MPI_DOUBLE,0,world);
MPI_Bcast(&setfl->negativity[i],1,MPI_DOUBLE,0,world);
@@ -515,7 +515,7 @@ void PairEIM::read_file(char *filename)
else ij = nelements*(j+1) - (j+1)*(j+2)/2 + i;
if (me == 0)
if (grabpair(fptr,i,j) == 0)
- error->one(FLERR,"Could not grab pair entry from EIM potential file");
+ error->one(FLERR,"Could not grab pair entry from EIM potential file");
MPI_Bcast(&setfl->rcutphiA[ij],1,MPI_DOUBLE,0,world);
MPI_Bcast(&setfl->rcutphiR[ij],1,MPI_DOUBLE,0,world);
MPI_Bcast(&setfl->Eb[ij],1,MPI_DOUBLE,0,world);
@@ -556,21 +556,21 @@ void PairEIM::read_file(char *filename)
ij = nelements*(i+1) - (i+1)*(i+2)/2 + j;
}
setfl->cuts[i][j] = setfl->rcutphiA[ij];
- if (setfl->cuts[i][j] < setfl->rcutphiR[ij])
- setfl->cuts[i][j] = setfl->rcutphiR[ij];
- if (setfl->cuts[i][j] < setfl->rcutq[ij])
- setfl->cuts[i][j] = setfl->rcutq[ij];
- if (setfl->cuts[i][j] < setfl->rcutsigma[ij])
- setfl->cuts[i][j] = setfl->rcutsigma[ij];
+ if (setfl->cuts[i][j] < setfl->rcutphiR[ij])
+ setfl->cuts[i][j] = setfl->rcutphiR[ij];
+ if (setfl->cuts[i][j] < setfl->rcutq[ij])
+ setfl->cuts[i][j] = setfl->rcutq[ij];
+ if (setfl->cuts[i][j] < setfl->rcutsigma[ij])
+ setfl->cuts[i][j] = setfl->rcutsigma[ij];
}
}
}
-
+
memory->create(setfl->Fij,nelements,nelements,setfl->nr+1,"pair:Fij");
memory->create(setfl->Gij,nelements,nelements,setfl->nr+1,"pair:Gij");
memory->create(setfl->phiij,nelements,nelements,setfl->nr+1,"pair:phiij");
- for (int i = 0; i < nelements; i++)
+ for (int i = 0; i < nelements; i++)
for (int j = 0; j < nelements; j++) {
for (int k = 0; k < setfl->nr; k++) {
if (i > j) {
@@ -701,11 +701,11 @@ void PairEIM::file2array()
}
// add extra Fij of zeroes for non-EIM types to point to (pair hybrid)
-
+
for (m = 1; m <= nr; m++) Fij[nFij-1][m] = 0.0;
-
+
// type2Fij[i][j] = which Fij array (0 to nFij-1) each type pair maps to
- // setfl of Fij arrays
+ // setfl of Fij arrays
// value = n = sum over rows of matrix until reach irow,icol
// if atom type doesn't point to element (non-EIM atom in pair hybrid)
// then map it to last Fij array of zeroes
@@ -793,7 +793,7 @@ void PairEIM::file2array()
for (m = 1; m <= nr; m++) phiij[nphiij-1][m] = 0.0;
- // type2phiij[i][j] = which phiij array (0 to nphiij-1)
+ // type2phiij[i][j] = which phiij array (0 to nphiij-1)
// each type pair maps to
// setfl of phiij arrays only fill lower triangular Nelement matrix
// value = n = sum over rows of lower-triangular matrix until reach irow,icol
@@ -847,8 +847,8 @@ void PairEIM::array2spline()
/* ---------------------------------------------------------------------- */
-void PairEIM::interpolate(int n, double delta, double *f,
- double **spline, double origin)
+void PairEIM::interpolate(int n, double delta, double *f,
+ double **spline, double origin)
{
for (int m = 1; m <= n; m++) spline[m][6] = f[m];
@@ -856,21 +856,21 @@ void PairEIM::interpolate(int n, double delta, double *f,
spline[2][5] = 0.5 * (spline[3][6]-spline[1][6]);
spline[n-1][5] = 0.5 * (spline[n][6]-spline[n-2][6]);
spline[n][5] = 0.0;
-
+
for (int m = 3; m <= n-2; m++)
- spline[m][5] = ((spline[m-2][6]-spline[m+2][6]) +
- 8.0*(spline[m+1][6]-spline[m-1][6])) / 12.0;
-
+ spline[m][5] = ((spline[m-2][6]-spline[m+2][6]) +
+ 8.0*(spline[m+1][6]-spline[m-1][6])) / 12.0;
+
for (int m = 1; m <= n-1; m++) {
- spline[m][4] = 3.0*(spline[m+1][6]-spline[m][6]) -
+ spline[m][4] = 3.0*(spline[m+1][6]-spline[m][6]) -
2.0*spline[m][5] - spline[m+1][5];
- spline[m][3] = spline[m][5] + spline[m+1][5] -
+ spline[m][3] = spline[m][5] + spline[m+1][5] -
2.0*(spline[m+1][6]-spline[m][6]);
}
-
+
spline[n][4] = 0.0;
spline[n][3] = 0.0;
-
+
for (int m = 1; m <= n; m++) {
spline[m][2] = spline[m][5]/delta;
spline[m][1] = 2.0*spline[m][4]/delta;
@@ -992,7 +992,7 @@ double PairEIM::funccutoff(double rp, double rc, double r)
{
double rbig = setfl->rbig;
double rsmall = setfl->rsmall;
-
+
double a = (rsmall-rbig)/(rc-rp)*(r-rp)+rbig;
a = erfc(a);
double b = erfc(rbig);
@@ -1013,9 +1013,9 @@ double PairEIM::funcphi(int i, int j, double r)
else ij = nelements*(j+1) - (j+1)*(j+2)/2 + i;
if (r < 0.2) r = 0.2;
if (setfl->tp[ij] == 1) {
- double a = setfl->Eb[ij]*setfl->alpha[ij] /
+ double a = setfl->Eb[ij]*setfl->alpha[ij] /
(setfl->beta[ij]-setfl->alpha[ij]);
- double b = setfl->Eb[ij]*setfl->beta[ij] /
+ double b = setfl->Eb[ij]*setfl->beta[ij] /
(setfl->beta[ij]-setfl->alpha[ij]);
if (r < setfl->rcutphiA[ij]) {
value -= a*exp(-setfl->beta[ij]*(r/setfl->r0[ij]-1.0))*
@@ -1085,7 +1085,7 @@ double PairEIM::funccoul(int i, int j, double r)
int PairEIM::pack_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
{
int i,j,m;
-
+
m = 0;
if (rhofp == 1) {
for (i = 0; i < n; i++) {
@@ -1107,7 +1107,7 @@ int PairEIM::pack_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
void PairEIM::unpack_comm(int n, int first, double *buf)
{
int i,m,last;
-
+
m = 0;
last = first + n;
if (rhofp == 1) {
@@ -1148,7 +1148,7 @@ void PairEIM::unpack_reverse_comm(int n, int *list, double *buf)
rho[j] += buf[m++];
}
}
- if (rhofp == 2) {
+ if (rhofp == 2) {
for (i = 0; i < n; i++) {
j = list[i];
fp[j] += buf[m++];
@@ -1157,7 +1157,7 @@ void PairEIM::unpack_reverse_comm(int n, int *list, double *buf)
}
/* ----------------------------------------------------------------------
- memory usage of local atom-based arrays
+ memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double PairEIM::memory_usage()
diff --git a/src/MANYBODY/pair_eim.h b/src/MANYBODY/pair_eim.h
index f34cc6cc3f4b1e2701d97378b4d97e6e79506282..687c61564b1574375dd4346c0bd7140f63ca35c6 100644
--- a/src/MANYBODY/pair_eim.h
+++ b/src/MANYBODY/pair_eim.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -71,7 +71,7 @@ class PairEIM : public Pair {
int nFij,nGij,nphiij;
double **Fij,**Gij,**phiij;
int **type2Fij,**type2Gij,**type2phiij;
-
+
// potentials in spline form used for force computation
double dr,rdr;
@@ -81,7 +81,7 @@ class PairEIM : public Pair {
void allocate();
void array2spline();
void interpolate(int, double, double *, double **, double);
- int grabglobal(FILE *);
+ int grabglobal(FILE *);
int grabsingle(FILE *, int);
int grabpair(FILE *, int, int);
diff --git a/src/MANYBODY/pair_lcbop.cpp b/src/MANYBODY/pair_lcbop.cpp
index 882cf1686d4c1b00c87137a2663c3ca7dd964a16..97c1bfef0bc9199f321429fec56ab4a3e290419e 100644
--- a/src/MANYBODY/pair_lcbop.cpp
+++ b/src/MANYBODY/pair_lcbop.cpp
@@ -678,11 +678,11 @@ double PairLCBOP::bondorder(int i, int j, double rij[3],
dNconj_dNij = 0;
dNconj_dNji = 0;
dNconj_dNel = 0;
- } else {
+ } else {
dNconj_dNij = (
( (Nji+1)*(Nij_el + Nji_el)-4)
- Nconj*( (Nji+1)*(3-2*Nij) + Nji*(3-Nji) )
- ) /den_Nconj;
+ ) /den_Nconj;
dNconj_dNji = (
( (Nij+1)*(Nji_el + Nij_el)-4)
- Nconj*( (Nij+1)*(3-2*Nji) + Nij*(3-Nij) )
diff --git a/src/MANYBODY/pair_rebo.cpp b/src/MANYBODY/pair_rebo.cpp
index efda8c2c9e18d7f6fa0983bc0d38263f86ae8737..f2ca30df7fcfc204ef3408d52cae643346acd093 100644
--- a/src/MANYBODY/pair_rebo.cpp
+++ b/src/MANYBODY/pair_rebo.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/MANYBODY/pair_rebo.h b/src/MANYBODY/pair_rebo.h
index aefe145b2657905b99542536f536582d91e6ccb3..75e9d8037043de8890b9ff348cdaf5295503d44b 100644
--- a/src/MANYBODY/pair_rebo.h
+++ b/src/MANYBODY/pair_rebo.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/MANYBODY/pair_sw.cpp b/src/MANYBODY/pair_sw.cpp
index deae3cb26ff91b623121a2bdf4fdc3ef53224adc..7af668d37fb57c8ed027235f36940cfebc2b0c17 100755
--- a/src/MANYBODY/pair_sw.cpp
+++ b/src/MANYBODY/pair_sw.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -118,13 +118,13 @@ void PairSW::compute(int eflag, int vflag)
jtag = tag[j];
if (itag > jtag) {
- if ((itag+jtag) % 2 == 0) continue;
+ if ((itag+jtag) % 2 == 0) continue;
} else if (itag < jtag) {
- if ((itag+jtag) % 2 == 1) continue;
+ if ((itag+jtag) % 2 == 1) continue;
} else {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
- if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
+ if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
}
jtype = map[type[j]];
@@ -147,7 +147,7 @@ void PairSW::compute(int eflag, int vflag)
f[j][2] -= delz*fpair;
if (evflag) ev_tally(i,j,nlocal,newton_pair,
- evdwl,0.0,fpair,delx,dely,delz);
+ evdwl,0.0,fpair,delx,dely,delz);
}
jnumm1 = jnum - 1;
@@ -164,32 +164,32 @@ void PairSW::compute(int eflag, int vflag)
if (rsq1 > params[ijparam].cutsq) continue;
for (kk = jj+1; kk < jnum; kk++) {
- k = jlist[kk];
- k &= NEIGHMASK;
- ktype = map[type[k]];
- ikparam = elem2param[itype][ktype][ktype];
- ijkparam = elem2param[itype][jtype][ktype];
-
- delr2[0] = x[k][0] - xtmp;
- delr2[1] = x[k][1] - ytmp;
- delr2[2] = x[k][2] - ztmp;
- rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
- if (rsq2 > params[ikparam].cutsq) continue;
-
- threebody(¶ms[ijparam],¶ms[ikparam],¶ms[ijkparam],
- rsq1,rsq2,delr1,delr2,fj,fk,eflag,evdwl);
-
- f[i][0] -= fj[0] + fk[0];
- f[i][1] -= fj[1] + fk[1];
- f[i][2] -= fj[2] + fk[2];
- f[j][0] += fj[0];
- f[j][1] += fj[1];
- f[j][2] += fj[2];
- f[k][0] += fk[0];
- f[k][1] += fk[1];
- f[k][2] += fk[2];
-
- if (evflag) ev_tally3(i,j,k,evdwl,0.0,fj,fk,delr1,delr2);
+ k = jlist[kk];
+ k &= NEIGHMASK;
+ ktype = map[type[k]];
+ ikparam = elem2param[itype][ktype][ktype];
+ ijkparam = elem2param[itype][jtype][ktype];
+
+ delr2[0] = x[k][0] - xtmp;
+ delr2[1] = x[k][1] - ytmp;
+ delr2[2] = x[k][2] - ztmp;
+ rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
+ if (rsq2 > params[ikparam].cutsq) continue;
+
+ threebody(¶ms[ijparam],¶ms[ikparam],¶ms[ijkparam],
+ rsq1,rsq2,delr1,delr2,fj,fk,eflag,evdwl);
+
+ f[i][0] -= fj[0] + fk[0];
+ f[i][1] -= fj[1] + fk[1];
+ f[i][2] -= fj[2] + fk[2];
+ f[j][0] += fj[0];
+ f[j][1] += fj[1];
+ f[j][2] += fj[2];
+ f[k][0] += fk[0];
+ f[k][1] += fk[1];
+ f[k][2] += fk[2];
+
+ if (evflag) ev_tally3(i,j,k,evdwl,0.0,fj,fk,delr1,delr2);
}
}
}
@@ -211,7 +211,7 @@ void PairSW::allocate()
}
/* ----------------------------------------------------------------------
- global settings
+ global settings
------------------------------------------------------------------------- */
void PairSW::settings(int narg, char **arg)
@@ -267,7 +267,7 @@ void PairSW::coeff(int narg, char **arg)
}
// read potential file and initialize potential parameters
-
+
read_file(arg[2]);
setup();
@@ -284,8 +284,8 @@ void PairSW::coeff(int narg, char **arg)
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
if (map[i] >= 0 && map[j] >= 0) {
- setflag[i][j] = 1;
- count++;
+ setflag[i][j] = 1;
+ count++;
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
@@ -355,8 +355,8 @@ void PairSW::read_file(char *file)
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fp);
if (ptr == NULL) {
- eof = 1;
- fclose(fp);
+ eof = 1;
+ fclose(fp);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
@@ -377,8 +377,8 @@ void PairSW::read_file(char *file)
if (comm->me == 0) {
ptr = fgets(&line[n],MAXLINE-n,fp);
if (ptr == NULL) {
- eof = 1;
- fclose(fp);
+ eof = 1;
+ fclose(fp);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
@@ -417,7 +417,7 @@ void PairSW::read_file(char *file)
if (nparams == maxparam) {
maxparam += DELTA;
params = (Param *) memory->srealloc(params,maxparam*sizeof(Param),
- "pair:params");
+ "pair:params");
}
params[nparams].ielement = ielement;
@@ -435,11 +435,11 @@ void PairSW::read_file(char *file)
params[nparams].powerq = atof(words[12]);
params[nparams].tol = atof(words[13]);
- if (params[nparams].epsilon < 0.0 || params[nparams].sigma < 0.0 ||
- params[nparams].littlea < 0.0 || params[nparams].lambda < 0.0 ||
- params[nparams].gamma < 0.0 || params[nparams].biga < 0.0 ||
- params[nparams].bigb < 0.0 || params[nparams].powerp < 0.0 ||
- params[nparams].powerq < 0.0 || params[nparams].tol < 0.0)
+ if (params[nparams].epsilon < 0.0 || params[nparams].sigma < 0.0 ||
+ params[nparams].littlea < 0.0 || params[nparams].lambda < 0.0 ||
+ params[nparams].gamma < 0.0 || params[nparams].biga < 0.0 ||
+ params[nparams].bigb < 0.0 || params[nparams].powerp < 0.0 ||
+ params[nparams].powerq < 0.0 || params[nparams].tol < 0.0)
error->all(FLERR,"Illegal Stillinger-Weber parameter");
nparams++;
@@ -465,16 +465,16 @@ void PairSW::setup()
for (i = 0; i < nelements; i++)
for (j = 0; j < nelements; j++)
for (k = 0; k < nelements; k++) {
- n = -1;
- for (m = 0; m < nparams; m++) {
- if (i == params[m].ielement && j == params[m].jelement &&
- k == params[m].kelement) {
- if (n >= 0) error->all(FLERR,"Potential file has duplicate entry");
- n = m;
- }
- }
- if (n < 0) error->all(FLERR,"Potential file is missing an entry");
- elem2param[i][j][k] = n;
+ n = -1;
+ for (m = 0; m < nparams; m++) {
+ if (i == params[m].ielement && j == params[m].jelement &&
+ k == params[m].kelement) {
+ if (n >= 0) error->all(FLERR,"Potential file has duplicate entry");
+ n = m;
+ }
+ }
+ if (n < 0) error->all(FLERR,"Potential file is missing an entry");
+ elem2param[i][j][k] = n;
}
@@ -482,7 +482,7 @@ void PairSW::setup()
// set cutsq using shortcut to reduce neighbor list for accelerated
// calculations. cut must remain unchanged as it is a potential parameter
- // (cut = a*sigma)
+ // (cut = a*sigma)
for (m = 0; m < nparams; m++) {
params[m].cut = params[m].sigma*params[m].littlea;
@@ -493,24 +493,24 @@ void PairSW::setup()
if (params[m].gamma < 1.0)
rtmp = rtmp +
params[m].gamma * params[m].sigma / log(params[m].tol);
- else rtmp = rtmp +
- params[m].sigma / log(params[m].tol);
+ else rtmp = rtmp +
+ params[m].sigma / log(params[m].tol);
}
params[m].cutsq = rtmp * rtmp;
params[m].sigma_gamma = params[m].sigma*params[m].gamma;
params[m].lambda_epsilon = params[m].lambda*params[m].epsilon;
params[m].lambda_epsilon2 = 2.0*params[m].lambda*params[m].epsilon;
- params[m].c1 = params[m].biga*params[m].epsilon *
- params[m].powerp*params[m].bigb *
+ params[m].c1 = params[m].biga*params[m].epsilon *
+ params[m].powerp*params[m].bigb *
pow(params[m].sigma,params[m].powerp);
- params[m].c2 = params[m].biga*params[m].epsilon*params[m].powerq *
+ params[m].c2 = params[m].biga*params[m].epsilon*params[m].powerq *
pow(params[m].sigma,params[m].powerq);
- params[m].c3 = params[m].biga*params[m].epsilon*params[m].bigb *
+ params[m].c3 = params[m].biga*params[m].epsilon*params[m].bigb *
pow(params[m].sigma,params[m].powerp+1.0);
- params[m].c4 = params[m].biga*params[m].epsilon *
+ params[m].c4 = params[m].biga*params[m].epsilon *
pow(params[m].sigma,params[m].powerq+1.0);
- params[m].c5 = params[m].biga*params[m].epsilon*params[m].bigb *
+ params[m].c5 = params[m].biga*params[m].epsilon*params[m].bigb *
pow(params[m].sigma,params[m].powerp);
params[m].c6 = params[m].biga*params[m].epsilon *
pow(params[m].sigma,params[m].powerq);
@@ -523,12 +523,12 @@ void PairSW::setup()
rtmp = sqrt(params[m].cutsq);
if (rtmp > cutmax) cutmax = rtmp;
}
-}
+}
/* ---------------------------------------------------------------------- */
void PairSW::twobody(Param *param, double rsq, double &fforce,
- int eflag, double &eng)
+ int eflag, double &eng)
{
double r,rinvsq,rp,rq,rainv,rainvsq,expsrainv;
@@ -537,19 +537,19 @@ void PairSW::twobody(Param *param, double rsq, double &fforce,
rp = pow(r,-param->powerp);
rq = pow(r,-param->powerq);
rainv = 1.0 / (r - param->cut);
- rainvsq = rainv*rainv*r;
+ rainvsq = rainv*rainv*r;
expsrainv = exp(param->sigma * rainv);
fforce = (param->c1*rp - param->c2*rq +
- (param->c3*rp -param->c4*rq) * rainvsq) * expsrainv * rinvsq;
+ (param->c3*rp -param->c4*rq) * rainvsq) * expsrainv * rinvsq;
if (eflag) eng = (param->c5*rp - param->c6*rq) * expsrainv;
}
/* ---------------------------------------------------------------------- */
void PairSW::threebody(Param *paramij, Param *paramik, Param *paramijk,
- double rsq1, double rsq2,
- double *delr1, double *delr2,
- double *fj, double *fk, int eflag, double &eng)
+ double rsq1, double rsq2,
+ double *delr1, double *delr2,
+ double *fj, double *fk, int eflag, double &eng)
{
double r1,rinvsq1,rainv1,gsrainv1,gsrainvsq1,expgsrainv1;
double r2,rinvsq2,rainv2,gsrainv2,gsrainvsq2,expgsrainv2;
@@ -560,14 +560,14 @@ void PairSW::threebody(Param *paramij, Param *paramik, Param *paramijk,
rinvsq1 = 1.0/rsq1;
rainv1 = 1.0/(r1 - paramij->cut);
gsrainv1 = paramij->sigma_gamma * rainv1;
- gsrainvsq1 = gsrainv1*rainv1/r1;
+ gsrainvsq1 = gsrainv1*rainv1/r1;
expgsrainv1 = exp(gsrainv1);
r2 = sqrt(rsq2);
rinvsq2 = 1.0/rsq2;
rainv2 = 1.0/(r2 - paramik->cut);
gsrainv2 = paramik->sigma_gamma * rainv2;
- gsrainvsq2 = gsrainv2*rainv2/r2;
+ gsrainvsq2 = gsrainv2*rainv2/r2;
expgsrainv2 = exp(gsrainv2);
rinv12 = 1.0/(r1*r2);
@@ -587,11 +587,11 @@ void PairSW::threebody(Param *paramij, Param *paramik, Param *paramijk,
facang12 = rinv12*facang;
csfacang = cs*facang;
csfac1 = rinvsq1*csfacang;
-
+
fj[0] = delr1[0]*(frad1+csfac1)-delr2[0]*facang12;
fj[1] = delr1[1]*(frad1+csfac1)-delr2[1]*facang12;
fj[2] = delr1[2]*(frad1+csfac1)-delr2[2]*facang12;
-
+
csfac2 = rinvsq2*csfacang;
fk[0] = delr2[0]*(frad2+csfac2)-delr1[0]*facang12;
@@ -600,4 +600,3 @@ void PairSW::threebody(Param *paramij, Param *paramik, Param *paramijk,
if (eflag) eng = facrad;
}
-
diff --git a/src/MANYBODY/pair_sw.h b/src/MANYBODY/pair_sw.h
index 76b3d5528f7e68d9521e3d758f49a2f4b5399bb7..76db031dae6f44759c6b51ef063e00756774a606 100755
--- a/src/MANYBODY/pair_sw.h
+++ b/src/MANYBODY/pair_sw.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -46,7 +46,7 @@ class PairSW : public Pair {
double c1,c2,c3,c4,c5,c6;
int ielement,jelement,kelement;
};
-
+
double cutmax; // max cutoff for all elements
int nelements; // # of unique elements
char **elements; // names of unique elements
@@ -61,7 +61,7 @@ class PairSW : public Pair {
void setup();
void twobody(Param *, double, double &, int, double &);
void threebody(Param *, Param *, Param *, double, double, double *, double *,
- double *, double *, int, double &);
+ double *, double *, int, double &);
};
}
diff --git a/src/MANYBODY/pair_tersoff.cpp b/src/MANYBODY/pair_tersoff.cpp
index f284f12fd1368aad0636114d6398f11a0920f934..6c3c006b12e4947d8516e00c0484e16240730eae 100755
--- a/src/MANYBODY/pair_tersoff.cpp
+++ b/src/MANYBODY/pair_tersoff.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -120,13 +120,13 @@ void PairTersoff::compute(int eflag, int vflag)
jtag = tag[j];
if (itag > jtag) {
- if ((itag+jtag) % 2 == 0) continue;
+ if ((itag+jtag) % 2 == 0) continue;
} else if (itag < jtag) {
- if ((itag+jtag) % 2 == 1) continue;
+ if ((itag+jtag) % 2 == 1) continue;
} else {
- if (x[j][2] < x[i][2]) continue;
- if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
- if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
+ if (x[j][2] < x[i][2]) continue;
+ if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
+ if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
}
jtype = map[type[j]];
@@ -149,7 +149,7 @@ void PairTersoff::compute(int eflag, int vflag)
f[j][2] -= delz*fpair;
if (evflag) ev_tally(i,j,nlocal,newton_pair,
- evdwl,0.0,fpair,delx,dely,delz);
+ evdwl,0.0,fpair,delx,dely,delz);
}
// three-body interactions
@@ -172,19 +172,19 @@ void PairTersoff::compute(int eflag, int vflag)
zeta_ij = 0.0;
for (kk = 0; kk < jnum; kk++) {
- if (jj == kk) continue;
- k = jlist[kk];
- k &= NEIGHMASK;
- ktype = map[type[k]];
- iparam_ijk = elem2param[itype][jtype][ktype];
-
- delr2[0] = x[k][0] - xtmp;
- delr2[1] = x[k][1] - ytmp;
- delr2[2] = x[k][2] - ztmp;
- rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
- if (rsq2 > params[iparam_ijk].cutsq) continue;
-
- zeta_ij += zeta(¶ms[iparam_ijk],rsq1,rsq2,delr1,delr2);
+ if (jj == kk) continue;
+ k = jlist[kk];
+ k &= NEIGHMASK;
+ ktype = map[type[k]];
+ iparam_ijk = elem2param[itype][jtype][ktype];
+
+ delr2[0] = x[k][0] - xtmp;
+ delr2[1] = x[k][1] - ytmp;
+ delr2[2] = x[k][2] - ztmp;
+ rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
+ if (rsq2 > params[iparam_ijk].cutsq) continue;
+
+ zeta_ij += zeta(¶ms[iparam_ijk],rsq1,rsq2,delr1,delr2);
}
// pairwise force due to zeta
@@ -199,37 +199,37 @@ void PairTersoff::compute(int eflag, int vflag)
f[j][2] -= delr1[2]*fpair;
if (evflag) ev_tally(i,j,nlocal,newton_pair,
- evdwl,0.0,-fpair,-delr1[0],-delr1[1],-delr1[2]);
+ evdwl,0.0,-fpair,-delr1[0],-delr1[1],-delr1[2]);
// attractive term via loop over k
for (kk = 0; kk < jnum; kk++) {
- if (jj == kk) continue;
- k = jlist[kk];
- k &= NEIGHMASK;
- ktype = map[type[k]];
- iparam_ijk = elem2param[itype][jtype][ktype];
-
- delr2[0] = x[k][0] - xtmp;
- delr2[1] = x[k][1] - ytmp;
- delr2[2] = x[k][2] - ztmp;
- rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
- if (rsq2 > params[iparam_ijk].cutsq) continue;
-
- attractive(¶ms[iparam_ijk],prefactor,
- rsq1,rsq2,delr1,delr2,fi,fj,fk);
-
- f[i][0] += fi[0];
- f[i][1] += fi[1];
- f[i][2] += fi[2];
- f[j][0] += fj[0];
- f[j][1] += fj[1];
- f[j][2] += fj[2];
- f[k][0] += fk[0];
- f[k][1] += fk[1];
- f[k][2] += fk[2];
-
- if (vflag_atom) v_tally3(i,j,k,fj,fk,delr1,delr2);
+ if (jj == kk) continue;
+ k = jlist[kk];
+ k &= NEIGHMASK;
+ ktype = map[type[k]];
+ iparam_ijk = elem2param[itype][jtype][ktype];
+
+ delr2[0] = x[k][0] - xtmp;
+ delr2[1] = x[k][1] - ytmp;
+ delr2[2] = x[k][2] - ztmp;
+ rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
+ if (rsq2 > params[iparam_ijk].cutsq) continue;
+
+ attractive(¶ms[iparam_ijk],prefactor,
+ rsq1,rsq2,delr1,delr2,fi,fj,fk);
+
+ f[i][0] += fi[0];
+ f[i][1] += fi[1];
+ f[i][2] += fi[2];
+ f[j][0] += fj[0];
+ f[j][1] += fj[1];
+ f[j][2] += fj[2];
+ f[k][0] += fk[0];
+ f[k][1] += fk[1];
+ f[k][2] += fk[2];
+
+ if (vflag_atom) v_tally3(i,j,k,fj,fk,delr1,delr2);
}
}
}
@@ -251,7 +251,7 @@ void PairTersoff::allocate()
}
/* ----------------------------------------------------------------------
- global settings
+ global settings
------------------------------------------------------------------------- */
void PairTersoff::settings(int narg, char **arg)
@@ -307,7 +307,7 @@ void PairTersoff::coeff(int narg, char **arg)
}
// read potential file and initialize potential parameters
-
+
read_file(arg[2]);
setup();
@@ -324,8 +324,8 @@ void PairTersoff::coeff(int narg, char **arg)
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
if (map[i] >= 0 && map[j] >= 0) {
- setflag[i][j] = 1;
- count++;
+ setflag[i][j] = 1;
+ count++;
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
@@ -394,8 +394,8 @@ void PairTersoff::read_file(char *file)
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fp);
if (ptr == NULL) {
- eof = 1;
- fclose(fp);
+ eof = 1;
+ fclose(fp);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
@@ -416,8 +416,8 @@ void PairTersoff::read_file(char *file)
if (comm->me == 0) {
ptr = fgets(&line[n],MAXLINE-n,fp);
if (ptr == NULL) {
- eof = 1;
- fclose(fp);
+ eof = 1;
+ fclose(fp);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
@@ -456,7 +456,7 @@ void PairTersoff::read_file(char *file)
if (nparams == maxparam) {
maxparam += DELTA;
params = (Param *) memory->srealloc(params,maxparam*sizeof(Param),
- "pair:params");
+ "pair:params");
}
params[nparams].ielement = ielement;
@@ -481,15 +481,15 @@ void PairTersoff::read_file(char *file)
params[nparams].powermint = int(params[nparams].powerm);
- if (params[nparams].c < 0.0 || params[nparams].d < 0.0 ||
- params[nparams].powern < 0.0 || params[nparams].beta < 0.0 ||
- params[nparams].lam2 < 0.0 || params[nparams].bigb < 0.0 ||
- params[nparams].bigr < 0.0 ||params[nparams].bigd < 0.0 ||
- params[nparams].bigd > params[nparams].bigr ||
- params[nparams].lam1 < 0.0 || params[nparams].biga < 0.0 ||
- params[nparams].powerm - params[nparams].powermint != 0.0 ||
+ if (params[nparams].c < 0.0 || params[nparams].d < 0.0 ||
+ params[nparams].powern < 0.0 || params[nparams].beta < 0.0 ||
+ params[nparams].lam2 < 0.0 || params[nparams].bigb < 0.0 ||
+ params[nparams].bigr < 0.0 ||params[nparams].bigd < 0.0 ||
+ params[nparams].bigd > params[nparams].bigr ||
+ params[nparams].lam1 < 0.0 || params[nparams].biga < 0.0 ||
+ params[nparams].powerm - params[nparams].powermint != 0.0 ||
(params[nparams].powermint != 3 && params[nparams].powermint != 1) ||
- params[nparams].gamma < 0.0)
+ params[nparams].gamma < 0.0)
error->all(FLERR,"Illegal Tersoff parameter");
nparams++;
@@ -514,16 +514,16 @@ void PairTersoff::setup()
for (i = 0; i < nelements; i++)
for (j = 0; j < nelements; j++)
for (k = 0; k < nelements; k++) {
- n = -1;
- for (m = 0; m < nparams; m++) {
- if (i == params[m].ielement && j == params[m].jelement &&
- k == params[m].kelement) {
- if (n >= 0) error->all(FLERR,"Potential file has duplicate entry");
- n = m;
- }
- }
- if (n < 0) error->all(FLERR,"Potential file is missing an entry");
- elem2param[i][j][k] = n;
+ n = -1;
+ for (m = 0; m < nparams; m++) {
+ if (i == params[m].ielement && j == params[m].jelement &&
+ k == params[m].kelement) {
+ if (n >= 0) error->all(FLERR,"Potential file has duplicate entry");
+ n = m;
+ }
+ }
+ if (n < 0) error->all(FLERR,"Potential file is missing an entry");
+ elem2param[i][j][k] = n;
}
@@ -544,12 +544,12 @@ void PairTersoff::setup()
cutmax = 0.0;
for (m = 0; m < nparams; m++)
if (params[m].cut > cutmax) cutmax = params[m].cut;
-}
+}
/* ---------------------------------------------------------------------- */
void PairTersoff::repulsive(Param *param, double rsq, double &fforce,
- int eflag, double &eng)
+ int eflag, double &eng)
{
double r,tmp_fc,tmp_fc_d,tmp_exp;
@@ -564,14 +564,14 @@ void PairTersoff::repulsive(Param *param, double rsq, double &fforce,
/* ---------------------------------------------------------------------- */
double PairTersoff::zeta(Param *param, double rsqij, double rsqik,
- double *delrij, double *delrik)
+ double *delrij, double *delrik)
{
double rij,rik,costheta,arg,ex_delr;
rij = sqrt(rsqij);
rik = sqrt(rsqik);
- costheta = (delrij[0]*delrik[0] + delrij[1]*delrik[1] +
- delrij[2]*delrik[2]) / (rij*rik);
+ costheta = (delrij[0]*delrik[0] + delrij[1]*delrik[1] +
+ delrij[2]*delrik[2]) / (rij*rik);
if (param->powermint == 3) arg = pow(param->lam3 * (rij-rik),3.0);
else arg = param->lam3 * (rij-rik);
@@ -579,15 +579,15 @@ double PairTersoff::zeta(Param *param, double rsqij, double rsqik,
if (arg > 69.0776) ex_delr = 1.e30;
else if (arg < -69.0776) ex_delr = 0.0;
else ex_delr = exp(arg);
-
+
return ters_fc(rik,param) * ters_gijk(costheta,param) * ex_delr;
}
/* ---------------------------------------------------------------------- */
void PairTersoff::force_zeta(Param *param, double rsq, double zeta_ij,
- double &fforce, double &prefactor,
- int eflag, double &eng)
+ double &fforce, double &prefactor,
+ int eflag, double &eng)
{
double r,fa,fa_d,bij;
@@ -607,9 +607,9 @@ void PairTersoff::force_zeta(Param *param, double rsq, double zeta_ij,
------------------------------------------------------------------------- */
void PairTersoff::attractive(Param *param, double prefactor,
- double rsqij, double rsqik,
- double *delrij, double *delrik,
- double *fi, double *fj, double *fk)
+ double rsqij, double rsqik,
+ double *delrij, double *delrik,
+ double *fi, double *fj, double *fk)
{
double rij_hat[3],rik_hat[3];
double rij,rijinv,rik,rikinv;
@@ -617,7 +617,7 @@ void PairTersoff::attractive(Param *param, double prefactor,
rij = sqrt(rsqij);
rijinv = 1.0/rij;
vec3_scale(rijinv,delrij,rij_hat);
-
+
rik = sqrt(rsqik);
rikinv = 1.0/rik;
vec3_scale(rikinv,delrik,rik_hat);
@@ -631,7 +631,7 @@ double PairTersoff::ters_fc(double r, Param *param)
{
double ters_R = param->bigr;
double ters_D = param->bigd;
-
+
if (r < ters_R-ters_D) return 1.0;
if (r > ters_R+ters_D) return 0.0;
return 0.5*(1.0 - sin(MY_PI2*(r - ters_R)/ters_D));
@@ -643,7 +643,7 @@ double PairTersoff::ters_fc_d(double r, Param *param)
{
double ters_R = param->bigr;
double ters_D = param->bigd;
-
+
if (r < ters_R-ters_D) return 0.0;
if (r > ters_R+ters_D) return 0.0;
return -(MY_PI4/ters_D) * cos(MY_PI2*(r - ters_R)/ters_D);
@@ -655,7 +655,7 @@ double PairTersoff::ters_fa(double r, Param *param)
{
if (r > param->bigr + param->bigd) return 0.0;
return -param->bigb * exp(-param->lam2 * r) * ters_fc(r,param);
-}
+}
/* ---------------------------------------------------------------------- */
@@ -687,13 +687,13 @@ double PairTersoff::ters_bij_d(double zeta, Param *param)
double tmp = param->beta * zeta;
if (tmp > param->c1) return param->beta * -0.5*pow(tmp,-1.5);
if (tmp > param->c2)
- return param->beta * (-0.5*pow(tmp,-1.5) *
- (1.0 - 0.5*(1.0 + 1.0/(2.0*param->powern)) *
- pow(tmp,-param->powern)));
+ return param->beta * (-0.5*pow(tmp,-1.5) *
+ (1.0 - 0.5*(1.0 + 1.0/(2.0*param->powern)) *
+ pow(tmp,-param->powern)));
if (tmp < param->c4) return 0.0;
if (tmp < param->c3)
return -0.5*param->beta * pow(tmp,param->powern-1.0);
-
+
double tmp_n = pow(tmp,param->powern);
return -0.5 * pow(1.0+tmp_n, -1.0-(1.0/(2.0*param->powern)))*tmp_n / zeta;
}
@@ -701,10 +701,10 @@ double PairTersoff::ters_bij_d(double zeta, Param *param)
/* ---------------------------------------------------------------------- */
void PairTersoff::ters_zetaterm_d(double prefactor,
- double *rij_hat, double rij,
- double *rik_hat, double rik,
- double *dri, double *drj, double *drk,
- Param *param)
+ double *rij_hat, double rij,
+ double *rik_hat, double rik,
+ double *dri, double *drj, double *drk,
+ Param *param)
{
double gijk,gijk_d,ex_delr,ex_delr_d,fc,dfc,cos_theta,tmp;
double dcosdri[3],dcosdrj[3],dcosdrk[3];
@@ -760,8 +760,8 @@ void PairTersoff::ters_zetaterm_d(double prefactor,
/* ---------------------------------------------------------------------- */
void PairTersoff::costheta_d(double *rij_hat, double rij,
- double *rik_hat, double rik,
- double *dri, double *drj, double *drk)
+ double *rik_hat, double rik,
+ double *dri, double *drj, double *drk)
{
// first element is devative wrt Ri, second wrt Rj, third wrt Rk
diff --git a/src/MANYBODY/pair_tersoff.h b/src/MANYBODY/pair_tersoff.h
index b5902abba89a9ec98a8cb0ea78db743783a5fe2b..a2913b22f30fc7bb49eab39d37f59c40d1d906da 100755
--- a/src/MANYBODY/pair_tersoff.h
+++ b/src/MANYBODY/pair_tersoff.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -48,7 +48,7 @@ class PairTersoff : public Pair {
double Z_i,Z_j;
double ZBLcut,ZBLexpscale;
};
-
+
Param *params; // parameter set for an I-J-K interaction
char **elements; // names of unique elements
int ***elem2param; // mapping from element triplets to parameters
@@ -63,10 +63,10 @@ class PairTersoff : public Pair {
void setup();
virtual void repulsive(Param *, double, double &, int, double &);
double zeta(Param *, double, double, double *, double *);
- virtual void force_zeta(Param *, double, double, double &,
- double &, int, double &);
+ virtual void force_zeta(Param *, double, double, double &,
+ double &, int, double &);
void attractive(Param *, double, double, double, double *, double *,
- double *, double *, double *);
+ double *, double *, double *);
double ters_fc(double, Param *);
double ters_fc_d(double, Param *);
@@ -76,14 +76,14 @@ class PairTersoff : public Pair {
double ters_bij_d(double, Param *);
void ters_zetaterm_d(double, double *, double, double *, double,
- double *, double *, double *, Param *);
+ double *, double *, double *, Param *);
void costheta_d(double *, double, double *, double,
- double *, double *, double *);
+ double *, double *, double *);
// inlined functions for efficiency
- inline double ters_gijk(const double costheta,
- const Param * const param) const {
+ inline double ters_gijk(const double costheta,
+ const Param * const param) const {
const double ters_c = param->c * param->c;
const double ters_d = param->d * param->d;
const double hcth = param->h - costheta;
@@ -91,8 +91,8 @@ class PairTersoff : public Pair {
return param->gamma*(1.0 + ters_c/ters_d - ters_c / (ters_d + hcth*hcth));
}
- inline double ters_gijk_d(const double costheta,
- const Param * const param) const {
+ inline double ters_gijk_d(const double costheta,
+ const Param * const param) const {
const double ters_c = param->c * param->c;
const double ters_d = param->d * param->d;
const double hcth = param->h - costheta;
@@ -105,18 +105,18 @@ class PairTersoff : public Pair {
return x[0]*y[0] + x[1]*y[1] + x[2]*y[2];
}
- inline void vec3_add(const double x[3], const double y[3],
- double * const z) const {
+ inline void vec3_add(const double x[3], const double y[3],
+ double * const z) const {
z[0] = x[0]+y[0]; z[1] = x[1]+y[1]; z[2] = x[2]+y[2];
}
inline void vec3_scale(const double k, const double x[3],
- double y[3]) const {
+ double y[3]) const {
y[0] = k*x[0]; y[1] = k*x[1]; y[2] = k*x[2];
}
- inline void vec3_scaleadd(const double k, const double x[3],
- const double y[3], double * const z) const {
+ inline void vec3_scaleadd(const double k, const double x[3],
+ const double y[3], double * const z) const {
z[0] = k*x[0]+y[0];
z[1] = k*x[1]+y[1];
z[2] = k*x[2]+y[2];
diff --git a/src/MANYBODY/pair_tersoff_zbl.cpp b/src/MANYBODY/pair_tersoff_zbl.cpp
index d8e044e078b8a236bf57f602e643a7b42ad7052e..67633525e864902be45980d8e625a4b61177ed96 100644
--- a/src/MANYBODY/pair_tersoff_zbl.cpp
+++ b/src/MANYBODY/pair_tersoff_zbl.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -93,8 +93,8 @@ void PairTersoffZBL::read_file(char *file)
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fp);
if (ptr == NULL) {
- eof = 1;
- fclose(fp);
+ eof = 1;
+ fclose(fp);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
@@ -115,8 +115,8 @@ void PairTersoffZBL::read_file(char *file)
if (comm->me == 0) {
ptr = fgets(&line[n],MAXLINE-n,fp);
if (ptr == NULL) {
- eof = 1;
- fclose(fp);
+ eof = 1;
+ fclose(fp);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
@@ -155,7 +155,7 @@ void PairTersoffZBL::read_file(char *file)
if (nparams == maxparam) {
maxparam += DELTA;
params = (Param *) memory->srealloc(params,maxparam*sizeof(Param),
- "pair:params");
+ "pair:params");
}
params[nparams].ielement = ielement;
@@ -185,18 +185,18 @@ void PairTersoffZBL::read_file(char *file)
params[nparams].powermint = int(params[nparams].powerm);
if (
- params[nparams].lam3 < 0.0 || params[nparams].c < 0.0 ||
- params[nparams].d < 0.0 || params[nparams].powern < 0.0 ||
- params[nparams].beta < 0.0 || params[nparams].lam2 < 0.0 ||
- params[nparams].bigb < 0.0 || params[nparams].bigr < 0.0 ||
- params[nparams].bigd < 0.0 ||
- params[nparams].bigd > params[nparams].bigr ||
- params[nparams].lam3 < 0.0 || params[nparams].biga < 0.0 ||
- params[nparams].powerm - params[nparams].powermint != 0.0 ||
+ params[nparams].lam3 < 0.0 || params[nparams].c < 0.0 ||
+ params[nparams].d < 0.0 || params[nparams].powern < 0.0 ||
+ params[nparams].beta < 0.0 || params[nparams].lam2 < 0.0 ||
+ params[nparams].bigb < 0.0 || params[nparams].bigr < 0.0 ||
+ params[nparams].bigd < 0.0 ||
+ params[nparams].bigd > params[nparams].bigr ||
+ params[nparams].lam3 < 0.0 || params[nparams].biga < 0.0 ||
+ params[nparams].powerm - params[nparams].powermint != 0.0 ||
(params[nparams].powermint != 3 && params[nparams].powermint != 1) ||
- params[nparams].gamma < 0.0 ||
- params[nparams].Z_i < 1.0 || params[nparams].Z_j < 1.0 ||
- params[nparams].ZBLcut < 0.0 || params[nparams].ZBLexpscale < 0.0)
+ params[nparams].gamma < 0.0 ||
+ params[nparams].Z_i < 1.0 || params[nparams].Z_j < 1.0 ||
+ params[nparams].ZBLcut < 0.0 || params[nparams].ZBLexpscale < 0.0)
error->all(FLERR,"Illegal Tersoff parameter");
nparams++;
@@ -208,7 +208,7 @@ void PairTersoffZBL::read_file(char *file)
/* ---------------------------------------------------------------------- */
void PairTersoffZBL::repulsive(Param *param, double rsq, double &fforce,
- int eflag, double &eng)
+ int eflag, double &eng)
{
double r,tmp_fc,tmp_fc_d,tmp_exp;
@@ -220,29 +220,29 @@ void PairTersoffZBL::repulsive(Param *param, double rsq, double &fforce,
tmp_exp = exp(-param->lam1 * r);
double fforce_ters = param->biga * tmp_exp * (tmp_fc_d - tmp_fc*param->lam1);
double eng_ters = tmp_fc * param->biga * tmp_exp;
-
+
// ZBL repulsive portion
double esq = pow(global_e,2.0);
- double a_ij = (0.8854*global_a_0) /
+ double a_ij = (0.8854*global_a_0) /
(pow(param->Z_i,0.23) + pow(param->Z_j,0.23));
double premult = (param->Z_i * param->Z_j * esq)/(4.0*MY_PI*global_epsilon_0);
double r_ov_a = r/a_ij;
- double phi = 0.1818*exp(-3.2*r_ov_a) + 0.5099*exp(-0.9423*r_ov_a) +
+ double phi = 0.1818*exp(-3.2*r_ov_a) + 0.5099*exp(-0.9423*r_ov_a) +
0.2802*exp(-0.4029*r_ov_a) + 0.02817*exp(-0.2016*r_ov_a);
- double dphi = (1.0/a_ij) * (-3.2*0.1818*exp(-3.2*r_ov_a) -
- 0.9423*0.5099*exp(-0.9423*r_ov_a) -
- 0.4029*0.2802*exp(-0.4029*r_ov_a) -
- 0.2016*0.02817*exp(-0.2016*r_ov_a));
+ double dphi = (1.0/a_ij) * (-3.2*0.1818*exp(-3.2*r_ov_a) -
+ 0.9423*0.5099*exp(-0.9423*r_ov_a) -
+ 0.4029*0.2802*exp(-0.4029*r_ov_a) -
+ 0.2016*0.02817*exp(-0.2016*r_ov_a));
double fforce_ZBL = premult*-phi/rsq + premult*dphi/r;
double eng_ZBL = premult*(1.0/r)*phi;
-
+
// combine two parts with smoothing by Fermi-like function
- fforce = -(-F_fermi_d(r,param) * eng_ZBL +
- (1.0 - F_fermi(r,param))*fforce_ZBL +
- F_fermi_d(r,param)*eng_ters + F_fermi(r,param)*fforce_ters) / r;
-
+ fforce = -(-F_fermi_d(r,param) * eng_ZBL +
+ (1.0 - F_fermi(r,param))*fforce_ZBL +
+ F_fermi_d(r,param)*eng_ters + F_fermi(r,param)*fforce_ters) / r;
+
if (eflag)
eng = (1.0 - F_fermi(r,param))*eng_ZBL + F_fermi(r,param)*eng_ters;
}
@@ -252,9 +252,9 @@ void PairTersoffZBL::repulsive(Param *param, double rsq, double &fforce,
double PairTersoffZBL::ters_fa(double r, Param *param)
{
if (r > param->bigr + param->bigd) return 0.0;
- return -param->bigb * exp(-param->lam2 * r) * ters_fc(r,param) *
+ return -param->bigb * exp(-param->lam2 * r) * ters_fc(r,param) *
F_fermi(r,param);
-}
+}
/* ---------------------------------------------------------------------- */
@@ -262,8 +262,8 @@ double PairTersoffZBL::ters_fa_d(double r, Param *param)
{
if (r > param->bigr + param->bigd) return 0.0;
return param->bigb * exp(-param->lam2 * r) *
- (param->lam2 * ters_fc(r,param) * F_fermi(r,param) -
- ters_fc_d(r,param) * F_fermi(r,param) - ters_fc(r,param) *
+ (param->lam2 * ters_fc(r,param) * F_fermi(r,param) -
+ ters_fc_d(r,param) * F_fermi(r,param) - ters_fc(r,param) *
F_fermi_d(r,param));
}
@@ -282,6 +282,6 @@ double PairTersoffZBL::F_fermi(double r, Param *param)
double PairTersoffZBL::F_fermi_d(double r, Param *param)
{
- return param->ZBLexpscale*exp(-param->ZBLexpscale*(r-param->ZBLcut)) /
+ return param->ZBLexpscale*exp(-param->ZBLexpscale*(r-param->ZBLcut)) /
pow(1.0 + exp(-param->ZBLexpscale*(r-param->ZBLcut)),2.0);
}
diff --git a/src/MANYBODY/pair_tersoff_zbl.h b/src/MANYBODY/pair_tersoff_zbl.h
index c464120983f48ff5053723f6d5f62da42300c92b..01e296e92c252157305a04d84dc33333415a4c10 100755
--- a/src/MANYBODY/pair_tersoff_zbl.h
+++ b/src/MANYBODY/pair_tersoff_zbl.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -30,16 +30,16 @@ class PairTersoffZBL : public PairTersoff {
~PairTersoffZBL() {}
private:
- double global_a_0; // Bohr radius for Coulomb repulsion
- double global_epsilon_0; // permittivity of vacuum for Coulomb repulsion
- double global_e; // proton charge (negative of electron charge)
+ double global_a_0; // Bohr radius for Coulomb repulsion
+ double global_epsilon_0; // permittivity of vacuum for Coulomb repulsion
+ double global_e; // proton charge (negative of electron charge)
void read_file(char *);
void repulsive(Param *, double, double &, int, double &);
double ters_fa(double, Param *);
double ters_fa_d(double, Param *);
-
+
double F_fermi(double, Param *);
double F_fermi_d(double, Param *);
};
diff --git a/src/MC/fix_bond_break.cpp b/src/MC/fix_bond_break.cpp
index a68c173d29ad9233b67ae5e7e40ada708f9e2634..e24e733f660a684fb6dd1f8a56db838432cb3bf0 100755
--- a/src/MC/fix_bond_break.cpp
+++ b/src/MC/fix_bond_break.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -70,7 +70,7 @@ FixBondBreak::FixBondBreak(LAMMPS *lmp, int narg, char **arg) :
fraction = atof(arg[iarg+1]);
seed = atoi(arg[iarg+2]);
if (fraction < 0.0 || fraction > 1.0)
- error->all(FLERR,"Illegal fix bond/break command");
+ error->all(FLERR,"Illegal fix bond/break command");
if (seed <= 0) error->all(FLERR,"Illegal fix bond/break command");
iarg += 3;
} else error->all(FLERR,"Illegal fix bond/break command");
@@ -140,9 +140,9 @@ void FixBondBreak::init()
// warn if angles, dihedrals, impropers are being used
if (force->angle || force->dihedral || force->improper) {
- if (me == 0)
+ if (me == 0)
error->warning(FLERR,"Broken bonds will not alter angles, "
- "dihedrals, or impropers");
+ "dihedrals, or impropers");
}
if (strstr(update->integrate_style,"respa"))
@@ -263,12 +263,12 @@ void FixBondBreak::post_integrate()
for (m = 0; m < num_bond[i]; m++) {
if (bond_atom[i][m] == partner[i]) {
- for (k = m; k < num_bond[i]-1; k++) {
- bond_atom[i][k] = bond_atom[i][k+1];
- bond_type[i][k] = bond_type[i][k+1];
- }
- num_bond[i]--;
- break;
+ for (k = m; k < num_bond[i]-1; k++) {
+ bond_atom[i][k] = bond_atom[i][k+1];
+ bond_type[i][k] = bond_type[i][k+1];
+ }
+ num_bond[i]--;
+ break;
}
}
@@ -284,7 +284,7 @@ void FixBondBreak::post_integrate()
nspecial[i][0]--;
nspecial[i][1]--;
nspecial[i][2]--;
-
+
// count the broken bond once
if (tag[i] < tag[j]) nbreak++;
@@ -311,7 +311,7 @@ void FixBondBreak::post_integrate_respa(int ilevel, int iloop)
/* ---------------------------------------------------------------------- */
int FixBondBreak::pack_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
@@ -378,7 +378,7 @@ double FixBondBreak::compute_vector(int n)
}
/* ----------------------------------------------------------------------
- memory usage of local atom-based arrays
+ memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double FixBondBreak::memory_usage()
diff --git a/src/MC/fix_bond_break.h b/src/MC/fix_bond_break.h
index daac664fa4af8723b8558cf4402835a5fa750185..a625e0ff80501c4fcb6ac10bca09eddb849a93e3 100755
--- a/src/MC/fix_bond_break.h
+++ b/src/MC/fix_bond_break.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/MC/fix_bond_create.cpp b/src/MC/fix_bond_create.cpp
index 577d5a7f8e74cbc066f07102f27fc4337b3ffd1d..7b62d3c81327e8f9f8f640519472281bf8f62a11 100755
--- a/src/MC/fix_bond_create.cpp
+++ b/src/MC/fix_bond_create.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -58,7 +58,7 @@ FixBondCreate::FixBondCreate(LAMMPS *lmp, int narg, char **arg) :
double cutoff = atof(arg[6]);
btype = atoi(arg[7]);
- if (iatomtype < 1 || iatomtype > atom->ntypes ||
+ if (iatomtype < 1 || iatomtype > atom->ntypes ||
jatomtype < 1 || jatomtype > atom->ntypes)
error->all(FLERR,"Invalid atom type in fix bond/create command");
if (cutoff < 0.0) error->all(FLERR,"Illegal fix bond/create command");
@@ -84,7 +84,7 @@ FixBondCreate::FixBondCreate(LAMMPS *lmp, int narg, char **arg) :
inewtype = atoi(arg[iarg+2]);
if (imaxbond < 0) error->all(FLERR,"Illegal fix bond/create command");
if (inewtype < 1 || inewtype > atom->ntypes)
- error->all(FLERR,"Invalid atom type in fix bond/create command");
+ error->all(FLERR,"Invalid atom type in fix bond/create command");
iarg += 3;
} else if (strcmp(arg[iarg],"jparam") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix bond/create command");
@@ -92,14 +92,14 @@ FixBondCreate::FixBondCreate(LAMMPS *lmp, int narg, char **arg) :
jnewtype = atoi(arg[iarg+2]);
if (jmaxbond < 0) error->all(FLERR,"Illegal fix bond/create command");
if (jnewtype < 1 || jnewtype > atom->ntypes)
- error->all(FLERR,"Invalid atom type in fix bond/create command");
+ error->all(FLERR,"Invalid atom type in fix bond/create command");
iarg += 3;
} else if (strcmp(arg[iarg],"prob") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix bond/create command");
fraction = atof(arg[iarg+1]);
seed = atoi(arg[iarg+2]);
if (fraction < 0.0 || fraction > 1.0)
- error->all(FLERR,"Illegal fix bond/create command");
+ error->all(FLERR,"Illegal fix bond/create command");
if (seed <= 0) error->all(FLERR,"Illegal fix bond/create command");
iarg += 3;
} else error->all(FLERR,"Illegal fix bond/create command");
@@ -109,10 +109,10 @@ FixBondCreate::FixBondCreate(LAMMPS *lmp, int narg, char **arg) :
if (atom->molecular == 0)
error->all(FLERR,"Cannot use fix bond/create with non-molecular systems");
- if (iatomtype == jatomtype &&
+ if (iatomtype == jatomtype &&
((imaxbond != jmaxbond) || (inewtype != jnewtype)))
error->all(FLERR,
- "Inconsistent iparam/jparam values in fix bond/create command");
+ "Inconsistent iparam/jparam values in fix bond/create command");
// initialize Marsaglia RNG with processor-unique seed
@@ -177,9 +177,9 @@ void FixBondCreate::init()
{
// check cutoff for iatomtype,jatomtype
- if (force->pair == NULL || cutsq > force->pair->cutsq[iatomtype][jatomtype])
+ if (force->pair == NULL || cutsq > force->pair->cutsq[iatomtype][jatomtype])
error->all(FLERR,"Fix bond/create cutoff is longer than pairwise cutoff");
-
+
// require special bonds = 0,1,1
if (force->special_lj[1] != 0.0 || force->special_lj[2] != 1.0 ||
@@ -188,15 +188,15 @@ void FixBondCreate::init()
if (atom->q_flag)
if (force->special_coul[1] != 0.0 || force->special_coul[2] != 1.0 ||
- force->special_coul[3] != 1.0)
+ force->special_coul[3] != 1.0)
error->all(FLERR,"Fix bond/create requires special_bonds coul = 0,1,1");
// warn if angles, dihedrals, impropers are being used
if (force->angle || force->dihedral || force->improper) {
- if (me == 0)
+ if (me == 0)
error->warning(FLERR,"Created bonds will not create angles, "
- "dihedrals, or impropers");
+ "dihedrals, or impropers");
}
// need a half neighbor list, built when ever re-neighboring occurs
@@ -232,7 +232,7 @@ void FixBondCreate::setup(int vflag)
// if newton bond is not set, just increment count on atom I
// if newton bond is set, also increment count on atom J even if ghost
// bondcount is long enough to tally ghost atom counts
-
+
int *num_bond = atom->num_bond;
int **bond_type = atom->bond_type;
int **bond_atom = atom->bond_atom;
@@ -247,13 +247,13 @@ void FixBondCreate::setup(int vflag)
for (j = 0; j < num_bond[i]; j++) {
if (bond_type[i][j] == btype) {
bondcount[i]++;
- if (newton_bond) {
- m = atom->map(bond_atom[i][j]);
- if (m < 0)
- error->one(FLERR,
- "Could not count initial bonds in fix bond/create");
- bondcount[m]++;
- }
+ if (newton_bond) {
+ m = atom->map(bond_atom[i][j]);
+ if (m < 0)
+ error->one(FLERR,
+ "Could not count initial bonds in fix bond/create");
+ bondcount[m]++;
+ }
}
}
@@ -325,7 +325,7 @@ void FixBondCreate::post_integrate()
ztmp = x[i][2];
jlist = firstneigh[i];
jnum = numneigh[i];
-
+
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
@@ -334,13 +334,13 @@ void FixBondCreate::post_integrate()
possible = 0;
if (itype == iatomtype && jtype == jatomtype) {
- if ((imaxbond == 0 || bondcount[i] < imaxbond) &&
- (jmaxbond == 0 || bondcount[j] < jmaxbond))
- possible = 1;
+ if ((imaxbond == 0 || bondcount[i] < imaxbond) &&
+ (jmaxbond == 0 || bondcount[j] < jmaxbond))
+ possible = 1;
} else if (itype == jatomtype && jtype == iatomtype) {
- if ((jmaxbond == 0 || bondcount[i] < jmaxbond) &&
- (imaxbond == 0 || bondcount[j] < imaxbond))
- possible = 1;
+ if ((jmaxbond == 0 || bondcount[i] < jmaxbond) &&
+ (imaxbond == 0 || bondcount[j] < imaxbond))
+ possible = 1;
}
if (!possible) continue;
@@ -351,12 +351,12 @@ void FixBondCreate::post_integrate()
if (rsq >= cutsq) continue;
if (rsq < distsq[i]) {
- partner[i] = tag[j];
- distsq[i] = rsq;
+ partner[i] = tag[j];
+ distsq[i] = rsq;
}
if (rsq < distsq[j]) {
- partner[j] = tag[i];
- distsq[j] = rsq;
+ partner[j] = tag[i];
+ distsq[j] = rsq;
}
}
}
@@ -375,7 +375,7 @@ void FixBondCreate::post_integrate()
for (i = 0; i < nlocal; i++)
if (partner[i]) probability[i] = random->uniform();
}
-
+
commflag = 1;
comm->forward_comm_fix(this);
@@ -411,7 +411,7 @@ void FixBondCreate::post_integrate()
if (!newton_bond || tag[i] < tag[j]) {
if (num_bond[i] == atom->bond_per_atom)
- error->one(FLERR,"New bond exceeded bonds per atom in fix bond/create");
+ error->one(FLERR,"New bond exceeded bonds per atom in fix bond/create");
bond_type[i][num_bond[i]] = btype;
bond_atom[i][num_bond[i]] = tag[j];
num_bond[i]++;
@@ -425,7 +425,7 @@ void FixBondCreate::post_integrate()
n3 = nspecial[i][2];
if (n3 == atom->maxspecial)
error->one(FLERR,
- "New bond exceeded special list size in fix bond/create");
+ "New bond exceeded special list size in fix bond/create");
for (m = n3; m > n1; m--) slist[m+1] = slist[m];
slist[n1] = tag[j];
nspecial[i][0]++;
@@ -467,7 +467,7 @@ void FixBondCreate::post_integrate_respa(int ilevel, int iloop)
/* ---------------------------------------------------------------------- */
int FixBondCreate::pack_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
@@ -521,7 +521,7 @@ int FixBondCreate::pack_reverse_comm(int n, int first, double *buf)
last = first + n;
if (commflag == 0) {
- for (i = first; i < last; i++)
+ for (i = first; i < last; i++)
buf[m++] = bondcount[i];
return 1;
@@ -552,15 +552,15 @@ void FixBondCreate::unpack_reverse_comm(int n, int *list, double *buf)
for (i = 0; i < n; i++) {
j = list[i];
if (buf[m] < distsq[j]) {
- distsq[j] = buf[m++];
- partner[j] = static_cast<int> (buf[m++]);
+ distsq[j] = buf[m++];
+ partner[j] = static_cast<int> (buf[m++]);
} else m += 2;
}
}
}
/* ----------------------------------------------------------------------
- allocate local atom-based arrays
+ allocate local atom-based arrays
------------------------------------------------------------------------- */
void FixBondCreate::grow_arrays(int nmax)
@@ -569,7 +569,7 @@ void FixBondCreate::grow_arrays(int nmax)
}
/* ----------------------------------------------------------------------
- copy values within local atom-based arrays
+ copy values within local atom-based arrays
------------------------------------------------------------------------- */
void FixBondCreate::copy_arrays(int i, int j)
@@ -578,7 +578,7 @@ void FixBondCreate::copy_arrays(int i, int j)
}
/* ----------------------------------------------------------------------
- pack values in local atom-based arrays for exchange with another proc
+ pack values in local atom-based arrays for exchange with another proc
------------------------------------------------------------------------- */
int FixBondCreate::pack_exchange(int i, double *buf)
@@ -588,7 +588,7 @@ int FixBondCreate::pack_exchange(int i, double *buf)
}
/* ----------------------------------------------------------------------
- unpack values in local atom-based arrays from exchange with another proc
+ unpack values in local atom-based arrays from exchange with another proc
------------------------------------------------------------------------- */
int FixBondCreate::unpack_exchange(int nlocal, double *buf)
@@ -606,7 +606,7 @@ double FixBondCreate::compute_vector(int n)
}
/* ----------------------------------------------------------------------
- memory usage of local atom-based arrays
+ memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double FixBondCreate::memory_usage()
diff --git a/src/MC/fix_bond_create.h b/src/MC/fix_bond_create.h
index 08d229accba9bf968bd2868d283989e945f0dc8e..9f2d904ec39b9fc3c384d659539cce67c4dac825 100755
--- a/src/MC/fix_bond_create.h
+++ b/src/MC/fix_bond_create.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -95,7 +95,7 @@ Self-explanatory.
E: Inconsistent iparam/jparam values in fix bond/create command
-If itype and jtype are the same, then their maxbond and newtype
+If itype and jtype are the same, then their maxbond and newtype
settings must also be the same.
E: Fix bond/create cutoff is longer than pairwise cutoff
diff --git a/src/MC/fix_bond_swap.cpp b/src/MC/fix_bond_swap.cpp
index c02f3fcd3d4551b13e0075857d13f693354f80c8..c5aee7f294d7181a310c0039972fe1a55d4d150c 100644
--- a/src/MC/fix_bond_swap.cpp
+++ b/src/MC/fix_bond_swap.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -115,7 +115,7 @@ void FixBondSwap::init()
error->all(FLERR,"Must use atom style with molecule IDs with fix bond/swap");
int icompute = modify->find_compute(id_temp);
- if (icompute < 0)
+ if (icompute < 0)
error->all(FLERR,"Temperature ID for fix bond/swap does not exist");
temperature = modify->compute[icompute];
@@ -257,141 +257,141 @@ void FixBondSwap::pre_neighbor()
// all 4 old and new bonds must have length < cutoff
for (ibond = 0; ibond < num_bond[i]; ibond++) {
- inext = atom->map(bond_atom[i][ibond]);
- if (inext >= nlocal || inext < 0) continue;
- ibondtype = bond_type[i][ibond];
-
- for (jbond = 0; jbond < num_bond[j]; jbond++) {
- jnext = atom->map(bond_atom[j][jbond]);
- if (jnext >= nlocal || jnext < 0) continue;
- jbondtype = bond_type[j][jbond];
-
- if (molecule[inext] != molecule[jnext]) continue;
- if (inext == jnext || inext == j) continue;
- if (dist_rsq(i,inext) >= cutsq) continue;
- if (dist_rsq(j,jnext) >= cutsq) continue;
- if (dist_rsq(i,jnext) >= cutsq) continue;
- if (dist_rsq(j,inext) >= cutsq) continue;
-
- // if angles are enabled:
- // find other atoms i,inext,j,jnext are in angles with
- // and angletypes: i/j angletype, i/j nextangletype
- // use num_angle for this, not special list, so also find angletypes
- // 4 atoms consecutively along 1st chain: iprev,i,inext,ilast
- // 4 atoms consecutively along 2nd chain: jprev,j,jnext,jlast
- // prev or last atom can be non-existent at end of chain
- // set prev/last = -1 in this case
- // if newton bond = 0, then angles are stored by all 4 atoms
- // so require that iprev,ilast,jprev,jlast be owned by this proc
- // so all copies of angles can be updated if a swap takes place
-
- if (angleflag) {
- itag = tag[i];
- inexttag = tag[inext];
- jtag = tag[j];
- jnexttag = tag[jnext];
-
- iprev = -1;
- for (iangle = 0; iangle < num_angle[i]; iangle++) {
- i1 = angle_atom1[i][iangle];
- i2 = angle_atom2[i][iangle];
- i3 = angle_atom3[i][iangle];
- if (i2 == itag && i3 == inexttag) iprev = atom->map(i1);
- else if (i1 == inexttag && i2 == itag) iprev = atom->map(i3);
- if (iprev >= 0) {
- iangletype = angle_type[i][iangle];
- break;
- }
- }
- if (!newton_bond && iprev >= nlocal) continue;
-
- ilast = -1;
- for (iangle = 0; iangle < num_angle[inext]; iangle++) {
- i1 = angle_atom1[inext][iangle];
- i2 = angle_atom2[inext][iangle];
- i3 = angle_atom3[inext][iangle];
- if (i1 == itag && i2 == inexttag) ilast = atom->map(i3);
- else if (i2 == inexttag && i3 == itag) ilast = atom->map(i1);
- if (ilast >= 0) {
- inextangletype = angle_type[inext][iangle];
- break;
- }
- }
- if (!newton_bond && ilast >= nlocal) continue;
-
- jprev = -1;
- for (jangle = 0; jangle < num_angle[j]; jangle++) {
- j1 = angle_atom1[j][jangle];
- j2 = angle_atom2[j][jangle];
- j3 = angle_atom3[j][jangle];
- if (j2 == jtag && j3 == jnexttag) jprev = atom->map(j1);
- else if (j1 == jnexttag && j2 == jtag) jprev = atom->map(j3);
- if (jprev >= 0) {
- jangletype = angle_type[j][jangle];
- break;
- }
- }
- if (!newton_bond && jprev >= nlocal) continue;
-
- jlast = -1;
- for (jangle = 0; jangle < num_angle[jnext]; jangle++) {
- j1 = angle_atom1[jnext][jangle];
- j2 = angle_atom2[jnext][jangle];
- j3 = angle_atom3[jnext][jangle];
- if (j1 == jtag && j2 == jnexttag) jlast = atom->map(j3);
- else if (j2 == jnexttag && j3 == jtag) jlast = atom->map(j1);
- if (jlast >= 0) {
- jnextangletype = angle_type[jnext][jangle];
- break;
- }
- }
- if (!newton_bond && jlast >= nlocal) continue;
- }
-
- // valid foursome found between 2 chains:
- // chains = iprev-i-inext-ilast and jprev-j-jnext-jlast
- // prev or last values are -1 if do not exist due to end of chain
- // OK to call angle_eng with -1 atom, since just return 0.0
- // current energy of foursome =
- // E_nb(i,j) + E_nb(i,jnext) + E_nb(inext,j) + E_nb(inext,jnext) +
- // E_bond(i,inext) + E_bond(j,jnext) +
- // E_angle(iprev,i,inext) + E_angle(i,inext,ilast) +
- // E_angle(jprev,j,jnext) + E_angle(j,jnext,jlast)
- // new energy of foursome with swapped bonds =
- // E_nb(i,j) + E_nb(i,inext) + E_nb(j,jnext) + E_nb(inext,jnext) +
- // E_bond(i,jnext) + E_bond(j,inext) +
- // E_angle(iprev,i,jnext) + E_angle(i,jnext,jlast) +
- // E_angle(jprev,j,inext) + E_angle(j,inext,ilast)
- // energy delta = add/subtract differing terms between 2 formulas
-
- foursome++;
-
- delta = pair_eng(i,inext) + pair_eng(j,jnext) -
- pair_eng(i,jnext) - pair_eng(inext,j);
- delta += bond_eng(ibondtype,i,jnext) + bond_eng(jbondtype,j,inext) -
- bond_eng(ibondtype,i,inext) - bond_eng(jbondtype,j,jnext);
- if (angleflag)
- delta += angle_eng(iangletype,iprev,i,jnext) +
- angle_eng(jnextangletype,i,jnext,jlast) +
- angle_eng(jangletype,jprev,j,inext) +
- angle_eng(inextangletype,j,inext,ilast) -
- angle_eng(iangletype,iprev,i,inext) -
- angle_eng(inextangletype,i,inext,ilast) -
- angle_eng(jangletype,jprev,j,jnext) -
- angle_eng(jnextangletype,j,jnext,jlast);
-
- // if delta <= 0, accept swap
- // if delta > 0, compute Boltzmann factor with current temperature
- // only accept if greater than random value
- // whether accept or not, exit test loop
-
- if (delta < 0.0) accept = 1;
- else {
- factor = exp(-delta/force->boltz/t_current);
- if (random->uniform() < factor) accept = 1;
- }
- goto done;
- }
+ inext = atom->map(bond_atom[i][ibond]);
+ if (inext >= nlocal || inext < 0) continue;
+ ibondtype = bond_type[i][ibond];
+
+ for (jbond = 0; jbond < num_bond[j]; jbond++) {
+ jnext = atom->map(bond_atom[j][jbond]);
+ if (jnext >= nlocal || jnext < 0) continue;
+ jbondtype = bond_type[j][jbond];
+
+ if (molecule[inext] != molecule[jnext]) continue;
+ if (inext == jnext || inext == j) continue;
+ if (dist_rsq(i,inext) >= cutsq) continue;
+ if (dist_rsq(j,jnext) >= cutsq) continue;
+ if (dist_rsq(i,jnext) >= cutsq) continue;
+ if (dist_rsq(j,inext) >= cutsq) continue;
+
+ // if angles are enabled:
+ // find other atoms i,inext,j,jnext are in angles with
+ // and angletypes: i/j angletype, i/j nextangletype
+ // use num_angle for this, not special list, so also find angletypes
+ // 4 atoms consecutively along 1st chain: iprev,i,inext,ilast
+ // 4 atoms consecutively along 2nd chain: jprev,j,jnext,jlast
+ // prev or last atom can be non-existent at end of chain
+ // set prev/last = -1 in this case
+ // if newton bond = 0, then angles are stored by all 4 atoms
+ // so require that iprev,ilast,jprev,jlast be owned by this proc
+ // so all copies of angles can be updated if a swap takes place
+
+ if (angleflag) {
+ itag = tag[i];
+ inexttag = tag[inext];
+ jtag = tag[j];
+ jnexttag = tag[jnext];
+
+ iprev = -1;
+ for (iangle = 0; iangle < num_angle[i]; iangle++) {
+ i1 = angle_atom1[i][iangle];
+ i2 = angle_atom2[i][iangle];
+ i3 = angle_atom3[i][iangle];
+ if (i2 == itag && i3 == inexttag) iprev = atom->map(i1);
+ else if (i1 == inexttag && i2 == itag) iprev = atom->map(i3);
+ if (iprev >= 0) {
+ iangletype = angle_type[i][iangle];
+ break;
+ }
+ }
+ if (!newton_bond && iprev >= nlocal) continue;
+
+ ilast = -1;
+ for (iangle = 0; iangle < num_angle[inext]; iangle++) {
+ i1 = angle_atom1[inext][iangle];
+ i2 = angle_atom2[inext][iangle];
+ i3 = angle_atom3[inext][iangle];
+ if (i1 == itag && i2 == inexttag) ilast = atom->map(i3);
+ else if (i2 == inexttag && i3 == itag) ilast = atom->map(i1);
+ if (ilast >= 0) {
+ inextangletype = angle_type[inext][iangle];
+ break;
+ }
+ }
+ if (!newton_bond && ilast >= nlocal) continue;
+
+ jprev = -1;
+ for (jangle = 0; jangle < num_angle[j]; jangle++) {
+ j1 = angle_atom1[j][jangle];
+ j2 = angle_atom2[j][jangle];
+ j3 = angle_atom3[j][jangle];
+ if (j2 == jtag && j3 == jnexttag) jprev = atom->map(j1);
+ else if (j1 == jnexttag && j2 == jtag) jprev = atom->map(j3);
+ if (jprev >= 0) {
+ jangletype = angle_type[j][jangle];
+ break;
+ }
+ }
+ if (!newton_bond && jprev >= nlocal) continue;
+
+ jlast = -1;
+ for (jangle = 0; jangle < num_angle[jnext]; jangle++) {
+ j1 = angle_atom1[jnext][jangle];
+ j2 = angle_atom2[jnext][jangle];
+ j3 = angle_atom3[jnext][jangle];
+ if (j1 == jtag && j2 == jnexttag) jlast = atom->map(j3);
+ else if (j2 == jnexttag && j3 == jtag) jlast = atom->map(j1);
+ if (jlast >= 0) {
+ jnextangletype = angle_type[jnext][jangle];
+ break;
+ }
+ }
+ if (!newton_bond && jlast >= nlocal) continue;
+ }
+
+ // valid foursome found between 2 chains:
+ // chains = iprev-i-inext-ilast and jprev-j-jnext-jlast
+ // prev or last values are -1 if do not exist due to end of chain
+ // OK to call angle_eng with -1 atom, since just return 0.0
+ // current energy of foursome =
+ // E_nb(i,j) + E_nb(i,jnext) + E_nb(inext,j) + E_nb(inext,jnext) +
+ // E_bond(i,inext) + E_bond(j,jnext) +
+ // E_angle(iprev,i,inext) + E_angle(i,inext,ilast) +
+ // E_angle(jprev,j,jnext) + E_angle(j,jnext,jlast)
+ // new energy of foursome with swapped bonds =
+ // E_nb(i,j) + E_nb(i,inext) + E_nb(j,jnext) + E_nb(inext,jnext) +
+ // E_bond(i,jnext) + E_bond(j,inext) +
+ // E_angle(iprev,i,jnext) + E_angle(i,jnext,jlast) +
+ // E_angle(jprev,j,inext) + E_angle(j,inext,ilast)
+ // energy delta = add/subtract differing terms between 2 formulas
+
+ foursome++;
+
+ delta = pair_eng(i,inext) + pair_eng(j,jnext) -
+ pair_eng(i,jnext) - pair_eng(inext,j);
+ delta += bond_eng(ibondtype,i,jnext) + bond_eng(jbondtype,j,inext) -
+ bond_eng(ibondtype,i,inext) - bond_eng(jbondtype,j,jnext);
+ if (angleflag)
+ delta += angle_eng(iangletype,iprev,i,jnext) +
+ angle_eng(jnextangletype,i,jnext,jlast) +
+ angle_eng(jangletype,jprev,j,inext) +
+ angle_eng(inextangletype,j,inext,ilast) -
+ angle_eng(iangletype,iprev,i,inext) -
+ angle_eng(inextangletype,i,inext,ilast) -
+ angle_eng(jangletype,jprev,j,jnext) -
+ angle_eng(jnextangletype,j,jnext,jlast);
+
+ // if delta <= 0, accept swap
+ // if delta > 0, compute Boltzmann factor with current temperature
+ // only accept if greater than random value
+ // whether accept or not, exit test loop
+
+ if (delta < 0.0) accept = 1;
+ else {
+ factor = exp(-delta/force->boltz/t_current);
+ if (random->uniform() < factor) accept = 1;
+ }
+ goto done;
+ }
}
}
}
@@ -399,7 +399,7 @@ void FixBondSwap::pre_neighbor()
done:
if (!accept) return;
naccept++;
-
+
// change bond partners of affected atoms
// on atom i: bond i-inext changes to i-jnext
// on atom j: bond j-jnext changes to j-inext
@@ -533,7 +533,7 @@ void FixBondSwap::pre_neighbor()
angle_atom3[jnext][jangle] = iprevtag;
} else if (j1 == jtag && j2 == jnexttag && j3 == jlasttag)
angle_atom1[jnext][jangle] = itag;
- else if (j1 == jlasttag && j2 == jnexttag && j3 == jtag)
+ else if (j1 == jlasttag && j2 == jnexttag && j3 == jtag)
angle_atom3[jnext][jangle] = itag;
}
@@ -551,7 +551,7 @@ void FixBondSwap::pre_neighbor()
i1 = angle_atom1[iprev][iangle];
i2 = angle_atom2[iprev][iangle];
i3 = angle_atom3[iprev][iangle];
-
+
if (i1 == iprevtag && i2 == itag && i3 == inexttag)
angle_atom3[iprev][iangle] = jnexttag;
else if (i1 == inexttag && i2 == itag && i3 == iprevtag)
@@ -562,7 +562,7 @@ void FixBondSwap::pre_neighbor()
j1 = angle_atom1[jprev][jangle];
j2 = angle_atom2[jprev][jangle];
j3 = angle_atom3[jprev][jangle];
-
+
if (j1 == jprevtag && j2 == jtag && j3 == jnexttag)
angle_atom3[jprev][jangle] = inexttag;
else if (j1 == jnexttag && j2 == jtag && j3 == jprevtag)
@@ -573,7 +573,7 @@ void FixBondSwap::pre_neighbor()
i1 = angle_atom1[ilast][iangle];
i2 = angle_atom2[ilast][iangle];
i3 = angle_atom3[ilast][iangle];
-
+
if (i1 == itag && i2 == inexttag && i3 == ilasttag)
angle_atom1[ilast][iangle] = jtag;
else if (i1 == ilasttag && i2 == inexttag && i3 == itag)
@@ -584,7 +584,7 @@ void FixBondSwap::pre_neighbor()
j1 = angle_atom1[jlast][jangle];
j2 = angle_atom2[jlast][jangle];
j3 = angle_atom3[jlast][jangle];
-
+
if (j1 == jtag && j2 == jnexttag && j3 == jlasttag)
angle_atom1[jlast][jangle] = itag;
else if (j1 == jlasttag && j2 == jnexttag && j3 == jtag)
diff --git a/src/MC/fix_bond_swap.h b/src/MC/fix_bond_swap.h
index ce549c4849534aa73afa016249932e3b7898add9..2804a5f9e91db1e356c9684e72d6a0d993df3611 100644
--- a/src/MC/fix_bond_swap.h
+++ b/src/MC/fix_bond_swap.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -46,7 +46,7 @@ class FixBondSwap : public Fix {
char *id_temp;
int *type;
double **x;
-
+
class NeighList *list;
class Compute *temperature;
class RanMars *random;
diff --git a/src/MC/fix_gcmc.cpp b/src/MC/fix_gcmc.cpp
index 6a699a06527d3325ea804fc3323a94db97b08580..dd314d772d7df05a8b2d826112e1c62e1a56adf8 100644
--- a/src/MC/fix_gcmc.cpp
+++ b/src/MC/fix_gcmc.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -53,7 +53,7 @@ FixGCMC::FixGCMC(LAMMPS *lmp, int narg, char **arg) :
time_depend = 1;
// required args
-
+
nevery = atoi(arg[3]);
nexchanges = atoi(arg[4]);
nmcmoves = atoi(arg[5]);
@@ -63,22 +63,22 @@ FixGCMC::FixGCMC(LAMMPS *lmp, int narg, char **arg) :
chemical_potential = atof(arg[9]);
displace = atof(arg[10]);
- if (ntype <= 0 || ntype > atom->ntypes)
+ if (ntype <= 0 || ntype > atom->ntypes)
error->all(FLERR,"Invalid atom type in fix GCMC command");
if (nexchanges < 0) error->all(FLERR,"Illegal fix GCMC command");
if (nmcmoves < 0) error->all(FLERR,"Illegal fix GCMC command");
if (seed <= 0) error->all(FLERR,"Illegal fix GCMC command");
- if (reservoir_temperature < 0.0)
- error->all(FLERR,"Illegal fix GCMC command");
- if (displace < 0.0) error->all(FLERR,"Illegal fix GCMC command");
+ if (reservoir_temperature < 0.0)
+ error->all(FLERR,"Illegal fix GCMC command");
+ if (displace < 0.0) error->all(FLERR,"Illegal fix GCMC command");
// compute beta, lambda, sigma, and the zz factor
-
+
beta = 1.0/(force->boltz*reservoir_temperature);
double gas_mass = atom->mass[ntype];
double lambda = sqrt(force->hplanck*force->hplanck/
- (2.0*MY_PI*gas_mass*force->mvv2e*
- force->boltz*reservoir_temperature));
+ (2.0*MY_PI*gas_mass*force->mvv2e*
+ force->boltz*reservoir_temperature));
sigma = sqrt(force->boltz*reservoir_temperature/gas_mass/force->mvv2e);
zz = exp(beta*chemical_potential)/(pow(lambda,3.0));
@@ -97,23 +97,23 @@ FixGCMC::FixGCMC(LAMMPS *lmp, int narg, char **arg) :
// random number generator, not the same for all procs
random_unequal = new RanPark(lmp,seed);
-
+
// compute the number of MC cycles that occur nevery timesteps
-
+
ncycles = nexchanges + nmcmoves;
-
+
// set up reneighboring
force_reneighbor = 1;
next_reneighbor = update->ntimestep + 1;
// zero out counters
-
- nmove_attempts = 0.0;
- nmove_successes = 0.0;
- ndel_attempts = 0.0;
- ndel_successes = 0.0;
- ninsert_attempts = 0.0;
+
+ nmove_attempts = 0.0;
+ nmove_successes = 0.0;
+ ndel_attempts = 0.0;
+ ndel_successes = 0.0;
+ ninsert_attempts = 0.0;
ninsert_successes = 0.0;
nmax = 0;
@@ -146,7 +146,7 @@ void FixGCMC::init()
// deleting such an atom would not leave firstgroup atoms first
int *type = atom->type;
-
+
if (atom->firstgroup >= 0) {
int *mask = atom->mask;
int nlocal = atom->nlocal;
@@ -177,17 +177,17 @@ void FixGCMC::init()
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall && comm->me == 0)
error->warning(FLERR,
- "Fix GCMC may delete atom with non-zero molecule ID");
+ "Fix GCMC may delete atom with non-zero molecule ID");
}
if (molflag && atom->molecule_flag == 0)
error->all(FLERR,
- "Fix GCMC molecule command requires atom attribute molecule");
-
- if (molflag != 0)
- error->all(FLERR,"Fix GCMC molecule feature does not yet work");
-
- if (force->pair->single_enable == 0)
+ "Fix GCMC molecule command requires atom attribute molecule");
+
+ if (molflag != 0)
+ error->all(FLERR,"Fix GCMC molecule feature does not yet work");
+
+ if (force->pair->single_enable == 0)
error->all(FLERR,"Fix GCMC incompatible with given pair_style");
}
@@ -200,7 +200,7 @@ void FixGCMC::init()
void FixGCMC::pre_exchange()
{
// just return if should not be called on this timestep
-
+
if (next_reneighbor != update->ntimestep) return;
if (domain->triclinic == 0) {
@@ -221,34 +221,34 @@ void FixGCMC::pre_exchange()
zhi = domain->boxhi_bound[2];
sublo = domain->sublo_lamda;
subhi = domain->subhi_lamda;
- }
-
+ }
+
volume = domain->xprd * domain->yprd * domain->zprd;
-
+
// grow local_gas_list array if necessary
if (atom->nlocal > nmax) {
memory->sfree(local_gas_list);
nmax = atom->nmax;
local_gas_list = (int *) memory->smalloc(nmax*sizeof(int),
- "GCMC:local_gas_list");
+ "GCMC:local_gas_list");
}
-
+
int *type = atom->type;
ngas_local = 0;
for (int i = 0; i < atom->nlocal; i++)
if (type[i] == ntype)
local_gas_list[ngas_local++] = i;
-
+
MPI_Allreduce(&ngas_local,&ngas,1,MPI_INT,MPI_SUM,world);
MPI_Scan(&ngas_local,&ngas_before,1,MPI_INT,MPI_SUM,world);
ngas_before -= ngas_local;
-
+
// perform ncycles MC cycles
-
+
for (int i = 0; i < ncycles; i++) {
- int random_int_fraction =
- static_cast<int>(random_equal->uniform()*ncycles) + 1;
+ int random_int_fraction =
+ static_cast<int>(random_equal->uniform()*ncycles) + 1;
if (random_int_fraction <= nmcmoves) {
attempt_move();
} else {
@@ -256,26 +256,26 @@ void FixGCMC::pre_exchange()
else attempt_insertion();
}
}
-
+
next_reneighbor = update->ntimestep + nevery;
-}
+}
/* ----------------------------------------------------------------------
choose particle randomly across all procs and attempt displacement
------------------------------------------------------------------------- */
void FixGCMC::attempt_move()
-{
+{
int i,iwhichglobal,iwhichlocal;
double rx,ry,rz;
double coord[3];
double **x = atom->x;
nmove_attempts += 1.0;
-
+
int success = 0;
iwhichglobal = static_cast<int> (ngas*random_equal->uniform());
- if ((iwhichglobal >= ngas_before) &&
+ if ((iwhichglobal >= ngas_before) &&
(iwhichglobal < ngas_before + ngas_local)) {
iwhichlocal = iwhichglobal - ngas_before;
i = local_gas_list[iwhichlocal];
@@ -293,19 +293,19 @@ void FixGCMC::attempt_move()
coord[2] = x[i][2] + displace*rz;
double energy_after = energy(i,coord);
if (random_unequal->uniform() < exp(-beta*(energy_after - energy_before))) {
- x[i][0] = coord[0];
- x[i][1] = coord[1];
+ x[i][0] = coord[0];
+ x[i][1] = coord[1];
x[i][2] = coord[2];
success = 1;
}
- }
-
+ }
+
int success_all = 0;
MPI_Allreduce(&success,&success_all,1,MPI_INT,MPI_MAX,world);
-
+
if (success_all) {
- nmove_successes += 1.0;
- comm->borders();
+ nmove_successes += 1.0;
+ comm->borders();
}
}
@@ -314,7 +314,7 @@ void FixGCMC::attempt_move()
------------------------------------------------------------------------- */
void FixGCMC::attempt_deletion()
-{
+{
ndel_attempts += 1.0;
if (ngas == 0) return;
@@ -325,32 +325,32 @@ void FixGCMC::attempt_deletion()
// choose particle randomly across all procs and delete it
// keep ngas, ngas_local, ngas_before, and local_gas_list current
// after each deletion
-
+
int success = 0;
iwhichglobal = static_cast<int> (ngas*random_equal->uniform());
- if ((iwhichglobal >= ngas_before) &&
+ if ((iwhichglobal >= ngas_before) &&
(iwhichglobal < ngas_before + ngas_local)) {
iwhichlocal = iwhichglobal - ngas_before;
i = local_gas_list[iwhichlocal];
- double deletion_energy = energy(i,atom->x[i]);
- if (random_unequal->uniform() <
- ngas*exp(beta*deletion_energy)/(zz*volume)) {
+ double deletion_energy = energy(i,atom->x[i]);
+ if (random_unequal->uniform() <
+ ngas*exp(beta*deletion_energy)/(zz*volume)) {
avec->copy(atom->nlocal-1,i,1);
atom->nlocal--;
local_gas_list[iwhichlocal] = local_gas_list[ngas_local-1];
ngas_local--;
- success = 1;
+ success = 1;
}
}
-
+
int success_all = 0;
MPI_Allreduce(&success,&success_all,1,MPI_INT,MPI_MAX,world);
-
+
if (success_all) {
ngas--;
ndel_successes += 1.0;
atom->natoms--;
- if (iwhichglobal < ngas_before) ngas_before--;
+ if (iwhichglobal < ngas_before) ngas_before--;
comm->borders();
if (atom->tag_enable) {
atom->tag_extend();
@@ -367,13 +367,13 @@ void FixGCMC::attempt_deletion()
------------------------------------------------------------------------- */
void FixGCMC::attempt_insertion()
-{
+{
int flag,success;
double coord[3],lamda[3];
- double *newcoord;
-
+ double *newcoord;
+
ninsert_attempts += 1.0;
-
+
// choose random position for new atom within box
coord[0] = xlo + random_equal->uniform() * (xhi-xlo);
@@ -384,7 +384,7 @@ void FixGCMC::attempt_insertion()
// if so, add to my list via create_atom()
// initialize info about the atoms
// set group mask to "all" plus fix group
-
+
if (domain->triclinic) {
domain->x2lamda(coord,lamda);
newcoord = lamda;
@@ -394,21 +394,21 @@ void FixGCMC::attempt_insertion()
if (newcoord[0] >= sublo[0] && newcoord[0] < subhi[0] &&
newcoord[1] >= sublo[1] && newcoord[1] < subhi[1] &&
newcoord[2] >= sublo[2] && newcoord[2] < subhi[2]) flag = 1;
-
+
success = 0;
if (flag) {
int nall = atom->nlocal + atom->nghost;
double insertion_energy = energy(nall,coord);
- if (random_unequal->uniform() <
- zz*volume*exp(-beta*insertion_energy)/(ngas+1)) {
- atom->avec->create_atom(ntype,coord);
+ if (random_unequal->uniform() <
+ zz*volume*exp(-beta*insertion_energy)/(ngas+1)) {
+ atom->avec->create_atom(ntype,coord);
int m = atom->nlocal - 1;
atom->type[m] = ntype;
atom->mask[m] = 1 | groupbit;
atom->v[m][0] = random_unequal->gaussian()*sigma;
atom->v[m][1] = random_unequal->gaussian()*sigma;
atom->v[m][2] = random_unequal->gaussian()*sigma;
-
+
int nfix = modify->nfix;
Fix **fix = modify->fix;
for (int j = 0; j < nfix; j++)
@@ -416,20 +416,20 @@ void FixGCMC::attempt_insertion()
if (atom->nlocal > nmax) {
nmax = atom->nmax;
- local_gas_list = (int *)
- memory->srealloc(local_gas_list,nmax*sizeof(int),
- "GCMC:local_gas_list");
+ local_gas_list = (int *)
+ memory->srealloc(local_gas_list,nmax*sizeof(int),
+ "GCMC:local_gas_list");
}
-
+
local_gas_list[ngas_local] = atom->nlocal;
- ngas_local++;
- success = 1;
+ ngas_local++;
+ success = 1;
}
}
-
+
int success_all = 0;
MPI_Allreduce(&success,&success_all,1,MPI_INT,MPI_MAX,world);
-
+
if (success_all) {
ngas++;
ninsert_successes += 1.0;
@@ -443,15 +443,15 @@ void FixGCMC::attempt_insertion()
atom->map_init();
atom->map_set();
}
- }
- }
+ }
+ }
}
/* ----------------------------------------------------------------------
compute particle's interaction energy with the rest of the system
------------------------------------------------------------------------- */
-double FixGCMC::energy(int i, double *coord)
+double FixGCMC::energy(int i, double *coord)
{
double delx,dely,delz,rsq;
@@ -464,7 +464,7 @@ double FixGCMC::energy(int i, double *coord)
double fpair = 0.0;
double factor_coul = 1.0;
double factor_lj = 1.0;
-
+
double total_energy = 0.0;
for (int j = 0; j < nall; j++) {
@@ -477,15 +477,15 @@ double FixGCMC::energy(int i, double *coord)
int jtype = type[j];
if (rsq < cutsq[ntype][jtype])
- total_energy +=
- pair->single(i,j,ntype,jtype,rsq,factor_coul,factor_lj,fpair);
+ total_energy +=
+ pair->single(i,j,ntype,jtype,rsq,factor_coul,factor_lj,fpair);
}
return total_energy;
}
/* ----------------------------------------------------------------------
- parse optional parameters at end of input line
+ parse optional parameters at end of input line
------------------------------------------------------------------------- */
void FixGCMC::options(int narg, char **arg)
@@ -530,7 +530,7 @@ double FixGCMC::memory_usage()
}
/* ----------------------------------------------------------------------
- pack entire state of Fix into one write
+ pack entire state of Fix into one write
------------------------------------------------------------------------- */
void FixGCMC::write_restart(FILE *fp)
@@ -549,7 +549,7 @@ void FixGCMC::write_restart(FILE *fp)
}
/* ----------------------------------------------------------------------
- use state info from restart file to restart the Fix
+ use state info from restart file to restart the Fix
------------------------------------------------------------------------- */
void FixGCMC::restart(char *buf)
@@ -559,9 +559,9 @@ void FixGCMC::restart(char *buf)
seed = static_cast<int> (list[n++]);
random_equal->reset(seed);
-
+
seed = static_cast<int> (list[n++]);
random_unequal->reset(seed);
-
+
next_reneighbor = static_cast<int> (list[n++]);
}
diff --git a/src/MC/fix_gcmc.h b/src/MC/fix_gcmc.h
index b19286bfa6bcb6e181b819144bcbee8c5365acad..9c2b322723b84cf9998dbe074bac03e1c7b53e16 100644
--- a/src/MC/fix_gcmc.h
+++ b/src/MC/fix_gcmc.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -44,18 +44,18 @@ class FixGCMC : public Fix {
private:
int ntype,nevery,seed;
int ncycles,nexchanges,nmcmoves;
- int ngas; // # of gas molecules (or atoms) on all procs
- int ngas_local; // # of gas molecules (or atoms) on this proc
+ int ngas; // # of gas molecules (or atoms) on all procs
+ int ngas_local; // # of gas molecules (or atoms) on this proc
int ngas_before; // # of gas molecules (or atoms) on procs < this proc
int molflag; // 0 = atomic, 1 = molecular system
- double nmove_attempts;
- double nmove_successes;
- double ndel_attempts;
- double ndel_successes;
- double ninsert_attempts;
+ double nmove_attempts;
+ double nmove_successes;
+ double ndel_attempts;
+ double ndel_successes;
+ double ninsert_attempts;
double ninsert_successes;
-
+
int nmax;
double reservoir_temperature;
double chemical_potential;
@@ -63,10 +63,10 @@ class FixGCMC : public Fix {
double beta,zz,sigma,volume;
double xlo,xhi,ylo,yhi,zlo,zhi;
double *sublo,*subhi;
- int *local_gas_list;
+ int *local_gas_list;
double **cutsq;
class Pair *pair;
-
+
class RanPark *random_equal;
class RanPark *random_unequal;
diff --git a/src/MC/pair_dsmc.cpp b/src/MC/pair_dsmc.cpp
index 39a0f50133f322bfa0bd2a62a5c4139c30af4d5d..b54075453b4e4f1952b65efaf270323dde8f0492 100644
--- a/src/MC/pair_dsmc.cpp
+++ b/src/MC/pair_dsmc.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -68,7 +68,7 @@ PairDSMC::~PairDSMC()
void PairDSMC::compute(int eflag, int vflag)
{
double **x = atom->x;
- double *mass = atom->mass;
+ double *mass = atom->mass;
int *type = atom->type;
int nlocal = atom->nlocal;
@@ -111,7 +111,7 @@ void PairDSMC::compute(int eflag, int vflag)
if (number_of_A > max_particle_list) {
max_particle_list = number_of_A;
memory->grow(particle_list,atom->ntypes+1,max_particle_list,
- "pair:particle_list");
+ "pair:particle_list");
}
int m = first[itype][icell];
@@ -128,7 +128,7 @@ void PairDSMC::compute(int eflag, int vflag)
for (jtype = itype; jtype <= atom->ntypes; ++jtype) {
jmass = mass[jtype];
number_of_B = number[jtype][icell];
-
+
reduced_mass = imass*jmass/(imass + jmass);
total_mass = imass + jmass;
jmass_tmass = jmass/total_mass;
@@ -136,27 +136,27 @@ void PairDSMC::compute(int eflag, int vflag)
// if necessary, recompute V_sigma_max values
- if (recompute_vsigmamax_stride &&
- (update->ntimestep % recompute_vsigmamax_stride == 0))
+ if (recompute_vsigmamax_stride &&
+ (update->ntimestep % recompute_vsigmamax_stride == 0))
recompute_V_sigma_max(icell);
// # of collisions to perform for itype-jtype pairs
double &Vs_max = V_sigma_max[itype][jtype];
- double num_of_collisions_double = number_of_A * number_of_B *
- weighting * Vs_max * update->dt / vol;
+ double num_of_collisions_double = number_of_A * number_of_B *
+ weighting * Vs_max * update->dt / vol;
- if ((itype == jtype) and number_of_B)
- num_of_collisions_double *=
- 0.5 * double(number_of_B - 1) / double(number_of_B);
+ if ((itype == jtype) and number_of_B)
+ num_of_collisions_double *=
+ 0.5 * double(number_of_B - 1) / double(number_of_B);
- int num_of_collisions =
- convert_double_to_equivalent_int(num_of_collisions_double);
+ int num_of_collisions =
+ convert_double_to_equivalent_int(num_of_collisions_double);
- if (num_of_collisions > number_of_A)
- error->warning(FLERR,"Pair dsmc: num_of_collisions > number_of_A",0);
- if (num_of_collisions > number_of_B)
- error->warning(FLERR,"Pair dsmc: num_of_collisions > number_of_B",0);
+ if (num_of_collisions > number_of_A)
+ error->warning(FLERR,"Pair dsmc: num_of_collisions > number_of_A",0);
+ if (num_of_collisions > number_of_B)
+ error->warning(FLERR,"Pair dsmc: num_of_collisions > number_of_B",0);
// perform collisions on pairs of particles in icell
@@ -230,7 +230,7 @@ void PairDSMC::settings(int narg, char **arg)
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
- if (setflag[i][j]) cut[i][j] = cut_global;
+ if (setflag[i][j]) cut[i][j] = cut_global;
}
}
@@ -272,22 +272,22 @@ void PairDSMC::coeff(int narg, char **arg)
void PairDSMC::init_style()
{
ncellsx = ncellsy = ncellsz = 1;
- while (((domain->boxhi[0] - domain->boxlo[0])/ncellsx) > max_cell_size)
+ while (((domain->boxhi[0] - domain->boxlo[0])/ncellsx) > max_cell_size)
ncellsx++;
- while (((domain->boxhi[1] - domain->boxlo[1])/ncellsy) > max_cell_size)
+ while (((domain->boxhi[1] - domain->boxlo[1])/ncellsy) > max_cell_size)
ncellsy++;
- while (((domain->boxhi[2] - domain->boxlo[2])/ncellsz) > max_cell_size)
+ while (((domain->boxhi[2] - domain->boxlo[2])/ncellsz) > max_cell_size)
ncellsz++;
cellx = (domain->boxhi[0] - domain->boxlo[0])/ncellsx;
celly = (domain->boxhi[1] - domain->boxlo[1])/ncellsy;
cellz = (domain->boxhi[2] - domain->boxlo[2])/ncellsz;
-
+
if (comm->me == 0) {
if (screen) fprintf(screen,"DSMC cell size = %g x %g x %g\n",
- cellx,celly,cellz);
+ cellx,celly,cellz);
if (logfile) fprintf(logfile,"DSMC cell size = %g x %g x %g\n",
- cellx,celly,cellz);
+ cellx,celly,cellz);
}
total_ncells = ncellsx*ncellsy*ncellsz;
@@ -327,7 +327,7 @@ void PairDSMC::write_restart(FILE *fp)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
- fwrite(&sigma[i][j],sizeof(double),1,fp);
+ fwrite(&sigma[i][j],sizeof(double),1,fp);
fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
@@ -349,12 +349,12 @@ void PairDSMC::read_restart(FILE *fp)
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
- if (me == 0) {
+ if (me == 0) {
fread(&sigma[i][j],sizeof(double),1,fp);
fread(&cut[i][j],sizeof(double),1,fp);
}
- MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
@@ -400,7 +400,7 @@ void PairDSMC::read_restart_settings(FILE *fp)
}
/*-------------------------------------------------------------------------
- rezero and recompute the V_sigma_max values this timestep for use during
+ rezero and recompute the V_sigma_max values this timestep for use during
the next nrezero timesteps
-------------------------------------------------------------------------*/
@@ -412,9 +412,9 @@ void PairDSMC::recompute_V_sigma_max(int icell)
if (number_of_A && number_of_B) {
for (k = 0; k < vsigmamax_samples; k++) {
i = particle_list[itype]
- [static_cast<int>(random->uniform()*number_of_A)];
+ [static_cast<int>(random->uniform()*number_of_A)];
j = particle_list[jtype]
- [static_cast<int>(random->uniform()*number_of_B)];
+ [static_cast<int>(random->uniform()*number_of_B)];
if (i == j) continue;
Vsigma_max = MAX(Vsigma_max,V_sigma(i,j));
}
@@ -444,9 +444,9 @@ double PairDSMC::V_sigma(int i, int j)
// (omega - 0.5) = 0.17
// 1/GAMMA(2.5 - omega) = 1.06418029298371
- if (relative_velocity_sq != 0.0)
+ if (relative_velocity_sq != 0.0)
pair_sigma = sigma[itype][jtype]*
- pow(kT_ref/(0.5*reduced_mass*relative_velocity_sq),0.17) *
+ pow(kT_ref/(0.5*reduced_mass*relative_velocity_sq),0.17) *
1.06418029298371;
else
pair_sigma = 0.0;
@@ -498,15 +498,15 @@ void PairDSMC::scatter_random(int i, int j, int icell)
vj[1] = vcm[1] - delv[1]*imass_tmass;
vj[2] = vcm[2] - delv[2]*imass_tmass;
}
-
+
total_number_of_collisions++;
}
-/* ----------------------------------------------------------------------
- This method converts the double supplied by the calling function into
- an int, which is returned. By adding a random number between 0 and 1
- to the double before converting it to an int, we ensure that,
- statistically, we round down with probability identical to the
+/* ----------------------------------------------------------------------
+ This method converts the double supplied by the calling function into
+ an int, which is returned. By adding a random number between 0 and 1
+ to the double before converting it to an int, we ensure that,
+ statistically, we round down with probability identical to the
remainder and up the rest of the time. So even though we're using an
integer, we're statistically matching the exact expression represented
by the double.
diff --git a/src/MC/pair_dsmc.h b/src/MC/pair_dsmc.h
index 66c2f767dc40c88d6e43d06b7cbe731cec65c4ee..ee1139130b6246b5a7afbee60da2d8b0a67e7178 100644
--- a/src/MC/pair_dsmc.h
+++ b/src/MC/pair_dsmc.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -97,9 +97,9 @@ class PairDSMC : public Pair {
v3[1] = v2[1] - v1[1];
v3[2] = v2[2] - v1[2];
}
-
+
inline double dot3d(const double *v1, const double *v2) {
- return( v1[0]*v2[0] + v1[1]*v2[1] + v1[2]*v2[2] );
+ return( v1[0]*v2[0] + v1[1]*v2[1] + v1[2]*v2[2] );
}
};
diff --git a/src/MEAM/pair_meam.cpp b/src/MEAM/pair_meam.cpp
index 4afb5e1d0f857aeaead885317d5d4692fb53668c..4a3b15898c6ec97d36c9957285a4c8719c548bed 100644
--- a/src/MEAM/pair_meam.cpp
+++ b/src/MEAM/pair_meam.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -37,10 +37,10 @@ using namespace LAMMPS_NS;
enum{FCC,BCC,HCP,DIM,DIAMOND,B1,C11,L12,B2};
int nkeywords = 21;
const char *keywords[] = {"Ec","alpha","rho0","delta","lattce",
- "attrac","repuls","nn2","Cmin","Cmax","rc","delr",
- "augt1","gsmooth_factor","re","ialloy",
- "mixture_ref_t","erose_form","zbl",
- "emb_lin_neg","bkgd_dyn"};
+ "attrac","repuls","nn2","Cmin","Cmax","rc","delr",
+ "augt1","gsmooth_factor","re","ialloy",
+ "mixture_ref_t","erose_form","zbl",
+ "emb_lin_neg","bkgd_dyn"};
/* ---------------------------------------------------------------------- */
@@ -99,7 +99,7 @@ PairMEAM::~PairMEAM()
memory->destroy(scrfcn);
memory->destroy(dscrfcn);
memory->destroy(fcpair);
-
+
for (int i = 0; i < nelements; i++) delete [] elements[i];
delete [] elements;
delete [] mass;
@@ -124,7 +124,7 @@ void PairMEAM::compute(int eflag, int vflag)
evdwl = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = eflag_global = vflag_global =
- eflag_atom = vflag_atom = 0;
+ eflag_atom = vflag_atom = 0;
// grow local arrays if necessary
@@ -237,11 +237,11 @@ void PairMEAM::compute(int eflag, int vflag)
i = ilist_half[ii];
ifort = i+1;
meam_dens_init_(&ifort,&nmax,&ntype,type,fmap,&x[0][0],
- &numneigh_half[i],firstneigh_half[i],
- &numneigh_full[i],firstneigh_full[i],
- &scrfcn[offset],&dscrfcn[offset],&fcpair[offset],
- rho0,&arho1[0][0],&arho2[0][0],arho2b,
- &arho3[0][0],&arho3b[0][0],&t_ave[0][0],&tsq_ave[0][0],
+ &numneigh_half[i],firstneigh_half[i],
+ &numneigh_full[i],firstneigh_full[i],
+ &scrfcn[offset],&dscrfcn[offset],&fcpair[offset],
+ rho0,&arho1[0][0],&arho2[0][0],arho2b,
+ &arho3[0][0],&arho3b[0][0],&t_ave[0][0],&tsq_ave[0][0],
&errorflag);
if (errorflag) {
char str[128];
@@ -254,10 +254,10 @@ void PairMEAM::compute(int eflag, int vflag)
comm->reverse_comm_pair(this);
meam_dens_final_(&nlocal,&nmax,&eflag_either,&eflag_global,&eflag_atom,
- &eng_vdwl,eatom,&ntype,type,fmap,
- &arho1[0][0],&arho2[0][0],arho2b,&arho3[0][0],
- &arho3b[0][0],&t_ave[0][0],&tsq_ave[0][0],gamma,dgamma1,
- dgamma2,dgamma3,rho,rho0,rho1,rho2,rho3,frhop,&errorflag);
+ &eng_vdwl,eatom,&ntype,type,fmap,
+ &arho1[0][0],&arho2[0][0],arho2b,&arho3[0][0],
+ &arho3b[0][0],&t_ave[0][0],&tsq_ave[0][0],gamma,dgamma1,
+ dgamma2,dgamma3,rho,rho0,rho1,rho2,rho3,frhop,&errorflag);
if (errorflag) {
char str[128];
sprintf(str,"MEAM library error %d",errorflag);
@@ -279,13 +279,13 @@ void PairMEAM::compute(int eflag, int vflag)
i = ilist_half[ii];
ifort = i+1;
meam_force_(&ifort,&nmax,&eflag_either,&eflag_global,&eflag_atom,
- &vflag_atom,&eng_vdwl,eatom,&ntype,type,fmap,&x[0][0],
- &numneigh_half[i],firstneigh_half[i],
- &numneigh_full[i],firstneigh_full[i],
- &scrfcn[offset],&dscrfcn[offset],&fcpair[offset],
- dgamma1,dgamma2,dgamma3,rho0,rho1,rho2,rho3,frhop,
- &arho1[0][0],&arho2[0][0],arho2b,&arho3[0][0],&arho3b[0][0],
- &t_ave[0][0],&tsq_ave[0][0],&f[0][0],vptr,&errorflag);
+ &vflag_atom,&eng_vdwl,eatom,&ntype,type,fmap,&x[0][0],
+ &numneigh_half[i],firstneigh_half[i],
+ &numneigh_full[i],firstneigh_full[i],
+ &scrfcn[offset],&dscrfcn[offset],&fcpair[offset],
+ dgamma1,dgamma2,dgamma3,rho0,rho1,rho2,rho3,frhop,
+ &arho1[0][0],&arho2[0][0],arho2b,&arho3[0][0],&arho3b[0][0],
+ &t_ave[0][0],&tsq_ave[0][0],&f[0][0],vptr,&errorflag);
if (errorflag) {
char str[128];
sprintf(str,"MEAM library error %d",errorflag);
@@ -317,7 +317,7 @@ void PairMEAM::allocate()
}
/* ----------------------------------------------------------------------
- global settings
+ global settings
------------------------------------------------------------------------- */
void PairMEAM::settings(int narg, char **arg)
@@ -355,7 +355,7 @@ void PairMEAM::coeff(int narg, char **arg)
if (nelements < 1) error->all(FLERR,"Incorrect args for pair coefficients");
elements = new char*[nelements];
mass = new double[nelements];
-
+
for (i = 0; i < nelements; i++) {
n = strlen(arg[i+3]) + 1;
elements[i] = new char[n];
@@ -368,7 +368,7 @@ void PairMEAM::coeff(int narg, char **arg)
read_files(arg[2],arg[2+nelements+1]);
meam_setup_done_(&cutmax);
-
+
// read args that map atom types to MEAM elements
// map[i] = which element the Ith atom type is, -1 if not mapped
@@ -395,9 +395,9 @@ void PairMEAM::coeff(int narg, char **arg)
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
if (map[i] >= 0 && map[j] >= 0) {
- setflag[i][j] = 1;
- if (i == j) atom->set_mass(i,mass[map[i]]);
- count++;
+ setflag[i][j] = 1;
+ if (i == j) atom->set_mass(i,mass[map[i]]);
+ count++;
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
@@ -508,8 +508,8 @@ void PairMEAM::read_files(char *globalfile, char *userfile)
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fp);
if (ptr == NULL) {
- eof = 1;
- fclose(fp);
+ eof = 1;
+ fclose(fp);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
@@ -530,8 +530,8 @@ void PairMEAM::read_files(char *globalfile, char *userfile)
if (comm->me == 0) {
ptr = fgets(&line[n],MAXLINE-n,fp);
if (ptr == NULL) {
- eof = 1;
- fclose(fp);
+ eof = 1;
+ fclose(fp);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
@@ -603,7 +603,7 @@ void PairMEAM::read_files(char *globalfile, char *userfile)
// pass element parameters to MEAM package
meam_setup_global_(&nelements,lat,z,ielement,atwt,alpha,b0,b1,b2,b3,
- alat,esub,asub,t0,t1,t2,t3,rozero,ibar);
+ alat,esub,asub,t0,t1,t2,t3,rozero,ibar);
// set element masses
@@ -664,8 +664,8 @@ void PairMEAM::read_files(char *globalfile, char *userfile)
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fp);
if (ptr == NULL) {
- eof = 1;
- fclose(fp);
+ eof = 1;
+ fclose(fp);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
@@ -683,8 +683,8 @@ void PairMEAM::read_files(char *globalfile, char *userfile)
nparams = 0;
params[nparams++] = strtok(line,"=(), '\t\n\r\f");
- while (nparams < maxparams &&
- (params[nparams++] = strtok(NULL,"=(), '\t\n\r\f")))
+ while (nparams < maxparams &&
+ (params[nparams++] = strtok(NULL,"=(), '\t\n\r\f")))
continue;
nparams--;
@@ -693,7 +693,7 @@ void PairMEAM::read_files(char *globalfile, char *userfile)
if (which == nkeywords) {
char str[128];
sprintf(str,"Keyword %s in MEAM parameter file not recognized",
- params[0]);
+ params[0]);
error->all(FLERR,str);
}
nindex = nparams - 2;
@@ -881,7 +881,7 @@ void PairMEAM::unpack_reverse_comm(int n, int *list, double *buf)
}
/* ----------------------------------------------------------------------
- memory usage of local atom-based arrays
+ memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double PairMEAM::memory_usage()
@@ -899,8 +899,8 @@ double PairMEAM::memory_usage()
done once per reneighbor so that neigh_f2c and neigh_c2f don't see them
------------------------------------------------------------------------- */
-void PairMEAM::neigh_strip(int inum, int *ilist,
- int *numneigh, int **firstneigh)
+void PairMEAM::neigh_strip(int inum, int *ilist,
+ int *numneigh, int **firstneigh)
{
int i,j,ii,jnum;
int *jlist;
diff --git a/src/MEAM/pair_meam.h b/src/MEAM/pair_meam.h
index 7c99150d46a621e8bde9df11bb41133760b78bc4..9d73ee0489686d36a3faecf1302d5cecfed30024 100644
--- a/src/MEAM/pair_meam.h
+++ b/src/MEAM/pair_meam.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -22,33 +22,33 @@ PairStyle(meam,PairMEAM)
extern "C" {
void meam_setup_global_(int *, int *, double *, int *, double *, double *,
- double *, double *, double *, double *, double *,
- double *, double *, double *, double *, double *,
- double *, double *, int *);
+ double *, double *, double *, double *, double *,
+ double *, double *, double *, double *, double *,
+ double *, double *, int *);
void meam_setup_param_(int *, double *, int *, int *, int *);
void meam_setup_done_(double *);
void meam_dens_init_(int *, int *, int *, int *, int *,
- double *, int *, int *, int *, int *,
- double *, double *, double *, double *,
- double *, double *,
- double *, double *, double *, double *, double *,
+ double *, int *, int *, int *, int *,
+ double *, double *, double *, double *,
+ double *, double *,
+ double *, double *, double *, double *, double *,
int *);
-
+
void meam_dens_final_(int *, int *, int *, int *, int *, double *, double *,
- int *, int *, int *,
- double *, double *, double *, double *,
- double *, double *, double *,
- double *, double *, double *, double *,
- double *, double *,
- double *, double *, double *, double *, int *);
-
+ int *, int *, int *,
+ double *, double *, double *, double *,
+ double *, double *, double *,
+ double *, double *, double *, double *,
+ double *, double *,
+ double *, double *, double *, double *, int *);
+
void meam_force_(int *, int *, int *, int *, int *, int *,
- double *, double *, int *, int *, int *,
- double *, int *, int *, int *, int *, double *, double *,
- double *, double *, double *, double *, double *, double *,
- double *, double *, double *, double *, double *, double *,
- double *, double *, double *, double *, double *, double *, int *);
+ double *, double *, int *, int *, int *,
+ double *, int *, int *, int *, int *, double *, double *,
+ double *, double *, double *, double *, double *, double *,
+ double *, double *, double *, double *, double *, double *,
+ double *, double *, double *, double *, double *, double *, int *);
void meam_cleanup_();
}
diff --git a/src/MOLECULE/angle_charmm.cpp b/src/MOLECULE/angle_charmm.cpp
index 0361209e661df4b3176bf9689afdfcbbd92ebb0f..8d086838fd1575c3a02adc8355801dbae72cb3f5 100644
--- a/src/MOLECULE/angle_charmm.cpp
+++ b/src/MOLECULE/angle_charmm.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -121,10 +121,10 @@ void AngleCharmm::compute(int eflag, int vflag)
c = delx1*delx2 + dely1*dely2 + delz1*delz2;
c /= r1*r2;
-
+
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
-
+
s = sqrt(1.0 - c*c);
if (s < SMALL) s = SMALL;
s = 1.0/s;
@@ -170,7 +170,7 @@ void AngleCharmm::compute(int eflag, int vflag)
}
if (evflag) ev_tally(i1,i2,i3,nlocal,newton_bond,eangle,f1,f3,
- delx1,dely1,delz1,delx2,dely2,delz2);
+ delx1,dely1,delz1,delx2,dely2,delz2);
}
}
@@ -241,7 +241,7 @@ void AngleCharmm::write_restart(FILE *fp)
}
/* ----------------------------------------------------------------------
- proc 0 reads coeffs from restart file, bcasts them
+ proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void AngleCharmm::read_restart(FILE *fp)
@@ -273,7 +273,7 @@ double AngleCharmm::single(int type, int i1, int i2, int i3)
double delz1 = x[i1][2] - x[i2][2];
domain->minimum_image(delx1,dely1,delz1);
double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1);
-
+
double delx2 = x[i3][0] - x[i2][0];
double dely2 = x[i3][1] - x[i2][1];
double delz2 = x[i3][2] - x[i2][2];
diff --git a/src/MOLECULE/angle_charmm.h b/src/MOLECULE/angle_charmm.h
index 51a4554fe730c36ac0a77798da9eb4accaf381d9..b55e7eb9f8f72f87dcf95e363f0667b200f08303 100644
--- a/src/MOLECULE/angle_charmm.h
+++ b/src/MOLECULE/angle_charmm.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/MOLECULE/angle_cosine.cpp b/src/MOLECULE/angle_cosine.cpp
index dc82378083aea9b2be0361d6d8599966d8ddf371..d6bd3965d7009e84f93eb9e36b1fd8417ffed4c7 100644
--- a/src/MOLECULE/angle_cosine.cpp
+++ b/src/MOLECULE/angle_cosine.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -103,7 +103,7 @@ void AngleCosine::compute(int eflag, int vflag)
a11 = a*c / rsq1;
a12 = -a / (r1*r2);
a22 = a*c / rsq2;
-
+
f1[0] = a11*delx1 + a12*delx2;
f1[1] = a11*dely1 + a12*dely2;
f1[2] = a11*delz1 + a12*delz2;
@@ -132,7 +132,7 @@ void AngleCosine::compute(int eflag, int vflag)
}
if (evflag) ev_tally(i1,i2,i3,nlocal,newton_bond,eangle,f1,f3,
- delx1,dely1,delz1,delx2,dely2,delz2);
+ delx1,dely1,delz1,delx2,dely2,delz2);
}
}
@@ -180,7 +180,7 @@ double AngleCosine::equilibrium_angle(int i)
}
/* ----------------------------------------------------------------------
- proc 0 writes out coeffs to restart file
+ proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void AngleCosine::write_restart(FILE *fp)
@@ -189,7 +189,7 @@ void AngleCosine::write_restart(FILE *fp)
}
/* ----------------------------------------------------------------------
- proc 0 reads coeffs from restart file, bcasts them
+ proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void AngleCosine::read_restart(FILE *fp)
@@ -213,7 +213,7 @@ double AngleCosine::single(int type, int i1, int i2, int i3)
double delz1 = x[i1][2] - x[i2][2];
domain->minimum_image(delx1,dely1,delz1);
double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1);
-
+
double delx2 = x[i3][0] - x[i2][0];
double dely2 = x[i3][1] - x[i2][1];
double delz2 = x[i3][2] - x[i2][2];
diff --git a/src/MOLECULE/angle_cosine.h b/src/MOLECULE/angle_cosine.h
index 064bd43bd5877b7b3a9cd9ef163bfde7df50d9df..903794c8b4b1ac4dbd1a7c49e763e03129699d90 100644
--- a/src/MOLECULE/angle_cosine.h
+++ b/src/MOLECULE/angle_cosine.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/MOLECULE/angle_cosine_delta.cpp b/src/MOLECULE/angle_cosine_delta.cpp
index 3697bb87c77c6066fab770ae906902e7a519acda..b7cceb61861e9d51f8d0b5357230dfa82a06efad 100644
--- a/src/MOLECULE/angle_cosine_delta.cpp
+++ b/src/MOLECULE/angle_cosine_delta.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -84,21 +84,21 @@ void AngleCosineDelta::compute(int eflag, int vflag)
c = delx1*delx2 + dely1*dely2 + delz1*delz2;
c /= r1*r2;
-
+
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
-
+
theta = acos(c);
-
+
s = sqrt(1.0 - c*c);
if (s < SMALL) s = SMALL;
s = 1.0/s;
-
+
cot = c/s;
-
+
// force & energy
-
- dtheta = theta - theta0[type];
+
+ dtheta = theta - theta0[type];
dcostheta = cos(dtheta);
tk = k[type] * (1.0-dcostheta);
@@ -107,15 +107,15 @@ void AngleCosineDelta::compute(int eflag, int vflag)
a = -k[type];
// expand dtheta for cos and sin contribution to force
-
+
a11 = a*c / rsq1;
a12 = -a / (r1*r2);
a22 = a*c / rsq2;
-
+
b11 = -a*c*cot / rsq1;
b12 = a*cot / (r1*r2);
b22 = -a*c*cot / rsq2;
-
+
c0 = cos(theta0[type]);
s0 = sin(theta0[type]);
@@ -147,7 +147,7 @@ void AngleCosineDelta::compute(int eflag, int vflag)
}
if (evflag) ev_tally(i1,i2,i3,nlocal,newton_bond,eangle,f1,f3,
- delx1,dely1,delz1,delx2,dely2,delz2);
+ delx1,dely1,delz1,delx2,dely2,delz2);
}
}
@@ -162,7 +162,7 @@ double AngleCosineDelta::single(int type, int i1, int i2, int i3)
double delz1 = x[i1][2] - x[i2][2];
domain->minimum_image(delx1,dely1,delz1);
double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1);
-
+
double delx2 = x[i3][0] - x[i2][0];
double dely2 = x[i3][1] - x[i2][1];
double delz2 = x[i3][2] - x[i2][2];
diff --git a/src/MOLECULE/angle_cosine_delta.h b/src/MOLECULE/angle_cosine_delta.h
index 08dede2baffd242b29fa7a80b1e9805b5b2ad21b..305e3ea673190b6d67a5d6235c2ec7b9ef50dc86 100644
--- a/src/MOLECULE/angle_cosine_delta.h
+++ b/src/MOLECULE/angle_cosine_delta.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/MOLECULE/angle_cosine_periodic.cpp b/src/MOLECULE/angle_cosine_periodic.cpp
index f3b429061374c2592c5c1d69450b7d4939dfe721..7c676d309b0009b3dce59e58d5249bbcf1448df3 100644
--- a/src/MOLECULE/angle_cosine_periodic.cpp
+++ b/src/MOLECULE/angle_cosine_periodic.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -116,7 +116,7 @@ void AngleCosinePeriodic::compute(int eflag, int vflag)
tn = 1.0;
tn_1 = 1.0;
tn_2 = 0.0;
- un = 1.0;
+ un = 1.0;
un_1 = 2.0;
un_2 = 0.0;
@@ -147,7 +147,7 @@ void AngleCosinePeriodic::compute(int eflag, int vflag)
a11 = a*c / rsq1;
a12 = -a / (r1*r2);
a22 = a*c / rsq2;
-
+
f1[0] = a11*delx1 + a12*delx2;
f1[1] = a11*dely1 + a12*dely2;
f1[2] = a11*delz1 + a12*delz2;
@@ -176,7 +176,7 @@ void AngleCosinePeriodic::compute(int eflag, int vflag)
}
if (evflag) ev_tally(i1,i2,i3,nlocal,newton_bond,eangle,f1,f3,
- delx1,dely1,delz1,delx2,dely2,delz2);
+ delx1,dely1,delz1,delx2,dely2,delz2);
}
}
@@ -232,7 +232,7 @@ double AngleCosinePeriodic::equilibrium_angle(int i)
}
/* ----------------------------------------------------------------------
- proc 0 writes out coeffs to restart file
+ proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void AngleCosinePeriodic::write_restart(FILE *fp)
@@ -243,7 +243,7 @@ void AngleCosinePeriodic::write_restart(FILE *fp)
}
/* ----------------------------------------------------------------------
- proc 0 reads coeffs from restart file, bcasts them
+ proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void AngleCosinePeriodic::read_restart(FILE *fp)
@@ -273,7 +273,7 @@ double AngleCosinePeriodic::single(int type, int i1, int i2, int i3)
double delz1 = x[i1][2] - x[i2][2];
domain->minimum_image(delx1,dely1,delz1);
double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1);
-
+
double delx2 = x[i3][0] - x[i2][0];
double dely2 = x[i3][1] - x[i2][1];
double delz2 = x[i3][2] - x[i2][2];
diff --git a/src/MOLECULE/angle_cosine_periodic.h b/src/MOLECULE/angle_cosine_periodic.h
index 5c0aeb11957dadb7db544af5801a8de1e3c682a7..0b9ce0938516d6e771c4feca286d5f38a18b3228 100644
--- a/src/MOLECULE/angle_cosine_periodic.h
+++ b/src/MOLECULE/angle_cosine_periodic.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -37,7 +37,7 @@ class AngleCosinePeriodic : public Angle {
double single(int, int, int, int);
protected:
- double *k;
+ double *k;
int *multiplicity,*b;
void allocate();
diff --git a/src/MOLECULE/angle_cosine_squared.cpp b/src/MOLECULE/angle_cosine_squared.cpp
index 95c1a3b9223dc908cb384a74c042ed115935a1a9..f9275589e8f7ec53f390072eb92aacd438cfc93f 100644
--- a/src/MOLECULE/angle_cosine_squared.cpp
+++ b/src/MOLECULE/angle_cosine_squared.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -98,12 +98,12 @@ void AngleCosineSquared::compute(int eflag, int vflag)
c = delx1*delx2 + dely1*dely2 + delz1*delz2;
c /= r1*r2;
-
+
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
-
+
// force & energy
-
+
dcostheta = c - cos(theta0[type]);
tk = k[type] * dcostheta;
@@ -142,7 +142,7 @@ void AngleCosineSquared::compute(int eflag, int vflag)
}
if (evflag) ev_tally(i1,i2,i3,nlocal,newton_bond,eangle,f1,f3,
- delx1,dely1,delz1,delx2,dely2,delz2);
+ delx1,dely1,delz1,delx2,dely2,delz2);
}
}
@@ -206,7 +206,7 @@ void AngleCosineSquared::write_restart(FILE *fp)
}
/* ----------------------------------------------------------------------
- proc 0 reads coeffs from restart file, bcasts them
+ proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void AngleCosineSquared::read_restart(FILE *fp)
@@ -234,7 +234,7 @@ double AngleCosineSquared::single(int type, int i1, int i2, int i3)
double delz1 = x[i1][2] - x[i2][2];
domain->minimum_image(delx1,dely1,delz1);
double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1);
-
+
double delx2 = x[i3][0] - x[i2][0];
double dely2 = x[i3][1] - x[i2][1];
double delz2 = x[i3][2] - x[i2][2];
@@ -245,7 +245,7 @@ double AngleCosineSquared::single(int type, int i1, int i2, int i3)
c /= r1*r2;
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
-
+
double dcostheta = c - cos(theta0[type]);
double tk = k[type] * dcostheta;
return tk*dcostheta;
diff --git a/src/MOLECULE/angle_cosine_squared.h b/src/MOLECULE/angle_cosine_squared.h
index e3d1f52da4070a1ad2f6535c04f1c99b161c0985..3b8b3114ef9418a01521cb3b7d8a5ca7ed1142f4 100644
--- a/src/MOLECULE/angle_cosine_squared.h
+++ b/src/MOLECULE/angle_cosine_squared.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/MOLECULE/angle_harmonic.cpp b/src/MOLECULE/angle_harmonic.cpp
index 8a462abaede8cbd3b56989fb420b6a8d5eeebf42..a1d36aca6ee1bc2f54636ac93002b96a5cdfc0a6 100644
--- a/src/MOLECULE/angle_harmonic.cpp
+++ b/src/MOLECULE/angle_harmonic.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -94,10 +94,10 @@ void AngleHarmonic::compute(int eflag, int vflag)
c = delx1*delx2 + dely1*dely2 + delz1*delz2;
c /= r1*r2;
-
+
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
-
+
s = sqrt(1.0 - c*c);
if (s < SMALL) s = SMALL;
s = 1.0/s;
@@ -142,7 +142,7 @@ void AngleHarmonic::compute(int eflag, int vflag)
}
if (evflag) ev_tally(i1,i2,i3,nlocal,newton_bond,eangle,f1,f3,
- delx1,dely1,delz1,delx2,dely2,delz2);
+ delx1,dely1,delz1,delx2,dely2,delz2);
}
}
@@ -206,7 +206,7 @@ void AngleHarmonic::write_restart(FILE *fp)
}
/* ----------------------------------------------------------------------
- proc 0 reads coeffs from restart file, bcasts them
+ proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void AngleHarmonic::read_restart(FILE *fp)
@@ -234,7 +234,7 @@ double AngleHarmonic::single(int type, int i1, int i2, int i3)
double delz1 = x[i1][2] - x[i2][2];
domain->minimum_image(delx1,dely1,delz1);
double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1);
-
+
double delx2 = x[i3][0] - x[i2][0];
double dely2 = x[i3][1] - x[i2][1];
double delz2 = x[i3][2] - x[i2][2];
diff --git a/src/MOLECULE/angle_harmonic.h b/src/MOLECULE/angle_harmonic.h
index 84d219ee1f42e5c53fc8dacea84a092ad368ad8c..bc9cb7fdb25b30e6a81f6b810a3405b3d8b14db4 100644
--- a/src/MOLECULE/angle_harmonic.h
+++ b/src/MOLECULE/angle_harmonic.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/MOLECULE/angle_hybrid.cpp b/src/MOLECULE/angle_hybrid.cpp
index 6cd641e73b4de601b338c37277f9994bb64636b4..f492a4e0de6912f2acb65a572c9708daabd22143 100644
--- a/src/MOLECULE/angle_hybrid.cpp
+++ b/src/MOLECULE/angle_hybrid.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -80,9 +80,9 @@ void AngleHybrid::compute(int eflag, int vflag)
}
for (m = 0; m < nstyles; m++) {
if (nanglelist[m] > maxangle[m]) {
- memory->destroy(anglelist[m]);
- maxangle[m] = nanglelist[m] + EXTRA;
- memory->create(anglelist[m],maxangle[m],4,"angle_hybrid:anglelist");
+ memory->destroy(anglelist[m]);
+ maxangle[m] = nanglelist[m] + EXTRA;
+ memory->create(anglelist[m],maxangle[m],4,"angle_hybrid:anglelist");
}
nanglelist[m] = 0;
}
@@ -97,7 +97,7 @@ void AngleHybrid::compute(int eflag, int vflag)
nanglelist[m]++;
}
}
-
+
// call each sub-style's compute function
// set neighbor->anglelist to sub-style anglelist before call
// accumulate sub-style global/peratom energy/virial in hybrid
@@ -125,8 +125,8 @@ void AngleHybrid::compute(int eflag, int vflag)
if (force->newton_bond) n += atom->nghost;
double **vatom_substyle = styles[m]->vatom;
for (i = 0; i < n; i++)
- for (j = 0; j < 6; j++)
- vatom[i][j] += vatom_substyle[i][j];
+ for (j = 0; j < 6; j++)
+ vatom[i][j] += vatom_substyle[i][j];
}
}
@@ -213,11 +213,11 @@ void AngleHybrid::settings(int narg, char **arg)
while (i < narg) {
for (m = 0; m < nstyles; m++)
- if (strcmp(arg[i],keywords[m]) == 0)
- error->all(FLERR,"Angle style hybrid cannot use same pair style twice");
- if (strcmp(arg[i],"hybrid") == 0)
+ if (strcmp(arg[i],keywords[m]) == 0)
+ error->all(FLERR,"Angle style hybrid cannot use same pair style twice");
+ if (strcmp(arg[i],"hybrid") == 0)
error->all(FLERR,"Angle style hybrid cannot have hybrid as an argument");
- if (strcmp(arg[i],"none") == 0)
+ if (strcmp(arg[i],"none") == 0)
error->all(FLERR,"Angle style hybrid cannot have none as an argument");
styles[nstyles] = force->new_angle(arg[i],lmp->suffix,dummy);
keywords[nstyles] = new char[strlen(arg[i])+1];
@@ -293,7 +293,7 @@ void AngleHybrid::init_style()
}
/* ----------------------------------------------------------------------
- return an equilbrium angle length
+ return an equilbrium angle length
------------------------------------------------------------------------- */
double AngleHybrid::equilibrium_angle(int i)
@@ -332,7 +332,7 @@ void AngleHybrid::read_restart(FILE *fp)
keywords = new char*[nstyles];
allocate();
-
+
int n,dummy;
for (int m = 0; m < nstyles; m++) {
if (me == 0) fread(&n,sizeof(int),1,fp);
@@ -361,7 +361,7 @@ double AngleHybrid::memory_usage()
double bytes = maxeatom * sizeof(double);
bytes += maxvatom*6 * sizeof(double);
for (int m = 0; m < nstyles; m++) bytes += maxangle[m]*4 * sizeof(int);
- for (int m = 0; m < nstyles; m++)
+ for (int m = 0; m < nstyles; m++)
if (styles[m]) bytes += styles[m]->memory_usage();
return bytes;
}
diff --git a/src/MOLECULE/angle_hybrid.h b/src/MOLECULE/angle_hybrid.h
index 8f00c7adaf84f7160558c7cd2ca192c01215776c..7fd7d7af2e28b7e90be772008ba17245150f2236 100644
--- a/src/MOLECULE/angle_hybrid.h
+++ b/src/MOLECULE/angle_hybrid.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -49,7 +49,7 @@ class AngleHybrid : public Angle {
int *nanglelist; // # of angles in sub-style anglelists
int *maxangle; // max # of angles sub-style lists can store
int ***anglelist; // anglelist for each sub-style
-
+
void allocate();
};
diff --git a/src/MOLECULE/angle_table.cpp b/src/MOLECULE/angle_table.cpp
index 8a8841f7825a061690955269849b06074a534696..a5d16910d13d57cd5b7a0d8ce9fb3fbc465999a3 100644
--- a/src/MOLECULE/angle_table.cpp
+++ b/src/MOLECULE/angle_table.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -39,7 +39,7 @@ enum{LINEAR,SPLINE};
/* ---------------------------------------------------------------------- */
-AngleTable::AngleTable(LAMMPS *lmp) : Angle(lmp)
+AngleTable::AngleTable(LAMMPS *lmp) : Angle(lmp)
{
ntables = 0;
tables = NULL;
@@ -51,7 +51,7 @@ AngleTable::~AngleTable()
{
for (int m = 0; m < ntables; m++) free_table(&tables[m]);
memory->sfree(tables);
-
+
if (allocated) {
memory->destroy(setflag);
memory->destroy(theta0);
@@ -110,10 +110,10 @@ void AngleTable::compute(int eflag, int vflag)
c = delx1*delx2 + dely1*dely2 + delz1*delz2;
c /= r1*r2;
-
+
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
-
+
s = sqrt(1.0 - c*c);
if (s < SMALL) s = SMALL;
s = 1.0/s;
@@ -122,10 +122,10 @@ void AngleTable::compute(int eflag, int vflag)
theta = acos(c);
uf_lookup(type,theta,u,mdu);
-
+
if (eflag) eangle = u;
- a = mdu * s;
+ a = mdu * s;
a11 = a*c / rsq1;
a12 = -a / (r1*r2);
a22 = a*c / rsq2;
@@ -158,7 +158,7 @@ void AngleTable::compute(int eflag, int vflag)
}
if (evflag) ev_tally(i1,i2,i3,nlocal,newton_bond,eangle,f1,f3,
- delx1,dely1,delz1,delx2,dely2,delz2);
+ delx1,dely1,delz1,delx2,dely2,delz2);
}
}
@@ -177,7 +177,7 @@ void AngleTable::allocate()
}
/* ----------------------------------------------------------------------
- global settings
+ global settings
------------------------------------------------------------------------- */
void AngleTable::settings(int narg, char **arg)
@@ -217,10 +217,10 @@ void AngleTable::coeff(int narg, char **arg)
int ilo,ihi;
force->bounds(arg[0],atom->nangletypes,ilo,ihi);
-
+
int me;
MPI_Comm_rank(world,&me);
- tables = (Table *)
+ tables = (Table *)
memory->srealloc(tables,(ntables+1)*sizeof(Table),"angle:tables");
Table *tb = &tables[ntables];
null_table(tb);
@@ -236,12 +236,12 @@ void AngleTable::coeff(int narg, char **arg)
ahi = tb->afile[tb->ninput-1];
if (fabs(alo-0.0) > TINY || fabs(ahi-180.0) > TINY)
error->all(FLERR,"Angle table must range from 0 to 180 degrees");
-
+
// convert theta from degrees to radians
for (int i = 0; i < tb->ninput; i++){
tb->afile[i] *= MY_PI/180.0;
- tb->ffile[i] *= 180.0/MY_PI;
+ tb->ffile[i] *= 180.0/MY_PI;
}
// spline read-in and compute a,e,f vectors within table
@@ -310,7 +310,7 @@ double AngleTable::single(int type, int i1, int i2, int i3)
double delz1 = x[i1][2] - x[i2][2];
domain->minimum_image(delx1,dely1,delz1);
double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1);
-
+
double delx2 = x[i3][0] - x[i2][0];
double dely2 = x[i3][1] - x[i2][1];
double delz2 = x[i3][2] - x[i2][2];
@@ -347,7 +347,7 @@ void AngleTable::free_table(Table *tb)
memory->destroy(tb->ffile);
memory->destroy(tb->e2file);
memory->destroy(tb->f2file);
-
+
memory->destroy(tb->ang);
memory->destroy(tb->e);
memory->destroy(tb->de);
@@ -426,7 +426,7 @@ void AngleTable::spline_table(Table *tb)
if (tb->fpflag == 0) {
tb->fplo = (tb->ffile[1] - tb->ffile[0]) / (tb->afile[1] - tb->afile[0]);
- tb->fphi = (tb->ffile[tb->ninput-1] - tb->ffile[tb->ninput-2]) /
+ tb->fphi = (tb->ffile[tb->ninput-1] - tb->ffile[tb->ninput-2]) /
(tb->afile[tb->ninput-1] - tb->afile[tb->ninput-2]);
}
@@ -447,7 +447,7 @@ void AngleTable::compute_table(Table *tb)
tb->delta = MY_PI / tlm1;
tb->invdelta = 1.0/tb->delta;
tb->deltasq6 = tb->delta*tb->delta / 6.0;
-
+
// N-1 evenly spaced bins in angle from 0 to PI
// ang,e,f = value at lower edge of bin
// de,df values = delta values of e,f
@@ -465,18 +465,18 @@ void AngleTable::compute_table(Table *tb)
for (int i = 0; i < tablength; i++) {
a = i*tb->delta;
tb->ang[i] = a;
- tb->e[i] = splint(tb->afile,tb->efile,tb->e2file,tb->ninput,a);
- tb->f[i] = splint(tb->afile,tb->ffile,tb->f2file,tb->ninput,a);
+ tb->e[i] = splint(tb->afile,tb->efile,tb->e2file,tb->ninput,a);
+ tb->f[i] = splint(tb->afile,tb->ffile,tb->f2file,tb->ninput,a);
}
-
+
for (int i = 0; i < tlm1; i++) {
tb->de[i] = tb->e[i+1] - tb->e[i];
tb->df[i] = tb->f[i+1] - tb->f[i];
}
-
+
double ep0 = - tb->f[0];
double epn = - tb->f[tlm1];
- spline(tb->ang,tb->e,tablength,ep0,epn,tb->e2);
+ spline(tb->ang,tb->e,tablength,ep0,epn,tb->e2);
spline(tb->ang,tb->f,tablength,tb->fplo,tb->fphi,tb->f2);
}
@@ -490,8 +490,8 @@ void AngleTable::param_extract(Table *tb, char *line)
{
tb->ninput = 0;
tb->fpflag = 0;
- tb->theta0 = 180.0;
-
+ tb->theta0 = 180.0;
+
char *word = strtok(line," \t\n\r\f");
while (word) {
if (strcmp(word,"N") == 0) {
@@ -552,7 +552,7 @@ void AngleTable::bcast_table(Table *tb)
------------------------------------------------------------------------- */
void AngleTable::spline(double *x, double *y, int n,
- double yp1, double ypn, double *y2)
+ double yp1, double ypn, double *y2)
{
int i,k;
double p,qn,sig,un;
@@ -598,7 +598,7 @@ double AngleTable::splint(double *xa, double *ya, double *y2a, int n, double x)
h = xa[khi]-xa[klo];
a = (xa[khi]-x) / h;
b = (x-xa[klo]) / h;
- y = a*ya[klo] + b*ya[khi] +
+ y = a*ya[klo] + b*ya[khi] +
((a*a*a-a)*y2a[klo] + (b*b*b-b)*y2a[khi]) * (h*h)/6.0;
return y;
}
@@ -613,7 +613,7 @@ void AngleTable::uf_lookup(int type, double x, double &u, double &f)
double fraction,a,b;
Table *tb = &tables[tabindex[type]];
-
+
if (tabstyle == LINEAR) {
itable = static_cast<int> ( x * tb->invdelta);
fraction = (x - tb->ang[itable]) * tb->invdelta;
@@ -622,16 +622,16 @@ void AngleTable::uf_lookup(int type, double x, double &u, double &f)
} else if (tabstyle == SPLINE) {
itable = static_cast<int> ( x * tb->invdelta);
fraction = (x - tb->ang[itable]) * tb->invdelta;
-
+
b = (x - tb->ang[itable]) * tb->invdelta;
a = 1.0 - b;
- u = a * tb->e[itable] + b * tb->e[itable+1] +
- ((a*a*a-a)*tb->e2[itable] + (b*b*b-b)*tb->e2[itable+1]) *
+ u = a * tb->e[itable] + b * tb->e[itable+1] +
+ ((a*a*a-a)*tb->e2[itable] + (b*b*b-b)*tb->e2[itable+1]) *
tb->deltasq6;
- f = a * tb->f[itable] + b * tb->f[itable+1] +
- ((a*a*a-a)*tb->f2[itable] + (b*b*b-b)*tb->f2[itable+1]) *
+ f = a * tb->f[itable] + b * tb->f[itable+1] +
+ ((a*a*a-a)*tb->f2[itable] + (b*b*b-b)*tb->f2[itable+1]) *
tb->deltasq6;
- }
+ }
}
/* ----------------------------------------------------------------------
@@ -644,7 +644,7 @@ void AngleTable::u_lookup(int type, double x, double &u)
double fraction,a,b;
Table *tb = &tables[tabindex[type]];
-
+
if (tabstyle == LINEAR) {
itable = static_cast<int> ( x * tb->invdelta);
fraction = (x - tb->ang[itable]) * tb->invdelta;
@@ -652,11 +652,11 @@ void AngleTable::u_lookup(int type, double x, double &u)
} else if (tabstyle == SPLINE) {
itable = static_cast<int> ( x * tb->invdelta);
fraction = (x - tb->ang[itable]) * tb->invdelta;
-
+
b = (x - tb->ang[itable]) * tb->invdelta;
a = 1.0 - b;
- u = a * tb->e[itable] + b * tb->e[itable+1] +
- ((a*a*a-a)*tb->e2[itable] + (b*b*b-b)*tb->e2[itable+1]) *
+ u = a * tb->e[itable] + b * tb->e[itable+1] +
+ ((a*a*a-a)*tb->e2[itable] + (b*b*b-b)*tb->e2[itable+1]) *
tb->deltasq6;
- }
+ }
}
diff --git a/src/MOLECULE/angle_table.h b/src/MOLECULE/angle_table.h
index fe3df9cae879618909c4739da36ccb9e6a76de03..2cfc3d3eea50a63683b94b97af221f96d9c495ef 100644
--- a/src/MOLECULE/angle_table.h
+++ b/src/MOLECULE/angle_table.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -53,7 +53,7 @@ class AngleTable : public Angle {
int ntables;
Table *tables;
int *tabindex;
-
+
void allocate();
void null_table(Table *);
void free_table(Table *);
diff --git a/src/MOLECULE/atom_vec_angle.cpp b/src/MOLECULE/atom_vec_angle.cpp
index c1c0c19be32ac67ba741d3b15314e1113f572a7a..ceda77751879d5ebca96263e06986311f8694a14 100644
--- a/src/MOLECULE/atom_vec_angle.cpp
+++ b/src/MOLECULE/atom_vec_angle.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -49,7 +49,7 @@ AtomVecAngle::AtomVecAngle(LAMMPS *lmp, int narg, char **arg) :
/* ----------------------------------------------------------------------
grow atom arrays
n = 0 grows arrays by DELTA
- n > 0 allocates arrays to size n
+ n > 0 allocates arrays to size n
------------------------------------------------------------------------- */
void AtomVecAngle::grow(int n)
@@ -69,28 +69,28 @@ void AtomVecAngle::grow(int n)
f = memory->grow(atom->f,nmax*comm->nthreads,3,"atom:f");
molecule = memory->grow(atom->molecule,nmax,"atom:molecule");
-
+
nspecial = memory->grow(atom->nspecial,nmax,3,"atom:nspecial");
special = memory->grow(atom->special,nmax,atom->maxspecial,"atom:special");
num_bond = memory->grow(atom->num_bond,nmax,"atom:num_bond");
bond_type = memory->grow(atom->bond_type,nmax,atom->bond_per_atom,
- "atom:bond_type");
+ "atom:bond_type");
bond_atom = memory->grow(atom->bond_atom,nmax,atom->bond_per_atom,
- "atom:bond_atom");
+ "atom:bond_atom");
num_angle = memory->grow(atom->num_angle,nmax,"atom:num_angle");
angle_type = memory->grow(atom->angle_type,nmax,atom->angle_per_atom,
- "atom:angle_type");
+ "atom:angle_type");
angle_atom1 = memory->grow(atom->angle_atom1,nmax,atom->angle_per_atom,
- "atom:angle_atom1");
+ "atom:angle_atom1");
angle_atom2 = memory->grow(atom->angle_atom2,nmax,atom->angle_per_atom,
- "atom:angle_atom2");
+ "atom:angle_atom2");
angle_atom3 = memory->grow(atom->angle_atom3,nmax,atom->angle_per_atom,
- "atom:angle_atom3");
+ "atom:angle_atom3");
if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
}
@@ -153,14 +153,14 @@ void AtomVecAngle::copy(int i, int j, int delflag)
for (k = 0; k < nspecial[j][2]; k++) special[j][k] = special[i][k];
if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j);
}
/* ---------------------------------------------------------------------- */
int AtomVecAngle::pack_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
@@ -196,7 +196,7 @@ int AtomVecAngle::pack_comm(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
int AtomVecAngle::pack_comm_vel(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz,dvx,dvy,dvz;
@@ -224,32 +224,32 @@ int AtomVecAngle::pack_comm_vel(int n, int *list, double *buf,
}
if (!deform_vremap) {
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
}
} else {
dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
dvz = pbc[2]*h_rate[2];
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- if (mask[i] & deform_groupbit) {
- buf[m++] = v[j][0] + dvx;
- buf[m++] = v[j][1] + dvy;
- buf[m++] = v[j][2] + dvz;
- } else {
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
- }
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ if (mask[i] & deform_groupbit) {
+ buf[m++] = v[j][0] + dvx;
+ buf[m++] = v[j][1] + dvy;
+ buf[m++] = v[j][2] + dvz;
+ } else {
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
+ }
}
}
}
@@ -323,7 +323,7 @@ void AtomVecAngle::unpack_reverse(int n, int *list, double *buf)
/* ---------------------------------------------------------------------- */
int AtomVecAngle::pack_border(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
@@ -367,7 +367,7 @@ int AtomVecAngle::pack_border(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
int AtomVecAngle::pack_border_vel(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz,dvx,dvy,dvz;
@@ -399,40 +399,40 @@ int AtomVecAngle::pack_border_vel(int n, int *list, double *buf,
}
if (!deform_vremap) {
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = tag[j];
- buf[m++] = type[j];
- buf[m++] = mask[j];
- buf[m++] = molecule[j];
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = tag[j];
+ buf[m++] = type[j];
+ buf[m++] = mask[j];
+ buf[m++] = molecule[j];
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
}
} else {
dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
dvz = pbc[2]*h_rate[2];
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = tag[j];
- buf[m++] = type[j];
- buf[m++] = mask[j];
- buf[m++] = molecule[j];
- if (mask[i] & deform_groupbit) {
- buf[m++] = v[j][0] + dvx;
- buf[m++] = v[j][1] + dvy;
- buf[m++] = v[j][2] + dvz;
- } else {
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
- }
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = tag[j];
+ buf[m++] = type[j];
+ buf[m++] = mask[j];
+ buf[m++] = molecule[j];
+ if (mask[i] & deform_groupbit) {
+ buf[m++] = v[j][0] + dvx;
+ buf[m++] = v[j][1] + dvy;
+ buf[m++] = v[j][2] + dvz;
+ } else {
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
+ }
}
}
}
@@ -511,7 +511,7 @@ int AtomVecAngle::unpack_border_hybrid(int n, int first, double *buf)
/* ----------------------------------------------------------------------
pack data for atom I for sending to another proc
- xyz must be 1st 3 values, so comm::exchange() can test on them
+ xyz must be 1st 3 values, so comm::exchange() can test on them
------------------------------------------------------------------------- */
int AtomVecAngle::pack_exchange(int i, double *buf)
@@ -552,7 +552,7 @@ int AtomVecAngle::pack_exchange(int i, double *buf)
for (k = 0; k < nspecial[i][2]; k++) buf[m++] = special[i][k];
if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]);
buf[0] = m;
@@ -603,9 +603,9 @@ int AtomVecAngle::unpack_exchange(double *buf)
special[nlocal][k] = static_cast<int> (buf[m++]);
if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->
- unpack_exchange(nlocal,&buf[m]);
+ unpack_exchange(nlocal,&buf[m]);
atom->nlocal++;
return m;
@@ -626,9 +626,9 @@ int AtomVecAngle::size_restart()
n += 14 + 2*num_bond[i] + 4*num_angle[i];
if (atom->nextra_restart)
- for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
for (i = 0; i < nlocal; i++)
- n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
+ n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
return n;
}
@@ -636,7 +636,7 @@ int AtomVecAngle::size_restart()
/* ----------------------------------------------------------------------
pack atom I's data for restart file including extra quantities
xyz must be 1st 3 values, so that read_restart can test on them
- molecular types may be negative, but write as positive
+ molecular types may be negative, but write as positive
------------------------------------------------------------------------- */
int AtomVecAngle::pack_restart(int i, double *buf)
@@ -656,7 +656,7 @@ int AtomVecAngle::pack_restart(int i, double *buf)
buf[m++] = v[i][2];
buf[m++] = molecule[i];
-
+
buf[m++] = num_bond[i];
for (k = 0; k < num_bond[i]; k++) {
buf[m++] = MAX(bond_type[i][k],-bond_type[i][k]);
@@ -672,7 +672,7 @@ int AtomVecAngle::pack_restart(int i, double *buf)
}
if (atom->nextra_restart)
- for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]);
buf[0] = m;
@@ -707,7 +707,7 @@ int AtomVecAngle::unpack_restart(double *buf)
v[nlocal][2] = buf[m++];
molecule[nlocal] = static_cast<int> (buf[m++]);
-
+
num_bond[nlocal] = static_cast<int> (buf[m++]);
for (k = 0; k < num_bond[nlocal]; k++) {
bond_type[nlocal][k] = static_cast<int> (buf[m++]);
@@ -813,7 +813,7 @@ int AtomVecAngle::data_atom_hybrid(int nlocal, char **values)
}
/* ----------------------------------------------------------------------
- return # of bytes of allocated memory
+ return # of bytes of allocated memory
------------------------------------------------------------------------- */
bigint AtomVecAngle::memory_usage()
@@ -830,23 +830,23 @@ bigint AtomVecAngle::memory_usage()
if (atom->memcheck("molecule")) bytes += memory->usage(molecule,nmax);
if (atom->memcheck("nspecial")) bytes += memory->usage(nspecial,nmax,3);
- if (atom->memcheck("special"))
+ if (atom->memcheck("special"))
bytes += memory->usage(special,nmax,atom->maxspecial);
if (atom->memcheck("num_bond")) bytes += memory->usage(num_bond,nmax);
- if (atom->memcheck("bond_type"))
+ if (atom->memcheck("bond_type"))
bytes += memory->usage(bond_type,nmax,atom->bond_per_atom);
- if (atom->memcheck("bond_atom"))
+ if (atom->memcheck("bond_atom"))
bytes += memory->usage(bond_atom,nmax,atom->bond_per_atom);
if (atom->memcheck("num_angle")) bytes += memory->usage(num_angle,nmax);
- if (atom->memcheck("angle_type"))
+ if (atom->memcheck("angle_type"))
bytes += memory->usage(angle_type,nmax,atom->angle_per_atom);
- if (atom->memcheck("angle_atom1"))
+ if (atom->memcheck("angle_atom1"))
bytes += memory->usage(angle_atom1,nmax,atom->angle_per_atom);
- if (atom->memcheck("angle_atom2"))
+ if (atom->memcheck("angle_atom2"))
bytes += memory->usage(angle_atom2,nmax,atom->angle_per_atom);
- if (atom->memcheck("angle_atom3"))
+ if (atom->memcheck("angle_atom3"))
bytes += memory->usage(angle_atom3,nmax,atom->angle_per_atom);
return bytes;
diff --git a/src/MOLECULE/atom_vec_angle.h b/src/MOLECULE/atom_vec_angle.h
index e340c3296cdd24660484ae9619dd62ee0ec88dd4..56a6e359788251626b8d7bf74463ffa2f345cfe7 100644
--- a/src/MOLECULE/atom_vec_angle.h
+++ b/src/MOLECULE/atom_vec_angle.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/MOLECULE/atom_vec_bond.cpp b/src/MOLECULE/atom_vec_bond.cpp
index 8fd65ab1e86d6446aee4330f7e6c85d52f236bf8..ee4aabb6f662499a6371d055884bc0ffd3233074 100644
--- a/src/MOLECULE/atom_vec_bond.cpp
+++ b/src/MOLECULE/atom_vec_bond.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -49,7 +49,7 @@ AtomVecBond::AtomVecBond(LAMMPS *lmp, int narg, char **arg) :
/* ----------------------------------------------------------------------
grow atom arrays
n = 0 grows arrays by DELTA
- n > 0 allocates arrays to size n
+ n > 0 allocates arrays to size n
------------------------------------------------------------------------- */
void AtomVecBond::grow(int n)
@@ -75,12 +75,12 @@ void AtomVecBond::grow(int n)
num_bond = memory->grow(atom->num_bond,nmax,"atom:num_bond");
bond_type = memory->grow(atom->bond_type,nmax,atom->bond_per_atom,
- "atom:bond_type");
+ "atom:bond_type");
bond_atom = memory->grow(atom->bond_atom,nmax,atom->bond_per_atom,
- "atom:bond_atom");
-
+ "atom:bond_atom");
+
if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
}
@@ -132,14 +132,14 @@ void AtomVecBond::copy(int i, int j, int delflag)
for (k = 0; k < nspecial[j][2]; k++) special[j][k] = special[i][k];
if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j);
}
/* ---------------------------------------------------------------------- */
int AtomVecBond::pack_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
@@ -175,7 +175,7 @@ int AtomVecBond::pack_comm(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
int AtomVecBond::pack_comm_vel(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz,dvx,dvy,dvz;
@@ -203,32 +203,32 @@ int AtomVecBond::pack_comm_vel(int n, int *list, double *buf,
}
if (!deform_vremap) {
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
}
} else {
dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
dvz = pbc[2]*h_rate[2];
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- if (mask[i] & deform_groupbit) {
- buf[m++] = v[j][0] + dvx;
- buf[m++] = v[j][1] + dvy;
- buf[m++] = v[j][2] + dvz;
- } else {
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
- }
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ if (mask[i] & deform_groupbit) {
+ buf[m++] = v[j][0] + dvx;
+ buf[m++] = v[j][1] + dvy;
+ buf[m++] = v[j][2] + dvz;
+ } else {
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
+ }
}
}
}
@@ -302,7 +302,7 @@ void AtomVecBond::unpack_reverse(int n, int *list, double *buf)
/* ---------------------------------------------------------------------- */
int AtomVecBond::pack_border(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
@@ -346,7 +346,7 @@ int AtomVecBond::pack_border(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
int AtomVecBond::pack_border_vel(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz,dvx,dvy,dvz;
@@ -378,40 +378,40 @@ int AtomVecBond::pack_border_vel(int n, int *list, double *buf,
}
if (!deform_vremap) {
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = tag[j];
- buf[m++] = type[j];
- buf[m++] = mask[j];
- buf[m++] = molecule[j];
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = tag[j];
+ buf[m++] = type[j];
+ buf[m++] = mask[j];
+ buf[m++] = molecule[j];
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
}
} else {
dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
dvz = pbc[2]*h_rate[2];
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = tag[j];
- buf[m++] = type[j];
- buf[m++] = mask[j];
- buf[m++] = molecule[j];
- if (mask[i] & deform_groupbit) {
- buf[m++] = v[j][0] + dvx;
- buf[m++] = v[j][1] + dvy;
- buf[m++] = v[j][2] + dvz;
- } else {
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
- }
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = tag[j];
+ buf[m++] = type[j];
+ buf[m++] = mask[j];
+ buf[m++] = molecule[j];
+ if (mask[i] & deform_groupbit) {
+ buf[m++] = v[j][0] + dvx;
+ buf[m++] = v[j][1] + dvy;
+ buf[m++] = v[j][2] + dvz;
+ } else {
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
+ }
}
}
}
@@ -490,7 +490,7 @@ int AtomVecBond::unpack_border_hybrid(int n, int first, double *buf)
/* ----------------------------------------------------------------------
pack data for atom I for sending to another proc
- xyz must be 1st 3 values, so comm::exchange() can test on them
+ xyz must be 1st 3 values, so comm::exchange() can test on them
------------------------------------------------------------------------- */
int AtomVecBond::pack_exchange(int i, double *buf)
@@ -523,7 +523,7 @@ int AtomVecBond::pack_exchange(int i, double *buf)
for (k = 0; k < nspecial[i][2]; k++) buf[m++] = special[i][k];
if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]);
buf[0] = m;
@@ -566,9 +566,9 @@ int AtomVecBond::unpack_exchange(double *buf)
special[nlocal][k] = static_cast<int> (buf[m++]);
if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->
- unpack_exchange(nlocal,&buf[m]);
+ unpack_exchange(nlocal,&buf[m]);
atom->nlocal++;
return m;
@@ -589,9 +589,9 @@ int AtomVecBond::size_restart()
n += 13 + 2*num_bond[i];
if (atom->nextra_restart)
- for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
for (i = 0; i < nlocal; i++)
- n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
+ n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
return n;
}
@@ -599,7 +599,7 @@ int AtomVecBond::size_restart()
/* ----------------------------------------------------------------------
pack atom I's data for restart file including extra quantities
xyz must be 1st 3 values, so that read_restart can test on them
- molecular types may be negative, but write as positive
+ molecular types may be negative, but write as positive
------------------------------------------------------------------------- */
int AtomVecBond::pack_restart(int i, double *buf)
@@ -627,7 +627,7 @@ int AtomVecBond::pack_restart(int i, double *buf)
}
if (atom->nextra_restart)
- for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]);
buf[0] = m;
@@ -662,7 +662,7 @@ int AtomVecBond::unpack_restart(double *buf)
v[nlocal][2] = buf[m++];
molecule[nlocal] = static_cast<int> (buf[m++]);
-
+
num_bond[nlocal] = static_cast<int> (buf[m++]);
for (k = 0; k < num_bond[nlocal]; k++) {
bond_type[nlocal][k] = static_cast<int> (buf[m++]);
@@ -757,7 +757,7 @@ int AtomVecBond::data_atom_hybrid(int nlocal, char **values)
}
/* ----------------------------------------------------------------------
- return # of bytes of allocated memory
+ return # of bytes of allocated memory
------------------------------------------------------------------------- */
bigint AtomVecBond::memory_usage()
@@ -774,13 +774,13 @@ bigint AtomVecBond::memory_usage()
if (atom->memcheck("molecule")) bytes += memory->usage(molecule,nmax);
if (atom->memcheck("nspecial")) bytes += memory->usage(nspecial,nmax,3);
- if (atom->memcheck("special"))
+ if (atom->memcheck("special"))
bytes += memory->usage(special,nmax,atom->maxspecial);
if (atom->memcheck("num_bond")) bytes += memory->usage(num_bond,nmax);
- if (atom->memcheck("bond_type"))
+ if (atom->memcheck("bond_type"))
bytes += memory->usage(bond_type,nmax,atom->bond_per_atom);
- if (atom->memcheck("bond_atom"))
+ if (atom->memcheck("bond_atom"))
bytes += memory->usage(bond_atom,nmax,atom->bond_per_atom);
return bytes;
diff --git a/src/MOLECULE/atom_vec_bond.h b/src/MOLECULE/atom_vec_bond.h
index 0da71d3b215d446d970e23441ac143e96464164b..19b301441ceec5f4318b5a4cb51adb1bfdedd640 100644
--- a/src/MOLECULE/atom_vec_bond.h
+++ b/src/MOLECULE/atom_vec_bond.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/MOLECULE/atom_vec_full.cpp b/src/MOLECULE/atom_vec_full.cpp
index 793237b447da77bf9293abef7d8e502e9d625cf7..0a8a3785deeb97fd3ae28caa0e03f11e65c5c045 100644
--- a/src/MOLECULE/atom_vec_full.cpp
+++ b/src/MOLECULE/atom_vec_full.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -27,7 +27,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-AtomVecFull::AtomVecFull(LAMMPS *lmp, int narg, char **arg) :
+AtomVecFull::AtomVecFull(LAMMPS *lmp, int narg, char **arg) :
AtomVec(lmp, narg, arg)
{
molecular = 1;
@@ -49,7 +49,7 @@ AtomVecFull::AtomVecFull(LAMMPS *lmp, int narg, char **arg) :
/* ----------------------------------------------------------------------
grow atom arrays
n = 0 grows arrays by DELTA
- n > 0 allocates arrays to size n
+ n > 0 allocates arrays to size n
------------------------------------------------------------------------- */
void AtomVecFull::grow(int n)
@@ -73,58 +73,58 @@ void AtomVecFull::grow(int n)
nspecial = memory->grow(atom->nspecial,nmax,3,"atom:nspecial");
special = memory->grow(atom->special,nmax,atom->maxspecial,"atom:special");
-
+
num_bond = memory->grow(atom->num_bond,nmax,"atom:num_bond");
bond_type = memory->grow(atom->bond_type,nmax,atom->bond_per_atom,
- "atom:bond_type");
+ "atom:bond_type");
bond_atom = memory->grow(atom->bond_atom,nmax,atom->bond_per_atom,
- "atom:bond_atom");
+ "atom:bond_atom");
num_angle = memory->grow(atom->num_angle,nmax,"atom:num_angle");
angle_type = memory->grow(atom->angle_type,nmax,atom->angle_per_atom,
- "atom:angle_type");
+ "atom:angle_type");
angle_atom1 = memory->grow(atom->angle_atom1,nmax,atom->angle_per_atom,
- "atom:angle_atom1");
+ "atom:angle_atom1");
angle_atom2 = memory->grow(atom->angle_atom2,nmax,atom->angle_per_atom,
- "atom:angle_atom2");
+ "atom:angle_atom2");
angle_atom3 = memory->grow(atom->angle_atom3,nmax,atom->angle_per_atom,
- "atom:angle_atom3");
-
+ "atom:angle_atom3");
+
num_dihedral = memory->grow(atom->num_dihedral,nmax,"atom:num_dihedral");
dihedral_type = memory->grow(atom->dihedral_type,nmax,
- atom->dihedral_per_atom,"atom:dihedral_type");
- dihedral_atom1 =
+ atom->dihedral_per_atom,"atom:dihedral_type");
+ dihedral_atom1 =
memory->grow(atom->dihedral_atom1,nmax,atom->dihedral_per_atom,
- "atom:dihedral_atom1");
- dihedral_atom2 =
+ "atom:dihedral_atom1");
+ dihedral_atom2 =
memory->grow(atom->dihedral_atom2,nmax,atom->dihedral_per_atom,
- "atom:dihedral_atom2");
- dihedral_atom3 =
+ "atom:dihedral_atom2");
+ dihedral_atom3 =
memory->grow(atom->dihedral_atom3,nmax,atom->dihedral_per_atom,
- "atom:dihedral_atom3");
- dihedral_atom4 =
+ "atom:dihedral_atom3");
+ dihedral_atom4 =
memory->grow(atom->dihedral_atom4,nmax,atom->dihedral_per_atom,
- "atom:dihedral_atom4");
+ "atom:dihedral_atom4");
num_improper = memory->grow(atom->num_improper,nmax,"atom:num_improper");
- improper_type =
+ improper_type =
memory->grow(atom->improper_type,nmax,atom->improper_per_atom,
- "atom:improper_type");
- improper_atom1 =
+ "atom:improper_type");
+ improper_atom1 =
memory->grow(atom->improper_atom1,nmax,atom->improper_per_atom,
- "atom:improper_atom1");
- improper_atom2 =
+ "atom:improper_atom1");
+ improper_atom2 =
memory->grow(atom->improper_atom2,nmax,atom->improper_per_atom,
- "atom:improper_atom2");
- improper_atom3 =
+ "atom:improper_atom2");
+ improper_atom3 =
memory->grow(atom->improper_atom3,nmax,atom->improper_per_atom,
- "atom:improper_atom3");
- improper_atom4 =
+ "atom:improper_atom3");
+ improper_atom4 =
memory->grow(atom->improper_atom4,nmax,atom->improper_per_atom,
- "atom:improper_atom4");
+ "atom:improper_atom4");
if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
}
@@ -212,14 +212,14 @@ void AtomVecFull::copy(int i, int j, int delflag)
for (k = 0; k < nspecial[j][2]; k++) special[j][k] = special[i][k];
if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j);
}
/* ---------------------------------------------------------------------- */
int AtomVecFull::pack_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
@@ -255,7 +255,7 @@ int AtomVecFull::pack_comm(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
int AtomVecFull::pack_comm_vel(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz,dvx,dvy,dvz;
@@ -283,32 +283,32 @@ int AtomVecFull::pack_comm_vel(int n, int *list, double *buf,
}
if (!deform_vremap) {
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
}
} else {
dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
dvz = pbc[2]*h_rate[2];
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- if (mask[i] & deform_groupbit) {
- buf[m++] = v[j][0] + dvx;
- buf[m++] = v[j][1] + dvy;
- buf[m++] = v[j][2] + dvz;
- } else {
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
- }
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ if (mask[i] & deform_groupbit) {
+ buf[m++] = v[j][0] + dvx;
+ buf[m++] = v[j][1] + dvy;
+ buf[m++] = v[j][2] + dvz;
+ } else {
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
+ }
}
}
}
@@ -382,7 +382,7 @@ void AtomVecFull::unpack_reverse(int n, int *list, double *buf)
/* ---------------------------------------------------------------------- */
int AtomVecFull::pack_border(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
@@ -428,7 +428,7 @@ int AtomVecFull::pack_border(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
int AtomVecFull::pack_border_vel(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz,dvx,dvy,dvz;
@@ -461,42 +461,42 @@ int AtomVecFull::pack_border_vel(int n, int *list, double *buf,
}
if (!deform_vremap) {
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = tag[j];
- buf[m++] = type[j];
- buf[m++] = mask[j];
- buf[m++] = q[j];
- buf[m++] = molecule[j];
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = tag[j];
+ buf[m++] = type[j];
+ buf[m++] = mask[j];
+ buf[m++] = q[j];
+ buf[m++] = molecule[j];
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
}
} else {
dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
dvz = pbc[2]*h_rate[2];
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = tag[j];
- buf[m++] = type[j];
- buf[m++] = mask[j];
- buf[m++] = q[j];
- buf[m++] = molecule[j];
- if (mask[i] & deform_groupbit) {
- buf[m++] = v[j][0] + dvx;
- buf[m++] = v[j][1] + dvy;
- buf[m++] = v[j][2] + dvz;
- } else {
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
- }
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = tag[j];
+ buf[m++] = type[j];
+ buf[m++] = mask[j];
+ buf[m++] = q[j];
+ buf[m++] = molecule[j];
+ if (mask[i] & deform_groupbit) {
+ buf[m++] = v[j][0] + dvx;
+ buf[m++] = v[j][1] + dvy;
+ buf[m++] = v[j][2] + dvz;
+ } else {
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
+ }
}
}
}
@@ -580,7 +580,7 @@ int AtomVecFull::unpack_border_hybrid(int n, int first, double *buf)
/* ----------------------------------------------------------------------
pack data for atom I for sending to another proc
- xyz must be 1st 3 values, so comm::exchange() can test on them
+ xyz must be 1st 3 values, so comm::exchange() can test on them
------------------------------------------------------------------------- */
int AtomVecFull::pack_exchange(int i, double *buf)
@@ -640,7 +640,7 @@ int AtomVecFull::pack_exchange(int i, double *buf)
for (k = 0; k < nspecial[i][2]; k++) buf[m++] = special[i][k];
if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]);
buf[0] = m;
@@ -710,9 +710,9 @@ int AtomVecFull::unpack_exchange(double *buf)
special[nlocal][k] = static_cast<int> (buf[m++]);
if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->
- unpack_exchange(nlocal,&buf[m]);
+ unpack_exchange(nlocal,&buf[m]);
atom->nlocal++;
return m;
@@ -734,9 +734,9 @@ int AtomVecFull::size_restart()
5*num_dihedral[i] + 5*num_improper[i];
if (atom->nextra_restart)
- for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
for (i = 0; i < nlocal; i++)
- n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
+ n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
return n;
}
@@ -744,7 +744,7 @@ int AtomVecFull::size_restart()
/* ----------------------------------------------------------------------
pack atom I's data for restart file including extra quantities
xyz must be 1st 3 values, so that read_restart can test on them
- molecular types may be negative, but write as positive
+ molecular types may be negative, but write as positive
------------------------------------------------------------------------- */
int AtomVecFull::pack_restart(int i, double *buf)
@@ -765,13 +765,13 @@ int AtomVecFull::pack_restart(int i, double *buf)
buf[m++] = q[i];
buf[m++] = molecule[i];
-
+
buf[m++] = num_bond[i];
for (k = 0; k < num_bond[i]; k++) {
buf[m++] = MAX(bond_type[i][k],-bond_type[i][k]);
buf[m++] = bond_atom[i][k];
}
-
+
buf[m++] = num_angle[i];
for (k = 0; k < num_angle[i]; k++) {
buf[m++] = MAX(angle_type[i][k],-angle_type[i][k]);
@@ -799,7 +799,7 @@ int AtomVecFull::pack_restart(int i, double *buf)
}
if (atom->nextra_restart)
- for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]);
buf[0] = m;
@@ -835,7 +835,7 @@ int AtomVecFull::unpack_restart(double *buf)
q[nlocal] = buf[m++];
molecule[nlocal] = static_cast<int> (buf[m++]);
-
+
num_bond[nlocal] = static_cast<int> (buf[m++]);
for (k = 0; k < num_bond[nlocal]; k++) {
bond_type[nlocal][k] = static_cast<int> (buf[m++]);
@@ -969,7 +969,7 @@ int AtomVecFull::data_atom_hybrid(int nlocal, char **values)
}
/* ----------------------------------------------------------------------
- return # of bytes of allocated memory
+ return # of bytes of allocated memory
------------------------------------------------------------------------- */
bigint AtomVecFull::memory_usage()
@@ -987,47 +987,47 @@ bigint AtomVecFull::memory_usage()
if (atom->memcheck("q")) bytes += memory->usage(q,nmax);
if (atom->memcheck("molecule")) bytes += memory->usage(molecule,nmax);
if (atom->memcheck("nspecial")) bytes += memory->usage(nspecial,nmax,3);
- if (atom->memcheck("special"))
+ if (atom->memcheck("special"))
bytes += memory->usage(special,nmax,atom->maxspecial);
if (atom->memcheck("num_bond")) bytes += memory->usage(num_bond,nmax);
- if (atom->memcheck("bond_type"))
+ if (atom->memcheck("bond_type"))
bytes += memory->usage(bond_type,nmax,atom->bond_per_atom);
- if (atom->memcheck("bond_atom"))
+ if (atom->memcheck("bond_atom"))
bytes += memory->usage(bond_atom,nmax,atom->bond_per_atom);
if (atom->memcheck("num_angle")) bytes += memory->usage(num_angle,nmax);
- if (atom->memcheck("angle_type"))
+ if (atom->memcheck("angle_type"))
bytes += memory->usage(angle_type,nmax,atom->angle_per_atom);
- if (atom->memcheck("angle_atom1"))
+ if (atom->memcheck("angle_atom1"))
bytes += memory->usage(angle_atom1,nmax,atom->angle_per_atom);
- if (atom->memcheck("angle_atom2"))
+ if (atom->memcheck("angle_atom2"))
bytes += memory->usage(angle_atom2,nmax,atom->angle_per_atom);
- if (atom->memcheck("angle_atom3"))
+ if (atom->memcheck("angle_atom3"))
bytes += memory->usage(angle_atom3,nmax,atom->angle_per_atom);
if (atom->memcheck("num_dihedral")) bytes += memory->usage(num_dihedral,nmax);
- if (atom->memcheck("dihedral_type"))
+ if (atom->memcheck("dihedral_type"))
bytes += memory->usage(dihedral_type,nmax,atom->dihedral_per_atom);
- if (atom->memcheck("dihedral_atom1"))
+ if (atom->memcheck("dihedral_atom1"))
bytes += memory->usage(dihedral_atom1,nmax,atom->dihedral_per_atom);
- if (atom->memcheck("dihedral_atom2"))
+ if (atom->memcheck("dihedral_atom2"))
bytes += memory->usage(dihedral_atom2,nmax,atom->dihedral_per_atom);
- if (atom->memcheck("dihedral_atom3"))
+ if (atom->memcheck("dihedral_atom3"))
bytes += memory->usage(dihedral_atom3,nmax,atom->dihedral_per_atom);
- if (atom->memcheck("dihedral_atom4"))
+ if (atom->memcheck("dihedral_atom4"))
bytes += memory->usage(dihedral_atom4,nmax,atom->dihedral_per_atom);
if (atom->memcheck("num_improper")) bytes += memory->usage(num_improper,nmax);
- if (atom->memcheck("improper_type"))
+ if (atom->memcheck("improper_type"))
bytes += memory->usage(improper_type,nmax,atom->improper_per_atom);
- if (atom->memcheck("improper_atom1"))
+ if (atom->memcheck("improper_atom1"))
bytes += memory->usage(improper_atom1,nmax,atom->improper_per_atom);
- if (atom->memcheck("improper_atom2"))
+ if (atom->memcheck("improper_atom2"))
bytes += memory->usage(improper_atom2,nmax,atom->improper_per_atom);
- if (atom->memcheck("improper_atom3"))
+ if (atom->memcheck("improper_atom3"))
bytes += memory->usage(improper_atom3,nmax,atom->improper_per_atom);
- if (atom->memcheck("improper_atom4"))
+ if (atom->memcheck("improper_atom4"))
bytes += memory->usage(improper_atom4,nmax,atom->improper_per_atom);
return bytes;
diff --git a/src/MOLECULE/atom_vec_full.h b/src/MOLECULE/atom_vec_full.h
index c188c14265430fcff80c8c92deb511a1be5d225c..f21c736acfb7cd6d6d5c1157bb6342fe19dbba9f 100644
--- a/src/MOLECULE/atom_vec_full.h
+++ b/src/MOLECULE/atom_vec_full.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/MOLECULE/atom_vec_molecular.cpp b/src/MOLECULE/atom_vec_molecular.cpp
index b29dc143741e12f3ec90895fc0544a7e4a60302e..c2d2ca9fc51faac5a9972b0fda065e0547cf3fb4 100644
--- a/src/MOLECULE/atom_vec_molecular.cpp
+++ b/src/MOLECULE/atom_vec_molecular.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -27,7 +27,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-AtomVecMolecular::AtomVecMolecular(LAMMPS *lmp, int narg, char **arg) :
+AtomVecMolecular::AtomVecMolecular(LAMMPS *lmp, int narg, char **arg) :
AtomVec(lmp, narg, arg)
{
molecular = 1;
@@ -49,7 +49,7 @@ AtomVecMolecular::AtomVecMolecular(LAMMPS *lmp, int narg, char **arg) :
/* ----------------------------------------------------------------------
grow atom arrays
n = 0 grows arrays by DELTA
- n > 0 allocates arrays to size n
+ n > 0 allocates arrays to size n
------------------------------------------------------------------------- */
void AtomVecMolecular::grow(int n)
@@ -72,58 +72,58 @@ void AtomVecMolecular::grow(int n)
nspecial = memory->grow(atom->nspecial,nmax,3,"atom:nspecial");
special = memory->grow(atom->special,nmax,atom->maxspecial,"atom:special");
-
+
num_bond = memory->grow(atom->num_bond,nmax,"atom:num_bond");
bond_type = memory->grow(atom->bond_type,nmax,atom->bond_per_atom,
- "atom:bond_type");
+ "atom:bond_type");
bond_atom = memory->grow(atom->bond_atom,nmax,atom->bond_per_atom,
- "atom:bond_atom");
+ "atom:bond_atom");
num_angle = memory->grow(atom->num_angle,nmax,"atom:num_angle");
angle_type = memory->grow(atom->angle_type,nmax,atom->angle_per_atom,
- "atom:angle_type");
+ "atom:angle_type");
angle_atom1 = memory->grow(atom->angle_atom1,nmax,atom->angle_per_atom,
- "atom:angle_atom1");
+ "atom:angle_atom1");
angle_atom2 = memory->grow(atom->angle_atom2,nmax,atom->angle_per_atom,
- "atom:angle_atom2");
+ "atom:angle_atom2");
angle_atom3 = memory->grow(atom->angle_atom3,nmax,atom->angle_per_atom,
- "atom:angle_atom3");
+ "atom:angle_atom3");
num_dihedral = memory->grow(atom->num_dihedral,nmax,"atom:num_dihedral");
dihedral_type = memory->grow(atom->dihedral_type,nmax,
- atom->dihedral_per_atom,"atom:dihedral_type");
- dihedral_atom1 =
+ atom->dihedral_per_atom,"atom:dihedral_type");
+ dihedral_atom1 =
memory->grow(atom->dihedral_atom1,nmax,atom->dihedral_per_atom,
- "atom:dihedral_atom1");
- dihedral_atom2 =
+ "atom:dihedral_atom1");
+ dihedral_atom2 =
memory->grow(atom->dihedral_atom2,nmax,atom->dihedral_per_atom,
- "atom:dihedral_atom2");
- dihedral_atom3 =
+ "atom:dihedral_atom2");
+ dihedral_atom3 =
memory->grow(atom->dihedral_atom3,nmax,atom->dihedral_per_atom,
- "atom:dihedral_atom3");
- dihedral_atom4 =
+ "atom:dihedral_atom3");
+ dihedral_atom4 =
memory->grow(atom->dihedral_atom4,nmax,atom->dihedral_per_atom,
- "atom:dihedral_atom4");
+ "atom:dihedral_atom4");
num_improper = memory->grow(atom->num_improper,nmax,"atom:num_improper");
- improper_type =
+ improper_type =
memory->grow(atom->improper_type,nmax,atom->improper_per_atom,
- "atom:improper_type");
- improper_atom1 =
+ "atom:improper_type");
+ improper_atom1 =
memory->grow(atom->improper_atom1,nmax,atom->improper_per_atom,
- "atom:improper_atom1");
- improper_atom2 =
+ "atom:improper_atom1");
+ improper_atom2 =
memory->grow(atom->improper_atom2,nmax,atom->improper_per_atom,
- "atom:improper_atom2");
- improper_atom3 =
+ "atom:improper_atom2");
+ improper_atom3 =
memory->grow(atom->improper_atom3,nmax,atom->improper_per_atom,
- "atom:improper_atom3");
- improper_atom4 =
+ "atom:improper_atom3");
+ improper_atom4 =
memory->grow(atom->improper_atom4,nmax,atom->improper_per_atom,
- "atom:improper_atom4");
+ "atom:improper_atom4");
if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
}
@@ -210,14 +210,14 @@ void AtomVecMolecular::copy(int i, int j, int delflag)
for (k = 0; k < nspecial[j][2]; k++) special[j][k] = special[i][k];
if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j);
}
/* ---------------------------------------------------------------------- */
-int AtomVecMolecular::pack_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+int AtomVecMolecular::pack_comm(int n, int *list, double *buf,
+ int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
@@ -252,8 +252,8 @@ int AtomVecMolecular::pack_comm(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
-int AtomVecMolecular::pack_comm_vel(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+int AtomVecMolecular::pack_comm_vel(int n, int *list, double *buf,
+ int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz,dvx,dvy,dvz;
@@ -281,32 +281,32 @@ int AtomVecMolecular::pack_comm_vel(int n, int *list, double *buf,
}
if (!deform_vremap) {
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
}
} else {
dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
dvz = pbc[2]*h_rate[2];
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- if (mask[i] & deform_groupbit) {
- buf[m++] = v[j][0] + dvx;
- buf[m++] = v[j][1] + dvy;
- buf[m++] = v[j][2] + dvz;
- } else {
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
- }
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ if (mask[i] & deform_groupbit) {
+ buf[m++] = v[j][0] + dvx;
+ buf[m++] = v[j][1] + dvy;
+ buf[m++] = v[j][2] + dvz;
+ } else {
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
+ }
}
}
}
@@ -380,7 +380,7 @@ void AtomVecMolecular::unpack_reverse(int n, int *list, double *buf)
/* ---------------------------------------------------------------------- */
int AtomVecMolecular::pack_border(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
@@ -424,7 +424,7 @@ int AtomVecMolecular::pack_border(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
int AtomVecMolecular::pack_border_vel(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz,dvx,dvy,dvz;
@@ -456,40 +456,40 @@ int AtomVecMolecular::pack_border_vel(int n, int *list, double *buf,
}
if (!deform_vremap) {
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = tag[j];
- buf[m++] = type[j];
- buf[m++] = mask[j];
- buf[m++] = molecule[j];
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = tag[j];
+ buf[m++] = type[j];
+ buf[m++] = mask[j];
+ buf[m++] = molecule[j];
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
}
} else {
dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
dvz = pbc[2]*h_rate[2];
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = tag[j];
- buf[m++] = type[j];
- buf[m++] = mask[j];
- buf[m++] = molecule[j];
- if (mask[i] & deform_groupbit) {
- buf[m++] = v[j][0] + dvx;
- buf[m++] = v[j][1] + dvy;
- buf[m++] = v[j][2] + dvz;
- } else {
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
- }
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = tag[j];
+ buf[m++] = type[j];
+ buf[m++] = mask[j];
+ buf[m++] = molecule[j];
+ if (mask[i] & deform_groupbit) {
+ buf[m++] = v[j][0] + dvx;
+ buf[m++] = v[j][1] + dvy;
+ buf[m++] = v[j][2] + dvz;
+ } else {
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
+ }
}
}
}
@@ -568,7 +568,7 @@ int AtomVecMolecular::unpack_border_hybrid(int n, int first, double *buf)
/* ----------------------------------------------------------------------
pack data for atom I for sending to another proc
- xyz must be 1st 3 values, so comm::exchange() can test on them
+ xyz must be 1st 3 values, so comm::exchange() can test on them
------------------------------------------------------------------------- */
int AtomVecMolecular::pack_exchange(int i, double *buf)
@@ -627,7 +627,7 @@ int AtomVecMolecular::pack_exchange(int i, double *buf)
for (k = 0; k < nspecial[i][2]; k++) buf[m++] = special[i][k];
if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]);
buf[0] = m;
@@ -696,9 +696,9 @@ int AtomVecMolecular::unpack_exchange(double *buf)
special[nlocal][k] = static_cast<int> (buf[m++]);
if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->
- unpack_exchange(nlocal,&buf[m]);
+ unpack_exchange(nlocal,&buf[m]);
atom->nlocal++;
return m;
@@ -720,9 +720,9 @@ int AtomVecMolecular::size_restart()
5*num_dihedral[i] + 5*num_improper[i];
if (atom->nextra_restart)
- for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
for (i = 0; i < nlocal; i++)
- n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
+ n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
return n;
}
@@ -730,7 +730,7 @@ int AtomVecMolecular::size_restart()
/* ----------------------------------------------------------------------
pack atom I's data for restart file including extra quantities
xyz must be 1st 3 values, so that read_restart can test on them
- molecular types may be negative, but write as positive
+ molecular types may be negative, but write as positive
------------------------------------------------------------------------- */
int AtomVecMolecular::pack_restart(int i, double *buf)
@@ -750,13 +750,13 @@ int AtomVecMolecular::pack_restart(int i, double *buf)
buf[m++] = v[i][2];
buf[m++] = molecule[i];
-
+
buf[m++] = num_bond[i];
for (k = 0; k < num_bond[i]; k++) {
buf[m++] = MAX(bond_type[i][k],-bond_type[i][k]);
buf[m++] = bond_atom[i][k];
}
-
+
buf[m++] = num_angle[i];
for (k = 0; k < num_angle[i]; k++) {
buf[m++] = MAX(angle_type[i][k],-angle_type[i][k]);
@@ -784,7 +784,7 @@ int AtomVecMolecular::pack_restart(int i, double *buf)
}
if (atom->nextra_restart)
- for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]);
buf[0] = m;
@@ -819,7 +819,7 @@ int AtomVecMolecular::unpack_restart(double *buf)
v[nlocal][2] = buf[m++];
molecule[nlocal] = static_cast<int> (buf[m++]);
-
+
num_bond[nlocal] = static_cast<int> (buf[m++]);
for (k = 0; k < num_bond[nlocal]; k++) {
bond_type[nlocal][k] = static_cast<int> (buf[m++]);
@@ -949,7 +949,7 @@ int AtomVecMolecular::data_atom_hybrid(int nlocal, char **values)
}
/* ----------------------------------------------------------------------
- return # of bytes of allocated memory
+ return # of bytes of allocated memory
------------------------------------------------------------------------- */
bigint AtomVecMolecular::memory_usage()
@@ -966,47 +966,47 @@ bigint AtomVecMolecular::memory_usage()
if (atom->memcheck("molecule")) bytes += memory->usage(molecule,nmax);
if (atom->memcheck("nspecial")) bytes += memory->usage(nspecial,nmax,3);
- if (atom->memcheck("special"))
+ if (atom->memcheck("special"))
bytes += memory->usage(special,nmax,atom->maxspecial);
if (atom->memcheck("num_bond")) bytes += memory->usage(num_bond,nmax);
- if (atom->memcheck("bond_type"))
+ if (atom->memcheck("bond_type"))
bytes += memory->usage(bond_type,nmax,atom->bond_per_atom);
- if (atom->memcheck("bond_atom"))
+ if (atom->memcheck("bond_atom"))
bytes += memory->usage(bond_atom,nmax,atom->bond_per_atom);
if (atom->memcheck("num_angle")) bytes += memory->usage(num_angle,nmax);
- if (atom->memcheck("angle_type"))
+ if (atom->memcheck("angle_type"))
bytes += memory->usage(angle_type,nmax,atom->angle_per_atom);
- if (atom->memcheck("angle_atom1"))
+ if (atom->memcheck("angle_atom1"))
bytes += memory->usage(angle_atom1,nmax,atom->angle_per_atom);
- if (atom->memcheck("angle_atom2"))
+ if (atom->memcheck("angle_atom2"))
bytes += memory->usage(angle_atom2,nmax,atom->angle_per_atom);
- if (atom->memcheck("angle_atom3"))
+ if (atom->memcheck("angle_atom3"))
bytes += memory->usage(angle_atom3,nmax,atom->angle_per_atom);
if (atom->memcheck("num_dihedral")) bytes += memory->usage(num_dihedral,nmax);
- if (atom->memcheck("dihedral_type"))
+ if (atom->memcheck("dihedral_type"))
bytes += memory->usage(dihedral_type,nmax,atom->dihedral_per_atom);
- if (atom->memcheck("dihedral_atom1"))
+ if (atom->memcheck("dihedral_atom1"))
bytes += memory->usage(dihedral_atom1,nmax,atom->dihedral_per_atom);
- if (atom->memcheck("dihedral_atom2"))
+ if (atom->memcheck("dihedral_atom2"))
bytes += memory->usage(dihedral_atom2,nmax,atom->dihedral_per_atom);
- if (atom->memcheck("dihedral_atom3"))
+ if (atom->memcheck("dihedral_atom3"))
bytes += memory->usage(dihedral_atom3,nmax,atom->dihedral_per_atom);
- if (atom->memcheck("dihedral_atom4"))
+ if (atom->memcheck("dihedral_atom4"))
bytes += memory->usage(dihedral_atom4,nmax,atom->dihedral_per_atom);
if (atom->memcheck("num_improper")) bytes += memory->usage(num_improper,nmax);
- if (atom->memcheck("improper_type"))
+ if (atom->memcheck("improper_type"))
bytes += memory->usage(improper_type,nmax,atom->improper_per_atom);
- if (atom->memcheck("improper_atom1"))
+ if (atom->memcheck("improper_atom1"))
bytes += memory->usage(improper_atom1,nmax,atom->improper_per_atom);
- if (atom->memcheck("improper_atom2"))
+ if (atom->memcheck("improper_atom2"))
bytes += memory->usage(improper_atom2,nmax,atom->improper_per_atom);
- if (atom->memcheck("improper_atom3"))
+ if (atom->memcheck("improper_atom3"))
bytes += memory->usage(improper_atom3,nmax,atom->improper_per_atom);
- if (atom->memcheck("improper_atom4"))
+ if (atom->memcheck("improper_atom4"))
bytes += memory->usage(improper_atom4,nmax,atom->improper_per_atom);
return bytes;
diff --git a/src/MOLECULE/atom_vec_molecular.h b/src/MOLECULE/atom_vec_molecular.h
index 66c1ddb1ae2b4272f5dc5812ef32ece45c5e3de3..046d9cc0a773a448b483a4bbb6baf3947f857543 100644
--- a/src/MOLECULE/atom_vec_molecular.h
+++ b/src/MOLECULE/atom_vec_molecular.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/MOLECULE/bond_fene.cpp b/src/MOLECULE/bond_fene.cpp
index bc94ef9b270ae366534127216377fb7c1c677a46..27880ee1e3d2093668fc90f6f1e35f4bb48cf156 100644
--- a/src/MOLECULE/bond_fene.cpp
+++ b/src/MOLECULE/bond_fene.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -87,7 +87,7 @@ void BondFENE::compute(int eflag, int vflag)
if (rlogarg < 0.1) {
char str[128];
sprintf(str,"FENE bond too long: " BIGINT_FORMAT " %d %d %g",
- update->ntimestep,atom->tag[i1],atom->tag[i2],sqrt(rsq));
+ update->ntimestep,atom->tag[i1],atom->tag[i2],sqrt(rsq));
error->warning(FLERR,str,0);
if (rlogarg <= -3.0) error->one(FLERR,"Bad FENE bond");
rlogarg = 0.1;
@@ -108,7 +108,7 @@ void BondFENE::compute(int eflag, int vflag)
if (eflag) {
ebond = -0.5 * k[type]*r0sq*log(rlogarg);
if (rsq < TWO_1_3*sigma[type]*sigma[type])
- ebond += 4.0*epsilon[type]*sr6*(sr6-1.0) + epsilon[type];
+ ebond += 4.0*epsilon[type]*sr6*(sr6-1.0) + epsilon[type];
}
// apply force to each of 2 atoms
@@ -244,7 +244,7 @@ double BondFENE::single(int type, double rsq, int i, int j)
if (rlogarg < 0.1) {
char str[128];
sprintf(str,"FENE bond too long: " BIGINT_FORMAT " %g",
- update->ntimestep,sqrt(rsq));
+ update->ntimestep,sqrt(rsq));
error->warning(FLERR,str,0);
if (rlogarg <= -3.0) error->one(FLERR,"Bad FENE bond");
rlogarg = 0.1;
diff --git a/src/MOLECULE/bond_fene.h b/src/MOLECULE/bond_fene.h
index e90c61c0379e742e668bab80085df85059795dae..55216b05ad9490b7f4522b7bb12b1f3c6d6f7d45 100644
--- a/src/MOLECULE/bond_fene.h
+++ b/src/MOLECULE/bond_fene.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/MOLECULE/bond_fene_expand.cpp b/src/MOLECULE/bond_fene_expand.cpp
index eb0b9cf0c795be7553b9114b7ed8ed1c5b4ae77b..6b80478e513fbd9fab26a48c063f18b7777995b8 100644
--- a/src/MOLECULE/bond_fene_expand.cpp
+++ b/src/MOLECULE/bond_fene_expand.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -92,7 +92,7 @@ void BondFENEExpand::compute(int eflag, int vflag)
if (rlogarg < 0.1) {
char str[128];
sprintf(str,"FENE bond too long: " BIGINT_FORMAT " %d %d %g",
- update->ntimestep,atom->tag[i1],atom->tag[i2],sqrt(rsq));
+ update->ntimestep,atom->tag[i1],atom->tag[i2],sqrt(rsq));
error->warning(FLERR,str,0);
if (rlogarg <= -3.0) error->one(FLERR,"Bad FENE bond");
rlogarg = 0.1;
@@ -113,7 +113,7 @@ void BondFENEExpand::compute(int eflag, int vflag)
if (eflag) {
ebond = -0.5 * k[type]*r0sq*log(rlogarg);
if (rshiftsq < TWO_1_3*sigma[type]*sigma[type])
- ebond += 4.0*epsilon[type]*sr6*(sr6-1.0) + epsilon[type];
+ ebond += 4.0*epsilon[type]*sr6*(sr6-1.0) + epsilon[type];
}
// apply force to each of 2 atoms
@@ -258,7 +258,7 @@ double BondFENEExpand::single(int type, double rsq, int i, int j)
if (rlogarg < 0.1) {
char str[128];
sprintf(str,"FENE bond too long: " BIGINT_FORMAT " %g",
- update->ntimestep,sqrt(rsq));
+ update->ntimestep,sqrt(rsq));
error->warning(FLERR,str,0);
if (rlogarg <= -3.0) error->one(FLERR,"Bad FENE bond");
rlogarg = 0.1;
diff --git a/src/MOLECULE/bond_fene_expand.h b/src/MOLECULE/bond_fene_expand.h
index 449c32b308b9eff3f3e9977d5503cb58f055b2fa..1d8e3a3ede658f54eeac230fd1d8122854439a44 100644
--- a/src/MOLECULE/bond_fene_expand.h
+++ b/src/MOLECULE/bond_fene_expand.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/MOLECULE/bond_harmonic.cpp b/src/MOLECULE/bond_harmonic.cpp
index 63af84bf98f37afc975e3cbfce79ebe6f702bc58..ab67e8bec67809474a36c47d5013f3d9e21d1c69 100644
--- a/src/MOLECULE/bond_harmonic.cpp
+++ b/src/MOLECULE/bond_harmonic.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -139,7 +139,7 @@ void BondHarmonic::coeff(int narg, char **arg)
}
/* ----------------------------------------------------------------------
- return an equilbrium bond length
+ return an equilbrium bond length
------------------------------------------------------------------------- */
double BondHarmonic::equilibrium_distance(int i)
@@ -148,7 +148,7 @@ double BondHarmonic::equilibrium_distance(int i)
}
/* ----------------------------------------------------------------------
- proc 0 writes out coeffs to restart file
+ proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void BondHarmonic::write_restart(FILE *fp)
@@ -158,7 +158,7 @@ void BondHarmonic::write_restart(FILE *fp)
}
/* ----------------------------------------------------------------------
- proc 0 reads coeffs from restart file, bcasts them
+ proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void BondHarmonic::read_restart(FILE *fp)
diff --git a/src/MOLECULE/bond_harmonic.h b/src/MOLECULE/bond_harmonic.h
index 7594fe2251c7df31877becd8012dfc01cb5469cf..90bc0e1fb7cf3cc966862a05fe1b34633a4d12a7 100644
--- a/src/MOLECULE/bond_harmonic.h
+++ b/src/MOLECULE/bond_harmonic.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/MOLECULE/bond_morse.cpp b/src/MOLECULE/bond_morse.cpp
index 135c6f8df5ef728f217bb6f4883551b5a2e7bdbf..070c30113688c7217405df3abe8ee0b6f0e4d856 100644
--- a/src/MOLECULE/bond_morse.cpp
+++ b/src/MOLECULE/bond_morse.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -146,7 +146,7 @@ void BondMorse::coeff(int narg, char **arg)
}
/* ----------------------------------------------------------------------
- return an equilbrium bond length
+ return an equilbrium bond length
------------------------------------------------------------------------- */
double BondMorse::equilibrium_distance(int i)
diff --git a/src/MOLECULE/bond_morse.h b/src/MOLECULE/bond_morse.h
index e5bcdbe8f2693ee93b2cdc7f15d6ae6d5e226138..87303e4bc7292e2d48b883e5879cadecf7947100 100644
--- a/src/MOLECULE/bond_morse.h
+++ b/src/MOLECULE/bond_morse.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/MOLECULE/bond_nonlinear.cpp b/src/MOLECULE/bond_nonlinear.cpp
index 1a31b4c4b1801ac4499271fa59da7eb5218fef4e..5bc12e650d82313d599ffcff5159e06bb36ffde1 100644
--- a/src/MOLECULE/bond_nonlinear.cpp
+++ b/src/MOLECULE/bond_nonlinear.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/MOLECULE/bond_nonlinear.h b/src/MOLECULE/bond_nonlinear.h
index c3051af18bc9562ea16303a9141fcb5c6016488c..02efaa969f48057246de2184188512d066134d67 100644
--- a/src/MOLECULE/bond_nonlinear.h
+++ b/src/MOLECULE/bond_nonlinear.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/MOLECULE/bond_quartic.cpp b/src/MOLECULE/bond_quartic.cpp
index c8fc882d57b8d8ae721ea5d5b576720da2bb06a2..8b5264bacdaedc0845193684347684c0916859c5 100755
--- a/src/MOLECULE/bond_quartic.cpp
+++ b/src/MOLECULE/bond_quartic.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -102,12 +102,12 @@ void BondQuartic::compute(int eflag, int vflag)
if (rsq > rc[type]*rc[type]) {
bondlist[n][2] = 0;
for (m = 0; m < atom->num_bond[i1]; m++)
- if (atom->bond_atom[i1][m] == atom->tag[i2])
- atom->bond_type[i1][m] = 0;
+ if (atom->bond_atom[i1][m] == atom->tag[i2])
+ atom->bond_type[i1][m] = 0;
if (i2 < atom->nlocal)
- for (m = 0; m < atom->num_bond[i2]; m++)
- if (atom->bond_atom[i2][m] == atom->tag[i1])
- atom->bond_type[i2][m] = 0;
+ for (m = 0; m < atom->num_bond[i2]; m++)
+ if (atom->bond_atom[i2][m] == atom->tag[i1])
+ atom->bond_type[i2][m] = 0;
continue;
}
@@ -121,7 +121,7 @@ void BondQuartic::compute(int eflag, int vflag)
ra = dr - b1[type];
rb = dr - b2[type];
fbond = -k[type]/r * (r2*(ra+rb) + 2.0*dr*ra*rb);
-
+
if (rsq < TWO_1_3) {
sr2 = 1.0/rsq;
sr6 = sr2*sr2*sr2;
@@ -161,18 +161,18 @@ void BondQuartic::compute(int eflag, int vflag)
fpair = -fpair;
if (newton_bond || i1 < nlocal) {
- f[i1][0] += delx*fpair;
- f[i1][1] += dely*fpair;
- f[i1][2] += delz*fpair;
+ f[i1][0] += delx*fpair;
+ f[i1][1] += dely*fpair;
+ f[i1][2] += delz*fpair;
}
if (newton_bond || i2 < nlocal) {
- f[i2][0] -= delx*fpair;
- f[i2][1] -= dely*fpair;
- f[i2][2] -= delz*fpair;
+ f[i2][0] -= delx*fpair;
+ f[i2][1] -= dely*fpair;
+ f[i2][2] -= delz*fpair;
}
if (evflag) force->pair->ev_tally(i1,i2,nlocal,newton_bond,
- evdwl,0.0,fpair,delx,dely,delz);
+ evdwl,0.0,fpair,delx,dely,delz);
}
}
}
@@ -249,7 +249,7 @@ void BondQuartic::init_style()
}
/* ----------------------------------------------------------------------
- return an equilbrium bond length
+ return an equilbrium bond length
------------------------------------------------------------------------- */
double BondQuartic::equilibrium_distance(int i)
@@ -258,7 +258,7 @@ double BondQuartic::equilibrium_distance(int i)
}
/* ----------------------------------------------------------------------
- proc 0 writes out coeffs to restart file
+ proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void BondQuartic::write_restart(FILE *fp)
@@ -271,7 +271,7 @@ void BondQuartic::write_restart(FILE *fp)
}
/* ----------------------------------------------------------------------
- proc 0 reads coeffs from restart file, bcasts them
+ proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void BondQuartic::read_restart(FILE *fp)
@@ -309,7 +309,7 @@ double BondQuartic::single(int type, double rsq, int i, int j)
int itype = atom->type[i];
int jtype = atom->type[j];
-
+
if (rsq < force->pair->cutsq[itype][jtype]) {
double tmp;
eng = -force->pair->single(i,j,itype,jtype,rsq,1.0,1.0,tmp);
diff --git a/src/MOLECULE/bond_quartic.h b/src/MOLECULE/bond_quartic.h
index 528e76e09d5ccdd662eab04070371c839232f54f..4fb144c65522ecadb5b933eb8ad854d49fbbc484 100644
--- a/src/MOLECULE/bond_quartic.h
+++ b/src/MOLECULE/bond_quartic.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/MOLECULE/bond_table.cpp b/src/MOLECULE/bond_table.cpp
index a47c3db75a30f4faa580dfe2f16f1d5b41413f42..19b3f66402888d94dc81973a2048220b957cc074 100644
--- a/src/MOLECULE/bond_table.cpp
+++ b/src/MOLECULE/bond_table.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -35,7 +35,7 @@ enum{LINEAR,SPLINE};
/* ---------------------------------------------------------------------- */
-BondTable::BondTable(LAMMPS *lmp) : Bond(lmp)
+BondTable::BondTable(LAMMPS *lmp) : Bond(lmp)
{
ntables = 0;
tables = NULL;
@@ -127,7 +127,7 @@ void BondTable::allocate()
/* ----------------------------------------------------------------------
- global settings
+ global settings
------------------------------------------------------------------------- */
void BondTable::settings(int narg, char **arg)
@@ -167,10 +167,10 @@ void BondTable::coeff(int narg, char **arg)
int ilo,ihi;
force->bounds(arg[0],atom->nbondtypes,ilo,ihi);
-
+
int me;
MPI_Comm_rank(world,&me);
- tables = (Table *)
+ tables = (Table *)
memory->srealloc(tables,(ntables+1)*sizeof(Table),"bond:tables");
Table *tb = &tables[ntables];
null_table(tb);
@@ -269,7 +269,7 @@ void BondTable::free_table(Table *tb)
memory->destroy(tb->ffile);
memory->destroy(tb->e2file);
memory->destroy(tb->f2file);
-
+
memory->destroy(tb->r);
memory->destroy(tb->e);
memory->destroy(tb->de);
@@ -348,7 +348,7 @@ void BondTable::spline_table(Table *tb)
if (tb->fpflag == 0) {
tb->fplo = (tb->ffile[1] - tb->ffile[0]) / (tb->rfile[1] - tb->rfile[0]);
- tb->fphi = (tb->ffile[tb->ninput-1] - tb->ffile[tb->ninput-2]) /
+ tb->fphi = (tb->ffile[tb->ninput-1] - tb->ffile[tb->ninput-2]) /
(tb->rfile[tb->ninput-1] - tb->rfile[tb->ninput-2]);
}
@@ -370,7 +370,7 @@ void BondTable::compute_table(Table *tb)
tb->delta = (tb->hi - tb->lo)/ tlm1;
tb->invdelta = 1.0/tb->delta;
tb->deltasq6 = tb->delta*tb->delta / 6.0;
-
+
// N-1 evenly spaced bins in r from min to max
// r,e,f = value at lower edge of bin
// de,df values = delta values of e,f
@@ -391,15 +391,15 @@ void BondTable::compute_table(Table *tb)
tb->e[i] = splint(tb->rfile,tb->efile,tb->e2file,tb->ninput,a);
tb->f[i] = splint(tb->rfile,tb->ffile,tb->f2file,tb->ninput,a);
}
-
+
for (int i = 0; i < tlm1; i++) {
tb->de[i] = tb->e[i+1] - tb->e[i];
tb->df[i] = tb->f[i+1] - tb->f[i];
}
-
+
double ep0 = - tb->f[0];
double epn = - tb->f[tlm1];
- spline(tb->r,tb->e,tablength,ep0,epn,tb->e2);
+ spline(tb->r,tb->e,tablength,ep0,epn,tb->e2);
spline(tb->r,tb->f,tablength,tb->fplo,tb->fphi,tb->f2);
}
@@ -414,7 +414,7 @@ void BondTable::param_extract(Table *tb, char *line)
tb->ninput = 0;
tb->fpflag = 0;
tb->r0 = 0.0;
-
+
char *word = strtok(line," \t\n\r\f");
while (word) {
if (strcmp(word,"N") == 0) {
@@ -474,7 +474,7 @@ void BondTable::bcast_table(Table *tb)
------------------------------------------------------------------------- */
void BondTable::spline(double *x, double *y, int n,
- double yp1, double ypn, double *y2)
+ double yp1, double ypn, double *y2)
{
int i,k;
double p,qn,sig,un;
@@ -520,7 +520,7 @@ double BondTable::splint(double *xa, double *ya, double *y2a, int n, double x)
h = xa[khi]-xa[klo];
a = (xa[khi]-x) / h;
b = (x-xa[klo]) / h;
- y = a*ya[klo] + b*ya[khi] +
+ y = a*ya[klo] + b*ya[khi] +
((a*a*a-a)*y2a[klo] + (b*b*b-b)*y2a[khi]) * (h*h)/6.0;
return y;
}
@@ -547,16 +547,16 @@ void BondTable::uf_lookup(int type, double x, double &u, double &f)
} else if (tabstyle == SPLINE) {
itable = static_cast<int> ((x - tb->lo) * tb->invdelta);
fraction = (x - tb->r[itable]) * tb->invdelta;
-
+
b = (x - tb->r[itable]) * tb->invdelta;
a = 1.0 - b;
- u = a * tb->e[itable] + b * tb->e[itable+1] +
- ((a*a*a-a)*tb->e2[itable] + (b*b*b-b)*tb->e2[itable+1]) *
+ u = a * tb->e[itable] + b * tb->e[itable+1] +
+ ((a*a*a-a)*tb->e2[itable] + (b*b*b-b)*tb->e2[itable+1]) *
tb->deltasq6;
- f = a * tb->f[itable] + b * tb->f[itable+1] +
- ((a*a*a-a)*tb->f2[itable] + (b*b*b-b)*tb->f2[itable+1]) *
+ f = a * tb->f[itable] + b * tb->f[itable+1] +
+ ((a*a*a-a)*tb->f2[itable] + (b*b*b-b)*tb->f2[itable+1]) *
tb->deltasq6;
- }
+ }
}
/* ----------------------------------------------------------------------
@@ -572,7 +572,7 @@ void BondTable::u_lookup(int type, double x, double &u)
Table *tb = &tables[tabindex[type]];
x = MAX(x,tb->lo);
x = MIN(x,tb->hi);
-
+
if (tabstyle == LINEAR) {
itable = static_cast<int> ((x - tb->lo) * tb->invdelta);
fraction = (x - tb->r[itable]) * tb->invdelta;
@@ -580,11 +580,11 @@ void BondTable::u_lookup(int type, double x, double &u)
} else if (tabstyle == SPLINE) {
itable = static_cast<int> ((x - tb->lo) * tb->invdelta);
fraction = (x - tb->r[itable]) * tb->invdelta;
-
+
b = (x - tb->r[itable]) * tb->invdelta;
a = 1.0 - b;
- u = a * tb->e[itable] + b * tb->e[itable+1] +
- ((a*a*a-a)*tb->e2[itable] + (b*b*b-b)*tb->e2[itable+1]) *
+ u = a * tb->e[itable] + b * tb->e[itable+1] +
+ ((a*a*a-a)*tb->e2[itable] + (b*b*b-b)*tb->e2[itable+1]) *
tb->deltasq6;
- }
+ }
}
diff --git a/src/MOLECULE/bond_table.h b/src/MOLECULE/bond_table.h
index 31c335cb429a3428cdac7375566a255b4eec0a70..3a6f75d89b2c63c78ed572687c9db726fffad5c2 100644
--- a/src/MOLECULE/bond_table.h
+++ b/src/MOLECULE/bond_table.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -54,7 +54,7 @@ class BondTable : public Bond {
int ntables;
Table *tables;
int *tabindex;
-
+
void allocate();
void null_table(Table *);
void free_table(Table *);
diff --git a/src/MOLECULE/dihedral_charmm.cpp b/src/MOLECULE/dihedral_charmm.cpp
index 6e4c8745a307b0387b0868703c4dcfece9c20204..644655f589be41829a875aed12c11d967120ed6e 100644
--- a/src/MOLECULE/dihedral_charmm.cpp
+++ b/src/MOLECULE/dihedral_charmm.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -64,7 +64,7 @@ void DihedralCharmm::compute(int eflag, int vflag)
double edihedral,f1[3],f2[3],f3[3],f4[3];
double ax,ay,az,bx,by,bz,rasq,rbsq,rgsq,rg,rginv,ra2inv,rb2inv,rabinv;
double df,df1,ddf1,fg,hg,fga,hgb,gaa,gbb;
- double dtfx,dtfy,dtfz,dtgx,dtgy,dtgz,dthx,dthy,dthz;
+ double dtfx,dtfy,dtfz,dtgx,dtgy,dtgz,dthx,dthy,dthz;
double c,s,p,sx2,sy2,sz2;
int itype,jtype;
double delx,dely,delz,rsq,r2inv,r6inv;
@@ -121,7 +121,7 @@ void DihedralCharmm::compute(int eflag, int vflag)
vb3y = x[i4][1] - x[i3][1];
vb3z = x[i4][2] - x[i3][2];
domain->minimum_image(vb3x,vb3y,vb3z);
-
+
ax = vb1y*vb2zm - vb1z*vb2ym;
ay = vb1z*vb2xm - vb1x*vb2zm;
az = vb1x*vb2ym - vb1y*vb2xm;
@@ -133,7 +133,7 @@ void DihedralCharmm::compute(int eflag, int vflag)
rbsq = bx*bx + by*by + bz*bz;
rgsq = vb2xm*vb2xm + vb2ym*vb2ym + vb2zm*vb2zm;
rg = sqrt(rgsq);
-
+
rginv = ra2inv = rb2inv = 0.0;
if (rg > 0) rginv = 1.0/rg;
if (rasq > 0) ra2inv = 1.0/rasq;
@@ -149,29 +149,29 @@ void DihedralCharmm::compute(int eflag, int vflag)
int me;
MPI_Comm_rank(world,&me);
if (screen) {
- char str[128];
- sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " %d %d %d %d",
- me,update->ntimestep,
- atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
- error->warning(FLERR,str,0);
- fprintf(screen," 1st atom: %d %g %g %g\n",
- me,x[i1][0],x[i1][1],x[i1][2]);
- fprintf(screen," 2nd atom: %d %g %g %g\n",
- me,x[i2][0],x[i2][1],x[i2][2]);
- fprintf(screen," 3rd atom: %d %g %g %g\n",
- me,x[i3][0],x[i3][1],x[i3][2]);
- fprintf(screen," 4th atom: %d %g %g %g\n",
- me,x[i4][0],x[i4][1],x[i4][2]);
+ char str[128];
+ sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " %d %d %d %d",
+ me,update->ntimestep,
+ atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
+ error->warning(FLERR,str,0);
+ fprintf(screen," 1st atom: %d %g %g %g\n",
+ me,x[i1][0],x[i1][1],x[i1][2]);
+ fprintf(screen," 2nd atom: %d %g %g %g\n",
+ me,x[i2][0],x[i2][1],x[i2][2]);
+ fprintf(screen," 3rd atom: %d %g %g %g\n",
+ me,x[i3][0],x[i3][1],x[i3][2]);
+ fprintf(screen," 4th atom: %d %g %g %g\n",
+ me,x[i4][0],x[i4][1],x[i4][2]);
}
}
-
+
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
-
+
m = multiplicity[type];
p = 1.0;
ddf1 = df1 = 0.0;
-
+
for (i = 0; i < m; i++) {
ddf1 = p*c - df1*s;
df1 = p*s + df1*c;
@@ -182,21 +182,21 @@ void DihedralCharmm::compute(int eflag, int vflag)
df1 = df1*cos_shift[type] - ddf1*sin_shift[type];
df1 *= -m;
p += 1.0;
-
+
if (m == 0) {
p = 1.0 + cos_shift[type];
df1 = 0.0;
}
- if (eflag) edihedral = k[type] * p;
-
+ if (eflag) edihedral = k[type] * p;
+
fg = vb1x*vb2xm + vb1y*vb2ym + vb1z*vb2zm;
hg = vb3x*vb2xm + vb3y*vb2ym + vb3z*vb2zm;
fga = fg*ra2inv*rginv;
hgb = hg*rb2inv*rginv;
gaa = -ra2inv*rg;
gbb = rb2inv*rg;
-
+
dtfx = gaa*ax;
dtfy = gaa*ay;
dtfz = gaa*az;
@@ -206,9 +206,9 @@ void DihedralCharmm::compute(int eflag, int vflag)
dthx = gbb*bx;
dthy = gbb*by;
dthz = gbb*bz;
-
+
df = -k[type] * df1;
-
+
sx2 = df*dtgx;
sy2 = df*dtgy;
sz2 = df*dtgz;
@@ -257,7 +257,7 @@ void DihedralCharmm::compute(int eflag, int vflag)
if (evflag)
ev_tally(i1,i2,i3,i4,nlocal,newton_bond,edihedral,f1,f3,f4,
- vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
+ vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
// 1-4 LJ and Coulomb interactions
// tally energy/virial in pair, using newton_bond as newton flag
@@ -280,24 +280,24 @@ void DihedralCharmm::compute(int eflag, int vflag)
fpair = weight[type] * (forcelj+forcecoul)*r2inv;
if (eflag) {
- ecoul = weight[type] * forcecoul;
- evdwl = r6inv * (lj14_3[itype][jtype]*r6inv - lj14_4[itype][jtype]);
- evdwl *= weight[type];
+ ecoul = weight[type] * forcecoul;
+ evdwl = r6inv * (lj14_3[itype][jtype]*r6inv - lj14_4[itype][jtype]);
+ evdwl *= weight[type];
}
if (newton_bond || i1 < nlocal) {
- f[i1][0] += delx*fpair;
- f[i1][1] += dely*fpair;
- f[i1][2] += delz*fpair;
+ f[i1][0] += delx*fpair;
+ f[i1][1] += dely*fpair;
+ f[i1][2] += delz*fpair;
}
if (newton_bond || i4 < nlocal) {
- f[i4][0] -= delx*fpair;
- f[i4][1] -= dely*fpair;
- f[i4][2] -= delz*fpair;
+ f[i4][0] -= delx*fpair;
+ f[i4][1] -= dely*fpair;
+ f[i4][2] -= delz*fpair;
}
if (evflag) force->pair->ev_tally(i1,i4,nlocal,newton_bond,
- evdwl,ecoul,fpair,delx,dely,delz);
+ evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
@@ -331,11 +331,11 @@ void DihedralCharmm::coeff(int narg, char **arg)
int ilo,ihi;
force->bounds(arg[0],atom->ndihedraltypes,ilo,ihi);
-
+
// require integer values of shift for backwards compatibility
// arbitrary phase angle shift could be allowed, but would break
// backwards compatibility and is probably not needed
-
+
double k_one = force->numeric(arg[1]);
int multiplicity_one = force->inumeric(arg[2]);
int shift_one = force->inumeric(arg[3]);
@@ -343,7 +343,7 @@ void DihedralCharmm::coeff(int narg, char **arg)
if (multiplicity_one < 0)
error->all(FLERR,"Incorrect multiplicity arg for dihedral coefficients");
- if (weight_one < 0.0 || weight_one > 1.0)
+ if (weight_one < 0.0 || weight_one > 1.0)
error->all(FLERR,"Incorrect weight arg for dihedral coefficients");
int count = 0;
@@ -362,7 +362,7 @@ void DihedralCharmm::coeff(int narg, char **arg)
}
/* ----------------------------------------------------------------------
- error check and initialize all values needed for force computation
+ error check and initialize all values needed for force computation
------------------------------------------------------------------------- */
void DihedralCharmm::init_style()
@@ -390,7 +390,7 @@ void DihedralCharmm::init_style()
}
/* ----------------------------------------------------------------------
- proc 0 writes out coeffs to restart file
+ proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void DihedralCharmm::write_restart(FILE *fp)
@@ -402,7 +402,7 @@ void DihedralCharmm::write_restart(FILE *fp)
}
/* ----------------------------------------------------------------------
- proc 0 reads coeffs from restart file, bcasts them
+ proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void DihedralCharmm::read_restart(FILE *fp)
diff --git a/src/MOLECULE/dihedral_charmm.h b/src/MOLECULE/dihedral_charmm.h
index be0e7c58476e2c6889748885568e6d0ca6e56e44..591de5f5a8b5e940648a474818ea2a18dd6433ad 100644
--- a/src/MOLECULE/dihedral_charmm.h
+++ b/src/MOLECULE/dihedral_charmm.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/MOLECULE/dihedral_harmonic.cpp b/src/MOLECULE/dihedral_harmonic.cpp
index 43d4333dd86fc6c7db47654a2add817103e8667c..a951f3816bd79e3823f9f265fff8ea9f29558d37 100644
--- a/src/MOLECULE/dihedral_harmonic.cpp
+++ b/src/MOLECULE/dihedral_harmonic.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -61,7 +61,7 @@ void DihedralHarmonic::compute(int eflag, int vflag)
double edihedral,f1[3],f2[3],f3[3],f4[3];
double ax,ay,az,bx,by,bz,rasq,rbsq,rgsq,rg,rginv,ra2inv,rb2inv,rabinv;
double df,df1,ddf1,fg,hg,fga,hgb,gaa,gbb;
- double dtfx,dtfy,dtfz,dtgx,dtgy,dtgz,dthx,dthy,dthz;
+ double dtfx,dtfy,dtfz,dtgx,dtgy,dtgz,dthx,dthy,dthz;
double c,s,p,sx2,sy2,sz2;
edihedral = 0.0;
@@ -107,7 +107,7 @@ void DihedralHarmonic::compute(int eflag, int vflag)
vb3y = x[i4][1] - x[i3][1];
vb3z = x[i4][2] - x[i3][2];
domain->minimum_image(vb3x,vb3y,vb3z);
-
+
// c,s calculation
ax = vb1y*vb2zm - vb1z*vb2ym;
@@ -121,7 +121,7 @@ void DihedralHarmonic::compute(int eflag, int vflag)
rbsq = bx*bx + by*by + bz*bz;
rgsq = vb2xm*vb2xm + vb2ym*vb2ym + vb2zm*vb2zm;
rg = sqrt(rgsq);
-
+
rginv = ra2inv = rb2inv = 0.0;
if (rg > 0) rginv = 1.0/rg;
if (rasq > 0) ra2inv = 1.0/rasq;
@@ -137,29 +137,29 @@ void DihedralHarmonic::compute(int eflag, int vflag)
int me;
MPI_Comm_rank(world,&me);
if (screen) {
- char str[128];
- sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " %d %d %d %d",
- me,update->ntimestep,
- atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
- error->warning(FLERR,str,0);
- fprintf(screen," 1st atom: %d %g %g %g\n",
- me,x[i1][0],x[i1][1],x[i1][2]);
- fprintf(screen," 2nd atom: %d %g %g %g\n",
- me,x[i2][0],x[i2][1],x[i2][2]);
- fprintf(screen," 3rd atom: %d %g %g %g\n",
- me,x[i3][0],x[i3][1],x[i3][2]);
- fprintf(screen," 4th atom: %d %g %g %g\n",
- me,x[i4][0],x[i4][1],x[i4][2]);
+ char str[128];
+ sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " %d %d %d %d",
+ me,update->ntimestep,
+ atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
+ error->warning(FLERR,str,0);
+ fprintf(screen," 1st atom: %d %g %g %g\n",
+ me,x[i1][0],x[i1][1],x[i1][2]);
+ fprintf(screen," 2nd atom: %d %g %g %g\n",
+ me,x[i2][0],x[i2][1],x[i2][2]);
+ fprintf(screen," 3rd atom: %d %g %g %g\n",
+ me,x[i3][0],x[i3][1],x[i3][2]);
+ fprintf(screen," 4th atom: %d %g %g %g\n",
+ me,x[i4][0],x[i4][1],x[i4][2]);
}
}
-
+
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
-
+
m = multiplicity[type];
p = 1.0;
ddf1 = df1 = 0.0;
-
+
for (i = 0; i < m; i++) {
ddf1 = p*c - df1*s;
df1 = p*s + df1*c;
@@ -170,21 +170,21 @@ void DihedralHarmonic::compute(int eflag, int vflag)
df1 = df1*cos_shift[type] - ddf1*sin_shift[type];
df1 *= -m;
p += 1.0;
-
+
if (m == 0) {
p = 1.0 + cos_shift[type];
df1 = 0.0;
}
- if (eflag) edihedral = k[type] * p;
-
+ if (eflag) edihedral = k[type] * p;
+
fg = vb1x*vb2xm + vb1y*vb2ym + vb1z*vb2zm;
hg = vb3x*vb2xm + vb3y*vb2ym + vb3z*vb2zm;
fga = fg*ra2inv*rginv;
hgb = hg*rb2inv*rginv;
gaa = -ra2inv*rg;
gbb = rb2inv*rg;
-
+
dtfx = gaa*ax;
dtfy = gaa*ay;
dtfz = gaa*az;
@@ -194,9 +194,9 @@ void DihedralHarmonic::compute(int eflag, int vflag)
dthx = gbb*bx;
dthy = gbb*by;
dthz = gbb*bz;
-
+
df = -k[type] * df1;
-
+
sx2 = df*dtgx;
sy2 = df*dtgy;
sz2 = df*dtgz;
@@ -216,7 +216,7 @@ void DihedralHarmonic::compute(int eflag, int vflag)
f3[0] = -sx2 - f4[0];
f3[1] = -sy2 - f4[1];
f3[2] = -sz2 - f4[2];
-
+
// apply force to each of 4 atoms
if (newton_bond || i1 < nlocal) {
@@ -245,7 +245,7 @@ void DihedralHarmonic::compute(int eflag, int vflag)
if (evflag)
ev_tally(i1,i2,i3,i4,nlocal,newton_bond,edihedral,f1,f3,f4,
- vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
+ vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
}
}
@@ -285,12 +285,12 @@ void DihedralHarmonic::coeff(int narg, char **arg)
// require sign = +/- 1 for backwards compatibility
// arbitrary phase angle shift could be allowed, but would break
// backwards compatibility and is probably not needed
-
+
if (sign_one != -1 && sign_one != 1)
error->all(FLERR,"Incorrect sign arg for dihedral coefficients");
if (multiplicity_one < 0)
error->all(FLERR,"Incorrect multiplicity arg for dihedral coefficients");
-
+
int count = 0;
for (int i = ilo; i <= ihi; i++) {
k[i] = k_one;
@@ -311,7 +311,7 @@ void DihedralHarmonic::coeff(int narg, char **arg)
}
/* ----------------------------------------------------------------------
- proc 0 writes out coeffs to restart file
+ proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void DihedralHarmonic::write_restart(FILE *fp)
@@ -322,7 +322,7 @@ void DihedralHarmonic::write_restart(FILE *fp)
}
/* ----------------------------------------------------------------------
- proc 0 reads coeffs from restart file, bcasts them
+ proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void DihedralHarmonic::read_restart(FILE *fp)
@@ -337,7 +337,7 @@ void DihedralHarmonic::read_restart(FILE *fp)
MPI_Bcast(&k[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&sign[1],atom->ndihedraltypes,MPI_INT,0,world);
MPI_Bcast(&multiplicity[1],atom->ndihedraltypes,MPI_INT,0,world);
-
+
for (int i = 1; i <= atom->ndihedraltypes; i++) {
setflag[i] = 1;
if (sign[i] == 1) {
@@ -345,7 +345,7 @@ void DihedralHarmonic::read_restart(FILE *fp)
sin_shift[i] = 0;
} else {
cos_shift[i] = -1;
- sin_shift[i] = 0;
+ sin_shift[i] = 0;
}
}
}
diff --git a/src/MOLECULE/dihedral_harmonic.h b/src/MOLECULE/dihedral_harmonic.h
index 5eafdb61f3cd16b2b0d066d3a5c4707715be7b31..195bd1b357a5c20df06cbcb3bdb46cb9738724cc 100644
--- a/src/MOLECULE/dihedral_harmonic.h
+++ b/src/MOLECULE/dihedral_harmonic.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/MOLECULE/dihedral_helix.cpp b/src/MOLECULE/dihedral_helix.cpp
index 8079de6f06f5a0a48f0b8e923bfafc639b4c2028..c9da759d2111c714dc955c87db5ca639393faf3c 100644
--- a/src/MOLECULE/dihedral_helix.cpp
+++ b/src/MOLECULE/dihedral_helix.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -112,18 +112,18 @@ void DihedralHelix::compute(int eflag, int vflag)
domain->minimum_image(vb3x,vb3y,vb3z);
// c0 calculation
-
+
sb1 = 1.0 / (vb1x*vb1x + vb1y*vb1y + vb1z*vb1z);
sb2 = 1.0 / (vb2x*vb2x + vb2y*vb2y + vb2z*vb2z);
sb3 = 1.0 / (vb3x*vb3x + vb3y*vb3y + vb3z*vb3z);
-
+
rb1 = sqrt(sb1);
rb3 = sqrt(sb3);
-
+
c0 = (vb1x*vb3x + vb1y*vb3y + vb1z*vb3z) * rb1*rb3;
// 1st and 2nd angle
-
+
b1mag2 = vb1x*vb1x + vb1y*vb1y + vb1z*vb1z;
b1mag = sqrt(b1mag2);
b2mag2 = vb2x*vb2x + vb2y*vb2y + vb2z*vb2z;
@@ -161,29 +161,29 @@ void DihedralHelix::compute(int eflag, int vflag)
cz = vb1x*vb2y - vb1y*vb2x;
cmag = sqrt(cx*cx + cy*cy + cz*cz);
dx = (cx*vb3x + cy*vb3y + cz*vb3z)/cmag/b3mag;
-
+
// error check
if (c > 1.0 + TOLERANCE || c < (-1.0 - TOLERANCE)) {
int me;
MPI_Comm_rank(world,&me);
if (screen) {
- char str[128];
- sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " %d %d %d %d",
- me,update->ntimestep,
- atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
- error->warning(FLERR,str,0);
- fprintf(screen," 1st atom: %d %g %g %g\n",
- me,x[i1][0],x[i1][1],x[i1][2]);
- fprintf(screen," 2nd atom: %d %g %g %g\n",
- me,x[i2][0],x[i2][1],x[i2][2]);
- fprintf(screen," 3rd atom: %d %g %g %g\n",
- me,x[i3][0],x[i3][1],x[i3][2]);
- fprintf(screen," 4th atom: %d %g %g %g\n",
- me,x[i4][0],x[i4][1],x[i4][2]);
+ char str[128];
+ sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " %d %d %d %d",
+ me,update->ntimestep,
+ atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
+ error->warning(FLERR,str,0);
+ fprintf(screen," 1st atom: %d %g %g %g\n",
+ me,x[i1][0],x[i1][1],x[i1][2]);
+ fprintf(screen," 2nd atom: %d %g %g %g\n",
+ me,x[i2][0],x[i2][1],x[i2][2]);
+ fprintf(screen," 3rd atom: %d %g %g %g\n",
+ me,x[i3][0],x[i3][1],x[i3][2]);
+ fprintf(screen," 4th atom: %d %g %g %g\n",
+ me,x[i4][0],x[i4][1],x[i4][2]);
}
}
-
+
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
@@ -258,7 +258,7 @@ void DihedralHelix::compute(int eflag, int vflag)
if (evflag)
ev_tally(i1,i2,i3,i4,nlocal,newton_bond,edihedral,f1,f3,f4,
- vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
+ vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
}
}
@@ -306,7 +306,7 @@ void DihedralHelix::coeff(int narg, char **arg)
}
/* ----------------------------------------------------------------------
- proc 0 writes out coeffs to restart file
+ proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void DihedralHelix::write_restart(FILE *fp)
@@ -317,7 +317,7 @@ void DihedralHelix::write_restart(FILE *fp)
}
/* ----------------------------------------------------------------------
- proc 0 reads coeffs from restart file, bcasts them
+ proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void DihedralHelix::read_restart(FILE *fp)
diff --git a/src/MOLECULE/dihedral_helix.h b/src/MOLECULE/dihedral_helix.h
index f28b9db28e22369819124076044b3f61cce9e27e..1e34ff4712786b7a0448ea8ca91cc328da61cfca 100644
--- a/src/MOLECULE/dihedral_helix.h
+++ b/src/MOLECULE/dihedral_helix.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/MOLECULE/dihedral_hybrid.cpp b/src/MOLECULE/dihedral_hybrid.cpp
index 131762be282f41a80e0b93a208d3f520173e816a..e66cf7e328044930b439c83b6580a091276833da 100644
--- a/src/MOLECULE/dihedral_hybrid.cpp
+++ b/src/MOLECULE/dihedral_hybrid.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -79,10 +79,10 @@ void DihedralHybrid::compute(int eflag, int vflag)
}
for (m = 0; m < nstyles; m++) {
if (ndihedrallist[m] > maxdihedral[m]) {
- memory->destroy(dihedrallist[m]);
- maxdihedral[m] = ndihedrallist[m] + EXTRA;
- memory->create(dihedrallist[m],maxdihedral[m],5,
- "dihedral_hybrid:dihedrallist");
+ memory->destroy(dihedrallist[m]);
+ maxdihedral[m] = ndihedrallist[m] + EXTRA;
+ memory->create(dihedrallist[m],maxdihedral[m],5,
+ "dihedral_hybrid:dihedrallist");
}
ndihedrallist[m] = 0;
}
@@ -98,7 +98,7 @@ void DihedralHybrid::compute(int eflag, int vflag)
ndihedrallist[m]++;
}
}
-
+
// call each sub-style's compute function
// set neighbor->dihedrallist to sub-style dihedrallist before call
// accumulate sub-style global/peratom energy/virial in hybrid
@@ -126,8 +126,8 @@ void DihedralHybrid::compute(int eflag, int vflag)
if (force->newton_bond) n += atom->nghost;
double **vatom_substyle = styles[m]->vatom;
for (i = 0; i < n; i++)
- for (j = 0; j < 6; j++)
- vatom[i][j] += vatom_substyle[i][j];
+ for (j = 0; j < 6; j++)
+ vatom[i][j] += vatom_substyle[i][j];
}
}
@@ -169,13 +169,13 @@ void DihedralHybrid::settings(int narg, char **arg)
for (int m = 0; m < nstyles; m++) {
for (int i = 0; i < m; i++)
- if (strcmp(arg[m],arg[i]) == 0)
- error->all(FLERR,"Dihedral style hybrid cannot use "
- "same dihedral style twice");
- if (strcmp(arg[m],"hybrid") == 0)
+ if (strcmp(arg[m],arg[i]) == 0)
+ error->all(FLERR,"Dihedral style hybrid cannot use "
+ "same dihedral style twice");
+ if (strcmp(arg[m],"hybrid") == 0)
error->all(FLERR,
- "Dihedral style hybrid cannot have hybrid as an argument");
- if (strcmp(arg[m],"none") == 0)
+ "Dihedral style hybrid cannot have hybrid as an argument");
+ if (strcmp(arg[m],"none") == 0)
error->all(FLERR,"Dihedral style hybrid cannot have none as an argument");
styles[m] = force->new_dihedral(arg[m],lmp->suffix,dummy);
keywords[m] = new char[strlen(arg[m])+1];
@@ -292,7 +292,7 @@ double DihedralHybrid::memory_usage()
double bytes = maxeatom * sizeof(double);
bytes += maxvatom*6 * sizeof(double);
for (int m = 0; m < nstyles; m++) bytes += maxdihedral[m]*5 * sizeof(int);
- for (int m = 0; m < nstyles; m++)
+ for (int m = 0; m < nstyles; m++)
if (styles[m]) bytes += styles[m]->memory_usage();
return bytes;
}
diff --git a/src/MOLECULE/dihedral_hybrid.h b/src/MOLECULE/dihedral_hybrid.h
index bee1e58b20f0b6df0fe150db74b6efe19f8f17cd..c847dd2e9c3830dee0215bd7483058f2fa1a05e0 100644
--- a/src/MOLECULE/dihedral_hybrid.h
+++ b/src/MOLECULE/dihedral_hybrid.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -47,7 +47,7 @@ class DihedralHybrid : public Dihedral {
int *ndihedrallist; // # of dihedrals in sub-style dihedrallists
int *maxdihedral; // max # of dihedrals sub-style lists can store
int ***dihedrallist; // dihedrallist for each sub-style
-
+
void allocate();
};
diff --git a/src/MOLECULE/dihedral_multi_harmonic.cpp b/src/MOLECULE/dihedral_multi_harmonic.cpp
index f44a9dccf37085dc24cde44d370a8f30d9bda2c6..cff19447f778a63eb87d22b33477ff8cad4a91b5 100644
--- a/src/MOLECULE/dihedral_multi_harmonic.cpp
+++ b/src/MOLECULE/dihedral_multi_harmonic.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -108,18 +108,18 @@ void DihedralMultiHarmonic::compute(int eflag, int vflag)
domain->minimum_image(vb3x,vb3y,vb3z);
// c0 calculation
-
+
sb1 = 1.0 / (vb1x*vb1x + vb1y*vb1y + vb1z*vb1z);
sb2 = 1.0 / (vb2x*vb2x + vb2y*vb2y + vb2z*vb2z);
sb3 = 1.0 / (vb3x*vb3x + vb3y*vb3y + vb3z*vb3z);
-
+
rb1 = sqrt(sb1);
rb3 = sqrt(sb3);
-
+
c0 = (vb1x*vb3x + vb1y*vb3y + vb1z*vb3z) * rb1*rb3;
// 1st and 2nd angle
-
+
b1mag2 = vb1x*vb1x + vb1y*vb1y + vb1z*vb1z;
b1mag = sqrt(b1mag2);
b2mag2 = vb2x*vb2x + vb2y*vb2y + vb2z*vb2z;
@@ -158,22 +158,22 @@ void DihedralMultiHarmonic::compute(int eflag, int vflag)
int me;
MPI_Comm_rank(world,&me);
if (screen) {
- char str[128];
- sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " %d %d %d %d",
- me,update->ntimestep,
- atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
- error->warning(FLERR,str,0);
- fprintf(screen," 1st atom: %d %g %g %g\n",
- me,x[i1][0],x[i1][1],x[i1][2]);
- fprintf(screen," 2nd atom: %d %g %g %g\n",
- me,x[i2][0],x[i2][1],x[i2][2]);
- fprintf(screen," 3rd atom: %d %g %g %g\n",
- me,x[i3][0],x[i3][1],x[i3][2]);
- fprintf(screen," 4th atom: %d %g %g %g\n",
- me,x[i4][0],x[i4][1],x[i4][2]);
+ char str[128];
+ sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " %d %d %d %d",
+ me,update->ntimestep,
+ atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
+ error->warning(FLERR,str,0);
+ fprintf(screen," 1st atom: %d %g %g %g\n",
+ me,x[i1][0],x[i1][1],x[i1][2]);
+ fprintf(screen," 2nd atom: %d %g %g %g\n",
+ me,x[i2][0],x[i2][1],x[i2][2]);
+ fprintf(screen," 3rd atom: %d %g %g %g\n",
+ me,x[i3][0],x[i3][1],x[i3][2]);
+ fprintf(screen," 4th atom: %d %g %g %g\n",
+ me,x[i4][0],x[i4][1],x[i4][2]);
}
}
-
+
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
@@ -244,7 +244,7 @@ void DihedralMultiHarmonic::compute(int eflag, int vflag)
if (evflag)
ev_tally(i1,i2,i3,i4,nlocal,newton_bond,edihedral,f1,f3,f4,
- vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
+ vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
}
}
@@ -298,7 +298,7 @@ void DihedralMultiHarmonic::coeff(int narg, char **arg)
}
/* ----------------------------------------------------------------------
- proc 0 writes out coeffs to restart file
+ proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void DihedralMultiHarmonic::write_restart(FILE *fp)
@@ -311,7 +311,7 @@ void DihedralMultiHarmonic::write_restart(FILE *fp)
}
/* ----------------------------------------------------------------------
- proc 0 reads coeffs from restart file, bcasts them
+ proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void DihedralMultiHarmonic::read_restart(FILE *fp)
diff --git a/src/MOLECULE/dihedral_multi_harmonic.h b/src/MOLECULE/dihedral_multi_harmonic.h
index a768cb6d62521826611dc0d7af1a26ba11900392..c8331681397684c6a600e863e26159e4dd8835ca 100644
--- a/src/MOLECULE/dihedral_multi_harmonic.h
+++ b/src/MOLECULE/dihedral_multi_harmonic.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/MOLECULE/dihedral_opls.cpp b/src/MOLECULE/dihedral_opls.cpp
index e60585deab900f9e7cd6cdcbf458586046a64f41..676434a061815bb8396c97d0cb1acfd9a1cb038e 100644
--- a/src/MOLECULE/dihedral_opls.cpp
+++ b/src/MOLECULE/dihedral_opls.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -164,22 +164,22 @@ void DihedralOPLS::compute(int eflag, int vflag)
int me;
MPI_Comm_rank(world,&me);
if (screen) {
- char str[128];
- sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " %d %d %d %d",
- me,update->ntimestep,
- atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
- error->warning(FLERR,str,0);
- fprintf(screen," 1st atom: %d %g %g %g\n",
- me,x[i1][0],x[i1][1],x[i1][2]);
- fprintf(screen," 2nd atom: %d %g %g %g\n",
- me,x[i2][0],x[i2][1],x[i2][2]);
- fprintf(screen," 3rd atom: %d %g %g %g\n",
- me,x[i3][0],x[i3][1],x[i3][2]);
- fprintf(screen," 4th atom: %d %g %g %g\n",
- me,x[i4][0],x[i4][1],x[i4][2]);
+ char str[128];
+ sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " %d %d %d %d",
+ me,update->ntimestep,
+ atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
+ error->warning(FLERR,str,0);
+ fprintf(screen," 1st atom: %d %g %g %g\n",
+ me,x[i1][0],x[i1][1],x[i1][2]);
+ fprintf(screen," 2nd atom: %d %g %g %g\n",
+ me,x[i2][0],x[i2][1],x[i2][2]);
+ fprintf(screen," 3rd atom: %d %g %g %g\n",
+ me,x[i3][0],x[i3][1],x[i3][2]);
+ fprintf(screen," 4th atom: %d %g %g %g\n",
+ me,x[i4][0],x[i4][1],x[i4][2]);
}
}
-
+
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
@@ -195,10 +195,10 @@ void DihedralOPLS::compute(int eflag, int vflag)
p = k1[type]*(1.0 + c) + k2[type]*(1.0 - cos(2.0*phi)) +
k3[type]*(1.0 + cos(3.0*phi)) + k4[type]*(1.0 - cos(4.0*phi)) ;
- pd = k1[type] - 2.0*k2[type]*sin(2.0*phi)*siinv +
+ pd = k1[type] - 2.0*k2[type]*sin(2.0*phi)*siinv +
3.0*k3[type]*sin(3.0*phi)*siinv - 4.0*k4[type]*sin(4.0*phi)*siinv;
- if (eflag) edihedral = p;
+ if (eflag) edihedral = p;
a = pd;
c = c * a;
@@ -258,7 +258,7 @@ void DihedralOPLS::compute(int eflag, int vflag)
if (evflag)
ev_tally(i1,i2,i3,i4,nlocal,newton_bond,edihedral,f1,f3,f4,
- vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
+ vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
}
}
@@ -311,7 +311,7 @@ void DihedralOPLS::coeff(int narg, char **arg)
}
/* ----------------------------------------------------------------------
- proc 0 writes out coeffs to restart file
+ proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void DihedralOPLS::write_restart(FILE *fp)
@@ -323,7 +323,7 @@ void DihedralOPLS::write_restart(FILE *fp)
}
/* ----------------------------------------------------------------------
- proc 0 reads coeffs from restart file, bcasts them
+ proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void DihedralOPLS::read_restart(FILE *fp)
@@ -340,6 +340,6 @@ void DihedralOPLS::read_restart(FILE *fp)
MPI_Bcast(&k2[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&k3[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&k4[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
-
+
for (int i = 1; i <= atom->ndihedraltypes; i++) setflag[i] = 1;
}
diff --git a/src/MOLECULE/dihedral_opls.h b/src/MOLECULE/dihedral_opls.h
index e2c0d6b2c4f1f0d6953c88ab0038cc9ed1232e77..500a5927a11762a35823d59ab22a3d51d1d57daf 100644
--- a/src/MOLECULE/dihedral_opls.h
+++ b/src/MOLECULE/dihedral_opls.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/MOLECULE/improper_cvff.cpp b/src/MOLECULE/improper_cvff.cpp
index 401bcad85a1f702c8d8613be49f81501d07da1d7..a75d6c077d4bdd28a16a3c04072c4814f6c46490 100644
--- a/src/MOLECULE/improper_cvff.cpp
+++ b/src/MOLECULE/improper_cvff.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -103,18 +103,18 @@ void ImproperCvff::compute(int eflag, int vflag)
domain->minimum_image(vb3x,vb3y,vb3z);
// c0 calculation
-
+
sb1 = 1.0 / (vb1x*vb1x + vb1y*vb1y + vb1z*vb1z);
sb2 = 1.0 / (vb2x*vb2x + vb2y*vb2y + vb2z*vb2z);
sb3 = 1.0 / (vb3x*vb3x + vb3y*vb3y + vb3z*vb3z);
-
+
rb1 = sqrt(sb1);
rb3 = sqrt(sb3);
-
+
c0 = (vb1x*vb3x + vb1y*vb3y + vb1z*vb3z) * rb1*rb3;
// 1st and 2nd angle
-
+
b1mag2 = vb1x*vb1x + vb1y*vb1y + vb1z*vb1z;
b1mag = sqrt(b1mag2);
b2mag2 = vb2x*vb2x + vb2y*vb2y + vb2z*vb2z;
@@ -151,23 +151,23 @@ void ImproperCvff::compute(int eflag, int vflag)
int me;
MPI_Comm_rank(world,&me);
if (screen) {
- char str[128];
- sprintf(str,
- "Improper problem: %d " BIGINT_FORMAT " %d %d %d %d",
- me,update->ntimestep,
- atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
- error->warning(FLERR,str,0);
- fprintf(screen," 1st atom: %d %g %g %g\n",
- me,x[i1][0],x[i1][1],x[i1][2]);
- fprintf(screen," 2nd atom: %d %g %g %g\n",
- me,x[i2][0],x[i2][1],x[i2][2]);
- fprintf(screen," 3rd atom: %d %g %g %g\n",
- me,x[i3][0],x[i3][1],x[i3][2]);
- fprintf(screen," 4th atom: %d %g %g %g\n",
- me,x[i4][0],x[i4][1],x[i4][2]);
+ char str[128];
+ sprintf(str,
+ "Improper problem: %d " BIGINT_FORMAT " %d %d %d %d",
+ me,update->ntimestep,
+ atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
+ error->warning(FLERR,str,0);
+ fprintf(screen," 1st atom: %d %g %g %g\n",
+ me,x[i1][0],x[i1][1],x[i1][2]);
+ fprintf(screen," 2nd atom: %d %g %g %g\n",
+ me,x[i2][0],x[i2][1],x[i2][2]);
+ fprintf(screen," 3rd atom: %d %g %g %g\n",
+ me,x[i3][0],x[i3][1],x[i3][2]);
+ fprintf(screen," 4th atom: %d %g %g %g\n",
+ me,x[i4][0],x[i4][1],x[i4][2]);
}
}
-
+
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
@@ -175,7 +175,7 @@ void ImproperCvff::compute(int eflag, int vflag)
// p = 1 + cos(n*phi) for d = 1
// p = 1 - cos(n*phi) for d = -1
// pd = dp/dc / 2
-
+
m = multiplicity[type];
if (m == 2) {
@@ -204,7 +204,7 @@ void ImproperCvff::compute(int eflag, int vflag)
p = 2.0;
pd = 0.0;
}
-
+
if (sign[type] == -1) {
p = 2.0 - p;
pd = -pd;
@@ -270,7 +270,7 @@ void ImproperCvff::compute(int eflag, int vflag)
if (evflag)
ev_tally(i1,i2,i3,i4,nlocal,newton_bond,eimproper,f1,f3,f4,
- vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
+ vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
}
}
@@ -318,7 +318,7 @@ void ImproperCvff::coeff(int narg, char **arg)
}
/* ----------------------------------------------------------------------
- proc 0 writes out coeffs to restart file
+ proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void ImproperCvff::write_restart(FILE *fp)
@@ -329,7 +329,7 @@ void ImproperCvff::write_restart(FILE *fp)
}
/* ----------------------------------------------------------------------
- proc 0 reads coeffs from restart file, bcasts them
+ proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void ImproperCvff::read_restart(FILE *fp)
diff --git a/src/MOLECULE/improper_cvff.h b/src/MOLECULE/improper_cvff.h
index 5f8755b30cbd749410dd22c7fd3f1949df331be5..f6d6c36d1c9981ccc021e6c43841db4217a4f117 100644
--- a/src/MOLECULE/improper_cvff.h
+++ b/src/MOLECULE/improper_cvff.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/MOLECULE/improper_harmonic.cpp b/src/MOLECULE/improper_harmonic.cpp
index 87d94079bd5452418d32d6f738943ba8d63589a3..dae70277c9afdb713d7b256695eaa40925e2431b 100644
--- a/src/MOLECULE/improper_harmonic.cpp
+++ b/src/MOLECULE/improper_harmonic.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -96,13 +96,13 @@ void ImproperHarmonic::compute(int eflag, int vflag)
ss1 = 1.0 / (vb1x*vb1x + vb1y*vb1y + vb1z*vb1z);
ss2 = 1.0 / (vb2x*vb2x + vb2y*vb2y + vb2z*vb2z);
ss3 = 1.0 / (vb3x*vb3x + vb3y*vb3y + vb3z*vb3z);
-
+
r1 = sqrt(ss1);
r2 = sqrt(ss2);
r3 = sqrt(ss3);
-
+
// sin and cos of angle
-
+
c0 = (vb1x * vb3x + vb1y * vb3y + vb1z * vb3z) * r1 * r3;
c1 = (vb1x * vb2x + vb1y * vb2y + vb1z * vb2z) * r1 * r2;
c2 = -(vb3x * vb2x + vb3y * vb2y + vb3z * vb2z) * r3 * r2;
@@ -124,23 +124,23 @@ void ImproperHarmonic::compute(int eflag, int vflag)
int me;
MPI_Comm_rank(world,&me);
if (screen) {
- char str[128];
- sprintf(str,
- "Improper problem: %d " BIGINT_FORMAT " %d %d %d %d",
- me,update->ntimestep,
- atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
- error->warning(FLERR,str,0);
- fprintf(screen," 1st atom: %d %g %g %g\n",
- me,x[i1][0],x[i1][1],x[i1][2]);
- fprintf(screen," 2nd atom: %d %g %g %g\n",
- me,x[i2][0],x[i2][1],x[i2][2]);
- fprintf(screen," 3rd atom: %d %g %g %g\n",
- me,x[i3][0],x[i3][1],x[i3][2]);
- fprintf(screen," 4th atom: %d %g %g %g\n",
- me,x[i4][0],x[i4][1],x[i4][2]);
+ char str[128];
+ sprintf(str,
+ "Improper problem: %d " BIGINT_FORMAT " %d %d %d %d",
+ me,update->ntimestep,
+ atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
+ error->warning(FLERR,str,0);
+ fprintf(screen," 1st atom: %d %g %g %g\n",
+ me,x[i1][0],x[i1][1],x[i1][2]);
+ fprintf(screen," 2nd atom: %d %g %g %g\n",
+ me,x[i2][0],x[i2][1],x[i2][2]);
+ fprintf(screen," 3rd atom: %d %g %g %g\n",
+ me,x[i3][0],x[i3][1],x[i3][2]);
+ fprintf(screen," 4th atom: %d %g %g %g\n",
+ me,x[i4][0],x[i4][1],x[i4][2]);
}
}
-
+
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
@@ -212,7 +212,7 @@ void ImproperHarmonic::compute(int eflag, int vflag)
if (evflag)
ev_tally(i1,i2,i3,i4,nlocal,newton_bond,eimproper,f1,f3,f4,
- vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
+ vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
}
}
@@ -259,7 +259,7 @@ void ImproperHarmonic::coeff(int narg, char **arg)
}
/* ----------------------------------------------------------------------
- proc 0 writes out coeffs to restart file
+ proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void ImproperHarmonic::write_restart(FILE *fp)
@@ -269,7 +269,7 @@ void ImproperHarmonic::write_restart(FILE *fp)
}
/* ----------------------------------------------------------------------
- proc 0 reads coeffs from restart file, bcasts them
+ proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void ImproperHarmonic::read_restart(FILE *fp)
diff --git a/src/MOLECULE/improper_harmonic.h b/src/MOLECULE/improper_harmonic.h
index f75df37dc562c820b3b3b660d85f839375066614..621582edff65a62edeec01900de7b53baa5735dc 100644
--- a/src/MOLECULE/improper_harmonic.h
+++ b/src/MOLECULE/improper_harmonic.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/MOLECULE/improper_hybrid.cpp b/src/MOLECULE/improper_hybrid.cpp
index 898b3cd3500f5a24ef6139e2d69e8eb503906f07..e89e644ced899498e6a91ddb294dacb6e526ce41 100644
--- a/src/MOLECULE/improper_hybrid.cpp
+++ b/src/MOLECULE/improper_hybrid.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -79,10 +79,10 @@ void ImproperHybrid::compute(int eflag, int vflag)
}
for (m = 0; m < nstyles; m++) {
if (nimproperlist[m] > maximproper[m]) {
- memory->destroy(improperlist[m]);
- maximproper[m] = nimproperlist[m] + EXTRA;
- memory->create(improperlist[m],maximproper[m],5,
- "improper_hybrid:improperlist");
+ memory->destroy(improperlist[m]);
+ maximproper[m] = nimproperlist[m] + EXTRA;
+ memory->create(improperlist[m],maximproper[m],5,
+ "improper_hybrid:improperlist");
}
nimproperlist[m] = 0;
}
@@ -98,7 +98,7 @@ void ImproperHybrid::compute(int eflag, int vflag)
nimproperlist[m]++;
}
}
-
+
// call each sub-style's compute function
// set neighbor->improperlist to sub-style improperlist before call
// accumulate sub-style global/peratom energy/virial in hybrid
@@ -126,8 +126,8 @@ void ImproperHybrid::compute(int eflag, int vflag)
if (force->newton_bond) n += atom->nghost;
double **vatom_substyle = styles[m]->vatom;
for (i = 0; i < n; i++)
- for (j = 0; j < 6; j++)
- vatom[i][j] += vatom_substyle[i][j];
+ for (j = 0; j < 6; j++)
+ vatom[i][j] += vatom_substyle[i][j];
}
}
@@ -169,13 +169,13 @@ void ImproperHybrid::settings(int narg, char **arg)
for (int m = 0; m < nstyles; m++) {
for (int i = 0; i < m; i++)
- if (strcmp(arg[m],arg[i]) == 0)
- error->all(FLERR,
- "Improper style hybrid cannot use same improper style twice");
- if (strcmp(arg[m],"hybrid") == 0)
+ if (strcmp(arg[m],arg[i]) == 0)
+ error->all(FLERR,
+ "Improper style hybrid cannot use same improper style twice");
+ if (strcmp(arg[m],"hybrid") == 0)
error->all(FLERR,
- "Improper style hybrid cannot have hybrid as an argument");
- if (strcmp(arg[m],"none") == 0)
+ "Improper style hybrid cannot have hybrid as an argument");
+ if (strcmp(arg[m],"none") == 0)
error->all(FLERR,"Improper style hybrid cannot have none as an argument");
styles[m] = force->new_improper(arg[m],lmp->suffix,dummy);
keywords[m] = new char[strlen(arg[m])+1];
@@ -259,7 +259,7 @@ void ImproperHybrid::read_restart(FILE *fp)
keywords = new char*[nstyles];
allocate();
-
+
int n,dummy;
for (int m = 0; m < nstyles; m++) {
if (me == 0) fread(&n,sizeof(int),1,fp);
@@ -280,7 +280,7 @@ double ImproperHybrid::memory_usage()
double bytes = maxeatom * sizeof(double);
bytes += maxvatom*6 * sizeof(double);
for (int m = 0; m < nstyles; m++) bytes += maximproper[m]*5 * sizeof(int);
- for (int m = 0; m < nstyles; m++)
+ for (int m = 0; m < nstyles; m++)
if (styles[m]) bytes += styles[m]->memory_usage();
return bytes;
}
diff --git a/src/MOLECULE/improper_hybrid.h b/src/MOLECULE/improper_hybrid.h
index 6a542811bf3df7afd8de9b9a4902d649c8b93aad..a54eb6fe5c47797da1b47eb5bc9433de686fe684 100644
--- a/src/MOLECULE/improper_hybrid.h
+++ b/src/MOLECULE/improper_hybrid.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -46,7 +46,7 @@ class ImproperHybrid : public Improper {
int *nimproperlist; // # of impropers in sub-style improperlists
int *maximproper; // max # of impropers sub-style lists can store
int ***improperlist; // improperlist for each sub-style
-
+
void allocate();
};
diff --git a/src/MOLECULE/improper_umbrella.cpp b/src/MOLECULE/improper_umbrella.cpp
index 5858e485564d8997a17e30ca323760e311269de8..61055a95986aa4aeee34537add6cea3b6753d665 100644
--- a/src/MOLECULE/improper_umbrella.cpp
+++ b/src/MOLECULE/improper_umbrella.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -130,23 +130,23 @@ void ImproperUmbrella::compute(int eflag, int vflag)
int me;
MPI_Comm_rank(world,&me);
if (screen) {
- char str[128];
- sprintf(str,
- "Improper problem: %d " BIGINT_FORMAT " %d %d %d %d",
- me,update->ntimestep,
- atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
- error->warning(FLERR,str,0);
- fprintf(screen," 1st atom: %d %g %g %g\n",
- me,x[i1][0],x[i1][1],x[i1][2]);
- fprintf(screen," 2nd atom: %d %g %g %g\n",
- me,x[i2][0],x[i2][1],x[i2][2]);
- fprintf(screen," 3rd atom: %d %g %g %g\n",
- me,x[i3][0],x[i3][1],x[i3][2]);
- fprintf(screen," 4th atom: %d %g %g %g\n",
- me,x[i4][0],x[i4][1],x[i4][2]);
+ char str[128];
+ sprintf(str,
+ "Improper problem: %d " BIGINT_FORMAT " %d %d %d %d",
+ me,update->ntimestep,
+ atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
+ error->warning(FLERR,str,0);
+ fprintf(screen," 1st atom: %d %g %g %g\n",
+ me,x[i1][0],x[i1][1],x[i1][2]);
+ fprintf(screen," 2nd atom: %d %g %g %g\n",
+ me,x[i2][0],x[i2][1],x[i2][2]);
+ fprintf(screen," 3rd atom: %d %g %g %g\n",
+ me,x[i3][0],x[i3][1],x[i3][2]);
+ fprintf(screen," 4th atom: %d %g %g %g\n",
+ me,x[i4][0],x[i4][1],x[i4][2]);
}
}
-
+
if (c > 1.0) s = 1.0;
if (c < -1.0) s = -1.0;
@@ -154,15 +154,15 @@ void ImproperUmbrella::compute(int eflag, int vflag)
if (s < SMALL) s = SMALL;
cotphi = c/s;
- projhfg = (vb3x*vb1x+vb3y*vb1y+vb3z*vb1z) /
- sqrt(vb1x*vb1x+vb1y*vb1y+vb1z*vb1z);
- projhfg += (vb3x*vb2x+vb3y*vb2y+vb3z*vb2z) /
+ projhfg = (vb3x*vb1x+vb3y*vb1y+vb3z*vb1z) /
+ sqrt(vb1x*vb1x+vb1y*vb1y+vb1z*vb1z);
+ projhfg += (vb3x*vb2x+vb3y*vb2y+vb3z*vb2z) /
sqrt(vb2x*vb2x+vb2y*vb2y+vb2z*vb2z);
if (projhfg > 0.0) {
s *= -1.0;
cotphi *= -1.0;
}
-
+
// force and energy
// if w0 = 0: E = k * (1 - cos w)
// if w0 != 0: E = 0.5 * C (cos w - cos w0)^2, C = k/(sin(w0)^2
@@ -232,7 +232,7 @@ void ImproperUmbrella::compute(int eflag, int vflag)
if (evflag)
ev_tally(i1,i2,i3,i4,nlocal,newton_bond,eimproper,f1,f3,f4,
- vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
+ vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
}
}
@@ -282,7 +282,7 @@ void ImproperUmbrella::coeff(int narg, char **arg)
}
/* ----------------------------------------------------------------------
- proc 0 writes out coeffs to restart file
+ proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void ImproperUmbrella::write_restart(FILE *fp)
@@ -293,7 +293,7 @@ void ImproperUmbrella::write_restart(FILE *fp)
}
/* ----------------------------------------------------------------------
- proc 0 reads coeffs from restart file, bcasts them
+ proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void ImproperUmbrella::read_restart(FILE *fp)
diff --git a/src/MOLECULE/improper_umbrella.h b/src/MOLECULE/improper_umbrella.h
index fd3d47127f581049dc8c486693ae793faa06f252..3d005aa105bab36022b568da6a794a8f1cba7149 100644
--- a/src/MOLECULE/improper_umbrella.h
+++ b/src/MOLECULE/improper_umbrella.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/MOLECULE/pair_hbond_dreiding_lj.cpp b/src/MOLECULE/pair_hbond_dreiding_lj.cpp
index 77302e66940f94e65099b16cd2424eccb4ead10e..c5fd2b0269f762600fbb245be23d24643ac4b18d 100644
--- a/src/MOLECULE/pair_hbond_dreiding_lj.cpp
+++ b/src/MOLECULE/pair_hbond_dreiding_lj.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -39,7 +39,7 @@ using namespace MathConst;
/* ---------------------------------------------------------------------- */
-PairHbondDreidingLJ::PairHbondDreidingLJ(LAMMPS *lmp) : Pair(lmp)
+PairHbondDreidingLJ::PairHbondDreidingLJ(LAMMPS *lmp) : Pair(lmp)
{
// hbond cannot compute virial as F dot r
// due to using map() to find bonded H atoms which are not near donor atom
@@ -88,19 +88,19 @@ void PairHbondDreidingLJ::compute(int eflag, int vflag)
evdwl = ehbond = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
-
+
double **x = atom->x;
double **f = atom->f;
int **special = atom->special;
int *type = atom->type;
int **nspecial = atom->nspecial;
double *special_lj = force->special_lj;
-
+
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// ii = loop over donors
// jj = loop over acceptors
// kk = loop over hydrogens bonded to donor
@@ -115,7 +115,7 @@ void PairHbondDreidingLJ::compute(int eflag, int vflag)
knum = nspecial[i][0];
jlist = firstneigh[i];
jnum = numneigh[i];
-
+
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_hb = special_lj[sbmask(j)];
@@ -130,110 +130,110 @@ void PairHbondDreidingLJ::compute(int eflag, int vflag)
rsq = delx*delx + dely*dely + delz*delz;
for (kk = 0; kk < knum; kk++) {
- k = atom->map(klist[kk]);
- if (k < 0) continue;
- ktype = type[k];
- m = type2param[itype][jtype][ktype];
- if (m < 0) continue;
- pm = ¶ms[m];
-
- if (rsq < pm->cut_outersq) {
- delr1[0] = x[i][0] - x[k][0];
- delr1[1] = x[i][1] - x[k][1];
- delr1[2] = x[i][2] - x[k][2];
- domain->minimum_image(delr1);
- rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2];
- r1 = sqrt(rsq1);
-
- delr2[0] = x[j][0] - x[k][0];
- delr2[1] = x[j][1] - x[k][1];
- delr2[2] = x[j][2] - x[k][2];
- domain->minimum_image(delr2);
- rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
- r2 = sqrt(rsq2);
-
- // angle (cos and sin)
-
- c = delr1[0]*delr2[0] + delr1[1]*delr2[1] + delr1[2]*delr2[2];
- c /= r1*r2;
- if (c > 1.0) c = 1.0;
- if (c < -1.0) c = -1.0;
- ac = acos(c);
-
- if (ac > pm->cut_angle && ac < (2.0*MY_PI - pm->cut_angle)) {
- s = sqrt(1.0 - c*c);
- if (s < SMALL) s = SMALL;
-
- // LJ-specific kernel
-
- r2inv = 1.0/rsq;
- r10inv = r2inv*r2inv*r2inv*r2inv*r2inv;
- force_kernel = r10inv*(pm->lj1*r2inv - pm->lj2)*r2inv *
- pow(c,(double)pm->ap);
- force_angle = pm->ap * r10inv*(pm->lj3*r2inv - pm->lj4) *
- pow(c,(double)pm->ap-1.0)*s;
-
- eng_lj = r10inv*(pm->lj3*r2inv - pm->lj4);
- if (rsq > pm->cut_innersq) {
- switch1 = (pm->cut_outersq-rsq) * (pm->cut_outersq-rsq) *
- (pm->cut_outersq + 2.0*rsq - 3.0*pm->cut_innersq) /
- pm->denom_vdw;
- switch2 = 12.0*rsq * (pm->cut_outersq-rsq) *
- (rsq-pm->cut_innersq) / pm->denom_vdw;
- force_kernel = force_kernel*switch1 + eng_lj*switch2;
- eng_lj *= switch1;
- }
-
- if (eflag) {
- evdwl = eng_lj * pow(c,(double)pm->ap);
- evdwl *= factor_hb;
- ehbond += evdwl;
- }
-
- a = factor_hb*force_angle/s;
- b = factor_hb*force_kernel;
-
- a11 = a*c / rsq1;
- a12 = -a / (r1*r2);
- a22 = a*c / rsq2;
-
- vx1 = a11*delr1[0] + a12*delr2[0];
- vx2 = a22*delr2[0] + a12*delr1[0];
- vy1 = a11*delr1[1] + a12*delr2[1];
- vy2 = a22*delr2[1] + a12*delr1[1];
- vz1 = a11*delr1[2] + a12*delr2[2];
- vz2 = a22*delr2[2] + a12*delr1[2];
-
- fi[0] = vx1 + b*delx;
- fi[1] = vy1 + b*dely;
- fi[2] = vz1 + b*delz;
- fj[0] = vx2 - b*delx;
- fj[1] = vy2 - b*dely;
- fj[2] = vz2 - b*delz;
-
- f[i][0] += fi[0];
- f[i][1] += fi[1];
- f[i][2] += fi[2];
-
- f[j][0] += fj[0];
- f[j][1] += fj[1];
- f[j][2] += fj[2];
-
- f[k][0] -= vx1 + vx2;
- f[k][1] -= vy1 + vy2;
- f[k][2] -= vz1 + vz2;
-
- // KIJ instead of IJK b/c delr1/delr2 are both with respect to k
-
- if (evflag) ev_tally3(k,i,j,evdwl,0.0,fi,fj,delr1,delr2);
-
- hbcount++;
- }
+ k = atom->map(klist[kk]);
+ if (k < 0) continue;
+ ktype = type[k];
+ m = type2param[itype][jtype][ktype];
+ if (m < 0) continue;
+ pm = ¶ms[m];
+
+ if (rsq < pm->cut_outersq) {
+ delr1[0] = x[i][0] - x[k][0];
+ delr1[1] = x[i][1] - x[k][1];
+ delr1[2] = x[i][2] - x[k][2];
+ domain->minimum_image(delr1);
+ rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2];
+ r1 = sqrt(rsq1);
+
+ delr2[0] = x[j][0] - x[k][0];
+ delr2[1] = x[j][1] - x[k][1];
+ delr2[2] = x[j][2] - x[k][2];
+ domain->minimum_image(delr2);
+ rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
+ r2 = sqrt(rsq2);
+
+ // angle (cos and sin)
+
+ c = delr1[0]*delr2[0] + delr1[1]*delr2[1] + delr1[2]*delr2[2];
+ c /= r1*r2;
+ if (c > 1.0) c = 1.0;
+ if (c < -1.0) c = -1.0;
+ ac = acos(c);
+
+ if (ac > pm->cut_angle && ac < (2.0*MY_PI - pm->cut_angle)) {
+ s = sqrt(1.0 - c*c);
+ if (s < SMALL) s = SMALL;
+
+ // LJ-specific kernel
+
+ r2inv = 1.0/rsq;
+ r10inv = r2inv*r2inv*r2inv*r2inv*r2inv;
+ force_kernel = r10inv*(pm->lj1*r2inv - pm->lj2)*r2inv *
+ pow(c,(double)pm->ap);
+ force_angle = pm->ap * r10inv*(pm->lj3*r2inv - pm->lj4) *
+ pow(c,(double)pm->ap-1.0)*s;
+
+ eng_lj = r10inv*(pm->lj3*r2inv - pm->lj4);
+ if (rsq > pm->cut_innersq) {
+ switch1 = (pm->cut_outersq-rsq) * (pm->cut_outersq-rsq) *
+ (pm->cut_outersq + 2.0*rsq - 3.0*pm->cut_innersq) /
+ pm->denom_vdw;
+ switch2 = 12.0*rsq * (pm->cut_outersq-rsq) *
+ (rsq-pm->cut_innersq) / pm->denom_vdw;
+ force_kernel = force_kernel*switch1 + eng_lj*switch2;
+ eng_lj *= switch1;
+ }
+
+ if (eflag) {
+ evdwl = eng_lj * pow(c,(double)pm->ap);
+ evdwl *= factor_hb;
+ ehbond += evdwl;
+ }
+
+ a = factor_hb*force_angle/s;
+ b = factor_hb*force_kernel;
+
+ a11 = a*c / rsq1;
+ a12 = -a / (r1*r2);
+ a22 = a*c / rsq2;
+
+ vx1 = a11*delr1[0] + a12*delr2[0];
+ vx2 = a22*delr2[0] + a12*delr1[0];
+ vy1 = a11*delr1[1] + a12*delr2[1];
+ vy2 = a22*delr2[1] + a12*delr1[1];
+ vz1 = a11*delr1[2] + a12*delr2[2];
+ vz2 = a22*delr2[2] + a12*delr1[2];
+
+ fi[0] = vx1 + b*delx;
+ fi[1] = vy1 + b*dely;
+ fi[2] = vz1 + b*delz;
+ fj[0] = vx2 - b*delx;
+ fj[1] = vy2 - b*dely;
+ fj[2] = vz2 - b*delz;
+
+ f[i][0] += fi[0];
+ f[i][1] += fi[1];
+ f[i][2] += fi[2];
+
+ f[j][0] += fj[0];
+ f[j][1] += fj[1];
+ f[j][2] += fj[2];
+
+ f[k][0] -= vx1 + vx2;
+ f[k][1] -= vy1 + vy2;
+ f[k][2] -= vz1 + vz2;
+
+ // KIJ instead of IJK b/c delr1/delr2 are both with respect to k
+
+ if (evflag) ev_tally3(k,i,j,evdwl,0.0,fi,fj,delr1,delr2);
+
+ hbcount++;
+ }
}
}
}
}
-
+
if (eflag_global) {
pvector[0] = hbcount;
pvector[1] = ehbond;
@@ -241,7 +241,7 @@ void PairHbondDreidingLJ::compute(int eflag, int vflag)
}
/* ----------------------------------------------------------------------
- allocate all arrays
+ allocate all arrays
------------------------------------------------------------------------- */
void PairHbondDreidingLJ::allocate()
@@ -257,27 +257,27 @@ void PairHbondDreidingLJ::allocate()
setflag[i][j] = 1;
memory->create(cutsq,n+1,n+1,"pair:cutsq");
-
+
donor = new int[n+1];
acceptor = new int[n+1];
memory->create(type2param,n+1,n+1,n+1,"pair:type2param");
int i,j,k;
for (i = 1; i <= n; i++)
- for (j = 1; j <= n; j++)
+ for (j = 1; j <= n; j++)
for (k = 1; k <= n; k++)
type2param[i][j][k] = -1;
}
/* ----------------------------------------------------------------------
- global settings
+ global settings
------------------------------------------------------------------------- */
void PairHbondDreidingLJ::settings(int narg, char **arg)
{
if (narg != 4) error->all(FLERR,"Illegal pair_style command");
-
- ap_global = force->inumeric(arg[0]);
+
+ ap_global = force->inumeric(arg[0]);
cut_inner_global = force->numeric(arg[1]);
cut_outer_global = force->numeric(arg[2]);
cut_angle_global = force->numeric(arg[3]) * MY_PI/180.0;
@@ -292,12 +292,12 @@ void PairHbondDreidingLJ::coeff(int narg, char **arg)
if (narg < 6 || narg > 9)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
-
+
int ilo,ihi,jlo,jhi,klo,khi;
force->bounds(arg[0],atom->ntypes,ilo,ihi);
force->bounds(arg[1],atom->ntypes,jlo,jhi);
force->bounds(arg[2],atom->ntypes,klo,khi);
-
+
int donor_flag;
if (strcmp(arg[3],"i") == 0) donor_flag = 0;
else if (strcmp(arg[3],"j") == 0) donor_flag = 1;
@@ -305,7 +305,7 @@ void PairHbondDreidingLJ::coeff(int narg, char **arg)
double epsilon_one = force->numeric(arg[4]);
double sigma_one = force->numeric(arg[5]);
-
+
int ap_one = ap_global;
if (narg > 6) ap_one = force->inumeric(arg[6]);
double cut_inner_one = cut_inner_global;
@@ -323,7 +323,7 @@ void PairHbondDreidingLJ::coeff(int narg, char **arg)
if (nparams == maxparam) {
maxparam += CHUNK;
params = (Param *) memory->srealloc(params,maxparam*sizeof(Param),
- "pair:params");
+ "pair:params");
}
params[nparams].epsilon = epsilon_one;
@@ -334,10 +334,10 @@ void PairHbondDreidingLJ::coeff(int narg, char **arg)
params[nparams].cut_innersq = cut_inner_one*cut_inner_one;
params[nparams].cut_outersq = cut_outer_one*cut_outer_one;
params[nparams].cut_angle = cut_angle_one;
- params[nparams].denom_vdw =
+ params[nparams].denom_vdw =
(params[nparams].cut_outersq-params[nparams].cut_innersq) *
(params[nparams].cut_outersq-params[nparams].cut_innersq) *
- (params[nparams].cut_outersq-params[nparams].cut_innersq);
+ (params[nparams].cut_outersq-params[nparams].cut_innersq);
// flag type2param with either i,j = D,A or j,i = D,A
@@ -345,9 +345,9 @@ void PairHbondDreidingLJ::coeff(int narg, char **arg)
for (int i = ilo; i <= ihi; i++)
for (int j = MAX(jlo,i); j <= jhi; j++)
for (int k = klo; k <= khi; k++) {
- if (donor_flag == 0) type2param[i][j][k] = nparams;
- else type2param[j][i][k] = nparams;
- count++;
+ if (donor_flag == 0) type2param[i][j][k] = nparams;
+ else type2param[j][i][k] = nparams;
+ count++;
}
nparams++;
@@ -369,9 +369,9 @@ void PairHbondDreidingLJ::init_style()
error->all(FLERR,"Pair style hbond/dreiding requires molecular system");
if (atom->tag_enable == 0)
error->all(FLERR,"Pair style hbond/dreiding requires atom IDs");
- if (atom->map_style == 0)
+ if (atom->map_style == 0)
error->all(FLERR,"Pair style hbond/dreiding requires an atom map, "
- "see atom_modify");
+ "see atom_modify");
if (force->newton_pair == 0)
error->all(FLERR,"Pair style hbond/dreiding requires newton pair on");
@@ -383,11 +383,11 @@ void PairHbondDreidingLJ::init_style()
for (int i = 1; i <= n; i++)
for (int j = 1; j <= n; j++)
for (int k = 1; k <= n; k++)
- if (type2param[i][j][k] >= 0) {
- anyflag = 1;
- donor[i] = 1;
- acceptor[j] = 1;
- }
+ if (type2param[i][j][k] >= 0) {
+ anyflag = 1;
+ donor[i] = 1;
+ acceptor[j] = 1;
+ }
if (!anyflag) error->all(FLERR,"No pair hbond/dreiding coefficients set");
@@ -399,21 +399,21 @@ void PairHbondDreidingLJ::init_style()
params[m].lj2 = 60.0*params[m].epsilon*pow(params[m].sigma,10.0);
params[m].lj3 = 5.0*params[m].epsilon*pow(params[m].sigma,12.0);
params[m].lj4 = 6.0*params[m].epsilon*pow(params[m].sigma,10.0);
-
+
/*
if (offset_flag) {
double ratio = params[m].sigma / params[m].cut_outer;
- params[m].offset = params[m].epsilon *
- ((2.0*pow(ratio,9.0)) - (3.0*pow(ratio,6.0)));
+ params[m].offset = params[m].epsilon *
+ ((2.0*pow(ratio,9.0)) - (3.0*pow(ratio,6.0)));
} else params[m].offset = 0.0;
*/
}
-
+
// full neighbor list request
int irequest = neighbor->request(this);
neighbor->requests[irequest]->half = 0;
- neighbor->requests[irequest]->full = 1;
+ neighbor->requests[irequest]->full = 1;
}
/* ----------------------------------------------------------------------
@@ -460,7 +460,7 @@ double PairHbondDreidingLJ::single(int i, int j, int itype, int jtype,
eng = 0.0;
fforce = 0;
-
+
// sanity check
if (!donor[itype]) return 0.0;
@@ -468,7 +468,7 @@ double PairHbondDreidingLJ::single(int i, int j, int itype, int jtype,
klist = special[i];
knum = nspecial[i][0];
-
+
factor_hb = special_lj[sbmask(j)];
for (kk = 0; kk < knum; kk++) {
@@ -485,16 +485,16 @@ double PairHbondDreidingLJ::single(int i, int j, int itype, int jtype,
domain->minimum_image(delr1);
rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2];
r1 = sqrt(rsq1);
-
+
delr2[0] = x[j][0] - x[k][0];
delr2[1] = x[j][1] - x[k][1];
delr2[2] = x[j][2] - x[k][2];
domain->minimum_image(delr2);
rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
r2 = sqrt(rsq2);
-
+
// angle (cos and sin)
-
+
c = delr1[0]*delr2[0] + delr1[1]*delr2[1] + delr1[2]*delr2[2];
c /= r1*r2;
if (c > 1.0) c = 1.0;
@@ -509,20 +509,20 @@ double PairHbondDreidingLJ::single(int i, int j, int itype, int jtype,
r2inv = 1.0/rsq;
r10inv = r2inv*r2inv*r2inv*r2inv*r2inv;
- force_kernel = r10inv*(pm->lj1*r2inv - pm->lj2)*r2inv *
+ force_kernel = r10inv*(pm->lj1*r2inv - pm->lj2)*r2inv *
pow(c,(double)pm->ap);
- force_angle = pm->ap * r10inv*(pm->lj3*r2inv - pm->lj4) *
+ force_angle = pm->ap * r10inv*(pm->lj3*r2inv - pm->lj4) *
pow(c,(double)pm->ap-1.0)*s;
// only lj part for now
- eng_lj = r10inv*(pm->lj3*r2inv - pm->lj4);
+ eng_lj = r10inv*(pm->lj3*r2inv - pm->lj4);
if (rsq > pm->cut_innersq) {
- switch1 = (pm->cut_outersq-rsq) * (pm->cut_outersq-rsq) *
- (pm->cut_outersq + 2.0*rsq - 3.0*pm->cut_innersq) /
- pm->denom_vdw;
+ switch1 = (pm->cut_outersq-rsq) * (pm->cut_outersq-rsq) *
+ (pm->cut_outersq + 2.0*rsq - 3.0*pm->cut_innersq) /
+ pm->denom_vdw;
switch2 = 12.0*rsq * (pm->cut_outersq-rsq) *
- (rsq-pm->cut_innersq) / pm->denom_vdw;
+ (rsq-pm->cut_innersq) / pm->denom_vdw;
force_kernel = force_kernel*switch1 + eng_lj*switch2;
eng_lj *= switch1;
}
diff --git a/src/MOLECULE/pair_hbond_dreiding_lj.h b/src/MOLECULE/pair_hbond_dreiding_lj.h
index 942a5bfa477e0884405f64b413aaaa790511dcf1..588ec8ab74e6f0fa186b2967037a86cf84dd3637 100644
--- a/src/MOLECULE/pair_hbond_dreiding_lj.h
+++ b/src/MOLECULE/pair_hbond_dreiding_lj.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/MOLECULE/pair_hbond_dreiding_morse.cpp b/src/MOLECULE/pair_hbond_dreiding_morse.cpp
index 185dbc84e01d13b1f602d1ccb16d4fb5857fbdeb..044946bd13428bcbd28899e4351b5f57246fb464 100644
--- a/src/MOLECULE/pair_hbond_dreiding_morse.cpp
+++ b/src/MOLECULE/pair_hbond_dreiding_morse.cpp
@@ -5,9 +5,9 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
-
+
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@@ -39,7 +39,7 @@ using namespace MathConst;
/* ---------------------------------------------------------------------- */
-PairHbondDreidingMorse::PairHbondDreidingMorse(LAMMPS *lmp) :
+PairHbondDreidingMorse::PairHbondDreidingMorse(LAMMPS *lmp) :
PairHbondDreidingLJ(lmp) {}
/* ---------------------------------------------------------------------- */
@@ -58,19 +58,19 @@ void PairHbondDreidingMorse::compute(int eflag, int vflag)
evdwl = ehbond = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
-
+
double **x = atom->x;
double **f = atom->f;
int **special = atom->special;
int *type = atom->type;
int **nspecial = atom->nspecial;
double *special_lj = force->special_lj;
-
+
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// ii = loop over donors
// jj = loop over acceptors
// kk = loop over hydrogens bonded to donor
@@ -85,7 +85,7 @@ void PairHbondDreidingMorse::compute(int eflag, int vflag)
knum = nspecial[i][0];
jlist = firstneigh[i];
jnum = numneigh[i];
-
+
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_hb = special_lj[sbmask(j)];
@@ -98,106 +98,106 @@ void PairHbondDreidingMorse::compute(int eflag, int vflag)
dely = x[i][1] - x[j][1];
delz = x[i][2] - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
-
+
for (kk = 0; kk < knum; kk++) {
- k = atom->map(klist[kk]);
- if (k < 0) continue;
- ktype = type[k];
- m = type2param[itype][jtype][ktype];
- if (m < 0) continue;
- pm = ¶ms[m];
-
- if (rsq < pm->cut_outersq) {
- delr1[0] = x[i][0] - x[k][0];
- delr1[1] = x[i][1] - x[k][1];
- delr1[2] = x[i][2] - x[k][2];
- domain->minimum_image(delr1);
- rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2];
- r1 = sqrt(rsq1);
-
- delr2[0] = x[j][0] - x[k][0];
- delr2[1] = x[j][1] - x[k][1];
- delr2[2] = x[j][2] - x[k][2];
- domain->minimum_image(delr2);
- rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
- r2 = sqrt(rsq2);
-
- // angle (cos and sin)
-
- c = delr1[0]*delr2[0] + delr1[1]*delr2[1] + delr1[2]*delr2[2];
- c /= r1*r2;
- if (c > 1.0) c = 1.0;
- if (c < -1.0) c = -1.0;
- ac = acos(c);
-
- if (ac > pm->cut_angle && ac < (2.0*MY_PI - pm->cut_angle)) {
- s = sqrt(1.0 - c*c);
- if (s < SMALL) s = SMALL;
-
- // Morse-specific kernel
-
- r = sqrt(rsq);
- dr = r - pm->r0;
- dexp = exp(-pm->alpha * dr);
- force_kernel = pm->morse1*(dexp*dexp - dexp)/r * pow(c,(double)pm->ap);
- force_angle = pm->ap * eng_morse * pow(c,pm->ap-1.0)*s;
-
- eng_morse = pm->d0 * (dexp*dexp - 2.0*dexp);
- if (rsq > pm->cut_innersq) {
- switch1 = (pm->cut_outersq-rsq) * (pm->cut_outersq-rsq) *
- (pm->cut_outersq + 2.0*rsq - 3.0*pm->cut_innersq) /
- pm->denom_vdw;
- switch2 = 12.0*rsq * (pm->cut_outersq-rsq) *
- (rsq-pm->cut_innersq) / pm->denom_vdw;
- force_kernel = force_kernel*switch1 + eng_morse*switch2;
- eng_morse *= switch1;
- }
-
- if (eflag) {
- evdwl = eng_morse * pow(c,(double)params[m].ap);
- evdwl *= factor_hb;
- ehbond += evdwl;
- }
-
- a = factor_hb*force_angle/s;
- b = factor_hb*force_kernel;
-
- a11 = a*c / rsq1;
- a12 = -a / (r1*r2);
- a22 = a*c / rsq2;
-
- vx1 = a11*delr1[0] + a12*delr2[0];
- vx2 = a22*delr2[0] + a12*delr1[0];
- vy1 = a11*delr1[1] + a12*delr2[1];
- vy2 = a22*delr2[1] + a12*delr1[1];
- vz1 = a11*delr1[2] + a12*delr2[2];
- vz2 = a22*delr2[2] + a12*delr1[2];
-
- fi[0] = vx1 + b*delx;
- fi[1] = vy1 + b*dely;
- fi[2] = vz1 + b*delz;
- fj[0] = vx2 - b*delx;
- fj[1] = vy2 - b*dely;
- fj[2] = vz2 - b*delz;
-
- f[i][0] += fi[0];
- f[i][1] += fi[1];
- f[i][2] += fi[2];
-
- f[j][0] += fj[0];
- f[j][1] += fj[1];
- f[j][2] += fj[2];
-
- f[k][0] -= vx1 + vx2;
- f[k][1] -= vy1 + vy2;
- f[k][2] -= vz1 + vz2;
-
- // KIJ instead of IJK b/c delr1/delr2 are both with respect to k
-
- if (evflag) ev_tally3(k,i,j,evdwl,0.0,fi,fj,delr1,delr2);
-
- hbcount++;
- }
+ k = atom->map(klist[kk]);
+ if (k < 0) continue;
+ ktype = type[k];
+ m = type2param[itype][jtype][ktype];
+ if (m < 0) continue;
+ pm = ¶ms[m];
+
+ if (rsq < pm->cut_outersq) {
+ delr1[0] = x[i][0] - x[k][0];
+ delr1[1] = x[i][1] - x[k][1];
+ delr1[2] = x[i][2] - x[k][2];
+ domain->minimum_image(delr1);
+ rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2];
+ r1 = sqrt(rsq1);
+
+ delr2[0] = x[j][0] - x[k][0];
+ delr2[1] = x[j][1] - x[k][1];
+ delr2[2] = x[j][2] - x[k][2];
+ domain->minimum_image(delr2);
+ rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
+ r2 = sqrt(rsq2);
+
+ // angle (cos and sin)
+
+ c = delr1[0]*delr2[0] + delr1[1]*delr2[1] + delr1[2]*delr2[2];
+ c /= r1*r2;
+ if (c > 1.0) c = 1.0;
+ if (c < -1.0) c = -1.0;
+ ac = acos(c);
+
+ if (ac > pm->cut_angle && ac < (2.0*MY_PI - pm->cut_angle)) {
+ s = sqrt(1.0 - c*c);
+ if (s < SMALL) s = SMALL;
+
+ // Morse-specific kernel
+
+ r = sqrt(rsq);
+ dr = r - pm->r0;
+ dexp = exp(-pm->alpha * dr);
+ force_kernel = pm->morse1*(dexp*dexp - dexp)/r * pow(c,(double)pm->ap);
+ force_angle = pm->ap * eng_morse * pow(c,pm->ap-1.0)*s;
+
+ eng_morse = pm->d0 * (dexp*dexp - 2.0*dexp);
+ if (rsq > pm->cut_innersq) {
+ switch1 = (pm->cut_outersq-rsq) * (pm->cut_outersq-rsq) *
+ (pm->cut_outersq + 2.0*rsq - 3.0*pm->cut_innersq) /
+ pm->denom_vdw;
+ switch2 = 12.0*rsq * (pm->cut_outersq-rsq) *
+ (rsq-pm->cut_innersq) / pm->denom_vdw;
+ force_kernel = force_kernel*switch1 + eng_morse*switch2;
+ eng_morse *= switch1;
+ }
+
+ if (eflag) {
+ evdwl = eng_morse * pow(c,(double)params[m].ap);
+ evdwl *= factor_hb;
+ ehbond += evdwl;
+ }
+
+ a = factor_hb*force_angle/s;
+ b = factor_hb*force_kernel;
+
+ a11 = a*c / rsq1;
+ a12 = -a / (r1*r2);
+ a22 = a*c / rsq2;
+
+ vx1 = a11*delr1[0] + a12*delr2[0];
+ vx2 = a22*delr2[0] + a12*delr1[0];
+ vy1 = a11*delr1[1] + a12*delr2[1];
+ vy2 = a22*delr2[1] + a12*delr1[1];
+ vz1 = a11*delr1[2] + a12*delr2[2];
+ vz2 = a22*delr2[2] + a12*delr1[2];
+
+ fi[0] = vx1 + b*delx;
+ fi[1] = vy1 + b*dely;
+ fi[2] = vz1 + b*delz;
+ fj[0] = vx2 - b*delx;
+ fj[1] = vy2 - b*dely;
+ fj[2] = vz2 - b*delz;
+
+ f[i][0] += fi[0];
+ f[i][1] += fi[1];
+ f[i][2] += fi[2];
+
+ f[j][0] += fj[0];
+ f[j][1] += fj[1];
+ f[j][2] += fj[2];
+
+ f[k][0] -= vx1 + vx2;
+ f[k][1] -= vy1 + vy2;
+ f[k][2] -= vz1 + vz2;
+
+ // KIJ instead of IJK b/c delr1/delr2 are both with respect to k
+
+ if (evflag) ev_tally3(k,i,j,evdwl,0.0,fi,fj,delr1,delr2);
+
+ hbcount++;
+ }
}
}
}
@@ -223,7 +223,7 @@ void PairHbondDreidingMorse::coeff(int narg, char **arg)
force->bounds(arg[0],atom->ntypes,ilo,ihi);
force->bounds(arg[1],atom->ntypes,jlo,jhi);
force->bounds(arg[2],atom->ntypes,klo,khi);
-
+
int donor_flag;
if (strcmp(arg[3],"i") == 0) donor_flag = 0;
else if (strcmp(arg[3],"j") == 0) donor_flag = 1;
@@ -251,7 +251,7 @@ void PairHbondDreidingMorse::coeff(int narg, char **arg)
if (nparams == maxparam) {
maxparam += CHUNK;
params = (Param *) memory->srealloc(params,maxparam*sizeof(Param),
- "pair:params");
+ "pair:params");
}
params[nparams].d0 = d0_one;
@@ -263,20 +263,20 @@ void PairHbondDreidingMorse::coeff(int narg, char **arg)
params[nparams].cut_innersq = cut_inner_one*cut_inner_one;
params[nparams].cut_outersq = cut_outer_one*cut_outer_one;
params[nparams].cut_angle = cut_angle_one;
- params[nparams].denom_vdw =
+ params[nparams].denom_vdw =
(params[nparams].cut_outersq-params[nparams].cut_innersq) *
(params[nparams].cut_outersq-params[nparams].cut_innersq) *
(params[nparams].cut_outersq-params[nparams].cut_innersq);
-
+
// flag type2param with either i,j = D,A or j,i = D,A
int count = 0;
for (int i = ilo; i <= ihi; i++)
for (int j = MAX(jlo,i); j <= jhi; j++)
for (int k = klo; k <= khi; k++) {
- if (donor_flag == 0) type2param[i][j][k] = nparams;
- else type2param[j][i][k] = nparams;
- count++;
+ if (donor_flag == 0) type2param[i][j][k] = nparams;
+ else type2param[j][i][k] = nparams;
+ count++;
}
nparams++;
@@ -298,9 +298,9 @@ void PairHbondDreidingMorse::init_style()
error->all(FLERR,"Pair style hbond/dreiding requires molecular system");
if (atom->tag_enable == 0)
error->all(FLERR,"Pair style hbond/dreiding requires atom IDs");
- if (atom->map_style == 0)
+ if (atom->map_style == 0)
error->all(FLERR,"Pair style hbond/dreiding requires an atom map, "
- "see atom_modify");
+ "see atom_modify");
if (force->newton_pair == 0)
error->all(FLERR,"Pair style hbond/dreiding requires newton pair on");
@@ -312,11 +312,11 @@ void PairHbondDreidingMorse::init_style()
for (int i = 1; i <= n; i++)
for (int j = 1; j <= n; j++)
for (int k = 1; k <= n; k++)
- if (type2param[i][j][k] >= 0) {
- anyflag = 1;
- donor[i] = 1;
- acceptor[j] = 1;
- }
+ if (type2param[i][j][k] >= 0) {
+ anyflag = 1;
+ donor[i] = 1;
+ acceptor[j] = 1;
+ }
if (!anyflag) error->all(FLERR,"No pair hbond/dreiding coefficients set");
@@ -329,8 +329,8 @@ void PairHbondDreidingMorse::init_style()
/*
if (offset_flag) {
double alpha_dr = -params[m].alpha * (params[m].cut - params[m].r0);
- params[m].offset = params[m].d0 *
- ((exp(2.0*alpha_dr)) - (2.0*exp(alpha_dr)));
+ params[m].offset = params[m].d0 *
+ ((exp(2.0*alpha_dr)) - (2.0*exp(alpha_dr)));
} else params[m].offset = 0.0;
*/
}
@@ -339,7 +339,7 @@ void PairHbondDreidingMorse::init_style()
int irequest = neighbor->request(this);
neighbor->requests[irequest]->half = 0;
- neighbor->requests[irequest]->full = 1;
+ neighbor->requests[irequest]->full = 1;
}
/* ---------------------------------------------------------------------- */
@@ -421,18 +421,17 @@ double PairHbondDreidingMorse::single(int i, int j, int itype, int jtype,
eng_morse = pm->d0 * (dexp*dexp - 2.0*dexp);
if (rsq > pm->cut_innersq) {
switch1 = (pm->cut_outersq-rsq) * (pm->cut_outersq-rsq) *
- (pm->cut_outersq + 2.0*rsq - 3.0*pm->cut_innersq) /
- pm->denom_vdw;
+ (pm->cut_outersq + 2.0*rsq - 3.0*pm->cut_innersq) /
+ pm->denom_vdw;
switch2 = 12.0*rsq * (pm->cut_outersq-rsq) *
- (rsq-pm->cut_innersq) / pm->denom_vdw;
+ (rsq-pm->cut_innersq) / pm->denom_vdw;
force_kernel = force_kernel*switch1 + eng_morse*switch2;
eng_morse *= switch1;
}
-
+
eng += eng_morse * pow(c,(double)params[m].ap)* factor_hb;
fforce += force_kernel*pow(c,(double)pm->ap) + eng_morse*force_angle;
}
return eng;
}
-
diff --git a/src/MOLECULE/pair_hbond_dreiding_morse.h b/src/MOLECULE/pair_hbond_dreiding_morse.h
index a9cd5037bead184855cc381c009862b09691396e..fcd96aebc605bf3a301ec904b17cbd28f126c92d 100644
--- a/src/MOLECULE/pair_hbond_dreiding_morse.h
+++ b/src/MOLECULE/pair_hbond_dreiding_morse.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp b/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp
index 9f04882a1b68dcc2e4aff3fd0708e9cf7687e39f..60d00fb56059356b2505ff24bf1da567020b2b5f 100644
--- a/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp
+++ b/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -114,68 +114,68 @@ void PairLJCharmmCoulCharmm::compute(int eflag, int vflag)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cut_bothsq) {
- r2inv = 1.0/rsq;
-
- if (rsq < cut_coulsq) {
- forcecoul = qqrd2e * qtmp*q[j]*sqrt(r2inv);
- if (rsq > cut_coul_innersq) {
- switch1 = (cut_coulsq-rsq) * (cut_coulsq-rsq) *
- (cut_coulsq + 2.0*rsq - 3.0*cut_coul_innersq) / denom_coul;
- switch2 = 12.0*rsq * (cut_coulsq-rsq) *
- (rsq-cut_coul_innersq) / denom_coul;
- forcecoul *= switch1 + switch2;
- }
- } else forcecoul = 0.0;
-
- if (rsq < cut_ljsq) {
- r6inv = r2inv*r2inv*r2inv;
- jtype = type[j];
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- if (rsq > cut_lj_innersq) {
- switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
- (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
- switch2 = 12.0*rsq * (cut_ljsq-rsq) *
- (rsq-cut_lj_innersq) / denom_lj;
- philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
- forcelj = forcelj*switch1 + philj*switch2;
- }
- } else forcelj = 0.0;
-
- fpair = (factor_coul*forcecoul + factor_lj*forcelj) * r2inv;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (eflag) {
- if (rsq < cut_coulsq) {
- ecoul = qqrd2e * qtmp*q[j]*sqrt(r2inv);
- if (rsq > cut_coul_innersq) {
- switch1 = (cut_coulsq-rsq) * (cut_coulsq-rsq) *
- (cut_coulsq + 2.0*rsq - 3.0*cut_coul_innersq) /
- denom_coul;
- ecoul *= switch1;
- }
- ecoul *= factor_coul;
- } else ecoul = 0.0;
- if (rsq < cut_ljsq) {
- evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
- if (rsq > cut_lj_innersq) {
- switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
- (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
- evdwl *= switch1;
- }
- evdwl *= factor_lj;
- } else evdwl = 0.0;
- }
-
- if (evflag) ev_tally(i,j,nlocal,newton_pair,
- evdwl,ecoul,fpair,delx,dely,delz);
+ r2inv = 1.0/rsq;
+
+ if (rsq < cut_coulsq) {
+ forcecoul = qqrd2e * qtmp*q[j]*sqrt(r2inv);
+ if (rsq > cut_coul_innersq) {
+ switch1 = (cut_coulsq-rsq) * (cut_coulsq-rsq) *
+ (cut_coulsq + 2.0*rsq - 3.0*cut_coul_innersq) / denom_coul;
+ switch2 = 12.0*rsq * (cut_coulsq-rsq) *
+ (rsq-cut_coul_innersq) / denom_coul;
+ forcecoul *= switch1 + switch2;
+ }
+ } else forcecoul = 0.0;
+
+ if (rsq < cut_ljsq) {
+ r6inv = r2inv*r2inv*r2inv;
+ jtype = type[j];
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ if (rsq > cut_lj_innersq) {
+ switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
+ (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
+ switch2 = 12.0*rsq * (cut_ljsq-rsq) *
+ (rsq-cut_lj_innersq) / denom_lj;
+ philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
+ forcelj = forcelj*switch1 + philj*switch2;
+ }
+ } else forcelj = 0.0;
+
+ fpair = (factor_coul*forcecoul + factor_lj*forcelj) * r2inv;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (eflag) {
+ if (rsq < cut_coulsq) {
+ ecoul = qqrd2e * qtmp*q[j]*sqrt(r2inv);
+ if (rsq > cut_coul_innersq) {
+ switch1 = (cut_coulsq-rsq) * (cut_coulsq-rsq) *
+ (cut_coulsq + 2.0*rsq - 3.0*cut_coul_innersq) /
+ denom_coul;
+ ecoul *= switch1;
+ }
+ ecoul *= factor_coul;
+ } else ecoul = 0.0;
+ if (rsq < cut_ljsq) {
+ evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
+ if (rsq > cut_lj_innersq) {
+ switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
+ (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
+ evdwl *= switch1;
+ }
+ evdwl *= factor_lj;
+ } else evdwl = 0.0;
+ }
+
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
@@ -221,7 +221,7 @@ void PairLJCharmmCoulCharmm::allocate()
void PairLJCharmmCoulCharmm::settings(int narg, char **arg)
{
- if (narg != 2 && narg != 4)
+ if (narg != 2 && narg != 4)
error->all(FLERR,"Illegal pair_style command");
cut_lj_inner = force->numeric(arg[0]);
@@ -241,7 +241,7 @@ void PairLJCharmmCoulCharmm::settings(int narg, char **arg)
void PairLJCharmmCoulCharmm::coeff(int narg, char **arg)
{
- if (narg != 4 && narg != 6)
+ if (narg != 4 && narg != 6)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
@@ -281,7 +281,7 @@ void PairLJCharmmCoulCharmm::init_style()
{
if (!atom->q_flag)
error->all(FLERR,
- "Pair style lj/charmm/coul/charmm requires atom attribute q");
+ "Pair style lj/charmm/coul/charmm requires atom attribute q");
neighbor->request(this);
@@ -296,9 +296,9 @@ void PairLJCharmmCoulCharmm::init_style()
cut_coulsq = cut_coul * cut_coul;
cut_bothsq = MAX(cut_ljsq,cut_coulsq);
- denom_lj = (cut_ljsq-cut_lj_innersq) * (cut_ljsq-cut_lj_innersq) *
+ denom_lj = (cut_ljsq-cut_lj_innersq) * (cut_ljsq-cut_lj_innersq) *
(cut_ljsq-cut_lj_innersq);
- denom_coul = (cut_coulsq-cut_coul_innersq) * (cut_coulsq-cut_coul_innersq) *
+ denom_coul = (cut_coulsq-cut_coul_innersq) * (cut_coulsq-cut_coul_innersq) *
(cut_coulsq-cut_coul_innersq);
}
@@ -310,10 +310,10 @@ double PairLJCharmmCoulCharmm::init_one(int i, int j)
{
if (setflag[i][j] == 0) {
epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j],
- sigma[i][i],sigma[j][j]);
+ sigma[i][i],sigma[j][j]);
sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]);
eps14[i][j] = mix_energy(eps14[i][i],eps14[j][j],
- sigma14[i][i],sigma14[j][j]);
+ sigma14[i][i],sigma14[j][j]);
sigma14[i][j] = mix_distance(sigma14[i][i],sigma14[j][j]);
}
@@ -327,7 +327,7 @@ double PairLJCharmmCoulCharmm::init_one(int i, int j)
lj14_2[i][j] = 24.0 * eps14[i][j] * pow(sigma14[i][j],6.0);
lj14_3[i][j] = 4.0 * eps14[i][j] * pow(sigma14[i][j],12.0);
lj14_4[i][j] = 4.0 * eps14[i][j] * pow(sigma14[i][j],6.0);
-
+
lj1[j][i] = lj1[i][j];
lj2[j][i] = lj2[i][j];
lj3[j][i] = lj3[i][j];
@@ -353,10 +353,10 @@ void PairLJCharmmCoulCharmm::write_restart(FILE *fp)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
- fwrite(&epsilon[i][j],sizeof(double),1,fp);
- fwrite(&sigma[i][j],sizeof(double),1,fp);
- fwrite(&eps14[i][j],sizeof(double),1,fp);
- fwrite(&sigma14[i][j],sizeof(double),1,fp);
+ fwrite(&epsilon[i][j],sizeof(double),1,fp);
+ fwrite(&sigma[i][j],sizeof(double),1,fp);
+ fwrite(&eps14[i][j],sizeof(double),1,fp);
+ fwrite(&sigma14[i][j],sizeof(double),1,fp);
}
}
}
@@ -378,16 +378,16 @@ void PairLJCharmmCoulCharmm::read_restart(FILE *fp)
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
- if (me == 0) {
- fread(&epsilon[i][j],sizeof(double),1,fp);
- fread(&sigma[i][j],sizeof(double),1,fp);
- fread(&eps14[i][j],sizeof(double),1,fp);
- fread(&sigma14[i][j],sizeof(double),1,fp);
- }
- MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&eps14[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&sigma14[i][j],1,MPI_DOUBLE,0,world);
+ if (me == 0) {
+ fread(&epsilon[i][j],sizeof(double),1,fp);
+ fread(&sigma[i][j],sizeof(double),1,fp);
+ fread(&eps14[i][j],sizeof(double),1,fp);
+ fread(&sigma14[i][j],sizeof(double),1,fp);
+ }
+ MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&eps14[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&sigma14[i][j],1,MPI_DOUBLE,0,world);
}
}
}
@@ -431,9 +431,9 @@ void PairLJCharmmCoulCharmm::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairLJCharmmCoulCharmm::single(int i, int j, int itype, int jtype,
- double rsq,
- double factor_coul, double factor_lj,
- double &fforce)
+ double rsq,
+ double factor_coul, double factor_lj,
+ double &fforce)
{
double r2inv,r6inv,forcecoul,forcelj,phicoul,philj;
double switch1,switch2;
@@ -443,9 +443,9 @@ double PairLJCharmmCoulCharmm::single(int i, int j, int itype, int jtype,
forcecoul = force->qqrd2e * atom->q[i]*atom->q[j]*sqrt(r2inv);
if (rsq > cut_coul_innersq) {
switch1 = (cut_coulsq-rsq) * (cut_coulsq-rsq) *
- (cut_coulsq + 2.0*rsq - 3.0*cut_coul_innersq) / denom_coul;
- switch2 = 12.0*rsq * (cut_coulsq-rsq) *
- (rsq-cut_coul_innersq) / denom_coul;
+ (cut_coulsq + 2.0*rsq - 3.0*cut_coul_innersq) / denom_coul;
+ switch2 = 12.0*rsq * (cut_coulsq-rsq) *
+ (rsq-cut_coul_innersq) / denom_coul;
forcecoul *= switch1 + switch2;
}
} else forcecoul = 0.0;
@@ -455,9 +455,9 @@ double PairLJCharmmCoulCharmm::single(int i, int j, int itype, int jtype,
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
- (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
- switch2 = 12.0*rsq * (cut_ljsq-rsq) *
- (rsq-cut_lj_innersq) / denom_lj;
+ (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
+ switch2 = 12.0*rsq * (cut_ljsq-rsq) *
+ (rsq-cut_lj_innersq) / denom_lj;
philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
forcelj = forcelj*switch1 + philj*switch2;
}
@@ -470,8 +470,8 @@ double PairLJCharmmCoulCharmm::single(int i, int j, int itype, int jtype,
phicoul = force->qqrd2e * atom->q[i]*atom->q[j]*sqrt(r2inv);
if (rsq > cut_coul_innersq) {
switch1 = (cut_coulsq-rsq) * (cut_coulsq-rsq) *
- (cut_coulsq + 2.0*rsq - 3.0*cut_coul_innersq) /
- denom_coul;
+ (cut_coulsq + 2.0*rsq - 3.0*cut_coul_innersq) /
+ denom_coul;
phicoul *= switch1;
}
eng += factor_coul*phicoul;
@@ -480,7 +480,7 @@ double PairLJCharmmCoulCharmm::single(int i, int j, int itype, int jtype,
philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
- (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
+ (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
philj *= switch1;
}
eng += factor_lj*philj;
diff --git a/src/MOLECULE/pair_lj_charmm_coul_charmm.h b/src/MOLECULE/pair_lj_charmm_coul_charmm.h
index 03e453d9ee1813a4a1d634d1143c2f79eb014794..9723d84bc91f70e6ff6d7f954f881ea0d3691d31 100644
--- a/src/MOLECULE/pair_lj_charmm_coul_charmm.h
+++ b/src/MOLECULE/pair_lj_charmm_coul_charmm.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.cpp b/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.cpp
index 785e62fd039c9a5d23e2e449a59111d0b8fad033..2cb524a241fb9c9aa9358c29e745787f83163faa 100644
--- a/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.cpp
+++ b/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -56,7 +56,7 @@ void PairLJCharmmCoulCharmmImplicit::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@@ -81,68 +81,68 @@ void PairLJCharmmCoulCharmmImplicit::compute(int eflag, int vflag)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cut_bothsq) {
- r2inv = 1.0/rsq;
-
- if (rsq < cut_coulsq) {
- forcecoul = 2.0 * qqrd2e * qtmp*q[j]*r2inv;
- if (rsq > cut_coul_innersq) {
- switch1 = (cut_coulsq-rsq) * (cut_coulsq-rsq) *
- (cut_coulsq + 2.0*rsq - 3.0*cut_coul_innersq) / denom_coul;
- switch2 = 12.0*rsq * (cut_coulsq-rsq) *
- (rsq-cut_coul_innersq) / denom_coul;
- forcecoul *= switch1 + switch2;
- }
- } else forcecoul = 0.0;
-
- if (rsq < cut_ljsq) {
- r6inv = r2inv*r2inv*r2inv;
- jtype = type[j];
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- if (rsq > cut_lj_innersq) {
- switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
- (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
- switch2 = 12.0*rsq * (cut_ljsq-rsq) *
- (rsq-cut_lj_innersq) / denom_lj;
- philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
- forcelj = forcelj*switch1 + philj*switch2;
- }
- } else forcelj = 0.0;
-
- fpair = (factor_coul*forcecoul + factor_lj*forcelj) * r2inv;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (eflag) {
- if (rsq < cut_coulsq) {
- ecoul = qqrd2e * qtmp*q[j]*r2inv;
- if (rsq > cut_coul_innersq) {
- switch1 = (cut_coulsq-rsq) * (cut_coulsq-rsq) *
- (cut_coulsq + 2.0*rsq - 3.0*cut_coul_innersq) /
- denom_coul;
- ecoul *= switch1;
- }
- ecoul *= factor_coul;
- } else ecoul = 0.0;
- if (rsq < cut_ljsq) {
- evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
- if (rsq > cut_lj_innersq) {
- switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
- (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
- evdwl *= switch1;
- }
- evdwl *= factor_lj;
- } else evdwl = 0.0;
- }
-
- if (evflag) ev_tally(i,j,nlocal,newton_pair,
- evdwl,ecoul,fpair,delx,dely,delz);
+ r2inv = 1.0/rsq;
+
+ if (rsq < cut_coulsq) {
+ forcecoul = 2.0 * qqrd2e * qtmp*q[j]*r2inv;
+ if (rsq > cut_coul_innersq) {
+ switch1 = (cut_coulsq-rsq) * (cut_coulsq-rsq) *
+ (cut_coulsq + 2.0*rsq - 3.0*cut_coul_innersq) / denom_coul;
+ switch2 = 12.0*rsq * (cut_coulsq-rsq) *
+ (rsq-cut_coul_innersq) / denom_coul;
+ forcecoul *= switch1 + switch2;
+ }
+ } else forcecoul = 0.0;
+
+ if (rsq < cut_ljsq) {
+ r6inv = r2inv*r2inv*r2inv;
+ jtype = type[j];
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ if (rsq > cut_lj_innersq) {
+ switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
+ (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
+ switch2 = 12.0*rsq * (cut_ljsq-rsq) *
+ (rsq-cut_lj_innersq) / denom_lj;
+ philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
+ forcelj = forcelj*switch1 + philj*switch2;
+ }
+ } else forcelj = 0.0;
+
+ fpair = (factor_coul*forcecoul + factor_lj*forcelj) * r2inv;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (eflag) {
+ if (rsq < cut_coulsq) {
+ ecoul = qqrd2e * qtmp*q[j]*r2inv;
+ if (rsq > cut_coul_innersq) {
+ switch1 = (cut_coulsq-rsq) * (cut_coulsq-rsq) *
+ (cut_coulsq + 2.0*rsq - 3.0*cut_coul_innersq) /
+ denom_coul;
+ ecoul *= switch1;
+ }
+ ecoul *= factor_coul;
+ } else ecoul = 0.0;
+ if (rsq < cut_ljsq) {
+ evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
+ if (rsq > cut_lj_innersq) {
+ switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
+ (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
+ evdwl *= switch1;
+ }
+ evdwl *= factor_lj;
+ } else evdwl = 0.0;
+ }
+
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
@@ -153,11 +153,11 @@ void PairLJCharmmCoulCharmmImplicit::compute(int eflag, int vflag)
/* ---------------------------------------------------------------------- */
double PairLJCharmmCoulCharmmImplicit::single(int i, int j,
- int itype, int jtype,
- double rsq,
- double factor_coul,
- double factor_lj,
- double &fforce)
+ int itype, int jtype,
+ double rsq,
+ double factor_coul,
+ double factor_lj,
+ double &fforce)
{
double r2inv,r6inv,switch1,switch2,forcecoul,forcelj,phicoul,philj;
@@ -166,9 +166,9 @@ double PairLJCharmmCoulCharmmImplicit::single(int i, int j,
forcecoul = 2.0 * force->qqrd2e * atom->q[i]*atom->q[j]*r2inv;
if (rsq > cut_coul_innersq) {
switch1 = (cut_coulsq-rsq) * (cut_coulsq-rsq) *
- (cut_coulsq + 2.0*rsq - 3.0*cut_coul_innersq) / denom_coul;
- switch2 = 12.0*rsq * (cut_coulsq-rsq) *
- (rsq-cut_coul_innersq) / denom_coul;
+ (cut_coulsq + 2.0*rsq - 3.0*cut_coul_innersq) / denom_coul;
+ switch2 = 12.0*rsq * (cut_coulsq-rsq) *
+ (rsq-cut_coul_innersq) / denom_coul;
forcecoul *= switch1 + switch2;
}
} else forcecoul = 0.0;
@@ -177,9 +177,9 @@ double PairLJCharmmCoulCharmmImplicit::single(int i, int j,
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
- (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
- switch2 = 12.0*rsq * (cut_ljsq-rsq) *
- (rsq-cut_lj_innersq) / denom_lj;
+ (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
+ switch2 = 12.0*rsq * (cut_ljsq-rsq) *
+ (rsq-cut_lj_innersq) / denom_lj;
philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
forcelj = forcelj*switch1 + philj*switch2;
}
@@ -191,8 +191,8 @@ double PairLJCharmmCoulCharmmImplicit::single(int i, int j,
phicoul = force->qqrd2e * atom->q[i]*atom->q[j]*r2inv;
if (rsq > cut_coul_innersq) {
switch1 = (cut_coulsq-rsq) * (cut_coulsq-rsq) *
- (cut_coulsq + 2.0*rsq - 3.0*cut_coul_innersq) /
- denom_coul;
+ (cut_coulsq + 2.0*rsq - 3.0*cut_coul_innersq) /
+ denom_coul;
phicoul *= switch1;
}
eng += factor_coul*phicoul;
@@ -201,7 +201,7 @@ double PairLJCharmmCoulCharmmImplicit::single(int i, int j,
philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
- (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
+ (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
philj *= switch1;
}
eng += factor_lj*philj;
diff --git a/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.h b/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.h
index c5882a74956bdd83505f0bb988e26e806bdd63c3..747f2caa6d879497f6ea24e34906f4dc92848139 100644
--- a/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.h
+++ b/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/OPT/pair_eam_alloy_opt.cpp b/src/OPT/pair_eam_alloy_opt.cpp
index 0deaf8b43079bcc9782a247344cfbb3cf44b0c5e..1e13fc1fa3752cbf25937d970249e680179d250f 100644
--- a/src/OPT/pair_eam_alloy_opt.cpp
+++ b/src/OPT/pair_eam_alloy_opt.cpp
@@ -5,14 +5,14 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
- Contributing authors:
+ Contributing authors:
James Fischer, High Performance Technologies, Inc.
Charles Cornwell, High Performance Technologies, Inc.
David Richie, Stone Ridge Technology
diff --git a/src/OPT/pair_eam_alloy_opt.h b/src/OPT/pair_eam_alloy_opt.h
index 5435f00fa4a89579e01335bca2053d471a6cbae9..04afac8c653cf281f35f969181ada66bdc3d2a46 100644
--- a/src/OPT/pair_eam_alloy_opt.h
+++ b/src/OPT/pair_eam_alloy_opt.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/OPT/pair_eam_fs_opt.cpp b/src/OPT/pair_eam_fs_opt.cpp
index a097eec2b6411706294cf81c9c662c7c248b51b8..7b30532f4f3d12560e076661add95334f1c0417a 100644
--- a/src/OPT/pair_eam_fs_opt.cpp
+++ b/src/OPT/pair_eam_fs_opt.cpp
@@ -5,14 +5,14 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
- Contributing authors:
+ Contributing authors:
James Fischer, High Performance Technologies, Inc.
Charles Cornwell, High Performance Technologies, Inc.
David Richie, Stone Ridge Technology
diff --git a/src/OPT/pair_eam_fs_opt.h b/src/OPT/pair_eam_fs_opt.h
index b5bfdad4bf4f9fd71cc8f47a470622b965c32933..64da344ec87dd34814b33ffad20834582dcfe5b5 100644
--- a/src/OPT/pair_eam_fs_opt.h
+++ b/src/OPT/pair_eam_fs_opt.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/OPT/pair_eam_opt.cpp b/src/OPT/pair_eam_opt.cpp
index 616234b69bfee8ed70ac3c01f165565f1074c323..c0cb4165ec99d7b86d382a441bf754cbd9900be7 100644
--- a/src/OPT/pair_eam_opt.cpp
+++ b/src/OPT/pair_eam_opt.cpp
@@ -5,14 +5,14 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
- Contributing authors:
+ Contributing authors:
James Fischer, High Performance Technologies, Inc.
Charles Cornwell, High Performance Technologies, Inc.
David Richie, Stone Ridge Technology
@@ -61,30 +61,30 @@ template < int EVFLAG, int EFLAG, int NEWTON_PAIR >
void PairEAMOpt::eval()
{
typedef struct { double x,y,z; } vec3_t;
-
+
typedef struct {
double rhor0i,rhor1i,rhor2i,rhor3i;
double rhor0j,rhor1j,rhor2j,rhor3j;
} fast_alpha_t;
-
+
typedef struct {
double frho0,frho1,frho2,frho3,frho4,frho5,frho6;
double _pad[1];
} fast_beta_t;
-
+
typedef struct {
double rhor4i,rhor5i,rhor6i;
double rhor4j,rhor5j,rhor6j;
double z2r0,z2r1,z2r2,z2r3,z2r4,z2r5,z2r6;
double _pad[3];
} fast_gamma_t;
-
+
int i,j,ii,jj,inum,jnum,itype,jtype;
double evdwl = 0.0;
double* __restrict__ coeff;
// grow energy array if necessary
-
+
if (atom->nmax > nmax) {
memory->sfree(rho);
memory->sfree(fp);
@@ -92,96 +92,96 @@ void PairEAMOpt::eval()
rho = (double *) memory->smalloc(nmax*sizeof(double),"pair:rho");
fp = (double *) memory->smalloc(nmax*sizeof(double),"pair:fp");
}
-
+
double** __restrict__ x = atom->x;
double** __restrict__ f = atom->f;
int* __restrict__ type = atom->type;
int nlocal = atom->nlocal;
-
+
vec3_t* __restrict__ xx = (vec3_t*)x[0];
vec3_t* __restrict__ ff = (vec3_t*)f[0];
-
+
double tmp_cutforcesq = cutforcesq;
double tmp_rdr = rdr;
int nr2 = nr-2;
int nr1 = nr-1;
-
+
inum = list->inum;
int* __restrict__ ilist = list->ilist;
int** __restrict__ firstneigh = list->firstneigh;
int* __restrict__ numneigh = list->numneigh;
-
+
int ntypes = atom->ntypes;
int ntypes2 = ntypes*ntypes;
-
- fast_alpha_t* __restrict__ fast_alpha =
+
+ fast_alpha_t* __restrict__ fast_alpha =
(fast_alpha_t*) malloc(ntypes2*(nr+1)*sizeof(fast_alpha_t));
for (i = 0; i < ntypes; i++) for (j = 0; j < ntypes; j++) {
fast_alpha_t* __restrict__ tab = &fast_alpha[i*ntypes*nr+j*nr];
if (type2rhor[i+1][j+1] >= 0) {
for(int m = 1; m <= nr; m++) {
- tab[m].rhor0i = rhor_spline[type2rhor[i+1][j+1]][m][6];
- tab[m].rhor1i = rhor_spline[type2rhor[i+1][j+1]][m][5];
- tab[m].rhor2i = rhor_spline[type2rhor[i+1][j+1]][m][4];
- tab[m].rhor3i = rhor_spline[type2rhor[i+1][j+1]][m][3];
+ tab[m].rhor0i = rhor_spline[type2rhor[i+1][j+1]][m][6];
+ tab[m].rhor1i = rhor_spline[type2rhor[i+1][j+1]][m][5];
+ tab[m].rhor2i = rhor_spline[type2rhor[i+1][j+1]][m][4];
+ tab[m].rhor3i = rhor_spline[type2rhor[i+1][j+1]][m][3];
}
}
if (type2rhor[j+1][i+1] >= 0) {
for(int m = 1; m <= nr; m++) {
- tab[m].rhor0j = rhor_spline[type2rhor[j+1][i+1]][m][6];
- tab[m].rhor1j = rhor_spline[type2rhor[j+1][i+1]][m][5];
- tab[m].rhor2j = rhor_spline[type2rhor[j+1][i+1]][m][4];
- tab[m].rhor3j = rhor_spline[type2rhor[j+1][i+1]][m][3];
+ tab[m].rhor0j = rhor_spline[type2rhor[j+1][i+1]][m][6];
+ tab[m].rhor1j = rhor_spline[type2rhor[j+1][i+1]][m][5];
+ tab[m].rhor2j = rhor_spline[type2rhor[j+1][i+1]][m][4];
+ tab[m].rhor3j = rhor_spline[type2rhor[j+1][i+1]][m][3];
}
}
}
fast_alpha_t* __restrict__ tabeight = fast_alpha;
-
- fast_gamma_t* __restrict__ fast_gamma =
+
+ fast_gamma_t* __restrict__ fast_gamma =
(fast_gamma_t*) malloc(ntypes2*(nr+1)*sizeof(fast_gamma_t));
for (i = 0; i < ntypes; i++) for (j = 0; j < ntypes; j++) {
fast_gamma_t* __restrict__ tab = &fast_gamma[i*ntypes*nr+j*nr];
if (type2rhor[i+1][j+1] >= 0) {
for(int m = 1; m <= nr; m++) {
- tab[m].rhor4i = rhor_spline[type2rhor[i+1][j+1]][m][2];
- tab[m].rhor5i = rhor_spline[type2rhor[i+1][j+1]][m][1];
- tab[m].rhor6i = rhor_spline[type2rhor[i+1][j+1]][m][0];
+ tab[m].rhor4i = rhor_spline[type2rhor[i+1][j+1]][m][2];
+ tab[m].rhor5i = rhor_spline[type2rhor[i+1][j+1]][m][1];
+ tab[m].rhor6i = rhor_spline[type2rhor[i+1][j+1]][m][0];
}
}
if (type2rhor[j+1][i+1] >= 0) {
for(int m = 1; m <= nr; m++) {
- tab[m].rhor4j = rhor_spline[type2rhor[j+1][i+1]][m][2];
- tab[m].rhor5j = rhor_spline[type2rhor[j+1][i+1]][m][1];
- tab[m].rhor6j = rhor_spline[type2rhor[j+1][i+1]][m][0];
- tab[m].z2r6 = z2r_spline[type2z2r[i+1][j+1]][m][0];
+ tab[m].rhor4j = rhor_spline[type2rhor[j+1][i+1]][m][2];
+ tab[m].rhor5j = rhor_spline[type2rhor[j+1][i+1]][m][1];
+ tab[m].rhor6j = rhor_spline[type2rhor[j+1][i+1]][m][0];
+ tab[m].z2r6 = z2r_spline[type2z2r[i+1][j+1]][m][0];
}
}
if (type2z2r[i+1][j+1] >= 0) {
for(int m = 1; m <= nr; m++) {
- tab[m].z2r0 = z2r_spline[type2z2r[i+1][j+1]][m][6];
- tab[m].z2r1 = z2r_spline[type2z2r[i+1][j+1]][m][5];
- tab[m].z2r2 = z2r_spline[type2z2r[i+1][j+1]][m][4];
- tab[m].z2r3 = z2r_spline[type2z2r[i+1][j+1]][m][3];
- tab[m].z2r4 = z2r_spline[type2z2r[i+1][j+1]][m][2];
- tab[m].z2r5 = z2r_spline[type2z2r[i+1][j+1]][m][1];
- tab[m].z2r6 = z2r_spline[type2z2r[i+1][j+1]][m][0];
+ tab[m].z2r0 = z2r_spline[type2z2r[i+1][j+1]][m][6];
+ tab[m].z2r1 = z2r_spline[type2z2r[i+1][j+1]][m][5];
+ tab[m].z2r2 = z2r_spline[type2z2r[i+1][j+1]][m][4];
+ tab[m].z2r3 = z2r_spline[type2z2r[i+1][j+1]][m][3];
+ tab[m].z2r4 = z2r_spline[type2z2r[i+1][j+1]][m][2];
+ tab[m].z2r5 = z2r_spline[type2z2r[i+1][j+1]][m][1];
+ tab[m].z2r6 = z2r_spline[type2z2r[i+1][j+1]][m][0];
}
}
}
fast_gamma_t* __restrict__ tabss = fast_gamma;
-
+
// zero out density
-
+
if (NEWTON_PAIR) {
int m = nlocal + atom->nghost;
for (i = 0; i < m; i++) rho[i] = 0.0;
} else for (i = 0; i < nlocal; i++) rho[i] = 0.0;
-
+
// rho = density at each atom
// loop over neighbors of my atoms
-
+
// loop over neighbors of my atoms
-
+
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
double xtmp = xx[i].x;
@@ -190,7 +190,7 @@ void PairEAMOpt::eval()
itype = type[i] - 1;
int* __restrict__ jlist = firstneigh[i];
jnum = numneigh[i];
-
+
double tmprho = rho[i];
fast_alpha_t* __restrict__ tabeighti = &tabeight[itype*ntypes*nr];
@@ -202,38 +202,38 @@ void PairEAMOpt::eval()
double dely = ytmp - xx[j].y;
double delz = ztmp - xx[j].z;
double rsq = delx*delx + dely*dely + delz*delz;
-
+
if (rsq < tmp_cutforcesq) {
- jtype = type[j] - 1;
-
- double p = sqrt(rsq)*tmp_rdr;
- if ( (int)p <= nr2 ) {
- int m = (int)p + 1;
- p -= (double)((int)p);
- fast_alpha_t& a = tabeighti[jtype*nr+m];
- tmprho += ((a.rhor3j*p+a.rhor2j)*p+a.rhor1j)*p+a.rhor0j;
- if (NEWTON_PAIR || j < nlocal) {
- rho[j] += ((a.rhor3i*p+a.rhor2i)*p+a.rhor1i)*p+a.rhor0i;
- }
- } else {
- fast_alpha_t& a = tabeighti[jtype*nr+nr1];
- tmprho += a.rhor3j+a.rhor2j+a.rhor1j+a.rhor0j;
- if (NEWTON_PAIR || j < nlocal) {
- rho[j] += a.rhor3i+a.rhor2i+a.rhor1i+a.rhor0i;
- }
- }
+ jtype = type[j] - 1;
+
+ double p = sqrt(rsq)*tmp_rdr;
+ if ( (int)p <= nr2 ) {
+ int m = (int)p + 1;
+ p -= (double)((int)p);
+ fast_alpha_t& a = tabeighti[jtype*nr+m];
+ tmprho += ((a.rhor3j*p+a.rhor2j)*p+a.rhor1j)*p+a.rhor0j;
+ if (NEWTON_PAIR || j < nlocal) {
+ rho[j] += ((a.rhor3i*p+a.rhor2i)*p+a.rhor1i)*p+a.rhor0i;
+ }
+ } else {
+ fast_alpha_t& a = tabeighti[jtype*nr+nr1];
+ tmprho += a.rhor3j+a.rhor2j+a.rhor1j+a.rhor0j;
+ if (NEWTON_PAIR || j < nlocal) {
+ rho[j] += a.rhor3i+a.rhor2i+a.rhor1i+a.rhor0i;
+ }
+ }
}
}
rho[i] = tmprho;
}
-
+
// communicate and sum densities
-
+
if (NEWTON_PAIR) comm->reverse_comm_pair(this);
-
+
// fp = derivative of embedding energy at each atom
// phi = embedding energy at each atom
-
+
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
double p = rho[i]*rdrho;
@@ -248,11 +248,11 @@ void PairEAMOpt::eval()
if (eflag_atom) eatom[i] += phi;
}
}
-
+
// communicate derivative of embedding function
-
+
comm->forward_comm_pair(this);
-
+
// compute forces on each atom
// loop over neighbors of my atoms
@@ -264,11 +264,11 @@ void PairEAMOpt::eval()
int itype1 = type[i] - 1;
int* __restrict__ jlist = firstneigh[i];
jnum = numneigh[i];
-
+
double tmpfx = 0.0;
double tmpfy = 0.0;
double tmpfz = 0.0;
-
+
fast_gamma_t* __restrict__ tabssi = &tabss[itype1*ntypes*nr];
for (jj = 0; jj < jnum; jj++) {
@@ -279,60 +279,60 @@ void PairEAMOpt::eval()
double dely = ytmp - xx[j].y;
double delz = ztmp - xx[j].z;
double rsq = delx*delx + dely*dely + delz*delz;
-
+
if (rsq < tmp_cutforcesq) {
- jtype = type[j] - 1;
- double r = sqrt(rsq);
- double rhoip,rhojp,z2,z2p;
- double p = r*tmp_rdr;
- if ( (int)p <= nr2 ) {
- int m = (int) p + 1;
- p -= (double)((int) p);
-
- fast_gamma_t& a = tabssi[jtype*nr+m];
- rhoip = (a.rhor6i*p + a.rhor5i)*p + a.rhor4i;
- rhojp = (a.rhor6j*p + a.rhor5j)*p + a.rhor4j;
- z2 = ((a.z2r3*p + a.z2r2)*p + a.z2r1)*p + a.z2r0;
- z2p = (a.z2r6*p + a.z2r5)*p + a.z2r4;
-
- } else {
-
- fast_gamma_t& a = tabssi[jtype*nr+nr1];
- rhoip = a.rhor6i + a.rhor5i + a.rhor4i;
- rhojp = a.rhor6j + a.rhor5j + a.rhor4j;
- z2 = a.z2r3 + a.z2r2 + a.z2r1 + a.z2r0;
- z2p = a.z2r6 + a.z2r5 + a.z2r4;
- }
-
- // rhoip = derivative of (density at atom j due to atom i)
- // rhojp = derivative of (density at atom i due to atom j)
- // phi = pair potential energy
- // phip = phi'
- // z2 = phi * r
- // z2p = (phi * r)' = (phi' r) + phi
- // psip needs both fp[i] and fp[j] terms since r_ij appears in two
- // terms of embed eng: Fi(sum rho_ij) and Fj(sum rho_ji)
- // hence embed' = Fi(sum rho_ij) rhojp + Fj(sum rho_ji) rhoip
-
- double recip = 1.0/r;
- double phi = z2*recip;
- double phip = z2p*recip - phi*recip;
- double psip = fp[i]*rhojp + fp[j]*rhoip + phip;
- double fpair = -psip*recip;
-
- tmpfx += delx*fpair;
- tmpfy += dely*fpair;
- tmpfz += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- ff[j].x -= delx*fpair;
- ff[j].y -= dely*fpair;
- ff[j].z -= delz*fpair;
- }
-
- if (EFLAG) evdwl = phi;
-
- if (EVFLAG) ev_tally(i,j,nlocal,NEWTON_PAIR,
- evdwl,0.0,fpair,delx,dely,delz);
+ jtype = type[j] - 1;
+ double r = sqrt(rsq);
+ double rhoip,rhojp,z2,z2p;
+ double p = r*tmp_rdr;
+ if ( (int)p <= nr2 ) {
+ int m = (int) p + 1;
+ p -= (double)((int) p);
+
+ fast_gamma_t& a = tabssi[jtype*nr+m];
+ rhoip = (a.rhor6i*p + a.rhor5i)*p + a.rhor4i;
+ rhojp = (a.rhor6j*p + a.rhor5j)*p + a.rhor4j;
+ z2 = ((a.z2r3*p + a.z2r2)*p + a.z2r1)*p + a.z2r0;
+ z2p = (a.z2r6*p + a.z2r5)*p + a.z2r4;
+
+ } else {
+
+ fast_gamma_t& a = tabssi[jtype*nr+nr1];
+ rhoip = a.rhor6i + a.rhor5i + a.rhor4i;
+ rhojp = a.rhor6j + a.rhor5j + a.rhor4j;
+ z2 = a.z2r3 + a.z2r2 + a.z2r1 + a.z2r0;
+ z2p = a.z2r6 + a.z2r5 + a.z2r4;
+ }
+
+ // rhoip = derivative of (density at atom j due to atom i)
+ // rhojp = derivative of (density at atom i due to atom j)
+ // phi = pair potential energy
+ // phip = phi'
+ // z2 = phi * r
+ // z2p = (phi * r)' = (phi' r) + phi
+ // psip needs both fp[i] and fp[j] terms since r_ij appears in two
+ // terms of embed eng: Fi(sum rho_ij) and Fj(sum rho_ji)
+ // hence embed' = Fi(sum rho_ij) rhojp + Fj(sum rho_ji) rhoip
+
+ double recip = 1.0/r;
+ double phi = z2*recip;
+ double phip = z2p*recip - phi*recip;
+ double psip = fp[i]*rhojp + fp[j]*rhoip + phip;
+ double fpair = -psip*recip;
+
+ tmpfx += delx*fpair;
+ tmpfy += dely*fpair;
+ tmpfz += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ ff[j].x -= delx*fpair;
+ ff[j].y -= dely*fpair;
+ ff[j].z -= delz*fpair;
+ }
+
+ if (EFLAG) evdwl = phi;
+
+ if (EVFLAG) ev_tally(i,j,nlocal,NEWTON_PAIR,
+ evdwl,0.0,fpair,delx,dely,delz);
}
}
@@ -340,9 +340,9 @@ void PairEAMOpt::eval()
ff[i].y += tmpfy;
ff[i].z += tmpfz;
}
-
+
free(fast_alpha); fast_alpha = 0;
free(fast_gamma); fast_gamma = 0;
-
+
if (vflag_fdotr) virial_fdotr_compute();
}
diff --git a/src/OPT/pair_eam_opt.h b/src/OPT/pair_eam_opt.h
index afc7764da9d5a09322c4ccde33e019279eb90197..e174dae6475850b925afdec1b9541b2203e7cfe6 100644
--- a/src/OPT/pair_eam_opt.h
+++ b/src/OPT/pair_eam_opt.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/OPT/pair_lj_charmm_coul_long_opt.cpp b/src/OPT/pair_lj_charmm_coul_long_opt.cpp
index 49519d476110b20b9a4e512f7f80d2dc087525f5..5979141e3c8550161a659260ac0b4e866adeb4bc 100644
--- a/src/OPT/pair_lj_charmm_coul_long_opt.cpp
+++ b/src/OPT/pair_lj_charmm_coul_long_opt.cpp
@@ -5,14 +5,14 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
- Contributing authors:
+ Contributing authors:
James Fischer, High Performance Technologies, Inc.
David Richie, Stone Ridge Technology
Vincent Natoli, Stone Ridge Technology
@@ -67,23 +67,23 @@ template < int EVFLAG, int EFLAG, int NEWTON_PAIR >
void PairLJCharmmCoulLongOpt::eval()
{
typedef struct { double x,y,z; } vec3_t;
-
+
typedef struct {
double cutsq,lj1,lj2,lj3,lj4,offset;
double _pad[2];
} fast_alpha_t;
-
+
int i,j,ii,jj,inum,jnum,itype,jtype,itable,sbindex;
double fraction,table;
double r,r2inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj;
double grij,expm2,prefactor,t,erfc;
double philj,switch1,switch2;
-
- double rsq;
-
+
+ double rsq;
+
double evdwl = 0.0;
double ecoul = 0.0;
-
+
double** __restrict__ x = atom->x;
double** __restrict__ f = atom->f;
double* __restrict__ q = atom->q;
@@ -97,17 +97,17 @@ void PairLJCharmmCoulLongOpt::eval()
int* __restrict__ ilist = list->ilist;
int** __restrict__ firstneigh = list->firstneigh;
int* __restrict__ numneigh = list->numneigh;
-
+
vec3_t* __restrict__ xx = (vec3_t*)x[0];
vec3_t* __restrict__ ff = (vec3_t*)f[0];
-
+
int ntypes = atom->ntypes;
int ntypes2 = ntypes*ntypes;
-
+
double tmp_coef1 = 1.0/denom_lj;
double tmp_coef2 = cut_ljsq - 3.0*cut_lj_innersq;
-
- fast_alpha_t* __restrict__ fast_alpha =
+
+ fast_alpha_t* __restrict__ fast_alpha =
(fast_alpha_t*)malloc(ntypes2*sizeof(fast_alpha_t));
for (i = 0; i < ntypes; i++) for (j = 0; j < ntypes; j++) {
fast_alpha_t& a = fast_alpha[i*ntypes+j];
@@ -118,9 +118,9 @@ void PairLJCharmmCoulLongOpt::eval()
a.lj4 = lj4[i+1][j+1];
}
fast_alpha_t* __restrict__ tabsix = fast_alpha;
-
+
// loop over neighbors of my atoms
-
+
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
double qtmp = q[i];
@@ -130,11 +130,11 @@ void PairLJCharmmCoulLongOpt::eval()
itype = type[i] - 1;
int* __restrict__ jlist = firstneigh[i];
jnum = numneigh[i];
-
+
double tmpfx = 0.0;
double tmpfy = 0.0;
double tmpfz = 0.0;
-
+
fast_alpha_t* __restrict__ tabsixi = (fast_alpha_t*) &tabsix[itype*ntypes];
for (jj = 0; jj < jnum; jj++) {
@@ -142,189 +142,189 @@ void PairLJCharmmCoulLongOpt::eval()
sbindex = sbmask(j);
if (sbindex == 0) {
- double delx = xtmp - xx[j].x;
- double dely = ytmp - xx[j].y;
- double delz = ztmp - xx[j].z;
- rsq = delx*delx + dely*dely + delz*delz;
- double tmp_coef3 = qtmp*q[j];
-
- if (rsq < cut_bothsq) {
- r2inv = 1.0/rsq;
-
- forcecoul = 0.0;
- if (rsq < cut_coulsq) {
- if (!ncoultablebits || rsq <= tabinnersq) {
- r = sqrt(rsq);
- grij = g_ewald * r;
- expm2 = exp(-grij*grij);
- t = 1.0 / (1.0 + EWALD_P*grij);
- erfc = t *
- (EWALD_A1+t*(EWALD_A2+t*(EWALD_A3+t*(EWALD_A4+t*EWALD_A5)))) *
- expm2;
- prefactor = qqrd2e * tmp_coef3/r;
- forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
- } else {
- union_int_float_t rsq_lookup;
- rsq_lookup.f = rsq;
- itable = rsq_lookup.i & ncoulmask;
- itable >>= ncoulshiftbits;
- fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
- table = ftable[itable] + fraction*dftable[itable];
- forcecoul = tmp_coef3 * table;
- }
- }
-
- forcelj = 0.0;
- if (rsq < cut_ljsq) {
- r6inv = r2inv*r2inv*r2inv;
- jtype = type[j] - 1;
- fast_alpha_t& a = tabsixi[jtype];
- forcelj = r6inv * (a.lj1*r6inv - a.lj2);
- if (rsq > cut_lj_innersq) {
- switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
- (tmp_coef2 + 2.0*rsq) * tmp_coef1;
- switch2 = 12.0*rsq * (cut_ljsq-rsq) *
- (rsq-cut_lj_innersq) * tmp_coef1;
- philj = r6inv * (a.lj3*r6inv - a.lj4);
- forcelj = forcelj*switch1 + philj*switch2;
- }
- }
-
- double fpair = (forcecoul + forcelj) * r2inv;
-
- tmpfx += delx*fpair;
- tmpfy += dely*fpair;
- tmpfz += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- ff[j].x -= delx*fpair;
- ff[j].y -= dely*fpair;
- ff[j].z -= delz*fpair;
- }
-
- if (EFLAG) {
- if (rsq < cut_coulsq) {
- if (!ncoultablebits || rsq <= tabinnersq)
- ecoul = prefactor*erfc;
- else {
- table = etable[itable] + fraction*detable[itable];
- ecoul = tmp_coef3 * table;
- }
- } else ecoul = 0.0;
-
- if (rsq < cut_ljsq) {
- fast_alpha_t& a = tabsixi[jtype];
- evdwl = r6inv*(a.lj3*r6inv-a.lj4);
- if (rsq > cut_lj_innersq) {
- switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
- (tmp_coef2 + 2.0*rsq) * tmp_coef1;
- evdwl *= switch1;
- }
- } else evdwl = 0.0;
- }
-
- if (EVFLAG) ev_tally(i,j,nlocal,NEWTON_PAIR,
- evdwl,ecoul,fpair,delx,dely,delz);
- }
+ double delx = xtmp - xx[j].x;
+ double dely = ytmp - xx[j].y;
+ double delz = ztmp - xx[j].z;
+ rsq = delx*delx + dely*dely + delz*delz;
+ double tmp_coef3 = qtmp*q[j];
+
+ if (rsq < cut_bothsq) {
+ r2inv = 1.0/rsq;
+
+ forcecoul = 0.0;
+ if (rsq < cut_coulsq) {
+ if (!ncoultablebits || rsq <= tabinnersq) {
+ r = sqrt(rsq);
+ grij = g_ewald * r;
+ expm2 = exp(-grij*grij);
+ t = 1.0 / (1.0 + EWALD_P*grij);
+ erfc = t *
+ (EWALD_A1+t*(EWALD_A2+t*(EWALD_A3+t*(EWALD_A4+t*EWALD_A5)))) *
+ expm2;
+ prefactor = qqrd2e * tmp_coef3/r;
+ forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
+ } else {
+ union_int_float_t rsq_lookup;
+ rsq_lookup.f = rsq;
+ itable = rsq_lookup.i & ncoulmask;
+ itable >>= ncoulshiftbits;
+ fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
+ table = ftable[itable] + fraction*dftable[itable];
+ forcecoul = tmp_coef3 * table;
+ }
+ }
+
+ forcelj = 0.0;
+ if (rsq < cut_ljsq) {
+ r6inv = r2inv*r2inv*r2inv;
+ jtype = type[j] - 1;
+ fast_alpha_t& a = tabsixi[jtype];
+ forcelj = r6inv * (a.lj1*r6inv - a.lj2);
+ if (rsq > cut_lj_innersq) {
+ switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
+ (tmp_coef2 + 2.0*rsq) * tmp_coef1;
+ switch2 = 12.0*rsq * (cut_ljsq-rsq) *
+ (rsq-cut_lj_innersq) * tmp_coef1;
+ philj = r6inv * (a.lj3*r6inv - a.lj4);
+ forcelj = forcelj*switch1 + philj*switch2;
+ }
+ }
+
+ double fpair = (forcecoul + forcelj) * r2inv;
+
+ tmpfx += delx*fpair;
+ tmpfy += dely*fpair;
+ tmpfz += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ ff[j].x -= delx*fpair;
+ ff[j].y -= dely*fpair;
+ ff[j].z -= delz*fpair;
+ }
+
+ if (EFLAG) {
+ if (rsq < cut_coulsq) {
+ if (!ncoultablebits || rsq <= tabinnersq)
+ ecoul = prefactor*erfc;
+ else {
+ table = etable[itable] + fraction*detable[itable];
+ ecoul = tmp_coef3 * table;
+ }
+ } else ecoul = 0.0;
+
+ if (rsq < cut_ljsq) {
+ fast_alpha_t& a = tabsixi[jtype];
+ evdwl = r6inv*(a.lj3*r6inv-a.lj4);
+ if (rsq > cut_lj_innersq) {
+ switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
+ (tmp_coef2 + 2.0*rsq) * tmp_coef1;
+ evdwl *= switch1;
+ }
+ } else evdwl = 0.0;
+ }
+
+ if (EVFLAG) ev_tally(i,j,nlocal,NEWTON_PAIR,
+ evdwl,ecoul,fpair,delx,dely,delz);
+ }
} else {
- factor_lj = special_lj[sbindex];
- factor_coul = special_coul[sbindex];
- j &= NEIGHMASK;
-
- double delx = xtmp - xx[j].x;
- double dely = ytmp - xx[j].y;
- double delz = ztmp - xx[j].z;
- rsq = delx*delx + dely*dely + delz*delz;
- double tmp_coef3 = qtmp*q[j];
-
- if (rsq < cut_bothsq) {
- r2inv = 1.0/rsq;
-
- forcecoul = 0.0;
- if (rsq < cut_coulsq) {
- if (!ncoultablebits || rsq <= tabinnersq) {
- r = sqrt(rsq);
- grij = g_ewald * r;
- expm2 = exp(-grij*grij);
- t = 1.0 / (1.0 + EWALD_P*grij);
- erfc = t *
- (EWALD_A1+t*(EWALD_A2+t*(EWALD_A3+t*(EWALD_A4+t*EWALD_A5)))) *
- expm2;
- prefactor = qqrd2e * tmp_coef3/r;
- forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
- if (factor_coul < 1.0) {
- forcecoul -= (1.0-factor_coul)*prefactor;
- }
- } else {
- union_int_float_t rsq_lookup;
- rsq_lookup.f = rsq;
- itable = rsq_lookup.i & ncoulmask;
- itable >>= ncoulshiftbits;
- fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
- table = ftable[itable] + fraction*dftable[itable];
- forcecoul = tmp_coef3 * table;
- if (factor_coul < 1.0) {
- table = ctable[itable] + fraction*dctable[itable];
- prefactor = tmp_coef3 * table;
- forcecoul -= (1.0-factor_coul)*prefactor;
- }
- }
- }
-
- forcelj = 0.0;
- if (rsq < cut_ljsq) {
- r6inv = r2inv*r2inv*r2inv;
- jtype = type[j] - 1;
- fast_alpha_t& a = tabsixi[jtype];
- forcelj = r6inv * (a.lj1*r6inv - a.lj2);
- if (rsq > cut_lj_innersq) {
- switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
- (tmp_coef2 + 2.0*rsq) * tmp_coef1;
- switch2 = 12.0*rsq * (cut_ljsq-rsq) *
- (rsq-cut_lj_innersq) * tmp_coef1;
- fast_alpha_t& a = tabsixi[jtype];
- philj = r6inv * (a.lj3*r6inv - a.lj4);
- forcelj = forcelj*switch1 + philj*switch2;
- }
- }
-
- double fpair = (forcecoul + factor_lj*forcelj) * r2inv;
-
- tmpfx += delx*fpair;
- tmpfy += dely*fpair;
- tmpfz += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- ff[j].x -= delx*fpair;
- ff[j].y -= dely*fpair;
- ff[j].z -= delz*fpair;
- }
-
- if (EFLAG) {
- if (rsq < cut_coulsq) {
- if (!ncoultablebits || rsq <= tabinnersq)
- ecoul = prefactor*erfc;
- else {
- table = etable[itable] + fraction*detable[itable];
- ecoul = tmp_coef3 * table;
- }
- if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
- } else ecoul = 0.0;
-
- if (rsq < cut_ljsq) {
- fast_alpha_t& a = tabsixi[jtype];
- evdwl = r6inv*(a.lj3*r6inv-a.lj4);
- if (rsq > cut_lj_innersq) {
- switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
- (tmp_coef2 + 2.0*rsq) * tmp_coef1;
- evdwl *= switch1;
- }
- evdwl *= factor_lj;
- } else evdwl = 0.0;
- }
-
- if (EVFLAG) ev_tally(i,j,nlocal,NEWTON_PAIR,
- evdwl,ecoul,fpair,delx,dely,delz);
- }
+ factor_lj = special_lj[sbindex];
+ factor_coul = special_coul[sbindex];
+ j &= NEIGHMASK;
+
+ double delx = xtmp - xx[j].x;
+ double dely = ytmp - xx[j].y;
+ double delz = ztmp - xx[j].z;
+ rsq = delx*delx + dely*dely + delz*delz;
+ double tmp_coef3 = qtmp*q[j];
+
+ if (rsq < cut_bothsq) {
+ r2inv = 1.0/rsq;
+
+ forcecoul = 0.0;
+ if (rsq < cut_coulsq) {
+ if (!ncoultablebits || rsq <= tabinnersq) {
+ r = sqrt(rsq);
+ grij = g_ewald * r;
+ expm2 = exp(-grij*grij);
+ t = 1.0 / (1.0 + EWALD_P*grij);
+ erfc = t *
+ (EWALD_A1+t*(EWALD_A2+t*(EWALD_A3+t*(EWALD_A4+t*EWALD_A5)))) *
+ expm2;
+ prefactor = qqrd2e * tmp_coef3/r;
+ forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
+ if (factor_coul < 1.0) {
+ forcecoul -= (1.0-factor_coul)*prefactor;
+ }
+ } else {
+ union_int_float_t rsq_lookup;
+ rsq_lookup.f = rsq;
+ itable = rsq_lookup.i & ncoulmask;
+ itable >>= ncoulshiftbits;
+ fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
+ table = ftable[itable] + fraction*dftable[itable];
+ forcecoul = tmp_coef3 * table;
+ if (factor_coul < 1.0) {
+ table = ctable[itable] + fraction*dctable[itable];
+ prefactor = tmp_coef3 * table;
+ forcecoul -= (1.0-factor_coul)*prefactor;
+ }
+ }
+ }
+
+ forcelj = 0.0;
+ if (rsq < cut_ljsq) {
+ r6inv = r2inv*r2inv*r2inv;
+ jtype = type[j] - 1;
+ fast_alpha_t& a = tabsixi[jtype];
+ forcelj = r6inv * (a.lj1*r6inv - a.lj2);
+ if (rsq > cut_lj_innersq) {
+ switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
+ (tmp_coef2 + 2.0*rsq) * tmp_coef1;
+ switch2 = 12.0*rsq * (cut_ljsq-rsq) *
+ (rsq-cut_lj_innersq) * tmp_coef1;
+ fast_alpha_t& a = tabsixi[jtype];
+ philj = r6inv * (a.lj3*r6inv - a.lj4);
+ forcelj = forcelj*switch1 + philj*switch2;
+ }
+ }
+
+ double fpair = (forcecoul + factor_lj*forcelj) * r2inv;
+
+ tmpfx += delx*fpair;
+ tmpfy += dely*fpair;
+ tmpfz += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ ff[j].x -= delx*fpair;
+ ff[j].y -= dely*fpair;
+ ff[j].z -= delz*fpair;
+ }
+
+ if (EFLAG) {
+ if (rsq < cut_coulsq) {
+ if (!ncoultablebits || rsq <= tabinnersq)
+ ecoul = prefactor*erfc;
+ else {
+ table = etable[itable] + fraction*detable[itable];
+ ecoul = tmp_coef3 * table;
+ }
+ if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
+ } else ecoul = 0.0;
+
+ if (rsq < cut_ljsq) {
+ fast_alpha_t& a = tabsixi[jtype];
+ evdwl = r6inv*(a.lj3*r6inv-a.lj4);
+ if (rsq > cut_lj_innersq) {
+ switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
+ (tmp_coef2 + 2.0*rsq) * tmp_coef1;
+ evdwl *= switch1;
+ }
+ evdwl *= factor_lj;
+ } else evdwl = 0.0;
+ }
+
+ if (EVFLAG) ev_tally(i,j,nlocal,NEWTON_PAIR,
+ evdwl,ecoul,fpair,delx,dely,delz);
+ }
}
}
@@ -337,4 +337,3 @@ void PairLJCharmmCoulLongOpt::eval()
if (vflag_fdotr) virial_fdotr_compute();
}
-
diff --git a/src/OPT/pair_lj_charmm_coul_long_opt.h b/src/OPT/pair_lj_charmm_coul_long_opt.h
index e2cc1af8ed69028fb3c3ca7cd63a9844fedfe56f..2e6b30e5766f86111918ec09dc548b506ede64c4 100644
--- a/src/OPT/pair_lj_charmm_coul_long_opt.h
+++ b/src/OPT/pair_lj_charmm_coul_long_opt.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -32,7 +32,7 @@ class PairLJCharmmCoulLongOpt : public PairLJCharmmCoulLong {
private:
template < int EVFLAG, int EFLAG, int NEWTON_PAIR > void eval();
};
-
+
}
#endif
diff --git a/src/OPT/pair_lj_cut_coul_long_opt.cpp b/src/OPT/pair_lj_cut_coul_long_opt.cpp
index da09305270f98c0c7317a4dadbc8e86e95c5efab..2ff5fc7bd6b00c61623147921cc9986b8b29356c 100644
--- a/src/OPT/pair_lj_cut_coul_long_opt.cpp
+++ b/src/OPT/pair_lj_cut_coul_long_opt.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -99,7 +99,7 @@ void PairLJCutCoulLongOpt::eval()
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@@ -126,70 +126,70 @@ void PairLJCutCoulLongOpt::eval()
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
-
- if (rsq < cut_coulsq) {
- if (!CTABLE || rsq <= tabinnersq) {
- r = sqrt(rsq);
- grij = g_ewald * r;
- expm2 = exp(-grij*grij);
- t = 1.0 / (1.0 + EWALD_P*grij);
- erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
- prefactor = qqrd2e * qtmp*q[j]/r;
- forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
- if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
- } else {
- union_int_float_t rsq_lookup;
- rsq_lookup.f = rsq;
- itable = rsq_lookup.i & ncoulmask;
- itable >>= ncoulshiftbits;
- fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
- table = ftable[itable] + fraction*dftable[itable];
- forcecoul = qtmp*q[j] * table;
- if (factor_coul < 1.0) {
- table = ctable[itable] + fraction*dctable[itable];
- prefactor = qtmp*q[j] * table;
- forcecoul -= (1.0-factor_coul)*prefactor;
- }
- }
- } else forcecoul = 0.0;
-
- if (rsq < cut_ljsq[itype][jtype]) {
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- } else forcelj = 0.0;
-
- fpair = (forcecoul + factor_lj*forcelj) * r2inv;
-
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (EFLAG) {
- if (rsq < cut_coulsq) {
- if (!CTABLE || rsq <= tabinnersq)
- ecoul = prefactor*erfc;
- else {
- table = etable[itable] + fraction*detable[itable];
- ecoul = qtmp*q[j] * table;
- }
- if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
- } else ecoul = 0.0;
-
- if (rsq < cut_ljsq[itype][jtype]) {
- evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
- offset[itype][jtype];
- evdwl *= factor_lj;
- } else evdwl = 0.0;
- }
-
- if (EVFLAG) ev_tally(i,j,nlocal,NEWTON_PAIR,
- evdwl,ecoul,fpair,delx,dely,delz);
+ r2inv = 1.0/rsq;
+
+ if (rsq < cut_coulsq) {
+ if (!CTABLE || rsq <= tabinnersq) {
+ r = sqrt(rsq);
+ grij = g_ewald * r;
+ expm2 = exp(-grij*grij);
+ t = 1.0 / (1.0 + EWALD_P*grij);
+ erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
+ prefactor = qqrd2e * qtmp*q[j]/r;
+ forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
+ if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
+ } else {
+ union_int_float_t rsq_lookup;
+ rsq_lookup.f = rsq;
+ itable = rsq_lookup.i & ncoulmask;
+ itable >>= ncoulshiftbits;
+ fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
+ table = ftable[itable] + fraction*dftable[itable];
+ forcecoul = qtmp*q[j] * table;
+ if (factor_coul < 1.0) {
+ table = ctable[itable] + fraction*dctable[itable];
+ prefactor = qtmp*q[j] * table;
+ forcecoul -= (1.0-factor_coul)*prefactor;
+ }
+ }
+ } else forcecoul = 0.0;
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ } else forcelj = 0.0;
+
+ fpair = (forcecoul + factor_lj*forcelj) * r2inv;
+
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (EFLAG) {
+ if (rsq < cut_coulsq) {
+ if (!CTABLE || rsq <= tabinnersq)
+ ecoul = prefactor*erfc;
+ else {
+ table = etable[itable] + fraction*detable[itable];
+ ecoul = qtmp*q[j] * table;
+ }
+ if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
+ } else ecoul = 0.0;
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
+ offset[itype][jtype];
+ evdwl *= factor_lj;
+ } else evdwl = 0.0;
+ }
+
+ if (EVFLAG) ev_tally(i,j,nlocal,NEWTON_PAIR,
+ evdwl,ecoul,fpair,delx,dely,delz);
}
}
f[i][0] += fxtmp;
diff --git a/src/OPT/pair_lj_cut_coul_long_opt.h b/src/OPT/pair_lj_cut_coul_long_opt.h
index 4c19ee9b5d78f743b203a0e26526c868fea5c959..5afd3ffc775b9d8d5abfcfc46eac42ded847ba6a 100644
--- a/src/OPT/pair_lj_cut_coul_long_opt.h
+++ b/src/OPT/pair_lj_cut_coul_long_opt.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -30,7 +30,7 @@ class PairLJCutCoulLongOpt : public PairLJCutCoulLong {
virtual void compute(int, int);
protected:
- template <const int EVFLAG, const int EFLAG,
+ template <const int EVFLAG, const int EFLAG,
const int NEWTON_PAIR, const int CTABLE >
void eval();
};
diff --git a/src/OPT/pair_lj_cut_coul_long_tip4p_opt.cpp b/src/OPT/pair_lj_cut_coul_long_tip4p_opt.cpp
index 4cb1e11bffb7a37a4490bc7b144e307b61bd3a54..35388811beb88be872d66354392b72274975102d 100644
--- a/src/OPT/pair_lj_cut_coul_long_tip4p_opt.cpp
+++ b/src/OPT/pair_lj_cut_coul_long_tip4p_opt.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -101,21 +101,21 @@ void PairLJCutCoulLongTIP4POpt::compute(int eflag, int vflag)
if (!ncoultablebits) {
if (evflag) {
if (eflag) {
- if (vflag) return eval<1,1,1,1>();
- else return eval<1,1,1,0>();
+ if (vflag) return eval<1,1,1,1>();
+ else return eval<1,1,1,0>();
} else {
- if (vflag) return eval<1,1,0,1>();
- else return eval<1,1,0,0>();
+ if (vflag) return eval<1,1,0,1>();
+ else return eval<1,1,0,0>();
}
} else return eval<1,0,0,0>();
} else {
if (evflag) {
if (eflag) {
- if (vflag) return eval<0,1,1,1>();
- else return eval<0,1,1,0>();
+ if (vflag) return eval<0,1,1,1>();
+ else return eval<0,1,1,0>();
} else {
- if (vflag) return eval<0,1,0,1>();
- else return eval<0,1,0,0>();
+ if (vflag) return eval<0,1,0,1>();
+ else return eval<0,1,0,0>();
}
} else return eval<0,0,0,0>();
}
@@ -123,8 +123,8 @@ void PairLJCutCoulLongTIP4POpt::compute(int eflag, int vflag)
/* ---------------------------------------------------------------------- */
-template < const int CTABLE, const int EVFLAG,
- const int EFLAG, const int VFLAG>
+template < const int CTABLE, const int EVFLAG,
+ const int EFLAG, const int VFLAG>
void PairLJCutCoulLongTIP4POpt::eval()
{
int i,j,ii,jj,inum,jnum,itype,jtype,itable;
@@ -159,7 +159,7 @@ void PairLJCutCoulLongTIP4POpt::eval()
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@@ -192,26 +192,26 @@ void PairLJCutCoulLongTIP4POpt::eval()
// LJ interaction based on true rsq
if (rsq < cut_ljsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- forcelj *= factor_lj * r2inv;
-
- fxtmp += delx*forcelj;
- fytmp += dely*forcelj;
- fztmp += delz*forcelj;
- f[j][0] -= delx*forcelj;
- f[j][1] -= dely*forcelj;
- f[j][2] -= delz*forcelj;
-
- if (EFLAG) {
- evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
- offset[itype][jtype];
- evdwl *= factor_lj;
- } else evdwl = 0.0;
-
- if (EVFLAG) ev_tally(i,j,nlocal,/* newton_pair = */ 1,
- evdwl,0.0,forcelj,delx,dely,delz);
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ forcelj *= factor_lj * r2inv;
+
+ fxtmp += delx*forcelj;
+ fytmp += dely*forcelj;
+ fztmp += delz*forcelj;
+ f[j][0] -= delx*forcelj;
+ f[j][1] -= dely*forcelj;
+ f[j][2] -= delz*forcelj;
+
+ if (EFLAG) {
+ evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
+ offset[itype][jtype];
+ evdwl *= factor_lj;
+ } else evdwl = 0.0;
+
+ if (EVFLAG) ev_tally(i,j,nlocal,/* newton_pair = */ 1,
+ evdwl,0.0,forcelj,delx,dely,delz);
}
// adjust rsq and delxyz for off-site O charge(s),
@@ -219,210 +219,210 @@ void PairLJCutCoulLongTIP4POpt::eval()
if (rsq < cut_coulsqplus) {
- if (itype == typeO || jtype == typeO) {
- x2 = mpos[j];
- jH1 = h1idx[j];
- jH2 = h2idx[j];
- if (jtype == typeO && ( jH1 < 0 || jH2 < 0))
- error->one(FLERR,"TIP4P hydrogen is missing");
- delx = x1[0] - x2[0];
- dely = x1[1] - x2[1];
- delz = x1[2] - x2[2];
- rsq = delx*delx + dely*dely + delz*delz;
- }
-
- // Coulombic interaction based on modified rsq
-
- if (rsq < cut_coulsq) {
- r2inv = 1 / rsq;
- if (CTABLE || rsq <= tabinnersq) {
- r = sqrt(rsq);
- grij = g_ewald * r;
- expm2 = exp(-grij*grij);
- t = 1.0 / (1.0 + EWALD_P*grij);
- erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
- prefactor = qqrd2e * qtmp*q[j]/r;
- forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
- if (factor_coul < 1.0) {
- forcecoul -= (1.0-factor_coul)*prefactor;
- }
- } else {
- union_int_float_t rsq_lookup;
- rsq_lookup.f = rsq;
- itable = rsq_lookup.i & ncoulmask;
- itable >>= ncoulshiftbits;
- fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
- table = ftable[itable] + fraction*dftable[itable];
- forcecoul = qtmp*q[j] * table;
- if (factor_coul < 1.0) {
- table = ctable[itable] + fraction*dctable[itable];
- prefactor = qtmp*q[j] * table;
- forcecoul -= (1.0-factor_coul)*prefactor;
- }
- }
-
- cforce = forcecoul * r2inv;
-
- // if i,j are not O atoms, force is applied directly
- // if i or j are O atoms, force is on fictitious atom & partitioned
- // force partitioning due to Feenstra, J Comp Chem, 20, 786 (1999)
- // f_f = fictitious force, fO = f_f (1 - 2 alpha), fH = alpha f_f
- // preserves total force and torque on water molecule
- // virial = sum(r x F) where each water's atoms are near xi and xj
- // vlist stores 2,4,6 atoms whose forces contribute to virial
-
- n = 0;
-
- if (itype != typeO) {
- fxtmp += delx * cforce;
- fytmp += dely * cforce;
- fztmp += delz * cforce;
-
- if (VFLAG) {
- v[0] = x[i][0] * delx * cforce;
- v[1] = x[i][1] * dely * cforce;
- v[2] = x[i][2] * delz * cforce;
- v[3] = x[i][0] * dely * cforce;
- v[4] = x[i][0] * delz * cforce;
- v[5] = x[i][1] * delz * cforce;
- vlist[n++] = i;
- }
-
- } else {
-
- fdx = delx*cforce;
- fdy = dely*cforce;
- fdz = delz*cforce;
-
- delxOM = x[i][0] - x1[0];
- delyOM = x[i][1] - x1[1];
- delzOM = x[i][2] - x1[2];
-
- ddotf = (delxOM * fdx + delyOM * fdy + delzOM * fdz) /
- (qdist*qdist);
-
- f1x = alpha * (fdx - ddotf * delxOM);
- f1y = alpha * (fdy - ddotf * delyOM);
- f1z = alpha * (fdz - ddotf * delzOM);
-
- fOx = fdx - f1x;
- fOy = fdy - f1y;
- fOz = fdz - f1z;
-
- fHx = 0.5 * f1x;
- fHy = 0.5 * f1y;
- fHz = 0.5 * f1z;
-
- fxtmp += fOx;
- fytmp += fOy;
- fztmp += fOz;
-
- f[iH1][0] += fHx;
- f[iH1][1] += fHy;
- f[iH1][2] += fHz;
-
- f[iH2][0] += fHx;
- f[iH2][1] += fHy;
- f[iH2][2] += fHz;
-
- if (VFLAG) {
- domain->closest_image(x[i],x[iH1],xH1);
- domain->closest_image(x[i],x[iH2],xH2);
-
- v[0] = x[i][0]*fOx + xH1[0]*fHx + xH2[0]*fHx;
- v[1] = x[i][1]*fOy + xH1[1]*fHy + xH2[1]*fHy;
- v[2] = x[i][2]*fOz + xH1[2]*fHz + xH2[2]*fHz;
- v[3] = x[i][0]*fOy + xH1[0]*fHy + xH2[0]*fHy;
- v[4] = x[i][0]*fOz + xH1[0]*fHz + xH2[0]*fHz;
- v[5] = x[i][1]*fOz + xH1[1]*fHz + xH2[1]*fHz;
-
- vlist[n++] = i;
- vlist[n++] = iH1;
- vlist[n++] = iH2;
- }
- }
-
- if (jtype != typeO) {
- f[j][0] -= delx * cforce;
- f[j][1] -= dely * cforce;
- f[j][2] -= delz * cforce;
-
- if (VFLAG) {
- v[0] -= x[j][0] * delx * cforce;
- v[1] -= x[j][1] * dely * cforce;
- v[2] -= x[j][2] * delz * cforce;
- v[3] -= x[j][0] * dely * cforce;
- v[4] -= x[j][0] * delz * cforce;
- v[5] -= x[j][1] * delz * cforce;
- vlist[n++] = j;
- }
-
- } else {
-
- fdx = -delx*cforce;
- fdy = -dely*cforce;
- fdz = -delz*cforce;
-
- delxOM = x[j][0] - x2[0];
- delyOM = x[j][1] - x2[1];
- delzOM = x[j][2] - x2[2];
-
- ddotf = (delxOM * fdx + delyOM * fdy + delzOM * fdz) /
- (qdist*qdist);
-
- f1x = alpha * (fdx - ddotf * delxOM);
- f1y = alpha * (fdy - ddotf * delyOM);
- f1z = alpha * (fdz - ddotf * delzOM);
-
- fOx = fdx - f1x;
- fOy = fdy - f1y;
- fOz = fdz - f1z;
-
- fHx = 0.5 * f1x;
- fHy = 0.5 * f1y;
- fHz = 0.5 * f1z;
-
- f[j][0] += fOx;
- f[j][1] += fOy;
- f[j][2] += fOz;
-
- f[jH1][0] += fHx;
- f[jH1][1] += fHy;
- f[jH1][2] += fHz;
-
- f[jH2][0] += fHx;
- f[jH2][1] += fHy;
- f[jH2][2] += fHz;
-
- if (VFLAG) {
- domain->closest_image(x[j],x[jH1],xH1);
- domain->closest_image(x[j],x[jH2],xH2);
-
- v[0] += x[j][0]*fOx + xH1[0]*fHx + xH2[0]*fHx;
- v[1] += x[j][1]*fOy + xH1[1]*fHy + xH2[1]*fHy;
- v[2] += x[j][2]*fOz + xH1[2]*fHz + xH2[2]*fHz;
- v[3] += x[j][0]*fOy + xH1[0]*fHy + xH2[0]*fHy;
- v[4] += x[j][0]*fOz + xH1[0]*fHz + xH2[0]*fHz;
- v[5] += x[j][1]*fOz + xH1[1]*fHz + xH2[1]*fHz;
-
- vlist[n++] = j;
- vlist[n++] = jH1;
- vlist[n++] = jH2;
- }
- }
-
- if (EFLAG) {
- if (CTABLE || rsq <= tabinnersq)
- ecoul = prefactor*erfc;
- else {
- table = etable[itable] + fraction*detable[itable];
- ecoul = qtmp*q[j] * table;
- }
- if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
- } else ecoul = 0.0;
-
- if (EVFLAG) ev_tally_list(n,vlist,ecoul,v);
- }
+ if (itype == typeO || jtype == typeO) {
+ x2 = mpos[j];
+ jH1 = h1idx[j];
+ jH2 = h2idx[j];
+ if (jtype == typeO && ( jH1 < 0 || jH2 < 0))
+ error->one(FLERR,"TIP4P hydrogen is missing");
+ delx = x1[0] - x2[0];
+ dely = x1[1] - x2[1];
+ delz = x1[2] - x2[2];
+ rsq = delx*delx + dely*dely + delz*delz;
+ }
+
+ // Coulombic interaction based on modified rsq
+
+ if (rsq < cut_coulsq) {
+ r2inv = 1 / rsq;
+ if (CTABLE || rsq <= tabinnersq) {
+ r = sqrt(rsq);
+ grij = g_ewald * r;
+ expm2 = exp(-grij*grij);
+ t = 1.0 / (1.0 + EWALD_P*grij);
+ erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
+ prefactor = qqrd2e * qtmp*q[j]/r;
+ forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
+ if (factor_coul < 1.0) {
+ forcecoul -= (1.0-factor_coul)*prefactor;
+ }
+ } else {
+ union_int_float_t rsq_lookup;
+ rsq_lookup.f = rsq;
+ itable = rsq_lookup.i & ncoulmask;
+ itable >>= ncoulshiftbits;
+ fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
+ table = ftable[itable] + fraction*dftable[itable];
+ forcecoul = qtmp*q[j] * table;
+ if (factor_coul < 1.0) {
+ table = ctable[itable] + fraction*dctable[itable];
+ prefactor = qtmp*q[j] * table;
+ forcecoul -= (1.0-factor_coul)*prefactor;
+ }
+ }
+
+ cforce = forcecoul * r2inv;
+
+ // if i,j are not O atoms, force is applied directly
+ // if i or j are O atoms, force is on fictitious atom & partitioned
+ // force partitioning due to Feenstra, J Comp Chem, 20, 786 (1999)
+ // f_f = fictitious force, fO = f_f (1 - 2 alpha), fH = alpha f_f
+ // preserves total force and torque on water molecule
+ // virial = sum(r x F) where each water's atoms are near xi and xj
+ // vlist stores 2,4,6 atoms whose forces contribute to virial
+
+ n = 0;
+
+ if (itype != typeO) {
+ fxtmp += delx * cforce;
+ fytmp += dely * cforce;
+ fztmp += delz * cforce;
+
+ if (VFLAG) {
+ v[0] = x[i][0] * delx * cforce;
+ v[1] = x[i][1] * dely * cforce;
+ v[2] = x[i][2] * delz * cforce;
+ v[3] = x[i][0] * dely * cforce;
+ v[4] = x[i][0] * delz * cforce;
+ v[5] = x[i][1] * delz * cforce;
+ vlist[n++] = i;
+ }
+
+ } else {
+
+ fdx = delx*cforce;
+ fdy = dely*cforce;
+ fdz = delz*cforce;
+
+ delxOM = x[i][0] - x1[0];
+ delyOM = x[i][1] - x1[1];
+ delzOM = x[i][2] - x1[2];
+
+ ddotf = (delxOM * fdx + delyOM * fdy + delzOM * fdz) /
+ (qdist*qdist);
+
+ f1x = alpha * (fdx - ddotf * delxOM);
+ f1y = alpha * (fdy - ddotf * delyOM);
+ f1z = alpha * (fdz - ddotf * delzOM);
+
+ fOx = fdx - f1x;
+ fOy = fdy - f1y;
+ fOz = fdz - f1z;
+
+ fHx = 0.5 * f1x;
+ fHy = 0.5 * f1y;
+ fHz = 0.5 * f1z;
+
+ fxtmp += fOx;
+ fytmp += fOy;
+ fztmp += fOz;
+
+ f[iH1][0] += fHx;
+ f[iH1][1] += fHy;
+ f[iH1][2] += fHz;
+
+ f[iH2][0] += fHx;
+ f[iH2][1] += fHy;
+ f[iH2][2] += fHz;
+
+ if (VFLAG) {
+ domain->closest_image(x[i],x[iH1],xH1);
+ domain->closest_image(x[i],x[iH2],xH2);
+
+ v[0] = x[i][0]*fOx + xH1[0]*fHx + xH2[0]*fHx;
+ v[1] = x[i][1]*fOy + xH1[1]*fHy + xH2[1]*fHy;
+ v[2] = x[i][2]*fOz + xH1[2]*fHz + xH2[2]*fHz;
+ v[3] = x[i][0]*fOy + xH1[0]*fHy + xH2[0]*fHy;
+ v[4] = x[i][0]*fOz + xH1[0]*fHz + xH2[0]*fHz;
+ v[5] = x[i][1]*fOz + xH1[1]*fHz + xH2[1]*fHz;
+
+ vlist[n++] = i;
+ vlist[n++] = iH1;
+ vlist[n++] = iH2;
+ }
+ }
+
+ if (jtype != typeO) {
+ f[j][0] -= delx * cforce;
+ f[j][1] -= dely * cforce;
+ f[j][2] -= delz * cforce;
+
+ if (VFLAG) {
+ v[0] -= x[j][0] * delx * cforce;
+ v[1] -= x[j][1] * dely * cforce;
+ v[2] -= x[j][2] * delz * cforce;
+ v[3] -= x[j][0] * dely * cforce;
+ v[4] -= x[j][0] * delz * cforce;
+ v[5] -= x[j][1] * delz * cforce;
+ vlist[n++] = j;
+ }
+
+ } else {
+
+ fdx = -delx*cforce;
+ fdy = -dely*cforce;
+ fdz = -delz*cforce;
+
+ delxOM = x[j][0] - x2[0];
+ delyOM = x[j][1] - x2[1];
+ delzOM = x[j][2] - x2[2];
+
+ ddotf = (delxOM * fdx + delyOM * fdy + delzOM * fdz) /
+ (qdist*qdist);
+
+ f1x = alpha * (fdx - ddotf * delxOM);
+ f1y = alpha * (fdy - ddotf * delyOM);
+ f1z = alpha * (fdz - ddotf * delzOM);
+
+ fOx = fdx - f1x;
+ fOy = fdy - f1y;
+ fOz = fdz - f1z;
+
+ fHx = 0.5 * f1x;
+ fHy = 0.5 * f1y;
+ fHz = 0.5 * f1z;
+
+ f[j][0] += fOx;
+ f[j][1] += fOy;
+ f[j][2] += fOz;
+
+ f[jH1][0] += fHx;
+ f[jH1][1] += fHy;
+ f[jH1][2] += fHz;
+
+ f[jH2][0] += fHx;
+ f[jH2][1] += fHy;
+ f[jH2][2] += fHz;
+
+ if (VFLAG) {
+ domain->closest_image(x[j],x[jH1],xH1);
+ domain->closest_image(x[j],x[jH2],xH2);
+
+ v[0] += x[j][0]*fOx + xH1[0]*fHx + xH2[0]*fHx;
+ v[1] += x[j][1]*fOy + xH1[1]*fHy + xH2[1]*fHy;
+ v[2] += x[j][2]*fOz + xH1[2]*fHz + xH2[2]*fHz;
+ v[3] += x[j][0]*fOy + xH1[0]*fHy + xH2[0]*fHy;
+ v[4] += x[j][0]*fOz + xH1[0]*fHz + xH2[0]*fHz;
+ v[5] += x[j][1]*fOz + xH1[1]*fHz + xH2[1]*fHz;
+
+ vlist[n++] = j;
+ vlist[n++] = jH1;
+ vlist[n++] = jH2;
+ }
+ }
+
+ if (EFLAG) {
+ if (CTABLE || rsq <= tabinnersq)
+ ecoul = prefactor*erfc;
+ else {
+ table = etable[itable] + fraction*detable[itable];
+ ecoul = qtmp*q[j] * table;
+ }
+ if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
+ } else ecoul = 0.0;
+
+ if (EVFLAG) ev_tally_list(n,vlist,ecoul,v);
+ }
}
}
f[i][0] += fxtmp;
diff --git a/src/OPT/pair_lj_cut_coul_long_tip4p_opt.h b/src/OPT/pair_lj_cut_coul_long_tip4p_opt.h
index 4f77ca7c020a4ff79e69ab958e619c2a5dafb0b7..45c5e0c147f062a9603b40bbe77c19592411dd42 100644
--- a/src/OPT/pair_lj_cut_coul_long_tip4p_opt.h
+++ b/src/OPT/pair_lj_cut_coul_long_tip4p_opt.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/OPT/pair_lj_cut_opt.cpp b/src/OPT/pair_lj_cut_opt.cpp
index 8f855da5662ae46f17f5522e1bf954a6af538e75..a3d90eae501ee276502ec5aa819d7efbfab3b12b 100644
--- a/src/OPT/pair_lj_cut_opt.cpp
+++ b/src/OPT/pair_lj_cut_opt.cpp
@@ -5,14 +5,14 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
- Contributing authors:
+ Contributing authors:
James Fischer, High Performance Technologies, Inc.
David Richie, Stone Ridge Technology
Vincent Natoli, Stone Ridge Technology
@@ -57,16 +57,16 @@ template < int EVFLAG, int EFLAG, int NEWTON_PAIR >
void PairLJCutOpt::eval()
{
typedef struct { double x,y,z; } vec3_t;
-
+
typedef struct {
double cutsq,lj1,lj2,lj3,lj4,offset;
double _pad[2];
} fast_alpha_t;
-
+
int i,j,ii,jj,inum,jnum,itype,jtype,sbindex;
double factor_lj;
double evdwl = 0.0;
-
+
double** __restrict__ x = atom->x;
double** __restrict__ f = atom->f;
int* __restrict__ type = atom->type;
@@ -77,14 +77,14 @@ void PairLJCutOpt::eval()
int* __restrict__ ilist = list->ilist;
int** __restrict__ firstneigh = list->firstneigh;
int* __restrict__ numneigh = list->numneigh;
-
+
vec3_t* __restrict__ xx = (vec3_t*)x[0];
vec3_t* __restrict__ ff = (vec3_t*)f[0];
-
+
int ntypes = atom->ntypes;
int ntypes2 = ntypes*ntypes;
-
- fast_alpha_t* __restrict__ fast_alpha =
+
+ fast_alpha_t* __restrict__ fast_alpha =
(fast_alpha_t*) malloc(ntypes2*sizeof(fast_alpha_t));
for (i = 0; i < ntypes; i++) for (j = 0; j < ntypes; j++) {
fast_alpha_t& a = fast_alpha[i*ntypes+j];
@@ -96,9 +96,9 @@ void PairLJCutOpt::eval()
a.offset = offset[i+1][j+1];
}
fast_alpha_t* __restrict__ tabsix = fast_alpha;
-
+
// loop over neighbors of my atoms
-
+
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
double xtmp = xx[i].x;
@@ -107,86 +107,86 @@ void PairLJCutOpt::eval()
itype = type[i] - 1;
int* __restrict__ jlist = firstneigh[i];
jnum = numneigh[i];
-
+
double tmpfx = 0.0;
double tmpfy = 0.0;
double tmpfz = 0.0;
-
+
fast_alpha_t* __restrict__ tabsixi = (fast_alpha_t*)&tabsix[itype*ntypes];
-
+
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
sbindex = sbmask(j);
if (sbindex == 0) {
- double delx = xtmp - xx[j].x;
- double dely = ytmp - xx[j].y;
- double delz = ztmp - xx[j].z;
- double rsq = delx*delx + dely*dely + delz*delz;
-
- jtype = type[j] - 1;
-
- fast_alpha_t& a = tabsixi[jtype];
-
- if (rsq < a.cutsq) {
- double r2inv = 1.0/rsq;
- double r6inv = r2inv*r2inv*r2inv;
- double forcelj = r6inv * (a.lj1*r6inv - a.lj2);
- double fpair = forcelj*r2inv;
-
- tmpfx += delx*fpair;
- tmpfy += dely*fpair;
- tmpfz += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- ff[j].x -= delx*fpair;
- ff[j].y -= dely*fpair;
- ff[j].z -= delz*fpair;
- }
-
- if (EFLAG) evdwl = r6inv*(a.lj3*r6inv-a.lj4) - a.offset;
-
- if (EVFLAG)
- ev_tally(i,j,nlocal,NEWTON_PAIR,
- evdwl,0.0,fpair,delx,dely,delz);
- }
+ double delx = xtmp - xx[j].x;
+ double dely = ytmp - xx[j].y;
+ double delz = ztmp - xx[j].z;
+ double rsq = delx*delx + dely*dely + delz*delz;
+
+ jtype = type[j] - 1;
+
+ fast_alpha_t& a = tabsixi[jtype];
+
+ if (rsq < a.cutsq) {
+ double r2inv = 1.0/rsq;
+ double r6inv = r2inv*r2inv*r2inv;
+ double forcelj = r6inv * (a.lj1*r6inv - a.lj2);
+ double fpair = forcelj*r2inv;
+
+ tmpfx += delx*fpair;
+ tmpfy += dely*fpair;
+ tmpfz += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ ff[j].x -= delx*fpair;
+ ff[j].y -= dely*fpair;
+ ff[j].z -= delz*fpair;
+ }
+
+ if (EFLAG) evdwl = r6inv*(a.lj3*r6inv-a.lj4) - a.offset;
+
+ if (EVFLAG)
+ ev_tally(i,j,nlocal,NEWTON_PAIR,
+ evdwl,0.0,fpair,delx,dely,delz);
+ }
} else {
- factor_lj = special_lj[sbindex];
- j &= NEIGHMASK;
-
- double delx = xtmp - xx[j].x;
- double dely = ytmp - xx[j].y;
- double delz = ztmp - xx[j].z;
- double rsq = delx*delx + dely*dely + delz*delz;
-
- int jtype1 = type[j];
- jtype = jtype1 - 1;
-
- fast_alpha_t& a = tabsixi[jtype];
- if (rsq < a.cutsq) {
- double r2inv = 1.0/rsq;
- double r6inv = r2inv*r2inv*r2inv;
- fast_alpha_t& a = tabsixi[jtype];
- double forcelj = r6inv * (a.lj1*r6inv - a.lj2);
- double fpair = factor_lj*forcelj*r2inv;
-
- tmpfx += delx*fpair;
- tmpfy += dely*fpair;
- tmpfz += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- ff[j].x -= delx*fpair;
- ff[j].y -= dely*fpair;
- ff[j].z -= delz*fpair;
- }
-
- if (EFLAG) {
- evdwl = r6inv*(a.lj3*r6inv-a.lj4) - a.offset;
- evdwl *= factor_lj;
- }
-
- if (EVFLAG) ev_tally(i,j,nlocal,NEWTON_PAIR,
- evdwl,0.0,fpair,delx,dely,delz);
- }
+ factor_lj = special_lj[sbindex];
+ j &= NEIGHMASK;
+
+ double delx = xtmp - xx[j].x;
+ double dely = ytmp - xx[j].y;
+ double delz = ztmp - xx[j].z;
+ double rsq = delx*delx + dely*dely + delz*delz;
+
+ int jtype1 = type[j];
+ jtype = jtype1 - 1;
+
+ fast_alpha_t& a = tabsixi[jtype];
+ if (rsq < a.cutsq) {
+ double r2inv = 1.0/rsq;
+ double r6inv = r2inv*r2inv*r2inv;
+ fast_alpha_t& a = tabsixi[jtype];
+ double forcelj = r6inv * (a.lj1*r6inv - a.lj2);
+ double fpair = factor_lj*forcelj*r2inv;
+
+ tmpfx += delx*fpair;
+ tmpfy += dely*fpair;
+ tmpfz += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ ff[j].x -= delx*fpair;
+ ff[j].y -= dely*fpair;
+ ff[j].z -= delz*fpair;
+ }
+
+ if (EFLAG) {
+ evdwl = r6inv*(a.lj3*r6inv-a.lj4) - a.offset;
+ evdwl *= factor_lj;
+ }
+
+ if (EVFLAG) ev_tally(i,j,nlocal,NEWTON_PAIR,
+ evdwl,0.0,fpair,delx,dely,delz);
+ }
}
}
@@ -196,6 +196,6 @@ void PairLJCutOpt::eval()
}
free(fast_alpha); fast_alpha = 0;
-
+
if (vflag_fdotr) virial_fdotr_compute();
}
diff --git a/src/OPT/pair_lj_cut_opt.h b/src/OPT/pair_lj_cut_opt.h
index 0bdd00481185f8921b444fd396354b4d8c0594f8..0b01d169f8d87e6a80556176d83a210be02808c0 100644
--- a/src/OPT/pair_lj_cut_opt.h
+++ b/src/OPT/pair_lj_cut_opt.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/OPT/pair_morse_opt.cpp b/src/OPT/pair_morse_opt.cpp
index 5a9bfe7bed47f7900e09485c2cab0329fd91d4b6..c27dd053ff5a3fdaa7397e6d5dbb2124e48c9ba6 100644
--- a/src/OPT/pair_morse_opt.cpp
+++ b/src/OPT/pair_morse_opt.cpp
@@ -5,14 +5,14 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
- Contributing authors:
+ Contributing authors:
James Fischer, High Performance Technologies, Inc.
David Richie, Stone Ridge Technology
Vincent Natoli, Stone Ridge Technology
@@ -58,34 +58,34 @@ template < int EVFLAG, int EFLAG, int NEWTON_PAIR >
void PairMorseOpt::eval()
{
typedef struct { double x,y,z; } vec3_t;
-
+
typedef struct {
double cutsq,r0,alpha,morse1,d0,offset;
double _pad[2];
} fast_alpha_t;
-
+
int i,j,ii,jj,inum,jnum,itype,jtype,sbindex;
double factor_lj;
double evdwl = 0.0;
-
+
double** __restrict__ x = atom->x;
double** __restrict__ f = atom->f;
int* __restrict__ type = atom->type;
int nlocal = atom->nlocal;
double* __restrict__ special_lj = force->special_lj;
-
+
inum = list->inum;
int* __restrict__ ilist = list->ilist;
int** __restrict__ firstneigh = list->firstneigh;
int* __restrict__ numneigh = list->numneigh;
-
+
vec3_t* __restrict__ xx = (vec3_t*)x[0];
vec3_t* __restrict__ ff = (vec3_t*)f[0];
-
+
int ntypes = atom->ntypes;
int ntypes2 = ntypes*ntypes;
-
- fast_alpha_t* __restrict__ fast_alpha =
+
+ fast_alpha_t* __restrict__ fast_alpha =
(fast_alpha_t*) malloc(ntypes2*sizeof(fast_alpha_t));
for (i = 0; i < ntypes; i++) for (j = 0; j < ntypes; j++) {
fast_alpha_t& a = fast_alpha[i*ntypes+j];
@@ -97,9 +97,9 @@ void PairMorseOpt::eval()
a.offset = offset[i+1][j+1];
}
fast_alpha_t* __restrict__ tabsix = fast_alpha;
-
+
// loop over neighbors of my atoms
-
+
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
double xtmp = xx[i].x;
@@ -108,82 +108,82 @@ void PairMorseOpt::eval()
itype = type[i] - 1;
int* __restrict__ jlist = firstneigh[i];
jnum = numneigh[i];
-
+
double tmpfx = 0.0;
double tmpfy = 0.0;
double tmpfz = 0.0;
-
+
fast_alpha_t* __restrict__ tabsixi = (fast_alpha_t*)&tabsix[itype*ntypes];
-
+
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
sbindex = sbmask(j);
if (sbindex == 0) {
- double delx = xtmp - xx[j].x;
- double dely = ytmp - xx[j].y;
- double delz = ztmp - xx[j].z;
- double rsq = delx*delx + dely*dely + delz*delz;
-
- jtype = type[j] - 1;
-
- fast_alpha_t& a = tabsixi[jtype];
- if (rsq < a.cutsq) {
- double r = sqrt(rsq);
- double dr = r - a.r0;
- double dexp = exp(-a.alpha * dr);
- double fpair = a.morse1 * (dexp*dexp - dexp) / r;
-
- tmpfx += delx*fpair;
- tmpfy += dely*fpair;
- tmpfz += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- ff[j].x -= delx*fpair;
- ff[j].y -= dely*fpair;
- ff[j].z -= delz*fpair;
- }
-
- if (EFLAG) evdwl = a.d0 * (dexp*dexp - 2.0*dexp) - a.offset;
-
- if (EVFLAG) ev_tally(i,j,nlocal,NEWTON_PAIR,
- evdwl,0.0,fpair,delx,dely,delz);
- }
+ double delx = xtmp - xx[j].x;
+ double dely = ytmp - xx[j].y;
+ double delz = ztmp - xx[j].z;
+ double rsq = delx*delx + dely*dely + delz*delz;
+
+ jtype = type[j] - 1;
+
+ fast_alpha_t& a = tabsixi[jtype];
+ if (rsq < a.cutsq) {
+ double r = sqrt(rsq);
+ double dr = r - a.r0;
+ double dexp = exp(-a.alpha * dr);
+ double fpair = a.morse1 * (dexp*dexp - dexp) / r;
+
+ tmpfx += delx*fpair;
+ tmpfy += dely*fpair;
+ tmpfz += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ ff[j].x -= delx*fpair;
+ ff[j].y -= dely*fpair;
+ ff[j].z -= delz*fpair;
+ }
+
+ if (EFLAG) evdwl = a.d0 * (dexp*dexp - 2.0*dexp) - a.offset;
+
+ if (EVFLAG) ev_tally(i,j,nlocal,NEWTON_PAIR,
+ evdwl,0.0,fpair,delx,dely,delz);
+ }
} else {
- factor_lj = special_lj[sbindex];
- j &= NEIGHMASK;
-
- double delx = xtmp - xx[j].x;
- double dely = ytmp - xx[j].y;
- double delz = ztmp - xx[j].z;
- double rsq = delx*delx + dely*dely + delz*delz;
-
- jtype = type[j] - 1;
-
- fast_alpha_t& a = tabsixi[jtype];
- if (rsq < a.cutsq) {
- double r = sqrt(rsq);
- double dr = r - a.r0;
- double dexp = exp(-a.alpha * dr);
- double fpair = factor_lj * a.morse1 * (dexp*dexp - dexp) / r;
-
- tmpfx += delx*fpair;
- tmpfy += dely*fpair;
- tmpfz += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- ff[j].x -= delx*fpair;
- ff[j].y -= dely*fpair;
- ff[j].z -= delz*fpair;
- }
-
- if (EFLAG) {
- evdwl = a.d0 * (dexp*dexp - 2.0*dexp) - a.offset;
- evdwl *= factor_lj;
- }
-
- if (EVFLAG) ev_tally(i,j,nlocal,NEWTON_PAIR,
- evdwl,0.0,fpair,delx,dely,delz);
- }
+ factor_lj = special_lj[sbindex];
+ j &= NEIGHMASK;
+
+ double delx = xtmp - xx[j].x;
+ double dely = ytmp - xx[j].y;
+ double delz = ztmp - xx[j].z;
+ double rsq = delx*delx + dely*dely + delz*delz;
+
+ jtype = type[j] - 1;
+
+ fast_alpha_t& a = tabsixi[jtype];
+ if (rsq < a.cutsq) {
+ double r = sqrt(rsq);
+ double dr = r - a.r0;
+ double dexp = exp(-a.alpha * dr);
+ double fpair = factor_lj * a.morse1 * (dexp*dexp - dexp) / r;
+
+ tmpfx += delx*fpair;
+ tmpfy += dely*fpair;
+ tmpfz += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ ff[j].x -= delx*fpair;
+ ff[j].y -= dely*fpair;
+ ff[j].z -= delz*fpair;
+ }
+
+ if (EFLAG) {
+ evdwl = a.d0 * (dexp*dexp - 2.0*dexp) - a.offset;
+ evdwl *= factor_lj;
+ }
+
+ if (EVFLAG) ev_tally(i,j,nlocal,NEWTON_PAIR,
+ evdwl,0.0,fpair,delx,dely,delz);
+ }
}
}
diff --git a/src/OPT/pair_morse_opt.h b/src/OPT/pair_morse_opt.h
index 0e80ac4d742beaf6e73bf9eb167de99ad03ee069..535430015e6d15816867f7849aebaeb5ee2b2b48 100644
--- a/src/OPT/pair_morse_opt.h
+++ b/src/OPT/pair_morse_opt.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/PERI/atom_vec_peri.cpp b/src/PERI/atom_vec_peri.cpp
index cbd95e966adfa298bf44ba53ca2a2f55610e3cfb..586823e71d93bfe5b5707b08287db144d0ed8a19 100644
--- a/src/PERI/atom_vec_peri.cpp
+++ b/src/PERI/atom_vec_peri.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -32,8 +32,8 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-AtomVecPeri::AtomVecPeri(LAMMPS *lmp, int narg, char **arg) :
- AtomVec(lmp, narg, arg)
+AtomVecPeri::AtomVecPeri(LAMMPS *lmp, int narg, char **arg) :
+ AtomVec(lmp, narg, arg)
{
molecular = 0;
@@ -56,7 +56,7 @@ AtomVecPeri::AtomVecPeri(LAMMPS *lmp, int narg, char **arg) :
n = 0 grows arrays by DELTA
n > 0 allocates arrays to size n
------------------------------------------------------------------------- */
-
+
void AtomVecPeri::grow(int n)
{
if (n == 0) nmax += DELTA;
@@ -77,7 +77,7 @@ void AtomVecPeri::grow(int n)
rmass = memory->grow(atom->rmass,nmax,"atom:rmass");
s0 = memory->grow(atom->s0,nmax,"atom:s0");
x0 = memory->grow(atom->x0,nmax,3,"atom:x0");
-
+
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
@@ -121,7 +121,7 @@ void AtomVecPeri::copy(int i, int j, int delflag)
x0[j][2] = x0[i][2];
if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j);
}
@@ -167,7 +167,7 @@ int AtomVecPeri::pack_comm(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
int AtomVecPeri::pack_comm_vel(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
@@ -197,34 +197,34 @@ int AtomVecPeri::pack_comm_vel(int n, int *list, double *buf,
}
if (!deform_vremap) {
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = s0[j];
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = s0[j];
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
}
} else {
dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
dvz = pbc[2]*h_rate[2];
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = s0[j];
- if (mask[i] & deform_groupbit) {
- buf[m++] = v[j][0] + dvx;
- buf[m++] = v[j][1] + dvy;
- buf[m++] = v[j][2] + dvz;
- } else {
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
- }
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = s0[j];
+ if (mask[i] & deform_groupbit) {
+ buf[m++] = v[j][0] + dvx;
+ buf[m++] = v[j][1] + dvy;
+ buf[m++] = v[j][2] + dvz;
+ } else {
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
+ }
}
}
}
@@ -379,7 +379,7 @@ int AtomVecPeri::pack_border(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
int AtomVecPeri::pack_border_vel(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz,dvx,dvy,dvz;
@@ -415,48 +415,48 @@ int AtomVecPeri::pack_border_vel(int n, int *list, double *buf,
}
if (!deform_vremap) {
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = tag[j];
- buf[m++] = type[j];
- buf[m++] = mask[j];
- buf[m++] = vfrac[j];
- buf[m++] = s0[j];
- buf[m++] = x0[j][0];
- buf[m++] = x0[j][1];
- buf[m++] = x0[j][2];
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = tag[j];
+ buf[m++] = type[j];
+ buf[m++] = mask[j];
+ buf[m++] = vfrac[j];
+ buf[m++] = s0[j];
+ buf[m++] = x0[j][0];
+ buf[m++] = x0[j][1];
+ buf[m++] = x0[j][2];
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
}
} else {
dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
dvz = pbc[2]*h_rate[2];
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = tag[j];
- buf[m++] = type[j];
- buf[m++] = mask[j];
- buf[m++] = vfrac[j];
- buf[m++] = s0[j];
- buf[m++] = x0[j][0];
- buf[m++] = x0[j][1];
- buf[m++] = x0[j][2];
- if (mask[i] & deform_groupbit) {
- buf[m++] = v[j][0] + dvx;
- buf[m++] = v[j][1] + dvy;
- buf[m++] = v[j][2] + dvz;
- } else {
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
- }
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = tag[j];
+ buf[m++] = type[j];
+ buf[m++] = mask[j];
+ buf[m++] = vfrac[j];
+ buf[m++] = s0[j];
+ buf[m++] = x0[j][0];
+ buf[m++] = x0[j][1];
+ buf[m++] = x0[j][2];
+ if (mask[i] & deform_groupbit) {
+ buf[m++] = v[j][0] + dvx;
+ buf[m++] = v[j][1] + dvy;
+ buf[m++] = v[j][2] + dvz;
+ } else {
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
+ }
}
}
}
@@ -533,7 +533,7 @@ void AtomVecPeri::unpack_border_vel(int n, int first, double *buf)
}
/* ---------------------------------------------------------------------- */
-
+
int AtomVecPeri::unpack_border_hybrid(int n, int first, double *buf)
{
int i,m,last;
@@ -577,7 +577,7 @@ int AtomVecPeri::pack_exchange(int i, double *buf)
buf[m++] = x0[i][2];
if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]);
buf[0] = m;
@@ -611,9 +611,9 @@ int AtomVecPeri::unpack_exchange(double *buf)
x0[nlocal][2] = buf[m++];
if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->
- unpack_exchange(nlocal,&buf[m]);
+ unpack_exchange(nlocal,&buf[m]);
atom->nlocal++;
return m;
@@ -624,19 +624,19 @@ int AtomVecPeri::unpack_exchange(double *buf)
size of restart data for all atoms owned by this proc
include extra data stored by fixes
------------------------------------------------------------------------- */
-
+
int AtomVecPeri::size_restart()
{
int i;
-
+
int nlocal = atom->nlocal;
int n = 17 * nlocal;
-
+
if (atom->nextra_restart)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
for (i = 0; i < nlocal; i++)
n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
-
+
return n;
}
@@ -645,7 +645,7 @@ int AtomVecPeri::size_restart()
xyz must be 1st 3 values, so that read_restart can test on them
molecular types may be negative, but write as positive
------------------------------------------------------------------------- */
-
+
int AtomVecPeri::pack_restart(int i, double *buf)
{
int m = 1;
@@ -659,18 +659,18 @@ int AtomVecPeri::pack_restart(int i, double *buf)
buf[m++] = v[i][0];
buf[m++] = v[i][1];
buf[m++] = v[i][2];
-
+
buf[m++] = vfrac[i];
buf[m++] = rmass[i];
buf[m++] = s0[i];
buf[m++] = x0[i][0];
buf[m++] = x0[i][1];
buf[m++] = x0[i][2];
-
+
if (atom->nextra_restart)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]);
-
+
buf[0] = m;
return m;
}
@@ -678,7 +678,7 @@ int AtomVecPeri::pack_restart(int i, double *buf)
/* ----------------------------------------------------------------------
unpack data for one atom from restart file including extra quantities
------------------------------------------------------------------------- */
-
+
int AtomVecPeri::unpack_restart(double *buf)
{
int nlocal = atom->nlocal;
@@ -687,7 +687,7 @@ int AtomVecPeri::unpack_restart(double *buf)
if (atom->nextra_store)
memory->grow(atom->extra,nmax,atom->nextra_store,"atom:extra");
}
-
+
int m = 1;
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
@@ -699,20 +699,20 @@ int AtomVecPeri::unpack_restart(double *buf)
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
-
+
vfrac[nlocal] = buf[m++];
rmass[nlocal] = buf[m++];
s0[nlocal] = buf[m++];
x0[nlocal][0] = buf[m++];
x0[nlocal][1] = buf[m++];
x0[nlocal][2] = buf[m++];
-
+
double **extra = atom->extra;
if (atom->nextra_store) {
int size = static_cast<int> (buf[0]) - m;
for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++];
}
-
+
atom->nlocal++;
return m;
}
@@ -721,12 +721,12 @@ int AtomVecPeri::unpack_restart(double *buf)
create one atom of itype at coord
set other values to defaults
------------------------------------------------------------------------- */
-
+
void AtomVecPeri::create_atom(int itype, double *coord)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
-
+
tag[nlocal] = 0;
type[nlocal] = itype;
x[nlocal][0] = coord[0];
@@ -737,14 +737,14 @@ void AtomVecPeri::create_atom(int itype, double *coord)
v[nlocal][0] = 0.0;
v[nlocal][1] = 0.0;
v[nlocal][2] = 0.0;
-
+
vfrac[nlocal] = 1.0;
rmass[nlocal] = 1.0;
s0[nlocal] = DBL_MAX;
x0[nlocal][0] = coord[0];
x0[nlocal][1] = coord[1];
x0[nlocal][2] = coord[2];
-
+
atom->nlocal++;
}
@@ -752,7 +752,7 @@ void AtomVecPeri::create_atom(int itype, double *coord)
unpack one line from Atoms section of data file
initialize other atom quantities
------------------------------------------------------------------------- */
-
+
void AtomVecPeri::data_atom(double *coord, int imagetmp, char **values)
{
int nlocal = atom->nlocal;
@@ -761,7 +761,7 @@ void AtomVecPeri::data_atom(double *coord, int imagetmp, char **values)
tag[nlocal] = atoi(values[0]);
if (tag[nlocal] <= 0)
error->one(FLERR,"Invalid atom ID in Atoms section of data file");
-
+
type[nlocal] = atoi(values[1]);
if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
error->one(FLERR,"Invalid atom type in Atoms section of data file");
@@ -775,7 +775,7 @@ void AtomVecPeri::data_atom(double *coord, int imagetmp, char **values)
x[nlocal][2] = coord[2];
image[nlocal] = imagetmp;
-
+
mask[nlocal] = 1;
v[nlocal][0] = 0.0;
v[nlocal][1] = 0.0;
@@ -785,16 +785,16 @@ void AtomVecPeri::data_atom(double *coord, int imagetmp, char **values)
x0[nlocal][0] = coord[0];
x0[nlocal][1] = coord[1];
x0[nlocal][2] = coord[2];
-
+
atom->nlocal++;
}
-
+
/* ----------------------------------------------------------------------
unpack hybrid quantities from one line in Atoms section of data file
initialize other atom quantities for this sub-style
------------------------------------------------------------------------- */
-
+
int AtomVecPeri::data_atom_hybrid(int nlocal, char **values)
{
vfrac[nlocal] = atof(values[0]);
@@ -805,14 +805,14 @@ int AtomVecPeri::data_atom_hybrid(int nlocal, char **values)
x0[nlocal][0] = x[nlocal][0];
x0[nlocal][1] = x[nlocal][1];
x0[nlocal][2] = x[nlocal][2];
-
+
return 2;
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
------------------------------------------------------------------------- */
-
+
bigint AtomVecPeri::memory_usage()
{
bigint bytes = 0;
@@ -829,6 +829,6 @@ bigint AtomVecPeri::memory_usage()
if (atom->memcheck("rmass")) bytes += memory->usage(rmass,nmax);
if (atom->memcheck("s0")) bytes += memory->usage(s0,nmax);
if (atom->memcheck("x0")) bytes += memory->usage(x0,nmax,3);
-
+
return bytes;
}
diff --git a/src/PERI/atom_vec_peri.h b/src/PERI/atom_vec_peri.h
index 6b5c59511a86e15d3fee8fdc87de4d3dd447e7f1..b7479414de6226bd2276ee805b81ffdf96a85e64 100755
--- a/src/PERI/atom_vec_peri.h
+++ b/src/PERI/atom_vec_peri.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/PERI/compute_damage_atom.cpp b/src/PERI/compute_damage_atom.cpp
index 92407985c81f2dc1d1df8a8b2933f380c983cb71..bd8228faf516c07c4e54e3a46c12554284bb732a 100644
--- a/src/PERI/compute_damage_atom.cpp
+++ b/src/PERI/compute_damage_atom.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -110,8 +110,8 @@ void ComputeDamageAtom::compute_peratom()
j = atom->map(partner[i][jj]);
if (j < 0) continue;
- damage_temp += vfrac[j];
- }
+ damage_temp += vfrac[j];
+ }
}
else damage_temp = vinter[i];
diff --git a/src/PERI/compute_damage_atom.h b/src/PERI/compute_damage_atom.h
index a09272faf4434d16509203476fb9b73bbdcf8888..cafff63798c61434a05c0022cacaf960e3d20ff1 100644
--- a/src/PERI/compute_damage_atom.h
+++ b/src/PERI/compute_damage_atom.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/PERI/fix_peri_neigh.cpp b/src/PERI/fix_peri_neigh.cpp
index 5a504b7330604f6bf0c3d714109cc29648ad7c09..12e7a2b47b30e5d9110f831c19cf5afb9a9bb7e6 100644
--- a/src/PERI/fix_peri_neigh.cpp
+++ b/src/PERI/fix_peri_neigh.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -37,7 +37,7 @@ using namespace FixConst;
/* ---------------------------------------------------------------------- */
-FixPeriNeigh::FixPeriNeigh(LAMMPS *lmp,int narg, char **arg) :
+FixPeriNeigh::FixPeriNeigh(LAMMPS *lmp,int narg, char **arg) :
Fix(lmp, narg, arg)
{
restart_global = 1;
@@ -106,25 +106,25 @@ void FixPeriNeigh::init()
int irequest = neighbor->request((void *) this);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->fix = 1;
- neighbor->requests[irequest]->half = 0;
+ neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->occasional = 1;
}
/* ---------------------------------------------------------------------- */
-
+
void FixPeriNeigh::init_list(int id, NeighList *ptr)
{
list = ptr;
}
-/* ----------------------------------------------------------------------
- For minimization: setup as with dynamics
+/* ----------------------------------------------------------------------
+ For minimization: setup as with dynamics
------------------------------------------------------------------------- */
void FixPeriNeigh::min_setup(int vflag)
{
- setup(vflag);
+ setup(vflag);
}
/* ----------------------------------------------------------------------
@@ -241,7 +241,7 @@ void FixPeriNeigh::setup(int vflag)
}
// sanity check: does any atom appear twice in any neigborlist?
- // should only be possible if using pbc and domain < 2*delta
+ // should only be possible if using pbc and domain < 2*delta
if (domain->xperiodic || domain->yperiodic || domain->zperiodic) {
for (i = 0; i < nlocal; i++) {
@@ -249,8 +249,8 @@ void FixPeriNeigh::setup(int vflag)
for (jj = 0; jj < jnum; jj++) {
for (int kk = jj+1; kk < jnum; kk++) {
if (partner[i][jj] == partner[i][kk])
- error->one(FLERR,"Duplicate particle in PeriDynamic bond - "
- "simulation box is too small");
+ error->one(FLERR,"Duplicate particle in PeriDynamic bond - "
+ "simulation box is too small");
}
}
}
@@ -304,8 +304,8 @@ void FixPeriNeigh::setup(int vflag)
if (pairpmb != NULL) // define influence function to be 1.0
wvolume[i] += 1.0 * rsq0 * vfrac[j] * vfrac_scale;
else if (pairlps != NULL) // call the PairPeriLPS influence function
- wvolume[i] += pairlps->influence_function(delx0,dely0,delz0) *
- rsq0 * vfrac[j] * vfrac_scale;
+ wvolume[i] += pairlps->influence_function(delx0,dely0,delz0) *
+ rsq0 * vfrac[j] * vfrac_scale;
}
}
diff --git a/src/PERI/fix_peri_neigh.h b/src/PERI/fix_peri_neigh.h
index 19fda12d6ae11063edd4de61ef083608669607b1..e5715aa0a68fd67d6eaea4415e30e5320b506319 100644
--- a/src/PERI/fix_peri_neigh.h
+++ b/src/PERI/fix_peri_neigh.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/PERI/pair_peri_lps.cpp b/src/PERI/pair_peri_lps.cpp
index 10002f8d45735ffb229f92fc1002b2806862434a..70d3530c6b356774c1c329d8cd53161e7542b895 100644
--- a/src/PERI/pair_peri_lps.cpp
+++ b/src/PERI/pair_peri_lps.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -18,7 +18,7 @@
#include "math.h"
#include "stdlib.h"
#include "string.h"
-#include "pair_peri_lps.h"
+#include "pair_peri_lps.h"
#include "atom.h"
#include "domain.h"
#include "lattice.h"
@@ -32,13 +32,13 @@
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
-#include "update.h"
+#include "update.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-PairPeriLPS::PairPeriLPS(LAMMPS *lmp) : Pair(lmp)
+PairPeriLPS::PairPeriLPS(LAMMPS *lmp) : Pair(lmp)
{
for (int i = 0; i < 6; i++) virial[i] = 0.0;
no_virial_fdotr_compute = 1;
@@ -47,11 +47,11 @@ PairPeriLPS::PairPeriLPS(LAMMPS *lmp) : Pair(lmp)
nmax = 0;
s0_new = NULL;
- theta = NULL;
+ theta = NULL;
- bulkmodulus = NULL;
- shearmodulus = NULL;
- s00 = alpha = NULL;
+ bulkmodulus = NULL;
+ shearmodulus = NULL;
+ s00 = alpha = NULL;
cut = NULL;
// set comm size needed by this Pair
@@ -62,33 +62,33 @@ PairPeriLPS::PairPeriLPS(LAMMPS *lmp) : Pair(lmp)
/* ---------------------------------------------------------------------- */
-PairPeriLPS::~PairPeriLPS()
+PairPeriLPS::~PairPeriLPS()
{
if (ifix_peri >= 0) modify->delete_fix("PERI_NEIGH");
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
- memory->destroy(bulkmodulus);
- memory->destroy(shearmodulus);
- memory->destroy(s00);
- memory->destroy(alpha);
+ memory->destroy(bulkmodulus);
+ memory->destroy(shearmodulus);
+ memory->destroy(s00);
+ memory->destroy(alpha);
memory->destroy(cut);
- memory->destroy(theta);
- memory->destroy(s0_new);
+ memory->destroy(theta);
+ memory->destroy(s0_new);
}
}
/* ---------------------------------------------------------------------- */
-void PairPeriLPS::compute(int eflag, int vflag)
+void PairPeriLPS::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz;
double xtmp0,ytmp0,ztmp0,delx0,dely0,delz0,rsq0;
double rsq,r,dr,rk,evdwl,fpair,fbond;
int *ilist,*jlist,*numneigh,**firstneigh;
- double d_ij,delta,stretch;
+ double d_ij,delta,stretch;
evdwl = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
@@ -142,7 +142,7 @@ void PairPeriLPS::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
-
+
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
@@ -154,7 +154,7 @@ void PairPeriLPS::compute(int eflag, int vflag)
if (periodic) domain->minimum_image(delx0,dely0,delz0);
rsq0 = delx0*delx0 + dely0*dely0 + delz0*delz0;
jtype = type[j];
-
+
r = sqrt(rsq);
// short-range interaction distance based on initial particle position
@@ -170,10 +170,10 @@ void PairPeriLPS::compute(int eflag, int vflag)
dr = r - d_ij;
// kshort based upon short-range force constant
- // of the bond-based theory used in PMB model
+ // of the bond-based theory used in PMB model
double kshort = (15.0 * 18.0 * bulkmodulus[itype][itype]) /
- (3.141592653589793 * cutsq[itype][jtype] * cutsq[itype][jtype]);
+ (3.141592653589793 * cutsq[itype][jtype] * cutsq[itype][jtype]);
rk = (kshort * vfrac[j]) * (dr / cut[itype][jtype]);
if (r > 0.0) fpair = -(rk/r);
@@ -189,8 +189,8 @@ void PairPeriLPS::compute(int eflag, int vflag)
}
if (eflag) evdwl = 0.5*rk*dr;
- if (evflag) ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,
- fpair*vfrac[i],delx,dely,delz);
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,
+ fpair*vfrac[i],delx,dely,delz);
}
}
}
@@ -198,17 +198,17 @@ void PairPeriLPS::compute(int eflag, int vflag)
// grow bond forces array if necessary
if (atom->nmax > nmax) {
- memory->destroy(s0_new);
- memory->destroy(theta);
+ memory->destroy(s0_new);
+ memory->destroy(theta);
nmax = atom->nmax;
memory->create(s0_new,nmax,"pair:s0_new");
memory->create(theta,nmax,"pair:theta");
}
- // Compute the dilatation on each particle
- compute_dilatation();
+ // Compute the dilatation on each particle
+ compute_dilatation();
- // communicate dilatation (theta) of each particle
+ // communicate dilatation (theta) of each particle
comm->forward_comm_pair(this);
// communicate wighted volume (wvolume) upon every reneighbor
if (neighbor->ago == 0)
@@ -216,12 +216,12 @@ void PairPeriLPS::compute(int eflag, int vflag)
// Volume-dependent part of the energy
if (eflag) {
- for (i = 0; i < nlocal; i++) {
+ for (i = 0; i < nlocal; i++) {
itype = type[i];
if (eflag_global)
- eng_vdwl += 0.5 * bulkmodulus[itype][itype] * (theta[i] * theta[i]);
+ eng_vdwl += 0.5 * bulkmodulus[itype][itype] * (theta[i] * theta[i]);
if (eflag_atom)
- eatom[i] += 0.5 * bulkmodulus[itype][itype] * (theta[i] * theta[i]);
+ eatom[i] += 0.5 * bulkmodulus[itype][itype] * (theta[i] * theta[i]);
}
}
@@ -237,9 +237,9 @@ void PairPeriLPS::compute(int eflag, int vflag)
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
- xtmp0 = x0[i][0];
- ytmp0 = x0[i][1];
- ztmp0 = x0[i][2];
+ xtmp0 = x0[i][0];
+ ytmp0 = x0[i][1];
+ ztmp0 = x0[i][2];
itype = type[i];
jnum = npartner[i];
first = true;
@@ -262,10 +262,10 @@ void PairPeriLPS::compute(int eflag, int vflag)
delz = ztmp - x[j][2];
if (periodic) domain->minimum_image(delx,dely,delz);
rsq = delx*delx + dely*dely + delz*delz;
- delx0 = xtmp0 - x0[j][0];
- dely0 = ytmp0 - x0[j][1];
- delz0 = ztmp0 - x0[j][2];
- if (periodic) domain->minimum_image(delx0,dely0,delz0);
+ delx0 = xtmp0 - x0[j][0];
+ dely0 = ytmp0 - x0[j][1];
+ delz0 = ztmp0 - x0[j][2];
+ if (periodic) domain->minimum_image(delx0,dely0,delz0);
jtype = type[j];
delta = cut[itype][jtype];
r = sqrt(rsq);
@@ -278,18 +278,18 @@ void PairPeriLPS::compute(int eflag, int vflag)
// scale vfrac[j] if particle j near the horizon
if ((fabs(r0[i][jj] - delta)) <= half_lc)
- vfrac_scale = (-1.0/(2*half_lc))*(r0[i][jj]) +
- (1.0 + ((delta - half_lc)/(2*half_lc) ) );
+ vfrac_scale = (-1.0/(2*half_lc))*(r0[i][jj]) +
+ (1.0 + ((delta - half_lc)/(2*half_lc) ) );
else vfrac_scale = 1.0;
omega_plus = influence_function(-1.0*delx0,-1.0*dely0,-1.0*delz0);
omega_minus = influence_function(delx0,dely0,delz0);
- rk = ( (3.0 * bulkmodulus[itype][itype]) -
- (5.0 * shearmodulus[itype][itype]) ) * vfrac[j] * vfrac_scale *
- ( (omega_plus * theta[i] / wvolume[i]) +
- ( omega_minus * theta[j] / wvolume[j] ) ) * r0[i][jj];
+ rk = ( (3.0 * bulkmodulus[itype][itype]) -
+ (5.0 * shearmodulus[itype][itype]) ) * vfrac[j] * vfrac_scale *
+ ( (omega_plus * theta[i] / wvolume[i]) +
+ ( omega_minus * theta[j] / wvolume[j] ) ) * r0[i][jj];
rk += 15.0 * ( shearmodulus[itype][itype] * vfrac[j] * vfrac_scale ) *
- ( (omega_plus / wvolume[i]) + (omega_minus / wvolume[j]) ) * dr;
+ ( (omega_plus / wvolume[i]) + (omega_minus / wvolume[j]) ) * dr;
if (r > 0.0) fbond = -(rk/r);
else fbond = 0.0;
@@ -298,14 +298,14 @@ void PairPeriLPS::compute(int eflag, int vflag)
f[i][1] += dely*fbond;
f[i][2] += delz*fbond;
- // since I-J is double counted, set newton off & use 1/2 factor and I,I
+ // since I-J is double counted, set newton off & use 1/2 factor and I,I
double deviatoric_extension = dr - (theta[i]* r0[i][jj] / 3.0);
- if (eflag) evdwl = 0.5 * 15 * (shearmodulus[itype][itype]/wvolume[i]) *
- omega_plus*(deviatoric_extension * deviatoric_extension) *
- vfrac[j] * vfrac_scale;
+ if (eflag) evdwl = 0.5 * 15 * (shearmodulus[itype][itype]/wvolume[i]) *
+ omega_plus*(deviatoric_extension * deviatoric_extension) *
+ vfrac[j] * vfrac_scale;
if (evflag) ev_tally(i,i,nlocal,0,0.5*evdwl,0.0,
- 0.5*fbond*vfrac[i],delx,dely,delz);
+ 0.5*fbond*vfrac[i],delx,dely,delz);
// find stretch in bond I-J and break if necessary
// use s0 from previous timestep
@@ -318,8 +318,8 @@ void PairPeriLPS::compute(int eflag, int vflag)
if (first)
s0_new[i] = s00[itype][jtype] - (alpha[itype][jtype] * stretch);
else
- s0_new[i] = MAX(s0_new[i],s00[itype][jtype] -
- (alpha[itype][jtype] * stretch));
+ s0_new[i] = MAX(s0_new[i],s00[itype][jtype] -
+ (alpha[itype][jtype] * stretch));
first = false;
}
@@ -334,7 +334,7 @@ void PairPeriLPS::compute(int eflag, int vflag)
allocate all arrays
------------------------------------------------------------------------- */
-void PairPeriLPS::allocate()
+void PairPeriLPS::allocate()
{
allocated = 1;
int n = atom->ntypes;
@@ -347,8 +347,8 @@ void PairPeriLPS::allocate()
memory->create(cutsq,n+1,n+1,"pair:cutsq");
memory->create(bulkmodulus,n+1,n+1,"pair:bulkmodulus");
memory->create(shearmodulus,n+1,n+1,"pair:shearmodulus");
- memory->create(s00,n+1,n+1,"pair:s00");
- memory->create(alpha,n+1,n+1,"pair:alpha");
+ memory->create(s00,n+1,n+1,"pair:s00");
+ memory->create(alpha,n+1,n+1,"pair:alpha");
memory->create(cut,n+1,n+1,"pair:cut");
}
@@ -356,7 +356,7 @@ void PairPeriLPS::allocate()
global settings
------------------------------------------------------------------------- */
-void PairPeriLPS::settings(int narg, char **arg)
+void PairPeriLPS::settings(int narg, char **arg)
{
if (narg) error->all(FLERR,"Illegal pair_style command");
}
@@ -365,9 +365,9 @@ void PairPeriLPS::settings(int narg, char **arg)
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
-void PairPeriLPS::coeff(int narg, char **arg)
+void PairPeriLPS::coeff(int narg, char **arg)
{
- if (narg != 7) error->all(FLERR,"Incorrect args for pair coefficients");
+ if (narg != 7) error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
int ilo,ihi,jlo,jhi;
@@ -383,8 +383,8 @@ void PairPeriLPS::coeff(int narg, char **arg)
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
- bulkmodulus[i][j] = bulkmodulus_one;
- shearmodulus[i][j] = shearmodulus_one;
+ bulkmodulus[i][j] = bulkmodulus_one;
+ shearmodulus[i][j] = shearmodulus_one;
cut[i][j] = cut_one;
s00[i][j] = s00_one;
alpha[i][j] = alpha_one;
@@ -400,7 +400,7 @@ void PairPeriLPS::coeff(int narg, char **arg)
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
-double PairPeriLPS::init_one(int i, int j)
+double PairPeriLPS::init_one(int i, int j)
{
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
@@ -417,18 +417,18 @@ double PairPeriLPS::init_one(int i, int j)
init specific to this pair style
------------------------------------------------------------------------- */
-void PairPeriLPS::init_style()
+void PairPeriLPS::init_style()
{
// error checks
if (!atom->peri_flag) error->all(FLERR,"Pair style peri requires atom style peri");
- if (atom->map_style == 0)
+ if (atom->map_style == 0)
error->all(FLERR,"Pair peri requires an atom map, see atom_modify");
if (domain->lattice == NULL)
error->all(FLERR,"Pair peri requires a lattice be defined");
- if (domain->lattice->xlattice != domain->lattice->ylattice ||
- domain->lattice->xlattice != domain->lattice->zlattice ||
+ if (domain->lattice->xlattice != domain->lattice->ylattice ||
+ domain->lattice->xlattice != domain->lattice->zlattice ||
domain->lattice->ylattice != domain->lattice->zlattice)
error->all(FLERR,"Pair peri lattice is not identical in x, y, and z");
@@ -457,18 +457,18 @@ void PairPeriLPS::init_style()
proc 0 writes to restart file
------------------------------------------------------------------------- */
-void PairPeriLPS::write_restart(FILE *fp)
+void PairPeriLPS::write_restart(FILE *fp)
{
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
- fwrite(&bulkmodulus[i][j],sizeof(double),1,fp);
- fwrite(&shearmodulus[i][j],sizeof(double),1,fp);
- fwrite(&s00[i][j],sizeof(double),1,fp);
- fwrite(&alpha[i][j],sizeof(double),1,fp);
- fwrite(&cut[i][j],sizeof(double),1,fp);
+ fwrite(&bulkmodulus[i][j],sizeof(double),1,fp);
+ fwrite(&shearmodulus[i][j],sizeof(double),1,fp);
+ fwrite(&s00[i][j],sizeof(double),1,fp);
+ fwrite(&alpha[i][j],sizeof(double),1,fp);
+ fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
@@ -477,7 +477,7 @@ void PairPeriLPS::write_restart(FILE *fp)
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
-void PairPeriLPS::read_restart(FILE *fp)
+void PairPeriLPS::read_restart(FILE *fp)
{
allocate();
@@ -488,18 +488,18 @@ void PairPeriLPS::read_restart(FILE *fp)
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
- if (me == 0) {
- fread(&bulkmodulus[i][j],sizeof(double),1,fp);
- fread(&shearmodulus[i][j],sizeof(double),1,fp);
- fread(&s00[i][j],sizeof(double),1,fp);
- fread(&alpha[i][j],sizeof(double),1,fp);
- fread(&cut[i][j],sizeof(double),1,fp);
- }
- MPI_Bcast(&bulkmodulus[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&shearmodulus[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&s00[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&alpha[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
+ if (me == 0) {
+ fread(&bulkmodulus[i][j],sizeof(double),1,fp);
+ fread(&shearmodulus[i][j],sizeof(double),1,fp);
+ fread(&s00[i][j],sizeof(double),1,fp);
+ fread(&alpha[i][j],sizeof(double),1,fp);
+ fread(&cut[i][j],sizeof(double),1,fp);
+ }
+ MPI_Bcast(&bulkmodulus[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&shearmodulus[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&s00[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&alpha[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
@@ -507,8 +507,8 @@ void PairPeriLPS::read_restart(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairPeriLPS::single(int i, int j, int itype, int jtype,
- double rsq, double factor_coul, double factor_lj,
- double &fforce)
+ double rsq, double factor_coul, double factor_lj,
+ double &fforce)
{
double delx0,dely0,delz0,rsq0;
double d_ij,r,dr,rk,vfrac_scale;
@@ -523,8 +523,8 @@ double PairPeriLPS::single(int i, int j, int itype, int jtype,
double lc = domain->lattice->xlattice;
double half_lc = 0.5*lc;
- double kshort;
-
+ double kshort;
+
delx0 = x0[i][0] - x0[j][0];
dely0 = x0[i][1] - x0[j][1];
delz0 = x0[i][2] - x0[j][2];
@@ -545,17 +545,17 @@ double PairPeriLPS::single(int i, int j, int itype, int jtype,
( 3.141592653589793 * cutsq[itype][jtype] * cutsq[itype][jtype]);
rk = ( kshort * vfrac[j]) * (dr / sqrt(cutsq[itype][jtype]));
if (r > 0.0) fforce += -(rk/r);
- energy += 0.5*rk*dr;
+ energy += 0.5*rk*dr;
}
-
+
if (atom->nmax > nmax) {
memory->destroy(theta);
nmax = atom->nmax;
memory->create(theta,nmax,"pair:theta");
}
- // Compute the dilatation on each particle
- compute_dilatation();
+ // Compute the dilatation on each particle
+ compute_dilatation();
// communicate dilatation (theta) of each particle
comm->forward_comm_pair(this);
@@ -563,7 +563,7 @@ double PairPeriLPS::single(int i, int j, int itype, int jtype,
if (neighbor->ago == 0)
comm->forward_comm_fix(modify->fix[ifix_peri]);
- double omega_plus, omega_minus;
+ double omega_plus, omega_minus;
int jnum = npartner[i];
for (int jj = 0; jj < jnum; jj++) {
@@ -576,23 +576,23 @@ double PairPeriLPS::single(int i, int j, int itype, int jtype,
// scale vfrac[j] if particle j near the horizon
if ( (fabs(r0[i][jj] - sqrt(cutsq[itype][jtype]))) <= half_lc)
- vfrac_scale = (-1.0/(2*half_lc))*(r0[i][jj]) +
- (1.0 + ((sqrt(cutsq[itype][jtype]) - half_lc)/(2*half_lc)));
+ vfrac_scale = (-1.0/(2*half_lc))*(r0[i][jj]) +
+ (1.0 + ((sqrt(cutsq[itype][jtype]) - half_lc)/(2*half_lc)));
else vfrac_scale = 1.0;
omega_plus = influence_function(-1.0*delx0,-1.0*dely0,-1.0*delz0);
- omega_minus = influence_function(delx0,dely0,delz0);
+ omega_minus = influence_function(delx0,dely0,delz0);
rk = (3.0* bulkmodulus[itype][itype] -5.0 * shearmodulus[itype][itype]) *
- vfrac[j] * vfrac_scale * ( (omega_plus * theta[i] / wvolume[i]) +
- (omega_minus * theta[j] / wvolume[j])) *
- r0[i][jj];
- rk += 15.0 * ( shearmodulus[itype][itype] * vfrac[j] * vfrac_scale ) *
- ( (omega_plus / wvolume[i]) + (omega_minus / wvolume[j]) ) * dr;
+ vfrac[j] * vfrac_scale * ( (omega_plus * theta[i] / wvolume[i]) +
+ (omega_minus * theta[j] / wvolume[j])) *
+ r0[i][jj];
+ rk += 15.0 * ( shearmodulus[itype][itype] * vfrac[j] * vfrac_scale ) *
+ ( (omega_plus / wvolume[i]) + (omega_minus / wvolume[j]) ) * dr;
if (r > 0.0) fforce += -(rk/r);
- energy += 0.5 * 15 * (shearmodulus[itype][itype]/wvolume[i]) *
- omega_plus * ( dr - theta[i]* r0[i][jj] / 3.0 ) *
- ( dr - theta[i]* r0[i][jj] / 3.0 ) * vfrac[j] * vfrac_scale;
+ energy += 0.5 * 15 * (shearmodulus[itype][itype]/wvolume[i]) *
+ omega_plus * ( dr - theta[i]* r0[i][jj] / 3.0 ) *
+ ( dr - theta[i]* r0[i][jj] / 3.0 ) * vfrac[j] * vfrac_scale;
}
}
@@ -601,7 +601,7 @@ double PairPeriLPS::single(int i, int j, int itype, int jtype,
}
/* ----------------------------------------------------------------------
- memory usage of local atom-based arrays
+ memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double PairPeriLPS::memory_usage()
@@ -641,7 +641,7 @@ void PairPeriLPS::compute_dilatation()
int nlocal = atom->nlocal;
double *vfrac = atom->vfrac;
double vfrac_scale = 1.0;
-
+
double lc = domain->lattice->xlattice;
double half_lc = 0.5*lc;
@@ -702,12 +702,12 @@ void PairPeriLPS::compute_dilatation()
else vfrac_scale = 1.0;
theta[i] += influence_function(delx0, dely0, delz0) * r0[i][jj] * dr *
- vfrac[j] * vfrac_scale;
+ vfrac[j] * vfrac_scale;
}
// if wvolume[i] is zero, then particle i has no bonds
- // therefore, the dilatation is set to
+ // therefore, the dilatation is set to
if (wvolume[i] != 0.0) theta[i] = (3.0/wvolume[i]) * theta[i];
else theta[i] = 0;
@@ -717,13 +717,13 @@ void PairPeriLPS::compute_dilatation()
/* ----------------------------------------------------------------------
communication routines
---------------------------------------------------------------------- */
-
+
int PairPeriLPS::pack_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
-
+
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
@@ -731,18 +731,16 @@ int PairPeriLPS::pack_comm(int n, int *list, double *buf,
}
return 1;
}
-
+
/* ---------------------------------------------------------------------- */
-
+
void PairPeriLPS::unpack_comm(int n, int first, double *buf)
{
int i,m,last;
-
+
m = 0;
last = first + n;
for (i = first; i < last; i++) {
theta[i] = buf[m++];
}
}
-
-
diff --git a/src/PERI/pair_peri_lps.h b/src/PERI/pair_peri_lps.h
index aa2ab23c3b6486dc724b0dd061d27c3190985056..e6cfee15f509f731ee5b461bff2ab42f4527b1d6 100644
--- a/src/PERI/pair_peri_lps.h
+++ b/src/PERI/pair_peri_lps.h
@@ -5,31 +5,31 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#ifdef PAIR_CLASS
+#ifdef PAIR_CLASS
-PairStyle(peri/lps,PairPeriLPS)
+PairStyle(peri/lps,PairPeriLPS)
-#else
+#else
-#ifndef LMP_PAIR_PERI_LPS_H
-#define LMP_PAIR_PERI_LPS_H
+#ifndef LMP_PAIR_PERI_LPS_H
+#define LMP_PAIR_PERI_LPS_H
#include "pair.h"
namespace LAMMPS_NS {
-class PairPeriLPS : public Pair {
+class PairPeriLPS : public Pair {
public:
- PairPeriLPS(class LAMMPS *);
- virtual ~PairPeriLPS();
- int pack_comm(int, int *, double *, int, int *);
- void unpack_comm(int, int, double *);
+ PairPeriLPS(class LAMMPS *);
+ virtual ~PairPeriLPS();
+ int pack_comm(int, int *, double *, int, int *);
+ void unpack_comm(int, int, double *);
virtual void compute(int, int);
void settings(int, char **);
@@ -43,17 +43,17 @@ class PairPeriLPS : public Pair {
double single(int, int, int, int, double, double, double, double &);
double memory_usage();
double influence_function(double, double, double);
- void compute_dilatation();
+ void compute_dilatation();
protected:
int ifix_peri;
- double **bulkmodulus;
- double **shearmodulus;
- double **s00, **alpha;
+ double **bulkmodulus;
+ double **shearmodulus;
+ double **s00, **alpha;
double **cut;
-
- double *s0_new;
- double *theta;
+
+ double *s0_new;
+ double *theta;
int nmax;
void allocate();
diff --git a/src/PERI/pair_peri_pmb.cpp b/src/PERI/pair_peri_pmb.cpp
index 2d0ae40725e9102696c05c03818eb1c41fea8854..a4623f2517abf0a97eb9019ff466ab1a250a0b14 100644
--- a/src/PERI/pair_peri_pmb.cpp
+++ b/src/PERI/pair_peri_pmb.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -134,7 +134,7 @@ void PairPeriPMB::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
-
+
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
@@ -145,7 +145,7 @@ void PairPeriPMB::compute(int eflag, int vflag)
if (periodic) domain->minimum_image(delx0,dely0,delz0);
rsq0 = delx0*delx0 + dely0*dely0 + delz0*delz0;
jtype = type[j];
-
+
r = sqrt(rsq);
// short-range interaction distance based on initial particle position
@@ -160,8 +160,8 @@ void PairPeriPMB::compute(int eflag, int vflag)
if (r < d_ij) {
dr = r - d_ij;
- rk = (15.0 * kspring[itype][jtype] * vfrac[j]) *
- (dr / cut[itype][jtype]);
+ rk = (15.0 * kspring[itype][jtype] * vfrac[j]) *
+ (dr / cut[itype][jtype]);
if (r > 0.0) fpair = -(rk/r);
else fpair = 0.0;
@@ -175,7 +175,7 @@ void PairPeriPMB::compute(int eflag, int vflag)
}
if (eflag) evdwl = 0.5*rk*dr;
- if (evflag) ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair*vfrac[i],delx,dely,delz);
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair*vfrac[i],delx,dely,delz);
}
}
}
@@ -234,8 +234,8 @@ void PairPeriPMB::compute(int eflag, int vflag)
// scale vfrac[j] if particle j near the horizon
if ((fabs(r0[i][jj] - delta)) <= half_lc)
- vfrac_scale = (-1.0/(2*half_lc))*(r0[i][jj]) +
- (1.0 + ((delta - half_lc)/(2*half_lc) ) );
+ vfrac_scale = (-1.0/(2*half_lc))*(r0[i][jj]) +
+ (1.0 + ((delta - half_lc)/(2*half_lc) ) );
else vfrac_scale = 1.0;
stretch = dr / r0[i][jj];
@@ -247,7 +247,7 @@ void PairPeriPMB::compute(int eflag, int vflag)
f[i][1] += dely*fbond;
f[i][2] += delz*fbond;
- // since I-J is double counted, set newton off & use 1/2 factor and I,I
+ // since I-J is double counted, set newton off & use 1/2 factor and I,I
if (eflag) evdwl = 0.5*rk*dr;
if (evflag) ev_tally(i,i,nlocal,0,0.5*evdwl,0.0,0.5*fbond*vfrac[i],delx,dely,delz);
@@ -268,7 +268,7 @@ void PairPeriPMB::compute(int eflag, int vflag)
}
// store new s0
- for (i = 0; i < nlocal; i++) s0[i] = s0_new[i];
+ for (i = 0; i < nlocal; i++) s0[i] = s0_new[i];
}
/* ----------------------------------------------------------------------
@@ -359,13 +359,13 @@ void PairPeriPMB::init_style()
// error checks
if (!atom->peri_flag) error->all(FLERR,"Pair style peri requires atom style peri");
- if (atom->map_style == 0)
+ if (atom->map_style == 0)
error->all(FLERR,"Pair peri requires an atom map, see atom_modify");
if (domain->lattice == NULL)
error->all(FLERR,"Pair peri requires a lattice be defined");
- if (domain->lattice->xlattice != domain->lattice->ylattice ||
- domain->lattice->xlattice != domain->lattice->zlattice ||
+ if (domain->lattice->xlattice != domain->lattice->ylattice ||
+ domain->lattice->xlattice != domain->lattice->zlattice ||
domain->lattice->ylattice != domain->lattice->zlattice)
error->all(FLERR,"Pair peri lattice is not identical in x, y, and z");
@@ -401,10 +401,10 @@ void PairPeriPMB::write_restart(FILE *fp)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
- fwrite(&kspring[i][j],sizeof(double),1,fp);
- fwrite(&s00[i][j],sizeof(double),1,fp);
- fwrite(&alpha[i][j],sizeof(double),1,fp);
- fwrite(&cut[i][j],sizeof(double),1,fp);
+ fwrite(&kspring[i][j],sizeof(double),1,fp);
+ fwrite(&s00[i][j],sizeof(double),1,fp);
+ fwrite(&alpha[i][j],sizeof(double),1,fp);
+ fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
@@ -424,16 +424,16 @@ void PairPeriPMB::read_restart(FILE *fp)
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
- if (me == 0) {
- fread(&kspring[i][j],sizeof(double),1,fp);
- fread(&s00[i][j],sizeof(double),1,fp);
- fread(&alpha[i][j],sizeof(double),1,fp);
- fread(&cut[i][j],sizeof(double),1,fp);
- }
- MPI_Bcast(&kspring[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&s00[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&alpha[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
+ if (me == 0) {
+ fread(&kspring[i][j],sizeof(double),1,fp);
+ fread(&s00[i][j],sizeof(double),1,fp);
+ fread(&alpha[i][j],sizeof(double),1,fp);
+ fread(&cut[i][j],sizeof(double),1,fp);
+ }
+ MPI_Bcast(&kspring[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&s00[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&alpha[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
@@ -441,8 +441,8 @@ void PairPeriPMB::read_restart(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairPeriPMB::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
- double &fforce)
+ double factor_coul, double factor_lj,
+ double &fforce)
{
double delx0,dely0,delz0,rsq0;
double d_ij,r,dr,rk,vfrac_scale;
@@ -471,12 +471,12 @@ double PairPeriPMB::single(int i, int j, int itype, int jtype, double rsq,
if (r < d_ij) {
dr = r - d_ij;
- rk = (15.0 * kspring[itype][jtype] * vfrac[j]) *
+ rk = (15.0 * kspring[itype][jtype] * vfrac[j]) *
(dr / sqrt(cutsq[itype][jtype]));
if (r > 0.0) fforce += -(rk/r);
energy += 0.5*rk*dr;
}
-
+
int jnum = npartner[i];
for (int jj = 0; jj < jnum; jj++) {
if (partner[i][jj] == 0) continue;
@@ -485,11 +485,11 @@ double PairPeriPMB::single(int i, int j, int itype, int jtype, double rsq,
dr = r - r0[i][jj];
if (fabs(dr) < 2.2204e-016) dr = 0.0;
if ( (fabs(r0[i][jj] - sqrt(cutsq[itype][jtype]))) <= half_lc)
- vfrac_scale = (-1.0/(2*half_lc))*(r0[i][jj]) +
- (1.0 + ((sqrt(cutsq[itype][jtype]) - half_lc)/(2*half_lc)));
+ vfrac_scale = (-1.0/(2*half_lc))*(r0[i][jj]) +
+ (1.0 + ((sqrt(cutsq[itype][jtype]) - half_lc)/(2*half_lc)));
else vfrac_scale = 1.0;
- rk = (kspring[itype][jtype] * vfrac[j] * vfrac_scale) *
- (dr / r0[i][jj]);
+ rk = (kspring[itype][jtype] * vfrac[j] * vfrac_scale) *
+ (dr / r0[i][jj]);
if (r > 0.0) fforce += -(rk/r);
energy += 0.5*rk*dr;
}
@@ -499,7 +499,7 @@ double PairPeriPMB::single(int i, int j, int itype, int jtype, double rsq,
}
/* ----------------------------------------------------------------------
- memory usage of local atom-based arrays
+ memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double PairPeriPMB::memory_usage()
diff --git a/src/PERI/pair_peri_pmb.h b/src/PERI/pair_peri_pmb.h
index 3a53351070218db6a67452dff45fbddcaebe1ab6..81e78bb368593a773433b77d1bef81d503e86e61 100644
--- a/src/PERI/pair_peri_pmb.h
+++ b/src/PERI/pair_peri_pmb.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -45,7 +45,7 @@ class PairPeriPMB : public Pair {
double **kspring;
double **s00, **alpha;
double **cut;
-
+
double *s0_new;
int nmax;
diff --git a/src/POEMS/fix_poems.cpp b/src/POEMS/fix_poems.cpp
index c718f72c05e919c3b8e2e461567fcd3c7c61de2e..73330823df69ae5bd58f7e09e4b7ec2fa1a98414 100644
--- a/src/POEMS/fix_poems.cpp
+++ b/src/POEMS/fix_poems.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -100,23 +100,23 @@ FixPOEMS::FixPOEMS(LAMMPS *lmp, int narg, char **arg) :
int *igroups = new int[nbody];
for (ibody = 0; ibody < nbody; ibody++) {
igroups[ibody] = group->find(arg[ibody+4]);
- if (igroups[ibody] == -1)
- error->all(FLERR,"Could not find fix poems group ID");
+ if (igroups[ibody] == -1)
+ error->all(FLERR,"Could not find fix poems group ID");
}
int *mask = atom->mask;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit)
- for (ibody = 0; ibody < nbody; ibody++)
- if (mask[i] & group->bitmask[igroups[ibody]]) {
- if (natom2body[i] < MAXBODY) atom2body[i][natom2body[i]] = ibody;
- natom2body[i]++;
- }
+ for (ibody = 0; ibody < nbody; ibody++)
+ if (mask[i] & group->bitmask[igroups[ibody]]) {
+ if (natom2body[i] < MAXBODY) atom2body[i][natom2body[i]] = ibody;
+ natom2body[i]++;
+ }
}
delete [] igroups;
-
+
// file = read bodies from file
// file read doesn't pay attention to fix group,
// so after read, reset natom2body = 0 if atom is not in fix group
@@ -169,11 +169,11 @@ FixPOEMS::FixPOEMS(LAMMPS *lmp, int narg, char **arg) :
for (i = 0; i < nlocal; i++) {
natom2body[i] = 0;
if (mask[i] & groupbit) {
- natom2body[i] = 1;
- atom2body[i][0] = nall[molecule[i]];
+ natom2body[i] = 1;
+ atom2body[i][0] = nall[molecule[i]];
}
}
-
+
delete [] ncount;
delete [] nall;
@@ -208,11 +208,11 @@ FixPOEMS::FixPOEMS(LAMMPS *lmp, int narg, char **arg) :
memory->create(sum,nbody,6,"poems:sum");
memory->create(all,nbody,6,"poems:all");
-
+
// nrigid[n] = # of atoms in Nth rigid body
// double count joint atoms as being in multiple bodies
// error if one or zero atoms
-
+
int *ncount = new int[nbody];
for (ibody = 0; ibody < nbody; ibody++) ncount[ibody] = 0;
@@ -224,12 +224,12 @@ FixPOEMS::FixPOEMS(LAMMPS *lmp, int narg, char **arg) :
delete [] ncount;
for (ibody = 0; ibody < nbody; ibody++)
- if (nrigid[ibody] <= 1) error->all(FLERR,"One or zero atoms in rigid body");
+ if (nrigid[ibody] <= 1) error->all(FLERR,"One or zero atoms in rigid body");
// build list of joint connections and check for cycles and trees
jointbuild();
-
+
// delete temporary atom map
if (mapflag) {
@@ -237,23 +237,23 @@ FixPOEMS::FixPOEMS(LAMMPS *lmp, int narg, char **arg) :
atom->map_style = 0;
}
- // create POEMS instance
-
+ // create POEMS instance
+
poems = new Workspace;
-
+
// print statistics
int nsum = 0;
for (ibody = 0; ibody < nbody; ibody++) nsum += nrigid[ibody];
nsum -= njoint;
-
+
if (me == 0) {
if (screen)
fprintf(screen,"%d clusters, %d bodies, %d joints, %d atoms\n",
- ncluster,nbody,njoint,nsum);
+ ncluster,nbody,njoint,nsum);
if (logfile)
fprintf(logfile,"%d clusters, %d bodies, %d joints, %d atoms\n",
- ncluster,nbody,njoint,nsum);
+ ncluster,nbody,njoint,nsum);
}
}
@@ -314,7 +314,7 @@ int FixPOEMS::setmask()
mask |= POST_FORCE;
mask |= INITIAL_INTEGRATE_RESPA;
mask |= FINAL_INTEGRATE_RESPA;
- mask |= POST_FORCE_RESPA;
+ mask |= POST_FORCE_RESPA;
return mask;
}
@@ -340,13 +340,13 @@ void FixPOEMS::init()
if (i < modify->nfix) {
for (int j = i; j < modify->nfix; j++)
if (strcmp(modify->fix[j]->style,"poems") == 0)
- error->all(FLERR,"POEMS fix must come before NPT/NPH fix");
+ error->all(FLERR,"POEMS fix must come before NPT/NPH fix");
}
// timestep info
- dtv = update->dt;
- dtf = 0.5 * update->dt * force->ftm2v;
+ dtv = update->dt;
+ dtf = 0.5 * update->dt * force->ftm2v;
dthalf = 0.5 * update->dt;
// rRESPA info
@@ -382,13 +382,13 @@ void FixPOEMS::init()
xbox = (image[i] & 1023) - 512;
ybox = (image[i] >> 10 & 1023) - 512;
zbox = (image[i] >> 20) - 512;
- massone = mass[type[i]];
+ massone = mass[type[i]];
sum[ibody][0] += (x[i][0] + xbox*xprd) * massone;
sum[ibody][1] += (x[i][1] + ybox*yprd) * massone;
sum[ibody][2] += (x[i][2] + zbox*zprd) * massone;
sum[ibody][3] += massone;
sum[ibody][4] += massone *
- (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]);
+ (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]);
}
}
@@ -423,7 +423,7 @@ void FixPOEMS::init()
dy = x[i][1] + ybox*yprd - xcm[ibody][1];
dz = x[i][2] + zbox*zprd - xcm[ibody][2];
massone = mass[type[i]];
-
+
sum[ibody][0] += massone * (dy*dy + dz*dz);
sum[ibody][1] += massone * (dx*dx + dz*dz);
sum[ibody][2] += massone * (dx*dx + dy*dy);
@@ -452,46 +452,46 @@ void FixPOEMS::init()
tensor[0][1] = tensor[1][0] = all[ibody][3];
tensor[1][2] = tensor[2][1] = all[ibody][4];
tensor[0][2] = tensor[2][0] = all[ibody][5];
-
+
ierror = jacobi(tensor,inertia[ibody],evectors);
if (ierror) error->all(FLERR,"Insufficient Jacobi rotations for POEMS body");
ex_space[ibody][0] = evectors[0][0];
ex_space[ibody][1] = evectors[1][0];
ex_space[ibody][2] = evectors[2][0];
-
+
ey_space[ibody][0] = evectors[0][1];
ey_space[ibody][1] = evectors[1][1];
ey_space[ibody][2] = evectors[2][1];
-
+
ez_space[ibody][0] = evectors[0][2];
ez_space[ibody][1] = evectors[1][2];
ez_space[ibody][2] = evectors[2][2];
-
+
// if any principal moment < scaled EPSILON, error
// this is b/c POEMS cannot yet handle degenerate bodies
-
+
double max;
max = MAX(inertia[ibody][0],inertia[ibody][1]);
max = MAX(max,inertia[ibody][2]);
-
+
if (inertia[ibody][0] < EPSILON*max ||
- inertia[ibody][1] < EPSILON*max ||
- inertia[ibody][2] < EPSILON*max)
+ inertia[ibody][1] < EPSILON*max ||
+ inertia[ibody][2] < EPSILON*max)
error->all(FLERR,"Rigid body has degenerate moment of inertia");
// enforce 3 evectors as a right-handed coordinate system
// flip 3rd evector if needed
-
+
ez0 = ex_space[ibody][1]*ey_space[ibody][2] -
ex_space[ibody][2]*ey_space[ibody][1];
ez1 = ex_space[ibody][2]*ey_space[ibody][0] -
ex_space[ibody][0]*ey_space[ibody][2];
ez2 = ex_space[ibody][0]*ey_space[ibody][1] -
ex_space[ibody][1]*ey_space[ibody][0];
-
- if (ez0*ez_space[ibody][0] + ez1*ez_space[ibody][1] +
- ez2*ez_space[ibody][2] < 0.0) {
+
+ if (ez0*ez_space[ibody][0] + ez1*ez_space[ibody][1] +
+ ez2*ez_space[ibody][2] < 0.0) {
ez_space[ibody][0] = -ez_space[ibody][0];
ez_space[ibody][1] = -ez_space[ibody][1];
ez_space[ibody][2] = -ez_space[ibody][2];
@@ -499,7 +499,7 @@ void FixPOEMS::init()
}
// free temporary memory
-
+
memory->destroy(tensor);
memory->destroy(evectors);
@@ -517,15 +517,15 @@ void FixPOEMS::init()
dx = x[i][0] + xbox*xprd - xcm[ibody][0];
dy = x[i][1] + ybox*yprd - xcm[ibody][1];
dz = x[i][2] + zbox*zprd - xcm[ibody][2];
-
+
displace[i][0] = dx*ex_space[ibody][0] + dy*ex_space[ibody][1] +
- dz*ex_space[ibody][2];
+ dz*ex_space[ibody][2];
displace[i][1] = dx*ey_space[ibody][0] + dy*ey_space[ibody][1] +
- dz*ey_space[ibody][2];
+ dz*ey_space[ibody][2];
displace[i][2] = dx*ez_space[ibody][0] + dy*ez_space[ibody][1] +
- dz*ez_space[ibody][2];
+ dz*ez_space[ibody][2];
} else displace[i][0] = displace[i][1] = displace[i][2] = 0.0;
- }
+ }
// test for valid principal moments & axes
// recompute moments of inertia around new axes
@@ -552,12 +552,12 @@ void FixPOEMS::init()
dz = x[i][2] + zbox*zprd - xcm[ibody][2];
massone = mass[type[i]];
- ddx = dx*ex_space[ibody][0] + dy*ex_space[ibody][1] +
- dz*ex_space[ibody][2];
+ ddx = dx*ex_space[ibody][0] + dy*ex_space[ibody][1] +
+ dz*ex_space[ibody][2];
ddy = dx*ey_space[ibody][0] + dy*ey_space[ibody][1] +
- dz*ey_space[ibody][2];
+ dz*ey_space[ibody][2];
ddz = dx*ez_space[ibody][0] + dy*ez_space[ibody][1] +
- dz*ez_space[ibody][2];
+ dz*ez_space[ibody][2];
sum[ibody][0] += massone * (ddy*ddy + ddz*ddz);
sum[ibody][1] += massone * (ddx*ddx + ddz*ddz);
@@ -567,17 +567,17 @@ void FixPOEMS::init()
sum[ibody][5] -= massone * ddx*ddz;
}
}
-
+
MPI_Allreduce(sum[0],all[0],6*nbody,MPI_DOUBLE,MPI_SUM,world);
-
+
for (ibody = 0; ibody < nbody; ibody++) {
- if (fabs(all[ibody][0]-inertia[ibody][0]) > TOLERANCE ||
- fabs(all[ibody][1]-inertia[ibody][1]) > TOLERANCE ||
- fabs(all[ibody][2]-inertia[ibody][2]) > TOLERANCE)
+ if (fabs(all[ibody][0]-inertia[ibody][0]) > TOLERANCE ||
+ fabs(all[ibody][1]-inertia[ibody][1]) > TOLERANCE ||
+ fabs(all[ibody][2]-inertia[ibody][2]) > TOLERANCE)
error->all(FLERR,"Bad principal moments");
- if (fabs(all[ibody][3]) > TOLERANCE ||
- fabs(all[ibody][4]) > TOLERANCE ||
- fabs(all[ibody][5]) > TOLERANCE)
+ if (fabs(all[ibody][3]) > TOLERANCE ||
+ fabs(all[ibody][4]) > TOLERANCE ||
+ fabs(all[ibody][5]) > TOLERANCE)
error->all(FLERR,"Bad principal moments");
}
}
@@ -629,7 +629,7 @@ void FixPOEMS::setup(int vflag)
sum[ibody][2] += v[i][2] * massone;
sum[ibody][3] += dy * massone*v[i][2] - dz * massone*v[i][1];
sum[ibody][4] += dz * massone*v[i][0] - dx * massone*v[i][2];
- sum[ibody][5] += dx * massone*v[i][1] - dy * massone*v[i][0];
+ sum[ibody][5] += dx * massone*v[i][1] - dy * massone*v[i][0];
}
}
@@ -641,7 +641,7 @@ void FixPOEMS::setup(int vflag)
vcm[ibody][2] = all[ibody][2]/masstotal[ibody];
angmom[ibody][0] = all[ibody][3];
angmom[ibody][1] = all[ibody][4];
- angmom[ibody][2] = all[ibody][5];
+ angmom[ibody][2] = all[ibody][5];
}
// virial setup before call to set_v
@@ -653,7 +653,7 @@ void FixPOEMS::setup(int vflag)
for (ibody = 0; ibody < nbody; ibody++)
omega_from_mq(angmom[ibody],ex_space[ibody],ey_space[ibody],
- ez_space[ibody],inertia[ibody],omega[ibody]);
+ ez_space[ibody],inertia[ibody],omega[ibody]);
set_v();
// guestimate virial as 2x the set_v contribution
@@ -663,7 +663,7 @@ void FixPOEMS::setup(int vflag)
if (vflag_atom) {
for (i = 0; i < nlocal; i++)
for (n = 0; n < 6; n++)
- vatom[i][n] *= 2.0;
+ vatom[i][n] *= 2.0;
}
// use post_force() to compute initial fcm & torque
@@ -673,9 +673,9 @@ void FixPOEMS::setup(int vflag)
// setup for POEMS
poems->MakeSystem(nbody,masstotal,inertia,xcm,vcm,omega,
- ex_space,ey_space,ez_space,
- njoint,jointbody,xjoint,nfree,freelist,
- dthalf,dtv,force->ftm2v,total_ke);
+ ex_space,ey_space,ez_space,
+ njoint,jointbody,xjoint,nfree,freelist,
+ dthalf,dtv,force->ftm2v,total_ke);
}
/* ----------------------------------------------------------------------
@@ -695,7 +695,7 @@ void FixPOEMS::initial_integrate(int vflag)
else evflag = 0;
// set coords and velocities of atoms in rigid bodies
-
+
set_xv();
}
@@ -714,14 +714,14 @@ void FixPOEMS::post_force(int vflag)
double **x = atom->x;
double **f = atom->f;
int nlocal = atom->nlocal;
-
+
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
-
+
for (ibody = 0; ibody < nbody; ibody++)
for (i = 0; i < 6; i++) sum[ibody][i] = 0.0;
-
+
for (i = 0; i < nlocal; i++) {
if (natom2body[i]) {
ibody = atom2body[i][0];
@@ -729,20 +729,20 @@ void FixPOEMS::post_force(int vflag)
sum[ibody][0] += f[i][0];
sum[ibody][1] += f[i][1];
sum[ibody][2] += f[i][2];
-
+
xbox = (image[i] & 1023) - 512;
ybox = (image[i] >> 10 & 1023) - 512;
zbox = (image[i] >> 20) - 512;
dx = x[i][0] + xbox*xprd - xcm[ibody][0];
dy = x[i][1] + ybox*yprd - xcm[ibody][1];
dz = x[i][2] + zbox*zprd - xcm[ibody][2];
-
+
sum[ibody][3] += dy*f[i][2] - dz*f[i][1];
sum[ibody][4] += dz*f[i][0] - dx*f[i][2];
sum[ibody][5] += dx*f[i][1] - dy*f[i][0];
}
}
-
+
MPI_Allreduce(sum[0],all[0],6*nbody,MPI_DOUBLE,MPI_SUM,world);
for (ibody = 0; ibody < nbody; ibody++) {
@@ -763,7 +763,7 @@ void FixPOEMS::post_force(int vflag)
void FixPOEMS::final_integrate()
{
// perform POEMS integration
-
+
poems->LobattoTwo(vcm,omega,torque,fcm);
// set velocities of atoms in rigid bodies
@@ -805,18 +805,18 @@ void FixPOEMS::final_integrate_respa(int ilevel, int iloop)
and after fix_deform::pre_exchange() may have flipped box
if don't do this, then atoms of a body which drifts far away
from a triclinic box will be remapped back into box
- with huge displacements when the box tilt changes via set_x()
+ with huge displacements when the box tilt changes via set_x()
NOTE: cannot do this by changing xcm of each body in cluster
or even 1st body in cluster
- b/c POEMS library does not see xcm but only sets xcm
- so remap needs to be coordinated with POEMS library
- thus this routine does nothing for now
+ b/c POEMS library does not see xcm but only sets xcm
+ so remap needs to be coordinated with POEMS library
+ thus this routine does nothing for now
------------------------------------------------------------------------- */
void FixPOEMS::pre_neighbor() {}
/* ----------------------------------------------------------------------
- count # of degrees-of-freedom removed by fix_poems for atoms in igroup
+ count # of degrees-of-freedom removed by fix_poems for atoms in igroup
------------------------------------------------------------------------- */
int FixPOEMS::dof(int igroup)
@@ -868,9 +868,9 @@ int FixPOEMS::dof(int igroup)
flag = 0/1 means map from box to lamda coords or vice versa
NOTE: cannot do this by changing xcm of each body in cluster
or even 1st body in cluster
- b/c POEMS library does not see xcm but only sets xcm
- so deform needs to be coordinated with POEMS library
- thus this routine does nothing for now
+ b/c POEMS library does not see xcm but only sets xcm
+ so deform needs to be coordinated with POEMS library
+ thus this routine does nothing for now
------------------------------------------------------------------------- */
void FixPOEMS::deform(int flag) {}
@@ -1006,10 +1006,10 @@ void FixPOEMS::jointbuild()
if (njoint) {
if (mjoint)
MPI_Allgatherv(mylist[0],3*mjoint,MPI_INT,jlist[0],
- recvcounts,displs,MPI_INT,world);
+ recvcounts,displs,MPI_INT,world);
else
MPI_Allgatherv(NULL,3*mjoint,MPI_INT,jlist[0],
- recvcounts,displs,MPI_INT,world);
+ recvcounts,displs,MPI_INT,world);
}
delete [] recvcounts;
@@ -1065,8 +1065,8 @@ void FixPOEMS::jointbuild()
myjoint[i][2] = x[j][2];
} else myjoint[i][0] = myjoint[i][1] = myjoint[i][2] = 0.0;
}
-
- if (njoint)
+
+ if (njoint)
MPI_Allreduce(myjoint[0],xjoint[0],3*njoint,MPI_DOUBLE,MPI_SUM,world);
// compute freelist of nfree single unconnected bodies
@@ -1116,17 +1116,17 @@ void FixPOEMS::sortlist(int n, int **list)
v2 = list[i-1][2];
j = i;
flag = 0;
- if (list[j-inc-1][0] > v0 ||
- (list[j-inc-1][0] == v0 && list[j-inc-1][1] > v1)) flag = 1;
+ if (list[j-inc-1][0] > v0 ||
+ (list[j-inc-1][0] == v0 && list[j-inc-1][1] > v1)) flag = 1;
while (flag) {
- list[j-1][0] = list[j-inc-1][0];
- list[j-1][1] = list[j-inc-1][1];
- list[j-1][2] = list[j-inc-1][2];
- j -= inc;
- if (j <= inc) break;
- flag = 0;
- if (list[j-inc-1][0] > v0 ||
- (list[j-inc-1][0] == v0 && list[j-inc-1][1] > v1)) flag = 1;
+ list[j-1][0] = list[j-inc-1][0];
+ list[j-1][1] = list[j-inc-1][1];
+ list[j-1][2] = list[j-inc-1][2];
+ j -= inc;
+ if (j <= inc) break;
+ flag = 0;
+ if (list[j-inc-1][0] > v0 ||
+ (list[j-inc-1][0] == v0 && list[j-inc-1][1] > v1)) flag = 1;
}
list[j-1][0] = v0;
list[j-1][1] = v1;
@@ -1156,7 +1156,7 @@ int FixPOEMS::loopcheck(int nvert, int nedge, int **elist)
int emax = 0;
for (i = 0; i < nvert; i++) emax = MAX(emax,ecount[i]);
-
+
int **elistfull;
memory->create(elistfull,nvert,emax,"poems:elistfull");
for (i = 0; i < nvert; i++) ecount[i] = 0;
@@ -1197,12 +1197,12 @@ int FixPOEMS::loopcheck(int nvert, int nedge, int **elist)
while (nstack) {
i = stack[--nstack];
for (k = 0; k < ecount[i]; k++) {
- j = elistfull[i][k];
- if (j == parent[i]) continue;
- if (mark[j]) return 1;
- stack[nstack++] = j;
- mark[j] = 1;
- parent[j] = i;
+ j = elistfull[i][k];
+ if (j == parent[i]) continue;
+ if (mark[j]) return 1;
+ stack[nstack++] = j;
+ mark[j] = 1;
+ parent[j] = i;
}
}
ncluster++;
@@ -1229,7 +1229,7 @@ int FixPOEMS::jacobi(double **matrix, double *evalues, double **evectors)
{
int i,j,k;
double tresh,theta,tau,t,sm,s,h,g,c,b[3],z[3];
-
+
for (i = 0; i < 3; i++) {
for (j = 0; j < 3; j++) evectors[i][j] = 0.0;
evectors[i][i] = 1.0;
@@ -1238,48 +1238,48 @@ int FixPOEMS::jacobi(double **matrix, double *evalues, double **evectors)
b[i] = evalues[i] = matrix[i][i];
z[i] = 0.0;
}
-
+
for (int iter = 1; iter <= MAXJACOBI; iter++) {
sm = 0.0;
for (i = 0; i < 2; i++)
for (j = i+1; j < 3; j++)
- sm += fabs(matrix[i][j]);
+ sm += fabs(matrix[i][j]);
if (sm == 0.0) return 0;
-
+
if (iter < 4) tresh = 0.2*sm/(3*3);
else tresh = 0.0;
-
+
for (i = 0; i < 2; i++) {
for (j = i+1; j < 3; j++) {
- g = 100.0*fabs(matrix[i][j]);
- if (iter > 4 && fabs(evalues[i])+g == fabs(evalues[i])
- && fabs(evalues[j])+g == fabs(evalues[j]))
- matrix[i][j] = 0.0;
- else if (fabs(matrix[i][j]) > tresh) {
- h = evalues[j]-evalues[i];
- if (fabs(h)+g == fabs(h)) t = (matrix[i][j])/h;
- else {
- theta = 0.5*h/(matrix[i][j]);
- t = 1.0/(fabs(theta)+sqrt(1.0+theta*theta));
- if (theta < 0.0) t = -t;
- }
- c = 1.0/sqrt(1.0+t*t);
- s = t*c;
- tau = s/(1.0+c);
- h = t*matrix[i][j];
- z[i] -= h;
- z[j] += h;
- evalues[i] -= h;
- evalues[j] += h;
- matrix[i][j] = 0.0;
- for (k = 0; k < i; k++) rotate(matrix,k,i,k,j,s,tau);
- for (k = i+1; k < j; k++) rotate(matrix,i,k,k,j,s,tau);
- for (k = j+1; k < 3; k++) rotate(matrix,i,k,j,k,s,tau);
- for (k = 0; k < 3; k++) rotate(evectors,k,i,k,j,s,tau);
- }
+ g = 100.0*fabs(matrix[i][j]);
+ if (iter > 4 && fabs(evalues[i])+g == fabs(evalues[i])
+ && fabs(evalues[j])+g == fabs(evalues[j]))
+ matrix[i][j] = 0.0;
+ else if (fabs(matrix[i][j]) > tresh) {
+ h = evalues[j]-evalues[i];
+ if (fabs(h)+g == fabs(h)) t = (matrix[i][j])/h;
+ else {
+ theta = 0.5*h/(matrix[i][j]);
+ t = 1.0/(fabs(theta)+sqrt(1.0+theta*theta));
+ if (theta < 0.0) t = -t;
+ }
+ c = 1.0/sqrt(1.0+t*t);
+ s = t*c;
+ tau = s/(1.0+c);
+ h = t*matrix[i][j];
+ z[i] -= h;
+ z[j] += h;
+ evalues[i] -= h;
+ evalues[j] += h;
+ matrix[i][j] = 0.0;
+ for (k = 0; k < i; k++) rotate(matrix,k,i,k,j,s,tau);
+ for (k = i+1; k < j; k++) rotate(matrix,i,k,k,j,s,tau);
+ for (k = j+1; k < 3; k++) rotate(matrix,i,k,j,k,s,tau);
+ for (k = 0; k < 3; k++) rotate(evectors,k,i,k,j,s,tau);
+ }
}
}
-
+
for (i = 0; i < 3; i++) {
evalues[i] = b[i] += z[i];
z[i] = 0.0;
@@ -1293,7 +1293,7 @@ int FixPOEMS::jacobi(double **matrix, double *evalues, double **evectors)
------------------------------------------------------------------------- */
void FixPOEMS::rotate(double **matrix, int i, int j, int k, int l,
- double s, double tau)
+ double s, double tau)
{
double g = matrix[i][j];
double h = matrix[k][l];
@@ -1312,7 +1312,7 @@ void FixPOEMS::rotate(double **matrix, int i, int j, int k, int l,
------------------------------------------------------------------------- */
void FixPOEMS::omega_from_mq(double *m, double *ex, double *ey, double *ez,
- double *inertia, double *w)
+ double *inertia, double *w)
{
double wbody[3];
@@ -1345,14 +1345,14 @@ void FixPOEMS::set_xv()
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
- double *mass = atom->mass;
+ double *mass = atom->mass;
int *type = atom->type;
int nlocal = atom->nlocal;
-
+
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
-
+
// set x and v of each atom
// only set joint atoms for 1st rigid body they belong to
@@ -1380,13 +1380,13 @@ void FixPOEMS::set_xv()
// v = vcm + omega around center-of-mass
x[i][0] = ex_space[ibody][0]*displace[i][0] +
- ey_space[ibody][0]*displace[i][1] +
+ ey_space[ibody][0]*displace[i][1] +
ez_space[ibody][0]*displace[i][2];
x[i][1] = ex_space[ibody][1]*displace[i][0] +
- ey_space[ibody][1]*displace[i][1] +
+ ey_space[ibody][1]*displace[i][1] +
ez_space[ibody][1]*displace[i][2];
x[i][2] = ex_space[ibody][2]*displace[i][0] +
- ey_space[ibody][2]*displace[i][1] +
+ ey_space[ibody][2]*displace[i][1] +
ez_space[ibody][2]*displace[i][2];
v[i][0] = omega[ibody][1]*x[i][2] - omega[ibody][2]*x[i][1] +
@@ -1395,7 +1395,7 @@ void FixPOEMS::set_xv()
vcm[ibody][1];
v[i][2] = omega[ibody][0]*x[i][1] - omega[ibody][1]*x[i][0] +
vcm[ibody][2];
-
+
// add center of mass to displacement
// map back into periodic box via xbox,ybox,zbox
@@ -1413,7 +1413,7 @@ void FixPOEMS::set_xv()
massone = mass[type[i]];
fc0 = massone*(v[i][0] - v0)/dtf - f[i][0];
fc1 = massone*(v[i][1] - v1)/dtf - f[i][1];
- fc2 = massone*(v[i][2] - v2)/dtf - f[i][2];
+ fc2 = massone*(v[i][2] - v2)/dtf - f[i][2];
vr[0] = 0.5*fc0*x0;
vr[1] = 0.5*fc1*x1;
@@ -1440,7 +1440,7 @@ void FixPOEMS::set_v()
double x0,x1,x2,v0,v1,v2,fc0,fc1,fc2,massone;
double vr[6];
- double *mass = atom->mass;
+ double *mass = atom->mass;
double **f = atom->f;
double **x = atom->x;
double **v = atom->v;
@@ -1460,13 +1460,13 @@ void FixPOEMS::set_v()
ibody = atom2body[i][0];
dx = ex_space[ibody][0]*displace[i][0] +
- ey_space[ibody][0]*displace[i][1] +
+ ey_space[ibody][0]*displace[i][1] +
ez_space[ibody][0]*displace[i][2];
dy = ex_space[ibody][1]*displace[i][0] +
- ey_space[ibody][1]*displace[i][1] +
+ ey_space[ibody][1]*displace[i][1] +
ez_space[ibody][1]*displace[i][2];
dz = ex_space[ibody][2]*displace[i][0] +
- ey_space[ibody][2]*displace[i][1] +
+ ey_space[ibody][2]*displace[i][1] +
ez_space[ibody][2]*displace[i][2];
// save old velocities for virial
@@ -1491,7 +1491,7 @@ void FixPOEMS::set_v()
massone = mass[type[i]];
fc0 = massone*(v[i][0] - v0)/dtf - f[i][0];
fc1 = massone*(v[i][1] - v1)/dtf - f[i][1];
- fc2 = massone*(v[i][2] - v2)/dtf - f[i][2];
+ fc2 = massone*(v[i][2] - v2)/dtf - f[i][2];
xbox = (image[i] & 1023) - 512;
ybox = (image[i] >> 10 & 1023) - 512;
@@ -1514,7 +1514,7 @@ void FixPOEMS::set_v()
}
/* ----------------------------------------------------------------------
- allocate local atom-based arrays
+ allocate local atom-based arrays
------------------------------------------------------------------------- */
void FixPOEMS::grow_arrays(int nmax)
@@ -1525,7 +1525,7 @@ void FixPOEMS::grow_arrays(int nmax)
}
/* ----------------------------------------------------------------------
- copy values within local atom-based arrays
+ copy values within local atom-based arrays
------------------------------------------------------------------------- */
void FixPOEMS::copy_arrays(int i, int j)
@@ -1538,7 +1538,7 @@ void FixPOEMS::copy_arrays(int i, int j)
}
/* ----------------------------------------------------------------------
- memory usage of local atom-based arrays
+ memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double FixPOEMS::memory_usage()
@@ -1551,14 +1551,14 @@ double FixPOEMS::memory_usage()
}
/* ----------------------------------------------------------------------
- pack values in local atom-based arrays for exchange with another proc
+ pack values in local atom-based arrays for exchange with another proc
------------------------------------------------------------------------- */
int FixPOEMS::pack_exchange(int i, double *buf)
{
int m = 0;
buf[m++] = static_cast<double> (natom2body[i]);
- for (int j = 0; j < natom2body[i]; j++)
+ for (int j = 0; j < natom2body[i]; j++)
buf[m++] = static_cast<double> (atom2body[i][j]);
buf[m++] = displace[i][0];
buf[m++] = displace[i][1];
@@ -1567,7 +1567,7 @@ int FixPOEMS::pack_exchange(int i, double *buf)
}
/* ----------------------------------------------------------------------
- unpack values in local atom-based arrays from exchange with another proc
+ unpack values in local atom-based arrays from exchange with another proc
------------------------------------------------------------------------- */
int FixPOEMS::unpack_exchange(int nlocal, double *buf)
@@ -1586,7 +1586,7 @@ int FixPOEMS::unpack_exchange(int nlocal, double *buf)
void FixPOEMS::reset_dt()
{
- dtv = update->dt;
- dtf = 0.5 * update->dt * force->ftm2v;
+ dtv = update->dt;
+ dtf = 0.5 * update->dt * force->ftm2v;
dthalf = 0.5 * update->dt;
}
diff --git a/src/POEMS/fix_poems.h b/src/POEMS/fix_poems.h
index 7bb2ab22afd1a47ca40fc732efb6632f63f97e66..f1606ab7a74e4dcf54f054f8f1c0109601fd172c 100644
--- a/src/POEMS/fix_poems.h
+++ b/src/POEMS/fix_poems.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -62,7 +62,7 @@ class FixPOEMS : public Fix {
int *natom2body; // # of bodies each atom is part of
int **atom2body; // list of bodies each atom is part of
double **displace; // atom displace in body coords for 1st body it's in
-
+
// rigid body properties
// only nrigid double counts joint atoms as being in multiple bodies
// other quantities only count a joint atom as being in 1st body
@@ -104,7 +104,7 @@ class FixPOEMS : public Fix {
int jacobi(double **, double *, double **);
void rotate(double **, int, int, int, int, double, double);
void omega_from_mq(double *, double *, double *, double *,
- double *, double *);
+ double *, double *);
void set_v();
void set_xv();
};
diff --git a/src/REAX/fix_reax_bonds.cpp b/src/REAX/fix_reax_bonds.cpp
index fea4fa67d1af13900423d01f758e7b19a0cf438d..1044a4f83402c447f96c69530075d6f2ed113fa8 100644
--- a/src/REAX/fix_reax_bonds.cpp
+++ b/src/REAX/fix_reax_bonds.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -99,7 +99,7 @@ void FixReaxBonds::end_of_step()
/* ---------------------------------------------------------------------- */
-void FixReaxBonds::OutputReaxBonds(bigint ntimestep, FILE *fp)
+void FixReaxBonds::OutputReaxBonds(bigint ntimestep, FILE *fp)
{
int nparticles,nparticles_tot,nbuf,nbuf_local,most,j;
int ii,jn,mbond,numbonds,nsbmax,nsbmax_most;
@@ -111,36 +111,36 @@ void FixReaxBonds::OutputReaxBonds(bigint ntimestep, FILE *fp)
MPI_Status istatus;
MPI_Comm_size(world,&nprocs);
-
+
nparticles = atom->nlocal;
nparticles_tot = static_cast<int> (atom->natoms);
-
+
jn = ReaxParams::nat;
mbond = ReaxParams::mbond;
FORTRAN(getnsbmax,GETNSBMAX)(&nsbmax);
FORTRAN(getcutof3,GETCUTOF3)(&cutof3);
MPI_Allreduce(&nparticles,&most,1,MPI_INT,MPI_MAX,world);
MPI_Allreduce(&nsbmax,&nsbmax_most,1,MPI_INT,MPI_MAX,world);
-
+
if (me == 0) {
fprintf(fp,"# Timestep " BIGINT_FORMAT " \n",ntimestep);
fprintf(fp,"# \n");
fprintf(fp,"# Number of particles %d \n",nparticles_tot);
fprintf(fp,"# \n");
fprintf(fp,"# Max number of bonds per atom %d with "
- "coarse bond order cutoff %5.3f \n",
- nsbmax_most,cutof3);
+ "coarse bond order cutoff %5.3f \n",
+ nsbmax_most,cutof3);
fprintf(fp,"# Particle connection table and bond orders \n");
fprintf(fp,"# id type nb id_1...id_nb mol bo_1...bo_nb abo nlp q \n");
}
-
+
// allocate a temporary buffer for the snapshot info
// big enough for largest number of atoms on any one proc
// nbuf_local = size of local buffer for table of atom bonds
-
+
nbuf = 1+(2*nsbmax_most+7)*most;
memory->create(buf,nbuf,"reax/bonds:buf");
-
+
j = 0;
buf[j++] = nparticles;
for (int iparticle=0;iparticle<nparticles;iparticle++) {
@@ -155,9 +155,9 @@ void FixReaxBonds::OutputReaxBonds(bigint ntimestep, FILE *fp)
for (k=0;k<numbonds;k++) {
ii = FORTRAN(cbknubon2,CBKNUBON2).nubon1[iparticle+jn*k];
if (FORTRAN(cbkbo,CBKBO).bo[ii-1] > cutof3) {
- kk++;
- jj = FORTRAN(cbkia,CBKIA).iag[iparticle+jn*(k+2)];
- buf[j++] = FORTRAN(cbkc,CBKC).itag[jj-1];
+ kk++;
+ jj = FORTRAN(cbkia,CBKIA).iag[iparticle+jn*(k+2)];
+ buf[j++] = FORTRAN(cbkc,CBKC).itag[jj-1];
}
}
buf[jbufknum] = kk; //no.bonds
@@ -169,8 +169,8 @@ void FixReaxBonds::OutputReaxBonds(bigint ntimestep, FILE *fp)
for (k=0;k<numbonds;k++) {
ii = FORTRAN(cbknubon2,CBKNUBON2).nubon1[iparticle+jn*k];
if (FORTRAN(cbkbo,CBKBO).bo[ii-1] > cutof3) {
- kk++;
- buf[j++] = FORTRAN(cbkbo,CBKBO).bo[ii-1];
+ kk++;
+ buf[j++] = FORTRAN(cbkbo,CBKBO).bo[ii-1];
}
}
@@ -181,54 +181,54 @@ void FixReaxBonds::OutputReaxBonds(bigint ntimestep, FILE *fp)
buf[j++] = atom->q[iparticle];
}
nbuf_local = j-1;
-
+
// node 0 pings each node, receives their buffer, writes to file
// all other nodes wait for ping, send buffer to node 0
-
+
if (me == 0) {
for (int inode = 0; inode<nprocs; inode++) {
j = 0;
if (inode == 0) {
- nlocal_tmp = nparticles;
- j++;
+ nlocal_tmp = nparticles;
+ j++;
} else {
- MPI_Irecv(&buf[0],nbuf,MPI_DOUBLE,inode,0,world,&irequest);
+ MPI_Irecv(&buf[0],nbuf,MPI_DOUBLE,inode,0,world,&irequest);
MPI_Send(&itmp,0,MPI_INT,inode,0,world);
MPI_Wait(&irequest,&istatus);
- nlocal_tmp = nint(buf[j++]);
+ nlocal_tmp = nint(buf[j++]);
}
-
+
for (int iparticle=0;iparticle<nlocal_tmp;iparticle++) {
- // print atom tag, atom type, no.bonds
+ // print atom tag, atom type, no.bonds
- numbonds = nint(buf[j+2]);
- fprintf(fp," %d %d %d",nint(buf[j]),nint(buf[j+1]),numbonds);
- j += 3;
- if (numbonds > nsbmax_most) {
- char str[128];
- sprintf(str,"Fix reax/bonds numbonds > nsbmax_most");
- error->one(FLERR,str);
- }
+ numbonds = nint(buf[j+2]);
+ fprintf(fp," %d %d %d",nint(buf[j]),nint(buf[j+1]),numbonds);
+ j += 3;
+ if (numbonds > nsbmax_most) {
+ char str[128];
+ sprintf(str,"Fix reax/bonds numbonds > nsbmax_most");
+ error->one(FLERR,str);
+ }
- // print connection table
+ // print connection table
- for (k=0;k<numbonds;k++)
- fprintf(fp," %d",nint(buf[j++]));
+ for (k=0;k<numbonds;k++)
+ fprintf(fp," %d",nint(buf[j++]));
- // print molecule id
+ // print molecule id
- fprintf(fp," %d",nint(buf[j++]));
+ fprintf(fp," %d",nint(buf[j++]));
- // print bond orders
+ // print bond orders
- for (k=0;k<numbonds;k++)
- fprintf(fp,"%14.3f",buf[j++]);
+ for (k=0;k<numbonds;k++)
+ fprintf(fp,"%14.3f",buf[j++]);
- // print sum of bond orders, no. of lone pairs, charge
+ // print sum of bond orders, no. of lone pairs, charge
- fprintf(fp,"%14.3f%14.3f%14.3f\n",buf[j],buf[j+1],buf[j+2]);
- j+=3;
+ fprintf(fp,"%14.3f%14.3f%14.3f\n",buf[j],buf[j+1],buf[j+2]);
+ j+=3;
}
}
diff --git a/src/REAX/fix_reax_bonds.h b/src/REAX/fix_reax_bonds.h
index dadf0a7db0f1a4d642576d8d4f8a92f8919caac1..3206f8b9f3921b1845f16bf44c5b0d6e6b260f8f 100644
--- a/src/REAX/fix_reax_bonds.h
+++ b/src/REAX/fix_reax_bonds.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/REAX/pair_reax.cpp b/src/REAX/pair_reax.cpp
index 30f787d8d08a21203a6de59bea1388c1daa3dfc0..9d2a4e441675a5cc0f1fffff0f983a806a3058ad 100644
--- a/src/REAX/pair_reax.cpp
+++ b/src/REAX/pair_reax.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -49,7 +49,7 @@ PairREAX::PairREAX(LAMMPS *lmp) : Pair(lmp)
restartinfo = 0;
one_coeff = 1;
no_virial_fdotr_compute = 1;
-
+
nextra = 14;
pvector = new double[nextra];
@@ -155,7 +155,7 @@ void PairREAX::compute(int eflag, int vflag)
}
// calculate the atomic charge distribution
-
+
compute_charge(energy_charge_equilibration);
// transfer LAMMPS positions and neighbor lists to REAX
@@ -203,14 +203,14 @@ void PairREAX::compute(int eflag, int vflag)
ecoul += FORTRAN(cbkenergies, CBKENERGIES).ep;
ecoul += energy_charge_equilibration;
-
+
eng_vdwl += evdwl;
eng_coul += ecoul;
// Store the different parts of the energy
// in a list for output by compute pair command
- pvector[0] = FORTRAN(cbkenergies, CBKENERGIES).eb;
+ pvector[0] = FORTRAN(cbkenergies, CBKENERGIES).eb;
pvector[1] = FORTRAN(cbkenergies, CBKENERGIES).ea;
pvector[2] = FORTRAN(cbkenergies, CBKENERGIES).elp;
pvector[3] = FORTRAN(cbkenergies, CBKENERGIES).emol;
@@ -223,8 +223,8 @@ void PairREAX::compute(int eflag, int vflag)
pvector[10] = FORTRAN(cbkenergies, CBKENERGIES).ew;
pvector[11] = FORTRAN(cbkenergies, CBKENERGIES).ep;
pvector[12] = FORTRAN(cbkenergies, CBKENERGIES).efi;
- pvector[13] = energy_charge_equilibration;
-
+ pvector[13] = energy_charge_equilibration;
+
}
if (eflag_atom) {
@@ -334,7 +334,7 @@ void PairREAX::write_reax_vlist()
itag = tag[i];
jlist = firstneigh[i];
jnum = numneigh[i];
-
+
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
@@ -343,50 +343,50 @@ void PairREAX::write_reax_vlist()
yjtmp = x[j][1];
zjtmp = x[j][2];
jtag = tag[j];
-
+
delx = xitmp - xjtmp;
dely = yitmp - yjtmp;
delz = zitmp - zjtmp;
-
+
delr2 = delx*delx+dely*dely+delz*delz;
-
+
if (delr2 <= rcutvsq) {
- if (i < j) {
- iii = i+1;
- jjj = j+1;
- } else {
- iii = j+1;
- jjj = i+1;
- }
- if (nvpair >= nvpairmax)
- error->one(FLERR,"Reax_defs.h setting for NNEIGHMAXDEF is too small");
-
- FORTRAN(cbkpairs, CBKPAIRS).nvl1[nvpair] = iii;
- FORTRAN(cbkpairs, CBKPAIRS).nvl2[nvpair] = jjj;
- FORTRAN(cbknvlbo, CBKNVLBO).nvlbo[nvpair] = 0;
-
- if (delr2 <= rcutbsq) {
- FORTRAN(cbknvlbo, CBKNVLBO).nvlbo[nvpair] = 1;
- nbond++;
- }
-
- FORTRAN(cbknvlown, CBKNVLOWN).nvlown[nvpair] = 0;
-
- if (j < nlocal)
- FORTRAN(cbknvlown, CBKNVLOWN).nvlown[nvpair] = 1;
- else if (itag < jtag)
- FORTRAN(cbknvlown, CBKNVLOWN).nvlown[nvpair] = 1;
- else if (itag == jtag) {
- if (delz > SMALL)
- FORTRAN(cbknvlown, CBKNVLOWN).nvlown[nvpair] = 1;
- else if (fabs(delz) < SMALL) {
- if (dely > SMALL)
- FORTRAN(cbknvlown, CBKNVLOWN).nvlown[nvpair] = 1;
- else if (fabs(dely) < SMALL && delx > SMALL)
- FORTRAN(cbknvlown, CBKNVLOWN).nvlown[nvpair] = 1;
- }
- }
- nvpair++;
+ if (i < j) {
+ iii = i+1;
+ jjj = j+1;
+ } else {
+ iii = j+1;
+ jjj = i+1;
+ }
+ if (nvpair >= nvpairmax)
+ error->one(FLERR,"Reax_defs.h setting for NNEIGHMAXDEF is too small");
+
+ FORTRAN(cbkpairs, CBKPAIRS).nvl1[nvpair] = iii;
+ FORTRAN(cbkpairs, CBKPAIRS).nvl2[nvpair] = jjj;
+ FORTRAN(cbknvlbo, CBKNVLBO).nvlbo[nvpair] = 0;
+
+ if (delr2 <= rcutbsq) {
+ FORTRAN(cbknvlbo, CBKNVLBO).nvlbo[nvpair] = 1;
+ nbond++;
+ }
+
+ FORTRAN(cbknvlown, CBKNVLOWN).nvlown[nvpair] = 0;
+
+ if (j < nlocal)
+ FORTRAN(cbknvlown, CBKNVLOWN).nvlown[nvpair] = 1;
+ else if (itag < jtag)
+ FORTRAN(cbknvlown, CBKNVLOWN).nvlown[nvpair] = 1;
+ else if (itag == jtag) {
+ if (delz > SMALL)
+ FORTRAN(cbknvlown, CBKNVLOWN).nvlown[nvpair] = 1;
+ else if (fabs(delz) < SMALL) {
+ if (dely > SMALL)
+ FORTRAN(cbknvlown, CBKNVLOWN).nvlown[nvpair] = 1;
+ else if (fabs(dely) < SMALL && delx > SMALL)
+ FORTRAN(cbknvlown, CBKNVLOWN).nvlown[nvpair] = 1;
+ }
+ }
+ nvpair++;
}
}
}
@@ -404,33 +404,33 @@ void PairREAX::write_reax_vlist()
yjtmp = x[j][1];
zjtmp = x[j][2];
jtag = tag[j];
-
+
delx = xitmp - xjtmp;
dely = yitmp - yjtmp;
delz = zitmp - zjtmp;
-
+
delr2 = delx*delx+dely*dely+delz*delz;
-
+
// don't need to check the double count since i < j in the ghost region
if (delr2 <= rcutvsq) {
- iii = i+1;
- jjj = j+1;
-
- if (nvpair >= nvpairmax)
- error->one(FLERR,"Reax_defs.h setting for NNEIGHMAXDEF is too small");
-
- FORTRAN(cbkpairs, CBKPAIRS).nvl1[nvpair] = iii;
- FORTRAN(cbkpairs, CBKPAIRS).nvl2[nvpair] = jjj;
- FORTRAN(cbknvlbo, CBKNVLBO).nvlbo[nvpair] = 0;
-
- if (delr2 <= rcutbsq) {
- FORTRAN(cbknvlbo, CBKNVLBO).nvlbo[nvpair] = 1;
- nbond++;
- }
-
- FORTRAN(cbknvlown, CBKNVLOWN).nvlown[nvpair] = 0;
- nvpair++;
+ iii = i+1;
+ jjj = j+1;
+
+ if (nvpair >= nvpairmax)
+ error->one(FLERR,"Reax_defs.h setting for NNEIGHMAXDEF is too small");
+
+ FORTRAN(cbkpairs, CBKPAIRS).nvl1[nvpair] = iii;
+ FORTRAN(cbkpairs, CBKPAIRS).nvl2[nvpair] = jjj;
+ FORTRAN(cbknvlbo, CBKNVLBO).nvlbo[nvpair] = 0;
+
+ if (delr2 <= rcutbsq) {
+ FORTRAN(cbknvlbo, CBKNVLBO).nvlbo[nvpair] = 1;
+ nbond++;
+ }
+
+ FORTRAN(cbknvlown, CBKNVLOWN).nvlown[nvpair] = 0;
+ nvpair++;
}
}
}
@@ -438,7 +438,7 @@ void PairREAX::write_reax_vlist()
FORTRAN(cbkpairs, CBKPAIRS).nvpair = nvpair;
FORTRAN(cbkpairs, CBKPAIRS).nvlself = nvlself;
}
-
+
/* ---------------------------------------------------------------------- */
void PairREAX::read_reax_forces()
@@ -478,23 +478,23 @@ void PairREAX::allocate()
}
/* ----------------------------------------------------------------------
- global settings
+ global settings
------------------------------------------------------------------------- */
void PairREAX::settings(int narg, char **arg)
{
if (narg != 0 && narg !=4) error->all(FLERR,"Illegal pair_style command");
-
+
if (narg == 4) {
hbcut = force->numeric(arg[0]);
ihbnew = static_cast<int> (force->numeric(arg[1]));
itripstaball = static_cast<int> (force->numeric(arg[2]));
precision = force->numeric(arg[3]);
- if (hbcut <= 0.0 ||
- (ihbnew != 0 && ihbnew != 1) ||
- (itripstaball != 0 && itripstaball != 1) ||
- precision <= 0.0)
+ if (hbcut <= 0.0 ||
+ (ihbnew != 0 && ihbnew != 1) ||
+ (itripstaball != 0 && itripstaball != 1) ||
+ precision <= 0.0)
error->all(FLERR,"Illegal pair_style command");
}
}
@@ -517,7 +517,7 @@ void PairREAX::coeff(int narg, char **arg)
// insure filename is ffield.reax
- if (strcmp(arg[2],"ffield.reax") != 0)
+ if (strcmp(arg[2],"ffield.reax") != 0)
error->all(FLERR,"Incorrect args for pair coefficients");
// read args that map atom types to elements in potential file
@@ -576,7 +576,7 @@ void PairREAX::init_style()
// initial setup for cutoff radius of VLIST and BLIST in ReaxFF
double vlbora;
-
+
FORTRAN(getswb, GETSWB)(&swb);
cutmax=MAX(swb, hbcut);
rcutvsq=cutmax*cutmax;
@@ -669,7 +669,7 @@ int PairREAX::pack_reverse_comm(int n, int first, double *buf)
m = 0;
last = first + n;
- for (i = first; i < last; i++)
+ for (i = first; i < last; i++)
buf[m++] = wcg[i];
return 1;
@@ -704,7 +704,7 @@ void PairREAX::taper_setup()
swa3=swa2*swa;
swb2=swb*swb;
swb3=swb2*swb;
-
+
swc7= 20.0e0/d7;
swc6= -70.0e0*(swa+swb)/d7;
swc5= 84.0e0*(swa2+3.0e0*swa*swb+swb2)/d7;
@@ -713,7 +713,7 @@ void PairREAX::taper_setup()
swc2=-210.0e0*(swa3*swb2+swa2*swb3)/d7;
swc1= 140.0e0*swa3*swb3/d7;
swc0=(-35.0e0*swa3*swb2*swb2+21.0e0*swa2*swb3*swb2+
- 7.0e0*swa*swb3*swb3+swb3*swb3*swb)/d7;
+ 7.0e0*swa*swb3*swb3+swb3*swb3*swb)/d7;
}
/* ---------------------------------------------------------------------- */
@@ -792,16 +792,16 @@ void PairREAX::compute_charge(double &energy_charge_equilibration)
itag = tag[i];
jlist = firstneigh[i];
jnum = numneigh[i];
-
+
arow_ptr[i] = nmatentries;
aval[nmatentries] = 2.0*param_list[itype].params[1];
acol_ind[nmatentries] = i;
nmatentries++;
-
+
aval[nmatentries] = 1.0;
acol_ind[nmatentries] = nlocal + nghost;
- nmatentries++;
-
+ nmatentries++;
+
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
@@ -811,39 +811,39 @@ void PairREAX::compute_charge(double &energy_charge_equilibration)
zjtmp = x[j][2];
jtype = type[j];
jtag = tag[j];
-
+
delx = xitmp - xjtmp;
dely = yitmp - yjtmp;
delz = zitmp - zjtmp;
-
+
delr2 = delx*delx+dely*dely+delz*delz;
-
+
// avoid counting local-ghost pair twice since
// ReaxFF uses half neigh list with newton off
if (j >= nlocal) {
- if (itag > jtag) {
- if ((itag+jtag) % 2 == 0) continue;
- } else if (itag < jtag) {
- if ((itag+jtag) % 2 == 1) continue;
- } else {
- if (zjtmp < zitmp) continue;
- if (zjtmp == zitmp && yjtmp < yitmp) continue;
- if (zjtmp == zitmp && yjtmp == yitmp && xjtmp < xitmp) continue;
- }
+ if (itag > jtag) {
+ if ((itag+jtag) % 2 == 0) continue;
+ } else if (itag < jtag) {
+ if ((itag+jtag) % 2 == 1) continue;
+ } else {
+ if (zjtmp < zitmp) continue;
+ if (zjtmp == zitmp && yjtmp < yitmp) continue;
+ if (zjtmp == zitmp && yjtmp == yitmp && xjtmp < xitmp) continue;
+ }
}
// rcutvsq = cutmax*cutmax, in ReaxFF
if (delr2 <= rcutvsq) {
- gamt = sqrt(param_list[itype].params[2]*param_list[jtype].params[2]);
- delr_norm = sqrt(delr2);
- sw = taper_E(delr_norm, delr2);
- hulp1=(delr_norm*delr2+(1.0/(gamt*gamt*gamt)));
- hulp2=sw*14.40/cbrt(hulp1);
- aval[nmatentries] = hulp2;
- acol_ind[nmatentries] = j;
- nmatentries++;
+ gamt = sqrt(param_list[itype].params[2]*param_list[jtype].params[2]);
+ delr_norm = sqrt(delr2);
+ sw = taper_E(delr_norm, delr2);
+ hulp1=(delr_norm*delr2+(1.0/(gamt*gamt*gamt)));
+ hulp2=sw*14.40/cbrt(hulp1);
+ aval[nmatentries] = hulp2;
+ acol_ind[nmatentries] = j;
+ nmatentries++;
}
}
}
@@ -857,7 +857,7 @@ void PairREAX::compute_charge(double &energy_charge_equilibration)
arow_ptr[nlocal+nghost] = nmatentries;
// add rhs matentries to linear system
-
+
for (ii =0; ii<inum; ii++) {
i = ilist[ii];
itype = type[i];
@@ -907,7 +907,7 @@ void PairREAX::compute_charge(double &energy_charge_equilibration)
// if want other units would have to change params[] in file
qi = 23.02 * (param_list[itype].params[0]*ch[i]+
- param_list[itype].params[1]*ch[i]*ch[i]);
+ param_list[itype].params[1]*ch[i]*ch[i]);
energy_charge_equilibration += qi;
if (eflag_atom) eatom[i] += qi;
}
@@ -921,8 +921,8 @@ void PairREAX::compute_charge(double &energy_charge_equilibration)
/* ---------------------------------------------------------------------- */
void PairREAX::charge_reax(const int & nlocal, const int & nghost,
- double ch[], double aval[], int acol_ind[],
- int arow_ptr[], double elcvec[])
+ double ch[], double aval[], int acol_ind[],
+ int arow_ptr[], double elcvec[])
{
cg_solve(nlocal,nghost,aval,acol_ind,arow_ptr,ch,elcvec);
}
@@ -931,9 +931,9 @@ void PairREAX::charge_reax(const int & nlocal, const int & nghost,
CG solver for linear systems
------------------------------------------------------------------------- */
-void PairREAX::cg_solve(const int & nlocal, const int & nghost,
- double aval[], int acol_ind[], int arow_ptr[],
- double x[], double b[])
+void PairREAX::cg_solve(const int & nlocal, const int & nghost,
+ double aval[], int acol_ind[], int arow_ptr[],
+ double x[], double b[])
{
double one, zero, rho, rho_old, alpha, beta, gamma;
int iter, maxiter;
@@ -945,7 +945,7 @@ void PairREAX::cg_solve(const int & nlocal, const int & nghost,
// accumulated (full) vectors: x, w, p
// r = b-A.x
// w = r (ReverseComm + Comm)
-
+
double *r = rcg;
double *w = wcg;
double *p = pcg;
@@ -959,22 +959,22 @@ void PairREAX::cg_solve(const int & nlocal, const int & nghost,
maxiter = 100;
for (int i = 0; i < n; i++) w[i] = 0;
-
+
// construct r = b-Ax
sparse_product(n, nlocal, nghost, aval, acol_ind, arow_ptr, x, r);
-
+
// not using BLAS library
for (int i=0; i<n; i++) {
r[i] = b[i] - r[i];
w[i] = r[i];
}
-
+
packflag = 1;
comm->reverse_comm_pair(this);
comm->forward_comm_pair(this);
-
+
MPI_Allreduce(&w[n-1], &sumtmp, 1, MPI_DOUBLE, MPI_SUM, world);
w[n-1] = sumtmp;
rho_old = one;
@@ -995,7 +995,7 @@ void PairREAX::cg_solve(const int & nlocal, const int & nghost,
}
sparse_product(n, nlocal, nghost, aval, acol_ind, arow_ptr, p, q);
-
+
gamma = 0.0;
for (int i=0; i<n; i++) gamma += p[i]*q[i];
MPI_Allreduce(&gamma, &sumtmp, 1, MPI_DOUBLE, MPI_SUM, world);
@@ -1008,7 +1008,7 @@ void PairREAX::cg_solve(const int & nlocal, const int & nghost,
r[i] -= alpha*q[i];
w[i] = r[i];
}
-
+
comm->reverse_comm_pair(this);
comm->forward_comm_pair(this);
@@ -1025,9 +1025,9 @@ void PairREAX::cg_solve(const int & nlocal, const int & nghost,
------------------------------------------------------------------------- */
void PairREAX::sparse_product(const int &n, const int &nlocal,
- const int &nghost,
- double aval[], int acol_ind[], int arow_ptr[],
- double *x, double *r)
+ const int &nghost,
+ double aval[], int acol_ind[], int arow_ptr[],
+ double *x, double *r)
{
int i,j,jj;
@@ -1041,7 +1041,7 @@ void PairREAX::sparse_product(const int &n, const int &nlocal,
r[jj] += aval[j]*x[i];
}
}
-
+
for (i=nlocal; i<nlocal+nghost; i++)
for (j=arow_ptr[i]; j<arow_ptr[i+1]; j++) {
jj = acol_ind[j];
@@ -1051,7 +1051,7 @@ void PairREAX::sparse_product(const int &n, const int &nlocal,
}
/* ----------------------------------------------------------------------
- memory usage of local atom-based arrays
+ memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double PairREAX::memory_usage()
diff --git a/src/REAX/pair_reax.h b/src/REAX/pair_reax.h
index f9f87dd00320542852c332ad6577f4c53d5f792d..4062dc7e11806b16fe99299316cf977eaad972d7 100644
--- a/src/REAX/pair_reax.h
+++ b/src/REAX/pair_reax.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -40,10 +40,10 @@ class PairREAX : public Pair {
void unpack_comm(int, int, double *);
int pack_reverse_comm(int, int, double *);
void unpack_reverse_comm(int, int *, double *);
-
+
private:
double cutmax;
- double rcutvsq,rcutbsq;
+ double rcutvsq,rcutbsq;
int iprune,ihb,ihbnew,itripstaball;
double hbcut,swb;
double swa;
@@ -83,11 +83,11 @@ class PairREAX : public Pair {
void compute_charge(double &);
void sparse_product(const int &, const int &, const int &, double[],
- int[], int[], double[], double[]);
- void cg_solve(const int &, const int &, double[], int[],
- int[], double[], double[]);
+ int[], int[], double[], double[]);
+ void cg_solve(const int &, const int &, double[], int[],
+ int[], double[], double[]);
void charge_reax(const int &, const int &, double[],
- double[], int[], int[], double[]);
+ double[], int[], int[], double[]);
};
}
diff --git a/src/REAX/pair_reax_fortran.h b/src/REAX/pair_reax_fortran.h
index 057ff7c1e1801afa533822c43349280ecb99353e..50246b7ee7886593a65afd937c73203fa190e573 100644
--- a/src/REAX/pair_reax_fortran.h
+++ b/src/REAX/pair_reax_fortran.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -19,12 +19,12 @@
// corresponding macro at compile time using -D e.g. -D_IBM
// CONS(a,b) should return ab, the concatenation of its arguments.
-// If compiler is using strict ISO C standards, the ## works.
+// If compiler is using strict ISO C standards, the ## works.
// Otherwise try the old /**/ trick and test.
-// If that fails, you will need to figure out
+// If that fails, you will need to figure out
// a definition for the FORTRAN macro that works on your machine.
-#if __STDC__
+#if __STDC__
#define CONS(a,b) a##b
#elif defined(_IBM)
#define CONS(a,b) a##b
@@ -56,11 +56,11 @@ static int my_applesoroanges = CONS(my_apples,_my_oranges);
class ReaxParams {
public:
- enum {nneighmax=NNEIGHMAXDEF,
- nat=NATDEF,
- nattot=NATTOTDEF,
+ enum {nneighmax=NNEIGHMAXDEF,
+ nat=NATDEF,
+ nattot=NATTOTDEF,
nsort=NSORTDEF,
- mbond=MBONDDEF,
+ mbond=MBONDDEF,
nbomax=NBOMAXDEF,
};
};
@@ -96,7 +96,7 @@ extern "C" struct {
extern "C" struct {
double atomvirial[6*ReaxParams::nat];
- double virial[6];
+ double virial[6];
int Lvirial;
int Latomvirial;
} FORTRAN(cbkvirial,CBKVIRIAL);
@@ -160,15 +160,15 @@ extern "C" struct {
} FORTRAN(cbkenergies,CBKENERGIES);
extern "C" struct {
- double tset;
- double dseed;
- double tempmd;
- double ts2;
- double ts22;
- int nmolo;
- int nmolo5;
- int nbon;
- int na;
+ double tset;
+ double dseed;
+ double tempmd;
+ double ts2;
+ double ts22;
+ int nmolo;
+ int nmolo5;
+ int nbon;
+ int na;
int namov;
int na_local;
} FORTRAN(rsmall,RSMALL);
@@ -208,4 +208,3 @@ extern "C" void FORTRAN(mdsav,MDSAV)(int*);
extern "C" void FORTRAN(getnsbmax,GETNSBMAX)(int*);
extern "C" void FORTRAN(getnsbma2,GETNSBMA2)(int*);
extern "C" void FORTRAN(getcutof3,GETCUTOF3)(double*);
-
diff --git a/src/REPLICA/compute_event_displace.cpp b/src/REPLICA/compute_event_displace.cpp
index fb2e13298d07e8f1155b0a3832ea274a46a464ce..8cfe64461d07ec4a971b9387b0a12960536aa6f5 100644
--- a/src/REPLICA/compute_event_displace.cpp
+++ b/src/REPLICA/compute_event_displace.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -43,7 +43,7 @@ ComputeEventDisplace::ComputeEventDisplace(LAMMPS *lmp, int narg, char **arg) :
extscalar = 0;
double displace_dist = atof(arg[3]);
- if (displace_dist <= 0.0)
+ if (displace_dist <= 0.0)
error->all(FLERR,"Distance must be > 0 for compute event/displace");
displace_distsq = displace_dist * displace_dist;
@@ -70,11 +70,11 @@ void ComputeEventDisplace::init()
if (id_event != NULL) {
int ifix = modify->find_fix(id_event);
if (ifix < 0) error->all(FLERR,
- "Could not find compute event/displace fix ID");
+ "Could not find compute event/displace fix ID");
fix_event = (FixEvent*) modify->fix[ifix];
-
+
if (strcmp(fix_event->style,"EVENT/PRD") != 0 &&
- strcmp(fix_event->style,"EVENT/TAD") != 0)
+ strcmp(fix_event->style,"EVENT/TAD") != 0)
error->all(FLERR,"Compute event/displace has invalid fix event assigned");
}
@@ -109,12 +109,12 @@ double ComputeEventDisplace::compute_scalar()
if (triclinic == 0) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- xbox = (image[i] & 1023) - 512;
- ybox = (image[i] >> 10 & 1023) - 512;
- zbox = (image[i] >> 20) - 512;
- dx = x[i][0] + xbox*xprd - xevent[i][0];
- dy = x[i][1] + ybox*yprd - xevent[i][1];
- dz = x[i][2] + zbox*zprd - xevent[i][2];
+ xbox = (image[i] & 1023) - 512;
+ ybox = (image[i] >> 10 & 1023) - 512;
+ zbox = (image[i] >> 20) - 512;
+ dx = x[i][0] + xbox*xprd - xevent[i][0];
+ dy = x[i][1] + ybox*yprd - xevent[i][1];
+ dz = x[i][2] + zbox*zprd - xevent[i][2];
rsq = dx*dx + dy*dy + dz*dz;
if (rsq >= displace_distsq) {
event = 1.0;
@@ -124,12 +124,12 @@ double ComputeEventDisplace::compute_scalar()
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- xbox = (image[i] & 1023) - 512;
- ybox = (image[i] >> 10 & 1023) - 512;
- zbox = (image[i] >> 20) - 512;
- dx = x[i][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox - xevent[i][0];
- dy = x[i][1] + h[1]*ybox + h[3]*zbox - xevent[i][1];
- dz = x[i][2] + h[2]*zbox - xevent[i][2];
+ xbox = (image[i] & 1023) - 512;
+ ybox = (image[i] >> 10 & 1023) - 512;
+ zbox = (image[i] >> 20) - 512;
+ dx = x[i][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox - xevent[i][0];
+ dy = x[i][1] + h[1]*ybox + h[3]*zbox - xevent[i][1];
+ dz = x[i][2] + h[2]*zbox - xevent[i][2];
rsq = dx*dx + dy*dy + dz*dz;
if (rsq >= displace_distsq) {
event = 1.0;
diff --git a/src/REPLICA/compute_event_displace.h b/src/REPLICA/compute_event_displace.h
index 87135d2be485a748375b0e52599f9c0f9b84ae78..3d3fb23c49016e69488d574461e916953ed858bf 100644
--- a/src/REPLICA/compute_event_displace.h
+++ b/src/REPLICA/compute_event_displace.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/REPLICA/fix_event.cpp b/src/REPLICA/fix_event.cpp
index 700b9e33414a56371aeb983b26fcea3bfb3d1e75..4f59530573bd0d6a5bf72bbbd3a86f202142165f 100644
--- a/src/REPLICA/fix_event.cpp
+++ b/src/REPLICA/fix_event.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -55,7 +55,7 @@ FixEvent::FixEvent(LAMMPS *lmp, int narg, char **arg) :
FixEvent::~FixEvent()
{
// unregister callbacks to this fix from Atom class
-
+
atom->delete_callback(id,0);
// delete locally stored array
@@ -84,7 +84,7 @@ void FixEvent::store_event()
int *image = atom->image;
int nlocal = atom->nlocal;
- for (int i = 0; i < nlocal; i++)
+ for (int i = 0; i < nlocal; i++)
domain->unmap(x[i],image[i],xevent[i]);
}
@@ -248,7 +248,7 @@ int FixEvent::unpack_exchange(int nlocal, double *buf)
}
/* ----------------------------------------------------------------------
- pack entire state of Fix into one write
+ pack entire state of Fix into one write
------------------------------------------------------------------------- */
void FixEvent::write_restart(FILE *fp)
@@ -256,7 +256,7 @@ void FixEvent::write_restart(FILE *fp)
}
/* ----------------------------------------------------------------------
- use state info from restart file to restart the Fix
+ use state info from restart file to restart the Fix
------------------------------------------------------------------------- */
void FixEvent::restart(char *buf)
diff --git a/src/REPLICA/fix_event.h b/src/REPLICA/fix_event.h
index 6f8db48788a24ae106e6a74daf8fd22c0641e714..5f70ff9dca476cda0d905df43ec16b4d85bf74a5 100644
--- a/src/REPLICA/fix_event.h
+++ b/src/REPLICA/fix_event.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/REPLICA/fix_event_prd.cpp b/src/REPLICA/fix_event_prd.cpp
index cc8192a0af38399725f90c2427d67ceef980ac95..338c6a2f76bf30b1ca0dc2d2181c8efe9df8f01a 100644
--- a/src/REPLICA/fix_event_prd.cpp
+++ b/src/REPLICA/fix_event_prd.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -60,7 +60,7 @@ void FixEventPRD::store_event_prd(bigint ntimestep, int delta_clock)
}
/* ----------------------------------------------------------------------
- pack entire state of Fix into one write
+ pack entire state of Fix into one write
------------------------------------------------------------------------- */
void FixEventPRD::write_restart(FILE *fp)
@@ -82,7 +82,7 @@ void FixEventPRD::write_restart(FILE *fp)
}
/* ----------------------------------------------------------------------
- use state info from restart file to restart the Fix
+ use state info from restart file to restart the Fix
------------------------------------------------------------------------- */
void FixEventPRD::restart(char *buf)
@@ -97,5 +97,3 @@ void FixEventPRD::restart(char *buf)
correlated_event = static_cast<int> (list[n++]);
ncoincident = static_cast<int> (list[n++]);
}
-
-
diff --git a/src/REPLICA/fix_event_prd.h b/src/REPLICA/fix_event_prd.h
index 11dcbb361edc41f97c4fd29cc72817529bf8c0db..8cf7ef7846b1acb129738afde2f668d88a37fbca 100644
--- a/src/REPLICA/fix_event_prd.h
+++ b/src/REPLICA/fix_event_prd.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/REPLICA/fix_event_tad.cpp b/src/REPLICA/fix_event_tad.cpp
index 197a0904d14018e726dd8caffb566515186137bc..aed1d75437cdd081f1fb80b10fcb0776844f8784 100644
--- a/src/REPLICA/fix_event_tad.cpp
+++ b/src/REPLICA/fix_event_tad.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -58,7 +58,7 @@ void FixEventTAD::store_event_tad(bigint ntimestep)
}
/* ----------------------------------------------------------------------
- pack entire state of Fix into one write
+ pack entire state of Fix into one write
------------------------------------------------------------------------- */
void FixEventTAD::write_restart(FILE *fp)
@@ -78,7 +78,7 @@ void FixEventTAD::write_restart(FILE *fp)
}
/* ----------------------------------------------------------------------
- use state info from restart file to restart the Fix
+ use state info from restart file to restart the Fix
------------------------------------------------------------------------- */
void FixEventTAD::restart(char *buf)
@@ -91,5 +91,3 @@ void FixEventTAD::restart(char *buf)
tlo = list[n++];
ebarrier = list[n++];
}
-
-
diff --git a/src/REPLICA/fix_event_tad.h b/src/REPLICA/fix_event_tad.h
index e754504771c6e7d7dc5852cded4d229397ba91c4..91e2045ecccf493cb238c8b95a4e1b9736a0483d 100644
--- a/src/REPLICA/fix_event_tad.h
+++ b/src/REPLICA/fix_event_tad.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -28,7 +28,7 @@ class FixEventTAD : public FixEvent {
public:
int event_number; // event counter
bigint event_timestep; // timestep of last event
- double tlo; // event time at low temperature
+ double tlo; // event time at low temperature
double ebarrier; // energy barrier for this event
FixEventTAD(class LAMMPS *, int, char **);
diff --git a/src/REPLICA/fix_neb.cpp b/src/REPLICA/fix_neb.cpp
index 73116fac2576391e9689803e0b672e52942ba02c..6aabea3ebcbb4288ac1eae3c8c45721438a785bc 100644
--- a/src/REPLICA/fix_neb.cpp
+++ b/src/REPLICA/fix_neb.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -142,7 +142,7 @@ void FixNEB::min_post_force(int vflag)
if (ireplica < nreplica-1) MPI_Send(&veng,1,MPI_DOUBLE,procnext,0,uworld);
if (ireplica > 0) MPI_Recv(&vprev,1,MPI_DOUBLE,procprev,0,uworld,&status);
-
+
if (ireplica > 0) MPI_Send(&veng,1,MPI_DOUBLE,procprev,0,uworld);
if (ireplica < nreplica-1)
MPI_Recv(&vnext,1,MPI_DOUBLE,procnext,0,uworld,&status);
@@ -199,41 +199,41 @@ void FixNEB::min_post_force(int vflag)
if (vnext > veng && veng > vprev) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- tangent[i][0] = xnext[i][0] - x[i][0];
- tangent[i][1] = xnext[i][1] - x[i][1];
- tangent[i][2] = xnext[i][2] - x[i][2];
- domain->minimum_image(tangent[i]);
+ tangent[i][0] = xnext[i][0] - x[i][0];
+ tangent[i][1] = xnext[i][1] - x[i][1];
+ tangent[i][2] = xnext[i][2] - x[i][2];
+ domain->minimum_image(tangent[i]);
}
} else if (vnext < veng && veng < vprev) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- tangent[i][0] = x[i][0] - xprev[i][0];
- tangent[i][1] = x[i][1] - xprev[i][1];
- tangent[i][2] = x[i][2] - xprev[i][2];
- domain->minimum_image(tangent[i]);
+ tangent[i][0] = x[i][0] - xprev[i][0];
+ tangent[i][1] = x[i][1] - xprev[i][1];
+ tangent[i][2] = x[i][2] - xprev[i][2];
+ domain->minimum_image(tangent[i]);
}
} else {
vmax = MAX(fabs(vnext-veng),fabs(vprev-veng));
vmin = MIN(fabs(vnext-veng),fabs(vprev-veng));
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- delta1[0] = xnext[i][0] - x[i][0];
- delta1[1] = xnext[i][1] - x[i][1];
- delta1[2] = xnext[i][2] - x[i][2];
- domain->minimum_image(delta1);
- delta2[0] = x[i][0] - xprev[i][0];
- delta2[1] = x[i][1] - xprev[i][1];
- delta2[2] = x[i][2] - xprev[i][2];
- domain->minimum_image(delta2);
- if (vnext > vprev) {
- tangent[i][0] = vmax*delta1[0] + vmin*delta2[0];
- tangent[i][1] = vmax*delta1[1] + vmin*delta2[1];
- tangent[i][2] = vmax*delta1[2] + vmin*delta2[2];
- } else {
- tangent[i][0] = vmin*delta1[0] + vmax*delta2[0];
- tangent[i][1] = vmin*delta1[1] + vmax*delta2[1];
- tangent[i][2] = vmin*delta1[2] + vmax*delta2[2];
- }
+ delta1[0] = xnext[i][0] - x[i][0];
+ delta1[1] = xnext[i][1] - x[i][1];
+ delta1[2] = xnext[i][2] - x[i][2];
+ domain->minimum_image(delta1);
+ delta2[0] = x[i][0] - xprev[i][0];
+ delta2[1] = x[i][1] - xprev[i][1];
+ delta2[2] = x[i][2] - xprev[i][2];
+ domain->minimum_image(delta2);
+ if (vnext > vprev) {
+ tangent[i][0] = vmax*delta1[0] + vmin*delta2[0];
+ tangent[i][1] = vmax*delta1[1] + vmin*delta2[1];
+ tangent[i][2] = vmax*delta1[2] + vmin*delta2[2];
+ } else {
+ tangent[i][0] = vmin*delta1[0] + vmax*delta2[0];
+ tangent[i][1] = vmin*delta1[1] + vmax*delta2[1];
+ tangent[i][2] = vmin*delta1[2] + vmax*delta2[2];
+ }
}
}
@@ -245,9 +245,9 @@ void FixNEB::min_post_force(int vflag)
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- tlen += tangent[i][0]*tangent[i][0] + tangent[i][1]*tangent[i][1] +
- tangent[i][2]*tangent[i][2];
-
+ tlen += tangent[i][0]*tangent[i][0] + tangent[i][1]*tangent[i][1] +
+ tangent[i][2]*tangent[i][2];
+
delx = x[i][0] - xprev[i][0];
dely = x[i][1] - xprev[i][1];
delz = x[i][2] - xprev[i][2];
@@ -271,9 +271,9 @@ void FixNEB::min_post_force(int vflag)
double tleninv = 1.0/tlen;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- tangent[i][0] *= tleninv;
- tangent[i][1] *= tleninv;
- tangent[i][2] *= tleninv;
+ tangent[i][0] *= tleninv;
+ tangent[i][1] *= tleninv;
+ tangent[i][2] *= tleninv;
}
}
@@ -292,8 +292,8 @@ void FixNEB::min_post_force(int vflag)
double dot = 0.0;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit)
- dot += f[i][0]*tangent[i][0] + f[i][1]*tangent[i][1] +
- f[i][2]*tangent[i][2];
+ dot += f[i][0]*tangent[i][0] + f[i][1]*tangent[i][1] +
+ f[i][2]*tangent[i][2];
}
double prefactor;
diff --git a/src/REPLICA/fix_neb.h b/src/REPLICA/fix_neb.h
index 140ad60694ddf9d98e62ac4b29639f1f2222f324..b4e72a5a9f0b78c47c5d16c821bd285c1f84cef3 100644
--- a/src/REPLICA/fix_neb.h
+++ b/src/REPLICA/fix_neb.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/REPLICA/neb.cpp b/src/REPLICA/neb.cpp
index b700ffde9bea96eb9fbae0c9aff6c5df902b333d..86922826d35a73e63a5ecf0820548ab70b100d0b 100644
--- a/src/REPLICA/neb.cpp
+++ b/src/REPLICA/neb.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -46,8 +46,8 @@ NEB::NEB(LAMMPS *lmp) : Pointers(lmp) {}
------------------------------------------------------------------------- */
NEB::NEB(LAMMPS *lmp, double etol_in, double ftol_in, int n1steps_in,
- int n2steps_in, int nevery_in, double *buf_init, double *buf_final)
- : Pointers(lmp)
+ int n2steps_in, int nevery_in, double *buf_init, double *buf_final)
+ : Pointers(lmp)
{
double delx,dely,delz;
@@ -100,11 +100,11 @@ NEB::~NEB()
void NEB::command(int narg, char **arg)
{
- if (domain->box_exist == 0)
+ if (domain->box_exist == 0)
error->all(FLERR,"NEB command before simulation box is defined");
if (narg != 6) error->universe_all(FLERR,"Illegal NEB command");
-
+
etol = atof(arg[0]);
ftol = atof(arg[1]);
n1steps = atoi(arg[2]);
@@ -135,7 +135,7 @@ void NEB::command(int narg, char **arg)
error->all(FLERR,"Can only use NEB with 1-processor replicas");
if (atom->sortfreq > 0)
error->all(FLERR,"Cannot use NEB with atom_modify sort enabled");
- if (atom->map_style == 0)
+ if (atom->map_style == 0)
error->all(FLERR,"Cannot use NEB unless atom map exists");
// read in file of final state atom coords and reset my coords
@@ -186,7 +186,7 @@ void NEB::run()
if (me_universe == 0 && universe->uscreen)
fprintf(universe->uscreen,"Setting up regular NEB ...\n");
-
+
update->beginstep = update->firststep = update->ntimestep;
update->endstep = update->laststep = update->firststep + n1steps;
update->nsteps = n1steps;
@@ -195,21 +195,21 @@ void NEB::run()
error->all(FLERR,"Too many timesteps for NEB");
update->minimize->setup();
-
+
if (me_universe == 0) {
if (universe->uscreen)
fprintf(universe->uscreen,"Step MaxReplicaForce MaxAtomForce "
- "GradV0 GradV1 GradVc "
- "EBF EBR RDT "
- "RD1 PE1 RD2 PE2 ... RDN PEN\n");
+ "GradV0 GradV1 GradVc "
+ "EBF EBR RDT "
+ "RD1 PE1 RD2 PE2 ... RDN PEN\n");
if (universe->ulogfile)
fprintf(universe->ulogfile,"Step MaxReplicaForce MaxAtomForce "
- "GradV0 GradV1 GradVc "
- "EBF EBR RDT "
- "RD1 PE1 RD2 PE2 ... RDN PEN\n");
+ "GradV0 GradV1 GradVc "
+ "EBF EBR RDT "
+ "RD1 PE1 RD2 PE2 ... RDN PEN\n");
}
print_status();
-
+
// perform regular NEB for n1steps or until replicas converge
// retrieve PE values from fix NEB and print every nevery iterations
// break induced if converged
@@ -217,13 +217,13 @@ void NEB::run()
timer->init();
timer->barrier_start(TIME_LOOP);
-
+
while (update->minimize->niter < n1steps) {
update->minimize->run(nevery);
print_status();
if (update->minimize->stop_condition) break;
}
-
+
timer->barrier_stop(TIME_LOOP);
update->minimize->cleanup();
@@ -254,7 +254,7 @@ void NEB::run()
if (universe->ulogfile)
fprintf(universe->ulogfile,"Climbing replica = %d\n",top+1);
}
-
+
update->beginstep = update->firststep = update->ntimestep;
update->endstep = update->laststep = update->firststep + n2steps;
update->nsteps = n2steps;
@@ -269,22 +269,22 @@ void NEB::run()
if (me_universe == 0) {
if (universe->uscreen)
fprintf(universe->uscreen,"Step MaxReplicaForce MaxAtomForce "
- "GradV0 GradV1 GradVc "
- "EBF EBR RDT "
- "RD1 PE1 RD2 PE2 ... RDN PEN\n");
+ "GradV0 GradV1 GradVc "
+ "EBF EBR RDT "
+ "RD1 PE1 RD2 PE2 ... RDN PEN\n");
if (universe->ulogfile)
fprintf(universe->ulogfile,"Step MaxReplicaForce MaxAtomForce "
- "GradV0 GradV1 GradVc "
- "EBF EBR RDT "
- "RD1 PE1 RD2 PE2 ... RDN PEN\n");
+ "GradV0 GradV1 GradVc "
+ "EBF EBR RDT "
+ "RD1 PE1 RD2 PE2 ... RDN PEN\n");
}
print_status();
-
+
// perform climbing NEB for n2steps or until replicas converge
// retrieve PE values from fix NEB and print every nevery iterations
// break induced if converged
// damped dynamic min styles insure all replicas converge together
-
+
timer->init();
timer->barrier_start(TIME_LOOP);
@@ -293,7 +293,7 @@ void NEB::run()
print_status();
if (update->minimize->stop_condition) break;
}
-
+
timer->barrier_stop(TIME_LOOP);
update->minimize->cleanup();
@@ -337,9 +337,9 @@ void NEB::readfile(char *file)
if (me_universe == 0) {
m = 0;
for (nlines = 0; nlines < CHUNK; nlines++) {
- ptr = fgets(&buffer[m],MAXLINE,fp);
- if (ptr == NULL) break;
- m += strlen(&buffer[m]);
+ ptr = fgets(&buffer[m],MAXLINE,fp);
+ if (ptr == NULL) break;
+ m += strlen(&buffer[m]);
}
if (ptr == NULL) eof = 1;
buffer[m++] = '\n';
@@ -356,8 +356,8 @@ void NEB::readfile(char *file)
*next = '\0';
if (firstline) {
- if (atom->count_words(bufptr) == 4) firstline = 0;
- else error->all(FLERR,"Incorrect format in NEB coordinate file");
+ if (atom->count_words(bufptr) == 4) firstline = 0;
+ else error->all(FLERR,"Incorrect format in NEB coordinate file");
}
sscanf(bufptr,"%d %lg %lg %lg",&tag,&xx,&yy,&zz);
@@ -372,14 +372,14 @@ void NEB::readfile(char *file)
m = atom->map(tag);
if (m >= 0 && m < nlocal) {
- delx = xx - x[m][0];
- dely = yy - x[m][1];
- delz = zz - x[m][2];
- domain->minimum_image(delx,dely,delz);
- x[m][0] += fraction*delx;
- x[m][1] += fraction*dely;
- x[m][2] += fraction*delz;
- ncount++;
+ delx = xx - x[m][0];
+ dely = yy - x[m][1];
+ delz = zz - x[m][2];
+ domain->minimum_image(delx,dely,delz);
+ x[m][0] += fraction*delx;
+ x[m][1] += fraction*dely;
+ x[m][2] += fraction*delz;
+ ncount++;
}
bufptr = next + 1;
@@ -476,8 +476,8 @@ void NEB::print_status()
int top = 0;
for (int m = 1; m < nreplica; m++)
if (vmax < all[m][0]) {
- vmax = all[m][0];
- top = m;
+ vmax = all[m][0];
+ top = m;
}
irep = top;
gradvnormc = all[irep][3];
@@ -488,22 +488,22 @@ void NEB::print_status()
if (me_universe == 0) {
if (universe->uscreen) {
fprintf(universe->uscreen,BIGINT_FORMAT " %12.8g %12.8g ",
- update->ntimestep,fmaxreplica,fmaxatom);
+ update->ntimestep,fmaxreplica,fmaxatom);
fprintf(universe->uscreen,"%12.8g %12.8g %12.8g ",
- gradvnorm0,gradvnorm1,gradvnormc);
+ gradvnorm0,gradvnorm1,gradvnormc);
fprintf(universe->uscreen,"%12.8g %12.8g %12.8g ",ebf,ebr,endpt);
- for (int i = 0; i < nreplica; i++)
- fprintf(universe->uscreen,"%12.8g %12.8g ",rdist[i],all[i][0]);
+ for (int i = 0; i < nreplica; i++)
+ fprintf(universe->uscreen,"%12.8g %12.8g ",rdist[i],all[i][0]);
fprintf(universe->uscreen,"\n");
}
if (universe->ulogfile) {
fprintf(universe->ulogfile,BIGINT_FORMAT " %12.8g %12.8g ",
- update->ntimestep,fmaxreplica,fmaxatom);
+ update->ntimestep,fmaxreplica,fmaxatom);
fprintf(universe->ulogfile,"%12.8g %12.8g %12.8g ",
- gradvnorm0,gradvnorm1,gradvnormc);
+ gradvnorm0,gradvnorm1,gradvnormc);
fprintf(universe->ulogfile,"%12.8g %12.8g %12.8g ",ebf,ebr,endpt);
for (int i = 0; i < nreplica; i++)
- fprintf(universe->ulogfile,"%12.8g %12.8g ",rdist[i],all[i][0]);
+ fprintf(universe->ulogfile,"%12.8g %12.8g ",rdist[i],all[i][0]);
fprintf(universe->ulogfile,"\n");
fflush(universe->ulogfile);
}
diff --git a/src/REPLICA/neb.h b/src/REPLICA/neb.h
index 02eac60495b6b244a46a382f9fb8664c7caa7bef..1e1b47cc6a98b48f0cb24d41a33c7242e118557a 100644
--- a/src/REPLICA/neb.h
+++ b/src/REPLICA/neb.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -101,7 +101,7 @@ Use a different minimization style.
E: Too many timesteps for NEB
-You must use a number of timesteps that fit in a 32-bit integer
+You must use a number of timesteps that fit in a 32-bit integer
for NEB.
E: Too many timesteps
diff --git a/src/REPLICA/prd.cpp b/src/REPLICA/prd.cpp
index 24cd52f9e91e139daeeaed49cde95dc5df0d1731..17e83a9090363eb8f190c9fa2e0c6ae4c842c95a 100644
--- a/src/REPLICA/prd.cpp
+++ b/src/REPLICA/prd.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -35,7 +35,7 @@
#include "compute.h"
#include "fix.h"
#include "fix_event_prd.h"
-#include "force.h"
+#include "force.h"
#include "pair.h"
#include "random_park.h"
#include "random_mars.h"
@@ -62,13 +62,13 @@ void PRD::command(int narg, char **arg)
// error checks
- if (domain->box_exist == 0)
+ if (domain->box_exist == 0)
error->all(FLERR,"PRD command before simulation box is defined");
- if (universe->nworlds != universe->nprocs &&
- atom->map_style == 0)
+ if (universe->nworlds != universe->nprocs &&
+ atom->map_style == 0)
error->all(FLERR,"Cannot use PRD with multi-processor replicas "
- "unless atom map exists");
- if (universe->nworlds == 1 && comm->me == 0)
+ "unless atom map exists");
+ if (universe->nworlds == 1 && comm->me == 0)
error->warning(FLERR,"Running PRD with only one replica");
if (narg < 7) error->universe_all(FLERR,"Illegal prd command");
@@ -82,13 +82,13 @@ void PRD::command(int narg, char **arg)
char *id_compute = new char[strlen(arg[5])+1];
strcpy(id_compute,arg[5]);
int seed = atoi(arg[6]);
-
+
options(narg-7,&arg[7]);
// total # of timesteps must be multiple of t_event
if (t_event <= 0) error->universe_all(FLERR,"Invalid t_event in prd command");
- if (nsteps % t_event)
+ if (nsteps % t_event)
error->universe_all(FLERR,"PRD nsteps must be multiple of t_event");
if (t_corr % t_event)
error->universe_all(FLERR,"PRD t_corr must be multiple of t_event");
@@ -137,7 +137,7 @@ void PRD::command(int narg, char **arg)
random_dephase = new RanMars(lmp,seed+iworld);
// create ComputeTemp class to monitor temperature
-
+
char **args = new char*[3];
args[0] = (char *) "prd_temp";
args[1] = (char *) "all";
@@ -195,7 +195,7 @@ void PRD::command(int narg, char **arg)
neigh_dist_check = neighbor->dist_check;
if (neigh_every != 1 || neigh_delay != 0 || neigh_dist_check != 1) {
- if (me == 0)
+ if (me == 0)
error->warning(FLERR,"Resetting reneighboring criteria during PRD");
}
@@ -238,16 +238,16 @@ void PRD::command(int narg, char **arg)
// perform PRD simulation
- if (me_universe == 0 && universe->uscreen)
+ if (me_universe == 0 && universe->uscreen)
fprintf(universe->uscreen,"Setting up PRD ...\n");
if (me_universe == 0) {
- if (universe->uscreen)
+ if (universe->uscreen)
fprintf(universe->uscreen,"Step CPU Clock Event "
- "Correlated Coincident Replica\n");
- if (universe->ulogfile)
+ "Correlated Coincident Replica\n");
+ if (universe->ulogfile)
fprintf(universe->ulogfile,"Step CPU Clock Event "
- "Correlated Coincident Replica\n");
+ "Correlated Coincident Replica\n");
}
// store hot state and quenched event for replica 0
@@ -312,14 +312,14 @@ void PRD::command(int narg, char **arg)
share_event(ireplica,1);
log_event();
-
+
int restart_flag = 0;
if (output->restart_flag && universe->iworld == 0) {
- if (output->restart_every_single &&
- fix_event->event_number % output->restart_every_single == 0)
+ if (output->restart_every_single &&
+ fix_event->event_number % output->restart_every_single == 0)
restart_flag = 1;
- if (output->restart_every_double &&
- fix_event->event_number % output->restart_every_double == 0)
+ if (output->restart_every_double &&
+ fix_event->event_number % output->restart_every_double == 0)
restart_flag = 1;
}
@@ -342,7 +342,7 @@ void PRD::command(int narg, char **arg)
corr_endstep = update->ntimestep + t_corr;
} else fix_event->restore_state();
}
-
+
// full init/setup since are starting all replicas after event
// event replica bcasts temp to all replicas if temp_dephase is not set
@@ -355,14 +355,14 @@ void PRD::command(int narg, char **arg)
if (t_corr > 0) replicate(ireplica);
if (temp_flag == 0) {
if (ireplica == universe->iworld)
- temp_dephase = temperature->compute_scalar();
+ temp_dephase = temperature->compute_scalar();
MPI_Bcast(&temp_dephase,1,MPI_DOUBLE,universe->root_proc[ireplica],
- universe->uworld);
+ universe->uworld);
}
timer->barrier_stop(TIME_LOOP);
time_comm += timer->array[TIME_LOOP];
-
+
// write restart file of hot coords
if (restart_flag) {
@@ -388,20 +388,20 @@ void PRD::command(int narg, char **arg)
neighbor->ndanger = ndanger;
if (me_universe == 0) {
- if (universe->uscreen)
+ if (universe->uscreen)
fprintf(universe->uscreen,
- "Loop time of %g on %d procs for %d steps with " BIGINT_FORMAT
- " atoms\n",
- timer->array[TIME_LOOP],nprocs_universe,nsteps,atom->natoms);
- if (universe->ulogfile)
+ "Loop time of %g on %d procs for %d steps with " BIGINT_FORMAT
+ " atoms\n",
+ timer->array[TIME_LOOP],nprocs_universe,nsteps,atom->natoms);
+ if (universe->ulogfile)
fprintf(universe->ulogfile,
- "Loop time of %g on %d procs for %d steps with " BIGINT_FORMAT
- " atoms\n",
+ "Loop time of %g on %d procs for %d steps with " BIGINT_FORMAT
+ " atoms\n",
timer->array[TIME_LOOP],nprocs_universe,nsteps,atom->natoms);
}
-
+
finish->end(2);
-
+
update->whichflag = 0;
update->firststep = update->laststep = 0;
update->beginstep = update->endstep = 0;
@@ -419,7 +419,7 @@ void PRD::command(int narg, char **arg)
memory->destroy(tagall);
memory->destroy(xall);
memory->destroy(imageall);
-
+
delete [] id_compute;
MPI_Comm_free(&comm_replica);
delete random_select;
@@ -503,7 +503,7 @@ void PRD::quench()
bigint ntimestep_hold = update->ntimestep;
bigint endstep_hold = update->endstep;
- // need to change whichflag so that minimize->setup() calling
+ // need to change whichflag so that minimize->setup() calling
// modify->setup() will call fix->min_setup()
update->whichflag = 2;
@@ -546,7 +546,7 @@ void PRD::quench()
/* ----------------------------------------------------------------------
check for an event in any replica
- if replica_num is non-negative only check for event on replica_num
+ if replica_num is non-negative only check for event on replica_num
if multiple events, choose one at random
return -1 if no event
else return ireplica = world in which event occured
@@ -559,19 +559,19 @@ int PRD::check_event(int replica_num)
worldflag = 0;
if (compute_event->compute_scalar() > 0.0) worldflag = 1;
if (replica_num >= 0 && replica_num != universe->iworld) worldflag = 0;
-
+
timer->barrier_start(TIME_LOOP);
if (me == 0) MPI_Allreduce(&worldflag,&universeflag,1,
- MPI_INT,MPI_SUM,comm_replica);
+ MPI_INT,MPI_SUM,comm_replica);
MPI_Bcast(&universeflag,1,MPI_INT,0,world);
- ncoincident = universeflag;
+ ncoincident = universeflag;
if (!universeflag) ireplica = -1;
else {
if (universeflag > 1) {
- int iwhich = static_cast<int>
- (universeflag*random_select->uniform()) + 1;
+ int iwhich = static_cast<int>
+ (universeflag*random_select->uniform()) + 1;
if (me == 0) MPI_Scan(&worldflag,&scanflag,1,
- MPI_INT,MPI_SUM,comm_replica);
+ MPI_INT,MPI_SUM,comm_replica);
MPI_Bcast(&scanflag,1,MPI_INT,0,world);
if (scanflag != iwhich) worldflag = 0;
}
@@ -579,7 +579,7 @@ int PRD::check_event(int replica_num)
if (worldflag) replicaflag = universe->iworld;
else replicaflag = 0;
if (me == 0) MPI_Allreduce(&replicaflag,&ireplica,1,
- MPI_INT,MPI_SUM,comm_replica);
+ MPI_INT,MPI_SUM,comm_replica);
MPI_Bcast(&ireplica,1,MPI_INT,0,world);
}
timer->barrier_stop(TIME_LOOP);
@@ -606,7 +606,7 @@ void PRD::share_event(int ireplica, int flag)
replicate(ireplica);
timer->barrier_stop(TIME_LOOP);
time_comm += timer->array[TIME_LOOP];
-
+
// adjust time for last correlated event check (not on first event)
int corr_adjust = t_corr;
@@ -623,7 +623,7 @@ void PRD::share_event(int ireplica, int flag)
// don't change the clock or timestep if this is a restart
- if (flag == 0 && fix_event->event_number != 0)
+ if (flag == 0 && fix_event->event_number != 0)
fix_event->store_event_prd(fix_event->event_timestep,0);
else {
fix_event->store_event_prd(update->ntimestep,delta);
@@ -631,7 +631,7 @@ void PRD::share_event(int ireplica, int flag)
fix_event->correlated_event = 0;
if (flag == 2) fix_event->correlated_event = 1;
fix_event->ncoincident = ncoincident;
- }
+ }
if (flag == 0) fix_event->event_number--;
// dump snapshot of quenched coords
@@ -667,21 +667,21 @@ void PRD::log_event()
if (universe->me == 0) {
if (universe->uscreen)
fprintf(universe->uscreen,
- BIGINT_FORMAT " %.3f %d %d %d %d %d\n",
+ BIGINT_FORMAT " %.3f %d %d %d %d %d\n",
fix_event->event_timestep,
- timer->elapsed(TIME_LOOP),
- fix_event->clock,
+ timer->elapsed(TIME_LOOP),
+ fix_event->clock,
fix_event->event_number,fix_event->correlated_event,
- fix_event->ncoincident,
+ fix_event->ncoincident,
fix_event->replica_number);
if (universe->ulogfile)
fprintf(universe->ulogfile,
- BIGINT_FORMAT " %.3f %d %d %d %d %d\n",
+ BIGINT_FORMAT " %.3f %d %d %d %d %d\n",
fix_event->event_timestep,
- timer->elapsed(TIME_LOOP),
- fix_event->clock,
+ timer->elapsed(TIME_LOOP),
+ fix_event->clock,
fix_event->event_number,fix_event->correlated_event,
- fix_event->ncoincident,
+ fix_event->ncoincident,
fix_event->replica_number);
}
}
@@ -726,12 +726,12 @@ void PRD::replicate(int ireplica)
MPI_Gatherv(atom->tag,atom->nlocal,MPI_INT,
tagall,counts,displacements,MPI_INT,0,world);
MPI_Gatherv(atom->image,atom->nlocal,MPI_INT,
- imageall,counts,displacements,MPI_INT,0,world);
+ imageall,counts,displacements,MPI_INT,0,world);
for (i = 0; i < nprocs; i++) counts[i] *= 3;
for (i = 0; i < nprocs-1; i++)
displacements[i+1] = displacements[i] + counts[i];
MPI_Gatherv(atom->x[0],3*atom->nlocal,MPI_DOUBLE,
- xall[0],counts,displacements,MPI_DOUBLE,0,world);
+ xall[0],counts,displacements,MPI_DOUBLE,0,world);
}
if (me == 0) {
@@ -762,7 +762,7 @@ void PRD::replicate(int ireplica)
}
/* ----------------------------------------------------------------------
- parse optional parameters at end of PRD input line
+ parse optional parameters at end of PRD input line
------------------------------------------------------------------------- */
void PRD::options(int narg, char **arg)
@@ -770,7 +770,7 @@ void PRD::options(int narg, char **arg)
if (narg < 0) error->all(FLERR,"Illegal prd command");
// set defaults
-
+
etol = 0.1;
ftol = 0.1;
maxiter = 40;
diff --git a/src/REPLICA/prd.h b/src/REPLICA/prd.h
index 0e5b4db5ca39be9be3582e813defb1d98b65a193..45192480b3929d9d906db1589163a7383bd7483b 100644
--- a/src/REPLICA/prd.h
+++ b/src/REPLICA/prd.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -50,7 +50,7 @@ class PRD : protected Pointers {
double **xall;
int ncoincident;
-
+
class RanPark *random_select;
class RanMars *random_dephase;
class Compute *compute_event;
@@ -137,7 +137,7 @@ which is enabled by default, via the atom_modify command.
E: Too many iterations
-You must use a number of iterations that fit in a 32-bit integer
+You must use a number of iterations that fit in a 32-bit integer
for minimization.
*/
diff --git a/src/REPLICA/tad.cpp b/src/REPLICA/tad.cpp
index 6fb3a6cf8501fa5c5352dd3801df7a718ecf159e..9102bac1a077c6c7953d2ac417e0067b65573586 100644
--- a/src/REPLICA/tad.cpp
+++ b/src/REPLICA/tad.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -37,7 +37,7 @@
#include "fix.h"
#include "fix_event_tad.h"
#include "fix_store_state.h"
-#include "force.h"
+#include "force.h"
#include "pair.h"
#include "random_park.h"
#include "random_mars.h"
@@ -79,15 +79,15 @@ void TAD::command(int narg, char **arg)
// error checks
- if (domain->box_exist == 0)
+ if (domain->box_exist == 0)
error->all(FLERR,"Tad command before simulation box is defined");
- if (universe->nworlds == 1)
+ if (universe->nworlds == 1)
error->all(FLERR,"Cannot use TAD with a single replica for NEB");
if (universe->nworlds != universe->nprocs)
error->all(FLERR,"Can only use TAD with 1-processor replicas for NEB");
if (atom->sortfreq > 0)
error->all(FLERR,"Cannot use TAD with atom_modify sort enabled for NEB");
- if (atom->map_style == 0)
+ if (atom->map_style == 0)
error->all(FLERR,"Cannot use TAD unless atom map exists for NEB");
if (narg < 7) error->universe_all(FLERR,"Illegal tad command");
@@ -98,22 +98,22 @@ void TAD::command(int narg, char **arg)
temphi = atof(arg[3]);
delta_conf = atof(arg[4]);
tmax = atof(arg[5]);
-
+
char *id_compute = new char[strlen(arg[6])+1];
strcpy(id_compute,arg[6]);
-
+
options(narg-7,&arg[7]);
// total # of timesteps must be multiple of t_event
if (t_event <= 0) error->universe_all(FLERR,"Invalid t_event in tad command");
- if (nsteps % t_event)
+ if (nsteps % t_event)
error->universe_all(FLERR,"TAD nsteps must be multiple of t_event");
- if (delta_conf <= 0.0 || delta_conf >= 1.0)
+ if (delta_conf <= 0.0 || delta_conf >= 1.0)
error->universe_all(FLERR,"Invalid delta_conf in tad command");
- if (tmax <= 0.0)
+ if (tmax <= 0.0)
error->universe_all(FLERR,"Invalid tmax in tad command");
// deltconf = (ln(1/delta))/freq_min (timestep units)
@@ -129,7 +129,7 @@ void TAD::command(int narg, char **arg)
MPI_Comm_size(world,&nprocs);
delta_beta = (1.0/templo - 1.0/temphi) / force->boltz;
- ratio_beta = templo/temphi;
+ ratio_beta = templo/temphi;
// create FixEventTAD object to store last event
@@ -182,7 +182,7 @@ void TAD::command(int narg, char **arg)
neigh_dist_check = neighbor->dist_check;
if (neigh_every != 1 || neigh_delay != 0 || neigh_dist_check != 1) {
- if (me_universe == 0)
+ if (me_universe == 0)
error->warning(FLERR,"Resetting reneighboring criteria during TAD");
}
@@ -222,25 +222,25 @@ void TAD::command(int narg, char **arg)
// perform TAD simulation
- if (me_universe == 0 && universe->uscreen)
+ if (me_universe == 0 && universe->uscreen)
fprintf(universe->uscreen,"Setting up TAD ...\n");
if (me_universe == 0) {
- if (universe->uscreen)
+ if (universe->uscreen)
fprintf(universe->uscreen,
- "Step CPU N M Status Barrier Margin t_lo delt_lo\n"
- );
- if (universe->ulogfile)
+ "Step CPU N M Status Barrier Margin t_lo delt_lo\n"
+ );
+ if (universe->ulogfile)
fprintf(universe->ulogfile,
- "Step CPU N M Status Barrier Margin t_lo delt_lo\n"
- );
+ "Step CPU N M Status Barrier Margin t_lo delt_lo\n"
+ );
}
ulogfile_lammps = universe->ulogfile;
uscreen_lammps = universe->uscreen;
ulogfile_neb = NULL;
uscreen_neb = NULL;
- if (me_universe == 0 && neb_logfilename)
+ if (me_universe == 0 && neb_logfilename)
ulogfile_neb = fopen(neb_logfilename,"w");
// store hot state and quenched event, only on replica 0
@@ -262,86 +262,86 @@ void TAD::command(int narg, char **arg)
fix_event->restore_state();
// do full init/setup
-
+
update->whichflag = 1;
lmp->init();
update->integrate->setup();
// }
-
+
// main loop: look for events until out of time
// (1) dynamics, store state, quench, check event, restore state
// (2) if event, perform NEB, record in fix_event_list
- // (3) if confident, pick earliest event
+ // (3) if confident, pick earliest event
nbuild = ndanger = 0;
time_neb = time_dynamics = time_quench = time_comm = time_output = 0.0;
timer->barrier_start(TIME_LOOP);
time_start = timer->array[TIME_LOOP];
-
+
int confident_flag, event_flag;
if (universe->iworld == 0) {
while (update->ntimestep < update->endstep) {
// initialize list of possible events
-
+
initialize_event_list();
confident_flag = 0;
while (update->ntimestep < update->endstep) {
- event_flag = 0;
- while (update->ntimestep < update->endstep) {
+ event_flag = 0;
+ while (update->ntimestep < update->endstep) {
- dynamics();
+ dynamics();
- fix_event->store_state();
+ fix_event->store_state();
- quench();
+ quench();
- event_flag = check_event();
- MPI_Bcast(&event_flag,1,MPI_INT,0,universe->uworld);
+ event_flag = check_event();
+ MPI_Bcast(&event_flag,1,MPI_INT,0,universe->uworld);
- if (event_flag) break;
+ if (event_flag) break;
- // restore hot state
+ // restore hot state
- fix_event->restore_state();
+ fix_event->restore_state();
- // store hot state in revert
+ // store hot state in revert
- fix_revert->end_of_step();
- }
- if (!event_flag) break;
+ fix_revert->end_of_step();
+ }
+ if (!event_flag) break;
- add_event();
+ add_event();
- perform_neb(n_event_list-1);
- compute_tlo(n_event_list-1);
- confident_flag = check_confidence();
- MPI_Bcast(&confident_flag,1,MPI_INT,0,universe->uworld);
- if (confident_flag) break;
- if (universe->iworld == 0) revert();
+ perform_neb(n_event_list-1);
+ compute_tlo(n_event_list-1);
+ confident_flag = check_confidence();
+ MPI_Bcast(&confident_flag,1,MPI_INT,0,universe->uworld);
+ if (confident_flag) break;
+ if (universe->iworld == 0) revert();
}
if (!confident_flag) break;
-
+
perform_event(event_first);
- // need to sync timestep with TAD
+ // need to sync timestep with TAD
MPI_Bcast(&(update->ntimestep),1,MPI_INT,0,universe->uworld);
-
+
int restart_flag = 0;
if (output->restart_flag && universe->iworld == 0) {
- if (output->restart_every_single &&
- fix_event->event_number % output->restart_every_single == 0)
- restart_flag = 1;
- if (output->restart_every_double &&
- fix_event->event_number % output->restart_every_double == 0)
- restart_flag = 1;
+ if (output->restart_every_single &&
+ fix_event->event_number % output->restart_every_single == 0)
+ restart_flag = 1;
+ if (output->restart_every_double &&
+ fix_event->event_number % output->restart_every_double == 0)
+ restart_flag = 1;
}
// full init/setup since are starting after event
@@ -353,10 +353,10 @@ void TAD::command(int narg, char **arg)
// write restart file of hot coords
if (restart_flag) {
- timer->barrier_start(TIME_LOOP);
- output->write_restart(update->ntimestep);
- timer->barrier_stop(TIME_LOOP);
- time_output += timer->array[TIME_LOOP];
+ timer->barrier_start(TIME_LOOP);
+ output->write_restart(update->ntimestep);
+ timer->barrier_stop(TIME_LOOP);
+ time_output += timer->array[TIME_LOOP];
}
}
@@ -365,21 +365,21 @@ void TAD::command(int narg, char **arg)
while (update->ntimestep < update->endstep) {
confident_flag = 0;
while (update->ntimestep < update->endstep) {
- event_flag = 0;
- while (update->ntimestep < update->endstep) {
- update->ntimestep += t_event;
- MPI_Bcast(&event_flag,1,MPI_INT,0,universe->uworld);
-
- if (event_flag) break;
- }
- if (!event_flag) break;
- perform_neb(-1);
- MPI_Bcast(&confident_flag,1,MPI_INT,0,universe->uworld);
- if (confident_flag) break;
+ event_flag = 0;
+ while (update->ntimestep < update->endstep) {
+ update->ntimestep += t_event;
+ MPI_Bcast(&event_flag,1,MPI_INT,0,universe->uworld);
+
+ if (event_flag) break;
+ }
+ if (!event_flag) break;
+ perform_neb(-1);
+ MPI_Bcast(&confident_flag,1,MPI_INT,0,universe->uworld);
+ if (confident_flag) break;
}
if (!confident_flag) break;
-
- // need to sync timestep with TAD
+
+ // need to sync timestep with TAD
MPI_Bcast(&(update->ntimestep),1,MPI_INT,0,universe->uworld);
}
@@ -400,22 +400,22 @@ void TAD::command(int narg, char **arg)
neighbor->ndanger = ndanger;
if (me_universe == 0) {
- if (universe->uscreen)
+ if (universe->uscreen)
fprintf(universe->uscreen,
- "Loop time of %g on %d procs for %d steps with " BIGINT_FORMAT
- " atoms\n",
- timer->array[TIME_LOOP],nprocs_universe,nsteps,atom->natoms);
- if (universe->ulogfile)
+ "Loop time of %g on %d procs for %d steps with " BIGINT_FORMAT
+ " atoms\n",
+ timer->array[TIME_LOOP],nprocs_universe,nsteps,atom->natoms);
+ if (universe->ulogfile)
fprintf(universe->ulogfile,
- "Loop time of %g on %d procs for %d steps with " BIGINT_FORMAT
- " atoms\n",
+ "Loop time of %g on %d procs for %d steps with " BIGINT_FORMAT
+ " atoms\n",
timer->array[TIME_LOOP],nprocs_universe,nsteps,atom->natoms);
}
if (me_universe == 0) fclose(ulogfile_neb);
-
+
finish->end(3);
-
+
update->whichflag = 0;
update->firststep = update->laststep = 0;
update->beginstep = update->endstep = 0;
@@ -427,7 +427,7 @@ void TAD::command(int narg, char **arg)
neighbor->delay = neigh_delay;
neighbor->dist_check = neigh_dist_check;
-
+
delete [] id_compute;
delete finish;
modify->delete_fix("tad_event");
@@ -473,7 +473,7 @@ void TAD::quench()
bigint ntimestep_hold = update->ntimestep;
bigint endstep_hold = update->endstep;
- // need to change whichflag so that minimize->setup() calling
+ // need to change whichflag so that minimize->setup() calling
// modify->setup() will call fix->min_setup()
update->whichflag = 2;
@@ -541,28 +541,28 @@ void TAD::log_event(int ievent)
double tfrac = 0.0;
if (universe->uscreen)
fprintf(universe->uscreen,
- BIGINT_FORMAT " %.3f %d %d %s %.3f %.3f %.3f %.3f\n",
- fix_event->event_timestep,
- timer->elapsed(TIME_LOOP),
- fix_event->event_number,ievent,
- "E ",
- fix_event->ebarrier,tfrac,
- fix_event->tlo,deltfirst);
+ BIGINT_FORMAT " %.3f %d %d %s %.3f %.3f %.3f %.3f\n",
+ fix_event->event_timestep,
+ timer->elapsed(TIME_LOOP),
+ fix_event->event_number,ievent,
+ "E ",
+ fix_event->ebarrier,tfrac,
+ fix_event->tlo,deltfirst);
if (universe->ulogfile)
fprintf(universe->ulogfile,
- BIGINT_FORMAT " %.3f %d %d %s %.3f %.3f %.3f %.3f\n",
- fix_event->event_timestep,
- timer->elapsed(TIME_LOOP),
- fix_event->event_number,ievent,
- "E ",
- fix_event->ebarrier,tfrac,
- fix_event->tlo,deltfirst);
+ BIGINT_FORMAT " %.3f %d %d %s %.3f %.3f %.3f %.3f\n",
+ fix_event->event_timestep,
+ timer->elapsed(TIME_LOOP),
+ fix_event->event_number,ievent,
+ "E ",
+ fix_event->ebarrier,tfrac,
+ fix_event->tlo,deltfirst);
}
// dump snapshot of quenched coords
// must reneighbor and compute forces before dumping
// addstep_compute_all insures eng/virial are calculated if needed
-
+
if (output->ndump && universe->iworld == 0) {
timer->barrier_start(TIME_LOOP);
modify->addstep_compute_all(update->ntimestep);
@@ -575,7 +575,7 @@ void TAD::log_event(int ievent)
}
/* ----------------------------------------------------------------------
- parse optional parameters at end of TAD input line
+ parse optional parameters at end of TAD input line
------------------------------------------------------------------------- */
void TAD::options(int narg, char **arg)
@@ -583,7 +583,7 @@ void TAD::options(int narg, char **arg)
if (narg < 0) error->all(FLERR,"Illegal tad command");
// set defaults
-
+
etol = 0.1;
ftol = 0.1;
maxiter = 40;
@@ -609,9 +609,9 @@ void TAD::options(int narg, char **arg)
ftol = atof(arg[iarg+2]);
maxiter = atoi(arg[iarg+3]);
maxeval = atoi(arg[iarg+4]);
- if (maxiter < 0 || maxeval < 0 ||
- etol < 0.0 || ftol < 0.0 )
- error->all(FLERR,"Illegal tad command");
+ if (maxiter < 0 || maxeval < 0 ||
+ etol < 0.0 || ftol < 0.0 )
+ error->all(FLERR,"Illegal tad command");
iarg += 5;
} else if (strcmp(arg[iarg],"neb") == 0) {
@@ -621,11 +621,11 @@ void TAD::options(int narg, char **arg)
n1steps_neb = atoi(arg[iarg+3]);
n2steps_neb = atoi(arg[iarg+4]);
nevery_neb = atoi(arg[iarg+5]);
- if (etol_neb < 0.0 || ftol_neb < 0.0 ||
- n1steps_neb < 0 || n2steps_neb < 0 ||
- nevery_neb < 0) error->all(FLERR,"Illegal tad command");
+ if (etol_neb < 0.0 || ftol_neb < 0.0 ||
+ n1steps_neb < 0 || n2steps_neb < 0 ||
+ nevery_neb < 0) error->all(FLERR,"Illegal tad command");
iarg += 6;
-
+
} else if (strcmp(arg[iarg],"min_style") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal tad command");
int n = strlen(arg[iarg+1]) + 1;
@@ -647,9 +647,9 @@ void TAD::options(int narg, char **arg)
if (iarg+2 > narg) error->all(FLERR,"Illegal tad command");
if (strcmp(arg[iarg+1],"none") == 0) neb_logfilename = NULL;
else {
- int n = strlen(arg[iarg+1]) + 1;
- neb_logfilename = new char[n];
- strcpy(neb_logfilename,arg[iarg+1]);
+ int n = strlen(arg[iarg+1]) + 1;
+ neb_logfilename = new char[n];
+ strcpy(neb_logfilename,arg[iarg+1]);
}
iarg += 2;
} else error->all(FLERR,"Illegal tad command");
@@ -677,18 +677,18 @@ void TAD::perform_neb(int ievent)
int ii = 0;
for (int i = 0; i < nlocal; i++) {
- buf_final[ii++] = x[i][0];
- buf_final[ii++] = x[i][1];
- buf_final[ii++] = x[i][2];
+ buf_final[ii++] = x[i][0];
+ buf_final[ii++] = x[i][1];
+ buf_final[ii++] = x[i][2];
}
}
MPI_Bcast(buf_final,3*nlocal,MPI_DOUBLE,universe->root_proc[0],
- universe->uworld);
+ universe->uworld);
double *buf_init;
memory->create(buf_init,3*nlocal,"tad:bufinit");
-
+
// set system to quenched state of fix_event
if (universe->iworld == 0) {
@@ -697,14 +697,14 @@ void TAD::perform_neb(int ievent)
int ii = 0;
for (int i = 0; i < nlocal; i++) {
- buf_init[ii++] = x[i][0];
- buf_init[ii++] = x[i][1];
- buf_init[ii++] = x[i][2];
+ buf_init[ii++] = x[i][0];
+ buf_init[ii++] = x[i][1];
+ buf_init[ii++] = x[i][2];
}
}
MPI_Bcast(buf_init,3*nlocal,MPI_DOUBLE,universe->root_proc[0],
- universe->uworld);
+ universe->uworld);
// create FixNEB object to support NEB
@@ -714,7 +714,7 @@ void TAD::perform_neb(int ievent)
args[1] = (char *) "all";
args[2] = (char *) "neb";
char str[128];
- args[3] = str;
+ args[3] = str;
double kspring = 1.0;
sprintf(args[3],"%f",kspring);
modify->add_fix(narg2,args);
@@ -733,8 +733,8 @@ void TAD::perform_neb(int ievent)
// create NEB object
- neb = new NEB(lmp,etol_neb,ftol_neb,n1steps_neb,
- n2steps_neb,nevery_neb,buf_init,buf_final);
+ neb = new NEB(lmp,etol_neb,ftol_neb,n1steps_neb,
+ n2steps_neb,nevery_neb,buf_init,buf_final);
// free up temporary arrays
@@ -796,7 +796,7 @@ void TAD::perform_neb(int ievent)
delete [] args;
- // clean up
+ // clean up
modify->delete_fix("neb");
delete neb;
@@ -902,7 +902,7 @@ void TAD::add_event()
args[2] = (char *) "EVENT/TAD";
modify->add_fix(narg,args);
- if (n_event_list == nmax_event_list)
+ if (n_event_list == nmax_event_list)
grow_event_list(nmax_event_list+nmin_event_list);
n_event_list += 1;
int ievent = n_event_list-1;
@@ -932,7 +932,7 @@ void TAD::compute_tlo(int ievent)
double deltlo,delthi,ebarrier;
ebarrier = fix_event_list[ievent]->ebarrier;
- delthi = fix_event_list[ievent]->event_timestep
+ delthi = fix_event_list[ievent]->event_timestep
- fix_event->event_timestep;
deltlo = delthi*exp(ebarrier*delta_beta);
fix_event_list[ievent]->tlo = fix_event->tlo + deltlo;
@@ -952,29 +952,29 @@ void TAD::compute_tlo(int ievent)
}
// first-replica output about each event
-
+
timer->array[TIME_LOOP] = time_start;
if (universe->me == 0) {
double tfrac = 0.0;
if (ievent > 0) tfrac = delthi/deltstop;
- if (universe->uscreen)
+ if (universe->uscreen)
fprintf(universe->uscreen,
- BIGINT_FORMAT " %.3f %d %d %s %.3f %.3f %.3f %.3f\n",
- fix_event_list[ievent]->event_timestep,
- timer->elapsed(TIME_LOOP),
- fix_event->event_number,
- ievent,statstr,ebarrier,tfrac,
- fix_event->tlo,deltlo);
-
- if (universe->ulogfile)
+ BIGINT_FORMAT " %.3f %d %d %s %.3f %.3f %.3f %.3f\n",
+ fix_event_list[ievent]->event_timestep,
+ timer->elapsed(TIME_LOOP),
+ fix_event->event_number,
+ ievent,statstr,ebarrier,tfrac,
+ fix_event->tlo,deltlo);
+
+ if (universe->ulogfile)
fprintf(universe->ulogfile,
- BIGINT_FORMAT " %.3f %d %d %s %.3f %.3f %.3f %.3f\n",
- fix_event_list[ievent]->event_timestep,
- timer->elapsed(TIME_LOOP),
- fix_event->event_number,
- ievent,statstr,ebarrier,tfrac,
- fix_event->tlo,deltlo);
+ BIGINT_FORMAT " %.3f %d %d %s %.3f %.3f %.3f %.3f\n",
+ fix_event_list[ievent]->event_timestep,
+ timer->elapsed(TIME_LOOP),
+ fix_event->event_number,
+ ievent,statstr,ebarrier,tfrac,
+ fix_event->tlo,deltlo);
}
}
@@ -1014,8 +1014,7 @@ void TAD::perform_event(int ievent)
void TAD::grow_event_list(int nmax) {
if (nmax_event_list > nmax) return;
- fix_event_list = (FixEventTAD **)
+ fix_event_list = (FixEventTAD **)
memory->srealloc(fix_event_list,nmax*sizeof(FixEventTAD *),"tad:eventlist");
nmax_event_list = nmax;
}
-
diff --git a/src/REPLICA/tad.h b/src/REPLICA/tad.h
index e5f1c38be8421f119366772df104208f0ef3fc9f..8b370f1e94f06a298faa0bbe2b07538293e1324c 100644
--- a/src/REPLICA/tad.h
+++ b/src/REPLICA/tad.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -148,7 +148,7 @@ The cummulative timesteps must fit in a 64-bit integer.
E: Too many iterations
-You must use a number of iterations that fit in a 32-bit integer
+You must use a number of iterations that fit in a 32-bit integer
for minimization.
*/
diff --git a/src/REPLICA/temper.cpp b/src/REPLICA/temper.cpp
index 32261989cb182096c3a2ec4d9d3022528a1077d9..f0e0a931904d4a49b79731bd2068332738197a68 100644
--- a/src/REPLICA/temper.cpp
+++ b/src/REPLICA/temper.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -63,11 +63,11 @@ Temper::~Temper()
void Temper::command(int narg, char **arg)
{
- if (universe->nworlds == 1)
+ if (universe->nworlds == 1)
error->all(FLERR,"Must have more than one processor partition to temper");
- if (domain->box_exist == 0)
+ if (domain->box_exist == 0)
error->all(FLERR,"Temper command before simulation box is defined");
- if (narg != 6 && narg != 7)
+ if (narg != 6 && narg != 7)
error->universe_all(FLERR,"Illegal temper command");
int nsteps = atoi(arg[0]);
@@ -76,7 +76,7 @@ void Temper::command(int narg, char **arg)
for (whichfix = 0; whichfix < modify->nfix; whichfix++)
if (strcmp(arg[3],modify->fix[whichfix]->id) == 0) break;
- if (whichfix == modify->nfix)
+ if (whichfix == modify->nfix)
error->universe_all(FLERR,"Tempering fix ID is not defined");
seed_swap = atoi(arg[4]);
@@ -87,10 +87,10 @@ void Temper::command(int narg, char **arg)
// swap frequency must evenly divide total # of timesteps
- if (nevery == 0)
+ if (nevery == 0)
error->universe_all(FLERR,"Invalid frequency in temper command");
nswaps = nsteps/nevery;
- if (nswaps*nevery != nsteps)
+ if (nswaps*nevery != nsteps)
error->universe_all(FLERR,"Non integer # of swaps in temper command");
// fix style must be appropriate for temperature control
@@ -146,7 +146,7 @@ void Temper::command(int narg, char **arg)
// world2root[i] = global proc that is root proc of world i
world2root = new int[nworlds];
- if (me == 0)
+ if (me == 0)
MPI_Allgather(&me_universe,1,MPI_INT,world2root,1,MPI_INT,roots);
MPI_Bcast(world2root,nworlds,MPI_INT,0,world);
@@ -183,7 +183,7 @@ void Temper::command(int narg, char **arg)
double pe,pe_partner,boltz_factor,new_temp;
MPI_Status status;
- if (me_universe == 0 && universe->uscreen)
+ if (me_universe == 0 && universe->uscreen)
fprintf(universe->uscreen,"Setting up tempering ...\n");
update->integrate->setup();
@@ -192,13 +192,13 @@ void Temper::command(int narg, char **arg)
if (universe->uscreen) {
fprintf(universe->uscreen,"Step");
for (int i = 0; i < nworlds; i++)
- fprintf(universe->uscreen," T%d",i);
+ fprintf(universe->uscreen," T%d",i);
fprintf(universe->uscreen,"\n");
}
if (universe->ulogfile) {
fprintf(universe->ulogfile,"Step");
for (int i = 0; i < nworlds; i++)
- fprintf(universe->ulogfile," T%d",i);
+ fprintf(universe->ulogfile," T%d",i);
fprintf(universe->ulogfile,"\n");
}
print_status();
@@ -208,11 +208,11 @@ void Temper::command(int narg, char **arg)
timer->barrier_start(TIME_LOOP);
for (int iswap = 0; iswap < nswaps; iswap++) {
-
+
// run for nevery timesteps
update->integrate->run(nevery);
-
+
// compute PE
// notify compute it will be called at next swap
@@ -251,29 +251,29 @@ void Temper::command(int narg, char **arg)
swap = 0;
if (partner != -1) {
- if (me_universe > partner)
- MPI_Send(&pe,1,MPI_DOUBLE,partner,0,universe->uworld);
+ if (me_universe > partner)
+ MPI_Send(&pe,1,MPI_DOUBLE,partner,0,universe->uworld);
else
- MPI_Recv(&pe_partner,1,MPI_DOUBLE,partner,0,universe->uworld,&status);
+ MPI_Recv(&pe_partner,1,MPI_DOUBLE,partner,0,universe->uworld,&status);
if (me_universe < partner) {
- boltz_factor = (pe - pe_partner) *
- (1.0/(boltz*set_temp[my_set_temp]) -
- 1.0/(boltz*set_temp[partner_set_temp]));
- if (boltz_factor >= 0.0) swap = 1;
- else if (ranboltz->uniform() < exp(boltz_factor)) swap = 1;
+ boltz_factor = (pe - pe_partner) *
+ (1.0/(boltz*set_temp[my_set_temp]) -
+ 1.0/(boltz*set_temp[partner_set_temp]));
+ if (boltz_factor >= 0.0) swap = 1;
+ else if (ranboltz->uniform() < exp(boltz_factor)) swap = 1;
}
- if (me_universe < partner)
- MPI_Send(&swap,1,MPI_INT,partner,0,universe->uworld);
+ if (me_universe < partner)
+ MPI_Send(&swap,1,MPI_INT,partner,0,universe->uworld);
else
- MPI_Recv(&swap,1,MPI_INT,partner,0,universe->uworld,&status);
+ MPI_Recv(&swap,1,MPI_INT,partner,0,universe->uworld,&status);
#ifdef TEMPER_DEBUG
if (me_universe < partner)
- printf("SWAP %d & %d: yes = %d,Ts = %d %d, PEs = %g %g, Bz = %g %g\n",
- me_universe,partner,swap,my_set_temp,partner_set_temp,
- pe,pe_partner,boltz_factor,exp(boltz_factor));
+ printf("SWAP %d & %d: yes = %d,Ts = %d %d, PEs = %g %g, Bz = %g %g\n",
+ me_universe,partner,swap,my_set_temp,partner_set_temp,
+ pe,pe_partner,boltz_factor,exp(boltz_factor));
#endif
}
@@ -285,7 +285,7 @@ void Temper::command(int narg, char **arg)
// rescale kinetic energy via velocities if move is accepted
if (swap) scale_velocities(partner_set_temp,my_set_temp);
-
+
// if my world swapped, all procs in world reset temp target of Fix
if (swap) {
@@ -348,7 +348,7 @@ void Temper::print_status()
{
if (universe->uscreen) {
fprintf(universe->uscreen,BIGINT_FORMAT,update->ntimestep);
- for (int i = 0; i < nworlds; i++)
+ for (int i = 0; i < nworlds; i++)
fprintf(universe->uscreen," %d",world2temp[i]);
fprintf(universe->uscreen,"\n");
}
diff --git a/src/REPLICA/temper.h b/src/REPLICA/temper.h
index e61ee6711c08262d97b5d897919ccb8c66318f12..bde985d344d029f84215409f3e9c177297493231 100644
--- a/src/REPLICA/temper.h
+++ b/src/REPLICA/temper.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/REPLICA/verlet_split.cpp b/src/REPLICA/verlet_split.cpp
index 4272cc247413be08e2bd175b9004f4d4ff53833f..c8754ac6816e5b576a9293e06a7c7e9acddf91e4 100644
--- a/src/REPLICA/verlet_split.cpp
+++ b/src/REPLICA/verlet_split.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -46,11 +46,11 @@ VerletSplit::VerletSplit(LAMMPS *lmp, int narg, char **arg) :
{
// error checks on partitions
- if (universe->nworlds != 2)
+ if (universe->nworlds != 2)
error->universe_all(FLERR,"Verlet/split requires 2 partitions");
if (universe->procs_per_world[0] % universe->procs_per_world[1])
error->universe_all(FLERR,"Verlet/split requires Rspace partition "
- "size be multiple of Kspace partition size");
+ "size be multiple of Kspace partition size");
// master = 1 for Rspace procs, 0 for Kspace procs
@@ -72,18 +72,18 @@ VerletSplit::VerletSplit(LAMMPS *lmp, int narg, char **arg) :
int ***kspace_grid2proc;
memory->create(kspace_grid2proc,kspace_procgrid[0],
- kspace_procgrid[1],kspace_procgrid[2],
- "verlet/split:kspace_grid2proc");
+ kspace_procgrid[1],kspace_procgrid[2],
+ "verlet/split:kspace_grid2proc");
if (universe->me == universe->root_proc[1]) {
for (int i = 0; i < comm->procgrid[0]; i++)
for (int j = 0; j < comm->procgrid[1]; j++)
- for (int k = 0; k < comm->procgrid[2]; k++)
- kspace_grid2proc[i][j][k] = comm->grid2proc[i][j][k];
+ for (int k = 0; k < comm->procgrid[2]; k++)
+ kspace_grid2proc[i][j][k] = comm->grid2proc[i][j][k];
}
MPI_Bcast(&kspace_grid2proc[0][0][0],
- kspace_procgrid[0]*kspace_procgrid[1]*kspace_procgrid[2],MPI_INT,
- universe->root_proc[1],universe->uworld);
+ kspace_procgrid[0]*kspace_procgrid[1]*kspace_procgrid[2],MPI_INT,
+ universe->root_proc[1],universe->uworld);
// Rspace partition must be multiple of Kspace partition in each dim
// so atoms of one Kspace proc coincide with atoms of several Rspace procs
@@ -95,8 +95,8 @@ VerletSplit::VerletSplit(LAMMPS *lmp, int narg, char **arg) :
if (comm->procgrid[2] % kspace_procgrid[2]) flag = 1;
if (flag)
error->one(FLERR,
- "Verlet/split requires Rspace partition layout be "
- "multiple of Kspace partition layout in each dim");
+ "Verlet/split requires Rspace partition layout be "
+ "multiple of Kspace partition layout in each dim");
}
// block = 1 Kspace proc with set of Rspace procs it overlays
@@ -133,45 +133,45 @@ VerletSplit::VerletSplit(LAMMPS *lmp, int narg, char **arg) :
if (universe->me == 0) {
if (universe->uscreen) {
fprintf(universe->uscreen,
- "Per-block Rspace/Kspace proc IDs (original proc IDs):\n");
+ "Per-block Rspace/Kspace proc IDs (original proc IDs):\n");
int m = 0;
for (int i = 0; i < universe->nprocs/(ratio+1); i++) {
- fprintf(universe->uscreen," block %d:",i);
- int kspace_proc = bmapall[m];
- for (int j = 1; j <= ratio; j++)
- fprintf(universe->uscreen," %d",bmapall[m+j]);
- fprintf(universe->uscreen," %d",kspace_proc);
- kspace_proc = bmapall[m];
- for (int j = 1; j <= ratio; j++) {
- if (j == 1) fprintf(universe->uscreen," (");
- else fprintf(universe->uscreen," ");
- fprintf(universe->uscreen,"%d",
- universe->uni2orig[bmapall[m+j]]);
- }
- fprintf(universe->uscreen," %d)\n",universe->uni2orig[kspace_proc]);
- m += ratio + 1;
+ fprintf(universe->uscreen," block %d:",i);
+ int kspace_proc = bmapall[m];
+ for (int j = 1; j <= ratio; j++)
+ fprintf(universe->uscreen," %d",bmapall[m+j]);
+ fprintf(universe->uscreen," %d",kspace_proc);
+ kspace_proc = bmapall[m];
+ for (int j = 1; j <= ratio; j++) {
+ if (j == 1) fprintf(universe->uscreen," (");
+ else fprintf(universe->uscreen," ");
+ fprintf(universe->uscreen,"%d",
+ universe->uni2orig[bmapall[m+j]]);
+ }
+ fprintf(universe->uscreen," %d)\n",universe->uni2orig[kspace_proc]);
+ m += ratio + 1;
}
}
if (universe->ulogfile) {
fprintf(universe->ulogfile,
- "Per-block Rspace/Kspace proc IDs (original proc IDs):\n");
+ "Per-block Rspace/Kspace proc IDs (original proc IDs):\n");
int m = 0;
for (int i = 0; i < universe->nprocs/(ratio+1); i++) {
- fprintf(universe->ulogfile," block %d:",i);
- int kspace_proc = bmapall[m];
- for (int j = 1; j <= ratio; j++)
- fprintf(universe->ulogfile," %d",bmapall[m+j]);
-
- fprintf(universe->ulogfile," %d",kspace_proc);
- kspace_proc = bmapall[m];
- for (int j = 1; j <= ratio; j++) {
- if (j == 1) fprintf(universe->ulogfile," (");
- else fprintf(universe->ulogfile," ");
- fprintf(universe->ulogfile,"%d",
- universe->uni2orig[bmapall[m+j]]);
- }
- fprintf(universe->ulogfile," %d)\n",universe->uni2orig[kspace_proc]);
- m += ratio + 1;
+ fprintf(universe->ulogfile," block %d:",i);
+ int kspace_proc = bmapall[m];
+ for (int j = 1; j <= ratio; j++)
+ fprintf(universe->ulogfile," %d",bmapall[m+j]);
+
+ fprintf(universe->ulogfile," %d",kspace_proc);
+ kspace_proc = bmapall[m];
+ for (int j = 1; j <= ratio; j++) {
+ if (j == 1) fprintf(universe->ulogfile," (");
+ else fprintf(universe->ulogfile," ");
+ fprintf(universe->ulogfile,"%d",
+ universe->uni2orig[bmapall[m+j]]);
+ }
+ fprintf(universe->ulogfile," %d)\n",universe->uni2orig[kspace_proc]);
+ m += ratio + 1;
}
}
}
@@ -213,7 +213,7 @@ VerletSplit::~VerletSplit()
void VerletSplit::init()
{
- if (!force->kspace && comm->me == 0)
+ if (!force->kspace && comm->me == 0)
error->warning(FLERR,"No Kspace calculation with verlet/split");
if (force->kspace_match("tip4p",0)) tip4p_flag = 1;
@@ -290,7 +290,7 @@ void VerletSplit::run(int n)
ev_set(ntimestep);
// initial time integration
-
+
if (master) {
modify->initial_integrate(vflag);
if (n_post_integrate) modify->post_integrate();
@@ -303,36 +303,36 @@ void VerletSplit::run(int n)
if (master) {
if (nflag == 0) {
- timer->stamp();
- comm->forward_comm();
- timer->stamp(TIME_COMM);
+ timer->stamp();
+ comm->forward_comm();
+ timer->stamp(TIME_COMM);
} else {
- if (n_pre_exchange) modify->pre_exchange();
- if (triclinic) domain->x2lamda(atom->nlocal);
- domain->pbc();
- if (domain->box_change) {
- domain->reset_box();
- comm->setup();
- if (neighbor->style) neighbor->setup_bins();
- }
- timer->stamp();
- comm->exchange();
- if (sortflag && ntimestep >= atom->nextsort) atom->sort();
- comm->borders();
- if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
- timer->stamp(TIME_COMM);
- if (n_pre_neighbor) modify->pre_neighbor();
- neighbor->build();
- timer->stamp(TIME_NEIGHBOR);
+ if (n_pre_exchange) modify->pre_exchange();
+ if (triclinic) domain->x2lamda(atom->nlocal);
+ domain->pbc();
+ if (domain->box_change) {
+ domain->reset_box();
+ comm->setup();
+ if (neighbor->style) neighbor->setup_bins();
+ }
+ timer->stamp();
+ comm->exchange();
+ if (sortflag && ntimestep >= atom->nextsort) atom->sort();
+ comm->borders();
+ if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
+ timer->stamp(TIME_COMM);
+ if (n_pre_neighbor) modify->pre_neighbor();
+ neighbor->build();
+ timer->stamp(TIME_NEIGHBOR);
}
}
-
+
// if reneighboring occurred, re-setup Rspace <-> Kspace comm params
// comm Rspace atom coords to Kspace procs
if (nflag) rk_setup();
r2k_comm();
-
+
// force computations
force_clear();
@@ -345,7 +345,7 @@ void VerletSplit::run(int n)
force->pair->compute(eflag,vflag);
timer->stamp(TIME_PAIR);
}
-
+
if (atom->molecular) {
if (force->bond) force->bond->compute(eflag,vflag);
if (force->angle) force->angle->compute(eflag,vflag);
@@ -355,8 +355,8 @@ void VerletSplit::run(int n)
}
if (force->newton) {
- comm->reverse_comm();
- timer->stamp(TIME_COMM);
+ comm->reverse_comm();
+ timer->stamp(TIME_COMM);
}
} else {
@@ -369,8 +369,8 @@ void VerletSplit::run(int n)
// TIP4P PPPM puts forces on ghost atoms, so must reverse_comm()
if (tip4p_flag && force->newton) {
- comm->reverse_comm();
- timer->stamp(TIME_COMM);
+ comm->reverse_comm();
+ timer->stamp(TIME_COMM);
}
}
@@ -387,9 +387,9 @@ void VerletSplit::run(int n)
if (n_end_of_step) modify->end_of_step();
if (ntimestep == output->next) {
- timer->stamp();
- output->write(ntimestep);
- timer->stamp(TIME_OUTPUT);
+ timer->stamp();
+ output->write(ntimestep);
+ timer->stamp(TIME_OUTPUT);
}
}
}
@@ -424,7 +424,7 @@ void VerletSplit::rk_setup()
// set Kspace nlocal to sum of Rspace nlocals
// insure Kspace atom arrays are large enough
- if (!master) {
+ if (!master) {
qsize[0] = qdisp[0] = xsize[0] = xdisp[0] = 0;
for (int i = 1; i <= ratio; i++) {
qdisp[i] = qdisp[i-1]+qsize[i-1];
@@ -436,7 +436,7 @@ void VerletSplit::rk_setup()
while (atom->nmax <= atom->nlocal) atom->avec->grow(0);
atom->nghost = 0;
}
-
+
// one-time gather of Rspace atom charges to Kspace proc
MPI_Gatherv(atom->q,n,MPI_DOUBLE,atom->q,qsize,qdisp,MPI_DOUBLE,0,block);
@@ -477,7 +477,7 @@ void VerletSplit::r2k_comm()
int n = 0;
if (master) n = atom->nlocal;
MPI_Gatherv(atom->x[0],n*3,MPI_DOUBLE,atom->x[0],xsize,xdisp,
- MPI_DOUBLE,0,block);
+ MPI_DOUBLE,0,block);
// send eflag,vflag from Rspace to Kspace
@@ -527,8 +527,8 @@ void VerletSplit::k2r_comm()
int n = 0;
if (master) n = atom->nlocal;
MPI_Scatterv(atom->f[0],xsize,xdisp,MPI_DOUBLE,
- f_kspace[0],n*3,MPI_DOUBLE,0,block);
-
+ f_kspace[0],n*3,MPI_DOUBLE,0,block);
+
if (master) {
double **f = atom->f;
int nlocal = atom->nlocal;
diff --git a/src/REPLICA/verlet_split.h b/src/REPLICA/verlet_split.h
index 2819bac619ef675687c770c2f4e4cbbef903aadd..f109d477227339ca2470588226fb033da8373a3a 100644
--- a/src/REPLICA/verlet_split.h
+++ b/src/REPLICA/verlet_split.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -44,7 +44,7 @@ class VerletSplit : public Verlet {
double **f_kspace; // copy of Kspace forces on Rspace procs
int maxatom;
-
+
void rk_setup();
void r2k_comm();
void k2r_comm();
diff --git a/src/SHOCK/fix_append_atoms.cpp b/src/SHOCK/fix_append_atoms.cpp
index 63d68ddaf49e28c820bd2723cac11b2d6320c742..66580c6bfa8bfc53d30ce503f2e8f60fcddbe3a5 100644
--- a/src/SHOCK/fix_append_atoms.cpp
+++ b/src/SHOCK/fix_append_atoms.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -67,37 +67,37 @@ FixAppendAtoms::FixAppendAtoms(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,"Only zhi currently implemented for fix append/atoms");
xloflag = 1;
iarg++;
- if (domain->boundary[0][0] != 3)
- error->all(FLERR,"Append boundary must be shrink/minimum");
+ if (domain->boundary[0][0] != 3)
+ error->all(FLERR,"Append boundary must be shrink/minimum");
} else if (strcmp(arg[iarg],"xhi") == 0) {
error->all(FLERR,"Only zhi currently implemented for fix append/atoms");
xhiflag = 1;
iarg++;
- if (domain->boundary[0][1] != 3)
- error->all(FLERR,"Append boundary must be shrink/minimum");
+ if (domain->boundary[0][1] != 3)
+ error->all(FLERR,"Append boundary must be shrink/minimum");
} else if (strcmp(arg[iarg],"ylo") == 0) {
error->all(FLERR,"Only zhi currently implemented for fix append/atoms");
yloflag = 1;
iarg++;
- if (domain->boundary[1][0] != 3)
- error->all(FLERR,"Append boundary must be shrink/minimum");
+ if (domain->boundary[1][0] != 3)
+ error->all(FLERR,"Append boundary must be shrink/minimum");
} else if (strcmp(arg[iarg],"yhi") == 0) {
error->all(FLERR,"Only zhi currently implemented for fix append/atoms");
yhiflag = 1;
iarg++;
- if (domain->boundary[1][1] != 3)
- error->all(FLERR,"Append boundary must be shrink/minimum");
+ if (domain->boundary[1][1] != 3)
+ error->all(FLERR,"Append boundary must be shrink/minimum");
} else if (strcmp(arg[iarg],"zlo") == 0) {
error->all(FLERR,"Only zhi currently implemented for fix append/atoms");
zloflag = 1;
iarg++;
- if (domain->boundary[2][0] != 3)
- error->all(FLERR,"Append boundary must be shrink/minimum");
+ if (domain->boundary[2][0] != 3)
+ error->all(FLERR,"Append boundary must be shrink/minimum");
} else if (strcmp(arg[iarg],"zhi") == 0) {
zhiflag = 1;
iarg++;
- if (domain->boundary[2][1] != 3)
- error->all(FLERR,"Append boundary must be shrink/minimum");
+ if (domain->boundary[2][1] != 3)
+ error->all(FLERR,"Append boundary must be shrink/minimum");
} else if (strcmp(arg[iarg],"freq") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix append/atoms command");
freq = atoi(arg[iarg+1]);
@@ -105,8 +105,8 @@ FixAppendAtoms::FixAppendAtoms(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"spatial") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix append/atoms command");
if (strcmp(arg[iarg+1],"f_") == 0)
- error->all(FLERR,
- "Bad fix ID in fix append/atoms command");
+ error->all(FLERR,
+ "Bad fix ID in fix append/atoms command");
spatflag = 1;
int n = strlen(arg[iarg+1]);
spatlead = atof(arg[iarg+2]);
@@ -162,7 +162,7 @@ FixAppendAtoms::FixAppendAtoms(LAMMPS *lmp, int narg, char **arg) :
if ((zloflag || zhiflag) && domain->zperiodic)
error->all(FLERR,"Cannot use append/atoms in periodic dimension");
- if (domain->triclinic == 1)
+ if (domain->triclinic == 1)
error->all(FLERR,"Cannot append atoms to a triclinic box");
// setup scaling
@@ -223,7 +223,7 @@ void FixAppendAtoms::initial_integrate(int vflag)
void FixAppendAtoms::setup(int vflag)
{
- /*** CALL TO CREATE GROUP? SEE POST_FORCE ***/
+ /*** CALL TO CREATE GROUP? SEE POST_FORCE ***/
post_force(vflag);
}
@@ -236,16 +236,16 @@ int FixAppendAtoms::get_spatial()
int ifix = modify->find_fix(spatialid);
if (ifix < 0)
error->all(FLERR,"Fix ID for fix ave/spatial does not exist");
- Fix *fix = modify->fix[ifix];
+ Fix *fix = modify->fix[ifix];
- int failed = 0;
- int count = 0;
+ int failed = 0;
+ int count = 0;
while (failed < 2) {
double tmp = fix->compute_vector(2*count);
if (tmp == 0.0) failed++;
else failed = 0;
count++;
- }
+ }
double *pos = new double[count-2];
double *val = new double[count-2];
for (int loop=0; loop < count-2; loop++) {
@@ -255,7 +255,7 @@ int FixAppendAtoms::get_spatial()
// always ignore the first and last
- double binsize = 2.0;
+ double binsize = 2.0;
double min_energy=0.0;
double max_energy=0.0;
int header = static_cast<int> (size / binsize);
@@ -288,22 +288,22 @@ int FixAppendAtoms::get_spatial()
front_found2=1;
}
}
- if (front_found1 + front_found2 == 0) shockfront_loc = 0.0;
- else if (front_found1 + front_found2 == 1)
+ if (front_found1 + front_found2 == 0) shockfront_loc = 0.0;
+ else if (front_found1 + front_found2 == 1)
shockfront_loc = shockfront_max + shockfront_min;
- else if (front_found1 == 1 && front_found2 == 1 &&
- shockfront_max-shockfront_min > spatlead/2.0)
+ else if (front_found1 == 1 && front_found2 == 1 &&
+ shockfront_max-shockfront_min > spatlead/2.0)
shockfront_loc = shockfront_max;
else shockfront_loc = (shockfront_max + shockfront_min) / 2.0;
- if (comm->me == 0)
- printf("SHOCK: %g %g %g %g %g\n", shockfront_loc, shockfront_min,
- shockfront_max, domain->boxlo[2], domain->boxhi[2]);
+ if (comm->me == 0)
+ printf("SHOCK: %g %g %g %g %g\n", shockfront_loc, shockfront_min,
+ shockfront_max, domain->boxlo[2], domain->boxhi[2]);
if (domain->boxhi[2] - shockfront_loc < spatlead) advance = 1;
delete [] pos,val;
}
-
+
advance_sum = 0;
MPI_Allreduce(&advance,&advance_sum,1,MPI_INT,MPI_SUM,world);
@@ -394,12 +394,12 @@ void FixAppendAtoms::pre_exchange()
int addnode = 0;
if (ntimestep % freq == 0) {
- if (spatflag==1) if (get_spatial()==0) return;
+ if (spatflag==1) if (get_spatial()==0) return;
if (comm->myloc[2] == comm->procgrid[2]-1) {
if (domain->lattice) {
- nbasis = domain->lattice->nbasis;
- basistype = new int[nbasis];
- for (int i = 0; i < nbasis; i++) basistype[i] = 1;
+ nbasis = domain->lattice->nbasis;
+ basistype = new int[nbasis];
+ for (int i = 0; i < nbasis; i++) basistype[i] = 1;
} else error->all(FLERR,"Must define lattice to append/atoms");
double bboxlo[3],bboxhi[3];
@@ -413,21 +413,21 @@ void FixAppendAtoms::pre_exchange()
xmax = ymax = zmax = -BIG;
domain->lattice->bbox(1,bboxlo[0],bboxlo[1],bboxlo[2],
- xmin,ymin,zmin,xmax,ymax,zmax);
+ xmin,ymin,zmin,xmax,ymax,zmax);
domain->lattice->bbox(1,bboxhi[0],bboxlo[1],bboxlo[2],
- xmin,ymin,zmin,xmax,ymax,zmax);
+ xmin,ymin,zmin,xmax,ymax,zmax);
domain->lattice->bbox(1,bboxlo[0],bboxhi[1],bboxlo[2],
- xmin,ymin,zmin,xmax,ymax,zmax);
+ xmin,ymin,zmin,xmax,ymax,zmax);
domain->lattice->bbox(1,bboxhi[0],bboxhi[1],bboxlo[2],
- xmin,ymin,zmin,xmax,ymax,zmax);
+ xmin,ymin,zmin,xmax,ymax,zmax);
domain->lattice->bbox(1,bboxlo[0],bboxlo[1],bboxhi[2],
- xmin,ymin,zmin,xmax,ymax,zmax);
+ xmin,ymin,zmin,xmax,ymax,zmax);
domain->lattice->bbox(1,bboxhi[0],bboxlo[1],bboxhi[2],
- xmin,ymin,zmin,xmax,ymax,zmax);
+ xmin,ymin,zmin,xmax,ymax,zmax);
domain->lattice->bbox(1,bboxlo[0],bboxhi[1],bboxhi[2],
- xmin,ymin,zmin,xmax,ymax,zmax);
+ xmin,ymin,zmin,xmax,ymax,zmax);
domain->lattice->bbox(1,bboxhi[0],bboxhi[1],bboxhi[2],
- xmin,ymin,zmin,xmax,ymax,zmax);
+ xmin,ymin,zmin,xmax,ymax,zmax);
int ilo,ihi,jlo,jhi,klo,khi;
ilo = static_cast<int> (xmin);
@@ -449,36 +449,36 @@ void FixAppendAtoms::pre_exchange()
int i,j,k,m;
for (k = klo; k <= khi; k++) {
- for (j = jlo; j <= jhi; j++) {
- for (i = ilo; i <= ihi; i++) {
- for (m = 0; m < nbasis; m++) {
- x[0] = i + basis[m][0];
- x[1] = j + basis[m][1];
- x[2] = k + basis[m][2];
-
- int flag = 0;
- // convert from lattice coords to box coords
- domain->lattice->lattice2box(x[0],x[1],x[2]);
-
- if (x[0] >= sublo[0] && x[0] < subhi[0] &&
- x[1] >= sublo[1] && x[1] < subhi[1] &&
- x[2] >= subhi[2] && x[2] < subhi[2]+size) flag = 1;
- else if (domain->dimension == 2 && x[1] >= domain->boxhi[1] &&
- comm->myloc[1] == comm->procgrid[1]-1 &&
- x[0] >= sublo[0] && x[0] < subhi[0]) flag = 1;
-
- if (flag) {
- if (ranflag) {
- x[0] += ranx * 2.0*(randomx->uniform()-0.5);
- x[1] += rany * 2.0*(randomx->uniform()-0.5);
- x[2] += ranz * 2.0*(randomx->uniform()-0.5);
- }
+ for (j = jlo; j <= jhi; j++) {
+ for (i = ilo; i <= ihi; i++) {
+ for (m = 0; m < nbasis; m++) {
+ x[0] = i + basis[m][0];
+ x[1] = j + basis[m][1];
+ x[2] = k + basis[m][2];
+
+ int flag = 0;
+ // convert from lattice coords to box coords
+ domain->lattice->lattice2box(x[0],x[1],x[2]);
+
+ if (x[0] >= sublo[0] && x[0] < subhi[0] &&
+ x[1] >= sublo[1] && x[1] < subhi[1] &&
+ x[2] >= subhi[2] && x[2] < subhi[2]+size) flag = 1;
+ else if (domain->dimension == 2 && x[1] >= domain->boxhi[1] &&
+ comm->myloc[1] == comm->procgrid[1]-1 &&
+ x[0] >= sublo[0] && x[0] < subhi[0]) flag = 1;
+
+ if (flag) {
+ if (ranflag) {
+ x[0] += ranx * 2.0*(randomx->uniform()-0.5);
+ x[1] += rany * 2.0*(randomx->uniform()-0.5);
+ x[2] += ranz * 2.0*(randomx->uniform()-0.5);
+ }
addnode++;
- atom->avec->create_atom(basistype[m],x);
- }
- }
- }
- }
+ atom->avec->create_atom(basistype[m],x);
+ }
+ }
+ }
+ }
}
}
int addtotal = 0;
@@ -488,13 +488,13 @@ void FixAppendAtoms::pre_exchange()
if (addtotal) {
domain->reset_box();
if (atom->tag_enable) {
- atom->tag_extend();
- atom->natoms += addtotal;
- if (atom->map_style) {
- atom->nghost = 0;
- atom->map_init();
- atom->map_set();
- }
+ atom->tag_extend();
+ atom->natoms += addtotal;
+ if (atom->map_style) {
+ atom->nghost = 0;
+ atom->map_init();
+ atom->map_set();
+ }
}
}
}
diff --git a/src/SHOCK/fix_append_atoms.h b/src/SHOCK/fix_append_atoms.h
index 6d8801be01061a25617516ef523069b0e3a1a465..d22abbfcb323af1e53cf85689932aba9a75bfca5 100644
--- a/src/SHOCK/fix_append_atoms.h
+++ b/src/SHOCK/fix_append_atoms.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -70,7 +70,7 @@ Self-explanatory.
E: Append boundary must be shrink/minimum
The boundary style of the face where atoms are added
-must be of type m (shrink/minimum).
+must be of type m (shrink/minimum).
E: Bad fix ID in fix append/atoms command
diff --git a/src/SHOCK/fix_msst.cpp b/src/SHOCK/fix_msst.cpp
index 04d207880ddba3443c9e790840673e98b014549e..3ee57d060f10a47884ab1f759b0a1b1b442a1969 100644
--- a/src/SHOCK/fix_msst.cpp
+++ b/src/SHOCK/fix_msst.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -18,7 +18,7 @@
------------------------------------------------------------------------- */
#include "string.h"
-#include "stdlib.h"
+#include "stdlib.h"
#include "math.h"
#include "fix_msst.h"
#include "atom.h"
@@ -68,7 +68,7 @@ FixMSST::FixMSST(LAMMPS *lmp, int narg, char **arg) :
p0_set = 0;
v0_set = 0;
e0_set = 0;
- tscale = 0.01;
+ tscale = 0.01;
if ( strcmp(arg[3],"x") == 0 )
direction = 0;
@@ -80,7 +80,7 @@ FixMSST::FixMSST(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,"Illegal fix msst command");
}
- velocity = atof(arg[4]);
+ velocity = atof(arg[4]);
if ( velocity < 0 )
error->all(FLERR,"Illegal fix msst command");
@@ -106,7 +106,7 @@ FixMSST::FixMSST(LAMMPS *lmp, int narg, char **arg) :
} else if ( strcmp(arg[iarg],"tscale") == 0 ) {
tscale = atof(arg[iarg+1]);
if (tscale < 0.0 || tscale > 1.0)
- error->all(FLERR,"Fix msst tscale must satisfy 0 <= tscale < 1");
+ error->all(FLERR,"Fix msst tscale must satisfy 0 <= tscale < 1");
iarg++;
} else error->all(FLERR,"Illegal fix msst command");
}
@@ -118,21 +118,21 @@ FixMSST::FixMSST(LAMMPS *lmp, int narg, char **arg) :
else if (direction == 1) fprintf(screen," Shock in y direction\n");
else if (direction == 2) fprintf(screen," Shock in z direction\n");
fprintf(screen," Cell mass-like parameter qmass "
- "(units of mass^2/length^4) = %12.5e\n", qmass);
+ "(units of mass^2/length^4) = %12.5e\n", qmass);
fprintf(screen," Shock velocity = %12.5e\n", velocity);
fprintf(screen," Artificial viscosity "
- "(units of mass/length/time) = %12.5e\n", mu);
-
+ "(units of mass/length/time) = %12.5e\n", mu);
+
if (p0_set)
- fprintf(screen," Initial pressure specified to be %12.5e\n", p0);
+ fprintf(screen," Initial pressure specified to be %12.5e\n", p0);
else fprintf(screen," Initial pressure calculated on first step\n");
-
+
if (v0_set)
- fprintf(screen," Initial volume specified to be %12.5e\n", v0);
+ fprintf(screen," Initial volume specified to be %12.5e\n", v0);
else fprintf(screen," Initial volume calculated on first step\n");
-
- if (e0_set)
- fprintf(screen," Initial energy specified to be %12.5e\n", e0);
+
+ if (e0_set)
+ fprintf(screen," Initial energy specified to be %12.5e\n", e0);
else fprintf(screen," Initial energy calculated on first step\n");
}
if (logfile) {
@@ -141,21 +141,21 @@ FixMSST::FixMSST(LAMMPS *lmp, int narg, char **arg) :
else if (direction == 1) fprintf(logfile," Shock in y direction\n");
else if (direction == 2) fprintf(logfile," Shock in z direction\n");
fprintf(logfile," Cell mass-like parameter qmass "
- "(units of mass^2/length^4) = %12.5e\n", qmass);
+ "(units of mass^2/length^4) = %12.5e\n", qmass);
fprintf(logfile," Shock velocity = %12.5e\n", velocity);
fprintf(logfile," Artificial viscosity "
- "(units of mass/length/time) = %12.5e\n", mu);
-
- if (p0_set)
- fprintf(logfile," Initial pressure specified to be %12.5e\n", p0);
+ "(units of mass/length/time) = %12.5e\n", mu);
+
+ if (p0_set)
+ fprintf(logfile," Initial pressure specified to be %12.5e\n", p0);
else fprintf(logfile," Initial pressure calculated on first step\n");
-
- if (v0_set)
- fprintf(logfile," Initial volume specified to be %12.5e\n", v0);
+
+ if (v0_set)
+ fprintf(logfile," Initial volume specified to be %12.5e\n", v0);
else fprintf(logfile," Initial volume calculated on first step\n");
-
- if (e0_set)
- fprintf(logfile," Initial energy specified to be %12.5e\n", e0);
+
+ if (e0_set)
+ fprintf(logfile," Initial energy specified to be %12.5e\n", e0);
else fprintf(logfile," Initial energy calculated on first step\n");
}
}
@@ -217,7 +217,7 @@ FixMSST::FixMSST(LAMMPS *lmp, int narg, char **arg) :
// initialize the time derivative of the volume.
omega[0] = omega[1] = omega[2] = 0.0;
-
+
nrigid = 0;
rfix = NULL;
@@ -313,19 +313,19 @@ void FixMSST::init()
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"rigid") == 0 ||
- strcmp(modify->fix[i]->style,"poems") == 0) nrigid++;
+ strcmp(modify->fix[i]->style,"poems") == 0) nrigid++;
if (nrigid) {
rfix = new int[nrigid];
nrigid = 0;
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"rigid") == 0 ||
- strcmp(modify->fix[i]->style,"poems") == 0) rfix[nrigid++] = i;
+ strcmp(modify->fix[i]->style,"poems") == 0) rfix[nrigid++] = i;
}
}
/* ----------------------------------------------------------------------
- compute T,P before integrator starts
+ compute T,P before integrator starts
------------------------------------------------------------------------- */
void FixMSST::setup(int vflag)
@@ -344,7 +344,7 @@ void FixMSST::setup(int vflag)
if ( screen ) fprintf(screen,"Fix MSST v0 = %12.5e\n", v0);
if ( logfile ) fprintf(logfile,"Fix MSST v0 = %12.5e\n", v0);
}
- }
+ }
if ( p0_set == 0 ) {
p0 = p_current[direction];
@@ -370,10 +370,10 @@ void FixMSST::setup(int vflag)
temperature->compute_vector();
double *ke_tensor = temperature->vector;
double ke_temp = ke_tensor[0]+ke_tensor[1]+ke_tensor[2];
- if (ke_temp > 0.0 && tscale > 0.0 ) {
+ if (ke_temp > 0.0 && tscale > 0.0 ) {
// transfer energy from atom velocities to cell volume motion
- // to bias initial compression
+ // to bias initial compression
double **v = atom->v;
int *mask = atom->mask;
@@ -386,22 +386,22 @@ void FixMSST::setup(int vflag)
if ( comm->me == 0 && tscale != 1.0) {
if ( screen )
- fprintf(screen,"Fix MSST initial strain rate of %12.5e established "
- "by reducing temperature by factor of %12.5e\n",
- fac2,tscale);
+ fprintf(screen,"Fix MSST initial strain rate of %12.5e established "
+ "by reducing temperature by factor of %12.5e\n",
+ fac2,tscale);
if ( logfile )
- fprintf(logfile,"Fix MSST initial strain rate of %12.5e established "
- "by reducing temperature by factor of %12.5e\n",
- fac2,tscale);
+ fprintf(logfile,"Fix MSST initial strain rate of %12.5e established "
+ "by reducing temperature by factor of %12.5e\n",
+ fac2,tscale);
}
for (int i = 0; i < atom->nlocal; i++) {
if (mask[i] & groupbit) {
for (int k = 0; k < 3; k++ ) {
v[i][k]*=sqrt_initial_temperature_scaling;
- }
+ }
}
}
- }
+ }
// trigger virial computation on next timestep
@@ -409,7 +409,7 @@ void FixMSST::setup(int vflag)
}
/* ----------------------------------------------------------------------
- 1st half of Verlet update
+ 1st half of Verlet update
------------------------------------------------------------------------- */
void FixMSST::initial_integrate(int vflag)
@@ -417,7 +417,7 @@ void FixMSST::initial_integrate(int vflag)
int sd;
double p_msst; // MSST driving pressure.
int i, k;
- double vol;
+ double vol;
int nlocal = atom->nlocal;
int *mask = atom->mask;
double **v = atom->v;
@@ -438,12 +438,12 @@ void FixMSST::initial_integrate(int vflag)
couple();
vol = compute_vol();
- // propagate the time derivative of
+ // propagate the time derivative of
// the volume 1/2 step at fixed vol, r, rdot.
p_msst = nktv2p * mvv2e * velocity * velocity * total_mass *
( v0 - vol)/( v0 * v0);
- double A = total_mass * ( p_current[sd] - p0 - p_msst ) /
+ double A = total_mass * ( p_current[sd] - p0 - p_msst ) /
(qmass * nktv2p * mvv2e);
double B = total_mass * mu / ( qmass * vol );
@@ -456,34 +456,34 @@ void FixMSST::initial_integrate(int vflag)
// use taylor expansion to avoid singularity at B == 0.
if ( B * dthalf > 1.0e-06 ) {
- omega[sd] = ( omega[sd] + A * ( exp(B * dthalf) - 1.0 ) / B )
+ omega[sd] = ( omega[sd] + A * ( exp(B * dthalf) - 1.0 ) / B )
* exp(-B * dthalf);
} else {
omega[sd] = omega[sd] + (A - B * omega[sd]) * dthalf +
0.5 * (B * B * omega[sd] - A * B ) * dthalf * dthalf;
}
-
- // propagate velocity sum 1/2 step by
+
+ // propagate velocity sum 1/2 step by
// temporarily propagating the velocities.
velocity_sum = compute_vsum();
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
for ( k = 0; k < 3; k++ ) {
- double C = f[i][k] * force->ftm2v / mass[type[i]];
- double D = mu * omega[sd] * omega[sd] /
- (velocity_sum * mass[type[i]] * vol );
- old_velocity[i][k] = v[i][k];
- if ( k == direction ) {
- D = D - 2.0 * omega[sd] / vol;
- }
- if ( fabs(dthalf * D) > 1.0e-06 ) {
- double expd = exp(D * dthalf);
- v[i][k] = expd * ( C + D * v[i][k] - C / expd ) / D;
- } else {
- v[i][k] = v[i][k] + ( C + D * v[i][k] ) * dthalf +
- 0.5 * (D * D * v[i][k] + C * D ) * dthalf * dthalf;
- }
+ double C = f[i][k] * force->ftm2v / mass[type[i]];
+ double D = mu * omega[sd] * omega[sd] /
+ (velocity_sum * mass[type[i]] * vol );
+ old_velocity[i][k] = v[i][k];
+ if ( k == direction ) {
+ D = D - 2.0 * omega[sd] / vol;
+ }
+ if ( fabs(dthalf * D) > 1.0e-06 ) {
+ double expd = exp(D * dthalf);
+ v[i][k] = expd * ( C + D * v[i][k] - C / expd ) / D;
+ } else {
+ v[i][k] = v[i][k] + ( C + D * v[i][k] ) * dthalf +
+ 0.5 * (D * D * v[i][k] + C * D ) * dthalf * dthalf;
+ }
}
}
}
@@ -494,7 +494,7 @@ void FixMSST::initial_integrate(int vflag)
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
for ( k = 0; k < 3; k++ ) {
- v[i][k] = old_velocity[i][k];
+ v[i][k] = old_velocity[i][k];
}
}
}
@@ -504,23 +504,23 @@ void FixMSST::initial_integrate(int vflag)
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
for ( k = 0; k < 3; k++ ) {
- double C = f[i][k] * force->ftm2v / mass[type[i]];
- double D = mu * omega[sd] * omega[sd] /
- (velocity_sum * mass[type[i]] * vol );
- if ( k == direction ) {
- D = D - 2.0 * omega[sd] / vol;
- }
- if ( fabs(dthalf * D) > 1.0e-06 ) {
- double expd = exp(D * dthalf);
- v[i][k] = expd * ( C + D * v[i][k] - C / expd ) / D;
- } else {
- v[i][k] = v[i][k] + ( C + D * v[i][k] ) * dthalf +
- 0.5 * (D * D * v[i][k] + C * D ) * dthalf * dthalf;
- }
+ double C = f[i][k] * force->ftm2v / mass[type[i]];
+ double D = mu * omega[sd] * omega[sd] /
+ (velocity_sum * mass[type[i]] * vol );
+ if ( k == direction ) {
+ D = D - 2.0 * omega[sd] / vol;
+ }
+ if ( fabs(dthalf * D) > 1.0e-06 ) {
+ double expd = exp(D * dthalf);
+ v[i][k] = expd * ( C + D * v[i][k] - C / expd ) / D;
+ } else {
+ v[i][k] = v[i][k] + ( C + D * v[i][k] ) * dthalf +
+ 0.5 * (D * D * v[i][k] + C * D ) * dthalf * dthalf;
+ }
}
}
}
-
+
// propagate the volume 1/2 step.
double vol1 = vol + omega[sd] * dthalf;
@@ -539,7 +539,7 @@ void FixMSST::initial_integrate(int vflag)
x[i][2] += dtv * v[i][2];
}
}
-
+
// propagate the volume 1/2 step.
double vol2 = vol1 + omega[sd] * dthalf;
@@ -553,7 +553,7 @@ void FixMSST::initial_integrate(int vflag)
}
/* ----------------------------------------------------------------------
- 2nd half of Verlet update
+ 2nd half of Verlet update
------------------------------------------------------------------------- */
void FixMSST::final_integrate()
@@ -577,19 +577,19 @@ void FixMSST::final_integrate()
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
for ( int k = 0; k < 3; k++ ) {
- double C = f[i][k] * force->ftm2v / mass[type[i]];
- double D = mu * omega[sd] * omega[sd] /
- (velocity_sum * mass[type[i]] * vol );
- if ( k == direction ) {
- D = D - 2.0 * omega[sd] / vol;
- }
- if ( fabs(dthalf * D) > 1.0e-06 ) {
- double expd = exp(D * dthalf);
- v[i][k] = expd * ( C + D * v[i][k] - C / expd ) / D;
- } else {
- v[i][k] = v[i][k] + ( C + D * v[i][k] ) * dthalf +
- 0.5 * (D * D * v[i][k] + C * D ) * dthalf * dthalf;
- }
+ double C = f[i][k] * force->ftm2v / mass[type[i]];
+ double D = mu * omega[sd] * omega[sd] /
+ (velocity_sum * mass[type[i]] * vol );
+ if ( k == direction ) {
+ D = D - 2.0 * omega[sd] / vol;
+ }
+ if ( fabs(dthalf * D) > 1.0e-06 ) {
+ double expd = exp(D * dthalf);
+ v[i][k] = expd * ( C + D * v[i][k] - C / expd ) / D;
+ } else {
+ v[i][k] = v[i][k] + ( C + D * v[i][k] ) * dthalf +
+ 0.5 * (D * D * v[i][k] + C * D ) * dthalf * dthalf;
+ }
}
}
}
@@ -607,7 +607,7 @@ void FixMSST::final_integrate()
p_msst = nktv2p * mvv2e * velocity * velocity * total_mass *
( v0 - vol )/( v0 * v0 );
- double A = total_mass * ( p_current[sd] - p0 - p_msst ) /
+ double A = total_mass * ( p_current[sd] - p0 - p_msst ) /
( qmass * nktv2p * mvv2e );
double B = total_mass * mu / ( qmass * vol );
@@ -620,12 +620,12 @@ void FixMSST::final_integrate()
// use taylor expansion to avoid singularity at B == 0.
if ( B * dthalf > 1.0e-06 ) {
- omega[sd] = ( omega[sd] + A *
- ( exp(B * dthalf) - 1.0 ) / B ) * exp(-B * dthalf);
+ omega[sd] = ( omega[sd] + A *
+ ( exp(B * dthalf) - 1.0 ) / B ) * exp(-B * dthalf);
} else {
omega[sd] = omega[sd] + (A - B * omega[sd]) * dthalf +
0.5 * (B * B * omega[sd] - A * B ) * dthalf * dthalf;
- }
+ }
// calculate Lagrangian position of computational cell
@@ -694,13 +694,13 @@ void FixMSST::remap(int flag)
modify->fix[rfix[i]]->deform(1);
for (i = 0; i < n; i++) {
- v[i][direction] = v[i][direction] *
+ v[i][direction] = v[i][direction] *
dilation[direction];
}
}
/* ----------------------------------------------------------------------
- pack entire state of Fix into one write
+ pack entire state of Fix into one write
------------------------------------------------------------------------- */
void FixMSST::write_restart(FILE *fp)
@@ -719,7 +719,7 @@ void FixMSST::write_restart(FILE *fp)
}
/* ----------------------------------------------------------------------
- use state info from restart file to restart the Fix
+ use state info from restart file to restart the Fix
------------------------------------------------------------------------- */
void FixMSST::restart(char *buf)
@@ -800,7 +800,7 @@ double FixMSST::compute_scalar()
i = direction;
energy = qmass * omega[i] * omega[i] / (2.0 * total_mass) * mvv2e;
- energy -= 0.5 * total_mass * velocity * velocity *
+ energy -= 0.5 * total_mass * velocity * velocity *
(1.0 - volume/ v0) *
(1.0 - volume/ v0) * mvv2e;
energy -= p0 * ( v0 - volume ) / nktv2p;
@@ -809,7 +809,7 @@ double FixMSST::compute_scalar()
}
/* ----------------------------------------------------------------------
- return a single element from the following vector,
+ return a single element from the following vector,
[dhug,dray,lgr_vel,lgr_pos]
------------------------------------------------------------------------- */
@@ -828,7 +828,7 @@ double FixMSST::compute_vector(int n)
}
/* ----------------------------------------------------------------------
- Computes the deviation of the current point
+ Computes the deviation of the current point
from the Hugoniot in Kelvin for the MSST.
------------------------------------------------------------------------- */
@@ -836,24 +836,24 @@ double FixMSST::compute_hugoniot()
{
double v, e, p;
double dhugo;
-
+
e = compute_etotal();
-
+
temperature->compute_vector();
pressure->compute_vector();
p = pressure->vector[direction];
-
+
v = compute_vol();
-
- dhugo = (0.5 * (p + p0 ) * ( v0 - v)) /
+
+ dhugo = (0.5 * (p + p0 ) * ( v0 - v)) /
force->nktv2p + e0 - e;
dhugo /= temperature->dof * force->boltz;
-
+
return dhugo;
}
/* ----------------------------------------------------------------------
- Computes the deviation of the current point from the Rayleigh
+ Computes the deviation of the current point from the Rayleigh
in pressure units for the MSST.
------------------------------------------------------------------------- */
@@ -876,7 +876,7 @@ double FixMSST::compute_rayleigh()
}
/* ----------------------------------------------------------------------
- Computes the speed of the MSST computational cell in the
+ Computes the speed of the MSST computational cell in the
unshocked material rest-frame
------------------------------------------------------------------------- */
@@ -887,7 +887,7 @@ double FixMSST::compute_lagrangian_speed()
}
/* ----------------------------------------------------------------------
- Computes the distance behind the
+ Computes the distance behind the
shock front of the MSST computational cell.
------------------------------------------------------------------------- */
@@ -958,4 +958,3 @@ double FixMSST::compute_vsum()
MPI_Allreduce(&t,&vsum,1,MPI_DOUBLE,MPI_SUM,world);
return vsum;
}
-
diff --git a/src/SHOCK/fix_msst.h b/src/SHOCK/fix_msst.h
index 26ce3b1c9f52fdfc3e0204a889e3961056e912ef..13eed1828e368e86ee1b316f593619a3b98f0a98 100644
--- a/src/SHOCK/fix_msst.h
+++ b/src/SHOCK/fix_msst.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -52,9 +52,9 @@ class FixMSST : public Fix {
double p_current[3],dilation[3];
double qmass; // Effective cell mass.
double mu; // Effective cell viscosity.
- double tscale; // Converts thermal energy to compressive
+ double tscale; // Converts thermal energy to compressive
// strain ke at simulation start
-
+
double velocity_sum; // Sum of the velocities squared.
double **old_velocity; // Saved velocities.
@@ -66,7 +66,7 @@ class FixMSST : public Fix {
char *id_temp,*id_press; // Strings with identifiers of
char *id_pe; // created computes.
- class Compute *temperature; // Computes created to evaluate
+ class Compute *temperature; // Computes created to evaluate
class Compute *pressure; // thermodynamic quantities.
class Compute *pe;
int tflag,pflag,vsflag,peflag; // Flags to keep track of computes that
@@ -78,15 +78,15 @@ class FixMSST : public Fix {
double v0; // Initial volume
double p0; // Initial pressure
double velocity; // Velocity of the shock.
- double lagrangian_position; // Lagrangian location of computational cell
+ double lagrangian_position; // Lagrangian location of computational cell
int direction; // Direction of shock
int p0_set; // Is pressure set.
int v0_set; // Is volume set.
int e0_set; // Is energy set.
-
+
int atoms_allocated; // The number of allocated atoms in old_velocity.
- // functions
+ // functions
void couple();
void remap(int);
diff --git a/src/SHOCK/fix_nphug.cpp b/src/SHOCK/fix_nphug.cpp
index ed3c8f74e242bc930e43a8ae5348bda592487ef8..48b33db4e6607242b19309f6833458f17b4e7b53 100644
--- a/src/SHOCK/fix_nphug.cpp
+++ b/src/SHOCK/fix_nphug.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -59,7 +59,7 @@ FixNPHug::FixNPHug(LAMMPS *lmp, int narg, char **arg) :
// check pressure settings
if (p_start[0] != p_stop[0] ||
- p_start[1] != p_stop[1] ||
+ p_start[1] != p_stop[1] ||
p_start[2] != p_stop[2])
error->all(FLERR,"Pstart and Pstop must have the same value");
@@ -78,22 +78,22 @@ FixNPHug::FixNPHug(LAMMPS *lmp, int narg, char **arg) :
// anisotropic hydrostatic compression
- if (p_start[0] == p_start[1] &&
- p_start[0] == p_start[2] )
+ if (p_start[0] == p_start[1] &&
+ p_start[0] == p_start[2] )
uniaxial = 0;
// uniaxial compression
- else if (p_flag[0] == 1 && p_flag[1] == 0
- && p_flag[2] == 0) {
+ else if (p_flag[0] == 1 && p_flag[1] == 0
+ && p_flag[2] == 0) {
uniaxial = 1;
idir = 0;
- } else if (p_flag[0] == 0 && p_flag[1] == 1
- && p_flag[2] == 0) {
+ } else if (p_flag[0] == 0 && p_flag[1] == 1
+ && p_flag[2] == 0) {
uniaxial = 1;
idir = 1;
- } else if (p_flag[0] == 0 && p_flag[1] == 0
- && p_flag[2] == 1) {
+ } else if (p_flag[0] == 0 && p_flag[1] == 0
+ && p_flag[2] == 1) {
uniaxial = 1;
idir = 2;
@@ -103,11 +103,11 @@ FixNPHug::FixNPHug(LAMMPS *lmp, int narg, char **arg) :
} else if (pstyle == TRICLINIC) {
- if (p_start[0] == p_start[1] &&
- p_start[0] == p_start[2] &&
- p_start[3] == 0.0 &&
- p_start[4] == 0.0 &&
- p_start[5] == 0.0 )
+ if (p_start[0] == p_start[1] &&
+ p_start[0] == p_start[2] &&
+ p_start[3] == 0.0 &&
+ p_start[4] == 0.0 &&
+ p_start[5] == 0.0 )
uniaxial = 0;
else error->all(FLERR,"For triclinic deformation, specified target stress must be hydrostatic");
@@ -127,7 +127,7 @@ FixNPHug::FixNPHug(LAMMPS *lmp, int narg, char **arg) :
id_temp = new char[n];
strcpy(id_temp,id);
strcat(id_temp,"_temp");
-
+
char **newarg = new char*[3];
newarg[0] = id_temp;
newarg[1] = (char *) "all";
@@ -145,7 +145,7 @@ FixNPHug::FixNPHug(LAMMPS *lmp, int narg, char **arg) :
id_press = new char[n];
strcpy(id_press,id);
strcat(id_press,"_press");
-
+
newarg = new char*[4];
newarg[0] = id_press;
newarg[1] = (char *) "all";
@@ -195,14 +195,14 @@ void FixNPHug::init()
// set pe ptr
int icompute = modify->find_compute(id_pe);
- if (icompute < 0)
+ if (icompute < 0)
error->all(FLERR,"Potential energy ID for fix nvt/nph/npt does not exist");
pe = modify->compute[icompute];
}
/* ----------------------------------------------------------------------
- compute initial state before integrator starts
+ compute initial state before integrator starts
------------------------------------------------------------------------- */
void FixNPHug::setup(int vflag)
@@ -212,7 +212,7 @@ void FixNPHug::setup(int vflag)
if ( v0_set == 0 ) {
v0 = compute_vol();
v0_set = 1;
- }
+ }
if ( p0_set == 0 ) {
p0_set = 1;
@@ -270,7 +270,7 @@ double FixNPHug::compute_vol()
}
/* ----------------------------------------------------------------------
- Computes the deviation of the current point
+ Computes the deviation of the current point
from the Hugoniot in temperature units.
------------------------------------------------------------------------- */
@@ -278,21 +278,21 @@ double FixNPHug::compute_hugoniot()
{
double v,e,p;
double dhugo;
-
+
e = compute_etotal();
-
+
temperature->compute_vector();
if (uniaxial == 1) {
pressure->compute_vector();
p = pressure->vector[idir];
- } else
+ } else
p = pressure->compute_scalar();
-
+
v = compute_vol();
-
- dhugo = (0.5 * (p + p0 ) * ( v0 - v)) /
+
+ dhugo = (0.5 * (p + p0 ) * ( v0 - v)) /
force->nktv2p + e0 - e;
dhugo /= tdof * boltz;
@@ -308,24 +308,24 @@ double FixNPHug::compute_us()
{
double v,p;
double eps,us;
-
+
temperature->compute_vector();
if (uniaxial == 1) {
pressure->compute_vector();
p = pressure->vector[idir];
- } else
+ } else
p = pressure->compute_scalar();
-
+
v = compute_vol();
-
+
// Us^2 = (p-p0)/(rho0*eps)
eps = 1.0 - v/v0;
if (eps < 1.0e-10) us = 0.0;
- else if (p < p0) us = 0.0;
+ else if (p < p0) us = 0.0;
else us = sqrt((p-p0)/(rho0*eps));
-
+
return us;
}
@@ -337,7 +337,7 @@ double FixNPHug::compute_up()
{
double v;
double eps,us,up;
-
+
v = compute_vol();
us = compute_us();
@@ -380,7 +380,7 @@ double FixNPHug::compute_vector(int n)
}
/* ----------------------------------------------------------------------
- pack restart data
+ pack restart data
------------------------------------------------------------------------- */
int FixNPHug::pack_restart_data(double *list)
@@ -414,7 +414,7 @@ int FixNPHug::size_restart_global()
}
/* ----------------------------------------------------------------------
- use state info from restart file to restart the Fix
+ use state info from restart file to restart the Fix
------------------------------------------------------------------------- */
void FixNPHug::restart(char *buf)
diff --git a/src/SHOCK/fix_nphug.h b/src/SHOCK/fix_nphug.h
index 082a30539311c83de509d0f3d04da1938fea33a5..3cdd6ec508b1daa448dbce02aa90517319bedbdc 100644
--- a/src/SHOCK/fix_nphug.h
+++ b/src/SHOCK/fix_nphug.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -33,7 +33,7 @@ class FixNPHug : public FixNH {
int modify_param(int, char **);
int pack_restart_data(double *); // pack restart data
void restart(char *);
-
+
private:
class Compute *pe; // PE compute pointer
diff --git a/src/SHOCK/fix_wall_piston.cpp b/src/SHOCK/fix_wall_piston.cpp
index 7f45e61220e14c3e9163b1bb389f3caf78f72e97..18d097d97b30b1ef847f218020d512b0423694fa 100644
--- a/src/SHOCK/fix_wall_piston.cpp
+++ b/src/SHOCK/fix_wall_piston.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -63,8 +63,8 @@ FixWallPiston::FixWallPiston(LAMMPS *lmp, int narg, char **arg) :
else if (strcmp(arg[iarg],"zlo") == 0) {
zloflag = 1;
iarg++;
- if (domain->boundary[2][0] != 2)
- error->all(FLERR,"Must shrink-wrap piston boundary");
+ if (domain->boundary[2][0] != 2)
+ error->all(FLERR,"Must shrink-wrap piston boundary");
} else if (strcmp(arg[iarg],"xhi") == 0)
error->all(FLERR,"Fix wall/piston command only available at zlo");
else if (strcmp(arg[iarg],"yhi") == 0)
@@ -129,7 +129,7 @@ FixWallPiston::FixWallPiston(LAMMPS *lmp, int narg, char **arg) :
} else error->all(FLERR,"Illegal fix wall/piston command");
}
- if (vx < 0.0 || vy < 0.0 || vz < 0.0)
+ if (vx < 0.0 || vy < 0.0 || vz < 0.0)
error->all(FLERR,"Illegal fix wall/piston velocity");
if ((xloflag || xhiflag) && domain->xperiodic)
error->all(FLERR,"Cannot use wall in periodic dimension");
@@ -159,7 +159,7 @@ FixWallPiston::FixWallPiston(LAMMPS *lmp, int narg, char **arg) :
z0 *= zscale;
roughdist *= zscale;
- if (rampflag || rampNL1flag || rampNL2flag || rampNL3flag ||
+ if (rampflag || rampNL1flag || rampNL2flag || rampNL3flag ||
rampNL4flag || rampNL5flag) {
maxvx = vx;
maxvy = vy;
@@ -217,12 +217,12 @@ void FixWallPiston::post_integrate()
angfreq = MY_2PI / (0.5 * tott);
if (zloflag) {
- zlo = z0 + paccelz * (0.5*tt + 1.0/(angfreq*angfreq) -
- 1.0/(angfreq*angfreq)*cos(angfreq*t));
+ zlo = z0 + paccelz * (0.5*tt + 1.0/(angfreq*angfreq) -
+ 1.0/(angfreq*angfreq)*cos(angfreq*t));
vz = paccelz * (t + 1.0/angfreq*sin(angfreq*t));
}
else error->all(FLERR,
- "NL ramp in wall/piston only implemented in zlo for now");
+ "NL ramp in wall/piston only implemented in zlo for now");
}
else if (rampNL2flag) {
paccelz = maxvz / tott;
@@ -230,13 +230,13 @@ void FixWallPiston::post_integrate()
if (zloflag) {
zlo = z0 + paccelz * (0.5*tt + 4.0/(3.0*angfreq*angfreq)*
- (1.0-cos(angfreq*t)) +
- 1.0/(6.0*angfreq*angfreq)*(1.0-cos(2.0*angfreq*t)));
- vz = paccelz * (t + 4.0/(3.0*angfreq)*sin(angfreq*t) +
- 1.0/(3.0*angfreq)*sin(2.0*angfreq*t));
+ (1.0-cos(angfreq*t)) +
+ 1.0/(6.0*angfreq*angfreq)*(1.0-cos(2.0*angfreq*t)));
+ vz = paccelz * (t + 4.0/(3.0*angfreq)*sin(angfreq*t) +
+ 1.0/(3.0*angfreq)*sin(2.0*angfreq*t));
}
else error->all(FLERR,
- "NL ramp in wall/piston only implemented in zlo for now");
+ "NL ramp in wall/piston only implemented in zlo for now");
}
else if (rampNL3flag) {
paccelz = maxvz / tott;
@@ -246,7 +246,7 @@ void FixWallPiston::post_integrate()
vz = paccelz * tott * (t1p5 );
}
else error->all(FLERR,
- "NL ramp in wall/piston only implemented in zlo for now");
+ "NL ramp in wall/piston only implemented in zlo for now");
}
else if (rampNL4flag) {
paccelz = maxvz / tott;
@@ -256,7 +256,7 @@ void FixWallPiston::post_integrate()
vz = paccelz / tott * (tt);
}
else error->all(FLERR,
- "NL ramp in wall/piston only implemented in zlo for now");
+ "NL ramp in wall/piston only implemented in zlo for now");
}
else if (rampNL5flag) {
paccelz = maxvz / tott;
@@ -266,7 +266,7 @@ void FixWallPiston::post_integrate()
vz = paccelz / tott / tott * (ttt);
}
else error->all(FLERR,
- "NL ramp in wall/piston only implemented in zlo for now");
+ "NL ramp in wall/piston only implemented in zlo for now");
}
else {
if (zloflag) { zlo = z0 + vz * t; }
@@ -275,13 +275,13 @@ void FixWallPiston::post_integrate()
if (update->ntimestep % 1000 == 0)
if (comm->me == 0) {
if (screen)
- fprintf(screen,"SHOCK: step " BIGINT_FORMAT
- " t %g zpos %g vz %g az %g zlo %g\n",
- update->ntimestep, t, zlo, vz, paccelz, domain->boxlo[2]);
+ fprintf(screen,"SHOCK: step " BIGINT_FORMAT
+ " t %g zpos %g vz %g az %g zlo %g\n",
+ update->ntimestep, t, zlo, vz, paccelz, domain->boxlo[2]);
if (logfile)
- fprintf(logfile,"SHOCK: step " BIGINT_FORMAT
- " t %g zpos %g vz %g az %g zlo %g\n",
- update->ntimestep, t, zlo, vz, paccelz, domain->boxlo[2]);
+ fprintf(logfile,"SHOCK: step " BIGINT_FORMAT
+ " t %g zpos %g vz %g az %g zlo %g\n",
+ update->ntimestep, t, zlo, vz, paccelz, domain->boxlo[2]);
}
// VIRIAL PRESSURE CONTRIBUTION?
@@ -291,22 +291,22 @@ void FixWallPiston::post_integrate()
roughoff = 0.0;
if (roughflag) {
roughoff += roughdist*fabs((x[i][0] - domain->boxlo[0])/
- (domain->boxhi[0]-domain->boxlo[0])-0.5);
+ (domain->boxhi[0]-domain->boxlo[0])-0.5);
roughoff += roughdist*fabs((x[i][1] - domain->boxlo[1])/
- (domain->boxhi[1]-domain->boxlo[1])-0.5);
+ (domain->boxhi[1]-domain->boxlo[1])-0.5);
}
if (zloflag && x[i][2] < zlo - roughoff) {
- x[i][2] = 2.0 * (zlo - roughoff) - x[i][2];
- v[i][2] = 2.0 * vz - v[i][2];
+ x[i][2] = 2.0 * (zlo - roughoff) - x[i][2];
+ v[i][2] = 2.0 * vz - v[i][2];
}
}
}
double **f = atom->f;
int *type = atom->type;
-
+
double gamma1,gamma2;
double tsqrt = sqrt(t_target);
-
+
if (atom->mass) {
if (tempflag) {
for (int i = 1; i <= atom->ntypes; i++) {
diff --git a/src/SHOCK/fix_wall_piston.h b/src/SHOCK/fix_wall_piston.h
index 2ebd9ab8f39eea0552e4c832d9b6a0814e4ee1a7..15e4d9c0ef30d1fed8cc74127340d7adfa46de60 100644
--- a/src/SHOCK/fix_wall_piston.h
+++ b/src/SHOCK/fix_wall_piston.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/SRD/fix_srd.cpp b/src/SRD/fix_srd.cpp
index 7cbb604a492299c92df657e86a36a9fe3fcd22e5..5484ab3fbc43b569f40b3d536e7ccdb5db6af421 100644
--- a/src/SRD/fix_srd.cpp
+++ b/src/SRD/fix_srd.cpp
@@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
-
+
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
-
+
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@@ -174,7 +174,7 @@ FixSRD::FixSRD(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
// error check
if (nevery <= 0) error->all(FLERR,"Illegal fix srd command");
- if (bigexist && biggroup < 0)
+ if (bigexist && biggroup < 0)
error->all(FLERR,"Could not find fix srd group ID");
if (gridsrd <= 0.0) error->all(FLERR,"Illegal fix srd command");
if (temperature_srd <= 0.0) error->all(FLERR,"Illegal fix srd command");
@@ -183,9 +183,9 @@ FixSRD::FixSRD(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
if (maxbounceallow < 0) error->all(FLERR,"Illegal fix srd command");
if (lamdaflag && lamda <= 0.0) error->all(FLERR,"Illegal fix srd command");
if (gridsearch <= 0.0) error->all(FLERR,"Illegal fix srd command");
- if (cubictol < 0.0 || cubictol > 1.0)
+ if (cubictol < 0.0 || cubictol > 1.0)
error->all(FLERR,"Illegal fix srd command");
- if ((shiftuser == SHIFT_YES || shiftuser == SHIFT_POSSIBLE) &&
+ if ((shiftuser == SHIFT_YES || shiftuser == SHIFT_POSSIBLE) &&
shiftseed <= 0) error->all(FLERR,"Illegal fix srd command");
// initialize Marsaglia RNG with processor-unique seed
@@ -219,8 +219,8 @@ FixSRD::FixSRD(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
shifts[0].maxbinsq = shifts[1].maxbinsq = 0;
for (int ishift = 0; ishift < 2; ishift++)
for (int iswap = 0; iswap < 6; iswap++)
- shifts[ishift].bcomm[iswap].sendlist =
- shifts[ishift].bcomm[iswap].recvlist = NULL;
+ shifts[ishift].bcomm[iswap].sendlist =
+ shifts[ishift].bcomm[iswap].recvlist = NULL;
maxbin2 = 0;
nbinbig = NULL;
@@ -299,7 +299,7 @@ void FixSRD::init()
{
// error checks
- if (force->newton_pair == 0)
+ if (force->newton_pair == 0)
error->all(FLERR,"Fix srd requires newton pair on");
if (bigexist && comm->ghost_velocity == 0)
error->all(FLERR,"Fix srd requires ghost atoms store velocity");
@@ -330,8 +330,8 @@ void FixSRD::init()
fwall = wallfix->fwall;
walltrigger = 0.5 * neighbor->skin;
if (wallfix->overlap && overlap == 0 && me == 0)
- error->warning(FLERR,
- "Fix SRD walls overlap but fix srd overlap not set");
+ error->warning(FLERR,
+ "Fix SRD walls overlap but fix srd overlap not set");
}
}
@@ -344,17 +344,17 @@ void FixSRD::init()
if (modify->fix[i]->box_change_size) change_size = 1;
if (modify->fix[i]->box_change_shape) change_shape = 1;
if (strcmp(modify->fix[i]->style,"deform") == 0) {
- deformflag = 1;
- FixDeform *deform = (FixDeform *) modify->fix[i];
- if (deform->box_change_shape && deform->remapflag != V_REMAP)
- error->all(FLERR,"Using fix srd with inconsistent "
- "fix deform remap option");
+ deformflag = 1;
+ FixDeform *deform = (FixDeform *) modify->fix[i];
+ if (deform->box_change_shape && deform->remapflag != V_REMAP)
+ error->all(FLERR,"Using fix srd with inconsistent "
+ "fix deform remap option");
}
}
if (deformflag && tstat == 0 && me == 0)
error->warning(FLERR,
- "Using fix srd with box deformation but no SRD thermostat");
+ "Using fix srd with box deformation but no SRD thermostat");
// parameterize based on current box volume
@@ -374,8 +374,8 @@ void FixSRD::init()
if (mask[i] & groupbit) {
vsq = v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2];
if (vsq > vmaxsq) {
- nrescale++;
- MathExtra::scale3(vmax/sqrt(vsq),v[i]);
+ nrescale++;
+ MathExtra::scale3(vmax/sqrt(vsq),v[i]);
}
}
@@ -409,7 +409,7 @@ void FixSRD::setup(int vflag)
if (dist_srd_reneigh < nevery*dt_big*vmax && me == 0)
error->warning(FLERR,
- "Fix srd SRD moves may trigger frequent reneighboring");
+ "Fix srd SRD moves may trigger frequent reneighboring");
// setup search bins and search stencil based on these distances
@@ -455,11 +455,11 @@ void FixSRD::pre_neighbor()
if (bigexist) {
if (biggroup == atom->firstgroup) nbig = atom->nfirst + atom->nghost;
else {
- int *mask = atom->mask;
- int nlocal = atom->nlocal;
- nbig = atom->nghost;
- for (i = 0; i < nlocal; i++)
- if (mask[i] & biggroupbit) nbig++;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+ nbig = atom->nghost;
+ for (i = 0; i < nlocal; i++)
+ if (mask[i] & biggroupbit) nbig++;
}
} else nbig = 0;
@@ -478,17 +478,17 @@ void FixSRD::pre_neighbor()
if (biggroup == atom->firstgroup) nlocal = atom->nfirst;
nbig = 0;
for (i = 0; i < nlocal; i++)
- if (mask[i] & biggroupbit) biglist[nbig++].index = i;
+ if (mask[i] & biggroupbit) biglist[nbig++].index = i;
int nall = atom->nlocal + atom->nghost;
for (i = atom->nlocal; i < nall; i++)
- if (mask[i] & biggroupbit) biglist[nbig++].index = i;
+ if (mask[i] & biggroupbit) biglist[nbig++].index = i;
big_static();
}
if (wallexist) {
for (m = 0; m < nwall; m++) {
- biglist[nbig+m].index = m;
- biglist[nbig+m].type = WALL;
+ biglist[nbig+m].index = m;
+ biglist[nbig+m].type = WALL;
}
wallfix->wall_params(1);
}
@@ -525,38 +525,38 @@ void FixSRD::pre_neighbor()
i = nbig = 0;
while (i < nall) {
if (mask[i] & biggroupbit) {
- ix = static_cast<int> ((x[i][0]-xblo2)*bininv2x);
- iy = static_cast<int> ((x[i][1]-yblo2)*bininv2y);
- iz = static_cast<int> ((x[i][2]-zblo2)*bininv2z);
- ibin = iz*nbin2y*nbin2x + iy*nbin2x + ix;
-
- if (ix < 0 || ix >= nbin2x || iy < 0 || iy >= nbin2y ||
- iz < 0 || iz >= nbin2z)
- error->one(FLERR,"Fix SRD: bad search bin assignment");
-
- cutbinsq = biglist[nbig].cutbinsq;
- for (j = 0; j < nstencil; j++) {
- jx = ix + stencil[j][0];
- jy = iy + stencil[j][1];
- jz = iz + stencil[j][2];
-
- if (jx < 0 || jx >= nbin2x || jy < 0 || jy >= nbin2y ||
- jz < 0 || jz >= nbin2z) {
- printf("Big particle %d %d %g %g %g\n",
- atom->tag[i],i,x[i][0],x[i][1],x[i][2]);
- printf("Bin indices: %d %d %d, %d %d %d, %d %d %d\n",
- ix,iy,iz,jx,jy,jz,nbin2x,nbin2y,nbin2z);
- error->one(FLERR,"Fix SRD: bad stencil bin for big particle");
- }
- rsq = point_bin_distance(x[i],jx,jy,jz);
- if (rsq < cutbinsq) {
- jbin = ibin + stencil[j][3];
- if (nbinbig[jbin] == ATOMPERBIN)
- error->one(FLERR,"Fix SRD: too many big particles in bin");
- binbig[jbin][nbinbig[jbin]++] = nbig;
- }
- }
- nbig++;
+ ix = static_cast<int> ((x[i][0]-xblo2)*bininv2x);
+ iy = static_cast<int> ((x[i][1]-yblo2)*bininv2y);
+ iz = static_cast<int> ((x[i][2]-zblo2)*bininv2z);
+ ibin = iz*nbin2y*nbin2x + iy*nbin2x + ix;
+
+ if (ix < 0 || ix >= nbin2x || iy < 0 || iy >= nbin2y ||
+ iz < 0 || iz >= nbin2z)
+ error->one(FLERR,"Fix SRD: bad search bin assignment");
+
+ cutbinsq = biglist[nbig].cutbinsq;
+ for (j = 0; j < nstencil; j++) {
+ jx = ix + stencil[j][0];
+ jy = iy + stencil[j][1];
+ jz = iz + stencil[j][2];
+
+ if (jx < 0 || jx >= nbin2x || jy < 0 || jy >= nbin2y ||
+ jz < 0 || jz >= nbin2z) {
+ printf("Big particle %d %d %g %g %g\n",
+ atom->tag[i],i,x[i][0],x[i][1],x[i][2]);
+ printf("Bin indices: %d %d %d, %d %d %d, %d %d %d\n",
+ ix,iy,iz,jx,jy,jz,nbin2x,nbin2y,nbin2z);
+ error->one(FLERR,"Fix SRD: bad stencil bin for big particle");
+ }
+ rsq = point_bin_distance(x[i],jx,jy,jz);
+ if (rsq < cutbinsq) {
+ jbin = ibin + stencil[j][3];
+ if (nbinbig[jbin] == ATOMPERBIN)
+ error->one(FLERR,"Fix SRD: too many big particles in bin");
+ binbig[jbin][nbinbig[jbin]++] = nbig;
+ }
+ }
+ nbig++;
}
i++;
@@ -578,73 +578,73 @@ void FixSRD::pre_neighbor()
int side = wallwhich[m] % 2;
if (dim == 0) {
- if (side == 0) {
- hi = static_cast<int> ((xwall[m]+delta-xblo2)*bininv2x);
- if (hi < 0) continue;
- if (hi >= nbin2x) error->all(FLERR,
- "Fix SRD: bad search bin assignment");
- lo = 0;
- } else {
- lo = static_cast<int> ((xwall[m]-delta-xblo2)*bininv2x);
- if (lo >= nbin2x) continue;
- if (lo < 0) error->all(FLERR,"Fix SRD: bad search bin assignment");
- hi = nbin2x-1;
- }
-
- for (ix = lo; ix <= hi; ix++)
- for (iy = 0; iy < nbin2y; iy++)
- for (iz = 0; iz < nbin2z; iz++) {
- ibin = iz*nbin2y*nbin2x + iy*nbin2x + ix;
- if (nbinbig[ibin] == ATOMPERBIN)
- error->all(FLERR,"Fix SRD: too many walls in bin");
- binbig[ibin][nbinbig[ibin]++] = nbig+m;
- }
+ if (side == 0) {
+ hi = static_cast<int> ((xwall[m]+delta-xblo2)*bininv2x);
+ if (hi < 0) continue;
+ if (hi >= nbin2x) error->all(FLERR,
+ "Fix SRD: bad search bin assignment");
+ lo = 0;
+ } else {
+ lo = static_cast<int> ((xwall[m]-delta-xblo2)*bininv2x);
+ if (lo >= nbin2x) continue;
+ if (lo < 0) error->all(FLERR,"Fix SRD: bad search bin assignment");
+ hi = nbin2x-1;
+ }
+
+ for (ix = lo; ix <= hi; ix++)
+ for (iy = 0; iy < nbin2y; iy++)
+ for (iz = 0; iz < nbin2z; iz++) {
+ ibin = iz*nbin2y*nbin2x + iy*nbin2x + ix;
+ if (nbinbig[ibin] == ATOMPERBIN)
+ error->all(FLERR,"Fix SRD: too many walls in bin");
+ binbig[ibin][nbinbig[ibin]++] = nbig+m;
+ }
} else if (dim == 1) {
- if (side == 0) {
- hi = static_cast<int> ((xwall[m]+delta-yblo2)*bininv2y);
- if (hi < 0) continue;
- if (hi >= nbin2y) error->all(FLERR,
- "Fix SRD: bad search bin assignment");
- lo = 0;
- } else {
- lo = static_cast<int> ((xwall[m]-delta-yblo2)*bininv2y);
- if (lo >= nbin2y) continue;
- if (lo < 0) error->all(FLERR,"Fix SRD: bad search bin assignment");
- hi = nbin2y-1;
- }
-
- for (iy = lo; iy <= hi; iy++)
- for (ix = 0; ix < nbin2x; ix++)
- for (iz = 0; iz < nbin2z; iz++) {
- ibin = iz*nbin2y*nbin2x + iy*nbin2x + ix;
- if (nbinbig[ibin] == ATOMPERBIN)
- error->all(FLERR,"Fix SRD: too many walls in bin");
- binbig[ibin][nbinbig[ibin]++] = nbig+m;
- }
+ if (side == 0) {
+ hi = static_cast<int> ((xwall[m]+delta-yblo2)*bininv2y);
+ if (hi < 0) continue;
+ if (hi >= nbin2y) error->all(FLERR,
+ "Fix SRD: bad search bin assignment");
+ lo = 0;
+ } else {
+ lo = static_cast<int> ((xwall[m]-delta-yblo2)*bininv2y);
+ if (lo >= nbin2y) continue;
+ if (lo < 0) error->all(FLERR,"Fix SRD: bad search bin assignment");
+ hi = nbin2y-1;
+ }
+
+ for (iy = lo; iy <= hi; iy++)
+ for (ix = 0; ix < nbin2x; ix++)
+ for (iz = 0; iz < nbin2z; iz++) {
+ ibin = iz*nbin2y*nbin2x + iy*nbin2x + ix;
+ if (nbinbig[ibin] == ATOMPERBIN)
+ error->all(FLERR,"Fix SRD: too many walls in bin");
+ binbig[ibin][nbinbig[ibin]++] = nbig+m;
+ }
} else if (dim == 2) {
- if (side == 0) {
- hi = static_cast<int> ((xwall[m]+delta-zblo2)*bininv2z);
- if (hi < 0) continue;
- if (hi >= nbin2z) error->all(FLERR,
- "Fix SRD: bad search bin assignment");
- lo = 0;
- } else {
- lo = static_cast<int> ((xwall[m]-delta-zblo2)*bininv2z);
- if (lo >= nbin2z) continue;
- if (lo < 0) error->all(FLERR,"Fix SRD: bad search bin assignment");
- hi = nbin2z-1;
- }
-
- for (iz = lo; iz < hi; iz++)
- for (ix = 0; ix < nbin2x; ix++)
- for (iy = 0; iy < nbin2y; iy++) {
- ibin = iz*nbin2y*nbin2x + iy*nbin2x + ix;
- if (nbinbig[ibin] == ATOMPERBIN)
- error->all(FLERR,"Fix SRD: too many walls in bin");
- binbig[ibin][nbinbig[ibin]++] = nbig+m;
- }
+ if (side == 0) {
+ hi = static_cast<int> ((xwall[m]+delta-zblo2)*bininv2z);
+ if (hi < 0) continue;
+ if (hi >= nbin2z) error->all(FLERR,
+ "Fix SRD: bad search bin assignment");
+ lo = 0;
+ } else {
+ lo = static_cast<int> ((xwall[m]-delta-zblo2)*bininv2z);
+ if (lo >= nbin2z) continue;
+ if (lo < 0) error->all(FLERR,"Fix SRD: bad search bin assignment");
+ hi = nbin2z-1;
+ }
+
+ for (iz = lo; iz < hi; iz++)
+ for (ix = 0; ix < nbin2x; ix++)
+ for (iy = 0; iy < nbin2y; iy++) {
+ ibin = iz*nbin2y*nbin2x + iy*nbin2x + ix;
+ if (nbinbig[ibin] == ATOMPERBIN)
+ error->all(FLERR,"Fix SRD: too many walls in bin");
+ binbig[ibin][nbinbig[ibin]++] = nbig+m;
+ }
}
}
}
@@ -700,35 +700,35 @@ void FixSRD::post_force(int vflag)
if (bigexist || wallexist) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- x[i][0] += dt_big*v[i][0];
- x[i][1] += dt_big*v[i][1];
- x[i][2] += dt_big*v[i][2];
-
- ix = static_cast<int> ((x[i][0]-xblo2)*bininv2x);
- iy = static_cast<int> ((x[i][1]-yblo2)*bininv2y);
- iz = static_cast<int> ((x[i][2]-zblo2)*bininv2z);
- binsrd[i] = iz*nbin2y*nbin2x + iy*nbin2x + ix;
-
- if (ix < 0 || ix >= nbin2x || iy < 0 || iy >= nbin2y ||
- iz < 0 || iz >= nbin2z) {
- if (screen) {
- fprintf(screen,"SRD particle %d on step " BIGINT_FORMAT "\n",
- atom->tag[i],update->ntimestep);
- fprintf(screen,"v = %g %g %g\n",v[i][0],v[i][1],v[i][2]);
- fprintf(screen,"x = %g %g %g\n",x[i][0],x[i][1],x[i][2]);
- fprintf(screen,"ix,iy,iz nx,ny,nz = %d %d %d %d %d %d\n",
- ix,iy,iz,nbin2x,nbin2y,nbin2z);
- }
- error->one(FLERR,"Fix SRD: bad bin assignment for SRD advection");
- }
+ x[i][0] += dt_big*v[i][0];
+ x[i][1] += dt_big*v[i][1];
+ x[i][2] += dt_big*v[i][2];
+
+ ix = static_cast<int> ((x[i][0]-xblo2)*bininv2x);
+ iy = static_cast<int> ((x[i][1]-yblo2)*bininv2y);
+ iz = static_cast<int> ((x[i][2]-zblo2)*bininv2z);
+ binsrd[i] = iz*nbin2y*nbin2x + iy*nbin2x + ix;
+
+ if (ix < 0 || ix >= nbin2x || iy < 0 || iy >= nbin2y ||
+ iz < 0 || iz >= nbin2z) {
+ if (screen) {
+ fprintf(screen,"SRD particle %d on step " BIGINT_FORMAT "\n",
+ atom->tag[i],update->ntimestep);
+ fprintf(screen,"v = %g %g %g\n",v[i][0],v[i][1],v[i][2]);
+ fprintf(screen,"x = %g %g %g\n",x[i][0],x[i][1],x[i][2]);
+ fprintf(screen,"ix,iy,iz nx,ny,nz = %d %d %d %d %d %d\n",
+ ix,iy,iz,nbin2x,nbin2y,nbin2z);
+ }
+ error->one(FLERR,"Fix SRD: bad bin assignment for SRD advection");
+ }
}
} else {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- x[i][0] += dt_big*v[i][0];
- x[i][1] += dt_big*v[i][1];
- x[i][2] += dt_big*v[i][2];
+ x[i][0] += dt_big*v[i][0];
+ x[i][1] += dt_big*v[i][1];
+ x[i][2] += dt_big*v[i][2];
}
}
@@ -758,8 +758,8 @@ void FixSRD::post_force(int vflag)
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (x[i][0] < srdlo_reneigh[0] || x[i][0] > srdhi_reneigh[0] ||
- x[i][1] < srdlo_reneigh[1] || x[i][1] > srdhi_reneigh[1] ||
- x[i][2] < srdlo_reneigh[2] || x[i][2] > srdhi_reneigh[2]) flag = 1;
+ x[i][1] < srdlo_reneigh[1] || x[i][1] > srdhi_reneigh[1] ||
+ x[i][2] < srdlo_reneigh[2] || x[i][2] > srdhi_reneigh[2]) flag = 1;
}
if (triclinic) domain->lamda2x(nlocal);
@@ -776,7 +776,7 @@ void FixSRD::post_force(int vflag)
if (wallexist) {
for (m = 0; m < nwall; m++)
if (fabs(xwall[m]-xwallhold[m]) > walltrigger)
- next_reneighbor = update->ntimestep + 1;
+ next_reneighbor = update->ntimestep + 1;
}
// if next timestep is SRD timestep, trigger reneigh
@@ -928,17 +928,17 @@ void FixSRD::reset_velocities()
vsq = 0.0;
for (j = binhead[i]; j >= 0; j = binnext[j]) {
if (axis == 0) {
- u[0] = v[j][0]-vave[0];
- u[1] = sign ? v[j][2]-vave[2] : vave[2]-v[j][2];
- u[2] = sign ? vave[1]-v[j][1] : v[j][1]-vave[1];
+ u[0] = v[j][0]-vave[0];
+ u[1] = sign ? v[j][2]-vave[2] : vave[2]-v[j][2];
+ u[2] = sign ? vave[1]-v[j][1] : v[j][1]-vave[1];
} else if (axis == 1) {
- u[1] = v[j][1]-vave[1];
- u[0] = sign ? v[j][2]-vave[2] : vave[2]-v[j][2];
- u[2] = sign ? vave[0]-v[j][0] : v[j][0]-vave[0];
+ u[1] = v[j][1]-vave[1];
+ u[0] = sign ? v[j][2]-vave[2] : vave[2]-v[j][2];
+ u[2] = sign ? vave[0]-v[j][0] : v[j][0]-vave[0];
} else {
- u[2] = v[j][2]-vave[2];
- u[1] = sign ? v[j][0]-vave[0] : vave[0]-v[j][0];
- u[0] = sign ? vave[1]-v[j][1] : v[j][1]-vave[1];
+ u[2] = v[j][2]-vave[2];
+ u[1] = sign ? v[j][0]-vave[0] : vave[0]-v[j][0];
+ u[0] = sign ? vave[1]-v[j][1] : v[j][1]-vave[1];
}
vsq += u[0]*u[0] + u[1]*u[1] + u[2]*u[2];
v[j][0] = u[0] + vave[0];
@@ -948,15 +948,15 @@ void FixSRD::reset_velocities()
if (tstat && n > 1) {
if (deformflag) {
- xlamda = vbin[i].xctr;
- vstream[0] = h_rate[0]*xlamda[0] + h_rate[5]*xlamda[1] +
- h_rate[4]*xlamda[2] + h_ratelo[0];
- vstream[1] = h_rate[1]*xlamda[1] + h_rate[3]*xlamda[2] + h_ratelo[1];
- vstream[2] = h_rate[2]*xlamda[2] + h_ratelo[2];
+ xlamda = vbin[i].xctr;
+ vstream[0] = h_rate[0]*xlamda[0] + h_rate[5]*xlamda[1] +
+ h_rate[4]*xlamda[2] + h_ratelo[0];
+ vstream[1] = h_rate[1]*xlamda[1] + h_rate[3]*xlamda[2] + h_ratelo[1];
+ vstream[2] = h_rate[2]*xlamda[2] + h_ratelo[2];
} else {
- vstream[0] = vave[0];
- vstream[1] = vave[1];
- vstream[2] = vave[2];
+ vstream[0] = vave[0];
+ vstream[1] = vave[1];
+ vstream[2] = vave[2];
}
// tbin = thermal temperature of particles in bin
@@ -967,13 +967,13 @@ void FixSRD::reset_velocities()
vsq = 0.0;
for (j = binhead[i]; j >= 0; j = binnext[j]) {
- u[0] = (v[j][0] - vave[0]) * scale;
- u[1] = (v[j][1] - vave[1]) * scale;
- u[2] = (v[j][2] - vave[2]) * scale;
- vsq += u[0]*u[0] + u[1]*u[1] + u[2]*u[2];
- v[j][0] = u[0] + vstream[0];
- v[j][1] = u[1] + vstream[1];
- v[j][2] = u[2] + vstream[2];
+ u[0] = (v[j][0] - vave[0]) * scale;
+ u[1] = (v[j][1] - vave[1]) * scale;
+ u[2] = (v[j][2] - vave[2]) * scale;
+ vsq += u[0]*u[0] + u[1]*u[1] + u[2]*u[2];
+ v[j][0] = u[0] + vstream[0];
+ v[j][1] = u[1] + vstream[1];
+ v[j][2] = u[2] + vstream[2];
}
}
@@ -986,14 +986,14 @@ void FixSRD::reset_velocities()
srd_bin_temp *= tfactor;
- // rescale any too-large velocities
+ // rescale any too-large velocities
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
vsq = v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2];
if (vsq > vmaxsq) {
- nrescale++;
- MathExtra::scale3(vmax/sqrt(vsq),v[i]);
+ nrescale++;
+ MathExtra::scale3(vmax/sqrt(vsq),v[i]);
}
}
}
@@ -1007,7 +1007,7 @@ void FixSRD::vbin_comm(int ishift)
BinComm *bcomm1,*bcomm2;
MPI_Request request1,request2;
MPI_Status status;
-
+
// send/recv bins in both directions in each dimension
// don't send if nsend = 0
// due to static bins aliging with proc boundary
@@ -1017,7 +1017,7 @@ void FixSRD::vbin_comm(int ishift)
// don't recv if nrecv = 0
// copy from self if recvproc = me
// MPI recv from another proc if recvproc != me
-
+
BinAve *vbin = shifts[ishift].vbin;
int *procgrid = comm->procgrid;
@@ -1025,41 +1025,41 @@ void FixSRD::vbin_comm(int ishift)
for (int idim = 0; idim < dimension; idim++) {
bcomm1 = &shifts[ishift].bcomm[iswap++];
bcomm2 = &shifts[ishift].bcomm[iswap++];
-
+
if (procgrid[idim] == 1) {
if (bcomm1->nsend)
- vbin_pack(vbin,bcomm1->nsend,bcomm1->sendlist,sbuf1);
+ vbin_pack(vbin,bcomm1->nsend,bcomm1->sendlist,sbuf1);
if (bcomm2->nsend)
- vbin_pack(vbin,bcomm2->nsend,bcomm2->sendlist,sbuf2);
+ vbin_pack(vbin,bcomm2->nsend,bcomm2->sendlist,sbuf2);
if (bcomm1->nrecv)
- vbin_unpack(sbuf1,vbin,bcomm1->nrecv,bcomm1->recvlist);
+ vbin_unpack(sbuf1,vbin,bcomm1->nrecv,bcomm1->recvlist);
if (bcomm2->nrecv)
- vbin_unpack(sbuf2,vbin,bcomm2->nrecv,bcomm2->recvlist);
+ vbin_unpack(sbuf2,vbin,bcomm2->nrecv,bcomm2->recvlist);
} else {
if (bcomm1->nrecv)
- MPI_Irecv(rbuf1,bcomm1->nrecv*VBINSIZE,MPI_DOUBLE,bcomm1->recvproc,0,
- world,&request1);
+ MPI_Irecv(rbuf1,bcomm1->nrecv*VBINSIZE,MPI_DOUBLE,bcomm1->recvproc,0,
+ world,&request1);
if (bcomm2->nrecv)
- MPI_Irecv(rbuf2,bcomm2->nrecv*VBINSIZE,MPI_DOUBLE,bcomm2->recvproc,0,
- world,&request2);
+ MPI_Irecv(rbuf2,bcomm2->nrecv*VBINSIZE,MPI_DOUBLE,bcomm2->recvproc,0,
+ world,&request2);
if (bcomm1->nsend) {
- vbin_pack(vbin,bcomm1->nsend,bcomm1->sendlist,sbuf1);
- MPI_Send(sbuf1,bcomm1->nsend*VBINSIZE,MPI_DOUBLE,
- bcomm1->sendproc,0,world);
+ vbin_pack(vbin,bcomm1->nsend,bcomm1->sendlist,sbuf1);
+ MPI_Send(sbuf1,bcomm1->nsend*VBINSIZE,MPI_DOUBLE,
+ bcomm1->sendproc,0,world);
}
if (bcomm2->nsend) {
- vbin_pack(vbin,bcomm2->nsend,bcomm2->sendlist,sbuf2);
- MPI_Send(sbuf2,bcomm2->nsend*VBINSIZE,MPI_DOUBLE,
- bcomm2->sendproc,0,world);
+ vbin_pack(vbin,bcomm2->nsend,bcomm2->sendlist,sbuf2);
+ MPI_Send(sbuf2,bcomm2->nsend*VBINSIZE,MPI_DOUBLE,
+ bcomm2->sendproc,0,world);
}
if (bcomm1->nrecv) {
- MPI_Wait(&request1,&status);
- vbin_unpack(rbuf1,vbin,bcomm1->nrecv,bcomm1->recvlist);
+ MPI_Wait(&request1,&status);
+ vbin_unpack(rbuf1,vbin,bcomm1->nrecv,bcomm1->recvlist);
}
if (bcomm2->nrecv) {
- MPI_Wait(&request2,&status);
- vbin_unpack(rbuf2,vbin,bcomm2->nrecv,bcomm2->recvlist);
+ MPI_Wait(&request2,&status);
+ vbin_unpack(rbuf2,vbin,bcomm2->nrecv,bcomm2->recvlist);
}
}
}
@@ -1146,102 +1146,102 @@ void FixSRD::collisions_single()
collide_flag = 0;
for (m = 0; m < nbig; m++) {
- k = binbig[ibin][m];
- big = &biglist[k];
- j = big->index;
- type = big->type;
-
- if (type == SPHERE) inside = inside_sphere(x[i],x[j],big);
- else if (type == ELLIPSOID) inside = inside_ellipsoid(x[i],x[j],big);
- else inside = inside_wall(x[i],j);
-
- if (inside) {
- if (exactflag) {
- if (type == SPHERE)
- t_remain = collision_sphere_exact(x[i],x[j],v[i],v[j],big,
- xscoll,xbcoll,norm);
- else if (type == ELLIPSOID)
- t_remain = collision_ellipsoid_exact(x[i],x[j],v[i],v[j],big,
- xscoll,xbcoll,norm);
- else
- t_remain = collision_wall_exact(x[i],j,v[i],xscoll,xbcoll,norm);
-
- } else {
- t_remain = 0.5*dt;
- if (type == SPHERE)
- collision_sphere_inexact(x[i],x[j],big,xscoll,xbcoll,norm);
- else if (type == ELLIPSOID)
- collision_ellipsoid_inexact(x[i],x[j],big,xscoll,xbcoll,norm);
- else
- collision_wall_inexact(x[i],j,xscoll,xbcoll,norm);
- }
+ k = binbig[ibin][m];
+ big = &biglist[k];
+ j = big->index;
+ type = big->type;
+
+ if (type == SPHERE) inside = inside_sphere(x[i],x[j],big);
+ else if (type == ELLIPSOID) inside = inside_ellipsoid(x[i],x[j],big);
+ else inside = inside_wall(x[i],j);
+
+ if (inside) {
+ if (exactflag) {
+ if (type == SPHERE)
+ t_remain = collision_sphere_exact(x[i],x[j],v[i],v[j],big,
+ xscoll,xbcoll,norm);
+ else if (type == ELLIPSOID)
+ t_remain = collision_ellipsoid_exact(x[i],x[j],v[i],v[j],big,
+ xscoll,xbcoll,norm);
+ else
+ t_remain = collision_wall_exact(x[i],j,v[i],xscoll,xbcoll,norm);
+
+ } else {
+ t_remain = 0.5*dt;
+ if (type == SPHERE)
+ collision_sphere_inexact(x[i],x[j],big,xscoll,xbcoll,norm);
+ else if (type == ELLIPSOID)
+ collision_ellipsoid_inexact(x[i],x[j],big,xscoll,xbcoll,norm);
+ else
+ collision_wall_inexact(x[i],j,xscoll,xbcoll,norm);
+ }
#ifdef SRD_DEBUG
- if (update->ntimestep == SRD_DEBUG_TIMESTEP &&
- atom->tag[i] == SRD_DEBUG_ATOMID)
- print_collision(i,j,ibounce,t_remain,dt,xscoll,xbcoll,norm,type);
+ if (update->ntimestep == SRD_DEBUG_TIMESTEP &&
+ atom->tag[i] == SRD_DEBUG_ATOMID)
+ print_collision(i,j,ibounce,t_remain,dt,xscoll,xbcoll,norm,type);
#endif
- if (t_remain > dt) {
- ninside++;
- if (insideflag == INSIDE_ERROR || insideflag == INSIDE_WARN) {
- char str[128];
- if (type != WALL)
- sprintf(str,
- "SRD particle %d started "
- "inside big particle %d on step " BIGINT_FORMAT
- " bounce %d",
- atom->tag[i],atom->tag[j],update->ntimestep,ibounce+1);
- else
- sprintf(str,
- "SRD particle %d started "
- "inside big particle %d on step " BIGINT_FORMAT
- " bounce %d",
- atom->tag[i],atom->tag[j],update->ntimestep,ibounce+1);
- if (insideflag == INSIDE_ERROR) error->one(FLERR,str);
- error->warning(FLERR,str);
- }
- break;
- }
-
- if (collidestyle == SLIP) {
- if (type != WALL) slip(v[i],v[j],x[j],big,xscoll,norm,vsnew);
- else slip_wall(v[i],j,norm,vsnew);
- } else {
- if (type != WALL) noslip(v[i],v[j],x[j],big,-1, xscoll,norm,vsnew);
- else noslip(v[i],NULL,x[j],big,j,xscoll,norm,vsnew);
- }
-
- if (dimension == 2) vsnew[2] = 0.0;
-
- // check on rescaling of vsnew
-
- double vsq = vsnew[0]*vsnew[0] + vsnew[1]*vsnew[1] +
- vsnew[2]*vsnew[2];
- if (vsq > vmaxsq) {
- nrescale++;
- MathExtra::scale3(vmax/sqrt(vsq),vsnew);
- }
-
- // update BIG particle and WALL and SRD
- // BIG particle is not torqued if sphere and SLIP collision
-
- if (collidestyle == SLIP && type == SPHERE)
- force_torque(v[i],vsnew,xscoll,xbcoll,f[j],NULL);
- else if (type != WALL)
- force_torque(v[i],vsnew,xscoll,xbcoll,f[j],torque[j]);
- else if (type == WALL)
- force_wall(v[i],vsnew,j);
-
- ibin = binsrd[i] = update_srd(i,t_remain,xscoll,vsnew,x[i],v[i]);
-
- if (ibounce == 0) ncollide++;
- ibounce++;
- if (ibounce < maxbounceallow || maxbounceallow == 0)
- collide_flag = 1;
- dt = t_remain;
- break;
- }
+ if (t_remain > dt) {
+ ninside++;
+ if (insideflag == INSIDE_ERROR || insideflag == INSIDE_WARN) {
+ char str[128];
+ if (type != WALL)
+ sprintf(str,
+ "SRD particle %d started "
+ "inside big particle %d on step " BIGINT_FORMAT
+ " bounce %d",
+ atom->tag[i],atom->tag[j],update->ntimestep,ibounce+1);
+ else
+ sprintf(str,
+ "SRD particle %d started "
+ "inside big particle %d on step " BIGINT_FORMAT
+ " bounce %d",
+ atom->tag[i],atom->tag[j],update->ntimestep,ibounce+1);
+ if (insideflag == INSIDE_ERROR) error->one(FLERR,str);
+ error->warning(FLERR,str);
+ }
+ break;
+ }
+
+ if (collidestyle == SLIP) {
+ if (type != WALL) slip(v[i],v[j],x[j],big,xscoll,norm,vsnew);
+ else slip_wall(v[i],j,norm,vsnew);
+ } else {
+ if (type != WALL) noslip(v[i],v[j],x[j],big,-1, xscoll,norm,vsnew);
+ else noslip(v[i],NULL,x[j],big,j,xscoll,norm,vsnew);
+ }
+
+ if (dimension == 2) vsnew[2] = 0.0;
+
+ // check on rescaling of vsnew
+
+ double vsq = vsnew[0]*vsnew[0] + vsnew[1]*vsnew[1] +
+ vsnew[2]*vsnew[2];
+ if (vsq > vmaxsq) {
+ nrescale++;
+ MathExtra::scale3(vmax/sqrt(vsq),vsnew);
+ }
+
+ // update BIG particle and WALL and SRD
+ // BIG particle is not torqued if sphere and SLIP collision
+
+ if (collidestyle == SLIP && type == SPHERE)
+ force_torque(v[i],vsnew,xscoll,xbcoll,f[j],NULL);
+ else if (type != WALL)
+ force_torque(v[i],vsnew,xscoll,xbcoll,f[j],torque[j]);
+ else if (type == WALL)
+ force_wall(v[i],vsnew,j);
+
+ ibin = binsrd[i] = update_srd(i,t_remain,xscoll,vsnew,x[i],v[i]);
+
+ if (ibounce == 0) ncollide++;
+ ibounce++;
+ if (ibounce < maxbounceallow || maxbounceallow == 0)
+ collide_flag = 1;
+ dt = t_remain;
+ break;
+ }
}
}
@@ -1298,76 +1298,76 @@ void FixSRD::collisions_multi()
t_first = 0.0;
for (m = 0; m < nbig; m++) {
- k = binbig[ibin][m];
- big = &biglist[k];
- j = big->index;
- if (j == jlast) continue;
- type = big->type;
-
- if (type == SPHERE)
- inside = inside_sphere(x[i],x[j],big);
- else if (type == ELLIPSOID)
- inside = inside_ellipsoid(x[i],x[j],big);
- else if (type == LINE)
- inside = inside_line(x[i],x[j],v[i],v[j],big,dt);
- else if (type == TRIANGLE)
- inside = inside_tri(x[i],x[j],v[i],v[j],big,dt);
- else
- inside = inside_wall(x[i],j);
-
- if (inside) {
- if (type == SPHERE)
- t_remain = collision_sphere_exact(x[i],x[j],v[i],v[j],big,
- xscoll,xbcoll,norm);
- else if (type == ELLIPSOID)
- t_remain = collision_ellipsoid_exact(x[i],x[j],v[i],v[j],big,
- xscoll,xbcoll,norm);
- else if (type == LINE)
- t_remain = collision_line_exact(x[i],x[j],v[i],v[j],big,dt,
- xscoll,xbcoll,norm);
- else if (type == TRIANGLE)
- t_remain = collision_tri_exact(x[i],x[j],v[i],v[j],big,dt,
- xscoll,xbcoll,norm);
- else
- t_remain = collision_wall_exact(x[i],j,v[i],xscoll,xbcoll,norm);
+ k = binbig[ibin][m];
+ big = &biglist[k];
+ j = big->index;
+ if (j == jlast) continue;
+ type = big->type;
+
+ if (type == SPHERE)
+ inside = inside_sphere(x[i],x[j],big);
+ else if (type == ELLIPSOID)
+ inside = inside_ellipsoid(x[i],x[j],big);
+ else if (type == LINE)
+ inside = inside_line(x[i],x[j],v[i],v[j],big,dt);
+ else if (type == TRIANGLE)
+ inside = inside_tri(x[i],x[j],v[i],v[j],big,dt);
+ else
+ inside = inside_wall(x[i],j);
+
+ if (inside) {
+ if (type == SPHERE)
+ t_remain = collision_sphere_exact(x[i],x[j],v[i],v[j],big,
+ xscoll,xbcoll,norm);
+ else if (type == ELLIPSOID)
+ t_remain = collision_ellipsoid_exact(x[i],x[j],v[i],v[j],big,
+ xscoll,xbcoll,norm);
+ else if (type == LINE)
+ t_remain = collision_line_exact(x[i],x[j],v[i],v[j],big,dt,
+ xscoll,xbcoll,norm);
+ else if (type == TRIANGLE)
+ t_remain = collision_tri_exact(x[i],x[j],v[i],v[j],big,dt,
+ xscoll,xbcoll,norm);
+ else
+ t_remain = collision_wall_exact(x[i],j,v[i],xscoll,xbcoll,norm);
#ifdef SRD_DEBUG
- if (update->ntimestep == SRD_DEBUG_TIMESTEP &&
- atom->tag[i] == SRD_DEBUG_ATOMID)
- print_collision(i,j,ibounce,t_remain,dt,xscoll,xbcoll,norm,type);
+ if (update->ntimestep == SRD_DEBUG_TIMESTEP &&
+ atom->tag[i] == SRD_DEBUG_ATOMID)
+ print_collision(i,j,ibounce,t_remain,dt,xscoll,xbcoll,norm,type);
#endif
- if (t_remain > dt || t_remain < 0.0) {
- ninside++;
- if (insideflag == INSIDE_ERROR || insideflag == INSIDE_WARN) {
- char str[128];
- sprintf(str,
- "SRD particle %d started "
- "inside big particle %d on step " BIGINT_FORMAT
- " bounce %d",
- atom->tag[i],atom->tag[j],update->ntimestep,ibounce+1);
- if (insideflag == INSIDE_ERROR) error->one(FLERR,str);
- error->warning(FLERR,str);
- }
- t_first = 0.0;
- break;
- }
-
- if (t_remain > t_first) {
- t_first = t_remain;
- jfirst = j;
- typefirst = type;
- xscollfirst[0] = xscoll[0];
- xscollfirst[1] = xscoll[1];
- xscollfirst[2] = xscoll[2];
- xbcollfirst[0] = xbcoll[0];
- xbcollfirst[1] = xbcoll[1];
- xbcollfirst[2] = xbcoll[2];
- normfirst[0] = norm[0];
- normfirst[1] = norm[1];
- normfirst[2] = norm[2];
- }
- }
+ if (t_remain > dt || t_remain < 0.0) {
+ ninside++;
+ if (insideflag == INSIDE_ERROR || insideflag == INSIDE_WARN) {
+ char str[128];
+ sprintf(str,
+ "SRD particle %d started "
+ "inside big particle %d on step " BIGINT_FORMAT
+ " bounce %d",
+ atom->tag[i],atom->tag[j],update->ntimestep,ibounce+1);
+ if (insideflag == INSIDE_ERROR) error->one(FLERR,str);
+ error->warning(FLERR,str);
+ }
+ t_first = 0.0;
+ break;
+ }
+
+ if (t_remain > t_first) {
+ t_first = t_remain;
+ jfirst = j;
+ typefirst = type;
+ xscollfirst[0] = xscoll[0];
+ xscollfirst[1] = xscoll[1];
+ xscollfirst[2] = xscoll[2];
+ xbcollfirst[0] = xbcoll[0];
+ xbcollfirst[1] = xbcoll[1];
+ xbcollfirst[2] = xbcoll[2];
+ normfirst[0] = norm[0];
+ normfirst[1] = norm[1];
+ normfirst[2] = norm[2];
+ }
+ }
}
if (t_first == 0.0) break;
@@ -1384,11 +1384,11 @@ void FixSRD::collisions_multi()
norm[2] = normfirst[2];
if (collidestyle == SLIP) {
- if (type != WALL) slip(v[i],v[j],x[j],big,xscoll,norm,vsnew);
- else slip_wall(v[i],j,norm,vsnew);
+ if (type != WALL) slip(v[i],v[j],x[j],big,xscoll,norm,vsnew);
+ else slip_wall(v[i],j,norm,vsnew);
} else {
- if (type != WALL) noslip(v[i],v[j],x[j],big,-1,xscoll,norm,vsnew);
- else noslip(v[i],NULL,x[j],big,j,xscoll,norm,vsnew);
+ if (type != WALL) noslip(v[i],v[j],x[j],big,-1,xscoll,norm,vsnew);
+ else noslip(v[i],NULL,x[j],big,j,xscoll,norm,vsnew);
}
if (dimension == 2) vsnew[2] = 0.0;
@@ -1397,19 +1397,19 @@ void FixSRD::collisions_multi()
double vsq = vsnew[0]*vsnew[0] + vsnew[1]*vsnew[1] + vsnew[2]*vsnew[2];
if (vsq > vmaxsq) {
- nrescale++;
- MathExtra::scale3(vmax/sqrt(vsq),vsnew);
+ nrescale++;
+ MathExtra::scale3(vmax/sqrt(vsq),vsnew);
}
// update BIG particle and WALL and SRD
// BIG particle is not torqued if sphere and SLIP collision
if (collidestyle == SLIP && type == SPHERE)
- force_torque(v[i],vsnew,xscoll,xbcoll,f[j],NULL);
+ force_torque(v[i],vsnew,xscoll,xbcoll,f[j],NULL);
else if (type != WALL)
- force_torque(v[i],vsnew,xscoll,xbcoll,f[j],torque[j]);
+ force_torque(v[i],vsnew,xscoll,xbcoll,f[j],torque[j]);
else if (type == WALL)
- force_wall(v[i],vsnew,j);
+ force_wall(v[i],vsnew,j);
ibin = binsrd[i] = update_srd(i,t_first,xscoll,vsnew,x[i],v[i]);
@@ -1481,7 +1481,7 @@ int FixSRD::inside_ellipsoid(double *xs, double *xb, Big *big)
------------------------------------------------------------------------- */
int FixSRD::inside_line(double *xs, double *xb, double *vs, double *vb,
- Big *big, double dt_step)
+ Big *big, double dt_step)
{
double pmc0[2],pmc1[2],n0[2],n1[2];
double n1_n0[2],pmc1_pmc0[2];
@@ -1535,10 +1535,10 @@ int FixSRD::inside_line(double *xs, double *xb, double *vs, double *vb,
pmc1_pmc0[0] = pmc1[0]-pmc0[0]; pmc1_pmc0[1] = pmc1[1]-pmc0[1];
double a = pmc1_pmc0[0]*n1_n0[0] + pmc1_pmc0[1]*n1_n0[1];
- double b = pmc1_pmc0[0]*n0[0] + pmc1_pmc0[1]*n0[1] +
+ double b = pmc1_pmc0[0]*n0[0] + pmc1_pmc0[1]*n0[1] +
n1_n0[0]*pmc0[0] + n1_n0[1]*pmc0[1];
double c = pmc0[0]*n0[0] + pmc0[1]*n0[1];
-
+
if (a == 0.0) {
double dot0 = pmc0[0]*n0[0] + pmc0[1]*n0[1];
double dot1 = pmc1[0]*n0[0] + pmc1[1]*n0[1];
@@ -1553,11 +1553,11 @@ int FixSRD::inside_line(double *xs, double *xb, double *vs, double *vb,
double root2 = (-b - term) / (2.0*a);
//printf("ABC vecs: %g %g: %g %g\n",
- // pmc1_pmc0[0],pmc1_pmc0[1],n1_n0[0],n1_n0[1]);
+ // pmc1_pmc0[0],pmc1_pmc0[1],n1_n0[0],n1_n0[1]);
//printf("ABC vecs: %g %g: %g %g: %g %g %g\n",
- // n0[0],n0[1],n1[0],n1[1],theta0,theta1,big->omega[2]);
+ // n0[0],n0[1],n1[0],n1[1],theta0,theta1,big->omega[2]);
//printf("ABC root: %g %g %g: %g %g %g\n",a,b,c,root1,root2,tfraction);
-
+
if (0.0 <= root1 && root1 <= 1.0) tfraction = root1;
else if (0.0 <= root2 && root2 <= 1.0) tfraction = root2;
else error->one(FLERR,"Bad quadratic solve for particle/line collision");
@@ -1597,7 +1597,7 @@ int FixSRD::inside_line(double *xs, double *xb, double *vs, double *vb,
------------------------------------------------------------------------- */
int FixSRD::inside_tri(double *xs, double *xb, double *vs, double *vb,
- Big *big, double dt_step)
+ Big *big, double dt_step)
{
double pmc0[3],pmc1[3],n0[3];
double n1_n0[3],pmc1_pmc0[3];
@@ -1643,7 +1643,7 @@ int FixSRD::inside_tri(double *xs, double *xb, double *vs, double *vb,
pmc1_pmc0[0] = pmc1[0]-pmc0[0];
pmc1_pmc0[1] = pmc1[1]-pmc0[1];
pmc1_pmc0[2] = pmc1[2]-pmc0[2];
-
+
double a = MathExtra::dot3(pmc1_pmc0,n1_n0);
double b = MathExtra::dot3(pmc1_pmc0,n0) + MathExtra::dot3(n1_n0,pmc0);
double c = MathExtra::dot3(pmc0,n0);
@@ -1761,9 +1761,9 @@ int FixSRD::inside_wall(double *xs, int iwall)
------------------------------------------------------------------------- */
double FixSRD::collision_sphere_exact(double *xs, double *xb,
- double *vs, double *vb, Big *big,
- double *xscoll, double *xbcoll,
- double *norm)
+ double *vs, double *vb, Big *big,
+ double *xscoll, double *xbcoll,
+ double *norm)
{
double vs_dot_vs,vb_dot_vb,vs_dot_vb;
double vs_dot_xb,vb_dot_xs,vs_dot_xs,vb_dot_xb;
@@ -1818,9 +1818,9 @@ double FixSRD::collision_sphere_exact(double *xs, double *xb,
------------------------------------------------------------------------- */
void FixSRD::collision_sphere_inexact(double *xs, double *xb,
- Big *big,
- double *xscoll, double *xbcoll,
- double *norm)
+ Big *big,
+ double *xscoll, double *xbcoll,
+ double *norm)
{
double scale;
@@ -1851,9 +1851,9 @@ void FixSRD::collision_sphere_inexact(double *xs, double *xb,
------------------------------------------------------------------------- */
double FixSRD::collision_ellipsoid_exact(double *xs, double *xb,
- double *vs, double *vb, Big *big,
- double *xscoll, double *xbcoll,
- double *norm)
+ double *vs, double *vb, Big *big,
+ double *xscoll, double *xbcoll,
+ double *norm)
{
double vs_vb[3],xs_xb[3],omega_ex[3],omega_ey[3],omega_ez[3];
double excoll[3],eycoll[3],ezcoll[3],delta[3],xbody[3],nbody[3];
@@ -1888,10 +1888,10 @@ double FixSRD::collision_ellipsoid_exact(double *xs, double *xb,
cz = xs_xb[0]*ez[0] + xs_xb[1]*ez[1] + xs_xb[2]*ez[2];
a = (bx*bx + 2.0*ax*cx)*big->aradsqinv +
- (by*by + 2.0*ay*cy)*big->bradsqinv +
+ (by*by + 2.0*ay*cy)*big->bradsqinv +
(bz*bz + 2.0*az*cz)*big->cradsqinv;
b = 2.0 * (bx*cx*big->aradsqinv + by*cy*big->bradsqinv +
- bz*cz*big->cradsqinv);
+ bz*cz*big->cradsqinv);
c = cx*cx*big->aradsqinv + cy*cy*big->bradsqinv +
cz*cz*big->cradsqinv - 1.0;
@@ -1946,9 +1946,9 @@ double FixSRD::collision_ellipsoid_exact(double *xs, double *xb,
------------------------------------------------------------------------- */
void FixSRD::collision_ellipsoid_inexact(double *xs, double *xb,
- Big *big,
- double *xscoll, double *xbcoll,
- double *norm)
+ Big *big,
+ double *xscoll, double *xbcoll,
+ double *norm)
{
double xs_xb[3],delta[3],xbody[3],nbody[3];
@@ -1962,7 +1962,7 @@ void FixSRD::collision_ellipsoid_inexact(double *xs, double *xb,
double z = MathExtra::dot3(xs_xb,ez);
double scale = 1.0/sqrt(x*x*big->aradsqinv + y*y*big->bradsqinv +
- z*z*big->cradsqinv);
+ z*z*big->cradsqinv);
x *= scale;
y *= scale;
z *= scale;
@@ -2001,10 +2001,10 @@ void FixSRD::collision_ellipsoid_inexact(double *xs, double *xb,
------------------------------------------------------------------------- */
double FixSRD::collision_line_exact(double *xs, double *xb,
- double *vs, double *vb, Big *big,
- double dt_step,
- double *xscoll, double *xbcoll,
- double *norm)
+ double *vs, double *vb, Big *big,
+ double dt_step,
+ double *xscoll, double *xbcoll,
+ double *norm)
{
xscoll[0] = xsc[0];
xscoll[1] = xsc[1];
@@ -2030,10 +2030,10 @@ double FixSRD::collision_line_exact(double *xs, double *xb,
------------------------------------------------------------------------- */
double FixSRD::collision_tri_exact(double *xs, double *xb,
- double *vs, double *vb, Big *big,
- double dt_step,
- double *xscoll, double *xbcoll,
- double *norm)
+ double *vs, double *vb, Big *big,
+ double dt_step,
+ double *xscoll, double *xbcoll,
+ double *norm)
{
xscoll[0] = xsc[0];
xscoll[1] = xsc[1];
@@ -2059,8 +2059,8 @@ double FixSRD::collision_tri_exact(double *xs, double *xb,
------------------------------------------------------------------------- */
double FixSRD::collision_wall_exact(double *xs, int iwall, double *vs,
- double *xscoll, double *xbcoll,
- double *norm)
+ double *xscoll, double *xbcoll,
+ double *norm)
{
int dim = wallwhich[iwall] / 2;
@@ -2089,8 +2089,8 @@ double FixSRD::collision_wall_exact(double *xs, int iwall, double *vs,
norm = surface normal of collision pt at time of collision
------------------------------------------------------------------------- */
-void FixSRD::collision_wall_inexact(double *xs, int iwall, double *xscoll,
- double *xbcoll, double *norm)
+void FixSRD::collision_wall_inexact(double *xs, int iwall, double *xscoll,
+ double *xbcoll, double *norm)
{
int dim = wallwhich[iwall] / 2;
@@ -2120,7 +2120,7 @@ void FixSRD::collision_wall_inexact(double *xs, int iwall, double *xscoll,
------------------------------------------------------------------------- */
void FixSRD::slip(double *vs, double *vb, double *xb, Big *big,
- double *xsurf, double *norm, double *vsnew)
+ double *xsurf, double *norm, double *vsnew)
{
double r1,r2,vnmag,vs_dot_n,vsurf_dot_n;
double tangent[3],vsurf[3];
@@ -2173,7 +2173,7 @@ void FixSRD::slip_wall(double *vs, int iwall, double *norm, double *vsnew)
tangent1[1] = vs[1] - vs_dot_n*norm[1];
tangent1[2] = vs[2] - vs_dot_n*norm[2];
scale = 1.0/sqrt(tangent1[0]*tangent1[0] + tangent1[1]*tangent1[1] +
- tangent1[2]*tangent1[2]);
+ tangent1[2]*tangent1[2]);
tangent1[0] *= scale;
tangent1[1] *= scale;
tangent1[2] *= scale;
@@ -2213,7 +2213,7 @@ void FixSRD::slip_wall(double *vs, int iwall, double *norm, double *vsnew)
------------------------------------------------------------------------- */
void FixSRD::noslip(double *vs, double *vb, double *xb, Big *big, int iwall,
- double *xsurf, double *norm, double *vsnew)
+ double *xsurf, double *norm, double *vsnew)
{
double vs_dot_n,scale,r1,r2,vnmag,vtmag1,vtmag2;
double tangent1[3],tangent2[3];
@@ -2224,7 +2224,7 @@ void FixSRD::noslip(double *vs, double *vb, double *xb, Big *big, int iwall,
tangent1[1] = vs[1] - vs_dot_n*norm[1];
tangent1[2] = vs[2] - vs_dot_n*norm[2];
scale = 1.0/sqrt(tangent1[0]*tangent1[0] + tangent1[1]*tangent1[1] +
- tangent1[2]*tangent1[2]);
+ tangent1[2]*tangent1[2]);
tangent1[0] *= scale;
tangent1[1] *= scale;
tangent1[2] *= scale;
@@ -2269,8 +2269,8 @@ void FixSRD::noslip(double *vs, double *vb, double *xb, Big *big, int iwall,
------------------------------------------------------------------------- */
void FixSRD::force_torque(double *vsold, double *vsnew,
- double *xs, double *xb,
- double *fb, double *tb)
+ double *xs, double *xb,
+ double *fb, double *tb)
{
double dpdt[3],xs_xb[3];
@@ -2322,7 +2322,7 @@ void FixSRD::force_wall(double *vsold, double *vsnew, int iwall)
------------------------------------------------------------------------- */
int FixSRD::update_srd(int i, double dt, double *xscoll, double *vsnew,
- double *xs, double *vs)
+ double *xs, double *vs)
{
int ix,iy,iz;
@@ -2336,13 +2336,13 @@ int FixSRD::update_srd(int i, double dt, double *xscoll, double *vsnew,
if (triclinic) domain->x2lamda(xs,xs);
- if (xs[0] < srdlo[0] || xs[0] > srdhi[0] ||
- xs[1] < srdlo[1] || xs[1] > srdhi[1] ||
+ if (xs[0] < srdlo[0] || xs[0] > srdhi[0] ||
+ xs[1] < srdlo[1] || xs[1] > srdhi[1] ||
xs[2] < srdlo[2] || xs[2] > srdhi[2]) {
if (screen) {
error->warning(FLERR,"Fix srd particle moved outside valid domain");
fprintf(screen," particle %d on proc %d at timestep " BIGINT_FORMAT,
- atom->tag[i],me,update->ntimestep);
+ atom->tag[i],me,update->ntimestep);
fprintf(screen," xnew %g %g %g\n",xs[0],xs[1],xs[2]);
fprintf(screen," srdlo/hi x %g %g\n",srdlo[0],srdhi[0]);
fprintf(screen," srdlo/hi y %g %g\n",srdlo[1],srdhi[1]);
@@ -2395,33 +2395,33 @@ void FixSRD::parameterize()
for (int i = 0; i < nlocal; i++)
if (mask[i] & biggroupbit) {
if (radius && radius[i] > 0.0) {
- maxbigdiam = MAX(maxbigdiam,2.0*radius[i]);
- minbigdiam = MIN(minbigdiam,2.0*radius[i]);
+ maxbigdiam = MAX(maxbigdiam,2.0*radius[i]);
+ minbigdiam = MIN(minbigdiam,2.0*radius[i]);
} else if (ellipsoid && ellipsoid[i] >= 0) {
- any_ellipsoids = 1;
- double *shape = ebonus[ellipsoid[i]].shape;
- maxbigdiam = MAX(maxbigdiam,2.0*shape[0]);
- maxbigdiam = MAX(maxbigdiam,2.0*shape[1]);
- maxbigdiam = MAX(maxbigdiam,2.0*shape[2]);
- minbigdiam = MIN(minbigdiam,2.0*shape[0]);
- minbigdiam = MIN(minbigdiam,2.0*shape[1]);
- minbigdiam = MIN(minbigdiam,2.0*shape[2]);
+ any_ellipsoids = 1;
+ double *shape = ebonus[ellipsoid[i]].shape;
+ maxbigdiam = MAX(maxbigdiam,2.0*shape[0]);
+ maxbigdiam = MAX(maxbigdiam,2.0*shape[1]);
+ maxbigdiam = MAX(maxbigdiam,2.0*shape[2]);
+ minbigdiam = MIN(minbigdiam,2.0*shape[0]);
+ minbigdiam = MIN(minbigdiam,2.0*shape[1]);
+ minbigdiam = MIN(minbigdiam,2.0*shape[2]);
} else if (line && line[i] >= 0) {
- any_lines = 1;
- double length = lbonus[line[i]].length;
- maxbigdiam = MAX(maxbigdiam,length);
- minbigdiam = MIN(minbigdiam,length);
+ any_lines = 1;
+ double length = lbonus[line[i]].length;
+ maxbigdiam = MAX(maxbigdiam,length);
+ minbigdiam = MIN(minbigdiam,length);
} else if (tri && tri[i] >= 0) {
- any_tris = 1;
- double length1 = MathExtra::len3(tbonus[tri[i]].c1);
- double length2 = MathExtra::len3(tbonus[tri[i]].c2);
- double length3 = MathExtra::len3(tbonus[tri[i]].c3);
- double length = MAX(length1,length2);
- length = MAX(length,length3);
- maxbigdiam = MAX(maxbigdiam,length);
- minbigdiam = MIN(minbigdiam,length);
- } else
- error->one(FLERR,"Big particle in fix srd cannot be point particle");
+ any_tris = 1;
+ double length1 = MathExtra::len3(tbonus[tri[i]].c1);
+ double length2 = MathExtra::len3(tbonus[tri[i]].c2);
+ double length3 = MathExtra::len3(tbonus[tri[i]].c3);
+ double length = MAX(length1,length2);
+ length = MAX(length,length3);
+ maxbigdiam = MAX(maxbigdiam,length);
+ minbigdiam = MIN(minbigdiam,length);
+ } else
+ error->one(FLERR,"Big particle in fix srd cannot be point particle");
}
double tmp = maxbigdiam;
@@ -2462,17 +2462,17 @@ void FixSRD::parameterize()
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (rmass) {
- if (mass_srd == 0.0) mass_srd = rmass[i];
- else if (rmass[i] != mass_srd) flag = 1;
+ if (mass_srd == 0.0) mass_srd = rmass[i];
+ else if (rmass[i] != mass_srd) flag = 1;
} else {
- if (mass_srd == 0.0) mass_srd = mass[type[i]];
- else if (mass[type[i]] != mass_srd) flag = 1;
+ if (mass_srd == 0.0) mass_srd = mass[type[i]];
+ else if (mass[type[i]] != mass_srd) flag = 1;
}
}
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_MAX,world);
- if (flagall)
+ if (flagall)
error->all(FLERR,"Fix srd requires SRD particles all have same mass");
// set temperature and lamda of SRD particles from each other
@@ -2481,7 +2481,7 @@ void FixSRD::parameterize()
if (lamdaflag == 0)
lamda = dt_srd * sqrt(force->boltz*temperature_srd/mass_srd/force->mvv2e);
else
- temperature_srd = force->mvv2e *
+ temperature_srd = force->mvv2e *
(lamda/dt_srd)*(lamda/dt_srd) * mass_srd/force->boltz;
// vmax = maximum velocity of an SRD particle
@@ -2503,37 +2503,37 @@ void FixSRD::parameterize()
if (dimension == 3) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & biggroupbit) {
- if (radius && radius[i] > 0.0) {
- double r = radfactor * radius[i];
- volbig += 4.0/3.0*MY_PI * r*r*r;;
- } else if (ellipsoid && ellipsoid[i] >= 0) {
- double *shape = ebonus[ellipsoid[i]].shape;
- volbig += 4.0/3.0*MY_PI * shape[0]*shape[1]*shape[2] *
- radfactor*radfactor*radfactor;
- } else if (tri && tri[i] >= 0) {
- double *c1 = tbonus[tri[i]].c1;
- double *c2 = tbonus[tri[i]].c2;
- double *c3 = tbonus[tri[i]].c3;
- double c2mc1[3],c3mc1[3],cross[3];
- MathExtra::sub3(c2,c1,c2mc1);
- MathExtra::sub3(c3,c1,c3mc1);
- MathExtra::cross3(c2mc1,c3mc1,cross);
- volbig += 0.5 * MathExtra::len3(cross);
- }
+ if (radius && radius[i] > 0.0) {
+ double r = radfactor * radius[i];
+ volbig += 4.0/3.0*MY_PI * r*r*r;;
+ } else if (ellipsoid && ellipsoid[i] >= 0) {
+ double *shape = ebonus[ellipsoid[i]].shape;
+ volbig += 4.0/3.0*MY_PI * shape[0]*shape[1]*shape[2] *
+ radfactor*radfactor*radfactor;
+ } else if (tri && tri[i] >= 0) {
+ double *c1 = tbonus[tri[i]].c1;
+ double *c2 = tbonus[tri[i]].c2;
+ double *c3 = tbonus[tri[i]].c3;
+ double c2mc1[3],c3mc1[3],cross[3];
+ MathExtra::sub3(c2,c1,c2mc1);
+ MathExtra::sub3(c3,c1,c3mc1);
+ MathExtra::cross3(c2mc1,c3mc1,cross);
+ volbig += 0.5 * MathExtra::len3(cross);
+ }
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & biggroupbit) {
- if (radius && radius[i] > 0.0) {
- double r = radfactor * radius[i];
- volbig += MY_PI * r*r;
- } else if (ellipsoid && ellipsoid[i] >= 0) {
- double *shape = ebonus[ellipsoid[i]].shape;
- volbig += MY_PI * shape[0]*shape[1] * radfactor*radfactor;
- } else if (line && line[i] >= 0) {
- double length = lbonus[line[i]].length;
- volbig += length * WIDTH;
- }
+ if (radius && radius[i] > 0.0) {
+ double r = radfactor * radius[i];
+ volbig += MY_PI * r*r;
+ } else if (ellipsoid && ellipsoid[i] >= 0) {
+ double *shape = ebonus[ellipsoid[i]].shape;
+ volbig += MY_PI * shape[0]*shape[1] * radfactor*radfactor;
+ } else if (line && line[i] >= 0) {
+ double length = lbonus[line[i]].length;
+ volbig += length * WIDTH;
+ }
}
}
@@ -2566,7 +2566,7 @@ void FixSRD::parameterize()
double volsrd,density_srd;
if (dimension == 3) {
volsrd = (domain->xprd * domain->yprd * domain->zprd) - volbig;
- density_srd = nsrd * mass_srd /
+ density_srd = nsrd * mass_srd /
(domain->xprd*domain->yprd*domain->zprd - volbig);
} else {
volsrd = (domain->xprd * domain->yprd) - volbig;
@@ -2606,15 +2606,15 @@ void FixSRD::parameterize()
double viscosity;
if (dimension == 3)
- viscosity = gridsrd*gridsrd/(18.0*dt_srd) *
- (1.0-(1.0-exp(-srd_per_cell))/srd_per_cell) +
+ viscosity = gridsrd*gridsrd/(18.0*dt_srd) *
+ (1.0-(1.0-exp(-srd_per_cell))/srd_per_cell) +
(force->boltz*temperature_srd*dt_srd/(4.0*mass_srd*force->mvv2e)) *
((srd_per_cell+2.0)/(srd_per_cell-1.0));
else
- viscosity =
+ viscosity =
(force->boltz*temperature_srd*dt_srd/(2.0*mass_srd*force->mvv2e)) *
(srd_per_cell/(srd_per_cell-1.0 + exp(-srd_per_cell)) - 1.0) +
- (gridsrd*gridsrd)/(12.0*dt_srd) *
+ (gridsrd*gridsrd)/(12.0*dt_srd) *
((srd_per_cell-1.0 + exp(-srd_per_cell))/srd_per_cell);
viscosity *= force->xxt2kmu;
@@ -2624,16 +2624,16 @@ void FixSRD::parameterize()
if (screen) {
fprintf(screen,"SRD info:\n");
fprintf(screen,
- " SRD/big particles = " BIGINT_FORMAT " " BIGINT_FORMAT "\n",
- nsrd,mbig);
+ " SRD/big particles = " BIGINT_FORMAT " " BIGINT_FORMAT "\n",
+ nsrd,mbig);
fprintf(screen," big particle diameter max/min = %g %g\n",
- maxbigdiam,minbigdiam);
+ maxbigdiam,minbigdiam);
fprintf(screen," SRD temperature & lamda = %g %g\n",
- temperature_srd,lamda);
+ temperature_srd,lamda);
fprintf(screen," SRD max distance & max velocity = %g %g\n",dmax,vmax);
fprintf(screen," SRD grid counts: %d %d %d\n",nbin1x,nbin1y,nbin1z);
fprintf(screen," SRD grid size: request, actual (xyz) = %g, %g %g %g\n",
- gridsrd,binsize3x,binsize3y,binsize3z);
+ gridsrd,binsize3x,binsize3y,binsize3z);
fprintf(screen," SRD per actual grid cell = %g\n",srd_per_cell);
fprintf(screen," SRD viscosity = %g\n",viscosity);
fprintf(screen," big/SRD mass density ratio = %g\n",mdratio);
@@ -2641,16 +2641,16 @@ void FixSRD::parameterize()
if (logfile) {
fprintf(logfile,"SRD info:\n");
fprintf(logfile,
- " SRD/big particles = " BIGINT_FORMAT " " BIGINT_FORMAT "\n",
- nsrd,mbig);
+ " SRD/big particles = " BIGINT_FORMAT " " BIGINT_FORMAT "\n",
+ nsrd,mbig);
fprintf(logfile," big particle diameter max/min = %g %g\n",
- maxbigdiam,minbigdiam);
+ maxbigdiam,minbigdiam);
fprintf(logfile," SRD temperature & lamda = %g %g\n",
- temperature_srd,lamda);
+ temperature_srd,lamda);
fprintf(logfile," SRD max distance & max velocity = %g %g\n",dmax,vmax);
fprintf(logfile," SRD grid counts: %d %d %d\n",nbin1x,nbin1y,nbin1z);
fprintf(logfile," SRD grid size: request, actual (xyz) = %g, %g %g %g\n",
- gridsrd,binsize3x,binsize3y,binsize3z);
+ gridsrd,binsize3x,binsize3y,binsize3z);
fprintf(logfile," SRD per actual grid cell = %g\n",srd_per_cell);
fprintf(logfile," SRD viscosity = %g\n",viscosity);
fprintf(logfile," big/SRD mass density ratio = %g\n",mdratio);
@@ -2659,8 +2659,8 @@ void FixSRD::parameterize()
// error if less than 1 SRD bin per processor in some dim
- if (nbin1x < comm->procgrid[0] || nbin1y < comm->procgrid[1] ||
- nbin1z < comm->procgrid[2])
+ if (nbin1x < comm->procgrid[0] || nbin1y < comm->procgrid[1] ||
+ nbin1z < comm->procgrid[2])
error->all(FLERR,"Fewer SRD bins than processors in some dimension");
// check if SRD bins are within tolerance for shape and size
@@ -2670,7 +2670,7 @@ void FixSRD::parameterize()
binsize3x/binsize3y > 1.0+cubictol) tolflag = 1;
if (dimension == 3) {
if (binsize3z/binsize3x > 1.0+cubictol ||
- binsize3x/binsize3z > 1.0+cubictol) tolflag = 1;
+ binsize3x/binsize3z > 1.0+cubictol) tolflag = 1;
}
if (tolflag) {
@@ -2695,7 +2695,7 @@ void FixSRD::parameterize()
error->all(FLERR,"SRD bin size for fix srd differs from user request");
if (me == 0)
error->warning(FLERR,
- "SRD bin size for fix srd differs from user request");
+ "SRD bin size for fix srd differs from user request");
}
// error if lamda < 0.6 of SRD grid size and no shifting allowed
@@ -2709,7 +2709,7 @@ void FixSRD::parameterize()
error->all(FLERR,"Fix srd lamda must be >= 0.6 of SRD grid size");
else if (lamda < 0.6*maxgridsrd && shiftuser == SHIFT_POSSIBLE) {
shiftflag = 1;
- if (me == 0)
+ if (me == 0)
error->warning(FLERR,"SRD bin shifting turned on due to small lamda");
} else if (shiftuser == SHIFT_YES) shiftflag = 1;
@@ -2858,8 +2858,8 @@ void FixSRD::big_dynamic()
inertiaone[1] = EINERTIA*rmass[i] * (shape[0]*shape[0]+shape[2]*shape[2]);
inertiaone[2] = EINERTIA*rmass[i] * (shape[0]*shape[0]+shape[1]*shape[1]);
MathExtra::angmom_to_omega(angmom[i],
- biglist[k].ex,biglist[k].ey,biglist[k].ez,
- inertiaone,biglist[k].omega);
+ biglist[k].ex,biglist[k].ey,biglist[k].ez,
+ inertiaone,biglist[k].omega);
// line
// set omega from atom->omega directly
@@ -2880,10 +2880,10 @@ void FixSRD::big_dynamic()
MathExtra::q_to_exyz(quat,biglist[k].ex,biglist[k].ey,biglist[k].ez);
inertia = tbonus[tri[i]].inertia;
MathExtra::angmom_to_omega(angmom[i],
- biglist[k].ex,biglist[k].ey,biglist[k].ez,
- inertia,biglist[k].omega);
+ biglist[k].ex,biglist[k].ey,biglist[k].ez,
+ inertia,biglist[k].omega);
MathExtra::matvec(biglist[k].ex,biglist[k].ey,biglist[k].ez,
- biglist[k].normbody,biglist[k].norm);
+ biglist[k].normbody,biglist[k].norm);
MathExtra::norm3(biglist[k].norm);
}
}
@@ -2926,7 +2926,7 @@ void FixSRD::setup_bounds()
// dist_ghost = 0.0, since not used
// if no big particles or walls:
// dist_ghost and dist_srd = 0.0, since not used since no search bins
- // dist_srd_reneigh = subsize - onemove =
+ // dist_srd_reneigh = subsize - onemove =
// max distance to move without being lost during comm->exchange()
// subsize = perp distance between sub-domain faces (orthog or triclinic)
@@ -2947,13 +2947,13 @@ void FixSRD::setup_bounds()
if (triclinic == 0) {
subsize = domain->prd[0]/comm->procgrid[0];
subsize = MIN(subsize,domain->prd[1]/comm->procgrid[1]);
- if (dimension == 3)
- subsize = MIN(subsize,domain->prd[2]/comm->procgrid[2]);
+ if (dimension == 3)
+ subsize = MIN(subsize,domain->prd[2]/comm->procgrid[2]);
} else {
subsize = 1.0/comm->procgrid[0]/length0;
subsize = MIN(subsize,1.0/comm->procgrid[1]/length1);
- if (dimension == 3)
- subsize = MIN(subsize,1.0/comm->procgrid[2]/length2);
+ if (dimension == 3)
+ subsize = MIN(subsize,1.0/comm->procgrid[2]/length2);
}
dist_srd_reneigh = subsize - onemove;
}
@@ -3135,12 +3135,12 @@ void FixSRD::setup_velocity_shift(int ishift, int dynamic)
double *corner = shifts[ishift].corner;
int *procgrid = comm->procgrid;
int *myloc = comm->myloc;
-
+
binlo[0] = static_cast<int> ((sublo[0]-corner[0])*bininv1x);
binlo[1] = static_cast<int> ((sublo[1]-corner[1])*bininv1y);
binlo[2] = static_cast<int> ((sublo[2]-corner[2])*bininv1z);
if (dimension == 2) shifts[ishift].binlo[2] = 0;
-
+
binhi[0] = static_cast<int> ((subhi[0]-corner[0])*bininv1x);
binhi[1] = static_cast<int> ((subhi[1]-corner[1])*bininv1y);
binhi[2] = static_cast<int> ((subhi[2]-corner[2])*bininv1z);
@@ -3153,7 +3153,7 @@ void FixSRD::setup_velocity_shift(int ishift, int dynamic)
binlo[1] = myloc[1]*nbin1y/procgrid[1];
if (myloc[2]*nbin1z % procgrid[2] == 0)
binlo[2] = myloc[2]*nbin1z/procgrid[2];
-
+
if ((myloc[0]+1)*nbin1x % procgrid[0] == 0)
binhi[0] = (myloc[0]+1)*nbin1x/procgrid[0] - 1;
if ((myloc[1]+1)*nbin1y % procgrid[1] == 0)
@@ -3161,25 +3161,25 @@ void FixSRD::setup_velocity_shift(int ishift, int dynamic)
if ((myloc[2]+1)*nbin1z % procgrid[2] == 0)
binhi[2] = (myloc[2]+1)*nbin1z/procgrid[2] - 1;
}
-
+
int nbinx = binhi[0] - binlo[0] + 1;
int nbiny = binhi[1] - binlo[1] + 1;
int nbinz = binhi[2] - binlo[2] + 1;
// allow for one extra bin if shifting will occur
-
+
if (ishift == 1 && dynamic == 0) {
nbinx++;
nbiny++;
if (dimension == 3) nbinz++;
}
-
+
int nbins = nbinx*nbiny*nbinz;
int nbinxy = nbinx*nbiny;
int nbinsq = nbinx*nbiny;
nbinsq = MAX(nbiny*nbinz,nbinsq);
nbinsq = MAX(nbinx*nbinz,nbinsq);
-
+
shifts[ishift].nbins = nbins;
shifts[ishift].nbinx = nbinx;
shifts[ishift].nbiny = nbiny;
@@ -3194,7 +3194,7 @@ void FixSRD::setup_velocity_shift(int ishift, int dynamic)
// bcomm neighbors
// first = send in lo direction, recv from hi direction
// second = send in hi direction, recv from lo direction
-
+
if (dynamic == 0) {
shifts[ishift].bcomm[0].sendproc = comm->procneigh[0][0];
shifts[ishift].bcomm[0].recvproc = comm->procneigh[0][1];
@@ -3209,15 +3209,15 @@ void FixSRD::setup_velocity_shift(int ishift, int dynamic)
shifts[ishift].bcomm[5].sendproc = comm->procneigh[2][1];
shifts[ishift].bcomm[5].recvproc = comm->procneigh[2][0];
}
-
+
// set nsend,nrecv and sendlist,recvlist for each swap in x,y,z
// set nsend,nrecv = 0 if static bins align with proc boundary
// or to prevent dynamic bin swapping across non-periodic global boundary
// allocate sendlist,recvlist only for dynamic = 0
-
+
first = &shifts[ishift].bcomm[0];
second = &shifts[ishift].bcomm[1];
-
+
first->nsend = first->nrecv = second->nsend = second->nrecv = nbiny*nbinz;
if (ishift == 0) {
if (myloc[0]*nbin1x % procgrid[0] == 0)
@@ -3244,7 +3244,7 @@ void FixSRD::setup_velocity_shift(int ishift, int dynamic)
m = 0;
i = 0;
- for (j = 0; j < nbiny; j++)
+ for (j = 0; j < nbiny; j++)
for (k = 0; k < nbinz; k++) {
id = k*nbinxy + j*nbinx + i;
first->sendlist[m] = second->recvlist[m] = id;
@@ -3252,16 +3252,16 @@ void FixSRD::setup_velocity_shift(int ishift, int dynamic)
}
m = 0;
i = nbinx-1;
- for (j = 0; j < nbiny; j++)
+ for (j = 0; j < nbiny; j++)
for (k = 0; k < nbinz; k++) {
id = k*nbinxy + j*nbinx + i;
second->sendlist[m] = first->recvlist[m] = id;
m++;
}
-
+
first = &shifts[ishift].bcomm[2];
second = &shifts[ishift].bcomm[3];
-
+
first->nsend = first->nrecv = second->nsend = second->nrecv = nbinx*nbinz;
if (ishift == 0) {
if (myloc[1]*nbin1y % procgrid[1] == 0)
@@ -3274,7 +3274,7 @@ void FixSRD::setup_velocity_shift(int ishift, int dynamic)
if (myloc[1] == procgrid[1]-1) second->nsend = first->nrecv = 0;
}
}
-
+
if (reallocflag) {
memory->destroy(first->sendlist);
memory->destroy(first->recvlist);
@@ -3285,10 +3285,10 @@ void FixSRD::setup_velocity_shift(int ishift, int dynamic)
memory->create(second->sendlist,nbinsq,"fix/srd:sendlist");
memory->create(second->recvlist,nbinsq,"fix/srd:sendlist");
}
-
+
m = 0;
j = 0;
- for (i = 0; i < nbinx; i++)
+ for (i = 0; i < nbinx; i++)
for (k = 0; k < nbinz; k++) {
id = k*nbinxy + j*nbinx + i;
first->sendlist[m] = second->recvlist[m] = id;
@@ -3296,30 +3296,30 @@ void FixSRD::setup_velocity_shift(int ishift, int dynamic)
}
m = 0;
j = nbiny-1;
- for (i = 0; i < nbinx; i++)
+ for (i = 0; i < nbinx; i++)
for (k = 0; k < nbinz; k++) {
id = k*nbinxy + j*nbinx + i;
second->sendlist[m] = first->recvlist[m] = id;
m++;
}
-
+
if (dimension == 3) {
first = &shifts[ishift].bcomm[4];
second = &shifts[ishift].bcomm[5];
-
+
first->nsend = first->nrecv = second->nsend = second->nrecv = nbinx*nbiny;
if (ishift == 0) {
if (myloc[2]*nbin1z % procgrid[2] == 0)
- first->nsend = second->nrecv = 0;
+ first->nsend = second->nrecv = 0;
if ((myloc[2]+1)*nbin1z % procgrid[2] == 0)
- second->nsend = first->nrecv = 0;
+ second->nsend = first->nrecv = 0;
} else {
if (domain->zperiodic == 0) {
- if (myloc[2] == 0) first->nsend = second->nrecv = 0;
- if (myloc[2] == procgrid[2]-1) second->nsend = first->nrecv = 0;
+ if (myloc[2] == 0) first->nsend = second->nrecv = 0;
+ if (myloc[2] == procgrid[2]-1) second->nsend = first->nrecv = 0;
}
}
-
+
if (reallocflag) {
memory->destroy(first->sendlist);
memory->destroy(first->recvlist);
@@ -3330,39 +3330,39 @@ void FixSRD::setup_velocity_shift(int ishift, int dynamic)
memory->create(second->sendlist,nbinx*nbiny,"fix/srd:sendlist");
memory->create(second->recvlist,nbinx*nbiny,"fix/srd:sendlist");
}
-
+
m = 0;
k = 0;
- for (i = 0; i < nbinx; i++)
+ for (i = 0; i < nbinx; i++)
for (j = 0; j < nbiny; j++) {
- id = k*nbinxy + j*nbinx + i;
- first->sendlist[m] = second->recvlist[m] = id;
- m++;
+ id = k*nbinxy + j*nbinx + i;
+ first->sendlist[m] = second->recvlist[m] = id;
+ m++;
}
m = 0;
k = nbinz-1;
- for (i = 0; i < nbinx; i++)
+ for (i = 0; i < nbinx; i++)
for (j = 0; j < nbiny; j++) {
- id = k*nbinxy + j*nbinx + i;
- second->sendlist[m] = first->recvlist[m] = id;
- m++;
+ id = k*nbinxy + j*nbinx + i;
+ second->sendlist[m] = first->recvlist[m] = id;
+ m++;
}
}
-
+
// allocate vbins, only for dynamic = 0
-
+
if (dynamic == 0 && nbins > shifts[ishift].maxvbin) {
memory->destroy(shifts[ishift].vbin);
shifts[ishift].maxvbin = nbins;
- shifts[ishift].vbin = (BinAve *)
+ shifts[ishift].vbin = (BinAve *)
memory->smalloc(nbins*sizeof(BinAve),"fix/srd:vbin");
}
-
+
// for vbins I own, set owner = 1
// if bin never sent to anyone, I own it
// if bin sent to lower numbered proc, I do not own it
// if bin sent to self, I do not own it on even swap (avoids double counting)
-
+
vbin = shifts[ishift].vbin;
for (i = 0; i < nbins; i++) vbin[i].owner = 1;
for (int iswap = 0; iswap < 2*dimension; iswap++) {
@@ -3380,12 +3380,12 @@ void FixSRD::setup_velocity_shift(int ishift, int dynamic)
m = 0;
for (k = 0; k < nbinz; k++)
for (j = 0; j < nbiny; j++)
- for (i = 0; i < nbinx; i++) {
- vbin[m].xctr[0] = corner[0] + (i+binlo[0]+0.5)/nbin1x;
- vbin[m].xctr[1] = corner[1] + (j+binlo[1]+0.5)/nbin1y;
- vbin[m].xctr[2] = corner[2] + (k+binlo[2]+0.5)/nbin1z;
- m++;
- }
+ for (i = 0; i < nbinx; i++) {
+ vbin[m].xctr[0] = corner[0] + (i+binlo[0]+0.5)/nbin1x;
+ vbin[m].xctr[1] = corner[1] + (j+binlo[1]+0.5)/nbin1y;
+ vbin[m].xctr[2] = corner[2] + (k+binlo[2]+0.5)/nbin1z;
+ m++;
+ }
}
}
@@ -3403,7 +3403,7 @@ void FixSRD::setup_velocity_shift(int ishift, int dynamic)
void FixSRD::setup_search_bins()
{
- // subboxlo/hi = real space bbox which
+ // subboxlo/hi = real space bbox which
// owned/ghost big particles or walls can be in
// start with bounding box for my sub-domain, add dist_ghost
// for triclinic, need to:
@@ -3525,13 +3525,13 @@ void FixSRD::setup_search_stencil()
for (int k = -nz; k <= nz; k++)
for (int j = -ny; j <= ny; j++)
for (int i = -nx; i <= nx; i++)
- if (bin_bin_distance(i,j,k) < radsq) {
- stencil[nstencil][0] = i;
- stencil[nstencil][1] = j;
- stencil[nstencil][2] = k;
- stencil[nstencil][3] = k*nbin2y*nbin2x + j*nbin2x + i;
- nstencil++;
- }
+ if (bin_bin_distance(i,j,k) < radsq) {
+ stencil[nstencil][0] = i;
+ stencil[nstencil][1] = j;
+ stencil[nstencil][2] = k;
+ stencil[nstencil][3] = k*nbin2y*nbin2x + j*nbin2x + i;
+ nstencil++;
+ }
}
/* ----------------------------------------------------------------------
@@ -3713,10 +3713,10 @@ void FixSRD::velocity_stats(int groupnum)
if (me == 0) {
if (screen)
fprintf(screen," ave/max %s velocity = %g %g\n",
- group->names[groupnum],vave,vmax);
+ group->names[groupnum],vave,vmax);
if (logfile)
fprintf(logfile," ave/max %s velocity = %g %g\n",
- group->names[groupnum],vave,vmax);
+ group->names[groupnum],vave,vmax);
}
}
@@ -3743,7 +3743,7 @@ double FixSRD::newton_raphson(double t1, double t2)
double temp;
for (int i = 0; i < MAXITER; i++) {
if ((((t-thi)*df - f)*((t-tlo)*df - f) > 0.0) ||
- (fabs(2.0*f) > fabs(dtold*df))) {
+ (fabs(2.0*f) > fabs(dtold*df))) {
dtold = dt;
dt = 0.5 * (thi-tlo);
t = tlo + dt;
@@ -3780,7 +3780,7 @@ void FixSRD::lineside(double t, double &f, double &df)
double sinT = sin(theta);
f = (p[1]-c[1]) * cosT - (p[0]-c[0]) * sinT;
- df = ((xs1[1]-xs0[1]) - (xb1[1]-xb0[1]))*cosT - (p[1]-c[1])*sinT*dtheta -
+ df = ((xs1[1]-xs0[1]) - (xb1[1]-xb0[1]))*cosT - (p[1]-c[1])*sinT*dtheta -
((xs1[0]-xs0[0]) - (xb1[0]-xb0[0]))*sinT - (p[0]-c[0])*cosT*dtheta;
}
@@ -3800,7 +3800,7 @@ void FixSRD::triside(double t, double &f, double &df)
double sinT = sin(theta);
f = (p[1]-c[1]) * cosT - (p[0]-c[0]) * sinT;
- df = ((xs1[1]-xs0[1]) - (xb1[1]-xb0[1]))*cosT - (p[1]-c[1])*sinT*dtheta -
+ df = ((xs1[1]-xs0[1]) - (xb1[1]-xb0[1]))*cosT - (p[1]-c[1])*sinT*dtheta -
((xs1[0]-xs0[0]) - (xb1[0]-xb0[0]))*sinT - (p[0]-c[0])*cosT*dtheta;
}
@@ -3834,9 +3834,9 @@ double FixSRD::distance(int i, int j)
/* ---------------------------------------------------------------------- */
void FixSRD::print_collision(int i, int j, int ibounce,
- double t_remain, double dt,
- double *xscoll, double *xbcoll, double *norm,
- int type)
+ double t_remain, double dt,
+ double *xscoll, double *xbcoll, double *norm,
+ int type)
{
double xsstart[3],xbstart[3];
double **x = atom->x;
@@ -3848,7 +3848,7 @@ void FixSRD::print_collision(int i, int j, int ibounce,
printf(" local indices: %d %d\n",i,j);
printf(" timestep = %g\n",dt);
printf(" time remaining post-collision = %g\n",t_remain);
-
+
xsstart[0] = x[i][0] - dt*v[i][0];
xsstart[1] = x[i][1] - dt*v[i][1];
xsstart[2] = x[i][2] - dt*v[i][2];
@@ -3857,30 +3857,30 @@ void FixSRD::print_collision(int i, int j, int ibounce,
xbstart[2] = x[j][2] - dt*v[j][2];
printf(" SRD start position = %g %g %g\n",
- xsstart[0],xsstart[1],xsstart[2]);
+ xsstart[0],xsstart[1],xsstart[2]);
printf(" BIG start position = %g %g %g\n",
- xbstart[0],xbstart[1],xbstart[2]);
+ xbstart[0],xbstart[1],xbstart[2]);
printf(" SRD coll position = %g %g %g\n",
- xscoll[0],xscoll[1],xscoll[2]);
+ xscoll[0],xscoll[1],xscoll[2]);
printf(" BIG coll position = %g %g %g\n",
- xbcoll[0],xbcoll[1],xbcoll[2]);
+ xbcoll[0],xbcoll[1],xbcoll[2]);
printf(" SRD end position = %g %g %g\n",x[i][0],x[i][1],x[i][2]);
printf(" BIG end position = %g %g %g\n",x[j][0],x[j][1],x[j][2]);
printf(" SRD vel = %g %g %g\n",v[i][0],v[i][1],v[i][2]);
printf(" BIG vel = %g %g %g\n",v[j][0],v[j][1],v[j][2]);
printf(" surf norm = %g %g %g\n",norm[0],norm[1],norm[2]);
-
+
double rstart = sqrt((xsstart[0]-xbstart[0])*(xsstart[0]-xbstart[0]) +
- (xsstart[1]-xbstart[1])*(xsstart[1]-xbstart[1]) +
- (xsstart[2]-xbstart[2])*(xsstart[2]-xbstart[2]));
+ (xsstart[1]-xbstart[1])*(xsstart[1]-xbstart[1]) +
+ (xsstart[2]-xbstart[2])*(xsstart[2]-xbstart[2]));
double rcoll = sqrt((xscoll[0]-xbcoll[0])*(xscoll[0]-xbcoll[0]) +
- (xscoll[1]-xbcoll[1])*(xscoll[1]-xbcoll[1]) +
- (xscoll[2]-xbcoll[2])*(xscoll[2]-xbcoll[2]));
+ (xscoll[1]-xbcoll[1])*(xscoll[1]-xbcoll[1]) +
+ (xscoll[2]-xbcoll[2])*(xscoll[2]-xbcoll[2]));
double rend = sqrt((x[i][0]-x[j][0])*(x[i][0]-x[j][0]) +
- (x[i][1]-x[j][1])*(x[i][1]-x[j][1]) +
- (x[i][2]-x[j][2])*(x[i][2]-x[j][2]));
-
+ (x[i][1]-x[j][1])*(x[i][1]-x[j][1]) +
+ (x[i][2]-x[j][2])*(x[i][2]-x[j][2]));
+
printf(" separation at start = %g\n",rstart);
printf(" separation at coll = %g\n",rcoll);
printf(" separation at end = %g\n",rend);
@@ -3893,7 +3893,7 @@ void FixSRD::print_collision(int i, int j, int ibounce,
printf(" local indices: %d %d\n",i,j);
printf(" timestep = %g\n",dt);
printf(" time remaining post-collision = %g\n",t_remain);
-
+
xsstart[0] = x[i][0] - dt*v[i][0];
xsstart[1] = x[i][1] - dt*v[i][1];
xsstart[2] = x[i][2] - dt*v[i][2];
@@ -3901,10 +3901,10 @@ void FixSRD::print_collision(int i, int j, int ibounce,
xbstart[dim] = xwall[j] - dt*vwall[j];
printf(" SRD start position = %g %g %g\n",
- xsstart[0],xsstart[1],xsstart[2]);
+ xsstart[0],xsstart[1],xsstart[2]);
printf(" WALL start position = %g\n",xbstart[dim]);
printf(" SRD coll position = %g %g %g\n",
- xscoll[0],xscoll[1],xscoll[2]);
+ xscoll[0],xscoll[1],xscoll[2]);
printf(" WALL coll position = %g\n",xbcoll[dim]);
printf(" SRD end position = %g %g %g\n",x[i][0],x[i][1],x[i][2]);
printf(" WALL end position = %g\n",xwall[j]);
@@ -3912,11 +3912,11 @@ void FixSRD::print_collision(int i, int j, int ibounce,
printf(" SRD vel = %g %g %g\n",v[i][0],v[i][1],v[i][2]);
printf(" WALL vel = %g\n",vwall[j]);
printf(" surf norm = %g %g %g\n",norm[0],norm[1],norm[2]);
-
+
double rstart = xsstart[dim]-xbstart[dim];
double rcoll = xscoll[dim]-xbcoll[dim];
double rend = x[dim][0]-xwall[j];
-
+
printf(" separation at start = %g\n",rstart);
printf(" separation at coll = %g\n",rcoll);
printf(" separation at end = %g\n",rend);
diff --git a/src/SRD/fix_srd.h b/src/SRD/fix_srd.h
index 4d72e1badebedb8522c96f15ab61c49451d53e2c..3bb2cdda7bd8eb96ca0944aae2ba39fac2354715 100644
--- a/src/SRD/fix_srd.h
+++ b/src/SRD/fix_srd.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -46,7 +46,7 @@ class FixSRD : public Fix {
int cubicflag,shiftuser,shiftseed,shiftflag,tstat;
double gridsrd,gridsearch,lamda,radfactor,cubictol;
int triclinic,change_size,change_shape,deformflag;
-
+
double dt_big,dt_srd;
double mass_big,mass_srd;
double temperature_srd;
@@ -198,29 +198,29 @@ class FixSRD : public Fix {
int inside_wall(double *, int);
double collision_sphere_exact(double *, double *, double *, double *,
- Big *, double *, double *, double *);
+ Big *, double *, double *, double *);
void collision_sphere_inexact(double *, double *,
- Big *, double *, double *, double *);
+ Big *, double *, double *, double *);
double collision_ellipsoid_exact(double *, double *, double *, double *,
- Big *, double *, double *, double *);
+ Big *, double *, double *, double *);
void collision_ellipsoid_inexact(double *, double *,
- Big *, double *, double *, double *);
+ Big *, double *, double *, double *);
double collision_line_exact(double *, double *, double *, double *,
- Big *, double, double *, double *, double *);
+ Big *, double, double *, double *, double *);
double collision_tri_exact(double *, double *, double *, double *,
- Big *, double, double *, double *, double *);
+ Big *, double, double *, double *, double *);
double collision_wall_exact(double *, int, double *,
- double *, double *, double *);
+ double *, double *, double *);
void collision_wall_inexact(double *, int, double *, double *, double *);
void slip(double *, double *, double *, Big *,
- double *, double *, double *);
+ double *, double *, double *);
void slip_wall(double *, int, double *, double *);
void noslip(double *, double *, double *, Big *, int,
- double *, double *, double *);
+ double *, double *, double *);
void force_torque(double *, double *, double *,
- double *, double *, double *);
+ double *, double *, double *);
void force_wall(double *, double *, int);
int update_srd(int, double, double *, double *, double *, double *);
@@ -244,7 +244,7 @@ class FixSRD : public Fix {
double distance(int, int);
void print_collision(int, int, int, double, double,
- double *, double *, double *, int);
+ double *, double *, double *, int);
};
}
diff --git a/src/SRD/fix_wall_srd.cpp b/src/SRD/fix_wall_srd.cpp
index a951e13c9220ff70f0c1226a2e79394b35c3dda9..cd3b8df4373f2b0fc9b2a1bc6f164b5f30711674 100644
--- a/src/SRD/fix_wall_srd.cpp
+++ b/src/SRD/fix_wall_srd.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -47,8 +47,8 @@ FixWallSRD::FixWallSRD(LAMMPS *lmp, int narg, char **arg) :
int iarg = 3;
while (iarg < narg) {
if ((strcmp(arg[iarg],"xlo") == 0) || (strcmp(arg[iarg],"xhi") == 0) ||
- (strcmp(arg[iarg],"ylo") == 0) || (strcmp(arg[iarg],"yhi") == 0) ||
- (strcmp(arg[iarg],"zlo") == 0) || (strcmp(arg[iarg],"zhi") == 0)) {
+ (strcmp(arg[iarg],"ylo") == 0) || (strcmp(arg[iarg],"yhi") == 0) ||
+ (strcmp(arg[iarg],"zlo") == 0) || (strcmp(arg[iarg],"zhi") == 0)) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix wall/srd command");
int newwall;
@@ -60,24 +60,24 @@ FixWallSRD::FixWallSRD(LAMMPS *lmp, int narg, char **arg) :
else if (strcmp(arg[iarg],"zhi") == 0) newwall = ZHI;
for (int m = 0; m < nwall; m++)
- if (newwall == wallwhich[m])
- error->all(FLERR,"Wall defined twice in fix wall/srd command");
+ if (newwall == wallwhich[m])
+ error->all(FLERR,"Wall defined twice in fix wall/srd command");
wallwhich[nwall] = newwall;
if (strcmp(arg[iarg+1],"EDGE") == 0) {
- wallstyle[nwall] = EDGE;
- int dim = wallwhich[nwall] / 2;
- int side = wallwhich[nwall] % 2;
- if (side == 0) coord0[nwall] = domain->boxlo[dim];
- else coord0[nwall] = domain->boxhi[dim];
+ wallstyle[nwall] = EDGE;
+ int dim = wallwhich[nwall] / 2;
+ int side = wallwhich[nwall] % 2;
+ if (side == 0) coord0[nwall] = domain->boxlo[dim];
+ else coord0[nwall] = domain->boxhi[dim];
} else if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) {
- wallstyle[nwall] = VARIABLE;
- int n = strlen(&arg[iarg+1][2]) + 1;
- varstr[nwall] = new char[n];
- strcpy(varstr[nwall],&arg[iarg+1][2]);
+ wallstyle[nwall] = VARIABLE;
+ int n = strlen(&arg[iarg+1][2]) + 1;
+ varstr[nwall] = new char[n];
+ strcpy(varstr[nwall],&arg[iarg+1][2]);
} else {
- wallstyle[nwall] = CONSTANT;
- coord0[nwall] = atof(arg[iarg+1]);
+ wallstyle[nwall] = CONSTANT;
+ coord0[nwall] = atof(arg[iarg+1]);
}
nwall++;
@@ -213,7 +213,7 @@ double FixWallSRD::compute_array(int i, int j)
if (force_flag == 0) {
MPI_Allreduce(&fwall[0][0],&fwall_all[0][0],3*nwall,
- MPI_DOUBLE,MPI_SUM,world);
+ MPI_DOUBLE,MPI_SUM,world);
force_flag = 1;
}
return fwall_all[i][j];
@@ -245,7 +245,7 @@ void FixWallSRD::wall_params(int flag)
xwalllast[m] = xwall[m];
xwall[m] = xnew;
vwall[m] = (xwall[m] - xwalllast[m]) / dt;
- }
+ }
fwall[m][0] = fwall[m][1] = fwall[m][2] = 0.0;
}
diff --git a/src/SRD/fix_wall_srd.h b/src/SRD/fix_wall_srd.h
index d3d1eb68c9d835a32261f5e505c44ffefe1ffb87..99265ad2c88c6ef9273fc99910b3e1dc7d9f8549 100644
--- a/src/SRD/fix_wall_srd.h
+++ b/src/SRD/fix_wall_srd.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -48,7 +48,7 @@ class FixWallSRD : public Fix {
double dt;
double xwalllast[6];
bigint laststep;
-
+
double **fwall_all;
int force_flag;
};
diff --git a/src/STUBS/mpi.h b/src/STUBS/mpi.h
index e3db304874b1781438e6f1cb1e56e657924cfe52..75a4cd7aac9b0029a14166f734a4390af74401a0 100644
--- a/src/STUBS/mpi.h
+++ b/src/STUBS/mpi.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -87,12 +87,12 @@ int MPI_Irecv(void *buf, int count, MPI_Datatype datatype,
int source, int tag, MPI_Comm comm, MPI_Request *request);
int MPI_Wait(MPI_Request *request, MPI_Status *status);
int MPI_Waitall(int n, MPI_Request *request, MPI_Status *status);
-int MPI_Waitany(int count, MPI_Request *request, int *index,
+int MPI_Waitany(int count, MPI_Request *request, int *index,
MPI_Status *status);
int MPI_Sendrecv(void *sbuf, int scount, MPI_Datatype sdatatype,
- int dest, int stag, void *rbuf, int rcount,
- MPI_Datatype rdatatype, int source, int rtag,
- MPI_Comm comm, MPI_Status *status);
+ int dest, int stag, void *rbuf, int rcount,
+ MPI_Datatype rdatatype, int source, int rtag,
+ MPI_Comm comm, MPI_Status *status);
int MPI_Get_count(MPI_Status *status, MPI_Datatype datatype, int *count);
int MPI_Comm_split(MPI_Comm comm, int color, int key, MPI_Comm *comm_out);
@@ -113,7 +113,7 @@ int MPI_Bcast(void *buf, int count, MPI_Datatype datatype,
int MPI_Allreduce(void *sendbuf, void *recvbuf, int count,
MPI_Datatype datatype, MPI_Op op, MPI_Comm comm);
int MPI_Reduce(void *sendbuf, void *recvbuf, int count,
- MPI_Datatype datatype, MPI_Op op, int root, MPI_Comm comm);
+ MPI_Datatype datatype, MPI_Op op, int root, MPI_Comm comm);
int MPI_Scan(void *sendbuf, void *recvbuf, int count,
MPI_Datatype datatype, MPI_Op op, MPI_Comm comm);
int MPI_Allgather(void *sendbuf, int sendcount, MPI_Datatype sendtype,
@@ -128,11 +128,11 @@ int MPI_Gather(void *sendbuf, int sendcount, MPI_Datatype sendtype,
void *recvbuf, int recvcount, MPI_Datatype recvtype,
int root, MPI_Comm comm);
int MPI_Gatherv(void *sendbuf, int sendcount, MPI_Datatype sendtype,
- void *recvbuf, int *recvcounts, int *displs,
- MPI_Datatype recvtype, int root, MPI_Comm comm);
+ void *recvbuf, int *recvcounts, int *displs,
+ MPI_Datatype recvtype, int root, MPI_Comm comm);
int MPI_Scatterv(void *sendbuf, int *sendcounts, int *displs,
- MPI_Datatype sendtype, void *recvbuf, int recvcount,
- MPI_Datatype recvtype, int root, MPI_Comm comm);
+ MPI_Datatype sendtype, void *recvbuf, int recvcount,
+ MPI_Datatype recvtype, int root, MPI_Comm comm);
#ifdef __cplusplus
}
diff --git a/src/USER-ATC/fix_atc.cpp b/src/USER-ATC/fix_atc.cpp
index 62e4979216874bae193bf587c2a8c08d77da47f2..2aaf89ace6186e6b1b8d06470e840704b1e27709 100644
--- a/src/USER-ATC/fix_atc.cpp
+++ b/src/USER-ATC/fix_atc.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -33,7 +33,7 @@
#include "comm.h"
#include "error.h"
-using namespace LAMMPS_NS;
+using namespace LAMMPS_NS;
using namespace FixConst;
// main page of doxygen documentation
@@ -53,7 +53,7 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
// Set LAMMPS pointer on LammpsInterface
ATC::LammpsInterface::instance()->set_lammps(lmp);
- /*! \page man_fix_atc fix atc command
+ /*! \page man_fix_atc fix atc command
\section syntax
fix AtC transfer <type> <parameter_file>
- type\n
@@ -71,10 +71,10 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
fix do Verlet integration and the Hardy/post-processing does not.
After instantiating this fix, several other fix_modify commands will be
needed to set up the problem, e.g. define the finite element mesh and
- prescribe initial and boundary conditions.
+ prescribe initial and boundary conditions.
The following coupling example is typical, but non-exhaustive:\n
-
+
<TT>
# ... commands to create and initialize the MD system \n
@@ -122,7 +122,7 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
run 1000 \n
</TT>
- Note coupling and post-processing can be combined in the same simulations
+ Note coupling and post-processing can be combined in the same simulations
using separate fixes.
\n
For detailed exposition of the theory and algorithms please see:\n
@@ -131,21 +131,21 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
Special Issue of Computer Methods and Applied Mechanics (2008) 197:3351.
- Zimmerman, JA; Webb, EB; Hoyt, JJ;. Jones, RE; Klein, PA; Bammann, DJ,
<VAR> Calculation of stress in atomistic simulation </VAR>
- Special Issue of Modelling and Simulation in Materials Science and
+ Special Issue of Modelling and Simulation in Materials Science and
Engineering (2004), 12:S319
Please refer to the standard
- finite element (FE) texts, e.g. T.J.R Hughes <VAR> The finite element
+ finite element (FE) texts, e.g. T.J.R Hughes <VAR> The finite element
method </VAR>, Dover 2003, for the basics of FE simulation.
\section restrictions
- Thermal and two_temperature (coupling) types use a Verlet time-integration
+ Thermal and two_temperature (coupling) types use a Verlet time-integration
algorithm.
- The hardy type does not contain its own time-integrator and must be used
+ The hardy type does not contain its own time-integrator and must be used
with a separate fix that does contain one, e.g. nve, nvt, etc.
- Currently,
- - the coupling is restricted to thermal physics
+ Currently,
+ - the coupling is restricted to thermal physics
- the FE computations are done in serial on each processor.
\section related
@@ -197,7 +197,7 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
- \ref man_atom_element_map
- \ref man_neighbor_reset_frequency
- Note: a set of example input files with the attendant material files are
+ Note: a set of example input files with the attendant material files are
included with this package
\section default
none
@@ -212,34 +212,34 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
// Postprocessing
try {
- if (strcmp(arg[3],"hardy")==0)
+ if (strcmp(arg[3],"hardy")==0)
{
if (narg < 5) {
if (me==0) printf("Constructing ATC transfer (hardy)\n");
atcTransfer_ = new ATC::ATC_TransferHardy(groupName);
- }
- else {
+ }
+ else {
if (me==0) printf("Constructing ATC transfer (hardy) with parameter file %s\n",arg[4]);
std::string matParamFile = arg[4];
atcTransfer_ = new ATC::ATC_TransferHardy(groupName,matParamFile);
}
}
// PhysicsTypes
- else if (strcmp(arg[3],"thermal")==0)
+ else if (strcmp(arg[3],"thermal")==0)
{
std::string matParamFile = arg[4];
if (me==0) printf("Constructing ATC transfer (thermal) with parameter file %s\n",arg[4]);
atcTransfer_ = new ATC::ATC_TransferThermal(groupName,matParamFile);
lmp->atom->add_callback(0); // NOTE what is this?
}
- else if (strcmp(arg[3],"two_temperature")==0)
+ else if (strcmp(arg[3],"two_temperature")==0)
{
std::string matParamFile = arg[4];
if (me==0) printf("Constructing ATC transfer (two_temperature) with parameter file %s\n",arg[4]);
atcTransfer_ = new ATC::ATC_TransferThermal(groupName,matParamFile,
ATC::TWO_TEMPERATURE);
}
- else
+ else
{
lmp->error->all(FLERR,"Unknown physics type in ATC");
}
@@ -293,7 +293,7 @@ int FixATC::setmask()
int FixATC::modify_param(int narg, char** arg)
{
- bool match;
+ bool match;
// pass on to transfer layer
try {
@@ -406,15 +406,15 @@ void FixATC::unpack_restart(int nlocal, int nth){
/* ----------------------------------------------------------------------
maxsize of any atom's restart data
------------------------------------------------------------------------- */
-
+
int FixATC::maxsize_restart(){
return 0;
}
-
+
/* ----------------------------------------------------------------------
size of atom nlocal's restart data
------------------------------------------------------------------------- */
-
+
int FixATC::size_restart(int nlocal){
return 0;
}
diff --git a/src/USER-ATC/fix_atc.h b/src/USER-ATC/fix_atc.h
index de9f1539ef5616a6038b786cc4967cb50f44cd70..879b465bd3f5abf9d4bea0add992fc3ccd813658 100644
--- a/src/USER-ATC/fix_atc.h
+++ b/src/USER-ATC/fix_atc.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -34,12 +34,12 @@ namespace LAMMPS_NS {
class NeighList;
class FixATC : public Fix {
- public:
+ public:
/** constructor & destructor */
FixATC(class LAMMPS *, int, char **);
~FixATC();
- /** calls ATC_Transfer */
+ /** calls ATC_Transfer */
void init();
void init_list(int id, NeighList *ptr) {
ATC::LammpsInterface::instance()->init_list(id,ptr);
@@ -63,7 +63,7 @@ namespace LAMMPS_NS {
void copy_arrays(int, int);
int pack_exchange(int, double *);
int unpack_exchange(int, double *);
- int pack_comm(int , int *, double *, int, int *);
+ int pack_comm(int , int *, double *, int, int *);
void unpack_comm(int, int, double *);
/** modify atc parameters (parser) */
diff --git a/src/USER-AWPMD/atom_vec_wavepacket.cpp b/src/USER-AWPMD/atom_vec_wavepacket.cpp
index 16cda89c52bc188e690c7d9286056096c4291593..52aa2c18225158c8a02847b2708f2f8121762931 100644
--- a/src/USER-AWPMD/atom_vec_wavepacket.cpp
+++ b/src/USER-AWPMD/atom_vec_wavepacket.cpp
@@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
-
+
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
-
+
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@@ -38,21 +38,21 @@ AtomVecWavepacket::AtomVecWavepacket(LAMMPS *lmp, int narg, char **arg) :
AtomVec(lmp, narg, arg)
{
comm_x_only = comm_f_only = 0;
-
+
mass_type = 1;
molecular = 0;
-
+
size_forward = 4; // coords[3]+radius[1]
- size_reverse = 10; // force[3]+erforce[1]+ervelforce[1]+vforce[3]+csforce[2]
- size_border = 10; // coords[3]+tag[1]+type[1]+mask[1]+q[1]+spin[1]+eradius[1]+etag[1]
- size_velocity = 6; // +velocities[3]+ ervel[1]+cs[2]
+ size_reverse = 10; // force[3]+erforce[1]+ervelforce[1]+vforce[3]+csforce[2]
+ size_border = 10; // coords[3]+tag[1]+type[1]+mask[1]+q[1]+spin[1]+eradius[1]+etag[1]
+ size_velocity = 6; // +velocities[3]+ ervel[1]+cs[2]
size_data_atom = 11; // for input file: 1-tag 2-type 3-q 4-spin 5-eradius 6-etag 7-cs_re 8-cs_im 9-x 10-y 11-z
size_data_vel = 5; // for input file: vx vy vz ervel <??>
xcol_data = 9; // starting column for x data
-
- atom->wavepacket_flag = 1;
+
+ atom->wavepacket_flag = 1;
atom->electron_flag = 1; // compatible with eff
- atom->q_flag = atom->spin_flag = atom->eradius_flag =
+ atom->q_flag = atom->spin_flag = atom->eradius_flag =
atom->ervel_flag = atom->erforce_flag = 1;
atom->cs_flag = atom->csforce_flag = atom->vforce_flag = atom->ervelforce_flag = atom->etag_flag = 1;
@@ -63,7 +63,7 @@ AtomVecWavepacket::AtomVecWavepacket(LAMMPS *lmp, int narg, char **arg) :
/* ----------------------------------------------------------------------
grow atom-electron arrays
n = 0 grows arrays by DELTA
- n > 0 allocates arrays to size n
+ n > 0 allocates arrays to size n
------------------------------------------------------------------------- */
void AtomVecWavepacket::grow(int n)
@@ -71,7 +71,7 @@ void AtomVecWavepacket::grow(int n)
if (n == 0) nmax += DELTA;
else nmax = n;
atom->nmax = nmax;
-
+
tag = memory->grow(atom->tag,nmax,"atom:tag");
type = memory->grow(atom->type,nmax,"atom:type");
mask = memory->grow(atom->mask,nmax,"atom:mask");
@@ -90,10 +90,10 @@ void AtomVecWavepacket::grow(int n)
csforce = memory->grow(atom->csforce,2*nmax,"atom:csforce");
vforce = memory->grow(atom->vforce,3*nmax,"atom:vforce");
ervelforce = memory->grow(atom->ervelforce,nmax,"atom:ervelforce");
- etag = memory->grow(atom->etag,nmax,"atom:etag");
-
+ etag = memory->grow(atom->etag,nmax,"atom:etag");
+
if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
}
@@ -113,7 +113,7 @@ void AtomVecWavepacket::grow_reset()
csforce = atom->csforce;
vforce = atom->vforce;
ervelforce = atom->ervelforce;
- etag = atom->etag;
+ etag = atom->etag;
}
@@ -133,19 +133,19 @@ void AtomVecWavepacket::copy(int i, int j, int delflag)
v[j][0] = v[i][0];
v[j][1] = v[i][1];
v[j][2] = v[i][2];
-
+
q[j] = q[i];
spin[j] = spin[i];
eradius[j] = eradius[i];
ervel[j] = ervel[i];
-
+
cs[2*j] = cs[2*i];
- cs[2*j+1] = cs[2*i+1];
- etag[j] = etag[i];
+ cs[2*j+1] = cs[2*i+1];
+ etag[j] = etag[i];
if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j);
}
@@ -153,7 +153,7 @@ void AtomVecWavepacket::copy(int i, int j, int delflag)
// this will be used as partial pack for unsplit Hartree packets (v, ervel not regarded as separate variables)
int AtomVecWavepacket::pack_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
@@ -192,7 +192,7 @@ int AtomVecWavepacket::pack_comm(int n, int *list, double *buf,
// this is a complete pack of all 'position' variables of AWPMD
int AtomVecWavepacket::pack_comm_vel(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz,dvx,dvy,dvz;
@@ -225,14 +225,14 @@ int AtomVecWavepacket::pack_comm_vel(int n, int *list, double *buf,
}
if (!deform_vremap) {
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = eradius[j];
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = eradius[j];
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
buf[m++] = ervel[j];
buf[m++] = cs[2*j];
@@ -243,20 +243,20 @@ int AtomVecWavepacket::pack_comm_vel(int n, int *list, double *buf,
dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
dvz = pbc[2]*h_rate[2];
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = eradius[j];
- if (mask[i] & deform_groupbit) {
- buf[m++] = v[j][0] + dvx;
- buf[m++] = v[j][1] + dvy;
- buf[m++] = v[j][2] + dvz;
- } else {
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
- }
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = eradius[j];
+ if (mask[i] & deform_groupbit) {
+ buf[m++] = v[j][0] + dvx;
+ buf[m++] = v[j][1] + dvy;
+ buf[m++] = v[j][2] + dvz;
+ } else {
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
+ }
buf[m++] = ervel[j];
buf[m++] = cs[2*j];
buf[m++] = cs[2*j+1];
@@ -288,7 +288,7 @@ int AtomVecWavepacket::pack_comm_hybrid(int n, int *list, double *buf)
void AtomVecWavepacket::unpack_comm(int n, int first, double *buf)
{
int i,m,last;
-
+
m = 0;
last = first + n;
for (i = first; i < last; i++) {
@@ -304,7 +304,7 @@ void AtomVecWavepacket::unpack_comm(int n, int first, double *buf)
void AtomVecWavepacket::unpack_comm_vel(int n, int first, double *buf)
{
int i,m,last;
-
+
m = 0;
last = first + n;
for (i = first; i < last; i++) {
@@ -317,7 +317,7 @@ void AtomVecWavepacket::unpack_comm_vel(int n, int first, double *buf)
v[i][2] = buf[m++];
ervel[i] = buf[m++];
- cs[2*i] = buf[m++];
+ cs[2*i] = buf[m++];
cs[2*i+1] = buf[m++];
}
}
@@ -333,7 +333,7 @@ int AtomVecWavepacket::unpack_comm_hybrid(int n, int first, double *buf)
for (i = first; i < last; i++){
eradius[i] = buf[m++];
ervel[i] = buf[m++];
- cs[2*i] = buf[m++];
+ cs[2*i] = buf[m++];
cs[2*i+1] = buf[m++];
}
return m;
@@ -344,7 +344,7 @@ int AtomVecWavepacket::unpack_comm_hybrid(int n, int first, double *buf)
int AtomVecWavepacket::pack_reverse(int n, int first, double *buf)
{
int i,m,last;
-
+
m = 0;
last = first + n;
for (i = first; i < last; i++) { //10
@@ -352,7 +352,7 @@ int AtomVecWavepacket::pack_reverse(int n, int first, double *buf)
buf[m++] = f[i][1];
buf[m++] = f[i][2];
buf[m++] = erforce[i];
-
+
buf[m++] = ervelforce[i];
buf[m++] = vforce[3*i];
buf[m++] = vforce[3*i+1];
@@ -373,7 +373,7 @@ int AtomVecWavepacket::pack_reverse_hybrid(int n, int first, double *buf)
last = first + n;
for (i = first; i < last; i++){
buf[m++] = erforce[i];
-
+
buf[m++] = ervelforce[i];
buf[m++] = vforce[3*i];
buf[m++] = vforce[3*i+1];
@@ -389,7 +389,7 @@ int AtomVecWavepacket::pack_reverse_hybrid(int n, int first, double *buf)
void AtomVecWavepacket::unpack_reverse(int n, int *list, double *buf)
{
int i,j,m;
-
+
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
@@ -431,7 +431,7 @@ int AtomVecWavepacket::unpack_reverse_hybrid(int n, int *list, double *buf)
/* ---------------------------------------------------------------------- */
// will be used for Hartree unsplit version (the etag is added however)
int AtomVecWavepacket::pack_border(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
@@ -481,7 +481,7 @@ int AtomVecWavepacket::pack_border(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
int AtomVecWavepacket::pack_border_vel(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz,dvx,dvy,dvz;
@@ -522,23 +522,23 @@ int AtomVecWavepacket::pack_border_vel(int n, int *list, double *buf,
}
if (domain->triclinic == 0) {
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = tag[j];
- buf[m++] = type[j];
- buf[m++] = mask[j];
- buf[m++] = q[j];
- buf[m++] = spin[j];
- buf[m++] = eradius[j];
- buf[m++] = etag[j];
-
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = tag[j];
+ buf[m++] = type[j];
+ buf[m++] = mask[j];
+ buf[m++] = q[j];
+ buf[m++] = spin[j];
+ buf[m++] = eradius[j];
+ buf[m++] = etag[j];
+
buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
+
-
buf[m++] = ervel[j];
buf[m++] = cs[2*j];
buf[m++] = cs[2*j+1];
@@ -548,27 +548,27 @@ int AtomVecWavepacket::pack_border_vel(int n, int *list, double *buf,
dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
dvz = pbc[2]*h_rate[2];
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = tag[j];
- buf[m++] = type[j];
- buf[m++] = mask[j];
- buf[m++] = q[j];
- buf[m++] = spin[j];
- buf[m++] = eradius[j];
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = tag[j];
+ buf[m++] = type[j];
+ buf[m++] = mask[j];
+ buf[m++] = q[j];
+ buf[m++] = spin[j];
+ buf[m++] = eradius[j];
buf[m++] = etag[j];
- if (mask[i] & deform_groupbit) {
- buf[m++] = v[j][0] + dvx;
- buf[m++] = v[j][1] + dvy;
- buf[m++] = v[j][2] + dvz;
- } else {
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
- }
+ if (mask[i] & deform_groupbit) {
+ buf[m++] = v[j][0] + dvx;
+ buf[m++] = v[j][1] + dvy;
+ buf[m++] = v[j][2] + dvz;
+ } else {
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
+ }
buf[m++] = ervel[j];
buf[m++] = cs[2*j];
@@ -605,7 +605,7 @@ int AtomVecWavepacket::pack_border_hybrid(int n, int *list, double *buf)
void AtomVecWavepacket::unpack_border(int n, int first, double *buf)
{
int i,m,last;
-
+
m = 0;
last = first + n;
for (i = first; i < last; i++) {
@@ -615,7 +615,7 @@ void AtomVecWavepacket::unpack_border(int n, int first, double *buf)
x[i][2] = buf[m++];
tag[i] = static_cast<int> (buf[m++]);
type[i] = static_cast<int> (buf[m++]);
- mask[i] = static_cast<int> (buf[m++]);
+ mask[i] = static_cast<int> (buf[m++]);
q[i] = buf[m++];
spin[i] = static_cast<int> (buf[m++]);
eradius[i] = buf[m++];
@@ -628,7 +628,7 @@ void AtomVecWavepacket::unpack_border(int n, int first, double *buf)
void AtomVecWavepacket::unpack_border_vel(int n, int first, double *buf)
{
int i,m,last;
-
+
m = 0;
last = first + n;
for (i = first; i < last; i++) {
@@ -648,7 +648,7 @@ void AtomVecWavepacket::unpack_border_vel(int n, int first, double *buf)
v[i][1] = buf[m++];
v[i][2] = buf[m++];
-
+
ervel[i] = buf[m++];
cs[2*i] = buf[m++];
cs[2*i+1] = buf[m++];
@@ -678,7 +678,7 @@ int AtomVecWavepacket::unpack_border_hybrid(int n, int first, double *buf)
/* ----------------------------------------------------------------------
pack data for atom I for sending to another proc
- xyz must be 1st 3 values, so comm::exchange() can test on them
+ xyz must be 1st 3 values, so comm::exchange() can test on them
------------------------------------------------------------------------- */
int AtomVecWavepacket::pack_exchange(int i, double *buf)
@@ -693,7 +693,7 @@ int AtomVecWavepacket::pack_exchange(int i, double *buf)
buf[m++] = tag[i];
buf[m++] = type[i];
buf[m++] = mask[i];
- buf[m++] = image[i];
+ buf[m++] = image[i];
buf[m++] = q[i];
buf[m++] = spin[i];
buf[m++] = eradius[i];
@@ -702,11 +702,11 @@ int AtomVecWavepacket::pack_exchange(int i, double *buf)
buf[m++] = etag[i];
buf[m++] = cs[2*i];
buf[m++] = cs[2*i+1];
-
+
if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]);
-
+
buf[0] = m;
return m;
}
@@ -717,7 +717,7 @@ int AtomVecWavepacket::unpack_exchange(double *buf)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
-
+
int m = 1;
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
@@ -728,7 +728,7 @@ int AtomVecWavepacket::unpack_exchange(double *buf)
tag[nlocal] = static_cast<int> (buf[m++]);
type[nlocal] = static_cast<int> (buf[m++]);
mask[nlocal] = static_cast<int> (buf[m++]);
- image[nlocal] = static_cast<int> (buf[m++]);
+ image[nlocal] = static_cast<int> (buf[m++]);
q[nlocal] = buf[m++];
spin[nlocal] = static_cast<int> (buf[m++]);
eradius[nlocal] = buf[m++];
@@ -737,12 +737,12 @@ int AtomVecWavepacket::unpack_exchange(double *buf)
etag[nlocal] = buf[m++];
cs[2*nlocal] = buf[m++];
cs[2*nlocal+1] = buf[m++];
-
+
if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->
- unpack_exchange(nlocal,&buf[m]);
-
+ unpack_exchange(nlocal,&buf[m]);
+
atom->nlocal++;
return m;
}
@@ -755,22 +755,22 @@ int AtomVecWavepacket::unpack_exchange(double *buf)
int AtomVecWavepacket::size_restart()
{
int i;
-
+
int nlocal = atom->nlocal;
- int n = 18 * nlocal; // Associated with pack_restart
-
+ int n = 18 * nlocal; // Associated with pack_restart
+
if (atom->nextra_restart)
- for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
for (i = 0; i < nlocal; i++)
- n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
-
+ n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
+
return n;
}
/* ----------------------------------------------------------------------
pack atom I's data for restart file including extra quantities
xyz must be 1st 3 values, so that read_restart can test on them
- molecular types may be negative, but write as positive
+ molecular types may be negative, but write as positive
------------------------------------------------------------------------- */
int AtomVecWavepacket::pack_restart(int i, double *buf)
@@ -786,7 +786,7 @@ int AtomVecWavepacket::pack_restart(int i, double *buf)
buf[m++] = v[i][0];
buf[m++] = v[i][1];
buf[m++] = v[i][2];
-
+
buf[m++] = q[i];
buf[m++] = spin[i];
buf[m++] = eradius[i];
@@ -795,11 +795,11 @@ int AtomVecWavepacket::pack_restart(int i, double *buf)
buf[m++] = etag[i];
buf[m++] = cs[2*i];
buf[m++] = cs[2*i+1];
-
+
if (atom->nextra_restart)
- for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]);
-
+
buf[0] = m;
return m;
}
@@ -816,7 +816,7 @@ int AtomVecWavepacket::unpack_restart(double *buf)
if (atom->nextra_store)
memory->grow(atom->extra,nmax,atom->nextra_store,"atom:extra");
}
-
+
int m = 1;
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
@@ -828,7 +828,7 @@ int AtomVecWavepacket::unpack_restart(double *buf)
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
-
+
q[nlocal] = buf[m++];
spin[nlocal] = static_cast<int> (buf[m++]);
eradius[nlocal] = buf[m++];
@@ -837,13 +837,13 @@ int AtomVecWavepacket::unpack_restart(double *buf)
etag[nlocal] = buf[m++];
cs[2*nlocal] = buf[m++];
cs[2*nlocal+1] = buf[m++];
-
+
double **extra = atom->extra;
if (atom->nextra_store) {
int size = static_cast<int> (buf[0]) - m;
for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++];
}
-
+
atom->nlocal++;
return m;
}
@@ -858,7 +858,7 @@ void AtomVecWavepacket::create_atom(int itype, double *coord)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
-
+
tag[nlocal] = 0;
type[nlocal] = itype;
x[nlocal][0] = coord[0];
@@ -869,12 +869,12 @@ void AtomVecWavepacket::create_atom(int itype, double *coord)
v[nlocal][0] = 0.0;
v[nlocal][1] = 0.0;
v[nlocal][2] = 0.0;
-
+
q[nlocal] = 1.;
spin[nlocal] = 0.;
- eradius[nlocal] = 0.0;
- ervel[nlocal] = 0.0;
-
+ eradius[nlocal] = 0.0;
+ ervel[nlocal] = 0.0;
+
etag[nlocal]= 0.;
cs[2*nlocal] = 0.;
cs[2*nlocal+1] = 0.;
@@ -891,41 +891,41 @@ void AtomVecWavepacket::create_atom(int itype, double *coord)
void AtomVecWavepacket::data_atom(double *coord, int imagetmp, char **values)
{
int nlocal = atom->nlocal;
-
+
if (nlocal == nmax) grow(0);
-
+
tag[nlocal] = atoi(values[0]);
if (tag[nlocal] <= 0)
error->one(FLERR,"Invalid atom ID in Atoms section of data file (ID tag must be >0)");
-
+
type[nlocal] = atoi(values[1]);
if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
error->one(FLERR,"Invalid atom type in Atoms section of data file");
-
+
q[nlocal] = atof(values[2]);
spin[nlocal] = atoi(values[3]);
eradius[nlocal] = atof(values[4]);
if (eradius[nlocal] < 0.0)
error->one(FLERR,"Invalid eradius in Atoms section of data file");
-
+
etag[nlocal] = atoi(values[5]);
cs[2*nlocal] = atoi(values[6]);
cs[2*nlocal+1] = atof(values[7]);
-
-
+
+
x[nlocal][0] = coord[0];
x[nlocal][1] = coord[1];
x[nlocal][2] = coord[2];
-
+
image[nlocal] = imagetmp;
-
+
mask[nlocal] = 1;
v[nlocal][0] = 0.0;
v[nlocal][1] = 0.0;
v[nlocal][2] = 0.0;
ervel[nlocal] = 0.0;
-
+
atom->nlocal++;
}
@@ -941,17 +941,17 @@ int AtomVecWavepacket::data_atom_hybrid(int nlocal, char **values)
eradius[nlocal] = atof(values[2]);
if (eradius[nlocal] < 0.0)
error->one(FLERR,"Invalid eradius in Atoms section of data file");
-
+
etag[nlocal] = atoi(values[3]);
cs[2*nlocal] = atoi(values[4]);
cs[2*nlocal+1] = atof(values[5]);
-
-
+
+
v[nlocal][0] = 0.0;
v[nlocal][1] = 0.0;
v[nlocal][2] = 0.0;
ervel[nlocal] = 0.0;
-
+
return 3;
}
@@ -978,13 +978,13 @@ int AtomVecWavepacket::data_vel_hybrid(int m, char **values)
}
/* ----------------------------------------------------------------------
- return # of bytes of allocated memory
+ return # of bytes of allocated memory
------------------------------------------------------------------------- */
bigint AtomVecWavepacket::memory_usage()
{
bigint bytes = 0;
-
+
if (atom->memcheck("tag")) bytes += memory->usage(tag,nmax);
if (atom->memcheck("type")) bytes += memory->usage(type,nmax);
if (atom->memcheck("mask")) bytes += memory->usage(mask,nmax);
@@ -992,7 +992,7 @@ bigint AtomVecWavepacket::memory_usage()
if (atom->memcheck("x")) bytes += memory->usage(x,nmax,3);
if (atom->memcheck("v")) bytes += memory->usage(v,nmax,3);
if (atom->memcheck("f")) bytes += memory->usage(f,nmax*comm->nthreads,3);
-
+
if (atom->memcheck("q")) bytes += memory->usage(q,nmax);
if (atom->memcheck("spin")) bytes += memory->usage(spin,nmax);
if (atom->memcheck("eradius")) bytes += memory->usage(eradius,nmax);
@@ -1004,6 +1004,6 @@ bigint AtomVecWavepacket::memory_usage()
if (atom->memcheck("csforce")) bytes += memory->usage(csforce,2*nmax);
if (atom->memcheck("vforce")) bytes += memory->usage(vforce,3*nmax);
if (atom->memcheck("etag")) bytes += memory->usage(etag,nmax);
-
+
return bytes;
}
diff --git a/src/USER-AWPMD/atom_vec_wavepacket.h b/src/USER-AWPMD/atom_vec_wavepacket.h
index 4515dcf0fb5486265491590f3c38b04c1079b3b2..f98caca33cf9f426f6cea6ecd16cee7ed5eb3f9d 100644
--- a/src/USER-AWPMD/atom_vec_wavepacket.h
+++ b/src/USER-AWPMD/atom_vec_wavepacket.h
@@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
-
+
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
-
+
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@@ -28,7 +28,7 @@ AtomStyle(wavepacket,AtomVecWavepacket)
#include "atom_vec.h"
namespace LAMMPS_NS {
-
+
class AtomVecWavepacket : public AtomVec {
public:
AtomVecWavepacket(class LAMMPS *, int, char **);
@@ -63,11 +63,11 @@ public:
void data_vel(int, char **);
int data_vel_hybrid(int, char **);
bigint memory_usage();
-
+
private:
int *tag,*type,*mask,*image;
double **x,**v,**f;
-
+
///\en spin: -1 or 1 for electron, 0 for ion (compatible with eff)
int *spin;
///\en charge: must be specified in the corresponding units (-1 for electron in real units, eff compatible)
@@ -91,7 +91,7 @@ private:
///\en (generalized) force on radius velocity, size is N
double *ervelforce;
};
-
+
}
#endif
diff --git a/src/USER-AWPMD/fix_nve_awpmd.cpp b/src/USER-AWPMD/fix_nve_awpmd.cpp
index 8fbf2fa8a55949914f7287640ef77f4e83a582f7..377d42b37e872e35434cfa60f517dc187cfe7f75 100644
--- a/src/USER-AWPMD/fix_nve_awpmd.cpp
+++ b/src/USER-AWPMD/fix_nve_awpmd.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -36,9 +36,9 @@ using namespace FixConst;
FixNVEAwpmd::FixNVEAwpmd(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
- if (!atom->wavepacket_flag)
+ if (!atom->wavepacket_flag)
error->all(FLERR,"Fix nve/awpmd requires atom style wavepacket");
- //if (!atom->mass_type != 1)
+ //if (!atom->mass_type != 1)
// error->all(FLERR,"Fix nve/awpmd requires per type mass");
time_integrate = 1;
@@ -47,7 +47,7 @@ FixNVEAwpmd::FixNVEAwpmd(LAMMPS *lmp, int narg, char **arg) :
/* ---------------------------------------------------------------------- */
int FixNVEAwpmd::setmask()
-{
+{
int mask = 0;
mask |= INITIAL_INTEGRATE;
mask |= FINAL_INTEGRATE;
@@ -76,7 +76,7 @@ void FixNVEAwpmd::init()
void FixNVEAwpmd::initial_integrate(int vflag)
{
-
+
// update v,vr and x,radius of atoms in group
@@ -90,8 +90,8 @@ void FixNVEAwpmd::initial_integrate(int vflag)
double *ervelforce=atom->ervelforce;
double *cs=atom->cs;
double *csforce=atom->csforce;
-
-
+
+
double *mass = atom->mass;
int *spin = atom->spin;
int *type = atom->type;
@@ -100,7 +100,7 @@ void FixNVEAwpmd::initial_integrate(int vflag)
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
// x + dt * [v + 0.5 * dt * (f / m)];
-
+
// simple Euler update
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
@@ -150,4 +150,3 @@ void FixNVEAwpmd::reset_dt()
dtv = update->dt;
dtf = 0.5 * update->dt * force->ftm2v;
}
-
diff --git a/src/USER-AWPMD/fix_nve_awpmd.h b/src/USER-AWPMD/fix_nve_awpmd.h
index 9bc6d3ebb8ba856c4531e243764922d5c8c34cdd..364196c1f8694f5a9bdd857023873cad1bb54ec0 100644
--- a/src/USER-AWPMD/fix_nve_awpmd.h
+++ b/src/USER-AWPMD/fix_nve_awpmd.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-AWPMD/pair_awpmd_cut.cpp b/src/USER-AWPMD/pair_awpmd_cut.cpp
index 4644f1a2ce53789413e0022384fcec85b0c3441d..da7825398e4fd33a1499f763d1d94486fd3709ce 100644
--- a/src/USER-AWPMD/pair_awpmd_cut.cpp
+++ b/src/USER-AWPMD/pair_awpmd_cut.cpp
@@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
-
+
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
-
+
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@@ -92,7 +92,7 @@ struct cmp_x{
d=xx[left.second][2]-xx[right.second][2];
if(d<-tol)
return true;
- else
+ else
return false;
}
else
@@ -104,13 +104,13 @@ struct cmp_x{
void PairAWPMDCut::compute(int eflag, int vflag)
{
-
+
// pvector = [KE, Pauli, ecoul, radial_restraint]
for (int i=0; i<4; i++) pvector[i] = 0.0;
- if (eflag || vflag)
+ if (eflag || vflag)
ev_setup(eflag,vflag);
- else
+ else
evflag = vflag_fdotr = 0; //??
double **x = atom->x;
@@ -118,7 +118,7 @@ void PairAWPMDCut::compute(int eflag, int vflag)
double *q = atom->q;
double *erforce = atom->erforce;
double *eradius = atom->eradius;
- int *spin = atom->spin;
+ int *spin = atom->spin;
int *type = atom->type;
int *etag = atom->etag;
double **v = atom->v;
@@ -135,15 +135,15 @@ void PairAWPMDCut::compute(int eflag, int vflag)
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
-
-
+
+
// width pbc
if(width_pbc<0)
wpmd->Lextra=2*half_box_length;
- else
+ else
wpmd->Lextra=width_pbc;
-
+
wpmd->newton_pair=newton_pair;
@@ -151,7 +151,7 @@ void PairAWPMDCut::compute(int eflag, int vflag)
# if 1
// mapping of the LAMMPS numbers to the AWPMC numbers
vector<int> gmap(ntot,-1);
-
+
for (int ii = 0; ii < inum; ii++) {
int i = ilist[ii];
// local particles are all there
@@ -168,19 +168,19 @@ void PairAWPMDCut::compute(int eflag, int vflag)
int jtype = type[j];
double rsq=(ri-rj).norm2();
if (rsq < cutsq[itype][jtype])
- gmap[j]=0; //bingo, this ghost is really needed
-
+ gmap[j]=0; //bingo, this ghost is really needed
+
}
}
}
-
-# else // old mapping
+
+# else // old mapping
// mapping of the LAMMPS numbers to the AWPMC numbers
vector<int> gmap(ntot,-1);
// map for filtering the clones out: [tag,image] -> id
typedef map< pair<int,int>, int, cmp_x > map_t;
cmp_x cmp(x);
- map_t idmap(cmp);
+ map_t idmap(cmp);
for (int ii = 0; ii < inum; ii++) {
int i = ilist[ii];
// local particles are all there
@@ -205,7 +205,7 @@ void PairAWPMDCut::compute(int eflag, int vflag)
gmap[j]=-1; // filter out
continue;
}
-
+
bool j_local= j<nlocal ? true : false;
if((i_local && !j_local) || (j_local && !i_local)){ // some of them is a ghost
Vector_3 rj=Vector_3(x[j][0],x[j][1],x[j][2]);
@@ -217,7 +217,7 @@ void PairAWPMDCut::compute(int eflag, int vflag)
break; // don't need to continue j loop
}
else
- gmap[j]=0; //bingo, this ghost is really needed
+ gmap[j]=0; //bingo, this ghost is really needed
}
}
}
@@ -231,11 +231,11 @@ void PairAWPMDCut::compute(int eflag, int vflag)
for (int i = 0; i < ntot; i++) {
//int i = ilist[ii];
if(gmap[i]<0) // this particle was filtered out
- continue;
+ continue;
if(spin[i]==0) // this is an ion
gmap[i]=wpmd->add_ion(q[i], Vector_3(x[i][0],x[i][1],x[i][2]),i<nlocal ? atom->tag[i] : -atom->tag[i]);
else if(spin[i]==1 || spin[i]==-1){ // electron, sort them according to the tag
- etmap[etag[i]].push_back(i);
+ etmap[etag[i]].push_back(i);
}
else
error->all(FLERR,fmt("Invalid spin value (%d) for particle %d !",spin[i],i));
@@ -245,7 +245,7 @@ void PairAWPMDCut::compute(int eflag, int vflag)
if(wpmd->ni)
fi= new Vector_3[wpmd->ni];
- // adding electrons
+ // adding electrons
for(map<int,vector<int> >::iterator it=etmap.begin(); it!= etmap.end(); ++it){
vector<int> &el=it->second;
if(!el.size()) // should not happen
@@ -276,7 +276,7 @@ void PairAWPMDCut::compute(int eflag, int vflag)
for (int ii = 0; ii < inum; ii++) {
int i = ilist[ii];
if(gmap[i]<0) // this particle was filtered out
- continue;
+ continue;
if(spin[i]==0){ // this is an ion, copying forces
int ion=gmap[i];
f[i][0]=fi[ion][0];
@@ -286,8 +286,8 @@ void PairAWPMDCut::compute(int eflag, int vflag)
else { // electron
int iel=gmap[i];
int s=spin[i] >0 ? 0 : 1;
- wpmd->get_wp_force(s,iel,(Vector_3 *)f[i],(Vector_3 *)(atom->vforce+3*i),atom->erforce+i,atom->ervelforce+i,(Vector_2 *)(atom->csforce+2*i));
- }
+ wpmd->get_wp_force(s,iel,(Vector_3 *)f[i],(Vector_3 *)(atom->vforce+3*i),atom->erforce+i,atom->ervelforce+i,(Vector_2 *)(atom->csforce+2*i));
+ }
}
if(fi)
@@ -295,7 +295,7 @@ void PairAWPMDCut::compute(int eflag, int vflag)
// update LAMMPS energy
if (eflag_either) {
- if (eflag_global){
+ if (eflag_global){
eng_coul+= wpmd->get_energy();
// pvector = [KE, Pauli, ecoul, radial_restraint]
pvector[0] = wpmd->Ee[0]+wpmd->Ee[1];
@@ -303,12 +303,12 @@ void PairAWPMDCut::compute(int eflag, int vflag)
pvector[1] = pvector[0] + pvector[2] - wpmd->Edk - wpmd->Edc - wpmd->Eii; // All except diagonal terms
pvector[3] = wpmd->Ew;
}
-
+
if (eflag_atom) {
// transfer per-atom energies here
for (int i = 0; i < ntot; i++) {
if(gmap[i]<0) // this particle was filtered out
- continue;
+ continue;
if(spin[i]==0){
eatom[i]=wpmd->Eiep[gmap[i]]+wpmd->Eiip[gmap[i]];
}
@@ -321,10 +321,10 @@ void PairAWPMDCut::compute(int eflag, int vflag)
}
if (vflag_fdotr) {
virial_fdotr_compute();
- if (flexible_pressure_flag)
+ if (flexible_pressure_flag)
virial_eradius_compute();
}
-}
+}
/* ----------------------------------------------------------------------
electron width-specific contribution to global virial
@@ -338,7 +338,7 @@ void PairAWPMDCut::virial_eradius_compute()
int *spin = atom->spin;
// sum over force on all particles including ghosts
-
+
if (neighbor->includegroup == 0) {
int nall = atom->nlocal + atom->nghost;
for (int i = 0; i < nall; i++) {
@@ -349,10 +349,10 @@ void PairAWPMDCut::virial_eradius_compute()
virial[2] += e_virial;
}
}
-
+
// neighbor includegroup flag is set
// sum over force on initial nfirst particles and ghosts
-
+
} else {
int nall = atom->nfirst;
for (int i = 0; i < nall; i++) {
@@ -363,7 +363,7 @@ void PairAWPMDCut::virial_eradius_compute()
virial[2] += e_virial;
}
}
-
+
nall = atom->nlocal + atom->nghost;
for (int i = atom->nlocal; i < nall; i++) {
if (spin[i]) {
@@ -386,12 +386,12 @@ void PairAWPMDCut::allocate()
{
allocated = 1;
int n = atom->ntypes;
-
+
memory->create(setflag,n+1,n+1,"pair:setflag");
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
-
+
memory->create(cutsq,n+1,n+1,"pair:cutsq");
memory->create(cut,n+1,n+1,"pair:cut");
}
@@ -407,11 +407,11 @@ void PairAWPMDCut::allocate()
// [flex_press] -- set flexible pressure flag
// -1 for length means default setting (L/2 for cutoff and L for width PBC)
-void PairAWPMDCut::settings(int narg, char **arg){
+void PairAWPMDCut::settings(int narg, char **arg){
if (narg < 1) error->all(FLERR,"Illegal pair_style command");
cut_global = force->numeric(arg[0]);
-
+
ermscale=1.;
width_pbc=0.;
@@ -465,7 +465,7 @@ void PairAWPMDCut::settings(int narg, char **arg){
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
- if (setflag[i][j]) cut[i][j] = cut_global;
+ if (setflag[i][j]) cut[i][j] = cut_global;
}*/
}
@@ -476,8 +476,8 @@ void PairAWPMDCut::settings(int narg, char **arg){
void PairAWPMDCut::coeff(int narg, char **arg)
{
if (narg < 2 || narg > 3) error->all(FLERR,"Incorrect args for pair coefficients");
-
- /*if(domain->xperiodic == 1 || domain->yperiodic == 1 ||
+
+ /*if(domain->xperiodic == 1 || domain->yperiodic == 1 ||
domain->zperiodic == 1) {*/
double delx = domain->boxhi[0]-domain->boxlo[0];
double dely = domain->boxhi[1]-domain->boxlo[1];
@@ -487,22 +487,22 @@ void PairAWPMDCut::coeff(int narg, char **arg)
if(cut_global<0)
cut_global=half_box_length;
- if (!allocated)
+ if (!allocated)
allocate();
else{
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
- if (setflag[i][j]) cut[i][j] = cut_global;
+ if (setflag[i][j]) cut[i][j] = cut_global;
}
-
+
int ilo,ihi,jlo,jhi;
force->bounds(arg[0],atom->ntypes,ilo,ihi);
force->bounds(arg[1],atom->ntypes,jlo,jhi);
-
+
double cut_one = cut_global;
if (narg == 3) cut_one = atof(arg[2]);
-
+
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
@@ -511,7 +511,7 @@ void PairAWPMDCut::coeff(int narg, char **arg)
count++;
}
}
-
+
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
@@ -523,10 +523,10 @@ void PairAWPMDCut::init_style()
{
// error and warning checks
- if (!atom->q_flag || !atom->spin_flag ||
+ if (!atom->q_flag || !atom->spin_flag ||
!atom->eradius_flag || !atom->erforce_flag ) // TO DO: adjust this to match approximation used
error->all(FLERR,"Pair awpmd/cut requires atom attributes "
- "q, spin, eradius, erforce");
+ "q, spin, eradius, erforce");
/*
if(vflag_atom){ // can't compute virial per atom
@@ -536,32 +536,32 @@ void PairAWPMDCut::init_style()
// add hook to minimizer for eradius and erforce
- if (update->whichflag == 2)
+ if (update->whichflag == 2)
int ignore = update->minimize->request(this,1,0.01);
// make sure to use the appropriate timestep when using real units
- /*if (update->whichflag == 1) {
+ /*if (update->whichflag == 1) {
if (force->qqr2e == 332.06371 && update->dt == 1.0)
error->all(FLERR,"You must lower the default real units timestep for pEFF ");
}*/
// need a half neigh list and optionally a granular history neigh list
-
+
//int irequest = neighbor->request(this);
//if (atom->tag_enable == 0)
// error->all(FLERR,"Pair style reax requires atom IDs");
-
+
//if (force->newton_pair == 0)
//error->all(FLERR,"Pair style awpmd requires newton pair on");
-
+
//if (strcmp(update->unit_style,"real") != 0 && comm->me == 0)
//error->warning(FLERR,"Not using real units with pair reax");
int irequest = neighbor->request(this);
neighbor->requests[irequest]->newton = 2;
-
+
if(force->e_mass==0. || force->hhmrr2e==0. || force->mvh2r==0.)
error->all(FLERR,"Pair style awpmd requires e_mass and conversions hhmrr2e, mvh2r to be properly set for unit system");
@@ -581,7 +581,7 @@ double PairAWPMDCut::init_one(int i, int j)
{
if (setflag[i][j] == 0)
cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
-
+
return cut[i][j];
}
@@ -592,7 +592,7 @@ double PairAWPMDCut::init_one(int i, int j)
void PairAWPMDCut::write_restart(FILE *fp)
{
write_restart_settings(fp);
-
+
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
@@ -609,7 +609,7 @@ void PairAWPMDCut::read_restart(FILE *fp)
{
read_restart_settings(fp);
allocate();
-
+
int i,j;
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
@@ -617,8 +617,8 @@ void PairAWPMDCut::read_restart(FILE *fp)
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
- if (me == 0) fread(&cut[i][j],sizeof(double),1,fp);
- MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
+ if (me == 0) fread(&cut[i][j],sizeof(double),1,fp);
+ MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
@@ -724,7 +724,7 @@ void PairAWPMDCut::min_x_set(int ignore)
double **v=atom->v;
double *ervel=atom->ervel;
double *cs=atom->cs;
-
+
int *spin = atom->spin;
int nlocal = atom->nlocal;
@@ -741,7 +741,7 @@ void PairAWPMDCut::min_x_set(int ignore)
}
/* ----------------------------------------------------------------------
- memory usage of local atom-based arrays
+ memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double PairAWPMDCut::memory_usage()
diff --git a/src/USER-AWPMD/pair_awpmd_cut.h b/src/USER-AWPMD/pair_awpmd_cut.h
index b1511d449aa66fce17147bbf6436abc9391d06ec..96a2b16fa11d773b5672133aa74a41b260ae7eb1 100644
--- a/src/USER-AWPMD/pair_awpmd_cut.h
+++ b/src/USER-AWPMD/pair_awpmd_cut.h
@@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
-
+
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
-
+
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
@@ -47,34 +47,34 @@ class PairAWPMDCut : public Pair {
void read_restart(FILE *);
virtual void write_restart_settings(FILE *);
virtual void read_restart_settings(FILE *);
-
+
void min_xf_pointers(int, double **, double **);
void min_xf_get(int);
void min_x_set(int);
double memory_usage();
private:
-
+
int flexible_pressure_flag;
double cut_global;
double **cut;
-
-
+
+
int nmax; // number of additional variables for minimizer
double *min_var,*min_varforce; // additional variables for minimizer
void allocate();
void virial_eradius_compute();
-
+
AWPMD_split *wpmd; // solver oblect
double ermscale; // scale of width mass for motion
double width_pbc; // setting for width pbc
double half_box_length; // calculated by coeff function
};
-
+
}
#endif
diff --git a/src/USER-CG-CMM/angle_cg_cmm.cpp b/src/USER-CG-CMM/angle_cg_cmm.cpp
index 070d65c5b8d4b6bd289b42eb416f06f84c5067d3..f147a8723777efe3d87e8963b61fba1b9fd611cf 100644
--- a/src/USER-CG-CMM/angle_cg_cmm.cpp
+++ b/src/USER-CG-CMM/angle_cg_cmm.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -54,7 +54,7 @@ AngleCGCMM::~AngleCGCMM()
/* ---------------------------------------------------------------------- */
-void AngleCGCMM::ev_tally_lj13(int i, int j, int nlocal, int newton_bond,
+void AngleCGCMM::ev_tally_lj13(int i, int j, int nlocal, int newton_bond,
double evdwl, double fpair,
double delx, double dely, double delz)
{
@@ -76,7 +76,7 @@ void AngleCGCMM::ev_tally_lj13(int i, int j, int nlocal, int newton_bond,
if (newton_bond || j < nlocal) eatom[i] += 0.5*evdwl;
}
}
-
+
if (vflag_either) {
v[0] = delx*delx*fpair;
v[1] = dely*dely*fpair;
@@ -185,15 +185,15 @@ void AngleCGCMM::compute(int eflag, int vflag)
c = delx1*delx2 + dely1*dely2 + delz1*delz2;
c /= r1*r2;
-
+
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
-
+
s = sqrt(1.0 - c*c);
if (s < SMALL) s = SMALL;
s = 1.0/s;
- // 1-3 LJ interaction.
+ // 1-3 LJ interaction.
// we only want to use the repulsive part,
// so this has to be done here and not in the
// general non-bonded code.
@@ -206,20 +206,20 @@ void AngleCGCMM::compute(int eflag, int vflag)
f13=0.0;
e13=0.0;
-
+
if (r3 < rcut[type]) {
const int cgt = cg_type[type];
const double cgpow1 = cg_pow1[cgt];
const double cgpow2 = cg_pow2[cgt];
const double cgpref = cg_prefact[cgt];
-
+
const double ratio = sigma[type]/r3;
const double eps = epsilon[type];
- f13 = cgpref*eps / rsq3 * (cgpow1*pow(ratio,cgpow1)
+ f13 = cgpref*eps / rsq3 * (cgpow1*pow(ratio,cgpow1)
- cgpow2*pow(ratio,cgpow2));
- if (eflag) e13 = eps + cgpref*eps * (pow(ratio,cgpow1)
+ if (eflag) e13 = eps + cgpref*eps * (pow(ratio,cgpow1)
- pow(ratio,cgpow2));
}
@@ -264,7 +264,7 @@ void AngleCGCMM::compute(int eflag, int vflag)
}
if (evflag) ev_tally(i1,i2,i3,nlocal,newton_bond,eangle,f1,f3,
- delx1,dely1,delz1,delx2,dely2,delz2);
+ delx1,dely1,delz1,delx2,dely2,delz2);
if (evflag) ev_tally_lj13(i1,i3,nlocal,newton_bond,
e13,f13,delx3,dely3,delz3);
@@ -310,7 +310,7 @@ void AngleCGCMM::coeff(int narg, char **arg)
int cg_type_one=find_cg_type(arg[3]);
if (cg_type_one == CG_NOT_SET) error->all(FLERR,"Error reading CG type flag.");
-
+
double epsilon_one = atof(arg[4]);
double sigma_one = atof(arg[5]);
@@ -328,7 +328,7 @@ void AngleCGCMM::coeff(int narg, char **arg)
theta0[i] = theta0_one/180.0 * MY_PI;
epsilon[i] = epsilon_one;
sigma[i] = sigma_one;
- rcut[i] = rcut_one;
+ rcut[i] = rcut_one;
cg_type[i] = cg_type_one;
setflag[i] = 1;
count++;
@@ -359,7 +359,7 @@ void AngleCGCMM::write_restart(FILE *fp)
}
/* ----------------------------------------------------------------------
- proc 0 reads coeffs from restart file, bcasts them
+ proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void AngleCGCMM::read_restart(FILE *fp)
@@ -395,7 +395,7 @@ double AngleCGCMM::single(int type, int i1, int i2, int i3)
double delz1 = x[i1][2] - x[i2][2];
domain->minimum_image(delx1,dely1,delz1);
double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1);
-
+
double delx2 = x[i3][0] - x[i2][0];
double dely2 = x[i3][1] - x[i2][1];
double delz2 = x[i3][2] - x[i2][2];
@@ -407,7 +407,7 @@ double AngleCGCMM::single(int type, int i1, int i2, int i3)
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
- // 1-3 LJ interaction.
+ // 1-3 LJ interaction.
double delx3 = x[i1][0] - x[i3][0];
double dely3 = x[i1][1] - x[i3][1];
double delz3 = x[i1][2] - x[i3][2];
@@ -416,17 +416,17 @@ double AngleCGCMM::single(int type, int i1, int i2, int i3)
const double r3 = sqrt(delx3*delx3 + dely3*dely3 + delz3*delz3);
double e13=0.0;
-
+
if (r3 < rcut[type]) {
const int cgt = cg_type[type];
const double cgpow1 = cg_pow1[cgt];
const double cgpow2 = cg_pow2[cgt];
const double cgpref = cg_prefact[cgt];
-
+
const double ratio = sigma[type]/r3;
const double eps = epsilon[type];
- e13 = eps + cgpref*eps * (pow(ratio,cgpow1)
+ e13 = eps + cgpref*eps * (pow(ratio,cgpow1)
- pow(ratio,cgpow2));
}
diff --git a/src/USER-CG-CMM/angle_cg_cmm.h b/src/USER-CG-CMM/angle_cg_cmm.h
index 506041584271124b82d7a6d0df4cbe331e670709..fa467ab0d7faee00afcc21f571c41664fbf983cb 100644
--- a/src/USER-CG-CMM/angle_cg_cmm.h
+++ b/src/USER-CG-CMM/angle_cg_cmm.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -38,9 +38,9 @@ class AngleCGCMM : public Angle, public CGCMMParms {
double single(int, int, int, int);
protected:
- void ev_tally_lj13(int, int, int, int, double, double,
+ void ev_tally_lj13(int, int, int, int, double, double,
double, double, double);
-
+
private:
double *k,*theta0;
int *cg_type;
diff --git a/src/USER-CG-CMM/angle_sdk.cpp b/src/USER-CG-CMM/angle_sdk.cpp
index bc6deef88cebc333c9df539cd19b88a52b2b5974..35c4416af19a906eebf727f0ec08d4f429c5747e 100644
--- a/src/USER-CG-CMM/angle_sdk.cpp
+++ b/src/USER-CG-CMM/angle_sdk.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -107,15 +107,15 @@ void AngleSDK::compute(int eflag, int vflag)
c = delx1*delx2 + dely1*dely2 + delz1*delz2;
c /= r1*r2;
-
+
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
-
+
s = sqrt(1.0 - c*c);
if (s < SMALL) s = SMALL;
s = 1.0/s;
- // 1-3 LJ interaction.
+ // 1-3 LJ interaction.
// we only want to use the repulsive part,
// and it can be scaled (or off).
// so this has to be done here and not in the
@@ -124,7 +124,7 @@ void AngleSDK::compute(int eflag, int vflag)
f13 = e13 = delx3 = dely3 = delz3 = 0.0;
if (repflag) {
-
+
delx3 = x[i1][0] - x[i3][0];
dely3 = x[i1][1] - x[i3][1];
delz3 = x[i1][2] - x[i3][2];
@@ -133,38 +133,38 @@ void AngleSDK::compute(int eflag, int vflag)
const int type1 = atom->type[i1];
const int type3 = atom->type[i3];
-
+
f13=0.0;
e13=0.0;
-
+
if (rsq3 < rminsq[type1][type3]) {
- const int ljt = lj_type[type1][type3];
- const double r2inv = 1.0/rsq3;
+ const int ljt = lj_type[type1][type3];
+ const double r2inv = 1.0/rsq3;
+
+ if (ljt == LJ12_4) {
+ const double r4inv=r2inv*r2inv;
- if (ljt == LJ12_4) {
- const double r4inv=r2inv*r2inv;
+ f13 = r4inv*(lj1[type1][type3]*r4inv*r4inv - lj2[type1][type3]);
+ if (eflag) e13 = r4inv*(lj3[type1][type3]*r4inv*r4inv - lj4[type1][type3]);
- f13 = r4inv*(lj1[type1][type3]*r4inv*r4inv - lj2[type1][type3]);
- if (eflag) e13 = r4inv*(lj3[type1][type3]*r4inv*r4inv - lj4[type1][type3]);
-
- } else if (ljt == LJ9_6) {
- const double r3inv = r2inv*sqrt(r2inv);
- const double r6inv = r3inv*r3inv;
+ } else if (ljt == LJ9_6) {
+ const double r3inv = r2inv*sqrt(r2inv);
+ const double r6inv = r3inv*r3inv;
- f13 = r6inv*(lj1[type1][type3]*r3inv - lj2[type1][type3]);
- if (eflag) e13 = r6inv*(lj3[type1][type3]*r3inv - lj4[type1][type3]);
+ f13 = r6inv*(lj1[type1][type3]*r3inv - lj2[type1][type3]);
+ if (eflag) e13 = r6inv*(lj3[type1][type3]*r3inv - lj4[type1][type3]);
- } else if (ljt == LJ12_6) {
- const double r6inv = r2inv*r2inv*r2inv;
+ } else if (ljt == LJ12_6) {
+ const double r6inv = r2inv*r2inv*r2inv;
- f13 = r6inv*(lj1[type1][type3]*r6inv - lj2[type1][type3]);
- if (eflag) e13 = r6inv*(lj3[type1][type3]*r6inv - lj4[type1][type3]);
- }
+ f13 = r6inv*(lj1[type1][type3]*r6inv - lj2[type1][type3]);
+ if (eflag) e13 = r6inv*(lj3[type1][type3]*r6inv - lj4[type1][type3]);
+ }
- // make sure energy is 0.0 at the cutoff.
- if (eflag) e13 -= emin[type1][type3];
+ // make sure energy is 0.0 at the cutoff.
+ if (eflag) e13 -= emin[type1][type3];
- f13 *= r2inv;
+ f13 *= r2inv;
}
}
@@ -209,9 +209,9 @@ void AngleSDK::compute(int eflag, int vflag)
if (evflag) {
ev_tally(i1,i2,i3,nlocal,newton_bond,eangle,f1,f3,
- delx1,dely1,delz1,delx2,dely2,delz2);
+ delx1,dely1,delz1,delx2,dely2,delz2);
if (repflag)
- ev_tally13(i1,i3,nlocal,newton_bond,e13,f13,delx3,dely3,delz3);
+ ev_tally13(i1,i3,nlocal,newton_bond,e13,f13,delx3,dely3,delz3);
}
}
}
@@ -252,7 +252,7 @@ void AngleSDK::coeff(int narg, char **arg)
// backward compatibility with old cg/cmm style input:
// this had <lj_type> <epsilon> <sigma>
// if epsilon is set to 0.0 we accept it as repscale 0.0
- // otherwise assume repscale 1.0, since we were using
+ // otherwise assume repscale 1.0, since we were using
// epsilon to turn repulsion on or off.
if (narg == 6) {
repscale_one = force->numeric(arg[4]);
@@ -276,7 +276,7 @@ void AngleSDK::coeff(int narg, char **arg)
}
/* ----------------------------------------------------------------------
- error check and initialize all values needed for force computation
+ error check and initialize all values needed for force computation
------------------------------------------------------------------------- */
void AngleSDK::init_style()
@@ -327,7 +327,7 @@ void AngleSDK::write_restart(FILE *fp)
}
/* ----------------------------------------------------------------------
- proc 0 reads coeffs from restart file, bcasts them
+ proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void AngleSDK::read_restart(FILE *fp)
@@ -348,9 +348,9 @@ void AngleSDK::read_restart(FILE *fp)
/* ---------------------------------------------------------------------- */
-void AngleSDK::ev_tally13(int i, int j, int nlocal, int newton_bond,
- double evdwl, double fpair,
- double delx, double dely, double delz)
+void AngleSDK::ev_tally13(int i, int j, int nlocal, int newton_bond,
+ double evdwl, double fpair,
+ double delx, double dely, double delz)
{
double v[6];
@@ -370,7 +370,7 @@ void AngleSDK::ev_tally13(int i, int j, int nlocal, int newton_bond,
if (newton_bond || j < nlocal) eatom[i] += 0.5*evdwl;
}
}
-
+
if (vflag_either) {
v[0] = delx*delx*fpair;
v[1] = dely*dely*fpair;
@@ -439,7 +439,7 @@ double AngleSDK::single(int type, int i1, int i2, int i3)
double delz1 = x[i1][2] - x[i2][2];
domain->minimum_image(delx1,dely1,delz1);
double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1);
-
+
double delx2 = x[i3][0] - x[i2][0];
double dely2 = x[i3][1] - x[i2][1];
double delz2 = x[i3][2] - x[i2][2];
@@ -454,7 +454,7 @@ double AngleSDK::single(int type, int i1, int i2, int i3)
double e13=0.0;
if (repflag) {
- // 1-3 LJ interaction.
+ // 1-3 LJ interaction.
double delx3 = x[i1][0] - x[i3][0];
double dely3 = x[i1][1] - x[i3][1];
double delz3 = x[i1][2] - x[i3][2];
@@ -462,28 +462,28 @@ double AngleSDK::single(int type, int i1, int i2, int i3)
const int type1 = atom->type[i1];
const int type3 = atom->type[i3];
-
+
const double rsq3 = delx3*delx3 + dely3*dely3 + delz3*delz3;
-
+
if (rsq3 < rminsq[type1][type3]) {
const int ljt = lj_type[type1][type3];
const double r2inv = 1.0/rsq3;
if (ljt == LJ12_4) {
- const double r4inv=r2inv*r2inv;
+ const double r4inv=r2inv*r2inv;
+
+ e13 = r4inv*(lj3[type1][type3]*r4inv*r4inv - lj4[type1][type3]);
- e13 = r4inv*(lj3[type1][type3]*r4inv*r4inv - lj4[type1][type3]);
-
} else if (ljt == LJ9_6) {
- const double r3inv = r2inv*sqrt(r2inv);
- const double r6inv = r3inv*r3inv;
+ const double r3inv = r2inv*sqrt(r2inv);
+ const double r6inv = r3inv*r3inv;
- e13 = r6inv*(lj3[type1][type3]*r3inv - lj4[type1][type3]);
+ e13 = r6inv*(lj3[type1][type3]*r3inv - lj4[type1][type3]);
} else if (ljt == LJ12_6) {
- const double r6inv = r2inv*r2inv*r2inv;
+ const double r6inv = r2inv*r2inv*r2inv;
- e13 = r6inv*(lj3[type1][type3]*r6inv - lj4[type1][type3]);
+ e13 = r6inv*(lj3[type1][type3]*r6inv - lj4[type1][type3]);
}
// make sure energy is 0.0 at the cutoff.
diff --git a/src/USER-CG-CMM/angle_sdk.h b/src/USER-CG-CMM/angle_sdk.h
index 91da40abeb03babeed673e83f6016d8bf2a17f5d..8dd7d737053340d2988dd8da3885f590680d6f6a 100644
--- a/src/USER-CG-CMM/angle_sdk.h
+++ b/src/USER-CG-CMM/angle_sdk.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -50,9 +50,9 @@ class AngleSDK : public Angle {
int repflag; // 1 if we have to handle 1-3 repulsion
- void ev_tally13(int, int, int, int, double, double,
- double, double, double);
-
+ void ev_tally13(int, int, int, int, double, double,
+ double, double, double);
+
void allocate();
};
diff --git a/src/USER-CG-CMM/cg_cmm_parms.cpp b/src/USER-CG-CMM/cg_cmm_parms.cpp
index 4483c550c8a9de8f0f0e036591490313c67de6e5..57decc68ec5a349f198ace3665c0462e3783a212 100644
--- a/src/USER-CG-CMM/cg_cmm_parms.cpp
+++ b/src/USER-CG-CMM/cg_cmm_parms.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-CG-CMM/cg_cmm_parms.h b/src/USER-CG-CMM/cg_cmm_parms.h
index f696759d7a585c431814e10801b285396c1780da..f14f8f797c82f493306c0091f97fc86e39e8c3e4 100644
--- a/src/USER-CG-CMM/cg_cmm_parms.h
+++ b/src/USER-CG-CMM/cg_cmm_parms.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-CG-CMM/lj_sdk_common.h b/src/USER-CG-CMM/lj_sdk_common.h
index 9b151b8a356e2bc297e84dad65ac54ff5d7be5aa..ddf14eb01f083498ce7056abb19a239cf13958d0 100644
--- a/src/USER-CG-CMM/lj_sdk_common.h
+++ b/src/USER-CG-CMM/lj_sdk_common.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -21,14 +21,14 @@
#include "string.h"
-namespace LAMMPS_NS {
+namespace LAMMPS_NS {
namespace LJSDKParms {
// LJ type flags. list of supported LJ exponent combinations
enum {LJ_NOT_SET=0, LJ9_6, LJ12_4, LJ12_6, NUM_LJ_TYPES};
static int find_lj_type(const char *label,
- const char * const * const list) {
+ const char * const * const list) {
for (int i=0; i < NUM_LJ_TYPES; ++i)
if (strcmp(label,list[i]) == 0) return i;
@@ -41,4 +41,3 @@ namespace LJSDKParms {
static const double lj_pow2[] = {0.0, 6.00, 4.0, 6.0};
}}
#endif
-
diff --git a/src/USER-CG-CMM/pair_cg_cmm.cpp b/src/USER-CG-CMM/pair_cg_cmm.cpp
index 3ff948d1a156b1269df69b291e18de28b35d49cc..03c792c3c34005fab12e5adb610034d11ae9b2c7 100644
--- a/src/USER-CG-CMM/pair_cg_cmm.cpp
+++ b/src/USER-CG-CMM/pair_cg_cmm.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -19,7 +19,7 @@
#include "pair_cg_cmm.h"
using namespace LAMMPS_NS;
-
+
/* ---------------------------------------------------------------------- */
PairCGCMM::PairCGCMM(LAMMPS *lmp) : PairCMMCommon(lmp)
@@ -39,9 +39,9 @@ PairCGCMM::~PairCGCMM()
/* ---------------------------------------------------------------------- *
* the real compute work is done in the PairCMMCommon::eval_XXX<>() templates
- * in the common PairCG class. Through using templates we can have one
- * implementation for all CG varieties _and_ gain speed through having
- * the compiler optimize away conditionals within the innerloops that
+ * in the common PairCG class. Through using templates we can have one
+ * implementation for all CG varieties _and_ gain speed through having
+ * the compiler optimize away conditionals within the innerloops that
* can be predetermined outside the loop through instantiation of the
* different combination of template flags.
* ---------------------------------------------------------------------- */
@@ -150,7 +150,7 @@ void PairCGCMM::compute_outer(int eflag, int vflag)
/* ---------------------------------------------------------------------- */
-void PairCGCMM::write_restart(FILE *fp)
+void PairCGCMM::write_restart(FILE *fp)
{
write_restart_settings(fp);
PairCMMCommon::write_restart(fp);
@@ -168,7 +168,7 @@ void PairCGCMM::read_restart(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairCGCMM::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj, double &fforce)
+ double factor_coul, double factor_lj, double &fforce)
{
return eval_single(CG_COUL_NONE,i,j,itype,jtype,rsq,factor_coul,factor_lj,fforce);
}
diff --git a/src/USER-CG-CMM/pair_cg_cmm.h b/src/USER-CG-CMM/pair_cg_cmm.h
index 74eee884e3c4192b1111664e6794809672da65f0..fe24321587e791236a9e572b744f8652e2d358ab 100644
--- a/src/USER-CG-CMM/pair_cg_cmm.h
+++ b/src/USER-CG-CMM/pair_cg_cmm.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-CG-CMM/pair_cg_cmm_coul_cut.cpp b/src/USER-CG-CMM/pair_cg_cmm_coul_cut.cpp
index 10cee8919b22faec714246ae573b76a2b9cb6e14..211a07050182097f831dd9a91b33664eb2886a44 100644
--- a/src/USER-CG-CMM/pair_cg_cmm_coul_cut.cpp
+++ b/src/USER-CG-CMM/pair_cg_cmm_coul_cut.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -92,9 +92,9 @@ double PairCGCMMCoulCut::init_one(int i, int j)
/* ---------------------------------------------------------------------- *
* the real compute work is done in the PairCMMCommon::eval_XXX<>() templates
- * in the common PairCG class. Through using templates we can have one
- * implementation for all CG varieties _and_ gain speed through having
- * the compiler optimize away conditionals within the innerloops that
+ * in the common PairCG class. Through using templates we can have one
+ * implementation for all CG varieties _and_ gain speed through having
+ * the compiler optimize away conditionals within the innerloops that
* can be predetermined outside the loop through instantiation of the
* different combination of template flags.
* ---------------------------------------------------------------------- */
@@ -203,7 +203,7 @@ void PairCGCMMCoulCut::compute_outer(int eflag, int vflag)
/* ---------------------------------------------------------------------- */
-void PairCGCMMCoulCut::write_restart(FILE *fp)
+void PairCGCMMCoulCut::write_restart(FILE *fp)
{
write_restart_settings(fp);
PairCMMCommon::write_restart(fp);
@@ -223,19 +223,19 @@ void PairCGCMMCoulCut::read_restart(FILE *fp)
double PairCGCMMCoulCut::memory_usage()
{
double bytes=PairCMMCommon::memory_usage();
-
+
int n = atom->ntypes;
// cut_coul/cut_coulsq/cut_lj/cut_ljsq;
- bytes += (n+1)*(n+1)*sizeof(double)*4;
-
+ bytes += (n+1)*(n+1)*sizeof(double)*4;
+
return bytes;
}
/* ---------------------------------------------------------------------- */
double PairCGCMMCoulCut::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj, double &fforce)
+ double factor_coul, double factor_lj, double &fforce)
{
return eval_single(CG_COUL_CUT,i,j,itype,jtype,rsq,factor_coul,factor_lj,fforce);
}
diff --git a/src/USER-CG-CMM/pair_cg_cmm_coul_cut.h b/src/USER-CG-CMM/pair_cg_cmm_coul_cut.h
index 2732fa4d523d6917c71c7ab49897fb3a3e75f1a6..418ee2674fec597c2d5a01bcab641a2d94b1895e 100644
--- a/src/USER-CG-CMM/pair_cg_cmm_coul_cut.h
+++ b/src/USER-CG-CMM/pair_cg_cmm_coul_cut.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-CG-CMM/pair_cg_cmm_coul_long.cpp b/src/USER-CG-CMM/pair_cg_cmm_coul_long.cpp
index 89eda915f18592e98aba8950c191143f74de9348..a13f316ac01711f2945e7ceda28ebca577889484 100644
--- a/src/USER-CG-CMM/pair_cg_cmm_coul_long.cpp
+++ b/src/USER-CG-CMM/pair_cg_cmm_coul_long.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -90,7 +90,7 @@ void PairCGCMMCoulLong::init_style()
{
if (!atom->q_flag)
error->all(FLERR,"Pair style cg/cut/coul/long requires atom attribute q");
-
+
PairCMMCommon::init_style();
// set rRESPA cutoffs
@@ -102,7 +102,7 @@ void PairCGCMMCoulLong::init_style()
// ensure use of KSpace long-range solver, set g_ewald
- if (force->kspace == NULL)
+ if (force->kspace == NULL)
error->all(FLERR,"Pair style is incompatible with KSpace style");
g_ewald = force->kspace->g_ewald;
@@ -136,16 +136,16 @@ void PairCGCMMCoulLong::init_tables()
tabinnersq = tabinner*tabinner;
init_bitmap(tabinner,cut_coul_global,ncoultablebits,
masklo,maskhi,ncoulmask,ncoulshiftbits);
-
+
int ntable = 1;
for (int i = 0; i < ncoultablebits; i++) ntable *= 2;
-
+
// linear lookup tables of length N = 2^ncoultablebits
// stored value = value at lower edge of bin
// d values = delta from lower edge to upper edge of bin
if (ftable) free_tables();
-
+
memory->create(rtable,ntable,"pair:rtable");
memory->create(ftable,ntable,"pair:ftable");
memory->create(ctable,ntable,"pair:ctable");
@@ -194,7 +194,7 @@ void PairCGCMMCoulLong::init_tables()
vtable[i] = qqrd2e/r * (derfc + EWALD_F*grij*expm2);
if (rsq_lookup.f > cut_respa[2]*cut_respa[2]) {
if (rsq_lookup.f < cut_respa[3]*cut_respa[3]) {
- rsw = (r - cut_respa[2])/(cut_respa[3] - cut_respa[2]);
+ rsw = (r - cut_respa[2])/(cut_respa[3] - cut_respa[2]);
ftable[i] += qqrd2e/r * rsw*rsw*(3.0 - 2.0*rsw);
ctable[i] = qqrd2e/r * rsw*rsw*(3.0 - 2.0*rsw);
} else {
@@ -206,9 +206,9 @@ void PairCGCMMCoulLong::init_tables()
minrsq_lookup.f = MIN(minrsq_lookup.f,rsq_lookup.f);
}
tabinnersq = minrsq_lookup.f;
-
+
int ntablem1 = ntable - 1;
-
+
for (int i = 0; i < ntablem1; i++) {
drtable[i] = 1.0/(rtable[i+1] - rtable[i]);
dftable[i] = ftable[i+1] - ftable[i];
@@ -222,10 +222,10 @@ void PairCGCMMCoulLong::init_tables()
dptable[i] = ptable[i+1] - ptable[i];
}
}
-
- // get the delta values for the last table entries
+
+ // get the delta values for the last table entries
// tables are connected periodically between 0 and ntablem1
-
+
drtable[ntablem1] = 1.0/(rtable[0] - rtable[ntablem1]);
dftable[ntablem1] = ftable[0] - ftable[ntablem1];
dctable[ntablem1] = ctable[0] - ctable[ntablem1];
@@ -235,22 +235,22 @@ void PairCGCMMCoulLong::init_tables()
dptable[ntablem1] = ptable[0] - ptable[ntablem1];
}
- // get the correct delta values at itablemax
+ // get the correct delta values at itablemax
// smallest r is in bin itablemin
// largest r is in bin itablemax, which is itablemin-1,
// or ntablem1 if itablemin=0
// deltas at itablemax only needed if corresponding rsq < cut*cut
- // if so, compute deltas between rsq and cut*cut
-
+ // if so, compute deltas between rsq and cut*cut
+
double f_tmp,c_tmp,e_tmp,p_tmp,v_tmp;
itablemin = minrsq_lookup.i & ncoulmask;
- itablemin >>= ncoulshiftbits;
- int itablemax = itablemin - 1;
- if (itablemin == 0) itablemax = ntablem1;
+ itablemin >>= ncoulshiftbits;
+ int itablemax = itablemin - 1;
+ if (itablemin == 0) itablemax = ntablem1;
rsq_lookup.i = itablemax << ncoulshiftbits;
rsq_lookup.i |= maskhi;
if (rsq_lookup.f < cut_coulsq_global) {
- rsq_lookup.f = cut_coulsq_global;
+ rsq_lookup.f = cut_coulsq_global;
r = sqrtf(rsq_lookup.f);
grij = g_ewald * r;
expm2 = exp(-grij*grij);
@@ -268,7 +268,7 @@ void PairCGCMMCoulLong::init_tables()
v_tmp = qqrd2e/r * (derfc + EWALD_F*grij*expm2);
if (rsq_lookup.f > cut_respa[2]*cut_respa[2]) {
if (rsq_lookup.f < cut_respa[3]*cut_respa[3]) {
- rsw = (r - cut_respa[2])/(cut_respa[3] - cut_respa[2]);
+ rsw = (r - cut_respa[2])/(cut_respa[3] - cut_respa[2]);
f_tmp += qqrd2e/r * rsw*rsw*(3.0 - 2.0*rsw);
c_tmp = qqrd2e/r * rsw*rsw*(3.0 - 2.0*rsw);
} else {
@@ -278,25 +278,25 @@ void PairCGCMMCoulLong::init_tables()
}
}
- drtable[itablemax] = 1.0/(rsq_lookup.f - rtable[itablemax]);
+ drtable[itablemax] = 1.0/(rsq_lookup.f - rtable[itablemax]);
dftable[itablemax] = f_tmp - ftable[itablemax];
dctable[itablemax] = c_tmp - ctable[itablemax];
detable[itablemax] = e_tmp - etable[itablemax];
if (cut_respa) {
dvtable[itablemax] = v_tmp - vtable[itablemax];
dptable[itablemax] = p_tmp - ptable[itablemax];
- }
+ }
}
-
+
}
/* ---------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- *
* the real compute work is done in the PairCMMCommon::eval_XXX<>() templates
- * in the common PairCG class. Through using templates we can have one
- * implementation for all CG varieties _and_ gain speed through having
- * the compiler optimize away conditionals within the innerloops that
+ * in the common PairCG class. Through using templates we can have one
+ * implementation for all CG varieties _and_ gain speed through having
+ * the compiler optimize away conditionals within the innerloops that
* can be predetermined outside the loop through instantiation of the
* different combination of template flags.
* ---------------------------------------------------------------------- */
@@ -405,7 +405,7 @@ void PairCGCMMCoulLong::compute_outer(int eflag, int vflag)
/* ---------------------------------------------------------------------- */
-void PairCGCMMCoulLong::write_restart(FILE *fp)
+void PairCGCMMCoulLong::write_restart(FILE *fp)
{
write_restart_settings(fp);
PairCMMCommon::write_restart(fp);
@@ -425,18 +425,18 @@ void PairCGCMMCoulLong::read_restart(FILE *fp)
double PairCGCMMCoulLong::memory_usage()
{
double bytes=PairCMMCommon::memory_usage();
-
+
int n = atom->ntypes;
// cut_coul/cut_coulsq/cut_ljsq
- bytes += (n+1)*(n+1)*sizeof(double)*4;
-
+ bytes += (n+1)*(n+1)*sizeof(double)*4;
+
return bytes;
}
/* ---------------------------------------------------------------------- */
-double PairCGCMMCoulLong::single(int i, int j, int itype, int jtype, double rsq,
+double PairCGCMMCoulLong::single(int i, int j, int itype, int jtype, double rsq,
double factor_coul, double factor_lj, double &fforce)
{
return eval_single(CG_COUL_LONG,i,j,itype,jtype,rsq,factor_coul,factor_lj,fforce);
diff --git a/src/USER-CG-CMM/pair_cg_cmm_coul_long.h b/src/USER-CG-CMM/pair_cg_cmm_coul_long.h
index ce1fa044bc35c38a2363ef3e1b59067be759ac74..cf05f389451883d2d0cd79cede2a09120dd768ff 100644
--- a/src/USER-CG-CMM/pair_cg_cmm_coul_long.h
+++ b/src/USER-CG-CMM/pair_cg_cmm_coul_long.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-CG-CMM/pair_cmm_common.cpp b/src/USER-CG-CMM/pair_cmm_common.cpp
index 4e1606d58762966313fb24d0301423a1c9e25a4e..f5f5f5799e066a44010d6d3568d6b2cf34bf39b8 100644
--- a/src/USER-CG-CMM/pair_cmm_common.cpp
+++ b/src/USER-CG-CMM/pair_cmm_common.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -38,7 +38,7 @@ PairCMMCommon::PairCMMCommon(class LAMMPS *lmp) : Pair(lmp)
allocated_coul = 0;
kappa = 0.0;
respa_enable = 0;
- single_enable = 0;
+ single_enable = 0;
}
/* ---------------------------------------------------------------------- *
@@ -73,7 +73,7 @@ void PairCMMCommon::allocate()
{
allocated = 1;
int n = atom->ntypes;
-
+
memory->create(setflag,n+1,n+1,"paircg:setflag");
memory->create(cg_type,n+1,n+1,"paircg:cg_type");
for (int i = 1; i <= n; i++) {
@@ -87,7 +87,7 @@ void PairCMMCommon::allocate()
memory->create(cutsq,n+1,n+1,"paircg:cutsq");
memory->create(epsilon,n+1,n+1,"paircg:epsilon");
memory->create(sigma,n+1,n+1,"paircg:sigma");
- memory->create(offset,n+1,n+1,"paircg:offset");
+ memory->create(offset,n+1,n+1,"paircg:offset");
memory->create(lj1,n+1,n+1,"paircg:lj1");
memory->create(lj2,n+1,n+1,"paircg:lj2");
@@ -96,7 +96,7 @@ void PairCMMCommon::allocate()
}
/* ----------------------------------------------------------------------
- global settings
+ global settings
------------------------------------------------------------------------- */
// arguments to the pair_style command (global version)
@@ -109,7 +109,7 @@ void PairCMMCommon::settings(int narg, char **arg)
if (narg == 1) cut_coul_global = cut_lj_global;
else cut_coul_global = force->numeric(arg[1]);
cut_coulsq_global = cut_coul_global*cut_coul_global;
-
+
// exponential coulomb screening (optional)
if (narg == 3) kappa = force->numeric(arg[2]);
if (fabs(kappa) < SMALL) kappa=0.0;
@@ -147,7 +147,7 @@ void PairCMMCommon::coeff(int narg, char **arg)
int cg_type_one=find_cg_type(arg[2]);
if (cg_type_one == CG_NOT_SET) error->all(FLERR,"Error reading CG type flag.");
-
+
double epsilon_one = force->numeric(arg[3]);
double sigma_one = force->numeric(arg[4]);
@@ -248,7 +248,7 @@ double PairCMMCommon::init_one(int i, int j)
if (cgt == CG_NOT_SET)
error->all(FLERR,"unrecognized LJ parameter flag");
-
+
lj1[i][j] = cg_prefact[cgt] * cg_pow1[cgt] * epsilon[i][j] * pow(sigma[i][j],cg_pow1[cgt]);
lj2[i][j] = cg_prefact[cgt] * cg_pow2[cgt] * epsilon[i][j] * pow(sigma[i][j],cg_pow2[cgt]);
lj3[i][j] = cg_prefact[cgt] * epsilon[i][j] * pow(sigma[i][j],cg_pow1[cgt]);
@@ -270,7 +270,7 @@ double PairCMMCommon::init_one(int i, int j)
offset[i][j] = cg_prefact[cgt] * epsilon[i][j] * (pow(ratio,cg_pow1[cgt]) - pow(ratio,cg_pow2[cgt]));
} else offset[i][j] = 0.0;
}
-
+
// make sure data is stored symmetrically
lj1[j][i] = lj1[i][j];
lj2[j][i] = lj2[i][j];
@@ -279,7 +279,7 @@ double PairCMMCommon::init_one(int i, int j)
offset[j][i] = offset[i][j];
cg_type[j][i] = cg_type[i][j];
cut[j][i] = mycut;
-
+
if (allocated_coul) {
cut_lj[j][i]=cut_lj[i][j];
cut_ljsq[j][i]=cut_ljsq[i][j];
@@ -303,24 +303,24 @@ double PairCMMCommon::init_one(int i, int j)
if (type[k] == j) count[1] += 1.0;
}
MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world);
-
+
double sig2 = sigma[i][j]*sigma[i][j];
double sig6 = sig2*sig2*sig2;
double rc3 = cut[i][j]*cut[i][j]*cut[i][j];
double rc6 = rc3*rc3;
double rc9 = rc3*rc6;
- etail_ij = 8.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
- sig6 * (sig6 - 3.0*rc6) / (9.0*rc9);
- ptail_ij = 16.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
- sig6 * (2.0*sig6 - 3.0*rc6) / (9.0*rc9);
+ etail_ij = 8.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
+ sig6 * (sig6 - 3.0*rc6) / (9.0*rc9);
+ ptail_ij = 16.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
+ sig6 * (2.0*sig6 - 3.0*rc6) / (9.0*rc9);
#endif
- }
+ }
return mycut;
}
/* ----------------------------------------------------------------------
- proc 0 writes to restart file
+ proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairCMMCommon::write_restart(FILE *fp)
@@ -419,41 +419,41 @@ void PairCMMCommon::read_restart_settings(FILE *fp)
double PairCMMCommon::memory_usage()
{
double bytes=Pair::memory_usage();
-
+
int n = atom->ntypes;
// setflag/cg_type
- bytes += (n+1)*(n+1)*sizeof(int)*2;
+ bytes += (n+1)*(n+1)*sizeof(int)*2;
// cut/cutsq/epsilon/sigma/offset/lj1/lj2/lj3/lj4
- bytes += (n+1)*(n+1)*sizeof(double)*9;
-
+ bytes += (n+1)*(n+1)*sizeof(double)*9;
+
return bytes;
}
/* ------------------------------------------------------------------------ */
-double PairCMMCommon::eval_single(int coul_type, int i, int j, int itype, int jtype,
- double rsq, double factor_coul, double factor_lj,
+double PairCMMCommon::eval_single(int coul_type, int i, int j, int itype, int jtype,
+ double rsq, double factor_coul, double factor_lj,
double &fforce)
{
double lj_force, lj_erg, coul_force, coul_erg;
lj_force=lj_erg=coul_force=coul_erg=0.0;
if (rsq < cut_ljsq[itype][jtype]) {
-
+
const int cgt = cg_type[itype][jtype];
const double cgpow1 = cg_pow1[cgt];
const double cgpow2 = cg_pow2[cgt];
const double cgpref = cg_prefact[cgt];
-
+
const double ratio = sigma[itype][jtype]/sqrt(rsq);
const double eps = epsilon[itype][jtype];
- lj_force = cgpref*eps * (cgpow1*pow(ratio,cgpow1)
+ lj_force = cgpref*eps * (cgpow1*pow(ratio,cgpow1)
- cgpow2*pow(ratio,cgpow2))/rsq;
lj_erg = cgpref*eps * (pow(ratio,cgpow1) - pow(ratio,cgpow2));
}
-
+
if (rsq < cut_coul[itype][jtype]) {
if(coul_type == CG_COUL_LONG) {
error->all(FLERR,"single energy computation with long-range coulomb not supported by CG potentials.");
diff --git a/src/USER-CG-CMM/pair_cmm_common.h b/src/USER-CG-CMM/pair_cmm_common.h
index 1b4fe1eb44849b3f205d20ea0273e1987b4a2022..9b5f3fbb2c579b2eea7a3d73fea225d81ccfc013 100644
--- a/src/USER-CG-CMM/pair_cmm_common.h
+++ b/src/USER-CG-CMM/pair_cmm_common.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -67,7 +67,7 @@ namespace LAMMPS_NS {
// coarse grain flags
int **cg_type;
-
+
// lennard jones parameters
double cut_lj_global, **cut, **cut_lj, **cut_ljsq;
double **epsilon, **sigma;
@@ -83,7 +83,7 @@ namespace LAMMPS_NS {
double *rtable,*drtable,*ftable,*dftable,*ctable,*dctable;
double *etable,*detable,*ptable,*dptable,*vtable,*dvtable;
int ncoulshiftbits,ncoulmask;
-
+
// r-RESPA parameters
double *cut_respa;
@@ -97,19 +97,19 @@ namespace LAMMPS_NS {
protected:
// general optimizeable real space loops
- template < const int EVFLAG, const int EFLAG,
- const int NEWTON_PAIR, const int COUL_TYPE >
+ template < const int EVFLAG, const int EFLAG,
+ const int NEWTON_PAIR, const int COUL_TYPE >
void eval_verlet();
- template < const int NEWTON_PAIR, const int COUL_TYPE >
+ template < const int NEWTON_PAIR, const int COUL_TYPE >
void eval_inner();
- template < const int NEWTON_PAIR, const int COUL_TYPE >
+ template < const int NEWTON_PAIR, const int COUL_TYPE >
void eval_middle();
- template < const int EVFLAG, const int EFLAG, const int VFLAG,
- const int NEWTON_PAIR, const int COUL_TYPE >
+ template < const int EVFLAG, const int EFLAG, const int VFLAG,
+ const int NEWTON_PAIR, const int COUL_TYPE >
void eval_outer();
// this one is not performance critical... no template needed.
- double eval_single(int, int, int, int, int,
+ double eval_single(int, int, int, int, int,
double, double, double, double &);
};
@@ -173,11 +173,11 @@ namespace LAMMPS_NS {
; \
} \
} \
-
-
- template < const int EVFLAG, const int EFLAG,
- const int NEWTON_PAIR, const int COUL_TYPE >
+
+
+ template < const int EVFLAG, const int EFLAG,
+ const int NEWTON_PAIR, const int COUL_TYPE >
void PairCMMCommon::eval_verlet()
{
double ** const x = atom->x;
@@ -194,7 +194,7 @@ namespace LAMMPS_NS {
const int * const ilist = list->ilist;
const int * const numneigh = list->numneigh;
int * const * const firstneigh = list->firstneigh;
-
+
// loop over neighbors of my atoms
int ii,jj;
@@ -211,9 +211,9 @@ namespace LAMMPS_NS {
for (jj = 0; jj < jnum; jj++) {
int j2 = jlist[jj];
- factor_lj = special_lj[sbmask(j2)];
- factor_coul = special_coul[sbmask(j2)];
- const int j = j2 & NEIGHMASK;
+ factor_lj = special_lj[sbmask(j2)];
+ factor_coul = special_coul[sbmask(j2)];
+ const int j = j2 & NEIGHMASK;
const double delx = xtmp - x[j][0];
const double dely = ytmp - x[j][1];
@@ -235,7 +235,7 @@ namespace LAMMPS_NS {
} else {
double forcelj = 0.0;
double forcecoul = 0.0;
-
+
if (rsq < cut_ljsq[itype][jtype]) {
CG_LJ_INNER(EFLAG,forcelj);
}
@@ -247,7 +247,7 @@ namespace LAMMPS_NS {
double qscreen=exp(-kappa*r);
forcecoul = factor_coul * qqrd2e
* qtmp * q[j] * qscreen * (kappa + 1.0/r);
- if (EFLAG) ecoul=factor_coul*qqrd2e
+ if (EFLAG) ecoul=factor_coul*qqrd2e
* qtmp*q[j] * qscreen / r;
}
}
@@ -256,7 +256,7 @@ namespace LAMMPS_NS {
if (rsq < cut_coulsq_global) {
if (!ncoultablebits || rsq <= tabinnersq) {
const double r = sqrt(rsq);
-
+
const double grij = g_ewald * r;
const double expm2 = exp(-grij*grij);
const double t = 1.0 / (1.0 + EWALD_P*grij);
@@ -309,7 +309,7 @@ namespace LAMMPS_NS {
/* ---------------------------------------------------------------------- */
- template < const int NEWTON_PAIR, const int COUL_TYPE >
+ template < const int NEWTON_PAIR, const int COUL_TYPE >
void PairCMMCommon::eval_inner()
{
double ** const x = atom->x;
@@ -326,14 +326,14 @@ namespace LAMMPS_NS {
const int * const ilist = listinner->ilist;
const int * const numneigh = listinner->numneigh;
int * const * const firstneigh = listinner->firstneigh;
-
+
const double cut_out_on = cut_respa[0];
const double cut_out_off = cut_respa[1];
-
+
const double cut_out_diff = cut_out_off - cut_out_on;
const double cut_out_on_sq = cut_out_on*cut_out_on;
const double cut_out_off_sq = cut_out_off*cut_out_off;
-
+
// loop over neighbors of my atoms
int ii,jj;
@@ -349,9 +349,9 @@ namespace LAMMPS_NS {
for (jj = 0; jj < jnum; jj++) {
int j2 = jlist[jj];
- factor_lj = special_lj[sbmask(j2)];
- factor_coul = special_coul[sbmask(j2)];
- const int j = j2 & NEIGHMASK;
+ factor_lj = special_lj[sbmask(j2)];
+ factor_coul = special_coul[sbmask(j2)];
+ const int j = j2 & NEIGHMASK;
const double delx = xtmp - x[j][0];
const double dely = ytmp - x[j][1];
@@ -371,7 +371,7 @@ namespace LAMMPS_NS {
CG_LJ_INNER(0,fpair);
fpair *= r2inv;
if (rsq > cut_out_on_sq) {
- const double rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
+ const double rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
fpair *= 1.0 - rsw*rsw*(3.0 - 2.0*rsw);
}
} else {
@@ -387,7 +387,7 @@ namespace LAMMPS_NS {
fpair = (forcecoul + forcelj) * r2inv;
if (rsq > cut_out_on_sq) {
- const double rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
+ const double rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
fpair *= 1.0 - rsw*rsw*(3.0 - 2.0*rsw);
}
}
@@ -407,7 +407,7 @@ namespace LAMMPS_NS {
/* ---------------------------------------------------------------------- */
- template < const int NEWTON_PAIR, const int COUL_TYPE >
+ template < const int NEWTON_PAIR, const int COUL_TYPE >
void PairCMMCommon::eval_middle()
{
double ** const x = atom->x;
@@ -424,7 +424,7 @@ namespace LAMMPS_NS {
const int * const ilist = listmiddle->ilist;
const int * const numneigh = listmiddle->numneigh;
int * const * const firstneigh = listmiddle->firstneigh;
-
+
const double cut_in_off = cut_respa[0];
const double cut_in_on = cut_respa[1];
const double cut_out_on = cut_respa[2];
@@ -436,7 +436,7 @@ namespace LAMMPS_NS {
const double cut_in_on_sq = cut_in_on*cut_in_on;
const double cut_out_on_sq = cut_out_on*cut_out_on;
const double cut_out_off_sq = cut_out_off*cut_out_off;
-
+
// loop over neighbors of my atoms
int ii,jj;
@@ -452,9 +452,9 @@ namespace LAMMPS_NS {
for (jj = 0; jj < jnum; jj++) {
int j2 = jlist[jj];
- factor_lj = special_lj[sbmask(j2)];
- factor_coul = special_coul[sbmask(j2)];
- const int j = j2 & NEIGHMASK;
+ factor_lj = special_lj[sbmask(j2)];
+ factor_coul = special_coul[sbmask(j2)];
+ const int j = j2 & NEIGHMASK;
const double delx = xtmp - x[j][0];
const double dely = ytmp - x[j][1];
@@ -474,11 +474,11 @@ namespace LAMMPS_NS {
CG_LJ_INNER(0,fpair);
fpair *= r2inv;
if (rsq < cut_in_on_sq) {
- const double rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff;
+ const double rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff;
fpair *= rsw*rsw*(3.0 - 2.0*rsw);
}
if (rsq > cut_out_on_sq) {
- const double rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
+ const double rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
fpair *= 1.0 + rsw*rsw*(2.0*rsw - 3.0);
}
} else {
@@ -494,11 +494,11 @@ namespace LAMMPS_NS {
fpair = (forcecoul + forcelj) * r2inv;
if (rsq < cut_in_on_sq) {
- const double rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff;
+ const double rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff;
fpair *= rsw*rsw*(3.0 - 2.0*rsw);
}
if (rsq > cut_out_on_sq) {
- const double rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
+ const double rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
fpair *= 1.0 + rsw*rsw*(2.0*rsw - 3.0);
}
}
@@ -519,7 +519,7 @@ namespace LAMMPS_NS {
/* ---------------------------------------------------------------------- */
template < const int EVFLAG, const int EFLAG, const int VFLAG,
- const int NEWTON_PAIR, const int COUL_TYPE >
+ const int NEWTON_PAIR, const int COUL_TYPE >
void PairCMMCommon::eval_outer()
{
double ** const x = atom->x;
@@ -536,7 +536,7 @@ namespace LAMMPS_NS {
const int * const ilist = listouter->ilist;
const int * const numneigh = listouter->numneigh;
int * const * const firstneigh = listouter->firstneigh;
-
+
const double cut_in_off = cut_respa[2];
const double cut_in_on = cut_respa[3];
@@ -559,9 +559,9 @@ namespace LAMMPS_NS {
for (jj = 0; jj < jnum; jj++) {
int j2 = jlist[jj];
- factor_lj = special_lj[sbmask(j2)];
- factor_coul = special_coul[sbmask(j2)];
- const int j = j2 & NEIGHMASK;
+ factor_lj = special_lj[sbmask(j2)];
+ factor_coul = special_coul[sbmask(j2)];
+ const int j = j2 & NEIGHMASK;
const double delx = xtmp - x[j][0];
const double dely = ytmp - x[j][1];
@@ -579,7 +579,7 @@ namespace LAMMPS_NS {
if (rsq < cutsq[itype][jtype]) {
if (COUL_TYPE == CG_COUL_NONE) {
double forcelj=0.0;
-
+
if (rsq > cut_in_off_sq) {
CG_LJ_INNER(0,forcelj);
fpair = forcelj*r2inv;
@@ -599,7 +599,7 @@ namespace LAMMPS_NS {
}
CG_LJ_ENERGY(EFLAG);
-
+
if (VFLAG) {
if (rsq <= cut_in_off_sq) {
CG_LJ_INNER(0,fpair);
@@ -608,13 +608,13 @@ namespace LAMMPS_NS {
fpair = forcelj*r2inv;
}
}
-
+
if (EVFLAG) ev_tally(i,j,nlocal,NEWTON_PAIR,
evdwl,ecoul,fpair,delx,dely,delz);
} else {
double forcelj = 0.0;
double forcecoul = 0.0;
-
+
if (rsq < cut_ljsq[itype][jtype]) {
CG_LJ_INNER(EFLAG,forcelj);
}
@@ -626,7 +626,7 @@ namespace LAMMPS_NS {
double qscreen=exp(-kappa*r);
forcecoul = factor_coul * qqrd2e
* qtmp * q[j] * qscreen * (kappa + 1.0/r);
- if (EFLAG) ecoul=factor_coul*qqrd2e
+ if (EFLAG) ecoul=factor_coul*qqrd2e
* qtmp*q[j] * qscreen / r;
}
}
@@ -635,7 +635,7 @@ namespace LAMMPS_NS {
if (rsq < cut_coulsq_global) {
if (!ncoultablebits || rsq <= tabinnersq) {
const double r = sqrt(rsq);
-
+
const double grij = g_ewald * r;
const double expm2 = exp(-grij*grij);
const double t = 1.0 / (1.0 + EWALD_P*grij);
diff --git a/src/USER-CG-CMM/pair_lj_sdk.cpp b/src/USER-CG-CMM/pair_lj_sdk.cpp
index 9dac84d313d111f99e061f68c8c7f6f9084a8c07..681260993f0423107a846c58ff8226590f00a902 100644
--- a/src/USER-CG-CMM/pair_lj_sdk.cpp
+++ b/src/USER-CG-CMM/pair_lj_sdk.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -68,7 +68,7 @@ PairLJSDK::~PairLJSDK()
memory->destroy(rminsq);
memory->destroy(emin);
- allocated = 0;
+ allocated = 0;
}
}
@@ -94,7 +94,7 @@ void PairLJSDK::compute(int eflag, int vflag)
}
if (vflag_fdotr) virial_fdotr_compute();
-}
+}
/* ---------------------------------------------------------------------- */
@@ -145,50 +145,50 @@ void PairLJSDK::eval()
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- const int ljt = lj_type[itype][jtype];
-
- if (ljt == LJ12_4) {
- const double r4inv=r2inv*r2inv;
- forcelj = r4inv*(lj1[itype][jtype]*r4inv*r4inv
- - lj2[itype][jtype]);
-
- if (EFLAG)
- evdwl = r4inv*(lj3[itype][jtype]*r4inv*r4inv
- - lj4[itype][jtype]) - offset[itype][jtype];
-
- } else if (ljt == LJ9_6) {
- const double r3inv = r2inv*sqrt(r2inv);
- const double r6inv = r3inv*r3inv;
- forcelj = r6inv*(lj1[itype][jtype]*r3inv
- - lj2[itype][jtype]);
- if (EFLAG)
- evdwl = r6inv*(lj3[itype][jtype]*r3inv
- - lj4[itype][jtype]) - offset[itype][jtype];
-
- } else if (ljt == LJ12_6) {
- const double r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv*(lj1[itype][jtype]*r6inv
- - lj2[itype][jtype]);
- if (EFLAG)
- evdwl = r6inv*(lj3[itype][jtype]*r6inv
- - lj4[itype][jtype]) - offset[itype][jtype];
- } else continue;
-
- fpair = factor_lj*forcelj*r2inv;
-
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (EFLAG) evdwl *= factor_lj;
- if (EVFLAG) ev_tally(i,j,nlocal,NEWTON_PAIR,
- evdwl,0.0,fpair,delx,dely,delz);
+ r2inv = 1.0/rsq;
+ const int ljt = lj_type[itype][jtype];
+
+ if (ljt == LJ12_4) {
+ const double r4inv=r2inv*r2inv;
+ forcelj = r4inv*(lj1[itype][jtype]*r4inv*r4inv
+ - lj2[itype][jtype]);
+
+ if (EFLAG)
+ evdwl = r4inv*(lj3[itype][jtype]*r4inv*r4inv
+ - lj4[itype][jtype]) - offset[itype][jtype];
+
+ } else if (ljt == LJ9_6) {
+ const double r3inv = r2inv*sqrt(r2inv);
+ const double r6inv = r3inv*r3inv;
+ forcelj = r6inv*(lj1[itype][jtype]*r3inv
+ - lj2[itype][jtype]);
+ if (EFLAG)
+ evdwl = r6inv*(lj3[itype][jtype]*r3inv
+ - lj4[itype][jtype]) - offset[itype][jtype];
+
+ } else if (ljt == LJ12_6) {
+ const double r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv*(lj1[itype][jtype]*r6inv
+ - lj2[itype][jtype]);
+ if (EFLAG)
+ evdwl = r6inv*(lj3[itype][jtype]*r6inv
+ - lj4[itype][jtype]) - offset[itype][jtype];
+ } else continue;
+
+ fpair = factor_lj*forcelj*r2inv;
+
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (EFLAG) evdwl *= factor_lj;
+ if (EVFLAG) ev_tally(i,j,nlocal,NEWTON_PAIR,
+ evdwl,0.0,fpair,delx,dely,delz);
}
}
f[i][0] += fxtmp;
@@ -248,7 +248,7 @@ void PairLJSDK::settings(int narg, char **arg)
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
- if (setflag[i][j]) cut[i][j] = cut_global;
+ if (setflag[i][j]) cut[i][j] = cut_global;
}
}
@@ -298,13 +298,13 @@ double PairLJSDK::init_one(int i, int j)
{
if (setflag[i][j] == 0)
error->all(FLERR,"No mixing support for lj/sdk. "
- "Coefficients for all pairs need to be set explicitly.");
+ "Coefficients for all pairs need to be set explicitly.");
const int ljt = lj_type[i][j];
if (ljt == LJ_NOT_SET)
error->all(FLERR,"unrecognized LJ parameter flag");
-
+
lj1[i][j] = lj_prefact[ljt] * lj_pow1[ljt] * epsilon[i][j] * pow(sigma[i][j],lj_pow1[ljt]);
lj2[i][j] = lj_prefact[ljt] * lj_pow2[ljt] * epsilon[i][j] * pow(sigma[i][j],lj_pow2[ljt]);
lj3[i][j] = lj_prefact[ljt] * epsilon[i][j] * pow(sigma[i][j],lj_pow1[ljt]);
@@ -329,12 +329,12 @@ double PairLJSDK::init_one(int i, int j)
const double eps = epsilon[i][j];
const double sig = sigma[i][j];
const double rmin = sig*exp(1.0/(lj_pow1[ljt]-lj_pow2[ljt])
- *log(lj_pow1[ljt]/lj_pow2[ljt]) );
+ *log(lj_pow1[ljt]/lj_pow2[ljt]) );
rminsq[j][i] = rminsq[i][j] = rmin*rmin;
const double ratio = sig/rmin;
const double emin_one = lj_prefact[ljt] * eps * (pow(ratio,lj_pow1[ljt])
- - pow(ratio,lj_pow2[ljt]));
+ - pow(ratio,lj_pow2[ljt]));
emin[j][i] = emin[i][j] = emin_one;
// compute I,J contribution to long-range tail correction
@@ -347,7 +347,7 @@ double PairLJSDK::init_one(int i, int j)
}
/* ----------------------------------------------------------------------
- proc 0 writes to restart file
+ proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairLJSDK::write_restart(FILE *fp)
@@ -360,9 +360,9 @@ void PairLJSDK::write_restart(FILE *fp)
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
fwrite(&lj_type[i][j],sizeof(int),1,fp);
- fwrite(&epsilon[i][j],sizeof(double),1,fp);
- fwrite(&sigma[i][j],sizeof(double),1,fp);
- fwrite(&cut[i][j],sizeof(double),1,fp);
+ fwrite(&epsilon[i][j],sizeof(double),1,fp);
+ fwrite(&sigma[i][j],sizeof(double),1,fp);
+ fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
@@ -383,16 +383,16 @@ void PairLJSDK::read_restart(FILE *fp)
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
- if (me == 0) {
- fread(&lj_type[i][j],sizeof(int),1,fp);
- fread(&epsilon[i][j],sizeof(double),1,fp);
- fread(&sigma[i][j],sizeof(double),1,fp);
- fread(&cut[i][j],sizeof(double),1,fp);
- }
- MPI_Bcast(&lj_type[i][j],1,MPI_INT,0,world);
- MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
+ if (me == 0) {
+ fread(&lj_type[i][j],sizeof(int),1,fp);
+ fread(&epsilon[i][j],sizeof(double),1,fp);
+ fread(&sigma[i][j],sizeof(double),1,fp);
+ fread(&cut[i][j],sizeof(double),1,fp);
+ }
+ MPI_Bcast(&lj_type[i][j],1,MPI_INT,0,world);
+ MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
@@ -428,23 +428,23 @@ void PairLJSDK::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairLJSDK::single(int, int, int itype, int jtype, double rsq,
- double, double factor_lj, double &fforce)
+ double, double factor_lj, double &fforce)
{
if (rsq < cutsq[itype][jtype]) {
-
+
const int ljt = lj_type[itype][jtype];
const double ljpow1 = lj_pow1[ljt];
const double ljpow2 = lj_pow2[ljt];
const double ljpref = lj_prefact[ljt];
-
+
const double ratio = sigma[itype][jtype]/sqrt(rsq);
const double eps = epsilon[itype][jtype];
- fforce = factor_lj * ljpref*eps * (ljpow1*pow(ratio,ljpow1)
- - ljpow2*pow(ratio,ljpow2))/rsq;
+ fforce = factor_lj * ljpref*eps * (ljpow1*pow(ratio,ljpow1)
+ - ljpow2*pow(ratio,ljpow2))/rsq;
return factor_lj * (ljpref*eps * (pow(ratio,ljpow1) - pow(ratio,ljpow2))
- - offset[itype][jtype]);
+ - offset[itype][jtype]);
} else fforce=0.0;
@@ -476,9 +476,9 @@ double PairLJSDK::memory_usage()
int n = atom->ntypes;
// setflag/lj_type
- bytes += 2 * (n+1)*(n+1)*sizeof(int);
+ bytes += 2 * (n+1)*(n+1)*sizeof(int);
// cut/cutsq/epsilon/sigma/offset/lj1/lj2/lj3/lj4/rminsq/emin
- bytes += 11 * (n+1)*(n+1)*sizeof(double);
+ bytes += 11 * (n+1)*(n+1)*sizeof(double);
return bytes;
}
diff --git a/src/USER-CG-CMM/pair_lj_sdk.h b/src/USER-CG-CMM/pair_lj_sdk.h
index 9953b4aede6e735fc318c7e5af1e7e726b502312..fd764c6e838ac6429bca591a71fea70ad93bc626 100644
--- a/src/USER-CG-CMM/pair_lj_sdk.h
+++ b/src/USER-CG-CMM/pair_lj_sdk.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -29,7 +29,7 @@ PairStyle(cg/cmm,PairLJSDK)
namespace LAMMPS_NS {
class LAMMPS;
-
+
class PairLJSDK : public Pair {
public:
PairLJSDK(LAMMPS *);
@@ -54,7 +54,7 @@ class PairLJSDK : public Pair {
double **lj1,**lj2,**lj3,**lj4,**offset;
// cutoff and offset for minimum of LJ potential
- // to be used in SDK angle potential, which
+ // to be used in SDK angle potential, which
// uses only the repulsive part of the potential
double **rminsq, **emin;
diff --git a/src/USER-CG-CMM/pair_lj_sdk_coul_long.cpp b/src/USER-CG-CMM/pair_lj_sdk_coul_long.cpp
index 2b86f87ec25b08b530c4f706b68c197023753084..8d57401245270fb8cd7945bdbc2b1cd339ed8c6e 100644
--- a/src/USER-CG-CMM/pair_lj_sdk_coul_long.cpp
+++ b/src/USER-CG-CMM/pair_lj_sdk_coul_long.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -78,7 +78,7 @@ PairLJSDKCoulLong::~PairLJSDKCoulLong()
memory->destroy(rminsq);
memory->destroy(emin);
- allocated = 0;
+ allocated = 0;
}
if (ftable) free_tables();
}
@@ -105,7 +105,7 @@ void PairLJSDKCoulLong::compute(int eflag, int vflag)
}
if (vflag_fdotr) virial_fdotr_compute();
-}
+}
/* ---------------------------------------------------------------------- */
@@ -163,86 +163,86 @@ void PairLJSDKCoulLong::eval()
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- const int ljt = lj_type[itype][jtype];
-
- if (rsq < cut_coulsq) {
- if (!ncoultablebits || rsq <= tabinnersq) {
- r = sqrt(rsq);
- grij = g_ewald * r;
- expm2 = exp(-grij*grij);
- t = 1.0 / (1.0 + EWALD_P*grij);
- erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
- prefactor = qqrd2e * qtmp*q[j]/r;
- forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
- if (EFLAG) ecoul = prefactor*erfc;
- if (factor_coul < 1.0) {
- forcecoul -= (1.0-factor_coul)*prefactor;
- if (EFLAG) ecoul -= (1.0-factor_coul)*prefactor;
- }
- } else {
- union_int_float_t rsq_lookup;
- rsq_lookup.f = rsq;
- itable = rsq_lookup.i & ncoulmask;
- itable >>= ncoulshiftbits;
- fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
- table = ftable[itable] + fraction*dftable[itable];
- forcecoul = qtmp*q[j] * table;
- if (EFLAG) ecoul = qtmp*q[j] * (etable[itable] + fraction*detable[itable]);
- if (factor_coul < 1.0) {
- table = ctable[itable] + fraction*dctable[itable];
- prefactor = qtmp*q[j] * table;
- forcecoul -= (1.0-factor_coul)*prefactor;
- if (EFLAG) ecoul -= (1.0-factor_coul)*prefactor;
- }
- }
- }
-
- if (rsq < cut_ljsq[itype][jtype]) {
-
- if (ljt == LJ12_4) {
- const double r4inv=r2inv*r2inv;
- forcelj = r4inv*(lj1[itype][jtype]*r4inv*r4inv
- - lj2[itype][jtype]);
-
- if (EFLAG)
- evdwl = r4inv*(lj3[itype][jtype]*r4inv*r4inv
- - lj4[itype][jtype]) - offset[itype][jtype];
-
- } else if (ljt == LJ9_6) {
- const double r3inv = r2inv*sqrt(r2inv);
- const double r6inv = r3inv*r3inv;
- forcelj = r6inv*(lj1[itype][jtype]*r3inv
- - lj2[itype][jtype]);
- if (EFLAG)
- evdwl = r6inv*(lj3[itype][jtype]*r3inv
- - lj4[itype][jtype]) - offset[itype][jtype];
-
- } else if (ljt == LJ12_6) {
- const double r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv*(lj1[itype][jtype]*r6inv
- - lj2[itype][jtype]);
- if (EFLAG)
- evdwl = r6inv*(lj3[itype][jtype]*r6inv
- - lj4[itype][jtype]) - offset[itype][jtype];
- }
- forcelj *= factor_lj;
- if (EFLAG) evdwl *= factor_lj;
- }
-
- fpair = (forcecoul + forcelj) * r2inv;
-
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (EVFLAG) ev_tally(i,j,nlocal,NEWTON_PAIR,
- evdwl,ecoul,fpair,delx,dely,delz);
+ r2inv = 1.0/rsq;
+ const int ljt = lj_type[itype][jtype];
+
+ if (rsq < cut_coulsq) {
+ if (!ncoultablebits || rsq <= tabinnersq) {
+ r = sqrt(rsq);
+ grij = g_ewald * r;
+ expm2 = exp(-grij*grij);
+ t = 1.0 / (1.0 + EWALD_P*grij);
+ erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
+ prefactor = qqrd2e * qtmp*q[j]/r;
+ forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
+ if (EFLAG) ecoul = prefactor*erfc;
+ if (factor_coul < 1.0) {
+ forcecoul -= (1.0-factor_coul)*prefactor;
+ if (EFLAG) ecoul -= (1.0-factor_coul)*prefactor;
+ }
+ } else {
+ union_int_float_t rsq_lookup;
+ rsq_lookup.f = rsq;
+ itable = rsq_lookup.i & ncoulmask;
+ itable >>= ncoulshiftbits;
+ fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
+ table = ftable[itable] + fraction*dftable[itable];
+ forcecoul = qtmp*q[j] * table;
+ if (EFLAG) ecoul = qtmp*q[j] * (etable[itable] + fraction*detable[itable]);
+ if (factor_coul < 1.0) {
+ table = ctable[itable] + fraction*dctable[itable];
+ prefactor = qtmp*q[j] * table;
+ forcecoul -= (1.0-factor_coul)*prefactor;
+ if (EFLAG) ecoul -= (1.0-factor_coul)*prefactor;
+ }
+ }
+ }
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+
+ if (ljt == LJ12_4) {
+ const double r4inv=r2inv*r2inv;
+ forcelj = r4inv*(lj1[itype][jtype]*r4inv*r4inv
+ - lj2[itype][jtype]);
+
+ if (EFLAG)
+ evdwl = r4inv*(lj3[itype][jtype]*r4inv*r4inv
+ - lj4[itype][jtype]) - offset[itype][jtype];
+
+ } else if (ljt == LJ9_6) {
+ const double r3inv = r2inv*sqrt(r2inv);
+ const double r6inv = r3inv*r3inv;
+ forcelj = r6inv*(lj1[itype][jtype]*r3inv
+ - lj2[itype][jtype]);
+ if (EFLAG)
+ evdwl = r6inv*(lj3[itype][jtype]*r3inv
+ - lj4[itype][jtype]) - offset[itype][jtype];
+
+ } else if (ljt == LJ12_6) {
+ const double r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv*(lj1[itype][jtype]*r6inv
+ - lj2[itype][jtype]);
+ if (EFLAG)
+ evdwl = r6inv*(lj3[itype][jtype]*r6inv
+ - lj4[itype][jtype]) - offset[itype][jtype];
+ }
+ forcelj *= factor_lj;
+ if (EFLAG) evdwl *= factor_lj;
+ }
+
+ fpair = (forcecoul + forcelj) * r2inv;
+
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (EVFLAG) ev_tally(i,j,nlocal,NEWTON_PAIR,
+ evdwl,ecoul,fpair,delx,dely,delz);
}
}
f[i][0] += fxtmp;
@@ -306,7 +306,7 @@ void PairLJSDKCoulLong::settings(int narg, char **arg)
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
- if (setflag[i][j]) cut_lj[i][j] = cut_lj_global;
+ if (setflag[i][j]) cut_lj[i][j] = cut_lj_global;
}
}
@@ -380,7 +380,7 @@ double PairLJSDKCoulLong::init_one(int i, int j)
{
if (setflag[i][j] == 0)
error->all(FLERR,"No mixing support for lj/sdk/coul/long. "
- "Coefficients for all pairs need to be set explicitly.");
+ "Coefficients for all pairs need to be set explicitly.");
const int ljt = lj_type[i][j];
@@ -414,12 +414,12 @@ double PairLJSDKCoulLong::init_one(int i, int j)
const double eps = epsilon[i][j];
const double sig = sigma[i][j];
const double rmin = sig*exp(1.0/(lj_pow1[ljt]-lj_pow2[ljt])
- *log(lj_pow1[ljt]/lj_pow2[ljt]) );
+ *log(lj_pow1[ljt]/lj_pow2[ljt]) );
rminsq[j][i] = rminsq[i][j] = rmin*rmin;
const double ratio = sig/rmin;
const double emin_one = lj_prefact[ljt] * eps * (pow(ratio,lj_pow1[ljt])
- - pow(ratio,lj_pow2[ljt]));
+ - pow(ratio,lj_pow2[ljt]));
emin[j][i] = emin[i][j] = emin_one;
// compute I,J contribution to long-range tail correction
@@ -443,17 +443,17 @@ void PairLJSDKCoulLong::init_tables()
tabinnersq = tabinner*tabinner;
init_bitmap(tabinner,cut_coul,ncoultablebits,
- masklo,maskhi,ncoulmask,ncoulshiftbits);
-
+ masklo,maskhi,ncoulmask,ncoulshiftbits);
+
int ntable = 1;
for (int i = 0; i < ncoultablebits; i++) ntable *= 2;
-
+
// linear lookup tables of length N = 2^ncoultablebits
// stored value = value at lower edge of bin
// d values = delta from lower edge to upper edge of bin
if (ftable) free_tables();
-
+
memory->create(rtable,ntable,"pair:rtable");
memory->create(ftable,ntable,"pair:ftable");
memory->create(ctable,ntable,"pair:ctable");
@@ -468,7 +468,7 @@ void PairLJSDKCoulLong::init_tables()
int itablemin;
minrsq_lookup.i = 0 << ncoulshiftbits;
minrsq_lookup.i |= maskhi;
-
+
for (int i = 0; i < ntable; i++) {
rsq_lookup.i = i << ncoulshiftbits;
rsq_lookup.i |= masklo;
@@ -489,9 +489,9 @@ void PairLJSDKCoulLong::init_tables()
}
tabinnersq = minrsq_lookup.f;
-
+
int ntablem1 = ntable - 1;
-
+
for (int i = 0; i < ntablem1; i++) {
drtable[i] = 1.0/(rtable[i+1] - rtable[i]);
dftable[i] = ftable[i+1] - ftable[i];
@@ -499,31 +499,31 @@ void PairLJSDKCoulLong::init_tables()
detable[i] = etable[i+1] - etable[i];
}
- // get the delta values for the last table entries
+ // get the delta values for the last table entries
// tables are connected periodically between 0 and ntablem1
-
+
drtable[ntablem1] = 1.0/(rtable[0] - rtable[ntablem1]);
dftable[ntablem1] = ftable[0] - ftable[ntablem1];
dctable[ntablem1] = ctable[0] - ctable[ntablem1];
detable[ntablem1] = etable[0] - etable[ntablem1];
- // get the correct delta values at itablemax
+ // get the correct delta values at itablemax
// smallest r is in bin itablemin
// largest r is in bin itablemax, which is itablemin-1,
// or ntablem1 if itablemin=0
// deltas at itablemax only needed if corresponding rsq < cut*cut
- // if so, compute deltas between rsq and cut*cut
+ // if so, compute deltas between rsq and cut*cut
double f_tmp,c_tmp,e_tmp;
itablemin = minrsq_lookup.i & ncoulmask;
- itablemin >>= ncoulshiftbits;
- int itablemax = itablemin - 1;
- if (itablemin == 0) itablemax = ntablem1;
+ itablemin >>= ncoulshiftbits;
+ int itablemax = itablemin - 1;
+ if (itablemin == 0) itablemax = ntablem1;
rsq_lookup.i = itablemax << ncoulshiftbits;
rsq_lookup.i |= maskhi;
if (rsq_lookup.f < cut_coulsq) {
- rsq_lookup.f = cut_coulsq;
+ rsq_lookup.f = cut_coulsq;
r = sqrtf(rsq_lookup.f);
grij = g_ewald * r;
expm2 = exp(-grij*grij);
@@ -533,7 +533,7 @@ void PairLJSDKCoulLong::init_tables()
c_tmp = qqrd2e/r;
e_tmp = qqrd2e/r * derfc;
- drtable[itablemax] = 1.0/(rsq_lookup.f - rtable[itablemax]);
+ drtable[itablemax] = 1.0/(rsq_lookup.f - rtable[itablemax]);
dftable[itablemax] = f_tmp - ftable[itablemax];
dctable[itablemax] = c_tmp - ctable[itablemax];
detable[itablemax] = e_tmp - etable[itablemax];
@@ -554,9 +554,9 @@ void PairLJSDKCoulLong::write_restart(FILE *fp)
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
fwrite(&lj_type[i][j],sizeof(int),1,fp);
- fwrite(&epsilon[i][j],sizeof(double),1,fp);
- fwrite(&sigma[i][j],sizeof(double),1,fp);
- fwrite(&cut_lj[i][j],sizeof(double),1,fp);
+ fwrite(&epsilon[i][j],sizeof(double),1,fp);
+ fwrite(&sigma[i][j],sizeof(double),1,fp);
+ fwrite(&cut_lj[i][j],sizeof(double),1,fp);
}
}
}
@@ -577,16 +577,16 @@ void PairLJSDKCoulLong::read_restart(FILE *fp)
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
- if (me == 0) {
- fread(&lj_type[i][j],sizeof(int),1,fp);
- fread(&epsilon[i][j],sizeof(double),1,fp);
- fread(&sigma[i][j],sizeof(double),1,fp);
- fread(&cut_lj[i][j],sizeof(double),1,fp);
- }
- MPI_Bcast(&lj_type[i][j],1,MPI_INT,0,world);
- MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world);
+ if (me == 0) {
+ fread(&lj_type[i][j],sizeof(int),1,fp);
+ fread(&epsilon[i][j],sizeof(double),1,fp);
+ fread(&sigma[i][j],sizeof(double),1,fp);
+ fread(&cut_lj[i][j],sizeof(double),1,fp);
+ }
+ MPI_Bcast(&lj_type[i][j],1,MPI_INT,0,world);
+ MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world);
}
}
}
@@ -640,9 +640,9 @@ void PairLJSDKCoulLong::free_tables()
/* ---------------------------------------------------------------------- */
double PairLJSDKCoulLong::single(int i, int j, int itype, int jtype,
- double rsq,
- double factor_coul, double factor_lj,
- double &fforce)
+ double rsq,
+ double factor_coul, double factor_lj,
+ double &fforce)
{
double r2inv,r,grij,expm2,t,erfc,prefactor;
double fraction,table,forcecoul,forcelj,phicoul,philj;
@@ -662,8 +662,8 @@ double PairLJSDKCoulLong::single(int i, int j, int itype, int jtype,
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
phicoul = prefactor*erfc;
if (factor_coul < 1.0) {
- forcecoul -= (1.0-factor_coul)*prefactor;
- phicoul -= (1.0-factor_coul)*prefactor;
+ forcecoul -= (1.0-factor_coul)*prefactor;
+ phicoul -= (1.0-factor_coul)*prefactor;
}
} else {
union_int_float_t rsq_lookup_single;
@@ -676,10 +676,10 @@ double PairLJSDKCoulLong::single(int i, int j, int itype, int jtype,
table = etable[itable] + fraction*detable[itable];
phicoul = atom->q[i]*atom->q[j] * table;
if (factor_coul < 1.0) {
- table = ctable[itable] + fraction*dctable[itable];
- prefactor = atom->q[i]*atom->q[j] * table;
- forcecoul -= (1.0-factor_coul)*prefactor;
- phicoul -= (1.0-factor_coul)*prefactor;
+ table = ctable[itable] + fraction*dctable[itable];
+ prefactor = atom->q[i]*atom->q[j] * table;
+ forcecoul -= (1.0-factor_coul)*prefactor;
+ phicoul -= (1.0-factor_coul)*prefactor;
}
}
}
@@ -689,14 +689,14 @@ double PairLJSDKCoulLong::single(int i, int j, int itype, int jtype,
const double ljpow1 = lj_pow1[ljt];
const double ljpow2 = lj_pow2[ljt];
const double ljpref = lj_prefact[ljt];
-
+
const double ratio = sigma[itype][jtype]/sqrt(rsq);
const double eps = epsilon[itype][jtype];
- forcelj = factor_lj * ljpref*eps * (ljpow1*pow(ratio,ljpow1)
- - ljpow2*pow(ratio,ljpow2))/rsq;
+ forcelj = factor_lj * ljpref*eps * (ljpow1*pow(ratio,ljpow1)
+ - ljpow2*pow(ratio,ljpow2))/rsq;
philj = factor_lj * (ljpref*eps * (pow(ratio,ljpow1) - pow(ratio,ljpow2))
- - offset[itype][jtype]);
+ - offset[itype][jtype]);
}
fforce = (forcecoul + forcelj) * r2inv;
@@ -718,7 +718,7 @@ void *PairLJSDKCoulLong::extract(const char *str, int &dim)
if (strcmp(str,"lj4") == 0) return (void *) lj4;
if (strcmp(str,"rminsq") == 0) return (void *) rminsq;
if (strcmp(str,"emin") == 0) return (void *) emin;
-
+
dim = 0;
if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul;
return NULL;
@@ -732,7 +732,7 @@ double PairLJSDKCoulLong::memory_usage()
int n = atom->ntypes;
// setflag/lj_type
- bytes += 2 * (n+1)*(n+1)*sizeof(int);
+ bytes += 2 * (n+1)*(n+1)*sizeof(int);
// lj_cut/lj_cutsq/epsilon/sigma/offset/lj1/lj2/lj3/lj4/rminsq/emin
bytes += 11 * (n+1)*(n+1)*sizeof(double);
diff --git a/src/USER-CG-CMM/pair_lj_sdk_coul_long.h b/src/USER-CG-CMM/pair_lj_sdk_coul_long.h
index 61043ad2b0dac691b0ab42b4a15499e63b1126ee..c929712ec1fb1fca4834e2d36f0333f73c99907d 100644
--- a/src/USER-CG-CMM/pair_lj_sdk_coul_long.h
+++ b/src/USER-CG-CMM/pair_lj_sdk_coul_long.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -54,7 +54,7 @@ class PairLJSDKCoulLong : public Pair {
int **lj_type;
// cutoff and offset for minimum of LJ potential
- // to be used in SDK angle potential, which
+ // to be used in SDK angle potential, which
// uses only the repulsive part of the potential
double **rminsq, **emin;
diff --git a/src/USER-COLVARS/colvarproxy_lammps.cpp b/src/USER-COLVARS/colvarproxy_lammps.cpp
index e7b256d0e787362d1dad221ce269c00e19974837..f5a0a5df68efbb145e2fe50685d2488d7e980aae 100644
--- a/src/USER-COLVARS/colvarproxy_lammps.cpp
+++ b/src/USER-COLVARS/colvarproxy_lammps.cpp
@@ -47,7 +47,7 @@ static void my_backup_file(const char *filename, const char *extension)
char *sys_err_msg = strerror(errno);
if ( !sys_err_msg ) sys_err_msg = (char *) "(unknown error)";
fprintf(stderr,"Error renaming file %s to %s: %s\n",
- filename, backup, sys_err_msg);
+ filename, backup, sys_err_msg);
}
delete [] backup;
}
@@ -56,12 +56,12 @@ static void my_backup_file(const char *filename, const char *extension)
////////////////////////////////////////////////////////////////////////
colvarproxy_lammps::colvarproxy_lammps(LAMMPS_NS::LAMMPS *lmp,
- const char *conf_file,
- const char *inp_name,
- const char *out_name,
- const int seed,
- const double temp,
- const int *typemap)
+ const char *conf_file,
+ const char *inp_name,
+ const char *out_name,
+ const int seed,
+ const double temp,
+ const int *typemap)
: _lmp(lmp), _typemap(typemap)
{
if (cvm::debug())
@@ -127,7 +127,7 @@ colvarproxy_lammps::~colvarproxy_lammps()
}
}
-// trigger colvars computation
+// trigger colvars computation
double colvarproxy_lammps::compute()
{
if (first_timestep) {
@@ -145,8 +145,8 @@ double colvarproxy_lammps::compute()
if (cvm::debug()) {
cvm::log(cvm::line_marker+
- "colvarproxy_lammps, step no. "+cvm::to_str(colvars->it)+"\n"+
- "Updating internal data.\n");
+ "colvarproxy_lammps, step no. "+cvm::to_str(colvars->it)+"\n"+
+ "Updating internal data.\n");
}
// call the collective variable module
@@ -155,9 +155,9 @@ double colvarproxy_lammps::compute()
#if 0
for (int i=0; i < colvars_atoms.size(); ++i) {
fprintf(stderr,"CV: atom %d/%d/%d pos: %g %g %g for: %g %g %g\n",
- colvars_atoms[i], colvars_atoms_ncopies[i],
- positions[i].type, positions[i].x, positions[i].y, positions[i].z,
- applied_forces[i].x, applied_forces[i].y, applied_forces[i].z);
+ colvars_atoms[i], colvars_atoms_ncopies[i],
+ positions[i].type, positions[i].x, positions[i].y, positions[i].z,
+ applied_forces[i].x, applied_forces[i].y, applied_forces[i].z);
}
#endif
@@ -165,7 +165,7 @@ double colvarproxy_lammps::compute()
}
cvm::rvector colvarproxy_lammps::position_distance(cvm::atom_pos const &pos1,
- cvm::atom_pos const &pos2)
+ cvm::atom_pos const &pos2)
{
double xtmp = pos2.x - pos1.x;
double ytmp = pos2.y - pos1.y;
@@ -175,7 +175,7 @@ cvm::rvector colvarproxy_lammps::position_distance(cvm::atom_pos const &pos1,
}
cvm::real colvarproxy_lammps::position_dist2(cvm::atom_pos const &pos1,
- cvm::atom_pos const &pos2)
+ cvm::atom_pos const &pos2)
{
double xtmp = pos2.x - pos1.x;
double ytmp = pos2.y - pos1.y;
@@ -186,7 +186,7 @@ cvm::real colvarproxy_lammps::position_dist2(cvm::atom_pos const &pos1,
inline void colvarproxy_lammps::select_closest_image(cvm::atom_pos &pos,
- cvm::atom_pos const &ref)
+ cvm::atom_pos const &ref)
{
double xtmp = pos.x - ref.x;
double ytmp = pos.y - ref.y;
@@ -214,10 +214,10 @@ void colvarproxy_lammps::fatal_error(std::string const &message)
log(message);
if (!cvm::debug())
log("If this error message is unclear, try recompiling the "
- "colvars library and LAMMPS with -DCOLVARS_DEBUG.\n");
+ "colvars library and LAMMPS with -DCOLVARS_DEBUG.\n");
_lmp->error->one(FLERR,
- "Fatal error in the collective variables module.\n");
+ "Fatal error in the collective variables module.\n");
}
void colvarproxy_lammps::exit(std::string const &message)
@@ -256,7 +256,7 @@ e_pdb_field pdb_field_str2enum(std::string const &pdb_field_str)
colvarparse::to_lower_cppstr("X")) {
pdb_field = e_pdb_x;
}
-
+
if (colvarparse::to_lower_cppstr(pdb_field_str) ==
colvarparse::to_lower_cppstr("Y")) {
pdb_field = e_pdb_y;
@@ -283,7 +283,7 @@ void colvarproxy_lammps::load_coords(char const *pdb_filename,
{
cvm::fatal_error("Reading collective variable coordinates "
- "from a PDB file is currently not supported.\n");
+ "from a PDB file is currently not supported.\n");
}
void colvarproxy_lammps::load_atoms(char const *pdb_filename,
@@ -292,7 +292,7 @@ void colvarproxy_lammps::load_atoms(char const *pdb_filename,
double const pdb_field_value)
{
cvm::fatal_error("Selecting collective variable atoms "
- "from a PDB file is currently not supported.\n");
+ "from a PDB file is currently not supported.\n");
}
void colvarproxy_lammps::backup_file(char const *filename)
@@ -339,11 +339,11 @@ cvm::atom::atom(const int &id)
if (cvm::debug())
cvm::log("Adding atom "+cvm::to_str(id)+
- " for collective variables calculation.\n");
+ " for collective variables calculation.\n");
if (id < 0)
cvm::fatal_error("Error: invalid atom ID specified, "+
- cvm::to_str(id)+"\n");
+ cvm::to_str(id)+"\n");
int idx = ((colvarproxy_lammps *) cvm::proxy)->init_lammps_atom(id,this);
if (idx < 0)
@@ -352,7 +352,7 @@ cvm::atom::atom(const int &id)
this->index = idx;
if (cvm::debug())
cvm::log("The index of this atom in the colvarproxy_lammps arrays is "+
- cvm::to_str(this->index)+".\n");
+ cvm::to_str(this->index)+".\n");
this->reset_data();
}
@@ -362,11 +362,11 @@ cvm::atom::atom(const int &id)
/// "MAIN" (the segment id assigned by NAMD's AMBER topology parser),
/// and is therefore optional when an AMBER topology is used
cvm::atom::atom(cvm::residue_id const &residue,
- std::string const &atom_name,
- std::string const &segment_id)
+ std::string const &atom_name,
+ std::string const &segment_id)
{
cvm::fatal_error("Creating collective variable atoms "
- "from a PDB file is currently not supported.\n");
+ "from a PDB file is currently not supported.\n");
}
@@ -383,7 +383,7 @@ cvm::atom::atom(cvm::atom const &a)
}
-cvm::atom::~atom()
+cvm::atom::~atom()
{
colvarproxy_lammps *cp = (colvarproxy_lammps *) cvm::proxy;
if (cp->colvars_atoms_ncopies[this->index] > 0)
@@ -422,4 +422,3 @@ void cvm::atom::apply_force(cvm::rvector const &new_force)
cp->applied_forces[this->index].y = new_force.y;
cp->applied_forces[this->index].z = new_force.z;
}
-
diff --git a/src/USER-COLVARS/colvarproxy_lammps.h b/src/USER-COLVARS/colvarproxy_lammps.h
index 8786f07482e30f197951e6aaabc606c7cff9cb65..7d2f3b7fe5a81a1e38b21b024e6bb1bfb0cc2056 100644
--- a/src/USER-COLVARS/colvarproxy_lammps.h
+++ b/src/USER-COLVARS/colvarproxy_lammps.h
@@ -15,19 +15,19 @@
#include <iostream>
/* struct for packed data communication of coordinates and forces. */
-struct commdata {
- int tag,type;
- double x,y,z;
+struct commdata {
+ int tag,type;
+ double x,y,z;
};
inline std::ostream & operator<< (std::ostream &out, const commdata &cd)
{
- out << " (" << cd.tag << "/" << cd.type << ": "
+ out << " (" << cd.tag << "/" << cd.type << ": "
<< cd.x << ", " << cd.y << ", " << cd.z << ") ";
return out;
};
-/// \brief Communication between colvars and LAMMPS
+/// \brief Communication between colvars and LAMMPS
/// (implementation of \link colvarproxy \endlink)
class colvarproxy_lammps : public colvarproxy {
@@ -64,7 +64,7 @@ class colvarproxy_lammps : public colvarproxy {
public:
friend class cvm::atom;
colvarproxy_lammps (LAMMPS_NS::LAMMPS *lmp, const char *, const char *,
- const char *, const int, const double, const int *);
+ const char *, const int, const double, const int *);
virtual ~colvarproxy_lammps();
// disable default and copy constructor
diff --git a/src/USER-COLVARS/fix_colvars.cpp b/src/USER-COLVARS/fix_colvars.cpp
index 2ef1893b90bb92d03e77ac8e08ef06dbc8a72b20..2f8ca857cb763fd5af37923812d12140d807c4aa 100644
--- a/src/USER-COLVARS/fix_colvars.cpp
+++ b/src/USER-COLVARS/fix_colvars.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -78,7 +78,7 @@ static int inthash(const inthash_t *tptr, int key) {
hashvalue = (((key*1103515249)>>tptr->downshift) & tptr->mask);
if (hashvalue < 0) {
hashvalue = 0;
- }
+ }
return hashvalue;
}
@@ -205,7 +205,7 @@ int inthash_insert(inthash_t *tptr, int key, int data) {
/*
* inthash_destroy() - Delete the entire table, and all remaining entries.
- *
+ *
*/
void inthash_destroy(inthash_t *tptr) {
inthash_node_t *node, *last;
@@ -213,12 +213,12 @@ void inthash_destroy(inthash_t *tptr) {
for (i=0; i<tptr->size; i++) {
node = tptr->bucket[i];
- while (node != NULL) {
- last = node;
+ while (node != NULL) {
+ last = node;
node = node->next;
free(last);
}
- }
+ }
/* free the entire array of buckets */
if (tptr->bucket != NULL) {
@@ -274,7 +274,7 @@ using namespace FixConst;
int FixColvars::instances=0;
/***************************************************************
- create class and parse arguments in LAMMPS script. Syntax:
+ create class and parse arguments in LAMMPS script. Syntax:
fix ID group-ID colvars <config_file> [optional flags...]
@@ -310,7 +310,7 @@ FixColvars::FixColvars(LAMMPS *lmp, int narg, char **arg) :
extscalar = 1;
me = comm->me;
-
+
conf_file = strdup(arg[3]);
rng_seed = 1966;
@@ -457,7 +457,7 @@ void FixColvars::init()
MPI_Get_count(&status, MPI_INT, &ndata);
for (int k=0; k<ndata; k+=2)
- typemap[type_buf[k]] = type_buf[k+1];
+ typemap[type_buf[k]] = type_buf[k+1];
}
} else { // me != 0
@@ -480,25 +480,25 @@ void FixColvars::init()
if (inp_name) {
if (strcmp(inp_name,"NULL") == 0) {
- memory->sfree(inp_name);
- inp_name = NULL;
+ memory->sfree(inp_name);
+ inp_name = NULL;
}
}
double t_target = 0.0;
if (tmp_name) {
if (strcmp(tmp_name,"NULL") == 0)
- tstat_id = -1;
+ tstat_id = -1;
else {
- tstat_id = modify->find_fix(tmp_name);
- if (tstat_id < 0) error->one(FLERR,"Could not find tstat fix ID");
- double *tt = (double*)modify->fix[tstat_id]->extract("t_target",tmp);
- if (tt) t_target = *tt;
+ tstat_id = modify->find_fix(tmp_name);
+ if (tstat_id < 0) error->one(FLERR,"Could not find tstat fix ID");
+ double *tt = (double*)modify->fix[tstat_id]->extract("t_target",tmp);
+ if (tt) t_target = *tt;
}
}
proxy = new colvarproxy_lammps(lmp,conf_file,inp_name,out_name,
- rng_seed,t_target,typemap);
+ rng_seed,t_target,typemap);
coords = proxy->get_coords();
forces = proxy->get_forces();
oforce = proxy->get_oforce();
@@ -549,12 +549,12 @@ void FixColvars::init()
for (i=0; i<num_coords; ++i) {
const int k = atom->map(taglist[i]);
if ((k >= 0) && (k < nlocal)) {
- of[i].tag = cd[i].tag = tag[k];
- of[i].type = cd[i].type = type[k];
- cd[i].x = x[k][0];
- cd[i].y = x[k][1];
- cd[i].z = x[k][2];
- of[i].x = of[i].y = of[i].z = 0.0;
+ of[i].tag = cd[i].tag = tag[k];
+ of[i].type = cd[i].type = type[k];
+ cd[i].x = x[k][0];
+ cd[i].y = x[k][1];
+ cd[i].z = x[k][2];
+ of[i].x = of[i].y = of[i].z = 0.0;
}
}
@@ -569,15 +569,15 @@ void FixColvars::init()
ndata /= size_one;
for (int k=0; k<ndata; ++k) {
- const int j = inthash_lookup(idmap, comm_buf[k].tag);
- if (j != HASH_FAIL) {
- of[j].tag = cd[j].tag = comm_buf[k].tag;
- of[j].type = cd[j].type = comm_buf[k].type;
- cd[j].x = comm_buf[k].x;
- cd[j].y = comm_buf[k].y;
- cd[j].z = comm_buf[k].z;
- of[j].x = of[j].y = of[j].z = 0.0;
- }
+ const int j = inthash_lookup(idmap, comm_buf[k].tag);
+ if (j != HASH_FAIL) {
+ of[j].tag = cd[j].tag = comm_buf[k].tag;
+ of[j].type = cd[j].type = comm_buf[k].type;
+ cd[j].x = comm_buf[k].x;
+ cd[j].y = comm_buf[k].y;
+ cd[j].z = comm_buf[k].z;
+ of[j].x = of[j].y = of[j].z = 0.0;
+ }
}
}
} else { // me != 0
@@ -588,12 +588,12 @@ void FixColvars::init()
for (i=0; i<num_coords; ++i) {
const int k = atom->map(taglist[i]);
if ((k >= 0) && (k < nlocal)) {
- comm_buf[nme].tag = tag[k];
- comm_buf[nme].type = type[k];
- comm_buf[nme].x = x[k][0];
- comm_buf[nme].y = x[k][1];
- comm_buf[nme].z = x[k][2];
- ++nme;
+ comm_buf[nme].tag = tag[k];
+ comm_buf[nme].type = type[k];
+ comm_buf[nme].x = x[k][0];
+ comm_buf[nme].y = x[k][1];
+ comm_buf[nme].z = x[k][2];
+ ++nme;
}
}
/* blocking receive to wait until it is our turn to send data. */
@@ -633,10 +633,10 @@ void FixColvars::post_force(int vflag)
// get thermostat target temperature from corresponding fix,
// if the fix supports extraction.
double *tt = (double *) modify->fix[tstat_id]->extract("t_target",tmp);
- if (tt)
- proxy->set_temperature(*tt);
- else
- proxy->set_temperature(0.0);
+ if (tt)
+ proxy->set_temperature(*tt);
+ else
+ proxy->set_temperature(0.0);
}
}
@@ -671,9 +671,9 @@ void FixColvars::post_force(int vflag)
for (i=0; i<num_coords; ++i) {
const int k = atom->map(taglist[i]);
if ((k >= 0) && (k < nlocal)) {
- cd[i].x = x[k][0];
- cd[i].y = x[k][1];
- cd[i].z = x[k][2];
+ cd[i].x = x[k][0];
+ cd[i].y = x[k][1];
+ cd[i].z = x[k][2];
}
}
@@ -687,12 +687,12 @@ void FixColvars::post_force(int vflag)
ndata /= size_one;
for (int k=0; k<ndata; ++k) {
- const int j = inthash_lookup(idmap, comm_buf[k].tag);
- if (j != HASH_FAIL) {
- cd[j].x = comm_buf[k].x;
- cd[j].y = comm_buf[k].y;
- cd[j].z = comm_buf[k].z;
- }
+ const int j = inthash_lookup(idmap, comm_buf[k].tag);
+ if (j != HASH_FAIL) {
+ cd[j].x = comm_buf[k].x;
+ cd[j].y = comm_buf[k].y;
+ cd[j].z = comm_buf[k].z;
+ }
}
}
@@ -702,11 +702,11 @@ void FixColvars::post_force(int vflag)
for (i=0; i<num_coords; ++i) {
const int k = atom->map(taglist[i]);
if ((k >= 0) && (k < nlocal)) {
- comm_buf[nme].tag = tag[k];
- comm_buf[nme].x = x[k][0];
- comm_buf[nme].y = x[k][1];
- comm_buf[nme].z = x[k][2];
- ++nme;
+ comm_buf[nme].tag = tag[k];
+ comm_buf[nme].x = x[k][0];
+ comm_buf[nme].y = x[k][1];
+ comm_buf[nme].z = x[k][2];
+ ++nme;
}
}
/* blocking receive to wait until it is our turn to send data. */
@@ -724,7 +724,7 @@ void FixColvars::post_force(int vflag)
// broadcast store_forces flag and energy data to all processors
MPI_Bcast(&energy, 1, MPI_DOUBLE, 0, world);
- MPI_Bcast(&store_forces, 1, MPI_INT, 0, world);
+ MPI_Bcast(&store_forces, 1, MPI_INT, 0, world);
// broadcast and apply biasing forces
@@ -738,7 +738,7 @@ void FixColvars::post_force(int vflag)
}
}
MPI_Bcast(force_buf, 3*num_coords, MPI_DOUBLE, 0, world);
-
+
for (int i=0; i < num_coords; ++i) {
const int k = atom->map(taglist[i]);
if ((k >= 0) && (k < nlocal)) {
@@ -767,7 +767,7 @@ void FixColvars::post_force_respa(int vflag, int ilevel, int iloop)
void FixColvars::end_of_step()
{
if (store_forces) {
-
+
const int * const tag = atom->tag;
double * const * const f = atom->f;
const int nlocal = atom->nlocal;
@@ -777,7 +777,7 @@ void FixColvars::end_of_step()
for (i=0; i < num_coords; ++i) {
const int k = atom->map(taglist[i]);
if ((k >= 0) && (k < nlocal))
- ++nme;
+ ++nme;
}
MPI_Allreduce(&nme,&nmax_new,1,MPI_INT,MPI_MAX,world);
@@ -789,56 +789,56 @@ void FixColvars::end_of_step()
MPI_Status status;
MPI_Request request;
int tmp, ndata;
-
+
if (me == 0) {
// store old force data
std::vector<struct commdata> &of = *oforce;
for (i=0; i<num_coords; ++i) {
- const int k = atom->map(taglist[i]);
- if ((k >= 0) && (k < nlocal)) {
-
- const int j = inthash_lookup(idmap, tag[k]);
- if (j != HASH_FAIL) {
- of[j].x = f[k][0];
- of[j].y = f[k][1];
- of[j].z = f[k][2];
- }
- }
+ const int k = atom->map(taglist[i]);
+ if ((k >= 0) && (k < nlocal)) {
+
+ const int j = inthash_lookup(idmap, tag[k]);
+ if (j != HASH_FAIL) {
+ of[j].x = f[k][0];
+ of[j].y = f[k][1];
+ of[j].z = f[k][2];
+ }
+ }
}
/* loop over procs to receive remote data */
for (i=1; i < comm->nprocs; ++i) {
- int maxbuf = nmax*size_one;
- MPI_Irecv(comm_buf, maxbuf, MPI_BYTE, i, 0, world, &request);
- MPI_Send(&tmp, 0, MPI_INT, i, 0, world);
- MPI_Wait(&request, &status);
- MPI_Get_count(&status, MPI_BYTE, &ndata);
- ndata /= size_one;
-
- for (int k=0; k<ndata; ++k) {
- const int j = inthash_lookup(idmap, comm_buf[k].tag);
- if (j != HASH_FAIL) {
- of[j].x = comm_buf[k].x;
- of[j].y = comm_buf[k].y;
- of[j].z = comm_buf[k].z;
- }
- }
+ int maxbuf = nmax*size_one;
+ MPI_Irecv(comm_buf, maxbuf, MPI_BYTE, i, 0, world, &request);
+ MPI_Send(&tmp, 0, MPI_INT, i, 0, world);
+ MPI_Wait(&request, &status);
+ MPI_Get_count(&status, MPI_BYTE, &ndata);
+ ndata /= size_one;
+
+ for (int k=0; k<ndata; ++k) {
+ const int j = inthash_lookup(idmap, comm_buf[k].tag);
+ if (j != HASH_FAIL) {
+ of[j].x = comm_buf[k].x;
+ of[j].y = comm_buf[k].y;
+ of[j].z = comm_buf[k].z;
+ }
+ }
}
} else { // me != 0
/* copy total force data into communication buffer */
nme = 0;
for (i=0; i<num_coords; ++i) {
- const int k = atom->map(taglist[i]);
- if ((k >= 0) && (k < nlocal)) {
- comm_buf[nme].tag = tag[k];
- comm_buf[nme].x = f[k][0];
- comm_buf[nme].y = f[k][1];
- comm_buf[nme].z = f[k][2];
- ++nme;
- }
+ const int k = atom->map(taglist[i]);
+ if ((k >= 0) && (k < nlocal)) {
+ comm_buf[nme].tag = tag[k];
+ comm_buf[nme].x = f[k][0];
+ comm_buf[nme].y = f[k][1];
+ comm_buf[nme].z = f[k][2];
+ ++nme;
+ }
}
/* blocking receive to wait until it is our turn to send data. */
MPI_Recv(&tmp, 0, MPI_INT, 0, 0, world, &status);
diff --git a/src/USER-COLVARS/fix_colvars.h b/src/USER-COLVARS/fix_colvars.h
index fda88391f035ba03e1094b6e7e6c70f56d6fbeeb..de144edc58d4cf7db05ca276bd4cab502ae966b8 100644
--- a/src/USER-COLVARS/fix_colvars.h
+++ b/src/USER-COLVARS/fix_colvars.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -42,8 +42,8 @@ class FixColvars : public Fix {
virtual int setmask();
virtual void init();
virtual void setup(int);
- virtual void min_post_force(int);
- virtual void post_force(int);
+ virtual void min_post_force(int);
+ virtual void post_force(int);
virtual void post_force_respa(int, int, int);
virtual void post_run();
virtual void end_of_step();
@@ -59,7 +59,7 @@ class FixColvars : public Fix {
char *inp_name; // name/prefix of colvars restart file
char *out_name; // prefix string for all output files
char *tmp_name; // name of thermostat fix.
- int rng_seed; // seed to initialize random number generator
+ int rng_seed; // seed to initialize random number generator
int tstat_id; // id of the thermostat fix
double energy; // biasing energy of the fix
@@ -69,7 +69,7 @@ class FixColvars : public Fix {
std::vector<struct commdata> *coords; // coordinates of colvar atoms
std::vector<struct commdata> *forces; // received forces of colvar atoms
std::vector<struct commdata> *oforce; // old total forces of colvar atoms
-
+
int nmax; // size of atom communication buffer.
int size_one; // bytes per atom in communication buffer.
struct commdata *comm_buf; // communication buffer
@@ -79,7 +79,7 @@ class FixColvars : public Fix {
int *rev_idmap; // list of the hash keys for reverse mapping.
int nlevels_respa; // flag to determine respa levels.
- int store_forces; // flag to determine whether to store total forces
+ int store_forces; // flag to determine whether to store total forces
static int instances; // count fix instances, since colvars currently
// only supports one instance at a time
};
diff --git a/src/USER-CUDA/atom_vec_angle_cuda.cpp b/src/USER-CUDA/atom_vec_angle_cuda.cpp
index 08ba9761ede019d6387384d8023805f61814220e..f7795a3148ce1263615873d3bb801213438f8c6f 100644
--- a/src/USER-CUDA/atom_vec_angle_cuda.cpp
+++ b/src/USER-CUDA/atom_vec_angle_cuda.cpp
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -28,7 +28,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -64,8 +64,8 @@ AtomVecAngleCuda::AtomVecAngleCuda(LAMMPS *lmp, int narg, char **arg) :
AtomVecAngle(lmp, narg, arg)
{
cuda = lmp->cuda;
- if(cuda == NULL)
- error->all(FLERR,"You cannot use a /cuda class, without activating 'cuda' acceleration. Provide '-c on' as command-line argument to LAMMPS..");
+ if(cuda == NULL)
+ error->all(FLERR,"You cannot use a /cuda class, without activating 'cuda' acceleration. Provide '-c on' as command-line argument to LAMMPS..");
maxsend=0;
cudable=true;
@@ -100,13 +100,13 @@ void AtomVecAngleCuda::grow_send(int n,double** buf_send,int flag) //need to be
if(*buf_send) CudaWrapper_FreePinnedHostData((void*) (*buf_send));
*buf_send = (double*) CudaWrapper_AllocPinnedHostData((*maxsend+BUFEXTRA)*sizeof(double),false);
memcpy(*buf_send,tmp,old_maxsend*sizeof(double));
- delete [] tmp;
+ delete [] tmp;
}
else
{
- *buf_send = (double *)
+ *buf_send = (double *)
memory->srealloc(*buf_send,(*maxsend+BUFEXTRA)*sizeof(double),
- "comm:buf_send");
+ "comm:buf_send");
}
}
else {
@@ -119,7 +119,7 @@ void AtomVecAngleCuda::grow_send(int n,double** buf_send,int flag) //need to be
{
memory->sfree(*buf_send);
*buf_send = (double *) memory->smalloc((*maxsend+BUFEXTRA)*sizeof(double),
- "comm:buf_send");
+ "comm:buf_send");
}
}
}
@@ -141,27 +141,27 @@ void AtomVecAngleCuda::grow_both(int n)
}
int AtomVecAngleCuda::pack_comm(int n, int* iswap, double *buf,
- int pbc_flag, int *pbc) //usually this should not be called since comm->communicate handles the communication if only positions are exchanged
+ int pbc_flag, int *pbc) //usually this should not be called since comm->communicate handles the communication if only positions are exchanged
{
if(not cuda->finished_setup || cuda->oncpu)
- return AtomVecAngle::pack_comm(n,iswap,buf,pbc_flag,pbc);
-
- int m = Cuda_CommCuda_PackComm(&cuda->shared_data,n,*iswap,(void*) buf,pbc,pbc_flag);
- if((sizeof(X_FLOAT)!=sizeof(double)) && m)
- m=(m+1)*sizeof(X_FLOAT)/sizeof(double);
- return m;
+ return AtomVecAngle::pack_comm(n,iswap,buf,pbc_flag,pbc);
+
+ int m = Cuda_CommCuda_PackComm(&cuda->shared_data,n,*iswap,(void*) buf,pbc,pbc_flag);
+ if((sizeof(X_FLOAT)!=sizeof(double)) && m)
+ m=(m+1)*sizeof(X_FLOAT)/sizeof(double);
+ return m;
}
int AtomVecAngleCuda::pack_comm_vel(int n, int* iswap, double *buf,
- int pbc_flag, int *pbc) //usually this should not be called since comm->communicate handles the communication if only positions are exchanged
+ int pbc_flag, int *pbc) //usually this should not be called since comm->communicate handles the communication if only positions are exchanged
{
if(not cuda->finished_setup || cuda->oncpu)
- return AtomVecAngle::pack_comm_vel(n,iswap,buf,pbc_flag,pbc);
-
- int m = Cuda_CommCuda_PackCommVel(&cuda->shared_data,n,*iswap,(void*) buf,pbc,pbc_flag);
- if((sizeof(X_FLOAT)!=sizeof(double)) && m)
- m=(m+1)*sizeof(X_FLOAT)/sizeof(double);
- return m;
+ return AtomVecAngle::pack_comm_vel(n,iswap,buf,pbc_flag,pbc);
+
+ int m = Cuda_CommCuda_PackCommVel(&cuda->shared_data,n,*iswap,(void*) buf,pbc,pbc_flag);
+ if((sizeof(X_FLOAT)!=sizeof(double)) && m)
+ m=(m+1)*sizeof(X_FLOAT)/sizeof(double);
+ return m;
}
/* ---------------------------------------------------------------------- */
@@ -169,7 +169,7 @@ int AtomVecAngleCuda::pack_comm_vel(int n, int* iswap, double *buf,
void AtomVecAngleCuda::unpack_comm(int n, int first, double *buf) //usually this should not be called since comm->communicate handles the communication if only positions are exchanged
{
if(not cuda->finished_setup || cuda->oncpu)
- {AtomVecAngle::unpack_comm(n,first,buf); return;}
+ {AtomVecAngle::unpack_comm(n,first,buf); return;}
Cuda_CommCuda_UnpackComm(&cuda->shared_data,n,first,(void*)buf);
}
@@ -177,7 +177,7 @@ void AtomVecAngleCuda::unpack_comm(int n, int first, double *buf) //usually this
void AtomVecAngleCuda::unpack_comm_vel(int n, int first, double *buf) //usually this should not be called since comm->communicate handles the communication if only positions are exchanged
{
if(not cuda->finished_setup || cuda->oncpu)
- {AtomVecAngle::unpack_comm_vel(n,first,buf); return;}
+ {AtomVecAngle::unpack_comm_vel(n,first,buf); return;}
Cuda_CommCuda_UnpackCommVel(&cuda->shared_data,n,first,(void*)buf);
}
@@ -187,7 +187,7 @@ void AtomVecAngleCuda::unpack_comm_vel(int n, int first, double *buf) //usually
int AtomVecAngleCuda::pack_reverse(int n, int first, double *buf) //usually this should not be called since comm->communicate handles the communication if only forces are exchanged
{
if(not cuda->finished_setup || cuda->oncpu)
- return AtomVecAngle::pack_reverse(n,first,buf);
+ return AtomVecAngle::pack_reverse(n,first,buf);
int i,m,last;
cuda->cu_f->download();
@@ -207,7 +207,7 @@ int AtomVecAngleCuda::pack_reverse(int n, int first, double *buf) //usually this
void AtomVecAngleCuda::unpack_reverse(int n, int *list, double *buf)//usually this should not be called since comm->communicate handles the communication if only forces are exchanged
{
if(not cuda->finished_setup || cuda->oncpu)
- {AtomVecAngle::unpack_reverse(n,list,buf); return;}
+ {AtomVecAngle::unpack_reverse(n,list,buf); return;}
int i,j,m;
@@ -225,23 +225,23 @@ void AtomVecAngleCuda::unpack_reverse(int n, int *list, double *buf)//usually th
/* ---------------------------------------------------------------------- */
int AtomVecAngleCuda::pack_border(int n, int *iswap, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
if(not cuda->finished_setup || cuda->oncpu)
- return AtomVecAngle::pack_border(n,iswap,buf,pbc_flag,pbc);
-
- int m = Cuda_AtomVecAngleCuda_PackBorder(&cuda->shared_data,n,*iswap,(void*) buf,pbc,pbc_flag);
+ return AtomVecAngle::pack_border(n,iswap,buf,pbc_flag,pbc);
+
+ int m = Cuda_AtomVecAngleCuda_PackBorder(&cuda->shared_data,n,*iswap,(void*) buf,pbc,pbc_flag);
return m;
}
int AtomVecAngleCuda::pack_border_vel(int n, int *iswap, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
if(not cuda->finished_setup || cuda->oncpu)
- return AtomVecAngle::pack_border_vel(n,iswap,buf,pbc_flag,pbc);
-
- int m = Cuda_AtomVecAngleCuda_PackBorderVel(&cuda->shared_data,n,*iswap,(void*) buf,pbc,pbc_flag);
-
+ return AtomVecAngle::pack_border_vel(n,iswap,buf,pbc_flag,pbc);
+
+ int m = Cuda_AtomVecAngleCuda_PackBorderVel(&cuda->shared_data,n,*iswap,(void*) buf,pbc,pbc_flag);
+
return m;
}
@@ -250,10 +250,10 @@ int AtomVecAngleCuda::pack_border_vel(int n, int *iswap, double *buf,
void AtomVecAngleCuda::unpack_border(int n, int first, double *buf)
{
if(not cuda->finished_setup || cuda->oncpu)
- {AtomVecAngle::unpack_border(n,first,buf); return;}
+ {AtomVecAngle::unpack_border(n,first,buf); return;}
while(atom->nghost+atom->nlocal+n>=cuda->shared_data.atom.nmax) //ensure there is enough space on device to unpack data
{
- grow_both(0);
+ grow_both(0);
}
int flag=Cuda_AtomVecAngleCuda_UnpackBorder(&cuda->shared_data,n,first,(void*)buf);
if(flag) {printf(" # CUDA: Error: Failed to unpack Border atoms (This might be a bug).\n");}
@@ -262,10 +262,10 @@ void AtomVecAngleCuda::unpack_border(int n, int first, double *buf)
void AtomVecAngleCuda::unpack_border_vel(int n, int first, double *buf)
{
if(not cuda->finished_setup || cuda->oncpu)
- {AtomVecAngle::unpack_border_vel(n,first,buf); return;}
+ {AtomVecAngle::unpack_border_vel(n,first,buf); return;}
while(atom->nghost+atom->nlocal+n>=cuda->shared_data.atom.nmax) //ensure there is enough space on device to unpack data
{
- grow_both(0);
+ grow_both(0);
}
int flag=Cuda_AtomVecAngleCuda_UnpackBorderVel(&cuda->shared_data,n,first,(void*)buf);
if(flag) {printf(" # CUDA: Error: Failed to unpack Border atoms (This might be a bug).\n");}
@@ -273,67 +273,67 @@ void AtomVecAngleCuda::unpack_border_vel(int n, int first, double *buf)
/* ----------------------------------------------------------------------
pack data for atom I for sending to another proc
- xyz must be 1st 3 values, so comm::exchange() can test on them
+ xyz must be 1st 3 values, so comm::exchange() can test on them
------------------------------------------------------------------------- */
int AtomVecAngleCuda::pack_exchange(int dim, double *buf)
{
if(cuda->oncpu)
- return AtomVecAngle::pack_exchange(dim,buf);
+ return AtomVecAngle::pack_exchange(dim,buf);
if(not cuda_init_done||domain->box_change)
{
- Cuda_AtomVecAngleCuda_Init(&cuda->shared_data);
- cuda_init_done=true;
+ Cuda_AtomVecAngleCuda_Init(&cuda->shared_data);
+ cuda_init_done=true;
}
double** buf_pointer=(double**) buf;
if(*maxsend<atom->nghost || *buf_pointer==NULL)
{
- grow_send(atom->nghost>*maxsend?atom->nghost:*maxsend,buf_pointer,0);
- *maxsend=atom->nghost>*maxsend?atom->nghost:*maxsend;
+ grow_send(atom->nghost>*maxsend?atom->nghost:*maxsend,buf_pointer,0);
+ *maxsend=atom->nghost>*maxsend?atom->nghost:*maxsend;
}
-
+
if(max_nsend==0) grow_copylist(200);
int nsend_atoms = Cuda_AtomVecAngleCuda_PackExchangeList(&cuda->shared_data,*maxsend,dim,*buf_pointer);
-
+
if(nsend_atoms>max_nsend) grow_copylist(nsend_atoms+100);
- if(nsend_atoms*NCUDAEXCHANGE>*maxsend)
+ if(nsend_atoms*NCUDAEXCHANGE>*maxsend)
{
- grow_send((int) (nsend_atoms+100)*NCUDAEXCHANGE,buf_pointer,0);
- Cuda_AtomVecAngleCuda_PackExchangeList(&cuda->shared_data,*maxsend,dim,*buf_pointer);
+ grow_send((int) (nsend_atoms+100)*NCUDAEXCHANGE,buf_pointer,0);
+ Cuda_AtomVecAngleCuda_PackExchangeList(&cuda->shared_data,*maxsend,dim,*buf_pointer);
}
int nlocal=atom->nlocal-nsend_atoms;
-
+
for(int i=0;i<nsend_atoms;i++) copylist2[i]=1;
for(int j=1;j<nsend_atoms+1;j++)
{
- int i = static_cast <int> ((*buf_pointer)[j]);
- if(i>=nlocal) copylist2[i-nlocal]=-1;
+ int i = static_cast <int> ((*buf_pointer)[j]);
+ if(i>=nlocal) copylist2[i-nlocal]=-1;
}
-
+
int actpos=0;
for(int j=1;j<nsend_atoms+1;j++)
{
- int i = static_cast <int> ((*buf_pointer)[j]);
- if(i<nlocal)
- {
- while(copylist2[actpos]==-1) actpos++;
- copylist[j-1]=nlocal+actpos;
- actpos++;
- }
+ int i = static_cast <int> ((*buf_pointer)[j]);
+ if(i<nlocal)
+ {
+ while(copylist2[actpos]==-1) actpos++;
+ copylist[j-1]=nlocal+actpos;
+ actpos++;
+ }
}
cu_copylist->upload();
-
+
cuda->shared_data.atom.nlocal=nlocal;
-
+
int m = Cuda_AtomVecAngleCuda_PackExchange(&cuda->shared_data,nsend_atoms,*buf_pointer,cu_copylist->dev_data());
-
+
timespec time1,time2;
clock_gettime(CLOCK_REALTIME,&time1);
-
+
double* buf_p=*buf_pointer;
for(int j=0;j<nsend_atoms;j++)
{
@@ -364,23 +364,23 @@ int AtomVecAngleCuda::pack_exchange(int dim, double *buf)
for (k = 0; k < nspecial[i][2]; k++) buf_p[m++] = special[i][k];
nextra+=nspecial[i][2]+3;
if(m>*maxsend) {grow_send(m,buf_pointer,1); buf_p=*buf_pointer;}
-
+
if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
{
int dm= modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf_p[m]);
m+=dm;
- nextra+=dm;
+ nextra+=dm;
if(i<nlocal)modify->fix[atom->extra_grow[iextra]]->copy_arrays(copylist[j],i);
- if(m>*maxsend) {grow_send(m,buf_pointer,1); buf_p=*buf_pointer;}
+ if(m>*maxsend) {grow_send(m,buf_pointer,1); buf_p=*buf_pointer;}
}
- if(i<nlocal)AtomVecAngle::copy(copylist[j],i,1);
+ if(i<nlocal)AtomVecAngle::copy(copylist[j],i,1);
(*buf_pointer)[j+1] = nextra;
}
-
- clock_gettime(CLOCK_REALTIME,&time2);
- cuda->shared_data.cuda_timings.comm_exchange_cpu_pack+=
+
+ clock_gettime(CLOCK_REALTIME,&time2);
+ cuda->shared_data.cuda_timings.comm_exchange_cpu_pack+=
time2.tv_sec-time1.tv_sec+1.0*(time2.tv_nsec-time1.tv_nsec)/1000000000;
(*buf_pointer)[0] = nsend_atoms;
@@ -397,11 +397,11 @@ int AtomVecAngleCuda::unpack_exchange(double *buf)
{
// printf("Begin UnPack Exchange\n");
if(cuda->oncpu)
- return AtomVecAngle::unpack_exchange(buf);
-
+ return AtomVecAngle::unpack_exchange(buf);
+
double *sublo,*subhi;
int dim=cuda->shared_data.exchange_dim;
- if(domain->box_change)
+ if(domain->box_change)
Cuda_AtomVecAngleCuda_Init(&cuda->shared_data);
if (domain->triclinic == 0) {
sublo = domain->sublo;
@@ -417,7 +417,7 @@ int AtomVecAngleCuda::unpack_exchange(double *buf)
int nlocal = atom->nlocal;
int nsend_atoms=static_cast<int> (buf[0]);
if(nsend_atoms>max_nsend) grow_copylist(nsend_atoms+100);
-
+
if (nlocal+nsend_atoms+atom->nghost>=atom->nmax) grow_both(nlocal+nsend_atoms*2+atom->nghost); //ensure there is enough space on device to unpack data
int naccept = Cuda_AtomVecAngleCuda_UnpackExchange(&cuda->shared_data,nsend_atoms,buf,cu_copylist->dev_data());
cu_copylist->download();
@@ -431,40 +431,40 @@ int AtomVecAngleCuda::unpack_exchange(double *buf)
{
if(copylist[j]>-1)
{
- int k;
- int i=copylist[j];
+ int k;
+ int i=copylist[j];
num_bond[i] = static_cast<int> (buf[m++]);
for (k = 0; k < num_bond[i]; k++) {
- bond_type[i][k] = static_cast<int> (buf[m++]);
- bond_atom[i][k] = static_cast<int> (buf[m++]);
- }
-
- num_angle[i] = static_cast<int> (buf[m++]);
- for (k = 0; k < num_angle[i]; k++) {
- angle_type[i][k] = static_cast<int> (buf[m++]);
- angle_atom1[i][k] = static_cast<int> (buf[m++]);
- angle_atom2[i][k] = static_cast<int> (buf[m++]);
- angle_atom3[i][k] = static_cast<int> (buf[m++]);
- }
-
- nspecial[i][0] = static_cast<int> (buf[m++]);
- nspecial[i][1] = static_cast<int> (buf[m++]);
- nspecial[i][2] = static_cast<int> (buf[m++]);
- for (k = 0; k < nspecial[i][2]; k++)
- special[i][k] = static_cast<int> (buf[m++]);
-
- if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
- m += modify->fix[atom->extra_grow[iextra]]->
- unpack_exchange(i,&buf[m]);
-
+ bond_type[i][k] = static_cast<int> (buf[m++]);
+ bond_atom[i][k] = static_cast<int> (buf[m++]);
+ }
+
+ num_angle[i] = static_cast<int> (buf[m++]);
+ for (k = 0; k < num_angle[i]; k++) {
+ angle_type[i][k] = static_cast<int> (buf[m++]);
+ angle_atom1[i][k] = static_cast<int> (buf[m++]);
+ angle_atom2[i][k] = static_cast<int> (buf[m++]);
+ angle_atom3[i][k] = static_cast<int> (buf[m++]);
+ }
+
+ nspecial[i][0] = static_cast<int> (buf[m++]);
+ nspecial[i][1] = static_cast<int> (buf[m++]);
+ nspecial[i][2] = static_cast<int> (buf[m++]);
+ for (k = 0; k < nspecial[i][2]; k++)
+ special[i][k] = static_cast<int> (buf[m++]);
+
+ if (atom->nextra_grow)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ m += modify->fix[atom->extra_grow[iextra]]->
+ unpack_exchange(i,&buf[m]);
+
}
- else
+ else
m+=static_cast <int> (buf[j+1]);
}
-
- clock_gettime(CLOCK_REALTIME,&time2);
- cuda->shared_data.cuda_timings.comm_exchange_cpu_pack+=
+
+ clock_gettime(CLOCK_REALTIME,&time2);
+ cuda->shared_data.cuda_timings.comm_exchange_cpu_pack+=
time2.tv_sec-time1.tv_sec+1.0*(time2.tv_nsec-time1.tv_nsec)/1000000000;
cuda->shared_data.atom.nlocal=nlocal;
@@ -475,6 +475,3 @@ int AtomVecAngleCuda::unpack_exchange(double *buf)
}
return mfirst;
}
-
-
-
diff --git a/src/USER-CUDA/atom_vec_angle_cuda.h b/src/USER-CUDA/atom_vec_angle_cuda.h
index 0687058acae31cb0eb6b7951e2400435aca3acf4..1c2956e8377c70e8ef3a4ecdeab258dc348ae886 100644
--- a/src/USER-CUDA/atom_vec_angle_cuda.h
+++ b/src/USER-CUDA/atom_vec_angle_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
diff --git a/src/USER-CUDA/atom_vec_atomic_cuda.cpp b/src/USER-CUDA/atom_vec_atomic_cuda.cpp
index f6b2d76b854068d9205e41b8543ca294ca39194d..51ce230b8ce5e61b5f2fc458975389951a7a16b2 100644
--- a/src/USER-CUDA/atom_vec_atomic_cuda.cpp
+++ b/src/USER-CUDA/atom_vec_atomic_cuda.cpp
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -28,7 +28,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -100,13 +100,13 @@ void AtomVecAtomicCuda::grow_send(int n,double** buf_send,int flag)
if(*buf_send) CudaWrapper_FreePinnedHostData((void*) (*buf_send));
*buf_send = (double*) CudaWrapper_AllocPinnedHostData((*maxsend+BUFEXTRA)*sizeof(double),false);
memcpy(*buf_send,tmp,old_maxsend*sizeof(double));
- delete [] tmp;
+ delete [] tmp;
}
else
{
- *buf_send = (double *)
+ *buf_send = (double *)
memory->srealloc(*buf_send,(*maxsend+BUFEXTRA)*sizeof(double),
- "comm:buf_send");
+ "comm:buf_send");
}
}
else {
@@ -119,7 +119,7 @@ void AtomVecAtomicCuda::grow_send(int n,double** buf_send,int flag)
{
memory->sfree(*buf_send);
*buf_send = (double *) memory->smalloc((*maxsend+BUFEXTRA)*sizeof(double),
- "comm:buf_send");
+ "comm:buf_send");
}
}
}
@@ -127,7 +127,7 @@ void AtomVecAtomicCuda::grow_send(int n,double** buf_send,int flag)
void AtomVecAtomicCuda::grow_both(int n)
{
if(cuda->finished_setup)
- cuda->downloadAll();
+ cuda->downloadAll();
AtomVecAtomic::grow(n);
if(cuda->finished_setup)
{
@@ -137,34 +137,34 @@ void AtomVecAtomicCuda::grow_both(int n)
}
int AtomVecAtomicCuda::pack_comm(int n, int* iswap, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
if(not cuda->finished_setup || cuda->oncpu)
- return AtomVecAtomic::pack_comm(n,iswap,buf,pbc_flag,pbc);
-
- int m = Cuda_CommCuda_PackComm(&cuda->shared_data,n,*iswap,(void*) buf,pbc,pbc_flag);
- if((sizeof(X_FLOAT)!=sizeof(double)) && m)
- m=(m+1)*sizeof(X_FLOAT)/sizeof(double);
- return m;
+ return AtomVecAtomic::pack_comm(n,iswap,buf,pbc_flag,pbc);
+
+ int m = Cuda_CommCuda_PackComm(&cuda->shared_data,n,*iswap,(void*) buf,pbc,pbc_flag);
+ if((sizeof(X_FLOAT)!=sizeof(double)) && m)
+ m=(m+1)*sizeof(X_FLOAT)/sizeof(double);
+ return m;
}
int AtomVecAtomicCuda::pack_comm_vel(int n, int* iswap, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
if(not cuda->finished_setup || cuda->oncpu)
- return AtomVecAtomic::pack_comm_vel(n,iswap,buf,pbc_flag,pbc);
-
- int m = Cuda_CommCuda_PackCommVel(&cuda->shared_data,n,*iswap,(void*) buf,pbc,pbc_flag);
- if((sizeof(X_FLOAT)!=sizeof(double)) && m)
- m=(m+1)*sizeof(X_FLOAT)/sizeof(double);
- return m;
+ return AtomVecAtomic::pack_comm_vel(n,iswap,buf,pbc_flag,pbc);
+
+ int m = Cuda_CommCuda_PackCommVel(&cuda->shared_data,n,*iswap,(void*) buf,pbc,pbc_flag);
+ if((sizeof(X_FLOAT)!=sizeof(double)) && m)
+ m=(m+1)*sizeof(X_FLOAT)/sizeof(double);
+ return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecAtomicCuda::unpack_comm(int n, int first, double *buf)
{
if(not cuda->finished_setup || cuda->oncpu)
- {AtomVecAtomic::unpack_comm(n,first,buf); return;}
+ {AtomVecAtomic::unpack_comm(n,first,buf); return;}
Cuda_CommCuda_UnpackComm(&cuda->shared_data,n,first,(void*)buf);
}
@@ -172,7 +172,7 @@ void AtomVecAtomicCuda::unpack_comm(int n, int first, double *buf)
void AtomVecAtomicCuda::unpack_comm_vel(int n, int first, double *buf)
{
if(not cuda->finished_setup || cuda->oncpu)
- {AtomVecAtomic::unpack_comm_vel(n,first,buf); return;}
+ {AtomVecAtomic::unpack_comm_vel(n,first,buf); return;}
Cuda_CommCuda_UnpackCommVel(&cuda->shared_data,n,first,(void*)buf);
}
@@ -181,7 +181,7 @@ void AtomVecAtomicCuda::unpack_comm_vel(int n, int first, double *buf)
int AtomVecAtomicCuda::pack_reverse(int n, int first, double *buf)
{
if(not cuda->finished_setup || cuda->oncpu)
- return AtomVecAtomic::pack_reverse(n,first,buf);
+ return AtomVecAtomic::pack_reverse(n,first,buf);
int i,m,last;
@@ -200,7 +200,7 @@ int AtomVecAtomicCuda::pack_reverse(int n, int first, double *buf)
void AtomVecAtomicCuda::unpack_reverse(int n, int *list, double *buf)
{
if(not cuda->finished_setup || cuda->oncpu)
- {AtomVecAtomic::unpack_reverse(n,list,buf); return;}
+ {AtomVecAtomic::unpack_reverse(n,list,buf); return;}
int i,j,m;
@@ -216,22 +216,22 @@ void AtomVecAtomicCuda::unpack_reverse(int n, int *list, double *buf)
/* ---------------------------------------------------------------------- */
int AtomVecAtomicCuda::pack_border(int n, int *iswap, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
if(not cuda->finished_setup || cuda->oncpu)
- return AtomVecAtomic::pack_border(n,iswap,buf,pbc_flag,pbc);
-
+ return AtomVecAtomic::pack_border(n,iswap,buf,pbc_flag,pbc);
+
int m = Cuda_AtomVecAtomicCuda_PackBorder(&cuda->shared_data,n,*iswap,(void*) buf,pbc,pbc_flag);
return m;
}
int AtomVecAtomicCuda::pack_border_vel(int n, int *iswap, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
if(not cuda->finished_setup || cuda->oncpu)
- return AtomVecAtomic::pack_border_vel(n,iswap,buf,pbc_flag,pbc);
-
+ return AtomVecAtomic::pack_border_vel(n,iswap,buf,pbc_flag,pbc);
+
int m = Cuda_AtomVecAtomicCuda_PackBorderVel(&cuda->shared_data,n,*iswap,(void*) buf,pbc,pbc_flag);
return m;
@@ -241,10 +241,10 @@ int AtomVecAtomicCuda::pack_border_vel(int n, int *iswap, double *buf,
void AtomVecAtomicCuda::unpack_border(int n, int first, double *buf)
{
if(not cuda->finished_setup || cuda->oncpu)
- {AtomVecAtomic::unpack_border(n,first,buf); return;}
- while(atom->nghost+atom->nlocal+n>=cuda->shared_data.atom.nmax)
+ {AtomVecAtomic::unpack_border(n,first,buf); return;}
+ while(atom->nghost+atom->nlocal+n>=cuda->shared_data.atom.nmax)
{
- grow_both(0);
+ grow_both(0);
}
int flag=Cuda_AtomVecAtomicCuda_UnpackBorder(&cuda->shared_data,n,first,(void*)buf);
if(flag) {printf(" # CUDA: Error: Failed to unpack Border atoms (This might be a bug).\n");}
@@ -254,72 +254,72 @@ void AtomVecAtomicCuda::unpack_border(int n, int first, double *buf)
void AtomVecAtomicCuda::unpack_border_vel(int n, int first, double *buf)
{
if(not cuda->finished_setup || cuda->oncpu)
- {AtomVecAtomic::unpack_border_vel(n,first,buf); return;}
- while(atom->nghost+atom->nlocal+n>=cuda->shared_data.atom.nmax)
+ {AtomVecAtomic::unpack_border_vel(n,first,buf); return;}
+ while(atom->nghost+atom->nlocal+n>=cuda->shared_data.atom.nmax)
{
- grow_both(0);
+ grow_both(0);
}
int flag=Cuda_AtomVecAtomicCuda_UnpackBorderVel(&cuda->shared_data,n,first,(void*)buf);
if(flag) {printf(" # CUDA: Error: Failed to unpack Border atoms (This might be a bug).\n");}
}
/* ----------------------------------------------------------------------
pack data for atom I for sending to another proc
- xyz must be 1st 3 values, so comm::exchange() can test on them
+ xyz must be 1st 3 values, so comm::exchange() can test on them
------------------------------------------------------------------------- */
int AtomVecAtomicCuda::pack_exchange(int dim, double *buf)
{
if(cuda->oncpu)
- return AtomVecAtomic::pack_exchange(dim,buf);
+ return AtomVecAtomic::pack_exchange(dim,buf);
if(not cuda_init_done||domain->box_change)
{
- Cuda_AtomVecAtomicCuda_Init(&cuda->shared_data);
- cuda_init_done=true;
+ Cuda_AtomVecAtomicCuda_Init(&cuda->shared_data);
+ cuda_init_done=true;
}
double** buf_pointer=(double**) buf;
if(*maxsend<atom->nghost || *buf_pointer==NULL)
{
- grow_send(atom->nghost>*maxsend?atom->nghost:*maxsend,buf_pointer,0);
- *maxsend=atom->nghost>*maxsend?atom->nghost:*maxsend;
+ grow_send(atom->nghost>*maxsend?atom->nghost:*maxsend,buf_pointer,0);
+ *maxsend=atom->nghost>*maxsend?atom->nghost:*maxsend;
}
-
+
if(max_nsend==0) grow_copylist(200);
int nsend_atoms = Cuda_AtomVecAtomicCuda_PackExchangeList(&cuda->shared_data,*maxsend,dim,*buf_pointer);
-
+
if(nsend_atoms>max_nsend) {grow_copylist(nsend_atoms+100);}
- if(nsend_atoms*NCUDAEXCHANGE>*maxsend)
+ if(nsend_atoms*NCUDAEXCHANGE>*maxsend)
{
- grow_send((int) (nsend_atoms+100)*NCUDAEXCHANGE,buf_pointer,0);
- Cuda_AtomVecAtomicCuda_PackExchangeList(&cuda->shared_data,*maxsend,dim,*buf_pointer);
+ grow_send((int) (nsend_atoms+100)*NCUDAEXCHANGE,buf_pointer,0);
+ Cuda_AtomVecAtomicCuda_PackExchangeList(&cuda->shared_data,*maxsend,dim,*buf_pointer);
}
-
+
int nlocal=atom->nlocal-nsend_atoms;
-
+
for(int i=0;i<nsend_atoms;i++) copylist2[i]=1;
for(int j=1;j<nsend_atoms+1;j++)
{
- int i = static_cast <int> ((*buf_pointer)[j]);
- if(i>=nlocal) copylist2[i-nlocal]=-1;
+ int i = static_cast <int> ((*buf_pointer)[j]);
+ if(i>=nlocal) copylist2[i-nlocal]=-1;
}
-
+
int actpos=0;
for(int j=1;j<nsend_atoms+1;j++)
{
- int i = static_cast <int> ((*buf_pointer)[j]);
- if(i<nlocal)
- {
- while(copylist2[actpos]==-1) actpos++;
- copylist[j-1]=nlocal+actpos;
- actpos++;
- }
+ int i = static_cast <int> ((*buf_pointer)[j]);
+ if(i<nlocal)
+ {
+ while(copylist2[actpos]==-1) actpos++;
+ copylist[j-1]=nlocal+actpos;
+ actpos++;
+ }
}
cu_copylist->upload();
-
+
cuda->shared_data.atom.nlocal=nlocal;
-
+
int m = Cuda_AtomVecAtomicCuda_PackExchange(&cuda->shared_data,nsend_atoms,*buf_pointer,cu_copylist->dev_data());
if (atom->nextra_grow)
for(int j=0;j<nsend_atoms;j++)
@@ -327,15 +327,15 @@ int AtomVecAtomicCuda::pack_exchange(int dim, double *buf)
int i=static_cast <int> ((*buf_pointer)[j+1]);
int nextra=0;
for (int iextra = 0; iextra < atom->nextra_grow; iextra++) {
-
+
int dm = modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&((*buf_pointer)[m]));
m+=dm;
- nextra+=dm;
+ nextra+=dm;
if(i<nlocal)modify->fix[atom->extra_grow[iextra]]->copy_arrays(copylist[j],i);
if(m>*maxsend) grow_send(m,buf_pointer,1);
}
(*buf_pointer)[j+1] = nextra;
-
+
}
(*buf_pointer)[0] = nsend_atoms;
@@ -352,12 +352,12 @@ int AtomVecAtomicCuda::unpack_exchange(double *buf)
{
//printf("Unpack Begin\n");
if(cuda->oncpu)
- return AtomVecAtomic::unpack_exchange(buf);
+ return AtomVecAtomic::unpack_exchange(buf);
double *sublo,*subhi;
int dim=cuda->shared_data.exchange_dim;
- if(domain->box_change)
+ if(domain->box_change)
Cuda_AtomVecAtomicCuda_Init(&cuda->shared_data);
if (domain->triclinic == 0) {
sublo = domain->sublo;
@@ -371,10 +371,10 @@ int AtomVecAtomicCuda::unpack_exchange(double *buf)
for(int pi=0;pi<(comm->procgrid[dim]>2?2:1);pi++)
{
int nlocal = atom->nlocal;
-
+
int nsend_atoms=static_cast<int> (buf[0]);
if(nsend_atoms>max_nsend) grow_copylist(nsend_atoms+100);
-
+
if (nlocal+nsend_atoms+atom->nghost>=atom->nmax) grow_both(nlocal+nsend_atoms*2+atom->nghost);
int naccept = Cuda_AtomVecAtomicCuda_UnpackExchange(&cuda->shared_data,nsend_atoms,buf,cu_copylist->dev_data());
cu_copylist->download();
@@ -385,9 +385,9 @@ int AtomVecAtomicCuda::unpack_exchange(double *buf)
{
if(copylist[j]>-1)
{
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
- m += modify->fix[atom->extra_grow[iextra]]->
- unpack_exchange(copylist[j],&buf[m]);
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ m += modify->fix[atom->extra_grow[iextra]]->
+ unpack_exchange(copylist[j],&buf[m]);
}
else
{
@@ -403,6 +403,3 @@ int AtomVecAtomicCuda::unpack_exchange(double *buf)
}
return mfirst;
}
-
-
-
diff --git a/src/USER-CUDA/atom_vec_atomic_cuda.h b/src/USER-CUDA/atom_vec_atomic_cuda.h
index da6dfb4d3a7108d126d95108ce0625784678063f..17b803d8ad383497ffcef1c2cc9b93a29614f469 100644
--- a/src/USER-CUDA/atom_vec_atomic_cuda.h
+++ b/src/USER-CUDA/atom_vec_atomic_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -28,7 +28,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-CUDA/atom_vec_charge_cuda.cpp b/src/USER-CUDA/atom_vec_charge_cuda.cpp
index a15836c45b74ed4c61b37f9371f419f598d3590d..991038debb43e4d80a5cdbcb562c07dae62d6315 100644
--- a/src/USER-CUDA/atom_vec_charge_cuda.cpp
+++ b/src/USER-CUDA/atom_vec_charge_cuda.cpp
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -28,7 +28,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -99,13 +99,13 @@ void AtomVecChargeCuda::grow_send(int n,double** buf_send,int flag) //need to b
if(*buf_send) CudaWrapper_FreePinnedHostData((void*) (*buf_send));
*buf_send = (double*) CudaWrapper_AllocPinnedHostData((*maxsend+BUFEXTRA)*sizeof(double),false);
memcpy(*buf_send,tmp,old_maxsend*sizeof(double));
- delete [] tmp;
+ delete [] tmp;
}
else
{
- *buf_send = (double *)
+ *buf_send = (double *)
memory->srealloc(*buf_send,(*maxsend+BUFEXTRA)*sizeof(double),
- "comm:buf_send");
+ "comm:buf_send");
}
}
else {
@@ -118,7 +118,7 @@ void AtomVecChargeCuda::grow_send(int n,double** buf_send,int flag) //need to b
{
memory->sfree(*buf_send);
*buf_send = (double *) memory->smalloc((*maxsend+BUFEXTRA)*sizeof(double),
- "comm:buf_send");
+ "comm:buf_send");
}
}
}
@@ -126,7 +126,7 @@ void AtomVecChargeCuda::grow_send(int n,double** buf_send,int flag) //need to b
void AtomVecChargeCuda::grow_both(int n)
{
if(cuda->finished_setup)
- cuda->downloadAll();
+ cuda->downloadAll();
AtomVecCharge::grow(n);
if(cuda->finished_setup)
{
@@ -136,27 +136,27 @@ void AtomVecChargeCuda::grow_both(int n)
}
int AtomVecChargeCuda::pack_comm(int n, int* iswap, double *buf,
- int pbc_flag, int *pbc) //usually this should not be called since comm->communicate handles the communication if only positions are exchanged
+ int pbc_flag, int *pbc) //usually this should not be called since comm->communicate handles the communication if only positions are exchanged
{
if(not cuda->finished_setup || cuda->oncpu)
- return AtomVecCharge::pack_comm(n,iswap,buf,pbc_flag,pbc);
-
- int m = Cuda_CommCuda_PackComm(&cuda->shared_data,n,*iswap,(void*) buf,pbc,pbc_flag);
- if((sizeof(X_FLOAT)!=sizeof(double)) && m)
- m=(m+1)*sizeof(X_FLOAT)/sizeof(double);
- return m;
+ return AtomVecCharge::pack_comm(n,iswap,buf,pbc_flag,pbc);
+
+ int m = Cuda_CommCuda_PackComm(&cuda->shared_data,n,*iswap,(void*) buf,pbc,pbc_flag);
+ if((sizeof(X_FLOAT)!=sizeof(double)) && m)
+ m=(m+1)*sizeof(X_FLOAT)/sizeof(double);
+ return m;
}
int AtomVecChargeCuda::pack_comm_vel(int n, int* iswap, double *buf,
- int pbc_flag, int *pbc) //usually this should not be called since comm->communicate handles the communication if only positions are exchanged
+ int pbc_flag, int *pbc) //usually this should not be called since comm->communicate handles the communication if only positions are exchanged
{
if(not cuda->finished_setup || cuda->oncpu)
- return AtomVecCharge::pack_comm_vel(n,iswap,buf,pbc_flag,pbc);
-
- int m = Cuda_CommCuda_PackCommVel(&cuda->shared_data,n,*iswap,(void*) buf,pbc,pbc_flag);
- if((sizeof(X_FLOAT)!=sizeof(double)) && m)
- m=(m+1)*sizeof(X_FLOAT)/sizeof(double);
- return m;
+ return AtomVecCharge::pack_comm_vel(n,iswap,buf,pbc_flag,pbc);
+
+ int m = Cuda_CommCuda_PackCommVel(&cuda->shared_data,n,*iswap,(void*) buf,pbc,pbc_flag);
+ if((sizeof(X_FLOAT)!=sizeof(double)) && m)
+ m=(m+1)*sizeof(X_FLOAT)/sizeof(double);
+ return m;
}
/* ---------------------------------------------------------------------- */
@@ -164,7 +164,7 @@ int AtomVecChargeCuda::pack_comm_vel(int n, int* iswap, double *buf,
void AtomVecChargeCuda::unpack_comm(int n, int first, double *buf) //usually this should not be called since comm->communicate handles the communication if only positions are exchanged
{
if(not cuda->finished_setup || cuda->oncpu)
- {AtomVecCharge::unpack_comm(n,first,buf); return;}
+ {AtomVecCharge::unpack_comm(n,first,buf); return;}
Cuda_CommCuda_UnpackComm(&cuda->shared_data,n,first,(void*)buf);
}
@@ -172,7 +172,7 @@ void AtomVecChargeCuda::unpack_comm(int n, int first, double *buf) //usually thi
void AtomVecChargeCuda::unpack_comm_vel(int n, int first, double *buf) //usually this should not be called since comm->communicate handles the communication if only positions are exchanged
{
if(not cuda->finished_setup || cuda->oncpu)
- {AtomVecCharge::unpack_comm_vel(n,first,buf); return;}
+ {AtomVecCharge::unpack_comm_vel(n,first,buf); return;}
Cuda_CommCuda_UnpackCommVel(&cuda->shared_data,n,first,(void*)buf);
}
@@ -182,7 +182,7 @@ void AtomVecChargeCuda::unpack_comm_vel(int n, int first, double *buf) //usually
int AtomVecChargeCuda::pack_reverse(int n, int first, double *buf) //usually this should not be called since comm->communicate handles the communication if only forces are exchanged
{
if(not cuda->finished_setup || cuda->oncpu)
- return AtomVecCharge::pack_reverse(n,first,buf);
+ return AtomVecCharge::pack_reverse(n,first,buf);
int i,m,last;
cuda->cu_f->download();
@@ -202,7 +202,7 @@ int AtomVecChargeCuda::pack_reverse(int n, int first, double *buf) //usually thi
void AtomVecChargeCuda::unpack_reverse(int n, int *list, double *buf)//usually this should not be called since comm->communicate handles the communication if only forces are exchanged
{
if(not cuda->finished_setup || cuda->oncpu)
- {AtomVecCharge::unpack_reverse(n,list,buf); return;}
+ {AtomVecCharge::unpack_reverse(n,list,buf); return;}
int i,j,m;
@@ -220,24 +220,24 @@ void AtomVecChargeCuda::unpack_reverse(int n, int *list, double *buf)//usually t
/* ---------------------------------------------------------------------- */
int AtomVecChargeCuda::pack_border(int n, int *iswap, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
if(not cuda->finished_setup || cuda->oncpu)
- return AtomVecCharge::pack_border(n,iswap,buf,pbc_flag,pbc);
-
- int m = Cuda_AtomVecChargeCuda_PackBorder(&cuda->shared_data,n,*iswap,(void*) buf,pbc,pbc_flag);
-
+ return AtomVecCharge::pack_border(n,iswap,buf,pbc_flag,pbc);
+
+ int m = Cuda_AtomVecChargeCuda_PackBorder(&cuda->shared_data,n,*iswap,(void*) buf,pbc,pbc_flag);
+
return m;
}
int AtomVecChargeCuda::pack_border_vel(int n, int *iswap, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
if(not cuda->finished_setup || cuda->oncpu)
- return AtomVecCharge::pack_border_vel(n,iswap,buf,pbc_flag,pbc);
-
- int m = Cuda_AtomVecChargeCuda_PackBorderVel(&cuda->shared_data,n,*iswap,(void*) buf,pbc,pbc_flag);
-
+ return AtomVecCharge::pack_border_vel(n,iswap,buf,pbc_flag,pbc);
+
+ int m = Cuda_AtomVecChargeCuda_PackBorderVel(&cuda->shared_data,n,*iswap,(void*) buf,pbc,pbc_flag);
+
return m;
}
@@ -246,10 +246,10 @@ int AtomVecChargeCuda::pack_border_vel(int n, int *iswap, double *buf,
void AtomVecChargeCuda::unpack_border(int n, int first, double *buf)
{
if(not cuda->finished_setup || cuda->oncpu)
- {AtomVecCharge::unpack_border(n,first,buf); return;}
+ {AtomVecCharge::unpack_border(n,first,buf); return;}
while(atom->nghost+atom->nlocal+n>=cuda->shared_data.atom.nmax) //ensure there is enough space on device to unpack data
{
- grow_both(0);
+ grow_both(0);
}
int flag=Cuda_AtomVecChargeCuda_UnpackBorder(&cuda->shared_data,n,first,(void*)buf);
if(flag) {printf(" # CUDA: Error: Failed to unpack Border atoms (This might be a bug).\n");}
@@ -258,10 +258,10 @@ void AtomVecChargeCuda::unpack_border(int n, int first, double *buf)
void AtomVecChargeCuda::unpack_border_vel(int n, int first, double *buf)
{
if(not cuda->finished_setup || cuda->oncpu)
- {AtomVecCharge::unpack_border_vel(n,first,buf); return;}
+ {AtomVecCharge::unpack_border_vel(n,first,buf); return;}
while(atom->nghost+atom->nlocal+n>=cuda->shared_data.atom.nmax) //ensure there is enough space on device to unpack data
{
- grow_both(0);
+ grow_both(0);
}
int flag=Cuda_AtomVecChargeCuda_UnpackBorderVel(&cuda->shared_data,n,first,(void*)buf);
if(flag) {printf(" # CUDA: Error: Failed to unpack Border atoms (This might be a bug).\n");}
@@ -269,74 +269,74 @@ void AtomVecChargeCuda::unpack_border_vel(int n, int first, double *buf)
/* ----------------------------------------------------------------------
pack data for atom I for sending to another proc
- xyz must be 1st 3 values, so comm::exchange() can test on them
+ xyz must be 1st 3 values, so comm::exchange() can test on them
------------------------------------------------------------------------- */
int AtomVecChargeCuda::pack_exchange(int dim, double *buf)
{
if(cuda->oncpu)
- return AtomVecCharge::pack_exchange(dim,buf);
+ return AtomVecCharge::pack_exchange(dim,buf);
if(not cuda_init_done||domain->box_change)
{
- Cuda_AtomVecChargeCuda_Init(&cuda->shared_data);
- cuda_init_done=true;
+ Cuda_AtomVecChargeCuda_Init(&cuda->shared_data);
+ cuda_init_done=true;
}
double** buf_pointer=(double**) buf;
if(*maxsend<atom->nghost || *buf_pointer==NULL)
{
- grow_send(atom->nghost>*maxsend?atom->nghost:*maxsend,buf_pointer,0);
- *maxsend=atom->nghost>*maxsend?atom->nghost:*maxsend;
+ grow_send(atom->nghost>*maxsend?atom->nghost:*maxsend,buf_pointer,0);
+ *maxsend=atom->nghost>*maxsend?atom->nghost:*maxsend;
}
-
+
if(max_nsend==0) grow_copylist(200);
int nsend_atoms = Cuda_AtomVecChargeCuda_PackExchangeList(&cuda->shared_data,*maxsend,dim,*buf_pointer);
-
+
if(nsend_atoms>max_nsend) grow_copylist(nsend_atoms+100);
- if(nsend_atoms*NCUDAEXCHANGE>*maxsend)
+ if(nsend_atoms*NCUDAEXCHANGE>*maxsend)
{
- grow_send((int) (nsend_atoms+100)*NCUDAEXCHANGE,buf_pointer,0);
- Cuda_AtomVecChargeCuda_PackExchangeList(&cuda->shared_data,*maxsend,dim,*buf_pointer);
+ grow_send((int) (nsend_atoms+100)*NCUDAEXCHANGE,buf_pointer,0);
+ Cuda_AtomVecChargeCuda_PackExchangeList(&cuda->shared_data,*maxsend,dim,*buf_pointer);
}
-
+
int nlocal=atom->nlocal-nsend_atoms;
-
+
for(int i=0;i<nsend_atoms;i++) copylist2[i]=1;
for(int j=1;j<nsend_atoms+1;j++)
{
- int i = static_cast <int> ((*buf_pointer)[j]);
- if(i>=nlocal) copylist2[i-nlocal]=-1;
+ int i = static_cast <int> ((*buf_pointer)[j]);
+ if(i>=nlocal) copylist2[i-nlocal]=-1;
}
-
+
int actpos=0;
for(int j=1;j<nsend_atoms+1;j++)
{
- int i = static_cast <int> ((*buf_pointer)[j]);
- if(i<nlocal)
- {
- while(copylist2[actpos]==-1) actpos++;
- copylist[j-1]=nlocal+actpos;
- actpos++;
- }
+ int i = static_cast <int> ((*buf_pointer)[j]);
+ if(i<nlocal)
+ {
+ while(copylist2[actpos]==-1) actpos++;
+ copylist[j-1]=nlocal+actpos;
+ actpos++;
+ }
}
cu_copylist->upload();
-
+
cuda->shared_data.atom.nlocal=nlocal;
-
+
int m = Cuda_AtomVecChargeCuda_PackExchange(&cuda->shared_data,nsend_atoms,*buf_pointer,cu_copylist->dev_data());
-
+
if (atom->nextra_grow)
for(int j=0;j<nsend_atoms;j++)
{
int i=static_cast <int> ((*buf_pointer)[j+1]);
int nextra=0;
for (int iextra = 0; iextra < atom->nextra_grow; iextra++) {
-
+
int dm = modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&((*buf_pointer)[m]));
m+=dm;
- nextra+=dm;
+ nextra+=dm;
if(i<nlocal)modify->fix[atom->extra_grow[iextra]]->copy_arrays(copylist[j],i);
if(m>*maxsend) grow_send(m,buf_pointer,1);
}
@@ -356,11 +356,11 @@ int AtomVecChargeCuda::pack_exchange(int dim, double *buf)
int AtomVecChargeCuda::unpack_exchange(double *buf)
{
if(cuda->oncpu)
- return AtomVecCharge::unpack_exchange(buf);
+ return AtomVecCharge::unpack_exchange(buf);
double *sublo,*subhi;
int dim=cuda->shared_data.exchange_dim;
- if(domain->box_change)
+ if(domain->box_change)
Cuda_AtomVecChargeCuda_Init(&cuda->shared_data);
if (domain->triclinic == 0) {
sublo = domain->sublo;
@@ -376,7 +376,7 @@ int AtomVecChargeCuda::unpack_exchange(double *buf)
int nlocal = atom->nlocal;
int nsend_atoms=static_cast<int> (buf[0]);
if(nsend_atoms>max_nsend) grow_copylist(nsend_atoms+100);
-
+
if (nlocal+nsend_atoms+atom->nghost>=atom->nmax) grow_both(nlocal+nsend_atoms*2+atom->nghost);
int naccept = Cuda_AtomVecChargeCuda_UnpackExchange(&cuda->shared_data,nsend_atoms,buf,cu_copylist->dev_data());
cu_copylist->download();
@@ -387,9 +387,9 @@ int AtomVecChargeCuda::unpack_exchange(double *buf)
{
if(copylist[j]>-1)
{
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
- m += modify->fix[atom->extra_grow[iextra]]->
- unpack_exchange(copylist[j],&buf[m]);
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ m += modify->fix[atom->extra_grow[iextra]]->
+ unpack_exchange(copylist[j],&buf[m]);
}
else
m+=static_cast <int> (buf[j+1]);
@@ -402,6 +402,3 @@ int AtomVecChargeCuda::unpack_exchange(double *buf)
}
return mfirst;
}
-
-
-
diff --git a/src/USER-CUDA/atom_vec_charge_cuda.h b/src/USER-CUDA/atom_vec_charge_cuda.h
index 924dd55c853e3278026350b0863f33c5719627f1..ba7b57e75f0d2d40a967cde7d277597525f2856e 100644
--- a/src/USER-CUDA/atom_vec_charge_cuda.h
+++ b/src/USER-CUDA/atom_vec_charge_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
diff --git a/src/USER-CUDA/atom_vec_full_cuda.cpp b/src/USER-CUDA/atom_vec_full_cuda.cpp
index 9816a7c5c9c75aa6c0ee01d230bb02480a172847..ce56c719cc2d57cc3d361661637e0d59b392af80 100644
--- a/src/USER-CUDA/atom_vec_full_cuda.cpp
+++ b/src/USER-CUDA/atom_vec_full_cuda.cpp
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -28,7 +28,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -100,13 +100,13 @@ void AtomVecFullCuda::grow_send(int n,double** buf_send,int flag) //need to be
if(*buf_send) CudaWrapper_FreePinnedHostData((void*) (*buf_send));
*buf_send = (double*) CudaWrapper_AllocPinnedHostData((*maxsend+BUFEXTRA)*sizeof(double),false);
memcpy(*buf_send,tmp,old_maxsend*sizeof(double));
- delete [] tmp;
+ delete [] tmp;
}
else
{
- *buf_send = (double *)
+ *buf_send = (double *)
memory->srealloc(*buf_send,(*maxsend+BUFEXTRA)*sizeof(double),
- "comm:buf_send");
+ "comm:buf_send");
}
}
else {
@@ -119,7 +119,7 @@ void AtomVecFullCuda::grow_send(int n,double** buf_send,int flag) //need to be
{
memory->sfree(*buf_send);
*buf_send = (double *) memory->smalloc((*maxsend+BUFEXTRA)*sizeof(double),
- "comm:buf_send");
+ "comm:buf_send");
}
}
}
@@ -141,27 +141,27 @@ void AtomVecFullCuda::grow_both(int n)
}
int AtomVecFullCuda::pack_comm(int n, int* iswap, double *buf,
- int pbc_flag, int *pbc) //usually this should not be called since comm->communicate handles the communication if only positions are exchanged
+ int pbc_flag, int *pbc) //usually this should not be called since comm->communicate handles the communication if only positions are exchanged
{
if(not cuda->finished_setup || cuda->oncpu)
- return AtomVecFull::pack_comm(n,iswap,buf,pbc_flag,pbc);
-
- int m = Cuda_CommCuda_PackComm(&cuda->shared_data,n,*iswap,(void*) buf,pbc,pbc_flag);
- if((sizeof(X_FLOAT)!=sizeof(double)) && m)
- m=(m+1)*sizeof(X_FLOAT)/sizeof(double);
- return m;
+ return AtomVecFull::pack_comm(n,iswap,buf,pbc_flag,pbc);
+
+ int m = Cuda_CommCuda_PackComm(&cuda->shared_data,n,*iswap,(void*) buf,pbc,pbc_flag);
+ if((sizeof(X_FLOAT)!=sizeof(double)) && m)
+ m=(m+1)*sizeof(X_FLOAT)/sizeof(double);
+ return m;
}
int AtomVecFullCuda::pack_comm_vel(int n, int* iswap, double *buf,
- int pbc_flag, int *pbc) //usually this should not be called since comm->communicate handles the communication if only positions are exchanged
+ int pbc_flag, int *pbc) //usually this should not be called since comm->communicate handles the communication if only positions are exchanged
{
if(not cuda->finished_setup || cuda->oncpu)
- return AtomVecFull::pack_comm_vel(n,iswap,buf,pbc_flag,pbc);
-
- int m = Cuda_CommCuda_PackCommVel(&cuda->shared_data,n,*iswap,(void*) buf,pbc,pbc_flag);
- if((sizeof(X_FLOAT)!=sizeof(double)) && m)
- m=(m+1)*sizeof(X_FLOAT)/sizeof(double);
- return m;
+ return AtomVecFull::pack_comm_vel(n,iswap,buf,pbc_flag,pbc);
+
+ int m = Cuda_CommCuda_PackCommVel(&cuda->shared_data,n,*iswap,(void*) buf,pbc,pbc_flag);
+ if((sizeof(X_FLOAT)!=sizeof(double)) && m)
+ m=(m+1)*sizeof(X_FLOAT)/sizeof(double);
+ return m;
}
/* ---------------------------------------------------------------------- */
@@ -169,7 +169,7 @@ int AtomVecFullCuda::pack_comm_vel(int n, int* iswap, double *buf,
void AtomVecFullCuda::unpack_comm(int n, int first, double *buf) //usually this should not be called since comm->communicate handles the communication if only positions are exchanged
{
if(not cuda->finished_setup || cuda->oncpu)
- {AtomVecFull::unpack_comm(n,first,buf); return;}
+ {AtomVecFull::unpack_comm(n,first,buf); return;}
Cuda_CommCuda_UnpackComm(&cuda->shared_data,n,first,(void*)buf);
}
@@ -177,7 +177,7 @@ void AtomVecFullCuda::unpack_comm(int n, int first, double *buf) //usually this
void AtomVecFullCuda::unpack_comm_vel(int n, int first, double *buf) //usually this should not be called since comm->communicate handles the communication if only positions are exchanged
{
if(not cuda->finished_setup || cuda->oncpu)
- {AtomVecFull::unpack_comm_vel(n,first,buf); return;}
+ {AtomVecFull::unpack_comm_vel(n,first,buf); return;}
Cuda_CommCuda_UnpackCommVel(&cuda->shared_data,n,first,(void*)buf);
}
@@ -187,7 +187,7 @@ void AtomVecFullCuda::unpack_comm_vel(int n, int first, double *buf) //usually t
int AtomVecFullCuda::pack_reverse(int n, int first, double *buf) //usually this should not be called since comm->communicate handles the communication if only forces are exchanged
{
if(not cuda->finished_setup || cuda->oncpu)
- return AtomVecFull::pack_reverse(n,first,buf);
+ return AtomVecFull::pack_reverse(n,first,buf);
int i,m,last;
cuda->cu_f->download();
@@ -207,7 +207,7 @@ int AtomVecFullCuda::pack_reverse(int n, int first, double *buf) //usually this
void AtomVecFullCuda::unpack_reverse(int n, int *list, double *buf)//usually this should not be called since comm->communicate handles the communication if only forces are exchanged
{
if(not cuda->finished_setup || cuda->oncpu)
- {AtomVecFull::unpack_reverse(n,list,buf); return;}
+ {AtomVecFull::unpack_reverse(n,list,buf); return;}
int i,j,m;
@@ -225,23 +225,23 @@ void AtomVecFullCuda::unpack_reverse(int n, int *list, double *buf)//usually thi
/* ---------------------------------------------------------------------- */
int AtomVecFullCuda::pack_border(int n, int *iswap, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
if(not cuda->finished_setup || cuda->oncpu)
- return AtomVecFull::pack_border(n,iswap,buf,pbc_flag,pbc);
-
- int m = Cuda_AtomVecFullCuda_PackBorder(&cuda->shared_data,n,*iswap,(void*) buf,pbc,pbc_flag);
+ return AtomVecFull::pack_border(n,iswap,buf,pbc_flag,pbc);
+
+ int m = Cuda_AtomVecFullCuda_PackBorder(&cuda->shared_data,n,*iswap,(void*) buf,pbc,pbc_flag);
return m;
}
int AtomVecFullCuda::pack_border_vel(int n, int *iswap, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
if(not cuda->finished_setup || cuda->oncpu)
- return AtomVecFull::pack_border_vel(n,iswap,buf,pbc_flag,pbc);
-
- int m = Cuda_AtomVecFullCuda_PackBorderVel(&cuda->shared_data,n,*iswap,(void*) buf,pbc,pbc_flag);
-
+ return AtomVecFull::pack_border_vel(n,iswap,buf,pbc_flag,pbc);
+
+ int m = Cuda_AtomVecFullCuda_PackBorderVel(&cuda->shared_data,n,*iswap,(void*) buf,pbc,pbc_flag);
+
return m;
}
@@ -250,10 +250,10 @@ int AtomVecFullCuda::pack_border_vel(int n, int *iswap, double *buf,
void AtomVecFullCuda::unpack_border(int n, int first, double *buf)
{
if(not cuda->finished_setup || cuda->oncpu)
- {AtomVecFull::unpack_border(n,first,buf); return;}
+ {AtomVecFull::unpack_border(n,first,buf); return;}
while(atom->nghost+atom->nlocal+n>=cuda->shared_data.atom.nmax) //ensure there is enough space on device to unpack data
{
- grow_both(0);
+ grow_both(0);
}
int flag=Cuda_AtomVecFullCuda_UnpackBorder(&cuda->shared_data,n,first,(void*)buf);
if(flag) {printf(" # CUDA: Error: Failed to unpack Border atoms (This might be a bug).\n");}
@@ -262,10 +262,10 @@ void AtomVecFullCuda::unpack_border(int n, int first, double *buf)
void AtomVecFullCuda::unpack_border_vel(int n, int first, double *buf)
{
if(not cuda->finished_setup || cuda->oncpu)
- {AtomVecFull::unpack_border_vel(n,first,buf); return;}
+ {AtomVecFull::unpack_border_vel(n,first,buf); return;}
while(atom->nghost+atom->nlocal+n>=cuda->shared_data.atom.nmax) //ensure there is enough space on device to unpack data
{
- grow_both(0);
+ grow_both(0);
}
int flag=Cuda_AtomVecFullCuda_UnpackBorderVel(&cuda->shared_data,n,first,(void*)buf);
if(flag) {printf(" # CUDA: Error: Failed to unpack Border atoms (This might be a bug).\n");}
@@ -273,67 +273,67 @@ void AtomVecFullCuda::unpack_border_vel(int n, int first, double *buf)
/* ----------------------------------------------------------------------
pack data for atom I for sending to another proc
- xyz must be 1st 3 values, so comm::exchange() can test on them
+ xyz must be 1st 3 values, so comm::exchange() can test on them
------------------------------------------------------------------------- */
int AtomVecFullCuda::pack_exchange(int dim, double *buf)
{
if(cuda->oncpu)
- return AtomVecFull::pack_exchange(dim,buf);
+ return AtomVecFull::pack_exchange(dim,buf);
if(not cuda_init_done||domain->box_change)
{
- Cuda_AtomVecFullCuda_Init(&cuda->shared_data);
- cuda_init_done=true;
+ Cuda_AtomVecFullCuda_Init(&cuda->shared_data);
+ cuda_init_done=true;
}
double** buf_pointer=(double**) buf;
if(*maxsend<atom->nghost || *buf_pointer==NULL)
{
- grow_send(atom->nghost>*maxsend?atom->nghost:*maxsend,buf_pointer,0);
- *maxsend=atom->nghost>*maxsend?atom->nghost:*maxsend;
+ grow_send(atom->nghost>*maxsend?atom->nghost:*maxsend,buf_pointer,0);
+ *maxsend=atom->nghost>*maxsend?atom->nghost:*maxsend;
}
-
+
if(max_nsend==0) grow_copylist(200);
int nsend_atoms = Cuda_AtomVecFullCuda_PackExchangeList(&cuda->shared_data,*maxsend,dim,*buf_pointer);
-
+
if(nsend_atoms>max_nsend) grow_copylist(nsend_atoms+100);
- if(nsend_atoms*NCUDAEXCHANGE>*maxsend)
+ if(nsend_atoms*NCUDAEXCHANGE>*maxsend)
{
- grow_send((int) (nsend_atoms+100)*NCUDAEXCHANGE,buf_pointer,0);
- Cuda_AtomVecFullCuda_PackExchangeList(&cuda->shared_data,*maxsend,dim,*buf_pointer);
+ grow_send((int) (nsend_atoms+100)*NCUDAEXCHANGE,buf_pointer,0);
+ Cuda_AtomVecFullCuda_PackExchangeList(&cuda->shared_data,*maxsend,dim,*buf_pointer);
}
int nlocal=atom->nlocal-nsend_atoms;
-
+
for(int i=0;i<nsend_atoms;i++) copylist2[i]=1;
for(int j=1;j<nsend_atoms+1;j++)
{
- int i = static_cast <int> ((*buf_pointer)[j]);
- if(i>=nlocal) copylist2[i-nlocal]=-1;
+ int i = static_cast <int> ((*buf_pointer)[j]);
+ if(i>=nlocal) copylist2[i-nlocal]=-1;
}
-
+
int actpos=0;
for(int j=1;j<nsend_atoms+1;j++)
{
- int i = static_cast <int> ((*buf_pointer)[j]);
- if(i<nlocal)
- {
- while(copylist2[actpos]==-1) actpos++;
- copylist[j-1]=nlocal+actpos;
- actpos++;
- }
+ int i = static_cast <int> ((*buf_pointer)[j]);
+ if(i<nlocal)
+ {
+ while(copylist2[actpos]==-1) actpos++;
+ copylist[j-1]=nlocal+actpos;
+ actpos++;
+ }
}
cu_copylist->upload();
-
+
cuda->shared_data.atom.nlocal=nlocal;
-
+
int m = Cuda_AtomVecFullCuda_PackExchange(&cuda->shared_data,nsend_atoms,*buf_pointer,cu_copylist->dev_data());
-
+
timespec time1,time2;
clock_gettime(CLOCK_REALTIME,&time1);
-
+
double* buf_p=*buf_pointer;
for(int j=0;j<nsend_atoms;j++)
{
@@ -347,7 +347,7 @@ int AtomVecFullCuda::pack_exchange(int dim, double *buf)
}
nextra+=2*num_bond[i]+1;
if(m>*maxsend) {grow_send(m,buf_pointer,1); buf_p=*buf_pointer;}
-
+
buf_p[m++] = num_angle[i];
for (k = 0; k < num_angle[i]; k++) {
buf_p[m++] = angle_type[i][k];
@@ -386,23 +386,23 @@ int AtomVecFullCuda::pack_exchange(int dim, double *buf)
for (k = 0; k < nspecial[i][2]; k++) buf_p[m++] = special[i][k];
nextra+=nspecial[i][2]+3;
if(m>*maxsend) {grow_send(m,buf_pointer,1); buf_p=*buf_pointer;}
-
+
if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
{
int dm= modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf_p[m]);
m+=dm;
- nextra+=dm;
+ nextra+=dm;
if(i<nlocal)modify->fix[atom->extra_grow[iextra]]->copy_arrays(copylist[j],i);
if(m>*maxsend) {grow_send(m,buf_pointer,1); buf_p=*buf_pointer;}
}
- if(i<nlocal)AtomVecFull::copy(copylist[j],i,1);
+ if(i<nlocal)AtomVecFull::copy(copylist[j],i,1);
(*buf_pointer)[j+1] = nextra;
}
-
- clock_gettime(CLOCK_REALTIME,&time2);
- cuda->shared_data.cuda_timings.comm_exchange_cpu_pack+=
+
+ clock_gettime(CLOCK_REALTIME,&time2);
+ cuda->shared_data.cuda_timings.comm_exchange_cpu_pack+=
time2.tv_sec-time1.tv_sec+1.0*(time2.tv_nsec-time1.tv_nsec)/1000000000;
(*buf_pointer)[0] = nsend_atoms;
@@ -419,11 +419,11 @@ int AtomVecFullCuda::unpack_exchange(double *buf)
{
// printf("Begin UnPack Exchange\n");
if(cuda->oncpu)
- return AtomVecFull::unpack_exchange(buf);
-
+ return AtomVecFull::unpack_exchange(buf);
+
double *sublo,*subhi;
int dim=cuda->shared_data.exchange_dim;
- if(domain->box_change)
+ if(domain->box_change)
Cuda_AtomVecFullCuda_Init(&cuda->shared_data);
if (domain->triclinic == 0) {
sublo = domain->sublo;
@@ -439,7 +439,7 @@ int AtomVecFullCuda::unpack_exchange(double *buf)
int nlocal = atom->nlocal;
int nsend_atoms=static_cast<int> (buf[0]);
if(nsend_atoms>max_nsend) grow_copylist(nsend_atoms+100);
-
+
if (nlocal+nsend_atoms+atom->nghost>=atom->nmax) grow_both(nlocal+nsend_atoms*2+atom->nghost); //ensure there is enough space on device to unpack data
int naccept = Cuda_AtomVecFullCuda_UnpackExchange(&cuda->shared_data,nsend_atoms,buf,cu_copylist->dev_data());
cu_copylist->download();
@@ -453,58 +453,58 @@ int AtomVecFullCuda::unpack_exchange(double *buf)
{
if(copylist[j]>-1)
{
- int k;
- int i=copylist[j];
+ int k;
+ int i=copylist[j];
num_bond[i] = static_cast<int> (buf[m++]);
for (k = 0; k < num_bond[i]; k++) {
- bond_type[i][k] = static_cast<int> (buf[m++]);
- bond_atom[i][k] = static_cast<int> (buf[m++]);
- }
-
- num_angle[i] = static_cast<int> (buf[m++]);
- for (k = 0; k < num_angle[i]; k++) {
- angle_type[i][k] = static_cast<int> (buf[m++]);
- angle_atom1[i][k] = static_cast<int> (buf[m++]);
- angle_atom2[i][k] = static_cast<int> (buf[m++]);
- angle_atom3[i][k] = static_cast<int> (buf[m++]);
- }
-
- num_dihedral[i] = static_cast<int> (buf[m++]);
- for (k = 0; k < num_dihedral[i]; k++) {
- dihedral_type[i][k] = static_cast<int> (buf[m++]);
- dihedral_atom1[i][k] = static_cast<int> (buf[m++]);
- dihedral_atom2[i][k] = static_cast<int> (buf[m++]);
- dihedral_atom3[i][k] = static_cast<int> (buf[m++]);
- dihedral_atom4[i][k] = static_cast<int> (buf[m++]);
- }
-
- num_improper[i] = static_cast<int> (buf[m++]);
- for (k = 0; k < num_improper[i]; k++) {
- improper_type[i][k] = static_cast<int> (buf[m++]);
- improper_atom1[i][k] = static_cast<int> (buf[m++]);
- improper_atom2[i][k] = static_cast<int> (buf[m++]);
- improper_atom3[i][k] = static_cast<int> (buf[m++]);
- improper_atom4[i][k] = static_cast<int> (buf[m++]);
- }
-
- nspecial[i][0] = static_cast<int> (buf[m++]);
- nspecial[i][1] = static_cast<int> (buf[m++]);
- nspecial[i][2] = static_cast<int> (buf[m++]);
- for (k = 0; k < nspecial[i][2]; k++)
- special[i][k] = static_cast<int> (buf[m++]);
-
- if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
- m += modify->fix[atom->extra_grow[iextra]]->
- unpack_exchange(i,&buf[m]);
-
+ bond_type[i][k] = static_cast<int> (buf[m++]);
+ bond_atom[i][k] = static_cast<int> (buf[m++]);
+ }
+
+ num_angle[i] = static_cast<int> (buf[m++]);
+ for (k = 0; k < num_angle[i]; k++) {
+ angle_type[i][k] = static_cast<int> (buf[m++]);
+ angle_atom1[i][k] = static_cast<int> (buf[m++]);
+ angle_atom2[i][k] = static_cast<int> (buf[m++]);
+ angle_atom3[i][k] = static_cast<int> (buf[m++]);
+ }
+
+ num_dihedral[i] = static_cast<int> (buf[m++]);
+ for (k = 0; k < num_dihedral[i]; k++) {
+ dihedral_type[i][k] = static_cast<int> (buf[m++]);
+ dihedral_atom1[i][k] = static_cast<int> (buf[m++]);
+ dihedral_atom2[i][k] = static_cast<int> (buf[m++]);
+ dihedral_atom3[i][k] = static_cast<int> (buf[m++]);
+ dihedral_atom4[i][k] = static_cast<int> (buf[m++]);
+ }
+
+ num_improper[i] = static_cast<int> (buf[m++]);
+ for (k = 0; k < num_improper[i]; k++) {
+ improper_type[i][k] = static_cast<int> (buf[m++]);
+ improper_atom1[i][k] = static_cast<int> (buf[m++]);
+ improper_atom2[i][k] = static_cast<int> (buf[m++]);
+ improper_atom3[i][k] = static_cast<int> (buf[m++]);
+ improper_atom4[i][k] = static_cast<int> (buf[m++]);
+ }
+
+ nspecial[i][0] = static_cast<int> (buf[m++]);
+ nspecial[i][1] = static_cast<int> (buf[m++]);
+ nspecial[i][2] = static_cast<int> (buf[m++]);
+ for (k = 0; k < nspecial[i][2]; k++)
+ special[i][k] = static_cast<int> (buf[m++]);
+
+ if (atom->nextra_grow)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ m += modify->fix[atom->extra_grow[iextra]]->
+ unpack_exchange(i,&buf[m]);
+
}
- else
+ else
m+=static_cast <int> (buf[j+1]);
}
-
- clock_gettime(CLOCK_REALTIME,&time2);
- cuda->shared_data.cuda_timings.comm_exchange_cpu_pack+=
+
+ clock_gettime(CLOCK_REALTIME,&time2);
+ cuda->shared_data.cuda_timings.comm_exchange_cpu_pack+=
time2.tv_sec-time1.tv_sec+1.0*(time2.tv_nsec-time1.tv_nsec)/1000000000;
cuda->shared_data.atom.nlocal=nlocal;
@@ -515,6 +515,3 @@ int AtomVecFullCuda::unpack_exchange(double *buf)
}
return mfirst;
}
-
-
-
diff --git a/src/USER-CUDA/atom_vec_full_cuda.h b/src/USER-CUDA/atom_vec_full_cuda.h
index f16fd7703da7056d19917a0c89f07dd6cc824aaf..5ce96a203c0264b1fe960ff73805d291a277644a 100644
--- a/src/USER-CUDA/atom_vec_full_cuda.h
+++ b/src/USER-CUDA/atom_vec_full_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
diff --git a/src/USER-CUDA/comm_cuda.cpp b/src/USER-CUDA/comm_cuda.cpp
index 4e9b9e6cad21682480a6bfb6c1e1cc753ea00df4..0c2e8e8ff0bb1eddb44f25ce64f0b7cf1ef4135d 100644
--- a/src/USER-CUDA/comm_cuda.cpp
+++ b/src/USER-CUDA/comm_cuda.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -49,10 +49,10 @@ using namespace LAMMPS_NS;
enum{SINGLE,MULTI};
/* ----------------------------------------------------------------------
- setup MPI and allocate buffer space
+ setup MPI and allocate buffer space
------------------------------------------------------------------------- */
-CommCuda::CommCuda(LAMMPS *lmp):Comm(lmp)
+CommCuda::CommCuda(LAMMPS *lmp):Comm(lmp)
{
cuda = lmp->cuda;
if(cuda == NULL)
@@ -123,11 +123,11 @@ void CommCuda::init()
delete cu_slabhi;
cu_slabhi = new cCudaData<double, X_FLOAT,x>(slabhi,cuda->shared_data.comm.maxswap);
cu_slabhi->upload();
-
+
cuda->shared_data.comm.pbc.dev_data=cu_pbc->dev_data();
cuda->shared_data.comm.slablo.dev_data=cu_slablo->dev_data();
cuda->shared_data.comm.slabhi.dev_data=cu_slabhi->dev_data();
-
+
Comm::init();
}
@@ -142,17 +142,17 @@ void CommCuda::setup()
{
if(cuda->shared_data.pair.neighall) cutghostuser = MAX(2.0*neighbor->cutneighmax,cutghostuser);
Comm::setup();
-
+
//upload changed geometry to device
if(style == SINGLE)
{
- if(cu_slablo) cu_slablo->upload();
- if(cu_slabhi) cu_slabhi->upload();
+ if(cu_slablo) cu_slablo->upload();
+ if(cu_slabhi) cu_slabhi->upload();
}
- else
+ else
{
- if(cu_multilo) cu_multilo->upload();
- if(cu_multihi) cu_multihi->upload();
+ if(cu_multilo) cu_multilo->upload();
+ if(cu_multihi) cu_multihi->upload();
}
}
@@ -176,7 +176,7 @@ void CommCuda::forward_comm_cuda()
static double kerneltime=0.0;
static double copytime=0.0;
timespec time1,time2,time3;
-
+
int n;
MPI_Request request;
MPI_Status status;
@@ -190,112 +190,112 @@ void CommCuda::forward_comm_cuda()
cuda->shared_data.domain.prd[1]=domain->prd[1];
cuda->shared_data.domain.prd[2]=domain->prd[2];
cuda->shared_data.domain.triclinic=domain->triclinic;
- if(not comm_x_only && not avec->cudable)
+ if(not comm_x_only && not avec->cudable)
{
- cuda->downloadAll();
+ cuda->downloadAll();
Comm::forward_comm();
cuda->uploadAll();
return;
- }
-
+ }
+
// exchange data with another proc
// if other proc is self, just copy
// if comm_x_only set, exchange or copy directly to x, don't unpack
for (int iswap = 0; iswap < nswap; iswap++) {
- if (sendproc[iswap] != me)
- {
- if (comm_x_only)
+ if (sendproc[iswap] != me)
+ {
+ if (comm_x_only)
{
int size_forward_recv_now=0;
-
+
if((sizeof(X_FLOAT)!=sizeof(double)) && size_forward_recv[iswap]) //some complicated way to safe some transfer size if single precision is used
size_forward_recv_now=(size_forward_recv[iswap]+1)*sizeof(X_FLOAT)/sizeof(double);
else
size_forward_recv_now=size_forward_recv[iswap];
clock_gettime(CLOCK_REALTIME,&time1);
-
+
MPI_Irecv(buf_recv,size_forward_recv_now,MPI_DOUBLE,
recvproc[iswap],0,world,&request);
n = Cuda_CommCuda_PackComm(&cuda->shared_data,sendnum[iswap],iswap,(void*) buf_send,pbc[iswap],pbc_flag[iswap]);
-
+
clock_gettime(CLOCK_REALTIME,&time2);
-
+
if((sizeof(X_FLOAT)!=sizeof(double)) && n) //some complicated way to safe some transfer size if single precision is used
n=(n+1)*sizeof(X_FLOAT)/sizeof(double);
- //printf("RecvSize: %i SendSize: %i\n",size_forward_recv_now,n);
- MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap],0,world);
- MPI_Wait(&request,&status);
-
+ //printf("RecvSize: %i SendSize: %i\n",size_forward_recv_now,n);
+ MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap],0,world);
+ MPI_Wait(&request,&status);
+
clock_gettime(CLOCK_REALTIME,&time3);
cuda->shared_data.cuda_timings.comm_forward_mpi_upper+=
time3.tv_sec-time1.tv_sec+1.0*(time3.tv_nsec-time1.tv_nsec)/1000000000;
cuda->shared_data.cuda_timings.comm_forward_mpi_lower+=
time3.tv_sec-time2.tv_sec+1.0*(time3.tv_nsec-time2.tv_nsec)/1000000000;
-
+
Cuda_CommCuda_UnpackComm(&cuda->shared_data,recvnum[iswap],firstrecv[iswap],(void*)buf_recv,iswap); //Unpack for cpu exchange happens implicitely since buf==x[firstrecv]
-
- }
- else if (ghost_velocity)
+
+ }
+ else if (ghost_velocity)
{
- MPI_Irecv(buf_recv,size_forward_recv[iswap],MPI_DOUBLE,
- recvproc[iswap],0,world,&request);
-
+ MPI_Irecv(buf_recv,size_forward_recv[iswap],MPI_DOUBLE,
+ recvproc[iswap],0,world,&request);
+
if(avec->cudable)
n = avec->pack_comm_vel(sendnum[iswap],&iswap,
buf_send,pbc_flag[iswap],pbc[iswap]);
else
- n = avec->pack_comm_vel(sendnum[iswap],sendlist[iswap],
- buf_send,pbc_flag[iswap],pbc[iswap]);
-
- MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap],0,world);
- MPI_Wait(&request,&status);
- avec->unpack_comm_vel(recvnum[iswap],firstrecv[iswap],buf_recv);
- }
- else
+ n = avec->pack_comm_vel(sendnum[iswap],sendlist[iswap],
+ buf_send,pbc_flag[iswap],pbc[iswap]);
+
+ MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap],0,world);
+ MPI_Wait(&request,&status);
+ avec->unpack_comm_vel(recvnum[iswap],firstrecv[iswap],buf_recv);
+ }
+ else
{
- MPI_Irecv(buf_recv,size_forward_recv[iswap],MPI_DOUBLE,
- recvproc[iswap],0,world,&request);
-
+ MPI_Irecv(buf_recv,size_forward_recv[iswap],MPI_DOUBLE,
+ recvproc[iswap],0,world,&request);
+
if(avec->cudable)
n = avec->pack_comm(sendnum[iswap],&iswap,
buf_send,pbc_flag[iswap],pbc[iswap]);
else
- n = avec->pack_comm(sendnum[iswap],sendlist[iswap],
- buf_send,pbc_flag[iswap],pbc[iswap]);
-
- MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap],0,world);
- MPI_Wait(&request,&status);
- avec->unpack_comm(recvnum[iswap],firstrecv[iswap],buf_recv);
+ n = avec->pack_comm(sendnum[iswap],sendlist[iswap],
+ buf_send,pbc_flag[iswap],pbc[iswap]);
+
+ MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap],0,world);
+ MPI_Wait(&request,&status);
+ avec->unpack_comm(recvnum[iswap],firstrecv[iswap],buf_recv);
}
}
else //sendproc == me
{
cuda->self_comm=1;
- if (comm_x_only)
- {
- if (sendnum[iswap])
- {
+ if (comm_x_only)
+ {
+ if (sendnum[iswap])
+ {
n = Cuda_CommCuda_PackComm_Self(&cuda->shared_data,sendnum[iswap],iswap,firstrecv[iswap],pbc[iswap],pbc_flag[iswap]);
if(n<0) error->all(FLERR," # CUDA ERRROR on PackComm_Self");
if((sizeof(X_FLOAT)!=sizeof(double)) && n)
n=(n+1)*sizeof(X_FLOAT)/sizeof(double);
- }
- }
- else if (ghost_velocity)
+ }
+ }
+ else if (ghost_velocity)
{
- n = avec->pack_comm_vel(sendnum[iswap],&iswap,
- (double*) firstrecv,pbc_flag[iswap],pbc[iswap]);
- //avec->unpack_comm_vel(recvnum[iswap],firstrecv[iswap],(double*) firstrecv);
- }
- else
+ n = avec->pack_comm_vel(sendnum[iswap],&iswap,
+ (double*) firstrecv,pbc_flag[iswap],pbc[iswap]);
+ //avec->unpack_comm_vel(recvnum[iswap],firstrecv[iswap],(double*) firstrecv);
+ }
+ else
{
- n = avec->pack_comm(sendnum[iswap],&iswap,
- (double*) firstrecv,pbc_flag[iswap],pbc[iswap]);
- //avec->unpack_comm(recvnum[iswap],firstrecv[iswap],(double*) firstrecv);
+ n = avec->pack_comm(sendnum[iswap],&iswap,
+ (double*) firstrecv,pbc_flag[iswap],pbc[iswap]);
+ //avec->unpack_comm(recvnum[iswap],firstrecv[iswap],(double*) firstrecv);
}
cuda->self_comm=0;
}
@@ -304,9 +304,9 @@ cuda->shared_data.cuda_timings.comm_forward_mpi_lower+=
void CommCuda::forward_comm_pack_cuda()
{
- static int count=0;
- static double kerneltime=0.0;
- static double copytime=0.0;
+ static int count=0;
+ static double kerneltime=0.0;
+ static double copytime=0.0;
timespec time1,time2,time3;
int n; // initialize comm buffers & exchange memory
@@ -322,94 +322,94 @@ void CommCuda::forward_comm_pack_cuda()
cuda->shared_data.domain.prd[1]=domain->prd[1];
cuda->shared_data.domain.prd[2]=domain->prd[2];
cuda->shared_data.domain.triclinic=domain->triclinic;
- if(not comm_x_only && not avec->cudable) cuda->downloadAll(); //if not comm_x_only the communication routine of the atom_vec style class is used
+ if(not comm_x_only && not avec->cudable) cuda->downloadAll(); //if not comm_x_only the communication routine of the atom_vec style class is used
// exchange data with another proc
// if other proc is self, just copy
// if comm_x_only set, exchange or copy directly to x, don't unpack
for (int iswap = 0; iswap < nswap; iswap++) {
- if (sendproc[iswap] != me)
- {
- if (comm_x_only)
+ if (sendproc[iswap] != me)
+ {
+ if (comm_x_only)
{
-
+
clock_gettime(CLOCK_REALTIME,&time1);
-
+
// n = Cuda_CommCuda_PackComm(&cuda->shared_data,sendnum[iswap],iswap,(void*) cuda->shared_data.comm.buf_send[iswap],pbc[iswap],pbc_flag[iswap]);
- n = Cuda_CommCuda_PackComm(&cuda->shared_data,sendnum[iswap],iswap,(void*)buf_send,pbc[iswap],pbc_flag[iswap]);
-
+ n = Cuda_CommCuda_PackComm(&cuda->shared_data,sendnum[iswap],iswap,(void*)buf_send,pbc[iswap],pbc_flag[iswap]);
+
clock_gettime(CLOCK_REALTIME,&time2);
-
+
if((sizeof(X_FLOAT)!=sizeof(double)) && n) //some complicated way to safe some transfer size if single precision is used
n=(n+1)*sizeof(X_FLOAT)/sizeof(double);
- cuda->shared_data.comm.send_size[iswap]=n;
- }
- else if (ghost_velocity)
+ cuda->shared_data.comm.send_size[iswap]=n;
+ }
+ else if (ghost_velocity)
{
clock_gettime(CLOCK_REALTIME,&time1);
// n = Cuda_CommCuda_PackComm_Vel(&cuda->shared_data,sendnum[iswap],iswap,(void*) &buf_send[iswap*maxsend],pbc[iswap],pbc_flag[iswap]);
-
+
clock_gettime(CLOCK_REALTIME,&time2);
-
+
if((sizeof(X_FLOAT)!=sizeof(double)) && n) //some complicated way to safe some transfer size if single precision is used
n=(n+1)*sizeof(X_FLOAT)/sizeof(double);
- cuda->shared_data.comm.send_size[iswap]=n;
- }
- else
+ cuda->shared_data.comm.send_size[iswap]=n;
+ }
+ else
{
- MPI_Irecv(buf_recv,size_forward_recv[iswap],MPI_DOUBLE,
- recvproc[iswap],0,world,&request);
-
+ MPI_Irecv(buf_recv,size_forward_recv[iswap],MPI_DOUBLE,
+ recvproc[iswap],0,world,&request);
+
if(avec->cudable)
n = avec->pack_comm(sendnum[iswap],&iswap,
cuda->shared_data.comm.buf_send[iswap],pbc_flag[iswap],pbc[iswap]);
else
- n = avec->pack_comm(sendnum[iswap],sendlist[iswap],
- cuda->shared_data.comm.buf_send[iswap],pbc_flag[iswap],pbc[iswap]);
-
- MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap],0,world);
- MPI_Wait(&request,&status);
- avec->unpack_comm(recvnum[iswap],firstrecv[iswap],buf_recv);
+ n = avec->pack_comm(sendnum[iswap],sendlist[iswap],
+ cuda->shared_data.comm.buf_send[iswap],pbc_flag[iswap],pbc[iswap]);
+
+ MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap],0,world);
+ MPI_Wait(&request,&status);
+ avec->unpack_comm(recvnum[iswap],firstrecv[iswap],buf_recv);
}
}
else //sendproc == me
{
- if (comm_x_only)
- {
- if (sendnum[iswap])
- {
+ if (comm_x_only)
+ {
+ if (sendnum[iswap])
+ {
n = Cuda_CommCuda_PackComm_Self(&cuda->shared_data,sendnum[iswap],iswap,firstrecv[iswap],pbc[iswap],pbc_flag[iswap]);
if(n<0) error->all(FLERR," # CUDA ERRROR on PackComm_Self");
if((sizeof(X_FLOAT)!=sizeof(double)) && n)
n=(n+1)*sizeof(X_FLOAT)/sizeof(double);
- }
- }
- else if (ghost_velocity)
+ }
+ }
+ else if (ghost_velocity)
{
- n = avec->pack_comm_vel(sendnum[iswap],sendlist[iswap],
- buf_send,pbc_flag[iswap],pbc[iswap]);
- avec->unpack_comm_vel(recvnum[iswap],firstrecv[iswap],buf_send);
- }
- else
+ n = avec->pack_comm_vel(sendnum[iswap],sendlist[iswap],
+ buf_send,pbc_flag[iswap],pbc[iswap]);
+ avec->unpack_comm_vel(recvnum[iswap],firstrecv[iswap],buf_send);
+ }
+ else
{
- n = avec->pack_comm(sendnum[iswap],sendlist[iswap],
- buf_send,pbc_flag[iswap],pbc[iswap]);
- avec->unpack_comm(recvnum[iswap],firstrecv[iswap],buf_send);
+ n = avec->pack_comm(sendnum[iswap],sendlist[iswap],
+ buf_send,pbc_flag[iswap],pbc[iswap]);
+ avec->unpack_comm(recvnum[iswap],firstrecv[iswap],buf_send);
}
}
}
- if(not comm_x_only && not avec->cudable) cuda->uploadAll();
+ if(not comm_x_only && not avec->cudable) cuda->uploadAll();
}
void CommCuda::forward_comm_transfer_cuda()
{
- static int count=0;
- static double kerneltime=0.0;
- static double copytime=0.0;
+ static int count=0;
+ static double kerneltime=0.0;
+ static double copytime=0.0;
timespec time1,time2,time3;
int n;
MPI_Request request;
@@ -423,51 +423,51 @@ void CommCuda::forward_comm_transfer_cuda()
cuda->shared_data.domain.prd[1]=domain->prd[1];
cuda->shared_data.domain.prd[2]=domain->prd[2];
cuda->shared_data.domain.triclinic=domain->triclinic;
- if(not comm_x_only && not avec->cudable) cuda->downloadAll(); //if not comm_x_only the communication routine of the atom_vec style class is used
+ if(not comm_x_only && not avec->cudable) cuda->downloadAll(); //if not comm_x_only the communication routine of the atom_vec style class is used
//printf("A\n");
// exchange data with another proc
// if other proc is self, just copy
// if comm_x_only set, exchange or copy directly to x, don't unpack
for (int iswap = 0; iswap < nswap; iswap++) {
- if (sendproc[iswap] != me)
- {
- if (comm_x_only)
+ if (sendproc[iswap] != me)
+ {
+ if (comm_x_only)
{
int size_forward_recv_now=0;
-
+
if((sizeof(X_FLOAT)!=sizeof(double)) && size_forward_recv[iswap]) //some complicated way to safe some transfer size if single precision is used
size_forward_recv_now=(size_forward_recv[iswap]+1)*sizeof(X_FLOAT)/sizeof(double);
else
size_forward_recv_now=size_forward_recv[iswap];
-
+
//printf("A: %i \n",size_forward_recv_now/1024*4);
//MPI_Irecv(cuda->shared_data.comm.buf_recv[iswap],size_forward_recv_now,MPI_DOUBLE,
// recvproc[iswap],0,world,&request);
MPI_Irecv(buf_recv,size_forward_recv_now,MPI_DOUBLE,
recvproc[iswap],0,world,&request);
- //printf("%p %p %i\n",buf_send, cuda->shared_data.comm.buf_send_dev[iswap], cuda->shared_data.comm.send_size[iswap]*sizeof(double));
+ //printf("%p %p %i\n",buf_send, cuda->shared_data.comm.buf_send_dev[iswap], cuda->shared_data.comm.send_size[iswap]*sizeof(double));
//memcpy(buf_send,cuda->shared_data.comm.buf_send[iswap],cuda->shared_data.comm.send_size[iswap]*sizeof(double));
- // CudaWrapper_SyncStream(1);
+ // CudaWrapper_SyncStream(1);
//printf("B: %i \n",cuda->shared_data.comm.send_size[iswap]/1024*4);
- CudaWrapper_DownloadCudaDataAsync((void*) buf_send, cuda->shared_data.comm.buf_send_dev[iswap], cuda->shared_data.comm.send_size[iswap]*sizeof(double),2);
- //MPI_Send(cuda->shared_data.comm.buf_send[iswap],cuda->shared_data.comm.send_size[iswap],MPI_DOUBLE,sendproc[iswap],0,world);
+ CudaWrapper_DownloadCudaDataAsync((void*) buf_send, cuda->shared_data.comm.buf_send_dev[iswap], cuda->shared_data.comm.send_size[iswap]*sizeof(double),2);
+ //MPI_Send(cuda->shared_data.comm.buf_send[iswap],cuda->shared_data.comm.send_size[iswap],MPI_DOUBLE,sendproc[iswap],0,world);
clock_gettime(CLOCK_REALTIME,&time1);
CudaWrapper_SyncStream(2);
//printf("C: %i \n",cuda->shared_data.comm.send_size[iswap]/1024*4);
clock_gettime(CLOCK_REALTIME,&time2);
cuda->shared_data.cuda_timings.comm_forward_download+=
time2.tv_sec-time1.tv_sec+1.0*(time2.tv_nsec-time1.tv_nsec)/1000000000;
- MPI_Send(buf_send,cuda->shared_data.comm.send_size[iswap],MPI_DOUBLE,sendproc[iswap],0,world);
- MPI_Wait(&request,&status);
+ MPI_Send(buf_send,cuda->shared_data.comm.send_size[iswap],MPI_DOUBLE,sendproc[iswap],0,world);
+ MPI_Wait(&request,&status);
//printf("D: %i \n",cuda->shared_data.comm.send_size[iswap]/1024*4);
- CudaWrapper_UploadCudaDataAsync((void*) buf_recv,cuda->shared_data.comm.buf_recv_dev[iswap], size_forward_recv_now*sizeof(double),2);
+ CudaWrapper_UploadCudaDataAsync((void*) buf_recv,cuda->shared_data.comm.buf_recv_dev[iswap], size_forward_recv_now*sizeof(double),2);
clock_gettime(CLOCK_REALTIME,&time1);
CudaWrapper_SyncStream(2);
//printf("E: %i \n",cuda->shared_data.comm.send_size[iswap]/1024*4);
//memcpy(cuda->shared_data.comm.buf_recv[iswap],buf_recv,size_forward_recv_now*sizeof(double));
- //printf("RecvSize: %i SendSize: %i\n",size_forward_recv_now*sizeof(double),cuda->shared_data.comm.send_size[iswap]*sizeof(double));
+ //printf("RecvSize: %i SendSize: %i\n",size_forward_recv_now*sizeof(double),cuda->shared_data.comm.send_size[iswap]*sizeof(double));
clock_gettime(CLOCK_REALTIME,&time3);
cuda->shared_data.cuda_timings.comm_forward_upload+=
time3.tv_sec-time1.tv_sec+1.0*(time3.tv_nsec-time1.tv_nsec)/1000000000;
@@ -476,78 +476,78 @@ cuda->shared_data.cuda_timings.comm_forward_mpi_lower+=
clock_gettime(CLOCK_REALTIME,&time3);
cuda->shared_data.cuda_timings.comm_forward_mpi_upper+=
time3.tv_sec-time1.tv_sec+1.0*(time3.tv_nsec-time1.tv_nsec)/1000000000;
- }
- else if (ghost_velocity)
+ }
+ else if (ghost_velocity)
{
/* int size_forward_recv_now=0;
-
+
if((sizeof(X_FLOAT)!=sizeof(double)) && size_forward_recv[iswap]) //some complicated way to safe some transfer size if single precision is used
size_forward_recv_now=(size_forward_recv[iswap]+1)*sizeof(X_FLOAT)/sizeof(double);
else
size_forward_recv_now=size_forward_recv[iswap];
-
+
clock_gettime(CLOCK_REALTIME,&time1);
-
+
MPI_Irecv(cuda->shared_data.comm.buf_recv[iswap],size_forward_recv_now,MPI_DOUBLE,
recvproc[iswap],0,world,&request);
-
+
clock_gettime(CLOCK_REALTIME,&time2);
-
- MPI_Send(cuda->shared_data.comm.buf_send[iswap],cuda->shared_data.comm.send_size[iswap],MPI_DOUBLE,sendproc[iswap],0,world);
- MPI_Wait(&request,&status);
-
+
+ MPI_Send(cuda->shared_data.comm.buf_send[iswap],cuda->shared_data.comm.send_size[iswap],MPI_DOUBLE,sendproc[iswap],0,world);
+ MPI_Wait(&request,&status);
+
clock_gettime(CLOCK_REALTIME,&time3);
cuda->shared_data.cuda_timings.comm_forward_mpi_upper+=
time3.tv_sec-time1.tv_sec+1.0*(time3.tv_nsec-time1.tv_nsec)/1000000000;
cuda->shared_data.cuda_timings.comm_forward_mpi_lower+=
time3.tv_sec-time2.tv_sec+1.0*(time3.tv_nsec-time2.tv_nsec)/1000000000;*/
-
- }
- else
+
+ }
+ else
{
- MPI_Irecv(buf_recv,size_forward_recv[iswap],MPI_DOUBLE,
- recvproc[iswap],0,world,&request);
-
+ MPI_Irecv(buf_recv,size_forward_recv[iswap],MPI_DOUBLE,
+ recvproc[iswap],0,world,&request);
+
if(avec->cudable)
n = avec->pack_comm(sendnum[iswap],&iswap,
buf_send,pbc_flag[iswap],pbc[iswap]);
else
- n = avec->pack_comm(sendnum[iswap],sendlist[iswap],
- buf_send,pbc_flag[iswap],pbc[iswap]);
-
- MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap],0,world);
- MPI_Wait(&request,&status);
- avec->unpack_comm(recvnum[iswap],firstrecv[iswap],buf_recv);
+ n = avec->pack_comm(sendnum[iswap],sendlist[iswap],
+ buf_send,pbc_flag[iswap],pbc[iswap]);
+
+ MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap],0,world);
+ MPI_Wait(&request,&status);
+ avec->unpack_comm(recvnum[iswap],firstrecv[iswap],buf_recv);
}
}
else //sendproc == me
{
- if (comm_x_only)
- {
- if (sendnum[iswap])
- {
- }
- }
- else if (ghost_velocity)
+ if (comm_x_only)
{
- }
- else
+ if (sendnum[iswap])
+ {
+ }
+ }
+ else if (ghost_velocity)
{
- n = avec->pack_comm(sendnum[iswap],sendlist[iswap],
- buf_send,pbc_flag[iswap],pbc[iswap]);
- avec->unpack_comm(recvnum[iswap],firstrecv[iswap],buf_send);
+ }
+ else
+ {
+ n = avec->pack_comm(sendnum[iswap],sendlist[iswap],
+ buf_send,pbc_flag[iswap],pbc[iswap]);
+ avec->unpack_comm(recvnum[iswap],firstrecv[iswap],buf_send);
}
}
}
- if(not comm_x_only && not avec->cudable) cuda->uploadAll();
+ if(not comm_x_only && not avec->cudable) cuda->uploadAll();
}
void CommCuda::forward_comm_unpack_cuda()
{
- static int count=0;
- static double kerneltime=0.0;
- static double copytime=0.0;
+ static int count=0;
+ static double kerneltime=0.0;
+ static double copytime=0.0;
timespec time1,time2,time3;
int n;
MPI_Request request;
@@ -562,73 +562,73 @@ void CommCuda::forward_comm_unpack_cuda()
cuda->shared_data.domain.prd[1]=domain->prd[1];
cuda->shared_data.domain.prd[2]=domain->prd[2];
cuda->shared_data.domain.triclinic=domain->triclinic;
- if(not comm_x_only && not avec->cudable) cuda->downloadAll(); //if not comm_x_only the communication routine of the atom_vec style class is used
+ if(not comm_x_only && not avec->cudable) cuda->downloadAll(); //if not comm_x_only the communication routine of the atom_vec style class is used
// exchange data with another proc
// if other proc is self, just copy
// if comm_x_only set, exchange or copy directly to x, don't unpack
for (int iswap = 0; iswap < nswap; iswap++) {
- if (sendproc[iswap] != me)
- {
- if (comm_x_only)
- {
-
+ if (sendproc[iswap] != me)
+ {
+ if (comm_x_only)
+ {
+
//Cuda_CommCuda_UnpackComm(&cuda->shared_data,recvnum[iswap],firstrecv[iswap],cuda->shared_data.comm.buf_recv[iswap],iswap); //Unpack for cpu exchange happens implicitely since buf==x[firstrecv]
Cuda_CommCuda_UnpackComm(&cuda->shared_data,recvnum[iswap],firstrecv[iswap],buf_recv,iswap); //Unpack for cpu exchange happens implicitely since buf==x[firstrecv]
-
- }
- else if (ghost_velocity)
- {
+
+ }
+ else if (ghost_velocity)
+ {
//Cuda_CommCuda_UnpackComm_Vel(&cuda->shared_data,recvnum[iswap],firstrecv[iswap],(void*)&buf_recv[iswap*maxrecv]); //Unpack for cpu exchange happens implicitely since buf==x[firstrecv]
- }
- else
+ }
+ else
{
- MPI_Irecv(buf_recv,size_forward_recv[iswap],MPI_DOUBLE,
- recvproc[iswap],0,world,&request);
-
+ MPI_Irecv(buf_recv,size_forward_recv[iswap],MPI_DOUBLE,
+ recvproc[iswap],0,world,&request);
+
if(avec->cudable)
n = avec->pack_comm(sendnum[iswap],&iswap,
buf_send,pbc_flag[iswap],pbc[iswap]);
else
- n = avec->pack_comm(sendnum[iswap],sendlist[iswap],
- buf_send,pbc_flag[iswap],pbc[iswap]);
-
- MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap],0,world);
- MPI_Wait(&request,&status);
- avec->unpack_comm(recvnum[iswap],firstrecv[iswap],buf_recv);
+ n = avec->pack_comm(sendnum[iswap],sendlist[iswap],
+ buf_send,pbc_flag[iswap],pbc[iswap]);
+
+ MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap],0,world);
+ MPI_Wait(&request,&status);
+ avec->unpack_comm(recvnum[iswap],firstrecv[iswap],buf_recv);
}
}
else //sendproc == me
{
- if (comm_x_only)
- {
- if (sendnum[iswap])
- {
- }
- }
- else if (ghost_velocity)
+ if (comm_x_only)
{
- }
- else
+ if (sendnum[iswap])
+ {
+ }
+ }
+ else if (ghost_velocity)
{
- n = avec->pack_comm(sendnum[iswap],sendlist[iswap],
- buf_send,pbc_flag[iswap],pbc[iswap]);
- avec->unpack_comm(recvnum[iswap],firstrecv[iswap],buf_send);
+ }
+ else
+ {
+ n = avec->pack_comm(sendnum[iswap],sendlist[iswap],
+ buf_send,pbc_flag[iswap],pbc[iswap]);
+ avec->unpack_comm(recvnum[iswap],firstrecv[iswap],buf_send);
}
}
}
- if(not comm_x_only && not avec->cudable) cuda->uploadAll();
+ if(not comm_x_only && not avec->cudable) cuda->uploadAll();
}
void CommCuda::forward_comm_pair(Pair *pair)
{
if(not cuda->shared_data.pair.cudable_force)
{
- return Comm::forward_comm_pair(pair);
+ return Comm::forward_comm_pair(pair);
}
-
+
int iswap,n;
double *buf;
MPI_Request request;
@@ -639,18 +639,18 @@ void CommCuda::forward_comm_pair(Pair *pair)
// pack buffer
n = pair->pack_comm(sendnum[iswap],&iswap,
- buf_send,pbc_flag[iswap],pbc[iswap]);
- int nrecv = recvnum[iswap]*n;
- if(nrecv<0) nrecv=-(nrecv+1)/2;
- int nsend = sendnum[iswap]*n;
- if(nsend<0) nsend=-(nsend+1)/2;
-
+ buf_send,pbc_flag[iswap],pbc[iswap]);
+ int nrecv = recvnum[iswap]*n;
+ if(nrecv<0) nrecv=-(nrecv+1)/2;
+ int nsend = sendnum[iswap]*n;
+ if(nsend<0) nsend=-(nsend+1)/2;
+
// exchange with another proc
// if self, set recv buffer to send buffer
if (sendproc[iswap] != me) {
MPI_Irecv(buf_recv,nrecv,MPI_DOUBLE,recvproc[iswap],0,
- world,&request);
+ world,&request);
MPI_Send(buf_send,nsend,MPI_DOUBLE,sendproc[iswap],0,world);
MPI_Wait(&request,&status);
buf = buf_recv;
@@ -663,10 +663,10 @@ void CommCuda::forward_comm_pair(Pair *pair)
}
/* ----------------------------------------------------------------------
- reverse communication of forces on atoms every timestep
+ reverse communication of forces on atoms every timestep
other per-atom attributes may also be sent via pack/unpack routines
------------------------------------------------------------------------- */
-
+
void CommCuda::reverse_comm()
{
int n;
@@ -687,10 +687,10 @@ void CommCuda::reverse_comm()
if (comm_f_only) {
int size_recv_now=size_reverse_recv[iswap];
- if((sizeof(F_FLOAT)!=sizeof(double))&& size_reverse_recv[iswap])
- size_recv_now=(size_recv_now+1)*sizeof(F_FLOAT)/sizeof(double);
- MPI_Irecv(buf_recv,size_recv_now,MPI_DOUBLE,
- sendproc[iswap],0,world,&request);
+ if((sizeof(F_FLOAT)!=sizeof(double))&& size_reverse_recv[iswap])
+ size_recv_now=(size_recv_now+1)*sizeof(F_FLOAT)/sizeof(double);
+ MPI_Irecv(buf_recv,size_recv_now,MPI_DOUBLE,
+ sendproc[iswap],0,world,&request);
buf=buf_send;
if (size_reverse_send[iswap])
@@ -699,30 +699,30 @@ void CommCuda::reverse_comm()
}
else buf=NULL;
int size_reverse_send_now=size_reverse_send[iswap];
- if((sizeof(F_FLOAT)!=sizeof(double))&& size_reverse_send[iswap])
- size_reverse_send_now=(size_reverse_send_now+1)*sizeof(F_FLOAT)/sizeof(double);
- MPI_Send(buf,size_reverse_send_now,MPI_DOUBLE,
- recvproc[iswap],0,world);
- MPI_Wait(&request,&status);
- Cuda_CommCuda_UnpackReverse(&cuda->shared_data,sendnum[iswap],iswap,buf_recv);
+ if((sizeof(F_FLOAT)!=sizeof(double))&& size_reverse_send[iswap])
+ size_reverse_send_now=(size_reverse_send_now+1)*sizeof(F_FLOAT)/sizeof(double);
+ MPI_Send(buf,size_reverse_send_now,MPI_DOUBLE,
+ recvproc[iswap],0,world);
+ MPI_Wait(&request,&status);
+ Cuda_CommCuda_UnpackReverse(&cuda->shared_data,sendnum[iswap],iswap,buf_recv);
} else {
- MPI_Irecv(buf_recv,size_reverse_recv[iswap],MPI_DOUBLE,
- sendproc[iswap],0,world,&request);
- n = avec->pack_reverse(recvnum[iswap],firstrecv[iswap],buf_send);
- MPI_Send(buf_send,n,MPI_DOUBLE,recvproc[iswap],0,world);
- MPI_Wait(&request,&status);
+ MPI_Irecv(buf_recv,size_reverse_recv[iswap],MPI_DOUBLE,
+ sendproc[iswap],0,world,&request);
+ n = avec->pack_reverse(recvnum[iswap],firstrecv[iswap],buf_send);
+ MPI_Send(buf_send,n,MPI_DOUBLE,recvproc[iswap],0,world);
+ MPI_Wait(&request,&status);
avec->unpack_reverse(sendnum[iswap],sendlist[iswap],buf_recv);
}
} else {
if (comm_f_only) {
- if (sendnum[iswap])
- Cuda_CommCuda_UnpackReverse_Self(&cuda->shared_data,sendnum[iswap],iswap,firstrecv[iswap]);
+ if (sendnum[iswap])
+ Cuda_CommCuda_UnpackReverse_Self(&cuda->shared_data,sendnum[iswap],iswap,firstrecv[iswap]);
} else {
- n = avec->pack_reverse(recvnum[iswap],firstrecv[iswap],buf_send);
- avec->unpack_reverse(sendnum[iswap],sendlist[iswap],buf_send);
+ n = avec->pack_reverse(recvnum[iswap],firstrecv[iswap],buf_send);
+ avec->unpack_reverse(sendnum[iswap],sendlist[iswap],buf_send);
}
}
}
@@ -743,12 +743,12 @@ void CommCuda::reverse_comm()
void CommCuda::exchange()
{
AtomVec *avec = atom->avec;
-
+
if(not cuda->oncpu && avec->cudable)
- return exchange_cuda();
+ return exchange_cuda();
+
+ if(not cuda->oncpu) cuda->downloadAll();
- if(not cuda->oncpu) cuda->downloadAll();
-
Comm::exchange();
}
@@ -765,11 +765,11 @@ void CommCuda::exchange_cuda()
timespec time1,time2,time3;
// clear global->local map for owned and ghost atoms
- // b/c atoms migrate to new procs in exchange() and
+ // b/c atoms migrate to new procs in exchange() and
// new ghosts are created in borders()
// map_set() is done at end of borders()
-
+
if(map_style) cuda->cu_tag->download();
if (map_style) atom->map_clear();
@@ -785,13 +785,13 @@ void CommCuda::exchange_cuda()
}
// loop over dimensions
-
+
for (int dim = 0; dim < 3; dim++) {
// fill buffer with atoms leaving my box, using < and >=
// when atom is deleted, fill it in with last atom
- cuda->shared_data.exchange_dim=dim;
-
+ cuda->shared_data.exchange_dim=dim;
+
nlocal = atom->nlocal;
avec->maxsend=&maxsend;
nsend=avec->pack_exchange(dim,(double*) &buf_send);
@@ -806,39 +806,39 @@ void CommCuda::exchange_cuda()
// if more than 2 procs in dimension, send/recv to both neighbors
clock_gettime(CLOCK_REALTIME,&time1);
-
+
if (procgrid[dim] == 1) {
nrecv = nsend;
buf = buf_send;
} else {
MPI_Sendrecv(&nsend,1,MPI_INT,procneigh[dim][0],0,
- &nrecv1,1,MPI_INT,procneigh[dim][1],0,world,&status);
+ &nrecv1,1,MPI_INT,procneigh[dim][1],0,world,&status);
nrecv = nrecv1;
if (procgrid[dim] > 2) {
- MPI_Sendrecv(&nsend,1,MPI_INT,procneigh[dim][1],0,
- &nrecv2,1,MPI_INT,procneigh[dim][0],0,world,&status);
- nrecv += nrecv2;
+ MPI_Sendrecv(&nsend,1,MPI_INT,procneigh[dim][1],0,
+ &nrecv2,1,MPI_INT,procneigh[dim][0],0,world,&status);
+ nrecv += nrecv2;
}
if (nrecv+1 > maxrecv) grow_recv(nrecv+1);
-
+
MPI_Irecv(buf_recv,nrecv1,MPI_DOUBLE,procneigh[dim][1],0,
- world,&request);
+ world,&request);
MPI_Send(buf_send,nsend,MPI_DOUBLE,procneigh[dim][0],0,world);
MPI_Wait(&request,&status);
-
+
if (procgrid[dim] > 2) {
- MPI_Irecv(&buf_recv[nrecv1],nrecv2,MPI_DOUBLE,procneigh[dim][0],0,
- world,&request);
- MPI_Send(buf_send,nsend,MPI_DOUBLE,procneigh[dim][1],0,world);
- MPI_Wait(&request,&status);
+ MPI_Irecv(&buf_recv[nrecv1],nrecv2,MPI_DOUBLE,procneigh[dim][0],0,
+ world,&request);
+ MPI_Send(buf_send,nsend,MPI_DOUBLE,procneigh[dim][1],0,world);
+ MPI_Wait(&request,&status);
- if((nrecv1==0)||(nrecv2==0)) buf_recv[nrecv]=0;
+ if((nrecv1==0)||(nrecv2==0)) buf_recv[nrecv]=0;
}
-
+
buf = buf_recv;
}
- //printf("nsend: %i nrecv: %i\n",nsend,nrecv);
+ //printf("nsend: %i nrecv: %i\n",nsend,nrecv);
// check incoming atoms to see if they are in my box
// if so, add to my list
clock_gettime(CLOCK_REALTIME,&time2);
@@ -856,7 +856,7 @@ cuda->shared_data.cuda_timings.comm_exchange_mpi+=
if(atom->firstgroupname) atom->first_reorder();
- if(atom->firstgroupname) cuda->uploadAll();
+ if(atom->firstgroupname) cuda->uploadAll();
}
/* ----------------------------------------------------------------------
@@ -875,19 +875,19 @@ void CommCuda::borders()
AtomVec *avec = atom->avec;
if(not cuda->oncpu && avec->cudable)
{
- if(cuda->shared_data.overlap_comm&&cuda->finished_setup)
- borders_cuda_overlap_forward_comm();
- else
- borders_cuda();
-
- return;
+ if(cuda->shared_data.overlap_comm&&cuda->finished_setup)
+ borders_cuda_overlap_forward_comm();
+ else
+ borders_cuda();
+
+ return;
}
Comm::borders();
-
+
cuda->setSystemParams();
if(cuda->finished_setup) {cuda->checkResize(); cuda->uploadAll();}
- cuda->shared_data.atom.nghost=atom->nghost;
+ cuda->shared_data.atom.nghost=atom->nghost;
cu_sendlist->upload();
}
@@ -912,7 +912,7 @@ void CommCuda::borders_cuda()
iswap = 0;
smax = rmax = 0;
-
+
cuda->shared_data.comm.nsend=0;
for (dim = 0; dim < 3; dim++) {
nlast = 0;
@@ -927,16 +927,16 @@ void CommCuda::borders_cuda()
x = atom->x;
if (style == SINGLE) {
- lo = slablo[iswap];
- hi = slabhi[iswap];
+ lo = slablo[iswap];
+ hi = slabhi[iswap];
} else {
- type = atom->type;
- mlo = multilo[iswap];
- mhi = multihi[iswap];
+ type = atom->type;
+ mlo = multilo[iswap];
+ mhi = multihi[iswap];
}
if (ineed % 2 == 0) {
- nfirst = nlast;
- nlast = atom->nlocal + atom->nghost;
+ nfirst = nlast;
+ nlast = atom->nlocal + atom->nghost;
}
nsend = 0;
@@ -948,13 +948,13 @@ void CommCuda::borders_cuda()
do
{
if(nsend>=maxsendlist[iswap]) grow_list(iswap,static_cast <int> (nsend*1.05));
- nsend=Cuda_CommCuda_BuildSendlist(&cuda->shared_data,bordergroup,ineed,style==SINGLE?1:0,atom->nfirst,nfirst,nlast,dim,iswap);
+ nsend=Cuda_CommCuda_BuildSendlist(&cuda->shared_data,bordergroup,ineed,style==SINGLE?1:0,atom->nfirst,nfirst,nlast,dim,iswap);
}while(nsend>=maxsendlist[iswap]);
// pack up list of border atoms
if (nsend*size_border > maxsend)
- grow_send(nsend*size_border,0);
-
+ grow_send(nsend*size_border,0);
+
if (ghost_velocity)
n = avec->pack_border_vel(nsend,&iswap,buf_send,
pbc_flag[iswap],pbc[iswap]);
@@ -968,18 +968,18 @@ void CommCuda::borders_cuda()
clock_gettime(CLOCK_REALTIME,&time1);
if (sendproc[iswap] != me) {
- MPI_Sendrecv(&nsend,1,MPI_INT,sendproc[iswap],0,
- &nrecv,1,MPI_INT,recvproc[iswap],0,world,&status);
- if (nrecv*size_border > maxrecv)
- grow_recv(nrecv*size_border);
- MPI_Irecv(buf_recv,nrecv*size_border,MPI_DOUBLE,
- recvproc[iswap],0,world,&request);
- MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap],0,world);
- MPI_Wait(&request,&status);
- buf = buf_recv;
+ MPI_Sendrecv(&nsend,1,MPI_INT,sendproc[iswap],0,
+ &nrecv,1,MPI_INT,recvproc[iswap],0,world,&status);
+ if (nrecv*size_border > maxrecv)
+ grow_recv(nrecv*size_border);
+ MPI_Irecv(buf_recv,nrecv*size_border,MPI_DOUBLE,
+ recvproc[iswap],0,world,&request);
+ MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap],0,world);
+ MPI_Wait(&request,&status);
+ buf = buf_recv;
} else {
- nrecv = nsend;
- buf = buf_send;
+ nrecv = nsend;
+ buf = buf_send;
}
clock_gettime(CLOCK_REALTIME,&time2);
@@ -989,9 +989,9 @@ cuda->shared_data.cuda_timings.comm_border_mpi+=
// unpack buffer
if (ghost_velocity)
- avec->unpack_border_vel(nrecv,atom->nlocal+atom->nghost,buf);
+ avec->unpack_border_vel(nrecv,atom->nlocal+atom->nghost,buf);
else
- avec->unpack_border(nrecv,atom->nlocal+atom->nghost,buf);
+ avec->unpack_border(nrecv,atom->nlocal+atom->nghost,buf);
// set all pointers & counters
@@ -1016,14 +1016,14 @@ cuda->shared_data.cuda_timings.comm_border_mpi+=
if (max > maxrecv) grow_recv(max);
// reset global->local map
- if(map_style)
+ if(map_style)
{
- cuda->cu_tag->download();
- atom->map_set();
+ cuda->cu_tag->download();
+ atom->map_set();
}
-
+
cuda->setSystemParams();
- cuda->shared_data.atom.nghost+=n;
+ cuda->shared_data.atom.nghost+=n;
}
void CommCuda::borders_cuda_overlap_forward_comm()
@@ -1047,7 +1047,7 @@ void CommCuda::borders_cuda_overlap_forward_comm()
iswap = 0;
smax = rmax = 0;
-
+
cuda->shared_data.comm.nsend=0;
for (dim = 0; dim < 3; dim++) {
nlast = 0;
@@ -1062,16 +1062,16 @@ void CommCuda::borders_cuda_overlap_forward_comm()
x = atom->x;
if (style == SINGLE) {
- lo = slablo[iswap];
- hi = slabhi[iswap];
+ lo = slablo[iswap];
+ hi = slabhi[iswap];
} else {
- type = atom->type;
- mlo = multilo[iswap];
- mhi = multihi[iswap];
+ type = atom->type;
+ mlo = multilo[iswap];
+ mhi = multihi[iswap];
}
if (ineed % 2 == 0) {
- nfirst = nlast;
- nlast = atom->nlocal + atom->nghost;
+ nfirst = nlast;
+ nlast = atom->nlocal + atom->nghost;
}
nsend = 0;
@@ -1083,14 +1083,14 @@ void CommCuda::borders_cuda_overlap_forward_comm()
do
{
if(nsend>=maxsendlist[iswap]) grow_list(iswap,static_cast <int> (nsend*1.05));
- nsend=Cuda_CommCuda_BuildSendlist(&cuda->shared_data,bordergroup,ineed,style==SINGLE?1:0,atom->nfirst,nfirst,nlast,dim,iswap);
+ nsend=Cuda_CommCuda_BuildSendlist(&cuda->shared_data,bordergroup,ineed,style==SINGLE?1:0,atom->nfirst,nfirst,nlast,dim,iswap);
}while(nsend>=maxsendlist[iswap]);
- cuda->shared_data.comm.nsend_swap[iswap]=nsend;
- // pack up list of border atoms
+ cuda->shared_data.comm.nsend_swap[iswap]=nsend;
+ // pack up list of border atoms
if (nsend*size_border > maxsend)
- grow_send(nsend*size_border,0);
-
+ grow_send(nsend*size_border,0);
+
if (ghost_velocity)
n = avec->pack_border_vel(nsend,&iswap,buf_send,
pbc_flag[iswap],pbc[iswap]);
@@ -1104,18 +1104,18 @@ void CommCuda::borders_cuda_overlap_forward_comm()
clock_gettime(CLOCK_REALTIME,&time1);
if (sendproc[iswap] != me) {
- MPI_Sendrecv(&nsend,1,MPI_INT,sendproc[iswap],0,
- &nrecv,1,MPI_INT,recvproc[iswap],0,world,&status);
- if (nrecv*size_border > maxrecv)
- grow_recv(nrecv*size_border);
- MPI_Irecv(buf_recv,nrecv*size_border,MPI_DOUBLE,
- recvproc[iswap],0,world,&request);
- MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap],0,world);
- MPI_Wait(&request,&status);
- buf = buf_recv;
+ MPI_Sendrecv(&nsend,1,MPI_INT,sendproc[iswap],0,
+ &nrecv,1,MPI_INT,recvproc[iswap],0,world,&status);
+ if (nrecv*size_border > maxrecv)
+ grow_recv(nrecv*size_border);
+ MPI_Irecv(buf_recv,nrecv*size_border,MPI_DOUBLE,
+ recvproc[iswap],0,world,&request);
+ MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap],0,world);
+ MPI_Wait(&request,&status);
+ buf = buf_recv;
} else {
- nrecv = nsend;
- buf = buf_send;
+ nrecv = nsend;
+ buf = buf_send;
}
clock_gettime(CLOCK_REALTIME,&time2);
@@ -1125,9 +1125,9 @@ cuda->shared_data.cuda_timings.comm_border_mpi+=
// unpack buffer
if (ghost_velocity)
- avec->unpack_border_vel(nrecv,atom->nlocal+atom->nghost,buf);
+ avec->unpack_border_vel(nrecv,atom->nlocal+atom->nghost,buf);
else
- avec->unpack_border(nrecv,atom->nlocal+atom->nghost,buf);
+ avec->unpack_border(nrecv,atom->nlocal+atom->nghost,buf);
// set all pointers & counters
@@ -1152,14 +1152,14 @@ cuda->shared_data.cuda_timings.comm_border_mpi+=
if (max > maxrecv) grow_recv(max);
// reset global->local map
- if(map_style)
+ if(map_style)
{
- cuda->cu_tag->download();
- atom->map_set();
+ cuda->cu_tag->download();
+ atom->map_set();
}
-
+
cuda->setSystemParams();
- cuda->shared_data.atom.nghost+=n;
+ cuda->shared_data.atom.nghost+=n;
}
@@ -1176,27 +1176,27 @@ void CommCuda::forward_comm_fix(Fix *fix)
// pack buffer
if(fix->cudable_comm&&cuda->finished_setup)
{
- int swap=iswap;
+ int swap=iswap;
if(sendproc[iswap] == me) {swap=-iswap-1; buf=(double*)&(firstrecv[iswap]);}
else buf=buf_send;
-
+
n = fix->pack_comm(sendnum[iswap],&swap,
buf,pbc_flag[iswap],pbc[iswap]);
- if(sendproc[iswap] == me)
+ if(sendproc[iswap] == me)
{
- continue;
+ continue;
}
}
else
n = fix->pack_comm(sendnum[iswap],sendlist[iswap],
- buf_send,pbc_flag[iswap],pbc[iswap]);
+ buf_send,pbc_flag[iswap],pbc[iswap]);
// exchange with another proc
// if self, set recv buffer to send buffer
if (sendproc[iswap] != me) {
MPI_Irecv(buf_recv,n*recvnum[iswap],MPI_DOUBLE,recvproc[iswap],0,
- world,&request);
+ world,&request);
MPI_Send(buf_send,n*sendnum[iswap],MPI_DOUBLE,sendproc[iswap],0,world);
MPI_Wait(&request,&status);
buf = buf_recv;
@@ -1221,13 +1221,13 @@ void CommCuda::grow_send(int n, int flag)
if(buf_send) CudaWrapper_FreePinnedHostData((void*) (buf_send));
buf_send = (double*) CudaWrapper_AllocPinnedHostData((maxsend+BUFEXTRA)*sizeof(double),false);
memcpy(buf_send,tmp,oldmaxsend*sizeof(double));
- delete [] tmp;
+ delete [] tmp;
}
else
{
- buf_send = (double *)
+ buf_send = (double *)
memory->srealloc(buf_send,(maxsend+BUFEXTRA)*sizeof(double),
- "comm:buf_send");printf("srealloc\n");
+ "comm:buf_send");printf("srealloc\n");
}
}
else {
@@ -1240,7 +1240,7 @@ void CommCuda::grow_send(int n, int flag)
{
memory->sfree(buf_send);
buf_send = (double *) memory->smalloc((maxsend+BUFEXTRA)*sizeof(double),
- "comm:buf_send");
+ "comm:buf_send");
}
for(int i=0;i<maxswap;i++)
{
@@ -1250,7 +1250,7 @@ void CommCuda::grow_send(int n, int flag)
}
}
/* ----------------------------------------------------------------------
- free/malloc the size of the recv buffer as needed with BUFFACTOR
+ free/malloc the size of the recv buffer as needed with BUFFACTOR
------------------------------------------------------------------------- */
@@ -1267,7 +1267,7 @@ void CommCuda::grow_recv(int n)
{
memory->sfree(buf_recv);
buf_recv = (double *) memory->smalloc(maxrecv*sizeof(double),
- "comm:buf_recv");
+ "comm:buf_recv");
}
for(int i=0;i<maxswap;i++)
{
@@ -1277,33 +1277,33 @@ void CommCuda::grow_recv(int n)
}
/* ----------------------------------------------------------------------
- realloc the size of the iswap sendlist as needed with BUFFACTOR
+ realloc the size of the iswap sendlist as needed with BUFFACTOR
------------------------------------------------------------------------- */
void CommCuda::grow_list(int iswap, int n)
{
-
+
MYDBG(printf(" # CUDA CommCuda::grow_list\n");)
if(cuda->finished_setup&&cu_sendlist) cu_sendlist->download();
if(!cu_sendlist||n*BUFFACTOR>cu_sendlist->get_dim()[1]||n*BUFFACTOR>maxsendlist[iswap])
{
- for(int i=0;i<maxswap;i++)
- {
- maxsendlist[i] = static_cast<int> (BUFFACTOR * n);
- sendlist[i] = (int *)
- memory->srealloc(sendlist[i],maxsendlist[i]*sizeof(int),
- "comm:sendlist[iswap]");
- }
- delete cu_sendlist;
- cu_sendlist=new cCudaData<int, int, xy> ((int*)sendlist,maxswap,maxsendlist[iswap]);
- cuda->shared_data.comm.sendlist.dev_data=cu_sendlist->dev_data();
+ for(int i=0;i<maxswap;i++)
+ {
+ maxsendlist[i] = static_cast<int> (BUFFACTOR * n);
+ sendlist[i] = (int *)
+ memory->srealloc(sendlist[i],maxsendlist[i]*sizeof(int),
+ "comm:sendlist[iswap]");
+ }
+ delete cu_sendlist;
+ cu_sendlist=new cCudaData<int, int, xy> ((int*)sendlist,maxswap,maxsendlist[iswap]);
+ cuda->shared_data.comm.sendlist.dev_data=cu_sendlist->dev_data();
cuda->shared_data.comm.maxlistlength=maxsendlist[iswap];
cu_sendlist->upload();
}
}
/* ----------------------------------------------------------------------
- realloc the buffers needed for swaps
+ realloc the buffers needed for swaps
------------------------------------------------------------------------- */
void CommCuda::grow_swap(int n)
@@ -1313,22 +1313,22 @@ void CommCuda::grow_swap(int n)
if(n>cu_sendlist->get_dim()[0])
{
MYDBG(printf(" # CUDA CommCuda::grow_swap\n");)
-
- delete cu_sendlist;
- cu_sendlist=new cCudaData<int, int, xy> ((int*)sendlist,n,BUFMIN);
- cuda->shared_data.comm.sendlist.dev_data=cu_sendlist->dev_data();
+
+ delete cu_sendlist;
+ cu_sendlist=new cCudaData<int, int, xy> ((int*)sendlist,n,BUFMIN);
+ cuda->shared_data.comm.sendlist.dev_data=cu_sendlist->dev_data();
cuda->shared_data.comm.maxlistlength=BUFMIN;
cuda->shared_data.comm.maxswap=n;
cuda->shared_data.comm.nsend_swap=new int[n];
cuda->shared_data.comm.send_size=new int[n];
- cuda->shared_data.comm.recv_size=new int[n];
+ cuda->shared_data.comm.recv_size=new int[n];
}
for(int i=0;i<oldmaxswap;i++)
{
if(cuda->shared_data.comm.buf_recv_dev[i]) CudaWrapper_FreeCudaData(cuda->shared_data.comm.buf_recv_dev[i],maxrecv*sizeof(double));
if(cuda->shared_data.comm.buf_send_dev[i]) CudaWrapper_FreeCudaData(cuda->shared_data.comm.buf_send_dev[i],maxsend*sizeof(double));
cuda->shared_data.comm.buf_recv_dev[i]=NULL;
- cuda->shared_data.comm.buf_send_dev[i]=NULL;
+ cuda->shared_data.comm.buf_send_dev[i]=NULL;
}
cuda->shared_data.comm.buf_send= new double*[n];
cuda->shared_data.comm.buf_recv= new double*[n];
@@ -1337,9 +1337,9 @@ void CommCuda::grow_swap(int n)
for(int i=0;i<n;i++)
{
cuda->shared_data.comm.buf_recv[i]=NULL;
- cuda->shared_data.comm.buf_send[i]=NULL;
+ cuda->shared_data.comm.buf_send[i]=NULL;
cuda->shared_data.comm.buf_recv_dev[i]=NULL;
- cuda->shared_data.comm.buf_send_dev[i]=NULL;
+ cuda->shared_data.comm.buf_send_dev[i]=NULL;
}
grow_send(maxsend,0);
grow_recv(maxrecv);
@@ -1348,28 +1348,28 @@ void CommCuda::grow_swap(int n)
}
/* ----------------------------------------------------------------------
- allocation of swap info
+ allocation of swap info
------------------------------------------------------------------------- */
void CommCuda::allocate_swap(int n)
{
Comm::allocate_swap(n);
-
- delete cu_pbc;
- delete cu_slablo;
- delete cu_slabhi;
-
+
+ delete cu_pbc;
+ delete cu_slablo;
+ delete cu_slabhi;
+
cuda->shared_data.comm.maxswap=n;
- if(cu_sendlist)
- {
- cu_pbc=new cCudaData<int, int, xy> ((int*)pbc,n,6);
- cu_slablo = new cCudaData<double, X_FLOAT,x>(slablo,n);
- cu_slabhi = new cCudaData<double, X_FLOAT,x>(slabhi,n);
-
- cuda->shared_data.comm.pbc.dev_data=cu_pbc->dev_data();
- cuda->shared_data.comm.slablo.dev_data=cu_slablo->dev_data();
- cuda->shared_data.comm.slabhi.dev_data=cu_slabhi->dev_data();
- }
+ if(cu_sendlist)
+ {
+ cu_pbc=new cCudaData<int, int, xy> ((int*)pbc,n,6);
+ cu_slablo = new cCudaData<double, X_FLOAT,x>(slablo,n);
+ cu_slabhi = new cCudaData<double, X_FLOAT,x>(slabhi,n);
+
+ cuda->shared_data.comm.pbc.dev_data=cu_pbc->dev_data();
+ cuda->shared_data.comm.slablo.dev_data=cu_slablo->dev_data();
+ cuda->shared_data.comm.slabhi.dev_data=cu_slabhi->dev_data();
+ }
cuda->shared_data.comm.nsend_swap=new int[n];
cuda->shared_data.comm.send_size=new int[n];
cuda->shared_data.comm.recv_size=new int[n];
@@ -1390,17 +1390,17 @@ void CommCuda::allocate_multi(int n)
{
Comm::allocate_multi(n);
- delete cu_multilo;
- delete cu_multihi;
- cu_multilo = new cCudaData<double, X_FLOAT,xy>(slablo,n,atom->ntypes+1);
- cu_multihi = new cCudaData<double, X_FLOAT,xy>(slabhi,n,atom->ntypes+1);
-
- cuda->shared_data.comm.multilo.dev_data=cu_multilo->dev_data();
- cuda->shared_data.comm.multihi.dev_data=cu_multihi->dev_data();
+ delete cu_multilo;
+ delete cu_multihi;
+ cu_multilo = new cCudaData<double, X_FLOAT,xy>(slablo,n,atom->ntypes+1);
+ cu_multihi = new cCudaData<double, X_FLOAT,xy>(slabhi,n,atom->ntypes+1);
+
+ cuda->shared_data.comm.multilo.dev_data=cu_multilo->dev_data();
+ cuda->shared_data.comm.multihi.dev_data=cu_multihi->dev_data();
}
/* ----------------------------------------------------------------------
- free memory for swaps
+ free memory for swaps
------------------------------------------------------------------------- */
void CommCuda::free_swap()
@@ -1417,7 +1417,7 @@ void CommCuda::free_swap()
if(cuda->shared_data.comm.buf_recv_dev[i]) CudaWrapper_FreeCudaData(cuda->shared_data.comm.buf_recv_dev[i],maxrecv*sizeof(double));
if(cuda->shared_data.comm.buf_send_dev[i]) CudaWrapper_FreeCudaData(cuda->shared_data.comm.buf_send_dev[i],maxsend*sizeof(double));
}
-
+
}
@@ -1431,4 +1431,3 @@ void CommCuda::free_multi()
delete cu_multilo; cu_multilo = NULL;
delete cu_multihi; cu_multihi = NULL;
}
-
diff --git a/src/USER-CUDA/comm_cuda.h b/src/USER-CUDA/comm_cuda.h
index 933d7364c1205046c87325437b441baab546f8f8..125441af1b9dd43031c07d52fbcb5df5a03a403b 100644
--- a/src/USER-CUDA/comm_cuda.h
+++ b/src/USER-CUDA/comm_cuda.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -33,7 +33,7 @@ public:
virtual void forward_comm_pack_cuda();
virtual void forward_comm_transfer_cuda();
virtual void forward_comm_unpack_cuda();
- virtual void forward_comm_pair(Pair *pair);
+ virtual void forward_comm_pair(Pair *pair);
virtual void reverse_comm(); // reverse communication of forces
virtual void exchange(); // move atoms to new procs
virtual void exchange_cuda(); // move atoms to new procs
@@ -43,7 +43,7 @@ public:
virtual void forward_comm_fix(class Fix *); // forward comm from a Fix
-
+
protected:
class Cuda *cuda;
@@ -52,7 +52,7 @@ public:
cCudaData<double, X_FLOAT, x>* cu_slabhi;
cCudaData<double, X_FLOAT, xy>* cu_multilo;
cCudaData<double, X_FLOAT, xy>* cu_multihi;
-
+
cCudaData<int, int, xy>* cu_sendlist;
virtual void grow_send(int,int); // reallocate send buffer
virtual void grow_recv(int); // free/allocate recv buffer
diff --git a/src/USER-CUDA/compute_pe_cuda.cpp b/src/USER-CUDA/compute_pe_cuda.cpp
index 0d93aea2499cda4a4d815e47938844143f328119..57685e52f3f934910642cee31f730bb673ed603b 100644
--- a/src/USER-CUDA/compute_pe_cuda.cpp
+++ b/src/USER-CUDA/compute_pe_cuda.cpp
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -28,7 +28,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -54,7 +54,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-ComputePECuda::ComputePECuda(LAMMPS *lmp, int narg, char **arg) :
+ComputePECuda::ComputePECuda(LAMMPS *lmp, int narg, char **arg) :
ComputePE(lmp, narg, arg)
{
cudable = 1;
diff --git a/src/USER-CUDA/compute_pe_cuda.h b/src/USER-CUDA/compute_pe_cuda.h
index 71444f671c018c41e8d92d5df55c1702486ac8b5..11bb163685d58799f60f956f8601349996faec8c 100644
--- a/src/USER-CUDA/compute_pe_cuda.h
+++ b/src/USER-CUDA/compute_pe_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -28,7 +28,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-CUDA/compute_pressure_cuda.cpp b/src/USER-CUDA/compute_pressure_cuda.cpp
index 27de7e58508c7348fb0131f58bd3fa46a94d53b7..339374308eaeba399946c66e23162c1452d49ba6 100644
--- a/src/USER-CUDA/compute_pressure_cuda.cpp
+++ b/src/USER-CUDA/compute_pressure_cuda.cpp
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -28,7 +28,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -66,7 +66,7 @@ ComputePressureCuda::ComputePressureCuda(LAMMPS *lmp, int narg, char **arg) :
if(cuda == NULL)
error->all(FLERR,"You cannot use a /cuda class, without activating 'cuda' acceleration. Provide '-c on' as command-line argument to LAMMPS..");
cudable = 1;
-
+
// store temperature ID used by pressure computation
// insure it is valid for temperature computation
@@ -81,7 +81,7 @@ ComputePressureCuda::ComputePressureCuda(LAMMPS *lmp, int narg, char **arg) :
error->warning(FLERR,"Compute pressure/cuda temperature ID is not cudable! Try a temp/cuda style.");
cudable = 0;
}
-
+
}
double ComputePressureCuda::compute_scalar()
diff --git a/src/USER-CUDA/compute_pressure_cuda.h b/src/USER-CUDA/compute_pressure_cuda.h
index d99f4a5cca77dc43ea9718439e6002d0cf701c66..f08fbde973dfb5a1b43cd67a5501d4b28edf7136 100644
--- a/src/USER-CUDA/compute_pressure_cuda.h
+++ b/src/USER-CUDA/compute_pressure_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -28,7 +28,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-CUDA/compute_temp_cuda.cpp b/src/USER-CUDA/compute_temp_cuda.cpp
index 0b560f536611ac3cd5d1a7e83c961780af2cfa59..4830add2727908d3ecf5a7ab795b00fe36eda68d 100644
--- a/src/USER-CUDA/compute_temp_cuda.cpp
+++ b/src/USER-CUDA/compute_temp_cuda.cpp
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -28,7 +28,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -54,7 +54,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-ComputeTempCuda::ComputeTempCuda(LAMMPS *lmp, int narg, char **arg) :
+ComputeTempCuda::ComputeTempCuda(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
cuda = lmp->cuda;
@@ -73,7 +73,7 @@ ComputeTempCuda::ComputeTempCuda(LAMMPS *lmp, int narg, char **arg) :
cu_t_vector = 0;
cu_t_scalar = 0;
cudable=true;
-
+
}
/* ---------------------------------------------------------------------- */
@@ -112,8 +112,8 @@ double ComputeTempCuda::compute_scalar()
{
if(cuda->begin_setup)
{
- if(not cu_t_vector) cu_t_vector = new cCudaData<double, ENERGY_FLOAT, x> (t_vector,6);
- if(not cu_t_scalar) cu_t_scalar = new cCudaData<double, ENERGY_FLOAT, x> (&t_scalar,1);
+ if(not cu_t_vector) cu_t_vector = new cCudaData<double, ENERGY_FLOAT, x> (t_vector,6);
+ if(not cu_t_scalar) cu_t_scalar = new cCudaData<double, ENERGY_FLOAT, x> (&t_scalar,1);
invoked_scalar = update->ntimestep;
Cuda_ComputeTempCuda_Scalar(&cuda->shared_data,groupbit,(ENERGY_FLOAT*) cu_t_scalar->dev_data());
cu_t_scalar->download();
@@ -134,31 +134,31 @@ double ComputeTempCuda::compute_scalar()
if (rmass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
- t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) * rmass[i];
+ t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) * rmass[i];
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
- t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
- mass[type[i]];
+ t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
+ mass[type[i]];
}
t_scalar=t;
}
-
+
MPI_Allreduce(&t_scalar,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
if (dynamic) dof_compute();
scalar *= tfactor;
- if(scalar>1e15)
+ if(scalar>1e15)
{
- cuda->cu_v->download();
- cuda->cu_x->download();
- cuda->cu_type->download();
+ cuda->cu_v->download();
+ cuda->cu_x->download();
+ cuda->cu_type->download();
double **v = atom->v;
double **x = atom->x;
- printf("Out of v-range atoms: \n");
- for(int i=0;i<atom->nlocal;i++)
- if((v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2])>1e5)
- printf("%i %i // %lf %lf %lf // %lf %lf %lf\n",atom->tag[i],atom->type[i],x[i][0], x[i][1], x[i][2],v[i][0], v[i][1], v[i][2]);
- error->all(FLERR,"Temperature out of range. Simulations will be abortet.\n");
+ printf("Out of v-range atoms: \n");
+ for(int i=0;i<atom->nlocal;i++)
+ if((v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2])>1e5)
+ printf("%i %i // %lf %lf %lf // %lf %lf %lf\n",atom->tag[i],atom->type[i],x[i][0], x[i][1], x[i][2],v[i][0], v[i][1], v[i][2]);
+ error->all(FLERR,"Temperature out of range. Simulations will be abortet.\n");
}
return scalar;
}
@@ -170,8 +170,8 @@ void ComputeTempCuda::compute_vector()
int i;
if(cuda->begin_setup)
{
- if(not cu_t_vector) cu_t_vector = new cCudaData<double, ENERGY_FLOAT, x> (t_vector,6);
- if(not cu_t_scalar) cu_t_scalar = new cCudaData<double, ENERGY_FLOAT, x> (&t_scalar,1);
+ if(not cu_t_vector) cu_t_vector = new cCudaData<double, ENERGY_FLOAT, x> (t_vector,6);
+ if(not cu_t_scalar) cu_t_scalar = new cCudaData<double, ENERGY_FLOAT, x> (&t_scalar,1);
invoked_vector = update->ntimestep;
@@ -180,7 +180,7 @@ void ComputeTempCuda::compute_vector()
}
else
{
-
+
invoked_vector = update->ntimestep;
double **v = atom->v;
@@ -204,7 +204,7 @@ void ComputeTempCuda::compute_vector()
t[4] += massone * v[i][0]*v[i][2];
t[5] += massone * v[i][1]*v[i][2];
}
-
+
for (i = 0; i < 6; i++) t_vector[i]=t[i];
}
MPI_Allreduce(t_vector,vector,6,MPI_DOUBLE,MPI_SUM,world);
diff --git a/src/USER-CUDA/compute_temp_cuda.h b/src/USER-CUDA/compute_temp_cuda.h
index 35ae0bbf3fca6a70a6c1f6ca11de0da29084a2b7..df7559d0480118fe63deeabb4014686ec3e0f857 100644
--- a/src/USER-CUDA/compute_temp_cuda.h
+++ b/src/USER-CUDA/compute_temp_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -28,7 +28,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -64,9 +64,9 @@ class ComputeTempCuda : public Compute {
void dof_compute();
double t_vector[6];
double t_scalar;
- cCudaData<double , ENERGY_FLOAT , x>* cu_t_scalar;
- cCudaData<double , ENERGY_FLOAT , x>* cu_t_vector;
-
+ cCudaData<double , ENERGY_FLOAT , x>* cu_t_scalar;
+ cCudaData<double , ENERGY_FLOAT , x>* cu_t_vector;
+
};
}
diff --git a/src/USER-CUDA/compute_temp_partial_cuda.cpp b/src/USER-CUDA/compute_temp_partial_cuda.cpp
index e39484c83580844496d7ce79ac56ba19f5b761a0..c3ac1b4d89a1df84419e23387934636058367b1d 100644
--- a/src/USER-CUDA/compute_temp_partial_cuda.cpp
+++ b/src/USER-CUDA/compute_temp_partial_cuda.cpp
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -28,7 +28,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -55,7 +55,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-ComputeTempPartialCuda::ComputeTempPartialCuda(LAMMPS *lmp, int narg, char **arg) :
+ComputeTempPartialCuda::ComputeTempPartialCuda(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
cuda = lmp->cuda;
@@ -70,7 +70,7 @@ ComputeTempPartialCuda::ComputeTempPartialCuda(LAMMPS *lmp, int narg, char **arg
extvector = 1;
tempflag = 1;
tempbias = 1;
-
+
xflag = atoi(arg[3]);
yflag = atoi(arg[4]);
zflag = atoi(arg[5]);
@@ -85,7 +85,7 @@ ComputeTempPartialCuda::ComputeTempPartialCuda(LAMMPS *lmp, int narg, char **arg
cu_t_scalar = 0;
cu_vbiasall=NULL;
cudable=true;
-
+
}
/* ---------------------------------------------------------------------- */
@@ -135,8 +135,8 @@ double ComputeTempPartialCuda::compute_scalar()
{
if(cuda->begin_setup)
{
- if(not cu_t_vector) cu_t_vector = new cCudaData<double, ENERGY_FLOAT, x> (t_vector,6);
- if(not cu_t_scalar) cu_t_scalar = new cCudaData<double, ENERGY_FLOAT, x> (&t_scalar,1);
+ if(not cu_t_vector) cu_t_vector = new cCudaData<double, ENERGY_FLOAT, x> (t_vector,6);
+ if(not cu_t_scalar) cu_t_scalar = new cCudaData<double, ENERGY_FLOAT, x> (&t_scalar,1);
invoked_scalar = update->ntimestep;
Cuda_ComputeTempPartialCuda_Scalar(&cuda->shared_data,groupbit,(ENERGY_FLOAT*) cu_t_scalar->dev_data(),xflag,yflag,zflag);
cu_t_scalar->download();
@@ -157,31 +157,31 @@ double ComputeTempPartialCuda::compute_scalar()
if (rmass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
- t += (xflag*v[i][0]*v[i][0] + yflag*v[i][1]*v[i][1] + zflag*v[i][2]*v[i][2]) * rmass[i];
+ t += (xflag*v[i][0]*v[i][0] + yflag*v[i][1]*v[i][1] + zflag*v[i][2]*v[i][2]) * rmass[i];
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
- t += (xflag*v[i][0]*v[i][0] + yflag*v[i][1]*v[i][1] + zflag*v[i][2]*v[i][2]) *
- mass[type[i]];
+ t += (xflag*v[i][0]*v[i][0] + yflag*v[i][1]*v[i][1] + zflag*v[i][2]*v[i][2]) *
+ mass[type[i]];
}
t_scalar=t;
}
-
+
MPI_Allreduce(&t_scalar,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
if (dynamic) dof_compute();
scalar *= tfactor;
- if(scalar>1e15)
+ if(scalar>1e15)
{
- cuda->cu_v->download();
- cuda->cu_x->download();
- cuda->cu_type->download();
+ cuda->cu_v->download();
+ cuda->cu_x->download();
+ cuda->cu_type->download();
double **v = atom->v;
double **x = atom->x;
- printf("Out of v-range atoms: \n");
- for(int i=0;i<atom->nlocal;i++)
- if((v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2])>1e5)
- printf("%i %i // %lf %lf %lf // %lf %lf %lf\n",atom->tag[i],atom->type[i],x[i][0], x[i][1], x[i][2],v[i][0], v[i][1], v[i][2]);
- error->all(FLERR,"Temperature out of range. Simulations will be abortet.\n");
+ printf("Out of v-range atoms: \n");
+ for(int i=0;i<atom->nlocal;i++)
+ if((v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2])>1e5)
+ printf("%i %i // %lf %lf %lf // %lf %lf %lf\n",atom->tag[i],atom->type[i],x[i][0], x[i][1], x[i][2],v[i][0], v[i][1], v[i][2]);
+ error->all(FLERR,"Temperature out of range. Simulations will be abortet.\n");
}
return scalar;
}
@@ -193,8 +193,8 @@ void ComputeTempPartialCuda::compute_vector()
int i;
if(cuda->begin_setup)
{
- if(not cu_t_vector) cu_t_vector = new cCudaData<double, ENERGY_FLOAT, x> (t_vector,6);
- if(not cu_t_scalar) cu_t_scalar = new cCudaData<double, ENERGY_FLOAT, x> (&t_scalar,1);
+ if(not cu_t_vector) cu_t_vector = new cCudaData<double, ENERGY_FLOAT, x> (t_vector,6);
+ if(not cu_t_scalar) cu_t_scalar = new cCudaData<double, ENERGY_FLOAT, x> (&t_scalar,1);
invoked_vector = update->ntimestep;
@@ -203,7 +203,7 @@ void ComputeTempPartialCuda::compute_vector()
}
else
{
-
+
invoked_vector = update->ntimestep;
double **v = atom->v;
@@ -227,7 +227,7 @@ void ComputeTempPartialCuda::compute_vector()
t[4] += massone * xflag*zflag*v[i][0]*v[i][2];
t[5] += massone * yflag*zflag*v[i][1]*v[i][2];
}
-
+
for (i = 0; i < 6; i++) t_vector[i]=t[i];
}
MPI_Allreduce(t_vector,vector,6,MPI_DOUBLE,MPI_SUM,world);
@@ -268,34 +268,34 @@ void ComputeTempPartialCuda::remove_bias_all()
memory->destroy(vbiasall);
maxbias = atom->nmax;
memory->create(vbiasall,maxbias,3,"temp/partial:vbiasall");
- delete cu_vbiasall;
- cu_vbiasall = new cCudaData<double, V_FLOAT, yx> ((double*)vbiasall, atom->nmax, 3);
+ delete cu_vbiasall;
+ cu_vbiasall = new cCudaData<double, V_FLOAT, yx> ((double*)vbiasall, atom->nmax, 3);
}
if(cuda->begin_setup)
{
- Cuda_ComputeTempPartialCuda_RemoveBiasAll(&cuda->shared_data,groupbit,xflag,yflag,zflag,cu_vbiasall->dev_data());
+ Cuda_ComputeTempPartialCuda_RemoveBiasAll(&cuda->shared_data,groupbit,xflag,yflag,zflag,cu_vbiasall->dev_data());
}
else
{
if (!xflag) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- vbiasall[i][0] = v[i][0];
- v[i][0] = 0.0;
+ vbiasall[i][0] = v[i][0];
+ v[i][0] = 0.0;
}
}
if (!yflag) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- vbiasall[i][1] = v[i][1];
- v[i][1] = 0.0;
+ vbiasall[i][1] = v[i][1];
+ v[i][1] = 0.0;
}
}
if (!zflag) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- vbiasall[i][2] = v[i][2];
- v[i][2] = 0.0;
+ vbiasall[i][2] = v[i][2];
+ v[i][2] = 0.0;
}
}
}
@@ -325,7 +325,7 @@ void ComputeTempPartialCuda::restore_bias_all()
int nlocal = atom->nlocal;
if(cuda->begin_setup)
{
- Cuda_ComputeTempPartialCuda_RestoreBiasAll(&cuda->shared_data,groupbit,xflag,yflag,zflag,cu_vbiasall->dev_data());
+ Cuda_ComputeTempPartialCuda_RestoreBiasAll(&cuda->shared_data,groupbit,xflag,yflag,zflag,cu_vbiasall->dev_data());
}
else
{
@@ -333,17 +333,17 @@ void ComputeTempPartialCuda::restore_bias_all()
if (!xflag) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
- v[i][0] += vbiasall[i][0];
+ v[i][0] += vbiasall[i][0];
}
if (!yflag) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
- v[i][1] += vbiasall[i][1];
+ v[i][1] += vbiasall[i][1];
}
if (!zflag) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
- v[i][2] += vbiasall[i][2];
+ v[i][2] += vbiasall[i][2];
}
}
}
diff --git a/src/USER-CUDA/compute_temp_partial_cuda.h b/src/USER-CUDA/compute_temp_partial_cuda.h
index 4412adc88af407a764388d5b0e13564d6d69ea92..f7d34b8ce9ffcc24a41df6424cb88c5fb3a838e9 100644
--- a/src/USER-CUDA/compute_temp_partial_cuda.h
+++ b/src/USER-CUDA/compute_temp_partial_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -28,7 +28,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -72,8 +72,8 @@ class ComputeTempPartialCuda : public Compute {
void dof_compute();
double t_vector[6];
double t_scalar;
- cCudaData<double , ENERGY_FLOAT , x>* cu_t_scalar;
- cCudaData<double , ENERGY_FLOAT , x>* cu_t_vector;
+ cCudaData<double , ENERGY_FLOAT , x>* cu_t_scalar;
+ cCudaData<double , ENERGY_FLOAT , x>* cu_t_vector;
cCudaData<double, V_FLOAT, yx>* cu_vbiasall;
};
diff --git a/src/USER-CUDA/cuda.cpp b/src/USER-CUDA/cuda.cpp
index 50c896fbbaa52c69c277f7462f1c9f5e12c8b2c3..723f5f8f08da358d9c3a86700f782a9c77e4b60e 100644
--- a/src/USER-CUDA/cuda.cpp
+++ b/src/USER-CUDA/cuda.cpp
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -50,362 +50,362 @@ using namespace LAMMPS_NS;
Cuda::Cuda(LAMMPS *lmp) : Pointers(lmp)
{
- cuda_exists=true;
- lmp->cuda=this;
- if(universe->me==0)
- printf("# Using LAMMPS_CUDA \n");
- shared_data.me=universe->me;
- device_set=false;
-
- Cuda_Cuda_GetCompileSettings(&shared_data);
-
- if(shared_data.compile_settings.prec_glob!=sizeof(CUDA_FLOAT)/4) printf("\n\n # CUDA WARNING: Compile Settings of cuda and cpp code differ! \n # CUDA WARNING: Global Precision: cuda %i cpp %i\n\n",shared_data.compile_settings.prec_glob, sizeof(CUDA_FLOAT)/4);
- if(shared_data.compile_settings.prec_x!=sizeof(X_FLOAT)/4) printf("\n\n # CUDA WARNING: Compile Settings of cuda and cpp code differ! \n # CUDA WARNING: X Precision: cuda %i cpp %i\n\n",shared_data.compile_settings.prec_x, sizeof(X_FLOAT)/4);
- if(shared_data.compile_settings.prec_v!=sizeof(V_FLOAT)/4) printf("\n\n # CUDA WARNING: Compile Settings of cuda and cpp code differ! \n # CUDA WARNING: V Precision: cuda %i cpp %i\n\n",shared_data.compile_settings.prec_v, sizeof(V_FLOAT)/4);
- if(shared_data.compile_settings.prec_f!=sizeof(F_FLOAT)/4) printf("\n\n # CUDA WARNING: Compile Settings of cuda and cpp code differ! \n # CUDA WARNING: F Precision: cuda %i cpp %i\n\n",shared_data.compile_settings.prec_f, sizeof(F_FLOAT)/4);
- if(shared_data.compile_settings.prec_pppm!=sizeof(PPPM_FLOAT)/4) printf("\n\n # CUDA WARNING: Compile Settings of cuda and cpp code differ! \n # CUDA WARNING: PPPM Precision: cuda %i cpp %i\n\n",shared_data.compile_settings.prec_pppm, sizeof(PPPM_FLOAT)/4);
- if(shared_data.compile_settings.prec_fft!=sizeof(FFT_FLOAT)/4) printf("\n\n # CUDA WARNING: Compile Settings of cuda and cpp code differ! \n # CUDA WARNING: FFT Precision: cuda %i cpp %i\n\n",shared_data.compile_settings.prec_fft, sizeof(FFT_FLOAT)/4);
+ cuda_exists=true;
+ lmp->cuda=this;
+ if(universe->me==0)
+ printf("# Using LAMMPS_CUDA \n");
+ shared_data.me=universe->me;
+ device_set=false;
+
+ Cuda_Cuda_GetCompileSettings(&shared_data);
+
+ if(shared_data.compile_settings.prec_glob!=sizeof(CUDA_FLOAT)/4) printf("\n\n # CUDA WARNING: Compile Settings of cuda and cpp code differ! \n # CUDA WARNING: Global Precision: cuda %i cpp %i\n\n",shared_data.compile_settings.prec_glob, sizeof(CUDA_FLOAT)/4);
+ if(shared_data.compile_settings.prec_x!=sizeof(X_FLOAT)/4) printf("\n\n # CUDA WARNING: Compile Settings of cuda and cpp code differ! \n # CUDA WARNING: X Precision: cuda %i cpp %i\n\n",shared_data.compile_settings.prec_x, sizeof(X_FLOAT)/4);
+ if(shared_data.compile_settings.prec_v!=sizeof(V_FLOAT)/4) printf("\n\n # CUDA WARNING: Compile Settings of cuda and cpp code differ! \n # CUDA WARNING: V Precision: cuda %i cpp %i\n\n",shared_data.compile_settings.prec_v, sizeof(V_FLOAT)/4);
+ if(shared_data.compile_settings.prec_f!=sizeof(F_FLOAT)/4) printf("\n\n # CUDA WARNING: Compile Settings of cuda and cpp code differ! \n # CUDA WARNING: F Precision: cuda %i cpp %i\n\n",shared_data.compile_settings.prec_f, sizeof(F_FLOAT)/4);
+ if(shared_data.compile_settings.prec_pppm!=sizeof(PPPM_FLOAT)/4) printf("\n\n # CUDA WARNING: Compile Settings of cuda and cpp code differ! \n # CUDA WARNING: PPPM Precision: cuda %i cpp %i\n\n",shared_data.compile_settings.prec_pppm, sizeof(PPPM_FLOAT)/4);
+ if(shared_data.compile_settings.prec_fft!=sizeof(FFT_FLOAT)/4) printf("\n\n # CUDA WARNING: Compile Settings of cuda and cpp code differ! \n # CUDA WARNING: FFT Precision: cuda %i cpp %i\n\n",shared_data.compile_settings.prec_fft, sizeof(FFT_FLOAT)/4);
#ifdef FFT_CUFFT
if(shared_data.compile_settings.cufft!=1) printf("\n\n # CUDA WARNING: Compile Settings of cuda and cpp code differ! \n # CUDA WARNING: cufft: cuda %i cpp %i\n\n",shared_data.compile_settings.cufft, 1);
- #else
+ #else
if(shared_data.compile_settings.cufft!=0) printf("\n\n # CUDA WARNING: Compile Settings of cuda and cpp code differ! \n # CUDA WARNING: cufft: cuda %i cpp %i\n\n",shared_data.compile_settings.cufft, 0);
#endif
-
+
if(shared_data.compile_settings.arch!=CUDA_ARCH) printf("\n\n # CUDA WARNING: Compile Settings of cuda and cpp code differ! \n # CUDA WARNING: arch: cuda %i cpp %i\n\n",shared_data.compile_settings.cufft, CUDA_ARCH);
-
- cu_x = 0;
- cu_v = 0;
- cu_f = 0;
- cu_tag = 0;
- cu_type = 0;
- cu_mask = 0;
- cu_image = 0;
- cu_xhold = 0;
- cu_q = 0;
- cu_rmass = 0;
- cu_mass = 0;
- cu_virial = 0;
- cu_eatom = 0;
- cu_vatom = 0;
- cu_radius = 0;
- cu_density = 0;
- cu_omega = 0;
- cu_torque = 0;
-
- cu_special = 0;
- cu_nspecial = 0;
-
- cu_molecule = 0;
-
- cu_x_type = 0;
- x_type = 0;
- cu_v_radius = 0;
- v_radius = 0;
- cu_omega_rmass = 0;
- omega_rmass = 0;
-
- binned_id = 0;
- cu_binned_id = 0;
- binned_idnew = 0;
- cu_binned_idnew = 0;
-
- cu_map_array = 0;
-
- copy_buffer=0;
- copy_buffersize=0;
-
- neighbor_decide_by_integrator=0;
- pinned=true;
-
- debugdata=0;
- new int[2*CUDA_MAX_DEBUG_SIZE];
-
- finished_setup = false;
- begin_setup = false;
- finished_run = false;
-
- setSharedDataZero();
-
- uploadtime=0;
- downloadtime=0;
- dotiming=false;
+
+ cu_x = 0;
+ cu_v = 0;
+ cu_f = 0;
+ cu_tag = 0;
+ cu_type = 0;
+ cu_mask = 0;
+ cu_image = 0;
+ cu_xhold = 0;
+ cu_q = 0;
+ cu_rmass = 0;
+ cu_mass = 0;
+ cu_virial = 0;
+ cu_eatom = 0;
+ cu_vatom = 0;
+ cu_radius = 0;
+ cu_density = 0;
+ cu_omega = 0;
+ cu_torque = 0;
+
+ cu_special = 0;
+ cu_nspecial = 0;
+
+ cu_molecule = 0;
+
+ cu_x_type = 0;
+ x_type = 0;
+ cu_v_radius = 0;
+ v_radius = 0;
+ cu_omega_rmass = 0;
+ omega_rmass = 0;
+
+ binned_id = 0;
+ cu_binned_id = 0;
+ binned_idnew = 0;
+ cu_binned_idnew = 0;
+
+ cu_map_array = 0;
+
+ copy_buffer=0;
+ copy_buffersize=0;
+
+ neighbor_decide_by_integrator=0;
+ pinned=true;
+
+ debugdata=0;
+ new int[2*CUDA_MAX_DEBUG_SIZE];
+
+ finished_setup = false;
+ begin_setup = false;
+ finished_run = false;
+
+ setSharedDataZero();
+
+ uploadtime=0;
+ downloadtime=0;
+ dotiming=false;
dotestatom = false;
testatom = 0;
- oncpu = true;
+ oncpu = true;
self_comm = 0;
- MYDBG( printf("# CUDA: Cuda::Cuda Done...\n");)
- //cCudaData<double, float, yx >
+ MYDBG( printf("# CUDA: Cuda::Cuda Done...\n");)
+ //cCudaData<double, float, yx >
}
Cuda::~Cuda()
{
-
- print_timings();
-
- if(universe->me==0) printf("# CUDA: Free memory...\n");
-
- delete cu_q;
- delete cu_x;
- delete cu_v;
- delete cu_f;
- delete cu_tag;
- delete cu_type;
- delete cu_mask;
- delete cu_image;
- delete cu_xhold;
- delete cu_mass;
- delete cu_rmass;
- delete cu_virial;
- delete cu_eng_vdwl;
- delete cu_eng_coul;
- delete cu_eatom;
- delete cu_vatom;
- delete cu_radius;
- delete cu_density;
- delete cu_omega;
- delete cu_torque;
- delete cu_molecule;
-
- delete cu_x_type;
- delete [] x_type;
- delete cu_v_radius;
- delete [] v_radius;
- delete cu_omega_rmass;
- delete [] omega_rmass;
-
- delete cu_map_array;
-
- std::map<NeighList*, CudaNeighList*>::iterator p = neigh_lists.begin();
- while(p != neigh_lists.end())
- {
- delete p->second;
- ++p;
- }
+
+ print_timings();
+
+ if(universe->me==0) printf("# CUDA: Free memory...\n");
+
+ delete cu_q;
+ delete cu_x;
+ delete cu_v;
+ delete cu_f;
+ delete cu_tag;
+ delete cu_type;
+ delete cu_mask;
+ delete cu_image;
+ delete cu_xhold;
+ delete cu_mass;
+ delete cu_rmass;
+ delete cu_virial;
+ delete cu_eng_vdwl;
+ delete cu_eng_coul;
+ delete cu_eatom;
+ delete cu_vatom;
+ delete cu_radius;
+ delete cu_density;
+ delete cu_omega;
+ delete cu_torque;
+ delete cu_molecule;
+
+ delete cu_x_type;
+ delete [] x_type;
+ delete cu_v_radius;
+ delete [] v_radius;
+ delete cu_omega_rmass;
+ delete [] omega_rmass;
+
+ delete cu_map_array;
+
+ std::map<NeighList*, CudaNeighList*>::iterator p = neigh_lists.begin();
+ while(p != neigh_lists.end())
+ {
+ delete p->second;
+ ++p;
+ }
}
void Cuda::accelerator(int narg, char** arg)
{
- if(device_set) return;
- if(universe->me==0)
- printf("# CUDA: Activate GPU \n");
-
- int* devicelist=NULL;
- int pppn=2;
+ if(device_set) return;
+ if(universe->me==0)
+ printf("# CUDA: Activate GPU \n");
+
+ int* devicelist=NULL;
+ int pppn=2;
for(int i=0;i<narg;i++)
- {
- if(strcmp(arg[i],"gpu/node")==0)
- {
- if(++i==narg)
- error->all(FLERR,"Invalid Options for 'accelerator' command. Expecting a number after 'gpu/node' option.");
- pppn=atoi(arg[i]);
- }
-
- if(strcmp(arg[i],"gpu/node/special")==0)
- {
- if(++i==narg)
- error->all(FLERR,"Invalid Options for 'accelerator' command. Expecting number of GPUs to be used per node after keyword 'gpu/node/special'.");
- pppn=atoi(arg[i]);
- if(pppn<1) error->all(FLERR,"Invalid Options for 'accelerator' command. Expecting number of GPUs to be used per node after keyword 'gpu/node special'.");
- if(i+pppn==narg)
- error->all(FLERR,"Invalid Options for 'accelerator' command. Expecting list of device ids after keyword 'gpu/node special'.");
- devicelist=new int[pppn];
- for(int k=0;k<pppn;k++)
- {i++;devicelist[k]=atoi(arg[i]);}
- }
-
- if(strcmp(arg[i],"pinned")==0)
- {
- if(++i==narg)
- error->all(FLERR,"Invalid Options for 'accelerator' command. Expecting a number after 'pinned' option.");
- pinned=atoi(arg[i])==0?false:true;
+ {
+ if(strcmp(arg[i],"gpu/node")==0)
+ {
+ if(++i==narg)
+ error->all(FLERR,"Invalid Options for 'accelerator' command. Expecting a number after 'gpu/node' option.");
+ pppn=atoi(arg[i]);
+ }
+
+ if(strcmp(arg[i],"gpu/node/special")==0)
+ {
+ if(++i==narg)
+ error->all(FLERR,"Invalid Options for 'accelerator' command. Expecting number of GPUs to be used per node after keyword 'gpu/node/special'.");
+ pppn=atoi(arg[i]);
+ if(pppn<1) error->all(FLERR,"Invalid Options for 'accelerator' command. Expecting number of GPUs to be used per node after keyword 'gpu/node special'.");
+ if(i+pppn==narg)
+ error->all(FLERR,"Invalid Options for 'accelerator' command. Expecting list of device ids after keyword 'gpu/node special'.");
+ devicelist=new int[pppn];
+ for(int k=0;k<pppn;k++)
+ {i++;devicelist[k]=atoi(arg[i]);}
+ }
+
+ if(strcmp(arg[i],"pinned")==0)
+ {
+ if(++i==narg)
+ error->all(FLERR,"Invalid Options for 'accelerator' command. Expecting a number after 'pinned' option.");
+ pinned=atoi(arg[i])==0?false:true;
if((pinned==false)&&(universe->me==0)) printf(" #CUDA: Pinned memory is not used for communication\n");
- }
-
- if(strcmp(arg[i],"timing")==0)
- {
- dotiming=true;
- }
-
- if(strcmp(arg[i],"suffix")==0)
- {
- if(++i==narg)
- error->all(FLERR,"Invalid Options for 'accelerator' command. Expecting a string after 'suffix' option.");
- strcpy(lmp->suffix,arg[i]);
- }
-
- if(strcmp(arg[i],"overlap_comm")==0)
- {
- shared_data.overlap_comm=1;
- }
-
- if(strcmp(arg[i],"test")==0)
- {
- if(++i==narg)
- error->all(FLERR,"Invalid Options for 'accelerator' command. Expecting a number after 'test' option.");
- testatom=atof(arg[i]);
- dotestatom=true;
- }
-
- if(strcmp(arg[i],"override/bpa")==0)
- {
- if(++i==narg)
- error->all(FLERR,"Invalid Options for 'accelerator' command. Expecting a number after 'override/bpa' option.");
- shared_data.pair.override_block_per_atom = atoi(arg[i]);
- }
- }
-
- CudaWrapper_Init(0, (char**)0,universe->me,pppn,devicelist);
- //if(shared_data.overlap_comm)
- CudaWrapper_AddStreams(3);
- cu_x = 0;
- cu_v = 0;
- cu_f = 0;
- cu_tag = 0;
- cu_type = 0;
- cu_mask = 0;
- cu_image = 0;
- cu_xhold = 0;
- cu_q = 0;
- cu_rmass = 0;
- cu_mass = 0;
- cu_virial = 0;
- cu_eatom = 0;
- cu_vatom = 0;
- cu_radius = 0;
- cu_density = 0;
- cu_omega = 0;
- cu_torque = 0;
-
- cu_special = 0;
- cu_nspecial = 0;
-
- cu_molecule = 0;
-
- cu_x_type = 0;
- cu_v_radius = 0;
- cu_omega_rmass = 0;
-
- cu_binned_id = 0;
- cu_binned_idnew = 0;
- device_set=true;
- allocate();
- delete devicelist;
+ }
+
+ if(strcmp(arg[i],"timing")==0)
+ {
+ dotiming=true;
+ }
+
+ if(strcmp(arg[i],"suffix")==0)
+ {
+ if(++i==narg)
+ error->all(FLERR,"Invalid Options for 'accelerator' command. Expecting a string after 'suffix' option.");
+ strcpy(lmp->suffix,arg[i]);
+ }
+
+ if(strcmp(arg[i],"overlap_comm")==0)
+ {
+ shared_data.overlap_comm=1;
+ }
+
+ if(strcmp(arg[i],"test")==0)
+ {
+ if(++i==narg)
+ error->all(FLERR,"Invalid Options for 'accelerator' command. Expecting a number after 'test' option.");
+ testatom=atof(arg[i]);
+ dotestatom=true;
+ }
+
+ if(strcmp(arg[i],"override/bpa")==0)
+ {
+ if(++i==narg)
+ error->all(FLERR,"Invalid Options for 'accelerator' command. Expecting a number after 'override/bpa' option.");
+ shared_data.pair.override_block_per_atom = atoi(arg[i]);
+ }
+ }
+
+ CudaWrapper_Init(0, (char**)0,universe->me,pppn,devicelist);
+ //if(shared_data.overlap_comm)
+ CudaWrapper_AddStreams(3);
+ cu_x = 0;
+ cu_v = 0;
+ cu_f = 0;
+ cu_tag = 0;
+ cu_type = 0;
+ cu_mask = 0;
+ cu_image = 0;
+ cu_xhold = 0;
+ cu_q = 0;
+ cu_rmass = 0;
+ cu_mass = 0;
+ cu_virial = 0;
+ cu_eatom = 0;
+ cu_vatom = 0;
+ cu_radius = 0;
+ cu_density = 0;
+ cu_omega = 0;
+ cu_torque = 0;
+
+ cu_special = 0;
+ cu_nspecial = 0;
+
+ cu_molecule = 0;
+
+ cu_x_type = 0;
+ cu_v_radius = 0;
+ cu_omega_rmass = 0;
+
+ cu_binned_id = 0;
+ cu_binned_idnew = 0;
+ device_set=true;
+ allocate();
+ delete devicelist;
}
void Cuda::setSharedDataZero()
{
- MYDBG(printf("# CUDA: Cuda::setSharedDataZero ...\n");)
- shared_data.atom.nlocal = 0;
- shared_data.atom.nghost = 0;
- shared_data.atom.nall = 0;
- shared_data.atom.nmax = 0;
- shared_data.atom.ntypes = 0;
- shared_data.atom.q_flag = 0;
- shared_data.atom.need_eatom = 0;
- shared_data.atom.need_vatom = 0;
+ MYDBG(printf("# CUDA: Cuda::setSharedDataZero ...\n");)
+ shared_data.atom.nlocal = 0;
+ shared_data.atom.nghost = 0;
+ shared_data.atom.nall = 0;
+ shared_data.atom.nmax = 0;
+ shared_data.atom.ntypes = 0;
+ shared_data.atom.q_flag = 0;
+ shared_data.atom.need_eatom = 0;
+ shared_data.atom.need_vatom = 0;
shared_data.atom.update_nmax = 1;
shared_data.atom.update_nlocal = 1;
shared_data.atom.update_neigh = 1;
-
+
shared_data.pair.cudable_force = 0;
- shared_data.pair.collect_forces_later = 0;
- shared_data.pair.use_block_per_atom = 0;
- shared_data.pair.override_block_per_atom = -1;
- shared_data.pair.cut = 0;
- shared_data.pair.cutsq = 0;
- shared_data.pair.cut_inner = 0;
- shared_data.pair.cut_coul = 0;
- shared_data.pair.special_lj = 0;
- shared_data.pair.special_coul = 0;
-
- shared_data.pair.neighall = false;
-
- shared_data.pppm.cudable_force = 0;
-
- shared_data.buffersize = 0;
- shared_data.buffer_new = 1;
- shared_data.buffer = NULL;
-
- shared_data.comm.comm_phase=0;
- shared_data.overlap_comm=0;
-
- shared_data.comm.buffer = NULL;
- shared_data.comm.buffer_size=0;
- shared_data.comm.overlap_split_ratio=0;
+ shared_data.pair.collect_forces_later = 0;
+ shared_data.pair.use_block_per_atom = 0;
+ shared_data.pair.override_block_per_atom = -1;
+ shared_data.pair.cut = 0;
+ shared_data.pair.cutsq = 0;
+ shared_data.pair.cut_inner = 0;
+ shared_data.pair.cut_coul = 0;
+ shared_data.pair.special_lj = 0;
+ shared_data.pair.special_coul = 0;
+
+ shared_data.pair.neighall = false;
+
+ shared_data.pppm.cudable_force = 0;
+
+ shared_data.buffersize = 0;
+ shared_data.buffer_new = 1;
+ shared_data.buffer = NULL;
+
+ shared_data.comm.comm_phase=0;
+ shared_data.overlap_comm=0;
+
+ shared_data.comm.buffer = NULL;
+ shared_data.comm.buffer_size=0;
+ shared_data.comm.overlap_split_ratio=0;
// setTimingsZero();
}
void Cuda::allocate()
{
- accelerator(0,NULL);
- MYDBG(printf("# CUDA: Cuda::allocate ...\n");)
- if(not cu_virial)
- {
- cu_virial = new cCudaData<double, ENERGY_FLOAT, x > (NULL, & shared_data.pair.virial , 6);
- cu_eng_vdwl = new cCudaData<double, ENERGY_FLOAT, x > (NULL, & shared_data.pair.eng_vdwl ,1);
- cu_eng_coul = new cCudaData<double, ENERGY_FLOAT, x > (NULL, & shared_data.pair.eng_coul ,1);
- cu_extent = new cCudaData<double, double, x> (extent, 6);
- shared_data.flag = CudaWrapper_AllocCudaData(sizeof(int));
- int size=2*CUDA_MAX_DEBUG_SIZE;
- debugdata = new int[size];
- cu_debugdata = new cCudaData<int, int, x > (debugdata , size);
- shared_data.debugdata=cu_debugdata->dev_data();
- }
- checkResize();
- setSystemParams();
- MYDBG(printf("# CUDA: Cuda::allocate done...\n");)
+ accelerator(0,NULL);
+ MYDBG(printf("# CUDA: Cuda::allocate ...\n");)
+ if(not cu_virial)
+ {
+ cu_virial = new cCudaData<double, ENERGY_FLOAT, x > (NULL, & shared_data.pair.virial , 6);
+ cu_eng_vdwl = new cCudaData<double, ENERGY_FLOAT, x > (NULL, & shared_data.pair.eng_vdwl ,1);
+ cu_eng_coul = new cCudaData<double, ENERGY_FLOAT, x > (NULL, & shared_data.pair.eng_coul ,1);
+ cu_extent = new cCudaData<double, double, x> (extent, 6);
+ shared_data.flag = CudaWrapper_AllocCudaData(sizeof(int));
+ int size=2*CUDA_MAX_DEBUG_SIZE;
+ debugdata = new int[size];
+ cu_debugdata = new cCudaData<int, int, x > (debugdata , size);
+ shared_data.debugdata=cu_debugdata->dev_data();
+ }
+ checkResize();
+ setSystemParams();
+ MYDBG(printf("# CUDA: Cuda::allocate done...\n");)
}
void Cuda::setSystemParams()
{
MYDBG(printf("# CUDA: Cuda::setSystemParams ...\n");)
- shared_data.atom.nlocal = atom->nlocal;
- shared_data.atom.nghost = atom->nghost;
- shared_data.atom.nall = atom->nlocal + atom->nghost;
- shared_data.atom.ntypes = atom->ntypes;
- shared_data.atom.q_flag = atom->q_flag;
- shared_data.atom.rmass_flag = atom->rmass_flag;
+ shared_data.atom.nlocal = atom->nlocal;
+ shared_data.atom.nghost = atom->nghost;
+ shared_data.atom.nall = atom->nlocal + atom->nghost;
+ shared_data.atom.ntypes = atom->ntypes;
+ shared_data.atom.q_flag = atom->q_flag;
+ shared_data.atom.rmass_flag = atom->rmass_flag;
MYDBG(printf("# CUDA: Cuda::setSystemParams done ...\n");)
}
void Cuda::setDomainParams()
{
MYDBG(printf("# CUDA: Cuda::setDomainParams ...\n");)
- cuda_shared_domain* cu_domain = &shared_data.domain;
-
+ cuda_shared_domain* cu_domain = &shared_data.domain;
+
cu_domain->triclinic = domain->triclinic;
- for(short i=0; i<3; ++i)
- {
- cu_domain->periodicity[i] = domain->periodicity[i];
- cu_domain->sublo[i] = domain->sublo[i];
- cu_domain->subhi[i] = domain->subhi[i];
- cu_domain->boxlo[i] = domain->boxlo[i];
- cu_domain->boxhi[i] = domain->boxhi[i];
- cu_domain->prd[i] = domain->prd[i];
- }
- if(domain->triclinic)
+ for(short i=0; i<3; ++i)
+ {
+ cu_domain->periodicity[i] = domain->periodicity[i];
+ cu_domain->sublo[i] = domain->sublo[i];
+ cu_domain->subhi[i] = domain->subhi[i];
+ cu_domain->boxlo[i] = domain->boxlo[i];
+ cu_domain->boxhi[i] = domain->boxhi[i];
+ cu_domain->prd[i] = domain->prd[i];
+ }
+ if(domain->triclinic)
{
- for(short i=0; i<3; ++i)
- {
- cu_domain->boxlo_lamda[i] = domain->boxlo_lamda[i];
- cu_domain->boxhi_lamda[i] = domain->boxhi_lamda[i];
- cu_domain->prd_lamda[i] = domain->prd_lamda[i];
- }
- cu_domain->xy = domain->xy;
- cu_domain->xz = domain->xz;
- cu_domain->yz = domain->yz;
- }
-
- for(int i=0;i<6;i++)
- {
- cu_domain->h[i]=domain->h[i];
- cu_domain->h_inv[i]=domain->h_inv[i];
- cu_domain->h_rate[i]=domain->h_rate[i];
- }
-
- cu_domain->update=2;
+ for(short i=0; i<3; ++i)
+ {
+ cu_domain->boxlo_lamda[i] = domain->boxlo_lamda[i];
+ cu_domain->boxhi_lamda[i] = domain->boxhi_lamda[i];
+ cu_domain->prd_lamda[i] = domain->prd_lamda[i];
+ }
+ cu_domain->xy = domain->xy;
+ cu_domain->xz = domain->xz;
+ cu_domain->yz = domain->yz;
+ }
+
+ for(int i=0;i<6;i++)
+ {
+ cu_domain->h[i]=domain->h[i];
+ cu_domain->h_inv[i]=domain->h_inv[i];
+ cu_domain->h_rate[i]=domain->h_rate[i];
+ }
+
+ cu_domain->update=2;
MYDBG(printf("# CUDA: Cuda::setDomainParams done ...\n");)
}
@@ -413,283 +413,283 @@ void Cuda::checkResize()
{
MYDBG(printf("# CUDA: Cuda::checkResize ...\n");)
accelerator(0,NULL);
- cuda_shared_atom* cu_atom = & shared_data.atom;
- cuda_shared_pair* cu_pair = & shared_data.pair;
- cu_atom->q_flag = atom->q_flag;
- cu_atom->rmass_flag = atom->rmass ? 1 : 0;
- cu_atom->nall = atom->nlocal + atom->nghost;
- cu_atom->nlocal = atom->nlocal;
- cu_atom->nghost = atom->nghost;
-
- // do we have more atoms to upload than currently allocated memory on device? (also true if nothing yet allocated)
- if(atom->nmax > cu_atom->nmax || cu_tag == NULL)
- {
- delete cu_x; cu_x = new cCudaData<double, X_FLOAT, yx> ((double*)atom->x , & cu_atom->x , atom->nmax, 3,0,true); //cu_x->set_buffer(&(shared_data.buffer),&(shared_data.buffersize),true);
- delete cu_v; cu_v = new cCudaData<double, V_FLOAT, yx> ((double*)atom->v, & cu_atom->v , atom->nmax, 3);
- delete cu_f; cu_f = new cCudaData<double, F_FLOAT, yx> ((double*)atom->f, & cu_atom->f , atom->nmax, 3,0,true);
- delete cu_tag; cu_tag = new cCudaData<int , int , x > (atom->tag , & cu_atom->tag , atom->nmax );
- delete cu_type; cu_type = new cCudaData<int , int , x > (atom->type , & cu_atom->type , atom->nmax );
- delete cu_mask; cu_mask = new cCudaData<int , int , x > (atom->mask , & cu_atom->mask , atom->nmax );
- delete cu_image; cu_image = new cCudaData<int , int , x > (atom->image , & cu_atom->image , atom->nmax );
-
- if(atom->rmass)
- {delete cu_rmass; cu_rmass = new cCudaData<double, V_FLOAT, x > (atom->rmass , & cu_atom->rmass , atom->nmax );}
-
- if(cu_atom->q_flag)
- {delete cu_q; cu_q = new cCudaData<double, F_FLOAT, x > ((double*)atom->q, & cu_atom->q , atom->nmax );}// cu_q->set_buffer(&(copy_buffer),&(copy_buffersize),true);}
-
- if(atom->radius)
- {
- delete cu_radius; cu_radius = new cCudaData<double, X_FLOAT, x > (atom->radius , & cu_atom->radius , atom->nmax );
- delete cu_v_radius; cu_v_radius = new cCudaData<V_FLOAT, V_FLOAT, x> (v_radius , & cu_atom->v_radius , atom->nmax*4);
- delete cu_omega_rmass; cu_omega_rmass = new cCudaData<V_FLOAT, V_FLOAT, x> (omega_rmass , & cu_atom->omega_rmass , atom->nmax*4);
- }
-
- if(atom->omega)
- {delete cu_omega; cu_omega = new cCudaData<double, V_FLOAT, yx > (((double*) atom->omega) , & cu_atom->omega , atom->nmax,3 );}
-
- if(atom->torque)
- {delete cu_torque; cu_torque = new cCudaData<double, F_FLOAT, yx > (((double*) atom->torque) , & cu_atom->torque , atom->nmax,3 );}
-
- if(atom->special)
- {delete cu_special; cu_special = new cCudaData<int, int, yx > (((int*) &(atom->special[0][0])) , & cu_atom->special , atom->nmax,atom->maxspecial ); shared_data.atom.maxspecial=atom->maxspecial;}
- if(atom->nspecial)
- {delete cu_nspecial; cu_nspecial = new cCudaData<int, int, yx > (((int*) atom->nspecial) , & cu_atom->nspecial , atom->nmax,3 );}
- if(atom->molecule)
- {delete cu_molecule; cu_molecule = new cCudaData<int, int, x > (((int*) atom->molecule) , & cu_atom->molecule , atom->nmax );}
- shared_data.atom.special_flag = neighbor->special_flag;
- shared_data.atom.molecular = atom->molecular;
-
+ cuda_shared_atom* cu_atom = & shared_data.atom;
+ cuda_shared_pair* cu_pair = & shared_data.pair;
+ cu_atom->q_flag = atom->q_flag;
+ cu_atom->rmass_flag = atom->rmass ? 1 : 0;
+ cu_atom->nall = atom->nlocal + atom->nghost;
+ cu_atom->nlocal = atom->nlocal;
+ cu_atom->nghost = atom->nghost;
+
+ // do we have more atoms to upload than currently allocated memory on device? (also true if nothing yet allocated)
+ if(atom->nmax > cu_atom->nmax || cu_tag == NULL)
+ {
+ delete cu_x; cu_x = new cCudaData<double, X_FLOAT, yx> ((double*)atom->x , & cu_atom->x , atom->nmax, 3,0,true); //cu_x->set_buffer(&(shared_data.buffer),&(shared_data.buffersize),true);
+ delete cu_v; cu_v = new cCudaData<double, V_FLOAT, yx> ((double*)atom->v, & cu_atom->v , atom->nmax, 3);
+ delete cu_f; cu_f = new cCudaData<double, F_FLOAT, yx> ((double*)atom->f, & cu_atom->f , atom->nmax, 3,0,true);
+ delete cu_tag; cu_tag = new cCudaData<int , int , x > (atom->tag , & cu_atom->tag , atom->nmax );
+ delete cu_type; cu_type = new cCudaData<int , int , x > (atom->type , & cu_atom->type , atom->nmax );
+ delete cu_mask; cu_mask = new cCudaData<int , int , x > (atom->mask , & cu_atom->mask , atom->nmax );
+ delete cu_image; cu_image = new cCudaData<int , int , x > (atom->image , & cu_atom->image , atom->nmax );
+
+ if(atom->rmass)
+ {delete cu_rmass; cu_rmass = new cCudaData<double, V_FLOAT, x > (atom->rmass , & cu_atom->rmass , atom->nmax );}
+
+ if(cu_atom->q_flag)
+ {delete cu_q; cu_q = new cCudaData<double, F_FLOAT, x > ((double*)atom->q, & cu_atom->q , atom->nmax );}// cu_q->set_buffer(&(copy_buffer),&(copy_buffersize),true);}
+
+ if(atom->radius)
+ {
+ delete cu_radius; cu_radius = new cCudaData<double, X_FLOAT, x > (atom->radius , & cu_atom->radius , atom->nmax );
+ delete cu_v_radius; cu_v_radius = new cCudaData<V_FLOAT, V_FLOAT, x> (v_radius , & cu_atom->v_radius , atom->nmax*4);
+ delete cu_omega_rmass; cu_omega_rmass = new cCudaData<V_FLOAT, V_FLOAT, x> (omega_rmass , & cu_atom->omega_rmass , atom->nmax*4);
+ }
+
+ if(atom->omega)
+ {delete cu_omega; cu_omega = new cCudaData<double, V_FLOAT, yx > (((double*) atom->omega) , & cu_atom->omega , atom->nmax,3 );}
+
+ if(atom->torque)
+ {delete cu_torque; cu_torque = new cCudaData<double, F_FLOAT, yx > (((double*) atom->torque) , & cu_atom->torque , atom->nmax,3 );}
+
+ if(atom->special)
+ {delete cu_special; cu_special = new cCudaData<int, int, yx > (((int*) &(atom->special[0][0])) , & cu_atom->special , atom->nmax,atom->maxspecial ); shared_data.atom.maxspecial=atom->maxspecial;}
+ if(atom->nspecial)
+ {delete cu_nspecial; cu_nspecial = new cCudaData<int, int, yx > (((int*) atom->nspecial) , & cu_atom->nspecial , atom->nmax,3 );}
+ if(atom->molecule)
+ {delete cu_molecule; cu_molecule = new cCudaData<int, int, x > (((int*) atom->molecule) , & cu_atom->molecule , atom->nmax );}
+ shared_data.atom.special_flag = neighbor->special_flag;
+ shared_data.atom.molecular = atom->molecular;
+
cu_atom->update_nmax = 2;
cu_atom->nmax = atom->nmax;
-
- delete cu_x_type; cu_x_type = new cCudaData<X_FLOAT, X_FLOAT, x> (x_type , & cu_atom->x_type , atom->nmax*4);
- }
-
- if(((cu_xhold==NULL)||(cu_xhold->get_dim()[0]<neighbor->maxhold))&&neighbor->xhold)
- {
- delete cu_xhold; cu_xhold = new cCudaData<double, X_FLOAT, yx> ((double*)neighbor->xhold, & cu_atom->xhold , neighbor->maxhold, 3);
- shared_data.atom.maxhold=neighbor->maxhold;
- }
-
- if(atom->mass && !cu_mass)
- {cu_mass = new cCudaData<double, V_FLOAT, x > (atom->mass , & cu_atom->mass , atom->ntypes+1);}
- cu_atom->mass_host = atom->mass;
-
- if(atom->map_style==1)
- {
- if((cu_map_array==NULL))
- {
- cu_map_array = new cCudaData<int, int, x > (atom->get_map_array() , & cu_atom->map_array , atom->get_map_size() );
- }
- else
- if(cu_map_array->dev_size()/sizeof(int)<atom->get_map_size())
- {
- delete cu_map_array;
+
+ delete cu_x_type; cu_x_type = new cCudaData<X_FLOAT, X_FLOAT, x> (x_type , & cu_atom->x_type , atom->nmax*4);
+ }
+
+ if(((cu_xhold==NULL)||(cu_xhold->get_dim()[0]<neighbor->maxhold))&&neighbor->xhold)
+ {
+ delete cu_xhold; cu_xhold = new cCudaData<double, X_FLOAT, yx> ((double*)neighbor->xhold, & cu_atom->xhold , neighbor->maxhold, 3);
+ shared_data.atom.maxhold=neighbor->maxhold;
+ }
+
+ if(atom->mass && !cu_mass)
+ {cu_mass = new cCudaData<double, V_FLOAT, x > (atom->mass , & cu_atom->mass , atom->ntypes+1);}
+ cu_atom->mass_host = atom->mass;
+
+ if(atom->map_style==1)
+ {
+ if((cu_map_array==NULL))
+ {
+ cu_map_array = new cCudaData<int, int, x > (atom->get_map_array() , & cu_atom->map_array , atom->get_map_size() );
+ }
+ else
+ if(cu_map_array->dev_size()/sizeof(int)<atom->get_map_size())
+ {
+ delete cu_map_array;
cu_map_array = new cCudaData<int, int, x > (atom->get_map_array() , & cu_atom->map_array , atom->get_map_size() );
- }
- }
-
-
- // if any of the host pointers have changed (e.g. re-allocated somewhere else), set to correct pointer
- if(cu_x ->get_host_data() != atom->x) cu_x ->set_host_data((double*) (atom->x));
- if(cu_v ->get_host_data() != atom->v) cu_v ->set_host_data((double*) (atom->v));
- if(cu_f ->get_host_data() != atom->f) cu_f ->set_host_data((double*) (atom->f));
- if(cu_tag ->get_host_data() != atom->tag) cu_tag ->set_host_data(atom->tag);
- if(cu_type->get_host_data() != atom->type) cu_type->set_host_data(atom->type);
- if(cu_mask->get_host_data() != atom->mask) cu_mask->set_host_data(atom->mask);
- if(cu_image->get_host_data() != atom->image) cu_mask->set_host_data(atom->image);
-
- if(cu_xhold)
- if(cu_xhold->get_host_data()!= neighbor->xhold) cu_xhold->set_host_data((double*)(neighbor->xhold));
-
- if(atom->rmass)
- if(cu_rmass->get_host_data() != atom->rmass) cu_rmass->set_host_data((double*) (atom->rmass));
-
- if(cu_atom->q_flag)
- if(cu_q->get_host_data() != atom->q) cu_q->set_host_data((double*) (atom->q));
-
- if(atom->radius)
- if(cu_radius->get_host_data() != atom->radius) cu_radius->set_host_data((double*) (atom->radius));
-
- if(atom->omega)
- if(cu_omega->get_host_data() != atom->omega) cu_omega->set_host_data((double*) (atom->omega));
-
- if(atom->torque)
- if(cu_torque->get_host_data() != atom->torque) cu_torque->set_host_data((double*) (atom->torque));
-
- if(atom->special)
- if(cu_special->get_host_data() != atom->special)
- {delete cu_special; cu_special = new cCudaData<int, int, yx > (((int*) atom->special) , & cu_atom->special , atom->nmax,atom->maxspecial ); shared_data.atom.maxspecial=atom->maxspecial;}
-
- if(atom->nspecial)
- if(cu_nspecial->get_host_data() != atom->nspecial) cu_nspecial->set_host_data((int*) (atom->nspecial));
-
- if(atom->molecule)
- if(cu_molecule->get_host_data() != atom->molecule) cu_molecule->set_host_data((int*) (atom->molecule));
-
- if(force)
- if(cu_virial ->get_host_data() != force->pair->virial) cu_virial ->set_host_data(force->pair->virial);
- if(force)
- if(cu_eng_vdwl ->get_host_data() != &force->pair->eng_vdwl) cu_eng_vdwl ->set_host_data(&force->pair->eng_vdwl);
- if(force)
- if(cu_eng_coul ->get_host_data() != &force->pair->eng_coul) cu_eng_coul ->set_host_data(&force->pair->eng_coul);
-
- cu_atom->update_nlocal = 2;
- MYDBG(printf("# CUDA: Cuda::checkResize done...\n");)
+ }
+ }
+
+
+ // if any of the host pointers have changed (e.g. re-allocated somewhere else), set to correct pointer
+ if(cu_x ->get_host_data() != atom->x) cu_x ->set_host_data((double*) (atom->x));
+ if(cu_v ->get_host_data() != atom->v) cu_v ->set_host_data((double*) (atom->v));
+ if(cu_f ->get_host_data() != atom->f) cu_f ->set_host_data((double*) (atom->f));
+ if(cu_tag ->get_host_data() != atom->tag) cu_tag ->set_host_data(atom->tag);
+ if(cu_type->get_host_data() != atom->type) cu_type->set_host_data(atom->type);
+ if(cu_mask->get_host_data() != atom->mask) cu_mask->set_host_data(atom->mask);
+ if(cu_image->get_host_data() != atom->image) cu_mask->set_host_data(atom->image);
+
+ if(cu_xhold)
+ if(cu_xhold->get_host_data()!= neighbor->xhold) cu_xhold->set_host_data((double*)(neighbor->xhold));
+
+ if(atom->rmass)
+ if(cu_rmass->get_host_data() != atom->rmass) cu_rmass->set_host_data((double*) (atom->rmass));
+
+ if(cu_atom->q_flag)
+ if(cu_q->get_host_data() != atom->q) cu_q->set_host_data((double*) (atom->q));
+
+ if(atom->radius)
+ if(cu_radius->get_host_data() != atom->radius) cu_radius->set_host_data((double*) (atom->radius));
+
+ if(atom->omega)
+ if(cu_omega->get_host_data() != atom->omega) cu_omega->set_host_data((double*) (atom->omega));
+
+ if(atom->torque)
+ if(cu_torque->get_host_data() != atom->torque) cu_torque->set_host_data((double*) (atom->torque));
+
+ if(atom->special)
+ if(cu_special->get_host_data() != atom->special)
+ {delete cu_special; cu_special = new cCudaData<int, int, yx > (((int*) atom->special) , & cu_atom->special , atom->nmax,atom->maxspecial ); shared_data.atom.maxspecial=atom->maxspecial;}
+
+ if(atom->nspecial)
+ if(cu_nspecial->get_host_data() != atom->nspecial) cu_nspecial->set_host_data((int*) (atom->nspecial));
+
+ if(atom->molecule)
+ if(cu_molecule->get_host_data() != atom->molecule) cu_molecule->set_host_data((int*) (atom->molecule));
+
+ if(force)
+ if(cu_virial ->get_host_data() != force->pair->virial) cu_virial ->set_host_data(force->pair->virial);
+ if(force)
+ if(cu_eng_vdwl ->get_host_data() != &force->pair->eng_vdwl) cu_eng_vdwl ->set_host_data(&force->pair->eng_vdwl);
+ if(force)
+ if(cu_eng_coul ->get_host_data() != &force->pair->eng_coul) cu_eng_coul ->set_host_data(&force->pair->eng_coul);
+
+ cu_atom->update_nlocal = 2;
+ MYDBG(printf("# CUDA: Cuda::checkResize done...\n");)
}
void Cuda::evsetup_eatom_vatom(int eflag_atom,int vflag_atom)
{
if(eflag_atom)
{
- if(not cu_eatom)
- cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > (force->pair->eatom, & (shared_data.atom.eatom) , atom->nmax );// cu_eatom->set_buffer(&(copy_buffer),&(copy_buffersize),true);}
- if(cu_eatom->get_dim()[0]!=atom->nmax)
- {
- //delete cu_eatom;
+ if(not cu_eatom)
+ cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > (force->pair->eatom, & (shared_data.atom.eatom) , atom->nmax );// cu_eatom->set_buffer(&(copy_buffer),&(copy_buffersize),true);}
+ if(cu_eatom->get_dim()[0]!=atom->nmax)
+ {
+ //delete cu_eatom;
//cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > (force->pair->eatom, & (shared_data.atom.eatom) , atom->nmax );// cu_eatom->set_buffer(&(copy_buffer),&(copy_buffersize),true);}
- shared_data.atom.update_nmax=2;
- }
+ shared_data.atom.update_nmax=2;
+ }
- cu_eatom->set_host_data(force->pair->eatom);
- cu_eatom->memset_device(0);
+ cu_eatom->set_host_data(force->pair->eatom);
+ cu_eatom->memset_device(0);
}
if(vflag_atom)
- {
- if(not cu_vatom)
- cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)force->pair->vatom, & (shared_data.atom.vatom) , atom->nmax ,6 );// cu_vatom->set_buffer(&(copy_buffer),&(copy_buffersize),true);}
+ {
+ if(not cu_vatom)
+ cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)force->pair->vatom, & (shared_data.atom.vatom) , atom->nmax ,6 );// cu_vatom->set_buffer(&(copy_buffer),&(copy_buffersize),true);}
if(cu_vatom->get_dim()[0]!=atom->nmax)
{
//delete cu_vatom;
//cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)force->pair->vatom, & (shared_data.atom.vatom) , atom->nmax ,6 );// cu_vatom->set_buffer(&(copy_buffer),&(copy_buffersize),true);}
shared_data.atom.update_nmax=2;
}
- cu_vatom->set_host_data((double*)force->pair->vatom);
- cu_vatom->memset_device(0);
+ cu_vatom->set_host_data((double*)force->pair->vatom);
+ cu_vatom->memset_device(0);
}
}
void Cuda::uploadAll()
{
- MYDBG(printf("# CUDA: Cuda::uploadAll() ... start\n");)
- timespec starttime;
- timespec endtime;
-
- if(atom->nmax!=shared_data.atom.nmax) checkResize();
- clock_gettime(CLOCK_REALTIME,&starttime);
- cu_x ->upload();
- cu_v ->upload();
- cu_f ->upload();
- cu_tag ->upload();
- cu_type->upload();
- cu_mask->upload();
- cu_image->upload();
- if(shared_data.atom.q_flag) cu_q ->upload();
-
- if(atom->rmass) cu_rmass->upload();
-
- if(atom->radius) cu_radius->upload();
- if(atom->omega) cu_omega->upload();
- if(atom->torque) cu_torque->upload();
- if(atom->special) cu_special->upload();
- if(atom->nspecial) cu_nspecial->upload();
- if(atom->molecule) cu_molecule->upload();
- if(cu_eatom) cu_eatom->upload();
- if(cu_vatom) cu_vatom->upload();
-
- clock_gettime(CLOCK_REALTIME,&endtime);
- uploadtime+=(endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000);
- CUDA_IF_BINNING(Cuda_PreBinning(& shared_data);)
- CUDA_IF_BINNING(Cuda_Binning (& shared_data);)
-
- shared_data.atom.triggerneighsq=neighbor->triggersq;
- MYDBG(printf("# CUDA: Cuda::uploadAll() ... end\n");)
+ MYDBG(printf("# CUDA: Cuda::uploadAll() ... start\n");)
+ timespec starttime;
+ timespec endtime;
+
+ if(atom->nmax!=shared_data.atom.nmax) checkResize();
+ clock_gettime(CLOCK_REALTIME,&starttime);
+ cu_x ->upload();
+ cu_v ->upload();
+ cu_f ->upload();
+ cu_tag ->upload();
+ cu_type->upload();
+ cu_mask->upload();
+ cu_image->upload();
+ if(shared_data.atom.q_flag) cu_q ->upload();
+
+ if(atom->rmass) cu_rmass->upload();
+
+ if(atom->radius) cu_radius->upload();
+ if(atom->omega) cu_omega->upload();
+ if(atom->torque) cu_torque->upload();
+ if(atom->special) cu_special->upload();
+ if(atom->nspecial) cu_nspecial->upload();
+ if(atom->molecule) cu_molecule->upload();
+ if(cu_eatom) cu_eatom->upload();
+ if(cu_vatom) cu_vatom->upload();
+
+ clock_gettime(CLOCK_REALTIME,&endtime);
+ uploadtime+=(endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000);
+ CUDA_IF_BINNING(Cuda_PreBinning(& shared_data);)
+ CUDA_IF_BINNING(Cuda_Binning (& shared_data);)
+
+ shared_data.atom.triggerneighsq=neighbor->triggersq;
+ MYDBG(printf("# CUDA: Cuda::uploadAll() ... end\n");)
}
void Cuda::downloadAll()
{
- MYDBG(printf("# CUDA: Cuda::downloadAll() ... start\n");)
- timespec starttime;
- timespec endtime;
-
- if(atom->nmax!=shared_data.atom.nmax) checkResize();
-
- CUDA_IF_BINNING( Cuda_ReverseBinning(& shared_data); )
- clock_gettime(CLOCK_REALTIME,&starttime);
- cu_x ->download();
- cu_v ->download();
- cu_f ->download();
- cu_type->download();
- cu_tag ->download();
- cu_mask->download();
- cu_image->download();
-
- //if(shared_data.atom.need_eatom) cu_eatom->download();
- //if(shared_data.atom.need_vatom) cu_vatom->download();
-
- if(shared_data.atom.q_flag) cu_q ->download();
- if(atom->rmass) cu_rmass->download();
-
- if(atom->radius) cu_radius->download();
- if(atom->omega) cu_omega->download();
- if(atom->torque) cu_torque->download();
- if(atom->special) cu_special->download();
- if(atom->nspecial) cu_nspecial->download();
- if(atom->molecule) cu_molecule->download();
- if(cu_eatom) cu_eatom->download();
- if(cu_vatom) cu_vatom->download();
-
- clock_gettime(CLOCK_REALTIME,&endtime);
- downloadtime+=(endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000);
- MYDBG(printf("# CUDA: Cuda::downloadAll() ... end\n");)
+ MYDBG(printf("# CUDA: Cuda::downloadAll() ... start\n");)
+ timespec starttime;
+ timespec endtime;
+
+ if(atom->nmax!=shared_data.atom.nmax) checkResize();
+
+ CUDA_IF_BINNING( Cuda_ReverseBinning(& shared_data); )
+ clock_gettime(CLOCK_REALTIME,&starttime);
+ cu_x ->download();
+ cu_v ->download();
+ cu_f ->download();
+ cu_type->download();
+ cu_tag ->download();
+ cu_mask->download();
+ cu_image->download();
+
+ //if(shared_data.atom.need_eatom) cu_eatom->download();
+ //if(shared_data.atom.need_vatom) cu_vatom->download();
+
+ if(shared_data.atom.q_flag) cu_q ->download();
+ if(atom->rmass) cu_rmass->download();
+
+ if(atom->radius) cu_radius->download();
+ if(atom->omega) cu_omega->download();
+ if(atom->torque) cu_torque->download();
+ if(atom->special) cu_special->download();
+ if(atom->nspecial) cu_nspecial->download();
+ if(atom->molecule) cu_molecule->download();
+ if(cu_eatom) cu_eatom->download();
+ if(cu_vatom) cu_vatom->download();
+
+ clock_gettime(CLOCK_REALTIME,&endtime);
+ downloadtime+=(endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000);
+ MYDBG(printf("# CUDA: Cuda::downloadAll() ... end\n");)
}
void Cuda::downloadX()
{
- Cuda_Pair_RevertXType(& this->shared_data);
- cu_x->download();
+ Cuda_Pair_RevertXType(& this->shared_data);
+ cu_x->download();
}
CudaNeighList* Cuda::registerNeighborList(class NeighList* neigh_list)
{
- MYDBG(printf("# CUDA: Cuda::registerNeighborList() ... start a\n");)
- std::map<NeighList*, CudaNeighList*>::iterator p = neigh_lists.find(neigh_list);
-
- if(p != neigh_lists.end()) return p->second;
- else
- {
- CudaNeighList* neigh_list_cuda = new CudaNeighList(lmp, neigh_list);
- neigh_lists.insert(std::pair<NeighList*, CudaNeighList*>(neigh_list, neigh_list_cuda));
- return neigh_list_cuda;
- }
- MYDBG(printf("# CUDA: Cuda::registerNeighborList() ... end b\n");)
+ MYDBG(printf("# CUDA: Cuda::registerNeighborList() ... start a\n");)
+ std::map<NeighList*, CudaNeighList*>::iterator p = neigh_lists.find(neigh_list);
+
+ if(p != neigh_lists.end()) return p->second;
+ else
+ {
+ CudaNeighList* neigh_list_cuda = new CudaNeighList(lmp, neigh_list);
+ neigh_lists.insert(std::pair<NeighList*, CudaNeighList*>(neigh_list, neigh_list_cuda));
+ return neigh_list_cuda;
+ }
+ MYDBG(printf("# CUDA: Cuda::registerNeighborList() ... end b\n");)
}
void Cuda::uploadAllNeighborLists()
{
- MYDBG(printf("# CUDA: Cuda::uploadAllNeighborList() ... start\n");)
- std::map<NeighList*, CudaNeighList*>::iterator p = neigh_lists.begin();
- while(p != neigh_lists.end())
- {
- p->second->nl_upload();
- if(not (p->second->neigh_list->cuda_list->build_cuda))
- for(int i=0;i<atom->nlocal;i++)
- p->second->sneighlist.maxneighbors=MAX(p->second->neigh_list->numneigh[i],p->second->sneighlist.maxneighbors) ;
- ++p;
- }
- MYDBG(printf("# CUDA: Cuda::uploadAllNeighborList() ... done\n");)
+ MYDBG(printf("# CUDA: Cuda::uploadAllNeighborList() ... start\n");)
+ std::map<NeighList*, CudaNeighList*>::iterator p = neigh_lists.begin();
+ while(p != neigh_lists.end())
+ {
+ p->second->nl_upload();
+ if(not (p->second->neigh_list->cuda_list->build_cuda))
+ for(int i=0;i<atom->nlocal;i++)
+ p->second->sneighlist.maxneighbors=MAX(p->second->neigh_list->numneigh[i],p->second->sneighlist.maxneighbors) ;
+ ++p;
+ }
+ MYDBG(printf("# CUDA: Cuda::uploadAllNeighborList() ... done\n");)
}
void Cuda::downloadAllNeighborLists()
{
- MYDBG(printf("# CUDA: Cuda::downloadAllNeighborList() ... start\n");)
- std::map<NeighList*, CudaNeighList*>::iterator p = neigh_lists.begin();
- while(p != neigh_lists.end())
- {
- p->second->nl_download();
- ++p;
- }
+ MYDBG(printf("# CUDA: Cuda::downloadAllNeighborList() ... start\n");)
+ std::map<NeighList*, CudaNeighList*>::iterator p = neigh_lists.begin();
+ while(p != neigh_lists.end())
+ {
+ p->second->nl_download();
+ ++p;
+ }
}
void Cuda::update_xhold(int &maxhold,double* xhold)
@@ -697,142 +697,142 @@ void Cuda::update_xhold(int &maxhold,double* xhold)
if(this->shared_data.atom.maxhold<atom->nmax)
{
maxhold = atom->nmax;
- delete this->cu_xhold; this->cu_xhold = new cCudaData<double, X_FLOAT, yx> ((double*)xhold, & this->shared_data.atom.xhold , maxhold, 3);
+ delete this->cu_xhold; this->cu_xhold = new cCudaData<double, X_FLOAT, yx> ((double*)xhold, & this->shared_data.atom.xhold , maxhold, 3);
}
this->shared_data.atom.maxhold=maxhold;
- CudaWrapper_CopyData(this->cu_xhold->dev_data(),this->cu_x->dev_data(),3*atom->nmax*sizeof(X_FLOAT));
+ CudaWrapper_CopyData(this->cu_xhold->dev_data(),this->cu_x->dev_data(),3*atom->nmax*sizeof(X_FLOAT));
}
void Cuda::setTimingsZero()
{
- shared_data.cuda_timings.test1=0;
- shared_data.cuda_timings.test2=0;
-
- //communication
- shared_data.cuda_timings.comm_forward_total = 0;
- shared_data.cuda_timings.comm_forward_mpi_upper = 0;
- shared_data.cuda_timings.comm_forward_mpi_lower = 0;
- shared_data.cuda_timings.comm_forward_kernel_pack = 0;
- shared_data.cuda_timings.comm_forward_kernel_unpack = 0;
- shared_data.cuda_timings.comm_forward_upload = 0;
- shared_data.cuda_timings.comm_forward_download = 0;
-
- shared_data.cuda_timings.comm_exchange_total = 0;
- shared_data.cuda_timings.comm_exchange_mpi = 0;
- shared_data.cuda_timings.comm_exchange_kernel_pack = 0;
- shared_data.cuda_timings.comm_exchange_kernel_unpack = 0;
- shared_data.cuda_timings.comm_exchange_kernel_fill = 0;
- shared_data.cuda_timings.comm_exchange_cpu_pack= 0;
- shared_data.cuda_timings.comm_exchange_upload = 0;
- shared_data.cuda_timings.comm_exchange_download = 0;
-
- shared_data.cuda_timings.comm_border_total = 0;
- shared_data.cuda_timings.comm_border_mpi = 0;
- shared_data.cuda_timings.comm_border_kernel_pack = 0;
- shared_data.cuda_timings.comm_border_kernel_unpack = 0;
- shared_data.cuda_timings.comm_border_kernel_buildlist = 0;
- shared_data.cuda_timings.comm_border_kernel_self = 0;
- shared_data.cuda_timings.comm_border_upload = 0;
- shared_data.cuda_timings.comm_border_download = 0;
-
- //pair forces
- shared_data.cuda_timings.pair_xtype_conversion = 0;
- shared_data.cuda_timings.pair_kernel = 0;
- shared_data.cuda_timings.pair_virial = 0;
- shared_data.cuda_timings.pair_force_collection = 0;
-
- //neighbor
- shared_data.cuda_timings.neigh_bin = 0;
- shared_data.cuda_timings.neigh_build = 0;
- shared_data.cuda_timings.neigh_special = 0;
-
- //PPPM
- shared_data.cuda_timings.pppm_particle_map = 0;
+ shared_data.cuda_timings.test1=0;
+ shared_data.cuda_timings.test2=0;
+
+ //communication
+ shared_data.cuda_timings.comm_forward_total = 0;
+ shared_data.cuda_timings.comm_forward_mpi_upper = 0;
+ shared_data.cuda_timings.comm_forward_mpi_lower = 0;
+ shared_data.cuda_timings.comm_forward_kernel_pack = 0;
+ shared_data.cuda_timings.comm_forward_kernel_unpack = 0;
+ shared_data.cuda_timings.comm_forward_upload = 0;
+ shared_data.cuda_timings.comm_forward_download = 0;
+
+ shared_data.cuda_timings.comm_exchange_total = 0;
+ shared_data.cuda_timings.comm_exchange_mpi = 0;
+ shared_data.cuda_timings.comm_exchange_kernel_pack = 0;
+ shared_data.cuda_timings.comm_exchange_kernel_unpack = 0;
+ shared_data.cuda_timings.comm_exchange_kernel_fill = 0;
+ shared_data.cuda_timings.comm_exchange_cpu_pack= 0;
+ shared_data.cuda_timings.comm_exchange_upload = 0;
+ shared_data.cuda_timings.comm_exchange_download = 0;
+
+ shared_data.cuda_timings.comm_border_total = 0;
+ shared_data.cuda_timings.comm_border_mpi = 0;
+ shared_data.cuda_timings.comm_border_kernel_pack = 0;
+ shared_data.cuda_timings.comm_border_kernel_unpack = 0;
+ shared_data.cuda_timings.comm_border_kernel_buildlist = 0;
+ shared_data.cuda_timings.comm_border_kernel_self = 0;
+ shared_data.cuda_timings.comm_border_upload = 0;
+ shared_data.cuda_timings.comm_border_download = 0;
+
+ //pair forces
+ shared_data.cuda_timings.pair_xtype_conversion = 0;
+ shared_data.cuda_timings.pair_kernel = 0;
+ shared_data.cuda_timings.pair_virial = 0;
+ shared_data.cuda_timings.pair_force_collection = 0;
+
+ //neighbor
+ shared_data.cuda_timings.neigh_bin = 0;
+ shared_data.cuda_timings.neigh_build = 0;
+ shared_data.cuda_timings.neigh_special = 0;
+
+ //PPPM
+ shared_data.cuda_timings.pppm_particle_map = 0;
shared_data.cuda_timings.pppm_make_rho = 0;
shared_data.cuda_timings.pppm_brick2fft = 0;
shared_data.cuda_timings.pppm_poisson = 0;
shared_data.cuda_timings.pppm_fillbrick = 0;
shared_data.cuda_timings.pppm_fieldforce = 0;
shared_data.cuda_timings.pppm_compute = 0;
-
- CudaWrapper_CheckUploadTime(true);
- CudaWrapper_CheckDownloadTime(true);
- CudaWrapper_CheckCPUBufUploadTime(true);
- CudaWrapper_CheckCPUBufDownloadTime(true);
+
+ CudaWrapper_CheckUploadTime(true);
+ CudaWrapper_CheckDownloadTime(true);
+ CudaWrapper_CheckCPUBufUploadTime(true);
+ CudaWrapper_CheckCPUBufDownloadTime(true);
}
void Cuda::print_timings()
{
- if(universe->me!=0) return;
- if(not dotiming) return;
- printf("\n # CUDA: Special timings\n\n");
- printf("\n Transfer Times\n");
- printf(" PCIe Upload: \t %lf s\n",CudaWrapper_CheckUploadTime());
- printf(" PCIe Download:\t %lf s\n",CudaWrapper_CheckDownloadTime());
- printf(" CPU Tempbbuf Upload: \t %lf \n",CudaWrapper_CheckCPUBufUploadTime());
- printf(" CPU Tempbbuf Download: \t %lf \n",CudaWrapper_CheckCPUBufDownloadTime());
-
- printf("\n Communication \n");
-
- printf(" Forward Total \t %lf \n",shared_data.cuda_timings.comm_forward_total);
- printf(" Forward MPI Upper Bound \t %lf \n",shared_data.cuda_timings.comm_forward_mpi_upper);
- printf(" Forward MPI Lower Bound \t %lf \n",shared_data.cuda_timings.comm_forward_mpi_lower);
- printf(" Forward Kernel Pack \t %lf \n",shared_data.cuda_timings.comm_forward_kernel_pack);
- printf(" Forward Kernel Unpack \t %lf \n",shared_data.cuda_timings.comm_forward_kernel_unpack);
- printf(" Forward Kernel Self \t %lf \n",shared_data.cuda_timings.comm_forward_kernel_self);
- printf(" Forward Upload \t %lf \n",shared_data.cuda_timings.comm_forward_upload);
- printf(" Forward Download \t %lf \n",shared_data.cuda_timings.comm_forward_download);
- printf(" Forward Overlap Split Ratio\t %lf \n",shared_data.comm.overlap_split_ratio);
- printf("\n");
-
- printf(" Exchange Total \t %lf \n",shared_data.cuda_timings.comm_exchange_total);
- printf(" Exchange MPI \t %lf \n",shared_data.cuda_timings.comm_exchange_mpi);
- printf(" Exchange Kernel Pack \t %lf \n",shared_data.cuda_timings.comm_exchange_kernel_pack);
- printf(" Exchange Kernel Unpack \t %lf \n",shared_data.cuda_timings.comm_exchange_kernel_unpack);
+ if(universe->me!=0) return;
+ if(not dotiming) return;
+ printf("\n # CUDA: Special timings\n\n");
+ printf("\n Transfer Times\n");
+ printf(" PCIe Upload: \t %lf s\n",CudaWrapper_CheckUploadTime());
+ printf(" PCIe Download:\t %lf s\n",CudaWrapper_CheckDownloadTime());
+ printf(" CPU Tempbbuf Upload: \t %lf \n",CudaWrapper_CheckCPUBufUploadTime());
+ printf(" CPU Tempbbuf Download: \t %lf \n",CudaWrapper_CheckCPUBufDownloadTime());
+
+ printf("\n Communication \n");
+
+ printf(" Forward Total \t %lf \n",shared_data.cuda_timings.comm_forward_total);
+ printf(" Forward MPI Upper Bound \t %lf \n",shared_data.cuda_timings.comm_forward_mpi_upper);
+ printf(" Forward MPI Lower Bound \t %lf \n",shared_data.cuda_timings.comm_forward_mpi_lower);
+ printf(" Forward Kernel Pack \t %lf \n",shared_data.cuda_timings.comm_forward_kernel_pack);
+ printf(" Forward Kernel Unpack \t %lf \n",shared_data.cuda_timings.comm_forward_kernel_unpack);
+ printf(" Forward Kernel Self \t %lf \n",shared_data.cuda_timings.comm_forward_kernel_self);
+ printf(" Forward Upload \t %lf \n",shared_data.cuda_timings.comm_forward_upload);
+ printf(" Forward Download \t %lf \n",shared_data.cuda_timings.comm_forward_download);
+ printf(" Forward Overlap Split Ratio\t %lf \n",shared_data.comm.overlap_split_ratio);
+ printf("\n");
+
+ printf(" Exchange Total \t %lf \n",shared_data.cuda_timings.comm_exchange_total);
+ printf(" Exchange MPI \t %lf \n",shared_data.cuda_timings.comm_exchange_mpi);
+ printf(" Exchange Kernel Pack \t %lf \n",shared_data.cuda_timings.comm_exchange_kernel_pack);
+ printf(" Exchange Kernel Unpack \t %lf \n",shared_data.cuda_timings.comm_exchange_kernel_unpack);
printf(" Exchange Kernel Fill \t %lf \n",shared_data.cuda_timings.comm_exchange_kernel_fill);
- printf(" Exchange CPU Pack \t %lf \n",shared_data.cuda_timings.comm_exchange_cpu_pack);
- printf(" Exchange Upload \t %lf \n",shared_data.cuda_timings.comm_exchange_upload);
- printf(" Exchange Download \t %lf \n",shared_data.cuda_timings.comm_exchange_download);
- printf("\n");
-
- printf(" Border Total \t %lf \n",shared_data.cuda_timings.comm_border_total);
- printf(" Border MPI \t %lf \n",shared_data.cuda_timings.comm_border_mpi);
- printf(" Border Kernel Pack \t %lf \n",shared_data.cuda_timings.comm_border_kernel_pack);
- printf(" Border Kernel Unpack \t %lf \n",shared_data.cuda_timings.comm_border_kernel_unpack);
- printf(" Border Kernel Self \t %lf \n",shared_data.cuda_timings.comm_border_kernel_self);
- printf(" Border Kernel BuildList \t %lf \n",shared_data.cuda_timings.comm_border_kernel_buildlist);
- printf(" Border Upload \t %lf \n",shared_data.cuda_timings.comm_border_upload);
- printf(" Border Download \t %lf \n",shared_data.cuda_timings.comm_border_download);
- printf("\n");
-
- //pair forces
- printf(" Pair XType Conversion \t %lf \n",shared_data.cuda_timings.pair_xtype_conversion );
- printf(" Pair Kernel \t %lf \n",shared_data.cuda_timings.pair_kernel );
- printf(" Pair Virial \t %lf \n",shared_data.cuda_timings.pair_virial );
- printf(" Pair Force Collection \t %lf \n",shared_data.cuda_timings.pair_force_collection );
- printf("\n");
-
- //neighbor
- printf(" Neighbor Binning \t %lf \n",shared_data.cuda_timings.neigh_bin );
- printf(" Neighbor Build \t %lf \n",shared_data.cuda_timings.neigh_build );
- printf(" Neighbor Special \t %lf \n",shared_data.cuda_timings.neigh_special );
- printf("\n");
-
- //pppm
- if(force->kspace)
- {
- printf(" PPPM Total \t %lf \n",shared_data.cuda_timings.pppm_compute );
- printf(" PPPM Particle Map \t %lf \n",shared_data.cuda_timings.pppm_particle_map );
- printf(" PPPM Make Rho \t %lf \n",shared_data.cuda_timings.pppm_make_rho );
- printf(" PPPM Brick2fft \t %lf \n",shared_data.cuda_timings.pppm_brick2fft );
- printf(" PPPM Poisson \t %lf \n",shared_data.cuda_timings.pppm_poisson );
- printf(" PPPM Fillbrick \t %lf \n",shared_data.cuda_timings.pppm_fillbrick );
- printf(" PPPM Fieldforce \t %lf \n",shared_data.cuda_timings.pppm_fieldforce );
- printf("\n");
- }
-
- printf(" Debug Test 1 \t %lf \n",shared_data.cuda_timings.test1);
- printf(" Debug Test 2 \t %lf \n",shared_data.cuda_timings.test2);
-
- printf("\n");
+ printf(" Exchange CPU Pack \t %lf \n",shared_data.cuda_timings.comm_exchange_cpu_pack);
+ printf(" Exchange Upload \t %lf \n",shared_data.cuda_timings.comm_exchange_upload);
+ printf(" Exchange Download \t %lf \n",shared_data.cuda_timings.comm_exchange_download);
+ printf("\n");
+
+ printf(" Border Total \t %lf \n",shared_data.cuda_timings.comm_border_total);
+ printf(" Border MPI \t %lf \n",shared_data.cuda_timings.comm_border_mpi);
+ printf(" Border Kernel Pack \t %lf \n",shared_data.cuda_timings.comm_border_kernel_pack);
+ printf(" Border Kernel Unpack \t %lf \n",shared_data.cuda_timings.comm_border_kernel_unpack);
+ printf(" Border Kernel Self \t %lf \n",shared_data.cuda_timings.comm_border_kernel_self);
+ printf(" Border Kernel BuildList \t %lf \n",shared_data.cuda_timings.comm_border_kernel_buildlist);
+ printf(" Border Upload \t %lf \n",shared_data.cuda_timings.comm_border_upload);
+ printf(" Border Download \t %lf \n",shared_data.cuda_timings.comm_border_download);
+ printf("\n");
+
+ //pair forces
+ printf(" Pair XType Conversion \t %lf \n",shared_data.cuda_timings.pair_xtype_conversion );
+ printf(" Pair Kernel \t %lf \n",shared_data.cuda_timings.pair_kernel );
+ printf(" Pair Virial \t %lf \n",shared_data.cuda_timings.pair_virial );
+ printf(" Pair Force Collection \t %lf \n",shared_data.cuda_timings.pair_force_collection );
+ printf("\n");
+
+ //neighbor
+ printf(" Neighbor Binning \t %lf \n",shared_data.cuda_timings.neigh_bin );
+ printf(" Neighbor Build \t %lf \n",shared_data.cuda_timings.neigh_build );
+ printf(" Neighbor Special \t %lf \n",shared_data.cuda_timings.neigh_special );
+ printf("\n");
+
+ //pppm
+ if(force->kspace)
+ {
+ printf(" PPPM Total \t %lf \n",shared_data.cuda_timings.pppm_compute );
+ printf(" PPPM Particle Map \t %lf \n",shared_data.cuda_timings.pppm_particle_map );
+ printf(" PPPM Make Rho \t %lf \n",shared_data.cuda_timings.pppm_make_rho );
+ printf(" PPPM Brick2fft \t %lf \n",shared_data.cuda_timings.pppm_brick2fft );
+ printf(" PPPM Poisson \t %lf \n",shared_data.cuda_timings.pppm_poisson );
+ printf(" PPPM Fillbrick \t %lf \n",shared_data.cuda_timings.pppm_fillbrick );
+ printf(" PPPM Fieldforce \t %lf \n",shared_data.cuda_timings.pppm_fieldforce );
+ printf("\n");
+ }
+
+ printf(" Debug Test 1 \t %lf \n",shared_data.cuda_timings.test1);
+ printf(" Debug Test 2 \t %lf \n",shared_data.cuda_timings.test2);
+
+ printf("\n");
}
diff --git a/src/USER-CUDA/cuda.h b/src/USER-CUDA/cuda.h
index 21d47610fb558315783282b686ccbf5fc7978d68..2494796da2d743d91669ad2f46815b946a27a7ef 100644
--- a/src/USER-CUDA/cuda.h
+++ b/src/USER-CUDA/cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -33,121 +33,121 @@
#ifdef _DEBUG
#define MYDBG(a) a
#else
-#define MYDBG(a)
+#define MYDBG(a)
#endif
namespace LAMMPS_NS
{
- class Cuda : protected Pointers
- {
- public:
- Cuda(class LAMMPS *);
- ~Cuda();
- //static void setDevice(class LAMMPS*);
- void allocate();
-
- void accelerator(int, char **);
-
- void setSharedDataZero();
- void setSystemParams();
-
- void setDomainParams();
-
- void checkResize();
- void evsetup_eatom_vatom(int eflag_atom,int vflag_atom);
- void uploadAll();
- void downloadAll();
- void downloadX();
-
- class CudaNeighList* registerNeighborList(class NeighList* neigh_list);
- void uploadAllNeighborLists();
- void downloadAllNeighborLists();
- void set_neighinit(int dist_check, double triggerneighsq)
- {
- shared_data.atom.dist_check=dist_check;
- shared_data.atom.triggerneighsq = triggerneighsq;
- }
- bool decide_by_integrator()
- {
- return neighbor_decide_by_integrator && cu_xhold && finished_setup;
- }
- void update_xhold(int &maxhold,double* xhold);
-
- void setTimingsZero();
- void print_timings();
-
- void cu_x_download() {cu_x->download();}
- bool device_set;
- bool dotiming;
- bool dotestatom;
- int testatom;
-
- double uploadtime,downloadtime;
- bool finished_setup,begin_setup;
- bool oncpu;
- bool finished_run;
-
- int self_comm;
-
- int cuda_exists;
-
- double extent[6];
- int* debugdata;
- // data shared between host code and device code
- // (number of atoms, device pointers for up- & download)
- cuda_shared_data shared_data;
-
- cCudaData<double , F_FLOAT , x >* cu_q;
- cCudaData<double , F_FLOAT , yx>* cu_f;
- cCudaData<double , V_FLOAT , x >* cu_mass;
- cCudaData<double , V_FLOAT , x >* cu_rmass;
- cCudaData<double , V_FLOAT , yx>* cu_v;
- cCudaData<double , X_FLOAT , yx>* cu_x;
- cCudaData<double , X_FLOAT , yx>* cu_xhold;
- cCudaData<int , int , x >* cu_mask;
- cCudaData<int , int , x >* cu_tag;
- cCudaData<int , int , x >* cu_type;
- cCudaData<int , int , x >* cu_image;
- cCudaData<double , ENERGY_FLOAT, x >* cu_eatom;
- cCudaData<double , ENERGY_FLOAT, yx>* cu_vatom;
- cCudaData<double , ENERGY_FLOAT, x >* cu_virial;
- cCudaData<double , ENERGY_FLOAT, x >* cu_eng_vdwl;
- cCudaData<double , ENERGY_FLOAT, x >* cu_eng_coul;
- cCudaData<double , double , x >* cu_extent;
- int* binned_id;
- cCudaData<int , int , xx >* cu_binned_id;
- int* binned_idnew;
- cCudaData<int , int , xx >* cu_binned_idnew;
- cCudaData<int , int , x >* cu_debugdata;
- cCudaData<double , X_FLOAT , x>* cu_radius;
- cCudaData<double , F_FLOAT , x>* cu_density;
- cCudaData<double , V_FLOAT , yx>* cu_omega;
- cCudaData<double , F_FLOAT , yx>* cu_torque;
- cCudaData<int , int , yx >* cu_special;
- cCudaData<int , int , yx >* cu_nspecial;
- cCudaData<int , int , x >* cu_molecule;
-
-
- cCudaData<X_FLOAT , X_FLOAT , x>* cu_x_type;
- X_FLOAT* x_type;
-
- cCudaData<V_FLOAT , V_FLOAT , x>* cu_v_radius;
- V_FLOAT* v_radius;
-
- cCudaData<V_FLOAT , V_FLOAT , x>* cu_omega_rmass;
- V_FLOAT* omega_rmass;
-
- cCudaData<int , int , x >* cu_map_array;
- int neighbor_decide_by_integrator;
+ class Cuda : protected Pointers
+ {
+ public:
+ Cuda(class LAMMPS *);
+ ~Cuda();
+ //static void setDevice(class LAMMPS*);
+ void allocate();
+
+ void accelerator(int, char **);
+
+ void setSharedDataZero();
+ void setSystemParams();
+
+ void setDomainParams();
+
+ void checkResize();
+ void evsetup_eatom_vatom(int eflag_atom,int vflag_atom);
+ void uploadAll();
+ void downloadAll();
+ void downloadX();
+
+ class CudaNeighList* registerNeighborList(class NeighList* neigh_list);
+ void uploadAllNeighborLists();
+ void downloadAllNeighborLists();
+ void set_neighinit(int dist_check, double triggerneighsq)
+ {
+ shared_data.atom.dist_check=dist_check;
+ shared_data.atom.triggerneighsq = triggerneighsq;
+ }
+ bool decide_by_integrator()
+ {
+ return neighbor_decide_by_integrator && cu_xhold && finished_setup;
+ }
+ void update_xhold(int &maxhold,double* xhold);
+
+ void setTimingsZero();
+ void print_timings();
+
+ void cu_x_download() {cu_x->download();}
+ bool device_set;
+ bool dotiming;
+ bool dotestatom;
+ int testatom;
+
+ double uploadtime,downloadtime;
+ bool finished_setup,begin_setup;
+ bool oncpu;
+ bool finished_run;
+
+ int self_comm;
+
+ int cuda_exists;
+
+ double extent[6];
+ int* debugdata;
+ // data shared between host code and device code
+ // (number of atoms, device pointers for up- & download)
+ cuda_shared_data shared_data;
+
+ cCudaData<double , F_FLOAT , x >* cu_q;
+ cCudaData<double , F_FLOAT , yx>* cu_f;
+ cCudaData<double , V_FLOAT , x >* cu_mass;
+ cCudaData<double , V_FLOAT , x >* cu_rmass;
+ cCudaData<double , V_FLOAT , yx>* cu_v;
+ cCudaData<double , X_FLOAT , yx>* cu_x;
+ cCudaData<double , X_FLOAT , yx>* cu_xhold;
+ cCudaData<int , int , x >* cu_mask;
+ cCudaData<int , int , x >* cu_tag;
+ cCudaData<int , int , x >* cu_type;
+ cCudaData<int , int , x >* cu_image;
+ cCudaData<double , ENERGY_FLOAT, x >* cu_eatom;
+ cCudaData<double , ENERGY_FLOAT, yx>* cu_vatom;
+ cCudaData<double , ENERGY_FLOAT, x >* cu_virial;
+ cCudaData<double , ENERGY_FLOAT, x >* cu_eng_vdwl;
+ cCudaData<double , ENERGY_FLOAT, x >* cu_eng_coul;
+ cCudaData<double , double , x >* cu_extent;
+ int* binned_id;
+ cCudaData<int , int , xx >* cu_binned_id;
+ int* binned_idnew;
+ cCudaData<int , int , xx >* cu_binned_idnew;
+ cCudaData<int , int , x >* cu_debugdata;
+ cCudaData<double , X_FLOAT , x>* cu_radius;
+ cCudaData<double , F_FLOAT , x>* cu_density;
+ cCudaData<double , V_FLOAT , yx>* cu_omega;
+ cCudaData<double , F_FLOAT , yx>* cu_torque;
+ cCudaData<int , int , yx >* cu_special;
+ cCudaData<int , int , yx >* cu_nspecial;
+ cCudaData<int , int , x >* cu_molecule;
+
+
+ cCudaData<X_FLOAT , X_FLOAT , x>* cu_x_type;
+ X_FLOAT* x_type;
+
+ cCudaData<V_FLOAT , V_FLOAT , x>* cu_v_radius;
+ V_FLOAT* v_radius;
+
+ cCudaData<V_FLOAT , V_FLOAT , x>* cu_omega_rmass;
+ V_FLOAT* omega_rmass;
+
+ cCudaData<int , int , x >* cu_map_array;
+ int neighbor_decide_by_integrator;
bool pinned;
-
- void* copy_buffer;
- int copy_buffersize;
- private:
- std::map<class NeighList*, class CudaNeighList*> neigh_lists;
- };
+ void* copy_buffer;
+ int copy_buffersize;
+
+ private:
+ std::map<class NeighList*, class CudaNeighList*> neigh_lists;
+ };
}
#endif // CUDA_H
diff --git a/src/USER-CUDA/cuda_data.h b/src/USER-CUDA/cuda_data.h
index 6311598332885f7794e8cacbb6ddca23272d822e..ed8a9ff7aa81f082d2d33b11013305f06d48134d 100644
--- a/src/USER-CUDA/cuda_data.h
+++ b/src/USER-CUDA/cuda_data.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -37,46 +37,46 @@ enum copy_mode {x, xx, xy, yx, xyz, xzy}; // yxz, yzx, zxy, zyx not yet implemen
template <typename host_type, typename dev_type, copy_mode mode>
class cCudaData
{
- protected:
- void** buffer;
- int* buf_size;
- host_type* host_data;
- dev_array* dev_data_array;
- dev_type* temp_data;
- unsigned nbytes;
- bool owns_dev_array;
- bool current_data_on_device; //this is not yet working as intended and therefore deactivated
- bool current_data_on_host;
- bool is_continues;
- bool pinned;
-
- public:
- cCudaData(host_type* host_data, dev_array* dev_data_array, unsigned dim_x, unsigned dim_y=0, unsigned dim_z=0, bool is_pinned=false);
- cCudaData(host_type* host_data, unsigned dim_x, unsigned dim_y=0, unsigned dim_z=0, bool is_pinned=false);
- ~cCudaData();
- void* dev_data() {if(dev_data_array!=NULL) return dev_data_array->dev_data; else return NULL;};
- void set_dev_data(void* adev_data) {dev_data_array->dev_data=adev_data;};
- void set_dev_array(dev_array* adev_array) {dev_data_array=adev_array;};
- void set_host_data(host_type* host_data);
- void* get_host_data() { return host_data;};
- void set_buffer(void** buffer,int* buf_size,bool ais_continues);
- unsigned int* get_dim() {return dev_data_array->dim;};
- // if you want to upload data to the gpu, which will not change there, then set will_be_changed=false
- // if you want to upload data to the gpu and update it there, then set will_be_changed=true (default)
- void upload(bool will_be_changed=true);
- void uploadAsync(int stream, bool will_be_changed=true );
- // if you want to download data just to have a look at it, then set will_be_changed=false
- // if you are going to modify the downloaded data, then set will_be_changed=true (default)
- void download(bool will_be_changed=true);
- void downloadAsync(int stream);
- void memset_device(int value);
- void device_data_has_changed() {current_data_on_device=false;}
- void host_data_has_changed() {current_data_on_host=false;}
- int dev_size() {
- int size = dev_data_array->dim[0]*sizeof(dev_type);
- if(dev_data_array->dim[1]) size*=dev_data_array->dim[1];
- if(dev_data_array->dim[2]) size*=dev_data_array->dim[2];
- return size;}
+ protected:
+ void** buffer;
+ int* buf_size;
+ host_type* host_data;
+ dev_array* dev_data_array;
+ dev_type* temp_data;
+ unsigned nbytes;
+ bool owns_dev_array;
+ bool current_data_on_device; //this is not yet working as intended and therefore deactivated
+ bool current_data_on_host;
+ bool is_continues;
+ bool pinned;
+
+ public:
+ cCudaData(host_type* host_data, dev_array* dev_data_array, unsigned dim_x, unsigned dim_y=0, unsigned dim_z=0, bool is_pinned=false);
+ cCudaData(host_type* host_data, unsigned dim_x, unsigned dim_y=0, unsigned dim_z=0, bool is_pinned=false);
+ ~cCudaData();
+ void* dev_data() {if(dev_data_array!=NULL) return dev_data_array->dev_data; else return NULL;};
+ void set_dev_data(void* adev_data) {dev_data_array->dev_data=adev_data;};
+ void set_dev_array(dev_array* adev_array) {dev_data_array=adev_array;};
+ void set_host_data(host_type* host_data);
+ void* get_host_data() { return host_data;};
+ void set_buffer(void** buffer,int* buf_size,bool ais_continues);
+ unsigned int* get_dim() {return dev_data_array->dim;};
+ // if you want to upload data to the gpu, which will not change there, then set will_be_changed=false
+ // if you want to upload data to the gpu and update it there, then set will_be_changed=true (default)
+ void upload(bool will_be_changed=true);
+ void uploadAsync(int stream, bool will_be_changed=true );
+ // if you want to download data just to have a look at it, then set will_be_changed=false
+ // if you are going to modify the downloaded data, then set will_be_changed=true (default)
+ void download(bool will_be_changed=true);
+ void downloadAsync(int stream);
+ void memset_device(int value);
+ void device_data_has_changed() {current_data_on_device=false;}
+ void host_data_has_changed() {current_data_on_host=false;}
+ int dev_size() {
+ int size = dev_data_array->dim[0]*sizeof(dev_type);
+ if(dev_data_array->dim[1]) size*=dev_data_array->dim[1];
+ if(dev_data_array->dim[2]) size*=dev_data_array->dim[2];
+ return size;}
};
@@ -84,685 +84,685 @@ template <typename host_type, typename dev_type, copy_mode mode>
cCudaData<host_type, dev_type, mode>
::cCudaData(host_type* host_data, dev_array* dev_data_array, unsigned dim_x, unsigned dim_y, unsigned dim_z, bool is_pinned)
{
- pinned=is_pinned;
- owns_dev_array = false;
- current_data_on_device = false;
- current_data_on_host = false;
- is_continues = false;
- this->host_data = host_data;
- this->dev_data_array = dev_data_array;
- unsigned ndev;
- if((mode == x)||(mode==xx))
- {
- ndev = dim_x;
- dev_data_array->dim[0] = dim_x;
- dev_data_array->dim[1] = 0;
- dev_data_array->dim[2] = 0;
- }
- else if(mode == xy || mode == yx )
- {
- ndev = dim_x * dim_y;
- dev_data_array->dim[0] = dim_x;
- dev_data_array->dim[1] = dim_y;
- dev_data_array->dim[2] = 0;
- }
- else
- {
- ndev = dim_x * dim_y * dim_z;
- dev_data_array->dim[0] = dim_x;
- dev_data_array->dim[1] = dim_y;
- dev_data_array->dim[2] = dim_z;
- }
- nbytes = ndev * sizeof(dev_type);
- if(nbytes<=0)
- {
- host_data=NULL;
- temp_data=NULL;
- dev_data_array->dev_data=NULL;
- return;
- }
-
- dev_data_array->dev_data = CudaWrapper_AllocCudaData(nbytes);
- if(((mode!=x)&&(mode!=xx)) || typeid(host_type) != typeid(dev_type))
- {
- if(not pinned)
- temp_data = new dev_type[ndev];
- else
- {
- temp_data = (dev_type*) CudaWrapper_AllocPinnedHostData(ndev*sizeof(dev_type));
- }
- }
+ pinned=is_pinned;
+ owns_dev_array = false;
+ current_data_on_device = false;
+ current_data_on_host = false;
+ is_continues = false;
+ this->host_data = host_data;
+ this->dev_data_array = dev_data_array;
+ unsigned ndev;
+ if((mode == x)||(mode==xx))
+ {
+ ndev = dim_x;
+ dev_data_array->dim[0] = dim_x;
+ dev_data_array->dim[1] = 0;
+ dev_data_array->dim[2] = 0;
+ }
+ else if(mode == xy || mode == yx )
+ {
+ ndev = dim_x * dim_y;
+ dev_data_array->dim[0] = dim_x;
+ dev_data_array->dim[1] = dim_y;
+ dev_data_array->dim[2] = 0;
+ }
+ else
+ {
+ ndev = dim_x * dim_y * dim_z;
+ dev_data_array->dim[0] = dim_x;
+ dev_data_array->dim[1] = dim_y;
+ dev_data_array->dim[2] = dim_z;
+ }
+ nbytes = ndev * sizeof(dev_type);
+ if(nbytes<=0)
+ {
+ host_data=NULL;
+ temp_data=NULL;
+ dev_data_array->dev_data=NULL;
+ return;
+ }
+
+ dev_data_array->dev_data = CudaWrapper_AllocCudaData(nbytes);
+ if(((mode!=x)&&(mode!=xx)) || typeid(host_type) != typeid(dev_type))
+ {
+ if(not pinned)
+ temp_data = new dev_type[ndev];
+ else
+ {
+ temp_data = (dev_type*) CudaWrapper_AllocPinnedHostData(ndev*sizeof(dev_type));
+ }
+ }
}
template <typename host_type, typename dev_type, copy_mode mode>
cCudaData<host_type, dev_type, mode>
::cCudaData(host_type* host_data, unsigned dim_x, unsigned dim_y, unsigned dim_z, bool is_pinned)
{
- pinned=is_pinned;
- this->dev_data_array = new dev_array;
- this->owns_dev_array = true;
- current_data_on_device = false;
- current_data_on_host = false;
- is_continues = false;
- this->host_data = host_data;
- unsigned ndev;
- if((mode == x)||(mode==xx))
- {
- ndev = dim_x;
- dev_data_array->dim[0] = dim_x;
- dev_data_array->dim[1] = 0;
- dev_data_array->dim[2] = 0;
- }
- else if(mode == xy || mode == yx )
- {
- ndev = dim_x * dim_y;
- dev_data_array->dim[0] = dim_x;
- dev_data_array->dim[1] = dim_y;
- dev_data_array->dim[2] = 0;
- }
- else
- {
- ndev = dim_x * dim_y * dim_z;
- dev_data_array->dim[0] = dim_x;
- dev_data_array->dim[1] = dim_y;
- dev_data_array->dim[2] = dim_z;
- }
- nbytes = ndev * sizeof(dev_type);
- if(nbytes<=0)
- {
- host_data=NULL;
- temp_data=NULL;
- dev_data_array->dev_data=NULL;
- return;
- }
-
- dev_data_array->dev_data = CudaWrapper_AllocCudaData(nbytes);
- if(((mode!=x)&&(mode!=xx)) || (typeid(host_type) != typeid(dev_type)))
- {
- if(not pinned)
- temp_data = new dev_type[ndev];
- else
- {
- temp_data = (dev_type*) CudaWrapper_AllocPinnedHostData(ndev*sizeof(dev_type));
- }
- }
+ pinned=is_pinned;
+ this->dev_data_array = new dev_array;
+ this->owns_dev_array = true;
+ current_data_on_device = false;
+ current_data_on_host = false;
+ is_continues = false;
+ this->host_data = host_data;
+ unsigned ndev;
+ if((mode == x)||(mode==xx))
+ {
+ ndev = dim_x;
+ dev_data_array->dim[0] = dim_x;
+ dev_data_array->dim[1] = 0;
+ dev_data_array->dim[2] = 0;
+ }
+ else if(mode == xy || mode == yx )
+ {
+ ndev = dim_x * dim_y;
+ dev_data_array->dim[0] = dim_x;
+ dev_data_array->dim[1] = dim_y;
+ dev_data_array->dim[2] = 0;
+ }
+ else
+ {
+ ndev = dim_x * dim_y * dim_z;
+ dev_data_array->dim[0] = dim_x;
+ dev_data_array->dim[1] = dim_y;
+ dev_data_array->dim[2] = dim_z;
+ }
+ nbytes = ndev * sizeof(dev_type);
+ if(nbytes<=0)
+ {
+ host_data=NULL;
+ temp_data=NULL;
+ dev_data_array->dev_data=NULL;
+ return;
+ }
+
+ dev_data_array->dev_data = CudaWrapper_AllocCudaData(nbytes);
+ if(((mode!=x)&&(mode!=xx)) || (typeid(host_type) != typeid(dev_type)))
+ {
+ if(not pinned)
+ temp_data = new dev_type[ndev];
+ else
+ {
+ temp_data = (dev_type*) CudaWrapper_AllocPinnedHostData(ndev*sizeof(dev_type));
+ }
+ }
}
template <typename host_type, typename dev_type, copy_mode mode>
cCudaData<host_type, dev_type, mode>
::~cCudaData()
{
- if(((mode!=x)&&(mode!=xx)) || typeid(host_type) != typeid(dev_type))
- {
- if(not pinned)
- delete [] temp_data;
- else
- {
- CudaWrapper_FreePinnedHostData((void*)temp_data);
- }
- }
- if((dev_data_array->dev_data)&&(nbytes>0))
- CudaWrapper_FreeCudaData(dev_data_array->dev_data,nbytes);
- if(owns_dev_array) delete dev_data_array;
+ if(((mode!=x)&&(mode!=xx)) || typeid(host_type) != typeid(dev_type))
+ {
+ if(not pinned)
+ delete [] temp_data;
+ else
+ {
+ CudaWrapper_FreePinnedHostData((void*)temp_data);
+ }
+ }
+ if((dev_data_array->dev_data)&&(nbytes>0))
+ CudaWrapper_FreeCudaData(dev_data_array->dev_data,nbytes);
+ if(owns_dev_array) delete dev_data_array;
}
template <typename host_type, typename dev_type, copy_mode mode>
void cCudaData<host_type, dev_type, mode>
::set_host_data(host_type* host_data)
{
- this->host_data = host_data;
+ this->host_data = host_data;
}
template <typename host_type, typename dev_type, copy_mode mode>
void cCudaData<host_type, dev_type, mode>
::upload(bool will_be_changed)
{
- // if current data is already up, do not re-upload it
-// if(current_data_on_device) return;
+ // if current data is already up, do not re-upload it
+// if(current_data_on_device) return;
if(buffer&&is_continues)
{
- printf("Actual Buffer: %p %i\n",*buffer,*buf_size);
- if(typeid(host_type)==typeid(double))
- {
- if(typeid(dev_type)==typeid(double))
- {
- CudaData_Upload_DoubleDouble((void*) host_data,dev_data_array->dev_data,
- dev_data_array->dim,mode,*buffer);
- current_data_on_device = true;
- if(will_be_changed) current_data_on_host = false;
- return;
- }
- else if(typeid(dev_type)==typeid(float))
- {
- CudaData_Upload_DoubleFloat((void*) host_data,dev_data_array->dev_data,
- dev_data_array->dim,mode,*buffer);
- current_data_on_device = true;
- if(will_be_changed) current_data_on_host = false;
- return;
- }
- }
- else if(typeid(host_type)==typeid(float))
- {
- if(typeid(dev_type)==typeid(double))
- {
- CudaData_Upload_FloatDouble((void*) host_data,dev_data_array->dev_data,
- dev_data_array->dim,mode,*buffer);
- current_data_on_device = true;
- if(will_be_changed) current_data_on_host = false;
- return;
- }
- else if(typeid(dev_type)==typeid(float))
- {
- CudaData_Upload_FloatFloat((void*) host_data,dev_data_array->dev_data,
- dev_data_array->dim,mode,*buffer);
- current_data_on_device = true;
- if(will_be_changed) current_data_on_host = false;
- return;
- }
- }
- else if(typeid(host_type)==typeid(int))
- {
- if(typeid(dev_type)==typeid(int))
- {
- CudaData_Upload_IntInt((void*) host_data,dev_data_array->dev_data,
- dev_data_array->dim,mode,*buffer);
- current_data_on_device = true;
- if(will_be_changed) current_data_on_host = false;
- return;
- }
- }
+ printf("Actual Buffer: %p %i\n",*buffer,*buf_size);
+ if(typeid(host_type)==typeid(double))
+ {
+ if(typeid(dev_type)==typeid(double))
+ {
+ CudaData_Upload_DoubleDouble((void*) host_data,dev_data_array->dev_data,
+ dev_data_array->dim,mode,*buffer);
+ current_data_on_device = true;
+ if(will_be_changed) current_data_on_host = false;
+ return;
+ }
+ else if(typeid(dev_type)==typeid(float))
+ {
+ CudaData_Upload_DoubleFloat((void*) host_data,dev_data_array->dev_data,
+ dev_data_array->dim,mode,*buffer);
+ current_data_on_device = true;
+ if(will_be_changed) current_data_on_host = false;
+ return;
+ }
+ }
+ else if(typeid(host_type)==typeid(float))
+ {
+ if(typeid(dev_type)==typeid(double))
+ {
+ CudaData_Upload_FloatDouble((void*) host_data,dev_data_array->dev_data,
+ dev_data_array->dim,mode,*buffer);
+ current_data_on_device = true;
+ if(will_be_changed) current_data_on_host = false;
+ return;
+ }
+ else if(typeid(dev_type)==typeid(float))
+ {
+ CudaData_Upload_FloatFloat((void*) host_data,dev_data_array->dev_data,
+ dev_data_array->dim,mode,*buffer);
+ current_data_on_device = true;
+ if(will_be_changed) current_data_on_host = false;
+ return;
+ }
+ }
+ else if(typeid(host_type)==typeid(int))
+ {
+ if(typeid(dev_type)==typeid(int))
+ {
+ CudaData_Upload_IntInt((void*) host_data,dev_data_array->dev_data,
+ dev_data_array->dim,mode,*buffer);
+ current_data_on_device = true;
+ if(will_be_changed) current_data_on_host = false;
+ return;
+ }
+ }
}
- switch(mode)
- {
- case x:
- {
- if(typeid(host_type) == typeid(dev_type))
- CudaWrapper_UploadCudaData(host_data, dev_data_array->dev_data, nbytes);
- else
- {
+ switch(mode)
+ {
+ case x:
+ {
+ if(typeid(host_type) == typeid(dev_type))
+ CudaWrapper_UploadCudaData(host_data, dev_data_array->dev_data, nbytes);
+ else
+ {
timespec time1,time2;
clock_gettime(CLOCK_REALTIME,&time1);
- for(unsigned i=0; i<dev_data_array->dim[0]; ++i) temp_data[i] = static_cast<dev_type>(host_data[i]);
- clock_gettime(CLOCK_REALTIME,&time2);
- CudaWrapper_AddCPUBufUploadTime(
+ for(unsigned i=0; i<dev_data_array->dim[0]; ++i) temp_data[i] = static_cast<dev_type>(host_data[i]);
+ clock_gettime(CLOCK_REALTIME,&time2);
+ CudaWrapper_AddCPUBufUploadTime(
time2.tv_sec-time1.tv_sec+1.0*(time2.tv_nsec-time1.tv_nsec)/1000000000);
- CudaWrapper_UploadCudaData(temp_data, dev_data_array->dev_data, nbytes);
- }
- break;
- }
-
- case xx:
- {
- if(typeid(host_type) == typeid(dev_type))
- CudaWrapper_UploadCudaData(host_data, dev_data_array->dev_data, nbytes);
- else
- {
+ CudaWrapper_UploadCudaData(temp_data, dev_data_array->dev_data, nbytes);
+ }
+ break;
+ }
+
+ case xx:
+ {
+ if(typeid(host_type) == typeid(dev_type))
+ CudaWrapper_UploadCudaData(host_data, dev_data_array->dev_data, nbytes);
+ else
+ {
timespec time1,time2;
clock_gettime(CLOCK_REALTIME,&time1);
- for(unsigned i=0; i<dev_data_array->dim[0]; ++i) temp_data[i] = static_cast<dev_type>(host_data[i]);
- clock_gettime(CLOCK_REALTIME,&time2);
- CudaWrapper_AddCPUBufUploadTime(
+ for(unsigned i=0; i<dev_data_array->dim[0]; ++i) temp_data[i] = static_cast<dev_type>(host_data[i]);
+ clock_gettime(CLOCK_REALTIME,&time2);
+ CudaWrapper_AddCPUBufUploadTime(
time2.tv_sec-time1.tv_sec+1.0*(time2.tv_nsec-time1.tv_nsec)/1000000000);
- CudaWrapper_UploadCudaData(temp_data, dev_data_array->dev_data, nbytes);
- }
- break;
- }
+ CudaWrapper_UploadCudaData(temp_data, dev_data_array->dev_data, nbytes);
+ }
+ break;
+ }
- case xy:
- {
+ case xy:
+ {
timespec time1,time2;
clock_gettime(CLOCK_REALTIME,&time1);
- for(unsigned i=0; i<dev_data_array->dim[0]; ++i)
- {
- dev_type* temp = &temp_data[i * dev_data_array->dim[1]];
- for(unsigned j=0; j<dev_data_array->dim[1]; ++j)
- {
- temp[j] = static_cast<dev_type>((reinterpret_cast<host_type**>(host_data))[i][j]);
- }
- }
- clock_gettime(CLOCK_REALTIME,&time2);
- CudaWrapper_AddCPUBufUploadTime(
+ for(unsigned i=0; i<dev_data_array->dim[0]; ++i)
+ {
+ dev_type* temp = &temp_data[i * dev_data_array->dim[1]];
+ for(unsigned j=0; j<dev_data_array->dim[1]; ++j)
+ {
+ temp[j] = static_cast<dev_type>((reinterpret_cast<host_type**>(host_data))[i][j]);
+ }
+ }
+ clock_gettime(CLOCK_REALTIME,&time2);
+ CudaWrapper_AddCPUBufUploadTime(
time2.tv_sec-time1.tv_sec+1.0*(time2.tv_nsec-time1.tv_nsec)/1000000000);
- CudaWrapper_UploadCudaData(temp_data, dev_data_array->dev_data, nbytes);
- break;
- }
-
- case yx:
- {
+ CudaWrapper_UploadCudaData(temp_data, dev_data_array->dev_data, nbytes);
+ break;
+ }
+
+ case yx:
+ {
timespec time1,time2;
clock_gettime(CLOCK_REALTIME,&time1);
- for(unsigned j=0; j<dev_data_array->dim[1]; ++j)
- {
- dev_type* temp = &temp_data[j*dev_data_array->dim[0]];
- for(unsigned i=0; i<dev_data_array->dim[0]; ++i)
- {
- temp[i] = static_cast<dev_type>(reinterpret_cast<host_type**>(host_data)[i][j]);
- }
- }
- clock_gettime(CLOCK_REALTIME,&time2);
- CudaWrapper_AddCPUBufUploadTime(
+ for(unsigned j=0; j<dev_data_array->dim[1]; ++j)
+ {
+ dev_type* temp = &temp_data[j*dev_data_array->dim[0]];
+ for(unsigned i=0; i<dev_data_array->dim[0]; ++i)
+ {
+ temp[i] = static_cast<dev_type>(reinterpret_cast<host_type**>(host_data)[i][j]);
+ }
+ }
+ clock_gettime(CLOCK_REALTIME,&time2);
+ CudaWrapper_AddCPUBufUploadTime(
time2.tv_sec-time1.tv_sec+1.0*(time2.tv_nsec-time1.tv_nsec)/1000000000);
- CudaWrapper_UploadCudaData(temp_data, dev_data_array->dev_data, nbytes);
- break;
- }
- case xyz:
- {
+ CudaWrapper_UploadCudaData(temp_data, dev_data_array->dev_data, nbytes);
+ break;
+ }
+ case xyz:
+ {
timespec time1,time2;
clock_gettime(CLOCK_REALTIME,&time1);
- for(unsigned i=0; i<dev_data_array->dim[0]; ++i)
- for(unsigned j=0; j<dev_data_array->dim[1]; ++j)
- {
- dev_type* temp = &temp_data[(i*dev_data_array->dim[1]+j)*dev_data_array->dim[2]];
- for(unsigned k=0; k<dev_data_array->dim[2]; ++k)
- {
- temp[k] = static_cast<dev_type>(reinterpret_cast<host_type***>(host_data)[i][j][k]);
- }
- }
- clock_gettime(CLOCK_REALTIME,&time2);
- CudaWrapper_AddCPUBufUploadTime(
+ for(unsigned i=0; i<dev_data_array->dim[0]; ++i)
+ for(unsigned j=0; j<dev_data_array->dim[1]; ++j)
+ {
+ dev_type* temp = &temp_data[(i*dev_data_array->dim[1]+j)*dev_data_array->dim[2]];
+ for(unsigned k=0; k<dev_data_array->dim[2]; ++k)
+ {
+ temp[k] = static_cast<dev_type>(reinterpret_cast<host_type***>(host_data)[i][j][k]);
+ }
+ }
+ clock_gettime(CLOCK_REALTIME,&time2);
+ CudaWrapper_AddCPUBufUploadTime(
time2.tv_sec-time1.tv_sec+1.0*(time2.tv_nsec-time1.tv_nsec)/1000000000);
- CudaWrapper_UploadCudaData(temp_data, dev_data_array->dev_data, nbytes);
- break;
- }
+ CudaWrapper_UploadCudaData(temp_data, dev_data_array->dev_data, nbytes);
+ break;
+ }
- case xzy:
- {
+ case xzy:
+ {
timespec time1,time2;
clock_gettime(CLOCK_REALTIME,&time1);
- for(unsigned i=0; i<dev_data_array->dim[0]; ++i)
- for(unsigned k=0; k<dev_data_array->dim[2]; ++k)
- {
- dev_type* temp = &temp_data[(i*dev_data_array->dim[2]+k)*dev_data_array->dim[1]];
- for(unsigned j=0; j<dev_data_array->dim[1]; ++j)
- {
- temp[j] = static_cast<dev_type>(reinterpret_cast<host_type***>(host_data)[i][j][k]);
- }
- }
- clock_gettime(CLOCK_REALTIME,&time2);
- CudaWrapper_AddCPUBufUploadTime(
+ for(unsigned i=0; i<dev_data_array->dim[0]; ++i)
+ for(unsigned k=0; k<dev_data_array->dim[2]; ++k)
+ {
+ dev_type* temp = &temp_data[(i*dev_data_array->dim[2]+k)*dev_data_array->dim[1]];
+ for(unsigned j=0; j<dev_data_array->dim[1]; ++j)
+ {
+ temp[j] = static_cast<dev_type>(reinterpret_cast<host_type***>(host_data)[i][j][k]);
+ }
+ }
+ clock_gettime(CLOCK_REALTIME,&time2);
+ CudaWrapper_AddCPUBufUploadTime(
time2.tv_sec-time1.tv_sec+1.0*(time2.tv_nsec-time1.tv_nsec)/1000000000);
- CudaWrapper_UploadCudaData(temp_data, dev_data_array->dev_data, nbytes);
- break;
- }
- }
- // we have uploaded the data to the device, i.e.:
- current_data_on_device = true;
- // the data is going to change on the device, making the host data out-dated
- if(will_be_changed) current_data_on_host = false;
+ CudaWrapper_UploadCudaData(temp_data, dev_data_array->dev_data, nbytes);
+ break;
+ }
+ }
+ // we have uploaded the data to the device, i.e.:
+ current_data_on_device = true;
+ // the data is going to change on the device, making the host data out-dated
+ if(will_be_changed) current_data_on_host = false;
}
template <typename host_type, typename dev_type, copy_mode mode>
void cCudaData<host_type, dev_type, mode>
::uploadAsync(int stream,bool will_be_changed)
{
- // if current data is already up, do not re-upload it
-// if(current_data_on_device) return;
+ // if current data is already up, do not re-upload it
+// if(current_data_on_device) return;
if(buffer&&is_continues)
{
- printf("Actual Buffer: %p %i\n",*buffer,*buf_size);
- if(typeid(host_type)==typeid(double))
- {
- if(typeid(dev_type)==typeid(double))
- {
- CudaData_Upload_DoubleDouble((void*) host_data,dev_data_array->dev_data,
- dev_data_array->dim,mode,*buffer);
- current_data_on_device = true;
- if(will_be_changed) current_data_on_host = false;
- return;
- }
- else if(typeid(dev_type)==typeid(float))
- {
- CudaData_Upload_DoubleFloat((void*) host_data,dev_data_array->dev_data,
- dev_data_array->dim,mode,*buffer);
- current_data_on_device = true;
- if(will_be_changed) current_data_on_host = false;
- return;
- }
- }
- else if(typeid(host_type)==typeid(float))
- {
- if(typeid(dev_type)==typeid(double))
- {
- CudaData_Upload_FloatDouble((void*) host_data,dev_data_array->dev_data,
- dev_data_array->dim,mode,*buffer);
- current_data_on_device = true;
- if(will_be_changed) current_data_on_host = false;
- return;
- }
- else if(typeid(dev_type)==typeid(float))
- {
- CudaData_Upload_FloatFloat((void*) host_data,dev_data_array->dev_data,
- dev_data_array->dim,mode,*buffer);
- current_data_on_device = true;
- if(will_be_changed) current_data_on_host = false;
- return;
- }
- }
- else if(typeid(host_type)==typeid(int))
- {
- if(typeid(dev_type)==typeid(int))
- {
- CudaData_Upload_IntInt((void*) host_data,dev_data_array->dev_data,
- dev_data_array->dim,mode,*buffer);
- current_data_on_device = true;
- if(will_be_changed) current_data_on_host = false;
- return;
- }
- }
+ printf("Actual Buffer: %p %i\n",*buffer,*buf_size);
+ if(typeid(host_type)==typeid(double))
+ {
+ if(typeid(dev_type)==typeid(double))
+ {
+ CudaData_Upload_DoubleDouble((void*) host_data,dev_data_array->dev_data,
+ dev_data_array->dim,mode,*buffer);
+ current_data_on_device = true;
+ if(will_be_changed) current_data_on_host = false;
+ return;
+ }
+ else if(typeid(dev_type)==typeid(float))
+ {
+ CudaData_Upload_DoubleFloat((void*) host_data,dev_data_array->dev_data,
+ dev_data_array->dim,mode,*buffer);
+ current_data_on_device = true;
+ if(will_be_changed) current_data_on_host = false;
+ return;
+ }
+ }
+ else if(typeid(host_type)==typeid(float))
+ {
+ if(typeid(dev_type)==typeid(double))
+ {
+ CudaData_Upload_FloatDouble((void*) host_data,dev_data_array->dev_data,
+ dev_data_array->dim,mode,*buffer);
+ current_data_on_device = true;
+ if(will_be_changed) current_data_on_host = false;
+ return;
+ }
+ else if(typeid(dev_type)==typeid(float))
+ {
+ CudaData_Upload_FloatFloat((void*) host_data,dev_data_array->dev_data,
+ dev_data_array->dim,mode,*buffer);
+ current_data_on_device = true;
+ if(will_be_changed) current_data_on_host = false;
+ return;
+ }
+ }
+ else if(typeid(host_type)==typeid(int))
+ {
+ if(typeid(dev_type)==typeid(int))
+ {
+ CudaData_Upload_IntInt((void*) host_data,dev_data_array->dev_data,
+ dev_data_array->dim,mode,*buffer);
+ current_data_on_device = true;
+ if(will_be_changed) current_data_on_host = false;
+ return;
+ }
+ }
}
- switch(mode)
- {
- case x:
- {
- if(typeid(host_type) == typeid(dev_type))
- CudaWrapper_UploadCudaDataAsync(host_data, dev_data_array->dev_data, nbytes,stream);
- else
- {
+ switch(mode)
+ {
+ case x:
+ {
+ if(typeid(host_type) == typeid(dev_type))
+ CudaWrapper_UploadCudaDataAsync(host_data, dev_data_array->dev_data, nbytes,stream);
+ else
+ {
timespec time1,time2;
clock_gettime(CLOCK_REALTIME,&time1);
- for(unsigned i=0; i<dev_data_array->dim[0]; ++i) temp_data[i] = static_cast<dev_type>(host_data[i]);
- clock_gettime(CLOCK_REALTIME,&time2);
- CudaWrapper_AddCPUBufUploadTime(
+ for(unsigned i=0; i<dev_data_array->dim[0]; ++i) temp_data[i] = static_cast<dev_type>(host_data[i]);
+ clock_gettime(CLOCK_REALTIME,&time2);
+ CudaWrapper_AddCPUBufUploadTime(
time2.tv_sec-time1.tv_sec+1.0*(time2.tv_nsec-time1.tv_nsec)/1000000000);
- CudaWrapper_UploadCudaDataAsync(temp_data, dev_data_array->dev_data, nbytes,stream);
- }
- break;
- }
-
- case xx:
- {
- if(typeid(host_type) == typeid(dev_type))
- CudaWrapper_UploadCudaDataAsync(host_data, dev_data_array->dev_data, nbytes,stream);
- else
- {
+ CudaWrapper_UploadCudaDataAsync(temp_data, dev_data_array->dev_data, nbytes,stream);
+ }
+ break;
+ }
+
+ case xx:
+ {
+ if(typeid(host_type) == typeid(dev_type))
+ CudaWrapper_UploadCudaDataAsync(host_data, dev_data_array->dev_data, nbytes,stream);
+ else
+ {
timespec time1,time2;
clock_gettime(CLOCK_REALTIME,&time1);
- for(unsigned i=0; i<dev_data_array->dim[0]; ++i) temp_data[i] = static_cast<dev_type>(host_data[i]);
- clock_gettime(CLOCK_REALTIME,&time2);
- CudaWrapper_AddCPUBufUploadTime(
+ for(unsigned i=0; i<dev_data_array->dim[0]; ++i) temp_data[i] = static_cast<dev_type>(host_data[i]);
+ clock_gettime(CLOCK_REALTIME,&time2);
+ CudaWrapper_AddCPUBufUploadTime(
time2.tv_sec-time1.tv_sec+1.0*(time2.tv_nsec-time1.tv_nsec)/1000000000);
- CudaWrapper_UploadCudaDataAsync(temp_data, dev_data_array->dev_data, nbytes,stream);
- }
- break;
- }
+ CudaWrapper_UploadCudaDataAsync(temp_data, dev_data_array->dev_data, nbytes,stream);
+ }
+ break;
+ }
- case xy:
- {
+ case xy:
+ {
timespec time1,time2;
clock_gettime(CLOCK_REALTIME,&time1);
- for(unsigned i=0; i<dev_data_array->dim[0]; ++i)
- {
- dev_type* temp = &temp_data[i * dev_data_array->dim[1]];
- for(unsigned j=0; j<dev_data_array->dim[1]; ++j)
- {
- temp[j] = static_cast<dev_type>((reinterpret_cast<host_type**>(host_data))[i][j]);
- }
- }
- clock_gettime(CLOCK_REALTIME,&time2);
- CudaWrapper_AddCPUBufUploadTime(
+ for(unsigned i=0; i<dev_data_array->dim[0]; ++i)
+ {
+ dev_type* temp = &temp_data[i * dev_data_array->dim[1]];
+ for(unsigned j=0; j<dev_data_array->dim[1]; ++j)
+ {
+ temp[j] = static_cast<dev_type>((reinterpret_cast<host_type**>(host_data))[i][j]);
+ }
+ }
+ clock_gettime(CLOCK_REALTIME,&time2);
+ CudaWrapper_AddCPUBufUploadTime(
time2.tv_sec-time1.tv_sec+1.0*(time2.tv_nsec-time1.tv_nsec)/1000000000);
- CudaWrapper_UploadCudaDataAsync(temp_data, dev_data_array->dev_data, nbytes,stream);
- break;
- }
-
- case yx:
- {
+ CudaWrapper_UploadCudaDataAsync(temp_data, dev_data_array->dev_data, nbytes,stream);
+ break;
+ }
+
+ case yx:
+ {
timespec time1,time2;
clock_gettime(CLOCK_REALTIME,&time1);
- for(unsigned j=0; j<dev_data_array->dim[1]; ++j)
- {
- dev_type* temp = &temp_data[j*dev_data_array->dim[0]];
- for(unsigned i=0; i<dev_data_array->dim[0]; ++i)
- {
- temp[i] = static_cast<dev_type>(reinterpret_cast<host_type**>(host_data)[i][j]);
- }
- }
- clock_gettime(CLOCK_REALTIME,&time2);
- CudaWrapper_AddCPUBufUploadTime(
+ for(unsigned j=0; j<dev_data_array->dim[1]; ++j)
+ {
+ dev_type* temp = &temp_data[j*dev_data_array->dim[0]];
+ for(unsigned i=0; i<dev_data_array->dim[0]; ++i)
+ {
+ temp[i] = static_cast<dev_type>(reinterpret_cast<host_type**>(host_data)[i][j]);
+ }
+ }
+ clock_gettime(CLOCK_REALTIME,&time2);
+ CudaWrapper_AddCPUBufUploadTime(
time2.tv_sec-time1.tv_sec+1.0*(time2.tv_nsec-time1.tv_nsec)/1000000000);
- CudaWrapper_UploadCudaDataAsync(temp_data, dev_data_array->dev_data, nbytes,stream);
- break;
- }
- case xyz:
- {
+ CudaWrapper_UploadCudaDataAsync(temp_data, dev_data_array->dev_data, nbytes,stream);
+ break;
+ }
+ case xyz:
+ {
timespec time1,time2;
clock_gettime(CLOCK_REALTIME,&time1);
- for(unsigned i=0; i<dev_data_array->dim[0]; ++i)
- for(unsigned j=0; j<dev_data_array->dim[1]; ++j)
- {
- dev_type* temp = &temp_data[(i*dev_data_array->dim[1]+j)*dev_data_array->dim[2]];
- for(unsigned k=0; k<dev_data_array->dim[2]; ++k)
- {
- temp[k] = static_cast<dev_type>(reinterpret_cast<host_type***>(host_data)[i][j][k]);
- }
- }
- clock_gettime(CLOCK_REALTIME,&time2);
- CudaWrapper_AddCPUBufUploadTime(
+ for(unsigned i=0; i<dev_data_array->dim[0]; ++i)
+ for(unsigned j=0; j<dev_data_array->dim[1]; ++j)
+ {
+ dev_type* temp = &temp_data[(i*dev_data_array->dim[1]+j)*dev_data_array->dim[2]];
+ for(unsigned k=0; k<dev_data_array->dim[2]; ++k)
+ {
+ temp[k] = static_cast<dev_type>(reinterpret_cast<host_type***>(host_data)[i][j][k]);
+ }
+ }
+ clock_gettime(CLOCK_REALTIME,&time2);
+ CudaWrapper_AddCPUBufUploadTime(
time2.tv_sec-time1.tv_sec+1.0*(time2.tv_nsec-time1.tv_nsec)/1000000000);
- CudaWrapper_UploadCudaDataAsync(temp_data, dev_data_array->dev_data, nbytes,stream);
- break;
- }
+ CudaWrapper_UploadCudaDataAsync(temp_data, dev_data_array->dev_data, nbytes,stream);
+ break;
+ }
- case xzy:
- {
+ case xzy:
+ {
timespec time1,time2;
clock_gettime(CLOCK_REALTIME,&time1);
- for(unsigned i=0; i<dev_data_array->dim[0]; ++i)
- for(unsigned k=0; k<dev_data_array->dim[2]; ++k)
- {
- dev_type* temp = &temp_data[(i*dev_data_array->dim[2]+k)*dev_data_array->dim[1]];
- for(unsigned j=0; j<dev_data_array->dim[1]; ++j)
- {
- temp[j] = static_cast<dev_type>(reinterpret_cast<host_type***>(host_data)[i][j][k]);
- }
- }
- clock_gettime(CLOCK_REALTIME,&time2);
- CudaWrapper_AddCPUBufUploadTime(
+ for(unsigned i=0; i<dev_data_array->dim[0]; ++i)
+ for(unsigned k=0; k<dev_data_array->dim[2]; ++k)
+ {
+ dev_type* temp = &temp_data[(i*dev_data_array->dim[2]+k)*dev_data_array->dim[1]];
+ for(unsigned j=0; j<dev_data_array->dim[1]; ++j)
+ {
+ temp[j] = static_cast<dev_type>(reinterpret_cast<host_type***>(host_data)[i][j][k]);
+ }
+ }
+ clock_gettime(CLOCK_REALTIME,&time2);
+ CudaWrapper_AddCPUBufUploadTime(
time2.tv_sec-time1.tv_sec+1.0*(time2.tv_nsec-time1.tv_nsec)/1000000000);
- CudaWrapper_UploadCudaDataAsync(temp_data, dev_data_array->dev_data, nbytes,stream);
- break;
- }
- }
- // we have uploaded the data to the device, i.e.:
- current_data_on_device = true;
- // the data is going to change on the device, making the host data out-dated
- if(will_be_changed) current_data_on_host = false;
+ CudaWrapper_UploadCudaDataAsync(temp_data, dev_data_array->dev_data, nbytes,stream);
+ break;
+ }
+ }
+ // we have uploaded the data to the device, i.e.:
+ current_data_on_device = true;
+ // the data is going to change on the device, making the host data out-dated
+ if(will_be_changed) current_data_on_host = false;
}
template <typename host_type, typename dev_type, copy_mode mode>
void cCudaData<host_type, dev_type, mode>
::download(bool will_be_changed)
{
- // if current data is already down, do not re-download it
-// if(current_data_on_host) return;
- switch(mode)
- {
- case x:
- {
- if(typeid(host_type) == typeid(dev_type))
- CudaWrapper_DownloadCudaData(host_data, dev_data_array->dev_data, nbytes);
- else
- {
- CudaWrapper_DownloadCudaData(temp_data, dev_data_array->dev_data, nbytes);
+ // if current data is already down, do not re-download it
+// if(current_data_on_host) return;
+ switch(mode)
+ {
+ case x:
+ {
+ if(typeid(host_type) == typeid(dev_type))
+ CudaWrapper_DownloadCudaData(host_data, dev_data_array->dev_data, nbytes);
+ else
+ {
+ CudaWrapper_DownloadCudaData(temp_data, dev_data_array->dev_data, nbytes);
timespec time1,time2;
clock_gettime(CLOCK_REALTIME,&time1);
- for(unsigned i=0; i<dev_data_array->dim[0]; ++i) host_data[i] = static_cast<host_type>(temp_data[i]);
- clock_gettime(CLOCK_REALTIME,&time2);
- CudaWrapper_AddCPUBufDownloadTime(
+ for(unsigned i=0; i<dev_data_array->dim[0]; ++i) host_data[i] = static_cast<host_type>(temp_data[i]);
+ clock_gettime(CLOCK_REALTIME,&time2);
+ CudaWrapper_AddCPUBufDownloadTime(
time2.tv_sec-time1.tv_sec+1.0*(time2.tv_nsec-time1.tv_nsec)/1000000000);
- }
- break;
- }
-
- case xx:
- {
- if(typeid(host_type) == typeid(dev_type))
- CudaWrapper_DownloadCudaData(host_data, dev_data_array->dev_data, nbytes);
- else
- {
- CudaWrapper_DownloadCudaData(temp_data, dev_data_array->dev_data, nbytes);
+ }
+ break;
+ }
+
+ case xx:
+ {
+ if(typeid(host_type) == typeid(dev_type))
+ CudaWrapper_DownloadCudaData(host_data, dev_data_array->dev_data, nbytes);
+ else
+ {
+ CudaWrapper_DownloadCudaData(temp_data, dev_data_array->dev_data, nbytes);
timespec time1,time2;
clock_gettime(CLOCK_REALTIME,&time1);
- for(unsigned i=0; i<dev_data_array->dim[0]; ++i) host_data[i] = static_cast<host_type>(temp_data[i]);
- clock_gettime(CLOCK_REALTIME,&time2);
- CudaWrapper_AddCPUBufDownloadTime(
+ for(unsigned i=0; i<dev_data_array->dim[0]; ++i) host_data[i] = static_cast<host_type>(temp_data[i]);
+ clock_gettime(CLOCK_REALTIME,&time2);
+ CudaWrapper_AddCPUBufDownloadTime(
time2.tv_sec-time1.tv_sec+1.0*(time2.tv_nsec-time1.tv_nsec)/1000000000);
- }
- break;
- }
-
- case xy:
- {
- CudaWrapper_DownloadCudaData(temp_data, dev_data_array->dev_data, nbytes);
+ }
+ break;
+ }
+
+ case xy:
+ {
+ CudaWrapper_DownloadCudaData(temp_data, dev_data_array->dev_data, nbytes);
timespec time1,time2;
clock_gettime(CLOCK_REALTIME,&time1);
- for(unsigned i=0; i<dev_data_array->dim[0]; ++i)
- {
- dev_type* temp = &temp_data[i * dev_data_array->dim[1]];
- for(unsigned j=0; j<dev_data_array->dim[1]; ++j)
- {
- reinterpret_cast<host_type**>(host_data)[i][j] = static_cast<host_type>(temp[j]);
- }
- }
- clock_gettime(CLOCK_REALTIME,&time2);
- CudaWrapper_AddCPUBufDownloadTime(
+ for(unsigned i=0; i<dev_data_array->dim[0]; ++i)
+ {
+ dev_type* temp = &temp_data[i * dev_data_array->dim[1]];
+ for(unsigned j=0; j<dev_data_array->dim[1]; ++j)
+ {
+ reinterpret_cast<host_type**>(host_data)[i][j] = static_cast<host_type>(temp[j]);
+ }
+ }
+ clock_gettime(CLOCK_REALTIME,&time2);
+ CudaWrapper_AddCPUBufDownloadTime(
time2.tv_sec-time1.tv_sec+1.0*(time2.tv_nsec-time1.tv_nsec)/1000000000);
- break;
- }
-
- case yx:
- {
- CudaWrapper_DownloadCudaData(temp_data, dev_data_array->dev_data, nbytes);
+ break;
+ }
+
+ case yx:
+ {
+ CudaWrapper_DownloadCudaData(temp_data, dev_data_array->dev_data, nbytes);
timespec time1,time2;
clock_gettime(CLOCK_REALTIME,&time1);
- for(unsigned j=0; j<dev_data_array->dim[1]; ++j)
- {
- dev_type* temp = &temp_data[j*dev_data_array->dim[0]];
- for(unsigned i=0; i<dev_data_array->dim[0]; ++i)
- {
- reinterpret_cast<host_type**>(host_data)[i][j] = static_cast<host_type>(temp[i]);
- }
- }
- clock_gettime(CLOCK_REALTIME,&time2);
- CudaWrapper_AddCPUBufDownloadTime(
+ for(unsigned j=0; j<dev_data_array->dim[1]; ++j)
+ {
+ dev_type* temp = &temp_data[j*dev_data_array->dim[0]];
+ for(unsigned i=0; i<dev_data_array->dim[0]; ++i)
+ {
+ reinterpret_cast<host_type**>(host_data)[i][j] = static_cast<host_type>(temp[i]);
+ }
+ }
+ clock_gettime(CLOCK_REALTIME,&time2);
+ CudaWrapper_AddCPUBufDownloadTime(
time2.tv_sec-time1.tv_sec+1.0*(time2.tv_nsec-time1.tv_nsec)/1000000000);
- break;
- }
+ break;
+ }
- case xyz:
- {
- CudaWrapper_DownloadCudaData(temp_data, dev_data_array->dev_data, nbytes);
+ case xyz:
+ {
+ CudaWrapper_DownloadCudaData(temp_data, dev_data_array->dev_data, nbytes);
timespec time1,time2;
clock_gettime(CLOCK_REALTIME,&time1);
- for(unsigned i=0; i<dev_data_array->dim[0]; ++i)
- for(unsigned j=0; j<dev_data_array->dim[1]; ++j)
- {
- dev_type* temp = &temp_data[(i * dev_data_array->dim[1]+j)*dev_data_array->dim[2]];
- for(unsigned k=0; k<dev_data_array->dim[2]; ++k)
- {
- reinterpret_cast<host_type***>(host_data)[i][j][k] = static_cast<host_type>(temp[k]);
- }
- }
- clock_gettime(CLOCK_REALTIME,&time2);
- CudaWrapper_AddCPUBufDownloadTime(
+ for(unsigned i=0; i<dev_data_array->dim[0]; ++i)
+ for(unsigned j=0; j<dev_data_array->dim[1]; ++j)
+ {
+ dev_type* temp = &temp_data[(i * dev_data_array->dim[1]+j)*dev_data_array->dim[2]];
+ for(unsigned k=0; k<dev_data_array->dim[2]; ++k)
+ {
+ reinterpret_cast<host_type***>(host_data)[i][j][k] = static_cast<host_type>(temp[k]);
+ }
+ }
+ clock_gettime(CLOCK_REALTIME,&time2);
+ CudaWrapper_AddCPUBufDownloadTime(
time2.tv_sec-time1.tv_sec+1.0*(time2.tv_nsec-time1.tv_nsec)/1000000000);
- break;
- }
+ break;
+ }
- case xzy:
- {
- CudaWrapper_DownloadCudaData(temp_data, dev_data_array->dev_data, nbytes);
+ case xzy:
+ {
+ CudaWrapper_DownloadCudaData(temp_data, dev_data_array->dev_data, nbytes);
timespec time1,time2;
clock_gettime(CLOCK_REALTIME,&time1);
- for(unsigned i=0; i<dev_data_array->dim[0]; ++i)
- for(unsigned k=0; k<dev_data_array->dim[2]; ++k)
- {
- dev_type* temp = &temp_data[(i * dev_data_array->dim[2]+k)*dev_data_array->dim[1]];
- for(unsigned j=0; j<dev_data_array->dim[1]; ++j)
- {
- reinterpret_cast<host_type***>(host_data)[i][j][k] = static_cast<host_type>(temp[j]);
- }
- }
- clock_gettime(CLOCK_REALTIME,&time2);
- CudaWrapper_AddCPUBufDownloadTime(
+ for(unsigned i=0; i<dev_data_array->dim[0]; ++i)
+ for(unsigned k=0; k<dev_data_array->dim[2]; ++k)
+ {
+ dev_type* temp = &temp_data[(i * dev_data_array->dim[2]+k)*dev_data_array->dim[1]];
+ for(unsigned j=0; j<dev_data_array->dim[1]; ++j)
+ {
+ reinterpret_cast<host_type***>(host_data)[i][j][k] = static_cast<host_type>(temp[j]);
+ }
+ }
+ clock_gettime(CLOCK_REALTIME,&time2);
+ CudaWrapper_AddCPUBufDownloadTime(
time2.tv_sec-time1.tv_sec+1.0*(time2.tv_nsec-time1.tv_nsec)/1000000000);
- break;
- }
- }
- // we have downloaded the data to the host, i.e.:
- current_data_on_host = true;
- // the data is going to change on the host, making the device data out-dated
- if(will_be_changed) current_data_on_device = false;
+ break;
+ }
+ }
+ // we have downloaded the data to the host, i.e.:
+ current_data_on_host = true;
+ // the data is going to change on the host, making the device data out-dated
+ if(will_be_changed) current_data_on_device = false;
}
template <typename host_type, typename dev_type, copy_mode mode>
void cCudaData<host_type, dev_type, mode>
::downloadAsync(int stream)
{
- switch(mode)
- {
- case x:
- {
- if(typeid(host_type) == typeid(dev_type))
- {
- CudaWrapper_DownloadCudaDataAsync(host_data, dev_data_array->dev_data, nbytes, stream);
- CudaWrapper_SyncStream(stream);
- }
- else
- {
- CudaWrapper_DownloadCudaDataAsync(temp_data, dev_data_array->dev_data, nbytes, stream);
- CudaWrapper_SyncStream(stream);
- for(unsigned i=0; i<dev_data_array->dim[0]; ++i) host_data[i] = static_cast<host_type>(temp_data[i]);
- }
- break;
- }
-
- case xx:
- {
- if(typeid(host_type) == typeid(dev_type))
- {
- CudaWrapper_DownloadCudaDataAsync(host_data, dev_data_array->dev_data, nbytes, stream);
- CudaWrapper_SyncStream(stream);
- }
- else
- {
- CudaWrapper_DownloadCudaDataAsync(temp_data, dev_data_array->dev_data, nbytes, stream);
- CudaWrapper_SyncStream(stream);
- for(unsigned i=0; i<dev_data_array->dim[0]; ++i) host_data[i] = static_cast<host_type>(temp_data[i]);
- }
- break;
- }
-
- case xy:
- {
- CudaWrapper_DownloadCudaDataAsync(temp_data, dev_data_array->dev_data, nbytes, stream);
- CudaWrapper_SyncStream(stream);
- for(unsigned i=0; i<dev_data_array->dim[0]; ++i)
- {
- dev_type* temp = &temp_data[i * dev_data_array->dim[1]];
- for(unsigned j=0; j<dev_data_array->dim[1]; ++j)
- {
- reinterpret_cast<host_type**>(host_data)[i][j] = static_cast<host_type>(temp[j]);
- }
- }
- break;
- }
-
- case yx:
- {
- CudaWrapper_DownloadCudaDataAsync(temp_data, dev_data_array->dev_data, nbytes, stream);
- CudaWrapper_SyncStream(stream);
- for(unsigned j=0; j<dev_data_array->dim[1]; ++j)
- {
- dev_type* temp = &temp_data[j*dev_data_array->dim[0]];
- for(unsigned i=0; i<dev_data_array->dim[0]; ++i)
- {
- reinterpret_cast<host_type**>(host_data)[i][j] = static_cast<host_type>(temp[i]);
- }
- }
- break;
- }
- }
+ switch(mode)
+ {
+ case x:
+ {
+ if(typeid(host_type) == typeid(dev_type))
+ {
+ CudaWrapper_DownloadCudaDataAsync(host_data, dev_data_array->dev_data, nbytes, stream);
+ CudaWrapper_SyncStream(stream);
+ }
+ else
+ {
+ CudaWrapper_DownloadCudaDataAsync(temp_data, dev_data_array->dev_data, nbytes, stream);
+ CudaWrapper_SyncStream(stream);
+ for(unsigned i=0; i<dev_data_array->dim[0]; ++i) host_data[i] = static_cast<host_type>(temp_data[i]);
+ }
+ break;
+ }
+
+ case xx:
+ {
+ if(typeid(host_type) == typeid(dev_type))
+ {
+ CudaWrapper_DownloadCudaDataAsync(host_data, dev_data_array->dev_data, nbytes, stream);
+ CudaWrapper_SyncStream(stream);
+ }
+ else
+ {
+ CudaWrapper_DownloadCudaDataAsync(temp_data, dev_data_array->dev_data, nbytes, stream);
+ CudaWrapper_SyncStream(stream);
+ for(unsigned i=0; i<dev_data_array->dim[0]; ++i) host_data[i] = static_cast<host_type>(temp_data[i]);
+ }
+ break;
+ }
+
+ case xy:
+ {
+ CudaWrapper_DownloadCudaDataAsync(temp_data, dev_data_array->dev_data, nbytes, stream);
+ CudaWrapper_SyncStream(stream);
+ for(unsigned i=0; i<dev_data_array->dim[0]; ++i)
+ {
+ dev_type* temp = &temp_data[i * dev_data_array->dim[1]];
+ for(unsigned j=0; j<dev_data_array->dim[1]; ++j)
+ {
+ reinterpret_cast<host_type**>(host_data)[i][j] = static_cast<host_type>(temp[j]);
+ }
+ }
+ break;
+ }
+
+ case yx:
+ {
+ CudaWrapper_DownloadCudaDataAsync(temp_data, dev_data_array->dev_data, nbytes, stream);
+ CudaWrapper_SyncStream(stream);
+ for(unsigned j=0; j<dev_data_array->dim[1]; ++j)
+ {
+ dev_type* temp = &temp_data[j*dev_data_array->dim[0]];
+ for(unsigned i=0; i<dev_data_array->dim[0]; ++i)
+ {
+ reinterpret_cast<host_type**>(host_data)[i][j] = static_cast<host_type>(temp[i]);
+ }
+ }
+ break;
+ }
+ }
}
@@ -783,13 +783,13 @@ void cCudaData<host_type, dev_type, mode>
if(buffer!=NULL)
if(not((typeid(host_type) == typeid(dev_type))&&(mode == x || mode == xx)))
{
- printf("Allocate Buffer: %p %i\n",*buffer,*buf_size);
- if(((*buffer)!=NULL)&&(*buf_size<nbytes_buf))
- CudaWrapper_FreeCudaData(*buffer,*buf_size);
- if(*buf_size<nbytes_buf)
- {*buffer=CudaWrapper_AllocCudaData(nbytes_buf);*buf_size=nbytes_buf;}
- printf("Allocate Buffer2: %p %i\n",*buffer,*buf_size);
-
+ printf("Allocate Buffer: %p %i\n",*buffer,*buf_size);
+ if(((*buffer)!=NULL)&&(*buf_size<nbytes_buf))
+ CudaWrapper_FreeCudaData(*buffer,*buf_size);
+ if(*buf_size<nbytes_buf)
+ {*buffer=CudaWrapper_AllocCudaData(nbytes_buf);*buf_size=nbytes_buf;}
+ printf("Allocate Buffer2: %p %i\n",*buffer,*buf_size);
+
}
is_continues=ais_continues;
}
diff --git a/src/USER-CUDA/cuda_modify_flags.h b/src/USER-CUDA/cuda_modify_flags.h
index 8863fe60d4bf87f651a6dc9725c46a2fd5bf6b5d..e683456d272b5b4861bfcc2fe271aaaac8bf1b5c 100644
--- a/src/USER-CUDA/cuda_modify_flags.h
+++ b/src/USER-CUDA/cuda_modify_flags.h
@@ -1,22 +1,22 @@
/* -*- c++ -*- ----------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
diff --git a/src/USER-CUDA/cuda_neigh_list.cpp b/src/USER-CUDA/cuda_neigh_list.cpp
index 01f8e0c6a86f4dd3e700588506abe2a6e07d90be..c34fb22ed4625e7f18c7a35caba0470cebed9a22 100644
--- a/src/USER-CUDA/cuda_neigh_list.cpp
+++ b/src/USER-CUDA/cuda_neigh_list.cpp
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -39,147 +39,146 @@ CudaNeighList::CudaNeighList(LAMMPS *lmp, class NeighList* neigh_list) : Pointer
if(cuda == NULL)
error->all(FLERR,"You cannot use a /cuda class, without activating 'cuda' acceleration. Provide '-c on' as command-line argument to LAMMPS..");
- MYDBG(printf("# CUDA: CudaNeighList::cudaNeighList() ... start\n");)
- this->neigh_list = neigh_list;
- neigh_list->cuda_list=this;
- sneighlist.maxlocal = neigh_list->get_maxlocal();
- sneighlist.maxneighbors = 32;
- sneighlist.maxcut = 0.0;
- sneighlist.cutneighsq = NULL;
- cu_neighbors = NULL;
- cu_neighbors_border = NULL;
- cu_neighbors_inner = NULL;
- cu_numneigh_border = NULL;
- cu_numneigh_inner = NULL;
- cu_numneigh = NULL;
- cu_ilist = NULL;
- cu_ilist_border = NULL;
- cu_inum_border = NULL;
- inum_border = 0;
- neighbors = NULL;
- neighbors_inner = NULL;
- neighbors_border = NULL;
- numneigh_border = NULL;
- numneigh_inner = NULL;
- ilist_border = NULL;
-
- build_cuda = false;
- sneighlist.binned_id=NULL;
- sneighlist.bin_dim=new int[3];
- sneighlist.bin_dim[0]=0;
- sneighlist.bin_dim[1]=0;
- sneighlist.bin_dim[2]=0;
-
- cu_ex_type = NULL;
- cu_ex1_bit = NULL;
- cu_ex2_bit = NULL;
- cu_ex_mol_bit = NULL;
- sneighlist.nex_type=0;
- sneighlist.nex_group=0;
- sneighlist.nex_mol=0;
-
- sneighlist.bin_nmax=0;
- sneighlist.bin_extraspace=0.05;
- MYDBG(printf("# CUDA: CudaNeighList::cudaNeighList() ... end\n");)
-
+ MYDBG(printf("# CUDA: CudaNeighList::cudaNeighList() ... start\n");)
+ this->neigh_list = neigh_list;
+ neigh_list->cuda_list=this;
+ sneighlist.maxlocal = neigh_list->get_maxlocal();
+ sneighlist.maxneighbors = 32;
+ sneighlist.maxcut = 0.0;
+ sneighlist.cutneighsq = NULL;
+ cu_neighbors = NULL;
+ cu_neighbors_border = NULL;
+ cu_neighbors_inner = NULL;
+ cu_numneigh_border = NULL;
+ cu_numneigh_inner = NULL;
+ cu_numneigh = NULL;
+ cu_ilist = NULL;
+ cu_ilist_border = NULL;
+ cu_inum_border = NULL;
+ inum_border = 0;
+ neighbors = NULL;
+ neighbors_inner = NULL;
+ neighbors_border = NULL;
+ numneigh_border = NULL;
+ numneigh_inner = NULL;
+ ilist_border = NULL;
+
+ build_cuda = false;
+ sneighlist.binned_id=NULL;
+ sneighlist.bin_dim=new int[3];
+ sneighlist.bin_dim[0]=0;
+ sneighlist.bin_dim[1]=0;
+ sneighlist.bin_dim[2]=0;
+
+ cu_ex_type = NULL;
+ cu_ex1_bit = NULL;
+ cu_ex2_bit = NULL;
+ cu_ex_mol_bit = NULL;
+ sneighlist.nex_type=0;
+ sneighlist.nex_group=0;
+ sneighlist.nex_mol=0;
+
+ sneighlist.bin_nmax=0;
+ sneighlist.bin_extraspace=0.05;
+ MYDBG(printf("# CUDA: CudaNeighList::cudaNeighList() ... end\n");)
+
}
CudaNeighList::~CudaNeighList()
{
- dev_free();
+ dev_free();
}
void CudaNeighList::dev_alloc()
-{
- MYDBG( printf("# CUDA: CudaNeighList::dev_alloc() ... start\n"); )
- cu_ilist = new cCudaData<int , int , x> (neigh_list->ilist , & sneighlist.ilist , sneighlist.maxlocal );
- cu_numneigh = new cCudaData<int , int , x> (neigh_list->numneigh, & sneighlist.numneigh , sneighlist.maxlocal );
- neighbors = new int[atom->nmax*sneighlist.maxneighbors];
- cu_neighbors= new cCudaData<int, int, x> (neighbors , & sneighlist.neighbors, atom->nmax*sneighlist.maxneighbors );
-
- if(cuda->shared_data.overlap_comm)
- {
- ilist_border = new int[sneighlist.maxlocal];
- numneigh_border = new int[sneighlist.maxlocal];
- numneigh_inner = new int[sneighlist.maxlocal];
- cu_inum_border = new cCudaData<int , int , x> (&inum_border , & sneighlist.inum_border , 1 );
- cu_ilist_border = new cCudaData<int , int , x> (ilist_border , & sneighlist.ilist_border , sneighlist.maxlocal );
- cu_numneigh_border = new cCudaData<int , int , x> (numneigh_border , & sneighlist.numneigh_border , sneighlist.maxlocal );
- cu_numneigh_inner = new cCudaData<int , int , x> (numneigh_inner , & sneighlist.numneigh_inner , sneighlist.maxlocal );
- neighbors_border = new int[sneighlist.maxlocal*sneighlist.maxneighbors];
- cu_neighbors_border= new cCudaData<int, int, x> (neighbors_border , & sneighlist.neighbors_border, sneighlist.maxlocal*sneighlist.maxneighbors );
- neighbors_inner = new int[sneighlist.maxlocal*sneighlist.maxneighbors];
- cu_neighbors_inner = new cCudaData<int, int, x> (neighbors_inner , & sneighlist.neighbors_inner , sneighlist.maxlocal*sneighlist.maxneighbors );
- }
- cuda->shared_data.atom.update_neigh=2;
- MYDBG( printf("# CUDA: CudaNeighList::dev_alloc() ... end\n"); )
+{
+ MYDBG( printf("# CUDA: CudaNeighList::dev_alloc() ... start\n"); )
+ cu_ilist = new cCudaData<int , int , x> (neigh_list->ilist , & sneighlist.ilist , sneighlist.maxlocal );
+ cu_numneigh = new cCudaData<int , int , x> (neigh_list->numneigh, & sneighlist.numneigh , sneighlist.maxlocal );
+ neighbors = new int[atom->nmax*sneighlist.maxneighbors];
+ cu_neighbors= new cCudaData<int, int, x> (neighbors , & sneighlist.neighbors, atom->nmax*sneighlist.maxneighbors );
+
+ if(cuda->shared_data.overlap_comm)
+ {
+ ilist_border = new int[sneighlist.maxlocal];
+ numneigh_border = new int[sneighlist.maxlocal];
+ numneigh_inner = new int[sneighlist.maxlocal];
+ cu_inum_border = new cCudaData<int , int , x> (&inum_border , & sneighlist.inum_border , 1 );
+ cu_ilist_border = new cCudaData<int , int , x> (ilist_border , & sneighlist.ilist_border , sneighlist.maxlocal );
+ cu_numneigh_border = new cCudaData<int , int , x> (numneigh_border , & sneighlist.numneigh_border , sneighlist.maxlocal );
+ cu_numneigh_inner = new cCudaData<int , int , x> (numneigh_inner , & sneighlist.numneigh_inner , sneighlist.maxlocal );
+ neighbors_border = new int[sneighlist.maxlocal*sneighlist.maxneighbors];
+ cu_neighbors_border= new cCudaData<int, int, x> (neighbors_border , & sneighlist.neighbors_border, sneighlist.maxlocal*sneighlist.maxneighbors );
+ neighbors_inner = new int[sneighlist.maxlocal*sneighlist.maxneighbors];
+ cu_neighbors_inner = new cCudaData<int, int, x> (neighbors_inner , & sneighlist.neighbors_inner , sneighlist.maxlocal*sneighlist.maxneighbors );
+ }
+ cuda->shared_data.atom.update_neigh=2;
+ MYDBG( printf("# CUDA: CudaNeighList::dev_alloc() ... end\n"); )
}
void CudaNeighList::dev_free()
{
- MYDBG( printf("# CUDA: CudaNeighList::dev_free() ... start\n"); )
- delete cu_numneigh;
- delete cu_ilist;
- delete [] neighbors;
- delete cu_neighbors;
-
- if(cuda->shared_data.overlap_comm)
- {
- delete [] ilist_border;
- delete [] numneigh_border;
- delete [] numneigh_inner;
- delete [] neighbors_border;
- delete [] neighbors_inner;
- delete cu_inum_border;
- delete cu_neighbors_border;
- delete cu_neighbors_inner;
- delete cu_numneigh_border;
- delete cu_numneigh_inner;
- delete cu_ilist_border;
- }
- MYDBG( printf("# CUDA: CudaNeighList::dev_free() ... end\n"); )
+ MYDBG( printf("# CUDA: CudaNeighList::dev_free() ... start\n"); )
+ delete cu_numneigh;
+ delete cu_ilist;
+ delete [] neighbors;
+ delete cu_neighbors;
+
+ if(cuda->shared_data.overlap_comm)
+ {
+ delete [] ilist_border;
+ delete [] numneigh_border;
+ delete [] numneigh_inner;
+ delete [] neighbors_border;
+ delete [] neighbors_inner;
+ delete cu_inum_border;
+ delete cu_neighbors_border;
+ delete cu_neighbors_inner;
+ delete cu_numneigh_border;
+ delete cu_numneigh_inner;
+ delete cu_ilist_border;
+ }
+ MYDBG( printf("# CUDA: CudaNeighList::dev_free() ... end\n"); )
}
void CudaNeighList::grow_device()
{
- MYDBG(printf("# CUDA: CudaNeighList::grow_device() ... start\n");)
- // if host has allocated more memory for atom arrays than device has, then allocate more memory on device
- int new_maxlocal = neigh_list->get_maxlocal();
- if(sneighlist.maxlocal < new_maxlocal)
- {
- sneighlist.maxlocal = new_maxlocal;
- dev_free();
- dev_alloc();
- }
-
- if(!cu_ilist || !cu_numneigh) dev_alloc();
-
- // check, if hosts data has been allocated somewhere else
- if(cu_ilist ->get_host_data() != neigh_list->ilist) cu_ilist ->set_host_data(neigh_list->ilist);
- if(cu_numneigh->get_host_data() != neigh_list->numneigh) cu_numneigh->set_host_data(neigh_list->numneigh);
-
- MYDBG(printf("# CUDA: CudaNeighList::grow_device() ... end\n");)
+ MYDBG(printf("# CUDA: CudaNeighList::grow_device() ... start\n");)
+ // if host has allocated more memory for atom arrays than device has, then allocate more memory on device
+ int new_maxlocal = neigh_list->get_maxlocal();
+ if(sneighlist.maxlocal < new_maxlocal)
+ {
+ sneighlist.maxlocal = new_maxlocal;
+ dev_free();
+ dev_alloc();
+ }
+
+ if(!cu_ilist || !cu_numneigh) dev_alloc();
+
+ // check, if hosts data has been allocated somewhere else
+ if(cu_ilist ->get_host_data() != neigh_list->ilist) cu_ilist ->set_host_data(neigh_list->ilist);
+ if(cu_numneigh->get_host_data() != neigh_list->numneigh) cu_numneigh->set_host_data(neigh_list->numneigh);
+
+ MYDBG(printf("# CUDA: CudaNeighList::grow_device() ... end\n");)
}
void CudaNeighList::nl_upload(bool will_be_changed)
{
- //return;
- MYDBG(printf("# CUDA: CudaNeighList::nl_upload() ... start\n");)
- if(cu_ilist)
- cu_ilist->upload();
- if(cu_numneigh)
- cu_numneigh->upload();
- MYDBG(printf("# CUDA: CudaNeighList::nl_upload() ... end\n");)
+ //return;
+ MYDBG(printf("# CUDA: CudaNeighList::nl_upload() ... start\n");)
+ if(cu_ilist)
+ cu_ilist->upload();
+ if(cu_numneigh)
+ cu_numneigh->upload();
+ MYDBG(printf("# CUDA: CudaNeighList::nl_upload() ... end\n");)
}
void CudaNeighList::nl_download(bool will_be_changed)
{
- MYDBG(printf("# CUDA: CudaNeighList::nl_download() ... start\n");)
- if(cu_ilist)
- cu_ilist->download();
- if(cu_numneigh)
- cu_numneigh->download();
- MYDBG(printf("# CUDA: CudaNeighList::nl_download() ... end\n");)
+ MYDBG(printf("# CUDA: CudaNeighList::nl_download() ... start\n");)
+ if(cu_ilist)
+ cu_ilist->download();
+ if(cu_numneigh)
+ cu_numneigh->download();
+ MYDBG(printf("# CUDA: CudaNeighList::nl_download() ... end\n");)
}
-
diff --git a/src/USER-CUDA/cuda_neigh_list.h b/src/USER-CUDA/cuda_neigh_list.h
index 97e75b9390fa2d05194a52dfc81b3bd2e11f8b16..8a8963dbbdd9392e2fcce7bc30127b2499c12c27 100644
--- a/src/USER-CUDA/cuda_neigh_list.h
+++ b/src/USER-CUDA/cuda_neigh_list.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -33,46 +33,46 @@ namespace LAMMPS_NS
class CudaNeighList : protected Pointers
{
- public:
- cCudaData<int , int , x>* cu_ilist;
- cCudaData<int , int , x>* cu_numneigh;
- cCudaData<int , int , x>* cu_inum_border;
- cCudaData<int , int , x>* cu_ilist_border;
- cCudaData<int , int , x>* cu_numneigh_border;
- cCudaData<int , int , x>* cu_numneigh_inner;
- cCudaData<int , int , x>* cu_neighbors;
- cCudaData<int , int , x>* cu_neighbors_border;
- cCudaData<int , int , x>* cu_neighbors_inner;
- cCudaData<int , int , x>* cu_ex_type;
- cCudaData<int , int , x>* cu_ex1_bit;
- cCudaData<int , int , x>* cu_ex2_bit;
- cCudaData<int , int , x>* cu_ex_mol_bit;
-
-
- cuda_shared_neighlist sneighlist;
-
- int* neighbors;
- int* neighbors_inner;
- int* neighbors_border;
- int inum_border;
- int* ilist_border;
- int* numneigh_border;
- int* numneigh_inner;
- int nex_type;
- int nex_group;
- int nex_mol;
-
- bool build_cuda;
-
- CudaNeighList(class LAMMPS *, class NeighList* neigh_list);
- ~CudaNeighList();
- void grow_device(); // will grow pages memory on device, keeping old pages. will grow lists memory on device, deleting old lists
- void nl_upload(bool will_be_changed=true);
- void nl_download(bool will_be_changed=true);
- NeighList* neigh_list;
-
- void dev_alloc();
- void dev_free();
+ public:
+ cCudaData<int , int , x>* cu_ilist;
+ cCudaData<int , int , x>* cu_numneigh;
+ cCudaData<int , int , x>* cu_inum_border;
+ cCudaData<int , int , x>* cu_ilist_border;
+ cCudaData<int , int , x>* cu_numneigh_border;
+ cCudaData<int , int , x>* cu_numneigh_inner;
+ cCudaData<int , int , x>* cu_neighbors;
+ cCudaData<int , int , x>* cu_neighbors_border;
+ cCudaData<int , int , x>* cu_neighbors_inner;
+ cCudaData<int , int , x>* cu_ex_type;
+ cCudaData<int , int , x>* cu_ex1_bit;
+ cCudaData<int , int , x>* cu_ex2_bit;
+ cCudaData<int , int , x>* cu_ex_mol_bit;
+
+
+ cuda_shared_neighlist sneighlist;
+
+ int* neighbors;
+ int* neighbors_inner;
+ int* neighbors_border;
+ int inum_border;
+ int* ilist_border;
+ int* numneigh_border;
+ int* numneigh_inner;
+ int nex_type;
+ int nex_group;
+ int nex_mol;
+
+ bool build_cuda;
+
+ CudaNeighList(class LAMMPS *, class NeighList* neigh_list);
+ ~CudaNeighList();
+ void grow_device(); // will grow pages memory on device, keeping old pages. will grow lists memory on device, deleting old lists
+ void nl_upload(bool will_be_changed=true);
+ void nl_download(bool will_be_changed=true);
+ NeighList* neigh_list;
+
+ void dev_alloc();
+ void dev_free();
private:
class Cuda *cuda;
diff --git a/src/USER-CUDA/domain_cuda.cpp b/src/USER-CUDA/domain_cuda.cpp
index b241b16a294fd14d74ba6915f1964ad625afce10..eb5a242457047b21c4cb3aeb5e5fc97cd1f54cfc 100644
--- a/src/USER-CUDA/domain_cuda.cpp
+++ b/src/USER-CUDA/domain_cuda.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -46,7 +46,7 @@ using namespace LAMMPS_NS;
enum{NO_REMAP,X_REMAP,V_REMAP}; // same as fix_deform.cpp
/* ----------------------------------------------------------------------
- default is periodic
+ default is periodic
------------------------------------------------------------------------- */
DomainCuda::DomainCuda(LAMMPS *lmp) : Domain(lmp)
@@ -229,11 +229,11 @@ void DomainCuda::pbc()
{
if(cuda->finished_setup&&(!cuda->oncpu))
{
- cuda->setDomainParams();
+ cuda->setDomainParams();
Cuda_Domain_PBC(&cuda->shared_data, deform_vremap, deform_groupbit,cuda->extent);
return;
}
-
+
Domain::pbc();
}
@@ -266,6 +266,6 @@ void DomainCuda::x2lamda(int n)
Cuda_Domain_x2lamda(&cuda->shared_data,n);
return;
}
-
+
Domain::x2lamda(n);
}
diff --git a/src/USER-CUDA/domain_cuda.h b/src/USER-CUDA/domain_cuda.h
index 1ff4f75946eececcd4eb7977e7a8c2d661f7ef57..7d0186ee798a17045b2fce2b37ddb8569a8cf4f3 100644
--- a/src/USER-CUDA/domain_cuda.h
+++ b/src/USER-CUDA/domain_cuda.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -28,7 +28,7 @@ class DomainCuda : public Domain {
void set_local_box();
void reset_box();
void pbc();
-
+
void lamda2x(int);
void x2lamda(int);
diff --git a/src/USER-CUDA/fft3d_cuda.cpp b/src/USER-CUDA/fft3d_cuda.cpp
index c6882f459748c9c47b4e297dbba72c20f296da7b..c09654d977f6d7a9c76f8c751fdf0e979b452f57 100644
--- a/src/USER-CUDA/fft3d_cuda.cpp
+++ b/src/USER-CUDA/fft3d_cuda.cpp
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -28,7 +28,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -63,9 +63,9 @@
my subsection must not overlap with any other proc's subsection,
i.e. the union of all proc's input (or output) subsections must
exactly tile the global Nfast x Nmid x Nslow data set
- when called from C, all subsection indices are
+ when called from C, all subsection indices are
C-style from 0 to N-1 where N = Nfast or Nmid or Nslow
- when called from F77, all subsection indices are
+ when called from F77, all subsection indices are
F77-style from 1 to N where N = Nfast or Nmid or Nslow
a proc can own 0 elements on input or output
by specifying hi index < lo index
@@ -74,7 +74,7 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
- Perform 3d FFT
+ Perform 3d FFT
Arguments:
in starting address of input data on this proc
@@ -90,15 +90,15 @@ void fft_3d_cuda(FFT_DATA *in, FFT_DATA *out, int flag, struct fft_plan_3d *plan
plan->iterate++;
timespec starttime,starttime2;
timespec endtime,endtime2;
-
+
int i,total,length,offset,num;
double norm;
FFT_DATA *data,*copy;
- // system specific constants
+ // system specific constants
// pre-remap to prepare for 1st FFTs if needed
- // copy = loc for remap result
+ // copy = loc for remap result
int nprocs=plan->nprocs;
if(nprocs>1)
{
@@ -116,8 +116,8 @@ if(nprocs>1)
cufftResult retvalc;
if(plan->init)
{
- if(nprocs>1)
- {
+ if(nprocs>1)
+ {
if(sizeof(FFT_FLOAT)==sizeof(double))cudaMemcpy((void*) (plan->cudata2), (void*) data, plan->cudatasize/2,cudaMemcpyHostToDevice);
if(sizeof(FFT_FLOAT)==sizeof(float)) cudaMemcpy((void*) (plan->cudata2), (void*) data, plan->cudatasize,cudaMemcpyHostToDevice);
initfftdata((double*)plan->cudata2,(FFT_FLOAT*)plan->cudata,plan->nfast,plan->nmid,plan->nslow);
@@ -137,7 +137,7 @@ if(nprocs>1)
#endif
}
/* ----------------------------------------------------------------------
- Create plan for performing a 3d FFT
+ Create plan for performing a 3d FFT
Arguments:
comm MPI communicator for the P procs which own the data
@@ -151,8 +151,8 @@ if(nprocs>1)
scaled 0 = no scaling of result, 1 = scaling
permute permutation in storage order of indices on output
0 = no permutation
- 1 = permute once = mid->fast, slow->mid, fast->slow
- 2 = permute twice = slow->fast, fast->mid, mid->slow
+ 1 = permute once = mid->fast, slow->mid, fast->slow
+ 2 = permute twice = slow->fast, fast->mid, mid->slow
nbuf returns size of internal storage buffers used by FFT
------------------------------------------------------------------------- */
@@ -175,9 +175,9 @@ struct fft_plan_3d *fft_3d_create_plan_cuda(
int np1,np2,ip1,ip2;
int list[50];
- // system specific variables
+ // system specific variables
- // query MPI info
+ // query MPI info
MPI_Comm_rank(comm,&me);
MPI_Comm_size(comm,&nprocs);
@@ -185,7 +185,7 @@ struct fft_plan_3d *fft_3d_create_plan_cuda(
#ifndef FFT_CUFFT
error->all(FLERR,"ERROR: Trying to use cuda fft without FFT_CUFFT set. Recompile with make option 'cufft=1'.");
#endif
- // compute division of procs in 2 dimensions not on-processor
+ // compute division of procs in 2 dimensions not on-processor
bifactor_cuda(nprocs,&np1,&np2);
ip1 = me % np1;
ip2 = me/np1;
@@ -196,13 +196,13 @@ struct fft_plan_3d *fft_3d_create_plan_cuda(
int ip2out = ip2;
int np1out = np1;
int np2out = np2;
-
+
ip1 = 0;
ip2 = 0;
np1 = 1;
np2 = 1;
- // allocate memory for plan data struct
+ // allocate memory for plan data struct
plan = (struct fft_plan_3d *) malloc(sizeof(struct fft_plan_3d));
if (plan == NULL) return NULL;
@@ -210,7 +210,7 @@ struct fft_plan_3d *fft_3d_create_plan_cuda(
// remap from initial distribution to layout needed for 1st set of 1d FFTs
// not needed if all procs own entire fast axis initially
- // first indices = distribution after 1st set of FFTs
+ // first indices = distribution after 1st set of FFTs
if (in_ilo == 0 && in_ihi == nfast-1)
flag = 0;
@@ -241,20 +241,20 @@ struct fft_plan_3d *fft_3d_create_plan_cuda(
if(plan->init) members=1;
plan->pre_plan =
remap_3d_create_plan(comm,in_ilo,in_ihi,in_jlo,in_jhi,in_klo,in_khi,
- first_ilo,first_ihi,first_jlo,first_jhi,
- first_klo,first_khi,
- members,0,0,2);
+ first_ilo,first_ihi,first_jlo,first_jhi,
+ first_klo,first_khi,
+ members,0,0,2);
if (plan->pre_plan == NULL) return NULL;
}
- // 1d FFTs along fast axis
+ // 1d FFTs along fast axis
plan->length1 = nfast;
plan->total1 = nfast * nmid * nslow;
// remap from 1st to 2nd FFT
// choose which axis is split over np1 vs np2 to minimize communication
- // second indices = distribution after 2nd set of FFTs
+ // second indices = distribution after 2nd set of FFTs
second_ilo = ip1*nfast/np1;
second_ihi = (ip1+1)*nfast/np1 - 1;
@@ -264,14 +264,14 @@ struct fft_plan_3d *fft_3d_create_plan_cuda(
second_khi = (ip2+1)*nslow/np2 - 1;
plan->mid1_plan =
remap_3d_create_plan(comm,
- first_ilo,first_ihi,first_jlo,first_jhi,
- first_klo,first_khi,
- second_ilo,second_ihi,second_jlo,second_jhi,
- second_klo,second_khi,
- 2,1,0,2);
+ first_ilo,first_ihi,first_jlo,first_jhi,
+ first_klo,first_khi,
+ second_ilo,second_ihi,second_jlo,second_jhi,
+ second_klo,second_khi,
+ 2,1,0,2);
if (plan->mid1_plan == NULL) return NULL;
- // 1d FFTs along mid axis
+ // 1d FFTs along mid axis
plan->length2 = nmid;
plan->total2 = nfast * nmid * nslow;
@@ -279,7 +279,7 @@ struct fft_plan_3d *fft_3d_create_plan_cuda(
// remap from 2nd to 3rd FFT
// if final distribution is permute=2 with all procs owning entire slow axis
// then this remapping goes directly to final distribution
- // third indices = distribution after 3rd set of FFTs
+ // third indices = distribution after 3rd set of FFTs
flag=1;
@@ -301,23 +301,23 @@ struct fft_plan_3d *fft_3d_create_plan_cuda(
third_klo = 0;
third_khi = nslow - 1;
}
-
+
plan->mid2_plan =
remap_3d_create_plan(comm,
- second_jlo,second_jhi,second_klo,second_khi,
- second_ilo,second_ihi,
- third_jlo,third_jhi,third_klo,third_khi,
- third_ilo,third_ihi,
- 2,1,0,2);
+ second_jlo,second_jhi,second_klo,second_khi,
+ second_ilo,second_ihi,
+ third_jlo,third_jhi,third_klo,third_khi,
+ third_ilo,third_ihi,
+ 2,1,0,2);
if (plan->mid2_plan == NULL) return NULL;
- // 1d FFTs along slow axis
+ // 1d FFTs along slow axis
plan->length3 = nslow;
plan->total3 = nfast * nmid * nslow;
// remap from 3rd FFT to final distribution
- // not needed if permute = 2 and third indices = out indices on all procs
+ // not needed if permute = 2 and third indices = out indices on all procs
flag=1;
@@ -328,11 +328,11 @@ struct fft_plan_3d *fft_3d_create_plan_cuda(
else {
plan->post_plan =
remap_3d_create_plan(comm,
- third_klo,third_khi,third_ilo,third_ihi,
- third_jlo,third_jhi,
- out_klo,out_khi,out_ilo,out_ihi,
- out_jlo,out_jhi,
- 2,(permute+1)%3,0,2);
+ third_klo,third_khi,third_ilo,third_ihi,
+ third_jlo,third_jhi,
+ out_klo,out_khi,out_ilo,out_ihi,
+ out_jlo,out_jhi,
+ 2,(permute+1)%3,0,2);
if (plan->post_plan == NULL) return NULL;
}
@@ -343,14 +343,14 @@ struct fft_plan_3d *fft_3d_create_plan_cuda(
// scratch_size = amount needed internally for remap scratch space
// for each remap:
// out space used for result if big enough, else require copy buffer
- // accumulate largest required remap scratch space
+ // accumulate largest required remap scratch space
out_size = (out_ihi-out_ilo+1) * (out_jhi-out_jlo+1) * (out_khi-out_klo+1);
- first_size = (first_ihi-first_ilo+1) * (first_jhi-first_jlo+1) *
+ first_size = (first_ihi-first_ilo+1) * (first_jhi-first_jlo+1) *
(first_khi-first_klo+1);
- second_size = (second_ihi-second_ilo+1) * (second_jhi-second_jlo+1) *
+ second_size = (second_ihi-second_ilo+1) * (second_jhi-second_jlo+1) *
(second_khi-second_klo+1);
- third_size = (third_ihi-third_ilo+1) * (third_jhi-third_jlo+1) *
+ third_size = (third_ihi-third_ilo+1) * (third_jhi-third_jlo+1) *
(third_khi-third_klo+1);
plan->ihi_out=out_ihi;
@@ -410,15 +410,15 @@ struct fft_plan_3d *fft_3d_create_plan_cuda(
}
else plan->scratch = NULL;
- // system specific pre-computation of 1d FFT coeffs
- // and scaling normalization
+ // system specific pre-computation of 1d FFT coeffs
+ // and scaling normalization
cufftResult retvalc;
int nfft = (in_ihi-in_ilo+1) * (in_jhi-in_jlo+1) *
(in_khi-in_klo+1);
int nfft_brick = (out_ihi-out_ilo+1) * (out_jhi-out_jlo+1) *
(out_khi-out_klo+1);
-
+
int nfft_both = MAX(nfft,nfft_brick);
nfft_both=nfast*nmid*nslow;
@@ -458,7 +458,7 @@ struct fft_plan_3d *fft_3d_create_plan_cuda(
}
/* ----------------------------------------------------------------------
- Destroy a 3d fft plan
+ Destroy a 3d fft plan
------------------------------------------------------------------------- */
void fft_3d_destroy_plan_cuda(struct fft_plan_3d *plan)
@@ -528,7 +528,7 @@ void factor_cuda(int n, int *num, int *list)
}
/* ----------------------------------------------------------------------
- divide n into 2 factors of as equal size as possible
+ divide n into 2 factors of as equal size as possible
------------------------------------------------------------------------- */
void bifactor_cuda(int n, int *factor1, int *factor2)
@@ -564,7 +564,7 @@ void fft_1d_only_cuda(FFT_DATA *data, int nsize, int flag, struct fft_plan_3d *p
int i,total,length,offset,num;
double norm;
- // system specific constants
+ // system specific constants
@@ -602,7 +602,7 @@ void fft_1d_only_cuda(FFT_DATA *data, int nsize, int flag, struct fft_plan_3d *p
}
cudaMemcpy((void*) data, (void**) &(plan->cudata), plan->cudatasize,cudaMemcpyDeviceToHost);
- // scaling if required
+ // scaling if required
// limit num to size of data
#endif
diff --git a/src/USER-CUDA/fft3d_cuda.h b/src/USER-CUDA/fft3d_cuda.h
index 648d7d658444e2f35c064325f4af7cb5b7825960..5ec3871bbba00e892500ed17f72a6a2034d06f52 100644
--- a/src/USER-CUDA/fft3d_cuda.h
+++ b/src/USER-CUDA/fft3d_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -28,22 +28,22 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-// User-settable FFT precision
+// User-settable FFT precision
-// FFT_PRECISION = 1 is single-precision complex (4-byte real, 4-byte imag)
-// FFT_PRECISION = 2 is double-precision complex (8-byte real, 8-byte imag)
+// FFT_PRECISION = 1 is single-precision complex (4-byte real, 4-byte imag)
+// FFT_PRECISION = 2 is double-precision complex (8-byte real, 8-byte imag)
#include "cuda_precision.h"
//#define FFT_PRECISION 2
-// -------------------------------------------------------------------------
+// -------------------------------------------------------------------------
-// Data types for single-precision complex
+// Data types for single-precision complex
#if FFT_PRECISION_CU == 1
@@ -69,9 +69,9 @@ typedef struct {
#endif
-// -------------------------------------------------------------------------
+// -------------------------------------------------------------------------
-// Data types for double-precision complex
+// Data types for double-precision complex
#if FFT_PRECISION_CU == 2
@@ -93,29 +93,29 @@ typedef struct {
#endif
-// -------------------------------------------------------------------------
+// -------------------------------------------------------------------------
-// details of how to do a 3d FFT
+// details of how to do a 3d FFT
struct fft_plan_3d {
- struct remap_plan_3d *pre_plan; // remap from input -> 1st FFTs
- struct remap_plan_3d *mid1_plan; // remap from 1st -> 2nd FFTs
- struct remap_plan_3d *mid2_plan; // remap from 2nd -> 3rd FFTs
- struct remap_plan_3d *post_plan; // remap from 3rd FFTs -> output
- FFT_DATA *copy; // memory for remap results (if needed)
- FFT_DATA *scratch; // scratch space for remaps
- int total1,total2,total3; // # of 1st,2nd,3rd FFTs (times length)
- int length1,length2,length3; // length of 1st,2nd,3rd FFTs
- int pre_target; // where to put remap results
+ struct remap_plan_3d *pre_plan; // remap from input -> 1st FFTs
+ struct remap_plan_3d *mid1_plan; // remap from 1st -> 2nd FFTs
+ struct remap_plan_3d *mid2_plan; // remap from 2nd -> 3rd FFTs
+ struct remap_plan_3d *post_plan; // remap from 3rd FFTs -> output
+ FFT_DATA *copy; // memory for remap results (if needed)
+ FFT_DATA *scratch; // scratch space for remaps
+ int total1,total2,total3; // # of 1st,2nd,3rd FFTs (times length)
+ int length1,length2,length3; // length of 1st,2nd,3rd FFTs
+ int pre_target; // where to put remap results
int mid1_target,mid2_target;
- int scaled; // whether to scale FFT results
- int normnum; // # of values to rescale
- double norm; // normalization factor for rescaling
+ int scaled; // whether to scale FFT results
+ int normnum; // # of values to rescale
+ double norm; // normalization factor for rescaling
double coretime;
double ffttime;
int iterate;
- // system specific 1d FFT info
+ // system specific 1d FFT info
#ifdef FFT_CUFFT
//CUdeviceptr cudata;
@@ -135,7 +135,7 @@ struct fft_plan_3d {
int init;
};
-// function prototypes
+// function prototypes
void fft_3d_destroy_plan_cuda(struct fft_plan_3d *);
void factor_cuda(int, int *, int *);
diff --git a/src/USER-CUDA/fft3d_wrap_cuda.cpp b/src/USER-CUDA/fft3d_wrap_cuda.cpp
index eab2f82e795b069051acc1d36a61bcee5aee63cc..059924066258e8ad8196e9854e2d20ba83f1f31a 100644
--- a/src/USER-CUDA/fft3d_wrap_cuda.cpp
+++ b/src/USER-CUDA/fft3d_wrap_cuda.cpp
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -28,7 +28,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -43,23 +43,23 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
FFT3dCuda::FFT3dCuda(LAMMPS *lmp, MPI_Comm comm, int nfast, int nmid, int nslow,
- int in_ilo, int in_ihi, int in_jlo, int in_jhi,
- int in_klo, int in_khi,
- int out_ilo, int out_ihi, int out_jlo, int out_jhi,
- int out_klo, int out_khi,
- int scaled, int permute, int *nbuf,bool init) : Pointers(lmp)
+ int in_ilo, int in_ihi, int in_jlo, int in_jhi,
+ int in_klo, int in_khi,
+ int out_ilo, int out_ihi, int out_jlo, int out_jhi,
+ int out_klo, int out_khi,
+ int scaled, int permute, int *nbuf,bool init) : Pointers(lmp)
{
#ifdef FFT_CUFFT
plan = fft_3d_create_plan_cuda(comm,nfast,nmid,nslow,
- in_ilo,in_ihi,in_jlo,in_jhi,in_klo,in_khi,
- out_ilo,out_ihi,out_jlo,out_jhi,out_klo,out_khi,
- scaled,permute,nbuf,init);
+ in_ilo,in_ihi,in_jlo,in_jhi,in_klo,in_khi,
+ out_ilo,out_ihi,out_jlo,out_jhi,out_klo,out_khi,
+ scaled,permute,nbuf,init);
#endif
#ifndef FFT_CUFFT
plan = fft_3d_create_plan(comm,nfast,nmid,nslow,
- in_ilo,in_ihi,in_jlo,in_jhi,in_klo,in_khi,
- out_ilo,out_ihi,out_jlo,out_jhi,out_klo,out_khi,
- scaled,permute,nbuf);
+ in_ilo,in_ihi,in_jlo,in_jhi,in_klo,in_khi,
+ out_ilo,out_ihi,out_jlo,out_jhi,out_klo,out_khi,
+ scaled,permute,nbuf);
#endif
if (plan == NULL) error->one(FLERR,"Could not create 3d FFT plan");
}
@@ -102,10 +102,10 @@ void FFT3dCuda::timing1d(double *in, int nsize, int flag)
#ifdef FFT_CUFFT
void FFT3dCuda::set_cudata(void* cudata,void* cudata2)
-{
-
+{
+
plan->cudata=(cufftData*) cudata;
plan->cudata2=(cufftData*) cudata2;
-
+
}
#endif
diff --git a/src/USER-CUDA/fft3d_wrap_cuda.h b/src/USER-CUDA/fft3d_wrap_cuda.h
index 911057cbecabc9b4fa68ac3a5c69c25bc585179c..1d3680facd61de95f3fce7a7adad3b68ce91041d 100644
--- a/src/USER-CUDA/fft3d_wrap_cuda.h
+++ b/src/USER-CUDA/fft3d_wrap_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -28,7 +28,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -51,7 +51,7 @@ namespace LAMMPS_NS {
class FFT3dCuda : protected Pointers {
public:
FFT3dCuda(class LAMMPS *, MPI_Comm,int,int,int,int,int,int,int,int,int,
- int,int,int,int,int,int,int,int,int *,bool);
+ int,int,int,int,int,int,int,int,int *,bool);
~FFT3dCuda();
void compute(double *, double *, int);
void timing1d(double *, int, int);
diff --git a/src/USER-CUDA/fix_addforce_cuda.cpp b/src/USER-CUDA/fix_addforce_cuda.cpp
index 4b8d3fc03eeedc577f58b87fd7a2be440006efaf..03519b80a9102b843ba484be9eef1e9cb358dcb0 100644
--- a/src/USER-CUDA/fix_addforce_cuda.cpp
+++ b/src/USER-CUDA/fix_addforce_cuda.cpp
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -75,9 +75,9 @@ FixAddForceCuda::FixAddForceCuda(LAMMPS *lmp, int narg, char **arg) :
iarg += 2;
} else error->all(FLERR,"Illegal fix addforce/cuda command");
}
-
+
if(iregion!=-1) error->all(FLERR,"Error: fix addforce/cuda does not currently support 'region' option");
-
+
force_flag = 0;
foriginal[0] = foriginal[1] = foriginal[2] = foriginal[3] = 0.0;
cu_foriginal = NULL;
@@ -100,7 +100,7 @@ int FixAddForceCuda::setmask()
void FixAddForceCuda::init()
{
if(not cu_foriginal)
- cu_foriginal = new cCudaData<double, F_FLOAT, x> (foriginal,4);
+ cu_foriginal = new cCudaData<double, F_FLOAT, x> (foriginal,4);
if (strstr(update->integrate_style,"respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;
}
@@ -110,14 +110,14 @@ void FixAddForceCuda::init()
void FixAddForceCuda::setup(int vflag)
{
MYDBG( printf("# CUDA: FixAddForceCuda::setup\n"); )
-
+
if (strstr(update->integrate_style,"verlet"))
{
Cuda_FixAddForceCuda_Init(&cuda->shared_data);
cuda->cu_f->upload();
post_force(vflag);
cuda->cu_f->download();
-
+
}
else {
((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
diff --git a/src/USER-CUDA/fix_addforce_cuda.h b/src/USER-CUDA/fix_addforce_cuda.h
index 38efa0528d540adb7830139843adc0ccf16765a2..1bf3251f46c5722e31fb80903660fb34afe4665e 100644
--- a/src/USER-CUDA/fix_addforce_cuda.h
+++ b/src/USER-CUDA/fix_addforce_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -53,7 +53,7 @@ class FixAddForceCuda : public Fix {
int iregion;
double xvalue,yvalue,zvalue;
double foriginal[4],foriginal_all[4];
- cCudaData<double , F_FLOAT , x>* cu_foriginal;
+ cCudaData<double , F_FLOAT , x>* cu_foriginal;
int force_flag;
int nlevels_respa;
};
diff --git a/src/USER-CUDA/fix_aveforce_cuda.cpp b/src/USER-CUDA/fix_aveforce_cuda.cpp
index c2fcaa98f27346f495127aace3b88cef90828ca4..ed2ca925a63729320029912eac03e38109e834ab 100644
--- a/src/USER-CUDA/fix_aveforce_cuda.cpp
+++ b/src/USER-CUDA/fix_aveforce_cuda.cpp
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -77,13 +77,13 @@ FixAveForceCuda::FixAveForceCuda(LAMMPS *lmp, int narg, char **arg) :
} else error->all(FLERR,"Illegal fix aveforce command");
}
-
+
if(iregion!=-1) error->all(FLERR,"Error: fix aveforce/cuda does not currently support 'region' option");
foriginal_all[0] = foriginal_all[1] = foriginal_all[2] = foriginal_all[3] = 0.0;
foriginal[0] = foriginal[1] = foriginal[2] = foriginal[3] = 0.0;
cu_foriginal = NULL;
-
+
}
/* ---------------------------------------------------------------------- */
@@ -102,7 +102,7 @@ int FixAveForceCuda::setmask()
void FixAveForceCuda::init()
{
if(not cu_foriginal)
- cu_foriginal = new cCudaData<double, F_FLOAT, x> (foriginal,4);
+ cu_foriginal = new cCudaData<double, F_FLOAT, x> (foriginal,4);
if (strstr(update->integrate_style,"respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;
@@ -122,7 +122,7 @@ void FixAveForceCuda::setup(int vflag)
cuda->cu_f->upload();
post_force(vflag);
cuda->cu_f->download();
-
+
}
else
{
@@ -189,11 +189,11 @@ void FixAveForceCuda::post_force_respa(int vflag, int ilevel, int iloop)
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- foriginal[0] += f[i][0];
- foriginal[1] += f[i][1];
- foriginal[2] += f[i][2];
- foriginal[3] += 1;
-
+ foriginal[0] += f[i][0];
+ foriginal[1] += f[i][1];
+ foriginal[2] += f[i][2];
+ foriginal[3] += 1;
+
}
MPI_Allreduce(foriginal,foriginal_all,4,MPI_DOUBLE,MPI_SUM,world);
@@ -206,9 +206,9 @@ void FixAveForceCuda::post_force_respa(int vflag, int ilevel, int iloop)
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- if (xflag) f[i][0] = fave[0];
- if (yflag) f[i][1] = fave[1];
- if (zflag) f[i][2] = fave[2];
+ if (xflag) f[i][0] = fave[0];
+ if (yflag) f[i][1] = fave[1];
+ if (zflag) f[i][2] = fave[2];
}
cuda->cu_f->upload();
}
diff --git a/src/USER-CUDA/fix_aveforce_cuda.h b/src/USER-CUDA/fix_aveforce_cuda.h
index 987ee9d9969448617408b63cda1b17d97e9e2f53..418210e472bf53aea5376599c0bf9ddc75c67a4b 100644
--- a/src/USER-CUDA/fix_aveforce_cuda.h
+++ b/src/USER-CUDA/fix_aveforce_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -54,7 +54,7 @@ class FixAveForceCuda : public Fix {
double xvalue,yvalue,zvalue;
double foriginal_all[4];
double foriginal[4];
- cCudaData<double , F_FLOAT , x>* cu_foriginal;
+ cCudaData<double , F_FLOAT , x>* cu_foriginal;
int nlevels_respa;
};
diff --git a/src/USER-CUDA/fix_enforce2d_cuda.cpp b/src/USER-CUDA/fix_enforce2d_cuda.cpp
index 3cf64a2f3c7d032de934becc30a0cb34cedd77c3..8e482c1478dccf48ad656cbfd06fa0a342790a72 100644
--- a/src/USER-CUDA/fix_enforce2d_cuda.cpp
+++ b/src/USER-CUDA/fix_enforce2d_cuda.cpp
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -28,7 +28,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -78,13 +78,13 @@ void FixEnforce2DCuda::init()
{
if (domain->dimension == 3)
error->all(FLERR,"Cannot use fix enforce2d/cuda with 3d simulation");
- if (atom->omega_flag)
+ if (atom->omega_flag)
error->warning(FLERR,"Enforce2d/cuda does not support omega_flag on gpu yet. Will be handled on cpu.");
-
+
if (atom->angmom_flag)
error->warning(FLERR,"Enforce2d/cuda does not support angmom_flag (angular momentum) on gpu yet. Will be handled on cpu.");
- if (atom->torque_flag)
+ if (atom->torque_flag)
error->warning(FLERR,"Enforce2d/cuda does not support torque_flag on gpu yet. Will be handled on cpu.");
}
@@ -127,13 +127,13 @@ void FixEnforce2DCuda::post_force(int vflag)
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
-
+
if (atom->omega_flag) {
double **omega = atom->omega;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- omega[i][0] = 0.0;
- omega[i][1] = 0.0;
+ omega[i][0] = 0.0;
+ omega[i][1] = 0.0;
}
}
@@ -141,8 +141,8 @@ void FixEnforce2DCuda::post_force(int vflag)
double **angmom = atom->angmom;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- angmom[i][0] = 0.0;
- angmom[i][1] = 0.0;
+ angmom[i][0] = 0.0;
+ angmom[i][1] = 0.0;
}
}
@@ -150,10 +150,10 @@ void FixEnforce2DCuda::post_force(int vflag)
double **torque = atom->torque;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- torque[i][0] = 0.0;
- torque[i][1] = 0.0;
+ torque[i][0] = 0.0;
+ torque[i][1] = 0.0;
}
- }
+ }
}
/* ---------------------------------------------------------------------- */
diff --git a/src/USER-CUDA/fix_enforce2d_cuda.h b/src/USER-CUDA/fix_enforce2d_cuda.h
index 2abb1ffa18dd0e25e0fbd0c1fe036155994eb8c4..c8b01e6bede81ff7402103e58866fbe41911d5c6 100644
--- a/src/USER-CUDA/fix_enforce2d_cuda.h
+++ b/src/USER-CUDA/fix_enforce2d_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
diff --git a/src/USER-CUDA/fix_freeze_cuda.cpp b/src/USER-CUDA/fix_freeze_cuda.cpp
index 818d1be5601a77b3bafaa7f2ab4d8767274716bd..c9f9b4366d7d6005f2e24b043a54df28fd7f50cd 100644
--- a/src/USER-CUDA/fix_freeze_cuda.cpp
+++ b/src/USER-CUDA/fix_freeze_cuda.cpp
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -79,7 +79,7 @@ int FixFreezeCuda::setmask()
void FixFreezeCuda::init()
{
if(not cu_foriginal)
- cu_foriginal = new cCudaData<double, F_FLOAT, x> (foriginal,3);
+ cu_foriginal = new cCudaData<double, F_FLOAT, x> (foriginal,3);
int count = 0;
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"freeze") == 0) count++;
@@ -91,14 +91,14 @@ void FixFreezeCuda::init()
void FixFreezeCuda::setup(int vflag)
{
MYDBG( printf("# CUDA: FixFreezeCuda::setup\n"); )
-
+
if (strstr(update->integrate_style,"verlet"))
{
Cuda_FixFreezeCuda_Init(&cuda->shared_data);
cuda->cu_f->upload();
post_force(vflag);
cuda->cu_f->download();
-
+
}
MYDBG( printf("# CUDA: FixFreezeCuda::setup done\n"); )
diff --git a/src/USER-CUDA/fix_freeze_cuda.h b/src/USER-CUDA/fix_freeze_cuda.h
index 019301096ca2424e51eaa546cf4c99287279634c..7808a59d6276983333ac99541a36fdcf14626ff8 100644
--- a/src/USER-CUDA/fix_freeze_cuda.h
+++ b/src/USER-CUDA/fix_freeze_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -47,7 +47,7 @@ class FixFreezeCuda : public Fix {
private:
class Cuda *cuda;
double foriginal[3],foriginal_all[3];
- cCudaData<double , F_FLOAT , x>* cu_foriginal;
+ cCudaData<double , F_FLOAT , x>* cu_foriginal;
int force_flag;
};
diff --git a/src/USER-CUDA/fix_gravity_cuda.cpp b/src/USER-CUDA/fix_gravity_cuda.cpp
index 6c61c13e78a1fbbf76336a0169e7a37221bb3805..549f95edbf8dddef4b7b3da70527521e791b6a54 100644
--- a/src/USER-CUDA/fix_gravity_cuda.cpp
+++ b/src/USER-CUDA/fix_gravity_cuda.cpp
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -134,14 +134,14 @@ void FixGravityCuda::init()
void FixGravityCuda::setup(int vflag)
{
MYDBG( printf("# CUDA: FixGravityCuda::setup\n"); )
-
+
if (strstr(update->integrate_style,"verlet"))
{
Cuda_FixGravityCuda_Init(&cuda->shared_data);
cuda->cu_f->upload();
post_force(vflag);
cuda->cu_f->download();
-
+
}
else {
}
@@ -156,16 +156,16 @@ void FixGravityCuda::post_force(int vflag)
if (style == GRADIENT) {
if (domain->dimension == 3) {
- double phi_current = degree2rad *
- (phi + (update->ntimestep - time_origin)*dt*phigrad*360.0);
- double theta_current = degree2rad *
- (theta + (update->ntimestep - time_origin)*dt*thetagrad*360.0);
+ double phi_current = degree2rad *
+ (phi + (update->ntimestep - time_origin)*dt*phigrad*360.0);
+ double theta_current = degree2rad *
+ (theta + (update->ntimestep - time_origin)*dt*thetagrad*360.0);
xgrav = sin(theta_current) * cos(phi_current);
ygrav = sin(theta_current) * sin(phi_current);
zgrav = cos(theta_current);
} else {
- double theta_current = degree2rad *
- (theta + (update->ntimestep - time_origin)*dt*thetagrad*360.0);
+ double theta_current = degree2rad *
+ (theta + (update->ntimestep - time_origin)*dt*thetagrad*360.0);
xgrav = sin(theta_current);
ygrav = cos(theta_current);
}
@@ -177,5 +177,3 @@ void FixGravityCuda::post_force(int vflag)
MYDBG( printf("# CUDA: FixGravityCuda::postforce start\n"); )
Cuda_FixGravityCuda_PostForce(&cuda->shared_data, groupbit, xacc,yacc,zacc);
}
-
-
diff --git a/src/USER-CUDA/fix_gravity_cuda.h b/src/USER-CUDA/fix_gravity_cuda.h
index f4aef37790864a7f5a990c972baa79f854d7dc03..23d0b2102e14a3ac77829d45fc8e2375cf7676cb 100644
--- a/src/USER-CUDA/fix_gravity_cuda.h
+++ b/src/USER-CUDA/fix_gravity_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
diff --git a/src/USER-CUDA/fix_nh_cuda.cpp b/src/USER-CUDA/fix_nh_cuda.cpp
index 439a92156832bb97ae59a61575f0ac613345b5a2..6a426dd50c7998a02ce6bed8bf7234cdee5b8362 100644
--- a/src/USER-CUDA/fix_nh_cuda.cpp
+++ b/src/USER-CUDA/fix_nh_cuda.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -45,7 +45,7 @@ enum{NONE,XYZ,XY,YZ,XZ};
enum{ISO,ANISO,TRICLINIC};
/* ----------------------------------------------------------------------
- NVT,NPH,NPT integrators for improved Nose-Hoover equations of motion
+ NVT,NPH,NPT integrators for improved Nose-Hoover equations of motion
---------------------------------------------------------------------- */
FixNHCuda::FixNHCuda(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
@@ -76,7 +76,7 @@ FixNHCuda::FixNHCuda(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
deviatoric_flag = 0;
nreset_h0 = 0;
- // Used by FixNVTSllod to preserve non-default value
+ // Used by FixNVTSllod to preserve non-default value
mtchain_default_flag = 1;
@@ -103,7 +103,7 @@ FixNHCuda::FixNHCuda(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
t_stop = atof(arg[iarg+2]);
t_period = atof(arg[iarg+3]);
if (t_start < 0.0 || t_stop <= 0.0)
- error->all(FLERR,"Target T for fix nvt/npt/nph cannot be 0.0");
+ error->all(FLERR,"Target T for fix nvt/npt/nph cannot be 0.0");
iarg += 4;
} else if (strcmp(arg[iarg],"iso") == 0) {
@@ -114,10 +114,10 @@ FixNHCuda::FixNHCuda(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
p_period[0] = p_period[1] = p_period[2] = atof(arg[iarg+3]);
p_flag[0] = p_flag[1] = p_flag[2] = 1;
if (dimension == 2) {
- p_start[2] = p_stop[2] = p_period[2] = 0.0;
- p_flag[2] = 0;
+ p_start[2] = p_stop[2] = p_period[2] = 0.0;
+ p_flag[2] = 0;
}
- iarg += 4;
+ iarg += 4;
} else if (strcmp(arg[iarg],"aniso") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
pcouple = NONE;
@@ -126,8 +126,8 @@ FixNHCuda::FixNHCuda(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
p_period[0] = p_period[1] = p_period[2] = atof(arg[iarg+3]);
p_flag[0] = p_flag[1] = p_flag[2] = 1;
if (dimension == 2) {
- p_start[2] = p_stop[2] = p_period[2] = 0.0;
- p_flag[2] = 0;
+ p_start[2] = p_stop[2] = p_period[2] = 0.0;
+ p_flag[2] = 0;
}
iarg += 4;
} else if (strcmp(arg[iarg],"tri") == 0) {
@@ -142,12 +142,12 @@ FixNHCuda::FixNHCuda(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
p_period[3] = p_period[4] = p_period[5] = atof(arg[iarg+3]);
p_flag[3] = p_flag[4] = p_flag[5] = 1;
if (dimension == 2) {
- p_start[2] = p_stop[2] = p_period[2] = 0.0;
- p_flag[2] = 0;
- p_start[3] = p_stop[3] = p_period[3] = 0.0;
- p_flag[3] = 0;
- p_start[4] = p_stop[4] = p_period[4] = 0.0;
- p_flag[4] = 0;
+ p_start[2] = p_stop[2] = p_period[2] = 0.0;
+ p_flag[2] = 0;
+ p_start[3] = p_stop[3] = p_period[3] = 0.0;
+ p_flag[3] = 0;
+ p_start[4] = p_stop[4] = p_period[4] = 0.0;
+ p_flag[4] = 0;
}
iarg += 4;
@@ -158,7 +158,7 @@ FixNHCuda::FixNHCuda(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
p_period[0] = atof(arg[iarg+3]);
p_flag[0] = 1;
deviatoric_flag = 1;
- iarg += 4;
+ iarg += 4;
} else if (strcmp(arg[iarg],"y") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
p_start[1] = atof(arg[iarg+1]);
@@ -166,7 +166,7 @@ FixNHCuda::FixNHCuda(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
p_period[1] = atof(arg[iarg+3]);
p_flag[1] = 1;
deviatoric_flag = 1;
- iarg += 4;
+ iarg += 4;
} else if (strcmp(arg[iarg],"z") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
p_start[2] = atof(arg[iarg+1]);
@@ -174,9 +174,9 @@ FixNHCuda::FixNHCuda(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
p_period[2] = atof(arg[iarg+3]);
p_flag[2] = 1;
deviatoric_flag = 1;
- iarg += 4;
+ iarg += 4;
if (dimension == 2)
- error->all(FLERR,"Invalid fix nvt/npt/nph command for a 2d simulation");
+ error->all(FLERR,"Invalid fix nvt/npt/nph command for a 2d simulation");
} else if (strcmp(arg[iarg],"yz") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
@@ -185,9 +185,9 @@ FixNHCuda::FixNHCuda(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
p_period[3] = atof(arg[iarg+3]);
p_flag[3] = 1;
deviatoric_flag = 1;
- iarg += 4;
+ iarg += 4;
if (dimension == 2)
- error->all(FLERR,"Invalid fix nvt/npt/nph command for a 2d simulation");
+ error->all(FLERR,"Invalid fix nvt/npt/nph command for a 2d simulation");
} else if (strcmp(arg[iarg],"xz") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
p_start[4] = atof(arg[iarg+1]);
@@ -195,9 +195,9 @@ FixNHCuda::FixNHCuda(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
p_period[4] = atof(arg[iarg+3]);
p_flag[4] = 1;
deviatoric_flag = 1;
- iarg += 4;
+ iarg += 4;
if (dimension == 2)
- error->all(FLERR,"Invalid fix nvt/npt/nph command for a 2d simulation");
+ error->all(FLERR,"Invalid fix nvt/npt/nph command for a 2d simulation");
} else if (strcmp(arg[iarg],"xy") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
p_start[5] = atof(arg[iarg+1]);
@@ -205,7 +205,7 @@ FixNHCuda::FixNHCuda(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
p_period[5] = atof(arg[iarg+3]);
p_flag[5] = 1;
deviatoric_flag = 1;
- iarg += 4;
+ iarg += 4;
} else if (strcmp(arg[iarg],"couple") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
@@ -293,38 +293,38 @@ FixNHCuda::FixNHCuda(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
if (p_flag[5] && domain->yperiodic == 0)
error->all(FLERR,"Cannot use fix nvt/npt/nph on a 2nd non-periodic dimension");
- if (!domain->triclinic && (p_flag[3] || p_flag[4] || p_flag[5]))
+ if (!domain->triclinic && (p_flag[3] || p_flag[4] || p_flag[5]))
error->all(FLERR,"Can not specify Pxy/Pxz/Pyz in "
- "fix nvt/npt/nph with non-triclinic box");
+ "fix nvt/npt/nph with non-triclinic box");
if (pcouple == XYZ && dimension == 3 &&
- (p_start[0] != p_start[1] || p_start[0] != p_start[2] ||
- p_stop[0] != p_stop[1] || p_stop[0] != p_stop[2] ||
+ (p_start[0] != p_start[1] || p_start[0] != p_start[2] ||
+ p_stop[0] != p_stop[1] || p_stop[0] != p_stop[2] ||
p_period[0] != p_period[1] || p_period[0] != p_period[2]))
error->all(FLERR,"Invalid fix nvt/npt/nph pressure settings");
if (pcouple == XYZ && dimension == 2 &&
- (p_start[0] != p_start[1] || p_stop[0] != p_stop[1] ||
+ (p_start[0] != p_start[1] || p_stop[0] != p_stop[1] ||
p_period[0] != p_period[1]))
error->all(FLERR,"Invalid fix nvt/npt/nph pressure settings");
- if (pcouple == XY &&
- (p_start[0] != p_start[1] || p_stop[0] != p_stop[1] ||
+ if (pcouple == XY &&
+ (p_start[0] != p_start[1] || p_stop[0] != p_stop[1] ||
p_period[0] != p_period[1]))
error->all(FLERR,"Invalid fix nvt/npt/nph pressure settings");
- if (pcouple == YZ &&
+ if (pcouple == YZ &&
(p_start[1] != p_start[2] || p_stop[1] != p_stop[2] ||
p_period[1] != p_period[2]))
error->all(FLERR,"Invalid fix nvt/npt/nph pressure settings");
- if (pcouple == XZ &&
+ if (pcouple == XZ &&
(p_start[0] != p_start[2] || p_stop[0] != p_stop[2] ||
p_period[0] != p_period[2]))
error->all(FLERR,"Invalid fix nvt/npt/nph pressure settings");
- if ((tstat_flag && t_period <= 0.0) ||
- (p_flag[0] && p_period[0] <= 0.0) ||
- (p_flag[1] && p_period[1] <= 0.0) ||
+ if ((tstat_flag && t_period <= 0.0) ||
+ (p_flag[0] && p_period[0] <= 0.0) ||
+ (p_flag[1] && p_period[1] <= 0.0) ||
(p_flag[2] && p_period[2] <= 0.0) ||
- (p_flag[3] && p_period[3] <= 0.0) ||
- (p_flag[4] && p_period[4] <= 0.0) ||
+ (p_flag[3] && p_period[3] <= 0.0) ||
+ (p_flag[4] && p_period[4] <= 0.0) ||
(p_flag[5] && p_period[5] <= 0.0))
error->all(FLERR,"Fix nvt/npt/nph damping parameters must be > 0.0");
@@ -393,7 +393,7 @@ FixNHCuda::FixNHCuda(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
if (pstyle == ISO) size_vector += 2*2*1;
else if (pstyle == ANISO) size_vector += 2*2*3;
else if (pstyle == TRICLINIC) size_vector += 2*2*6;
-
+
if (mpchain) {
int ich;
etap = new double[mpchain];
@@ -404,8 +404,8 @@ FixNHCuda::FixNHCuda(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
etap_dot[mpchain] = 0.0;
etap_dotdot = new double[mpchain];
for (ich = 0; ich < mpchain; ich++) {
- etap[ich] = etap_dot[ich] =
- etap_dotdot[ich] = 0.0;
+ etap[ich] = etap_dot[ich] =
+ etap_dotdot[ich] = 0.0;
}
etap_mass = new double[mpchain];
size_vector += 2*2*mpchain;
@@ -422,9 +422,9 @@ FixNHCuda::FixNHCuda(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
vol0 = t0 = 0.0;
}
-
+
/* ---------------------------------------------------------------------- */
-
+
FixNHCuda::~FixNHCuda()
{
delete [] rfix;
@@ -475,18 +475,18 @@ void FixNHCuda::init()
if (pstat_flag)
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"deform") == 0) {
- int *dimflag = ((FixDeform *) modify->fix[i])->dimflag;
- if ((p_flag[0] && dimflag[0]) || (p_flag[1] && dimflag[1]) ||
- (p_flag[2] && dimflag[2]) || (p_flag[3] && dimflag[3]) ||
- (p_flag[4] && dimflag[4]) || (p_flag[5] && dimflag[5]))
- error->all(FLERR,"Cannot use fix npt and fix deform on "
- "same component of stress tensor");
+ int *dimflag = ((FixDeform *) modify->fix[i])->dimflag;
+ if ((p_flag[0] && dimflag[0]) || (p_flag[1] && dimflag[1]) ||
+ (p_flag[2] && dimflag[2]) || (p_flag[3] && dimflag[3]) ||
+ (p_flag[4] && dimflag[4]) || (p_flag[5] && dimflag[5]))
+ error->all(FLERR,"Cannot use fix npt and fix deform on "
+ "same component of stress tensor");
}
// set temperature and pressure ptrs
int icompute = modify->find_compute(id_temp);
- if (icompute < 0)
+ if (icompute < 0)
error->all(FLERR,"Temperature ID for fix nvt/nph/npt does not exist");
temperature = modify->compute[icompute];
@@ -524,7 +524,7 @@ void FixNHCuda::init()
tdrag_factor = 1.0 - (update->dt * t_freq * drag / nc_tchain);
// tally the number of dimensions that are barostatted
- // also compute the initial volume and reference cell
+ // also compute the initial volume and reference cell
// set initial volume and reference cell, if not already done
if (pstat_flag) {
@@ -571,11 +571,11 @@ void FixNHCuda::init()
triggerneighsq= cuda->shared_data.atom.triggerneighsq;
cuda->neighbor_decide_by_integrator=1;
Cuda_FixNHCuda_Init(&cuda->shared_data,dtv,dtf);
-
+
}
/* ----------------------------------------------------------------------
- compute T,P before integrator starts
+ compute T,P before integrator starts
------------------------------------------------------------------------- */
void FixNHCuda::setup(int vflag)
@@ -588,7 +588,7 @@ void FixNHCuda::setup(int vflag)
// t_target is used by compute_scalar(), even for NPH
- if (tstat_flag) t_target = t_start;
+ if (tstat_flag) t_target = t_start;
else if (pstat_flag) {
// t0 = initial value for piston mass and energy conservation
@@ -600,8 +600,8 @@ void FixNHCuda::setup(int vflag)
if (t0 == 0.0) {
t0 = temperature->compute_scalar();
if (t0 == 0.0) {
- if (strcmp(update->unit_style,"lj") == 0) t0 = 1.0;
- else t0 = 300.0;
+ if (strcmp(update->unit_style,"lj") == 0) t0 = 1.0;
+ else t0 = 300.0;
}
}
t_target = t0;
@@ -625,7 +625,7 @@ void FixNHCuda::setup(int vflag)
eta_mass[ich] = boltz * t_target / (t_freq*t_freq);
for (int ich = 1; ich < mtchain; ich++) {
eta_dotdot[ich] = (eta_mass[ich-1]*eta_dot[ich-1]*eta_dot[ich-1] -
- boltz*t_target) / eta_mass[ich];
+ boltz*t_target) / eta_mass[ich];
}
}
@@ -635,11 +635,11 @@ void FixNHCuda::setup(int vflag)
for (int i = 0; i < 3; i++)
if (p_flag[i])
- omega_mass[i] = nkt/(p_freq[i]*p_freq[i]);
+ omega_mass[i] = nkt/(p_freq[i]*p_freq[i]);
if (pstyle == TRICLINIC) {
for (int i = 3; i < 6; i++)
- if (p_flag[i]) omega_mass[i] = nkt/(p_freq[i]*p_freq[i]);
+ if (p_flag[i]) omega_mass[i] = nkt/(p_freq[i]*p_freq[i]);
}
// initial forces on barostat thermostat variables
@@ -647,11 +647,11 @@ void FixNHCuda::setup(int vflag)
if (mpchain) {
etap_mass[0] = boltz * t_target / (p_freq_max*p_freq_max);
for (int ich = 1; ich < mpchain; ich++)
- etap_mass[ich] = boltz * t_target / (p_freq_max*p_freq_max);
+ etap_mass[ich] = boltz * t_target / (p_freq_max*p_freq_max);
for (int ich = 1; ich < mpchain; ich++)
- etap_dotdot[ich] =
- (etap_mass[ich-1]*etap_dot[ich-1]*etap_dot[ich-1] -
- boltz*t_target) / etap_mass[ich];
+ etap_dotdot[ich] =
+ (etap_mass[ich-1]*etap_dot[ich-1]*etap_dot[ich-1] -
+ boltz*t_target) / etap_mass[ich];
}
// compute appropriately coupled elements of mvv_current
@@ -661,17 +661,17 @@ void FixNHCuda::setup(int vflag)
}
/* ----------------------------------------------------------------------
- 1st half of Verlet update
+ 1st half of Verlet update
------------------------------------------------------------------------- */
void FixNHCuda::initial_integrate(int vflag)
{
if(!temperature->cudable) cuda->downloadAll();
- if(triggerneighsq!=cuda->shared_data.atom.triggerneighsq)
+ if(triggerneighsq!=cuda->shared_data.atom.triggerneighsq)
{
- triggerneighsq= cuda->shared_data.atom.triggerneighsq;
- Cuda_FixNHCuda_Init(&cuda->shared_data,dtv,dtf);
+ triggerneighsq= cuda->shared_data.atom.triggerneighsq;
+ Cuda_FixNHCuda_Init(&cuda->shared_data,dtv,dtf);
}
// update eta_press_dot
@@ -713,8 +713,8 @@ void FixNHCuda::initial_integrate(int vflag)
compute_press_target();
nh_omega_dot();
factor[0] = exp(-dt4*(omega_dot[0]+mtk_term2));
- factor[1] = exp(-dt4*(omega_dot[1]+mtk_term2));
- factor[2] = exp(-dt4*(omega_dot[2]+mtk_term2));
+ factor[1] = exp(-dt4*(omega_dot[1]+mtk_term2));
+ factor[2] = exp(-dt4*(omega_dot[2]+mtk_term2));
Cuda_FixNHCuda_nh_v_press_and_nve_v_NoBias(&cuda->shared_data, groupbit, factor,(igroup == atom->firstgroup)?atom->nfirst:atom->nlocal,(pstyle == TRICLINIC)?1:0);
}
else
@@ -722,28 +722,28 @@ void FixNHCuda::initial_integrate(int vflag)
}
else if(which==BIAS)
{
- if(pstat_flag)
- {
+ if(pstat_flag)
+ {
compute_press_target();
nh_omega_dot();
- factor[0] = exp(-dt4*(omega_dot[0]+mtk_term2));
- factor[1] = exp(-dt4*(omega_dot[1]+mtk_term2));
- factor[2] = exp(-dt4*(omega_dot[2]+mtk_term2));
- if(!temperature->cudable)
- {
- nh_v_press();
- cuda->cu_v->upload();
- }
- else
- {
- int groupbit_org=temperature->groupbit;
- temperature->groupbit=groupbit;
- temperature->remove_bias_all();
+ factor[0] = exp(-dt4*(omega_dot[0]+mtk_term2));
+ factor[1] = exp(-dt4*(omega_dot[1]+mtk_term2));
+ factor[2] = exp(-dt4*(omega_dot[2]+mtk_term2));
+ if(!temperature->cudable)
+ {
+ nh_v_press();
+ cuda->cu_v->upload();
+ }
+ else
+ {
+ int groupbit_org=temperature->groupbit;
+ temperature->groupbit=groupbit;
+ temperature->remove_bias_all();
Cuda_FixNHCuda_nh_v_press(&cuda->shared_data, groupbit, factor,(igroup == atom->firstgroup)?atom->nfirst:atom->nlocal,(pstyle == TRICLINIC)?1:0);
- temperature->restore_bias_all();
- temperature->groupbit=groupbit_org;
- }
- }
+ temperature->restore_bias_all();
+ temperature->groupbit=groupbit_org;
+ }
+ }
Cuda_FixNHCuda_nve_v(&cuda->shared_data,groupbit,(igroup == atom->firstgroup)?atom->nfirst:atom->nlocal);
}
@@ -763,7 +763,7 @@ void FixNHCuda::initial_integrate(int vflag)
}
/* ----------------------------------------------------------------------
- 2nd half of Verlet update
+ 2nd half of Verlet update
------------------------------------------------------------------------- */
void FixNHCuda::final_integrate()
@@ -786,33 +786,33 @@ void FixNHCuda::final_integrate()
else if(which==BIAS)
{
Cuda_FixNHCuda_nve_v(&cuda->shared_data,groupbit,(igroup == atom->firstgroup)?atom->nfirst:atom->nlocal);
-
- if(pstat_flag)
- {
+
+ if(pstat_flag)
+ {
factor[0] = exp(-dt4*(omega_dot[0]+mtk_term2));
factor[1] = exp(-dt4*(omega_dot[1]+mtk_term2));
factor[2] = exp(-dt4*(omega_dot[2]+mtk_term2));
- if(!temperature->cudable)
- {
- cuda->cu_v->download();
- nh_v_press();
- cuda->cu_v->upload();
- }
- else
- {
- int groupbit_org=temperature->groupbit;
- temperature->groupbit=groupbit;
- temperature->remove_bias_all();
+ if(!temperature->cudable)
+ {
+ cuda->cu_v->download();
+ nh_v_press();
+ cuda->cu_v->upload();
+ }
+ else
+ {
+ int groupbit_org=temperature->groupbit;
+ temperature->groupbit=groupbit;
+ temperature->remove_bias_all();
Cuda_FixNHCuda_nh_v_press(&cuda->shared_data, groupbit, factor,(igroup == atom->firstgroup)?atom->nfirst:atom->nlocal,(pstyle == TRICLINIC)?1:0);
- temperature->restore_bias_all();
- temperature->groupbit=groupbit_org;
- }
- }
+ temperature->restore_bias_all();
+ temperature->groupbit=groupbit_org;
+ }
+ }
}
// compute new T,P
// compute appropriately coupled elements of mvv_current
- if(!temperature->cudable) cuda->cu_v->download();
+ if(!temperature->cudable) cuda->cu_v->download();
t_current = temperature->compute_scalar();
if (pstat_flag) {
if (pstyle == ISO) double tmp = pressure->compute_scalar();
@@ -849,7 +849,7 @@ void FixNHCuda::initial_integrate_respa(int vflag, int ilevel, int iloop)
if (ilevel == nlevels_respa-1) {
// update eta_press_dot
-
+
if (pstat_flag && mpchain) nhc_press_integrate();
// update eta_dot
@@ -860,7 +860,7 @@ void FixNHCuda::initial_integrate_respa(int vflag, int ilevel, int iloop)
t_target = t_start + delta * (t_stop-t_start);
eta_mass[0] = tdof * boltz * t_target / (t_freq*t_freq);
for (int ich = 1; ich < mtchain; ich++)
- eta_mass[ich] = boltz * t_target / (t_freq*t_freq);
+ eta_mass[ich] = boltz * t_target / (t_freq*t_freq);
nhc_temp_integrate();
}
@@ -870,17 +870,17 @@ void FixNHCuda::initial_integrate_respa(int vflag, int ilevel, int iloop)
if (pstat_flag) {
if (pstyle == ISO) {
- temperature->compute_scalar();
- double tmp = pressure->compute_scalar();
+ temperature->compute_scalar();
+ double tmp = pressure->compute_scalar();
} else {
- temperature->compute_vector();
- pressure->compute_vector();
+ temperature->compute_vector();
+ pressure->compute_vector();
}
couple();
pressure->addstep(update->ntimestep+1);
if (mtk_flag) couple_ke();
}
-
+
if (pstat_flag) {
compute_press_target();
nh_omega_dot();
@@ -900,10 +900,10 @@ void FixNHCuda::initial_integrate_respa(int vflag, int ilevel, int iloop)
if (pstat_flag) remap();
}
- // if barostat, redo KSpace coeffs at outermost level,
+ // if barostat, redo KSpace coeffs at outermost level,
// since volume has changed
- if (ilevel == nlevels_respa-1 && kspace_flag && pstat_flag)
+ if (ilevel == nlevels_respa-1 && kspace_flag && pstat_flag)
force->kspace->setup();
}
@@ -951,9 +951,9 @@ void FixNHCuda::couple()
p_current[1] = tensor[1];
p_current[2] = tensor[2];
}
-
- // switch order from xy-xz-yz to Voigt
-
+
+ // switch order from xy-xz-yz to Voigt
+
if (pstyle == TRICLINIC) {
p_current[3] = tensor[5];
p_current[4] = tensor[4];
@@ -967,7 +967,7 @@ void FixNHCuda::couple_ke()
{
double *tensor = temperature->vector;
if (pstyle == ISO)
- mvv_current[0] = mvv_current[1] = mvv_current[2] =
+ mvv_current[0] = mvv_current[1] = mvv_current[2] =
tdof * boltz * t_current/dimension;
else if (pcouple == XYZ) {
double ave = 1.0/3.0 * (tensor[0] + tensor[1] + tensor[2]);
@@ -1016,7 +1016,7 @@ void FixNHCuda::remap()
else {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
- domain->x2lamda(x[i],x[i]);
+ domain->x2lamda(x[i],x[i]);
}
if (nrigid)
@@ -1026,16 +1026,16 @@ void FixNHCuda::remap()
// reset global and local box to new size/shape
// This operation corresponds to applying the
- // translate and scale operations
+ // translate and scale operations
// corresponding to the solution of the following ODE:
//
// h_dot = omega_dot * h
//
// where h_dot, omega_dot and h are all upper-triangular
- // 3x3 tensors. In Voigt notation, the elements of the
+ // 3x3 tensors. In Voigt notation, the elements of the
// RHS product tensor are:
// h_dot = [0*0, 1*1, 2*2, 1*3+3*2, 0*4+5*3+4*2, 0*5+5*1]
- //
+ //
// Ordering of operations preserves time symmetry.
double dto2 = dto/2.0;
@@ -1045,19 +1045,19 @@ void FixNHCuda::remap()
if (pstyle == TRICLINIC) {
h[4] *= exp(dto8*omega_dot[0]);
- h[4] += dto4*(omega_dot[5]*h[3]+omega_dot[4]*h[2]);
+ h[4] += dto4*(omega_dot[5]*h[3]+omega_dot[4]*h[2]);
h[4] *= exp(dto8*omega_dot[0]);
h[3] *= exp(dto4*omega_dot[1]);
- h[3] += dto2*(omega_dot[3]*h[2]);
+ h[3] += dto2*(omega_dot[3]*h[2]);
h[3] *= exp(dto4*omega_dot[1]);
h[5] *= exp(dto4*omega_dot[0]);
- h[5] += dto2*(omega_dot[5]*h[1]);
+ h[5] += dto2*(omega_dot[5]*h[1]);
h[5] *= exp(dto4*omega_dot[0]);
h[4] *= exp(dto8*omega_dot[0]);
- h[4] += dto4*(omega_dot[5]*h[3]+omega_dot[4]*h[2]);
+ h[4] += dto4*(omega_dot[5]*h[3]+omega_dot[4]*h[2]);
h[4] *= exp(dto8*omega_dot[0]);
}
@@ -1075,19 +1075,19 @@ void FixNHCuda::remap()
if (pstyle == TRICLINIC) {
h[4] *= exp(dto8*omega_dot[0]);
- h[4] += dto4*(omega_dot[5]*h[3]+omega_dot[4]*h[2]);
+ h[4] += dto4*(omega_dot[5]*h[3]+omega_dot[4]*h[2]);
h[4] *= exp(dto8*omega_dot[0]);
h[3] *= exp(dto4*omega_dot[1]);
- h[3] += dto2*(omega_dot[3]*h[2]);
+ h[3] += dto2*(omega_dot[3]*h[2]);
h[3] *= exp(dto4*omega_dot[1]);
h[5] *= exp(dto4*omega_dot[0]);
- h[5] += dto2*(omega_dot[5]*h[1]);
+ h[5] += dto2*(omega_dot[5]*h[1]);
h[5] *= exp(dto4*omega_dot[0]);
h[4] *= exp(dto8*omega_dot[0]);
- h[4] += dto4*(omega_dot[5]*h[3]+omega_dot[4]*h[2]);
+ h[4] += dto4*(omega_dot[5]*h[3]+omega_dot[4]*h[2]);
h[4] *= exp(dto8*omega_dot[0]);
domain->yz = h[3];
@@ -1095,10 +1095,10 @@ void FixNHCuda::remap()
domain->xy = h[5];
if (domain->yz < -0.5*domain->yprd || domain->yz > 0.5*domain->yprd ||
- domain->xz < -0.5*domain->xprd || domain->xz > 0.5*domain->xprd ||
- domain->xy < -0.5*domain->xprd || domain->xy > 0.5*domain->xprd)
+ domain->xz < -0.5*domain->xprd || domain->xz > 0.5*domain->xprd ||
+ domain->xy < -0.5*domain->xprd || domain->xy > 0.5*domain->xprd)
error->all(FLERR,"Fix npt/nph has tilted box too far - "
- "box flips are not yet implemented");
+ "box flips are not yet implemented");
}
domain->set_global_box();
@@ -1110,7 +1110,7 @@ void FixNHCuda::remap()
else {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
- domain->lamda2x(x[i],x[i]);
+ domain->lamda2x(x[i],x[i]);
}
if (nrigid)
@@ -1119,7 +1119,7 @@ void FixNHCuda::remap()
}
/* ----------------------------------------------------------------------
- pack entire state of Fix into one write
+ pack entire state of Fix into one write
------------------------------------------------------------------------- */
void FixNHCuda::write_restart(FILE *fp)
@@ -1163,9 +1163,9 @@ void FixNHCuda::write_restart(FILE *fp)
list[n++] = mpchain;
if (mpchain) {
for (int ich = 0; ich < mpchain; ich++)
- list[n++] = etap[ich];
+ list[n++] = etap[ich];
for (int ich = 0; ich < mpchain; ich++)
- list[n++] = etap_dot[ich];
+ list[n++] = etap_dot[ich];
}
list[n++] = deviatoric_flag;
@@ -1189,7 +1189,7 @@ void FixNHCuda::write_restart(FILE *fp)
}
/* ----------------------------------------------------------------------
- use state info from restart file to restart the Fix
+ use state info from restart file to restart the Fix
------------------------------------------------------------------------- */
void FixNHCuda::restart(char *buf)
@@ -1201,9 +1201,9 @@ void FixNHCuda::restart(char *buf)
int m = static_cast<int> (list[n++]);
if (tstat_flag && m == mtchain) {
for (int ich = 0; ich < mtchain; ich++)
- eta[ich] = list[n++];
+ eta[ich] = list[n++];
for (int ich = 0; ich < mtchain; ich++)
- eta_dot[ich] = list[n++];
+ eta_dot[ich] = list[n++];
} else n += 2*m;
}
flag = static_cast<int> (list[n++]);
@@ -1225,9 +1225,9 @@ void FixNHCuda::restart(char *buf)
int m = static_cast<int> (list[n++]);
if (pstat_flag && m == mpchain) {
for (int ich = 0; ich < mpchain; ich++)
- etap[ich] = list[n++];
+ etap[ich] = list[n++];
for (int ich = 0; ich < mpchain; ich++)
- etap_dot[ich] = list[n++];
+ etap_dot[ich] = list[n++];
} else n+=2*m;
flag = static_cast<int> (list[n++]);
if (flag) {
@@ -1269,8 +1269,8 @@ int FixNHCuda::modify_param(int narg, char **arg)
if (pstat_flag) {
icompute = modify->find_compute(id_press);
- if (icompute < 0)
- error->all(FLERR,"Pressure ID for fix modify does not exist");
+ if (icompute < 0)
+ error->all(FLERR,"Pressure ID for fix modify does not exist");
modify->compute[icompute]->reset_extra_compute_fix(id_temp);
}
@@ -1323,7 +1323,7 @@ double FixNHCuda::compute_scalar()
// M = mtchain
// p_eta_k = Q_k*eta_dot[k-1]
// Q_1 = L*k*T/t_freq^2
- // Q_k = k*T/t_freq^2, k > 1
+ // Q_k = k*T/t_freq^2, k > 1
if (tstat_flag) {
energy += lkt * eta[0] + 0.5*eta_mass[0]*eta_dot[0]*eta_dot[0];
@@ -1339,16 +1339,16 @@ double FixNHCuda::compute_scalar()
// W = N*k*T/p_freq^2
// sum is over barostatted dimensions
- if (pstat_flag) {
+ if (pstat_flag) {
for (i = 0; i < 3; i++)
if (p_flag[i])
- energy += 0.5*omega_dot[i]*omega_dot[i]*omega_mass[i] +
- p_hydro*(volume-vol0) / (pdim*nktv2p);
+ energy += 0.5*omega_dot[i]*omega_dot[i]*omega_mass[i] +
+ p_hydro*(volume-vol0) / (pdim*nktv2p);
if (pstyle == TRICLINIC) {
for (i = 3; i < 6; i++)
- if (p_flag[i])
- energy += 0.5*omega_dot[i]*omega_dot[i]*omega_mass[i];
+ if (p_flag[i])
+ energy += 0.5*omega_dot[i]*omega_dot[i]*omega_mass[i];
}
// extra contributions from thermostat chain for barostat
@@ -1356,8 +1356,8 @@ double FixNHCuda::compute_scalar()
if (mpchain) {
energy += lkt_press * etap[0] + 0.5*etap_mass[0]*etap_dot[0]*etap_dot[0];
for (ich = 1; ich < mpchain; ich++)
- energy += kt * etap[ich] +
- 0.5*etap_mass[ich]*etap_dot[ich]*etap_dot[ich];
+ energy += kt * etap[ich] +
+ 0.5*etap_mass[ich]*etap_dot[ich]*etap_dot[ich];
}
// extra contribution from strain energy
@@ -1383,7 +1383,7 @@ double FixNHCuda::compute_vector(int n)
{
int ilen;
- if (tstat_flag) {
+ if (tstat_flag) {
ilen = mtchain;
if (n < ilen) return eta[n];
n -= ilen;
@@ -1392,7 +1392,7 @@ double FixNHCuda::compute_vector(int n)
n -= ilen;
}
- if (pstat_flag) {
+ if (pstat_flag) {
if (pstyle == ISO) {
ilen = 1;
if (n < ilen) return omega[n];
@@ -1406,7 +1406,7 @@ double FixNHCuda::compute_vector(int n)
if (n < ilen) return omega[n];
n -= ilen;
}
-
+
if (pstyle == ISO) {
ilen = 1;
if (n < ilen) return omega_dot[n];
@@ -1420,7 +1420,7 @@ double FixNHCuda::compute_vector(int n)
if (n < ilen) return omega_dot[n];
n -= ilen;
}
-
+
if (mpchain) {
ilen = mpchain;
if (n < ilen) return etap[n];
@@ -1440,88 +1440,88 @@ double FixNHCuda::compute_vector(int n)
if (dimension == 3) volume = domain->xprd * domain->yprd * domain->zprd;
else volume = domain->xprd * domain->yprd;
- if (tstat_flag) {
+ if (tstat_flag) {
ilen = mtchain;
- if (n < ilen) {
+ if (n < ilen) {
ich = n;
if (ich == 0)
- return lkt * eta[0];
+ return lkt * eta[0];
else
- return kt * eta[ich];
+ return kt * eta[ich];
}
n -= ilen;
ilen = mtchain;
if (n < ilen) {
ich = n;
if (ich == 0)
- return 0.5*eta_mass[0]*eta_dot[0]*eta_dot[0];
+ return 0.5*eta_mass[0]*eta_dot[0]*eta_dot[0];
else
- return 0.5*eta_mass[ich]*eta_dot[ich]*eta_dot[ich];
+ return 0.5*eta_mass[ich]*eta_dot[ich]*eta_dot[ich];
}
n -= ilen;
}
- if (pstat_flag) {
+ if (pstat_flag) {
if (pstyle == ISO) {
ilen = 1;
- if (n < ilen)
- return p_hydro*(volume-vol0) / nktv2p;
+ if (n < ilen)
+ return p_hydro*(volume-vol0) / nktv2p;
n -= ilen;
} else if (pstyle == ANISO) {
ilen = 3;
- if (n < ilen)
- if (p_flag[n])
- return p_hydro*(volume-vol0) / (pdim*nktv2p);
- else
- return 0.0;
+ if (n < ilen)
+ if (p_flag[n])
+ return p_hydro*(volume-vol0) / (pdim*nktv2p);
+ else
+ return 0.0;
n -= ilen;
} else {
ilen = 6;
if (n < ilen)
- if (n > 2) return 0.0;
- else if (p_flag[n])
- return p_hydro*(volume-vol0) / (pdim*nktv2p);
- else
- return 0.0;
+ if (n > 2) return 0.0;
+ else if (p_flag[n])
+ return p_hydro*(volume-vol0) / (pdim*nktv2p);
+ else
+ return 0.0;
n -= ilen;
}
-
+
if (pstyle == ISO) {
ilen = 1;
- if (n < ilen)
- return pdim*0.5*omega_dot[n]*omega_dot[n]*omega_mass[n];
+ if (n < ilen)
+ return pdim*0.5*omega_dot[n]*omega_dot[n]*omega_mass[n];
n -= ilen;
} else if (pstyle == ANISO) {
ilen = 3;
- if (n < ilen)
- if (p_flag[n])
- return 0.5*omega_dot[n]*omega_dot[n]*omega_mass[n];
- else return 0.0;
+ if (n < ilen)
+ if (p_flag[n])
+ return 0.5*omega_dot[n]*omega_dot[n]*omega_mass[n];
+ else return 0.0;
n -= ilen;
} else {
ilen = 6;
if (n < ilen)
- if (p_flag[n])
- return 0.5*omega_dot[n]*omega_dot[n]*omega_mass[n];
- else return 0.0;
+ if (p_flag[n])
+ return 0.5*omega_dot[n]*omega_dot[n]*omega_mass[n];
+ else return 0.0;
n -= ilen;
}
-
+
if (mpchain) {
ilen = mpchain;
if (n < ilen) {
- ich = n;
- if (ich == 0) return lkt_press * etap[0];
- else return kt * etap[ich];
+ ich = n;
+ if (ich == 0) return lkt_press * etap[0];
+ else return kt * etap[ich];
}
n -= ilen;
ilen = mpchain;
if (n < ilen) {
- ich = n;
- if (ich == 0)
- return 0.5*etap_mass[0]*etap_dot[0]*etap_dot[0];
- else
- return 0.5*etap_mass[ich]*etap_dot[ich]*etap_dot[ich];
+ ich = n;
+ if (ich == 0)
+ return 0.5*etap_mass[0]*etap_dot[0]*etap_dot[0];
+ else
+ return 0.5*etap_mass[ich]*etap_dot[ich]*etap_dot[ich];
}
n -= ilen;
}
@@ -1529,7 +1529,7 @@ double FixNHCuda::compute_vector(int n)
if (deviatoric_flag) {
ilen = 1;
if (n < ilen)
- return compute_strain_energy();
+ return compute_strain_energy();
n -= ilen;
}
}
@@ -1549,10 +1549,10 @@ void FixNHCuda::reset_dt()
dto = dthalf;
// If using respa, then remap is performed in innermost level
-
+
if (strcmp(update->integrate_style,"respa") == 0)
dto = 0.5*step_respa[0];
-
+
p_freq_max = 0.0;
if (pstat_flag) {
p_freq_max = MAX(p_freq[0],p_freq[1]);
@@ -1598,48 +1598,48 @@ void FixNHCuda::nhc_temp_integrate()
eta_dot[0] += eta_dotdot[0] * ncfac*dt4;
eta_dot[0] *= tdrag_factor;
eta_dot[0] *= expfac;
-
+
factor_eta = exp(-ncfac*dthalf*eta_dot[0]);
- if(which==NOBIAS)
- Cuda_FixNHCuda_nh_v_temp(&cuda->shared_data,groupbit,factor_eta,(igroup == atom->firstgroup)?atom->nfirst:atom->nlocal);
+ if(which==NOBIAS)
+ Cuda_FixNHCuda_nh_v_temp(&cuda->shared_data,groupbit,factor_eta,(igroup == atom->firstgroup)?atom->nfirst:atom->nlocal);
else if(which==BIAS)
{
- if(!temperature->cudable)
- {
- cuda->downloadAll();
- nh_v_temp();
- cuda->cu_v->upload();
- }
- else
- {
- int groupbit_org=temperature->groupbit;
- temperature->groupbit=groupbit;
- temperature->remove_bias_all();
- Cuda_FixNHCuda_nh_v_temp(&cuda->shared_data,groupbit,factor_eta,(igroup == atom->firstgroup)?atom->nfirst:atom->nlocal);
- temperature->restore_bias_all();
- temperature->groupbit=groupbit_org;
- }
-
+ if(!temperature->cudable)
+ {
+ cuda->downloadAll();
+ nh_v_temp();
+ cuda->cu_v->upload();
+ }
+ else
+ {
+ int groupbit_org=temperature->groupbit;
+ temperature->groupbit=groupbit;
+ temperature->remove_bias_all();
+ Cuda_FixNHCuda_nh_v_temp(&cuda->shared_data,groupbit,factor_eta,(igroup == atom->firstgroup)?atom->nfirst:atom->nlocal);
+ temperature->restore_bias_all();
+ temperature->groupbit=groupbit_org;
+ }
+
}
// rescale temperature due to velocity scaling
- // should not be necessary to explicitly recompute the temperature
+ // should not be necessary to explicitly recompute the temperature
t_current *= factor_eta*factor_eta;
kecurrent = tdof * boltz * t_current;
eta_dotdot[0] = (kecurrent - lkt)/eta_mass[0];
-
+
for (ich = 0; ich < mtchain; ich++)
eta[ich] += ncfac*dthalf*eta_dot[ich];
-
+
eta_dot[0] *= expfac;
eta_dot[0] += eta_dotdot[0] * ncfac*dt4;
eta_dot[0] *= expfac;
-
+
for (ich = 1; ich < mtchain; ich++) {
expfac = exp(-ncfac*dt8*eta_dot[ich+1]);
eta_dot[ich] *= expfac;
- eta_dotdot[ich] = (eta_mass[ich-1]*eta_dot[ich-1]*eta_dot[ich-1]
- - boltz * t_target)/eta_mass[ich];
+ eta_dotdot[ich] = (eta_mass[ich-1]*eta_dot[ich-1]*eta_dot[ich-1]
+ - boltz * t_target)/eta_mass[ich];
eta_dot[ich] += eta_dotdot[ich] * ncfac*dt4;
eta_dot[ich] *= expfac;
}
@@ -1663,7 +1663,7 @@ void FixNHCuda::nhc_press_integrate()
if (p_flag[i]) kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i];
if (pstyle == TRICLINIC) {
- for (i = 3; i < 6; i++)
+ for (i = 3; i < 6; i++)
if (p_flag[i]) kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i];
}
@@ -1679,46 +1679,46 @@ void FixNHCuda::nhc_press_integrate()
etap_dot[ich] *= pdrag_factor;
etap_dot[ich] *= expfac;
}
-
+
expfac = exp(-ncfac*dt8*etap_dot[1]);
etap_dot[0] *= expfac;
etap_dot[0] += etap_dotdot[0] * ncfac*dt4;
etap_dot[0] *= pdrag_factor;
etap_dot[0] *= expfac;
-
+
for (ich = 0; ich < mpchain; ich++)
etap[ich] += ncfac*dthalf*etap_dot[ich];
-
+
factor_etap = exp(-ncfac*dthalf*etap_dot[0]);
for (i = 0; i < 3; i++)
if (p_flag[i]) omega_dot[i] *= factor_etap;
-
+
if (pstyle == TRICLINIC) {
for (i = 3; i < 6; i++)
- if (p_flag[i]) omega_dot[i] *= factor_etap;
+ if (p_flag[i]) omega_dot[i] *= factor_etap;
}
-
+
kecurrent = 0.0;
for (i = 0; i < 3; i++)
if (p_flag[i]) kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i];
-
+
if (pstyle == TRICLINIC) {
- for (i = 3; i < 6; i++)
- if (p_flag[i]) kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i];
+ for (i = 3; i < 6; i++)
+ if (p_flag[i]) kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i];
}
-
+
etap_dotdot[0] = (kecurrent - lkt_press)/etap_mass[0];
-
+
etap_dot[0] *= expfac;
etap_dot[0] += etap_dotdot[0] * ncfac*dt4;
etap_dot[0] *= expfac;
-
+
for (ich = 1; ich < mpchain; ich++) {
expfac = exp(-ncfac*dt8*etap_dot[ich+1]);
etap_dot[ich] *= expfac;
- etap_dotdot[ich] =
- (etap_mass[ich-1]*etap_dot[ich-1]*etap_dot[ich-1] - boltz*t_target) /
- etap_mass[ich];
+ etap_dotdot[ich] =
+ (etap_mass[ich-1]*etap_dot[ich-1]*etap_dot[ich-1] - boltz*t_target) /
+ etap_mass[ich];
etap_dot[ich] += etap_dotdot[ich] * ncfac*dt4;
etap_dot[ich] *= expfac;
}
@@ -1744,33 +1744,33 @@ void FixNHCuda::nh_v_press()
if (which == NOBIAS) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
- v[i][0] *= factor[0];
- v[i][1] *= factor[1];
- v[i][2] *= factor[2];
- if (pstyle == TRICLINIC) {
- v[i][0] += -dthalf*(v[i][1]*omega_dot[5] + v[i][2]*omega_dot[4]);
- v[i][1] += -dthalf*v[i][2]*omega_dot[3];
- }
- v[i][0] *= factor[0];
- v[i][1] *= factor[1];
- v[i][2] *= factor[2];
+ v[i][0] *= factor[0];
+ v[i][1] *= factor[1];
+ v[i][2] *= factor[2];
+ if (pstyle == TRICLINIC) {
+ v[i][0] += -dthalf*(v[i][1]*omega_dot[5] + v[i][2]*omega_dot[4]);
+ v[i][1] += -dthalf*v[i][2]*omega_dot[3];
+ }
+ v[i][0] *= factor[0];
+ v[i][1] *= factor[1];
+ v[i][2] *= factor[2];
}
}
} else if (which == BIAS) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
- temperature->remove_bias(i,v[i]);
- v[i][0] *= factor[0];
- v[i][1] *= factor[1];
- v[i][2] *= factor[2];
- if (pstyle == TRICLINIC) {
- v[i][0] += -dthalf*(v[i][1]*omega_dot[5] + v[i][2]*omega_dot[4]);
- v[i][1] += -dthalf*v[i][2]*omega_dot[3];
- }
- v[i][0] *= factor[0];
- v[i][1] *= factor[1];
- v[i][2] *= factor[2];
- temperature->restore_bias(i,v[i]);
+ temperature->remove_bias(i,v[i]);
+ v[i][0] *= factor[0];
+ v[i][1] *= factor[1];
+ v[i][2] *= factor[2];
+ if (pstyle == TRICLINIC) {
+ v[i][0] += -dthalf*(v[i][1]*omega_dot[5] + v[i][2]*omega_dot[4]);
+ v[i][1] += -dthalf*v[i][2]*omega_dot[3];
+ }
+ v[i][0] *= factor[0];
+ v[i][1] *= factor[1];
+ v[i][2] *= factor[2];
+ temperature->restore_bias(i,v[i]);
}
}
}
@@ -1795,19 +1795,19 @@ void FixNHCuda::nve_v()
if (rmass) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
- dtfm = dtf / rmass[i];
- v[i][0] += dtfm*f[i][0];
- v[i][1] += dtfm*f[i][1];
- v[i][2] += dtfm*f[i][2];
+ dtfm = dtf / rmass[i];
+ v[i][0] += dtfm*f[i][0];
+ v[i][1] += dtfm*f[i][1];
+ v[i][2] += dtfm*f[i][2];
}
}
} else {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
- dtfm = dtf / mass[type[i]];
- v[i][0] += dtfm*f[i][0];
- v[i][1] += dtfm*f[i][1];
- v[i][2] += dtfm*f[i][2];
+ dtfm = dtf / mass[type[i]];
+ v[i][0] += dtfm*f[i][0];
+ v[i][1] += dtfm*f[i][1];
+ v[i][2] += dtfm*f[i][2];
}
}
}
@@ -1850,24 +1850,24 @@ void FixNHCuda::nh_v_temp()
if (which == NOBIAS) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
- v[i][0] *= factor_eta;
- v[i][1] *= factor_eta;
- v[i][2] *= factor_eta;
+ v[i][0] *= factor_eta;
+ v[i][1] *= factor_eta;
+ v[i][2] *= factor_eta;
}
}
} else if (which == BIAS) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
- temperature->remove_bias(i,v[i]);
- v[i][0] *= factor_eta;
- v[i][1] *= factor_eta;
- v[i][2] *= factor_eta;
- temperature->restore_bias(i,v[i]);
+ temperature->remove_bias(i,v[i]);
+ v[i][0] *= factor_eta;
+ v[i][1] *= factor_eta;
+ v[i][2] *= factor_eta;
+ temperature->restore_bias(i,v[i]);
}
}
}
}
-
+
/* ----------------------------------------------------------------------
compute sigma tensor
needed whenever p_target or h0_inv changes
@@ -1875,7 +1875,7 @@ void FixNHCuda::nh_v_temp()
void FixNHCuda::compute_sigma()
{
- // if nreset_h0 > 0, reset vol0 and h0_inv
+ // if nreset_h0 > 0, reset vol0 and h0_inv
// every nreset_h0 timesteps
if (nreset_h0 > 0) {
@@ -1894,37 +1894,37 @@ void FixNHCuda::compute_sigma()
// generate upper-triangular half of
// sigma = vol0*h0inv*(p_target-p_hydro)*h0inv^t
- // units of sigma are are PV/L^2 e.g. atm.A
+ // units of sigma are are PV/L^2 e.g. atm.A
//
// [ 0 5 4 ] [ 0 5 4 ] [ 0 5 4 ] [ 0 - - ]
// [ 5 1 3 ] = [ - 1 3 ] [ 5 1 3 ] [ 5 1 - ]
// [ 4 3 2 ] [ - - 2 ] [ 4 3 2 ] [ 4 3 2 ]
- sigma[0] =
+ sigma[0] =
vol0*(h0_inv[0]*((p_target[0]-p_hydro)*h0_inv[0] +
- p_target[5]*h0_inv[5]+p_target[4]*h0_inv[4]) +
- h0_inv[5]*(p_target[5]*h0_inv[0] +
- (p_target[1]-p_hydro)*h0_inv[5]+p_target[3]*h0_inv[4]) +
- h0_inv[4]*(p_target[4]*h0_inv[0]+p_target[3]*h0_inv[5] +
- (p_target[2]-p_hydro)*h0_inv[4]));
- sigma[1] =
+ p_target[5]*h0_inv[5]+p_target[4]*h0_inv[4]) +
+ h0_inv[5]*(p_target[5]*h0_inv[0] +
+ (p_target[1]-p_hydro)*h0_inv[5]+p_target[3]*h0_inv[4]) +
+ h0_inv[4]*(p_target[4]*h0_inv[0]+p_target[3]*h0_inv[5] +
+ (p_target[2]-p_hydro)*h0_inv[4]));
+ sigma[1] =
vol0*(h0_inv[1]*((p_target[1]-p_hydro)*h0_inv[1] +
- p_target[3]*h0_inv[3]) +
- h0_inv[3]*(p_target[3]*h0_inv[1] +
- (p_target[2]-p_hydro)*h0_inv[3]));
- sigma[2] =
+ p_target[3]*h0_inv[3]) +
+ h0_inv[3]*(p_target[3]*h0_inv[1] +
+ (p_target[2]-p_hydro)*h0_inv[3]));
+ sigma[2] =
vol0*(h0_inv[2]*((p_target[2]-p_hydro)*h0_inv[2]));
- sigma[3] =
+ sigma[3] =
vol0*(h0_inv[1]*(p_target[3]*h0_inv[2]) +
- h0_inv[3]*((p_target[2]-p_hydro)*h0_inv[2]));
- sigma[4] =
+ h0_inv[3]*((p_target[2]-p_hydro)*h0_inv[2]));
+ sigma[4] =
vol0*(h0_inv[0]*(p_target[4]*h0_inv[2]) +
- h0_inv[5]*(p_target[3]*h0_inv[2]) +
- h0_inv[4]*((p_target[2]-p_hydro)*h0_inv[2]));
- sigma[5] =
+ h0_inv[5]*(p_target[3]*h0_inv[2]) +
+ h0_inv[4]*((p_target[2]-p_hydro)*h0_inv[2]));
+ sigma[5] =
vol0*(h0_inv[0]*(p_target[5]*h0_inv[1]+p_target[4]*h0_inv[3]) +
- h0_inv[5]*((p_target[1]-p_hydro)*h0_inv[1]+p_target[3]*h0_inv[3]) +
- h0_inv[4]*(p_target[3]*h0_inv[1]+(p_target[2]-p_hydro)*h0_inv[3]));
+ h0_inv[5]*((p_target[1]-p_hydro)*h0_inv[1]+p_target[3]*h0_inv[3]) +
+ h0_inv[4]*(p_target[3]*h0_inv[1]+(p_target[2]-p_hydro)*h0_inv[3]));
}
/* ----------------------------------------------------------------------
@@ -1933,20 +1933,20 @@ void FixNHCuda::compute_sigma()
double FixNHCuda::compute_strain_energy()
{
- // compute strain energy = 0.5*Tr(sigma*h*h^t) in energy units
+ // compute strain energy = 0.5*Tr(sigma*h*h^t) in energy units
double* h = domain->h;
double d0,d1,d2;
- d0 =
+ d0 =
sigma[0]*(h[0]*h[0]+h[5]*h[5]+h[4]*h[4]) +
sigma[5]*( h[1]*h[5]+h[3]*h[4]) +
sigma[4]*( h[2]*h[4]);
- d1 =
+ d1 =
sigma[5]*( h[5]*h[1]+h[4]*h[3]) +
sigma[1]*( h[1]*h[1]+h[3]*h[3]) +
sigma[3]*( h[2]*h[3]);
- d2 =
+ d2 =
sigma[4]*( h[4]*h[2]) +
sigma[3]*( h[3]*h[2]) +
sigma[2]*( h[2]*h[2]);
@@ -1962,30 +1962,30 @@ double FixNHCuda::compute_strain_energy()
void FixNHCuda::compute_deviatoric()
{
// generate upper-triangular part of h*sigma*h^t
- // units of fdev are are PV, e.g. atm*A^3
+ // units of fdev are are PV, e.g. atm*A^3
// [ 0 5 4 ] [ 0 5 4 ] [ 0 5 4 ] [ 0 - - ]
// [ 5 1 3 ] = [ - 1 3 ] [ 5 1 3 ] [ 5 1 - ]
// [ 4 3 2 ] [ - - 2 ] [ 4 3 2 ] [ 4 3 2 ]
-
+
double* h = domain->h;
-
- fdev[0] =
+
+ fdev[0] =
h[0]*(sigma[0]*h[0]+sigma[5]*h[5]+sigma[4]*h[4]) +
h[5]*(sigma[5]*h[0]+sigma[1]*h[5]+sigma[3]*h[4]) +
h[4]*(sigma[4]*h[0]+sigma[3]*h[5]+sigma[2]*h[4]);
- fdev[1] =
+ fdev[1] =
h[1]*( sigma[1]*h[1]+sigma[3]*h[3]) +
h[3]*( sigma[3]*h[1]+sigma[2]*h[3]);
- fdev[2] =
+ fdev[2] =
h[2]*( sigma[2]*h[2]);
- fdev[3] =
+ fdev[3] =
h[1]*( sigma[3]*h[2]) +
h[3]*( sigma[2]*h[2]);
- fdev[4] =
+ fdev[4] =
h[0]*( sigma[4]*h[2]) +
h[5]*( sigma[3]*h[2]) +
h[4]*( sigma[2]*h[2]);
- fdev[5] =
+ fdev[5] =
h[0]*( sigma[5]*h[1]+sigma[4]*h[3]) +
h[5]*( sigma[1]*h[1]+sigma[3]*h[3]) +
h[4]*( sigma[3]*h[1]+sigma[2]*h[3]);
@@ -2001,7 +2001,7 @@ void FixNHCuda::compute_press_target()
if (update->endstep > update->beginstep)
delta /= update->endstep - update->beginstep;
else delta = 0.0;
-
+
p_hydro = 0.0;
for (int i = 0; i < 3; i++)
if (p_flag[i]) {
@@ -2034,21 +2034,21 @@ void FixNHCuda::nh_omega_dot()
mtk_term1 = 0.0;
if (mtk_flag)
- if (pstyle == ISO) {
+ if (pstyle == ISO) {
mtk_term1 = tdof * boltz * t_current;
mtk_term1 /= pdim * atom->natoms;
} else {
double *mvv_current = temperature->vector;
for (int i = 0; i < 3; i++)
- if (p_flag[i])
- mtk_term1 += mvv_current[i];
+ if (p_flag[i])
+ mtk_term1 += mvv_current[i];
mtk_term1 /= pdim * atom->natoms;
}
-
+
for (int i = 0; i < 3; i++)
if (p_flag[i]) {
f_omega = (p_current[i]-p_hydro)*volume /
- (omega_mass[i] * nktv2p) + mtk_term1 / omega_mass[i];
+ (omega_mass[i] * nktv2p) + mtk_term1 / omega_mass[i];
if (deviatoric_flag) f_omega -= fdev[i]/(omega_mass[i] * nktv2p);
omega_dot[i] += f_omega*dthalf;
omega_dot[i] *= pdrag_factor;
@@ -2058,20 +2058,19 @@ void FixNHCuda::nh_omega_dot()
if (mtk_flag) {
for (int i = 0; i < 3; i++)
if (p_flag[i])
- mtk_term2 += omega_dot[i];
+ mtk_term2 += omega_dot[i];
mtk_term2 /= pdim * atom->natoms;
}
if (pstyle == TRICLINIC) {
for (int i = 3; i < 6; i++) {
if (p_flag[i]) {
- f_omega = p_current[i]*volume/(omega_mass[i] * nktv2p);
- if (deviatoric_flag)
- f_omega -= fdev[i]/(omega_mass[i] * nktv2p);
- omega_dot[i] += f_omega*dthalf;
- omega_dot[i] *= pdrag_factor;
+ f_omega = p_current[i]*volume/(omega_mass[i] * nktv2p);
+ if (deviatoric_flag)
+ f_omega -= fdev[i]/(omega_mass[i] * nktv2p);
+ omega_dot[i] += f_omega*dthalf;
+ omega_dot[i] *= pdrag_factor;
}
- }
+ }
}
}
-
diff --git a/src/USER-CUDA/fix_nh_cuda.h b/src/USER-CUDA/fix_nh_cuda.h
index 8c192b56dd6c514c910813c285581f127ef80fef..e57afe896aed7f2573d966f33c310136c5fc9d72 100644
--- a/src/USER-CUDA/fix_nh_cuda.h
+++ b/src/USER-CUDA/fix_nh_cuda.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -76,13 +76,13 @@ class FixNHCuda : public Fix {
double *eta_dotdot;
double *eta_mass;
int mtchain; // length of chain
-
+
double *etap; // chain thermostat for barostat
double *etap_dot;
double *etap_dotdot;
double *etap_mass;
int mpchain; // length of chain
-
+
int mtk_flag; // 0 if using Hoover barostat
double mtk_term1,mtk_term2;
int mtchain_default_flag;
@@ -117,7 +117,7 @@ class FixNHCuda : public Fix {
double compute_strain_energy();
void compute_press_target();
void nh_omega_dot();
-
+
X_FLOAT triggerneighsq;
};
diff --git a/src/USER-CUDA/fix_npt_cuda.cpp b/src/USER-CUDA/fix_npt_cuda.cpp
index db77ec007253c97106718a34a06b6ebf361dc5b8..ea2dd1fe04e1d2319483fdcb4daf756dcc8d9750 100644
--- a/src/USER-CUDA/fix_npt_cuda.cpp
+++ b/src/USER-CUDA/fix_npt_cuda.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -45,7 +45,7 @@ FixNPTCuda::FixNPTCuda(LAMMPS *lmp, int narg, char **arg) :
id_temp = new char[n];
strcpy(id_temp,id);
strcat(id_temp,"_temp");
-
+
char **newarg = new char*[3];
newarg[0] = id_temp;
newarg[1] = (char *) "all";
@@ -63,7 +63,7 @@ FixNPTCuda::FixNPTCuda(LAMMPS *lmp, int narg, char **arg) :
id_press = new char[n];
strcpy(id_press,id);
strcat(id_press,"_press");
-
+
newarg = new char*[4];
newarg[0] = id_press;
newarg[1] = (char *) "all";
diff --git a/src/USER-CUDA/fix_npt_cuda.h b/src/USER-CUDA/fix_npt_cuda.h
index 1dc5f5af3547c62652dad62b156dd957a6072c80..37ff8ffc5363d09d0a1ef83ffde8404284c1567d 100644
--- a/src/USER-CUDA/fix_npt_cuda.h
+++ b/src/USER-CUDA/fix_npt_cuda.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-CUDA/fix_nve_cuda.cpp b/src/USER-CUDA/fix_nve_cuda.cpp
index 00ed8882455eea139ab0946af221cbf36986b2e6..992bb5d5d9151e9fc428cfc02852c83fa2536747 100644
--- a/src/USER-CUDA/fix_nve_cuda.cpp
+++ b/src/USER-CUDA/fix_nve_cuda.cpp
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -28,7 +28,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -61,37 +61,37 @@ FixNVECuda::FixNVECuda(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,"You cannot use a /cuda class, without activating 'cuda' acceleration. Provide '-c on' as command-line argument to LAMMPS..");
if (strcmp(style,"nve/sphere") != 0 && narg < 3)
- error->all(FLERR,"Illegal fix nve command");
-
- time_integrate = 1;
+ error->all(FLERR,"Illegal fix nve command");
+
+ time_integrate = 1;
}
/* ---------------------------------------------------------------------- */
int FixNVECuda::setmask()
{
- int mask = 0;
- mask |= INITIAL_INTEGRATE_CUDA;
- mask |= FINAL_INTEGRATE_CUDA;
- // mask |= INITIAL_INTEGRATE_RESPA_CUDA;
- // mask |= FINAL_INTEGRATE_RESPA_CUDA;
- return mask;
+ int mask = 0;
+ mask |= INITIAL_INTEGRATE_CUDA;
+ mask |= FINAL_INTEGRATE_CUDA;
+ // mask |= INITIAL_INTEGRATE_RESPA_CUDA;
+ // mask |= FINAL_INTEGRATE_RESPA_CUDA;
+ return mask;
}
/* ---------------------------------------------------------------------- */
void FixNVECuda::init()
{
- dtv = update->dt;
- dtf = 0.5 * update->dt * force->ftm2v;
-
- if (strstr(update->integrate_style,"respa"))
- step_respa = ((Respa *) update->integrate)->step;
-
- triggerneighsq= cuda->shared_data.atom.triggerneighsq;
+ dtv = update->dt;
+ dtf = 0.5 * update->dt * force->ftm2v;
+
+ if (strstr(update->integrate_style,"respa"))
+ step_respa = ((Respa *) update->integrate)->step;
+
+ triggerneighsq= cuda->shared_data.atom.triggerneighsq;
cuda->neighbor_decide_by_integrator=1;
Cuda_FixNVECuda_Init(&cuda->shared_data,dtv,dtf);
-
+
}
/* ----------------------------------------------------------------------
@@ -100,58 +100,58 @@ void FixNVECuda::init()
void FixNVECuda::initial_integrate(int vflag)
{
- if(triggerneighsq!=cuda->shared_data.atom.triggerneighsq)
- {
- triggerneighsq= cuda->shared_data.atom.triggerneighsq;
- Cuda_FixNVECuda_Init(&cuda->shared_data,dtv,dtf);
- }
- int nlocal = atom->nlocal;
- if(igroup == atom->firstgroup) nlocal = atom->nfirst;
-
- Cuda_FixNVECuda_InitialIntegrate(& cuda->shared_data, groupbit,nlocal);
+ if(triggerneighsq!=cuda->shared_data.atom.triggerneighsq)
+ {
+ triggerneighsq= cuda->shared_data.atom.triggerneighsq;
+ Cuda_FixNVECuda_Init(&cuda->shared_data,dtv,dtf);
+ }
+ int nlocal = atom->nlocal;
+ if(igroup == atom->firstgroup) nlocal = atom->nfirst;
+
+ Cuda_FixNVECuda_InitialIntegrate(& cuda->shared_data, groupbit,nlocal);
}
/* ---------------------------------------------------------------------- */
void FixNVECuda::final_integrate()
{
- int nlocal = atom->nlocal;
- if(igroup == atom->firstgroup) nlocal = atom->nfirst;
-
- Cuda_FixNVECuda_FinalIntegrate(& cuda->shared_data, groupbit,nlocal);
+ int nlocal = atom->nlocal;
+ if(igroup == atom->firstgroup) nlocal = atom->nfirst;
+
+ Cuda_FixNVECuda_FinalIntegrate(& cuda->shared_data, groupbit,nlocal);
}
/* ---------------------------------------------------------------------- */
void FixNVECuda::initial_integrate_respa(int vflag, int ilevel, int flag)
{
- //this point should not be reached yet since RESPA is not supported
- if (flag) return; // only used by NPT,NPH
-
- dtv = step_respa[ilevel];
- dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
-
- // innermost level - NVE update of v and x
- // all other levels - NVE update of v
-
- if(ilevel == 0) initial_integrate(vflag);
- else final_integrate();
+ //this point should not be reached yet since RESPA is not supported
+ if (flag) return; // only used by NPT,NPH
+
+ dtv = step_respa[ilevel];
+ dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
+
+ // innermost level - NVE update of v and x
+ // all other levels - NVE update of v
+
+ if(ilevel == 0) initial_integrate(vflag);
+ else final_integrate();
}
/* ---------------------------------------------------------------------- */
void FixNVECuda::final_integrate_respa(int ilevel, int iloop)
{
- //this point should not be reached yet since RESPA is not supported
- dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
- final_integrate();
+ //this point should not be reached yet since RESPA is not supported
+ dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
+ final_integrate();
}
/* ---------------------------------------------------------------------- */
void FixNVECuda::reset_dt()
{
- dtv = update->dt;
- dtf = 0.5 * update->dt * force->ftm2v;
- Cuda_FixNVECuda_Init(&cuda->shared_data,dtv,dtf);
+ dtv = update->dt;
+ dtf = 0.5 * update->dt * force->ftm2v;
+ Cuda_FixNVECuda_Init(&cuda->shared_data,dtv,dtf);
}
diff --git a/src/USER-CUDA/fix_nve_cuda.h b/src/USER-CUDA/fix_nve_cuda.h
index 6968297610a410ad4e5c61156bf4bb4cc0160284..f649db26a9882f3a9e652abcddc5053a738bcae4 100644
--- a/src/USER-CUDA/fix_nve_cuda.h
+++ b/src/USER-CUDA/fix_nve_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -37,24 +37,24 @@ namespace LAMMPS_NS {
class FixNVECuda : public Fix
{
- public:
- FixNVECuda(class LAMMPS *, int, char **);
- int setmask();
- virtual void init();
- virtual void initial_integrate(int);
- virtual void final_integrate();
- void initial_integrate_respa(int, int, int);
- void final_integrate_respa(int, int);
- void reset_dt();
-
- X_FLOAT triggerneighsq;
-
- protected:
- class Cuda *cuda;
- double dtv, dtf;
- double *step_respa;
- int mass_require;
-
+ public:
+ FixNVECuda(class LAMMPS *, int, char **);
+ int setmask();
+ virtual void init();
+ virtual void initial_integrate(int);
+ virtual void final_integrate();
+ void initial_integrate_respa(int, int, int);
+ void final_integrate_respa(int, int);
+ void reset_dt();
+
+ X_FLOAT triggerneighsq;
+
+ protected:
+ class Cuda *cuda;
+ double dtv, dtf;
+ double *step_respa;
+ int mass_require;
+
};
}
diff --git a/src/USER-CUDA/fix_nvt_cuda.cpp b/src/USER-CUDA/fix_nvt_cuda.cpp
index 8438f2d3f6b50ec52fdc5fbd7cd52f49dd993357..e1380b0005c976a845339906f9f5b274205b6987 100644
--- a/src/USER-CUDA/fix_nvt_cuda.cpp
+++ b/src/USER-CUDA/fix_nvt_cuda.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -40,7 +40,7 @@ FixNVTCuda::FixNVTCuda(LAMMPS *lmp, int narg, char **arg) :
id_temp = new char[n];
strcpy(id_temp,id);
strcat(id_temp,"_temp");
-
+
char **newarg = new char*[3];
newarg[0] = id_temp;
newarg[1] = group->names[igroup];
diff --git a/src/USER-CUDA/fix_nvt_cuda.h b/src/USER-CUDA/fix_nvt_cuda.h
index 02e5ca3d5813655f980242ad924352444a22b270..227dbf6a948e2e517eaf16481d5354afe700a140 100644
--- a/src/USER-CUDA/fix_nvt_cuda.h
+++ b/src/USER-CUDA/fix_nvt_cuda.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-CUDA/fix_set_force_cuda.cpp b/src/USER-CUDA/fix_set_force_cuda.cpp
index 4726cca0bb74ea2fa94d8e6c4d50a935e78ea35e..1010c087ad46525e2859c8568774089518074f16 100644
--- a/src/USER-CUDA/fix_set_force_cuda.cpp
+++ b/src/USER-CUDA/fix_set_force_cuda.cpp
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -45,7 +45,7 @@ FixSetForceCuda::FixSetForceCuda(LAMMPS *lmp, int narg, char **arg) :
cuda = lmp->cuda;
if(cuda == NULL)
error->all(FLERR,"You cannot use a /cuda class, without activating 'cuda' acceleration. Provide '-c on' as command-line argument to LAMMPS..");
-
+
if (narg != 6) error->all(FLERR,"Illegal fix setforce/cuda command");
vector_flag = 1;
@@ -83,7 +83,7 @@ int FixSetForceCuda::setmask()
void FixSetForceCuda::init()
{
if(not cu_foriginal)
- cu_foriginal = new cCudaData<double, F_FLOAT, x> (foriginal,3);
+ cu_foriginal = new cCudaData<double, F_FLOAT, x> (foriginal,3);
if (strstr(update->integrate_style,"respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;
}
@@ -93,14 +93,14 @@ void FixSetForceCuda::init()
void FixSetForceCuda::setup(int vflag)
{
MYDBG( printf("# CUDA: FixSetForceCuda::setup\n"); )
-
+
if (strstr(update->integrate_style,"verlet"))
{
Cuda_FixSetForceCuda_Init(&cuda->shared_data);
cuda->cu_f->upload();
post_force(vflag);
cuda->cu_f->download();
-
+
}
else {
((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
@@ -136,26 +136,26 @@ void FixSetForceCuda::post_force_respa(int vflag, int ilevel, int iloop)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
else {
- cuda->cu_f->download();
- cuda->cu_mask->download();
-
+ cuda->cu_f->download();
+ cuda->cu_mask->download();
+
double **f = atom->f;
int *mask = atom->mask;
int nlocal = atom->nlocal;
foriginal[0] = foriginal[1] = foriginal[2] = 0.0;
force_flag = 0;
-
+
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- foriginal[0] += f[i][0];
- foriginal[1] += f[i][1];
- foriginal[2] += f[i][2];
- if (flagx) f[i][0] = 0.0;
- if (flagy) f[i][1] = 0.0;
- if (flagz) f[i][2] = 0.0;
+ foriginal[0] += f[i][0];
+ foriginal[1] += f[i][1];
+ foriginal[2] += f[i][2];
+ if (flagx) f[i][0] = 0.0;
+ if (flagy) f[i][1] = 0.0;
+ if (flagz) f[i][2] = 0.0;
}
- cuda->cu_f->upload();
+ cuda->cu_f->upload();
}
}
diff --git a/src/USER-CUDA/fix_set_force_cuda.h b/src/USER-CUDA/fix_set_force_cuda.h
index c233294a5b1b8c7a5b43325cf4391313b9cc18ca..8fb523361cef0062e7a04c8708a0a1da8e2698d9 100644
--- a/src/USER-CUDA/fix_set_force_cuda.h
+++ b/src/USER-CUDA/fix_set_force_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -49,10 +49,10 @@ class FixSetForceCuda : public Fix {
private:
class Cuda *cuda;
- int flagx,flagy,flagz;
+ int flagx,flagy,flagz;
double xvalue,yvalue,zvalue;
double foriginal[3],foriginal_all[3];
- cCudaData<double , F_FLOAT , x>* cu_foriginal;
+ cCudaData<double , F_FLOAT , x>* cu_foriginal;
int force_flag;
int nlevels_respa;
};
diff --git a/src/USER-CUDA/fix_shake_cuda.cpp b/src/USER-CUDA/fix_shake_cuda.cpp
index 0fb8eaf6f642fb27dd00ca4cb7b0803f9854de7c..5b155921d7420cfe2a3c19881eb962662b029bc8 100644
--- a/src/USER-CUDA/fix_shake_cuda.cpp
+++ b/src/USER-CUDA/fix_shake_cuda.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -79,7 +79,7 @@ FixShakeCuda::FixShakeCuda(LAMMPS *lmp, int narg, char **arg) :
cu_list = NULL;
cu_bond_distance = NULL;
cu_angle_distance = NULL;
- cu_virial = new cCudaData<double , ENERGY_FLOAT , xx >(virial,6);
+ cu_virial = new cCudaData<double , ENERGY_FLOAT , xx >(virial,6);
grow_arrays(atom->nmax);
atom->add_callback(0);
@@ -123,20 +123,20 @@ FixShakeCuda::FixShakeCuda(LAMMPS *lmp, int narg, char **arg) :
} else if (mode == 'b') {
int i = atoi(arg[next]);
- if (i < 1 || i > atom->nbondtypes)
- error->all(FLERR,"Invalid bond type index for fix shake");
+ if (i < 1 || i > atom->nbondtypes)
+ error->all(FLERR,"Invalid bond type index for fix shake");
bond_flag[i] = 1;
} else if (mode == 'a') {
int i = atoi(arg[next]);
- if (i < 1 || i > atom->nangletypes)
- error->all(FLERR,"Invalid angle type index for fix shake");
+ if (i < 1 || i > atom->nangletypes)
+ error->all(FLERR,"Invalid angle type index for fix shake");
angle_flag[i] = 1;
} else if (mode == 't') {
int i = atoi(arg[next]);
- if (i < 1 || i > atom->ntypes)
- error->all(FLERR,"Invalid atom type index for fix shake");
+ if (i < 1 || i > atom->ntypes)
+ error->all(FLERR,"Invalid atom type index for fix shake");
type_flag[i] = 1;
} else if (mode == 'm') {
@@ -156,7 +156,7 @@ FixShakeCuda::FixShakeCuda(LAMMPS *lmp, int narg, char **arg) :
cu_bond_distance = new cCudaData<double, X_FLOAT, xx> (bond_distance, atom->nbondtypes+1);
cu_angle_distance = new cCudaData<double, X_FLOAT, xx> (angle_distance, atom->nangletypes+1);
-
+
// allocate statistics arrays
if (output_every) {
@@ -191,11 +191,11 @@ FixShakeCuda::FixShakeCuda(LAMMPS *lmp, int narg, char **arg) :
maxlist = 0;
list = NULL;
Cuda_FixShakeCuda_Init(&cuda->shared_data,dtv, dtfsq,
- cu_shake_flag->dev_data(),cu_shake_atom->dev_data(),cu_shake_type->dev_data(), cu_xshake->dev_data(),
- cu_bond_distance->dev_data(),cu_angle_distance->dev_data(),cu_virial->dev_data(),
- max_iter,tolerance);
-
-
+ cu_shake_flag->dev_data(),cu_shake_atom->dev_data(),cu_shake_type->dev_data(), cu_xshake->dev_data(),
+ cu_bond_distance->dev_data(),cu_angle_distance->dev_data(),cu_virial->dev_data(),
+ max_iter,tolerance);
+
+
}
/* ---------------------------------------------------------------------- */
@@ -300,7 +300,7 @@ int FixShakeCuda::setmask()
/* ----------------------------------------------------------------------
set bond and angle distances
- this init must happen after force->bond and force->angle inits
+ this init must happen after force->bond and force->angle inits
------------------------------------------------------------------------- */
void FixShakeCuda::init()
@@ -330,7 +330,7 @@ void FixShakeCuda::init()
if (i < modify->nfix) {
for (int j = i; j < modify->nfix; j++)
if (strcmp(modify->fix[j]->style,"shake") == 0)
- error->all(FLERR,"Shake fix must come before NPT/NPH fix");
+ error->all(FLERR,"Shake fix must come before NPT/NPH fix");
}
// if rRESPA, find associated fix that must exist
@@ -349,7 +349,7 @@ void FixShakeCuda::init()
if (force->bond == NULL)
error->all(FLERR,"Bond potential must be defined for SHAKE");
- for (i = 1; i <= atom->nbondtypes; i++)
+ for (i = 1; i <= atom->nbondtypes; i++)
bond_distance[i] = force->bond->equilibrium_distance(i);
// set equilibrium angle distances
@@ -365,7 +365,7 @@ void FixShakeCuda::init()
// extract bond types for the 2 bonds in the cluster
// bond types must be same in all clusters of this angle type,
// else set error flag
-
+
flag = 0;
bond1_type = bond2_type = 0;
for (m = 0; m < nlocal; m++) {
@@ -374,46 +374,46 @@ void FixShakeCuda::init()
type1 = MIN(shake_type[m][0],shake_type[m][1]);
type2 = MAX(shake_type[m][0],shake_type[m][1]);
if (bond1_type > 0) {
- if (type1 != bond1_type || type2 != bond2_type) {
- flag = 1;
- break;
- }
+ if (type1 != bond1_type || type2 != bond2_type) {
+ flag = 1;
+ break;
+ }
}
bond1_type = type1;
bond2_type = type2;
}
// error check for any bond types that are not the same
-
+
MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_MAX,world);
if (flag_all) error->all(FLERR,"Shake angles have different bond types");
-
+
// insure all procs have bond types
-
+
MPI_Allreduce(&bond1_type,&flag_all,1,MPI_INT,MPI_MAX,world);
bond1_type = flag_all;
MPI_Allreduce(&bond2_type,&flag_all,1,MPI_INT,MPI_MAX,world);
bond2_type = flag_all;
-
+
// if bond types are 0, no SHAKE angles of this type exist
// just skip this angle
-
+
if (bond1_type == 0) {
angle_distance[i] = 0.0;
continue;
}
// compute the angle distance as a function of 2 bond distances
-
+
angle = force->angle->equilibrium_angle(i);
- rsq = 2.0*bond_distance[bond1_type]*bond_distance[bond2_type] *
+ rsq = 2.0*bond_distance[bond1_type]*bond_distance[bond2_type] *
(1.0-cos(angle));
angle_distance[i] = sqrt(rsq);
}
}
/* ----------------------------------------------------------------------
- SHAKE as pre-integrator constraint
+ SHAKE as pre-integrator constraint
------------------------------------------------------------------------- */
void FixShakeCuda::setup(int vflag)
@@ -447,15 +447,15 @@ void FixShakeCuda::setup(int vflag)
dtf_inner = step_respa[0] * force->ftm2v;
}
Cuda_FixShakeCuda_Init(&cuda->shared_data,dtv, dtfsq,
- cu_shake_flag->dev_data(),cu_shake_atom->dev_data(),cu_shake_type->dev_data(), cu_xshake->dev_data(),
- cu_bond_distance->dev_data(),cu_angle_distance->dev_data(),cu_virial->dev_data(),
- max_iter,tolerance);
+ cu_shake_flag->dev_data(),cu_shake_atom->dev_data(),cu_shake_type->dev_data(), cu_xshake->dev_data(),
+ cu_bond_distance->dev_data(),cu_angle_distance->dev_data(),cu_virial->dev_data(),
+ max_iter,tolerance);
}
/* ----------------------------------------------------------------------
build list of SHAKE clusters to constrain
if one or more atoms in cluster are on this proc,
- this proc lists the cluster exactly once
+ this proc lists the cluster exactly once
------------------------------------------------------------------------- */
void FixShakeCuda::pre_neighbor()
@@ -479,7 +479,7 @@ void FixShakeCuda::pre_neighbor()
maxlist = nlocal;
memory->destroy(list);
memory->create(list,maxlist,"shake:list");
- delete cu_list; cu_list = new cCudaData<int , int , xx >(list,maxlist);
+ delete cu_list; cu_list = new cCudaData<int , int , xx >(list,maxlist);
}
// build list of SHAKE clusters I compute
@@ -488,53 +488,53 @@ void FixShakeCuda::pre_neighbor()
int count2=0,count3=0,count4=0,count3a=0;
for (int i = 0; i < nlocal; i++)
if (shake_flag[i]) {
- if(shake_flag[i] == 2) count2++;
- if(shake_flag[i] == 3) count3++;
- if(shake_flag[i] == 4) count4++;
- if(shake_flag[i] == 1) count3a++;
-
+ if(shake_flag[i] == 2) count2++;
+ if(shake_flag[i] == 3) count3++;
+ if(shake_flag[i] == 4) count4++;
+ if(shake_flag[i] == 1) count3a++;
+
if (shake_flag[i] == 2) {
- atom1 = atom->map(shake_atom[i][0]);
- atom2 = atom->map(shake_atom[i][1]);
- if (atom1 == -1 || atom2 == -1) {
- char str[128];
- sprintf(str,
- "Shake atoms %d %d missing on proc %d at step " BIGINT_FORMAT,
- shake_atom[i][0],shake_atom[i][1],me,update->ntimestep);
- error->one(FLERR,str);
- }
- if (i <= atom1 && i <= atom2) list[nlist++] = i;
+ atom1 = atom->map(shake_atom[i][0]);
+ atom2 = atom->map(shake_atom[i][1]);
+ if (atom1 == -1 || atom2 == -1) {
+ char str[128];
+ sprintf(str,
+ "Shake atoms %d %d missing on proc %d at step " BIGINT_FORMAT,
+ shake_atom[i][0],shake_atom[i][1],me,update->ntimestep);
+ error->one(FLERR,str);
+ }
+ if (i <= atom1 && i <= atom2) list[nlist++] = i;
} else if (shake_flag[i] % 2 == 1) {
- atom1 = atom->map(shake_atom[i][0]);
- atom2 = atom->map(shake_atom[i][1]);
- atom3 = atom->map(shake_atom[i][2]);
- if (atom1 == -1 || atom2 == -1 || atom3 == -1) {
- char str[128];
- sprintf(str,
- "Shake atoms %d %d %d missing on proc %d at step "
- BIGINT_FORMAT,
- shake_atom[i][0],shake_atom[i][1],shake_atom[i][2],
- me,update->ntimestep);
- error->one(FLERR,str);
- }
- if (i <= atom1 && i <= atom2 && i <= atom3) list[nlist++] = i;
+ atom1 = atom->map(shake_atom[i][0]);
+ atom2 = atom->map(shake_atom[i][1]);
+ atom3 = atom->map(shake_atom[i][2]);
+ if (atom1 == -1 || atom2 == -1 || atom3 == -1) {
+ char str[128];
+ sprintf(str,
+ "Shake atoms %d %d %d missing on proc %d at step "
+ BIGINT_FORMAT,
+ shake_atom[i][0],shake_atom[i][1],shake_atom[i][2],
+ me,update->ntimestep);
+ error->one(FLERR,str);
+ }
+ if (i <= atom1 && i <= atom2 && i <= atom3) list[nlist++] = i;
} else {
- atom1 = atom->map(shake_atom[i][0]);
- atom2 = atom->map(shake_atom[i][1]);
- atom3 = atom->map(shake_atom[i][2]);
- atom4 = atom->map(shake_atom[i][3]);
- if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
- char str[128];
- sprintf(str,
- "Shake atoms %d %d %d %d missing on proc %d at step "
- BIGINT_FORMAT,
- shake_atom[i][0],shake_atom[i][1],
- shake_atom[i][2],shake_atom[i][3],
- me,update->ntimestep);
- error->one(FLERR,str);
- }
- if (i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)
- list[nlist++] = i;
+ atom1 = atom->map(shake_atom[i][0]);
+ atom2 = atom->map(shake_atom[i][1]);
+ atom3 = atom->map(shake_atom[i][2]);
+ atom4 = atom->map(shake_atom[i][3]);
+ if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
+ char str[128];
+ sprintf(str,
+ "Shake atoms %d %d %d %d missing on proc %d at step "
+ BIGINT_FORMAT,
+ shake_atom[i][0],shake_atom[i][1],
+ shake_atom[i][2],shake_atom[i][3],
+ me,update->ntimestep);
+ error->one(FLERR,str);
+ }
+ if (i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)
+ list[nlist++] = i;
}
}
count2/=2;
@@ -553,7 +553,7 @@ void FixShakeCuda::pre_neighbor()
int tmp = list[k]; list[k]=list[l]; list[l]=tmp;
}
}
-
+
for(int k = count2,l = count3; k < count3; k++)
{
if(shake_flag[list[k]]!=3)
@@ -563,7 +563,7 @@ void FixShakeCuda::pre_neighbor()
int tmp = list[k]; list[k]=list[l]; list[l]=tmp;
}
}
-
+
for(int k = count3,l = count4; k < count4; k++)
{
if(shake_flag[list[k]]!=4)
@@ -573,42 +573,42 @@ void FixShakeCuda::pre_neighbor()
int tmp = list[k]; list[k]=list[l]; list[l]=tmp;
}
}
- cu_list->upload();
- cu_bond_distance->upload();
- cu_angle_distance->upload();
- cu_shake_flag->upload();
- cu_shake_atom->upload();
- cu_shake_type->upload();
-
+ cu_list->upload();
+ cu_bond_distance->upload();
+ cu_angle_distance->upload();
+ cu_shake_flag->upload();
+ cu_shake_atom->upload();
+ cu_shake_type->upload();
+
neighbor_step=true;
}
/* ----------------------------------------------------------------------
- compute the force adjustment for SHAKE constraint
+ compute the force adjustment for SHAKE constraint
------------------------------------------------------------------------- */
void FixShakeCuda::post_force(int vflag)
{
- timespec starttime;
- timespec endtime;
+ timespec starttime;
+ timespec endtime;
- if(cuda->finished_setup && neighbor_step)
- {
+ if(cuda->finished_setup && neighbor_step)
+ {
Cuda_FixShakeCuda_Init(&cuda->shared_data,dtv, dtfsq,
- cu_shake_flag->dev_data(),cu_shake_atom->dev_data(),cu_shake_type->dev_data(), cu_xshake->dev_data(),
- cu_bond_distance->dev_data(),cu_angle_distance->dev_data(),cu_virial->dev_data(),
- max_iter,tolerance);
-
- }
-
- if(not cuda->finished_setup)
- cuda->downloadAll();
- if (update->ntimestep == next_output)
+ cu_shake_flag->dev_data(),cu_shake_atom->dev_data(),cu_shake_type->dev_data(), cu_xshake->dev_data(),
+ cu_bond_distance->dev_data(),cu_angle_distance->dev_data(),cu_virial->dev_data(),
+ max_iter,tolerance);
+
+ }
+
+ if(not cuda->finished_setup)
+ cuda->downloadAll();
+ if (update->ntimestep == next_output)
{
- if(cuda->finished_setup)
- cuda->cu_x->download();
- stats();
+ if(cuda->finished_setup)
+ cuda->cu_x->download();
+ stats();
}
// xshake = unconstrained move with current v,f
@@ -616,15 +616,15 @@ void FixShakeCuda::post_force(int vflag)
unconstrained_update();
// communicate results if necessary
-
+
//if(cuda->finished_setup) cu_xshake->download();
- if (nprocs > 1)
+ if (nprocs > 1)
{
- //if(cuda->finished_setup)
+ //if(cuda->finished_setup)
//cu_xshake->download();
- comm->forward_comm_fix(this);
- //if(cuda->finished_setup)
+ comm->forward_comm_fix(this);
+ //if(cuda->finished_setup)
//cu_xshake->upload();
}
// virial setup
@@ -634,36 +634,36 @@ void FixShakeCuda::post_force(int vflag)
// loop over clusters
- clock_gettime(CLOCK_REALTIME,&starttime);
+ clock_gettime(CLOCK_REALTIME,&starttime);
if(cuda->finished_setup)
{
- cu_virial->upload();
- if(vflag_atom) cuda->cu_vatom->upload();
-
- Cuda_FixShakeCuda_Shake(&cuda->shared_data,vflag,vflag_atom,(int*)cu_list->dev_data(),nlist);
- cu_virial->download();
- if(vflag_atom) cuda->cu_vatom->download();
-
+ cu_virial->upload();
+ if(vflag_atom) cuda->cu_vatom->upload();
+
+ Cuda_FixShakeCuda_Shake(&cuda->shared_data,vflag,vflag_atom,(int*)cu_list->dev_data(),nlist);
+ cu_virial->download();
+ if(vflag_atom) cuda->cu_vatom->download();
+
}
else
for (int i = 0; i < nlist; i++) {
int m = list[i];
- if (shake_flag[m] == 2) shake2(m);
- else if (shake_flag[m] == 3) shake3(m);
- else if (shake_flag[m] == 4) shake4(m);
- else shake3angle(m);
+ if (shake_flag[m] == 2) shake2(m);
+ else if (shake_flag[m] == 3) shake3(m);
+ else if (shake_flag[m] == 4) shake4(m);
+ else shake3angle(m);
}
if((not cuda->finished_setup)) cuda->cu_f->upload();
- clock_gettime(CLOCK_REALTIME,&endtime);
- if(cuda->finished_setup)
- time_postforce+=(endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000);
- else
- time_postforce=0.0;
- //printf("Postforce time: %lf\n",time_postforce);
+ clock_gettime(CLOCK_REALTIME,&endtime);
+ if(cuda->finished_setup)
+ time_postforce+=(endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000);
+ else
+ time_postforce=0.0;
+ //printf("Postforce time: %lf\n",time_postforce);
}
/* ----------------------------------------------------------------------
- count # of degrees-of-freedom removed by SHAKE for atoms in igroup
+ count # of degrees-of-freedom removed by SHAKE for atoms in igroup
------------------------------------------------------------------------- */
int FixShakeCuda::dof(int igroup)
@@ -698,7 +698,7 @@ int FixShakeCuda::dof(int igroup)
only include atoms in fix group and those bonds/angles specified in input
test whether all clusters are valid
set shake_flag, shake_atom, shake_type values
- set bond,angle types negative so will be ignored in neighbor lists
+ set bond,angle types negative so will be ignored in neighbor lists
------------------------------------------------------------------------- */
void FixShakeCuda::find_clusters()
@@ -728,7 +728,7 @@ void FixShakeCuda::find_clusters()
// setup ring of procs
int next = me + 1;
- int prev = me -1;
+ int prev = me -1;
if (next == nprocs) next = 0;
if (prev < 0) prev = nprocs - 1;
@@ -795,19 +795,19 @@ void FixShakeCuda::find_clusters()
m = atom->map(partner_tag[i][j]);
if (m >= 0 && m < nlocal) {
- partner_mask[i][j] = mask[m];
- partner_type[i][j] = type[m];
- if (nmass) {
- if (rmass) massone = rmass[m];
- else massone = mass[type[m]];
- partner_massflag[i][j] = masscheck(massone);
- }
- n = bondfind(i,tag[i],partner_tag[i][j]);
- if (n >= 0) partner_bondtype[i][j] = bond_type[i][n];
- else {
- n = bondfind(m,tag[i],partner_tag[i][j]);
- if (n >= 0) partner_bondtype[i][j] = bond_type[m][n];
- }
+ partner_mask[i][j] = mask[m];
+ partner_type[i][j] = type[m];
+ if (nmass) {
+ if (rmass) massone = rmass[m];
+ else massone = mass[type[m]];
+ partner_massflag[i][j] = masscheck(massone);
+ }
+ n = bondfind(i,tag[i],partner_tag[i][j]);
+ if (n >= 0) partner_bondtype[i][j] = bond_type[i][n];
+ else {
+ n = bondfind(m,tag[i],partner_tag[i][j]);
+ if (n >= 0) partner_bondtype[i][j] = bond_type[m][n];
+ }
} else nbuf += nper;
}
}
@@ -824,15 +824,15 @@ void FixShakeCuda::find_clusters()
for (j = 0; j < npartner[i]; j++) {
m = atom->map(partner_tag[i][j]);
if (m < 0 || m >= nlocal) {
- buf[size] = tag[i];
- buf[size+1] = partner_tag[i][j];
- buf[size+2] = 0;
- buf[size+3] = 0;
- buf[size+4] = 0;
- n = bondfind(i,tag[i],partner_tag[i][j]);
- if (n >= 0) buf[size+5] = bond_type[i][n];
- else buf[size+5] = 0;
- size += nper;
+ buf[size] = tag[i];
+ buf[size+1] = partner_tag[i][j];
+ buf[size+2] = 0;
+ buf[size+3] = 0;
+ buf[size+4] = 0;
+ n = bondfind(i,tag[i],partner_tag[i][j]);
+ if (n >= 0) buf[size+5] = bond_type[i][n];
+ else buf[size+5] = 0;
+ size += nper;
}
}
}
@@ -849,17 +849,17 @@ void FixShakeCuda::find_clusters()
while (i < size) {
m = atom->map(buf[i+1]);
if (m >= 0 && m < nlocal) {
- buf[i+2] = mask[m];
- buf[i+3] = type[m];
- if (nmass) {
- if (rmass) massone = rmass[m];
- else massone = mass[type[m]];
- buf[i+4] = masscheck(massone);
- }
- if (buf[i+5] == 0) {
- n = bondfind(m,buf[i],buf[i+1]);
- if (n >= 0) buf[i+5] = bond_type[m][n];
- }
+ buf[i+2] = mask[m];
+ buf[i+3] = type[m];
+ if (nmass) {
+ if (rmass) massone = rmass[m];
+ else massone = mass[type[m]];
+ buf[i+4] = masscheck(massone);
+ }
+ if (buf[i+5] == 0) {
+ n = bondfind(m,buf[i],buf[i+1]);
+ if (n >= 0) buf[i+5] = bond_type[m][n];
+ }
}
i += nper;
}
@@ -932,29 +932,29 @@ void FixShakeCuda::find_clusters()
if (partner_bondtype[i][j] <= 0) continue;
if (bond_flag[partner_bondtype[i][j]]) {
- partner_shake[i][j] = 1;
- nshake[i]++;
- continue;
+ partner_shake[i][j] = 1;
+ nshake[i]++;
+ continue;
}
if (type_flag[type[i]] || type_flag[partner_type[i][j]]) {
- partner_shake[i][j] = 1;
- nshake[i]++;
- continue;
+ partner_shake[i][j] = 1;
+ nshake[i]++;
+ continue;
}
if (nmass) {
- if (partner_massflag[i][j]) {
- partner_shake[i][j] = 1;
- nshake[i]++;
- continue;
- } else {
- if (rmass) massone = rmass[i];
- else massone = mass[type[i]];
- if (masscheck(massone)) {
- partner_shake[i][j] = 1;
- nshake[i]++;
- continue;
- }
- }
+ if (partner_massflag[i][j]) {
+ partner_shake[i][j] = 1;
+ nshake[i]++;
+ continue;
+ } else {
+ if (rmass) massone = rmass[i];
+ else massone = mass[type[i]];
+ if (masscheck(massone)) {
+ partner_shake[i][j] = 1;
+ nshake[i]++;
+ continue;
+ }
+ }
}
}
}
@@ -977,7 +977,7 @@ void FixShakeCuda::find_clusters()
else nbuf += 3;
}
}
-
+
MPI_Allreduce(&nbuf,&nbufmax,1,MPI_INT,MPI_MAX,world);
buf = new int[nbufmax];
@@ -990,9 +990,9 @@ void FixShakeCuda::find_clusters()
for (j = 0; j < npartner[i]; j++) {
m = atom->map(partner_tag[i][j]);
if (m < 0 || m >= nlocal) {
- buf[size] = tag[i];
- buf[size+1] = partner_tag[i][j];
- size += 3;
+ buf[size] = tag[i];
+ buf[size+1] = partner_tag[i][j];
+ size += 3;
}
}
}
@@ -1055,7 +1055,7 @@ void FixShakeCuda::find_clusters()
// -----------------------------------------------------
// set SHAKE arrays that are stored with atoms & add angle constraints
// zero shake arrays for all owned atoms
- // if I am central atom set shake_flag & shake_atom & shake_type
+ // if I am central atom set shake_flag & shake_atom & shake_type
// for 2-atom clusters, I am central atom if my atom ID < partner ID
// for 3-atom clusters, test for angle constraint
// angle will be stored by this atom if it exists
@@ -1082,12 +1082,12 @@ void FixShakeCuda::find_clusters()
if (nshake[i] == 1) {
for (j = 0; j < npartner[i]; j++)
- if (partner_shake[i][j]) break;
+ if (partner_shake[i][j]) break;
if (partner_nshake[i][j] == 1 && tag[i] < partner_tag[i][j]) {
- shake_flag[i] = 2;
- shake_atom[i][0] = tag[i];
- shake_atom[i][1] = partner_tag[i][j];
- shake_type[i][0] = partner_bondtype[i][j];
+ shake_flag[i] = 2;
+ shake_atom[i][0] = tag[i];
+ shake_atom[i][1] = partner_tag[i][j];
+ shake_type[i][0] = partner_bondtype[i][j];
}
}
@@ -1095,12 +1095,12 @@ void FixShakeCuda::find_clusters()
shake_flag[i] = 1;
shake_atom[i][0] = tag[i];
for (j = 0; j < npartner[i]; j++)
- if (partner_shake[i][j]) {
- m = shake_flag[i];
- shake_atom[i][m] = partner_tag[i][j];
- shake_type[i][m-1] = partner_bondtype[i][j];
- shake_flag[i]++;
- }
+ if (partner_shake[i][j]) {
+ m = shake_flag[i];
+ shake_atom[i][m] = partner_tag[i][j];
+ shake_type[i][m-1] = partner_bondtype[i][j];
+ shake_flag[i]++;
+ }
}
if (nshake[i] == 2) {
@@ -1108,8 +1108,8 @@ void FixShakeCuda::find_clusters()
if (n < 0) continue;
if (angle_type[i][n] < 0) continue;
if (angle_flag[angle_type[i][n]]) {
- shake_flag[i] = 1;
- shake_type[i][2] = angle_type[i][n];
+ shake_flag[i] = 1;
+ shake_type[i][2] = angle_type[i][n];
}
}
}
@@ -1131,14 +1131,14 @@ void FixShakeCuda::find_clusters()
if (partner_shake[i][j] == 0) continue;
m = atom->map(partner_tag[i][j]);
if (m >= 0 && m < nlocal) {
- shake_flag[m] = shake_flag[i];
- shake_atom[m][0] = shake_atom[i][0];
- shake_atom[m][1] = shake_atom[i][1];
- shake_atom[m][2] = shake_atom[i][2];
- shake_atom[m][3] = shake_atom[i][3];
- shake_type[m][0] = shake_type[i][0];
- shake_type[m][1] = shake_type[i][1];
- shake_type[m][2] = shake_type[i][2];
+ shake_flag[m] = shake_flag[i];
+ shake_atom[m][0] = shake_atom[i][0];
+ shake_atom[m][1] = shake_atom[i][1];
+ shake_atom[m][2] = shake_atom[i][2];
+ shake_atom[m][3] = shake_atom[i][3];
+ shake_type[m][0] = shake_type[i][0];
+ shake_type[m][1] = shake_type[i][1];
+ shake_type[m][2] = shake_type[i][2];
} else nbuf += 9;
}
}
@@ -1157,16 +1157,16 @@ void FixShakeCuda::find_clusters()
if (partner_shake[i][j] == 0) continue;
m = atom->map(partner_tag[i][j]);
if (m < 0 || m >= nlocal) {
- buf[size] = partner_tag[i][j];
- buf[size+1] = shake_flag[i];
- buf[size+2] = shake_atom[i][0];
- buf[size+3] = shake_atom[i][1];
- buf[size+4] = shake_atom[i][2];
- buf[size+5] = shake_atom[i][3];
- buf[size+6] = shake_type[i][0];
- buf[size+7] = shake_type[i][1];
- buf[size+8] = shake_type[i][2];
- size += 9;
+ buf[size] = partner_tag[i][j];
+ buf[size+1] = shake_flag[i];
+ buf[size+2] = shake_atom[i][0];
+ buf[size+3] = shake_atom[i][1];
+ buf[size+4] = shake_atom[i][2];
+ buf[size+5] = shake_atom[i][3];
+ buf[size+6] = shake_type[i][0];
+ buf[size+7] = shake_type[i][1];
+ buf[size+8] = shake_type[i][2];
+ size += 9;
}
}
}
@@ -1181,14 +1181,14 @@ void FixShakeCuda::find_clusters()
while (i < size) {
m = atom->map(buf[i]);
if (m >= 0 && m < nlocal) {
- shake_flag[m] = buf[i+1];
- shake_atom[m][0] = buf[i+2];
- shake_atom[m][1] = buf[i+3];
- shake_atom[m][2] = buf[i+4];
- shake_atom[m][3] = buf[i+5];
- shake_type[m][0] = buf[i+6];
- shake_type[m][1] = buf[i+7];
- shake_type[m][2] = buf[i+8];
+ shake_flag[m] = buf[i+1];
+ shake_atom[m][0] = buf[i+2];
+ shake_atom[m][1] = buf[i+3];
+ shake_atom[m][2] = buf[i+4];
+ shake_atom[m][3] = buf[i+5];
+ shake_type[m][0] = buf[i+6];
+ shake_type[m][1] = buf[i+7];
+ shake_type[m][2] = buf[i+8];
}
i += 9;
}
@@ -1262,11 +1262,11 @@ void FixShakeCuda::find_clusters()
else if (shake_flag[i] == 3) count3++;
else if (shake_flag[i] == 4) count4++;
}
-
+
for(int i=0;i<nlocal;i++)
{
}
-
+
int tmp;
tmp = count1;
@@ -1296,23 +1296,23 @@ void FixShakeCuda::find_clusters()
cu_shake_atom->upload();
cu_shake_type->upload();
Cuda_FixShakeCuda_Init(&cuda->shared_data,dtv, dtfsq,
- cu_shake_flag->dev_data(),cu_shake_atom->dev_data(),cu_shake_type->dev_data(), cu_xshake->dev_data(),
- cu_bond_distance->dev_data(),cu_angle_distance->dev_data(),cu_virial->dev_data(),
- max_iter,tolerance);
-
+ cu_shake_flag->dev_data(),cu_shake_atom->dev_data(),cu_shake_type->dev_data(), cu_xshake->dev_data(),
+ cu_bond_distance->dev_data(),cu_angle_distance->dev_data(),cu_virial->dev_data(),
+ max_iter,tolerance);
+
}
void FixShakeCuda::swap_clusters(int i, int j)
{
- int tmp;
- tmp = shake_flag[i]; shake_flag[i] = shake_flag[j]; shake_flag[j] = tmp;
- tmp = shake_atom[i][0]; shake_atom[i][0] = shake_atom[j][0]; shake_atom[j][0] = tmp;
- tmp = shake_atom[i][1]; shake_atom[i][1] = shake_atom[j][1]; shake_atom[j][1] = tmp;
- tmp = shake_atom[i][2]; shake_atom[i][2] = shake_atom[j][2]; shake_atom[j][2] = tmp;
- tmp = shake_atom[i][3]; shake_atom[i][3] = shake_atom[j][3]; shake_atom[j][3] = tmp;
- tmp = shake_type[i][0]; shake_type[i][0] = shake_type[j][0]; shake_type[j][0] = tmp;
- tmp = shake_type[i][1]; shake_type[i][1] = shake_type[j][1]; shake_type[j][1] = tmp;
- tmp = shake_type[i][2]; shake_type[i][2] = shake_type[j][2]; shake_type[j][2] = tmp;
+ int tmp;
+ tmp = shake_flag[i]; shake_flag[i] = shake_flag[j]; shake_flag[j] = tmp;
+ tmp = shake_atom[i][0]; shake_atom[i][0] = shake_atom[j][0]; shake_atom[j][0] = tmp;
+ tmp = shake_atom[i][1]; shake_atom[i][1] = shake_atom[j][1]; shake_atom[j][1] = tmp;
+ tmp = shake_atom[i][2]; shake_atom[i][2] = shake_atom[j][2]; shake_atom[j][2] = tmp;
+ tmp = shake_atom[i][3]; shake_atom[i][3] = shake_atom[j][3]; shake_atom[j][3] = tmp;
+ tmp = shake_type[i][0]; shake_type[i][0] = shake_type[j][0]; shake_type[j][0] = tmp;
+ tmp = shake_type[i][1]; shake_type[i][1] = shake_type[j][1]; shake_type[j][1] = tmp;
+ tmp = shake_type[i][2]; shake_type[i][2] = shake_type[j][2]; shake_type[j][2] = tmp;
}
/* ----------------------------------------------------------------------
@@ -1330,7 +1330,7 @@ int FixShakeCuda::masscheck(double massone)
/* ----------------------------------------------------------------------
update the unconstrained position of each atom
only for SHAKE clusters, else set to 0.0
- assumes NVE update, seems to be accurate enough for NVT,NPT,NPH as well
+ assumes NVE update, seems to be accurate enough for NVT,NPT,NPH as well
------------------------------------------------------------------------- */
void FixShakeCuda::unconstrained_update()
@@ -1340,25 +1340,25 @@ void FixShakeCuda::unconstrained_update()
Cuda_FixShakeCuda_UnconstrainedUpdate(&cuda->shared_data);
return;
}
-
+
double dtfmsq;
-
+
if (rmass) {
for (int i = 0; i < nlocal; i++) {
if (shake_flag[i]) {
- dtfmsq = dtfsq / rmass[i];
- xshake[i][0] = x[i][0] + dtv*v[i][0] + dtfmsq*f[i][0];
- xshake[i][1] = x[i][1] + dtv*v[i][1] + dtfmsq*f[i][1];
- xshake[i][2] = x[i][2] + dtv*v[i][2] + dtfmsq*f[i][2];
+ dtfmsq = dtfsq / rmass[i];
+ xshake[i][0] = x[i][0] + dtv*v[i][0] + dtfmsq*f[i][0];
+ xshake[i][1] = x[i][1] + dtv*v[i][1] + dtfmsq*f[i][1];
+ xshake[i][2] = x[i][2] + dtv*v[i][2] + dtfmsq*f[i][2];
} else xshake[i][2] = xshake[i][1] = xshake[i][0] = 0.0;
}
} else {
for (int i = 0; i < nlocal; i++) {
if (shake_flag[i]) {
- dtfmsq = dtfsq / mass[type[i]];
- xshake[i][0] = x[i][0] + dtv*v[i][0] + dtfmsq*f[i][0];
- xshake[i][1] = x[i][1] + dtv*v[i][1] + dtfmsq*f[i][1];
- xshake[i][2] = x[i][2] + dtv*v[i][2] + dtfmsq*f[i][2];
+ dtfmsq = dtfsq / mass[type[i]];
+ xshake[i][0] = x[i][0] + dtv*v[i][0] + dtfmsq*f[i][0];
+ xshake[i][1] = x[i][1] + dtv*v[i][1] + dtfmsq*f[i][1];
+ xshake[i][2] = x[i][2] + dtv*v[i][2] + dtfmsq*f[i][2];
} else xshake[i][2] = xshake[i][1] = xshake[i][0] = 0.0;
}
}
@@ -1378,7 +1378,7 @@ void FixShakeCuda::shake2(int m)
int i0 = atom->map(shake_atom[m][0]);
int i1 = atom->map(shake_atom[m][1]);
double bond1 = bond_distance[shake_type[m][0]];
-
+
// r01 = distance vec between atoms, with PBC
double r01[3];
@@ -1401,7 +1401,7 @@ void FixShakeCuda::shake2(int m)
double s01sq = s01[0]*s01[0] + s01[1]*s01[1] + s01[2]*s01[2];
// a,b,c = coeffs in quadratic equation for lamda
-
+
if (rmass) {
invmass0 = 1.0/rmass[i0];
invmass1 = 1.0/rmass[i1];
@@ -1540,7 +1540,7 @@ void FixShakeCuda::shake3(int m)
double determ = a11*a22 - a12*a21;
if (determ == 0.0) error->one(FLERR,"Shake determinant = 0.0");
double determinv = 1.0/determ;
-
+
double a11inv = a22*determinv;
double a12inv = -a12*determinv;
double a21inv = -a21*determinv;
@@ -1568,14 +1568,14 @@ void FixShakeCuda::shake3(int m)
double quad1,quad2,b1,b2,lamda01_new,lamda02_new;
while (!done && niter < max_iter) {
- quad1 = quad1_0101 * lamda01*lamda01 + quad1_0202 * lamda02*lamda02 +
+ quad1 = quad1_0101 * lamda01*lamda01 + quad1_0202 * lamda02*lamda02 +
quad1_0102 * lamda01*lamda02;
- quad2 = quad2_0101 * lamda01*lamda01 + quad2_0202 * lamda02*lamda02 +
+ quad2 = quad2_0101 * lamda01*lamda01 + quad2_0202 * lamda02*lamda02 +
quad2_0102 * lamda01*lamda02;
-
+
b1 = bond1*bond1 - s01sq - quad1;
b2 = bond2*bond2 - s02sq - quad2;
-
+
lamda01_new = a11inv*b1 + a12inv*b2;
lamda02_new = a21inv*b1 + a22inv*b2;
@@ -1727,14 +1727,14 @@ void FixShakeCuda::shake4(int m)
(s03[0]*r02[0] + s03[1]*r02[1] + s03[2]*r02[2]);
double a33 = 2.0 * (invmass0+invmass3) *
(s03[0]*r03[0] + s03[1]*r03[1] + s03[2]*r03[2]);
-
+
// inverse of matrix;
double determ = a11*a22*a33 + a12*a23*a31 + a13*a21*a32 -
a11*a23*a32 - a12*a21*a33 - a13*a22*a31;
if (determ == 0.0) error->one(FLERR,"Shake determinant = 0.0");
double determinv = 1.0/determ;
-
+
double a11inv = determinv * (a22*a33 - a23*a32);
double a12inv = -determinv * (a12*a33 - a13*a32);
double a13inv = determinv * (a12*a23 - a13*a22);
@@ -1783,23 +1783,23 @@ void FixShakeCuda::shake4(int m)
double quad1,quad2,quad3,b1,b2,b3,lamda01_new,lamda02_new,lamda03_new;
while (!done && niter < max_iter) {
- quad1 = quad1_0101 * lamda01*lamda01 +
+ quad1 = quad1_0101 * lamda01*lamda01 +
quad1_0202 * lamda02*lamda02 +
- quad1_0303 * lamda03*lamda03 +
+ quad1_0303 * lamda03*lamda03 +
quad1_0102 * lamda01*lamda02 +
quad1_0103 * lamda01*lamda03 +
quad1_0203 * lamda02*lamda03;
- quad2 = quad2_0101 * lamda01*lamda01 +
+ quad2 = quad2_0101 * lamda01*lamda01 +
quad2_0202 * lamda02*lamda02 +
- quad2_0303 * lamda03*lamda03 +
+ quad2_0303 * lamda03*lamda03 +
quad2_0102 * lamda01*lamda02 +
quad2_0103 * lamda01*lamda03 +
quad2_0203 * lamda02*lamda03;
- quad3 = quad3_0101 * lamda01*lamda01 +
+ quad3 = quad3_0101 * lamda01*lamda01 +
quad3_0202 * lamda02*lamda02 +
- quad3_0303 * lamda03*lamda03 +
+ quad3_0303 * lamda03*lamda03 +
quad3_0102 * lamda01*lamda02 +
quad3_0103 * lamda01*lamda03 +
quad3_0203 * lamda02*lamda03;
@@ -1807,7 +1807,7 @@ void FixShakeCuda::shake4(int m)
b1 = bond1*bond1 - s01sq - quad1;
b2 = bond2*bond2 - s02sq - quad2;
b3 = bond3*bond3 - s03sq - quad3;
-
+
lamda01_new = a11inv*b1 + a12inv*b2 + a13inv*b3;
lamda02_new = a21inv*b1 + a22inv*b2 + a23inv*b3;
lamda03_new = a31inv*b1 + a32inv*b2 + a33inv*b3;
@@ -1975,7 +1975,7 @@ void FixShakeCuda::shake3angle(int m)
a11*a23*a32 - a12*a21*a33 - a13*a22*a31;
if (determ == 0.0) error->one(FLERR,"Shake determinant = 0.0");
double determinv = 1.0/determ;
-
+
double a11inv = determinv * (a22*a33 - a23*a32);
double a12inv = -determinv * (a12*a33 - a13*a32);
double a13inv = determinv * (a12*a23 - a13*a22);
@@ -2024,23 +2024,23 @@ void FixShakeCuda::shake3angle(int m)
double quad1,quad2,quad3,b1,b2,b3,lamda01_new,lamda02_new,lamda12_new;
while (!done && niter < max_iter) {
- quad1 = quad1_0101 * lamda01*lamda01 +
+ quad1 = quad1_0101 * lamda01*lamda01 +
quad1_0202 * lamda02*lamda02 +
- quad1_1212 * lamda12*lamda12 +
+ quad1_1212 * lamda12*lamda12 +
quad1_0102 * lamda01*lamda02 +
quad1_0112 * lamda01*lamda12 +
quad1_0212 * lamda02*lamda12;
- quad2 = quad2_0101 * lamda01*lamda01 +
+ quad2 = quad2_0101 * lamda01*lamda01 +
quad2_0202 * lamda02*lamda02 +
- quad2_1212 * lamda12*lamda12 +
+ quad2_1212 * lamda12*lamda12 +
quad2_0102 * lamda01*lamda02 +
quad2_0112 * lamda01*lamda12 +
quad2_0212 * lamda02*lamda12;
-
- quad3 = quad3_0101 * lamda01*lamda01 +
+
+ quad3 = quad3_0101 * lamda01*lamda01 +
quad3_0202 * lamda02*lamda02 +
- quad3_1212 * lamda12*lamda12 +
+ quad3_1212 * lamda12*lamda12 +
quad3_0102 * lamda01*lamda02 +
quad3_0112 * lamda01*lamda12 +
quad3_0212 * lamda02*lamda12;
@@ -2048,7 +2048,7 @@ void FixShakeCuda::shake3angle(int m)
b1 = bond1*bond1 - s01sq - quad1;
b2 = bond2*bond2 - s02sq - quad2;
b3 = bond12*bond12 - s12sq - quad3;
-
+
lamda01_new = a11inv*b1 + a12inv*b2 + a13inv*b3;
lamda02_new = a21inv*b1 + a22inv*b2 + a23inv*b3;
lamda12_new = a31inv*b1 + a32inv*b2 + a33inv*b3;
@@ -2106,7 +2106,7 @@ void FixShakeCuda::shake3angle(int m)
}
/* ----------------------------------------------------------------------
- print-out bond & angle statistics
+ print-out bond & angle statistics
------------------------------------------------------------------------- */
void FixShakeCuda::stats()
@@ -2152,7 +2152,7 @@ void FixShakeCuda::stats()
delz = x[iatom][2] - x[jatom][2];
domain->minimum_image(delx,dely,delz);
r = sqrt(delx*delx + dely*dely + delz*delz);
-
+
m = shake_type[i][j-1];
b_count[m]++;
b_ave[m] += r;
@@ -2212,29 +2212,29 @@ void FixShakeCuda::stats()
if (me == 0) {
if (screen) {
fprintf(screen,
- "SHAKE stats (type/ave/delta) on step " BIGINT_FORMAT "\n",
- update->ntimestep);
- for (i = 1; i < nb; i++)
- if (b_count_all[i])
- fprintf(screen," %d %g %g\n",i,
- b_ave_all[i]/b_count_all[i],b_max_all[i]-b_min_all[i]);
- for (i = 1; i < na; i++)
- if (a_count_all[i])
- fprintf(screen," %d %g %g\n",i,
- a_ave_all[i]/a_count_all[i],a_max_all[i]-a_min_all[i]);
+ "SHAKE stats (type/ave/delta) on step " BIGINT_FORMAT "\n",
+ update->ntimestep);
+ for (i = 1; i < nb; i++)
+ if (b_count_all[i])
+ fprintf(screen," %d %g %g\n",i,
+ b_ave_all[i]/b_count_all[i],b_max_all[i]-b_min_all[i]);
+ for (i = 1; i < na; i++)
+ if (a_count_all[i])
+ fprintf(screen," %d %g %g\n",i,
+ a_ave_all[i]/a_count_all[i],a_max_all[i]-a_min_all[i]);
}
if (logfile) {
fprintf(logfile,
- "SHAKE stats (type/ave/delta) on step " BIGINT_FORMAT "\n",
- update->ntimestep);
- for (i = 0; i < nb; i++)
- if (b_count_all[i])
- fprintf(logfile," %d %g %g\n",i,
- b_ave_all[i]/b_count_all[i],b_max_all[i]-b_min_all[i]);
- for (i = 0; i < na; i++)
- if (a_count_all[i])
- fprintf(logfile," %d %g %g\n",i,
- a_ave_all[i]/a_count_all[i],a_max_all[i]-a_min_all[i]);
+ "SHAKE stats (type/ave/delta) on step " BIGINT_FORMAT "\n",
+ update->ntimestep);
+ for (i = 0; i < nb; i++)
+ if (b_count_all[i])
+ fprintf(logfile," %d %g %g\n",i,
+ b_ave_all[i]/b_count_all[i],b_max_all[i]-b_min_all[i]);
+ for (i = 0; i < na; i++)
+ if (a_count_all[i])
+ fprintf(logfile," %d %g %g\n",i,
+ a_ave_all[i]/a_count_all[i],a_max_all[i]-a_min_all[i]);
}
}
@@ -2286,7 +2286,7 @@ int FixShakeCuda::anglefind(int i, int n1, int n2)
}
/* ----------------------------------------------------------------------
- memory usage of local atom-based arrays
+ memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double FixShakeCuda::memory_usage()
@@ -2301,7 +2301,7 @@ double FixShakeCuda::memory_usage()
}
/* ----------------------------------------------------------------------
- allocate local atom-based arrays
+ allocate local atom-based arrays
------------------------------------------------------------------------- */
void FixShakeCuda::grow_arrays(int nmax)
@@ -2321,13 +2321,13 @@ void FixShakeCuda::grow_arrays(int nmax)
cu_shake_type->upload();
if(cu_bond_distance)
Cuda_FixShakeCuda_Init(&cuda->shared_data,dtv, dtfsq,
- cu_shake_flag->dev_data(),cu_shake_atom->dev_data(),cu_shake_type->dev_data(), cu_xshake->dev_data(),
- cu_bond_distance->dev_data(),cu_angle_distance->dev_data(),cu_virial->dev_data(),
- max_iter,tolerance);
+ cu_shake_flag->dev_data(),cu_shake_atom->dev_data(),cu_shake_type->dev_data(), cu_xshake->dev_data(),
+ cu_bond_distance->dev_data(),cu_angle_distance->dev_data(),cu_virial->dev_data(),
+ max_iter,tolerance);
}
/* ----------------------------------------------------------------------
- copy values within local atom-based arrays
+ copy values within local atom-based arrays
------------------------------------------------------------------------- */
void FixShakeCuda::copy_arrays(int i, int j)
@@ -2371,7 +2371,7 @@ void FixShakeCuda::set_arrays(int i)
}
/* ----------------------------------------------------------------------
- pack values in local atom-based arrays for exchange with another proc
+ pack values in local atom-based arrays for exchange with another proc
------------------------------------------------------------------------- */
int FixShakeCuda::pack_exchange(int i, double *buf)
@@ -2409,7 +2409,7 @@ int FixShakeCuda::pack_exchange(int i, double *buf)
}
/* ----------------------------------------------------------------------
- unpack values in local atom-based arrays from exchange with another proc
+ unpack values in local atom-based arrays from exchange with another proc
------------------------------------------------------------------------- */
int FixShakeCuda::unpack_exchange(int nlocal, double *buf)
@@ -2461,7 +2461,7 @@ void FixShakeCuda::post_force_respa(int vflag, int ilevel, int iloop)
// except last loop iteration of inner levels
if (ilevel < nlevels_respa-1 && iloop == loop_respa[ilevel]-1) return;
-
+
// xshake = atom coords after next x update in innermost loop
// depends on rRESPA level
// for levels > 0 this includes more than one velocity update
@@ -2477,34 +2477,34 @@ void FixShakeCuda::post_force_respa(int vflag, int ilevel, int iloop)
if (rmass) {
for (int i = 0; i < nlocal; i++) {
if (shake_flag[i]) {
- invmass = 1.0 / rmass[i];
- dtfmsq = dtfsq * invmass;
- xshake[i][0] = x[i][0] + dtv*v[i][0] + dtfmsq*f[i][0];
- xshake[i][1] = x[i][1] + dtv*v[i][1] + dtfmsq*f[i][1];
- xshake[i][2] = x[i][2] + dtv*v[i][2] + dtfmsq*f[i][2];
- for (jlevel = 0; jlevel < ilevel; jlevel++) {
- dtfmsq = dtf_innerhalf * step_respa[jlevel] * invmass;
- xshake[i][0] += dtfmsq*f_level[i][jlevel][0];
- xshake[i][1] += dtfmsq*f_level[i][jlevel][1];
- xshake[i][2] += dtfmsq*f_level[i][jlevel][2];
- }
+ invmass = 1.0 / rmass[i];
+ dtfmsq = dtfsq * invmass;
+ xshake[i][0] = x[i][0] + dtv*v[i][0] + dtfmsq*f[i][0];
+ xshake[i][1] = x[i][1] + dtv*v[i][1] + dtfmsq*f[i][1];
+ xshake[i][2] = x[i][2] + dtv*v[i][2] + dtfmsq*f[i][2];
+ for (jlevel = 0; jlevel < ilevel; jlevel++) {
+ dtfmsq = dtf_innerhalf * step_respa[jlevel] * invmass;
+ xshake[i][0] += dtfmsq*f_level[i][jlevel][0];
+ xshake[i][1] += dtfmsq*f_level[i][jlevel][1];
+ xshake[i][2] += dtfmsq*f_level[i][jlevel][2];
+ }
} else xshake[i][2] = xshake[i][1] = xshake[i][0] = 0.0;
}
} else {
for (int i = 0; i < nlocal; i++) {
if (shake_flag[i]) {
- invmass = 1.0 / mass[type[i]];
- dtfmsq = dtfsq * invmass;
- xshake[i][0] = x[i][0] + dtv*v[i][0] + dtfmsq*f[i][0];
- xshake[i][1] = x[i][1] + dtv*v[i][1] + dtfmsq*f[i][1];
- xshake[i][2] = x[i][2] + dtv*v[i][2] + dtfmsq*f[i][2];
- for (jlevel = 0; jlevel < ilevel; jlevel++) {
- dtfmsq = dtf_innerhalf * step_respa[jlevel] * invmass;
- xshake[i][0] += dtfmsq*f_level[i][jlevel][0];
- xshake[i][1] += dtfmsq*f_level[i][jlevel][1];
- xshake[i][2] += dtfmsq*f_level[i][jlevel][2];
- }
+ invmass = 1.0 / mass[type[i]];
+ dtfmsq = dtfsq * invmass;
+ xshake[i][0] = x[i][0] + dtv*v[i][0] + dtfmsq*f[i][0];
+ xshake[i][1] = x[i][1] + dtv*v[i][1] + dtfmsq*f[i][1];
+ xshake[i][2] = x[i][2] + dtv*v[i][2] + dtfmsq*f[i][2];
+ for (jlevel = 0; jlevel < ilevel; jlevel++) {
+ dtfmsq = dtf_innerhalf * step_respa[jlevel] * invmass;
+ xshake[i][0] += dtfmsq*f_level[i][jlevel][0];
+ xshake[i][1] += dtfmsq*f_level[i][jlevel][1];
+ xshake[i][2] += dtfmsq*f_level[i][jlevel][2];
+ }
} else xshake[i][2] = xshake[i][1] = xshake[i][0] = 0.0;
}
}
@@ -2537,18 +2537,18 @@ int FixShakeCuda::pack_comm(int n, int *list, double *buf, int pbc_flag, int *pb
{
if(cuda->finished_setup)
{
- int iswap=*list;
- if(iswap<0)
- {
- iswap=-iswap-1;
- int first= ((int*) buf)[0];
- Cuda_FixShakeCuda_PackComm_Self(&cuda->shared_data,n,iswap,first,pbc,pbc_flag);
- }
- else
+ int iswap=*list;
+ if(iswap<0)
+ {
+ iswap=-iswap-1;
+ int first= ((int*) buf)[0];
+ Cuda_FixShakeCuda_PackComm_Self(&cuda->shared_data,n,iswap,first,pbc,pbc_flag);
+ }
+ else
Cuda_FixShakeCuda_PackComm(&cuda->shared_data,n,iswap,(void*) buf,pbc,pbc_flag);
return 3;
}
-
+
int i,j,m;
double dx,dy,dz;
@@ -2589,7 +2589,7 @@ void FixShakeCuda::unpack_comm(int n, int first, double *buf)
Cuda_FixShakeCuda_UnpackComm(&cuda->shared_data,n,first,(void*)buf);
return;
}
-
+
int i,m,last;
m = 0;
@@ -2615,7 +2615,7 @@ void FixShakeCuda::reset_dt()
}
if(cu_shake_atom)
Cuda_FixShakeCuda_Init(&cuda->shared_data,dtv, dtfsq,
- cu_shake_flag->dev_data(),cu_shake_atom->dev_data(),cu_shake_type->dev_data(), cu_xshake->dev_data(),
- cu_bond_distance->dev_data(),cu_angle_distance->dev_data(),cu_virial->dev_data(),
- max_iter,tolerance);
+ cu_shake_flag->dev_data(),cu_shake_atom->dev_data(),cu_shake_type->dev_data(), cu_xshake->dev_data(),
+ cu_bond_distance->dev_data(),cu_angle_distance->dev_data(),cu_virial->dev_data(),
+ max_iter,tolerance);
}
diff --git a/src/USER-CUDA/fix_shake_cuda.h b/src/USER-CUDA/fix_shake_cuda.h
index b0ebe584d744cae49005fd09632dc2bd809179c2..03cd5aa08660989422a5026228b38444077ba8bf 100644
--- a/src/USER-CUDA/fix_shake_cuda.h
+++ b/src/USER-CUDA/fix_shake_cuda.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -63,11 +63,11 @@ class FixShakeCuda : public Fix {
int *type_flag; // constrain bonds to these types
double *mass_list; // constrain bonds to these masses
int nmass; // # of masses in mass_list
- bool neighbor_step; // was neighboring done in this step -> need to run the Cuda_FixShake_Init
+ bool neighbor_step; // was neighboring done in this step -> need to run the Cuda_FixShake_Init
double *bond_distance,*angle_distance; // constraint distances
- cCudaData<double , X_FLOAT , xx >* cu_bond_distance;
- cCudaData<double , X_FLOAT , xx >* cu_angle_distance;
+ cCudaData<double , X_FLOAT , xx >* cu_bond_distance;
+ cCudaData<double , X_FLOAT , xx >* cu_angle_distance;
int ifix_respa; // rRESPA fix needed by SHAKE
int nlevels_respa; // copies of needed rRESPA variables
@@ -85,17 +85,17 @@ class FixShakeCuda : public Fix {
int **shake_atom; // global IDs of atoms in cluster
// central atom is 1st
// lowest global ID is 1st for size 2
-
+
int **shake_type; // bondtype of each bond in cluster
// for angle cluster, 3rd value
// is angletype
double **xshake; // unconstrained atom coords
- cCudaData<int , int , xx >* cu_shake_flag;
- cCudaData<int , int , yx >* cu_shake_atom;
- cCudaData<int , int , yx >* cu_shake_type;
- cCudaData<double , X_FLOAT , xy >* cu_xshake;
- cCudaData<int , int , xx >* cu_list;
- cCudaData<double , ENERGY_FLOAT , xx >* cu_virial;
+ cCudaData<int , int , xx >* cu_shake_flag;
+ cCudaData<int , int , yx >* cu_shake_atom;
+ cCudaData<int , int , yx >* cu_shake_type;
+ cCudaData<double , X_FLOAT , xy >* cu_xshake;
+ cCudaData<int , int , xx >* cu_list;
+ cCudaData<double , ENERGY_FLOAT , xx >* cu_virial;
int* countoccur;
int vflag; // virial flag
diff --git a/src/USER-CUDA/fix_temp_berendsen_cuda.cpp b/src/USER-CUDA/fix_temp_berendsen_cuda.cpp
index 32e86809e47eaa0bc0d98070f0bda61422186ea3..5f5e13dd3cc5cc203e96f4e760cb87d457954df7 100644
--- a/src/USER-CUDA/fix_temp_berendsen_cuda.cpp
+++ b/src/USER-CUDA/fix_temp_berendsen_cuda.cpp
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -28,7 +28,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -120,11 +120,11 @@ int FixTempBerendsenCuda::setmask()
void FixTempBerendsenCuda::init()
{
int icompute = modify->find_compute(id_temp);
- if (icompute < 0)
+ if (icompute < 0)
error->all(FLERR,"Temperature ID for fix temp/berendsen/cuda does not exist");
temperature = modify->compute[icompute];
- if(not temperature->cudable)
- error->warning(FLERR,"Fix temp/berendsen/cuda uses non cudable temperature compute");
+ if(not temperature->cudable)
+ error->warning(FLERR,"Fix temp/berendsen/cuda uses non cudable temperature compute");
if (temperature->tempbias) which = BIAS;
else which = NOBIAS;
@@ -154,32 +154,32 @@ void FixTempBerendsenCuda::end_of_step()
int nlocal = atom->nlocal;
if (which == NOBIAS) {
- Cuda_FixTempBerendsenCuda_EndOfStep(&cuda->shared_data, groupbit,lamda);
+ Cuda_FixTempBerendsenCuda_EndOfStep(&cuda->shared_data, groupbit,lamda);
} else {
if(not temperature->cudable)
{
- cuda->cu_x->download();cuda->cu_v->download();
+ cuda->cu_x->download();cuda->cu_v->download();
for (int i = 0; i < nlocal; i++) {
- if (mask[i] & groupbit) {
- temperature->remove_bias(i,v[i]);
- v[i][0] *= lamda;
- v[i][1] *= lamda;
- v[i][2] *= lamda;
- temperature->restore_bias(i,v[i]);
- }
+ if (mask[i] & groupbit) {
+ temperature->remove_bias(i,v[i]);
+ v[i][0] *= lamda;
+ v[i][1] *= lamda;
+ v[i][2] *= lamda;
+ temperature->restore_bias(i,v[i]);
+ }
}
- cuda->cu_v->upload();
+ cuda->cu_v->upload();
}
else
- {
- temperature->remove_bias_all();
- Cuda_FixTempBerendsenCuda_EndOfStep(&cuda->shared_data, groupbit,lamda);
- temperature->restore_bias_all();
- }
+ {
+ temperature->remove_bias_all();
+ Cuda_FixTempBerendsenCuda_EndOfStep(&cuda->shared_data, groupbit,lamda);
+ temperature->restore_bias_all();
+ }
}
-
+
}
/* ---------------------------------------------------------------------- */
@@ -217,6 +217,3 @@ void FixTempBerendsenCuda::reset_target(double t_new)
{
t_start = t_stop = t_new;
}
-
-
-
diff --git a/src/USER-CUDA/fix_temp_berendsen_cuda.h b/src/USER-CUDA/fix_temp_berendsen_cuda.h
index 391cd07e72f834160503f2dbaeaff6401cd031cb..076d24181370b9242ce226fdf287ccc91dac5828 100644
--- a/src/USER-CUDA/fix_temp_berendsen_cuda.h
+++ b/src/USER-CUDA/fix_temp_berendsen_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
diff --git a/src/USER-CUDA/fix_temp_rescale_cuda.cpp b/src/USER-CUDA/fix_temp_rescale_cuda.cpp
index 25826318873bbb661e089db10cdbe8100b2f3699..85684d9b46b7c51a2e2e9f3431b3841bfd4a9dba 100644
--- a/src/USER-CUDA/fix_temp_rescale_cuda.cpp
+++ b/src/USER-CUDA/fix_temp_rescale_cuda.cpp
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -112,11 +112,11 @@ int FixTempRescaleCuda::setmask()
void FixTempRescaleCuda::init()
{
int icompute = modify->find_compute(id_temp);
- if (icompute < 0)
+ if (icompute < 0)
error->all(FLERR,"Temperature ID for fix temp/rescale/cuda does not exist");
temperature = modify->compute[icompute];
- if(not temperature->cudable)
- error->warning(FLERR,"Fix temp/rescale/cuda uses non cudable temperature compute");
+ if(not temperature->cudable)
+ error->warning(FLERR,"Fix temp/rescale/cuda uses non cudable temperature compute");
if (temperature->tempbias) which = BIAS;
else which = NOBIAS;
}
@@ -149,29 +149,29 @@ void FixTempRescaleCuda::end_of_step()
if (which == NOBIAS) {
energy += (t_current-t_target) * efactor;
- Cuda_FixTempRescaleCuda_EndOfStep(&cuda->shared_data, groupbit,factor);
+ Cuda_FixTempRescaleCuda_EndOfStep(&cuda->shared_data, groupbit,factor);
} else if (which == BIAS) {
energy += (t_current-t_target) * efactor;
if(not temperature->cudable)
{
- cuda->cu_x->download();cuda->cu_v->download();
+ cuda->cu_x->download();cuda->cu_v->download();
for (int i = 0; i < nlocal; i++) {
- if (mask[i] & groupbit) {
- temperature->remove_bias(i,v[i]);
- v[i][0] *= factor;
- v[i][1] *= factor;
- v[i][2] *= factor;
- temperature->restore_bias(i,v[i]);
- }
+ if (mask[i] & groupbit) {
+ temperature->remove_bias(i,v[i]);
+ v[i][0] *= factor;
+ v[i][1] *= factor;
+ v[i][2] *= factor;
+ temperature->restore_bias(i,v[i]);
}
- cuda->cu_v->upload();
+ }
+ cuda->cu_v->upload();
}
else
{
- temperature->remove_bias_all();
- Cuda_FixTempRescaleCuda_EndOfStep(&cuda->shared_data, groupbit,factor);
- temperature->restore_bias_all();
+ temperature->remove_bias_all();
+ Cuda_FixTempRescaleCuda_EndOfStep(&cuda->shared_data, groupbit,factor);
+ temperature->restore_bias_all();
}
}
@@ -201,8 +201,8 @@ int FixTempRescaleCuda::modify_param(int narg, char **arg)
error->all(FLERR,"Fix_modify temperature ID does not compute temperature");
if (temperature->igroup != igroup && comm->me == 0)
error->warning(FLERR,"Group for fix_modify temp != fix group");
- if(not temperature->cudable)
- error->warning(FLERR,"Fix temp/rescale/cuda uses non cudable temperature compute");
+ if(not temperature->cudable)
+ error->warning(FLERR,"Fix temp/rescale/cuda uses non cudable temperature compute");
return 2;
}
return 0;
diff --git a/src/USER-CUDA/fix_temp_rescale_cuda.h b/src/USER-CUDA/fix_temp_rescale_cuda.h
index 75876e60d3baffbed6295e4acf7cf498402a613c..8e7fedfde161e8bb823005ba33272fa152ebf277 100644
--- a/src/USER-CUDA/fix_temp_rescale_cuda.h
+++ b/src/USER-CUDA/fix_temp_rescale_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
diff --git a/src/USER-CUDA/fix_temp_rescale_limit_cuda.cpp b/src/USER-CUDA/fix_temp_rescale_limit_cuda.cpp
index 6979078a4c2da0d62e4c151c1d4ce997a4a5aa6b..a7d4aaa4d79b4620e00f3dc89002db5b31565794 100644
--- a/src/USER-CUDA/fix_temp_rescale_limit_cuda.cpp
+++ b/src/USER-CUDA/fix_temp_rescale_limit_cuda.cpp
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -69,7 +69,7 @@ FixTempRescaleLimitCuda::FixTempRescaleLimitCuda(LAMMPS *lmp, int narg, char **a
fraction = atof(arg[7]);
limit = atof(arg[8]);
if (limit <= 1.0) error->all(FLERR,"Illegal fix temp/rescale/limit/cuda command (limit must be > 1.0)");
-
+
// create a new compute temp
// id = fix-ID + temp, compute group = fix group
@@ -115,11 +115,11 @@ int FixTempRescaleLimitCuda::setmask()
void FixTempRescaleLimitCuda::init()
{
int icompute = modify->find_compute(id_temp);
- if (icompute < 0)
+ if (icompute < 0)
error->all(FLERR,"Temperature ID for fix temp/rescale/limit/cuda does not exist");
temperature = modify->compute[icompute];
- if(not temperature->cudable)
- error->warning(FLERR,"Fix temp/rescale/limit/cuda uses non cudable temperature compute");
+ if(not temperature->cudable)
+ error->warning(FLERR,"Fix temp/rescale/limit/cuda uses non cudable temperature compute");
if (temperature->tempbias) which = BIAS;
else which = NOBIAS;
}
@@ -157,34 +157,34 @@ void FixTempRescaleLimitCuda::end_of_step()
if (which == NOBIAS) {
energy += (t_current-t_target) * efactor;
-
- Cuda_FixTempRescaleLimitCuda_EndOfStep(&cuda->shared_data, groupbit,factor,current_limit);
-
+
+ Cuda_FixTempRescaleLimitCuda_EndOfStep(&cuda->shared_data, groupbit,factor,current_limit);
+
} else if (which == BIAS) {
energy += (t_current-t_target) * efactor;
if(not temperature->cudable)
{
- cuda->cu_x->download();cuda->cu_v->download();
+ cuda->cu_x->download();cuda->cu_v->download();
for (int i = 0; i < nlocal; i++) {
- if (mask[i] & groupbit) {
- temperature->remove_bias(i,v[i]);
- double vx = v[i][0] * factor;
- double vy = v[i][1] * factor;
- double vz = v[i][2] * factor;
- v[i][0]=vx>0?MIN(vx,current_limit):MAX(vx,-current_limit);
- v[i][1]=vy>0?MIN(vy,current_limit):MAX(vy,-current_limit);
- v[i][2]=vz>0?MIN(vz,current_limit):MAX(vz,-current_limit);
-
- temperature->restore_bias(i,v[i]);
- }
+ if (mask[i] & groupbit) {
+ temperature->remove_bias(i,v[i]);
+ double vx = v[i][0] * factor;
+ double vy = v[i][1] * factor;
+ double vz = v[i][2] * factor;
+ v[i][0]=vx>0?MIN(vx,current_limit):MAX(vx,-current_limit);
+ v[i][1]=vy>0?MIN(vy,current_limit):MAX(vy,-current_limit);
+ v[i][2]=vz>0?MIN(vz,current_limit):MAX(vz,-current_limit);
+
+ temperature->restore_bias(i,v[i]);
+ }
}
- cuda->cu_v->upload();
+ cuda->cu_v->upload();
}
else
{
- temperature->remove_bias_all();
- Cuda_FixTempRescaleLimitCuda_EndOfStep(&cuda->shared_data, groupbit,factor,current_limit);
- temperature->restore_bias_all();
+ temperature->remove_bias_all();
+ Cuda_FixTempRescaleLimitCuda_EndOfStep(&cuda->shared_data, groupbit,factor,current_limit);
+ temperature->restore_bias_all();
}
}
@@ -214,8 +214,8 @@ int FixTempRescaleLimitCuda::modify_param(int narg, char **arg)
error->all(FLERR,"Fix_modify temperature ID does not compute temperature");
if (temperature->igroup != igroup && comm->me == 0)
error->warning(FLERR,"Group for fix_modify temp != fix group");
- if(not temperature->cudable)
- error->warning(FLERR,"Fix temp/rescale/limit/cuda uses non cudable temperature compute");
+ if(not temperature->cudable)
+ error->warning(FLERR,"Fix temp/rescale/limit/cuda uses non cudable temperature compute");
return 2;
}
return 0;
diff --git a/src/USER-CUDA/fix_temp_rescale_limit_cuda.h b/src/USER-CUDA/fix_temp_rescale_limit_cuda.h
index 7ee49d3c40f5db42885198045d3265a7f73de74c..de3ccffe32d87232f83cdb521e107ca532116b3f 100644
--- a/src/USER-CUDA/fix_temp_rescale_limit_cuda.h
+++ b/src/USER-CUDA/fix_temp_rescale_limit_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
diff --git a/src/USER-CUDA/fix_viscous_cuda.cpp b/src/USER-CUDA/fix_viscous_cuda.cpp
index a85ce1b31639fb02f1cad67b6adf176585e46c45..a95b5453c5e76e789e79a1ce9d3e03f5085bfff8 100644
--- a/src/USER-CUDA/fix_viscous_cuda.cpp
+++ b/src/USER-CUDA/fix_viscous_cuda.cpp
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -46,14 +46,14 @@ FixViscousCuda::FixViscousCuda(LAMMPS *lmp, int narg, char **arg) :
if(cuda == NULL)
error->all(FLERR,"You cannot use a /cuda class, without activating 'cuda' acceleration. Provide '-c on' as command-line argument to LAMMPS..");
- cu_gamma=NULL;
+ cu_gamma=NULL;
}
/* ---------------------------------------------------------------------- */
FixViscousCuda::~FixViscousCuda()
{
- delete cu_gamma;
+ delete cu_gamma;
}
/* ---------------------------------------------------------------------- */
diff --git a/src/USER-CUDA/fix_viscous_cuda.h b/src/USER-CUDA/fix_viscous_cuda.h
index 54e75cc0d29b1fb0c2adf942cbed9a010f38a72a..cfc7813110785dc123d0ee10961f19b4d27a1246 100644
--- a/src/USER-CUDA/fix_viscous_cuda.h
+++ b/src/USER-CUDA/fix_viscous_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
diff --git a/src/USER-CUDA/modify_cuda.cpp b/src/USER-CUDA/modify_cuda.cpp
index e1d0c385d86bb2653fd7f96959071c2764b776b8..7ac26873306f475cc165f71909b7ac824679af0d 100644
--- a/src/USER-CUDA/modify_cuda.cpp
+++ b/src/USER-CUDA/modify_cuda.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -137,7 +137,7 @@ void ModifyCuda::init()
n_final_integrate_host = n_final_integrate;
n_end_of_step_host = n_end_of_step;
n_thermo_energy_host = n_thermo_energy;
-
+
n_initial_integrate = n_initial_integrate_cuda+n_initial_integrate_host;
n_post_integrate = n_post_integrate_cuda+n_post_integrate_host;
n_pre_exchange = n_pre_exchange_cuda+n_pre_exchange_host;
@@ -147,17 +147,17 @@ void ModifyCuda::init()
n_final_integrate = n_final_integrate_cuda+n_final_integrate_host;
n_end_of_step = n_end_of_step_cuda+n_end_of_step_host;
n_thermo_energy = n_thermo_energy_cuda+n_thermo_energy_host;
-
+
list_init(INITIAL_INTEGRATE_RESPA,
- n_initial_integrate_respa,list_initial_integrate_respa);
+ n_initial_integrate_respa,list_initial_integrate_respa);
list_init(POST_INTEGRATE_RESPA,
- n_post_integrate_respa,list_post_integrate_respa);
+ n_post_integrate_respa,list_post_integrate_respa);
list_init(POST_FORCE_RESPA,
- n_post_force_respa,list_post_force_respa);
+ n_post_force_respa,list_post_force_respa);
list_init(PRE_FORCE_RESPA,
- n_pre_force_respa,list_pre_force_respa);
+ n_pre_force_respa,list_pre_force_respa);
list_init(FINAL_INTEGRATE_RESPA,
- n_final_integrate_respa,list_final_integrate_respa);
+ n_final_integrate_respa,list_final_integrate_respa);
list_init(MIN_PRE_EXCHANGE,n_min_pre_exchange,list_min_pre_exchange);
list_init(MIN_POST_FORCE,n_min_post_force,list_min_post_force);
@@ -231,16 +231,16 @@ void ModifyCuda::init()
void ModifyCuda::initial_integrate(int vflag)
{
- for(int i = 0; i < n_initial_integrate_cuda; i++)
- fix[list_initial_integrate_cuda[i]]->initial_integrate(vflag);
-
- if(n_initial_integrate_host != 0)
- {
- cuda->downloadAll(); cuda->oncpu = true;
- for (int i = 0; i < n_initial_integrate_host; i++)
- fix[list_initial_integrate[i]]->initial_integrate(vflag);
- cuda->uploadAll(); cuda->oncpu = false;
- }
+ for(int i = 0; i < n_initial_integrate_cuda; i++)
+ fix[list_initial_integrate_cuda[i]]->initial_integrate(vflag);
+
+ if(n_initial_integrate_host != 0)
+ {
+ cuda->downloadAll(); cuda->oncpu = true;
+ for (int i = 0; i < n_initial_integrate_host; i++)
+ fix[list_initial_integrate[i]]->initial_integrate(vflag);
+ cuda->uploadAll(); cuda->oncpu = false;
+ }
}
/* ----------------------------------------------------------------------
@@ -249,16 +249,16 @@ void ModifyCuda::initial_integrate(int vflag)
void ModifyCuda::post_integrate()
{
- for(int i = 0; i < n_post_integrate_cuda; i++)
- fix[list_post_integrate_cuda[i]]->post_integrate();
-
- if(n_post_integrate_host != 0)
- {
- cuda->downloadAll(); cuda->oncpu = true;
- for (int i = 0; i < n_post_integrate_host; i++)
- fix[list_post_integrate[i]]->post_integrate();
- cuda->uploadAll(); cuda->oncpu = false;
- }
+ for(int i = 0; i < n_post_integrate_cuda; i++)
+ fix[list_post_integrate_cuda[i]]->post_integrate();
+
+ if(n_post_integrate_host != 0)
+ {
+ cuda->downloadAll(); cuda->oncpu = true;
+ for (int i = 0; i < n_post_integrate_host; i++)
+ fix[list_post_integrate[i]]->post_integrate();
+ cuda->uploadAll(); cuda->oncpu = false;
+ }
}
/* ----------------------------------------------------------------------
@@ -267,16 +267,16 @@ void ModifyCuda::post_integrate()
void ModifyCuda::pre_exchange()
{
- for(int i = 0; i < n_pre_exchange_cuda; i++)
- fix[list_pre_exchange_cuda[i]]->pre_exchange();
-
- if(n_pre_exchange_host != 0)
- {
- cuda->downloadAll(); cuda->oncpu = true;
- for (int i = 0; i < n_pre_exchange_host; i++)
- fix[list_pre_exchange[i]]->pre_exchange();
- cuda->uploadAll(); cuda->oncpu = false;
- }
+ for(int i = 0; i < n_pre_exchange_cuda; i++)
+ fix[list_pre_exchange_cuda[i]]->pre_exchange();
+
+ if(n_pre_exchange_host != 0)
+ {
+ cuda->downloadAll(); cuda->oncpu = true;
+ for (int i = 0; i < n_pre_exchange_host; i++)
+ fix[list_pre_exchange[i]]->pre_exchange();
+ cuda->uploadAll(); cuda->oncpu = false;
+ }
}
/* ----------------------------------------------------------------------
@@ -285,16 +285,16 @@ void ModifyCuda::pre_exchange()
void ModifyCuda::pre_neighbor()
{
- for(int i = 0; i < n_pre_neighbor_cuda; i++)
- fix[list_pre_neighbor_cuda[i]]->pre_neighbor();
-
- if(n_pre_neighbor_host != 0)
- {
- cuda->downloadAll(); cuda->oncpu = true;
- for (int i = 0; i < n_pre_neighbor_host; i++)
- fix[list_pre_neighbor[i]]->pre_neighbor();
- cuda->uploadAll(); cuda->oncpu = false;
- }
+ for(int i = 0; i < n_pre_neighbor_cuda; i++)
+ fix[list_pre_neighbor_cuda[i]]->pre_neighbor();
+
+ if(n_pre_neighbor_host != 0)
+ {
+ cuda->downloadAll(); cuda->oncpu = true;
+ for (int i = 0; i < n_pre_neighbor_host; i++)
+ fix[list_pre_neighbor[i]]->pre_neighbor();
+ cuda->uploadAll(); cuda->oncpu = false;
+ }
}
/* ----------------------------------------------------------------------
@@ -303,30 +303,30 @@ void ModifyCuda::pre_neighbor()
void ModifyCuda::setup_pre_force(int vflag)
{
- for(int i = 0; i < n_pre_force_cuda; i++)
- fix[list_pre_force_cuda[i]]->pre_force(vflag);
-
- if(n_pre_force_host != 0)
- {
- cuda->downloadAll(); cuda->oncpu = true;
- for (int i = 0; i < n_pre_force_host; i++)
- fix[list_pre_force[i]]->pre_force(vflag);
- cuda->uploadAll(); cuda->oncpu = false;
- }
+ for(int i = 0; i < n_pre_force_cuda; i++)
+ fix[list_pre_force_cuda[i]]->pre_force(vflag);
+
+ if(n_pre_force_host != 0)
+ {
+ cuda->downloadAll(); cuda->oncpu = true;
+ for (int i = 0; i < n_pre_force_host; i++)
+ fix[list_pre_force[i]]->pre_force(vflag);
+ cuda->uploadAll(); cuda->oncpu = false;
+ }
}
void ModifyCuda::pre_force(int vflag)
{
- for(int i = 0; i < n_pre_force_cuda; i++)
- fix[list_pre_force_cuda[i]]->pre_force(vflag);
-
- if(n_pre_force_host != 0)
- {
- cuda->downloadAll(); cuda->oncpu = true;
- for (int i = 0; i < n_pre_force_host; i++)
- fix[list_pre_force[i]]->pre_force(vflag);
- cuda->uploadAll(); cuda->oncpu = false;
- }
+ for(int i = 0; i < n_pre_force_cuda; i++)
+ fix[list_pre_force_cuda[i]]->pre_force(vflag);
+
+ if(n_pre_force_host != 0)
+ {
+ cuda->downloadAll(); cuda->oncpu = true;
+ for (int i = 0; i < n_pre_force_host; i++)
+ fix[list_pre_force[i]]->pre_force(vflag);
+ cuda->uploadAll(); cuda->oncpu = false;
+ }
}
/* ----------------------------------------------------------------------
@@ -335,16 +335,16 @@ void ModifyCuda::pre_force(int vflag)
void ModifyCuda::post_force(int vflag)
{
- for(int i = 0; i < n_post_force_cuda; i++)
- fix[list_post_force_cuda[i]]->post_force(vflag);
-
- if(n_post_force_host != 0)
- {
- cuda->downloadAll(); cuda->oncpu = true;
- for (int i = 0; i < n_post_force_host; i++)
- fix[list_post_force[i]]->post_force(vflag);
- cuda->uploadAll(); cuda->oncpu = false;
- }
+ for(int i = 0; i < n_post_force_cuda; i++)
+ fix[list_post_force_cuda[i]]->post_force(vflag);
+
+ if(n_post_force_host != 0)
+ {
+ cuda->downloadAll(); cuda->oncpu = true;
+ for (int i = 0; i < n_post_force_host; i++)
+ fix[list_post_force[i]]->post_force(vflag);
+ cuda->uploadAll(); cuda->oncpu = false;
+ }
}
/* ----------------------------------------------------------------------
@@ -353,16 +353,16 @@ void ModifyCuda::post_force(int vflag)
void ModifyCuda::final_integrate()
{
- for (int i = 0; i < n_final_integrate_cuda; i++)
- fix[list_final_integrate_cuda[i]]->final_integrate();
-
- if(n_final_integrate_host != 0)
- {
- cuda->downloadAll(); cuda->oncpu = true;
- for (int i = 0; i < n_final_integrate_host; i++)
- fix[list_final_integrate[i]]->final_integrate();
- cuda->uploadAll(); cuda->oncpu = false;
- }
+ for (int i = 0; i < n_final_integrate_cuda; i++)
+ fix[list_final_integrate_cuda[i]]->final_integrate();
+
+ if(n_final_integrate_host != 0)
+ {
+ cuda->downloadAll(); cuda->oncpu = true;
+ for (int i = 0; i < n_final_integrate_host; i++)
+ fix[list_final_integrate[i]]->final_integrate();
+ cuda->uploadAll(); cuda->oncpu = false;
+ }
}
/* ----------------------------------------------------------------------
@@ -372,24 +372,24 @@ void ModifyCuda::final_integrate()
void ModifyCuda::end_of_step()
{
- for (int i = 0; i < n_end_of_step_cuda; i++)
- if (update->ntimestep % end_of_step_every_cuda[i] == 0)
- fix[list_end_of_step_cuda[i]]->end_of_step();
-
- if(n_end_of_step_host != 0)
- {
- int do_thisstep=0;
- for (int i = 0; i < n_end_of_step_host; i++)
- if (update->ntimestep % end_of_step_every[i] == 0) do_thisstep=1;
- if(do_thisstep)
- {
- cuda->downloadAll(); cuda->oncpu = true;
- for (int i = 0; i < n_end_of_step_host; i++)
- if (update->ntimestep % end_of_step_every[i] == 0)
- fix[list_end_of_step[i]]->end_of_step();
- cuda->uploadAll(); cuda->oncpu = false;
- }
- }
+ for (int i = 0; i < n_end_of_step_cuda; i++)
+ if (update->ntimestep % end_of_step_every_cuda[i] == 0)
+ fix[list_end_of_step_cuda[i]]->end_of_step();
+
+ if(n_end_of_step_host != 0)
+ {
+ int do_thisstep=0;
+ for (int i = 0; i < n_end_of_step_host; i++)
+ if (update->ntimestep % end_of_step_every[i] == 0) do_thisstep=1;
+ if(do_thisstep)
+ {
+ cuda->downloadAll(); cuda->oncpu = true;
+ for (int i = 0; i < n_end_of_step_host; i++)
+ if (update->ntimestep % end_of_step_every[i] == 0)
+ fix[list_end_of_step[i]]->end_of_step();
+ cuda->uploadAll(); cuda->oncpu = false;
+ }
+ }
}
/* ----------------------------------------------------------------------
@@ -400,20 +400,20 @@ void ModifyCuda::end_of_step()
double ModifyCuda::thermo_energy()
{
- double energy = 0.0;
-
- for (int i = 0; i < n_thermo_energy_cuda; i++)
- energy += fix[list_thermo_energy_cuda[i]]->compute_scalar();
-
- if(n_thermo_energy_host != 0)
- {
- cuda->downloadAll(); cuda->oncpu = true;
- for (int i = 0; i < n_thermo_energy_host; i++)
- energy += fix[list_thermo_energy[i]]->compute_scalar();
- cuda->uploadAll(); cuda->oncpu = false;
- }
-
- return energy;
+ double energy = 0.0;
+
+ for (int i = 0; i < n_thermo_energy_cuda; i++)
+ energy += fix[list_thermo_energy_cuda[i]]->compute_scalar();
+
+ if(n_thermo_energy_host != 0)
+ {
+ cuda->downloadAll(); cuda->oncpu = true;
+ for (int i = 0; i < n_thermo_energy_host; i++)
+ energy += fix[list_thermo_energy[i]]->compute_scalar();
+ cuda->uploadAll(); cuda->oncpu = false;
+ }
+
+ return energy;
}
diff --git a/src/USER-CUDA/modify_cuda.h b/src/USER-CUDA/modify_cuda.h
index 12c0ca25ec6eafa1e8c5048e4bfe5c73ee67e62e..bfea2170461d0fd5b560d5b465edb539be401058 100644
--- a/src/USER-CUDA/modify_cuda.h
+++ b/src/USER-CUDA/modify_cuda.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-CUDA/neigh_full_cuda.cpp b/src/USER-CUDA/neigh_full_cuda.cpp
index 14fe153ec9400bf5066585497a9f76847e8fe235..ba70497ef177ab3036223c89018492a0544527c2 100644
--- a/src/USER-CUDA/neigh_full_cuda.cpp
+++ b/src/USER-CUDA/neigh_full_cuda.cpp
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -43,21 +43,21 @@ void NeighborCuda::full_bin_cuda(NeighList *list)
if(includegroup) error->warning(FLERR,"Warning using inlcudegroup neighborbuild. This is not yet supported by CUDA neighborbuild styles.\n");
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
-
+
if(nlocal==0) return;
CudaNeighList* clist=list->cuda_list;
cuda_shared_neighlist* slist=&clist->sneighlist;
-
+
if(not clist) cuda->registerNeighborList(list);
-
+
clist->build_cuda=true;
-
+
if(slist->bin_extraspace<0.09)
{
for(int i=1;i<=atom->ntypes;i++)
for(int j=1;j<=atom->ntypes;j++)
{
- if(slist->maxcut<cutneighsq[i][j]) slist->maxcut=cutneighsq[i][j];
+ if(slist->maxcut<cutneighsq[i][j]) slist->maxcut=cutneighsq[i][j];
}
slist->maxcut=sqrt(slist->maxcut);
}
@@ -79,19 +79,19 @@ void NeighborCuda::full_bin_cuda(NeighList *list)
bin_dim_tmp[0]+=4;
bin_dim_tmp[1]+=4;
bin_dim_tmp[2]+=4;
- if(bin_nmax_tmp<32) slist->maxcut*=1.2;
- // printf("slist->maxcut: %lf\n", slist->maxcut);
+ if(bin_nmax_tmp<32) slist->maxcut*=1.2;
+ // printf("slist->maxcut: %lf\n", slist->maxcut);
} while(bin_nmax_tmp<32);
if((slist->bin_dim[0]!=bin_dim_tmp[0])||(slist->bin_dim[1]!=bin_dim_tmp[1])||(slist->bin_dim[2]!=bin_dim_tmp[2])||(slist->bin_nmax!=bin_nmax_tmp))
{
- if(slist->binned_id!=NULL)
- CudaWrapper_FreeCudaData(slist->binned_id,slist->bin_dim[0]*slist->bin_dim[1]*slist->bin_dim[2]*slist->bin_nmax*sizeof(int));
- slist->bin_dim[0] = bin_dim_tmp[0];
- slist->bin_dim[1] = bin_dim_tmp[1];
- slist->bin_dim[2] = bin_dim_tmp[2];
- slist->bin_nmax = bin_nmax_tmp;
- slist->binned_id=(int*) CudaWrapper_AllocCudaData(slist->bin_dim[0]*slist->bin_dim[1]*slist->bin_dim[2]*slist->bin_nmax*sizeof(int));
- //printf("slist->bin: %i %i %i %i \n", bin_dim_tmp[0],bin_dim_tmp[1],bin_dim_tmp[2],bin_nmax_tmp);
+ if(slist->binned_id!=NULL)
+ CudaWrapper_FreeCudaData(slist->binned_id,slist->bin_dim[0]*slist->bin_dim[1]*slist->bin_dim[2]*slist->bin_nmax*sizeof(int));
+ slist->bin_dim[0] = bin_dim_tmp[0];
+ slist->bin_dim[1] = bin_dim_tmp[1];
+ slist->bin_dim[2] = bin_dim_tmp[2];
+ slist->bin_nmax = bin_nmax_tmp;
+ slist->binned_id=(int*) CudaWrapper_AllocCudaData(slist->bin_dim[0]*slist->bin_dim[1]*slist->bin_dim[2]*slist->bin_nmax*sizeof(int));
+ //printf("slist->bin: %i %i %i %i \n", bin_dim_tmp[0],bin_dim_tmp[1],bin_dim_tmp[2],bin_nmax_tmp);
}
//if(list->cuda_list->sneighlist.bin_nmax>512) error->all(FLERR,"To many atoms per bin. Likely cause is very long pair cutoff. This needs major rewrite of code and is not yet scheduled to be done.\n");
}while(Cuda_BinAtoms(&cuda->shared_data, &list->cuda_list->sneighlist));
@@ -105,43 +105,43 @@ void NeighborCuda::full_bin_cuda(NeighList *list)
(nex_group!=slist->nex_group)||
(nex_mol!=slist->nex_mol))
{
- slist->nex_type=nex_type;
- slist->nex_group=nex_group;
- slist->nex_mol=nex_mol;
- //printf("%i %i %i\n",nex_type,nex_group,nex_mol);
- if(nex_type)
- {
- delete clist->cu_ex_type;
- clist->cu_ex_type=new cCudaData<int , int , x> (&ex_type[0][0] , & slist->ex_type , (atom->ntypes+1)*(atom->ntypes+1) );
- clist->cu_ex_type->upload();
- }
- //printf("AA %i %i %i\n",nex_type,nex_group,nex_mol);
- if(nex_group)
- {
- delete clist->cu_ex1_bit;
- clist->cu_ex1_bit=new cCudaData<int , int , x> (ex1_bit , & slist->ex1_bit , nex_group );
- clist->cu_ex1_bit->upload();
- //printf("A %i %i %i\n",nex_type,nex_group,nex_mol);
- delete clist->cu_ex2_bit;
- clist->cu_ex2_bit=new cCudaData<int , int , x> (ex2_bit , & slist->ex2_bit , nex_group );
- clist->cu_ex2_bit->upload();
- }
- //printf("B %i %i %i\n",nex_type,nex_group,nex_mol);
- if(nex_mol)
- {
- delete clist->cu_ex_mol_bit;
- clist->cu_ex_mol_bit=new cCudaData<int , int , x> (ex_mol_bit , & slist->ex_mol_bit , nex_mol );
- clist->cu_ex_mol_bit->upload();
- }
- //printf("C %i %i %i\n",nex_type,nex_group,nex_mol);
+ slist->nex_type=nex_type;
+ slist->nex_group=nex_group;
+ slist->nex_mol=nex_mol;
+ //printf("%i %i %i\n",nex_type,nex_group,nex_mol);
+ if(nex_type)
+ {
+ delete clist->cu_ex_type;
+ clist->cu_ex_type=new cCudaData<int , int , x> (&ex_type[0][0] , & slist->ex_type , (atom->ntypes+1)*(atom->ntypes+1) );
+ clist->cu_ex_type->upload();
+ }
+ //printf("AA %i %i %i\n",nex_type,nex_group,nex_mol);
+ if(nex_group)
+ {
+ delete clist->cu_ex1_bit;
+ clist->cu_ex1_bit=new cCudaData<int , int , x> (ex1_bit , & slist->ex1_bit , nex_group );
+ clist->cu_ex1_bit->upload();
+ //printf("A %i %i %i\n",nex_type,nex_group,nex_mol);
+ delete clist->cu_ex2_bit;
+ clist->cu_ex2_bit=new cCudaData<int , int , x> (ex2_bit , & slist->ex2_bit , nex_group );
+ clist->cu_ex2_bit->upload();
+ }
+ //printf("B %i %i %i\n",nex_type,nex_group,nex_mol);
+ if(nex_mol)
+ {
+ delete clist->cu_ex_mol_bit;
+ clist->cu_ex_mol_bit=new cCudaData<int , int , x> (ex_mol_bit , & slist->ex_mol_bit , nex_mol );
+ clist->cu_ex_mol_bit->upload();
+ }
+ //printf("C %i %i %i\n",nex_type,nex_group,nex_mol);
}
int overflow = 0;
int inum = 0;
int npnt = 0;
do
{
- npnt=0;
- inum=0;
+ npnt=0;
+ inum=0;
overflow=0;
clist->grow_device();
slist->cutneighsq=cutneighsq;
@@ -150,59 +150,59 @@ void NeighborCuda::full_bin_cuda(NeighList *list)
//list->cuda_list->grow_device();
if(cuda->shared_data.overlap_comm)
{
- list->cuda_list->inum_border=0;
- list->cuda_list->cu_inum_border->upload();
+ list->cuda_list->inum_border=0;
+ list->cuda_list->cu_inum_border->upload();
}
-
+
cuda->shared_data.atom.nall=nall;
//Cuda_NeighborReBuildFirstneigh(&cuda->shared_data, &list->cuda_list->sneighlist);
overflow= Cuda_NeighborBuildFullBin(&cuda->shared_data, &list->cuda_list->sneighlist);
-
- /*cuda->cu_debugdata->download();
- printf("Debugdata: %i ",cuda->debugdata[0]);
- for(int i=0;i<cuda->debugdata[0];i+=3) printf("// %i %i %i",cuda->debugdata[i+1],cuda->debugdata[i+2],cuda->debugdata[i+3]);
- printf("\n");*/
- //printf("maxneighborsA: %i %i %i %i\n",maxneighbors,pgsize,oneatom,atom->nmax);
-
- if(overflow<0)
+
+ /*cuda->cu_debugdata->download();
+ printf("Debugdata: %i ",cuda->debugdata[0]);
+ for(int i=0;i<cuda->debugdata[0];i+=3) printf("// %i %i %i",cuda->debugdata[i+1],cuda->debugdata[i+2],cuda->debugdata[i+3]);
+ printf("\n");*/
+ //printf("maxneighborsA: %i %i %i %i\n",maxneighbors,pgsize,oneatom,atom->nmax);
+
+ if(overflow<0)
{
- maxneighbors+=32;
- if(-overflow>maxneighbors) maxneighbors=((-overflow+37)/32)*32;
- delete list->cuda_list->cu_neighbors;
- delete [] list->cuda_list->neighbors;
- list->cuda_list->neighbors= new int[slist->maxlocal*maxneighbors];
- list->cuda_list->sneighlist.maxneighbors=maxneighbors;
- //printf("maxneighborsA1: %i %i %i %i %i\n",maxneighbors,pgsize,oneatom,atom->nmax,slist->maxlocal);
- list->cuda_list->cu_neighbors= new cCudaData<int, int, x> (list->cuda_list->neighbors , & list->cuda_list->sneighlist.neighbors, slist->maxlocal*maxneighbors );
- //printf("maxneighborsA2: %i %i %i %i\n",maxneighbors,pgsize,oneatom,atom->nmax);
-
- if(cuda->shared_data.overlap_comm)
- {
- list->cuda_list->sneighlist.maxneighbors=maxneighbors;
- list->cuda_list->dev_free();
- list->cuda_list->dev_alloc();
- }
- //printf("maxneighborsA3: %i %i %i %i\n",maxneighbors,pgsize,oneatom,atom->nmax);
+ maxneighbors+=32;
+ if(-overflow>maxneighbors) maxneighbors=((-overflow+37)/32)*32;
+ delete list->cuda_list->cu_neighbors;
+ delete [] list->cuda_list->neighbors;
+ list->cuda_list->neighbors= new int[slist->maxlocal*maxneighbors];
+ list->cuda_list->sneighlist.maxneighbors=maxneighbors;
+ //printf("maxneighborsA1: %i %i %i %i %i\n",maxneighbors,pgsize,oneatom,atom->nmax,slist->maxlocal);
+ list->cuda_list->cu_neighbors= new cCudaData<int, int, x> (list->cuda_list->neighbors , & list->cuda_list->sneighlist.neighbors, slist->maxlocal*maxneighbors );
+ //printf("maxneighborsA2: %i %i %i %i\n",maxneighbors,pgsize,oneatom,atom->nmax);
+
+ if(cuda->shared_data.overlap_comm)
+ {
+ list->cuda_list->sneighlist.maxneighbors=maxneighbors;
+ list->cuda_list->dev_free();
+ list->cuda_list->dev_alloc();
+ }
+ //printf("maxneighborsA3: %i %i %i %i\n",maxneighbors,pgsize,oneatom,atom->nmax);
}
- //printf("maxneighborsB: %i %i %i %i\n",maxneighbors,pgsize,oneatom,atom->nmax);
+ //printf("maxneighborsB: %i %i %i %i\n",maxneighbors,pgsize,oneatom,atom->nmax);
if(cuda->shared_data.overlap_comm)
{
- list->cuda_list->cu_inum_border->download();
- list->cuda_list->sneighlist.inum_border2=list->cuda_list->inum_border;
+ list->cuda_list->cu_inum_border->download();
+ list->cuda_list->sneighlist.inum_border2=list->cuda_list->inum_border;
}
}
while(overflow<0);
-
+
//cuda->cu_debugdata->download();
// printf("Differences in: %i\n",cuda->debugdata[0]);
// for(int i=0;i<20;i++) printf("%i %i %i %i// ",cuda->debugdata[4*i+1],cuda->debugdata[4*i+2],cuda->debugdata[4*i+3],cuda->debugdata[4*i+4]);
// printf("\n");
/*for(int i=0;i<10;i++)
{
- printf("%i %i // ",i,numneigh[i]);
- for(int j=0;j<numneigh[i];j++)
- printf("%i ",list->cuda_list->neighbors[i+j*nlocal]);
- printf("\n");
+ printf("%i %i // ",i,numneigh[i]);
+ for(int j=0;j<numneigh[i];j++)
+ printf("%i ",list->cuda_list->neighbors[i+j*nlocal]);
+ printf("\n");
}*/
/* int count=0;
if(cuda->shared_data.overlap_comm)
@@ -214,7 +214,7 @@ void NeighborCuda::full_bin_cuda(NeighList *list)
list->cuda_list->cu_neighbors->download();
list->cuda_list->cu_neighbors_inner->download();
list->cuda_list->cu_neighbors_border->download();
-
+
//list->cuda_list->cu_firstneigh->download();
// list->cuda_list->nl_download();
list->cuda_list->cu_numneigh->download();
@@ -222,53 +222,53 @@ void NeighborCuda::full_bin_cuda(NeighList *list)
//for(int i=0;i<nlocal;i++)*/
/* int i=123;
{
- int k=-1;
- //printf("inum_border: %i\n",list->cuda_list->inum_border);
- //for(int j=0;j<list->numneigh[i];j++) printf("%i ",list->firstneigh[i][j]);printf("\n");
- for(int j=0;j<list->cuda_list->inum_border;j++)
- if(list->cuda_list->ilist_border[j]==i) k=j;
- int d=numneigh[i]-list->cuda_list->numneigh_inner[i];
- if(k>-1) d-=list->cuda_list->numneigh_border[k];
- if(d!=0) {printf("Error at %i %i %i %i %i\n",i,k,d,numneigh[i],list->cuda_list->numneigh_inner[i]); diff++;}
- if(k>-1 && count<10)
- {
- printf("Numneighs: %i %i %i Border_i: %i %i\n",numneigh[i],list->cuda_list->numneigh_inner[i],list->cuda_list->numneigh_border[k],k,(int)list->cuda_list->cu_ilist_border->dev_data());
- cuda->shared_data.me=k;
- for(int j=0;j<numneigh[i];j++)
- printf("%i ",list->cuda_list->neighbors[i+j*nlocal]);
- printf("\n");
- for(int j=0;j<list->cuda_list->numneigh_inner[i];j++)
- printf("%i ",list->cuda_list->neighbors_inner[i+j*nlocal]);
- printf(" // ");
- for(int j=0;j<list->cuda_list->numneigh_border[k];j++)
- printf("%i ",list->cuda_list->neighbors_border[k+j*nlocal]);
- printf("\n");
- count++;
- }
+ int k=-1;
+ //printf("inum_border: %i\n",list->cuda_list->inum_border);
+ //for(int j=0;j<list->numneigh[i];j++) printf("%i ",list->firstneigh[i][j]);printf("\n");
+ for(int j=0;j<list->cuda_list->inum_border;j++)
+ if(list->cuda_list->ilist_border[j]==i) k=j;
+ int d=numneigh[i]-list->cuda_list->numneigh_inner[i];
+ if(k>-1) d-=list->cuda_list->numneigh_border[k];
+ if(d!=0) {printf("Error at %i %i %i %i %i\n",i,k,d,numneigh[i],list->cuda_list->numneigh_inner[i]); diff++;}
+ if(k>-1 && count<10)
+ {
+ printf("Numneighs: %i %i %i Border_i: %i %i\n",numneigh[i],list->cuda_list->numneigh_inner[i],list->cuda_list->numneigh_border[k],k,(int)list->cuda_list->cu_ilist_border->dev_data());
+ cuda->shared_data.me=k;
+ for(int j=0;j<numneigh[i];j++)
+ printf("%i ",list->cuda_list->neighbors[i+j*nlocal]);
+ printf("\n");
+ for(int j=0;j<list->cuda_list->numneigh_inner[i];j++)
+ printf("%i ",list->cuda_list->neighbors_inner[i+j*nlocal]);
+ printf(" // ");
+ for(int j=0;j<list->cuda_list->numneigh_border[k];j++)
+ printf("%i ",list->cuda_list->neighbors_border[k+j*nlocal]);
+ printf("\n");
+ count++;
+ }
}
printf("%i\n",diff);
}*/
list->cuda_list->cu_numneigh->download();
list->cuda_list->cu_ilist->download();
cuda->shared_data.atom.update_neigh=2;
- //printf("Done\n");
-
+ //printf("Done\n");
+
MYDBG(printf(" # CUDA::NeighFullBinCuda ... end\n");)
-
+
}
void NeighborCuda::full_nsq_cuda(NeighList *list)
{
- printf("Full_Nsq cuda neighbor list build is not implemented anymore.\n");
+ printf("Full_Nsq cuda neighbor list build is not implemented anymore.\n");
return;
/*
MYDBG(printf(" # CUDA::NeighFullNSQCuda ... start\n");)
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
-
+
if(cuda->cu_xhold) cuda->cu_xhold->upload();
-
+
if(not list->cuda_list) cuda->registerNeighborList(list);
list->cuda_list->build_cuda=true;
@@ -285,27 +285,27 @@ return;
int npnt = 0;
do
{
- npage=0;
- npnt=0;
- inum=0;
+ npage=0;
+ npnt=0;
+ inum=0;
overflow=0;
- neigh_lists_per_page=pgsize/maxneighbors;
+ neigh_lists_per_page=pgsize/maxneighbors;
npage=(2*nlocal*maxneighbors-1)/pgsize;
while(npage>list->maxpage) list->add_pages();
pages = list->pages;
npage=0;
- list->cuda_list->sneighlist.neigh_lists_per_page=pgsize/maxneighbors;
+ list->cuda_list->sneighlist.neigh_lists_per_page=pgsize/maxneighbors;
list->cuda_list->grow_device();
list->cuda_list->sneighlist.cutneighsq=cutneighsq;
list->cuda_list->sneighlist.maxneighbors=maxneighbors;
list->cuda_list->sneighlist.inum = list->inum = nlocal;
-
+
cuda->shared_data.atom.nall=nall;
Cuda_NeighborReBuildFirstneigh(&cuda->shared_data, &list->cuda_list->sneighlist);
overflow= not Cuda_NeighborBuildFullNsq(&cuda->shared_data, &list->cuda_list->sneighlist);
-
-
-
+
+
+
if(overflow) maxneighbors+=32;
}
while(overflow);
@@ -313,4 +313,3 @@ return;
MYDBG(printf(" # CUDA::NeighFullNSQCuda ... end\n");)
*/
}
-
diff --git a/src/USER-CUDA/neighbor_cuda.cpp b/src/USER-CUDA/neighbor_cuda.cpp
index dc5af9f2f8025b59be926cca208520fc0d2ee886..23953ebc1597cc9b653f2775233c08b0597d208a 100644
--- a/src/USER-CUDA/neighbor_cuda.cpp
+++ b/src/USER-CUDA/neighbor_cuda.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -58,7 +58,7 @@ void NeighborCuda::init()
void NeighborCuda::choose_build(int index, NeighRequest *rq)
{
Neighbor::choose_build(index,rq);
-
+
if (rq->full && style == NSQ && rq->cudable)
pair_build[index] = (Neighbor::PairPtr) &NeighborCuda::full_nsq_cuda;
else if (rq->full && style == BIN && rq->cudable)
@@ -88,12 +88,12 @@ int NeighborCuda::check_distance()
domain->box_corners();
delta1 = delta2 = 0.0;
for (int i = 0; i < 8; i++) {
- delx = corners[i][0] - corners_hold[i][0];
- dely = corners[i][1] - corners_hold[i][1];
- delz = corners[i][2] - corners_hold[i][2];
- delta = sqrt(delx*delx + dely*dely + delz*delz);
- if (delta > delta1) delta1 = delta;
- else if (delta > delta2) delta2 = delta;
+ delx = corners[i][0] - corners_hold[i][0];
+ dely = corners[i][1] - corners_hold[i][1];
+ delz = corners[i][2] - corners_hold[i][2];
+ delta = sqrt(delx*delx + dely*dely + delz*delz);
+ if (delta > delta1) delta1 = delta;
+ else if (delta > delta2) delta2 = delta;
}
delta = 0.5 * (skin - (delta1+delta2));
deltasq = delta*delta;
@@ -117,7 +117,7 @@ int NeighborCuda::check_distance()
}
}
else flag = cuda->shared_data.atom.reneigh_flag;
-
+
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_MAX,world);
if (flagall && ago == MAX(every,delay)) ndanger++;
@@ -140,43 +140,43 @@ void NeighborCuda::build()
cuda->update_xhold(maxhold, &xhold[0][0]);
else {
if (cuda->finished_setup) cuda->cu_x_download();
-
+
double **x = atom->x;
int nlocal = atom->nlocal;
if (includegroup) nlocal = atom->nfirst;
if (nlocal > maxhold) {
- maxhold = atom->nmax;
- memory->destroy(xhold);
- memory->create(xhold,maxhold,3,"neigh:xhold");
+ maxhold = atom->nmax;
+ memory->destroy(xhold);
+ memory->create(xhold,maxhold,3,"neigh:xhold");
}
for (i = 0; i < nlocal; i++) {
- xhold[i][0] = x[i][0];
- xhold[i][1] = x[i][1];
- xhold[i][2] = x[i][2];
+ xhold[i][0] = x[i][0];
+ xhold[i][1] = x[i][1];
+ xhold[i][2] = x[i][2];
}
if (boxcheck) {
- if (triclinic == 0) {
- boxlo_hold[0] = bboxlo[0];
- boxlo_hold[1] = bboxlo[1];
- boxlo_hold[2] = bboxlo[2];
- boxhi_hold[0] = bboxhi[0];
- boxhi_hold[1] = bboxhi[1];
- boxhi_hold[2] = bboxhi[2];
- } else {
- domain->box_corners();
- corners = domain->corners;
- for (i = 0; i < 8; i++) {
- corners_hold[i][0] = corners[i][0];
- corners_hold[i][1] = corners[i][1];
- corners_hold[i][2] = corners[i][2];
- }
- }
+ if (triclinic == 0) {
+ boxlo_hold[0] = bboxlo[0];
+ boxlo_hold[1] = bboxlo[1];
+ boxlo_hold[2] = bboxlo[2];
+ boxhi_hold[0] = bboxhi[0];
+ boxhi_hold[1] = bboxhi[1];
+ boxhi_hold[2] = bboxhi[2];
+ } else {
+ domain->box_corners();
+ corners = domain->corners;
+ for (i = 0; i < 8; i++) {
+ corners_hold[i][0] = corners[i][0];
+ corners_hold[i][1] = corners[i][1];
+ corners_hold[i][2] = corners[i][2];
+ }
+ }
}
}
}
-
+
if (not cudable && cuda->finished_setup && atom->avec->cudable)
- cuda->downloadAll();
+ cuda->downloadAll();
if (cudable && (not cuda->finished_setup)) {
cuda->checkResize();
cuda->uploadAll();
@@ -194,7 +194,7 @@ void NeighborCuda::build()
maxatom = atom->nmax;
for (i = 0; i < nglist; i++) lists[glist[i]]->grow(maxatom);
}
-
+
// extend atom bin list if necessary
if (style != NSQ && atom->nmax > maxbin) {
diff --git a/src/USER-CUDA/neighbor_cuda.h b/src/USER-CUDA/neighbor_cuda.h
index c171b23be3c20c3ebe16e532f6d12b547ca75f2d..847c5bcb1e9528b1ac05a357b2c8397d0e0c3ddc 100644
--- a/src/USER-CUDA/neighbor_cuda.h
+++ b/src/USER-CUDA/neighbor_cuda.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-CUDA/pair_born_coul_long_cuda.cpp b/src/USER-CUDA/pair_born_coul_long_cuda.cpp
index 0918be7ce8bab03e74a031699f8a4cc5660123ad..c5e65da3e2e7c4756d529056c6584cbeb9fd4cf3 100644
--- a/src/USER-CUDA/pair_born_coul_long_cuda.cpp
+++ b/src/USER-CUDA/pair_born_coul_long_cuda.cpp
@@ -1,23 +1,23 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
Contributing author: Paul Crozier (SNL)
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -61,10 +61,10 @@ PairBornCoulLongCuda::PairBornCoulLongCuda(LAMMPS *lmp) : PairBornCoulLong(lmp)
if(cuda == NULL)
error->all(FLERR,"You cannot use a /cuda class, without activating 'cuda' acceleration. Provide '-c on' as command-line argument to LAMMPS..");
- allocated2 = false;
- cuda->shared_data.pair.cudable_force = 1;
- cuda->shared_data.pair.use_block_per_atom = 0;
- cuda->setSystemParams();
+ allocated2 = false;
+ cuda->shared_data.pair.cudable_force = 1;
+ cuda->shared_data.pair.use_block_per_atom = 0;
+ cuda->setSystemParams();
}
/* ----------------------------------------------------------------------
@@ -73,59 +73,59 @@ PairBornCoulLongCuda::PairBornCoulLongCuda(LAMMPS *lmp) : PairBornCoulLong(lmp)
void PairBornCoulLongCuda::allocate()
{
- if(! allocated) PairBornCoulLong::allocate();
- if(! allocated2)
- {
- allocated2 = true;
- cuda->shared_data.pair.cut = cut_lj;
- cuda->shared_data.pair.coeff1 = rhoinv;
- cuda->shared_data.pair.coeff2 = sigma;
- cuda->shared_data.pair.coeff3 = a;
- cuda->shared_data.pair.coeff4 = c;
- cuda->shared_data.pair.coeff5 = d;
- cuda->shared_data.pair.offset = offset;
- cuda->shared_data.pair.special_lj = force->special_lj;
- cuda->shared_data.pair.special_coul = force->special_coul;
- }
+ if(! allocated) PairBornCoulLong::allocate();
+ if(! allocated2)
+ {
+ allocated2 = true;
+ cuda->shared_data.pair.cut = cut_lj;
+ cuda->shared_data.pair.coeff1 = rhoinv;
+ cuda->shared_data.pair.coeff2 = sigma;
+ cuda->shared_data.pair.coeff3 = a;
+ cuda->shared_data.pair.coeff4 = c;
+ cuda->shared_data.pair.coeff5 = d;
+ cuda->shared_data.pair.offset = offset;
+ cuda->shared_data.pair.special_lj = force->special_lj;
+ cuda->shared_data.pair.special_coul = force->special_coul;
+ }
}
/* ---------------------------------------------------------------------- */
void PairBornCoulLongCuda::compute(int eflag, int vflag)
{
- MYDBG( printf("PairBornCoulLongCuda compute start\n"); fflush(stdout);)
- if (eflag || vflag) ev_setup(eflag,vflag);
- if(eflag) cuda->cu_eng_vdwl->upload();
- if(eflag) cuda->cu_eng_coul->upload();
- if(vflag) cuda->cu_virial->upload();
- #ifdef CUDA_USE_BINNING
- Cuda_PairBornCoulLongCuda(& cuda->shared_data, eflag, vflag);
- #else
- Cuda_PairBornCoulLongCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);
- #endif
+ MYDBG( printf("PairBornCoulLongCuda compute start\n"); fflush(stdout);)
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ if(eflag) cuda->cu_eng_vdwl->upload();
+ if(eflag) cuda->cu_eng_coul->upload();
+ if(vflag) cuda->cu_virial->upload();
+ #ifdef CUDA_USE_BINNING
+ Cuda_PairBornCoulLongCuda(& cuda->shared_data, eflag, vflag);
+ #else
+ Cuda_PairBornCoulLongCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);
+ #endif
if(not cuda->shared_data.pair.collect_forces_later)
{
- if(eflag) cuda->cu_eng_vdwl->download();
- if(eflag) cuda->cu_eng_coul->download();
- if(vflag) cuda->cu_virial->download();
+ if(eflag) cuda->cu_eng_vdwl->download();
+ if(eflag) cuda->cu_eng_coul->download();
+ if(vflag) cuda->cu_virial->download();
}
- MYDBG( printf("PairBornCoulLongCuda compute end\n"); fflush(stdout);)
+ MYDBG( printf("PairBornCoulLongCuda compute end\n"); fflush(stdout);)
}
/* ---------------------------------------------------------------------- */
void PairBornCoulLongCuda::settings(int narg, char **arg)
{
- PairBornCoulLong::settings(narg, arg);
- cuda->shared_data.pair.cut_global = (F_FLOAT) cut_lj_global;
+ PairBornCoulLong::settings(narg, arg);
+ cuda->shared_data.pair.cut_global = (F_FLOAT) cut_lj_global;
}
/* ---------------------------------------------------------------------- */
void PairBornCoulLongCuda::coeff(int narg, char **arg)
{
- PairBornCoulLong::coeff(narg, arg);
- allocate();
+ PairBornCoulLong::coeff(narg, arg);
+ allocate();
}
void PairBornCoulLongCuda::init_style()
@@ -135,14 +135,14 @@ void PairBornCoulLongCuda::init_style()
// request regular or rRESPA neighbor lists
int irequest;
-
+
if (strstr(update->integrate_style,"respa")) error->all(FLERR,"Integrate Style Respa is not supported by pair style buck/coul/long/cuda");
-
- irequest = neighbor->request(this);
+
+ irequest = neighbor->request(this);
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->cudable = 1;
-
+
cut_coulsq = cut_coul * cut_coul;
cuda->shared_data.pair.cut_coulsq_global=cut_coulsq;
@@ -152,32 +152,32 @@ void PairBornCoulLongCuda::init_style()
g_ewald = force->kspace->g_ewald;
cuda->shared_data.pair.g_ewald=g_ewald;
cuda->shared_data.pppm.qqrd2e=force->qqrd2e;
-
+
if(ncoultablebits) error->warning(FLERR,"# CUDA: You asked for the usage of Coulomb Tables. This is not supported in CUDA Pair forces. Setting is ignored.\n");
}
void PairBornCoulLongCuda::init_list(int id, NeighList *ptr)
{
- MYDBG(printf("# CUDA PairBornCoulLongCuda::init_list\n");)
- PairBornCoulLong::init_list(id, ptr);
- #ifndef CUDA_USE_BINNING
- // right now we can only handle verlet (id 0), not respa
- if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
- // see Neighbor::init() for details on lammps lists' logic
- #endif
- MYDBG(printf("# CUDA PairBornCoulLongCuda::init_list end\n");)
+ MYDBG(printf("# CUDA PairBornCoulLongCuda::init_list\n");)
+ PairBornCoulLong::init_list(id, ptr);
+ #ifndef CUDA_USE_BINNING
+ // right now we can only handle verlet (id 0), not respa
+ if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
+ // see Neighbor::init() for details on lammps lists' logic
+ #endif
+ MYDBG(printf("# CUDA PairBornCoulLongCuda::init_list end\n");)
}
void PairBornCoulLongCuda::ev_setup(int eflag, int vflag)
{
- int maxeatomold=maxeatom;
- PairBornCoulLong::ev_setup(eflag,vflag);
+ int maxeatomold=maxeatom;
+ PairBornCoulLong::ev_setup(eflag,vflag);
+
+ if (eflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
- if (eflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
+ if (vflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
- if (vflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
-
}
diff --git a/src/USER-CUDA/pair_born_coul_long_cuda.h b/src/USER-CUDA/pair_born_coul_long_cuda.h
index 91f6f650ae6becf90e23bf1fd6db795e81868702..497c2d533e781382a33b0bbb022cd8aa61354a94 100644
--- a/src/USER-CUDA/pair_born_coul_long_cuda.h
+++ b/src/USER-CUDA/pair_born_coul_long_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -36,19 +36,19 @@ namespace LAMMPS_NS {
class PairBornCoulLongCuda : public PairBornCoulLong
{
- public:
- PairBornCoulLongCuda(class LAMMPS *);
- void compute(int, int);
- void settings(int, char **);
- void coeff(int, char **);
- void init_list(int, class NeighList *);
- void init_style();
- void ev_setup(int eflag, int vflag);
- protected:
- class Cuda *cuda;
- void allocate();
- bool allocated2;
- class CudaNeighList* cuda_neigh_list;
+ public:
+ PairBornCoulLongCuda(class LAMMPS *);
+ void compute(int, int);
+ void settings(int, char **);
+ void coeff(int, char **);
+ void init_list(int, class NeighList *);
+ void init_style();
+ void ev_setup(int eflag, int vflag);
+ protected:
+ class Cuda *cuda;
+ void allocate();
+ bool allocated2;
+ class CudaNeighList* cuda_neigh_list;
};
}
diff --git a/src/USER-CUDA/pair_buck_coul_cut_cuda.cpp b/src/USER-CUDA/pair_buck_coul_cut_cuda.cpp
index cc927fa5b0b74b43b8b708443944fbf2154336e7..00698ed81d5c095ae1d6c7218ba8da3d9d7b7ea9 100644
--- a/src/USER-CUDA/pair_buck_coul_cut_cuda.cpp
+++ b/src/USER-CUDA/pair_buck_coul_cut_cuda.cpp
@@ -1,23 +1,23 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
Contributing author: Paul Crozier (SNL)
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -54,10 +54,10 @@ PairBuckCoulCutCuda::PairBuckCoulCutCuda(LAMMPS *lmp) : PairBuckCoulCut(lmp)
if(cuda == NULL)
error->all(FLERR,"You cannot use a /cuda class, without activating 'cuda' acceleration. Provide '-c on' as command-line argument to LAMMPS..");
- allocated2 = false;
- cuda->shared_data.pair.cudable_force = 1;
- cuda->shared_data.pair.use_block_per_atom = 0;
- cuda->setSystemParams();
+ allocated2 = false;
+ cuda->shared_data.pair.cudable_force = 1;
+ cuda->shared_data.pair.use_block_per_atom = 0;
+ cuda->setSystemParams();
}
/* ----------------------------------------------------------------------
@@ -66,59 +66,59 @@ PairBuckCoulCutCuda::PairBuckCoulCutCuda(LAMMPS *lmp) : PairBuckCoulCut(lmp)
void PairBuckCoulCutCuda::allocate()
{
- if(! allocated) PairBuckCoulCut::allocate();
- if(! allocated2)
- {
- allocated2 = true;
- cuda->shared_data.pair.cut_coul = cut_coul;
- cuda->shared_data.pair.cut = cut_lj;
- cuda->shared_data.pair.coeff1 = rhoinv;
- cuda->shared_data.pair.coeff2 = buck1;
- cuda->shared_data.pair.coeff3 = buck2;
- cuda->shared_data.pair.coeff4 = a;
- cuda->shared_data.pair.coeff5 = c;
- cuda->shared_data.pair.offset = offset;
- cuda->shared_data.pair.special_lj = force->special_lj;
- cuda->shared_data.pair.special_coul = force->special_coul;
- }
+ if(! allocated) PairBuckCoulCut::allocate();
+ if(! allocated2)
+ {
+ allocated2 = true;
+ cuda->shared_data.pair.cut_coul = cut_coul;
+ cuda->shared_data.pair.cut = cut_lj;
+ cuda->shared_data.pair.coeff1 = rhoinv;
+ cuda->shared_data.pair.coeff2 = buck1;
+ cuda->shared_data.pair.coeff3 = buck2;
+ cuda->shared_data.pair.coeff4 = a;
+ cuda->shared_data.pair.coeff5 = c;
+ cuda->shared_data.pair.offset = offset;
+ cuda->shared_data.pair.special_lj = force->special_lj;
+ cuda->shared_data.pair.special_coul = force->special_coul;
+ }
}
/* ---------------------------------------------------------------------- */
void PairBuckCoulCutCuda::compute(int eflag, int vflag)
{
- MYDBG( printf("PairBuckCoulCutCuda compute start\n"); fflush(stdout);)
- if (eflag || vflag) ev_setup(eflag,vflag);
- if(eflag) cuda->cu_eng_vdwl->upload();
- if(eflag) cuda->cu_eng_coul->upload();
- if(vflag) cuda->cu_virial->upload();
-
- Cuda_PairBuckCoulCutCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);
-
+ MYDBG( printf("PairBuckCoulCutCuda compute start\n"); fflush(stdout);)
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ if(eflag) cuda->cu_eng_vdwl->upload();
+ if(eflag) cuda->cu_eng_coul->upload();
+ if(vflag) cuda->cu_virial->upload();
+
+ Cuda_PairBuckCoulCutCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);
+
if(not cuda->shared_data.pair.collect_forces_later)
{
- if(eflag) cuda->cu_eng_vdwl->download();
- if(eflag) cuda->cu_eng_coul->download();
- if(vflag) cuda->cu_virial->download();
+ if(eflag) cuda->cu_eng_vdwl->download();
+ if(eflag) cuda->cu_eng_coul->download();
+ if(vflag) cuda->cu_virial->download();
}
- MYDBG( printf("PairBuckCoulCutCuda compute end\n"); fflush(stdout);)
+ MYDBG( printf("PairBuckCoulCutCuda compute end\n"); fflush(stdout);)
}
/* ---------------------------------------------------------------------- */
void PairBuckCoulCutCuda::settings(int narg, char **arg)
{
- PairBuckCoulCut::settings(narg, arg);
- cuda->shared_data.pair.cut_coul_global = (F_FLOAT) cut_coul_global;
- cuda->shared_data.pair.cut_global = (F_FLOAT) cut_lj_global;
+ PairBuckCoulCut::settings(narg, arg);
+ cuda->shared_data.pair.cut_coul_global = (F_FLOAT) cut_coul_global;
+ cuda->shared_data.pair.cut_global = (F_FLOAT) cut_lj_global;
}
/* ---------------------------------------------------------------------- */
void PairBuckCoulCutCuda::coeff(int narg, char **arg)
{
- PairBuckCoulCut::coeff(narg, arg);
- allocate();
+ PairBuckCoulCut::coeff(narg, arg);
+ allocate();
}
void PairBuckCoulCutCuda::init_style()
@@ -128,17 +128,17 @@ void PairBuckCoulCutCuda::init_style()
// request regular or rRESPA neighbor lists
int irequest;
-
+
if (strstr(update->integrate_style,"respa")) error->all(FLERR,"Integrate Style Respa is not supported by pair style buck/coul/long/cuda");
-
- irequest = neighbor->request(this);
+
+ irequest = neighbor->request(this);
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->cudable = 1;
-
+
cuda->shared_data.pppm.qqrd2e=force->qqrd2e;
-
+
cuda->shared_data.pair.cut_coulsq_global=cut_coul_global * cut_coul_global;
if(ncoultablebits) error->warning(FLERR,"# CUDA: You asked for the usage of Coulomb Tables. This is not supported in CUDA Pair forces. Setting is ignored.\n");
@@ -146,25 +146,25 @@ void PairBuckCoulCutCuda::init_style()
void PairBuckCoulCutCuda::init_list(int id, NeighList *ptr)
{
- MYDBG(printf("# CUDA PairBuckCoulCutCuda::init_list\n");)
- PairBuckCoulCut::init_list(id, ptr);
- #ifndef CUDA_USE_BINNING
- // right now we can only handle verlet (id 0), not respa
- if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
- // see Neighbor::init() for details on lammps lists' logic
- #endif
- MYDBG(printf("# CUDA PairBuckCoulCutCuda::init_list end\n");)
+ MYDBG(printf("# CUDA PairBuckCoulCutCuda::init_list\n");)
+ PairBuckCoulCut::init_list(id, ptr);
+ #ifndef CUDA_USE_BINNING
+ // right now we can only handle verlet (id 0), not respa
+ if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
+ // see Neighbor::init() for details on lammps lists' logic
+ #endif
+ MYDBG(printf("# CUDA PairBuckCoulCutCuda::init_list end\n");)
}
void PairBuckCoulCutCuda::ev_setup(int eflag, int vflag)
{
- int maxeatomold=maxeatom;
- PairBuckCoulCut::ev_setup(eflag,vflag);
+ int maxeatomold=maxeatom;
+ PairBuckCoulCut::ev_setup(eflag,vflag);
+
+ if (eflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
- if (eflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
+ if (vflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
- if (vflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
-
}
diff --git a/src/USER-CUDA/pair_buck_coul_cut_cuda.h b/src/USER-CUDA/pair_buck_coul_cut_cuda.h
index b46a18364af3f5ebdd314cb8143db7e904ea7afe..c766eede1cea821296a38a1f07ecff87db7e402a 100644
--- a/src/USER-CUDA/pair_buck_coul_cut_cuda.h
+++ b/src/USER-CUDA/pair_buck_coul_cut_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -36,19 +36,19 @@ namespace LAMMPS_NS {
class PairBuckCoulCutCuda : public PairBuckCoulCut
{
- public:
- PairBuckCoulCutCuda(class LAMMPS *);
- void compute(int, int);
- void settings(int, char **);
- void coeff(int, char **);
- void init_list(int, class NeighList *);
- void init_style();
- void ev_setup(int eflag, int vflag);
- protected:
- class Cuda *cuda;
- void allocate();
- bool allocated2;
- class CudaNeighList* cuda_neigh_list;
+ public:
+ PairBuckCoulCutCuda(class LAMMPS *);
+ void compute(int, int);
+ void settings(int, char **);
+ void coeff(int, char **);
+ void init_list(int, class NeighList *);
+ void init_style();
+ void ev_setup(int eflag, int vflag);
+ protected:
+ class Cuda *cuda;
+ void allocate();
+ bool allocated2;
+ class CudaNeighList* cuda_neigh_list;
};
}
diff --git a/src/USER-CUDA/pair_buck_coul_long_cuda.cpp b/src/USER-CUDA/pair_buck_coul_long_cuda.cpp
index 01cc6243772b68ea947977c4fb7b820415ad4927..07948e5ee374a340444f5312134e99e265f94a0e 100644
--- a/src/USER-CUDA/pair_buck_coul_long_cuda.cpp
+++ b/src/USER-CUDA/pair_buck_coul_long_cuda.cpp
@@ -1,23 +1,23 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
Contributing author: Paul Crozier (SNL)
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -61,10 +61,10 @@ PairBuckCoulLongCuda::PairBuckCoulLongCuda(LAMMPS *lmp) : PairBuckCoulLong(lmp)
if(cuda == NULL)
error->all(FLERR,"You cannot use a /cuda class, without activating 'cuda' acceleration. Provide '-c on' as command-line argument to LAMMPS..");
- allocated2 = false;
- cuda->shared_data.pair.cudable_force = 1;
- cuda->shared_data.pair.use_block_per_atom = 0;
- cuda->setSystemParams();
+ allocated2 = false;
+ cuda->shared_data.pair.cudable_force = 1;
+ cuda->shared_data.pair.use_block_per_atom = 0;
+ cuda->setSystemParams();
}
/* ----------------------------------------------------------------------
@@ -73,57 +73,57 @@ PairBuckCoulLongCuda::PairBuckCoulLongCuda(LAMMPS *lmp) : PairBuckCoulLong(lmp)
void PairBuckCoulLongCuda::allocate()
{
- if(! allocated) PairBuckCoulLong::allocate();
- if(! allocated2)
- {
- allocated2 = true;
- cuda->shared_data.pair.cut = cut_lj;
- cuda->shared_data.pair.coeff1 = rhoinv;
- cuda->shared_data.pair.coeff2 = buck1;
- cuda->shared_data.pair.coeff3 = buck2;
- cuda->shared_data.pair.coeff4 = a;
- cuda->shared_data.pair.coeff5 = c;
- cuda->shared_data.pair.offset = offset;
- cuda->shared_data.pair.special_lj = force->special_lj;
- cuda->shared_data.pair.special_coul = force->special_coul;
- }
+ if(! allocated) PairBuckCoulLong::allocate();
+ if(! allocated2)
+ {
+ allocated2 = true;
+ cuda->shared_data.pair.cut = cut_lj;
+ cuda->shared_data.pair.coeff1 = rhoinv;
+ cuda->shared_data.pair.coeff2 = buck1;
+ cuda->shared_data.pair.coeff3 = buck2;
+ cuda->shared_data.pair.coeff4 = a;
+ cuda->shared_data.pair.coeff5 = c;
+ cuda->shared_data.pair.offset = offset;
+ cuda->shared_data.pair.special_lj = force->special_lj;
+ cuda->shared_data.pair.special_coul = force->special_coul;
+ }
}
/* ---------------------------------------------------------------------- */
void PairBuckCoulLongCuda::compute(int eflag, int vflag)
{
- MYDBG( printf("PairBuckCoulLongCuda compute start\n"); fflush(stdout);)
- if (eflag || vflag) ev_setup(eflag,vflag);
- if(eflag) cuda->cu_eng_vdwl->upload();
- if(eflag) cuda->cu_eng_coul->upload();
- if(vflag) cuda->cu_virial->upload();
+ MYDBG( printf("PairBuckCoulLongCuda compute start\n"); fflush(stdout);)
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ if(eflag) cuda->cu_eng_vdwl->upload();
+ if(eflag) cuda->cu_eng_coul->upload();
+ if(vflag) cuda->cu_virial->upload();
- Cuda_PairBuckCoulLongCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);
+ Cuda_PairBuckCoulLongCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);
if(not cuda->shared_data.pair.collect_forces_later)
{
- if(eflag) cuda->cu_eng_vdwl->download();
- if(eflag) cuda->cu_eng_coul->download();
- if(vflag) cuda->cu_virial->download();
+ if(eflag) cuda->cu_eng_vdwl->download();
+ if(eflag) cuda->cu_eng_coul->download();
+ if(vflag) cuda->cu_virial->download();
}
- MYDBG( printf("PairBuckCoulLongCuda compute end\n"); fflush(stdout);)
+ MYDBG( printf("PairBuckCoulLongCuda compute end\n"); fflush(stdout);)
}
/* ---------------------------------------------------------------------- */
void PairBuckCoulLongCuda::settings(int narg, char **arg)
{
- PairBuckCoulLong::settings(narg, arg);
- cuda->shared_data.pair.cut_global = (F_FLOAT) cut_lj_global;
+ PairBuckCoulLong::settings(narg, arg);
+ cuda->shared_data.pair.cut_global = (F_FLOAT) cut_lj_global;
}
/* ---------------------------------------------------------------------- */
void PairBuckCoulLongCuda::coeff(int narg, char **arg)
{
- PairBuckCoulLong::coeff(narg, arg);
- allocate();
+ PairBuckCoulLong::coeff(narg, arg);
+ allocate();
}
void PairBuckCoulLongCuda::init_style()
@@ -133,14 +133,14 @@ void PairBuckCoulLongCuda::init_style()
// request regular or rRESPA neighbor lists
int irequest;
-
+
if (strstr(update->integrate_style,"respa")) error->all(FLERR,"Integrate Style Respa is not supported by pair style buck/coul/long/cuda");
-
- irequest = neighbor->request(this);
+
+ irequest = neighbor->request(this);
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->cudable = 1;
-
+
cut_coulsq = cut_coul * cut_coul;
cuda->shared_data.pair.cut_coulsq_global=cut_coulsq;
@@ -150,32 +150,32 @@ void PairBuckCoulLongCuda::init_style()
g_ewald = force->kspace->g_ewald;
cuda->shared_data.pair.g_ewald=g_ewald;
cuda->shared_data.pppm.qqrd2e=force->qqrd2e;
-
+
if(ncoultablebits) error->warning(FLERR,"# CUDA: You asked for the usage of Coulomb Tables. This is not supported in CUDA Pair forces. Setting is ignored.\n");
}
void PairBuckCoulLongCuda::init_list(int id, NeighList *ptr)
{
- MYDBG(printf("# CUDA PairBuckCoulLongCuda::init_list\n");)
- PairBuckCoulLong::init_list(id, ptr);
- #ifndef CUDA_USE_BINNING
- // right now we can only handle verlet (id 0), not respa
- if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
- // see Neighbor::init() for details on lammps lists' logic
- #endif
- MYDBG(printf("# CUDA PairBuckCoulLongCuda::init_list end\n");)
+ MYDBG(printf("# CUDA PairBuckCoulLongCuda::init_list\n");)
+ PairBuckCoulLong::init_list(id, ptr);
+ #ifndef CUDA_USE_BINNING
+ // right now we can only handle verlet (id 0), not respa
+ if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
+ // see Neighbor::init() for details on lammps lists' logic
+ #endif
+ MYDBG(printf("# CUDA PairBuckCoulLongCuda::init_list end\n");)
}
void PairBuckCoulLongCuda::ev_setup(int eflag, int vflag)
{
- int maxeatomold=maxeatom;
- PairBuckCoulLong::ev_setup(eflag,vflag);
+ int maxeatomold=maxeatom;
+ PairBuckCoulLong::ev_setup(eflag,vflag);
+
+ if (eflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
- if (eflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
+ if (vflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
- if (vflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
-
}
diff --git a/src/USER-CUDA/pair_buck_coul_long_cuda.h b/src/USER-CUDA/pair_buck_coul_long_cuda.h
index 39a379103126b90f13939d9f13750159afe331eb..e9ef8b3e48d1ed9b5d3d3cfb8418a8197240f27c 100644
--- a/src/USER-CUDA/pair_buck_coul_long_cuda.h
+++ b/src/USER-CUDA/pair_buck_coul_long_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -36,19 +36,19 @@ namespace LAMMPS_NS {
class PairBuckCoulLongCuda : public PairBuckCoulLong
{
- public:
- PairBuckCoulLongCuda(class LAMMPS *);
- void compute(int, int);
- void settings(int, char **);
- void coeff(int, char **);
- void init_list(int, class NeighList *);
- void init_style();
- void ev_setup(int eflag, int vflag);
- protected:
- class Cuda *cuda;
- void allocate();
- bool allocated2;
- class CudaNeighList* cuda_neigh_list;
+ public:
+ PairBuckCoulLongCuda(class LAMMPS *);
+ void compute(int, int);
+ void settings(int, char **);
+ void coeff(int, char **);
+ void init_list(int, class NeighList *);
+ void init_style();
+ void ev_setup(int eflag, int vflag);
+ protected:
+ class Cuda *cuda;
+ void allocate();
+ bool allocated2;
+ class CudaNeighList* cuda_neigh_list;
};
}
diff --git a/src/USER-CUDA/pair_buck_cuda.cpp b/src/USER-CUDA/pair_buck_cuda.cpp
index 40dd8bd13b5d1ee183d6bc2a6ab2a844ca225153..6443f92d2f0e8a45570b9c07c7f62ac882cd53ab 100644
--- a/src/USER-CUDA/pair_buck_cuda.cpp
+++ b/src/USER-CUDA/pair_buck_cuda.cpp
@@ -1,23 +1,23 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
Contributing author: Paul Crozier (SNL)
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -54,10 +54,10 @@ PairBuckCuda::PairBuckCuda(LAMMPS *lmp) : PairBuck(lmp)
if(cuda == NULL)
error->all(FLERR,"You cannot use a /cuda class, without activating 'cuda' acceleration. Provide '-c on' as command-line argument to LAMMPS..");
- allocated2 = false;
- cuda->shared_data.pair.cudable_force = 1;
- cuda->shared_data.pair.use_block_per_atom = 0;
- cuda->setSystemParams();
+ allocated2 = false;
+ cuda->shared_data.pair.cudable_force = 1;
+ cuda->shared_data.pair.use_block_per_atom = 0;
+ cuda->setSystemParams();
}
/* ----------------------------------------------------------------------
@@ -66,56 +66,56 @@ PairBuckCuda::PairBuckCuda(LAMMPS *lmp) : PairBuck(lmp)
void PairBuckCuda::allocate()
{
- if(! allocated) PairBuck::allocate();
- if(! allocated2)
- {
- allocated2 = true;
- cuda->shared_data.pair.cut = cut;
- cuda->shared_data.pair.coeff1 = rhoinv;
- cuda->shared_data.pair.coeff2 = buck1;
- cuda->shared_data.pair.coeff3 = buck2;
- cuda->shared_data.pair.coeff4 = a;
- cuda->shared_data.pair.coeff5 = c;
- cuda->shared_data.pair.offset = offset;
- cuda->shared_data.pair.special_lj = force->special_lj;
- }
+ if(! allocated) PairBuck::allocate();
+ if(! allocated2)
+ {
+ allocated2 = true;
+ cuda->shared_data.pair.cut = cut;
+ cuda->shared_data.pair.coeff1 = rhoinv;
+ cuda->shared_data.pair.coeff2 = buck1;
+ cuda->shared_data.pair.coeff3 = buck2;
+ cuda->shared_data.pair.coeff4 = a;
+ cuda->shared_data.pair.coeff5 = c;
+ cuda->shared_data.pair.offset = offset;
+ cuda->shared_data.pair.special_lj = force->special_lj;
+ }
}
/* ---------------------------------------------------------------------- */
void PairBuckCuda::compute(int eflag, int vflag)
{
- MYDBG( printf("PairBuckCuda compute start\n"); fflush(stdout);)
- if (eflag || vflag) ev_setup(eflag,vflag);
- if(eflag) cuda->cu_eng_vdwl->upload();
- if(eflag) cuda->cu_eng_coul->upload();
- if(vflag) cuda->cu_virial->upload();
+ MYDBG( printf("PairBuckCuda compute start\n"); fflush(stdout);)
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ if(eflag) cuda->cu_eng_vdwl->upload();
+ if(eflag) cuda->cu_eng_coul->upload();
+ if(vflag) cuda->cu_virial->upload();
- Cuda_PairBuckCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);
+ Cuda_PairBuckCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);
if(not cuda->shared_data.pair.collect_forces_later)
{
- if(eflag) cuda->cu_eng_vdwl->download();
- if(eflag) cuda->cu_eng_coul->download();
- if(vflag) cuda->cu_virial->download();
+ if(eflag) cuda->cu_eng_vdwl->download();
+ if(eflag) cuda->cu_eng_coul->download();
+ if(vflag) cuda->cu_virial->download();
}
- MYDBG( printf("PairBuckCuda compute end\n"); fflush(stdout);)
+ MYDBG( printf("PairBuckCuda compute end\n"); fflush(stdout);)
}
/* ---------------------------------------------------------------------- */
void PairBuckCuda::settings(int narg, char **arg)
{
- PairBuck::settings(narg, arg);
- cuda->shared_data.pair.cut_global = (F_FLOAT) cut_global;
+ PairBuck::settings(narg, arg);
+ cuda->shared_data.pair.cut_global = (F_FLOAT) cut_global;
}
/* ---------------------------------------------------------------------- */
void PairBuckCuda::coeff(int narg, char **arg)
{
- PairBuck::coeff(narg, arg);
- allocate();
+ PairBuck::coeff(narg, arg);
+ allocate();
}
void PairBuckCuda::init_style()
@@ -125,42 +125,42 @@ void PairBuckCuda::init_style()
// request regular or rRESPA neighbor lists
int irequest;
-
+
if (strstr(update->integrate_style,"respa")) error->all(FLERR,"Integrate Style Respa is not supported by pair style buck/coul/long/cuda");
-
- irequest = neighbor->request(this);
+
+ irequest = neighbor->request(this);
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->cudable = 1;
-
+
cuda->shared_data.pppm.qqrd2e=force->qqrd2e;
-
+
if(ncoultablebits) error->warning(FLERR,"# CUDA: You asked for the usage of Coulomb Tables. This is not supported in CUDA Pair forces. Setting is ignored.\n");
}
void PairBuckCuda::init_list(int id, NeighList *ptr)
{
- MYDBG(printf("# CUDA PairBuckCuda::init_list\n");)
- PairBuck::init_list(id, ptr);
- #ifndef CUDA_USE_BINNING
- // right now we can only handle verlet (id 0), not respa
- if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
- // see Neighbor::init() for details on lammps lists' logic
- #endif
- MYDBG(printf("# CUDA PairBuckCuda::init_list end\n");)
+ MYDBG(printf("# CUDA PairBuckCuda::init_list\n");)
+ PairBuck::init_list(id, ptr);
+ #ifndef CUDA_USE_BINNING
+ // right now we can only handle verlet (id 0), not respa
+ if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
+ // see Neighbor::init() for details on lammps lists' logic
+ #endif
+ MYDBG(printf("# CUDA PairBuckCuda::init_list end\n");)
}
void PairBuckCuda::ev_setup(int eflag, int vflag)
{
- int maxeatomold=maxeatom;
- PairBuck::ev_setup(eflag,vflag);
+ int maxeatomold=maxeatom;
+ PairBuck::ev_setup(eflag,vflag);
+
+ if (eflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
- if (eflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
+ if (eflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
- if (eflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
-
}
diff --git a/src/USER-CUDA/pair_buck_cuda.h b/src/USER-CUDA/pair_buck_cuda.h
index 9ec29e166222d1723451d84925909c79017693a8..9ecb07d5b1fd48a66ae8658c3f481b1e438b3d9d 100644
--- a/src/USER-CUDA/pair_buck_cuda.h
+++ b/src/USER-CUDA/pair_buck_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -36,19 +36,19 @@ namespace LAMMPS_NS {
class PairBuckCuda : public PairBuck
{
- public:
- PairBuckCuda(class LAMMPS *);
- void compute(int, int);
- void settings(int, char **);
- void coeff(int, char **);
- void init_list(int, class NeighList *);
- void init_style();
- void ev_setup(int eflag, int vflag);
- protected:
- class Cuda *cuda;
- void allocate();
- bool allocated2;
- class CudaNeighList* cuda_neigh_list;
+ public:
+ PairBuckCuda(class LAMMPS *);
+ void compute(int, int);
+ void settings(int, char **);
+ void coeff(int, char **);
+ void init_list(int, class NeighList *);
+ void init_style();
+ void ev_setup(int eflag, int vflag);
+ protected:
+ class Cuda *cuda;
+ void allocate();
+ bool allocated2;
+ class CudaNeighList* cuda_neigh_list;
};
}
diff --git a/src/USER-CUDA/pair_cg_cmm_coul_cut_cuda.cpp b/src/USER-CUDA/pair_cg_cmm_coul_cut_cuda.cpp
index 5334e91f97f22b0619d1ff0474f58f67694c1bd1..e6d7954e3f4997569c085c857a65d4290ee247ed 100644
--- a/src/USER-CUDA/pair_cg_cmm_coul_cut_cuda.cpp
+++ b/src/USER-CUDA/pair_cg_cmm_coul_cut_cuda.cpp
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -28,7 +28,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -69,10 +69,10 @@ PairCGCMMCoulCutCuda::PairCGCMMCoulCutCuda(LAMMPS *lmp) : PairCGCMMCoulCut(lmp)
if(cuda == NULL)
error->all(FLERR,"You cannot use a /cuda class, without activating 'cuda' acceleration. Provide '-c on' as command-line argument to LAMMPS..");
- allocated2 = false;
- cg_type_double = NULL;
- cuda->shared_data.pair.cudable_force = 1;
- cuda->setSystemParams();
+ allocated2 = false;
+ cg_type_double = NULL;
+ cuda->shared_data.pair.cudable_force = 1;
+ cuda->setSystemParams();
}
/* ----------------------------------------------------------------------
@@ -81,27 +81,27 @@ PairCGCMMCoulCutCuda::PairCGCMMCoulCutCuda(LAMMPS *lmp) : PairCGCMMCoulCut(lmp)
void PairCGCMMCoulCutCuda::allocate()
{
- if(! allocated) PairCGCMMCoulCut::allocate();
- int n = atom->ntypes;
- if(! allocated2)
- {
- allocated2 = true;
-
-
- memory->create(cg_type_double,n+1,n+1,"paircg:cgtypedouble");
-
- cuda->shared_data.pair.cut = cut_lj;
- cuda->shared_data.pair.cut_coul= cut_coul;
- cuda->shared_data.pair.coeff1 = lj1;
- cuda->shared_data.pair.coeff2 = lj2;
- cuda->shared_data.pair.coeff3 = lj3;
- cuda->shared_data.pair.coeff4 = lj4;
- cuda->shared_data.pair.coeff5 = cg_type_double;
- cuda->shared_data.pair.offset = offset;
- cuda->shared_data.pair.special_lj = force->special_lj;
- cuda->shared_data.pair.special_coul = force->special_coul;
- }
- for (int i = 1; i <= n; i++) {
+ if(! allocated) PairCGCMMCoulCut::allocate();
+ int n = atom->ntypes;
+ if(! allocated2)
+ {
+ allocated2 = true;
+
+
+ memory->create(cg_type_double,n+1,n+1,"paircg:cgtypedouble");
+
+ cuda->shared_data.pair.cut = cut_lj;
+ cuda->shared_data.pair.cut_coul= cut_coul;
+ cuda->shared_data.pair.coeff1 = lj1;
+ cuda->shared_data.pair.coeff2 = lj2;
+ cuda->shared_data.pair.coeff3 = lj3;
+ cuda->shared_data.pair.coeff4 = lj4;
+ cuda->shared_data.pair.coeff5 = cg_type_double;
+ cuda->shared_data.pair.offset = offset;
+ cuda->shared_data.pair.special_lj = force->special_lj;
+ cuda->shared_data.pair.special_coul = force->special_coul;
+ }
+ for (int i = 1; i <= n; i++) {
for (int j = i; j <= n; j++) {
cg_type_double[i][j] = cg_type[i][j];
cg_type_double[j][i] = cg_type[i][j];
@@ -113,53 +113,53 @@ void PairCGCMMCoulCutCuda::allocate()
void PairCGCMMCoulCutCuda::compute(int eflag, int vflag)
{
- if (eflag || vflag) ev_setup(eflag,vflag);
- if(eflag) cuda->cu_eng_vdwl->upload();
- if(eflag) cuda->cu_eng_coul->upload();
- if(vflag) cuda->cu_virial->upload();
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ if(eflag) cuda->cu_eng_vdwl->upload();
+ if(eflag) cuda->cu_eng_coul->upload();
+ if(vflag) cuda->cu_virial->upload();
- Cuda_PairCGCMMCoulCutCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);
+ Cuda_PairCGCMMCoulCutCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);
if(not cuda->shared_data.pair.collect_forces_later)
{
- if(eflag) cuda->cu_eng_vdwl->download();
- if(eflag) cuda->cu_eng_coul->download();
- if(vflag) cuda->cu_virial->download();
+ if(eflag) cuda->cu_eng_vdwl->download();
+ if(eflag) cuda->cu_eng_coul->download();
+ if(vflag) cuda->cu_virial->download();
}
-
+
}
/* ---------------------------------------------------------------------- */
void PairCGCMMCoulCutCuda::settings(int narg, char **arg)
{
- PairCGCMMCoulCut::settings(narg, arg);
- cuda->shared_data.pair.cut_global = (F_FLOAT) cut_lj_global;
- cuda->shared_data.pair.cut_coul_global = (F_FLOAT) cut_coul_global;
- cuda->shared_data.pair.kappa = (F_FLOAT) kappa;
+ PairCGCMMCoulCut::settings(narg, arg);
+ cuda->shared_data.pair.cut_global = (F_FLOAT) cut_lj_global;
+ cuda->shared_data.pair.cut_coul_global = (F_FLOAT) cut_coul_global;
+ cuda->shared_data.pair.kappa = (F_FLOAT) kappa;
}
/* ---------------------------------------------------------------------- */
void PairCGCMMCoulCutCuda::coeff(int narg, char **arg)
{
- PairCGCMMCoulCut::coeff(narg, arg);
- allocate();
+ PairCGCMMCoulCut::coeff(narg, arg);
+ allocate();
}
void PairCGCMMCoulCutCuda::init_style()
{
- MYDBG(printf("# CUDA PairCGCMMCoulCutCuda::init_style start\n"); )
+ MYDBG(printf("# CUDA PairCGCMMCoulCutCuda::init_style start\n"); )
// request regular or rRESPA neighbor lists
int irequest;
-
+
if (update->whichflag == 0 && strstr(update->integrate_style,"respa")) {
- }
- else
+ }
+ else
{
- irequest = neighbor->request(this);
+ irequest = neighbor->request(this);
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->cudable = 1;
@@ -175,27 +175,25 @@ void PairCGCMMCoulCutCuda::init_style()
void PairCGCMMCoulCutCuda::init_list(int id, NeighList *ptr)
{
- MYDBG(printf("# CUDA PairCGCMMCoulCutCuda::init_list\n");)
- PairCGCMMCoulCut::init_list(id, ptr);
- #ifndef CUDA_USE_BINNING
- // right now we can only handle verlet (id 0), not respa
- if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
- // see Neighbor::init() for details on lammps lists' logic
- #endif
- MYDBG(printf("# CUDA PairCGCMMCoulCutCuda::init_list end\n");)
+ MYDBG(printf("# CUDA PairCGCMMCoulCutCuda::init_list\n");)
+ PairCGCMMCoulCut::init_list(id, ptr);
+ #ifndef CUDA_USE_BINNING
+ // right now we can only handle verlet (id 0), not respa
+ if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
+ // see Neighbor::init() for details on lammps lists' logic
+ #endif
+ MYDBG(printf("# CUDA PairCGCMMCoulCutCuda::init_list end\n");)
}
void PairCGCMMCoulCutCuda::ev_setup(int eflag, int vflag)
{
- int maxeatomold=maxeatom;
- PairCGCMMCoulCut::ev_setup(eflag,vflag);
-
- if (eflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
+ int maxeatomold=maxeatom;
+ PairCGCMMCoulCut::ev_setup(eflag,vflag);
- if (vflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
-
-}
+ if (eflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
+ if (vflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
+}
diff --git a/src/USER-CUDA/pair_cg_cmm_coul_cut_cuda.h b/src/USER-CUDA/pair_cg_cmm_coul_cut_cuda.h
index 467b8a3feb8747196c947ba874540434457611b7..9ae9ce5821572ef822e7623a7059f073eb0e0ed8 100644
--- a/src/USER-CUDA/pair_cg_cmm_coul_cut_cuda.h
+++ b/src/USER-CUDA/pair_cg_cmm_coul_cut_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -36,20 +36,20 @@ namespace LAMMPS_NS {
class PairCGCMMCoulCutCuda : public PairCGCMMCoulCut
{
- public:
- PairCGCMMCoulCutCuda(class LAMMPS *);
- void compute(int, int);
- void settings(int, char **);
- void coeff(int, char **);
- void init_list(int, class NeighList *);
- void init_style();
- void ev_setup(int eflag, int vflag);
- protected:
- class Cuda *cuda;
- void allocate();
- bool allocated2;
- class CudaNeighList* cuda_neigh_list;
- double** cg_type_double;
+ public:
+ PairCGCMMCoulCutCuda(class LAMMPS *);
+ void compute(int, int);
+ void settings(int, char **);
+ void coeff(int, char **);
+ void init_list(int, class NeighList *);
+ void init_style();
+ void ev_setup(int eflag, int vflag);
+ protected:
+ class Cuda *cuda;
+ void allocate();
+ bool allocated2;
+ class CudaNeighList* cuda_neigh_list;
+ double** cg_type_double;
};
}
diff --git a/src/USER-CUDA/pair_cg_cmm_coul_debye_cuda.cpp b/src/USER-CUDA/pair_cg_cmm_coul_debye_cuda.cpp
index 862d8e56b3ade1daec4e813d7c2ef07510763021..3c3818ac7c7b6bc189aa4c2c86cfccb99154818a 100644
--- a/src/USER-CUDA/pair_cg_cmm_coul_debye_cuda.cpp
+++ b/src/USER-CUDA/pair_cg_cmm_coul_debye_cuda.cpp
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -28,7 +28,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -69,10 +69,10 @@ PairCGCMMCoulDebyeCuda::PairCGCMMCoulDebyeCuda(LAMMPS *lmp) : PairCGCMMCoulCut(l
if(cuda == NULL)
error->all(FLERR,"You cannot use a /cuda class, without activating 'cuda' acceleration. Provide '-c on' as command-line argument to LAMMPS..");
- allocated2 = false;
- cg_type_double = NULL;
- cuda->shared_data.pair.cudable_force = 1;
- cuda->setSystemParams();
+ allocated2 = false;
+ cg_type_double = NULL;
+ cuda->shared_data.pair.cudable_force = 1;
+ cuda->setSystemParams();
}
/* ----------------------------------------------------------------------
@@ -81,27 +81,27 @@ PairCGCMMCoulDebyeCuda::PairCGCMMCoulDebyeCuda(LAMMPS *lmp) : PairCGCMMCoulCut(l
void PairCGCMMCoulDebyeCuda::allocate()
{
- if(! allocated) PairCGCMMCoulCut::allocate();
- int n = atom->ntypes;
- if(! allocated2)
- {
- allocated2 = true;
-
-
- memory->create(cg_type_double,n+1,n+1,"paircg:cgtypedouble");
-
- cuda->shared_data.pair.cut = cut_lj;
- cuda->shared_data.pair.cut_coul= cut_coul;
- cuda->shared_data.pair.coeff1 = lj1;
- cuda->shared_data.pair.coeff2 = lj2;
- cuda->shared_data.pair.coeff3 = lj3;
- cuda->shared_data.pair.coeff4 = lj4;
- cuda->shared_data.pair.coeff5 = cg_type_double;
- cuda->shared_data.pair.offset = offset;
- cuda->shared_data.pair.special_lj = force->special_lj;
- cuda->shared_data.pair.special_coul = force->special_coul;
- }
- for (int i = 1; i <= n; i++) {
+ if(! allocated) PairCGCMMCoulCut::allocate();
+ int n = atom->ntypes;
+ if(! allocated2)
+ {
+ allocated2 = true;
+
+
+ memory->create(cg_type_double,n+1,n+1,"paircg:cgtypedouble");
+
+ cuda->shared_data.pair.cut = cut_lj;
+ cuda->shared_data.pair.cut_coul= cut_coul;
+ cuda->shared_data.pair.coeff1 = lj1;
+ cuda->shared_data.pair.coeff2 = lj2;
+ cuda->shared_data.pair.coeff3 = lj3;
+ cuda->shared_data.pair.coeff4 = lj4;
+ cuda->shared_data.pair.coeff5 = cg_type_double;
+ cuda->shared_data.pair.offset = offset;
+ cuda->shared_data.pair.special_lj = force->special_lj;
+ cuda->shared_data.pair.special_coul = force->special_coul;
+ }
+ for (int i = 1; i <= n; i++) {
for (int j = i; j <= n; j++) {
cg_type_double[i][j] = cg_type[i][j];
cg_type_double[j][i] = cg_type[i][j];
@@ -113,53 +113,53 @@ void PairCGCMMCoulDebyeCuda::allocate()
void PairCGCMMCoulDebyeCuda::compute(int eflag, int vflag)
{
- if (eflag || vflag) ev_setup(eflag,vflag);
- if(eflag) cuda->cu_eng_vdwl->upload();
- if(eflag) cuda->cu_eng_coul->upload();
- if(vflag) cuda->cu_virial->upload();
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ if(eflag) cuda->cu_eng_vdwl->upload();
+ if(eflag) cuda->cu_eng_coul->upload();
+ if(vflag) cuda->cu_virial->upload();
- Cuda_PairCGCMMCoulDebyeCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);
+ Cuda_PairCGCMMCoulDebyeCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);
if(not cuda->shared_data.pair.collect_forces_later)
{
- if(eflag) cuda->cu_eng_vdwl->download();
- if(eflag) cuda->cu_eng_coul->download();
- if(vflag) cuda->cu_virial->download();
+ if(eflag) cuda->cu_eng_vdwl->download();
+ if(eflag) cuda->cu_eng_coul->download();
+ if(vflag) cuda->cu_virial->download();
}
-
+
}
/* ---------------------------------------------------------------------- */
void PairCGCMMCoulDebyeCuda::settings(int narg, char **arg)
{
- PairCGCMMCoulCut::settings(narg, arg);
- cuda->shared_data.pair.cut_global = (F_FLOAT) cut_lj_global;
- cuda->shared_data.pair.cut_coul_global = (F_FLOAT) cut_coul_global;
- cuda->shared_data.pair.kappa = (F_FLOAT) kappa;
+ PairCGCMMCoulCut::settings(narg, arg);
+ cuda->shared_data.pair.cut_global = (F_FLOAT) cut_lj_global;
+ cuda->shared_data.pair.cut_coul_global = (F_FLOAT) cut_coul_global;
+ cuda->shared_data.pair.kappa = (F_FLOAT) kappa;
}
/* ---------------------------------------------------------------------- */
void PairCGCMMCoulDebyeCuda::coeff(int narg, char **arg)
{
- PairCGCMMCoulCut::coeff(narg, arg);
- allocate();
+ PairCGCMMCoulCut::coeff(narg, arg);
+ allocate();
}
void PairCGCMMCoulDebyeCuda::init_style()
{
- MYDBG(printf("# CUDA PairCGCMMCoulDebyeCuda::init_style start\n"); )
+ MYDBG(printf("# CUDA PairCGCMMCoulDebyeCuda::init_style start\n"); )
// request regular or rRESPA neighbor lists
int irequest;
-
+
if (update->whichflag == 0 && strstr(update->integrate_style,"respa")) {
- }
- else
+ }
+ else
{
- irequest = neighbor->request(this);
+ irequest = neighbor->request(this);
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->cudable = 1;
@@ -175,27 +175,25 @@ void PairCGCMMCoulDebyeCuda::init_style()
void PairCGCMMCoulDebyeCuda::init_list(int id, NeighList *ptr)
{
- MYDBG(printf("# CUDA PairCGCMMCoulDebyeCuda::init_list\n");)
- PairCGCMMCoulCut::init_list(id, ptr);
- #ifndef CUDA_USE_BINNING
- // right now we can only handle verlet (id 0), not respa
- if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
- // see Neighbor::init() for details on lammps lists' logic
- #endif
- MYDBG(printf("# CUDA PairCGCMMCoulDebyeCuda::init_list end\n");)
+ MYDBG(printf("# CUDA PairCGCMMCoulDebyeCuda::init_list\n");)
+ PairCGCMMCoulCut::init_list(id, ptr);
+ #ifndef CUDA_USE_BINNING
+ // right now we can only handle verlet (id 0), not respa
+ if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
+ // see Neighbor::init() for details on lammps lists' logic
+ #endif
+ MYDBG(printf("# CUDA PairCGCMMCoulDebyeCuda::init_list end\n");)
}
void PairCGCMMCoulDebyeCuda::ev_setup(int eflag, int vflag)
{
- int maxeatomold=maxeatom;
- PairCGCMMCoulCut::ev_setup(eflag,vflag);
-
- if (eflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
+ int maxeatomold=maxeatom;
+ PairCGCMMCoulCut::ev_setup(eflag,vflag);
- if (vflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
-
-}
+ if (eflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
+ if (vflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
+}
diff --git a/src/USER-CUDA/pair_cg_cmm_coul_debye_cuda.h b/src/USER-CUDA/pair_cg_cmm_coul_debye_cuda.h
index a3921251614515a949edf3bcb47b10673ec8874e..98758e8d86a2012a2e98e136e54db63d91ed7a51 100644
--- a/src/USER-CUDA/pair_cg_cmm_coul_debye_cuda.h
+++ b/src/USER-CUDA/pair_cg_cmm_coul_debye_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -36,20 +36,20 @@ namespace LAMMPS_NS {
class PairCGCMMCoulDebyeCuda : public PairCGCMMCoulCut
{
- public:
- PairCGCMMCoulDebyeCuda(class LAMMPS *);
- void compute(int, int);
- void settings(int, char **);
- void coeff(int, char **);
- void init_list(int, class NeighList *);
- void init_style();
- void ev_setup(int eflag, int vflag);
- protected:
- class Cuda *cuda;
- void allocate();
- bool allocated2;
- class CudaNeighList* cuda_neigh_list;
- double** cg_type_double;
+ public:
+ PairCGCMMCoulDebyeCuda(class LAMMPS *);
+ void compute(int, int);
+ void settings(int, char **);
+ void coeff(int, char **);
+ void init_list(int, class NeighList *);
+ void init_style();
+ void ev_setup(int eflag, int vflag);
+ protected:
+ class Cuda *cuda;
+ void allocate();
+ bool allocated2;
+ class CudaNeighList* cuda_neigh_list;
+ double** cg_type_double;
};
}
diff --git a/src/USER-CUDA/pair_cg_cmm_coul_long_cuda.cpp b/src/USER-CUDA/pair_cg_cmm_coul_long_cuda.cpp
index c2d4ede4b4511850ba68d33284f6da912f16a6d6..3d276ad7e912283d4a356131c6b01d92d215fc64 100644
--- a/src/USER-CUDA/pair_cg_cmm_coul_long_cuda.cpp
+++ b/src/USER-CUDA/pair_cg_cmm_coul_long_cuda.cpp
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -28,7 +28,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -70,10 +70,10 @@ PairCGCMMCoulLongCuda::PairCGCMMCoulLongCuda(LAMMPS *lmp) : PairCGCMMCoulLong(lm
if(cuda == NULL)
error->all(FLERR,"You cannot use a /cuda class, without activating 'cuda' acceleration. Provide '-c on' as command-line argument to LAMMPS..");
- allocated2 = false;
- cg_type_double = NULL;
- cuda->shared_data.pair.cudable_force = 1;
- cuda->setSystemParams();
+ allocated2 = false;
+ cg_type_double = NULL;
+ cuda->shared_data.pair.cudable_force = 1;
+ cuda->setSystemParams();
}
/* ----------------------------------------------------------------------
@@ -82,27 +82,27 @@ PairCGCMMCoulLongCuda::PairCGCMMCoulLongCuda(LAMMPS *lmp) : PairCGCMMCoulLong(lm
void PairCGCMMCoulLongCuda::allocate()
{
- if(! allocated) PairCGCMMCoulLong::allocate();
- int n = atom->ntypes;
- if(! allocated2)
- {
- allocated2 = true;
-
-
- memory->create(cg_type_double,n+1,n+1,"paircg:cgtypedouble");
-
- cuda->shared_data.pair.cut = cut_lj;
- cuda->shared_data.pair.cut_coul= cut_coul;
- cuda->shared_data.pair.coeff1 = lj1;
- cuda->shared_data.pair.coeff2 = lj2;
- cuda->shared_data.pair.coeff3 = lj3;
- cuda->shared_data.pair.coeff4 = lj4;
- cuda->shared_data.pair.coeff5 = cg_type_double;
- cuda->shared_data.pair.offset = offset;
- cuda->shared_data.pair.special_lj = force->special_lj;
- cuda->shared_data.pair.special_coul = force->special_coul;
- }
- for (int i = 1; i <= n; i++) {
+ if(! allocated) PairCGCMMCoulLong::allocate();
+ int n = atom->ntypes;
+ if(! allocated2)
+ {
+ allocated2 = true;
+
+
+ memory->create(cg_type_double,n+1,n+1,"paircg:cgtypedouble");
+
+ cuda->shared_data.pair.cut = cut_lj;
+ cuda->shared_data.pair.cut_coul= cut_coul;
+ cuda->shared_data.pair.coeff1 = lj1;
+ cuda->shared_data.pair.coeff2 = lj2;
+ cuda->shared_data.pair.coeff3 = lj3;
+ cuda->shared_data.pair.coeff4 = lj4;
+ cuda->shared_data.pair.coeff5 = cg_type_double;
+ cuda->shared_data.pair.offset = offset;
+ cuda->shared_data.pair.special_lj = force->special_lj;
+ cuda->shared_data.pair.special_coul = force->special_coul;
+ }
+ for (int i = 1; i <= n; i++) {
for (int j = i; j <= n; j++) {
cg_type_double[i][j] = cg_type[i][j];
cg_type_double[j][i] = cg_type[i][j];
@@ -114,53 +114,53 @@ void PairCGCMMCoulLongCuda::allocate()
void PairCGCMMCoulLongCuda::compute(int eflag, int vflag)
{
- if (eflag || vflag) ev_setup(eflag,vflag);
- if(eflag) cuda->cu_eng_vdwl->upload();
- if(eflag) cuda->cu_eng_coul->upload();
- if(vflag) cuda->cu_virial->upload();
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ if(eflag) cuda->cu_eng_vdwl->upload();
+ if(eflag) cuda->cu_eng_coul->upload();
+ if(vflag) cuda->cu_virial->upload();
- Cuda_PairCGCMMCoulLongCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);
+ Cuda_PairCGCMMCoulLongCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);
if(not cuda->shared_data.pair.collect_forces_later)
{
- if(eflag) cuda->cu_eng_vdwl->download();
- if(eflag) cuda->cu_eng_coul->download();
- if(vflag) cuda->cu_virial->download();
+ if(eflag) cuda->cu_eng_vdwl->download();
+ if(eflag) cuda->cu_eng_coul->download();
+ if(vflag) cuda->cu_virial->download();
}
-
+
}
/* ---------------------------------------------------------------------- */
void PairCGCMMCoulLongCuda::settings(int narg, char **arg)
{
- PairCGCMMCoulLong::settings(narg, arg);
- cuda->shared_data.pair.cut_global = (F_FLOAT) cut_lj_global;
- cuda->shared_data.pair.cut_coul_global = (F_FLOAT) cut_coul_global;
- cuda->shared_data.pair.kappa = (F_FLOAT) kappa;
+ PairCGCMMCoulLong::settings(narg, arg);
+ cuda->shared_data.pair.cut_global = (F_FLOAT) cut_lj_global;
+ cuda->shared_data.pair.cut_coul_global = (F_FLOAT) cut_coul_global;
+ cuda->shared_data.pair.kappa = (F_FLOAT) kappa;
}
/* ---------------------------------------------------------------------- */
void PairCGCMMCoulLongCuda::coeff(int narg, char **arg)
{
- PairCGCMMCoulLong::coeff(narg, arg);
- allocate();
+ PairCGCMMCoulLong::coeff(narg, arg);
+ allocate();
}
void PairCGCMMCoulLongCuda::init_style()
{
- MYDBG(printf("# CUDA PairCGCMMCoulLongCuda::init_style start\n"); )
+ MYDBG(printf("# CUDA PairCGCMMCoulLongCuda::init_style start\n"); )
// request regular or rRESPA neighbor lists
int irequest;
-
+
if (update->whichflag == 0 && strstr(update->integrate_style,"respa")) {
- }
- else
+ }
+ else
{
- irequest = neighbor->request(this);
+ irequest = neighbor->request(this);
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->cudable = 1;
@@ -177,27 +177,25 @@ void PairCGCMMCoulLongCuda::init_style()
void PairCGCMMCoulLongCuda::init_list(int id, NeighList *ptr)
{
- MYDBG(printf("# CUDA PairCGCMMCoulLongCuda::init_list\n");)
- PairCGCMMCoulLong::init_list(id, ptr);
- #ifndef CUDA_USE_BINNING
- // right now we can only handle verlet (id 0), not respa
- if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
- // see Neighbor::init() for details on lammps lists' logic
- #endif
- MYDBG(printf("# CUDA PairCGCMMCoulLongCuda::init_list end\n");)
+ MYDBG(printf("# CUDA PairCGCMMCoulLongCuda::init_list\n");)
+ PairCGCMMCoulLong::init_list(id, ptr);
+ #ifndef CUDA_USE_BINNING
+ // right now we can only handle verlet (id 0), not respa
+ if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
+ // see Neighbor::init() for details on lammps lists' logic
+ #endif
+ MYDBG(printf("# CUDA PairCGCMMCoulLongCuda::init_list end\n");)
}
void PairCGCMMCoulLongCuda::ev_setup(int eflag, int vflag)
{
- int maxeatomold=maxeatom;
- PairCGCMMCoulLong::ev_setup(eflag,vflag);
-
- if (eflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
+ int maxeatomold=maxeatom;
+ PairCGCMMCoulLong::ev_setup(eflag,vflag);
- if (vflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
-
-}
+ if (eflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
+ if (vflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
+}
diff --git a/src/USER-CUDA/pair_cg_cmm_coul_long_cuda.h b/src/USER-CUDA/pair_cg_cmm_coul_long_cuda.h
index cad37fc8cae522287dd56b9ed870bc982290e3c4..d3021f8ab87b52c27bf344fd8a4eab5b3a1b0622 100644
--- a/src/USER-CUDA/pair_cg_cmm_coul_long_cuda.h
+++ b/src/USER-CUDA/pair_cg_cmm_coul_long_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -36,20 +36,20 @@ namespace LAMMPS_NS {
class PairCGCMMCoulLongCuda : public PairCGCMMCoulLong
{
- public:
- PairCGCMMCoulLongCuda(class LAMMPS *);
- void compute(int, int);
- void settings(int, char **);
- void coeff(int, char **);
- void init_list(int, class NeighList *);
- void init_style();
- void ev_setup(int eflag, int vflag);
- protected:
- class Cuda *cuda;
- void allocate();
- bool allocated2;
- class CudaNeighList* cuda_neigh_list;
- double** cg_type_double;
+ public:
+ PairCGCMMCoulLongCuda(class LAMMPS *);
+ void compute(int, int);
+ void settings(int, char **);
+ void coeff(int, char **);
+ void init_list(int, class NeighList *);
+ void init_style();
+ void ev_setup(int eflag, int vflag);
+ protected:
+ class Cuda *cuda;
+ void allocate();
+ bool allocated2;
+ class CudaNeighList* cuda_neigh_list;
+ double** cg_type_double;
};
}
diff --git a/src/USER-CUDA/pair_cg_cmm_cuda.cpp b/src/USER-CUDA/pair_cg_cmm_cuda.cpp
index cc3e5e585be36200ae1708c959ef198b7322dd85..4d89651cd907fdba489e2cb43561ddcc530a3230 100644
--- a/src/USER-CUDA/pair_cg_cmm_cuda.cpp
+++ b/src/USER-CUDA/pair_cg_cmm_cuda.cpp
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -28,7 +28,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -69,10 +69,10 @@ PairCGCMMCuda::PairCGCMMCuda(LAMMPS *lmp) : PairCGCMM(lmp)
if(cuda == NULL)
error->all(FLERR,"You cannot use a /cuda class, without activating 'cuda' acceleration. Provide '-c on' as command-line argument to LAMMPS..");
- allocated2 = false;
- cg_type_double = NULL;
- cuda->shared_data.pair.cudable_force = 1;
- cuda->setSystemParams();
+ allocated2 = false;
+ cg_type_double = NULL;
+ cuda->shared_data.pair.cudable_force = 1;
+ cuda->setSystemParams();
}
/* ----------------------------------------------------------------------
@@ -81,30 +81,30 @@ PairCGCMMCuda::PairCGCMMCuda(LAMMPS *lmp) : PairCGCMM(lmp)
void PairCGCMMCuda::allocate()
{
- if(! allocated) PairCGCMM::allocate();
- int n = atom->ntypes;
- if(! allocated2)
- {
- allocated2 = true;
-
-
- memory->create(cg_type_double,n+1,n+1,"paircg:cgtypedouble");
-
- cuda->shared_data.pair.cut = cut;
- cuda->shared_data.pair.coeff1 = lj1;
- cuda->shared_data.pair.coeff2 = lj2;
- cuda->shared_data.pair.coeff3 = lj3;
- cuda->shared_data.pair.coeff4 = lj4;
- cuda->shared_data.pair.coeff5 = cg_type_double;
- /*cu_lj1_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj1, &cuda->shared_data.pair.coeff1_gm, (atom->ntypes+1)*(atom->ntypes+1));
- cu_lj2_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj2, &cuda->shared_data.pair.coeff2_gm, (atom->ntypes+1)*(atom->ntypes+1));
- cu_lj3_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj3, &cuda->shared_data.pair.coeff3_gm, (atom->ntypes+1)*(atom->ntypes+1));
- cu_lj4_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj4, &cuda->shared_data.pair.coeff4_gm, (atom->ntypes+1)*(atom->ntypes+1));
- cu_cg_type_double_gm = new cCudaData<double, F_FLOAT, x> ((double*)cg_type_double, &cuda->shared_data.pair.coeff5_gm, (atom->ntypes+1)*(atom->ntypes+1));*/
- cuda->shared_data.pair.offset = offset;
- cuda->shared_data.pair.special_lj = force->special_lj;
- }
- for (int i = 1; i <= n; i++) {
+ if(! allocated) PairCGCMM::allocate();
+ int n = atom->ntypes;
+ if(! allocated2)
+ {
+ allocated2 = true;
+
+
+ memory->create(cg_type_double,n+1,n+1,"paircg:cgtypedouble");
+
+ cuda->shared_data.pair.cut = cut;
+ cuda->shared_data.pair.coeff1 = lj1;
+ cuda->shared_data.pair.coeff2 = lj2;
+ cuda->shared_data.pair.coeff3 = lj3;
+ cuda->shared_data.pair.coeff4 = lj4;
+ cuda->shared_data.pair.coeff5 = cg_type_double;
+ /*cu_lj1_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj1, &cuda->shared_data.pair.coeff1_gm, (atom->ntypes+1)*(atom->ntypes+1));
+ cu_lj2_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj2, &cuda->shared_data.pair.coeff2_gm, (atom->ntypes+1)*(atom->ntypes+1));
+ cu_lj3_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj3, &cuda->shared_data.pair.coeff3_gm, (atom->ntypes+1)*(atom->ntypes+1));
+ cu_lj4_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj4, &cuda->shared_data.pair.coeff4_gm, (atom->ntypes+1)*(atom->ntypes+1));
+ cu_cg_type_double_gm = new cCudaData<double, F_FLOAT, x> ((double*)cg_type_double, &cuda->shared_data.pair.coeff5_gm, (atom->ntypes+1)*(atom->ntypes+1));*/
+ cuda->shared_data.pair.offset = offset;
+ cuda->shared_data.pair.special_lj = force->special_lj;
+ }
+ for (int i = 1; i <= n; i++) {
for (int j = i; j <= n; j++) {
cg_type_double[i][j] = cg_type[i][j];
cg_type_double[j][i] = cg_type[i][j];
@@ -116,49 +116,49 @@ void PairCGCMMCuda::allocate()
void PairCGCMMCuda::compute(int eflag, int vflag)
{
- if (eflag || vflag) ev_setup(eflag,vflag);
- if(eflag) cuda->cu_eng_vdwl->upload();
- if(vflag) cuda->cu_virial->upload();
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ if(eflag) cuda->cu_eng_vdwl->upload();
+ if(vflag) cuda->cu_virial->upload();
- Cuda_PairCGCMMCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);
+ Cuda_PairCGCMMCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);
if(not cuda->shared_data.pair.collect_forces_later)
{
- if(eflag) cuda->cu_eng_vdwl->download();
- if(vflag) cuda->cu_virial->download();
+ if(eflag) cuda->cu_eng_vdwl->download();
+ if(vflag) cuda->cu_virial->download();
}
-
+
}
/* ---------------------------------------------------------------------- */
void PairCGCMMCuda::settings(int narg, char **arg)
{
- PairCGCMM::settings(narg, arg);
- cuda->shared_data.pair.cut_global = (F_FLOAT) cut_lj_global;
+ PairCGCMM::settings(narg, arg);
+ cuda->shared_data.pair.cut_global = (F_FLOAT) cut_lj_global;
}
/* ---------------------------------------------------------------------- */
void PairCGCMMCuda::coeff(int narg, char **arg)
{
- PairCGCMM::coeff(narg, arg);
- allocate();
+ PairCGCMM::coeff(narg, arg);
+ allocate();
}
void PairCGCMMCuda::init_style()
{
- MYDBG(printf("# CUDA PairCGCMMCuda::init_style start\n"); )
+ MYDBG(printf("# CUDA PairCGCMMCuda::init_style start\n"); )
// request regular or rRESPA neighbor lists
int irequest;
-
+
if (update->whichflag == 0 && strstr(update->integrate_style,"respa")) {
- }
- else
+ }
+ else
{
- irequest = neighbor->request(this);
+ irequest = neighbor->request(this);
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->cudable = 1;
@@ -172,27 +172,25 @@ void PairCGCMMCuda::init_style()
void PairCGCMMCuda::init_list(int id, NeighList *ptr)
{
- MYDBG(printf("# CUDA PairCGCMMCuda::init_list\n");)
- PairCGCMM::init_list(id, ptr);
- #ifndef CUDA_USE_BINNING
- // right now we can only handle verlet (id 0), not respa
- if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
- // see Neighbor::init() for details on lammps lists' logic
- #endif
- MYDBG(printf("# CUDA PairCGCMMCuda::init_list end\n");)
+ MYDBG(printf("# CUDA PairCGCMMCuda::init_list\n");)
+ PairCGCMM::init_list(id, ptr);
+ #ifndef CUDA_USE_BINNING
+ // right now we can only handle verlet (id 0), not respa
+ if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
+ // see Neighbor::init() for details on lammps lists' logic
+ #endif
+ MYDBG(printf("# CUDA PairCGCMMCuda::init_list end\n");)
}
void PairCGCMMCuda::ev_setup(int eflag, int vflag)
{
- int maxeatomold=maxeatom;
- PairCGCMM::ev_setup(eflag,vflag);
-
- if (eflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
+ int maxeatomold=maxeatom;
+ PairCGCMM::ev_setup(eflag,vflag);
- if (vflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
-
-}
+ if (eflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
+ if (vflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
+}
diff --git a/src/USER-CUDA/pair_cg_cmm_cuda.h b/src/USER-CUDA/pair_cg_cmm_cuda.h
index 74236b889f0ebe1e0d21b35258660faa79067765..32e204270fd3a71047f79c403240741786d13007 100644
--- a/src/USER-CUDA/pair_cg_cmm_cuda.h
+++ b/src/USER-CUDA/pair_cg_cmm_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -37,25 +37,25 @@ namespace LAMMPS_NS {
class PairCGCMMCuda : public PairCGCMM
{
- public:
- PairCGCMMCuda(class LAMMPS *);
- void compute(int, int);
- void settings(int, char **);
- void coeff(int, char **);
- void init_list(int, class NeighList *);
- void init_style();
- void ev_setup(int eflag, int vflag);
- protected:
- class Cuda *cuda;
- void allocate();
- bool allocated2;
- class CudaNeighList* cuda_neigh_list;
- double** cg_type_double;
- cCudaData<double , F_FLOAT , x >* cu_lj1_gm;
- cCudaData<double , F_FLOAT , x >* cu_lj2_gm;
- cCudaData<double , F_FLOAT , x >* cu_lj3_gm;
- cCudaData<double , F_FLOAT , x >* cu_lj4_gm;
- cCudaData<double , F_FLOAT , x >* cu_cg_type_double_gm;
+ public:
+ PairCGCMMCuda(class LAMMPS *);
+ void compute(int, int);
+ void settings(int, char **);
+ void coeff(int, char **);
+ void init_list(int, class NeighList *);
+ void init_style();
+ void ev_setup(int eflag, int vflag);
+ protected:
+ class Cuda *cuda;
+ void allocate();
+ bool allocated2;
+ class CudaNeighList* cuda_neigh_list;
+ double** cg_type_double;
+ cCudaData<double , F_FLOAT , x >* cu_lj1_gm;
+ cCudaData<double , F_FLOAT , x >* cu_lj2_gm;
+ cCudaData<double , F_FLOAT , x >* cu_lj3_gm;
+ cCudaData<double , F_FLOAT , x >* cu_lj4_gm;
+ cCudaData<double , F_FLOAT , x >* cu_cg_type_double_gm;
};
}
diff --git a/src/USER-CUDA/pair_eam_alloy_cuda.cpp b/src/USER-CUDA/pair_eam_alloy_cuda.cpp
index fd78c57133ebf40d370a21c4cd58555494f020eb..72cbb77d375dab628d4355ae60a986b3842538bd 100644
--- a/src/USER-CUDA/pair_eam_alloy_cuda.cpp
+++ b/src/USER-CUDA/pair_eam_alloy_cuda.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -100,9 +100,9 @@ void PairEAMAlloyCuda::coeff(int narg, char **arg)
for (i = 1; i <= n; i++) {
for (j = i; j <= n; j++) {
if (map[i] >= 0 && map[j] >= 0) {
- setflag[i][j] = 1;
- if (i == j) atom->set_mass(i,setfl->mass[map[i]]);
- count++;
+ setflag[i][j] = 1;
+ if (i == j) atom->set_mass(i,setfl->mass[map[i]]);
+ count++;
}
}
}
@@ -151,7 +151,7 @@ void PairEAMAlloyCuda::read_file(char *filename)
int nwords = atom->count_words(line);
if (nwords != file->nelements + 1)
error->all(FLERR,"Incorrect element names in EAM potential file");
-
+
char **words = new char*[file->nelements+1];
nwords = 0;
char *first = strtok(line," \t\n\r\f");
@@ -168,7 +168,7 @@ void PairEAMAlloyCuda::read_file(char *filename)
if (me == 0) {
fgets(line,MAXLINE,fptr);
sscanf(line,"%d %lg %d %lg %lg",
- &file->nrho,&file->drho,&file->nr,&file->dr,&file->cut);
+ &file->nrho,&file->drho,&file->nr,&file->dr,&file->cut);
}
MPI_Bcast(&file->nrho,1,MPI_INT,0,world);
@@ -181,7 +181,7 @@ void PairEAMAlloyCuda::read_file(char *filename)
memory->create(file->frho,file->nelements,file->nrho+1,"pair:frho");
memory->create(file->rhor,file->nelements,file->nr+1,"pair:rhor");
memory->create(file->z2r,file->nelements,file->nelements,file->nr+1,
- "pair:z2r");
+ "pair:z2r");
int i,j,tmp;
for (i = 0; i < file->nelements; i++) {
if (me == 0) {
@@ -229,7 +229,7 @@ void PairEAMAlloyCuda::file2array()
// allocate frho arrays
// nfrho = # of setfl elements + 1 for zero array
-
+
nfrho = setfl->nelements + 1;
memory->destroy(frho);
memory->create(frho,nfrho,nrho+1,"pair:frho");
@@ -310,12 +310,12 @@ void PairEAMAlloyCuda::file2array()
irow = map[i];
icol = map[j];
if (irow == -1 || icol == -1) {
- type2z2r[i][j] = 0;
- continue;
+ type2z2r[i][j] = 0;
+ continue;
}
if (irow < icol) {
- irow = map[j];
- icol = map[i];
+ irow = map[j];
+ icol = map[i];
}
n = 0;
for (m = 0; m < irow; m++) n += m + 1;
diff --git a/src/USER-CUDA/pair_eam_alloy_cuda.h b/src/USER-CUDA/pair_eam_alloy_cuda.h
index d17d9f5c79eee630ad03290f165aef5b5e0985a2..27ddcb1600d44c50b7580f61839bcf1c9b567716 100644
--- a/src/USER-CUDA/pair_eam_alloy_cuda.h
+++ b/src/USER-CUDA/pair_eam_alloy_cuda.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-CUDA/pair_eam_cuda.cpp b/src/USER-CUDA/pair_eam_cuda.cpp
index ee9a701b25276da99f07300a15a5c4a477a3c5d7..1e65aaf7190375bb1f0a614f9462d8ebcd2f3d5c 100644
--- a/src/USER-CUDA/pair_eam_cuda.cpp
+++ b/src/USER-CUDA/pair_eam_cuda.cpp
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -28,7 +28,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -70,13 +70,13 @@ PairEAMCuda::PairEAMCuda(LAMMPS *lmp) : PairEAM(lmp)
if(cuda == NULL)
error->all(FLERR,"You cannot use a /cuda class, without activating 'cuda' acceleration. Provide '-c on' as command-line argument to LAMMPS..");
- allocated2 = false;
- cuda->shared_data.pair.cudable_force = 1;
- cuda->shared_data.pair.override_block_per_atom = 0;
-
- cuda->setSystemParams();
- cu_rho=NULL;
- cu_fp=NULL;
+ allocated2 = false;
+ cuda->shared_data.pair.cudable_force = 1;
+ cuda->shared_data.pair.override_block_per_atom = 0;
+
+ cuda->setSystemParams();
+ cu_rho=NULL;
+ cu_fp=NULL;
cu_frho_spline = NULL;
cu_z2r_spline = NULL;
cu_rhor_spline = NULL;
@@ -88,16 +88,16 @@ PairEAMCuda::PairEAMCuda(LAMMPS *lmp) : PairEAM(lmp)
void PairEAMCuda::allocate()
{
- if(! allocated) PairEAM::allocate();
- cuda->shared_data.pair.cutsq = cutsq;
- cuda->shared_data.pair.cut_global = (F_FLOAT) cutforcesq;
+ if(! allocated) PairEAM::allocate();
+ cuda->shared_data.pair.cutsq = cutsq;
+ cuda->shared_data.pair.cut_global = (F_FLOAT) cutforcesq;
}
/* ---------------------------------------------------------------------- */
void PairEAMCuda::compute(int eflag, int vflag)
{
- cuda->shared_data.pair.cut_global = (F_FLOAT) cutforcesq;
+ cuda->shared_data.pair.cut_global = (F_FLOAT) cutforcesq;
cuda->shared_data.pair.use_block_per_atom = 0;
cuda->shared_data.pair.collect_forces_later = 0;
if (atom->nmax > nmax) {
@@ -106,84 +106,84 @@ void PairEAMCuda::compute(int eflag, int vflag)
nmax = atom->nmax;
memory->create(rho,nmax,"pair:rho");
memory->create(fp,nmax,"pair:fp");
- delete cu_rho;
- delete cu_fp;
- cu_rho = new cCudaData<double, F_FLOAT, x> (rho, atom->nmax);
- cu_fp = new cCudaData<double, F_FLOAT, x> (fp, atom->nmax);
- Cuda_PairEAMCuda_Init(&cuda->shared_data,rdr,rdrho,nfrho,nrhor,nr,nrho,nz2r,
- cu_frho_spline->dev_data(),cu_rhor_spline->dev_data(),cu_z2r_spline->dev_data(),
- cu_rho->dev_data(),cu_fp->dev_data(),type2frho,type2z2r,type2rhor);
- }
-
-
-
- if(eflag || vflag) ev_setup(eflag,vflag);
- if(eflag) cuda->cu_eng_vdwl->upload();
- if(vflag) cuda->cu_virial->upload();
-
- Cuda_PairEAM1Cuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag,eflag_atom,vflag_atom);
+ delete cu_rho;
+ delete cu_fp;
+ cu_rho = new cCudaData<double, F_FLOAT, x> (rho, atom->nmax);
+ cu_fp = new cCudaData<double, F_FLOAT, x> (fp, atom->nmax);
+ Cuda_PairEAMCuda_Init(&cuda->shared_data,rdr,rdrho,nfrho,nrhor,nr,nrho,nz2r,
+ cu_frho_spline->dev_data(),cu_rhor_spline->dev_data(),cu_z2r_spline->dev_data(),
+ cu_rho->dev_data(),cu_fp->dev_data(),type2frho,type2z2r,type2rhor);
+ }
+
+
+
+ if(eflag || vflag) ev_setup(eflag,vflag);
+ if(eflag) cuda->cu_eng_vdwl->upload();
+ if(vflag) cuda->cu_virial->upload();
+
+ Cuda_PairEAM1Cuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag,eflag_atom,vflag_atom);
comm->forward_comm_pair(this);
- Cuda_PairEAM2Cuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag,eflag_atom,vflag_atom);
-
- if(eflag) cuda->cu_eng_vdwl->download();
- if(vflag) cuda->cu_virial->download();
+ Cuda_PairEAM2Cuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag,eflag_atom,vflag_atom);
+
+ if(eflag) cuda->cu_eng_vdwl->download();
+ if(vflag) cuda->cu_virial->download();
}
/* ---------------------------------------------------------------------- */
void PairEAMCuda::settings(int narg, char **arg)
{
- PairEAM::settings(narg, arg);
- cuda->shared_data.pair.cut_global = (F_FLOAT) cutforcesq;
+ PairEAM::settings(narg, arg);
+ cuda->shared_data.pair.cut_global = (F_FLOAT) cutforcesq;
}
/* ---------------------------------------------------------------------- */
void PairEAMCuda::coeff(int narg, char **arg)
{
- PairEAM::coeff(narg, arg);
- allocate();
+ PairEAM::coeff(narg, arg);
+ allocate();
}
void PairEAMCuda::init_style()
{
- MYDBG(printf("# CUDA PairEAMCuda::init_style start\n"); )
+ MYDBG(printf("# CUDA PairEAMCuda::init_style start\n"); )
// request regular or rRESPA neighbor lists
file2array();
array2spline();
int irequest;
-
-
- irequest = neighbor->request(this);
+
+
+ irequest = neighbor->request(this);
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->cudable = 1;
- delete cu_rhor_spline;
- delete cu_z2r_spline;
- delete cu_frho_spline;
-
- cu_rhor_spline = new cCudaData<double, F_FLOAT, xyz>((double*)rhor_spline,nrhor,nr+1,EAM_COEFF_LENGTH);
- cu_z2r_spline = new cCudaData<double, F_FLOAT, xyz>((double*)z2r_spline,nz2r,nr+1,EAM_COEFF_LENGTH);
- cu_frho_spline = new cCudaData<double, F_FLOAT, xyz>((double*)frho_spline,nfrho,nrho+1,EAM_COEFF_LENGTH);
-
- cu_rhor_spline->upload();
- cu_z2r_spline->upload();
- cu_frho_spline->upload();
-
+ delete cu_rhor_spline;
+ delete cu_z2r_spline;
+ delete cu_frho_spline;
+
+ cu_rhor_spline = new cCudaData<double, F_FLOAT, xyz>((double*)rhor_spline,nrhor,nr+1,EAM_COEFF_LENGTH);
+ cu_z2r_spline = new cCudaData<double, F_FLOAT, xyz>((double*)z2r_spline,nz2r,nr+1,EAM_COEFF_LENGTH);
+ cu_frho_spline = new cCudaData<double, F_FLOAT, xyz>((double*)frho_spline,nfrho,nrho+1,EAM_COEFF_LENGTH);
+
+ cu_rhor_spline->upload();
+ cu_z2r_spline->upload();
+ cu_frho_spline->upload();
+
MYDBG(printf("# CUDA PairEAMCuda::init_style end\n"); )
}
void PairEAMCuda::init_list(int id, NeighList *ptr)
{
- MYDBG(printf("# CUDA PairEAMCuda::init_list\n");)
- PairEAM::init_list(id, ptr);
- #ifndef CUDA_USE_BINNING
- // right now we can only handle verlet (id 0), not respa
- if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
- // see Neighbor::init() for details on lammps lists' logic
- #endif
- MYDBG(printf("# CUDA PairEAMCuda::init_list end\n");)
+ MYDBG(printf("# CUDA PairEAMCuda::init_list\n");)
+ PairEAM::init_list(id, ptr);
+ #ifndef CUDA_USE_BINNING
+ // right now we can only handle verlet (id 0), not respa
+ if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
+ // see Neighbor::init() for details on lammps lists' logic
+ #endif
+ MYDBG(printf("# CUDA PairEAMCuda::init_list end\n");)
}
void PairEAMCuda::array2spline()
@@ -204,7 +204,7 @@ void PairEAMCuda::array2spline()
for(int j=0;j<nrho+1;j++)
frho_spline[i][j][7]=frho_spline[i][j][3];
}
-
+
for (int i = 0; i < nrhor; i++){
interpolate(nr,dr,rhor[i],rhor_spline[i]);
for(int j=0;j<nr+1;j++)
@@ -222,7 +222,7 @@ void PairEAMCuda::array2spline()
int PairEAMCuda::pack_comm(int n, int *iswap, double *buf, int pbc_flag, int *pbc)
{
- Cuda_PairEAMCuda_PackComm(&cuda->shared_data,n,*iswap,buf);
+ Cuda_PairEAMCuda_PackComm(&cuda->shared_data,n,*iswap,buf);
if(sizeof(F_FLOAT)<sizeof(double)) return 1;
else return 1;
}
@@ -231,7 +231,7 @@ int PairEAMCuda::pack_comm(int n, int *iswap, double *buf, int pbc_flag, int *pb
void PairEAMCuda::unpack_comm(int n, int first, double *buf)
{
- Cuda_PairEAMCuda_UnpackComm(&cuda->shared_data,n,first,buf,cu_fp->dev_data());
+ Cuda_PairEAMCuda_UnpackComm(&cuda->shared_data,n,first,buf,cu_fp->dev_data());
}
void PairEAMCuda::ev_setup(int eflag, int vflag)
@@ -239,10 +239,10 @@ void PairEAMCuda::ev_setup(int eflag, int vflag)
int maxeatomold=maxeatom;
PairEAM::ev_setup(eflag,vflag);
- if (eflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
+ if (eflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
- if (vflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
+ if (vflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
}
diff --git a/src/USER-CUDA/pair_eam_cuda.h b/src/USER-CUDA/pair_eam_cuda.h
index 2f1f251fac6a1782b136da4d222e6bc14c6e7d30..9d4a30ca0d177bf3230a4d53baa3e4e0a2fe7e84 100644
--- a/src/USER-CUDA/pair_eam_cuda.h
+++ b/src/USER-CUDA/pair_eam_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -28,7 +28,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -49,27 +49,27 @@ namespace LAMMPS_NS {
class PairEAMCuda : public PairEAM
{
- public:
- PairEAMCuda(class LAMMPS *);
- void compute(int, int);
- void settings(int, char **);
- void coeff(int, char **);
- void init_list(int, class NeighList *);
- void init_style();
- void array2spline();
- int pack_comm(int n, int *iswap, double *buf, int pbc_flag, int *pbc);
- void unpack_comm(int n, int first, double *buf);
- protected:
- class Cuda *cuda;
- void allocate();
- bool allocated2;
- virtual void ev_setup(int eflag, int vflag);
- class CudaNeighList* cuda_neigh_list;
- cCudaData<double, F_FLOAT, x>* cu_rho;
- cCudaData<double, F_FLOAT, x>* cu_fp;
- cCudaData<double, F_FLOAT, xyz>* cu_rhor_spline;
- cCudaData<double, F_FLOAT, xyz>* cu_z2r_spline;
- cCudaData<double, F_FLOAT, xyz>* cu_frho_spline;
+ public:
+ PairEAMCuda(class LAMMPS *);
+ void compute(int, int);
+ void settings(int, char **);
+ void coeff(int, char **);
+ void init_list(int, class NeighList *);
+ void init_style();
+ void array2spline();
+ int pack_comm(int n, int *iswap, double *buf, int pbc_flag, int *pbc);
+ void unpack_comm(int n, int first, double *buf);
+ protected:
+ class Cuda *cuda;
+ void allocate();
+ bool allocated2;
+ virtual void ev_setup(int eflag, int vflag);
+ class CudaNeighList* cuda_neigh_list;
+ cCudaData<double, F_FLOAT, x>* cu_rho;
+ cCudaData<double, F_FLOAT, x>* cu_fp;
+ cCudaData<double, F_FLOAT, xyz>* cu_rhor_spline;
+ cCudaData<double, F_FLOAT, xyz>* cu_z2r_spline;
+ cCudaData<double, F_FLOAT, xyz>* cu_frho_spline;
};
diff --git a/src/USER-CUDA/pair_eam_fs_cuda.cpp b/src/USER-CUDA/pair_eam_fs_cuda.cpp
index 13efb5a4feefa33e7bae1737570f188c80bf104e..1d6d6d5f3ba711b929cd49562be8f44b390d0844 100644
--- a/src/USER-CUDA/pair_eam_fs_cuda.cpp
+++ b/src/USER-CUDA/pair_eam_fs_cuda.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -100,9 +100,9 @@ void PairEAMFSCuda::coeff(int narg, char **arg)
for (i = 1; i <= n; i++) {
for (j = i; j <= n; j++) {
if (map[i] >= 0 && map[j] >= 0) {
- setflag[i][j] = 1;
- if (i == j) atom->set_mass(i,fs->mass[map[i]]);
- count++;
+ setflag[i][j] = 1;
+ if (i == j) atom->set_mass(i,fs->mass[map[i]]);
+ count++;
}
}
}
@@ -151,7 +151,7 @@ void PairEAMFSCuda::read_file(char *filename)
int nwords = atom->count_words(line);
if (nwords != file->nelements + 1)
error->all(FLERR,"Incorrect element names in EAM potential file");
-
+
char **words = new char*[file->nelements+1];
nwords = 0;
char *first = strtok(line," \t\n\r\f");
@@ -168,7 +168,7 @@ void PairEAMFSCuda::read_file(char *filename)
if (me == 0) {
fgets(line,MAXLINE,fptr);
sscanf(line,"%d %lg %d %lg %lg",
- &file->nrho,&file->drho,&file->nr,&file->dr,&file->cut);
+ &file->nrho,&file->drho,&file->nr,&file->dr,&file->cut);
}
MPI_Bcast(&file->nrho,1,MPI_INT,0,world);
@@ -179,11 +179,11 @@ void PairEAMFSCuda::read_file(char *filename)
file->mass = new double[file->nelements];
memory->create(file->frho,file->nelements,file->nrho+1,
- "pair:frho");
+ "pair:frho");
memory->create(file->rhor,file->nelements,file->nelements,
- file->nr+1,"pair:rhor");
+ file->nr+1,"pair:rhor");
memory->create(file->z2r,file->nelements,file->nelements,
- file->nr+1,"pair:z2r");
+ file->nr+1,"pair:z2r");
int i,j,tmp;
for (i = 0; i < file->nelements; i++) {
if (me == 0) {
@@ -234,7 +234,7 @@ void PairEAMFSCuda::file2array()
// allocate frho arrays
// nfrho = # of fs elements + 1 for zero array
-
+
nfrho = fs->nelements + 1;
memory->destroy(frho);
memory->create(frho,nfrho,nrho+1,"pair:frho");
@@ -319,12 +319,12 @@ void PairEAMFSCuda::file2array()
irow = map[i];
icol = map[j];
if (irow == -1 || icol == -1) {
- type2z2r[i][j] = 0;
- continue;
+ type2z2r[i][j] = 0;
+ continue;
}
if (irow < icol) {
- irow = map[j];
- icol = map[i];
+ irow = map[j];
+ icol = map[i];
}
n = 0;
for (m = 0; m < irow; m++) n += m + 1;
diff --git a/src/USER-CUDA/pair_eam_fs_cuda.h b/src/USER-CUDA/pair_eam_fs_cuda.h
index c2d4a5504d0fdc9b498806d695b6d021618f0786..a68501a0afd362bab5c6973eb4bb1595d8db4793 100644
--- a/src/USER-CUDA/pair_eam_fs_cuda.h
+++ b/src/USER-CUDA/pair_eam_fs_cuda.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-CUDA/pair_gran_hooke_cuda.cpp b/src/USER-CUDA/pair_gran_hooke_cuda.cpp
index 74a3dbca8d6b4e571fdd71a4a91900a10b1491b5..223d31ad76ce1f16f74f161fbab2266efc99177e 100644
--- a/src/USER-CUDA/pair_gran_hooke_cuda.cpp
+++ b/src/USER-CUDA/pair_gran_hooke_cuda.cpp
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -28,7 +28,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -71,9 +71,9 @@ PairGranHookeCuda::PairGranHookeCuda(LAMMPS *lmp) : PairGranHooke(lmp)
if(cuda == NULL)
error->all(FLERR,"You cannot use a /cuda class, without activating 'cuda' acceleration. Provide '-c on' as command-line argument to LAMMPS..");
- allocated2 = false;
- cuda->shared_data.pair.cudable_force = 1;
- cuda->setSystemParams();
+ allocated2 = false;
+ cuda->shared_data.pair.cudable_force = 1;
+ cuda->setSystemParams();
}
/* ----------------------------------------------------------------------
@@ -82,76 +82,76 @@ PairGranHookeCuda::PairGranHookeCuda(LAMMPS *lmp) : PairGranHooke(lmp)
void PairGranHookeCuda::allocate()
{
- if(! allocated) PairGranHooke::allocate();
- if(! allocated2)
- {
- allocated2 = true;
- int n = atom->ntypes;
- cuda->shared_data.pair.cutsq = cutsq;
- memory->create(cuda->shared_data.pair.coeff1,n+1,n+1,
- "pair:cuda_coeff1");
- memory->create(cuda->shared_data.pair.coeff2,
- n+1,n+1,"pair:cuda_coeff2");
- cuda->shared_data.pair.coeff1[0][0]=kn;
- cuda->shared_data.pair.coeff1[0][1]=kt;
- cuda->shared_data.pair.coeff1[1][0]=gamman;
- cuda->shared_data.pair.coeff1[1][1]=gammat;
- cuda->shared_data.pair.coeff2[0][0]=xmu;
- cuda->shared_data.pair.coeff2[0][1]=dampflag;
- }
+ if(! allocated) PairGranHooke::allocate();
+ if(! allocated2)
+ {
+ allocated2 = true;
+ int n = atom->ntypes;
+ cuda->shared_data.pair.cutsq = cutsq;
+ memory->create(cuda->shared_data.pair.coeff1,n+1,n+1,
+ "pair:cuda_coeff1");
+ memory->create(cuda->shared_data.pair.coeff2,
+ n+1,n+1,"pair:cuda_coeff2");
+ cuda->shared_data.pair.coeff1[0][0]=kn;
+ cuda->shared_data.pair.coeff1[0][1]=kt;
+ cuda->shared_data.pair.coeff1[1][0]=gamman;
+ cuda->shared_data.pair.coeff1[1][1]=gammat;
+ cuda->shared_data.pair.coeff2[0][0]=xmu;
+ cuda->shared_data.pair.coeff2[0][1]=dampflag;
+ }
}
/* ---------------------------------------------------------------------- */
void PairGranHookeCuda::compute(int eflag, int vflag)
{
- cuda->shared_data.pair.use_block_per_atom = 0;
- //cuda->cu_debugdata->memset_device(0);
- if (eflag || vflag) ev_setup(eflag,vflag);
- if(eflag) cuda->cu_eng_vdwl->upload();
- if(vflag) cuda->cu_virial->upload();
+ cuda->shared_data.pair.use_block_per_atom = 0;
+ //cuda->cu_debugdata->memset_device(0);
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ if(eflag) cuda->cu_eng_vdwl->upload();
+ if(vflag) cuda->cu_virial->upload();
- Cuda_PairGranHookeCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);
+ Cuda_PairGranHookeCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);
if(not cuda->shared_data.pair.collect_forces_later)
{
- if(eflag) cuda->cu_eng_vdwl->download();
- if(vflag) cuda->cu_virial->download();
+ if(eflag) cuda->cu_eng_vdwl->download();
+ if(vflag) cuda->cu_virial->download();
}
- //cuda->cu_debugdata->download();
- //printf("%lf %lf %lf %lf %lf %lf\n",1.0e-6*cuda->debugdata[0],1.0e-6*cuda->debugdata[1],1.0e-6*cuda->debugdata[2],1.0e-6*cuda->debugdata[3],1.0e-6*cuda->debugdata[4],1.0e-6*cuda->debugdata[5]);
-
+ //cuda->cu_debugdata->download();
+ //printf("%lf %lf %lf %lf %lf %lf\n",1.0e-6*cuda->debugdata[0],1.0e-6*cuda->debugdata[1],1.0e-6*cuda->debugdata[2],1.0e-6*cuda->debugdata[3],1.0e-6*cuda->debugdata[4],1.0e-6*cuda->debugdata[5]);
+
}
/* ---------------------------------------------------------------------- */
void PairGranHookeCuda::settings(int narg, char **arg)
{
- PairGranHooke::settings(narg, arg);
+ PairGranHooke::settings(narg, arg);
}
/* ---------------------------------------------------------------------- */
void PairGranHookeCuda::coeff(int narg, char **arg)
{
- PairGranHooke::coeff(narg, arg);
- allocate();
+ PairGranHooke::coeff(narg, arg);
+ allocate();
}
void PairGranHookeCuda::init_style()
{
- int i;
- MYDBG(printf("# CUDA PairGranHookeCuda::init_style start\n"); )
+ int i;
+ MYDBG(printf("# CUDA PairGranHookeCuda::init_style start\n"); )
// request regular or rRESPA neighbor lists
int irequest;
-
+
if (update->whichflag == 0 && strstr(update->integrate_style,"respa")) {
- }
- else
+ }
+ else
{
- irequest = neighbor->request(this);
+ irequest = neighbor->request(this);
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->gran = 1;
@@ -207,38 +207,36 @@ void PairGranHookeCuda::init_style()
else
onerad_dynamic[type[i]] = MAX(onerad_dynamic[type[i]],radius[i]);
}
-
+
MPI_Allreduce(&onerad_dynamic[1],&maxrad_dynamic[1],atom->ntypes,
- MPI_DOUBLE,MPI_MAX,world);
+ MPI_DOUBLE,MPI_MAX,world);
MPI_Allreduce(&onerad_frozen[1],&maxrad_frozen[1],atom->ntypes,
- MPI_DOUBLE,MPI_MAX,world);
+ MPI_DOUBLE,MPI_MAX,world);
MYDBG(printf("# CUDA PairGranHookeCuda::init_style end\n"); )
}
void PairGranHookeCuda::init_list(int id, NeighList *ptr)
{
- MYDBG(printf("# CUDA PairGranHookeCuda::init_list\n");)
- PairGranHooke::init_list(id, ptr);
- #ifndef CUDA_USE_BINNING
- // right now we can only handle verlet (id 0), not respa
- if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
- // see Neighbor::init() for details on lammps lists' logic
- #endif
- MYDBG(printf("# CUDA PairGranHookeCuda::init_list end\n");)
+ MYDBG(printf("# CUDA PairGranHookeCuda::init_list\n");)
+ PairGranHooke::init_list(id, ptr);
+ #ifndef CUDA_USE_BINNING
+ // right now we can only handle verlet (id 0), not respa
+ if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
+ // see Neighbor::init() for details on lammps lists' logic
+ #endif
+ MYDBG(printf("# CUDA PairGranHookeCuda::init_list end\n");)
}
void PairGranHookeCuda::ev_setup(int eflag, int vflag)
{
- int maxeatomold=maxeatom;
- PairGranHooke::ev_setup(eflag,vflag);
+ int maxeatomold=maxeatom;
+ PairGranHooke::ev_setup(eflag,vflag);
- if (eflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
-
- if (eflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.eatom , atom->nmax, 6 );}
-
-}
+ if (eflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
+ if (eflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.eatom , atom->nmax, 6 );}
+}
diff --git a/src/USER-CUDA/pair_gran_hooke_cuda.h b/src/USER-CUDA/pair_gran_hooke_cuda.h
index 727082f1f81d48218d721baf1e7bc8011e3b7fb6..b2aee0f9d204925e430f1b2e79378a7354d6118e 100644
--- a/src/USER-CUDA/pair_gran_hooke_cuda.h
+++ b/src/USER-CUDA/pair_gran_hooke_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -36,19 +36,19 @@ namespace LAMMPS_NS {
class PairGranHookeCuda : public PairGranHooke
{
- public:
- PairGranHookeCuda(class LAMMPS *);
- void compute(int, int);
- void settings(int, char **);
- void coeff(int, char **);
- void init_list(int, class NeighList *);
- void init_style();
- void ev_setup(int eflag, int vflag);
- protected:
- class Cuda *cuda;
- void allocate();
- bool allocated2;
- class CudaNeighList* cuda_neigh_list;
+ public:
+ PairGranHookeCuda(class LAMMPS *);
+ void compute(int, int);
+ void settings(int, char **);
+ void coeff(int, char **);
+ void init_list(int, class NeighList *);
+ void init_style();
+ void ev_setup(int eflag, int vflag);
+ protected:
+ class Cuda *cuda;
+ void allocate();
+ bool allocated2;
+ class CudaNeighList* cuda_neigh_list;
};
}
diff --git a/src/USER-CUDA/pair_lj96_cut_cuda.cpp b/src/USER-CUDA/pair_lj96_cut_cuda.cpp
index 408665d85e2d028e0529d85cba145435fe8f95fc..58d866528ac074aad56478acac362b6e034747b6 100644
--- a/src/USER-CUDA/pair_lj96_cut_cuda.cpp
+++ b/src/USER-CUDA/pair_lj96_cut_cuda.cpp
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -28,7 +28,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -69,9 +69,9 @@ PairLJ96CutCuda::PairLJ96CutCuda(LAMMPS *lmp) : PairLJ96Cut(lmp)
if(cuda == NULL)
error->all(FLERR,"You cannot use a /cuda class, without activating 'cuda' acceleration. Provide '-c on' as command-line argument to LAMMPS..");
- allocated2 = false;
- cuda->shared_data.pair.cudable_force = 1;
- cuda->setSystemParams();
+ allocated2 = false;
+ cuda->shared_data.pair.cudable_force = 1;
+ cuda->setSystemParams();
}
/* ----------------------------------------------------------------------
@@ -80,68 +80,68 @@ PairLJ96CutCuda::PairLJ96CutCuda(LAMMPS *lmp) : PairLJ96Cut(lmp)
void PairLJ96CutCuda::allocate()
{
- if(! allocated) PairLJ96Cut::allocate();
- if(! allocated2)
- {
- allocated2 = true;
- cuda->shared_data.pair.cut = cut;
- cuda->shared_data.pair.coeff1 = lj1;
- cuda->shared_data.pair.coeff2 = lj2;
- cuda->shared_data.pair.coeff3 = lj3;
- cuda->shared_data.pair.coeff4 = lj4;
- cuda->shared_data.pair.offset = offset;
- cuda->shared_data.pair.special_lj = force->special_lj;
- cuda->shared_data.pair.special_coul = force->special_coul;
- }
+ if(! allocated) PairLJ96Cut::allocate();
+ if(! allocated2)
+ {
+ allocated2 = true;
+ cuda->shared_data.pair.cut = cut;
+ cuda->shared_data.pair.coeff1 = lj1;
+ cuda->shared_data.pair.coeff2 = lj2;
+ cuda->shared_data.pair.coeff3 = lj3;
+ cuda->shared_data.pair.coeff4 = lj4;
+ cuda->shared_data.pair.offset = offset;
+ cuda->shared_data.pair.special_lj = force->special_lj;
+ cuda->shared_data.pair.special_coul = force->special_coul;
+ }
}
/* ---------------------------------------------------------------------- */
void PairLJ96CutCuda::compute(int eflag, int vflag)
{
- if (eflag || vflag) ev_setup(eflag,vflag);
- if(eflag) cuda->cu_eng_vdwl->upload();
- if(vflag) cuda->cu_virial->upload();
-
- Cuda_PairLJ96CutCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ if(eflag) cuda->cu_eng_vdwl->upload();
+ if(vflag) cuda->cu_virial->upload();
+
+ Cuda_PairLJ96CutCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);
if(not cuda->shared_data.pair.collect_forces_later)
{
- if(eflag) cuda->cu_eng_vdwl->download();
- if(vflag) cuda->cu_virial->download();
+ if(eflag) cuda->cu_eng_vdwl->download();
+ if(vflag) cuda->cu_virial->download();
}
-
+
}
/* ---------------------------------------------------------------------- */
void PairLJ96CutCuda::settings(int narg, char **arg)
{
- PairLJ96Cut::settings(narg, arg);
- cuda->shared_data.pair.cut_global = (F_FLOAT) cut_global;
+ PairLJ96Cut::settings(narg, arg);
+ cuda->shared_data.pair.cut_global = (F_FLOAT) cut_global;
}
/* ---------------------------------------------------------------------- */
void PairLJ96CutCuda::coeff(int narg, char **arg)
{
- PairLJ96Cut::coeff(narg, arg);
- allocate();
+ PairLJ96Cut::coeff(narg, arg);
+ allocate();
}
void PairLJ96CutCuda::init_style()
{
- MYDBG(printf("# CUDA PairLJ96CutCuda::init_style start\n"); )
+ MYDBG(printf("# CUDA PairLJ96CutCuda::init_style start\n"); )
// request regular or rRESPA neighbor lists
int irequest;
-
+
if (update->whichflag == 0 && strstr(update->integrate_style,"respa")) {
- }
- else
+ }
+ else
{
- irequest = neighbor->request(this);
+ irequest = neighbor->request(this);
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->cudable = 1;
@@ -155,27 +155,25 @@ void PairLJ96CutCuda::init_style()
void PairLJ96CutCuda::init_list(int id, NeighList *ptr)
{
- MYDBG(printf("# CUDA PairLJ96CutCuda::init_list\n");)
- PairLJ96Cut::init_list(id, ptr);
- #ifndef CUDA_USE_BINNING
- // right now we can only handle verlet (id 0), not respa
- if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
- // see Neighbor::init() for details on lammps lists' logic
- #endif
- MYDBG(printf("# CUDA PairLJ96CutCuda::init_list end\n");)
+ MYDBG(printf("# CUDA PairLJ96CutCuda::init_list\n");)
+ PairLJ96Cut::init_list(id, ptr);
+ #ifndef CUDA_USE_BINNING
+ // right now we can only handle verlet (id 0), not respa
+ if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
+ // see Neighbor::init() for details on lammps lists' logic
+ #endif
+ MYDBG(printf("# CUDA PairLJ96CutCuda::init_list end\n");)
}
void PairLJ96CutCuda::ev_setup(int eflag, int vflag)
{
- int maxeatomold=maxeatom;
- PairLJ96Cut::ev_setup(eflag,vflag);
+ int maxeatomold=maxeatom;
+ PairLJ96Cut::ev_setup(eflag,vflag);
- if (eflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
-
- if (vflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
-
-}
+ if (eflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
+ if (vflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
+}
diff --git a/src/USER-CUDA/pair_lj96_cut_cuda.h b/src/USER-CUDA/pair_lj96_cut_cuda.h
index 0abb66f6aa9bb0436edc7a296d8b37fc58959eb8..aeb02ca67089d23f5506fe8067c231a214ae3175 100644
--- a/src/USER-CUDA/pair_lj96_cut_cuda.h
+++ b/src/USER-CUDA/pair_lj96_cut_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -36,19 +36,19 @@ namespace LAMMPS_NS {
class PairLJ96CutCuda : public PairLJ96Cut
{
- public:
- PairLJ96CutCuda(class LAMMPS *);
- void compute(int, int);
- void settings(int, char **);
- void coeff(int, char **);
- void init_list(int, class NeighList *);
- void init_style();
- void ev_setup(int eflag, int vflag);
- protected:
- class Cuda *cuda;
- void allocate();
- bool allocated2;
- class CudaNeighList* cuda_neigh_list;
+ public:
+ PairLJ96CutCuda(class LAMMPS *);
+ void compute(int, int);
+ void settings(int, char **);
+ void coeff(int, char **);
+ void init_list(int, class NeighList *);
+ void init_style();
+ void ev_setup(int eflag, int vflag);
+ protected:
+ class Cuda *cuda;
+ void allocate();
+ bool allocated2;
+ class CudaNeighList* cuda_neigh_list;
};
}
diff --git a/src/USER-CUDA/pair_lj_charmm_coul_charmm_cuda.cpp b/src/USER-CUDA/pair_lj_charmm_coul_charmm_cuda.cpp
index bcd35690944acdd1b4ca7d71e726ebabb76c1da7..83dd79d7d22f9de82ed8bf00b3d57db55bf37d5a 100644
--- a/src/USER-CUDA/pair_lj_charmm_coul_charmm_cuda.cpp
+++ b/src/USER-CUDA/pair_lj_charmm_coul_charmm_cuda.cpp
@@ -1,23 +1,23 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
Contributing author: Paul Crozier (SNL)
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -54,10 +54,10 @@ PairLJCharmmCoulCharmmCuda::PairLJCharmmCoulCharmmCuda(LAMMPS *lmp) : PairLJChar
if(cuda == NULL)
error->all(FLERR,"You cannot use a /cuda class, without activating 'cuda' acceleration. Provide '-c on' as command-line argument to LAMMPS..");
- allocated2 = false;
- cuda->shared_data.pair.cudable_force = 1;
- cuda->shared_data.pair.use_block_per_atom = 0;
- cuda->setSystemParams();
+ allocated2 = false;
+ cuda->shared_data.pair.cudable_force = 1;
+ cuda->shared_data.pair.use_block_per_atom = 0;
+ cuda->setSystemParams();
}
/* ----------------------------------------------------------------------
@@ -66,62 +66,62 @@ PairLJCharmmCoulCharmmCuda::PairLJCharmmCoulCharmmCuda(LAMMPS *lmp) : PairLJChar
void PairLJCharmmCoulCharmmCuda::allocate()
{
- if(! allocated) PairLJCharmmCoulCharmm::allocate();
- if(! allocated2)
- {
- cuda->accelerator(0,NULL);
- allocated2 = true;
- cuda->shared_data.pair.coeff1 = lj1;
- cuda->shared_data.pair.coeff2 = lj2;
- cuda->shared_data.pair.coeff3 = lj3;
- cuda->shared_data.pair.coeff4 = lj4;
- cuda->shared_data.pair.special_lj = force->special_lj;
- cuda->shared_data.pair.special_coul = force->special_coul;
- cu_lj1_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj1, &cuda->shared_data.pair.coeff1_gm, (atom->ntypes+1)*(atom->ntypes+1));
- cu_lj2_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj2, &cuda->shared_data.pair.coeff2_gm, (atom->ntypes+1)*(atom->ntypes+1));
- cu_lj3_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj3, &cuda->shared_data.pair.coeff3_gm, (atom->ntypes+1)*(atom->ntypes+1));
- cu_lj4_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj4, &cuda->shared_data.pair.coeff4_gm, (atom->ntypes+1)*(atom->ntypes+1));
- }
+ if(! allocated) PairLJCharmmCoulCharmm::allocate();
+ if(! allocated2)
+ {
+ cuda->accelerator(0,NULL);
+ allocated2 = true;
+ cuda->shared_data.pair.coeff1 = lj1;
+ cuda->shared_data.pair.coeff2 = lj2;
+ cuda->shared_data.pair.coeff3 = lj3;
+ cuda->shared_data.pair.coeff4 = lj4;
+ cuda->shared_data.pair.special_lj = force->special_lj;
+ cuda->shared_data.pair.special_coul = force->special_coul;
+ cu_lj1_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj1, &cuda->shared_data.pair.coeff1_gm, (atom->ntypes+1)*(atom->ntypes+1));
+ cu_lj2_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj2, &cuda->shared_data.pair.coeff2_gm, (atom->ntypes+1)*(atom->ntypes+1));
+ cu_lj3_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj3, &cuda->shared_data.pair.coeff3_gm, (atom->ntypes+1)*(atom->ntypes+1));
+ cu_lj4_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj4, &cuda->shared_data.pair.coeff4_gm, (atom->ntypes+1)*(atom->ntypes+1));
+ }
}
/* ---------------------------------------------------------------------- */
void PairLJCharmmCoulCharmmCuda::compute(int eflag, int vflag)
{
- if (eflag || vflag) ev_setup(eflag,vflag);
- if(not cuda->shared_data.pair.collect_forces_later)
- {
- if(eflag) cuda->cu_eng_vdwl->upload();
- if(eflag) cuda->cu_eng_coul->upload();
- if(vflag) cuda->cu_virial->upload();
- }
-
- Cuda_PairLJCharmmCoulCharmmCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom,denom_lj,cut_coul_innersq,denom_coul);
-
- if(not cuda->shared_data.pair.collect_forces_later)
- {
- if(eflag) cuda->cu_eng_vdwl->download();
- if(eflag) cuda->cu_eng_coul->download();
- if(vflag) cuda->cu_virial->download();
- }
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ if(not cuda->shared_data.pair.collect_forces_later)
+ {
+ if(eflag) cuda->cu_eng_vdwl->upload();
+ if(eflag) cuda->cu_eng_coul->upload();
+ if(vflag) cuda->cu_virial->upload();
+ }
+
+ Cuda_PairLJCharmmCoulCharmmCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom,denom_lj,cut_coul_innersq,denom_coul);
+
+ if(not cuda->shared_data.pair.collect_forces_later)
+ {
+ if(eflag) cuda->cu_eng_vdwl->download();
+ if(eflag) cuda->cu_eng_coul->download();
+ if(vflag) cuda->cu_virial->download();
+ }
}
/* ---------------------------------------------------------------------- */
void PairLJCharmmCoulCharmmCuda::settings(int narg, char **arg)
{
- PairLJCharmmCoulCharmm::settings(narg, arg);
- cuda->shared_data.pair.cut_global = (X_FLOAT) cut_lj;
- cuda->shared_data.pair.cut_coulsq_global = (X_FLOAT) cut_coulsq;
- cuda->shared_data.pair.cut_inner_global = (F_FLOAT) cut_lj_inner;
+ PairLJCharmmCoulCharmm::settings(narg, arg);
+ cuda->shared_data.pair.cut_global = (X_FLOAT) cut_lj;
+ cuda->shared_data.pair.cut_coulsq_global = (X_FLOAT) cut_coulsq;
+ cuda->shared_data.pair.cut_inner_global = (F_FLOAT) cut_lj_inner;
}
/* ---------------------------------------------------------------------- */
void PairLJCharmmCoulCharmmCuda::coeff(int narg, char **arg)
{
- PairLJCharmmCoulCharmm::coeff(narg, arg);
- allocate();
+ PairLJCharmmCoulCharmm::coeff(narg, arg);
+ allocate();
}
void PairLJCharmmCoulCharmmCuda::init_style()
@@ -130,17 +130,17 @@ void PairLJCharmmCoulCharmmCuda::init_style()
error->all(FLERR,"Pair style lj/charmm/coul/long requires atom attribute q");
// request regular or rRESPA neighbor lists
- if(atom->molecular)
- {
- cuda->shared_data.pair.collect_forces_later = 1;
- }
-
+ if(atom->molecular)
+ {
+ cuda->shared_data.pair.collect_forces_later = 1;
+ }
+
int irequest;
-
- irequest = neighbor->request(this);
+
+ irequest = neighbor->request(this);
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->half = 0;
- neighbor->requests[irequest]->cudable = 1;
+ neighbor->requests[irequest]->cudable = 1;
if (cut_lj_inner >= cut_lj || cut_coul_inner >= cut_coul)
error->all(FLERR,"Pair inner cutoff >= Pair outer cutoff");
@@ -151,41 +151,39 @@ void PairLJCharmmCoulCharmmCuda::init_style()
cut_coulsq = cut_coul * cut_coul;
cut_bothsq = MAX(cut_ljsq,cut_coulsq);
- denom_lj = (cut_ljsq-cut_lj_innersq) * (cut_ljsq-cut_lj_innersq) *
+ denom_lj = (cut_ljsq-cut_lj_innersq) * (cut_ljsq-cut_lj_innersq) *
(cut_ljsq-cut_lj_innersq);
- denom_coul = (cut_coulsq-cut_coul_innersq) * (cut_coulsq-cut_coul_innersq) *
+ denom_coul = (cut_coulsq-cut_coul_innersq) * (cut_coulsq-cut_coul_innersq) *
(cut_coulsq-cut_coul_innersq);
cut_coulsq = cut_coul * cut_coul;
-
+
cuda->shared_data.pair.cut_coulsq_global=cut_coulsq;
-
+
cuda->shared_data.pppm.qqrd2e=force->qqrd2e;
}
void PairLJCharmmCoulCharmmCuda::init_list(int id, NeighList *ptr)
{
- MYDBG(printf("# CUDA PairLJCharmmCoulCharmmCuda::init_list\n");)
- PairLJCharmmCoulCharmm::init_list(id, ptr);
- #ifndef CUDA_USE_BINNING
- // right now we can only handle verlet (id 0), not respa
- if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
- // see Neighbor::init() for details on lammps lists' logic
- #endif
- MYDBG(printf("# CUDA PairLJCharmmCoulCharmmCuda::init_list end\n");)
+ MYDBG(printf("# CUDA PairLJCharmmCoulCharmmCuda::init_list\n");)
+ PairLJCharmmCoulCharmm::init_list(id, ptr);
+ #ifndef CUDA_USE_BINNING
+ // right now we can only handle verlet (id 0), not respa
+ if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
+ // see Neighbor::init() for details on lammps lists' logic
+ #endif
+ MYDBG(printf("# CUDA PairLJCharmmCoulCharmmCuda::init_list end\n");)
}
void PairLJCharmmCoulCharmmCuda::ev_setup(int eflag, int vflag)
{
- int maxeatomold=maxeatom;
- PairLJCharmmCoulCharmm::ev_setup(eflag,vflag);
+ int maxeatomold=maxeatom;
+ PairLJCharmmCoulCharmm::ev_setup(eflag,vflag);
- if (eflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
-
- if (vflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
-
-}
+ if (eflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
+ if (vflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
+}
diff --git a/src/USER-CUDA/pair_lj_charmm_coul_charmm_cuda.h b/src/USER-CUDA/pair_lj_charmm_coul_charmm_cuda.h
index 39ec4735ef7d8b096e4cb1908f4b2a8e8bd0da9f..bcc76b5b68922ae6ee5bdcac60b5c3d5c2f9ba7e 100644
--- a/src/USER-CUDA/pair_lj_charmm_coul_charmm_cuda.h
+++ b/src/USER-CUDA/pair_lj_charmm_coul_charmm_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -37,23 +37,23 @@ namespace LAMMPS_NS {
class PairLJCharmmCoulCharmmCuda : public PairLJCharmmCoulCharmm
{
- public:
- PairLJCharmmCoulCharmmCuda(class LAMMPS *);
- void compute(int, int);
- void settings(int, char **);
- void coeff(int, char **);
- void init_list(int, class NeighList *);
- void init_style();
- void ev_setup(int eflag, int vflag);
- protected:
- class Cuda *cuda;
- void allocate();
- bool allocated2;
- class CudaNeighList* cuda_neigh_list;
- cCudaData<double , F_FLOAT , x >* cu_lj1_gm;
- cCudaData<double , F_FLOAT , x >* cu_lj2_gm;
- cCudaData<double , F_FLOAT , x >* cu_lj3_gm;
- cCudaData<double , F_FLOAT , x >* cu_lj4_gm;
+ public:
+ PairLJCharmmCoulCharmmCuda(class LAMMPS *);
+ void compute(int, int);
+ void settings(int, char **);
+ void coeff(int, char **);
+ void init_list(int, class NeighList *);
+ void init_style();
+ void ev_setup(int eflag, int vflag);
+ protected:
+ class Cuda *cuda;
+ void allocate();
+ bool allocated2;
+ class CudaNeighList* cuda_neigh_list;
+ cCudaData<double , F_FLOAT , x >* cu_lj1_gm;
+ cCudaData<double , F_FLOAT , x >* cu_lj2_gm;
+ cCudaData<double , F_FLOAT , x >* cu_lj3_gm;
+ cCudaData<double , F_FLOAT , x >* cu_lj4_gm;
};
diff --git a/src/USER-CUDA/pair_lj_charmm_coul_charmm_implicit_cuda.cpp b/src/USER-CUDA/pair_lj_charmm_coul_charmm_implicit_cuda.cpp
index 10696094c05ac3a22655e0bf6e253de7b9690970..340116959c2d8510d6a3e61f0ed90917d61b3869 100644
--- a/src/USER-CUDA/pair_lj_charmm_coul_charmm_implicit_cuda.cpp
+++ b/src/USER-CUDA/pair_lj_charmm_coul_charmm_implicit_cuda.cpp
@@ -1,23 +1,23 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
Contributing author: Paul Crozier (SNL)
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -54,10 +54,10 @@ PairLJCharmmCoulCharmmImplicitCuda::PairLJCharmmCoulCharmmImplicitCuda(LAMMPS *l
if(cuda == NULL)
error->all(FLERR,"You cannot use a /cuda class, without activating 'cuda' acceleration. Provide '-c on' as command-line argument to LAMMPS..");
- allocated2 = false;
- cuda->shared_data.pair.cudable_force = 1;
- cuda->shared_data.pair.collect_forces_later = 1;
- cuda->setSystemParams();
+ allocated2 = false;
+ cuda->shared_data.pair.cudable_force = 1;
+ cuda->shared_data.pair.collect_forces_later = 1;
+ cuda->setSystemParams();
}
/* ----------------------------------------------------------------------
@@ -66,62 +66,62 @@ PairLJCharmmCoulCharmmImplicitCuda::PairLJCharmmCoulCharmmImplicitCuda(LAMMPS *l
void PairLJCharmmCoulCharmmImplicitCuda::allocate()
{
- if(! allocated) PairLJCharmmCoulCharmmImplicit::allocate();
- if(! allocated2)
- {
- cuda->accelerator(0,NULL);
- allocated2 = true;
- cuda->shared_data.pair.coeff1 = lj1;
- cuda->shared_data.pair.coeff2 = lj2;
- cuda->shared_data.pair.coeff3 = lj3;
- cuda->shared_data.pair.coeff4 = lj4;
- cuda->shared_data.pair.special_lj = force->special_lj;
- cuda->shared_data.pair.special_coul = force->special_coul;
- cu_lj1_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj1, &cuda->shared_data.pair.coeff1_gm, (atom->ntypes+1)*(atom->ntypes+1));
- cu_lj2_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj2, &cuda->shared_data.pair.coeff2_gm, (atom->ntypes+1)*(atom->ntypes+1));
- cu_lj3_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj3, &cuda->shared_data.pair.coeff3_gm, (atom->ntypes+1)*(atom->ntypes+1));
- cu_lj4_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj4, &cuda->shared_data.pair.coeff4_gm, (atom->ntypes+1)*(atom->ntypes+1));
- }
+ if(! allocated) PairLJCharmmCoulCharmmImplicit::allocate();
+ if(! allocated2)
+ {
+ cuda->accelerator(0,NULL);
+ allocated2 = true;
+ cuda->shared_data.pair.coeff1 = lj1;
+ cuda->shared_data.pair.coeff2 = lj2;
+ cuda->shared_data.pair.coeff3 = lj3;
+ cuda->shared_data.pair.coeff4 = lj4;
+ cuda->shared_data.pair.special_lj = force->special_lj;
+ cuda->shared_data.pair.special_coul = force->special_coul;
+ cu_lj1_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj1, &cuda->shared_data.pair.coeff1_gm, (atom->ntypes+1)*(atom->ntypes+1));
+ cu_lj2_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj2, &cuda->shared_data.pair.coeff2_gm, (atom->ntypes+1)*(atom->ntypes+1));
+ cu_lj3_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj3, &cuda->shared_data.pair.coeff3_gm, (atom->ntypes+1)*(atom->ntypes+1));
+ cu_lj4_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj4, &cuda->shared_data.pair.coeff4_gm, (atom->ntypes+1)*(atom->ntypes+1));
+ }
}
/* ---------------------------------------------------------------------- */
void PairLJCharmmCoulCharmmImplicitCuda::compute(int eflag, int vflag)
{
- if (eflag || vflag) ev_setup(eflag,vflag);
- if(not cuda->shared_data.pair.collect_forces_later)
- {
- if(eflag) cuda->cu_eng_vdwl->upload();
- if(eflag) cuda->cu_eng_coul->upload();
- if(vflag) cuda->cu_virial->upload();
- }
-
- Cuda_PairLJCharmmCoulCharmmImplicitCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom,denom_lj,cut_coul_innersq,denom_coul);
-
- if(not cuda->shared_data.pair.collect_forces_later)
- {
- if(eflag) cuda->cu_eng_vdwl->download();
- if(eflag) cuda->cu_eng_coul->download();
- if(vflag) cuda->cu_virial->download();
- }
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ if(not cuda->shared_data.pair.collect_forces_later)
+ {
+ if(eflag) cuda->cu_eng_vdwl->upload();
+ if(eflag) cuda->cu_eng_coul->upload();
+ if(vflag) cuda->cu_virial->upload();
+ }
+
+ Cuda_PairLJCharmmCoulCharmmImplicitCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom,denom_lj,cut_coul_innersq,denom_coul);
+
+ if(not cuda->shared_data.pair.collect_forces_later)
+ {
+ if(eflag) cuda->cu_eng_vdwl->download();
+ if(eflag) cuda->cu_eng_coul->download();
+ if(vflag) cuda->cu_virial->download();
+ }
}
/* ---------------------------------------------------------------------- */
void PairLJCharmmCoulCharmmImplicitCuda::settings(int narg, char **arg)
{
- PairLJCharmmCoulCharmmImplicit::settings(narg, arg);
- cuda->shared_data.pair.cut_global = (X_FLOAT) cut_lj;
- cuda->shared_data.pair.cut_coulsq_global = (X_FLOAT) cut_coulsq;
- cuda->shared_data.pair.cut_inner_global = (F_FLOAT) cut_lj_inner;
+ PairLJCharmmCoulCharmmImplicit::settings(narg, arg);
+ cuda->shared_data.pair.cut_global = (X_FLOAT) cut_lj;
+ cuda->shared_data.pair.cut_coulsq_global = (X_FLOAT) cut_coulsq;
+ cuda->shared_data.pair.cut_inner_global = (F_FLOAT) cut_lj_inner;
}
/* ---------------------------------------------------------------------- */
void PairLJCharmmCoulCharmmImplicitCuda::coeff(int narg, char **arg)
{
- PairLJCharmmCoulCharmmImplicit::coeff(narg, arg);
- allocate();
+ PairLJCharmmCoulCharmmImplicit::coeff(narg, arg);
+ allocate();
}
void PairLJCharmmCoulCharmmImplicitCuda::init_style()
@@ -131,11 +131,11 @@ void PairLJCharmmCoulCharmmImplicitCuda::init_style()
// request regular or rRESPA neighbor lists
int irequest;
-
- irequest = neighbor->request(this);
+
+ irequest = neighbor->request(this);
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->half = 0;
- neighbor->requests[irequest]->cudable = 1;
+ neighbor->requests[irequest]->cudable = 1;
if (cut_lj_inner >= cut_lj || cut_coul_inner >= cut_coul)
error->all(FLERR,"Pair inner cutoff >= Pair outer cutoff");
@@ -146,41 +146,39 @@ void PairLJCharmmCoulCharmmImplicitCuda::init_style()
cut_coulsq = cut_coul * cut_coul;
cut_bothsq = MAX(cut_ljsq,cut_coulsq);
- denom_lj = (cut_ljsq-cut_lj_innersq) * (cut_ljsq-cut_lj_innersq) *
+ denom_lj = (cut_ljsq-cut_lj_innersq) * (cut_ljsq-cut_lj_innersq) *
(cut_ljsq-cut_lj_innersq);
- denom_coul = (cut_coulsq-cut_coul_innersq) * (cut_coulsq-cut_coul_innersq) *
+ denom_coul = (cut_coulsq-cut_coul_innersq) * (cut_coulsq-cut_coul_innersq) *
(cut_coulsq-cut_coul_innersq);
cut_coulsq = cut_coul * cut_coul;
cuda->shared_data.pair.cut_coulsq_global=cut_coulsq;
-
+
cuda->shared_data.pppm.qqrd2e=force->qqrd2e;
}
void PairLJCharmmCoulCharmmImplicitCuda::init_list(int id, NeighList *ptr)
{
- MYDBG(printf("# CUDA PairLJCharmmCoulCharmmImplicitCuda::init_list\n");)
- PairLJCharmmCoulCharmmImplicit::init_list(id, ptr);
- #ifndef CUDA_USE_BINNING
- // right now we can only handle verlet (id 0), not respa
- if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
- // see Neighbor::init() for details on lammps lists' logic
- #endif
- MYDBG(printf("# CUDA PairLJCharmmCoulCharmmImplicitCuda::init_list end\n");)
+ MYDBG(printf("# CUDA PairLJCharmmCoulCharmmImplicitCuda::init_list\n");)
+ PairLJCharmmCoulCharmmImplicit::init_list(id, ptr);
+ #ifndef CUDA_USE_BINNING
+ // right now we can only handle verlet (id 0), not respa
+ if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
+ // see Neighbor::init() for details on lammps lists' logic
+ #endif
+ MYDBG(printf("# CUDA PairLJCharmmCoulCharmmImplicitCuda::init_list end\n");)
}
void PairLJCharmmCoulCharmmImplicitCuda::ev_setup(int eflag, int vflag)
{
- int maxeatomold=maxeatom;
- PairLJCharmmCoulCharmmImplicit::ev_setup(eflag,vflag);
+ int maxeatomold=maxeatom;
+ PairLJCharmmCoulCharmmImplicit::ev_setup(eflag,vflag);
- if (eflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
-
- if (vflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
-
-}
+ if (eflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
+ if (vflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
+}
diff --git a/src/USER-CUDA/pair_lj_charmm_coul_charmm_implicit_cuda.h b/src/USER-CUDA/pair_lj_charmm_coul_charmm_implicit_cuda.h
index 94d8d0954328c75e089ce3cd66faea3b04d07c8d..748b6b6bbc28dae29290ad44c4741b50208641c7 100644
--- a/src/USER-CUDA/pair_lj_charmm_coul_charmm_implicit_cuda.h
+++ b/src/USER-CUDA/pair_lj_charmm_coul_charmm_implicit_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -37,23 +37,23 @@ namespace LAMMPS_NS {
class PairLJCharmmCoulCharmmImplicitCuda : public PairLJCharmmCoulCharmmImplicit
{
- public:
- PairLJCharmmCoulCharmmImplicitCuda(class LAMMPS *);
- void compute(int, int);
- void settings(int, char **);
- void coeff(int, char **);
- void init_list(int, class NeighList *);
- void init_style();
- void ev_setup(int eflag, int vflag);
- protected:
- class Cuda *cuda;
- void allocate();
- bool allocated2;
- class CudaNeighList* cuda_neigh_list;
- cCudaData<double , F_FLOAT , x >* cu_lj1_gm;
- cCudaData<double , F_FLOAT , x >* cu_lj2_gm;
- cCudaData<double , F_FLOAT , x >* cu_lj3_gm;
- cCudaData<double , F_FLOAT , x >* cu_lj4_gm;
+ public:
+ PairLJCharmmCoulCharmmImplicitCuda(class LAMMPS *);
+ void compute(int, int);
+ void settings(int, char **);
+ void coeff(int, char **);
+ void init_list(int, class NeighList *);
+ void init_style();
+ void ev_setup(int eflag, int vflag);
+ protected:
+ class Cuda *cuda;
+ void allocate();
+ bool allocated2;
+ class CudaNeighList* cuda_neigh_list;
+ cCudaData<double , F_FLOAT , x >* cu_lj1_gm;
+ cCudaData<double , F_FLOAT , x >* cu_lj2_gm;
+ cCudaData<double , F_FLOAT , x >* cu_lj3_gm;
+ cCudaData<double , F_FLOAT , x >* cu_lj4_gm;
};
}
diff --git a/src/USER-CUDA/pair_lj_charmm_coul_long_cuda.cpp b/src/USER-CUDA/pair_lj_charmm_coul_long_cuda.cpp
index 833b16f5928dd1f850711cece13577ef91cf71ae..315f7ff80ecaf44ea9b321709f7b0f3c5e7cb657 100644
--- a/src/USER-CUDA/pair_lj_charmm_coul_long_cuda.cpp
+++ b/src/USER-CUDA/pair_lj_charmm_coul_long_cuda.cpp
@@ -1,23 +1,23 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
Contributing author: Paul Crozier (SNL)
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -61,10 +61,10 @@ PairLJCharmmCoulLongCuda::PairLJCharmmCoulLongCuda(LAMMPS *lmp) : PairLJCharmmCo
if(cuda == NULL)
error->all(FLERR,"You cannot use a /cuda class, without activating 'cuda' acceleration. Provide '-c on' as command-line argument to LAMMPS..");
- allocated2 = false;
- cuda->shared_data.pair.cudable_force = 1;
- cuda->shared_data.pair.collect_forces_later = 1;
- cuda->setSystemParams();
+ allocated2 = false;
+ cuda->shared_data.pair.cudable_force = 1;
+ cuda->shared_data.pair.collect_forces_later = 1;
+ cuda->setSystemParams();
}
/* ----------------------------------------------------------------------
@@ -73,64 +73,64 @@ PairLJCharmmCoulLongCuda::PairLJCharmmCoulLongCuda(LAMMPS *lmp) : PairLJCharmmCo
void PairLJCharmmCoulLongCuda::allocate()
{
- if(! allocated) PairLJCharmmCoulLong::allocate();
- if(! allocated2)
- {
- cuda->accelerator(0,NULL);
- allocated2 = true;
- //cuda->shared_data.pair.cut = cut_lj;
- cuda->shared_data.pair.coeff1 = lj1;
- cuda->shared_data.pair.coeff2 = lj2;
- cuda->shared_data.pair.coeff3 = lj3;
- cuda->shared_data.pair.coeff4 = lj4;
- cuda->shared_data.pair.offset = offset;
- cuda->shared_data.pair.special_lj = force->special_lj;
- cuda->shared_data.pair.special_coul = force->special_coul;
- cu_lj1_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj1, &cuda->shared_data.pair.coeff1_gm, (atom->ntypes+1)*(atom->ntypes+1));
- cu_lj2_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj2, &cuda->shared_data.pair.coeff2_gm, (atom->ntypes+1)*(atom->ntypes+1));
- cu_lj3_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj3, &cuda->shared_data.pair.coeff3_gm, (atom->ntypes+1)*(atom->ntypes+1));
- cu_lj4_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj4, &cuda->shared_data.pair.coeff4_gm, (atom->ntypes+1)*(atom->ntypes+1));
- }
+ if(! allocated) PairLJCharmmCoulLong::allocate();
+ if(! allocated2)
+ {
+ cuda->accelerator(0,NULL);
+ allocated2 = true;
+ //cuda->shared_data.pair.cut = cut_lj;
+ cuda->shared_data.pair.coeff1 = lj1;
+ cuda->shared_data.pair.coeff2 = lj2;
+ cuda->shared_data.pair.coeff3 = lj3;
+ cuda->shared_data.pair.coeff4 = lj4;
+ cuda->shared_data.pair.offset = offset;
+ cuda->shared_data.pair.special_lj = force->special_lj;
+ cuda->shared_data.pair.special_coul = force->special_coul;
+ cu_lj1_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj1, &cuda->shared_data.pair.coeff1_gm, (atom->ntypes+1)*(atom->ntypes+1));
+ cu_lj2_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj2, &cuda->shared_data.pair.coeff2_gm, (atom->ntypes+1)*(atom->ntypes+1));
+ cu_lj3_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj3, &cuda->shared_data.pair.coeff3_gm, (atom->ntypes+1)*(atom->ntypes+1));
+ cu_lj4_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj4, &cuda->shared_data.pair.coeff4_gm, (atom->ntypes+1)*(atom->ntypes+1));
+ }
}
/* ---------------------------------------------------------------------- */
void PairLJCharmmCoulLongCuda::compute(int eflag, int vflag)
{
- if (eflag || vflag) ev_setup(eflag,vflag);
- if(not cuda->shared_data.pair.collect_forces_later)
- {
- if(eflag) cuda->cu_eng_vdwl->upload();
- if(eflag) cuda->cu_eng_coul->upload();
- if(vflag) cuda->cu_virial->upload();
- }
-
- Cuda_PairLJCharmmCoulLongCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom,denom_lj);
-
- if(not cuda->shared_data.pair.collect_forces_later)
- {
- if(eflag) cuda->cu_eng_vdwl->download();
- if(eflag) cuda->cu_eng_coul->download();
- if(vflag) cuda->cu_virial->download();
- }
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ if(not cuda->shared_data.pair.collect_forces_later)
+ {
+ if(eflag) cuda->cu_eng_vdwl->upload();
+ if(eflag) cuda->cu_eng_coul->upload();
+ if(vflag) cuda->cu_virial->upload();
+ }
+
+ Cuda_PairLJCharmmCoulLongCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom,denom_lj);
+
+ if(not cuda->shared_data.pair.collect_forces_later)
+ {
+ if(eflag) cuda->cu_eng_vdwl->download();
+ if(eflag) cuda->cu_eng_coul->download();
+ if(vflag) cuda->cu_virial->download();
+ }
}
/* ---------------------------------------------------------------------- */
void PairLJCharmmCoulLongCuda::settings(int narg, char **arg)
{
- PairLJCharmmCoulLong::settings(narg, arg);
- cuda->shared_data.pair.cut_global = (X_FLOAT) cut_lj;
- cuda->shared_data.pair.cut_coulsq_global = (X_FLOAT) cut_coulsq;
- cuda->shared_data.pair.cut_inner_global = (F_FLOAT) cut_lj_inner;
+ PairLJCharmmCoulLong::settings(narg, arg);
+ cuda->shared_data.pair.cut_global = (X_FLOAT) cut_lj;
+ cuda->shared_data.pair.cut_coulsq_global = (X_FLOAT) cut_coulsq;
+ cuda->shared_data.pair.cut_inner_global = (F_FLOAT) cut_lj_inner;
}
/* ---------------------------------------------------------------------- */
void PairLJCharmmCoulLongCuda::coeff(int narg, char **arg)
{
- PairLJCharmmCoulLong::coeff(narg, arg);
- allocate();
+ PairLJCharmmCoulLong::coeff(narg, arg);
+ allocate();
}
void PairLJCharmmCoulLongCuda::init_style()
@@ -140,14 +140,14 @@ void PairLJCharmmCoulLongCuda::init_style()
// request regular or rRESPA neighbor lists
int irequest;
-
- irequest = neighbor->request(this);
+
+ irequest = neighbor->request(this);
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->half = 0;
- neighbor->requests[irequest]->cudable = 1;
-
- if (cut_lj_inner >= cut_lj)
+ neighbor->requests[irequest]->cudable = 1;
+
+ if (cut_lj_inner >= cut_lj)
error->all(FLERR,"Pair inner cutoff >= Pair outer cutoff");
cut_lj_innersq = cut_lj_inner * cut_lj_inner;
@@ -155,7 +155,7 @@ void PairLJCharmmCoulLongCuda::init_style()
cut_coulsq = cut_coul * cut_coul;
cut_bothsq = MAX(cut_ljsq,cut_coulsq);
- denom_lj = (cut_ljsq-cut_lj_innersq) * (cut_ljsq-cut_lj_innersq) *
+ denom_lj = (cut_ljsq-cut_lj_innersq) * (cut_ljsq-cut_lj_innersq) *
(cut_ljsq-cut_lj_innersq);
cut_coulsq = cut_coul * cut_coul;
@@ -166,34 +166,32 @@ void PairLJCharmmCoulLongCuda::init_style()
g_ewald = force->kspace->g_ewald;
cuda->shared_data.pair.g_ewald=g_ewald;
cuda->shared_data.pppm.qqrd2e=force->qqrd2e;
-
+
if(ncoultablebits) error->warning(FLERR,"# CUDA: You asked for the usage of Coulomb Tables. This is not supported in CUDA Pair forces. Setting is ignored.\n");
}
void PairLJCharmmCoulLongCuda::init_list(int id, NeighList *ptr)
{
- MYDBG(printf("# CUDA PairLJCharmmCoulLongCuda::init_list\n");)
- PairLJCharmmCoulLong::init_list(id, ptr);
- #ifndef CUDA_USE_BINNING
- // right now we can only handle verlet (id 0), not respa
- if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
- // see Neighbor::init() for details on lammps lists' logic
- #endif
- MYDBG(printf("# CUDA PairLJCharmmCoulLongCuda::init_list end\n");)
+ MYDBG(printf("# CUDA PairLJCharmmCoulLongCuda::init_list\n");)
+ PairLJCharmmCoulLong::init_list(id, ptr);
+ #ifndef CUDA_USE_BINNING
+ // right now we can only handle verlet (id 0), not respa
+ if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
+ // see Neighbor::init() for details on lammps lists' logic
+ #endif
+ MYDBG(printf("# CUDA PairLJCharmmCoulLongCuda::init_list end\n");)
}
void PairLJCharmmCoulLongCuda::ev_setup(int eflag, int vflag)
{
- int maxeatomold=maxeatom;
- PairLJCharmmCoulLong::ev_setup(eflag,vflag);
+ int maxeatomold=maxeatom;
+ PairLJCharmmCoulLong::ev_setup(eflag,vflag);
- if (eflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
-
- if (vflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
-
-}
+ if (eflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
+ if (vflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
+}
diff --git a/src/USER-CUDA/pair_lj_charmm_coul_long_cuda.h b/src/USER-CUDA/pair_lj_charmm_coul_long_cuda.h
index 4548883aaad4e55c585ddfde0ec1f9283105fb62..de575d5914ccc14c0df97e90d1d9631e2d43000f 100644
--- a/src/USER-CUDA/pair_lj_charmm_coul_long_cuda.h
+++ b/src/USER-CUDA/pair_lj_charmm_coul_long_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -37,23 +37,23 @@ namespace LAMMPS_NS {
class PairLJCharmmCoulLongCuda : public PairLJCharmmCoulLong
{
- public:
- PairLJCharmmCoulLongCuda(class LAMMPS *);
- void compute(int, int);
- void settings(int, char **);
- void coeff(int, char **);
- void init_list(int, class NeighList *);
- void init_style();
- void ev_setup(int eflag, int vflag);
- protected:
- class Cuda *cuda;
- void allocate();
- bool allocated2;
- class CudaNeighList* cuda_neigh_list;
- cCudaData<double , F_FLOAT , x >* cu_lj1_gm;
- cCudaData<double , F_FLOAT , x >* cu_lj2_gm;
- cCudaData<double , F_FLOAT , x >* cu_lj3_gm;
- cCudaData<double , F_FLOAT , x >* cu_lj4_gm;
+ public:
+ PairLJCharmmCoulLongCuda(class LAMMPS *);
+ void compute(int, int);
+ void settings(int, char **);
+ void coeff(int, char **);
+ void init_list(int, class NeighList *);
+ void init_style();
+ void ev_setup(int eflag, int vflag);
+ protected:
+ class Cuda *cuda;
+ void allocate();
+ bool allocated2;
+ class CudaNeighList* cuda_neigh_list;
+ cCudaData<double , F_FLOAT , x >* cu_lj1_gm;
+ cCudaData<double , F_FLOAT , x >* cu_lj2_gm;
+ cCudaData<double , F_FLOAT , x >* cu_lj3_gm;
+ cCudaData<double , F_FLOAT , x >* cu_lj4_gm;
};
}
diff --git a/src/USER-CUDA/pair_lj_class2_coul_cut_cuda.cpp b/src/USER-CUDA/pair_lj_class2_coul_cut_cuda.cpp
index 702f2089c9dbd14b246d9279aeca7667df966341..5c0aa6d32aef1c5e72d8d0ad5f2d0a63b1aaf370 100644
--- a/src/USER-CUDA/pair_lj_class2_coul_cut_cuda.cpp
+++ b/src/USER-CUDA/pair_lj_class2_coul_cut_cuda.cpp
@@ -1,23 +1,23 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
Contributing author: Paul Crozier (SNL)
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -54,9 +54,9 @@ PairLJClass2CoulCutCuda::PairLJClass2CoulCutCuda(LAMMPS *lmp) : PairLJClass2Coul
if(cuda == NULL)
error->all(FLERR,"You cannot use a /cuda class, without activating 'cuda' acceleration. Provide '-c on' as command-line argument to LAMMPS..");
- allocated2 = false;
- cuda->shared_data.pair.cudable_force = 1;
- cuda->setSystemParams();
+ allocated2 = false;
+ cuda->shared_data.pair.cudable_force = 1;
+ cuda->setSystemParams();
}
/* ----------------------------------------------------------------------
@@ -65,38 +65,38 @@ PairLJClass2CoulCutCuda::PairLJClass2CoulCutCuda(LAMMPS *lmp) : PairLJClass2Coul
void PairLJClass2CoulCutCuda::allocate()
{
- if(! allocated) PairLJClass2CoulCut::allocate();
- if(! allocated2)
- {
- allocated2 = true;
- cuda->shared_data.pair.cut = cut_lj;
- cuda->shared_data.pair.cut_coul= cut_coul;
- cuda->shared_data.pair.coeff1 = lj1;
- cuda->shared_data.pair.coeff2 = lj2;
- cuda->shared_data.pair.coeff3 = lj3;
- cuda->shared_data.pair.coeff4 = lj4;
- cuda->shared_data.pair.offset = offset;
- cuda->shared_data.pair.special_lj = force->special_lj;
- cuda->shared_data.pair.special_coul = force->special_coul;
- }
+ if(! allocated) PairLJClass2CoulCut::allocate();
+ if(! allocated2)
+ {
+ allocated2 = true;
+ cuda->shared_data.pair.cut = cut_lj;
+ cuda->shared_data.pair.cut_coul= cut_coul;
+ cuda->shared_data.pair.coeff1 = lj1;
+ cuda->shared_data.pair.coeff2 = lj2;
+ cuda->shared_data.pair.coeff3 = lj3;
+ cuda->shared_data.pair.coeff4 = lj4;
+ cuda->shared_data.pair.offset = offset;
+ cuda->shared_data.pair.special_lj = force->special_lj;
+ cuda->shared_data.pair.special_coul = force->special_coul;
+ }
}
/* ---------------------------------------------------------------------- */
void PairLJClass2CoulCutCuda::compute(int eflag, int vflag)
{
- if (eflag || vflag) ev_setup(eflag,vflag);
- if(eflag) cuda->cu_eng_vdwl->upload();
- if(eflag) cuda->cu_eng_coul->upload();
- if(vflag) cuda->cu_virial->upload();
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ if(eflag) cuda->cu_eng_vdwl->upload();
+ if(eflag) cuda->cu_eng_coul->upload();
+ if(vflag) cuda->cu_virial->upload();
- Cuda_PairLJClass2CoulCutCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);
+ Cuda_PairLJClass2CoulCutCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);
if(not cuda->shared_data.pair.collect_forces_later)
{
- if(eflag) cuda->cu_eng_vdwl->download();
- if(eflag) cuda->cu_eng_coul->download();
- if(vflag) cuda->cu_virial->download();
+ if(eflag) cuda->cu_eng_vdwl->download();
+ if(eflag) cuda->cu_eng_coul->download();
+ if(vflag) cuda->cu_virial->download();
}
}
@@ -104,17 +104,17 @@ void PairLJClass2CoulCutCuda::compute(int eflag, int vflag)
void PairLJClass2CoulCutCuda::settings(int narg, char **arg)
{
- PairLJClass2CoulCut::settings(narg, arg);
- cuda->shared_data.pair.cut_global = (F_FLOAT) cut_lj_global;
- cuda->shared_data.pair.cut_coul_global = (F_FLOAT) cut_coul_global;
+ PairLJClass2CoulCut::settings(narg, arg);
+ cuda->shared_data.pair.cut_global = (F_FLOAT) cut_lj_global;
+ cuda->shared_data.pair.cut_coul_global = (F_FLOAT) cut_coul_global;
}
/* ---------------------------------------------------------------------- */
void PairLJClass2CoulCutCuda::coeff(int narg, char **arg)
{
- PairLJClass2CoulCut::coeff(narg, arg);
- allocate();
+ PairLJClass2CoulCut::coeff(narg, arg);
+ allocate();
}
void PairLJClass2CoulCutCuda::init_style()
@@ -124,41 +124,39 @@ void PairLJClass2CoulCutCuda::init_style()
// request regular or rRESPA neighbor lists
int irequest;
-
-
+
+
irequest = neighbor->request(this);
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->cudable = 1;
-
+
cuda->shared_data.pppm.qqrd2e=force->qqrd2e;
-
+
}
void PairLJClass2CoulCutCuda::init_list(int id, NeighList *ptr)
{
- MYDBG(printf("# CUDA PairLJClass2CoulCutCuda::init_list\n");)
- PairLJClass2CoulCut::init_list(id, ptr);
- #ifndef CUDA_USE_BINNING
- // right now we can only handle verlet (id 0), not respa
- if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
- // see Neighbor::init() for details on lammps lists' logic
- #endif
- MYDBG(printf("# CUDA PairLJClass2CoulCutCuda::init_list end\n");)
+ MYDBG(printf("# CUDA PairLJClass2CoulCutCuda::init_list\n");)
+ PairLJClass2CoulCut::init_list(id, ptr);
+ #ifndef CUDA_USE_BINNING
+ // right now we can only handle verlet (id 0), not respa
+ if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
+ // see Neighbor::init() for details on lammps lists' logic
+ #endif
+ MYDBG(printf("# CUDA PairLJClass2CoulCutCuda::init_list end\n");)
}
void PairLJClass2CoulCutCuda::ev_setup(int eflag, int vflag)
{
- int maxeatomold=maxeatom;
- PairLJClass2CoulCut::ev_setup(eflag,vflag);
+ int maxeatomold=maxeatom;
+ PairLJClass2CoulCut::ev_setup(eflag,vflag);
- if (eflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
-
- if (vflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
-
-}
+ if (eflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
+ if (vflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
+}
diff --git a/src/USER-CUDA/pair_lj_class2_coul_cut_cuda.h b/src/USER-CUDA/pair_lj_class2_coul_cut_cuda.h
index e9edf9839bb1073ee874f78dacd85efa3e695c75..0baf24942ba3ffc3f0eb57bca287393223089a91 100644
--- a/src/USER-CUDA/pair_lj_class2_coul_cut_cuda.h
+++ b/src/USER-CUDA/pair_lj_class2_coul_cut_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -36,19 +36,19 @@ namespace LAMMPS_NS {
class PairLJClass2CoulCutCuda : public PairLJClass2CoulCut
{
- public:
- PairLJClass2CoulCutCuda(class LAMMPS *);
- void compute(int, int);
- void settings(int, char **);
- void coeff(int, char **);
- void init_list(int, class NeighList *);
- void init_style();
- void ev_setup(int eflag, int vflag);
- protected:
- class Cuda *cuda;
- void allocate();
- bool allocated2;
- class CudaNeighList* cuda_neigh_list;
+ public:
+ PairLJClass2CoulCutCuda(class LAMMPS *);
+ void compute(int, int);
+ void settings(int, char **);
+ void coeff(int, char **);
+ void init_list(int, class NeighList *);
+ void init_style();
+ void ev_setup(int eflag, int vflag);
+ protected:
+ class Cuda *cuda;
+ void allocate();
+ bool allocated2;
+ class CudaNeighList* cuda_neigh_list;
};
}
diff --git a/src/USER-CUDA/pair_lj_class2_coul_long_cuda.cpp b/src/USER-CUDA/pair_lj_class2_coul_long_cuda.cpp
index b0afe85554f178731966e2b017cf835efdb19d25..5de5787e08065fb38de7145b7abe64c12c3fbe0e 100644
--- a/src/USER-CUDA/pair_lj_class2_coul_long_cuda.cpp
+++ b/src/USER-CUDA/pair_lj_class2_coul_long_cuda.cpp
@@ -1,23 +1,23 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
Contributing author: Paul Crozier (SNL)
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -61,9 +61,9 @@ PairLJClass2CoulLongCuda::PairLJClass2CoulLongCuda(LAMMPS *lmp) : PairLJClass2Co
if(cuda == NULL)
error->all(FLERR,"You cannot use a /cuda class, without activating 'cuda' acceleration. Provide '-c on' as command-line argument to LAMMPS..");
- allocated2 = false;
- cuda->shared_data.pair.cudable_force = 1;
- cuda->setSystemParams();
+ allocated2 = false;
+ cuda->shared_data.pair.cudable_force = 1;
+ cuda->setSystemParams();
}
/* ----------------------------------------------------------------------
@@ -72,37 +72,37 @@ PairLJClass2CoulLongCuda::PairLJClass2CoulLongCuda(LAMMPS *lmp) : PairLJClass2Co
void PairLJClass2CoulLongCuda::allocate()
{
- if(! allocated) PairLJClass2CoulLong::allocate();
- if(! allocated2)
- {
- allocated2 = true;
- cuda->shared_data.pair.cut = cut_lj;
- cuda->shared_data.pair.coeff1 = lj1;
- cuda->shared_data.pair.coeff2 = lj2;
- cuda->shared_data.pair.coeff3 = lj3;
- cuda->shared_data.pair.coeff4 = lj4;
- cuda->shared_data.pair.offset = offset;
- cuda->shared_data.pair.special_lj = force->special_lj;
- cuda->shared_data.pair.special_coul = force->special_coul;
- }
+ if(! allocated) PairLJClass2CoulLong::allocate();
+ if(! allocated2)
+ {
+ allocated2 = true;
+ cuda->shared_data.pair.cut = cut_lj;
+ cuda->shared_data.pair.coeff1 = lj1;
+ cuda->shared_data.pair.coeff2 = lj2;
+ cuda->shared_data.pair.coeff3 = lj3;
+ cuda->shared_data.pair.coeff4 = lj4;
+ cuda->shared_data.pair.offset = offset;
+ cuda->shared_data.pair.special_lj = force->special_lj;
+ cuda->shared_data.pair.special_coul = force->special_coul;
+ }
}
/* ---------------------------------------------------------------------- */
void PairLJClass2CoulLongCuda::compute(int eflag, int vflag)
{
- if (eflag || vflag) ev_setup(eflag,vflag);
- if(eflag) cuda->cu_eng_vdwl->upload();
- if(eflag) cuda->cu_eng_coul->upload();
- if(vflag) cuda->cu_virial->upload();
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ if(eflag) cuda->cu_eng_vdwl->upload();
+ if(eflag) cuda->cu_eng_coul->upload();
+ if(vflag) cuda->cu_virial->upload();
- Cuda_PairLJClass2CoulLongCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);
+ Cuda_PairLJClass2CoulLongCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);
if(not cuda->shared_data.pair.collect_forces_later)
{
- if(eflag) cuda->cu_eng_vdwl->download();
- if(eflag) cuda->cu_eng_coul->download();
- if(vflag) cuda->cu_virial->download();
+ if(eflag) cuda->cu_eng_vdwl->download();
+ if(eflag) cuda->cu_eng_coul->download();
+ if(vflag) cuda->cu_virial->download();
}
}
@@ -110,16 +110,16 @@ void PairLJClass2CoulLongCuda::compute(int eflag, int vflag)
void PairLJClass2CoulLongCuda::settings(int narg, char **arg)
{
- PairLJClass2CoulLong::settings(narg, arg);
- cuda->shared_data.pair.cut_global = (F_FLOAT) cut_lj_global;
+ PairLJClass2CoulLong::settings(narg, arg);
+ cuda->shared_data.pair.cut_global = (F_FLOAT) cut_lj_global;
}
/* ---------------------------------------------------------------------- */
void PairLJClass2CoulLongCuda::coeff(int narg, char **arg)
{
- PairLJClass2CoulLong::coeff(narg, arg);
- allocate();
+ PairLJClass2CoulLong::coeff(narg, arg);
+ allocate();
}
void PairLJClass2CoulLongCuda::init_style()
@@ -129,9 +129,9 @@ void PairLJClass2CoulLongCuda::init_style()
// request regular or rRESPA neighbor lists
int irequest;
-
- irequest = neighbor->request(this);
+
+ irequest = neighbor->request(this);
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->cudable = 1;
@@ -147,31 +147,29 @@ void PairLJClass2CoulLongCuda::init_style()
g_ewald = force->kspace->g_ewald;
cuda->shared_data.pair.g_ewald=g_ewald;
cuda->shared_data.pppm.qqrd2e=force->qqrd2e;
-
+
if(ncoultablebits) error->warning(FLERR,"# CUDA: You asked for the usage of Coulomb Tables. This is not supported in CUDA Pair forces. Setting is ignored.\n");
}
void PairLJClass2CoulLongCuda::init_list(int id, NeighList *ptr)
{
- MYDBG(printf("# CUDA PairLJClass2CoulLongCuda::init_list\n");)
- PairLJClass2CoulLong::init_list(id, ptr);
- if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
- // see Neighbor::init() for details on lammps lists' logic
- MYDBG(printf("# CUDA PairLJClass2CoulLongCuda::init_list end\n");)
+ MYDBG(printf("# CUDA PairLJClass2CoulLongCuda::init_list\n");)
+ PairLJClass2CoulLong::init_list(id, ptr);
+ if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
+ // see Neighbor::init() for details on lammps lists' logic
+ MYDBG(printf("# CUDA PairLJClass2CoulLongCuda::init_list end\n");)
}
void PairLJClass2CoulLongCuda::ev_setup(int eflag, int vflag)
{
- int maxeatomold=maxeatom;
- PairLJClass2CoulLong::ev_setup(eflag,vflag);
+ int maxeatomold=maxeatom;
+ PairLJClass2CoulLong::ev_setup(eflag,vflag);
- if (eflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
-
- if (vflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
-
-}
+ if (eflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
+ if (vflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
+}
diff --git a/src/USER-CUDA/pair_lj_class2_coul_long_cuda.h b/src/USER-CUDA/pair_lj_class2_coul_long_cuda.h
index 6bf4a71e16b0104af33f834163fced22dff472c2..22ec5aa600215dcf851f765fdf72739f29dd269c 100644
--- a/src/USER-CUDA/pair_lj_class2_coul_long_cuda.h
+++ b/src/USER-CUDA/pair_lj_class2_coul_long_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -36,19 +36,19 @@ namespace LAMMPS_NS {
class PairLJClass2CoulLongCuda : public PairLJClass2CoulLong
{
- public:
- PairLJClass2CoulLongCuda(class LAMMPS *);
- void compute(int, int);
- void settings(int, char **);
- void coeff(int, char **);
- void init_list(int, class NeighList *);
- void init_style();
- void ev_setup(int eflag, int vflag);
- protected:
- class Cuda *cuda;
- void allocate();
- bool allocated2;
- class CudaNeighList* cuda_neigh_list;
+ public:
+ PairLJClass2CoulLongCuda(class LAMMPS *);
+ void compute(int, int);
+ void settings(int, char **);
+ void coeff(int, char **);
+ void init_list(int, class NeighList *);
+ void init_style();
+ void ev_setup(int eflag, int vflag);
+ protected:
+ class Cuda *cuda;
+ void allocate();
+ bool allocated2;
+ class CudaNeighList* cuda_neigh_list;
};
}
diff --git a/src/USER-CUDA/pair_lj_class2_cuda.cpp b/src/USER-CUDA/pair_lj_class2_cuda.cpp
index a218dc9cc805dc1463612f0597f7083f72499543..df0ba7a0de61476171485c87b1a3a063340752ed 100644
--- a/src/USER-CUDA/pair_lj_class2_cuda.cpp
+++ b/src/USER-CUDA/pair_lj_class2_cuda.cpp
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -28,7 +28,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -69,9 +69,9 @@ PairLJClass2Cuda::PairLJClass2Cuda(LAMMPS *lmp) : PairLJClass2(lmp)
if(cuda == NULL)
error->all(FLERR,"You cannot use a /cuda class, without activating 'cuda' acceleration. Provide '-c on' as command-line argument to LAMMPS..");
- allocated2 = false;
- cuda->shared_data.pair.cudable_force = 1;
- cuda->setSystemParams();
+ allocated2 = false;
+ cuda->shared_data.pair.cudable_force = 1;
+ cuda->setSystemParams();
}
/* ----------------------------------------------------------------------
@@ -80,63 +80,63 @@ PairLJClass2Cuda::PairLJClass2Cuda(LAMMPS *lmp) : PairLJClass2(lmp)
void PairLJClass2Cuda::allocate()
{
- if(! allocated) PairLJClass2::allocate();
- if(! allocated2)
- {
- allocated2 = true;
- cuda->shared_data.pair.cut = cut;
- cuda->shared_data.pair.coeff1 = lj1;
- cuda->shared_data.pair.coeff2 = lj2;
- cuda->shared_data.pair.coeff3 = lj3;
- cuda->shared_data.pair.coeff4 = lj4;
- cuda->shared_data.pair.offset = offset;
- cuda->shared_data.pair.special_lj = force->special_lj;
- cuda->shared_data.pair.special_coul = force->special_coul;
- }
+ if(! allocated) PairLJClass2::allocate();
+ if(! allocated2)
+ {
+ allocated2 = true;
+ cuda->shared_data.pair.cut = cut;
+ cuda->shared_data.pair.coeff1 = lj1;
+ cuda->shared_data.pair.coeff2 = lj2;
+ cuda->shared_data.pair.coeff3 = lj3;
+ cuda->shared_data.pair.coeff4 = lj4;
+ cuda->shared_data.pair.offset = offset;
+ cuda->shared_data.pair.special_lj = force->special_lj;
+ cuda->shared_data.pair.special_coul = force->special_coul;
+ }
}
/* ---------------------------------------------------------------------- */
void PairLJClass2Cuda::compute(int eflag, int vflag)
{
- if (eflag || vflag) ev_setup(eflag,vflag);
- if(eflag) cuda->cu_eng_vdwl->upload();
- if(vflag) cuda->cu_virial->upload();
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ if(eflag) cuda->cu_eng_vdwl->upload();
+ if(vflag) cuda->cu_virial->upload();
- Cuda_PairLJClass2Cuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);
+ Cuda_PairLJClass2Cuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);
if(not cuda->shared_data.pair.collect_forces_later)
{
- if(eflag) cuda->cu_eng_vdwl->download();
- if(vflag) cuda->cu_virial->download();
+ if(eflag) cuda->cu_eng_vdwl->download();
+ if(vflag) cuda->cu_virial->download();
}
-
+
}
/* ---------------------------------------------------------------------- */
void PairLJClass2Cuda::settings(int narg, char **arg)
{
- PairLJClass2::settings(narg, arg);
- cuda->shared_data.pair.cut_global = (F_FLOAT) cut_global;
+ PairLJClass2::settings(narg, arg);
+ cuda->shared_data.pair.cut_global = (F_FLOAT) cut_global;
}
/* ---------------------------------------------------------------------- */
void PairLJClass2Cuda::coeff(int narg, char **arg)
{
- PairLJClass2::coeff(narg, arg);
- allocate();
+ PairLJClass2::coeff(narg, arg);
+ allocate();
}
void PairLJClass2Cuda::init_style()
{
- MYDBG(printf("# CUDA PairLJClass2Cuda::init_style start\n"); )
+ MYDBG(printf("# CUDA PairLJClass2Cuda::init_style start\n"); )
// request regular or rRESPA neighbor lists
int irequest;
-
- irequest = neighbor->request(this);
+
+ irequest = neighbor->request(this);
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->cudable = 1;
@@ -146,24 +146,22 @@ void PairLJClass2Cuda::init_style()
void PairLJClass2Cuda::init_list(int id, NeighList *ptr)
{
- MYDBG(printf("# CUDA PairLJClass2Cuda::init_list\n");)
- PairLJClass2::init_list(id, ptr);
- if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
- // see Neighbor::init() for details on lammps lists' logic
- MYDBG(printf("# CUDA PairLJClass2Cuda::init_list end\n");)
+ MYDBG(printf("# CUDA PairLJClass2Cuda::init_list\n");)
+ PairLJClass2::init_list(id, ptr);
+ if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
+ // see Neighbor::init() for details on lammps lists' logic
+ MYDBG(printf("# CUDA PairLJClass2Cuda::init_list end\n");)
}
void PairLJClass2Cuda::ev_setup(int eflag, int vflag)
{
- int maxeatomold=maxeatom;
- PairLJClass2::ev_setup(eflag,vflag);
-
- if (eflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
+ int maxeatomold=maxeatom;
+ PairLJClass2::ev_setup(eflag,vflag);
- if (vflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
-
-}
+ if (eflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
+ if (vflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
+}
diff --git a/src/USER-CUDA/pair_lj_class2_cuda.h b/src/USER-CUDA/pair_lj_class2_cuda.h
index 8643ad94aa9a99c9882ea97da4d3d1170c429f72..789fd7dcf538f79fb3ba8449b833ce8e1f46d9eb 100644
--- a/src/USER-CUDA/pair_lj_class2_cuda.h
+++ b/src/USER-CUDA/pair_lj_class2_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -36,19 +36,19 @@ namespace LAMMPS_NS {
class PairLJClass2Cuda : public PairLJClass2
{
- public:
- PairLJClass2Cuda(class LAMMPS *);
- void compute(int, int);
- void settings(int, char **);
- void coeff(int, char **);
- void init_list(int, class NeighList *);
- void init_style();
- void ev_setup(int eflag, int vflag);
- protected:
- class Cuda *cuda;
- void allocate();
- bool allocated2;
- class CudaNeighList* cuda_neigh_list;
+ public:
+ PairLJClass2Cuda(class LAMMPS *);
+ void compute(int, int);
+ void settings(int, char **);
+ void coeff(int, char **);
+ void init_list(int, class NeighList *);
+ void init_style();
+ void ev_setup(int eflag, int vflag);
+ protected:
+ class Cuda *cuda;
+ void allocate();
+ bool allocated2;
+ class CudaNeighList* cuda_neigh_list;
};
}
diff --git a/src/USER-CUDA/pair_lj_cut_coul_cut_cuda.cpp b/src/USER-CUDA/pair_lj_cut_coul_cut_cuda.cpp
index ac80ff52146867871d7b48b7cb0d9a8f3ef73cb1..a702344f088acec8479d208028592294751bc14e 100644
--- a/src/USER-CUDA/pair_lj_cut_coul_cut_cuda.cpp
+++ b/src/USER-CUDA/pair_lj_cut_coul_cut_cuda.cpp
@@ -1,23 +1,23 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
Contributing author: Paul Crozier (SNL)
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -54,9 +54,9 @@ PairLJCutCoulCutCuda::PairLJCutCoulCutCuda(LAMMPS *lmp) : PairLJCutCoulCut(lmp)
if(cuda == NULL)
error->all(FLERR,"You cannot use a /cuda class, without activating 'cuda' acceleration. Provide '-c on' as command-line argument to LAMMPS..");
- allocated2 = false;
- cuda->shared_data.pair.cudable_force = 1;
- cuda->setSystemParams();
+ allocated2 = false;
+ cuda->shared_data.pair.cudable_force = 1;
+ cuda->setSystemParams();
}
/* ----------------------------------------------------------------------
@@ -65,38 +65,38 @@ PairLJCutCoulCutCuda::PairLJCutCoulCutCuda(LAMMPS *lmp) : PairLJCutCoulCut(lmp)
void PairLJCutCoulCutCuda::allocate()
{
- if(! allocated) PairLJCutCoulCut::allocate();
- if(! allocated2)
- {
- allocated2 = true;
- cuda->shared_data.pair.cut = cut_lj;
- cuda->shared_data.pair.cut_coul= cut_coul;
- cuda->shared_data.pair.coeff1 = lj1;
- cuda->shared_data.pair.coeff2 = lj2;
- cuda->shared_data.pair.coeff3 = lj3;
- cuda->shared_data.pair.coeff4 = lj4;
- cuda->shared_data.pair.offset = offset;
- cuda->shared_data.pair.special_lj = force->special_lj;
- cuda->shared_data.pair.special_coul = force->special_coul;
- }
+ if(! allocated) PairLJCutCoulCut::allocate();
+ if(! allocated2)
+ {
+ allocated2 = true;
+ cuda->shared_data.pair.cut = cut_lj;
+ cuda->shared_data.pair.cut_coul= cut_coul;
+ cuda->shared_data.pair.coeff1 = lj1;
+ cuda->shared_data.pair.coeff2 = lj2;
+ cuda->shared_data.pair.coeff3 = lj3;
+ cuda->shared_data.pair.coeff4 = lj4;
+ cuda->shared_data.pair.offset = offset;
+ cuda->shared_data.pair.special_lj = force->special_lj;
+ cuda->shared_data.pair.special_coul = force->special_coul;
+ }
}
/* ---------------------------------------------------------------------- */
void PairLJCutCoulCutCuda::compute(int eflag, int vflag)
{
- if (eflag || vflag) ev_setup(eflag,vflag);
- if(eflag) cuda->cu_eng_vdwl->upload();
- if(eflag) cuda->cu_eng_coul->upload();
- if(vflag) cuda->cu_virial->upload();
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ if(eflag) cuda->cu_eng_vdwl->upload();
+ if(eflag) cuda->cu_eng_coul->upload();
+ if(vflag) cuda->cu_virial->upload();
- Cuda_PairLJCutCoulCutCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);
+ Cuda_PairLJCutCoulCutCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);
if(not cuda->shared_data.pair.collect_forces_later)
{
- if(eflag) cuda->cu_eng_vdwl->download();
- if(eflag) cuda->cu_eng_coul->download();
- if(vflag) cuda->cu_virial->download();
+ if(eflag) cuda->cu_eng_vdwl->download();
+ if(eflag) cuda->cu_eng_coul->download();
+ if(vflag) cuda->cu_virial->download();
}
}
@@ -104,17 +104,17 @@ void PairLJCutCoulCutCuda::compute(int eflag, int vflag)
void PairLJCutCoulCutCuda::settings(int narg, char **arg)
{
- PairLJCutCoulCut::settings(narg, arg);
- cuda->shared_data.pair.cut_global = (F_FLOAT) cut_lj_global;
- cuda->shared_data.pair.cut_coul_global = (F_FLOAT) cut_coul_global;
+ PairLJCutCoulCut::settings(narg, arg);
+ cuda->shared_data.pair.cut_global = (F_FLOAT) cut_lj_global;
+ cuda->shared_data.pair.cut_coul_global = (F_FLOAT) cut_coul_global;
}
/* ---------------------------------------------------------------------- */
void PairLJCutCoulCutCuda::coeff(int narg, char **arg)
{
- PairLJCutCoulCut::coeff(narg, arg);
- allocate();
+ PairLJCutCoulCut::coeff(narg, arg);
+ allocate();
}
void PairLJCutCoulCutCuda::init_style()
@@ -124,41 +124,39 @@ void PairLJCutCoulCutCuda::init_style()
// request regular or rRESPA neighbor lists
int irequest;
-
-
+
+
irequest = neighbor->request(this);
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->cudable = 1;
-
+
cuda->shared_data.pppm.qqrd2e=force->qqrd2e;
-
+
}
void PairLJCutCoulCutCuda::init_list(int id, NeighList *ptr)
{
- MYDBG(printf("# CUDA PairLJCutCoulCutCuda::init_list\n");)
- PairLJCutCoulCut::init_list(id, ptr);
- #ifndef CUDA_USE_BINNING
- // right now we can only handle verlet (id 0), not respa
- if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
- // see Neighbor::init() for details on lammps lists' logic
- #endif
- MYDBG(printf("# CUDA PairLJCutCoulCutCuda::init_list end\n");)
+ MYDBG(printf("# CUDA PairLJCutCoulCutCuda::init_list\n");)
+ PairLJCutCoulCut::init_list(id, ptr);
+ #ifndef CUDA_USE_BINNING
+ // right now we can only handle verlet (id 0), not respa
+ if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
+ // see Neighbor::init() for details on lammps lists' logic
+ #endif
+ MYDBG(printf("# CUDA PairLJCutCoulCutCuda::init_list end\n");)
}
void PairLJCutCoulCutCuda::ev_setup(int eflag, int vflag)
{
- int maxeatomold=maxeatom;
- PairLJCutCoulCut::ev_setup(eflag,vflag);
+ int maxeatomold=maxeatom;
+ PairLJCutCoulCut::ev_setup(eflag,vflag);
- if (eflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
-
- if (vflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
-
-}
+ if (eflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
+ if (vflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
+}
diff --git a/src/USER-CUDA/pair_lj_cut_coul_cut_cuda.h b/src/USER-CUDA/pair_lj_cut_coul_cut_cuda.h
index 130140d6ce547a323625020994c12c8e30e0d7e6..23fe8344d66c9524c18e415ad41fada0b0fc04fe 100644
--- a/src/USER-CUDA/pair_lj_cut_coul_cut_cuda.h
+++ b/src/USER-CUDA/pair_lj_cut_coul_cut_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -36,19 +36,19 @@ namespace LAMMPS_NS {
class PairLJCutCoulCutCuda : public PairLJCutCoulCut
{
- public:
- PairLJCutCoulCutCuda(class LAMMPS *);
- void compute(int, int);
- void settings(int, char **);
- void coeff(int, char **);
- void init_list(int, class NeighList *);
- void init_style();
- void ev_setup(int eflag, int vflag);
- protected:
- class Cuda *cuda;
- void allocate();
- bool allocated2;
- class CudaNeighList* cuda_neigh_list;
+ public:
+ PairLJCutCoulCutCuda(class LAMMPS *);
+ void compute(int, int);
+ void settings(int, char **);
+ void coeff(int, char **);
+ void init_list(int, class NeighList *);
+ void init_style();
+ void ev_setup(int eflag, int vflag);
+ protected:
+ class Cuda *cuda;
+ void allocate();
+ bool allocated2;
+ class CudaNeighList* cuda_neigh_list;
};
}
diff --git a/src/USER-CUDA/pair_lj_cut_coul_debye_cuda.cpp b/src/USER-CUDA/pair_lj_cut_coul_debye_cuda.cpp
index bc9a6f33bab3b364c98de7552018b37327b4b9e4..0ed229fff4377b6f68c69aa4a69cd6f498216a77 100644
--- a/src/USER-CUDA/pair_lj_cut_coul_debye_cuda.cpp
+++ b/src/USER-CUDA/pair_lj_cut_coul_debye_cuda.cpp
@@ -1,23 +1,23 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
Contributing author: Paul Crozier (SNL)
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -54,9 +54,9 @@ PairLJCutCoulDebyeCuda::PairLJCutCoulDebyeCuda(LAMMPS *lmp) : PairLJCutCoulDebye
if(cuda == NULL)
error->all(FLERR,"You cannot use a /cuda class, without activating 'cuda' acceleration. Provide '-c on' as command-line argument to LAMMPS..");
- allocated2 = false;
- cuda->shared_data.pair.cudable_force = 1;
- cuda->setSystemParams();
+ allocated2 = false;
+ cuda->shared_data.pair.cudable_force = 1;
+ cuda->setSystemParams();
}
/* ----------------------------------------------------------------------
@@ -65,38 +65,38 @@ PairLJCutCoulDebyeCuda::PairLJCutCoulDebyeCuda(LAMMPS *lmp) : PairLJCutCoulDebye
void PairLJCutCoulDebyeCuda::allocate()
{
- if(! allocated) PairLJCutCoulDebye::allocate();
- if(! allocated2)
- {
- allocated2 = true;
- cuda->shared_data.pair.cut = cut_lj;
- cuda->shared_data.pair.cut_coul= cut_coul;
- cuda->shared_data.pair.coeff1 = lj1;
- cuda->shared_data.pair.coeff2 = lj2;
- cuda->shared_data.pair.coeff3 = lj3;
- cuda->shared_data.pair.coeff4 = lj4;
- cuda->shared_data.pair.offset = offset;
- cuda->shared_data.pair.special_lj = force->special_lj;
- cuda->shared_data.pair.special_coul = force->special_coul;
- }
+ if(! allocated) PairLJCutCoulDebye::allocate();
+ if(! allocated2)
+ {
+ allocated2 = true;
+ cuda->shared_data.pair.cut = cut_lj;
+ cuda->shared_data.pair.cut_coul= cut_coul;
+ cuda->shared_data.pair.coeff1 = lj1;
+ cuda->shared_data.pair.coeff2 = lj2;
+ cuda->shared_data.pair.coeff3 = lj3;
+ cuda->shared_data.pair.coeff4 = lj4;
+ cuda->shared_data.pair.offset = offset;
+ cuda->shared_data.pair.special_lj = force->special_lj;
+ cuda->shared_data.pair.special_coul = force->special_coul;
+ }
}
/* ---------------------------------------------------------------------- */
void PairLJCutCoulDebyeCuda::compute(int eflag, int vflag)
{
- if (eflag || vflag) ev_setup(eflag,vflag);
- if(eflag) cuda->cu_eng_vdwl->upload();
- if(eflag) cuda->cu_eng_coul->upload();
- if(vflag) cuda->cu_virial->upload();
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ if(eflag) cuda->cu_eng_vdwl->upload();
+ if(eflag) cuda->cu_eng_coul->upload();
+ if(vflag) cuda->cu_virial->upload();
- Cuda_PairLJCutCoulDebyeCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);
+ Cuda_PairLJCutCoulDebyeCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);
if(not cuda->shared_data.pair.collect_forces_later)
{
- if(eflag) cuda->cu_eng_vdwl->download();
- if(eflag) cuda->cu_eng_coul->download();
- if(vflag) cuda->cu_virial->download();
+ if(eflag) cuda->cu_eng_vdwl->download();
+ if(eflag) cuda->cu_eng_coul->download();
+ if(vflag) cuda->cu_virial->download();
}
}
@@ -104,18 +104,18 @@ void PairLJCutCoulDebyeCuda::compute(int eflag, int vflag)
void PairLJCutCoulDebyeCuda::settings(int narg, char **arg)
{
- PairLJCutCoulDebye::settings(narg, arg);
- cuda->shared_data.pair.cut_global = (F_FLOAT) cut_lj_global;
- cuda->shared_data.pair.cut_coul_global = (F_FLOAT) cut_coul_global;
- cuda->shared_data.pair.kappa = (F_FLOAT) kappa;
+ PairLJCutCoulDebye::settings(narg, arg);
+ cuda->shared_data.pair.cut_global = (F_FLOAT) cut_lj_global;
+ cuda->shared_data.pair.cut_coul_global = (F_FLOAT) cut_coul_global;
+ cuda->shared_data.pair.kappa = (F_FLOAT) kappa;
}
/* ---------------------------------------------------------------------- */
void PairLJCutCoulDebyeCuda::coeff(int narg, char **arg)
{
- PairLJCutCoulDebye::coeff(narg, arg);
- allocate();
+ PairLJCutCoulDebye::coeff(narg, arg);
+ allocate();
}
void PairLJCutCoulDebyeCuda::init_style()
@@ -125,41 +125,39 @@ void PairLJCutCoulDebyeCuda::init_style()
// request regular or rRESPA neighbor lists
int irequest;
-
-
+
+
irequest = neighbor->request(this);
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->cudable = 1;
-
+
cuda->shared_data.pppm.qqrd2e=force->qqrd2e;
-
+
}
void PairLJCutCoulDebyeCuda::init_list(int id, NeighList *ptr)
{
- MYDBG(printf("# CUDA PairLJCutCoulDebyeCuda::init_list\n");)
- PairLJCutCoulDebye::init_list(id, ptr);
- #ifndef CUDA_USE_BINNING
- // right now we can only handle verlet (id 0), not respa
- if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
- // see Neighbor::init() for details on lammps lists' logic
- #endif
- MYDBG(printf("# CUDA PairLJCutCoulDebyeCuda::init_list end\n");)
+ MYDBG(printf("# CUDA PairLJCutCoulDebyeCuda::init_list\n");)
+ PairLJCutCoulDebye::init_list(id, ptr);
+ #ifndef CUDA_USE_BINNING
+ // right now we can only handle verlet (id 0), not respa
+ if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
+ // see Neighbor::init() for details on lammps lists' logic
+ #endif
+ MYDBG(printf("# CUDA PairLJCutCoulDebyeCuda::init_list end\n");)
}
void PairLJCutCoulDebyeCuda::ev_setup(int eflag, int vflag)
{
- int maxeatomold=maxeatom;
- PairLJCutCoulDebye::ev_setup(eflag,vflag);
+ int maxeatomold=maxeatom;
+ PairLJCutCoulDebye::ev_setup(eflag,vflag);
- if (eflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
-
- if (vflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
-
-}
+ if (eflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
+ if (vflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
+}
diff --git a/src/USER-CUDA/pair_lj_cut_coul_debye_cuda.h b/src/USER-CUDA/pair_lj_cut_coul_debye_cuda.h
index 853c4281431e824119321235e848e8c9056a337c..0f3ff9b1c11bc66a9a169d8d7f9b85a4e1958141 100644
--- a/src/USER-CUDA/pair_lj_cut_coul_debye_cuda.h
+++ b/src/USER-CUDA/pair_lj_cut_coul_debye_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -36,19 +36,19 @@ namespace LAMMPS_NS {
class PairLJCutCoulDebyeCuda : public PairLJCutCoulDebye
{
- public:
- PairLJCutCoulDebyeCuda(class LAMMPS *);
- void compute(int, int);
- void settings(int, char **);
- void coeff(int, char **);
- void init_list(int, class NeighList *);
- void init_style();
- void ev_setup(int eflag, int vflag);
- protected:
- class Cuda *cuda;
- void allocate();
- bool allocated2;
- class CudaNeighList* cuda_neigh_list;
+ public:
+ PairLJCutCoulDebyeCuda(class LAMMPS *);
+ void compute(int, int);
+ void settings(int, char **);
+ void coeff(int, char **);
+ void init_list(int, class NeighList *);
+ void init_style();
+ void ev_setup(int eflag, int vflag);
+ protected:
+ class Cuda *cuda;
+ void allocate();
+ bool allocated2;
+ class CudaNeighList* cuda_neigh_list;
};
}
diff --git a/src/USER-CUDA/pair_lj_cut_coul_long_cuda.cpp b/src/USER-CUDA/pair_lj_cut_coul_long_cuda.cpp
index cf6081221788bc9e78f59098c10820703b6f8431..37825a66b9952c3e1a3d5f6448a7d00dfbeecc5e 100644
--- a/src/USER-CUDA/pair_lj_cut_coul_long_cuda.cpp
+++ b/src/USER-CUDA/pair_lj_cut_coul_long_cuda.cpp
@@ -1,23 +1,23 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
Contributing author: Paul Crozier (SNL)
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -61,9 +61,9 @@ PairLJCutCoulLongCuda::PairLJCutCoulLongCuda(LAMMPS *lmp) : PairLJCutCoulLong(lm
if(cuda == NULL)
error->all(FLERR,"You cannot use a /cuda class, without activating 'cuda' acceleration. Provide '-c on' as command-line argument to LAMMPS..");
- allocated2 = false;
- cuda->shared_data.pair.cudable_force = 1;
- cuda->setSystemParams();
+ allocated2 = false;
+ cuda->shared_data.pair.cudable_force = 1;
+ cuda->setSystemParams();
}
/* ----------------------------------------------------------------------
@@ -72,37 +72,37 @@ PairLJCutCoulLongCuda::PairLJCutCoulLongCuda(LAMMPS *lmp) : PairLJCutCoulLong(lm
void PairLJCutCoulLongCuda::allocate()
{
- if(! allocated) PairLJCutCoulLong::allocate();
- if(! allocated2)
- {
- allocated2 = true;
- cuda->shared_data.pair.cut = cut_lj;
- cuda->shared_data.pair.coeff1 = lj1;
- cuda->shared_data.pair.coeff2 = lj2;
- cuda->shared_data.pair.coeff3 = lj3;
- cuda->shared_data.pair.coeff4 = lj4;
- cuda->shared_data.pair.offset = offset;
- cuda->shared_data.pair.special_lj = force->special_lj;
- cuda->shared_data.pair.special_coul = force->special_coul;
- }
+ if(! allocated) PairLJCutCoulLong::allocate();
+ if(! allocated2)
+ {
+ allocated2 = true;
+ cuda->shared_data.pair.cut = cut_lj;
+ cuda->shared_data.pair.coeff1 = lj1;
+ cuda->shared_data.pair.coeff2 = lj2;
+ cuda->shared_data.pair.coeff3 = lj3;
+ cuda->shared_data.pair.coeff4 = lj4;
+ cuda->shared_data.pair.offset = offset;
+ cuda->shared_data.pair.special_lj = force->special_lj;
+ cuda->shared_data.pair.special_coul = force->special_coul;
+ }
}
/* ---------------------------------------------------------------------- */
void PairLJCutCoulLongCuda::compute(int eflag, int vflag)
{
- if (eflag || vflag) ev_setup(eflag,vflag);
- if(eflag) cuda->cu_eng_vdwl->upload();
- if(eflag) cuda->cu_eng_coul->upload();
- if(vflag) cuda->cu_virial->upload();
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ if(eflag) cuda->cu_eng_vdwl->upload();
+ if(eflag) cuda->cu_eng_coul->upload();
+ if(vflag) cuda->cu_virial->upload();
- Cuda_PairLJCutCoulLongCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);
+ Cuda_PairLJCutCoulLongCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);
if(not cuda->shared_data.pair.collect_forces_later)
{
- if(eflag) cuda->cu_eng_vdwl->download();
- if(eflag) cuda->cu_eng_coul->download();
- if(vflag) cuda->cu_virial->download();
+ if(eflag) cuda->cu_eng_vdwl->download();
+ if(eflag) cuda->cu_eng_coul->download();
+ if(vflag) cuda->cu_virial->download();
}
}
@@ -110,16 +110,16 @@ void PairLJCutCoulLongCuda::compute(int eflag, int vflag)
void PairLJCutCoulLongCuda::settings(int narg, char **arg)
{
- PairLJCutCoulLong::settings(narg, arg);
- cuda->shared_data.pair.cut_global = (F_FLOAT) cut_lj_global;
+ PairLJCutCoulLong::settings(narg, arg);
+ cuda->shared_data.pair.cut_global = (F_FLOAT) cut_lj_global;
}
/* ---------------------------------------------------------------------- */
void PairLJCutCoulLongCuda::coeff(int narg, char **arg)
{
- PairLJCutCoulLong::coeff(narg, arg);
- allocate();
+ PairLJCutCoulLong::coeff(narg, arg);
+ allocate();
}
void PairLJCutCoulLongCuda::init_style()
@@ -129,7 +129,7 @@ void PairLJCutCoulLongCuda::init_style()
// request regular or rRESPA neighbor lists
int irequest;
-
+
if (update->whichflag == 0 && strstr(update->integrate_style,"respa")) {
int respa = 0;
if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
@@ -160,10 +160,10 @@ void PairLJCutCoulLongCuda::init_style()
neighbor->requests[irequest]->respaouter = 1;
}
- }
- else
+ }
+ else
{
- irequest = neighbor->request(this);
+ irequest = neighbor->request(this);
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->cudable = 1;
@@ -185,34 +185,32 @@ void PairLJCutCoulLongCuda::init_style()
g_ewald = force->kspace->g_ewald;
cuda->shared_data.pair.g_ewald=g_ewald;
cuda->shared_data.pppm.qqrd2e=force->qqrd2e;
-
+
if(ncoultablebits) error->warning(FLERR,"# CUDA: You asked for the usage of Coulomb Tables. This is not supported in CUDA Pair forces. Setting is ignored.\n");
}
void PairLJCutCoulLongCuda::init_list(int id, NeighList *ptr)
{
- MYDBG(printf("# CUDA PairLJCutCoulLongCuda::init_list\n");)
- PairLJCutCoulLong::init_list(id, ptr);
- #ifndef CUDA_USE_BINNING
- // right now we can only handle verlet (id 0), not respa
- if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
- // see Neighbor::init() for details on lammps lists' logic
- #endif
- MYDBG(printf("# CUDA PairLJCutCoulLongCuda::init_list end\n");)
+ MYDBG(printf("# CUDA PairLJCutCoulLongCuda::init_list\n");)
+ PairLJCutCoulLong::init_list(id, ptr);
+ #ifndef CUDA_USE_BINNING
+ // right now we can only handle verlet (id 0), not respa
+ if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
+ // see Neighbor::init() for details on lammps lists' logic
+ #endif
+ MYDBG(printf("# CUDA PairLJCutCoulLongCuda::init_list end\n");)
}
void PairLJCutCoulLongCuda::ev_setup(int eflag, int vflag)
{
- int maxeatomold=maxeatom;
- PairLJCutCoulLong::ev_setup(eflag,vflag);
+ int maxeatomold=maxeatom;
+ PairLJCutCoulLong::ev_setup(eflag,vflag);
- if (eflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
-
- if (vflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
-
-}
+ if (eflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
+ if (vflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
+}
diff --git a/src/USER-CUDA/pair_lj_cut_coul_long_cuda.h b/src/USER-CUDA/pair_lj_cut_coul_long_cuda.h
index 2f14357408f5c4262c2493b3c388bb1f0727fe3e..ca1d5fed947e70560090bcf00e6cb762cac178c4 100644
--- a/src/USER-CUDA/pair_lj_cut_coul_long_cuda.h
+++ b/src/USER-CUDA/pair_lj_cut_coul_long_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -36,19 +36,19 @@ namespace LAMMPS_NS {
class PairLJCutCoulLongCuda : public PairLJCutCoulLong
{
- public:
- PairLJCutCoulLongCuda(class LAMMPS *);
- void compute(int, int);
- void settings(int, char **);
- void coeff(int, char **);
- void init_list(int, class NeighList *);
- void init_style();
- void ev_setup(int eflag, int vflag);
- protected:
- class Cuda *cuda;
- void allocate();
- bool allocated2;
- class CudaNeighList* cuda_neigh_list;
+ public:
+ PairLJCutCoulLongCuda(class LAMMPS *);
+ void compute(int, int);
+ void settings(int, char **);
+ void coeff(int, char **);
+ void init_list(int, class NeighList *);
+ void init_style();
+ void ev_setup(int eflag, int vflag);
+ protected:
+ class Cuda *cuda;
+ void allocate();
+ bool allocated2;
+ class CudaNeighList* cuda_neigh_list;
};
}
diff --git a/src/USER-CUDA/pair_lj_cut_cuda.cpp b/src/USER-CUDA/pair_lj_cut_cuda.cpp
index c865f2136177e797036ed80b59942bc9277ee22b..7f35db0918a4154fb63edd80a0411e880e8a2981 100644
--- a/src/USER-CUDA/pair_lj_cut_cuda.cpp
+++ b/src/USER-CUDA/pair_lj_cut_cuda.cpp
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -28,7 +28,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -69,9 +69,9 @@ PairLJCutCuda::PairLJCutCuda(LAMMPS *lmp) : PairLJCut(lmp)
if(cuda == NULL)
error->all(FLERR,"You cannot use a /cuda class, without activating 'cuda' acceleration. Provide '-c on' as command-line argument to LAMMPS..");
- allocated2 = false;
- cuda->shared_data.pair.cudable_force = 1;
- cuda->setSystemParams();
+ allocated2 = false;
+ cuda->shared_data.pair.cudable_force = 1;
+ cuda->setSystemParams();
}
/* ----------------------------------------------------------------------
@@ -80,68 +80,68 @@ PairLJCutCuda::PairLJCutCuda(LAMMPS *lmp) : PairLJCut(lmp)
void PairLJCutCuda::allocate()
{
- if(! allocated) PairLJCut::allocate();
- if(! allocated2)
- {
- allocated2 = true;
- cuda->shared_data.pair.cut = cut;
- cuda->shared_data.pair.coeff1 = lj1;
- cuda->shared_data.pair.coeff2 = lj2;
- cuda->shared_data.pair.coeff3 = lj3;
- cuda->shared_data.pair.coeff4 = lj4;
- cuda->shared_data.pair.offset = offset;
- cuda->shared_data.pair.special_lj = force->special_lj;
- cuda->shared_data.pair.special_coul = force->special_coul;
- }
+ if(! allocated) PairLJCut::allocate();
+ if(! allocated2)
+ {
+ allocated2 = true;
+ cuda->shared_data.pair.cut = cut;
+ cuda->shared_data.pair.coeff1 = lj1;
+ cuda->shared_data.pair.coeff2 = lj2;
+ cuda->shared_data.pair.coeff3 = lj3;
+ cuda->shared_data.pair.coeff4 = lj4;
+ cuda->shared_data.pair.offset = offset;
+ cuda->shared_data.pair.special_lj = force->special_lj;
+ cuda->shared_data.pair.special_coul = force->special_coul;
+ }
}
/* ---------------------------------------------------------------------- */
void PairLJCutCuda::compute(int eflag, int vflag)
{
- if (eflag || vflag) ev_setup(eflag,vflag);
- if(eflag) cuda->cu_eng_vdwl->upload();
- if(vflag) cuda->cu_virial->upload();
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ if(eflag) cuda->cu_eng_vdwl->upload();
+ if(vflag) cuda->cu_virial->upload();
- Cuda_PairLJCutCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);
+ Cuda_PairLJCutCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);
if(not cuda->shared_data.pair.collect_forces_later)
{
- if(eflag) cuda->cu_eng_vdwl->download();
- if(vflag) cuda->cu_virial->download();
+ if(eflag) cuda->cu_eng_vdwl->download();
+ if(vflag) cuda->cu_virial->download();
}
-
+
}
/* ---------------------------------------------------------------------- */
void PairLJCutCuda::settings(int narg, char **arg)
{
- PairLJCut::settings(narg, arg);
- cuda->shared_data.pair.cut_global = (F_FLOAT) cut_global;
+ PairLJCut::settings(narg, arg);
+ cuda->shared_data.pair.cut_global = (F_FLOAT) cut_global;
}
/* ---------------------------------------------------------------------- */
void PairLJCutCuda::coeff(int narg, char **arg)
{
- PairLJCut::coeff(narg, arg);
- allocate();
+ PairLJCut::coeff(narg, arg);
+ allocate();
}
void PairLJCutCuda::init_style()
{
- MYDBG(printf("# CUDA PairLJCutCuda::init_style start\n"); )
+ MYDBG(printf("# CUDA PairLJCutCuda::init_style start\n"); )
// request regular or rRESPA neighbor lists
int irequest;
-
+
if (update->whichflag == 0 && strstr(update->integrate_style,"respa")) {
- }
- else
+ }
+ else
{
- irequest = neighbor->request(this);
+ irequest = neighbor->request(this);
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->cudable = 1;
@@ -155,27 +155,25 @@ void PairLJCutCuda::init_style()
void PairLJCutCuda::init_list(int id, NeighList *ptr)
{
- MYDBG(printf("# CUDA PairLJCutCuda::init_list\n");)
- PairLJCut::init_list(id, ptr);
- #ifndef CUDA_USE_BINNING
- // right now we can only handle verlet (id 0), not respa
- if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
- // see Neighbor::init() for details on lammps lists' logic
- #endif
- MYDBG(printf("# CUDA PairLJCutCuda::init_list end\n");)
+ MYDBG(printf("# CUDA PairLJCutCuda::init_list\n");)
+ PairLJCut::init_list(id, ptr);
+ #ifndef CUDA_USE_BINNING
+ // right now we can only handle verlet (id 0), not respa
+ if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
+ // see Neighbor::init() for details on lammps lists' logic
+ #endif
+ MYDBG(printf("# CUDA PairLJCutCuda::init_list end\n");)
}
void PairLJCutCuda::ev_setup(int eflag, int vflag)
{
- int maxeatomold=maxeatom;
- PairLJCut::ev_setup(eflag,vflag);
-
- if (eflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
+ int maxeatomold=maxeatom;
+ PairLJCut::ev_setup(eflag,vflag);
- if (vflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
-
-}
+ if (eflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
+ if (vflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
+}
diff --git a/src/USER-CUDA/pair_lj_cut_cuda.h b/src/USER-CUDA/pair_lj_cut_cuda.h
index f81d47952d5a3ef1fe295be3d3353ff3e319808d..602a1e3d13f57f7bae47d17ec01209474d25f8d6 100644
--- a/src/USER-CUDA/pair_lj_cut_cuda.h
+++ b/src/USER-CUDA/pair_lj_cut_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -36,19 +36,19 @@ namespace LAMMPS_NS {
class PairLJCutCuda : public PairLJCut
{
- public:
- PairLJCutCuda(class LAMMPS *);
- void compute(int, int);
- void settings(int, char **);
- void coeff(int, char **);
- void init_list(int, class NeighList *);
- void init_style();
- void ev_setup(int eflag, int vflag);
- protected:
- class Cuda *cuda;
- void allocate();
- bool allocated2;
- class CudaNeighList* cuda_neigh_list;
+ public:
+ PairLJCutCuda(class LAMMPS *);
+ void compute(int, int);
+ void settings(int, char **);
+ void coeff(int, char **);
+ void init_list(int, class NeighList *);
+ void init_style();
+ void ev_setup(int eflag, int vflag);
+ protected:
+ class Cuda *cuda;
+ void allocate();
+ bool allocated2;
+ class CudaNeighList* cuda_neigh_list;
};
}
diff --git a/src/USER-CUDA/pair_lj_cut_experimental_cuda.cpp b/src/USER-CUDA/pair_lj_cut_experimental_cuda.cpp
index 50dfaa5fa9a3742b5b03160c7e397b3394b15c4e..ffc9533b45d6ef16e387f18084aabafb41174584 100644
--- a/src/USER-CUDA/pair_lj_cut_experimental_cuda.cpp
+++ b/src/USER-CUDA/pair_lj_cut_experimental_cuda.cpp
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -28,7 +28,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -69,9 +69,9 @@ PairLJCutExperimentalCuda::PairLJCutExperimentalCuda(LAMMPS *lmp) : PairLJCut(lm
if(cuda == NULL)
error->all(FLERR,"You cannot use a /cuda class, without activating 'cuda' acceleration. Provide '-c on' as command-line argument to LAMMPS..");
- allocated2 = false;
- cuda->shared_data.pair.cudable_force = 1;
- cuda->setSystemParams();
+ allocated2 = false;
+ cuda->shared_data.pair.cudable_force = 1;
+ cuda->setSystemParams();
}
/* ----------------------------------------------------------------------
@@ -80,35 +80,35 @@ PairLJCutExperimentalCuda::PairLJCutExperimentalCuda(LAMMPS *lmp) : PairLJCut(lm
void PairLJCutExperimentalCuda::allocate()
{
- if(! allocated) PairLJCut::allocate();
- if(! allocated2)
- {
- allocated2 = true;
- cuda->shared_data.pair.cut = cut;
- cuda->shared_data.pair.coeff1 = lj1;
- cuda->shared_data.pair.coeff2 = lj2;
- cuda->shared_data.pair.coeff3 = lj3;
- cuda->shared_data.pair.coeff4 = lj4;
- cuda->shared_data.pair.offset = offset;
- cuda->shared_data.pair.special_lj = force->special_lj;
- cuda->shared_data.pair.special_coul = force->special_coul;
- }
+ if(! allocated) PairLJCut::allocate();
+ if(! allocated2)
+ {
+ allocated2 = true;
+ cuda->shared_data.pair.cut = cut;
+ cuda->shared_data.pair.coeff1 = lj1;
+ cuda->shared_data.pair.coeff2 = lj2;
+ cuda->shared_data.pair.coeff3 = lj3;
+ cuda->shared_data.pair.coeff4 = lj4;
+ cuda->shared_data.pair.offset = offset;
+ cuda->shared_data.pair.special_lj = force->special_lj;
+ cuda->shared_data.pair.special_coul = force->special_coul;
+ }
}
/* ---------------------------------------------------------------------- */
void PairLJCutExperimentalCuda::compute(int eflag, int vflag)
{
- if (eflag || vflag) ev_setup(eflag,vflag);
- if(eflag) cuda->cu_eng_vdwl->upload();
- if(vflag) cuda->cu_virial->upload();
- Cuda_PairLJCutExperimentalCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ if(eflag) cuda->cu_eng_vdwl->upload();
+ if(vflag) cuda->cu_virial->upload();
+ Cuda_PairLJCutExperimentalCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);
if(not cuda->shared_data.pair.collect_forces_later)
{
- CudaWrapper_Sync();
- if(eflag) cuda->cu_eng_vdwl->download();
- if(vflag) cuda->cu_virial->download();
+ CudaWrapper_Sync();
+ if(eflag) cuda->cu_eng_vdwl->download();
+ if(vflag) cuda->cu_virial->download();
}
}
@@ -116,31 +116,31 @@ void PairLJCutExperimentalCuda::compute(int eflag, int vflag)
void PairLJCutExperimentalCuda::settings(int narg, char **arg)
{
- PairLJCut::settings(narg, arg);
- cuda->shared_data.pair.cut_global = (F_FLOAT) cut_global;
+ PairLJCut::settings(narg, arg);
+ cuda->shared_data.pair.cut_global = (F_FLOAT) cut_global;
}
/* ---------------------------------------------------------------------- */
void PairLJCutExperimentalCuda::coeff(int narg, char **arg)
{
- PairLJCut::coeff(narg, arg);
- allocate();
+ PairLJCut::coeff(narg, arg);
+ allocate();
}
void PairLJCutExperimentalCuda::init_style()
{
- MYDBG(printf("# CUDA PairLJCutExperimentalCuda::init_style start\n"); )
+ MYDBG(printf("# CUDA PairLJCutExperimentalCuda::init_style start\n"); )
// request regular or rRESPA neighbor lists
int irequest;
-
+
if (update->whichflag == 0 && strstr(update->integrate_style,"respa")) {
- }
- else
+ }
+ else
{
- irequest = neighbor->request(this);
+ irequest = neighbor->request(this);
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->cudable = 1;
@@ -154,27 +154,25 @@ void PairLJCutExperimentalCuda::init_style()
void PairLJCutExperimentalCuda::init_list(int id, NeighList *ptr)
{
- MYDBG(printf("# CUDA PairLJCutExperimentalCuda::init_list\n");)
- PairLJCut::init_list(id, ptr);
- #ifndef CUDA_USE_BINNING
- // right now we can only handle verlet (id 0), not respa
- if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
- // see Neighbor::init() for details on lammps lists' logic
- #endif
- MYDBG(printf("# CUDA PairLJCutExperimentalCuda::init_list end\n");)
+ MYDBG(printf("# CUDA PairLJCutExperimentalCuda::init_list\n");)
+ PairLJCut::init_list(id, ptr);
+ #ifndef CUDA_USE_BINNING
+ // right now we can only handle verlet (id 0), not respa
+ if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
+ // see Neighbor::init() for details on lammps lists' logic
+ #endif
+ MYDBG(printf("# CUDA PairLJCutExperimentalCuda::init_list end\n");)
}
void PairLJCutExperimentalCuda::ev_setup(int eflag, int vflag)
{
- int maxeatomold=maxeatom;
- PairLJCut::ev_setup(eflag,vflag);
-
- if (eflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
+ int maxeatomold=maxeatom;
+ PairLJCut::ev_setup(eflag,vflag);
- if (vflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
-
-}
+ if (eflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
+ if (vflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
+}
diff --git a/src/USER-CUDA/pair_lj_cut_experimental_cuda.h b/src/USER-CUDA/pair_lj_cut_experimental_cuda.h
index 9deb686524e56ec3751a4c97bbe9b16b81f0b6f7..25cf38624c4f8a071954d857b03743fb8ac1d665 100644
--- a/src/USER-CUDA/pair_lj_cut_experimental_cuda.h
+++ b/src/USER-CUDA/pair_lj_cut_experimental_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -36,19 +36,19 @@ namespace LAMMPS_NS {
class PairLJCutExperimentalCuda : public PairLJCut
{
- public:
- PairLJCutExperimentalCuda(class LAMMPS *);
- void compute(int, int);
- void settings(int, char **);
- void coeff(int, char **);
- void init_list(int, class NeighList *);
- void init_style();
- void ev_setup(int eflag, int vflag);
- protected:
- class Cuda *cuda;
- void allocate();
- bool allocated2;
- class CudaNeighList* cuda_neigh_list;
+ public:
+ PairLJCutExperimentalCuda(class LAMMPS *);
+ void compute(int, int);
+ void settings(int, char **);
+ void coeff(int, char **);
+ void init_list(int, class NeighList *);
+ void init_style();
+ void ev_setup(int eflag, int vflag);
+ protected:
+ class Cuda *cuda;
+ void allocate();
+ bool allocated2;
+ class CudaNeighList* cuda_neigh_list;
};
}
diff --git a/src/USER-CUDA/pair_lj_expand_cuda.cpp b/src/USER-CUDA/pair_lj_expand_cuda.cpp
index 79f5f77c80a9689b15eb08b4ed11ba9d5c2fa2aa..4420fb7c5808133753ea0dd087d5268190ab6f35 100644
--- a/src/USER-CUDA/pair_lj_expand_cuda.cpp
+++ b/src/USER-CUDA/pair_lj_expand_cuda.cpp
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -28,7 +28,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -69,9 +69,9 @@ PairLJExpandCuda::PairLJExpandCuda(LAMMPS *lmp) : PairLJExpand(lmp)
if(cuda == NULL)
error->all(FLERR,"You cannot use a /cuda class, without activating 'cuda' acceleration. Provide '-c on' as command-line argument to LAMMPS..");
- allocated2 = false;
- cuda->shared_data.pair.cudable_force = 1;
- cuda->setSystemParams();
+ allocated2 = false;
+ cuda->shared_data.pair.cudable_force = 1;
+ cuda->setSystemParams();
}
/* ----------------------------------------------------------------------
@@ -80,70 +80,70 @@ PairLJExpandCuda::PairLJExpandCuda(LAMMPS *lmp) : PairLJExpand(lmp)
void PairLJExpandCuda::allocate()
{
- if(! allocated) PairLJExpand::allocate();
- if(! allocated2)
- {
- allocated2 = true;
- cuda->shared_data.pair.cut = cut;
- cuda->shared_data.pair.cutsq = cutsq;
- cuda->shared_data.pair.coeff1 = lj1;
- cuda->shared_data.pair.coeff2 = lj2;
- cuda->shared_data.pair.coeff3 = lj3;
- cuda->shared_data.pair.coeff4 = lj4;
- cuda->shared_data.pair.coeff5 = shift;
- cuda->shared_data.pair.offset = offset;
- cuda->shared_data.pair.special_lj = force->special_lj;
- cuda->shared_data.pair.special_coul = force->special_coul;
- }
+ if(! allocated) PairLJExpand::allocate();
+ if(! allocated2)
+ {
+ allocated2 = true;
+ cuda->shared_data.pair.cut = cut;
+ cuda->shared_data.pair.cutsq = cutsq;
+ cuda->shared_data.pair.coeff1 = lj1;
+ cuda->shared_data.pair.coeff2 = lj2;
+ cuda->shared_data.pair.coeff3 = lj3;
+ cuda->shared_data.pair.coeff4 = lj4;
+ cuda->shared_data.pair.coeff5 = shift;
+ cuda->shared_data.pair.offset = offset;
+ cuda->shared_data.pair.special_lj = force->special_lj;
+ cuda->shared_data.pair.special_coul = force->special_coul;
+ }
}
/* ---------------------------------------------------------------------- */
void PairLJExpandCuda::compute(int eflag, int vflag)
{
- if (eflag || vflag) ev_setup(eflag,vflag);
- if(eflag) cuda->cu_eng_vdwl->upload();
- if(vflag) cuda->cu_virial->upload();
-
- Cuda_PairLJExpandCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);
-
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ if(eflag) cuda->cu_eng_vdwl->upload();
+ if(vflag) cuda->cu_virial->upload();
+
+ Cuda_PairLJExpandCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);
+
if(not cuda->shared_data.pair.collect_forces_later)
{
- if(eflag) cuda->cu_eng_vdwl->download();
- if(vflag) cuda->cu_virial->download();
+ if(eflag) cuda->cu_eng_vdwl->download();
+ if(vflag) cuda->cu_virial->download();
}
-
+
}
/* ---------------------------------------------------------------------- */
void PairLJExpandCuda::settings(int narg, char **arg)
{
- PairLJExpand::settings(narg, arg);
- cuda->shared_data.pair.cut_global = (F_FLOAT) cut_global;
+ PairLJExpand::settings(narg, arg);
+ cuda->shared_data.pair.cut_global = (F_FLOAT) cut_global;
}
/* ---------------------------------------------------------------------- */
void PairLJExpandCuda::coeff(int narg, char **arg)
{
- PairLJExpand::coeff(narg, arg);
- allocate();
+ PairLJExpand::coeff(narg, arg);
+ allocate();
}
void PairLJExpandCuda::init_style()
{
- MYDBG(printf("# CUDA PairLJExpandCuda::init_style start\n"); )
+ MYDBG(printf("# CUDA PairLJExpandCuda::init_style start\n"); )
// request regular or rRESPA neighbor lists
int irequest;
-
+
if (update->whichflag == 0 && strstr(update->integrate_style,"respa")) {
- }
- else
+ }
+ else
{
- irequest = neighbor->request(this);
+ irequest = neighbor->request(this);
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->cudable = 1;
@@ -156,27 +156,25 @@ void PairLJExpandCuda::init_style()
void PairLJExpandCuda::init_list(int id, NeighList *ptr)
{
- MYDBG(printf("# CUDA PairLJExpandCuda::init_list\n");)
- PairLJExpand::init_list(id, ptr);
- #ifndef CUDA_USE_BINNING
- // right now we can only handle verlet (id 0), not respa
- if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
- // see Neighbor::init() for details on lammps lists' logic
- #endif
- MYDBG(printf("# CUDA PairLJExpandCuda::init_list end\n");)
+ MYDBG(printf("# CUDA PairLJExpandCuda::init_list\n");)
+ PairLJExpand::init_list(id, ptr);
+ #ifndef CUDA_USE_BINNING
+ // right now we can only handle verlet (id 0), not respa
+ if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
+ // see Neighbor::init() for details on lammps lists' logic
+ #endif
+ MYDBG(printf("# CUDA PairLJExpandCuda::init_list end\n");)
}
void PairLJExpandCuda::ev_setup(int eflag, int vflag)
{
- int maxeatomold=maxeatom;
- PairLJExpand::ev_setup(eflag,vflag);
+ int maxeatomold=maxeatom;
+ PairLJExpand::ev_setup(eflag,vflag);
- if (eflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
-
- if (vflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
-
-}
+ if (eflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
+ if (vflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
+}
diff --git a/src/USER-CUDA/pair_lj_expand_cuda.h b/src/USER-CUDA/pair_lj_expand_cuda.h
index 67d1030edbc6997d12a6abfe51ba0784696a020a..4cc905a578ee8b324bfd2f30b81ab54683982fec 100644
--- a/src/USER-CUDA/pair_lj_expand_cuda.h
+++ b/src/USER-CUDA/pair_lj_expand_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -36,19 +36,19 @@ namespace LAMMPS_NS {
class PairLJExpandCuda : public PairLJExpand
{
- public:
- PairLJExpandCuda(class LAMMPS *);
- void compute(int, int);
- void settings(int, char **);
- void coeff(int, char **);
- void init_list(int, class NeighList *);
- void init_style();
- void ev_setup(int eflag, int vflag);
- protected:
- class Cuda *cuda;
- void allocate();
- bool allocated2;
- class CudaNeighList* cuda_neigh_list;
+ public:
+ PairLJExpandCuda(class LAMMPS *);
+ void compute(int, int);
+ void settings(int, char **);
+ void coeff(int, char **);
+ void init_list(int, class NeighList *);
+ void init_style();
+ void ev_setup(int eflag, int vflag);
+ protected:
+ class Cuda *cuda;
+ void allocate();
+ bool allocated2;
+ class CudaNeighList* cuda_neigh_list;
};
}
diff --git a/src/USER-CUDA/pair_lj_gromacs_coul_gromacs_cuda.cpp b/src/USER-CUDA/pair_lj_gromacs_coul_gromacs_cuda.cpp
index 862d180e96a727b9aeb24d84fa00736f8d2ef0ab..44ead2c2fc350eb1a2582bd07db8d6d32ec95752 100644
--- a/src/USER-CUDA/pair_lj_gromacs_coul_gromacs_cuda.cpp
+++ b/src/USER-CUDA/pair_lj_gromacs_coul_gromacs_cuda.cpp
@@ -1,23 +1,23 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
Contributing author: Paul Crozier (SNL)
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -54,10 +54,10 @@ PairLJGromacsCoulGromacsCuda::PairLJGromacsCoulGromacsCuda(LAMMPS *lmp) : PairLJ
if(cuda == NULL)
error->all(FLERR,"You cannot use a /cuda class, without activating 'cuda' acceleration. Provide '-c on' as command-line argument to LAMMPS..");
- allocated2 = false;
- cuda->shared_data.pair.cudable_force = 1;
- cuda->shared_data.pair.use_block_per_atom = 0;
- cuda->setSystemParams();
+ allocated2 = false;
+ cuda->shared_data.pair.cudable_force = 1;
+ cuda->shared_data.pair.use_block_per_atom = 0;
+ cuda->setSystemParams();
}
/* ----------------------------------------------------------------------
@@ -66,72 +66,72 @@ PairLJGromacsCoulGromacsCuda::PairLJGromacsCoulGromacsCuda(LAMMPS *lmp) : PairLJ
void PairLJGromacsCoulGromacsCuda::allocate()
{
- if(! allocated) PairLJGromacsCoulGromacs::allocate();
- if(! allocated2)
- {
- cuda->accelerator(0,NULL);
- allocated2 = true;
- cuda->shared_data.pair.coeff1 = lj1;
- cuda->shared_data.pair.coeff2 = lj2;
- cuda->shared_data.pair.coeff3 = lj3;
- cuda->shared_data.pair.coeff4 = lj4;
- cuda->shared_data.pair.coeff5 = ljsw1;
- cuda->shared_data.pair.coeff6 = ljsw2;
- cuda->shared_data.pair.coeff7 = ljsw3;
- cuda->shared_data.pair.coeff8 = ljsw4;
- cuda->shared_data.pair.coeff9 = ljsw5;
- cuda->shared_data.pair.special_lj = force->special_lj;
- cuda->shared_data.pair.special_coul = force->special_coul;
- cu_lj1_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj1, &cuda->shared_data.pair.coeff1_gm, (atom->ntypes+1)*(atom->ntypes+1));
- cu_lj2_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj2, &cuda->shared_data.pair.coeff2_gm, (atom->ntypes+1)*(atom->ntypes+1));
- cu_lj3_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj3, &cuda->shared_data.pair.coeff3_gm, (atom->ntypes+1)*(atom->ntypes+1));
- cu_lj4_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj4, &cuda->shared_data.pair.coeff4_gm, (atom->ntypes+1)*(atom->ntypes+1));
- cu_ljsw1_gm = new cCudaData<double, F_FLOAT, x> ((double*)ljsw1, &cuda->shared_data.pair.coeff5_gm, (atom->ntypes+1)*(atom->ntypes+1));
- cu_ljsw2_gm = new cCudaData<double, F_FLOAT, x> ((double*)ljsw2, &cuda->shared_data.pair.coeff6_gm, (atom->ntypes+1)*(atom->ntypes+1));
- cu_ljsw3_gm = new cCudaData<double, F_FLOAT, x> ((double*)ljsw3, &cuda->shared_data.pair.coeff7_gm, (atom->ntypes+1)*(atom->ntypes+1));
- cu_ljsw4_gm = new cCudaData<double, F_FLOAT, x> ((double*)ljsw4, &cuda->shared_data.pair.coeff8_gm, (atom->ntypes+1)*(atom->ntypes+1));
- cu_ljsw5_gm = new cCudaData<double, F_FLOAT, x> ((double*)ljsw5, &cuda->shared_data.pair.coeff9_gm, (atom->ntypes+1)*(atom->ntypes+1));
- }
+ if(! allocated) PairLJGromacsCoulGromacs::allocate();
+ if(! allocated2)
+ {
+ cuda->accelerator(0,NULL);
+ allocated2 = true;
+ cuda->shared_data.pair.coeff1 = lj1;
+ cuda->shared_data.pair.coeff2 = lj2;
+ cuda->shared_data.pair.coeff3 = lj3;
+ cuda->shared_data.pair.coeff4 = lj4;
+ cuda->shared_data.pair.coeff5 = ljsw1;
+ cuda->shared_data.pair.coeff6 = ljsw2;
+ cuda->shared_data.pair.coeff7 = ljsw3;
+ cuda->shared_data.pair.coeff8 = ljsw4;
+ cuda->shared_data.pair.coeff9 = ljsw5;
+ cuda->shared_data.pair.special_lj = force->special_lj;
+ cuda->shared_data.pair.special_coul = force->special_coul;
+ cu_lj1_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj1, &cuda->shared_data.pair.coeff1_gm, (atom->ntypes+1)*(atom->ntypes+1));
+ cu_lj2_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj2, &cuda->shared_data.pair.coeff2_gm, (atom->ntypes+1)*(atom->ntypes+1));
+ cu_lj3_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj3, &cuda->shared_data.pair.coeff3_gm, (atom->ntypes+1)*(atom->ntypes+1));
+ cu_lj4_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj4, &cuda->shared_data.pair.coeff4_gm, (atom->ntypes+1)*(atom->ntypes+1));
+ cu_ljsw1_gm = new cCudaData<double, F_FLOAT, x> ((double*)ljsw1, &cuda->shared_data.pair.coeff5_gm, (atom->ntypes+1)*(atom->ntypes+1));
+ cu_ljsw2_gm = new cCudaData<double, F_FLOAT, x> ((double*)ljsw2, &cuda->shared_data.pair.coeff6_gm, (atom->ntypes+1)*(atom->ntypes+1));
+ cu_ljsw3_gm = new cCudaData<double, F_FLOAT, x> ((double*)ljsw3, &cuda->shared_data.pair.coeff7_gm, (atom->ntypes+1)*(atom->ntypes+1));
+ cu_ljsw4_gm = new cCudaData<double, F_FLOAT, x> ((double*)ljsw4, &cuda->shared_data.pair.coeff8_gm, (atom->ntypes+1)*(atom->ntypes+1));
+ cu_ljsw5_gm = new cCudaData<double, F_FLOAT, x> ((double*)ljsw5, &cuda->shared_data.pair.coeff9_gm, (atom->ntypes+1)*(atom->ntypes+1));
+ }
}
/* ---------------------------------------------------------------------- */
void PairLJGromacsCoulGromacsCuda::compute(int eflag, int vflag)
{
- if (eflag || vflag) ev_setup(eflag,vflag);
- if(not cuda->shared_data.pair.collect_forces_later)
- {
- if(eflag) cuda->cu_eng_vdwl->upload();
- if(eflag) cuda->cu_eng_coul->upload();
- if(vflag) cuda->cu_virial->upload();
- }
-
- Cuda_PairLJGromacsCoulGromacsCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom,cut_coul_inner,coulsw1,coulsw2,coulsw5);
-
- if(not cuda->shared_data.pair.collect_forces_later)
- {
- if(eflag) cuda->cu_eng_vdwl->download();
- if(eflag) cuda->cu_eng_coul->download();
- if(vflag) cuda->cu_virial->download();
- }
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ if(not cuda->shared_data.pair.collect_forces_later)
+ {
+ if(eflag) cuda->cu_eng_vdwl->upload();
+ if(eflag) cuda->cu_eng_coul->upload();
+ if(vflag) cuda->cu_virial->upload();
+ }
+
+ Cuda_PairLJGromacsCoulGromacsCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom,cut_coul_inner,coulsw1,coulsw2,coulsw5);
+
+ if(not cuda->shared_data.pair.collect_forces_later)
+ {
+ if(eflag) cuda->cu_eng_vdwl->download();
+ if(eflag) cuda->cu_eng_coul->download();
+ if(vflag) cuda->cu_virial->download();
+ }
}
/* ---------------------------------------------------------------------- */
void PairLJGromacsCoulGromacsCuda::settings(int narg, char **arg)
{
- PairLJGromacsCoulGromacs::settings(narg, arg);
- cuda->shared_data.pair.cut_global = (X_FLOAT) cut_lj;
- cuda->shared_data.pair.cut_coulsq_global = (X_FLOAT) cut_coulsq;
- cuda->shared_data.pair.cut_inner_global = (F_FLOAT) cut_lj_inner;
+ PairLJGromacsCoulGromacs::settings(narg, arg);
+ cuda->shared_data.pair.cut_global = (X_FLOAT) cut_lj;
+ cuda->shared_data.pair.cut_coulsq_global = (X_FLOAT) cut_coulsq;
+ cuda->shared_data.pair.cut_inner_global = (F_FLOAT) cut_lj_inner;
}
/* ---------------------------------------------------------------------- */
void PairLJGromacsCoulGromacsCuda::coeff(int narg, char **arg)
{
- PairLJGromacsCoulGromacs::coeff(narg, arg);
- allocate();
+ PairLJGromacsCoulGromacs::coeff(narg, arg);
+ allocate();
}
void PairLJGromacsCoulGromacsCuda::init_style()
@@ -140,17 +140,17 @@ void PairLJGromacsCoulGromacsCuda::init_style()
error->all(FLERR,"Pair style lj/gromacs/coul/gromacs requires atom attribute q");
// request regular or rRESPA neighbor lists
- if(atom->molecular)
- {
- cuda->shared_data.pair.collect_forces_later = 1;
- }
-
+ if(atom->molecular)
+ {
+ cuda->shared_data.pair.collect_forces_later = 1;
+ }
+
int irequest;
-
- irequest = neighbor->request(this);
+
+ irequest = neighbor->request(this);
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->half = 0;
- neighbor->requests[irequest]->cudable = 1;
+ neighbor->requests[irequest]->cudable = 1;
if (cut_lj_inner >= cut_lj || cut_coul_inner >= cut_coul)
error->all(FLERR,"Pair inner cutoff >= Pair outer cutoff");
@@ -161,37 +161,35 @@ void PairLJGromacsCoulGromacsCuda::init_style()
cut_coulsq = cut_coul * cut_coul;
cut_bothsq = MAX(cut_ljsq,cut_coulsq);
-
+
cut_coulsq = cut_coul * cut_coul;
-
+
cuda->shared_data.pair.cut_coulsq_global=cut_coulsq;
-
+
cuda->shared_data.pppm.qqrd2e=force->qqrd2e;
}
void PairLJGromacsCoulGromacsCuda::init_list(int id, NeighList *ptr)
{
- MYDBG(printf("# CUDA PairLJGromacsCoulGromacsCuda::init_list\n");)
- PairLJGromacsCoulGromacs::init_list(id, ptr);
- #ifndef CUDA_USE_BINNING
- // right now we can only handle verlet (id 0), not respa
- if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
- // see Neighbor::init() for details on lammps lists' logic
- #endif
- MYDBG(printf("# CUDA PairLJGromacsCoulGromacsCuda::init_list end\n");)
+ MYDBG(printf("# CUDA PairLJGromacsCoulGromacsCuda::init_list\n");)
+ PairLJGromacsCoulGromacs::init_list(id, ptr);
+ #ifndef CUDA_USE_BINNING
+ // right now we can only handle verlet (id 0), not respa
+ if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
+ // see Neighbor::init() for details on lammps lists' logic
+ #endif
+ MYDBG(printf("# CUDA PairLJGromacsCoulGromacsCuda::init_list end\n");)
}
void PairLJGromacsCoulGromacsCuda::ev_setup(int eflag, int vflag)
{
- int maxeatomold=maxeatom;
- PairLJGromacsCoulGromacs::ev_setup(eflag,vflag);
-
- if (eflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
+ int maxeatomold=maxeatom;
+ PairLJGromacsCoulGromacs::ev_setup(eflag,vflag);
- if (vflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
-
-}
+ if (eflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
+ if (vflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
+}
diff --git a/src/USER-CUDA/pair_lj_gromacs_coul_gromacs_cuda.h b/src/USER-CUDA/pair_lj_gromacs_coul_gromacs_cuda.h
index 333bbc00883980e4e8dab3b5323c9221d9985c59..32f781bc8e7bd8278a2c057588e432a3719c006d 100644
--- a/src/USER-CUDA/pair_lj_gromacs_coul_gromacs_cuda.h
+++ b/src/USER-CUDA/pair_lj_gromacs_coul_gromacs_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -37,28 +37,28 @@ namespace LAMMPS_NS {
class PairLJGromacsCoulGromacsCuda : public PairLJGromacsCoulGromacs
{
- public:
- PairLJGromacsCoulGromacsCuda(class LAMMPS *);
- void compute(int, int);
- void settings(int, char **);
- void coeff(int, char **);
- void init_list(int, class NeighList *);
- void init_style();
- void ev_setup(int eflag, int vflag);
- protected:
- class Cuda *cuda;
- void allocate();
- bool allocated2;
- class CudaNeighList* cuda_neigh_list;
- cCudaData<double , F_FLOAT , x >* cu_lj1_gm;
- cCudaData<double , F_FLOAT , x >* cu_lj2_gm;
- cCudaData<double , F_FLOAT , x >* cu_lj3_gm;
- cCudaData<double , F_FLOAT , x >* cu_lj4_gm;
- cCudaData<double , F_FLOAT , x >* cu_ljsw1_gm;
- cCudaData<double , F_FLOAT , x >* cu_ljsw2_gm;
- cCudaData<double , F_FLOAT , x >* cu_ljsw3_gm;
- cCudaData<double , F_FLOAT , x >* cu_ljsw4_gm;
- cCudaData<double , F_FLOAT , x >* cu_ljsw5_gm;
+ public:
+ PairLJGromacsCoulGromacsCuda(class LAMMPS *);
+ void compute(int, int);
+ void settings(int, char **);
+ void coeff(int, char **);
+ void init_list(int, class NeighList *);
+ void init_style();
+ void ev_setup(int eflag, int vflag);
+ protected:
+ class Cuda *cuda;
+ void allocate();
+ bool allocated2;
+ class CudaNeighList* cuda_neigh_list;
+ cCudaData<double , F_FLOAT , x >* cu_lj1_gm;
+ cCudaData<double , F_FLOAT , x >* cu_lj2_gm;
+ cCudaData<double , F_FLOAT , x >* cu_lj3_gm;
+ cCudaData<double , F_FLOAT , x >* cu_lj4_gm;
+ cCudaData<double , F_FLOAT , x >* cu_ljsw1_gm;
+ cCudaData<double , F_FLOAT , x >* cu_ljsw2_gm;
+ cCudaData<double , F_FLOAT , x >* cu_ljsw3_gm;
+ cCudaData<double , F_FLOAT , x >* cu_ljsw4_gm;
+ cCudaData<double , F_FLOAT , x >* cu_ljsw5_gm;
};
diff --git a/src/USER-CUDA/pair_lj_gromacs_cuda.cpp b/src/USER-CUDA/pair_lj_gromacs_cuda.cpp
index 518ab5632579e956a8ba5014e0fd60efb89e535b..c8a09aaf7f5669c4f9febd58f95aec8769909e09 100644
--- a/src/USER-CUDA/pair_lj_gromacs_cuda.cpp
+++ b/src/USER-CUDA/pair_lj_gromacs_cuda.cpp
@@ -1,23 +1,23 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
Contributing author: Paul Crozier (SNL)
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -54,10 +54,10 @@ PairLJGromacsCuda::PairLJGromacsCuda(LAMMPS *lmp) : PairLJGromacs(lmp)
if(cuda == NULL)
error->all(FLERR,"You cannot use a /cuda class, without activating 'cuda' acceleration. Provide '-c on' as command-line argument to LAMMPS..");
- allocated2 = false;
- cuda->shared_data.pair.cudable_force = 1;
- cuda->shared_data.pair.use_block_per_atom = 0;
- cuda->setSystemParams();
+ allocated2 = false;
+ cuda->shared_data.pair.cudable_force = 1;
+ cuda->shared_data.pair.use_block_per_atom = 0;
+ cuda->setSystemParams();
}
/* ----------------------------------------------------------------------
@@ -66,115 +66,113 @@ PairLJGromacsCuda::PairLJGromacsCuda(LAMMPS *lmp) : PairLJGromacs(lmp)
void PairLJGromacsCuda::allocate()
{
- if(! allocated) PairLJGromacs::allocate();
- if(! allocated2)
- {
- cuda->accelerator(0,NULL);
- allocated2 = true;
- cuda->shared_data.pair.cut = cut;
- cuda->shared_data.pair.cut_inner = cut_inner;
- cuda->shared_data.pair.coeff1 = lj1;
- cuda->shared_data.pair.coeff2 = lj2;
- cuda->shared_data.pair.coeff3 = lj3;
- cuda->shared_data.pair.coeff4 = lj4;
- cuda->shared_data.pair.coeff5 = ljsw1;
- cuda->shared_data.pair.coeff6 = ljsw2;
- cuda->shared_data.pair.coeff7 = ljsw3;
- cuda->shared_data.pair.coeff8 = ljsw4;
- cuda->shared_data.pair.coeff9 = ljsw5;
- cuda->shared_data.pair.special_lj = force->special_lj;
- cu_lj1_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj1, &cuda->shared_data.pair.coeff1_gm, (atom->ntypes+1)*(atom->ntypes+1));
- cu_lj2_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj2, &cuda->shared_data.pair.coeff2_gm, (atom->ntypes+1)*(atom->ntypes+1));
- cu_lj3_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj3, &cuda->shared_data.pair.coeff3_gm, (atom->ntypes+1)*(atom->ntypes+1));
- cu_lj4_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj4, &cuda->shared_data.pair.coeff4_gm, (atom->ntypes+1)*(atom->ntypes+1));
- cu_ljsw1_gm = new cCudaData<double, F_FLOAT, x> ((double*)ljsw1, &cuda->shared_data.pair.coeff5_gm, (atom->ntypes+1)*(atom->ntypes+1));
- cu_ljsw2_gm = new cCudaData<double, F_FLOAT, x> ((double*)ljsw2, &cuda->shared_data.pair.coeff6_gm, (atom->ntypes+1)*(atom->ntypes+1));
- cu_ljsw3_gm = new cCudaData<double, F_FLOAT, x> ((double*)ljsw3, &cuda->shared_data.pair.coeff7_gm, (atom->ntypes+1)*(atom->ntypes+1));
- cu_ljsw4_gm = new cCudaData<double, F_FLOAT, x> ((double*)ljsw4, &cuda->shared_data.pair.coeff8_gm, (atom->ntypes+1)*(atom->ntypes+1));
- cu_ljsw5_gm = new cCudaData<double, F_FLOAT, x> ((double*)ljsw5, &cuda->shared_data.pair.coeff9_gm, (atom->ntypes+1)*(atom->ntypes+1));
- }
+ if(! allocated) PairLJGromacs::allocate();
+ if(! allocated2)
+ {
+ cuda->accelerator(0,NULL);
+ allocated2 = true;
+ cuda->shared_data.pair.cut = cut;
+ cuda->shared_data.pair.cut_inner = cut_inner;
+ cuda->shared_data.pair.coeff1 = lj1;
+ cuda->shared_data.pair.coeff2 = lj2;
+ cuda->shared_data.pair.coeff3 = lj3;
+ cuda->shared_data.pair.coeff4 = lj4;
+ cuda->shared_data.pair.coeff5 = ljsw1;
+ cuda->shared_data.pair.coeff6 = ljsw2;
+ cuda->shared_data.pair.coeff7 = ljsw3;
+ cuda->shared_data.pair.coeff8 = ljsw4;
+ cuda->shared_data.pair.coeff9 = ljsw5;
+ cuda->shared_data.pair.special_lj = force->special_lj;
+ cu_lj1_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj1, &cuda->shared_data.pair.coeff1_gm, (atom->ntypes+1)*(atom->ntypes+1));
+ cu_lj2_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj2, &cuda->shared_data.pair.coeff2_gm, (atom->ntypes+1)*(atom->ntypes+1));
+ cu_lj3_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj3, &cuda->shared_data.pair.coeff3_gm, (atom->ntypes+1)*(atom->ntypes+1));
+ cu_lj4_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj4, &cuda->shared_data.pair.coeff4_gm, (atom->ntypes+1)*(atom->ntypes+1));
+ cu_ljsw1_gm = new cCudaData<double, F_FLOAT, x> ((double*)ljsw1, &cuda->shared_data.pair.coeff5_gm, (atom->ntypes+1)*(atom->ntypes+1));
+ cu_ljsw2_gm = new cCudaData<double, F_FLOAT, x> ((double*)ljsw2, &cuda->shared_data.pair.coeff6_gm, (atom->ntypes+1)*(atom->ntypes+1));
+ cu_ljsw3_gm = new cCudaData<double, F_FLOAT, x> ((double*)ljsw3, &cuda->shared_data.pair.coeff7_gm, (atom->ntypes+1)*(atom->ntypes+1));
+ cu_ljsw4_gm = new cCudaData<double, F_FLOAT, x> ((double*)ljsw4, &cuda->shared_data.pair.coeff8_gm, (atom->ntypes+1)*(atom->ntypes+1));
+ cu_ljsw5_gm = new cCudaData<double, F_FLOAT, x> ((double*)ljsw5, &cuda->shared_data.pair.coeff9_gm, (atom->ntypes+1)*(atom->ntypes+1));
+ }
}
/* ---------------------------------------------------------------------- */
void PairLJGromacsCuda::compute(int eflag, int vflag)
{
- if (eflag || vflag) ev_setup(eflag,vflag);
- if(not cuda->shared_data.pair.collect_forces_later)
- {
- if(eflag) cuda->cu_eng_vdwl->upload();
- if(vflag) cuda->cu_virial->upload();
- }
-
- Cuda_PairLJGromacsCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);
-
- if(not cuda->shared_data.pair.collect_forces_later)
- {
- if(eflag) cuda->cu_eng_vdwl->download();
- if(vflag) cuda->cu_virial->download();
- }
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ if(not cuda->shared_data.pair.collect_forces_later)
+ {
+ if(eflag) cuda->cu_eng_vdwl->upload();
+ if(vflag) cuda->cu_virial->upload();
+ }
+
+ Cuda_PairLJGromacsCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);
+
+ if(not cuda->shared_data.pair.collect_forces_later)
+ {
+ if(eflag) cuda->cu_eng_vdwl->download();
+ if(vflag) cuda->cu_virial->download();
+ }
}
/* ---------------------------------------------------------------------- */
void PairLJGromacsCuda::settings(int narg, char **arg)
{
- PairLJGromacs::settings(narg, arg);
- cuda->shared_data.pair.cut_global = (F_FLOAT) cut_global;
- cuda->shared_data.pair.cut_inner_global = (F_FLOAT) cut_inner_global;
+ PairLJGromacs::settings(narg, arg);
+ cuda->shared_data.pair.cut_global = (F_FLOAT) cut_global;
+ cuda->shared_data.pair.cut_inner_global = (F_FLOAT) cut_inner_global;
}
/* ---------------------------------------------------------------------- */
void PairLJGromacsCuda::coeff(int narg, char **arg)
{
- PairLJGromacs::coeff(narg, arg);
- allocate();
+ PairLJGromacs::coeff(narg, arg);
+ allocate();
}
void PairLJGromacsCuda::init_style()
{
// request regular or rRESPA neighbor lists
- if(atom->molecular)
- {
- cuda->shared_data.pair.collect_forces_later = 1;
- }
-
+ if(atom->molecular)
+ {
+ cuda->shared_data.pair.collect_forces_later = 1;
+ }
+
int irequest;
-
- irequest = neighbor->request(this);
+
+ irequest = neighbor->request(this);
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->half = 0;
- neighbor->requests[irequest]->cudable = 1;
+ neighbor->requests[irequest]->cudable = 1;
+
-
}
void PairLJGromacsCuda::init_list(int id, NeighList *ptr)
{
- MYDBG(printf("# CUDA PairLJGromacsCuda::init_list\n");)
- PairLJGromacs::init_list(id, ptr);
- #ifndef CUDA_USE_BINNING
- // right now we can only handle verlet (id 0), not respa
- if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
- // see Neighbor::init() for details on lammps lists' logic
- #endif
- MYDBG(printf("# CUDA PairLJGromacsCuda::init_list end\n");)
+ MYDBG(printf("# CUDA PairLJGromacsCuda::init_list\n");)
+ PairLJGromacs::init_list(id, ptr);
+ #ifndef CUDA_USE_BINNING
+ // right now we can only handle verlet (id 0), not respa
+ if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
+ // see Neighbor::init() for details on lammps lists' logic
+ #endif
+ MYDBG(printf("# CUDA PairLJGromacsCuda::init_list end\n");)
}
void PairLJGromacsCuda::ev_setup(int eflag, int vflag)
{
- int maxeatomold=maxeatom;
- PairLJGromacs::ev_setup(eflag,vflag);
+ int maxeatomold=maxeatom;
+ PairLJGromacs::ev_setup(eflag,vflag);
- if (eflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
-
- if (vflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
-
-}
+ if (eflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
+ if (vflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
+}
diff --git a/src/USER-CUDA/pair_lj_gromacs_cuda.h b/src/USER-CUDA/pair_lj_gromacs_cuda.h
index 64e38aa763329c10f605d7e664e905c6435141ab..87ee71f8819263dcef77d54b86952f1d25ec869b 100644
--- a/src/USER-CUDA/pair_lj_gromacs_cuda.h
+++ b/src/USER-CUDA/pair_lj_gromacs_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -37,28 +37,28 @@ namespace LAMMPS_NS {
class PairLJGromacsCuda : public PairLJGromacs
{
- public:
- PairLJGromacsCuda(class LAMMPS *);
- void compute(int, int);
- void settings(int, char **);
- void coeff(int, char **);
- void init_list(int, class NeighList *);
- void init_style();
- void ev_setup(int eflag, int vflag);
- protected:
- class Cuda *cuda;
- void allocate();
- bool allocated2;
- class CudaNeighList* cuda_neigh_list;
- cCudaData<double , F_FLOAT , x >* cu_lj1_gm;
- cCudaData<double , F_FLOAT , x >* cu_lj2_gm;
- cCudaData<double , F_FLOAT , x >* cu_lj3_gm;
- cCudaData<double , F_FLOAT , x >* cu_lj4_gm;
- cCudaData<double , F_FLOAT , x >* cu_ljsw1_gm;
- cCudaData<double , F_FLOAT , x >* cu_ljsw2_gm;
- cCudaData<double , F_FLOAT , x >* cu_ljsw3_gm;
- cCudaData<double , F_FLOAT , x >* cu_ljsw4_gm;
- cCudaData<double , F_FLOAT , x >* cu_ljsw5_gm;
+ public:
+ PairLJGromacsCuda(class LAMMPS *);
+ void compute(int, int);
+ void settings(int, char **);
+ void coeff(int, char **);
+ void init_list(int, class NeighList *);
+ void init_style();
+ void ev_setup(int eflag, int vflag);
+ protected:
+ class Cuda *cuda;
+ void allocate();
+ bool allocated2;
+ class CudaNeighList* cuda_neigh_list;
+ cCudaData<double , F_FLOAT , x >* cu_lj1_gm;
+ cCudaData<double , F_FLOAT , x >* cu_lj2_gm;
+ cCudaData<double , F_FLOAT , x >* cu_lj3_gm;
+ cCudaData<double , F_FLOAT , x >* cu_lj4_gm;
+ cCudaData<double , F_FLOAT , x >* cu_ljsw1_gm;
+ cCudaData<double , F_FLOAT , x >* cu_ljsw2_gm;
+ cCudaData<double , F_FLOAT , x >* cu_ljsw3_gm;
+ cCudaData<double , F_FLOAT , x >* cu_ljsw4_gm;
+ cCudaData<double , F_FLOAT , x >* cu_ljsw5_gm;
};
diff --git a/src/USER-CUDA/pair_lj_sdk_coul_cut_cuda.cpp b/src/USER-CUDA/pair_lj_sdk_coul_cut_cuda.cpp
index 458973525df9fe1c92f6fbf776956f0eaf473718..c74cc0c4ee99a26b9b99f0518bf4951544375a19 100644
--- a/src/USER-CUDA/pair_lj_sdk_coul_cut_cuda.cpp
+++ b/src/USER-CUDA/pair_lj_sdk_coul_cut_cuda.cpp
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -28,7 +28,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -69,10 +69,10 @@ PairLJSDKCoulCutCuda::PairLJSDKCoulCutCuda(LAMMPS *lmp) : PairLJSDKCoulCut(lmp)
if(cuda == NULL)
error->all(FLERR,"You cannot use a /cuda class, without activating 'cuda' acceleration. Provide '-c on' as command-line argument to LAMMPS..");
- allocated2 = false;
- lj_type_double = NULL;
- cuda->shared_data.pair.cudable_force = 1;
- cuda->setSystemParams();
+ allocated2 = false;
+ lj_type_double = NULL;
+ cuda->shared_data.pair.cudable_force = 1;
+ cuda->setSystemParams();
}
/* ----------------------------------------------------------------------
@@ -81,27 +81,27 @@ PairLJSDKCoulCutCuda::PairLJSDKCoulCutCuda(LAMMPS *lmp) : PairLJSDKCoulCut(lmp)
void PairLJSDKCoulCutCuda::allocate()
{
- if(! allocated) PairLJSDKCoulCut::allocate();
- int n = atom->ntypes;
- if(! allocated2)
- {
- allocated2 = true;
-
-
- memory->create(lj_type_double,n+1,n+1,"pairlj:ljtypedouble");
-
- cuda->shared_data.pair.cut = cut_lj;
- cuda->shared_data.pair.cut_coul= cut_coul;
- cuda->shared_data.pair.coeff1 = lj1;
- cuda->shared_data.pair.coeff2 = lj2;
- cuda->shared_data.pair.coeff3 = lj3;
- cuda->shared_data.pair.coeff4 = lj4;
- cuda->shared_data.pair.coeff5 = lj_type_double;
- cuda->shared_data.pair.offset = offset;
- cuda->shared_data.pair.special_lj = force->special_lj;
- cuda->shared_data.pair.special_coul = force->special_coul;
- }
- for (int i = 1; i <= n; i++) {
+ if(! allocated) PairLJSDKCoulCut::allocate();
+ int n = atom->ntypes;
+ if(! allocated2)
+ {
+ allocated2 = true;
+
+
+ memory->create(lj_type_double,n+1,n+1,"pairlj:ljtypedouble");
+
+ cuda->shared_data.pair.cut = cut_lj;
+ cuda->shared_data.pair.cut_coul= cut_coul;
+ cuda->shared_data.pair.coeff1 = lj1;
+ cuda->shared_data.pair.coeff2 = lj2;
+ cuda->shared_data.pair.coeff3 = lj3;
+ cuda->shared_data.pair.coeff4 = lj4;
+ cuda->shared_data.pair.coeff5 = lj_type_double;
+ cuda->shared_data.pair.offset = offset;
+ cuda->shared_data.pair.special_lj = force->special_lj;
+ cuda->shared_data.pair.special_coul = force->special_coul;
+ }
+ for (int i = 1; i <= n; i++) {
for (int j = i; j <= n; j++) {
lj_type_double[i][j] = lj_type[i][j];
lj_type_double[j][i] = lj_type[i][j];
@@ -113,53 +113,53 @@ void PairLJSDKCoulCutCuda::allocate()
void PairLJSDKCoulCutCuda::compute(int eflag, int vflag)
{
- if (eflag || vflag) ev_setup(eflag,vflag);
- if(eflag) cuda->cu_eng_vdwl->upload();
- if(eflag) cuda->cu_eng_coul->upload();
- if(vflag) cuda->cu_virial->upload();
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ if(eflag) cuda->cu_eng_vdwl->upload();
+ if(eflag) cuda->cu_eng_coul->upload();
+ if(vflag) cuda->cu_virial->upload();
- Cuda_PairLJSDKCoulCutCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);
+ Cuda_PairLJSDKCoulCutCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);
if(not cuda->shared_data.pair.collect_forces_later)
{
- if(eflag) cuda->cu_eng_vdwl->download();
- if(eflag) cuda->cu_eng_coul->download();
- if(vflag) cuda->cu_virial->download();
+ if(eflag) cuda->cu_eng_vdwl->download();
+ if(eflag) cuda->cu_eng_coul->download();
+ if(vflag) cuda->cu_virial->download();
}
-
+
}
/* ---------------------------------------------------------------------- */
void PairLJSDKCoulCutCuda::settings(int narg, char **arg)
{
- PairLJSDKCoulCut::settings(narg, arg);
- cuda->shared_data.pair.cut_global = (F_FLOAT) cut_lj_global;
- cuda->shared_data.pair.cut_coul_global = (F_FLOAT) cut_coul_global;
- cuda->shared_data.pair.kappa = (F_FLOAT) kappa;
+ PairLJSDKCoulCut::settings(narg, arg);
+ cuda->shared_data.pair.cut_global = (F_FLOAT) cut_lj_global;
+ cuda->shared_data.pair.cut_coul_global = (F_FLOAT) cut_coul_global;
+ cuda->shared_data.pair.kappa = (F_FLOAT) kappa;
}
/* ---------------------------------------------------------------------- */
void PairLJSDKCoulCutCuda::coeff(int narg, char **arg)
{
- PairLJSDKCoulCut::coeff(narg, arg);
- allocate();
+ PairLJSDKCoulCut::coeff(narg, arg);
+ allocate();
}
void PairLJSDKCoulCutCuda::init_style()
{
- MYDBG(printf("# CUDA PairLJSDKCoulCutCuda::init_style start\n"); )
+ MYDBG(printf("# CUDA PairLJSDKCoulCutCuda::init_style start\n"); )
// request regular or rRESPA neighbor lists
int irequest;
-
+
if (update->whichflag == 0 && strstr(update->integrate_style,"respa")) {
- }
- else
+ }
+ else
{
- irequest = neighbor->request(this);
+ irequest = neighbor->request(this);
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->cudable = 1;
@@ -175,27 +175,25 @@ void PairLJSDKCoulCutCuda::init_style()
void PairLJSDKCoulCutCuda::init_list(int id, NeighList *ptr)
{
- MYDBG(printf("# CUDA PairLJSDKCoulCutCuda::init_list\n");)
- PairLJSDKCoulCut::init_list(id, ptr);
- #ifndef CUDA_USE_BINNING
- // right now we can only handle verlet (id 0), not respa
- if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
- // see Neighbor::init() for details on lammps lists' logic
- #endif
- MYDBG(printf("# CUDA PairLJSDKCoulCutCuda::init_list end\n");)
+ MYDBG(printf("# CUDA PairLJSDKCoulCutCuda::init_list\n");)
+ PairLJSDKCoulCut::init_list(id, ptr);
+ #ifndef CUDA_USE_BINNING
+ // right now we can only handle verlet (id 0), not respa
+ if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
+ // see Neighbor::init() for details on lammps lists' logic
+ #endif
+ MYDBG(printf("# CUDA PairLJSDKCoulCutCuda::init_list end\n");)
}
void PairLJSDKCoulCutCuda::ev_setup(int eflag, int vflag)
{
- int maxeatomold=maxeatom;
- PairLJSDKCoulCut::ev_setup(eflag,vflag);
-
- if (eflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
+ int maxeatomold=maxeatom;
+ PairLJSDKCoulCut::ev_setup(eflag,vflag);
- if (vflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
-
-}
+ if (eflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
+ if (vflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
+}
diff --git a/src/USER-CUDA/pair_lj_sdk_coul_cut_cuda.h b/src/USER-CUDA/pair_lj_sdk_coul_cut_cuda.h
index e254a63f69fb4f006d4edaf200e89e5e23e57175..0e78ae775782cef0beefb939d5718eabd0c1d532 100644
--- a/src/USER-CUDA/pair_lj_sdk_coul_cut_cuda.h
+++ b/src/USER-CUDA/pair_lj_sdk_coul_cut_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -36,20 +36,20 @@ namespace LAMMPS_NS {
class PairLJSDKCoulCutCuda : public PairLJSDKCoulCut
{
- public:
- PairLJSDKCoulCutCuda(class LAMMPS *);
- void compute(int, int);
- void settings(int, char **);
- void coeff(int, char **);
- void init_list(int, class NeighList *);
- void init_style();
- void ev_setup(int eflag, int vflag);
- protected:
- class Cuda *cuda;
- void allocate();
- bool allocated2;
- class CudaNeighList* cuda_neigh_list;
- double** lj_type_double;
+ public:
+ PairLJSDKCoulCutCuda(class LAMMPS *);
+ void compute(int, int);
+ void settings(int, char **);
+ void coeff(int, char **);
+ void init_list(int, class NeighList *);
+ void init_style();
+ void ev_setup(int eflag, int vflag);
+ protected:
+ class Cuda *cuda;
+ void allocate();
+ bool allocated2;
+ class CudaNeighList* cuda_neigh_list;
+ double** lj_type_double;
};
}
diff --git a/src/USER-CUDA/pair_lj_sdk_coul_debye_cuda.cpp b/src/USER-CUDA/pair_lj_sdk_coul_debye_cuda.cpp
index 418bdb0c647985d39956b414cb3c37612bedb6e9..afd140207e1fc24b766a22ecd5d4b3a0d2bb1564 100644
--- a/src/USER-CUDA/pair_lj_sdk_coul_debye_cuda.cpp
+++ b/src/USER-CUDA/pair_lj_sdk_coul_debye_cuda.cpp
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -28,7 +28,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -69,10 +69,10 @@ PairLJSDKCoulDebyeCuda::PairLJSDKCoulDebyeCuda(LAMMPS *lmp) : PairLJSDKCoulCut(l
if(cuda == NULL)
error->all(FLERR,"You cannot use a /cuda class, without activating 'cuda' acceleration. Provide '-c on' as command-line argument to LAMMPS..");
- allocated2 = false;
- lj_type_double = NULL;
- cuda->shared_data.pair.cudable_force = 1;
- cuda->setSystemParams();
+ allocated2 = false;
+ lj_type_double = NULL;
+ cuda->shared_data.pair.cudable_force = 1;
+ cuda->setSystemParams();
}
/* ----------------------------------------------------------------------
@@ -81,27 +81,27 @@ PairLJSDKCoulDebyeCuda::PairLJSDKCoulDebyeCuda(LAMMPS *lmp) : PairLJSDKCoulCut(l
void PairLJSDKCoulDebyeCuda::allocate()
{
- if(! allocated) PairLJSDKCoulCut::allocate();
- int n = atom->ntypes;
- if(! allocated2)
- {
- allocated2 = true;
-
-
- memory->create(lj_type_double,n+1,n+1,"pairlj:ljtypedouble");
-
- cuda->shared_data.pair.cut = cut_lj;
- cuda->shared_data.pair.cut_coul= cut_coul;
- cuda->shared_data.pair.coeff1 = lj1;
- cuda->shared_data.pair.coeff2 = lj2;
- cuda->shared_data.pair.coeff3 = lj3;
- cuda->shared_data.pair.coeff4 = lj4;
- cuda->shared_data.pair.coeff5 = lj_type_double;
- cuda->shared_data.pair.offset = offset;
- cuda->shared_data.pair.special_lj = force->special_lj;
- cuda->shared_data.pair.special_coul = force->special_coul;
- }
- for (int i = 1; i <= n; i++) {
+ if(! allocated) PairLJSDKCoulCut::allocate();
+ int n = atom->ntypes;
+ if(! allocated2)
+ {
+ allocated2 = true;
+
+
+ memory->create(lj_type_double,n+1,n+1,"pairlj:ljtypedouble");
+
+ cuda->shared_data.pair.cut = cut_lj;
+ cuda->shared_data.pair.cut_coul= cut_coul;
+ cuda->shared_data.pair.coeff1 = lj1;
+ cuda->shared_data.pair.coeff2 = lj2;
+ cuda->shared_data.pair.coeff3 = lj3;
+ cuda->shared_data.pair.coeff4 = lj4;
+ cuda->shared_data.pair.coeff5 = lj_type_double;
+ cuda->shared_data.pair.offset = offset;
+ cuda->shared_data.pair.special_lj = force->special_lj;
+ cuda->shared_data.pair.special_coul = force->special_coul;
+ }
+ for (int i = 1; i <= n; i++) {
for (int j = i; j <= n; j++) {
lj_type_double[i][j] = lj_type[i][j];
lj_type_double[j][i] = lj_type[i][j];
@@ -113,53 +113,53 @@ void PairLJSDKCoulDebyeCuda::allocate()
void PairLJSDKCoulDebyeCuda::compute(int eflag, int vflag)
{
- if (eflag || vflag) ev_setup(eflag,vflag);
- if(eflag) cuda->cu_eng_vdwl->upload();
- if(eflag) cuda->cu_eng_coul->upload();
- if(vflag) cuda->cu_virial->upload();
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ if(eflag) cuda->cu_eng_vdwl->upload();
+ if(eflag) cuda->cu_eng_coul->upload();
+ if(vflag) cuda->cu_virial->upload();
- Cuda_PairLJSDKCoulDebyeCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);
+ Cuda_PairLJSDKCoulDebyeCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);
if(not cuda->shared_data.pair.collect_forces_later)
{
- if(eflag) cuda->cu_eng_vdwl->download();
- if(eflag) cuda->cu_eng_coul->download();
- if(vflag) cuda->cu_virial->download();
+ if(eflag) cuda->cu_eng_vdwl->download();
+ if(eflag) cuda->cu_eng_coul->download();
+ if(vflag) cuda->cu_virial->download();
}
-
+
}
/* ---------------------------------------------------------------------- */
void PairLJSDKCoulDebyeCuda::settings(int narg, char **arg)
{
- PairLJSDKCoulCut::settings(narg, arg);
- cuda->shared_data.pair.cut_global = (F_FLOAT) cut_lj_global;
- cuda->shared_data.pair.cut_coul_global = (F_FLOAT) cut_coul_global;
- cuda->shared_data.pair.kappa = (F_FLOAT) kappa;
+ PairLJSDKCoulCut::settings(narg, arg);
+ cuda->shared_data.pair.cut_global = (F_FLOAT) cut_lj_global;
+ cuda->shared_data.pair.cut_coul_global = (F_FLOAT) cut_coul_global;
+ cuda->shared_data.pair.kappa = (F_FLOAT) kappa;
}
/* ---------------------------------------------------------------------- */
void PairLJSDKCoulDebyeCuda::coeff(int narg, char **arg)
{
- PairLJSDKCoulCut::coeff(narg, arg);
- allocate();
+ PairLJSDKCoulCut::coeff(narg, arg);
+ allocate();
}
void PairLJSDKCoulDebyeCuda::init_style()
{
- MYDBG(printf("# CUDA PairLJSDKCoulDebyeCuda::init_style start\n"); )
+ MYDBG(printf("# CUDA PairLJSDKCoulDebyeCuda::init_style start\n"); )
// request regular or rRESPA neighbor lists
int irequest;
-
+
if (update->whichflag == 0 && strstr(update->integrate_style,"respa")) {
- }
- else
+ }
+ else
{
- irequest = neighbor->request(this);
+ irequest = neighbor->request(this);
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->cudable = 1;
@@ -175,27 +175,25 @@ void PairLJSDKCoulDebyeCuda::init_style()
void PairLJSDKCoulDebyeCuda::init_list(int id, NeighList *ptr)
{
- MYDBG(printf("# CUDA PairLJSDKCoulDebyeCuda::init_list\n");)
- PairLJSDKCoulCut::init_list(id, ptr);
- #ifndef CUDA_USE_BINNING
- // right now we can only handle verlet (id 0), not respa
- if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
- // see Neighbor::init() for details on lammps lists' logic
- #endif
- MYDBG(printf("# CUDA PairLJSDKCoulDebyeCuda::init_list end\n");)
+ MYDBG(printf("# CUDA PairLJSDKCoulDebyeCuda::init_list\n");)
+ PairLJSDKCoulCut::init_list(id, ptr);
+ #ifndef CUDA_USE_BINNING
+ // right now we can only handle verlet (id 0), not respa
+ if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
+ // see Neighbor::init() for details on lammps lists' logic
+ #endif
+ MYDBG(printf("# CUDA PairLJSDKCoulDebyeCuda::init_list end\n");)
}
void PairLJSDKCoulDebyeCuda::ev_setup(int eflag, int vflag)
{
- int maxeatomold=maxeatom;
- PairLJSDKCoulCut::ev_setup(eflag,vflag);
-
- if (eflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
+ int maxeatomold=maxeatom;
+ PairLJSDKCoulCut::ev_setup(eflag,vflag);
- if (vflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
-
-}
+ if (eflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
+ if (vflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
+}
diff --git a/src/USER-CUDA/pair_lj_sdk_coul_debye_cuda.h b/src/USER-CUDA/pair_lj_sdk_coul_debye_cuda.h
index 9f193fc33307e0245ac9468570b9a086857d20d7..cceffdbfe7b7ccce3740db427a70c663e101f7f9 100644
--- a/src/USER-CUDA/pair_lj_sdk_coul_debye_cuda.h
+++ b/src/USER-CUDA/pair_lj_sdk_coul_debye_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -36,20 +36,20 @@ namespace LAMMPS_NS {
class PairLJSDKCoulDebyeCuda : public PairLJSDKCoulCut
{
- public:
- PairLJSDKCoulDebyeCuda(class LAMMPS *);
- void compute(int, int);
- void settings(int, char **);
- void coeff(int, char **);
- void init_list(int, class NeighList *);
- void init_style();
- void ev_setup(int eflag, int vflag);
- protected:
- class Cuda *cuda;
- void allocate();
- bool allocated2;
- class CudaNeighList* cuda_neigh_list;
- double** lj_type_double;
+ public:
+ PairLJSDKCoulDebyeCuda(class LAMMPS *);
+ void compute(int, int);
+ void settings(int, char **);
+ void coeff(int, char **);
+ void init_list(int, class NeighList *);
+ void init_style();
+ void ev_setup(int eflag, int vflag);
+ protected:
+ class Cuda *cuda;
+ void allocate();
+ bool allocated2;
+ class CudaNeighList* cuda_neigh_list;
+ double** lj_type_double;
};
}
diff --git a/src/USER-CUDA/pair_lj_sdk_coul_long_cuda.cpp b/src/USER-CUDA/pair_lj_sdk_coul_long_cuda.cpp
index 85b6f4a138863de3bb30e08dcd00e70ad1aa9d63..89134d7e3744073fa311e7128582e6b644ee013f 100644
--- a/src/USER-CUDA/pair_lj_sdk_coul_long_cuda.cpp
+++ b/src/USER-CUDA/pair_lj_sdk_coul_long_cuda.cpp
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -28,7 +28,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -70,10 +70,10 @@ PairLJSDKCoulLongCuda::PairLJSDKCoulLongCuda(LAMMPS *lmp) : PairLJSDKCoulLong(lm
if(cuda == NULL)
error->all(FLERR,"You cannot use a /cuda class, without activating 'cuda' acceleration. Provide '-c on' as command-line argument to LAMMPS..");
- allocated2 = false;
- lj_type_double = NULL;
- cuda->shared_data.pair.cudable_force = 1;
- cuda->setSystemParams();
+ allocated2 = false;
+ lj_type_double = NULL;
+ cuda->shared_data.pair.cudable_force = 1;
+ cuda->setSystemParams();
}
/* ----------------------------------------------------------------------
@@ -82,28 +82,28 @@ PairLJSDKCoulLongCuda::PairLJSDKCoulLongCuda(LAMMPS *lmp) : PairLJSDKCoulLong(lm
void PairLJSDKCoulLongCuda::allocate()
{
- if(! allocated) PairLJSDKCoulLong::allocate();
- int n = atom->ntypes;
- if(! allocated2)
- {
- allocated2 = true;
-
-
- memory->create(lj_type_double,n+1,n+1,"pairlj:ljtypedouble");
-
- cuda->shared_data.pair.cut = cut_lj;
- cuda->shared_data.pair.cut_coul= NULL;
- cuda->shared_data.pair.coeff1 = lj1;
- cuda->shared_data.pair.coeff2 = lj2;
- cuda->shared_data.pair.coeff3 = lj3;
- cuda->shared_data.pair.coeff4 = lj4;
- cuda->shared_data.pair.coeff5 = lj_type_double;
- cuda->shared_data.pair.offset = offset;
- cuda->shared_data.pair.special_lj = force->special_lj;
+ if(! allocated) PairLJSDKCoulLong::allocate();
+ int n = atom->ntypes;
+ if(! allocated2)
+ {
+ allocated2 = true;
+
+
+ memory->create(lj_type_double,n+1,n+1,"pairlj:ljtypedouble");
+
+ cuda->shared_data.pair.cut = cut_lj;
+ cuda->shared_data.pair.cut_coul= NULL;
+ cuda->shared_data.pair.coeff1 = lj1;
+ cuda->shared_data.pair.coeff2 = lj2;
+ cuda->shared_data.pair.coeff3 = lj3;
+ cuda->shared_data.pair.coeff4 = lj4;
+ cuda->shared_data.pair.coeff5 = lj_type_double;
+ cuda->shared_data.pair.offset = offset;
+ cuda->shared_data.pair.special_lj = force->special_lj;
cuda->shared_data.pair.special_coul = force->special_coul;
- }
- for (int i = 1; i <= n; i++) {
+ }
+ for (int i = 1; i <= n; i++) {
for (int j = i; j <= n; j++) {
lj_type_double[i][j] = lj_type[i][j];
lj_type_double[j][i] = lj_type[i][j];
@@ -115,47 +115,47 @@ void PairLJSDKCoulLongCuda::allocate()
void PairLJSDKCoulLongCuda::compute(int eflag, int vflag)
{
- if (eflag || vflag) ev_setup(eflag,vflag);
- if(eflag) cuda->cu_eng_vdwl->upload();
- if(eflag) cuda->cu_eng_coul->upload();
- if(vflag) cuda->cu_virial->upload();
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ if(eflag) cuda->cu_eng_vdwl->upload();
+ if(eflag) cuda->cu_eng_coul->upload();
+ if(vflag) cuda->cu_virial->upload();
- Cuda_PairLJSDKCoulLongCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);
+ Cuda_PairLJSDKCoulLongCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);
if(not cuda->shared_data.pair.collect_forces_later)
{
- if(eflag) cuda->cu_eng_vdwl->download();
- if(eflag) cuda->cu_eng_coul->download();
- if(vflag) cuda->cu_virial->download();
+ if(eflag) cuda->cu_eng_vdwl->download();
+ if(eflag) cuda->cu_eng_coul->download();
+ if(vflag) cuda->cu_virial->download();
}
-
+
}
/* ---------------------------------------------------------------------- */
void PairLJSDKCoulLongCuda::settings(int narg, char **arg)
{
- PairLJSDKCoulLong::settings(narg, arg);
- cuda->shared_data.pair.cut_global = (F_FLOAT) cut_lj_global;
- cuda->shared_data.pair.cut_coul_global = (F_FLOAT) cut_coul;
+ PairLJSDKCoulLong::settings(narg, arg);
+ cuda->shared_data.pair.cut_global = (F_FLOAT) cut_lj_global;
+ cuda->shared_data.pair.cut_coul_global = (F_FLOAT) cut_coul;
}
/* ---------------------------------------------------------------------- */
void PairLJSDKCoulLongCuda::coeff(int narg, char **arg)
{
- PairLJSDKCoulLong::coeff(narg, arg);
- allocate();
+ PairLJSDKCoulLong::coeff(narg, arg);
+ allocate();
}
void PairLJSDKCoulLongCuda::init_style()
{
- MYDBG(printf("# CUDA PairLJSDKCoulLongCuda::init_style start\n"); )
+ MYDBG(printf("# CUDA PairLJSDKCoulLongCuda::init_style start\n"); )
// request regular or rRESPA neighbor lists
int irequest;
-
- irequest = neighbor->request(this);
+
+ irequest = neighbor->request(this);
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->cudable = 1;
@@ -169,27 +169,25 @@ void PairLJSDKCoulLongCuda::init_style()
void PairLJSDKCoulLongCuda::init_list(int id, NeighList *ptr)
{
- MYDBG(printf("# CUDA PairLJSDKCoulLongCuda::init_list\n");)
- PairLJSDKCoulLong::init_list(id, ptr);
- #ifndef CUDA_USE_BINNING
- // right now we can only handle verlet (id 0), not respa
- if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
- // see Neighbor::init() for details on lammps lists' logic
- #endif
- MYDBG(printf("# CUDA PairLJSDKCoulLongCuda::init_list end\n");)
+ MYDBG(printf("# CUDA PairLJSDKCoulLongCuda::init_list\n");)
+ PairLJSDKCoulLong::init_list(id, ptr);
+ #ifndef CUDA_USE_BINNING
+ // right now we can only handle verlet (id 0), not respa
+ if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
+ // see Neighbor::init() for details on lammps lists' logic
+ #endif
+ MYDBG(printf("# CUDA PairLJSDKCoulLongCuda::init_list end\n");)
}
void PairLJSDKCoulLongCuda::ev_setup(int eflag, int vflag)
{
- int maxeatomold=maxeatom;
- PairLJSDKCoulLong::ev_setup(eflag,vflag);
-
- if (eflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
+ int maxeatomold=maxeatom;
+ PairLJSDKCoulLong::ev_setup(eflag,vflag);
- if (vflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
-
-}
+ if (eflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
+ if (vflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
+}
diff --git a/src/USER-CUDA/pair_lj_sdk_coul_long_cuda.h b/src/USER-CUDA/pair_lj_sdk_coul_long_cuda.h
index 5b678837115958501abd520dc9578999511b50ee..8debb816660798786fb92dac738b80a5a89e447f 100644
--- a/src/USER-CUDA/pair_lj_sdk_coul_long_cuda.h
+++ b/src/USER-CUDA/pair_lj_sdk_coul_long_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -36,20 +36,20 @@ namespace LAMMPS_NS {
class PairLJSDKCoulLongCuda : public PairLJSDKCoulLong
{
- public:
- PairLJSDKCoulLongCuda(class LAMMPS *);
- void compute(int, int);
- void settings(int, char **);
- void coeff(int, char **);
- void init_list(int, class NeighList *);
- void init_style();
- void ev_setup(int eflag, int vflag);
- protected:
- class Cuda *cuda;
- void allocate();
- bool allocated2;
- class CudaNeighList* cuda_neigh_list;
- double** lj_type_double;
+ public:
+ PairLJSDKCoulLongCuda(class LAMMPS *);
+ void compute(int, int);
+ void settings(int, char **);
+ void coeff(int, char **);
+ void init_list(int, class NeighList *);
+ void init_style();
+ void ev_setup(int eflag, int vflag);
+ protected:
+ class Cuda *cuda;
+ void allocate();
+ bool allocated2;
+ class CudaNeighList* cuda_neigh_list;
+ double** lj_type_double;
};
}
diff --git a/src/USER-CUDA/pair_lj_sdk_cuda.cpp b/src/USER-CUDA/pair_lj_sdk_cuda.cpp
index 6ce34418d40d2cb08fcc27fc00c80ad85761dee1..64a7a483115e37759162b3c6549e7d0a741a1ee1 100644
--- a/src/USER-CUDA/pair_lj_sdk_cuda.cpp
+++ b/src/USER-CUDA/pair_lj_sdk_cuda.cpp
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -28,7 +28,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -69,10 +69,10 @@ PairLJSDKCuda::PairLJSDKCuda(LAMMPS *lmp) : PairLJSDK(lmp)
if(cuda == NULL)
error->all(FLERR,"You cannot use a /cuda class, without activating 'cuda' acceleration. Provide '-c on' as command-line argument to LAMMPS..");
- allocated2 = false;
- lj_type_double = NULL;
- cuda->shared_data.pair.cudable_force = 1;
- cuda->setSystemParams();
+ allocated2 = false;
+ lj_type_double = NULL;
+ cuda->shared_data.pair.cudable_force = 1;
+ cuda->setSystemParams();
}
/* ----------------------------------------------------------------------
@@ -81,30 +81,30 @@ PairLJSDKCuda::PairLJSDKCuda(LAMMPS *lmp) : PairLJSDK(lmp)
void PairLJSDKCuda::allocate()
{
- if(! allocated) PairLJSDK::allocate();
- int n = atom->ntypes;
- if(! allocated2)
- {
- allocated2 = true;
-
-
- memory->create(lj_type_double,n+1,n+1,"pairlj:ljtypedouble");
-
- cuda->shared_data.pair.cut = cut;
- cuda->shared_data.pair.coeff1 = lj1;
- cuda->shared_data.pair.coeff2 = lj2;
- cuda->shared_data.pair.coeff3 = lj3;
- cuda->shared_data.pair.coeff4 = lj4;
- cuda->shared_data.pair.coeff5 = lj_type_double;
- /*cu_lj1_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj1, &cuda->shared_data.pair.coeff1_gm, (atom->ntypes+1)*(atom->ntypes+1));
- cu_lj2_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj2, &cuda->shared_data.pair.coeff2_gm, (atom->ntypes+1)*(atom->ntypes+1));
- cu_lj3_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj3, &cuda->shared_data.pair.coeff3_gm, (atom->ntypes+1)*(atom->ntypes+1));
- cu_lj4_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj4, &cuda->shared_data.pair.coeff4_gm, (atom->ntypes+1)*(atom->ntypes+1));
- cu_lj_type_double_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj_type_double, &cuda->shared_data.pair.coeff5_gm, (atom->ntypes+1)*(atom->ntypes+1));*/
- cuda->shared_data.pair.offset = offset;
- cuda->shared_data.pair.special_lj = force->special_lj;
- }
- for (int i = 1; i <= n; i++) {
+ if(! allocated) PairLJSDK::allocate();
+ int n = atom->ntypes;
+ if(! allocated2)
+ {
+ allocated2 = true;
+
+
+ memory->create(lj_type_double,n+1,n+1,"pairlj:ljtypedouble");
+
+ cuda->shared_data.pair.cut = cut;
+ cuda->shared_data.pair.coeff1 = lj1;
+ cuda->shared_data.pair.coeff2 = lj2;
+ cuda->shared_data.pair.coeff3 = lj3;
+ cuda->shared_data.pair.coeff4 = lj4;
+ cuda->shared_data.pair.coeff5 = lj_type_double;
+ /*cu_lj1_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj1, &cuda->shared_data.pair.coeff1_gm, (atom->ntypes+1)*(atom->ntypes+1));
+ cu_lj2_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj2, &cuda->shared_data.pair.coeff2_gm, (atom->ntypes+1)*(atom->ntypes+1));
+ cu_lj3_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj3, &cuda->shared_data.pair.coeff3_gm, (atom->ntypes+1)*(atom->ntypes+1));
+ cu_lj4_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj4, &cuda->shared_data.pair.coeff4_gm, (atom->ntypes+1)*(atom->ntypes+1));
+ cu_lj_type_double_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj_type_double, &cuda->shared_data.pair.coeff5_gm, (atom->ntypes+1)*(atom->ntypes+1));*/
+ cuda->shared_data.pair.offset = offset;
+ cuda->shared_data.pair.special_lj = force->special_lj;
+ }
+ for (int i = 1; i <= n; i++) {
for (int j = i; j <= n; j++) {
lj_type_double[i][j] = lj_type[i][j];
lj_type_double[j][i] = lj_type[i][j];
@@ -116,40 +116,40 @@ void PairLJSDKCuda::allocate()
void PairLJSDKCuda::compute(int eflag, int vflag)
{
- if (eflag || vflag) ev_setup(eflag,vflag);
- if(eflag) cuda->cu_eng_vdwl->upload();
- if(vflag) cuda->cu_virial->upload();
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ if(eflag) cuda->cu_eng_vdwl->upload();
+ if(vflag) cuda->cu_virial->upload();
- Cuda_PairLJSDKCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);
+ Cuda_PairLJSDKCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);
if(not cuda->shared_data.pair.collect_forces_later)
{
- if(eflag) cuda->cu_eng_vdwl->download();
- if(vflag) cuda->cu_virial->download();
+ if(eflag) cuda->cu_eng_vdwl->download();
+ if(vflag) cuda->cu_virial->download();
}
-
+
}
/* ---------------------------------------------------------------------- */
void PairLJSDKCuda::settings(int narg, char **arg)
{
- PairLJSDK::settings(narg, arg);
- cuda->shared_data.pair.cut_global = (F_FLOAT) cut_global;
+ PairLJSDK::settings(narg, arg);
+ cuda->shared_data.pair.cut_global = (F_FLOAT) cut_global;
}
/* ---------------------------------------------------------------------- */
void PairLJSDKCuda::coeff(int narg, char **arg)
{
- PairLJSDK::coeff(narg, arg);
- allocate();
+ PairLJSDK::coeff(narg, arg);
+ allocate();
}
void PairLJSDKCuda::init_style()
{
MYDBG(printf("# CUDA PairLJSDKCuda::init_style start\n"); )
-
+
int irequest = neighbor->request(this);
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->half = 0;
@@ -160,27 +160,25 @@ void PairLJSDKCuda::init_style()
void PairLJSDKCuda::init_list(int id, NeighList *ptr)
{
- MYDBG(printf("# CUDA PairLJSDKCuda::init_list\n");)
- PairLJSDK::init_list(id, ptr);
- #ifndef CUDA_USE_BINNING
- // right now we can only handle verlet (id 0), not respa
- if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
- // see Neighbor::init() for details on lammps lists' logic
- #endif
- MYDBG(printf("# CUDA PairLJSDKCuda::init_list end\n");)
+ MYDBG(printf("# CUDA PairLJSDKCuda::init_list\n");)
+ PairLJSDK::init_list(id, ptr);
+ #ifndef CUDA_USE_BINNING
+ // right now we can only handle verlet (id 0), not respa
+ if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
+ // see Neighbor::init() for details on lammps lists' logic
+ #endif
+ MYDBG(printf("# CUDA PairLJSDKCuda::init_list end\n");)
}
void PairLJSDKCuda::ev_setup(int eflag, int vflag)
{
- int maxeatomold=maxeatom;
- PairLJSDK::ev_setup(eflag,vflag);
-
- if (eflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
+ int maxeatomold=maxeatom;
+ PairLJSDK::ev_setup(eflag,vflag);
- if (vflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
-
-}
+ if (eflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
+ if (vflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
+}
diff --git a/src/USER-CUDA/pair_lj_sdk_cuda.h b/src/USER-CUDA/pair_lj_sdk_cuda.h
index adc50410218d58076854a03ee8a427db09f0f56f..f5737adadc8da045dadc663ae97d5fc33e3f66b7 100644
--- a/src/USER-CUDA/pair_lj_sdk_cuda.h
+++ b/src/USER-CUDA/pair_lj_sdk_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -37,25 +37,25 @@ namespace LAMMPS_NS {
class PairLJSDKCuda : public PairLJSDK
{
- public:
- PairLJSDKCuda(class LAMMPS *);
- void compute(int, int);
- void settings(int, char **);
- void coeff(int, char **);
- void init_list(int, class NeighList *);
- void init_style();
- void ev_setup(int eflag, int vflag);
- protected:
- class Cuda *cuda;
- void allocate();
- bool allocated2;
- class CudaNeighList* cuda_neigh_list;
- double** lj_type_double;
- cCudaData<double , F_FLOAT , x >* cu_lj1_gm;
- cCudaData<double , F_FLOAT , x >* cu_lj2_gm;
- cCudaData<double , F_FLOAT , x >* cu_lj3_gm;
- cCudaData<double , F_FLOAT , x >* cu_lj4_gm;
- cCudaData<double , F_FLOAT , x >* cu_lj_type_double_gm;
+ public:
+ PairLJSDKCuda(class LAMMPS *);
+ void compute(int, int);
+ void settings(int, char **);
+ void coeff(int, char **);
+ void init_list(int, class NeighList *);
+ void init_style();
+ void ev_setup(int eflag, int vflag);
+ protected:
+ class Cuda *cuda;
+ void allocate();
+ bool allocated2;
+ class CudaNeighList* cuda_neigh_list;
+ double** lj_type_double;
+ cCudaData<double , F_FLOAT , x >* cu_lj1_gm;
+ cCudaData<double , F_FLOAT , x >* cu_lj2_gm;
+ cCudaData<double , F_FLOAT , x >* cu_lj3_gm;
+ cCudaData<double , F_FLOAT , x >* cu_lj4_gm;
+ cCudaData<double , F_FLOAT , x >* cu_lj_type_double_gm;
};
}
diff --git a/src/USER-CUDA/pair_lj_smooth_cuda.cpp b/src/USER-CUDA/pair_lj_smooth_cuda.cpp
index 84a4d9086a5e1a09354d71897ef7bac1da1163a5..62a7a7378d8f9f52ac35e102ea70d21f38a1ad6a 100644
--- a/src/USER-CUDA/pair_lj_smooth_cuda.cpp
+++ b/src/USER-CUDA/pair_lj_smooth_cuda.cpp
@@ -1,23 +1,23 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
Contributing author: Paul Crozier (SNL)
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -54,10 +54,10 @@ PairLJSmoothCuda::PairLJSmoothCuda(LAMMPS *lmp) : PairLJSmooth(lmp)
if(cuda == NULL)
error->all(FLERR,"You cannot use a /cuda class, without activating 'cuda' acceleration. Provide '-c on' as command-line argument to LAMMPS..");
- allocated2 = false;
- cuda->shared_data.pair.cudable_force = 1;
- cuda->shared_data.pair.use_block_per_atom = 0;
- cuda->setSystemParams();
+ allocated2 = false;
+ cuda->shared_data.pair.cudable_force = 1;
+ cuda->shared_data.pair.use_block_per_atom = 0;
+ cuda->setSystemParams();
}
/* ----------------------------------------------------------------------
@@ -66,115 +66,113 @@ PairLJSmoothCuda::PairLJSmoothCuda(LAMMPS *lmp) : PairLJSmooth(lmp)
void PairLJSmoothCuda::allocate()
{
- if(! allocated) PairLJSmooth::allocate();
- if(! allocated2)
- {
- cuda->accelerator(0,NULL);
- allocated2 = true;
- cuda->shared_data.pair.cut = cut;
- cuda->shared_data.pair.cut_inner = cut_inner;
- cuda->shared_data.pair.coeff1 = lj1;
- cuda->shared_data.pair.coeff2 = lj2;
- cuda->shared_data.pair.coeff3 = lj3;
- cuda->shared_data.pair.coeff4 = lj4;
- cuda->shared_data.pair.coeff5 = ljsw1;
- cuda->shared_data.pair.coeff6 = ljsw2;
- cuda->shared_data.pair.coeff7 = ljsw3;
- cuda->shared_data.pair.coeff8 = ljsw4;
- cuda->shared_data.pair.coeff9 = ljsw0;
- cuda->shared_data.pair.special_lj = force->special_lj;
- cu_lj1_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj1, &cuda->shared_data.pair.coeff1_gm, (atom->ntypes+1)*(atom->ntypes+1));
- cu_lj2_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj2, &cuda->shared_data.pair.coeff2_gm, (atom->ntypes+1)*(atom->ntypes+1));
- cu_lj3_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj3, &cuda->shared_data.pair.coeff3_gm, (atom->ntypes+1)*(atom->ntypes+1));
- cu_lj4_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj4, &cuda->shared_data.pair.coeff4_gm, (atom->ntypes+1)*(atom->ntypes+1));
- cu_ljsw0_gm = new cCudaData<double, F_FLOAT, x> ((double*)ljsw0, &cuda->shared_data.pair.coeff9_gm, (atom->ntypes+1)*(atom->ntypes+1));
- cu_ljsw1_gm = new cCudaData<double, F_FLOAT, x> ((double*)ljsw1, &cuda->shared_data.pair.coeff5_gm, (atom->ntypes+1)*(atom->ntypes+1));
- cu_ljsw2_gm = new cCudaData<double, F_FLOAT, x> ((double*)ljsw2, &cuda->shared_data.pair.coeff6_gm, (atom->ntypes+1)*(atom->ntypes+1));
- cu_ljsw3_gm = new cCudaData<double, F_FLOAT, x> ((double*)ljsw3, &cuda->shared_data.pair.coeff7_gm, (atom->ntypes+1)*(atom->ntypes+1));
- cu_ljsw4_gm = new cCudaData<double, F_FLOAT, x> ((double*)ljsw4, &cuda->shared_data.pair.coeff8_gm, (atom->ntypes+1)*(atom->ntypes+1));
- }
+ if(! allocated) PairLJSmooth::allocate();
+ if(! allocated2)
+ {
+ cuda->accelerator(0,NULL);
+ allocated2 = true;
+ cuda->shared_data.pair.cut = cut;
+ cuda->shared_data.pair.cut_inner = cut_inner;
+ cuda->shared_data.pair.coeff1 = lj1;
+ cuda->shared_data.pair.coeff2 = lj2;
+ cuda->shared_data.pair.coeff3 = lj3;
+ cuda->shared_data.pair.coeff4 = lj4;
+ cuda->shared_data.pair.coeff5 = ljsw1;
+ cuda->shared_data.pair.coeff6 = ljsw2;
+ cuda->shared_data.pair.coeff7 = ljsw3;
+ cuda->shared_data.pair.coeff8 = ljsw4;
+ cuda->shared_data.pair.coeff9 = ljsw0;
+ cuda->shared_data.pair.special_lj = force->special_lj;
+ cu_lj1_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj1, &cuda->shared_data.pair.coeff1_gm, (atom->ntypes+1)*(atom->ntypes+1));
+ cu_lj2_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj2, &cuda->shared_data.pair.coeff2_gm, (atom->ntypes+1)*(atom->ntypes+1));
+ cu_lj3_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj3, &cuda->shared_data.pair.coeff3_gm, (atom->ntypes+1)*(atom->ntypes+1));
+ cu_lj4_gm = new cCudaData<double, F_FLOAT, x> ((double*)lj4, &cuda->shared_data.pair.coeff4_gm, (atom->ntypes+1)*(atom->ntypes+1));
+ cu_ljsw0_gm = new cCudaData<double, F_FLOAT, x> ((double*)ljsw0, &cuda->shared_data.pair.coeff9_gm, (atom->ntypes+1)*(atom->ntypes+1));
+ cu_ljsw1_gm = new cCudaData<double, F_FLOAT, x> ((double*)ljsw1, &cuda->shared_data.pair.coeff5_gm, (atom->ntypes+1)*(atom->ntypes+1));
+ cu_ljsw2_gm = new cCudaData<double, F_FLOAT, x> ((double*)ljsw2, &cuda->shared_data.pair.coeff6_gm, (atom->ntypes+1)*(atom->ntypes+1));
+ cu_ljsw3_gm = new cCudaData<double, F_FLOAT, x> ((double*)ljsw3, &cuda->shared_data.pair.coeff7_gm, (atom->ntypes+1)*(atom->ntypes+1));
+ cu_ljsw4_gm = new cCudaData<double, F_FLOAT, x> ((double*)ljsw4, &cuda->shared_data.pair.coeff8_gm, (atom->ntypes+1)*(atom->ntypes+1));
+ }
}
/* ---------------------------------------------------------------------- */
void PairLJSmoothCuda::compute(int eflag, int vflag)
{
- if (eflag || vflag) ev_setup(eflag,vflag);
- if(not cuda->shared_data.pair.collect_forces_later)
- {
- if(eflag) cuda->cu_eng_vdwl->upload();
- if(vflag) cuda->cu_virial->upload();
- }
-
- Cuda_PairLJSmoothCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);
-
- if(not cuda->shared_data.pair.collect_forces_later)
- {
- if(eflag) cuda->cu_eng_vdwl->download();
- if(vflag) cuda->cu_virial->download();
- }
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ if(not cuda->shared_data.pair.collect_forces_later)
+ {
+ if(eflag) cuda->cu_eng_vdwl->upload();
+ if(vflag) cuda->cu_virial->upload();
+ }
+
+ Cuda_PairLJSmoothCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);
+
+ if(not cuda->shared_data.pair.collect_forces_later)
+ {
+ if(eflag) cuda->cu_eng_vdwl->download();
+ if(vflag) cuda->cu_virial->download();
+ }
}
/* ---------------------------------------------------------------------- */
void PairLJSmoothCuda::settings(int narg, char **arg)
{
- PairLJSmooth::settings(narg, arg);
- cuda->shared_data.pair.cut_global = (F_FLOAT) cut_global;
- cuda->shared_data.pair.cut_inner_global = (F_FLOAT) cut_inner_global;
+ PairLJSmooth::settings(narg, arg);
+ cuda->shared_data.pair.cut_global = (F_FLOAT) cut_global;
+ cuda->shared_data.pair.cut_inner_global = (F_FLOAT) cut_inner_global;
}
/* ---------------------------------------------------------------------- */
void PairLJSmoothCuda::coeff(int narg, char **arg)
{
- PairLJSmooth::coeff(narg, arg);
- allocate();
+ PairLJSmooth::coeff(narg, arg);
+ allocate();
}
void PairLJSmoothCuda::init_style()
{
// request regular or rRESPA neighbor lists
- if(atom->molecular)
- {
- cuda->shared_data.pair.collect_forces_later = 1;
- }
-
+ if(atom->molecular)
+ {
+ cuda->shared_data.pair.collect_forces_later = 1;
+ }
+
int irequest;
-
- irequest = neighbor->request(this);
+
+ irequest = neighbor->request(this);
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->half = 0;
- neighbor->requests[irequest]->cudable = 1;
+ neighbor->requests[irequest]->cudable = 1;
+
-
}
void PairLJSmoothCuda::init_list(int id, NeighList *ptr)
{
- MYDBG(printf("# CUDA PairLJSmoothCuda::init_list\n");)
- PairLJSmooth::init_list(id, ptr);
- #ifndef CUDA_USE_BINNING
- // right now we can only handle verlet (id 0), not respa
- if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
- // see Neighbor::init() for details on lammps lists' logic
- #endif
- MYDBG(printf("# CUDA PairLJSmoothCuda::init_list end\n");)
+ MYDBG(printf("# CUDA PairLJSmoothCuda::init_list\n");)
+ PairLJSmooth::init_list(id, ptr);
+ #ifndef CUDA_USE_BINNING
+ // right now we can only handle verlet (id 0), not respa
+ if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
+ // see Neighbor::init() for details on lammps lists' logic
+ #endif
+ MYDBG(printf("# CUDA PairLJSmoothCuda::init_list end\n");)
}
void PairLJSmoothCuda::ev_setup(int eflag, int vflag)
{
- int maxeatomold=maxeatom;
- PairLJSmooth::ev_setup(eflag,vflag);
+ int maxeatomold=maxeatom;
+ PairLJSmooth::ev_setup(eflag,vflag);
- if (eflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
-
- if (vflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
-
-}
+ if (eflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
+ if (vflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
+}
diff --git a/src/USER-CUDA/pair_lj_smooth_cuda.h b/src/USER-CUDA/pair_lj_smooth_cuda.h
index 32f6b4fabc045642c58cb02105d356768c3fe6c7..909ac186af2b99114e131791c16cc0275b5a08cb 100644
--- a/src/USER-CUDA/pair_lj_smooth_cuda.h
+++ b/src/USER-CUDA/pair_lj_smooth_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -37,28 +37,28 @@ namespace LAMMPS_NS {
class PairLJSmoothCuda : public PairLJSmooth
{
- public:
- PairLJSmoothCuda(class LAMMPS *);
- void compute(int, int);
- void settings(int, char **);
- void coeff(int, char **);
- void init_list(int, class NeighList *);
- void init_style();
- void ev_setup(int eflag, int vflag);
- protected:
- class Cuda *cuda;
- void allocate();
- bool allocated2;
- class CudaNeighList* cuda_neigh_list;
- cCudaData<double , F_FLOAT , x >* cu_lj1_gm;
- cCudaData<double , F_FLOAT , x >* cu_lj2_gm;
- cCudaData<double , F_FLOAT , x >* cu_lj3_gm;
- cCudaData<double , F_FLOAT , x >* cu_lj4_gm;
- cCudaData<double , F_FLOAT , x >* cu_ljsw0_gm;
- cCudaData<double , F_FLOAT , x >* cu_ljsw1_gm;
- cCudaData<double , F_FLOAT , x >* cu_ljsw2_gm;
- cCudaData<double , F_FLOAT , x >* cu_ljsw3_gm;
- cCudaData<double , F_FLOAT , x >* cu_ljsw4_gm;
+ public:
+ PairLJSmoothCuda(class LAMMPS *);
+ void compute(int, int);
+ void settings(int, char **);
+ void coeff(int, char **);
+ void init_list(int, class NeighList *);
+ void init_style();
+ void ev_setup(int eflag, int vflag);
+ protected:
+ class Cuda *cuda;
+ void allocate();
+ bool allocated2;
+ class CudaNeighList* cuda_neigh_list;
+ cCudaData<double , F_FLOAT , x >* cu_lj1_gm;
+ cCudaData<double , F_FLOAT , x >* cu_lj2_gm;
+ cCudaData<double , F_FLOAT , x >* cu_lj3_gm;
+ cCudaData<double , F_FLOAT , x >* cu_lj4_gm;
+ cCudaData<double , F_FLOAT , x >* cu_ljsw0_gm;
+ cCudaData<double , F_FLOAT , x >* cu_ljsw1_gm;
+ cCudaData<double , F_FLOAT , x >* cu_ljsw2_gm;
+ cCudaData<double , F_FLOAT , x >* cu_ljsw3_gm;
+ cCudaData<double , F_FLOAT , x >* cu_ljsw4_gm;
};
diff --git a/src/USER-CUDA/pair_morse_cuda.cpp b/src/USER-CUDA/pair_morse_cuda.cpp
index ec2375fb924593f0d0275e4043f301a36282c4b4..ec5fabd5e89802bb6c96f39e2f2eccfd8ca14efe 100644
--- a/src/USER-CUDA/pair_morse_cuda.cpp
+++ b/src/USER-CUDA/pair_morse_cuda.cpp
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -28,7 +28,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -69,9 +69,9 @@ PairMorseCuda::PairMorseCuda(LAMMPS *lmp) : PairMorse(lmp)
if(cuda == NULL)
error->all(FLERR,"You cannot use a /cuda class, without activating 'cuda' acceleration. Provide '-c on' as command-line argument to LAMMPS..");
- allocated2 = false;
- cuda->shared_data.pair.cudable_force = 1;
- cuda->setSystemParams();
+ allocated2 = false;
+ cuda->shared_data.pair.cudable_force = 1;
+ cuda->setSystemParams();
}
/* ----------------------------------------------------------------------
@@ -80,67 +80,67 @@ PairMorseCuda::PairMorseCuda(LAMMPS *lmp) : PairMorse(lmp)
void PairMorseCuda::allocate()
{
- if(! allocated) PairMorse::allocate();
- if(! allocated2)
- {
- allocated2 = true;
- cuda->shared_data.pair.cut = cut;
- cuda->shared_data.pair.coeff1 = r0;
- cuda->shared_data.pair.coeff2 = alpha;
- cuda->shared_data.pair.coeff3 = morse1;
- cuda->shared_data.pair.coeff4 = d0;
- cuda->shared_data.pair.offset = offset;
- cuda->shared_data.pair.special_lj = force->special_lj;
- }
+ if(! allocated) PairMorse::allocate();
+ if(! allocated2)
+ {
+ allocated2 = true;
+ cuda->shared_data.pair.cut = cut;
+ cuda->shared_data.pair.coeff1 = r0;
+ cuda->shared_data.pair.coeff2 = alpha;
+ cuda->shared_data.pair.coeff3 = morse1;
+ cuda->shared_data.pair.coeff4 = d0;
+ cuda->shared_data.pair.offset = offset;
+ cuda->shared_data.pair.special_lj = force->special_lj;
+ }
}
/* ---------------------------------------------------------------------- */
void PairMorseCuda::compute(int eflag, int vflag)
{
- if (eflag || vflag) ev_setup(eflag,vflag);
- if(eflag) cuda->cu_eng_vdwl->upload();
- if(vflag) cuda->cu_virial->upload();
-
- Cuda_PairMorseCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ if(eflag) cuda->cu_eng_vdwl->upload();
+ if(vflag) cuda->cu_virial->upload();
+
+ Cuda_PairMorseCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);
if(not cuda->shared_data.pair.collect_forces_later)
{
- if(eflag) cuda->cu_eng_vdwl->download();
- if(vflag) cuda->cu_virial->download();
+ if(eflag) cuda->cu_eng_vdwl->download();
+ if(vflag) cuda->cu_virial->download();
}
-
+
}
/* ---------------------------------------------------------------------- */
void PairMorseCuda::settings(int narg, char **arg)
{
- PairMorse::settings(narg, arg);
- cuda->shared_data.pair.cut_global = (F_FLOAT) cut_global;
+ PairMorse::settings(narg, arg);
+ cuda->shared_data.pair.cut_global = (F_FLOAT) cut_global;
}
/* ---------------------------------------------------------------------- */
void PairMorseCuda::coeff(int narg, char **arg)
{
- PairMorse::coeff(narg, arg);
- allocate();
+ PairMorse::coeff(narg, arg);
+ allocate();
}
void PairMorseCuda::init_style()
{
- MYDBG(printf("# CUDA PairMorseCuda::init_style start\n"); )
+ MYDBG(printf("# CUDA PairMorseCuda::init_style start\n"); )
// request regular or rRESPA neighbor lists
int irequest;
-
+
if (update->whichflag == 0 && strstr(update->integrate_style,"respa")) {
- }
- else
+ }
+ else
{
- irequest = neighbor->request(this);
+ irequest = neighbor->request(this);
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->cudable = 1;
@@ -153,27 +153,25 @@ void PairMorseCuda::init_style()
void PairMorseCuda::init_list(int id, NeighList *ptr)
{
- MYDBG(printf("# CUDA PairMorseCuda::init_list\n");)
- PairMorse::init_list(id, ptr);
- #ifndef CUDA_USE_BINNING
- // right now we can only handle verlet (id 0), not respa
- if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
- // see Neighbor::init() for details on lammps lists' logic
- #endif
- MYDBG(printf("# CUDA PairMorseCuda::init_list end\n");)
+ MYDBG(printf("# CUDA PairMorseCuda::init_list\n");)
+ PairMorse::init_list(id, ptr);
+ #ifndef CUDA_USE_BINNING
+ // right now we can only handle verlet (id 0), not respa
+ if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
+ // see Neighbor::init() for details on lammps lists' logic
+ #endif
+ MYDBG(printf("# CUDA PairMorseCuda::init_list end\n");)
}
void PairMorseCuda::ev_setup(int eflag, int vflag)
{
- int maxeatomold=maxeatom;
- PairMorse::ev_setup(eflag,vflag);
+ int maxeatomold=maxeatom;
+ PairMorse::ev_setup(eflag,vflag);
- if (eflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
-
- if (vflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
-
-}
+ if (eflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
+ if (vflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
+}
diff --git a/src/USER-CUDA/pair_morse_cuda.h b/src/USER-CUDA/pair_morse_cuda.h
index aae40294bafc060ae73db578ae4b5b4cb627aa88..1ce784631d34f4fbbabab06405ba4b71db61f2b0 100644
--- a/src/USER-CUDA/pair_morse_cuda.h
+++ b/src/USER-CUDA/pair_morse_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -36,19 +36,19 @@ namespace LAMMPS_NS {
class PairMorseCuda : public PairMorse
{
- public:
- PairMorseCuda(class LAMMPS *);
- void compute(int, int);
- void settings(int, char **);
- void coeff(int, char **);
- void init_list(int, class NeighList *);
- void init_style();
- void ev_setup(int eflag, int vflag);
- protected:
- class Cuda *cuda;
- void allocate();
- bool allocated2;
- class CudaNeighList* cuda_neigh_list;
+ public:
+ PairMorseCuda(class LAMMPS *);
+ void compute(int, int);
+ void settings(int, char **);
+ void coeff(int, char **);
+ void init_list(int, class NeighList *);
+ void init_style();
+ void ev_setup(int eflag, int vflag);
+ protected:
+ class Cuda *cuda;
+ void allocate();
+ bool allocated2;
+ class CudaNeighList* cuda_neigh_list;
};
}
diff --git a/src/USER-CUDA/pair_sw_cuda.cpp b/src/USER-CUDA/pair_sw_cuda.cpp
index 601ad7f2cffd28e8c67e5116973a508de0cabfa6..89d1d744c94a164cfeddcb5343359e4964422930 100644
--- a/src/USER-CUDA/pair_sw_cuda.cpp
+++ b/src/USER-CUDA/pair_sw_cuda.cpp
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -28,7 +28,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -71,9 +71,9 @@ PairSWCuda::PairSWCuda(LAMMPS *lmp) : PairSW(lmp)
if(cuda == NULL)
error->all(FLERR,"You cannot use a /cuda class, without activating 'cuda' acceleration. Provide '-c on' as command-line argument to LAMMPS..");
- allocated2 = false;
- params_f = NULL;
- cuda->setSystemParams();
+ allocated2 = false;
+ params_f = NULL;
+ cuda->setSystemParams();
cuda->shared_data.pair.cudable_force = 1;
cuda->shared_data.pair.override_block_per_atom = 0;
cuda->shared_data.pair.neighall = true;
@@ -86,14 +86,14 @@ PairSWCuda::PairSWCuda(LAMMPS *lmp) : PairSW(lmp)
void PairSWCuda::allocate()
{
- if(! allocated) PairSW::allocate();
- if(! allocated2)
- {
- allocated2 = true;
- cuda->shared_data.pair.cutsq = cutsq;
- cuda->shared_data.pair.special_lj = force->special_lj;
- cuda->shared_data.pair.special_coul = force->special_coul;
- }
+ if(! allocated) PairSW::allocate();
+ if(! allocated2)
+ {
+ allocated2 = true;
+ cuda->shared_data.pair.cutsq = cutsq;
+ cuda->shared_data.pair.special_lj = force->special_lj;
+ cuda->shared_data.pair.special_coul = force->special_coul;
+ }
}
/* ---------------------------------------------------------------------- */
@@ -101,15 +101,15 @@ void PairSWCuda::allocate()
void PairSWCuda::compute(int eflag, int vflag)
{
if(!init) {Cuda_PairSWCuda_Init(&cuda->shared_data,params_f,map, &elem2param[0][0][0],nelements); init=true;}
- if (eflag || vflag) ev_setup(eflag,vflag);
- if(eflag) cuda->cu_eng_vdwl->upload();
- if(vflag) cuda->cu_virial->upload();
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ if(eflag) cuda->cu_eng_vdwl->upload();
+ if(vflag) cuda->cu_virial->upload();
- Cuda_PairSWCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);//,&elem2param[0][0][0],map
+ Cuda_PairSWCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);//,&elem2param[0][0][0],map
if(not cuda->shared_data.pair.collect_forces_later)
{
- if(eflag) cuda->cu_eng_vdwl->download();
- if(vflag) cuda->cu_virial->download();
+ if(eflag) cuda->cu_eng_vdwl->download();
+ if(vflag) cuda->cu_virial->download();
}
}
@@ -117,15 +117,15 @@ void PairSWCuda::compute(int eflag, int vflag)
void PairSWCuda::settings(int narg, char **arg)
{
- PairSW::settings(narg, arg);
+ PairSW::settings(narg, arg);
}
/* ---------------------------------------------------------------------- */
void PairSWCuda::coeff(int narg, char **arg)
{
- PairSW::coeff(narg, arg);
- allocate();
+ PairSW::coeff(narg, arg);
+ allocate();
params_f = (ParamSW_Float *) memory->srealloc(params_f,maxparam*sizeof(ParamSW_Float),
"pair:params_f");
for(int i=0;i<maxparam;i++)
@@ -164,11 +164,11 @@ void PairSWCuda::coeff(int narg, char **arg)
void PairSWCuda::init_style()
{
- MYDBG(printf("# CUDA PairSWCuda::init_style start\n"); )
+ MYDBG(printf("# CUDA PairSWCuda::init_style start\n"); )
int irequest;
-
- irequest = neighbor->request(this);
+
+ irequest = neighbor->request(this);
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->cudable = 1;
@@ -180,12 +180,12 @@ void PairSWCuda::init_style()
void PairSWCuda::init_list(int id, NeighList *ptr)
{
- MYDBG(printf("# CUDA PairSWCuda::init_list\n");)
- PairSW::init_list(id, ptr);
- // right now we can only handle verlet (id 0), not respa
- if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
- // see Neighbor::init() for details on lammps lists' logic
- MYDBG(printf("# CUDA PairSWCuda::init_list end\n");)
+ MYDBG(printf("# CUDA PairSWCuda::init_list\n");)
+ PairSW::init_list(id, ptr);
+ // right now we can only handle verlet (id 0), not respa
+ if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
+ // see Neighbor::init() for details on lammps lists' logic
+ MYDBG(printf("# CUDA PairSWCuda::init_list end\n");)
cu_params_f = (ParamSW_Float*) CudaWrapper_AllocCudaData(sizeof(ParamSW_Float)*maxparam);
CudaWrapper_UploadCudaData((void*) params_f,(void*) cu_params_f,sizeof(ParamSW_Float)*maxparam);
cu_elem2param = new cCudaData<int, int, xyz > ((int*) elem2param, nelements,nelements,nelements);
@@ -196,14 +196,12 @@ void PairSWCuda::init_list(int id, NeighList *ptr)
void PairSWCuda::ev_setup(int eflag, int vflag)
{
- int maxeatomold=maxeatom;
- PairSW::ev_setup(eflag,vflag);
+ int maxeatomold=maxeatom;
+ PairSW::ev_setup(eflag,vflag);
- if (eflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
+ if (eflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
- if (vflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
+ if (vflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
}
-
-
diff --git a/src/USER-CUDA/pair_sw_cuda.h b/src/USER-CUDA/pair_sw_cuda.h
index be9ba9bb3d9d7afeed3f4c79aa4ab38e17e9093c..8a871d9d40517500e5c818310453df9a5ba2ad74 100644
--- a/src/USER-CUDA/pair_sw_cuda.h
+++ b/src/USER-CUDA/pair_sw_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -38,23 +38,23 @@ namespace LAMMPS_NS {
class PairSWCuda : public PairSW
{
- public:
- PairSWCuda(class LAMMPS *);
- void compute(int, int);
- void settings(int, char **);
- void coeff(int, char **);
- void init_list(int, class NeighList *);
- void init_style();
- void ev_setup(int eflag, int vflag);
- protected:
-
- class Cuda *cuda;
- void allocate();
- bool allocated2;
- class CudaNeighList* cuda_neigh_list;
- ParamSW_Float* params_f;
- ParamSW_Float* cu_params_f;
- cCudaData<int, int, xyz >* cu_elem2param;
+ public:
+ PairSWCuda(class LAMMPS *);
+ void compute(int, int);
+ void settings(int, char **);
+ void coeff(int, char **);
+ void init_list(int, class NeighList *);
+ void init_style();
+ void ev_setup(int eflag, int vflag);
+ protected:
+
+ class Cuda *cuda;
+ void allocate();
+ bool allocated2;
+ class CudaNeighList* cuda_neigh_list;
+ ParamSW_Float* params_f;
+ ParamSW_Float* cu_params_f;
+ cCudaData<int, int, xyz >* cu_elem2param;
cCudaData<int, int, x >* cu_map;
bool init;
bool iszbl;
diff --git a/src/USER-CUDA/pair_tersoff_cuda.cpp b/src/USER-CUDA/pair_tersoff_cuda.cpp
index 4f1dba4e31e583e35130abe8e6ff783540c0687e..9ce69ae3a60f0f1ad3e8c8aea016c54b0c0a50bd 100644
--- a/src/USER-CUDA/pair_tersoff_cuda.cpp
+++ b/src/USER-CUDA/pair_tersoff_cuda.cpp
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -28,7 +28,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -71,9 +71,9 @@ PairTersoffCuda::PairTersoffCuda(LAMMPS *lmp) : PairTersoff(lmp)
if(cuda == NULL)
error->all(FLERR,"You cannot use a /cuda class, without activating 'cuda' acceleration. Provide '-c on' as command-line argument to LAMMPS..");
- allocated2 = false;
- params_f = NULL;
- cuda->setSystemParams();
+ allocated2 = false;
+ params_f = NULL;
+ cuda->setSystemParams();
cuda->shared_data.pair.cudable_force = 1;
cuda->shared_data.pair.override_block_per_atom = 0;
cuda->shared_data.pair.neighall = true;
@@ -87,14 +87,14 @@ PairTersoffCuda::PairTersoffCuda(LAMMPS *lmp) : PairTersoff(lmp)
void PairTersoffCuda::allocate()
{
- if(! allocated) PairTersoff::allocate();
- if(! allocated2)
- {
- allocated2 = true;
- cuda->shared_data.pair.cutsq = cutsq;
- cuda->shared_data.pair.special_lj = force->special_lj;
- cuda->shared_data.pair.special_coul = force->special_coul;
- }
+ if(! allocated) PairTersoff::allocate();
+ if(! allocated2)
+ {
+ allocated2 = true;
+ cuda->shared_data.pair.cutsq = cutsq;
+ cuda->shared_data.pair.special_lj = force->special_lj;
+ cuda->shared_data.pair.special_coul = force->special_coul;
+ }
}
/* ---------------------------------------------------------------------- */
@@ -102,15 +102,15 @@ void PairTersoffCuda::allocate()
void PairTersoffCuda::compute(int eflag, int vflag)
{
if(!init) {Cuda_PairTersoffCuda_Init(&cuda->shared_data,params_f,map, &elem2param[0][0][0],nelements,iszbl); init=true;}
- if (eflag || vflag) ev_setup(eflag,vflag);
- if(eflag) cuda->cu_eng_vdwl->upload();
- if(vflag) cuda->cu_virial->upload();
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ if(eflag) cuda->cu_eng_vdwl->upload();
+ if(vflag) cuda->cu_virial->upload();
- Cuda_PairTersoffCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);//,&elem2param[0][0][0],map
+ Cuda_PairTersoffCuda(& cuda->shared_data, & cuda_neigh_list->sneighlist, eflag, vflag, eflag_atom, vflag_atom);//,&elem2param[0][0][0],map
if(not cuda->shared_data.pair.collect_forces_later)
{
- if(eflag) cuda->cu_eng_vdwl->download();
- if(vflag) cuda->cu_virial->download();
+ if(eflag) cuda->cu_eng_vdwl->download();
+ if(vflag) cuda->cu_virial->download();
}
}
@@ -118,15 +118,15 @@ void PairTersoffCuda::compute(int eflag, int vflag)
void PairTersoffCuda::settings(int narg, char **arg)
{
- PairTersoff::settings(narg, arg);
+ PairTersoff::settings(narg, arg);
}
/* ---------------------------------------------------------------------- */
void PairTersoffCuda::coeff(int narg, char **arg)
{
- PairTersoff::coeff(narg, arg);
- allocate();
+ PairTersoff::coeff(narg, arg);
+ allocate();
params_f = (Param_Float *) memory->srealloc(params_f,maxparam*sizeof(Param_Float),
"pair:params_f");
for(int i=0;i<maxparam;i++)
@@ -161,11 +161,11 @@ void PairTersoffCuda::coeff(int narg, char **arg)
void PairTersoffCuda::init_style()
{
- MYDBG(printf("# CUDA PairTersoffCuda::init_style start\n"); )
+ MYDBG(printf("# CUDA PairTersoffCuda::init_style start\n"); )
int irequest;
-
- irequest = neighbor->request(this);
+
+ irequest = neighbor->request(this);
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->cudable = 1;
@@ -177,12 +177,12 @@ void PairTersoffCuda::init_style()
void PairTersoffCuda::init_list(int id, NeighList *ptr)
{
- MYDBG(printf("# CUDA PairTersoffCuda::init_list\n");)
- PairTersoff::init_list(id, ptr);
- // right now we can only handle verlet (id 0), not respa
- if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
- // see Neighbor::init() for details on lammps lists' logic
- MYDBG(printf("# CUDA PairTersoffCuda::init_list end\n");)
+ MYDBG(printf("# CUDA PairTersoffCuda::init_list\n");)
+ PairTersoff::init_list(id, ptr);
+ // right now we can only handle verlet (id 0), not respa
+ if(id == 0) cuda_neigh_list = cuda->registerNeighborList(ptr);
+ // see Neighbor::init() for details on lammps lists' logic
+ MYDBG(printf("# CUDA PairTersoffCuda::init_list end\n");)
cu_params_f = (Param_Float*) CudaWrapper_AllocCudaData(sizeof(Param_Float)*maxparam);
CudaWrapper_UploadCudaData((void*) params_f,(void*) cu_params_f,sizeof(Param_Float)*maxparam);
cu_elem2param = new cCudaData<int, int, xyz > ((int*) elem2param, nelements,nelements,nelements);
@@ -193,14 +193,12 @@ void PairTersoffCuda::init_list(int id, NeighList *ptr)
void PairTersoffCuda::ev_setup(int eflag, int vflag)
{
- int maxeatomold=maxeatom;
- PairTersoff::ev_setup(eflag,vflag);
+ int maxeatomold=maxeatom;
+ PairTersoff::ev_setup(eflag,vflag);
- if (eflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
+ if (eflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_eatom; cuda->cu_eatom = new cCudaData<double, ENERGY_FLOAT, x > ((double*)eatom, & cuda->shared_data.atom.eatom , atom->nmax );}
- if (vflag_atom && atom->nmax > maxeatomold)
- {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
+ if (vflag_atom && atom->nmax > maxeatomold)
+ {delete cuda->cu_vatom; cuda->cu_vatom = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)vatom, & cuda->shared_data.atom.vatom , atom->nmax, 6 );}
}
-
-
diff --git a/src/USER-CUDA/pair_tersoff_cuda.h b/src/USER-CUDA/pair_tersoff_cuda.h
index 34a06f91a9dc7ba4da4beaea0a6e85950689ade7..02885dbb30125b2f379978b524a74aab9d1fa236 100644
--- a/src/USER-CUDA/pair_tersoff_cuda.h
+++ b/src/USER-CUDA/pair_tersoff_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -38,23 +38,23 @@ namespace LAMMPS_NS {
class PairTersoffCuda : public PairTersoff
{
- public:
- PairTersoffCuda(class LAMMPS *);
- void compute(int, int);
- void settings(int, char **);
- void coeff(int, char **);
- void init_list(int, class NeighList *);
- void init_style();
- void ev_setup(int eflag, int vflag);
- protected:
-
- class Cuda *cuda;
- void allocate();
- bool allocated2;
- class CudaNeighList* cuda_neigh_list;
- Param_Float* params_f;
- Param_Float* cu_params_f;
- cCudaData<int, int, xyz >* cu_elem2param;
+ public:
+ PairTersoffCuda(class LAMMPS *);
+ void compute(int, int);
+ void settings(int, char **);
+ void coeff(int, char **);
+ void init_list(int, class NeighList *);
+ void init_style();
+ void ev_setup(int eflag, int vflag);
+ protected:
+
+ class Cuda *cuda;
+ void allocate();
+ bool allocated2;
+ class CudaNeighList* cuda_neigh_list;
+ Param_Float* params_f;
+ Param_Float* cu_params_f;
+ cCudaData<int, int, xyz >* cu_elem2param;
cCudaData<int, int, x >* cu_map;
bool init;
bool iszbl;
diff --git a/src/USER-CUDA/pair_tersoff_zbl_cuda.cpp b/src/USER-CUDA/pair_tersoff_zbl_cuda.cpp
index 45236da51538e20ed37f7efcab06d742a19f89b0..1ac3b81ec67132b5389f95f36f031debcf261927 100644
--- a/src/USER-CUDA/pair_tersoff_zbl_cuda.cpp
+++ b/src/USER-CUDA/pair_tersoff_zbl_cuda.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -94,8 +94,8 @@ void PairTersoffZBLCuda::read_file(char *file)
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fp);
if (ptr == NULL) {
- eof = 1;
- fclose(fp);
+ eof = 1;
+ fclose(fp);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
@@ -116,8 +116,8 @@ void PairTersoffZBLCuda::read_file(char *file)
if (comm->me == 0) {
ptr = fgets(&line[n],MAXLINE-n,fp);
if (ptr == NULL) {
- eof = 1;
- fclose(fp);
+ eof = 1;
+ fclose(fp);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
@@ -156,7 +156,7 @@ void PairTersoffZBLCuda::read_file(char *file)
if (nparams == maxparam) {
maxparam += DELTA;
params = (Param *) memory->srealloc(params,maxparam*sizeof(Param),
- "pair:params");
+ "pair:params");
}
params[nparams].ielement = ielement;
@@ -186,18 +186,18 @@ void PairTersoffZBLCuda::read_file(char *file)
params[nparams].powermint = int(params[nparams].powerm);
if (
- params[nparams].lam3 < 0.0 || params[nparams].c < 0.0 ||
- params[nparams].d < 0.0 || params[nparams].powern < 0.0 ||
- params[nparams].beta < 0.0 || params[nparams].lam2 < 0.0 ||
- params[nparams].bigb < 0.0 || params[nparams].bigr < 0.0 ||
- params[nparams].bigd < 0.0 ||
- params[nparams].bigd > params[nparams].bigr ||
- params[nparams].lam3 < 0.0 || params[nparams].biga < 0.0 ||
- params[nparams].powerm - params[nparams].powermint != 0.0 ||
+ params[nparams].lam3 < 0.0 || params[nparams].c < 0.0 ||
+ params[nparams].d < 0.0 || params[nparams].powern < 0.0 ||
+ params[nparams].beta < 0.0 || params[nparams].lam2 < 0.0 ||
+ params[nparams].bigb < 0.0 || params[nparams].bigr < 0.0 ||
+ params[nparams].bigd < 0.0 ||
+ params[nparams].bigd > params[nparams].bigr ||
+ params[nparams].lam3 < 0.0 || params[nparams].biga < 0.0 ||
+ params[nparams].powerm - params[nparams].powermint != 0.0 ||
(params[nparams].powermint != 3 && params[nparams].powermint != 1) ||
- params[nparams].gamma < 0.0 ||
- params[nparams].Z_i < 1.0 || params[nparams].Z_j < 1.0 ||
- params[nparams].ZBLcut < 0.0 || params[nparams].ZBLexpscale < 0.0)
+ params[nparams].gamma < 0.0 ||
+ params[nparams].Z_i < 1.0 || params[nparams].Z_j < 1.0 ||
+ params[nparams].ZBLcut < 0.0 || params[nparams].ZBLexpscale < 0.0)
error->all(FLERR,"Illegal Tersoff parameter");
nparams++;
diff --git a/src/USER-CUDA/pair_tersoff_zbl_cuda.h b/src/USER-CUDA/pair_tersoff_zbl_cuda.h
index bd91a2abfa4eff61323913b6d67eb9c6d0fa6e71..59f1dc757fd428cccd78ee6b1887319b07cc22f4 100644
--- a/src/USER-CUDA/pair_tersoff_zbl_cuda.h
+++ b/src/USER-CUDA/pair_tersoff_zbl_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -36,15 +36,15 @@ namespace LAMMPS_NS {
class PairTersoffZBLCuda : public PairTersoffCuda
{
- public:
- PairTersoffZBLCuda(class LAMMPS *);
- private:
- double global_a_0; // Bohr radius for Coulomb repulsion
- double global_epsilon_0; // permittivity of vacuum for Coulomb repulsion
- double global_e; // proton charge (negative of electron charge)
-
- void read_file(char *);
- void coeff(int narg, char **arg);
+ public:
+ PairTersoffZBLCuda(class LAMMPS *);
+ private:
+ double global_a_0; // Bohr radius for Coulomb repulsion
+ double global_epsilon_0; // permittivity of vacuum for Coulomb repulsion
+ double global_e; // proton charge (negative of electron charge)
+
+ void read_file(char *);
+ void coeff(int narg, char **arg);
};
}
diff --git a/src/USER-CUDA/pppm_cuda.cpp b/src/USER-CUDA/pppm_cuda.cpp
index afcc1fb52cd1d4a9d47dc1eaeda1a133584f1f32..60504bf5564f39b85d0dbf59f76ecf5b15e2f615 100644
--- a/src/USER-CUDA/pppm_cuda.cpp
+++ b/src/USER-CUDA/pppm_cuda.cpp
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -28,7 +28,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -78,23 +78,23 @@ void printArray(double* data,int nx, int ny, int nz)
for(int i=0;i<nz;i++)
for(int j=0;j<ny;j++)
{
- printf("%i %i\n",i,j);
- for(int k=0;k<nx;k++)
- printf("%e ",data[2*(i*ny*nx+j*nx+k)]);
- printf("\n\n");
+ printf("%i %i\n",i,j);
+ for(int k=0;k<nx;k++)
+ printf("%e ",data[2*(i*ny*nx+j*nx+k)]);
+ printf("\n\n");
}
-}
+}
void printArray(double*** data,int nx, int ny, int nz)
{
for(int i=0;i<nx;i++)
for(int j=0;j<ny;j++)
{
- printf("%i %i\n",i,j);
- for(int k=0;k<nz;k++)
- printf("%e ",data[i][j][k]);
- printf("\n\n");
+ printf("%i %i\n",i,j);
+ for(int k=0;k<nz;k++)
+ printf("%e ",data[i][j][k]);
+ printf("\n\n");
}
-}
+}
/* ---------------------------------------------------------------------- */
PPPMCuda::PPPMCuda(LAMMPS *lmp, int narg, char **arg) : PPPM(lmp, (narg==2?1:narg), arg)
@@ -108,7 +108,7 @@ PPPMCuda::PPPMCuda(LAMMPS *lmp, int narg, char **arg) : PPPM(lmp, (narg==2?1:nar
error->all(FLERR,"Using kspace_style pppm/cuda without cufft is not possible. Compile with cufft=1 to include cufft. Aborting.");
#endif
accuracy_relative = atof(arg[0]);
-
+
nfactors = 3;
factors = new int[nfactors];
factors[0] = 2;
@@ -131,7 +131,7 @@ PPPMCuda::PPPMCuda(LAMMPS *lmp, int narg, char **arg) : PPPM(lmp, (narg==2?1:nar
fft1c = fft2c = NULL;
remap = NULL;
-
+
density_brick_int=NULL;
density_intScale=1000000;
cu_vdx_brick = cu_vdy_brick = cu_vdz_brick = NULL;
@@ -143,43 +143,43 @@ PPPMCuda::PPPMCuda(LAMMPS *lmp, int narg, char **arg) : PPPM(lmp, (narg==2?1:nar
cu_work1 = cu_work2 = cu_work3 = NULL;
cu_vg = NULL;
cu_fkx = cu_fky = cu_fkz = NULL;
-
+
cu_flag = NULL;
cu_debugdata = NULL;
cu_rho_coeff = NULL;
cu_virial = NULL;
-
+
cu_gf_b = NULL;
-
+
cu_slabbuf = NULL;
slabbuf = NULL;
-
+
nmax = 0;
part2grid = NULL;
cu_part2grid = NULL;
adev_data_array=NULL;
poissontime=0;
old_nmax=0;
- cu_pppm_grid_n=NULL;
- cu_pppm_grid_ids=NULL;
-
+ cu_pppm_grid_n=NULL;
+ cu_pppm_grid_ids=NULL;
+
pppm_grid_nmax=0;
pppm2partgrid=new int[3];
- pppm_grid=new int[3];
+ pppm_grid=new int[3];
firstpass=true;
scale = 1.0;
}
/* ----------------------------------------------------------------------
- free all memory
+ free all memory
------------------------------------------------------------------------- */
PPPMCuda::~PPPMCuda()
{
delete [] slabbuf;
delete cu_slabbuf;
-
+
delete [] factors;
factors=NULL;
deallocate();
@@ -190,16 +190,16 @@ PPPMCuda::~PPPMCuda()
}
/* ----------------------------------------------------------------------
- called once before run
+ called once before run
------------------------------------------------------------------------- */
void PPPMCuda::init()
{
-
+
cuda->shared_data.pppm.cudable_force=1;
-
+
//if(cuda->finished_run) {PPPM::init(); return;}
-
+
if (me == 0) {
if (screen) fprintf(screen,"PPPMCuda initialization ...\n");
if (logfile) fprintf(logfile,"PPPMCuda initialization ...\n");
@@ -216,8 +216,8 @@ void PPPMCuda::init()
if (slabflag == 0 && domain->nonperiodic > 0)
error->all(FLERR,"Cannot use nonperiodic boundaries with PPPMCuda");
if (slabflag == 1) {
- if (domain->xperiodic != 1 || domain->yperiodic != 1 ||
- domain->boundary[2][0] != 1 || domain->boundary[2][1] != 1)
+ if (domain->xperiodic != 1 || domain->yperiodic != 1 ||
+ domain->boundary[2][0] != 1 || domain->boundary[2][1] != 1)
error->all(FLERR,"Incorrect boundaries with slab PPPMCuda");
}
@@ -305,7 +305,7 @@ void PPPMCuda::init()
while (order > 1) {
if (iteration && me == 0)
error->warning(FLERR,"Reducing PPPMCuda order b/c stencil extends "
- "beyond neighbor processor");
+ "beyond neighbor processor");
iteration++;
set_grid();
@@ -322,9 +322,9 @@ void PPPMCuda::init()
nxhi_in = (comm->myloc[0]+1)*nx_pppm / comm->procgrid[0] - 1;
nylo_in = comm->myloc[1]*ny_pppm / comm->procgrid[1];
nyhi_in = (comm->myloc[1]+1)*ny_pppm / comm->procgrid[1] - 1;
- nzlo_in = comm->myloc[2] *
+ nzlo_in = comm->myloc[2] *
(static_cast<int> (nz_pppm/slab_volfactor)) / comm->procgrid[2];
- nzhi_in = (comm->myloc[2]+1) *
+ nzhi_in = (comm->myloc[2]+1) *
(static_cast<int> (nz_pppm/slab_volfactor)) / comm->procgrid[2] - 1;
// nlower,nupper = stencil size for mapping particles to PPPMCuda grid
@@ -380,27 +380,27 @@ void PPPMCuda::init()
dist[1] = cuthalf/domain->prd[1];
dist[2] = cuthalf/domain->prd[2];
}
-
+
int nlo,nhi;
-
- nlo = static_cast<int> ((sublo[0]-dist[0]-boxlo[0]) *
- nx_pppm/xprd + shift) - OFFSET;
- nhi = static_cast<int> ((subhi[0]+dist[0]-boxlo[0]) *
- nx_pppm/xprd + shift) - OFFSET;
+
+ nlo = static_cast<int> ((sublo[0]-dist[0]-boxlo[0]) *
+ nx_pppm/xprd + shift) - OFFSET;
+ nhi = static_cast<int> ((subhi[0]+dist[0]-boxlo[0]) *
+ nx_pppm/xprd + shift) - OFFSET;
nxlo_out = nlo + nlower;
nxhi_out = nhi + nupper;
- nlo = static_cast<int> ((sublo[1]-dist[1]-boxlo[1]) *
- ny_pppm/yprd + shift) - OFFSET;
- nhi = static_cast<int> ((subhi[1]+dist[1]-boxlo[1]) *
- ny_pppm/yprd + shift) - OFFSET;
+ nlo = static_cast<int> ((sublo[1]-dist[1]-boxlo[1]) *
+ ny_pppm/yprd + shift) - OFFSET;
+ nhi = static_cast<int> ((subhi[1]+dist[1]-boxlo[1]) *
+ ny_pppm/yprd + shift) - OFFSET;
nylo_out = nlo + nlower;
nyhi_out = nhi + nupper;
- nlo = static_cast<int> ((sublo[2]-dist[2]-boxlo[2]) *
- nz_pppm/zprd_slab + shift) - OFFSET;
- nhi = static_cast<int> ((subhi[2]+dist[2]-boxlo[2]) *
- nz_pppm/zprd_slab + shift) - OFFSET;
+ nlo = static_cast<int> ((sublo[2]-dist[2]-boxlo[2]) *
+ nz_pppm/zprd_slab + shift) - OFFSET;
+ nhi = static_cast<int> ((subhi[2]+dist[2]-boxlo[2]) *
+ nz_pppm/zprd_slab + shift) - OFFSET;
nzlo_out = nlo + nlower;
nzhi_out = nhi + nupper;
@@ -415,7 +415,7 @@ void PPPMCuda::init()
nzhi_in = nz_pppm - 1;
nzhi_out = nz_pppm - 1;
}
-
+
// nlo_ghost,nhi_ghost = # of planes I will recv from 6 directions
// that overlay domain I own
// proc in that direction tells me via sendrecv()
@@ -427,43 +427,43 @@ void PPPMCuda::init()
nplanes = nxlo_in - nxlo_out;
if (comm->procneigh[0][0] != me)
MPI_Sendrecv(&nplanes,1,MPI_INT,comm->procneigh[0][0],0,
- &nxhi_ghost,1,MPI_INT,comm->procneigh[0][1],0,
- world,&status);
+ &nxhi_ghost,1,MPI_INT,comm->procneigh[0][1],0,
+ world,&status);
else nxhi_ghost = nplanes;
nplanes = nxhi_out - nxhi_in;
if (comm->procneigh[0][1] != me)
MPI_Sendrecv(&nplanes,1,MPI_INT,comm->procneigh[0][1],0,
- &nxlo_ghost,1,MPI_INT,comm->procneigh[0][0],
- 0,world,&status);
+ &nxlo_ghost,1,MPI_INT,comm->procneigh[0][0],
+ 0,world,&status);
else nxlo_ghost = nplanes;
nplanes = nylo_in - nylo_out;
if (comm->procneigh[1][0] != me)
MPI_Sendrecv(&nplanes,1,MPI_INT,comm->procneigh[1][0],0,
- &nyhi_ghost,1,MPI_INT,comm->procneigh[1][1],0,
- world,&status);
+ &nyhi_ghost,1,MPI_INT,comm->procneigh[1][1],0,
+ world,&status);
else nyhi_ghost = nplanes;
nplanes = nyhi_out - nyhi_in;
if (comm->procneigh[1][1] != me)
MPI_Sendrecv(&nplanes,1,MPI_INT,comm->procneigh[1][1],0,
- &nylo_ghost,1,MPI_INT,comm->procneigh[1][0],0,
- world,&status);
+ &nylo_ghost,1,MPI_INT,comm->procneigh[1][0],0,
+ world,&status);
else nylo_ghost = nplanes;
nplanes = nzlo_in - nzlo_out;
if (comm->procneigh[2][0] != me)
MPI_Sendrecv(&nplanes,1,MPI_INT,comm->procneigh[2][0],0,
- &nzhi_ghost,1,MPI_INT,comm->procneigh[2][1],0,
- world,&status);
+ &nzhi_ghost,1,MPI_INT,comm->procneigh[2][1],0,
+ world,&status);
else nzhi_ghost = nplanes;
nplanes = nzhi_out - nzhi_in;
if (comm->procneigh[2][1] != me)
MPI_Sendrecv(&nplanes,1,MPI_INT,comm->procneigh[2][1],0,
- &nzlo_ghost,1,MPI_INT,comm->procneigh[2][0],0,
- world,&status);
+ &nzlo_ghost,1,MPI_INT,comm->procneigh[2][0],0,
+ world,&status);
else nzlo_ghost = nplanes;
// test that ghost overlap is not bigger than my sub-domain
@@ -570,9 +570,9 @@ void PPPMCuda::init()
if (me == 0) {
if (screen) fprintf(screen," brick FFT buffer size/proc = %d %d %d\n",
- ngrid_max,nfft_both_max,nbuf_max);
+ ngrid_max,nfft_both_max,nbuf_max);
if (logfile) fprintf(logfile," brick FFT buffer size/proc = %d %d %d\n",
- ngrid_max,nfft_both_max,nbuf_max);
+ ngrid_max,nfft_both_max,nbuf_max);
}
cuda_shared_pppm* ap=&(cuda->shared_data.pppm);
@@ -608,7 +608,7 @@ void PPPMCuda::init()
ap->nlower=nlower;
ap->nupper=nupper;
ap->shiftone=shiftone;
-
+
// allocate K-space dependent memory
@@ -622,7 +622,7 @@ void PPPMCuda::init()
}
/* ----------------------------------------------------------------------
- adjust PPPMCuda coeffs, called initially and whenever volume has changed
+ adjust PPPMCuda coeffs, called initially and whenever volume has changed
------------------------------------------------------------------------- */
void PPPMCuda::setup()
@@ -641,7 +641,7 @@ void PPPMCuda::setup()
double zprd = prd[2];
double zprd_slab = zprd*slab_volfactor;
volume = xprd * yprd * zprd_slab;
-
+
delxinv = nx_pppm/xprd;
delyinv = ny_pppm/yprd;
delzinv = nz_pppm/zprd_slab;
@@ -655,20 +655,20 @@ void PPPMCuda::setup()
// fkx,fky,fkz for my FFT grid pts
Cuda_PPPM_Setup_fkxyz_vg(nx_pppm, ny_pppm,nz_pppm,unitkx,unitky,unitkz,g_ewald);
-
+
// modified (Hockney-Eastwood) Coulomb Green's function
- int nbx = static_cast<int> ((g_ewald*xprd/(MY_PI*nx_pppm)) *
- pow(-log(EPS_HOC),0.25));
- int nby = static_cast<int> ((g_ewald*yprd/(MY_PI*ny_pppm)) *
- pow(-log(EPS_HOC),0.25));
- int nbz = static_cast<int> ((g_ewald*zprd_slab/(MY_PI*nz_pppm)) *
- pow(-log(EPS_HOC),0.25));
+ int nbx = static_cast<int> ((g_ewald*xprd/(MY_PI*nx_pppm)) *
+ pow(-log(EPS_HOC),0.25));
+ int nby = static_cast<int> ((g_ewald*yprd/(MY_PI*ny_pppm)) *
+ pow(-log(EPS_HOC),0.25));
+ int nbz = static_cast<int> ((g_ewald*zprd_slab/(MY_PI*nz_pppm)) *
+ pow(-log(EPS_HOC),0.25));
Cuda_PPPM_setup_greensfn(nx_pppm,ny_pppm,nz_pppm,unitkx,unitky,unitkz,g_ewald,
nbx,nby,nbz,xprd,yprd,zprd_slab);
-
+
#ifdef FFT_CUFFT
cu_vdx_brick->upload();
cu_vdy_brick->upload();
@@ -680,7 +680,7 @@ nbx,nby,nbz,xprd,yprd,zprd_slab);
}
/* ----------------------------------------------------------------------
- compute the PPPMCuda long-range force, energy, virial
+ compute the PPPMCuda long-range force, energy, virial
------------------------------------------------------------------------- */
void PPPMCuda::compute(int eflag, int vflag)
@@ -693,7 +693,7 @@ void PPPMCuda::compute(int eflag, int vflag)
timespec starttotal;
timespec endtotal;
// convert atoms from box to lamda coords
-
+
if (triclinic == 0) boxlo = domain->boxlo;
else {
boxlo = domain->boxlo_lamda;
@@ -706,21 +706,21 @@ void PPPMCuda::compute(int eflag, int vflag)
memory->destroy(part2grid);
nmax = atom->nmax;
memory->create(part2grid,nmax,3,"pppm:part2grid");
- delete cu_part2grid;
- delete [] adev_data_array;
- adev_data_array=new dev_array[1];
- cu_part2grid = new cCudaData<int , int , yx > ((int*)part2grid,adev_data_array, nmax,3);
+ delete cu_part2grid;
+ delete [] adev_data_array;
+ adev_data_array=new dev_array[1];
+ cu_part2grid = new cCudaData<int , int , yx > ((int*)part2grid,adev_data_array, nmax,3);
- pppm_device_update(&cuda->shared_data,cu_part2grid->dev_data(),atom->nlocal,atom->nmax);
+ pppm_device_update(&cuda->shared_data,cu_part2grid->dev_data(),atom->nlocal,atom->nmax);
old_nmax=nmax;
}
if(cu_atom->update_nlocal) {pppm_update_nlocal(cu_atom->nlocal);}
-
+
energy = 0.0;
- if (vflag)
+ if (vflag)
{
- for (i = 0; i < 6; i++) virial[i] = 0.0;
- cu_virial->memset_device(0);
+ for (i = 0; i < 6; i++) virial[i] = 0.0;
+ cu_virial->memset_device(0);
}
if(eflag) cu_energy->memset_device(0);
clock_gettime(CLOCK_REALTIME,&starttotal);
@@ -745,7 +745,7 @@ void PPPMCuda::compute(int eflag, int vflag)
// all procs communicate density values from their ghost cells
// to fully sum contribution in their 3d bricks
// remap from 3d decomposition to FFT decomposition
-
+
int nprocs=comm->nprocs;
clock_gettime(CLOCK_REALTIME,&starttime);
@@ -768,7 +768,7 @@ void PPPMCuda::compute(int eflag, int vflag)
// compute potential gradient on my FFT grid and
// portion of e_long on this proc's FFT grid
// return gradients (electric fields) in 3d brick decomposition
-
+
clock_gettime(CLOCK_REALTIME,&starttime);
poisson(eflag,vflag);
clock_gettime(CLOCK_REALTIME,&endtime);
@@ -778,7 +778,7 @@ void PPPMCuda::compute(int eflag, int vflag)
// surrounding their 3d bricks
// not necessary since all the calculations are done on one proc
-
+
// calculate the force on my particles
@@ -796,7 +796,7 @@ void PPPMCuda::compute(int eflag, int vflag)
double energy_all;
MPI_Allreduce(&energy,&energy_all,1,MPI_DOUBLE,MPI_SUM,world);
energy = energy_all;
-
+
energy *= 0.5*volume;
energy -= g_ewald*qsqsum/1.772453851 +
MY_PI2*qsum*qsum / (g_ewald*g_ewald*volume);
@@ -816,15 +816,15 @@ void PPPMCuda::compute(int eflag, int vflag)
if (slabflag) slabcorr(eflag);
// convert atoms back from lamda to box coords
-
+
if (triclinic) domain->lamda2x(atom->nlocal);
-
+
if(firstpass) firstpass=false;
}
/* ----------------------------------------------------------------------
- allocate memory that depends on # of K-vectors and order
+ allocate memory that depends on # of K-vectors and order
------------------------------------------------------------------------- */
@@ -836,41 +836,41 @@ void PPPMCuda::allocate()
memory->create3d_offset(density_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
- nxlo_out,nxhi_out,"pppm:density_brick");
+ nxlo_out,nxhi_out,"pppm:density_brick");
memory->create3d_offset(density_brick_int,nzlo_out,nzhi_out,nylo_out,nyhi_out,
- nxlo_out,nxhi_out,"pppm:density_brick_int");
+ nxlo_out,nxhi_out,"pppm:density_brick_int");
cu_density_brick = new cCudaData<double, PPPM_FLOAT, x> ((double*) &(density_brick[nzlo_out][nylo_out][nxlo_out]), & (dev_tmp[n_cudata++]),
- (nzhi_out-nzlo_out+1)*(nyhi_out-nylo_out+1)*(nxhi_out-nxlo_out+1));
+ (nzhi_out-nzlo_out+1)*(nyhi_out-nylo_out+1)*(nxhi_out-nxlo_out+1));
cu_density_brick_int = new cCudaData<int, int, x> ((int*) &(density_brick_int[nzlo_out][nylo_out][nxlo_out]), & (dev_tmp[n_cudata++]),
- (nzhi_out-nzlo_out+1)*(nyhi_out-nylo_out+1)*(nxhi_out-nxlo_out+1));
+ (nzhi_out-nzlo_out+1)*(nyhi_out-nylo_out+1)*(nxhi_out-nxlo_out+1));
memory->create3d_offset(vdx_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
- nxlo_out,nxhi_out,"pppm:vdx_brick");
+ nxlo_out,nxhi_out,"pppm:vdx_brick");
memory->create3d_offset(vdx_brick_tmp,nzlo_out,nzhi_out,nylo_out,nyhi_out,
- nxlo_out,nxhi_out,"pppm:vdx_brick_tmp");
+ nxlo_out,nxhi_out,"pppm:vdx_brick_tmp");
cu_vdx_brick = new cCudaData<double, PPPM_FLOAT, x> ((double*) &(vdx_brick[nzlo_out][nylo_out][nxlo_out]), & (dev_tmp[n_cudata++]),
- (nzhi_out-nzlo_out+1)*(nyhi_out-nylo_out+1)*(nxhi_out-nxlo_out+1));
+ (nzhi_out-nzlo_out+1)*(nyhi_out-nylo_out+1)*(nxhi_out-nxlo_out+1));
memory->create3d_offset(vdy_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
- nxlo_out,nxhi_out,"pppm:vdy_brick");
+ nxlo_out,nxhi_out,"pppm:vdy_brick");
cu_vdy_brick = new cCudaData<double, PPPM_FLOAT, x> ((double*) &(vdy_brick[nzlo_out][nylo_out][nxlo_out]), & (dev_tmp[n_cudata++]),
- (nzhi_out-nzlo_out+1)*(nyhi_out-nylo_out+1)*(nxhi_out-nxlo_out+1));
+ (nzhi_out-nzlo_out+1)*(nyhi_out-nylo_out+1)*(nxhi_out-nxlo_out+1));
memory->create3d_offset(vdz_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
- nxlo_out,nxhi_out,"pppm:vdz_brick");
+ nxlo_out,nxhi_out,"pppm:vdz_brick");
cu_vdz_brick = new cCudaData<double, PPPM_FLOAT, x> ((double*) &(vdz_brick[nzlo_out][nylo_out][nxlo_out]), & (dev_tmp[n_cudata++]),
- (nzhi_out-nzlo_out+1)*(nyhi_out-nylo_out+1)*(nxhi_out-nxlo_out+1));
+ (nzhi_out-nzlo_out+1)*(nyhi_out-nylo_out+1)*(nxhi_out-nxlo_out+1));
memory->create(density_fft,nfft_both,"pppm:density_fft");
cu_density_fft = new cCudaData<double, PPPM_FLOAT, x> (density_fft, & (dev_tmp[n_cudata++]),nfft_both);
- cu_energy = new cCudaData<double, ENERGY_FLOAT, x> (NULL, &(dev_tmp[n_cudata++]),ny_pppm*nz_pppm);
- cu_virial = new cCudaData<double, ENERGY_FLOAT, x> (NULL, &(dev_tmp[n_cudata++]),ny_pppm*nz_pppm*6);
+ cu_energy = new cCudaData<double, ENERGY_FLOAT, x> (NULL, &(dev_tmp[n_cudata++]),ny_pppm*nz_pppm);
+ cu_virial = new cCudaData<double, ENERGY_FLOAT, x> (NULL, &(dev_tmp[n_cudata++]),ny_pppm*nz_pppm*6);
memory->create(greensfn,nfft_both,"pppm:greensfn");
cu_greensfn = new cCudaData<double, PPPM_FLOAT, x> (greensfn, & (dev_tmp[n_cudata++]) , nx_pppm*ny_pppm*nz_pppm);
@@ -878,11 +878,11 @@ void PPPMCuda::allocate()
memory->create(work1,2*nx_pppm*ny_pppm*nz_pppm,"pppm:work1");
memory->create(work2,2*nx_pppm*ny_pppm*nz_pppm,"pppm:work2");
memory->create(work3,2*nx_pppm*ny_pppm*nz_pppm,"pppm:work3");
-
+
cu_work1 = new cCudaData<double, FFT_FLOAT, x> (work1, & (dev_tmp[n_cudata++]) , 2*nx_pppm*ny_pppm*nz_pppm);
cu_work2 = new cCudaData<double, FFT_FLOAT, x> (work2, & (dev_tmp[n_cudata++]) , 2*nx_pppm*ny_pppm*nz_pppm);
cu_work3 = new cCudaData<double, FFT_FLOAT, x> (work3, & (dev_tmp[n_cudata++]) , 2*nx_pppm*ny_pppm*nz_pppm);
-
+
memory->create(fkx,nx_pppm,"pppmcuda:fkx");
cu_fkx = new cCudaData<double, PPPM_FLOAT, x> (fkx, & (dev_tmp[n_cudata++]) , nx_pppm);
@@ -912,7 +912,7 @@ void PPPMCuda::allocate()
debugdata=new PPPM_FLOAT[100];
cu_debugdata = new cCudaData<PPPM_FLOAT, PPPM_FLOAT, x> (debugdata,& (dev_tmp[n_cudata++]),100);
cu_flag = new cCudaData<int, int, x> (&global_flag,& (dev_tmp[n_cudata++]),3);
-
+
// create 2 FFTs and a Remap
// 1st FFT keeps data in FFT decompostion
// 2nd FFT returns data in 3d brick decomposition
@@ -924,39 +924,39 @@ void PPPMCuda::allocate()
fft1c = new FFT3dCuda(lmp,world,nx_pppm,ny_pppm,nz_pppm,
- nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
- nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
- 0,0,&tmp,true);
+ nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
+ nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
+ 0,0,&tmp,true);
fft2c = new FFT3dCuda(lmp,world,nx_pppm,ny_pppm,nz_pppm,
- nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
- nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in,
- 0,0,&tmp,false);
+ nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
+ nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in,
+ 0,0,&tmp,false);
-
-#ifdef FFT_CUFFT
+
+#ifdef FFT_CUFFT
fft1c->set_cudata(cu_work2->dev_data(),cu_work1->dev_data());
fft2c->set_cudata(cu_work2->dev_data(),cu_work3->dev_data());
#endif
remap = new Remap(lmp,world,
- nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in,
- nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
- 1,0,0,2);
+ nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in,
+ nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
+ 1,0,0,2);
pppm_device_init(cu_density_brick->dev_data(), cu_vdx_brick->dev_data(), cu_vdy_brick->dev_data(), cu_vdz_brick->dev_data(), cu_density_fft->dev_data(),cu_energy->dev_data(),cu_virial->dev_data()
- , cu_work1->dev_data(), cu_work2->dev_data(), cu_work3->dev_data(), cu_greensfn->dev_data(), cu_fkx->dev_data(), cu_fky->dev_data(), cu_fkz->dev_data(), cu_vg->dev_data()
- ,nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in,nxlo_out,nxhi_out,nylo_out,nyhi_out,nzlo_out,nzhi_out,nx_pppm,ny_pppm,nz_pppm
- ,nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,cu_gf_b->dev_data()
- ,qqrd2e,order,cu_rho_coeff->dev_data(),cu_debugdata->dev_data(),cu_density_brick_int->dev_data(),slabflag
- );
+ , cu_work1->dev_data(), cu_work2->dev_data(), cu_work3->dev_data(), cu_greensfn->dev_data(), cu_fkx->dev_data(), cu_fky->dev_data(), cu_fkz->dev_data(), cu_vg->dev_data()
+ ,nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in,nxlo_out,nxhi_out,nylo_out,nyhi_out,nzlo_out,nzhi_out,nx_pppm,ny_pppm,nz_pppm
+ ,nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,cu_gf_b->dev_data()
+ ,qqrd2e,order,cu_rho_coeff->dev_data(),cu_debugdata->dev_data(),cu_density_brick_int->dev_data(),slabflag
+ );
}
/* ----------------------------------------------------------------------
- deallocate memory that depends on # of K-vectors and order
+ deallocate memory that depends on # of K-vectors and order
---------------------------------------------------------------------- */
void PPPMCuda::deallocate()
@@ -965,7 +965,7 @@ void PPPMCuda::deallocate()
memory->destroy3d_offset(vdx_brick,nzlo_out,nylo_out,nxlo_out);
memory->destroy3d_offset(vdy_brick,nzlo_out,nylo_out,nxlo_out);
memory->destroy3d_offset(vdz_brick,nzlo_out,nylo_out,nxlo_out);
-
+
density_brick = vdx_brick = vdy_brick = vdz_brick = NULL;
memory->destroy(density_fft);
@@ -996,7 +996,7 @@ void PPPMCuda::deallocate()
delete cu_density_fft;
delete cu_energy;
delete cu_virial;
-#ifdef FFT_CUFFT
+#ifdef FFT_CUFFT
delete cu_greensfn;
delete cu_gf_b;
delete cu_vg;
@@ -1012,7 +1012,7 @@ void PPPMCuda::deallocate()
delete cu_debugdata;
delete cu_rho_coeff;
-
+
cu_vdx_brick = cu_vdy_brick = cu_vdz_brick = NULL;
cu_density_brick = NULL;
cu_density_brick_int = NULL;
@@ -1026,12 +1026,12 @@ void PPPMCuda::deallocate()
cu_vg = NULL;
cu_fkx = cu_fky = cu_fkz = NULL;
#endif
-
+
cu_flag = NULL;
cu_debugdata = NULL;
cu_rho_coeff = NULL;
cu_part2grid = NULL;
-
+
memory->destroy(buf1);
memory->destroy(buf2);
@@ -1052,7 +1052,7 @@ void PPPMCuda::deallocate()
}
/* ----------------------------------------------------------------------
- set size of FFT grid (nx,ny,nz_pppm) and g_ewald
+ set size of FFT grid (nx,ny,nz_pppm) and g_ewald
-------------------------------------------------------------------------*/
void PPPMCuda::set_grid()
@@ -1103,7 +1103,7 @@ void PPPMCuda::set_grid()
double yprd = domain->yprd;
double zprd = domain->zprd;
double zprd_slab = zprd*slab_volfactor;
-
+
// make initial g_ewald estimate
// based on desired error and real space cutoff
// fluid-occupied volume used to estimate real-space error
@@ -1113,7 +1113,7 @@ void PPPMCuda::set_grid()
if (!gewaldflag)
g_ewald = sqrt(-log(accuracy*sqrt(natoms*cutoff*xprd*yprd*zprd) /
- (2.0*q2))) / cutoff;
+ (2.0*q2))) / cutoff;
// set optimal nx_pppm,ny_pppm,nz_pppm based on order and precision
// nz_pppm uses extended zprd_slab instead of zprd
@@ -1122,7 +1122,7 @@ void PPPMCuda::set_grid()
if (!gridflag) {
double err;
- h_x = h_y = h_z = 1/g_ewald;
+ h_x = h_y = h_z = 1/g_ewald;
nx_pppm = static_cast<int> (xprd/h_x + 1);
ny_pppm = static_cast<int> (yprd/h_y + 1);
@@ -1156,7 +1156,7 @@ void PPPMCuda::set_grid()
while (!factorable(ny_pppm)) ny_pppm++;
while (!factorable(nz_pppm)) nz_pppm++;
-
+
// adjust g_ewald for new grid size
h_x = xprd/nx_pppm;
@@ -1182,7 +1182,7 @@ void PPPMCuda::set_grid()
while (fabs(dgew) > SMALL && fmid != 0.0) {
dgew *= 0.5;
g_ewald = rtb + dgew;
- fmid = diffpr(h_x,h_y,h_z,q2,acons);
+ fmid = diffpr(h_x,h_y,h_z,q2,acons);
if (fmid <= 0.0) rtb = g_ewald;
ncount++;
if (ncount > LARGE) error->all(FLERR,"Cannot compute PPPMCuda G");
@@ -1195,7 +1195,7 @@ void PPPMCuda::set_grid()
double lpry = rms(h_y,yprd,natoms,q2,acons);
double lprz = rms(h_z,zprd_slab,natoms,q2,acons);
double lpr = sqrt(lprx*lprx + lpry*lpry + lprz*lprz) / sqrt(3.0);
- double spr = 2.0*q2 * exp(-g_ewald*g_ewald*cutoff*cutoff) /
+ double spr = 2.0*q2 * exp(-g_ewald*g_ewald*cutoff*cutoff) /
sqrt(natoms*cutoff*xprd*yprd*zprd_slab);
// free local memory
@@ -1211,7 +1211,7 @@ void PPPMCuda::set_grid()
fprintf(screen," stencil order = %d\n",order);
fprintf(screen," absolute RMS force accuracy = %g\n",MAX(lpr,spr));
fprintf(screen," relative force accuracy = %g\n",
- MAX(lpr,spr)/two_charge_force);
+ MAX(lpr,spr)/two_charge_force);
}
if (logfile) {
fprintf(logfile," G vector = %g\n",g_ewald);
@@ -1219,7 +1219,7 @@ void PPPMCuda::set_grid()
fprintf(logfile," stencil order = %d\n",order);
fprintf(logfile," absolute RMS force accuracy = %g\n",MAX(lpr,spr));
fprintf(logfile," relative force accuracy = %g\n",
- MAX(lpr,spr)/two_charge_force);
+ MAX(lpr,spr)/two_charge_force);
}
}
}
@@ -1228,13 +1228,13 @@ void PPPMCuda::set_grid()
/* ----------------------------------------------------------------------
find center grid pt for each of my particles
check that full stencil for the particle will fit in my 3d brick
- store central grid pt indices in part2grid array
+ store central grid pt indices in part2grid array
------------------------------------------------------------------------- */
void PPPMCuda::particle_map()
{
- MYDBG(printf("# CUDA PPPMCuda::particle_map() ... start\n");)
+ MYDBG(printf("# CUDA PPPMCuda::particle_map() ... start\n");)
int flag = 0;
cu_flag->memset_device(0);
@@ -1249,25 +1249,25 @@ void PPPMCuda::particle_map()
printf("z: %e ",debugdata[9]);
printf("nx: %e ",debugdata[4]);
printf("ny: %e ",debugdata[5]);
-
+
printf("\n");
//printf("debugdata: cpu: %e %e %e %i\n",boxlo[0],boxlo[1],boxlo[2],atom->nlocal);
cuda->cu_x->download();
- int nx,ny,nz;
+ int nx,ny,nz;
- double **x = atom->x;
+ double **x = atom->x;
int nlocal = atom->nlocal;
- for (int i = 0; i < nlocal; i++) {
+ for (int i = 0; i < nlocal; i++) {
nx = static_cast<int> ((x[i][0]-boxlo[0])*delxinv+shift) - OFFSET;
ny = static_cast<int> ((x[i][1]-boxlo[1])*delyinv+shift) - OFFSET;
- nz = static_cast<int> ((x[i][2]-boxlo[2])*delzinv+shift) - OFFSET;
-
- if(i==1203)printf("Outside Atom: %i %e %e %e (%i %i %i)\n",i,x[i][0],x[i][1],x[i][2],nx,ny,nz);
- if (nx+nlower < nxlo_out || nx+nupper > nxhi_out ||
- ny+nlower < nylo_out || ny+nupper > nyhi_out ||
- nz+nlower < nzlo_out || nz+nupper > nzhi_out || i==1203) {printf("Outside Atom: %i %e %e %e (%i %i %i)\n",i,x[i][0],x[i][1],x[i][2],nx,ny,nz); }
- }
-
+ nz = static_cast<int> ((x[i][2]-boxlo[2])*delzinv+shift) - OFFSET;
+
+ if(i==1203)printf("Outside Atom: %i %e %e %e (%i %i %i)\n",i,x[i][0],x[i][1],x[i][2],nx,ny,nz);
+ if (nx+nlower < nxlo_out || nx+nupper > nxhi_out ||
+ ny+nlower < nylo_out || ny+nupper > nyhi_out ||
+ nz+nlower < nzlo_out || nz+nupper > nzhi_out || i==1203) {printf("Outside Atom: %i %e %e %e (%i %i %i)\n",i,x[i][0],x[i][1],x[i][2],nx,ny,nz); }
+ }
+
}
int flag_all;
@@ -1279,7 +1279,7 @@ void PPPMCuda::particle_map()
create discretized "density" on section of global grid due to my particles
density(x,y,z) = charge "density" at grid points of my 3d brick
(nxlo:nxhi,nylo:nyhi,nzlo:nzhi) is extent of my brick (including ghosts)
- in global grid
+ in global grid
------------------------------------------------------------------------- */
@@ -1290,7 +1290,7 @@ void PPPMCuda::make_rho()
/* ----------------------------------------------------------------------
- FFT-based Poisson solver
+ FFT-based Poisson solver
------------------------------------------------------------------------- */
void PPPMCuda::poisson(int eflag, int vflag)
{
@@ -1302,27 +1302,27 @@ void PPPMCuda::poisson(int eflag, int vflag)
#ifdef FFT_CUFFT
timespec starttime;
timespec endtime;
-
+
clock_gettime(CLOCK_REALTIME,&starttime);
fft1c->compute(density_fft,work1,1);
-
+
clock_gettime(CLOCK_REALTIME,&endtime);
poissontime+=(endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000);
-
+
if (eflag || vflag) {
poisson_energy(nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,vflag);
ENERGY_FLOAT gpuvirial[6];
energy+=sum_energy(cu_virial->dev_data(),cu_energy->dev_data(),nx_pppm,ny_pppm,nz_pppm,vflag,gpuvirial);
- if(vflag)
+ if(vflag)
{
for(int j=0;j<6;j++) virial[j]+=gpuvirial[j];
}
}
-
-
+
+
// scale by 1/total-grid-pts to get rho(k)
// multiply by Green's function to get V(k)
@@ -1333,8 +1333,8 @@ void PPPMCuda::poisson(int eflag, int vflag)
// copy it into inner portion of vdx,vdy,vdz arrays
// x direction gradient
-
-
+
+
poisson_xgrad(nx_pppm,ny_pppm,nz_pppm);
@@ -1342,10 +1342,10 @@ void PPPMCuda::poisson(int eflag, int vflag)
fft2c->compute(work2,work2,-1);
clock_gettime(CLOCK_REALTIME,&endtime);
poissontime+=(endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000);
-
+
poisson_vdx_brick(nxhi_out,nxlo_out,nyhi_out,nylo_out,nzhi_out,nzlo_out,nx_pppm,ny_pppm,nz_pppm);
-
-
+
+
// y direction gradient
poisson_ygrad(nx_pppm,ny_pppm,nz_pppm);
@@ -1356,7 +1356,7 @@ void PPPMCuda::poisson(int eflag, int vflag)
poissontime+=(endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000);
poisson_vdy_brick(nxhi_out,nxlo_out,nyhi_out,nylo_out,nzhi_out,nzlo_out,nx_pppm,ny_pppm,nz_pppm);
-
+
// z direction gradient
poisson_zgrad(nx_pppm,ny_pppm,nz_pppm);
@@ -1371,7 +1371,7 @@ void PPPMCuda::poisson(int eflag, int vflag)
}
/*----------------------------------------------------------------------
- interpolate from grid to get electric field & force on my particles
+ interpolate from grid to get electric field & force on my particles
-------------------------------------------------------------------------*/
void PPPMCuda::fieldforce()
@@ -1429,30 +1429,30 @@ void PPPMCuda::slabcorr(int eflag)
// compute local contribution to global dipole moment
if(slabbuf==NULL)
{
- slabbuf=new ENERGY_FLOAT[(atom->nmax+31)/32];
- cu_slabbuf = new cCudaData<ENERGY_FLOAT,ENERGY_FLOAT, x> (slabbuf, (atom->nmax+31)/32);
+ slabbuf=new ENERGY_FLOAT[(atom->nmax+31)/32];
+ cu_slabbuf = new cCudaData<ENERGY_FLOAT,ENERGY_FLOAT, x> (slabbuf, (atom->nmax+31)/32);
}
if(unsigned((atom->nlocal+31)/32)*sizeof(ENERGY_FLOAT)>=unsigned(cu_slabbuf->dev_size()))
{
- delete [] slabbuf;
- delete cu_slabbuf;
- slabbuf=new ENERGY_FLOAT[(atom->nmax+31)/32];
- cu_slabbuf = new cCudaData<ENERGY_FLOAT,ENERGY_FLOAT, x> (slabbuf, (atom->nmax+31)/32);
+ delete [] slabbuf;
+ delete cu_slabbuf;
+ slabbuf=new ENERGY_FLOAT[(atom->nmax+31)/32];
+ cu_slabbuf = new cCudaData<ENERGY_FLOAT,ENERGY_FLOAT, x> (slabbuf, (atom->nmax+31)/32);
}
-
-
+
+
double dipole = cuda_slabcorr_energy(&cuda->shared_data,slabbuf,(ENERGY_FLOAT*) cu_slabbuf->dev_data());
double dipole_all;
MPI_Allreduce(&dipole,&dipole_all,1,MPI_DOUBLE,MPI_SUM,world);
// compute corrections
-
+
double e_slabcorr = 2.0*MY_PI*dipole_all*dipole_all/volume;
-
+
if (eflag) energy += qqrd2e*scale * e_slabcorr;
-
- double ffact = -4.0*MY_PI*dipole_all/volume;
-
+
+ double ffact = -4.0*MY_PI*dipole_all/volume;
+
cuda_slabcorr_force(&cuda->shared_data,ffact);
}
diff --git a/src/USER-CUDA/pppm_cuda.h b/src/USER-CUDA/pppm_cuda.h
index ac12cd96235cd76749fb2168ebb3bb42151b9731..2237155a1193364f0a1e571be50ba5d1321a28be 100644
--- a/src/USER-CUDA/pppm_cuda.h
+++ b/src/USER-CUDA/pppm_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -51,7 +51,7 @@ class PPPMCuda : public PPPM {
class Cuda *cuda;
class FFT3dCuda *fft1c,*fft2c;
double* work3;
-
+
cCudaData<double , FFT_FLOAT , x >* cu_work1;
cCudaData<double , FFT_FLOAT , x >* cu_work2;
cCudaData<double , FFT_FLOAT , x >* cu_work3;
@@ -62,39 +62,39 @@ class PPPMCuda : public PPPM {
cCudaData<double , PPPM_FLOAT , x >* cu_fkz;
cCudaData<double , PPPM_FLOAT , xy>* cu_vg;
cCudaData<double , PPPM_FLOAT , x >* cu_density_brick;
- cCudaData<int , int , x >* cu_density_brick_int;
+ cCudaData<int , int , x >* cu_density_brick_int;
cCudaData<double , PPPM_FLOAT , x >* cu_vdx_brick;
cCudaData<double , PPPM_FLOAT , x >* cu_vdy_brick;
cCudaData<double , PPPM_FLOAT , x >* cu_vdz_brick;
cCudaData<double , PPPM_FLOAT , x >* cu_density_fft;
cCudaData<double , ENERGY_FLOAT , x >* cu_energy;
cCudaData<double , ENERGY_FLOAT , x >* cu_virial;
- cCudaData<double , X_FLOAT , yx>* cu_x;
- cCudaData<double , V_FLOAT , yx>* cu_v;
- cCudaData<double , F_FLOAT , yx>* cu_f;
- cCudaData<double , F_FLOAT , yx>* cu_q;
- cCudaData<int , int , yx>* cu_part2grid;
- cCudaData<double , PPPM_FLOAT , x >* cu_rho_coeff;
- cCudaData<PPPM_FLOAT , PPPM_FLOAT , x >* cu_debugdata;
- cCudaData<int , int , x >* cu_flag;
- cCudaData<int , int , x >* cu_pppm_grid_n;
- cCudaData<int , int , x >* cu_pppm_grid_ids;
-
+ cCudaData<double , X_FLOAT , yx>* cu_x;
+ cCudaData<double , V_FLOAT , yx>* cu_v;
+ cCudaData<double , F_FLOAT , yx>* cu_f;
+ cCudaData<double , F_FLOAT , yx>* cu_q;
+ cCudaData<int , int , yx>* cu_part2grid;
+ cCudaData<double , PPPM_FLOAT , x >* cu_rho_coeff;
+ cCudaData<PPPM_FLOAT , PPPM_FLOAT , x >* cu_debugdata;
+ cCudaData<int , int , x >* cu_flag;
+ cCudaData<int , int , x >* cu_pppm_grid_n;
+ cCudaData<int , int , x >* cu_pppm_grid_ids;
+
ENERGY_FLOAT* slabbuf;
cCudaData<ENERGY_FLOAT, ENERGY_FLOAT, x >* cu_slabbuf;
-
+
int*** density_brick_int;
PPPM_FLOAT density_intScale;
int pppm_grid_nmax;
int* pppm2partgrid;
- int* pppm_grid;
+ int* pppm_grid;
PPPM_FLOAT* debugdata;
bool firstpass;
-
+
void set_grid();
void allocate();
void deallocate();
-
+
virtual void particle_map();
virtual void make_rho();
void poisson(int, int);
diff --git a/src/USER-CUDA/verlet_cuda.cpp b/src/USER-CUDA/verlet_cuda.cpp
index 4079f3a6c57f6ee1d47fb32523e25ee7709c28c2..a1df9fe3f0b8a6aa6f035a95418ae27e0082ff4a 100644
--- a/src/USER-CUDA/verlet_cuda.cpp
+++ b/src/USER-CUDA/verlet_cuda.cpp
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -58,12 +58,12 @@ using namespace LAMMPS_NS;
#define MAKETIMEING
-VerletCuda::VerletCuda(LAMMPS *lmp, int narg, char **arg) : Verlet(lmp, narg, arg) {
+VerletCuda::VerletCuda(LAMMPS *lmp, int narg, char **arg) : Verlet(lmp, narg, arg) {
cuda = lmp->cuda;
if(cuda == NULL)
error->all(FLERR,"You cannot use a /cuda class, without activating 'cuda' acceleration. Provide '-c on' as command-line argument to LAMMPS..");
- modify_cuda=(ModifyCuda*) modify;
+ modify_cuda=(ModifyCuda*) modify;
int ifix = modify->find_fix("package_omp");
if (ifix >= 0) external_force_clear = 1;
}
@@ -74,44 +74,44 @@ VerletCuda::VerletCuda(LAMMPS *lmp, int narg, char **arg) : Verlet(lmp, narg, ar
void VerletCuda::setup()
{
- //debug related variables
- cuda->debugdata[0]=0;
- cuda->cu_debugdata->upload();
- dotestatom=cuda->dotestatom;
- int testatom=cuda->testatom;//48267;
- if(atom->nlocal==0)
- error->warning(FLERR,"# CUDA: There are currently no atoms on one of the MPI processes. This is known to cause errors with the USER-CUDA package. Please use the 'processors' keyword to enforce more balanced processor layout.");
- MYDBG(printf("# CUDA VerletCuda::setup start\n"); )
-
- cuda->oncpu = true;
- cuda->begin_setup = true;
- cuda->finished_run = false;
-
- time_pair=0;
- time_kspace=0;
- time_comm=0;
- time_modify=0;
- time_fulliterate=0;
-
+ //debug related variables
+ cuda->debugdata[0]=0;
+ cuda->cu_debugdata->upload();
+ dotestatom=cuda->dotestatom;
+ int testatom=cuda->testatom;//48267;
+ if(atom->nlocal==0)
+ error->warning(FLERR,"# CUDA: There are currently no atoms on one of the MPI processes. This is known to cause errors with the USER-CUDA package. Please use the 'processors' keyword to enforce more balanced processor layout.");
+ MYDBG(printf("# CUDA VerletCuda::setup start\n"); )
+
+ cuda->oncpu = true;
+ cuda->begin_setup = true;
+ cuda->finished_run = false;
+
+ time_pair=0;
+ time_kspace=0;
+ time_comm=0;
+ time_modify=0;
+ time_fulliterate=0;
+
atom->setup();
-
- cuda_shared_atom* cu_atom = & cuda->shared_data.atom;
- cuda_shared_domain* cu_domain = & cuda->shared_data.domain;
- cuda_shared_pair* cu_pair = & cuda->shared_data.pair;
- cu_atom->update_nlocal=1;
- cu_atom->update_nmax=1;
-
- if(atom->molecular||(force->kspace&&(not cuda->shared_data.pppm.cudable_force))) cuda->shared_data.pair.collect_forces_later = true;
-
- cuda->setDomainParams();
-
-
- if(cuda->shared_data.me==0)
- printf("# CUDA: VerletCuda::setup: Allocate memory on device for maximum of %i atoms...\n", atom->nmax);
- if(cuda->shared_data.me==0)
- printf("# CUDA: Using precision: Global: %u X: %u V: %u F: %u PPPM: %u \n", CUDA_PRECISION==1?4:8,sizeof(X_FLOAT),sizeof(V_FLOAT),sizeof(F_FLOAT),sizeof(PPPM_FLOAT));
- cuda->allocate();
-
+
+ cuda_shared_atom* cu_atom = & cuda->shared_data.atom;
+ cuda_shared_domain* cu_domain = & cuda->shared_data.domain;
+ cuda_shared_pair* cu_pair = & cuda->shared_data.pair;
+ cu_atom->update_nlocal=1;
+ cu_atom->update_nmax=1;
+
+ if(atom->molecular||(force->kspace&&(not cuda->shared_data.pppm.cudable_force))) cuda->shared_data.pair.collect_forces_later = true;
+
+ cuda->setDomainParams();
+
+
+ if(cuda->shared_data.me==0)
+ printf("# CUDA: VerletCuda::setup: Allocate memory on device for maximum of %i atoms...\n", atom->nmax);
+ if(cuda->shared_data.me==0)
+ printf("# CUDA: Using precision: Global: %u X: %u V: %u F: %u PPPM: %u \n", CUDA_PRECISION==1?4:8,sizeof(X_FLOAT),sizeof(V_FLOAT),sizeof(F_FLOAT),sizeof(PPPM_FLOAT));
+ cuda->allocate();
+
if (comm->me == 0 && screen) fprintf(screen,"Setting up run ...\n");
@@ -140,7 +140,7 @@ void VerletCuda::setup()
if(atom->mass)
cuda->cu_mass->upload();
-
+
if(cuda->cu_map_array)
cuda->cu_map_array->upload();
@@ -157,7 +157,7 @@ void VerletCuda::setup()
#ifdef NO_PREC_TIMING
double startsec,endsec;
#endif
- //if(atom->molecular||(force->kspace&&(not cuda->shared_data.pppm.cudable_force))) cuda->shared_data.pair.collect_forces_later = false;
+ //if(atom->molecular||(force->kspace&&(not cuda->shared_data.pppm.cudable_force))) cuda->shared_data.pair.collect_forces_later = false;
if(test_BpA_vs_TpA && cuda->shared_data.pair.cudable_force && force->pair &&(cuda->shared_data.pair.override_block_per_atom<0))
{
int StyleLoops=10;
@@ -166,10 +166,10 @@ void VerletCuda::setup()
cuda->shared_data.pair.use_block_per_atom = 0;
neighbor->build();
Cuda_Pair_GenerateXType(&cuda->shared_data);
- if(cuda->cu_v_radius)
- Cuda_Pair_GenerateVRadius(&cuda->shared_data);
- if(cuda->cu_omega_rmass)
- Cuda_Pair_GenerateOmegaRmass(&cuda->shared_data);
+ if(cuda->cu_v_radius)
+ Cuda_Pair_GenerateVRadius(&cuda->shared_data);
+ if(cuda->cu_omega_rmass)
+ Cuda_Pair_GenerateOmegaRmass(&cuda->shared_data);
force->pair->compute(eflag,vflag);
CudaWrapper_Sync();
#ifdef NO_PREC_TIMING
@@ -178,17 +178,17 @@ void VerletCuda::setup()
clock_gettime(CLOCK_REALTIME,&starttime);
for(int i=0;i<StyleLoops;i++)
{
- Cuda_Pair_GenerateXType(&cuda->shared_data);
- if(cuda->cu_v_radius)
- Cuda_Pair_GenerateVRadius(&cuda->shared_data);
- if(cuda->cu_omega_rmass)
- Cuda_Pair_GenerateOmegaRmass(&cuda->shared_data);
+ Cuda_Pair_GenerateXType(&cuda->shared_data);
+ if(cuda->cu_v_radius)
+ Cuda_Pair_GenerateVRadius(&cuda->shared_data);
+ if(cuda->cu_omega_rmass)
+ Cuda_Pair_GenerateOmegaRmass(&cuda->shared_data);
force->pair->compute(eflag,vflag);
CudaWrapper_Sync();
}
clock_gettime(CLOCK_REALTIME,&endtime);
-
- double TpAtime=endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000;
+
+ double TpAtime=endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000;
#ifdef NO_PREC_TIMING
endsec = 1.0*clock()/CLOCKS_PER_SEC;
TpAtime = endsec - startsec;
@@ -198,10 +198,10 @@ void VerletCuda::setup()
cuda->shared_data.pair.use_block_per_atom = 1;
neighbor->build();
Cuda_Pair_GenerateXType(&cuda->shared_data);
- if(cuda->cu_v_radius)
- Cuda_Pair_GenerateVRadius(&cuda->shared_data);
- if(cuda->cu_omega_rmass)
- Cuda_Pair_GenerateOmegaRmass(&cuda->shared_data);
+ if(cuda->cu_v_radius)
+ Cuda_Pair_GenerateVRadius(&cuda->shared_data);
+ if(cuda->cu_omega_rmass)
+ Cuda_Pair_GenerateOmegaRmass(&cuda->shared_data);
force->pair->compute(eflag,vflag);
CudaWrapper_Sync();
@@ -211,26 +211,26 @@ void VerletCuda::setup()
#endif
for(int i=0;i<StyleLoops;i++)
{
- Cuda_Pair_GenerateXType(&cuda->shared_data);
- if(cuda->cu_v_radius)
- Cuda_Pair_GenerateVRadius(&cuda->shared_data);
- if(cuda->cu_omega_rmass)
- Cuda_Pair_GenerateOmegaRmass(&cuda->shared_data);
+ Cuda_Pair_GenerateXType(&cuda->shared_data);
+ if(cuda->cu_v_radius)
+ Cuda_Pair_GenerateVRadius(&cuda->shared_data);
+ if(cuda->cu_omega_rmass)
+ Cuda_Pair_GenerateOmegaRmass(&cuda->shared_data);
force->pair->compute(eflag,vflag);
CudaWrapper_Sync();
}
clock_gettime(CLOCK_REALTIME,&endtime);
- double BpAtime=endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000;
+ double BpAtime=endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000;
#ifdef NO_PREC_TIMING
endsec = 1.0*clock()/CLOCKS_PER_SEC;
BpAtime = endsec - startsec;
#endif
-
- if(cuda->shared_data.me==0)
- printf("\n# CUDA: Timing of parallelisation layout with %i loops:\n",StyleLoops);
- if(cuda->shared_data.me==0)
- printf("# CUDA: BpA TpA\n %lf %lf\n",BpAtime,TpAtime);
- if(BpAtime>TpAtime) cuda->shared_data.pair.use_block_per_atom = 0;
+
+ if(cuda->shared_data.me==0)
+ printf("\n# CUDA: Timing of parallelisation layout with %i loops:\n",StyleLoops);
+ if(cuda->shared_data.me==0)
+ printf("# CUDA: BpA TpA\n %lf %lf\n",BpAtime,TpAtime);
+ if(BpAtime>TpAtime) cuda->shared_data.pair.use_block_per_atom = 0;
}
else
cuda->shared_data.pair.use_block_per_atom = cuda->shared_data.pair.override_block_per_atom;
@@ -238,7 +238,7 @@ void VerletCuda::setup()
if(atom->molecular||(force->kspace&&(not cuda->shared_data.pppm.cudable_force))) cuda->shared_data.pair.collect_forces_later = true;
neighbor->build();
neighbor->ncalls = 0;
-
+
force_clear();
modify->setup_pre_force(vflag);
@@ -246,38 +246,38 @@ void VerletCuda::setup()
cuda->cu_f->download();
if(cuda->cu_torque)
cuda->cu_torque->download();
-
+
//printf("# Verlet::setup: g f[0] = (%f, %f, %f)\n", atom->f[0][0], atom->f[0][1], atom->f[0][2]);
-
+
MYDBG( printf("# CUDA: VerletCuda::setup: initial force compute\n"); )
//test_atom(testatom,"pre pair force");
-
+
if(cuda->shared_data.pair.cudable_force)
{
- cuda->uploadAll();
- Cuda_Pair_GenerateXType(&cuda->shared_data);
- if(cuda->cu_v_radius)
- Cuda_Pair_GenerateVRadius(&cuda->shared_data);
- if(cuda->cu_omega_rmass)
- Cuda_Pair_GenerateOmegaRmass(&cuda->shared_data);
+ cuda->uploadAll();
+ Cuda_Pair_GenerateXType(&cuda->shared_data);
+ if(cuda->cu_v_radius)
+ Cuda_Pair_GenerateVRadius(&cuda->shared_data);
+ if(cuda->cu_omega_rmass)
+ Cuda_Pair_GenerateOmegaRmass(&cuda->shared_data);
}
if (force->pair) force->pair->compute(eflag,vflag);
-
+
if(cuda->shared_data.pair.cudable_force)
{
- if(cuda->shared_data.pair.collect_forces_later)
- {
- if(eflag) cuda->cu_eng_vdwl->upload();
- if(eflag) cuda->cu_eng_coul->upload();
- if(vflag) cuda->cu_virial->upload();
+ if(cuda->shared_data.pair.collect_forces_later)
+ {
+ if(eflag) cuda->cu_eng_vdwl->upload();
+ if(eflag) cuda->cu_eng_coul->upload();
+ if(vflag) cuda->cu_virial->upload();
Cuda_Pair_CollectForces(&cuda->shared_data,eflag,vflag);
- if(eflag) cuda->cu_eng_vdwl->download();
- if(eflag) cuda->cu_eng_coul->download();
- if(vflag) cuda->cu_virial->download();
- }
- cuda->downloadAll();
+ if(eflag) cuda->cu_eng_vdwl->download();
+ if(eflag) cuda->cu_eng_coul->download();
+ if(vflag) cuda->cu_virial->download();
+ }
+ cuda->downloadAll();
}
test_atom(testatom,"post pair force");
@@ -295,12 +295,12 @@ void VerletCuda::setup()
if(cuda->shared_data.pppm.cudable_force)
{
- cuda->cu_tag ->upload();
- cuda->cu_type->upload();
- cuda->cu_x ->upload();
- cuda->cu_v ->upload();
- cuda->cu_f ->upload();
- if(cu_atom->q_flag) cuda->cu_q->upload();
+ cuda->cu_tag ->upload();
+ cuda->cu_type->upload();
+ cuda->cu_x ->upload();
+ cuda->cu_v ->upload();
+ cuda->cu_f ->upload();
+ if(cu_atom->q_flag) cuda->cu_q->upload();
}
if (force->kspace) {
force->kspace->setup();
@@ -308,9 +308,9 @@ void VerletCuda::setup()
}
if(cuda->shared_data.pppm.cudable_force)
{
- cuda->cu_f ->download();
+ cuda->cu_f ->download();
}
-
+
test_atom(testatom,"post kspace");
cuda->uploadAll();
@@ -318,7 +318,7 @@ void VerletCuda::setup()
cuda->downloadAll();
test_atom(testatom,"post reverse comm");
-
+
if(cuda->shared_data.me==0)
printf("# CUDA: Total Device Memory useage post setup: %lf MB\n",1.0*CudaWrapper_CheckMemUseage()/1024/1024);
@@ -329,7 +329,7 @@ void VerletCuda::setup()
output->setup(1);
test_atom(testatom,"post setup");
-
+
MYDBG( printf("# CUDA: VerletCuda::setup: done\n"); )
cuda->finished_setup = true;
cuda->oncpu = false;
@@ -340,38 +340,38 @@ void VerletCuda::setup()
void VerletCuda::setup_minimal(int flag)
{
-
- dotestatom=0;
- int testatom=104;
- cuda->oncpu = true;
- cuda->begin_setup = true;
- cuda->finished_run = false;
- MYDBG(printf("# CUDA VerletCuda::setup start\n"); )
- time_pair=0;
- time_kspace=0;
- time_comm=0;
- time_modify=0;
- time_fulliterate=0;
-
- //cuda->allocate();
-
- cuda_shared_atom* cu_atom = & cuda->shared_data.atom;
- cuda_shared_domain* cu_domain = & cuda->shared_data.domain;
- cuda_shared_pair* cu_pair = & cuda->shared_data.pair;
- cu_atom->update_nlocal=1;
- cu_atom->update_nmax=1;
-
- if(atom->molecular) cuda->shared_data.pair.collect_forces_later = true;
-
- cuda->setDomainParams();
-
-
-
- if(cuda->shared_data.me==0)
- printf("# CUDA: VerletCuda::setup: Allocate memory on device for maximum of %i atoms...\n", atom->nmax);
- cuda->allocate();
-
-
+
+ dotestatom=0;
+ int testatom=104;
+ cuda->oncpu = true;
+ cuda->begin_setup = true;
+ cuda->finished_run = false;
+ MYDBG(printf("# CUDA VerletCuda::setup start\n"); )
+ time_pair=0;
+ time_kspace=0;
+ time_comm=0;
+ time_modify=0;
+ time_fulliterate=0;
+
+ //cuda->allocate();
+
+ cuda_shared_atom* cu_atom = & cuda->shared_data.atom;
+ cuda_shared_domain* cu_domain = & cuda->shared_data.domain;
+ cuda_shared_pair* cu_pair = & cuda->shared_data.pair;
+ cu_atom->update_nlocal=1;
+ cu_atom->update_nmax=1;
+
+ if(atom->molecular) cuda->shared_data.pair.collect_forces_later = true;
+
+ cuda->setDomainParams();
+
+
+
+ if(cuda->shared_data.me==0)
+ printf("# CUDA: VerletCuda::setup: Allocate memory on device for maximum of %i atoms...\n", atom->nmax);
+ cuda->allocate();
+
+
// setup domain, communication and neighboring
@@ -393,60 +393,60 @@ void VerletCuda::setup_minimal(int flag)
neighbor->ncalls = 0;
}
- if(cuda->shared_data.me==0)
- printf("# CUDA: VerletCuda::setup: Upload data...\n");
- cuda->uploadAll();
+ if(cuda->shared_data.me==0)
+ printf("# CUDA: VerletCuda::setup: Upload data...\n");
+ cuda->uploadAll();
cuda->uploadAllNeighborLists();
- if(atom->mass)
- cuda->cu_mass->upload();
-
- if(cuda->cu_map_array)
- cuda->cu_map_array->upload();
-
+ if(atom->mass)
+ cuda->cu_mass->upload();
+
+ if(cuda->cu_map_array)
+ cuda->cu_map_array->upload();
+
// compute all forces
ev_set(update->ntimestep);
if(elist_atom) cuda->shared_data.atom.need_eatom = 1;
if(vlist_atom) cuda->shared_data.atom.need_vatom = 1;
if(elist_atom||vlist_atom) cuda->checkResize();
-
+
force_clear();
cuda->cu_f->download();
-
+
//printf("# Verlet::setup: g f[0] = (%f, %f, %f)\n", atom->f[0][0], atom->f[0][1], atom->f[0][2]);
-
+
cuda->cu_mass->upload();
MYDBG( printf("# CUDA: VerletCuda::setup: initial force compute\n"); )
test_atom(testatom,"pre pair force");
-
+
if(cuda->shared_data.pair.cudable_force)
{
- cuda->uploadAll();
- Cuda_Pair_GenerateXType(&cuda->shared_data);
- if(cuda->cu_v_radius)
- Cuda_Pair_GenerateVRadius(&cuda->shared_data);
- if(cuda->cu_omega_rmass)
- Cuda_Pair_GenerateOmegaRmass(&cuda->shared_data);
+ cuda->uploadAll();
+ Cuda_Pair_GenerateXType(&cuda->shared_data);
+ if(cuda->cu_v_radius)
+ Cuda_Pair_GenerateVRadius(&cuda->shared_data);
+ if(cuda->cu_omega_rmass)
+ Cuda_Pair_GenerateOmegaRmass(&cuda->shared_data);
}
-
+
if (force->pair) force->pair->compute(eflag,vflag);
-
+
if(cuda->shared_data.pair.cudable_force)
{
- if(cuda->shared_data.pair.collect_forces_later)
- {
- if(eflag) cuda->cu_eng_vdwl->upload();
- if(eflag) cuda->cu_eng_coul->upload();
- if(vflag) cuda->cu_virial->upload();
+ if(cuda->shared_data.pair.collect_forces_later)
+ {
+ if(eflag) cuda->cu_eng_vdwl->upload();
+ if(eflag) cuda->cu_eng_coul->upload();
+ if(vflag) cuda->cu_virial->upload();
Cuda_Pair_CollectForces(&cuda->shared_data,eflag,vflag);
- if(eflag) cuda->cu_eng_vdwl->download();
- if(eflag) cuda->cu_eng_coul->download();
- if(vflag) cuda->cu_virial->download();
- }
- cuda->downloadAll();
+ if(eflag) cuda->cu_eng_vdwl->download();
+ if(eflag) cuda->cu_eng_coul->download();
+ if(vflag) cuda->cu_virial->download();
+ }
+ cuda->downloadAll();
}
-
+
test_atom(testatom,"post pair force");
MYDBG( printf("# CUDA: VerletCuda::setup: initial force compute done\n"); )
@@ -462,12 +462,12 @@ void VerletCuda::setup_minimal(int flag)
if(cuda->shared_data.pppm.cudable_force)
{
- cuda->cu_tag ->upload();
- cuda->cu_type->upload();
- cuda->cu_x ->upload();
- cuda->cu_v ->upload();
- cuda->cu_f ->upload();
- if(cu_atom->q_flag) cuda->cu_q->upload();
+ cuda->cu_tag ->upload();
+ cuda->cu_type->upload();
+ cuda->cu_x ->upload();
+ cuda->cu_v ->upload();
+ cuda->cu_f ->upload();
+ if(cu_atom->q_flag) cuda->cu_q->upload();
}
if (force->kspace) {
force->kspace->setup();
@@ -475,9 +475,9 @@ void VerletCuda::setup_minimal(int flag)
}
if(cuda->shared_data.pppm.cudable_force)
{
- cuda->cu_f ->download();
+ cuda->cu_f ->download();
}
-
+
test_atom(testatom,"post kspace");
cuda->uploadAll();
@@ -485,7 +485,7 @@ void VerletCuda::setup_minimal(int flag)
cuda->downloadAll();
test_atom(testatom,"post reverse comm");
-
+
if(cuda->shared_data.me==0)
printf("# CUDA: Total Device Memory useage post setup: %lf MB\n",1.0*CudaWrapper_CheckMemUseage()/1024/1024);
@@ -516,16 +516,16 @@ void VerletCuda::run(int n)
cuda->setTimingsZero();
static double testtime=0.0;
-// clock_gettime(CLOCK_REALTIME,&starttime);
-// clock_gettime(CLOCK_REALTIME,&endtime);
-// testtime+=endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000;
-// printf("Time: %lf\n",testtime);*/
+// clock_gettime(CLOCK_REALTIME,&starttime);
+// clock_gettime(CLOCK_REALTIME,&endtime);
+// testtime+=endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000;
+// printf("Time: %lf\n",testtime);*/
cuda_shared_domain* cu_domain = & cuda->shared_data.domain;
int nflag,ntimestep,sortflag;
-
+
int n_initial_integrate = modify_cuda->n_initial_integrate;
int n_post_integrate = modify_cuda->n_post_integrate;
int n_final_integrate = modify_cuda->n_final_integrate;
@@ -535,37 +535,37 @@ void VerletCuda::run(int n)
int n_post_force = modify_cuda->n_post_force;
int n_end_of_step = modify_cuda->n_end_of_step;
MYDBG(printf("# CUDA: Fixes: i_int: %i p_int: %i f_int: %i pr_exc: %i pr_neigh: %i pr_f: %i p_f: %i eos: %i\n",
- n_initial_integrate,n_post_integrate,n_final_integrate,n_pre_exchange,n_pre_neighbor,n_pre_force,n_post_force,n_end_of_step);)
+ n_initial_integrate,n_post_integrate,n_final_integrate,n_pre_exchange,n_pre_neighbor,n_pre_force,n_post_force,n_end_of_step);)
if (atom->sortfreq > 0) sortflag = 1;
else sortflag = 0;
- if(cuda->shared_data.me==0)
- {
- if((not cuda->shared_data.pair.cudable_force)&&(force->pair))
- error->warning(FLERR,"# CUDA: You asked for a Verlet integration using Cuda, "
- "but selected a pair force which has not yet been ported to Cuda");
- if((not cuda->shared_data.pppm.cudable_force)&&(force->kspace))
- error->warning(FLERR,"# CUDA: You asked for a Verlet integration using Cuda, "
- "but selected a kspace force which has not yet been ported to Cuda");
+ if(cuda->shared_data.me==0)
+ {
+ if((not cuda->shared_data.pair.cudable_force)&&(force->pair))
+ error->warning(FLERR,"# CUDA: You asked for a Verlet integration using Cuda, "
+ "but selected a pair force which has not yet been ported to Cuda");
+ if((not cuda->shared_data.pppm.cudable_force)&&(force->kspace))
+ error->warning(FLERR,"# CUDA: You asked for a Verlet integration using Cuda, "
+ "but selected a kspace force which has not yet been ported to Cuda");
if(modify_cuda->n_post_integrate_host+modify_cuda->n_pre_exchange_host+modify_cuda->n_pre_neighbor_host+modify_cuda->n_pre_force_host+modify_cuda->n_post_force_host+modify_cuda->n_end_of_step_host+modify_cuda->n_initial_integrate_host+modify_cuda->n_final_integrate_host)
- error->warning(FLERR,"# CUDA: You asked for a Verlet integration using Cuda, "
- "but several fixes have not yet been ported to Cuda.\n"
- "This can cause a severe speed penalty due to frequent data synchronization between host and GPU.");
- if(atom->firstgroupname)
- error->warning(FLERR,"Warning: firstgroupname is used, this will cause additional data transfers.");
- }
+ error->warning(FLERR,"# CUDA: You asked for a Verlet integration using Cuda, "
+ "but several fixes have not yet been ported to Cuda.\n"
+ "This can cause a severe speed penalty due to frequent data synchronization between host and GPU.");
+ if(atom->firstgroupname)
+ error->warning(FLERR,"Warning: firstgroupname is used, this will cause additional data transfers.");
+ }
cuda->uploadAll();
-
+
if(cuda->neighbor_decide_by_integrator && cuda->cu_xhold)
{
- const int n=cuda->shared_data.atom.maxhold;
- CudaWrapper_CopyData(cuda->cu_xhold->dev_data(),cuda->cu_x->dev_data(),n*sizeof(X_FLOAT));
- CudaWrapper_CopyData((void*) &((X_FLOAT*)cuda->cu_xhold->dev_data())[n],(void*) &((X_FLOAT*)cuda->cu_x->dev_data())[atom->nmax],n*sizeof(X_FLOAT));
- CudaWrapper_CopyData((void*) &((X_FLOAT*)cuda->cu_xhold->dev_data())[2*n],(void*) &((X_FLOAT*)cuda->cu_x->dev_data())[2*atom->nmax],n*sizeof(X_FLOAT));
+ const int n=cuda->shared_data.atom.maxhold;
+ CudaWrapper_CopyData(cuda->cu_xhold->dev_data(),cuda->cu_x->dev_data(),n*sizeof(X_FLOAT));
+ CudaWrapper_CopyData((void*) &((X_FLOAT*)cuda->cu_xhold->dev_data())[n],(void*) &((X_FLOAT*)cuda->cu_x->dev_data())[atom->nmax],n*sizeof(X_FLOAT));
+ CudaWrapper_CopyData((void*) &((X_FLOAT*)cuda->cu_xhold->dev_data())[2*n],(void*) &((X_FLOAT*)cuda->cu_x->dev_data())[2*atom->nmax],n*sizeof(X_FLOAT));
}
-
+
cuda->shared_data.atom.reneigh_flag=0;
cuda->shared_data.atom.update_nlocal=1;
cuda->shared_data.atom.update_nmax=1;
@@ -576,422 +576,422 @@ void VerletCuda::run(int n)
cuda->downloadtime=0;
int firstreneigh=1;
- for(int i = 0; i < n; i++)
- {
- if(atom->nlocal==0)
- error->warning(FLERR,"# CUDA: There are currently no atoms on one of the MPI processes. This is currently prone to encountering errors with USER-CUDA package. Please use the 'processors' keyword to use a more balanced processor layout.");
- ntimestep = ++update->ntimestep;
- ev_set(ntimestep);
-
- // initial time integration
-
- test_atom(testatom,"Pre initial");
-
- MYDBG( printf("# CUDA VerletCuda::iterate: before initial_integrate\n"); )
-
- modify->initial_integrate(vflag);
-
- MYDBG( printf("# CUDA VerletCuda::iterate: after initial_integrate\n"); )
-
- if(n_post_integrate) modify->post_integrate();
-
-
-
- // regular communication vs neighbor list rebuild
-
- test_atom(testatom,"Pre Exchange");
-
- MYDBG( printf("# CUDA VerletCuda::iterate: before neighbor decide\n"); )
- nflag = neighbor->decide();
- if(nflag == 0)
- {
- MYDBG( printf("# CUDA VerletCuda::iterate: communicate\n"); )
- timer->stamp();
-
- if((not (eflag||vflag))&&(cuda->shared_data.overlap_comm))
- {
- //overlap forward communication of ghost atom positions with inner force calculation (interactions between local atoms)
- //build communication buffers
- // printf("Pre forward_comm(1)\n");
- clock_gettime(CLOCK_REALTIME,&starttotal);
- cuda->shared_data.atom.reneigh_flag=0;
- clock_gettime(CLOCK_REALTIME,&starttime);
- timer->stamp();
- comm->forward_comm(1);
- timer->stamp(TIME_COMM);
- clock_gettime(CLOCK_REALTIME,&endtime);
- cuda->shared_data.cuda_timings.comm_forward_total+=
- endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000;
-
- //prepare force calculation
- // printf("Pre force_clear\n");
- force_clear();
- // printf("Pre Generate XType\n");
- Cuda_Pair_GenerateXType(&cuda->shared_data);
- if(cuda->cu_v_radius)
- Cuda_Pair_GenerateVRadius(&cuda->shared_data);
- if(cuda->cu_omega_rmass)
- Cuda_Pair_GenerateOmegaRmass(&cuda->shared_data);
-
- //start force calculation asynchronus
- cuda->shared_data.comm.comm_phase=1;
- force->pair->compute(eflag, vflag);
- timer->stamp(TIME_PAIR);
+ for(int i = 0; i < n; i++)
+ {
+ if(atom->nlocal==0)
+ error->warning(FLERR,"# CUDA: There are currently no atoms on one of the MPI processes. This is currently prone to encountering errors with USER-CUDA package. Please use the 'processors' keyword to use a more balanced processor layout.");
+ ntimestep = ++update->ntimestep;
+ ev_set(ntimestep);
+
+ // initial time integration
+
+ test_atom(testatom,"Pre initial");
+
+ MYDBG( printf("# CUDA VerletCuda::iterate: before initial_integrate\n"); )
+
+ modify->initial_integrate(vflag);
+
+ MYDBG( printf("# CUDA VerletCuda::iterate: after initial_integrate\n"); )
+
+ if(n_post_integrate) modify->post_integrate();
+
+
+
+ // regular communication vs neighbor list rebuild
+
+ test_atom(testatom,"Pre Exchange");
+
+ MYDBG( printf("# CUDA VerletCuda::iterate: before neighbor decide\n"); )
+ nflag = neighbor->decide();
+ if(nflag == 0)
+ {
+ MYDBG( printf("# CUDA VerletCuda::iterate: communicate\n"); )
+ timer->stamp();
+
+ if((not (eflag||vflag))&&(cuda->shared_data.overlap_comm))
+ {
+ //overlap forward communication of ghost atom positions with inner force calculation (interactions between local atoms)
+ //build communication buffers
+ // printf("Pre forward_comm(1)\n");
+ clock_gettime(CLOCK_REALTIME,&starttotal);
+ cuda->shared_data.atom.reneigh_flag=0;
+ clock_gettime(CLOCK_REALTIME,&starttime);
+ timer->stamp();
+ comm->forward_comm(1);
+ timer->stamp(TIME_COMM);
+ clock_gettime(CLOCK_REALTIME,&endtime);
+ cuda->shared_data.cuda_timings.comm_forward_total+=
+ endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000;
+
+ //prepare force calculation
+ // printf("Pre force_clear\n");
+ force_clear();
+ // printf("Pre Generate XType\n");
+ Cuda_Pair_GenerateXType(&cuda->shared_data);
+ if(cuda->cu_v_radius)
+ Cuda_Pair_GenerateVRadius(&cuda->shared_data);
+ if(cuda->cu_omega_rmass)
+ Cuda_Pair_GenerateOmegaRmass(&cuda->shared_data);
+
+ //start force calculation asynchronus
+ cuda->shared_data.comm.comm_phase=1;
+ force->pair->compute(eflag, vflag);
+ timer->stamp(TIME_PAIR);
//CudaWrapper_Sync();
-
- //download comm buffers from GPU, perform MPI communication and upload buffers again
- clock_gettime(CLOCK_REALTIME,&starttime);
- comm->forward_comm(2);
- clock_gettime(CLOCK_REALTIME,&endtime);
- cuda->shared_data.cuda_timings.comm_forward_total+=
- endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000;
- timer->stamp(TIME_COMM);
-
- //wait for force calculation
- CudaWrapper_Sync();
- timer->stamp(TIME_PAIR);
-
- //unpack communication buffers
- clock_gettime(CLOCK_REALTIME,&starttime);
- comm->forward_comm(3);
- clock_gettime(CLOCK_REALTIME,&endtime);
- cuda->shared_data.cuda_timings.comm_forward_total+=
- endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000;
-
- timer->stamp(TIME_COMM);
- MYDBG( printf("# CUDA VerletCuda::iterate: communicate done\n"); )
- cuda->shared_data.cuda_timings.test1+=
- endtotal.tv_sec-starttotal.tv_sec+1.0*(endtotal.tv_nsec-starttotal.tv_nsec)/1000000000;
- }
- else
- {
- //perform standard forward communication
- clock_gettime(CLOCK_REALTIME,&starttime);
- comm->forward_comm();
- clock_gettime(CLOCK_REALTIME,&endtime);
- cuda->shared_data.cuda_timings.comm_forward_total+=
- endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000;
- timer->stamp(TIME_COMM);
- MYDBG( printf("# CUDA VerletCuda::iterate: communicate done\n"); )
- }
- }
- else
- {
- int nlocalold=cuda->shared_data.atom.nlocal;
- if(firstreneigh)
- {
- cuda->shared_data.atom.update_nlocal=1;
- cuda->shared_data.atom.update_nmax=1;
- firstreneigh=0;
- }
- cuda->shared_data.buffer_new=1;
- MYDBG( printf("# CUDA VerletCuda::iterate: neighbor\n"); )
- cuda->setDomainParams();
- if(n_pre_exchange) modify->pre_exchange();
- if(atom->nlocal!=cuda->shared_data.atom.nlocal) //did someone add atoms during pre_exchange?
- {
- cuda->checkResize();
- cuda->uploadAll();
- }
-
- //check domain changes
- if(domain->triclinic) domain->x2lamda(atom->nlocal);
- MYDBG( printf("# CUDA VerletCuda::iterate: neighbor pbc\n"); )
- domain->pbc();
- if(domain->box_change)
- {
- domain->reset_box();
- comm->setup();
- if (neighbor->style) neighbor->setup_bins();
-
- }
- timer->stamp();
- MYDBG( printf("# CUDA VerletCuda::iterate: neighbor exchange\n"); )
-
- //perform exchange of local atoms
- clock_gettime(CLOCK_REALTIME,&starttime);
- comm->exchange();
- clock_gettime(CLOCK_REALTIME,&endtime);
-
- //special and nspecial fields of the atom data are not currently transfered via the GPU buffer might be changed in the future
- if(comm->nprocs>1)
- {
- clock_gettime(CLOCK_REALTIME,&starttime);
- if(atom->special)
- cuda->cu_special->upload();
- if(atom->nspecial)
- cuda->cu_nspecial->upload();
- clock_gettime(CLOCK_REALTIME,&endtime);
- cuda->shared_data.cuda_timings.test1+=
- endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000;
- }
-
- cuda->shared_data.cuda_timings.comm_exchange_total+=
- endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000;
-
- if(nlocalold!=cuda->shared_data.atom.nlocal) cuda->shared_data.atom.update_nlocal=2;
-
- //sort atoms
- if (sortflag && ntimestep >= atom->nextsort) atom->sort();
- MYDBG( printf("# CUDA VerletCuda::iterate: neighbor borders\n"); )
-
- //generate ghost atom lists, and transfer ghost atom data
- clock_gettime(CLOCK_REALTIME,&starttime);
- comm->borders();
- clock_gettime(CLOCK_REALTIME,&endtime);
- cuda->shared_data.cuda_timings.comm_border_total+=
- endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000;
-
- clock_gettime(CLOCK_REALTIME,&starttime);
- //atom index maps are generated on CPU, and need to be transfered to GPU if they are used
- if(cuda->cu_map_array)
- cuda->cu_map_array->upload();
-
-
- if(domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
-
- if(n_pre_neighbor) modify->pre_neighbor();
-
- cuda->shared_data.buffer_new=2;
- if(atom->molecular) cuda->cu_molecule->download();
- MYDBG( printf("# CUDA VerletCuda::iterate: neighbor build\n"); )
- timer->stamp(TIME_COMM);
- clock_gettime(CLOCK_REALTIME,&endtime);
- cuda->shared_data.cuda_timings.test2+=
- endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000;
-
- //rebuild neighbor list
- test_atom(testatom,"Pre Neighbor");
- neighbor->build();
- timer->stamp(TIME_NEIGHBOR);
- MYDBG( printf("# CUDA VerletCuda::iterate: neighbor done\n"); )
-
- //if bonded interactions are used (in this case collect_forces_later is true), transfer data which only changes upon exchange/border routines from GPU to CPU
- if(cuda->shared_data.pair.collect_forces_later)
- {
- if(cuda->cu_molecule) cuda->cu_molecule->download();
- cuda->cu_tag->download();
- cuda->cu_type->download();
- cuda->cu_mask->download();
- if(cuda->cu_q) cuda->cu_q->download();
- }
- cuda->shared_data.comm.comm_phase=3;
- }
-
- test_atom(testatom,"Post Exchange");
-
- // force computations
-
- //only do force_clear if it has not been done during overlap of communication with local interactions
- if(not((not (eflag||vflag))&&(cuda->shared_data.overlap_comm)&&(cuda->shared_data.comm.comm_phase<3)))
- force_clear();
-
- if(n_pre_force) modify->pre_force(vflag);
-
- timer->stamp();
-
- //if overlap of bonded interactions with nonbonded interactions takes place, download forces and positions
- /* if(cuda->shared_data.pair.collect_forces_later)
- {
- cuda->cu_x->downloadAsync(2);
- cuda->cu_f->downloadAsync(2);
- }*/
-
- if(force->pair)
- {
- if((not (eflag||vflag))&&(cuda->shared_data.overlap_comm)&&(cuda->shared_data.comm.comm_phase<3)&&cuda->shared_data.pair.cudable_force)
- {
- //second part of force calculations in case of overlaping it with commuincation. Only interactions between local and ghost atoms are done now
- //regenerate data layout for force computations, its actually only needed for the ghost atoms
- cuda->shared_data.comm.comm_phase=2;
-
- timespec atime1,atime2;
- clock_gettime(CLOCK_REALTIME,&atime1);
-
- Cuda_Pair_GenerateXType(&cuda->shared_data);
- if(cuda->cu_v_radius)
- Cuda_Pair_GenerateVRadius(&cuda->shared_data);
- if(cuda->cu_omega_rmass)
- Cuda_Pair_GenerateOmegaRmass(&cuda->shared_data);
-
- clock_gettime(CLOCK_REALTIME,&atime2);
- cuda->shared_data.cuda_timings.pair_xtype_conversion+=
- atime2.tv_sec-atime1.tv_sec+1.0*(atime2.tv_nsec-atime1.tv_nsec)/1000000000;
- force->pair->compute(eflag, vflag);
-
- }
- else
- {
- //calculate complete pair interactions
- if(not cuda->shared_data.pair.cudable_force) cuda->downloadAll();
- else
- {
- //regenerate data layout for force computations, its actually only needed for the ghost atoms
- timespec atime1,atime2;
- clock_gettime(CLOCK_REALTIME,&atime1);
-
- Cuda_Pair_GenerateXType(&cuda->shared_data);
- if(cuda->cu_v_radius)
- Cuda_Pair_GenerateVRadius(&cuda->shared_data);
- if(cuda->cu_omega_rmass)
- Cuda_Pair_GenerateOmegaRmass(&cuda->shared_data);
-
- clock_gettime(CLOCK_REALTIME,&atime2);
- cuda->shared_data.cuda_timings.pair_xtype_conversion+=
- atime2.tv_sec-atime1.tv_sec+1.0*(atime2.tv_nsec-atime1.tv_nsec)/1000000000;
- }
- cuda->shared_data.comm.comm_phase=0;
- force->pair->compute(eflag, vflag);
- }
-
- if(not cuda->shared_data.pair.cudable_force) cuda->uploadAll();
-
- //wait for force calculation in case of not using overlap with bonded interactions
- if(not cuda->shared_data.pair.collect_forces_later)
- CudaWrapper_Sync();
-
- timer->stamp(TIME_PAIR);
- }
-
- //calculate bonded interactions
- if(atom->molecular)
- {
- cuda->cu_x->downloadAsync(2);
- if(n_pre_force==0) Verlet::force_clear();
- else cuda->cu_f->downloadAsync(2);
-
- timer->stamp(TIME_PAIR);
-
- test_atom(testatom,"pre bond force");
- if(force->bond) force->bond->compute(eflag, vflag);
- if(force->angle) force->angle->compute(eflag, vflag);
- if(force->dihedral) force->dihedral->compute(eflag, vflag);
- if(force->improper) force->improper->compute(eflag, vflag);
- timer->stamp(TIME_BOND);
- }
-
- //collect forces in case pair force and bonded interactions were overlapped, and either no KSPACE or a GPU KSPACE style is used
- if(cuda->shared_data.pair.collect_forces_later&&cuda->shared_data.pair.cudable_force&&(not (force->kspace&&(not cuda->shared_data.pppm.cudable_force))))
- {
- clock_gettime(CLOCK_REALTIME,&starttime);
- cuda->cu_f->uploadAsync(2);
-
- test_atom(testatom,"post molecular force");
-
-
- if(eflag) cuda->cu_eng_vdwl->upload();
- if(eflag) cuda->cu_eng_coul->upload();
- if(vflag) cuda->cu_virial->upload();
+
+ //download comm buffers from GPU, perform MPI communication and upload buffers again
+ clock_gettime(CLOCK_REALTIME,&starttime);
+ comm->forward_comm(2);
+ clock_gettime(CLOCK_REALTIME,&endtime);
+ cuda->shared_data.cuda_timings.comm_forward_total+=
+ endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000;
+ timer->stamp(TIME_COMM);
+
+ //wait for force calculation
+ CudaWrapper_Sync();
+ timer->stamp(TIME_PAIR);
+
+ //unpack communication buffers
+ clock_gettime(CLOCK_REALTIME,&starttime);
+ comm->forward_comm(3);
+ clock_gettime(CLOCK_REALTIME,&endtime);
+ cuda->shared_data.cuda_timings.comm_forward_total+=
+ endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000;
+
+ timer->stamp(TIME_COMM);
+ MYDBG( printf("# CUDA VerletCuda::iterate: communicate done\n"); )
+ cuda->shared_data.cuda_timings.test1+=
+ endtotal.tv_sec-starttotal.tv_sec+1.0*(endtotal.tv_nsec-starttotal.tv_nsec)/1000000000;
+ }
+ else
+ {
+ //perform standard forward communication
+ clock_gettime(CLOCK_REALTIME,&starttime);
+ comm->forward_comm();
+ clock_gettime(CLOCK_REALTIME,&endtime);
+ cuda->shared_data.cuda_timings.comm_forward_total+=
+ endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000;
+ timer->stamp(TIME_COMM);
+ MYDBG( printf("# CUDA VerletCuda::iterate: communicate done\n"); )
+ }
+ }
+ else
+ {
+ int nlocalold=cuda->shared_data.atom.nlocal;
+ if(firstreneigh)
+ {
+ cuda->shared_data.atom.update_nlocal=1;
+ cuda->shared_data.atom.update_nmax=1;
+ firstreneigh=0;
+ }
+ cuda->shared_data.buffer_new=1;
+ MYDBG( printf("# CUDA VerletCuda::iterate: neighbor\n"); )
+ cuda->setDomainParams();
+ if(n_pre_exchange) modify->pre_exchange();
+ if(atom->nlocal!=cuda->shared_data.atom.nlocal) //did someone add atoms during pre_exchange?
+ {
+ cuda->checkResize();
+ cuda->uploadAll();
+ }
+
+ //check domain changes
+ if(domain->triclinic) domain->x2lamda(atom->nlocal);
+ MYDBG( printf("# CUDA VerletCuda::iterate: neighbor pbc\n"); )
+ domain->pbc();
+ if(domain->box_change)
+ {
+ domain->reset_box();
+ comm->setup();
+ if (neighbor->style) neighbor->setup_bins();
+
+ }
+ timer->stamp();
+ MYDBG( printf("# CUDA VerletCuda::iterate: neighbor exchange\n"); )
+
+ //perform exchange of local atoms
+ clock_gettime(CLOCK_REALTIME,&starttime);
+ comm->exchange();
+ clock_gettime(CLOCK_REALTIME,&endtime);
+
+ //special and nspecial fields of the atom data are not currently transfered via the GPU buffer might be changed in the future
+ if(comm->nprocs>1)
+ {
+ clock_gettime(CLOCK_REALTIME,&starttime);
+ if(atom->special)
+ cuda->cu_special->upload();
+ if(atom->nspecial)
+ cuda->cu_nspecial->upload();
+ clock_gettime(CLOCK_REALTIME,&endtime);
+ cuda->shared_data.cuda_timings.test1+=
+ endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000;
+ }
+
+ cuda->shared_data.cuda_timings.comm_exchange_total+=
+ endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000;
+
+ if(nlocalold!=cuda->shared_data.atom.nlocal) cuda->shared_data.atom.update_nlocal=2;
+
+ //sort atoms
+ if (sortflag && ntimestep >= atom->nextsort) atom->sort();
+ MYDBG( printf("# CUDA VerletCuda::iterate: neighbor borders\n"); )
+
+ //generate ghost atom lists, and transfer ghost atom data
+ clock_gettime(CLOCK_REALTIME,&starttime);
+ comm->borders();
+ clock_gettime(CLOCK_REALTIME,&endtime);
+ cuda->shared_data.cuda_timings.comm_border_total+=
+ endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000;
+
+ clock_gettime(CLOCK_REALTIME,&starttime);
+ //atom index maps are generated on CPU, and need to be transfered to GPU if they are used
+ if(cuda->cu_map_array)
+ cuda->cu_map_array->upload();
+
+
+ if(domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
+
+ if(n_pre_neighbor) modify->pre_neighbor();
+
+ cuda->shared_data.buffer_new=2;
+ if(atom->molecular) cuda->cu_molecule->download();
+ MYDBG( printf("# CUDA VerletCuda::iterate: neighbor build\n"); )
+ timer->stamp(TIME_COMM);
+ clock_gettime(CLOCK_REALTIME,&endtime);
+ cuda->shared_data.cuda_timings.test2+=
+ endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000;
+
+ //rebuild neighbor list
+ test_atom(testatom,"Pre Neighbor");
+ neighbor->build();
+ timer->stamp(TIME_NEIGHBOR);
+ MYDBG( printf("# CUDA VerletCuda::iterate: neighbor done\n"); )
+
+ //if bonded interactions are used (in this case collect_forces_later is true), transfer data which only changes upon exchange/border routines from GPU to CPU
+ if(cuda->shared_data.pair.collect_forces_later)
+ {
+ if(cuda->cu_molecule) cuda->cu_molecule->download();
+ cuda->cu_tag->download();
+ cuda->cu_type->download();
+ cuda->cu_mask->download();
+ if(cuda->cu_q) cuda->cu_q->download();
+ }
+ cuda->shared_data.comm.comm_phase=3;
+ }
+
+ test_atom(testatom,"Post Exchange");
+
+ // force computations
+
+ //only do force_clear if it has not been done during overlap of communication with local interactions
+ if(not((not (eflag||vflag))&&(cuda->shared_data.overlap_comm)&&(cuda->shared_data.comm.comm_phase<3)))
+ force_clear();
+
+ if(n_pre_force) modify->pre_force(vflag);
+
+ timer->stamp();
+
+ //if overlap of bonded interactions with nonbonded interactions takes place, download forces and positions
+ /* if(cuda->shared_data.pair.collect_forces_later)
+ {
+ cuda->cu_x->downloadAsync(2);
+ cuda->cu_f->downloadAsync(2);
+ }*/
+
+ if(force->pair)
+ {
+ if((not (eflag||vflag))&&(cuda->shared_data.overlap_comm)&&(cuda->shared_data.comm.comm_phase<3)&&cuda->shared_data.pair.cudable_force)
+ {
+ //second part of force calculations in case of overlaping it with commuincation. Only interactions between local and ghost atoms are done now
+ //regenerate data layout for force computations, its actually only needed for the ghost atoms
+ cuda->shared_data.comm.comm_phase=2;
+
+ timespec atime1,atime2;
+ clock_gettime(CLOCK_REALTIME,&atime1);
+
+ Cuda_Pair_GenerateXType(&cuda->shared_data);
+ if(cuda->cu_v_radius)
+ Cuda_Pair_GenerateVRadius(&cuda->shared_data);
+ if(cuda->cu_omega_rmass)
+ Cuda_Pair_GenerateOmegaRmass(&cuda->shared_data);
+
+ clock_gettime(CLOCK_REALTIME,&atime2);
+ cuda->shared_data.cuda_timings.pair_xtype_conversion+=
+ atime2.tv_sec-atime1.tv_sec+1.0*(atime2.tv_nsec-atime1.tv_nsec)/1000000000;
+ force->pair->compute(eflag, vflag);
+
+ }
+ else
+ {
+ //calculate complete pair interactions
+ if(not cuda->shared_data.pair.cudable_force) cuda->downloadAll();
+ else
+ {
+ //regenerate data layout for force computations, its actually only needed for the ghost atoms
+ timespec atime1,atime2;
+ clock_gettime(CLOCK_REALTIME,&atime1);
+
+ Cuda_Pair_GenerateXType(&cuda->shared_data);
+ if(cuda->cu_v_radius)
+ Cuda_Pair_GenerateVRadius(&cuda->shared_data);
+ if(cuda->cu_omega_rmass)
+ Cuda_Pair_GenerateOmegaRmass(&cuda->shared_data);
+
+ clock_gettime(CLOCK_REALTIME,&atime2);
+ cuda->shared_data.cuda_timings.pair_xtype_conversion+=
+ atime2.tv_sec-atime1.tv_sec+1.0*(atime2.tv_nsec-atime1.tv_nsec)/1000000000;
+ }
+ cuda->shared_data.comm.comm_phase=0;
+ force->pair->compute(eflag, vflag);
+ }
+
+ if(not cuda->shared_data.pair.cudable_force) cuda->uploadAll();
+
+ //wait for force calculation in case of not using overlap with bonded interactions
+ if(not cuda->shared_data.pair.collect_forces_later)
+ CudaWrapper_Sync();
+
+ timer->stamp(TIME_PAIR);
+ }
+
+ //calculate bonded interactions
+ if(atom->molecular)
+ {
+ cuda->cu_x->downloadAsync(2);
+ if(n_pre_force==0) Verlet::force_clear();
+ else cuda->cu_f->downloadAsync(2);
+
+ timer->stamp(TIME_PAIR);
+
+ test_atom(testatom,"pre bond force");
+ if(force->bond) force->bond->compute(eflag, vflag);
+ if(force->angle) force->angle->compute(eflag, vflag);
+ if(force->dihedral) force->dihedral->compute(eflag, vflag);
+ if(force->improper) force->improper->compute(eflag, vflag);
+ timer->stamp(TIME_BOND);
+ }
+
+ //collect forces in case pair force and bonded interactions were overlapped, and either no KSPACE or a GPU KSPACE style is used
+ if(cuda->shared_data.pair.collect_forces_later&&cuda->shared_data.pair.cudable_force&&(not (force->kspace&&(not cuda->shared_data.pppm.cudable_force))))
+ {
+ clock_gettime(CLOCK_REALTIME,&starttime);
+ cuda->cu_f->uploadAsync(2);
+
+ test_atom(testatom,"post molecular force");
+
+
+ if(eflag) cuda->cu_eng_vdwl->upload();
+ if(eflag) cuda->cu_eng_coul->upload();
+ if(vflag) cuda->cu_virial->upload();
Cuda_Pair_CollectForces(&cuda->shared_data,eflag,vflag);
- if(eflag) cuda->cu_eng_vdwl->download();
- if(eflag) cuda->cu_eng_coul->download();
- if(vflag) cuda->cu_virial->download();
- timer->stamp(TIME_PAIR);
-
- clock_gettime(CLOCK_REALTIME,&endtime);
- cuda->shared_data.cuda_timings.pair_force_collection+=
- endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000;
- }
-
- //compute kspace force
- if(force->kspace)
- {
- if((not cuda->shared_data.pppm.cudable_force) && (not cuda->shared_data.pair.collect_forces_later))
- cuda->downloadAll();
- if((not cuda->shared_data.pppm.cudable_force) && (cuda->shared_data.pair.collect_forces_later) && (not atom->molecular))
- {
- cuda->cu_x->downloadAsync(2);
- if(n_pre_force==0) Verlet::force_clear();
- else cuda->cu_f->downloadAsync(2);
-
- timer->stamp(TIME_PAIR);
- }
-
- force->kspace->compute(eflag,vflag);
- if((not cuda->shared_data.pppm.cudable_force) && (not cuda->shared_data.pair.collect_forces_later))
- cuda->uploadAll();
- timer->stamp(TIME_KSPACE);
- }
-
- //collect forces in case pair forces and kspace was overlaped
- if(cuda->shared_data.pair.collect_forces_later&&cuda->shared_data.pair.cudable_force&&((force->kspace&&(not cuda->shared_data.pppm.cudable_force))))
- {
- cuda->cu_f->uploadAsync(2);
-
- clock_gettime(CLOCK_REALTIME,&starttime);
-
- if(eflag) cuda->cu_eng_vdwl->upload();
- if(eflag) cuda->cu_eng_coul->upload();
- if(vflag) cuda->cu_virial->upload();
- Cuda_Pair_CollectForces(&cuda->shared_data,eflag,vflag);
- if(eflag) cuda->cu_eng_vdwl->download();
- if(eflag) cuda->cu_eng_coul->download();
- if(vflag) cuda->cu_virial->download();
- timer->stamp(TIME_PAIR);
-
- clock_gettime(CLOCK_REALTIME,&endtime);
- cuda->shared_data.cuda_timings.pair_force_collection+=
- endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000;
- }
-
- //send forces on ghost atoms back to other GPU: THIS SHOULD NEVER HAPPEN
- if(force->newton)
- {
- comm->reverse_comm();
- timer->stamp(TIME_COMM);
- }
- test_atom(testatom,"post force");
- // force modifications, final time integration, diagnostics
-
- if(n_post_force) modify->post_force(vflag);
-
- test_atom(testatom,"pre final");
-
- modify->final_integrate();
-
- test_atom(testatom,"post final");
-
- if(n_end_of_step) modify->end_of_step();
-
- // all output
-
- test_atom(testatom,"pre output");
-
- if(ntimestep == output->next)
- {
- if(not output->thermo->cudable)
- cuda->downloadAll();
- timer->stamp();
- output->write(ntimestep);
- timer->stamp(TIME_OUTPUT);
- }
-
-
- test_atom(testatom,"post output");
-
- if(cuda->shared_data.atom.update_nlocal>0)
- cuda->shared_data.atom.update_nlocal--;
- if(cuda->shared_data.atom.update_nmax>0)
- cuda->shared_data.atom.update_nmax--;
+ if(eflag) cuda->cu_eng_vdwl->download();
+ if(eflag) cuda->cu_eng_coul->download();
+ if(vflag) cuda->cu_virial->download();
+ timer->stamp(TIME_PAIR);
+
+ clock_gettime(CLOCK_REALTIME,&endtime);
+ cuda->shared_data.cuda_timings.pair_force_collection+=
+ endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000;
+ }
+
+ //compute kspace force
+ if(force->kspace)
+ {
+ if((not cuda->shared_data.pppm.cudable_force) && (not cuda->shared_data.pair.collect_forces_later))
+ cuda->downloadAll();
+ if((not cuda->shared_data.pppm.cudable_force) && (cuda->shared_data.pair.collect_forces_later) && (not atom->molecular))
+ {
+ cuda->cu_x->downloadAsync(2);
+ if(n_pre_force==0) Verlet::force_clear();
+ else cuda->cu_f->downloadAsync(2);
+
+ timer->stamp(TIME_PAIR);
+ }
+
+ force->kspace->compute(eflag,vflag);
+ if((not cuda->shared_data.pppm.cudable_force) && (not cuda->shared_data.pair.collect_forces_later))
+ cuda->uploadAll();
+ timer->stamp(TIME_KSPACE);
+ }
+
+ //collect forces in case pair forces and kspace was overlaped
+ if(cuda->shared_data.pair.collect_forces_later&&cuda->shared_data.pair.cudable_force&&((force->kspace&&(not cuda->shared_data.pppm.cudable_force))))
+ {
+ cuda->cu_f->uploadAsync(2);
+
+ clock_gettime(CLOCK_REALTIME,&starttime);
+
+ if(eflag) cuda->cu_eng_vdwl->upload();
+ if(eflag) cuda->cu_eng_coul->upload();
+ if(vflag) cuda->cu_virial->upload();
+ Cuda_Pair_CollectForces(&cuda->shared_data,eflag,vflag);
+ if(eflag) cuda->cu_eng_vdwl->download();
+ if(eflag) cuda->cu_eng_coul->download();
+ if(vflag) cuda->cu_virial->download();
+ timer->stamp(TIME_PAIR);
+
+ clock_gettime(CLOCK_REALTIME,&endtime);
+ cuda->shared_data.cuda_timings.pair_force_collection+=
+ endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000;
+ }
+
+ //send forces on ghost atoms back to other GPU: THIS SHOULD NEVER HAPPEN
+ if(force->newton)
+ {
+ comm->reverse_comm();
+ timer->stamp(TIME_COMM);
+ }
+ test_atom(testatom,"post force");
+ // force modifications, final time integration, diagnostics
+
+ if(n_post_force) modify->post_force(vflag);
+
+ test_atom(testatom,"pre final");
+
+ modify->final_integrate();
+
+ test_atom(testatom,"post final");
+
+ if(n_end_of_step) modify->end_of_step();
+
+ // all output
+
+ test_atom(testatom,"pre output");
+
+ if(ntimestep == output->next)
+ {
+ if(not output->thermo->cudable)
+ cuda->downloadAll();
+ timer->stamp();
+ output->write(ntimestep);
+ timer->stamp(TIME_OUTPUT);
+ }
+
+
+ test_atom(testatom,"post output");
+
+ if(cuda->shared_data.atom.update_nlocal>0)
+ cuda->shared_data.atom.update_nlocal--;
+ if(cuda->shared_data.atom.update_nmax>0)
+ cuda->shared_data.atom.update_nmax--;
if(cuda->shared_data.atom.update_neigh>0)
cuda->shared_data.atom.update_neigh--;
- if(cuda->shared_data.domain.update>0)
- cuda->shared_data.domain.update--;
- if(cuda->shared_data.buffer_new>0)
- cuda->shared_data.buffer_new--;
- cuda->shared_data.atom.reneigh_flag=0;
- }
-
-
- cuda->downloadAll();
- cuda->downloadAllNeighborLists();
- cuda->shared_data.atom.update_nlocal=1;
- cuda->shared_data.atom.update_nmax=1;
+ if(cuda->shared_data.domain.update>0)
+ cuda->shared_data.domain.update--;
+ if(cuda->shared_data.buffer_new>0)
+ cuda->shared_data.buffer_new--;
+ cuda->shared_data.atom.reneigh_flag=0;
+ }
+
+
+ cuda->downloadAll();
+ cuda->downloadAllNeighborLists();
+ cuda->shared_data.atom.update_nlocal=1;
+ cuda->shared_data.atom.update_nmax=1;
cuda->shared_data.atom.update_neigh=1;
- cuda->shared_data.buffer_new=1;
- cuda->shared_data.domain.update=1;
- cuda->oncpu = true;
- cuda->finished_run = true;
+ cuda->shared_data.buffer_new=1;
+ cuda->shared_data.domain.update=1;
+ cuda->oncpu = true;
+ cuda->finished_run = true;
}
@@ -1005,14 +1005,14 @@ void VerletCuda::force_clear()
cuda->cu_f->memset_device(0);
if(cuda->cu_torque) cuda->cu_torque->memset_device(0);
return;
-
+
//The rest should not be necessary
int i;
for(i=0;i<atom->nlocal;i++)
{
- atom->f[i][0]=0.0;
- atom->f[i][1]=0.0;
- atom->f[i][2]=0.0;
+ atom->f[i][0]=0.0;
+ atom->f[i][1]=0.0;
+ atom->f[i][2]=0.0;
}
// clear force on all particles
// if either newton flag is set, also include ghosts
@@ -1024,9 +1024,9 @@ void VerletCuda::force_clear()
if (torqueflag) {
double **torque = atom->torque;
for (i = 0; i < nall; i++) {
- torque[i][0] = 0.0;
- torque[i][1] = 0.0;
- torque[i][2] = 0.0;
+ torque[i][0] = 0.0;
+ torque[i][1] = 0.0;
+ torque[i][2] = 0.0;
}
}
@@ -1037,26 +1037,26 @@ void VerletCuda::force_clear()
} else {
int nall = atom->nfirst;
-
+
if (torqueflag) {
double **torque = atom->torque;
for (i = 0; i < nall; i++) {
- torque[i][0] = 0.0;
- torque[i][1] = 0.0;
- torque[i][2] = 0.0;
+ torque[i][0] = 0.0;
+ torque[i][1] = 0.0;
+ torque[i][2] = 0.0;
}
}
if (force->newton) {
nall = atom->nlocal + atom->nghost;
-
+
if (torqueflag) {
- double **torque = atom->torque;
- for (i = atom->nlocal; i < nall; i++) {
- torque[i][0] = 0.0;
- torque[i][1] = 0.0;
- torque[i][2] = 0.0;
- }
+ double **torque = atom->torque;
+ for (i = atom->nlocal; i < nall; i++) {
+ torque[i][0] = 0.0;
+ torque[i][1] = 0.0;
+ torque[i][2] = 0.0;
+ }
}
}
}
@@ -1070,35 +1070,35 @@ void VerletCuda::test_atom(int aatom, char* string) //printing properties of on
for(int i=0;i<atom->nlocal+atom->nghost;i++)
{
if((atom->tag[i]==aatom)&&(i<atom->nlocal))
- {
-
- printf("%i # CUDA %s: %i %i %e %e %e %i ",comm->me,string,update->ntimestep,atom->tag[i],atom->x[i][0],atom->v[i][0],atom->f[i][0],i);
- if(atom->molecular && (i<atom->nlocal))
- {
- printf(" // %i %i %i ",atom->num_bond[i],atom->num_angle[i],atom->num_dihedral[i]);
- for(int k=0;k<atom->num_bond[i];k++)
- printf("// %i %i ",atom->bond_type[i][k],atom->bond_atom[i][k]);
- }
- printf("\n");
- }
+ {
+
+ printf("%i # CUDA %s: %i %i %e %e %e %i ",comm->me,string,update->ntimestep,atom->tag[i],atom->x[i][0],atom->v[i][0],atom->f[i][0],i);
+ if(atom->molecular && (i<atom->nlocal))
+ {
+ printf(" // %i %i %i ",atom->num_bond[i],atom->num_angle[i],atom->num_dihedral[i]);
+ for(int k=0;k<atom->num_bond[i];k++)
+ printf("// %i %i ",atom->bond_type[i][k],atom->bond_atom[i][k]);
+ }
+ printf("\n");
+ }
if(i<atom->nlocal)
{
if((atom->v[i][0]<-100||atom->v[i][0]>100)||
- (atom->v[i][1]<-100||atom->v[i][1]>100)||
- (atom->v[i][2]<-100||atom->v[i][2]>100)||
- (atom->v[i][0]!=atom->v[i][0])||
- (atom->v[i][1]!=atom->v[i][1])||
- (atom->v[i][2]!=atom->v[i][2]))
- {printf("%i # CUDA %s velocity: %i %e %e %e %i\n",comm->me,string,atom->tag[i],atom->x[i][0],atom->v[i][0],atom->f[i][0],i); check=true;}
+ (atom->v[i][1]<-100||atom->v[i][1]>100)||
+ (atom->v[i][2]<-100||atom->v[i][2]>100)||
+ (atom->v[i][0]!=atom->v[i][0])||
+ (atom->v[i][1]!=atom->v[i][1])||
+ (atom->v[i][2]!=atom->v[i][2]))
+ {printf("%i # CUDA %s velocity: %i %e %e %e %i\n",comm->me,string,atom->tag[i],atom->x[i][0],atom->v[i][0],atom->f[i][0],i); check=true;}
if((atom->f[i][0]<-10000||atom->f[i][0]>10000)||
- (atom->f[i][1]<-10000||atom->f[i][1]>10000)||
- (atom->f[i][2]<-10000||atom->f[i][2]>10000)||
- (atom->f[i][0]!=atom->f[i][0])||
- (atom->f[i][1]!=atom->f[i][1])||
- (atom->f[i][2]!=atom->f[i][2]))
- {printf("%i # CUDA %s force: %i %e %e %e %i\n",comm->me,string,atom->tag[i],atom->x[i][0],atom->v[i][0],atom->f[i][0],i); check=true;}
+ (atom->f[i][1]<-10000||atom->f[i][1]>10000)||
+ (atom->f[i][2]<-10000||atom->f[i][2]>10000)||
+ (atom->f[i][0]!=atom->f[i][0])||
+ (atom->f[i][1]!=atom->f[i][1])||
+ (atom->f[i][2]!=atom->f[i][2]))
+ {printf("%i # CUDA %s force: %i %e %e %e %i\n",comm->me,string,atom->tag[i],atom->x[i][0],atom->v[i][0],atom->f[i][0],i); check=true;}
if(atom->tag[i]<=0)
- printf("%i # CUDA %s tag: %i %e %e %e %i\n",comm->me,string,atom->tag[i],atom->x[i][0],atom->v[i][0],atom->f[i][0],i);
+ printf("%i # CUDA %s tag: %i %e %e %e %i\n",comm->me,string,atom->tag[i],atom->x[i][0],atom->v[i][0],atom->f[i][0],i);
}
}
if(check) exit(0);
diff --git a/src/USER-CUDA/verlet_cuda.h b/src/USER-CUDA/verlet_cuda.h
index 6992f438a45e34cb75ba7c6a9ffa8e5140ffa671..21f1a049bc2794d67dc4b24ef43e6ee27d938a94 100644
--- a/src/USER-CUDA/verlet_cuda.h
+++ b/src/USER-CUDA/verlet_cuda.h
@@ -1,22 +1,22 @@
/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
+ Steve Plimpton, sjplimp@sandia.gov
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level LAMMPS directory.
- -----------------------------------------------------------------------
+ -----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
- https://sourceforge.net/projects/lammpscuda/
+ https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
- Theoretical Physics II, University of Technology Ilmenau, Germany
+ Theoretical Physics II, University of Technology Ilmenau, Germany
- See the README file in the USER-CUDA directory.
+ See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
@@ -37,24 +37,24 @@ namespace LAMMPS_NS {
class VerletCuda : public Verlet
{
- public:
- VerletCuda(class LAMMPS *, int, char **);
- void setup();
- void setup_minimal(int);
- void run(int);
-
- void test_atom(int atom,char* astring); //debugging purpose
- int dotestatom; //debugging purpose
-
- protected:
- class Cuda *cuda;
- void force_clear();
- double time_pair;
- double time_kspace;
- double time_comm;
- double time_modify;
- double time_fulliterate;
- ModifyCuda* modify_cuda;
+ public:
+ VerletCuda(class LAMMPS *, int, char **);
+ void setup();
+ void setup_minimal(int);
+ void run(int);
+
+ void test_atom(int atom,char* astring); //debugging purpose
+ int dotestatom; //debugging purpose
+
+ protected:
+ class Cuda *cuda;
+ void force_clear();
+ double time_pair;
+ double time_kspace;
+ double time_comm;
+ double time_modify;
+ double time_fulliterate;
+ ModifyCuda* modify_cuda;
};
}
diff --git a/src/USER-EFF/atom_vec_electron.cpp b/src/USER-EFF/atom_vec_electron.cpp
index 4f73254c31e8e4a0fe868509381511820f44a328..9cbdf22cbbfbcd6b8f15c9f196921524ee9a65e0 100644
--- a/src/USER-EFF/atom_vec_electron.cpp
+++ b/src/USER-EFF/atom_vec_electron.cpp
@@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
-
+
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
-
+
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@@ -37,27 +37,27 @@ AtomVecElectron::AtomVecElectron(LAMMPS *lmp, int narg, char **arg) :
AtomVec(lmp, narg, arg)
{
comm_x_only = comm_f_only = 0;
-
+
mass_type = 1;
molecular = 0;
-
+
size_forward = 4;
- size_reverse = 4;
- size_border = 9;
+ size_reverse = 4;
+ size_border = 9;
size_velocity = 3;
size_data_atom = 8;
size_data_vel = 5;
xcol_data = 6;
-
+
atom->electron_flag = 1;
- atom->q_flag = atom->spin_flag = atom->eradius_flag =
+ atom->q_flag = atom->spin_flag = atom->eradius_flag =
atom->ervel_flag = atom->erforce_flag = 1;
}
/* ----------------------------------------------------------------------
grow atom-electron arrays
n = 0 grows arrays by DELTA
- n > 0 allocates arrays to size n
+ n > 0 allocates arrays to size n
------------------------------------------------------------------------- */
void AtomVecElectron::grow(int n)
@@ -65,7 +65,7 @@ void AtomVecElectron::grow(int n)
if (n == 0) nmax += DELTA;
else nmax = n;
atom->nmax = nmax;
-
+
tag = memory->grow(atom->tag,nmax,"atom:tag");
type = memory->grow(atom->type,nmax,"atom:type");
mask = memory->grow(atom->mask,nmax,"atom:mask");
@@ -81,7 +81,7 @@ void AtomVecElectron::grow(int n)
erforce = memory->grow(atom->erforce,nmax*comm->nthreads,"atom:erforce");
if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
}
@@ -114,21 +114,21 @@ void AtomVecElectron::copy(int i, int j, int delflag)
v[j][0] = v[i][0];
v[j][1] = v[i][1];
v[j][2] = v[i][2];
-
+
q[j] = q[i];
spin[j] = spin[i];
eradius[j] = eradius[i];
ervel[j] = ervel[i];
-
+
if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j);
}
/* ---------------------------------------------------------------------- */
int AtomVecElectron::pack_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
@@ -166,7 +166,7 @@ int AtomVecElectron::pack_comm(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
int AtomVecElectron::pack_comm_vel(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz,dvx,dvy,dvz;
@@ -195,34 +195,34 @@ int AtomVecElectron::pack_comm_vel(int n, int *list, double *buf,
}
if (!deform_vremap) {
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = eradius[j];
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = eradius[j];
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
}
} else {
dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
dvz = pbc[2]*h_rate[2];
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = eradius[j];
- if (mask[i] & deform_groupbit) {
- buf[m++] = v[j][0] + dvx;
- buf[m++] = v[j][1] + dvy;
- buf[m++] = v[j][2] + dvz;
- } else {
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
- }
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = eradius[j];
+ if (mask[i] & deform_groupbit) {
+ buf[m++] = v[j][0] + dvx;
+ buf[m++] = v[j][1] + dvy;
+ buf[m++] = v[j][2] + dvz;
+ } else {
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
+ }
}
}
}
@@ -248,7 +248,7 @@ int AtomVecElectron::pack_comm_hybrid(int n, int *list, double *buf)
void AtomVecElectron::unpack_comm(int n, int first, double *buf)
{
int i,m,last;
-
+
m = 0;
last = first + n;
for (i = first; i < last; i++) {
@@ -264,7 +264,7 @@ void AtomVecElectron::unpack_comm(int n, int first, double *buf)
void AtomVecElectron::unpack_comm_vel(int n, int first, double *buf)
{
int i,m,last;
-
+
m = 0;
last = first + n;
for (i = first; i < last; i++) {
@@ -296,7 +296,7 @@ int AtomVecElectron::unpack_comm_hybrid(int n, int first, double *buf)
int AtomVecElectron::pack_reverse(int n, int first, double *buf)
{
int i,m,last;
-
+
m = 0;
last = first + n;
for (i = first; i < last; i++) {
@@ -326,7 +326,7 @@ int AtomVecElectron::pack_reverse_hybrid(int n, int first, double *buf)
void AtomVecElectron::unpack_reverse(int n, int *list, double *buf)
{
int i,j,m;
-
+
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
@@ -354,7 +354,7 @@ int AtomVecElectron::unpack_reverse_hybrid(int n, int *list, double *buf)
/* ---------------------------------------------------------------------- */
int AtomVecElectron::pack_border(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
@@ -402,7 +402,7 @@ int AtomVecElectron::pack_border(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
int AtomVecElectron::pack_border_vel(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz,dvx,dvy,dvz;
@@ -436,44 +436,44 @@ int AtomVecElectron::pack_border_vel(int n, int *list, double *buf,
}
if (domain->triclinic == 0) {
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = tag[j];
- buf[m++] = type[j];
- buf[m++] = mask[j];
- buf[m++] = q[j];
- buf[m++] = spin[j];
- buf[m++] = eradius[j];
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = tag[j];
+ buf[m++] = type[j];
+ buf[m++] = mask[j];
+ buf[m++] = q[j];
+ buf[m++] = spin[j];
+ buf[m++] = eradius[j];
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
}
} else {
dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
dvz = pbc[2]*h_rate[2];
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = tag[j];
- buf[m++] = type[j];
- buf[m++] = mask[j];
- buf[m++] = q[j];
- buf[m++] = spin[j];
- buf[m++] = eradius[j];
- if (mask[i] & deform_groupbit) {
- buf[m++] = v[j][0] + dvx;
- buf[m++] = v[j][1] + dvy;
- buf[m++] = v[j][2] + dvz;
- } else {
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
- }
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = tag[j];
+ buf[m++] = type[j];
+ buf[m++] = mask[j];
+ buf[m++] = q[j];
+ buf[m++] = spin[j];
+ buf[m++] = eradius[j];
+ if (mask[i] & deform_groupbit) {
+ buf[m++] = v[j][0] + dvx;
+ buf[m++] = v[j][1] + dvy;
+ buf[m++] = v[j][2] + dvz;
+ } else {
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
+ }
}
}
}
@@ -501,7 +501,7 @@ int AtomVecElectron::pack_border_hybrid(int n, int *list, double *buf)
void AtomVecElectron::unpack_border(int n, int first, double *buf)
{
int i,m,last;
-
+
m = 0;
last = first + n;
for (i = first; i < last; i++) {
@@ -511,7 +511,7 @@ void AtomVecElectron::unpack_border(int n, int first, double *buf)
x[i][2] = buf[m++];
tag[i] = static_cast<int> (buf[m++]);
type[i] = static_cast<int> (buf[m++]);
- mask[i] = static_cast<int> (buf[m++]);
+ mask[i] = static_cast<int> (buf[m++]);
q[i] = buf[m++];
spin[i] = static_cast<int> (buf[m++]);
eradius[i] = buf[m++];
@@ -523,7 +523,7 @@ void AtomVecElectron::unpack_border(int n, int first, double *buf)
void AtomVecElectron::unpack_border_vel(int n, int first, double *buf)
{
int i,m,last;
-
+
m = 0;
last = first + n;
for (i = first; i < last; i++) {
@@ -561,7 +561,7 @@ int AtomVecElectron::unpack_border_hybrid(int n, int first, double *buf)
/* ----------------------------------------------------------------------
pack data for atom I for sending to another proc
- xyz must be 1st 3 values, so comm::exchange() can test on them
+ xyz must be 1st 3 values, so comm::exchange() can test on them
------------------------------------------------------------------------- */
int AtomVecElectron::pack_exchange(int i, double *buf)
@@ -576,16 +576,16 @@ int AtomVecElectron::pack_exchange(int i, double *buf)
buf[m++] = tag[i];
buf[m++] = type[i];
buf[m++] = mask[i];
- buf[m++] = image[i];
+ buf[m++] = image[i];
buf[m++] = q[i];
buf[m++] = spin[i];
buf[m++] = eradius[i];
buf[m++] = ervel[i];
-
+
if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]);
-
+
buf[0] = m;
return m;
}
@@ -596,7 +596,7 @@ int AtomVecElectron::unpack_exchange(double *buf)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
-
+
int m = 1;
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
@@ -607,17 +607,17 @@ int AtomVecElectron::unpack_exchange(double *buf)
tag[nlocal] = static_cast<int> (buf[m++]);
type[nlocal] = static_cast<int> (buf[m++]);
mask[nlocal] = static_cast<int> (buf[m++]);
- image[nlocal] = static_cast<int> (buf[m++]);
+ image[nlocal] = static_cast<int> (buf[m++]);
q[nlocal] = buf[m++];
spin[nlocal] = static_cast<int> (buf[m++]);
eradius[nlocal] = buf[m++];
ervel[nlocal] = buf[m++];
-
+
if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->
- unpack_exchange(nlocal,&buf[m]);
-
+ unpack_exchange(nlocal,&buf[m]);
+
atom->nlocal++;
return m;
}
@@ -630,22 +630,22 @@ int AtomVecElectron::unpack_exchange(double *buf)
int AtomVecElectron::size_restart()
{
int i;
-
+
int nlocal = atom->nlocal;
- int n = 15 * nlocal; // Associated with pack_restart
-
+ int n = 15 * nlocal; // Associated with pack_restart
+
if (atom->nextra_restart)
- for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
for (i = 0; i < nlocal; i++)
- n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
-
+ n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
+
return n;
}
/* ----------------------------------------------------------------------
pack atom I's data for restart file including extra quantities
xyz must be 1st 3 values, so that read_restart can test on them
- molecular types may be negative, but write as positive
+ molecular types may be negative, but write as positive
------------------------------------------------------------------------- */
int AtomVecElectron::pack_restart(int i, double *buf)
@@ -661,16 +661,16 @@ int AtomVecElectron::pack_restart(int i, double *buf)
buf[m++] = v[i][0];
buf[m++] = v[i][1];
buf[m++] = v[i][2];
-
+
buf[m++] = q[i];
buf[m++] = spin[i];
buf[m++] = eradius[i];
buf[m++] = ervel[i];
-
+
if (atom->nextra_restart)
- for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]);
-
+
buf[0] = m;
return m;
}
@@ -687,7 +687,7 @@ int AtomVecElectron::unpack_restart(double *buf)
if (atom->nextra_store)
memory->grow(atom->extra,nmax,atom->nextra_store,"atom:extra");
}
-
+
int m = 1;
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
@@ -699,18 +699,18 @@ int AtomVecElectron::unpack_restart(double *buf)
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
-
+
q[nlocal] = buf[m++];
spin[nlocal] = static_cast<int> (buf[m++]);
eradius[nlocal] = buf[m++];
ervel[nlocal] = buf[m++];
-
+
double **extra = atom->extra;
if (atom->nextra_store) {
int size = static_cast<int> (buf[0]) - m;
for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++];
}
-
+
atom->nlocal++;
return m;
}
@@ -724,7 +724,7 @@ void AtomVecElectron::create_atom(int itype, double *coord)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
-
+
tag[nlocal] = 0;
type[nlocal] = itype;
x[nlocal][0] = coord[0];
@@ -735,12 +735,12 @@ void AtomVecElectron::create_atom(int itype, double *coord)
v[nlocal][0] = 0.0;
v[nlocal][1] = 0.0;
v[nlocal][2] = 0.0;
-
+
q[nlocal] = 0.0;
spin[nlocal] = 1;
- eradius[nlocal] = 1.0;
- ervel[nlocal] = 0.0;
-
+ eradius[nlocal] = 1.0;
+ ervel[nlocal] = 0.0;
+
atom->nlocal++;
}
@@ -752,33 +752,33 @@ void AtomVecElectron::create_atom(int itype, double *coord)
void AtomVecElectron::data_atom(double *coord, int imagetmp, char **values)
{
int nlocal = atom->nlocal;
-
+
if (nlocal == nmax) grow(0);
-
+
tag[nlocal] = atoi(values[0]);
if (tag[nlocal] <= 0)
error->one(FLERR,"Invalid atom ID in Atoms section of data file");
-
+
type[nlocal] = atoi(values[1]);
if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
error->one(FLERR,"Invalid atom type in Atoms section of data file");
-
+
q[nlocal] = atof(values[2]);
spin[nlocal] = atoi(values[3]);
eradius[nlocal] = atof(values[4]);
-
+
x[nlocal][0] = coord[0];
x[nlocal][1] = coord[1];
x[nlocal][2] = coord[2];
-
+
image[nlocal] = imagetmp;
-
+
mask[nlocal] = 1;
v[nlocal][0] = 0.0;
v[nlocal][1] = 0.0;
v[nlocal][2] = 0.0;
ervel[nlocal] = 0.0;
-
+
atom->nlocal++;
}
@@ -794,12 +794,12 @@ int AtomVecElectron::data_atom_hybrid(int nlocal, char **values)
eradius[nlocal] = atof(values[2]);
if (eradius[nlocal] < 0.0)
error->one(FLERR,"Invalid eradius in Atoms section of data file");
-
+
v[nlocal][0] = 0.0;
v[nlocal][1] = 0.0;
v[nlocal][2] = 0.0;
ervel[nlocal] = 0.0;
-
+
return 3;
}
@@ -826,13 +826,13 @@ int AtomVecElectron::data_vel_hybrid(int m, char **values)
}
/* ----------------------------------------------------------------------
- return # of bytes of allocated memory
+ return # of bytes of allocated memory
------------------------------------------------------------------------- */
bigint AtomVecElectron::memory_usage()
{
bigint bytes = 0;
-
+
if (atom->memcheck("tag")) bytes += memory->usage(tag,nmax);
if (atom->memcheck("type")) bytes += memory->usage(type,nmax);
if (atom->memcheck("mask")) bytes += memory->usage(mask,nmax);
@@ -840,12 +840,12 @@ bigint AtomVecElectron::memory_usage()
if (atom->memcheck("x")) bytes += memory->usage(x,nmax,3);
if (atom->memcheck("v")) bytes += memory->usage(v,nmax,3);
if (atom->memcheck("f")) bytes += memory->usage(f,nmax*comm->nthreads,3);
-
+
if (atom->memcheck("q")) bytes += memory->usage(q,nmax);
if (atom->memcheck("spin")) bytes += memory->usage(spin,nmax);
if (atom->memcheck("eradius")) bytes += memory->usage(eradius,nmax);
if (atom->memcheck("ervel")) bytes += memory->usage(ervel,nmax);
if (atom->memcheck("erforce")) bytes += memory->usage(erforce,nmax*comm->nthreads);
-
+
return bytes;
}
diff --git a/src/USER-EFF/atom_vec_electron.h b/src/USER-EFF/atom_vec_electron.h
index 6c527cacdd7faec95001602ef424b87e540843a2..cfe8f3ea9ec0410211e2c435ab5635c005ff6938 100644
--- a/src/USER-EFF/atom_vec_electron.h
+++ b/src/USER-EFF/atom_vec_electron.h
@@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
-
+
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
-
+
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@@ -23,7 +23,7 @@ AtomStyle(electron,AtomVecElectron)
#include "atom_vec.h"
namespace LAMMPS_NS {
-
+
class AtomVecElectron : public AtomVec {
public:
AtomVecElectron(class LAMMPS *, int, char **);
@@ -58,14 +58,14 @@ class AtomVecElectron : public AtomVec {
void data_vel(int, char **);
int data_vel_hybrid(int, char **);
bigint memory_usage();
-
+
private:
int *tag,*type,*mask,*image;
double **x,**v,**f;
int *spin;
- double *q,*eradius,*ervel,*erforce;
+ double *q,*eradius,*ervel,*erforce;
};
-
+
}
#endif
diff --git a/src/USER-EFF/compute_ke_atom_eff.cpp b/src/USER-EFF/compute_ke_atom_eff.cpp
index 695cdc8874f4c1676886c7c1cb34cf2f94fac7e4..165a3c401db597c5ce4348f915e18105ea08e835 100644
--- a/src/USER-EFF/compute_ke_atom_eff.cpp
+++ b/src/USER-EFF/compute_ke_atom_eff.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -44,7 +44,7 @@ ComputeKEAtomEff::ComputeKEAtomEff(LAMMPS *lmp, int narg, char **arg) :
// error check
- if (!atom->electron_flag)
+ if (!atom->electron_flag)
error->all(FLERR,"Compute ke/atom/eff requires atom style electron");
}
@@ -80,9 +80,9 @@ void ComputeKEAtomEff::compute_peratom()
memory->create(ke,nmax,"compute/ke/atom/eff:ke");
vector_atom = ke;
}
-
+
// compute kinetic energy for each atom in group
-
+
double mvv2e = force->mvv2e;
double **v = atom->v;
double *ervel = atom->ervel;
@@ -92,11 +92,11 @@ void ComputeKEAtomEff::compute_peratom()
int *type = atom->type;
int nlocal = atom->nlocal;
double mefactor = domain->dimension/4.0;
-
+
if (mass)
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
- ke[i] = 0.5 * mvv2e * mass[type[i]] *
+ ke[i] = 0.5 * mvv2e * mass[type[i]] *
(v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]);
if (fabs(spin[i])==1)
ke[i] += 0.5 * mvv2e * mefactor * mass[type[i]] * ervel[i]*ervel[i];
diff --git a/src/USER-EFF/compute_ke_atom_eff.h b/src/USER-EFF/compute_ke_atom_eff.h
index 1f04412e502ceacff25e743cf6a7448320547f91..16ac96fc94800c21d83cb52b9e8327b924d4b883 100644
--- a/src/USER-EFF/compute_ke_atom_eff.h
+++ b/src/USER-EFF/compute_ke_atom_eff.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -32,7 +32,7 @@ class ComputeKEAtomEff : public Compute {
void init();
void compute_peratom();
double memory_usage();
-
+
private:
int nmax;
double *ke;
diff --git a/src/USER-EFF/compute_ke_eff.cpp b/src/USER-EFF/compute_ke_eff.cpp
index 5da7d257408749841664deb1253d2a2cd34d56a4..2549ca93aad70003cefc28605cbc2ea4b7759e26 100644
--- a/src/USER-EFF/compute_ke_eff.cpp
+++ b/src/USER-EFF/compute_ke_eff.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -39,7 +39,7 @@ ComputeKEEff::ComputeKEEff(LAMMPS *lmp, int narg, char **arg) :
// error check
- if (!atom->electron_flag)
+ if (!atom->electron_flag)
error->all(FLERR,"Compute ke/eff requires atom style electron");
}
@@ -70,7 +70,7 @@ double ComputeKEEff::compute_scalar()
if (mass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- ke += mass[type[i]]*(v[i][0]*v[i][0] + v[i][1]*v[i][1] +
+ ke += mass[type[i]]*(v[i][0]*v[i][0] + v[i][1]*v[i][1] +
v[i][2]*v[i][2]);
if (fabs(spin[i])==1) ke += mefactor*mass[type[i]]*ervel[i]*ervel[i];
}
diff --git a/src/USER-EFF/compute_ke_eff.h b/src/USER-EFF/compute_ke_eff.h
index e8a31db55115577f112ca1bb15a23f129771526c..cd71dd59f5133b1d0c749179a28b446c2de620b9 100644
--- a/src/USER-EFF/compute_ke_eff.h
+++ b/src/USER-EFF/compute_ke_eff.h
@@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
-
+
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
-
+
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@@ -30,11 +30,11 @@ class ComputeKEEff : public Compute {
~ComputeKEEff() {};
void init();
double compute_scalar();
-
+
private:
double pfactor;
};
-
+
}
#endif
diff --git a/src/USER-EFF/compute_temp_deform_eff.cpp b/src/USER-EFF/compute_temp_deform_eff.cpp
index 68e73a83d1e6af77fd63b540fb4b11b4f3e407fe..69237259128ccb523ce78e3cca25686428262de3 100644
--- a/src/USER-EFF/compute_temp_deform_eff.cpp
+++ b/src/USER-EFF/compute_temp_deform_eff.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -43,7 +43,7 @@ ComputeTempDeformEff::ComputeTempDeformEff(LAMMPS *lmp, int narg, char **arg) :
{
if (narg != 3) error->all(FLERR,"Illegal compute temp/deform/eff command");
- if (!atom->electron_flag)
+ if (!atom->electron_flag)
error->all(FLERR,"Compute temp/deform/eff requires atom style electron");
scalar_flag = vector_flag = 1;
@@ -79,7 +79,7 @@ void ComputeTempDeformEff::init()
// check fix deform remap settings
- for (i = 0; i < modify->nfix; i++)
+ for (i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"deform") == 0) {
if (((FixDeform *) modify->fix[i])->remapflag == X_REMAP &&
comm->me == 0)
@@ -98,7 +98,7 @@ void ComputeTempDeformEff::dof_compute()
double natoms = group->count(igroup);
dof = domain->dimension * natoms;
dof -= extra_dof + fix_dof;
-
+
// just include nuclear dof
int *spin = atom->spin;
@@ -113,9 +113,9 @@ void ComputeTempDeformEff::dof_compute()
int nelectrons;
MPI_Allreduce(&one,&nelectrons,1,MPI_INT,MPI_SUM,world);
- // Assume 3/2 k T per nucleus
+ // Assume 3/2 k T per nucleus
dof -= domain->dimension * nelectrons;
-
+
if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz);
else tfactor = 0.0;
}
@@ -125,9 +125,9 @@ void ComputeTempDeformEff::dof_compute()
double ComputeTempDeformEff::compute_scalar()
{
double lamda[3],vstream[3],vthermal[3];
-
+
invoked_scalar = update->ntimestep;
-
+
double **x = atom->x;
double **v = atom->v;
double *ervel = atom->ervel;
@@ -141,30 +141,30 @@ double ComputeTempDeformEff::compute_scalar()
// lamda = 0-1 triclinic lamda coords
// vstream = streaming velocity = Hrate*lamda + Hratelo
// vthermal = thermal velocity = v - vstream
-
+
double *h_rate = domain->h_rate;
double *h_ratelo = domain->h_ratelo;
-
- double t = 0.0;
-
+
+ double t = 0.0;
+
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
domain->x2lamda(x[i],lamda);
- vstream[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
+ vstream[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
h_rate[4]*lamda[2] + h_ratelo[0];
vstream[1] = h_rate[1]*lamda[1] + h_rate[3]*lamda[2] + h_ratelo[1];
vstream[2] = h_rate[2]*lamda[2] + h_ratelo[2];
vthermal[0] = v[i][0] - vstream[0];
vthermal[1] = v[i][1] - vstream[1];
vthermal[2] = v[i][2] - vstream[2];
-
+
if (mass) {
- t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] +
+ t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] +
vthermal[2]*vthermal[2])* mass[type[i]];
if (fabs(spin[i])==1) t += mefactor*mass[type[i]]*ervel[i]*ervel[i];
}
}
-
+
MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
if (dynamic) dof_compute();
scalar *= tfactor;
@@ -176,14 +176,14 @@ double ComputeTempDeformEff::compute_scalar()
void ComputeTempDeformEff::compute_vector()
{
double lamda[3],vstream[3],vthermal[3];
-
+
invoked_vector = update->ntimestep;
-
+
double **x = atom->x;
double **v = atom->v;
double *ervel = atom->ervel;
double *mass = atom->mass;
- int *spin = atom->spin;
+ int *spin = atom->spin;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
@@ -191,23 +191,23 @@ void ComputeTempDeformEff::compute_vector()
double *h_rate = domain->h_rate;
double *h_ratelo = domain->h_ratelo;
-
+
double massone,t[6];
for (int i = 0; i < 6; i++) t[i] = 0.0;
-
+
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
domain->x2lamda(x[i],lamda);
- vstream[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
+ vstream[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
h_rate[4]*lamda[2] + h_ratelo[0];
vstream[1] = h_rate[1]*lamda[1] + h_rate[3]*lamda[2] + h_ratelo[1];
vstream[2] = h_rate[2]*lamda[2] + h_ratelo[2];
vthermal[0] = v[i][0] - vstream[0];
vthermal[1] = v[i][1] - vstream[1];
vthermal[2] = v[i][2] - vstream[2];
-
+
massone = mass[type[i]];
- t[0] += massone * vthermal[0]*vthermal[0];
+ t[0] += massone * vthermal[0]*vthermal[0];
t[1] += massone * vthermal[1]*vthermal[1];
t[2] += massone * vthermal[2]*vthermal[2];
t[3] += massone * vthermal[0]*vthermal[1];
@@ -219,7 +219,7 @@ void ComputeTempDeformEff::compute_vector()
t[2] += mefactor * massone * ervel[i]*ervel[i];
}
}
-
+
MPI_Allreduce(t,vector,6,MPI_DOUBLE,MPI_SUM,world);
for (int i = 0; i < 6; i++) vector[i] *= force->mvv2e;
}
@@ -316,4 +316,3 @@ double ComputeTempDeformEff::memory_usage()
double bytes = maxbias * sizeof(double);
return bytes;
}
-
diff --git a/src/USER-EFF/compute_temp_deform_eff.h b/src/USER-EFF/compute_temp_deform_eff.h
index 47f440942225e8fff3fbfc32a6776ab673bb5b23..c5be07430154797a06d74baad4fdfd9e70fac077 100644
--- a/src/USER-EFF/compute_temp_deform_eff.h
+++ b/src/USER-EFF/compute_temp_deform_eff.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-EFF/compute_temp_eff.cpp b/src/USER-EFF/compute_temp_eff.cpp
index cf406c53e6afa241134b302104346d6978610000..ea4474eb0cf65d108100f8086345ba9c9d64d529 100644
--- a/src/USER-EFF/compute_temp_eff.cpp
+++ b/src/USER-EFF/compute_temp_eff.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -32,18 +32,18 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-ComputeTempEff::ComputeTempEff(LAMMPS *lmp, int narg, char **arg) :
+ComputeTempEff::ComputeTempEff(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
- if (!atom->electron_flag)
+ if (!atom->electron_flag)
error->all(FLERR,"Compute temp/eff requires atom style electron");
scalar_flag = vector_flag = 1;
size_vector = 6;
- extscalar = 0;
+ extscalar = 0;
extvector = 1;
tempflag = 1;
-
+
vector = new double[size_vector];
}
@@ -70,7 +70,7 @@ void ComputeTempEff::dof_compute()
{
double natoms = group->count(igroup);
dof = domain->dimension * natoms;
- dof -= extra_dof + fix_dof;
+ dof -= extra_dof + fix_dof;
int *spin = atom->spin;
int *mask = atom->mask;
@@ -84,7 +84,7 @@ void ComputeTempEff::dof_compute()
int nelectrons;
MPI_Allreduce(&one,&nelectrons,1,MPI_INT,MPI_SUM,world);
- // Assume 3/2 k T per nucleus
+ // Assume 3/2 k T per nucleus
dof -= domain->dimension * nelectrons;
@@ -108,11 +108,11 @@ double ComputeTempEff::compute_scalar()
double mefactor = domain->dimension/4.0;
double t = 0.0;
-
+
if (mass) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
- t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
+ t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
mass[type[i]];
if (fabs(spin[i])==1) t += mefactor*mass[type[i]]*ervel[i]*ervel[i];
}
diff --git a/src/USER-EFF/compute_temp_eff.h b/src/USER-EFF/compute_temp_eff.h
index 197dd4dbc576a21dd1aae5764caf9c0b9e5d1668..18a6a6ecb58c0817ee1a5efc3521f2ef84193909 100644
--- a/src/USER-EFF/compute_temp_eff.h
+++ b/src/USER-EFF/compute_temp_eff.h
@@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
-
+
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
-
+
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@@ -23,7 +23,7 @@ ComputeStyle(temp/eff,ComputeTempEff)
#include "compute.h"
namespace LAMMPS_NS {
-
+
class ComputeTempEff : public Compute {
public:
ComputeTempEff(class LAMMPS *, int, char **);
@@ -31,7 +31,7 @@ class ComputeTempEff : public Compute {
void init();
double compute_scalar();
void compute_vector();
-
+
private:
int fix_dof;
double tfactor;
@@ -39,7 +39,7 @@ class ComputeTempEff : public Compute {
void dof_compute();
};
-
+
}
#endif
diff --git a/src/USER-EFF/compute_temp_region_eff.cpp b/src/USER-EFF/compute_temp_region_eff.cpp
index 0dd2bf3cf60fa2d69d7e85a583d339c67ca99b84..5e8a42421b2d21f1501ff0c0bfb17bbb58657328 100644
--- a/src/USER-EFF/compute_temp_region_eff.cpp
+++ b/src/USER-EFF/compute_temp_region_eff.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -32,10 +32,10 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-ComputeTempRegionEff::ComputeTempRegionEff(LAMMPS *lmp, int narg, char **arg) :
+ComputeTempRegionEff::ComputeTempRegionEff(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
- if (!atom->electron_flag)
+ if (!atom->electron_flag)
error->all(FLERR,"Compute temp/region/eff requires atom style electron");
if (narg != 4) error->all(FLERR,"Illegal compute temp/region/eff command");
@@ -46,14 +46,14 @@ ComputeTempRegionEff::ComputeTempRegionEff(LAMMPS *lmp, int narg, char **arg) :
int n = strlen(arg[3]) + 1;
idregion = new char[n];
strcpy(idregion,arg[3]);
-
+
scalar_flag = vector_flag = 1;
size_vector = 6;
extscalar = 0;
extvector = 1;
tempflag = 1;
tempbias = 1;
-
+
maxbias = 0;
vbiasall = NULL;
vector = new double[6];
@@ -62,7 +62,7 @@ ComputeTempRegionEff::ComputeTempRegionEff(LAMMPS *lmp, int narg, char **arg) :
/* ---------------------------------------------------------------------- */
ComputeTempRegionEff::~ComputeTempRegionEff()
-{
+{
delete [] idregion;
memory->destroy(vbiasall);
delete [] vector;
@@ -115,7 +115,7 @@ double ComputeTempRegionEff::compute_scalar()
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
count++;
- t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
+ t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
mass[type[i]];
if (fabs(spin[i])==1) {
t += mefactor*mass[type[i]]*ervel[i]*ervel[i];
@@ -130,7 +130,7 @@ double ComputeTempRegionEff::compute_scalar()
tarray[1] = t;
MPI_Allreduce(tarray,tarray_all,2,MPI_DOUBLE,MPI_SUM,world);
dof = domain->dimension * tarray_all[0] - extra_dof;
-
+
int one = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
@@ -166,7 +166,7 @@ void ComputeTempRegionEff::compute_vector()
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
- massone = mass[type[i]];
+ massone = mass[type[i]];
t[0] += massone * v[i][0]*v[i][0];
t[1] += massone * v[i][1]*v[i][1];
@@ -174,7 +174,7 @@ void ComputeTempRegionEff::compute_vector()
t[3] += massone * v[i][0]*v[i][1];
t[4] += massone * v[i][0]*v[i][2];
t[5] += massone * v[i][1]*v[i][2];
-
+
if (fabs(spin[i])==1) {
t[0] += mefactor * massone * ervel[i]*ervel[i];
t[1] += mefactor * massone * ervel[i]*ervel[i];
@@ -190,7 +190,7 @@ void ComputeTempRegionEff::compute_vector()
remove velocity bias from atom I to leave thermal velocity
NOTE: the following commands do not bias the radial electron velocities
------------------------------------------------------------------------- */
-
+
void ComputeTempRegionEff::remove_bias(int i, double *v)
{
double *x = atom->x[i];
@@ -201,13 +201,13 @@ void ComputeTempRegionEff::remove_bias(int i, double *v)
vbias[1] = v[1];
vbias[2] = v[2];
v[0] = v[1] = v[2] = 0.0;
- }
+ }
}
/* ----------------------------------------------------------------------
remove velocity bias from all atoms to leave thermal velocity
------------------------------------------------------------------------- */
-
+
void ComputeTempRegionEff::remove_bias_all()
{
double **x = atom->x;
@@ -219,10 +219,10 @@ void ComputeTempRegionEff::remove_bias_all()
memory->destroy(vbiasall);
maxbias = atom->nmax;
memory->create(vbiasall,maxbias,3,"temp/region:vbiasall");
- }
+ }
Region *region = domain->regions[iregion];
-
+
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (region->match(x[i][0],x[i][1],x[i][2]))
@@ -274,4 +274,3 @@ double ComputeTempRegionEff::memory_usage()
double bytes = maxbias * sizeof(double);
return bytes;
}
-
diff --git a/src/USER-EFF/compute_temp_region_eff.h b/src/USER-EFF/compute_temp_region_eff.h
index 3340fe8261bea3da8625b965d486f7d086010bc6..5d6d7561d6dcbe84e94f40b0b1f4ec76ce3c4d57 100644
--- a/src/USER-EFF/compute_temp_region_eff.h
+++ b/src/USER-EFF/compute_temp_region_eff.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -38,7 +38,7 @@ class ComputeTempRegionEff : public Compute {
void restore_bias(int, double *);
void restore_bias_all();
double memory_usage();
-
+
protected:
int iregion;
char *idregion;
diff --git a/src/USER-EFF/fix_langevin_eff.cpp b/src/USER-EFF/fix_langevin_eff.cpp
index 88f38ab83aee499d1133c93e501f35202a0480f7..8e90f1995f092843f4c3b1b1330b53b2abfb9356 100644
--- a/src/USER-EFF/fix_langevin_eff.cpp
+++ b/src/USER-EFF/fix_langevin_eff.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -93,20 +93,20 @@ void FixLangevinEff::post_force_no_tally()
if (tstyle == EQUAL) {
t_target = input->variable->compute_equal(tvar);
if (t_target < 0.0)
- error->one(FLERR,"Fix langevin/eff variable returned negative temperature");
+ error->one(FLERR,"Fix langevin/eff variable returned negative temperature");
tsqrt = sqrt(t_target);
} else {
if (nlocal > maxatom2) {
- maxatom2 = atom->nmax;
- memory->destroy(tforce);
- memory->create(tforce,maxatom2,"langevin/eff:tforce");
+ maxatom2 = atom->nmax;
+ memory->destroy(tforce);
+ memory->create(tforce,maxatom2,"langevin/eff:tforce");
}
input->variable->compute_atom(tvar,igroup,tforce,1,0);
for (int i = 0; i < nlocal; i++)
- if (mask[i] & groupbit)
- if (tforce[i] < 0.0)
- error->one(FLERR,
- "Fix langevin/eff variable returned negative temperature");
+ if (mask[i] & groupbit)
+ if (tforce[i] < 0.0)
+ error->one(FLERR,
+ "Fix langevin/eff variable returned negative temperature");
}
modify->addstep_compute(update->ntimestep + 1);
}
@@ -119,7 +119,7 @@ void FixLangevinEff::post_force_no_tally()
// and added force has extra term not multiplied by v = 0
// for ZEROFLAG:
// sum random force over all atoms in group
- // subtract sum/particles from each atom in group
+ // subtract sum/particles from each atom in group
double fran[4],fsum[4],fsumall[4];
fsum[0] = fsum[1] = fsum[2] = fsum[3] = 0.0;
@@ -155,7 +155,7 @@ void FixLangevinEff::post_force_no_tally()
dofelectrons = domain->dimension*nelectrons;
dofnuclei = dof-dofelectrons;
- // thermal partitioning factor between nuclei and electrons
+ // thermal partitioning factor between nuclei and electrons
// extra dof from electron size
double gfactor3=(double) (dof+nelectrons)/dofnuclei;
@@ -163,17 +163,17 @@ void FixLangevinEff::post_force_no_tally()
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
- gamma1 = gfactor1[type[i]] * gfactor3;
- gamma2 = gfactor2[type[i]] * tsqrt;
- fran[0] = gamma2*(random->uniform()-0.5);
- fran[1] = gamma2*(random->uniform()-0.5);
- fran[2] = gamma2*(random->uniform()-0.5);
- f[i][0] += gamma1*v[i][0] + fran[0];
- f[i][1] += gamma1*v[i][1] + fran[1];
- f[i][2] += gamma1*v[i][2] + fran[2];
- fsum[0] += fran[0];
- fsum[1] += fran[1];
- fsum[2] += fran[2];
+ gamma1 = gfactor1[type[i]] * gfactor3;
+ gamma2 = gfactor2[type[i]] * tsqrt;
+ fran[0] = gamma2*(random->uniform()-0.5);
+ fran[1] = gamma2*(random->uniform()-0.5);
+ fran[2] = gamma2*(random->uniform()-0.5);
+ f[i][0] += gamma1*v[i][0] + fran[0];
+ f[i][1] += gamma1*v[i][1] + fran[1];
+ f[i][2] += gamma1*v[i][2] + fran[2];
+ fsum[0] += fran[0];
+ fsum[1] += fran[1];
+ fsum[2] += fran[2];
if (fabs(spin[i])==1) {
fran[3] = sqrtmefactor*gamma2*(random->uniform()-0.5);
erforce[i] += mefactor*gamma1*ervel[i]+fran[3];
@@ -185,28 +185,28 @@ void FixLangevinEff::post_force_no_tally()
temperature->compute_scalar();
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
- if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
- gamma1 = gfactor1[type[i]] * gfactor3;
- gamma2 = gfactor2[type[i]] * tsqrt;
- temperature->remove_bias(i,v[i]);
- fran[0] = gamma2*(random->uniform()-0.5);
- fran[1] = gamma2*(random->uniform()-0.5);
- fran[2] = gamma2*(random->uniform()-0.5);
- if (v[i][0] != 0.0)
- f[i][0] += gamma1*v[i][0] + fran[0];
- if (v[i][1] != 0.0)
- f[i][1] += gamma1*v[i][1] + fran[1];
- if (v[i][2] != 0.0)
- f[i][2] += gamma1*v[i][2] + fran[2];
- fsum[0] += fran[0];
- fsum[1] += fran[1];
- fsum[2] += fran[2];
+ if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
+ gamma1 = gfactor1[type[i]] * gfactor3;
+ gamma2 = gfactor2[type[i]] * tsqrt;
+ temperature->remove_bias(i,v[i]);
+ fran[0] = gamma2*(random->uniform()-0.5);
+ fran[1] = gamma2*(random->uniform()-0.5);
+ fran[2] = gamma2*(random->uniform()-0.5);
+ if (v[i][0] != 0.0)
+ f[i][0] += gamma1*v[i][0] + fran[0];
+ if (v[i][1] != 0.0)
+ f[i][1] += gamma1*v[i][1] + fran[1];
+ if (v[i][2] != 0.0)
+ f[i][2] += gamma1*v[i][2] + fran[2];
+ fsum[0] += fran[0];
+ fsum[1] += fran[1];
+ fsum[2] += fran[2];
if (fabs(spin[i])==1) {
fran[3] = sqrtmefactor*gamma2*(random->uniform()-0.5);
if (ervel[i] != 0.0) erforce[i] += mefactor*gamma1*ervel[i]+fran[3];
fsum[3] += fran[3];
}
- temperature->restore_bias(i,v[i]);
+ temperature->restore_bias(i,v[i]);
}
}
}
@@ -221,9 +221,9 @@ void FixLangevinEff::post_force_no_tally()
fsumall[3] /= nelectrons;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
- f[i][0] -= fsumall[0];
- f[i][1] -= fsumall[1];
- f[i][2] -= fsumall[2];
+ f[i][0] -= fsumall[0];
+ f[i][1] -= fsumall[1];
+ f[i][2] -= fsumall[2];
if (fabs(spin[i])==1) erforce[i] -= fsumall[3];
}
}
@@ -273,20 +273,20 @@ void FixLangevinEff::post_force_tally()
if (tstyle == EQUAL) {
t_target = input->variable->compute_equal(tvar);
if (t_target < 0.0)
- error->one(FLERR,"Fix langevin/eff variable returned negative temperature");
+ error->one(FLERR,"Fix langevin/eff variable returned negative temperature");
tsqrt = sqrt(t_target);
} else {
if (nlocal > maxatom2) {
- maxatom2 = atom->nmax;
- memory->destroy(tforce);
- memory->create(tforce,maxatom2,"langevin/eff:tforce");
+ maxatom2 = atom->nmax;
+ memory->destroy(tforce);
+ memory->create(tforce,maxatom2,"langevin/eff:tforce");
}
input->variable->compute_atom(tvar,igroup,tforce,1,0);
for (int i = 0; i < nlocal; i++)
- if (mask[i] & groupbit)
- if (tforce[i] < 0.0)
- error->one(FLERR,
- "Fix langevin/eff variable returned negative temperature");
+ if (mask[i] & groupbit)
+ if (tforce[i] < 0.0)
+ error->one(FLERR,
+ "Fix langevin/eff variable returned negative temperature");
}
modify->addstep_compute(update->ntimestep + 1);
}
@@ -336,15 +336,15 @@ void FixLangevinEff::post_force_tally()
if (which == NOBIAS) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
- if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
- gamma1 = gfactor1[type[i]] * gfactor3;
- gamma2 = gfactor2[type[i]] * tsqrt;
- flangevin[i][0] = gamma1*v[i][0] + gamma2*(random->uniform()-0.5);
- flangevin[i][1] = gamma1*v[i][1] + gamma2*(random->uniform()-0.5);
- flangevin[i][2] = gamma1*v[i][2] + gamma2*(random->uniform()-0.5);
- f[i][0] += flangevin[i][0];
- f[i][1] += flangevin[i][1];
- f[i][2] += flangevin[i][2];
+ if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
+ gamma1 = gfactor1[type[i]] * gfactor3;
+ gamma2 = gfactor2[type[i]] * tsqrt;
+ flangevin[i][0] = gamma1*v[i][0] + gamma2*(random->uniform()-0.5);
+ flangevin[i][1] = gamma1*v[i][1] + gamma2*(random->uniform()-0.5);
+ flangevin[i][2] = gamma1*v[i][2] + gamma2*(random->uniform()-0.5);
+ f[i][0] += flangevin[i][0];
+ f[i][1] += flangevin[i][1];
+ f[i][2] += flangevin[i][2];
if (fabs(spin[i])==1) {
erforcelangevin[i] = mefactor*gamma1*ervel[i]+sqrtmefactor*gamma2*(random->uniform()-0.5);
erforce[i] += erforcelangevin[i];
@@ -355,25 +355,25 @@ void FixLangevinEff::post_force_tally()
temperature->compute_scalar();
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
- if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
- gamma1 = gfactor1[type[i]] * gfactor3;
- gamma2 = gfactor2[type[i]] * tsqrt;
- temperature->remove_bias(i,v[i]);
- flangevin[i][0] = gamma1*v[i][0] + gamma2*(random->uniform()-0.5);
- flangevin[i][1] = gamma1*v[i][1] + gamma2*(random->uniform()-0.5);
- flangevin[i][2] = gamma1*v[i][2] + gamma2*(random->uniform()-0.5);
- if (v[i][0] != 0.0) f[i][0] += flangevin[i][0];
- else flangevin[i][0] = 0.0;
- if (v[i][1] != 0.0) f[i][1] += flangevin[i][1];
- else flangevin[i][1] = 0.0;
- if (v[i][2] != 0.0) f[i][2] += flangevin[i][2];
- else flangevin[i][2] = 0.0;
+ if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
+ gamma1 = gfactor1[type[i]] * gfactor3;
+ gamma2 = gfactor2[type[i]] * tsqrt;
+ temperature->remove_bias(i,v[i]);
+ flangevin[i][0] = gamma1*v[i][0] + gamma2*(random->uniform()-0.5);
+ flangevin[i][1] = gamma1*v[i][1] + gamma2*(random->uniform()-0.5);
+ flangevin[i][2] = gamma1*v[i][2] + gamma2*(random->uniform()-0.5);
+ if (v[i][0] != 0.0) f[i][0] += flangevin[i][0];
+ else flangevin[i][0] = 0.0;
+ if (v[i][1] != 0.0) f[i][1] += flangevin[i][1];
+ else flangevin[i][1] = 0.0;
+ if (v[i][2] != 0.0) f[i][2] += flangevin[i][2];
+ else flangevin[i][2] = 0.0;
if (fabs(spin[i])==1) {
erforcelangevin[i] = mefactor*gamma1*ervel[i]+sqrtmefactor*gamma2*(random->uniform()-0.5);
if (ervel[i] != 0.0) erforce[i] += erforcelangevin[i];
else erforcelangevin[i] = 0.0;
}
- temperature->restore_bias(i,v[i]);
+ temperature->restore_bias(i,v[i]);
}
}
}
@@ -389,14 +389,14 @@ void FixLangevinEff::end_of_step()
double **v = atom->v;
int *mask = atom->mask;
- int nlocal = atom->nlocal;
+ int nlocal = atom->nlocal;
int *spin = atom->spin;
energy_onestep = 0.0;
-
+
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- energy_onestep += flangevin[i][0]*v[i][0] + flangevin[i][1]*v[i][1] +
+ energy_onestep += flangevin[i][0]*v[i][0] + flangevin[i][1]*v[i][1] +
flangevin[i][2]*v[i][2];
if (fabs(spin[i])==1) energy_onestep += erforcelangevin[i];
}
@@ -413,15 +413,15 @@ double FixLangevinEff::compute_scalar()
double **v = atom->v;
int *mask = atom->mask;
- int nlocal = atom->nlocal;
+ int nlocal = atom->nlocal;
int *spin = atom->spin;
if (update->ntimestep == update->beginstep) {
energy_onestep = 0.0;
- for (int i = 0; i < nlocal; i++)
+ for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- energy_onestep += flangevin[i][0]*v[i][0] + flangevin[i][1]*v[i][1] +
- flangevin[i][2]*v[i][2];
+ energy_onestep += flangevin[i][0]*v[i][0] + flangevin[i][1]*v[i][1] +
+ flangevin[i][2]*v[i][2];
if (fabs(spin[i])==1) energy_onestep += erforcelangevin[i];
}
energy = 0.5*energy_onestep*update->dt;
@@ -429,8 +429,7 @@ double FixLangevinEff::compute_scalar()
double energy_me = energy - 0.5*energy_onestep*update->dt;
- double energy_all;
- MPI_Allreduce(&energy_me,&energy_all,1,MPI_DOUBLE,MPI_SUM,world);
+ double energy_all;
+ MPI_Allreduce(&energy_me,&energy_all,1,MPI_DOUBLE,MPI_SUM,world);
return -energy_all;
}
-
diff --git a/src/USER-EFF/fix_langevin_eff.h b/src/USER-EFF/fix_langevin_eff.h
index 6eb78ff9b9ca23d51f29a37ff585e564813d6446..81d831291648750fdb8da20fac722fcab34accda 100644
--- a/src/USER-EFF/fix_langevin_eff.h
+++ b/src/USER-EFF/fix_langevin_eff.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-EFF/fix_nh_eff.cpp b/src/USER-EFF/fix_nh_eff.cpp
index 4258a081bafbf105b922b2befe3d405e65f50fff..fb1a968ec5b34d316e7e619c8c326216763c7f61 100644
--- a/src/USER-EFF/fix_nh_eff.cpp
+++ b/src/USER-EFF/fix_nh_eff.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -32,12 +32,12 @@ enum{NOBIAS,BIAS};
FixNHEff::FixNHEff(LAMMPS *lmp, int narg, char **arg) : FixNH(lmp, narg, arg)
{
- if (!atom->electron_flag)
+ if (!atom->electron_flag)
error->all(FLERR,"Fix nvt/nph/npt/eff requires atom style electron");
}
/* ----------------------------------------------------------------------
- perform half-step update of electron radial velocities
+ perform half-step update of electron radial velocities
-----------------------------------------------------------------------*/
void FixNHEff::nve_v()
@@ -59,11 +59,11 @@ void FixNHEff::nve_v()
int itype;
double dtfm;
- for (int i = 0; i < nlocal; i++) {
+ for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (fabs(spin[i])==1) {
- dtfm = dtf / mass[type[i]];
- ervel[i] = dtfm * erforce[i] / mefactor;
+ dtfm = dtf / mass[type[i]];
+ ervel[i] = dtfm * erforce[i] / mefactor;
}
}
}
diff --git a/src/USER-EFF/fix_nh_eff.h b/src/USER-EFF/fix_nh_eff.h
index c51b6be0140c78fb0994784c5dcf93ee93de55ae..74c30f978e2b699739f10a220b086ca2d2ea9da3 100644
--- a/src/USER-EFF/fix_nh_eff.h
+++ b/src/USER-EFF/fix_nh_eff.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-EFF/fix_nph_eff.cpp b/src/USER-EFF/fix_nph_eff.cpp
index f75dbee35afd70ffa0040707863631347751959a..e580a3fc735a654ab094b81bd297490fea46170c 100644
--- a/src/USER-EFF/fix_nph_eff.cpp
+++ b/src/USER-EFF/fix_nph_eff.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -38,7 +38,7 @@ FixNPHEff::FixNPHEff(LAMMPS *lmp, int narg, char **arg) :
id_temp = new char[n];
strcpy(id_temp,id);
strcat(id_temp,"_temp");
-
+
char **newarg = new char*[3];
newarg[0] = id_temp;
newarg[1] = (char *) "all";
@@ -56,7 +56,7 @@ FixNPHEff::FixNPHEff(LAMMPS *lmp, int narg, char **arg) :
id_press = new char[n];
strcpy(id_press,id);
strcat(id_press,"_press");
-
+
newarg = new char*[4];
newarg[0] = id_press;
newarg[1] = (char *) "all";
diff --git a/src/USER-EFF/fix_nph_eff.h b/src/USER-EFF/fix_nph_eff.h
index 9862bf8d99022d78bb9a0185bfa03b4b4b999767..10766ec96c9ce4d377c4f1115e262785d9a520bc 100644
--- a/src/USER-EFF/fix_nph_eff.h
+++ b/src/USER-EFF/fix_nph_eff.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-EFF/fix_npt_eff.cpp b/src/USER-EFF/fix_npt_eff.cpp
index 53b3ab11e2fa0fcd6b9059eefa505b3c4ffe2b24..baea9a16eadb12df63eaf64419e43f1b82870f6e 100644
--- a/src/USER-EFF/fix_npt_eff.cpp
+++ b/src/USER-EFF/fix_npt_eff.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -38,7 +38,7 @@ FixNPTEff::FixNPTEff(LAMMPS *lmp, int narg, char **arg) :
id_temp = new char[n];
strcpy(id_temp,id);
strcat(id_temp,"_temp");
-
+
char **newarg = new char*[3];
newarg[0] = id_temp;
newarg[1] = (char *) "all";
@@ -56,7 +56,7 @@ FixNPTEff::FixNPTEff(LAMMPS *lmp, int narg, char **arg) :
id_press = new char[n];
strcpy(id_press,id);
strcat(id_press,"_press");
-
+
newarg = new char*[4];
newarg[0] = id_press;
newarg[1] = (char *) "all";
diff --git a/src/USER-EFF/fix_npt_eff.h b/src/USER-EFF/fix_npt_eff.h
index ace91a596def1a0d4dbc2aa87ea9e3ec93c9bd7d..11f059d73335194b0bbc26f973fd9fc196134561 100644
--- a/src/USER-EFF/fix_npt_eff.h
+++ b/src/USER-EFF/fix_npt_eff.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-EFF/fix_nve_eff.cpp b/src/USER-EFF/fix_nve_eff.cpp
index 6ddff5e30c4fe6234a147af69319c0e1b0e08351..afe442ba5e88c0f4b280a33802370d3b1c7909f4 100644
--- a/src/USER-EFF/fix_nve_eff.cpp
+++ b/src/USER-EFF/fix_nve_eff.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -35,7 +35,7 @@ using namespace FixConst;
FixNVEEff::FixNVEEff(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
- if (!atom->electron_flag)
+ if (!atom->electron_flag)
error->all(FLERR,"Fix nve/eff requires atom style electron");
time_integrate = 1;
@@ -44,7 +44,7 @@ FixNVEEff::FixNVEEff(LAMMPS *lmp, int narg, char **arg) :
/* ---------------------------------------------------------------------- */
int FixNVEEff::setmask()
-{
+{
int mask = 0;
mask |= INITIAL_INTEGRATE;
mask |= FINAL_INTEGRATE;
@@ -89,7 +89,7 @@ void FixNVEEff::initial_integrate(int vflag)
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
// x + dt * [v + 0.5 * dt * (f / m)];
-
+
if (mass) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
@@ -114,7 +114,7 @@ void FixNVEEff::initial_integrate(int vflag)
void FixNVEEff::final_integrate()
{
double dtfm;
-
+
double **v = atom->v;
double *ervel = atom->ervel;
double *erforce = atom->erforce;
@@ -126,7 +126,7 @@ void FixNVEEff::final_integrate()
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
-
+
// dyn_v[i] += m * dt * dyn_f[i];
if (mass) {
@@ -172,4 +172,3 @@ void FixNVEEff::reset_dt()
dtv = update->dt;
dtf = 0.5 * update->dt * force->ftm2v;
}
-
diff --git a/src/USER-EFF/fix_nve_eff.h b/src/USER-EFF/fix_nve_eff.h
index 68be95295f252a47e9349614665c60771aa30081..de01aa9b3d955e5e5a51ca3229af3727deb2318d 100644
--- a/src/USER-EFF/fix_nve_eff.h
+++ b/src/USER-EFF/fix_nve_eff.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-EFF/fix_nvt_eff.cpp b/src/USER-EFF/fix_nvt_eff.cpp
index 0236f406e055d7893bdcbdd7a84c4eaee2c701cd..17e01a31bb2adf8bbd5542a1a2ccf4c2a7edb88b 100644
--- a/src/USER-EFF/fix_nvt_eff.cpp
+++ b/src/USER-EFF/fix_nvt_eff.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -38,7 +38,7 @@ FixNVTEff::FixNVTEff(LAMMPS *lmp, int narg, char **arg) :
id_temp = new char[n];
strcpy(id_temp,id);
strcat(id_temp,"_temp");
-
+
char **newarg = new char*[3];
newarg[0] = id_temp;
newarg[1] = group->names[igroup];
diff --git a/src/USER-EFF/fix_nvt_eff.h b/src/USER-EFF/fix_nvt_eff.h
index 139febcf3d6620b434e91e54ab00293afe50eea7..9b63345ef24eac6095fd96ce0ee3fd9742213550 100644
--- a/src/USER-EFF/fix_nvt_eff.h
+++ b/src/USER-EFF/fix_nvt_eff.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-EFF/fix_nvt_sllod_eff.cpp b/src/USER-EFF/fix_nvt_sllod_eff.cpp
index 17d58664db63d7612bd097b325a9220d6d04cd0f..4aecdd4fdeb0732028174a8e92f5595bf18f6d77 100644
--- a/src/USER-EFF/fix_nvt_sllod_eff.cpp
+++ b/src/USER-EFF/fix_nvt_sllod_eff.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -78,8 +78,8 @@ void FixNVTSllodEff::init()
for (i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"deform") == 0) {
if (((FixDeform *) modify->fix[i])->remapflag != V_REMAP)
- error->all(FLERR,"Using fix nvt/sllod/eff with inconsistent fix deform "
- "remap option");
+ error->all(FLERR,"Using fix nvt/sllod/eff with inconsistent fix deform "
+ "remap option");
break;
}
if (i == modify->nfix)
diff --git a/src/USER-EFF/fix_nvt_sllod_eff.h b/src/USER-EFF/fix_nvt_sllod_eff.h
index 852ffb89c4b1084bca64d586c40099005c682c89..29676b6e30edf12ab3e1d76ea91da934e0d5ddb6 100644
--- a/src/USER-EFF/fix_nvt_sllod_eff.h
+++ b/src/USER-EFF/fix_nvt_sllod_eff.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-EFF/fix_temp_rescale_eff.cpp b/src/USER-EFF/fix_temp_rescale_eff.cpp
index 8d9fce342abec46df3965fcec4013b8b693c1bf0..0482ae36d5637446ec078d447bde41b280257f4e 100644
--- a/src/USER-EFF/fix_temp_rescale_eff.cpp
+++ b/src/USER-EFF/fix_temp_rescale_eff.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -137,26 +137,26 @@ void FixTempRescaleEff::end_of_step()
if (which == NOBIAS) {
energy += (t_current-t_target) * efactor;
for (int i = 0; i < nlocal; i++) {
- if (mask[i] & groupbit) {
- v[i][0] *= factor;
- v[i][1] *= factor;
- v[i][2] *= factor;
- if (abs(spin[i])==1)
+ if (mask[i] & groupbit) {
+ v[i][0] *= factor;
+ v[i][1] *= factor;
+ v[i][2] *= factor;
+ if (abs(spin[i])==1)
ervel[i] *= factor;
- }
+ }
}
} else {
energy += (t_current-t_target) * efactor;
for (int i = 0; i < nlocal; i++) {
- if (mask[i] & groupbit) {
- temperature->remove_bias(i,v[i]);
- v[i][0] *= factor;
- v[i][1] *= factor;
- v[i][2] *= factor;
+ if (mask[i] & groupbit) {
+ temperature->remove_bias(i,v[i]);
+ v[i][0] *= factor;
+ v[i][1] *= factor;
+ v[i][2] *= factor;
if (abs(spin[i])==1)
- ervel[i] *= factor;
- temperature->restore_bias(i,v[i]);
- }
+ ervel[i] *= factor;
+ temperature->restore_bias(i,v[i]);
+ }
}
}
@@ -204,4 +204,3 @@ double FixTempRescaleEff::compute_scalar()
{
return energy;
}
-
diff --git a/src/USER-EFF/fix_temp_rescale_eff.h b/src/USER-EFF/fix_temp_rescale_eff.h
index 9ac4c003adb8d73c82ca3da4343a70cf3fd32616..54155bcc533ec97ce814fb8244a470cc1ac49f93 100644
--- a/src/USER-EFF/fix_temp_rescale_eff.h
+++ b/src/USER-EFF/fix_temp_rescale_eff.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-EFF/pair_eff_cut.cpp b/src/USER-EFF/pair_eff_cut.cpp
index 3641bf372d66203b77cbadc9dc03ca5b4b1e108a..ae67bac2a015bffc053e0f9ccddb7f02414d8191 100644
--- a/src/USER-EFF/pair_eff_cut.cpp
+++ b/src/USER-EFF/pair_eff_cut.cpp
@@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
-
+
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
-
+
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@@ -75,7 +75,7 @@ void PairEffCut::compute(int eflag, int vflag)
double ecp_epauli, ecp_fpair, ecp_e1rforce, ecp_e2rforce;
double rsq,rc;
int *ilist,*jlist,*numneigh,**firstneigh;
-
+
energy = eke = epauli = ecoul = errestrain = 0.0;
// pvector = [KE, Pauli, ecoul, radial_restraint]
for (i=0; i<4; i++) pvector[i] = 0.0;
@@ -88,7 +88,7 @@ void PairEffCut::compute(int eflag, int vflag)
double *q = atom->q;
double *erforce = atom->erforce;
double *eradius = atom->eradius;
- int *spin = atom->spin;
+ int *spin = atom->spin;
int *type = atom->type;
int nlocal = atom->nlocal;
@@ -99,7 +99,7 @@ void PairEffCut::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@@ -110,7 +110,7 @@ void PairEffCut::compute(int eflag, int vflag)
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
-
+
// add electron wavefuntion kinetic energy (not pairwise)
if (abs(spin[i])==1 || spin[i]==2) {
@@ -120,7 +120,7 @@ void PairEffCut::compute(int eflag, int vflag)
s_fpair = 0.0;
KinElec(eradius[i],&eke,&e1rforce);
-
+
// Fixed-core
if (spin[i] == 2) {
// KE(2s)+Coul(1s-1s)+Coul(2s-nuclei)+Pauli(2s)
@@ -144,10 +144,10 @@ void PairEffCut::compute(int eflag, int vflag)
epauli *= hhmss2e;
s_fpair *= hhmss2e;
e1rforce *= hhmss2e;
-
+
// Sum up contributions
energy = eke + epauli + ecoul;
- fpair = fpair + s_fpair;
+ fpair = fpair + s_fpair;
erforce[i] += e1rforce;
@@ -173,26 +173,26 @@ void PairEffCut::compute(int eflag, int vflag)
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
rc = sqrt(rsq);
-
+
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
-
+
energy = ecoul = epauli = ecp_epauli = 0.0;
fx = fy = fz = fpair = s_fpair = ecp_fpair = 0.0;
double taper = sqrt(cutsq[itype][jtype]);
double dist = rc / taper;
- double spline = cutoff(dist);
+ double spline = cutoff(dist);
double dspline = dcutoff(dist) / taper;
- // nucleus (i) - nucleus (j) Coul interaction
+ // nucleus (i) - nucleus (j) Coul interaction
- if (spin[i] == 0 && spin[j] == 0) {
- double qxq = q[i]*q[j];
+ if (spin[i] == 0 && spin[j] == 0) {
+ double qxq = q[i]*q[j];
ElecNucNuc(qxq, rc, &ecoul, &fpair);
- }
+ }
// fixed-core (i) - nucleus (j) nuclear Coul interaction
else if (spin[i] == 2 && spin[j] == 0) {
@@ -228,39 +228,39 @@ void PairEffCut::compute(int eflag, int vflag)
ElecCoreNuc(qxq, rc, eradius[j], &ecoul, &fpair);
}
- // nucleus (i) - electron (j) Coul interaction
+ // nucleus (i) - electron (j) Coul interaction
- else if (spin[i] == 0 && abs(spin[j]) == 1) {
+ else if (spin[i] == 0 && abs(spin[j]) == 1) {
e1rforce = 0.0;
ElecNucElec(q[i],rc,eradius[j],&ecoul,&fpair,&e1rforce);
- e1rforce = spline * qqrd2e * e1rforce;
- erforce[j] += e1rforce;
-
+ e1rforce = spline * qqrd2e * e1rforce;
+ erforce[j] += e1rforce;
+
// Radial electron virial, iff flexible pressure flag set
- if (evflag && flexible_pressure_flag) {
+ if (evflag && flexible_pressure_flag) {
e1rvirial = eradius[j] * e1rforce;
ev_tally_eff(j,j,nlocal,newton_pair,0.0,e1rvirial);
}
- }
+ }
- // electron (i) - nucleus (j) Coul interaction
+ // electron (i) - nucleus (j) Coul interaction
- else if (abs(spin[i]) == 1 && spin[j] == 0) {
+ else if (abs(spin[i]) == 1 && spin[j] == 0) {
e1rforce = 0.0;
ElecNucElec(q[j],rc,eradius[i],&ecoul,&fpair,&e1rforce);
- e1rforce = spline * qqrd2e * e1rforce;
- erforce[i] += e1rforce;
-
+ e1rforce = spline * qqrd2e * e1rforce;
+ erforce[i] += e1rforce;
+
// Radial electron virial, iff flexible pressure flag set
- if (evflag && flexible_pressure_flag) {
+ if (evflag && flexible_pressure_flag) {
e1rvirial = eradius[i] * e1rforce;
ev_tally_eff(i,i,nlocal,newton_pair,0.0,e1rvirial);
}
- }
+ }
// electron (i) - electron (j) interactions
@@ -342,7 +342,7 @@ void PairEffCut::compute(int eflag, int vflag)
epauli *= hhmss2e;
s_fpair *= hhmss2e;
- // only update virial for i electron
+ // only update virial for i electron
e2rforce = spline * (qqrd2e * e2rforce + hhmss2e * s_e2rforce);
erforce[i] += e2rforce;
@@ -373,7 +373,7 @@ void PairEffCut::compute(int eflag, int vflag)
&e1rforce,&e2rforce);
ElecElecElec(rc,eradius[i],eradius[j],&ecoul,&fpair,
&e1rforce,&e2rforce);
-
+
PauliElecElec(0,rc,eradius[i],eradius[j],&epauli,
&s_fpair,&s_e1rforce,&s_e2rforce);
PauliElecElec(1,rc,eradius[i],eradius[j],&epauli,
@@ -473,7 +473,7 @@ void PairEffCut::compute(int eflag, int vflag)
else if (spin[i] == 3 && abs(spin[j]) == 3) {
double qxq = q[i]*q[j];
- ElecCoreCore(qxq,rc,eradius[i],eradius[j],&ecoul,&fpair);
+ ElecCoreCore(qxq,rc,eradius[i],eradius[j],&ecoul,&fpair);
}
// Apply Coulomb conversion factor for all cases
@@ -506,41 +506,41 @@ void PairEffCut::compute(int eflag, int vflag)
if (eflag_global) {
if (newton_pair) {
pvector[1] += spline * epauli;
- pvector[2] += spline * ecoul;
+ pvector[2] += spline * ecoul;
}
else {
halfpauli = 0.5 * spline * epauli;
halfcoul = 0.5 * spline * ecoul;
if (i < nlocal) {
pvector[1] += halfpauli;
- pvector[2] += halfcoul;
+ pvector[2] += halfcoul;
}
if (j < nlocal) {
pvector[1] += halfpauli;
- pvector[2] += halfcoul;
+ pvector[2] += halfcoul;
}
}
}
}
}
-
+
// limit electron stifness (size) for periodic systems, to max=half-box-size
if (abs(spin[i]) == 1 && limit_size_flag) {
- double half_box_length=0, dr, kfactor=hhmss2e*1.0;
+ double half_box_length=0, dr, kfactor=hhmss2e*1.0;
e1rforce = errestrain = 0.0;
if (domain->xperiodic == 1 || domain->yperiodic == 1 ||
- domain->zperiodic == 1) {
- delx = domain->boxhi[0]-domain->boxlo[0];
- dely = domain->boxhi[1]-domain->boxlo[1];
- delz = domain->boxhi[2]-domain->boxlo[2];
- half_box_length = 0.5 * MIN(delx, MIN(dely, delz));
- if (eradius[i] > half_box_length) {
- dr = eradius[i]-half_box_length;
- errestrain=0.5*kfactor*dr*dr;
- e1rforce=-kfactor*dr;
+ domain->zperiodic == 1) {
+ delx = domain->boxhi[0]-domain->boxlo[0];
+ dely = domain->boxhi[1]-domain->boxlo[1];
+ delz = domain->boxhi[2]-domain->boxlo[2];
+ half_box_length = 0.5 * MIN(delx, MIN(dely, delz));
+ if (eradius[i] > half_box_length) {
+ dr = eradius[i]-half_box_length;
+ errestrain=0.5*kfactor*dr*dr;
+ e1rforce=-kfactor*dr;
if (eflag_global) pvector[3] += errestrain;
erforce[i] += e1rforce;
@@ -560,7 +560,7 @@ void PairEffCut::compute(int eflag, int vflag)
virial_fdotr_compute();
if (flexible_pressure_flag) virial_eff_compute();
}
-}
+}
/* ----------------------------------------------------------------------
eff-specific contribution to global virial
@@ -574,7 +574,7 @@ void PairEffCut::virial_eff_compute()
int *spin = atom->spin;
// sum over force on all particles including ghosts
-
+
if (neighbor->includegroup == 0) {
int nall = atom->nlocal + atom->nghost;
for (int i = 0; i < nall; i++) {
@@ -585,10 +585,10 @@ void PairEffCut::virial_eff_compute()
virial[2] += e_virial;
}
}
-
+
// neighbor includegroup flag is set
// sum over force on initial nfirst particles and ghosts
-
+
} else {
int nall = atom->nfirst;
for (int i = 0; i < nall; i++) {
@@ -599,7 +599,7 @@ void PairEffCut::virial_eff_compute()
virial[2] += e_virial;
}
}
-
+
nall = atom->nlocal + atom->nghost;
for (int i = atom->nlocal; i < nall; i++) {
if (spin[i]) {
@@ -618,7 +618,7 @@ void PairEffCut::virial_eff_compute()
------------------------------------------------------------------------- */
void PairEffCut::ev_tally_eff(int i, int j, int nlocal, int newton_pair,
- double energy, double e_virial)
+ double energy, double e_virial)
{
double energyhalf;
double partial_evirial = e_virial/3.0;
@@ -634,7 +634,7 @@ void PairEffCut::ev_tally_eff(int i, int j, int nlocal, int newton_pair,
energyhalf = 0.5*energy;
if (i < nlocal)
eng_coul += energyhalf;
- if (j < nlocal)
+ if (j < nlocal)
eng_coul += energyhalf;
}
}
@@ -665,7 +665,7 @@ void PairEffCut::ev_tally_eff(int i, int j, int nlocal, int newton_pair,
vatom[i][2] += half_partial_evirial;
}
}
- if (spin[j]) {
+ if (spin[j]) {
if (newton_pair || j < nlocal) {
vatom[j][0] += half_partial_evirial;
vatom[j][1] += half_partial_evirial;
@@ -684,12 +684,12 @@ void PairEffCut::allocate()
{
allocated = 1;
int n = atom->ntypes;
-
+
memory->create(setflag,n+1,n+1,"pair:setflag");
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
-
+
memory->create(cutsq,n+1,n+1,"pair:cutsq");
memory->create(cut,n+1,n+1,"pair:cut");
}
@@ -700,7 +700,7 @@ void PairEffCut::allocate()
void PairEffCut::settings(int narg, char **arg)
{
- if (narg != 1 && narg != 3 && narg != 5 && narg != 7)
+ if (narg != 1 && narg != 3 && narg != 5 && narg != 7)
error->all(FLERR,"Illegal pair_style command");
// Defaults ECP parameters for Si
@@ -739,23 +739,23 @@ void PairEffCut::settings(int narg, char **arg)
PAULI_CORE_C = force->numeric(arg[6]);
}
}
-
+
// Need to introduce 2 new constants w/out changing update.cpp
- if (force->qqr2e==332.06371) { // i.e. Real units chosen
- h2e = 627.509; // hartree->kcal/mol
+ if (force->qqr2e==332.06371) { // i.e. Real units chosen
+ h2e = 627.509; // hartree->kcal/mol
hhmss2e = 175.72044219620075; // hartree->kcal/mol * (Bohr->Angstrom)^2
- } else if (force->qqr2e==1.0) { // electron units
+ } else if (force->qqr2e==1.0) { // electron units
h2e = 1.0;
hhmss2e = 1.0;
} else error->all(FLERR,"Check your units");
// reset cutoffs that have been explicitly set
-
+
if (allocated) {
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
- if (setflag[i][j]) cut[i][j] = cut_global;
+ if (setflag[i][j]) cut[i][j] = cut_global;
}
}
@@ -767,14 +767,14 @@ void PairEffCut::coeff(int narg, char **arg)
{
if (narg < 2 || narg > 3) error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
-
+
int ilo,ihi,jlo,jhi;
force->bounds(arg[0],atom->ntypes,ilo,ihi);
force->bounds(arg[1],atom->ntypes,jlo,jhi);
-
+
double cut_one = cut_global;
if (narg == 3) cut_one = atof(arg[2]);
-
+
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
@@ -783,7 +783,7 @@ void PairEffCut::coeff(int narg, char **arg)
count++;
}
}
-
+
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
@@ -795,25 +795,25 @@ void PairEffCut::init_style()
{
// error and warning checks
- if (!atom->q_flag || !atom->spin_flag ||
+ if (!atom->q_flag || !atom->spin_flag ||
!atom->eradius_flag || !atom->erforce_flag)
error->all(FLERR,"Pair eff/cut requires atom attributes "
- "q, spin, eradius, erforce");
+ "q, spin, eradius, erforce");
// add hook to minimizer for eradius and erforce
- if (update->whichflag == 2)
+ if (update->whichflag == 2)
int ignore = update->minimize->request(this,1,0.01);
// make sure to use the appropriate timestep when using real units
- if (update->whichflag == 1) {
+ if (update->whichflag == 1) {
if (force->qqr2e == 332.06371 && update->dt == 1.0)
error->all(FLERR,"You must lower the default real units timestep for pEFF ");
}
// need a half neigh list and optionally a granular history neigh list
-
+
int irequest = neighbor->request(this);
}
@@ -825,7 +825,7 @@ double PairEffCut::init_one(int i, int j)
{
if (setflag[i][j] == 0)
cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
-
+
return cut[i][j];
}
@@ -836,7 +836,7 @@ double PairEffCut::init_one(int i, int j)
void PairEffCut::write_restart(FILE *fp)
{
write_restart_settings(fp);
-
+
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
@@ -853,7 +853,7 @@ void PairEffCut::read_restart(FILE *fp)
{
read_restart_settings(fp);
allocate();
-
+
int i,j;
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
@@ -861,8 +861,8 @@ void PairEffCut::read_restart(FILE *fp)
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
- if (me == 0) fread(&cut[i][j],sizeof(double),1,fp);
- MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
+ if (me == 0) fread(&cut[i][j],sizeof(double),1,fp);
+ MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
@@ -947,12 +947,12 @@ void PairEffCut::min_x_set(int ignore)
int *spin = atom->spin;
int nlocal = atom->nlocal;
- for (int i = 0; i < nlocal; i++)
+ for (int i = 0; i < nlocal; i++)
if (spin[i]) eradius[i] = exp(min_eradius[i]);
}
/* ----------------------------------------------------------------------
- memory usage of local atom-based arrays
+ memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double PairEffCut::memory_usage()
diff --git a/src/USER-EFF/pair_eff_cut.h b/src/USER-EFF/pair_eff_cut.h
index 7519d7335d6b175b1994c89a1f77b86abf65a7d3..0253359883e9a2865be624fa3a7b1adb79b6e94e 100644
--- a/src/USER-EFF/pair_eff_cut.h
+++ b/src/USER-EFF/pair_eff_cut.h
@@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
-
+
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
-
+
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@@ -38,7 +38,7 @@ class PairEffCut : public Pair {
void read_restart(FILE *);
virtual void write_restart_settings(FILE *);
virtual void read_restart_settings(FILE *);
-
+
void min_xf_pointers(int, double **, double **);
void min_xf_get(int);
void min_x_set(int);
@@ -50,7 +50,7 @@ class PairEffCut : public Pair {
double **cut;
double PAULI_CORE_A, PAULI_CORE_B, PAULI_CORE_C;
double hhmss2e, h2e;
-
+
int nmax;
double *min_eradius,*min_erforce;
@@ -58,7 +58,7 @@ class PairEffCut : public Pair {
void virial_eff_compute();
void ev_tally_eff(int, int, int, int, double, double);
};
-
+
}
#endif
diff --git a/src/USER-EFF/pair_eff_inline.h b/src/USER-EFF/pair_eff_inline.h
index 6bd44fb7c29555450ec4528cbe21cc8e914f122a..30aad413b8924a10315c0f8f15429074743341e4 100644
--- a/src/USER-EFF/pair_eff_inline.h
+++ b/src/USER-EFF/pair_eff_inline.h
@@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
-
+
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
-
+
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@@ -194,7 +194,7 @@ inline double ipoly1(double x)
/* First derivative P'(x) in the range x < 2 */
int i;
double b0, b1, b2;
-
+
b1 = 0.0; b0 = 0.0; x *= 2;
for (i = DERF_TERMS; i >= 0; i--)
{
@@ -228,11 +228,11 @@ inline double ipoly01(double x)
inline double ierfoverx1(double x, double *df)
{
// Computes Erf(x)/x and its first derivative
-
+
double t, f;
double x2; // x squared
double exp_term, recip_x;
-
+
if (x < 2.0)
{
/* erf(x) = x * y(t) */
@@ -261,7 +261,7 @@ inline void KinElec(double radius, double *eke, double *frc)
{
*eke += 1.5 / (radius * radius);
*frc += 3.0 / (radius * radius * radius);
-}
+}
/* ---------------------------------------------------------------------- */
@@ -273,28 +273,28 @@ inline void ElecNucNuc(double q, double rc, double *ecoul, double *frc)
/* ---------------------------------------------------------------------- */
-inline void ElecNucElec(double q, double rc, double re1,
- double *ecoul, double *frc, double *fre1)
+inline void ElecNucElec(double q, double rc, double re1,
+ double *ecoul, double *frc, double *fre1)
{
double a, arc;
double coeff_a;
-
+
/* sqrt(2) */
coeff_a = 1.4142135623730951;
-
+
/* E = -Z/r Erf(a r / re) */
/* constants: sqrt(2), 2 / sqrt(pi) */
a = coeff_a / re1;
arc = a * rc;
-
+
/* Interaction between nuclear point charge and Gaussian electron */
double E, dEdr, dEdr1, f, df;
-
+
f = ierfoverx1(arc, &df);
dEdr = q * a * a * df;
dEdr1 = -q * (a / re1) * (f + arc * df);
E = -q * a * f;
-
+
*ecoul += E;
*frc += dEdr;
*fre1 += dEdr1;
@@ -302,40 +302,40 @@ inline void ElecNucElec(double q, double rc, double re1,
/* ---------------------------------------------------------------------- */
-inline void ElecElecElec(double rc, double re1, double re2,
- double *ecoul, double *frc, double *fre1,
- double *fre2)
+inline void ElecElecElec(double rc, double re1, double re2,
+ double *ecoul, double *frc, double *fre1,
+ double *fre2)
{
double a, arc, re, fre;
double coeff_a;
-
+
/* sqrt(2) */
coeff_a = 1.4142135623730951;
-
+
re = sqrt(re1 * re1 + re2 * re2);
-
+
double ratio;
ratio = rc / re;
-
+
/* constants: sqrt(2), 2 / sqrt(pi) */
a = coeff_a / re;
arc = a * rc;
-
+
/* V_elecelec = E * F */
/* where E = -Z/r Erf(a r / re) */
/* F = (1 - (b s + c s^2) exp(-d s^2)) */
/* and s = r / re */
-
+
double E, dEdr, dEdr1, dEdr2, f, df;
-
+
f = ierfoverx1(arc, &df);
dEdr = -a * a * df;
fre = a * (f + arc * df) / (re * re);
dEdr1 = fre * re1;
dEdr2 = fre * re2;
-
+
E = a * f;
-
+
*ecoul += E;
*frc += dEdr;
*fre1 += dEdr1;
@@ -355,7 +355,7 @@ inline void ElecCoreNuc(double q, double rc, double re1, double *ecoul, double *
arc = a * rc;
f = ierfoverx1(arc, &df);
- dEdr = -q * a * a * df;
+ dEdr = -q * a * a * df;
E = q * a * f;
*ecoul += E;
@@ -364,7 +364,7 @@ inline void ElecCoreNuc(double q, double rc, double re1, double *ecoul, double *
/* ---------------------------------------------------------------------- */
-inline void ElecCoreCore(double q, double rc, double re1, double re2,
+inline void ElecCoreCore(double q, double rc, double re1, double re2,
double *ecoul, double *frc)
{
double a, arc, re;
@@ -376,7 +376,7 @@ inline void ElecCoreCore(double q, double rc, double re1, double re2,
re = sqrt(re1 * re1 + re2 * re2);
a = coeff_a / re;
arc = a * rc;
-
+
f = ierfoverx1(arc, &df);
dEdr = -q * a * a * df;
fre = q * a * (f + arc * df) / (re * re);
@@ -388,7 +388,7 @@ inline void ElecCoreCore(double q, double rc, double re1, double re2,
/* ---------------------------------------------------------------------- */
-inline void ElecCoreElec(double q, double rc, double re1, double re2,
+inline void ElecCoreElec(double q, double rc, double re1, double re2,
double *ecoul, double *frc, double *fre2)
{
double a,arc, re;
@@ -401,7 +401,7 @@ inline void ElecCoreElec(double q, double rc, double re1, double re2,
/*
re1: core size
re2: electron size
- re3: size of the core, obtained from the electron density function rho(r) of core
+ re3: size of the core, obtained from the electron density function rho(r) of core
e.g. rho(r) = a1*exp(-((r)/b1)^2), a1 =157.9, b1 = 0.1441 -> re3 = 0.1441 for Si4+
*/
@@ -423,45 +423,45 @@ inline void ElecCoreElec(double q, double rc, double re1, double re2,
/* ---------------------------------------------------------------------- */
-inline void PauliElecElec(int samespin, double rc,
- double re1, double re2, double *epauli,
- double *frc, double *fre1, double *fre2)
+inline void PauliElecElec(int samespin, double rc,
+ double re1, double re2, double *epauli,
+ double *frc, double *fre1, double *fre2)
{
double ree, rem;
double S, t1, t2, tt;
double dSdr1, dSdr2, dSdr;
double dTdr1, dTdr2, dTdr;
double O, dOdS, ratio;
-
+
re1 *= PAULI_RE; re2 *= PAULI_RE; rc *= PAULI_RC;
ree = re1 * re1 + re2 * re2;
rem = re1 * re1 - re2 * re2;
-
- S = (2.82842712474619 / pow((re2 / re1 + re1 / re2), 1.5)) *
+
+ S = (2.82842712474619 / pow((re2 / re1 + re1 / re2), 1.5)) *
exp(-rc * rc / ree);
-
+
t1 = 1.5 * (1 / (re1 * re1) + 1 / (re2 * re2));
t2 = 2.0 * (3 * ree - 2 * rc * rc) / (ree * ree);
tt = t1 - t2;
-
+
dSdr1 = (-1.5 / re1) * (rem / ree) + 2 * re1 * rc * rc / (ree * ree);
dSdr2 = (1.5 / re2) * (rem / ree) + 2 * re2 * rc * rc / (ree * ree);
dSdr = -2 * rc / ree;
- dTdr1 = -3 / (re1 * re1 * re1) - 12 * re1 / (ree * ree) + 8 * re1 *
+ dTdr1 = -3 / (re1 * re1 * re1) - 12 * re1 / (ree * ree) + 8 * re1 *
(-2 * rc * rc + 3 * ree) / (ree * ree * ree);
- dTdr2 = -3 / (re2 * re2 * re2) - 12 * re2 / (ree * ree) + 8 * re2 *
+ dTdr2 = -3 / (re2 * re2 * re2) - 12 * re2 / (ree * ree) + 8 * re2 *
(-2 * rc * rc + 3 * ree) / (ree * ree * ree);
dTdr = 8 * rc / (ree * ree);
-
+
if (samespin == 1) {
O = S * S / (1.0 - S * S) + (1 - PAULI_RHO) * S * S / (1.0 + S * S);
- dOdS = 2 * S / ((1.0 - S * S) * (1.0 - S * S)) +
+ dOdS = 2 * S / ((1.0 - S * S) * (1.0 - S * S)) +
(1 - PAULI_RHO) * 2 * S / ((1.0 + S * S) * (1.0 + S * S));
} else {
O = -PAULI_RHO * S * S / (1.0 + S * S);
dOdS = -PAULI_RHO * 2 * S / ((1.0 + S * S) * (1.0 + S * S));
}
-
+
ratio = tt * dOdS * S;
*fre1 -= PAULI_RE * (dTdr1 * O + ratio * dSdr1);
*fre2 -= PAULI_RE * (dTdr2 * O + ratio * dSdr2);
@@ -471,16 +471,16 @@ inline void PauliElecElec(int samespin, double rc,
/* ---------------------------------------------------------------------- */
-inline void PauliCoreElec(double rc, double re2, double *epauli, double *frc,
+inline void PauliCoreElec(double rc, double re2, double *epauli, double *frc,
double *fre2, double PAULI_CORE_A, double PAULI_CORE_B, double PAULI_CORE_C)
{
double E, dEdrc, dEdre2, rcsq, ssq;
-
+
rcsq = rc * rc;
ssq = re2 * re2;
E = PAULI_CORE_A * exp((-PAULI_CORE_B * rcsq) / (ssq + PAULI_CORE_C));
-
+
dEdrc = -2 * PAULI_CORE_A * PAULI_CORE_B * rc * exp(-PAULI_CORE_B * rcsq /
(ssq + PAULI_CORE_C)) / (ssq + PAULI_CORE_C);
@@ -494,8 +494,8 @@ inline void PauliCoreElec(double rc, double re2, double *epauli, double *frc,
/* ---------------------------------------------------------------------- */
-inline void RForce(double dx, double dy, double dz,
- double rc, double force, double *fx, double *fy, double *fz)
+inline void RForce(double dx, double dy, double dz,
+ double rc, double force, double *fx, double *fy, double *fz)
{
force /= rc;
*fx = force * dx;
@@ -505,25 +505,25 @@ inline void RForce(double dx, double dy, double dz,
/* ---------------------------------------------------------------------- */
-inline void SmallRForce(double dx, double dy, double dz,
- double rc, double force,
- double *fx, double *fy, double *fz)
+inline void SmallRForce(double dx, double dy, double dz,
+ double rc, double force,
+ double *fx, double *fy, double *fz)
{
/* Handles case where rc is small to avoid division by zero */
-
+
if (rc > 0.000001){
force /= rc;
*fx = force * dx; *fy = force * dy; *fz = force * dz;
} else {
- if (dx != 0) *fx = force / sqrt(1 + (dy * dy + dz * dz) / (dx * dx));
+ if (dx != 0) *fx = force / sqrt(1 + (dy * dy + dz * dz) / (dx * dx));
else *fx = 0.0;
- if (dy != 0) *fy = force / sqrt(1 + (dx * dx + dz * dz) / (dy * dy));
+ if (dy != 0) *fy = force / sqrt(1 + (dx * dx + dz * dz) / (dy * dy));
else *fy = 0.0;
- if (dz != 0) *fz = force / sqrt(1 + (dx * dx + dy * dy) / (dz * dz));
+ if (dz != 0) *fz = force / sqrt(1 + (dx * dx + dy * dy) / (dz * dz));
else *fz = 0.0;
- // if (dx < 0) *fx = -*fx;
- // if (dy < 0) *fy = -*fy;
- // if (dz < 0) *fz = -*fz;
+ // if (dx < 0) *fx = -*fx;
+ // if (dy < 0) *fy = -*fy;
+ // if (dz < 0) *fz = -*fz;
}
}
@@ -533,7 +533,7 @@ inline double cutoff(double x)
{
/* cubic: return x * x * (2.0 * x - 3.0) + 1.0; */
/* quintic: return -6 * pow(x, 5) + 15 * pow(x, 4) - 10 * pow(x, 3) + 1; */
-
+
/* Seventh order spline */
// return 20 * pow(x, 7) - 70 * pow(x, 6) + 84 * pow(x, 5) - 35 * pow(x, 4) + 1;
return (((20 * x - 70) * x + 84) * x - 35) * x * x * x * x + 1;
@@ -545,7 +545,7 @@ inline double dcutoff(double x)
{
/* cubic: return (6.0 * x * x - 6.0 * x); */
/* quintic: return -30 * pow(x, 4) + 60 * pow(x, 3) - 30 * pow(x, 2); */
-
+
/* Seventh order spline */
// return 140 * pow(x, 6) - 420 * pow(x, 5) + 420 * pow(x, 4) - 140 * pow(x, 3);
return (((140 * x - 420) * x + 420) * x - 140) * x * x * x;
diff --git a/src/USER-EWALDN/ewald_n.cpp b/src/USER-EWALDN/ewald_n.cpp
index b6291cb5dec513cc1debb39a922e024ef9f48d4f..8dd262a6e15f5810157dc48049a21514bdea13a3 100644
--- a/src/USER-EWALDN/ewald_n.cpp
+++ b/src/USER-EWALDN/ewald_n.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -36,9 +36,9 @@ using namespace MathConst;
#define SMALL 0.00001
-#define KSPACE_ILLEGAL "Illegal kspace_style ewald/n command"
-#define KSPACE_ORDER "Unsupported order in kspace_style ewald/n for"
-#define KSPACE_MIX "Unsupported mixing rule in kspace_style ewald/n for"
+#define KSPACE_ILLEGAL "Illegal kspace_style ewald/n command"
+#define KSPACE_ORDER "Unsupported order in kspace_style ewald/n for"
+#define KSPACE_MIX "Unsupported mixing rule in kspace_style ewald/n for"
enum{GEOMETRIC,ARITHMETIC,SIXTHPOWER}; // same as in pair.h
@@ -83,18 +83,18 @@ void EwaldN::init()
nbox = -1;
bytes = 0.0;
- if (!comm->me) { // output message
+ if (!comm->me) { // output message
if (screen) fprintf(screen,"EwaldN initialization ...\n");
if (logfile) fprintf(logfile,"EwaldN initialization ...\n");
}
- if (domain->dimension == 2) // check for errors
+ if (domain->dimension == 2) // check for errors
error->all(FLERR,"Cannot use EwaldN with 2d simulation");
if (slabflag == 0 && domain->nonperiodic > 0)
error->all(FLERR,"Cannot use nonperiodic boundaries with EwaldN");
if (slabflag == 1) {
- if (domain->xperiodic != 1 || domain->yperiodic != 1 ||
- domain->boundary[2][0] != 1 || domain->boundary[2][1] != 1)
+ if (domain->xperiodic != 1 || domain->yperiodic != 1 ||
+ domain->boundary[2][0] != 1 || domain->boundary[2][1] != 1)
error->all(FLERR,"Incorrect boundaries with slab EwaldN");
}
@@ -102,44 +102,44 @@ void EwaldN::init()
//mumurd2e = force->mumurd2e;
//dielectric = force->dielectric;
mumurd2e = dielectric = 1.0;
-
+
int tmp;
Pair *pair = force->pair;
int *ptr = pair ? (int *) pair->extract("ewald_order",tmp) : NULL;
double *cutoff = pair ? (double *) pair->extract("cut_coul",tmp) : NULL;
- if (!(ptr||cutoff))
+ if (!(ptr||cutoff))
error->all(FLERR,"KSpace style is incompatible with Pair style");
int ewald_order = ptr ? *((int *) ptr) : 1<<1;
int ewald_mix = ptr ? *((int *) pair->extract("ewald_mix",tmp)) : GEOMETRIC;
memset(function, 0, EWALD_NFUNCS*sizeof(int));
- for (int i=0; i<=EWALD_NORDER; ++i) // transcribe order
- if (ewald_order&(1<<i)) { // from pair_style
+ for (int i=0; i<=EWALD_NORDER; ++i) // transcribe order
+ if (ewald_order&(1<<i)) { // from pair_style
int n[] = EWALD_NSUMS, k = 0;
char str[128];
switch (i) {
- case 1:
- k = 0; break;
- case 3:
- k = 3; break;
- case 6:
- if (ewald_mix==GEOMETRIC) { k = 1; break; }
- else if (ewald_mix==ARITHMETIC) { k = 2; break; }
- sprintf(str, "%s pair_style %s", KSPACE_MIX, force->pair_style);
- error->all(FLERR,str);
- default:
- sprintf(str, "%s pair_style %s", KSPACE_ORDER, force->pair_style);
- error->all(FLERR,str);
+ case 1:
+ k = 0; break;
+ case 3:
+ k = 3; break;
+ case 6:
+ if (ewald_mix==GEOMETRIC) { k = 1; break; }
+ else if (ewald_mix==ARITHMETIC) { k = 2; break; }
+ sprintf(str, "%s pair_style %s", KSPACE_MIX, force->pair_style);
+ error->all(FLERR,str);
+ default:
+ sprintf(str, "%s pair_style %s", KSPACE_ORDER, force->pair_style);
+ error->all(FLERR,str);
}
nfunctions += function[k] = 1;
nsums += n[k];
}
-
-
+
+
g_ewald = 0;
pair->init(); // so B is defined
init_coeffs();
- init_coeff_sums();
-
+ init_coeff_sums();
+
double qsum, qsqsum, bsbsum;
qsum = qsqsum = bsbsum = 0.0;
if (function[0]) {
@@ -148,12 +148,12 @@ void EwaldN::init()
}
if (function[1]) {
bsbsum = sum[1].x2;
- }
+ }
if (function[2]) {
bsbsum = sum[2].x2;
- }
-
-
+ }
+
+
if (qsqsum == 0.0 && bsbsum == 0.0)
error->all(FLERR,"Cannot use Ewald/n solver on system with no charge or LJ particles");
if (fabs(qsum) > SMALL && comm->me == 0) {
@@ -161,18 +161,18 @@ void EwaldN::init()
sprintf(str,"System is not charge neutral, net charge = %g",qsum);
error->warning(FLERR,str);
}
-
+
//set accuracy (force units) from accuracy_relative or accuracy_absolute
-
+
if (accuracy_absolute >= 0.0) accuracy = accuracy_absolute;
else accuracy = accuracy_relative * two_charge_force;
-
+
// setup K-space resolution
-
+
q2 = qsqsum * force->qqrd2e / force->dielectric;
b2 = bsbsum; //Are these units right?
bigint natoms = atom->natoms;
-
+
if (function[0]) { //Coulombic
g_ewald = accuracy*sqrt(natoms*(*cutoff)*shape_det(domain->h)) / (2.0*q2);
if (g_ewald >= 1.0)
@@ -182,49 +182,49 @@ void EwaldN::init()
else if (function[1] || function[2]) { //Only LJ
double *cutoffLJ = pair ? (double *) pair->extract("cut_LJ",tmp) : NULL;
-
+
//Try Newton Solver
-
+
//Use old method to get guess
g_ewald = (1.35 - 0.15*log(accuracy))/ *cutoffLJ;
-
+
double g_ewald_new = NewtonSolve(g_ewald,(*cutoffLJ),natoms,shape_det(domain->h),b2);
-
+
if (g_ewald_new > 0.0) g_ewald = g_ewald_new;
- else error->warning(FLERR,"Ewald/n Newton solver failed, using old method to estimate g_ewald");
-
+ else error->warning(FLERR,"Ewald/n Newton solver failed, using old method to estimate g_ewald");
+
if (g_ewald >= 1.0)
error->all(FLERR,"KSpace accuracy too large to estimate G vector");
}
-
- if (!comm->me) { // output results
+
+ if (!comm->me) { // output results
if (screen) fprintf(screen, " G vector = %g\n", g_ewald);
if (logfile) fprintf(logfile, " G vector = %g\n", g_ewald);
- }
-
-
+ }
+
+
deallocate_peratom();
peratom_allocate_flag = 0;
}
/* ----------------------------------------------------------------------
- adjust EwaldN coeffs, called initially and whenever volume has changed
+ adjust EwaldN coeffs, called initially and whenever volume has changed
------------------------------------------------------------------------- */
void EwaldN::setup()
{
- volume = shape_det(domain->h)*slab_volfactor; // cell volume
- memcpy(unit, domain->h_inv, sizeof(shape)); // wave vector units
+ volume = shape_det(domain->h)*slab_volfactor; // cell volume
+ memcpy(unit, domain->h_inv, sizeof(shape)); // wave vector units
shape_scalar_mult(unit, 2.0*MY_PI);
unit[2] /= slab_volfactor;
-
+
//int nbox_old = nbox, nkvec_old = nkvec;
if (accuracy>=1) {
nbox = 0;
- error->all(FLERR,"KSpace accuracy too low");
+ error->all(FLERR,"KSpace accuracy too low");
}
-
+
bigint natoms = atom->natoms;
double err;
int kxmax = 1;
@@ -244,7 +244,7 @@ void EwaldN::setup()
while (err > accuracy) {
kzmax++;
err = rms(kzmax,domain->h[2]*slab_volfactor,natoms,q2,b2);
- }
+ }
nbox = MAX(kxmax,kymax);
nbox = MAX(nbox,kzmax);
double gsqxmx = unit[0]*unit[0]*kxmax*kxmax;
@@ -253,20 +253,20 @@ void EwaldN::setup()
gsqmx = MAX(gsqxmx,gsqymx);
gsqmx = MAX(gsqmx,gsqzmx);
gsqmx *= 1.00001;
-
+
reallocate();
- coefficients(); // compute coeffs
+ coefficients(); // compute coeffs
init_coeffs();
init_coeff_sums();
init_self();
- if (!(first_output||comm->me)) { // output on first
+ if (!(first_output||comm->me)) { // output on first
first_output = 1;
if (screen) fprintf(screen,
- " vectors: nbox = %d, nkvec = %d\n", nbox, nkvec);
+ " vectors: nbox = %d, nkvec = %d\n", nbox, nkvec);
if (logfile) fprintf(logfile,
- " vectors: nbox = %d, nkvec = %d\n", nbox, nkvec);
- }
+ " vectors: nbox = %d, nkvec = %d\n", nbox, nkvec);
+ }
}
/* ----------------------------------------------------------------------
@@ -274,80 +274,80 @@ void EwaldN::setup()
------------------------------------------------------------------------- */
double EwaldN::rms(int km, double prd, bigint natoms, double q2, double b2)
-{
+{
double value = 0.0;
-
- //Coulombic
-
+
+ //Coulombic
+
double g2 = g_ewald*g_ewald;
-
- value += 2.0*q2*g_ewald/prd *
- sqrt(1.0/(MY_PI*km*natoms)) *
+
+ value += 2.0*q2*g_ewald/prd *
+ sqrt(1.0/(MY_PI*km*natoms)) *
exp(-MY_PI*MY_PI*km*km/(g2*prd*prd));
-
- //Lennard-Jones
-
+
+ //Lennard-Jones
+
double g7 = g2*g2*g2*g_ewald;
-
- value += 4.0*b2*g7/3.0 *
- sqrt(1.0/(MY_PI*natoms)) *
+
+ value += 4.0*b2*g7/3.0 *
+ sqrt(1.0/(MY_PI*natoms)) *
(exp(-MY_PI*MY_PI*km*km/(g2*prd*prd)) *
(MY_PI*km/(g_ewald*prd) + 1));
-
+
return value;
}
-void EwaldN::reallocate() // allocate memory
+void EwaldN::reallocate() // allocate memory
{
int ix, iy, iz;
int nkvec_max = nkvec;
vector h;
- nkvec = 0; // determine size(kvec)
+ nkvec = 0; // determine size(kvec)
int *kflag = new int[(nbox+1)*(2*nbox+1)*(2*nbox+1)];
int *flag = kflag;
for (ix=0; ix<=nbox; ++ix)
for (iy=-nbox; iy<=nbox; ++iy)
for (iz=-nbox; iz<=nbox; ++iz)
- if (!(ix||iy||iz)) *(flag++) = 0;
- else if ((!ix)&&(iy<0)) *(flag++) = 0;
- else if ((!(ix||iy))&&(iz<0)) *(flag++) = 0; // use symmetry
- else {
- h[0] = unit[0]*ix;
- h[1] = unit[5]*ix+unit[1]*iy;
- h[2] = unit[4]*ix+unit[3]*iy+unit[2]*iz;
- if ((*(flag++) = h[0]*h[0]+h[1]*h[1]+h[2]*h[2]<=gsqmx)) ++nkvec;
- }
-
+ if (!(ix||iy||iz)) *(flag++) = 0;
+ else if ((!ix)&&(iy<0)) *(flag++) = 0;
+ else if ((!(ix||iy))&&(iz<0)) *(flag++) = 0; // use symmetry
+ else {
+ h[0] = unit[0]*ix;
+ h[1] = unit[5]*ix+unit[1]*iy;
+ h[2] = unit[4]*ix+unit[3]*iy+unit[2]*iz;
+ if ((*(flag++) = h[0]*h[0]+h[1]*h[1]+h[2]*h[2]<=gsqmx)) ++nkvec;
+ }
+
if (nkvec>nkvec_max) {
- deallocate(); // free memory
- hvec = new hvector[nkvec]; // hvec
+ deallocate(); // free memory
+ hvec = new hvector[nkvec]; // hvec
bytes += (nkvec-nkvec_max)*sizeof(hvector);
- kvec = new kvector[nkvec]; // kvec
+ kvec = new kvector[nkvec]; // kvec
bytes += (nkvec-nkvec_max)*sizeof(kvector);
- kenergy = new double[nkvec*nfunctions]; // kenergy
+ kenergy = new double[nkvec*nfunctions]; // kenergy
bytes += (nkvec-nkvec_max)*nfunctions*sizeof(double);
- kvirial = new double[6*nkvec*nfunctions]; // kvirial
+ kvirial = new double[6*nkvec*nfunctions]; // kvirial
bytes += 6*(nkvec-nkvec_max)*nfunctions*sizeof(double);
- cek_local = new complex[nkvec*nsums]; // cek_local
+ cek_local = new complex[nkvec*nsums]; // cek_local
bytes += (nkvec-nkvec_max)*nsums*sizeof(complex);
- cek_global = new complex[nkvec*nsums]; // cek_global
+ cek_global = new complex[nkvec*nsums]; // cek_global
bytes += (nkvec-nkvec_max)*nsums*sizeof(complex);
nkvec_max = nkvec;
}
- flag = kflag; // create index and
- kvector *k = kvec; // wave vectors
+ flag = kflag; // create index and
+ kvector *k = kvec; // wave vectors
hvector *hi = hvec;
for (ix=0; ix<=nbox; ++ix)
for (iy=-nbox; iy<=nbox; ++iy)
for (iz=-nbox; iz<=nbox; ++iz)
- if (*(flag++)) {
- hi->x = unit[0]*ix;
- hi->y = unit[5]*ix+unit[1]*iy;
- (hi++)->z = unit[4]*ix+unit[3]*iy+unit[2]*iz;
- k->x = ix+nbox; k->y = iy+nbox; (k++)->z = iz+nbox; }
+ if (*(flag++)) {
+ hi->x = unit[0]*ix;
+ hi->y = unit[5]*ix+unit[1]*iy;
+ (hi++)->z = unit[4]*ix+unit[3]*iy+unit[2]*iz;
+ k->x = ix+nbox; k->y = iy+nbox; (k++)->z = iz+nbox; }
delete [] kflag;
}
@@ -361,7 +361,7 @@ void EwaldN::reallocate_atoms()
allocate_peratom();
nmax = atom->nmax;
}
-
+
if ((nevec = atom->nmax*(2*nbox+1))<=nevec_max) return;
delete [] ekr_local;
ekr_local = new cvector[nevec];
@@ -370,7 +370,7 @@ void EwaldN::reallocate_atoms()
}
-void EwaldN::allocate_peratom()
+void EwaldN::allocate_peratom()
{
memory->create(energy_self_peratom,
atom->nmax,EWALD_NFUNCS,"ewald/n:energy_self_peratom");
@@ -379,25 +379,25 @@ void EwaldN::allocate_peratom()
}
-void EwaldN::deallocate_peratom() // free memory
+void EwaldN::deallocate_peratom() // free memory
{
memory->destroy(energy_self_peratom);
memory->destroy(virial_self_peratom);
}
-void EwaldN::deallocate() // free memory
+void EwaldN::deallocate() // free memory
{
- delete [] hvec; hvec = NULL;
- delete [] kvec; kvec = NULL;
- delete [] kenergy; kenergy = NULL;
- delete [] kvirial; kvirial = NULL;
- delete [] cek_local; cek_local = NULL;
- delete [] cek_global; cek_global = NULL;
+ delete [] hvec; hvec = NULL;
+ delete [] kvec; kvec = NULL;
+ delete [] kenergy; kenergy = NULL;
+ delete [] kvirial; kvirial = NULL;
+ delete [] cek_local; cek_local = NULL;
+ delete [] cek_global; cek_global = NULL;
}
-void EwaldN::coefficients() // set up pre-factors
+void EwaldN::coefficients() // set up pre-factors
{
vector h;
hvector *hi = hvec, *nh;
@@ -407,35 +407,35 @@ void EwaldN::coefficients() // set up pre-factors
int func0 = function[0], func12 = function[1]||function[2],
func3 = function[3];
- for (nh = (hi = hvec)+nkvec; hi<nh; ++hi) { // wave vectors
+ for (nh = (hi = hvec)+nkvec; hi<nh; ++hi) { // wave vectors
memcpy(h, hi, sizeof(vector));
expb2 = exp(-(b2 = (h2 = vec_dot(h, h))*eta2));
- if (func0) { // qi*qj/r coeffs
+ if (func0) { // qi*qj/r coeffs
*(ke++) = c1 = expb2/h2;
*(kv++) = c1-(c2 = 2.0*c1*(1.0+b2)/h2)*h[0]*h[0];
- *(kv++) = c1-c2*h[1]*h[1]; // lammps convention
- *(kv++) = c1-c2*h[2]*h[2]; // instead of voigt
- *(kv++) = -c2*h[1]*h[0];
+ *(kv++) = c1-c2*h[1]*h[1]; // lammps convention
+ *(kv++) = c1-c2*h[2]*h[2]; // instead of voigt
+ *(kv++) = -c2*h[1]*h[0];
*(kv++) = -c2*h[2]*h[0];
*(kv++) = -c2*h[2]*h[1];
}
- if (func12) { // -Bij/r^6 coeffs
- b1 = sqrt(b2); // minus sign folded
- h1 = sqrt(h2); // into constants
+ if (func12) { // -Bij/r^6 coeffs
+ b1 = sqrt(b2); // minus sign folded
+ h1 = sqrt(h2); // into constants
*(ke++) = c1 = -h1*h2*((c2=sqrt(MY_PI)*erfc(b1))+(0.5/b2-1.0)*expb2/b1);
*(kv++) = c1-(c2 = 3.0*h1*(c2-expb2/b1))*h[0]*h[0];
- *(kv++) = c1-c2*h[1]*h[1]; // lammps convention
- *(kv++) = c1-c2*h[2]*h[2]; // instead of voigt
+ *(kv++) = c1-c2*h[1]*h[1]; // lammps convention
+ *(kv++) = c1-c2*h[2]*h[2]; // instead of voigt
*(kv++) = -c2*h[1]*h[0];
*(kv++) = -c2*h[2]*h[0];
*(kv++) = -c2*h[2]*h[1];
}
- if (func3) { // dipole coeffs
+ if (func3) { // dipole coeffs
*(ke++) = c1 = expb2/h2;
*(kv++) = c1-(c2 = 2.0*c1*(1.0+b2)/h2)*h[0]*h[0];
- *(kv++) = c1-c2*h[1]*h[1]; // lammps convention
- *(kv++) = c1-c2*h[2]*h[2]; // instead of voigt
- *(kv++) = -c2*h[1]*h[0];
+ *(kv++) = c1-c2*h[1]*h[1]; // lammps convention
+ *(kv++) = c1-c2*h[2]*h[2]; // instead of voigt
+ *(kv++) = -c2*h[1]*h[0];
*(kv++) = -c2*h[2]*h[0];
*(kv++) = -c2*h[2]*h[1];
}
@@ -443,19 +443,19 @@ void EwaldN::coefficients() // set up pre-factors
}
-void EwaldN::init_coeffs() // local pair coeffs
+void EwaldN::init_coeffs() // local pair coeffs
{
int tmp;
int n = atom->ntypes;
- if (function[1]) { // geometric 1/r^6
+ if (function[1]) { // geometric 1/r^6
double **b = (double **) force->pair->extract("B",tmp);
delete [] B;
B = new double[n+1];
bytes += (n+1)*sizeof(double);
for (int i=0; i<=n; ++i) B[i] = sqrt(fabs(b[i][i]));
}
- if (function[2]) { // arithmetic 1/r^6
+ if (function[2]) { // arithmetic 1/r^6
double **epsilon = (double **) force->pair->extract("epsilon",tmp);
double **sigma = (double **) force->pair->extract("sigma",tmp);
double eps_i, sigma_i, sigma_n, *bi = B = new double[7*n+7];
@@ -464,47 +464,47 @@ void EwaldN::init_coeffs() // local pair coeffs
if (!(epsilon&&sigma))
error->all(
- FLERR,"epsilon or sigma reference not set by pair style in ewald/n");
+ FLERR,"epsilon or sigma reference not set by pair style in ewald/n");
for (int i=0; i<=n; ++i) {
eps_i = sqrt(epsilon[i][i]);
sigma_i = sigma[i][i];
sigma_n = 1.0;
for (int j=0; j<7; ++j) {
- *(bi++) = sigma_n*eps_i*c[j]; sigma_n *= sigma_i;
+ *(bi++) = sigma_n*eps_i*c[j]; sigma_n *= sigma_i;
}
}
}
}
-void EwaldN::init_coeff_sums() // sums based on atoms
+void EwaldN::init_coeff_sums() // sums based on atoms
{
- if (sums) return; // calculated only once
+ if (sums) return; // calculated only once
sums = 1;
Sum sum_local[EWALD_MAX_NSUMS];
memset(sum_local, 0, EWALD_MAX_NSUMS*sizeof(Sum));
- if (function[0]) { // 1/r
+ if (function[0]) { // 1/r
double *q = atom->q, *qn = q+atom->nlocal;
for (double *i=q; i<qn; ++i) {
sum_local[0].x += i[0]; sum_local[0].x2 += i[0]*i[0]; }
}
- if (function[1]) { // geometric 1/r^6
+ if (function[1]) { // geometric 1/r^6
int *type = atom->type, *ntype = type+atom->nlocal;
for (int *i=type; i<ntype; ++i) {
sum_local[1].x += B[i[0]]; sum_local[1].x2 += B[i[0]]*B[i[0]]; }
}
- if (function[2]) { // arithmetic 1/r^6
+ if (function[2]) { // arithmetic 1/r^6
double *bi;
int *type = atom->type, *ntype = type+atom->nlocal;
for (int *i=type; i<ntype; ++i) {
bi = B+7*i[0];
sum_local[2].x2 += bi[0]*bi[6];
- for (int k=2; k<9; ++k) sum_local[k].x += *(bi++);
+ for (int k=2; k<9; ++k) sum_local[k].x += *(bi++);
}
}
- if (function[3]&&atom->mu) { // dipole
+ if (function[3]&&atom->mu) { // dipole
double *mu = atom->mu[0], *nmu = mu+4*atom->nlocal;
for (double *i = mu; i < nmu; i += 4)
sum_local[9].x2 += i[3]*i[3];
@@ -518,24 +518,24 @@ void EwaldN::init_self()
double g1 = g_ewald, g2 = g1*g1, g3 = g1*g2;
const double qscale = force->qqrd2e * scale;
- memset(energy_self, 0, EWALD_NFUNCS*sizeof(double)); // self energy
+ memset(energy_self, 0, EWALD_NFUNCS*sizeof(double)); // self energy
memset(virial_self, 0, EWALD_NFUNCS*sizeof(double));
- if (function[0]) { // 1/r
+ if (function[0]) { // 1/r
virial_self[0] = -0.5*MY_PI*qscale/(g2*volume)*sum[0].x*sum[0].x;
energy_self[0] = sum[0].x2*qscale*g1/sqrt(MY_PI)-virial_self[0];
}
- if (function[1]) { // geometric 1/r^6
+ if (function[1]) { // geometric 1/r^6
virial_self[1] = MY_PI*sqrt(MY_PI)*g3/(6.0*volume)*sum[1].x*sum[1].x;
energy_self[1] = -sum[1].x2*g3*g3/12.0+virial_self[1];
}
- if (function[2]) { // arithmetic 1/r^6
+ if (function[2]) { // arithmetic 1/r^6
virial_self[2] = MY_PI*sqrt(MY_PI)*g3/(48.0*volume)*(sum[2].x*sum[8].x+
- sum[3].x*sum[7].x+sum[4].x*sum[6].x+0.5*sum[5].x*sum[5].x);
+ sum[3].x*sum[7].x+sum[4].x*sum[6].x+0.5*sum[5].x*sum[5].x);
energy_self[2] = -sum[2].x2*g3*g3/3.0+virial_self[2];
}
- if (function[3]) { // dipole
- virial_self[3] = 0; // in surface
+ if (function[3]) { // dipole
+ virial_self[3] = 0; // in surface
energy_self[3] = sum[9].x2*mumurd2e*2.0*g3/3.0/sqrt(MY_PI)-virial_self[3];
}
}
@@ -543,18 +543,18 @@ void EwaldN::init_self()
void EwaldN::init_self_peratom()
{
- if (!(vflag_atom || eflag_atom)) return;
+ if (!(vflag_atom || eflag_atom)) return;
double g1 = g_ewald, g2 = g1*g1, g3 = g1*g2;
const double qscale = force->qqrd2e * scale;
double *energy = energy_self_peratom[0];
double *virial = virial_self_peratom[0];
int nlocal = atom->nlocal;
-
+
memset(energy, 0, EWALD_NFUNCS*nlocal*sizeof(double));
memset(virial, 0, EWALD_NFUNCS*nlocal*sizeof(double));
- if (function[0]) { // 1/r
+ if (function[0]) { // 1/r
double *ei = energy;
double *vi = virial;
double ce = qscale*g1/sqrt(MY_PI);
@@ -566,7 +566,7 @@ void EwaldN::init_self_peratom()
*ei = ce*q*q-vi[0];
}
}
- if (function[1]) { // geometric 1/r^6
+ if (function[1]) { // geometric 1/r^6
double *ei = energy+1;
double *vi = virial+1;
double ce = -g3*g3/12.0;
@@ -578,7 +578,7 @@ void EwaldN::init_self_peratom()
*ei = ce*b*b+vi[0];
}
}
- if (function[2]) { // arithmetic 1/r^6
+ if (function[2]) { // arithmetic 1/r^6
double *bi;
double *ei = energy+2;
double *vi = virial+2;
@@ -586,30 +586,30 @@ void EwaldN::init_self_peratom()
double cv = 0.5*MY_PI*sqrt(MY_PI)*g3/(48.0*volume);
int *typei = atom->type, *typen = typei + atom->nlocal;
for (; typei < typen; typei++, vi += EWALD_NFUNCS, ei += EWALD_NFUNCS) {
- bi = B+7*typei[0]+7;
+ bi = B+7*typei[0]+7;
for (int k=2; k<9; ++k) *vi += cv*sum[k].x*(--bi)[0];
- /* PJV 20120225:
+ /* PJV 20120225:
should this be this instead? above implies an inverse dependence
- seems to be the above way in original; i recall having tested
- arithmetic mixing in the conception phase, but an extra test would
- be prudent (pattern repeats in multiple functions below)
+ seems to be the above way in original; i recall having tested
+ arithmetic mixing in the conception phase, but an extra test would
+ be prudent (pattern repeats in multiple functions below)
- bi = B+7*typei[0];
+ bi = B+7*typei[0];
for (int k=2; k<9; ++k) *vi += cv*sum[k].x*(bi++)[0];
-
+
*/
*ei = ce*bi[0]*bi[6]+vi[0];
}
}
- if (function[3]&&atom->mu) { // dipole
+ if (function[3]&&atom->mu) { // dipole
double *ei = energy+3;
double *vi = virial+3;
double *imu = atom->mu[0], *nmu = imu+4*atom->nlocal;
double ce = mumurd2e*2.0*g3/3.0/sqrt(MY_PI);
for (; imu < nmu; imu += 4, vi += EWALD_NFUNCS, ei += EWALD_NFUNCS) {
- *vi = 0; // in surface
+ *vi = 0; // in surface
*ei = ce*imu[3]*imu[3]-vi[0];
}
}
@@ -617,25 +617,25 @@ void EwaldN::init_self_peratom()
/* ----------------------------------------------------------------------
- compute the EwaldN long-range force, energy, virial
+ compute the EwaldN long-range force, energy, virial
------------------------------------------------------------------------- */
void EwaldN::compute(int eflag, int vflag)
{
if (!nbox) return;
-
+
// set energy/virial flags
// invoke allocate_peratom() if needed for first time
-
+
if (eflag || vflag) ev_setup(eflag,vflag);
- else evflag = eflag_global = vflag_global = eflag_atom = vflag_atom = 0;
-
+ else evflag = eflag_global = vflag_global = eflag_atom = vflag_atom = 0;
+
if (!peratom_allocate_flag && (eflag_atom || vflag_atom)) {
allocate_peratom();
peratom_allocate_flag = 1;
nmax = atom->nmax;
}
-
+
reallocate_atoms();
init_self_peratom();
compute_ek();
@@ -665,22 +665,22 @@ void EwaldN::compute_ek()
int func[EWALD_NFUNCS];
memcpy(func, function, EWALD_NFUNCS*sizeof(int));
- memset(cek_local, 0, n*sizeof(complex)); // reset sums
+ memset(cek_local, 0, n*sizeof(complex)); // reset sums
while (x<xn) {
zx = (zy = (zz = z+nbox)+1)-2;
- C_SET(zz->x, 1, 0); C_SET(zz->y, 1, 0); C_SET(zz->z, 1, 0); // z[0]
- if (tri) { // triclinic z[1]
+ C_SET(zz->x, 1, 0); C_SET(zz->y, 1, 0); C_SET(zz->z, 1, 0); // z[0]
+ if (tri) { // triclinic z[1]
C_ANGLE(z1.x, unit[0]*x[0]+unit[5]*x[1]+unit[4]*x[2]);
C_ANGLE(z1.y, unit[1]*x[1]+unit[3]*x[2]);
C_ANGLE(z1.z, x[2]*unit[2]); x += 3;
}
- else { // orthogonal z[1]
+ else { // orthogonal z[1]
C_ANGLE(z1.x, *(x++)*unit[0]);
C_ANGLE(z1.y, *(x++)*unit[1]);
C_ANGLE(z1.z, *(x++)*unit[2]);
}
- for (; zz<zn; --zx, ++zy, ++zz) { // set up z[k]=e^(ik.r)
- C_RMULT(zy->x, zz->x, z1.x); // 3D k-vector
+ for (; zz<zn; --zx, ++zy, ++zz) { // set up z[k]=e^(ik.r)
+ C_RMULT(zy->x, zz->x, z1.x); // 3D k-vector
C_RMULT(zy->y, zz->y, z1.y); C_CONJ(zx->y, zy->y);
C_RMULT(zy->z, zz->z, z1.z); C_CONJ(zx->z, zy->z);
}
@@ -689,30 +689,30 @@ void EwaldN::compute_ek()
if (func[0]) qi = *(q++);
if (func[1]) bi = B[*type];
if (func[2]) memcpy(ci, B+7*type[0], 7*sizeof(double));
- if (func[3]) {
+ if (func[3]) {
memcpy(mui, mu, sizeof(vector));
vec_scalar_mult(mui, mu[3]);
mu += 4;
h = hvec;
}
- for (k=kvec; k<nk; ++k) { // compute rho(k)
- if (ky!=k->y) { // based on order in
- if (kx!=k->x) cx = z[kx = k->x].x; // reallocate
- C_RMULT(zxy, z[ky = k->y].y, cx);
+ for (k=kvec; k<nk; ++k) { // compute rho(k)
+ if (ky!=k->y) { // based on order in
+ if (kx!=k->x) cx = z[kx = k->x].x; // reallocate
+ C_RMULT(zxy, z[ky = k->y].y, cx);
}
C_RMULT(zxyz, z[k->z].z, zxy);
if (func[0]) {
- cek->re += zxyz.re*qi; (cek++)->im += zxyz.im*qi;
+ cek->re += zxyz.re*qi; (cek++)->im += zxyz.im*qi;
}
if (func[1]) {
- cek->re += zxyz.re*bi; (cek++)->im += zxyz.im*bi;
+ cek->re += zxyz.re*bi; (cek++)->im += zxyz.im*bi;
}
if (func[2]) for (i=0; i<7; ++i) {
- cek->re += zxyz.re*ci[i]; (cek++)->im += zxyz.im*ci[i];
+ cek->re += zxyz.re*ci[i]; (cek++)->im += zxyz.im*ci[i];
}
if (func[3]) {
- register double muk = mui[0]*h->x+mui[1]*h->y+mui[2]*h->z; ++h;
- cek->re += zxyz.re*muk; (cek++)->im += zxyz.im*muk;
+ register double muk = mui[0]*h->x+mui[1]*h->y+mui[2]*h->z; ++h;
+ cek->re += zxyz.re*muk; (cek++)->im += zxyz.im*muk;
}
}
ekr = (cvector *) ((char *) memcpy(ekr, z, lbytes)+lbytes);
@@ -743,63 +743,63 @@ void EwaldN::compute_force()
if (atom->torque) t = atom->torque[0];
memcpy(func, function, EWALD_NFUNCS*sizeof(int));
- memset(sum, 0, EWALD_MAX_NSUMS*sizeof(vector)); // fj = -dE/dr =
- for (; f<fn; f+=3) { // -i*qj*fac*
- k = kvec; // Sum[conj(d)-d]
- kx = ky = -1; // d = k*conj(ekj)*ek
+ memset(sum, 0, EWALD_MAX_NSUMS*sizeof(vector)); // fj = -dE/dr =
+ for (; f<fn; f+=3) { // -i*qj*fac*
+ k = kvec; // Sum[conj(d)-d]
+ kx = ky = -1; // d = k*conj(ekj)*ek
ke = kenergy;
cek = cek_global;
memset(sum, 0, EWALD_MAX_NSUMS*sizeof(vector));
- if (func[3]) {
+ if (func[3]) {
register double di = mu[3] * c[3];
mui[0] = di*(mu++)[0]; mui[1] = di*(mu++)[0]; mui[2] = di*(mu++)[0];
mu++;
}
for (nh = (h = hvec)+nkvec; h<nh; ++h, ++k) {
- if (ky!=k->y) { // based on order in
- if (kx!=k->x) zx = z[kx = k->x].x; // reallocate
- C_RMULT(zxy, z[ky = k->y].y, zx);
+ if (ky!=k->y) { // based on order in
+ if (kx!=k->x) zx = z[kx = k->x].x; // reallocate
+ C_RMULT(zxy, z[ky = k->y].y, zx);
}
C_CRMULT(zc, z[k->z].z, zxy);
- if (func[0]) { // 1/r
- register double im = *(ke++)*(zc.im*cek->re+cek->im*zc.re); ++cek;
- sum[0][0] += h->x*im; sum[0][1] += h->y*im; sum[0][2] += h->z*im;
+ if (func[0]) { // 1/r
+ register double im = *(ke++)*(zc.im*cek->re+cek->im*zc.re); ++cek;
+ sum[0][0] += h->x*im; sum[0][1] += h->y*im; sum[0][2] += h->z*im;
}
- if (func[1]) { // geometric 1/r^6
- register double im = *(ke++)*(zc.im*cek->re+cek->im*zc.re); ++cek;
- sum[1][0] += h->x*im; sum[1][1] += h->y*im; sum[1][2] += h->z*im;
+ if (func[1]) { // geometric 1/r^6
+ register double im = *(ke++)*(zc.im*cek->re+cek->im*zc.re); ++cek;
+ sum[1][0] += h->x*im; sum[1][1] += h->y*im; sum[1][2] += h->z*im;
}
- if (func[2]) { // arithmetic 1/r^6
- register double im, c = *(ke++);
- for (i=2; i<9; ++i) {
- im = c*(zc.im*cek->re+cek->im*zc.re); ++cek;
- sum[i][0] += h->x*im; sum[i][1] += h->y*im; sum[i][2] += h->z*im;
- }
+ if (func[2]) { // arithmetic 1/r^6
+ register double im, c = *(ke++);
+ for (i=2; i<9; ++i) {
+ im = c*(zc.im*cek->re+cek->im*zc.re); ++cek;
+ sum[i][0] += h->x*im; sum[i][1] += h->y*im; sum[i][2] += h->z*im;
+ }
}
- if (func[3]) { // dipole
- register double im = *(ke++)*(zc.im*cek->re+
- cek->im*zc.re)*(mui[0]*h->x+mui[1]*h->y+mui[2]*h->z); ++cek;
- sum[9][0] += h->x*im; sum[9][1] += h->y*im; sum[9][2] += h->z*im;
+ if (func[3]) { // dipole
+ register double im = *(ke++)*(zc.im*cek->re+
+ cek->im*zc.re)*(mui[0]*h->x+mui[1]*h->y+mui[2]*h->z); ++cek;
+ sum[9][0] += h->x*im; sum[9][1] += h->y*im; sum[9][2] += h->z*im;
}
}
- if (func[0]) { // 1/r
+ if (func[0]) { // 1/r
register double qi = *(q++)*c[0];
f[0] -= sum[0][0]*qi; f[1] -= sum[0][1]*qi; f[2] -= sum[0][2]*qi;
}
- if (func[1]) { // geometric 1/r^6
+ if (func[1]) { // geometric 1/r^6
register double bi = B[*type]*c[1];
f[0] -= sum[1][0]*bi; f[1] -= sum[1][1]*bi; f[2] -= sum[1][2]*bi;
}
- if (func[2]) { // arithmetic 1/r^6
+ if (func[2]) { // arithmetic 1/r^6
register double *bi = B+7*type[0]+7;
for (i=2; i<9; ++i) {
- register double c2 = (--bi)[0]*c[2];
- f[0] -= sum[i][0]*c2; f[1] -= sum[i][1]*c2; f[2] -= sum[i][2]*c2;
+ register double c2 = (--bi)[0]*c[2];
+ f[0] -= sum[i][0]*c2; f[1] -= sum[i][1]*c2; f[2] -= sum[i][2]*c2;
}
}
- if (func[3]) { // dipole
+ if (func[3]) { // dipole
f[0] -= sum[9][0]; f[1] -= sum[9][1]; f[2] -= sum[9][2];
- *(t++) -= mui[1]*sum[0][2]+mui[2]*sum[0][1]-mui[0]*kt; // torque
+ *(t++) -= mui[1]*sum[0][2]+mui[2]*sum[0][1]-mui[0]*kt; // torque
*(t++) -= mui[2]*sum[0][0]+mui[0]*sum[0][2]-mui[1]*kt;
*(t++) -= mui[0]*sum[0][1]+mui[1]*sum[0][0]-mui[2]*kt;
}
@@ -832,7 +832,7 @@ void EwaldN::compute_surface()
energy_self[3] -= virial_self[3];
if (!(vflag_atom || eflag_atom)) return;
-
+
double *ei = energy_self_peratom[0]+3;
double *vi = virial_self_peratom[0]+3;
double cv = 2.0*mumurd2e*MY_PI/(2.0*dielectric+1)/volume;
@@ -849,7 +849,7 @@ void EwaldN::compute_energy()
{
energy = 0.0;
if (!eflag_global) return;
-
+
complex *cek = cek_global;
double *ke = kenergy;
const double qscale = force->qqrd2e * scale;
@@ -860,23 +860,23 @@ void EwaldN::compute_energy()
int func[EWALD_NFUNCS];
memcpy(func, function, EWALD_NFUNCS*sizeof(int));
- memset(sum, 0, EWALD_NFUNCS*sizeof(double)); // reset sums
- for (int k=0; k<nkvec; ++k) { // sum over k vectors
- if (func[0]) { // 1/r
+ memset(sum, 0, EWALD_NFUNCS*sizeof(double)); // reset sums
+ for (int k=0; k<nkvec; ++k) { // sum over k vectors
+ if (func[0]) { // 1/r
sum[0] += *(ke++)*(cek->re*cek->re+cek->im*cek->im); ++cek; }
- if (func[1]) { // geometric 1/r^6
+ if (func[1]) { // geometric 1/r^6
sum[1] += *(ke++)*(cek->re*cek->re+cek->im*cek->im); ++cek; }
- if (func[2]) { // arithmetic 1/r^6
+ if (func[2]) { // arithmetic 1/r^6
register double r =
- (cek[0].re*cek[6].re+cek[0].im*cek[6].im)+
- (cek[1].re*cek[5].re+cek[1].im*cek[5].im)+
- (cek[2].re*cek[4].re+cek[2].im*cek[4].im)+
- 0.5*(cek[3].re*cek[3].re+cek[3].im*cek[3].im); cek += 7;
+ (cek[0].re*cek[6].re+cek[0].im*cek[6].im)+
+ (cek[1].re*cek[5].re+cek[1].im*cek[5].im)+
+ (cek[2].re*cek[4].re+cek[2].im*cek[4].im)+
+ 0.5*(cek[3].re*cek[3].re+cek[3].im*cek[3].im); cek += 7;
sum[2] += *(ke++)*r;
}
- if (func[3]) { // dipole
+ if (func[3]) { // dipole
sum[3] += *(ke++)*(cek->re*cek->re+cek->im*cek->im); ++cek; }
- }
+ }
for (int k=0; k<EWALD_NFUNCS; ++k) energy += c[k]*sum[k]-energy_self[k];
if (slabflag) compute_slabcorr();
}
@@ -885,7 +885,7 @@ void EwaldN::compute_energy()
void EwaldN::compute_energy_peratom()
{
if (!eflag_atom) return;
-
+
kvector *k;
hvector *h, *nh;
cvector *z = ekr_local;
@@ -902,63 +902,63 @@ void EwaldN::compute_energy_peratom()
2.0*MY_PI*sqrt(MY_PI)/(192.0*volume), 4.0*MY_PI*mumurd2e/volume};
int i, kx, ky, lbytes = (2*nbox+1)*sizeof(cvector), *type = atom->type;
int func[EWALD_NFUNCS];
-
+
memcpy(func, function, EWALD_NFUNCS*sizeof(int));
for (int j = 0; j < atom->nlocal; j++, ++eatomj) {
- k = kvec;
- kx = ky = -1;
+ k = kvec;
+ kx = ky = -1;
ke = kenergy;
cek = cek_global;
memset(sum, 0, EWALD_MAX_NSUMS*sizeof(double));
- if (func[3]) {
+ if (func[3]) {
register double di = mu[3] * c[3];
mui[0] = di*(mu++)[0]; mui[1] = di*(mu++)[0]; mui[2] = di*(mu++)[0];
mu++;
}
for (nh = (h = hvec)+nkvec; h<nh; ++h, ++k) {
- if (ky!=k->y) { // based on order in
- if (kx!=k->x) zx = z[kx = k->x].x; // reallocate
- C_RMULT(zxy, z[ky = k->y].y, zx);
+ if (ky!=k->y) { // based on order in
+ if (kx!=k->x) zx = z[kx = k->x].x; // reallocate
+ C_RMULT(zxy, z[ky = k->y].y, zx);
}
C_CRMULT(zc, z[k->z].z, zxy);
- if (func[0]) { // 1/r
- sum[0] += *(ke++)*(cek->re*zc.re - cek->im*zc.im); ++cek; }
- if (func[1]) { // geometric 1/r^6
- sum[1] += *(ke++)*(cek->re*zc.re - cek->im*zc.im); ++cek; }
- if (func[2]) { // arithmetic 1/r^6
- register double im, c = *(ke++);
- for (i=2; i<9; ++i) {
- im = c*(cek->re*zc.re - cek->im*zc.im); ++cek;
- sum[i] += im;
- }
+ if (func[0]) { // 1/r
+ sum[0] += *(ke++)*(cek->re*zc.re - cek->im*zc.im); ++cek; }
+ if (func[1]) { // geometric 1/r^6
+ sum[1] += *(ke++)*(cek->re*zc.re - cek->im*zc.im); ++cek; }
+ if (func[2]) { // arithmetic 1/r^6
+ register double im, c = *(ke++);
+ for (i=2; i<9; ++i) {
+ im = c*(cek->re*zc.re - cek->im*zc.im); ++cek;
+ sum[i] += im;
+ }
}
- if (func[3]) { // dipole
- sum[9] += *(ke++)*(cek->re*zc.re +
- cek->im*zc.im)*(mui[0]*h->x+mui[1]*h->y+mui[2]*h->z); ++cek;
+ if (func[3]) { // dipole
+ sum[9] += *(ke++)*(cek->re*zc.re +
+ cek->im*zc.im)*(mui[0]*h->x+mui[1]*h->y+mui[2]*h->z); ++cek;
}
}
-
- if (func[0]) { // 1/r
+
+ if (func[0]) { // 1/r
register double qj = *(q++)*c[0];
*eatomj += sum[0]*qj - energy_self_peratom[j][0];
}
- if (func[1]) { // geometric 1/r^6
+ if (func[1]) { // geometric 1/r^6
register double bj = B[*type]*c[1];
*eatomj += sum[1]*bj - energy_self_peratom[j][1];
}
- if (func[2]) { // arithmetic 1/r^6
+ if (func[2]) { // arithmetic 1/r^6
register double *bj = B+7*type[0]+7;
for (i=2; i<9; ++i) {
- register double c2 = (--bj)[0]*c[2];
- *eatomj += 0.5*sum[i]*c2;
- }
- *eatomj -= energy_self_peratom[j][2];
+ register double c2 = (--bj)[0]*c[2];
+ *eatomj += 0.5*sum[i]*c2;
+ }
+ *eatomj -= energy_self_peratom[j][2];
}
- if (func[3]) { // dipole
+ if (func[3]) { // dipole
*eatomj += sum[9] - energy_self_peratom[j][3];
}
z = (cvector *) ((char *) z+lbytes);
- ++type;
+ ++type;
}
}
@@ -981,23 +981,23 @@ void EwaldN::compute_virial()
memcpy(func, function, EWALD_NFUNCS*sizeof(int));
memset(sum, 0, EWALD_NFUNCS*sizeof(shape));
- for (int k=0; k<nkvec; ++k) { // sum over k vectors
- if (func[0]) { // 1/r
+ for (int k=0; k<nkvec; ++k) { // sum over k vectors
+ if (func[0]) { // 1/r
register double r = cek->re*cek->re+cek->im*cek->im; ++cek;
sum[0][0] += *(kv++)*r; sum[0][1] += *(kv++)*r; sum[0][2] += *(kv++)*r;
sum[0][3] += *(kv++)*r; sum[0][4] += *(kv++)*r; sum[0][5] += *(kv++)*r;
}
- if (func[1]) { // geometric 1/r^6
+ if (func[1]) { // geometric 1/r^6
register double r = cek->re*cek->re+cek->im*cek->im; ++cek;
sum[1][0] += *(kv++)*r; sum[1][1] += *(kv++)*r; sum[1][2] += *(kv++)*r;
sum[1][3] += *(kv++)*r; sum[1][4] += *(kv++)*r; sum[1][5] += *(kv++)*r;
}
- if (func[2]) { // arithmetic 1/r^6
+ if (func[2]) { // arithmetic 1/r^6
register double r =
- (cek[0].re*cek[6].re+cek[0].im*cek[6].im)+
- (cek[1].re*cek[5].re+cek[1].im*cek[5].im)+
- (cek[2].re*cek[4].re+cek[2].im*cek[4].im)+
- 0.5*(cek[3].re*cek[3].re+cek[3].im*cek[3].im); cek += 7;
+ (cek[0].re*cek[6].re+cek[0].im*cek[6].im)+
+ (cek[1].re*cek[5].re+cek[1].im*cek[5].im)+
+ (cek[2].re*cek[4].re+cek[2].im*cek[4].im)+
+ 0.5*(cek[3].re*cek[3].re+cek[3].im*cek[3].im); cek += 7;
sum[2][0] += *(kv++)*r; sum[2][1] += *(kv++)*r; sum[2][2] += *(kv++)*r;
sum[2][3] += *(kv++)*r; sum[2][4] += *(kv++)*r; sum[2][5] += *(kv++)*r;
}
@@ -1019,7 +1019,7 @@ void EwaldN::compute_virial()
void EwaldN::compute_virial_peratom()
{
if (!vflag_atom) return;
-
+
kvector *k;
hvector *h, *nh;
cvector *z = ekr_local;
@@ -1038,93 +1038,93 @@ void EwaldN::compute_virial_peratom()
memcpy(func, function, EWALD_NFUNCS*sizeof(int));
int i, kx, ky, lbytes = (2*nbox+1)*sizeof(cvector), *type = atom->type;
- for (int j = 0; j < atom->nlocal; j++, vatomj += 6) {
- k = kvec;
- kx = ky = -1;
+ for (int j = 0; j < atom->nlocal; j++, vatomj += 6) {
+ k = kvec;
+ kx = ky = -1;
kv = kvirial;
cek = cek_global;
memset(sum, 0, EWALD_MAX_NSUMS*sizeof(shape));
- if (func[3]) {
+ if (func[3]) {
register double di = mu[3] * c[3];
mui[0] = di*(mu++)[0]; mui[1] = di*(mu++)[1]; mui[2] = di*(mu++)[2];
mu++;
}
for (nh = (h = hvec)+nkvec; h<nh; ++h, ++k) {
- if (ky!=k->y) { // based on order in
- if (kx!=k->x) zx = z[kx = k->x].x; // reallocate
- C_RMULT(zxy, z[ky = k->y].y, zx);
+ if (ky!=k->y) { // based on order in
+ if (kx!=k->x) zx = z[kx = k->x].x; // reallocate
+ C_RMULT(zxy, z[ky = k->y].y, zx);
}
C_CRMULT(zc, z[k->z].z, zxy);
- if (func[0]) { // 1/r
- register double r = cek->re*zc.re - cek->im*zc.im; ++cek;
- sum[0][0] += *(kv++)*r;
- sum[0][1] += *(kv++)*r;
- sum[0][2] += *(kv++)*r;
- sum[0][3] += *(kv++)*r;
- sum[0][4] += *(kv++)*r;
- sum[0][5] += *(kv++)*r;
+ if (func[0]) { // 1/r
+ register double r = cek->re*zc.re - cek->im*zc.im; ++cek;
+ sum[0][0] += *(kv++)*r;
+ sum[0][1] += *(kv++)*r;
+ sum[0][2] += *(kv++)*r;
+ sum[0][3] += *(kv++)*r;
+ sum[0][4] += *(kv++)*r;
+ sum[0][5] += *(kv++)*r;
}
- if (func[1]) { // geometric 1/r^6
- register double r = cek->re*zc.re - cek->im*zc.im; ++cek;
- sum[1][0] += *(kv++)*r;
- sum[1][1] += *(kv++)*r;
- sum[1][2] += *(kv++)*r;
- sum[1][3] += *(kv++)*r;
- sum[1][4] += *(kv++)*r;
- sum[1][5] += *(kv++)*r;
+ if (func[1]) { // geometric 1/r^6
+ register double r = cek->re*zc.re - cek->im*zc.im; ++cek;
+ sum[1][0] += *(kv++)*r;
+ sum[1][1] += *(kv++)*r;
+ sum[1][2] += *(kv++)*r;
+ sum[1][3] += *(kv++)*r;
+ sum[1][4] += *(kv++)*r;
+ sum[1][5] += *(kv++)*r;
}
- if (func[2]) { // arithmetic 1/r^6
- register double r;
- for (i=2; i<9; ++i) {
- r = cek->re*zc.re - cek->im*zc.im; ++cek;
- sum[i][0] += *(kv++)*r;
- sum[i][1] += *(kv++)*r;
- sum[i][2] += *(kv++)*r;
- sum[i][3] += *(kv++)*r;
- sum[i][4] += *(kv++)*r;
- sum[i][5] += *(kv++)*r;
+ if (func[2]) { // arithmetic 1/r^6
+ register double r;
+ for (i=2; i<9; ++i) {
+ r = cek->re*zc.re - cek->im*zc.im; ++cek;
+ sum[i][0] += *(kv++)*r;
+ sum[i][1] += *(kv++)*r;
+ sum[i][2] += *(kv++)*r;
+ sum[i][3] += *(kv++)*r;
+ sum[i][4] += *(kv++)*r;
+ sum[i][5] += *(kv++)*r;
kv -= 6;
- }
+ }
kv += 6;
}
- if (func[3]) { // dipole
- register double
- r = (cek->re*zc.re - cek->im*zc.im)
- *(mui[0]*h->x+mui[1]*h->y+mui[2]*h->z); ++cek;
- sum[9][0] += *(kv++)*r;
- sum[9][1] += *(kv++)*r;
- sum[9][2] += *(kv++)*r;
- sum[9][3] += *(kv++)*r;
- sum[9][4] += *(kv++)*r;
- sum[9][5] += *(kv++)*r;
+ if (func[3]) { // dipole
+ register double
+ r = (cek->re*zc.re - cek->im*zc.im)
+ *(mui[0]*h->x+mui[1]*h->y+mui[2]*h->z); ++cek;
+ sum[9][0] += *(kv++)*r;
+ sum[9][1] += *(kv++)*r;
+ sum[9][2] += *(kv++)*r;
+ sum[9][3] += *(kv++)*r;
+ sum[9][4] += *(kv++)*r;
+ sum[9][5] += *(kv++)*r;
}
}
-
- if (func[0]) { // 1/r
+
+ if (func[0]) { // 1/r
register double qi = *(q++)*c[0];
for (int n = 0; n < 6; n++) vatomj[n] += sum[0][n]*qi;
}
- if (func[1]) { // geometric 1/r^6
+ if (func[1]) { // geometric 1/r^6
register double bi = B[*type]*c[1];
for (int n = 0; n < 6; n++) vatomj[n] += sum[1][n]*bi;
}
- if (func[2]) { // arithmetic 1/r^6
+ if (func[2]) { // arithmetic 1/r^6
register double *bj = B+7*type[0]+7;
for (i=2; i<9; ++i) {
- register double c2 = (--bj)[0]*c[2];
- for (int n = 0; n < 6; n++) vatomj[n] += 0.5*sum[i][n]*c2;
+ register double c2 = (--bj)[0]*c[2];
+ for (int n = 0; n < 6; n++) vatomj[n] += 0.5*sum[i][n]*c2;
}
}
- if (func[3]) { // dipole
+ if (func[3]) { // dipole
for (int n = 0; n < 6; n++) vatomj[n] += sum[9][n];
}
for (int k=0; k<EWALD_NFUNCS; ++k) {
if (func[k]) {
- for (int n = 0; n < 3; n++) vatomj[n] -= virial_self_peratom[j][k];
+ for (int n = 0; n < 3; n++) vatomj[n] -= virial_self_peratom[j][k];
}
}
-
+
z = (cvector *) ((char *) z+lbytes);
++type;
}
@@ -1133,46 +1133,46 @@ void EwaldN::compute_virial_peratom()
/* ----------------------------------------------------------------------
Slab-geometry correction term to dampen inter-slab interactions between
- periodically repeating slabs. Yields good approximation to 2-D EwaldN if
- adequate empty space is left between repeating slabs (J. Chem. Phys.
- 111, 3155). Slabs defined here to be parallel to the xy plane.
+ periodically repeating slabs. Yields good approximation to 2-D EwaldN if
+ adequate empty space is left between repeating slabs (J. Chem. Phys.
+ 111, 3155). Slabs defined here to be parallel to the xy plane.
------------------------------------------------------------------------- */
void EwaldN::compute_slabcorr()
{
// compute local contribution to global dipole moment
-
+
double *q = atom->q;
double **x = atom->x;
int nlocal = atom->nlocal;
-
+
double dipole = 0.0;
for (int i = 0; i < nlocal; i++) dipole += q[i]*x[i][2];
-
+
// sum local contributions to get global dipole moment
-
+
double dipole_all;
MPI_Allreduce(&dipole,&dipole_all,1,MPI_DOUBLE,MPI_SUM,world);
-
+
// compute corrections
-
+
const double e_slabcorr = 2.0*MY_PI*dipole_all*dipole_all/volume;
const double qscale = force->qqrd2e * scale;
-
+
if (eflag_global) energy += qscale * e_slabcorr;
-
+
// per-atom energy
-
+
if (eflag_atom) {
- double efact = 2.0*MY_PI*dipole_all/volume;
+ double efact = 2.0*MY_PI*dipole_all/volume;
for (int i = 0; i < nlocal; i++) eatom[i] += qscale * q[i]*x[i][2]*efact;
}
-
+
// add on force corrections
-
- double ffact = -4.0*MY_PI*dipole_all/volume;
+
+ double ffact = -4.0*MY_PI*dipole_all/volume;
double **f = atom->f;
-
+
for (int i = 0; i < nlocal; i++) f[i][2] += qscale * q[i]*ffact;
}
@@ -1187,11 +1187,11 @@ double EwaldN::NewtonSolve(double x, double Rc, bigint natoms, double vol, doubl
maxit = 10000; //Maximum number of iterations
tol = 0.00001; //Convergence tolerance
-
+
//Begin algorithm
-
+
for (int i = 0; i < maxit; i++) {
- dx = f(x,Rc,natoms,vol,b2) / derivf(x,Rc,natoms,vol,b2);
+ dx = f(x,Rc,natoms,vol,b2) / derivf(x,Rc,natoms,vol,b2);
x = x - dx; //Update x
if (fabs(dx) < tol) return x;
}
@@ -1213,10 +1213,9 @@ double EwaldN::f(double x, double Rc, bigint natoms, double vol, double b2)
/* ----------------------------------------------------------------------
Calculate numerical derivative f'(x)
------------------------------------------------------------------------- */
-
+
double EwaldN::derivf(double x, double Rc, bigint natoms, double vol, double b2)
-{
+{
double h = 0.000001; //Derivative step-size
return (f(x + h,Rc,natoms,vol,b2) - f(x,Rc,natoms,vol,b2)) / h;
-}
-
+}
diff --git a/src/USER-EWALDN/ewald_n.h b/src/USER-EWALDN/ewald_n.h
index 874704877099e90deccf871cbe6d704fbdc1edf7..4bc4bc1d83bb3ea0ad2bf5ed16b6e882bb9cc388 100644
--- a/src/USER-EWALDN/ewald_n.h
+++ b/src/USER-EWALDN/ewald_n.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -25,10 +25,10 @@ KSpaceStyle(ewald/n,EwaldN)
namespace LAMMPS_NS {
-#define EWALD_NORDER 6
-#define EWALD_NFUNCS 4
-#define EWALD_MAX_NSUMS 10
-#define EWALD_NSUMS {1, 1, 7, 1}
+#define EWALD_NORDER 6
+#define EWALD_NFUNCS 4
+#define EWALD_MAX_NSUMS 10
+#define EWALD_NSUMS {1, 1, 7, 1}
typedef struct cvector { complex x, y, z; } cvector;
typedef struct hvector { double x, y, z; } hvector;
@@ -64,7 +64,7 @@ class EwaldN : public KSpace {
double mumurd2e, dielectric, *B, volume;
struct Sum { double x, x2; } sum[EWALD_MAX_NSUMS];
complex *cek_local, *cek_global;
-
+
double rms(int, double, bigint, double, double);
void reallocate();
void allocate_peratom();
diff --git a/src/USER-EWALDN/math_complex.h b/src/USER-EWALDN/math_complex.h
index 1540af012f1bdc8b0022ed4c1a036e4154b907cb..4f53b452881e37182907072584921b062f7533e2 100644
--- a/src/USER-EWALDN/math_complex.h
+++ b/src/USER-EWALDN/math_complex.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -18,7 +18,7 @@
#ifndef LMP_MATH_COMPLEX_H
#define LMP_MATH_COMPLEX_H
-#define COMPLEX_NULL {0, 0}
+#define COMPLEX_NULL {0, 0}
namespace LAMMPS_NS {
@@ -70,4 +70,3 @@ typedef struct complex {
memcpy(&d, &x, sizeof(complex)); }
#endif
-
diff --git a/src/USER-EWALDN/math_vector.h b/src/USER-EWALDN/math_vector.h
index b7473b5d89ff9e4601c8c6bcb06400ad377ba924..da65e069bd2b57e32cf2e5175770d452a8f9f03b 100644
--- a/src/USER-EWALDN/math_vector.h
+++ b/src/USER-EWALDN/math_vector.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -21,80 +21,80 @@
#include "math.h"
#include "string.h"
-#define VECTOR_NULL {0, 0, 0}
-#define SHAPE_NULL {0, 0, 0, 0, 0, 0}
-#define FORM_NULL {0, 0, 0, 0, 0, 0}
-#define MATRIX_NULL {VECTOR_NULL, VECTOR_NULL, VECTOR_NULL}
-#define VECTOR4_NULL {0, 0, 0, 0}
-#define QUATERNION_NULL {0, 0, 0, 0}
-#define FORM4_NULL {0, 0, 0, 0, 0, 0, 0, 0, 0, 0}
+#define VECTOR_NULL {0, 0, 0}
+#define SHAPE_NULL {0, 0, 0, 0, 0, 0}
+#define FORM_NULL {0, 0, 0, 0, 0, 0}
+#define MATRIX_NULL {VECTOR_NULL, VECTOR_NULL, VECTOR_NULL}
+#define VECTOR4_NULL {0, 0, 0, 0}
+#define QUATERNION_NULL {0, 0, 0, 0}
+#define FORM4_NULL {0, 0, 0, 0, 0, 0, 0, 0, 0, 0}
#define FZERO 1e-15
#define fzero(x) (((x)>-FZERO) && ((x)<FZERO))
namespace LAMMPS_NS {
-typedef double vector[3]; // 0:x 1:y 2:z
+typedef double vector[3]; // 0:x 1:y 2:z
typedef int lvector[3];
-typedef double shape[6]; // 0:xx 1:yy 2:zz 3:zy 4:zx 5:yx
-typedef int lshape[6]; // xy=0 xz=0 yz=0;
-typedef double form[6]; // 0:xx 1:yy 2:zz 3:zy 4:zx 5:yx
-typedef int lform[6]; // xy=yx xz=zx yz=zy;
-typedef vector matrix[3]; // 00:xx 11:yy 22:zz 21:zy 20:zx 10:yx
+typedef double shape[6]; // 0:xx 1:yy 2:zz 3:zy 4:zx 5:yx
+typedef int lshape[6]; // xy=0 xz=0 yz=0;
+typedef double form[6]; // 0:xx 1:yy 2:zz 3:zy 4:zx 5:yx
+typedef int lform[6]; // xy=yx xz=zx yz=zy;
+typedef vector matrix[3]; // 00:xx 11:yy 22:zz 21:zy 20:zx 10:yx
typedef lvector lmatrix[3];
-typedef double vector4[4]; // 4D vector
-typedef double form4[10]; // 0:00 1:11 2:22 3:33 4:32
- // 5:31 6:30 7:21 8:20 9:10
- // 01=10 02=20 03=30 etc
-typedef double quaternion[4]; // quaternion
+typedef double vector4[4]; // 4D vector
+typedef double form4[10]; // 0:00 1:11 2:22 3:33 4:32
+ // 5:31 6:30 7:21 8:20 9:10
+ // 01=10 02=20 03=30 etc
+typedef double quaternion[4]; // quaternion
// vector operators
-inline double vec_dot(vector &a, vector &b) { // a.b
+inline double vec_dot(vector &a, vector &b) { // a.b
return a[0]*b[0]+a[1]*b[1]+a[2]*b[2]; }
inline void vec_null(vector &dest) {
memset(dest, 0, sizeof(vector)); }
-inline void vec_neg(vector &dest) { // -a
+inline void vec_neg(vector &dest) { // -a
dest[0] = -dest[0];
dest[1] = -dest[1];
dest[2] = -dest[2]; }
-inline void vec_norm(vector &dest) { // a/|a|
- register double f = sqrt(vec_dot(dest, dest));
- dest[0] /= f;
- dest[1] /= f;
+inline void vec_norm(vector &dest) { // a/|a|
+ register double f = sqrt(vec_dot(dest, dest));
+ dest[0] /= f;
+ dest[1] /= f;
dest[2] /= f; }
-inline void vec_add(vector &dest, vector &src) { // a+b
+inline void vec_add(vector &dest, vector &src) { // a+b
dest[0] += src[0];
dest[1] += src[1];
dest[2] += src[2]; }
-inline void vec_subtr(vector &dest, vector &src) { // a-b
+inline void vec_subtr(vector &dest, vector &src) { // a-b
dest[0] -= src[0];
dest[1] -= src[1];
dest[2] -= src[2]; }
-inline void vec_mult(vector &dest, vector &src) { // a*b
+inline void vec_mult(vector &dest, vector &src) { // a*b
dest[0] *= src[0];
dest[1] *= src[1];
dest[2] *= src[2]; }
-inline void vec_div(vector &dest, vector &src) { // a/b
+inline void vec_div(vector &dest, vector &src) { // a/b
dest[0] /= src[0];
dest[1] /= src[1];
dest[2] /= src[2]; }
-inline void vec_cross(vector &dest, vector &src) { // a x b
+inline void vec_cross(vector &dest, vector &src) { // a x b
vector t = {
dest[1]*src[2]-dest[2]*src[1],
dest[2]*src[0]-dest[0]*src[2],
dest[0]*src[1]-dest[1]*src[0]};
memcpy(dest, t, sizeof(vector)); }
-inline void vec_scalar_mult(vector &dest, double f) { // f*a
+inline void vec_scalar_mult(vector &dest, double f) { // f*a
dest[0] *= f;
dest[1] *= f;
dest[2] *= f; }
@@ -121,27 +121,27 @@ inline void shape_unit(shape &dest) {
memset(dest, 0, sizeof(shape));
dest[0] = dest[1] = dest[2] = 1.0; }
-inline void shape_add(shape &dest, shape &src) { // h_a+h_b
+inline void shape_add(shape &dest, shape &src) { // h_a+h_b
dest[0] += src[0]; dest[1] += src[1]; dest[2] += src[2];
dest[3] += src[3]; dest[4] += src[4]; dest[5] += src[5]; }
-inline void shape_subtr(shape &dest, shape &src) { // h_a-h_b
+inline void shape_subtr(shape &dest, shape &src) { // h_a-h_b
dest[0] -= src[0]; dest[1] -= src[1]; dest[2] -= src[2];
dest[3] -= src[3]; dest[4] -= src[4]; dest[5] -= src[5]; }
-inline void shape_inv(shape &h_inv, shape &h) { // h^-1
+inline void shape_inv(shape &h_inv, shape &h) { // h^-1
h_inv[0] = 1.0/h[0]; h_inv[1] = 1.0/h[1]; h_inv[2] = 1.0/h[2];
h_inv[3] = -h[3]/(h[1]*h[2]);
h_inv[4] = (h[3]*h[5]-h[1]*h[4])/(h[0]*h[1]*h[2]);
- h_inv[5] = -h[5]/(h[0]*h[1]); }
+ h_inv[5] = -h[5]/(h[0]*h[1]); }
-inline void shape_dot(shape &dest, shape &src) { // h_a.h_b
+inline void shape_dot(shape &dest, shape &src) { // h_a.h_b
dest[3] = dest[1]*src[3]+dest[3]*src[2];
dest[4] = dest[0]*src[4]+dest[5]*src[3]+dest[4]*src[2];
dest[5] = dest[0]*src[5]+dest[5]*src[1];
dest[0] *= src[0]; dest[1] *= src[1]; dest[2] *= src[2]; }
-inline void shape_scalar_mult(shape &dest, double f) { // f*h
+inline void shape_scalar_mult(shape &dest, double f) { // f*h
dest[0] *= f; dest[1] *= f; dest[2] *= f;
dest[3] *= f; dest[4] *= f; dest[5] *= f; }
@@ -155,7 +155,7 @@ inline void vec_shape_dot(vector &dest, shape &h, vector &src) {// a.h
dest[1] = h[5]*src[0]+h[1]*src[1];
dest[0] = h[0]*src[0]; }
-inline void shape_to_matrix(matrix &dest, shape &h) { // m = h
+inline void shape_to_matrix(matrix &dest, shape &h) { // m = h
dest[0][0] = h[0]; dest[1][0] = h[5]; dest[2][0] = h[4];
dest[0][1] = 0.0; dest[1][1] = h[1]; dest[2][1] = h[3];
dest[0][2] = 0.0; dest[1][2] = 0.0; dest[2][2] = h[2]; }
@@ -170,10 +170,10 @@ inline void lshape_to_shape(shape &dest, lshape &src) {
// form operators
-inline double form_det(form &m) { // |m|
+inline double form_det(form &m) { // |m|
return m[0]*(m[1]*m[2]-m[3]*m[3])+
m[4]*(2.0*m[3]*m[5]-m[1]*m[4])-m[2]*m[5]*m[5]; }
-
+
inline void form_null(form &dest) {
memset(dest, 0, sizeof(form)); }
@@ -181,15 +181,15 @@ inline void form_unit(form &dest) {
memset(dest, 0, sizeof(form));
dest[0] = dest[1] = dest[2] = 1.0; }
-inline void form_add(form &dest, form &src) { // m_a+m_b
+inline void form_add(form &dest, form &src) { // m_a+m_b
dest[0] += src[0]; dest[1] += src[1]; dest[2] += src[2];
dest[3] += src[3]; dest[4] += src[4]; dest[5] += src[5]; }
-inline void form_subtr(shape &dest, form &src) { // m_a-m_b
+inline void form_subtr(shape &dest, form &src) { // m_a-m_b
dest[0] -= src[0]; dest[1] -= src[1]; dest[2] -= src[2];
dest[3] -= src[3]; dest[4] -= src[4]; dest[5] -= src[5]; }
-inline int form_inv(form &m_inv, form &m) { // m^-1
+inline int form_inv(form &m_inv, form &m) { // m^-1
register double det = form_det(m);
if (fzero(det)) return 0;
m_inv[0] = (m[1]*m[2]-m[3]*m[3])/det;
@@ -200,7 +200,7 @@ inline int form_inv(form &m_inv, form &m) { // m^-1
m_inv[5] = (m[3]*m[4]-m[2]*m[5])/det;
return 1; }
-inline void form_dot(form &dest, form &src) { // m_a.m_b
+inline void form_dot(form &dest, form &src) { // m_a.m_b
form m;
memcpy(m, dest, sizeof(form));
dest[0] = m[0]*src[0]+m[4]*src[4]+m[5]*src[5];
@@ -210,7 +210,7 @@ inline void form_dot(form &dest, form &src) { // m_a.m_b
dest[4] = m[4]*src[2]+m[5]*src[3]+m[0]*src[4];
dest[5] = m[5]*src[1]+m[4]*src[3]+m[0]*src[5]; }
-inline void form_vec_dot(vector &dest, form &m) { // m.a
+inline void form_vec_dot(vector &dest, form &m) { // m.a
vector a;
memcpy(a, dest, sizeof(vector));
dest[0] = m[0]*a[0]+m[5]*a[1]+m[4]*a[2];
@@ -227,12 +227,12 @@ inline void lform_to_form(form &dest, lform &src) {
// matrix operators
-inline double matrix_det(matrix &m) { // |m|
+inline double matrix_det(matrix &m) { // |m|
vector axb;
memcpy(&axb, m[0], sizeof(vector));
vec_cross(axb, m[1]);
return vec_dot(axb, m[2]); }
-
+
inline void matrix_null(matrix &dest) {
memset(dest, 0, sizeof(dest)); }
@@ -240,19 +240,19 @@ inline void matrix_unit(matrix &dest) {
memset(dest, 0, sizeof(dest));
dest[0][0] = dest[1][1] = dest[2][2] = 1.0; }
-inline void matrix_scalar_mult(matrix &dest, double f) { // f*m
+inline void matrix_scalar_mult(matrix &dest, double f) { // f*m
vec_scalar_mult(dest[0], f);
vec_scalar_mult(dest[1], f);
vec_scalar_mult(dest[2], f); }
-inline void matrix_trans(matrix &dest) { // m^t
+inline void matrix_trans(matrix &dest) { // m^t
double f = dest[0][1]; dest[0][1] = dest[1][0]; dest[1][0] = f;
f = dest[0][2]; dest[0][2] = dest[2][0]; dest[2][0] = f;
f = dest[1][2]; dest[1][2] = dest[2][1]; dest[2][1] = f; }
-inline int matrix_inv(matrix &dest, matrix &src) { // m^-1
+inline int matrix_inv(matrix &dest, matrix &src) { // m^-1
double f = matrix_det(src);
- if (fzero(f)) return 0; // singular matrix
+ if (fzero(f)) return 0; // singular matrix
memcpy(dest[0], src[1], sizeof(vector));
memcpy(dest[1], src[2], sizeof(vector));
memcpy(dest[2], src[0], sizeof(vector));
@@ -262,16 +262,16 @@ inline int matrix_inv(matrix &dest, matrix &src) { // m^-1
matrix_scalar_mult(dest, 1.0/f);
matrix_trans(dest);
return 0; }
-
+
inline void matrix_vec_dot(vector &dest, vector &src, matrix &m) { // m.a
dest[0] = m[0][0]*src[0]+m[1][0]*src[1]+m[2][0]*src[2];
dest[1] = m[0][1]*src[0]+m[1][1]*src[1]+m[2][1]*src[2];
dest[2] = m[0][2]*src[0]+m[1][2]*src[1]+m[2][2]*src[2]; }
-inline void matrix_to_shape(shape &dest, matrix &src) { // h = m
+inline void matrix_to_shape(shape &dest, matrix &src) { // h = m
dest[0] = src[0][0]; dest[1] = src[1][1]; dest[2] = src[2][2];
dest[3] = src[2][1]; dest[4] = src[2][0]; dest[5] = src[1][0]; }
-
+
inline void matrix_to_lmatrix(lmatrix &dest, matrix &src) {
vec_to_lvec(dest[0], src[0]);
vec_to_lvec(dest[1], src[1]);
@@ -284,20 +284,20 @@ inline void lmatrix_to_matrix(matrix &dest, lmatrix &src) {
// quaternion operators
-inline double quat_dot(quaternion &p, quaternion &q) { // p.q
+inline double quat_dot(quaternion &p, quaternion &q) { // p.q
return p[0]*q[0]+p[1]*q[1]+p[2]*q[2]+p[3]*q[3];
}
-inline void quat_norm(quaternion &q) { // q = q/|q|
+inline void quat_norm(quaternion &q) { // q = q/|q|
double f = sqrt(q[0]*q[0]+q[1]*q[1]+q[2]*q[2]+q[3]*q[3]);
q[0] /= f; q[1] /= f; q[2] /= f; q[3] /= f;
}
-inline void quat_conj(quaternion &q) { // q = conj(q)
+inline void quat_conj(quaternion &q) { // q = conj(q)
q[1] = -q[1]; q[2] = -q[2]; q[3] = -q[3];
}
-inline void quat_mult(quaternion &dest, quaternion &src) { // dest *= src
+inline void quat_mult(quaternion &dest, quaternion &src) { // dest *= src
quaternion q;
memcpy(q, dest, sizeof(quaternion));
dest[0] = src[0]*q[3]+src[1]*q[2]-src[2]*q[1]+src[3]*q[0];
@@ -306,7 +306,7 @@ inline void quat_mult(quaternion &dest, quaternion &src) { // dest *= src
dest[3] = -src[0]*q[0]-src[1]*q[1]-src[2]*q[2]+src[3]*q[3];
}
-inline void quat_div(quaternion &dest, quaternion &src) { // dest /= src
+inline void quat_div(quaternion &dest, quaternion &src) { // dest /= src
quaternion q;
memcpy(q, dest, sizeof(quaternion));
dest[0] = src[0]*q[3]-src[1]*q[2]+src[2]*q[1]-src[3]*q[0];
@@ -314,16 +314,16 @@ inline void quat_div(quaternion &dest, quaternion &src) { // dest /= src
dest[2] = src[0]*q[1]+src[1]*q[0]-src[2]*q[3]-src[3]*q[2];
dest[3] = -src[0]*q[0]+src[1]*q[1]+src[2]*q[2]-src[3]*q[3];
}
- // dest = q*src*conj(q)
+ // dest = q*src*conj(q)
inline void quat_vec_rot(vector &dest, vector &src, quaternion &q) {
quaternion aa={q[0]*q[0], q[1]*q[1], q[2]*q[2], q[3]*q[3]};
form ab={q[0]*q[1], q[0]*q[2], q[0]*q[3], q[1]*q[2], q[1]*q[3], q[2]*q[3]};
dest[0] = (aa[0]+aa[1]-aa[2]-aa[3])*src[0]+
- ((ab[3]-ab[2])*src[1]+(ab[1]+ab[4])*src[2])*2.0;
+ ((ab[3]-ab[2])*src[1]+(ab[1]+ab[4])*src[2])*2.0;
dest[1] = (aa[0]-aa[1]+aa[2]-aa[3])*src[1]+
- ((ab[2]+ab[3])*src[0]+(ab[5]-ab[0])*src[2])*2.0;
+ ((ab[2]+ab[3])*src[0]+(ab[5]-ab[0])*src[2])*2.0;
dest[2] = (aa[0]-aa[1]-aa[2]+aa[3])*src[2]+
- ((ab[4]-ab[1])*src[0]+(ab[0]+ab[5])*src[1])*2.0;
+ ((ab[4]-ab[1])*src[0]+(ab[0]+ab[5])*src[1])*2.0;
}
// vector4 operators
@@ -334,7 +334,7 @@ inline void vec4_null(vector4 &dest) {
inline double vec4_dot(vector4 &a, vector4 &b) {
return a[0]*b[0]+a[1]*b[1]+a[2]*b[2]+a[3]*b[3]; }
-
+
// form operators
inline void form4_null(form4 &dest) {
@@ -351,8 +351,8 @@ inline double form4_det(form4 &m) {
m[5]*(2.0*m[4]*m[7]-m[2]*m[5])-m[3]*m[7]*m[7])+f*f+
-m[1]*(m[2]*m[6]*m[6]+m[8]*(m[3]*m[8]-2.0*m[4]*m[6]))+
m[9]*(
- 2.0*(m[2]*m[5]*m[6]+m[3]*m[7]*m[8]-m[4]*(m[6]*m[7]+m[5]*m[8]))+
- m[9]*(m[4]*m[4]-m[2]*m[3])); }
+ 2.0*(m[2]*m[5]*m[6]+m[3]*m[7]*m[8]-m[4]*(m[6]*m[7]+m[5]*m[8]))+
+ m[9]*(m[4]*m[4]-m[2]*m[3])); }
inline int form4_inv(form4 &m_inv, form4 &m) {
register double det = form4_det(m);
@@ -394,10 +394,10 @@ inline int regress2(vector &eqn, int order, double *x, double *y, int n) {
vector xty = VECTOR_NULL;
double xn, xi, yi;
int i;
-
+
vec_null(eqn);
xtx[0] = n;
- if ((order = order%2)<0) order = -order; // max: quad regress
+ if ((order = order%2)<0) order = -order; // max: quad regress
if (order<1) xtx[1] = 1.0;
if (order<2) xtx[2] = 1.0;
for (i=0; i<n; ++i) {
@@ -420,10 +420,10 @@ inline int regress3(vector4 &eqn, int order, double *x, double *y, int n) {
vector4 xty = VECTOR4_NULL;
double xn, xi, yi;
int i;
-
+
vec4_null(eqn);
xtx[0] = n;
- if ((order = order%3)<0) order = -order; // max: cubic regress
+ if ((order = order%3)<0) order = -order; // max: cubic regress
if (order<1) xtx[1] = 1.0;
if (order<2) xtx[2] = 1.0;
if (order<3) xtx[3] = 1.0;
diff --git a/src/USER-EWALDN/pair_buck_coul.cpp b/src/USER-EWALDN/pair_buck_coul.cpp
index 512f10aedc71886081cdd207d97148b521ed54c4..dd7d323852dfeb830cf4d74a7d4fd6a4674e58c9 100644
--- a/src/USER-EWALDN/pair_buck_coul.cpp
+++ b/src/USER-EWALDN/pair_buck_coul.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -56,13 +56,13 @@ PairBuckCoul::PairBuckCoul(LAMMPS *lmp) : Pair(lmp)
global settings
------------------------------------------------------------------------- */
-#define PAIR_ILLEGAL "Illegal pair_style buck/coul command"
-#define PAIR_CUTOFF "Only one cut-off allowed when requesting all long"
-#define PAIR_MISSING "Cut-offs missing in pair_style buck/coul"
-#define PAIR_LJ_OFF "LJ6 off not supported in pair_style buck/coul"
-#define PAIR_COUL_CUT "Coulombic cut not supported in pair_style buck/coul"
-#define PAIR_LARGEST "Using largest cut-off for buck/coul long long"
-#define PAIR_MIX "Geometric mixing assumed for 1/r^6 coefficients"
+#define PAIR_ILLEGAL "Illegal pair_style buck/coul command"
+#define PAIR_CUTOFF "Only one cut-off allowed when requesting all long"
+#define PAIR_MISSING "Cut-offs missing in pair_style buck/coul"
+#define PAIR_LJ_OFF "LJ6 off not supported in pair_style buck/coul"
+#define PAIR_COUL_CUT "Coulombic cut not supported in pair_style buck/coul"
+#define PAIR_LARGEST "Using largest cut-off for buck/coul long long"
+#define PAIR_MIX "Geometric mixing assumed for 1/r^6 coefficients"
void PairBuckCoul::options(char **arg, int order)
{
@@ -73,8 +73,8 @@ void PairBuckCoul::options(char **arg, int order)
for (i=0; option[i]&&strcmp(arg[0], option[i]); ++i);
switch (i) {
default: error->all(FLERR,PAIR_ILLEGAL);
- case 0: ewald_order |= 1<<order; break; // set kspace r^-order
- case 2: ewald_off |= 1<<order; // turn r^-order off
+ case 0: ewald_order |= 1<<order; break; // set kspace r^-order
+ case 2: ewald_off |= 1<<order; // turn r^-order off
case 1: break;
}
}
@@ -83,7 +83,7 @@ void PairBuckCoul::options(char **arg, int order)
void PairBuckCoul::settings(int narg, char **arg)
{
if (narg != 3 && narg != 4) error->all(FLERR,"Illegal pair_style command");
-
+
ewald_order = 0;
ewald_off = 0;
options(arg, 6);
@@ -98,11 +98,11 @@ void PairBuckCoul::settings(int narg, char **arg)
if (narg == 4) cut_coul = force->numeric(*arg);
else cut_coul = cut_buck_global;
- if (allocated) { // reset explicit cuts
+ if (allocated) { // reset explicit cuts
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
- if (setflag[i][j]) cut_buck[i][j] = cut_buck_global;
+ if (setflag[i][j]) cut_buck[i][j] = cut_buck_global;
}
}
@@ -228,7 +228,7 @@ void PairBuckCoul::init_style()
if (!atom->q_flag && (ewald_order&(1<<1)))
error->all(FLERR,
- "Invoking coulombic in pair style lj/coul requires atom attribute q");
+ "Invoking coulombic in pair style lj/coul requires atom attribute q");
// request regular or rRESPA neighbor lists
@@ -277,12 +277,12 @@ void PairBuckCoul::init_style()
// ensure use of KSpace long-range solver, set g_ewald
- if (ewald_order&(1<<1)) { // r^-1 kspace
- if (force->kspace == NULL)
+ if (ewald_order&(1<<1)) { // r^-1 kspace
+ if (force->kspace == NULL)
error->all(FLERR,"Pair style is incompatible with KSpace style");
g_ewald = force->kspace->g_ewald;
}
- if (ewald_order&(1<<6)) { // r^-6 kspace
+ if (ewald_order&(1<<6)) { // r^-6 kspace
if (!force->kspace && strcmp(force->kspace_style,"ewald/n"))
error->all(FLERR,"Pair style is incompatible with KSpace style");
g_ewald = force->kspace->g_ewald;
@@ -331,7 +331,7 @@ double PairBuckCoul::init_one(int i, int j)
if (cut_respa && MIN(cut_buck[i][j],cut_coul) < cut_respa[3])
error->all(FLERR,"Pair cutoff < Respa interior cutoff");
-
+
if (offset_flag) {
double rexp = exp(-cut_buck[i][j]/buck_rho[i][j]);
offset[i][j] = buck_a[i][j]*rexp - buck_c[i][j]/pow(cut_buck[i][j],6.0);
@@ -362,10 +362,10 @@ void PairBuckCoul::write_restart(FILE *fp)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
- fwrite(&buck_a_read[i][j],sizeof(double),1,fp);
- fwrite(&buck_rho_read[i][j],sizeof(double),1,fp);
- fwrite(&buck_c_read[i][j],sizeof(double),1,fp);
- fwrite(&cut_buck_read[i][j],sizeof(double),1,fp);
+ fwrite(&buck_a_read[i][j],sizeof(double),1,fp);
+ fwrite(&buck_rho_read[i][j],sizeof(double),1,fp);
+ fwrite(&buck_c_read[i][j],sizeof(double),1,fp);
+ fwrite(&cut_buck_read[i][j],sizeof(double),1,fp);
}
}
}
@@ -387,16 +387,16 @@ void PairBuckCoul::read_restart(FILE *fp)
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
- if (me == 0) {
- fread(&buck_a_read[i][j],sizeof(double),1,fp);
- fread(&buck_rho_read[i][j],sizeof(double),1,fp);
- fread(&buck_c_read[i][j],sizeof(double),1,fp);
- fread(&cut_buck_read[i][j],sizeof(double),1,fp);
- }
- MPI_Bcast(&buck_a_read[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&buck_rho_read[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&buck_c_read[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&cut_buck_read[i][j],1,MPI_DOUBLE,0,world);
+ if (me == 0) {
+ fread(&buck_a_read[i][j],sizeof(double),1,fp);
+ fread(&buck_rho_read[i][j],sizeof(double),1,fp);
+ fread(&buck_c_read[i][j],sizeof(double),1,fp);
+ fread(&cut_buck_read[i][j],sizeof(double),1,fp);
+ }
+ MPI_Bcast(&buck_a_read[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&buck_rho_read[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&buck_c_read[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut_buck_read[i][j],1,MPI_DOUBLE,0,world);
}
}
}
@@ -458,16 +458,16 @@ void PairBuckCoul::compute(int eflag, int vflag)
int i, j, order1 = ewald_order&(1<<1), order6 = ewald_order&(1<<6);
int *ineigh, *ineighn, *jneigh, *jneighn, typei, typej, ni;
double qi = 0.0, qri = 0.0, *cutsqi, *cut_bucksqi,
- *buck1i, *buck2i, *buckai, *buckci, *rhoinvi, *offseti;
+ *buck1i, *buck2i, *buckai, *buckci, *rhoinvi, *offseti;
double r, rsq, r2inv, force_coul, force_buck;
double g2 = g_ewald*g_ewald, g6 = g2*g2*g2, g8 = g6*g2;
vector xi, d;
ineighn = (ineigh = list->ilist)+list->inum;
- for (; ineigh<ineighn; ++ineigh) { // loop over my atoms
+ for (; ineigh<ineighn; ++ineigh) { // loop over my atoms
i = *ineigh; fi = f0+3*i;
- if (order1) qri = (qi = q[i])*qqrd2e; // initialize constants
+ if (order1) qri = (qi = q[i])*qqrd2e; // initialize constants
offseti = offset[typei = type[i]];
buck1i = buck1[typei]; buck2i = buck2[typei];
buckai = buck_a[typei]; buckci = buck_c[typei], rhoinvi = rhoinv[typei];
@@ -475,105 +475,105 @@ void PairBuckCoul::compute(int eflag, int vflag)
memcpy(xi, x0+(i+(i<<1)), sizeof(vector));
jneighn = (jneigh = list->firstneigh[i])+list->numneigh[i];
- for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
+ for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
j = *jneigh;
ni = sbmask(j);
j &= NEIGHMASK;
-
+
{ register double *xj = x0+(j+(j<<1));
- d[0] = xi[0] - xj[0]; // pair vector
- d[1] = xi[1] - xj[1];
- d[2] = xi[2] - xj[2]; }
+ d[0] = xi[0] - xj[0]; // pair vector
+ d[1] = xi[1] - xj[1];
+ d[2] = xi[2] - xj[2]; }
if ((rsq = vec_dot(d, d)) >= cutsqi[typej = type[j]]) continue;
r2inv = 1.0/rsq;
r = sqrt(rsq);
- if (order1 && (rsq < cut_coulsq)) { // coulombic
- if (!ncoultablebits || rsq <= tabinnersq) { // series real space
- register double x = g_ewald*r;
- register double s = qri*q[j], t = 1.0/(1.0+EWALD_P*x);
- if (ni == 0) {
- s *= g_ewald*exp(-x*x);
- force_coul = (t *= ((((t*A5+A4)*t+A3)*t+A2)*t+A1)*s/x)+EWALD_F*s;
- if (eflag) ecoul = t;
- }
- else { // special case
- register double f = s*(1.0-special_coul[ni])/r;
- s *= g_ewald*exp(-x*x);
- force_coul = (t *= ((((t*A5+A4)*t+A3)*t+A2)*t+A1)*s/x)+EWALD_F*s-f;
- if (eflag) ecoul = t-f;
- }
- } // table real space
- else {
- register union_int_float_t t;
- t.f = rsq;
- register const int k = (t.i & ncoulmask) >> ncoulshiftbits;
- register double f = (rsq-rtable[k])*drtable[k], qiqj = qi*q[j];
- if (ni == 0) {
- force_coul = qiqj*(ftable[k]+f*dftable[k]);
- if (eflag) ecoul = qiqj*(etable[k]+f*detable[k]);
- }
- else { // special case
- t.f = (1.0-special_coul[ni])*(ctable[k]+f*dctable[k]);
- force_coul = qiqj*(ftable[k]+f*dftable[k]-t.f);
- if (eflag) ecoul = qiqj*(etable[k]+f*detable[k]-t.f);
- }
- }
+ if (order1 && (rsq < cut_coulsq)) { // coulombic
+ if (!ncoultablebits || rsq <= tabinnersq) { // series real space
+ register double x = g_ewald*r;
+ register double s = qri*q[j], t = 1.0/(1.0+EWALD_P*x);
+ if (ni == 0) {
+ s *= g_ewald*exp(-x*x);
+ force_coul = (t *= ((((t*A5+A4)*t+A3)*t+A2)*t+A1)*s/x)+EWALD_F*s;
+ if (eflag) ecoul = t;
+ }
+ else { // special case
+ register double f = s*(1.0-special_coul[ni])/r;
+ s *= g_ewald*exp(-x*x);
+ force_coul = (t *= ((((t*A5+A4)*t+A3)*t+A2)*t+A1)*s/x)+EWALD_F*s-f;
+ if (eflag) ecoul = t-f;
+ }
+ } // table real space
+ else {
+ register union_int_float_t t;
+ t.f = rsq;
+ register const int k = (t.i & ncoulmask) >> ncoulshiftbits;
+ register double f = (rsq-rtable[k])*drtable[k], qiqj = qi*q[j];
+ if (ni == 0) {
+ force_coul = qiqj*(ftable[k]+f*dftable[k]);
+ if (eflag) ecoul = qiqj*(etable[k]+f*detable[k]);
+ }
+ else { // special case
+ t.f = (1.0-special_coul[ni])*(ctable[k]+f*dctable[k]);
+ force_coul = qiqj*(ftable[k]+f*dftable[k]-t.f);
+ if (eflag) ecoul = qiqj*(etable[k]+f*detable[k]-t.f);
+ }
+ }
}
else force_coul = ecoul = 0.0;
- if (rsq < cut_bucksqi[typej]) { // buckingham
- register double rn = r2inv*r2inv*r2inv,
- expr = exp(-r*rhoinvi[typej]);
- if (order6) { // long-range
- register double x2 = g2*rsq, a2 = 1.0/x2;
- x2 = a2*exp(-x2)*buckci[typej];
- if (ni == 0) {
- force_buck =
- r*expr*buck1i[typej]-g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq;
- if (eflag) evdwl = expr*buckai[typej]-g6*((a2+1.0)*a2+0.5)*x2;
- }
- else { // special case
- register double f = special_lj[ni], t = rn*(1.0-f);
- force_buck = f*r*expr*buck1i[typej]-
- g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq+t*buck2i[typej];
- if (eflag) evdwl = f*expr*buckai[typej] -
- g6*((a2+1.0)*a2+0.5)*x2+t*buckci[typej];
- }
- }
- else { // cut
- if (ni == 0) {
- force_buck = r*expr*buck1i[typej]-rn*buck2i[typej];
- if (eflag) evdwl = expr*buckai[typej] -
- rn*buckci[typej]-offseti[typej];
- }
- else { // special case
- register double f = special_lj[ni];
- force_buck = f*(r*expr*buck1i[typej]-rn*buck2i[typej]);
- if (eflag)
- evdwl = f*(expr*buckai[typej]-rn*buckci[typej]-offseti[typej]);
- }
- }
+ if (rsq < cut_bucksqi[typej]) { // buckingham
+ register double rn = r2inv*r2inv*r2inv,
+ expr = exp(-r*rhoinvi[typej]);
+ if (order6) { // long-range
+ register double x2 = g2*rsq, a2 = 1.0/x2;
+ x2 = a2*exp(-x2)*buckci[typej];
+ if (ni == 0) {
+ force_buck =
+ r*expr*buck1i[typej]-g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq;
+ if (eflag) evdwl = expr*buckai[typej]-g6*((a2+1.0)*a2+0.5)*x2;
+ }
+ else { // special case
+ register double f = special_lj[ni], t = rn*(1.0-f);
+ force_buck = f*r*expr*buck1i[typej]-
+ g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq+t*buck2i[typej];
+ if (eflag) evdwl = f*expr*buckai[typej] -
+ g6*((a2+1.0)*a2+0.5)*x2+t*buckci[typej];
+ }
+ }
+ else { // cut
+ if (ni == 0) {
+ force_buck = r*expr*buck1i[typej]-rn*buck2i[typej];
+ if (eflag) evdwl = expr*buckai[typej] -
+ rn*buckci[typej]-offseti[typej];
+ }
+ else { // special case
+ register double f = special_lj[ni];
+ force_buck = f*(r*expr*buck1i[typej]-rn*buck2i[typej]);
+ if (eflag)
+ evdwl = f*(expr*buckai[typej]-rn*buckci[typej]-offseti[typej]);
+ }
+ }
}
else force_buck = evdwl = 0.0;
fpair = (force_coul+force_buck)*r2inv;
if (newton_pair || j < nlocal) {
- register double *fj = f0+(j+(j<<1)), f;
- fi[0] += f = d[0]*fpair; fj[0] -= f;
- fi[1] += f = d[1]*fpair; fj[1] -= f;
- fi[2] += f = d[2]*fpair; fj[2] -= f;
+ register double *fj = f0+(j+(j<<1)), f;
+ fi[0] += f = d[0]*fpair; fj[0] -= f;
+ fi[1] += f = d[1]*fpair; fj[1] -= f;
+ fi[2] += f = d[2]*fpair; fj[2] -= f;
}
else {
- fi[0] += d[0]*fpair;
- fi[1] += d[1]*fpair;
- fi[2] += d[2]*fpair;
+ fi[0] += d[0]*fpair;
+ fi[1] += d[1]*fpair;
+ fi[2] += d[2]*fpair;
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
- evdwl,ecoul,fpair,d[0],d[1],d[2]);
+ evdwl,ecoul,fpair,d[0],d[1],d[2]);
}
}
@@ -596,7 +596,7 @@ void PairBuckCoul::compute_inner()
double cut_out_on = cut_respa[0];
double cut_out_off = cut_respa[1];
-
+
double cut_out_diff = cut_out_off - cut_out_on;
double cut_out_on_sq = cut_out_on*cut_out_on;
double cut_out_off_sq = cut_out_off*cut_out_off;
@@ -608,7 +608,7 @@ void PairBuckCoul::compute_inner()
ineighn = (ineigh = listinner->ilist)+listinner->inum;
- for (; ineigh<ineighn; ++ineigh) { // loop over my atoms
+ for (; ineigh<ineighn; ++ineigh) { // loop over my atoms
i = *ineigh; fi = f0+3*i;
qri = qqrd2e*q[i];
memcpy(xi, x0+(i+(i<<1)), sizeof(vector));
@@ -616,50 +616,50 @@ void PairBuckCoul::compute_inner()
buck1i = buck1[typei]; buck2i = buck2[typei]; rhoinvi = rhoinv[typei];
jneighn = (jneigh = listinner->firstneigh[i])+listinner->numneigh[i];
- for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
+ for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
j = *jneigh;
ni = sbmask(j);
j &= NEIGHMASK;
-
+
{ register double *xj = x0+(j+(j<<1));
- d[0] = xi[0] - xj[0]; // pair vector
- d[1] = xi[1] - xj[1];
- d[2] = xi[2] - xj[2]; }
+ d[0] = xi[0] - xj[0]; // pair vector
+ d[1] = xi[1] - xj[1];
+ d[2] = xi[2] - xj[2]; }
if ((rsq = vec_dot(d, d)) >= cut_out_off_sq) continue;
r2inv = 1.0/rsq;
r = sqrt(rsq);
- if (order1 && (rsq < cut_coulsq)) // coulombic
- force_coul = ni == 0 ?
- qri*q[j]/r : qri*q[j]/r*special_coul[ni];
+ if (order1 && (rsq < cut_coulsq)) // coulombic
+ force_coul = ni == 0 ?
+ qri*q[j]/r : qri*q[j]/r*special_coul[ni];
- if (rsq < cut_bucksqi[typej = type[j]]) { // buckingham
- register double rn = r2inv*r2inv*r2inv,
- expr = exp(-r*rhoinvi[typej]);
- force_buck = ni == 0 ?
- (r*expr*buck1i[typej]-rn*buck2i[typej]) :
- (r*expr*buck1i[typej]-rn*buck2i[typej])*special_lj[ni];
+ if (rsq < cut_bucksqi[typej = type[j]]) { // buckingham
+ register double rn = r2inv*r2inv*r2inv,
+ expr = exp(-r*rhoinvi[typej]);
+ force_buck = ni == 0 ?
+ (r*expr*buck1i[typej]-rn*buck2i[typej]) :
+ (r*expr*buck1i[typej]-rn*buck2i[typej])*special_lj[ni];
}
else force_buck = 0.0;
fpair = (force_coul + force_buck) * r2inv;
-
- if (rsq > cut_out_on_sq) { // switching
- register double rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
- fpair *= 1.0 + rsw*rsw*(2.0*rsw-3.0);
+
+ if (rsq > cut_out_on_sq) { // switching
+ register double rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
+ fpair *= 1.0 + rsw*rsw*(2.0*rsw-3.0);
}
- if (newton_pair || j < nlocal) { // force update
- register double *fj = f0+(j+(j<<1)), f;
- fi[0] += f = d[0]*fpair; fj[0] -= f;
- fi[1] += f = d[1]*fpair; fj[1] -= f;
- fi[2] += f = d[2]*fpair; fj[2] -= f;
+ if (newton_pair || j < nlocal) { // force update
+ register double *fj = f0+(j+(j<<1)), f;
+ fi[0] += f = d[0]*fpair; fj[0] -= f;
+ fi[1] += f = d[1]*fpair; fj[1] -= f;
+ fi[2] += f = d[2]*fpair; fj[2] -= f;
}
else {
- fi[0] += d[0]*fpair;
- fi[1] += d[1]*fpair;
- fi[2] += d[2]*fpair;
+ fi[0] += d[0]*fpair;
+ fi[1] += d[1]*fpair;
+ fi[2] += d[2]*fpair;
}
}
}
@@ -698,7 +698,7 @@ void PairBuckCoul::compute_middle()
ineighn = (ineigh = listmiddle->ilist)+listmiddle->inum;
- for (; ineigh<ineighn; ++ineigh) { // loop over my atoms
+ for (; ineigh<ineighn; ++ineigh) { // loop over my atoms
i = *ineigh; fi = f0+3*i;
qri = qqrd2e*q[i];
memcpy(xi, x0+(i+(i<<1)), sizeof(vector));
@@ -706,55 +706,55 @@ void PairBuckCoul::compute_middle()
buck1i = buck1[typei]; buck2i = buck2[typei]; rhoinvi = rhoinv[typei];
jneighn = (jneigh = listmiddle->firstneigh[i])+listmiddle->numneigh[i];
- for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
+ for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
j = *jneigh;
ni = sbmask(j);
j &= NEIGHMASK;
-
+
{ register double *xj = x0+(j+(j<<1));
- d[0] = xi[0] - xj[0]; // pair vector
- d[1] = xi[1] - xj[1];
- d[2] = xi[2] - xj[2]; }
+ d[0] = xi[0] - xj[0]; // pair vector
+ d[1] = xi[1] - xj[1];
+ d[2] = xi[2] - xj[2]; }
if ((rsq = vec_dot(d, d)) >= cut_out_off_sq) continue;
if (rsq <= cut_in_off_sq) continue;
r2inv = 1.0/rsq;
r = sqrt(rsq);
- if (order1 && (rsq < cut_coulsq)) // coulombic
- force_coul = ni == 0 ?
- qri*q[j]/r : qri*q[j]/r*special_coul[ni];
+ if (order1 && (rsq < cut_coulsq)) // coulombic
+ force_coul = ni == 0 ?
+ qri*q[j]/r : qri*q[j]/r*special_coul[ni];
- if (rsq < cut_bucksqi[typej = type[j]]) { // buckingham
- register double rn = r2inv*r2inv*r2inv,
- expr = exp(-r*rhoinvi[typej]);
- force_buck = ni == 0 ?
- (r*expr*buck1i[typej]-rn*buck2i[typej]) :
- (r*expr*buck1i[typej]-rn*buck2i[typej])*special_lj[ni];
+ if (rsq < cut_bucksqi[typej = type[j]]) { // buckingham
+ register double rn = r2inv*r2inv*r2inv,
+ expr = exp(-r*rhoinvi[typej]);
+ force_buck = ni == 0 ?
+ (r*expr*buck1i[typej]-rn*buck2i[typej]) :
+ (r*expr*buck1i[typej]-rn*buck2i[typej])*special_lj[ni];
}
else force_buck = 0.0;
fpair = (force_coul + force_buck) * r2inv;
-
- if (rsq < cut_in_on_sq) { // switching
- register double rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff;
- fpair *= rsw*rsw*(3.0 - 2.0*rsw);
+
+ if (rsq < cut_in_on_sq) { // switching
+ register double rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff;
+ fpair *= rsw*rsw*(3.0 - 2.0*rsw);
}
if (rsq > cut_out_on_sq) {
- register double rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
- fpair *= 1.0 + rsw*rsw*(2.0*rsw-3.0);
+ register double rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
+ fpair *= 1.0 + rsw*rsw*(2.0*rsw-3.0);
}
- if (newton_pair || j < nlocal) { // force update
- register double *fj = f0+(j+(j<<1)), f;
- fi[0] += f = d[0]*fpair; fj[0] -= f;
- fi[1] += f = d[1]*fpair; fj[1] -= f;
- fi[2] += f = d[2]*fpair; fj[2] -= f;
+ if (newton_pair || j < nlocal) { // force update
+ register double *fj = f0+(j+(j<<1)), f;
+ fi[0] += f = d[0]*fpair; fj[0] -= f;
+ fi[1] += f = d[1]*fpair; fj[1] -= f;
+ fi[2] += f = d[2]*fpair; fj[2] -= f;
}
else {
- fi[0] += d[0]*fpair;
- fi[1] += d[1]*fpair;
- fi[2] += d[2]*fpair;
+ fi[0] += d[0]*fpair;
+ fi[1] += d[1]*fpair;
+ fi[2] += d[2]*fpair;
}
}
}
@@ -782,7 +782,7 @@ void PairBuckCoul::compute_outer(int eflag, int vflag)
int i, j, order1 = ewald_order&(1<<1), order6 = ewald_order&(1<<6);
int *ineigh, *ineighn, *jneigh, *jneighn, typei, typej, ni, respa_flag;
double qi = 0.0, qri = 0.0, *cutsqi, *cut_bucksqi,
- *buck1i, *buck2i, *buckai, *buckci, *rhoinvi, *offseti;
+ *buck1i, *buck2i, *buckai, *buckci, *rhoinvi, *offseti;
double r, rsq, r2inv, force_coul, force_buck;
double g2 = g_ewald*g_ewald, g6 = g2*g2*g2, g8 = g6*g2;
double respa_buck = 0.0, respa_coul = 0.0, frespa = 0.0;
@@ -797,9 +797,9 @@ void PairBuckCoul::compute_outer(int eflag, int vflag)
ineighn = (ineigh = listouter->ilist)+listouter->inum;
- for (; ineigh<ineighn; ++ineigh) { // loop over my atoms
+ for (; ineigh<ineighn; ++ineigh) { // loop over my atoms
i = *ineigh; fi = f0+3*i;
- if (order1) qri = (qi = q[i])*qqrd2e; // initialize constants
+ if (order1) qri = (qi = q[i])*qqrd2e; // initialize constants
offseti = offset[typei = type[i]];
buck1i = buck1[typei]; buck2i = buck2[typei];
buckai = buck_a[typei]; buckci = buck_c[typei]; rhoinvi = rhoinv[typei];
@@ -807,98 +807,98 @@ void PairBuckCoul::compute_outer(int eflag, int vflag)
memcpy(xi, x0+(i+(i<<1)), sizeof(vector));
jneighn = (jneigh = listouter->firstneigh[i])+listouter->numneigh[i];
- for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
+ for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
j = *jneigh;
ni = sbmask(j);
j &= NEIGHMASK;
-
+
{ register double *xj = x0+(j+(j<<1));
- d[0] = xi[0] - xj[0]; // pair vector
- d[1] = xi[1] - xj[1];
- d[2] = xi[2] - xj[2]; }
+ d[0] = xi[0] - xj[0]; // pair vector
+ d[1] = xi[1] - xj[1];
+ d[2] = xi[2] - xj[2]; }
if ((rsq = vec_dot(d, d)) >= cutsqi[typej = type[j]]) continue;
r2inv = 1.0/rsq;
r = sqrt(rsq);
if ((respa_flag = (rsq>cut_in_off_sq)&&(rsq<cut_in_on_sq))) {
- register double rsw = (r-cut_in_off)/cut_in_diff;
- frespa = rsw*rsw*(3.0-2.0*rsw);
+ register double rsw = (r-cut_in_off)/cut_in_diff;
+ frespa = rsw*rsw*(3.0-2.0*rsw);
}
- if (order1 && (rsq < cut_coulsq)) { // coulombic
- if (!ncoultablebits || rsq <= tabinnersq) { // series real space
- register double s = qri*q[j];
- if (respa_flag) // correct for respa
- respa_coul = ni == 0 ? frespa*s/r : frespa*s/r*special_coul[ni];
- register double x = g_ewald*r, t = 1.0/(1.0+EWALD_P*x);
- if (ni == 0) {
- s *= g_ewald*exp(-x*x);
- force_coul = (t *= ((((t*A5+A4)*t+A3)*t+A2)*t+A1)*s/x)+EWALD_F*s;
- if (eflag) ecoul = t;
- }
- else { // correct for special
- r = s*(1.0-special_coul[ni])/r; s *= g_ewald*exp(-x*x);
- force_coul = (t *= ((((t*A5+A4)*t+A3)*t+A2)*t+A1)*s/x)+EWALD_F*s-r;
- if (eflag) ecoul = t-r;
- }
- } // table real space
- else {
- if (respa_flag) respa_coul = ni == 0 ? // correct for respa
- frespa*qri*q[j]/r :
- frespa*qri*q[j]/r*special_coul[ni];
- register union_int_float_t t;
- t.f = rsq;
- register const int k = (t.i & ncoulmask) >> ncoulshiftbits;
- register double f = (rsq-rtable[k])*drtable[k], qiqj = qi*q[j];
- if (ni == 0) {
- force_coul = qiqj*(ftable[k]+f*dftable[k]);
- if (eflag) ecoul = qiqj*(etable[k]+f*detable[k]);
- }
- else { // correct for special
- t.f = (1.0-special_coul[ni])*(ctable[k]+f*dctable[k]);
- force_coul = qiqj*(ftable[k]+f*dftable[k]-t.f);
- if (eflag) ecoul = qiqj*(etable[k]+f*detable[k]-t.f);
- }
- }
+ if (order1 && (rsq < cut_coulsq)) { // coulombic
+ if (!ncoultablebits || rsq <= tabinnersq) { // series real space
+ register double s = qri*q[j];
+ if (respa_flag) // correct for respa
+ respa_coul = ni == 0 ? frespa*s/r : frespa*s/r*special_coul[ni];
+ register double x = g_ewald*r, t = 1.0/(1.0+EWALD_P*x);
+ if (ni == 0) {
+ s *= g_ewald*exp(-x*x);
+ force_coul = (t *= ((((t*A5+A4)*t+A3)*t+A2)*t+A1)*s/x)+EWALD_F*s;
+ if (eflag) ecoul = t;
+ }
+ else { // correct for special
+ r = s*(1.0-special_coul[ni])/r; s *= g_ewald*exp(-x*x);
+ force_coul = (t *= ((((t*A5+A4)*t+A3)*t+A2)*t+A1)*s/x)+EWALD_F*s-r;
+ if (eflag) ecoul = t-r;
+ }
+ } // table real space
+ else {
+ if (respa_flag) respa_coul = ni == 0 ? // correct for respa
+ frespa*qri*q[j]/r :
+ frespa*qri*q[j]/r*special_coul[ni];
+ register union_int_float_t t;
+ t.f = rsq;
+ register const int k = (t.i & ncoulmask) >> ncoulshiftbits;
+ register double f = (rsq-rtable[k])*drtable[k], qiqj = qi*q[j];
+ if (ni == 0) {
+ force_coul = qiqj*(ftable[k]+f*dftable[k]);
+ if (eflag) ecoul = qiqj*(etable[k]+f*detable[k]);
+ }
+ else { // correct for special
+ t.f = (1.0-special_coul[ni])*(ctable[k]+f*dctable[k]);
+ force_coul = qiqj*(ftable[k]+f*dftable[k]-t.f);
+ if (eflag) ecoul = qiqj*(etable[k]+f*detable[k]-t.f);
+ }
+ }
}
else force_coul = respa_coul = ecoul = 0.0;
- if (rsq < cut_bucksqi[typej]) { // buckingham
- register double rn = r2inv*r2inv*r2inv,
- expr = exp(-r*rhoinvi[typej]);
- if (respa_flag) respa_buck = ni == 0 ? // correct for respa
- frespa*(r*expr*buck1i[typej]-rn*buck2i[typej]) :
- frespa*(r*expr*buck1i[typej]-rn*buck2i[typej])*special_lj[ni];
- if (order6) { // long-range form
- register double x2 = g2*rsq, a2 = 1.0/x2;
- x2 = a2*exp(-x2)*buckci[typej];
- if (ni == 0) {
- force_buck =
- r*expr*buck1i[typej]-g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq;
- if (eflag) evdwl = expr*buckai[typej]-g6*((a2+1.0)*a2+0.5)*x2;
- }
- else { // correct for special
- register double f = special_lj[ni], t = rn*(1.0-f);
- force_buck = f*r*expr*buck1i[typej]-
- g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq+t*buck2i[typej];
- if (eflag) evdwl = f*expr*buckai[typej] -
- g6*((a2+1.0)*a2+0.5)*x2+t*buckci[typej];
- }
- }
- else { // cut form
- if (ni == 0) {
- force_buck = r*expr*buck1i[typej]-rn*buck2i[typej];
- if (eflag)
- evdwl = expr*buckai[typej]-rn*buckci[typej]-offseti[typej];
- }
- else { // correct for special
- register double f = special_lj[ni];
- force_buck = f*(r*expr*buck1i[typej]-rn*buck2i[typej]);
- if (eflag)
- evdwl = f*(expr*buckai[typej]-rn*buckci[typej]-offseti[typej]);
- }
- }
+ if (rsq < cut_bucksqi[typej]) { // buckingham
+ register double rn = r2inv*r2inv*r2inv,
+ expr = exp(-r*rhoinvi[typej]);
+ if (respa_flag) respa_buck = ni == 0 ? // correct for respa
+ frespa*(r*expr*buck1i[typej]-rn*buck2i[typej]) :
+ frespa*(r*expr*buck1i[typej]-rn*buck2i[typej])*special_lj[ni];
+ if (order6) { // long-range form
+ register double x2 = g2*rsq, a2 = 1.0/x2;
+ x2 = a2*exp(-x2)*buckci[typej];
+ if (ni == 0) {
+ force_buck =
+ r*expr*buck1i[typej]-g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq;
+ if (eflag) evdwl = expr*buckai[typej]-g6*((a2+1.0)*a2+0.5)*x2;
+ }
+ else { // correct for special
+ register double f = special_lj[ni], t = rn*(1.0-f);
+ force_buck = f*r*expr*buck1i[typej]-
+ g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq+t*buck2i[typej];
+ if (eflag) evdwl = f*expr*buckai[typej] -
+ g6*((a2+1.0)*a2+0.5)*x2+t*buckci[typej];
+ }
+ }
+ else { // cut form
+ if (ni == 0) {
+ force_buck = r*expr*buck1i[typej]-rn*buck2i[typej];
+ if (eflag)
+ evdwl = expr*buckai[typej]-rn*buckci[typej]-offseti[typej];
+ }
+ else { // correct for special
+ register double f = special_lj[ni];
+ force_buck = f*(r*expr*buck1i[typej]-rn*buck2i[typej]);
+ if (eflag)
+ evdwl = f*(expr*buckai[typej]-rn*buckci[typej]-offseti[typej]);
+ }
+ }
}
else force_buck = respa_buck = evdwl = 0.0;
@@ -906,19 +906,19 @@ void PairBuckCoul::compute_outer(int eflag, int vflag)
frespa = fpair-(respa_coul+respa_buck)*r2inv;
if (newton_pair || j < nlocal) {
- register double *fj = f0+(j+(j<<1)), f;
- fi[0] += f = d[0]*frespa; fj[0] -= f;
- fi[1] += f = d[1]*frespa; fj[1] -= f;
- fi[2] += f = d[2]*frespa; fj[2] -= f;
+ register double *fj = f0+(j+(j<<1)), f;
+ fi[0] += f = d[0]*frespa; fj[0] -= f;
+ fi[1] += f = d[1]*frespa; fj[1] -= f;
+ fi[2] += f = d[2]*frespa; fj[2] -= f;
}
else {
- fi[0] += d[0]*frespa;
- fi[1] += d[1]*frespa;
- fi[2] += d[2]*frespa;
+ fi[0] += d[0]*frespa;
+ fi[1] += d[1]*frespa;
+ fi[2] += d[2]*frespa;
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
- evdwl,ecoul,fpair,d[0],d[1],d[2]);
+ evdwl,ecoul,fpair,d[0],d[1],d[2]);
}
}
}
@@ -935,17 +935,17 @@ void PairBuckCoul::init_tables()
tabinnersq = tabinner*tabinner;
init_bitmap(tabinner,cut_coul,ncoultablebits,
- masklo,maskhi,ncoulmask,ncoulshiftbits);
-
+ masklo,maskhi,ncoulmask,ncoulshiftbits);
+
int ntable = 1;
for (int i = 0; i < ncoultablebits; i++) ntable *= 2;
-
+
// linear lookup tables of length N = 2^ncoultablebits
// stored value = value at lower edge of bin
// d values = delta from lower edge to upper edge of bin
if (ftable) free_tables();
-
+
memory->create(rtable,ntable,"pair:rtable");
memory->create(ftable,ntable,"pair:ftable");
memory->create(ctable,ntable,"pair:ctable");
@@ -969,7 +969,7 @@ void PairBuckCoul::init_tables()
int itablemin;
minrsq_lookup.i = 0 << ncoulshiftbits;
minrsq_lookup.i |= maskhi;
-
+
for (int i = 0; i < ntable; i++) {
rsq_lookup.i = i << ncoulshiftbits;
rsq_lookup.i |= masklo;
@@ -994,23 +994,23 @@ void PairBuckCoul::init_tables()
ptable[i] = qqrd2e/r;
vtable[i] = qqrd2e/r * (derfc + EWALD_F*grij*expm2);
if (rsq_lookup.f > cut_respa[2]*cut_respa[2]) {
- if (rsq_lookup.f < cut_respa[3]*cut_respa[3]) {
- rsw = (r - cut_respa[2])/(cut_respa[3] - cut_respa[2]);
- ftable[i] += qqrd2e/r * rsw*rsw*(3.0 - 2.0*rsw);
- ctable[i] = qqrd2e/r * rsw*rsw*(3.0 - 2.0*rsw);
- } else {
- ftable[i] = qqrd2e/r * (derfc + EWALD_F*grij*expm2);
- ctable[i] = qqrd2e/r;
- }
+ if (rsq_lookup.f < cut_respa[3]*cut_respa[3]) {
+ rsw = (r - cut_respa[2])/(cut_respa[3] - cut_respa[2]);
+ ftable[i] += qqrd2e/r * rsw*rsw*(3.0 - 2.0*rsw);
+ ctable[i] = qqrd2e/r * rsw*rsw*(3.0 - 2.0*rsw);
+ } else {
+ ftable[i] = qqrd2e/r * (derfc + EWALD_F*grij*expm2);
+ ctable[i] = qqrd2e/r;
+ }
}
}
minrsq_lookup.f = MIN(minrsq_lookup.f,rsq_lookup.f);
}
tabinnersq = minrsq_lookup.f;
-
+
int ntablem1 = ntable - 1;
-
+
for (int i = 0; i < ntablem1; i++) {
drtable[i] = 1.0/(rtable[i+1] - rtable[i]);
dftable[i] = ftable[i+1] - ftable[i];
@@ -1024,10 +1024,10 @@ void PairBuckCoul::init_tables()
dptable[i] = ptable[i+1] - ptable[i];
}
}
-
- // get the delta values for the last table entries
+
+ // get the delta values for the last table entries
// tables are connected periodically between 0 and ntablem1
-
+
drtable[ntablem1] = 1.0/(rtable[0] - rtable[ntablem1]);
dftable[ntablem1] = ftable[0] - ftable[ntablem1];
dctable[ntablem1] = ctable[0] - ctable[ntablem1];
@@ -1037,23 +1037,23 @@ void PairBuckCoul::init_tables()
dptable[ntablem1] = ptable[0] - ptable[ntablem1];
}
- // get the correct delta values at itablemax
+ // get the correct delta values at itablemax
// smallest r is in bin itablemin
// largest r is in bin itablemax, which is itablemin-1,
// or ntablem1 if itablemin=0
// deltas at itablemax only needed if corresponding rsq < cut*cut
- // if so, compute deltas between rsq and cut*cut
-
+ // if so, compute deltas between rsq and cut*cut
+
double f_tmp,c_tmp,e_tmp,p_tmp = 0.0,v_tmp = 0.0;
itablemin = minrsq_lookup.i & ncoulmask;
- itablemin >>= ncoulshiftbits;
- int itablemax = itablemin - 1;
- if (itablemin == 0) itablemax = ntablem1;
+ itablemin >>= ncoulshiftbits;
+ int itablemax = itablemin - 1;
+ if (itablemin == 0) itablemax = ntablem1;
rsq_lookup.i = itablemax << ncoulshiftbits;
rsq_lookup.i |= maskhi;
if (rsq_lookup.f < cut_coulsq) {
- rsq_lookup.f = cut_coulsq;
+ rsq_lookup.f = cut_coulsq;
r = sqrtf(rsq_lookup.f);
grij = g_ewald * r;
expm2 = exp(-grij*grij);
@@ -1071,7 +1071,7 @@ void PairBuckCoul::init_tables()
v_tmp = qqrd2e/r * (derfc + EWALD_F*grij*expm2);
if (rsq_lookup.f > cut_respa[2]*cut_respa[2]) {
if (rsq_lookup.f < cut_respa[3]*cut_respa[3]) {
- rsw = (r - cut_respa[2])/(cut_respa[3] - cut_respa[2]);
+ rsw = (r - cut_respa[2])/(cut_respa[3] - cut_respa[2]);
f_tmp += qqrd2e/r * rsw*rsw*(3.0 - 2.0*rsw);
c_tmp = qqrd2e/r * rsw*rsw*(3.0 - 2.0*rsw);
} else {
@@ -1081,14 +1081,14 @@ void PairBuckCoul::init_tables()
}
}
- drtable[itablemax] = 1.0/(rsq_lookup.f - rtable[itablemax]);
+ drtable[itablemax] = 1.0/(rsq_lookup.f - rtable[itablemax]);
dftable[itablemax] = f_tmp - ftable[itablemax];
dctable[itablemax] = c_tmp - ctable[itablemax];
detable[itablemax] = e_tmp - etable[itablemax];
if (cut_respa) {
dvtable[itablemax] = v_tmp - vtable[itablemax];
dptable[itablemax] = p_tmp - ptable[itablemax];
- }
+ }
}
}
@@ -1115,8 +1115,8 @@ void PairBuckCoul::free_tables()
/* ---------------------------------------------------------------------- */
double PairBuckCoul::single(int i, int j, int itype, int jtype,
- double rsq, double factor_coul, double factor_buck,
- double &fforce)
+ double rsq, double factor_coul, double factor_buck,
+ double &fforce)
{
double f, r, r2inv, r6inv, force_coul, force_buck;
double g2 = g_ewald*g_ewald, g6 = g2*g2*g2, g8 = g6*g2, *q = atom->q;
@@ -1125,15 +1125,15 @@ double PairBuckCoul::single(int i, int j, int itype, int jtype,
r2inv = 1.0/rsq;
double eng = 0.0;
- if ((ewald_order&2) && (rsq < cut_coulsq)) { // coulombic
- if (!ncoultablebits || rsq <= tabinnersq) { // series real space
+ if ((ewald_order&2) && (rsq < cut_coulsq)) { // coulombic
+ if (!ncoultablebits || rsq <= tabinnersq) { // series real space
register double x = g_ewald*r;
register double s = force->qqrd2e*q[i]*q[j], t = 1.0/(1.0+EWALD_P*x);
f = s*(1.0-factor_coul)/r; s *= g_ewald*exp(-x*x);
force_coul = (t *= ((((t*A5+A4)*t+A3)*t+A2)*t+A1)*s/x)+EWALD_F*s-f;
eng += t-f;
}
- else { // table real space
+ else { // table real space
register union_int_float_t t;
t.f = rsq;
register const int k = (t.i & ncoulmask) >> ncoulshiftbits;
@@ -1143,23 +1143,23 @@ double PairBuckCoul::single(int i, int j, int itype, int jtype,
eng += qiqj*(etable[k]+f*detable[k]-t.f);
}
} else force_coul = 0.0;
-
- if (rsq < cut_bucksq[itype][jtype]) { // buckingham
+
+ if (rsq < cut_bucksq[itype][jtype]) { // buckingham
register double expr = factor_buck*exp(-sqrt(rsq)*rhoinv[itype][jtype]);
r6inv = r2inv*r2inv*r2inv;
- if (ewald_order&64) { // long-range
+ if (ewald_order&64) { // long-range
register double x2 = g2*rsq, a2 = 1.0/x2, t = r6inv*(1.0-factor_buck);
x2 = a2*exp(-x2)*buck_c[itype][jtype];
force_buck = buck1[itype][jtype]*r*expr-
- g8*(((6.0*a2+6.0)*a2+3.0)*a2+a2)*x2*rsq+t*buck2[itype][jtype];
+ g8*(((6.0*a2+6.0)*a2+3.0)*a2+a2)*x2*rsq+t*buck2[itype][jtype];
eng += buck_a[itype][jtype]*expr-
- g6*((a2+1.0)*a2+0.5)*x2+t*buck_c[itype][jtype];
+ g6*((a2+1.0)*a2+0.5)*x2+t*buck_c[itype][jtype];
}
- else { // cut
- force_buck =
- buck1[itype][jtype]*r*expr-factor_buck*buck_c[itype][jtype]*r6inv;
+ else { // cut
+ force_buck =
+ buck1[itype][jtype]*r*expr-factor_buck*buck_c[itype][jtype]*r6inv;
eng += buck_a[itype][jtype]*expr-
- factor_buck*(buck_c[itype][jtype]*r6inv-offset[itype][jtype]);
+ factor_buck*(buck_c[itype][jtype]*r6inv-offset[itype][jtype]);
}
} else force_buck = 0.0;
diff --git a/src/USER-EWALDN/pair_buck_coul.h b/src/USER-EWALDN/pair_buck_coul.h
index 5b9d406cbc87f411ba5f7b1d47fae7760b3eca9b..6c29b134195684cd9a47c681afcde660217c053a 100644
--- a/src/USER-EWALDN/pair_buck_coul.h
+++ b/src/USER-EWALDN/pair_buck_coul.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -39,7 +39,7 @@ class PairBuckCoul : public Pair {
double init_one(int, int);
void write_restart(FILE *);
void read_restart(FILE *);
-
+
void write_restart_settings(FILE *);
void read_restart_settings(FILE *);
double single(int, int, int, int, double, double, double, double &);
diff --git a/src/USER-EWALDN/pair_lj_coul.cpp b/src/USER-EWALDN/pair_lj_coul.cpp
index 181127870472952b3a8dddd241781dac52d2bab5..c38ad6b6f498626b2cb0ee58fabf24bfdcf8561a 100644
--- a/src/USER-EWALDN/pair_lj_coul.cpp
+++ b/src/USER-EWALDN/pair_lj_coul.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -56,12 +56,12 @@ PairLJCoul::PairLJCoul(LAMMPS *lmp) : Pair(lmp)
global settings
------------------------------------------------------------------------- */
-#define PAIR_ILLEGAL "Illegal pair_style lj/coul command"
-#define PAIR_CUTOFF "Only one cut-off allowed when requesting all long"
-#define PAIR_MISSING "Cut-offs missing in pair_style lj/coul"
-#define PAIR_COUL_CUT "Coulombic cut not supported in pair_style lj/coul"
-#define PAIR_LARGEST "Using largest cut-off for lj/coul long long"
-#define PAIR_MIX "Mixing forced for lj coefficients"
+#define PAIR_ILLEGAL "Illegal pair_style lj/coul command"
+#define PAIR_CUTOFF "Only one cut-off allowed when requesting all long"
+#define PAIR_MISSING "Cut-offs missing in pair_style lj/coul"
+#define PAIR_COUL_CUT "Coulombic cut not supported in pair_style lj/coul"
+#define PAIR_LARGEST "Using largest cut-off for lj/coul long long"
+#define PAIR_MIX "Mixing forced for lj coefficients"
void PairLJCoul::options(char **arg, int order)
{
@@ -72,8 +72,8 @@ void PairLJCoul::options(char **arg, int order)
for (i=0; option[i]&&strcmp(arg[0], option[i]); ++i);
switch (i) {
default: error->all(FLERR,PAIR_ILLEGAL);
- case 0: ewald_order |= 1<<order; break; // set kspace r^-order
- case 2: ewald_off |= 1<<order; // turn r^-order off
+ case 0: ewald_order |= 1<<order; break; // set kspace r^-order
+ case 2: ewald_off |= 1<<order; // turn r^-order off
case 1: break;
}
}
@@ -96,11 +96,11 @@ void PairLJCoul::settings(int narg, char **arg)
if (narg == 4) cut_coul = force->numeric(*arg);
else cut_coul = cut_lj_global;
- if (allocated) { // reset explicit cuts
+ if (allocated) { // reset explicit cuts
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
- if (setflag[i][j]) cut_lj[i][j] = cut_lj_global;
+ if (setflag[i][j]) cut_lj[i][j] = cut_lj_global;
}
}
@@ -226,7 +226,7 @@ void PairLJCoul::init_style()
if (!atom->q_flag && (ewald_order&(1<<1)))
error->all(FLERR,
- "Invoking coulombic in pair style lj/coul requires atom attribute q");
+ "Invoking coulombic in pair style lj/coul requires atom attribute q");
// request regular or rRESPA neighbor lists
@@ -275,14 +275,14 @@ void PairLJCoul::init_style()
// ensure use of KSpace long-range solver, set g_ewald
- if (ewald_order&(1<<1)) { // r^-1 kspace
- if (force->kspace == NULL)
+ if (ewald_order&(1<<1)) { // r^-1 kspace
+ if (force->kspace == NULL)
error->all(FLERR,"Pair style is incompatible with KSpace style");
for (i=0; style1[i]&&strcmp(force->kspace_style, style1[i]); ++i);
if (!style1[i]) error->all(FLERR,"Pair style is incompatible with KSpace style");
}
- if (ewald_order&(1<<6)) { // r^-6 kspace
- if (force->kspace == NULL)
+ if (ewald_order&(1<<6)) { // r^-6 kspace
+ if (force->kspace == NULL)
error->all(FLERR,"Pair style is incompatible with KSpace style");
for (i=0; style6[i]&&strcmp(force->kspace_style, style6[i]); ++i);
if (!style6[i]) error->all(FLERR,"Pair style is incompatible with KSpace style");
@@ -315,7 +315,7 @@ double PairLJCoul::init_one(int i, int j)
{
if ((ewald_order&(1<<6))||(setflag[i][j] == 0)) {
epsilon[i][j] = mix_energy(epsilon_read[i][i],epsilon_read[j][j],
- sigma_read[i][i],sigma_read[j][j]);
+ sigma_read[i][i],sigma_read[j][j]);
sigma[i][j] = mix_distance(sigma_read[i][i],sigma_read[j][j]);
if (ewald_order&(1<<6))
cut_lj[i][j] = cut_lj_global;
@@ -341,7 +341,7 @@ double PairLJCoul::init_one(int i, int j)
if (cut_respa && MIN(cut_lj[i][j],cut_coul) < cut_respa[3])
error->all(FLERR,"Pair cutoff < Respa interior cutoff");
-
+
if (offset_flag) {
double ratio = sigma[i][j] / cut_lj[i][j];
offset[i][j] = 4.0 * epsilon[i][j] * (pow(ratio,12.0) - pow(ratio,6.0));
@@ -371,9 +371,9 @@ void PairLJCoul::write_restart(FILE *fp)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
- fwrite(&epsilon_read[i][j],sizeof(double),1,fp);
- fwrite(&sigma_read[i][j],sizeof(double),1,fp);
- fwrite(&cut_lj_read[i][j],sizeof(double),1,fp);
+ fwrite(&epsilon_read[i][j],sizeof(double),1,fp);
+ fwrite(&sigma_read[i][j],sizeof(double),1,fp);
+ fwrite(&cut_lj_read[i][j],sizeof(double),1,fp);
}
}
}
@@ -395,14 +395,14 @@ void PairLJCoul::read_restart(FILE *fp)
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
- if (me == 0) {
- fread(&epsilon_read[i][j],sizeof(double),1,fp);
- fread(&sigma_read[i][j],sizeof(double),1,fp);
- fread(&cut_lj_read[i][j],sizeof(double),1,fp);
- }
- MPI_Bcast(&epsilon_read[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&sigma_read[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&cut_lj_read[i][j],1,MPI_DOUBLE,0,world);
+ if (me == 0) {
+ fread(&epsilon_read[i][j],sizeof(double),1,fp);
+ fread(&sigma_read[i][j],sizeof(double),1,fp);
+ fread(&cut_lj_read[i][j],sizeof(double),1,fp);
+ }
+ MPI_Bcast(&epsilon_read[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&sigma_read[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut_lj_read[i][j],1,MPI_DOUBLE,0,world);
}
}
}
@@ -450,7 +450,7 @@ void PairLJCoul::compute(int eflag, int vflag)
evdwl = ecoul = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
-
+
double **x = atom->x, *x0 = x[0];
double **f = atom->f, *f0 = f[0], *fi = f0;
double *q = atom->q;
@@ -471,112 +471,112 @@ void PairLJCoul::compute(int eflag, int vflag)
ineighn = (ineigh = list->ilist)+list->inum;
- for (; ineigh<ineighn; ++ineigh) { // loop over my atoms
+ for (; ineigh<ineighn; ++ineigh) { // loop over my atoms
i = *ineigh; fi = f0+3*i;
- if (order1) qri = (qi = q[i])*qqrd2e; // initialize constants
+ if (order1) qri = (qi = q[i])*qqrd2e; // initialize constants
offseti = offset[typei = type[i]];
lj1i = lj1[typei]; lj2i = lj2[typei]; lj3i = lj3[typei]; lj4i = lj4[typei];
cutsqi = cutsq[typei]; cut_ljsqi = cut_ljsq[typei];
memcpy(xi, x0+(i+(i<<1)), sizeof(vector));
jneighn = (jneigh = list->firstneigh[i])+list->numneigh[i];
- for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
+ for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
j = *jneigh;
ni = sbmask(j);
j &= NEIGHMASK;
-
+
{ register double *xj = x0+(j+(j<<1));
- d[0] = xi[0] - xj[0]; // pair vector
- d[1] = xi[1] - xj[1];
- d[2] = xi[2] - xj[2]; }
+ d[0] = xi[0] - xj[0]; // pair vector
+ d[1] = xi[1] - xj[1];
+ d[2] = xi[2] - xj[2]; }
if ((rsq = vec_dot(d, d)) >= cutsqi[typej = type[j]]) continue;
r2inv = 1.0/rsq;
- if (order1 && (rsq < cut_coulsq)) { // coulombic
- if (!ncoultablebits || rsq <= tabinnersq) { // series real space
- register double r = sqrt(rsq), x = g_ewald*r;
- register double s = qri*q[j], t = 1.0/(1.0+EWALD_P*x);
- if (ni == 0) {
- s *= g_ewald*exp(-x*x);
- force_coul = (t *= ((((t*A5+A4)*t+A3)*t+A2)*t+A1)*s/x)+EWALD_F*s;
- if (eflag) ecoul = t;
- }
- else { // special case
- r = s*(1.0-special_coul[ni])/r; s *= g_ewald*exp(-x*x);
- force_coul = (t *= ((((t*A5+A4)*t+A3)*t+A2)*t+A1)*s/x)+EWALD_F*s-r;
- if (eflag) ecoul = t-r;
- }
- } // table real space
- else {
- register union_int_float_t t;
- t.f = rsq;
- register const int k = (t.i & ncoulmask)>>ncoulshiftbits;
- register double f = (rsq-rtable[k])*drtable[k], qiqj = qi*q[j];
- if (ni == 0) {
- force_coul = qiqj*(ftable[k]+f*dftable[k]);
- if (eflag) ecoul = qiqj*(etable[k]+f*detable[k]);
- }
- else { // special case
- t.f = (1.0-special_coul[ni])*(ctable[k]+f*dctable[k]);
- force_coul = qiqj*(ftable[k]+f*dftable[k]-t.f);
- if (eflag) ecoul = qiqj*(etable[k]+f*detable[k]-t.f);
- }
- }
+ if (order1 && (rsq < cut_coulsq)) { // coulombic
+ if (!ncoultablebits || rsq <= tabinnersq) { // series real space
+ register double r = sqrt(rsq), x = g_ewald*r;
+ register double s = qri*q[j], t = 1.0/(1.0+EWALD_P*x);
+ if (ni == 0) {
+ s *= g_ewald*exp(-x*x);
+ force_coul = (t *= ((((t*A5+A4)*t+A3)*t+A2)*t+A1)*s/x)+EWALD_F*s;
+ if (eflag) ecoul = t;
+ }
+ else { // special case
+ r = s*(1.0-special_coul[ni])/r; s *= g_ewald*exp(-x*x);
+ force_coul = (t *= ((((t*A5+A4)*t+A3)*t+A2)*t+A1)*s/x)+EWALD_F*s-r;
+ if (eflag) ecoul = t-r;
+ }
+ } // table real space
+ else {
+ register union_int_float_t t;
+ t.f = rsq;
+ register const int k = (t.i & ncoulmask)>>ncoulshiftbits;
+ register double f = (rsq-rtable[k])*drtable[k], qiqj = qi*q[j];
+ if (ni == 0) {
+ force_coul = qiqj*(ftable[k]+f*dftable[k]);
+ if (eflag) ecoul = qiqj*(etable[k]+f*detable[k]);
+ }
+ else { // special case
+ t.f = (1.0-special_coul[ni])*(ctable[k]+f*dctable[k]);
+ force_coul = qiqj*(ftable[k]+f*dftable[k]-t.f);
+ if (eflag) ecoul = qiqj*(etable[k]+f*detable[k]-t.f);
+ }
+ }
}
else force_coul = ecoul = 0.0;
- if (rsq < cut_ljsqi[typej]) { // lj
- if (order6) { // long-range lj
- register double rn = r2inv*r2inv*r2inv;
- register double x2 = g2*rsq, a2 = 1.0/x2;
- x2 = a2*exp(-x2)*lj4i[typej];
- if (ni == 0) {
- force_lj =
- (rn*=rn)*lj1i[typej]-g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq;
- if (eflag)
- evdwl = rn*lj3i[typej]-g6*((a2+1.0)*a2+0.5)*x2;
- }
- else { // special case
- register double f = special_lj[ni], t = rn*(1.0-f);
- force_lj = f*(rn *= rn)*lj1i[typej]-
- g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq+t*lj2i[typej];
- if (eflag)
- evdwl = f*rn*lj3i[typej]-g6*((a2+1.0)*a2+0.5)*x2+t*lj4i[typej];
- }
- }
- else { // cut lj
- register double rn = r2inv*r2inv*r2inv;
- if (ni == 0) {
- force_lj = rn*(rn*lj1i[typej]-lj2i[typej]);
- if (eflag) evdwl = rn*(rn*lj3i[typej]-lj4i[typej])-offseti[typej];
- }
- else { // special case
- register double f = special_lj[ni];
- force_lj = f*rn*(rn*lj1i[typej]-lj2i[typej]);
- if (eflag)
- evdwl = f * (rn*(rn*lj3i[typej]-lj4i[typej])-offseti[typej]);
- }
- }
+ if (rsq < cut_ljsqi[typej]) { // lj
+ if (order6) { // long-range lj
+ register double rn = r2inv*r2inv*r2inv;
+ register double x2 = g2*rsq, a2 = 1.0/x2;
+ x2 = a2*exp(-x2)*lj4i[typej];
+ if (ni == 0) {
+ force_lj =
+ (rn*=rn)*lj1i[typej]-g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq;
+ if (eflag)
+ evdwl = rn*lj3i[typej]-g6*((a2+1.0)*a2+0.5)*x2;
+ }
+ else { // special case
+ register double f = special_lj[ni], t = rn*(1.0-f);
+ force_lj = f*(rn *= rn)*lj1i[typej]-
+ g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq+t*lj2i[typej];
+ if (eflag)
+ evdwl = f*rn*lj3i[typej]-g6*((a2+1.0)*a2+0.5)*x2+t*lj4i[typej];
+ }
+ }
+ else { // cut lj
+ register double rn = r2inv*r2inv*r2inv;
+ if (ni == 0) {
+ force_lj = rn*(rn*lj1i[typej]-lj2i[typej]);
+ if (eflag) evdwl = rn*(rn*lj3i[typej]-lj4i[typej])-offseti[typej];
+ }
+ else { // special case
+ register double f = special_lj[ni];
+ force_lj = f*rn*(rn*lj1i[typej]-lj2i[typej]);
+ if (eflag)
+ evdwl = f * (rn*(rn*lj3i[typej]-lj4i[typej])-offseti[typej]);
+ }
+ }
}
else force_lj = evdwl = 0.0;
fpair = (force_coul+force_lj)*r2inv;
if (newton_pair || j < nlocal) {
- register double *fj = f0+(j+(j<<1)), f;
- fi[0] += f = d[0]*fpair; fj[0] -= f;
- fi[1] += f = d[1]*fpair; fj[1] -= f;
- fi[2] += f = d[2]*fpair; fj[2] -= f;
+ register double *fj = f0+(j+(j<<1)), f;
+ fi[0] += f = d[0]*fpair; fj[0] -= f;
+ fi[1] += f = d[1]*fpair; fj[1] -= f;
+ fi[2] += f = d[2]*fpair; fj[2] -= f;
}
else {
- fi[0] += d[0]*fpair;
- fi[1] += d[1]*fpair;
- fi[2] += d[2]*fpair;
+ fi[0] += d[0]*fpair;
+ fi[1] += d[1]*fpair;
+ fi[2] += d[2]*fpair;
}
-
+
if (evflag) ev_tally(i,j,nlocal,newton_pair,
- evdwl,ecoul,fpair,d[0],d[1],d[2]);
+ evdwl,ecoul,fpair,d[0],d[1],d[2]);
}
}
@@ -599,7 +599,7 @@ void PairLJCoul::compute_inner()
double cut_out_on = cut_respa[0];
double cut_out_off = cut_respa[1];
-
+
double cut_out_diff = cut_out_off - cut_out_on;
double cut_out_on_sq = cut_out_on*cut_out_on;
double cut_out_off_sq = cut_out_off*cut_out_off;
@@ -611,7 +611,7 @@ void PairLJCoul::compute_inner()
ineighn = (ineigh = list->ilist)+list->inum;
- for (; ineigh<ineighn; ++ineigh) { // loop over my atoms
+ for (; ineigh<ineighn; ++ineigh) { // loop over my atoms
i = *ineigh; fi = f0+3*i;
qri = qqrd2e*q[i];
memcpy(xi, x0+(i+(i<<1)), sizeof(vector));
@@ -619,48 +619,48 @@ void PairLJCoul::compute_inner()
lj1i = lj1[typei]; lj2i = lj2[typei];
jneighn = (jneigh = list->firstneigh[i])+list->numneigh[i];
- for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
+ for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
j = *jneigh;
ni = sbmask(j);
j &= NEIGHMASK;
-
+
{ register double *xj = x0+(j+(j<<1));
- d[0] = xi[0] - xj[0]; // pair vector
- d[1] = xi[1] - xj[1];
- d[2] = xi[2] - xj[2]; }
+ d[0] = xi[0] - xj[0]; // pair vector
+ d[1] = xi[1] - xj[1];
+ d[2] = xi[2] - xj[2]; }
if ((rsq = vec_dot(d, d)) >= cut_out_off_sq) continue;
r2inv = 1.0/rsq;
- if (order1 && (rsq < cut_coulsq)) // coulombic
- force_coul = ni == 0 ?
- qri*q[j]*sqrt(r2inv) : qri*q[j]*sqrt(r2inv)*special_coul[ni];
+ if (order1 && (rsq < cut_coulsq)) // coulombic
+ force_coul = ni == 0 ?
+ qri*q[j]*sqrt(r2inv) : qri*q[j]*sqrt(r2inv)*special_coul[ni];
- if (rsq < cut_ljsqi[typej = type[j]]) { // lennard-jones
- register double rn = r2inv*r2inv*r2inv;
- force_lj = ni == 0 ?
- rn*(rn*lj1i[typej]-lj2i[typej]) :
- rn*(rn*lj1i[typej]-lj2i[typej])*special_lj[ni];
+ if (rsq < cut_ljsqi[typej = type[j]]) { // lennard-jones
+ register double rn = r2inv*r2inv*r2inv;
+ force_lj = ni == 0 ?
+ rn*(rn*lj1i[typej]-lj2i[typej]) :
+ rn*(rn*lj1i[typej]-lj2i[typej])*special_lj[ni];
}
else force_lj = 0.0;
fpair = (force_coul + force_lj) * r2inv;
-
- if (rsq > cut_out_on_sq) { // switching
- register double rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
- fpair *= 1.0 + rsw*rsw*(2.0*rsw-3.0);
+
+ if (rsq > cut_out_on_sq) { // switching
+ register double rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
+ fpair *= 1.0 + rsw*rsw*(2.0*rsw-3.0);
}
- if (newton_pair || j < nlocal) { // force update
- register double *fj = f0+(j+(j<<1)), f;
- fi[0] += f = d[0]*fpair; fj[0] -= f;
- fi[1] += f = d[1]*fpair; fj[1] -= f;
- fi[2] += f = d[2]*fpair; fj[2] -= f;
+ if (newton_pair || j < nlocal) { // force update
+ register double *fj = f0+(j+(j<<1)), f;
+ fi[0] += f = d[0]*fpair; fj[0] -= f;
+ fi[1] += f = d[1]*fpair; fj[1] -= f;
+ fi[2] += f = d[2]*fpair; fj[2] -= f;
}
else {
- fi[0] += d[0]*fpair;
- fi[1] += d[1]*fpair;
- fi[2] += d[2]*fpair;
+ fi[0] += d[0]*fpair;
+ fi[1] += d[1]*fpair;
+ fi[2] += d[2]*fpair;
}
}
}
@@ -699,7 +699,7 @@ void PairLJCoul::compute_middle()
ineighn = (ineigh = list->ilist)+list->inum;
- for (; ineigh<ineighn; ++ineigh) { // loop over my atoms
+ for (; ineigh<ineighn; ++ineigh) { // loop over my atoms
i = *ineigh; fi = f0+3*i;
qri = qqrd2e*q[i];
memcpy(xi, x0+(i+(i<<1)), sizeof(vector));
@@ -711,49 +711,49 @@ void PairLJCoul::compute_middle()
j = *jneigh;
ni = sbmask(j);
j &= NEIGHMASK;
-
+
{ register double *xj = x0+(j+(j<<1));
- d[0] = xi[0] - xj[0]; // pair vector
- d[1] = xi[1] - xj[1];
- d[2] = xi[2] - xj[2]; }
+ d[0] = xi[0] - xj[0]; // pair vector
+ d[1] = xi[1] - xj[1];
+ d[2] = xi[2] - xj[2]; }
if ((rsq = vec_dot(d, d)) >= cut_out_off_sq) continue;
if (rsq <= cut_in_off_sq) continue;
r2inv = 1.0/rsq;
- if (order1 && (rsq < cut_coulsq)) // coulombic
- force_coul = ni == 0 ?
- qri*q[j]*sqrt(r2inv) : qri*q[j]*sqrt(r2inv)*special_coul[ni];
+ if (order1 && (rsq < cut_coulsq)) // coulombic
+ force_coul = ni == 0 ?
+ qri*q[j]*sqrt(r2inv) : qri*q[j]*sqrt(r2inv)*special_coul[ni];
- if (rsq < cut_ljsqi[typej = type[j]]) { // lennard-jones
- register double rn = r2inv*r2inv*r2inv;
- force_lj = ni == 0 ?
- rn*(rn*lj1i[typej]-lj2i[typej]) :
- rn*(rn*lj1i[typej]-lj2i[typej])*special_lj[ni];
+ if (rsq < cut_ljsqi[typej = type[j]]) { // lennard-jones
+ register double rn = r2inv*r2inv*r2inv;
+ force_lj = ni == 0 ?
+ rn*(rn*lj1i[typej]-lj2i[typej]) :
+ rn*(rn*lj1i[typej]-lj2i[typej])*special_lj[ni];
}
else force_lj = 0.0;
fpair = (force_coul + force_lj) * r2inv;
-
- if (rsq < cut_in_on_sq) { // switching
- register double rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff;
- fpair *= rsw*rsw*(3.0 - 2.0*rsw);
+
+ if (rsq < cut_in_on_sq) { // switching
+ register double rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff;
+ fpair *= rsw*rsw*(3.0 - 2.0*rsw);
}
if (rsq > cut_out_on_sq) {
- register double rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
- fpair *= 1.0 + rsw*rsw*(2.0*rsw-3.0);
+ register double rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
+ fpair *= 1.0 + rsw*rsw*(2.0*rsw-3.0);
}
- if (newton_pair || j < nlocal) { // force update
- register double *fj = f0+(j+(j<<1)), f;
- fi[0] += f = d[0]*fpair; fj[0] -= f;
- fi[1] += f = d[1]*fpair; fj[1] -= f;
- fi[2] += f = d[2]*fpair; fj[2] -= f;
+ if (newton_pair || j < nlocal) { // force update
+ register double *fj = f0+(j+(j<<1)), f;
+ fi[0] += f = d[0]*fpair; fj[0] -= f;
+ fi[1] += f = d[1]*fpair; fj[1] -= f;
+ fi[2] += f = d[2]*fpair; fj[2] -= f;
}
else {
- fi[0] += d[0]*fpair;
- fi[1] += d[1]*fpair;
- fi[2] += d[2]*fpair;
+ fi[0] += d[0]*fpair;
+ fi[1] += d[1]*fpair;
+ fi[2] += d[2]*fpair;
}
}
}
@@ -780,7 +780,7 @@ void PairLJCoul::compute_outer(int eflag, int vflag)
int i, j, order1 = ewald_order&(1<<1), order6 = ewald_order&(1<<6);
int *ineigh, *ineighn, *jneigh, *jneighn, typei, typej, ni, respa_flag;
- double qi = 0.0, qri = 0.0;
+ double qi = 0.0, qri = 0.0;
double *cutsqi, *cut_ljsqi, *lj1i, *lj2i, *lj3i, *lj4i, *offseti;
double rsq, r2inv, force_coul, force_lj;
double g2 = g_ewald*g_ewald, g6 = g2*g2*g2, g8 = g6*g2;
@@ -796,104 +796,104 @@ void PairLJCoul::compute_outer(int eflag, int vflag)
ineighn = (ineigh = list->ilist)+list->inum;
- for (; ineigh<ineighn; ++ineigh) { // loop over my atoms
+ for (; ineigh<ineighn; ++ineigh) { // loop over my atoms
i = *ineigh; fi = f0+3*i;
- if (order1) qri = (qi = q[i])*qqrd2e; // initialize constants
+ if (order1) qri = (qi = q[i])*qqrd2e; // initialize constants
offseti = offset[typei = type[i]];
lj1i = lj1[typei]; lj2i = lj2[typei]; lj3i = lj3[typei]; lj4i = lj4[typei];
cutsqi = cutsq[typei]; cut_ljsqi = cut_ljsq[typei];
memcpy(xi, x0+(i+(i<<1)), sizeof(vector));
jneighn = (jneigh = list->firstneigh[i])+list->numneigh[i];
- for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
+ for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
j = *jneigh;
ni = sbmask(j);
j &= NEIGHMASK;
{ register double *xj = x0+(j+(j<<1));
- d[0] = xi[0] - xj[0]; // pair vector
- d[1] = xi[1] - xj[1];
- d[2] = xi[2] - xj[2]; }
+ d[0] = xi[0] - xj[0]; // pair vector
+ d[1] = xi[1] - xj[1];
+ d[2] = xi[2] - xj[2]; }
if ((rsq = vec_dot(d, d)) >= cutsqi[typej = type[j]]) continue;
r2inv = 1.0/rsq;
if ((respa_flag = (rsq>cut_in_off_sq)&&(rsq<cut_in_on_sq))) {
- register double rsw = (sqrt(rsq)-cut_in_off)/cut_in_diff;
- frespa = rsw*rsw*(3.0-2.0*rsw);
+ register double rsw = (sqrt(rsq)-cut_in_off)/cut_in_diff;
+ frespa = rsw*rsw*(3.0-2.0*rsw);
}
- if (order1 && (rsq < cut_coulsq)) { // coulombic
- if (!ncoultablebits || rsq <= tabinnersq) { // series real space
- register double r = sqrt(rsq), s = qri*q[j];
- if (respa_flag) // correct for respa
- respa_coul = ni == 0 ? frespa*s/r : frespa*s/r*special_coul[ni];
- register double x = g_ewald*r, t = 1.0/(1.0+EWALD_P*x);
- if (ni == 0) {
- s *= g_ewald*exp(-x*x);
- force_coul = (t *= ((((t*A5+A4)*t+A3)*t+A2)*t+A1)*s/x)+EWALD_F*s;
- if (eflag) ecoul = t;
- }
- else { // correct for special
- r = s*(1.0-special_coul[ni])/r; s *= g_ewald*exp(-x*x);
- force_coul = (t *= ((((t*A5+A4)*t+A3)*t+A2)*t+A1)*s/x)+EWALD_F*s-r;
- if (eflag) ecoul = t-r;
- }
- } // table real space
- else {
- if (respa_flag) respa_coul = ni == 0 ? // correct for respa
- frespa*qri*q[j]/sqrt(rsq) :
- frespa*qri*q[j]/sqrt(rsq)*special_coul[ni];
- register union_int_float_t t;
- t.f = rsq;
- register const int k = (t.i & ncoulmask) >> ncoulshiftbits;
- register double f = (rsq-rtable[k])*drtable[k], qiqj = qi*q[j];
- if (ni == 0) {
- force_coul = qiqj*(ftable[k]+f*dftable[k]);
- if (eflag) ecoul = qiqj*(etable[k]+f*detable[k]);
- }
- else { // correct for special
- t.f = (1.0-special_coul[ni])*(ctable[k]+f*dctable[k]);
- force_coul = qiqj*(ftable[k]+f*dftable[k]-t.f);
- if (eflag) ecoul = qiqj*(etable[k]+f*detable[k]-t.f);
- }
- }
+ if (order1 && (rsq < cut_coulsq)) { // coulombic
+ if (!ncoultablebits || rsq <= tabinnersq) { // series real space
+ register double r = sqrt(rsq), s = qri*q[j];
+ if (respa_flag) // correct for respa
+ respa_coul = ni == 0 ? frespa*s/r : frespa*s/r*special_coul[ni];
+ register double x = g_ewald*r, t = 1.0/(1.0+EWALD_P*x);
+ if (ni == 0) {
+ s *= g_ewald*exp(-x*x);
+ force_coul = (t *= ((((t*A5+A4)*t+A3)*t+A2)*t+A1)*s/x)+EWALD_F*s;
+ if (eflag) ecoul = t;
+ }
+ else { // correct for special
+ r = s*(1.0-special_coul[ni])/r; s *= g_ewald*exp(-x*x);
+ force_coul = (t *= ((((t*A5+A4)*t+A3)*t+A2)*t+A1)*s/x)+EWALD_F*s-r;
+ if (eflag) ecoul = t-r;
+ }
+ } // table real space
+ else {
+ if (respa_flag) respa_coul = ni == 0 ? // correct for respa
+ frespa*qri*q[j]/sqrt(rsq) :
+ frespa*qri*q[j]/sqrt(rsq)*special_coul[ni];
+ register union_int_float_t t;
+ t.f = rsq;
+ register const int k = (t.i & ncoulmask) >> ncoulshiftbits;
+ register double f = (rsq-rtable[k])*drtable[k], qiqj = qi*q[j];
+ if (ni == 0) {
+ force_coul = qiqj*(ftable[k]+f*dftable[k]);
+ if (eflag) ecoul = qiqj*(etable[k]+f*detable[k]);
+ }
+ else { // correct for special
+ t.f = (1.0-special_coul[ni])*(ctable[k]+f*dctable[k]);
+ force_coul = qiqj*(ftable[k]+f*dftable[k]-t.f);
+ if (eflag) ecoul = qiqj*(etable[k]+f*detable[k]-t.f);
+ }
+ }
}
else force_coul = respa_coul = ecoul = 0.0;
- if (rsq < cut_ljsqi[typej]) { // lennard-jones
- register double rn = r2inv*r2inv*r2inv;
- if (respa_flag) respa_lj = ni == 0 ? // correct for respa
- frespa*rn*(rn*lj1i[typej]-lj2i[typej]) :
- frespa*rn*(rn*lj1i[typej]-lj2i[typej])*special_lj[ni];
- if (order6) { // long-range form
- register double x2 = g2*rsq, a2 = 1.0/x2;
- x2 = a2*exp(-x2)*lj4i[typej];
- if (ni == 0) {
- force_lj =
- (rn*=rn)*lj1i[typej]-g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq;
- if (eflag) evdwl = rn*lj3i[typej]-g6*((a2+1.0)*a2+0.5)*x2;
- }
- else { // correct for special
- register double f = special_lj[ni], t = rn*(1.0-f);
- force_lj = f*(rn *= rn)*lj1i[typej]-
- g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq+t*lj2i[typej];
- if (eflag)
- evdwl = f*rn*lj3i[typej]-g6*((a2+1.0)*a2+0.5)*x2+t*lj4i[typej];
- }
- }
- else { // cut form
- if (ni == 0) {
- force_lj = rn*(rn*lj1i[typej]-lj2i[typej]);
- if (eflag) evdwl = rn*(rn*lj3i[typej]-lj4i[typej])-offseti[typej];
- }
- else { // correct for special
- register double f = special_lj[ni];
- force_lj = f*rn*(rn*lj1i[typej]-lj2i[typej]);
- if (eflag)
- evdwl = f*(rn*(rn*lj3i[typej]-lj4i[typej])-offseti[typej]);
- }
- }
+ if (rsq < cut_ljsqi[typej]) { // lennard-jones
+ register double rn = r2inv*r2inv*r2inv;
+ if (respa_flag) respa_lj = ni == 0 ? // correct for respa
+ frespa*rn*(rn*lj1i[typej]-lj2i[typej]) :
+ frespa*rn*(rn*lj1i[typej]-lj2i[typej])*special_lj[ni];
+ if (order6) { // long-range form
+ register double x2 = g2*rsq, a2 = 1.0/x2;
+ x2 = a2*exp(-x2)*lj4i[typej];
+ if (ni == 0) {
+ force_lj =
+ (rn*=rn)*lj1i[typej]-g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq;
+ if (eflag) evdwl = rn*lj3i[typej]-g6*((a2+1.0)*a2+0.5)*x2;
+ }
+ else { // correct for special
+ register double f = special_lj[ni], t = rn*(1.0-f);
+ force_lj = f*(rn *= rn)*lj1i[typej]-
+ g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq+t*lj2i[typej];
+ if (eflag)
+ evdwl = f*rn*lj3i[typej]-g6*((a2+1.0)*a2+0.5)*x2+t*lj4i[typej];
+ }
+ }
+ else { // cut form
+ if (ni == 0) {
+ force_lj = rn*(rn*lj1i[typej]-lj2i[typej]);
+ if (eflag) evdwl = rn*(rn*lj3i[typej]-lj4i[typej])-offseti[typej];
+ }
+ else { // correct for special
+ register double f = special_lj[ni];
+ force_lj = f*rn*(rn*lj1i[typej]-lj2i[typej]);
+ if (eflag)
+ evdwl = f*(rn*(rn*lj3i[typej]-lj4i[typej])-offseti[typej]);
+ }
+ }
}
else force_lj = respa_lj = evdwl = 0.0;
@@ -901,19 +901,19 @@ void PairLJCoul::compute_outer(int eflag, int vflag)
frespa = fpair-(respa_coul+respa_lj)*r2inv;
if (newton_pair || j < nlocal) {
- register double *fj = f0+(j+(j<<1)), f;
- fi[0] += f = d[0]*frespa; fj[0] -= f;
- fi[1] += f = d[1]*frespa; fj[1] -= f;
- fi[2] += f = d[2]*frespa; fj[2] -= f;
+ register double *fj = f0+(j+(j<<1)), f;
+ fi[0] += f = d[0]*frespa; fj[0] -= f;
+ fi[1] += f = d[1]*frespa; fj[1] -= f;
+ fi[2] += f = d[2]*frespa; fj[2] -= f;
}
else {
- fi[0] += d[0]*frespa;
- fi[1] += d[1]*frespa;
- fi[2] += d[2]*frespa;
+ fi[0] += d[0]*frespa;
+ fi[1] += d[1]*frespa;
+ fi[2] += d[2]*frespa;
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
- evdwl,ecoul,fpair,d[0],d[1],d[2]);
+ evdwl,ecoul,fpair,d[0],d[1],d[2]);
}
}
}
@@ -930,17 +930,17 @@ void PairLJCoul::init_tables()
tabinnersq = tabinner*tabinner;
init_bitmap(tabinner,cut_coul,ncoultablebits,
- masklo,maskhi,ncoulmask,ncoulshiftbits);
-
+ masklo,maskhi,ncoulmask,ncoulshiftbits);
+
int ntable = 1;
for (int i = 0; i < ncoultablebits; i++) ntable *= 2;
-
+
// linear lookup tables of length N = 2^ncoultablebits
// stored value = value at lower edge of bin
// d values = delta from lower edge to upper edge of bin
if (ftable) free_tables();
-
+
memory->create(rtable,ntable,"pair:rtable");
memory->create(ftable,ntable,"pair:ftable");
memory->create(ctable,ntable,"pair:ctable");
@@ -964,7 +964,7 @@ void PairLJCoul::init_tables()
int itablemin;
minrsq_lookup.i = 0 << ncoulshiftbits;
minrsq_lookup.i |= maskhi;
-
+
for (int i = 0; i < ntable; i++) {
rsq_lookup.i = i << ncoulshiftbits;
rsq_lookup.i |= masklo;
@@ -989,23 +989,23 @@ void PairLJCoul::init_tables()
ptable[i] = qqrd2e/r;
vtable[i] = qqrd2e/r * (derfc + EWALD_F*grij*expm2);
if (rsq_lookup.f > cut_respa[2]*cut_respa[2]) {
- if (rsq_lookup.f < cut_respa[3]*cut_respa[3]) {
- rsw = (r - cut_respa[2])/(cut_respa[3] - cut_respa[2]);
- ftable[i] += qqrd2e/r * rsw*rsw*(3.0 - 2.0*rsw);
- ctable[i] = qqrd2e/r * rsw*rsw*(3.0 - 2.0*rsw);
- } else {
- ftable[i] = qqrd2e/r * (derfc + EWALD_F*grij*expm2);
- ctable[i] = qqrd2e/r;
- }
+ if (rsq_lookup.f < cut_respa[3]*cut_respa[3]) {
+ rsw = (r - cut_respa[2])/(cut_respa[3] - cut_respa[2]);
+ ftable[i] += qqrd2e/r * rsw*rsw*(3.0 - 2.0*rsw);
+ ctable[i] = qqrd2e/r * rsw*rsw*(3.0 - 2.0*rsw);
+ } else {
+ ftable[i] = qqrd2e/r * (derfc + EWALD_F*grij*expm2);
+ ctable[i] = qqrd2e/r;
+ }
}
}
minrsq_lookup.f = MIN(minrsq_lookup.f,rsq_lookup.f);
}
tabinnersq = minrsq_lookup.f;
-
+
int ntablem1 = ntable - 1;
-
+
for (int i = 0; i < ntablem1; i++) {
drtable[i] = 1.0/(rtable[i+1] - rtable[i]);
dftable[i] = ftable[i+1] - ftable[i];
@@ -1019,10 +1019,10 @@ void PairLJCoul::init_tables()
dptable[i] = ptable[i+1] - ptable[i];
}
}
-
- // get the delta values for the last table entries
+
+ // get the delta values for the last table entries
// tables are connected periodically between 0 and ntablem1
-
+
drtable[ntablem1] = 1.0/(rtable[0] - rtable[ntablem1]);
dftable[ntablem1] = ftable[0] - ftable[ntablem1];
dctable[ntablem1] = ctable[0] - ctable[ntablem1];
@@ -1032,23 +1032,23 @@ void PairLJCoul::init_tables()
dptable[ntablem1] = ptable[0] - ptable[ntablem1];
}
- // get the correct delta values at itablemax
+ // get the correct delta values at itablemax
// smallest r is in bin itablemin
// largest r is in bin itablemax, which is itablemin-1,
// or ntablem1 if itablemin=0
// deltas at itablemax only needed if corresponding rsq < cut*cut
- // if so, compute deltas between rsq and cut*cut
-
+ // if so, compute deltas between rsq and cut*cut
+
double f_tmp,c_tmp,e_tmp,p_tmp = 0.0,v_tmp = 0.0;
itablemin = minrsq_lookup.i & ncoulmask;
- itablemin >>= ncoulshiftbits;
- int itablemax = itablemin - 1;
- if (itablemin == 0) itablemax = ntablem1;
+ itablemin >>= ncoulshiftbits;
+ int itablemax = itablemin - 1;
+ if (itablemin == 0) itablemax = ntablem1;
rsq_lookup.i = itablemax << ncoulshiftbits;
rsq_lookup.i |= maskhi;
if (rsq_lookup.f < cut_coulsq) {
- rsq_lookup.f = cut_coulsq;
+ rsq_lookup.f = cut_coulsq;
r = sqrtf(rsq_lookup.f);
grij = g_ewald * r;
expm2 = exp(-grij*grij);
@@ -1066,7 +1066,7 @@ void PairLJCoul::init_tables()
v_tmp = qqrd2e/r * (derfc + EWALD_F*grij*expm2);
if (rsq_lookup.f > cut_respa[2]*cut_respa[2]) {
if (rsq_lookup.f < cut_respa[3]*cut_respa[3]) {
- rsw = (r - cut_respa[2])/(cut_respa[3] - cut_respa[2]);
+ rsw = (r - cut_respa[2])/(cut_respa[3] - cut_respa[2]);
f_tmp += qqrd2e/r * rsw*rsw*(3.0 - 2.0*rsw);
c_tmp = qqrd2e/r * rsw*rsw*(3.0 - 2.0*rsw);
} else {
@@ -1076,14 +1076,14 @@ void PairLJCoul::init_tables()
}
}
- drtable[itablemax] = 1.0/(rsq_lookup.f - rtable[itablemax]);
+ drtable[itablemax] = 1.0/(rsq_lookup.f - rtable[itablemax]);
dftable[itablemax] = f_tmp - ftable[itablemax];
dctable[itablemax] = c_tmp - ctable[itablemax];
detable[itablemax] = e_tmp - etable[itablemax];
if (cut_respa) {
dvtable[itablemax] = v_tmp - vtable[itablemax];
dptable[itablemax] = p_tmp - ptable[itablemax];
- }
+ }
}
}
@@ -1110,8 +1110,8 @@ void PairLJCoul::free_tables()
/* ---------------------------------------------------------------------- */
double PairLJCoul::single(int i, int j, int itype, int jtype,
- double rsq, double factor_coul, double factor_lj,
- double &fforce)
+ double rsq, double factor_coul, double factor_lj,
+ double &fforce)
{
double r2inv, r6inv, force_coul, force_lj;
double g2 = g_ewald*g_ewald, g6 = g2*g2*g2, g8 = g6*g2, *q = atom->q;
@@ -1119,15 +1119,15 @@ double PairLJCoul::single(int i, int j, int itype, int jtype,
double eng = 0.0;
r2inv = 1.0/rsq;
- if ((ewald_order&2) && (rsq < cut_coulsq)) { // coulombic
- if (!ncoultablebits || rsq <= tabinnersq) { // series real space
+ if ((ewald_order&2) && (rsq < cut_coulsq)) { // coulombic
+ if (!ncoultablebits || rsq <= tabinnersq) { // series real space
register double r = sqrt(rsq), x = g_ewald*r;
register double s = force->qqrd2e*q[i]*q[j], t = 1.0/(1.0+EWALD_P*x);
r = s*(1.0-factor_coul)/r; s *= g_ewald*exp(-x*x);
force_coul = (t *= ((((t*A5+A4)*t+A3)*t+A2)*t+A1)*s/x)+EWALD_F*s-r;
eng += t-r;
}
- else { // table real space
+ else { // table real space
register union_int_float_t t;
t.f = rsq;
register const int k = (t.i & ncoulmask) >> ncoulshiftbits;
@@ -1137,21 +1137,21 @@ double PairLJCoul::single(int i, int j, int itype, int jtype,
eng += qiqj*(etable[k]+f*detable[k]-t.f);
}
} else force_coul = 0.0;
-
- if (rsq < cut_ljsq[itype][jtype]) { // lennard-jones
+
+ if (rsq < cut_ljsq[itype][jtype]) { // lennard-jones
r6inv = r2inv*r2inv*r2inv;
- if (ewald_order&64) { // long-range
+ if (ewald_order&64) { // long-range
register double x2 = g2*rsq, a2 = 1.0/x2, t = r6inv*(1.0-factor_lj);
x2 = a2*exp(-x2)*lj4[itype][jtype];
force_lj = factor_lj*(r6inv *= r6inv)*lj1[itype][jtype]-
- g8*(((6.0*a2+6.0)*a2+3.0)*a2+a2)*x2*rsq+t*lj2[itype][jtype];
+ g8*(((6.0*a2+6.0)*a2+3.0)*a2+a2)*x2*rsq+t*lj2[itype][jtype];
eng += factor_lj*r6inv*lj3[itype][jtype]-
- g6*((a2+1.0)*a2+0.5)*x2+t*lj4[itype][jtype];
+ g6*((a2+1.0)*a2+0.5)*x2+t*lj4[itype][jtype];
}
- else { // cut
+ else { // cut
force_lj = factor_lj*r6inv*(lj1[itype][jtype]*r6inv-lj2[itype][jtype]);
eng += factor_lj*(r6inv*(r6inv*lj3[itype][jtype]-
- lj4[itype][jtype])-offset[itype][jtype]);
+ lj4[itype][jtype])-offset[itype][jtype]);
}
} else force_lj = 0.0;
diff --git a/src/USER-EWALDN/pair_lj_coul.h b/src/USER-EWALDN/pair_lj_coul.h
index 4f17095770ee82adc19899dc19cfab334f24f4cd..b497cd254627feb49fd0c435f9de98e9b29e19c6 100644
--- a/src/USER-EWALDN/pair_lj_coul.h
+++ b/src/USER-EWALDN/pair_lj_coul.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -38,7 +38,7 @@ class PairLJCoul : public Pair {
double init_one(int, int);
void write_restart(FILE *);
void read_restart(FILE *);
-
+
void write_restart_settings(FILE *);
void read_restart_settings(FILE *);
double single(int, int, int, int, double, double, double, double &);
diff --git a/src/USER-MISC/angle_cosine_shift.cpp b/src/USER-MISC/angle_cosine_shift.cpp
index cc4e15378212164abb5d29544816578ef6f49ca6..11b4cd070ceba4c74ff8aec28d365093efe25753 100644
--- a/src/USER-MISC/angle_cosine_shift.cpp
+++ b/src/USER-MISC/angle_cosine_shift.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -102,11 +102,11 @@ void AngleCosineShift::compute(int eflag, int vflag)
// C= sine of angle
s = sqrt(1.0 - c*c);
if (s < SMALL) s = SMALL;
-
+
// force & energy
kcos=kcost[type];
ksin=ksint[type];
- if (eflag) eangle = -k[type]-kcos*c-ksin*s;
+ if (eflag) eangle = -k[type]-kcos*c-ksin*s;
cps = c/s; // NOTE absorbed one c
@@ -142,7 +142,7 @@ void AngleCosineShift::compute(int eflag, int vflag)
}
if (evflag) ev_tally(i1,i2,i3,nlocal,newton_bond,eangle,f1,f3,
- delx1,dely1,delz1,delx2,dely2,delz2);
+ delx1,dely1,delz1,delx2,dely2,delz2);
}
}
@@ -158,7 +158,7 @@ void AngleCosineShift::allocate()
memory->create(kcost ,n+1,"Angle:kcost");
memory->create(theta ,n+1,"Angle:theta");
memory->create(setflag,n+1, "Angle:setflag");
-
+
for (int i = 1; i <= n; i++) setflag[i] = 0;
}
@@ -201,7 +201,7 @@ double AngleCosineShift::equilibrium_angle(int i)
}
/* ----------------------------------------------------------------------
- proc 0 writes out coeffs to restart file
+ proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void AngleCosineShift::write_restart(FILE *fp)
@@ -213,14 +213,14 @@ void AngleCosineShift::write_restart(FILE *fp)
}
/* ----------------------------------------------------------------------
- proc 0 reads coeffs from restart file, bcasts them
+ proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void AngleCosineShift::read_restart(FILE *fp)
{
allocate();
- if (comm->me == 0)
+ if (comm->me == 0)
{
fread(&k[1],sizeof(double),atom->nangletypes,fp);
fread(&kcost[1],sizeof(double),atom->nangletypes,fp);
@@ -246,7 +246,7 @@ double AngleCosineShift::single(int type, int i1, int i2, int i3)
double delz1 = x[i1][2] - x[i2][2];
domain->minimum_image(delx1,dely1,delz1);
double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1);
-
+
double delx2 = x[i3][0] - x[i2][0];
double dely2 = x[i3][1] - x[i2][1];
double delz2 = x[i3][2] - x[i2][2];
@@ -259,5 +259,5 @@ double AngleCosineShift::single(int type, int i1, int i2, int i3)
if (c < -1.0) c = -1.0;
double s=sqrt(1.0-c*c);
- return -k[type]-kcost[type]*c-ksint[type]*s;
+ return -k[type]-kcost[type]*c-ksint[type]*s;
}
diff --git a/src/USER-MISC/angle_cosine_shift.h b/src/USER-MISC/angle_cosine_shift.h
index d8b7ea17411a9b5fdb42bc8916422998309813a1..3945161f0e51ae4eecffb3a72d4a393241f37b5c 100644
--- a/src/USER-MISC/angle_cosine_shift.h
+++ b/src/USER-MISC/angle_cosine_shift.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-MISC/angle_cosine_shift_exp.cpp b/src/USER-MISC/angle_cosine_shift_exp.cpp
index 031cfec5635df8fb4e4372394f0b5608ff80c6c6..0c607b4c43f5528e4088cc56432d17ea76f06270 100644
--- a/src/USER-MISC/angle_cosine_shift_exp.cpp
+++ b/src/USER-MISC/angle_cosine_shift_exp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -42,7 +42,7 @@ AngleCosineShiftExp::~AngleCosineShiftExp()
memory->destroy(setflag);
memory->destroy(umin);
memory->destroy(a);
- memory->destroy(opt1);
+ memory->destroy(opt1);
memory->destroy(cost);
memory->destroy(sint);
memory->destroy(theta0);
@@ -58,7 +58,7 @@ void AngleCosineShiftExp::compute(int eflag, int vflag)
double delx1,dely1,delz1,delx2,dely2,delz2;
double eangle,f1[3],f3[3],ff;
double rsq1,rsq2,r1,r2,c,s,a11,a12,a22;
- double exp2,aa,uumin,cccpsss,cssmscc;
+ double exp2,aa,uumin,cccpsss,cssmscc;
eangle = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
@@ -106,9 +106,9 @@ void AngleCosineShiftExp::compute(int eflag, int vflag)
// C= sine of angle
s = sqrt(1.0 - c*c);
if (s < SMALL) s = SMALL;
-
+
// force & energy
-
+
aa=a[type];
uumin=umin[type];
@@ -119,19 +119,19 @@ void AngleCosineShiftExp::compute(int eflag, int vflag)
{ // |a|<0.01 so use expansions relative precision <1e-5
// std::cout << "Using expansion\n";
if (eflag) eangle = -0.125*(1+cccpsss)*(4+aa*(cccpsss-1))*uumin;
- ff=0.25*uumin*cssmscc*(2+aa*cccpsss)/s;
+ ff=0.25*uumin*cssmscc*(2+aa*cccpsss)/s;
}
else
{
-// std::cout << "Not using expansion\n";
+// std::cout << "Not using expansion\n";
exp2=exp(0.5*aa*(1+cccpsss));
if (eflag) eangle = opt1[type]*(1-exp2);
- ff=0.5*a[type]*opt1[type]*exp2*cssmscc/s;
+ ff=0.5*a[type]*opt1[type]*exp2*cssmscc/s;
}
a11 = ff*c/ rsq1;
a12 = -ff / (r1*r2);
- a22 = ff*c/ rsq2;
+ a22 = ff*c/ rsq2;
f1[0] = a11*delx1 + a12*delx2;
f1[1] = a11*dely1 + a12*dely2;
@@ -161,7 +161,7 @@ void AngleCosineShiftExp::compute(int eflag, int vflag)
}
if (evflag) ev_tally(i1,i2,i3,nlocal,newton_bond,eangle,f1,f3,
- delx1,dely1,delz1,delx2,dely2,delz2);
+ delx1,dely1,delz1,delx2,dely2,delz2);
}
}
@@ -208,7 +208,7 @@ void AngleCosineShiftExp::coeff(int narg, char **arg)
cost[i] = cos(theta0_*3.14159265/180);
sint[i] = sin(theta0_*3.14159265/180);
theta0[i]= theta0_*3.14159265/180;
-
+
if (!doExpansion[i]) opt1[i]=umin_/(exp(a_)-1);
setflag[i] = 1;
@@ -226,7 +226,7 @@ double AngleCosineShiftExp::equilibrium_angle(int i)
}
/* ----------------------------------------------------------------------
- proc 0 writes out coeffs to restart file
+ proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void AngleCosineShiftExp::write_restart(FILE *fp)
@@ -239,7 +239,7 @@ void AngleCosineShiftExp::write_restart(FILE *fp)
}
/* ----------------------------------------------------------------------
- proc 0 reads coeffs from restart file, bcasts them
+ proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void AngleCosineShiftExp::read_restart(FILE *fp)
@@ -279,7 +279,7 @@ double AngleCosineShiftExp::single(int type, int i1, int i2, int i3)
double delz1 = x[i1][2] - x[i2][2];
domain->minimum_image(delx1,dely1,delz1);
double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1);
-
+
double delx2 = x[i3][0] - x[i2][0];
double dely2 = x[i3][1] - x[i2][1];
double delz2 = x[i3][2] - x[i2][2];
diff --git a/src/USER-MISC/angle_cosine_shift_exp.h b/src/USER-MISC/angle_cosine_shift_exp.h
index 50883dc0346551b68354855c990edd6745e4bac3..10c6d1ba6f9cfe2bf79a972aa48ad5da80a1cf29 100644
--- a/src/USER-MISC/angle_cosine_shift_exp.h
+++ b/src/USER-MISC/angle_cosine_shift_exp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-MISC/angle_dipole.cpp b/src/USER-MISC/angle_dipole.cpp
index f5bbf00b61225a090769b413c0f67566e3107427..4020842413736434750143e69b52465f6e5c762d 100644
--- a/src/USER-MISC/angle_dipole.cpp
+++ b/src/USER-MISC/angle_dipole.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -66,7 +66,7 @@ void AngleDipole::compute(int eflag, int vflag)
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
- if (!newton_bond)
+ if (!newton_bond)
error->all(FLERR,"'newton' flag for bonded interactions must be 'on'");
for (n = 0; n < nanglelist; n++) {
@@ -87,19 +87,19 @@ void AngleDipole::compute(int eflag, int vflag)
deltaGamma = cosGamma - cos(gamma0[type]);
kdg = k[type] * deltaGamma;
- if (eflag) eangle = kdg * deltaGamma; // energy
-
- tangle = 2.0 * kdg / rmu;
-
+ if (eflag) eangle = kdg * deltaGamma; // energy
+
+ tangle = 2.0 * kdg / rmu;
+
torque[iDip][0] += tangle * (dely*mu[iDip][2] - delz*mu[iDip][1]);
torque[iDip][1] += tangle * (delz*mu[iDip][0] - delx*mu[iDip][2]);
torque[iDip][2] += tangle * (delx*mu[iDip][1] - dely*mu[iDip][0]);
-
+
f1[0] = f1[1] = f1[2] = f3[0] = f3[1] = f3[2] = 0.0;
-
+
if (evflag) // tally energy (virial=0 because force=0)
ev_tally(iRef,iDip,iDummy,nlocal,newton_bond,eangle,f1,f3,
- 0.0,0.0,0.0,0.0,0.0,0.0);
+ 0.0,0.0,0.0,0.0,0.0,0.0);
}
}
@@ -165,7 +165,7 @@ void AngleDipole::write_restart(FILE *fp)
}
/* ----------------------------------------------------------------------
- proc 0 reads coeffs from restart file, bcasts them
+ proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void AngleDipole::read_restart(FILE *fp)
@@ -203,5 +203,5 @@ double AngleDipole::single(int type, int iRef, int iDip, int iDummy)
double deltaGamma = cosGamma - cos(gamma0[type]);
double kdg = k[type] * deltaGamma;
- return kdg * deltaGamma; // energy
+ return kdg * deltaGamma; // energy
}
diff --git a/src/USER-MISC/angle_dipole.h b/src/USER-MISC/angle_dipole.h
index 09dd6821cf0b8db040928769e8a289c89f9e52f5..f3138ad83cfdfdaa4880d009d1ae8f5a149ae0df 100644
--- a/src/USER-MISC/angle_dipole.h
+++ b/src/USER-MISC/angle_dipole.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-MISC/bond_harmonic_shift.cpp b/src/USER-MISC/bond_harmonic_shift.cpp
index 958dad69f811d7e3ec7f25f5f614d0f389bb40ea..e140892141676d7537b7fec034563dfcef825066 100644
--- a/src/USER-MISC/bond_harmonic_shift.cpp
+++ b/src/USER-MISC/bond_harmonic_shift.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -75,7 +75,7 @@ void BondHarmonicShift::compute(int eflag, int vflag)
rsq = delx*delx + dely*dely + delz*delz;
r = sqrt(rsq);
-
+
dr = r - r0[type];
rk = k[type] * dr;
@@ -115,7 +115,7 @@ void BondHarmonicShift::allocate()
memory->create(r0, n+1,"bond:r0");
memory->create(r1, n+1,"bond:r1");
memory->create(setflag,n+1,"bond:setflag");
-
+
for (int i = 1; i <= n; i++) setflag[i] = 0;
}
@@ -148,7 +148,7 @@ void BondHarmonicShift::coeff(int narg, char **arg)
}
/* ----------------------------------------------------------------------
- return an equilbrium bond length
+ return an equilbrium bond length
------------------------------------------------------------------------- */
double BondHarmonicShift::equilibrium_distance(int i)
@@ -157,7 +157,7 @@ double BondHarmonicShift::equilibrium_distance(int i)
}
/* ----------------------------------------------------------------------
- proc 0 writes out coeffs to restart file
+ proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void BondHarmonicShift::write_restart(FILE *fp)
@@ -168,7 +168,7 @@ void BondHarmonicShift::write_restart(FILE *fp)
}
/* ----------------------------------------------------------------------
- proc 0 reads coeffs from restart file, bcasts them
+ proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void BondHarmonicShift::read_restart(FILE *fp)
@@ -183,7 +183,7 @@ void BondHarmonicShift::read_restart(FILE *fp)
MPI_Bcast(&k[1],atom->nbondtypes,MPI_DOUBLE,0,world);
MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world);
MPI_Bcast(&r1[1],atom->nbondtypes,MPI_DOUBLE,0,world);
-
+
for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1;
}
@@ -191,9 +191,9 @@ void BondHarmonicShift::read_restart(FILE *fp)
double BondHarmonicShift::single(int type, double rsq, int i, int j)
{
- double r = sqrt(rsq);
+ double r = sqrt(rsq);
double dr = r - r0[type];
double dr2=r0[type]-r1[type];
-
+
return k[type]*(dr*dr - dr2*dr2);
}
diff --git a/src/USER-MISC/bond_harmonic_shift.h b/src/USER-MISC/bond_harmonic_shift.h
index b3378aea3f8dc0e1bed060be5e67056e32ad105f..74909a0becf1de5ff46f81d30514c356a40f7fe3 100644
--- a/src/USER-MISC/bond_harmonic_shift.h
+++ b/src/USER-MISC/bond_harmonic_shift.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-MISC/bond_harmonic_shift_cut.cpp b/src/USER-MISC/bond_harmonic_shift_cut.cpp
index da78a54aed8ea438b0e147d63f961d606a19cd65..8ebb820e0b6941d7f115b1d333d33e506f3b4732 100644
--- a/src/USER-MISC/bond_harmonic_shift_cut.cpp
+++ b/src/USER-MISC/bond_harmonic_shift_cut.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -75,9 +75,9 @@ void BondHarmonicShiftCut::compute(int eflag, int vflag)
rsq = delx*delx + dely*dely + delz*delz;
r = sqrt(rsq);
-
+
if (r>r1[type]) continue;
-
+
dr = r - r0[type];
rk = k[type] * dr;
@@ -149,7 +149,7 @@ void BondHarmonicShiftCut::coeff(int narg, char **arg)
}
/* ----------------------------------------------------------------------
- return an equilbrium bond length
+ return an equilbrium bond length
------------------------------------------------------------------------- */
double BondHarmonicShiftCut::equilibrium_distance(int i)
@@ -158,7 +158,7 @@ double BondHarmonicShiftCut::equilibrium_distance(int i)
}
/* ----------------------------------------------------------------------
- proc 0 writes out coeffs to restart file
+ proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void BondHarmonicShiftCut::write_restart(FILE *fp)
@@ -169,7 +169,7 @@ void BondHarmonicShiftCut::write_restart(FILE *fp)
}
/* ----------------------------------------------------------------------
- proc 0 reads coeffs from restart file, bcasts them
+ proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void BondHarmonicShiftCut::read_restart(FILE *fp)
@@ -184,7 +184,7 @@ void BondHarmonicShiftCut::read_restart(FILE *fp)
MPI_Bcast(&k[1],atom->nbondtypes,MPI_DOUBLE,0,world);
MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world);
MPI_Bcast(&r1[1],atom->nbondtypes,MPI_DOUBLE,0,world);
-
+
for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1;
}
@@ -192,10 +192,10 @@ void BondHarmonicShiftCut::read_restart(FILE *fp)
double BondHarmonicShiftCut::single(int type, double rsq, int i, int j)
{
- double r = sqrt(rsq);
-
+ double r = sqrt(rsq);
+
if (r>r1[type]) return 0;
-
+
double dr = r - r0[type];
double dr2=r0[type]-r1[type];
return k[type]*(dr*dr - dr2*dr2);
diff --git a/src/USER-MISC/bond_harmonic_shift_cut.h b/src/USER-MISC/bond_harmonic_shift_cut.h
index 6e957d286c413ae9d4a9f16fce15dc90e64415cf..9767f11580a2fd081c1a6fc522978481d680e956 100644
--- a/src/USER-MISC/bond_harmonic_shift_cut.h
+++ b/src/USER-MISC/bond_harmonic_shift_cut.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-MISC/compute_ackland_atom.cpp b/src/USER-MISC/compute_ackland_atom.cpp
index 650688b130989c05078a0857b035c8687d62abaa..2c70cf19f01f1fcbeebd9ffdb1d902c6a73e7586 100644
--- a/src/USER-MISC/compute_ackland_atom.cpp
+++ b/src/USER-MISC/compute_ackland_atom.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -140,15 +140,15 @@ void ComputeAcklandAtom::compute_peratom()
// ensure distsq and nearest arrays are long enough
if (jnum > maxneigh) {
- memory->destroy(distsq);
- memory->destroy(nearest);
- memory->destroy(nearest_n0);
- memory->destroy(nearest_n1);
- maxneigh = jnum;
- memory->create(distsq,maxneigh,"compute/ackland/atom:distsq");
- memory->create(nearest,maxneigh,"compute/ackland/atom:nearest");
- memory->create(nearest_n0,maxneigh,"compute/ackland/atom:nearest_n0");
- memory->create(nearest_n1,maxneigh,"compute/ackland/atom:nearest_n1");
+ memory->destroy(distsq);
+ memory->destroy(nearest);
+ memory->destroy(nearest_n0);
+ memory->destroy(nearest_n1);
+ maxneigh = jnum;
+ memory->create(distsq,maxneigh,"compute/ackland/atom:distsq");
+ memory->create(nearest,maxneigh,"compute/ackland/atom:nearest");
+ memory->create(nearest_n0,maxneigh,"compute/ackland/atom:nearest_n0");
+ memory->create(nearest_n1,maxneigh,"compute/ackland/atom:nearest_n1");
}
// loop over list of all neighbors within force cutoff
@@ -157,17 +157,17 @@ void ComputeAcklandAtom::compute_peratom()
n = 0;
for (jj = 0; jj < jnum; jj++) {
- j = jlist[jj];
- j &= NEIGHMASK;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
- if (rsq < cutsq) {
- distsq[n] = rsq;
- nearest[n++] = j;
- }
+ j = jlist[jj];
+ j &= NEIGHMASK;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+ if (rsq < cutsq) {
+ distsq[n] = rsq;
+ nearest[n++] = j;
+ }
}
// Select 6 nearest neighbors
@@ -177,15 +177,15 @@ void ComputeAcklandAtom::compute_peratom()
// Mean squared separation
double r0_sq = 0.;
- for (j = 0; j < 6; j++)
- r0_sq += distsq[j];
+ for (j = 0; j < 6; j++)
+ r0_sq += distsq[j];
r0_sq /= 6.;
// n0 near neighbors with: distsq<1.45*r0_sq
// n1 near neighbors with: distsq<1.55*r0_sq
double n0_dist_sq = 1.45*r0_sq,
- n1_dist_sq = 1.55*r0_sq;
+ n1_dist_sq = 1.55*r0_sq;
int n0 = 0, n1 = 0;
for (j = 0; j < n; j++) {
if (distsq[j] < n1_dist_sq) {
@@ -204,32 +204,32 @@ void ComputeAcklandAtom::compute_peratom()
chi[0] = chi[1] = chi[2] = chi[3] = chi[4] = chi[5] = chi[6] = chi[7] = 0;
double x_ij, y_ij, z_ij, x_ik, y_ik, z_ik;
for (j = 0; j < n0; j++) {
- x_ij = x[i][0]-x[nearest_n0[j]][0];
- y_ij = x[i][1]-x[nearest_n0[j]][1];
- z_ij = x[i][2]-x[nearest_n0[j]][2];
- norm_j = sqrt (x_ij*x_ij + y_ij*y_ij + z_ij*z_ij);
- if (norm_j <= 0.) continue;
- for (k = j+1; k < n0; k++) {
- x_ik = x[i][0]-x[nearest_n0[k]][0];
- y_ik = x[i][1]-x[nearest_n0[k]][1];
- z_ik = x[i][2]-x[nearest_n0[k]][2];
- norm_k = sqrt (x_ik*x_ik + y_ik*y_ik + z_ik*z_ik);
- if (norm_k <= 0.)
- continue;
-
- bond_angle = (x_ij*x_ik + y_ij*y_ik + z_ij*z_ik) / (norm_j*norm_k);
-
- // Histogram for identifying the relevant peaks
-
- if (bond_angle < -0.945) chi[0]++;
- else if (bond_angle < -0.915) chi[1]++;
- else if (bond_angle < -0.755) chi[2]++;
- else if (bond_angle < -0.195) chi[3]++;
- else if (bond_angle < 0.195) chi[4]++;
- else if (bond_angle < 0.245) chi[5]++;
- else if (bond_angle < 0.795) chi[6]++;
- else chi[7]++;
- }
+ x_ij = x[i][0]-x[nearest_n0[j]][0];
+ y_ij = x[i][1]-x[nearest_n0[j]][1];
+ z_ij = x[i][2]-x[nearest_n0[j]][2];
+ norm_j = sqrt (x_ij*x_ij + y_ij*y_ij + z_ij*z_ij);
+ if (norm_j <= 0.) continue;
+ for (k = j+1; k < n0; k++) {
+ x_ik = x[i][0]-x[nearest_n0[k]][0];
+ y_ik = x[i][1]-x[nearest_n0[k]][1];
+ z_ik = x[i][2]-x[nearest_n0[k]][2];
+ norm_k = sqrt (x_ik*x_ik + y_ik*y_ik + z_ik*z_ik);
+ if (norm_k <= 0.)
+ continue;
+
+ bond_angle = (x_ij*x_ik + y_ij*y_ik + z_ij*z_ik) / (norm_j*norm_k);
+
+ // Histogram for identifying the relevant peaks
+
+ if (bond_angle < -0.945) chi[0]++;
+ else if (bond_angle < -0.915) chi[1]++;
+ else if (bond_angle < -0.755) chi[2]++;
+ else if (bond_angle < -0.195) chi[3]++;
+ else if (bond_angle < 0.195) chi[4]++;
+ else if (bond_angle < 0.245) chi[5]++;
+ else if (bond_angle < 0.795) chi[6]++;
+ else chi[7]++;
+ }
}
// Deviations from the different lattice structures
@@ -237,41 +237,41 @@ void ComputeAcklandAtom::compute_peratom()
double delta_bcc = 0.35*chi[4]/(double)(chi[5]+chi[6]-chi[4]);
double delta_cp = fabs(1.-(double)chi[6]/24.);
double delta_fcc = 0.61*(fabs((double)(chi[0]+chi[1]-6.))+
- (double)chi[2])/6.0;
+ (double)chi[2])/6.0;
double delta_hcp = (fabs((double)chi[0]-3.)+
- fabs((double)chi[0]+(double)chi[1]+
- (double)chi[2]+(double)chi[3]-9.0))/12.0;
-
+ fabs((double)chi[0]+(double)chi[1]+
+ (double)chi[2]+(double)chi[3]-9.0))/12.0;
+
// Identification of the local structure according to the reference
if (chi[0] == 7) { delta_bcc = 0.; }
else if (chi[0] == 6) { delta_fcc = 0.; }
else if (chi[0] <= 3) { delta_hcp = 0.; }
- if (chi[7] > 0.)
- structure[i] = UNKNOWN;
- else
- if (chi[4] < 3.)
+ if (chi[7] > 0.)
+ structure[i] = UNKNOWN;
+ else
+ if (chi[4] < 3.)
{
- if (n1 > 13 || n1 < 11)
- structure[i] = UNKNOWN;
- else
- structure[i] = ICO;
- } else
- if (delta_bcc <= delta_cp)
+ if (n1 > 13 || n1 < 11)
+ structure[i] = UNKNOWN;
+ else
+ structure[i] = ICO;
+ } else
+ if (delta_bcc <= delta_cp)
{
- if (n1 < 11)
- structure[i] = UNKNOWN;
- else
- structure[i] = BCC;
- } else
- if (n1 > 12 || n1 < 11)
- structure[i] = UNKNOWN;
- else
- if (delta_fcc < delta_hcp)
- structure[i] = FCC;
- else
- structure[i] = HCP;
+ if (n1 < 11)
+ structure[i] = UNKNOWN;
+ else
+ structure[i] = BCC;
+ } else
+ if (n1 > 12 || n1 < 11)
+ structure[i] = UNKNOWN;
+ else
+ if (delta_fcc < delta_hcp)
+ structure[i] = FCC;
+ else
+ structure[i] = HCP;
} else structure[i] = 0.0;
}
@@ -297,29 +297,29 @@ void ComputeAcklandAtom::select(int k, int n, double *arr)
for (;;) {
if (ir <= l+1) {
if (ir == l+1 && arr[ir] < arr[l]) {
- SWAP(arr[l],arr[ir])
+ SWAP(arr[l],arr[ir])
}
return;
} else {
mid=(l+ir) >> 1;
SWAP(arr[mid],arr[l+1])
if (arr[l] > arr[ir]) {
- SWAP(arr[l],arr[ir])
+ SWAP(arr[l],arr[ir])
}
if (arr[l+1] > arr[ir]) {
- SWAP(arr[l+1],arr[ir])
+ SWAP(arr[l+1],arr[ir])
}
if (arr[l] > arr[l+1]) {
- SWAP(arr[l],arr[l+1])
+ SWAP(arr[l],arr[l+1])
}
i = l+1;
j = ir;
a = arr[l+1];
for (;;) {
- do i++; while (arr[i] < a);
- do j--; while (arr[j] > a);
- if (j < i) break;
- SWAP(arr[i],arr[j])
+ do i++; while (arr[i] < a);
+ do j--; while (arr[j] > a);
+ if (j < i) break;
+ SWAP(arr[i],arr[j])
}
arr[l+1] = arr[j];
arr[j] = a;
@@ -343,8 +343,8 @@ void ComputeAcklandAtom::select2(int k, int n, double *arr, int *iarr)
for (;;) {
if (ir <= l+1) {
if (ir == l+1 && arr[ir] < arr[l]) {
- SWAP(arr[l],arr[ir])
- ISWAP(iarr[l],iarr[ir])
+ SWAP(arr[l],arr[ir])
+ ISWAP(iarr[l],iarr[ir])
}
return;
} else {
@@ -352,27 +352,27 @@ void ComputeAcklandAtom::select2(int k, int n, double *arr, int *iarr)
SWAP(arr[mid],arr[l+1])
ISWAP(iarr[mid],iarr[l+1])
if (arr[l] > arr[ir]) {
- SWAP(arr[l],arr[ir])
- ISWAP(iarr[l],iarr[ir])
+ SWAP(arr[l],arr[ir])
+ ISWAP(iarr[l],iarr[ir])
}
if (arr[l+1] > arr[ir]) {
- SWAP(arr[l+1],arr[ir])
- ISWAP(iarr[l+1],iarr[ir])
+ SWAP(arr[l+1],arr[ir])
+ ISWAP(iarr[l+1],iarr[ir])
}
if (arr[l] > arr[l+1]) {
- SWAP(arr[l],arr[l+1])
- ISWAP(iarr[l],iarr[l+1])
+ SWAP(arr[l],arr[l+1])
+ ISWAP(iarr[l],iarr[l+1])
}
i = l+1;
j = ir;
a = arr[l+1];
ia = iarr[l+1];
for (;;) {
- do i++; while (arr[i] < a);
- do j--; while (arr[j] > a);
- if (j < i) break;
- SWAP(arr[i],arr[j])
- ISWAP(iarr[i],iarr[j])
+ do i++; while (arr[i] < a);
+ do j--; while (arr[j] > a);
+ if (j < i) break;
+ SWAP(arr[i],arr[j])
+ ISWAP(iarr[i],iarr[j])
}
arr[l+1] = arr[j];
arr[j] = a;
diff --git a/src/USER-MISC/compute_ackland_atom.h b/src/USER-MISC/compute_ackland_atom.h
index 946827c4064fd0cbc969163c6de88040a314a284..ec42aa66305af14b23e01b1352e921157d43e0d8 100644
--- a/src/USER-MISC/compute_ackland_atom.h
+++ b/src/USER-MISC/compute_ackland_atom.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-MISC/compute_temp_rotate.cpp b/src/USER-MISC/compute_temp_rotate.cpp
index 539683f4f438af059186b6f6d234c747d0c06480..69519249c790021f74d94db0625ad75e62e7727b 100644
--- a/src/USER-MISC/compute_temp_rotate.cpp
+++ b/src/USER-MISC/compute_temp_rotate.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -34,7 +34,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-ComputeTempRotate::ComputeTempRotate(LAMMPS *lmp, int narg, char **arg) :
+ComputeTempRotate::ComputeTempRotate(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 3) error->all(FLERR,"Illegal compute temp/rotate command");
@@ -120,10 +120,10 @@ double ComputeTempRotate::compute_scalar()
}
double t = 0.0;
-
+
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
-
+
xbox = (image[i] & 1023) - 512;
ybox = (image[i] >> 10 & 1023) - 512;
zbox = (image[i] >> 20) - 512;
@@ -138,11 +138,11 @@ double ComputeTempRotate::compute_scalar()
vthermal[1] = v[i][1] - vbiasall[i][1];
vthermal[2] = v[i][2] - vbiasall[i][2];
if (rmass)
- t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] +
- vthermal[2]*vthermal[2]) * rmass[i];
+ t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] +
+ vthermal[2]*vthermal[2]) * rmass[i];
else
- t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] +
- vthermal[2]*vthermal[2]) * mass[type[i]];
+ t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] +
+ vthermal[2]*vthermal[2]) * mass[type[i]];
}
MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
@@ -242,9 +242,9 @@ void ComputeTempRotate::remove_bias_all()
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
-
+
for (int i = 0; i < nlocal; i++)
- if (mask[i] & groupbit) {
+ if (mask[i] & groupbit) {
v[i][0] -= vbiasall[i][0];
v[i][1] -= vbiasall[i][1];
v[i][2] -= vbiasall[i][2];
@@ -273,7 +273,7 @@ void ComputeTempRotate::restore_bias_all()
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
-
+
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
v[i][0] += vbiasall[i][0];
diff --git a/src/USER-MISC/compute_temp_rotate.h b/src/USER-MISC/compute_temp_rotate.h
index c539f250f6302e8c0057b1faf3a3db49280eca09..8944f986bee21268f1a4b8818d8bdd69fb53b21b 100644
--- a/src/USER-MISC/compute_temp_rotate.h
+++ b/src/USER-MISC/compute_temp_rotate.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-MISC/dihedral_cosine_shift_exp.cpp b/src/USER-MISC/dihedral_cosine_shift_exp.cpp
index 29e15fe6cec1d55f46028d6e947b907c43f573bf..d607051d9f40db1cc06957773e4ec913fd7dc5db 100644
--- a/src/USER-MISC/dihedral_cosine_shift_exp.cpp
+++ b/src/USER-MISC/dihedral_cosine_shift_exp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -50,7 +50,7 @@ DihedralCosineShiftExp::~DihedralCosineShiftExp()
memory->destroy(cost);
memory->destroy(sint);
memory->destroy(theta);
- memory->destroy(doExpansion);
+ memory->destroy(doExpansion);
}
}
@@ -63,7 +63,7 @@ void DihedralCosineShiftExp::compute(int eflag, int vflag)
double edihedral,f1[3],f2[3],f3[3],f4[3];
double ax,ay,az,bx,by,bz,rasq,rbsq,rgsq,rg,rginv,ra2inv,rb2inv,rabinv;
double df,df1,ddf1,fg,hg,fga,hgb,gaa,gbb;
- double dtfx,dtfy,dtfz,dtgx,dtgy,dtgz,dthx,dthy,dthz;
+ double dtfx,dtfy,dtfz,dtgx,dtgy,dtgz,dthx,dthy,dthz;
double c,s,p,sx2,sy2,sz2;
double cccpsss,cssmscc,exp2;
@@ -110,7 +110,7 @@ void DihedralCosineShiftExp::compute(int eflag, int vflag)
vb3y = x[i4][1] - x[i3][1];
vb3z = x[i4][2] - x[i3][2];
domain->minimum_image(vb3x,vb3y,vb3z);
-
+
// c,s calculation
ax = vb1y*vb2zm - vb1z*vb2ym;
@@ -124,7 +124,7 @@ void DihedralCosineShiftExp::compute(int eflag, int vflag)
rbsq = bx*bx + by*by + bz*bz;
rgsq = vb2xm*vb2xm + vb2ym*vb2ym + vb2zm*vb2zm;
rg = sqrt(rgsq);
-
+
rginv = ra2inv = rb2inv = 0.0;
if (rg > 0) rginv = 1.0/rg;
if (rasq > 0) ra2inv = 1.0/rasq;
@@ -140,28 +140,28 @@ void DihedralCosineShiftExp::compute(int eflag, int vflag)
int me;
MPI_Comm_rank(world,&me);
if (screen) {
- char str[128];
- sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " %d %d %d %d",
- me,update->ntimestep,
- atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
- error->warning(FLERR,str,0);
- fprintf(screen," 1st atom: %d %g %g %g\n",
- me,x[i1][0],x[i1][1],x[i1][2]);
- fprintf(screen," 2nd atom: %d %g %g %g\n",
- me,x[i2][0],x[i2][1],x[i2][2]);
- fprintf(screen," 3rd atom: %d %g %g %g\n",
- me,x[i3][0],x[i3][1],x[i3][2]);
- fprintf(screen," 4th atom: %d %g %g %g\n",
- me,x[i4][0],x[i4][1],x[i4][2]);
+ char str[128];
+ sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " %d %d %d %d",
+ me,update->ntimestep,
+ atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
+ error->warning(FLERR,str,0);
+ fprintf(screen," 1st atom: %d %g %g %g\n",
+ me,x[i1][0],x[i1][1],x[i1][2]);
+ fprintf(screen," 2nd atom: %d %g %g %g\n",
+ me,x[i2][0],x[i2][1],x[i2][2]);
+ fprintf(screen," 3rd atom: %d %g %g %g\n",
+ me,x[i3][0],x[i3][1],x[i3][2]);
+ fprintf(screen," 4th atom: %d %g %g %g\n",
+ me,x[i4][0],x[i4][1],x[i4][2]);
}
}
-
+
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
-
+
double aa=a[type];
double uumin=umin[type];
-
+
cccpsss = c*cost[type]+s*sint[type];
cssmscc = c*sint[type]-s*cost[type];
@@ -185,7 +185,7 @@ void DihedralCosineShiftExp::compute(int eflag, int vflag)
hgb = hg*rb2inv*rginv;
gaa = -ra2inv*rg;
gbb = rb2inv*rg;
-
+
dtfx = gaa*ax;
dtfy = gaa*ay;
dtfz = gaa*az;
@@ -195,7 +195,7 @@ void DihedralCosineShiftExp::compute(int eflag, int vflag)
dthx = gbb*bx;
dthy = gbb*by;
dthz = gbb*bz;
-
+
sx2 = df*dtgx;
sy2 = df*dtgy;
sz2 = df*dtgz;
@@ -244,7 +244,7 @@ void DihedralCosineShiftExp::compute(int eflag, int vflag)
if (evflag)
ev_tally(i1,i2,i3,i4,nlocal,newton_bond,edihedral,f1,f3,f4,
- vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
+ vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
}
}
@@ -302,7 +302,7 @@ void DihedralCosineShiftExp::coeff(int narg, char **arg)
}
/* ----------------------------------------------------------------------
- proc 0 writes out coeffs to restart file
+ proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void DihedralCosineShiftExp::write_restart(FILE *fp)
@@ -315,14 +315,14 @@ void DihedralCosineShiftExp::write_restart(FILE *fp)
}
/* ----------------------------------------------------------------------
- proc 0 reads coeffs from restart file, bcasts them
+ proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void DihedralCosineShiftExp::read_restart(FILE *fp)
{
allocate();
- if (comm->me == 0) {
+ if (comm->me == 0) {
fread(&umin[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&a[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&cost[1],sizeof(double),atom->ndihedraltypes,fp);
@@ -334,7 +334,7 @@ void DihedralCosineShiftExp::read_restart(FILE *fp)
MPI_Bcast(&cost[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&sint[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&theta[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
-
+
for (int i = 1; i <= atom->ndihedraltypes; i++) {
setflag[i] = 1;
doExpansion[i]=(fabs(a[i])<0.01);
diff --git a/src/USER-MISC/dihedral_cosine_shift_exp.h b/src/USER-MISC/dihedral_cosine_shift_exp.h
index 3e77bf491490b7855738883ceafc96f0a80d972a..62008e425b03ca191a9494a03d29edfce11cf2ad 100644
--- a/src/USER-MISC/dihedral_cosine_shift_exp.h
+++ b/src/USER-MISC/dihedral_cosine_shift_exp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-MISC/dihedral_table.cpp b/src/USER-MISC/dihedral_table.cpp
index b493cc68bf531f28d60faa9a59ac92a7b40b61ec..89d4b6e39d0d48a34f6c44904dcfdc728f6ed380 100644
--- a/src/USER-MISC/dihedral_table.cpp
+++ b/src/USER-MISC/dihedral_table.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -90,19 +90,19 @@ void DihedralTable::compute(int eflag, int vflag)
// The dihedral angle "phi" is the angle between n123 and n234
// the planes defined by atoms i1,i2,i3, and i2,i3,i4.
//
- // Definitions of vectors: vb12, vb23, vb34, perp12on23
+ // Definitions of vectors: vb12, vb23, vb34, perp12on23
// proj12on23, perp43on32, proj43on32
//
// Note: The positions of the 4 atoms are labeled x[i1], x[i2], x[i3], x[i4]
// (which are also vectors)
//
- // proj12on23 proj34on23
- // ---------> ----------->
- // .
- // .
- // .
- // x[i2] . x[i3]
- // . __@----------vb23-------->@ . . . . .
+ // proj12on23 proj34on23
+ // ---------> ----------->
+ // .
+ // .
+ // .
+ // x[i2] . x[i3]
+ // . __@----------vb23-------->@ . . . . .
// /|\ /| \ |
// | / \ |
// | / \ |
@@ -115,9 +115,9 @@ void DihedralTable::compute(int eflag, int vflag)
// | / \ |
// @ \ |
// _\| \|/
- // x[i1] @
- //
- // x[i4]
+ // x[i1] @
+ //
+ // x[i4]
//
double vb12[g_dim]; // displacement vector from atom i1 towards atom i2
@@ -159,11 +159,11 @@ void DihedralTable::compute(int eflag, int vflag)
//
// Phi() calculates the dihedral angle.
- // This function also calculates the vectors:
+ // This function also calculates the vectors:
// vb12, vb23, vb34, n123, and n234, which we will need later.
- double phi = Phi(x[i1], x[i2], x[i3], x[i4], domain,
+ double phi = Phi(x[i1], x[i2], x[i3], x[i4], domain,
vb12, vb23, vb34, n123, n234);
@@ -171,7 +171,7 @@ void DihedralTable::compute(int eflag, int vflag)
//
// Gradient variables:
//
- // dphi_dx1, dphi_dx2, dphi_dx3, dphi_dx4 are the gradients of phi with
+ // dphi_dx1, dphi_dx2, dphi_dx3, dphi_dx4 are the gradients of phi with
// respect to the atomic positions of atoms i1, i2, i3, i4, respectively.
// As an example, consider dphi_dx1. The d'th element is:
double dphi_dx1[g_dim]; // d phi
@@ -223,8 +223,8 @@ void DihedralTable::compute(int eflag, int vflag)
// --- Compute the gradient vectors dphi/dx2 and dphi/dx3: ---
//
- // This is more tricky because atoms 2 and 3 are shared by both planes
- // 123 and 234 (the angle between which defines "phi"). Moving either
+ // This is more tricky because atoms 2 and 3 are shared by both planes
+ // 123 and 234 (the angle between which defines "phi"). Moving either
// one of these atoms effects both the 123 and 234 planes
// Both the 123 and 234 planes intersect with the plane perpendicular to the
// central bond axis (vb23). The two lines where these intersections occur
@@ -257,9 +257,9 @@ void DihedralTable::compute(int eflag, int vflag)
for (int d=0; d < g_dim; ++d) {
// Recall that the n123 and n234 plane normal vectors are proportional to
- // the dphi/dx1 and dphi/dx2 gradients vectors
+ // the dphi/dx1 and dphi/dx2 gradients vectors
// It turns out we can save slightly more CPU cycles by expressing
- // dphi/dx2 and dphi/dx3 as linear combinations of dphi/dx1 and dphi/dx2
+ // dphi/dx2 and dphi/dx3 as linear combinations of dphi/dx1 and dphi/dx2
// which we computed already (instead of n123 & n234).
dphi_dx2[d] = dphi123_dx2_coef*dphi_dx1[d] + dphi234_dx2_coef*dphi_dx4[d];
dphi_dx3[d] = dphi123_dx3_coef*dphi_dx1[d] + dphi234_dx3_coef*dphi_dx4[d];
@@ -274,7 +274,7 @@ void DihedralTable::compute(int eflag, int vflag)
cerr << " -- testing gradient for dihedral (n="<<n<<") for atoms ("
<< i1 << "," << i2 << "," << i3 << "," << i4 << ") --" << endl;
- PrintGradientComparison(*this, dphi_dx1, dphi_dx2, dphi_dx3, dphi_dx4,
+ PrintGradientComparison(*this, dphi_dx1, dphi_dx2, dphi_dx3, dphi_dx4,
domain, x[i1], x[i2], x[i3], x[i4]);
for (int d=0; d < g_dim; ++d) {
@@ -365,7 +365,7 @@ double DihedralTable::single(int type, int i1, int i2, int i3, int i4)
double **x = atom->x;
- double phi = Phi(x[i1], x[i2], x[i3], x[i4], domain,
+ double phi = Phi(x[i1], x[i2], x[i3], x[i4], domain,
vb12, vb23, vb34, n123, n234);
double u;
@@ -392,7 +392,7 @@ void DihedralTable::allocate()
/* ----------------------------------------------------------------------
- global settings
+ global settings
------------------------------------------------------------------------- */
void DihedralTable::settings(int narg, char **arg)
@@ -404,7 +404,7 @@ void DihedralTable::settings(int narg, char **arg)
else error->all(FLERR,"Unknown table style in dihedral style table");
tablength = force->inumeric(arg[1]);
- if (tablength < 3)
+ if (tablength < 3)
error->all(FLERR,"Illegal number of dihedral table entries");
// delete old tables, since cannot just change settings
@@ -438,7 +438,7 @@ void DihedralTable::coeff(int narg, char **arg)
int me;
MPI_Comm_rank(world,&me);
- tables = (Table *)
+ tables = (Table *)
memory->srealloc(tables,(ntables+1)*sizeof(Table), "dihedral:tables");
Table *tb = &tables[ntables];
null_table(tb);
@@ -461,11 +461,11 @@ void DihedralTable::coeff(int narg, char **arg)
if (tb->phifile[i] >= tb->phifile[i+1]) {
stringstream i_str;
i_str << i+1;
- string err_msg =
+ string err_msg =
string("Dihedral table values are not increasing (") +
- string(arg[2]) + string(", ")+i_str.str()+string("th entry)");
+ string(arg[2]) + string(", ")+i_str.str()+string("th entry)");
if (i==0)
- err_msg += string("\n(This is probably a mistake with your table format.)\n");
+ err_msg += string("\n(This is probably a mistake with your table format.)\n");
error->all(FLERR,err_msg.c_str());
}
}
@@ -477,7 +477,7 @@ void DihedralTable::coeff(int narg, char **arg)
if ((phihi - philo) >= 360) {
string err_msg;
err_msg = string("Dihedral table angle range must be < 360 degrees (")
- +string(arg[2]) + string(").");
+ +string(arg[2]) + string(").");
error->all(FLERR,err_msg.c_str());
}
}
@@ -485,7 +485,7 @@ void DihedralTable::coeff(int narg, char **arg)
if ((phihi - philo) >= TWOPI) {
string err_msg;
err_msg = string("Dihedral table angle range must be < 2*PI radians (")
- + string(arg[2]) + string(").");
+ + string(arg[2]) + string(").");
error->all(FLERR,err_msg.c_str());
}
}
@@ -505,13 +505,13 @@ void DihedralTable::coeff(int narg, char **arg)
// We also want the angles to be sorted in increasing order.
// This messy code fixes these problems with the user's data:
{
- double *phifile_tmp = new double [tb->ninput]; //temporary arrays
+ double *phifile_tmp = new double [tb->ninput]; //temporary arrays
double *ffile_tmp = new double [tb->ninput]; //used for sorting
double *efile_tmp = new double [tb->ninput];
// After re-imaging, does the range of angles cross the 0 or 2*PI boundary?
// If so, find the discontinuity:
- int i_discontinuity = tb->ninput;
+ int i_discontinuity = tb->ninput;
for (int i=0; i < tb->ninput; i++) {
double phi = tb->phifile[i];
// Add a multiple of 2*PI to phi until it lies in the range [0, 2*PI).
@@ -576,27 +576,27 @@ void DihedralTable::coeff(int narg, char **arg)
double phi = i*TWOPI/tablength;
double f;
if ((tabstyle == SPLINE) && (tb->f_unspecified)) {
- double dU_dphi =
+ double dU_dphi =
// (If the user did not specify the forces now, AND the user
- // selected the "spline" option, (as opposed to "linear")
- // THEN the tb->f array is uninitialized, so there's
- // no point to print out the contents of the tb->f[] array.
- // Instead, later on, we will calculate the force using the
- // -cyc_splintD() routine to calculate the derivative of the
- // energy spline, using the energy data (tb->e[]).
+ // selected the "spline" option, (as opposed to "linear")
+ // THEN the tb->f array is uninitialized, so there's
+ // no point to print out the contents of the tb->f[] array.
+ // Instead, later on, we will calculate the force using the
+ // -cyc_splintD() routine to calculate the derivative of the
+ // energy spline, using the energy data (tb->e[]).
// To be nice and report something, I do the same thing here.)
cyc_splintD(tb->phi, tb->e, tb->e2, tablength, TWOPI,phi);
f = -dU_dphi;
}
else
- // Otherwise we calculated the tb->f[] array. Report its contents.
+ // Otherwise we calculated the tb->f[] array. Report its contents.
f = tb->f[i];
if (tb->use_degrees) {
phi *= 180.0/PI;
- // If the user wants degree angle units, we should convert our
- // internal force tables (in energy/radians) to (energy/degrees)
- f *= PI/180.0;
- }
+ // If the user wants degree angle units, we should convert our
+ // internal force tables (in energy/radians) to (energy/degrees)
+ f *= PI/180.0;
+ }
checkF_file << phi << " " << f << "\n";
}
checkF_file.close();
@@ -614,7 +614,7 @@ void DihedralTable::coeff(int narg, char **arg)
}
ntables++;
- if (count == 0)
+ if (count == 0)
error->all(FLERR,"Illegal dihedral_coeff command");
} //DihedralTable::coeff()
@@ -667,7 +667,7 @@ void DihedralTable::free_table(Table *tb)
memory->destroy(tb->ffile);
memory->destroy(tb->e2file);
memory->destroy(tb->f2file);
-
+
memory->destroy(tb->phi);
memory->destroy(tb->e);
memory->destroy(tb->de);
@@ -698,7 +698,7 @@ void DihedralTable::read_table(Table *tb, char *file, char *keyword)
while (1) {
if (fgets(line,MAXLINE,fp) == NULL) {
string err_msg=string("Did not find keyword \"")
- +string(keyword)+string("\" in dihedral table file.");
+ +string(keyword)+string("\" in dihedral table file.");
error->one(FLERR, err_msg.c_str());
}
if (strspn(line," \t\n\r") == strlen(line)) continue; // blank line
@@ -736,25 +736,25 @@ void DihedralTable::read_table(Table *tb, char *file, char *keyword)
if (tb->f_unspecified) {
//sscanf(line,"%d %lg %lg",
// &itmp,&tb->phifile[i],&tb->efile[i]);
- line_ss >> itmp;
- line_ss >> tb->phifile[i];
- line_ss >> tb->efile[i];
+ line_ss >> itmp;
+ line_ss >> tb->phifile[i];
+ line_ss >> tb->efile[i];
}
else {
//sscanf(line,"%d %lg %lg %lg",
// &itmp,&tb->phifile[i],&tb->efile[i],&tb->ffile[i]);
- line_ss >> itmp;
- line_ss >> tb->phifile[i];
- line_ss >> tb->efile[i];
- line_ss >> tb->ffile[i];
+ line_ss >> itmp;
+ line_ss >> tb->phifile[i];
+ line_ss >> tb->efile[i];
+ line_ss >> tb->ffile[i];
}
if (! line_ss) {
- stringstream err_msg;
- err_msg << "Read error in table "<< keyword<<", near line "<<i+1<<"\n"
- << " (Check to make sure the number of colums is correct.)";
- if ((! tb->f_unspecified) && (i==0))
- err_msg << "\n (This sometimes occurs if users forget to specify the \"NOF\" option.)\n";
- error->one(FLERR, err_msg.str().c_str());
+ stringstream err_msg;
+ err_msg << "Read error in table "<< keyword<<", near line "<<i+1<<"\n"
+ << " (Check to make sure the number of colums is correct.)";
+ if ((! tb->f_unspecified) && (i==0))
+ err_msg << "\n (This sometimes occurs if users forget to specify the \"NOF\" option.)\n";
+ error->one(FLERR, err_msg.str().c_str());
}
}
else //if it is a blank line, then skip it.
@@ -766,7 +766,7 @@ void DihedralTable::read_table(Table *tb, char *file, char *keyword)
/* ----------------------------------------------------------------------
build spline representation of e,f over entire range of read-in table
- this function sets these values in e2file,f2file.
+ this function sets these values in e2file,f2file.
I also perform a crude check for force & energy consistency.
------------------------------------------------------------------------- */
@@ -781,7 +781,7 @@ void DihedralTable::spline_table(Table *tb)
cyc_spline(tb->phifile, tb->ffile, tb->ninput, TWOPI, tb->f2file);
}
- // CHECK to help make sure the user calculated forces in a way
+ // CHECK to help make sure the user calculated forces in a way
// which is grossly numerically consistent with the energy table.
// --------------------------------------------------
// This is an ugly piece of code
@@ -790,7 +790,7 @@ void DihedralTable::spline_table(Table *tb)
int num_disagreements = 0;
for (int i=0; i<tb->ninput; i++) {
- // Calculate what the force should be at the control points
+ // Calculate what the force should be at the control points
// by using linear interpolation of the derivatives of the energy:
double phi_i = tb->phifile[i];
@@ -802,14 +802,14 @@ void DihedralTable::spline_table(Table *tb)
im1 += tb->ninput;
phi_im1 = tb->phifile[im1] - TWOPI;
}
- else
+ else
phi_im1 = tb->phifile[im1];
int ip1 = i+1;
if (ip1 >= tb->ninput) {
ip1 -= tb->ninput;
phi_ip1 = tb->phifile[ip1] + TWOPI;
}
- else
+ else
phi_ip1 = tb->phifile[ip1];
// Now calculate the midpoints above and below phi_i = tb->phifile[i]
@@ -817,16 +817,16 @@ void DihedralTable::spline_table(Table *tb)
double phi_hi= 0.5*(phi_i + phi_ip1); //midpoint between phi_i and phi_ip1
// Use a linear approximation to the derivative at these two midpoints
- double dU_dphi_lo =
+ double dU_dphi_lo =
(tb->efile[i] - tb->efile[im1])
- /
- (phi_i - phi_im1);
- double dU_dphi_hi =
+ /
+ (phi_i - phi_im1);
+ double dU_dphi_hi =
(tb->efile[ip1] - tb->efile[i])
- /
- (phi_ip1 - phi_i);
+ /
+ (phi_ip1 - phi_i);
- // Now calculate the derivative at position
+ // Now calculate the derivative at position
// phi_i (=tb->phifile[i]) using linear interpolation
double a = (phi_i - phi_lo) / (phi_hi - phi_lo);
@@ -842,7 +842,7 @@ void DihedralTable::spline_table(Table *tb)
// anything important. It does not have to be perfect.
// We are only checking for stupid user errors here.
- if ((f != 0.0) &&
+ if ((f != 0.0) &&
(tb->ffile[i] != 0.0) &&
((f/tb->ffile[i] < 0.5) || (f/tb->ffile[i] > 2.0))) {
num_disagreements++;
@@ -883,7 +883,7 @@ void DihedralTable::compute_table(Table *tb)
memory->create(tb->e2,tablength,"dihedral:e2");
memory->create(tb->f2,tablength,"dihedral:f2");
- // Use cubic spline interpolation to calculate the entries in the
+ // Use cubic spline interpolation to calculate the entries in the
// internal table. (This is true regardless...even if tabstyle!=SPLINE.)
for (int i = 0; i < tablength; i++) {
double phi = i*tb->delta;
@@ -965,7 +965,7 @@ void DihedralTable::param_extract(Table *tb, char *line)
//else if (strcmp(word,"EQ") == 0) {
// word = strtok(NULL," \t\n\r\f");
// tb->theta0 = atof(word);
- //}
+ //}
else {
string err_msg("Invalid keyword in dihedral angle table parameters");
err_msg += string(" (") + string(word) + string(")");
@@ -974,7 +974,7 @@ void DihedralTable::param_extract(Table *tb, char *line)
word = strtok(NULL," \t\n\r\f");
}
- if (tb->ninput == 0)
+ if (tb->ninput == 0)
error->one(FLERR,"Dihedral table parameters did not set N");
} // DihedralTable::param_extract()
@@ -1010,7 +1010,7 @@ void DihedralTable::bcast_table(Table *tb)
//MPI_Bcast(&tb->theta0,1,MPI_DOUBLE,0,world);
}
-
+
namespace LAMMPS_NS {
namespace DIHEDRAL_TABLE_NS {
@@ -1042,7 +1042,7 @@ enum { //GSL status return codes.
};
-int
+int
solve_cyc_tridiag(
const double diag[], size_t d_stride,
const double offdiag[], size_t o_stride,
@@ -1068,7 +1068,7 @@ solve_cyc_tridiag(
/* factor */
- if (N == 1)
+ if (N == 1)
{
x[0] = b[0] / diag[0];
return GSL_SUCCESS;
@@ -1157,15 +1157,15 @@ solve_cyc_tridiag(
spline and splint routines modified from Numerical Recipes
------------------------------------------------------------------------- */
-void cyc_spline(double const *xa,
- double const *ya,
+void cyc_spline(double const *xa,
+ double const *ya,
int n,
- double period,
+ double period,
double *y2a)
{
- double *diag = new double[n];
- double *offdiag = new double[n];
+ double *diag = new double[n];
+ double *offdiag = new double[n];
double *rhs = new double[n];
double xa_im1, xa_ip1;
@@ -1175,7 +1175,7 @@ void cyc_spline(double const *xa,
for(int i=0; i < n; i++) {
- // I have to lookup xa[i+1] and xa[i-1]. This gets tricky because of
+ // I have to lookup xa[i+1] and xa[i-1]. This gets tricky because of
// periodic boundary conditions. We handle that now.
int im1 = i-1;
if (im1<0) {
@@ -1195,7 +1195,7 @@ void cyc_spline(double const *xa,
// Recall that we want to find the y2a[] parameters (there are n of them).
// To solve for them, we have a linear equation with n unknowns
- // (in the cyclic case that is). For details, the non-cyclic case is
+ // (in the cyclic case that is). For details, the non-cyclic case is
// explained in equation 3.3.7 in Numerical Recipes in C, p. 115.
diag[i] = (xa_ip1 - xa_im1) / 3.0;
offdiag[i] = (xa_ip1 - xa[i]) / 6.0;
@@ -1207,10 +1207,10 @@ void cyc_spline(double const *xa,
// thousands of rows and columns). However because this matix happens
// to be tridiagonal (and cyclic), we can use the following cheap method:
solve_cyc_tridiag(diag, 1,
- offdiag, 1,
- rhs, 1,
- y2a, 1,
- n);
+ offdiag, 1,
+ rhs, 1,
+ y2a, 1,
+ n);
delete [] diag;
delete [] offdiag;
@@ -1224,14 +1224,14 @@ void cyc_spline(double const *xa,
// cyc_splint(): Evaluates a spline at position x, with n control
// points located at xa[], ya[], and with parameters y2a[]
-// The xa[] must be monotonically increasing and their
-// range should not exceed period (ie xa[n-1] < xa[0] + period).
+// The xa[] must be monotonically increasing and their
+// range should not exceed period (ie xa[n-1] < xa[0] + period).
// x must lie in the range: [(xa[n-1]-period), (xa[0]+period)]
// "period" is typically 2*PI.
-double cyc_splint(double const *xa,
- double const *ya,
- double const *y2a,
- int n,
+double cyc_splint(double const *xa,
+ double const *ya,
+ double const *y2a,
+ int n,
double period,
double x)
{
@@ -1260,7 +1260,7 @@ double cyc_splint(double const *xa,
double h = xhi-xlo;
double a = (xhi-x) / h;
double b = (x-xlo) / h;
- double y = a*ya[klo] + b*ya[khi] +
+ double y = a*ya[klo] + b*ya[khi] +
((a*a*a-a)*y2a[klo] + (b*b*b-b)*y2a[khi]) * (h*h)/6.0;
return y;
@@ -1269,16 +1269,16 @@ double cyc_splint(double const *xa,
-// cyc_splintD(): Evaluate the deriviative of a cyclic spline at position x,
+// cyc_splintD(): Evaluate the deriviative of a cyclic spline at position x,
// with n control points at xa[], ya[], with parameters y2a[].
-// The xa[] must be monotonically increasing and their
-// range should not exceed period (ie xa[n-1] < xa[0] + period).
+// The xa[] must be monotonically increasing and their
+// range should not exceed period (ie xa[n-1] < xa[0] + period).
// x must lie in the range: [(xa[n-1]-period), (xa[0]+period)]
// "period" is typically 2*PI.
-double cyc_splintD(double const *xa,
- double const *ya,
- double const *y2a,
- int n,
+double cyc_splintD(double const *xa,
+ double const *ya,
+ double const *y2a,
+ int n,
double period,
double x)
{
@@ -1313,7 +1313,7 @@ double cyc_splintD(double const *xa,
// Formula below taken from equation 3.3.5 of "numerical recipes in c"
// "yD" = the derivative of y
double yD = g/h - ( (3.0*a*a-1.0)*y2a[klo] - (3.0*b*b-1.0)*y2a[khi] ) * h/6.0;
- // For rerefence: y = a*ylo + b*yhi +
+ // For rerefence: y = a*ylo + b*yhi +
// ((a*a*a-a)*y2a[klo] + (b*b*b-b)*y2a[khi]) * (h*h)/6.0;
return yD;
diff --git a/src/USER-MISC/dihedral_table.h b/src/USER-MISC/dihedral_table.h
index 12b8ce6a4950d1ac1041b2a3377f9eb54345faaf..4635e127b1c92381b5c0192ab7142a9e27663fe8 100644
--- a/src/USER-MISC/dihedral_table.h
+++ b/src/USER-MISC/dihedral_table.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -62,7 +62,7 @@ class DihedralTable : public Dihedral {
int ntables;
Table *tables;
int *tabindex;
-
+
void allocate();
void null_table(Table *);
void free_table(Table *);
@@ -78,7 +78,7 @@ class DihedralTable : public Dihedral {
// --------------------------------------------
// -----------------------------------------------------------
- // uf_lookup()
+ // uf_lookup()
// quickly calculate the potential u and force f at angle x,
// using the internal tables tb->e and tb->f (evenly spaced)
// -----------------------------------------------------------
@@ -97,24 +97,24 @@ class DihedralTable : public Dihedral {
switch(tabstyle) {
case LINEAR:
- u = tb->e[i] + b * tb->de[i];
- f = tb->f[i] + b * tb->df[i]; //<--works even if tb->f_unspecified==true
- break;
+ u = tb->e[i] + b * tb->de[i];
+ f = tb->f[i] + b * tb->df[i]; //<--works even if tb->f_unspecified==true
+ break;
case SPLINE:
- a = 1.0 - b;
- u = a * tb->e[i] + b * tb->e[ip1] +
- ((a*a*a-a)*tb->e2[i] + (b*b*b-b)*tb->e2[ip1]) *
- tb->deltasq6;
- if (tb->f_unspecified)
- //Formula below taken from equation3.3.5 of "numerical recipes in c"
- //"f"=-derivative of e with respect to x (or "phi" in this case)
- f = (tb->e[i]-tb->e[ip1])*tb->invdelta +
- ((3.0*a*a-1.0)*tb->e2[i]+(1.0-3.0*b*b)*tb->e2[ip1])*tb->delta/6.0;
- else
- f = a * tb->f[i] + b * tb->f[ip1] +
- ((a*a*a-a)*tb->f2[i] + (b*b*b-b)*tb->f2[ip1]) *
- tb->deltasq6;
- break;
+ a = 1.0 - b;
+ u = a * tb->e[i] + b * tb->e[ip1] +
+ ((a*a*a-a)*tb->e2[i] + (b*b*b-b)*tb->e2[ip1]) *
+ tb->deltasq6;
+ if (tb->f_unspecified)
+ //Formula below taken from equation3.3.5 of "numerical recipes in c"
+ //"f"=-derivative of e with respect to x (or "phi" in this case)
+ f = (tb->e[i]-tb->e[ip1])*tb->invdelta +
+ ((3.0*a*a-1.0)*tb->e2[i]+(1.0-3.0*b*b)*tb->e2[ip1])*tb->delta/6.0;
+ else
+ f = a * tb->f[i] + b * tb->f[ip1] +
+ ((a*a*a-a)*tb->f2[i] + (b*b*b-b)*tb->f2[ip1]) *
+ tb->deltasq6;
+ break;
} // switch(tabstyle)
} // uf_lookup()
@@ -143,10 +143,10 @@ class DihedralTable : public Dihedral {
}
else if (tabstyle == SPLINE) {
double a = 1.0 - b;
- u = a * tb->e[i] + b * tb->e[ip1] +
- ((a*a*a-a)*tb->e2[i] + (b*b*b-b)*tb->e2[ip1]) *
+ u = a * tb->e[i] + b * tb->e[ip1] +
+ ((a*a*a-a)*tb->e2[i] + (b*b*b-b)*tb->e2[ip1]) *
tb->deltasq6;
- }
+ }
} // u_lookup()
@@ -171,8 +171,8 @@ class DihedralTable : public Dihedral {
// ------------------------------------------------------------------------
-// The following auxiliary functions were left out of the
-// DihedralTable class either because they require template parameters,
+// The following auxiliary functions were left out of the
+// DihedralTable class either because they require template parameters,
// or because they have nothing to do with dihedral angles.
// ------------------------------------------------------------------------
@@ -184,37 +184,37 @@ static const double TWOPI = 6.2831853071795862;
// Determine the array of "y2" parameters of a cyclic spline from its control
// points at positions x[] and y[]. (spline() must be invoked before splint())
// The x[] positions should be sorted in order and not exceed period.
-void cyc_spline(double const *xa, double const *ya, int n,
+void cyc_spline(double const *xa, double const *ya, int n,
double period, double *y2a);
// Evaluate a cyclic spline at position x with n control points at xa[], ya[],
// (The y2a array must be calculated using cyc_spline() above in advance.)
// x (and all the xa[] positions) should lie in the range from 0 to period.
// (Typically period = 2*PI, but this is optional.)
-double cyc_splint(double const *xa, double const *ya, double const *y2a,
+double cyc_splint(double const *xa, double const *ya, double const *y2a,
int n, double period, double x);
// Evaluate the deriviative of a cyclic spline at position x:
-double cyc_splintD(double const *xa, double const *ya, double const *y2a,
+double cyc_splintD(double const *xa, double const *ya, double const *y2a,
int n, double period, double x);
// -----------------------------------------------------------
// ---- some simple vector operations are defined below. ----
// -----------------------------------------------------------
-// --- g_dim --- As elsewhere in the LAMMPS code, coordinates here are
+// --- g_dim --- As elsewhere in the LAMMPS code, coordinates here are
// represented as entries in an array, not as named variables "x" "y" "z".
-// (I like this style.) In this spirit, the vector operations here are
-// defined for vectors of arbitrary size. For this to work, the number
+// (I like this style.) In this spirit, the vector operations here are
+// defined for vectors of arbitrary size. For this to work, the number
// of dimensions, "g_dim", must be known at compile time:
const int g_dim = 3;
-// In LAMMPS at least, this constant is always 3, and is only used inside
+// In LAMMPS at least, this constant is always 3, and is only used inside
// the dihedral code here. (It should not conflict with 2-D simulations.)
// Note: Compiler optimizations should eliminate any performance overhead
// associated with loops like "for (int i=0; i<g_dim; i++)"
// If having a constant named "g_dim" is confusing people, I suppose
-// we can replace it with "3". Note: the supplemental file
-// "nd/dihedral_table_nd_mod.h" shows how to generalize the dihedral
+// we can replace it with "3". Note: the supplemental file
+// "nd/dihedral_table_nd_mod.h" shows how to generalize the dihedral
// code in higher dimensions.
template<class _Real>
@@ -229,7 +229,7 @@ DotProduct(_Real const *A, _Real const *B)
// Normalize() divides the components of the vector "v" by it's length.
// Normalize() silently ignores divide-by-zero errors but does not
-// crash. (If "v" has length 0, then we replace v with the unit vector in
+// crash. (If "v" has length 0, then we replace v with the unit vector in
// an arbitrary direction,(1,0,...).)
// It returns the length of v (useful for checking if the operation succeeded).
template<class _Real>
@@ -240,19 +240,19 @@ Normalize(_Real *v)
if (length != 0.0)
{
_Real one_over_length = 1.0 / length;
- for (int d=0; d < g_dim; ++d)
+ for (int d=0; d < g_dim; ++d)
v[d] *= one_over_length;
}
else {
v[0] = 1.0;
- for (int d=1; d < g_dim; ++d)
+ for (int d=1; d < g_dim; ++d)
v[d] = 0.0;
}
return length;
}
-// CrossProduct(A,B,dest) computes the cross-product (A x B)
+// CrossProduct(A,B,dest) computes the cross-product (A x B)
// and stores the result in "dest".
template<class _Real>
inline void
@@ -272,7 +272,7 @@ inline double Phi(double const *x1, //array holding x,y,z coords atom 1
double const *x2, // : : : : 2
double const *x3, // : : : : 3
double const *x4, // : : : : 4
- Domain *domain, //<-periodic boundary information
+ Domain *domain, //<-periodic boundary information
// The following arrays are of doubles with g_dim elements.
// (g_dim is a constant known at compile time, usually 3).
// Their contents is calculated by this function.
diff --git a/src/USER-MISC/fix_addtorque.cpp b/src/USER-MISC/fix_addtorque.cpp
index dd9ef8ffc436cdf90c943f9073aa94debe46a204..9d0d621fe7c571d8216f04407df153aa5373364f 100644
--- a/src/USER-MISC/fix_addtorque.cpp
+++ b/src/USER-MISC/fix_addtorque.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -75,7 +75,7 @@ FixAddTorque::FixAddTorque(LAMMPS *lmp, int narg, char **arg) :
zvalue = atof(arg[5]);
zstyle = CONSTANT;
}
-
+
force_flag = 0;
foriginal[0] = foriginal[1] = foriginal[2] = foriginal[3] = 0.0;
}
@@ -167,7 +167,7 @@ void FixAddTorque::post_force(int vflag)
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
double mvv2e = force->mvv2e;
-
+
int xbox,ybox,zbox;
double dx,dy,dz,vx,vy,vz,fx,fy,fz,massone,omegadotr;
double xprd = domain->xprd;
@@ -180,7 +180,7 @@ void FixAddTorque::post_force(int vflag)
// foriginal[123] = torque on atoms before extra force added
foriginal[0] = foriginal[1] = foriginal[2] = foriginal[3] = 0.0;
force_flag = 0;
-
+
if (varflag == EQUAL) {
// variable torque, wrap with clear/add
modify->clearstep_compute();
@@ -189,7 +189,7 @@ void FixAddTorque::post_force(int vflag)
if (zstyle == EQUAL) zvalue = input->variable->compute_equal(zvar);
modify->addstep_compute(update->ntimestep + 1);
}
-
+
atom->check_mass();
double masstotal = group->mass(igroup);
group->xcm(igroup,masstotal,xcm);
@@ -214,12 +214,12 @@ void FixAddTorque::post_force(int vflag)
tlocal[2] += massone * omegadotr * (dx*omega[1] - dy*omega[0]);
}
MPI_Allreduce(tlocal,itorque,3,MPI_DOUBLE,MPI_SUM,world);
-
+
tcm[0] = xvalue - mvv2e*itorque[0];
tcm[1] = yvalue - mvv2e*itorque[1];
tcm[2] = zvalue - mvv2e*itorque[2];
group->omega(tcm,inertia,domegadt);
-
+
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
xbox = (image[i] & 1023) - 512;
@@ -236,7 +236,7 @@ void FixAddTorque::post_force(int vflag)
fx = massone * (dz*domegadt[1]-dy*domegadt[2] + vz*omega[1]-vy*omega[2]);
fy = massone * (dx*domegadt[2]-dz*domegadt[0] + vx*omega[2]-vz*omega[0]);
fz = massone * (dy*domegadt[0]-dx*domegadt[1] + vy*omega[0]-vx*omega[1]);
-
+
// potential energy = - x dot f
foriginal[0] -= fx*x[i][0] + fy*x[i][1] + fz*x[i][2];
foriginal[1] += dy*f[i][2] - dz*f[i][1];
diff --git a/src/USER-MISC/fix_addtorque.h b/src/USER-MISC/fix_addtorque.h
index 238ed9f164551c338da42d9578488477c302fd45..08438ef91dbc2bf8659872e6c28b6ebaa62dfeb2 100644
--- a/src/USER-MISC/fix_addtorque.h
+++ b/src/USER-MISC/fix_addtorque.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-MISC/fix_imd.cpp b/src/USER-MISC/fix_imd.cpp
index 48606876f0b460b323056108702d8678efcaaada..69379c0f52aa51135c055ae741206df13fc94af0 100644
--- a/src/USER-MISC/fix_imd.cpp
+++ b/src/USER-MISC/fix_imd.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -13,37 +13,37 @@
/* ----------------------------------------------------------------------
The FixIMD class contains code from VMD and NAMD which is copyrighted
- by the Board of Trustees of the University of Illinois and is free to
+ by the Board of Trustees of the University of Illinois and is free to
use with LAMMPS according to point 2 of the UIUC license (10% clause):
-" Licensee may, at its own expense, create and freely distribute
-complimentary works that interoperate with the Software, directing others to
-the TCBG server to license and obtain the Software itself. Licensee may, at
-its own expense, modify the Software to make derivative works. Except as
-explicitly provided below, this License shall apply to any derivative work
-as it does to the original Software distributed by Illinois. Any derivative
-work should be clearly marked and renamed to notify users that it is a
-modified version and not the original Software distributed by Illinois.
-Licensee agrees to reproduce the copyright notice and other proprietary
-markings on any derivative work and to include in the documentation of such
+" Licensee may, at its own expense, create and freely distribute
+complimentary works that interoperate with the Software, directing others to
+the TCBG server to license and obtain the Software itself. Licensee may, at
+its own expense, modify the Software to make derivative works. Except as
+explicitly provided below, this License shall apply to any derivative work
+as it does to the original Software distributed by Illinois. Any derivative
+work should be clearly marked and renamed to notify users that it is a
+modified version and not the original Software distributed by Illinois.
+Licensee agrees to reproduce the copyright notice and other proprietary
+markings on any derivative work and to include in the documentation of such
work the acknowledgement:
- "This software includes code developed by the Theoretical and Computational
- Biophysics Group in the Beckman Institute for Advanced Science and
+ "This software includes code developed by the Theoretical and Computational
+ Biophysics Group in the Beckman Institute for Advanced Science and
Technology at the University of Illinois at Urbana-Champaign."
-Licensee may redistribute without restriction works with up to 1/2 of their
-non-comment source code derived from at most 1/10 of the non-comment source
-code developed by Illinois and contained in the Software, provided that the
-above directions for notice and acknowledgement are observed. Any other
-distribution of the Software or any derivative work requires a separate
-license with Illinois. Licensee may contact Illinois (vmd@ks.uiuc.edu) to
+Licensee may redistribute without restriction works with up to 1/2 of their
+non-comment source code derived from at most 1/10 of the non-comment source
+code developed by Illinois and contained in the Software, provided that the
+above directions for notice and acknowledgement are observed. Any other
+distribution of the Software or any derivative work requires a separate
+license with Illinois. Licensee may contact Illinois (vmd@ks.uiuc.edu) to
negotiate an appropriate license for such distribution."
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Axel Kohlmeyer (TempleU)
- IMD API, hash, and socket code written by: John E. Stone,
+ IMD API, hash, and socket code written by: John E. Stone,
Justin Gullingsrud, and James Phillips, (TCBG, Beckman Institute, UIUC)
------------------------------------------------------------------------- */
@@ -124,7 +124,7 @@ static int inthash(const inthash_t *tptr, int key) {
hashvalue = (((key*1103515249)>>tptr->downshift) & tptr->mask);
if (hashvalue < 0) {
hashvalue = 0;
- }
+ }
return hashvalue;
}
@@ -224,15 +224,15 @@ int *inthash_keys(inthash_t *tptr) {
int *keys;
inthash_node_t *node;
-
+
keys = (int *)calloc(tptr->entries, sizeof(int));
-
+
for (int i=0; i < tptr->size; ++i) {
for (node=tptr->bucket[i]; node != NULL; node=node->next) {
keys[node->data] = node->key;
}
}
-
+
return keys;
}
@@ -271,7 +271,7 @@ int inthash_insert(inthash_t *tptr, int key, int data) {
/*
* inthash_destroy() - Delete the entire table, and all remaining entries.
- *
+ *
*/
void inthash_destroy(inthash_t *tptr) {
inthash_node_t *node, *last;
@@ -279,12 +279,12 @@ void inthash_destroy(inthash_t *tptr) {
for (i=0; i<tptr->size; i++) {
node = tptr->bucket[i];
- while (node != NULL) {
- last = node;
+ while (node != NULL) {
+ last = node;
node = node->next;
free(last);
}
- }
+ }
/* free the entire array of buckets */
if (tptr->bucket != NULL) {
@@ -432,22 +432,22 @@ using namespace LAMMPS_NS;
using namespace FixConst;
/* struct for packed data communication of coordinates and forces. */
-struct commdata {
- int tag;
- float x,y,z;
+struct commdata {
+ int tag;
+ float x,y,z;
};
/***************************************************************
- * create class and parse arguments in LAMMPS script. Syntax:
- * fix ID group-ID imd <imd_trate> <imd_port> [unwrap (on|off)] [fscale <imd_fscale>]
+ * create class and parse arguments in LAMMPS script. Syntax:
+ * fix ID group-ID imd <imd_trate> <imd_port> [unwrap (on|off)] [fscale <imd_fscale>]
***************************************************************/
FixIMD::FixIMD(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
- if (narg < 4)
+ if (narg < 4)
error->all(FLERR,"Illegal fix imd command");
- imd_port = atoi(arg[3]);
+ imd_port = atoi(arg[3]);
if (imd_port < 1024)
error->all(FLERR,"Illegal fix imd parameter: port < 1024");
@@ -457,18 +457,18 @@ FixIMD::FixIMD(LAMMPS *lmp, int narg, char **arg) :
connect_msg = 1;
imd_fscale = 1.0;
imd_trate = 1;
-
+
/* parse optional arguments */
int argsdone = 4;
while (argsdone+1 < narg) {
if (0 == strcmp(arg[argsdone], "unwrap")) {
- if (0 == strcmp(arg[argsdone+1], "on")) {
+ if (0 == strcmp(arg[argsdone+1], "on")) {
unwrap_flag = 1;
} else {
unwrap_flag = 0;
}
} else if (0 == strcmp(arg[argsdone], "nowait")) {
- if (0 == strcmp(arg[argsdone+1], "on")) {
+ if (0 == strcmp(arg[argsdone+1], "on")) {
nowait_flag = 1;
} else {
nowait_flag = 0;
@@ -507,7 +507,7 @@ FixIMD::FixIMD(LAMMPS *lmp, int narg, char **arg) :
comm_buf = NULL;
idmap = NULL;
rev_idmap = NULL;
-
+
if (me == 0) {
/* set up incoming socket on MPI rank 0. */
imdsock_init();
@@ -524,7 +524,7 @@ FixIMD::FixIMD(LAMMPS *lmp, int narg, char **arg) :
MPI_Bcast(&imd_terminate, 1, MPI_INT, 0, world);
if (imd_terminate)
error->all(FLERR,"LAMMPS Terminated on error in IMD.");
-
+
/* storage required to communicate a single coordinate or force. */
size_one = sizeof(struct commdata);
@@ -618,7 +618,7 @@ int FixIMD::reconnect()
/* set up IMD communication, but only if needed. */
imd_inactive = 0;
imd_terminate = 0;
-
+
if (me == 0) {
if (clientsock) return 1;
if (screen && connect_msg)
@@ -626,7 +626,7 @@ int FixIMD::reconnect()
fprintf(screen,"Listening for IMD connection on port %d. Transfer rate %d.\n",imd_port, imd_trate);
else
fprintf(screen,"Waiting for IMD connection on port %d. Transfer rate %d.\n",imd_port, imd_trate);
-
+
connect_msg = 0;
clientsock = NULL;
if (nowait_flag) {
@@ -644,7 +644,7 @@ int FixIMD::reconnect()
} while (retval <= 0);
clientsock = imdsock_accept(localsock);
}
-
+
if (!imd_inactive && !clientsock) {
if (screen)
fprintf(screen, "IMD socket accept error. Dropping connection.\n");
@@ -677,7 +677,7 @@ int FixIMD::reconnect()
}
/* ---------------------------------------------------------------------- */
-/* wait for IMD client (e.g. VMD) to respond, initialize communication
+/* wait for IMD client (e.g. VMD) to respond, initialize communication
* buffers and collect tag/id maps. */
void FixIMD::setup(int)
{
@@ -709,7 +709,7 @@ void FixIMD::setup(int)
inthash_t *hashtable=new inthash_t;
inthash_init(hashtable, num_coords);
idmap = (void *)hashtable;
-
+
MPI_Status status;
MPI_Request request;
int tmp, ndata;
@@ -718,14 +718,14 @@ void FixIMD::setup(int)
if (me == 0) {
int *taglist = new int[num_coords];
int numtag=0; /* counter to map atom tags to a 0-based consecutive index list */
-
+
for (i=0; i < nlocal; ++i) {
if (mask[i] & groupbit) {
taglist[numtag] = tag[i];
++numtag;
}
}
-
+
/* loop over procs to receive remote data */
for (i=1; i < comm->nprocs; ++i) {
MPI_Irecv(comm_buf, maxbuf, MPI_BYTE, i, 0, world, &request);
@@ -740,7 +740,7 @@ void FixIMD::setup(int)
}
}
- /* sort list of tags by value to have consistently the
+ /* sort list of tags by value to have consistently the
* same list when running in parallel and build hash table. */
id_sort(taglist, 0, num_coords-1);
for (i=0; i < num_coords; ++i) {
@@ -748,7 +748,7 @@ void FixIMD::setup(int)
}
delete[] taglist;
- /* generate reverse index-to-tag map for communicating
+ /* generate reverse index-to-tag map for communicating
* IMD forces back to the proper atoms */
rev_idmap=inthash_keys(hashtable);
} else {
@@ -763,7 +763,7 @@ void FixIMD::setup(int)
MPI_Recv(&tmp, 0, MPI_INT, 0, 0, world, &status);
MPI_Rsend(comm_buf, nme*size_one, MPI_BYTE, 0, 0, world);
}
-
+
return;
}
@@ -834,7 +834,7 @@ void FixIMD::post_force(int vflag)
while ((imdsock_selread(clientsock, 0) > 0) || imd_paused) {
/* if something requested to turn off IMD while paused get out */
if (imd_inactive) break;
-
+
int32 length;
int msg = imd_recv_header(clientsock, &length);
@@ -881,7 +881,7 @@ void FixIMD::post_force(int vflag)
case IMD_PAUSE:
/* pause the running simulation. wait for second IMD_PAUSE to continue. */
if (imd_paused) {
- if (screen)
+ if (screen)
fprintf(screen, "Continuing run on IMD client request.\n");
imd_paused = 0;
} else {
@@ -893,9 +893,9 @@ void FixIMD::post_force(int vflag)
case IMD_TRATE:
/* change the IMD transmission data rate */
- if (length > 0)
+ if (length > 0)
imd_trate = length;
- if (screen)
+ if (screen)
fprintf(screen, "IMD client requested change of transfer rate. Now it is %d.\n", imd_trate);
break;
@@ -904,7 +904,7 @@ void FixIMD::post_force(int vflag)
imd_recv_energies(clientsock, &dummy_energies);
break;
}
-
+
case IMD_FCOORDS: {
float *dummy_coords = new float[3*length];
imd_recv_fcoords(clientsock, length, dummy_coords);
@@ -924,7 +924,7 @@ void FixIMD::post_force(int vflag)
}
imd_forces = length;
buf = static_cast<struct commdata *>(force_buf);
-
+
/* compare data to hash table */
for (int ii=0; ii < length; ++ii) {
buf[ii].tag = rev_idmap[imd_tags[ii]];
@@ -936,7 +936,7 @@ void FixIMD::post_force(int vflag)
delete[] imd_fdat;
break;
}
-
+
default:
if (screen)
fprintf(screen, "Unhandled incoming IMD message #%d. length=%d\n", msg, length);
@@ -944,11 +944,11 @@ void FixIMD::post_force(int vflag)
}
}
}
-
+
/* update all tasks with current settings. */
int old_imd_forces = imd_forces;
MPI_Bcast(&imd_trate, 1, MPI_INT, 0, world);
- MPI_Bcast(&imd_inactive, 1, MPI_INT, 0, world);
+ MPI_Bcast(&imd_inactive, 1, MPI_INT, 0, world);
MPI_Bcast(&imd_forces, 1, MPI_INT, 0, world);
MPI_Bcast(&imd_terminate, 1, MPI_INT, 0, world);
if (imd_terminate)
@@ -958,7 +958,7 @@ void FixIMD::post_force(int vflag)
/* check if we need to readjust the forces comm buffer on the receiving nodes. */
if (me != 0) {
if (old_imd_forces < imd_forces) { /* grow holding space for forces, if needed. */
- if (force_buf != NULL)
+ if (force_buf != NULL)
memory->sfree(force_buf);
force_buf = memory->smalloc(imd_forces*size_one, "imd:force_buf");
}
@@ -971,16 +971,16 @@ void FixIMD::post_force(int vflag)
* at the expense of a more jumpy display. Rather than using
* end_of_step() we do everything here in one go.
*
- * If we don't communicate, only check if we have forces
+ * If we don't communicate, only check if we have forces
* stored away and apply them. */
if (update->ntimestep % imd_trate) {
if (imd_forces > 0) {
double **f = atom->f;
buf = static_cast<struct commdata *>(force_buf);
- /* XXX. this is in principle O(N**2) == not good.
- * however we assume for now that the number of atoms
- * that we manipulate via IMD will be small compared
+ /* XXX. this is in principle O(N**2) == not good.
+ * however we assume for now that the number of atoms
+ * that we manipulate via IMD will be small compared
* to the total system size, so we don't hurt too much. */
for (int j=0; j < imd_forces; ++j) {
for (int i=0; i < nlocal; ++i) {
@@ -996,7 +996,7 @@ void FixIMD::post_force(int vflag)
}
return;
}
-
+
/* check and potentially grow local communication buffers. */
int i, k, nmax, nme=0;
for (i=0; i < nlocal; ++i)
@@ -1013,7 +1013,7 @@ void FixIMD::post_force(int vflag)
MPI_Request request;
int tmp, ndata;
buf = static_cast<struct commdata *>(comm_buf);
-
+
if (me == 0) {
/* collect data into new array. we bypass the IMD API to save
* us one extra copy of the data. */
@@ -1072,7 +1072,7 @@ void FixIMD::post_force(int vflag)
MPI_Wait(&request, &status);
MPI_Get_count(&status, MPI_BYTE, &ndata);
ndata /= size_one;
-
+
for (k=0; k<ndata; ++k) {
const int j = 3*inthash_lookup((inthash_t *)idmap, buf[k].tag);
if (j != HASH_FAIL) {
@@ -1169,12 +1169,12 @@ double FixIMD::memory_usage(void)
/***************************************************************************/
/* NOTE: the following code is the based on the example implementation
- * of the IMD protocol API from VMD and NAMD. The UIUC license allows
+ * of the IMD protocol API from VMD and NAMD. The UIUC license allows
* to re-use up to 10% of a project's code to be used in other software */
/***************************************************************************
* DESCRIPTION:
- * Socket interface, abstracts machine dependent APIs/routines.
+ * Socket interface, abstracts machine dependent APIs/routines.
***************************************************************************/
int imdsock_init(void) {
@@ -1190,7 +1190,7 @@ int imdsock_init(void) {
}
return rc;
-#else
+#else
return 0;
#endif
}
@@ -1201,7 +1201,7 @@ void * imdsock_create(void) {
s = (imdsocket *) malloc(sizeof(imdsocket));
if (s != NULL)
- memset(s, 0, sizeof(imdsocket));
+ memset(s, 0, sizeof(imdsocket));
if ((s->sd = socket(PF_INET, SOCK_STREAM, 0)) == -1) {
printf("Failed to open socket.");
@@ -1214,7 +1214,7 @@ void * imdsock_create(void) {
int imdsock_bind(void * v, int port) {
imdsocket *s = (imdsocket *) v;
- memset(&(s->addr), 0, sizeof(s->addr));
+ memset(&(s->addr), 0, sizeof(s->addr));
s->addr.sin_family = PF_INET;
s->addr.sin_port = htons(port);
@@ -1296,7 +1296,7 @@ void imdsock_destroy(void * v) {
#else
close(s->sd);
#endif
- free(s);
+ free(s);
}
int imdsock_selread(void *v, int sec) {
@@ -1304,9 +1304,9 @@ int imdsock_selread(void *v, int sec) {
fd_set rfd;
struct timeval tv;
int rc;
-
+
if (v == NULL) return 0;
-
+
FD_ZERO(&rfd);
FD_SET(s->sd, &rfd);
memset((void *)&tv, 0, sizeof(struct timeval));
@@ -1317,13 +1317,13 @@ int imdsock_selread(void *v, int sec) {
return rc;
}
-
+
int imdsock_selwrite(void *v, int sec) {
imdsocket *s = (imdsocket *)v;
fd_set wfd;
struct timeval tv;
int rc;
-
+
if (v == NULL) return 0;
FD_ZERO(&wfd);
@@ -1394,7 +1394,7 @@ static void swap_header(IMDheader *header) {
static int32 imd_readn(void *s, char *ptr, int32 n) {
int32 nleft;
int32 nread;
-
+
nleft = n;
while (nleft > 0) {
if ((nread = imdsock_read(s, ptr, nleft)) < 0) {
@@ -1449,7 +1449,7 @@ IMDType imd_recv_header(void *s, int32 *length) {
return IMD_IOERROR;
swap_header(&header);
*length = header.length;
- return IMDType(header.type);
+ return IMDType(header.type);
}
int imd_recv_mdcomm(void *s, int32 n, int32 *indices, float *forces) {
@@ -1474,4 +1474,3 @@ int imd_recv_fcoords(void *s, int32 n, float *coords) {
// fill-column: 76
// indent-tabs-mode: nil
// End:
-
diff --git a/src/USER-MISC/fix_imd.h b/src/USER-MISC/fix_imd.h
index a7c3cb36eb3e92d0cb4b2ccf43a2256b99129dd3..379742fb4d627ef7680ff03e80771db578630f80 100644
--- a/src/USER-MISC/fix_imd.h
+++ b/src/USER-MISC/fix_imd.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -13,31 +13,31 @@
/* ----------------------------------------------------------------------
The FixIMD class contains code from VMD and NAMD which is copyrighted
- by the Board of Trustees of the University of Illinois and is free to
+ by the Board of Trustees of the University of Illinois and is free to
use with LAMMPS according to point 2 of the UIUC license (10% clause):
-" Licensee may, at its own expense, create and freely distribute
-complimentary works that interoperate with the Software, directing others to
-the TCBG server to license and obtain the Software itself. Licensee may, at
-its own expense, modify the Software to make derivative works. Except as
-explicitly provided below, this License shall apply to any derivative work
-as it does to the original Software distributed by Illinois. Any derivative
-work should be clearly marked and renamed to notify users that it is a
-modified version and not the original Software distributed by Illinois.
-Licensee agrees to reproduce the copyright notice and other proprietary
-markings on any derivative work and to include in the documentation of such
+" Licensee may, at its own expense, create and freely distribute
+complimentary works that interoperate with the Software, directing others to
+the TCBG server to license and obtain the Software itself. Licensee may, at
+its own expense, modify the Software to make derivative works. Except as
+explicitly provided below, this License shall apply to any derivative work
+as it does to the original Software distributed by Illinois. Any derivative
+work should be clearly marked and renamed to notify users that it is a
+modified version and not the original Software distributed by Illinois.
+Licensee agrees to reproduce the copyright notice and other proprietary
+markings on any derivative work and to include in the documentation of such
work the acknowledgement:
- "This software includes code developed by the Theoretical and Computational
- Biophysics Group in the Beckman Institute for Advanced Science and
+ "This software includes code developed by the Theoretical and Computational
+ Biophysics Group in the Beckman Institute for Advanced Science and
Technology at the University of Illinois at Urbana-Champaign."
-Licensee may redistribute without restriction works with up to 1/2 of their
-non-comment source code derived from at most 1/10 of the non-comment source
-code developed by Illinois and contained in the Software, provided that the
-above directions for notice and acknowledgement are observed. Any other
-distribution of the Software or any derivative work requires a separate
-license with Illinois. Licensee may contact Illinois (vmd@ks.uiuc.edu) to
+Licensee may redistribute without restriction works with up to 1/2 of their
+non-comment source code derived from at most 1/10 of the non-comment source
+code developed by Illinois and contained in the Software, provided that the
+above directions for notice and acknowledgement are observed. Any other
+distribution of the Software or any derivative work requires a separate
+license with Illinois. Licensee may contact Illinois (vmd@ks.uiuc.edu) to
negotiate an appropriate license for such distribution."
------------------------------------------------------------------------- */
@@ -68,7 +68,7 @@ class FixIMD : public Fix {
int setmask();
void init();
void setup(int);
- void post_force(int);
+ void post_force(int);
void post_force_respa(int, int, int);
double memory_usage();
@@ -76,8 +76,8 @@ class FixIMD : public Fix {
int imd_port;
void *localsock;
void *clientsock;
-
- int num_coords; // total number of atoms controlled by this fix
+
+ int num_coords; // total number of atoms controlled by this fix
int size_one; // bytes per atom in communication buffer.
int maxbuf; // size of atom communication buffer.
void *comm_buf; // communication buffer
diff --git a/src/USER-MISC/fix_smd.cpp b/src/USER-MISC/fix_smd.cpp
index 25d26b98e0ab7c145a8c3fc941736cf148b7b939..32fc75066bb9b40990d7dbf36fd5ee3e1e100611 100644
--- a/src/USER-MISC/fix_smd.cpp
+++ b/src/USER-MISC/fix_smd.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -31,9 +31,9 @@
using namespace LAMMPS_NS;
using namespace FixConst;
-enum { SMD_NONE=0,
- SMD_TETHER=1<<0, SMD_COUPLE=1<<1,
- SMD_CVEL=1<<2, SMD_CFOR=1<<3,
+enum { SMD_NONE=0,
+ SMD_TETHER=1<<0, SMD_COUPLE=1<<1,
+ SMD_CVEL=1<<2, SMD_CFOR=1<<3,
SMD_AUTOX=1<<4, SMD_AUTOY=1<<5, SMD_AUTOZ=1<<6};
#define SMALL 0.001
@@ -69,7 +69,7 @@ FixSMD::FixSMD(LAMMPS *lmp, int narg, char **arg) :
f_smd = atof(arg[argoffs+1]);
argoffs += 2;
} else error->all(FLERR,"Illegal fix smd command");
-
+
if (strcmp(arg[argoffs],"tether") == 0) {
if (narg < argoffs+5) error->all(FLERR,"Illegal fix smd command");
styleflag |= SMD_TETHER;
@@ -86,10 +86,10 @@ FixSMD::FixSMD(LAMMPS *lmp, int narg, char **arg) :
if (narg < argoffs+6) error->all(FLERR,"Illegal fix smd command");
styleflag |= SMD_COUPLE;
igroup2 = group->find(arg[argoffs+1]);
- if (igroup2 == -1)
- error->all(FLERR,"Could not find fix smd couple group ID");
- if (igroup2 == igroup)
- error->all(FLERR,"Two groups cannot be the same in fix smd couple");
+ if (igroup2 == -1)
+ error->all(FLERR,"Could not find fix smd couple group ID");
+ if (igroup2 == igroup)
+ error->all(FLERR,"Two groups cannot be the same in fix smd couple");
group2bit = group->bitmask[igroup2];
if (strcmp(arg[argoffs+2],"NULL") == 0) xflag = 0;
@@ -101,7 +101,7 @@ FixSMD::FixSMD(LAMMPS *lmp, int narg, char **arg) :
if (strcmp(arg[argoffs+4],"NULL") == 0) zflag = 0;
else if (strcmp(arg[argoffs+4],"auto") == 0) styleflag |= SMD_AUTOZ;
else zc = atof(arg[argoffs+4]);
-
+
r0 = atof(arg[argoffs+5]);
if (r0 < 0) error->all(FLERR,"R0 < 0 for fix smd command");
argoffs +=6;
@@ -144,7 +144,7 @@ void FixSMD::init()
if (styleflag & SMD_AUTOZ) dz = xcm2[2] - xcm[2];
else dz = zc;
}
-
+
if (!xflag) dx = 0.0;
if (!yflag) dy = 0.0;
if (!zflag) dz = 0.0;
@@ -154,7 +154,7 @@ void FixSMD::init()
yn = dy/r_old;
zn = dz/r_old;
}
-
+
if (strstr(update->integrate_style,"respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;
}
@@ -190,14 +190,14 @@ void FixSMD::smd_tether()
group->xcm(igroup,masstotal,xcm);
// fx,fy,fz = components of k * (r-r0)
-
+
double dx,dy,dz,fx,fy,fz,r,dr;
-
+
dx = xcm[0] - xc;
dy = xcm[1] - yc;
dz = xcm[2] - zc;
r_now = sqrt(dx*dx + dy*dy + dz*dz);
-
+
if (!xflag) dx = 0.0;
if (!yflag) dy = 0.0;
if (!zflag) dz = 0.0;
@@ -218,7 +218,7 @@ void FixSMD::smd_tether()
fy = f_smd*dy/r;
fz = f_smd*dz/r;
}
-
+
// apply restoring force to atoms in group
// f = -k*(r-r0)*mass/masstotal
@@ -227,7 +227,7 @@ void FixSMD::smd_tether()
int *type = atom->type;
double *mass = atom->mass;
int nlocal = atom->nlocal;
-
+
ftotal[0] = ftotal[1] = ftotal[2] = 0.0;
force_flag = 0;
@@ -251,7 +251,7 @@ void FixSMD::smd_couple()
double xcm[3],xcm2[3];
group->xcm(igroup,masstotal,xcm);
group->xcm(igroup2,masstotal2,xcm2);
-
+
// renormalize direction of spring
double dx,dy,dz,r,dr;
if (styleflag & SMD_AUTOX) dx = xcm2[0] - xcm[0];
@@ -274,10 +274,10 @@ void FixSMD::smd_couple()
dy = xcm2[1] - xcm[1];
dz = xcm2[2] - xcm[2];
r_now = sqrt(dx*dx + dy*dy + dz*dz);
-
+
dx -= xn*r_old;
dy -= yn*r_old;
- dz -= zn*r_old;
+ dz -= zn*r_old;
if (!xflag) dx = 0.0;
if (!yflag) dy = 0.0;
@@ -320,7 +320,7 @@ void FixSMD::smd_couple()
force_flag = 0;
double massfrac;
- for (int i = 0; i < nlocal; i++) {
+ for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
massfrac = mass[type[i]]/masstotal;
f[i][0] += fx*massfrac;
@@ -345,7 +345,7 @@ void FixSMD::write_restart(FILE *fp)
{
#define RESTART_ITEMS 5
double buf[RESTART_ITEMS], fsign;
-
+
if (comm->me == 0) {
// make sure we project the force into the direction of the pulling.
fsign = (v_smd<0.0) ? -1.0 : 1.0;
diff --git a/src/USER-MISC/fix_smd.h b/src/USER-MISC/fix_smd.h
index 5319ca955868a20a9416e25e23cfc1ae31785cd0..339838d2729a0fa805da6d90caec5a9ea0bdb8cd 100644
--- a/src/USER-MISC/fix_smd.h
+++ b/src/USER-MISC/fix_smd.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -43,7 +43,7 @@ class FixSMD : public Fix {
int xflag,yflag,zflag;
int styleflag;
double r_old,r_now,pmf;
-
+
int igroup2,group2bit;
double masstotal,masstotal2;
int nlevels_respa;
diff --git a/src/USER-MISC/improper_cossq.cpp b/src/USER-MISC/improper_cossq.cpp
index a7684017d0f092c032a1cafd238f336aaf0706ca..9bd5be609fa33691196c591834f9c99b8e101430 100644
--- a/src/USER-MISC/improper_cossq.cpp
+++ b/src/USER-MISC/improper_cossq.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -76,7 +76,7 @@ void ImproperCossq::compute(int eflag, int vflag)
for (n = 0; n < nimproperlist; n++) {
/* Ask the improper list for the atom types. */
- i1 = improperlist[n][0];
+ i1 = improperlist[n][0];
i2 = improperlist[n][1];
i3 = improperlist[n][2];
i4 = improperlist[n][3];
@@ -105,9 +105,9 @@ void ImproperCossq::compute(int eflag, int vflag)
rlk = sqrt(rlksq);
cosphi = (vb3x*vb1x + vb3y*vb1y + vb3z*vb1z)/(rji * rlk);
-
- /* Check that cos(phi) is in the correct limits. */
- if (cosphi > 1.0 + TOLERANCE || cosphi < (-1.0 - TOLERANCE))
+
+ /* Check that cos(phi) is in the correct limits. */
+ if (cosphi > 1.0 + TOLERANCE || cosphi < (-1.0 - TOLERANCE))
{
int me;
MPI_Comm_rank(world,&me);
@@ -123,19 +123,19 @@ void ImproperCossq::compute(int eflag, int vflag)
}
}
-
+
/* Apply corrections to round-off errors. */
if (cosphi > 1.0) cosphi -= SMALL;
if (cosphi < -1.0) cosphi += SMALL;
-
+
/* Calculate the angle: */
double torangle = acos(cosphi);
cosphi = cos(torangle - chi[type]);
if (eflag) eimproper = 0.5 * k[type] * cosphi * cosphi;
-
+
/*
- printf("The tags: %d-%d-%d-%d, of type %d .\n",atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4],type);
+ printf("The tags: %d-%d-%d-%d, of type %d .\n",atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4],type);
printf("The ji vector: %f, %f, %f.\nThe lk vector: %f, %f, %f.\n", vb1x,vb1y,vb1z,vb3x,vb3y,vb3z);
printf("The cosine of the angle: %-1.16e.\n", cosphi);
printf("The energy of the improper: %-1.16e with prefactor %-1.16e.\n", eimproper, 0.5*k[type]);
@@ -147,7 +147,7 @@ void ImproperCossq::compute(int eflag, int vflag)
cjiji = rjisq;
clklk = rlksq;
/*CLKJI = RXLK * RXJI + RYLK * RYJI + RZLK * RZJI */
- clkji = vb3x*vb1x + vb3y*vb1y + vb3z*vb1z;
+ clkji = vb3x*vb1x + vb3y*vb1y + vb3z*vb1z;
/*CFACT1 = CLKLK * CJIJI
CFACT1 = SQRT(CFACT1)
@@ -171,7 +171,7 @@ void ImproperCossq::compute(int eflag, int vflag)
f2[0] = - f1[0];
f2[1] = - f1[1];
f2[2] = - f1[2];
-
+
/*FKX = CFACT2 * RXLK - RXJI
FKY = CFACT2 * RYLK - RYJI
FKZ = CFACT2 * RZLK - RZJI*/
@@ -190,7 +190,7 @@ void ImproperCossq::compute(int eflag, int vflag)
FIY = FIY * CFACT1
FIZ = FIZ * CFACT1*/
f1[0] *= cfact1;
- f1[1] *= cfact1;
+ f1[1] *= cfact1;
f1[2] *= cfact1;
/*FJX = FJX * CFACT1
@@ -203,15 +203,15 @@ void ImproperCossq::compute(int eflag, int vflag)
/*FKX = FKX * CFACT1
FKY = FKY * CFACT1
FKZ = FKZ * CFACT1*/
- f3[0] *= cfact1;
- f3[1] *= cfact1;
+ f3[0] *= cfact1;
+ f3[1] *= cfact1;
f3[2] *= cfact1;
/*FLX = FLX * CFACT1
FLY = FLY * CFACT1
FLZ = FLZ * CFACT1*/
f4[0] *= cfact1;
- f4[1] *= cfact1;
+ f4[1] *= cfact1;
f4[2] *= cfact1;
/* Apply force to each of 4 atoms */
@@ -241,7 +241,7 @@ void ImproperCossq::compute(int eflag, int vflag)
if (evflag)
ev_tally(i1,i2,i3,i4,nlocal,newton_bond,eimproper,f1,f3,f4,
- -vb1x,-vb1y,-vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
+ -vb1x,-vb1y,-vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
}
}
@@ -265,7 +265,7 @@ void ImproperCossq::allocate()
void ImproperCossq::coeff(int narg, char **arg)
{
- /* Check whether there exist sufficient number of arguments.
+ /* Check whether there exist sufficient number of arguments.
0: type of improper to be applied to
1: energetic constant
2: equilibrium angle in degrees */
@@ -290,7 +290,7 @@ void ImproperCossq::coeff(int narg, char **arg)
}
/* ----------------------------------------------------------------------
- proc 0 writes out coeffs to restart file
+ proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void ImproperCossq::write_restart(FILE *fp)
{
@@ -299,7 +299,7 @@ void ImproperCossq::write_restart(FILE *fp)
}
/* ----------------------------------------------------------------------
- proc 0 reads coeffs from restart file, bcasts them
+ proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void ImproperCossq::read_restart(FILE *fp)
{
diff --git a/src/USER-MISC/improper_cossq.h b/src/USER-MISC/improper_cossq.h
index d4b7ca64a77851ed788731ffb77cbc16245b3c92..498d3403b05cade6321532eed1c3fdea02e6c7ee 100644
--- a/src/USER-MISC/improper_cossq.h
+++ b/src/USER-MISC/improper_cossq.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-MISC/improper_ring.cpp b/src/USER-MISC/improper_ring.cpp
index cead4c87df2b0dbcf8178308d013afb96e94fa52..0afbb197caa7bc865608e1df55244ded933508d1 100644
--- a/src/USER-MISC/improper_ring.cpp
+++ b/src/USER-MISC/improper_ring.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -17,23 +17,23 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
- Description: This file implements the improper potential introduced
+ Description: This file implements the improper potential introduced
by Destree et al., in Equation 9 of:
- - M. Destree, F. Laupretre, A. Lyulin, and J.-P.
- Ryckaert, J. Chem. Phys. 112, 9632 (2000),
+ - M. Destree, F. Laupretre, A. Lyulin, and J.-P.
+ Ryckaert, J. Chem. Phys. 112, 9632 (2000),
and subsequently referred in:
- A.V. Lyulin, M.A.J Michels, Macromolecules, 35, 1463,
(2002)
This potential does not affect small amplitude vibrations
- but is used in an ad hoc way to prevent the onset of
- accidentially large amplitude fluctuations leading to
- the occurrence of a planar conformation of the three
- bonds i, i + 1 and i', an intermediate conformation
+ but is used in an ad hoc way to prevent the onset of
+ accidentially large amplitude fluctuations leading to
+ the occurrence of a planar conformation of the three
+ bonds i, i + 1 and i', an intermediate conformation
toward the chiral inversion of a methine carbon.
In the "Impropers" section of data file four atoms:
i, j, k and l are specified with i,j and l lying on the
backbone of the chain and k specifying the chirality
- of j.
+ of j.
------------------------------------------------------------------------- */
#include "lmptype.h"
@@ -79,20 +79,20 @@ void ImproperRing::compute(int eflag, int vflag)
/* Be careful!: "chi" is the equilibrium angle in radians. */
int i1,i2,i3,i4,n,type;
- double eimproper ;
+ double eimproper ;
/* Compatibility variables. */
double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z;
double f1[3], f3[3], f4[3];
-
+
/* Actual computation variables. */
int at1[3], at2[3], at3[3], icomb;
- double bvec1x[3], bvec1y[3], bvec1z[3],
- bvec2x[3], bvec2y[3], bvec2z[3],
+ double bvec1x[3], bvec1y[3], bvec1z[3],
+ bvec2x[3], bvec2y[3], bvec2z[3],
bvec1n[3], bvec2n[3], bend_angle[3];
double angle_summer, angfac, cfact1, cfact2, cfact3;
double cjiji, ckjji, ckjkj, fix, fiy, fiz, fjx, fjy, fjz, fkx, fky, fkz;
-
+
eimproper = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = 0;
@@ -106,9 +106,9 @@ void ImproperRing::compute(int eflag, int vflag)
int newton_bond = force->newton_bond;
- /* A description of the potential can be found in
+ /* A description of the potential can be found in
Macromolecules 35, pp. 1463-1472 (2002). */
- for (n = 0; n < nimproperlist; n++)
+ for (n = 0; n < nimproperlist; n++)
{
/* Take the ids of the atoms contributing to the improper potential. */
i1 = improperlist[n][0]; /* Atom "1" of Figure 1 from the above reference.*/
@@ -117,9 +117,9 @@ void ImproperRing::compute(int eflag, int vflag)
i4 = improperlist[n][3]; /* Atom "9" ... */
type = improperlist[n][4];
- /* Calculate the necessary variables for LAMMPS implementation.
+ /* Calculate the necessary variables for LAMMPS implementation.
if (evflag) ev_tally(i1,i2,i3,i4,nlocal,newton_bond,eimproper,f1,f3,f4,
- vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
+ vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
Although, they are irrelevant to the calculation of the potential, we keep
them for maximal compatibility. */
vb1x = x[i1][0] - x[i2][0]; vb1y = x[i1][1] - x[i2][1]; vb1z = x[i1][2] - x[i2][2];
@@ -131,27 +131,27 @@ void ImproperRing::compute(int eflag, int vflag)
vb3x = x[i4][0] - x[i3][0]; vb3y = x[i4][1] - x[i3][1]; vb3z = x[i4][2] - x[i3][2];
domain->minimum_image(vb3x,vb3y,vb3z);
-
+
/* Pass the atom tags to form the necessary combinations. */
at1[0] = i1; at2[0] = i2; at3[0] = i4; /* ids: 1-2-9 */
at1[1] = i1; at2[1] = i2; at3[1] = i3; /* ids: 1-2-3 */
at1[2] = i4; at2[2] = i2; at3[2] = i3; /* ids: 9-2-3 */
-
+
/* Initialize the sum of the angles differences. */
angle_summer = 0.0;
/* Take a loop over the three angles, defined by each triad: */
for (icomb = 0; icomb < 3; icomb ++)
{
-
+
/* Bond vector connecting the first and the second atom. */
bvec1x[icomb] = x[at2[icomb]][0] - x[at1[icomb]][0];
bvec1y[icomb] = x[at2[icomb]][1] - x[at1[icomb]][1];
bvec1z[icomb] = x[at2[icomb]][2] - x[at1[icomb]][2];
domain -> minimum_image(bvec1x[icomb], bvec1y[icomb], bvec1z[icomb]);
/* also calculate the norm of the vector: */
- bvec1n[icomb] = sqrt( bvec1x[icomb]*bvec1x[icomb]
- + bvec1y[icomb]*bvec1y[icomb]
+ bvec1n[icomb] = sqrt( bvec1x[icomb]*bvec1x[icomb]
+ + bvec1y[icomb]*bvec1y[icomb]
+ bvec1z[icomb]*bvec1z[icomb]);
/* Bond vector connecting the second and the third atom. */
bvec2x[icomb] = x[at3[icomb]][0] - x[at2[icomb]][0];
@@ -159,13 +159,13 @@ void ImproperRing::compute(int eflag, int vflag)
bvec2z[icomb] = x[at3[icomb]][2] - x[at2[icomb]][2];
domain -> minimum_image(bvec2x[icomb], bvec2y[icomb], bvec2z[icomb]);
/* also calculate the norm of the vector: */
- bvec2n[icomb] = sqrt( bvec2x[icomb]*bvec2x[icomb]
- + bvec2y[icomb]*bvec2y[icomb]
+ bvec2n[icomb] = sqrt( bvec2x[icomb]*bvec2x[icomb]
+ + bvec2y[icomb]*bvec2y[icomb]
+ bvec2z[icomb]*bvec2z[icomb]);
-
+
/* Calculate the bending angle of the atom triad: */
- bend_angle[icomb] = ( bvec2x[icomb]*bvec1x[icomb]
- + bvec2y[icomb]*bvec1y[icomb]
+ bend_angle[icomb] = ( bvec2x[icomb]*bvec1x[icomb]
+ + bvec2y[icomb]*bvec1y[icomb]
+ bvec2z[icomb]*bvec1z[icomb]);
bend_angle[icomb] /= (bvec1n[icomb] * bvec2n[icomb]);
if (bend_angle[icomb] > 1.0) bend_angle[icomb] -= SMALL;
@@ -173,38 +173,38 @@ void ImproperRing::compute(int eflag, int vflag)
/* Append the current angle to the sum of angle differences. */
angle_summer += (bend_angle[icomb] - chi[type]);
- }
- if (eflag) eimproper = (1.0/6.0) *k[type] * pow(angle_summer,6.0);
+ }
+ if (eflag) eimproper = (1.0/6.0) *k[type] * pow(angle_summer,6.0);
/*
- printf("The tags: %d-%d-%d-%d, of type %d .\n",atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4],type);
+ printf("The tags: %d-%d-%d-%d, of type %d .\n",atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4],type);
// printf("The coordinates of the first: %f, %f, %f.\n", x[i1][0], x[i1][1], x[i1][2]);
// printf("The coordinates of the second: %f, %f, %f.\n", x[i2][0], x[i2][1], x[i2][2]);
// printf("The coordinates of the third: %f, %f, %f.\n", x[i3][0], x[i3][1], x[i3][2]);
// printf("The coordinates of the fourth: %f, %f, %f.\n", x[i4][0], x[i4][1], x[i4][2]);
printf("The angles are: %f / %f / %f equilibrium: %f.\n", bend_angle[0], bend_angle[1], bend_angle[2],chi[type]);
printf("The energy of the improper: %f with prefactor %f.\n", eimproper,(1.0/6.0)*k[type]);
- printf("The sum of the angles: %f.\n", angle_summer);
+ printf("The sum of the angles: %f.\n", angle_summer);
*/
- /* Force calculation acting on all atoms.
+ /* Force calculation acting on all atoms.
Calculate the derivatives of the potential. */
angfac = k[type] * pow(angle_summer,5.0);
f1[0] = 0.0; f1[1] = 0.0; f1[2] = 0.0;
f3[0] = 0.0; f3[1] = 0.0; f3[2] = 0.0;
- f4[0] = 0.0; f4[1] = 0.0; f4[2] = 0.0;
-
+ f4[0] = 0.0; f4[1] = 0.0; f4[2] = 0.0;
+
/* Take a loop over the three angles, defined by each triad: */
for (icomb = 0; icomb < 3; icomb ++)
{
/* Calculate the squares of the distances. */
cjiji = bvec1n[icomb] * bvec1n[icomb]; ckjkj = bvec2n[icomb] * bvec2n[icomb];
-
- ckjji = bvec2x[icomb] * bvec1x[icomb]
+
+ ckjji = bvec2x[icomb] * bvec1x[icomb]
+ bvec2y[icomb] * bvec1y[icomb]
+ bvec2z[icomb] * bvec1z[icomb] ;
-
- cfact1 = angfac / (sqrt(ckjkj * cjiji));
+
+ cfact1 = angfac / (sqrt(ckjkj * cjiji));
cfact2 = ckjji / ckjkj;
cfact3 = ckjji / cjiji;
@@ -212,15 +212,15 @@ void ImproperRing::compute(int eflag, int vflag)
fkx = cfact2 * bvec2x[icomb] - bvec1x[icomb];
fky = cfact2 * bvec2y[icomb] - bvec1y[icomb];
fkz = cfact2 * bvec2z[icomb] - bvec1z[icomb];
-
+
/* Calculate the force acted on the first atom of the angle. */
fix = bvec2x[icomb] - cfact3 * bvec1x[icomb];
fiy = bvec2y[icomb] - cfact3 * bvec1y[icomb];
- fiz = bvec2z[icomb] - cfact3 * bvec1z[icomb];
+ fiz = bvec2z[icomb] - cfact3 * bvec1z[icomb];
/* Finally, calculate the force acted on the middle atom of the angle.*/
- fjx = - fix - fkx; fjy = - fiy - fky; fjz = - fiz - fkz;
-
+ fjx = - fix - fkx; fjy = - fiy - fky; fjz = - fiz - fkz;
+
/* Consider the appropriate scaling of the forces: */
fix *= cfact1; fiy *= cfact1; fiz *= cfact1;
fjx *= cfact1; fjy *= cfact1; fjz *= cfact1;
@@ -229,7 +229,7 @@ void ImproperRing::compute(int eflag, int vflag)
if (at1[icomb] == i1) {f1[0] += fix; f1[1] += fiy; f1[2] += fiz;}
else if (at2[icomb] == i1) {f1[0] += fjx; f1[1] += fjy; f1[2] += fjz;}
else if (at3[icomb] == i1) {f1[0] += fkx; f1[1] += fky; f1[2] += fkz;}
-
+
if (at1[icomb] == i3) {f3[0] += fix; f3[1] += fiy; f3[2] += fiz;}
else if (at2[icomb] == i3) {f3[0] += fjx; f3[1] += fjy; f3[2] += fjz;}
else if (at3[icomb] == i3) {f3[0] += fkx; f3[1] += fky; f3[2] += fkz;}
@@ -242,7 +242,7 @@ void ImproperRing::compute(int eflag, int vflag)
/* Store the contribution to the global arrays: */
/* Take the id of the atom from the at1[icomb] element, i1 = at1[icomb]. */
if (newton_bond || at1[icomb] < nlocal) {
- f[at1[icomb]][0] += fix;
+ f[at1[icomb]][0] += fix;
f[at1[icomb]][1] += fiy;
f[at1[icomb]][2] += fiz;
}
@@ -258,11 +258,11 @@ void ImproperRing::compute(int eflag, int vflag)
f[at3[icomb]][1] += fky;
f[at3[icomb]][2] += fkz;
}
-
+
}
if (evflag) ev_tally(i1,i2,i3,i4,nlocal,newton_bond,eimproper,f1,f3,f4,
- vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
+ vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
}
}
@@ -287,7 +287,7 @@ void ImproperRing::allocate()
void ImproperRing ::coeff(int narg, char **arg)
{
- /* Check whether there exist sufficient number of arguments.
+ /* Check whether there exist sufficient number of arguments.
0: type of improper to be applied to
1: energetic constant
2: equilibrium angle in degrees */
@@ -315,7 +315,7 @@ void ImproperRing ::coeff(int narg, char **arg)
}
/* ----------------------------------------------------------------------
- proc 0 writes out coeffs to restart file
+ proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void ImproperRing ::write_restart(FILE *fp)
@@ -325,7 +325,7 @@ void ImproperRing ::write_restart(FILE *fp)
}
/* ----------------------------------------------------------------------
- proc 0 reads coeffs from restart file, bcasts them
+ proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void ImproperRing::read_restart(FILE *fp)
diff --git a/src/USER-MISC/improper_ring.h b/src/USER-MISC/improper_ring.h
index f68d5a6d21203a3a54a5bc61013c8349a9bda5bc..0da0e5e05d035c91848091bfbf7fc717c411ae2b 100644
--- a/src/USER-MISC/improper_ring.h
+++ b/src/USER-MISC/improper_ring.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-MISC/pair_cdeam.cpp b/src/USER-MISC/pair_cdeam.cpp
index 4da0065ae769c3cfa58f7aefbf86fbc0ab3b2b1b..9d3a3cb084e6b5f0a4e2d7bc42d8339fd50fd4aa 100644
--- a/src/USER-MISC/pair_cdeam.cpp
+++ b/src/USER-MISC/pair_cdeam.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -35,420 +35,420 @@ using namespace LAMMPS_NS;
// This is for debugging purposes. The ASSERT() macro is used in the code to check
// if everything runs as expected. Change this to #if 0 if you don't need the checking.
#if 0
- #define ASSERT(cond) ((!(cond)) ? my_failure(error,__FILE__,__LINE__) : my_noop())
-
- inline void my_noop() {}
- inline void my_failure(Error* error, const char* file, int line) {
- char str[1024];
- sprintf(str,"Assertion failure: File %s, line %i", file, line);
- error->one(FLERR,str);
- }
+ #define ASSERT(cond) ((!(cond)) ? my_failure(error,__FILE__,__LINE__) : my_noop())
+
+ inline void my_noop() {}
+ inline void my_failure(Error* error, const char* file, int line) {
+ char str[1024];
+ sprintf(str,"Assertion failure: File %s, line %i", file, line);
+ error->one(FLERR,str);
+ }
#else
- #define ASSERT(cond)
+ #define ASSERT(cond)
#endif
-#define MAXLINE 1024 // This sets the maximum line length in EAM input files.
+#define MAXLINE 1024 // This sets the maximum line length in EAM input files.
PairCDEAM::PairCDEAM(LAMMPS *lmp, int _cdeamVersion) : PairEAM(lmp), PairEAMAlloy(lmp), cdeamVersion(_cdeamVersion)
{
- single_enable = 0;
- restartinfo = 0;
-
- rhoB = NULL;
- D_values = NULL;
- hcoeff = NULL;
-
- // Set communication buffer sizes needed by this pair style.
- if(cdeamVersion == 1) {
- comm_forward = 4;
- comm_reverse = 3;
- }
- else if(cdeamVersion == 2) {
- comm_forward = 3;
- comm_reverse = 2;
- }
- else {
- error->all(FLERR,"Invalid CD-EAM potential version.");
- }
+ single_enable = 0;
+ restartinfo = 0;
+
+ rhoB = NULL;
+ D_values = NULL;
+ hcoeff = NULL;
+
+ // Set communication buffer sizes needed by this pair style.
+ if(cdeamVersion == 1) {
+ comm_forward = 4;
+ comm_reverse = 3;
+ }
+ else if(cdeamVersion == 2) {
+ comm_forward = 3;
+ comm_reverse = 2;
+ }
+ else {
+ error->all(FLERR,"Invalid CD-EAM potential version.");
+ }
}
PairCDEAM::~PairCDEAM()
{
- memory->destroy(rhoB);
- memory->destroy(D_values);
- if(hcoeff) delete[] hcoeff;
+ memory->destroy(rhoB);
+ memory->destroy(D_values);
+ if(hcoeff) delete[] hcoeff;
}
void PairCDEAM::compute(int eflag, int vflag)
{
- int i,j,ii,jj,inum,jnum,itype,jtype;
- double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
- double rsq,rhoip,rhojp,recip,phi;
- int *ilist,*jlist,*numneigh,**firstneigh;
-
- evdwl = 0.0;
- if (eflag || vflag) ev_setup(eflag,vflag);
- else evflag = vflag_fdotr = eflag_global = eflag_atom = 0;
-
- // Grow per-atom arrays if necessary
- if(atom->nmax > nmax) {
- memory->destroy(rho);
- memory->destroy(fp);
- memory->destroy(rhoB);
- memory->destroy(D_values);
- nmax = atom->nmax;
- memory->create(rho,nmax,"pair:rho");
- memory->create(rhoB,nmax,"pair:rhoB");
- memory->create(fp,nmax,"pair:fp");
- memory->create(D_values,nmax,"pair:D_values");
- }
-
- double **x = atom->x;
- double **f = atom->f;
- int *type = atom->type;
- int nlocal = atom->nlocal;
- int newton_pair = force->newton_pair;
-
- inum = list->inum;
- ilist = list->ilist;
- numneigh = list->numneigh;
- firstneigh = list->firstneigh;
-
- // Zero out per-atom arrays.
- int m = nlocal + atom->nghost;
- for(i = 0; i < m; i++) {
- rho[i] = 0.0;
- rhoB[i] = 0.0;
- D_values[i] = 0.0;
- }
-
- // Stage I
-
- // Compute rho and rhoB at each local atom site.
- // Additionally calculate the D_i values here if we are using the one-site formulation.
- // For the two-site formulation we have to calculate the D values in an extra loop (Stage II).
- for(ii = 0; ii < inum; ii++) {
- i = ilist[ii];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- itype = type[i];
- jlist = firstneigh[i];
- jnum = numneigh[i];
-
- for(jj = 0; jj < jnum; jj++) {
- j = jlist[jj];
- j &= NEIGHMASK;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if(rsq < cutforcesq) {
- jtype = type[j];
- double r = sqrt(rsq);
- const EAMTableIndex index = radiusToTableIndex(r);
- double localrho = RhoOfR(index, jtype, itype);
- rho[i] += localrho;
- if(jtype == speciesB) rhoB[i] += localrho;
- if(newton_pair || j < nlocal) {
- localrho = RhoOfR(index, itype, jtype);
- rho[j] += localrho;
- if(itype == speciesB) rhoB[j] += localrho;
- }
-
- if(cdeamVersion == 1 && itype != jtype) {
- // Note: if the i-j interaction is not concentration dependent (because either
- // i or j are not species A or B) then its contribution to D_i and D_j should
- // be ignored.
- // This if-clause is only required for a ternary.
- if((itype == speciesA && jtype == speciesB) || (jtype == speciesA && itype == speciesB)) {
- double Phi_AB = PhiOfR(index, itype, jtype, 1.0 / r);
- D_values[i] += Phi_AB;
- if(newton_pair || j < nlocal)
- D_values[j] += Phi_AB;
- }
- }
- }
- }
- }
-
- // Communicate and sum densities.
- if(newton_pair) {
- communicationStage = 1;
- comm->reverse_comm_pair(this);
- }
-
- // fp = derivative of embedding energy at each atom
- // phi = embedding energy at each atom
- for(ii = 0; ii < inum; ii++) {
- i = ilist[ii];
- EAMTableIndex index = rhoToTableIndex(rho[i]);
- fp[i] = FPrimeOfRho(index, type[i]);
- if(eflag) {
- phi = FofRho(index, type[i]);
- if (eflag_global) eng_vdwl += phi;
- if (eflag_atom) eatom[i] += phi;
- }
- }
-
- // Communicate derivative of embedding function and densities
- // and D_values (this for one-site formulation only).
- communicationStage = 2;
- comm->forward_comm_pair(this);
-
- // The electron densities may not drop to zero because then the concentration would no longer be defined.
- // But the concentration is not needed anyway if there is no interaction with another atom, which is the case
- // if the electron density is exactly zero. That's why the following lines have been commented out.
- //
- //for(i = 0; i < nlocal + atom->nghost; i++) {
- // if(rho[i] == 0 && (type[i] == speciesA || type[i] == speciesB))
- // error->one(FLERR,"CD-EAM potential routine: Detected atom with zero electron density.");
- //}
-
- // Stage II
- // This is only required for the original two-site formulation of the CD-EAM potential.
-
- if(cdeamVersion == 2) {
- // Compute intermediate value D_i for each atom.
- for(ii = 0; ii < inum; ii++) {
- i = ilist[ii];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- itype = type[i];
- jlist = firstneigh[i];
- jnum = numneigh[i];
-
- // This code line is required for ternary alloys.
- if(itype != speciesA && itype != speciesB) continue;
-
- double x_i = rhoB[i] / rho[i]; // Concentration at atom i.
-
- for(jj = 0; jj < jnum; jj++) {
- j = jlist[jj];
- j &= NEIGHMASK;
- jtype = type[j];
- if(itype == jtype) continue;
-
- // This code line is required for ternary alloys.
- if(jtype != speciesA && jtype != speciesB) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if(rsq < cutforcesq) {
- double r = sqrt(rsq);
- const EAMTableIndex index = radiusToTableIndex(r);
-
- // The concentration independent part of the cross pair potential.
- double Phi_AB = PhiOfR(index, itype, jtype, 1.0 / r);
-
- // Average concentration of two sites
- double x_ij = 0.5 * (x_i + rhoB[j]/rho[j]);
-
- // Calculate derivative of h(x_ij) polynomial function.
- double h_prime = evalHprime(x_ij);
-
- D_values[i] += h_prime * Phi_AB / (2.0 * rho[i] * rho[i]);
- if(newton_pair || j < nlocal)
- D_values[j] += h_prime * Phi_AB / (2.0 * rho[j] * rho[j]);
- }
- }
- }
-
- // Communicate and sum D values.
- if(newton_pair) {
- communicationStage = 3;
- comm->reverse_comm_pair(this);
- }
- communicationStage = 4;
- comm->forward_comm_pair(this);
- }
-
- // Stage III
-
- // Compute force acting on each atom.
- for(ii = 0; ii < inum; ii++) {
- i = ilist[ii];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- itype = type[i];
-
- jlist = firstneigh[i];
- jnum = numneigh[i];
-
- // Concentration at site i
- double x_i = -1.0; // The value -1 indicates: no concentration dependence for all interactions of atom i.
- // It will be replaced by the concentration at site i if atom i is either A or B.
-
- double D_i, h_prime_i;
-
- // This if-clause is only required for ternary alloys.
- if((itype == speciesA || itype == speciesB) && rho[i] != 0.0) {
-
- // Compute local concentration at site i.
- x_i = rhoB[i]/rho[i];
- ASSERT(x_i >= 0 && x_i<=1.0);
-
- if(cdeamVersion == 1) {
- // Calculate derivative of h(x_i) polynomial function.
- h_prime_i = evalHprime(x_i);
- D_i = D_values[i] * h_prime_i / (2.0 * rho[i] * rho[i]);
- }
- else if(cdeamVersion == 2) {
- D_i = D_values[i];
- }
- else ASSERT(false);
- }
-
- for(jj = 0; jj < jnum; jj++) {
- j = jlist[jj];
- j &= NEIGHMASK;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if(rsq < cutforcesq) {
- jtype = type[j];
- double r = sqrt(rsq);
- const EAMTableIndex index = radiusToTableIndex(r);
-
- // rhoip = derivative of (density at atom j due to atom i)
- // rhojp = derivative of (density at atom i due to atom j)
- // psip needs both fp[i] and fp[j] terms since r_ij appears in two
- // terms of embed eng: Fi(sum rho_ij) and Fj(sum rho_ji)
- // hence embed' = Fi(sum rho_ij) rhojp + Fj(sum rho_ji) rhoip
- rhoip = RhoPrimeOfR(index, itype, jtype);
- rhojp = RhoPrimeOfR(index, jtype, itype);
- fpair = fp[i]*rhojp + fp[j]*rhoip;
- recip = 1.0/r;
-
- double x_j = -1; // The value -1 indicates: no concentration dependence for this i-j pair
- // because atom j is not of species A nor B.
-
- // This code line is required for ternary alloy.
- if(jtype == speciesA || jtype == speciesB) {
- ASSERT(rho[i] != 0.0);
- ASSERT(rho[j] != 0.0);
-
- // Compute local concentration at site j.
- x_j = rhoB[j]/rho[j];
- ASSERT(x_j >= 0 && x_j<=1.0);
-
- double D_j;
- if(cdeamVersion == 1) {
- // Calculate derivative of h(x_j) polynomial function.
- double h_prime_j = evalHprime(x_j);
- D_j = D_values[j] * h_prime_j / (2.0 * rho[j] * rho[j]);
- }
- else if(cdeamVersion == 2) {
- D_j = D_values[j];
- }
- else ASSERT(false);
-
- double t2 = -rhoB[j];
- if(itype == speciesB) t2 += rho[j];
- fpair += D_j * rhoip * t2;
- }
-
- // This if-clause is only required for a ternary alloy.
- // Actually we don't need it at all because D_i should be zero anyway if
- // atom i has no concentration dependent interactions (because it is not species A or B).
- if(x_i != -1.0) {
- double t1 = -rhoB[i];
- if(jtype == speciesB) t1 += rho[i];
- fpair += D_i * rhojp * t1;
- }
-
- double phip;
- double phi = PhiOfR(index, itype, jtype, recip, phip);
- if(itype == jtype || x_i == -1.0 || x_j == -1.0) {
- // Case of no concentration dependence.
- fpair += phip;
- }
- else {
- // We have a concentration dependence for the i-j interaction.
- double h;
- if(cdeamVersion == 1) {
- // Calculate h(x_i) polynomial function.
- double h_i = evalH(x_i);
- // Calculate h(x_j) polynomial function.
- double h_j = evalH(x_j);
- h = 0.5 * (h_i + h_j);
- }
- else if(cdeamVersion == 2) {
- // Average concentration.
- double x_ij = 0.5 * (x_i + x_j);
- // Calculate h(x_ij) polynomial function.
- h = evalH(x_ij);
- }
- else ASSERT(false);
- fpair += h * phip;
- phi *= h;
- }
-
- // Divide by r_ij and negate to get forces from gradient.
- fpair /= -r;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if(newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if(eflag) evdwl = phi;
- if(evflag) ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz);
- }
- }
- }
-
- if(vflag_fdotr) virial_fdotr_compute();
+ int i,j,ii,jj,inum,jnum,itype,jtype;
+ double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
+ double rsq,rhoip,rhojp,recip,phi;
+ int *ilist,*jlist,*numneigh,**firstneigh;
+
+ evdwl = 0.0;
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ else evflag = vflag_fdotr = eflag_global = eflag_atom = 0;
+
+ // Grow per-atom arrays if necessary
+ if(atom->nmax > nmax) {
+ memory->destroy(rho);
+ memory->destroy(fp);
+ memory->destroy(rhoB);
+ memory->destroy(D_values);
+ nmax = atom->nmax;
+ memory->create(rho,nmax,"pair:rho");
+ memory->create(rhoB,nmax,"pair:rhoB");
+ memory->create(fp,nmax,"pair:fp");
+ memory->create(D_values,nmax,"pair:D_values");
+ }
+
+ double **x = atom->x;
+ double **f = atom->f;
+ int *type = atom->type;
+ int nlocal = atom->nlocal;
+ int newton_pair = force->newton_pair;
+
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+
+ // Zero out per-atom arrays.
+ int m = nlocal + atom->nghost;
+ for(i = 0; i < m; i++) {
+ rho[i] = 0.0;
+ rhoB[i] = 0.0;
+ D_values[i] = 0.0;
+ }
+
+ // Stage I
+
+ // Compute rho and rhoB at each local atom site.
+ // Additionally calculate the D_i values here if we are using the one-site formulation.
+ // For the two-site formulation we have to calculate the D values in an extra loop (Stage II).
+ for(ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ itype = type[i];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+
+ for(jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
+ j &= NEIGHMASK;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if(rsq < cutforcesq) {
+ jtype = type[j];
+ double r = sqrt(rsq);
+ const EAMTableIndex index = radiusToTableIndex(r);
+ double localrho = RhoOfR(index, jtype, itype);
+ rho[i] += localrho;
+ if(jtype == speciesB) rhoB[i] += localrho;
+ if(newton_pair || j < nlocal) {
+ localrho = RhoOfR(index, itype, jtype);
+ rho[j] += localrho;
+ if(itype == speciesB) rhoB[j] += localrho;
+ }
+
+ if(cdeamVersion == 1 && itype != jtype) {
+ // Note: if the i-j interaction is not concentration dependent (because either
+ // i or j are not species A or B) then its contribution to D_i and D_j should
+ // be ignored.
+ // This if-clause is only required for a ternary.
+ if((itype == speciesA && jtype == speciesB) || (jtype == speciesA && itype == speciesB)) {
+ double Phi_AB = PhiOfR(index, itype, jtype, 1.0 / r);
+ D_values[i] += Phi_AB;
+ if(newton_pair || j < nlocal)
+ D_values[j] += Phi_AB;
+ }
+ }
+ }
+ }
+ }
+
+ // Communicate and sum densities.
+ if(newton_pair) {
+ communicationStage = 1;
+ comm->reverse_comm_pair(this);
+ }
+
+ // fp = derivative of embedding energy at each atom
+ // phi = embedding energy at each atom
+ for(ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+ EAMTableIndex index = rhoToTableIndex(rho[i]);
+ fp[i] = FPrimeOfRho(index, type[i]);
+ if(eflag) {
+ phi = FofRho(index, type[i]);
+ if (eflag_global) eng_vdwl += phi;
+ if (eflag_atom) eatom[i] += phi;
+ }
+ }
+
+ // Communicate derivative of embedding function and densities
+ // and D_values (this for one-site formulation only).
+ communicationStage = 2;
+ comm->forward_comm_pair(this);
+
+ // The electron densities may not drop to zero because then the concentration would no longer be defined.
+ // But the concentration is not needed anyway if there is no interaction with another atom, which is the case
+ // if the electron density is exactly zero. That's why the following lines have been commented out.
+ //
+ //for(i = 0; i < nlocal + atom->nghost; i++) {
+ // if(rho[i] == 0 && (type[i] == speciesA || type[i] == speciesB))
+ // error->one(FLERR,"CD-EAM potential routine: Detected atom with zero electron density.");
+ //}
+
+ // Stage II
+ // This is only required for the original two-site formulation of the CD-EAM potential.
+
+ if(cdeamVersion == 2) {
+ // Compute intermediate value D_i for each atom.
+ for(ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ itype = type[i];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+
+ // This code line is required for ternary alloys.
+ if(itype != speciesA && itype != speciesB) continue;
+
+ double x_i = rhoB[i] / rho[i]; // Concentration at atom i.
+
+ for(jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
+ j &= NEIGHMASK;
+ jtype = type[j];
+ if(itype == jtype) continue;
+
+ // This code line is required for ternary alloys.
+ if(jtype != speciesA && jtype != speciesB) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if(rsq < cutforcesq) {
+ double r = sqrt(rsq);
+ const EAMTableIndex index = radiusToTableIndex(r);
+
+ // The concentration independent part of the cross pair potential.
+ double Phi_AB = PhiOfR(index, itype, jtype, 1.0 / r);
+
+ // Average concentration of two sites
+ double x_ij = 0.5 * (x_i + rhoB[j]/rho[j]);
+
+ // Calculate derivative of h(x_ij) polynomial function.
+ double h_prime = evalHprime(x_ij);
+
+ D_values[i] += h_prime * Phi_AB / (2.0 * rho[i] * rho[i]);
+ if(newton_pair || j < nlocal)
+ D_values[j] += h_prime * Phi_AB / (2.0 * rho[j] * rho[j]);
+ }
+ }
+ }
+
+ // Communicate and sum D values.
+ if(newton_pair) {
+ communicationStage = 3;
+ comm->reverse_comm_pair(this);
+ }
+ communicationStage = 4;
+ comm->forward_comm_pair(this);
+ }
+
+ // Stage III
+
+ // Compute force acting on each atom.
+ for(ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ itype = type[i];
+
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+
+ // Concentration at site i
+ double x_i = -1.0; // The value -1 indicates: no concentration dependence for all interactions of atom i.
+ // It will be replaced by the concentration at site i if atom i is either A or B.
+
+ double D_i, h_prime_i;
+
+ // This if-clause is only required for ternary alloys.
+ if((itype == speciesA || itype == speciesB) && rho[i] != 0.0) {
+
+ // Compute local concentration at site i.
+ x_i = rhoB[i]/rho[i];
+ ASSERT(x_i >= 0 && x_i<=1.0);
+
+ if(cdeamVersion == 1) {
+ // Calculate derivative of h(x_i) polynomial function.
+ h_prime_i = evalHprime(x_i);
+ D_i = D_values[i] * h_prime_i / (2.0 * rho[i] * rho[i]);
+ }
+ else if(cdeamVersion == 2) {
+ D_i = D_values[i];
+ }
+ else ASSERT(false);
+ }
+
+ for(jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
+ j &= NEIGHMASK;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if(rsq < cutforcesq) {
+ jtype = type[j];
+ double r = sqrt(rsq);
+ const EAMTableIndex index = radiusToTableIndex(r);
+
+ // rhoip = derivative of (density at atom j due to atom i)
+ // rhojp = derivative of (density at atom i due to atom j)
+ // psip needs both fp[i] and fp[j] terms since r_ij appears in two
+ // terms of embed eng: Fi(sum rho_ij) and Fj(sum rho_ji)
+ // hence embed' = Fi(sum rho_ij) rhojp + Fj(sum rho_ji) rhoip
+ rhoip = RhoPrimeOfR(index, itype, jtype);
+ rhojp = RhoPrimeOfR(index, jtype, itype);
+ fpair = fp[i]*rhojp + fp[j]*rhoip;
+ recip = 1.0/r;
+
+ double x_j = -1; // The value -1 indicates: no concentration dependence for this i-j pair
+ // because atom j is not of species A nor B.
+
+ // This code line is required for ternary alloy.
+ if(jtype == speciesA || jtype == speciesB) {
+ ASSERT(rho[i] != 0.0);
+ ASSERT(rho[j] != 0.0);
+
+ // Compute local concentration at site j.
+ x_j = rhoB[j]/rho[j];
+ ASSERT(x_j >= 0 && x_j<=1.0);
+
+ double D_j;
+ if(cdeamVersion == 1) {
+ // Calculate derivative of h(x_j) polynomial function.
+ double h_prime_j = evalHprime(x_j);
+ D_j = D_values[j] * h_prime_j / (2.0 * rho[j] * rho[j]);
+ }
+ else if(cdeamVersion == 2) {
+ D_j = D_values[j];
+ }
+ else ASSERT(false);
+
+ double t2 = -rhoB[j];
+ if(itype == speciesB) t2 += rho[j];
+ fpair += D_j * rhoip * t2;
+ }
+
+ // This if-clause is only required for a ternary alloy.
+ // Actually we don't need it at all because D_i should be zero anyway if
+ // atom i has no concentration dependent interactions (because it is not species A or B).
+ if(x_i != -1.0) {
+ double t1 = -rhoB[i];
+ if(jtype == speciesB) t1 += rho[i];
+ fpair += D_i * rhojp * t1;
+ }
+
+ double phip;
+ double phi = PhiOfR(index, itype, jtype, recip, phip);
+ if(itype == jtype || x_i == -1.0 || x_j == -1.0) {
+ // Case of no concentration dependence.
+ fpair += phip;
+ }
+ else {
+ // We have a concentration dependence for the i-j interaction.
+ double h;
+ if(cdeamVersion == 1) {
+ // Calculate h(x_i) polynomial function.
+ double h_i = evalH(x_i);
+ // Calculate h(x_j) polynomial function.
+ double h_j = evalH(x_j);
+ h = 0.5 * (h_i + h_j);
+ }
+ else if(cdeamVersion == 2) {
+ // Average concentration.
+ double x_ij = 0.5 * (x_i + x_j);
+ // Calculate h(x_ij) polynomial function.
+ h = evalH(x_ij);
+ }
+ else ASSERT(false);
+ fpair += h * phip;
+ phi *= h;
+ }
+
+ // Divide by r_ij and negate to get forces from gradient.
+ fpair /= -r;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if(newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if(eflag) evdwl = phi;
+ if(evflag) ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz);
+ }
+ }
+ }
+
+ if(vflag_fdotr) virial_fdotr_compute();
}
/* ---------------------------------------------------------------------- */
void PairCDEAM::coeff(int narg, char **arg)
{
- PairEAMAlloy::coeff(narg, arg);
-
- // Make sure the EAM file is a CD-EAM binary alloy.
- if(setfl->nelements < 2)
- error->all(FLERR,"The EAM file must contain at least 2 elements to be used with the eam/cd pair style.");
-
- // Read in the coefficients of the h polynomial from the end of the EAM file.
- read_h_coeff(arg[2]);
-
- // Determine which atom type is the A species and which is the B species in the alloy.
- // By default take the first element (index 0) in the EAM file as the A species
- // and the second element (index 1) in the EAM file as the B species.
- speciesA = -1;
- speciesB = -1;
- for(int i = 1; i <= atom->ntypes; i++) {
- if(map[i] == 0) {
- if(speciesA >= 0)
- error->all(FLERR,"The first element from the EAM file may only be mapped to a single atom type.");
- speciesA = i;
- }
- if(map[i] == 1) {
- if(speciesB >= 0)
- error->all(FLERR,"The second element from the EAM file may only be mapped to a single atom type.");
- speciesB = i;
- }
- }
- if(speciesA < 0)
- error->all(FLERR,"The first element from the EAM file must be mapped to exactly one atom type.");
- if(speciesB < 0)
- error->all(FLERR,"The second element from the EAM file must be mapped to exactly one atom type.");
+ PairEAMAlloy::coeff(narg, arg);
+
+ // Make sure the EAM file is a CD-EAM binary alloy.
+ if(setfl->nelements < 2)
+ error->all(FLERR,"The EAM file must contain at least 2 elements to be used with the eam/cd pair style.");
+
+ // Read in the coefficients of the h polynomial from the end of the EAM file.
+ read_h_coeff(arg[2]);
+
+ // Determine which atom type is the A species and which is the B species in the alloy.
+ // By default take the first element (index 0) in the EAM file as the A species
+ // and the second element (index 1) in the EAM file as the B species.
+ speciesA = -1;
+ speciesB = -1;
+ for(int i = 1; i <= atom->ntypes; i++) {
+ if(map[i] == 0) {
+ if(speciesA >= 0)
+ error->all(FLERR,"The first element from the EAM file may only be mapped to a single atom type.");
+ speciesA = i;
+ }
+ if(map[i] == 1) {
+ if(speciesB >= 0)
+ error->all(FLERR,"The second element from the EAM file may only be mapped to a single atom type.");
+ speciesB = i;
+ }
+ }
+ if(speciesA < 0)
+ error->all(FLERR,"The first element from the EAM file must be mapped to exactly one atom type.");
+ if(speciesB < 0)
+ error->all(FLERR,"The second element from the EAM file must be mapped to exactly one atom type.");
}
/* ----------------------------------------------------------------------
@@ -456,41 +456,41 @@ void PairCDEAM::coeff(int narg, char **arg)
------------------------------------------------------------------------- */
void PairCDEAM::read_h_coeff(char *filename)
{
- if(comm->me == 0) {
- // Open potential file
- FILE *fp;
- char line[MAXLINE];
- char nextline[MAXLINE];
- fp = fopen(filename,"r");
- if (fp == NULL) {
- char str[128];
- sprintf(str,"Cannot open EAM potential file %s", filename);
- error->one(FLERR,str);
- }
-
- // h coefficients are stored at the end of the file.
- // Skip to last line of file.
- while(fgets(nextline, MAXLINE, fp) != NULL) {
- strcpy(line, nextline);
- }
- char* ptr = strtok(line, " \t\n\r\f");
- int degree = atoi(ptr);
- nhcoeff = degree+1;
- hcoeff = new double[nhcoeff];
- int i = 0;
- while((ptr = strtok(NULL," \t\n\r\f")) != NULL && i < nhcoeff) {
- hcoeff[i++] = atof(ptr);
- }
- if(i != nhcoeff || nhcoeff < 1)
- error->one(FLERR,"Failed to read h(x) function coefficients from EAM file.");
-
- // Close the potential file.
- fclose(fp);
- }
-
- MPI_Bcast(&nhcoeff, 1, MPI_INT, 0, world);
- if(comm->me != 0) hcoeff = new double[nhcoeff];
- MPI_Bcast(hcoeff, nhcoeff, MPI_DOUBLE, 0, world);
+ if(comm->me == 0) {
+ // Open potential file
+ FILE *fp;
+ char line[MAXLINE];
+ char nextline[MAXLINE];
+ fp = fopen(filename,"r");
+ if (fp == NULL) {
+ char str[128];
+ sprintf(str,"Cannot open EAM potential file %s", filename);
+ error->one(FLERR,str);
+ }
+
+ // h coefficients are stored at the end of the file.
+ // Skip to last line of file.
+ while(fgets(nextline, MAXLINE, fp) != NULL) {
+ strcpy(line, nextline);
+ }
+ char* ptr = strtok(line, " \t\n\r\f");
+ int degree = atoi(ptr);
+ nhcoeff = degree+1;
+ hcoeff = new double[nhcoeff];
+ int i = 0;
+ while((ptr = strtok(NULL," \t\n\r\f")) != NULL && i < nhcoeff) {
+ hcoeff[i++] = atof(ptr);
+ }
+ if(i != nhcoeff || nhcoeff < 1)
+ error->one(FLERR,"Failed to read h(x) function coefficients from EAM file.");
+
+ // Close the potential file.
+ fclose(fp);
+ }
+
+ MPI_Bcast(&nhcoeff, 1, MPI_INT, 0, world);
+ if(comm->me != 0) hcoeff = new double[nhcoeff];
+ MPI_Bcast(hcoeff, nhcoeff, MPI_DOUBLE, 0, world);
}
@@ -498,140 +498,140 @@ void PairCDEAM::read_h_coeff(char *filename)
int PairCDEAM::pack_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
{
- int i,j,m;
-
- m = 0;
- if(communicationStage == 2) {
- if(cdeamVersion == 1) {
- for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = fp[j];
- buf[m++] = rho[j];
- buf[m++] = rhoB[j];
- buf[m++] = D_values[j];
- }
- return 4;
- }
- else if(cdeamVersion == 2) {
- for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = fp[j];
- buf[m++] = rho[j];
- buf[m++] = rhoB[j];
- }
- return 3;
- }
- else { ASSERT(false); return 0; }
- }
- else if(communicationStage == 4) {
- for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = D_values[j];
- }
- return 1;
- }
- else return 0;
+ int i,j,m;
+
+ m = 0;
+ if(communicationStage == 2) {
+ if(cdeamVersion == 1) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = fp[j];
+ buf[m++] = rho[j];
+ buf[m++] = rhoB[j];
+ buf[m++] = D_values[j];
+ }
+ return 4;
+ }
+ else if(cdeamVersion == 2) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = fp[j];
+ buf[m++] = rho[j];
+ buf[m++] = rhoB[j];
+ }
+ return 3;
+ }
+ else { ASSERT(false); return 0; }
+ }
+ else if(communicationStage == 4) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = D_values[j];
+ }
+ return 1;
+ }
+ else return 0;
}
/* ---------------------------------------------------------------------- */
void PairCDEAM::unpack_comm(int n, int first, double *buf)
{
- int i,m,last;
-
- m = 0;
- last = first + n;
- if(communicationStage == 2) {
- if(cdeamVersion == 1) {
- for(i = first; i < last; i++) {
- fp[i] = buf[m++];
- rho[i] = buf[m++];
- rhoB[i] = buf[m++];
- D_values[i] = buf[m++];
- }
- }
- else if(cdeamVersion == 2) {
- for(i = first; i < last; i++) {
- fp[i] = buf[m++];
- rho[i] = buf[m++];
- rhoB[i] = buf[m++];
- }
- }
- else ASSERT(false);
- }
- else if(communicationStage == 4) {
- for(i = first; i < last; i++) {
- D_values[i] = buf[m++];
- }
- }
+ int i,m,last;
+
+ m = 0;
+ last = first + n;
+ if(communicationStage == 2) {
+ if(cdeamVersion == 1) {
+ for(i = first; i < last; i++) {
+ fp[i] = buf[m++];
+ rho[i] = buf[m++];
+ rhoB[i] = buf[m++];
+ D_values[i] = buf[m++];
+ }
+ }
+ else if(cdeamVersion == 2) {
+ for(i = first; i < last; i++) {
+ fp[i] = buf[m++];
+ rho[i] = buf[m++];
+ rhoB[i] = buf[m++];
+ }
+ }
+ else ASSERT(false);
+ }
+ else if(communicationStage == 4) {
+ for(i = first; i < last; i++) {
+ D_values[i] = buf[m++];
+ }
+ }
}
/* ---------------------------------------------------------------------- */
int PairCDEAM::pack_reverse_comm(int n, int first, double *buf)
{
- int i,m,last;
-
- m = 0;
- last = first + n;
-
- if(communicationStage == 1) {
- if(cdeamVersion == 1) {
- for(i = first; i < last; i++) {
- buf[m++] = rho[i];
- buf[m++] = rhoB[i];
- buf[m++] = D_values[i];
- }
- return 3;
- }
- else if(cdeamVersion == 2) {
- for(i = first; i < last; i++) {
- buf[m++] = rho[i];
- buf[m++] = rhoB[i];
- }
- return 2;
- }
- else { ASSERT(false); return 0; }
- }
- else if(communicationStage == 3) {
- for(i = first; i < last; i++) {
- buf[m++] = D_values[i];
- }
- return 1;
- }
- else return 0;
+ int i,m,last;
+
+ m = 0;
+ last = first + n;
+
+ if(communicationStage == 1) {
+ if(cdeamVersion == 1) {
+ for(i = first; i < last; i++) {
+ buf[m++] = rho[i];
+ buf[m++] = rhoB[i];
+ buf[m++] = D_values[i];
+ }
+ return 3;
+ }
+ else if(cdeamVersion == 2) {
+ for(i = first; i < last; i++) {
+ buf[m++] = rho[i];
+ buf[m++] = rhoB[i];
+ }
+ return 2;
+ }
+ else { ASSERT(false); return 0; }
+ }
+ else if(communicationStage == 3) {
+ for(i = first; i < last; i++) {
+ buf[m++] = D_values[i];
+ }
+ return 1;
+ }
+ else return 0;
}
/* ---------------------------------------------------------------------- */
void PairCDEAM::unpack_reverse_comm(int n, int *list, double *buf)
{
- int i,j,m;
-
- m = 0;
- if(communicationStage == 1) {
- if(cdeamVersion == 1) {
- for(i = 0; i < n; i++) {
- j = list[i];
- rho[j] += buf[m++];
- rhoB[j] += buf[m++];
- D_values[j] += buf[m++];
- }
- }
- else if(cdeamVersion == 2) {
- for(i = 0; i < n; i++) {
- j = list[i];
- rho[j] += buf[m++];
- rhoB[j] += buf[m++];
- }
- }
- else ASSERT(false);
- }
- else if(communicationStage == 3) {
- for(i = 0; i < n; i++) {
- j = list[i];
- D_values[j] += buf[m++];
- }
- }
+ int i,j,m;
+
+ m = 0;
+ if(communicationStage == 1) {
+ if(cdeamVersion == 1) {
+ for(i = 0; i < n; i++) {
+ j = list[i];
+ rho[j] += buf[m++];
+ rhoB[j] += buf[m++];
+ D_values[j] += buf[m++];
+ }
+ }
+ else if(cdeamVersion == 2) {
+ for(i = 0; i < n; i++) {
+ j = list[i];
+ rho[j] += buf[m++];
+ rhoB[j] += buf[m++];
+ }
+ }
+ else ASSERT(false);
+ }
+ else if(communicationStage == 3) {
+ for(i = 0; i < n; i++) {
+ j = list[i];
+ D_values[j] += buf[m++];
+ }
+ }
}
/* ----------------------------------------------------------------------
@@ -639,6 +639,6 @@ void PairCDEAM::unpack_reverse_comm(int n, int *list, double *buf)
------------------------------------------------------------------------- */
double PairCDEAM::memory_usage()
{
- double bytes = 2 * nmax * sizeof(double);
- return PairEAMAlloy::memory_usage() + bytes;
+ double bytes = 2 * nmax * sizeof(double);
+ return PairEAMAlloy::memory_usage() + bytes;
}
diff --git a/src/USER-MISC/pair_cdeam.h b/src/USER-MISC/pair_cdeam.h
index 836ad2fe7ccdd5c2481df501c6abbdf5e9dc2842..efc1b5801258acdd593d23c93b02e5f1123bc952 100644
--- a/src/USER-MISC/pair_cdeam.h
+++ b/src/USER-MISC/pair_cdeam.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -36,25 +36,25 @@ public:
/// Calculates the energies and forces for all atoms in the system.
virtual void compute(int, int);
-
+
/// Parses the pair_coeff command parameters for this pair style.
void coeff(int, char **);
-
+
/// This is for MPI communication with neighbor nodes.
int pack_comm(int, int *, double *, int, int *);
void unpack_comm(int, int, double *);
int pack_reverse_comm(int, int, double *);
void unpack_reverse_comm(int, int *, double *);
-
+
/// Reports the memory usage of this pair style to LAMMPS.
double memory_usage();
-
+
/// Parses the coefficients of the h polynomial from the end of the EAM file.
void read_h_coeff(char* filename);
-
+
public:
// The public interface exposed by this potential class.
-
+
// Evaluates the h(x) polynomial for a given local concentration x.
inline double evalH(double x) const {
double v = 0.0;
@@ -63,7 +63,7 @@ public:
}
return v + hcoeff[0];
};
-
+
// Calculates the derivative of the h(x) polynomial.
inline double evalHprime(double x) const {
double v = 0.0;
@@ -72,7 +72,7 @@ public:
}
return v + hcoeff[1];
};
-
+
// We have two versions of the CD-EAM potential. The user can choose which one he wants to use:
//
// Version 1 - One-site concentration: The h(x_i) function depends only on the concentration at the atomic site i.
@@ -82,39 +82,39 @@ public:
// Version 2 - Two-site concentration: The h(x_ij) function depends on the concentrations at two atomic sites i and j.
// This is the original version from the 2005 PRL paper.
int cdeamVersion;
-
+
// Per-atom arrays
-
+
// The partial density of B atoms at each atom site.
double *rhoB;
-
+
// The intermediate value D_i for each atom.
// The meaning of these values depend on the version of the CD-EAM potential used:
//
- // For the one-site concentration version these are the v_i values defined in equation (21)
+ // For the one-site concentration version these are the v_i values defined in equation (21)
// of the MSMSE paper.
//
- // For the old two-site concentration version these are the M_i values defined in equation (12)
+ // For the old two-site concentration version these are the M_i values defined in equation (12)
// of the MSMSE paper.
double *D_values;
-
+
// The atom type index that is considered to be the A species in the alloy.
int speciesA;
-
+
// The atom type index that is considered to be the B species in the alloy.
int speciesB;
-
+
protected:
-
+
// Evaluation functions:
-
- // This structure specifies an entry in one of the EAM spline tables
+
+ // This structure specifies an entry in one of the EAM spline tables
// and the corresponding floating point part.
typedef struct {
int m;
double p;
} EAMTableIndex;
-
+
// Converts a radius value to an index value to be used in a spline table lookup.
inline EAMTableIndex radiusToTableIndex(double r) const {
EAMTableIndex index;
@@ -125,7 +125,7 @@ public:
index.p = index.p <= 1.0 ? index.p : 1.0;
return index;
};
-
+
// Converts a density value to an index value to be used in a spline table lookup.
inline EAMTableIndex rhoToTableIndex(double rho) const {
EAMTableIndex index;
@@ -136,31 +136,31 @@ public:
index.p = index.p <= 1.0 ? index.p : 1.0;
return index;
};
-
+
// Computes the derivative of rho(r)
inline double RhoPrimeOfR(const EAMTableIndex& index, int itype, int jtype) const {
const double* coeff = rhor_spline[type2rhor[itype][jtype]][index.m];
return (coeff[0]*index.p + coeff[1])*index.p + coeff[2];
};
-
+
// Computes rho(r)
inline double RhoOfR(const EAMTableIndex& index, int itype, int jtype) const {
const double* coeff = rhor_spline[type2rhor[itype][jtype]][index.m];
return ((coeff[3]*index.p + coeff[4])*index.p + coeff[5])*index.p + coeff[6];
};
-
+
// Computes the derivative of F(rho)
inline double FPrimeOfRho(const EAMTableIndex& index, int itype) const {
const double* coeff = frho_spline[type2frho[itype]][index.m];
return (coeff[0]*index.p + coeff[1])*index.p + coeff[2];
};
-
+
// Computes F(rho)
inline double FofRho(const EAMTableIndex& index, int itype) const {
const double* coeff = frho_spline[type2frho[itype]][index.m];
return ((coeff[3]*index.p + coeff[4])*index.p + coeff[5])*index.p + coeff[6];
};
-
+
// Computes the derivative of z2(r)
inline double Z2PrimeOfR(const EAMTableIndex& index, int itype, int jtype) const {
const double* coeff = z2r_spline[type2z2r[itype][jtype]][index.m];
@@ -172,7 +172,7 @@ public:
const double* coeff = z2r_spline[type2z2r[itype][jtype]][index.m];
return ((coeff[3]*index.p + coeff[4])*index.p + coeff[5])*index.p + coeff[6];
};
-
+
// Computes pair potential V_ij(r).
inline double PhiOfR(const EAMTableIndex& index, int itype, int jtype, const double oneOverR) const {
// phi = pair potential energy
@@ -181,7 +181,7 @@ public:
const double z2 = ((coeff[3]*index.p + coeff[4])*index.p + coeff[5])*index.p + coeff[6];
return z2 * oneOverR;
};
-
+
// Computes pair potential V_ij(r) and its derivative.
inline double PhiOfR(const EAMTableIndex& index, int itype, int jtype, const double oneOverR, double& phid) const {
// phi = pair potential energy
@@ -195,19 +195,19 @@ public:
phid = z2p * oneOverR - phi * oneOverR;
return phi;
};
-
+
// Parameters
-
+
// h() polynomial function coefficients
double* hcoeff;
// The number of coefficients in the polynomial.
int nhcoeff;
-
+
// This specifies the calculation stage to let the pack/unpack communication routines know
// which data to exchange.
int communicationStage;
};
-
+
/// The one-site concentration formulation of CD-EAM.
class PairCDEAM_OneSite : public PairCDEAM
{
@@ -215,7 +215,7 @@ public:
/// Constructor.
PairCDEAM_OneSite(class LAMMPS* lmp) : PairEAM(lmp), PairCDEAM(lmp, 1) {}
};
-
+
/// The two-site concentration formulation of CD-EAM.
class PairCDEAM_TwoSite : public PairCDEAM
{
@@ -223,7 +223,7 @@ public:
/// Constructor.
PairCDEAM_TwoSite(class LAMMPS* lmp) : PairEAM(lmp), PairCDEAM(lmp, 2) {}
};
-
+
}
#endif
diff --git a/src/USER-MISC/pair_coul_diel.cpp b/src/USER-MISC/pair_coul_diel.cpp
index 7f63b1a20198069e479b7e4fdab175f4b796010e..8fb4ef6372bb9f423ce6342903f414697827c26b 100644
--- a/src/USER-MISC/pair_coul_diel.cpp
+++ b/src/USER-MISC/pair_coul_diel.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -100,31 +100,31 @@ void PairCoulDiel::compute(int eflag, int vflag)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r = sqrt(rsq);
- rarg = (r-rme[itype][jtype])/sigmae[itype][jtype];
- th=tanh(rarg);
- epsr=a_eps+b_eps*th;
- depsdr=b_eps * (1.0 - th*th) / sigmae[itype][jtype];
-
- forcecoul = qqrd2e*qtmp*q[j]*((eps_s*(epsr+r*depsdr)/epsr/epsr) -1.)/rsq;
- fpair = factor_coul*forcecoul/r;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (eflag) {
- ecoul = (qqrd2e*qtmp*q[j]*((eps_s/epsr) -1.)/r) - offset[itype][jtype];
- ecoul *= factor_coul;
- }
-
- if (evflag) ev_tally(i,j,nlocal,newton_pair,0.0,
- ecoul,fpair,delx,dely,delz);
+ r = sqrt(rsq);
+ rarg = (r-rme[itype][jtype])/sigmae[itype][jtype];
+ th=tanh(rarg);
+ epsr=a_eps+b_eps*th;
+ depsdr=b_eps * (1.0 - th*th) / sigmae[itype][jtype];
+
+ forcecoul = qqrd2e*qtmp*q[j]*((eps_s*(epsr+r*depsdr)/epsr/epsr) -1.)/rsq;
+ fpair = factor_coul*forcecoul/r;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (eflag) {
+ ecoul = (qqrd2e*qtmp*q[j]*((eps_s/epsr) -1.)/r) - offset[itype][jtype];
+ ecoul *= factor_coul;
+ }
+
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,0.0,
+ ecoul,fpair,delx,dely,delz);
}
}
}
@@ -169,7 +169,7 @@ void PairCoulDiel::settings(int narg, char **arg)
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
- if (setflag[i][j]) cut[i][j] = cut_global;
+ if (setflag[i][j]) cut[i][j] = cut_global;
}
}
@@ -189,8 +189,8 @@ void PairCoulDiel::coeff(int narg, char **arg)
eps_s = force->numeric(arg[2]);
double rme_one =force->numeric(arg[3]);
double sigmae_one = force->numeric(arg[4]);
-
- double cut_one = cut_global;
+
+ double cut_one = cut_global;
if (narg == 6) cut_one = force->numeric(arg[5]);
int count = 0;
@@ -234,14 +234,14 @@ double PairCoulDiel::init_one(int i, int j)
double *q = atom->q;
double qqrd2e = force->qqrd2e;
-
+
if (offset_flag) {
double rarg = (cut[i][j]-rme[i][j])/sigmae[i][j];
double epsr=a_eps+b_eps*tanh(rarg);
offset[i][j] = qqrd2e*q[i]*q[j]*((eps_s/epsr) -1.)/cut[i][j];
} else offset[i][j] = 0.0;
-
-
+
+
sigmae[j][i] = sigmae[i][j];
rme[j][i] = rme[i][j];
offset[j][i] = offset[i][j];
@@ -263,9 +263,9 @@ void PairCoulDiel::write_restart(FILE *fp)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
- fwrite(&rme[i][j],sizeof(double),1,fp);
- fwrite(&sigmae[i][j],sizeof(double),1,fp);
- fwrite(&cut[i][j],sizeof(double),1,fp);
+ fwrite(&rme[i][j],sizeof(double),1,fp);
+ fwrite(&sigmae[i][j],sizeof(double),1,fp);
+ fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
@@ -284,14 +284,14 @@ void PairCoulDiel::read_restart(FILE *fp)
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (setflag[i][j]) {
- if (me == 0) {
- fread(&rme[i][j],sizeof(double),1,fp);
- fread(&sigmae[i][j],sizeof(double),1,fp);
- fread(&cut[i][j],sizeof(double),1,fp);
- }
- MPI_Bcast(&rme[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&sigmae[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
+ if (me == 0) {
+ fread(&rme[i][j],sizeof(double),1,fp);
+ fread(&sigmae[i][j],sizeof(double),1,fp);
+ fread(&cut[i][j],sizeof(double),1,fp);
+ }
+ MPI_Bcast(&rme[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&sigmae[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
@@ -326,8 +326,8 @@ void PairCoulDiel::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairCoulDiel::single(int i, int j, int itype, int jtype,
- double rsq, double factor_coul, double factor_lj,
- double &fforce)
+ double rsq, double factor_coul, double factor_lj,
+ double &fforce)
{
double r, rarg,forcedielec,phidielec;
double th,epsr,depsdr;
@@ -339,10 +339,10 @@ double PairCoulDiel::single(int i, int j, int itype, int jtype,
th = tanh(rarg);
epsr=a_eps+b_eps*th;
depsdr=b_eps*(1.-th*th)/sigmae[itype][jtype];
-
+
forcedielec = qqrd2e*q[i]*q[j]*((eps_s*(epsr+r*depsdr)/epsr/epsr) -1.)/rsq;
fforce = factor_coul*forcedielec/r;
-
+
phidielec = (qqrd2e*q[i]*q[j]*((eps_s/epsr) -1.)/r)- offset[itype][jtype];
return factor_coul*phidielec;
}
diff --git a/src/USER-MISC/pair_coul_diel.h b/src/USER-MISC/pair_coul_diel.h
index 14d7b8b14329cb1494c7e8930f11ae6a5d4c76d0..2113e456808ac001b566de95d936093882e667e9 100644
--- a/src/USER-MISC/pair_coul_diel.h
+++ b/src/USER-MISC/pair_coul_diel.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-MISC/pair_dipole_sf.cpp b/src/USER-MISC/pair_dipole_sf.cpp
index bd9e900c528f25ddd0401dae5ce652f0531b2265..61534e6ec3fa450d1d6871442e0fb0388f82343b 100644
--- a/src/USER-MISC/pair_dipole_sf.cpp
+++ b/src/USER-MISC/pair_dipole_sf.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -93,7 +93,7 @@ void PairDipoleSF::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@@ -119,168 +119,168 @@ void PairDipoleSF::compute(int eflag, int vflag)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- rinv = sqrt(r2inv);
+ r2inv = 1.0/rsq;
+ rinv = sqrt(r2inv);
+
+ // atom can have both a charge and dipole
+ // i,j = charge-charge, dipole-dipole, dipole-charge, or charge-dipole
- // atom can have both a charge and dipole
- // i,j = charge-charge, dipole-dipole, dipole-charge, or charge-dipole
+ forcecoulx = forcecouly = forcecoulz = 0.0;
+ tixcoul = tiycoul = tizcoul = 0.0;
+ tjxcoul = tjycoul = tjzcoul = 0.0;
- forcecoulx = forcecouly = forcecoulz = 0.0;
- tixcoul = tiycoul = tizcoul = 0.0;
- tjxcoul = tjycoul = tjzcoul = 0.0;
-
- if (rsq < cut_coulsq[itype][jtype]) {
+ if (rsq < cut_coulsq[itype][jtype]) {
- if (qtmp != 0.0 && q[j] != 0.0) {
+ if (qtmp != 0.0 && q[j] != 0.0) {
pre1 = qtmp*q[j]*rinv*(r2inv-1.0/cut_coulsq[itype][jtype]);
- forcecoulx += pre1*delx;
- forcecouly += pre1*dely;
- forcecoulz += pre1*delz;
- }
+ forcecoulx += pre1*delx;
+ forcecouly += pre1*dely;
+ forcecoulz += pre1*delz;
+ }
- if (mu[i][3] > 0.0 && mu[j][3] > 0.0) {
+ if (mu[i][3] > 0.0 && mu[j][3] > 0.0) {
r3inv = r2inv*rinv;
r5inv = r3inv*r2inv;
- rcutcoul2inv=1.0/cut_coulsq[itype][jtype];
+ rcutcoul2inv=1.0/cut_coulsq[itype][jtype];
pdotp = mu[i][0]*mu[j][0] + mu[i][1]*mu[j][1] + mu[i][2]*mu[j][2];
pidotr = mu[i][0]*delx + mu[i][1]*dely + mu[i][2]*delz;
pjdotr = mu[j][0]*delx + mu[j][1]*dely + mu[j][2]*delz;
- afac = 1.0 - rsq*rsq * rcutcoul2inv*rcutcoul2inv;
- pre1 = afac * ( pdotp - 3.0 * r2inv * pidotr * pjdotr );
- aforcecoulx = pre1*delx;
- aforcecouly = pre1*dely;
- aforcecoulz = pre1*delz;
-
- bfac = 1.0 - 4.0*rsq*sqrt(rsq)*rcutcoul2inv*sqrt(rcutcoul2inv) +
- 3.0*rsq*rsq*rcutcoul2inv*rcutcoul2inv;
- presf = 2.0 * r2inv * pidotr * pjdotr;
- bforcecoulx = bfac * (pjdotr*mu[i][0]+pidotr*mu[j][0]-presf*delx);
- bforcecouly = bfac * (pjdotr*mu[i][1]+pidotr*mu[j][1]-presf*dely);
- bforcecoulz = bfac * (pjdotr*mu[i][2]+pidotr*mu[j][2]-presf*delz);
-
- forcecoulx += 3.0 * r5inv * ( aforcecoulx + bforcecoulx );
- forcecouly += 3.0 * r5inv * ( aforcecouly + bforcecouly );
- forcecoulz += 3.0 * r5inv * ( aforcecoulz + bforcecoulz );
-
- pre2 = 3.0 * bfac * r5inv * pjdotr;
- pre3 = 3.0 * bfac * r5inv * pidotr;
- pre4 = -bfac * r3inv;
-
- crossx = pre4 * (mu[i][1]*mu[j][2] - mu[i][2]*mu[j][1]);
- crossy = pre4 * (mu[i][2]*mu[j][0] - mu[i][0]*mu[j][2]);
- crossz = pre4 * (mu[i][0]*mu[j][1] - mu[i][1]*mu[j][0]);
-
- tixcoul += crossx + pre2 * (mu[i][1]*delz - mu[i][2]*dely);
- tiycoul += crossy + pre2 * (mu[i][2]*delx - mu[i][0]*delz);
- tizcoul += crossz + pre2 * (mu[i][0]*dely - mu[i][1]*delx);
- tjxcoul += -crossx + pre3 * (mu[j][1]*delz - mu[j][2]*dely);
- tjycoul += -crossy + pre3 * (mu[j][2]*delx - mu[j][0]*delz);
- tjzcoul += -crossz + pre3 * (mu[j][0]*dely - mu[j][1]*delx);
- }
-
- if (mu[i][3] > 0.0 && q[j] != 0.0) {
+ afac = 1.0 - rsq*rsq * rcutcoul2inv*rcutcoul2inv;
+ pre1 = afac * ( pdotp - 3.0 * r2inv * pidotr * pjdotr );
+ aforcecoulx = pre1*delx;
+ aforcecouly = pre1*dely;
+ aforcecoulz = pre1*delz;
+
+ bfac = 1.0 - 4.0*rsq*sqrt(rsq)*rcutcoul2inv*sqrt(rcutcoul2inv) +
+ 3.0*rsq*rsq*rcutcoul2inv*rcutcoul2inv;
+ presf = 2.0 * r2inv * pidotr * pjdotr;
+ bforcecoulx = bfac * (pjdotr*mu[i][0]+pidotr*mu[j][0]-presf*delx);
+ bforcecouly = bfac * (pjdotr*mu[i][1]+pidotr*mu[j][1]-presf*dely);
+ bforcecoulz = bfac * (pjdotr*mu[i][2]+pidotr*mu[j][2]-presf*delz);
+
+ forcecoulx += 3.0 * r5inv * ( aforcecoulx + bforcecoulx );
+ forcecouly += 3.0 * r5inv * ( aforcecouly + bforcecouly );
+ forcecoulz += 3.0 * r5inv * ( aforcecoulz + bforcecoulz );
+
+ pre2 = 3.0 * bfac * r5inv * pjdotr;
+ pre3 = 3.0 * bfac * r5inv * pidotr;
+ pre4 = -bfac * r3inv;
+
+ crossx = pre4 * (mu[i][1]*mu[j][2] - mu[i][2]*mu[j][1]);
+ crossy = pre4 * (mu[i][2]*mu[j][0] - mu[i][0]*mu[j][2]);
+ crossz = pre4 * (mu[i][0]*mu[j][1] - mu[i][1]*mu[j][0]);
+
+ tixcoul += crossx + pre2 * (mu[i][1]*delz - mu[i][2]*dely);
+ tiycoul += crossy + pre2 * (mu[i][2]*delx - mu[i][0]*delz);
+ tizcoul += crossz + pre2 * (mu[i][0]*dely - mu[i][1]*delx);
+ tjxcoul += -crossx + pre3 * (mu[j][1]*delz - mu[j][2]*dely);
+ tjycoul += -crossy + pre3 * (mu[j][2]*delx - mu[j][0]*delz);
+ tjzcoul += -crossz + pre3 * (mu[j][0]*dely - mu[j][1]*delx);
+ }
+
+ if (mu[i][3] > 0.0 && q[j] != 0.0) {
r3inv = r2inv*rinv;
r5inv = r3inv*r2inv;
pidotr = mu[i][0]*delx + mu[i][1]*dely + mu[i][2]*delz;
- rcutcoul2inv=1.0/cut_coulsq[itype][jtype];
- pre1 = 3.0 * q[j] * r5inv * pidotr * (1-rsq*rcutcoul2inv);
- pqfac = 1.0 - 3.0*rsq*rcutcoul2inv +
- 2.0*rsq*sqrt(rsq)*rcutcoul2inv*sqrt(rcutcoul2inv);
- pre2 = q[j] * r3inv * pqfac;
+ rcutcoul2inv=1.0/cut_coulsq[itype][jtype];
+ pre1 = 3.0 * q[j] * r5inv * pidotr * (1-rsq*rcutcoul2inv);
+ pqfac = 1.0 - 3.0*rsq*rcutcoul2inv +
+ 2.0*rsq*sqrt(rsq)*rcutcoul2inv*sqrt(rcutcoul2inv);
+ pre2 = q[j] * r3inv * pqfac;
- forcecoulx += pre2*mu[i][0] - pre1*delx;
+ forcecoulx += pre2*mu[i][0] - pre1*delx;
forcecouly += pre2*mu[i][1] - pre1*dely;
forcecoulz += pre2*mu[i][2] - pre1*delz;
- tixcoul += pre2 * (mu[i][1]*delz - mu[i][2]*dely);
- tiycoul += pre2 * (mu[i][2]*delx - mu[i][0]*delz);
- tizcoul += pre2 * (mu[i][0]*dely - mu[i][1]*delx);
- }
+ tixcoul += pre2 * (mu[i][1]*delz - mu[i][2]*dely);
+ tiycoul += pre2 * (mu[i][2]*delx - mu[i][0]*delz);
+ tizcoul += pre2 * (mu[i][0]*dely - mu[i][1]*delx);
+ }
- if (mu[j][3] > 0.0 && qtmp != 0.0) {
+ if (mu[j][3] > 0.0 && qtmp != 0.0) {
r3inv = r2inv*rinv;
r5inv = r3inv*r2inv;
pjdotr = mu[j][0]*delx + mu[j][1]*dely + mu[j][2]*delz;
- rcutcoul2inv=1.0/cut_coulsq[itype][jtype];
- pre1 = 3.0 * qtmp * r5inv * pjdotr * (1-rsq*rcutcoul2inv);
- qpfac = 1.0 - 3.0*rsq*rcutcoul2inv +
- 2.0*rsq*sqrt(rsq)*rcutcoul2inv*sqrt(rcutcoul2inv);
- pre2 = qtmp * r3inv * qpfac;
+ rcutcoul2inv=1.0/cut_coulsq[itype][jtype];
+ pre1 = 3.0 * qtmp * r5inv * pjdotr * (1-rsq*rcutcoul2inv);
+ qpfac = 1.0 - 3.0*rsq*rcutcoul2inv +
+ 2.0*rsq*sqrt(rsq)*rcutcoul2inv*sqrt(rcutcoul2inv);
+ pre2 = qtmp * r3inv * qpfac;
- forcecoulx += pre1*delx - pre2*mu[j][0];
+ forcecoulx += pre1*delx - pre2*mu[j][0];
forcecouly += pre1*dely - pre2*mu[j][1];
forcecoulz += pre1*delz - pre2*mu[j][2];
- tjxcoul += -pre2 * (mu[j][1]*delz - mu[j][2]*dely);
- tjycoul += -pre2 * (mu[j][2]*delx - mu[j][0]*delz);
- tjzcoul += -pre2 * (mu[j][0]*dely - mu[j][1]*delx);
- }
- }
-
- // LJ interaction
-
- if (rsq < cut_ljsq[itype][jtype]) {
- r6inv = r2inv*r2inv*r2inv;
- forceljcut = r6inv*(lj1[itype][jtype]*r6inv-lj2[itype][jtype])*r2inv;
-
- rcutlj2inv = 1.0 / cut_ljsq[itype][jtype];
- rcutlj6inv = rcutlj2inv * rcutlj2inv * rcutlj2inv;
- forceljsf = (lj1[itype][jtype]*rcutlj6inv - lj2[itype][jtype]) *
- rcutlj6inv * rcutlj2inv;
-
- forcelj = factor_lj * (forceljcut - forceljsf);
- } else forcelj = 0.0;
-
- // total force
-
- fq = factor_coul*qqrd2e;
- fx = fq*forcecoulx + delx*forcelj;
- fy = fq*forcecouly + dely*forcelj;
- fz = fq*forcecoulz + delz*forcelj;
-
- // force & torque accumulation
-
- f[i][0] += fx;
- f[i][1] += fy;
- f[i][2] += fz;
- torque[i][0] += fq*tixcoul;
- torque[i][1] += fq*tiycoul;
- torque[i][2] += fq*tizcoul;
-
- if (newton_pair || j < nlocal) {
- f[j][0] -= fx;
- f[j][1] -= fy;
- f[j][2] -= fz;
- torque[j][0] += fq*tjxcoul;
- torque[j][1] += fq*tjycoul;
- torque[j][2] += fq*tjzcoul;
- }
-
- if (eflag) {
- if (rsq < cut_coulsq[itype][jtype]) {
- ecoul = qtmp * q[j] * rinv *
- pow((1.0-sqrt(rsq)/sqrt(cut_coulsq[itype][jtype])),2.0);
- if (mu[i][3] > 0.0 && mu[j][3] > 0.0)
- ecoul += bfac * (r3inv*pdotp - 3.0*r5inv*pidotr*pjdotr);
- if (mu[i][3] > 0.0 && q[j] != 0.0)
- ecoul += -q[j] * r3inv * pqfac * pidotr;
- if (mu[j][3] > 0.0 && qtmp != 0.0)
- ecoul += qtmp * r3inv * qpfac * pjdotr;
- ecoul *= factor_coul*qqrd2e;
- } else ecoul = 0.0;
-
- if (rsq < cut_ljsq[itype][jtype]) {
- evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype])+
- rcutlj6inv*(6*lj3[itype][jtype]*rcutlj6inv-3*lj4[itype][jtype])*
- rsq*rcutlj2inv+
- rcutlj6inv*(-7*lj3[itype][jtype]*rcutlj6inv+4*lj4[itype][jtype]);
- evdwl *= factor_lj;
- } else evdwl = 0.0;
- }
-
- if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,
- evdwl,ecoul,fx,fy,fz,delx,dely,delz);
+ tjxcoul += -pre2 * (mu[j][1]*delz - mu[j][2]*dely);
+ tjycoul += -pre2 * (mu[j][2]*delx - mu[j][0]*delz);
+ tjzcoul += -pre2 * (mu[j][0]*dely - mu[j][1]*delx);
+ }
+ }
+
+ // LJ interaction
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ r6inv = r2inv*r2inv*r2inv;
+ forceljcut = r6inv*(lj1[itype][jtype]*r6inv-lj2[itype][jtype])*r2inv;
+
+ rcutlj2inv = 1.0 / cut_ljsq[itype][jtype];
+ rcutlj6inv = rcutlj2inv * rcutlj2inv * rcutlj2inv;
+ forceljsf = (lj1[itype][jtype]*rcutlj6inv - lj2[itype][jtype]) *
+ rcutlj6inv * rcutlj2inv;
+
+ forcelj = factor_lj * (forceljcut - forceljsf);
+ } else forcelj = 0.0;
+
+ // total force
+
+ fq = factor_coul*qqrd2e;
+ fx = fq*forcecoulx + delx*forcelj;
+ fy = fq*forcecouly + dely*forcelj;
+ fz = fq*forcecoulz + delz*forcelj;
+
+ // force & torque accumulation
+
+ f[i][0] += fx;
+ f[i][1] += fy;
+ f[i][2] += fz;
+ torque[i][0] += fq*tixcoul;
+ torque[i][1] += fq*tiycoul;
+ torque[i][2] += fq*tizcoul;
+
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= fx;
+ f[j][1] -= fy;
+ f[j][2] -= fz;
+ torque[j][0] += fq*tjxcoul;
+ torque[j][1] += fq*tjycoul;
+ torque[j][2] += fq*tjzcoul;
+ }
+
+ if (eflag) {
+ if (rsq < cut_coulsq[itype][jtype]) {
+ ecoul = qtmp * q[j] * rinv *
+ pow((1.0-sqrt(rsq)/sqrt(cut_coulsq[itype][jtype])),2.0);
+ if (mu[i][3] > 0.0 && mu[j][3] > 0.0)
+ ecoul += bfac * (r3inv*pdotp - 3.0*r5inv*pidotr*pjdotr);
+ if (mu[i][3] > 0.0 && q[j] != 0.0)
+ ecoul += -q[j] * r3inv * pqfac * pidotr;
+ if (mu[j][3] > 0.0 && qtmp != 0.0)
+ ecoul += qtmp * r3inv * qpfac * pjdotr;
+ ecoul *= factor_coul*qqrd2e;
+ } else ecoul = 0.0;
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype])+
+ rcutlj6inv*(6*lj3[itype][jtype]*rcutlj6inv-3*lj4[itype][jtype])*
+ rsq*rcutlj2inv+
+ rcutlj6inv*(-7*lj3[itype][jtype]*rcutlj6inv+4*lj4[itype][jtype]);
+ evdwl *= factor_lj;
+ } else evdwl = 0.0;
+ }
+
+ if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,
+ evdwl,ecoul,fx,fy,fz,delx,dely,delz);
}
}
}
@@ -289,7 +289,7 @@ void PairDipoleSF::compute(int eflag, int vflag)
}
/* ----------------------------------------------------------------------
- allocate all arrays
+ allocate all arrays
------------------------------------------------------------------------- */
void PairDipoleSF::allocate()
@@ -317,7 +317,7 @@ void PairDipoleSF::allocate()
}
/* ----------------------------------------------------------------------
- global settings
+ global settings
------------------------------------------------------------------------- */
void PairDipoleSF::settings(int narg, char **arg)
@@ -335,10 +335,10 @@ void PairDipoleSF::settings(int narg, char **arg)
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
- if (setflag[i][j]) {
- cut_lj[i][j] = cut_lj_global;
- cut_coul[i][j] = cut_coul_global;
- }
+ if (setflag[i][j]) {
+ cut_lj[i][j] = cut_lj_global;
+ cut_coul[i][j] = cut_coul_global;
+ }
}
}
@@ -348,7 +348,7 @@ void PairDipoleSF::settings(int narg, char **arg)
void PairDipoleSF::coeff(int narg, char **arg)
{
- if (narg < 4 || narg > 6)
+ if (narg < 4 || narg > 6)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
@@ -399,7 +399,7 @@ double PairDipoleSF::init_one(int i, int j)
{
if (setflag[i][j] == 0) {
epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j],
- sigma[i][i],sigma[j][j]);
+ sigma[i][i],sigma[j][j]);
sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]);
cut_lj[i][j] = mix_distance(cut_lj[i][i],cut_lj[j][j]);
cut_coul[i][j] = mix_distance(cut_coul[i][i],cut_coul[j][j]);
@@ -413,7 +413,7 @@ double PairDipoleSF::init_one(int i, int j)
lj2[i][j] = 24.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
-
+
cut_ljsq[j][i] = cut_ljsq[i][j];
cut_coulsq[j][i] = cut_coulsq[i][j];
lj1[j][i] = lj1[i][j];
@@ -437,10 +437,10 @@ void PairDipoleSF::write_restart(FILE *fp)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
- fwrite(&epsilon[i][j],sizeof(double),1,fp);
- fwrite(&sigma[i][j],sizeof(double),1,fp);
- fwrite(&cut_lj[i][j],sizeof(double),1,fp);
- fwrite(&cut_coul[i][j],sizeof(double),1,fp);
+ fwrite(&epsilon[i][j],sizeof(double),1,fp);
+ fwrite(&sigma[i][j],sizeof(double),1,fp);
+ fwrite(&cut_lj[i][j],sizeof(double),1,fp);
+ fwrite(&cut_coul[i][j],sizeof(double),1,fp);
}
}
}
@@ -462,16 +462,16 @@ void PairDipoleSF::read_restart(FILE *fp)
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
- if (me == 0) {
- fread(&epsilon[i][j],sizeof(double),1,fp);
- fread(&sigma[i][j],sizeof(double),1,fp);
- fread(&cut_lj[i][j],sizeof(double),1,fp);
- fread(&cut_coul[i][j],sizeof(double),1,fp);
- }
- MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&cut_coul[i][j],1,MPI_DOUBLE,0,world);
+ if (me == 0) {
+ fread(&epsilon[i][j],sizeof(double),1,fp);
+ fread(&sigma[i][j],sizeof(double),1,fp);
+ fread(&cut_lj[i][j],sizeof(double),1,fp);
+ fread(&cut_coul[i][j],sizeof(double),1,fp);
+ }
+ MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut_coul[i][j],1,MPI_DOUBLE,0,world);
}
}
}
diff --git a/src/USER-MISC/pair_dipole_sf.h b/src/USER-MISC/pair_dipole_sf.h
index 945f48694c78593b740e7866c6b84cb8b1daceda..57a577c61b1097419ec5ce5b9534a0eb4824ae52 100644
--- a/src/USER-MISC/pair_dipole_sf.h
+++ b/src/USER-MISC/pair_dipole_sf.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-MISC/pair_edip.cpp b/src/USER-MISC/pair_edip.cpp
index 008251f9347ccafcba82c9b75f4e9f8e299d9104..a9efb04820a4996d35c362ae568b313535f8147e 100755
--- a/src/USER-MISC/pair_edip.cpp
+++ b/src/USER-MISC/pair_edip.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -210,8 +210,8 @@ void PairEDIP::compute(int eflag, int vflag)
interpolY1 = exp3B[interpolIDX];
interpolY2 = exp3B[interpolIDX+1];
- exp3B_ij = interpolY1 + (interpolY2 - interpolY1) *
- (interpolTMP-interpolIDX);
+ exp3B_ij = interpolY1 + (interpolY2 - interpolY1) *
+ (interpolTMP-interpolIDX);
exp3BDerived_ij = - exp3B_ij * gammInvRMinusCutoffA * invRMinusCutoffA;
@@ -220,8 +220,8 @@ void PairEDIP::compute(int eflag, int vflag)
interpolY1 = exp2B[interpolIDX];
interpolY2 = exp2B[interpolIDX+1];
- exp2B_ij = interpolY1 + (interpolY2 - interpolY1) *
- (interpolTMP-interpolIDX);
+ exp2B_ij = interpolY1 + (interpolY2 - interpolY1) *
+ (interpolTMP-interpolIDX);
exp2BDerived_ij = - exp2B_ij * sigmaInvRMinusCutoffA * invRMinusCutoffA;
@@ -230,8 +230,8 @@ void PairEDIP::compute(int eflag, int vflag)
interpolY1 = pow2B[interpolIDX];
interpolY2 = pow2B[interpolIDX+1];
- pow2B_ij = interpolY1 + (interpolY2 - interpolY1) *
- (interpolTMP-interpolIDX);
+ pow2B_ij = interpolY1 + (interpolY2 - interpolY1) *
+ (interpolTMP-interpolIDX);
prePow2B_ij[neighbor_j] = pow2B_ij;
@@ -241,15 +241,15 @@ void PairEDIP::compute(int eflag, int vflag)
else {
interpolY1 = cutoffFunction[interpolIDX];
interpolY2 = cutoffFunction[interpolIDX+1];
- cutoffFunction_ij = interpolY1 + (interpolY2 - interpolY1) *
- (interpolTMP-interpolIDX);
+ cutoffFunction_ij = interpolY1 + (interpolY2 - interpolY1) *
+ (interpolTMP-interpolIDX);
zeta_i += cutoffFunction_ij;
interpolY1 = cutoffFunctionDerived[interpolIDX];
interpolY2 = cutoffFunctionDerived[interpolIDX+1];
- zeta_iDerived = interpolY1 + (interpolY2 - interpolY1) *
- (interpolTMP-interpolIDX);
+ zeta_iDerived = interpolY1 + (interpolY2 - interpolY1) *
+ (interpolTMP-interpolIDX);
zeta_iDerivedInvR_ij = zeta_iDerived * invR_ij;
@@ -271,22 +271,22 @@ void PairEDIP::compute(int eflag, int vflag)
interpolY1 = expMinusBetaZeta_iZeta_iGrid[interpolIDX];
interpolY2 = expMinusBetaZeta_iZeta_iGrid[interpolIDX+1];
- expMinusBetaZeta_iZeta_i = interpolY1 + (interpolY2 - interpolY1) *
+ expMinusBetaZeta_iZeta_i = interpolY1 + (interpolY2 - interpolY1) *
(interpolTMP-interpolIDX);
interpolY1 = qFunctionGrid[interpolIDX];
interpolY2 = qFunctionGrid[interpolIDX+1];
- qFunction = interpolY1 + (interpolY2 - interpolY1) *
+ qFunction = interpolY1 + (interpolY2 - interpolY1) *
(interpolTMP-interpolIDX);
interpolY1 = tauFunctionGrid[interpolIDX];
interpolY2 = tauFunctionGrid[interpolIDX+1];
- tauFunction = interpolY1 + (interpolY2 - interpolY1) *
+ tauFunction = interpolY1 + (interpolY2 - interpolY1) *
(interpolTMP-interpolIDX);
interpolY1 = tauFunctionDerivedGrid[interpolIDX];
interpolY2 = tauFunctionDerivedGrid[interpolIDX+1];
- tauFunctionDerived = interpolY1 + (interpolY2 - interpolY1) *
+ tauFunctionDerived = interpolY1 + (interpolY2 - interpolY1) *
(interpolTMP-interpolIDX);
qFunctionDerived = -mu * qFunction;
@@ -326,8 +326,8 @@ void PairEDIP::compute(int eflag, int vflag)
forceModCoord += (forceModCoord_factor*exp2B_ij);
exp2BDerived_ij = preExp2BDerived_ij[neighbor_j];
- forceMod2B = exp2BDerived_ij * potential2B_factor +
- exp2B_ij * pow2BDerived_ij;
+ forceMod2B = exp2BDerived_ij * potential2B_factor +
+ exp2B_ij * pow2BDerived_ij;
directorCos_ij_x = invR_ij * dr_ij[0];
directorCos_ij_y = invR_ij * dr_ij[1];
@@ -381,56 +381,56 @@ void PairEDIP::compute(int eflag, int vflag)
directorCos_ik_y = invR_ik * dr_ik[1];
directorCos_ik_z = invR_ik * dr_ik[2];
- cosTeta = directorCos_ij_x * directorCos_ik_x +
- directorCos_ij_y * directorCos_ik_y +
- directorCos_ij_z * directorCos_ik_z;
+ cosTeta = directorCos_ij_x * directorCos_ik_x +
+ directorCos_ij_y * directorCos_ik_y +
+ directorCos_ij_z * directorCos_ik_z;
cosTetaDiff = cosTeta + tauFunction;
cosTetaDiffCosTetaDiff = cosTetaDiff * cosTetaDiff;
qFunctionCosTetaDiffCosTetaDiff = cosTetaDiffCosTetaDiff * qFunction;
- expMinusQFunctionCosTetaDiffCosTetaDiff =
- exp(-qFunctionCosTetaDiffCosTetaDiff);
+ expMinusQFunctionCosTetaDiffCosTetaDiff =
+ exp(-qFunctionCosTetaDiffCosTetaDiff);
- potentia3B_factor = lambda *
- ((1.0 - expMinusQFunctionCosTetaDiffCosTetaDiff) +
- eta * qFunctionCosTetaDiffCosTetaDiff);
+ potentia3B_factor = lambda *
+ ((1.0 - expMinusQFunctionCosTetaDiffCosTetaDiff) +
+ eta * qFunctionCosTetaDiffCosTetaDiff);
exp3B_ik = preExp3B_ij[neighbor_k];
exp3BDerived_ik = preExp3BDerived_ij[neighbor_k];
- forceMod3B_factor1_ij = - exp3BDerived_ij * exp3B_ik *
- potentia3B_factor;
- forceMod3B_factor2 = 2.0 * lambda * exp3B_ij * exp3B_ik *
- qFunction * cosTetaDiff *
- (eta + expMinusQFunctionCosTetaDiffCosTetaDiff);
+ forceMod3B_factor1_ij = - exp3BDerived_ij * exp3B_ik *
+ potentia3B_factor;
+ forceMod3B_factor2 = 2.0 * lambda * exp3B_ij * exp3B_ik *
+ qFunction * cosTetaDiff *
+ (eta + expMinusQFunctionCosTetaDiffCosTetaDiff);
forceMod3B_factor2_ij = forceMod3B_factor2 * invR_ij;
- f_ij[0] = forceMod3B_factor1_ij * directorCos_ij_x +
- forceMod3B_factor2_ij *
- (cosTeta * directorCos_ij_x - directorCos_ik_x);
- f_ij[1] = forceMod3B_factor1_ij * directorCos_ij_y +
- forceMod3B_factor2_ij *
- (cosTeta * directorCos_ij_y - directorCos_ik_y);
- f_ij[2] = forceMod3B_factor1_ij * directorCos_ij_z +
- forceMod3B_factor2_ij *
- (cosTeta * directorCos_ij_z - directorCos_ik_z);
-
- forceMod3B_factor1_ik = - exp3BDerived_ik * exp3B_ij *
- potentia3B_factor;
+ f_ij[0] = forceMod3B_factor1_ij * directorCos_ij_x +
+ forceMod3B_factor2_ij *
+ (cosTeta * directorCos_ij_x - directorCos_ik_x);
+ f_ij[1] = forceMod3B_factor1_ij * directorCos_ij_y +
+ forceMod3B_factor2_ij *
+ (cosTeta * directorCos_ij_y - directorCos_ik_y);
+ f_ij[2] = forceMod3B_factor1_ij * directorCos_ij_z +
+ forceMod3B_factor2_ij *
+ (cosTeta * directorCos_ij_z - directorCos_ik_z);
+
+ forceMod3B_factor1_ik = - exp3BDerived_ik * exp3B_ij *
+ potentia3B_factor;
forceMod3B_factor2_ik = forceMod3B_factor2 * invR_ik;
- f_ik[0] = forceMod3B_factor1_ik * directorCos_ik_x +
- forceMod3B_factor2_ik *
- (cosTeta * directorCos_ik_x - directorCos_ij_x);
- f_ik[1] = forceMod3B_factor1_ik * directorCos_ik_y +
- forceMod3B_factor2_ik *
- (cosTeta * directorCos_ik_y - directorCos_ij_y);
- f_ik[2] = forceMod3B_factor1_ik * directorCos_ik_z +
- forceMod3B_factor2_ik *
- (cosTeta * directorCos_ik_z - directorCos_ij_z);
+ f_ik[0] = forceMod3B_factor1_ik * directorCos_ik_x +
+ forceMod3B_factor2_ik *
+ (cosTeta * directorCos_ik_x - directorCos_ij_x);
+ f_ik[1] = forceMod3B_factor1_ik * directorCos_ik_y +
+ forceMod3B_factor2_ik *
+ (cosTeta * directorCos_ik_y - directorCos_ij_y);
+ f_ik[2] = forceMod3B_factor1_ik * directorCos_ik_z +
+ forceMod3B_factor2_ik *
+ (cosTeta * directorCos_ik_z - directorCos_ij_z);
- forceModCoord += (forceMod3B_factor2 *
- (tauFunctionDerived - 0.5 * mu * cosTetaDiff));
+ forceModCoord += (forceMod3B_factor2 *
+ (tauFunctionDerived - 0.5 * mu * cosTetaDiff));
f[j][0] += f_ij[0];
f[j][1] += f_ij[1];
@@ -482,7 +482,7 @@ void PairEDIP::compute(int eflag, int vflag)
evdwl = 0.0;
if (evflag) ev_tally(i, j, nlocal, newton_pair, evdwl, 0.0,
- forceModCoord_ij, dr_ij[0], dr_ij[1], dr_ij[2]);
+ forceModCoord_ij, dr_ij[0], dr_ij[1], dr_ij[2]);
}
}
@@ -509,27 +509,27 @@ void PairEDIP::allocateGrids(void)
// tauFunctionGrid
maxArgumentTauFunctionGrid = leadDimInteractionList;
- numGridPointsTauFunctionGrid = (int)
+ numGridPointsTauFunctionGrid = (int)
((maxArgumentTauFunctionGrid) * GRIDDENSITY) + 2;
memory->create(tauFunctionGrid,numGridPointsTauFunctionGrid,
- "edip:tauFunctionGrid");
+ "edip:tauFunctionGrid");
memory->create(tauFunctionDerivedGrid,numGridPointsTauFunctionGrid,
- "edip:tauFunctionDerivedGrid");
+ "edip:tauFunctionDerivedGrid");
// expMinusBetaZeta_iZeta_iGrid
maxArgumentExpMinusBetaZeta_iZeta_i = leadDimInteractionList;
- numGridPointsExpMinusBetaZeta_iZeta_i = (int)
+ numGridPointsExpMinusBetaZeta_iZeta_i = (int)
((maxArgumentExpMinusBetaZeta_iZeta_i) * GRIDDENSITY) + 2;
memory->create(expMinusBetaZeta_iZeta_iGrid,
- numGridPointsExpMinusBetaZeta_iZeta_i,
- "edip:expMinusBetaZeta_iZeta_iGrid");
+ numGridPointsExpMinusBetaZeta_iZeta_i,
+ "edip:expMinusBetaZeta_iZeta_iGrid");
// qFunctionGrid
maxArgumentQFunctionGrid = leadDimInteractionList;
- numGridPointsQFunctionGrid = (int)
+ numGridPointsQFunctionGrid = (int)
((maxArgumentQFunctionGrid) * GRIDDENSITY) + 2;
memory->create(qFunctionGrid,numGridPointsQFunctionGrid,"edip:qFunctionGrid");
@@ -537,17 +537,17 @@ void PairEDIP::allocateGrids(void)
numGridPointsOneCutoffFunction = (int) ((cutoffC - GRIDSTART) * GRIDDENSITY);
numGridPointsNotOneCutoffFunction = (int) ((cutoffA-cutoffC) * GRIDDENSITY);
- numGridPointsCutoffFunction = numGridPointsOneCutoffFunction +
+ numGridPointsCutoffFunction = numGridPointsOneCutoffFunction +
numGridPointsNotOneCutoffFunction+2;
memory->create(cutoffFunction,numGridPointsCutoffFunction,
- "edip:cutoffFunction");
+ "edip:cutoffFunction");
memory->create(cutoffFunctionDerived,numGridPointsCutoffFunction,
- "edip:cutoffFunctionDerived");
+ "edip:cutoffFunctionDerived");
// pow2B
- numGridPointsR = (int)
+ numGridPointsR = (int)
((cutoffA + leftLimitToZero - GRIDSTART) * GRIDDENSITY);
numGridPointsRTotal = numGridPointsR + 2;
@@ -563,14 +563,14 @@ void PairEDIP::allocateGrids(void)
void PairEDIP::allocatePreLoops(void)
{
int nthreads = comm->nthreads;
-
+
memory->create(preInvR_ij,nthreads*leadDimInteractionList,"edip:preInvR_ij");
memory->create(preExp3B_ij,nthreads*leadDimInteractionList,"edip:preExp3B_ij");
memory->create(preExp3BDerived_ij,nthreads*leadDimInteractionList,
- "edip:preExp3BDerived_ij");
+ "edip:preExp3BDerived_ij");
memory->create(preExp2B_ij,nthreads*leadDimInteractionList,"edip:preExp2B_ij");
memory->create(preExp2BDerived_ij,nthreads*leadDimInteractionList,
- "edip:preExp2BDerived_ij");
+ "edip:preExp2BDerived_ij");
memory->create(prePow2B_ij,nthreads*leadDimInteractionList,"edip:prePow2B_ij");
memory->create(preForceCoord,5*nthreads*leadDimInteractionList,"edip:preForceCoord");
}
@@ -621,7 +621,7 @@ void PairEDIP::allocate()
}
/* ----------------------------------------------------------------------
- global settings
+ global settings
------------------------------------------------------------------------- */
void PairEDIP::settings(int narg, char **arg)
@@ -660,17 +660,17 @@ void PairEDIP::initGrids(void)
maxArgumentTauFunctionGrid = leadDimInteractionList;
- numGridPointsTauFunctionGrid = (int)
+ numGridPointsTauFunctionGrid = (int)
((maxArgumentTauFunctionGrid) * GRIDDENSITY) + 2;
r = 0.0;
deltaArgumentTauFunctionGrid = 1.0 / GRIDDENSITY;
for (l = 0; l < numGridPointsTauFunctionGrid; l++) {
- tauFunctionGrid[l] = u1 + u2 * u3 * exp(-u4 * r) -
- u2 * exp(-2.0 * u4 * r);
- tauFunctionDerivedGrid[l] = - u2 * u3 * u4 * exp(-u4 * r) +
- 2.0 * u2 * u4 * exp(-2.0 * u4 * r);
+ tauFunctionGrid[l] = u1 + u2 * u3 * exp(-u4 * r) -
+ u2 * exp(-2.0 * u4 * r);
+ tauFunctionDerivedGrid[l] = - u2 * u3 * u4 * exp(-u4 * r) +
+ 2.0 * u2 * u4 * exp(-2.0 * u4 * r);
r += deltaArgumentTauFunctionGrid;
}
@@ -678,7 +678,7 @@ void PairEDIP::initGrids(void)
maxArgumentExpMinusBetaZeta_iZeta_i = leadDimInteractionList;
- numGridPointsExpMinusBetaZeta_iZeta_i = (int)
+ numGridPointsExpMinusBetaZeta_iZeta_i = (int)
((maxArgumentExpMinusBetaZeta_iZeta_i) * GRIDDENSITY) + 2;
r = 0.0;
@@ -692,7 +692,7 @@ void PairEDIP::initGrids(void)
// qFunctionGrid
maxArgumentQFunctionGrid = leadDimInteractionList;
- numGridPointsQFunctionGrid =
+ numGridPointsQFunctionGrid =
(int) ((maxArgumentQFunctionGrid) * GRIDDENSITY) + 2;
r = 0.0;
@@ -705,11 +705,11 @@ void PairEDIP::initGrids(void)
// cutoffFunction
- numGridPointsOneCutoffFunction =
+ numGridPointsOneCutoffFunction =
(int) ((cutoffC - GRIDSTART) * GRIDDENSITY);
- numGridPointsNotOneCutoffFunction =
+ numGridPointsNotOneCutoffFunction =
(int) ((cutoffA-cutoffC) * GRIDDENSITY);
- numGridPointsCutoffFunction =
+ numGridPointsCutoffFunction =
numGridPointsOneCutoffFunction+numGridPointsNotOneCutoffFunction+2;
r = GRIDSTART;
@@ -721,20 +721,20 @@ void PairEDIP::initGrids(void)
r += deltaArgumentCutoffFunction;
}
- for (l = numGridPointsOneCutoffFunction;
+ for (l = numGridPointsOneCutoffFunction;
l < numGridPointsCutoffFunction; l++) {
temp = (cutoffA - cutoffC)/(r - cutoffC);
temp3 = temp * temp * temp;
temp4 = temp3 * temp;
cutoffFunction[l] = exp(alpha/(1.0-temp3));
- cutoffFunctionDerived[l] = (-3*alpha/(cutoffA-cutoffC)) *
- (temp4/((1-temp3)*(1-temp3)))*exp(alpha/(1.0-temp3));
+ cutoffFunctionDerived[l] = (-3*alpha/(cutoffA-cutoffC)) *
+ (temp4/((1-temp3)*(1-temp3)))*exp(alpha/(1.0-temp3));
r += deltaArgumentCutoffFunction;
}
// pow2B
- numGridPointsR = (int)
+ numGridPointsR = (int)
((cutoffA + leftLimitToZero - GRIDSTART) * GRIDDENSITY);
numGridPointsRTotal = numGridPointsR + 2;
@@ -804,7 +804,7 @@ void PairEDIP::coeff(int narg, char **arg)
}
// read potential file and initialize potential parameters
-
+
read_file(arg[2]);
setup();
@@ -821,8 +821,8 @@ void PairEDIP::coeff(int narg, char **arg)
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
if (map[i] >= 0 && map[j] >= 0) {
- setflag[i][j] = 1;
- count++;
+ setflag[i][j] = 1;
+ count++;
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
@@ -898,8 +898,8 @@ void PairEDIP::read_file(char *file)
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fp);
if (ptr == NULL) {
- eof = 1;
- fclose(fp);
+ eof = 1;
+ fclose(fp);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
@@ -920,8 +920,8 @@ void PairEDIP::read_file(char *file)
if (comm->me == 0) {
ptr = fgets(&line[n],MAXLINE-n,fp);
if (ptr == NULL) {
- eof = 1;
- fclose(fp);
+ eof = 1;
+ fclose(fp);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
@@ -960,7 +960,7 @@ void PairEDIP::read_file(char *file)
if (nparams == maxparam) {
maxparam += DELTA;
params = (Param *) memory->srealloc(params,maxparam*sizeof(Param),
- "pair:params");
+ "pair:params");
}
params[nparams].ielement = ielement;
@@ -985,13 +985,13 @@ void PairEDIP::read_file(char *file)
params[nparams].u4 = atof(words[19]);
if (params[nparams].A < 0.0 || params[nparams].B < 0.0 ||
- params[nparams].cutoffA < 0.0 || params[nparams].cutoffC < 0.0 ||
- params[nparams].alpha < 0.0 || params[nparams].beta < 0.0 ||
- params[nparams].eta < 0.0 || params[nparams].gamm < 0.0 ||
- params[nparams].lambda < 0.0 || params[nparams].mu < 0.0 ||
- params[nparams].rho < 0.0 || params[nparams].sigma < 0.0)
+ params[nparams].cutoffA < 0.0 || params[nparams].cutoffC < 0.0 ||
+ params[nparams].alpha < 0.0 || params[nparams].beta < 0.0 ||
+ params[nparams].eta < 0.0 || params[nparams].gamm < 0.0 ||
+ params[nparams].lambda < 0.0 || params[nparams].mu < 0.0 ||
+ params[nparams].rho < 0.0 || params[nparams].sigma < 0.0)
error->all(FLERR,"Illegal EDIP parameter");
-
+
nparams++;
}
@@ -1015,16 +1015,16 @@ void PairEDIP::setup()
for (i = 0; i < nelements; i++)
for (j = 0; j < nelements; j++)
for (k = 0; k < nelements; k++) {
- n = -1;
- for (m = 0; m < nparams; m++) {
- if (i == params[m].ielement && j == params[m].jelement &&
- k == params[m].kelement) {
- if (n >= 0) error->all(FLERR,"Potential file has duplicate entry");
- n = m;
- }
- }
- if (n < 0) error->all(FLERR,"Potential file is missing an entry");
- elem2param[i][j][k] = n;
+ n = -1;
+ for (m = 0; m < nparams; m++) {
+ if (i == params[m].ielement && j == params[m].jelement &&
+ k == params[m].kelement) {
+ if (n >= 0) error->all(FLERR,"Potential file has duplicate entry");
+ n = m;
+ }
+ }
+ if (n < 0) error->all(FLERR,"Potential file is missing an entry");
+ elem2param[i][j][k] = n;
}
// set cutoff square
diff --git a/src/USER-MISC/pair_edip.h b/src/USER-MISC/pair_edip.h
index f83c32ed3ec29ea29dca357b6b303d2593952b24..c3ad25fb3046ac895575be9851a6448a3fb6c997 100755
--- a/src/USER-MISC/pair_edip.h
+++ b/src/USER-MISC/pair_edip.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -51,7 +51,7 @@ class PairEDIP : public Pair {
double *preExp2BDerived_ij;
double *prePow2B_ij;
double *preForceCoord;
-
+
// grids
double *cutoffFunction;
diff --git a/src/USER-MISC/pair_gauss_cut.cpp b/src/USER-MISC/pair_gauss_cut.cpp
index 0568c40ea003a419d8d7eab0ae0466e0f89a3859..e70bada2f5f188de6202a68b05b27feca70ce3fd 100644
--- a/src/USER-MISC/pair_gauss_cut.cpp
+++ b/src/USER-MISC/pair_gauss_cut.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -107,27 +107,27 @@ void PairGaussCut::compute(int eflag, int vflag)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r = sqrt(rsq);
- rexp = (r-rmh[itype][jtype])/sigmah[itype][jtype];
- ugauss = pgauss[itype][jtype]*exp(-0.5*rexp*rexp);
- fpair = factor_lj*rexp/r*ugauss/sigmah[itype][jtype];
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (eflag) {
- evdwl = ugauss - offset[itype][jtype];
- evdwl *= factor_lj;
- }
-
- if (evflag) ev_tally(i,j,nlocal,newton_pair,
- evdwl,0.0,fpair,delx,dely,delz);
+ r = sqrt(rsq);
+ rexp = (r-rmh[itype][jtype])/sigmah[itype][jtype];
+ ugauss = pgauss[itype][jtype]*exp(-0.5*rexp*rexp);
+ fpair = factor_lj*rexp/r*ugauss/sigmah[itype][jtype];
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (eflag) {
+ evdwl = ugauss - offset[itype][jtype];
+ evdwl *= factor_lj;
+ }
+
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ evdwl,0.0,fpair,delx,dely,delz);
}
}
}
@@ -137,7 +137,7 @@ void PairGaussCut::compute(int eflag, int vflag)
/* ----------------------------------------------------------------------
- allocate all arrays
+ allocate all arrays
------------------------------------------------------------------------- */
void PairGaussCut::allocate()
@@ -161,7 +161,7 @@ void PairGaussCut::allocate()
}
/* ----------------------------------------------------------------------
- global settings
+ global settings
------------------------------------------------------------------------- */
void PairGaussCut::settings(int narg, char **arg)
@@ -176,7 +176,7 @@ void PairGaussCut::settings(int narg, char **arg)
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
- if (setflag[i][j]) cut[i][j] = cut_global;
+ if (setflag[i][j]) cut[i][j] = cut_global;
}
}
@@ -226,13 +226,13 @@ double PairGaussCut::init_one(int i, int j)
error->all(FLERR,"for gauss/cut pair style, parameters need to be set explicitly for all pairs.");
}
pgauss[i][j] = hgauss[i][j] / sqrt(MY_2PI)/ sigmah[i][j];
-
+
if (offset_flag) {
double rexp = (cut[i][j]-rmh[i][j])/sigmah[i][j];
offset[i][j] = pgauss[i][j] * exp(-0.5*rexp*rexp);
} else offset[i][j] = 0.0;
-
+
hgauss[j][i] = hgauss[i][j];
sigmah[j][i] = sigmah[i][j];
rmh[j][i] = rmh[i][j];
@@ -254,13 +254,13 @@ double PairGaussCut::init_one(int i, int j)
if (type[k] == j) count[1] += 1.0;
}
MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world);
- }
+ }
return cut[i][j];
}
/* ----------------------------------------------------------------------
- proc 0 writes to restart file
+ proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairGaussCut::write_restart(FILE *fp)
@@ -272,10 +272,10 @@ void PairGaussCut::write_restart(FILE *fp)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
- fwrite(&hgauss[i][j],sizeof(double),1,fp);
- fwrite(&rmh[i][j],sizeof(double),1,fp);
- fwrite(&sigmah[i][j],sizeof(double),1,fp);
- fwrite(&cut[i][j],sizeof(double),1,fp);
+ fwrite(&hgauss[i][j],sizeof(double),1,fp);
+ fwrite(&rmh[i][j],sizeof(double),1,fp);
+ fwrite(&sigmah[i][j],sizeof(double),1,fp);
+ fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
@@ -296,16 +296,16 @@ void PairGaussCut::read_restart(FILE *fp)
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
- if (me == 0) {
- fread(&hgauss[i][j],sizeof(double),1,fp);
- fread(&rmh[i][j],sizeof(double),1,fp);
- fread(&sigmah[i][j],sizeof(double),1,fp);
- fread(&cut[i][j],sizeof(double),1,fp);
- }
- MPI_Bcast(&hgauss[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&rmh[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&sigmah[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
+ if (me == 0) {
+ fread(&hgauss[i][j],sizeof(double),1,fp);
+ fread(&rmh[i][j],sizeof(double),1,fp);
+ fread(&sigmah[i][j],sizeof(double),1,fp);
+ fread(&cut[i][j],sizeof(double),1,fp);
+ }
+ MPI_Bcast(&hgauss[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&rmh[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&sigmah[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
@@ -341,15 +341,15 @@ void PairGaussCut::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairGaussCut::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
- double &fforce)
+ double factor_coul, double factor_lj,
+ double &fforce)
{
double r, rexp,ugauss,phigauss;
r=sqrt(rsq);
rexp = (r-rmh[itype][jtype])/sigmah[itype][jtype];
- ugauss = pgauss[itype][jtype]*exp(-0.5*rexp*rexp);
-
+ ugauss = pgauss[itype][jtype]*exp(-0.5*rexp*rexp);
+
fforce = factor_lj*rexp/r*ugauss/sigmah[itype][jtype];
phigauss = ugauss - offset[itype][jtype];
@@ -360,7 +360,7 @@ double PairGaussCut::single(int i, int j, int itype, int jtype, double rsq,
double PairGaussCut::memory_usage()
{
const int n=atom->ntypes;
-
+
double bytes = Pair::memory_usage();
bytes += 7*((n+1)*(n+1) * sizeof(double) + (n+1)*sizeof(double *));
@@ -368,4 +368,3 @@ double PairGaussCut::memory_usage()
return bytes;
}
-
diff --git a/src/USER-MISC/pair_gauss_cut.h b/src/USER-MISC/pair_gauss_cut.h
index 8a10308278cccb36a60d4494d1ec91aad36de42e..b43276fe7d8e25d5d8ac572415d7ae2034e32112 100644
--- a/src/USER-MISC/pair_gauss_cut.h
+++ b/src/USER-MISC/pair_gauss_cut.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-MISC/pair_lj_sf.cpp b/src/USER-MISC/pair_lj_sf.cpp
index 9745f296be15f079099adc480cc33cdca09504b3..d378cfab4eb8a872ba1a8f9acbf563c7e6897288 100644
--- a/src/USER-MISC/pair_lj_sf.cpp
+++ b/src/USER-MISC/pair_lj_sf.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -61,11 +61,11 @@ void PairLJShiftedForce::compute(int eflag, int vflag)
double rsq,r2inv,r6inv,forcelj,factor_lj;
double r,t;
int *ilist,*jlist,*numneigh,**firstneigh;
-
+
evdwl = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
-
+
double **x = atom->x;
double **f = atom->f;
int *type = atom->type;
@@ -73,14 +73,14 @@ void PairLJShiftedForce::compute(int eflag, int vflag)
int nall = nlocal + atom->nghost;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
-
+
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// loop over neighbors of my atoms
-
+
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
@@ -89,53 +89,53 @@ void PairLJShiftedForce::compute(int eflag, int vflag)
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
-
+
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
-
+
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
-
+
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
- r = sqrt(rsq);
- t = r/cut[itype][jtype];
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]) -
- t*foffset[itype][jtype];
- fpair = factor_lj*forcelj*r2inv;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (eflag) {
- evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) +
- (t-1.0)*foffset[itype][jtype] - offset[itype][jtype];
- evdwl *= factor_lj;
- }
-
- if (evflag) ev_tally(i,j,nlocal,newton_pair,
- evdwl,0.0,fpair,delx,dely,delz);
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
+ r = sqrt(rsq);
+ t = r/cut[itype][jtype];
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]) -
+ t*foffset[itype][jtype];
+ fpair = factor_lj*forcelj*r2inv;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (eflag) {
+ evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) +
+ (t-1.0)*foffset[itype][jtype] - offset[itype][jtype];
+ evdwl *= factor_lj;
+ }
+
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ evdwl,0.0,fpair,delx,dely,delz);
}
}
}
-
+
if (vflag_fdotr) virial_fdotr_compute();
}
/* ----------------------------------------------------------------------
- allocate all arrays
+ allocate all arrays
------------------------------------------------------------------------- */
void PairLJShiftedForce::allocate()
@@ -161,7 +161,7 @@ void PairLJShiftedForce::allocate()
}
/* ----------------------------------------------------------------------
- global settings
+ global settings
------------------------------------------------------------------------- */
void PairLJShiftedForce::settings(int narg, char **arg)
@@ -172,14 +172,14 @@ void PairLJShiftedForce::settings(int narg, char **arg)
if (cut_global <= 0.0)
error->all(FLERR,"Illegal pair_style command");
-
+
// reset cutoffs that have been explicitly set
if (allocated) {
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
- if (setflag[i][j]) cut[i][j] = cut_global;
+ if (setflag[i][j]) cut[i][j] = cut_global;
}
}
@@ -204,7 +204,7 @@ void PairLJShiftedForce::coeff(int narg, char **arg)
if (cut_one <= 0.0)
error->all(FLERR,"Incorrect args for pair coefficients");
-
+
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
@@ -227,7 +227,7 @@ double PairLJShiftedForce::init_one(int i, int j)
{
if (setflag[i][j] == 0) {
epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j],
- sigma[i][i],sigma[j][j]);
+ sigma[i][i],sigma[j][j]);
sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]);
cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
}
@@ -238,10 +238,10 @@ double PairLJShiftedForce::init_one(int i, int j)
lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
double ratio = sigma[i][j] / cut[i][j];
- foffset[i][j] = 4.0 * epsilon[i][j] * (12.0 * pow(ratio,12.0) -
- 6.0 * pow(ratio,6.0));
+ foffset[i][j] = 4.0 * epsilon[i][j] * (12.0 * pow(ratio,12.0) -
+ 6.0 * pow(ratio,6.0));
offset[i][j] = 4.0 * epsilon[i][j] * (pow(ratio,12.0) - pow(ratio,6.0));
-
+
cut[j][i] = cut[i][j];
lj1[j][i] = lj1[i][j];
lj2[j][i] = lj2[i][j];
@@ -249,12 +249,12 @@ double PairLJShiftedForce::init_one(int i, int j)
lj4[j][i] = lj4[i][j];
foffset[j][i] = foffset[i][j];
offset[j][i] = offset[i][j];
-
+
return cut[i][j];
}
/* ----------------------------------------------------------------------
- proc 0 writes to restart file
+ proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairLJShiftedForce::write_restart(FILE *fp)
@@ -266,9 +266,9 @@ void PairLJShiftedForce::write_restart(FILE *fp)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
- fwrite(&epsilon[i][j],sizeof(double),1,fp);
- fwrite(&sigma[i][j],sizeof(double),1,fp);
- fwrite(&cut[i][j],sizeof(double),1,fp);
+ fwrite(&epsilon[i][j],sizeof(double),1,fp);
+ fwrite(&sigma[i][j],sizeof(double),1,fp);
+ fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
@@ -289,14 +289,14 @@ void PairLJShiftedForce::read_restart(FILE *fp)
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
- if (me == 0) {
- fread(&epsilon[i][j],sizeof(double),1,fp);
- fread(&sigma[i][j],sizeof(double),1,fp);
- fread(&cut[i][j],sizeof(double),1,fp);
- }
- MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
+ if (me == 0) {
+ fread(&epsilon[i][j],sizeof(double),1,fp);
+ fread(&sigma[i][j],sizeof(double),1,fp);
+ fread(&cut[i][j],sizeof(double),1,fp);
+ }
+ MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
@@ -332,16 +332,16 @@ void PairLJShiftedForce::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairLJShiftedForce::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
- double &fforce)
+ double factor_coul, double factor_lj,
+ double &fforce)
{
double r2inv,r6inv,forcelj,philj,r,t;
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
- r = sqrt(rsq);
+ r = sqrt(rsq);
t = r/cut[itype][jtype];
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]) -
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]) -
t*foffset[itype][jtype];
fforce = factor_lj*forcelj*r2inv;
diff --git a/src/USER-MISC/pair_lj_sf.h b/src/USER-MISC/pair_lj_sf.h
index 819e46cf729db2c78a6b0ff34063a5129711c0f2..6252d4134a6f8a155403ddd11497b2cf74a23c03 100644
--- a/src/USER-MISC/pair_lj_sf.h
+++ b/src/USER-MISC/pair_lj_sf.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-MISC/pair_meam_spline.cpp b/src/USER-MISC/pair_meam_spline.cpp
index 8e563fb1748b1ea113e6ea6b54d5c050d56fee40..46224bb85351c7cac181a511addaa16fb68f21f8 100644
--- a/src/USER-MISC/pair_meam_spline.cpp
+++ b/src/USER-MISC/pair_meam_spline.cpp
@@ -91,7 +91,7 @@ PairMEAMSpline::PairMEAMSpline(LAMMPS *lmp) : Pair(lmp)
nmax = 0;
maxNeighbors = 0;
twoBodyInfo = NULL;
-
+
comm_forward = 1;
comm_reverse = 0;
}
@@ -106,7 +106,7 @@ PairMEAMSpline::~PairMEAMSpline()
delete[] twoBodyInfo;
memory->destroy(Uprime_values);
-
+
if(allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
@@ -119,8 +119,8 @@ PairMEAMSpline::~PairMEAMSpline()
void PairMEAMSpline::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag, vflag);
- else evflag = vflag_fdotr =
- eflag_global = vflag_global = eflag_atom = vflag_atom = 0;
+ else evflag = vflag_fdotr =
+ eflag_global = vflag_global = eflag_atom = vflag_atom = 0;
double cutforcesq = cutoff*cutoff;
@@ -157,7 +157,7 @@ void PairMEAMSpline::compute(int eflag, int vflag)
delete[] twoBodyInfo;
twoBodyInfo = new MEAM2Body[maxNeighbors];
}
-
+
// Sum three-body contributions to charge density and
// compute embedding energies
@@ -171,43 +171,43 @@ void PairMEAMSpline::compute(int eflag, int vflag)
double rho_value = 0;
int numBonds = 0;
MEAM2Body* nextTwoBodyInfo = twoBodyInfo;
-
+
for(int jj = 0; jj < jnum; jj++) {
int j = jlist[jj];
j &= NEIGHMASK;
-
+
double jdelx = x[j][0] - xtmp;
double jdely = x[j][1] - ytmp;
double jdelz = x[j][2] - ztmp;
double rij_sq = jdelx*jdelx + jdely*jdely + jdelz*jdelz;
-
+
if(rij_sq < cutforcesq) {
- double rij = sqrt(rij_sq);
- double partial_sum = 0;
-
- nextTwoBodyInfo->tag = j;
- nextTwoBodyInfo->r = rij;
- nextTwoBodyInfo->f = f.eval(rij, nextTwoBodyInfo->fprime);
- nextTwoBodyInfo->del[0] = jdelx / rij;
- nextTwoBodyInfo->del[1] = jdely / rij;
- nextTwoBodyInfo->del[2] = jdelz / rij;
-
- for(int kk = 0; kk < numBonds; kk++) {
- const MEAM2Body& bondk = twoBodyInfo[kk];
- double cos_theta = (nextTwoBodyInfo->del[0]*bondk.del[0] +
- nextTwoBodyInfo->del[1]*bondk.del[1] +
- nextTwoBodyInfo->del[2]*bondk.del[2]);
- partial_sum += bondk.f * g.eval(cos_theta);
- }
-
- rho_value += nextTwoBodyInfo->f * partial_sum;
- rho_value += rho.eval(rij);
-
- numBonds++;
- nextTwoBodyInfo++;
+ double rij = sqrt(rij_sq);
+ double partial_sum = 0;
+
+ nextTwoBodyInfo->tag = j;
+ nextTwoBodyInfo->r = rij;
+ nextTwoBodyInfo->f = f.eval(rij, nextTwoBodyInfo->fprime);
+ nextTwoBodyInfo->del[0] = jdelx / rij;
+ nextTwoBodyInfo->del[1] = jdely / rij;
+ nextTwoBodyInfo->del[2] = jdelz / rij;
+
+ for(int kk = 0; kk < numBonds; kk++) {
+ const MEAM2Body& bondk = twoBodyInfo[kk];
+ double cos_theta = (nextTwoBodyInfo->del[0]*bondk.del[0] +
+ nextTwoBodyInfo->del[1]*bondk.del[1] +
+ nextTwoBodyInfo->del[2]*bondk.del[2]);
+ partial_sum += bondk.f * g.eval(cos_theta);
+ }
+
+ rho_value += nextTwoBodyInfo->f * partial_sum;
+ rho_value += rho.eval(rij);
+
+ numBonds++;
+ nextTwoBodyInfo++;
}
}
-
+
// Compute embedding energy and its derivative
double Uprime_i;
@@ -217,76 +217,76 @@ void PairMEAMSpline::compute(int eflag, int vflag)
if(eflag_global) eng_vdwl += embeddingEnergy;
if(eflag_atom) eatom[i] += embeddingEnergy;
}
-
+
double forces_i[3] = {0, 0, 0};
-
+
// Compute three-body contributions to force
for(int jj = 0; jj < numBonds; jj++) {
const MEAM2Body bondj = twoBodyInfo[jj];
double rij = bondj.r;
int j = bondj.tag;
-
+
double f_rij_prime = bondj.fprime;
double f_rij = bondj.f;
-
+
double forces_j[3] = {0, 0, 0};
-
+
MEAM2Body const* bondk = twoBodyInfo;
for(int kk = 0; kk < jj; kk++, ++bondk) {
- double rik = bondk->r;
-
- double cos_theta = (bondj.del[0]*bondk->del[0] +
- bondj.del[1]*bondk->del[1] +
- bondj.del[2]*bondk->del[2]);
- double g_prime;
- double g_value = g.eval(cos_theta, g_prime);
- double f_rik_prime = bondk->fprime;
- double f_rik = bondk->f;
-
- double fij = -Uprime_i * g_value * f_rik * f_rij_prime;
- double fik = -Uprime_i * g_value * f_rij * f_rik_prime;
-
- double prefactor = Uprime_i * f_rij * f_rik * g_prime;
- double prefactor_ij = prefactor / rij;
- double prefactor_ik = prefactor / rik;
- fij += prefactor_ij * cos_theta;
- fik += prefactor_ik * cos_theta;
-
- double fj[3], fk[3];
-
- fj[0] = bondj.del[0] * fij - bondk->del[0] * prefactor_ij;
- fj[1] = bondj.del[1] * fij - bondk->del[1] * prefactor_ij;
- fj[2] = bondj.del[2] * fij - bondk->del[2] * prefactor_ij;
- forces_j[0] += fj[0];
- forces_j[1] += fj[1];
- forces_j[2] += fj[2];
-
- fk[0] = bondk->del[0] * fik - bondj.del[0] * prefactor_ik;
- fk[1] = bondk->del[1] * fik - bondj.del[1] * prefactor_ik;
- fk[2] = bondk->del[2] * fik - bondj.del[2] * prefactor_ik;
- forces_i[0] -= fk[0];
- forces_i[1] -= fk[1];
- forces_i[2] -= fk[2];
-
- int k = bondk->tag;
- forces[k][0] += fk[0];
- forces[k][1] += fk[1];
- forces[k][2] += fk[2];
-
- if(evflag) {
- double delta_ij[3];
- double delta_ik[3];
- delta_ij[0] = bondj.del[0] * rij;
- delta_ij[1] = bondj.del[1] * rij;
- delta_ij[2] = bondj.del[2] * rij;
- delta_ik[0] = bondk->del[0] * rik;
- delta_ik[1] = bondk->del[1] * rik;
- delta_ik[2] = bondk->del[2] * rik;
- ev_tally3(i, j, k, 0.0, 0.0, fj, fk, delta_ij, delta_ik);
- }
+ double rik = bondk->r;
+
+ double cos_theta = (bondj.del[0]*bondk->del[0] +
+ bondj.del[1]*bondk->del[1] +
+ bondj.del[2]*bondk->del[2]);
+ double g_prime;
+ double g_value = g.eval(cos_theta, g_prime);
+ double f_rik_prime = bondk->fprime;
+ double f_rik = bondk->f;
+
+ double fij = -Uprime_i * g_value * f_rik * f_rij_prime;
+ double fik = -Uprime_i * g_value * f_rij * f_rik_prime;
+
+ double prefactor = Uprime_i * f_rij * f_rik * g_prime;
+ double prefactor_ij = prefactor / rij;
+ double prefactor_ik = prefactor / rik;
+ fij += prefactor_ij * cos_theta;
+ fik += prefactor_ik * cos_theta;
+
+ double fj[3], fk[3];
+
+ fj[0] = bondj.del[0] * fij - bondk->del[0] * prefactor_ij;
+ fj[1] = bondj.del[1] * fij - bondk->del[1] * prefactor_ij;
+ fj[2] = bondj.del[2] * fij - bondk->del[2] * prefactor_ij;
+ forces_j[0] += fj[0];
+ forces_j[1] += fj[1];
+ forces_j[2] += fj[2];
+
+ fk[0] = bondk->del[0] * fik - bondj.del[0] * prefactor_ik;
+ fk[1] = bondk->del[1] * fik - bondj.del[1] * prefactor_ik;
+ fk[2] = bondk->del[2] * fik - bondj.del[2] * prefactor_ik;
+ forces_i[0] -= fk[0];
+ forces_i[1] -= fk[1];
+ forces_i[2] -= fk[2];
+
+ int k = bondk->tag;
+ forces[k][0] += fk[0];
+ forces[k][1] += fk[1];
+ forces[k][2] += fk[2];
+
+ if(evflag) {
+ double delta_ij[3];
+ double delta_ik[3];
+ delta_ij[0] = bondj.del[0] * rij;
+ delta_ij[1] = bondj.del[1] * rij;
+ delta_ij[2] = bondj.del[2] * rij;
+ delta_ik[0] = bondk->del[0] * rik;
+ delta_ik[1] = bondk->del[1] * rik;
+ delta_ik[2] = bondk->del[2] * rik;
+ ev_tally3(i, j, k, 0.0, 0.0, fj, fk, delta_ij, delta_ik);
+ }
}
-
+
forces[i][0] -= forces_j[0];
forces[i][1] -= forces_j[1];
forces[i][2] -= forces_j[2];
@@ -294,21 +294,21 @@ void PairMEAMSpline::compute(int eflag, int vflag)
forces[j][1] += forces_j[1];
forces[j][2] += forces_j[2];
}
-
+
forces[i][0] += forces_i[0];
forces[i][1] += forces_i[1];
forces[i][2] += forces_i[2];
}
-
+
// Communicate U'(rho) values
comm->forward_comm_pair(this);
-
+
int inum_half = listhalf->inum;
int* ilist_half = listhalf->ilist;
int* numneigh_half = listhalf->numneigh;
int** firstneigh_half = listhalf->firstneigh;
-
+
// Compute two-body pair interactions
for(int ii = 0; ii < inum_half; ii++) {
@@ -318,44 +318,44 @@ void PairMEAMSpline::compute(int eflag, int vflag)
double ztmp = x[i][2];
int* jlist = firstneigh_half[i];
int jnum = numneigh_half[i];
-
+
for(int jj = 0; jj < jnum; jj++) {
int j = jlist[jj];
j &= NEIGHMASK;
-
+
double jdel[3];
jdel[0] = x[j][0] - xtmp;
jdel[1] = x[j][1] - ytmp;
jdel[2] = x[j][2] - ztmp;
double rij_sq = jdel[0]*jdel[0] + jdel[1]*jdel[1] + jdel[2]*jdel[2];
-
+
if(rij_sq < cutforcesq) {
- double rij = sqrt(rij_sq);
-
- double rho_prime;
- rho.eval(rij, rho_prime);
- double fpair = rho_prime * (Uprime_values[i] + Uprime_values[j]);
-
- double pair_pot_deriv;
- double pair_pot = phi.eval(rij, pair_pot_deriv);
- fpair += pair_pot_deriv;
-
- // Divide by r_ij to get forces from gradient
-
- fpair /= rij;
-
- forces[i][0] += jdel[0]*fpair;
- forces[i][1] += jdel[1]*fpair;
- forces[i][2] += jdel[2]*fpair;
- forces[j][0] -= jdel[0]*fpair;
- forces[j][1] -= jdel[1]*fpair;
- forces[j][2] -= jdel[2]*fpair;
- if (evflag) ev_tally(i, j, nlocal, newton_pair,
- pair_pot, 0.0, -fpair, jdel[0], jdel[1], jdel[2]);
+ double rij = sqrt(rij_sq);
+
+ double rho_prime;
+ rho.eval(rij, rho_prime);
+ double fpair = rho_prime * (Uprime_values[i] + Uprime_values[j]);
+
+ double pair_pot_deriv;
+ double pair_pot = phi.eval(rij, pair_pot_deriv);
+ fpair += pair_pot_deriv;
+
+ // Divide by r_ij to get forces from gradient
+
+ fpair /= rij;
+
+ forces[i][0] += jdel[0]*fpair;
+ forces[i][1] += jdel[1]*fpair;
+ forces[i][2] += jdel[2]*fpair;
+ forces[j][0] -= jdel[0]*fpair;
+ forces[j][1] -= jdel[1]*fpair;
+ forces[j][2] -= jdel[2]*fpair;
+ if (evflag) ev_tally(i, j, nlocal, newton_pair,
+ pair_pot, 0.0, -fpair, jdel[0], jdel[1], jdel[2]);
}
}
}
-
+
if(vflag_fdotr) virial_fdotr_compute();
}
@@ -365,7 +365,7 @@ void PairMEAMSpline::allocate()
{
allocated = 1;
int n = atom->ntypes;
-
+
memory->create(setflag,n+1,n+1,"pair:setflag");
memory->create(cutsq,n+1,n+1,"pair:cutsq");
@@ -373,7 +373,7 @@ void PairMEAMSpline::allocate()
}
/* ----------------------------------------------------------------------
- global settings
+ global settings
------------------------------------------------------------------------- */
void PairMEAMSpline::settings(int narg, char **arg)
@@ -432,10 +432,10 @@ void PairMEAMSpline::coeff(int narg, char **arg)
if (nelements > 1)
error->all(FLERR,
- "Pair meam/spline only supports single element potentials");
+ "Pair meam/spline only supports single element potentials");
// read potential file
-
+
read_file(arg[2]);
// clear setflag since coeff() called once with I,J = * *
@@ -451,8 +451,8 @@ void PairMEAMSpline::coeff(int narg, char **arg)
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
if (map[i] >= 0 && map[j] >= 0) {
- setflag[i][j] = 1;
- count++;
+ setflag[i][j] = 1;
+ count++;
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
@@ -466,57 +466,57 @@ void PairMEAMSpline::coeff(int narg, char **arg)
void PairMEAMSpline::read_file(const char* filename)
{
- if(comm->me == 0) {
- FILE *fp = fopen(filename, "r");
- if(fp == NULL) {
- char str[1024];
- sprintf(str,"Cannot open spline MEAM potential file %s", filename);
- error->one(FLERR,str);
- }
-
- // Skip first line of file.
- char line[MAXLINE];
- fgets(line, MAXLINE, fp);
-
- // Parse spline functions.
- phi.parse(fp, error);
- rho.parse(fp, error);
- U.parse(fp, error);
- f.parse(fp, error);
- g.parse(fp, error);
-
- fclose(fp);
- }
-
- // Transfer spline functions from master processor to all other processors.
- phi.communicate(world, comm->me);
- rho.communicate(world, comm->me);
- f.communicate(world, comm->me);
- U.communicate(world, comm->me);
- g.communicate(world, comm->me);
-
- // Calculate 'zero-point energy' of single atom in vacuum.
- zero_atom_energy = U.eval(0.0);
-
- // Determine maximum cutoff radius of all relevant spline functions.
- cutoff = 0.0;
- if(phi.cutoff() > cutoff) cutoff = phi.cutoff();
- if(rho.cutoff() > cutoff) cutoff = rho.cutoff();
- if(f.cutoff() > cutoff) cutoff = f.cutoff();
-
- // Set LAMMPS pair interaction flags.
- for(int i = 1; i <= atom->ntypes; i++) {
- for(int j = 1; j <= atom->ntypes; j++) {
- setflag[i][j] = 1;
- cutsq[i][j] = cutoff;
- }
- }
-
- //phi.writeGnuplot("phi.gp", "Phi(r)");
- //rho.writeGnuplot("rho.gp", "Rho(r)");
- //f.writeGnuplot("f.gp", "f(r)");
- //U.writeGnuplot("U.gp", "U(rho)");
- //g.writeGnuplot("g.gp", "g(x)");
+ if(comm->me == 0) {
+ FILE *fp = fopen(filename, "r");
+ if(fp == NULL) {
+ char str[1024];
+ sprintf(str,"Cannot open spline MEAM potential file %s", filename);
+ error->one(FLERR,str);
+ }
+
+ // Skip first line of file.
+ char line[MAXLINE];
+ fgets(line, MAXLINE, fp);
+
+ // Parse spline functions.
+ phi.parse(fp, error);
+ rho.parse(fp, error);
+ U.parse(fp, error);
+ f.parse(fp, error);
+ g.parse(fp, error);
+
+ fclose(fp);
+ }
+
+ // Transfer spline functions from master processor to all other processors.
+ phi.communicate(world, comm->me);
+ rho.communicate(world, comm->me);
+ f.communicate(world, comm->me);
+ U.communicate(world, comm->me);
+ g.communicate(world, comm->me);
+
+ // Calculate 'zero-point energy' of single atom in vacuum.
+ zero_atom_energy = U.eval(0.0);
+
+ // Determine maximum cutoff radius of all relevant spline functions.
+ cutoff = 0.0;
+ if(phi.cutoff() > cutoff) cutoff = phi.cutoff();
+ if(rho.cutoff() > cutoff) cutoff = rho.cutoff();
+ if(f.cutoff() > cutoff) cutoff = f.cutoff();
+
+ // Set LAMMPS pair interaction flags.
+ for(int i = 1; i <= atom->ntypes; i++) {
+ for(int j = 1; j <= atom->ntypes; j++) {
+ setflag[i][j] = 1;
+ cutsq[i][j] = cutoff;
+ }
+ }
+
+ //phi.writeGnuplot("phi.gp", "Phi(r)");
+ //rho.writeGnuplot("rho.gp", "Rho(r)");
+ //f.writeGnuplot("f.gp", "f(r)");
+ //U.writeGnuplot("U.gp", "U(rho)");
+ //g.writeGnuplot("g.gp", "g(x)");
}
/* ----------------------------------------------------------------------
@@ -524,19 +524,19 @@ void PairMEAMSpline::read_file(const char* filename)
------------------------------------------------------------------------- */
void PairMEAMSpline::init_style()
{
- if(force->newton_pair == 0)
- error->all(FLERR,"Pair style meam/spline requires newton pair on");
-
- // Need both full and half neighbor list.
- int irequest_full = neighbor->request(this);
- neighbor->requests[irequest_full]->id = 1;
- neighbor->requests[irequest_full]->half = 0;
- neighbor->requests[irequest_full]->full = 1;
- int irequest_half = neighbor->request(this);
- neighbor->requests[irequest_half]->id = 2;
- neighbor->requests[irequest_half]->half = 0;
- neighbor->requests[irequest_half]->half_from_full = 1;
- neighbor->requests[irequest_half]->otherlist = irequest_full;
+ if(force->newton_pair == 0)
+ error->all(FLERR,"Pair style meam/spline requires newton pair on");
+
+ // Need both full and half neighbor list.
+ int irequest_full = neighbor->request(this);
+ neighbor->requests[irequest_full]->id = 1;
+ neighbor->requests[irequest_full]->half = 0;
+ neighbor->requests[irequest_full]->full = 1;
+ int irequest_half = neighbor->request(this);
+ neighbor->requests[irequest_half]->id = 2;
+ neighbor->requests[irequest_half]->half = 0;
+ neighbor->requests[irequest_half]->half_from_full = 1;
+ neighbor->requests[irequest_half]->otherlist = irequest_full;
}
/* ----------------------------------------------------------------------
@@ -545,8 +545,8 @@ void PairMEAMSpline::init_style()
------------------------------------------------------------------------- */
void PairMEAMSpline::init_list(int id, NeighList *ptr)
{
- if(id == 1) listfull = ptr;
- else if(id == 2) listhalf = ptr;
+ if(id == 1) listfull = ptr;
+ else if(id == 2) listhalf = ptr;
}
/* ----------------------------------------------------------------------
@@ -554,32 +554,32 @@ void PairMEAMSpline::init_list(int id, NeighList *ptr)
------------------------------------------------------------------------- */
double PairMEAMSpline::init_one(int i, int j)
{
- return cutoff;
+ return cutoff;
}
/* ---------------------------------------------------------------------- */
int PairMEAMSpline::pack_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
{
- int* list_iter = list;
- int* list_iter_end = list + n;
- while(list_iter != list_iter_end)
- *buf++ = Uprime_values[*list_iter++];
- return 1;
+ int* list_iter = list;
+ int* list_iter_end = list + n;
+ while(list_iter != list_iter_end)
+ *buf++ = Uprime_values[*list_iter++];
+ return 1;
}
/* ---------------------------------------------------------------------- */
void PairMEAMSpline::unpack_comm(int n, int first, double *buf)
{
- memcpy(&Uprime_values[first], buf, n * sizeof(buf[0]));
+ memcpy(&Uprime_values[first], buf, n * sizeof(buf[0]));
}
/* ---------------------------------------------------------------------- */
int PairMEAMSpline::pack_reverse_comm(int n, int first, double *buf)
{
- return 0;
+ return 0;
}
/* ---------------------------------------------------------------------- */
@@ -593,116 +593,116 @@ void PairMEAMSpline::unpack_reverse_comm(int n, int *list, double *buf)
------------------------------------------------------------------------- */
double PairMEAMSpline::memory_usage()
{
- return nmax * sizeof(double); // The Uprime_values array.
+ return nmax * sizeof(double); // The Uprime_values array.
}
/// Parses the spline knots from a text file.
void PairMEAMSpline::SplineFunction::parse(FILE* fp, Error* error)
{
- char line[MAXLINE];
-
- // Parse number of spline knots.
- fgets(line, MAXLINE, fp);
- int n = atoi(line);
- if(n < 2)
- error->one(FLERR,"Invalid number of spline knots in MEAM potential file");
-
- // Parse first derivatives at beginning and end of spline.
- fgets(line, MAXLINE, fp);
- double d0 = atof(strtok(line, " \t\n\r\f"));
- double dN = atof(strtok(NULL, " \t\n\r\f"));
- init(n, d0, dN);
-
- // Skip line.
- fgets(line, MAXLINE, fp);
-
- // Parse knot coordinates.
- for(int i=0; i<n; i++) {
- fgets(line, MAXLINE, fp);
- double x, y, y2;
- if(sscanf(line, "%lg %lg %lg", &x, &y, &y2) != 3) {
- error->one(FLERR,"Invalid knot line in MEAM potential file");
- }
- setKnot(i, x, y);
- }
-
- prepareSpline(error);
+ char line[MAXLINE];
+
+ // Parse number of spline knots.
+ fgets(line, MAXLINE, fp);
+ int n = atoi(line);
+ if(n < 2)
+ error->one(FLERR,"Invalid number of spline knots in MEAM potential file");
+
+ // Parse first derivatives at beginning and end of spline.
+ fgets(line, MAXLINE, fp);
+ double d0 = atof(strtok(line, " \t\n\r\f"));
+ double dN = atof(strtok(NULL, " \t\n\r\f"));
+ init(n, d0, dN);
+
+ // Skip line.
+ fgets(line, MAXLINE, fp);
+
+ // Parse knot coordinates.
+ for(int i=0; i<n; i++) {
+ fgets(line, MAXLINE, fp);
+ double x, y, y2;
+ if(sscanf(line, "%lg %lg %lg", &x, &y, &y2) != 3) {
+ error->one(FLERR,"Invalid knot line in MEAM potential file");
+ }
+ setKnot(i, x, y);
+ }
+
+ prepareSpline(error);
}
/// Calculates the second derivatives at the knots of the cubic spline.
void PairMEAMSpline::SplineFunction::prepareSpline(Error* error)
{
- xmin = X[0];
- xmax = X[N-1];
-
- isGridSpline = true;
- h = (xmax-xmin)/(N-1);
- hsq = h*h;
-
- double* u = new double[N];
- Y2[0] = -0.5;
- u[0] = (3.0/(X[1]-X[0])) * ((Y[1]-Y[0])/(X[1]-X[0]) - deriv0);
- for(int i = 1; i <= N-2; i++) {
- double sig = (X[i]-X[i-1]) / (X[i+1]-X[i-1]);
- double p = sig * Y2[i-1] + 2.0;
- Y2[i] = (sig - 1.0) / p;
- u[i] = (Y[i+1]-Y[i]) / (X[i+1]-X[i]) - (Y[i]-Y[i-1])/(X[i]-X[i-1]);
- u[i] = (6.0 * u[i]/(X[i+1]-X[i-1]) - sig*u[i-1])/p;
-
- if(fabs(h*i+xmin - X[i]) > 1e-8)
- isGridSpline = false;
- }
-
- double qn = 0.5;
- double un = (3.0/(X[N-1]-X[N-2])) * (derivN - (Y[N-1]-Y[N-2])/(X[N-1]-X[N-2]));
- Y2[N-1] = (un - qn*u[N-2]) / (qn * Y2[N-2] + 1.0);
- for(int k = N-2; k >= 0; k--) {
- Y2[k] = Y2[k] * Y2[k+1] + u[k];
- }
-
- delete[] u;
+ xmin = X[0];
+ xmax = X[N-1];
+
+ isGridSpline = true;
+ h = (xmax-xmin)/(N-1);
+ hsq = h*h;
+
+ double* u = new double[N];
+ Y2[0] = -0.5;
+ u[0] = (3.0/(X[1]-X[0])) * ((Y[1]-Y[0])/(X[1]-X[0]) - deriv0);
+ for(int i = 1; i <= N-2; i++) {
+ double sig = (X[i]-X[i-1]) / (X[i+1]-X[i-1]);
+ double p = sig * Y2[i-1] + 2.0;
+ Y2[i] = (sig - 1.0) / p;
+ u[i] = (Y[i+1]-Y[i]) / (X[i+1]-X[i]) - (Y[i]-Y[i-1])/(X[i]-X[i-1]);
+ u[i] = (6.0 * u[i]/(X[i+1]-X[i-1]) - sig*u[i-1])/p;
+
+ if(fabs(h*i+xmin - X[i]) > 1e-8)
+ isGridSpline = false;
+ }
+
+ double qn = 0.5;
+ double un = (3.0/(X[N-1]-X[N-2])) * (derivN - (Y[N-1]-Y[N-2])/(X[N-1]-X[N-2]));
+ Y2[N-1] = (un - qn*u[N-2]) / (qn * Y2[N-2] + 1.0);
+ for(int k = N-2; k >= 0; k--) {
+ Y2[k] = Y2[k] * Y2[k+1] + u[k];
+ }
+
+ delete[] u;
#if !SPLINE_MEAM_SUPPORT_NON_GRID_SPLINES
- if(!isGridSpline)
- error->one(FLERR,"Support for MEAM potentials with non-uniform cubic splines has not been enabled in the MEAM potential code. Set SPLINE_MEAM_SUPPORT_NON_GRID_SPLINES in pair_spline_meam.h to 1 to enable it");
+ if(!isGridSpline)
+ error->one(FLERR,"Support for MEAM potentials with non-uniform cubic splines has not been enabled in the MEAM potential code. Set SPLINE_MEAM_SUPPORT_NON_GRID_SPLINES in pair_spline_meam.h to 1 to enable it");
#endif
- // Shift the spline to X=0 to speed up interpolation.
- for(int i = 0; i < N; i++) {
- Xs[i] = X[i] - xmin;
+ // Shift the spline to X=0 to speed up interpolation.
+ for(int i = 0; i < N; i++) {
+ Xs[i] = X[i] - xmin;
#if !SPLINE_MEAM_SUPPORT_NON_GRID_SPLINES
- if(i < N-1) Ydelta[i] = (Y[i+1]-Y[i])/h;
- Y2[i] /= h*6.0;
+ if(i < N-1) Ydelta[i] = (Y[i+1]-Y[i])/h;
+ Y2[i] /= h*6.0;
#endif
- }
- xmax_shifted = xmax - xmin;
+ }
+ xmax_shifted = xmax - xmin;
}
/// Broadcasts the spline function parameters to all processors.
void PairMEAMSpline::SplineFunction::communicate(MPI_Comm& world, int me)
{
- MPI_Bcast(&N, 1, MPI_INT, 0, world);
- MPI_Bcast(&deriv0, 1, MPI_DOUBLE, 0, world);
- MPI_Bcast(&derivN, 1, MPI_DOUBLE, 0, world);
- MPI_Bcast(&xmin, 1, MPI_DOUBLE, 0, world);
- MPI_Bcast(&xmax, 1, MPI_DOUBLE, 0, world);
- MPI_Bcast(&xmax_shifted, 1, MPI_DOUBLE, 0, world);
- MPI_Bcast(&isGridSpline, 1, MPI_INT, 0, world);
- MPI_Bcast(&h, 1, MPI_DOUBLE, 0, world);
- MPI_Bcast(&hsq, 1, MPI_DOUBLE, 0, world);
- if(me != 0) {
- X = new double[N];
- Xs = new double[N];
- Y = new double[N];
- Y2 = new double[N];
- Ydelta = new double[N];
- }
- MPI_Bcast(X, N, MPI_DOUBLE, 0, world);
- MPI_Bcast(Xs, N, MPI_DOUBLE, 0, world);
- MPI_Bcast(Y, N, MPI_DOUBLE, 0, world);
- MPI_Bcast(Y2, N, MPI_DOUBLE, 0, world);
- MPI_Bcast(Ydelta, N, MPI_DOUBLE, 0, world);
+ MPI_Bcast(&N, 1, MPI_INT, 0, world);
+ MPI_Bcast(&deriv0, 1, MPI_DOUBLE, 0, world);
+ MPI_Bcast(&derivN, 1, MPI_DOUBLE, 0, world);
+ MPI_Bcast(&xmin, 1, MPI_DOUBLE, 0, world);
+ MPI_Bcast(&xmax, 1, MPI_DOUBLE, 0, world);
+ MPI_Bcast(&xmax_shifted, 1, MPI_DOUBLE, 0, world);
+ MPI_Bcast(&isGridSpline, 1, MPI_INT, 0, world);
+ MPI_Bcast(&h, 1, MPI_DOUBLE, 0, world);
+ MPI_Bcast(&hsq, 1, MPI_DOUBLE, 0, world);
+ if(me != 0) {
+ X = new double[N];
+ Xs = new double[N];
+ Y = new double[N];
+ Y2 = new double[N];
+ Ydelta = new double[N];
+ }
+ MPI_Bcast(X, N, MPI_DOUBLE, 0, world);
+ MPI_Bcast(Xs, N, MPI_DOUBLE, 0, world);
+ MPI_Bcast(Y, N, MPI_DOUBLE, 0, world);
+ MPI_Bcast(Y2, N, MPI_DOUBLE, 0, world);
+ MPI_Bcast(Ydelta, N, MPI_DOUBLE, 0, world);
}
/// Writes a Gnuplot script that plots the spline function.
@@ -710,23 +710,22 @@ void PairMEAMSpline::SplineFunction::communicate(MPI_Comm& world, int me)
/// This function is for debugging only!
void PairMEAMSpline::SplineFunction::writeGnuplot(const char* filename, const char* title) const
{
- FILE* fp = fopen(filename, "w");
- fprintf(fp, "#!/usr/bin/env gnuplot\n");
- if(title) fprintf(fp, "set title \"%s\"\n", title);
- double tmin = X[0] - (X[N-1] - X[0]) * 0.05;
- double tmax = X[N-1] + (X[N-1] - X[0]) * 0.05;
- double delta = (tmax - tmin) / (N*200);
- fprintf(fp, "set xrange [%f:%f]\n", tmin, tmax);
- fprintf(fp, "plot '-' with lines notitle, '-' with points notitle pt 3 lc 3\n");
- for(double x = tmin; x <= tmax+1e-8; x += delta) {
- double y = eval(x);
- fprintf(fp, "%f %f\n", x, y);
- }
- fprintf(fp, "e\n");
- for(int i = 0; i < N; i++) {
- fprintf(fp, "%f %f\n", X[i], Y[i]);
- }
- fprintf(fp, "e\n");
- fclose(fp);
+ FILE* fp = fopen(filename, "w");
+ fprintf(fp, "#!/usr/bin/env gnuplot\n");
+ if(title) fprintf(fp, "set title \"%s\"\n", title);
+ double tmin = X[0] - (X[N-1] - X[0]) * 0.05;
+ double tmax = X[N-1] + (X[N-1] - X[0]) * 0.05;
+ double delta = (tmax - tmin) / (N*200);
+ fprintf(fp, "set xrange [%f:%f]\n", tmin, tmax);
+ fprintf(fp, "plot '-' with lines notitle, '-' with points notitle pt 3 lc 3\n");
+ for(double x = tmin; x <= tmax+1e-8; x += delta) {
+ double y = eval(x);
+ fprintf(fp, "%f %f\n", x, y);
+ }
+ fprintf(fp, "e\n");
+ for(int i = 0; i < N; i++) {
+ fprintf(fp, "%f %f\n", X[i], Y[i]);
+ }
+ fprintf(fp, "e\n");
+ fclose(fp);
}
-
diff --git a/src/USER-MISC/pair_meam_spline.h b/src/USER-MISC/pair_meam_spline.h
index 733a05cf936cae1b997b3785d3bcbc077712225d..fdf8972e63265c78515c525c16f5ef1622ee8c40 100644
--- a/src/USER-MISC/pair_meam_spline.h
+++ b/src/USER-MISC/pair_meam_spline.h
@@ -76,199 +76,199 @@ namespace LAMMPS_NS {
class PairMEAMSpline : public Pair
{
public:
- PairMEAMSpline(class LAMMPS *);
- virtual ~PairMEAMSpline();
- virtual void compute(int, int);
- void settings(int, char **);
- void coeff(int, char **);
- void init_style();
- void init_list(int, class NeighList *);
- double init_one(int, int);
-
- int pack_comm(int, int *, double *, int, int *);
- void unpack_comm(int, int, double *);
- int pack_reverse_comm(int, int, double *);
- void unpack_reverse_comm(int, int *, double *);
- double memory_usage();
+ PairMEAMSpline(class LAMMPS *);
+ virtual ~PairMEAMSpline();
+ virtual void compute(int, int);
+ void settings(int, char **);
+ void coeff(int, char **);
+ void init_style();
+ void init_list(int, class NeighList *);
+ double init_one(int, int);
+
+ int pack_comm(int, int *, double *, int, int *);
+ void unpack_comm(int, int, double *);
+ int pack_reverse_comm(int, int, double *);
+ void unpack_reverse_comm(int, int *, double *);
+ double memory_usage();
protected:
char **elements; // names of unique elements
int *map; // mapping from atom types to elements
int nelements; // # of unique elements
- class SplineFunction {
- public:
-
- /// Default constructor.
- SplineFunction() : X(NULL), Xs(NULL), Y(NULL), Y2(NULL), Ydelta(NULL), N(0) {}
-
- /// Destructor.
- ~SplineFunction() {
- delete[] X;
- delete[] Xs;
- delete[] Y;
- delete[] Y2;
- delete[] Ydelta;
- }
-
- /// Initialization of spline function.
- void init(int _N, double _deriv0, double _derivN) {
- N = _N;
- deriv0 = _deriv0;
- derivN = _derivN;
- delete[] X;
- delete[] Xs;
- delete[] Y;
- delete[] Y2;
- delete[] Ydelta;
- X = new double[N];
- Xs = new double[N];
- Y = new double[N];
- Y2 = new double[N];
- Ydelta = new double[N];
- }
-
- /// Adds a knot to the spline.
- void setKnot(int n, double x, double y) { X[n] = x; Y[n] = y; }
-
- /// Returns the number of knots.
- int numKnots() const { return N; }
-
- /// Parses the spline knots from a text file.
- void parse(FILE* fp, Error* error);
-
- /// Calculates the second derivatives of the cubic spline.
- void prepareSpline(Error* error);
-
- /// Evaluates the spline function at position x.
- inline double eval(double x) const
- {
- x -= xmin;
- if(x <= 0.0) { // Left extrapolation.
- return Y[0] + deriv0 * x;
- }
- else if(x >= xmax_shifted) { // Right extrapolation.
- return Y[N-1] + derivN * (x - xmax_shifted);
- }
- else {
+ class SplineFunction {
+ public:
+
+ /// Default constructor.
+ SplineFunction() : X(NULL), Xs(NULL), Y(NULL), Y2(NULL), Ydelta(NULL), N(0) {}
+
+ /// Destructor.
+ ~SplineFunction() {
+ delete[] X;
+ delete[] Xs;
+ delete[] Y;
+ delete[] Y2;
+ delete[] Ydelta;
+ }
+
+ /// Initialization of spline function.
+ void init(int _N, double _deriv0, double _derivN) {
+ N = _N;
+ deriv0 = _deriv0;
+ derivN = _derivN;
+ delete[] X;
+ delete[] Xs;
+ delete[] Y;
+ delete[] Y2;
+ delete[] Ydelta;
+ X = new double[N];
+ Xs = new double[N];
+ Y = new double[N];
+ Y2 = new double[N];
+ Ydelta = new double[N];
+ }
+
+ /// Adds a knot to the spline.
+ void setKnot(int n, double x, double y) { X[n] = x; Y[n] = y; }
+
+ /// Returns the number of knots.
+ int numKnots() const { return N; }
+
+ /// Parses the spline knots from a text file.
+ void parse(FILE* fp, Error* error);
+
+ /// Calculates the second derivatives of the cubic spline.
+ void prepareSpline(Error* error);
+
+ /// Evaluates the spline function at position x.
+ inline double eval(double x) const
+ {
+ x -= xmin;
+ if(x <= 0.0) { // Left extrapolation.
+ return Y[0] + deriv0 * x;
+ }
+ else if(x >= xmax_shifted) { // Right extrapolation.
+ return Y[N-1] + derivN * (x - xmax_shifted);
+ }
+ else {
#if SPLINE_MEAM_SUPPORT_NON_GRID_SPLINES
- // Do interval search.
- int klo = 0;
- int khi = N-1;
- while(khi - klo > 1) {
- int k = (khi + klo) / 2;
- if(Xs[k] > x) khi = k;
- else klo = k;
- }
- double h = Xs[khi] - Xs[klo];
- // Do spline interpolation.
- double a = (Xs[khi] - x)/h;
- double b = 1.0 - a; // = (x - X[klo])/h
- return a * Y[klo] + b * Y[khi] + ((a*a*a - a) * Y2[klo] + (b*b*b - b) * Y2[khi])*(h*h)/6.0;
+ // Do interval search.
+ int klo = 0;
+ int khi = N-1;
+ while(khi - klo > 1) {
+ int k = (khi + klo) / 2;
+ if(Xs[k] > x) khi = k;
+ else klo = k;
+ }
+ double h = Xs[khi] - Xs[klo];
+ // Do spline interpolation.
+ double a = (Xs[khi] - x)/h;
+ double b = 1.0 - a; // = (x - X[klo])/h
+ return a * Y[klo] + b * Y[khi] + ((a*a*a - a) * Y2[klo] + (b*b*b - b) * Y2[khi])*(h*h)/6.0;
#else
- // For a spline with grid points, we can directly calculate the interval X is in.
- int klo = (int)(x / h);
- int khi = klo + 1;
- double a = Xs[khi] - x;
- double b = h - a;
- return Y[khi] - a * Ydelta[klo] + ((a*a - hsq) * a * Y2[klo] + (b*b - hsq) * b * Y2[khi]);
+ // For a spline with grid points, we can directly calculate the interval X is in.
+ int klo = (int)(x / h);
+ int khi = klo + 1;
+ double a = Xs[khi] - x;
+ double b = h - a;
+ return Y[khi] - a * Ydelta[klo] + ((a*a - hsq) * a * Y2[klo] + (b*b - hsq) * b * Y2[khi]);
#endif
- }
- }
-
- /// Evaluates the spline function and its first derivative at position x.
- inline double eval(double x, double& deriv) const
- {
- x -= xmin;
- if(x <= 0.0) { // Left extrapolation.
- deriv = deriv0;
- return Y[0] + deriv0 * x;
- }
- else if(x >= xmax_shifted) { // Right extrapolation.
- deriv = derivN;
- return Y[N-1] + derivN * (x - xmax_shifted);
- }
- else {
+ }
+ }
+
+ /// Evaluates the spline function and its first derivative at position x.
+ inline double eval(double x, double& deriv) const
+ {
+ x -= xmin;
+ if(x <= 0.0) { // Left extrapolation.
+ deriv = deriv0;
+ return Y[0] + deriv0 * x;
+ }
+ else if(x >= xmax_shifted) { // Right extrapolation.
+ deriv = derivN;
+ return Y[N-1] + derivN * (x - xmax_shifted);
+ }
+ else {
#if SPLINE_MEAM_SUPPORT_NON_GRID_SPLINES
- // Do interval search.
- int klo = 0;
- int khi = N-1;
- while(khi - klo > 1) {
- int k = (khi + klo) / 2;
- if(Xs[k] > x) khi = k;
- else klo = k;
- }
- double h = Xs[khi] - Xs[klo];
- // Do spline interpolation.
- double a = (Xs[khi] - x)/h;
- double b = 1.0 - a; // = (x - X[klo])/h
- deriv = (Y[khi] - Y[klo]) / h + ((3.0*b*b - 1.0) * Y2[khi] - (3.0*a*a - 1.0) * Y2[klo]) * h / 6.0;
- return a * Y[klo] + b * Y[khi] + ((a*a*a - a) * Y2[klo] + (b*b*b - b) * Y2[khi]) * (h*h) / 6.0;
+ // Do interval search.
+ int klo = 0;
+ int khi = N-1;
+ while(khi - klo > 1) {
+ int k = (khi + klo) / 2;
+ if(Xs[k] > x) khi = k;
+ else klo = k;
+ }
+ double h = Xs[khi] - Xs[klo];
+ // Do spline interpolation.
+ double a = (Xs[khi] - x)/h;
+ double b = 1.0 - a; // = (x - X[klo])/h
+ deriv = (Y[khi] - Y[klo]) / h + ((3.0*b*b - 1.0) * Y2[khi] - (3.0*a*a - 1.0) * Y2[klo]) * h / 6.0;
+ return a * Y[klo] + b * Y[khi] + ((a*a*a - a) * Y2[klo] + (b*b*b - b) * Y2[khi]) * (h*h) / 6.0;
#else
- // For a spline with grid points, we can directly calculate the interval X is in.
- int klo = (int)(x / h);
- int khi = klo + 1;
- double a = Xs[khi] - x;
- double b = h - a;
- deriv = Ydelta[klo] + ((3.0*b*b - hsq) * Y2[khi] - (3.0*a*a - hsq) * Y2[klo]);
- return Y[khi] - a * Ydelta[klo] + ((a*a - hsq) * a * Y2[klo] + (b*b - hsq) * b * Y2[khi]);
+ // For a spline with grid points, we can directly calculate the interval X is in.
+ int klo = (int)(x / h);
+ int khi = klo + 1;
+ double a = Xs[khi] - x;
+ double b = h - a;
+ deriv = Ydelta[klo] + ((3.0*b*b - hsq) * Y2[khi] - (3.0*a*a - hsq) * Y2[klo]);
+ return Y[khi] - a * Ydelta[klo] + ((a*a - hsq) * a * Y2[klo] + (b*b - hsq) * b * Y2[khi]);
#endif
- }
- }
-
- /// Returns the number of bytes used by this function object.
- double memory_usage() const { return sizeof(*this) + sizeof(X[0]) * N * 3; }
-
- /// Returns the cutoff radius of this function.
- double cutoff() const { return X[N-1]; }
-
- /// Writes a Gnuplot script that plots the spline function.
- void writeGnuplot(const char* filename, const char* title = NULL) const;
-
- /// Broadcasts the spline function parameters to all processors.
- void communicate(MPI_Comm& world, int me);
-
- private:
- double* X; // Positions of spline knots
- double* Xs; // Shifted positions of spline knots
- double* Y; // Function values at spline knots
- double* Y2; // Second derivatives at spline knots
- double* Ydelta; // If this is a grid spline, Ydelta[i] = (Y[i+1]-Y[i])/h
- int N; // Number of spline knots
- double deriv0; // First derivative at knot 0
- double derivN; // First derivative at knot (N-1)
- double xmin; // The beginning of the interval on which the spline function is defined.
- double xmax; // The end of the interval on which the spline function is defined.
- int isGridSpline; // Indicates that all spline knots are on a regular grid.
- double h; // The distance between knots if this is a grid spline with equidistant knots.
- double hsq; // The squared distance between knots if this is a grid spline with equidistant knots.
- double xmax_shifted; // The end of the spline interval after it has been shifted to begin at X=0.
- };
-
- /// Helper data structure for potential routine.
- struct MEAM2Body {
- int tag;
- double r;
- double f, fprime;
- double del[3];
- };
-
- SplineFunction phi; // Phi(r_ij)
- SplineFunction rho; // Rho(r_ij)
- SplineFunction f; // f(r_ij)
- SplineFunction U; // U(rho)
- SplineFunction g; // g(cos_theta)
- double zero_atom_energy; // Shift embedding energy by this value to make it zero for a single atom in vacuum.
-
- double cutoff; // The cutoff radius
-
- double* Uprime_values; // Used for temporary storage of U'(rho) values
- int nmax; // Size of temporary array.
- int maxNeighbors; // The last maximum number of neighbors a single atoms has.
- MEAM2Body* twoBodyInfo; // Temporary array.
-
- void read_file(const char* filename);
- void allocate();
+ }
+ }
+
+ /// Returns the number of bytes used by this function object.
+ double memory_usage() const { return sizeof(*this) + sizeof(X[0]) * N * 3; }
+
+ /// Returns the cutoff radius of this function.
+ double cutoff() const { return X[N-1]; }
+
+ /// Writes a Gnuplot script that plots the spline function.
+ void writeGnuplot(const char* filename, const char* title = NULL) const;
+
+ /// Broadcasts the spline function parameters to all processors.
+ void communicate(MPI_Comm& world, int me);
+
+ private:
+ double* X; // Positions of spline knots
+ double* Xs; // Shifted positions of spline knots
+ double* Y; // Function values at spline knots
+ double* Y2; // Second derivatives at spline knots
+ double* Ydelta; // If this is a grid spline, Ydelta[i] = (Y[i+1]-Y[i])/h
+ int N; // Number of spline knots
+ double deriv0; // First derivative at knot 0
+ double derivN; // First derivative at knot (N-1)
+ double xmin; // The beginning of the interval on which the spline function is defined.
+ double xmax; // The end of the interval on which the spline function is defined.
+ int isGridSpline; // Indicates that all spline knots are on a regular grid.
+ double h; // The distance between knots if this is a grid spline with equidistant knots.
+ double hsq; // The squared distance between knots if this is a grid spline with equidistant knots.
+ double xmax_shifted; // The end of the spline interval after it has been shifted to begin at X=0.
+ };
+
+ /// Helper data structure for potential routine.
+ struct MEAM2Body {
+ int tag;
+ double r;
+ double f, fprime;
+ double del[3];
+ };
+
+ SplineFunction phi; // Phi(r_ij)
+ SplineFunction rho; // Rho(r_ij)
+ SplineFunction f; // f(r_ij)
+ SplineFunction U; // U(rho)
+ SplineFunction g; // g(cos_theta)
+ double zero_atom_energy; // Shift embedding energy by this value to make it zero for a single atom in vacuum.
+
+ double cutoff; // The cutoff radius
+
+ double* Uprime_values; // Used for temporary storage of U'(rho) values
+ int nmax; // Size of temporary array.
+ int maxNeighbors; // The last maximum number of neighbors a single atoms has.
+ MEAM2Body* twoBodyInfo; // Temporary array.
+
+ void read_file(const char* filename);
+ void allocate();
};
}
diff --git a/src/USER-MISC/pair_tersoff_table.cpp b/src/USER-MISC/pair_tersoff_table.cpp
index 74997af935d462b9a6a9389347d4017ea4cdd02a..ce25a86393b9ee89868bdf94e175f81a884c0068 100644
--- a/src/USER-MISC/pair_tersoff_table.cpp
+++ b/src/USER-MISC/pair_tersoff_table.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -80,7 +80,7 @@ PairTersoffTable::~PairTersoffTable()
memory->destroy(setflag);
memory->destroy(cutsq);
delete [] map;
-
+
deallocateGrids();
deallocatePreLoops();
}
@@ -103,7 +103,7 @@ void PairTersoffTable::compute(int eflag, int vflag)
double invR_ij, invR_ik, cosTeta;
double repulsivePotential, attractivePotential;
double exponentRepulsivePotential, exponentAttractivePotential,interpolTMP,interpolDeltaX,interpolY1;
- double interpolY2, cutoffFunctionIJ, attractiveExponential, repulsiveExponential, cutoffFunctionDerivedIJ,zeta;
+ double interpolY2, cutoffFunctionIJ, attractiveExponential, repulsiveExponential, cutoffFunctionDerivedIJ,zeta;
double gtetaFunctionIJK,gtetaFunctionDerivedIJK,cutoffFunctionIK;
double cutoffFunctionDerivedIK,factor_force3_ij,factor_1_force3_ik;
double factor_2_force3_ik,betaZetaPowerIJK,betaZetaPowerDerivedIJK,factor_force_tot;
@@ -142,8 +142,8 @@ void PairTersoffTable::compute(int eflag, int vflag)
if (jnum > leadingDimensionInteractionList) {
char errmsg[256];
sprintf(errmsg,"Too many neighbors for interaction list: %d vs %d.\n"
- "Check your system or increase 'leadingDimensionInteractionList'",
- jnum, leadingDimensionInteractionList);
+ "Check your system or increase 'leadingDimensionInteractionList'",
+ jnum, leadingDimensionInteractionList);
error->one(FLERR,errmsg);
}
@@ -168,11 +168,11 @@ void PairTersoffTable::compute(int eflag, int vflag)
r_ij = sqrt(r_ij);
invR_ij = 1.0 / r_ij;
-
+
directorCos_ij_x = invR_ij * dr_ij[0];
directorCos_ij_y = invR_ij * dr_ij[1];
directorCos_ij_z = invR_ij * dr_ij[2];
-
+
// preCutoffFunction
interpolDeltaX = r_ij - GRIDSTART;
interpolTMP = (interpolDeltaX * GRIDDENSITY_FCUTOFF);
@@ -187,47 +187,47 @@ void PairTersoffTable::compute(int eflag, int vflag)
for (int neighbor_k = neighbor_j + 1; neighbor_k < jnum; neighbor_k++) {
- double dr_ik[3], r_ik;
-
- k = jlist[neighbor_k];
- k &= NEIGHMASK;
- ktype = map[type[k]];
- ikparam = elem2param[itype][ktype][ktype];
- ijkparam = elem2param[itype][jtype][ktype];
-
- dr_ik[0] = xtmp -x[k][0];
- dr_ik[1] = ytmp -x[k][1];
- dr_ik[2] = ztmp -x[k][2];
- r_ik = dr_ik[0]*dr_ik[0] + dr_ik[1]*dr_ik[1] + dr_ik[2]*dr_ik[2];
-
- if (r_ik > params[ikparam].cutsq) continue;
-
- r_ik = sqrt(r_ik);
-
- invR_ik = 1.0 / r_ik;
-
- directorCos_ik_x = invR_ik * dr_ik[0];
- directorCos_ik_y = invR_ik * dr_ik[1];
- directorCos_ik_z = invR_ik * dr_ik[2];
-
- cosTeta = directorCos_ij_x * directorCos_ik_x + directorCos_ij_y * directorCos_ik_y + directorCos_ij_z * directorCos_ik_z;
-
- // preGtetaFunction
- interpolDeltaX=cosTeta+1.0;
- interpolTMP = (interpolDeltaX * GRIDDENSITY_GTETA);
- interpolIDX = (int) interpolTMP;
- interpolY1 = gtetaFunction[itype][interpolIDX];
- interpolY2 = gtetaFunction[itype][interpolIDX+1];
- gtetaFunction_temp = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
- // preGtetaFunctionDerived
- interpolY1 = gtetaFunctionDerived[itype][interpolIDX];
- interpolY2 = gtetaFunctionDerived[itype][interpolIDX+1];
- gtetaFunctionDerived_temp = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
-
- preGtetaFunction[neighbor_j][neighbor_k]=params[ijkparam].gamma*gtetaFunction_temp;
- preGtetaFunctionDerived[neighbor_j][neighbor_k]=params[ijkparam].gamma*gtetaFunctionDerived_temp;
- preGtetaFunction[neighbor_k][neighbor_j]=params[ijkparam].gamma*gtetaFunction_temp;
- preGtetaFunctionDerived[neighbor_k][neighbor_j]=params[ijkparam].gamma*gtetaFunctionDerived_temp;
+ double dr_ik[3], r_ik;
+
+ k = jlist[neighbor_k];
+ k &= NEIGHMASK;
+ ktype = map[type[k]];
+ ikparam = elem2param[itype][ktype][ktype];
+ ijkparam = elem2param[itype][jtype][ktype];
+
+ dr_ik[0] = xtmp -x[k][0];
+ dr_ik[1] = ytmp -x[k][1];
+ dr_ik[2] = ztmp -x[k][2];
+ r_ik = dr_ik[0]*dr_ik[0] + dr_ik[1]*dr_ik[1] + dr_ik[2]*dr_ik[2];
+
+ if (r_ik > params[ikparam].cutsq) continue;
+
+ r_ik = sqrt(r_ik);
+
+ invR_ik = 1.0 / r_ik;
+
+ directorCos_ik_x = invR_ik * dr_ik[0];
+ directorCos_ik_y = invR_ik * dr_ik[1];
+ directorCos_ik_z = invR_ik * dr_ik[2];
+
+ cosTeta = directorCos_ij_x * directorCos_ik_x + directorCos_ij_y * directorCos_ik_y + directorCos_ij_z * directorCos_ik_z;
+
+ // preGtetaFunction
+ interpolDeltaX=cosTeta+1.0;
+ interpolTMP = (interpolDeltaX * GRIDDENSITY_GTETA);
+ interpolIDX = (int) interpolTMP;
+ interpolY1 = gtetaFunction[itype][interpolIDX];
+ interpolY2 = gtetaFunction[itype][interpolIDX+1];
+ gtetaFunction_temp = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
+ // preGtetaFunctionDerived
+ interpolY1 = gtetaFunctionDerived[itype][interpolIDX];
+ interpolY2 = gtetaFunctionDerived[itype][interpolIDX+1];
+ gtetaFunctionDerived_temp = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
+
+ preGtetaFunction[neighbor_j][neighbor_k]=params[ijkparam].gamma*gtetaFunction_temp;
+ preGtetaFunctionDerived[neighbor_j][neighbor_k]=params[ijkparam].gamma*gtetaFunctionDerived_temp;
+ preGtetaFunction[neighbor_k][neighbor_j]=params[ijkparam].gamma*gtetaFunction_temp;
+ preGtetaFunctionDerived[neighbor_k][neighbor_j]=params[ijkparam].gamma*gtetaFunctionDerived_temp;
} // loop on K
@@ -254,7 +254,7 @@ void PairTersoffTable::compute(int eflag, int vflag)
r_ij = sqrt(r_ij);
invR_ij = 1.0 / r_ij;
-
+
directorCos_ij_x = invR_ij * dr_ij[0];
directorCos_ij_y = invR_ij * dr_ij[1];
directorCos_ij_z = invR_ij * dr_ij[2];
@@ -284,72 +284,72 @@ void PairTersoffTable::compute(int eflag, int vflag)
cutoffFunctionDerivedIJ = preCutoffFunctionDerived[neighbor_j];
zeta = 0.0;
-
+
// first loop over neighbours of atom i except j - part 1/2
for (int neighbor_k = 0; neighbor_k < neighbor_j; neighbor_k++) {
- double dr_ik[3], r_ik;
-
- k = jlist[neighbor_k];
- k &= NEIGHMASK;
- ktype = map[type[k]];
- ikparam = elem2param[itype][ktype][ktype];
- ijkparam = elem2param[itype][jtype][ktype];
-
- dr_ik[0] = xtmp -x[k][0];
- dr_ik[1] = ytmp -x[k][1];
- dr_ik[2] = ztmp -x[k][2];
- r_ik = dr_ik[0]*dr_ik[0] + dr_ik[1]*dr_ik[1] + dr_ik[2]*dr_ik[2];
-
- if (r_ik > params[ikparam].cutsq) continue;
-
- r_ik = sqrt(r_ik);
-
- invR_ik = 1.0 / r_ik;
-
- directorCos_ik_x = invR_ik * r_ik_x;
- directorCos_ik_y = invR_ik * r_ik_y;
- directorCos_ik_z = invR_ik * r_ik_z;
-
- gtetaFunctionIJK = preGtetaFunction[neighbor_j][neighbor_k];
-
- cutoffFunctionIK = preCutoffFunction[neighbor_k];
-
- zeta += cutoffFunctionIK * gtetaFunctionIJK;
-
+ double dr_ik[3], r_ik;
+
+ k = jlist[neighbor_k];
+ k &= NEIGHMASK;
+ ktype = map[type[k]];
+ ikparam = elem2param[itype][ktype][ktype];
+ ijkparam = elem2param[itype][jtype][ktype];
+
+ dr_ik[0] = xtmp -x[k][0];
+ dr_ik[1] = ytmp -x[k][1];
+ dr_ik[2] = ztmp -x[k][2];
+ r_ik = dr_ik[0]*dr_ik[0] + dr_ik[1]*dr_ik[1] + dr_ik[2]*dr_ik[2];
+
+ if (r_ik > params[ikparam].cutsq) continue;
+
+ r_ik = sqrt(r_ik);
+
+ invR_ik = 1.0 / r_ik;
+
+ directorCos_ik_x = invR_ik * r_ik_x;
+ directorCos_ik_y = invR_ik * r_ik_y;
+ directorCos_ik_z = invR_ik * r_ik_z;
+
+ gtetaFunctionIJK = preGtetaFunction[neighbor_j][neighbor_k];
+
+ cutoffFunctionIK = preCutoffFunction[neighbor_k];
+
+ zeta += cutoffFunctionIK * gtetaFunctionIJK;
+
}
// first loop over neighbours of atom i except j - part 2/2
for (int neighbor_k = neighbor_j+1; neighbor_k < jnum; neighbor_k++) {
- double dr_ik[3], r_ik;
-
- k = jlist[neighbor_k];
- k &= NEIGHMASK;
- ktype = map[type[k]];
- ikparam = elem2param[itype][ktype][ktype];
- ijkparam = elem2param[itype][jtype][ktype];
-
- dr_ik[0] = xtmp -x[k][0];
- dr_ik[1] = ytmp -x[k][1];
- dr_ik[2] = ztmp -x[k][2];
- r_ik = dr_ik[0]*dr_ik[0] + dr_ik[1]*dr_ik[1] + dr_ik[2]*dr_ik[2];
-
- if (r_ik > params[ikparam].cutsq) continue;
-
- r_ik = sqrt(r_ik);
- invR_ik = 1.0 / r_ik;
-
- directorCos_ik_x = invR_ik * dr_ik[0];
- directorCos_ik_y = invR_ik * dr_ik[1];
- directorCos_ik_z = invR_ik * dr_ik[2];
-
- gtetaFunctionIJK = preGtetaFunction[neighbor_j][neighbor_k];
-
- cutoffFunctionIK = preCutoffFunction[neighbor_k];
-
- zeta += cutoffFunctionIK * gtetaFunctionIJK;
+ double dr_ik[3], r_ik;
+
+ k = jlist[neighbor_k];
+ k &= NEIGHMASK;
+ ktype = map[type[k]];
+ ikparam = elem2param[itype][ktype][ktype];
+ ijkparam = elem2param[itype][jtype][ktype];
+
+ dr_ik[0] = xtmp -x[k][0];
+ dr_ik[1] = ytmp -x[k][1];
+ dr_ik[2] = ztmp -x[k][2];
+ r_ik = dr_ik[0]*dr_ik[0] + dr_ik[1]*dr_ik[1] + dr_ik[2]*dr_ik[2];
+
+ if (r_ik > params[ikparam].cutsq) continue;
+
+ r_ik = sqrt(r_ik);
+ invR_ik = 1.0 / r_ik;
+
+ directorCos_ik_x = invR_ik * dr_ik[0];
+ directorCos_ik_y = invR_ik * dr_ik[1];
+ directorCos_ik_z = invR_ik * dr_ik[2];
+
+ gtetaFunctionIJK = preGtetaFunction[neighbor_j][neighbor_k];
+
+ cutoffFunctionIK = preCutoffFunction[neighbor_k];
+
+ zeta += cutoffFunctionIK * gtetaFunctionIJK;
}
-
- // betaZetaPowerIJK
+
+ // betaZetaPowerIJK
interpolDeltaX= params[ijparam].beta * zeta;
interpolTMP = (interpolDeltaX * GRIDDENSITY_BIJ);
interpolIDX = (int) interpolTMP;
@@ -386,133 +386,133 @@ void PairTersoffTable::compute(int eflag, int vflag)
// second loop over neighbours of atom i except j, forces and virial only - part 1/2
for (int neighbor_k = 0; neighbor_k < neighbor_j; neighbor_k++) {
- double dr_ik[3], r_ik, f_ik[3];
-
- k = jlist[neighbor_k];
- k &= NEIGHMASK;
- ktype = map[type[k]];
- ikparam = elem2param[itype][ktype][ktype];
- ijkparam = elem2param[itype][jtype][ktype];
-
- dr_ik[0] = xtmp -x[k][0];
- dr_ik[1] = ytmp -x[k][1];
- dr_ik[2] = ztmp -x[k][2];
- r_ik = dr_ik[0]*dr_ik[0] + dr_ik[1]*dr_ik[1] + dr_ik[2]*dr_ik[2];
-
- if (r_ik > params[ikparam].cutsq) continue;
-
- r_ik = sqrt(r_ik);
- invR_ik = 1.0 / r_ik;
-
- directorCos_ik_x = invR_ik * dr_ik[0];
- directorCos_ik_y = invR_ik * dr_ik[1];
- directorCos_ik_z = invR_ik * dr_ik[2];
-
- cosTeta = directorCos_ij_x * directorCos_ik_x + directorCos_ij_y * directorCos_ik_y + directorCos_ij_z * directorCos_ik_z;
-
- gtetaFunctionIJK = preGtetaFunction[neighbor_j][neighbor_k];
-
- gtetaFunctionDerivedIJK = preGtetaFunctionDerived[neighbor_j][neighbor_k];
-
- cutoffFunctionIK = preCutoffFunction[neighbor_k];
-
- cutoffFunctionDerivedIK = preCutoffFunctionDerived[neighbor_k];
-
- factor_force3_ij= cutoffFunctionIK * gtetaFunctionDerivedIJK * invR_ij *factor_force_tot;
-
- f_ij[0] = factor_force3_ij * (directorCos_ij_x*cosTeta - directorCos_ik_x);
- f_ij[1] = factor_force3_ij * (directorCos_ij_y*cosTeta - directorCos_ik_y);
- f_ij[2] = factor_force3_ij * (directorCos_ij_z*cosTeta - directorCos_ik_z);
-
- factor_1_force3_ik = (cutoffFunctionIK * gtetaFunctionDerivedIJK * invR_ik)*factor_force_tot;
- factor_2_force3_ik = -(cutoffFunctionDerivedIK * gtetaFunctionIJK)*factor_force_tot;
-
- f_ik[0] = factor_1_force3_ik * (directorCos_ik_x*cosTeta - directorCos_ij_x) + factor_2_force3_ik * directorCos_ik_x;
- f_ik[1] = factor_1_force3_ik * (directorCos_ik_y*cosTeta - directorCos_ij_y) + factor_2_force3_ik * directorCos_ik_y;
- f_ik[2] = factor_1_force3_ik * (directorCos_ik_z*cosTeta - directorCos_ij_z) + factor_2_force3_ik * directorCos_ik_z;
-
- f[j][0] -= f_ij[0];
- f[j][1] -= f_ij[1];
- f[j][2] -= f_ij[2];
-
- f[k][0] -= f_ik[0];
- f[k][1] -= f_ik[1];
- f[k][2] -= f_ik[2];
-
- fxtmp += f_ij[0] + f_ik[0];
- fytmp += f_ij[1] + f_ik[1];
- fztmp += f_ij[2] + f_ik[2];
-
- // potential energy
- evdwl = 0.0;
-
- if (evflag) ev_tally3(i,j,k,evdwl,0.0,f_ij,f_ik,dr_ij,dr_ik);
+ double dr_ik[3], r_ik, f_ik[3];
+
+ k = jlist[neighbor_k];
+ k &= NEIGHMASK;
+ ktype = map[type[k]];
+ ikparam = elem2param[itype][ktype][ktype];
+ ijkparam = elem2param[itype][jtype][ktype];
+
+ dr_ik[0] = xtmp -x[k][0];
+ dr_ik[1] = ytmp -x[k][1];
+ dr_ik[2] = ztmp -x[k][2];
+ r_ik = dr_ik[0]*dr_ik[0] + dr_ik[1]*dr_ik[1] + dr_ik[2]*dr_ik[2];
+
+ if (r_ik > params[ikparam].cutsq) continue;
+
+ r_ik = sqrt(r_ik);
+ invR_ik = 1.0 / r_ik;
+
+ directorCos_ik_x = invR_ik * dr_ik[0];
+ directorCos_ik_y = invR_ik * dr_ik[1];
+ directorCos_ik_z = invR_ik * dr_ik[2];
+
+ cosTeta = directorCos_ij_x * directorCos_ik_x + directorCos_ij_y * directorCos_ik_y + directorCos_ij_z * directorCos_ik_z;
+
+ gtetaFunctionIJK = preGtetaFunction[neighbor_j][neighbor_k];
+
+ gtetaFunctionDerivedIJK = preGtetaFunctionDerived[neighbor_j][neighbor_k];
+
+ cutoffFunctionIK = preCutoffFunction[neighbor_k];
+
+ cutoffFunctionDerivedIK = preCutoffFunctionDerived[neighbor_k];
+
+ factor_force3_ij= cutoffFunctionIK * gtetaFunctionDerivedIJK * invR_ij *factor_force_tot;
+
+ f_ij[0] = factor_force3_ij * (directorCos_ij_x*cosTeta - directorCos_ik_x);
+ f_ij[1] = factor_force3_ij * (directorCos_ij_y*cosTeta - directorCos_ik_y);
+ f_ij[2] = factor_force3_ij * (directorCos_ij_z*cosTeta - directorCos_ik_z);
+
+ factor_1_force3_ik = (cutoffFunctionIK * gtetaFunctionDerivedIJK * invR_ik)*factor_force_tot;
+ factor_2_force3_ik = -(cutoffFunctionDerivedIK * gtetaFunctionIJK)*factor_force_tot;
+
+ f_ik[0] = factor_1_force3_ik * (directorCos_ik_x*cosTeta - directorCos_ij_x) + factor_2_force3_ik * directorCos_ik_x;
+ f_ik[1] = factor_1_force3_ik * (directorCos_ik_y*cosTeta - directorCos_ij_y) + factor_2_force3_ik * directorCos_ik_y;
+ f_ik[2] = factor_1_force3_ik * (directorCos_ik_z*cosTeta - directorCos_ij_z) + factor_2_force3_ik * directorCos_ik_z;
+
+ f[j][0] -= f_ij[0];
+ f[j][1] -= f_ij[1];
+ f[j][2] -= f_ij[2];
+
+ f[k][0] -= f_ik[0];
+ f[k][1] -= f_ik[1];
+ f[k][2] -= f_ik[2];
+
+ fxtmp += f_ij[0] + f_ik[0];
+ fytmp += f_ij[1] + f_ik[1];
+ fztmp += f_ij[2] + f_ik[2];
+
+ // potential energy
+ evdwl = 0.0;
+
+ if (evflag) ev_tally3(i,j,k,evdwl,0.0,f_ij,f_ik,dr_ij,dr_ik);
}
-
+
// second loop over neighbours of atom i except j, forces and virial only - part 2/2
for (int neighbor_k = neighbor_j+1; neighbor_k < jnum; neighbor_k++) {
- double dr_ik[3], r_ik, f_ik[3];
-
- k = jlist[neighbor_k];
- k &= NEIGHMASK;
- ktype = map[type[k]];
- ikparam = elem2param[itype][ktype][ktype];
- ijkparam = elem2param[itype][jtype][ktype];
-
- dr_ik[0] = xtmp -x[k][0];
- dr_ik[1] = ytmp -x[k][1];
- dr_ik[2] = ztmp -x[k][2];
- r_ik = dr_ik[0]*dr_ik[0] + dr_ik[1]*dr_ik[1] + dr_ik[2]*dr_ik[2];
-
- if (r_ik > params[ikparam].cutsq) continue;
-
- r_ik = sqrt(r_ik);
- invR_ik = 1.0 / r_ik;
-
- directorCos_ik_x = invR_ik * dr_ik[0];
- directorCos_ik_y = invR_ik * dr_ik[1];
- directorCos_ik_z = invR_ik * dr_ik[2];
-
- cosTeta = directorCos_ij_x * directorCos_ik_x + directorCos_ij_y * directorCos_ik_y + directorCos_ij_z * directorCos_ik_z;
-
- gtetaFunctionIJK = preGtetaFunction[neighbor_j][neighbor_k];
-
- gtetaFunctionDerivedIJK = preGtetaFunctionDerived[neighbor_j][neighbor_k];
-
- cutoffFunctionIK = preCutoffFunction[neighbor_k];
-
- cutoffFunctionDerivedIK = preCutoffFunctionDerived[neighbor_k];
-
- factor_force3_ij= cutoffFunctionIK * gtetaFunctionDerivedIJK * invR_ij *factor_force_tot;
-
- f_ij[0] = factor_force3_ij * (directorCos_ij_x*cosTeta - directorCos_ik_x);
- f_ij[1] = factor_force3_ij * (directorCos_ij_y*cosTeta - directorCos_ik_y);
- f_ij[2] = factor_force3_ij * (directorCos_ij_z*cosTeta - directorCos_ik_z);
-
- factor_1_force3_ik = (cutoffFunctionIK * gtetaFunctionDerivedIJK * invR_ik)*factor_force_tot;
- factor_2_force3_ik = -(cutoffFunctionDerivedIK * gtetaFunctionIJK)*factor_force_tot;
-
- f_ik[0] = factor_1_force3_ik * (directorCos_ik_x*cosTeta - directorCos_ij_x) + factor_2_force3_ik * directorCos_ik_x;
- f_ik[1] = factor_1_force3_ik * (directorCos_ik_y*cosTeta - directorCos_ij_y) + factor_2_force3_ik * directorCos_ik_y;
- f_ik[2] = factor_1_force3_ik * (directorCos_ik_z*cosTeta - directorCos_ij_z) + factor_2_force3_ik * directorCos_ik_z;
-
- f[j][0] -= f_ij[0];
- f[j][1] -= f_ij[1];
- f[j][2] -= f_ij[2];
-
- f[k][0] -= f_ik[0];
- f[k][1] -= f_ik[1];
- f[k][2] -= f_ik[2];
-
- fxtmp += f_ij[0] + f_ik[0];
- fytmp += f_ij[1] + f_ik[1];
- fztmp += f_ij[2] + f_ik[2];
-
- // potential energy
- evdwl = 0.0;
-
- if (evflag) ev_tally3(i,j,k,evdwl,0.0,f_ij,f_ik,dr_ij,dr_ik);
-
+ double dr_ik[3], r_ik, f_ik[3];
+
+ k = jlist[neighbor_k];
+ k &= NEIGHMASK;
+ ktype = map[type[k]];
+ ikparam = elem2param[itype][ktype][ktype];
+ ijkparam = elem2param[itype][jtype][ktype];
+
+ dr_ik[0] = xtmp -x[k][0];
+ dr_ik[1] = ytmp -x[k][1];
+ dr_ik[2] = ztmp -x[k][2];
+ r_ik = dr_ik[0]*dr_ik[0] + dr_ik[1]*dr_ik[1] + dr_ik[2]*dr_ik[2];
+
+ if (r_ik > params[ikparam].cutsq) continue;
+
+ r_ik = sqrt(r_ik);
+ invR_ik = 1.0 / r_ik;
+
+ directorCos_ik_x = invR_ik * dr_ik[0];
+ directorCos_ik_y = invR_ik * dr_ik[1];
+ directorCos_ik_z = invR_ik * dr_ik[2];
+
+ cosTeta = directorCos_ij_x * directorCos_ik_x + directorCos_ij_y * directorCos_ik_y + directorCos_ij_z * directorCos_ik_z;
+
+ gtetaFunctionIJK = preGtetaFunction[neighbor_j][neighbor_k];
+
+ gtetaFunctionDerivedIJK = preGtetaFunctionDerived[neighbor_j][neighbor_k];
+
+ cutoffFunctionIK = preCutoffFunction[neighbor_k];
+
+ cutoffFunctionDerivedIK = preCutoffFunctionDerived[neighbor_k];
+
+ factor_force3_ij= cutoffFunctionIK * gtetaFunctionDerivedIJK * invR_ij *factor_force_tot;
+
+ f_ij[0] = factor_force3_ij * (directorCos_ij_x*cosTeta - directorCos_ik_x);
+ f_ij[1] = factor_force3_ij * (directorCos_ij_y*cosTeta - directorCos_ik_y);
+ f_ij[2] = factor_force3_ij * (directorCos_ij_z*cosTeta - directorCos_ik_z);
+
+ factor_1_force3_ik = (cutoffFunctionIK * gtetaFunctionDerivedIJK * invR_ik)*factor_force_tot;
+ factor_2_force3_ik = -(cutoffFunctionDerivedIK * gtetaFunctionIJK)*factor_force_tot;
+
+ f_ik[0] = factor_1_force3_ik * (directorCos_ik_x*cosTeta - directorCos_ij_x) + factor_2_force3_ik * directorCos_ik_x;
+ f_ik[1] = factor_1_force3_ik * (directorCos_ik_y*cosTeta - directorCos_ij_y) + factor_2_force3_ik * directorCos_ik_y;
+ f_ik[2] = factor_1_force3_ik * (directorCos_ik_z*cosTeta - directorCos_ij_z) + factor_2_force3_ik * directorCos_ik_z;
+
+ f[j][0] -= f_ij[0];
+ f[j][1] -= f_ij[1];
+ f[j][2] -= f_ij[2];
+
+ f[k][0] -= f_ik[0];
+ f[k][1] -= f_ik[1];
+ f[k][2] -= f_ik[2];
+
+ fxtmp += f_ij[0] + f_ik[0];
+ fytmp += f_ij[1] + f_ik[1];
+ fztmp += f_ij[2] + f_ik[2];
+
+ // potential energy
+ evdwl = 0.0;
+
+ if (evflag) ev_tally3(i,j,k,evdwl,0.0,f_ij,f_ik,dr_ij,dr_ik);
+
}
} // loop on J
f[i][0] += fxtmp;
@@ -525,7 +525,7 @@ void PairTersoffTable::compute(int eflag, int vflag)
/* ---------------------------------------------------------------------- */
-void PairTersoffTable::deallocatePreLoops(void)
+void PairTersoffTable::deallocatePreLoops(void)
{
memory->destroy (preGtetaFunction);
memory->destroy (preGtetaFunctionDerived);
@@ -538,14 +538,14 @@ void PairTersoffTable::allocatePreLoops(void)
memory->create(preGtetaFunction,leadingDimensionInteractionList,leadingDimensionInteractionList,"tersofftable:preGtetaFunction");
memory->create(preGtetaFunctionDerived,leadingDimensionInteractionList,leadingDimensionInteractionList,"tersofftable:preGtetaFunctionDerived");
-
+
memory->create(preCutoffFunction,leadingDimensionInteractionList,"tersofftable:preCutoffFunction");
-
+
memory->create(preCutoffFunctionDerived,leadingDimensionInteractionList,"tersofftable:preCutoffFunctionDerived");
}
-void PairTersoffTable::deallocateGrids()
-{
+void PairTersoffTable::deallocateGrids()
+{
int i,j;
memory->destroy(exponential);
@@ -560,7 +560,7 @@ void PairTersoffTable::deallocateGrids()
void PairTersoffTable::allocateGrids(void)
{
int i, j, l;
-
+
int numGridPointsExponential, numGridPointsGtetaFunction, numGridPointsOneCutoffFunction;
int numGridPointsNotOneCutoffFunction, numGridPointsCutoffFunction, numGridPointsBetaZetaPower;
// double minArgumentExponential;
@@ -569,7 +569,7 @@ void PairTersoffTable::allocateGrids(void)
double r, minMu, maxLambda, maxCutoff;
double const PI=acos(-1.0);
- // exponential
+ // exponential
// find min and max argument
minMu=params[0].lam2;
@@ -579,9 +579,9 @@ void PairTersoffTable::allocateGrids(void)
if (params[i].lam1 > maxLambda) maxLambda = params[i].lam1;
}
maxCutoff=cutmax;
-
+
minArgumentExponential=minMu*GRIDSTART;
-
+
numGridPointsExponential=(int)((maxLambda*maxCutoff-minArgumentExponential)*GRIDDENSITY_EXP)+2;
memory->create(exponential,numGridPointsExponential,"tersofftable:exponential");
@@ -593,7 +593,7 @@ void PairTersoffTable::allocateGrids(void)
exponential[i] = exp(-r);
r += deltaArgumentExponential;
}
-
+
// gtetaFunction
@@ -601,12 +601,12 @@ void PairTersoffTable::allocateGrids(void)
memory->create(gtetaFunction,nelements,numGridPointsGtetaFunction,"tersofftable:gtetaFunction");
memory->create(gtetaFunctionDerived,nelements,numGridPointsGtetaFunction,"tersofftable:gtetaFunctionDerived");
-
+
r = minArgumentExponential;
for (i=0; i<nelements; i++) {
r = -1.0;
deltaArgumentGtetaFunction = 1.0 / GRIDDENSITY_GTETA;
-
+
int iparam = elem2param[i][i][i];
double c = params[iparam].c;
double d = params[iparam].d;
@@ -619,7 +619,7 @@ void PairTersoffTable::allocateGrids(void)
}
}
-
+
// cutoffFunction, zetaFunction, find grids.
int ngrid_max = -1;
@@ -638,55 +638,55 @@ void PairTersoffTable::allocateGrids(void)
for (j=0; j<nelements; j++) {
for (j=0; j<nelements; j++) {
- int ijparam = elem2param[i][j][j];
- double cutoffR = params[ijparam].cutoffR;
- double cutoffS = params[ijparam].cutoffS;
+ int ijparam = elem2param[i][j][j];
+ double cutoffR = params[ijparam].cutoffR;
+ double cutoffS = params[ijparam].cutoffS;
- numGridPointsOneCutoffFunction=(int) ((cutoffR-GRIDSTART)*GRIDDENSITY_FCUTOFF)+1;
- numGridPointsNotOneCutoffFunction=(int) ((cutoffS-cutoffR)*GRIDDENSITY_FCUTOFF)+2;
- numGridPointsCutoffFunction=numGridPointsOneCutoffFunction+numGridPointsNotOneCutoffFunction;
+ numGridPointsOneCutoffFunction=(int) ((cutoffR-GRIDSTART)*GRIDDENSITY_FCUTOFF)+1;
+ numGridPointsNotOneCutoffFunction=(int) ((cutoffS-cutoffR)*GRIDDENSITY_FCUTOFF)+2;
+ numGridPointsCutoffFunction=numGridPointsOneCutoffFunction+numGridPointsNotOneCutoffFunction;
- ngrid_max = MAX(ngrid_max,numGridPointsCutoffFunction);
+ ngrid_max = MAX(ngrid_max,numGridPointsCutoffFunction);
}
}
}
-
+
memory->create(cutoffFunction,nelements,nelements,ngrid_max,"tersoff:cutfunc");
memory->create(cutoffFunctionDerived,nelements,nelements,ngrid_max,"tersoff:cutfuncD");
-
+
// cutoffFunction, compute.
for (i=0; i<nelements; i++) {
for (j=0; j<nelements; j++) {
for (j=0; j<nelements; j++) {
- int ijparam = elem2param[i][j][j];
- double cutoffR = params[ijparam].cutoffR;
- double cutoffS = params[ijparam].cutoffS;
-
- numGridPointsOneCutoffFunction=(int) ((cutoffR-GRIDSTART)*GRIDDENSITY_FCUTOFF)+1;
- numGridPointsNotOneCutoffFunction=(int) ((cutoffS-cutoffR)*GRIDDENSITY_FCUTOFF)+2;
- numGridPointsCutoffFunction=numGridPointsOneCutoffFunction+numGridPointsNotOneCutoffFunction;
-
- r = GRIDSTART;
- deltaArgumentCutoffFunction = 1.0 / GRIDDENSITY_FCUTOFF;
-
- for (l = 0; l < numGridPointsOneCutoffFunction; l++) {
- cutoffFunction[i][j][l] = 1.0;
- cutoffFunctionDerived[i][j][l]=0.0;
- r += deltaArgumentCutoffFunction;
- }
-
- for (l = numGridPointsOneCutoffFunction; l < numGridPointsCutoffFunction; l++) {
- cutoffFunction[i][j][l] = 0.5 + 0.5 * cos (PI * (r - cutoffR)/(cutoffS-cutoffR)) ;
- cutoffFunctionDerived[i][j][l] = -0.5 * PI * sin (PI * (r - cutoffR)/(cutoffS-cutoffR)) / (cutoffS-cutoffR) ;
- r += deltaArgumentCutoffFunction;
- }
+ int ijparam = elem2param[i][j][j];
+ double cutoffR = params[ijparam].cutoffR;
+ double cutoffS = params[ijparam].cutoffS;
+
+ numGridPointsOneCutoffFunction=(int) ((cutoffR-GRIDSTART)*GRIDDENSITY_FCUTOFF)+1;
+ numGridPointsNotOneCutoffFunction=(int) ((cutoffS-cutoffR)*GRIDDENSITY_FCUTOFF)+2;
+ numGridPointsCutoffFunction=numGridPointsOneCutoffFunction+numGridPointsNotOneCutoffFunction;
+
+ r = GRIDSTART;
+ deltaArgumentCutoffFunction = 1.0 / GRIDDENSITY_FCUTOFF;
+
+ for (l = 0; l < numGridPointsOneCutoffFunction; l++) {
+ cutoffFunction[i][j][l] = 1.0;
+ cutoffFunctionDerived[i][j][l]=0.0;
+ r += deltaArgumentCutoffFunction;
+ }
+
+ for (l = numGridPointsOneCutoffFunction; l < numGridPointsCutoffFunction; l++) {
+ cutoffFunction[i][j][l] = 0.5 + 0.5 * cos (PI * (r - cutoffR)/(cutoffS-cutoffR)) ;
+ cutoffFunctionDerived[i][j][l] = -0.5 * PI * sin (PI * (r - cutoffR)/(cutoffS-cutoffR)) / (cutoffS-cutoffR) ;
+ r += deltaArgumentCutoffFunction;
+ }
}
}
}
// betaZetaPower, compute
-
+
memory->create(betaZetaPower,nelements,zeta_max,"tersoff:zetafunc");
memory->create(betaZetaPowerDerived,nelements,zeta_max,"tersoff:zetafuncD");
@@ -701,11 +701,11 @@ void PairTersoffTable::allocateGrids(void)
r=0.0;
deltaArgumentBetaZetaPower = 1.0 / GRIDDENSITY_BIJ;
-
+
betaZetaPower[i][0]=1.0;
r += deltaArgumentBetaZetaPower;
-
+
for (j = 1; j < numGridPointsBetaZetaPower; j++) {
double powern=params[iparam].powern;
betaZetaPower[i][j]=pow((1+pow(r,powern)),-1/(2*powern));
@@ -728,7 +728,7 @@ void PairTersoffTable::allocate()
}
/* ----------------------------------------------------------------------
- global settings
+ global settings
------------------------------------------------------------------------- */
void PairTersoffTable::settings(int narg, char **arg)
@@ -784,7 +784,7 @@ void PairTersoffTable::coeff(int narg, char **arg)
}
// read potential file and initialize potential parameters
-
+
read_file(arg[2]);
setup();
@@ -801,8 +801,8 @@ void PairTersoffTable::coeff(int narg, char **arg)
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
if (map[i] >= 0 && map[j] >= 0) {
- setflag[i][j] = 1;
- count++;
+ setflag[i][j] = 1;
+ count++;
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
@@ -876,8 +876,8 @@ void PairTersoffTable::read_file(char *file)
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fp);
if (ptr == NULL) {
- eof = 1;
- fclose(fp);
+ eof = 1;
+ fclose(fp);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
@@ -898,8 +898,8 @@ void PairTersoffTable::read_file(char *file)
if (comm->me == 0) {
ptr = fgets(&line[n],MAXLINE-n,fp);
if (ptr == NULL) {
- eof = 1;
- fclose(fp);
+ eof = 1;
+ fclose(fp);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
@@ -938,7 +938,7 @@ void PairTersoffTable::read_file(char *file)
if (nparams == maxparam) {
maxparam += DELTA;
params = (Param *) memory->srealloc(params,maxparam*sizeof(Param),
- "pair:params");
+ "pair:params");
}
params[nparams].ielement = ielement;
@@ -966,16 +966,16 @@ void PairTersoffTable::read_file(char *file)
// currently only allow m exponent of 1 or 3
params[nparams].powermint = int(params[nparams].powerm);
- if (params[nparams].c < 0.0 || params[nparams].d < 0.0 ||
- params[nparams].powern < 0.0 || params[nparams].beta < 0.0 ||
- params[nparams].lam2 < 0.0 || params[nparams].bigb < 0.0 ||
- params[nparams].cutoffR < 0.0 ||params[nparams].cutoffS < 0.0 ||
- params[nparams].cutoffR > params[nparams].cutoffS ||
- params[nparams].lam1 < 0.0 || params[nparams].biga < 0.0
+ if (params[nparams].c < 0.0 || params[nparams].d < 0.0 ||
+ params[nparams].powern < 0.0 || params[nparams].beta < 0.0 ||
+ params[nparams].lam2 < 0.0 || params[nparams].bigb < 0.0 ||
+ params[nparams].cutoffR < 0.0 ||params[nparams].cutoffS < 0.0 ||
+ params[nparams].cutoffR > params[nparams].cutoffS ||
+ params[nparams].lam1 < 0.0 || params[nparams].biga < 0.0
) error->all(FLERR,"Illegal Tersoff parameter");
// only tersoff_2 parametrization is implemented
- if (params[nparams].gamma != 1.0 || params[nparams].lam3 != 0.0)
+ if (params[nparams].gamma != 1.0 || params[nparams].lam3 != 0.0)
error->all(FLERR,"Current tersoff/table pair_style implements only tersoff_2 parametrization");
nparams++;
}
@@ -999,16 +999,16 @@ void PairTersoffTable::setup()
for (i = 0; i < nelements; i++)
for (j = 0; j < nelements; j++)
for (k = 0; k < nelements; k++) {
- n = -1;
- for (m = 0; m < nparams; m++) {
- if (i == params[m].ielement && j == params[m].jelement &&
- k == params[m].kelement) {
- if (n >= 0) error->all(FLERR,"Potential file has duplicate entry");
- n = m;
- }
- }
- if (n < 0) error->all(FLERR,"Potential file is missing an entry");
- elem2param[i][j][k] = n;
+ n = -1;
+ for (m = 0; m < nparams; m++) {
+ if (i == params[m].ielement && j == params[m].jelement &&
+ k == params[m].kelement) {
+ if (n >= 0) error->all(FLERR,"Potential file has duplicate entry");
+ n = m;
+ }
+ }
+ if (n < 0) error->all(FLERR,"Potential file is missing an entry");
+ elem2param[i][j][k] = n;
}
// set cutoff square
@@ -1022,4 +1022,4 @@ void PairTersoffTable::setup()
for (m = 0; m < nparams; m++) {
if (params[m].cut > cutmax) cutmax = params[m].cut;
}
-}
+}
diff --git a/src/USER-MISC/pair_tersoff_table.h b/src/USER-MISC/pair_tersoff_table.h
index fb7550c3b5a13b6d19b6c7a8969ba9e46b26533d..82e9087a48f75608644b8666535cd8569769978c 100644
--- a/src/USER-MISC/pair_tersoff_table.h
+++ b/src/USER-MISC/pair_tersoff_table.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -54,8 +54,8 @@ class PairTersoffTable : public Pair {
int ielement,jelement,kelement;
int powermint;
};
-
-
+
+
double cutmax; // max cutoff for all elements
int nelements; // # of unique elements
char **elements; // names of unique elements
diff --git a/src/USER-OMP/angle_charmm_omp.cpp b/src/USER-OMP/angle_charmm_omp.cpp
index 36a5127ccf0797d94a8a7c36e1c02529d231ee51..1efe62d4d3c42354cae07f72a4a5c3ab20ca0880 100644
--- a/src/USER-OMP/angle_charmm_omp.cpp
+++ b/src/USER-OMP/angle_charmm_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -65,11 +65,11 @@ void AngleCharmmOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_bond) eval<0,0,1>(ifrom, ito, thr);
@@ -145,10 +145,10 @@ void AngleCharmmOMP::eval(int nfrom, int nto, ThrData * const thr)
c = delx1*delx2 + dely1*dely2 + delz1*delz2;
c /= r1*r2;
-
+
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
-
+
s = sqrt(1.0 - c*c);
if (s < SMALL) s = SMALL;
s = 1.0/s;
@@ -194,6 +194,6 @@ void AngleCharmmOMP::eval(int nfrom, int nto, ThrData * const thr)
}
if (EVFLAG) ev_tally_thr(this,i1,i2,i3,nlocal,NEWTON_BOND,eangle,f1,f3,
- delx1,dely1,delz1,delx2,dely2,delz2,thr);
+ delx1,dely1,delz1,delx2,dely2,delz2,thr);
}
}
diff --git a/src/USER-OMP/angle_charmm_omp.h b/src/USER-OMP/angle_charmm_omp.h
index f9f13cad333288a388351d2bc48632b185a62662..8cbb992c3b3190967e6b2186137d9e7be95b80ed 100644
--- a/src/USER-OMP/angle_charmm_omp.h
+++ b/src/USER-OMP/angle_charmm_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/angle_class2_omp.cpp b/src/USER-OMP/angle_class2_omp.cpp
index 37b28343e1f61937fbc811f8726c4e3f56af2fd4..0dbd0cbfda29fbc5fc628d064a28d2c176789eb9 100644
--- a/src/USER-OMP/angle_class2_omp.cpp
+++ b/src/USER-OMP/angle_class2_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -65,11 +65,11 @@ void AngleClass2OMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_bond) eval<0,0,1>(ifrom, ito, thr);
@@ -126,10 +126,10 @@ void AngleClass2OMP::eval(int nfrom, int nto, ThrData * const thr)
c = delx1*delx2 + dely1*dely2 + delz1*delz2;
c /= r1*r2;
-
+
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
-
+
s = sqrt(1.0 - c*c);
if (s < SMALL) s = SMALL;
s = 1.0/s;
@@ -141,7 +141,7 @@ void AngleClass2OMP::eval(int nfrom, int nto, ThrData * const thr)
dtheta3 = dtheta2*dtheta;
dtheta4 = dtheta3*dtheta;
- de_angle = 2.0*k2[type]*dtheta + 3.0*k3[type]*dtheta2 +
+ de_angle = 2.0*k2[type]*dtheta + 3.0*k3[type]*dtheta2 +
4.0*k4[type]*dtheta3;
a = -de_angle*s;
@@ -237,6 +237,6 @@ void AngleClass2OMP::eval(int nfrom, int nto, ThrData * const thr)
}
if (EVFLAG) ev_tally_thr(this,i1,i2,i3,nlocal,NEWTON_BOND,eangle,f1,f3,
- delx1,dely1,delz1,delx2,dely2,delz2,thr);
+ delx1,dely1,delz1,delx2,dely2,delz2,thr);
}
}
diff --git a/src/USER-OMP/angle_class2_omp.h b/src/USER-OMP/angle_class2_omp.h
index 5317f7c447f934fcd531919d31daa465d07916ad..fcfdae51a7d1632cb20a4beff7cc283f0a5fb8f0 100644
--- a/src/USER-OMP/angle_class2_omp.h
+++ b/src/USER-OMP/angle_class2_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/angle_cosine_delta_omp.cpp b/src/USER-OMP/angle_cosine_delta_omp.cpp
index 8c14513ca8ac8751bafc4c3138edf930d6e85a68..5ba57d20b5ea77348db30718dcbb351b752d3e32 100644
--- a/src/USER-OMP/angle_cosine_delta_omp.cpp
+++ b/src/USER-OMP/angle_cosine_delta_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -65,11 +65,11 @@ void AngleCosineDeltaOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_bond) eval<0,0,1>(ifrom, ito, thr);
@@ -123,21 +123,21 @@ void AngleCosineDeltaOMP::eval(int nfrom, int nto, ThrData * const thr)
c = delx1*delx2 + dely1*dely2 + delz1*delz2;
c /= r1*r2;
-
+
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
-
+
theta = acos(c);
-
+
s = sqrt(1.0 - c*c);
if (s < SMALL) s = SMALL;
s = 1.0/s;
-
+
cot = c/s;
-
+
// force & energy
-
- dtheta = theta - theta0[type];
+
+ dtheta = theta - theta0[type];
dcostheta = cos(dtheta);
tk = k[type] * (1.0-dcostheta);
@@ -146,15 +146,15 @@ void AngleCosineDeltaOMP::eval(int nfrom, int nto, ThrData * const thr)
a = -k[type];
// expand dtheta for cos and sin contribution to force
-
+
a11 = a*c / rsq1;
a12 = -a / (r1*r2);
a22 = a*c / rsq2;
-
+
b11 = -a*c*cot / rsq1;
b12 = a*cot / (r1*r2);
b22 = -a*c*cot / rsq2;
-
+
c0 = cos(theta0[type]);
s0 = sin(theta0[type]);
@@ -186,6 +186,6 @@ void AngleCosineDeltaOMP::eval(int nfrom, int nto, ThrData * const thr)
}
if (EVFLAG) ev_tally_thr(this,i1,i2,i3,nlocal,NEWTON_BOND,eangle,f1,f3,
- delx1,dely1,delz1,delx2,dely2,delz2,thr);
+ delx1,dely1,delz1,delx2,dely2,delz2,thr);
}
}
diff --git a/src/USER-OMP/angle_cosine_delta_omp.h b/src/USER-OMP/angle_cosine_delta_omp.h
index aecc30f7944508bb218ca1d41decbb81b5b6436b..57b1d9364da43d362f2eea8bebe0d6b7ee852ce5 100644
--- a/src/USER-OMP/angle_cosine_delta_omp.h
+++ b/src/USER-OMP/angle_cosine_delta_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/angle_cosine_omp.cpp b/src/USER-OMP/angle_cosine_omp.cpp
index 4bc93e95ac8e6d9e60e05281567cc9df8fa21cf3..a773f94c5040eaef7864a77a26508e37e6cb0a98 100644
--- a/src/USER-OMP/angle_cosine_omp.cpp
+++ b/src/USER-OMP/angle_cosine_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -65,11 +65,11 @@ void AngleCosineOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_bond) eval<0,0,1>(ifrom, ito, thr);
@@ -163,6 +163,6 @@ void AngleCosineOMP::eval(int nfrom, int nto, ThrData * const thr)
}
if (EVFLAG) ev_tally_thr(this,i1,i2,i3,nlocal,NEWTON_BOND,eangle,f1,f3,
- delx1,dely1,delz1,delx2,dely2,delz2,thr);
+ delx1,dely1,delz1,delx2,dely2,delz2,thr);
}
}
diff --git a/src/USER-OMP/angle_cosine_omp.h b/src/USER-OMP/angle_cosine_omp.h
index 6d2995ba0fa39d34d6f8e5122cc27cdc24619a61..16eb3ff944838c8f9d6a3abab347722379875787 100644
--- a/src/USER-OMP/angle_cosine_omp.h
+++ b/src/USER-OMP/angle_cosine_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/angle_cosine_periodic_omp.cpp b/src/USER-OMP/angle_cosine_periodic_omp.cpp
index 0f121efd73fcac31f4b8f29d8f7cc7fa9caa1c70..a86b68611f81329496e78b1b1a6c784e1661408f 100644
--- a/src/USER-OMP/angle_cosine_periodic_omp.cpp
+++ b/src/USER-OMP/angle_cosine_periodic_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -65,11 +65,11 @@ void AngleCosinePeriodicOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_bond) eval<0,0,1>(ifrom, ito, thr);
@@ -141,7 +141,7 @@ void AngleCosinePeriodicOMP::eval(int nfrom, int nto, ThrData * const thr)
tn = 1.0;
tn_1 = 1.0;
tn_2 = 0.0;
- un = 1.0;
+ un = 1.0;
un_1 = 2.0;
un_2 = 0.0;
@@ -172,7 +172,7 @@ void AngleCosinePeriodicOMP::eval(int nfrom, int nto, ThrData * const thr)
a11 = a*c / rsq1;
a12 = -a / (r1*r2);
a22 = a*c / rsq2;
-
+
f1[0] = a11*delx1 + a12*delx2;
f1[1] = a11*dely1 + a12*dely2;
f1[2] = a11*delz1 + a12*delz2;
@@ -201,6 +201,6 @@ void AngleCosinePeriodicOMP::eval(int nfrom, int nto, ThrData * const thr)
}
if (EVFLAG) ev_tally_thr(this,i1,i2,i3,nlocal,NEWTON_BOND,eangle,f1,f3,
- delx1,dely1,delz1,delx2,dely2,delz2,thr);
+ delx1,dely1,delz1,delx2,dely2,delz2,thr);
}
}
diff --git a/src/USER-OMP/angle_cosine_periodic_omp.h b/src/USER-OMP/angle_cosine_periodic_omp.h
index 9d05b3e07105bcba85adc22c17f947064cbd1fc9..3c7da10cebd67c9212ccae1b7c33e186952d55b8 100644
--- a/src/USER-OMP/angle_cosine_periodic_omp.h
+++ b/src/USER-OMP/angle_cosine_periodic_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/angle_cosine_shift_exp_omp.cpp b/src/USER-OMP/angle_cosine_shift_exp_omp.cpp
index 26ad2976cf820062ca27148bd88890d2588c9fad..81cd8ecad3e795739fe33cb9a8e5d31c2b989630 100644
--- a/src/USER-OMP/angle_cosine_shift_exp_omp.cpp
+++ b/src/USER-OMP/angle_cosine_shift_exp_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -65,11 +65,11 @@ void AngleCosineShiftExpOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_bond) eval<0,0,1>(ifrom, ito, thr);
@@ -87,7 +87,7 @@ void AngleCosineShiftExpOMP::eval(int nfrom, int nto, ThrData * const thr)
double delx1,dely1,delz1,delx2,dely2,delz2;
double eangle,f1[3],f3[3],ff;
double rsq1,rsq2,r1,r2,c,s,a11,a12,a22;
- double exp2,aa,uumin,cccpsss,cssmscc;
+ double exp2,aa,uumin,cccpsss,cssmscc;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
@@ -129,9 +129,9 @@ void AngleCosineShiftExpOMP::eval(int nfrom, int nto, ThrData * const thr)
// C= sine of angle
s = sqrt(1.0 - c*c);
if (s < SMALL) s = SMALL;
-
+
// force & energy
-
+
aa=a[type];
uumin=umin[type];
@@ -142,19 +142,19 @@ void AngleCosineShiftExpOMP::eval(int nfrom, int nto, ThrData * const thr)
{ // |a|<0.01 so use expansions relative precision <1e-5
// std::cout << "Using expansion\n";
if (EFLAG) eangle = -0.125*(1+cccpsss)*(4+aa*(cccpsss-1))*uumin;
- ff=0.25*uumin*cssmscc*(2+aa*cccpsss)/s;
+ ff=0.25*uumin*cssmscc*(2+aa*cccpsss)/s;
}
else
{
-// std::cout << "Not using expansion\n";
+// std::cout << "Not using expansion\n";
exp2=exp(0.5*aa*(1+cccpsss));
if (EFLAG) eangle = opt1[type]*(1-exp2);
- ff=0.5*a[type]*opt1[type]*exp2*cssmscc/s;
+ ff=0.5*a[type]*opt1[type]*exp2*cssmscc/s;
}
a11 = ff*c/ rsq1;
a12 = -ff / (r1*r2);
- a22 = ff*c/ rsq2;
+ a22 = ff*c/ rsq2;
f1[0] = a11*delx1 + a12*delx2;
f1[1] = a11*dely1 + a12*dely2;
@@ -184,6 +184,6 @@ void AngleCosineShiftExpOMP::eval(int nfrom, int nto, ThrData * const thr)
}
if (EVFLAG) ev_tally_thr(this,i1,i2,i3,nlocal,NEWTON_BOND,eangle,f1,f3,
- delx1,dely1,delz1,delx2,dely2,delz2,thr);
+ delx1,dely1,delz1,delx2,dely2,delz2,thr);
}
}
diff --git a/src/USER-OMP/angle_cosine_shift_exp_omp.h b/src/USER-OMP/angle_cosine_shift_exp_omp.h
index b70045b890bf612cdb0636d185caeff542f8d22a..aba70f8a3cd2aba3218e13bde64c80f8b0e924e5 100644
--- a/src/USER-OMP/angle_cosine_shift_exp_omp.h
+++ b/src/USER-OMP/angle_cosine_shift_exp_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/angle_cosine_shift_omp.cpp b/src/USER-OMP/angle_cosine_shift_omp.cpp
index 6024f9976631c5c0b55dfe2f622d6421191d37ec..2c830cf39341fd9439f0c9426a5b2eb98757df95 100644
--- a/src/USER-OMP/angle_cosine_shift_omp.cpp
+++ b/src/USER-OMP/angle_cosine_shift_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -65,11 +65,11 @@ void AngleCosineShiftOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_bond) eval<0,0,1>(ifrom, ito, thr);
@@ -129,11 +129,11 @@ void AngleCosineShiftOMP::eval(int nfrom, int nto, ThrData * const thr)
// C= sine of angle
s = sqrt(1.0 - c*c);
if (s < SMALL) s = SMALL;
-
+
// force & energy
const double kcos=kcost[type];
const double ksin=ksint[type];
- if (EFLAG) eangle = -k[type]-kcos*c-ksin*s;
+ if (EFLAG) eangle = -k[type]-kcos*c-ksin*s;
cps = c/s; // NOTE absorbed one c
@@ -169,6 +169,6 @@ void AngleCosineShiftOMP::eval(int nfrom, int nto, ThrData * const thr)
}
if (EVFLAG) ev_tally_thr(this,i1,i2,i3,nlocal,NEWTON_BOND,eangle,f1,f3,
- delx1,dely1,delz1,delx2,dely2,delz2,thr);
+ delx1,dely1,delz1,delx2,dely2,delz2,thr);
}
}
diff --git a/src/USER-OMP/angle_cosine_shift_omp.h b/src/USER-OMP/angle_cosine_shift_omp.h
index 4afe4a233e71fa7cfcbc271f8367350683dfd706..09402fb34121b55929588b807f6160567398a60e 100644
--- a/src/USER-OMP/angle_cosine_shift_omp.h
+++ b/src/USER-OMP/angle_cosine_shift_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/angle_cosine_squared_omp.cpp b/src/USER-OMP/angle_cosine_squared_omp.cpp
index d518167508ec9ece67b052e3e83d9ea075101b37..ccdaf2bdbc69cd0a9922305eae105bcfb3a590a7 100644
--- a/src/USER-OMP/angle_cosine_squared_omp.cpp
+++ b/src/USER-OMP/angle_cosine_squared_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -65,11 +65,11 @@ void AngleCosineSquaredOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_bond) eval<0,0,1>(ifrom, ito, thr);
@@ -124,12 +124,12 @@ void AngleCosineSquaredOMP::eval(int nfrom, int nto, ThrData * const thr)
c = delx1*delx2 + dely1*dely2 + delz1*delz2;
c /= r1*r2;
-
+
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
-
+
// force & energy
-
+
dcostheta = c - cos(theta0[type]);
tk = k[type] * dcostheta;
@@ -168,6 +168,6 @@ void AngleCosineSquaredOMP::eval(int nfrom, int nto, ThrData * const thr)
}
if (EVFLAG) ev_tally_thr(this,i1,i2,i3,nlocal,NEWTON_BOND,eangle,f1,f3,
- delx1,dely1,delz1,delx2,dely2,delz2,thr);
+ delx1,dely1,delz1,delx2,dely2,delz2,thr);
}
}
diff --git a/src/USER-OMP/angle_cosine_squared_omp.h b/src/USER-OMP/angle_cosine_squared_omp.h
index aeadd2e95d640eeef79d86b4cf97565628be6e34..758863e61277230973dde79dd54b03e8c60ab9ce 100644
--- a/src/USER-OMP/angle_cosine_squared_omp.h
+++ b/src/USER-OMP/angle_cosine_squared_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/angle_dipole_omp.cpp b/src/USER-OMP/angle_dipole_omp.cpp
index 6499c484691d2cdac9e0711fdd4a2aa91a99a13a..f9cbc6f51d5247d3c8a08ecceb7025f8da3fcdb8 100644
--- a/src/USER-OMP/angle_dipole_omp.cpp
+++ b/src/USER-OMP/angle_dipole_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -50,7 +50,7 @@ void AngleDipoleOMP::compute(int eflag, int vflag)
ev_setup(eflag,vflag);
} else evflag = 0;
- if (!force->newton_bond)
+ if (!force->newton_bond)
error->all(FLERR,"'newton' flag for bonded interactions must be 'on'");
const int nall = atom->nlocal + atom->nghost;
@@ -111,16 +111,16 @@ void AngleDipoleOMP::eval(int nfrom, int nto, ThrData * const thr)
deltaGamma = cosGamma - cos(gamma0[type]);
kdg = k[type] * deltaGamma;
- if (EFLAG) eangle = kdg * deltaGamma; // energy
-
- tangle = 2.0 * kdg / rmu;
-
+ if (EFLAG) eangle = kdg * deltaGamma; // energy
+
+ tangle = 2.0 * kdg / rmu;
+
torque[iDip][0] += tangle * (dely*mu[iDip][2] - delz*mu[iDip][1]);
torque[iDip][1] += tangle * (delz*mu[iDip][0] - delx*mu[iDip][2]);
torque[iDip][2] += tangle * (delx*mu[iDip][1] - dely*mu[iDip][0]);
if (EFLAG) // tally energy (virial=0 because force=0)
ev_tally_thr(this,iRef,iDip,iDummy,nlocal,/* NEWTON_BOND */ 1,
- eangle,f1,f3,0.0,0.0,0.0,0.0,0.0,0.0,thr);
+ eangle,f1,f3,0.0,0.0,0.0,0.0,0.0,0.0,thr);
}
}
diff --git a/src/USER-OMP/angle_dipole_omp.h b/src/USER-OMP/angle_dipole_omp.h
index 23e69ad5eeeee325b871d30bd35ab4332c1f062f..ab7133da34171d3d141f7c9d7a75f30ace5a2317 100644
--- a/src/USER-OMP/angle_dipole_omp.h
+++ b/src/USER-OMP/angle_dipole_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/angle_harmonic_omp.cpp b/src/USER-OMP/angle_harmonic_omp.cpp
index 1ebfa3fdde8b55c573ed56a23623833c737397d6..b6ff1a1ddd72d3443313052a9a4c35a4f6fe8220 100644
--- a/src/USER-OMP/angle_harmonic_omp.cpp
+++ b/src/USER-OMP/angle_harmonic_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -65,11 +65,11 @@ void AngleHarmonicOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_bond) eval<0,0,1>(ifrom, ito, thr);
@@ -124,10 +124,10 @@ void AngleHarmonicOMP::eval(int nfrom, int nto, ThrData * const thr)
c = delx1*delx2 + dely1*dely2 + delz1*delz2;
c /= r1*r2;
-
+
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
-
+
s = sqrt(1.0 - c*c);
if (s < SMALL) s = SMALL;
s = 1.0/s;
@@ -172,6 +172,6 @@ void AngleHarmonicOMP::eval(int nfrom, int nto, ThrData * const thr)
}
if (EVFLAG) ev_tally_thr(this,i1,i2,i3,nlocal,NEWTON_BOND,eangle,f1,f3,
- delx1,dely1,delz1,delx2,dely2,delz2,thr);
+ delx1,dely1,delz1,delx2,dely2,delz2,thr);
}
}
diff --git a/src/USER-OMP/angle_harmonic_omp.h b/src/USER-OMP/angle_harmonic_omp.h
index f8169de117ea75a8cd8a961c9f48b37feacfc9a2..80c8f491aa83f3381a08a62b187a334a51c1b115 100644
--- a/src/USER-OMP/angle_harmonic_omp.h
+++ b/src/USER-OMP/angle_harmonic_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/angle_sdk_omp.cpp b/src/USER-OMP/angle_sdk_omp.cpp
index e5d9552982fef9fa004ea36644396c98222a1a13..43e0049e1614215231652bde9213651574b0c704 100644
--- a/src/USER-OMP/angle_sdk_omp.cpp
+++ b/src/USER-OMP/angle_sdk_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -67,11 +67,11 @@ void AngleSDKOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_bond) eval<0,0,1>(ifrom, ito, thr);
@@ -126,15 +126,15 @@ void AngleSDKOMP::eval(int nfrom, int nto, ThrData * const thr)
c = delx1*delx2 + dely1*dely2 + delz1*delz2;
c /= r1*r2;
-
+
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
-
+
s = sqrt(1.0 - c*c);
if (s < SMALL) s = SMALL;
s = 1.0/s;
- // 1-3 LJ interaction.
+ // 1-3 LJ interaction.
// we only want to use the repulsive part,
// and it can be scaled (or off).
// so this has to be done here and not in the
@@ -143,7 +143,7 @@ void AngleSDKOMP::eval(int nfrom, int nto, ThrData * const thr)
f13 = e13 = delx3 = dely3 = delz3 = 0.0;
if (repflag) {
-
+
delx3 = x[i1][0] - x[i3][0];
dely3 = x[i1][1] - x[i3][1];
delz3 = x[i1][2] - x[i3][2];
@@ -152,35 +152,35 @@ void AngleSDKOMP::eval(int nfrom, int nto, ThrData * const thr)
const int type1 = atom->type[i1];
const int type3 = atom->type[i3];
-
+
if (rsq3 < rminsq[type1][type3]) {
- const int ljt = lj_type[type1][type3];
- const double r2inv = 1.0/rsq3;
+ const int ljt = lj_type[type1][type3];
+ const double r2inv = 1.0/rsq3;
+
+ if (ljt == LJ12_4) {
+ const double r4inv=r2inv*r2inv;
- if (ljt == LJ12_4) {
- const double r4inv=r2inv*r2inv;
+ f13 = r4inv*(lj1[type1][type3]*r4inv*r4inv - lj2[type1][type3]);
+ if (EFLAG) e13 = r4inv*(lj3[type1][type3]*r4inv*r4inv - lj4[type1][type3]);
- f13 = r4inv*(lj1[type1][type3]*r4inv*r4inv - lj2[type1][type3]);
- if (EFLAG) e13 = r4inv*(lj3[type1][type3]*r4inv*r4inv - lj4[type1][type3]);
-
- } else if (ljt == LJ9_6) {
- const double r3inv = r2inv*sqrt(r2inv);
- const double r6inv = r3inv*r3inv;
+ } else if (ljt == LJ9_6) {
+ const double r3inv = r2inv*sqrt(r2inv);
+ const double r6inv = r3inv*r3inv;
- f13 = r6inv*(lj1[type1][type3]*r3inv - lj2[type1][type3]);
- if (EFLAG) e13 = r6inv*(lj3[type1][type3]*r3inv - lj4[type1][type3]);
+ f13 = r6inv*(lj1[type1][type3]*r3inv - lj2[type1][type3]);
+ if (EFLAG) e13 = r6inv*(lj3[type1][type3]*r3inv - lj4[type1][type3]);
- } else if (ljt == LJ12_6) {
- const double r6inv = r2inv*r2inv*r2inv;
+ } else if (ljt == LJ12_6) {
+ const double r6inv = r2inv*r2inv*r2inv;
- f13 = r6inv*(lj1[type1][type3]*r6inv - lj2[type1][type3]);
- if (EFLAG) e13 = r6inv*(lj3[type1][type3]*r6inv - lj4[type1][type3]);
- }
+ f13 = r6inv*(lj1[type1][type3]*r6inv - lj2[type1][type3]);
+ if (EFLAG) e13 = r6inv*(lj3[type1][type3]*r6inv - lj4[type1][type3]);
+ }
- // make sure energy is 0.0 at the cutoff.
- if (EFLAG) e13 -= emin[type1][type3];
+ // make sure energy is 0.0 at the cutoff.
+ if (EFLAG) e13 -= emin[type1][type3];
- f13 *= r2inv;
+ f13 *= r2inv;
}
}
@@ -225,9 +225,9 @@ void AngleSDKOMP::eval(int nfrom, int nto, ThrData * const thr)
if (EVFLAG) {
ev_tally_thr(this,i1,i2,i3,nlocal,NEWTON_BOND,eangle,f1,f3,
- delx1,dely1,delz1,delx2,dely2,delz2,thr);
+ delx1,dely1,delz1,delx2,dely2,delz2,thr);
if (repflag) ev_tally13_thr(this,i1,i3,nlocal,NEWTON_BOND,
- e13,f13,delx3,dely3,delz3,thr);
+ e13,f13,delx3,dely3,delz3,thr);
}
}
}
diff --git a/src/USER-OMP/angle_sdk_omp.h b/src/USER-OMP/angle_sdk_omp.h
index 350490811fce55cb085736c637dcc342c4d6732e..9ab75904ceb54b8ce60997836829cb63868efde1 100644
--- a/src/USER-OMP/angle_sdk_omp.h
+++ b/src/USER-OMP/angle_sdk_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/angle_table_omp.cpp b/src/USER-OMP/angle_table_omp.cpp
index edb162d9833606b1c16db12101f6c21d7df85884..8eb73b4c2b1ffdbb6d96be7fd0b85a779e8ef1c5 100644
--- a/src/USER-OMP/angle_table_omp.cpp
+++ b/src/USER-OMP/angle_table_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -65,11 +65,11 @@ void AngleTableOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_bond) eval<0,0,1>(ifrom, ito, thr);
@@ -124,10 +124,10 @@ void AngleTableOMP::eval(int nfrom, int nto, ThrData * const thr)
c = delx1*delx2 + dely1*dely2 + delz1*delz2;
c /= r1*r2;
-
+
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
-
+
s = sqrt(1.0 - c*c);
if (s < SMALL) s = SMALL;
s = 1.0/s;
@@ -136,10 +136,10 @@ void AngleTableOMP::eval(int nfrom, int nto, ThrData * const thr)
theta = acos(c);
uf_lookup(type,theta,u,mdu);
-
+
if (EFLAG) eangle = u;
- a = mdu * s;
+ a = mdu * s;
a11 = a*c / rsq1;
a12 = -a / (r1*r2);
a22 = a*c / rsq2;
@@ -172,6 +172,6 @@ void AngleTableOMP::eval(int nfrom, int nto, ThrData * const thr)
}
if (EVFLAG) ev_tally_thr(this,i1,i2,i3,nlocal,NEWTON_BOND,eangle,f1,f3,
- delx1,dely1,delz1,delx2,dely2,delz2,thr);
+ delx1,dely1,delz1,delx2,dely2,delz2,thr);
}
}
diff --git a/src/USER-OMP/angle_table_omp.h b/src/USER-OMP/angle_table_omp.h
index 31d7db60b6bfc87fd0491b85e6c6790d7c3f5a02..97c9bb65a7a1964efd757fdad2e35f39bd70eb0f 100644
--- a/src/USER-OMP/angle_table_omp.h
+++ b/src/USER-OMP/angle_table_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/bond_class2_omp.cpp b/src/USER-OMP/bond_class2_omp.cpp
index 1d0efe3862addada3ac60fbc3426d2f6acf5298c..a31ac2e3aa1dcd2fa6d9b72007d7bafdbb8ae593 100644
--- a/src/USER-OMP/bond_class2_omp.cpp
+++ b/src/USER-OMP/bond_class2_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -61,11 +61,11 @@ void BondClass2OMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_bond) eval<0,0,1>(ifrom, ito, thr);
@@ -128,6 +128,6 @@ void BondClass2OMP::eval(int nfrom, int nto, ThrData * const thr)
}
if (EVFLAG) ev_tally_thr(this,i1,i2,nlocal,NEWTON_BOND,
- ebond,fbond,delx,dely,delz,thr);
+ ebond,fbond,delx,dely,delz,thr);
}
}
diff --git a/src/USER-OMP/bond_class2_omp.h b/src/USER-OMP/bond_class2_omp.h
index ab41ae401e28ac555694eceeda39a3633195efb6..845e28f5921499d99fbbad08718c006111fa12eb 100644
--- a/src/USER-OMP/bond_class2_omp.h
+++ b/src/USER-OMP/bond_class2_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/bond_fene_expand_omp.cpp b/src/USER-OMP/bond_fene_expand_omp.cpp
index 42de952298c21ff71d4c43f0c692df769587a678..39c43d978ef489b9de392ff7a5c2ef399cd33f34 100644
--- a/src/USER-OMP/bond_fene_expand_omp.cpp
+++ b/src/USER-OMP/bond_fene_expand_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -62,11 +62,11 @@ void BondFENEExpandOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_bond) eval<0,0,1>(ifrom, ito, thr);
@@ -116,11 +116,11 @@ void BondFENEExpandOMP::eval(int nfrom, int nto, ThrData * const thr)
char str[128];
sprintf(str,"FENE bond too long: " BIGINT_FORMAT " %d %d %g",
- update->ntimestep,atom->tag[i1],atom->tag[i2],sqrt(rsq));
+ update->ntimestep,atom->tag[i1],atom->tag[i2],sqrt(rsq));
error->warning(FLERR,str,0);
if (check_error_thr((rlogarg <= -3.0),tid,FLERR,"Bad FENE bond"))
- return;
+ return;
rlogarg = 0.1;
}
@@ -140,7 +140,7 @@ void BondFENEExpandOMP::eval(int nfrom, int nto, ThrData * const thr)
if (EFLAG) {
ebond = -0.5 * k[type]*r0sq*log(rlogarg);
if (rshiftsq < TWO_1_3*sigma[type]*sigma[type])
- ebond += 4.0*epsilon[type]*sr6*(sr6-1.0) + epsilon[type];
+ ebond += 4.0*epsilon[type]*sr6*(sr6-1.0) + epsilon[type];
}
// apply force to each of 2 atoms
@@ -158,6 +158,6 @@ void BondFENEExpandOMP::eval(int nfrom, int nto, ThrData * const thr)
}
if (EVFLAG) ev_tally_thr(this,i1,i2,nlocal,NEWTON_BOND,
- ebond,fbond,delx,dely,delz,thr);
+ ebond,fbond,delx,dely,delz,thr);
}
}
diff --git a/src/USER-OMP/bond_fene_expand_omp.h b/src/USER-OMP/bond_fene_expand_omp.h
index a383fe58a732540c41835b2b484fb7510cee3702..317b81e5debba4925081cc0798adfcdd8a9cebc0 100644
--- a/src/USER-OMP/bond_fene_expand_omp.h
+++ b/src/USER-OMP/bond_fene_expand_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/bond_fene_omp.cpp b/src/USER-OMP/bond_fene_omp.cpp
index f9556392fb61abb0b4246a7440980f1ff1ab65bd..72596d1864f16116f6a28872fa05e3dd5254a279 100644
--- a/src/USER-OMP/bond_fene_omp.cpp
+++ b/src/USER-OMP/bond_fene_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -62,11 +62,11 @@ void BondFENEOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_bond) eval<0,0,1>(ifrom, ito, thr);
@@ -112,11 +112,11 @@ void BondFENEOMP::eval(int nfrom, int nto, ThrData * const thr)
char str[128];
sprintf(str,"FENE bond too long: " BIGINT_FORMAT " %d %d %g",
- update->ntimestep,atom->tag[i1],atom->tag[i2],sqrt(rsq));
+ update->ntimestep,atom->tag[i1],atom->tag[i2],sqrt(rsq));
error->warning(FLERR,str,0);
if (check_error_thr((rlogarg <= -3.0),tid,FLERR,"Bad FENE bond"))
- return;
+ return;
rlogarg = 0.1;
}
@@ -136,7 +136,7 @@ void BondFENEOMP::eval(int nfrom, int nto, ThrData * const thr)
if (EFLAG) {
ebond = -0.5 * k[type]*r0sq*log(rlogarg);
if (rsq < TWO_1_3*sigma[type]*sigma[type])
- ebond += 4.0*epsilon[type]*sr6*(sr6-1.0) + epsilon[type];
+ ebond += 4.0*epsilon[type]*sr6*(sr6-1.0) + epsilon[type];
}
// apply force to each of 2 atoms
@@ -154,6 +154,6 @@ void BondFENEOMP::eval(int nfrom, int nto, ThrData * const thr)
}
if (EVFLAG) ev_tally_thr(this,i1,i2,nlocal,NEWTON_BOND,
- ebond,fbond,delx,dely,delz,thr);
+ ebond,fbond,delx,dely,delz,thr);
}
}
diff --git a/src/USER-OMP/bond_fene_omp.h b/src/USER-OMP/bond_fene_omp.h
index c3b0348e93047ace634fb24dd707703c8e5cc198..13e843fe136ad8e32500eeb9c54844a646b7dd5c 100644
--- a/src/USER-OMP/bond_fene_omp.h
+++ b/src/USER-OMP/bond_fene_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/bond_harmonic_omp.cpp b/src/USER-OMP/bond_harmonic_omp.cpp
index 19b03194bea61dc3e3b3c86f5652ff1d0f7cd2fa..9c8c6d2c712416242807870d4137ded227944b73 100644
--- a/src/USER-OMP/bond_harmonic_omp.cpp
+++ b/src/USER-OMP/bond_harmonic_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -60,11 +60,11 @@ void BondHarmonicOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_bond) eval<0,0,1>(ifrom, ito, thr);
@@ -124,6 +124,6 @@ void BondHarmonicOMP::eval(int nfrom, int nto, ThrData * const thr)
}
if (EVFLAG) ev_tally_thr(this,i1,i2,nlocal,NEWTON_BOND,
- ebond,fbond,delx,dely,delz,thr);
+ ebond,fbond,delx,dely,delz,thr);
}
}
diff --git a/src/USER-OMP/bond_harmonic_omp.h b/src/USER-OMP/bond_harmonic_omp.h
index c542033d5e07c71a945dbbe051cd63a60d50977f..0a81b52f4157fdf7593cc4775a75916884573b64 100644
--- a/src/USER-OMP/bond_harmonic_omp.h
+++ b/src/USER-OMP/bond_harmonic_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp b/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp
index e5f1b49f23761ae2186b7b0b017667ba60f2d87d..de2c72e89026543be02453a38f7f730a117ba70d 100644
--- a/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp
+++ b/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -60,11 +60,11 @@ void BondHarmonicShiftCutOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_bond) eval<0,0,1>(ifrom, ito, thr);
@@ -127,6 +127,6 @@ void BondHarmonicShiftCutOMP::eval(int nfrom, int nto, ThrData * const thr)
}
if (EVFLAG) ev_tally_thr(this,i1,i2,nlocal,NEWTON_BOND,
- ebond,fbond,delx,dely,delz,thr);
+ ebond,fbond,delx,dely,delz,thr);
}
}
diff --git a/src/USER-OMP/bond_harmonic_shift_cut_omp.h b/src/USER-OMP/bond_harmonic_shift_cut_omp.h
index fd4f6185f027d6cbf446b42bf92c4a99ca131c34..f465ff5b3a13daa0cb1511c25a85b561453cbf16 100644
--- a/src/USER-OMP/bond_harmonic_shift_cut_omp.h
+++ b/src/USER-OMP/bond_harmonic_shift_cut_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/bond_harmonic_shift_omp.cpp b/src/USER-OMP/bond_harmonic_shift_omp.cpp
index 87d62afd1579c01d24a55b4e44e79df4bd262c70..2d566f771b62f2a5ab041fbfc78a4e3dd2cb9be5 100644
--- a/src/USER-OMP/bond_harmonic_shift_omp.cpp
+++ b/src/USER-OMP/bond_harmonic_shift_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -60,11 +60,11 @@ void BondHarmonicShiftOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_bond) eval<0,0,1>(ifrom, ito, thr);
@@ -124,6 +124,6 @@ void BondHarmonicShiftOMP::eval(int nfrom, int nto, ThrData * const thr)
}
if (EVFLAG) ev_tally_thr(this,i1,i2,nlocal,NEWTON_BOND,
- ebond,fbond,delx,dely,delz,thr);
+ ebond,fbond,delx,dely,delz,thr);
}
}
diff --git a/src/USER-OMP/bond_harmonic_shift_omp.h b/src/USER-OMP/bond_harmonic_shift_omp.h
index 6c5aa1324eabf397e540175ecf6a9d3df23fa832..58ee6ce23d309b79acafe2cb90678c9dad1a4aae 100644
--- a/src/USER-OMP/bond_harmonic_shift_omp.h
+++ b/src/USER-OMP/bond_harmonic_shift_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/bond_morse_omp.cpp b/src/USER-OMP/bond_morse_omp.cpp
index 39979edf391cc172edc9935f1c3106a63200fa32..0a91857c8eb6ef06f54ae6ed05212f5e71b8db67 100644
--- a/src/USER-OMP/bond_morse_omp.cpp
+++ b/src/USER-OMP/bond_morse_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -60,11 +60,11 @@ void BondMorseOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_bond) eval<0,0,1>(ifrom, ito, thr);
@@ -125,6 +125,6 @@ void BondMorseOMP::eval(int nfrom, int nto, ThrData * const thr)
}
if (EVFLAG) ev_tally_thr(this,i1,i2,nlocal,NEWTON_BOND,
- ebond,fbond,delx,dely,delz,thr);
+ ebond,fbond,delx,dely,delz,thr);
}
}
diff --git a/src/USER-OMP/bond_morse_omp.h b/src/USER-OMP/bond_morse_omp.h
index e6a91778680f561455fd5292f5c4f637534e6f80..09d3a4458d6675edd645cd980c4dc865e020a652 100644
--- a/src/USER-OMP/bond_morse_omp.h
+++ b/src/USER-OMP/bond_morse_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/bond_nonlinear_omp.cpp b/src/USER-OMP/bond_nonlinear_omp.cpp
index cfb046bf6765da0ea0a36d9ed50cf929d73604d6..46eed47604cf18dd3745620ae737c33861a5ff16 100644
--- a/src/USER-OMP/bond_nonlinear_omp.cpp
+++ b/src/USER-OMP/bond_nonlinear_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -60,11 +60,11 @@ void BondNonlinearOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_bond) eval<0,0,1>(ifrom, ito, thr);
@@ -125,6 +125,6 @@ void BondNonlinearOMP::eval(int nfrom, int nto, ThrData * const thr)
}
if (EVFLAG) ev_tally_thr(this,i1,i2,nlocal,NEWTON_BOND,
- ebond,fbond,delx,dely,delz,thr);
+ ebond,fbond,delx,dely,delz,thr);
}
}
diff --git a/src/USER-OMP/bond_nonlinear_omp.h b/src/USER-OMP/bond_nonlinear_omp.h
index ae1b671ad4fc11ec1635224c17adc5cf90196c4e..fcb0fa325d4b5fe1dff34333e3d5e0df1cee6cb6 100644
--- a/src/USER-OMP/bond_nonlinear_omp.h
+++ b/src/USER-OMP/bond_nonlinear_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/bond_quartic_omp.cpp b/src/USER-OMP/bond_quartic_omp.cpp
index d4ce470cdea820cbb3bbd8179acea44ac6af7581..d07ee9aca614cffa257a4723453bcef784d745d8 100644
--- a/src/USER-OMP/bond_quartic_omp.cpp
+++ b/src/USER-OMP/bond_quartic_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -66,11 +66,11 @@ void BondQuarticOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_bond) eval<0,0,1>(ifrom, ito, thr);
@@ -122,12 +122,12 @@ void BondQuarticOMP::eval(int nfrom, int nto, ThrData * const thr)
if (rsq > rc[type]*rc[type]) {
bondlist[n][2] = 0;
for (m = 0; m < atom->num_bond[i1]; m++)
- if (atom->bond_atom[i1][m] == atom->tag[i2])
- atom->bond_type[i1][m] = 0;
+ if (atom->bond_atom[i1][m] == atom->tag[i2])
+ atom->bond_type[i1][m] = 0;
if (i2 < atom->nlocal)
- for (m = 0; m < atom->num_bond[i2]; m++)
- if (atom->bond_atom[i2][m] == atom->tag[i1])
- atom->bond_type[i2][m] = 0;
+ for (m = 0; m < atom->num_bond[i2]; m++)
+ if (atom->bond_atom[i2][m] == atom->tag[i1])
+ atom->bond_type[i2][m] = 0;
continue;
}
@@ -141,7 +141,7 @@ void BondQuarticOMP::eval(int nfrom, int nto, ThrData * const thr)
ra = dr - b1[type];
rb = dr - b2[type];
fbond = -k[type]/r * (r2*(ra+rb) + 2.0*dr*ra*rb);
-
+
if (rsq < TWO_1_3) {
sr2 = 1.0/rsq;
sr6 = sr2*sr2*sr2;
@@ -181,18 +181,18 @@ void BondQuarticOMP::eval(int nfrom, int nto, ThrData * const thr)
fpair = -fpair;
if (NEWTON_BOND || i1 < nlocal) {
- f[i1][0] += delx*fpair;
- f[i1][1] += dely*fpair;
- f[i1][2] += delz*fpair;
+ f[i1][0] += delx*fpair;
+ f[i1][1] += dely*fpair;
+ f[i1][2] += delz*fpair;
}
if (NEWTON_BOND || i2 < nlocal) {
- f[i2][0] -= delx*fpair;
- f[i2][1] -= dely*fpair;
- f[i2][2] -= delz*fpair;
+ f[i2][0] -= delx*fpair;
+ f[i2][1] -= dely*fpair;
+ f[i2][2] -= delz*fpair;
}
if (EVFLAG) ev_tally_thr(force->pair,i1,i2,nlocal,NEWTON_BOND,
- evdwl,0.0,fpair,delx,dely,delz,thr);
+ evdwl,0.0,fpair,delx,dely,delz,thr);
}
}
}
diff --git a/src/USER-OMP/bond_quartic_omp.h b/src/USER-OMP/bond_quartic_omp.h
index bdc7d229e2bc06895d7566c2ea84085e2a9f59fb..3a249a6cac0dcf4fd2f2a0cd00c71901a2c59c05 100644
--- a/src/USER-OMP/bond_quartic_omp.h
+++ b/src/USER-OMP/bond_quartic_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/bond_table_omp.cpp b/src/USER-OMP/bond_table_omp.cpp
index fe344dcfbe3174183af5b122eaa658f6d23440b2..fefadfc44ab18c30166e2dd1d42946bf7422ad21 100644
--- a/src/USER-OMP/bond_table_omp.cpp
+++ b/src/USER-OMP/bond_table_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -60,11 +60,11 @@ void BondTableOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_bond) eval<0,0,1>(ifrom, ito, thr);
@@ -122,6 +122,6 @@ void BondTableOMP::eval(int nfrom, int nto, ThrData * const thr)
}
if (EVFLAG) ev_tally_thr(this,i1,i2,nlocal,NEWTON_BOND,
- ebond,fbond,delx,dely,delz,thr);
+ ebond,fbond,delx,dely,delz,thr);
}
}
diff --git a/src/USER-OMP/bond_table_omp.h b/src/USER-OMP/bond_table_omp.h
index 17e48463d3375c8d217bf4bbdea7d2b6c992ef97..37e057ee26844638c7bd2b16c9a81f81ac52a385 100644
--- a/src/USER-OMP/bond_table_omp.h
+++ b/src/USER-OMP/bond_table_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/dihedral_charmm_omp.cpp b/src/USER-OMP/dihedral_charmm_omp.cpp
index 9b9cbca6fe6967dce6de67af891e1861045998ec..fbebfbaaacdd5f42a765a36592704632a86a4d50 100644
--- a/src/USER-OMP/dihedral_charmm_omp.cpp
+++ b/src/USER-OMP/dihedral_charmm_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -72,11 +72,11 @@ void DihedralCharmmOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_bond) eval<0,0,1>(ifrom, ito, thr);
@@ -90,13 +90,13 @@ void DihedralCharmmOMP::compute(int eflag, int vflag)
template <int EVFLAG, int EFLAG, int NEWTON_BOND>
void DihedralCharmmOMP::eval(int nfrom, int nto, ThrData * const thr)
{
-
+
int i1,i2,i3,i4,i,m,n,type;
double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm;
double edihedral,f1[3],f2[3],f3[3],f4[3];
double ax,ay,az,bx,by,bz,rasq,rbsq,rgsq,rg,rginv,ra2inv,rb2inv,rabinv;
double df,df1,ddf1,fg,hg,fga,hgb,gaa,gbb;
- double dtfx,dtfy,dtfz,dtgx,dtgy,dtgz,dthx,dthy,dthz;
+ double dtfx,dtfy,dtfz,dtgx,dtgy,dtgz,dthx,dthy,dthz;
double c,s,p,sx2,sy2,sz2;
int itype,jtype;
double delx,dely,delz,rsq,r2inv,r6inv;
@@ -144,7 +144,7 @@ void DihedralCharmmOMP::eval(int nfrom, int nto, ThrData * const thr)
vb3y = x[i4][1] - x[i3][1];
vb3z = x[i4][2] - x[i3][2];
domain->minimum_image(vb3x,vb3y,vb3z);
-
+
// c,s calculation
ax = vb1y*vb2zm - vb1z*vb2ym;
@@ -158,7 +158,7 @@ void DihedralCharmmOMP::eval(int nfrom, int nto, ThrData * const thr)
rbsq = bx*bx + by*by + bz*bz;
rgsq = vb2xm*vb2xm + vb2ym*vb2ym + vb2zm*vb2zm;
rg = sqrt(rgsq);
-
+
rginv = ra2inv = rb2inv = 0.0;
if (rg > 0) rginv = 1.0/rg;
if (rasq > 0) ra2inv = 1.0/rasq;
@@ -174,29 +174,29 @@ void DihedralCharmmOMP::eval(int nfrom, int nto, ThrData * const thr)
int me = comm->me;
if (screen) {
- char str[128];
- sprintf(str,"Dihedral problem: %d/%d " BIGINT_FORMAT " %d %d %d %d",
- me,thr->get_tid(),update->ntimestep,
- atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
- error->warning(FLERR,str,0);
- fprintf(screen," 1st atom: %d %g %g %g\n",
- me,x[i1][0],x[i1][1],x[i1][2]);
- fprintf(screen," 2nd atom: %d %g %g %g\n",
- me,x[i2][0],x[i2][1],x[i2][2]);
- fprintf(screen," 3rd atom: %d %g %g %g\n",
- me,x[i3][0],x[i3][1],x[i3][2]);
- fprintf(screen," 4th atom: %d %g %g %g\n",
- me,x[i4][0],x[i4][1],x[i4][2]);
+ char str[128];
+ sprintf(str,"Dihedral problem: %d/%d " BIGINT_FORMAT " %d %d %d %d",
+ me,thr->get_tid(),update->ntimestep,
+ atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
+ error->warning(FLERR,str,0);
+ fprintf(screen," 1st atom: %d %g %g %g\n",
+ me,x[i1][0],x[i1][1],x[i1][2]);
+ fprintf(screen," 2nd atom: %d %g %g %g\n",
+ me,x[i2][0],x[i2][1],x[i2][2]);
+ fprintf(screen," 3rd atom: %d %g %g %g\n",
+ me,x[i3][0],x[i3][1],x[i3][2]);
+ fprintf(screen," 4th atom: %d %g %g %g\n",
+ me,x[i4][0],x[i4][1],x[i4][2]);
}
}
-
+
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
-
+
m = multiplicity[type];
p = 1.0;
ddf1 = df1 = 0.0;
-
+
for (i = 0; i < m; i++) {
ddf1 = p*c - df1*s;
df1 = p*s + df1*c;
@@ -207,21 +207,21 @@ void DihedralCharmmOMP::eval(int nfrom, int nto, ThrData * const thr)
df1 = df1*cos_shift[type] - ddf1*sin_shift[type];
df1 *= -m;
p += 1.0;
-
+
if (m == 0) {
p = 1.0 + cos_shift[type];
df1 = 0.0;
}
- if (EFLAG) edihedral = k[type] * p;
-
+ if (EFLAG) edihedral = k[type] * p;
+
fg = vb1x*vb2xm + vb1y*vb2ym + vb1z*vb2zm;
hg = vb3x*vb2xm + vb3y*vb2ym + vb3z*vb2zm;
fga = fg*ra2inv*rginv;
hgb = hg*rb2inv*rginv;
gaa = -ra2inv*rg;
gbb = rb2inv*rg;
-
+
dtfx = gaa*ax;
dtfy = gaa*ay;
dtfz = gaa*az;
@@ -231,9 +231,9 @@ void DihedralCharmmOMP::eval(int nfrom, int nto, ThrData * const thr)
dthx = gbb*bx;
dthy = gbb*by;
dthz = gbb*bz;
-
+
df = -k[type] * df1;
-
+
sx2 = df*dtgx;
sy2 = df*dtgy;
sz2 = df*dtgz;
@@ -253,7 +253,7 @@ void DihedralCharmmOMP::eval(int nfrom, int nto, ThrData * const thr)
f3[0] = -sx2 - f4[0];
f3[1] = -sy2 - f4[1];
f3[2] = -sz2 - f4[2];
-
+
// apply force to each of 4 atoms
if (NEWTON_BOND || i1 < nlocal) {
@@ -282,7 +282,7 @@ void DihedralCharmmOMP::eval(int nfrom, int nto, ThrData * const thr)
if (EVFLAG)
ev_tally_thr(this,i1,i2,i3,i4,nlocal,NEWTON_BOND,edihedral,f1,f3,f4,
- vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,thr);
+ vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,thr);
// 1-4 LJ and Coulomb interactions
// tally energy/virial in pair, using newton_bond as newton flag
@@ -304,25 +304,24 @@ void DihedralCharmmOMP::eval(int nfrom, int nto, ThrData * const thr)
fpair = weight[type] * (forcelj+forcecoul)*r2inv;
if (EFLAG) {
- ecoul = weight[type] * forcecoul;
- evdwl = r6inv * (lj14_3[itype][jtype]*r6inv - lj14_4[itype][jtype]);
- evdwl *= weight[type];
+ ecoul = weight[type] * forcecoul;
+ evdwl = r6inv * (lj14_3[itype][jtype]*r6inv - lj14_4[itype][jtype]);
+ evdwl *= weight[type];
}
if (NEWTON_BOND || i1 < nlocal) {
- f[i1][0] += delx*fpair;
- f[i1][1] += dely*fpair;
- f[i1][2] += delz*fpair;
+ f[i1][0] += delx*fpair;
+ f[i1][1] += dely*fpair;
+ f[i1][2] += delz*fpair;
}
if (NEWTON_BOND || i4 < nlocal) {
- f[i4][0] -= delx*fpair;
- f[i4][1] -= dely*fpair;
- f[i4][2] -= delz*fpair;
+ f[i4][0] -= delx*fpair;
+ f[i4][1] -= dely*fpair;
+ f[i4][2] -= delz*fpair;
}
if (EVFLAG) ev_tally_thr(force->pair,i1,i4,nlocal,NEWTON_BOND,
- evdwl,ecoul,fpair,delx,dely,delz,thr);
+ evdwl,ecoul,fpair,delx,dely,delz,thr);
}
}
}
-
diff --git a/src/USER-OMP/dihedral_charmm_omp.h b/src/USER-OMP/dihedral_charmm_omp.h
index 6705b89fbcee88508189f1b91d5d7016b086f8d8..cd0ae5f8ea51c56851436da2726aba3961ed1325 100644
--- a/src/USER-OMP/dihedral_charmm_omp.h
+++ b/src/USER-OMP/dihedral_charmm_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/dihedral_class2_omp.cpp b/src/USER-OMP/dihedral_class2_omp.cpp
index 1c473ca4b1f6304d3584c543633e34cd169e1477..0d150851c8a0c636271782f5d1cff90a00c05903 100644
--- a/src/USER-OMP/dihedral_class2_omp.cpp
+++ b/src/USER-OMP/dihedral_class2_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -64,11 +64,11 @@ void DihedralClass2OMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_bond) eval<0,0,1>(ifrom, ito, thr);
@@ -82,7 +82,7 @@ void DihedralClass2OMP::compute(int eflag, int vflag)
template <int EVFLAG, int EFLAG, int NEWTON_BOND>
void DihedralClass2OMP::eval(int nfrom, int nto, ThrData * const thr)
{
-
+
int i1,i2,i3,i4,i,j,k,n,type;
double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm;
double edihedral;
@@ -136,7 +136,7 @@ void DihedralClass2OMP::eval(int nfrom, int nto, ThrData * const thr)
vb3y = x[i4][1] - x[i3][1];
vb3z = x[i4][2] - x[i3][2];
domain->minimum_image(vb3x,vb3y,vb3z);
-
+
// distances
r1mag2 = vb1x*vb1x + vb1y*vb1y + vb1z*vb1z;
@@ -162,14 +162,14 @@ void DihedralClass2OMP::eval(int nfrom, int nto, ThrData * const thr)
costh12 = (vb1x*vb2x + vb1y*vb2y + vb1z*vb2z) * r12c1;
costh13 = c0;
costh23 = (vb2xm*vb3x + vb2ym*vb3y + vb2zm*vb3z) * r12c2;
-
+
// cos and sin of 2 angles and final c
sin2 = MAX(1.0 - costh12*costh12,0.0);
sc1 = sqrt(sin2);
if (sc1 < SMALL) sc1 = SMALL;
sc1 = 1.0/sc1;
-
+
sin2 = MAX(1.0 - costh23*costh23,0.0);
sc2 = sqrt(sin2);
if (sc2 < SMALL) sc2 = SMALL;
@@ -186,19 +186,19 @@ void DihedralClass2OMP::eval(int nfrom, int nto, ThrData * const thr)
int me = comm->me;
if (screen) {
- char str[128];
- sprintf(str,"Dihedral problem: %d/%d " BIGINT_FORMAT " %d %d %d %d",
- me,thr->get_tid(),update->ntimestep,
- atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
- error->warning(FLERR,str,0);
- fprintf(screen," 1st atom: %d %g %g %g\n",
- me,x[i1][0],x[i1][1],x[i1][2]);
- fprintf(screen," 2nd atom: %d %g %g %g\n",
- me,x[i2][0],x[i2][1],x[i2][2]);
- fprintf(screen," 3rd atom: %d %g %g %g\n",
- me,x[i3][0],x[i3][1],x[i3][2]);
- fprintf(screen," 4th atom: %d %g %g %g\n",
- me,x[i4][0],x[i4][1],x[i4][2]);
+ char str[128];
+ sprintf(str,"Dihedral problem: %d/%d " BIGINT_FORMAT " %d %d %d %d",
+ me,thr->get_tid(),update->ntimestep,
+ atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
+ error->warning(FLERR,str,0);
+ fprintf(screen," 1st atom: %d %g %g %g\n",
+ me,x[i1][0],x[i1][1],x[i1][2]);
+ fprintf(screen," 2nd atom: %d %g %g %g\n",
+ me,x[i2][0],x[i2][1],x[i2][2]);
+ fprintf(screen," 3rd atom: %d %g %g %g\n",
+ me,x[i3][0],x[i3][1],x[i3][2]);
+ fprintf(screen," 4th atom: %d %g %g %g\n",
+ me,x[i4][0],x[i4][1],x[i4][2]);
}
}
@@ -216,7 +216,7 @@ void DihedralClass2OMP::eval(int nfrom, int nto, ThrData * const thr)
a12 = r12c1 * (costh12*c*s1 + costh23*s12);
a13 = rb1*rb3*s12;
a23 = r12c2 * (-costh23*c*s2 - costh12*s12);
-
+
sx1 = a11*vb1x + a12*vb2x + a13*vb3x;
sx2 = a12*vb1x + a22*vb2x + a23*vb3x;
sx12 = a13*vb1x + a23*vb2x + a33*vb3x;
@@ -244,18 +244,18 @@ void DihedralClass2OMP::eval(int nfrom, int nto, ThrData * const thr)
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
- dphidr[i][j] = -dcosphidr[i][j] / sinphi;
+ dphidr[i][j] = -dcosphidr[i][j] / sinphi;
// energy
dphi1 = phi - phi1[type];
dphi2 = 2.0*phi - phi2[type];
dphi3 = 3.0*phi - phi3[type];
-
+
if (EFLAG) edihedral = k1[type]*(1.0 - cos(dphi1)) +
- k2[type]*(1.0 - cos(dphi2)) +
- k3[type]*(1.0 - cos(dphi3));
-
+ k2[type]*(1.0 - cos(dphi2)) +
+ k3[type]*(1.0 - cos(dphi3));
+
de_dihedral = k1[type]*sin(dphi1) + 2.0*k2[type]*sin(dphi2) +
3.0*k3[type]*sin(dphi3);
@@ -263,18 +263,18 @@ void DihedralClass2OMP::eval(int nfrom, int nto, ThrData * const thr)
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
- fabcd[i][j] = de_dihedral*dphidr[i][j];
+ fabcd[i][j] = de_dihedral*dphidr[i][j];
// set up d(bond)/d(r) array
// dbonddr(i,j,k) = bond i, atom j, coordinate k
for (i = 0; i < 3; i++)
for (j = 0; j < 4; j++)
- for (k = 0; k < 3; k++)
- dbonddr[i][j][k] = 0.0;
-
+ for (k = 0; k < 3; k++)
+ dbonddr[i][j][k] = 0.0;
+
// bond1
-
+
dbonddr[0][0][0] = vb1x / r1;
dbonddr[0][0][1] = vb1y / r1;
dbonddr[0][0][2] = vb1z / r1;
@@ -292,7 +292,7 @@ void DihedralClass2OMP::eval(int nfrom, int nto, ThrData * const thr)
dbonddr[1][2][2] = -vb2z / r2;
// bond3
-
+
dbonddr[2][2][0] = vb3x / r3;
dbonddr[2][2][1] = vb3y / r3;
dbonddr[2][2][2] = vb3z / r3;
@@ -305,71 +305,71 @@ void DihedralClass2OMP::eval(int nfrom, int nto, ThrData * const thr)
for (i = 0; i < 2; i++)
for (j = 0; j < 4; j++)
- for (k = 0; k < 3; k++)
- dthetadr[i][j][k] = 0.0;
-
+ for (k = 0; k < 3; k++)
+ dthetadr[i][j][k] = 0.0;
+
t1 = costh12 / r1mag2;
t2 = costh23 / r2mag2;
t3 = costh12 / r2mag2;
t4 = costh23 / r3mag2;
-
+
// angle12
-
+
dthetadr[0][0][0] = sc1 * ((t1 * vb1x) - (vb2x * r12c1));
dthetadr[0][0][1] = sc1 * ((t1 * vb1y) - (vb2y * r12c1));
dthetadr[0][0][2] = sc1 * ((t1 * vb1z) - (vb2z * r12c1));
-
+
dthetadr[0][1][0] = sc1 * ((-t1 * vb1x) + (vb2x * r12c1) +
- (-t3 * vb2x) + (vb1x * r12c1));
+ (-t3 * vb2x) + (vb1x * r12c1));
dthetadr[0][1][1] = sc1 * ((-t1 * vb1y) + (vb2y * r12c1) +
- (-t3 * vb2y) + (vb1y * r12c1));
+ (-t3 * vb2y) + (vb1y * r12c1));
dthetadr[0][1][2] = sc1 * ((-t1 * vb1z) + (vb2z * r12c1) +
- (-t3 * vb2z) + (vb1z * r12c1));
-
- dthetadr[0][2][0] = sc1 * ((t3 * vb2x) - (vb1x * r12c1));
+ (-t3 * vb2z) + (vb1z * r12c1));
+
+ dthetadr[0][2][0] = sc1 * ((t3 * vb2x) - (vb1x * r12c1));
dthetadr[0][2][1] = sc1 * ((t3 * vb2y) - (vb1y * r12c1));
dthetadr[0][2][2] = sc1 * ((t3 * vb2z) - (vb1z * r12c1));
-
+
// angle23
-
+
dthetadr[1][1][0] = sc2 * ((t2 * vb2x) + (vb3x * r12c2));
dthetadr[1][1][1] = sc2 * ((t2 * vb2y) + (vb3y * r12c2));
dthetadr[1][1][2] = sc2 * ((t2 * vb2z) + (vb3z * r12c2));
-
+
dthetadr[1][2][0] = sc2 * ((-t2 * vb2x) - (vb3x * r12c2) +
- (t4 * vb3x) + (vb2x * r12c2));
+ (t4 * vb3x) + (vb2x * r12c2));
dthetadr[1][2][1] = sc2 * ((-t2 * vb2y) - (vb3y * r12c2) +
- (t4 * vb3y) + (vb2y * r12c2));
+ (t4 * vb3y) + (vb2y * r12c2));
dthetadr[1][2][2] = sc2 * ((-t2 * vb2z) - (vb3z * r12c2) +
- (t4 * vb3z) + (vb2z * r12c2));
-
+ (t4 * vb3z) + (vb2z * r12c2));
+
dthetadr[1][3][0] = -sc2 * ((t4 * vb3x) + (vb2x * r12c2));
dthetadr[1][3][1] = -sc2 * ((t4 * vb3y) + (vb2y * r12c2));
dthetadr[1][3][2] = -sc2 * ((t4 * vb3z) + (vb2z * r12c2));
-
+
// mid-bond/torsion coupling
// energy on bond2 (middle bond)
-
+
cos2phi = cos(2.0*phi);
cos3phi = cos(3.0*phi);
-
+
bt1 = mbt_f1[type] * cosphi;
bt2 = mbt_f2[type] * cos2phi;
bt3 = mbt_f3[type] * cos3phi;
sumbte = bt1 + bt2 + bt3;
db = r2 - mbt_r0[type];
if (EFLAG) edihedral += db * sumbte;
-
+
// force on bond2
-
+
bt1 = -mbt_f1[type] * sinphi;
bt2 = -2.0 * mbt_f2[type] * sin(2.0*phi);
bt3 = -3.0 * mbt_f3[type] * sin(3.0*phi);
sumbtf = bt1 + bt2 + bt3;
-
+
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
- fabcd[i][j] += db*sumbtf*dphidr[i][j] + sumbte*dbonddr[1][i][j];
+ fabcd[i][j] += db*sumbtf*dphidr[i][j] + sumbte*dbonddr[1][i][j];
// end-bond/torsion coupling
// energy on bond1 (first bond)
@@ -391,7 +391,7 @@ void DihedralClass2OMP::eval(int nfrom, int nto, ThrData * const thr)
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
- fabcd[i][j] -= db*sumbtf*dphidr[i][j] + sumbte*dbonddr[0][i][j];
+ fabcd[i][j] -= db*sumbtf*dphidr[i][j] + sumbte*dbonddr[0][i][j];
// end-bond/torsion coupling
// energy on bond3 (last bond)
@@ -413,7 +413,7 @@ void DihedralClass2OMP::eval(int nfrom, int nto, ThrData * const thr)
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
- fabcd[i][j] += db*sumbtf*dphidr[i][j] + sumbte*dbonddr[2][i][j];
+ fabcd[i][j] += db*sumbtf*dphidr[i][j] + sumbte*dbonddr[2][i][j];
// angle/torsion coupling
// energy on angle1
@@ -435,7 +435,7 @@ void DihedralClass2OMP::eval(int nfrom, int nto, ThrData * const thr)
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
- fabcd[i][j] -= da*sumbtf*dphidr[i][j] + sumbte*dthetadr[0][i][j];
+ fabcd[i][j] -= da*sumbtf*dphidr[i][j] + sumbte*dthetadr[0][i][j];
// energy on angle2
@@ -456,20 +456,20 @@ void DihedralClass2OMP::eval(int nfrom, int nto, ThrData * const thr)
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
- fabcd[i][j] += da*sumbtf*dphidr[i][j] + sumbte*dthetadr[1][i][j];
+ fabcd[i][j] += da*sumbtf*dphidr[i][j] + sumbte*dthetadr[1][i][j];
// angle/angle/torsion coupling
da1 = acos(costh12) - aat_theta0_1[type];
da2 = acos(costh23) - aat_theta0_2[type];
-
+
if (EFLAG) edihedral += aat_k[type]*da1*da2*cosphi;
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
- fabcd[i][j] -= aat_k[type] *
- (cosphi * (da2*dthetadr[0][i][j] - da1*dthetadr[1][i][j]) +
- sinphi * da1*da2*dphidr[i][j]);
+ fabcd[i][j] -= aat_k[type] *
+ (cosphi * (da2*dthetadr[0][i][j] - da1*dthetadr[1][i][j]) +
+ sinphi * da1*da2*dphidr[i][j]);
// bond1/bond3 coupling
@@ -483,7 +483,7 @@ void DihedralClass2OMP::eval(int nfrom, int nto, ThrData * const thr)
tk2 = -bb13t_k[type] * dr2 / r1;
if (EFLAG) edihedral += bb13t_k[type]*dr1*dr2;
-
+
fabcd[0][0] += tk2 * vb1x;
fabcd[0][1] += tk2 * vb1y;
fabcd[0][2] += tk2 * vb1z;
@@ -491,7 +491,7 @@ void DihedralClass2OMP::eval(int nfrom, int nto, ThrData * const thr)
fabcd[1][0] -= tk2 * vb1x;
fabcd[1][1] -= tk2 * vb1y;
fabcd[1][2] -= tk2 * vb1z;
-
+
fabcd[2][0] -= tk1 * vb3x;
fabcd[2][1] -= tk1 * vb3y;
fabcd[2][2] -= tk1 * vb3z;
@@ -529,8 +529,7 @@ void DihedralClass2OMP::eval(int nfrom, int nto, ThrData * const thr)
if (EVFLAG)
ev_tally_thr(this,i1,i2,i3,i4,nlocal,NEWTON_BOND,edihedral,
- fabcd[0],fabcd[2],fabcd[3],
- vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,thr);
+ fabcd[0],fabcd[2],fabcd[3],
+ vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,thr);
}
}
-
diff --git a/src/USER-OMP/dihedral_class2_omp.h b/src/USER-OMP/dihedral_class2_omp.h
index ac7b21cb4b39d00768b277798db1a5aceeb7ec50..889bbaf9208b23ef565b0f10089b9452491801c5 100644
--- a/src/USER-OMP/dihedral_class2_omp.h
+++ b/src/USER-OMP/dihedral_class2_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp b/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp
index 29a7e48f52022a98425720cc10f3df0c58e2880a..15f4dd97c10559ae15edf9e752a3a12f18fa79bb 100644
--- a/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp
+++ b/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -64,11 +64,11 @@ void DihedralCosineShiftExpOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_bond) eval<0,0,1>(ifrom, ito, thr);
@@ -82,13 +82,13 @@ void DihedralCosineShiftExpOMP::compute(int eflag, int vflag)
template <int EVFLAG, int EFLAG, int NEWTON_BOND>
void DihedralCosineShiftExpOMP::eval(int nfrom, int nto, ThrData * const thr)
{
-
+
int i1,i2,i3,i4,n,type;
double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm;
double edihedral,f1[3],f2[3],f3[3],f4[3];
double ax,ay,az,bx,by,bz,rasq,rbsq,rgsq,rg,rginv,ra2inv,rb2inv,rabinv;
double df,fg,hg,fga,hgb,gaa,gbb;
- double dtfx,dtfy,dtfz,dtgx,dtgy,dtgz,dthx,dthy,dthz;
+ double dtfx,dtfy,dtfz,dtgx,dtgy,dtgz,dthx,dthy,dthz;
double c,s,sx2,sy2,sz2;
double cccpsss,cssmscc,exp2;
@@ -131,7 +131,7 @@ void DihedralCosineShiftExpOMP::eval(int nfrom, int nto, ThrData * const thr)
vb3y = x[i4][1] - x[i3][1];
vb3z = x[i4][2] - x[i3][2];
domain->minimum_image(vb3x,vb3y,vb3z);
-
+
// c,s calculation
ax = vb1y*vb2zm - vb1z*vb2ym;
@@ -145,7 +145,7 @@ void DihedralCosineShiftExpOMP::eval(int nfrom, int nto, ThrData * const thr)
rbsq = bx*bx + by*by + bz*bz;
rgsq = vb2xm*vb2xm + vb2ym*vb2ym + vb2zm*vb2zm;
rg = sqrt(rgsq);
-
+
rginv = ra2inv = rb2inv = 0.0;
if (rg > 0) rginv = 1.0/rg;
if (rasq > 0) ra2inv = 1.0/rasq;
@@ -161,19 +161,19 @@ void DihedralCosineShiftExpOMP::eval(int nfrom, int nto, ThrData * const thr)
int me = comm->me;
if (screen) {
- char str[128];
- sprintf(str,"Dihedral problem: %d/%d " BIGINT_FORMAT " %d %d %d %d",
- me,thr->get_tid(),update->ntimestep,
- atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
- error->warning(FLERR,str,0);
- fprintf(screen," 1st atom: %d %g %g %g\n",
- me,x[i1][0],x[i1][1],x[i1][2]);
- fprintf(screen," 2nd atom: %d %g %g %g\n",
- me,x[i2][0],x[i2][1],x[i2][2]);
- fprintf(screen," 3rd atom: %d %g %g %g\n",
- me,x[i3][0],x[i3][1],x[i3][2]);
- fprintf(screen," 4th atom: %d %g %g %g\n",
- me,x[i4][0],x[i4][1],x[i4][2]);
+ char str[128];
+ sprintf(str,"Dihedral problem: %d/%d " BIGINT_FORMAT " %d %d %d %d",
+ me,thr->get_tid(),update->ntimestep,
+ atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
+ error->warning(FLERR,str,0);
+ fprintf(screen," 1st atom: %d %g %g %g\n",
+ me,x[i1][0],x[i1][1],x[i1][2]);
+ fprintf(screen," 2nd atom: %d %g %g %g\n",
+ me,x[i2][0],x[i2][1],x[i2][2]);
+ fprintf(screen," 3rd atom: %d %g %g %g\n",
+ me,x[i3][0],x[i3][1],x[i3][2]);
+ fprintf(screen," 4th atom: %d %g %g %g\n",
+ me,x[i4][0],x[i4][1],x[i4][2]);
}
}
@@ -182,11 +182,11 @@ void DihedralCosineShiftExpOMP::eval(int nfrom, int nto, ThrData * const thr)
double aa=a[type];
double uumin=umin[type];
-
+
cccpsss = c*cost[type]+s*sint[type];
cssmscc = c*sint[type]-s*cost[type];
- if (doExpansion[type]) {
+ if (doExpansion[type]) {
// |a|<0.001 so use expansions relative precision <1e-5
if (EFLAG) edihedral = -0.125*(1+cccpsss)*(4+aa*(cccpsss-1))*uumin;
df=0.5*uumin*( cssmscc + 0.5*aa*cccpsss);
@@ -195,14 +195,14 @@ void DihedralCosineShiftExpOMP::eval(int nfrom, int nto, ThrData * const thr)
if (EFLAG) edihedral = opt1[type]*(1-exp2);
df= 0.5*opt1[type]*aa* ( exp2*cssmscc );
}
-
+
fg = vb1x*vb2xm + vb1y*vb2ym + vb1z*vb2zm;
hg = vb3x*vb2xm + vb3y*vb2ym + vb3z*vb2zm;
fga = fg*ra2inv*rginv;
hgb = hg*rb2inv*rginv;
gaa = -ra2inv*rg;
gbb = rb2inv*rg;
-
+
dtfx = gaa*ax;
dtfy = gaa*ay;
dtfz = gaa*az;
@@ -261,7 +261,6 @@ void DihedralCosineShiftExpOMP::eval(int nfrom, int nto, ThrData * const thr)
if (EVFLAG)
ev_tally_thr(this,i1,i2,i3,i4,nlocal,NEWTON_BOND,edihedral,f1,f3,f4,
- vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,thr);
+ vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,thr);
}
}
-
diff --git a/src/USER-OMP/dihedral_cosine_shift_exp_omp.h b/src/USER-OMP/dihedral_cosine_shift_exp_omp.h
index 502c2c01e90b2cff663a640a7c62e6db47bcbbb6..7e1accebf1ab130f38275172169b95d37449d717 100644
--- a/src/USER-OMP/dihedral_cosine_shift_exp_omp.h
+++ b/src/USER-OMP/dihedral_cosine_shift_exp_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/dihedral_harmonic_omp.cpp b/src/USER-OMP/dihedral_harmonic_omp.cpp
index 2f5dfb01fd593378d360156c4ff7d54264bfff1b..11023ee36cee14db5a582c0d488279e5516746e0 100644
--- a/src/USER-OMP/dihedral_harmonic_omp.cpp
+++ b/src/USER-OMP/dihedral_harmonic_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -34,7 +34,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
DihedralHarmonicOMP::DihedralHarmonicOMP(class LAMMPS *lmp)
- : DihedralHarmonic(lmp), ThrOMP(lmp,THR_DIHEDRAL)
+ : DihedralHarmonic(lmp), ThrOMP(lmp,THR_DIHEDRAL)
{
suffix_flag |= Suffix::OMP;
}
@@ -64,11 +64,11 @@ void DihedralHarmonicOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_bond) eval<0,0,1>(ifrom, ito, thr);
@@ -82,13 +82,13 @@ void DihedralHarmonicOMP::compute(int eflag, int vflag)
template <int EVFLAG, int EFLAG, int NEWTON_BOND>
void DihedralHarmonicOMP::eval(int nfrom, int nto, ThrData * const thr)
{
-
+
int i1,i2,i3,i4,i,m,n,type;
double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm;
double edihedral,f1[3],f2[3],f3[3],f4[3];
double ax,ay,az,bx,by,bz,rasq,rbsq,rgsq,rg,rginv,ra2inv,rb2inv,rabinv;
double df,df1,ddf1,fg,hg,fga,hgb,gaa,gbb;
- double dtfx,dtfy,dtfz,dtgx,dtgy,dtgz,dthx,dthy,dthz;
+ double dtfx,dtfy,dtfz,dtgx,dtgy,dtgz,dthx,dthy,dthz;
double c,s,p,sx2,sy2,sz2;
edihedral = 0.0;
@@ -130,7 +130,7 @@ void DihedralHarmonicOMP::eval(int nfrom, int nto, ThrData * const thr)
vb3y = x[i4][1] - x[i3][1];
vb3z = x[i4][2] - x[i3][2];
domain->minimum_image(vb3x,vb3y,vb3z);
-
+
// c,s calculation
ax = vb1y*vb2zm - vb1z*vb2ym;
@@ -144,7 +144,7 @@ void DihedralHarmonicOMP::eval(int nfrom, int nto, ThrData * const thr)
rbsq = bx*bx + by*by + bz*bz;
rgsq = vb2xm*vb2xm + vb2ym*vb2ym + vb2zm*vb2zm;
rg = sqrt(rgsq);
-
+
rginv = ra2inv = rb2inv = 0.0;
if (rg > 0) rginv = 1.0/rg;
if (rasq > 0) ra2inv = 1.0/rasq;
@@ -160,29 +160,29 @@ void DihedralHarmonicOMP::eval(int nfrom, int nto, ThrData * const thr)
int me = comm->me;
if (screen) {
- char str[128];
- sprintf(str,"Dihedral problem: %d/%d " BIGINT_FORMAT " %d %d %d %d",
- me,thr->get_tid(),update->ntimestep,
- atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
- error->warning(FLERR,str,0);
- fprintf(screen," 1st atom: %d %g %g %g\n",
- me,x[i1][0],x[i1][1],x[i1][2]);
- fprintf(screen," 2nd atom: %d %g %g %g\n",
- me,x[i2][0],x[i2][1],x[i2][2]);
- fprintf(screen," 3rd atom: %d %g %g %g\n",
- me,x[i3][0],x[i3][1],x[i3][2]);
- fprintf(screen," 4th atom: %d %g %g %g\n",
- me,x[i4][0],x[i4][1],x[i4][2]);
+ char str[128];
+ sprintf(str,"Dihedral problem: %d/%d " BIGINT_FORMAT " %d %d %d %d",
+ me,thr->get_tid(),update->ntimestep,
+ atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
+ error->warning(FLERR,str,0);
+ fprintf(screen," 1st atom: %d %g %g %g\n",
+ me,x[i1][0],x[i1][1],x[i1][2]);
+ fprintf(screen," 2nd atom: %d %g %g %g\n",
+ me,x[i2][0],x[i2][1],x[i2][2]);
+ fprintf(screen," 3rd atom: %d %g %g %g\n",
+ me,x[i3][0],x[i3][1],x[i3][2]);
+ fprintf(screen," 4th atom: %d %g %g %g\n",
+ me,x[i4][0],x[i4][1],x[i4][2]);
}
}
-
+
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
-
+
m = multiplicity[type];
p = 1.0;
ddf1 = df1 = 0.0;
-
+
for (i = 0; i < m; i++) {
ddf1 = p*c - df1*s;
df1 = p*s + df1*c;
@@ -193,21 +193,21 @@ void DihedralHarmonicOMP::eval(int nfrom, int nto, ThrData * const thr)
df1 = df1*cos_shift[type] - ddf1*sin_shift[type];
df1 *= -m;
p += 1.0;
-
+
if (m == 0) {
p = 1.0 + cos_shift[type];
df1 = 0.0;
}
- if (EFLAG) edihedral = k[type] * p;
-
+ if (EFLAG) edihedral = k[type] * p;
+
fg = vb1x*vb2xm + vb1y*vb2ym + vb1z*vb2zm;
hg = vb3x*vb2xm + vb3y*vb2ym + vb3z*vb2zm;
fga = fg*ra2inv*rginv;
hgb = hg*rb2inv*rginv;
gaa = -ra2inv*rg;
gbb = rb2inv*rg;
-
+
dtfx = gaa*ax;
dtfy = gaa*ay;
dtfz = gaa*az;
@@ -217,9 +217,9 @@ void DihedralHarmonicOMP::eval(int nfrom, int nto, ThrData * const thr)
dthx = gbb*bx;
dthy = gbb*by;
dthz = gbb*bz;
-
+
df = -k[type] * df1;
-
+
sx2 = df*dtgx;
sy2 = df*dtgy;
sz2 = df*dtgz;
@@ -239,7 +239,7 @@ void DihedralHarmonicOMP::eval(int nfrom, int nto, ThrData * const thr)
f3[0] = -sx2 - f4[0];
f3[1] = -sy2 - f4[1];
f3[2] = -sz2 - f4[2];
-
+
// apply force to each of 4 atoms
if (NEWTON_BOND || i1 < nlocal) {
@@ -268,6 +268,6 @@ void DihedralHarmonicOMP::eval(int nfrom, int nto, ThrData * const thr)
if (EVFLAG)
ev_tally_thr(this,i1,i2,i3,i4,nlocal,NEWTON_BOND,edihedral,f1,f3,f4,
- vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,thr);
+ vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,thr);
}
}
diff --git a/src/USER-OMP/dihedral_harmonic_omp.h b/src/USER-OMP/dihedral_harmonic_omp.h
index 744054ae43e37c341c3c75539ed24bd54eab19ab..b55bf015f2cc105c5f6b19331636160630c993f3 100644
--- a/src/USER-OMP/dihedral_harmonic_omp.h
+++ b/src/USER-OMP/dihedral_harmonic_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/dihedral_helix_omp.cpp b/src/USER-OMP/dihedral_helix_omp.cpp
index dc9673699d588745e2597f999a908148f665b52b..a869367bdbd5ba0ee24b2625cb66d7d9f48b91f6 100644
--- a/src/USER-OMP/dihedral_helix_omp.cpp
+++ b/src/USER-OMP/dihedral_helix_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -67,11 +67,11 @@ void DihedralHelixOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_bond) eval<0,0,1>(ifrom, ito, thr);
@@ -85,7 +85,7 @@ void DihedralHelixOMP::compute(int eflag, int vflag)
template <int EVFLAG, int EFLAG, int NEWTON_BOND>
void DihedralHelixOMP::eval(int nfrom, int nto, ThrData * const thr)
{
-
+
int i1,i2,i3,i4,n,type;
double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm;
double edihedral,f1[3],f2[3],f3[3],f4[3];
@@ -134,7 +134,7 @@ void DihedralHelixOMP::eval(int nfrom, int nto, ThrData * const thr)
vb3y = x[i4][1] - x[i3][1];
vb3z = x[i4][2] - x[i3][2];
domain->minimum_image(vb3x,vb3y,vb3z);
-
+
// c0 calculation
sb1 = 1.0 / (vb1x*vb1x + vb1y*vb1y + vb1z*vb1z);
@@ -192,19 +192,19 @@ void DihedralHelixOMP::eval(int nfrom, int nto, ThrData * const thr)
int me = comm->me;
if (screen) {
- char str[128];
- sprintf(str,"Dihedral problem: %d/%d " BIGINT_FORMAT " %d %d %d %d",
- me,thr->get_tid(),update->ntimestep,
- atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
- error->warning(FLERR,str,0);
- fprintf(screen," 1st atom: %d %g %g %g\n",
- me,x[i1][0],x[i1][1],x[i1][2]);
- fprintf(screen," 2nd atom: %d %g %g %g\n",
- me,x[i2][0],x[i2][1],x[i2][2]);
- fprintf(screen," 3rd atom: %d %g %g %g\n",
- me,x[i3][0],x[i3][1],x[i3][2]);
- fprintf(screen," 4th atom: %d %g %g %g\n",
- me,x[i4][0],x[i4][1],x[i4][2]);
+ char str[128];
+ sprintf(str,"Dihedral problem: %d/%d " BIGINT_FORMAT " %d %d %d %d",
+ me,thr->get_tid(),update->ntimestep,
+ atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
+ error->warning(FLERR,str,0);
+ fprintf(screen," 1st atom: %d %g %g %g\n",
+ me,x[i1][0],x[i1][1],x[i1][2]);
+ fprintf(screen," 2nd atom: %d %g %g %g\n",
+ me,x[i2][0],x[i2][1],x[i2][2]);
+ fprintf(screen," 3rd atom: %d %g %g %g\n",
+ me,x[i3][0],x[i3][1],x[i3][2]);
+ fprintf(screen," 4th atom: %d %g %g %g\n",
+ me,x[i4][0],x[i4][1],x[i4][2]);
}
}
@@ -221,7 +221,7 @@ void DihedralHelixOMP::eval(int nfrom, int nto, ThrData * const thr)
cphi[type]*sin(phi + MY_PI4)*siinv;
if (EFLAG) edihedral = aphi[type]*(1.0 - c) + bphi[type]*(1.0 + cos(3.0*phi)) +
- cphi[type]*(1.0 + cos(phi + MY_PI4));
+ cphi[type]*(1.0 + cos(phi + MY_PI4));
a = pd;
c = c * a;
@@ -281,6 +281,6 @@ void DihedralHelixOMP::eval(int nfrom, int nto, ThrData * const thr)
if (EVFLAG)
ev_tally_thr(this,i1,i2,i3,i4,nlocal,NEWTON_BOND,edihedral,f1,f3,f4,
- vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,thr);
+ vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,thr);
}
}
diff --git a/src/USER-OMP/dihedral_helix_omp.h b/src/USER-OMP/dihedral_helix_omp.h
index de3d5b8f30aa93282df51a9eeb0f5eaf46865bc3..24f16c4d7e8fa0a80890b298f9683e9c9e63cba0 100644
--- a/src/USER-OMP/dihedral_helix_omp.h
+++ b/src/USER-OMP/dihedral_helix_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/dihedral_multi_harmonic_omp.cpp b/src/USER-OMP/dihedral_multi_harmonic_omp.cpp
index decc12e75a6a437b5ad574aed0d3b2b7aa8d0d5a..a40bdba955ab833e170ffe8b6381955179bb2c30 100644
--- a/src/USER-OMP/dihedral_multi_harmonic_omp.cpp
+++ b/src/USER-OMP/dihedral_multi_harmonic_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -64,11 +64,11 @@ void DihedralMultiHarmonicOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_bond) eval<0,0,1>(ifrom, ito, thr);
@@ -82,7 +82,7 @@ void DihedralMultiHarmonicOMP::compute(int eflag, int vflag)
template <int EVFLAG, int EFLAG, int NEWTON_BOND>
void DihedralMultiHarmonicOMP::eval(int nfrom, int nto, ThrData * const thr)
{
-
+
int i1,i2,i3,i4,n,type;
double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm;
double edihedral,f1[3],f2[3],f3[3],f4[3];
@@ -131,20 +131,20 @@ void DihedralMultiHarmonicOMP::eval(int nfrom, int nto, ThrData * const thr)
vb3y = x[i4][1] - x[i3][1];
vb3z = x[i4][2] - x[i3][2];
domain->minimum_image(vb3x,vb3y,vb3z);
-
+
// c0 calculation
-
+
sb1 = 1.0 / (vb1x*vb1x + vb1y*vb1y + vb1z*vb1z);
sb2 = 1.0 / (vb2x*vb2x + vb2y*vb2y + vb2z*vb2z);
sb3 = 1.0 / (vb3x*vb3x + vb3y*vb3y + vb3z*vb3z);
-
+
rb1 = sqrt(sb1);
rb3 = sqrt(sb3);
-
+
c0 = (vb1x*vb3x + vb1y*vb3y + vb1z*vb3z) * rb1*rb3;
// 1st and 2nd angle
-
+
b1mag2 = vb1x*vb1x + vb1y*vb1y + vb1z*vb1z;
b1mag = sqrt(b1mag2);
b2mag2 = vb2x*vb2x + vb2y*vb2y + vb2z*vb2z;
@@ -182,22 +182,22 @@ void DihedralMultiHarmonicOMP::eval(int nfrom, int nto, ThrData * const thr)
if (c > 1.0 + TOLERANCE || c < (-1.0 - TOLERANCE)) {
int me = comm->me;
if (screen) {
- char str[128];
- sprintf(str,"Dihedral problem: %d/%d " BIGINT_FORMAT " %d %d %d %d",
- me,thr->get_tid(),update->ntimestep,
- atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
- error->warning(FLERR,str,0);
- fprintf(screen," 1st atom: %d %g %g %g\n",
- me,x[i1][0],x[i1][1],x[i1][2]);
- fprintf(screen," 2nd atom: %d %g %g %g\n",
- me,x[i2][0],x[i2][1],x[i2][2]);
- fprintf(screen," 3rd atom: %d %g %g %g\n",
- me,x[i3][0],x[i3][1],x[i3][2]);
- fprintf(screen," 4th atom: %d %g %g %g\n",
- me,x[i4][0],x[i4][1],x[i4][2]);
+ char str[128];
+ sprintf(str,"Dihedral problem: %d/%d " BIGINT_FORMAT " %d %d %d %d",
+ me,thr->get_tid(),update->ntimestep,
+ atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
+ error->warning(FLERR,str,0);
+ fprintf(screen," 1st atom: %d %g %g %g\n",
+ me,x[i1][0],x[i1][1],x[i1][2]);
+ fprintf(screen," 2nd atom: %d %g %g %g\n",
+ me,x[i2][0],x[i2][1],x[i2][2]);
+ fprintf(screen," 3rd atom: %d %g %g %g\n",
+ me,x[i3][0],x[i3][1],x[i3][2]);
+ fprintf(screen," 4th atom: %d %g %g %g\n",
+ me,x[i4][0],x[i4][1],x[i4][2]);
}
}
-
+
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
@@ -207,7 +207,7 @@ void DihedralMultiHarmonicOMP::eval(int nfrom, int nto, ThrData * const thr)
pd = a2[type] + c*(2.0*a3[type] + c*(3.0*a4[type] + c*4.0*a5[type]));
- if (EFLAG)
+ if (EFLAG)
edihedral = a1[type] + c*(a2[type] + c*(a3[type] + c*(a4[type] + c*a5[type])));
a = pd;
@@ -268,6 +268,6 @@ void DihedralMultiHarmonicOMP::eval(int nfrom, int nto, ThrData * const thr)
if (EVFLAG)
ev_tally_thr(this,i1,i2,i3,i4,nlocal,NEWTON_BOND,edihedral,f1,f3,f4,
- vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,thr);
+ vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,thr);
}
}
diff --git a/src/USER-OMP/dihedral_multi_harmonic_omp.h b/src/USER-OMP/dihedral_multi_harmonic_omp.h
index 73e34a49e55f61588e1c323d1243b94cf410da26..c6b80237a5872bd843fa545c80c6e47fda2582ad 100644
--- a/src/USER-OMP/dihedral_multi_harmonic_omp.h
+++ b/src/USER-OMP/dihedral_multi_harmonic_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/dihedral_opls_omp.cpp b/src/USER-OMP/dihedral_opls_omp.cpp
index 5beee8a8cb9ca200f537ca7104b9d22b5bc370e6..30b805611b0e8738c2864cd5bbc0cff090ec27ad 100644
--- a/src/USER-OMP/dihedral_opls_omp.cpp
+++ b/src/USER-OMP/dihedral_opls_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -65,11 +65,11 @@ void DihedralOPLSOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_bond) eval<0,0,1>(ifrom, ito, thr);
@@ -83,7 +83,7 @@ void DihedralOPLSOMP::compute(int eflag, int vflag)
template <int EVFLAG, int EFLAG, int NEWTON_BOND>
void DihedralOPLSOMP::eval(int nfrom, int nto, ThrData * const thr)
{
-
+
int i1,i2,i3,i4,n,type;
double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm;
double edihedral,f1[3],f2[3],f3[3],f4[3];
@@ -132,7 +132,7 @@ void DihedralOPLSOMP::eval(int nfrom, int nto, ThrData * const thr)
vb3y = x[i4][1] - x[i3][1];
vb3z = x[i4][2] - x[i3][2];
domain->minimum_image(vb3x,vb3y,vb3z);
-
+
// c0 calculation
sb1 = 1.0 / (vb1x*vb1x + vb1y*vb1y + vb1z*vb1z);
@@ -190,19 +190,19 @@ void DihedralOPLSOMP::eval(int nfrom, int nto, ThrData * const thr)
int me = comm->me;
if (screen) {
- char str[128];
- sprintf(str,"Dihedral problem: %d/%d " BIGINT_FORMAT " %d %d %d %d",
- me,thr->get_tid(),update->ntimestep,
- atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
- error->warning(FLERR,str,0);
- fprintf(screen," 1st atom: %d %g %g %g\n",
- me,x[i1][0],x[i1][1],x[i1][2]);
- fprintf(screen," 2nd atom: %d %g %g %g\n",
- me,x[i2][0],x[i2][1],x[i2][2]);
- fprintf(screen," 3rd atom: %d %g %g %g\n",
- me,x[i3][0],x[i3][1],x[i3][2]);
- fprintf(screen," 4th atom: %d %g %g %g\n",
- me,x[i4][0],x[i4][1],x[i4][2]);
+ char str[128];
+ sprintf(str,"Dihedral problem: %d/%d " BIGINT_FORMAT " %d %d %d %d",
+ me,thr->get_tid(),update->ntimestep,
+ atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
+ error->warning(FLERR,str,0);
+ fprintf(screen," 1st atom: %d %g %g %g\n",
+ me,x[i1][0],x[i1][1],x[i1][2]);
+ fprintf(screen," 2nd atom: %d %g %g %g\n",
+ me,x[i2][0],x[i2][1],x[i2][2]);
+ fprintf(screen," 3rd atom: %d %g %g %g\n",
+ me,x[i3][0],x[i3][1],x[i3][2]);
+ fprintf(screen," 4th atom: %d %g %g %g\n",
+ me,x[i4][0],x[i4][1],x[i4][2]);
}
}
@@ -219,7 +219,7 @@ void DihedralOPLSOMP::eval(int nfrom, int nto, ThrData * const thr)
if (fabs(si) < SMALLER) si = SMALLER;
siinv = 1.0/si;
- pd = k1[type] - 2.0*k2[type]*sin(2.0*phi)*siinv +
+ pd = k1[type] - 2.0*k2[type]*sin(2.0*phi)*siinv +
3.0*k3[type]*sin(3.0*phi)*siinv - 4.0*k4[type]*sin(4.0*phi)*siinv;
if (EFLAG) edihedral = k1[type]*(1.0 + c) + k2[type]*(1.0 - cos(2.0*phi))
@@ -284,7 +284,6 @@ void DihedralOPLSOMP::eval(int nfrom, int nto, ThrData * const thr)
if (EVFLAG)
ev_tally_thr(this,i1,i2,i3,i4,nlocal,NEWTON_BOND,edihedral,f1,f3,f4,
- vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,thr);
+ vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,thr);
}
}
-
diff --git a/src/USER-OMP/dihedral_opls_omp.h b/src/USER-OMP/dihedral_opls_omp.h
index 4092ab167e7a9eb049a555533d63edbb5618d2e8..fbb5455f9ca8224ba1bc9964b5ee6a4b73933d79 100644
--- a/src/USER-OMP/dihedral_opls_omp.h
+++ b/src/USER-OMP/dihedral_opls_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/dihedral_table_omp.cpp b/src/USER-OMP/dihedral_table_omp.cpp
index c2ed9d63b8245c23fad6c57b8454226efccb54de..55f5ffd97bcc12a24f813e16cd01db33960e12eb 100644
--- a/src/USER-OMP/dihedral_table_omp.cpp
+++ b/src/USER-OMP/dihedral_table_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -64,11 +64,11 @@ void DihedralTableOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_bond) eval<0,0,1>(ifrom, ito, thr);
@@ -93,19 +93,19 @@ void DihedralTableOMP::eval(int nfrom, int nto, ThrData * const thr)
// The dihedral angle "phi" is the angle between n123 and n234
// the planes defined by atoms i1,i2,i3, and i2,i3,i4.
//
- // Definitions of vectors: vb12, vb23, vb34, perp12on23
+ // Definitions of vectors: vb12, vb23, vb34, perp12on23
// proj12on23, perp43on32, proj43on32
//
// Note: The positions of the 4 atoms are labeled x[i1], x[i2], x[i3], x[i4]
// (which are also vectors)
//
- // proj12on23 proj34on23
- // ---------> ----------->
- // .
- // .
- // .
- // x[i2] . x[i3]
- // . __@----------vb23-------->@ . . . . .
+ // proj12on23 proj34on23
+ // ---------> ----------->
+ // .
+ // .
+ // .
+ // x[i2] . x[i3]
+ // . __@----------vb23-------->@ . . . . .
// /|\ /| \ |
// | / \ |
// | / \ |
@@ -118,9 +118,9 @@ void DihedralTableOMP::eval(int nfrom, int nto, ThrData * const thr)
// | / \ |
// @ \ |
// _\| \|/
- // x[i1] @
- //
- // x[i4]
+ // x[i1] @
+ //
+ // x[i4]
//
double vb12[g_dim]; // displacement vector from atom i1 towards atom i2
@@ -158,11 +158,11 @@ void DihedralTableOMP::eval(int nfrom, int nto, ThrData * const thr)
//
// Phi() calculates the dihedral angle.
- // This function also calculates the vectors:
+ // This function also calculates the vectors:
// vb12, vb23, vb34, n123, and n234, which we will need later.
- double phi = Phi(x[i1], x[i2], x[i3], x[i4], domain,
+ double phi = Phi(x[i1], x[i2], x[i3], x[i4], domain,
vb12, vb23, vb34, n123, n234);
@@ -170,7 +170,7 @@ void DihedralTableOMP::eval(int nfrom, int nto, ThrData * const thr)
//
// Gradient variables:
//
- // dphi_dx1, dphi_dx2, dphi_dx3, dphi_dx4 are the gradients of phi with
+ // dphi_dx1, dphi_dx2, dphi_dx3, dphi_dx4 are the gradients of phi with
// respect to the atomic positions of atoms i1, i2, i3, i4, respectively.
// As an example, consider dphi_dx1. The d'th element is:
double dphi_dx1[g_dim]; // d phi
@@ -222,8 +222,8 @@ void DihedralTableOMP::eval(int nfrom, int nto, ThrData * const thr)
// --- Compute the gradient vectors dphi/dx2 and dphi/dx3: ---
//
- // This is more tricky because atoms 2 and 3 are shared by both planes
- // 123 and 234 (the angle between which defines "phi"). Moving either
+ // This is more tricky because atoms 2 and 3 are shared by both planes
+ // 123 and 234 (the angle between which defines "phi"). Moving either
// one of these atoms effects both the 123 and 234 planes
// Both the 123 and 234 planes intersect with the plane perpendicular to the
// central bond axis (vb23). The two lines where these intersections occur
@@ -256,9 +256,9 @@ void DihedralTableOMP::eval(int nfrom, int nto, ThrData * const thr)
for (int d=0; d < g_dim; ++d) {
// Recall that the n123 and n234 plane normal vectors are proportional to
- // the dphi/dx1 and dphi/dx2 gradients vectors
+ // the dphi/dx1 and dphi/dx2 gradients vectors
// It turns out we can save slightly more CPU cycles by expressing
- // dphi/dx2 and dphi/dx3 as linear combinations of dphi/dx1 and dphi/dx2
+ // dphi/dx2 and dphi/dx3 as linear combinations of dphi/dx1 and dphi/dx2
// which we computed already (instead of n123 & n234).
dphi_dx2[d] = dphi123_dx2_coef*dphi_dx1[d] + dphi234_dx2_coef*dphi_dx4[d];
dphi_dx3[d] = dphi123_dx3_coef*dphi_dx1[d] + dphi234_dx3_coef*dphi_dx4[d];
@@ -273,7 +273,7 @@ void DihedralTableOMP::eval(int nfrom, int nto, ThrData * const thr)
cerr << " -- testing gradient for dihedral (n="<<n<<") for atoms ("
<< i1 << "," << i2 << "," << i3 << "," << i4 << ") --" << endl;
- PrintGradientComparison(*this, dphi_dx1, dphi_dx2, dphi_dx3, dphi_dx4,
+ PrintGradientComparison(*this, dphi_dx1, dphi_dx2, dphi_dx3, dphi_dx4,
domain, x[i1], x[i2], x[i3], x[i4]);
for (int d=0; d < g_dim; ++d) {
@@ -339,7 +339,7 @@ void DihedralTableOMP::eval(int nfrom, int nto, ThrData * const thr)
if (EVFLAG)
ev_tally_thr(this,i1,i2,i3,i4,nlocal,NEWTON_BOND,edihedral,f1,f3,f4,
- vb12[0],vb12[1],vb12[2],vb23[0],vb23[1],vb23[2],vb34[0],
- vb34[1],vb34[2],thr);
+ vb12[0],vb12[1],vb12[2],vb23[0],vb23[1],vb23[2],vb34[0],
+ vb34[1],vb34[2],thr);
}
}
diff --git a/src/USER-OMP/dihedral_table_omp.h b/src/USER-OMP/dihedral_table_omp.h
index 638834b104cad099bf477031ac988f7076c65b43..fadb57ed1d778a7725763b5a5f39523bce69db38 100644
--- a/src/USER-OMP/dihedral_table_omp.h
+++ b/src/USER-OMP/dihedral_table_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/ewald_omp.cpp b/src/USER-OMP/ewald_omp.cpp
index 1461ea4ad68f7f885552838b4cc326e3320ea874..93b61af186ca645752661abcd3e44e6595319c1a 100644
--- a/src/USER-OMP/ewald_omp.cpp
+++ b/src/USER-OMP/ewald_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -34,7 +34,7 @@ using namespace MathConst;
/* ---------------------------------------------------------------------- */
-EwaldOMP::EwaldOMP(LAMMPS *lmp, int narg, char **arg)
+EwaldOMP::EwaldOMP(LAMMPS *lmp, int narg, char **arg)
: Ewald(lmp, narg, arg), ThrOMP(lmp, THR_KSPACE)
{
suffix_flag |= Suffix::OMP;
@@ -54,7 +54,7 @@ void EwaldOMP::allocate()
}
/* ----------------------------------------------------------------------
- compute the Ewald long-range force, energy, virial
+ compute the Ewald long-range force, energy, virial
------------------------------------------------------------------------- */
void EwaldOMP::compute(int eflag, int vflag)
@@ -123,22 +123,22 @@ void EwaldOMP::compute(int eflag, int vflag)
kz = kzvecs[k];
for (i = ifrom; i < ito; i++) {
- cypz = cs[ky][1][i]*cs[kz][2][i] - sn[ky][1][i]*sn[kz][2][i];
- sypz = sn[ky][1][i]*cs[kz][2][i] + cs[ky][1][i]*sn[kz][2][i];
- exprl = cs[kx][0][i]*cypz - sn[kx][0][i]*sypz;
- expim = sn[kx][0][i]*cypz + cs[kx][0][i]*sypz;
- partial = expim*sfacrl_all[k] - exprl*sfacim_all[k];
- ek[i][0] += partial*eg[k][0];
- ek[i][1] += partial*eg[k][1];
- ek[i][2] += partial*eg[k][2];
-
- if (evflag_atom) {
- const double partial_peratom = exprl*sfacrl_all[k] + expim*sfacim_all[k];
- if (eflag_atom) eatom[i] += q[i]*ug[k]*partial_peratom;
- if (vflag_atom)
- for (j = 0; j < 6; j++)
- vatom[i][j] += ug[k]*vg[k][j]*partial_peratom;
- }
+ cypz = cs[ky][1][i]*cs[kz][2][i] - sn[ky][1][i]*sn[kz][2][i];
+ sypz = sn[ky][1][i]*cs[kz][2][i] + cs[ky][1][i]*sn[kz][2][i];
+ exprl = cs[kx][0][i]*cypz - sn[kx][0][i]*sypz;
+ expim = sn[kx][0][i]*cypz + cs[kx][0][i]*sypz;
+ partial = expim*sfacrl_all[k] - exprl*sfacim_all[k];
+ ek[i][0] += partial*eg[k][0];
+ ek[i][1] += partial*eg[k][1];
+ ek[i][2] += partial*eg[k][2];
+
+ if (evflag_atom) {
+ const double partial_peratom = exprl*sfacrl_all[k] + expim*sfacim_all[k];
+ if (eflag_atom) eatom[i] += q[i]*ug[k]*partial_peratom;
+ if (vflag_atom)
+ for (j = 0; j < 6; j++)
+ vatom[i][j] += ug[k]*vg[k][j]*partial_peratom;
+ }
}
}
@@ -150,7 +150,7 @@ void EwaldOMP::compute(int eflag, int vflag)
f[i][1] += fac*ek[i][1];
f[i][2] += fac*ek[i][2];
}
-
+
// global energy
if (eflag_global) {
@@ -158,8 +158,8 @@ void EwaldOMP::compute(int eflag, int vflag)
#pragma omp for private(k)
#endif
for (k = 0; k < kcount; k++)
- eng_tmp += ug[k] * (sfacrl_all[k]*sfacrl_all[k] +
- sfacim_all[k]*sfacim_all[k]);
+ eng_tmp += ug[k] * (sfacrl_all[k]*sfacrl_all[k] +
+ sfacim_all[k]*sfacim_all[k]);
}
// global virial
@@ -169,13 +169,13 @@ void EwaldOMP::compute(int eflag, int vflag)
#pragma omp for private(k)
#endif
for (k = 0; k < kcount; k++) {
- double uk = ug[k] * (sfacrl_all[k]*sfacrl_all[k] + sfacim_all[k]*sfacim_all[k]);
- v0 += uk*vg[k][0];
- v1 += uk*vg[k][1];
- v2 += uk*vg[k][2];
- v3 += uk*vg[k][3];
- v4 += uk*vg[k][4];
- v5 += uk*vg[k][5];
+ double uk = ug[k] * (sfacrl_all[k]*sfacrl_all[k] + sfacim_all[k]*sfacim_all[k]);
+ v0 += uk*vg[k][0];
+ v1 += uk*vg[k][1];
+ v2 += uk*vg[k][2];
+ v3 += uk*vg[k][3];
+ v4 += uk*vg[k][4];
+ v5 += uk*vg[k][5];
}
}
@@ -184,16 +184,16 @@ void EwaldOMP::compute(int eflag, int vflag)
if (evflag_atom) {
if (eflag_atom) {
- for (i = ifrom; i < ito; i++) {
- eatom[i] -= g_ewald*q[i]*q[i]/MY_PIS + MY_PI2*q[i]*qsum /
- (g_ewald*g_ewald*volume);
- eatom[i] *= qscale;
- }
+ for (i = ifrom; i < ito; i++) {
+ eatom[i] -= g_ewald*q[i]*q[i]/MY_PIS + MY_PI2*q[i]*qsum /
+ (g_ewald*g_ewald*volume);
+ eatom[i] *= qscale;
+ }
}
if (vflag_atom)
- for (i = ifrom; i < ito; i++)
- for (j = 0; j < 6; j++) vatom[i][j] *= q[i]*qscale;
+ for (i = ifrom; i < ito; i++)
+ for (j = 0; j < 6; j++) vatom[i][j] *= q[i]*qscale;
}
reduce_thr(this, eflag,vflag,thr);
@@ -233,9 +233,9 @@ void EwaldOMP::eik_dot_r()
int i,ifrom,ito,k,l,m,n,ic,tid;
double cstr1,sstr1,cstr2,sstr2,cstr3,sstr3,cstr4,sstr4;
double sqk,clpm,slpm;
-
+
loop_setup_thr(ifrom, ito, tid, nlocal, nthreads);
-
+
double * const sfacrl_thr = sfacrl + tid*kmax3d;
double * const sfacim_thr = sfacim + tid*kmax3d;
@@ -246,42 +246,42 @@ void EwaldOMP::eik_dot_r()
for (ic = 0; ic < 3; ic++) {
sqk = unitk[ic]*unitk[ic];
if (sqk <= gsqmx) {
- cstr1 = 0.0;
- sstr1 = 0.0;
- for (i = ifrom; i < ito; i++) {
- cs[0][ic][i] = 1.0;
- sn[0][ic][i] = 0.0;
- cs[1][ic][i] = cos(unitk[ic]*x[i][ic]);
- sn[1][ic][i] = sin(unitk[ic]*x[i][ic]);
- cs[-1][ic][i] = cs[1][ic][i];
- sn[-1][ic][i] = -sn[1][ic][i];
- cstr1 += q[i]*cs[1][ic][i];
- sstr1 += q[i]*sn[1][ic][i];
- }
- sfacrl_thr[n] = cstr1;
- sfacim_thr[n++] = sstr1;
+ cstr1 = 0.0;
+ sstr1 = 0.0;
+ for (i = ifrom; i < ito; i++) {
+ cs[0][ic][i] = 1.0;
+ sn[0][ic][i] = 0.0;
+ cs[1][ic][i] = cos(unitk[ic]*x[i][ic]);
+ sn[1][ic][i] = sin(unitk[ic]*x[i][ic]);
+ cs[-1][ic][i] = cs[1][ic][i];
+ sn[-1][ic][i] = -sn[1][ic][i];
+ cstr1 += q[i]*cs[1][ic][i];
+ sstr1 += q[i]*sn[1][ic][i];
+ }
+ sfacrl_thr[n] = cstr1;
+ sfacim_thr[n++] = sstr1;
}
}
for (m = 2; m <= kmax; m++) {
for (ic = 0; ic < 3; ic++) {
- sqk = m*unitk[ic] * m*unitk[ic];
- if (sqk <= gsqmx) {
- cstr1 = 0.0;
- sstr1 = 0.0;
- for (i = ifrom; i < ito; i++) {
- cs[m][ic][i] = cs[m-1][ic][i]*cs[1][ic][i] -
- sn[m-1][ic][i]*sn[1][ic][i];
- sn[m][ic][i] = sn[m-1][ic][i]*cs[1][ic][i] +
- cs[m-1][ic][i]*sn[1][ic][i];
- cs[-m][ic][i] = cs[m][ic][i];
- sn[-m][ic][i] = -sn[m][ic][i];
- cstr1 += q[i]*cs[m][ic][i];
- sstr1 += q[i]*sn[m][ic][i];
- }
- sfacrl_thr[n] = cstr1;
- sfacim_thr[n++] = sstr1;
- }
+ sqk = m*unitk[ic] * m*unitk[ic];
+ if (sqk <= gsqmx) {
+ cstr1 = 0.0;
+ sstr1 = 0.0;
+ for (i = ifrom; i < ito; i++) {
+ cs[m][ic][i] = cs[m-1][ic][i]*cs[1][ic][i] -
+ sn[m-1][ic][i]*sn[1][ic][i];
+ sn[m][ic][i] = sn[m-1][ic][i]*cs[1][ic][i] +
+ cs[m-1][ic][i]*sn[1][ic][i];
+ cs[-m][ic][i] = cs[m][ic][i];
+ sn[-m][ic][i] = -sn[m][ic][i];
+ cstr1 += q[i]*cs[m][ic][i];
+ sstr1 += q[i]*sn[m][ic][i];
+ }
+ sfacrl_thr[n] = cstr1;
+ sfacim_thr[n++] = sstr1;
+ }
}
}
@@ -289,23 +289,23 @@ void EwaldOMP::eik_dot_r()
for (k = 1; k <= kxmax; k++) {
for (l = 1; l <= kymax; l++) {
- sqk = (k*unitk[0] * k*unitk[0]) + (l*unitk[1] * l*unitk[1]);
- if (sqk <= gsqmx) {
- cstr1 = 0.0;
- sstr1 = 0.0;
- cstr2 = 0.0;
- sstr2 = 0.0;
- for (i = ifrom; i < ito; i++) {
- cstr1 += q[i]*(cs[k][0][i]*cs[l][1][i] - sn[k][0][i]*sn[l][1][i]);
- sstr1 += q[i]*(sn[k][0][i]*cs[l][1][i] + cs[k][0][i]*sn[l][1][i]);
- cstr2 += q[i]*(cs[k][0][i]*cs[l][1][i] + sn[k][0][i]*sn[l][1][i]);
- sstr2 += q[i]*(sn[k][0][i]*cs[l][1][i] - cs[k][0][i]*sn[l][1][i]);
- }
- sfacrl_thr[n] = cstr1;
- sfacim_thr[n++] = sstr1;
- sfacrl_thr[n] = cstr2;
- sfacim_thr[n++] = sstr2;
- }
+ sqk = (k*unitk[0] * k*unitk[0]) + (l*unitk[1] * l*unitk[1]);
+ if (sqk <= gsqmx) {
+ cstr1 = 0.0;
+ sstr1 = 0.0;
+ cstr2 = 0.0;
+ sstr2 = 0.0;
+ for (i = ifrom; i < ito; i++) {
+ cstr1 += q[i]*(cs[k][0][i]*cs[l][1][i] - sn[k][0][i]*sn[l][1][i]);
+ sstr1 += q[i]*(sn[k][0][i]*cs[l][1][i] + cs[k][0][i]*sn[l][1][i]);
+ cstr2 += q[i]*(cs[k][0][i]*cs[l][1][i] + sn[k][0][i]*sn[l][1][i]);
+ sstr2 += q[i]*(sn[k][0][i]*cs[l][1][i] - cs[k][0][i]*sn[l][1][i]);
+ }
+ sfacrl_thr[n] = cstr1;
+ sfacim_thr[n++] = sstr1;
+ sfacrl_thr[n] = cstr2;
+ sfacim_thr[n++] = sstr2;
+ }
}
}
@@ -313,23 +313,23 @@ void EwaldOMP::eik_dot_r()
for (l = 1; l <= kymax; l++) {
for (m = 1; m <= kzmax; m++) {
- sqk = (l*unitk[1] * l*unitk[1]) + (m*unitk[2] * m*unitk[2]);
- if (sqk <= gsqmx) {
- cstr1 = 0.0;
- sstr1 = 0.0;
- cstr2 = 0.0;
- sstr2 = 0.0;
- for (i = ifrom; i < ito; i++) {
- cstr1 += q[i]*(cs[l][1][i]*cs[m][2][i] - sn[l][1][i]*sn[m][2][i]);
- sstr1 += q[i]*(sn[l][1][i]*cs[m][2][i] + cs[l][1][i]*sn[m][2][i]);
- cstr2 += q[i]*(cs[l][1][i]*cs[m][2][i] + sn[l][1][i]*sn[m][2][i]);
- sstr2 += q[i]*(sn[l][1][i]*cs[m][2][i] - cs[l][1][i]*sn[m][2][i]);
- }
- sfacrl_thr[n] = cstr1;
- sfacim_thr[n++] = sstr1;
- sfacrl_thr[n] = cstr2;
- sfacim_thr[n++] = sstr2;
- }
+ sqk = (l*unitk[1] * l*unitk[1]) + (m*unitk[2] * m*unitk[2]);
+ if (sqk <= gsqmx) {
+ cstr1 = 0.0;
+ sstr1 = 0.0;
+ cstr2 = 0.0;
+ sstr2 = 0.0;
+ for (i = ifrom; i < ito; i++) {
+ cstr1 += q[i]*(cs[l][1][i]*cs[m][2][i] - sn[l][1][i]*sn[m][2][i]);
+ sstr1 += q[i]*(sn[l][1][i]*cs[m][2][i] + cs[l][1][i]*sn[m][2][i]);
+ cstr2 += q[i]*(cs[l][1][i]*cs[m][2][i] + sn[l][1][i]*sn[m][2][i]);
+ sstr2 += q[i]*(sn[l][1][i]*cs[m][2][i] - cs[l][1][i]*sn[m][2][i]);
+ }
+ sfacrl_thr[n] = cstr1;
+ sfacim_thr[n++] = sstr1;
+ sfacrl_thr[n] = cstr2;
+ sfacim_thr[n++] = sstr2;
+ }
}
}
@@ -337,23 +337,23 @@ void EwaldOMP::eik_dot_r()
for (k = 1; k <= kxmax; k++) {
for (m = 1; m <= kzmax; m++) {
- sqk = (k*unitk[0] * k*unitk[0]) + (m*unitk[2] * m*unitk[2]);
- if (sqk <= gsqmx) {
- cstr1 = 0.0;
- sstr1 = 0.0;
- cstr2 = 0.0;
- sstr2 = 0.0;
- for (i = ifrom; i < ito; i++) {
- cstr1 += q[i]*(cs[k][0][i]*cs[m][2][i] - sn[k][0][i]*sn[m][2][i]);
- sstr1 += q[i]*(sn[k][0][i]*cs[m][2][i] + cs[k][0][i]*sn[m][2][i]);
- cstr2 += q[i]*(cs[k][0][i]*cs[m][2][i] + sn[k][0][i]*sn[m][2][i]);
- sstr2 += q[i]*(sn[k][0][i]*cs[m][2][i] - cs[k][0][i]*sn[m][2][i]);
- }
- sfacrl_thr[n] = cstr1;
- sfacim_thr[n++] = sstr1;
- sfacrl_thr[n] = cstr2;
- sfacim_thr[n++] = sstr2;
- }
+ sqk = (k*unitk[0] * k*unitk[0]) + (m*unitk[2] * m*unitk[2]);
+ if (sqk <= gsqmx) {
+ cstr1 = 0.0;
+ sstr1 = 0.0;
+ cstr2 = 0.0;
+ sstr2 = 0.0;
+ for (i = ifrom; i < ito; i++) {
+ cstr1 += q[i]*(cs[k][0][i]*cs[m][2][i] - sn[k][0][i]*sn[m][2][i]);
+ sstr1 += q[i]*(sn[k][0][i]*cs[m][2][i] + cs[k][0][i]*sn[m][2][i]);
+ cstr2 += q[i]*(cs[k][0][i]*cs[m][2][i] + sn[k][0][i]*sn[m][2][i]);
+ sstr2 += q[i]*(sn[k][0][i]*cs[m][2][i] - cs[k][0][i]*sn[m][2][i]);
+ }
+ sfacrl_thr[n] = cstr1;
+ sfacim_thr[n++] = sstr1;
+ sfacrl_thr[n] = cstr2;
+ sfacim_thr[n++] = sstr2;
+ }
}
}
@@ -361,49 +361,49 @@ void EwaldOMP::eik_dot_r()
for (k = 1; k <= kxmax; k++) {
for (l = 1; l <= kymax; l++) {
- for (m = 1; m <= kzmax; m++) {
- sqk = (k*unitk[0] * k*unitk[0]) + (l*unitk[1] * l*unitk[1]) +
- (m*unitk[2] * m*unitk[2]);
- if (sqk <= gsqmx) {
- cstr1 = 0.0;
- sstr1 = 0.0;
- cstr2 = 0.0;
- sstr2 = 0.0;
- cstr3 = 0.0;
- sstr3 = 0.0;
- cstr4 = 0.0;
- sstr4 = 0.0;
- for (i = ifrom; i < ito; i++) {
- clpm = cs[l][1][i]*cs[m][2][i] - sn[l][1][i]*sn[m][2][i];
- slpm = sn[l][1][i]*cs[m][2][i] + cs[l][1][i]*sn[m][2][i];
- cstr1 += q[i]*(cs[k][0][i]*clpm - sn[k][0][i]*slpm);
- sstr1 += q[i]*(sn[k][0][i]*clpm + cs[k][0][i]*slpm);
-
- clpm = cs[l][1][i]*cs[m][2][i] + sn[l][1][i]*sn[m][2][i];
- slpm = -sn[l][1][i]*cs[m][2][i] + cs[l][1][i]*sn[m][2][i];
- cstr2 += q[i]*(cs[k][0][i]*clpm - sn[k][0][i]*slpm);
- sstr2 += q[i]*(sn[k][0][i]*clpm + cs[k][0][i]*slpm);
-
- clpm = cs[l][1][i]*cs[m][2][i] + sn[l][1][i]*sn[m][2][i];
- slpm = sn[l][1][i]*cs[m][2][i] - cs[l][1][i]*sn[m][2][i];
- cstr3 += q[i]*(cs[k][0][i]*clpm - sn[k][0][i]*slpm);
- sstr3 += q[i]*(sn[k][0][i]*clpm + cs[k][0][i]*slpm);
-
- clpm = cs[l][1][i]*cs[m][2][i] - sn[l][1][i]*sn[m][2][i];
- slpm = -sn[l][1][i]*cs[m][2][i] - cs[l][1][i]*sn[m][2][i];
- cstr4 += q[i]*(cs[k][0][i]*clpm - sn[k][0][i]*slpm);
- sstr4 += q[i]*(sn[k][0][i]*clpm + cs[k][0][i]*slpm);
- }
- sfacrl_thr[n] = cstr1;
- sfacim_thr[n++] = sstr1;
- sfacrl_thr[n] = cstr2;
- sfacim_thr[n++] = sstr2;
- sfacrl_thr[n] = cstr3;
- sfacim_thr[n++] = sstr3;
- sfacrl_thr[n] = cstr4;
- sfacim_thr[n++] = sstr4;
- }
- }
+ for (m = 1; m <= kzmax; m++) {
+ sqk = (k*unitk[0] * k*unitk[0]) + (l*unitk[1] * l*unitk[1]) +
+ (m*unitk[2] * m*unitk[2]);
+ if (sqk <= gsqmx) {
+ cstr1 = 0.0;
+ sstr1 = 0.0;
+ cstr2 = 0.0;
+ sstr2 = 0.0;
+ cstr3 = 0.0;
+ sstr3 = 0.0;
+ cstr4 = 0.0;
+ sstr4 = 0.0;
+ for (i = ifrom; i < ito; i++) {
+ clpm = cs[l][1][i]*cs[m][2][i] - sn[l][1][i]*sn[m][2][i];
+ slpm = sn[l][1][i]*cs[m][2][i] + cs[l][1][i]*sn[m][2][i];
+ cstr1 += q[i]*(cs[k][0][i]*clpm - sn[k][0][i]*slpm);
+ sstr1 += q[i]*(sn[k][0][i]*clpm + cs[k][0][i]*slpm);
+
+ clpm = cs[l][1][i]*cs[m][2][i] + sn[l][1][i]*sn[m][2][i];
+ slpm = -sn[l][1][i]*cs[m][2][i] + cs[l][1][i]*sn[m][2][i];
+ cstr2 += q[i]*(cs[k][0][i]*clpm - sn[k][0][i]*slpm);
+ sstr2 += q[i]*(sn[k][0][i]*clpm + cs[k][0][i]*slpm);
+
+ clpm = cs[l][1][i]*cs[m][2][i] + sn[l][1][i]*sn[m][2][i];
+ slpm = sn[l][1][i]*cs[m][2][i] - cs[l][1][i]*sn[m][2][i];
+ cstr3 += q[i]*(cs[k][0][i]*clpm - sn[k][0][i]*slpm);
+ sstr3 += q[i]*(sn[k][0][i]*clpm + cs[k][0][i]*slpm);
+
+ clpm = cs[l][1][i]*cs[m][2][i] - sn[l][1][i]*sn[m][2][i];
+ slpm = -sn[l][1][i]*cs[m][2][i] - cs[l][1][i]*sn[m][2][i];
+ cstr4 += q[i]*(cs[k][0][i]*clpm - sn[k][0][i]*slpm);
+ sstr4 += q[i]*(sn[k][0][i]*clpm + cs[k][0][i]*slpm);
+ }
+ sfacrl_thr[n] = cstr1;
+ sfacim_thr[n++] = sstr1;
+ sfacrl_thr[n] = cstr2;
+ sfacim_thr[n++] = sstr2;
+ sfacrl_thr[n] = cstr3;
+ sfacim_thr[n++] = sstr3;
+ sfacrl_thr[n] = cstr4;
+ sfacim_thr[n++] = sstr4;
+ }
+ }
}
}
diff --git a/src/USER-OMP/ewald_omp.h b/src/USER-OMP/ewald_omp.h
index 515a74ed35eef2a07a4769fadf15e008586399da..222806f15a227f4f3043ba69ae7ec7422a4064b9 100644
--- a/src/USER-OMP/ewald_omp.h
+++ b/src/USER-OMP/ewald_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/fix_gravity_omp.cpp b/src/USER-OMP/fix_gravity_omp.cpp
index 3b55d1e7faf4aa7a242aff71a899e0db4b91305a..fd32a00e5849e2c2d4480f0b0e996de6d24ad977 100644
--- a/src/USER-OMP/fix_gravity_omp.cpp
+++ b/src/USER-OMP/fix_gravity_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -82,11 +82,11 @@ void FixGravityOMP::post_force(int vflag)
#endif
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- massone = rmass[i];
- f[i][0] += massone*xacc_thr;
- f[i][1] += massone*yacc_thr;
- f[i][2] += massone*zacc_thr;
- grav -= massone * (xacc_thr*x[i][0] + yacc_thr*x[i][1] + zacc_thr*x[i][2]);
+ massone = rmass[i];
+ f[i][0] += massone*xacc_thr;
+ f[i][1] += massone*yacc_thr;
+ f[i][2] += massone*zacc_thr;
+ grav -= massone * (xacc_thr*x[i][0] + yacc_thr*x[i][1] + zacc_thr*x[i][2]);
}
} else {
#if defined(_OPENMP)
@@ -94,11 +94,11 @@ void FixGravityOMP::post_force(int vflag)
#endif
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- massone = mass[type[i]];
- f[i][0] += massone*xacc_thr;
- f[i][1] += massone*yacc_thr;
- f[i][2] += massone*zacc_thr;
- grav -= massone * (xacc_thr*x[i][0] + yacc_thr*x[i][1] + zacc_thr*x[i][2]);
+ massone = mass[type[i]];
+ f[i][0] += massone*xacc_thr;
+ f[i][1] += massone*yacc_thr;
+ f[i][2] += massone*zacc_thr;
+ grav -= massone * (xacc_thr*x[i][0] + yacc_thr*x[i][1] + zacc_thr*x[i][2]);
}
}
egrav = grav;
@@ -110,4 +110,3 @@ void FixGravityOMP::post_force_respa(int vflag, int ilevel, int iloop)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
}
-
diff --git a/src/USER-OMP/fix_gravity_omp.h b/src/USER-OMP/fix_gravity_omp.h
index dd0144410e624b17c5d93cb512a65668300c1118..ca104a1a9a9fd5a6bd4b1bfc94c35cdb476e2770 100644
--- a/src/USER-OMP/fix_gravity_omp.h
+++ b/src/USER-OMP/fix_gravity_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/fix_nve_sphere_omp.cpp b/src/USER-OMP/fix_nve_sphere_omp.cpp
index 6ac5afe55e8fb6f286fa52a15d5f3c5b9279c57f..bbe009ecc9e0b49265b21a545d8f575d109ebb64 100644
--- a/src/USER-OMP/fix_nve_sphere_omp.cpp
+++ b/src/USER-OMP/fix_nve_sphere_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -45,7 +45,7 @@ void FixNVESphereOMP::initial_integrate(int vflag)
const int * const mask = atom->mask;
const int nlocal = (igroup == atom->firstgroup) ? atom->nfirst : atom->nlocal;
int i;
-
+
// set timestep here since dt may have changed or come via rRESPA
const double dtfrotate = dtf / INERTIA;
@@ -63,7 +63,7 @@ void FixNVESphereOMP::initial_integrate(int vflag)
x[i][0] += dtv * v[i][0];
x[i][1] += dtv * v[i][1];
x[i][2] += dtv * v[i][2];
-
+
const double dtirotate = dtfrotate / (radius[i]*radius[i]*rmass[i]);
omega[i][0] += dtirotate * torque[i][0];
omega[i][1] += dtirotate * torque[i][1];
@@ -80,19 +80,19 @@ void FixNVESphereOMP::initial_integrate(int vflag)
#if defined(_OPENMP)
#pragma omp parallel for private(i) default(none)
#endif
- for (i = 0; i < nlocal; i++) {
+ for (i = 0; i < nlocal; i++) {
double g0,g1,g2,msq,scale;
if (mask[i] & groupbit) {
- if (mu[i][3] > 0.0) {
- g0 = mu[i][0] + dtv * (omega[i][1]*mu[i][2]-omega[i][2]*mu[i][1]);
- g1 = mu[i][1] + dtv * (omega[i][2]*mu[i][0]-omega[i][0]*mu[i][2]);
- g2 = mu[i][2] + dtv * (omega[i][0]*mu[i][1]-omega[i][1]*mu[i][0]);
- msq = g0*g0 + g1*g1 + g2*g2;
- scale = mu[i][3]/sqrt(msq);
- mu[i][0] = g0*scale;
- mu[i][1] = g1*scale;
- mu[i][2] = g2*scale;
- }
+ if (mu[i][3] > 0.0) {
+ g0 = mu[i][0] + dtv * (omega[i][1]*mu[i][2]-omega[i][2]*mu[i][1]);
+ g1 = mu[i][1] + dtv * (omega[i][2]*mu[i][0]-omega[i][0]*mu[i][2]);
+ g2 = mu[i][2] + dtv * (omega[i][0]*mu[i][1]-omega[i][1]*mu[i][0]);
+ msq = g0*g0 + g1*g1 + g2*g2;
+ scale = mu[i][3]/sqrt(msq);
+ mu[i][0] = g0*scale;
+ mu[i][1] = g1*scale;
+ mu[i][2] = g2*scale;
+ }
}
}
}
@@ -111,7 +111,7 @@ void FixNVESphereOMP::final_integrate()
const int * const mask = atom->mask;
const int nlocal = (igroup == atom->firstgroup) ? atom->nfirst : atom->nlocal;
int i;
-
+
// set timestep here since dt may have changed or come via rRESPA
const double dtfrotate = dtf / INERTIA;
@@ -128,7 +128,7 @@ void FixNVESphereOMP::final_integrate()
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
-
+
const double dtirotate = dtfrotate / (radius[i]*radius[i]*rmass[i]);
omega[i][0] += dtirotate * torque[i][0];
omega[i][1] += dtirotate * torque[i][1];
diff --git a/src/USER-OMP/fix_nve_sphere_omp.h b/src/USER-OMP/fix_nve_sphere_omp.h
index fe86039b18b207d3b5667362c87a55c0c761a494..ea965f1bb14c72105ba7c60333770f1a372f475a 100644
--- a/src/USER-OMP/fix_nve_sphere_omp.h
+++ b/src/USER-OMP/fix_nve_sphere_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/fix_omp.cpp b/src/USER-OMP/fix_omp.cpp
index 53e431dba4fbc3a52656cd31c9c6c82d47357f34..7e770ce907e23591dca6ec9ec530527f20a27d3c 100644
--- a/src/USER-OMP/fix_omp.cpp
+++ b/src/USER-OMP/fix_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -92,9 +92,9 @@ FixOMP::FixOMP(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
comm->nthreads = nthreads;
if (comm->me == 0) {
if (screen)
- fprintf(screen," reset %d OpenMP thread(s) per MPI task\n", nthreads);
+ fprintf(screen," reset %d OpenMP thread(s) per MPI task\n", nthreads);
if (logfile)
- fprintf(logfile," reset %d OpenMP thread(s) per MPI task\n", nthreads);
+ fprintf(logfile," reset %d OpenMP thread(s) per MPI task\n", nthreads);
}
}
@@ -108,11 +108,11 @@ FixOMP::FixOMP(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
if (comm->me == 0) {
const char * const mode = _neighbor ? "OpenMP capable" : "serial";
-
+
if (screen)
- fprintf(screen," using %s neighbor list subroutines\n", mode);
+ fprintf(screen," using %s neighbor list subroutines\n", mode);
if (logfile)
- fprintf(logfile," using %s neighbor list subroutines\n", mode);
+ fprintf(logfile," using %s neighbor list subroutines\n", mode);
}
}
@@ -121,23 +121,23 @@ FixOMP::FixOMP(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
if (strcmp(arg[5],"neigh/half") == 0)
_newton = true;
else if (strcmp(arg[5],"neigh/full") == 0)
- _newton = false;
+ _newton = false;
else
error->all(FLERR,"Illegal fix OMP command");
if (comm->me == 0) {
const char * const mode = _newton ? "half" : "full";
-
+
if (screen)
- fprintf(screen," using /omp styles with %s neighbor list builds\n", mode);
+ fprintf(screen," using /omp styles with %s neighbor list builds\n", mode);
if (logfile)
- fprintf(logfile," using /omp styles with %s neighbor list builds\n", mode);
+ fprintf(logfile," using /omp styles with %s neighbor list builds\n", mode);
}
}
#endif
// allocate list for per thread accumulator manager class instances
- // and then have each thread create an instance of this class to
+ // and then have each thread create an instance of this class to
// encourage the OS to use storage that is "close" to each thread's CPU.
thr = new ThrData *[nthreads];
_nthr = nthreads;
@@ -204,29 +204,29 @@ void FixOMP::init()
// determine which is the last force style with OpenMP
// support as this is the one that has to reduce the forces
-#define CheckStyleForOMP(name) \
- check_hybrid = 0; \
- if (force->name) { \
- if ( (strcmp(force->name ## _style,"hybrid") == 0) || \
- (strcmp(force->name ## _style,"hybrid/overlay") == 0) ) \
- check_hybrid=1; \
- if (force->name->suffix_flag & Suffix::OMP) { \
- last_force_name = (const char *) #name; \
- last_omp_name = force->name ## _style; \
- last_omp_style = (void *) force->name; \
- } \
+#define CheckStyleForOMP(name) \
+ check_hybrid = 0; \
+ if (force->name) { \
+ if ( (strcmp(force->name ## _style,"hybrid") == 0) || \
+ (strcmp(force->name ## _style,"hybrid/overlay") == 0) ) \
+ check_hybrid=1; \
+ if (force->name->suffix_flag & Suffix::OMP) { \
+ last_force_name = (const char *) #name; \
+ last_omp_name = force->name ## _style; \
+ last_omp_style = (void *) force->name; \
+ } \
}
-#define CheckHybridForOMP(name,Class) \
- if (check_hybrid) { \
- Class ## Hybrid *style = (Class ## Hybrid *) force->name; \
- for (int i=0; i < style->nstyles; i++) { \
- if (style->styles[i]->suffix_flag & Suffix::OMP) { \
- last_force_name = (const char *) #name; \
- last_omp_name = style->keywords[i]; \
- last_omp_style = style->styles[i]; \
- } \
- } \
+#define CheckHybridForOMP(name,Class) \
+ if (check_hybrid) { \
+ Class ## Hybrid *style = (Class ## Hybrid *) force->name; \
+ for (int i=0; i < style->nstyles; i++) { \
+ if (style->styles[i]->suffix_flag & Suffix::OMP) { \
+ last_force_name = (const char *) #name; \
+ last_omp_name = style->keywords[i]; \
+ last_omp_style = style->styles[i]; \
+ } \
+ } \
}
CheckStyleForOMP(pair);
@@ -258,22 +258,22 @@ void FixOMP::init()
if (comm->me == 0) {
if (last_omp_style) {
if (last_pair_hybrid) {
- if (screen)
- fprintf(screen,"Hybrid pair style last /omp style %s\n", last_hybrid_name);
- if (logfile)
- fprintf(logfile,"Hybrid pair style last /omp style %s\n", last_hybrid_name);
+ if (screen)
+ fprintf(screen,"Hybrid pair style last /omp style %s\n", last_hybrid_name);
+ if (logfile)
+ fprintf(logfile,"Hybrid pair style last /omp style %s\n", last_hybrid_name);
}
if (screen)
- fprintf(screen,"Last active /omp style is %s_style %s\n",
- last_force_name, last_omp_name);
+ fprintf(screen,"Last active /omp style is %s_style %s\n",
+ last_force_name, last_omp_name);
if (logfile)
- fprintf(logfile,"Last active /omp style is %s_style %s\n",
- last_force_name, last_omp_name);
+ fprintf(logfile,"Last active /omp style is %s_style %s\n",
+ last_force_name, last_omp_name);
} else {
if (screen)
- fprintf(screen,"No /omp style for force computation currently active\n");
+ fprintf(screen,"No /omp style for force computation currently active\n");
if (logfile)
- fprintf(screen,"No /omp style for force computation currently active\n");
+ fprintf(screen,"No /omp style for force computation currently active\n");
}
}
}
@@ -325,6 +325,6 @@ double FixOMP::memory_usage()
{
double bytes = comm->nthreads * (sizeof(ThrData *) + sizeof(ThrData));
bytes += comm->nthreads * thr[0]->memory_usage();
-
+
return bytes;
}
diff --git a/src/USER-OMP/fix_omp.h b/src/USER-OMP/fix_omp.h
index 6fa2c11cd5fc42d8d02db2e0c4145b33724f941d..d797b084188225dc4e215ef12da4e43079fd4f41 100644
--- a/src/USER-OMP/fix_omp.h
+++ b/src/USER-OMP/fix_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -54,7 +54,7 @@ class FixOMP : public Fix {
// to do the general force reduction
void *last_pair_hybrid; // pointer to the pair style that needs
// to call virial_fdot_compute()
-
+
public:
bool get_neighbor() const {return _neighbor;};
bool get_newton() const {return _newton;};
diff --git a/src/USER-OMP/fix_peri_neigh_omp.cpp b/src/USER-OMP/fix_peri_neigh_omp.cpp
index 2b3780f41e78ddae69dcdb284a2fa2533a79a648..000278c8b7cf596044ba7ddffab23dd5389d219f 100644
--- a/src/USER-OMP/fix_peri_neigh_omp.cpp
+++ b/src/USER-OMP/fix_peri_neigh_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -43,9 +43,8 @@ void FixPeriNeighOMP::init()
int irequest = neighbor->request((void *) this);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->fix = 1;
- neighbor->requests[irequest]->half = 0;
+ neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->omp = use_omp;
neighbor->requests[irequest]->occasional = 1;
}
-
diff --git a/src/USER-OMP/fix_peri_neigh_omp.h b/src/USER-OMP/fix_peri_neigh_omp.h
index 11a383a2feaf48a71abab32339db59e9e3b23d37..6d91f39be1efd5341cc357e404e10c7eeaa41b31 100644
--- a/src/USER-OMP/fix_peri_neigh_omp.h
+++ b/src/USER-OMP/fix_peri_neigh_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -27,7 +27,7 @@ namespace LAMMPS_NS {
class FixPeriNeighOMP : public FixPeriNeigh {
public:
- FixPeriNeighOMP(class LAMMPS *lmp, int narg, char **argv) :
+ FixPeriNeighOMP(class LAMMPS *lmp, int narg, char **argv) :
FixPeriNeigh(lmp,narg,argv) {};
virtual void init();
};
diff --git a/src/USER-OMP/fix_qeq_comb_omp.cpp b/src/USER-OMP/fix_qeq_comb_omp.cpp
index d283e6793b6c1102bce130c1a2c1947a2551954d..db3c9fcf770bd8083bcf6b7d187c9e0993014bbf 100644
--- a/src/USER-OMP/fix_qeq_comb_omp.cpp
+++ b/src/USER-OMP/fix_qeq_comb_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -35,7 +35,7 @@ using namespace FixConst;
/* ---------------------------------------------------------------------- */
-FixQEQCombOMP::FixQEQCombOMP(LAMMPS *lmp, int narg, char **arg)
+FixQEQCombOMP::FixQEQCombOMP(LAMMPS *lmp, int narg, char **arg)
: FixQEQComb(lmp, narg, arg)
{
if (narg < 5) error->all(FLERR,"Illegal fix qeq/comb/omp command");
@@ -88,7 +88,7 @@ void FixQEQCombOMP::post_force(int vflag)
// more loops for first-time charge equilibrium
- iloop = 0;
+ iloop = 0;
if (firstflag) loopmax = 5000;
else loopmax = 2000;
@@ -96,7 +96,7 @@ void FixQEQCombOMP::post_force(int vflag)
if (me == 0 && fp)
fprintf(fp,"Charge equilibration on step " BIGINT_FORMAT "\n",
- update->ntimestep);
+ update->ntimestep);
heatpq = 0.05;
qmass = 0.000548580;
@@ -104,7 +104,7 @@ void FixQEQCombOMP::post_force(int vflag)
dtq2 = 0.5*dtq*dtq/qmass;
double enegchk = 0.0;
- double enegtot = 0.0;
+ double enegtot = 0.0;
double enegmax = 0.0;
double *q = atom->q;
@@ -117,8 +117,8 @@ void FixQEQCombOMP::post_force(int vflag)
for (iloop = 0; iloop < loopmax; iloop ++ ) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- q1[i] += qf[i]*dtq2 - heatpq*q1[i];
- q[i] += q1[i];
+ q1[i] += qf[i]*dtq2 - heatpq*q1[i];
+ q[i] += q1[i];
}
enegtot = comb->yasu_char(qf,igroup);
@@ -127,10 +127,10 @@ void FixQEQCombOMP::post_force(int vflag)
for (i = 0; i < nlocal ; i++)
if (mask[i] & groupbit) {
- q2[i] = enegtot-qf[i];
- enegmax = MAX(enegmax,fabs(q2[i]));
- enegchk += fabs(q2[i]);
- qf[i] = q2[i];
+ q2[i] = enegtot-qf[i];
+ enegmax = MAX(enegmax,fabs(q2[i]));
+ enegchk += fabs(q2[i]);
+ qf[i] = q2[i];
}
MPI_Allreduce(&enegchk,&enegchkall,1,MPI_DOUBLE,MPI_SUM,world);
@@ -142,20 +142,19 @@ void FixQEQCombOMP::post_force(int vflag)
if (me == 0 && fp)
fprintf(fp," iteration: %d, enegtot %.6g, "
- "enegmax %.6g, fq deviation: %.6g\n",
- iloop,enegtot,enegmax,enegchk);
+ "enegmax %.6g, fq deviation: %.6g\n",
+ iloop,enegtot,enegmax,enegchk);
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
- q1[i] += qf[i]*dtq2 - heatpq*q1[i];
- }
+ q1[i] += qf[i]*dtq2 - heatpq*q1[i];
+ }
if (me == 0 && fp) {
if (iloop == loopmax)
fprintf(fp,"Charges did not converge in %d iterations\n",iloop);
else
fprintf(fp,"Charges converged in %d iterations to %.10f tolerance\n",
- iloop,enegchk);
+ iloop,enegchk);
}
}
-
diff --git a/src/USER-OMP/fix_shear_history_omp.cpp b/src/USER-OMP/fix_shear_history_omp.cpp
index d539b69709ac3a164bb2d4545af5ac3fbc446fd2..b5aa41b90b12f89349d49782d0bb40af00aad73a 100644
--- a/src/USER-OMP/fix_shear_history_omp.cpp
+++ b/src/USER-OMP/fix_shear_history_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -69,7 +69,7 @@ void FixShearHistoryOMP::pre_exchange()
const int gmax = gfrom + gdelta;
const int gto = (gmax > nall) ? nall : gmax;
-
+
int i,j,ii,jj,m,inum,jnum;
int *ilist,*jlist,*numneigh,**firstneigh;
int *touch,**firsttouch;
@@ -99,45 +99,45 @@ void FixShearHistoryOMP::pre_exchange()
touch = firsttouch[i];
for (jj = 0; jj < jnum; jj++) {
- if (touch[jj]) {
- j = jlist[jj];
- j &= NEIGHMASK;
- shear = &allshear[3*jj];
-
- if ((i >= lfrom) && (i < lto)) {
- if (npartner[i] < MAXTOUCH) {
- m = npartner[i];
- partner[i][m] = tag[j];
- shearpartner[i][m][0] = shear[0];
- shearpartner[i][m][1] = shear[1];
- shearpartner[i][m][2] = shear[2];
- }
- npartner[i]++;
- }
-
- if ((j >= lfrom) && (j < lto)) {
- if (npartner[j] < MAXTOUCH) {
- m = npartner[j];
- partner[j][m] = tag[i];
- shearpartner[j][m][0] = -shear[0];
- shearpartner[j][m][1] = -shear[1];
- shearpartner[j][m][2] = -shear[2];
- }
- npartner[j]++;
- }
-
- if ((j >= gfrom) && (j < gto)) {
- npartner[j]++;
- }
- }
+ if (touch[jj]) {
+ j = jlist[jj];
+ j &= NEIGHMASK;
+ shear = &allshear[3*jj];
+
+ if ((i >= lfrom) && (i < lto)) {
+ if (npartner[i] < MAXTOUCH) {
+ m = npartner[i];
+ partner[i][m] = tag[j];
+ shearpartner[i][m][0] = shear[0];
+ shearpartner[i][m][1] = shear[1];
+ shearpartner[i][m][2] = shear[2];
+ }
+ npartner[i]++;
+ }
+
+ if ((j >= lfrom) && (j < lto)) {
+ if (npartner[j] < MAXTOUCH) {
+ m = npartner[j];
+ partner[j][m] = tag[i];
+ shearpartner[j][m][0] = -shear[0];
+ shearpartner[j][m][1] = -shear[1];
+ shearpartner[j][m][2] = -shear[2];
+ }
+ npartner[j]++;
+ }
+
+ if ((j >= gfrom) && (j < gto)) {
+ npartner[j]++;
+ }
+ }
}
}
-
+
// test for too many touching neighbors
int myflag = 0;
for (i = lfrom; i < lto; i++)
if (npartner[i] >= MAXTOUCH) myflag = 1;
-
+
if (myflag)
#if defined(_OPENMP)
#pragma omp atomic
diff --git a/src/USER-OMP/fix_shear_history_omp.h b/src/USER-OMP/fix_shear_history_omp.h
index 9a360b7923040e8f53412a3cb8d88d73c35b1702..aa581ff6a7ac8f7778bb6947a16c02f0056a1292 100644
--- a/src/USER-OMP/fix_shear_history_omp.h
+++ b/src/USER-OMP/fix_shear_history_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/fix_wall_gran_omp.cpp b/src/USER-OMP/fix_wall_gran_omp.cpp
index 5b38d411598fe3b49dfd3dd191dd93be6844ab23..030bf1267970640142e35ddc04d5dc013c18d1de 100644
--- a/src/USER-OMP/fix_wall_gran_omp.cpp
+++ b/src/USER-OMP/fix_wall_gran_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -81,7 +81,7 @@ void FixWallGranOMP::post_force(int vflag)
int i;
#if defined(_OPENMP)
#pragma omp parallel for private(i) default(none) firstprivate(vwall,wlo,whi)
-#endif
+#endif
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
@@ -90,53 +90,53 @@ void FixWallGranOMP::post_force(int vflag)
dx = dy = dz = 0.0;
if (wallstyle == XPLANE) {
- del1 = x[i][0] - wlo;
- del2 = whi - x[i][0];
- if (del1 < del2) dx = del1;
- else dx = -del2;
+ del1 = x[i][0] - wlo;
+ del2 = whi - x[i][0];
+ if (del1 < del2) dx = del1;
+ else dx = -del2;
} else if (wallstyle == YPLANE) {
- del1 = x[i][1] - wlo;
- del2 = whi - x[i][1];
- if (del1 < del2) dy = del1;
- else dy = -del2;
+ del1 = x[i][1] - wlo;
+ del2 = whi - x[i][1];
+ if (del1 < del2) dy = del1;
+ else dy = -del2;
} else if (wallstyle == ZPLANE) {
- del1 = x[i][2] - wlo;
- del2 = whi - x[i][2];
- if (del1 < del2) dz = del1;
- else dz = -del2;
+ del1 = x[i][2] - wlo;
+ del2 = whi - x[i][2];
+ if (del1 < del2) dz = del1;
+ else dz = -del2;
} else if (wallstyle == ZCYLINDER) {
delxy = sqrt(x[i][0]*x[i][0] + x[i][1]*x[i][1]);
- delr = cylradius - delxy;
- if (delr > radius[i]) dz = cylradius;
- else {
- dx = -delr/delxy * x[i][0];
- dy = -delr/delxy * x[i][1];
- if (wshear && axis != 2) {
- vwall[0] = vshear * x[i][1]/delxy;
- vwall[1] = -vshear * x[i][0]/delxy;
- vwall[2] = 0.0;
- }
- }
+ delr = cylradius - delxy;
+ if (delr > radius[i]) dz = cylradius;
+ else {
+ dx = -delr/delxy * x[i][0];
+ dy = -delr/delxy * x[i][1];
+ if (wshear && axis != 2) {
+ vwall[0] = vshear * x[i][1]/delxy;
+ vwall[1] = -vshear * x[i][0]/delxy;
+ vwall[2] = 0.0;
+ }
+ }
}
rsq = dx*dx + dy*dy + dz*dz;
if (rsq > radius[i]*radius[i]) {
- if (pairstyle != HOOKE) {
- shear[i][0] = 0.0;
- shear[i][1] = 0.0;
- shear[i][2] = 0.0;
- }
+ if (pairstyle != HOOKE) {
+ shear[i][0] = 0.0;
+ shear[i][1] = 0.0;
+ shear[i][2] = 0.0;
+ }
} else {
- if (pairstyle == HOOKE)
- hooke(rsq,dx,dy,dz,vwall,v[i],f[i],omega[i],torque[i],
- radius[i],rmass[i]);
- else if (pairstyle == HOOKE_HISTORY)
- hooke_history(rsq,dx,dy,dz,vwall,v[i],f[i],omega[i],torque[i],
- radius[i],rmass[i],shear[i]);
- else if (pairstyle == HERTZ_HISTORY)
- hertz_history(rsq,dx,dy,dz,vwall,v[i],f[i],omega[i],torque[i],
- radius[i],rmass[i],shear[i]);
+ if (pairstyle == HOOKE)
+ hooke(rsq,dx,dy,dz,vwall,v[i],f[i],omega[i],torque[i],
+ radius[i],rmass[i]);
+ else if (pairstyle == HOOKE_HISTORY)
+ hooke_history(rsq,dx,dy,dz,vwall,v[i],f[i],omega[i],torque[i],
+ radius[i],rmass[i],shear[i]);
+ else if (pairstyle == HERTZ_HISTORY)
+ hertz_history(rsq,dx,dy,dz,vwall,v[i],f[i],omega[i],torque[i],
+ radius[i],rmass[i],shear[i]);
}
}
}
@@ -150,4 +150,3 @@ void FixWallGranOMP::post_force_respa(int vflag, int ilevel, int iloop)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
}
-
diff --git a/src/USER-OMP/fix_wall_gran_omp.h b/src/USER-OMP/fix_wall_gran_omp.h
index cfdfb9c75d90d5c71ba611f901ad47f619c18064..cd26a7b40a3c4f4d7161b3f134c331ad40a4fe3c 100644
--- a/src/USER-OMP/fix_wall_gran_omp.h
+++ b/src/USER-OMP/fix_wall_gran_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/improper_class2_omp.cpp b/src/USER-OMP/improper_class2_omp.cpp
index 42045023968c2f073f1834706289c162e0ac345e..0a4758f55e2c76602b627015af211f9b14f490c4 100644
--- a/src/USER-OMP/improper_class2_omp.cpp
+++ b/src/USER-OMP/improper_class2_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -64,11 +64,11 @@ void ImproperClass2OMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_bond) eval<0,0,1>(ifrom, ito, thr);
@@ -104,7 +104,7 @@ void ImproperClass2OMP::eval(int nfrom, int nto, ThrData * const thr)
double fabcd[4][3];
eimproper = 0.0;
-
+
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const * const improperlist = neighbor->improperlist;
@@ -113,10 +113,10 @@ void ImproperClass2OMP::eval(int nfrom, int nto, ThrData * const thr)
for (i = 0; i < 3; i++)
for (j = 0; j < 4; j++)
for (k = 0; k < 3; k++) {
- dthetadr[i][j][k] = 0.0;
- drAB[i][j][k] = 0.0;
- drCB[i][j][k] = 0.0;
- drDB[i][j][k] = 0.0;
+ dthetadr[i][j][k] = 0.0;
+ drAB[i][j][k] = 0.0;
+ drCB[i][j][k] = 0.0;
+ drDB[i][j][k] = 0.0;
}
for (n = nfrom; n < nto; n++) {
@@ -148,42 +148,42 @@ void ImproperClass2OMP::eval(int nfrom, int nto, ThrData * const thr)
// bond lengths and associated values
for (i = 0; i < 3; i++) {
- rmag2[i] = delr[i][0]*delr[i][0] + delr[i][1]*delr[i][1] +
- delr[i][2]*delr[i][2];
+ rmag2[i] = delr[i][0]*delr[i][0] + delr[i][1]*delr[i][1] +
+ delr[i][2]*delr[i][2];
rmag[i] = sqrt(rmag2[i]);
rinvmag[i] = 1.0/rmag[i];
}
// angle ABC, CBD, ABD
- costheta[0] = (delr[0][0]*delr[1][0] + delr[0][1]*delr[1][1] +
- delr[0][2]*delr[1][2]) / (rmag[0]*rmag[1]);
- costheta[1] = (delr[1][0]*delr[2][0] + delr[1][1]*delr[2][1] +
- delr[1][2]*delr[2][2]) / (rmag[1]*rmag[2]);
- costheta[2] = (delr[0][0]*delr[2][0] + delr[0][1]*delr[2][1] +
- delr[0][2]*delr[2][2]) / (rmag[0]*rmag[2]);
+ costheta[0] = (delr[0][0]*delr[1][0] + delr[0][1]*delr[1][1] +
+ delr[0][2]*delr[1][2]) / (rmag[0]*rmag[1]);
+ costheta[1] = (delr[1][0]*delr[2][0] + delr[1][1]*delr[2][1] +
+ delr[1][2]*delr[2][2]) / (rmag[1]*rmag[2]);
+ costheta[2] = (delr[0][0]*delr[2][0] + delr[0][1]*delr[2][1] +
+ delr[0][2]*delr[2][2]) / (rmag[0]*rmag[2]);
// angle error check
for (i = 0; i < 3; i++) {
if (costheta[i] == -1.0) {
- int me = comm->me;
- if (screen) {
- char str[128];
- sprintf(str,
- "Improper problem: %d/%d " BIGINT_FORMAT " %d %d %d %d",
- me, thr->get_tid(),update->ntimestep,
- atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
- error->warning(FLERR,str,0);
- fprintf(screen," 1st atom: %d %g %g %g\n",
- me,x[i1][0],x[i1][1],x[i1][2]);
- fprintf(screen," 2nd atom: %d %g %g %g\n",
- me,x[i2][0],x[i2][1],x[i2][2]);
- fprintf(screen," 3rd atom: %d %g %g %g\n",
- me,x[i3][0],x[i3][1],x[i3][2]);
- fprintf(screen," 4th atom: %d %g %g %g\n",
- me,x[i4][0],x[i4][1],x[i4][2]);
- }
+ int me = comm->me;
+ if (screen) {
+ char str[128];
+ sprintf(str,
+ "Improper problem: %d/%d " BIGINT_FORMAT " %d %d %d %d",
+ me, thr->get_tid(),update->ntimestep,
+ atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
+ error->warning(FLERR,str,0);
+ fprintf(screen," 1st atom: %d %g %g %g\n",
+ me,x[i1][0],x[i1][1],x[i1][2]);
+ fprintf(screen," 2nd atom: %d %g %g %g\n",
+ me,x[i2][0],x[i2][1],x[i2][2]);
+ fprintf(screen," 3rd atom: %d %g %g %g\n",
+ me,x[i3][0],x[i3][1],x[i3][2]);
+ fprintf(screen," 4th atom: %d %g %g %g\n",
+ me,x[i4][0],x[i4][1],x[i4][2]);
+ }
}
}
@@ -254,19 +254,19 @@ void ImproperClass2OMP::eval(int nfrom, int nto, ThrData * const thr)
for (i = 0; i < 3; i++)
for (j = 0; j < 4; j++)
- for (k = 0; k < 3; k++) {
- dr[i][j][k] = delr[i][k] * ddelr[i][j] / rmag[i];
- dinvr[i][j][k] = -dr[i][j][k] / rmag2[i];
- }
+ for (k = 0; k < 3; k++) {
+ dr[i][j][k] = delr[i][k] * ddelr[i][j] / rmag[i];
+ dinvr[i][j][k] = -dr[i][j][k] / rmag2[i];
+ }
// compute d(1 / (|r_AB| * |r_CB| * |r_DB|) / dr
// i = atom A/B/C/D, j = X/Y/Z
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
- dinv3r[i][j] = rinvmag[1] * (rinvmag[2] * dinvr[0][i][j] +
- rinvmag[0] * dinvr[2][i][j]) +
- rinvmag[2] * rinvmag[0] * dinvr[1][i][j];
+ dinv3r[i][j] = rinvmag[1] * (rinvmag[2] * dinvr[0][i][j] +
+ rinvmag[0] * dinvr[2][i][j]) +
+ rinvmag[2] * rinvmag[0] * dinvr[1][i][j];
// compute d(theta)/d(r) for 3 angles
// angleABC
@@ -275,30 +275,30 @@ void ImproperClass2OMP::eval(int nfrom, int nto, ThrData * const thr)
tt3 = costheta[0] / rmag2[1];
sc1 = 1.0 / sqrt(1.0 - cossqtheta[0]);
- dthetadr[0][0][0] = sc1 * ((tt1 * delr[0][0]) -
- (delr[1][0] * rinvmag[0] * rinvmag[1]));
- dthetadr[0][0][1] = sc1 * ((tt1 * delr[0][1]) -
- (delr[1][1] * rinvmag[0] * rinvmag[1]));
- dthetadr[0][0][2] = sc1 * ((tt1 * delr[0][2]) -
- (delr[1][2] * rinvmag[0] * rinvmag[1]));
- dthetadr[0][1][0] = -sc1 * ((tt1 * delr[0][0]) -
- (delr[1][0] * rinvmag[0] * rinvmag[1]) +
- (tt3 * delr[1][0]) -
- (delr[0][0] * rinvmag[0] * rinvmag[1]));
- dthetadr[0][1][1] = -sc1 * ((tt1 * delr[0][1]) -
- (delr[1][1] * rinvmag[0] * rinvmag[1]) +
- (tt3 * delr[1][1]) -
- (delr[0][1] * rinvmag[0] * rinvmag[1]));
- dthetadr[0][1][2] = -sc1 * ((tt1 * delr[0][2]) -
- (delr[1][2] * rinvmag[0] * rinvmag[1]) +
- (tt3 * delr[1][2]) -
- (delr[0][2] * rinvmag[0] * rinvmag[1]));
- dthetadr[0][2][0] = sc1 * ((tt3 * delr[1][0]) -
- (delr[0][0] * rinvmag[0] * rinvmag[1]));
- dthetadr[0][2][1] = sc1 * ((tt3 * delr[1][1]) -
- (delr[0][1] * rinvmag[0] * rinvmag[1]));
- dthetadr[0][2][2] = sc1 * ((tt3 * delr[1][2]) -
- (delr[0][2] * rinvmag[0] * rinvmag[1]));
+ dthetadr[0][0][0] = sc1 * ((tt1 * delr[0][0]) -
+ (delr[1][0] * rinvmag[0] * rinvmag[1]));
+ dthetadr[0][0][1] = sc1 * ((tt1 * delr[0][1]) -
+ (delr[1][1] * rinvmag[0] * rinvmag[1]));
+ dthetadr[0][0][2] = sc1 * ((tt1 * delr[0][2]) -
+ (delr[1][2] * rinvmag[0] * rinvmag[1]));
+ dthetadr[0][1][0] = -sc1 * ((tt1 * delr[0][0]) -
+ (delr[1][0] * rinvmag[0] * rinvmag[1]) +
+ (tt3 * delr[1][0]) -
+ (delr[0][0] * rinvmag[0] * rinvmag[1]));
+ dthetadr[0][1][1] = -sc1 * ((tt1 * delr[0][1]) -
+ (delr[1][1] * rinvmag[0] * rinvmag[1]) +
+ (tt3 * delr[1][1]) -
+ (delr[0][1] * rinvmag[0] * rinvmag[1]));
+ dthetadr[0][1][2] = -sc1 * ((tt1 * delr[0][2]) -
+ (delr[1][2] * rinvmag[0] * rinvmag[1]) +
+ (tt3 * delr[1][2]) -
+ (delr[0][2] * rinvmag[0] * rinvmag[1]));
+ dthetadr[0][2][0] = sc1 * ((tt3 * delr[1][0]) -
+ (delr[0][0] * rinvmag[0] * rinvmag[1]));
+ dthetadr[0][2][1] = sc1 * ((tt3 * delr[1][1]) -
+ (delr[0][1] * rinvmag[0] * rinvmag[1]));
+ dthetadr[0][2][2] = sc1 * ((tt3 * delr[1][2]) -
+ (delr[0][2] * rinvmag[0] * rinvmag[1]));
// angleCBD
@@ -306,30 +306,30 @@ void ImproperClass2OMP::eval(int nfrom, int nto, ThrData * const thr)
tt3 = costheta[1] / rmag2[2];
sc1 = 1.0 / sqrt(1.0 - cossqtheta[1]);
- dthetadr[1][2][0] = sc1 * ((tt1 * delr[1][0]) -
- (delr[2][0] * rinvmag[1] * rinvmag[2]));
- dthetadr[1][2][1] = sc1 * ((tt1 * delr[1][1]) -
- (delr[2][1] * rinvmag[1] * rinvmag[2]));
- dthetadr[1][2][2] = sc1 * ((tt1 * delr[1][2]) -
- (delr[2][2] * rinvmag[1] * rinvmag[2]));
- dthetadr[1][1][0] = -sc1 * ((tt1 * delr[1][0]) -
- (delr[2][0] * rinvmag[1] * rinvmag[2]) +
- (tt3 * delr[2][0]) -
- (delr[1][0] * rinvmag[2] * rinvmag[1]));
- dthetadr[1][1][1] = -sc1 * ((tt1 * delr[1][1]) -
- (delr[2][1] * rinvmag[1] * rinvmag[2]) +
- (tt3 * delr[2][1]) -
- (delr[1][1] * rinvmag[2] * rinvmag[1]));
- dthetadr[1][1][2] = -sc1 * ((tt1 * delr[1][2]) -
- (delr[2][2] * rinvmag[1] * rinvmag[2]) +
- (tt3 * delr[2][2]) -
- (delr[1][2] * rinvmag[2] * rinvmag[1]));
- dthetadr[1][3][0] = sc1 * ((tt3 * delr[2][0]) -
- (delr[1][0] * rinvmag[2] * rinvmag[1]));
- dthetadr[1][3][1] = sc1 * ((tt3 * delr[2][1]) -
- (delr[1][1] * rinvmag[2] * rinvmag[1]));
- dthetadr[1][3][2] = sc1 * ((tt3 * delr[2][2]) -
- (delr[1][2] * rinvmag[2] * rinvmag[1]));
+ dthetadr[1][2][0] = sc1 * ((tt1 * delr[1][0]) -
+ (delr[2][0] * rinvmag[1] * rinvmag[2]));
+ dthetadr[1][2][1] = sc1 * ((tt1 * delr[1][1]) -
+ (delr[2][1] * rinvmag[1] * rinvmag[2]));
+ dthetadr[1][2][2] = sc1 * ((tt1 * delr[1][2]) -
+ (delr[2][2] * rinvmag[1] * rinvmag[2]));
+ dthetadr[1][1][0] = -sc1 * ((tt1 * delr[1][0]) -
+ (delr[2][0] * rinvmag[1] * rinvmag[2]) +
+ (tt3 * delr[2][0]) -
+ (delr[1][0] * rinvmag[2] * rinvmag[1]));
+ dthetadr[1][1][1] = -sc1 * ((tt1 * delr[1][1]) -
+ (delr[2][1] * rinvmag[1] * rinvmag[2]) +
+ (tt3 * delr[2][1]) -
+ (delr[1][1] * rinvmag[2] * rinvmag[1]));
+ dthetadr[1][1][2] = -sc1 * ((tt1 * delr[1][2]) -
+ (delr[2][2] * rinvmag[1] * rinvmag[2]) +
+ (tt3 * delr[2][2]) -
+ (delr[1][2] * rinvmag[2] * rinvmag[1]));
+ dthetadr[1][3][0] = sc1 * ((tt3 * delr[2][0]) -
+ (delr[1][0] * rinvmag[2] * rinvmag[1]));
+ dthetadr[1][3][1] = sc1 * ((tt3 * delr[2][1]) -
+ (delr[1][1] * rinvmag[2] * rinvmag[1]));
+ dthetadr[1][3][2] = sc1 * ((tt3 * delr[2][2]) -
+ (delr[1][2] * rinvmag[2] * rinvmag[1]));
// angleABD
@@ -337,30 +337,30 @@ void ImproperClass2OMP::eval(int nfrom, int nto, ThrData * const thr)
tt3 = costheta[2] / rmag2[2];
sc1 = 1.0 / sqrt(1.0 - cossqtheta[2]);
- dthetadr[2][0][0] = sc1 * ((tt1 * delr[0][0]) -
- (delr[2][0] * rinvmag[0] * rinvmag[2]));
- dthetadr[2][0][1] = sc1 * ((tt1 * delr[0][1]) -
- (delr[2][1] * rinvmag[0] * rinvmag[2]));
- dthetadr[2][0][2] = sc1 * ((tt1 * delr[0][2]) -
- (delr[2][2] * rinvmag[0] * rinvmag[2]));
- dthetadr[2][1][0] = -sc1 * ((tt1 * delr[0][0]) -
- (delr[2][0] * rinvmag[0] * rinvmag[2]) +
- (tt3 * delr[2][0]) -
- (delr[0][0] * rinvmag[2] * rinvmag[0]));
- dthetadr[2][1][1] = -sc1 * ((tt1 * delr[0][1]) -
- (delr[2][1] * rinvmag[0] * rinvmag[2]) +
- (tt3 * delr[2][1]) -
- (delr[0][1] * rinvmag[2] * rinvmag[0]));
- dthetadr[2][1][2] = -sc1 * ((tt1 * delr[0][2]) -
- (delr[2][2] * rinvmag[0] * rinvmag[2]) +
- (tt3 * delr[2][2]) -
- (delr[0][2] * rinvmag[2] * rinvmag[0]));
- dthetadr[2][3][0] = sc1 * ((tt3 * delr[2][0]) -
- (delr[0][0] * rinvmag[2] * rinvmag[0]));
- dthetadr[2][3][1] = sc1 * ((tt3 * delr[2][1]) -
- (delr[0][1] * rinvmag[2] * rinvmag[0]));
- dthetadr[2][3][2] = sc1 * ((tt3 * delr[2][2]) -
- (delr[0][2] * rinvmag[2] * rinvmag[0]));
+ dthetadr[2][0][0] = sc1 * ((tt1 * delr[0][0]) -
+ (delr[2][0] * rinvmag[0] * rinvmag[2]));
+ dthetadr[2][0][1] = sc1 * ((tt1 * delr[0][1]) -
+ (delr[2][1] * rinvmag[0] * rinvmag[2]));
+ dthetadr[2][0][2] = sc1 * ((tt1 * delr[0][2]) -
+ (delr[2][2] * rinvmag[0] * rinvmag[2]));
+ dthetadr[2][1][0] = -sc1 * ((tt1 * delr[0][0]) -
+ (delr[2][0] * rinvmag[0] * rinvmag[2]) +
+ (tt3 * delr[2][0]) -
+ (delr[0][0] * rinvmag[2] * rinvmag[0]));
+ dthetadr[2][1][1] = -sc1 * ((tt1 * delr[0][1]) -
+ (delr[2][1] * rinvmag[0] * rinvmag[2]) +
+ (tt3 * delr[2][1]) -
+ (delr[0][1] * rinvmag[2] * rinvmag[0]));
+ dthetadr[2][1][2] = -sc1 * ((tt1 * delr[0][2]) -
+ (delr[2][2] * rinvmag[0] * rinvmag[2]) +
+ (tt3 * delr[2][2]) -
+ (delr[0][2] * rinvmag[2] * rinvmag[0]));
+ dthetadr[2][3][0] = sc1 * ((tt3 * delr[2][0]) -
+ (delr[0][0] * rinvmag[2] * rinvmag[0]));
+ dthetadr[2][3][1] = sc1 * ((tt3 * delr[2][1]) -
+ (delr[0][1] * rinvmag[2] * rinvmag[0]));
+ dthetadr[2][3][2] = sc1 * ((tt3 * delr[2][2]) -
+ (delr[0][2] * rinvmag[2] * rinvmag[0]));
// compute d( 1 / sin(theta))/dr
// i = angle, j = atom, k = direction
@@ -368,8 +368,8 @@ void ImproperClass2OMP::eval(int nfrom, int nto, ThrData * const thr)
for (i = 0; i < 3; i++) {
cossin2 = -costheta[i] / sinsqtheta[i];
for (j = 0; j < 4; j++)
- for (k = 0; k < 3; k++)
- dinvsth[i][j][k] = cossin2 * dthetadr[i][j][k];
+ for (k = 0; k < 3; k++)
+ dinvsth[i][j][k] = cossin2 * dthetadr[i][j][k];
}
// compute d(1 / sin(theta) * |r_AB| * |r_CB| * |r_DB|)/dr
@@ -377,12 +377,12 @@ void ImproperClass2OMP::eval(int nfrom, int nto, ThrData * const thr)
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++) {
- dinvs3r[0][i][j] = (invstheta[1] * dinv3r[i][j]) +
- (inv3r * dinvsth[1][i][j]);
- dinvs3r[1][i][j] = (invstheta[2] * dinv3r[i][j]) +
- (inv3r * dinvsth[2][i][j]);
- dinvs3r[2][i][j] = (invstheta[0] * dinv3r[i][j]) +
- (inv3r * dinvsth[0][i][j]);
+ dinvs3r[0][i][j] = (invstheta[1] * dinv3r[i][j]) +
+ (inv3r * dinvsth[1][i][j]);
+ dinvs3r[1][i][j] = (invstheta[2] * dinv3r[i][j]) +
+ (inv3r * dinvsth[2][i][j]);
+ dinvs3r[2][i][j] = (invstheta[0] * dinv3r[i][j]) +
+ (inv3r * dinvsth[0][i][j]);
}
// drCB(i,j,k), etc
@@ -406,12 +406,12 @@ void ImproperClass2OMP::eval(int nfrom, int nto, ThrData * const thr)
for (i = 0; i < 3; i++)
for (j = 0; j < 4; j++) {
- cross(delr[1],drDB[i][j],rCBxdrDB);
- cross(drCB[i][j],delr[2],drCBxrDB);
- for (k = 0; k < 3; k++) dd[k] = rCBxdrDB[k] + drCBxrDB[k];
- dot1 = dot(dd,delr[0]);
- dot2 = dot(rCBxrDB,drAB[i][j]);
- fdot[0][j][i] = dot1 + dot2;
+ cross(delr[1],drDB[i][j],rCBxdrDB);
+ cross(drCB[i][j],delr[2],drCBxrDB);
+ for (k = 0; k < 3; k++) dd[k] = rCBxdrDB[k] + drCBxrDB[k];
+ dot1 = dot(dd,delr[0]);
+ dot2 = dot(rCBxrDB,drAB[i][j]);
+ fdot[0][j][i] = dot1 + dot2;
}
// d((r_DB x r_AB) dot r_CB)
@@ -423,12 +423,12 @@ void ImproperClass2OMP::eval(int nfrom, int nto, ThrData * const thr)
for (i = 0; i < 3; i++)
for (j = 0; j < 4; j++) {
- cross(delr[2],drAB[i][j],rDBxdrAB);
- cross(drDB[i][j],delr[0],drDBxrAB);
- for (k = 0; k < 3; k++) dd[k] = rDBxdrAB[k] + drDBxrAB[k];
- dot1 = dot(dd,delr[1]);
- dot2 = dot(rDBxrAB,drCB[i][j]);
- fdot[1][j][i] = dot1 + dot2;
+ cross(delr[2],drAB[i][j],rDBxdrAB);
+ cross(drDB[i][j],delr[0],drDBxrAB);
+ for (k = 0; k < 3; k++) dd[k] = rDBxdrAB[k] + drDBxrAB[k];
+ dot1 = dot(dd,delr[1]);
+ dot2 = dot(rDBxrAB,drCB[i][j]);
+ fdot[1][j][i] = dot1 + dot2;
}
// d((r_AB x r_CB) dot r_DB)
@@ -440,33 +440,33 @@ void ImproperClass2OMP::eval(int nfrom, int nto, ThrData * const thr)
for (i = 0; i < 3; i++)
for (j = 0; j < 4; j++) {
- cross(delr[0],drCB[i][j],rABxdrCB);
- cross(drAB[i][j],delr[1],drABxrCB);
- for (k = 0; k < 3; k++) dd[k] = rABxdrCB[k] + drABxrCB[k];
- dot1 = dot(dd,delr[2]);
- dot2 = dot(rABxrCB,drDB[i][j]);
- fdot[2][j][i] = dot1 + dot2;
+ cross(delr[0],drCB[i][j],rABxdrCB);
+ cross(drAB[i][j],delr[1],drABxrCB);
+ for (k = 0; k < 3; k++) dd[k] = rABxdrCB[k] + drABxrCB[k];
+ dot1 = dot(dd,delr[2]);
+ dot2 = dot(rABxrCB,drDB[i][j]);
+ fdot[2][j][i] = dot1 + dot2;
}
// force on each atom
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++) {
- ftmp = (fdot[0][i][j] * invs3r[0]) +
- (dinvs3r[0][i][j] * dotCBDBAB);
- dchi[0][i][j] = ftmp / cos(chiABCD);
- ftmp = (fdot[1][i][j] * invs3r[1]) +
- (dinvs3r[1][i][j] * dotDBABCB);
- dchi[1][i][j] = ftmp / cos(chiCBDA);
- ftmp = (fdot[2][i][j] * invs3r[2]) +
- (dinvs3r[2][i][j] * dotABCBDB);
- dchi[2][i][j] = ftmp / cos(chiDBAC);
- dtotalchi[i][j] = (dchi[0][i][j]+dchi[1][i][j]+dchi[2][i][j]) / 3.0;
+ ftmp = (fdot[0][i][j] * invs3r[0]) +
+ (dinvs3r[0][i][j] * dotCBDBAB);
+ dchi[0][i][j] = ftmp / cos(chiABCD);
+ ftmp = (fdot[1][i][j] * invs3r[1]) +
+ (dinvs3r[1][i][j] * dotDBABCB);
+ dchi[1][i][j] = ftmp / cos(chiCBDA);
+ ftmp = (fdot[2][i][j] * invs3r[2]) +
+ (dinvs3r[2][i][j] * dotABCBDB);
+ dchi[2][i][j] = ftmp / cos(chiDBAC);
+ dtotalchi[i][j] = (dchi[0][i][j]+dchi[1][i][j]+dchi[2][i][j]) / 3.0;
}
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
- fabcd[i][j] = -2.0*k0[type] * deltachi*dtotalchi[i][j];
+ fabcd[i][j] = -2.0*k0[type] * deltachi*dtotalchi[i][j];
// apply force to each of 4 atoms
@@ -496,11 +496,11 @@ void ImproperClass2OMP::eval(int nfrom, int nto, ThrData * const thr)
if (EVFLAG)
ev_tally_thr(this,i1,i2,i3,i4,nlocal,NEWTON_BOND,eimproper,
- fabcd[0],fabcd[2],fabcd[3],
- delr[0][0],delr[0][1],delr[0][2],
- delr[1][0],delr[1][1],delr[1][2],
- delr[2][0]-delr[1][0],delr[2][1]-delr[1][1],
- delr[2][2]-delr[1][2],thr);
+ fabcd[0],fabcd[2],fabcd[3],
+ delr[0][0],delr[0][1],delr[0][2],
+ delr[1][0],delr[1][1],delr[1][2],
+ delr[2][0]-delr[1][0],delr[2][1]-delr[1][1],
+ delr[2][2]-delr[1][2],thr);
}
// compute angle-angle interactions
@@ -562,7 +562,7 @@ void ImproperClass2OMP::angleangle_thr(int nfrom, int nto, ThrData * const thr)
rBC = sqrt(rBCmag2);
rBDmag2 = delxBD*delxBD + delyBD*delyBD + delzBD*delzBD;
rBD = sqrt(rBDmag2);
-
+
// angle ABC, ABD, CBD
costhABC = (delxAB*delxBC + delyAB*delyBC + delzAB*delzBC) / (rAB * rBC);
@@ -586,17 +586,17 @@ void ImproperClass2OMP::angleangle_thr(int nfrom, int nto, ThrData * const thr)
// energy
- if (EFLAG) eimproper = aa_k2[type] * dthABC * dthABD +
- aa_k1[type] * dthABC * dthCBD +
- aa_k3[type] * dthABD * dthCBD;
+ if (EFLAG) eimproper = aa_k2[type] * dthABC * dthABD +
+ aa_k1[type] * dthABC * dthCBD +
+ aa_k3[type] * dthABD * dthCBD;
// d(theta)/d(r) array
// angle i, atom j, coordinate k
for (i = 0; i < 3; i++)
for (j = 0; j < 4; j++)
- for (k = 0; k < 3; k++)
- dthetadr[i][j][k] = 0.0;
+ for (k = 0; k < 3; k++)
+ dthetadr[i][j][k] = 0.0;
// angle ABC
@@ -609,11 +609,11 @@ void ImproperClass2OMP::angleangle_thr(int nfrom, int nto, ThrData * const thr)
dthetadr[0][0][1] = sc1 * ((t1 * delyAB) - (delyBC * r12));
dthetadr[0][0][2] = sc1 * ((t1 * delzAB) - (delzBC * r12));
dthetadr[0][1][0] = sc1 * ((-t1 * delxAB) + (delxBC * r12) +
- (-t3 * delxBC) + (delxAB * r12));
+ (-t3 * delxBC) + (delxAB * r12));
dthetadr[0][1][1] = sc1 * ((-t1 * delyAB) + (delyBC * r12) +
- (-t3 * delyBC) + (delyAB * r12));
+ (-t3 * delyBC) + (delyAB * r12));
dthetadr[0][1][2] = sc1 * ((-t1 * delzAB) + (delzBC * r12) +
- (-t3 * delzBC) + (delzAB * r12));
+ (-t3 * delzBC) + (delzAB * r12));
dthetadr[0][2][0] = sc1 * ((t3 * delxBC) - (delxAB * r12));
dthetadr[0][2][1] = sc1 * ((t3 * delyBC) - (delyAB * r12));
dthetadr[0][2][2] = sc1 * ((t3 * delzBC) - (delzAB * r12));
@@ -629,11 +629,11 @@ void ImproperClass2OMP::angleangle_thr(int nfrom, int nto, ThrData * const thr)
dthetadr[1][2][1] = sc1 * ((t1 * delyBC) - (delyBD * r12));
dthetadr[1][2][2] = sc1 * ((t1 * delzBC) - (delzBD * r12));
dthetadr[1][1][0] = sc1 * ((-t1 * delxBC) + (delxBD * r12) +
- (-t3 * delxBD) + (delxBC * r12));
+ (-t3 * delxBD) + (delxBC * r12));
dthetadr[1][1][1] = sc1 * ((-t1 * delyBC) + (delyBD * r12) +
- (-t3 * delyBD) + (delyBC * r12));
+ (-t3 * delyBD) + (delyBC * r12));
dthetadr[1][1][2] = sc1 * ((-t1 * delzBC) + (delzBD * r12) +
- (-t3 * delzBD) + (delzBC * r12));
+ (-t3 * delzBD) + (delzBC * r12));
dthetadr[1][3][0] = sc1 * ((t3 * delxBD) - (delxBC * r12));
dthetadr[1][3][1] = sc1 * ((t3 * delyBD) - (delyBC * r12));
dthetadr[1][3][2] = sc1 * ((t3 * delzBD) - (delzBC * r12));
@@ -649,11 +649,11 @@ void ImproperClass2OMP::angleangle_thr(int nfrom, int nto, ThrData * const thr)
dthetadr[2][0][1] = sc1 * ((t1 * delyAB) - (delyBD * r12));
dthetadr[2][0][2] = sc1 * ((t1 * delzAB) - (delzBD * r12));
dthetadr[2][1][0] = sc1 * ((-t1 * delxAB) + (delxBD * r12) +
- (-t3 * delxBD) + (delxAB * r12));
+ (-t3 * delxBD) + (delxAB * r12));
dthetadr[2][1][1] = sc1 * ((-t1 * delyAB) + (delyBD * r12) +
- (-t3 * delyBD) + (delyAB * r12));
+ (-t3 * delyBD) + (delyAB * r12));
dthetadr[2][1][2] = sc1 * ((-t1 * delzAB) + (delzBD * r12) +
- (-t3 * delzBD) + (delzAB * r12));
+ (-t3 * delzBD) + (delzAB * r12));
dthetadr[2][3][0] = sc1 * ((t3 * delxBD) - (delxAB * r12));
dthetadr[2][3][1] = sc1 * ((t3 * delyBD) - (delyAB * r12));
dthetadr[2][3][2] = sc1 * ((t3 * delzBD) - (delzAB * r12));
@@ -662,13 +662,13 @@ void ImproperClass2OMP::angleangle_thr(int nfrom, int nto, ThrData * const thr)
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
- fabcd[i][j] = -
- ((aa_k1[type] *
- (dthABC*dthetadr[1][i][j] + dthCBD*dthetadr[0][i][j])) +
- (aa_k2[type] *
- (dthABC*dthetadr[2][i][j] + dthABD*dthetadr[0][i][j])) +
- (aa_k3[type] *
- (dthABD*dthetadr[1][i][j] + dthCBD*dthetadr[2][i][j])));
+ fabcd[i][j] = -
+ ((aa_k1[type] *
+ (dthABC*dthetadr[1][i][j] + dthCBD*dthetadr[0][i][j])) +
+ (aa_k2[type] *
+ (dthABC*dthetadr[2][i][j] + dthABD*dthetadr[0][i][j])) +
+ (aa_k3[type] *
+ (dthABD*dthetadr[1][i][j] + dthCBD*dthetadr[2][i][j])));
// apply force to each of 4 atoms
@@ -698,7 +698,7 @@ void ImproperClass2OMP::angleangle_thr(int nfrom, int nto, ThrData * const thr)
if (EVFLAG)
ev_tally_thr(this,i1,i2,i3,i4,nlocal,NEWTON_BOND,eimproper,
- fabcd[0],fabcd[2],fabcd[3],delxAB,delyAB,delzAB,
- delxBC,delyBC,delzBC,delxBD,delyBD,delzBD,thr);
+ fabcd[0],fabcd[2],fabcd[3],delxAB,delyAB,delzAB,
+ delxBC,delyBC,delzBC,delxBD,delyBD,delzBD,thr);
}
}
diff --git a/src/USER-OMP/improper_class2_omp.h b/src/USER-OMP/improper_class2_omp.h
index 8eca8cd8c197f667e205980a7df7641be30d6c56..6f668a00783f83d9bf7d2ee06dbd6959c77be422 100644
--- a/src/USER-OMP/improper_class2_omp.h
+++ b/src/USER-OMP/improper_class2_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -41,7 +41,7 @@ class ImproperClass2OMP : public ImproperClass2, public ThrOMP {
template <int EVFLAG, int EFLAG, int NEWTON_BOND>
void angleangle_thr(int, int, ThrData * const thr);
-
+
};
}
diff --git a/src/USER-OMP/improper_cossq_omp.cpp b/src/USER-OMP/improper_cossq_omp.cpp
index b7ddd2e59c20982b02af1328998ad3bf024da9b7..1e1b53eaf7045687567bc20b4b69108b9263fb38 100644
--- a/src/USER-OMP/improper_cossq_omp.cpp
+++ b/src/USER-OMP/improper_cossq_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -64,11 +64,11 @@ void ImproperCossqOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_bond) eval<0,0,1>(ifrom, ito, thr);
@@ -125,43 +125,43 @@ void ImproperCossqOMP::eval(int nfrom, int nto, ThrData * const thr)
rlk = sqrt(rlksq);
cosphi = (vb3x*vb1x + vb3y*vb1y + vb3z*vb1z)/(rji * rlk);
-
- /* Check that cos(phi) is in the correct limits. */
+
+ /* Check that cos(phi) is in the correct limits. */
if (cosphi > 1.0 + TOLERANCE || cosphi < (-1.0 - TOLERANCE)) {
int me = comm->me;
if (screen) {
- char str[128];
- sprintf(str,"Improper problem: %d/%d " BIGINT_FORMAT " %d %d %d %d",
- me,thr->get_tid(),update->ntimestep,
- atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
- error->warning(FLERR,str,0);
- fprintf(screen," 1st atom: %d %g %g %g\n",
- me,x[i1][0],x[i1][1],x[i1][2]);
- fprintf(screen," 2nd atom: %d %g %g %g\n",
- me,x[i2][0],x[i2][1],x[i2][2]);
- fprintf(screen," 3rd atom: %d %g %g %g\n",
- me,x[i3][0],x[i3][1],x[i3][2]);
- fprintf(screen," 4th atom: %d %g %g %g\n",
- me,x[i4][0],x[i4][1],x[i4][2]);
+ char str[128];
+ sprintf(str,"Improper problem: %d/%d " BIGINT_FORMAT " %d %d %d %d",
+ me,thr->get_tid(),update->ntimestep,
+ atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
+ error->warning(FLERR,str,0);
+ fprintf(screen," 1st atom: %d %g %g %g\n",
+ me,x[i1][0],x[i1][1],x[i1][2]);
+ fprintf(screen," 2nd atom: %d %g %g %g\n",
+ me,x[i2][0],x[i2][1],x[i2][2]);
+ fprintf(screen," 3rd atom: %d %g %g %g\n",
+ me,x[i3][0],x[i3][1],x[i3][2]);
+ fprintf(screen," 4th atom: %d %g %g %g\n",
+ me,x[i4][0],x[i4][1],x[i4][2]);
}
-
+
/* Apply corrections to round-off errors. */
if (cosphi > 1.0) cosphi -= SMALL;
if (cosphi < -1.0) cosphi += SMALL;
-
+
/* Calculate the angle: */
double torangle = acos(cosphi);
cosphi = cos(torangle - chi[type]);
if (EFLAG) eimproper = 0.5 * k[type] * cosphi * cosphi;
-
+
/*
- printf("The tags: %d-%d-%d-%d, of type %d .\n",atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4],type);
- printf("The ji vector: %f, %f, %f.\nThe lk vector: %f, %f, %f.\n", vb1x,vb1y,vb1z,vb3x,vb3y,vb3z);
- printf("The cosine of the angle: %-1.16e.\n", cosphi);
- printf("The energy of the improper: %-1.16e with prefactor %-1.16e.\n", eimproper, 0.5*k[type]);
+ printf("The tags: %d-%d-%d-%d, of type %d .\n",atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4],type);
+ printf("The ji vector: %f, %f, %f.\nThe lk vector: %f, %f, %f.\n", vb1x,vb1y,vb1z,vb3x,vb3y,vb3z);
+ printf("The cosine of the angle: %-1.16e.\n", cosphi);
+ printf("The energy of the improper: %-1.16e with prefactor %-1.16e.\n", eimproper, 0.5*k[type]);
*/
/* Work out forces. */
@@ -170,11 +170,11 @@ void ImproperCossqOMP::eval(int nfrom, int nto, ThrData * const thr)
cjiji = rjisq;
clklk = rlksq;
/*CLKJI = RXLK * RXJI + RYLK * RYJI + RZLK * RZJI */
- clkji = vb3x*vb1x + vb3y*vb1y + vb3z*vb1z;
+ clkji = vb3x*vb1x + vb3y*vb1y + vb3z*vb1z;
/*CFACT1 = CLKLK * CJIJI
- CFACT1 = SQRT(CFACT1)
- CFACT1 = ANGFAC / CFACT1*/
+ CFACT1 = SQRT(CFACT1)
+ CFACT1 = ANGFAC / CFACT1*/
cfact1 = angfac / sqrt(clklk * cjiji);
/*CFACT2 = CLKJI / CLKLK*/
cfact2 = clkji / clklk;
@@ -182,90 +182,89 @@ void ImproperCossqOMP::eval(int nfrom, int nto, ThrData * const thr)
cfact3 = clkji / cjiji;
/*FIX = -RXLK + CFACT3 * RXJI
- FIY = -RYLK + CFACT3 * RYJI
- FIZ = -RZLK + CFACT3 * RZJI*/
+ FIY = -RYLK + CFACT3 * RYJI
+ FIZ = -RZLK + CFACT3 * RZJI*/
f1[0] = - vb3x + cfact3 * vb1x;
f1[1] = - vb3y + cfact3 * vb1y;
f1[2] = - vb3z + cfact3 * vb1z;
/*FJX = -FIX
- FJY = -FIY
- FJZ = -FIZ*/
+ FJY = -FIY
+ FJZ = -FIZ*/
f2[0] = - f1[0];
f2[1] = - f1[1];
f2[2] = - f1[2];
-
+
/*FKX = CFACT2 * RXLK - RXJI
- FKY = CFACT2 * RYLK - RYJI
- FKZ = CFACT2 * RZLK - RZJI*/
+ FKY = CFACT2 * RYLK - RYJI
+ FKZ = CFACT2 * RZLK - RZJI*/
f3[0] = cfact2 * vb3x - vb1x;
f3[1] = cfact2 * vb3y - vb1y;
f3[2] = cfact2 * vb3z - vb1z;
/*FLX = -FKX
- FLY = -FKY
- FLZ = -FKZ*/
+ FLY = -FKY
+ FLZ = -FKZ*/
f4[0] = - f3[0];
f4[1] = - f3[1];
f4[2] = - f3[2];
/*FIX = FIX * CFACT1
- FIY = FIY * CFACT1
- FIZ = FIZ * CFACT1*/
+ FIY = FIY * CFACT1
+ FIZ = FIZ * CFACT1*/
f1[0] *= cfact1;
- f1[1] *= cfact1;
+ f1[1] *= cfact1;
f1[2] *= cfact1;
/*FJX = FJX * CFACT1
- FJY = FJY * CFACT1
- FJZ = FJZ * CFACT1*/
+ FJY = FJY * CFACT1
+ FJZ = FJZ * CFACT1*/
f2[0] *= cfact1;
f2[1] *= cfact1;
f2[2] *= cfact1;
/*FKX = FKX * CFACT1
- FKY = FKY * CFACT1
- FKZ = FKZ * CFACT1*/
- f3[0] *= cfact1;
- f3[1] *= cfact1;
+ FKY = FKY * CFACT1
+ FKZ = FKZ * CFACT1*/
+ f3[0] *= cfact1;
+ f3[1] *= cfact1;
f3[2] *= cfact1;
/*FLX = FLX * CFACT1
- FLY = FLY * CFACT1
- FLZ = FLZ * CFACT1*/
+ FLY = FLY * CFACT1
+ FLZ = FLZ * CFACT1*/
f4[0] *= cfact1;
- f4[1] *= cfact1;
+ f4[1] *= cfact1;
f4[2] *= cfact1;
/* Apply force to each of 4 atoms */
if (NEWTON_BOND || i1 < nlocal) {
- f[i1][0] += f1[0];
- f[i1][1] += f1[1];
- f[i1][2] += f1[2];
+ f[i1][0] += f1[0];
+ f[i1][1] += f1[1];
+ f[i1][2] += f1[2];
}
if (NEWTON_BOND || i2 < nlocal) {
- f[i2][0] += f2[0];
- f[i2][1] += f2[1];
- f[i2][2] += f2[2];
+ f[i2][0] += f2[0];
+ f[i2][1] += f2[1];
+ f[i2][2] += f2[2];
}
if (NEWTON_BOND || i3 < nlocal) {
- f[i3][0] += f3[0];
- f[i3][1] += f3[1];
- f[i3][2] += f3[2];
+ f[i3][0] += f3[0];
+ f[i3][1] += f3[1];
+ f[i3][2] += f3[2];
}
if (NEWTON_BOND || i4 < nlocal) {
- f[i4][0] += f4[0];
- f[i4][1] += f4[1];
- f[i4][2] += f4[2];
+ f[i4][0] += f4[0];
+ f[i4][1] += f4[1];
+ f[i4][2] += f4[2];
}
if (EVFLAG)
- ev_tally_thr(this,i1,i2,i3,i4,nlocal,NEWTON_BOND,eimproper,f1,f3,f4,
- -vb1x,-vb1y,-vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,thr);
+ ev_tally_thr(this,i1,i2,i3,i4,nlocal,NEWTON_BOND,eimproper,f1,f3,f4,
+ -vb1x,-vb1y,-vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,thr);
}
}
}
-
diff --git a/src/USER-OMP/improper_cossq_omp.h b/src/USER-OMP/improper_cossq_omp.h
index 4b98338cfa12ed7761186d6b6efbdcbf99059a58..8fd1bc09a04e39bd936b7c757ed7f44b3fc5deff 100644
--- a/src/USER-OMP/improper_cossq_omp.h
+++ b/src/USER-OMP/improper_cossq_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/improper_cvff_omp.cpp b/src/USER-OMP/improper_cvff_omp.cpp
index 11387a76bcbb25972f264d612b55f1b8070c5061..fd8b4aca1d5715b27dbfa727c6be29db8f4212d5 100644
--- a/src/USER-OMP/improper_cvff_omp.cpp
+++ b/src/USER-OMP/improper_cvff_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -64,11 +64,11 @@ void ImproperCvffOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_bond) eval<0,0,1>(ifrom, ito, thr);
@@ -131,18 +131,18 @@ void ImproperCvffOMP::eval(int nfrom, int nto, ThrData * const thr)
domain->minimum_image(vb3x,vb3y,vb3z);
// c0 calculation
-
+
sb1 = 1.0 / (vb1x*vb1x + vb1y*vb1y + vb1z*vb1z);
sb2 = 1.0 / (vb2x*vb2x + vb2y*vb2y + vb2z*vb2z);
sb3 = 1.0 / (vb3x*vb3x + vb3y*vb3y + vb3z*vb3z);
-
+
rb1 = sqrt(sb1);
rb3 = sqrt(sb3);
-
+
c0 = (vb1x*vb3x + vb1y*vb3y + vb1z*vb3z) * rb1*rb3;
// 1st and 2nd angle
-
+
b1mag2 = vb1x*vb1x + vb1y*vb1y + vb1z*vb1z;
b1mag = sqrt(b1mag2);
b2mag2 = vb2x*vb2x + vb2y*vb2y + vb2z*vb2z;
@@ -179,22 +179,22 @@ void ImproperCvffOMP::eval(int nfrom, int nto, ThrData * const thr)
int me = comm->me;
if (screen) {
- char str[128];
- sprintf(str,"Improper problem: %d/%d " BIGINT_FORMAT " %d %d %d %d",
- me,thr->get_tid(),update->ntimestep,
- atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
- error->warning(FLERR,str,0);
- fprintf(screen," 1st atom: %d %g %g %g\n",
- me,x[i1][0],x[i1][1],x[i1][2]);
- fprintf(screen," 2nd atom: %d %g %g %g\n",
- me,x[i2][0],x[i2][1],x[i2][2]);
- fprintf(screen," 3rd atom: %d %g %g %g\n",
- me,x[i3][0],x[i3][1],x[i3][2]);
- fprintf(screen," 4th atom: %d %g %g %g\n",
- me,x[i4][0],x[i4][1],x[i4][2]);
+ char str[128];
+ sprintf(str,"Improper problem: %d/%d " BIGINT_FORMAT " %d %d %d %d",
+ me,thr->get_tid(),update->ntimestep,
+ atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
+ error->warning(FLERR,str,0);
+ fprintf(screen," 1st atom: %d %g %g %g\n",
+ me,x[i1][0],x[i1][1],x[i1][2]);
+ fprintf(screen," 2nd atom: %d %g %g %g\n",
+ me,x[i2][0],x[i2][1],x[i2][2]);
+ fprintf(screen," 3rd atom: %d %g %g %g\n",
+ me,x[i3][0],x[i3][1],x[i3][2]);
+ fprintf(screen," 4th atom: %d %g %g %g\n",
+ me,x[i4][0],x[i4][1],x[i4][2]);
}
}
-
+
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
@@ -202,7 +202,7 @@ void ImproperCvffOMP::eval(int nfrom, int nto, ThrData * const thr)
// p = 1 + cos(n*phi) for d = 1
// p = 1 - cos(n*phi) for d = -1
// pd = dp/dc / 2
-
+
m = multiplicity[type];
if (m == 2) {
@@ -231,7 +231,7 @@ void ImproperCvffOMP::eval(int nfrom, int nto, ThrData * const thr)
p = 2.0;
pd = 0.0;
}
-
+
if (sign[type] == -1) {
p = 2.0 - p;
pd = -pd;
@@ -297,6 +297,6 @@ void ImproperCvffOMP::eval(int nfrom, int nto, ThrData * const thr)
if (EVFLAG)
ev_tally_thr(this,i1,i2,i3,i4,nlocal,NEWTON_BOND,eimproper,f1,f3,f4,
- vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,thr);
+ vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,thr);
}
}
diff --git a/src/USER-OMP/improper_cvff_omp.h b/src/USER-OMP/improper_cvff_omp.h
index 912da93b5da63a217460812c2db176ccb374748c..8ab8f1615cb5439ac55ab54c79e2e2fca232ee2d 100644
--- a/src/USER-OMP/improper_cvff_omp.h
+++ b/src/USER-OMP/improper_cvff_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/improper_harmonic_omp.cpp b/src/USER-OMP/improper_harmonic_omp.cpp
index 748afdd2ca2dcaa9369e1255d8f5333a3ba17317..77f1a1c596703c946cb80813807d36f6c2837cad 100644
--- a/src/USER-OMP/improper_harmonic_omp.cpp
+++ b/src/USER-OMP/improper_harmonic_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -64,11 +64,11 @@ void ImproperHarmonicOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_bond) eval<0,0,1>(ifrom, ito, thr);
@@ -123,13 +123,13 @@ void ImproperHarmonicOMP::eval(int nfrom, int nto, ThrData * const thr)
ss1 = 1.0 / (vb1x*vb1x + vb1y*vb1y + vb1z*vb1z);
ss2 = 1.0 / (vb2x*vb2x + vb2y*vb2y + vb2z*vb2z);
ss3 = 1.0 / (vb3x*vb3x + vb3y*vb3y + vb3z*vb3z);
-
+
r1 = sqrt(ss1);
r2 = sqrt(ss2);
r3 = sqrt(ss3);
-
+
// sin and cos of angle
-
+
c0 = (vb1x * vb3x + vb1y * vb3y + vb1z * vb3z) * r1 * r3;
c1 = (vb1x * vb2x + vb1y * vb2y + vb1z * vb2z) * r1 * r2;
c2 = -(vb3x * vb2x + vb3y * vb2y + vb3z * vb2z) * r3 * r2;
@@ -151,22 +151,22 @@ void ImproperHarmonicOMP::eval(int nfrom, int nto, ThrData * const thr)
int me = comm->me;
if (screen) {
- char str[128];
- sprintf(str,"Improper problem: %d/%d " BIGINT_FORMAT " %d %d %d %d",
- me,thr->get_tid(),update->ntimestep,
- atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
- error->warning(FLERR,str,0);
- fprintf(screen," 1st atom: %d %g %g %g\n",
- me,x[i1][0],x[i1][1],x[i1][2]);
- fprintf(screen," 2nd atom: %d %g %g %g\n",
- me,x[i2][0],x[i2][1],x[i2][2]);
- fprintf(screen," 3rd atom: %d %g %g %g\n",
- me,x[i3][0],x[i3][1],x[i3][2]);
- fprintf(screen," 4th atom: %d %g %g %g\n",
- me,x[i4][0],x[i4][1],x[i4][2]);
+ char str[128];
+ sprintf(str,"Improper problem: %d/%d " BIGINT_FORMAT " %d %d %d %d",
+ me,thr->get_tid(),update->ntimestep,
+ atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
+ error->warning(FLERR,str,0);
+ fprintf(screen," 1st atom: %d %g %g %g\n",
+ me,x[i1][0],x[i1][1],x[i1][2]);
+ fprintf(screen," 2nd atom: %d %g %g %g\n",
+ me,x[i2][0],x[i2][1],x[i2][2]);
+ fprintf(screen," 3rd atom: %d %g %g %g\n",
+ me,x[i3][0],x[i3][1],x[i3][2]);
+ fprintf(screen," 4th atom: %d %g %g %g\n",
+ me,x[i4][0],x[i4][1],x[i4][2]);
}
}
-
+
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
@@ -238,6 +238,6 @@ void ImproperHarmonicOMP::eval(int nfrom, int nto, ThrData * const thr)
if (EVFLAG)
ev_tally_thr(this,i1,i2,i3,i4,nlocal,NEWTON_BOND,eimproper,f1,f3,f4,
- vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,thr);
+ vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,thr);
}
}
diff --git a/src/USER-OMP/improper_harmonic_omp.h b/src/USER-OMP/improper_harmonic_omp.h
index 73cf6c21dbb254e69e62b3ce8296c31ade8193ba..d6325016a797938d65264e6f3d17e768938aefc6 100644
--- a/src/USER-OMP/improper_harmonic_omp.h
+++ b/src/USER-OMP/improper_harmonic_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/improper_ring_omp.cpp b/src/USER-OMP/improper_ring_omp.cpp
index 99ae6e532b40c695433510e8c17d7cbbb9331a60..6f8a73c41c7f6c55576f50792fa57b02fd8b6a49 100644
--- a/src/USER-OMP/improper_ring_omp.cpp
+++ b/src/USER-OMP/improper_ring_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -64,11 +64,11 @@ void ImproperRingOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_bond) eval<0,0,1>(ifrom, ito, thr);
@@ -90,15 +90,15 @@ void ImproperRingOMP::eval(int nfrom, int nto, ThrData * const thr)
/* Compatibility variables. */
double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z;
double f1[3], f3[3], f4[3];
-
+
/* Actual computation variables. */
int at1[3], at2[3], at3[3], icomb;
- double bvec1x[3], bvec1y[3], bvec1z[3],
- bvec2x[3], bvec2y[3], bvec2z[3],
+ double bvec1x[3], bvec1y[3], bvec1z[3],
+ bvec2x[3], bvec2y[3], bvec2z[3],
bvec1n[3], bvec2n[3], bend_angle[3];
double angle_summer, angfac, cfact1, cfact2, cfact3;
double cjiji, ckjji, ckjkj, fix, fiy, fiz, fjx, fjy, fjz, fkx, fky, fkz;
-
+
eimproper = 0.0;
const double * const * const x = atom->x;
@@ -106,7 +106,7 @@ void ImproperRingOMP::eval(int nfrom, int nto, ThrData * const thr)
const int * const * const improperlist = neighbor->improperlist;
const int nlocal = atom->nlocal;
- /* A description of the potential can be found in
+ /* A description of the potential can be found in
Macromolecules 35, pp. 1463-1472 (2002). */
for (n = nfrom; n < nto; n++) {
/* Take the ids of the atoms contributing to the improper potential. */
@@ -116,9 +116,9 @@ void ImproperRingOMP::eval(int nfrom, int nto, ThrData * const thr)
i4 = improperlist[n][3]; /* Atom "9" ... */
type = improperlist[n][4];
- /* Calculate the necessary variables for LAMMPS implementation.
+ /* Calculate the necessary variables for LAMMPS implementation.
if (evflag) ev_tally(i1,i2,i3,i4,nlocal,newton_bond,eimproper,f1,f3,f4,
- vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
+ vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
Although, they are irrelevant to the calculation of the potential, we keep
them for maximal compatibility. */
vb1x = x[i1][0] - x[i2][0]; vb1y = x[i1][1] - x[i2][1]; vb1z = x[i1][2] - x[i2][2];
@@ -130,137 +130,137 @@ void ImproperRingOMP::eval(int nfrom, int nto, ThrData * const thr)
vb3x = x[i4][0] - x[i3][0]; vb3y = x[i4][1] - x[i3][1]; vb3z = x[i4][2] - x[i3][2];
domain->minimum_image(vb3x,vb3y,vb3z);
-
+
/* Pass the atom tags to form the necessary combinations. */
at1[0] = i1; at2[0] = i2; at3[0] = i4; /* ids: 1-2-9 */
at1[1] = i1; at2[1] = i2; at3[1] = i3; /* ids: 1-2-3 */
at1[2] = i4; at2[2] = i2; at3[2] = i3; /* ids: 9-2-3 */
-
+
/* Initialize the sum of the angles differences. */
angle_summer = 0.0;
/* Take a loop over the three angles, defined by each triad: */
for (icomb = 0; icomb < 3; icomb ++) {
-
+
/* Bond vector connecting the first and the second atom. */
bvec1x[icomb] = x[at2[icomb]][0] - x[at1[icomb]][0];
bvec1y[icomb] = x[at2[icomb]][1] - x[at1[icomb]][1];
bvec1z[icomb] = x[at2[icomb]][2] - x[at1[icomb]][2];
domain -> minimum_image(bvec1x[icomb], bvec1y[icomb], bvec1z[icomb]);
/* also calculate the norm of the vector: */
- bvec1n[icomb] = sqrt( bvec1x[icomb]*bvec1x[icomb]
- + bvec1y[icomb]*bvec1y[icomb]
- + bvec1z[icomb]*bvec1z[icomb]);
+ bvec1n[icomb] = sqrt( bvec1x[icomb]*bvec1x[icomb]
+ + bvec1y[icomb]*bvec1y[icomb]
+ + bvec1z[icomb]*bvec1z[icomb]);
/* Bond vector connecting the second and the third atom. */
bvec2x[icomb] = x[at3[icomb]][0] - x[at2[icomb]][0];
bvec2y[icomb] = x[at3[icomb]][1] - x[at2[icomb]][1];
bvec2z[icomb] = x[at3[icomb]][2] - x[at2[icomb]][2];
domain -> minimum_image(bvec2x[icomb], bvec2y[icomb], bvec2z[icomb]);
/* also calculate the norm of the vector: */
- bvec2n[icomb] = sqrt( bvec2x[icomb]*bvec2x[icomb]
- + bvec2y[icomb]*bvec2y[icomb]
- + bvec2z[icomb]*bvec2z[icomb]);
-
+ bvec2n[icomb] = sqrt( bvec2x[icomb]*bvec2x[icomb]
+ + bvec2y[icomb]*bvec2y[icomb]
+ + bvec2z[icomb]*bvec2z[icomb]);
+
/* Calculate the bending angle of the atom triad: */
- bend_angle[icomb] = ( bvec2x[icomb]*bvec1x[icomb]
- + bvec2y[icomb]*bvec1y[icomb]
- + bvec2z[icomb]*bvec1z[icomb]);
+ bend_angle[icomb] = ( bvec2x[icomb]*bvec1x[icomb]
+ + bvec2y[icomb]*bvec1y[icomb]
+ + bvec2z[icomb]*bvec1z[icomb]);
bend_angle[icomb] /= (bvec1n[icomb] * bvec2n[icomb]);
if (bend_angle[icomb] > 1.0) bend_angle[icomb] -= SMALL;
if (bend_angle[icomb] < -1.0) bend_angle[icomb] += SMALL;
/* Append the current angle to the sum of angle differences. */
angle_summer += (bend_angle[icomb] - chi[type]);
- }
- if (EFLAG) eimproper = (1.0/6.0) *k[type] * pow(angle_summer,6.0);
+ }
+ if (EFLAG) eimproper = (1.0/6.0) *k[type] * pow(angle_summer,6.0);
/*
- printf("The tags: %d-%d-%d-%d, of type %d .\n",atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4],type);
+ printf("The tags: %d-%d-%d-%d, of type %d .\n",atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4],type);
// printf("The coordinates of the first: %f, %f, %f.\n", x[i1][0], x[i1][1], x[i1][2]);
// printf("The coordinates of the second: %f, %f, %f.\n", x[i2][0], x[i2][1], x[i2][2]);
// printf("The coordinates of the third: %f, %f, %f.\n", x[i3][0], x[i3][1], x[i3][2]);
// printf("The coordinates of the fourth: %f, %f, %f.\n", x[i4][0], x[i4][1], x[i4][2]);
printf("The angles are: %f / %f / %f equilibrium: %f.\n", bend_angle[0], bend_angle[1], bend_angle[2],chi[type]);
printf("The energy of the improper: %f with prefactor %f.\n", eimproper,(1.0/6.0)*k[type]);
- printf("The sum of the angles: %f.\n", angle_summer);
+ printf("The sum of the angles: %f.\n", angle_summer);
*/
- /* Force calculation acting on all atoms.
+ /* Force calculation acting on all atoms.
Calculate the derivatives of the potential. */
angfac = k[type] * pow(angle_summer,5.0);
f1[0] = 0.0; f1[1] = 0.0; f1[2] = 0.0;
f3[0] = 0.0; f3[1] = 0.0; f3[2] = 0.0;
- f4[0] = 0.0; f4[1] = 0.0; f4[2] = 0.0;
-
+ f4[0] = 0.0; f4[1] = 0.0; f4[2] = 0.0;
+
/* Take a loop over the three angles, defined by each triad: */
for (icomb = 0; icomb < 3; icomb ++)
{
- /* Calculate the squares of the distances. */
- cjiji = bvec1n[icomb] * bvec1n[icomb]; ckjkj = bvec2n[icomb] * bvec2n[icomb];
-
- ckjji = bvec2x[icomb] * bvec1x[icomb]
- + bvec2y[icomb] * bvec1y[icomb]
- + bvec2z[icomb] * bvec1z[icomb] ;
-
- cfact1 = angfac / (sqrt(ckjkj * cjiji));
- cfact2 = ckjji / ckjkj;
- cfact3 = ckjji / cjiji;
-
- /* Calculate the force acted on the thrid atom of the angle. */
- fkx = cfact2 * bvec2x[icomb] - bvec1x[icomb];
- fky = cfact2 * bvec2y[icomb] - bvec1y[icomb];
- fkz = cfact2 * bvec2z[icomb] - bvec1z[icomb];
-
- /* Calculate the force acted on the first atom of the angle. */
- fix = bvec2x[icomb] - cfact3 * bvec1x[icomb];
- fiy = bvec2y[icomb] - cfact3 * bvec1y[icomb];
- fiz = bvec2z[icomb] - cfact3 * bvec1z[icomb];
-
- /* Finally, calculate the force acted on the middle atom of the angle.*/
- fjx = - fix - fkx; fjy = - fiy - fky; fjz = - fiz - fkz;
-
- /* Consider the appropriate scaling of the forces: */
- fix *= cfact1; fiy *= cfact1; fiz *= cfact1;
- fjx *= cfact1; fjy *= cfact1; fjz *= cfact1;
- fkx *= cfact1; fky *= cfact1; fkz *= cfact1;
-
- if (at1[icomb] == i1) {f1[0] += fix; f1[1] += fiy; f1[2] += fiz;}
- else if (at2[icomb] == i1) {f1[0] += fjx; f1[1] += fjy; f1[2] += fjz;}
- else if (at3[icomb] == i1) {f1[0] += fkx; f1[1] += fky; f1[2] += fkz;}
-
- if (at1[icomb] == i3) {f3[0] += fix; f3[1] += fiy; f3[2] += fiz;}
- else if (at2[icomb] == i3) {f3[0] += fjx; f3[1] += fjy; f3[2] += fjz;}
- else if (at3[icomb] == i3) {f3[0] += fkx; f3[1] += fky; f3[2] += fkz;}
-
- if (at1[icomb] == i4) {f4[0] += fix; f4[1] += fiy; f4[2] += fiz;}
- else if (at2[icomb] == i4) {f4[0] += fjx; f4[1] += fjy; f4[2] += fjz;}
- else if (at3[icomb] == i4) {f4[0] += fkx; f4[1] += fky; f4[2] += fkz;}
-
-
- /* Store the contribution to the global arrays: */
- /* Take the id of the atom from the at1[icomb] element, i1 = at1[icomb]. */
- if (NEWTON_BOND || at1[icomb] < nlocal) {
- f[at1[icomb]][0] += fix;
- f[at1[icomb]][1] += fiy;
- f[at1[icomb]][2] += fiz;
- }
- /* Take the id of the atom from the at2[icomb] element, i2 = at2[icomb]. */
- if (NEWTON_BOND || at2[icomb] < nlocal) {
- f[at2[icomb]][0] += fjx;
- f[at2[icomb]][1] += fjy;
- f[at2[icomb]][2] += fjz;
- }
- /* Take the id of the atom from the at3[icomb] element, i3 = at3[icomb]. */
- if (NEWTON_BOND || at3[icomb] < nlocal) {
- f[at3[icomb]][0] += fkx;
- f[at3[icomb]][1] += fky;
- f[at3[icomb]][2] += fkz;
- }
-
+ /* Calculate the squares of the distances. */
+ cjiji = bvec1n[icomb] * bvec1n[icomb]; ckjkj = bvec2n[icomb] * bvec2n[icomb];
+
+ ckjji = bvec2x[icomb] * bvec1x[icomb]
+ + bvec2y[icomb] * bvec1y[icomb]
+ + bvec2z[icomb] * bvec1z[icomb] ;
+
+ cfact1 = angfac / (sqrt(ckjkj * cjiji));
+ cfact2 = ckjji / ckjkj;
+ cfact3 = ckjji / cjiji;
+
+ /* Calculate the force acted on the thrid atom of the angle. */
+ fkx = cfact2 * bvec2x[icomb] - bvec1x[icomb];
+ fky = cfact2 * bvec2y[icomb] - bvec1y[icomb];
+ fkz = cfact2 * bvec2z[icomb] - bvec1z[icomb];
+
+ /* Calculate the force acted on the first atom of the angle. */
+ fix = bvec2x[icomb] - cfact3 * bvec1x[icomb];
+ fiy = bvec2y[icomb] - cfact3 * bvec1y[icomb];
+ fiz = bvec2z[icomb] - cfact3 * bvec1z[icomb];
+
+ /* Finally, calculate the force acted on the middle atom of the angle.*/
+ fjx = - fix - fkx; fjy = - fiy - fky; fjz = - fiz - fkz;
+
+ /* Consider the appropriate scaling of the forces: */
+ fix *= cfact1; fiy *= cfact1; fiz *= cfact1;
+ fjx *= cfact1; fjy *= cfact1; fjz *= cfact1;
+ fkx *= cfact1; fky *= cfact1; fkz *= cfact1;
+
+ if (at1[icomb] == i1) {f1[0] += fix; f1[1] += fiy; f1[2] += fiz;}
+ else if (at2[icomb] == i1) {f1[0] += fjx; f1[1] += fjy; f1[2] += fjz;}
+ else if (at3[icomb] == i1) {f1[0] += fkx; f1[1] += fky; f1[2] += fkz;}
+
+ if (at1[icomb] == i3) {f3[0] += fix; f3[1] += fiy; f3[2] += fiz;}
+ else if (at2[icomb] == i3) {f3[0] += fjx; f3[1] += fjy; f3[2] += fjz;}
+ else if (at3[icomb] == i3) {f3[0] += fkx; f3[1] += fky; f3[2] += fkz;}
+
+ if (at1[icomb] == i4) {f4[0] += fix; f4[1] += fiy; f4[2] += fiz;}
+ else if (at2[icomb] == i4) {f4[0] += fjx; f4[1] += fjy; f4[2] += fjz;}
+ else if (at3[icomb] == i4) {f4[0] += fkx; f4[1] += fky; f4[2] += fkz;}
+
+
+ /* Store the contribution to the global arrays: */
+ /* Take the id of the atom from the at1[icomb] element, i1 = at1[icomb]. */
+ if (NEWTON_BOND || at1[icomb] < nlocal) {
+ f[at1[icomb]][0] += fix;
+ f[at1[icomb]][1] += fiy;
+ f[at1[icomb]][2] += fiz;
+ }
+ /* Take the id of the atom from the at2[icomb] element, i2 = at2[icomb]. */
+ if (NEWTON_BOND || at2[icomb] < nlocal) {
+ f[at2[icomb]][0] += fjx;
+ f[at2[icomb]][1] += fjy;
+ f[at2[icomb]][2] += fjz;
+ }
+ /* Take the id of the atom from the at3[icomb] element, i3 = at3[icomb]. */
+ if (NEWTON_BOND || at3[icomb] < nlocal) {
+ f[at3[icomb]][0] += fkx;
+ f[at3[icomb]][1] += fky;
+ f[at3[icomb]][2] += fkz;
+ }
+
}
if (EVFLAG)
ev_tally_thr(this,i1,i2,i3,i4,nlocal,NEWTON_BOND,eimproper,f1,f3,f4,
- vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,thr);
+ vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,thr);
}
}
diff --git a/src/USER-OMP/improper_ring_omp.h b/src/USER-OMP/improper_ring_omp.h
index 52743f8d84b2099be619dd6f17eb3853ee51ef1a..2b2616ab034d5b374d677ac86f9a83d737abf7b9 100644
--- a/src/USER-OMP/improper_ring_omp.h
+++ b/src/USER-OMP/improper_ring_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/improper_umbrella_omp.cpp b/src/USER-OMP/improper_umbrella_omp.cpp
index 4b792b6218ad63026d69338efb13946e4b267cda..ebc1fc299f86d6d2718db567545d1ec020b0214b 100644
--- a/src/USER-OMP/improper_umbrella_omp.cpp
+++ b/src/USER-OMP/improper_umbrella_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -64,11 +64,11 @@ void ImproperUmbrellaOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_bond) eval<0,0,1>(ifrom, ito, thr);
@@ -153,22 +153,22 @@ void ImproperUmbrellaOMP::eval(int nfrom, int nto, ThrData * const thr)
int me = comm->me;
if (screen) {
- char str[128];
- sprintf(str,"Improper problem: %d/%d " BIGINT_FORMAT " %d %d %d %d",
- me,thr->get_tid(),update->ntimestep,
- atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
- error->warning(FLERR,str,0);
- fprintf(screen," 1st atom: %d %g %g %g\n",
- me,x[i1][0],x[i1][1],x[i1][2]);
- fprintf(screen," 2nd atom: %d %g %g %g\n",
- me,x[i2][0],x[i2][1],x[i2][2]);
- fprintf(screen," 3rd atom: %d %g %g %g\n",
- me,x[i3][0],x[i3][1],x[i3][2]);
- fprintf(screen," 4th atom: %d %g %g %g\n",
- me,x[i4][0],x[i4][1],x[i4][2]);
+ char str[128];
+ sprintf(str,"Improper problem: %d/%d " BIGINT_FORMAT " %d %d %d %d",
+ me,thr->get_tid(),update->ntimestep,
+ atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
+ error->warning(FLERR,str,0);
+ fprintf(screen," 1st atom: %d %g %g %g\n",
+ me,x[i1][0],x[i1][1],x[i1][2]);
+ fprintf(screen," 2nd atom: %d %g %g %g\n",
+ me,x[i2][0],x[i2][1],x[i2][2]);
+ fprintf(screen," 3rd atom: %d %g %g %g\n",
+ me,x[i3][0],x[i3][1],x[i3][2]);
+ fprintf(screen," 4th atom: %d %g %g %g\n",
+ me,x[i4][0],x[i4][1],x[i4][2]);
}
}
-
+
if (c > 1.0) s = 1.0;
if (c < -1.0) s = -1.0;
@@ -176,15 +176,15 @@ void ImproperUmbrellaOMP::eval(int nfrom, int nto, ThrData * const thr)
if (s < SMALL) s = SMALL;
cotphi = c/s;
- projhfg = (vb3x*vb1x+vb3y*vb1y+vb3z*vb1z) /
- sqrt(vb1x*vb1x+vb1y*vb1y+vb1z*vb1z);
- projhfg += (vb3x*vb2x+vb3y*vb2y+vb3z*vb2z) /
+ projhfg = (vb3x*vb1x+vb3y*vb1y+vb3z*vb1z) /
+ sqrt(vb1x*vb1x+vb1y*vb1y+vb1z*vb1z);
+ projhfg += (vb3x*vb2x+vb3y*vb2y+vb3z*vb2z) /
sqrt(vb2x*vb2x+vb2y*vb2y+vb2z*vb2z);
if (projhfg > 0.0) {
s *= -1.0;
cotphi *= -1.0;
}
-
+
// force and energy
// if w0 = 0: E = k * (1 - cos w)
// if w0 != 0: E = 0.5 * C (cos w - cos w0)^2, C = k/(sin(w0)^2
@@ -254,6 +254,6 @@ void ImproperUmbrellaOMP::eval(int nfrom, int nto, ThrData * const thr)
if (EVFLAG)
ev_tally_thr(this,i1,i2,i3,i4,nlocal,NEWTON_BOND,eimproper,f1,f3,f4,
- vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,thr);
+ vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,thr);
}
}
diff --git a/src/USER-OMP/improper_umbrella_omp.h b/src/USER-OMP/improper_umbrella_omp.h
index 39feb6d7b3384b069f218dcce9406174f79212d8..41bdfed4d5d08be2d87155dddc8e51d1f156ef5a 100644
--- a/src/USER-OMP/improper_umbrella_omp.h
+++ b/src/USER-OMP/improper_umbrella_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/neigh_derive_omp.cpp b/src/USER-OMP/neigh_derive_omp.cpp
index 187a6c8753cf108b2793f8c2ee5a637f8f713011..4356f17b62388ae1bc60500e957ea4e6c4803491 100644
--- a/src/USER-OMP/neigh_derive_omp.cpp
+++ b/src/USER-OMP/neigh_derive_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -62,7 +62,7 @@ void Neighbor::half_from_full_no_newton_omp(NeighList *list)
if (pgsize - npnt < oneatom) {
npnt = 0;
npage += nthreads;
- // only one thread at a time may check whether we
+ // only one thread at a time may check whether we
// need new neighbor list pages and then add to them.
if (npage >= list->maxpage) list->add_pages(nthreads);
}
@@ -160,13 +160,13 @@ void Neighbor::half_from_full_newton_omp(NeighList *list)
joriginal = jlist[jj];
j = joriginal & NEIGHMASK;
if (j < nlocal) {
- if (i > j) continue;
+ if (i > j) continue;
} else {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp) {
- if (x[j][1] < ytmp) continue;
- if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
- }
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp) {
+ if (x[j][1] < ytmp) continue;
+ if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
+ }
}
neighptr[n++] = joriginal;
}
@@ -181,4 +181,3 @@ void Neighbor::half_from_full_newton_omp(NeighList *list)
NEIGH_OMP_CLOSE;
list->inum = inum_full;
}
-
diff --git a/src/USER-OMP/neigh_full_omp.cpp b/src/USER-OMP/neigh_full_omp.cpp
index dcfaad9a4917ece15389fb8ec3b6d89be6f5a78a..91fd0fd1d38544a8c9a829e802e75b96949f9398 100644
--- a/src/USER-OMP/neigh_full_omp.cpp
+++ b/src/USER-OMP/neigh_full_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -94,10 +94,10 @@ void Neighbor::full_nsq_omp(NeighList *list)
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- which = find_special(special[i],nspecial[i],tag[j]);
- if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
+ if (molecular) {
+ which = find_special(special[i],nspecial[i],tag[j]);
+ if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
}
}
@@ -177,35 +177,35 @@ void Neighbor::full_nsq_ghost_omp(NeighList *list)
if (i < nlocal) {
for (j = 0; j < nall; j++) {
- if (i == j) continue;
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- which = find_special(special[i],nspecial[i],tag[j]);
- if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
+ if (i == j) continue;
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ which = find_special(special[i],nspecial[i],tag[j]);
+ if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
}
} else {
for (j = 0; j < nall; j++) {
- if (i == j) continue;
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighghostsq[itype][jtype])
- neighptr[n++] = j;
+ if (i == j) continue;
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighghostsq[itype][jtype])
+ neighptr[n++] = j;
}
}
@@ -291,22 +291,22 @@ void Neighbor::full_bin_omp(NeighList *list)
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- if (i == j) continue;
-
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- which = find_special(special[i],nspecial[i],tag[j]);
- if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
+ if (i == j) continue;
+
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ which = find_special(special[i],nspecial[i],tag[j]);
+ if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
}
}
@@ -396,49 +396,49 @@ void Neighbor::full_bin_ghost_omp(NeighList *list)
if (i < nlocal) {
ibin = coord2bin(x[i]);
for (k = 0; k < nstencil; k++) {
- for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- if (i == j) continue;
-
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- which = find_special(special[i],nspecial[i],tag[j]);
- if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
- }
+ for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
+ if (i == j) continue;
+
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ which = find_special(special[i],nspecial[i],tag[j]);
+ if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
+ }
}
} else {
ibin = coord2bin(x[i],xbin,ybin,zbin);
for (k = 0; k < nstencil; k++) {
- xbin2 = xbin + stencilxyz[k][0];
- ybin2 = ybin + stencilxyz[k][1];
- zbin2 = zbin + stencilxyz[k][2];
- if (xbin2 < 0 || xbin2 >= mbinx ||
- ybin2 < 0 || ybin2 >= mbiny ||
- zbin2 < 0 || zbin2 >= mbinz) continue;
- for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- if (i == j) continue;
-
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighghostsq[itype][jtype])
- neighptr[n++] = j;
- }
+ xbin2 = xbin + stencilxyz[k][0];
+ ybin2 = ybin + stencilxyz[k][1];
+ zbin2 = zbin + stencilxyz[k][2];
+ if (xbin2 < 0 || xbin2 >= mbinx ||
+ ybin2 < 0 || ybin2 >= mbiny ||
+ zbin2 < 0 || zbin2 >= mbinz) continue;
+ for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
+ if (i == j) continue;
+
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighghostsq[itype][jtype])
+ neighptr[n++] = j;
+ }
}
}
@@ -531,23 +531,23 @@ void Neighbor::full_multi_omp(NeighList *list)
ns = nstencil_multi[itype];
for (k = 0; k < ns; k++) {
for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
- jtype = type[j];
- if (cutsq[jtype] < distsq[k]) continue;
- if (i == j) continue;
-
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- which = find_special(special[i],nspecial[i],tag[j]);
- if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
+ jtype = type[j];
+ if (cutsq[jtype] < distsq[k]) continue;
+ if (i == j) continue;
+
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ which = find_special(special[i],nspecial[i],tag[j]);
+ if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
}
}
diff --git a/src/USER-OMP/neigh_gran_omp.cpp b/src/USER-OMP/neigh_gran_omp.cpp
index 8a03da8e64ccbc1e9db47adbf7ef27e24b7319cc..71fee4ec4ff246c67bd0c29278541a66afe26c2c 100644
--- a/src/USER-OMP/neigh_gran_omp.cpp
+++ b/src/USER-OMP/neigh_gran_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -90,20 +90,20 @@ void Neighbor::granular_nsq_no_newton_omp(NeighList *list)
#endif
{
if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage += nthreads;
- if (npage >= list->maxpage) {
- list->add_pages(nthreads);
- if (fix_history)
- listgranhistory->add_pages(nthreads);
- }
+ npnt = 0;
+ npage += nthreads;
+ if (npage >= list->maxpage) {
+ list->add_pages(nthreads);
+ if (fix_history)
+ listgranhistory->add_pages(nthreads);
+ }
}
n = nn = 0;
neighptr = &(list->pages[npage][npnt]);
if (fix_history) {
- touchptr = &(listgranhistory->pages[npage][npnt]);
- shearptr = &(listgranhistory->dpages[npage][3*npnt]);
+ touchptr = &(listgranhistory->pages[npage][npnt]);
+ shearptr = &(listgranhistory->dpages[npage][3*npnt]);
}
}
@@ -126,32 +126,32 @@ void Neighbor::granular_nsq_no_newton_omp(NeighList *list)
cutsq = (radsum+skin) * (radsum+skin);
if (rsq <= cutsq) {
- neighptr[n] = j;
-
- if (fix_history) {
- if (rsq < radsum*radsum) {
- for (m = 0; m < npartner[i]; m++)
- if (partner[i][m] == tag[j]) break;
- if (m < npartner[i]) {
- touchptr[n] = 1;
- shearptr[nn++] = shearpartner[i][m][0];
- shearptr[nn++] = shearpartner[i][m][1];
- shearptr[nn++] = shearpartner[i][m][2];
- } else {
- touchptr[n] = 0;
- shearptr[nn++] = 0.0;
- shearptr[nn++] = 0.0;
- shearptr[nn++] = 0.0;
- }
- } else {
- touchptr[n] = 0;
- shearptr[nn++] = 0.0;
- shearptr[nn++] = 0.0;
- shearptr[nn++] = 0.0;
- }
- }
-
- n++;
+ neighptr[n] = j;
+
+ if (fix_history) {
+ if (rsq < radsum*radsum) {
+ for (m = 0; m < npartner[i]; m++)
+ if (partner[i][m] == tag[j]) break;
+ if (m < npartner[i]) {
+ touchptr[n] = 1;
+ shearptr[nn++] = shearpartner[i][m][0];
+ shearptr[nn++] = shearpartner[i][m][1];
+ shearptr[nn++] = shearpartner[i][m][2];
+ } else {
+ touchptr[n] = 0;
+ shearptr[nn++] = 0.0;
+ shearptr[nn++] = 0.0;
+ shearptr[nn++] = 0.0;
+ }
+ } else {
+ touchptr[n] = 0;
+ shearptr[nn++] = 0.0;
+ shearptr[nn++] = 0.0;
+ shearptr[nn++] = 0.0;
+ }
+ }
+
+ n++;
}
}
@@ -236,18 +236,18 @@ void Neighbor::granular_nsq_newton_omp(NeighList *list)
if (includegroup && !(mask[j] & bitmask)) continue;
if (j >= nlocal) {
- jtag = tag[j];
- if (itag > jtag) {
- if ((itag+jtag) % 2 == 0) continue;
- } else if (itag < jtag) {
- if ((itag+jtag) % 2 == 1) continue;
- } else {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp) {
- if (x[j][1] < ytmp) continue;
- if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
- }
- }
+ jtag = tag[j];
+ if (itag > jtag) {
+ if ((itag+jtag) % 2 == 0) continue;
+ } else if (itag < jtag) {
+ if ((itag+jtag) % 2 == 1) continue;
+ } else {
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp) {
+ if (x[j][1] < ytmp) continue;
+ if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
+ }
+ }
}
if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
@@ -258,7 +258,7 @@ void Neighbor::granular_nsq_newton_omp(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
radsum = radi + radius[j];
cutsq = (radsum+skin) * (radsum+skin);
-
+
if (rsq <= cutsq) neighptr[n++] = j;
}
@@ -348,20 +348,20 @@ void Neighbor::granular_bin_no_newton_omp(NeighList *list)
#endif
{
if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage += nthreads;
- if (npage >= list->maxpage) {
- list->add_pages(nthreads);
- if (fix_history)
- listgranhistory->add_pages(nthreads);
- }
+ npnt = 0;
+ npage += nthreads;
+ if (npage >= list->maxpage) {
+ list->add_pages(nthreads);
+ if (fix_history)
+ listgranhistory->add_pages(nthreads);
+ }
}
n = nn = 0;
neighptr = &(list->pages[npage][npnt]);
if (fix_history) {
- touchptr = &(listgranhistory->pages[npage][npnt]);
- shearptr = &(listgranhistory->dpages[npage][3*npnt]);
+ touchptr = &(listgranhistory->pages[npage][npnt]);
+ shearptr = &(listgranhistory->dpages[npage][3*npnt]);
}
}
@@ -378,44 +378,44 @@ void Neighbor::granular_bin_no_newton_omp(NeighList *list)
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- if (j <= i) continue;
- if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
- radsum = radi + radius[j];
- cutsq = (radsum+skin) * (radsum+skin);
-
- if (rsq <= cutsq) {
- neighptr[n] = j;
-
- if (fix_history) {
- if (rsq < radsum*radsum) {
- for (m = 0; m < npartner[i]; m++)
- if (partner[i][m] == tag[j]) break;
- if (m < npartner[i]) {
- touchptr[n] = 1;
- shearptr[nn++] = shearpartner[i][m][0];
- shearptr[nn++] = shearpartner[i][m][1];
- shearptr[nn++] = shearpartner[i][m][2];
- } else {
- touchptr[n] = 0;
- shearptr[nn++] = 0.0;
- shearptr[nn++] = 0.0;
- shearptr[nn++] = 0.0;
- }
- } else {
- touchptr[n] = 0;
- shearptr[nn++] = 0.0;
- shearptr[nn++] = 0.0;
- shearptr[nn++] = 0.0;
- }
- }
-
- n++;
- }
+ if (j <= i) continue;
+ if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+ radsum = radi + radius[j];
+ cutsq = (radsum+skin) * (radsum+skin);
+
+ if (rsq <= cutsq) {
+ neighptr[n] = j;
+
+ if (fix_history) {
+ if (rsq < radsum*radsum) {
+ for (m = 0; m < npartner[i]; m++)
+ if (partner[i][m] == tag[j]) break;
+ if (m < npartner[i]) {
+ touchptr[n] = 1;
+ shearptr[nn++] = shearpartner[i][m][0];
+ shearptr[nn++] = shearpartner[i][m][1];
+ shearptr[nn++] = shearpartner[i][m][2];
+ } else {
+ touchptr[n] = 0;
+ shearptr[nn++] = 0.0;
+ shearptr[nn++] = 0.0;
+ shearptr[nn++] = 0.0;
+ }
+ } else {
+ touchptr[n] = 0;
+ shearptr[nn++] = 0.0;
+ shearptr[nn++] = 0.0;
+ shearptr[nn++] = 0.0;
+ }
+ }
+
+ n++;
+ }
}
}
@@ -503,11 +503,11 @@ void Neighbor::granular_bin_newton_omp(NeighList *list)
for (j = bins[i]; j >= 0; j = bins[j]) {
if (j >= nlocal) {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp) {
- if (x[j][1] < ytmp) continue;
- if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
- }
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp) {
+ if (x[j][1] < ytmp) continue;
+ if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
+ }
}
if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
@@ -527,16 +527,16 @@ void Neighbor::granular_bin_newton_omp(NeighList *list)
ibin = coord2bin(x[i]);
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
+ if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
- radsum = radi + radius[j];
- cutsq = (radsum+skin) * (radsum+skin);
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+ radsum = radi + radius[j];
+ cutsq = (radsum+skin) * (radsum+skin);
- if (rsq <= cutsq) neighptr[n++] = j;
+ if (rsq <= cutsq) neighptr[n++] = j;
}
}
@@ -623,25 +623,25 @@ void Neighbor::granular_bin_newton_tri_omp(NeighList *list)
ibin = coord2bin(x[i]);
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp) {
- if (x[j][1] < ytmp) continue;
- if (x[j][1] == ytmp) {
- if (x[j][0] < xtmp) continue;
- if (x[j][0] == xtmp && j <= i) continue;
- }
- }
-
- if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
- radsum = radi + radius[j];
- cutsq = (radsum+skin) * (radsum+skin);
-
- if (rsq <= cutsq) neighptr[n++] = j;
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp) {
+ if (x[j][1] < ytmp) continue;
+ if (x[j][1] == ytmp) {
+ if (x[j][0] < xtmp) continue;
+ if (x[j][0] == xtmp && j <= i) continue;
+ }
+ }
+
+ if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+ radsum = radi + radius[j];
+ cutsq = (radsum+skin) * (radsum+skin);
+
+ if (rsq <= cutsq) neighptr[n++] = j;
}
}
diff --git a/src/USER-OMP/neigh_half_bin_omp.cpp b/src/USER-OMP/neigh_half_bin_omp.cpp
index 3ff15b11da2557afd0b962e908fc984a658b8528..6da44d4203a7941161941e5c557f5cbaa0c79b8d 100644
--- a/src/USER-OMP/neigh_half_bin_omp.cpp
+++ b/src/USER-OMP/neigh_half_bin_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -95,22 +95,22 @@ void Neighbor::half_bin_no_newton_omp(NeighList *list)
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- if (j <= i) continue;
-
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- which = find_special(special[i],nspecial[i],tag[j]);
- if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
+ if (j <= i) continue;
+
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ which = find_special(special[i],nspecial[i],tag[j]);
+ if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
}
}
@@ -196,11 +196,11 @@ void Neighbor::half_bin_newton_omp(NeighList *list)
for (j = bins[i]; j >= 0; j = bins[j]) {
if (j >= nlocal) {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp) {
- if (x[j][1] < ytmp) continue;
- if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
- }
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp) {
+ if (x[j][1] < ytmp) continue;
+ if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
+ }
}
jtype = type[j];
@@ -212,10 +212,10 @@ void Neighbor::half_bin_newton_omp(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- which = find_special(special[i],nspecial[i],tag[j]);
- if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
+ if (molecular) {
+ which = find_special(special[i],nspecial[i],tag[j]);
+ if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
}
}
@@ -224,20 +224,20 @@ void Neighbor::half_bin_newton_omp(NeighList *list)
ibin = coord2bin(x[i]);
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- which = find_special(special[i],nspecial[i],tag[j]);
- if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ which = find_special(special[i],nspecial[i],tag[j]);
+ if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
}
}
@@ -326,29 +326,29 @@ void Neighbor::half_bin_newton_tri_omp(NeighList *list)
ibin = coord2bin(x[i]);
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp) {
- if (x[j][1] < ytmp) continue;
- if (x[j][1] == ytmp) {
- if (x[j][0] < xtmp) continue;
- if (x[j][0] == xtmp && j <= i) continue;
- }
- }
-
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- which = find_special(special[i],nspecial[i],tag[j]);
- if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp) {
+ if (x[j][1] < ytmp) continue;
+ if (x[j][1] == ytmp) {
+ if (x[j][0] < xtmp) continue;
+ if (x[j][0] == xtmp && j <= i) continue;
+ }
+ }
+
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ which = find_special(special[i],nspecial[i],tag[j]);
+ if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
}
}
diff --git a/src/USER-OMP/neigh_half_multi_omp.cpp b/src/USER-OMP/neigh_half_multi_omp.cpp
index ca7427613941f1c6ae96d31ef1c9bb6f438dda6e..0dbe2530af4a778696301521834c3508b0da997e 100644
--- a/src/USER-OMP/neigh_half_multi_omp.cpp
+++ b/src/USER-OMP/neigh_half_multi_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -102,23 +102,23 @@ void Neighbor::half_multi_no_newton_omp(NeighList *list)
ns = nstencil_multi[itype];
for (k = 0; k < ns; k++) {
for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
- if (j <= i) continue;
- jtype = type[j];
- if (cutsq[jtype] < distsq[k]) continue;
-
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- which = find_special(special[i],nspecial[i],tag[j]);
- if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
+ if (j <= i) continue;
+ jtype = type[j];
+ if (cutsq[jtype] < distsq[k]) continue;
+
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ which = find_special(special[i],nspecial[i],tag[j]);
+ if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
}
}
@@ -207,11 +207,11 @@ void Neighbor::half_multi_newton_omp(NeighList *list)
for (j = bins[i]; j >= 0; j = bins[j]) {
if (j >= nlocal) {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp) {
- if (x[j][1] < ytmp) continue;
- if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
- }
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp) {
+ if (x[j][1] < ytmp) continue;
+ if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
+ }
}
jtype = type[j];
@@ -223,10 +223,10 @@ void Neighbor::half_multi_newton_omp(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- which = find_special(special[i],nspecial[i],tag[j]);
- if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
+ if (molecular) {
+ which = find_special(special[i],nspecial[i],tag[j]);
+ if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
}
}
@@ -240,22 +240,22 @@ void Neighbor::half_multi_newton_omp(NeighList *list)
ns = nstencil_multi[itype];
for (k = 0; k < ns; k++) {
for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
- jtype = type[j];
- if (cutsq[jtype] < distsq[k]) continue;
-
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- which = find_special(special[i],nspecial[i],tag[j]);
- if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
+ jtype = type[j];
+ if (cutsq[jtype] < distsq[k]) continue;
+
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ which = find_special(special[i],nspecial[i],tag[j]);
+ if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
}
}
@@ -353,30 +353,30 @@ void Neighbor::half_multi_newton_tri_omp(NeighList *list)
ns = nstencil_multi[itype];
for (k = 0; k < ns; k++) {
for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
- jtype = type[j];
- if (cutsq[jtype] < distsq[k]) continue;
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp) {
- if (x[j][1] < ytmp) continue;
- if (x[j][1] == ytmp) {
- if (x[j][0] < xtmp) continue;
- if (x[j][0] == xtmp && j <= i) continue;
- }
- }
-
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- which = find_special(special[i],nspecial[i],tag[j]);
- if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
+ jtype = type[j];
+ if (cutsq[jtype] < distsq[k]) continue;
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp) {
+ if (x[j][1] < ytmp) continue;
+ if (x[j][1] == ytmp) {
+ if (x[j][0] < xtmp) continue;
+ if (x[j][0] == xtmp && j <= i) continue;
+ }
+ }
+
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ which = find_special(special[i],nspecial[i],tag[j]);
+ if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
}
}
diff --git a/src/USER-OMP/neigh_half_nsq_omp.cpp b/src/USER-OMP/neigh_half_nsq_omp.cpp
index c557fe7d8494eb8df82b453f1a67897fb7effeaa..a8a9e398274c70987227d7736dd7e116532e2a0c 100644
--- a/src/USER-OMP/neigh_half_nsq_omp.cpp
+++ b/src/USER-OMP/neigh_half_nsq_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -94,10 +94,10 @@ void Neighbor::half_nsq_no_newton_omp(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- which = find_special(special[i],nspecial[i],tag[j]);
- if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
+ if (molecular) {
+ which = find_special(special[i],nspecial[i],tag[j]);
+ if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
}
}
@@ -180,18 +180,18 @@ void Neighbor::half_nsq_newton_omp(NeighList *list)
if (includegroup && !(mask[j] & bitmask)) continue;
if (j >= nlocal) {
- jtag = tag[j];
- if (itag > jtag) {
- if ((itag+jtag) % 2 == 0) continue;
- } else if (itag < jtag) {
- if ((itag+jtag) % 2 == 1) continue;
- } else {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp) {
- if (x[j][1] < ytmp) continue;
- if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
- }
- }
+ jtag = tag[j];
+ if (itag > jtag) {
+ if ((itag+jtag) % 2 == 0) continue;
+ } else if (itag < jtag) {
+ if ((itag+jtag) % 2 == 1) continue;
+ } else {
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp) {
+ if (x[j][1] < ytmp) continue;
+ if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
+ }
+ }
}
jtype = type[j];
@@ -203,10 +203,10 @@ void Neighbor::half_nsq_newton_omp(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- which = find_special(special[i],nspecial[i],tag[j]);
- if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
+ if (molecular) {
+ which = find_special(special[i],nspecial[i],tag[j]);
+ if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
}
}
diff --git a/src/USER-OMP/neigh_respa_omp.cpp b/src/USER-OMP/neigh_respa_omp.cpp
index e0817385d6ce86f08613f8c93feb02c0cfc52cca..de22caa6cc1b363221cfd9bc9bd282ff1b547e6a 100644
--- a/src/USER-OMP/neigh_respa_omp.cpp
+++ b/src/USER-OMP/neigh_respa_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -122,9 +122,9 @@ void Neighbor::respa_nsq_no_newton_omp(NeighList *list)
#endif
if (respamiddle) {
if (pgsize - npnt_middle < oneatom) {
- npnt_middle = 0;
- npage_middle += nthreads;
- if (npage_middle == listmiddle->maxpage) listmiddle->add_pages(nthreads);
+ npnt_middle = 0;
+ npage_middle += nthreads;
+ if (npage_middle == listmiddle->maxpage) listmiddle->add_pages(nthreads);
}
neighptr_middle = &(listmiddle->pages[npage_middle][npnt_middle]);
n_middle = 0;
@@ -148,20 +148,20 @@ void Neighbor::respa_nsq_no_newton_omp(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- which = find_special(special[i],nspecial[i],tag[j]);
- if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
+ if (molecular) {
+ which = find_special(special[i],nspecial[i],tag[j]);
+ if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
if (rsq < cut_inner_sq) {
- if (which == 0) neighptr_inner[n_inner++] = j;
- else if (which > 0) neighptr_inner[n_inner++] = j ^ (which << SBBITS);
+ if (which == 0) neighptr_inner[n_inner++] = j;
+ else if (which > 0) neighptr_inner[n_inner++] = j ^ (which << SBBITS);
}
if (respamiddle && rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
- if (which == 0) neighptr_middle[n_middle++] = j;
- else if (which > 0)
- neighptr_middle[n_middle++] = j ^ (which << SBBITS);
+ if (which == 0) neighptr_middle[n_middle++] = j;
+ else if (which > 0)
+ neighptr_middle[n_middle++] = j ^ (which << SBBITS);
}
}
}
@@ -186,7 +186,7 @@ void Neighbor::respa_nsq_no_newton_omp(NeighList *list)
numneigh_middle[i] = n_middle;
npnt_middle += n_middle;
if (n_middle > oneatom)
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
}
NEIGH_OMP_CLOSE;
@@ -297,9 +297,9 @@ void Neighbor::respa_nsq_newton_omp(NeighList *list)
#endif
if (respamiddle) {
if (pgsize - npnt_middle < oneatom) {
- npnt_middle = 0;
- npage_middle += nthreads;
- if (npage_middle == listmiddle->maxpage) listmiddle->add_pages(nthreads);
+ npnt_middle = 0;
+ npage_middle += nthreads;
+ if (npage_middle == listmiddle->maxpage) listmiddle->add_pages(nthreads);
}
neighptr_middle = &(listmiddle->pages[npage_middle][npnt_middle]);
n_middle = 0;
@@ -317,18 +317,18 @@ void Neighbor::respa_nsq_newton_omp(NeighList *list)
if (includegroup && !(mask[j] & bitmask)) continue;
if (j >= nlocal) {
- jtag = tag[j];
- if (itag > jtag) {
- if ((itag+jtag) % 2 == 0) continue;
- } else if (itag < jtag) {
- if ((itag+jtag) % 2 == 1) continue;
- } else {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp) {
- if (x[j][1] < ytmp) continue;
- if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
- }
- }
+ jtag = tag[j];
+ if (itag > jtag) {
+ if ((itag+jtag) % 2 == 0) continue;
+ } else if (itag < jtag) {
+ if ((itag+jtag) % 2 == 1) continue;
+ } else {
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp) {
+ if (x[j][1] < ytmp) continue;
+ if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
+ }
+ }
}
jtype = type[j];
@@ -340,21 +340,21 @@ void Neighbor::respa_nsq_newton_omp(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- which = find_special(special[i],nspecial[i],tag[j]);
- if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
+ if (molecular) {
+ which = find_special(special[i],nspecial[i],tag[j]);
+ if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
if (rsq < cut_inner_sq) {
- if (which == 0) neighptr_inner[n_inner++] = j;
- else if (which > 0) neighptr_inner[n_inner++] = j ^ (which << SBBITS);
+ if (which == 0) neighptr_inner[n_inner++] = j;
+ else if (which > 0) neighptr_inner[n_inner++] = j ^ (which << SBBITS);
}
- if (respamiddle &&
- rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
- if (which == 0) neighptr_middle[n_middle++] = j;
- else if (which > 0)
- neighptr_middle[n_middle++] = j ^ (which << SBBITS);
+ if (respamiddle &&
+ rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
+ if (which == 0) neighptr_middle[n_middle++] = j;
+ else if (which > 0)
+ neighptr_middle[n_middle++] = j ^ (which << SBBITS);
}
}
}
@@ -379,7 +379,7 @@ void Neighbor::respa_nsq_newton_omp(NeighList *list)
numneigh_middle[i] = n_middle;
npnt_middle += n_middle;
if (n_middle > oneatom)
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
}
NEIGH_OMP_CLOSE;
@@ -494,9 +494,9 @@ void Neighbor::respa_bin_no_newton_omp(NeighList *list)
#endif
if (respamiddle) {
if (pgsize - npnt_middle < oneatom) {
- npnt_middle = 0;
- npage_middle += nthreads;
- if (npage_middle == listmiddle->maxpage) listmiddle->add_pages(nthreads);
+ npnt_middle = 0;
+ npage_middle += nthreads;
+ if (npage_middle == listmiddle->maxpage) listmiddle->add_pages(nthreads);
}
neighptr_middle = &(listmiddle->pages[npage_middle][npnt_middle]);
n_middle = 0;
@@ -515,35 +515,35 @@ void Neighbor::respa_bin_no_newton_omp(NeighList *list)
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- if (j <= i) continue;
-
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- which = find_special(special[i],nspecial[i],tag[j]);
- if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
-
- if (rsq < cut_inner_sq) {
- if (which == 0) neighptr_inner[n_inner++] = j;
- else if (which > 0)
- neighptr_inner[n_inner++] = j ^ (which << SBBITS);
- }
-
- if (respamiddle &&
- rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
- if (which == 0) neighptr_middle[n_middle++] = j;
- else if (which > 0)
- neighptr_middle[n_middle++] = j ^ (which << SBBITS);
- }
- }
+ if (j <= i) continue;
+
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ which = find_special(special[i],nspecial[i],tag[j]);
+ if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+
+ if (rsq < cut_inner_sq) {
+ if (which == 0) neighptr_inner[n_inner++] = j;
+ else if (which > 0)
+ neighptr_inner[n_inner++] = j ^ (which << SBBITS);
+ }
+
+ if (respamiddle &&
+ rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
+ if (which == 0) neighptr_middle[n_middle++] = j;
+ else if (which > 0)
+ neighptr_middle[n_middle++] = j ^ (which << SBBITS);
+ }
+ }
}
}
@@ -567,7 +567,7 @@ void Neighbor::respa_bin_no_newton_omp(NeighList *list)
numneigh_middle[i] = n_middle;
npnt_middle += n_middle;
if (n_middle > oneatom)
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
}
NEIGH_OMP_CLOSE;
@@ -575,7 +575,7 @@ void Neighbor::respa_bin_no_newton_omp(NeighList *list)
listinner->inum = nlocal;
if (respamiddle) listmiddle->inum = nlocal;
}
-
+
/* ----------------------------------------------------------------------
multiple respa lists
binned neighbor list construction with full Newton's 3rd law
@@ -681,9 +681,9 @@ void Neighbor::respa_bin_newton_omp(NeighList *list)
#endif
if (respamiddle) {
if (pgsize - npnt_middle < oneatom) {
- npnt_middle = 0;
- npage_middle += nthreads;
- if (npage_middle == listmiddle->maxpage) listmiddle->add_pages(nthreads);
+ npnt_middle = 0;
+ npage_middle += nthreads;
+ if (npage_middle == listmiddle->maxpage) listmiddle->add_pages(nthreads);
}
neighptr_middle = &(listmiddle->pages[npage_middle][npnt_middle]);
n_middle = 0;
@@ -700,11 +700,11 @@ void Neighbor::respa_bin_newton_omp(NeighList *list)
for (j = bins[i]; j >= 0; j = bins[j]) {
if (j >= nlocal) {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp) {
- if (x[j][1] < ytmp) continue;
- if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
- }
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp) {
+ if (x[j][1] < ytmp) continue;
+ if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
+ }
}
jtype = type[j];
@@ -716,21 +716,21 @@ void Neighbor::respa_bin_newton_omp(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- which = find_special(special[i],nspecial[i],tag[j]);
- if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
+ if (molecular) {
+ which = find_special(special[i],nspecial[i],tag[j]);
+ if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
if (rsq < cut_inner_sq) {
- if (which == 0) neighptr_inner[n_inner++] = j;
- else if (which > 0) neighptr_inner[n_inner++] = j ^ (which << SBBITS);
+ if (which == 0) neighptr_inner[n_inner++] = j;
+ else if (which > 0) neighptr_inner[n_inner++] = j ^ (which << SBBITS);
}
- if (respamiddle &&
- rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
- if (which == 0) neighptr_middle[n_middle++] = j;
- else if (which > 0)
- neighptr_middle[n_middle++] = j ^ (which << SBBITS);
+ if (respamiddle &&
+ rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
+ if (which == 0) neighptr_middle[n_middle++] = j;
+ else if (which > 0)
+ neighptr_middle[n_middle++] = j ^ (which << SBBITS);
}
}
}
@@ -740,33 +740,33 @@ void Neighbor::respa_bin_newton_omp(NeighList *list)
ibin = coord2bin(x[i]);
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- which = find_special(special[i],nspecial[i],tag[j]);
- if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
-
- if (rsq < cut_inner_sq) {
- if (which == 0) neighptr_inner[n_inner++] = j;
- else if (which > 0)
- neighptr_inner[n_inner++] = j ^ (which << SBBITS);
- }
-
- if (respamiddle &&
- rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
- if (which == 0) neighptr_middle[n_middle++] = j;
- else if (which > 0)
- neighptr_middle[n_middle++] = j ^ (which << SBBITS);
- }
- }
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ which = find_special(special[i],nspecial[i],tag[j]);
+ if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+
+ if (rsq < cut_inner_sq) {
+ if (which == 0) neighptr_inner[n_inner++] = j;
+ else if (which > 0)
+ neighptr_inner[n_inner++] = j ^ (which << SBBITS);
+ }
+
+ if (respamiddle &&
+ rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
+ if (which == 0) neighptr_middle[n_middle++] = j;
+ else if (which > 0)
+ neighptr_middle[n_middle++] = j ^ (which << SBBITS);
+ }
+ }
}
}
@@ -790,7 +790,7 @@ void Neighbor::respa_bin_newton_omp(NeighList *list)
numneigh_middle[i] = n_middle;
npnt_middle += n_middle;
if (n_middle > oneatom)
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
}
NEIGH_OMP_CLOSE;
@@ -904,9 +904,9 @@ void Neighbor::respa_bin_newton_tri_omp(NeighList *list)
#endif
if (respamiddle) {
if (pgsize - npnt_middle < oneatom) {
- npnt_middle = 0;
- npage_middle += nthreads;
- if (npage_middle == listmiddle->maxpage) listmiddle->add_pages(nthreads);
+ npnt_middle = 0;
+ npage_middle += nthreads;
+ if (npage_middle == listmiddle->maxpage) listmiddle->add_pages(nthreads);
}
neighptr_middle = &(listmiddle->pages[npage_middle][npnt_middle]);
n_middle = 0;
@@ -926,42 +926,42 @@ void Neighbor::respa_bin_newton_tri_omp(NeighList *list)
ibin = coord2bin(x[i]);
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp) {
- if (x[j][1] < ytmp) continue;
- if (x[j][1] == ytmp) {
- if (x[j][0] < xtmp) continue;
- if (x[j][0] == xtmp && j <= i) continue;
- }
- }
-
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- which = find_special(special[i],nspecial[i],tag[j]);
- if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
-
- if (rsq < cut_inner_sq) {
- if (which == 0) neighptr_inner[n_inner++] = j;
- else if (which > 0)
- neighptr_inner[n_inner++] = j ^ (which << SBBITS);
- }
-
- if (respamiddle &&
- rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
- if (which == 0) neighptr_middle[n_middle++] = j;
- else if (which > 0)
- neighptr_middle[n_middle++] = j ^ (which << SBBITS);
- }
- }
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp) {
+ if (x[j][1] < ytmp) continue;
+ if (x[j][1] == ytmp) {
+ if (x[j][0] < xtmp) continue;
+ if (x[j][0] == xtmp && j <= i) continue;
+ }
+ }
+
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ which = find_special(special[i],nspecial[i],tag[j]);
+ if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+
+ if (rsq < cut_inner_sq) {
+ if (which == 0) neighptr_inner[n_inner++] = j;
+ else if (which > 0)
+ neighptr_inner[n_inner++] = j ^ (which << SBBITS);
+ }
+
+ if (respamiddle &&
+ rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
+ if (which == 0) neighptr_middle[n_middle++] = j;
+ else if (which > 0)
+ neighptr_middle[n_middle++] = j ^ (which << SBBITS);
+ }
+ }
}
}
@@ -985,7 +985,7 @@ void Neighbor::respa_bin_newton_tri_omp(NeighList *list)
numneigh_middle[i] = n_middle;
npnt_middle += n_middle;
if (n_middle > oneatom)
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
}
NEIGH_OMP_CLOSE;
diff --git a/src/USER-OMP/neighbor_omp.h b/src/USER-OMP/neighbor_omp.h
index 138ef96d5bfc2fc84409df404d6c3fddb93b962b..fd27ba8b61da5cce52780bf582555c3424795b09 100644
--- a/src/USER-OMP/neighbor_omp.h
+++ b/src/USER-OMP/neighbor_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -24,30 +24,30 @@ namespace LAMMPS_NS {
#if defined(_OPENMP)
// make sure we have at least one page for each thread
-#define NEIGH_OMP_INIT \
- const int nthreads = comm->nthreads; \
- if (nthreads > list->maxpage) \
+#define NEIGH_OMP_INIT \
+ const int nthreads = comm->nthreads; \
+ if (nthreads > list->maxpage) \
list->add_pages(nthreads - list->maxpage)
// get thread id and then assign each thread a fixed chunk of atoms
-#define NEIGH_OMP_SETUP(num) \
- { \
- const int tid = omp_get_thread_num(); \
- const int idelta = 1 + num/nthreads; \
- const int ifrom = tid*idelta; \
- const int ito = ((ifrom + idelta) > num) \
- ? num : (ifrom+idelta); \
+#define NEIGH_OMP_SETUP(num) \
+ { \
+ const int tid = omp_get_thread_num(); \
+ const int idelta = 1 + num/nthreads; \
+ const int ifrom = tid*idelta; \
+ const int ito = ((ifrom + idelta) > num) \
+ ? num : (ifrom+idelta); \
#define NEIGH_OMP_CLOSE }
#else /* !defined(_OPENMP) */
-#define NEIGH_OMP_INIT \
+#define NEIGH_OMP_INIT \
const int nthreads = comm->nthreads;
-#define NEIGH_OMP_SETUP(num) \
- const int tid = 0; \
- const int ifrom = 0; \
+#define NEIGH_OMP_SETUP(num) \
+ const int tid = 0; \
+ const int ifrom = 0; \
const int ito = num
#define NEIGH_OMP_CLOSE
diff --git a/src/USER-OMP/pair_adp_omp.cpp b/src/USER-OMP/pair_adp_omp.cpp
index 389144e1d1dd97f2e9515f7ed5216012b12a3e83..4d05b16c703579a7eb735b3cc173f0168ad31d0d 100644
--- a/src/USER-OMP/pair_adp_omp.cpp
+++ b/src/USER-OMP/pair_adp_omp.cpp
@@ -72,7 +72,7 @@ void PairADPOMP::compute(int eflag, int vflag)
loop_setup_thr(ifrom, ito, tid, inum, nthreads);
ThrData *thr = fix->get_thr(tid);
ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
-
+
if (force->newton_pair)
thr->init_adp(nall, rho, mu, lambda);
else
@@ -80,11 +80,11 @@ void PairADPOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -149,21 +149,21 @@ void PairADPOMP::eval(int iifrom, int iito, ThrData * const thr)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cutforcesq) {
- jtype = type[j];
- p = sqrt(rsq)*rdr + 1.0;
- m = static_cast<int> (p);
- m = MIN(m,nr-1);
- p -= m;
- p = MIN(p,1.0);
- coeff = rhor_spline[type2rhor[jtype][itype]][m];
- rho_t[i] += ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
+ jtype = type[j];
+ p = sqrt(rsq)*rdr + 1.0;
+ m = static_cast<int> (p);
+ m = MIN(m,nr-1);
+ p -= m;
+ p = MIN(p,1.0);
+ coeff = rhor_spline[type2rhor[jtype][itype]][m];
+ rho_t[i] += ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
coeff = u2r_spline[type2u2r[jtype][itype]][m];
- u2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
+ u2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
mu_t[i][0] += u2*delx;
mu_t[i][1] += u2*dely;
mu_t[i][2] += u2*delz;
coeff = w2r_spline[type2w2r[jtype][itype]][m];
- w2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
+ w2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
lambda_t[i][0] += w2*delx*delx;
lambda_t[i][1] += w2*dely*dely;
lambda_t[i][2] += w2*delz*delz;
@@ -171,24 +171,24 @@ void PairADPOMP::eval(int iifrom, int iito, ThrData * const thr)
lambda_t[i][4] += w2*delx*delz;
lambda_t[i][5] += w2*delx*dely;
- if (NEWTON_PAIR || j < nlocal) {
+ if (NEWTON_PAIR || j < nlocal) {
// verify sign difference for mu and lambda
- coeff = rhor_spline[type2rhor[itype][jtype]][m];
- rho_t[j] += ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
+ coeff = rhor_spline[type2rhor[itype][jtype]][m];
+ rho_t[j] += ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
coeff = u2r_spline[type2u2r[itype][jtype]][m];
u2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
mu_t[j][0] -= u2*delx;
mu_t[j][1] -= u2*dely;
mu_t[j][2] -= u2*delz;
coeff = w2r_spline[type2w2r[itype][jtype]][m];
- w2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
+ w2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
lambda_t[j][0] += w2*delx*delx;
lambda_t[j][1] += w2*dely*dely;
lambda_t[j][2] += w2*delz*delz;
lambda_t[j][3] += w2*dely*delz;
lambda_t[j][4] += w2*delx*delz;
lambda_t[j][5] += w2*delx*dely;
- }
+ }
}
}
}
@@ -214,7 +214,7 @@ void PairADPOMP::eval(int iifrom, int iito, ThrData * const thr)
// wait until master thread is done with communication
sync_threads();
-
+
} else {
// reduce per thread density
data_reduce_thr(&(rho[0]), nlocal, comm->nthreads, 1, tid);
@@ -224,7 +224,7 @@ void PairADPOMP::eval(int iifrom, int iito, ThrData * const thr)
// wait until reduction is complete
sync_threads();
}
-
+
// fp = derivative of embedding energy at each atom
// phi = embedding energy at each atom
@@ -241,11 +241,11 @@ void PairADPOMP::eval(int iifrom, int iito, ThrData * const thr)
phi = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
phi += 0.5*(mu[i][0]*mu[i][0]+mu[i][1]*mu[i][1]+mu[i][2]*mu[i][2]);
phi += 0.5*(lambda[i][0]*lambda[i][0]+lambda[i][1]*
- lambda[i][1]+lambda[i][2]*lambda[i][2]);
+ lambda[i][1]+lambda[i][2]*lambda[i][2]);
phi += 1.0*(lambda[i][3]*lambda[i][3]+lambda[i][4]*
- lambda[i][4]+lambda[i][5]*lambda[i][5]);
+ lambda[i][4]+lambda[i][5]*lambda[i][5]);
phi -= 1.0/6.0*(lambda[i][0]+lambda[i][1]+lambda[i][2])*
- (lambda[i][0]+lambda[i][1]+lambda[i][2]);
+ (lambda[i][0]+lambda[i][1]+lambda[i][2]);
e_tally_thr(this,i,i,nlocal,/* newton_pair */ 1, phi, 0.0, thr);
}
}
@@ -287,51 +287,51 @@ void PairADPOMP::eval(int iifrom, int iito, ThrData * const thr)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cutforcesq) {
- jtype = type[j];
- r = sqrt(rsq);
- p = r*rdr + 1.0;
- m = static_cast<int> (p);
- m = MIN(m,nr-1);
- p -= m;
- p = MIN(p,1.0);
-
- // rhoip = derivative of (density at atom j due to atom i)
- // rhojp = derivative of (density at atom i due to atom j)
- // phi = pair potential energy
- // phip = phi'
- // z2 = phi * r
- // z2p = (phi * r)' = (phi' r) + phi
+ jtype = type[j];
+ r = sqrt(rsq);
+ p = r*rdr + 1.0;
+ m = static_cast<int> (p);
+ m = MIN(m,nr-1);
+ p -= m;
+ p = MIN(p,1.0);
+
+ // rhoip = derivative of (density at atom j due to atom i)
+ // rhojp = derivative of (density at atom i due to atom j)
+ // phi = pair potential energy
+ // phip = phi'
+ // z2 = phi * r
+ // z2p = (phi * r)' = (phi' r) + phi
// u2 = u
// u2p = u'
// w2 = w
// w2p = w'
- // psip needs both fp[i] and fp[j] terms since r_ij appears in two
- // terms of embed eng: Fi(sum rho_ij) and Fj(sum rho_ji)
- // hence embed' = Fi(sum rho_ij) rhojp + Fj(sum rho_ji) rhoip
-
- coeff = rhor_spline[type2rhor[itype][jtype]][m];
- rhoip = (coeff[0]*p + coeff[1])*p + coeff[2];
- coeff = rhor_spline[type2rhor[jtype][itype]][m];
- rhojp = (coeff[0]*p + coeff[1])*p + coeff[2];
- coeff = z2r_spline[type2z2r[itype][jtype]][m];
- z2p = (coeff[0]*p + coeff[1])*p + coeff[2];
- z2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
+ // psip needs both fp[i] and fp[j] terms since r_ij appears in two
+ // terms of embed eng: Fi(sum rho_ij) and Fj(sum rho_ji)
+ // hence embed' = Fi(sum rho_ij) rhojp + Fj(sum rho_ji) rhoip
+
+ coeff = rhor_spline[type2rhor[itype][jtype]][m];
+ rhoip = (coeff[0]*p + coeff[1])*p + coeff[2];
+ coeff = rhor_spline[type2rhor[jtype][itype]][m];
+ rhojp = (coeff[0]*p + coeff[1])*p + coeff[2];
+ coeff = z2r_spline[type2z2r[itype][jtype]][m];
+ z2p = (coeff[0]*p + coeff[1])*p + coeff[2];
+ z2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
coeff = u2r_spline[type2u2r[itype][jtype]][m];
- u2p = (coeff[0]*p + coeff[1])*p + coeff[2];
- u2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
+ u2p = (coeff[0]*p + coeff[1])*p + coeff[2];
+ u2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
coeff = w2r_spline[type2w2r[itype][jtype]][m];
- w2p = (coeff[0]*p + coeff[1])*p + coeff[2];
- w2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
+ w2p = (coeff[0]*p + coeff[1])*p + coeff[2];
+ w2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
- recip = 1.0/r;
- phi = z2*recip;
- phip = z2p*recip - phi*recip;
- psip = fp[i]*rhojp + fp[j]*rhoip + phip;
- fpair = -psip*recip;
+ recip = 1.0/r;
+ phi = z2*recip;
+ phip = z2p*recip - phi*recip;
+ psip = fp[i]*rhojp + fp[j]*rhoip + phip;
+ fpair = -psip*recip;
delmux = mu[i][0]-mu[j][0];
- delmuy = mu[i][1]-mu[j][1];
- delmuz = mu[i][2]-mu[j][2];
+ delmuy = mu[i][1]-mu[j][1];
+ delmuz = mu[i][2]-mu[j][2];
trdelmu = delmux*delx+delmuy*dely+delmuz*delz;
sumlamxx = lambda[i][0]+lambda[j][0];
sumlamyy = lambda[i][1]+lambda[j][1];
@@ -340,37 +340,37 @@ void PairADPOMP::eval(int iifrom, int iito, ThrData * const thr)
sumlamxz = lambda[i][4]+lambda[j][4];
sumlamxy = lambda[i][5]+lambda[j][5];
tradellam = sumlamxx*delx*delx+sumlamyy*dely*dely+
- sumlamzz*delz*delz+2.0*sumlamxy*delx*dely+
- 2.0*sumlamxz*delx*delz+2.0*sumlamyz*dely*delz;
+ sumlamzz*delz*delz+2.0*sumlamxy*delx*dely+
+ 2.0*sumlamxz*delx*delz+2.0*sumlamyz*dely*delz;
nu = sumlamxx+sumlamyy+sumlamzz;
- adpx = delmux*u2 + trdelmu*u2p*delx*recip +
- 2.0*w2*(sumlamxx*delx+sumlamxy*dely+sumlamxz*delz) +
- w2p*delx*recip*tradellam - 1.0/3.0*nu*(w2p*r+2.0*w2)*delx;
- adpy = delmuy*u2 + trdelmu*u2p*dely*recip +
- 2.0*w2*(sumlamxy*delx+sumlamyy*dely+sumlamyz*delz) +
- w2p*dely*recip*tradellam - 1.0/3.0*nu*(w2p*r+2.0*w2)*dely;
- adpz = delmuz*u2 + trdelmu*u2p*delz*recip +
- 2.0*w2*(sumlamxz*delx+sumlamyz*dely+sumlamzz*delz) +
- w2p*delz*recip*tradellam - 1.0/3.0*nu*(w2p*r+2.0*w2)*delz;
+ adpx = delmux*u2 + trdelmu*u2p*delx*recip +
+ 2.0*w2*(sumlamxx*delx+sumlamxy*dely+sumlamxz*delz) +
+ w2p*delx*recip*tradellam - 1.0/3.0*nu*(w2p*r+2.0*w2)*delx;
+ adpy = delmuy*u2 + trdelmu*u2p*dely*recip +
+ 2.0*w2*(sumlamxy*delx+sumlamyy*dely+sumlamyz*delz) +
+ w2p*dely*recip*tradellam - 1.0/3.0*nu*(w2p*r+2.0*w2)*dely;
+ adpz = delmuz*u2 + trdelmu*u2p*delz*recip +
+ 2.0*w2*(sumlamxz*delx+sumlamyz*dely+sumlamzz*delz) +
+ w2p*delz*recip*tradellam - 1.0/3.0*nu*(w2p*r+2.0*w2)*delz;
adpx*=-1.0; adpy*=-1.0; adpz*=-1.0;
fx = delx*fpair+adpx;
- fy = dely*fpair+adpy;
- fz = delz*fpair+adpz;
-
- fxtmp += fx;
- fytmp += fy;
- fztmp += fz;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= fx;
- f[j][1] -= fy;
- f[j][2] -= fz;
- }
-
- if (EFLAG) evdwl = phi;
- if (EVFLAG) ev_tally_xyz_thr(this,i,j,nlocal,NEWTON_PAIR,evdwl,0.0,
- fx,fy,fz,delx,dely,delz,thr);
+ fy = dely*fpair+adpy;
+ fz = delz*fpair+adpz;
+
+ fxtmp += fx;
+ fytmp += fy;
+ fztmp += fz;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= fx;
+ f[j][1] -= fy;
+ f[j][2] -= fz;
+ }
+
+ if (EFLAG) evdwl = phi;
+ if (EVFLAG) ev_tally_xyz_thr(this,i,j,nlocal,NEWTON_PAIR,evdwl,0.0,
+ fx,fy,fz,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_adp_omp.h b/src/USER-OMP/pair_adp_omp.h
index 9a7f4023fb4ce674ab222609ef78ff67f3870e64..e5c4c4af9fa2a68a6205b74875a36e31ee12a6b0 100644
--- a/src/USER-OMP/pair_adp_omp.h
+++ b/src/USER-OMP/pair_adp_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_airebo_omp.cpp b/src/USER-OMP/pair_airebo_omp.cpp
index 35bc988fea66b8c42098424320edd3437f37b617..5000ea2a097ba883231a1b4fabc9d9f89ead3105 100644
--- a/src/USER-OMP/pair_airebo_omp.cpp
+++ b/src/USER-OMP/pair_airebo_omp.cpp
@@ -77,7 +77,7 @@ void PairAIREBOOMP::compute(int eflag, int vflag)
------------------------------------------------------------------------- */
double PairAIREBOOMP::bondorder_thr(int i, int j, double rij[3], double rijmag,
- double VA, int vflag_atom, ThrData * const thr)
+ double VA, int vflag_atom, ThrData * const thr)
{
int atomi,atomj,k,n,l,atomk,atoml,atomn,atom1,atom2,atom3,atom4;
int itype,jtype,ktype,ltype,ntype;
@@ -140,12 +140,12 @@ double PairAIREBOOMP::bondorder_thr(int i, int j, double rij[3], double rijmag,
rik[2] = x[atomi][2]-x[atomk][2];
rikmag = sqrt((rik[0]*rik[0])+(rik[1]*rik[1])+(rik[2]*rik[2]));
lamdajik = 4.0*kronecker(itype,1) *
- ((rho[ktype][1]-rikmag)-(rho[jtype][1]-rijmag));
+ ((rho[ktype][1]-rikmag)-(rho[jtype][1]-rijmag));
wik = Sp(rikmag,rcmin[itype][ktype],rcmax[itype][ktype],dS);
Nki = nC[atomk]-(wik*kronecker(itype,0))+nH[atomk] -
- (wik*kronecker(itype,1));
+ (wik*kronecker(itype,1));
cosjik = ((rij[0]*rik[0])+(rij[1]*rik[1])+(rij[2]*rik[2])) /
- (rijmag*rikmag);
+ (rijmag*rikmag);
cosjik = MIN(cosjik,1.0);
cosjik = MAX(cosjik,-1.0);
@@ -180,7 +180,7 @@ double PairAIREBOOMP::bondorder_thr(int i, int j, double rij[3], double rijmag,
rik[2] = x[atomi][2]-x[atomk][2];
rikmag = sqrt((rik[0]*rik[0])+(rik[1]*rik[1])+(rik[2]*rik[2]));
lamdajik = 4.0*kronecker(itype,1) *
- ((rho[ktype][1]-rikmag)-(rho[jtype][1]-rijmag));
+ ((rho[ktype][1]-rikmag)-(rho[jtype][1]-rijmag));
wik = Sp(rikmag,rcmin[itype][ktype],rcmax[itype][ktype],dwik);
const double invrikm = 1.0/rikmag;
@@ -192,11 +192,11 @@ double PairAIREBOOMP::bondorder_thr(int i, int j, double rij[3], double rijmag,
cosjik = MAX(cosjik,-1.0);
dcosjikdri[0] = ((rij[0]+rik[0])*invrijkm) -
- (cosjik*((rij[0]*invrijm2)+(rik[0]*invrikm2)));
+ (cosjik*((rij[0]*invrijm2)+(rik[0]*invrikm2)));
dcosjikdri[1] = ((rij[1]+rik[1])*invrijkm) -
- (cosjik*((rij[1]*invrijm2)+(rik[1]*invrikm2)));
+ (cosjik*((rij[1]*invrijm2)+(rik[1]*invrikm2)));
dcosjikdri[2] = ((rij[2]+rik[2])*invrijkm) -
- (cosjik*((rij[2]*invrijm2)+(rik[2]*invrikm2)));
+ (cosjik*((rij[2]*invrijm2)+(rik[2]*invrikm2)));
dcosjikdrk[0] = (-rij[0]*invrijkm) + (cosjik*(rik[0]*invrikm2));
dcosjikdrk[1] = (-rij[1]*invrijkm) + (cosjik*(rik[1]*invrikm2));
dcosjikdrk[2] = (-rij[2]*invrijkm) + (cosjik*(rik[2]*invrikm2));
@@ -264,9 +264,9 @@ double PairAIREBOOMP::bondorder_thr(int i, int j, double rij[3], double rijmag,
f[atomk][0] += fk[0]; f[atomk][1] += fk[1]; f[atomk][2] += fk[2];
if (vflag_atom) {
- rji[0] = -rij[0]; rji[1] = -rij[1]; rji[2] = -rij[2];
- rki[0] = -rik[0]; rki[1] = -rik[1]; rki[2] = -rik[2];
- v_tally3_thr(atomi,atomj,atomk,fj,fk,rji,rki,thr);
+ rji[0] = -rij[0]; rji[1] = -rij[1]; rji[2] = -rij[2];
+ rki[0] = -rik[0]; rki[1] = -rik[1]; rki[2] = -rik[2];
+ v_tally3_thr(atomi,atomj,atomk,fj,fk,rji,rki,thr);
}
}
}
@@ -286,12 +286,12 @@ double PairAIREBOOMP::bondorder_thr(int i, int j, double rij[3], double rijmag,
rjl[2] = x[atomj][2]-x[atoml][2];
rjlmag = sqrt((rjl[0]*rjl[0])+(rjl[1]*rjl[1])+(rjl[2]*rjl[2]));
lamdaijl = 4.0*kronecker(jtype,1) *
- ((rho[ltype][1]-rjlmag)-(rho[itype][1]-rijmag));
+ ((rho[ltype][1]-rjlmag)-(rho[itype][1]-rijmag));
wjl = Sp(rjlmag,rcmin[jtype][ltype],rcmax[jtype][ltype],dS);
Nlj = nC[atoml]-(wjl*kronecker(jtype,0)) +
- nH[atoml]-(wjl*kronecker(jtype,1));
+ nH[atoml]-(wjl*kronecker(jtype,1));
cosijl = -1.0*((rij[0]*rjl[0])+(rij[1]*rjl[1])+(rij[2]*rjl[2])) /
- (rijmag*rjlmag);
+ (rijmag*rjlmag);
cosijl = MIN(cosijl,1.0);
cosijl = MAX(cosijl,-1.0);
@@ -321,7 +321,7 @@ double PairAIREBOOMP::bondorder_thr(int i, int j, double rij[3], double rijmag,
rjl[2] = x[atomj][2]-x[atoml][2];
rjlmag = sqrt((rjl[0]*rjl[0])+(rjl[1]*rjl[1])+(rjl[2]*rjl[2]));
lamdaijl = 4.0*kronecker(jtype,1) *
- ((rho[ltype][1]-rjlmag)-(rho[itype][1]-rijmag));
+ ((rho[ltype][1]-rjlmag)-(rho[itype][1]-rijmag));
wjl = Sp(rjlmag,rcmin[jtype][ltype],rcmax[jtype][ltype],dwjl);
const double invrjlm = 1.0/rjlmag;
@@ -329,7 +329,7 @@ double PairAIREBOOMP::bondorder_thr(int i, int j, double rij[3], double rijmag,
const double invrjlm2 = invrjlm*invrjlm;
cosijl = (-1.0*((rij[0]*rjl[0])+(rij[1]*rjl[1])+(rij[2]*rjl[2])))
- * invrijlm;
+ * invrijlm;
cosijl = MIN(cosijl,1.0);
cosijl = MAX(cosijl,-1.0);
@@ -338,11 +338,11 @@ double PairAIREBOOMP::bondorder_thr(int i, int j, double rij[3], double rijmag,
dcosijldri[1] = (-rjl[1]*invrijlm) - (cosijl*rij[1]*invrijm2);
dcosijldri[2] = (-rjl[2]*invrijlm) - (cosijl*rij[2]*invrijm2);
dcosijldrj[0] = ((-rij[0]+rjl[0])*invrijlm) +
- (cosijl*((rij[0]*invrijm2)-(rjl[0]*invrjlm2)));
+ (cosijl*((rij[0]*invrijm2)-(rjl[0]*invrjlm2)));
dcosijldrj[1] = ((-rij[1]+rjl[1])*invrijlm) +
- (cosijl*((rij[1]*invrijm2)-(rjl[1]*invrjlm2)));
+ (cosijl*((rij[1]*invrijm2)-(rjl[1]*invrjlm2)));
dcosijldrj[2] = ((-rij[2]+rjl[2])*invrijlm) +
- (cosijl*((rij[2]*invrijm2)-(rjl[2]*invrjlm2)));
+ (cosijl*((rij[2]*invrijm2)-(rjl[2]*invrjlm2)));
dcosijldrl[0] = (rij[0]*invrijlm)+(cosijl*rjl[0]*invrjlm2);
dcosijldrl[1] = (rij[1]*invrijlm)+(cosijl*rjl[1]*invrjlm2);
dcosijldrl[2] = (rij[2]*invrijlm)+(cosijl*rjl[2]*invrjlm2);
@@ -409,8 +409,8 @@ double PairAIREBOOMP::bondorder_thr(int i, int j, double rij[3], double rijmag,
f[atoml][0] += fl[0]; f[atoml][1] += fl[1]; f[atoml][2] += fl[2];
if (vflag_atom) {
- rlj[0] = -rjl[0]; rlj[1] = -rjl[1]; rlj[2] = -rjl[2];
- v_tally3_thr(atomi,atomj,atoml,fi,fl,rij,rlj,thr);
+ rlj[0] = -rjl[0]; rlj[1] = -rjl[1]; rlj[2] = -rjl[2];
+ v_tally3_thr(atomi,atomj,atoml,fi,fl,rij,rlj,thr);
}
}
}
@@ -433,7 +433,7 @@ double PairAIREBOOMP::bondorder_thr(int i, int j, double rij[3], double rijmag,
rikmag = sqrt((rik[0]*rik[0])+(rik[1]*rik[1])+(rik[2]*rik[2]));
wik = Sp(rikmag,rcmin[itype][ktype],rcmax[itype][ktype],dwik);
Nki = nC[atomk]-(wik*kronecker(itype,0))+nH[atomk] -
- (wik*kronecker(itype,1));
+ (wik*kronecker(itype,1));
SpN = Sp(Nki,Nmin,Nmax,dNki);
tmp2 = VA*dN3[0]*dwik/rikmag;
@@ -457,28 +457,28 @@ double PairAIREBOOMP::bondorder_thr(int i, int j, double rij[3], double rijmag,
if (vflag_atom) v_tally2_thr(atomi,atomk,-tmp2,rik,thr);
if (fabs(dNki) > TOL) {
- REBO_neighs_k = REBO_firstneigh[atomk];
- for (n = 0; n < REBO_numneigh[atomk]; n++) {
- atomn = REBO_neighs_k[n];
- if (atomn != atomi) {
- ntype = map[type[atomn]];
- rkn[0] = x[atomk][0]-x[atomn][0];
- rkn[1] = x[atomk][1]-x[atomn][1];
- rkn[2] = x[atomk][2]-x[atomn][2];
- rknmag = sqrt((rkn[0]*rkn[0])+(rkn[1]*rkn[1])+(rkn[2]*rkn[2]));
- Sp(rknmag,rcmin[ktype][ntype],rcmax[ktype][ntype],dwkn);
-
- tmp2 = VA*dN3[2]*(2.0*NconjtmpI*wik*dNki*dwkn)/rknmag;
- f[atomk][0] -= tmp2*rkn[0];
- f[atomk][1] -= tmp2*rkn[1];
- f[atomk][2] -= tmp2*rkn[2];
- f[atomn][0] += tmp2*rkn[0];
- f[atomn][1] += tmp2*rkn[1];
- f[atomn][2] += tmp2*rkn[2];
-
- if (vflag_atom) v_tally2_thr(atomk,atomn,-tmp2,rkn,thr);
- }
- }
+ REBO_neighs_k = REBO_firstneigh[atomk];
+ for (n = 0; n < REBO_numneigh[atomk]; n++) {
+ atomn = REBO_neighs_k[n];
+ if (atomn != atomi) {
+ ntype = map[type[atomn]];
+ rkn[0] = x[atomk][0]-x[atomn][0];
+ rkn[1] = x[atomk][1]-x[atomn][1];
+ rkn[2] = x[atomk][2]-x[atomn][2];
+ rknmag = sqrt((rkn[0]*rkn[0])+(rkn[1]*rkn[1])+(rkn[2]*rkn[2]));
+ Sp(rknmag,rcmin[ktype][ntype],rcmax[ktype][ntype],dwkn);
+
+ tmp2 = VA*dN3[2]*(2.0*NconjtmpI*wik*dNki*dwkn)/rknmag;
+ f[atomk][0] -= tmp2*rkn[0];
+ f[atomk][1] -= tmp2*rkn[1];
+ f[atomk][2] -= tmp2*rkn[2];
+ f[atomn][0] += tmp2*rkn[0];
+ f[atomn][1] += tmp2*rkn[1];
+ f[atomn][2] += tmp2*rkn[2];
+
+ if (vflag_atom) v_tally2_thr(atomk,atomn,-tmp2,rkn,thr);
+ }
+ }
}
}
}
@@ -496,7 +496,7 @@ double PairAIREBOOMP::bondorder_thr(int i, int j, double rij[3], double rijmag,
rjlmag = sqrt((rjl[0]*rjl[0])+(rjl[1]*rjl[1])+(rjl[2]*rjl[2]));
wjl = Sp(rjlmag,rcmin[jtype][ltype],rcmax[jtype][ltype],dwjl);
Nlj = nC[atoml]-(wjl*kronecker(jtype,0))+nH[atoml] -
- (wjl*kronecker(jtype,1));
+ (wjl*kronecker(jtype,1));
SpN = Sp(Nlj,Nmin,Nmax,dNlj);
tmp2 = VA*dN3[1]*dwjl/rjlmag;
@@ -520,28 +520,28 @@ double PairAIREBOOMP::bondorder_thr(int i, int j, double rij[3], double rijmag,
if (vflag_atom) v_tally2_thr(atomj,atoml,-tmp2,rjl,thr);
if (fabs(dNlj) > TOL) {
- REBO_neighs_l = REBO_firstneigh[atoml];
- for (n = 0; n < REBO_numneigh[atoml]; n++) {
- atomn = REBO_neighs_l[n];
- if (atomn != atomj) {
- ntype = map[type[atomn]];
- rln[0] = x[atoml][0]-x[atomn][0];
- rln[1] = x[atoml][1]-x[atomn][1];
- rln[2] = x[atoml][2]-x[atomn][2];
- rlnmag = sqrt((rln[0]*rln[0])+(rln[1]*rln[1])+(rln[2]*rln[2]));
- Sp(rlnmag,rcmin[ltype][ntype],rcmax[ltype][ntype],dwln);
-
- tmp2 = VA*dN3[2]*(2.0*NconjtmpJ*wjl*dNlj*dwln)/rlnmag;
- f[atoml][0] -= tmp2*rln[0];
- f[atoml][1] -= tmp2*rln[1];
- f[atoml][2] -= tmp2*rln[2];
- f[atomn][0] += tmp2*rln[0];
- f[atomn][1] += tmp2*rln[1];
- f[atomn][2] += tmp2*rln[2];
-
- if (vflag_atom) v_tally2_thr(atoml,atomn,-tmp2,rln,thr);
- }
- }
+ REBO_neighs_l = REBO_firstneigh[atoml];
+ for (n = 0; n < REBO_numneigh[atoml]; n++) {
+ atomn = REBO_neighs_l[n];
+ if (atomn != atomj) {
+ ntype = map[type[atomn]];
+ rln[0] = x[atoml][0]-x[atomn][0];
+ rln[1] = x[atoml][1]-x[atomn][1];
+ rln[2] = x[atoml][2]-x[atomn][2];
+ rlnmag = sqrt((rln[0]*rln[0])+(rln[1]*rln[1])+(rln[2]*rln[2]));
+ Sp(rlnmag,rcmin[ltype][ntype],rcmax[ltype][ntype],dwln);
+
+ tmp2 = VA*dN3[2]*(2.0*NconjtmpJ*wjl*dNlj*dwln)/rlnmag;
+ f[atoml][0] -= tmp2*rln[0];
+ f[atoml][1] -= tmp2*rln[1];
+ f[atoml][2] -= tmp2*rln[2];
+ f[atomn][0] += tmp2*rln[0];
+ f[atomn][1] += tmp2*rln[1];
+ f[atomn][2] += tmp2*rln[2];
+
+ if (vflag_atom) v_tally2_thr(atoml,atomn,-tmp2,rln,thr);
+ }
+ }
}
}
}
@@ -571,197 +571,197 @@ double PairAIREBOOMP::bondorder_thr(int i, int j, double rij[3], double rijmag,
atom1 = atomk;
ktype = map[type[atomk]];
if (atomk != atomj) {
- r21[0] = x[atom2][0]-x[atom1][0];
- r21[1] = x[atom2][1]-x[atom1][1];
- r21[2] = x[atom2][2]-x[atom1][2];
- r21mag = sqrt(r21[0]*r21[0] + r21[1]*r21[1] + r21[2]*r21[2]);
- cos321 = -1.0*((r21[0]*r32[0])+(r21[1]*r32[1])+(r21[2]*r32[2])) /
- (r21mag*r32mag);
- cos321 = MIN(cos321,1.0);
- cos321 = MAX(cos321,-1.0);
- Sp2(cos321,thmin,thmax,dcut321);
- sin321 = sqrt(1.0 - cos321*cos321);
- sink2i = 1.0/(sin321*sin321);
- rik2i = 1.0/(r21mag*r21mag);
- if (sin321 != 0.0) {
- rr = (r23mag*r23mag)-(r21mag*r21mag);
- rjk[0] = r21[0]-r23[0];
- rjk[1] = r21[1]-r23[1];
- rjk[2] = r21[2]-r23[2];
- rjk2 = (rjk[0]*rjk[0])+(rjk[1]*rjk[1])+(rjk[2]*rjk[2]);
- rijrik = 2.0*r23mag*r21mag;
- rik2 = r21mag*r21mag;
- dctik = (-rr+rjk2)/(rijrik*rik2);
- dctij = (rr+rjk2)/(rijrik*r23mag*r23mag);
- dctjk = -2.0/rijrik;
- w21 = Sp(r21mag,rcmin[itype][ktype],rcmaxp[itype][ktype],dw21);
- rijmag = r32mag;
- rikmag = r21mag;
- rij2 = r32mag*r32mag;
- rik2 = r21mag*r21mag;
- costmp = 0.5*(rij2+rik2-rjk2)/rijmag/rikmag;
- tspjik = Sp2(costmp,thmin,thmax,dtsjik);
- dtsjik = -dtsjik;
-
- REBO_neighs_j = REBO_firstneigh[j];
- for (l = 0; l < REBO_numneigh[j]; l++) {
- atoml = REBO_neighs_j[l];
- atom4 = atoml;
- ltype = map[type[atoml]];
- if (!(atoml == atomi || atoml == atomk)) {
- r34[0] = x[atom3][0]-x[atom4][0];
- r34[1] = x[atom3][1]-x[atom4][1];
- r34[2] = x[atom3][2]-x[atom4][2];
- r34mag = sqrt((r34[0]*r34[0])+(r34[1]*r34[1])+(r34[2]*r34[2]));
- cos234 = (r32[0]*r34[0] + r32[1]*r34[1] + r32[2]*r34[2]) /
- (r32mag*r34mag);
- cos234 = MIN(cos234,1.0);
- cos234 = MAX(cos234,-1.0);
- sin234 = sqrt(1.0 - cos234*cos234);
- sinl2i = 1.0/(sin234*sin234);
- rjl2i = 1.0/(r34mag*r34mag);
-
- if (sin234 != 0.0) {
- w34 = Sp(r34mag,rcmin[jtype][ltype],rcmaxp[jtype][ltype],dw34);
- rr = (r23mag*r23mag)-(r34mag*r34mag);
- ril[0] = r23[0]+r34[0];
- ril[1] = r23[1]+r34[1];
- ril[2] = r23[2]+r34[2];
- ril2 = (ril[0]*ril[0])+(ril[1]*ril[1])+(ril[2]*ril[2]);
- rijrjl = 2.0*r23mag*r34mag;
- rjl2 = r34mag*r34mag;
- dctjl = (-rr+ril2)/(rijrjl*rjl2);
- dctji = (rr+ril2)/(rijrjl*r23mag*r23mag);
- dctil = -2.0/rijrjl;
- rjlmag = r34mag;
- rjl2 = r34mag*r34mag;
- costmp = 0.5*(rij2+rjl2-ril2)/rijmag/rjlmag;
- tspijl = Sp2(costmp,thmin,thmax,dtsijl);
- dtsijl = -dtsijl;
- prefactor = VA*Tij;
-
- cross321[0] = (r32[1]*r21[2])-(r32[2]*r21[1]);
- cross321[1] = (r32[2]*r21[0])-(r32[0]*r21[2]);
- cross321[2] = (r32[0]*r21[1])-(r32[1]*r21[0]);
- cross234[0] = (r23[1]*r34[2])-(r23[2]*r34[1]);
- cross234[1] = (r23[2]*r34[0])-(r23[0]*r34[2]);
- cross234[2] = (r23[0]*r34[1])-(r23[1]*r34[0]);
-
- cwnum = (cross321[0]*cross234[0]) +
- (cross321[1]*cross234[1]) + (cross321[2]*cross234[2]);
- cwnom = r21mag*r34mag*r23mag*r23mag*sin321*sin234;
- om1234 = cwnum/cwnom;
- cw = om1234;
- Etmp += ((1.0-(om1234*om1234))*w21*w34) *
- (1.0-tspjik)*(1.0-tspijl);
-
- dt1dik = (rik2i)-(dctik*sink2i*cos321);
- dt1djk = (-dctjk*sink2i*cos321);
- dt1djl = (rjl2i)-(dctjl*sinl2i*cos234);
- dt1dil = (-dctil*sinl2i*cos234);
- dt1dij = (2.0/(r23mag*r23mag))-(dctij*sink2i*cos321) -
- (dctji*sinl2i*cos234);
-
- dt2dik[0] = (-r23[2]*cross234[1])+(r23[1]*cross234[2]);
- dt2dik[1] = (-r23[0]*cross234[2])+(r23[2]*cross234[0]);
- dt2dik[2] = (-r23[1]*cross234[0])+(r23[0]*cross234[1]);
-
- dt2djl[0] = (-r23[1]*cross321[2])+(r23[2]*cross321[1]);
- dt2djl[1] = (-r23[2]*cross321[0])+(r23[0]*cross321[2]);
- dt2djl[2] = (-r23[0]*cross321[1])+(r23[1]*cross321[0]);
-
- dt2dij[0] = (r21[2]*cross234[1])-(r34[2]*cross321[1]) -
- (r21[1]*cross234[2])+(r34[1]*cross321[2]);
- dt2dij[1] = (r21[0]*cross234[2])-(r34[0]*cross321[2]) -
- (r21[2]*cross234[0])+(r34[2]*cross321[0]);
- dt2dij[2] = (r21[1]*cross234[0])-(r34[1]*cross321[0]) -
- (r21[0]*cross234[1])+(r34[0]*cross321[1]);
-
- aa = (prefactor*2.0*cw/cwnom)*w21*w34 *
- (1.0-tspjik)*(1.0-tspijl);
- aaa1 = -prefactor*(1.0-(om1234*om1234)) *
- (1.0-tspjik)*(1.0-tspijl);
- aaa2 = aaa1*w21*w34;
- at2 = aa*cwnum;
-
- fcijpc = (-dt1dij*at2)+(aaa2*dtsjik*dctij*(1.0-tspijl)) +
- (aaa2*dtsijl*dctji*(1.0-tspjik));
- fcikpc = (-dt1dik*at2)+(aaa2*dtsjik*dctik*(1.0-tspijl));
- fcjlpc = (-dt1djl*at2)+(aaa2*dtsijl*dctjl*(1.0-tspjik));
- fcjkpc = (-dt1djk*at2)+(aaa2*dtsjik*dctjk*(1.0-tspijl));
- fcilpc = (-dt1dil*at2)+(aaa2*dtsijl*dctil*(1.0-tspjik));
-
- F23[0] = (fcijpc*r23[0])+(aa*dt2dij[0]);
- F23[1] = (fcijpc*r23[1])+(aa*dt2dij[1]);
- F23[2] = (fcijpc*r23[2])+(aa*dt2dij[2]);
-
- F12[0] = (fcikpc*r21[0])+(aa*dt2dik[0]);
- F12[1] = (fcikpc*r21[1])+(aa*dt2dik[1]);
- F12[2] = (fcikpc*r21[2])+(aa*dt2dik[2]);
-
- F34[0] = (fcjlpc*r34[0])+(aa*dt2djl[0]);
- F34[1] = (fcjlpc*r34[1])+(aa*dt2djl[1]);
- F34[2] = (fcjlpc*r34[2])+(aa*dt2djl[2]);
-
- F31[0] = (fcjkpc*rjk[0]);
- F31[1] = (fcjkpc*rjk[1]);
- F31[2] = (fcjkpc*rjk[2]);
-
- F24[0] = (fcilpc*ril[0]);
- F24[1] = (fcilpc*ril[1]);
- F24[2] = (fcilpc*ril[2]);
-
- f1[0] = -F12[0]-F31[0];
- f1[1] = -F12[1]-F31[1];
- f1[2] = -F12[2]-F31[2];
- f2[0] = F23[0]+F12[0]+F24[0];
- f2[1] = F23[1]+F12[1]+F24[1];
- f2[2] = F23[2]+F12[2]+F24[2];
- f3[0] = -F23[0]+F34[0]+F31[0];
- f3[1] = -F23[1]+F34[1]+F31[1];
- f3[2] = -F23[2]+F34[2]+F31[2];
- f4[0] = -F34[0]-F24[0];
- f4[1] = -F34[1]-F24[1];
- f4[2] = -F34[2]-F24[2];
-
- // coordination forces
-
- tmp2 = VA*Tij*((1.0-(om1234*om1234))) *
- (1.0-tspjik)*(1.0-tspijl)*dw21*w34/r21mag;
- f2[0] -= tmp2*r21[0];
- f2[1] -= tmp2*r21[1];
- f2[2] -= tmp2*r21[2];
- f1[0] += tmp2*r21[0];
- f1[1] += tmp2*r21[1];
- f1[2] += tmp2*r21[2];
-
- tmp2 = VA*Tij*((1.0-(om1234*om1234))) *
- (1.0-tspjik)*(1.0-tspijl)*w21*dw34/r34mag;
- f3[0] -= tmp2*r34[0];
- f3[1] -= tmp2*r34[1];
- f3[2] -= tmp2*r34[2];
- f4[0] += tmp2*r34[0];
- f4[1] += tmp2*r34[1];
- f4[2] += tmp2*r34[2];
-
- f[atom1][0] += f1[0]; f[atom1][1] += f1[1];
- f[atom1][2] += f1[2];
- f[atom2][0] += f2[0]; f[atom2][1] += f2[1];
- f[atom2][2] += f2[2];
- f[atom3][0] += f3[0]; f[atom3][1] += f3[1];
- f[atom3][2] += f3[2];
- f[atom4][0] += f4[0]; f[atom4][1] += f4[1];
- f[atom4][2] += f4[2];
-
- if (vflag_atom) {
- r13[0] = -rjk[0]; r13[1] = -rjk[1]; r13[2] = -rjk[2];
- r43[0] = -r34[0]; r43[1] = -r34[1]; r43[2] = -r34[2];
- v_tally4_thr(atom1,atom2,atom3,atom4,f1,f2,f4,r13,r23,r43,thr);
- }
- }
- }
- }
- }
+ r21[0] = x[atom2][0]-x[atom1][0];
+ r21[1] = x[atom2][1]-x[atom1][1];
+ r21[2] = x[atom2][2]-x[atom1][2];
+ r21mag = sqrt(r21[0]*r21[0] + r21[1]*r21[1] + r21[2]*r21[2]);
+ cos321 = -1.0*((r21[0]*r32[0])+(r21[1]*r32[1])+(r21[2]*r32[2])) /
+ (r21mag*r32mag);
+ cos321 = MIN(cos321,1.0);
+ cos321 = MAX(cos321,-1.0);
+ Sp2(cos321,thmin,thmax,dcut321);
+ sin321 = sqrt(1.0 - cos321*cos321);
+ sink2i = 1.0/(sin321*sin321);
+ rik2i = 1.0/(r21mag*r21mag);
+ if (sin321 != 0.0) {
+ rr = (r23mag*r23mag)-(r21mag*r21mag);
+ rjk[0] = r21[0]-r23[0];
+ rjk[1] = r21[1]-r23[1];
+ rjk[2] = r21[2]-r23[2];
+ rjk2 = (rjk[0]*rjk[0])+(rjk[1]*rjk[1])+(rjk[2]*rjk[2]);
+ rijrik = 2.0*r23mag*r21mag;
+ rik2 = r21mag*r21mag;
+ dctik = (-rr+rjk2)/(rijrik*rik2);
+ dctij = (rr+rjk2)/(rijrik*r23mag*r23mag);
+ dctjk = -2.0/rijrik;
+ w21 = Sp(r21mag,rcmin[itype][ktype],rcmaxp[itype][ktype],dw21);
+ rijmag = r32mag;
+ rikmag = r21mag;
+ rij2 = r32mag*r32mag;
+ rik2 = r21mag*r21mag;
+ costmp = 0.5*(rij2+rik2-rjk2)/rijmag/rikmag;
+ tspjik = Sp2(costmp,thmin,thmax,dtsjik);
+ dtsjik = -dtsjik;
+
+ REBO_neighs_j = REBO_firstneigh[j];
+ for (l = 0; l < REBO_numneigh[j]; l++) {
+ atoml = REBO_neighs_j[l];
+ atom4 = atoml;
+ ltype = map[type[atoml]];
+ if (!(atoml == atomi || atoml == atomk)) {
+ r34[0] = x[atom3][0]-x[atom4][0];
+ r34[1] = x[atom3][1]-x[atom4][1];
+ r34[2] = x[atom3][2]-x[atom4][2];
+ r34mag = sqrt((r34[0]*r34[0])+(r34[1]*r34[1])+(r34[2]*r34[2]));
+ cos234 = (r32[0]*r34[0] + r32[1]*r34[1] + r32[2]*r34[2]) /
+ (r32mag*r34mag);
+ cos234 = MIN(cos234,1.0);
+ cos234 = MAX(cos234,-1.0);
+ sin234 = sqrt(1.0 - cos234*cos234);
+ sinl2i = 1.0/(sin234*sin234);
+ rjl2i = 1.0/(r34mag*r34mag);
+
+ if (sin234 != 0.0) {
+ w34 = Sp(r34mag,rcmin[jtype][ltype],rcmaxp[jtype][ltype],dw34);
+ rr = (r23mag*r23mag)-(r34mag*r34mag);
+ ril[0] = r23[0]+r34[0];
+ ril[1] = r23[1]+r34[1];
+ ril[2] = r23[2]+r34[2];
+ ril2 = (ril[0]*ril[0])+(ril[1]*ril[1])+(ril[2]*ril[2]);
+ rijrjl = 2.0*r23mag*r34mag;
+ rjl2 = r34mag*r34mag;
+ dctjl = (-rr+ril2)/(rijrjl*rjl2);
+ dctji = (rr+ril2)/(rijrjl*r23mag*r23mag);
+ dctil = -2.0/rijrjl;
+ rjlmag = r34mag;
+ rjl2 = r34mag*r34mag;
+ costmp = 0.5*(rij2+rjl2-ril2)/rijmag/rjlmag;
+ tspijl = Sp2(costmp,thmin,thmax,dtsijl);
+ dtsijl = -dtsijl;
+ prefactor = VA*Tij;
+
+ cross321[0] = (r32[1]*r21[2])-(r32[2]*r21[1]);
+ cross321[1] = (r32[2]*r21[0])-(r32[0]*r21[2]);
+ cross321[2] = (r32[0]*r21[1])-(r32[1]*r21[0]);
+ cross234[0] = (r23[1]*r34[2])-(r23[2]*r34[1]);
+ cross234[1] = (r23[2]*r34[0])-(r23[0]*r34[2]);
+ cross234[2] = (r23[0]*r34[1])-(r23[1]*r34[0]);
+
+ cwnum = (cross321[0]*cross234[0]) +
+ (cross321[1]*cross234[1]) + (cross321[2]*cross234[2]);
+ cwnom = r21mag*r34mag*r23mag*r23mag*sin321*sin234;
+ om1234 = cwnum/cwnom;
+ cw = om1234;
+ Etmp += ((1.0-(om1234*om1234))*w21*w34) *
+ (1.0-tspjik)*(1.0-tspijl);
+
+ dt1dik = (rik2i)-(dctik*sink2i*cos321);
+ dt1djk = (-dctjk*sink2i*cos321);
+ dt1djl = (rjl2i)-(dctjl*sinl2i*cos234);
+ dt1dil = (-dctil*sinl2i*cos234);
+ dt1dij = (2.0/(r23mag*r23mag))-(dctij*sink2i*cos321) -
+ (dctji*sinl2i*cos234);
+
+ dt2dik[0] = (-r23[2]*cross234[1])+(r23[1]*cross234[2]);
+ dt2dik[1] = (-r23[0]*cross234[2])+(r23[2]*cross234[0]);
+ dt2dik[2] = (-r23[1]*cross234[0])+(r23[0]*cross234[1]);
+
+ dt2djl[0] = (-r23[1]*cross321[2])+(r23[2]*cross321[1]);
+ dt2djl[1] = (-r23[2]*cross321[0])+(r23[0]*cross321[2]);
+ dt2djl[2] = (-r23[0]*cross321[1])+(r23[1]*cross321[0]);
+
+ dt2dij[0] = (r21[2]*cross234[1])-(r34[2]*cross321[1]) -
+ (r21[1]*cross234[2])+(r34[1]*cross321[2]);
+ dt2dij[1] = (r21[0]*cross234[2])-(r34[0]*cross321[2]) -
+ (r21[2]*cross234[0])+(r34[2]*cross321[0]);
+ dt2dij[2] = (r21[1]*cross234[0])-(r34[1]*cross321[0]) -
+ (r21[0]*cross234[1])+(r34[0]*cross321[1]);
+
+ aa = (prefactor*2.0*cw/cwnom)*w21*w34 *
+ (1.0-tspjik)*(1.0-tspijl);
+ aaa1 = -prefactor*(1.0-(om1234*om1234)) *
+ (1.0-tspjik)*(1.0-tspijl);
+ aaa2 = aaa1*w21*w34;
+ at2 = aa*cwnum;
+
+ fcijpc = (-dt1dij*at2)+(aaa2*dtsjik*dctij*(1.0-tspijl)) +
+ (aaa2*dtsijl*dctji*(1.0-tspjik));
+ fcikpc = (-dt1dik*at2)+(aaa2*dtsjik*dctik*(1.0-tspijl));
+ fcjlpc = (-dt1djl*at2)+(aaa2*dtsijl*dctjl*(1.0-tspjik));
+ fcjkpc = (-dt1djk*at2)+(aaa2*dtsjik*dctjk*(1.0-tspijl));
+ fcilpc = (-dt1dil*at2)+(aaa2*dtsijl*dctil*(1.0-tspjik));
+
+ F23[0] = (fcijpc*r23[0])+(aa*dt2dij[0]);
+ F23[1] = (fcijpc*r23[1])+(aa*dt2dij[1]);
+ F23[2] = (fcijpc*r23[2])+(aa*dt2dij[2]);
+
+ F12[0] = (fcikpc*r21[0])+(aa*dt2dik[0]);
+ F12[1] = (fcikpc*r21[1])+(aa*dt2dik[1]);
+ F12[2] = (fcikpc*r21[2])+(aa*dt2dik[2]);
+
+ F34[0] = (fcjlpc*r34[0])+(aa*dt2djl[0]);
+ F34[1] = (fcjlpc*r34[1])+(aa*dt2djl[1]);
+ F34[2] = (fcjlpc*r34[2])+(aa*dt2djl[2]);
+
+ F31[0] = (fcjkpc*rjk[0]);
+ F31[1] = (fcjkpc*rjk[1]);
+ F31[2] = (fcjkpc*rjk[2]);
+
+ F24[0] = (fcilpc*ril[0]);
+ F24[1] = (fcilpc*ril[1]);
+ F24[2] = (fcilpc*ril[2]);
+
+ f1[0] = -F12[0]-F31[0];
+ f1[1] = -F12[1]-F31[1];
+ f1[2] = -F12[2]-F31[2];
+ f2[0] = F23[0]+F12[0]+F24[0];
+ f2[1] = F23[1]+F12[1]+F24[1];
+ f2[2] = F23[2]+F12[2]+F24[2];
+ f3[0] = -F23[0]+F34[0]+F31[0];
+ f3[1] = -F23[1]+F34[1]+F31[1];
+ f3[2] = -F23[2]+F34[2]+F31[2];
+ f4[0] = -F34[0]-F24[0];
+ f4[1] = -F34[1]-F24[1];
+ f4[2] = -F34[2]-F24[2];
+
+ // coordination forces
+
+ tmp2 = VA*Tij*((1.0-(om1234*om1234))) *
+ (1.0-tspjik)*(1.0-tspijl)*dw21*w34/r21mag;
+ f2[0] -= tmp2*r21[0];
+ f2[1] -= tmp2*r21[1];
+ f2[2] -= tmp2*r21[2];
+ f1[0] += tmp2*r21[0];
+ f1[1] += tmp2*r21[1];
+ f1[2] += tmp2*r21[2];
+
+ tmp2 = VA*Tij*((1.0-(om1234*om1234))) *
+ (1.0-tspjik)*(1.0-tspijl)*w21*dw34/r34mag;
+ f3[0] -= tmp2*r34[0];
+ f3[1] -= tmp2*r34[1];
+ f3[2] -= tmp2*r34[2];
+ f4[0] += tmp2*r34[0];
+ f4[1] += tmp2*r34[1];
+ f4[2] += tmp2*r34[2];
+
+ f[atom1][0] += f1[0]; f[atom1][1] += f1[1];
+ f[atom1][2] += f1[2];
+ f[atom2][0] += f2[0]; f[atom2][1] += f2[1];
+ f[atom2][2] += f2[2];
+ f[atom3][0] += f3[0]; f[atom3][1] += f3[1];
+ f[atom3][2] += f3[2];
+ f[atom4][0] += f4[0]; f[atom4][1] += f4[1];
+ f[atom4][2] += f4[2];
+
+ if (vflag_atom) {
+ r13[0] = -rjk[0]; r13[1] = -rjk[1]; r13[2] = -rjk[2];
+ r43[0] = -r34[0]; r43[1] = -r34[1]; r43[2] = -r34[2];
+ v_tally4_thr(atom1,atom2,atom3,atom4,f1,f2,f4,r13,r23,r43,thr);
+ }
+ }
+ }
+ }
+ }
}
}
@@ -771,60 +771,60 @@ double PairAIREBOOMP::bondorder_thr(int i, int j, double rij[3], double rijmag,
for (k = 0; k < REBO_numneigh[i]; k++) {
atomk = REBO_neighs[k];
if (atomk != atomj) {
- ktype = map[type[atomk]];
- rik[0] = x[atomi][0]-x[atomk][0];
- rik[1] = x[atomi][1]-x[atomk][1];
- rik[2] = x[atomi][2]-x[atomk][2];
- rikmag = sqrt((rik[0]*rik[0])+(rik[1]*rik[1])+(rik[2]*rik[2]));
- wik = Sp(rikmag,rcmin[itype][ktype],rcmax[itype][ktype],dwik);
- Nki = nC[atomk]-(wik*kronecker(itype,0))+nH[atomk] -
- (wik*kronecker(itype,1));
- SpN = Sp(Nki,Nmin,Nmax,dNki);
-
- tmp2 = VA*dN3[0]*dwik*Etmp/rikmag;
- f[atomi][0] -= tmp2*rik[0];
- f[atomi][1] -= tmp2*rik[1];
- f[atomi][2] -= tmp2*rik[2];
- f[atomk][0] += tmp2*rik[0];
- f[atomk][1] += tmp2*rik[1];
- f[atomk][2] += tmp2*rik[2];
-
- if (vflag_atom) v_tally2_thr(atomi,atomk,-tmp2,rik,thr);
-
- tmp2 = VA*dN3[2]*(2.0*NconjtmpI*dwik*SpN)*Etmp/rikmag;
- f[atomi][0] -= tmp2*rik[0];
- f[atomi][1] -= tmp2*rik[1];
- f[atomi][2] -= tmp2*rik[2];
- f[atomk][0] += tmp2*rik[0];
- f[atomk][1] += tmp2*rik[1];
- f[atomk][2] += tmp2*rik[2];
-
- if (vflag_atom) v_tally2_thr(atomi,atomk,-tmp2,rik,thr);
-
- if (fabs(dNki) > TOL) {
- REBO_neighs_k = REBO_firstneigh[atomk];
- for (n = 0; n < REBO_numneigh[atomk]; n++) {
- atomn = REBO_neighs_k[n];
- ntype = map[type[atomn]];
- if (atomn != atomi) {
- rkn[0] = x[atomk][0]-x[atomn][0];
- rkn[1] = x[atomk][1]-x[atomn][1];
- rkn[2] = x[atomk][2]-x[atomn][2];
- rknmag = sqrt((rkn[0]*rkn[0])+(rkn[1]*rkn[1])+(rkn[2]*rkn[2]));
- Sp(rknmag,rcmin[ktype][ntype],rcmax[ktype][ntype],dwkn);
-
- tmp2 = VA*dN3[2]*(2.0*NconjtmpI*wik*dNki*dwkn)*Etmp/rknmag;
- f[atomk][0] -= tmp2*rkn[0];
- f[atomk][1] -= tmp2*rkn[1];
- f[atomk][2] -= tmp2*rkn[2];
- f[atomn][0] += tmp2*rkn[0];
- f[atomn][1] += tmp2*rkn[1];
- f[atomn][2] += tmp2*rkn[2];
-
- if (vflag_atom) v_tally2_thr(atomk,atomn,-tmp2,rkn,thr);
- }
- }
- }
+ ktype = map[type[atomk]];
+ rik[0] = x[atomi][0]-x[atomk][0];
+ rik[1] = x[atomi][1]-x[atomk][1];
+ rik[2] = x[atomi][2]-x[atomk][2];
+ rikmag = sqrt((rik[0]*rik[0])+(rik[1]*rik[1])+(rik[2]*rik[2]));
+ wik = Sp(rikmag,rcmin[itype][ktype],rcmax[itype][ktype],dwik);
+ Nki = nC[atomk]-(wik*kronecker(itype,0))+nH[atomk] -
+ (wik*kronecker(itype,1));
+ SpN = Sp(Nki,Nmin,Nmax,dNki);
+
+ tmp2 = VA*dN3[0]*dwik*Etmp/rikmag;
+ f[atomi][0] -= tmp2*rik[0];
+ f[atomi][1] -= tmp2*rik[1];
+ f[atomi][2] -= tmp2*rik[2];
+ f[atomk][0] += tmp2*rik[0];
+ f[atomk][1] += tmp2*rik[1];
+ f[atomk][2] += tmp2*rik[2];
+
+ if (vflag_atom) v_tally2_thr(atomi,atomk,-tmp2,rik,thr);
+
+ tmp2 = VA*dN3[2]*(2.0*NconjtmpI*dwik*SpN)*Etmp/rikmag;
+ f[atomi][0] -= tmp2*rik[0];
+ f[atomi][1] -= tmp2*rik[1];
+ f[atomi][2] -= tmp2*rik[2];
+ f[atomk][0] += tmp2*rik[0];
+ f[atomk][1] += tmp2*rik[1];
+ f[atomk][2] += tmp2*rik[2];
+
+ if (vflag_atom) v_tally2_thr(atomi,atomk,-tmp2,rik,thr);
+
+ if (fabs(dNki) > TOL) {
+ REBO_neighs_k = REBO_firstneigh[atomk];
+ for (n = 0; n < REBO_numneigh[atomk]; n++) {
+ atomn = REBO_neighs_k[n];
+ ntype = map[type[atomn]];
+ if (atomn != atomi) {
+ rkn[0] = x[atomk][0]-x[atomn][0];
+ rkn[1] = x[atomk][1]-x[atomn][1];
+ rkn[2] = x[atomk][2]-x[atomn][2];
+ rknmag = sqrt((rkn[0]*rkn[0])+(rkn[1]*rkn[1])+(rkn[2]*rkn[2]));
+ Sp(rknmag,rcmin[ktype][ntype],rcmax[ktype][ntype],dwkn);
+
+ tmp2 = VA*dN3[2]*(2.0*NconjtmpI*wik*dNki*dwkn)*Etmp/rknmag;
+ f[atomk][0] -= tmp2*rkn[0];
+ f[atomk][1] -= tmp2*rkn[1];
+ f[atomk][2] -= tmp2*rkn[2];
+ f[atomn][0] += tmp2*rkn[0];
+ f[atomn][1] += tmp2*rkn[1];
+ f[atomn][2] += tmp2*rkn[2];
+
+ if (vflag_atom) v_tally2_thr(atomk,atomn,-tmp2,rkn,thr);
+ }
+ }
+ }
}
}
@@ -834,60 +834,60 @@ double PairAIREBOOMP::bondorder_thr(int i, int j, double rij[3], double rijmag,
for (l = 0; l < REBO_numneigh[j]; l++) {
atoml = REBO_neighs[l];
if (atoml != atomi) {
- ltype = map[type[atoml]];
- rjl[0] = x[atomj][0]-x[atoml][0];
- rjl[1] = x[atomj][1]-x[atoml][1];
- rjl[2] = x[atomj][2]-x[atoml][2];
- rjlmag = sqrt((rjl[0]*rjl[0])+(rjl[1]*rjl[1])+(rjl[2]*rjl[2]));
- wjl = Sp(rjlmag,rcmin[jtype][ltype],rcmax[jtype][ltype],dwjl);
- Nlj = nC[atoml]-(wjl*kronecker(jtype,0))+nH[atoml] -
- (wjl*kronecker(jtype,1));
- SpN = Sp(Nlj,Nmin,Nmax,dNlj);
-
- tmp2 = VA*dN3[1]*dwjl*Etmp/rjlmag;
- f[atomj][0] -= tmp2*rjl[0];
- f[atomj][1] -= tmp2*rjl[1];
- f[atomj][2] -= tmp2*rjl[2];
- f[atoml][0] += tmp2*rjl[0];
- f[atoml][1] += tmp2*rjl[1];
- f[atoml][2] += tmp2*rjl[2];
-
- if (vflag_atom) v_tally2_thr(atomj,atoml,-tmp2,rjl,thr);
-
- tmp2 = VA*dN3[2]*(2.0*NconjtmpJ*dwjl*SpN)*Etmp/rjlmag;
- f[atomj][0] -= tmp2*rjl[0];
- f[atomj][1] -= tmp2*rjl[1];
- f[atomj][2] -= tmp2*rjl[2];
- f[atoml][0] += tmp2*rjl[0];
- f[atoml][1] += tmp2*rjl[1];
- f[atoml][2] += tmp2*rjl[2];
-
- if (vflag_atom) v_tally2_thr(atomj,atoml,-tmp2,rjl,thr);
-
- if (fabs(dNlj) > TOL) {
- REBO_neighs_l = REBO_firstneigh[atoml];
- for (n = 0; n < REBO_numneigh[atoml]; n++) {
- atomn = REBO_neighs_l[n];
- ntype = map[type[atomn]];
- if (atomn !=atomj) {
- rln[0] = x[atoml][0]-x[atomn][0];
- rln[1] = x[atoml][1]-x[atomn][1];
- rln[2] = x[atoml][2]-x[atomn][2];
- rlnmag = sqrt((rln[0]*rln[0])+(rln[1]*rln[1])+(rln[2]*rln[2]));
- Sp(rlnmag,rcmin[ltype][ntype],rcmax[ltype][ntype],dwln);
-
- tmp2 = VA*dN3[2]*(2.0*NconjtmpJ*wjl*dNlj*dwln)*Etmp/rlnmag;
- f[atoml][0] -= tmp2*rln[0];
- f[atoml][1] -= tmp2*rln[1];
- f[atoml][2] -= tmp2*rln[2];
- f[atomn][0] += tmp2*rln[0];
- f[atomn][1] += tmp2*rln[1];
- f[atomn][2] += tmp2*rln[2];
-
- if (vflag_atom) v_tally2_thr(atoml,atomn,-tmp2,rln,thr);
- }
- }
- }
+ ltype = map[type[atoml]];
+ rjl[0] = x[atomj][0]-x[atoml][0];
+ rjl[1] = x[atomj][1]-x[atoml][1];
+ rjl[2] = x[atomj][2]-x[atoml][2];
+ rjlmag = sqrt((rjl[0]*rjl[0])+(rjl[1]*rjl[1])+(rjl[2]*rjl[2]));
+ wjl = Sp(rjlmag,rcmin[jtype][ltype],rcmax[jtype][ltype],dwjl);
+ Nlj = nC[atoml]-(wjl*kronecker(jtype,0))+nH[atoml] -
+ (wjl*kronecker(jtype,1));
+ SpN = Sp(Nlj,Nmin,Nmax,dNlj);
+
+ tmp2 = VA*dN3[1]*dwjl*Etmp/rjlmag;
+ f[atomj][0] -= tmp2*rjl[0];
+ f[atomj][1] -= tmp2*rjl[1];
+ f[atomj][2] -= tmp2*rjl[2];
+ f[atoml][0] += tmp2*rjl[0];
+ f[atoml][1] += tmp2*rjl[1];
+ f[atoml][2] += tmp2*rjl[2];
+
+ if (vflag_atom) v_tally2_thr(atomj,atoml,-tmp2,rjl,thr);
+
+ tmp2 = VA*dN3[2]*(2.0*NconjtmpJ*dwjl*SpN)*Etmp/rjlmag;
+ f[atomj][0] -= tmp2*rjl[0];
+ f[atomj][1] -= tmp2*rjl[1];
+ f[atomj][2] -= tmp2*rjl[2];
+ f[atoml][0] += tmp2*rjl[0];
+ f[atoml][1] += tmp2*rjl[1];
+ f[atoml][2] += tmp2*rjl[2];
+
+ if (vflag_atom) v_tally2_thr(atomj,atoml,-tmp2,rjl,thr);
+
+ if (fabs(dNlj) > TOL) {
+ REBO_neighs_l = REBO_firstneigh[atoml];
+ for (n = 0; n < REBO_numneigh[atoml]; n++) {
+ atomn = REBO_neighs_l[n];
+ ntype = map[type[atomn]];
+ if (atomn !=atomj) {
+ rln[0] = x[atoml][0]-x[atomn][0];
+ rln[1] = x[atoml][1]-x[atomn][1];
+ rln[2] = x[atoml][2]-x[atomn][2];
+ rlnmag = sqrt((rln[0]*rln[0])+(rln[1]*rln[1])+(rln[2]*rln[2]));
+ Sp(rlnmag,rcmin[ltype][ntype],rcmax[ltype][ntype],dwln);
+
+ tmp2 = VA*dN3[2]*(2.0*NconjtmpJ*wjl*dNlj*dwln)*Etmp/rlnmag;
+ f[atoml][0] -= tmp2*rln[0];
+ f[atoml][1] -= tmp2*rln[1];
+ f[atoml][2] -= tmp2*rln[2];
+ f[atomn][0] += tmp2*rln[0];
+ f[atomn][1] += tmp2*rln[1];
+ f[atomn][2] += tmp2*rln[2];
+
+ if (vflag_atom) v_tally2_thr(atoml,atomn,-tmp2,rln,thr);
+ }
+ }
+ }
}
}
}
@@ -901,8 +901,8 @@ double PairAIREBOOMP::bondorder_thr(int i, int j, double rij[3], double rijmag,
------------------------------------------------------------------------- */
double PairAIREBOOMP::bondorderLJ_thr(int i, int j, double rij[3], double rijmag,
- double VA, double rij0[3], double rij0mag,
- int vflag_atom, ThrData * const thr)
+ double VA, double rij0[3], double rij0mag,
+ int vflag_atom, ThrData * const thr)
{
int k,n,l,atomk,atoml,atomn,atom1,atom2,atom3,atom4;
int atomi,atomj,itype,jtype,ktype,ltype,ntype;
@@ -970,12 +970,12 @@ double PairAIREBOOMP::bondorderLJ_thr(int i, int j, double rij[3], double rijmag
rik[2] = x[atomi][2]-x[atomk][2];
rikmag = sqrt((rik[0]*rik[0])+(rik[1]*rik[1])+(rik[2]*rik[2]));
lamdajik = 4.0*kronecker(itype,1) *
- ((rho[ktype][1]-rikmag)-(rho[jtype][1]-rijmag));
+ ((rho[ktype][1]-rikmag)-(rho[jtype][1]-rijmag));
wik = Sp(rikmag,rcmin[itype][ktype],rcmax[itype][ktype],dS);
Nki = nC[atomk]-(wik*kronecker(itype,0)) +
- nH[atomk]-(wik*kronecker(itype,1));
+ nH[atomk]-(wik*kronecker(itype,1));
cosjik = ((rij[0]*rik[0])+(rij[1]*rik[1])+(rij[2]*rik[2])) /
- (rijmag*rikmag);
+ (rijmag*rikmag);
cosjik = MIN(cosjik,1.0);
cosjik = MAX(cosjik,-1.0);
@@ -1010,12 +1010,12 @@ double PairAIREBOOMP::bondorderLJ_thr(int i, int j, double rij[3], double rijmag
rjl[2] = x[atomj][2]-x[atoml][2];
rjlmag = sqrt((rjl[0]*rjl[0])+(rjl[1]*rjl[1])+(rjl[2]*rjl[2]));
lamdaijl = 4.0*kronecker(jtype,1) *
- ((rho[ltype][1]-rjlmag)-(rho[itype][1]-rijmag));
+ ((rho[ltype][1]-rjlmag)-(rho[itype][1]-rijmag));
wjl = Sp(rjlmag,rcmin[jtype][ltype],rcmax[jtype][ltype],dS);
Nlj = nC[atoml]-(wjl*kronecker(jtype,0))+nH[atoml] -
- (wjl*kronecker(jtype,1));
+ (wjl*kronecker(jtype,1));
cosijl = -1.0*((rij[0]*rjl[0])+(rij[1]*rjl[1])+(rij[2]*rjl[2])) /
- (rijmag*rjlmag);
+ (rijmag*rjlmag);
cosijl = MIN(cosijl,1.0);
cosijl = MAX(cosijl,-1.0);
@@ -1054,73 +1054,73 @@ double PairAIREBOOMP::bondorderLJ_thr(int i, int j, double rij[3], double rijmag
atomk = REBO_neighs_i[k];
ktype = map[type[atomk]];
if (atomk != atomj) {
- rik[0] = x[atomi][0]-x[atomk][0];
- rik[1] = x[atomi][1]-x[atomk][1];
- rik[2] = x[atomi][2]-x[atomk][2];
- rikmag = sqrt((rik[0]*rik[0])+(rik[1]*rik[1])+(rik[2]*rik[2]));
- cos321 = ((rij[0]*rik[0])+(rij[1]*rik[1])+(rij[2]*rik[2])) /
- (rijmag*rikmag);
- cos321 = MIN(cos321,1.0);
- cos321 = MAX(cos321,-1.0);
-
- rjk[0] = rik[0]-rij[0];
- rjk[1] = rik[1]-rij[1];
- rjk[2] = rik[2]-rij[2];
- rjk2 = (rjk[0]*rjk[0])+(rjk[1]*rjk[1])+(rjk[2]*rjk[2]);
- rij2 = rijmag*rijmag;
- rik2 = rikmag*rikmag;
- costmp = 0.5*(rij2+rik2-rjk2)/rijmag/rikmag;
- tspjik = Sp2(costmp,thmin,thmax,dtsjik);
-
- if (sqrt(1.0 - cos321*cos321) > sqrt(TOL)) {
- wik = Sp(rikmag,rcmin[itype][ktype],rcmaxp[itype][ktype],dwik);
- REBO_neighs_j = REBO_firstneigh[j];
- for (l = 0; l < REBO_numneigh[j]; l++) {
- atoml = REBO_neighs_j[l];
- ltype = map[type[atoml]];
- if (!(atoml == atomi || atoml == atomk)) {
- rjl[0] = x[atomj][0]-x[atoml][0];
- rjl[1] = x[atomj][1]-x[atoml][1];
- rjl[2] = x[atomj][2]-x[atoml][2];
- rjlmag = sqrt(rjl[0]*rjl[0] + rjl[1]*rjl[1] + rjl[2]*rjl[2]);
- cos234 = -((rij[0]*rjl[0])+(rij[1]*rjl[1])+(rij[2]*rjl[2])) /
- (rijmag*rjlmag);
- cos234 = MIN(cos234,1.0);
- cos234 = MAX(cos234,-1.0);
-
- ril[0] = rij[0]+rjl[0];
- ril[1] = rij[1]+rjl[1];
- ril[2] = rij[2]+rjl[2];
- ril2 = (ril[0]*ril[0])+(ril[1]*ril[1])+(ril[2]*ril[2]);
- rijrjl = 2.0*rijmag*rjlmag;
- rjl2 = rjlmag*rjlmag;
- costmp = 0.5*(rij2+rjl2-ril2)/rijmag/rjlmag;
- tspijl = Sp2(costmp,thmin,thmax,dtsijl);
-
- if (sqrt(1.0 - cos234*cos234) > sqrt(TOL)) {
- wjl = Sp(rjlmag,rcmin[jtype][ltype],rcmaxp[jtype][ltype],dS);
- crosskij[0] = (rij[1]*rik[2]-rij[2]*rik[1]);
- crosskij[1] = (rij[2]*rik[0]-rij[0]*rik[2]);
- crosskij[2] = (rij[0]*rik[1]-rij[1]*rik[0]);
- crosskijmag = sqrt(crosskij[0]*crosskij[0] +
- crosskij[1]*crosskij[1] +
- crosskij[2]*crosskij[2]);
- crossijl[0] = (rij[1]*rjl[2]-rij[2]*rjl[1]);
- crossijl[1] = (rij[2]*rjl[0]-rij[0]*rjl[2]);
- crossijl[2] = (rij[0]*rjl[1]-rij[1]*rjl[0]);
- crossijlmag = sqrt(crossijl[0]*crossijl[0] +
- crossijl[1]*crossijl[1] +
- crossijl[2]*crossijl[2]);
- omkijl = -1.0*(((crosskij[0]*crossijl[0]) +
- (crosskij[1]*crossijl[1]) +
- (crosskij[2]*crossijl[2])) /
- (crosskijmag*crossijlmag));
- Etmp += ((1.0-(omkijl*omkijl))*wik*wjl) *
- (1.0-tspjik)*(1.0-tspijl);
- }
- }
- }
- }
+ rik[0] = x[atomi][0]-x[atomk][0];
+ rik[1] = x[atomi][1]-x[atomk][1];
+ rik[2] = x[atomi][2]-x[atomk][2];
+ rikmag = sqrt((rik[0]*rik[0])+(rik[1]*rik[1])+(rik[2]*rik[2]));
+ cos321 = ((rij[0]*rik[0])+(rij[1]*rik[1])+(rij[2]*rik[2])) /
+ (rijmag*rikmag);
+ cos321 = MIN(cos321,1.0);
+ cos321 = MAX(cos321,-1.0);
+
+ rjk[0] = rik[0]-rij[0];
+ rjk[1] = rik[1]-rij[1];
+ rjk[2] = rik[2]-rij[2];
+ rjk2 = (rjk[0]*rjk[0])+(rjk[1]*rjk[1])+(rjk[2]*rjk[2]);
+ rij2 = rijmag*rijmag;
+ rik2 = rikmag*rikmag;
+ costmp = 0.5*(rij2+rik2-rjk2)/rijmag/rikmag;
+ tspjik = Sp2(costmp,thmin,thmax,dtsjik);
+
+ if (sqrt(1.0 - cos321*cos321) > sqrt(TOL)) {
+ wik = Sp(rikmag,rcmin[itype][ktype],rcmaxp[itype][ktype],dwik);
+ REBO_neighs_j = REBO_firstneigh[j];
+ for (l = 0; l < REBO_numneigh[j]; l++) {
+ atoml = REBO_neighs_j[l];
+ ltype = map[type[atoml]];
+ if (!(atoml == atomi || atoml == atomk)) {
+ rjl[0] = x[atomj][0]-x[atoml][0];
+ rjl[1] = x[atomj][1]-x[atoml][1];
+ rjl[2] = x[atomj][2]-x[atoml][2];
+ rjlmag = sqrt(rjl[0]*rjl[0] + rjl[1]*rjl[1] + rjl[2]*rjl[2]);
+ cos234 = -((rij[0]*rjl[0])+(rij[1]*rjl[1])+(rij[2]*rjl[2])) /
+ (rijmag*rjlmag);
+ cos234 = MIN(cos234,1.0);
+ cos234 = MAX(cos234,-1.0);
+
+ ril[0] = rij[0]+rjl[0];
+ ril[1] = rij[1]+rjl[1];
+ ril[2] = rij[2]+rjl[2];
+ ril2 = (ril[0]*ril[0])+(ril[1]*ril[1])+(ril[2]*ril[2]);
+ rijrjl = 2.0*rijmag*rjlmag;
+ rjl2 = rjlmag*rjlmag;
+ costmp = 0.5*(rij2+rjl2-ril2)/rijmag/rjlmag;
+ tspijl = Sp2(costmp,thmin,thmax,dtsijl);
+
+ if (sqrt(1.0 - cos234*cos234) > sqrt(TOL)) {
+ wjl = Sp(rjlmag,rcmin[jtype][ltype],rcmaxp[jtype][ltype],dS);
+ crosskij[0] = (rij[1]*rik[2]-rij[2]*rik[1]);
+ crosskij[1] = (rij[2]*rik[0]-rij[0]*rik[2]);
+ crosskij[2] = (rij[0]*rik[1]-rij[1]*rik[0]);
+ crosskijmag = sqrt(crosskij[0]*crosskij[0] +
+ crosskij[1]*crosskij[1] +
+ crosskij[2]*crosskij[2]);
+ crossijl[0] = (rij[1]*rjl[2]-rij[2]*rjl[1]);
+ crossijl[1] = (rij[2]*rjl[0]-rij[0]*rjl[2]);
+ crossijl[2] = (rij[0]*rjl[1]-rij[1]*rjl[0]);
+ crossijlmag = sqrt(crossijl[0]*crossijl[0] +
+ crossijl[1]*crossijl[1] +
+ crossijl[2]*crossijl[2]);
+ omkijl = -1.0*(((crosskij[0]*crossijl[0]) +
+ (crosskij[1]*crossijl[1]) +
+ (crosskij[2]*crossijl[2])) /
+ (crosskijmag*crossijlmag));
+ Etmp += ((1.0-(omkijl*omkijl))*wik*wjl) *
+ (1.0-tspjik)*(1.0-tspijl);
+ }
+ }
+ }
+ }
}
}
}
@@ -1144,102 +1144,102 @@ double PairAIREBOOMP::bondorderLJ_thr(int i, int j, double rij[3], double rijmag
for (k = 0; k < REBO_numneigh[i]; k++) {
atomk = REBO_neighs_i[k];
if (atomk != atomj) {
- lamdajik = 0.0;
- rik[0] = x[atomi][0]-x[atomk][0];
- rik[1] = x[atomi][1]-x[atomk][1];
- rik[2] = x[atomi][2]-x[atomk][2];
- rikmag = sqrt(rik[0]*rik[0] + rik[1]*rik[1] + rik[2]*rik[2]);
- lamdajik = 4.0*kronecker(itype,1) *
- ((rho[ktype][1]-rikmag)-(rho[jtype][1]-rijmag));
- wik = Sp(rikmag,rcmin[itype][ktype],rcmax[itype][ktype],dwik);
-
- const double invrikm = 1.0/rikmag;
- const double invrijkm = invrijm*invrikm;
- const double invrikm2 = invrikm*invrikm;
-
- cosjik = ((rij[0]*rik[0])+(rij[1]*rik[1])+(rij[2]*rik[2]))
- * invrijkm;
- cosjik = MIN(cosjik,1.0);
- cosjik = MAX(cosjik,-1.0);
-
- dcosjikdri[0] = ((rij[0]+rik[0])*invrijkm) -
- (cosjik*((rij[0]*invrijm2)+(rik[0]*invrikm2)));
- dcosjikdri[1] = ((rij[1]+rik[1])*invrijkm) -
- (cosjik*((rij[1]*invrijm2)+(rik[1]*invrikm2)));
- dcosjikdri[2] = ((rij[2]+rik[2])*invrijkm) -
- (cosjik*((rij[2]*invrijm2)+(rik[2]*invrikm2)));
- dcosjikdrk[0] = (-rij[0]*invrijkm) + (cosjik*(rik[0]*invrikm2));
- dcosjikdrk[1] = (-rij[1]*invrijkm) + (cosjik*(rik[1]*invrikm2));
- dcosjikdrk[2] = (-rij[2]*invrijkm) + (cosjik*(rik[2]*invrikm2));
- dcosjikdrj[0] = (-rik[0]*invrijkm) + (cosjik*(rij[0]*invrijm2));
- dcosjikdrj[1] = (-rik[1]*invrijkm) + (cosjik*(rij[1]*invrijm2));
- dcosjikdrj[2] = (-rik[2]*invrijkm) + (cosjik*(rij[2]*invrijm2));
-
- g = gSpline(cosjik,(NijC+NijH),itype,&dgdc,&dgdN);
-
- tmp2 = VA*.5*(tmp*wik*dgdc*exp(lamdajik));
- fj[0] = -tmp2*dcosjikdrj[0];
- fj[1] = -tmp2*dcosjikdrj[1];
- fj[2] = -tmp2*dcosjikdrj[2];
- fi[0] = -tmp2*dcosjikdri[0];
- fi[1] = -tmp2*dcosjikdri[1];
- fi[2] = -tmp2*dcosjikdri[2];
- fk[0] = -tmp2*dcosjikdrk[0];
- fk[1] = -tmp2*dcosjikdrk[1];
- fk[2] = -tmp2*dcosjikdrk[2];
-
- tmp2 = VA*.5*(tmp*wik*g*exp(lamdajik)*4.0*kronecker(itype,1));
- fj[0] -= tmp2*(-rij[0]*invrijm);
- fj[1] -= tmp2*(-rij[1]*invrijm);
- fj[2] -= tmp2*(-rij[2]*invrijm);
- fi[0] -= tmp2*((-rik[0]/rikmag)+(rij[0]*invrijm));
- fi[1] -= tmp2*((-rik[1]/rikmag)+(rij[1]*invrijm));
- fi[2] -= tmp2*((-rik[2]/rikmag)+(rij[2]*invrijm));
- fk[0] -= tmp2*(rik[0]/rikmag);
- fk[1] -= tmp2*(rik[1]/rikmag);
- fk[2] -= tmp2*(rik[2]/rikmag);
-
- // coordination forces
-
- // dwik forces
-
- tmp2 = VA*.5*(tmp*dwik*g*exp(lamdajik))/rikmag;
- fi[0] -= tmp2*rik[0];
- fi[1] -= tmp2*rik[1];
- fi[2] -= tmp2*rik[2];
- fk[0] += tmp2*rik[0];
- fk[1] += tmp2*rik[1];
- fk[2] += tmp2*rik[2];
-
- // PIJ forces
-
- tmp2 = VA*.5*(tmp*dN2[ktype]*dwik)/rikmag;
- fi[0] -= tmp2*rik[0];
- fi[1] -= tmp2*rik[1];
- fi[2] -= tmp2*rik[2];
- fk[0] += tmp2*rik[0];
- fk[1] += tmp2*rik[1];
- fk[2] += tmp2*rik[2];
-
- // dgdN forces
-
- tmp2 = VA*.5*(tmp*tmp3*dwik)/rikmag;
- fi[0] -= tmp2*rik[0];
- fi[1] -= tmp2*rik[1];
- fi[2] -= tmp2*rik[2];
- fk[0] += tmp2*rik[0];
- fk[1] += tmp2*rik[1];
- fk[2] += tmp2*rik[2];
-
- f[atomi][0] += fi[0]; f[atomi][1] += fi[1]; f[atomi][2] += fi[2];
- f[atomj][0] += fj[0]; f[atomj][1] += fj[1]; f[atomj][2] += fj[2];
- f[atomk][0] += fk[0]; f[atomk][1] += fk[1]; f[atomk][2] += fk[2];
-
- if (vflag_atom) {
- rji[0] = -rij[0]; rji[1] = -rij[1]; rji[2] = -rij[2];
- rki[0] = -rik[0]; rki[1] = -rik[1]; rki[2] = -rik[2];
- v_tally3_thr(atomi,atomj,atomk,fj,fk,rji,rki,thr);
- }
+ lamdajik = 0.0;
+ rik[0] = x[atomi][0]-x[atomk][0];
+ rik[1] = x[atomi][1]-x[atomk][1];
+ rik[2] = x[atomi][2]-x[atomk][2];
+ rikmag = sqrt(rik[0]*rik[0] + rik[1]*rik[1] + rik[2]*rik[2]);
+ lamdajik = 4.0*kronecker(itype,1) *
+ ((rho[ktype][1]-rikmag)-(rho[jtype][1]-rijmag));
+ wik = Sp(rikmag,rcmin[itype][ktype],rcmax[itype][ktype],dwik);
+
+ const double invrikm = 1.0/rikmag;
+ const double invrijkm = invrijm*invrikm;
+ const double invrikm2 = invrikm*invrikm;
+
+ cosjik = ((rij[0]*rik[0])+(rij[1]*rik[1])+(rij[2]*rik[2]))
+ * invrijkm;
+ cosjik = MIN(cosjik,1.0);
+ cosjik = MAX(cosjik,-1.0);
+
+ dcosjikdri[0] = ((rij[0]+rik[0])*invrijkm) -
+ (cosjik*((rij[0]*invrijm2)+(rik[0]*invrikm2)));
+ dcosjikdri[1] = ((rij[1]+rik[1])*invrijkm) -
+ (cosjik*((rij[1]*invrijm2)+(rik[1]*invrikm2)));
+ dcosjikdri[2] = ((rij[2]+rik[2])*invrijkm) -
+ (cosjik*((rij[2]*invrijm2)+(rik[2]*invrikm2)));
+ dcosjikdrk[0] = (-rij[0]*invrijkm) + (cosjik*(rik[0]*invrikm2));
+ dcosjikdrk[1] = (-rij[1]*invrijkm) + (cosjik*(rik[1]*invrikm2));
+ dcosjikdrk[2] = (-rij[2]*invrijkm) + (cosjik*(rik[2]*invrikm2));
+ dcosjikdrj[0] = (-rik[0]*invrijkm) + (cosjik*(rij[0]*invrijm2));
+ dcosjikdrj[1] = (-rik[1]*invrijkm) + (cosjik*(rij[1]*invrijm2));
+ dcosjikdrj[2] = (-rik[2]*invrijkm) + (cosjik*(rij[2]*invrijm2));
+
+ g = gSpline(cosjik,(NijC+NijH),itype,&dgdc,&dgdN);
+
+ tmp2 = VA*.5*(tmp*wik*dgdc*exp(lamdajik));
+ fj[0] = -tmp2*dcosjikdrj[0];
+ fj[1] = -tmp2*dcosjikdrj[1];
+ fj[2] = -tmp2*dcosjikdrj[2];
+ fi[0] = -tmp2*dcosjikdri[0];
+ fi[1] = -tmp2*dcosjikdri[1];
+ fi[2] = -tmp2*dcosjikdri[2];
+ fk[0] = -tmp2*dcosjikdrk[0];
+ fk[1] = -tmp2*dcosjikdrk[1];
+ fk[2] = -tmp2*dcosjikdrk[2];
+
+ tmp2 = VA*.5*(tmp*wik*g*exp(lamdajik)*4.0*kronecker(itype,1));
+ fj[0] -= tmp2*(-rij[0]*invrijm);
+ fj[1] -= tmp2*(-rij[1]*invrijm);
+ fj[2] -= tmp2*(-rij[2]*invrijm);
+ fi[0] -= tmp2*((-rik[0]/rikmag)+(rij[0]*invrijm));
+ fi[1] -= tmp2*((-rik[1]/rikmag)+(rij[1]*invrijm));
+ fi[2] -= tmp2*((-rik[2]/rikmag)+(rij[2]*invrijm));
+ fk[0] -= tmp2*(rik[0]/rikmag);
+ fk[1] -= tmp2*(rik[1]/rikmag);
+ fk[2] -= tmp2*(rik[2]/rikmag);
+
+ // coordination forces
+
+ // dwik forces
+
+ tmp2 = VA*.5*(tmp*dwik*g*exp(lamdajik))/rikmag;
+ fi[0] -= tmp2*rik[0];
+ fi[1] -= tmp2*rik[1];
+ fi[2] -= tmp2*rik[2];
+ fk[0] += tmp2*rik[0];
+ fk[1] += tmp2*rik[1];
+ fk[2] += tmp2*rik[2];
+
+ // PIJ forces
+
+ tmp2 = VA*.5*(tmp*dN2[ktype]*dwik)/rikmag;
+ fi[0] -= tmp2*rik[0];
+ fi[1] -= tmp2*rik[1];
+ fi[2] -= tmp2*rik[2];
+ fk[0] += tmp2*rik[0];
+ fk[1] += tmp2*rik[1];
+ fk[2] += tmp2*rik[2];
+
+ // dgdN forces
+
+ tmp2 = VA*.5*(tmp*tmp3*dwik)/rikmag;
+ fi[0] -= tmp2*rik[0];
+ fi[1] -= tmp2*rik[1];
+ fi[2] -= tmp2*rik[2];
+ fk[0] += tmp2*rik[0];
+ fk[1] += tmp2*rik[1];
+ fk[2] += tmp2*rik[2];
+
+ f[atomi][0] += fi[0]; f[atomi][1] += fi[1]; f[atomi][2] += fi[2];
+ f[atomj][0] += fj[0]; f[atomj][1] += fj[1]; f[atomj][2] += fj[2];
+ f[atomk][0] += fk[0]; f[atomk][1] += fk[1]; f[atomk][2] += fk[2];
+
+ if (vflag_atom) {
+ rji[0] = -rij[0]; rji[1] = -rij[1]; rji[2] = -rij[2];
+ rki[0] = -rik[0]; rki[1] = -rik[1]; rki[2] = -rik[2];
+ v_tally3_thr(atomi,atomj,atomk,fj,fk,rji,rki,thr);
+ }
}
}
@@ -1251,101 +1251,101 @@ double PairAIREBOOMP::bondorderLJ_thr(int i, int j, double rij[3], double rijmag
for (l = 0; l < REBO_numneigh[j]; l++) {
atoml = REBO_neighs[l];
if (atoml !=atomi) {
- ltype = map[type[atoml]];
- rjl[0] = x[atomj][0]-x[atoml][0];
- rjl[1] = x[atomj][1]-x[atoml][1];
- rjl[2] = x[atomj][2]-x[atoml][2];
- rjlmag = sqrt((rjl[0]*rjl[0])+(rjl[1]*rjl[1])+(rjl[2]*rjl[2]));
- lamdaijl = 4.0*kronecker(jtype,1) *
- ((rho[ltype][1]-rjlmag)-(rho[itype][1]-rijmag));
- wjl = Sp(rjlmag,rcmin[jtype][ltype],rcmax[jtype][ltype],dwjl);
-
- const double invrjlm = 1.0/rjlmag;
- const double invrijlm = invrijm*invrjlm;
- const double invrjlm2 = invrjlm*invrjlm;
-
- cosijl = (-1.0*((rij[0]*rjl[0])+(rij[1]*rjl[1])+(rij[2]*rjl[2]))) *
- invrijlm;
- cosijl = MIN(cosijl,1.0);
- cosijl = MAX(cosijl,-1.0);
-
- dcosijldri[0] = (-rjl[0]*invrijlm) - (cosijl*rij[0]*invrijm2);
- dcosijldri[1] = (-rjl[1]*invrijlm) - (cosijl*rij[1]*invrijm2);
- dcosijldri[2] = (-rjl[2]*invrijlm) - (cosijl*rij[2]*invrijm2);
- dcosijldrj[0] = ((-rij[0]+rjl[0])*invrijlm) +
- (cosijl*((rij[0]*invrijm2)-(rjl[0]*invrjlm2)));
- dcosijldrj[1] = ((-rij[1]+rjl[1])*invrijlm) +
- (cosijl*((rij[1]*invrijm2)-(rjl[1]*invrjlm2)));
- dcosijldrj[2] = ((-rij[2]+rjl[2])*invrijlm) +
- (cosijl*((rij[2]*invrijm2)-(rjl[2]*invrjlm2)));
- dcosijldrl[0] = (rij[0]*invrijlm) + (cosijl*rjl[0]*invrjlm2);
- dcosijldrl[1] = (rij[1]*invrijlm) + (cosijl*rjl[1]*invrjlm2);
- dcosijldrl[2] = (rij[2]*invrijlm) + (cosijl*rjl[2]*invrjlm2);
-
- // evaluate splines g and derivatives dg
-
- g = gSpline(cosijl,NjiC+NjiH,jtype,&dgdc,&dgdN);
- tmp2 = VA*.5*(tmp*wjl*dgdc*exp(lamdaijl));
- fi[0] = -tmp2*dcosijldri[0];
- fi[1] = -tmp2*dcosijldri[1];
- fi[2] = -tmp2*dcosijldri[2];
- fj[0] = -tmp2*dcosijldrj[0];
- fj[1] = -tmp2*dcosijldrj[1];
- fj[2] = -tmp2*dcosijldrj[2];
- fl[0] = -tmp2*dcosijldrl[0];
- fl[1] = -tmp2*dcosijldrl[1];
- fl[2] = -tmp2*dcosijldrl[2];
-
- tmp2 = VA*.5*(tmp*wjl*g*exp(lamdaijl)*4.0*kronecker(jtype,1));
- fi[0] -= tmp2*(rij[0]*invrijm);
- fi[1] -= tmp2*(rij[1]*invrijm);
- fi[2] -= tmp2*(rij[2]*invrijm);
- fj[0] -= tmp2*((-rjl[0]*invrjlm)-(rij[0]*invrijm));
- fj[1] -= tmp2*((-rjl[1]*invrjlm)-(rij[1]*invrijm));
- fj[2] -= tmp2*((-rjl[2]*invrjlm)-(rij[2]*invrijm));
- fl[0] -= tmp2*(rjl[0]*invrjlm);
- fl[1] -= tmp2*(rjl[1]*invrjlm);
- fl[2] -= tmp2*(rjl[2]*invrjlm);
-
- // coordination forces
- // dwik forces
-
- tmp2 = VA*.5*(tmp*dwjl*g*exp(lamdaijl))*invrjlm;
- fj[0] -= tmp2*rjl[0];
- fj[1] -= tmp2*rjl[1];
- fj[2] -= tmp2*rjl[2];
- fl[0] += tmp2*rjl[0];
- fl[1] += tmp2*rjl[1];
- fl[2] += tmp2*rjl[2];
-
- // PIJ forces
-
- tmp2 = VA*.5*(tmp*dN2[ltype]*dwjl)*invrjlm;
- fj[0] -= tmp2*rjl[0];
- fj[1] -= tmp2*rjl[1];
- fj[2] -= tmp2*rjl[2];
- fl[0] += tmp2*rjl[0];
- fl[1] += tmp2*rjl[1];
- fl[2] += tmp2*rjl[2];
-
- // dgdN forces
-
- tmp2=VA*.5*(tmp*tmp3*dwjl)*invrjlm;
- fj[0] -= tmp2*rjl[0];
- fj[1] -= tmp2*rjl[1];
- fj[2] -= tmp2*rjl[2];
- fl[0] += tmp2*rjl[0];
- fl[1] += tmp2*rjl[1];
- fl[2] += tmp2*rjl[2];
-
- f[atomi][0] += fi[0]; f[atomi][1] += fi[1]; f[atomi][2] += fi[2];
- f[atomj][0] += fj[0]; f[atomj][1] += fj[1]; f[atomj][2] += fj[2];
- f[atoml][0] += fl[0]; f[atoml][1] += fl[1]; f[atoml][2] += fl[2];
-
- if (vflag_atom) {
- rlj[0] = -rjl[0]; rlj[1] = -rjl[1]; rlj[2] = -rjl[2];
- v_tally3_thr(atomi,atomj,atoml,fi,fl,rij,rlj,thr);
- }
+ ltype = map[type[atoml]];
+ rjl[0] = x[atomj][0]-x[atoml][0];
+ rjl[1] = x[atomj][1]-x[atoml][1];
+ rjl[2] = x[atomj][2]-x[atoml][2];
+ rjlmag = sqrt((rjl[0]*rjl[0])+(rjl[1]*rjl[1])+(rjl[2]*rjl[2]));
+ lamdaijl = 4.0*kronecker(jtype,1) *
+ ((rho[ltype][1]-rjlmag)-(rho[itype][1]-rijmag));
+ wjl = Sp(rjlmag,rcmin[jtype][ltype],rcmax[jtype][ltype],dwjl);
+
+ const double invrjlm = 1.0/rjlmag;
+ const double invrijlm = invrijm*invrjlm;
+ const double invrjlm2 = invrjlm*invrjlm;
+
+ cosijl = (-1.0*((rij[0]*rjl[0])+(rij[1]*rjl[1])+(rij[2]*rjl[2]))) *
+ invrijlm;
+ cosijl = MIN(cosijl,1.0);
+ cosijl = MAX(cosijl,-1.0);
+
+ dcosijldri[0] = (-rjl[0]*invrijlm) - (cosijl*rij[0]*invrijm2);
+ dcosijldri[1] = (-rjl[1]*invrijlm) - (cosijl*rij[1]*invrijm2);
+ dcosijldri[2] = (-rjl[2]*invrijlm) - (cosijl*rij[2]*invrijm2);
+ dcosijldrj[0] = ((-rij[0]+rjl[0])*invrijlm) +
+ (cosijl*((rij[0]*invrijm2)-(rjl[0]*invrjlm2)));
+ dcosijldrj[1] = ((-rij[1]+rjl[1])*invrijlm) +
+ (cosijl*((rij[1]*invrijm2)-(rjl[1]*invrjlm2)));
+ dcosijldrj[2] = ((-rij[2]+rjl[2])*invrijlm) +
+ (cosijl*((rij[2]*invrijm2)-(rjl[2]*invrjlm2)));
+ dcosijldrl[0] = (rij[0]*invrijlm) + (cosijl*rjl[0]*invrjlm2);
+ dcosijldrl[1] = (rij[1]*invrijlm) + (cosijl*rjl[1]*invrjlm2);
+ dcosijldrl[2] = (rij[2]*invrijlm) + (cosijl*rjl[2]*invrjlm2);
+
+ // evaluate splines g and derivatives dg
+
+ g = gSpline(cosijl,NjiC+NjiH,jtype,&dgdc,&dgdN);
+ tmp2 = VA*.5*(tmp*wjl*dgdc*exp(lamdaijl));
+ fi[0] = -tmp2*dcosijldri[0];
+ fi[1] = -tmp2*dcosijldri[1];
+ fi[2] = -tmp2*dcosijldri[2];
+ fj[0] = -tmp2*dcosijldrj[0];
+ fj[1] = -tmp2*dcosijldrj[1];
+ fj[2] = -tmp2*dcosijldrj[2];
+ fl[0] = -tmp2*dcosijldrl[0];
+ fl[1] = -tmp2*dcosijldrl[1];
+ fl[2] = -tmp2*dcosijldrl[2];
+
+ tmp2 = VA*.5*(tmp*wjl*g*exp(lamdaijl)*4.0*kronecker(jtype,1));
+ fi[0] -= tmp2*(rij[0]*invrijm);
+ fi[1] -= tmp2*(rij[1]*invrijm);
+ fi[2] -= tmp2*(rij[2]*invrijm);
+ fj[0] -= tmp2*((-rjl[0]*invrjlm)-(rij[0]*invrijm));
+ fj[1] -= tmp2*((-rjl[1]*invrjlm)-(rij[1]*invrijm));
+ fj[2] -= tmp2*((-rjl[2]*invrjlm)-(rij[2]*invrijm));
+ fl[0] -= tmp2*(rjl[0]*invrjlm);
+ fl[1] -= tmp2*(rjl[1]*invrjlm);
+ fl[2] -= tmp2*(rjl[2]*invrjlm);
+
+ // coordination forces
+ // dwik forces
+
+ tmp2 = VA*.5*(tmp*dwjl*g*exp(lamdaijl))*invrjlm;
+ fj[0] -= tmp2*rjl[0];
+ fj[1] -= tmp2*rjl[1];
+ fj[2] -= tmp2*rjl[2];
+ fl[0] += tmp2*rjl[0];
+ fl[1] += tmp2*rjl[1];
+ fl[2] += tmp2*rjl[2];
+
+ // PIJ forces
+
+ tmp2 = VA*.5*(tmp*dN2[ltype]*dwjl)*invrjlm;
+ fj[0] -= tmp2*rjl[0];
+ fj[1] -= tmp2*rjl[1];
+ fj[2] -= tmp2*rjl[2];
+ fl[0] += tmp2*rjl[0];
+ fl[1] += tmp2*rjl[1];
+ fl[2] += tmp2*rjl[2];
+
+ // dgdN forces
+
+ tmp2=VA*.5*(tmp*tmp3*dwjl)*invrjlm;
+ fj[0] -= tmp2*rjl[0];
+ fj[1] -= tmp2*rjl[1];
+ fj[2] -= tmp2*rjl[2];
+ fl[0] += tmp2*rjl[0];
+ fl[1] += tmp2*rjl[1];
+ fl[2] += tmp2*rjl[2];
+
+ f[atomi][0] += fi[0]; f[atomi][1] += fi[1]; f[atomi][2] += fi[2];
+ f[atomj][0] += fj[0]; f[atomj][1] += fj[1]; f[atomj][2] += fj[2];
+ f[atoml][0] += fl[0]; f[atoml][1] += fl[1]; f[atoml][2] += fl[2];
+
+ if (vflag_atom) {
+ rlj[0] = -rjl[0]; rlj[1] = -rjl[1]; rlj[2] = -rjl[2];
+ v_tally3_thr(atomi,atomj,atoml,fi,fl,rij,rlj,thr);
+ }
}
}
@@ -1359,60 +1359,60 @@ double PairAIREBOOMP::bondorderLJ_thr(int i, int j, double rij[3], double rijmag
for (k = 0; k < REBO_numneigh[i]; k++) {
atomk = REBO_neighs_i[k];
if (atomk != atomj) {
- ktype = map[type[atomk]];
- rik[0] = x[atomi][0]-x[atomk][0];
- rik[1] = x[atomi][1]-x[atomk][1];
- rik[2] = x[atomi][2]-x[atomk][2];
- rikmag = sqrt((rik[0]*rik[0])+(rik[1]*rik[1])+(rik[2]*rik[2]));
- wik = Sp(rikmag,rcmin[itype][ktype],rcmax[itype][ktype],dwik);
- Nki = nC[atomk]-(wik*kronecker(itype,0))+nH[atomk] -
- (wik*kronecker(itype,1));
- SpN = Sp(Nki,Nmin,Nmax,dNki);
-
- tmp2 = VA*dN3[0]*dwik/rikmag;
- f[atomi][0] -= tmp2*rik[0];
- f[atomi][1] -= tmp2*rik[1];
- f[atomi][2] -= tmp2*rik[2];
- f[atomk][0] += tmp2*rik[0];
- f[atomk][1] += tmp2*rik[1];
- f[atomk][2] += tmp2*rik[2];
-
- if (vflag_atom) v_tally2_thr(atomi,atomk,-tmp2,rik,thr);
-
- tmp2 = VA*dN3[2]*(2.0*NconjtmpI*dwik*SpN)/rikmag;
- f[atomi][0] -= tmp2*rik[0];
- f[atomi][1] -= tmp2*rik[1];
- f[atomi][2] -= tmp2*rik[2];
- f[atomk][0] += tmp2*rik[0];
- f[atomk][1] += tmp2*rik[1];
- f[atomk][2] += tmp2*rik[2];
-
- if (vflag_atom) v_tally2_thr(atomi,atomk,-tmp2,rik,thr);
-
- if (fabs(dNki) > TOL) {
- REBO_neighs_k = REBO_firstneigh[atomk];
- for (n = 0; n < REBO_numneigh[atomk]; n++) {
- atomn = REBO_neighs_k[n];
- if (atomn != atomi) {
- ntype = map[type[atomn]];
- rkn[0] = x[atomk][0]-x[atomn][0];
- rkn[1] = x[atomk][1]-x[atomn][1];
- rkn[2] = x[atomk][2]-x[atomn][2];
- rknmag = sqrt((rkn[0]*rkn[0])+(rkn[1]*rkn[1])+(rkn[2]*rkn[2]));
- Sp(rknmag,rcmin[ktype][ntype],rcmax[ktype][ntype],dwkn);
-
- tmp2 = VA*dN3[2]*(2.0*NconjtmpI*wik*dNki*dwkn)/rknmag;
- f[atomk][0] -= tmp2*rkn[0];
- f[atomk][1] -= tmp2*rkn[1];
- f[atomk][2] -= tmp2*rkn[2];
- f[atomn][0] += tmp2*rkn[0];
- f[atomn][1] += tmp2*rkn[1];
- f[atomn][2] += tmp2*rkn[2];
-
- if (vflag_atom) v_tally2_thr(atomk,atomn,-tmp2,rkn,thr);
- }
- }
- }
+ ktype = map[type[atomk]];
+ rik[0] = x[atomi][0]-x[atomk][0];
+ rik[1] = x[atomi][1]-x[atomk][1];
+ rik[2] = x[atomi][2]-x[atomk][2];
+ rikmag = sqrt((rik[0]*rik[0])+(rik[1]*rik[1])+(rik[2]*rik[2]));
+ wik = Sp(rikmag,rcmin[itype][ktype],rcmax[itype][ktype],dwik);
+ Nki = nC[atomk]-(wik*kronecker(itype,0))+nH[atomk] -
+ (wik*kronecker(itype,1));
+ SpN = Sp(Nki,Nmin,Nmax,dNki);
+
+ tmp2 = VA*dN3[0]*dwik/rikmag;
+ f[atomi][0] -= tmp2*rik[0];
+ f[atomi][1] -= tmp2*rik[1];
+ f[atomi][2] -= tmp2*rik[2];
+ f[atomk][0] += tmp2*rik[0];
+ f[atomk][1] += tmp2*rik[1];
+ f[atomk][2] += tmp2*rik[2];
+
+ if (vflag_atom) v_tally2_thr(atomi,atomk,-tmp2,rik,thr);
+
+ tmp2 = VA*dN3[2]*(2.0*NconjtmpI*dwik*SpN)/rikmag;
+ f[atomi][0] -= tmp2*rik[0];
+ f[atomi][1] -= tmp2*rik[1];
+ f[atomi][2] -= tmp2*rik[2];
+ f[atomk][0] += tmp2*rik[0];
+ f[atomk][1] += tmp2*rik[1];
+ f[atomk][2] += tmp2*rik[2];
+
+ if (vflag_atom) v_tally2_thr(atomi,atomk,-tmp2,rik,thr);
+
+ if (fabs(dNki) > TOL) {
+ REBO_neighs_k = REBO_firstneigh[atomk];
+ for (n = 0; n < REBO_numneigh[atomk]; n++) {
+ atomn = REBO_neighs_k[n];
+ if (atomn != atomi) {
+ ntype = map[type[atomn]];
+ rkn[0] = x[atomk][0]-x[atomn][0];
+ rkn[1] = x[atomk][1]-x[atomn][1];
+ rkn[2] = x[atomk][2]-x[atomn][2];
+ rknmag = sqrt((rkn[0]*rkn[0])+(rkn[1]*rkn[1])+(rkn[2]*rkn[2]));
+ Sp(rknmag,rcmin[ktype][ntype],rcmax[ktype][ntype],dwkn);
+
+ tmp2 = VA*dN3[2]*(2.0*NconjtmpI*wik*dNki*dwkn)/rknmag;
+ f[atomk][0] -= tmp2*rkn[0];
+ f[atomk][1] -= tmp2*rkn[1];
+ f[atomk][2] -= tmp2*rkn[2];
+ f[atomn][0] += tmp2*rkn[0];
+ f[atomn][1] += tmp2*rkn[1];
+ f[atomn][2] += tmp2*rkn[2];
+
+ if (vflag_atom) v_tally2_thr(atomk,atomn,-tmp2,rkn,thr);
+ }
+ }
+ }
}
}
@@ -1422,60 +1422,60 @@ double PairAIREBOOMP::bondorderLJ_thr(int i, int j, double rij[3], double rijmag
for (l = 0; l < REBO_numneigh[j]; l++) {
atoml = REBO_neighs[l];
if (atoml != atomi) {
- ltype = map[type[atoml]];
- rjl[0] = x[atomj][0]-x[atoml][0];
- rjl[1] = x[atomj][1]-x[atoml][1];
- rjl[2] = x[atomj][2]-x[atoml][2];
- rjlmag = sqrt((rjl[0]*rjl[0])+(rjl[1]*rjl[1])+(rjl[2]*rjl[2]));
- wjl = Sp(rjlmag,rcmin[jtype][ltype],rcmax[jtype][ltype],dwjl);
- Nlj = nC[atoml]-(wjl*kronecker(jtype,0))+nH[atoml] -
- (wjl*kronecker(jtype,1));
- SpN = Sp(Nlj,Nmin,Nmax,dNlj);
-
- tmp2 = VA*dN3[1]*dwjl/rjlmag;
- f[atomj][0] -= tmp2*rjl[0];
- f[atomj][1] -= tmp2*rjl[1];
- f[atomj][2] -= tmp2*rjl[2];
- f[atoml][0] += tmp2*rjl[0];
- f[atoml][1] += tmp2*rjl[1];
- f[atoml][2] += tmp2*rjl[2];
-
- if (vflag_atom) v_tally2_thr(atomj,atoml,-tmp2,rjl,thr);
-
- tmp2 = VA*dN3[2]*(2.0*NconjtmpJ*dwjl*SpN)/rjlmag;
- f[atomj][0] -= tmp2*rjl[0];
- f[atomj][1] -= tmp2*rjl[1];
- f[atomj][2] -= tmp2*rjl[2];
- f[atoml][0] += tmp2*rjl[0];
- f[atoml][1] += tmp2*rjl[1];
- f[atoml][2] += tmp2*rjl[2];
-
- if (vflag_atom) v_tally2_thr(atomj,atoml,-tmp2,rjl,thr);
-
- if (fabs(dNlj) > TOL) {
- REBO_neighs_l = REBO_firstneigh[atoml];
- for (n = 0; n < REBO_numneigh[atoml]; n++) {
- atomn = REBO_neighs_l[n];
- if (atomn != atomj) {
- ntype = map[type[atomn]];
- rln[0] = x[atoml][0]-x[atomn][0];
- rln[1] = x[atoml][1]-x[atomn][1];
- rln[2] = x[atoml][2]-x[atomn][2];
- rlnmag = sqrt((rln[0]*rln[0])+(rln[1]*rln[1])+(rln[2]*rln[2]));
- Sp(rlnmag,rcmin[ltype][ntype],rcmax[ltype][ntype],dwln);
-
- tmp2 = VA*dN3[2]*(2.0*NconjtmpJ*wjl*dNlj*dwln)/rlnmag;
- f[atoml][0] -= tmp2*rln[0];
- f[atoml][1] -= tmp2*rln[1];
- f[atoml][2] -= tmp2*rln[2];
- f[atomn][0] += tmp2*rln[0];
- f[atomn][1] += tmp2*rln[1];
- f[atomn][2] += tmp2*rln[2];
-
- if (vflag_atom) v_tally2_thr(atoml,atomn,-tmp2,rln,thr);
- }
- }
- }
+ ltype = map[type[atoml]];
+ rjl[0] = x[atomj][0]-x[atoml][0];
+ rjl[1] = x[atomj][1]-x[atoml][1];
+ rjl[2] = x[atomj][2]-x[atoml][2];
+ rjlmag = sqrt((rjl[0]*rjl[0])+(rjl[1]*rjl[1])+(rjl[2]*rjl[2]));
+ wjl = Sp(rjlmag,rcmin[jtype][ltype],rcmax[jtype][ltype],dwjl);
+ Nlj = nC[atoml]-(wjl*kronecker(jtype,0))+nH[atoml] -
+ (wjl*kronecker(jtype,1));
+ SpN = Sp(Nlj,Nmin,Nmax,dNlj);
+
+ tmp2 = VA*dN3[1]*dwjl/rjlmag;
+ f[atomj][0] -= tmp2*rjl[0];
+ f[atomj][1] -= tmp2*rjl[1];
+ f[atomj][2] -= tmp2*rjl[2];
+ f[atoml][0] += tmp2*rjl[0];
+ f[atoml][1] += tmp2*rjl[1];
+ f[atoml][2] += tmp2*rjl[2];
+
+ if (vflag_atom) v_tally2_thr(atomj,atoml,-tmp2,rjl,thr);
+
+ tmp2 = VA*dN3[2]*(2.0*NconjtmpJ*dwjl*SpN)/rjlmag;
+ f[atomj][0] -= tmp2*rjl[0];
+ f[atomj][1] -= tmp2*rjl[1];
+ f[atomj][2] -= tmp2*rjl[2];
+ f[atoml][0] += tmp2*rjl[0];
+ f[atoml][1] += tmp2*rjl[1];
+ f[atoml][2] += tmp2*rjl[2];
+
+ if (vflag_atom) v_tally2_thr(atomj,atoml,-tmp2,rjl,thr);
+
+ if (fabs(dNlj) > TOL) {
+ REBO_neighs_l = REBO_firstneigh[atoml];
+ for (n = 0; n < REBO_numneigh[atoml]; n++) {
+ atomn = REBO_neighs_l[n];
+ if (atomn != atomj) {
+ ntype = map[type[atomn]];
+ rln[0] = x[atoml][0]-x[atomn][0];
+ rln[1] = x[atoml][1]-x[atomn][1];
+ rln[2] = x[atoml][2]-x[atomn][2];
+ rlnmag = sqrt((rln[0]*rln[0])+(rln[1]*rln[1])+(rln[2]*rln[2]));
+ Sp(rlnmag,rcmin[ltype][ntype],rcmax[ltype][ntype],dwln);
+
+ tmp2 = VA*dN3[2]*(2.0*NconjtmpJ*wjl*dNlj*dwln)/rlnmag;
+ f[atoml][0] -= tmp2*rln[0];
+ f[atoml][1] -= tmp2*rln[1];
+ f[atoml][2] -= tmp2*rln[2];
+ f[atomn][0] += tmp2*rln[0];
+ f[atomn][1] += tmp2*rln[1];
+ f[atomn][2] += tmp2*rln[2];
+
+ if (vflag_atom) v_tally2_thr(atoml,atomn,-tmp2,rln,thr);
+ }
+ }
+ }
}
}
@@ -1496,329 +1496,329 @@ double PairAIREBOOMP::bondorderLJ_thr(int i, int j, double rij[3], double rijmag
REBO_neighs_i = REBO_firstneigh[i];
for (k = 0; k < REBO_numneigh[i]; k++) {
- atomk = REBO_neighs_i[k];
- atom1 = atomk;
- ktype = map[type[atomk]];
- if (atomk != atomj) {
- r21[0] = x[atom2][0]-x[atom1][0];
- r21[1] = x[atom2][1]-x[atom1][1];
- r21[2] = x[atom2][2]-x[atom1][2];
- r21mag = sqrt(r21[0]*r21[0] + r21[1]*r21[1] + r21[2]*r21[2]);
- cos321 = ((r21[0]*rij[0])+(r21[1]*rij[1])+(r21[2]*rij[2])) /
- (r21mag*rijmag);
- cos321 = MIN(cos321,1.0);
- cos321 = MAX(cos321,-1.0);
- sin321 = sqrt(1.0 - cos321*cos321);
- sink2i = 1.0/(sin321*sin321);
- rik2i = 1.0/(r21mag*r21mag);
-
- if (sin321 != 0.0) {
- rr = (rijmag*rijmag)-(r21mag*r21mag);
- rjk[0] = r21[0]-rij[0];
- rjk[1] = r21[1]-rij[1];
- rjk[2] = r21[2]-rij[2];
- rjk2 = (rjk[0]*rjk[0])+(rjk[1]*rjk[1])+(rjk[2]*rjk[2]);
- rijrik = 2.0*rijmag*r21mag;
- rik2 = r21mag*r21mag;
- dctik = (-rr+rjk2)/(rijrik*rik2);
- dctij = (rr+rjk2)/(rijrik*rijmag*rijmag);
- dctjk = -2.0/rijrik;
- w21 = Sp(r21mag,rcmin[itype][ktype],rcmaxp[itype][ktype],dw21);
- rikmag = r21mag;
- rij2 = r32mag*r32mag;
- rik2 = r21mag*r21mag;
- costmp = 0.5*(rij2+rik2-rjk2)/rijmag/rikmag;
- tspjik = Sp2(costmp,thmin,thmax,dtsjik);
- dtsjik = -dtsjik;
-
- REBO_neighs_j = REBO_firstneigh[j];
- for (l = 0; l < REBO_numneigh[j]; l++) {
- atoml = REBO_neighs_j[l];
- atom4 = atoml;
- ltype = map[type[atoml]];
- if (!(atoml == atomi || atoml == atomk)) {
- r34[0] = x[atom3][0]-x[atom4][0];
- r34[1] = x[atom3][1]-x[atom4][1];
- r34[2] = x[atom3][2]-x[atom4][2];
- r34mag = sqrt(r34[0]*r34[0] + r34[1]*r34[1] + r34[2]*r34[2]);
- cos234 = -1.0*((rij[0]*r34[0])+(rij[1]*r34[1]) +
- (rij[2]*r34[2]))/(rijmag*r34mag);
- cos234 = MIN(cos234,1.0);
- cos234 = MAX(cos234,-1.0);
- sin234 = sqrt(1.0 - cos234*cos234);
- sinl2i = 1.0/(sin234*sin234);
- rjl2i = 1.0/(r34mag*r34mag);
-
- if (sin234 != 0.0) {
- w34 = Sp(r34mag,rcmin[jtype][ltype],
- rcmaxp[jtype][ltype],dw34);
- rr = (r23mag*r23mag)-(r34mag*r34mag);
- ril[0] = r23[0]+r34[0];
- ril[1] = r23[1]+r34[1];
- ril[2] = r23[2]+r34[2];
- ril2 = (ril[0]*ril[0])+(ril[1]*ril[1])+(ril[2]*ril[2]);
- rijrjl = 2.0*r23mag*r34mag;
- rjl2 = r34mag*r34mag;
- dctjl = (-rr+ril2)/(rijrjl*rjl2);
- dctji = (rr+ril2)/(rijrjl*r23mag*r23mag);
- dctil = -2.0/rijrjl;
- rjlmag = r34mag;
- rjl2 = r34mag*r34mag;
- costmp = 0.5*(rij2+rjl2-ril2)/rijmag/rjlmag;
- tspijl = Sp2(costmp,thmin,thmax,dtsijl);
- dtsijl = -dtsijl; //need minus sign
- prefactor = VA*Tij;
-
- cross321[0] = (r32[1]*r21[2])-(r32[2]*r21[1]);
- cross321[1] = (r32[2]*r21[0])-(r32[0]*r21[2]);
- cross321[2] = (r32[0]*r21[1])-(r32[1]*r21[0]);
- cross234[0] = (r23[1]*r34[2])-(r23[2]*r34[1]);
- cross234[1] = (r23[2]*r34[0])-(r23[0]*r34[2]);
- cross234[2] = (r23[0]*r34[1])-(r23[1]*r34[0]);
-
- cwnum = (cross321[0]*cross234[0]) +
- (cross321[1]*cross234[1])+(cross321[2]*cross234[2]);
- cwnom = r21mag*r34mag*r23mag*r23mag*sin321*sin234;
- om1234 = cwnum/cwnom;
- cw = om1234;
- Etmp += ((1.0-(om1234*om1234))*w21*w34) *
- (1.0-tspjik)*(1.0-tspijl);
-
- dt1dik = (rik2i)-(dctik*sink2i*cos321);
- dt1djk = (-dctjk*sink2i*cos321);
- dt1djl = (rjl2i)-(dctjl*sinl2i*cos234);
- dt1dil = (-dctil*sinl2i*cos234);
- dt1dij = (2.0/(r23mag*r23mag)) -
- (dctij*sink2i*cos321)-(dctji*sinl2i*cos234);
-
- dt2dik[0] = (-r23[2]*cross234[1])+(r23[1]*cross234[2]);
- dt2dik[1] = (-r23[0]*cross234[2])+(r23[2]*cross234[0]);
- dt2dik[2] = (-r23[1]*cross234[0])+(r23[0]*cross234[1]);
-
- dt2djl[0] = (-r23[1]*cross321[2])+(r23[2]*cross321[1]);
- dt2djl[1] = (-r23[2]*cross321[0])+(r23[0]*cross321[2]);
- dt2djl[2] = (-r23[0]*cross321[1])+(r23[1]*cross321[0]);
-
- dt2dij[0] = (r21[2]*cross234[1]) -
- (r34[2]*cross321[1])-(r21[1]*cross234[2]) +
- (r34[1]*cross321[2]);
- dt2dij[1] = (r21[0]*cross234[2]) -
- (r34[0]*cross321[2])-(r21[2]*cross234[0]) +
- (r34[2]*cross321[0]);
- dt2dij[2] = (r21[1]*cross234[0]) -
- (r34[1]*cross321[0])-(r21[0]*cross234[1]) +
- (r34[0]*cross321[1]);
-
- aa = (prefactor*2.0*cw/cwnom)*w21*w34 *
- (1.0-tspjik)*(1.0-tspijl);
- aaa1 = -prefactor*(1.0-(om1234*om1234)) *
- (1.0-tspjik)*(1.0-tspijl);
- aaa2 = aaa1*w21*w34;
- at2 = aa*cwnum;
-
- fcijpc = (-dt1dij*at2)+(aaa2*dtsjik*dctij*(1.0-tspijl)) +
- (aaa2*dtsijl*dctji*(1.0-tspjik));
- fcikpc = (-dt1dik*at2)+(aaa2*dtsjik*dctik*(1.0-tspijl));
- fcjlpc = (-dt1djl*at2)+(aaa2*dtsijl*dctjl*(1.0-tspjik));
- fcjkpc = (-dt1djk*at2)+(aaa2*dtsjik*dctjk*(1.0-tspijl));
- fcilpc = (-dt1dil*at2)+(aaa2*dtsijl*dctil*(1.0-tspjik));
-
- F23[0] = (fcijpc*r23[0])+(aa*dt2dij[0]);
- F23[1] = (fcijpc*r23[1])+(aa*dt2dij[1]);
- F23[2] = (fcijpc*r23[2])+(aa*dt2dij[2]);
-
- F12[0] = (fcikpc*r21[0])+(aa*dt2dik[0]);
- F12[1] = (fcikpc*r21[1])+(aa*dt2dik[1]);
- F12[2] = (fcikpc*r21[2])+(aa*dt2dik[2]);
-
- F34[0] = (fcjlpc*r34[0])+(aa*dt2djl[0]);
- F34[1] = (fcjlpc*r34[1])+(aa*dt2djl[1]);
- F34[2] = (fcjlpc*r34[2])+(aa*dt2djl[2]);
-
- F31[0] = (fcjkpc*rjk[0]);
- F31[1] = (fcjkpc*rjk[1]);
- F31[2] = (fcjkpc*rjk[2]);
-
- F24[0] = (fcilpc*ril[0]);
- F24[1] = (fcilpc*ril[1]);
- F24[2] = (fcilpc*ril[2]);
-
- f1[0] = -F12[0]-F31[0];
- f1[1] = -F12[1]-F31[1];
- f1[2] = -F12[2]-F31[2];
- f2[0] = F23[0]+F12[0]+F24[0];
- f2[1] = F23[1]+F12[1]+F24[1];
- f2[2] = F23[2]+F12[2]+F24[2];
- f3[0] = -F23[0]+F34[0]+F31[0];
- f3[1] = -F23[1]+F34[1]+F31[1];
- f3[2] = -F23[2]+F34[2]+F31[2];
- f4[0] = -F34[0]-F24[0];
- f4[1] = -F34[1]-F24[1];
- f4[2] = -F34[2]-F24[2];
-
- // coordination forces
-
- tmp2 = VA*Tij*((1.0-(om1234*om1234))) *
- (1.0-tspjik)*(1.0-tspijl)*dw21*w34/r21mag;
- f2[0] -= tmp2*r21[0];
- f2[1] -= tmp2*r21[1];
- f2[2] -= tmp2*r21[2];
- f1[0] += tmp2*r21[0];
- f1[1] += tmp2*r21[1];
- f1[2] += tmp2*r21[2];
-
- tmp2 = VA*Tij*((1.0-(om1234*om1234))) *
- (1.0-tspjik)*(1.0-tspijl)*w21*dw34/r34mag;
- f3[0] -= tmp2*r34[0];
- f3[1] -= tmp2*r34[1];
- f3[2] -= tmp2*r34[2];
- f4[0] += tmp2*r34[0];
- f4[1] += tmp2*r34[1];
- f4[2] += tmp2*r34[2];
-
- f[atom1][0] += f1[0]; f[atom1][1] += f1[1];
- f[atom1][2] += f1[2];
- f[atom2][0] += f2[0]; f[atom2][1] += f2[1];
- f[atom2][2] += f2[2];
- f[atom3][0] += f3[0]; f[atom3][1] += f3[1];
- f[atom3][2] += f3[2];
- f[atom4][0] += f4[0]; f[atom4][1] += f4[1];
- f[atom4][2] += f4[2];
-
- if (vflag_atom) {
- r13[0] = -rjk[0]; r13[1] = -rjk[1]; r13[2] = -rjk[2];
- r43[0] = -r34[0]; r43[1] = -r34[1]; r43[2] = -r34[2];
- v_tally4_thr(atom1,atom2,atom3,atom4,f1,f2,f4,r13,r23,r43,thr);
- }
- }
- }
- }
- }
- }
+ atomk = REBO_neighs_i[k];
+ atom1 = atomk;
+ ktype = map[type[atomk]];
+ if (atomk != atomj) {
+ r21[0] = x[atom2][0]-x[atom1][0];
+ r21[1] = x[atom2][1]-x[atom1][1];
+ r21[2] = x[atom2][2]-x[atom1][2];
+ r21mag = sqrt(r21[0]*r21[0] + r21[1]*r21[1] + r21[2]*r21[2]);
+ cos321 = ((r21[0]*rij[0])+(r21[1]*rij[1])+(r21[2]*rij[2])) /
+ (r21mag*rijmag);
+ cos321 = MIN(cos321,1.0);
+ cos321 = MAX(cos321,-1.0);
+ sin321 = sqrt(1.0 - cos321*cos321);
+ sink2i = 1.0/(sin321*sin321);
+ rik2i = 1.0/(r21mag*r21mag);
+
+ if (sin321 != 0.0) {
+ rr = (rijmag*rijmag)-(r21mag*r21mag);
+ rjk[0] = r21[0]-rij[0];
+ rjk[1] = r21[1]-rij[1];
+ rjk[2] = r21[2]-rij[2];
+ rjk2 = (rjk[0]*rjk[0])+(rjk[1]*rjk[1])+(rjk[2]*rjk[2]);
+ rijrik = 2.0*rijmag*r21mag;
+ rik2 = r21mag*r21mag;
+ dctik = (-rr+rjk2)/(rijrik*rik2);
+ dctij = (rr+rjk2)/(rijrik*rijmag*rijmag);
+ dctjk = -2.0/rijrik;
+ w21 = Sp(r21mag,rcmin[itype][ktype],rcmaxp[itype][ktype],dw21);
+ rikmag = r21mag;
+ rij2 = r32mag*r32mag;
+ rik2 = r21mag*r21mag;
+ costmp = 0.5*(rij2+rik2-rjk2)/rijmag/rikmag;
+ tspjik = Sp2(costmp,thmin,thmax,dtsjik);
+ dtsjik = -dtsjik;
+
+ REBO_neighs_j = REBO_firstneigh[j];
+ for (l = 0; l < REBO_numneigh[j]; l++) {
+ atoml = REBO_neighs_j[l];
+ atom4 = atoml;
+ ltype = map[type[atoml]];
+ if (!(atoml == atomi || atoml == atomk)) {
+ r34[0] = x[atom3][0]-x[atom4][0];
+ r34[1] = x[atom3][1]-x[atom4][1];
+ r34[2] = x[atom3][2]-x[atom4][2];
+ r34mag = sqrt(r34[0]*r34[0] + r34[1]*r34[1] + r34[2]*r34[2]);
+ cos234 = -1.0*((rij[0]*r34[0])+(rij[1]*r34[1]) +
+ (rij[2]*r34[2]))/(rijmag*r34mag);
+ cos234 = MIN(cos234,1.0);
+ cos234 = MAX(cos234,-1.0);
+ sin234 = sqrt(1.0 - cos234*cos234);
+ sinl2i = 1.0/(sin234*sin234);
+ rjl2i = 1.0/(r34mag*r34mag);
+
+ if (sin234 != 0.0) {
+ w34 = Sp(r34mag,rcmin[jtype][ltype],
+ rcmaxp[jtype][ltype],dw34);
+ rr = (r23mag*r23mag)-(r34mag*r34mag);
+ ril[0] = r23[0]+r34[0];
+ ril[1] = r23[1]+r34[1];
+ ril[2] = r23[2]+r34[2];
+ ril2 = (ril[0]*ril[0])+(ril[1]*ril[1])+(ril[2]*ril[2]);
+ rijrjl = 2.0*r23mag*r34mag;
+ rjl2 = r34mag*r34mag;
+ dctjl = (-rr+ril2)/(rijrjl*rjl2);
+ dctji = (rr+ril2)/(rijrjl*r23mag*r23mag);
+ dctil = -2.0/rijrjl;
+ rjlmag = r34mag;
+ rjl2 = r34mag*r34mag;
+ costmp = 0.5*(rij2+rjl2-ril2)/rijmag/rjlmag;
+ tspijl = Sp2(costmp,thmin,thmax,dtsijl);
+ dtsijl = -dtsijl; //need minus sign
+ prefactor = VA*Tij;
+
+ cross321[0] = (r32[1]*r21[2])-(r32[2]*r21[1]);
+ cross321[1] = (r32[2]*r21[0])-(r32[0]*r21[2]);
+ cross321[2] = (r32[0]*r21[1])-(r32[1]*r21[0]);
+ cross234[0] = (r23[1]*r34[2])-(r23[2]*r34[1]);
+ cross234[1] = (r23[2]*r34[0])-(r23[0]*r34[2]);
+ cross234[2] = (r23[0]*r34[1])-(r23[1]*r34[0]);
+
+ cwnum = (cross321[0]*cross234[0]) +
+ (cross321[1]*cross234[1])+(cross321[2]*cross234[2]);
+ cwnom = r21mag*r34mag*r23mag*r23mag*sin321*sin234;
+ om1234 = cwnum/cwnom;
+ cw = om1234;
+ Etmp += ((1.0-(om1234*om1234))*w21*w34) *
+ (1.0-tspjik)*(1.0-tspijl);
+
+ dt1dik = (rik2i)-(dctik*sink2i*cos321);
+ dt1djk = (-dctjk*sink2i*cos321);
+ dt1djl = (rjl2i)-(dctjl*sinl2i*cos234);
+ dt1dil = (-dctil*sinl2i*cos234);
+ dt1dij = (2.0/(r23mag*r23mag)) -
+ (dctij*sink2i*cos321)-(dctji*sinl2i*cos234);
+
+ dt2dik[0] = (-r23[2]*cross234[1])+(r23[1]*cross234[2]);
+ dt2dik[1] = (-r23[0]*cross234[2])+(r23[2]*cross234[0]);
+ dt2dik[2] = (-r23[1]*cross234[0])+(r23[0]*cross234[1]);
+
+ dt2djl[0] = (-r23[1]*cross321[2])+(r23[2]*cross321[1]);
+ dt2djl[1] = (-r23[2]*cross321[0])+(r23[0]*cross321[2]);
+ dt2djl[2] = (-r23[0]*cross321[1])+(r23[1]*cross321[0]);
+
+ dt2dij[0] = (r21[2]*cross234[1]) -
+ (r34[2]*cross321[1])-(r21[1]*cross234[2]) +
+ (r34[1]*cross321[2]);
+ dt2dij[1] = (r21[0]*cross234[2]) -
+ (r34[0]*cross321[2])-(r21[2]*cross234[0]) +
+ (r34[2]*cross321[0]);
+ dt2dij[2] = (r21[1]*cross234[0]) -
+ (r34[1]*cross321[0])-(r21[0]*cross234[1]) +
+ (r34[0]*cross321[1]);
+
+ aa = (prefactor*2.0*cw/cwnom)*w21*w34 *
+ (1.0-tspjik)*(1.0-tspijl);
+ aaa1 = -prefactor*(1.0-(om1234*om1234)) *
+ (1.0-tspjik)*(1.0-tspijl);
+ aaa2 = aaa1*w21*w34;
+ at2 = aa*cwnum;
+
+ fcijpc = (-dt1dij*at2)+(aaa2*dtsjik*dctij*(1.0-tspijl)) +
+ (aaa2*dtsijl*dctji*(1.0-tspjik));
+ fcikpc = (-dt1dik*at2)+(aaa2*dtsjik*dctik*(1.0-tspijl));
+ fcjlpc = (-dt1djl*at2)+(aaa2*dtsijl*dctjl*(1.0-tspjik));
+ fcjkpc = (-dt1djk*at2)+(aaa2*dtsjik*dctjk*(1.0-tspijl));
+ fcilpc = (-dt1dil*at2)+(aaa2*dtsijl*dctil*(1.0-tspjik));
+
+ F23[0] = (fcijpc*r23[0])+(aa*dt2dij[0]);
+ F23[1] = (fcijpc*r23[1])+(aa*dt2dij[1]);
+ F23[2] = (fcijpc*r23[2])+(aa*dt2dij[2]);
+
+ F12[0] = (fcikpc*r21[0])+(aa*dt2dik[0]);
+ F12[1] = (fcikpc*r21[1])+(aa*dt2dik[1]);
+ F12[2] = (fcikpc*r21[2])+(aa*dt2dik[2]);
+
+ F34[0] = (fcjlpc*r34[0])+(aa*dt2djl[0]);
+ F34[1] = (fcjlpc*r34[1])+(aa*dt2djl[1]);
+ F34[2] = (fcjlpc*r34[2])+(aa*dt2djl[2]);
+
+ F31[0] = (fcjkpc*rjk[0]);
+ F31[1] = (fcjkpc*rjk[1]);
+ F31[2] = (fcjkpc*rjk[2]);
+
+ F24[0] = (fcilpc*ril[0]);
+ F24[1] = (fcilpc*ril[1]);
+ F24[2] = (fcilpc*ril[2]);
+
+ f1[0] = -F12[0]-F31[0];
+ f1[1] = -F12[1]-F31[1];
+ f1[2] = -F12[2]-F31[2];
+ f2[0] = F23[0]+F12[0]+F24[0];
+ f2[1] = F23[1]+F12[1]+F24[1];
+ f2[2] = F23[2]+F12[2]+F24[2];
+ f3[0] = -F23[0]+F34[0]+F31[0];
+ f3[1] = -F23[1]+F34[1]+F31[1];
+ f3[2] = -F23[2]+F34[2]+F31[2];
+ f4[0] = -F34[0]-F24[0];
+ f4[1] = -F34[1]-F24[1];
+ f4[2] = -F34[2]-F24[2];
+
+ // coordination forces
+
+ tmp2 = VA*Tij*((1.0-(om1234*om1234))) *
+ (1.0-tspjik)*(1.0-tspijl)*dw21*w34/r21mag;
+ f2[0] -= tmp2*r21[0];
+ f2[1] -= tmp2*r21[1];
+ f2[2] -= tmp2*r21[2];
+ f1[0] += tmp2*r21[0];
+ f1[1] += tmp2*r21[1];
+ f1[2] += tmp2*r21[2];
+
+ tmp2 = VA*Tij*((1.0-(om1234*om1234))) *
+ (1.0-tspjik)*(1.0-tspijl)*w21*dw34/r34mag;
+ f3[0] -= tmp2*r34[0];
+ f3[1] -= tmp2*r34[1];
+ f3[2] -= tmp2*r34[2];
+ f4[0] += tmp2*r34[0];
+ f4[1] += tmp2*r34[1];
+ f4[2] += tmp2*r34[2];
+
+ f[atom1][0] += f1[0]; f[atom1][1] += f1[1];
+ f[atom1][2] += f1[2];
+ f[atom2][0] += f2[0]; f[atom2][1] += f2[1];
+ f[atom2][2] += f2[2];
+ f[atom3][0] += f3[0]; f[atom3][1] += f3[1];
+ f[atom3][2] += f3[2];
+ f[atom4][0] += f4[0]; f[atom4][1] += f4[1];
+ f[atom4][2] += f4[2];
+
+ if (vflag_atom) {
+ r13[0] = -rjk[0]; r13[1] = -rjk[1]; r13[2] = -rjk[2];
+ r43[0] = -r34[0]; r43[1] = -r34[1]; r43[2] = -r34[2];
+ v_tally4_thr(atom1,atom2,atom3,atom4,f1,f2,f4,r13,r23,r43,thr);
+ }
+ }
+ }
+ }
+ }
+ }
}
REBO_neighs = REBO_firstneigh[i];
for (k = 0; k < REBO_numneigh[i]; k++) {
- atomk = REBO_neighs[k];
- if (atomk != atomj) {
- ktype = map[type[atomk]];
- rik[0] = x[atomi][0]-x[atomk][0];
- rik[1] = x[atomi][1]-x[atomk][1];
- rik[2] = x[atomi][2]-x[atomk][2];
- rikmag = sqrt((rik[0]*rik[0])+(rik[1]*rik[1])+(rik[2]*rik[2]));
- wik = Sp(rikmag,rcmin[itype][ktype],rcmax[itype][ktype],dwik);
- Nki = nC[atomk]-(wik*kronecker(itype,0))+nH[atomk] -
- (wik*kronecker(itype,1));
- SpN = Sp(Nki,Nmin,Nmax,dNki);
-
- tmp2 = VA*dN3[0]*dwik*Etmp/rikmag;
- f[atomi][0] -= tmp2*rik[0];
- f[atomi][1] -= tmp2*rik[1];
- f[atomi][2] -= tmp2*rik[2];
- f[atomk][0] += tmp2*rik[0];
- f[atomk][1] += tmp2*rik[1];
- f[atomk][2] += tmp2*rik[2];
-
- if (vflag_atom) v_tally2_thr(atomi,atomk,-tmp2,rik,thr);
-
- tmp2 = VA*dN3[2]*(2.0*NconjtmpI*dwik*SpN)*Etmp/rikmag;
- f[atomi][0] -= tmp2*rik[0];
- f[atomi][1] -= tmp2*rik[1];
- f[atomi][2] -= tmp2*rik[2];
- f[atomk][0] += tmp2*rik[0];
- f[atomk][1] += tmp2*rik[1];
- f[atomk][2] += tmp2*rik[2];
-
- if (vflag_atom) v_tally2_thr(atomi,atomk,-tmp2,rik,thr);
-
- if (fabs(dNki) >TOL) {
- REBO_neighs_k = REBO_firstneigh[atomk];
- for (n = 0; n < REBO_numneigh[atomk]; n++) {
- atomn = REBO_neighs_k[n];
- ntype = map[type[atomn]];
- if (atomn !=atomi) {
- rkn[0] = x[atomk][0]-x[atomn][0];
- rkn[1] = x[atomk][1]-x[atomn][1];
- rkn[2] = x[atomk][2]-x[atomn][2];
- rknmag = sqrt((rkn[0]*rkn[0])+(rkn[1]*rkn[1])+(rkn[2]*rkn[2]));
- Sp(rknmag,rcmin[ktype][ntype],rcmax[ktype][ntype],dwkn);
-
- tmp2 = VA*dN3[2]*(2.0*NconjtmpI*wik*dNki*dwkn)*Etmp/rknmag;
- f[atomk][0] -= tmp2*rkn[0];
- f[atomk][1] -= tmp2*rkn[1];
- f[atomk][2] -= tmp2*rkn[2];
- f[atomn][0] += tmp2*rkn[0];
- f[atomn][1] += tmp2*rkn[1];
- f[atomn][2] += tmp2*rkn[2];
-
- if (vflag_atom) v_tally2_thr(atomk,atomn,-tmp2,rkn,thr);
- }
- }
- }
- }
+ atomk = REBO_neighs[k];
+ if (atomk != atomj) {
+ ktype = map[type[atomk]];
+ rik[0] = x[atomi][0]-x[atomk][0];
+ rik[1] = x[atomi][1]-x[atomk][1];
+ rik[2] = x[atomi][2]-x[atomk][2];
+ rikmag = sqrt((rik[0]*rik[0])+(rik[1]*rik[1])+(rik[2]*rik[2]));
+ wik = Sp(rikmag,rcmin[itype][ktype],rcmax[itype][ktype],dwik);
+ Nki = nC[atomk]-(wik*kronecker(itype,0))+nH[atomk] -
+ (wik*kronecker(itype,1));
+ SpN = Sp(Nki,Nmin,Nmax,dNki);
+
+ tmp2 = VA*dN3[0]*dwik*Etmp/rikmag;
+ f[atomi][0] -= tmp2*rik[0];
+ f[atomi][1] -= tmp2*rik[1];
+ f[atomi][2] -= tmp2*rik[2];
+ f[atomk][0] += tmp2*rik[0];
+ f[atomk][1] += tmp2*rik[1];
+ f[atomk][2] += tmp2*rik[2];
+
+ if (vflag_atom) v_tally2_thr(atomi,atomk,-tmp2,rik,thr);
+
+ tmp2 = VA*dN3[2]*(2.0*NconjtmpI*dwik*SpN)*Etmp/rikmag;
+ f[atomi][0] -= tmp2*rik[0];
+ f[atomi][1] -= tmp2*rik[1];
+ f[atomi][2] -= tmp2*rik[2];
+ f[atomk][0] += tmp2*rik[0];
+ f[atomk][1] += tmp2*rik[1];
+ f[atomk][2] += tmp2*rik[2];
+
+ if (vflag_atom) v_tally2_thr(atomi,atomk,-tmp2,rik,thr);
+
+ if (fabs(dNki) >TOL) {
+ REBO_neighs_k = REBO_firstneigh[atomk];
+ for (n = 0; n < REBO_numneigh[atomk]; n++) {
+ atomn = REBO_neighs_k[n];
+ ntype = map[type[atomn]];
+ if (atomn !=atomi) {
+ rkn[0] = x[atomk][0]-x[atomn][0];
+ rkn[1] = x[atomk][1]-x[atomn][1];
+ rkn[2] = x[atomk][2]-x[atomn][2];
+ rknmag = sqrt((rkn[0]*rkn[0])+(rkn[1]*rkn[1])+(rkn[2]*rkn[2]));
+ Sp(rknmag,rcmin[ktype][ntype],rcmax[ktype][ntype],dwkn);
+
+ tmp2 = VA*dN3[2]*(2.0*NconjtmpI*wik*dNki*dwkn)*Etmp/rknmag;
+ f[atomk][0] -= tmp2*rkn[0];
+ f[atomk][1] -= tmp2*rkn[1];
+ f[atomk][2] -= tmp2*rkn[2];
+ f[atomn][0] += tmp2*rkn[0];
+ f[atomn][1] += tmp2*rkn[1];
+ f[atomn][2] += tmp2*rkn[2];
+
+ if (vflag_atom) v_tally2_thr(atomk,atomn,-tmp2,rkn,thr);
+ }
+ }
+ }
+ }
}
// Tij forces
REBO_neighs = REBO_firstneigh[j];
for (l = 0; l < REBO_numneigh[j]; l++) {
- atoml = REBO_neighs[l];
- if (atoml != atomi) {
- ltype = map[type[atoml]];
- rjl[0] = x[atomj][0]-x[atoml][0];
- rjl[1] = x[atomj][1]-x[atoml][1];
- rjl[2] = x[atomj][2]-x[atoml][2];
- rjlmag = sqrt((rjl[0]*rjl[0])+(rjl[1]*rjl[1])+(rjl[2]*rjl[2]));
- wjl = Sp(rjlmag,rcmin[jtype][ltype],rcmax[jtype][ltype],dwjl);
- Nlj = nC[atoml]-(wjl*kronecker(jtype,0))+nH[atoml] -
- (wjl*kronecker(jtype,1));
- SpN = Sp(Nlj,Nmin,Nmax,dNlj);
-
- tmp2 = VA*dN3[1]*dwjl*Etmp/rjlmag;
- f[atomj][0] -= tmp2*rjl[0];
- f[atomj][1] -= tmp2*rjl[1];
- f[atomj][2] -= tmp2*rjl[2];
- f[atoml][0] += tmp2*rjl[0];
- f[atoml][1] += tmp2*rjl[1];
- f[atoml][2] += tmp2*rjl[2];
-
- if (vflag_atom) v_tally2_thr(atomj,atoml,-tmp2,rjl,thr);
-
- tmp2 = VA*dN3[2]*(2.0*NconjtmpJ*dwjl*SpN)*Etmp/rjlmag;
- f[atomj][0] -= tmp2*rjl[0];
- f[atomj][1] -= tmp2*rjl[1];
- f[atomj][2] -= tmp2*rjl[2];
- f[atoml][0] += tmp2*rjl[0];
- f[atoml][1] += tmp2*rjl[1];
- f[atoml][2] += tmp2*rjl[2];
-
- if (vflag_atom) v_tally2_thr(atomj,atoml,-tmp2,rjl,thr);
-
- if (fabs(dNlj) > TOL) {
- REBO_neighs_l = REBO_firstneigh[atoml];
- for (n = 0; n < REBO_numneigh[atoml]; n++) {
- atomn = REBO_neighs_l[n];
- ntype = map[type[atomn]];
- if (atomn != atomj) {
- rln[0] = x[atoml][0]-x[atomn][0];
- rln[1] = x[atoml][1]-x[atomn][1];
- rln[2] = x[atoml][2]-x[atomn][2];
- rlnmag = sqrt((rln[0]*rln[0])+(rln[1]*rln[1])+(rln[2]*rln[2]));
- Sp(rlnmag,rcmin[ltype][ntype],rcmax[ltype][ntype],dwln);
-
- tmp2 = VA*dN3[2]*(2.0*NconjtmpJ*wjl*dNlj*dwln)*Etmp/rlnmag;
- f[atoml][0] -= tmp2*rln[0];
- f[atoml][1] -= tmp2*rln[1];
- f[atoml][2] -= tmp2*rln[2];
- f[atomn][0] += tmp2*rln[0];
- f[atomn][1] += tmp2*rln[1];
- f[atomn][2] += tmp2*rln[2];
-
- if (vflag_atom) v_tally2_thr(atoml,atomn,-tmp2,rln,thr);
- }
- }
- }
- }
+ atoml = REBO_neighs[l];
+ if (atoml != atomi) {
+ ltype = map[type[atoml]];
+ rjl[0] = x[atomj][0]-x[atoml][0];
+ rjl[1] = x[atomj][1]-x[atoml][1];
+ rjl[2] = x[atomj][2]-x[atoml][2];
+ rjlmag = sqrt((rjl[0]*rjl[0])+(rjl[1]*rjl[1])+(rjl[2]*rjl[2]));
+ wjl = Sp(rjlmag,rcmin[jtype][ltype],rcmax[jtype][ltype],dwjl);
+ Nlj = nC[atoml]-(wjl*kronecker(jtype,0))+nH[atoml] -
+ (wjl*kronecker(jtype,1));
+ SpN = Sp(Nlj,Nmin,Nmax,dNlj);
+
+ tmp2 = VA*dN3[1]*dwjl*Etmp/rjlmag;
+ f[atomj][0] -= tmp2*rjl[0];
+ f[atomj][1] -= tmp2*rjl[1];
+ f[atomj][2] -= tmp2*rjl[2];
+ f[atoml][0] += tmp2*rjl[0];
+ f[atoml][1] += tmp2*rjl[1];
+ f[atoml][2] += tmp2*rjl[2];
+
+ if (vflag_atom) v_tally2_thr(atomj,atoml,-tmp2,rjl,thr);
+
+ tmp2 = VA*dN3[2]*(2.0*NconjtmpJ*dwjl*SpN)*Etmp/rjlmag;
+ f[atomj][0] -= tmp2*rjl[0];
+ f[atomj][1] -= tmp2*rjl[1];
+ f[atomj][2] -= tmp2*rjl[2];
+ f[atoml][0] += tmp2*rjl[0];
+ f[atoml][1] += tmp2*rjl[1];
+ f[atoml][2] += tmp2*rjl[2];
+
+ if (vflag_atom) v_tally2_thr(atomj,atoml,-tmp2,rjl,thr);
+
+ if (fabs(dNlj) > TOL) {
+ REBO_neighs_l = REBO_firstneigh[atoml];
+ for (n = 0; n < REBO_numneigh[atoml]; n++) {
+ atomn = REBO_neighs_l[n];
+ ntype = map[type[atomn]];
+ if (atomn != atomj) {
+ rln[0] = x[atoml][0]-x[atomn][0];
+ rln[1] = x[atoml][1]-x[atomn][1];
+ rln[2] = x[atoml][2]-x[atomn][2];
+ rlnmag = sqrt((rln[0]*rln[0])+(rln[1]*rln[1])+(rln[2]*rln[2]));
+ Sp(rlnmag,rcmin[ltype][ntype],rcmax[ltype][ntype],dwln);
+
+ tmp2 = VA*dN3[2]*(2.0*NconjtmpJ*wjl*dNlj*dwln)*Etmp/rlnmag;
+ f[atoml][0] -= tmp2*rln[0];
+ f[atoml][1] -= tmp2*rln[1];
+ f[atoml][2] -= tmp2*rln[2];
+ f[atomn][0] += tmp2*rln[0];
+ f[atomn][1] += tmp2*rln[1];
+ f[atomn][2] += tmp2*rln[2];
+
+ if (vflag_atom) v_tally2_thr(atoml,atomn,-tmp2,rln,thr);
+ }
+ }
+ }
+ }
}
}
}
@@ -1831,7 +1831,7 @@ double PairAIREBOOMP::bondorderLJ_thr(int i, int j, double rij[3], double rijmag
------------------------------------------------------------------------- */
void PairAIREBOOMP::FREBO_thr(int ifrom, int ito, int evflag, int eflag,
- int vflag_atom, ThrData * const thr)
+ int vflag_atom, ThrData * const thr)
{
int i,j,k,m,ii,itype,jtype,itag,jtag;
double delx,dely,delz,evdwl,fpair,xtmp,ytmp,ztmp;
@@ -1866,13 +1866,13 @@ void PairAIREBOOMP::FREBO_thr(int ifrom, int ito, int evflag, int eflag,
jtag = tag[j];
if (itag > jtag) {
- if ((itag+jtag) % 2 == 0) continue;
+ if ((itag+jtag) % 2 == 0) continue;
} else if (itag < jtag) {
- if ((itag+jtag) % 2 == 1) continue;
+ if ((itag+jtag) % 2 == 1) continue;
} else {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
- if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
+ if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
}
jtype = map[type[j]];
@@ -1896,9 +1896,9 @@ void PairAIREBOOMP::FREBO_thr(int ifrom, int ito, int evflag, int eflag,
VA = dVA = 0.0;
for (m = 0; m < 3; m++) {
- term = -wij * BIJc[itype][jtype][m] * exp(-Beta[itype][jtype][m]*rij);
- VA += term;
- dVA += -Beta[itype][jtype][m] * term;
+ term = -wij * BIJc[itype][jtype][m] * exp(-Beta[itype][jtype][m]*rij);
+ VA += term;
+ dVA += -Beta[itype][jtype][m] * term;
}
dVA += VA/wij * dwij;
del[0] = delx;
@@ -1917,7 +1917,7 @@ void PairAIREBOOMP::FREBO_thr(int ifrom, int ito, int evflag, int eflag,
if (eflag) evdwl = VR + bij*VA;
if (evflag) ev_tally_thr(this,i,j,nlocal,/* newton_pair */ 1,
- evdwl,0.0,fpair,delx,dely,delz,thr);
+ evdwl,0.0,fpair,delx,dely,delz,thr);
}
}
}
@@ -1928,7 +1928,7 @@ void PairAIREBOOMP::FREBO_thr(int ifrom, int ito, int evflag, int eflag,
------------------------------------------------------------------------- */
void PairAIREBOOMP::FLJ_thr(int ifrom, int ito, int evflag, int eflag,
- int vflag_atom, ThrData * const thr)
+ int vflag_atom, ThrData * const thr)
{
int i,j,k,m,ii,jj,kk,mm,jnum,itype,jtype,ktype,mtype,itag,jtag;
int atomi,atomj,atomk,atomm;
@@ -1987,13 +1987,13 @@ void PairAIREBOOMP::FLJ_thr(int ifrom, int ito, int evflag, int eflag,
jtag = tag[j];
if (itag > jtag) {
- if ((itag+jtag) % 2 == 0) continue;
+ if ((itag+jtag) % 2 == 0) continue;
} else if (itag < jtag) {
- if ((itag+jtag) % 2 == 1) continue;
+ if ((itag+jtag) % 2 == 1) continue;
} else {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
- if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
+ if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
}
jtype = map[type[j]];
@@ -2013,133 +2013,133 @@ void PairAIREBOOMP::FLJ_thr(int ifrom, int ito, int evflag, int eflag,
if (rijsq >= cutljsq[itype][jtype]) continue;
rij = sqrt(rijsq);
if (rij >= cut3rebo) {
- best = 0.0;
- testpath = 0;
+ best = 0.0;
+ testpath = 0;
} else if (rij >= rcmax[itype][jtype]) {
- best = 0.0;
- testpath = 1;
+ best = 0.0;
+ testpath = 1;
} else {
- best = Sp(rij,rcmin[itype][jtype],rcmax[itype][jtype],dwij);
- npath = 2;
- if (best < 1.0) testpath = 1;
- else testpath = 0;
+ best = Sp(rij,rcmin[itype][jtype],rcmax[itype][jtype],dwij);
+ npath = 2;
+ if (best < 1.0) testpath = 1;
+ else testpath = 0;
}
done = 0;
if (testpath) {
- // test all 3-body paths = I-K-J
- // I-K interactions come from atom I's REBO neighbors
- // if wik > current best, compute wkj
- // if best = 1.0, done
-
- REBO_neighs_i = REBO_firstneigh[i];
- for (kk = 0; kk < REBO_numneigh[i] && done==0; kk++) {
- k = REBO_neighs_i[kk];
- if (k == j) continue;
- ktype = map[type[k]];
-
- delik[0] = x[i][0] - x[k][0];
- delik[1] = x[i][1] - x[k][1];
- delik[2] = x[i][2] - x[k][2];
- rsq = delik[0]*delik[0] + delik[1]*delik[1] + delik[2]*delik[2];
- if (rsq < rcmaxsq[itype][ktype]) {
- rik = sqrt(rsq);
- wik = Sp(rik,rcmin[itype][ktype],rcmax[itype][ktype],dwik);
- } else wik = 0.0;
-
- if (wik > best) {
- deljk[0] = x[j][0] - x[k][0];
- deljk[1] = x[j][1] - x[k][1];
- deljk[2] = x[j][2] - x[k][2];
- rsq = deljk[0]*deljk[0] + deljk[1]*deljk[1] + deljk[2]*deljk[2];
- if (rsq < rcmaxsq[ktype][jtype]) {
- rkj = sqrt(rsq);
- wkj = Sp(rkj,rcmin[ktype][jtype],rcmax[ktype][jtype],dwkj);
- if (wik*wkj > best) {
- best = wik*wkj;
- npath = 3;
- atomk = k;
- delikS[0] = delik[0];
- delikS[1] = delik[1];
- delikS[2] = delik[2];
- rikS = rik;
- wikS = wik;
- dwikS = dwik;
- deljkS[0] = deljk[0];
- deljkS[1] = deljk[1];
- deljkS[2] = deljk[2];
- rkjS = rkj;
- wkjS = wkj;
- dwkjS = dwkj;
- if (best == 1.0) {
- done = 1;
- break;
- }
- }
- }
-
- // test all 4-body paths = I-K-M-J
- // K-M interactions come from atom K's REBO neighbors
- // if wik*wkm > current best, compute wmj
- // if best = 1.0, done
-
- REBO_neighs_k = REBO_firstneigh[k];
- for (mm = 0; mm < REBO_numneigh[k] && done==0; mm++) {
- m = REBO_neighs_k[mm];
- if (m == i || m == j) continue;
- mtype = map[type[m]];
- delkm[0] = x[k][0] - x[m][0];
- delkm[1] = x[k][1] - x[m][1];
- delkm[2] = x[k][2] - x[m][2];
- rsq = delkm[0]*delkm[0] + delkm[1]*delkm[1] + delkm[2]*delkm[2];
- if (rsq < rcmaxsq[ktype][mtype]) {
- rkm = sqrt(rsq);
- wkm = Sp(rkm,rcmin[ktype][mtype],rcmax[ktype][mtype],dwkm);
- } else wkm = 0.0;
-
- if (wik*wkm > best) {
- deljm[0] = x[j][0] - x[m][0];
- deljm[1] = x[j][1] - x[m][1];
- deljm[2] = x[j][2] - x[m][2];
- rsq = deljm[0]*deljm[0] + deljm[1]*deljm[1] +
- deljm[2]*deljm[2];
- if (rsq < rcmaxsq[mtype][jtype]) {
- rmj = sqrt(rsq);
- wmj = Sp(rmj,rcmin[mtype][jtype],rcmax[mtype][jtype],dwmj);
- if (wik*wkm*wmj > best) {
- best = wik*wkm*wmj;
- npath = 4;
- atomk = k;
- delikS[0] = delik[0];
- delikS[1] = delik[1];
- delikS[2] = delik[2];
- rikS = rik;
- wikS = wik;
- dwikS = dwik;
- atomm = m;
- delkmS[0] = delkm[0];
- delkmS[1] = delkm[1];
- delkmS[2] = delkm[2];
- rkmS = rkm;
- wkmS = wkm;
- dwkmS = dwkm;
- deljmS[0] = deljm[0];
- deljmS[1] = deljm[1];
- deljmS[2] = deljm[2];
- rmjS = rmj;
- wmjS = wmj;
- dwmjS = dwmj;
- if (best == 1.0) {
- done = 1;
- break;
- }
- }
- }
- }
- }
- }
- }
+ // test all 3-body paths = I-K-J
+ // I-K interactions come from atom I's REBO neighbors
+ // if wik > current best, compute wkj
+ // if best = 1.0, done
+
+ REBO_neighs_i = REBO_firstneigh[i];
+ for (kk = 0; kk < REBO_numneigh[i] && done==0; kk++) {
+ k = REBO_neighs_i[kk];
+ if (k == j) continue;
+ ktype = map[type[k]];
+
+ delik[0] = x[i][0] - x[k][0];
+ delik[1] = x[i][1] - x[k][1];
+ delik[2] = x[i][2] - x[k][2];
+ rsq = delik[0]*delik[0] + delik[1]*delik[1] + delik[2]*delik[2];
+ if (rsq < rcmaxsq[itype][ktype]) {
+ rik = sqrt(rsq);
+ wik = Sp(rik,rcmin[itype][ktype],rcmax[itype][ktype],dwik);
+ } else wik = 0.0;
+
+ if (wik > best) {
+ deljk[0] = x[j][0] - x[k][0];
+ deljk[1] = x[j][1] - x[k][1];
+ deljk[2] = x[j][2] - x[k][2];
+ rsq = deljk[0]*deljk[0] + deljk[1]*deljk[1] + deljk[2]*deljk[2];
+ if (rsq < rcmaxsq[ktype][jtype]) {
+ rkj = sqrt(rsq);
+ wkj = Sp(rkj,rcmin[ktype][jtype],rcmax[ktype][jtype],dwkj);
+ if (wik*wkj > best) {
+ best = wik*wkj;
+ npath = 3;
+ atomk = k;
+ delikS[0] = delik[0];
+ delikS[1] = delik[1];
+ delikS[2] = delik[2];
+ rikS = rik;
+ wikS = wik;
+ dwikS = dwik;
+ deljkS[0] = deljk[0];
+ deljkS[1] = deljk[1];
+ deljkS[2] = deljk[2];
+ rkjS = rkj;
+ wkjS = wkj;
+ dwkjS = dwkj;
+ if (best == 1.0) {
+ done = 1;
+ break;
+ }
+ }
+ }
+
+ // test all 4-body paths = I-K-M-J
+ // K-M interactions come from atom K's REBO neighbors
+ // if wik*wkm > current best, compute wmj
+ // if best = 1.0, done
+
+ REBO_neighs_k = REBO_firstneigh[k];
+ for (mm = 0; mm < REBO_numneigh[k] && done==0; mm++) {
+ m = REBO_neighs_k[mm];
+ if (m == i || m == j) continue;
+ mtype = map[type[m]];
+ delkm[0] = x[k][0] - x[m][0];
+ delkm[1] = x[k][1] - x[m][1];
+ delkm[2] = x[k][2] - x[m][2];
+ rsq = delkm[0]*delkm[0] + delkm[1]*delkm[1] + delkm[2]*delkm[2];
+ if (rsq < rcmaxsq[ktype][mtype]) {
+ rkm = sqrt(rsq);
+ wkm = Sp(rkm,rcmin[ktype][mtype],rcmax[ktype][mtype],dwkm);
+ } else wkm = 0.0;
+
+ if (wik*wkm > best) {
+ deljm[0] = x[j][0] - x[m][0];
+ deljm[1] = x[j][1] - x[m][1];
+ deljm[2] = x[j][2] - x[m][2];
+ rsq = deljm[0]*deljm[0] + deljm[1]*deljm[1] +
+ deljm[2]*deljm[2];
+ if (rsq < rcmaxsq[mtype][jtype]) {
+ rmj = sqrt(rsq);
+ wmj = Sp(rmj,rcmin[mtype][jtype],rcmax[mtype][jtype],dwmj);
+ if (wik*wkm*wmj > best) {
+ best = wik*wkm*wmj;
+ npath = 4;
+ atomk = k;
+ delikS[0] = delik[0];
+ delikS[1] = delik[1];
+ delikS[2] = delik[2];
+ rikS = rik;
+ wikS = wik;
+ dwikS = dwik;
+ atomm = m;
+ delkmS[0] = delkm[0];
+ delkmS[1] = delkm[1];
+ delkmS[2] = delkm[2];
+ rkmS = rkm;
+ wkmS = wkm;
+ dwkmS = dwkm;
+ deljmS[0] = deljm[0];
+ deljmS[1] = deljm[1];
+ deljmS[2] = deljm[2];
+ rmjS = rmj;
+ wmjS = wmj;
+ dwmjS = dwmj;
+ if (best == 1.0) {
+ done = 1;
+ break;
+ }
+ }
+ }
+ }
+ }
+ }
+ }
}
cij = 1.0 - best;
@@ -2156,18 +2156,18 @@ void PairAIREBOOMP::FLJ_thr(int ifrom, int ito, int evflag, int eflag,
rljmin = sigmin * rljmin;
if (rij > rljmax) {
- slw = 0.0;
- dslw = 0.0;
+ slw = 0.0;
+ dslw = 0.0;
} else if (rij > rljmin) {
- drij = rij - rljmin;
- swidth = rljmax - rljmin;
- tee = drij / swidth;
- tee2 = tee*tee;
- slw = 1.0 - tee2 * (3.0 - 2.0 * tee);
- dslw = 6.0 * tee * (1.0 - tee) / rij / swidth;
+ drij = rij - rljmin;
+ swidth = rljmax - rljmin;
+ tee = drij / swidth;
+ tee2 = tee*tee;
+ slw = 1.0 - tee2 * (3.0 - 2.0 * tee);
+ dslw = 6.0 * tee * (1.0 - tee) / rij / swidth;
} else {
- slw = 1.0;
- dslw = 0.0;
+ slw = 1.0;
+ dslw = 0.0;
}
r2inv = 1.0/rijsq;
@@ -2184,16 +2184,16 @@ void PairAIREBOOMP::FLJ_thr(int ifrom, int ito, int evflag, int eflag,
Str = Sp2(rij,rcLJmin[itype][jtype],rcLJmax[itype][jtype],dStr);
VA = Str*cij*VLJ;
if (Str > 0.0) {
- scale = rcmin[itype][jtype] / rij;
- delscale[0] = scale * delij[0];
- delscale[1] = scale * delij[1];
- delscale[2] = scale * delij[2];
- Stb = bondorderLJ_thr(i,j,delscale,rcmin[itype][jtype],VA,
- delij,rij,vflag_atom,thr);
+ scale = rcmin[itype][jtype] / rij;
+ delscale[0] = scale * delij[0];
+ delscale[1] = scale * delij[1];
+ delscale[2] = scale * delij[2];
+ Stb = bondorderLJ_thr(i,j,delscale,rcmin[itype][jtype],VA,
+ delij,rij,vflag_atom,thr);
} else Stb = 0.0;
fpair = -(dStr * (Stb*cij*VLJ - cij*VLJ) +
- dVLJ * (Str*Stb*cij + cij - Str*cij)) / rij;
+ dVLJ * (Str*Stb*cij + cij - Str*cij)) / rij;
f[i][0] += delij[0]*fpair;
f[i][1] += delij[1]*fpair;
@@ -2204,84 +2204,84 @@ void PairAIREBOOMP::FLJ_thr(int ifrom, int ito, int evflag, int eflag,
if (eflag) evdwl = VA*Stb + (1.0-Str)*cij*VLJ;
if (evflag) ev_tally_thr(this,i,j,nlocal,/* newton_pair */ 1,
- evdwl,0.0,fpair,delij[0],delij[1],delij[2],thr);
+ evdwl,0.0,fpair,delij[0],delij[1],delij[2],thr);
if (cij < 1.0) {
- dC = Str*Stb*VLJ + (1.0-Str)*VLJ;
- if (npath == 2) {
- fpair = dC*dwij / rij;
- f[atomi][0] += delij[0]*fpair;
- f[atomi][1] += delij[1]*fpair;
- f[atomi][2] += delij[2]*fpair;
- f[atomj][0] -= delij[0]*fpair;
- f[atomj][1] -= delij[1]*fpair;
- f[atomj][2] -= delij[2]*fpair;
-
- if (vflag_atom) v_tally2_thr(atomi,atomj,fpair,delij,thr);
-
- } else if (npath == 3) {
- fpair1 = dC*dwikS*wkjS / rikS;
- fi[0] = delikS[0]*fpair1;
- fi[1] = delikS[1]*fpair1;
- fi[2] = delikS[2]*fpair1;
- fpair2 = dC*wikS*dwkjS / rkjS;
- fj[0] = deljkS[0]*fpair2;
- fj[1] = deljkS[1]*fpair2;
- fj[2] = deljkS[2]*fpair2;
-
- f[atomi][0] += fi[0];
- f[atomi][1] += fi[1];
- f[atomi][2] += fi[2];
- f[atomj][0] += fj[0];
- f[atomj][1] += fj[1];
- f[atomj][2] += fj[2];
- f[atomk][0] -= fi[0] + fj[0];
- f[atomk][1] -= fi[1] + fj[1];
- f[atomk][2] -= fi[2] + fj[2];
-
- if (vflag_atom)
- v_tally3_thr(atomi,atomj,atomk,fi,fj,delikS,deljkS,thr);
-
- } else {
- fpair1 = dC*dwikS*wkmS*wmjS / rikS;
- fi[0] = delikS[0]*fpair1;
- fi[1] = delikS[1]*fpair1;
- fi[2] = delikS[2]*fpair1;
-
- fpair2 = dC*wikS*dwkmS*wmjS / rkmS;
- fk[0] = delkmS[0]*fpair2 - fi[0];
- fk[1] = delkmS[1]*fpair2 - fi[1];
- fk[2] = delkmS[2]*fpair2 - fi[2];
-
- fpair3 = dC*wikS*wkmS*dwmjS / rmjS;
- fj[0] = deljmS[0]*fpair3;
- fj[1] = deljmS[1]*fpair3;
- fj[2] = deljmS[2]*fpair3;
-
- fm[0] = -delkmS[0]*fpair2 - fj[0];
- fm[1] = -delkmS[1]*fpair2 - fj[1];
- fm[2] = -delkmS[2]*fpair2 - fj[2];
-
- f[atomi][0] += fi[0];
- f[atomi][1] += fi[1];
- f[atomi][2] += fi[2];
- f[atomj][0] += fj[0];
- f[atomj][1] += fj[1];
- f[atomj][2] += fj[2];
- f[atomk][0] += fk[0];
- f[atomk][1] += fk[1];
- f[atomk][2] += fk[2];
- f[atomm][0] += fm[0];
- f[atomm][1] += fm[1];
- f[atomm][2] += fm[2];
-
- if (vflag_atom) {
- delimS[0] = delikS[0] + delkmS[0];
- delimS[1] = delikS[1] + delkmS[1];
- delimS[2] = delikS[2] + delkmS[2];
- v_tally4_thr(atomi,atomj,atomk,atomm,fi,fj,fk,delimS,deljmS,delkmS,thr);
- }
- }
+ dC = Str*Stb*VLJ + (1.0-Str)*VLJ;
+ if (npath == 2) {
+ fpair = dC*dwij / rij;
+ f[atomi][0] += delij[0]*fpair;
+ f[atomi][1] += delij[1]*fpair;
+ f[atomi][2] += delij[2]*fpair;
+ f[atomj][0] -= delij[0]*fpair;
+ f[atomj][1] -= delij[1]*fpair;
+ f[atomj][2] -= delij[2]*fpair;
+
+ if (vflag_atom) v_tally2_thr(atomi,atomj,fpair,delij,thr);
+
+ } else if (npath == 3) {
+ fpair1 = dC*dwikS*wkjS / rikS;
+ fi[0] = delikS[0]*fpair1;
+ fi[1] = delikS[1]*fpair1;
+ fi[2] = delikS[2]*fpair1;
+ fpair2 = dC*wikS*dwkjS / rkjS;
+ fj[0] = deljkS[0]*fpair2;
+ fj[1] = deljkS[1]*fpair2;
+ fj[2] = deljkS[2]*fpair2;
+
+ f[atomi][0] += fi[0];
+ f[atomi][1] += fi[1];
+ f[atomi][2] += fi[2];
+ f[atomj][0] += fj[0];
+ f[atomj][1] += fj[1];
+ f[atomj][2] += fj[2];
+ f[atomk][0] -= fi[0] + fj[0];
+ f[atomk][1] -= fi[1] + fj[1];
+ f[atomk][2] -= fi[2] + fj[2];
+
+ if (vflag_atom)
+ v_tally3_thr(atomi,atomj,atomk,fi,fj,delikS,deljkS,thr);
+
+ } else {
+ fpair1 = dC*dwikS*wkmS*wmjS / rikS;
+ fi[0] = delikS[0]*fpair1;
+ fi[1] = delikS[1]*fpair1;
+ fi[2] = delikS[2]*fpair1;
+
+ fpair2 = dC*wikS*dwkmS*wmjS / rkmS;
+ fk[0] = delkmS[0]*fpair2 - fi[0];
+ fk[1] = delkmS[1]*fpair2 - fi[1];
+ fk[2] = delkmS[2]*fpair2 - fi[2];
+
+ fpair3 = dC*wikS*wkmS*dwmjS / rmjS;
+ fj[0] = deljmS[0]*fpair3;
+ fj[1] = deljmS[1]*fpair3;
+ fj[2] = deljmS[2]*fpair3;
+
+ fm[0] = -delkmS[0]*fpair2 - fj[0];
+ fm[1] = -delkmS[1]*fpair2 - fj[1];
+ fm[2] = -delkmS[2]*fpair2 - fj[2];
+
+ f[atomi][0] += fi[0];
+ f[atomi][1] += fi[1];
+ f[atomi][2] += fi[2];
+ f[atomj][0] += fj[0];
+ f[atomj][1] += fj[1];
+ f[atomj][2] += fj[2];
+ f[atomk][0] += fk[0];
+ f[atomk][1] += fk[1];
+ f[atomk][2] += fk[2];
+ f[atomm][0] += fm[0];
+ f[atomm][1] += fm[1];
+ f[atomm][2] += fm[2];
+
+ if (vflag_atom) {
+ delimS[0] = delikS[0] + delkmS[0];
+ delimS[1] = delikS[1] + delkmS[1];
+ delimS[2] = delikS[2] + delkmS[2];
+ v_tally4_thr(atomi,atomj,atomk,atomm,fi,fj,fk,delimS,deljmS,delkmS,thr);
+ }
+ }
}
}
}
@@ -2292,7 +2292,7 @@ void PairAIREBOOMP::FLJ_thr(int ifrom, int ito, int evflag, int eflag,
------------------------------------------------------------------------- */
void PairAIREBOOMP::TORSION_thr(int ifrom, int ito,
- int evflag, int eflag, ThrData * const thr)
+ int evflag, int eflag, ThrData * const thr)
{
int i,j,k,l,ii,itag,jtag;
double evdwl,fpair,xtmp,ytmp,ztmp;
@@ -2338,13 +2338,13 @@ void PairAIREBOOMP::TORSION_thr(int ifrom, int ito,
jtag = tag[j];
if (itag > jtag) {
- if ((itag+jtag) % 2 == 0) continue;
+ if ((itag+jtag) % 2 == 0) continue;
} else if (itag < jtag) {
- if ((itag+jtag) % 2 == 1) continue;
+ if ((itag+jtag) % 2 == 1) continue;
} else {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
- if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
+ if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
}
jtype = map[type[j]];
@@ -2362,285 +2362,285 @@ void PairAIREBOOMP::TORSION_thr(int ifrom, int ito,
w23 = Sp(r23,rcmin[itype][jtype],rcmax[itype][jtype],dw23);
for (kk = 0; kk < REBO_numneigh[i]; kk++) {
- k = REBO_neighs_i[kk];
- ktype = map[type[k]];
- if (k == j) continue;
- del21[0] = x[i][0]-x[k][0];
- del21[1] = x[i][1]-x[k][1];
- del21[2] = x[i][2]-x[k][2];
- rsq = del21[0]*del21[0] + del21[1]*del21[1] + del21[2]*del21[2];
- r21 = sqrt(rsq);
- cos321 = - ((del21[0]*del32[0]) + (del21[1]*del32[1]) +
- (del21[2]*del32[2])) / (r21*r32);
- cos321 = MIN(cos321,1.0);
- cos321 = MAX(cos321,-1.0);
- sin321 = sqrt(1.0 - cos321*cos321);
- if (sin321 < TOL) continue;
-
- deljk[0] = del21[0]-del23[0];
- deljk[1] = del21[1]-del23[1];
- deljk[2] = del21[2]-del23[2];
- rjk2 = deljk[0]*deljk[0] + deljk[1]*deljk[1] + deljk[2]*deljk[2];
- rjk=sqrt(rjk2);
- rik2 = r21*r21;
- w21 = Sp(r21,rcmin[itype][ktype],rcmax[itype][ktype],dw21);
-
- rij = r32;
- rik = r21;
- rij2 = r32*r32;
- rik2 = r21*r21;
- costmp = 0.5*(rij2+rik2-rjk2)/rij/rik;
- tspjik = Sp2(costmp,thmin,thmax,dtsjik);
- dtsjik = -dtsjik;
-
- REBO_neighs_j = REBO_firstneigh[j];
- for (ll = 0; ll < REBO_numneigh[j]; ll++) {
- l = REBO_neighs_j[ll];
- ltype = map[type[l]];
- if (l == i || l == k) continue;
- del34[0] = x[j][0]-x[l][0];
- del34[1] = x[j][1]-x[l][1];
- del34[2] = x[j][2]-x[l][2];
- rsq = del34[0]*del34[0] + del34[1]*del34[1] + del34[2]*del34[2];
- r34 = sqrt(rsq);
- cos234 = (del32[0]*del34[0] + del32[1]*del34[1] +
- del32[2]*del34[2]) / (r32*r34);
- cos234 = MIN(cos234,1.0);
- cos234 = MAX(cos234,-1.0);
- sin234 = sqrt(1.0 - cos234*cos234);
- if (sin234 < TOL) continue;
- w34 = Sp(r34,rcmin[jtype][ltype],rcmax[jtype][ltype],dw34);
- delil[0] = del23[0] + del34[0];
- delil[1] = del23[1] + del34[1];
- delil[2] = del23[2] + del34[2];
- ril2 = delil[0]*delil[0] + delil[1]*delil[1] + delil[2]*delil[2];
- ril=sqrt(ril2);
- rjl2 = r34*r34;
-
- rjl = r34;
- rjl2 = r34*r34;
- costmp = 0.5*(rij2+rjl2-ril2)/rij/rjl;
- tspijl = Sp2(costmp,thmin,thmax,dtsijl);
- dtsijl = -dtsijl; //need minus sign
- cross321[0] = (del32[1]*del21[2])-(del32[2]*del21[1]);
- cross321[1] = (del32[2]*del21[0])-(del32[0]*del21[2]);
- cross321[2] = (del32[0]*del21[1])-(del32[1]*del21[0]);
- cross321mag = sqrt(cross321[0]*cross321[0]+
- cross321[1]*cross321[1]+
- cross321[2]*cross321[2]);
- cross234[0] = (del23[1]*del34[2])-(del23[2]*del34[1]);
- cross234[1] = (del23[2]*del34[0])-(del23[0]*del34[2]);
- cross234[2] = (del23[0]*del34[1])-(del23[1]*del34[0]);
- cross234mag = sqrt(cross234[0]*cross234[0]+
- cross234[1]*cross234[1]+
- cross234[2]*cross234[2]);
- cwnum = (cross321[0]*cross234[0]) +
- (cross321[1]*cross234[1])+(cross321[2]*cross234[2]);
- cwnom = r21*r34*r32*r32*sin321*sin234;
- cw = cwnum/cwnom;
-
- cw2 = (.5*(1.0-cw));
- ekijl = epsilonT[ktype][ltype];
- Ec = 256.0*ekijl/405.0;
- Vtors = (Ec*(pow(cw2,5.0)))-(ekijl/10.0);
-
- if (eflag) evdwl = Vtors*w21*w23*w34*(1.0-tspjik)*(1.0-tspijl);
-
- dndij[0] = (cross234[1]*del21[2])-(cross234[2]*del21[1]);
- dndij[1] = (cross234[2]*del21[0])-(cross234[0]*del21[2]);
- dndij[2] = (cross234[0]*del21[1])-(cross234[1]*del21[0]);
-
- tmpvec[0] = (del34[1]*cross321[2])-(del34[2]*cross321[1]);
- tmpvec[1] = (del34[2]*cross321[0])-(del34[0]*cross321[2]);
- tmpvec[2] = (del34[0]*cross321[1])-(del34[1]*cross321[0]);
-
- dndij[0] = dndij[0]+tmpvec[0];
- dndij[1] = dndij[1]+tmpvec[1];
- dndij[2] = dndij[2]+tmpvec[2];
-
- dndik[0] = (del23[1]*cross234[2])-(del23[2]*cross234[1]);
- dndik[1] = (del23[2]*cross234[0])-(del23[0]*cross234[2]);
- dndik[2] = (del23[0]*cross234[1])-(del23[1]*cross234[0]);
-
- dndjl[0] = (cross321[1]*del23[2])-(cross321[2]*del23[1]);
- dndjl[1] = (cross321[2]*del23[0])-(cross321[0]*del23[2]);
- dndjl[2] = (cross321[0]*del23[1])-(cross321[1]*del23[0]);
-
- dcidij = ((r23*r23)-(r21*r21)+(rjk*rjk))/(2.0*r23*r23*r21);
- dcidik = ((r21*r21)-(r23*r23)+(rjk*rjk))/(2.0*r23*r21*r21);
- dcidjk = (-rjk)/(r23*r21);
- dcjdji = ((r23*r23)-(r34*r34)+(ril*ril))/(2.0*r23*r23*r34);
- dcjdjl = ((r34*r34)-(r23*r23)+(ril*ril))/(2.0*r23*r34*r34);
- dcjdil = (-ril)/(r23*r34);
-
- dsidij = (-cos321/sin321)*dcidij;
- dsidik = (-cos321/sin321)*dcidik;
- dsidjk = (-cos321/sin321)*dcidjk;
-
- dsjdji = (-cos234/sin234)*dcjdji;
- dsjdjl = (-cos234/sin234)*dcjdjl;
- dsjdil = (-cos234/sin234)*dcjdil;
-
- dxidij = (r21*sin321)+(r23*r21*dsidij);
- dxidik = (r23*sin321)+(r23*r21*dsidik);
- dxidjk = (r23*r21*dsidjk);
-
- dxjdji = (r34*sin234)+(r23*r34*dsjdji);
- dxjdjl = (r23*sin234)+(r23*r34*dsjdjl);
- dxjdil = (r23*r34*dsjdil);
-
- ddndij = (dxidij*cross234mag)+(cross321mag*dxjdji);
- ddndik = dxidik*cross234mag;
- ddndjk = dxidjk*cross234mag;
- ddndjl = cross321mag*dxjdjl;
- ddndil = cross321mag*dxjdil;
- dcwddn = -cwnum/(cwnom*cwnom);
- dcwdn = 1.0/cwnom;
- dvpdcw = (-1.0)*Ec*(-.5)*5.0*pow(cw2,4.0) *
- w23*w21*w34*(1.0-tspjik)*(1.0-tspijl);
-
- Ftmp[0] = dvpdcw*((dcwdn*dndij[0])+(dcwddn*ddndij*del23[0]/r23));
- Ftmp[1] = dvpdcw*((dcwdn*dndij[1])+(dcwddn*ddndij*del23[1]/r23));
- Ftmp[2] = dvpdcw*((dcwdn*dndij[2])+(dcwddn*ddndij*del23[2]/r23));
- fi[0] = Ftmp[0];
- fi[1] = Ftmp[1];
- fi[2] = Ftmp[2];
- fj[0] = -Ftmp[0];
- fj[1] = -Ftmp[1];
- fj[2] = -Ftmp[2];
-
- Ftmp[0] = dvpdcw*((dcwdn*dndik[0])+(dcwddn*ddndik*del21[0]/r21));
- Ftmp[1] = dvpdcw*((dcwdn*dndik[1])+(dcwddn*ddndik*del21[1]/r21));
- Ftmp[2] = dvpdcw*((dcwdn*dndik[2])+(dcwddn*ddndik*del21[2]/r21));
- fi[0] += Ftmp[0];
- fi[1] += Ftmp[1];
- fi[2] += Ftmp[2];
- fk[0] = -Ftmp[0];
- fk[1] = -Ftmp[1];
- fk[2] = -Ftmp[2];
-
- Ftmp[0] = (dvpdcw*dcwddn*ddndjk*deljk[0])/rjk;
- Ftmp[1] = (dvpdcw*dcwddn*ddndjk*deljk[1])/rjk;
- Ftmp[2] = (dvpdcw*dcwddn*ddndjk*deljk[2])/rjk;
- fj[0] += Ftmp[0];
- fj[1] += Ftmp[1];
- fj[2] += Ftmp[2];
- fk[0] -= Ftmp[0];
- fk[1] -= Ftmp[1];
- fk[2] -= Ftmp[2];
-
- Ftmp[0] = dvpdcw*((dcwdn*dndjl[0])+(dcwddn*ddndjl*del34[0]/r34));
- Ftmp[1] = dvpdcw*((dcwdn*dndjl[1])+(dcwddn*ddndjl*del34[1]/r34));
- Ftmp[2] = dvpdcw*((dcwdn*dndjl[2])+(dcwddn*ddndjl*del34[2]/r34));
- fj[0] += Ftmp[0];
- fj[1] += Ftmp[1];
- fj[2] += Ftmp[2];
- fl[0] = -Ftmp[0];
- fl[1] = -Ftmp[1];
- fl[2] = -Ftmp[2];
-
- Ftmp[0] = (dvpdcw*dcwddn*ddndil*delil[0])/ril;
- Ftmp[1] = (dvpdcw*dcwddn*ddndil*delil[1])/ril;
- Ftmp[2] = (dvpdcw*dcwddn*ddndil*delil[2])/ril;
- fi[0] += Ftmp[0];
- fi[1] += Ftmp[1];
- fi[2] += Ftmp[2];
- fl[0] -= Ftmp[0];
- fl[1] -= Ftmp[1];
- fl[2] -= Ftmp[2];
-
- // coordination forces
-
- fpair = Vtors*dw21*w23*w34*(1.0-tspjik)*(1.0-tspijl) / r21;
- fi[0] -= del21[0]*fpair;
- fi[1] -= del21[1]*fpair;
- fi[2] -= del21[2]*fpair;
- fk[0] += del21[0]*fpair;
- fk[1] += del21[1]*fpair;
- fk[2] += del21[2]*fpair;
-
- fpair = Vtors*w21*dw23*w34*(1.0-tspjik)*(1.0-tspijl) / r23;
- fi[0] -= del23[0]*fpair;
- fi[1] -= del23[1]*fpair;
- fi[2] -= del23[2]*fpair;
- fj[0] += del23[0]*fpair;
- fj[1] += del23[1]*fpair;
- fj[2] += del23[2]*fpair;
-
- fpair = Vtors*w21*w23*dw34*(1.0-tspjik)*(1.0-tspijl) / r34;
- fj[0] -= del34[0]*fpair;
- fj[1] -= del34[1]*fpair;
- fj[2] -= del34[2]*fpair;
- fl[0] += del34[0]*fpair;
- fl[1] += del34[1]*fpair;
- fl[2] += del34[2]*fpair;
-
- // additional cut off function forces
-
- fcpc = -Vtors*w21*w23*w34*dtsjik*(1.0-tspijl);
- fpair = fcpc*dcidij/rij;
- fi[0] += fpair*del23[0];
- fi[1] += fpair*del23[1];
- fi[2] += fpair*del23[2];
- fj[0] -= fpair*del23[0];
- fj[1] -= fpair*del23[1];
- fj[2] -= fpair*del23[2];
-
- fpair = fcpc*dcidik/rik;
- fi[0] += fpair*del21[0];
- fi[1] += fpair*del21[1];
- fi[2] += fpair*del21[2];
- fk[0] -= fpair*del21[0];
- fk[1] -= fpair*del21[1];
- fk[2] -= fpair*del21[2];
-
- fpair = fcpc*dcidjk/rjk;
- fj[0] += fpair*deljk[0];
- fj[1] += fpair*deljk[1];
- fj[2] += fpair*deljk[2];
- fk[0] -= fpair*deljk[0];
- fk[1] -= fpair*deljk[1];
- fk[2] -= fpair*deljk[2];
-
- fcpc = -Vtors*w21*w23*w34*(1.0-tspjik)*dtsijl;
- fpair = fcpc*dcjdji/rij;
- fi[0] += fpair*del23[0];
- fi[1] += fpair*del23[1];
- fi[2] += fpair*del23[2];
- fj[0] -= fpair*del23[0];
- fj[1] -= fpair*del23[1];
- fj[2] -= fpair*del23[2];
-
- fpair = fcpc*dcjdjl/rjl;
- fj[0] += fpair*del34[0];
- fj[1] += fpair*del34[1];
- fj[2] += fpair*del34[2];
- fl[0] -= fpair*del34[0];
- fl[1] -= fpair*del34[1];
- fl[2] -= fpair*del34[2];
-
- fpair = fcpc*dcjdil/ril;
- fi[0] += fpair*delil[0];
- fi[1] += fpair*delil[1];
- fi[2] += fpair*delil[2];
- fl[0] -= fpair*delil[0];
- fl[1] -= fpair*delil[1];
- fl[2] -= fpair*delil[2];
-
- // sum per-atom forces into atom force array
-
- f[i][0] += fi[0]; f[i][1] += fi[1]; f[i][2] += fi[2];
- f[j][0] += fj[0]; f[j][1] += fj[1]; f[j][2] += fj[2];
- f[k][0] += fk[0]; f[k][1] += fk[1]; f[k][2] += fk[2];
- f[l][0] += fl[0]; f[l][1] += fl[1]; f[l][2] += fl[2];
-
- if (evflag) {
- delkl[0] = delil[0] - del21[0];
- delkl[1] = delil[1] - del21[1];
- delkl[2] = delil[2] - del21[2];
- ev_tally4_thr(this,i,j,k,l,evdwl,fi,fj,fk,delil,del34,delkl,thr);
- }
- }
+ k = REBO_neighs_i[kk];
+ ktype = map[type[k]];
+ if (k == j) continue;
+ del21[0] = x[i][0]-x[k][0];
+ del21[1] = x[i][1]-x[k][1];
+ del21[2] = x[i][2]-x[k][2];
+ rsq = del21[0]*del21[0] + del21[1]*del21[1] + del21[2]*del21[2];
+ r21 = sqrt(rsq);
+ cos321 = - ((del21[0]*del32[0]) + (del21[1]*del32[1]) +
+ (del21[2]*del32[2])) / (r21*r32);
+ cos321 = MIN(cos321,1.0);
+ cos321 = MAX(cos321,-1.0);
+ sin321 = sqrt(1.0 - cos321*cos321);
+ if (sin321 < TOL) continue;
+
+ deljk[0] = del21[0]-del23[0];
+ deljk[1] = del21[1]-del23[1];
+ deljk[2] = del21[2]-del23[2];
+ rjk2 = deljk[0]*deljk[0] + deljk[1]*deljk[1] + deljk[2]*deljk[2];
+ rjk=sqrt(rjk2);
+ rik2 = r21*r21;
+ w21 = Sp(r21,rcmin[itype][ktype],rcmax[itype][ktype],dw21);
+
+ rij = r32;
+ rik = r21;
+ rij2 = r32*r32;
+ rik2 = r21*r21;
+ costmp = 0.5*(rij2+rik2-rjk2)/rij/rik;
+ tspjik = Sp2(costmp,thmin,thmax,dtsjik);
+ dtsjik = -dtsjik;
+
+ REBO_neighs_j = REBO_firstneigh[j];
+ for (ll = 0; ll < REBO_numneigh[j]; ll++) {
+ l = REBO_neighs_j[ll];
+ ltype = map[type[l]];
+ if (l == i || l == k) continue;
+ del34[0] = x[j][0]-x[l][0];
+ del34[1] = x[j][1]-x[l][1];
+ del34[2] = x[j][2]-x[l][2];
+ rsq = del34[0]*del34[0] + del34[1]*del34[1] + del34[2]*del34[2];
+ r34 = sqrt(rsq);
+ cos234 = (del32[0]*del34[0] + del32[1]*del34[1] +
+ del32[2]*del34[2]) / (r32*r34);
+ cos234 = MIN(cos234,1.0);
+ cos234 = MAX(cos234,-1.0);
+ sin234 = sqrt(1.0 - cos234*cos234);
+ if (sin234 < TOL) continue;
+ w34 = Sp(r34,rcmin[jtype][ltype],rcmax[jtype][ltype],dw34);
+ delil[0] = del23[0] + del34[0];
+ delil[1] = del23[1] + del34[1];
+ delil[2] = del23[2] + del34[2];
+ ril2 = delil[0]*delil[0] + delil[1]*delil[1] + delil[2]*delil[2];
+ ril=sqrt(ril2);
+ rjl2 = r34*r34;
+
+ rjl = r34;
+ rjl2 = r34*r34;
+ costmp = 0.5*(rij2+rjl2-ril2)/rij/rjl;
+ tspijl = Sp2(costmp,thmin,thmax,dtsijl);
+ dtsijl = -dtsijl; //need minus sign
+ cross321[0] = (del32[1]*del21[2])-(del32[2]*del21[1]);
+ cross321[1] = (del32[2]*del21[0])-(del32[0]*del21[2]);
+ cross321[2] = (del32[0]*del21[1])-(del32[1]*del21[0]);
+ cross321mag = sqrt(cross321[0]*cross321[0]+
+ cross321[1]*cross321[1]+
+ cross321[2]*cross321[2]);
+ cross234[0] = (del23[1]*del34[2])-(del23[2]*del34[1]);
+ cross234[1] = (del23[2]*del34[0])-(del23[0]*del34[2]);
+ cross234[2] = (del23[0]*del34[1])-(del23[1]*del34[0]);
+ cross234mag = sqrt(cross234[0]*cross234[0]+
+ cross234[1]*cross234[1]+
+ cross234[2]*cross234[2]);
+ cwnum = (cross321[0]*cross234[0]) +
+ (cross321[1]*cross234[1])+(cross321[2]*cross234[2]);
+ cwnom = r21*r34*r32*r32*sin321*sin234;
+ cw = cwnum/cwnom;
+
+ cw2 = (.5*(1.0-cw));
+ ekijl = epsilonT[ktype][ltype];
+ Ec = 256.0*ekijl/405.0;
+ Vtors = (Ec*(pow(cw2,5.0)))-(ekijl/10.0);
+
+ if (eflag) evdwl = Vtors*w21*w23*w34*(1.0-tspjik)*(1.0-tspijl);
+
+ dndij[0] = (cross234[1]*del21[2])-(cross234[2]*del21[1]);
+ dndij[1] = (cross234[2]*del21[0])-(cross234[0]*del21[2]);
+ dndij[2] = (cross234[0]*del21[1])-(cross234[1]*del21[0]);
+
+ tmpvec[0] = (del34[1]*cross321[2])-(del34[2]*cross321[1]);
+ tmpvec[1] = (del34[2]*cross321[0])-(del34[0]*cross321[2]);
+ tmpvec[2] = (del34[0]*cross321[1])-(del34[1]*cross321[0]);
+
+ dndij[0] = dndij[0]+tmpvec[0];
+ dndij[1] = dndij[1]+tmpvec[1];
+ dndij[2] = dndij[2]+tmpvec[2];
+
+ dndik[0] = (del23[1]*cross234[2])-(del23[2]*cross234[1]);
+ dndik[1] = (del23[2]*cross234[0])-(del23[0]*cross234[2]);
+ dndik[2] = (del23[0]*cross234[1])-(del23[1]*cross234[0]);
+
+ dndjl[0] = (cross321[1]*del23[2])-(cross321[2]*del23[1]);
+ dndjl[1] = (cross321[2]*del23[0])-(cross321[0]*del23[2]);
+ dndjl[2] = (cross321[0]*del23[1])-(cross321[1]*del23[0]);
+
+ dcidij = ((r23*r23)-(r21*r21)+(rjk*rjk))/(2.0*r23*r23*r21);
+ dcidik = ((r21*r21)-(r23*r23)+(rjk*rjk))/(2.0*r23*r21*r21);
+ dcidjk = (-rjk)/(r23*r21);
+ dcjdji = ((r23*r23)-(r34*r34)+(ril*ril))/(2.0*r23*r23*r34);
+ dcjdjl = ((r34*r34)-(r23*r23)+(ril*ril))/(2.0*r23*r34*r34);
+ dcjdil = (-ril)/(r23*r34);
+
+ dsidij = (-cos321/sin321)*dcidij;
+ dsidik = (-cos321/sin321)*dcidik;
+ dsidjk = (-cos321/sin321)*dcidjk;
+
+ dsjdji = (-cos234/sin234)*dcjdji;
+ dsjdjl = (-cos234/sin234)*dcjdjl;
+ dsjdil = (-cos234/sin234)*dcjdil;
+
+ dxidij = (r21*sin321)+(r23*r21*dsidij);
+ dxidik = (r23*sin321)+(r23*r21*dsidik);
+ dxidjk = (r23*r21*dsidjk);
+
+ dxjdji = (r34*sin234)+(r23*r34*dsjdji);
+ dxjdjl = (r23*sin234)+(r23*r34*dsjdjl);
+ dxjdil = (r23*r34*dsjdil);
+
+ ddndij = (dxidij*cross234mag)+(cross321mag*dxjdji);
+ ddndik = dxidik*cross234mag;
+ ddndjk = dxidjk*cross234mag;
+ ddndjl = cross321mag*dxjdjl;
+ ddndil = cross321mag*dxjdil;
+ dcwddn = -cwnum/(cwnom*cwnom);
+ dcwdn = 1.0/cwnom;
+ dvpdcw = (-1.0)*Ec*(-.5)*5.0*pow(cw2,4.0) *
+ w23*w21*w34*(1.0-tspjik)*(1.0-tspijl);
+
+ Ftmp[0] = dvpdcw*((dcwdn*dndij[0])+(dcwddn*ddndij*del23[0]/r23));
+ Ftmp[1] = dvpdcw*((dcwdn*dndij[1])+(dcwddn*ddndij*del23[1]/r23));
+ Ftmp[2] = dvpdcw*((dcwdn*dndij[2])+(dcwddn*ddndij*del23[2]/r23));
+ fi[0] = Ftmp[0];
+ fi[1] = Ftmp[1];
+ fi[2] = Ftmp[2];
+ fj[0] = -Ftmp[0];
+ fj[1] = -Ftmp[1];
+ fj[2] = -Ftmp[2];
+
+ Ftmp[0] = dvpdcw*((dcwdn*dndik[0])+(dcwddn*ddndik*del21[0]/r21));
+ Ftmp[1] = dvpdcw*((dcwdn*dndik[1])+(dcwddn*ddndik*del21[1]/r21));
+ Ftmp[2] = dvpdcw*((dcwdn*dndik[2])+(dcwddn*ddndik*del21[2]/r21));
+ fi[0] += Ftmp[0];
+ fi[1] += Ftmp[1];
+ fi[2] += Ftmp[2];
+ fk[0] = -Ftmp[0];
+ fk[1] = -Ftmp[1];
+ fk[2] = -Ftmp[2];
+
+ Ftmp[0] = (dvpdcw*dcwddn*ddndjk*deljk[0])/rjk;
+ Ftmp[1] = (dvpdcw*dcwddn*ddndjk*deljk[1])/rjk;
+ Ftmp[2] = (dvpdcw*dcwddn*ddndjk*deljk[2])/rjk;
+ fj[0] += Ftmp[0];
+ fj[1] += Ftmp[1];
+ fj[2] += Ftmp[2];
+ fk[0] -= Ftmp[0];
+ fk[1] -= Ftmp[1];
+ fk[2] -= Ftmp[2];
+
+ Ftmp[0] = dvpdcw*((dcwdn*dndjl[0])+(dcwddn*ddndjl*del34[0]/r34));
+ Ftmp[1] = dvpdcw*((dcwdn*dndjl[1])+(dcwddn*ddndjl*del34[1]/r34));
+ Ftmp[2] = dvpdcw*((dcwdn*dndjl[2])+(dcwddn*ddndjl*del34[2]/r34));
+ fj[0] += Ftmp[0];
+ fj[1] += Ftmp[1];
+ fj[2] += Ftmp[2];
+ fl[0] = -Ftmp[0];
+ fl[1] = -Ftmp[1];
+ fl[2] = -Ftmp[2];
+
+ Ftmp[0] = (dvpdcw*dcwddn*ddndil*delil[0])/ril;
+ Ftmp[1] = (dvpdcw*dcwddn*ddndil*delil[1])/ril;
+ Ftmp[2] = (dvpdcw*dcwddn*ddndil*delil[2])/ril;
+ fi[0] += Ftmp[0];
+ fi[1] += Ftmp[1];
+ fi[2] += Ftmp[2];
+ fl[0] -= Ftmp[0];
+ fl[1] -= Ftmp[1];
+ fl[2] -= Ftmp[2];
+
+ // coordination forces
+
+ fpair = Vtors*dw21*w23*w34*(1.0-tspjik)*(1.0-tspijl) / r21;
+ fi[0] -= del21[0]*fpair;
+ fi[1] -= del21[1]*fpair;
+ fi[2] -= del21[2]*fpair;
+ fk[0] += del21[0]*fpair;
+ fk[1] += del21[1]*fpair;
+ fk[2] += del21[2]*fpair;
+
+ fpair = Vtors*w21*dw23*w34*(1.0-tspjik)*(1.0-tspijl) / r23;
+ fi[0] -= del23[0]*fpair;
+ fi[1] -= del23[1]*fpair;
+ fi[2] -= del23[2]*fpair;
+ fj[0] += del23[0]*fpair;
+ fj[1] += del23[1]*fpair;
+ fj[2] += del23[2]*fpair;
+
+ fpair = Vtors*w21*w23*dw34*(1.0-tspjik)*(1.0-tspijl) / r34;
+ fj[0] -= del34[0]*fpair;
+ fj[1] -= del34[1]*fpair;
+ fj[2] -= del34[2]*fpair;
+ fl[0] += del34[0]*fpair;
+ fl[1] += del34[1]*fpair;
+ fl[2] += del34[2]*fpair;
+
+ // additional cut off function forces
+
+ fcpc = -Vtors*w21*w23*w34*dtsjik*(1.0-tspijl);
+ fpair = fcpc*dcidij/rij;
+ fi[0] += fpair*del23[0];
+ fi[1] += fpair*del23[1];
+ fi[2] += fpair*del23[2];
+ fj[0] -= fpair*del23[0];
+ fj[1] -= fpair*del23[1];
+ fj[2] -= fpair*del23[2];
+
+ fpair = fcpc*dcidik/rik;
+ fi[0] += fpair*del21[0];
+ fi[1] += fpair*del21[1];
+ fi[2] += fpair*del21[2];
+ fk[0] -= fpair*del21[0];
+ fk[1] -= fpair*del21[1];
+ fk[2] -= fpair*del21[2];
+
+ fpair = fcpc*dcidjk/rjk;
+ fj[0] += fpair*deljk[0];
+ fj[1] += fpair*deljk[1];
+ fj[2] += fpair*deljk[2];
+ fk[0] -= fpair*deljk[0];
+ fk[1] -= fpair*deljk[1];
+ fk[2] -= fpair*deljk[2];
+
+ fcpc = -Vtors*w21*w23*w34*(1.0-tspjik)*dtsijl;
+ fpair = fcpc*dcjdji/rij;
+ fi[0] += fpair*del23[0];
+ fi[1] += fpair*del23[1];
+ fi[2] += fpair*del23[2];
+ fj[0] -= fpair*del23[0];
+ fj[1] -= fpair*del23[1];
+ fj[2] -= fpair*del23[2];
+
+ fpair = fcpc*dcjdjl/rjl;
+ fj[0] += fpair*del34[0];
+ fj[1] += fpair*del34[1];
+ fj[2] += fpair*del34[2];
+ fl[0] -= fpair*del34[0];
+ fl[1] -= fpair*del34[1];
+ fl[2] -= fpair*del34[2];
+
+ fpair = fcpc*dcjdil/ril;
+ fi[0] += fpair*delil[0];
+ fi[1] += fpair*delil[1];
+ fi[2] += fpair*delil[2];
+ fl[0] -= fpair*delil[0];
+ fl[1] -= fpair*delil[1];
+ fl[2] -= fpair*delil[2];
+
+ // sum per-atom forces into atom force array
+
+ f[i][0] += fi[0]; f[i][1] += fi[1]; f[i][2] += fi[2];
+ f[j][0] += fj[0]; f[j][1] += fj[1]; f[j][2] += fj[2];
+ f[k][0] += fk[0]; f[k][1] += fk[1]; f[k][2] += fk[2];
+ f[l][0] += fl[0]; f[l][1] += fl[1]; f[l][2] += fl[2];
+
+ if (evflag) {
+ delkl[0] = delil[0] - del21[0];
+ delkl[1] = delil[1] - del21[1];
+ delkl[2] = delil[2] - del21[2];
+ ev_tally4_thr(this,i,j,k,l,evdwl,fi,fj,fk,delil,del34,delkl,thr);
+ }
+ }
}
}
}
@@ -2664,7 +2664,7 @@ void PairAIREBOOMP::REBO_neigh_thr()
memory->destroy(nH);
memory->create(REBO_numneigh,maxlocal,"AIREBO:numneigh");
REBO_firstneigh = (int **) memory->smalloc(maxlocal*sizeof(int *),
- "AIREBO:firstneigh");
+ "AIREBO:firstneigh");
memory->create(nC,maxlocal,"AIREBO:nC");
memory->create(nH,maxlocal,"AIREBO:nH");
}
@@ -2712,9 +2712,9 @@ void PairAIREBOOMP::REBO_neigh_thr()
#pragma omp critical
#endif
if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage += nthreads;
- if (npage >= maxpage) add_pages(nthreads);
+ npnt = 0;
+ npage += nthreads;
+ if (npage >= maxpage) add_pages(nthreads);
}
neighptr = &(pages[npage][npnt]);
n = 0;
@@ -2728,21 +2728,21 @@ void PairAIREBOOMP::REBO_neigh_thr()
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
- j = jlist[jj];
- j &= NEIGHMASK;
- jtype = map[type[j]];
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq < rcmaxsq[itype][jtype]) {
- neighptr[n++] = j;
- if (jtype == 0)
- nC[i] += Sp(sqrt(rsq),rcmin[itype][jtype],rcmax[itype][jtype],dS);
- else
- nH[i] += Sp(sqrt(rsq),rcmin[itype][jtype],rcmax[itype][jtype],dS);
- }
+ j = jlist[jj];
+ j &= NEIGHMASK;
+ jtype = map[type[j]];
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq < rcmaxsq[itype][jtype]) {
+ neighptr[n++] = j;
+ if (jtype == 0)
+ nC[i] += Sp(sqrt(rsq),rcmin[itype][jtype],rcmax[itype][jtype],dS);
+ else
+ nH[i] += Sp(sqrt(rsq),rcmin[itype][jtype],rcmax[itype][jtype],dS);
+ }
}
REBO_firstneigh[i] = neighptr;
@@ -2750,7 +2750,7 @@ void PairAIREBOOMP::REBO_neigh_thr()
npnt += n;
if (npnt >= pgsize)
- error->one(FLERR,"REBO list overflow, boost neigh_modify one or page");
+ error->one(FLERR,"REBO list overflow, boost neigh_modify one or page");
}
}
}
diff --git a/src/USER-OMP/pair_airebo_omp.h b/src/USER-OMP/pair_airebo_omp.h
index 9ba598fa8fe60f7e89aeea04dcfe6483e5dddd91..03bc5e5f8ce6ef85b70aca3004ba57cc29630a15 100644
--- a/src/USER-OMP/pair_airebo_omp.h
+++ b/src/USER-OMP/pair_airebo_omp.h
@@ -34,15 +34,15 @@ class PairAIREBOOMP : public PairAIREBO, public ThrOMP {
protected:
double bondorder_thr(int i, int j, double rij[3], double rijmag,
- double VA, int vflag_atom, ThrData * const thr);
+ double VA, int vflag_atom, ThrData * const thr);
double bondorderLJ_thr(int i, int j, double rij[3], double rijmag,
- double VA, double rij0[3], double rijmag0,
- int vflag_atom, ThrData * const thr);
+ double VA, double rij0[3], double rijmag0,
+ int vflag_atom, ThrData * const thr);
void FREBO_thr(int ifrom, int ito, int evflag, int eflag,
- int vflag_atom, ThrData * const thr);
+ int vflag_atom, ThrData * const thr);
void FLJ_thr(int ifrom, int ito, int evflag, int eflag,
- int vflag_atom, ThrData * const thr);
+ int vflag_atom, ThrData * const thr);
void TORSION_thr(int ifrom, int ito, int evflag, int eflag, ThrData * const thr);
void REBO_neigh_thr();
};
diff --git a/src/USER-OMP/pair_beck_omp.cpp b/src/USER-OMP/pair_beck_omp.cpp
index 231aad039073fa1b69cabae92fbf444fc0418227..9bec6c0db2bd2c83f87e687afa584f9932fb8f68 100644
--- a/src/USER-OMP/pair_beck_omp.cpp
+++ b/src/USER-OMP/pair_beck_omp.cpp
@@ -56,11 +56,11 @@ void PairBeckOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -121,7 +121,7 @@ void PairBeckOMP::eval(int iifrom, int iito, ThrData * const thr)
if (rsq < cutsq[itype][jtype]) {
r = sqrt(rsq);
- r5 = rsq*rsq*r;
+ r5 = rsq*rsq*r;
aaij = aa[itype][jtype];
alphaij = alpha[itype][jtype];
betaij = beta[itype][jtype];
@@ -129,31 +129,31 @@ void PairBeckOMP::eval(int iifrom, int iito, ThrData * const thr)
term2 = 1.0/pow(term1,5.0);
term3 = 21.672 + 30.0*aaij*aaij + 6.0*rsq;
term4 = alphaij + r5*betaij;
- term5 = alphaij + 6.0*r5*betaij;
+ term5 = alphaij + 6.0*r5*betaij;
rinv = 1.0/r;
- force_beck = AA[itype][jtype]*exp(-1.0*r*term4)*term5;
- force_beck -= BB[itype][jtype]*r*term2*term3;
-
- fpair = factor_lj*force_beck*rinv;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (EFLAG) {
+ force_beck = AA[itype][jtype]*exp(-1.0*r*term4)*term5;
+ force_beck -= BB[itype][jtype]*r*term2*term3;
+
+ fpair = factor_lj*force_beck*rinv;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (EFLAG) {
term6 = 1.0/pow(term1,3.0);
term1inv = 1.0/term1;
evdwl = AA[itype][jtype]*exp(-1.0*r*term4);
evdwl -= BB[itype][jtype]*term6*(1.0+(2.709+3.0*aaij*aaij)*term1inv);
- }
+ }
- if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
- evdwl,0.0,fpair,delx,dely,delz,thr);
+ if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
+ evdwl,0.0,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_beck_omp.h b/src/USER-OMP/pair_beck_omp.h
index f079ff5ecb1f4cb8ece5f1c687c80132e89c5357..18a4401bbc457d115d9a8f7e9d222737cd55816f 100644
--- a/src/USER-OMP/pair_beck_omp.h
+++ b/src/USER-OMP/pair_beck_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_born_coul_long_omp.cpp b/src/USER-OMP/pair_born_coul_long_omp.cpp
index 73bf7e066bc73d6b50b5e1c19e536d062b46e013..f627f19bac5f01ee1e07c68c1063950ac7abc971 100644
--- a/src/USER-OMP/pair_born_coul_long_omp.cpp
+++ b/src/USER-OMP/pair_born_coul_long_omp.cpp
@@ -64,11 +64,11 @@ void PairBornCoulLongOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -133,51 +133,51 @@ void PairBornCoulLongOMP::eval(int iifrom, int iito, ThrData * const thr)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- r = sqrt(rsq);
-
- if (rsq < cut_coulsq) {
- grij = g_ewald * r;
- expm2 = exp(-grij*grij);
- t = 1.0 / (1.0 + EWALD_P*grij);
- erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
- prefactor = qqrd2e * qtmp*q[j]/r;
- forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
- if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
- } else forcecoul = 0.0;
-
- if (rsq < cut_ljsq[itype][jtype]) {
- r6inv = r2inv*r2inv*r2inv;
- rexp = exp((sigma[itype][jtype]-r)*rhoinv[itype][jtype]);
- forceborn = born1[itype][jtype]*r*rexp - born2[itype][jtype]*r6inv
- + born3[itype][jtype]*r2inv*r6inv;
- } else forceborn = 0.0;
-
- fpair = (forcecoul + factor_lj*forceborn)*r2inv;
-
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (EFLAG) {
- if (rsq < cut_coulsq) {
- ecoul = prefactor*erfc;
- if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
- } else ecoul = 0.0;
- if (rsq < cut_ljsq[itype][jtype]) {
- evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv
- + d[itype][jtype]*r6inv*r2inv - offset[itype][jtype];
- evdwl *= factor_lj;
- } else evdwl = 0.0;
- }
-
- if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
- evdwl,ecoul,fpair,delx,dely,delz,thr);
+ r2inv = 1.0/rsq;
+ r = sqrt(rsq);
+
+ if (rsq < cut_coulsq) {
+ grij = g_ewald * r;
+ expm2 = exp(-grij*grij);
+ t = 1.0 / (1.0 + EWALD_P*grij);
+ erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
+ prefactor = qqrd2e * qtmp*q[j]/r;
+ forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
+ if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
+ } else forcecoul = 0.0;
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ r6inv = r2inv*r2inv*r2inv;
+ rexp = exp((sigma[itype][jtype]-r)*rhoinv[itype][jtype]);
+ forceborn = born1[itype][jtype]*r*rexp - born2[itype][jtype]*r6inv
+ + born3[itype][jtype]*r2inv*r6inv;
+ } else forceborn = 0.0;
+
+ fpair = (forcecoul + factor_lj*forceborn)*r2inv;
+
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (EFLAG) {
+ if (rsq < cut_coulsq) {
+ ecoul = prefactor*erfc;
+ if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
+ } else ecoul = 0.0;
+ if (rsq < cut_ljsq[itype][jtype]) {
+ evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv
+ + d[itype][jtype]*r6inv*r2inv - offset[itype][jtype];
+ evdwl *= factor_lj;
+ } else evdwl = 0.0;
+ }
+
+ if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
+ evdwl,ecoul,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_born_coul_long_omp.h b/src/USER-OMP/pair_born_coul_long_omp.h
index 3271c566a48361e5692aa17f6df5dab67b42f24b..bdf81e514e9e0e3b7375cfebbd3d3416240118b7 100644
--- a/src/USER-OMP/pair_born_coul_long_omp.h
+++ b/src/USER-OMP/pair_born_coul_long_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_born_coul_wolf_omp.cpp b/src/USER-OMP/pair_born_coul_wolf_omp.cpp
index c1ec917a2b3e0ee35cac12b2444c02738fa8e2bc..35e0ac7443be72857a577b57c978001e660f6b51 100644
--- a/src/USER-OMP/pair_born_coul_wolf_omp.cpp
+++ b/src/USER-OMP/pair_born_coul_wolf_omp.cpp
@@ -58,11 +58,11 @@ void PairBornCoulWolfOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -100,10 +100,10 @@ void PairBornCoulWolfOMP::eval(int iifrom, int iito, ThrData * const thr)
// self and shifted coulombic energy
- e_self = v_sh = 0.0;
+ e_self = v_sh = 0.0;
e_shift = erfc(alf*cut_coul)/cut_coul;
- f_shift = -(e_shift+ 2.0*alf/MY_PIS * exp(-alf*alf*cut_coul*cut_coul)) /
- cut_coul;
+ f_shift = -(e_shift+ 2.0*alf/MY_PIS * exp(-alf*alf*cut_coul*cut_coul)) /
+ cut_coul;
ilist = list->ilist;
numneigh = list->numneigh;
@@ -140,51 +140,51 @@ void PairBornCoulWolfOMP::eval(int iifrom, int iito, ThrData * const thr)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- r = sqrt(rsq);
+ r2inv = 1.0/rsq;
+ r = sqrt(rsq);
- if (rsq < cut_coulsq) {
+ if (rsq < cut_coulsq) {
prefactor = qqrd2e*qtmp*q[j]/r;
- erfcc = erfc(alf*r);
+ erfcc = erfc(alf*r);
erfcd = exp(-alf*alf*r*r);
- v_sh = (erfcc - e_shift*r) * prefactor;
+ v_sh = (erfcc - e_shift*r) * prefactor;
dvdrr = (erfcc/rsq + 2.0*alf/MY_PIS * erfcd/r) + f_shift;
forcecoul = dvdrr*rsq*prefactor;
- if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
- } else forcecoul = 0.0;
-
- if (rsq < cut_ljsq[itype][jtype]) {
- r6inv = r2inv*r2inv*r2inv;
- rexp = exp((sigma[itype][jtype]-r)*rhoinv[itype][jtype]);
- forceborn = born1[itype][jtype]*r*rexp - born2[itype][jtype]*r6inv
- + born3[itype][jtype]*r2inv*r6inv;
- } else forceborn = 0.0;
-
- fpair = (forcecoul + factor_lj*forceborn)*r2inv;
-
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (EFLAG) {
- if (rsq < cut_coulsq) {
- ecoul = v_sh;
- if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
- } else ecoul = 0.0;
- if (rsq < cut_ljsq[itype][jtype]) {
- evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv +
- d[itype][jtype]*r6inv*r2inv - offset[itype][jtype];
- evdwl *= factor_lj;
- } else evdwl = 0.0;
- }
-
- if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
- evdwl,ecoul,fpair,delx,dely,delz,thr);
+ if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
+ } else forcecoul = 0.0;
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ r6inv = r2inv*r2inv*r2inv;
+ rexp = exp((sigma[itype][jtype]-r)*rhoinv[itype][jtype]);
+ forceborn = born1[itype][jtype]*r*rexp - born2[itype][jtype]*r6inv
+ + born3[itype][jtype]*r2inv*r6inv;
+ } else forceborn = 0.0;
+
+ fpair = (forcecoul + factor_lj*forceborn)*r2inv;
+
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (EFLAG) {
+ if (rsq < cut_coulsq) {
+ ecoul = v_sh;
+ if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
+ } else ecoul = 0.0;
+ if (rsq < cut_ljsq[itype][jtype]) {
+ evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv +
+ d[itype][jtype]*r6inv*r2inv - offset[itype][jtype];
+ evdwl *= factor_lj;
+ } else evdwl = 0.0;
+ }
+
+ if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
+ evdwl,ecoul,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_born_coul_wolf_omp.h b/src/USER-OMP/pair_born_coul_wolf_omp.h
index a190ad1a07100df477f54403da42818086ec7bf4..d714b32d29c5567e3c09866ac023747d4b05529f 100644
--- a/src/USER-OMP/pair_born_coul_wolf_omp.h
+++ b/src/USER-OMP/pair_born_coul_wolf_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_born_omp.cpp b/src/USER-OMP/pair_born_omp.cpp
index ebcdbf72bc5af33afb64fa61cb1a26feb485d668..847efaa013f8758604349175a3b5bdd555457545 100644
--- a/src/USER-OMP/pair_born_omp.cpp
+++ b/src/USER-OMP/pair_born_omp.cpp
@@ -56,11 +56,11 @@ void PairBornOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -117,31 +117,31 @@ void PairBornOMP::eval(int iifrom, int iito, ThrData * const thr)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
- r = sqrt(rsq);
- rexp = exp((sigma[itype][jtype]-r)*rhoinv[itype][jtype]);
- forceborn = born1[itype][jtype]*r*rexp - born2[itype][jtype]*r6inv
- + born3[itype][jtype]*r2inv*r6inv;
- fpair = factor_lj*forceborn*r2inv;
-
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (EFLAG) {
- evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv
- + d[itype][jtype]*r6inv*r2inv - offset[itype][jtype];
- evdwl *= factor_lj;
- }
-
- if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
- evdwl,0.0,fpair,delx,dely,delz,thr);
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
+ r = sqrt(rsq);
+ rexp = exp((sigma[itype][jtype]-r)*rhoinv[itype][jtype]);
+ forceborn = born1[itype][jtype]*r*rexp - born2[itype][jtype]*r6inv
+ + born3[itype][jtype]*r2inv*r6inv;
+ fpair = factor_lj*forceborn*r2inv;
+
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (EFLAG) {
+ evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv
+ + d[itype][jtype]*r6inv*r2inv - offset[itype][jtype];
+ evdwl *= factor_lj;
+ }
+
+ if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
+ evdwl,0.0,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_born_omp.h b/src/USER-OMP/pair_born_omp.h
index 726064472844e577465d5c35cff4994e3579f476..db3c768f7a89f64b0f23bc0484bf9897be1b481d 100644
--- a/src/USER-OMP/pair_born_omp.h
+++ b/src/USER-OMP/pair_born_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_brownian_omp.cpp b/src/USER-OMP/pair_brownian_omp.cpp
index 8da822134555a40000463d54ae197881cd5bdbe5..561c82abf528fab76a8573e08d3570f54da8157a 100644
--- a/src/USER-OMP/pair_brownian_omp.cpp
+++ b/src/USER-OMP/pair_brownian_omp.cpp
@@ -50,7 +50,7 @@ PairBrownianOMP::PairBrownianOMP(LAMMPS *lmp) :
/* ---------------------------------------------------------------------- */
-PairBrownianOMP::~PairBrownianOMP()
+PairBrownianOMP::~PairBrownianOMP()
{
if (random_thr) {
for (int i=1; i < comm->nthreads; ++i)
@@ -80,37 +80,37 @@ void PairBrownianOMP::compute(int eflag, int vflag)
if (flagVF) // Flag for volume fraction corrections
if (flagdeform || flagwall == 2){ // Possible changes in volume fraction
if (flagdeform && !flagwall)
- for (int j = 0; j < 3; j++)
- dims[j] = domain->prd[j];
+ for (int j = 0; j < 3; j++)
+ dims[j] = domain->prd[j];
else if (flagwall == 2 || (flagdeform && flagwall == 1)){
- double wallhi[3], walllo[3];
- for (int j = 0; j < 3; j++){
- wallhi[j] = domain->prd[j];
- walllo[j] = 0;
- }
- for (int m = 0; m < wallfix->nwall; m++){
- int dim = wallfix->wallwhich[m] / 2;
- int side = wallfix->wallwhich[m] % 2;
- if (wallfix->wallstyle[m] == VARIABLE){
- wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
- }
- else wallcoord = wallfix->coord0[m];
- if (side == 0) walllo[dim] = wallcoord;
- else wallhi[dim] = wallcoord;
- }
- for (int j = 0; j < 3; j++)
- dims[j] = wallhi[j] - walllo[j];
+ double wallhi[3], walllo[3];
+ for (int j = 0; j < 3; j++){
+ wallhi[j] = domain->prd[j];
+ walllo[j] = 0;
+ }
+ for (int m = 0; m < wallfix->nwall; m++){
+ int dim = wallfix->wallwhich[m] / 2;
+ int side = wallfix->wallwhich[m] % 2;
+ if (wallfix->wallstyle[m] == VARIABLE){
+ wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
+ }
+ else wallcoord = wallfix->coord0[m];
+ if (side == 0) walllo[dim] = wallcoord;
+ else wallhi[dim] = wallcoord;
+ }
+ for (int j = 0; j < 3; j++)
+ dims[j] = wallhi[j] - walllo[j];
}
double vol_T = dims[0]*dims[1]*dims[2];
double vol_f = vol_P/vol_T;
if (flaglog == 0) {
- R0 = 6*MY_PI*mu*rad*(1.0 + 2.16*vol_f);
- RT0 = 8*MY_PI*mu*pow(rad,3.0);
- //RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3)*(1.0 + 3.33*vol_f + 2.80*vol_f*vol_f);
+ R0 = 6*MY_PI*mu*rad*(1.0 + 2.16*vol_f);
+ RT0 = 8*MY_PI*mu*pow(rad,3.0);
+ //RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3)*(1.0 + 3.33*vol_f + 2.80*vol_f*vol_f);
} else {
- R0 = 6*MY_PI*mu*rad*(1.0 + 2.725*vol_f - 6.583*vol_f*vol_f);
- RT0 = 8*MY_PI*mu*pow(rad,3.0)*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
- //RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3)*(1.0 + 3.64*vol_f - 6.95*vol_f*vol_f);
+ R0 = 6*MY_PI*mu*rad*(1.0 + 2.725*vol_f - 6.583*vol_f*vol_f);
+ RT0 = 8*MY_PI*mu*pow(rad,3.0)*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
+ //RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3)*(1.0 + 3.64*vol_f - 6.95*vol_f*vol_f);
}
}
@@ -135,23 +135,23 @@ void PairBrownianOMP::compute(int eflag, int vflag)
// generate a random number generator instance for
// all threads != 0. make sure we use unique seeds.
if (random_thr && tid > 0)
- random_thr[tid] = new RanMars(Pair::lmp, seed + comm->me
- + comm->nprocs*tid);
+ random_thr[tid] = new RanMars(Pair::lmp, seed + comm->me
+ + comm->nprocs*tid);
if (flaglog) {
if (evflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
- } else {
+ } else {
if (evflag) {
- if (force->newton_pair) eval<0,1,1>(ifrom, ito, thr);
- else eval<0,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<0,1,1>(ifrom, ito, thr);
+ else eval<0,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
- else eval<0,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
+ else eval<0,0,0>(ifrom, ito, thr);
}
}
@@ -202,8 +202,8 @@ void PairBrownianOMP::eval(int iifrom, int iito, ThrData * const thr)
itype = type[i];
radi = radius[i];
jlist = firstneigh[i];
- jnum = numneigh[i];
-
+ jnum = numneigh[i];
+
// FLD contribution to force and torque due to isotropic terms
if (flagfld) {
@@ -211,12 +211,12 @@ void PairBrownianOMP::eval(int iifrom, int iito, ThrData * const thr)
f[i][1] += prethermostat*sqrt(R0)*(rng.uniform()-0.5);
f[i][2] += prethermostat*sqrt(R0)*(rng.uniform()-0.5);
if (FLAGLOG) {
- torque[i][0] += prethermostat*sqrt(RT0)*(rng.uniform()-0.5);
- torque[i][1] += prethermostat*sqrt(RT0)*(rng.uniform()-0.5);
- torque[i][2] += prethermostat*sqrt(RT0)*(rng.uniform()-0.5);
+ torque[i][0] += prethermostat*sqrt(RT0)*(rng.uniform()-0.5);
+ torque[i][1] += prethermostat*sqrt(RT0)*(rng.uniform()-0.5);
+ torque[i][2] += prethermostat*sqrt(RT0)*(rng.uniform()-0.5);
}
}
-
+
if (!flagHI) continue;
for (jj = 0; jj < jnum; jj++) {
@@ -230,25 +230,25 @@ void PairBrownianOMP::eval(int iifrom, int iito, ThrData * const thr)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r = sqrt(rsq);
-
+ r = sqrt(rsq);
+
// scalar resistances a_sq and a_sh
h_sep = r - 2.0*radi;
-
+
// check for overlaps
if (h_sep < 0.0) overlaps++;
-
+
// if less than minimum gap, use minimum gap instead
if (r < cut_inner[itype][jtype])
- h_sep = cut_inner[itype][jtype] - 2.0*radi;
-
+ h_sep = cut_inner[itype][jtype] - 2.0*radi;
+
// scale h_sep by radi
h_sep = h_sep/radi;
-
+
// scalar resistances
if (FLAGLOG) {
@@ -257,70 +257,70 @@ void PairBrownianOMP::eval(int iifrom, int iito, ThrData * const thr)
a_pu = 8.0*MY_PI*mu*pow(radi,3.0)*(3.0/160.0*log(1.0/h_sep));
} else
a_sq = 6.0*MY_PI*mu*radi*(1.0/4.0/h_sep);
-
+
// generate the Pairwise Brownian Force: a_sq
Fbmag = prethermostat*sqrt(a_sq);
-
+
// generate a random number
randr = rng.uniform()-0.5;
-
+
// contribution due to Brownian motion
fx = Fbmag*randr*delx/r;
fy = Fbmag*randr*dely/r;
fz = Fbmag*randr*delz/r;
-
+
// add terms due to a_sh
if (FLAGLOG) {
// generate two orthogonal vectors to the line of centers
- p1[0] = delx/r; p1[1] = dely/r; p1[2] = delz/r;
+ p1[0] = delx/r; p1[1] = dely/r; p1[2] = delz/r;
set_3_orthogonal_vectors(p1,p2,p3);
-
+
// magnitude
- Fbmag = prethermostat*sqrt(a_sh);
-
+ Fbmag = prethermostat*sqrt(a_sh);
+
// force in each of the two directions
randr = rng.uniform()-0.5;
fx += Fbmag*randr*p2[0];
fy += Fbmag*randr*p2[1];
fz += Fbmag*randr*p2[2];
-
+
randr = rng.uniform()-0.5;
fx += Fbmag*randr*p3[0];
fy += Fbmag*randr*p3[1];
- fz += Fbmag*randr*p3[2];
- }
-
+ fz += Fbmag*randr*p3[2];
+ }
+
// scale forces to appropriate units
fx = vxmu2f*fx;
fy = vxmu2f*fy;
fz = vxmu2f*fz;
-
+
// sum to total force
f[i][0] -= fx;
f[i][1] -= fy;
- f[i][2] -= fz;
-
- if (NEWTON_PAIR || j < nlocal) {
- //randr = rng.uniform()-0.5;
- //fx = Fbmag*randr*delx/r;
- //fy = Fbmag*randr*dely/r;
- //fz = Fbmag*randr*delz/r;
-
- f[j][0] += fx;
- f[j][1] += fy;
- f[j][2] += fz;
- }
-
+ f[i][2] -= fz;
+
+ if (NEWTON_PAIR || j < nlocal) {
+ //randr = rng.uniform()-0.5;
+ //fx = Fbmag*randr*delx/r;
+ //fy = Fbmag*randr*dely/r;
+ //fz = Fbmag*randr*delz/r;
+
+ f[j][0] += fx;
+ f[j][1] += fy;
+ f[j][2] += fz;
+ }
+
// torque due to the Brownian Force
if (FLAGLOG) {
@@ -330,56 +330,56 @@ void PairBrownianOMP::eval(int iifrom, int iito, ThrData * const thr)
xl[0] = -delx/r*radi;
xl[1] = -dely/r*radi;
xl[2] = -delz/r*radi;
-
+
// torque = xl_cross_F
tx = xl[1]*fz - xl[2]*fy;
ty = xl[2]*fx - xl[0]*fz;
- tz = xl[0]*fy - xl[1]*fx;
-
+ tz = xl[0]*fy - xl[1]*fx;
+
// torque is same on both particles
torque[i][0] -= tx;
torque[i][1] -= ty;
- torque[i][2] -= tz;
-
- if (NEWTON_PAIR || j < nlocal) {
- torque[j][0] -= tx;
- torque[j][1] -= ty;
- torque[j][2] -= tz;
- }
+ torque[i][2] -= tz;
+
+ if (NEWTON_PAIR || j < nlocal) {
+ torque[j][0] -= tx;
+ torque[j][1] -= ty;
+ torque[j][2] -= tz;
+ }
// torque due to a_pu
- Fbmag = prethermostat*sqrt(a_pu);
-
+ Fbmag = prethermostat*sqrt(a_pu);
+
// force in each direction
randr = rng.uniform()-0.5;
tx = Fbmag*randr*p2[0];
ty = Fbmag*randr*p2[1];
tz = Fbmag*randr*p2[2];
-
+
randr = rng.uniform()-0.5;
tx += Fbmag*randr*p3[0];
ty += Fbmag*randr*p3[1];
- tz += Fbmag*randr*p3[2];
-
+ tz += Fbmag*randr*p3[2];
+
// torque has opposite sign on two particles
torque[i][0] -= tx;
torque[i][1] -= ty;
- torque[i][2] -= tz;
-
- if (NEWTON_PAIR || j < nlocal) {
- torque[j][0] += tx;
- torque[j][1] += ty;
- torque[j][2] += tz;
- }
+ torque[i][2] -= tz;
+
+ if (NEWTON_PAIR || j < nlocal) {
+ torque[j][0] += tx;
+ torque[j][1] += ty;
+ torque[j][2] += tz;
+ }
}
if (EVFLAG) ev_tally_xyz(i,j,nlocal,NEWTON_PAIR,
- 0.0,0.0,-fx,-fy,-fz,delx,dely,delz);
+ 0.0,0.0,-fx,-fy,-fz,delx,dely,delz);
}
}
}
diff --git a/src/USER-OMP/pair_brownian_omp.h b/src/USER-OMP/pair_brownian_omp.h
index adf6d3362d5cc16cbcc935bea7c3b921f7b86dd7..cdabe08ba1eb688daa6e8e5e8fd0ef6cdcde4519 100644
--- a/src/USER-OMP/pair_brownian_omp.h
+++ b/src/USER-OMP/pair_brownian_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_brownian_poly_omp.cpp b/src/USER-OMP/pair_brownian_poly_omp.cpp
index 891d868c250668486d987f35380bf88c4d46f5e1..6affbf96cfaa4488619c4d2df2fefb41ccfdd62d 100644
--- a/src/USER-OMP/pair_brownian_poly_omp.cpp
+++ b/src/USER-OMP/pair_brownian_poly_omp.cpp
@@ -50,7 +50,7 @@ PairBrownianPolyOMP::PairBrownianPolyOMP(LAMMPS *lmp) :
/* ---------------------------------------------------------------------- */
-PairBrownianPolyOMP::~PairBrownianPolyOMP()
+PairBrownianPolyOMP::~PairBrownianPolyOMP()
{
if (random_thr) {
for (int i=1; i < comm->nthreads; ++i)
@@ -80,37 +80,37 @@ void PairBrownianPolyOMP::compute(int eflag, int vflag)
if (flagVF) // Flag for volume fraction corrections
if (flagdeform || flagwall == 2){ // Possible changes in volume fraction
if (flagdeform && !flagwall)
- for (int j = 0; j < 3; j++)
- dims[j] = domain->prd[j];
+ for (int j = 0; j < 3; j++)
+ dims[j] = domain->prd[j];
else if (flagwall == 2 || (flagdeform && flagwall == 1)){
- double wallhi[3], walllo[3];
- for (int j = 0; j < 3; j++){
- wallhi[j] = domain->prd[j];
- walllo[j] = 0;
- }
- for (int m = 0; m < wallfix->nwall; m++){
- int dim = wallfix->wallwhich[m] / 2;
- int side = wallfix->wallwhich[m] % 2;
- if (wallfix->wallstyle[m] == VARIABLE){
- wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
- }
- else wallcoord = wallfix->coord0[m];
- if (side == 0) walllo[dim] = wallcoord;
- else wallhi[dim] = wallcoord;
- }
- for (int j = 0; j < 3; j++)
- dims[j] = wallhi[j] - walllo[j];
+ double wallhi[3], walllo[3];
+ for (int j = 0; j < 3; j++){
+ wallhi[j] = domain->prd[j];
+ walllo[j] = 0;
+ }
+ for (int m = 0; m < wallfix->nwall; m++){
+ int dim = wallfix->wallwhich[m] / 2;
+ int side = wallfix->wallwhich[m] % 2;
+ if (wallfix->wallstyle[m] == VARIABLE){
+ wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
+ }
+ else wallcoord = wallfix->coord0[m];
+ if (side == 0) walllo[dim] = wallcoord;
+ else wallhi[dim] = wallcoord;
+ }
+ for (int j = 0; j < 3; j++)
+ dims[j] = wallhi[j] - walllo[j];
}
double vol_T = dims[0]*dims[1]*dims[2];
double vol_f = vol_P/vol_T;
if (flaglog == 0) {
- R0 = 6*MY_PI*mu*rad*(1.0 + 2.16*vol_f);
- RT0 = 8*MY_PI*mu*pow(rad,3.0);
- //RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3)*(1.0 + 3.33*vol_f + 2.80*vol_f*vol_f);
+ R0 = 6*MY_PI*mu*rad*(1.0 + 2.16*vol_f);
+ RT0 = 8*MY_PI*mu*pow(rad,3.0);
+ //RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3)*(1.0 + 3.33*vol_f + 2.80*vol_f*vol_f);
} else {
- R0 = 6*MY_PI*mu*rad*(1.0 + 2.725*vol_f - 6.583*vol_f*vol_f);
- RT0 = 8*MY_PI*mu*pow(rad,3.0)*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
- //RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3)*(1.0 + 3.64*vol_f - 6.95*vol_f*vol_f);
+ R0 = 6*MY_PI*mu*rad*(1.0 + 2.725*vol_f - 6.583*vol_f*vol_f);
+ RT0 = 8*MY_PI*mu*pow(rad,3.0)*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
+ //RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3)*(1.0 + 3.64*vol_f - 6.95*vol_f*vol_f);
}
}
@@ -135,16 +135,16 @@ void PairBrownianPolyOMP::compute(int eflag, int vflag)
// generate a random number generator instance for
// all threads != 0. make sure we use unique seeds.
if (random_thr && tid > 0)
- random_thr[tid] = new RanMars(Pair::lmp, seed + comm->me
- + comm->nprocs*tid);
+ random_thr[tid] = new RanMars(Pair::lmp, seed + comm->me
+ + comm->nprocs*tid);
if (flaglog) {
if (evflag)
- eval<1,1>(ifrom, ito, thr);
+ eval<1,1>(ifrom, ito, thr);
else
- eval<1,0>(ifrom, ito, thr);
- } else {
+ eval<1,0>(ifrom, ito, thr);
+ } else {
if (evflag)
- eval<0,1>(ifrom, ito, thr);
+ eval<0,1>(ifrom, ito, thr);
else eval<0,0>(ifrom, ito, thr);
}
@@ -175,7 +175,7 @@ void PairBrownianPolyOMP::eval(int iifrom, int iito, ThrData * const thr)
double prethermostat;
double xl[3],a_sq,a_sh,a_pu,Fbmag;
double p1[3],p2[3],p3[3];
-
+
// scale factor for Brownian moments
prethermostat = sqrt(24.0*force->boltz*t_target/update->dt);
@@ -195,8 +195,8 @@ void PairBrownianPolyOMP::eval(int iifrom, int iito, ThrData * const thr)
itype = type[i];
radi = radius[i];
jlist = firstneigh[i];
- jnum = numneigh[i];
-
+ jnum = numneigh[i];
+
// FLD contribution to force and torque due to isotropic terms
if (flagfld) {
@@ -204,13 +204,13 @@ void PairBrownianPolyOMP::eval(int iifrom, int iito, ThrData * const thr)
f[i][1] += prethermostat*sqrt(R0*radi)*(rng.uniform()-0.5);
f[i][2] += prethermostat*sqrt(R0*radi)*(rng.uniform()-0.5);
if (FLAGLOG) {
- const double rad3 = radi*radi*radi;
- torque[i][0] += prethermostat*sqrt(RT0*rad3)*(rng.uniform()-0.5);
- torque[i][1] += prethermostat*sqrt(RT0*rad3)*(rng.uniform()-0.5);
- torque[i][2] += prethermostat*sqrt(RT0*rad3)*(rng.uniform()-0.5);
+ const double rad3 = radi*radi*radi;
+ torque[i][0] += prethermostat*sqrt(RT0*rad3)*(rng.uniform()-0.5);
+ torque[i][1] += prethermostat*sqrt(RT0*rad3)*(rng.uniform()-0.5);
+ torque[i][2] += prethermostat*sqrt(RT0*rad3)*(rng.uniform()-0.5);
}
}
-
+
if (!flagHI) continue;
for (jj = 0; jj < jnum; jj++) {
@@ -225,99 +225,99 @@ void PairBrownianPolyOMP::eval(int iifrom, int iito, ThrData * const thr)
radj = radius[j];
if (rsq < cutsq[itype][jtype]) {
- r = sqrt(rsq);
-
+ r = sqrt(rsq);
+
// scalar resistances a_sq and a_sh
h_sep = r - radi-radj;
-
+
// check for overlaps
if (h_sep < 0.0) overlaps++;
-
+
// if less than minimum gap, use minimum gap instead
if (r < cut_inner[itype][jtype])
h_sep = cut_inner[itype][jtype] - radi-radj;
-
+
// scale h_sep by radi
h_sep = h_sep/radi;
beta0 = radj/radi;
beta1 = 1.0 + beta0;
-
+
// scalar resistances
if (FLAGLOG) {
- a_sq = beta0*beta0/beta1/beta1/h_sep +
- (1.0+7.0*beta0+beta0*beta0)/5.0/pow(beta1,3.0)*log(1.0/h_sep);
- a_sq += (1.0+18.0*beta0-29.0*beta0*beta0+18.0*pow(beta0,3.0) +
- pow(beta0,4.0))/21.0/pow(beta1,4.0)*h_sep*log(1.0/h_sep);
+ a_sq = beta0*beta0/beta1/beta1/h_sep +
+ (1.0+7.0*beta0+beta0*beta0)/5.0/pow(beta1,3.0)*log(1.0/h_sep);
+ a_sq += (1.0+18.0*beta0-29.0*beta0*beta0+18.0*pow(beta0,3.0) +
+ pow(beta0,4.0))/21.0/pow(beta1,4.0)*h_sep*log(1.0/h_sep);
a_sq *= 6.0*MY_PI*mu*radi;
- a_sh = 4.0*beta0*(2.0+beta0+2.0*beta0*beta0)/15.0/pow(beta1,3.0) *
- log(1.0/h_sep);
- a_sh += 4.0*(16.0-45.0*beta0+58.0*beta0*beta0-45.0*pow(beta0,3.0) +
- 16.0*pow(beta0,4.0))/375.0/pow(beta1,4.0) *
- h_sep*log(1.0/h_sep);
+ a_sh = 4.0*beta0*(2.0+beta0+2.0*beta0*beta0)/15.0/pow(beta1,3.0) *
+ log(1.0/h_sep);
+ a_sh += 4.0*(16.0-45.0*beta0+58.0*beta0*beta0-45.0*pow(beta0,3.0) +
+ 16.0*pow(beta0,4.0))/375.0/pow(beta1,4.0) *
+ h_sep*log(1.0/h_sep);
a_sh *= 6.0*MY_PI*mu*radi;
a_pu = beta0*(4.0+beta0)/10.0/beta1/beta1*log(1.0/h_sep);
- a_pu += (32.0-33.0*beta0+83.0*beta0*beta0+43.0 *
- pow(beta0,3.0))/250.0/pow(beta1,3.0)*h_sep*log(1.0/h_sep);
+ a_pu += (32.0-33.0*beta0+83.0*beta0*beta0+43.0 *
+ pow(beta0,3.0))/250.0/pow(beta1,3.0)*h_sep*log(1.0/h_sep);
a_pu *= 8.0*MY_PI*mu*pow(radi,3.0);
} else a_sq = 6.0*MY_PI*mu*radi*(beta0*beta0/beta1/beta1/h_sep);
-
+
// generate the Pairwise Brownian Force: a_sq
Fbmag = prethermostat*sqrt(a_sq);
-
+
// generate a random number
randr = rng.uniform()-0.5;
-
+
// contribution due to Brownian motion
fx = Fbmag*randr*delx/r;
fy = Fbmag*randr*dely/r;
fz = Fbmag*randr*delz/r;
-
+
// add terms due to a_sh
if (FLAGLOG) {
// generate two orthogonal vectors to the line of centers
- p1[0] = delx/r; p1[1] = dely/r; p1[2] = delz/r;
+ p1[0] = delx/r; p1[1] = dely/r; p1[2] = delz/r;
set_3_orthogonal_vectors(p1,p2,p3);
-
+
// magnitude
- Fbmag = prethermostat*sqrt(a_sh);
-
+ Fbmag = prethermostat*sqrt(a_sh);
+
// force in each of the two directions
randr = rng.uniform()-0.5;
fx += Fbmag*randr*p2[0];
fy += Fbmag*randr*p2[1];
fz += Fbmag*randr*p2[2];
-
+
randr = rng.uniform()-0.5;
fx += Fbmag*randr*p3[0];
fy += Fbmag*randr*p3[1];
- fz += Fbmag*randr*p3[2];
- }
-
+ fz += Fbmag*randr*p3[2];
+ }
+
// scale forces to appropriate units
fx = vxmu2f*fx;
fy = vxmu2f*fy;
fz = vxmu2f*fz;
-
+
// sum to total force
f[i][0] -= fx;
f[i][1] -= fy;
- f[i][2] -= fz;
+ f[i][2] -= fz;
// torque due to the Brownian Force
@@ -328,47 +328,47 @@ void PairBrownianPolyOMP::eval(int iifrom, int iito, ThrData * const thr)
xl[0] = -delx/r*radi;
xl[1] = -dely/r*radi;
xl[2] = -delz/r*radi;
-
+
// torque = xl_cross_F
tx = xl[1]*fz - xl[2]*fy;
ty = xl[2]*fx - xl[0]*fz;
- tz = xl[0]*fy - xl[1]*fx;
-
+ tz = xl[0]*fy - xl[1]*fx;
+
// torque is same on both particles
torque[i][0] -= tx;
torque[i][1] -= ty;
- torque[i][2] -= tz;
-
+ torque[i][2] -= tz;
+
// torque due to a_pu
- Fbmag = prethermostat*sqrt(a_pu);
-
+ Fbmag = prethermostat*sqrt(a_pu);
+
// force in each direction
randr = rng.uniform()-0.5;
tx = Fbmag*randr*p2[0];
ty = Fbmag*randr*p2[1];
tz = Fbmag*randr*p2[2];
-
+
randr = rng.uniform()-0.5;
tx += Fbmag*randr*p3[0];
ty += Fbmag*randr*p3[1];
- tz += Fbmag*randr*p3[2];
-
+ tz += Fbmag*randr*p3[2];
+
// torque has opposite sign on two particles
torque[i][0] -= tx;
torque[i][1] -= ty;
- torque[i][2] -= tz;
-
+ torque[i][2] -= tz;
+
}
- // set j = nlocal so that only I gets tallied
+ // set j = nlocal so that only I gets tallied
if (EVFLAG) ev_tally_xyz(i,nlocal,nlocal,/* newton_pair */ 0,
- 0.0,0.0,-fx,-fy,-fz,delx,dely,delz);
+ 0.0,0.0,-fx,-fy,-fz,delx,dely,delz);
}
}
}
diff --git a/src/USER-OMP/pair_brownian_poly_omp.h b/src/USER-OMP/pair_brownian_poly_omp.h
index 23443e51e048beff9a5252d34cc015b7738d1bfa..663696c6c6185b2a234f5cde9e4b143cb25ea80d 100644
--- a/src/USER-OMP/pair_brownian_poly_omp.h
+++ b/src/USER-OMP/pair_brownian_poly_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_buck_coul_cut_omp.cpp b/src/USER-OMP/pair_buck_coul_cut_omp.cpp
index a3152ee15acf5053dfcfd13089deba496043c58c..8b570ff1a0eba78894200d8a8ace3185fa06df2e 100644
--- a/src/USER-OMP/pair_buck_coul_cut_omp.cpp
+++ b/src/USER-OMP/pair_buck_coul_cut_omp.cpp
@@ -56,11 +56,11 @@ void PairBuckCoulCutOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -123,43 +123,43 @@ void PairBuckCoulCutOMP::eval(int iifrom, int iito, ThrData * const thr)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- r = sqrt(rsq);
-
- if (rsq < cut_coulsq[itype][jtype])
- forcecoul = qqrd2e * qtmp*q[j]/r;
- else forcecoul = 0.0;
-
- if (rsq < cut_ljsq[itype][jtype]) {
- r6inv = r2inv*r2inv*r2inv;
- rexp = exp(-r*rhoinv[itype][jtype]);
- forcebuck = buck1[itype][jtype]*r*rexp - buck2[itype][jtype]*r6inv;
- } else forcebuck = 0.0;
-
- fpair = (forcecoul + factor_lj*forcebuck)*r2inv;
-
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (EFLAG) {
- if (rsq < cut_coulsq[itype][jtype])
- ecoul = factor_coul * qqrd2e * qtmp*q[j]/r;
- else ecoul = 0.0;
- if (rsq < cut_ljsq[itype][jtype]) {
- evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv -
- offset[itype][jtype];
- evdwl *= factor_lj;
- } else evdwl = 0.0;
- }
-
- if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
- evdwl,ecoul,fpair,delx,dely,delz,thr);
+ r2inv = 1.0/rsq;
+ r = sqrt(rsq);
+
+ if (rsq < cut_coulsq[itype][jtype])
+ forcecoul = qqrd2e * qtmp*q[j]/r;
+ else forcecoul = 0.0;
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ r6inv = r2inv*r2inv*r2inv;
+ rexp = exp(-r*rhoinv[itype][jtype]);
+ forcebuck = buck1[itype][jtype]*r*rexp - buck2[itype][jtype]*r6inv;
+ } else forcebuck = 0.0;
+
+ fpair = (forcecoul + factor_lj*forcebuck)*r2inv;
+
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (EFLAG) {
+ if (rsq < cut_coulsq[itype][jtype])
+ ecoul = factor_coul * qqrd2e * qtmp*q[j]/r;
+ else ecoul = 0.0;
+ if (rsq < cut_ljsq[itype][jtype]) {
+ evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv -
+ offset[itype][jtype];
+ evdwl *= factor_lj;
+ } else evdwl = 0.0;
+ }
+
+ if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
+ evdwl,ecoul,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_buck_coul_cut_omp.h b/src/USER-OMP/pair_buck_coul_cut_omp.h
index 8fee0808c0007d2b10c91633d5a521f503f1cf9f..cf142b022aea26212aa3e43a993cf56e53121146 100644
--- a/src/USER-OMP/pair_buck_coul_cut_omp.h
+++ b/src/USER-OMP/pair_buck_coul_cut_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_buck_coul_long_omp.cpp b/src/USER-OMP/pair_buck_coul_long_omp.cpp
index 3347e728ea5254b9ecc95d6c0a3d25d5319a900b..85f2b48db9aa11835648bcf0c0e699dbf6048e73 100644
--- a/src/USER-OMP/pair_buck_coul_long_omp.cpp
+++ b/src/USER-OMP/pair_buck_coul_long_omp.cpp
@@ -64,11 +64,11 @@ void PairBuckCoulLongOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -134,50 +134,50 @@ void PairBuckCoulLongOMP::eval(int iifrom, int iito, ThrData * const thr)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- r = sqrt(rsq);
-
- if (rsq < cut_coulsq) {
- grij = g_ewald * r;
- expm2 = exp(-grij*grij);
- t = 1.0 / (1.0 + EWALD_P*grij);
- erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
- prefactor = qqrd2e * qtmp*q[j]/r;
- forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
- if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
- } else forcecoul = 0.0;
-
- if (rsq < cut_ljsq[itype][jtype]) {
- r6inv = r2inv*r2inv*r2inv;
- rexp = exp(-r*rhoinv[itype][jtype]);
- forcebuck = buck1[itype][jtype]*r*rexp - buck2[itype][jtype]*r6inv;
- } else forcebuck = 0.0;
-
- fpair = (forcecoul + factor_lj*forcebuck)*r2inv;
-
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (EFLAG) {
- if (rsq < cut_coulsq) {
- ecoul = prefactor*erfc;
- if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
- } else ecoul = 0.0;
- if (rsq < cut_ljsq[itype][jtype]) {
- evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv -
- offset[itype][jtype];
- evdwl *= factor_lj;
- } else evdwl = 0.0;
- }
-
- if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
- evdwl,ecoul,fpair,delx,dely,delz,thr);
+ r2inv = 1.0/rsq;
+ r = sqrt(rsq);
+
+ if (rsq < cut_coulsq) {
+ grij = g_ewald * r;
+ expm2 = exp(-grij*grij);
+ t = 1.0 / (1.0 + EWALD_P*grij);
+ erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
+ prefactor = qqrd2e * qtmp*q[j]/r;
+ forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
+ if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
+ } else forcecoul = 0.0;
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ r6inv = r2inv*r2inv*r2inv;
+ rexp = exp(-r*rhoinv[itype][jtype]);
+ forcebuck = buck1[itype][jtype]*r*rexp - buck2[itype][jtype]*r6inv;
+ } else forcebuck = 0.0;
+
+ fpair = (forcecoul + factor_lj*forcebuck)*r2inv;
+
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (EFLAG) {
+ if (rsq < cut_coulsq) {
+ ecoul = prefactor*erfc;
+ if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
+ } else ecoul = 0.0;
+ if (rsq < cut_ljsq[itype][jtype]) {
+ evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv -
+ offset[itype][jtype];
+ evdwl *= factor_lj;
+ } else evdwl = 0.0;
+ }
+
+ if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
+ evdwl,ecoul,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_buck_coul_long_omp.h b/src/USER-OMP/pair_buck_coul_long_omp.h
index a47e809eec074c709f5a4c28527f30a4aaf6ca9b..1309bc4c4b28e07f2eb00eb4f85716f62ee1e349 100644
--- a/src/USER-OMP/pair_buck_coul_long_omp.h
+++ b/src/USER-OMP/pair_buck_coul_long_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_buck_coul_omp.cpp b/src/USER-OMP/pair_buck_coul_omp.cpp
index 4ff10ba02c246de5a9819305e4de40843c2af711..d1e54f1b117c68ba723e996239242f3f12a990e5 100644
--- a/src/USER-OMP/pair_buck_coul_omp.cpp
+++ b/src/USER-OMP/pair_buck_coul_omp.cpp
@@ -66,11 +66,11 @@ void PairBuckCoulOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -108,14 +108,14 @@ void PairBuckCoulOMP::eval(int iifrom, int iito, ThrData * const thr)
int i, ii, j, order1 = ewald_order&(1<<1), order6 = ewald_order&(1<<6);
int *jneigh, *jneighn, typei, typej, ni;
double qi, qri, *cutsqi, *cut_bucksqi,
- *buck1i, *buck2i, *buckai, *buckci, *rhoinvi, *offseti;
+ *buck1i, *buck2i, *buckai, *buckci, *rhoinvi, *offseti;
double r, rsq, r2inv, force_coul, force_buck;
double g2 = g_ewald*g_ewald, g6 = g2*g2*g2, g8 = g6*g2;
vector xi, d;
- for (ii = iifrom; ii < iito; ++ii) { // loop over my atoms
+ for (ii = iifrom; ii < iito; ++ii) { // loop over my atoms
i = ilist[ii]; fi = f0+3*i;
- if (order1) qri = (qi = q[i])*qqrd2e; // initialize constants
+ if (order1) qri = (qi = q[i])*qqrd2e; // initialize constants
offseti = offset[typei = type[i]];
buck1i = buck1[typei]; buck2i = buck2[typei];
buckai = buck_a[typei]; buckci = buck_c[typei], rhoinvi = rhoinv[typei];
@@ -123,97 +123,97 @@ void PairBuckCoulOMP::eval(int iifrom, int iito, ThrData * const thr)
memcpy(xi, x0+(i+(i<<1)), sizeof(vector));
jneighn = (jneigh = list->firstneigh[i])+list->numneigh[i];
- for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
+ for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
j = *jneigh;
ni = sbmask(j);
j &= NEIGHMASK;
-
+
{ const register double *xj = x0+(j+(j<<1));
- d[0] = xi[0] - xj[0]; // pair vector
- d[1] = xi[1] - xj[1];
- d[2] = xi[2] - xj[2]; }
+ d[0] = xi[0] - xj[0]; // pair vector
+ d[1] = xi[1] - xj[1];
+ d[2] = xi[2] - xj[2]; }
if ((rsq = vec_dot(d, d)) >= cutsqi[typej = type[j]]) continue;
r2inv = 1.0/rsq;
r = sqrt(rsq);
- if (order1 && (rsq < cut_coulsq)) { // coulombic
- if (!ncoultablebits || rsq <= tabinnersq) { // series real space
- register double x = g_ewald*r;
- register double s = qri*q[j], t = 1.0/(1.0+EWALD_P*x);
- if (ni == 0) {
- s *= g_ewald*exp(-x*x);
- force_coul = (t *= ((((t*A5+A4)*t+A3)*t+A2)*t+A1)*s/x)+EWALD_F*s;
- if (EFLAG) ecoul = t;
- } else { // special case
- register double f = s*(1.0-special_coul[ni])/r;
- s *= g_ewald*exp(-x*x);
- force_coul = (t *= ((((t*A5+A4)*t+A3)*t+A2)*t+A1)*s/x)+EWALD_F*s-f;
- if (EFLAG) ecoul = t-f;
- } // table real space
- } else {
- register union_int_float_t t;
- t.f = rsq;
- register const int k = (t.i & ncoulmask) >> ncoulshiftbits;
- register double f = (rsq-rtable[k])*drtable[k], qiqj = qi*q[j];
- if (ni == 0) {
- force_coul = qiqj*(ftable[k]+f*dftable[k]);
- if (EFLAG) ecoul = qiqj*(etable[k]+f*detable[k]);
- }
- else { // special case
- t.f = (1.0-special_coul[ni])*(ctable[k]+f*dctable[k]);
- force_coul = qiqj*(ftable[k]+f*dftable[k]-t.f);
- if (EFLAG) ecoul = qiqj*(etable[k]+f*detable[k]-t.f);
- }
- }
+ if (order1 && (rsq < cut_coulsq)) { // coulombic
+ if (!ncoultablebits || rsq <= tabinnersq) { // series real space
+ register double x = g_ewald*r;
+ register double s = qri*q[j], t = 1.0/(1.0+EWALD_P*x);
+ if (ni == 0) {
+ s *= g_ewald*exp(-x*x);
+ force_coul = (t *= ((((t*A5+A4)*t+A3)*t+A2)*t+A1)*s/x)+EWALD_F*s;
+ if (EFLAG) ecoul = t;
+ } else { // special case
+ register double f = s*(1.0-special_coul[ni])/r;
+ s *= g_ewald*exp(-x*x);
+ force_coul = (t *= ((((t*A5+A4)*t+A3)*t+A2)*t+A1)*s/x)+EWALD_F*s-f;
+ if (EFLAG) ecoul = t-f;
+ } // table real space
+ } else {
+ register union_int_float_t t;
+ t.f = rsq;
+ register const int k = (t.i & ncoulmask) >> ncoulshiftbits;
+ register double f = (rsq-rtable[k])*drtable[k], qiqj = qi*q[j];
+ if (ni == 0) {
+ force_coul = qiqj*(ftable[k]+f*dftable[k]);
+ if (EFLAG) ecoul = qiqj*(etable[k]+f*detable[k]);
+ }
+ else { // special case
+ t.f = (1.0-special_coul[ni])*(ctable[k]+f*dctable[k]);
+ force_coul = qiqj*(ftable[k]+f*dftable[k]-t.f);
+ if (EFLAG) ecoul = qiqj*(etable[k]+f*detable[k]-t.f);
+ }
+ }
} else force_coul = ecoul = 0.0;
- if (rsq < cut_bucksqi[typej]) { // buckingham
- register double rn = r2inv*r2inv*r2inv,
- expr = exp(-r*rhoinvi[typej]);
- if (order6) { // long-range
- register double x2 = g2*rsq, a2 = 1.0/x2;
- x2 = a2*exp(-x2)*buckci[typej];
- if (ni == 0) {
- force_buck =
- r*expr*buck1i[typej]-g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq;
- if (EFLAG) evdwl = expr*buckai[typej]-g6*((a2+1.0)*a2+0.5)*x2;
- } else { // special case
- register double f = special_lj[ni], t = rn*(1.0-f);
- force_buck = f*r*expr*buck1i[typej]-
- g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq+t*buck2i[typej];
- if (EFLAG) evdwl = f*expr*buckai[typej] -
- g6*((a2+1.0)*a2+0.5)*x2+t*buckci[typej];
- }
- } else { // cut
- if (ni == 0) {
- force_buck = r*expr*buck1i[typej]-rn*buck2i[typej];
- if (EFLAG) evdwl = expr*buckai[typej] -
- rn*buckci[typej]-offseti[typej];
- } else { // special case
- register double f = special_lj[ni];
- force_buck = f*(r*expr*buck1i[typej]-rn*buck2i[typej]);
- if (EFLAG)
- evdwl = f*(expr*buckai[typej]-rn*buckci[typej]-offseti[typej]);
- }
- }
+ if (rsq < cut_bucksqi[typej]) { // buckingham
+ register double rn = r2inv*r2inv*r2inv,
+ expr = exp(-r*rhoinvi[typej]);
+ if (order6) { // long-range
+ register double x2 = g2*rsq, a2 = 1.0/x2;
+ x2 = a2*exp(-x2)*buckci[typej];
+ if (ni == 0) {
+ force_buck =
+ r*expr*buck1i[typej]-g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq;
+ if (EFLAG) evdwl = expr*buckai[typej]-g6*((a2+1.0)*a2+0.5)*x2;
+ } else { // special case
+ register double f = special_lj[ni], t = rn*(1.0-f);
+ force_buck = f*r*expr*buck1i[typej]-
+ g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq+t*buck2i[typej];
+ if (EFLAG) evdwl = f*expr*buckai[typej] -
+ g6*((a2+1.0)*a2+0.5)*x2+t*buckci[typej];
+ }
+ } else { // cut
+ if (ni == 0) {
+ force_buck = r*expr*buck1i[typej]-rn*buck2i[typej];
+ if (EFLAG) evdwl = expr*buckai[typej] -
+ rn*buckci[typej]-offseti[typej];
+ } else { // special case
+ register double f = special_lj[ni];
+ force_buck = f*(r*expr*buck1i[typej]-rn*buck2i[typej]);
+ if (EFLAG)
+ evdwl = f*(expr*buckai[typej]-rn*buckci[typej]-offseti[typej]);
+ }
+ }
} else force_buck = evdwl = 0.0;
fpair = (force_coul+force_buck)*r2inv;
if (NEWTON_PAIR || j < nlocal) {
- register double *fj = f0+(j+(j<<1)), f;
- fi[0] += f = d[0]*fpair; fj[0] -= f;
- fi[1] += f = d[1]*fpair; fj[1] -= f;
- fi[2] += f = d[2]*fpair; fj[2] -= f;
+ register double *fj = f0+(j+(j<<1)), f;
+ fi[0] += f = d[0]*fpair; fj[0] -= f;
+ fi[1] += f = d[1]*fpair; fj[1] -= f;
+ fi[2] += f = d[2]*fpair; fj[2] -= f;
} else {
- fi[0] += d[0]*fpair;
- fi[1] += d[1]*fpair;
- fi[2] += d[2]*fpair;
+ fi[0] += d[0]*fpair;
+ fi[1] += d[1]*fpair;
+ fi[2] += d[2]*fpair;
}
if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
- evdwl,ecoul,fpair,d[0],d[1],d[2],thr);
+ evdwl,ecoul,fpair,d[0],d[1],d[2],thr);
}
}
}
diff --git a/src/USER-OMP/pair_buck_coul_omp.h b/src/USER-OMP/pair_buck_coul_omp.h
index 823f64a4aba1a79425d3173b71989264d65f6c05..9fc11818a691f2c7c482a8dc090520dc49c8d534 100644
--- a/src/USER-OMP/pair_buck_coul_omp.h
+++ b/src/USER-OMP/pair_buck_coul_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_buck_omp.cpp b/src/USER-OMP/pair_buck_omp.cpp
index ae6cbcf4b743de67a657c2a0a9caf2294678b4e2..8b32e2cfa5fab9b1fa06a54e8dea356e933a0c3f 100644
--- a/src/USER-OMP/pair_buck_omp.cpp
+++ b/src/USER-OMP/pair_buck_omp.cpp
@@ -56,11 +56,11 @@ void PairBuckOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -117,33 +117,33 @@ void PairBuckOMP::eval(int iifrom, int iito, ThrData * const thr)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
- r = sqrt(rsq);
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
- r = sqrt(rsq);
- rexp = exp(-r*rhoinv[itype][jtype]);
- forcebuck = buck1[itype][jtype]*r*rexp - buck2[itype][jtype]*r6inv;
- fpair = factor_lj*forcebuck*r2inv;
-
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (EFLAG) {
- evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv -
- offset[itype][jtype];
- evdwl *= factor_lj;
- }
-
- if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
- evdwl,0.0,fpair,delx,dely,delz,thr);
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
+ r = sqrt(rsq);
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
+ r = sqrt(rsq);
+ rexp = exp(-r*rhoinv[itype][jtype]);
+ forcebuck = buck1[itype][jtype]*r*rexp - buck2[itype][jtype]*r6inv;
+ fpair = factor_lj*forcebuck*r2inv;
+
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (EFLAG) {
+ evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv -
+ offset[itype][jtype];
+ evdwl *= factor_lj;
+ }
+
+ if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
+ evdwl,0.0,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_buck_omp.h b/src/USER-OMP/pair_buck_omp.h
index c73e3f0d08c81d498712cbe3964b7f46bd2d7fed..72e1178803d7c63f4124ac43b5c3c831fc47b94e 100644
--- a/src/USER-OMP/pair_buck_omp.h
+++ b/src/USER-OMP/pair_buck_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_cdeam_omp.cpp b/src/USER-OMP/pair_cdeam_omp.cpp
index 4963528b7c017b228e88df0a2fb59927e8bf9536..bec3ce4b2533f03d462ee5b16db52797cb16df60 100644
--- a/src/USER-OMP/pair_cdeam_omp.cpp
+++ b/src/USER-OMP/pair_cdeam_omp.cpp
@@ -30,16 +30,16 @@ using namespace LAMMPS_NS;
// This is for debugging purposes. The ASSERT() macro is used in the code to check
// if everything runs as expected. Change this to #if 0 if you don't need the checking.
#if 0
- #define ASSERT(cond) ((!(cond)) ? my_failure(error,__FILE__,__LINE__) : my_noop())
-
- inline void my_noop() {}
- inline void my_failure(Error* error, const char* file, int line) {
- char str[1024];
- sprintf(str,"Assertion failure: File %s, line %i", file, line);
- error->one(FLERR,str);
- }
+ #define ASSERT(cond) ((!(cond)) ? my_failure(error,__FILE__,__LINE__) : my_noop())
+
+ inline void my_noop() {}
+ inline void my_failure(Error* error, const char* file, int line) {
+ char str[1024];
+ sprintf(str,"Assertion failure: File %s, line %i", file, line);
+ error->one(FLERR,str);
+ }
#else
- #define ASSERT(cond)
+ #define ASSERT(cond)
#endif
/* ---------------------------------------------------------------------- */
@@ -83,11 +83,11 @@ void PairCDEAMOMP::compute(int eflag, int vflag)
#endif
{
int ifrom, ito, tid;
-
+
loop_setup_thr(ifrom, ito, tid, inum, nthreads);
ThrData *thr = fix->get_thr(tid);
ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
-
+
if (force->newton_pair)
thr->init_cdeam(nall, rho, rhoB, D_values);
else
@@ -96,34 +96,34 @@ void PairCDEAMOMP::compute(int eflag, int vflag)
switch (cdeamVersion) {
case 1:
-
+
if (evflag) {
- if (eflag) {
- if (force->newton_pair) eval<1,1,1,1>(ifrom, ito, thr);
- else eval<1,1,0,1>(ifrom, ito, thr);
- } else {
- if (force->newton_pair) eval<1,0,1,1>(ifrom, ito, thr);
- else eval<1,0,0,1>(ifrom, ito, thr);
- }
+ if (eflag) {
+ if (force->newton_pair) eval<1,1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0,1>(ifrom, ito, thr);
+ } else {
+ if (force->newton_pair) eval<1,0,1,1>(ifrom, ito, thr);
+ else eval<1,0,0,1>(ifrom, ito, thr);
+ }
} else {
- if (force->newton_pair) eval<0,0,1,1>(ifrom, ito, thr);
- else eval<0,0,0,1>(ifrom, ito, thr);
+ if (force->newton_pair) eval<0,0,1,1>(ifrom, ito, thr);
+ else eval<0,0,0,1>(ifrom, ito, thr);
}
break;
case 2:
if (evflag) {
- if (eflag) {
- if (force->newton_pair) eval<1,1,1,2>(ifrom, ito, thr);
- else eval<1,1,0,2>(ifrom, ito, thr);
- } else {
- if (force->newton_pair) eval<1,0,1,2>(ifrom, ito, thr);
- else eval<1,0,0,2>(ifrom, ito, thr);
- }
+ if (eflag) {
+ if (force->newton_pair) eval<1,1,1,2>(ifrom, ito, thr);
+ else eval<1,1,0,2>(ifrom, ito, thr);
+ } else {
+ if (force->newton_pair) eval<1,0,1,2>(ifrom, ito, thr);
+ else eval<1,0,0,2>(ifrom, ito, thr);
+ }
} else {
- if (force->newton_pair) eval<0,0,1,2>(ifrom, ito, thr);
- else eval<0,0,0,2>(ifrom, ito, thr);
+ if (force->newton_pair) eval<0,0,1,2>(ifrom, ito, thr);
+ else eval<0,0,0,2>(ifrom, ito, thr);
}
break;
@@ -133,7 +133,7 @@ void PairCDEAMOMP::compute(int eflag, int vflag)
#endif
error->all(FLERR,"unsupported eam/cd pair style variant");
}
-
+
reduce_thr(this, eflag, vflag, thr);
} // end of omp parallel region
}
@@ -191,31 +191,31 @@ void PairCDEAMOMP::eval(int iifrom, int iito, ThrData * const thr)
rsq = delx*delx + dely*dely + delz*delz;
if(rsq < cutforcesq) {
- jtype = type[j];
- double r = sqrt(rsq);
- const EAMTableIndex index = radiusToTableIndex(r);
- double localrho = RhoOfR(index, jtype, itype);
- rho_t[i] += localrho;
- if(jtype == speciesB) rhoB_t[i] += localrho;
- if(NEWTON_PAIR || j < nlocal) {
- localrho = RhoOfR(index, itype, jtype);
- rho_t[j] += localrho;
- if(itype == speciesB) rhoB_t[j] += localrho;
- }
-
- if(CDEAMVERSION == 1 && itype != jtype) {
- // Note: if the i-j interaction is not concentration dependent (because either
- // i or j are not species A or B) then its contribution to D_i and D_j should
- // be ignored.
- // This if-clause is only required for a ternary.
- if((itype == speciesA && jtype == speciesB)
- || (jtype == speciesA && itype == speciesB)) {
- double Phi_AB = PhiOfR(index, itype, jtype, 1.0 / r);
- D_values_t[i] += Phi_AB;
- if(NEWTON_PAIR || j < nlocal)
- D_values_t[j] += Phi_AB;
- }
- }
+ jtype = type[j];
+ double r = sqrt(rsq);
+ const EAMTableIndex index = radiusToTableIndex(r);
+ double localrho = RhoOfR(index, jtype, itype);
+ rho_t[i] += localrho;
+ if(jtype == speciesB) rhoB_t[i] += localrho;
+ if(NEWTON_PAIR || j < nlocal) {
+ localrho = RhoOfR(index, itype, jtype);
+ rho_t[j] += localrho;
+ if(itype == speciesB) rhoB_t[j] += localrho;
+ }
+
+ if(CDEAMVERSION == 1 && itype != jtype) {
+ // Note: if the i-j interaction is not concentration dependent (because either
+ // i or j are not species A or B) then its contribution to D_i and D_j should
+ // be ignored.
+ // This if-clause is only required for a ternary.
+ if((itype == speciesA && jtype == speciesB)
+ || (jtype == speciesA && itype == speciesB)) {
+ double Phi_AB = PhiOfR(index, itype, jtype, 1.0 / r);
+ D_values_t[i] += Phi_AB;
+ if(NEWTON_PAIR || j < nlocal)
+ D_values_t[j] += Phi_AB;
+ }
+ }
}
}
}
@@ -243,7 +243,7 @@ void PairCDEAMOMP::eval(int iifrom, int iito, ThrData * const thr)
// wait until master thread is done with communication
sync_threads();
-
+
} else {
// reduce per thread density
data_reduce_thr(rho, nlocal, nthreads, 1, tid);
@@ -254,7 +254,7 @@ void PairCDEAMOMP::eval(int iifrom, int iito, ThrData * const thr)
// wait until reduction is complete
sync_threads();
}
-
+
// fp = derivative of embedding energy at each atom
// phi = embedding energy at each atom
@@ -288,8 +288,8 @@ void PairCDEAMOMP::eval(int iifrom, int iito, ThrData * const thr)
// if the electron density is exactly zero. That's why the following lines have been commented out.
//
//for(i = 0; i < nlocal + atom->nghost; i++) {
- // if(rho[i] == 0 && (type[i] == speciesA || type[i] == speciesB))
- // error->one(FLERR,"CD-EAM potential routine: Detected atom with zero electron density.");
+ // if(rho[i] == 0 && (type[i] == speciesA || type[i] == speciesB))
+ // error->one(FLERR,"CD-EAM potential routine: Detected atom with zero electron density.");
//}
// Stage II
@@ -309,39 +309,39 @@ void PairCDEAMOMP::eval(int iifrom, int iito, ThrData * const thr)
// This code line is required for ternary alloys.
if(itype != speciesA && itype != speciesB) continue;
- double x_i = rhoB[i] / rho[i]; // Concentration at atom i.
+ double x_i = rhoB[i] / rho[i]; // Concentration at atom i.
for(jj = 0; jj < jnum; jj++) {
- j = jlist[jj];
- j &= NEIGHMASK;
- jtype = type[j];
- if(itype == jtype) continue;
+ j = jlist[jj];
+ j &= NEIGHMASK;
+ jtype = type[j];
+ if(itype == jtype) continue;
- // This code line is required for ternary alloys.
- if(jtype != speciesA && jtype != speciesB) continue;
+ // This code line is required for ternary alloys.
+ if(jtype != speciesA && jtype != speciesB) continue;
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
- if(rsq < cutforcesq) {
- double r = sqrt(rsq);
- const EAMTableIndex index = radiusToTableIndex(r);
+ if(rsq < cutforcesq) {
+ double r = sqrt(rsq);
+ const EAMTableIndex index = radiusToTableIndex(r);
- // The concentration independent part of the cross pair potential.
- double Phi_AB = PhiOfR(index, itype, jtype, 1.0 / r);
+ // The concentration independent part of the cross pair potential.
+ double Phi_AB = PhiOfR(index, itype, jtype, 1.0 / r);
- // Average concentration of two sites
- double x_ij = 0.5 * (x_i + rhoB[j]/rho[j]);
+ // Average concentration of two sites
+ double x_ij = 0.5 * (x_i + rhoB[j]/rho[j]);
- // Calculate derivative of h(x_ij) polynomial function.
- double h_prime = evalHprime(x_ij);
+ // Calculate derivative of h(x_ij) polynomial function.
+ double h_prime = evalHprime(x_ij);
- D_values_t[i] += h_prime * Phi_AB / (2.0 * rho[i] * rho[i]);
- if(NEWTON_PAIR || j < nlocal)
- D_values_t[j] += h_prime * Phi_AB / (2.0 * rho[j] * rho[j]);
- }
+ D_values_t[i] += h_prime * Phi_AB / (2.0 * rho[i] * rho[i]);
+ if(NEWTON_PAIR || j < nlocal)
+ D_values_t[j] += h_prime * Phi_AB / (2.0 * rho[j] * rho[j]);
+ }
}
}
@@ -355,11 +355,11 @@ void PairCDEAMOMP::eval(int iifrom, int iito, ThrData * const thr)
#pragma omp master
#endif
{ communicationStage = 3;
- comm->reverse_comm_pair(this); }
+ comm->reverse_comm_pair(this); }
// wait until master thread is done with communication
sync_threads();
-
+
} else {
data_reduce_thr(D_values, nlocal, nthreads, 1, tid);
@@ -372,7 +372,7 @@ void PairCDEAMOMP::eval(int iifrom, int iito, ThrData * const thr)
#endif
{ communicationStage = 4;
comm->forward_comm_pair(this); }
-
+
// wait until master thread is done with communication
sync_threads();
}
@@ -392,7 +392,7 @@ void PairCDEAMOMP::eval(int iifrom, int iito, ThrData * const thr)
jnum = numneigh[i];
// Concentration at site i
- double x_i = -1.0; // The value -1 indicates: no concentration dependence for all interactions of atom i.
+ double x_i = -1.0; // The value -1 indicates: no concentration dependence for all interactions of atom i.
// It will be replaced by the concentration at site i if atom i is either A or B.
double D_i, h_prime_i;
@@ -405,11 +405,11 @@ void PairCDEAMOMP::eval(int iifrom, int iito, ThrData * const thr)
ASSERT(x_i >= 0 && x_i<=1.0);
if(CDEAMVERSION == 1) {
- // Calculate derivative of h(x_i) polynomial function.
- h_prime_i = evalHprime(x_i);
- D_i = D_values[i] * h_prime_i / (2.0 * rho[i] * rho[i]);
+ // Calculate derivative of h(x_i) polynomial function.
+ h_prime_i = evalHprime(x_i);
+ D_i = D_values[i] * h_prime_i / (2.0 * rho[i] * rho[i]);
} else if(CDEAMVERSION == 2) {
- D_i = D_values[i];
+ D_i = D_values[i];
} else ASSERT(false);
}
@@ -423,95 +423,95 @@ void PairCDEAMOMP::eval(int iifrom, int iito, ThrData * const thr)
rsq = delx*delx + dely*dely + delz*delz;
if(rsq < cutforcesq) {
- jtype = type[j];
- double r = sqrt(rsq);
- const EAMTableIndex index = radiusToTableIndex(r);
-
- // rhoip = derivative of (density at atom j due to atom i)
- // rhojp = derivative of (density at atom i due to atom j)
- // psip needs both fp[i] and fp[j] terms since r_ij appears in two
- // terms of embed eng: Fi(sum rho_ij) and Fj(sum rho_ji)
- // hence embed' = Fi(sum rho_ij) rhojp + Fj(sum rho_ji) rhoip
- rhoip = RhoPrimeOfR(index, itype, jtype);
- rhojp = RhoPrimeOfR(index, jtype, itype);
- fpair = fp[i]*rhojp + fp[j]*rhoip;
- recip = 1.0/r;
-
- double x_j = -1; // The value -1 indicates: no concentration dependence for this i-j pair
- // because atom j is not of species A nor B.
-
- // This code line is required for ternary alloy.
- if(jtype == speciesA || jtype == speciesB) {
- ASSERT(rho[i] != 0.0);
- ASSERT(rho[j] != 0.0);
-
- // Compute local concentration at site j.
- x_j = rhoB[j]/rho[j];
- ASSERT(x_j >= 0 && x_j<=1.0);
-
- double D_j;
- if(CDEAMVERSION == 1) {
- // Calculate derivative of h(x_j) polynomial function.
- double h_prime_j = evalHprime(x_j);
- D_j = D_values[j] * h_prime_j / (2.0 * rho[j] * rho[j]);
- } else if(CDEAMVERSION == 2) {
- D_j = D_values[j];
- } else ASSERT(false);
-
- double t2 = -rhoB[j];
- if(itype == speciesB) t2 += rho[j];
- fpair += D_j * rhoip * t2;
- }
-
- // This if-clause is only required for a ternary alloy.
- // Actually we don't need it at all because D_i should be zero anyway if
- // atom i has no concentration dependent interactions (because it is not species A or B).
- if(x_i != -1.0) {
- double t1 = -rhoB[i];
- if(jtype == speciesB) t1 += rho[i];
- fpair += D_i * rhojp * t1;
- }
-
- double phip;
- double phi = PhiOfR(index, itype, jtype, recip, phip);
- if(itype == jtype || x_i == -1.0 || x_j == -1.0) {
- // Case of no concentration dependence.
- fpair += phip;
- } else {
- // We have a concentration dependence for the i-j interaction.
- double h;
- if(CDEAMVERSION == 1) {
- // Calculate h(x_i) polynomial function.
- double h_i = evalH(x_i);
- // Calculate h(x_j) polynomial function.
- double h_j = evalH(x_j);
- h = 0.5 * (h_i + h_j);
- } else if(CDEAMVERSION == 2) {
- // Average concentration.
- double x_ij = 0.5 * (x_i + x_j);
- // Calculate h(x_ij) polynomial function.
- h = evalH(x_ij);
- } else ASSERT(false);
-
- fpair += h * phip;
- phi *= h;
- }
-
- // Divide by r_ij and negate to get forces from gradient.
- fpair /= -r;
-
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
- if(NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if(EFLAG) evdwl = phi;
- if(EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,evdwl,0.0,
- fpair,delx,dely,delz,thr);
+ jtype = type[j];
+ double r = sqrt(rsq);
+ const EAMTableIndex index = radiusToTableIndex(r);
+
+ // rhoip = derivative of (density at atom j due to atom i)
+ // rhojp = derivative of (density at atom i due to atom j)
+ // psip needs both fp[i] and fp[j] terms since r_ij appears in two
+ // terms of embed eng: Fi(sum rho_ij) and Fj(sum rho_ji)
+ // hence embed' = Fi(sum rho_ij) rhojp + Fj(sum rho_ji) rhoip
+ rhoip = RhoPrimeOfR(index, itype, jtype);
+ rhojp = RhoPrimeOfR(index, jtype, itype);
+ fpair = fp[i]*rhojp + fp[j]*rhoip;
+ recip = 1.0/r;
+
+ double x_j = -1; // The value -1 indicates: no concentration dependence for this i-j pair
+ // because atom j is not of species A nor B.
+
+ // This code line is required for ternary alloy.
+ if(jtype == speciesA || jtype == speciesB) {
+ ASSERT(rho[i] != 0.0);
+ ASSERT(rho[j] != 0.0);
+
+ // Compute local concentration at site j.
+ x_j = rhoB[j]/rho[j];
+ ASSERT(x_j >= 0 && x_j<=1.0);
+
+ double D_j;
+ if(CDEAMVERSION == 1) {
+ // Calculate derivative of h(x_j) polynomial function.
+ double h_prime_j = evalHprime(x_j);
+ D_j = D_values[j] * h_prime_j / (2.0 * rho[j] * rho[j]);
+ } else if(CDEAMVERSION == 2) {
+ D_j = D_values[j];
+ } else ASSERT(false);
+
+ double t2 = -rhoB[j];
+ if(itype == speciesB) t2 += rho[j];
+ fpair += D_j * rhoip * t2;
+ }
+
+ // This if-clause is only required for a ternary alloy.
+ // Actually we don't need it at all because D_i should be zero anyway if
+ // atom i has no concentration dependent interactions (because it is not species A or B).
+ if(x_i != -1.0) {
+ double t1 = -rhoB[i];
+ if(jtype == speciesB) t1 += rho[i];
+ fpair += D_i * rhojp * t1;
+ }
+
+ double phip;
+ double phi = PhiOfR(index, itype, jtype, recip, phip);
+ if(itype == jtype || x_i == -1.0 || x_j == -1.0) {
+ // Case of no concentration dependence.
+ fpair += phip;
+ } else {
+ // We have a concentration dependence for the i-j interaction.
+ double h;
+ if(CDEAMVERSION == 1) {
+ // Calculate h(x_i) polynomial function.
+ double h_i = evalH(x_i);
+ // Calculate h(x_j) polynomial function.
+ double h_j = evalH(x_j);
+ h = 0.5 * (h_i + h_j);
+ } else if(CDEAMVERSION == 2) {
+ // Average concentration.
+ double x_ij = 0.5 * (x_i + x_j);
+ // Calculate h(x_ij) polynomial function.
+ h = evalH(x_ij);
+ } else ASSERT(false);
+
+ fpair += h * phip;
+ phi *= h;
+ }
+
+ // Divide by r_ij and negate to get forces from gradient.
+ fpair /= -r;
+
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+ if(NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if(EFLAG) evdwl = phi;
+ if(EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,evdwl,0.0,
+ fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_cdeam_omp.h b/src/USER-OMP/pair_cdeam_omp.h
index 46f460f8fa07144c4235bd7fde547dc99fbe7575..2839ab0ed0088166d9badea7a9b7df29aaa6ab49 100644
--- a/src/USER-OMP/pair_cdeam_omp.h
+++ b/src/USER-OMP/pair_cdeam_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -50,7 +50,7 @@ class PairCDEAMOMP : public PairCDEAM, public ThrOMP {
/// Constructor.
PairCDEAM_OneSiteOMP(class LAMMPS* lmp) : PairEAM(lmp), PairCDEAMOMP(lmp, 1) {}
};
-
+
/// The two-site concentration formulation of CD-EAM.
class PairCDEAM_TwoSiteOMP : public PairCDEAMOMP
{
diff --git a/src/USER-OMP/pair_colloid_omp.cpp b/src/USER-OMP/pair_colloid_omp.cpp
index 803298436571b588e05842113e8d757b6a64d4c5..e2f5c56d99f2bf994ff8778f609a729a48a8ad63 100644
--- a/src/USER-OMP/pair_colloid_omp.cpp
+++ b/src/USER-OMP/pair_colloid_omp.cpp
@@ -57,11 +57,11 @@ void PairColloidOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -120,94 +120,94 @@ void PairColloidOMP::eval(int iifrom, int iito, ThrData * const thr)
jtype = type[j];
if (rsq >= cutsq[itype][jtype]) continue;
-
+
switch(form[itype][jtype]) {
case SMALL_SMALL:
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- fpair = factor_lj*forcelj*r2inv;
- if (EFLAG)
- evdwl = r6inv*(r6inv*lj3[itype][jtype]-lj4[itype][jtype]) -
- offset[itype][jtype];
- break;
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ fpair = factor_lj*forcelj*r2inv;
+ if (EFLAG)
+ evdwl = r6inv*(r6inv*lj3[itype][jtype]-lj4[itype][jtype]) -
+ offset[itype][jtype];
+ break;
case SMALL_LARGE:
- c2 = a2[itype][jtype];
- K[1] = c2*c2;
- K[2] = rsq;
- K[0] = K[1] - rsq;
- K[4] = rsq*rsq;
- K[3] = K[1] - K[2];
- K[3] *= K[3]*K[3];
- K[6] = K[3]*K[3];
- fR = sigma3[itype][jtype]*a12[itype][jtype]*c2*K[1]/K[3];
- fpair = 4.0/15.0*fR*factor_lj *
- (2.0*(K[1]+K[2]) * (K[1]*(5.0*K[1]+22.0*K[2])+5.0*K[4]) *
- sigma6[itype][jtype]/K[6]-5.0) / K[0];
- if (EFLAG)
- evdwl = 2.0/9.0*fR *
- (1.0-(K[1]*(K[1]*(K[1]/3.0+3.0*K[2])+4.2*K[4])+K[2]*K[4]) *
- sigma6[itype][jtype]/K[6]) - offset[itype][jtype];
-
- if (check_error_thr((rsq <= K[1]),tid,FLERR,
- "Overlapping small/large in pair colloid"))
- return;
-
- break;
+ c2 = a2[itype][jtype];
+ K[1] = c2*c2;
+ K[2] = rsq;
+ K[0] = K[1] - rsq;
+ K[4] = rsq*rsq;
+ K[3] = K[1] - K[2];
+ K[3] *= K[3]*K[3];
+ K[6] = K[3]*K[3];
+ fR = sigma3[itype][jtype]*a12[itype][jtype]*c2*K[1]/K[3];
+ fpair = 4.0/15.0*fR*factor_lj *
+ (2.0*(K[1]+K[2]) * (K[1]*(5.0*K[1]+22.0*K[2])+5.0*K[4]) *
+ sigma6[itype][jtype]/K[6]-5.0) / K[0];
+ if (EFLAG)
+ evdwl = 2.0/9.0*fR *
+ (1.0-(K[1]*(K[1]*(K[1]/3.0+3.0*K[2])+4.2*K[4])+K[2]*K[4]) *
+ sigma6[itype][jtype]/K[6]) - offset[itype][jtype];
+
+ if (check_error_thr((rsq <= K[1]),tid,FLERR,
+ "Overlapping small/large in pair colloid"))
+ return;
+
+ break;
case LARGE_LARGE:
- r = sqrt(rsq);
- c1 = a1[itype][jtype];
- c2 = a2[itype][jtype];
- K[0] = c1*c2;
- K[1] = c1+c2;
- K[2] = c1-c2;
- K[3] = K[1]+r;
- K[4] = K[1]-r;
- K[5] = K[2]+r;
- K[6] = K[2]-r;
- K[7] = 1.0/(K[3]*K[4]);
- K[8] = 1.0/(K[5]*K[6]);
- g[0] = pow(K[3],-7.0);
- g[1] = pow(K[4],-7.0);
- g[2] = pow(K[5],-7.0);
- g[3] = pow(K[6],-7.0);
- h[0] = ((K[3]+5.0*K[1])*K[3]+30.0*K[0])*g[0];
- h[1] = ((K[4]+5.0*K[1])*K[4]+30.0*K[0])*g[1];
- h[2] = ((K[5]+5.0*K[2])*K[5]-30.0*K[0])*g[2];
- h[3] = ((K[6]+5.0*K[2])*K[6]-30.0*K[0])*g[3];
- g[0] *= 42.0*K[0]/K[3]+6.0*K[1]+K[3];
- g[1] *= 42.0*K[0]/K[4]+6.0*K[1]+K[4];
- g[2] *= -42.0*K[0]/K[5]+6.0*K[2]+K[5];
- g[3] *= -42.0*K[0]/K[6]+6.0*K[2]+K[6];
-
- fR = a12[itype][jtype]*sigma6[itype][jtype]/r/37800.0;
- evdwl = fR * (h[0]-h[1]-h[2]+h[3]);
- dUR = evdwl/r + 5.0*fR*(g[0]+g[1]-g[2]-g[3]);
- dUA = -a12[itype][jtype]/3.0*r*((2.0*K[0]*K[7]+1.0)*K[7] +
- (2.0*K[0]*K[8]-1.0)*K[8]);
- fpair = factor_lj * (dUR+dUA)/r;
- if (EFLAG)
- evdwl += a12[itype][jtype]/6.0 *
- (2.0*K[0]*(K[7]+K[8])-log(K[8]/K[7])) - offset[itype][jtype];
- if (r <= K[1]) error->one(FLERR,"Overlapping large/large in pair colloid");
- break;
+ r = sqrt(rsq);
+ c1 = a1[itype][jtype];
+ c2 = a2[itype][jtype];
+ K[0] = c1*c2;
+ K[1] = c1+c2;
+ K[2] = c1-c2;
+ K[3] = K[1]+r;
+ K[4] = K[1]-r;
+ K[5] = K[2]+r;
+ K[6] = K[2]-r;
+ K[7] = 1.0/(K[3]*K[4]);
+ K[8] = 1.0/(K[5]*K[6]);
+ g[0] = pow(K[3],-7.0);
+ g[1] = pow(K[4],-7.0);
+ g[2] = pow(K[5],-7.0);
+ g[3] = pow(K[6],-7.0);
+ h[0] = ((K[3]+5.0*K[1])*K[3]+30.0*K[0])*g[0];
+ h[1] = ((K[4]+5.0*K[1])*K[4]+30.0*K[0])*g[1];
+ h[2] = ((K[5]+5.0*K[2])*K[5]-30.0*K[0])*g[2];
+ h[3] = ((K[6]+5.0*K[2])*K[6]-30.0*K[0])*g[3];
+ g[0] *= 42.0*K[0]/K[3]+6.0*K[1]+K[3];
+ g[1] *= 42.0*K[0]/K[4]+6.0*K[1]+K[4];
+ g[2] *= -42.0*K[0]/K[5]+6.0*K[2]+K[5];
+ g[3] *= -42.0*K[0]/K[6]+6.0*K[2]+K[6];
+
+ fR = a12[itype][jtype]*sigma6[itype][jtype]/r/37800.0;
+ evdwl = fR * (h[0]-h[1]-h[2]+h[3]);
+ dUR = evdwl/r + 5.0*fR*(g[0]+g[1]-g[2]-g[3]);
+ dUA = -a12[itype][jtype]/3.0*r*((2.0*K[0]*K[7]+1.0)*K[7] +
+ (2.0*K[0]*K[8]-1.0)*K[8]);
+ fpair = factor_lj * (dUR+dUA)/r;
+ if (EFLAG)
+ evdwl += a12[itype][jtype]/6.0 *
+ (2.0*K[0]*(K[7]+K[8])-log(K[8]/K[7])) - offset[itype][jtype];
+ if (r <= K[1]) error->one(FLERR,"Overlapping large/large in pair colloid");
+ break;
}
-
+
if (EFLAG) evdwl *= factor_lj;
-
+
fxtmp += delx*fpair;
fytmp += dely*fpair;
fztmp += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
}
if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
- evdwl,0.0,fpair,delx,dely,delz,thr);
+ evdwl,0.0,fpair,delx,dely,delz,thr);
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
diff --git a/src/USER-OMP/pair_colloid_omp.h b/src/USER-OMP/pair_colloid_omp.h
index cde7e9b6502686ca84f7a4d26a985466341e9656..6605fbce008741351424a3e2295da58b33af702f 100644
--- a/src/USER-OMP/pair_colloid_omp.h
+++ b/src/USER-OMP/pair_colloid_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_comb_omp.cpp b/src/USER-OMP/pair_comb_omp.cpp
index c44bd4027b175d9701dedddfe8c676de2b2260e5..eea2c6b61027d3a55aeccf3c75b2a31c3350ec07 100644
--- a/src/USER-OMP/pair_comb_omp.cpp
+++ b/src/USER-OMP/pair_comb_omp.cpp
@@ -64,11 +64,11 @@ void PairCombOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (vflag_atom) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (vflag_atom) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (vflag_atom) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (vflag_atom) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else eval<0,0,0>(ifrom, ito, thr);
@@ -89,7 +89,7 @@ void PairCombOMP::eval(int iifrom, int iito, ThrData * const thr)
int mr1,mr2,mr3;
int rsc,inty;
double elp_ij,filp[3],fjlp[3],fklp[3];
- double iq,jq;
+ double iq,jq;
double yaself;
double potal,fac11,fac11e;
double vionij,fvionij,sr1,sr2,sr3,Eov,Fov;
@@ -108,7 +108,7 @@ void PairCombOMP::eval(int iifrom, int iito, ThrData * const thr)
numneigh = list->numneigh;
firstneigh = list->firstneigh;
- yaself = vionij = fvionij = Eov = Fov = 0.0;
+ yaself = vionij = fvionij = Eov = Fov = 0.0;
double fxtmp,fytmp,fztmp;
double fjxtmp,fjytmp,fjztmp;
@@ -139,7 +139,7 @@ void PairCombOMP::eval(int iifrom, int iito, ThrData * const thr)
yaself = self(¶ms[iparam_i],iq,potal);
if (EVFLAG) ev_tally_thr(this,i,i,nlocal,0,yaself,
- 0.0,0.0,0.0,0.0,0.0,thr);
+ 0.0,0.0,0.0,0.0,0.0,thr);
// two-body interactions (long and short repulsive)
@@ -154,16 +154,16 @@ void PairCombOMP::eval(int iifrom, int iito, ThrData * const thr)
jtag = tag[j];
if (itag > jtag) {
- if ((itag+jtag) % 2 == 0) continue;
+ if ((itag+jtag) % 2 == 0) continue;
} else if (itag < jtag) {
- if ((itag+jtag) % 2 == 1) continue;
+ if ((itag+jtag) % 2 == 1) continue;
} else {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
- if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
+ if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
}
- // Qj calculates 2-body Coulombic
+ // Qj calculates 2-body Coulombic
jtype = map[type[j]];
jq = q[j];
@@ -188,7 +188,7 @@ void PairCombOMP::eval(int iifrom, int iito, ThrData * const thr)
// 1/r energy and forces
direct(inty,mr1,mr2,mr3,rsq,sr1,sr2,sr3,iq,jq,
- potal,fac11,fac11e,vionij,fvionij);
+ potal,fac11,fac11e,vionij,fvionij);
// field correction to self energy
@@ -204,9 +204,9 @@ void PairCombOMP::eval(int iifrom, int iito, ThrData * const thr)
f[j][1] -= dely*fvionij;
f[j][2] -= delz*fvionij;
- if (EVFLAG)
- ev_tally_thr(this,i,j,nlocal,/* newton_pair */ 1,
- 0.0,vionij,fvionij,delx,dely,delz,thr);
+ if (EVFLAG)
+ ev_tally_thr(this,i,j,nlocal,/* newton_pair */ 1,
+ 0.0,vionij,fvionij,delx,dely,delz,thr);
// short range q-independent
@@ -224,8 +224,8 @@ void PairCombOMP::eval(int iifrom, int iito, ThrData * const thr)
f[j][2] -= delz*fpair;
if (EVFLAG)
- ev_tally_thr(this,i,j,nlocal,/* newton_pair */ 1,
- evdwl,0.0,fpair,delx,dely,delz,thr);
+ ev_tally_thr(this,i,j,nlocal,/* newton_pair */ 1,
+ evdwl,0.0,fpair,delx,dely,delz,thr);
}
// accumulate coordination number information
@@ -234,23 +234,23 @@ void PairCombOMP::eval(int iifrom, int iito, ThrData * const thr)
int numcoor = 0;
for (jj = 0; jj < sht_jnum; jj++) {
j = sht_jlist[jj];
- jtype = map[type[j]];
- iparam_ij = elem2param[itype][jtype][jtype];
-
- if(params[iparam_ij].hfocor > 0.0 ) {
- delr1[0] = x[j][0] - xtmp;
- delr1[1] = x[j][1] - ytmp;
- delr1[2] = x[j][2] - ztmp;
- rsq1 = vec3_dot(delr1,delr1);
-
- if (rsq1 > params[iparam_ij].cutsq) continue;
- ++numcoor;
- }
+ jtype = map[type[j]];
+ iparam_ij = elem2param[itype][jtype][jtype];
+
+ if(params[iparam_ij].hfocor > 0.0 ) {
+ delr1[0] = x[j][0] - xtmp;
+ delr1[1] = x[j][1] - ytmp;
+ delr1[2] = x[j][2] - ztmp;
+ rsq1 = vec3_dot(delr1,delr1);
+
+ if (rsq1 > params[iparam_ij].cutsq) continue;
+ ++numcoor;
+ }
}
- NCo[i] = numcoor;
+ NCo[i] = numcoor;
}
- // three-body interactions
+ // three-body interactions
// half i-j loop
for (jj = 0; jj < sht_jnum; jj++) {
@@ -278,34 +278,34 @@ void PairCombOMP::eval(int iifrom, int iito, ThrData * const thr)
cuo_flag1 = 0; cuo_flag2 = 0;
for (kk = 0; kk < sht_jnum; kk++) {
- k = sht_jlist[kk];
- if (j == k) continue;
- ktype = map[type[k]];
- iparam_ijk = elem2param[itype][jtype][ktype];
+ k = sht_jlist[kk];
+ if (j == k) continue;
+ ktype = map[type[k]];
+ iparam_ijk = elem2param[itype][jtype][ktype];
- delr2[0] = x[k][0] - xtmp;
- delr2[1] = x[k][1] - ytmp;
- delr2[2] = x[k][2] - ztmp;
- rsq2 = vec3_dot(delr2,delr2);
+ delr2[0] = x[k][0] - xtmp;
+ delr2[1] = x[k][1] - ytmp;
+ delr2[2] = x[k][2] - ztmp;
+ rsq2 = vec3_dot(delr2,delr2);
- if (rsq2 > params[iparam_ijk].cutsq) continue;
+ if (rsq2 > params[iparam_ijk].cutsq) continue;
- zeta_ij += zeta(¶ms[iparam_ijk],rsq1,rsq2,delr1,delr2);
+ zeta_ij += zeta(¶ms[iparam_ijk],rsq1,rsq2,delr1,delr2);
- if (params[iparam_ijk].hfocor == -2.0) cuo_flag1 = 1;
- if (params[iparam_ijk].hfocor == -1.0) cuo_flag2 = 1;
+ if (params[iparam_ijk].hfocor == -2.0) cuo_flag1 = 1;
+ if (params[iparam_ijk].hfocor == -1.0) cuo_flag2 = 1;
}
if (cuo_flag1 && cuo_flag2) cuo_flag = 1;
else cuo_flag = 0;
force_zeta(¶ms[iparam_ij],EFLAG,i,nj,rsq1,zeta_ij,
- iq,jq,fpair,prefactor,evdwl);
+ iq,jq,fpair,prefactor,evdwl);
// over-coordination correction for HfO2
if (cor_flag && NCo[i] != 0)
- Over_cor(¶ms[iparam_ij],rsq1,NCo[i],Eov, Fov);
+ Over_cor(¶ms[iparam_ij],rsq1,NCo[i],Eov, Fov);
evdwl += Eov;
fpair += Fov;
@@ -317,47 +317,47 @@ void PairCombOMP::eval(int iifrom, int iito, ThrData * const thr)
fjztmp -= delr1[2]*fpair;
if (EVFLAG) ev_tally_thr(this,i,j,nlocal,/* newton_pair */ 1,evdwl,0.0,
- -fpair,-delr1[0],-delr1[1],-delr1[2],thr);
+ -fpair,-delr1[0],-delr1[1],-delr1[2],thr);
// attractive term via loop over k (3-body forces)
for (kk = 0; kk < sht_jnum; kk++) {
- k = sht_jlist[kk];
- if (j == k) continue;
- ktype = map[type[k]];
- iparam_ijk = elem2param[itype][jtype][ktype];
-
- delr2[0] = x[k][0] - xtmp;
- delr2[1] = x[k][1] - ytmp;
- delr2[2] = x[k][2] - ztmp;
- rsq2 = vec3_dot(delr2,delr2);
- if (rsq2 > params[iparam_ijk].cutsq) continue;
-
- for (rsc = 0; rsc < 3; rsc++)
- fi[rsc] = fj[rsc] = fk[rsc] = 0.0;
-
- attractive(¶ms[iparam_ijk],prefactor,
- rsq1,rsq2,delr1,delr2,fi,fj,fk);
-
- // 3-body LP and BB correction and forces
-
- elp_ij = elp(¶ms[iparam_ijk],rsq1,rsq2,delr1,delr2);
- flp(¶ms[iparam_ijk],rsq1,rsq2,delr1,delr2,filp,fjlp,fklp);
-
- fxtmp += fi[0] + filp[0];
- fytmp += fi[1] + filp[1];
- fztmp += fi[2] + filp[2];
- fjxtmp += fj[0] + fjlp[0];
- fjytmp += fj[1] + fjlp[1];
- fjztmp += fj[2] + fjlp[2];
- f[k][0] += fk[0] + fklp[0];
- f[k][1] += fk[1] + fklp[1];
- f[k][2] += fk[2] + fklp[2];
-
- if (EVFLAG)
- ev_tally_thr(this,i,j,nlocal,/* newton_pair */ 1,
- elp_ij,0.0,0.0,0.0,0.0,0.0, thr);
- if (VFLAG_ATOM) v_tally3_thr(i,j,k,fj,fk,delr1,delr2,thr);
+ k = sht_jlist[kk];
+ if (j == k) continue;
+ ktype = map[type[k]];
+ iparam_ijk = elem2param[itype][jtype][ktype];
+
+ delr2[0] = x[k][0] - xtmp;
+ delr2[1] = x[k][1] - ytmp;
+ delr2[2] = x[k][2] - ztmp;
+ rsq2 = vec3_dot(delr2,delr2);
+ if (rsq2 > params[iparam_ijk].cutsq) continue;
+
+ for (rsc = 0; rsc < 3; rsc++)
+ fi[rsc] = fj[rsc] = fk[rsc] = 0.0;
+
+ attractive(¶ms[iparam_ijk],prefactor,
+ rsq1,rsq2,delr1,delr2,fi,fj,fk);
+
+ // 3-body LP and BB correction and forces
+
+ elp_ij = elp(¶ms[iparam_ijk],rsq1,rsq2,delr1,delr2);
+ flp(¶ms[iparam_ijk],rsq1,rsq2,delr1,delr2,filp,fjlp,fklp);
+
+ fxtmp += fi[0] + filp[0];
+ fytmp += fi[1] + filp[1];
+ fztmp += fi[2] + filp[2];
+ fjxtmp += fj[0] + fjlp[0];
+ fjytmp += fj[1] + fjlp[1];
+ fjztmp += fj[2] + fjlp[2];
+ f[k][0] += fk[0] + fklp[0];
+ f[k][1] += fk[1] + fklp[1];
+ f[k][2] += fk[2] + fklp[2];
+
+ if (EVFLAG)
+ ev_tally_thr(this,i,j,nlocal,/* newton_pair */ 1,
+ elp_ij,0.0,0.0,0.0,0.0,0.0, thr);
+ if (VFLAG_ATOM) v_tally3_thr(i,j,k,fj,fk,delr1,delr2,thr);
}
f[j][0] += fjxtmp;
f[j][1] += fjytmp;
@@ -440,7 +440,7 @@ double PairCombOMP::yasu_char(double *qf_fix, int &igroup)
for (int jj = 0; jj < jnum; jj++) {
const int j = jlist[jj] & NEIGHMASK;
- const int jtag = tag[j];
+ const int jtag = tag[j];
if (itag > jtag) {
if ((itag+jtag) % 2 == 0) continue;
@@ -450,7 +450,7 @@ double PairCombOMP::yasu_char(double *qf_fix, int &igroup)
if (x[j][2] < ytmp) continue;
if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
- }
+ }
const int jtype = map[type[j]];
double jq = q[j];
@@ -485,32 +485,32 @@ double PairCombOMP::yasu_char(double *qf_fix, int &igroup)
#endif
qf[j] += (iq * fqij + fqjj);
}
-
+
// three-body interactions
-
+
for (int jj = 0; jj < jnum; jj++) {
- const int j = jlist[jj] & NEIGHMASK;
- const int jtype = map[type[j]];
- const double jq = q[j];
+ const int j = jlist[jj] & NEIGHMASK;
+ const int jtype = map[type[j]];
+ const double jq = q[j];
- delr1[0] = x[j][0] - xtmp;
- delr1[1] = x[j][1] - ytmp;
- delr1[2] = x[j][2] - ztmp;
- double rsq1 = vec3_dot(delr1,delr1);
+ delr1[0] = x[j][0] - xtmp;
+ delr1[1] = x[j][1] - ytmp;
+ delr1[2] = x[j][2] - ztmp;
+ double rsq1 = vec3_dot(delr1,delr1);
const int iparam_ij = elem2param[itype][jtype][jtype];
if (rsq1 > params[iparam_ij].cutsq) continue;
- nj ++;
+ nj ++;
// charge force in Aij and Bij
qfo_short(¶ms[iparam_ij],i,nj,rsq1,iq,jq,fqij,fqjj);
- fqi += fqij;
+ fqi += fqij;
#if defined(_OPENMP)
#pragma omp atomic
#endif
- qf[j] += fqjj;
+ qf[j] += fqjj;
}
#if defined(_OPENMP)
@@ -553,7 +553,7 @@ void PairCombOMP::Short_neigh_thr()
nmax = atom->nmax;
memory->sfree(sht_first);
sht_first = (int **) memory->smalloc(nmax*sizeof(int *),
- "pair:sht_first");
+ "pair:sht_first");
memory->grow(sht_num,nmax,"pair:sht_num");
memory->grow(NCo,nmax,"pair:NCo");
memory->grow(bbij,nmax,nmax,"pair:bbij");
@@ -596,42 +596,42 @@ void PairCombOMP::Short_neigh_thr()
if (iifrom < inum) {
for (ii = iifrom; ii < iito; ii++) {
- i = ilist[ii];
+ i = ilist[ii];
#if defined(_OPENMP)
#pragma omp critical
#endif
- if(pgsize - npntj < oneatom) {
- npntj = 0;
- npage += nthreads;
- if (npage >= maxpage) add_pages(nthreads);
- }
-
- neighptrj = &pages[npage][npntj];
- nj = 0;
-
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
-
- jlist = firstneigh[i];
- jnum = numneigh[i];
-
- for (jj = 0; jj < jnum; jj++) {
- j = jlist[jj];
- j &= NEIGHMASK;
-
- delrj[0] = xtmp - x[j][0];
- delrj[1] = ytmp - x[j][1];
- delrj[2] = ztmp - x[j][2];
- rsq = vec3_dot(delrj,delrj);
-
- if (rsq > cutmin) continue;
- neighptrj[nj++] = j;
- }
- sht_first[i] = neighptrj;
- sht_num[i] = nj;
- npntj += nj;
+ if(pgsize - npntj < oneatom) {
+ npntj = 0;
+ npage += nthreads;
+ if (npage >= maxpage) add_pages(nthreads);
+ }
+
+ neighptrj = &pages[npage][npntj];
+ nj = 0;
+
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
+ j &= NEIGHMASK;
+
+ delrj[0] = xtmp - x[j][0];
+ delrj[1] = ytmp - x[j][1];
+ delrj[2] = ztmp - x[j][2];
+ rsq = vec3_dot(delrj,delrj);
+
+ if (rsq > cutmin) continue;
+ neighptrj[nj++] = j;
+ }
+ sht_first[i] = neighptrj;
+ sht_num[i] = nj;
+ npntj += nj;
}
}
}
diff --git a/src/USER-OMP/pair_coul_cut_omp.cpp b/src/USER-OMP/pair_coul_cut_omp.cpp
index e485efdb3cc5a42a934ce6951011dba0cc22587d..37b311f93e4c45d6a135e3f7cf5696bdebb0aec6 100644
--- a/src/USER-OMP/pair_coul_cut_omp.cpp
+++ b/src/USER-OMP/pair_coul_cut_omp.cpp
@@ -56,11 +56,11 @@ void PairCoulCutOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -122,25 +122,25 @@ void PairCoulCutOMP::eval(int iifrom, int iito, ThrData * const thr)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- rinv = sqrt(r2inv);
- forcecoul = qqrd2e * scale[itype][jtype] * qtmp*q[j]*rinv;
- fpair = factor_coul*forcecoul * r2inv;
-
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (EFLAG)
- ecoul = factor_coul * qqrd2e * scale[itype][jtype] * qtmp*q[j]*rinv;
-
- if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
- 0.0,ecoul,fpair,delx,dely,delz,thr);
+ r2inv = 1.0/rsq;
+ rinv = sqrt(r2inv);
+ forcecoul = qqrd2e * scale[itype][jtype] * qtmp*q[j]*rinv;
+ fpair = factor_coul*forcecoul * r2inv;
+
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (EFLAG)
+ ecoul = factor_coul * qqrd2e * scale[itype][jtype] * qtmp*q[j]*rinv;
+
+ if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
+ 0.0,ecoul,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_coul_cut_omp.h b/src/USER-OMP/pair_coul_cut_omp.h
index 3499ee4ae639bbe8a10c8e5c2659fb07478a63b1..9e5fe81197cfa0e072680fcfe0057e61583412a8 100644
--- a/src/USER-OMP/pair_coul_cut_omp.h
+++ b/src/USER-OMP/pair_coul_cut_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_coul_debye_omp.cpp b/src/USER-OMP/pair_coul_debye_omp.cpp
index 580b85087e4d3ceebde238097f66fa9dd6bc8f7b..4c8aaba0078f3cb65f77fc261e0f287d0922c04d 100644
--- a/src/USER-OMP/pair_coul_debye_omp.cpp
+++ b/src/USER-OMP/pair_coul_debye_omp.cpp
@@ -56,11 +56,11 @@ void PairCoulDebyeOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -122,27 +122,27 @@ void PairCoulDebyeOMP::eval(int iifrom, int iito, ThrData * const thr)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- r = sqrt(rsq);
- rinv = 1.0/r;
- screening = exp(-kappa*r);
- forcecoul = qqrd2e * qtmp*q[j] * screening * (kappa + rinv);
- fpair = factor_coul*forcecoul * r2inv;
-
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (EFLAG)
- ecoul = factor_coul * qqrd2e * qtmp*q[j] * rinv * screening;
-
- if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
- 0.0,ecoul,fpair,delx,dely,delz,thr);
+ r2inv = 1.0/rsq;
+ r = sqrt(rsq);
+ rinv = 1.0/r;
+ screening = exp(-kappa*r);
+ forcecoul = qqrd2e * qtmp*q[j] * screening * (kappa + rinv);
+ fpair = factor_coul*forcecoul * r2inv;
+
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (EFLAG)
+ ecoul = factor_coul * qqrd2e * qtmp*q[j] * rinv * screening;
+
+ if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
+ 0.0,ecoul,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_coul_debye_omp.h b/src/USER-OMP/pair_coul_debye_omp.h
index f016de8b5d8e8a7e29de1ddb8a6f63f8e92decf1..dc0864755357e71d93b32ecbb98624c5806af731 100644
--- a/src/USER-OMP/pair_coul_debye_omp.h
+++ b/src/USER-OMP/pair_coul_debye_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_coul_diel_omp.cpp b/src/USER-OMP/pair_coul_diel_omp.cpp
index 29d83b387621d230908ec6aec07e471b09a73ae2..c583800004599553a4a749c9407744ec594d2f59 100644
--- a/src/USER-OMP/pair_coul_diel_omp.cpp
+++ b/src/USER-OMP/pair_coul_diel_omp.cpp
@@ -56,11 +56,11 @@ void PairCoulDielOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -123,31 +123,31 @@ void PairCoulDielOMP::eval(int iifrom, int iito, ThrData * const thr)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r = sqrt(rsq);
- rarg = (r-rme[itype][jtype])/sigmae[itype][jtype];
- th=tanh(rarg);
- epsr=a_eps+b_eps*th;
- depsdr=b_eps * (1.0 - th*th) / sigmae[itype][jtype];
-
- forcecoul = qqrd2e*qtmp*q[j]*((eps_s*(epsr+r*depsdr)/epsr/epsr) -1.)/rsq;
- fpair = factor_coul*forcecoul/r;
-
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (EFLAG) {
- ecoul = (qqrd2e*qtmp*q[j]*((eps_s/epsr) -1.)/r) - offset[itype][jtype];
- ecoul *= factor_coul;
- }
-
- if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
- 0.0,ecoul,fpair,delx,dely,delz,thr);
+ r = sqrt(rsq);
+ rarg = (r-rme[itype][jtype])/sigmae[itype][jtype];
+ th=tanh(rarg);
+ epsr=a_eps+b_eps*th;
+ depsdr=b_eps * (1.0 - th*th) / sigmae[itype][jtype];
+
+ forcecoul = qqrd2e*qtmp*q[j]*((eps_s*(epsr+r*depsdr)/epsr/epsr) -1.)/rsq;
+ fpair = factor_coul*forcecoul/r;
+
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (EFLAG) {
+ ecoul = (qqrd2e*qtmp*q[j]*((eps_s/epsr) -1.)/r) - offset[itype][jtype];
+ ecoul *= factor_coul;
+ }
+
+ if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
+ 0.0,ecoul,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_coul_diel_omp.h b/src/USER-OMP/pair_coul_diel_omp.h
index 2dc0083ae33a818a3646387359edc842d6916711..68206e4c280dcd3cd06fd7d2471057ba92ed25ac 100644
--- a/src/USER-OMP/pair_coul_diel_omp.h
+++ b/src/USER-OMP/pair_coul_diel_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_coul_long_omp.cpp b/src/USER-OMP/pair_coul_long_omp.cpp
index 8be5e35a0ff2606949ae641227333f37bc20b3da..5ae5478755e4d2f44d0afb3b17837dfe3d6b4b3c 100644
--- a/src/USER-OMP/pair_coul_long_omp.cpp
+++ b/src/USER-OMP/pair_coul_long_omp.cpp
@@ -65,11 +65,11 @@ void PairCoulLongOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -133,54 +133,54 @@ void PairCoulLongOMP::eval(int iifrom, int iito, ThrData * const thr)
jtype = type[j];
if (rsq < cut_coulsq) {
- r2inv = 1.0/rsq;
- if (!ncoultablebits || rsq <= tabinnersq) {
- r = sqrt(rsq);
- grij = g_ewald * r;
- expm2 = exp(-grij*grij);
- t = 1.0 / (1.0 + EWALD_P*grij);
- erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
- prefactor = qqrd2e * scale[itype][jtype] * qtmp*q[j]/r;
- forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
- if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
- } else {
- union_int_float_t rsq_lookup;
- rsq_lookup.f = rsq;
- itable = rsq_lookup.i & ncoulmask;
- itable >>= ncoulshiftbits;
- fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
- table = ftable[itable] + fraction*dftable[itable];
- forcecoul = scale[itype][jtype] * qtmp*q[j] * table;
- if (factor_coul < 1.0) {
- table = ctable[itable] + fraction*dctable[itable];
- prefactor = scale[itype][jtype] * qtmp*q[j] * table;
- forcecoul -= (1.0-factor_coul)*prefactor;
- }
- }
-
- fpair = forcecoul * r2inv;
-
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (EFLAG) {
- if (!ncoultablebits || rsq <= tabinnersq)
- ecoul = prefactor*erfc;
- else {
- table = etable[itable] + fraction*detable[itable];
- ecoul = scale[itype][jtype] * qtmp*q[j] * table;
- }
- if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
- }
-
- if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
- 0.0,ecoul,fpair,delx,dely,delz,thr);
+ r2inv = 1.0/rsq;
+ if (!ncoultablebits || rsq <= tabinnersq) {
+ r = sqrt(rsq);
+ grij = g_ewald * r;
+ expm2 = exp(-grij*grij);
+ t = 1.0 / (1.0 + EWALD_P*grij);
+ erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
+ prefactor = qqrd2e * scale[itype][jtype] * qtmp*q[j]/r;
+ forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
+ if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
+ } else {
+ union_int_float_t rsq_lookup;
+ rsq_lookup.f = rsq;
+ itable = rsq_lookup.i & ncoulmask;
+ itable >>= ncoulshiftbits;
+ fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
+ table = ftable[itable] + fraction*dftable[itable];
+ forcecoul = scale[itype][jtype] * qtmp*q[j] * table;
+ if (factor_coul < 1.0) {
+ table = ctable[itable] + fraction*dctable[itable];
+ prefactor = scale[itype][jtype] * qtmp*q[j] * table;
+ forcecoul -= (1.0-factor_coul)*prefactor;
+ }
+ }
+
+ fpair = forcecoul * r2inv;
+
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (EFLAG) {
+ if (!ncoultablebits || rsq <= tabinnersq)
+ ecoul = prefactor*erfc;
+ else {
+ table = etable[itable] + fraction*detable[itable];
+ ecoul = scale[itype][jtype] * qtmp*q[j] * table;
+ }
+ if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
+ }
+
+ if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
+ 0.0,ecoul,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_coul_long_omp.h b/src/USER-OMP/pair_coul_long_omp.h
index d7655637d0f84cffd7880521b890741777a66c93..d628d22b606cf00860cbe12d167b9742236e5f06 100644
--- a/src/USER-OMP/pair_coul_long_omp.h
+++ b/src/USER-OMP/pair_coul_long_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_coul_wolf_omp.cpp b/src/USER-OMP/pair_coul_wolf_omp.cpp
index f290d7e3da207ba10f0828f92c5e4930d5266e5c..16e0c4ed907797f861ff82a18f49995d85dff72b 100644
--- a/src/USER-OMP/pair_coul_wolf_omp.cpp
+++ b/src/USER-OMP/pair_coul_wolf_omp.cpp
@@ -58,11 +58,11 @@ void PairCoulWolfOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -99,10 +99,10 @@ void PairCoulWolfOMP::eval(int iifrom, int iito, ThrData * const thr)
// self and shifted coulombic energy
- e_self = v_sh = 0.0;
+ e_self = v_sh = 0.0;
e_shift = erfc(alf*cut_coul)/cut_coul;
- f_shift = -(e_shift+ 2.0*alf/MY_PIS * exp(-alf*alf*cut_coul*cut_coul)) /
- cut_coul;
+ f_shift = -(e_shift+ 2.0*alf/MY_PIS * exp(-alf*alf*cut_coul*cut_coul)) /
+ cut_coul;
ilist = list->ilist;
numneigh = list->numneigh;
@@ -136,34 +136,34 @@ void PairCoulWolfOMP::eval(int iifrom, int iito, ThrData * const thr)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cut_coulsq) {
- r = sqrt(rsq);
- prefactor = qqrd2e*qtmp*q[j]/r;
- erfcc = erfc(alf*r);
- erfcd = exp(-alf*alf*r*r);
- v_sh = (erfcc - e_shift*r) * prefactor;
- dvdrr = (erfcc/rsq + 2.0*alf/MY_PIS * erfcd/r) + f_shift;
- forcecoul = dvdrr*rsq*prefactor;
- if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
- fpair = forcecoul / rsq;
-
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (EFLAG) {
- if (rsq < cut_coulsq) {
- ecoul = v_sh;
- if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
- } else ecoul = 0.0;
- }
-
- if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
- 0.0,ecoul,fpair,delx,dely,delz,thr);
+ r = sqrt(rsq);
+ prefactor = qqrd2e*qtmp*q[j]/r;
+ erfcc = erfc(alf*r);
+ erfcd = exp(-alf*alf*r*r);
+ v_sh = (erfcc - e_shift*r) * prefactor;
+ dvdrr = (erfcc/rsq + 2.0*alf/MY_PIS * erfcd/r) + f_shift;
+ forcecoul = dvdrr*rsq*prefactor;
+ if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
+ fpair = forcecoul / rsq;
+
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (EFLAG) {
+ if (rsq < cut_coulsq) {
+ ecoul = v_sh;
+ if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
+ } else ecoul = 0.0;
+ }
+
+ if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
+ 0.0,ecoul,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_coul_wolf_omp.h b/src/USER-OMP/pair_coul_wolf_omp.h
index 0b474601f27807ffe1d420af258433cf1fe120b0..aef683d22cef2ddc0cef6de48a043fa260c465e8 100644
--- a/src/USER-OMP/pair_coul_wolf_omp.h
+++ b/src/USER-OMP/pair_coul_wolf_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_dipole_cut_omp.cpp b/src/USER-OMP/pair_dipole_cut_omp.cpp
index 9e278b9a219116200e3ec37632af384c5dff0fda..34d7e6c17e2471bf369384051cb69e6b6c02a8d5 100644
--- a/src/USER-OMP/pair_dipole_cut_omp.cpp
+++ b/src/USER-OMP/pair_dipole_cut_omp.cpp
@@ -56,11 +56,11 @@ void PairDipoleCutOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -128,142 +128,142 @@ void PairDipoleCutOMP::eval(int iifrom, int iito, ThrData * const thr)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- rinv = sqrt(r2inv);
+ r2inv = 1.0/rsq;
+ rinv = sqrt(r2inv);
- // atom can have both a charge and dipole
- // i,j = charge-charge, dipole-dipole, dipole-charge, or charge-dipole
+ // atom can have both a charge and dipole
+ // i,j = charge-charge, dipole-dipole, dipole-charge, or charge-dipole
- forcecoulx = forcecouly = forcecoulz = 0.0;
- tixcoul = tiycoul = tizcoul = 0.0;
- tjxcoul = tjycoul = tjzcoul = 0.0;
-
- if (rsq < cut_coulsq[itype][jtype]) {
+ forcecoulx = forcecouly = forcecoulz = 0.0;
+ tixcoul = tiycoul = tizcoul = 0.0;
+ tjxcoul = tjycoul = tjzcoul = 0.0;
- if (qtmp != 0.0 && q[j] != 0.0) {
+ if (rsq < cut_coulsq[itype][jtype]) {
+
+ if (qtmp != 0.0 && q[j] != 0.0) {
r3inv = r2inv*rinv;
- pre1 = qtmp*q[j]*r3inv;
+ pre1 = qtmp*q[j]*r3inv;
- forcecoulx += pre1*delx;
- forcecouly += pre1*dely;
- forcecoulz += pre1*delz;
- }
+ forcecoulx += pre1*delx;
+ forcecouly += pre1*dely;
+ forcecoulz += pre1*delz;
+ }
- if (mu[i][3] > 0.0 && mu[j][3] > 0.0) {
+ if (mu[i][3] > 0.0 && mu[j][3] > 0.0) {
r3inv = r2inv*rinv;
r5inv = r3inv*r2inv;
- r7inv = r5inv*r2inv;
+ r7inv = r5inv*r2inv;
pdotp = mu[i][0]*mu[j][0] + mu[i][1]*mu[j][1] + mu[i][2]*mu[j][2];
pidotr = mu[i][0]*delx + mu[i][1]*dely + mu[i][2]*delz;
pjdotr = mu[j][0]*delx + mu[j][1]*dely + mu[j][2]*delz;
- pre1 = 3.0*r5inv*pdotp - 15.0*r7inv*pidotr*pjdotr;
- pre2 = 3.0*r5inv*pjdotr;
- pre3 = 3.0*r5inv*pidotr;
- pre4 = -1.0*r3inv;
-
- forcecoulx += pre1*delx + pre2*mu[i][0] + pre3*mu[j][0];
- forcecouly += pre1*dely + pre2*mu[i][1] + pre3*mu[j][1];
- forcecoulz += pre1*delz + pre2*mu[i][2] + pre3*mu[j][2];
-
- crossx = pre4 * (mu[i][1]*mu[j][2] - mu[i][2]*mu[j][1]);
- crossy = pre4 * (mu[i][2]*mu[j][0] - mu[i][0]*mu[j][2]);
- crossz = pre4 * (mu[i][0]*mu[j][1] - mu[i][1]*mu[j][0]);
-
- tixcoul += crossx + pre2 * (mu[i][1]*delz - mu[i][2]*dely);
- tiycoul += crossy + pre2 * (mu[i][2]*delx - mu[i][0]*delz);
- tizcoul += crossz + pre2 * (mu[i][0]*dely - mu[i][1]*delx);
- tjxcoul += -crossx + pre3 * (mu[j][1]*delz - mu[j][2]*dely);
- tjycoul += -crossy + pre3 * (mu[j][2]*delx - mu[j][0]*delz);
- tjzcoul += -crossz + pre3 * (mu[j][0]*dely - mu[j][1]*delx);
- }
-
- if (mu[i][3] > 0.0 && q[j] != 0.0) {
+ pre1 = 3.0*r5inv*pdotp - 15.0*r7inv*pidotr*pjdotr;
+ pre2 = 3.0*r5inv*pjdotr;
+ pre3 = 3.0*r5inv*pidotr;
+ pre4 = -1.0*r3inv;
+
+ forcecoulx += pre1*delx + pre2*mu[i][0] + pre3*mu[j][0];
+ forcecouly += pre1*dely + pre2*mu[i][1] + pre3*mu[j][1];
+ forcecoulz += pre1*delz + pre2*mu[i][2] + pre3*mu[j][2];
+
+ crossx = pre4 * (mu[i][1]*mu[j][2] - mu[i][2]*mu[j][1]);
+ crossy = pre4 * (mu[i][2]*mu[j][0] - mu[i][0]*mu[j][2]);
+ crossz = pre4 * (mu[i][0]*mu[j][1] - mu[i][1]*mu[j][0]);
+
+ tixcoul += crossx + pre2 * (mu[i][1]*delz - mu[i][2]*dely);
+ tiycoul += crossy + pre2 * (mu[i][2]*delx - mu[i][0]*delz);
+ tizcoul += crossz + pre2 * (mu[i][0]*dely - mu[i][1]*delx);
+ tjxcoul += -crossx + pre3 * (mu[j][1]*delz - mu[j][2]*dely);
+ tjycoul += -crossy + pre3 * (mu[j][2]*delx - mu[j][0]*delz);
+ tjzcoul += -crossz + pre3 * (mu[j][0]*dely - mu[j][1]*delx);
+ }
+
+ if (mu[i][3] > 0.0 && q[j] != 0.0) {
r3inv = r2inv*rinv;
r5inv = r3inv*r2inv;
pidotr = mu[i][0]*delx + mu[i][1]*dely + mu[i][2]*delz;
- pre1 = 3.0*q[j]*r5inv * pidotr;
- pre2 = q[j]*r3inv;
+ pre1 = 3.0*q[j]*r5inv * pidotr;
+ pre2 = q[j]*r3inv;
- forcecoulx += pre2*mu[i][0] - pre1*delx;
+ forcecoulx += pre2*mu[i][0] - pre1*delx;
forcecouly += pre2*mu[i][1] - pre1*dely;
forcecoulz += pre2*mu[i][2] - pre1*delz;
- tixcoul += pre2 * (mu[i][1]*delz - mu[i][2]*dely);
- tiycoul += pre2 * (mu[i][2]*delx - mu[i][0]*delz);
- tizcoul += pre2 * (mu[i][0]*dely - mu[i][1]*delx);
- }
+ tixcoul += pre2 * (mu[i][1]*delz - mu[i][2]*dely);
+ tiycoul += pre2 * (mu[i][2]*delx - mu[i][0]*delz);
+ tizcoul += pre2 * (mu[i][0]*dely - mu[i][1]*delx);
+ }
- if (mu[j][3] > 0.0 && qtmp != 0.0) {
+ if (mu[j][3] > 0.0 && qtmp != 0.0) {
r3inv = r2inv*rinv;
r5inv = r3inv*r2inv;
pjdotr = mu[j][0]*delx + mu[j][1]*dely + mu[j][2]*delz;
- pre1 = 3.0*qtmp*r5inv * pjdotr;
- pre2 = qtmp*r3inv;
+ pre1 = 3.0*qtmp*r5inv * pjdotr;
+ pre2 = qtmp*r3inv;
- forcecoulx += pre1*delx - pre2*mu[j][0];
+ forcecoulx += pre1*delx - pre2*mu[j][0];
forcecouly += pre1*dely - pre2*mu[j][1];
forcecoulz += pre1*delz - pre2*mu[j][2];
- tjxcoul += -pre2 * (mu[j][1]*delz - mu[j][2]*dely);
- tjycoul += -pre2 * (mu[j][2]*delx - mu[j][0]*delz);
- tjzcoul += -pre2 * (mu[j][0]*dely - mu[j][1]*delx);
- }
- }
-
- // LJ interaction
-
- if (rsq < cut_ljsq[itype][jtype]) {
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- forcelj *= factor_lj * r2inv;
- } else forcelj = 0.0;
-
- // total force
-
- fq = factor_coul*qqrd2e;
- fx = fq*forcecoulx + delx*forcelj;
- fy = fq*forcecouly + dely*forcelj;
- fz = fq*forcecoulz + delz*forcelj;
-
- // force & torque accumulation
-
- fxtmp += fx;
- fytmp += fy;
- fztmp += fz;
- t1tmp += fq*tixcoul;
- t2tmp += fq*tiycoul;
- t3tmp += fq*tizcoul;
-
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= fx;
- f[j][1] -= fy;
- f[j][2] -= fz;
- torque[j][0] += fq*tjxcoul;
- torque[j][1] += fq*tjycoul;
- torque[j][2] += fq*tjzcoul;
- }
-
- if (EFLAG) {
- if (rsq < cut_coulsq[itype][jtype]) {
- ecoul = qtmp*q[j]*rinv;
- if (mu[i][3] > 0.0 && mu[j][3] > 0.0)
- ecoul += r3inv*pdotp - 3.0*r5inv*pidotr*pjdotr;
- if (mu[i][3] > 0.0 && q[j] != 0.0)
- ecoul += -q[j]*r3inv*pidotr;
- if (mu[j][3] > 0.0 && qtmp != 0.0)
- ecoul += qtmp*r3inv*pjdotr;
- ecoul *= factor_coul*qqrd2e;
- } else ecoul = 0.0;
-
- if (rsq < cut_ljsq[itype][jtype]) {
- evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
- offset[itype][jtype];
- evdwl *= factor_lj;
- } else evdwl = 0.0;
- }
-
- if (EVFLAG) ev_tally_xyz_thr(this,i,j,nlocal,NEWTON_PAIR,
- evdwl,ecoul,fx,fy,fz,delx,dely,delz,thr);
+ tjxcoul += -pre2 * (mu[j][1]*delz - mu[j][2]*dely);
+ tjycoul += -pre2 * (mu[j][2]*delx - mu[j][0]*delz);
+ tjzcoul += -pre2 * (mu[j][0]*dely - mu[j][1]*delx);
+ }
+ }
+
+ // LJ interaction
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ forcelj *= factor_lj * r2inv;
+ } else forcelj = 0.0;
+
+ // total force
+
+ fq = factor_coul*qqrd2e;
+ fx = fq*forcecoulx + delx*forcelj;
+ fy = fq*forcecouly + dely*forcelj;
+ fz = fq*forcecoulz + delz*forcelj;
+
+ // force & torque accumulation
+
+ fxtmp += fx;
+ fytmp += fy;
+ fztmp += fz;
+ t1tmp += fq*tixcoul;
+ t2tmp += fq*tiycoul;
+ t3tmp += fq*tizcoul;
+
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= fx;
+ f[j][1] -= fy;
+ f[j][2] -= fz;
+ torque[j][0] += fq*tjxcoul;
+ torque[j][1] += fq*tjycoul;
+ torque[j][2] += fq*tjzcoul;
+ }
+
+ if (EFLAG) {
+ if (rsq < cut_coulsq[itype][jtype]) {
+ ecoul = qtmp*q[j]*rinv;
+ if (mu[i][3] > 0.0 && mu[j][3] > 0.0)
+ ecoul += r3inv*pdotp - 3.0*r5inv*pidotr*pjdotr;
+ if (mu[i][3] > 0.0 && q[j] != 0.0)
+ ecoul += -q[j]*r3inv*pidotr;
+ if (mu[j][3] > 0.0 && qtmp != 0.0)
+ ecoul += qtmp*r3inv*pjdotr;
+ ecoul *= factor_coul*qqrd2e;
+ } else ecoul = 0.0;
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
+ offset[itype][jtype];
+ evdwl *= factor_lj;
+ } else evdwl = 0.0;
+ }
+
+ if (EVFLAG) ev_tally_xyz_thr(this,i,j,nlocal,NEWTON_PAIR,
+ evdwl,ecoul,fx,fy,fz,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_dipole_cut_omp.h b/src/USER-OMP/pair_dipole_cut_omp.h
index b175450c9f14d8692590a6b5fc7748259d55a856..4e874b1ffb5f06ebbb24da574dcc3bbc0a789bef 100644
--- a/src/USER-OMP/pair_dipole_cut_omp.h
+++ b/src/USER-OMP/pair_dipole_cut_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_dipole_sf_omp.cpp b/src/USER-OMP/pair_dipole_sf_omp.cpp
index 07721562b8161c8b3fcd35f9b48a5072afad2de8..4090bc3c022189df4df5adb02631e48d22909a96 100644
--- a/src/USER-OMP/pair_dipole_sf_omp.cpp
+++ b/src/USER-OMP/pair_dipole_sf_omp.cpp
@@ -56,11 +56,11 @@ void PairDipoleSFOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -132,170 +132,170 @@ void PairDipoleSFOMP::eval(int iifrom, int iito, ThrData * const thr)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- rinv = sqrt(r2inv);
+ r2inv = 1.0/rsq;
+ rinv = sqrt(r2inv);
- // atom can have both a charge and dipole
- // i,j = charge-charge, dipole-dipole, dipole-charge, or charge-dipole
- // atom can have both a charge and dipole
- // i,j = charge-charge, dipole-dipole, dipole-charge, or charge-dipole
+ // atom can have both a charge and dipole
+ // i,j = charge-charge, dipole-dipole, dipole-charge, or charge-dipole
+ // atom can have both a charge and dipole
+ // i,j = charge-charge, dipole-dipole, dipole-charge, or charge-dipole
- forcecoulx = forcecouly = forcecoulz = 0.0;
- tixcoul = tiycoul = tizcoul = 0.0;
- tjxcoul = tjycoul = tjzcoul = 0.0;
-
- if (rsq < cut_coulsq[itype][jtype]) {
+ forcecoulx = forcecouly = forcecoulz = 0.0;
+ tixcoul = tiycoul = tizcoul = 0.0;
+ tjxcoul = tjycoul = tjzcoul = 0.0;
- if (qtmp != 0.0 && q[j] != 0.0) {
+ if (rsq < cut_coulsq[itype][jtype]) {
+
+ if (qtmp != 0.0 && q[j] != 0.0) {
pre1 = qtmp*q[j]*rinv*(r2inv-1.0/cut_coulsq[itype][jtype]);
- forcecoulx += pre1*delx;
- forcecouly += pre1*dely;
- forcecoulz += pre1*delz;
- }
+ forcecoulx += pre1*delx;
+ forcecouly += pre1*dely;
+ forcecoulz += pre1*delz;
+ }
- if (mu[i][3] > 0.0 && mu[j][3] > 0.0) {
+ if (mu[i][3] > 0.0 && mu[j][3] > 0.0) {
r3inv = r2inv*rinv;
r5inv = r3inv*r2inv;
- rcutcoul2inv=1.0/cut_coulsq[itype][jtype];
+ rcutcoul2inv=1.0/cut_coulsq[itype][jtype];
pdotp = mu[i][0]*mu[j][0] + mu[i][1]*mu[j][1] + mu[i][2]*mu[j][2];
pidotr = mu[i][0]*delx + mu[i][1]*dely + mu[i][2]*delz;
pjdotr = mu[j][0]*delx + mu[j][1]*dely + mu[j][2]*delz;
- afac = 1.0 - rsq*rsq * rcutcoul2inv*rcutcoul2inv;
- pre1 = afac * ( pdotp - 3.0 * r2inv * pidotr * pjdotr );
- aforcecoulx = pre1*delx;
- aforcecouly = pre1*dely;
- aforcecoulz = pre1*delz;
-
- bfac = 1.0 - 4.0*rsq*sqrt(rsq)*rcutcoul2inv*sqrt(rcutcoul2inv) +
- 3.0*rsq*rsq*rcutcoul2inv*rcutcoul2inv;
- presf = 2.0 * r2inv * pidotr * pjdotr;
- bforcecoulx = bfac * (pjdotr*mu[i][0]+pidotr*mu[j][0]-presf*delx);
- bforcecouly = bfac * (pjdotr*mu[i][1]+pidotr*mu[j][1]-presf*dely);
- bforcecoulz = bfac * (pjdotr*mu[i][2]+pidotr*mu[j][2]-presf*delz);
-
- forcecoulx += 3.0 * r5inv * ( aforcecoulx + bforcecoulx );
- forcecouly += 3.0 * r5inv * ( aforcecouly + bforcecouly );
- forcecoulz += 3.0 * r5inv * ( aforcecoulz + bforcecoulz );
-
- pre2 = 3.0 * bfac * r5inv * pjdotr;
- pre3 = 3.0 * bfac * r5inv * pidotr;
- pre4 = -bfac * r3inv;
-
- crossx = pre4 * (mu[i][1]*mu[j][2] - mu[i][2]*mu[j][1]);
- crossy = pre4 * (mu[i][2]*mu[j][0] - mu[i][0]*mu[j][2]);
- crossz = pre4 * (mu[i][0]*mu[j][1] - mu[i][1]*mu[j][0]);
-
- tixcoul += crossx + pre2 * (mu[i][1]*delz - mu[i][2]*dely);
- tiycoul += crossy + pre2 * (mu[i][2]*delx - mu[i][0]*delz);
- tizcoul += crossz + pre2 * (mu[i][0]*dely - mu[i][1]*delx);
- tjxcoul += -crossx + pre3 * (mu[j][1]*delz - mu[j][2]*dely);
- tjycoul += -crossy + pre3 * (mu[j][2]*delx - mu[j][0]*delz);
- tjzcoul += -crossz + pre3 * (mu[j][0]*dely - mu[j][1]*delx);
- }
-
- if (mu[i][3] > 0.0 && q[j] != 0.0) {
+ afac = 1.0 - rsq*rsq * rcutcoul2inv*rcutcoul2inv;
+ pre1 = afac * ( pdotp - 3.0 * r2inv * pidotr * pjdotr );
+ aforcecoulx = pre1*delx;
+ aforcecouly = pre1*dely;
+ aforcecoulz = pre1*delz;
+
+ bfac = 1.0 - 4.0*rsq*sqrt(rsq)*rcutcoul2inv*sqrt(rcutcoul2inv) +
+ 3.0*rsq*rsq*rcutcoul2inv*rcutcoul2inv;
+ presf = 2.0 * r2inv * pidotr * pjdotr;
+ bforcecoulx = bfac * (pjdotr*mu[i][0]+pidotr*mu[j][0]-presf*delx);
+ bforcecouly = bfac * (pjdotr*mu[i][1]+pidotr*mu[j][1]-presf*dely);
+ bforcecoulz = bfac * (pjdotr*mu[i][2]+pidotr*mu[j][2]-presf*delz);
+
+ forcecoulx += 3.0 * r5inv * ( aforcecoulx + bforcecoulx );
+ forcecouly += 3.0 * r5inv * ( aforcecouly + bforcecouly );
+ forcecoulz += 3.0 * r5inv * ( aforcecoulz + bforcecoulz );
+
+ pre2 = 3.0 * bfac * r5inv * pjdotr;
+ pre3 = 3.0 * bfac * r5inv * pidotr;
+ pre4 = -bfac * r3inv;
+
+ crossx = pre4 * (mu[i][1]*mu[j][2] - mu[i][2]*mu[j][1]);
+ crossy = pre4 * (mu[i][2]*mu[j][0] - mu[i][0]*mu[j][2]);
+ crossz = pre4 * (mu[i][0]*mu[j][1] - mu[i][1]*mu[j][0]);
+
+ tixcoul += crossx + pre2 * (mu[i][1]*delz - mu[i][2]*dely);
+ tiycoul += crossy + pre2 * (mu[i][2]*delx - mu[i][0]*delz);
+ tizcoul += crossz + pre2 * (mu[i][0]*dely - mu[i][1]*delx);
+ tjxcoul += -crossx + pre3 * (mu[j][1]*delz - mu[j][2]*dely);
+ tjycoul += -crossy + pre3 * (mu[j][2]*delx - mu[j][0]*delz);
+ tjzcoul += -crossz + pre3 * (mu[j][0]*dely - mu[j][1]*delx);
+ }
+
+ if (mu[i][3] > 0.0 && q[j] != 0.0) {
r3inv = r2inv*rinv;
r5inv = r3inv*r2inv;
pidotr = mu[i][0]*delx + mu[i][1]*dely + mu[i][2]*delz;
- rcutcoul2inv=1.0/cut_coulsq[itype][jtype];
- pre1 = 3.0 * q[j] * r5inv * pidotr * (1-rsq*rcutcoul2inv);
- pqfac = 1.0 - 3.0*rsq*rcutcoul2inv +
- 2.0*rsq*sqrt(rsq)*rcutcoul2inv*sqrt(rcutcoul2inv);
- pre2 = q[j] * r3inv * pqfac;
+ rcutcoul2inv=1.0/cut_coulsq[itype][jtype];
+ pre1 = 3.0 * q[j] * r5inv * pidotr * (1-rsq*rcutcoul2inv);
+ pqfac = 1.0 - 3.0*rsq*rcutcoul2inv +
+ 2.0*rsq*sqrt(rsq)*rcutcoul2inv*sqrt(rcutcoul2inv);
+ pre2 = q[j] * r3inv * pqfac;
- forcecoulx += pre2*mu[i][0] - pre1*delx;
+ forcecoulx += pre2*mu[i][0] - pre1*delx;
forcecouly += pre2*mu[i][1] - pre1*dely;
forcecoulz += pre2*mu[i][2] - pre1*delz;
- tixcoul += pre2 * (mu[i][1]*delz - mu[i][2]*dely);
- tiycoul += pre2 * (mu[i][2]*delx - mu[i][0]*delz);
- tizcoul += pre2 * (mu[i][0]*dely - mu[i][1]*delx);
- }
+ tixcoul += pre2 * (mu[i][1]*delz - mu[i][2]*dely);
+ tiycoul += pre2 * (mu[i][2]*delx - mu[i][0]*delz);
+ tizcoul += pre2 * (mu[i][0]*dely - mu[i][1]*delx);
+ }
- if (mu[j][3] > 0.0 && qtmp != 0.0) {
+ if (mu[j][3] > 0.0 && qtmp != 0.0) {
r3inv = r2inv*rinv;
r5inv = r3inv*r2inv;
pjdotr = mu[j][0]*delx + mu[j][1]*dely + mu[j][2]*delz;
- rcutcoul2inv=1.0/cut_coulsq[itype][jtype];
- pre1 = 3.0 * qtmp * r5inv * pjdotr * (1-rsq*rcutcoul2inv);
- qpfac = 1.0 - 3.0*rsq*rcutcoul2inv +
- 2.0*rsq*sqrt(rsq)*rcutcoul2inv*sqrt(rcutcoul2inv);
- pre2 = qtmp * r3inv * qpfac;
+ rcutcoul2inv=1.0/cut_coulsq[itype][jtype];
+ pre1 = 3.0 * qtmp * r5inv * pjdotr * (1-rsq*rcutcoul2inv);
+ qpfac = 1.0 - 3.0*rsq*rcutcoul2inv +
+ 2.0*rsq*sqrt(rsq)*rcutcoul2inv*sqrt(rcutcoul2inv);
+ pre2 = qtmp * r3inv * qpfac;
- forcecoulx += pre1*delx - pre2*mu[j][0];
+ forcecoulx += pre1*delx - pre2*mu[j][0];
forcecouly += pre1*dely - pre2*mu[j][1];
forcecoulz += pre1*delz - pre2*mu[j][2];
- tjxcoul += -pre2 * (mu[j][1]*delz - mu[j][2]*dely);
- tjycoul += -pre2 * (mu[j][2]*delx - mu[j][0]*delz);
- tjzcoul += -pre2 * (mu[j][0]*dely - mu[j][1]*delx);
- }
- }
-
- // LJ interaction
-
- if (rsq < cut_ljsq[itype][jtype]) {
- r6inv = r2inv*r2inv*r2inv;
- forceljcut = r6inv*(lj1[itype][jtype]*r6inv-lj2[itype][jtype])*r2inv;
-
- rcutlj2inv = 1.0 / cut_ljsq[itype][jtype];
- rcutlj6inv = rcutlj2inv * rcutlj2inv * rcutlj2inv;
- forceljsf = (lj1[itype][jtype]*rcutlj6inv - lj2[itype][jtype]) *
- rcutlj6inv * rcutlj2inv;
-
- forcelj = factor_lj * (forceljcut - forceljsf);
- } else forcelj = 0.0;
-
- // total force
-
- fq = factor_coul*qqrd2e;
- fx = fq*forcecoulx + delx*forcelj;
- fy = fq*forcecouly + dely*forcelj;
- fz = fq*forcecoulz + delz*forcelj;
-
- // force & torque accumulation
-
- fxtmp += fx;
- fytmp += fy;
- fztmp += fz;
- t1tmp += fq*tixcoul;
- t2tmp += fq*tiycoul;
- t3tmp += fq*tizcoul;
-
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= fx;
- f[j][1] -= fy;
- f[j][2] -= fz;
- torque[j][0] += fq*tjxcoul;
- torque[j][1] += fq*tjycoul;
- torque[j][2] += fq*tjzcoul;
- }
-
- if (EFLAG) {
- if (rsq < cut_coulsq[itype][jtype]) {
- ecoul = qtmp * q[j] * rinv *
- pow((1.0-sqrt(rsq)/sqrt(cut_coulsq[itype][jtype])),2.0);
- if (mu[i][3] > 0.0 && mu[j][3] > 0.0)
- ecoul += bfac * (r3inv*pdotp - 3.0*r5inv*pidotr*pjdotr);
- if (mu[i][3] > 0.0 && q[j] != 0.0)
- ecoul += -q[j] * r3inv * pqfac * pidotr;
- if (mu[j][3] > 0.0 && qtmp != 0.0)
- ecoul += qtmp * r3inv * qpfac * pjdotr;
- ecoul *= factor_coul*qqrd2e;
- } else ecoul = 0.0;
-
- if (rsq < cut_ljsq[itype][jtype]) {
- evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype])+
- rcutlj6inv*(6*lj3[itype][jtype]*rcutlj6inv-3*lj4[itype][jtype])*
- rsq*rcutlj2inv+
- rcutlj6inv*(-7*lj3[itype][jtype]*rcutlj6inv+4*lj4[itype][jtype]);
- evdwl *= factor_lj;
- } else evdwl = 0.0;
- }
-
- if (EVFLAG) ev_tally_xyz_thr(this,i,j,nlocal,NEWTON_PAIR,
- evdwl,ecoul,fx,fy,fz,delx,dely,delz,thr);
+ tjxcoul += -pre2 * (mu[j][1]*delz - mu[j][2]*dely);
+ tjycoul += -pre2 * (mu[j][2]*delx - mu[j][0]*delz);
+ tjzcoul += -pre2 * (mu[j][0]*dely - mu[j][1]*delx);
+ }
+ }
+
+ // LJ interaction
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ r6inv = r2inv*r2inv*r2inv;
+ forceljcut = r6inv*(lj1[itype][jtype]*r6inv-lj2[itype][jtype])*r2inv;
+
+ rcutlj2inv = 1.0 / cut_ljsq[itype][jtype];
+ rcutlj6inv = rcutlj2inv * rcutlj2inv * rcutlj2inv;
+ forceljsf = (lj1[itype][jtype]*rcutlj6inv - lj2[itype][jtype]) *
+ rcutlj6inv * rcutlj2inv;
+
+ forcelj = factor_lj * (forceljcut - forceljsf);
+ } else forcelj = 0.0;
+
+ // total force
+
+ fq = factor_coul*qqrd2e;
+ fx = fq*forcecoulx + delx*forcelj;
+ fy = fq*forcecouly + dely*forcelj;
+ fz = fq*forcecoulz + delz*forcelj;
+
+ // force & torque accumulation
+
+ fxtmp += fx;
+ fytmp += fy;
+ fztmp += fz;
+ t1tmp += fq*tixcoul;
+ t2tmp += fq*tiycoul;
+ t3tmp += fq*tizcoul;
+
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= fx;
+ f[j][1] -= fy;
+ f[j][2] -= fz;
+ torque[j][0] += fq*tjxcoul;
+ torque[j][1] += fq*tjycoul;
+ torque[j][2] += fq*tjzcoul;
+ }
+
+ if (EFLAG) {
+ if (rsq < cut_coulsq[itype][jtype]) {
+ ecoul = qtmp * q[j] * rinv *
+ pow((1.0-sqrt(rsq)/sqrt(cut_coulsq[itype][jtype])),2.0);
+ if (mu[i][3] > 0.0 && mu[j][3] > 0.0)
+ ecoul += bfac * (r3inv*pdotp - 3.0*r5inv*pidotr*pjdotr);
+ if (mu[i][3] > 0.0 && q[j] != 0.0)
+ ecoul += -q[j] * r3inv * pqfac * pidotr;
+ if (mu[j][3] > 0.0 && qtmp != 0.0)
+ ecoul += qtmp * r3inv * qpfac * pjdotr;
+ ecoul *= factor_coul*qqrd2e;
+ } else ecoul = 0.0;
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype])+
+ rcutlj6inv*(6*lj3[itype][jtype]*rcutlj6inv-3*lj4[itype][jtype])*
+ rsq*rcutlj2inv+
+ rcutlj6inv*(-7*lj3[itype][jtype]*rcutlj6inv+4*lj4[itype][jtype]);
+ evdwl *= factor_lj;
+ } else evdwl = 0.0;
+ }
+
+ if (EVFLAG) ev_tally_xyz_thr(this,i,j,nlocal,NEWTON_PAIR,
+ evdwl,ecoul,fx,fy,fz,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_dipole_sf_omp.h b/src/USER-OMP/pair_dipole_sf_omp.h
index 89c80fa78809cd1708861dfd538a89d38d23a944..3ff008cef547005dd36947ae4d675360573b69f3 100644
--- a/src/USER-OMP/pair_dipole_sf_omp.h
+++ b/src/USER-OMP/pair_dipole_sf_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_dpd_omp.cpp b/src/USER-OMP/pair_dpd_omp.cpp
index f8d472f041d7feda91c730083ae1f4436e834e0f..cb7f560e058170abfc03ca07143b68f322c2fc8e 100644
--- a/src/USER-OMP/pair_dpd_omp.cpp
+++ b/src/USER-OMP/pair_dpd_omp.cpp
@@ -39,7 +39,7 @@ PairDPDOMP::PairDPDOMP(LAMMPS *lmp) :
/* ---------------------------------------------------------------------- */
-PairDPDOMP::~PairDPDOMP()
+PairDPDOMP::~PairDPDOMP()
{
if (random_thr) {
for (int i=1; i < comm->nthreads; ++i)
@@ -82,16 +82,16 @@ void PairDPDOMP::compute(int eflag, int vflag)
// generate a random number generator instance for
// all threads != 0. make sure we use unique seeds.
if (random_thr && tid > 0)
- random_thr[tid] = new RanMars(Pair::lmp, seed + comm->me
- + comm->nprocs*tid);
+ random_thr[tid] = new RanMars(Pair::lmp, seed + comm->me
+ + comm->nprocs*tid);
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -155,44 +155,44 @@ void PairDPDOMP::eval(int iifrom, int iito, ThrData * const thr)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r = sqrt(rsq);
- if (r < EPSILON) continue; // r can be 0.0 in DPD systems
- rinv = 1.0/r;
- delvx = vxtmp - v[j][0];
- delvy = vytmp - v[j][1];
- delvz = vztmp - v[j][2];
- dot = delx*delvx + dely*delvy + delz*delvz;
- wd = 1.0 - r/cut[itype][jtype];
- randnum = rng.gaussian();
-
- // conservative force = a0 * wd
- // drag force = -gamma * wd^2 * (delx dot delv) / r
- // random force = sigma * wd * rnd * dtinvsqrt;
-
- fpair = a0[itype][jtype]*wd;
- fpair -= gamma[itype][jtype]*wd*wd*dot*rinv;
- fpair += sigma[itype][jtype]*wd*randnum*dtinvsqrt;
- fpair *= factor_dpd*rinv;
-
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (EFLAG) {
+ r = sqrt(rsq);
+ if (r < EPSILON) continue; // r can be 0.0 in DPD systems
+ rinv = 1.0/r;
+ delvx = vxtmp - v[j][0];
+ delvy = vytmp - v[j][1];
+ delvz = vztmp - v[j][2];
+ dot = delx*delvx + dely*delvy + delz*delvz;
+ wd = 1.0 - r/cut[itype][jtype];
+ randnum = rng.gaussian();
+
+ // conservative force = a0 * wd
+ // drag force = -gamma * wd^2 * (delx dot delv) / r
+ // random force = sigma * wd * rnd * dtinvsqrt;
+
+ fpair = a0[itype][jtype]*wd;
+ fpair -= gamma[itype][jtype]*wd*wd*dot*rinv;
+ fpair += sigma[itype][jtype]*wd*randnum*dtinvsqrt;
+ fpair *= factor_dpd*rinv;
+
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (EFLAG) {
// unshifted eng of conservative term:
- // evdwl = -a0[itype][jtype]*r * (1.0-0.5*r/cut[itype][jtype]);
- // eng shifted to 0.0 at cutoff
- evdwl = 0.5*a0[itype][jtype]*cut[itype][jtype] * wd*wd;
- evdwl *= factor_dpd;
- }
-
- if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
- evdwl,0.0,fpair,delx,dely,delz,thr);
+ // evdwl = -a0[itype][jtype]*r * (1.0-0.5*r/cut[itype][jtype]);
+ // eng shifted to 0.0 at cutoff
+ evdwl = 0.5*a0[itype][jtype]*cut[itype][jtype] * wd*wd;
+ evdwl *= factor_dpd;
+ }
+
+ if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
+ evdwl,0.0,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_dpd_omp.h b/src/USER-OMP/pair_dpd_omp.h
index c3802f8e6000e4607617c374036027f0fd5933e9..470e6f1133ae93432e23afc848c9c4b826fede99 100644
--- a/src/USER-OMP/pair_dpd_omp.h
+++ b/src/USER-OMP/pair_dpd_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_dpd_tstat_omp.cpp b/src/USER-OMP/pair_dpd_tstat_omp.cpp
index 2074f12b1e8394ae2966481da7be2304a4a3c4b1..6965e693491a5b05179cfab274017e2cf33a11a2 100644
--- a/src/USER-OMP/pair_dpd_tstat_omp.cpp
+++ b/src/USER-OMP/pair_dpd_tstat_omp.cpp
@@ -39,7 +39,7 @@ PairDPDTstatOMP::PairDPDTstatOMP(LAMMPS *lmp) :
/* ---------------------------------------------------------------------- */
-PairDPDTstatOMP::~PairDPDTstatOMP()
+PairDPDTstatOMP::~PairDPDTstatOMP()
{
if (random_thr) {
for (int i=1; i < comm->nthreads; ++i)
@@ -64,7 +64,7 @@ void PairDPDTstatOMP::compute(int eflag, int vflag)
if (!random_thr)
random_thr = new RanMars*[nthreads];
-
+
// to ensure full compatibility with the serial DPD style
// we use is random number generator instance for thread 0
random_thr[0] = random;
@@ -82,16 +82,16 @@ void PairDPDTstatOMP::compute(int eflag, int vflag)
// generate a random number generator instance for
// all threads != 0. make sure we use unique seeds.
if (random_thr && tid > 0)
- random_thr[tid] = new RanMars(Pair::lmp, seed + comm->me
- + comm->nprocs*tid);
+ random_thr[tid] = new RanMars(Pair::lmp, seed + comm->me
+ + comm->nprocs*tid);
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -130,7 +130,7 @@ void PairDPDTstatOMP::eval(int iifrom, int iito, ThrData * const thr)
double boltz = force->boltz;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++)
- sigma[i][j] = sigma[j][i] = sqrt(2.0*boltz*temperature*gamma[i][j]);
+ sigma[i][j] = sigma[j][i] = sqrt(2.0*boltz*temperature*gamma[i][j]);
}
ilist = list->ilist;
@@ -165,34 +165,34 @@ void PairDPDTstatOMP::eval(int iifrom, int iito, ThrData * const thr)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r = sqrt(rsq);
- if (r < EPSILON) continue; // r can be 0.0 in DPD systems
- rinv = 1.0/r;
- delvx = vxtmp - v[j][0];
- delvy = vytmp - v[j][1];
- delvz = vztmp - v[j][2];
- dot = delx*delvx + dely*delvy + delz*delvz;
- wd = 1.0 - r/cut[itype][jtype];
- randnum = rng.gaussian();
-
- // drag force = -gamma * wd^2 * (delx dot delv) / r
- // random force = sigma * wd * rnd * dtinvsqrt;
-
- fpair = -gamma[itype][jtype]*wd*wd*dot*rinv;
- fpair += sigma[itype][jtype]*wd*randnum*dtinvsqrt;
- fpair *= factor_dpd*rinv;
-
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
- 0.0,0.0,fpair,delx,dely,delz,thr);
+ r = sqrt(rsq);
+ if (r < EPSILON) continue; // r can be 0.0 in DPD systems
+ rinv = 1.0/r;
+ delvx = vxtmp - v[j][0];
+ delvy = vytmp - v[j][1];
+ delvz = vztmp - v[j][2];
+ dot = delx*delvx + dely*delvy + delz*delvz;
+ wd = 1.0 - r/cut[itype][jtype];
+ randnum = rng.gaussian();
+
+ // drag force = -gamma * wd^2 * (delx dot delv) / r
+ // random force = sigma * wd * rnd * dtinvsqrt;
+
+ fpair = -gamma[itype][jtype]*wd*wd*dot*rinv;
+ fpair += sigma[itype][jtype]*wd*randnum*dtinvsqrt;
+ fpair *= factor_dpd*rinv;
+
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
+ 0.0,0.0,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_dpd_tstat_omp.h b/src/USER-OMP/pair_dpd_tstat_omp.h
index 87c9de5505db70fa491e1e9a178614634f7bb319..b04874efc20a1af57b5e5c9715a5fb39b9e95d8b 100644
--- a/src/USER-OMP/pair_dpd_tstat_omp.h
+++ b/src/USER-OMP/pair_dpd_tstat_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_eam_alloy_omp.cpp b/src/USER-OMP/pair_eam_alloy_omp.cpp
index 54be571b7fda504edad052c6713087216605b2f1..3dff868b6a4a9e267d040b16dc5316487453afde 100644
--- a/src/USER-OMP/pair_eam_alloy_omp.cpp
+++ b/src/USER-OMP/pair_eam_alloy_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -96,9 +96,9 @@ void PairEAMAlloyOMP::coeff(int narg, char **arg)
for (i = 1; i <= n; i++) {
for (j = i; j <= n; j++) {
if (map[i] >= 0 && map[j] >= 0) {
- setflag[i][j] = 1;
- if (i == j) atom->set_mass(i,setfl->mass[map[i]]);
- count++;
+ setflag[i][j] = 1;
+ if (i == j) atom->set_mass(i,setfl->mass[map[i]]);
+ count++;
}
}
}
@@ -147,7 +147,7 @@ void PairEAMAlloyOMP::read_file(char *filename)
int nwords = atom->count_words(line);
if (nwords != file->nelements + 1)
error->all(FLERR,"Incorrect element names in EAM potential file");
-
+
char **words = new char*[file->nelements+1];
nwords = 0;
strtok(line," \t\n\r\f");
@@ -164,7 +164,7 @@ void PairEAMAlloyOMP::read_file(char *filename)
if (me == 0) {
fgets(line,MAXLINE,fptr);
sscanf(line,"%d %lg %d %lg %lg",
- &file->nrho,&file->drho,&file->nr,&file->dr,&file->cut);
+ &file->nrho,&file->drho,&file->nr,&file->dr,&file->cut);
}
MPI_Bcast(&file->nrho,1,MPI_INT,0,world);
@@ -177,7 +177,7 @@ void PairEAMAlloyOMP::read_file(char *filename)
memory->create(file->frho,file->nelements,file->nrho+1,"pair:frho");
memory->create(file->rhor,file->nelements,file->nr+1,"pair:rhor");
memory->create(file->z2r,file->nelements,file->nelements,file->nr+1,
- "pair:z2r");
+ "pair:z2r");
int i,j,tmp;
for (i = 0; i < file->nelements; i++) {
@@ -226,7 +226,7 @@ void PairEAMAlloyOMP::file2array()
// allocate frho arrays
// nfrho = # of setfl elements + 1 for zero array
-
+
nfrho = setfl->nelements + 1;
memory->destroy(frho);
memory->create(frho,nfrho,nrho+1,"pair:frho");
@@ -307,12 +307,12 @@ void PairEAMAlloyOMP::file2array()
irow = map[i];
icol = map[j];
if (irow == -1 || icol == -1) {
- type2z2r[i][j] = 0;
- continue;
+ type2z2r[i][j] = 0;
+ continue;
}
if (irow < icol) {
- irow = map[j];
- icol = map[i];
+ irow = map[j];
+ icol = map[i];
}
n = 0;
for (m = 0; m < irow; m++) n += m + 1;
diff --git a/src/USER-OMP/pair_eam_alloy_omp.h b/src/USER-OMP/pair_eam_alloy_omp.h
index 7a71fbc17a8b94328e6bcbe0c90b0d5c0000bd7f..a044b18f60263fae271af71b01ac1cf056d2e770 100644
--- a/src/USER-OMP/pair_eam_alloy_omp.h
+++ b/src/USER-OMP/pair_eam_alloy_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_eam_fs_omp.cpp b/src/USER-OMP/pair_eam_fs_omp.cpp
index d0963fa62197c7c0d3ab994417410899fa8f810c..84101913c54f4c2fdbad79c7a4c8edc5a87fb19b 100644
--- a/src/USER-OMP/pair_eam_fs_omp.cpp
+++ b/src/USER-OMP/pair_eam_fs_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -96,9 +96,9 @@ void PairEAMFSOMP::coeff(int narg, char **arg)
for (i = 1; i <= n; i++) {
for (j = i; j <= n; j++) {
if (map[i] >= 0 && map[j] >= 0) {
- setflag[i][j] = 1;
- if (i == j) atom->set_mass(i,fs->mass[map[i]]);
- count++;
+ setflag[i][j] = 1;
+ if (i == j) atom->set_mass(i,fs->mass[map[i]]);
+ count++;
}
}
}
@@ -147,7 +147,7 @@ void PairEAMFSOMP::read_file(char *filename)
int nwords = atom->count_words(line);
if (nwords != file->nelements + 1)
error->all(FLERR,"Incorrect element names in EAM potential file");
-
+
char **words = new char*[file->nelements+1];
nwords = 0;
strtok(line," \t\n\r\f");
@@ -164,7 +164,7 @@ void PairEAMFSOMP::read_file(char *filename)
if (me == 0) {
fgets(line,MAXLINE,fptr);
sscanf(line,"%d %lg %d %lg %lg",
- &file->nrho,&file->drho,&file->nr,&file->dr,&file->cut);
+ &file->nrho,&file->drho,&file->nr,&file->dr,&file->cut);
}
MPI_Bcast(&file->nrho,1,MPI_INT,0,world);
@@ -175,11 +175,11 @@ void PairEAMFSOMP::read_file(char *filename)
file->mass = new double[file->nelements];
memory->create(file->frho,file->nelements,file->nrho+1,
- "pair:frho");
+ "pair:frho");
memory->create(file->rhor,file->nelements,file->nelements,
- file->nr+1,"pair:rhor");
+ file->nr+1,"pair:rhor");
memory->create(file->z2r,file->nelements,file->nelements,
- file->nr+1,"pair:z2r");
+ file->nr+1,"pair:z2r");
int i,j,tmp;
for (i = 0; i < file->nelements; i++) {
@@ -231,7 +231,7 @@ void PairEAMFSOMP::file2array()
// allocate frho arrays
// nfrho = # of fs elements + 1 for zero array
-
+
nfrho = fs->nelements + 1;
memory->destroy(frho);
memory->create(frho,nfrho,nrho+1,"pair:frho");
@@ -316,12 +316,12 @@ void PairEAMFSOMP::file2array()
irow = map[i];
icol = map[j];
if (irow == -1 || icol == -1) {
- type2z2r[i][j] = 0;
- continue;
+ type2z2r[i][j] = 0;
+ continue;
}
if (irow < icol) {
- irow = map[j];
- icol = map[i];
+ irow = map[j];
+ icol = map[i];
}
n = 0;
for (m = 0; m < irow; m++) n += m + 1;
diff --git a/src/USER-OMP/pair_eam_fs_omp.h b/src/USER-OMP/pair_eam_fs_omp.h
index bee6cef762e7d1389b234b9815b86b6f6216efec..42d4d59eb6ec03855959db9c0cbb4caa22db4fce 100644
--- a/src/USER-OMP/pair_eam_fs_omp.h
+++ b/src/USER-OMP/pair_eam_fs_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_eam_omp.cpp b/src/USER-OMP/pair_eam_omp.cpp
index 17efa59a5286a2947a5e0b34ecc7f9f5df548a8d..0d74a94ba0a5bcaf4a5df53a7cc0d1988ed6ae7d 100644
--- a/src/USER-OMP/pair_eam_omp.cpp
+++ b/src/USER-OMP/pair_eam_omp.cpp
@@ -67,7 +67,7 @@ void PairEAMOMP::compute(int eflag, int vflag)
loop_setup_thr(ifrom, ito, tid, inum, nthreads);
ThrData *thr = fix->get_thr(tid);
ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
-
+
if (force->newton_pair)
thr->init_eam(nall, rho);
else
@@ -75,11 +75,11 @@ void PairEAMOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -139,18 +139,18 @@ void PairEAMOMP::eval(int iifrom, int iito, ThrData * const thr)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cutforcesq) {
- jtype = type[j];
- p = sqrt(rsq)*rdr + 1.0;
- m = static_cast<int> (p);
- m = MIN(m,nr-1);
- p -= m;
- p = MIN(p,1.0);
- coeff = rhor_spline[type2rhor[jtype][itype]][m];
- rho_t[i] += ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
- if (NEWTON_PAIR || j < nlocal) {
- coeff = rhor_spline[type2rhor[itype][jtype]][m];
- rho_t[j] += ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
- }
+ jtype = type[j];
+ p = sqrt(rsq)*rdr + 1.0;
+ m = static_cast<int> (p);
+ m = MIN(m,nr-1);
+ p -= m;
+ p = MIN(p,1.0);
+ coeff = rhor_spline[type2rhor[jtype][itype]][m];
+ rho_t[i] += ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
+ if (NEWTON_PAIR || j < nlocal) {
+ coeff = rhor_spline[type2rhor[itype][jtype]][m];
+ rho_t[j] += ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
+ }
}
}
}
@@ -174,14 +174,14 @@ void PairEAMOMP::eval(int iifrom, int iito, ThrData * const thr)
// wait until master thread is done with communication
sync_threads();
-
+
} else {
data_reduce_thr(rho, nlocal, nthreads, 1, tid);
// wait until reduction is complete
sync_threads();
}
-
+
// fp = derivative of embedding energy at each atom
// phi = embedding energy at each atom
@@ -237,50 +237,50 @@ void PairEAMOMP::eval(int iifrom, int iito, ThrData * const thr)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cutforcesq) {
- jtype = type[j];
- r = sqrt(rsq);
- p = r*rdr + 1.0;
- m = static_cast<int> (p);
- m = MIN(m,nr-1);
- p -= m;
- p = MIN(p,1.0);
-
- // rhoip = derivative of (density at atom j due to atom i)
- // rhojp = derivative of (density at atom i due to atom j)
- // phi = pair potential energy
- // phip = phi'
- // z2 = phi * r
- // z2p = (phi * r)' = (phi' r) + phi
- // psip needs both fp[i] and fp[j] terms since r_ij appears in two
- // terms of embed eng: Fi(sum rho_ij) and Fj(sum rho_ji)
- // hence embed' = Fi(sum rho_ij) rhojp + Fj(sum rho_ji) rhoip
-
- coeff = rhor_spline[type2rhor[itype][jtype]][m];
- rhoip = (coeff[0]*p + coeff[1])*p + coeff[2];
- coeff = rhor_spline[type2rhor[jtype][itype]][m];
- rhojp = (coeff[0]*p + coeff[1])*p + coeff[2];
- coeff = z2r_spline[type2z2r[itype][jtype]][m];
- z2p = (coeff[0]*p + coeff[1])*p + coeff[2];
- z2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
-
- recip = 1.0/r;
- phi = z2*recip;
- phip = z2p*recip - phi*recip;
- psip = fp[i]*rhojp + fp[j]*rhoip + phip;
- fpair = -psip*recip;
-
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (EFLAG) evdwl = phi;
- if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
- evdwl,0.0,fpair,delx,dely,delz,thr);
+ jtype = type[j];
+ r = sqrt(rsq);
+ p = r*rdr + 1.0;
+ m = static_cast<int> (p);
+ m = MIN(m,nr-1);
+ p -= m;
+ p = MIN(p,1.0);
+
+ // rhoip = derivative of (density at atom j due to atom i)
+ // rhojp = derivative of (density at atom i due to atom j)
+ // phi = pair potential energy
+ // phip = phi'
+ // z2 = phi * r
+ // z2p = (phi * r)' = (phi' r) + phi
+ // psip needs both fp[i] and fp[j] terms since r_ij appears in two
+ // terms of embed eng: Fi(sum rho_ij) and Fj(sum rho_ji)
+ // hence embed' = Fi(sum rho_ij) rhojp + Fj(sum rho_ji) rhoip
+
+ coeff = rhor_spline[type2rhor[itype][jtype]][m];
+ rhoip = (coeff[0]*p + coeff[1])*p + coeff[2];
+ coeff = rhor_spline[type2rhor[jtype][itype]][m];
+ rhojp = (coeff[0]*p + coeff[1])*p + coeff[2];
+ coeff = z2r_spline[type2z2r[itype][jtype]][m];
+ z2p = (coeff[0]*p + coeff[1])*p + coeff[2];
+ z2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
+
+ recip = 1.0/r;
+ phi = z2*recip;
+ phip = z2p*recip - phi*recip;
+ psip = fp[i]*rhojp + fp[j]*rhoip + phip;
+ fpair = -psip*recip;
+
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (EFLAG) evdwl = phi;
+ if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
+ evdwl,0.0,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_eam_omp.h b/src/USER-OMP/pair_eam_omp.h
index 6b0f1274fcd9419934a7d43d35832581d0e9d40f..0f9d3cd51e1b36458f98e8ad13bf608958240538 100644
--- a/src/USER-OMP/pair_eam_omp.h
+++ b/src/USER-OMP/pair_eam_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_edip_omp.cpp b/src/USER-OMP/pair_edip_omp.cpp
index 4d1fc3e833b1caa2b8cb60f2e15bcbd222c55935..d9d68d7a070897716d2bc6f9dc1be6d49158a1ec 100644
--- a/src/USER-OMP/pair_edip_omp.cpp
+++ b/src/USER-OMP/pair_edip_omp.cpp
@@ -63,11 +63,11 @@ void PairEDIPOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (vflag_atom) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (vflag_atom) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (vflag_atom) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (vflag_atom) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else eval<0,0,0>(ifrom, ito, thr);
@@ -204,8 +204,8 @@ void PairEDIPOMP::eval(int iifrom, int iito, ThrData * const thr)
interpolY1 = exp3B[interpolIDX];
interpolY2 = exp3B[interpolIDX+1];
- exp3B_ij = interpolY1 + (interpolY2 - interpolY1) *
- (interpolTMP-interpolIDX);
+ exp3B_ij = interpolY1 + (interpolY2 - interpolY1) *
+ (interpolTMP-interpolIDX);
exp3BDerived_ij = - exp3B_ij * gammInvRMinusCutoffA * invRMinusCutoffA;
@@ -214,8 +214,8 @@ void PairEDIPOMP::eval(int iifrom, int iito, ThrData * const thr)
interpolY1 = exp2B[interpolIDX];
interpolY2 = exp2B[interpolIDX+1];
- exp2B_ij = interpolY1 + (interpolY2 - interpolY1) *
- (interpolTMP-interpolIDX);
+ exp2B_ij = interpolY1 + (interpolY2 - interpolY1) *
+ (interpolTMP-interpolIDX);
exp2BDerived_ij = - exp2B_ij * sigmaInvRMinusCutoffA * invRMinusCutoffA;
@@ -224,8 +224,8 @@ void PairEDIPOMP::eval(int iifrom, int iito, ThrData * const thr)
interpolY1 = pow2B[interpolIDX];
interpolY2 = pow2B[interpolIDX+1];
- pow2B_ij = interpolY1 + (interpolY2 - interpolY1) *
- (interpolTMP-interpolIDX);
+ pow2B_ij = interpolY1 + (interpolY2 - interpolY1) *
+ (interpolTMP-interpolIDX);
pre_thrPow2B_ij[neighbor_j] = pow2B_ij;
@@ -235,15 +235,15 @@ void PairEDIPOMP::eval(int iifrom, int iito, ThrData * const thr)
else {
interpolY1 = cutoffFunction[interpolIDX];
interpolY2 = cutoffFunction[interpolIDX+1];
- cutoffFunction_ij = interpolY1 + (interpolY2 - interpolY1) *
- (interpolTMP-interpolIDX);
+ cutoffFunction_ij = interpolY1 + (interpolY2 - interpolY1) *
+ (interpolTMP-interpolIDX);
zeta_i += cutoffFunction_ij;
interpolY1 = cutoffFunctionDerived[interpolIDX];
interpolY2 = cutoffFunctionDerived[interpolIDX+1];
- zeta_iDerived = interpolY1 + (interpolY2 - interpolY1) *
- (interpolTMP-interpolIDX);
+ zeta_iDerived = interpolY1 + (interpolY2 - interpolY1) *
+ (interpolTMP-interpolIDX);
zeta_iDerivedInvR_ij = zeta_iDerived * invR_ij;
@@ -265,22 +265,22 @@ void PairEDIPOMP::eval(int iifrom, int iito, ThrData * const thr)
interpolY1 = expMinusBetaZeta_iZeta_iGrid[interpolIDX];
interpolY2 = expMinusBetaZeta_iZeta_iGrid[interpolIDX+1];
- expMinusBetaZeta_iZeta_i = interpolY1 + (interpolY2 - interpolY1) *
+ expMinusBetaZeta_iZeta_i = interpolY1 + (interpolY2 - interpolY1) *
(interpolTMP-interpolIDX);
interpolY1 = qFunctionGrid[interpolIDX];
interpolY2 = qFunctionGrid[interpolIDX+1];
- qFunction = interpolY1 + (interpolY2 - interpolY1) *
+ qFunction = interpolY1 + (interpolY2 - interpolY1) *
(interpolTMP-interpolIDX);
interpolY1 = tauFunctionGrid[interpolIDX];
interpolY2 = tauFunctionGrid[interpolIDX+1];
- tauFunction = interpolY1 + (interpolY2 - interpolY1) *
+ tauFunction = interpolY1 + (interpolY2 - interpolY1) *
(interpolTMP-interpolIDX);
interpolY1 = tauFunctionDerivedGrid[interpolIDX];
interpolY2 = tauFunctionDerivedGrid[interpolIDX+1];
- tauFunctionDerived = interpolY1 + (interpolY2 - interpolY1) *
+ tauFunctionDerived = interpolY1 + (interpolY2 - interpolY1) *
(interpolTMP-interpolIDX);
qFunctionDerived = -mu * qFunction;
@@ -320,8 +320,8 @@ void PairEDIPOMP::eval(int iifrom, int iito, ThrData * const thr)
forceModCoord += (forceModCoord_factor*exp2B_ij);
exp2BDerived_ij = pre_thrExp2BDerived_ij[neighbor_j];
- forceMod2B = exp2BDerived_ij * potential2B_factor +
- exp2B_ij * pow2BDerived_ij;
+ forceMod2B = exp2BDerived_ij * potential2B_factor +
+ exp2B_ij * pow2BDerived_ij;
directorCos_ij_x = invR_ij * dr_ij[0];
directorCos_ij_y = invR_ij * dr_ij[1];
@@ -347,7 +347,7 @@ void PairEDIPOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl = (exp2B_ij * potential2B_factor);
if (EVFLAG) ev_tally_thr(this,i, j, nlocal, /* newton_pair */ 1, evdwl, 0.0,
- -forceMod2B*invR_ij, dr_ij[0], dr_ij[1], dr_ij[2],thr);
+ -forceMod2B*invR_ij, dr_ij[0], dr_ij[1], dr_ij[2],thr);
// three-body Forces
@@ -375,56 +375,56 @@ void PairEDIPOMP::eval(int iifrom, int iito, ThrData * const thr)
directorCos_ik_y = invR_ik * dr_ik[1];
directorCos_ik_z = invR_ik * dr_ik[2];
- cosTeta = directorCos_ij_x * directorCos_ik_x +
- directorCos_ij_y * directorCos_ik_y +
- directorCos_ij_z * directorCos_ik_z;
+ cosTeta = directorCos_ij_x * directorCos_ik_x +
+ directorCos_ij_y * directorCos_ik_y +
+ directorCos_ij_z * directorCos_ik_z;
cosTetaDiff = cosTeta + tauFunction;
cosTetaDiffCosTetaDiff = cosTetaDiff * cosTetaDiff;
qFunctionCosTetaDiffCosTetaDiff = cosTetaDiffCosTetaDiff * qFunction;
- expMinusQFunctionCosTetaDiffCosTetaDiff =
- exp(-qFunctionCosTetaDiffCosTetaDiff);
+ expMinusQFunctionCosTetaDiffCosTetaDiff =
+ exp(-qFunctionCosTetaDiffCosTetaDiff);
- potentia3B_factor = lambda *
- ((1.0 - expMinusQFunctionCosTetaDiffCosTetaDiff) +
- eta * qFunctionCosTetaDiffCosTetaDiff);
+ potentia3B_factor = lambda *
+ ((1.0 - expMinusQFunctionCosTetaDiffCosTetaDiff) +
+ eta * qFunctionCosTetaDiffCosTetaDiff);
exp3B_ik = pre_thrExp3B_ij[neighbor_k];
exp3BDerived_ik = pre_thrExp3BDerived_ij[neighbor_k];
- forceMod3B_factor1_ij = - exp3BDerived_ij * exp3B_ik *
- potentia3B_factor;
- forceMod3B_factor2 = 2.0 * lambda * exp3B_ij * exp3B_ik *
- qFunction * cosTetaDiff *
- (eta + expMinusQFunctionCosTetaDiffCosTetaDiff);
+ forceMod3B_factor1_ij = - exp3BDerived_ij * exp3B_ik *
+ potentia3B_factor;
+ forceMod3B_factor2 = 2.0 * lambda * exp3B_ij * exp3B_ik *
+ qFunction * cosTetaDiff *
+ (eta + expMinusQFunctionCosTetaDiffCosTetaDiff);
forceMod3B_factor2_ij = forceMod3B_factor2 * invR_ij;
- f_ij[0] = forceMod3B_factor1_ij * directorCos_ij_x +
- forceMod3B_factor2_ij *
- (cosTeta * directorCos_ij_x - directorCos_ik_x);
- f_ij[1] = forceMod3B_factor1_ij * directorCos_ij_y +
- forceMod3B_factor2_ij *
- (cosTeta * directorCos_ij_y - directorCos_ik_y);
- f_ij[2] = forceMod3B_factor1_ij * directorCos_ij_z +
- forceMod3B_factor2_ij *
- (cosTeta * directorCos_ij_z - directorCos_ik_z);
-
- forceMod3B_factor1_ik = - exp3BDerived_ik * exp3B_ij *
- potentia3B_factor;
+ f_ij[0] = forceMod3B_factor1_ij * directorCos_ij_x +
+ forceMod3B_factor2_ij *
+ (cosTeta * directorCos_ij_x - directorCos_ik_x);
+ f_ij[1] = forceMod3B_factor1_ij * directorCos_ij_y +
+ forceMod3B_factor2_ij *
+ (cosTeta * directorCos_ij_y - directorCos_ik_y);
+ f_ij[2] = forceMod3B_factor1_ij * directorCos_ij_z +
+ forceMod3B_factor2_ij *
+ (cosTeta * directorCos_ij_z - directorCos_ik_z);
+
+ forceMod3B_factor1_ik = - exp3BDerived_ik * exp3B_ij *
+ potentia3B_factor;
forceMod3B_factor2_ik = forceMod3B_factor2 * invR_ik;
- f_ik[0] = forceMod3B_factor1_ik * directorCos_ik_x +
- forceMod3B_factor2_ik *
- (cosTeta * directorCos_ik_x - directorCos_ij_x);
- f_ik[1] = forceMod3B_factor1_ik * directorCos_ik_y +
- forceMod3B_factor2_ik *
- (cosTeta * directorCos_ik_y - directorCos_ij_y);
- f_ik[2] = forceMod3B_factor1_ik * directorCos_ik_z +
- forceMod3B_factor2_ik *
- (cosTeta * directorCos_ik_z - directorCos_ij_z);
+ f_ik[0] = forceMod3B_factor1_ik * directorCos_ik_x +
+ forceMod3B_factor2_ik *
+ (cosTeta * directorCos_ik_x - directorCos_ij_x);
+ f_ik[1] = forceMod3B_factor1_ik * directorCos_ik_y +
+ forceMod3B_factor2_ik *
+ (cosTeta * directorCos_ik_y - directorCos_ij_y);
+ f_ik[2] = forceMod3B_factor1_ik * directorCos_ik_z +
+ forceMod3B_factor2_ik *
+ (cosTeta * directorCos_ik_z - directorCos_ij_z);
- forceModCoord += (forceMod3B_factor2 *
- (tauFunctionDerived - 0.5 * mu * cosTetaDiff));
+ forceModCoord += (forceMod3B_factor2 *
+ (tauFunctionDerived - 0.5 * mu * cosTetaDiff));
f[j][0] += f_ij[0];
f[j][1] += f_ij[1];
@@ -476,7 +476,7 @@ void PairEDIPOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl = 0.0;
if (EVFLAG) ev_tally_thr(this,i, j, nlocal, /* newton_pair */ 1, 0.0, 0.0,
- forceModCoord_ij, dr_ij[0], dr_ij[1], dr_ij[2],thr);
+ forceModCoord_ij, dr_ij[0], dr_ij[1], dr_ij[2],thr);
}
}
}
diff --git a/src/USER-OMP/pair_eim_omp.cpp b/src/USER-OMP/pair_eim_omp.cpp
index cf1fcf5e359503c2eea3f8aca30c07ed192dd399..ad0909f24219a091378aeaa9e63f5bf71c940f70 100644
--- a/src/USER-OMP/pair_eim_omp.cpp
+++ b/src/USER-OMP/pair_eim_omp.cpp
@@ -67,19 +67,19 @@ void PairEIMOMP::compute(int eflag, int vflag)
loop_setup_thr(ifrom, ito, tid, inum, nthreads);
ThrData *thr = fix->get_thr(tid);
ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
-
+
if (force->newton_pair)
thr->init_eim(nall, rho, fp);
else
thr->init_eim(atom->nlocal, rho, fp);
-
+
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -141,17 +141,17 @@ void PairEIMOMP::eval(int iifrom, int iito, ThrData * const thr)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cutforcesq[itype][jtype]) {
- p = sqrt(rsq)*rdr + 1.0;
- m = static_cast<int> (p);
- m = MIN(m,nr-1);
- p -= m;
- p = MIN(p,1.0);
- coeff = Fij_spline[type2Fij[itype][jtype]][m];
- rho_t[i] += ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
- if (NEWTON_PAIR || j < nlocal) {
- coeff = Fij_spline[type2Fij[jtype][itype]][m];
- rho_t[j] += ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
- }
+ p = sqrt(rsq)*rdr + 1.0;
+ m = static_cast<int> (p);
+ m = MIN(m,nr-1);
+ p -= m;
+ p = MIN(p,1.0);
+ coeff = Fij_spline[type2Fij[itype][jtype]][m];
+ rho_t[i] += ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
+ if (NEWTON_PAIR || j < nlocal) {
+ coeff = Fij_spline[type2Fij[jtype][itype]][m];
+ rho_t[j] += ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
+ }
}
}
}
@@ -170,9 +170,9 @@ void PairEIMOMP::eval(int iifrom, int iito, ThrData * const thr)
#if defined(_OPENMP)
#pragma omp master
#endif
- {
+ {
rhofp = 1;
- comm->reverse_comm_pair(this);
+ comm->reverse_comm_pair(this);
}
} else {
@@ -185,14 +185,14 @@ void PairEIMOMP::eval(int iifrom, int iito, ThrData * const thr)
#if defined(_OPENMP)
#pragma omp master
#endif
- {
+ {
rhofp = 1;
- comm->forward_comm_pair(this);
+ comm->forward_comm_pair(this);
}
// wait until master is finished communicating
sync_threads();
-
+
for (ii = iifrom; ii < iito; ii++) {
i = ilist[ii];
xtmp = x[i][0];
@@ -201,17 +201,17 @@ void PairEIMOMP::eval(int iifrom, int iito, ThrData * const thr)
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
-
+
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
jtype = type[j];
-
+
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
-
+
if (rsq < cutforcesq[itype][jtype]) {
p = sqrt(rsq)*rdr + 1.0;
m = static_cast<int> (p);
@@ -221,8 +221,8 @@ void PairEIMOMP::eval(int iifrom, int iito, ThrData * const thr)
coeff = Gij_spline[type2Gij[itype][jtype]][m];
fp_t[i] += rho[j]*(((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6]);
if (NEWTON_PAIR || j < nlocal) {
- fp_t[j] += rho[i]*(((coeff[3]*p + coeff[4])*p + coeff[5])*p +
- coeff[6]);
+ fp_t[j] += rho[i]*(((coeff[3]*p + coeff[4])*p + coeff[5])*p +
+ coeff[6]);
}
}
}
@@ -242,9 +242,9 @@ void PairEIMOMP::eval(int iifrom, int iito, ThrData * const thr)
#if defined(_OPENMP)
#pragma omp master
#endif
- {
+ {
rhofp = 2;
- comm->reverse_comm_pair(this);
+ comm->reverse_comm_pair(this);
}
} else {
@@ -257,9 +257,9 @@ void PairEIMOMP::eval(int iifrom, int iito, ThrData * const thr)
#if defined(_OPENMP)
#pragma omp master
#endif
- {
+ {
rhofp = 2;
- comm->forward_comm_pair(this);
+ comm->forward_comm_pair(this);
}
// wait until master is finished communicating
@@ -298,12 +298,12 @@ void PairEIMOMP::eval(int iifrom, int iito, ThrData * const thr)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cutforcesq[itype][jtype]) {
- r = sqrt(rsq);
- p = r*rdr + 1.0;
- m = static_cast<int> (p);
- m = MIN(m,nr-1);
- p -= m;
- p = MIN(p,1.0);
+ r = sqrt(rsq);
+ p = r*rdr + 1.0;
+ m = static_cast<int> (p);
+ m = MIN(m,nr-1);
+ p -= m;
+ p = MIN(p,1.0);
// rhoip = derivative of (density at atom j due to atom i)
// rhojp = derivative of (density at atom i due to atom j)
@@ -324,18 +324,18 @@ void PairEIMOMP::eval(int iifrom, int iito, ThrData * const thr)
fp[i]*rhojp + fp[j]*rhoip;
recip = 1.0/r;
fpair = -psip*recip;
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (EFLAG) evdwl = phi-q0[itype]*q0[jtype]*coul;
- if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
- evdwl,0.0,fpair,delx,dely,delz,thr);
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (EFLAG) evdwl = phi-q0[itype]*q0[jtype]*coul;
+ if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
+ evdwl,0.0,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_eim_omp.h b/src/USER-OMP/pair_eim_omp.h
index ad273e28eb480c5f6f38ab80f70b2b9f96c6a910..c63222d7fb6c69ef493fa3b16139183094af79f1 100644
--- a/src/USER-OMP/pair_eim_omp.h
+++ b/src/USER-OMP/pair_eim_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_gauss_cut_omp.cpp b/src/USER-OMP/pair_gauss_cut_omp.cpp
index 09e27c18f2300e4d45ca22f179c899da9d9008cf..cb54785627ecd94754366e6a4c9c50cbb82897be 100644
--- a/src/USER-OMP/pair_gauss_cut_omp.cpp
+++ b/src/USER-OMP/pair_gauss_cut_omp.cpp
@@ -56,11 +56,11 @@ void PairGaussCutOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -118,27 +118,27 @@ void PairGaussCutOMP::eval(int iifrom, int iito, ThrData * const thr)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r = sqrt(rsq);
- rexp = (r-rmh[itype][jtype])/sigmah[itype][jtype];
- ugauss = pgauss[itype][jtype]*exp(-0.5*rexp*rexp);
- fpair = factor_lj*rexp/r*ugauss/sigmah[itype][jtype];
-
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (EFLAG) {
- evdwl = ugauss - offset[itype][jtype];
- evdwl *= factor_lj;
- }
-
- if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
- evdwl,0.0,fpair,delx,dely,delz,thr);
+ r = sqrt(rsq);
+ rexp = (r-rmh[itype][jtype])/sigmah[itype][jtype];
+ ugauss = pgauss[itype][jtype]*exp(-0.5*rexp*rexp);
+ fpair = factor_lj*rexp/r*ugauss/sigmah[itype][jtype];
+
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (EFLAG) {
+ evdwl = ugauss - offset[itype][jtype];
+ evdwl *= factor_lj;
+ }
+
+ if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
+ evdwl,0.0,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_gauss_cut_omp.h b/src/USER-OMP/pair_gauss_cut_omp.h
index d3da26abede0b988bf7b74aba151fc302f76277d..2da2c14fdbde95c031f4f799d6be1a9c340d4645 100644
--- a/src/USER-OMP/pair_gauss_cut_omp.h
+++ b/src/USER-OMP/pair_gauss_cut_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_gauss_omp.cpp b/src/USER-OMP/pair_gauss_omp.cpp
index 3de24e18d2ef5b1791868422de163145c91cc19e..ae8af0d774a72bd127595f10cee5a5fe92a224ab 100644
--- a/src/USER-OMP/pair_gauss_omp.cpp
+++ b/src/USER-OMP/pair_gauss_omp.cpp
@@ -58,11 +58,11 @@ void PairGaussOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) occ = eval<1,1,1>(ifrom, ito, thr);
- else occ = eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) occ = eval<1,1,1>(ifrom, ito, thr);
+ else occ = eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) occ = eval<1,0,1>(ifrom, ito, thr);
- else occ = eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) occ = eval<1,0,1>(ifrom, ito, thr);
+ else occ = eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) occ = eval<0,0,1>(ifrom, ito, thr);
@@ -122,34 +122,34 @@ double PairGaussOMP::eval(int iifrom, int iito, ThrData * const thr)
jtype = type[j];
// define a Gaussian well to be occupied if
- // the site it interacts with is within the force maximum
-
+ // the site it interacts with is within the force maximum
+
if (EFLAG)
- if (eflag_global && rsq < 0.5/b[itype][jtype]) occ++;
+ if (eflag_global && rsq < 0.5/b[itype][jtype]) occ++;
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- forcelj = - 2.0*a[itype][jtype]*b[itype][jtype] * rsq *
- exp(-b[itype][jtype]*rsq);
- fpair = factor_lj*forcelj*r2inv;
-
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (EFLAG) {
- evdwl = -(a[itype][jtype]*exp(-b[itype][jtype]*rsq) -
- offset[itype][jtype]);
- evdwl *= factor_lj;
- }
-
- if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
- evdwl,0.0,fpair,delx,dely,delz,thr);
+ r2inv = 1.0/rsq;
+ forcelj = - 2.0*a[itype][jtype]*b[itype][jtype] * rsq *
+ exp(-b[itype][jtype]*rsq);
+ fpair = factor_lj*forcelj*r2inv;
+
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (EFLAG) {
+ evdwl = -(a[itype][jtype]*exp(-b[itype][jtype]*rsq) -
+ offset[itype][jtype]);
+ evdwl *= factor_lj;
+ }
+
+ if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
+ evdwl,0.0,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_gauss_omp.h b/src/USER-OMP/pair_gauss_omp.h
index 81d9d0ce3f2484847b2cdff9685fd18576c16fcc..a65a98730a6efd4a9efffe05be8d2a8a7026db16 100644
--- a/src/USER-OMP/pair_gauss_omp.h
+++ b/src/USER-OMP/pair_gauss_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_gayberne_omp.cpp b/src/USER-OMP/pair_gayberne_omp.cpp
index f12b84f3f5179bab451484d1232bfa748bfc9873..98fa5428a22a135b41e39b9c0c53d6d9f94adc53 100644
--- a/src/USER-OMP/pair_gayberne_omp.cpp
+++ b/src/USER-OMP/pair_gayberne_omp.cpp
@@ -58,11 +58,11 @@ void PairGayBerneOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -134,81 +134,81 @@ void PairGayBerneOMP::eval(int iifrom, int iito, ThrData * const thr)
if (rsq < cutsq[itype][jtype]) {
- switch (form[itype][jtype]) {
- case SPHERE_SPHERE:
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- forcelj *= -r2inv;
- if (EFLAG)
- one_eng = r6inv*(r6inv*lj3[itype][jtype]-lj4[itype][jtype]) -
- offset[itype][jtype];
- fforce[0] = r12[0]*forcelj;
- fforce[1] = r12[1]*forcelj;
- fforce[2] = r12[2]*forcelj;
- ttor[0] = ttor[1] = ttor[2] = 0.0;
- rtor[0] = rtor[1] = rtor[2] = 0.0;
- break;
+ switch (form[itype][jtype]) {
+ case SPHERE_SPHERE:
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ forcelj *= -r2inv;
+ if (EFLAG)
+ one_eng = r6inv*(r6inv*lj3[itype][jtype]-lj4[itype][jtype]) -
+ offset[itype][jtype];
+ fforce[0] = r12[0]*forcelj;
+ fforce[1] = r12[1]*forcelj;
+ fforce[2] = r12[2]*forcelj;
+ ttor[0] = ttor[1] = ttor[2] = 0.0;
+ rtor[0] = rtor[1] = rtor[2] = 0.0;
+ break;
case SPHERE_ELLIPSE:
- jquat = bonus[ellipsoid[j]].quat;
- MathExtra::quat_to_mat_trans(jquat,a2);
- MathExtra::diag_times3(well[jtype],a2,temp);
- MathExtra::transpose_times3(a2,temp,b2);
- MathExtra::diag_times3(shape2[jtype],a2,temp);
- MathExtra::transpose_times3(a2,temp,g2);
- one_eng = gayberne_lj(j,i,a2,b2,g2,r12,rsq,fforce,rtor);
- ttor[0] = ttor[1] = ttor[2] = 0.0;
- break;
+ jquat = bonus[ellipsoid[j]].quat;
+ MathExtra::quat_to_mat_trans(jquat,a2);
+ MathExtra::diag_times3(well[jtype],a2,temp);
+ MathExtra::transpose_times3(a2,temp,b2);
+ MathExtra::diag_times3(shape2[jtype],a2,temp);
+ MathExtra::transpose_times3(a2,temp,g2);
+ one_eng = gayberne_lj(j,i,a2,b2,g2,r12,rsq,fforce,rtor);
+ ttor[0] = ttor[1] = ttor[2] = 0.0;
+ break;
case ELLIPSE_SPHERE:
- one_eng = gayberne_lj(i,j,a1,b1,g1,r12,rsq,fforce,ttor);
- rtor[0] = rtor[1] = rtor[2] = 0.0;
- break;
-
- default:
- jquat = bonus[ellipsoid[j]].quat;
- MathExtra::quat_to_mat_trans(jquat,a2);
- MathExtra::diag_times3(well[jtype],a2,temp);
- MathExtra::transpose_times3(a2,temp,b2);
- MathExtra::diag_times3(shape2[jtype],a2,temp);
- MathExtra::transpose_times3(a2,temp,g2);
- one_eng = gayberne_analytic(i,j,a1,a2,b1,b2,g1,g2,r12,rsq,
- fforce,ttor,rtor);
- break;
- }
+ one_eng = gayberne_lj(i,j,a1,b1,g1,r12,rsq,fforce,ttor);
+ rtor[0] = rtor[1] = rtor[2] = 0.0;
+ break;
+
+ default:
+ jquat = bonus[ellipsoid[j]].quat;
+ MathExtra::quat_to_mat_trans(jquat,a2);
+ MathExtra::diag_times3(well[jtype],a2,temp);
+ MathExtra::transpose_times3(a2,temp,b2);
+ MathExtra::diag_times3(shape2[jtype],a2,temp);
+ MathExtra::transpose_times3(a2,temp,g2);
+ one_eng = gayberne_analytic(i,j,a1,a2,b1,b2,g1,g2,r12,rsq,
+ fforce,ttor,rtor);
+ break;
+ }
fforce[0] *= factor_lj;
- fforce[1] *= factor_lj;
- fforce[2] *= factor_lj;
+ fforce[1] *= factor_lj;
+ fforce[2] *= factor_lj;
ttor[0] *= factor_lj;
- ttor[1] *= factor_lj;
- ttor[2] *= factor_lj;
+ ttor[1] *= factor_lj;
+ ttor[2] *= factor_lj;
fxtmp += fforce[0];
- fytmp += fforce[1];
- fztmp += fforce[2];
+ fytmp += fforce[1];
+ fztmp += fforce[2];
t1tmp += ttor[0];
- t2tmp += ttor[1];
- t3tmp += ttor[2];
+ t2tmp += ttor[1];
+ t3tmp += ttor[2];
if (NEWTON_PAIR || j < nlocal) {
rtor[0] *= factor_lj;
- rtor[1] *= factor_lj;
- rtor[2] *= factor_lj;
+ rtor[1] *= factor_lj;
+ rtor[2] *= factor_lj;
f[j][0] -= fforce[0];
- f[j][1] -= fforce[1];
- f[j][2] -= fforce[2];
+ f[j][1] -= fforce[1];
+ f[j][2] -= fforce[2];
tor[j][0] += rtor[0];
- tor[j][1] += rtor[1];
- tor[j][2] += rtor[2];
+ tor[j][1] += rtor[1];
+ tor[j][2] += rtor[2];
}
if (EFLAG) evdwl = factor_lj*one_eng;
- if (EVFLAG) ev_tally_xyz_thr(this,i,j,nlocal,NEWTON_PAIR,
- evdwl,0.0,fforce[0],fforce[1],fforce[2],
- -r12[0],-r12[1],-r12[2],thr);
+ if (EVFLAG) ev_tally_xyz_thr(this,i,j,nlocal,NEWTON_PAIR,
+ evdwl,0.0,fforce[0],fforce[1],fforce[2],
+ -r12[0],-r12[1],-r12[2],thr);
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_gayberne_omp.h b/src/USER-OMP/pair_gayberne_omp.h
index 0bd0b8b086464597e51d1f18fb557a16046d1238..0e7b6708ff2eb3764030256e89748d27cbac209a 100644
--- a/src/USER-OMP/pair_gayberne_omp.h
+++ b/src/USER-OMP/pair_gayberne_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_gran_hertz_history_omp.cpp b/src/USER-OMP/pair_gran_hertz_history_omp.cpp
index 283b3532e34aa22a6c202691b5431a1b1bebb1e5..4de7f12bad2d6c0c0162075318329f2a6165113f 100644
--- a/src/USER-OMP/pair_gran_hertz_history_omp.cpp
+++ b/src/USER-OMP/pair_gran_hertz_history_omp.cpp
@@ -60,7 +60,7 @@ void PairGranHertzHistoryOMP::compute(int eflag, int vflag)
if (evflag)
if (shearupdate) eval<1,1>(ifrom, ito, thr);
else eval<1,0>(ifrom, ito, thr);
- else
+ else
if (shearupdate) eval<0,1>(ifrom, ito, thr);
else eval<0,0>(ifrom, ito, thr);
@@ -133,145 +133,145 @@ void PairGranHertzHistoryOMP::eval(int iifrom, int iito, ThrData * const thr)
if (rsq >= radsum*radsum) {
- // unset non-touching neighbors
+ // unset non-touching neighbors
touch[jj] = 0;
- shear = &allshear[3*jj];
+ shear = &allshear[3*jj];
shear[0] = 0.0;
shear[1] = 0.0;
shear[2] = 0.0;
} else {
- r = sqrt(rsq);
- rinv = 1.0/r;
- rsqinv = 1.0/rsq;
+ r = sqrt(rsq);
+ rinv = 1.0/r;
+ rsqinv = 1.0/rsq;
- // relative translational velocity
+ // relative translational velocity
- vr1 = v[i][0] - v[j][0];
- vr2 = v[i][1] - v[j][1];
- vr3 = v[i][2] - v[j][2];
+ vr1 = v[i][0] - v[j][0];
+ vr2 = v[i][1] - v[j][1];
+ vr3 = v[i][2] - v[j][2];
- // normal component
+ // normal component
- vnnr = vr1*delx + vr2*dely + vr3*delz;
- vn1 = delx*vnnr * rsqinv;
- vn2 = dely*vnnr * rsqinv;
- vn3 = delz*vnnr * rsqinv;
+ vnnr = vr1*delx + vr2*dely + vr3*delz;
+ vn1 = delx*vnnr * rsqinv;
+ vn2 = dely*vnnr * rsqinv;
+ vn3 = delz*vnnr * rsqinv;
- // tangential component
+ // tangential component
- vt1 = vr1 - vn1;
- vt2 = vr2 - vn2;
- vt3 = vr3 - vn3;
+ vt1 = vr1 - vn1;
+ vt2 = vr2 - vn2;
+ vt3 = vr3 - vn3;
- // relative rotational velocity
+ // relative rotational velocity
- wr1 = (radi*omega[i][0] + radj*omega[j][0]) * rinv;
- wr2 = (radi*omega[i][1] + radj*omega[j][1]) * rinv;
- wr3 = (radi*omega[i][2] + radj*omega[j][2]) * rinv;
+ wr1 = (radi*omega[i][0] + radj*omega[j][0]) * rinv;
+ wr2 = (radi*omega[i][1] + radj*omega[j][1]) * rinv;
+ wr3 = (radi*omega[i][2] + radj*omega[j][2]) * rinv;
- // normal force = Hertzian contact + normal velocity damping
+ // normal force = Hertzian contact + normal velocity damping
- if (rmass) {
- meff = rmass[i]*rmass[j] / (rmass[i]+rmass[j]);
- if (mask[i] & freeze_group_bit) meff = rmass[j];
- if (mask[j] & freeze_group_bit) meff = rmass[i];
- } else {
- itype = type[i];
- jtype = type[j];
- meff = mass[itype]*mass[jtype] / (mass[itype]+mass[jtype]);
- if (mask[i] & freeze_group_bit) meff = mass[jtype];
- if (mask[j] & freeze_group_bit) meff = mass[itype];
- }
+ if (rmass) {
+ meff = rmass[i]*rmass[j] / (rmass[i]+rmass[j]);
+ if (mask[i] & freeze_group_bit) meff = rmass[j];
+ if (mask[j] & freeze_group_bit) meff = rmass[i];
+ } else {
+ itype = type[i];
+ jtype = type[j];
+ meff = mass[itype]*mass[jtype] / (mass[itype]+mass[jtype]);
+ if (mask[i] & freeze_group_bit) meff = mass[jtype];
+ if (mask[j] & freeze_group_bit) meff = mass[itype];
+ }
- damp = meff*gamman*vnnr*rsqinv;
- ccel = kn*(radsum-r)*rinv - damp;
- polyhertz = sqrt((radsum-r)*radi*radj / radsum);
- ccel *= polyhertz;
+ damp = meff*gamman*vnnr*rsqinv;
+ ccel = kn*(radsum-r)*rinv - damp;
+ polyhertz = sqrt((radsum-r)*radi*radj / radsum);
+ ccel *= polyhertz;
- // relative velocities
+ // relative velocities
- vtr1 = vt1 - (delz*wr2-dely*wr3);
- vtr2 = vt2 - (delx*wr3-delz*wr1);
- vtr3 = vt3 - (dely*wr1-delx*wr2);
- vrel = vtr1*vtr1 + vtr2*vtr2 + vtr3*vtr3;
- vrel = sqrt(vrel);
+ vtr1 = vt1 - (delz*wr2-dely*wr3);
+ vtr2 = vt2 - (delx*wr3-delz*wr1);
+ vtr3 = vt3 - (dely*wr1-delx*wr2);
+ vrel = vtr1*vtr1 + vtr2*vtr2 + vtr3*vtr3;
+ vrel = sqrt(vrel);
- // shear history effects
+ // shear history effects
- touch[jj] = 1;
- shear = &allshear[3*jj];
+ touch[jj] = 1;
+ shear = &allshear[3*jj];
- if (SHEARUPDATE) {
- shear[0] += vtr1*dt;
- shear[1] += vtr2*dt;
- shear[2] += vtr3*dt;
- }
+ if (SHEARUPDATE) {
+ shear[0] += vtr1*dt;
+ shear[1] += vtr2*dt;
+ shear[2] += vtr3*dt;
+ }
shrmag = sqrt(shear[0]*shear[0] + shear[1]*shear[1] +
- shear[2]*shear[2]);
+ shear[2]*shear[2]);
- // rotate shear displacements
+ // rotate shear displacements
- rsht = shear[0]*delx + shear[1]*dely + shear[2]*delz;
- rsht *= rsqinv;
- if (SHEARUPDATE) {
- shear[0] -= rsht*delx;
- shear[1] -= rsht*dely;
- shear[2] -= rsht*delz;
- }
+ rsht = shear[0]*delx + shear[1]*dely + shear[2]*delz;
+ rsht *= rsqinv;
+ if (SHEARUPDATE) {
+ shear[0] -= rsht*delx;
+ shear[1] -= rsht*dely;
+ shear[2] -= rsht*delz;
+ }
- // tangential forces = shear + tangential velocity damping
+ // tangential forces = shear + tangential velocity damping
fs1 = -polyhertz * (kt*shear[0] + meff*gammat*vtr1);
fs2 = -polyhertz * (kt*shear[1] + meff*gammat*vtr2);
fs3 = -polyhertz * (kt*shear[2] + meff*gammat*vtr3);
- // rescale frictional displacements and forces if needed
-
- fs = sqrt(fs1*fs1 + fs2*fs2 + fs3*fs3);
- fn = xmu * fabs(ccel*r);
-
- if (fs > fn) {
- if (shrmag != 0.0) {
- const double fnfs = fn/fs;
- const double mgkt = meff*gammat/kt;
- shear[0] = fnfs * (shear[0] + mgkt*vtr1) - mgkt*vtr1;
- shear[1] = fnfs * (shear[1] + mgkt*vtr2) - mgkt*vtr2;
- shear[2] = fnfs * (shear[2] + mgkt*vtr3) - mgkt*vtr3;
- fs1 *= fnfs;
- fs2 *= fnfs;
- fs3 *= fnfs;
- } else fs1 = fs2 = fs3 = 0.0;
- }
-
- // forces & torques
-
- fx = delx*ccel + fs1;
- fy = dely*ccel + fs2;
- fz = delz*ccel + fs3;
- fxtmp += fx;
- fytmp += fy;
- fztmp += fz;
-
- tor1 = rinv * (dely*fs3 - delz*fs2);
- tor2 = rinv * (delz*fs1 - delx*fs3);
- tor3 = rinv * (delx*fs2 - dely*fs1);
- t1tmp -= radi*tor1;
- t2tmp -= radi*tor2;
- t3tmp -= radi*tor3;
-
- if (j < nlocal) {
- f[j][0] -= fx;
- f[j][1] -= fy;
- f[j][2] -= fz;
- torque[j][0] -= radj*tor1;
- torque[j][1] -= radj*tor2;
- torque[j][2] -= radj*tor3;
- }
-
- if (EVFLAG) ev_tally_xyz_thr(this,i,j,nlocal,/* newton_pair */ 0,
- 0.0,0.0,fx,fy,fz,delx,dely,delz,thr);
+ // rescale frictional displacements and forces if needed
+
+ fs = sqrt(fs1*fs1 + fs2*fs2 + fs3*fs3);
+ fn = xmu * fabs(ccel*r);
+
+ if (fs > fn) {
+ if (shrmag != 0.0) {
+ const double fnfs = fn/fs;
+ const double mgkt = meff*gammat/kt;
+ shear[0] = fnfs * (shear[0] + mgkt*vtr1) - mgkt*vtr1;
+ shear[1] = fnfs * (shear[1] + mgkt*vtr2) - mgkt*vtr2;
+ shear[2] = fnfs * (shear[2] + mgkt*vtr3) - mgkt*vtr3;
+ fs1 *= fnfs;
+ fs2 *= fnfs;
+ fs3 *= fnfs;
+ } else fs1 = fs2 = fs3 = 0.0;
+ }
+
+ // forces & torques
+
+ fx = delx*ccel + fs1;
+ fy = dely*ccel + fs2;
+ fz = delz*ccel + fs3;
+ fxtmp += fx;
+ fytmp += fy;
+ fztmp += fz;
+
+ tor1 = rinv * (dely*fs3 - delz*fs2);
+ tor2 = rinv * (delz*fs1 - delx*fs3);
+ tor3 = rinv * (delx*fs2 - dely*fs1);
+ t1tmp -= radi*tor1;
+ t2tmp -= radi*tor2;
+ t3tmp -= radi*tor3;
+
+ if (j < nlocal) {
+ f[j][0] -= fx;
+ f[j][1] -= fy;
+ f[j][2] -= fz;
+ torque[j][0] -= radj*tor1;
+ torque[j][1] -= radj*tor2;
+ torque[j][2] -= radj*tor3;
+ }
+
+ if (EVFLAG) ev_tally_xyz_thr(this,i,j,nlocal,/* newton_pair */ 0,
+ 0.0,0.0,fx,fy,fz,delx,dely,delz,thr);
}
}
diff --git a/src/USER-OMP/pair_gran_hertz_history_omp.h b/src/USER-OMP/pair_gran_hertz_history_omp.h
index 956e057093f0acf6b87b814a8adfae901e64a1c2..1a8d819920a175e0a66d893351de4f615a343f7e 100644
--- a/src/USER-OMP/pair_gran_hertz_history_omp.h
+++ b/src/USER-OMP/pair_gran_hertz_history_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_gran_hooke_history_omp.cpp b/src/USER-OMP/pair_gran_hooke_history_omp.cpp
index 42ba42a1bc0265e1b327b6e85688e8471a9275bf..dc298de7e5105c03b3be87fb0f3b7eaf38ff08c0 100644
--- a/src/USER-OMP/pair_gran_hooke_history_omp.cpp
+++ b/src/USER-OMP/pair_gran_hooke_history_omp.cpp
@@ -65,7 +65,7 @@ void PairGranHookeHistoryOMP::compute(int eflag, int vflag)
if (evflag)
if (shearupdate) eval<1,1>(ifrom, ito, thr);
else eval<1,0>(ifrom, ito, thr);
- else
+ else
if (shearupdate) eval<0,1>(ifrom, ito, thr);
else eval<0,0>(ifrom, ito, thr);
@@ -139,7 +139,7 @@ void PairGranHookeHistoryOMP::eval(int iifrom, int iito, ThrData * const thr)
if (rsq >= radsum*radsum) {
- // unset non-touching neighbors
+ // unset non-touching neighbors
touch[jj] = 0;
myshear[0] = 0.0;
@@ -147,133 +147,133 @@ void PairGranHookeHistoryOMP::eval(int iifrom, int iito, ThrData * const thr)
myshear[2] = 0.0;
} else {
- r = sqrt(rsq);
- rinv = 1.0/r;
- rsqinv = 1.0/rsq;
+ r = sqrt(rsq);
+ rinv = 1.0/r;
+ rsqinv = 1.0/rsq;
- // relative translational velocity
+ // relative translational velocity
- vr1 = v[i][0] - v[j][0];
- vr2 = v[i][1] - v[j][1];
- vr3 = v[i][2] - v[j][2];
+ vr1 = v[i][0] - v[j][0];
+ vr2 = v[i][1] - v[j][1];
+ vr3 = v[i][2] - v[j][2];
- // normal component
+ // normal component
- vnnr = vr1*delx + vr2*dely + vr3*delz;
- vn1 = delx*vnnr * rsqinv;
- vn2 = dely*vnnr * rsqinv;
- vn3 = delz*vnnr * rsqinv;
+ vnnr = vr1*delx + vr2*dely + vr3*delz;
+ vn1 = delx*vnnr * rsqinv;
+ vn2 = dely*vnnr * rsqinv;
+ vn3 = delz*vnnr * rsqinv;
- // tangential component
+ // tangential component
- vt1 = vr1 - vn1;
- vt2 = vr2 - vn2;
- vt3 = vr3 - vn3;
+ vt1 = vr1 - vn1;
+ vt2 = vr2 - vn2;
+ vt3 = vr3 - vn3;
- // relative rotational velocity
+ // relative rotational velocity
- wr1 = (radi*omega[i][0] + radj*omega[j][0]) * rinv;
- wr2 = (radi*omega[i][1] + radj*omega[j][1]) * rinv;
- wr3 = (radi*omega[i][2] + radj*omega[j][2]) * rinv;
+ wr1 = (radi*omega[i][0] + radj*omega[j][0]) * rinv;
+ wr2 = (radi*omega[i][1] + radj*omega[j][1]) * rinv;
+ wr3 = (radi*omega[i][2] + radj*omega[j][2]) * rinv;
- // normal forces = Hookian contact + normal velocity damping
+ // normal forces = Hookian contact + normal velocity damping
- if (rmass) {
- meff = rmass[i]*rmass[j] / (rmass[i]+rmass[j]);
- if (mask[i] & freeze_group_bit) meff = rmass[j];
- if (mask[j] & freeze_group_bit) meff = rmass[i];
- } else {
- jtype = type[j];
- meff = mass[itype]*mass[jtype] / (mass[itype]+mass[jtype]);
- if (mask[i] & freeze_group_bit) meff = mass[jtype];
- if (mask[j] & freeze_group_bit) meff = mass[itype];
- }
+ if (rmass) {
+ meff = rmass[i]*rmass[j] / (rmass[i]+rmass[j]);
+ if (mask[i] & freeze_group_bit) meff = rmass[j];
+ if (mask[j] & freeze_group_bit) meff = rmass[i];
+ } else {
+ jtype = type[j];
+ meff = mass[itype]*mass[jtype] / (mass[itype]+mass[jtype]);
+ if (mask[i] & freeze_group_bit) meff = mass[jtype];
+ if (mask[j] & freeze_group_bit) meff = mass[itype];
+ }
- damp = meff*gamman*vnnr*rsqinv;
- ccel = kn*(radsum-r)*rinv - damp;
+ damp = meff*gamman*vnnr*rsqinv;
+ ccel = kn*(radsum-r)*rinv - damp;
- // relative velocities
+ // relative velocities
- vtr1 = vt1 - (delz*wr2-dely*wr3);
- vtr2 = vt2 - (delx*wr3-delz*wr1);
- vtr3 = vt3 - (dely*wr1-delx*wr2);
- vrel = vtr1*vtr1 + vtr2*vtr2 + vtr3*vtr3;
- vrel = sqrt(vrel);
+ vtr1 = vt1 - (delz*wr2-dely*wr3);
+ vtr2 = vt2 - (delx*wr3-delz*wr1);
+ vtr3 = vt3 - (dely*wr1-delx*wr2);
+ vrel = vtr1*vtr1 + vtr2*vtr2 + vtr3*vtr3;
+ vrel = sqrt(vrel);
- // shear history effects
+ // shear history effects
- touch[jj] = 1;
- memcpy(myshear,allshear + 3*jj, 3*sizeof(double));
+ touch[jj] = 1;
+ memcpy(myshear,allshear + 3*jj, 3*sizeof(double));
- if (SHEARUPDATE) {
- myshear[0] += vtr1*dt;
- myshear[1] += vtr2*dt;
- myshear[2] += vtr3*dt;
- }
+ if (SHEARUPDATE) {
+ myshear[0] += vtr1*dt;
+ myshear[1] += vtr2*dt;
+ myshear[2] += vtr3*dt;
+ }
shrmag = sqrt(myshear[0]*myshear[0] + myshear[1]*myshear[1] +
- myshear[2]*myshear[2]);
-
- // rotate shear displacements
-
- rsht = myshear[0]*delx + myshear[1]*dely + myshear[2]*delz;
- rsht *= rsqinv;
- if (SHEARUPDATE) {
- myshear[0] -= rsht*delx;
- myshear[1] -= rsht*dely;
- myshear[2] -= rsht*delz;
- }
-
- // tangential forces = shear + tangential velocity damping
-
- fs1 = - (kt*myshear[0] + meff*gammat*vtr1);
- fs2 = - (kt*myshear[1] + meff*gammat*vtr2);
- fs3 = - (kt*myshear[2] + meff*gammat*vtr3);
-
- // rescale frictional displacements and forces if needed
-
- fs = sqrt(fs1*fs1 + fs2*fs2 + fs3*fs3);
- fn = xmu * fabs(ccel*r);
-
- if (fs > fn) {
- if (shrmag != 0.0) {
- const double fnfs = fn/fs;
- const double mgkt = meff*gammat/kt;
- myshear[0] = fnfs * (myshear[0] + mgkt*vtr1) - mgkt*vtr1;
- myshear[1] = fnfs * (myshear[1] + mgkt*vtr2) - mgkt*vtr2;
- myshear[2] = fnfs * (myshear[2] + mgkt*vtr3) - mgkt*vtr3;
- fs1 *= fnfs;
- fs2 *= fnfs;
- fs3 *= fnfs;
- } else fs1 = fs2 = fs3 = 0.0;
- }
-
- // forces & torques
-
- fx = delx*ccel + fs1;
- fy = dely*ccel + fs2;
- fz = delz*ccel + fs3;
- fxtmp += fx;
- fytmp += fy;
- fztmp += fz;
-
- tor1 = rinv * (dely*fs3 - delz*fs2);
- tor2 = rinv * (delz*fs1 - delx*fs3);
- tor3 = rinv * (delx*fs2 - dely*fs1);
- t1tmp -= radi*tor1;
- t2tmp -= radi*tor2;
- t3tmp -= radi*tor3;
-
- if (j < nlocal) {
- f[j][0] -= fx;
- f[j][1] -= fy;
- f[j][2] -= fz;
- torque[j][0] -= radj*tor1;
- torque[j][1] -= radj*tor2;
- torque[j][2] -= radj*tor3;
- }
-
- if (EVFLAG) ev_tally_xyz_thr(this,i,j,nlocal,/* newton_pair */ 0,
- 0.0,0.0,fx,fy,fz,delx,dely,delz,thr);
+ myshear[2]*myshear[2]);
+
+ // rotate shear displacements
+
+ rsht = myshear[0]*delx + myshear[1]*dely + myshear[2]*delz;
+ rsht *= rsqinv;
+ if (SHEARUPDATE) {
+ myshear[0] -= rsht*delx;
+ myshear[1] -= rsht*dely;
+ myshear[2] -= rsht*delz;
+ }
+
+ // tangential forces = shear + tangential velocity damping
+
+ fs1 = - (kt*myshear[0] + meff*gammat*vtr1);
+ fs2 = - (kt*myshear[1] + meff*gammat*vtr2);
+ fs3 = - (kt*myshear[2] + meff*gammat*vtr3);
+
+ // rescale frictional displacements and forces if needed
+
+ fs = sqrt(fs1*fs1 + fs2*fs2 + fs3*fs3);
+ fn = xmu * fabs(ccel*r);
+
+ if (fs > fn) {
+ if (shrmag != 0.0) {
+ const double fnfs = fn/fs;
+ const double mgkt = meff*gammat/kt;
+ myshear[0] = fnfs * (myshear[0] + mgkt*vtr1) - mgkt*vtr1;
+ myshear[1] = fnfs * (myshear[1] + mgkt*vtr2) - mgkt*vtr2;
+ myshear[2] = fnfs * (myshear[2] + mgkt*vtr3) - mgkt*vtr3;
+ fs1 *= fnfs;
+ fs2 *= fnfs;
+ fs3 *= fnfs;
+ } else fs1 = fs2 = fs3 = 0.0;
+ }
+
+ // forces & torques
+
+ fx = delx*ccel + fs1;
+ fy = dely*ccel + fs2;
+ fz = delz*ccel + fs3;
+ fxtmp += fx;
+ fytmp += fy;
+ fztmp += fz;
+
+ tor1 = rinv * (dely*fs3 - delz*fs2);
+ tor2 = rinv * (delz*fs1 - delx*fs3);
+ tor3 = rinv * (delx*fs2 - dely*fs1);
+ t1tmp -= radi*tor1;
+ t2tmp -= radi*tor2;
+ t3tmp -= radi*tor3;
+
+ if (j < nlocal) {
+ f[j][0] -= fx;
+ f[j][1] -= fy;
+ f[j][2] -= fz;
+ torque[j][0] -= radj*tor1;
+ torque[j][1] -= radj*tor2;
+ torque[j][2] -= radj*tor3;
+ }
+
+ if (EVFLAG) ev_tally_xyz_thr(this,i,j,nlocal,/* newton_pair */ 0,
+ 0.0,0.0,fx,fy,fz,delx,dely,delz,thr);
}
memcpy(allshear + 3*jj, myshear, 3*sizeof(double));
diff --git a/src/USER-OMP/pair_gran_hooke_history_omp.h b/src/USER-OMP/pair_gran_hooke_history_omp.h
index 7588469e744408815af12be7f0e1b97ac24d54a2..9cdebf7104b971cf3380cf92b9c2642857c59c07 100644
--- a/src/USER-OMP/pair_gran_hooke_history_omp.h
+++ b/src/USER-OMP/pair_gran_hooke_history_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_gran_hooke_omp.cpp b/src/USER-OMP/pair_gran_hooke_omp.cpp
index 223acdbd4a6c1757eb3ba8c55f7ae8fbf36ac535..519384105ee428209c8dfab65bd43a0cec04e8f7 100644
--- a/src/USER-OMP/pair_gran_hooke_omp.cpp
+++ b/src/USER-OMP/pair_gran_hooke_omp.cpp
@@ -57,7 +57,7 @@ void PairGranHookeOMP::compute(int eflag, int vflag)
if (evflag)
if (force->newton_pair) eval<1,1>(ifrom, ito, thr);
else eval<1,0>(ifrom, ito, thr);
- else
+ else
if (force->newton_pair) eval<0,1>(ifrom, ito, thr);
else eval<0,0>(ifrom, ito, thr);
@@ -121,100 +121,100 @@ void PairGranHookeOMP::eval(int iifrom, int iito, ThrData * const thr)
radsum = radi + radj;
if (rsq < radsum*radsum) {
- r = sqrt(rsq);
- rinv = 1.0/r;
- rsqinv = 1.0/rsq;
-
- // relative translational velocity
-
- vr1 = v[i][0] - v[j][0];
- vr2 = v[i][1] - v[j][1];
- vr3 = v[i][2] - v[j][2];
-
- // normal component
-
- vnnr = vr1*delx + vr2*dely + vr3*delz;
- vn1 = delx*vnnr * rsqinv;
- vn2 = dely*vnnr * rsqinv;
- vn3 = delz*vnnr * rsqinv;
-
- // tangential component
-
- vt1 = vr1 - vn1;
- vt2 = vr2 - vn2;
- vt3 = vr3 - vn3;
-
- // relative rotational velocity
-
- wr1 = (radi*omega[i][0] + radj*omega[j][0]) * rinv;
- wr2 = (radi*omega[i][1] + radj*omega[j][1]) * rinv;
- wr3 = (radi*omega[i][2] + radj*omega[j][2]) * rinv;
-
- // normal forces = Hookian contact + normal velocity damping
-
- if (rmass) {
- meff = rmass[i]*rmass[j] / (rmass[i]+rmass[j]);
- if (mask[i] & freeze_group_bit) meff = rmass[j];
- if (mask[j] & freeze_group_bit) meff = rmass[i];
- } else {
- itype = type[i];
- jtype = type[j];
- meff = mass[itype]*mass[jtype] / (mass[itype]+mass[jtype]);
- if (mask[i] & freeze_group_bit) meff = mass[jtype];
- if (mask[j] & freeze_group_bit) meff = mass[itype];
- }
-
- damp = meff*gamman*vnnr*rsqinv;
- ccel = kn*(radsum-r)*rinv - damp;
-
- // relative velocities
-
- vtr1 = vt1 - (delz*wr2-dely*wr3);
- vtr2 = vt2 - (delx*wr3-delz*wr1);
- vtr3 = vt3 - (dely*wr1-delx*wr2);
- vrel = vtr1*vtr1 + vtr2*vtr2 + vtr3*vtr3;
- vrel = sqrt(vrel);
-
- // force normalization
-
- fn = xmu * fabs(ccel*r);
- fs = meff*gammat*vrel;
- if (vrel != 0.0) ft = MIN(fn,fs) / vrel;
- else ft = 0.0;
-
- // tangential force due to tangential velocity damping
-
- fs1 = -ft*vtr1;
- fs2 = -ft*vtr2;
- fs3 = -ft*vtr3;
-
- // forces & torques
-
- fx = delx*ccel + fs1;
- fy = dely*ccel + fs2;
- fz = delz*ccel + fs3;
- fxtmp += fx;
- fytmp += fy;
- fztmp += fz;
-
- tor1 = rinv * (dely*fs3 - delz*fs2);
- tor2 = rinv * (delz*fs1 - delx*fs3);
- tor3 = rinv * (delx*fs2 - dely*fs1);
- t1tmp -= radi*tor1;
- t2tmp -= radi*tor2;
- t3tmp -= radi*tor3;
-
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= fx;
- f[j][1] -= fy;
- f[j][2] -= fz;
- torque[j][0] -= radj*tor1;
- torque[j][1] -= radj*tor2;
- torque[j][2] -= radj*tor3;
- }
-
- if (EVFLAG) ev_tally_xyz_thr(this,i,j,nlocal,NEWTON_PAIR,
- 0.0,0.0,fx,fy,fz,delx,dely,delz,thr);
+ r = sqrt(rsq);
+ rinv = 1.0/r;
+ rsqinv = 1.0/rsq;
+
+ // relative translational velocity
+
+ vr1 = v[i][0] - v[j][0];
+ vr2 = v[i][1] - v[j][1];
+ vr3 = v[i][2] - v[j][2];
+
+ // normal component
+
+ vnnr = vr1*delx + vr2*dely + vr3*delz;
+ vn1 = delx*vnnr * rsqinv;
+ vn2 = dely*vnnr * rsqinv;
+ vn3 = delz*vnnr * rsqinv;
+
+ // tangential component
+
+ vt1 = vr1 - vn1;
+ vt2 = vr2 - vn2;
+ vt3 = vr3 - vn3;
+
+ // relative rotational velocity
+
+ wr1 = (radi*omega[i][0] + radj*omega[j][0]) * rinv;
+ wr2 = (radi*omega[i][1] + radj*omega[j][1]) * rinv;
+ wr3 = (radi*omega[i][2] + radj*omega[j][2]) * rinv;
+
+ // normal forces = Hookian contact + normal velocity damping
+
+ if (rmass) {
+ meff = rmass[i]*rmass[j] / (rmass[i]+rmass[j]);
+ if (mask[i] & freeze_group_bit) meff = rmass[j];
+ if (mask[j] & freeze_group_bit) meff = rmass[i];
+ } else {
+ itype = type[i];
+ jtype = type[j];
+ meff = mass[itype]*mass[jtype] / (mass[itype]+mass[jtype]);
+ if (mask[i] & freeze_group_bit) meff = mass[jtype];
+ if (mask[j] & freeze_group_bit) meff = mass[itype];
+ }
+
+ damp = meff*gamman*vnnr*rsqinv;
+ ccel = kn*(radsum-r)*rinv - damp;
+
+ // relative velocities
+
+ vtr1 = vt1 - (delz*wr2-dely*wr3);
+ vtr2 = vt2 - (delx*wr3-delz*wr1);
+ vtr3 = vt3 - (dely*wr1-delx*wr2);
+ vrel = vtr1*vtr1 + vtr2*vtr2 + vtr3*vtr3;
+ vrel = sqrt(vrel);
+
+ // force normalization
+
+ fn = xmu * fabs(ccel*r);
+ fs = meff*gammat*vrel;
+ if (vrel != 0.0) ft = MIN(fn,fs) / vrel;
+ else ft = 0.0;
+
+ // tangential force due to tangential velocity damping
+
+ fs1 = -ft*vtr1;
+ fs2 = -ft*vtr2;
+ fs3 = -ft*vtr3;
+
+ // forces & torques
+
+ fx = delx*ccel + fs1;
+ fy = dely*ccel + fs2;
+ fz = delz*ccel + fs3;
+ fxtmp += fx;
+ fytmp += fy;
+ fztmp += fz;
+
+ tor1 = rinv * (dely*fs3 - delz*fs2);
+ tor2 = rinv * (delz*fs1 - delx*fs3);
+ tor3 = rinv * (delx*fs2 - dely*fs1);
+ t1tmp -= radi*tor1;
+ t2tmp -= radi*tor2;
+ t3tmp -= radi*tor3;
+
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= fx;
+ f[j][1] -= fy;
+ f[j][2] -= fz;
+ torque[j][0] -= radj*tor1;
+ torque[j][1] -= radj*tor2;
+ torque[j][2] -= radj*tor3;
+ }
+
+ if (EVFLAG) ev_tally_xyz_thr(this,i,j,nlocal,NEWTON_PAIR,
+ 0.0,0.0,fx,fy,fz,delx,dely,delz,thr);
}
}
diff --git a/src/USER-OMP/pair_gran_hooke_omp.h b/src/USER-OMP/pair_gran_hooke_omp.h
index b275992bfacd096687147ec575bcf43596f88003..81f831fcea61446251507fa0b11fd4ada66c68f9 100644
--- a/src/USER-OMP/pair_gran_hooke_omp.h
+++ b/src/USER-OMP/pair_gran_hooke_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp b/src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp
index 074271a193a3b5ec57180d79083aea9bc81df755..8e4b8a7a9001d337fd2c747f8a85269c88359e81 100644
--- a/src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp
+++ b/src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp
@@ -83,11 +83,11 @@ void PairHbondDreidingLJOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -135,7 +135,7 @@ void PairHbondDreidingLJOMP::eval(int iifrom, int iito, ThrData * const thr)
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// ii = loop over donors
// jj = loop over acceptors
// kk = loop over hydrogens bonded to donor
@@ -173,107 +173,107 @@ void PairHbondDreidingLJOMP::eval(int iifrom, int iito, ThrData * const thr)
rsq = delx*delx + dely*dely + delz*delz;
for (kk = 0; kk < knum; kk++) {
- k = atom->map(klist[kk]);
- if (k < 0) continue;
- ktype = type[k];
- m = type2param[itype][jtype][ktype];
- if (m < 0) continue;
- pm = ¶ms[m];
-
- if (rsq < pm->cut_outersq) {
- delr1[0] = xtmp - x[k][0];
- delr1[1] = ytmp - x[k][1];
- delr1[2] = ztmp - x[k][2];
- domain->minimum_image(delr1);
- rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2];
- r1 = sqrt(rsq1);
-
- delr2[0] = x[j][0] - x[k][0];
- delr2[1] = x[j][1] - x[k][1];
- delr2[2] = x[j][2] - x[k][2];
- domain->minimum_image(delr2);
- rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
- r2 = sqrt(rsq2);
-
- // angle (cos and sin)
-
- c = delr1[0]*delr2[0] + delr1[1]*delr2[1] + delr1[2]*delr2[2];
- c /= r1*r2;
- if (c > 1.0) c = 1.0;
- if (c < -1.0) c = -1.0;
- ac = acos(c);
-
- if (ac > pm->cut_angle && ac < (2.0*MY_PI - pm->cut_angle)) {
- s = sqrt(1.0 - c*c);
- if (s < SMALL) s = SMALL;
-
- // LJ-specific kernel
-
- r2inv = 1.0/rsq;
- r10inv = r2inv*r2inv*r2inv*r2inv*r2inv;
- force_kernel = r10inv*(pm->lj1*r2inv - pm->lj2)*r2inv *
- pow(c,(double)pm->ap);
- force_angle = pm->ap * r10inv*(pm->lj3*r2inv - pm->lj4) *
- pow(c,pm->ap-1.0)*s;
-
- eng_lj = r10inv*(pm->lj3*r2inv - pm->lj4);
- if (rsq > pm->cut_innersq) {
- switch1 = (pm->cut_outersq-rsq) * (pm->cut_outersq-rsq) *
- (pm->cut_outersq + 2.0*rsq - 3.0*pm->cut_innersq) /
- pm->denom_vdw;
- switch2 = 12.0*rsq * (pm->cut_outersq-rsq) *
- (rsq-pm->cut_innersq) / pm->denom_vdw;
- force_kernel = force_kernel*switch1 + eng_lj*switch2;
- eng_lj *= switch1;
- }
-
- if (EFLAG) {
- evdwl = eng_lj * pow(c,(double)pm->ap);
- evdwl *= factor_hb;
- }
-
- a = factor_hb*force_angle/s;
- b = factor_hb*force_kernel;
-
- a11 = a*c / rsq1;
- a12 = -a / (r1*r2);
- a22 = a*c / rsq2;
-
- vx1 = a11*delr1[0] + a12*delr2[0];
- vx2 = a22*delr2[0] + a12*delr1[0];
- vy1 = a11*delr1[1] + a12*delr2[1];
- vy2 = a22*delr2[1] + a12*delr1[1];
- vz1 = a11*delr1[2] + a12*delr2[2];
- vz2 = a22*delr2[2] + a12*delr1[2];
-
- fi[0] = vx1 + b*delx;
- fi[1] = vy1 + b*dely;
- fi[2] = vz1 + b*delz;
- fj[0] = vx2 - b*delx;
- fj[1] = vy2 - b*dely;
- fj[2] = vz2 - b*delz;
-
- fxtmp += fi[0];
- fytmp += fi[1];
- fztmp += fi[2];
-
- f[j][0] += fj[0];
- f[j][1] += fj[1];
- f[j][2] += fj[2];
-
- f[k][0] -= vx1 + vx2;
- f[k][1] -= vy1 + vy2;
- f[k][2] -= vz1 + vz2;
-
- // KIJ instead of IJK b/c delr1/delr2 are both with respect to k
-
- if (EVFLAG) ev_tally3_thr(this,k,i,j,evdwl,0.0,fi,fj,delr1,delr2,thr);
- if (EFLAG) {
- hbcount++;
- hbeng += evdwl;
- }
- }
- }
+ k = atom->map(klist[kk]);
+ if (k < 0) continue;
+ ktype = type[k];
+ m = type2param[itype][jtype][ktype];
+ if (m < 0) continue;
+ pm = ¶ms[m];
+
+ if (rsq < pm->cut_outersq) {
+ delr1[0] = xtmp - x[k][0];
+ delr1[1] = ytmp - x[k][1];
+ delr1[2] = ztmp - x[k][2];
+ domain->minimum_image(delr1);
+ rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2];
+ r1 = sqrt(rsq1);
+
+ delr2[0] = x[j][0] - x[k][0];
+ delr2[1] = x[j][1] - x[k][1];
+ delr2[2] = x[j][2] - x[k][2];
+ domain->minimum_image(delr2);
+ rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
+ r2 = sqrt(rsq2);
+
+ // angle (cos and sin)
+
+ c = delr1[0]*delr2[0] + delr1[1]*delr2[1] + delr1[2]*delr2[2];
+ c /= r1*r2;
+ if (c > 1.0) c = 1.0;
+ if (c < -1.0) c = -1.0;
+ ac = acos(c);
+
+ if (ac > pm->cut_angle && ac < (2.0*MY_PI - pm->cut_angle)) {
+ s = sqrt(1.0 - c*c);
+ if (s < SMALL) s = SMALL;
+
+ // LJ-specific kernel
+
+ r2inv = 1.0/rsq;
+ r10inv = r2inv*r2inv*r2inv*r2inv*r2inv;
+ force_kernel = r10inv*(pm->lj1*r2inv - pm->lj2)*r2inv *
+ pow(c,(double)pm->ap);
+ force_angle = pm->ap * r10inv*(pm->lj3*r2inv - pm->lj4) *
+ pow(c,pm->ap-1.0)*s;
+
+ eng_lj = r10inv*(pm->lj3*r2inv - pm->lj4);
+ if (rsq > pm->cut_innersq) {
+ switch1 = (pm->cut_outersq-rsq) * (pm->cut_outersq-rsq) *
+ (pm->cut_outersq + 2.0*rsq - 3.0*pm->cut_innersq) /
+ pm->denom_vdw;
+ switch2 = 12.0*rsq * (pm->cut_outersq-rsq) *
+ (rsq-pm->cut_innersq) / pm->denom_vdw;
+ force_kernel = force_kernel*switch1 + eng_lj*switch2;
+ eng_lj *= switch1;
+ }
+
+ if (EFLAG) {
+ evdwl = eng_lj * pow(c,(double)pm->ap);
+ evdwl *= factor_hb;
+ }
+
+ a = factor_hb*force_angle/s;
+ b = factor_hb*force_kernel;
+
+ a11 = a*c / rsq1;
+ a12 = -a / (r1*r2);
+ a22 = a*c / rsq2;
+
+ vx1 = a11*delr1[0] + a12*delr2[0];
+ vx2 = a22*delr2[0] + a12*delr1[0];
+ vy1 = a11*delr1[1] + a12*delr2[1];
+ vy2 = a22*delr2[1] + a12*delr1[1];
+ vz1 = a11*delr1[2] + a12*delr2[2];
+ vz2 = a22*delr2[2] + a12*delr1[2];
+
+ fi[0] = vx1 + b*delx;
+ fi[1] = vy1 + b*dely;
+ fi[2] = vz1 + b*delz;
+ fj[0] = vx2 - b*delx;
+ fj[1] = vy2 - b*dely;
+ fj[2] = vz2 - b*delz;
+
+ fxtmp += fi[0];
+ fytmp += fi[1];
+ fztmp += fi[2];
+
+ f[j][0] += fj[0];
+ f[j][1] += fj[1];
+ f[j][2] += fj[2];
+
+ f[k][0] -= vx1 + vx2;
+ f[k][1] -= vy1 + vy2;
+ f[k][2] -= vz1 + vz2;
+
+ // KIJ instead of IJK b/c delr1/delr2 are both with respect to k
+
+ if (EVFLAG) ev_tally3_thr(this,k,i,j,evdwl,0.0,fi,fj,delr1,delr2,thr);
+ if (EFLAG) {
+ hbcount++;
+ hbeng += evdwl;
+ }
+ }
+ }
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_hbond_dreiding_lj_omp.h b/src/USER-OMP/pair_hbond_dreiding_lj_omp.h
index 937391684967734441ea04df84e3782b5f41d55b..dc5108b3d7fd8ec0f8ea45ca35d26f22f094244e 100644
--- a/src/USER-OMP/pair_hbond_dreiding_lj_omp.h
+++ b/src/USER-OMP/pair_hbond_dreiding_lj_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp b/src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp
index fe0106473f031aff230ba3c4fde4ddc91c3d21c6..3dccd98dbfe6fffdcf42e356ee3b4a1d42bdae52 100644
--- a/src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp
+++ b/src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp
@@ -83,11 +83,11 @@ void PairHbondDreidingMorseOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -134,7 +134,7 @@ void PairHbondDreidingMorseOMP::eval(int iifrom, int iito, ThrData * const thr)
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// ii = loop over donors
// jj = loop over acceptors
// kk = loop over hydrogens bonded to donor
@@ -172,106 +172,106 @@ void PairHbondDreidingMorseOMP::eval(int iifrom, int iito, ThrData * const thr)
rsq = delx*delx + dely*dely + delz*delz;
for (kk = 0; kk < knum; kk++) {
- k = atom->map(klist[kk]);
- if (k < 0) continue;
- ktype = type[k];
- m = type2param[itype][jtype][ktype];
- if (m < 0) continue;
- pm = ¶ms[m];
-
- if (rsq < pm->cut_outersq) {
- delr1[0] = xtmp - x[k][0];
- delr1[1] = ytmp - x[k][1];
- delr1[2] = ztmp - x[k][2];
- domain->minimum_image(delr1);
- rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2];
- r1 = sqrt(rsq1);
-
- delr2[0] = x[j][0] - x[k][0];
- delr2[1] = x[j][1] - x[k][1];
- delr2[2] = x[j][2] - x[k][2];
- domain->minimum_image(delr2);
- rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
- r2 = sqrt(rsq2);
-
- // angle (cos and sin)
-
- c = delr1[0]*delr2[0] + delr1[1]*delr2[1] + delr1[2]*delr2[2];
- c /= r1*r2;
- if (c > 1.0) c = 1.0;
- if (c < -1.0) c = -1.0;
- ac = acos(c);
-
- if (ac > pm->cut_angle && ac < (2.0*MY_PI - pm->cut_angle)) {
- s = sqrt(1.0 - c*c);
- if (s < SMALL) s = SMALL;
-
- // Morse-specific kernel
-
- r = sqrt(rsq);
- dr = r - pm->r0;
- dexp = exp(-pm->alpha * dr);
- force_kernel = pm->morse1*(dexp*dexp - dexp)/r * pow(c,(double)pm->ap);
- force_angle = pm->ap * eng_morse * pow(c,(double)pm->ap-1.0)*s;
-
- eng_morse = pm->d0 * (dexp*dexp - 2.0*dexp);
- if (rsq > pm->cut_innersq) {
- switch1 = (pm->cut_outersq-rsq) * (pm->cut_outersq-rsq) *
- (pm->cut_outersq + 2.0*rsq - 3.0*pm->cut_innersq) /
- pm->denom_vdw;
- switch2 = 12.0*rsq * (pm->cut_outersq-rsq) *
- (rsq-pm->cut_innersq) / pm->denom_vdw;
- force_kernel = force_kernel*switch1 + eng_morse*switch2;
- eng_morse *= switch1;
- }
-
- if (EFLAG) {
- evdwl = eng_morse * pow(c,(double)params[m].ap);
- evdwl *= factor_hb;
- }
-
- a = factor_hb*force_angle/s;
- b = factor_hb*force_kernel;
-
- a11 = a*c / rsq1;
- a12 = -a / (r1*r2);
- a22 = a*c / rsq2;
-
- vx1 = a11*delr1[0] + a12*delr2[0];
- vx2 = a22*delr2[0] + a12*delr1[0];
- vy1 = a11*delr1[1] + a12*delr2[1];
- vy2 = a22*delr2[1] + a12*delr1[1];
- vz1 = a11*delr1[2] + a12*delr2[2];
- vz2 = a22*delr2[2] + a12*delr1[2];
-
- fi[0] = vx1 + b*delx;
- fi[1] = vy1 + b*dely;
- fi[2] = vz1 + b*delz;
- fj[0] = vx2 - b*delx;
- fj[1] = vy2 - b*dely;
- fj[2] = vz2 - b*delz;
-
- fxtmp += fi[0];
- fytmp += fi[1];
- fztmp += fi[2];
-
- f[j][0] += fj[0];
- f[j][1] += fj[1];
- f[j][2] += fj[2];
-
- f[k][0] -= vx1 + vx2;
- f[k][1] -= vy1 + vy2;
- f[k][2] -= vz1 + vz2;
-
- // KIJ instead of IJK b/c delr1/delr2 are both with respect to k
-
- if (EVFLAG) ev_tally3_thr(this,k,i,j,evdwl,0.0,fi,fj,delr1,delr2,thr);
- if (EFLAG) {
- hbcount++;
- hbeng += evdwl;
- }
- }
- }
+ k = atom->map(klist[kk]);
+ if (k < 0) continue;
+ ktype = type[k];
+ m = type2param[itype][jtype][ktype];
+ if (m < 0) continue;
+ pm = ¶ms[m];
+
+ if (rsq < pm->cut_outersq) {
+ delr1[0] = xtmp - x[k][0];
+ delr1[1] = ytmp - x[k][1];
+ delr1[2] = ztmp - x[k][2];
+ domain->minimum_image(delr1);
+ rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2];
+ r1 = sqrt(rsq1);
+
+ delr2[0] = x[j][0] - x[k][0];
+ delr2[1] = x[j][1] - x[k][1];
+ delr2[2] = x[j][2] - x[k][2];
+ domain->minimum_image(delr2);
+ rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
+ r2 = sqrt(rsq2);
+
+ // angle (cos and sin)
+
+ c = delr1[0]*delr2[0] + delr1[1]*delr2[1] + delr1[2]*delr2[2];
+ c /= r1*r2;
+ if (c > 1.0) c = 1.0;
+ if (c < -1.0) c = -1.0;
+ ac = acos(c);
+
+ if (ac > pm->cut_angle && ac < (2.0*MY_PI - pm->cut_angle)) {
+ s = sqrt(1.0 - c*c);
+ if (s < SMALL) s = SMALL;
+
+ // Morse-specific kernel
+
+ r = sqrt(rsq);
+ dr = r - pm->r0;
+ dexp = exp(-pm->alpha * dr);
+ force_kernel = pm->morse1*(dexp*dexp - dexp)/r * pow(c,(double)pm->ap);
+ force_angle = pm->ap * eng_morse * pow(c,(double)pm->ap-1.0)*s;
+
+ eng_morse = pm->d0 * (dexp*dexp - 2.0*dexp);
+ if (rsq > pm->cut_innersq) {
+ switch1 = (pm->cut_outersq-rsq) * (pm->cut_outersq-rsq) *
+ (pm->cut_outersq + 2.0*rsq - 3.0*pm->cut_innersq) /
+ pm->denom_vdw;
+ switch2 = 12.0*rsq * (pm->cut_outersq-rsq) *
+ (rsq-pm->cut_innersq) / pm->denom_vdw;
+ force_kernel = force_kernel*switch1 + eng_morse*switch2;
+ eng_morse *= switch1;
+ }
+
+ if (EFLAG) {
+ evdwl = eng_morse * pow(c,(double)params[m].ap);
+ evdwl *= factor_hb;
+ }
+
+ a = factor_hb*force_angle/s;
+ b = factor_hb*force_kernel;
+
+ a11 = a*c / rsq1;
+ a12 = -a / (r1*r2);
+ a22 = a*c / rsq2;
+
+ vx1 = a11*delr1[0] + a12*delr2[0];
+ vx2 = a22*delr2[0] + a12*delr1[0];
+ vy1 = a11*delr1[1] + a12*delr2[1];
+ vy2 = a22*delr2[1] + a12*delr1[1];
+ vz1 = a11*delr1[2] + a12*delr2[2];
+ vz2 = a22*delr2[2] + a12*delr1[2];
+
+ fi[0] = vx1 + b*delx;
+ fi[1] = vy1 + b*dely;
+ fi[2] = vz1 + b*delz;
+ fj[0] = vx2 - b*delx;
+ fj[1] = vy2 - b*dely;
+ fj[2] = vz2 - b*delz;
+
+ fxtmp += fi[0];
+ fytmp += fi[1];
+ fztmp += fi[2];
+
+ f[j][0] += fj[0];
+ f[j][1] += fj[1];
+ f[j][2] += fj[2];
+
+ f[k][0] -= vx1 + vx2;
+ f[k][1] -= vy1 + vy2;
+ f[k][2] -= vz1 + vz2;
+
+ // KIJ instead of IJK b/c delr1/delr2 are both with respect to k
+
+ if (EVFLAG) ev_tally3_thr(this,k,i,j,evdwl,0.0,fi,fj,delr1,delr2,thr);
+ if (EFLAG) {
+ hbcount++;
+ hbeng += evdwl;
+ }
+ }
+ }
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_hbond_dreiding_morse_omp.h b/src/USER-OMP/pair_hbond_dreiding_morse_omp.h
index d2edd7281b63d7da1800623e46b6792453f30e3c..5a8aaf2c5afda8438acfa0cbff1ed47b2763c1b5 100644
--- a/src/USER-OMP/pair_hbond_dreiding_morse_omp.h
+++ b/src/USER-OMP/pair_hbond_dreiding_morse_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_line_lj_omp.cpp b/src/USER-OMP/pair_line_lj_omp.cpp
index b4b1ea3a063e20bd166fa369ab8ca176464513df..27c630166ef7d7277e02768b2761029b7093a49e 100644
--- a/src/USER-OMP/pair_line_lj_omp.cpp
+++ b/src/USER-OMP/pair_line_lj_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -69,7 +69,7 @@ void PairLineLJOMP::compute(int eflag, int vflag)
for (int i = 0; i < nall; ++i)
if (line[i] >= 0)
if (dnum[i] == 0)
- discretize(i,sigma[type[i]][type[i]]);
+ discretize(i,sigma[type[i]][type[i]]);
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(eflag,vflag)
@@ -83,11 +83,11 @@ void PairLineLJOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -140,192 +140,192 @@ void PairLineLJOMP::eval(int iifrom, int iito, ThrData * const thr)
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
-
+
if (rsq >= cutsq[itype][jtype]) continue;
-
+
// line/line interactions = NxN particles
-
+
evdwl = 0.0;
if (line[i] >= 0 && line[j] >= 0) {
- npi = dnum[i];
- ifirst = dfirst[i];
- npj = dnum[j];
- jfirst = dfirst[j];
-
- fi[0] = fi[1] = fj[0] = fj[1] = ti = tj = 0.0;
-
- for (ni = 0; ni < npi; ni++) {
- dxi = discrete[ifirst+ni].dx;
- dyi = discrete[ifirst+ni].dy;
-
- for (nj = 0; nj < npj; nj++) {
- dxj = discrete[jfirst+nj].dx;
- dyj = discrete[jfirst+nj].dy;
-
- xi[0] = x[i][0] + dxi;
- xi[1] = x[i][1] + dyi;
- xj[0] = x[j][0] + dxj;
- xj[1] = x[j][1] + dyj;
-
- delx = xi[0] - xj[0];
- dely = xi[1] - xj[1];
- rsq = delx*delx + dely*dely;
-
- sig = 0.5 * (discrete[ifirst+ni].sigma+discrete[jfirst+nj].sigma);
- sig3 = sig*sig*sig;
- term2 = 24.0*epsilon[itype][jtype] * sig3*sig3;
- term1 = 2.0 * term2 * sig3*sig3;
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (term1*r6inv - term2);
- fpair = forcelj*r2inv;
-
- if (EFLAG) evdwl += r6inv*(term1/12.0*r6inv-term2/6.0);
-
- fi[0] += delx*fpair;
- fi[1] += dely*fpair;
- ti += fpair*(dxi*dely - dyi*delx);
-
- if (NEWTON_PAIR || j < nlocal) {
- fj[0] -= delx*fpair;
- fj[1] -= dely*fpair;
- tj += fpair*(dxj*dely - dyj*delx);
- }
- }
- }
-
- f[i][0] += fi[0];
- f[i][1] += fi[1];
- f[j][0] += fj[0];
- f[j][1] += fj[1];
- torque[i][2] += ti;
- torque[j][2] += tj;
+ npi = dnum[i];
+ ifirst = dfirst[i];
+ npj = dnum[j];
+ jfirst = dfirst[j];
+
+ fi[0] = fi[1] = fj[0] = fj[1] = ti = tj = 0.0;
+
+ for (ni = 0; ni < npi; ni++) {
+ dxi = discrete[ifirst+ni].dx;
+ dyi = discrete[ifirst+ni].dy;
+
+ for (nj = 0; nj < npj; nj++) {
+ dxj = discrete[jfirst+nj].dx;
+ dyj = discrete[jfirst+nj].dy;
+
+ xi[0] = x[i][0] + dxi;
+ xi[1] = x[i][1] + dyi;
+ xj[0] = x[j][0] + dxj;
+ xj[1] = x[j][1] + dyj;
+
+ delx = xi[0] - xj[0];
+ dely = xi[1] - xj[1];
+ rsq = delx*delx + dely*dely;
+
+ sig = 0.5 * (discrete[ifirst+ni].sigma+discrete[jfirst+nj].sigma);
+ sig3 = sig*sig*sig;
+ term2 = 24.0*epsilon[itype][jtype] * sig3*sig3;
+ term1 = 2.0 * term2 * sig3*sig3;
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (term1*r6inv - term2);
+ fpair = forcelj*r2inv;
+
+ if (EFLAG) evdwl += r6inv*(term1/12.0*r6inv-term2/6.0);
+
+ fi[0] += delx*fpair;
+ fi[1] += dely*fpair;
+ ti += fpair*(dxi*dely - dyi*delx);
+
+ if (NEWTON_PAIR || j < nlocal) {
+ fj[0] -= delx*fpair;
+ fj[1] -= dely*fpair;
+ tj += fpair*(dxj*dely - dyj*delx);
+ }
+ }
+ }
+
+ f[i][0] += fi[0];
+ f[i][1] += fi[1];
+ f[j][0] += fj[0];
+ f[j][1] += fj[1];
+ torque[i][2] += ti;
+ torque[j][2] += tj;
// line/particle interaction = Nx1 particles
// convert line into Np particles based on sigma and line length
} else if (line[i] >= 0) {
- npi = dnum[i];
- ifirst = dfirst[i];
-
- fi[0] = fi[1] = fj[0] = fj[1] = ti = tj = 0.0;
-
- for (ni = 0; ni < npi; ni++) {
- dxi = discrete[ifirst+ni].dx;
- dyi = discrete[ifirst+ni].dy;
-
- xi[0] = x[i][0] + dxi;
- xi[1] = x[i][1] + dyi;
- xj[0] = x[j][0];
- xj[1] = x[j][1];
-
- delx = xi[0] - xj[0];
- dely = xi[1] - xj[1];
- rsq = delx*delx + dely*dely;
-
- sig = 0.5 * (discrete[ifirst+ni].sigma+sigma[jtype][jtype]);
- sig3 = sig*sig*sig;
- term2 = 24.0*epsilon[itype][jtype] * sig3*sig3;
- term1 = 2.0 * term2 * sig3*sig3;
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (term1*r6inv - term2);
- fpair = forcelj*r2inv;
-
- if (EFLAG) evdwl += r6inv*(term1/12.0*r6inv-term2/6.0);
-
- fi[0] += delx*fpair;
- fi[1] += dely*fpair;
- ti += fpair*(dxi*dely - dyi*delx);
-
- if (NEWTON_PAIR || j < nlocal) {
- fj[0] -= delx*fpair;
- fj[1] -= dely*fpair;
- tj += fpair*(dxj*dely - dyj*delx);
- }
- }
-
- f[i][0] += fi[0];
- f[i][1] += fi[1];
- f[j][0] += fj[0];
- f[j][1] += fj[1];
- torque[i][2] += ti;
- torque[j][2] += tj;
+ npi = dnum[i];
+ ifirst = dfirst[i];
+
+ fi[0] = fi[1] = fj[0] = fj[1] = ti = tj = 0.0;
+
+ for (ni = 0; ni < npi; ni++) {
+ dxi = discrete[ifirst+ni].dx;
+ dyi = discrete[ifirst+ni].dy;
+
+ xi[0] = x[i][0] + dxi;
+ xi[1] = x[i][1] + dyi;
+ xj[0] = x[j][0];
+ xj[1] = x[j][1];
+
+ delx = xi[0] - xj[0];
+ dely = xi[1] - xj[1];
+ rsq = delx*delx + dely*dely;
+
+ sig = 0.5 * (discrete[ifirst+ni].sigma+sigma[jtype][jtype]);
+ sig3 = sig*sig*sig;
+ term2 = 24.0*epsilon[itype][jtype] * sig3*sig3;
+ term1 = 2.0 * term2 * sig3*sig3;
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (term1*r6inv - term2);
+ fpair = forcelj*r2inv;
+
+ if (EFLAG) evdwl += r6inv*(term1/12.0*r6inv-term2/6.0);
+
+ fi[0] += delx*fpair;
+ fi[1] += dely*fpair;
+ ti += fpair*(dxi*dely - dyi*delx);
+
+ if (NEWTON_PAIR || j < nlocal) {
+ fj[0] -= delx*fpair;
+ fj[1] -= dely*fpair;
+ tj += fpair*(dxj*dely - dyj*delx);
+ }
+ }
+
+ f[i][0] += fi[0];
+ f[i][1] += fi[1];
+ f[j][0] += fj[0];
+ f[j][1] += fj[1];
+ torque[i][2] += ti;
+ torque[j][2] += tj;
// particle/line interaction = Nx1 particles
// convert line into Np particles based on sigma and line length
} else if (line[j] >= 0) {
- npj = dnum[j];
- jfirst = dfirst[j];
-
- fi[0] = fi[1] = fj[0] = fj[1] = ti = tj = 0.0;
-
- for (nj = 0; nj < npj; nj++) {
- dxj = discrete[jfirst+nj].dx;
- dyj = discrete[jfirst+nj].dy;
-
- xi[0] = x[i][0];
- xi[1] = x[i][1];
- xj[0] = x[j][0] + dxj;
- xj[1] = x[j][1] + dyj;
-
- delx = xi[0] - xj[0];
- dely = xi[1] - xj[1];
- rsq = delx*delx + dely*dely;
-
- sig = 0.5 * (sigma[itype][itype]+discrete[jfirst+nj].sigma);
- sig3 = sig*sig*sig;
- term2 = 24.0*epsilon[itype][jtype] * sig3*sig3;
- term1 = 2.0 * term2 * sig3*sig3;
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (term1*r6inv - term2);
- fpair = forcelj*r2inv;
-
- if (EFLAG) evdwl += r6inv*(term1/12.0*r6inv-term2/6.0);
-
- fi[0] += delx*fpair;
- fi[1] += dely*fpair;
- ti += fpair*(dxi*dely - dyi*delx);
-
- if (NEWTON_PAIR || j < nlocal) {
- fj[0] -= delx*fpair;
- fj[1] -= dely*fpair;
- tj -= fpair*(dxj*dely - dyj*delx);
- }
- }
-
- f[i][0] += fi[0];
- f[i][1] += fi[1];
- f[j][0] += fj[0];
- f[j][1] += fj[1];
- torque[i][2] += ti;
- torque[j][2] += tj;
+ npj = dnum[j];
+ jfirst = dfirst[j];
+
+ fi[0] = fi[1] = fj[0] = fj[1] = ti = tj = 0.0;
+
+ for (nj = 0; nj < npj; nj++) {
+ dxj = discrete[jfirst+nj].dx;
+ dyj = discrete[jfirst+nj].dy;
+
+ xi[0] = x[i][0];
+ xi[1] = x[i][1];
+ xj[0] = x[j][0] + dxj;
+ xj[1] = x[j][1] + dyj;
+
+ delx = xi[0] - xj[0];
+ dely = xi[1] - xj[1];
+ rsq = delx*delx + dely*dely;
+
+ sig = 0.5 * (sigma[itype][itype]+discrete[jfirst+nj].sigma);
+ sig3 = sig*sig*sig;
+ term2 = 24.0*epsilon[itype][jtype] * sig3*sig3;
+ term1 = 2.0 * term2 * sig3*sig3;
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (term1*r6inv - term2);
+ fpair = forcelj*r2inv;
+
+ if (EFLAG) evdwl += r6inv*(term1/12.0*r6inv-term2/6.0);
+
+ fi[0] += delx*fpair;
+ fi[1] += dely*fpair;
+ ti += fpair*(dxi*dely - dyi*delx);
+
+ if (NEWTON_PAIR || j < nlocal) {
+ fj[0] -= delx*fpair;
+ fj[1] -= dely*fpair;
+ tj -= fpair*(dxj*dely - dyj*delx);
+ }
+ }
+
+ f[i][0] += fi[0];
+ f[i][1] += fi[1];
+ f[j][0] += fj[0];
+ f[j][1] += fj[1];
+ torque[i][2] += ti;
+ torque[j][2] += tj;
// particle/particle interaction = 1x1 particles
} else {
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- fpair = forcelj*r2inv;
-
- if (EFLAG)
- evdwl += r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ fpair = forcelj*r2inv;
+
+ if (EFLAG)
+ evdwl += r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
}
if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
- evdwl,0.0,fpair,delx,dely,delz,thr);
+ evdwl,0.0,fpair,delx,dely,delz,thr);
}
}
}
diff --git a/src/USER-OMP/pair_line_lj_omp.h b/src/USER-OMP/pair_line_lj_omp.h
index 93b38afaf0880b213e9835ee5b3dc2b34c7ed169..9a5e4333e01f4738af8a02ee4b18b2434ec36aa6 100644
--- a/src/USER-OMP/pair_line_lj_omp.h
+++ b/src/USER-OMP/pair_line_lj_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_lj96_cut_omp.cpp b/src/USER-OMP/pair_lj96_cut_omp.cpp
index b92749bf56aa750ec1bae4110874cca00da5fb0d..16827c7ee1966b8bc0cc32ed946a03c245bd275e 100644
--- a/src/USER-OMP/pair_lj96_cut_omp.cpp
+++ b/src/USER-OMP/pair_lj96_cut_omp.cpp
@@ -57,11 +57,11 @@ void PairLJ96CutOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -118,30 +118,30 @@ void PairLJ96CutOMP::eval(int iifrom, int iito, ThrData * const thr)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
- r3inv = sqrt(r6inv);
-
- forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
- fpair = factor_lj*forcelj*r2inv;
-
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (EFLAG) {
- evdwl = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype])
- - offset[itype][jtype];
- evdwl *= factor_lj;
- }
-
- if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
- evdwl,0.0,fpair,delx,dely,delz,thr);
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
+ r3inv = sqrt(r6inv);
+
+ forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
+ fpair = factor_lj*forcelj*r2inv;
+
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (EFLAG) {
+ evdwl = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype])
+ - offset[itype][jtype];
+ evdwl *= factor_lj;
+ }
+
+ if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
+ evdwl,0.0,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_lj96_cut_omp.h b/src/USER-OMP/pair_lj96_cut_omp.h
index a8040320c8a01f63256ba693665204c261191608..037c68fc03da8291c8135c7049d078484e1e2be4 100644
--- a/src/USER-OMP/pair_lj96_cut_omp.h
+++ b/src/USER-OMP/pair_lj96_cut_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp b/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp
index 811fdbcdac9ac809499190a1dd603eb89dfe81b0..739f754a23838a270423143315e13bb0479cfd2d 100644
--- a/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp
+++ b/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp
@@ -56,11 +56,11 @@ void PairLJCharmmCoulCharmmImplicitOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -127,70 +127,70 @@ void PairLJCharmmCoulCharmmImplicitOMP::eval(int iifrom, int iito, ThrData * con
jtype = type[j];
if (rsq < cut_bothsq) {
- r2inv = 1.0/rsq;
-
- if (rsq < cut_coulsq) {
- forcecoul = 2.0 * qqrd2e * qtmp*q[j]*r2inv;
- if (rsq > cut_coul_innersq) {
- switch1 = (cut_coulsq-rsq) * (cut_coulsq-rsq) *
- (cut_coulsq + 2.0*rsq - 3.0*cut_coul_innersq) * invdenom_coul;
- switch2 = 12.0*rsq * (cut_coulsq-rsq) *
- (rsq-cut_coul_innersq) * invdenom_coul;
- forcecoul *= switch1 + switch2;
- }
- forcecoul *= factor_coul;
- } else forcecoul = 0.0;
-
- if (rsq < cut_ljsq) {
- r6inv = r2inv*r2inv*r2inv;
- jtype = type[j];
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- if (rsq > cut_lj_innersq) {
- switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
- (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * invdenom_lj;
- switch2 = 12.0*rsq * (cut_ljsq-rsq) *
- (rsq-cut_lj_innersq) * invdenom_lj;
- philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
- forcelj = forcelj*switch1 + philj*switch2;
- }
- forcelj *= factor_lj;
- } else forcelj = 0.0;
-
- fpair = (forcecoul + forcelj) * r2inv;
-
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (EFLAG) {
- if (rsq < cut_coulsq) {
- ecoul = qqrd2e * qtmp*q[j]*r2inv;
- if (rsq > cut_coul_innersq) {
- switch1 = (cut_coulsq-rsq) * (cut_coulsq-rsq) *
- (cut_coulsq + 2.0*rsq - 3.0*cut_coul_innersq) *
- invdenom_coul;
- ecoul *= switch1;
- }
- ecoul *= factor_coul;
- } else ecoul = 0.0;
- if (rsq < cut_ljsq) {
- evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
- if (rsq > cut_lj_innersq) {
- switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
- (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * invdenom_lj;
- evdwl *= switch1;
- }
- evdwl *= factor_lj;
- } else evdwl = 0.0;
- }
-
- if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
- evdwl,ecoul,fpair,delx,dely,delz,thr);
+ r2inv = 1.0/rsq;
+
+ if (rsq < cut_coulsq) {
+ forcecoul = 2.0 * qqrd2e * qtmp*q[j]*r2inv;
+ if (rsq > cut_coul_innersq) {
+ switch1 = (cut_coulsq-rsq) * (cut_coulsq-rsq) *
+ (cut_coulsq + 2.0*rsq - 3.0*cut_coul_innersq) * invdenom_coul;
+ switch2 = 12.0*rsq * (cut_coulsq-rsq) *
+ (rsq-cut_coul_innersq) * invdenom_coul;
+ forcecoul *= switch1 + switch2;
+ }
+ forcecoul *= factor_coul;
+ } else forcecoul = 0.0;
+
+ if (rsq < cut_ljsq) {
+ r6inv = r2inv*r2inv*r2inv;
+ jtype = type[j];
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ if (rsq > cut_lj_innersq) {
+ switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
+ (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * invdenom_lj;
+ switch2 = 12.0*rsq * (cut_ljsq-rsq) *
+ (rsq-cut_lj_innersq) * invdenom_lj;
+ philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
+ forcelj = forcelj*switch1 + philj*switch2;
+ }
+ forcelj *= factor_lj;
+ } else forcelj = 0.0;
+
+ fpair = (forcecoul + forcelj) * r2inv;
+
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (EFLAG) {
+ if (rsq < cut_coulsq) {
+ ecoul = qqrd2e * qtmp*q[j]*r2inv;
+ if (rsq > cut_coul_innersq) {
+ switch1 = (cut_coulsq-rsq) * (cut_coulsq-rsq) *
+ (cut_coulsq + 2.0*rsq - 3.0*cut_coul_innersq) *
+ invdenom_coul;
+ ecoul *= switch1;
+ }
+ ecoul *= factor_coul;
+ } else ecoul = 0.0;
+ if (rsq < cut_ljsq) {
+ evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
+ if (rsq > cut_lj_innersq) {
+ switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
+ (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * invdenom_lj;
+ evdwl *= switch1;
+ }
+ evdwl *= factor_lj;
+ } else evdwl = 0.0;
+ }
+
+ if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
+ evdwl,ecoul,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.h b/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.h
index dff01ce499b724a3143a3553c2d5e0c37e890834..9fb2835353227b9e6ab71d33b12df8ed4bdcefb1 100644
--- a/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.h
+++ b/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp b/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp
index 7c1b1041829f8eeeaf8425c657bca2a2471f2720..318cb3aaa8f1777d4e0a6f3a7489178dc80362e1 100644
--- a/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp
+++ b/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp
@@ -56,11 +56,11 @@ void PairLJCharmmCoulCharmmOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -127,70 +127,70 @@ void PairLJCharmmCoulCharmmOMP::eval(int iifrom, int iito, ThrData * const thr)
jtype = type[j];
if (rsq < cut_bothsq) {
- r2inv = 1.0/rsq;
-
- if (rsq < cut_coulsq) {
- forcecoul = qqrd2e * qtmp*q[j]*sqrt(r2inv);
- if (rsq > cut_coul_innersq) {
- switch1 = (cut_coulsq-rsq) * (cut_coulsq-rsq) *
- (cut_coulsq + 2.0*rsq - 3.0*cut_coul_innersq) * invdenom_coul;
- switch2 = 12.0*rsq * (cut_coulsq-rsq) *
- (rsq-cut_coul_innersq) * invdenom_coul;
- forcecoul *= switch1 + switch2;
- }
- forcecoul *= factor_coul;
- } else forcecoul = 0.0;
-
- if (rsq < cut_ljsq) {
- r6inv = r2inv*r2inv*r2inv;
- jtype = type[j];
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- if (rsq > cut_lj_innersq) {
- switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
- (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * invdenom_lj;
- switch2 = 12.0*rsq * (cut_ljsq-rsq) *
- (rsq-cut_lj_innersq) * invdenom_lj;
- philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
- forcelj = forcelj*switch1 + philj*switch2;
- }
- forcelj *= factor_lj;
- } else forcelj = 0.0;
-
- fpair = (forcecoul + forcelj) * r2inv;
-
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (EFLAG) {
- if (rsq < cut_coulsq) {
- ecoul = qqrd2e * qtmp*q[j]*sqrt(r2inv);
- if (rsq > cut_coul_innersq) {
- switch1 = (cut_coulsq-rsq) * (cut_coulsq-rsq) *
- (cut_coulsq + 2.0*rsq - 3.0*cut_coul_innersq) *
- invdenom_coul;
- ecoul *= switch1;
- }
- ecoul *= factor_coul;
- } else ecoul = 0.0;
- if (rsq < cut_ljsq) {
- evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
- if (rsq > cut_lj_innersq) {
- switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
- (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * invdenom_lj;
- evdwl *= switch1;
- }
- evdwl *= factor_lj;
- } else evdwl = 0.0;
- }
-
- if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
- evdwl,ecoul,fpair,delx,dely,delz,thr);
+ r2inv = 1.0/rsq;
+
+ if (rsq < cut_coulsq) {
+ forcecoul = qqrd2e * qtmp*q[j]*sqrt(r2inv);
+ if (rsq > cut_coul_innersq) {
+ switch1 = (cut_coulsq-rsq) * (cut_coulsq-rsq) *
+ (cut_coulsq + 2.0*rsq - 3.0*cut_coul_innersq) * invdenom_coul;
+ switch2 = 12.0*rsq * (cut_coulsq-rsq) *
+ (rsq-cut_coul_innersq) * invdenom_coul;
+ forcecoul *= switch1 + switch2;
+ }
+ forcecoul *= factor_coul;
+ } else forcecoul = 0.0;
+
+ if (rsq < cut_ljsq) {
+ r6inv = r2inv*r2inv*r2inv;
+ jtype = type[j];
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ if (rsq > cut_lj_innersq) {
+ switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
+ (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * invdenom_lj;
+ switch2 = 12.0*rsq * (cut_ljsq-rsq) *
+ (rsq-cut_lj_innersq) * invdenom_lj;
+ philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
+ forcelj = forcelj*switch1 + philj*switch2;
+ }
+ forcelj *= factor_lj;
+ } else forcelj = 0.0;
+
+ fpair = (forcecoul + forcelj) * r2inv;
+
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (EFLAG) {
+ if (rsq < cut_coulsq) {
+ ecoul = qqrd2e * qtmp*q[j]*sqrt(r2inv);
+ if (rsq > cut_coul_innersq) {
+ switch1 = (cut_coulsq-rsq) * (cut_coulsq-rsq) *
+ (cut_coulsq + 2.0*rsq - 3.0*cut_coul_innersq) *
+ invdenom_coul;
+ ecoul *= switch1;
+ }
+ ecoul *= factor_coul;
+ } else ecoul = 0.0;
+ if (rsq < cut_ljsq) {
+ evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
+ if (rsq > cut_lj_innersq) {
+ switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
+ (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * invdenom_lj;
+ evdwl *= switch1;
+ }
+ evdwl *= factor_lj;
+ } else evdwl = 0.0;
+ }
+
+ if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
+ evdwl,ecoul,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.h b/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.h
index 0eda030ebd866631a574ecaf468bd8c4b6f56ca3..9591d62c85a4171d7cd337f9237f7bb97209a7fb 100644
--- a/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.h
+++ b/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp b/src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp
index 9a5b1300e3c69c81074710432a7f0dc442e42031..afdc527567fff7d8aa1fc4893b630a61fe056938 100644
--- a/src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp
+++ b/src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp
@@ -57,11 +57,11 @@ void PairLJCharmmCoulLongOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -122,88 +122,88 @@ void PairLJCharmmCoulLongOMP::eval(int iifrom, int iito, ThrData * const thr)
const int jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- const double r2inv = 1.0/rsq;
-
- if (rsq < cut_coulsq) {
- if (!ncoultablebits || rsq <= tabinnersq) {
- const double A1 = 0.254829592;
- const double A2 = -0.284496736;
- const double A3 = 1.421413741;
- const double A4 = -1.453152027;
- const double A5 = 1.061405429;
- const double EWALD_F = 1.12837917;
- const double INV_EWALD_P = 1.0/0.3275911;
-
- const double r = sqrt(rsq);
- const double grij = g_ewald * r;
- const double expm2 = exp(-grij*grij);
- const double t = INV_EWALD_P / (INV_EWALD_P + grij);
- const double erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
- const double prefactor = qqrd2e * qtmp*q[j]/r;
- forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
- if (EFLAG) ecoul = prefactor*erfc;
- if (sbindex) {
- const double adjust = (1.0-special_coul[sbindex])*prefactor;
- forcecoul -= adjust;
- if (EFLAG) ecoul -= adjust;
- }
- } else {
- union_int_float_t rsq_lookup;
- rsq_lookup.f = rsq;
- const int itable = (rsq_lookup.i & ncoulmask) >> ncoulshiftbits;
- const double fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
- const double table = ftable[itable] + fraction*dftable[itable];
- forcecoul = qtmp*q[j] * table;
- if (EFLAG) ecoul = qtmp*q[j] * (etable[itable] + fraction*detable[itable]);
- if (sbindex) {
- const double table2 = ctable[itable] + fraction*dctable[itable];
- const double prefactor = qtmp*q[j] * table2;
- const double adjust = (1.0-special_coul[sbindex])*prefactor;
- forcecoul -= adjust;
- if (EFLAG) ecoul -= adjust;
- }
- }
- }
-
- if (rsq < cut_ljsq) {
- const double r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- if (EFLAG) evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
-
- if (rsq > cut_lj_innersq) {
- const double drsq = cut_ljsq - rsq;
- const double cut2 = (rsq - cut_lj_innersq) * drsq;
- const double switch1 = drsq * (drsq*drsq + 3.0*cut2) * inv_denom_lj;
- const double switch2 = 12.0*rsq * cut2 * inv_denom_lj;
- if (EFLAG) {
- forcelj = forcelj*switch1 + evdwl*switch2;
- evdwl *= switch1;
- } else {
- const double philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
- forcelj = forcelj*switch1 + philj*switch2;
- }
- }
-
- if (sbindex) {
- const double factor_lj = special_lj[sbindex];
- forcelj *= factor_lj;
- if (EFLAG) evdwl *= factor_lj;
- }
-
- }
- const double fpair = (forcecoul + forcelj) * r2inv;
-
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
- evdwl,ecoul,fpair,delx,dely,delz,thr);
+ const double r2inv = 1.0/rsq;
+
+ if (rsq < cut_coulsq) {
+ if (!ncoultablebits || rsq <= tabinnersq) {
+ const double A1 = 0.254829592;
+ const double A2 = -0.284496736;
+ const double A3 = 1.421413741;
+ const double A4 = -1.453152027;
+ const double A5 = 1.061405429;
+ const double EWALD_F = 1.12837917;
+ const double INV_EWALD_P = 1.0/0.3275911;
+
+ const double r = sqrt(rsq);
+ const double grij = g_ewald * r;
+ const double expm2 = exp(-grij*grij);
+ const double t = INV_EWALD_P / (INV_EWALD_P + grij);
+ const double erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
+ const double prefactor = qqrd2e * qtmp*q[j]/r;
+ forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
+ if (EFLAG) ecoul = prefactor*erfc;
+ if (sbindex) {
+ const double adjust = (1.0-special_coul[sbindex])*prefactor;
+ forcecoul -= adjust;
+ if (EFLAG) ecoul -= adjust;
+ }
+ } else {
+ union_int_float_t rsq_lookup;
+ rsq_lookup.f = rsq;
+ const int itable = (rsq_lookup.i & ncoulmask) >> ncoulshiftbits;
+ const double fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
+ const double table = ftable[itable] + fraction*dftable[itable];
+ forcecoul = qtmp*q[j] * table;
+ if (EFLAG) ecoul = qtmp*q[j] * (etable[itable] + fraction*detable[itable]);
+ if (sbindex) {
+ const double table2 = ctable[itable] + fraction*dctable[itable];
+ const double prefactor = qtmp*q[j] * table2;
+ const double adjust = (1.0-special_coul[sbindex])*prefactor;
+ forcecoul -= adjust;
+ if (EFLAG) ecoul -= adjust;
+ }
+ }
+ }
+
+ if (rsq < cut_ljsq) {
+ const double r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ if (EFLAG) evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
+
+ if (rsq > cut_lj_innersq) {
+ const double drsq = cut_ljsq - rsq;
+ const double cut2 = (rsq - cut_lj_innersq) * drsq;
+ const double switch1 = drsq * (drsq*drsq + 3.0*cut2) * inv_denom_lj;
+ const double switch2 = 12.0*rsq * cut2 * inv_denom_lj;
+ if (EFLAG) {
+ forcelj = forcelj*switch1 + evdwl*switch2;
+ evdwl *= switch1;
+ } else {
+ const double philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
+ forcelj = forcelj*switch1 + philj*switch2;
+ }
+ }
+
+ if (sbindex) {
+ const double factor_lj = special_lj[sbindex];
+ forcelj *= factor_lj;
+ if (EFLAG) evdwl *= factor_lj;
+ }
+
+ }
+ const double fpair = (forcecoul + forcelj) * r2inv;
+
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
+ evdwl,ecoul,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_lj_charmm_coul_long_omp.h b/src/USER-OMP/pair_lj_charmm_coul_long_omp.h
index 91b9c01c1ab4de7aeac310d3866bbcb174a83d88..ba28d051141e7c233d1c2f25fb93c517910804df 100644
--- a/src/USER-OMP/pair_lj_charmm_coul_long_omp.h
+++ b/src/USER-OMP/pair_lj_charmm_coul_long_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_lj_charmm_coul_pppm_omp.cpp b/src/USER-OMP/pair_lj_charmm_coul_pppm_omp.cpp
index e19152ad6e76276b2ce69924a0abae4f203531e7..b5878dfe3d560e22243f422442734340423c84ca 100644
--- a/src/USER-OMP/pair_lj_charmm_coul_pppm_omp.cpp
+++ b/src/USER-OMP/pair_lj_charmm_coul_pppm_omp.cpp
@@ -90,19 +90,19 @@ void PairLJCharmmCoulPPPMOMP::compute(int eflag, int vflag)
kspace->compute_proxy(eflag,vflag);
} else {
if (evflag) {
- if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
- } else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
- }
+ if (eflag) {
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
+ } else {
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
+ }
} else {
- if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
- else eval<0,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
+ else eval<0,0,0>(ifrom, ito, thr);
}
}
-
+
sync_threads();
reduce_thr(this, eflag, vflag, thr, nproxy);
} // end of omp parallel region
@@ -164,84 +164,84 @@ void PairLJCharmmCoulPPPMOMP::eval(int iifrom, int iito, ThrData * const thr)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
-
- if (rsq < cut_coulsq) {
- if (!ncoultablebits || rsq <= tabinnersq) {
- r = sqrt(rsq);
- grij = g_ewald * r;
- expm2 = exp(-grij*grij);
- t = 1.0 / (1.0 + EWALD_P*grij);
- erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
- prefactor = qqrd2e * qtmp*q[j]/r;
- forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
- if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
- } else {
- union_int_float_t rsq_lookup;
- rsq_lookup.f = rsq;
- itable = rsq_lookup.i & ncoulmask;
- itable >>= ncoulshiftbits;
- fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
- table = ftable[itable] + fraction*dftable[itable];
- forcecoul = qtmp*q[j] * table;
- if (factor_coul < 1.0) {
- table = ctable[itable] + fraction*dctable[itable];
- prefactor = qtmp*q[j] * table;
- forcecoul -= (1.0-factor_coul)*prefactor;
- }
- }
- } else forcecoul = 0.0;
-
- if (rsq < cut_ljsq) {
- r6inv = r2inv*r2inv*r2inv;
- jtype = type[j];
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- if (rsq > cut_lj_innersq) {
- switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
- (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
- switch2 = 12.0*rsq * (cut_ljsq-rsq) *
- (rsq-cut_lj_innersq) / denom_lj;
- philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
- forcelj = forcelj*switch1 + philj*switch2;
- }
- forcelj *= factor_lj;
- } else forcelj = 0.0;
-
- fpair = (forcecoul + forcelj) * r2inv;
-
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (EFLAG) {
- if (rsq < cut_coulsq) {
- if (!ncoultablebits || rsq <= tabinnersq)
- ecoul = prefactor*erfc;
- else {
- table = etable[itable] + fraction*detable[itable];
- ecoul = qtmp*q[j] * table;
- }
- if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
- } else ecoul = 0.0;
-
- if (rsq < cut_ljsq) {
- evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
- if (rsq > cut_lj_innersq) {
- switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
- (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
- evdwl *= switch1;
- }
- evdwl *= factor_lj;
- } else evdwl = 0.0;
- }
-
- if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
- evdwl,ecoul,fpair,delx,dely,delz,thr);
+ r2inv = 1.0/rsq;
+
+ if (rsq < cut_coulsq) {
+ if (!ncoultablebits || rsq <= tabinnersq) {
+ r = sqrt(rsq);
+ grij = g_ewald * r;
+ expm2 = exp(-grij*grij);
+ t = 1.0 / (1.0 + EWALD_P*grij);
+ erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
+ prefactor = qqrd2e * qtmp*q[j]/r;
+ forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
+ if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
+ } else {
+ union_int_float_t rsq_lookup;
+ rsq_lookup.f = rsq;
+ itable = rsq_lookup.i & ncoulmask;
+ itable >>= ncoulshiftbits;
+ fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
+ table = ftable[itable] + fraction*dftable[itable];
+ forcecoul = qtmp*q[j] * table;
+ if (factor_coul < 1.0) {
+ table = ctable[itable] + fraction*dctable[itable];
+ prefactor = qtmp*q[j] * table;
+ forcecoul -= (1.0-factor_coul)*prefactor;
+ }
+ }
+ } else forcecoul = 0.0;
+
+ if (rsq < cut_ljsq) {
+ r6inv = r2inv*r2inv*r2inv;
+ jtype = type[j];
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ if (rsq > cut_lj_innersq) {
+ switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
+ (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
+ switch2 = 12.0*rsq * (cut_ljsq-rsq) *
+ (rsq-cut_lj_innersq) / denom_lj;
+ philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
+ forcelj = forcelj*switch1 + philj*switch2;
+ }
+ forcelj *= factor_lj;
+ } else forcelj = 0.0;
+
+ fpair = (forcecoul + forcelj) * r2inv;
+
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (EFLAG) {
+ if (rsq < cut_coulsq) {
+ if (!ncoultablebits || rsq <= tabinnersq)
+ ecoul = prefactor*erfc;
+ else {
+ table = etable[itable] + fraction*detable[itable];
+ ecoul = qtmp*q[j] * table;
+ }
+ if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
+ } else ecoul = 0.0;
+
+ if (rsq < cut_ljsq) {
+ evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
+ if (rsq > cut_lj_innersq) {
+ switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
+ (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
+ evdwl *= switch1;
+ }
+ evdwl *= factor_lj;
+ } else evdwl = 0.0;
+ }
+
+ if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
+ evdwl,ecoul,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_lj_charmm_coul_pppm_omp.h b/src/USER-OMP/pair_lj_charmm_coul_pppm_omp.h
index 1faee2c47980b74d86bd00e9d75b987dae3730f1..835f40389f1a923f62c8fd6c80518e6e2c26de21 100644
--- a/src/USER-OMP/pair_lj_charmm_coul_pppm_omp.h
+++ b/src/USER-OMP/pair_lj_charmm_coul_pppm_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp b/src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp
index a6a7f3044973387dd74cf038f8d6b3f3b332a625..361923cb54b1292308280d9d2effc432cb16048f 100644
--- a/src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp
+++ b/src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp
@@ -56,11 +56,11 @@ void PairLJClass2CoulCutOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -125,45 +125,45 @@ void PairLJClass2CoulCutOMP::eval(int iifrom, int iito, ThrData * const thr)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- rinv = sqrt(r2inv);
-
- if (rsq < cut_coulsq[itype][jtype]) {
- forcecoul = qqrd2e * qtmp*q[j]*rinv;
- forcecoul *= factor_coul;
- } else forcecoul = 0.0;
-
- if (rsq < cut_ljsq[itype][jtype]) {
- r3inv = r2inv*rinv;
- r6inv = r3inv*r3inv;
- forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
- forcelj *= factor_lj;
- } else forcelj = 0.0;
-
- fpair = (forcecoul + forcelj) * r2inv;
-
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (EFLAG) {
- if (rsq < cut_coulsq[itype][jtype])
- ecoul = factor_coul * qqrd2e * qtmp*q[j]*rinv;
- else ecoul = 0.0;
- if (rsq < cut_ljsq[itype][jtype]) {
- evdwl = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) -
- offset[itype][jtype];
- evdwl *= factor_lj;
- } else evdwl = 0.0;
- }
-
- if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
- evdwl,ecoul,fpair,delx,dely,delz,thr);
+ r2inv = 1.0/rsq;
+ rinv = sqrt(r2inv);
+
+ if (rsq < cut_coulsq[itype][jtype]) {
+ forcecoul = qqrd2e * qtmp*q[j]*rinv;
+ forcecoul *= factor_coul;
+ } else forcecoul = 0.0;
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ r3inv = r2inv*rinv;
+ r6inv = r3inv*r3inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
+ forcelj *= factor_lj;
+ } else forcelj = 0.0;
+
+ fpair = (forcecoul + forcelj) * r2inv;
+
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (EFLAG) {
+ if (rsq < cut_coulsq[itype][jtype])
+ ecoul = factor_coul * qqrd2e * qtmp*q[j]*rinv;
+ else ecoul = 0.0;
+ if (rsq < cut_ljsq[itype][jtype]) {
+ evdwl = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) -
+ offset[itype][jtype];
+ evdwl *= factor_lj;
+ } else evdwl = 0.0;
+ }
+
+ if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
+ evdwl,ecoul,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_lj_class2_coul_cut_omp.h b/src/USER-OMP/pair_lj_class2_coul_cut_omp.h
index b22a29aa184038007f0b1666b90a316d9c4cafc1..f03da67a15966fbf763818a183a968b97029d56c 100644
--- a/src/USER-OMP/pair_lj_class2_coul_cut_omp.h
+++ b/src/USER-OMP/pair_lj_class2_coul_cut_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_lj_class2_coul_long_omp.cpp b/src/USER-OMP/pair_lj_class2_coul_long_omp.cpp
index 6412beb247df132202856439f4de221a6521d47c..6049d7a98cb09a1890d99354af0d95465f3e9434 100644
--- a/src/USER-OMP/pair_lj_class2_coul_long_omp.cpp
+++ b/src/USER-OMP/pair_lj_class2_coul_long_omp.cpp
@@ -64,11 +64,11 @@ void PairLJClass2CoulLongOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -133,53 +133,53 @@ void PairLJClass2CoulLongOMP::eval(int iifrom, int iito, ThrData * const thr)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
-
- if (rsq < cut_coulsq) {
- r = sqrt(rsq);
- grij = g_ewald * r;
- expm2 = exp(-grij*grij);
- t = 1.0 / (1.0 + EWALD_P*grij);
- erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
- prefactor = qqrd2e * qtmp*q[j]/r;
- forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
- if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
- } else forcecoul = 0.0;
-
- if (rsq < cut_ljsq[itype][jtype]) {
- rinv = sqrt(r2inv);
- r3inv = r2inv*rinv;
- r6inv = r3inv*r3inv;
- forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
- forcelj *= factor_lj;
- } else forcelj = 0.0;
-
- fpair = (forcecoul + forcelj) * r2inv;
-
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (EFLAG) {
- if (rsq < cut_coulsq) {
- ecoul = prefactor*erfc;
- if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
- } else ecoul = 0.0;
-
- if (rsq < cut_ljsq[itype][jtype]) {
- evdwl = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) -
- offset[itype][jtype];
- evdwl *= factor_lj;
- } else evdwl = 0.0;
- }
-
- if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
- evdwl,ecoul,fpair,delx,dely,delz,thr);
+ r2inv = 1.0/rsq;
+
+ if (rsq < cut_coulsq) {
+ r = sqrt(rsq);
+ grij = g_ewald * r;
+ expm2 = exp(-grij*grij);
+ t = 1.0 / (1.0 + EWALD_P*grij);
+ erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
+ prefactor = qqrd2e * qtmp*q[j]/r;
+ forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
+ if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
+ } else forcecoul = 0.0;
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ rinv = sqrt(r2inv);
+ r3inv = r2inv*rinv;
+ r6inv = r3inv*r3inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
+ forcelj *= factor_lj;
+ } else forcelj = 0.0;
+
+ fpair = (forcecoul + forcelj) * r2inv;
+
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (EFLAG) {
+ if (rsq < cut_coulsq) {
+ ecoul = prefactor*erfc;
+ if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
+ } else ecoul = 0.0;
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ evdwl = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) -
+ offset[itype][jtype];
+ evdwl *= factor_lj;
+ } else evdwl = 0.0;
+ }
+
+ if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
+ evdwl,ecoul,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_lj_class2_coul_long_omp.h b/src/USER-OMP/pair_lj_class2_coul_long_omp.h
index b32799bf8494ae128a65ea6448e7fd3c08ee59c0..973850c25cfe35c8db561bdce7b9c52665db1d3e 100644
--- a/src/USER-OMP/pair_lj_class2_coul_long_omp.h
+++ b/src/USER-OMP/pair_lj_class2_coul_long_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_lj_class2_coul_pppm_omp.cpp b/src/USER-OMP/pair_lj_class2_coul_pppm_omp.cpp
index a32005ff9b30926edbe4bbcb7a69627fb95856b1..1b0ca0ec7d2f2d4808c1c8e4309b8b0ff25682ff 100644
--- a/src/USER-OMP/pair_lj_class2_coul_pppm_omp.cpp
+++ b/src/USER-OMP/pair_lj_class2_coul_pppm_omp.cpp
@@ -90,19 +90,19 @@ void PairLJClass2CoulPPPMOMP::compute(int eflag, int vflag)
kspace->compute_proxy(eflag,vflag);
} else {
if (evflag) {
- if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
- } else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
- }
+ if (eflag) {
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
+ } else {
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
+ }
} else {
- if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
- else eval<0,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
+ else eval<0,0,0>(ifrom, ito, thr);
}
}
-
+
sync_threads();
reduce_thr(this, eflag, vflag, thr, nproxy);
} // end of omp parallel region
@@ -162,53 +162,53 @@ void PairLJClass2CoulPPPMOMP::eval(int iifrom, int iito, ThrData * const thr)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
-
- if (rsq < cut_coulsq) {
- r = sqrt(rsq);
- grij = g_ewald * r;
- expm2 = exp(-grij*grij);
- t = 1.0 / (1.0 + EWALD_P*grij);
- erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
- prefactor = qqrd2e * qtmp*q[j]/r;
- forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
- if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
- } else forcecoul = 0.0;
-
- if (rsq < cut_ljsq[itype][jtype]) {
- rinv = sqrt(r2inv);
- r3inv = r2inv*rinv;
- r6inv = r3inv*r3inv;
- forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
- forcelj *= factor_lj;
- } else forcelj = 0.0;
-
- fpair = (forcecoul + forcelj) * r2inv;
-
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (EFLAG) {
- if (rsq < cut_coulsq) {
- ecoul = prefactor*erfc;
- if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
- } else ecoul = 0.0;
-
- if (rsq < cut_ljsq[itype][jtype]) {
- evdwl = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) -
- offset[itype][jtype];
- evdwl *= factor_lj;
- } else evdwl = 0.0;
- }
-
- if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
- evdwl,ecoul,fpair,delx,dely,delz,thr);
+ r2inv = 1.0/rsq;
+
+ if (rsq < cut_coulsq) {
+ r = sqrt(rsq);
+ grij = g_ewald * r;
+ expm2 = exp(-grij*grij);
+ t = 1.0 / (1.0 + EWALD_P*grij);
+ erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
+ prefactor = qqrd2e * qtmp*q[j]/r;
+ forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
+ if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
+ } else forcecoul = 0.0;
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ rinv = sqrt(r2inv);
+ r3inv = r2inv*rinv;
+ r6inv = r3inv*r3inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
+ forcelj *= factor_lj;
+ } else forcelj = 0.0;
+
+ fpair = (forcecoul + forcelj) * r2inv;
+
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (EFLAG) {
+ if (rsq < cut_coulsq) {
+ ecoul = prefactor*erfc;
+ if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
+ } else ecoul = 0.0;
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ evdwl = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) -
+ offset[itype][jtype];
+ evdwl *= factor_lj;
+ } else evdwl = 0.0;
+ }
+
+ if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
+ evdwl,ecoul,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_lj_class2_coul_pppm_omp.h b/src/USER-OMP/pair_lj_class2_coul_pppm_omp.h
index 3f77bf4f9ab12e92ea0990264057ad020f3200ea..8a5def6bcc6ffe07bba92388acf17ff3f05fa014 100644
--- a/src/USER-OMP/pair_lj_class2_coul_pppm_omp.h
+++ b/src/USER-OMP/pair_lj_class2_coul_pppm_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_lj_class2_omp.cpp b/src/USER-OMP/pair_lj_class2_omp.cpp
index 018c3320c1fc3d51ea8f6cac9f3313093cc9fa53..978335d21e245e1686de9bbe56801b2a40fcaf5e 100644
--- a/src/USER-OMP/pair_lj_class2_omp.cpp
+++ b/src/USER-OMP/pair_lj_class2_omp.cpp
@@ -56,11 +56,11 @@ void PairLJClass2OMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -117,30 +117,30 @@ void PairLJClass2OMP::eval(int iifrom, int iito, ThrData * const thr)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
- r3inv = sqrt(r6inv);
-
- forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
- fpair = factor_lj*forcelj*r2inv;
-
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (EFLAG) {
- evdwl = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype])
- - offset[itype][jtype];
- evdwl *= factor_lj;
- }
-
- if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
- evdwl,0.0,fpair,delx,dely,delz,thr);
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
+ r3inv = sqrt(r6inv);
+
+ forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
+ fpair = factor_lj*forcelj*r2inv;
+
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (EFLAG) {
+ evdwl = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype])
+ - offset[itype][jtype];
+ evdwl *= factor_lj;
+ }
+
+ if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
+ evdwl,0.0,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_lj_class2_omp.h b/src/USER-OMP/pair_lj_class2_omp.h
index 317c7376c5210c62d7d93ab5a1e65cd702f82923..5acd2cfb39a57e925aa65a2d3e715519a92e5324 100644
--- a/src/USER-OMP/pair_lj_class2_omp.h
+++ b/src/USER-OMP/pair_lj_class2_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_lj_coul_omp.cpp b/src/USER-OMP/pair_lj_coul_omp.cpp
index 28e4a47645b5e2522a67314ad39aa94f0ee59384..21fd9ff8cdf2794db675ba9f28d4a1218d5a303c 100644
--- a/src/USER-OMP/pair_lj_coul_omp.cpp
+++ b/src/USER-OMP/pair_lj_coul_omp.cpp
@@ -66,11 +66,11 @@ void PairLJCoulOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -112,112 +112,112 @@ void PairLJCoulOMP::eval(int iifrom, int iito, ThrData * const thr)
double g2 = g_ewald*g_ewald, g6 = g2*g2*g2, g8 = g6*g2;
vector xi, d;
- for (ii = iifrom; ii < iito; ++ii) { // loop over my atoms
+ for (ii = iifrom; ii < iito; ++ii) { // loop over my atoms
i = ilist[ii]; fi = f0+3*i;
- if (order1) qri = (qi = q[i])*qqrd2e; // initialize constants
+ if (order1) qri = (qi = q[i])*qqrd2e; // initialize constants
offseti = offset[typei = type[i]];
lj1i = lj1[typei]; lj2i = lj2[typei]; lj3i = lj3[typei]; lj4i = lj4[typei];
cutsqi = cutsq[typei]; cut_ljsqi = cut_ljsq[typei];
memcpy(xi, x0+(i+(i<<1)), sizeof(vector));
jneighn = (jneigh = list->firstneigh[i])+list->numneigh[i];
- for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
+ for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
j = *jneigh;
ni = sbmask(j);
j &= NEIGHMASK;
-
+
{ register const double *xj = x0+(j+(j<<1));
- d[0] = xi[0] - xj[0]; // pair vector
- d[1] = xi[1] - xj[1];
- d[2] = xi[2] - xj[2]; }
+ d[0] = xi[0] - xj[0]; // pair vector
+ d[1] = xi[1] - xj[1];
+ d[2] = xi[2] - xj[2]; }
if ((rsq = vec_dot(d, d)) >= cutsqi[typej = type[j]]) continue;
r2inv = 1.0/rsq;
- if (order1 && (rsq < cut_coulsq)) { // coulombic
- if (!ncoultablebits || rsq <= tabinnersq) { // series real space
- register double r = sqrt(rsq), x = g_ewald*r;
- register double s = qri*q[j], t = 1.0/(1.0+EWALD_P*x);
- if (ni == 0) {
- s *= g_ewald*exp(-x*x);
- force_coul = (t *= ((((t*A5+A4)*t+A3)*t+A2)*t+A1)*s/x)+EWALD_F*s;
- if (EFLAG) ecoul = t;
- }
- else { // special case
- r = s*(1.0-special_coul[ni])/r; s *= g_ewald*exp(-x*x);
- force_coul = (t *= ((((t*A5+A4)*t+A3)*t+A2)*t+A1)*s/x)+EWALD_F*s-r;
- if (EFLAG) ecoul = t-r;
- }
- } // table real space
- else {
- register union_int_float_t t;
- t.f = rsq;
- register const int k = (t.i & ncoulmask)>>ncoulshiftbits;
- register double f = (rsq-rtable[k])*drtable[k], qiqj = qi*q[j];
- if (ni == 0) {
- force_coul = qiqj*(ftable[k]+f*dftable[k]);
- if (EFLAG) ecoul = qiqj*(etable[k]+f*detable[k]);
- }
- else { // special case
- t.f = (1.0-special_coul[ni])*(ctable[k]+f*dctable[k]);
- force_coul = qiqj*(ftable[k]+f*dftable[k]-t.f);
- if (EFLAG) ecoul = qiqj*(etable[k]+f*detable[k]-t.f);
- }
- }
+ if (order1 && (rsq < cut_coulsq)) { // coulombic
+ if (!ncoultablebits || rsq <= tabinnersq) { // series real space
+ register double r = sqrt(rsq), x = g_ewald*r;
+ register double s = qri*q[j], t = 1.0/(1.0+EWALD_P*x);
+ if (ni == 0) {
+ s *= g_ewald*exp(-x*x);
+ force_coul = (t *= ((((t*A5+A4)*t+A3)*t+A2)*t+A1)*s/x)+EWALD_F*s;
+ if (EFLAG) ecoul = t;
+ }
+ else { // special case
+ r = s*(1.0-special_coul[ni])/r; s *= g_ewald*exp(-x*x);
+ force_coul = (t *= ((((t*A5+A4)*t+A3)*t+A2)*t+A1)*s/x)+EWALD_F*s-r;
+ if (EFLAG) ecoul = t-r;
+ }
+ } // table real space
+ else {
+ register union_int_float_t t;
+ t.f = rsq;
+ register const int k = (t.i & ncoulmask)>>ncoulshiftbits;
+ register double f = (rsq-rtable[k])*drtable[k], qiqj = qi*q[j];
+ if (ni == 0) {
+ force_coul = qiqj*(ftable[k]+f*dftable[k]);
+ if (EFLAG) ecoul = qiqj*(etable[k]+f*detable[k]);
+ }
+ else { // special case
+ t.f = (1.0-special_coul[ni])*(ctable[k]+f*dctable[k]);
+ force_coul = qiqj*(ftable[k]+f*dftable[k]-t.f);
+ if (EFLAG) ecoul = qiqj*(etable[k]+f*detable[k]-t.f);
+ }
+ }
}
else force_coul = ecoul = 0.0;
- if (rsq < cut_ljsqi[typej]) { // lj
- if (order6) { // long-range lj
- register double rn = r2inv*r2inv*r2inv;
- register double x2 = g2*rsq, a2 = 1.0/x2;
- x2 = a2*exp(-x2)*lj4i[typej];
- if (ni == 0) {
- force_lj =
- (rn*=rn)*lj1i[typej]-g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq;
- if (EFLAG)
- evdwl = rn*lj3i[typej]-g6*((a2+1.0)*a2+0.5)*x2;
- }
- else { // special case
- register double f = special_lj[ni], t = rn*(1.0-f);
- force_lj = f*(rn *= rn)*lj1i[typej]-
- g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq+t*lj2i[typej];
- if (EFLAG)
- evdwl = f*rn*lj3i[typej]-g6*((a2+1.0)*a2+0.5)*x2+t*lj4i[typej];
- }
- }
- else { // cut lj
- register double rn = r2inv*r2inv*r2inv;
- if (ni == 0) {
- force_lj = rn*(rn*lj1i[typej]-lj2i[typej]);
- if (EFLAG) evdwl = rn*(rn*lj3i[typej]-lj4i[typej])-offseti[typej];
- }
- else { // special case
- register double f = special_lj[ni];
- force_lj = f*rn*(rn*lj1i[typej]-lj2i[typej]);
- if (EFLAG)
- evdwl = f * (rn*(rn*lj3i[typej]-lj4i[typej])-offseti[typej]);
- }
- }
+ if (rsq < cut_ljsqi[typej]) { // lj
+ if (order6) { // long-range lj
+ register double rn = r2inv*r2inv*r2inv;
+ register double x2 = g2*rsq, a2 = 1.0/x2;
+ x2 = a2*exp(-x2)*lj4i[typej];
+ if (ni == 0) {
+ force_lj =
+ (rn*=rn)*lj1i[typej]-g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq;
+ if (EFLAG)
+ evdwl = rn*lj3i[typej]-g6*((a2+1.0)*a2+0.5)*x2;
+ }
+ else { // special case
+ register double f = special_lj[ni], t = rn*(1.0-f);
+ force_lj = f*(rn *= rn)*lj1i[typej]-
+ g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq+t*lj2i[typej];
+ if (EFLAG)
+ evdwl = f*rn*lj3i[typej]-g6*((a2+1.0)*a2+0.5)*x2+t*lj4i[typej];
+ }
+ }
+ else { // cut lj
+ register double rn = r2inv*r2inv*r2inv;
+ if (ni == 0) {
+ force_lj = rn*(rn*lj1i[typej]-lj2i[typej]);
+ if (EFLAG) evdwl = rn*(rn*lj3i[typej]-lj4i[typej])-offseti[typej];
+ }
+ else { // special case
+ register double f = special_lj[ni];
+ force_lj = f*rn*(rn*lj1i[typej]-lj2i[typej]);
+ if (EFLAG)
+ evdwl = f * (rn*(rn*lj3i[typej]-lj4i[typej])-offseti[typej]);
+ }
+ }
}
else force_lj = evdwl = 0.0;
fpair = (force_coul+force_lj)*r2inv;
if (NEWTON_PAIR || j < nlocal) {
- register double *fj = f0+(j+(j<<1)), f;
- fi[0] += f = d[0]*fpair; fj[0] -= f;
- fi[1] += f = d[1]*fpair; fj[1] -= f;
- fi[2] += f = d[2]*fpair; fj[2] -= f;
+ register double *fj = f0+(j+(j<<1)), f;
+ fi[0] += f = d[0]*fpair; fj[0] -= f;
+ fi[1] += f = d[1]*fpair; fj[1] -= f;
+ fi[2] += f = d[2]*fpair; fj[2] -= f;
}
else {
- fi[0] += d[0]*fpair;
- fi[1] += d[1]*fpair;
- fi[2] += d[2]*fpair;
+ fi[0] += d[0]*fpair;
+ fi[1] += d[1]*fpair;
+ fi[2] += d[2]*fpair;
}
-
+
if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
- evdwl,ecoul,fpair,d[0],d[1],d[2],thr);
+ evdwl,ecoul,fpair,d[0],d[1],d[2],thr);
}
}
}
diff --git a/src/USER-OMP/pair_lj_coul_omp.h b/src/USER-OMP/pair_lj_coul_omp.h
index e2259e16a0a031c1fcb63e1612aa28d7920ccadc..6e988126a36e5183162441a523f8df78ca2989eb 100644
--- a/src/USER-OMP/pair_lj_coul_omp.h
+++ b/src/USER-OMP/pair_lj_coul_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_lj_cubic_omp.cpp b/src/USER-OMP/pair_lj_cubic_omp.cpp
index 97cfdc68a34e6240a275090170f513f8a6f14aeb..bf4b2b2bc885183163507913affe8b0a66f1ee1b 100644
--- a/src/USER-OMP/pair_lj_cubic_omp.cpp
+++ b/src/USER-OMP/pair_lj_cubic_omp.cpp
@@ -57,11 +57,11 @@ void PairLJCubicOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -119,39 +119,39 @@ void PairLJCubicOMP::eval(int iifrom, int iito, ThrData * const thr)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
+ r2inv = 1.0/rsq;
if (rsq <= cut_inner_sq[itype][jtype]) {
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- } else {
- r = sqrt(rsq);
- rmin = sigma[itype][jtype]*RT6TWO;
- t = (r - cut_inner[itype][jtype])/rmin;
- forcelj = epsilon[itype][jtype]*(-DPHIDS + A3*t*t/2.0)*r/rmin;
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ } else {
+ r = sqrt(rsq);
+ rmin = sigma[itype][jtype]*RT6TWO;
+ t = (r - cut_inner[itype][jtype])/rmin;
+ forcelj = epsilon[itype][jtype]*(-DPHIDS + A3*t*t/2.0)*r/rmin;
}
- fpair = factor_lj*forcelj*r2inv;
-
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (EFLAG) {
+ fpair = factor_lj*forcelj*r2inv;
+
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (EFLAG) {
if (rsq <= cut_inner_sq[itype][jtype])
- evdwl = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
- else
- evdwl = epsilon[itype][jtype]*
- (PHIS + DPHIDS*t - A3*t*t*t/6.0);
+ evdwl = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
+ else
+ evdwl = epsilon[itype][jtype]*
+ (PHIS + DPHIDS*t - A3*t*t*t/6.0);
- evdwl *= factor_lj;
- }
+ evdwl *= factor_lj;
+ }
- if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
- evdwl,0.0,fpair,delx,dely,delz,thr);
+ if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
+ evdwl,0.0,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_lj_cubic_omp.h b/src/USER-OMP/pair_lj_cubic_omp.h
index a6ed7d2b97db9ce3cc23568f7f3a0e43c2549362..78b298bb35873913e96bd85d638b81d05d2d6f54 100644
--- a/src/USER-OMP/pair_lj_cubic_omp.h
+++ b/src/USER-OMP/pair_lj_cubic_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp
index b681ec5f0355e2c406524480f6c6ae97f586ff14..6c1bdedef4c09501ab1e3d93bf8cd30f781a32f3 100644
--- a/src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp
+++ b/src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp
@@ -56,11 +56,11 @@ void PairLJCutCoulCutOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -124,44 +124,44 @@ void PairLJCutCoulCutOMP::eval(int iifrom, int iito, ThrData * const thr)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
-
- if (rsq < cut_coulsq[itype][jtype]) {
- rinv = sqrt(r2inv);
- forcecoul = qqrd2e * qtmp*q[j]*rinv;
- forcecoul *= factor_coul;
- } else forcecoul = 0.0;
-
- if (rsq < cut_ljsq[itype][jtype]) {
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- forcelj *= factor_lj;
- } else forcelj = 0.0;
-
- fpair = (forcecoul + forcelj) * r2inv;
-
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (EFLAG) {
- if (rsq < cut_coulsq[itype][jtype])
- ecoul = factor_coul * qqrd2e * qtmp*q[j]*rinv;
- else ecoul = 0.0;
- if (rsq < cut_ljsq[itype][jtype]) {
- evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
- offset[itype][jtype];
- evdwl *= factor_lj;
- } else evdwl = 0.0;
- }
-
- if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
- evdwl,ecoul,fpair,delx,dely,delz,thr);
+ r2inv = 1.0/rsq;
+
+ if (rsq < cut_coulsq[itype][jtype]) {
+ rinv = sqrt(r2inv);
+ forcecoul = qqrd2e * qtmp*q[j]*rinv;
+ forcecoul *= factor_coul;
+ } else forcecoul = 0.0;
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ forcelj *= factor_lj;
+ } else forcelj = 0.0;
+
+ fpair = (forcecoul + forcelj) * r2inv;
+
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (EFLAG) {
+ if (rsq < cut_coulsq[itype][jtype])
+ ecoul = factor_coul * qqrd2e * qtmp*q[j]*rinv;
+ else ecoul = 0.0;
+ if (rsq < cut_ljsq[itype][jtype]) {
+ evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
+ offset[itype][jtype];
+ evdwl *= factor_lj;
+ } else evdwl = 0.0;
+ }
+
+ if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
+ evdwl,ecoul,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_lj_cut_coul_cut_omp.h b/src/USER-OMP/pair_lj_cut_coul_cut_omp.h
index 3d4be420e71cb9809a79aa0ad5edda22010ab326..0d5de5b7b7ea4677a5f6baa8f55eeb84c162cfe6 100644
--- a/src/USER-OMP/pair_lj_cut_coul_cut_omp.h
+++ b/src/USER-OMP/pair_lj_cut_coul_cut_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp
index 102259dd11c452603bd289924bc32b8011db429f..81a73d78b183dd2f684fb73da17a33549d3f472f 100644
--- a/src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp
+++ b/src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp
@@ -56,11 +56,11 @@ void PairLJCutCoulDebyeOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -125,46 +125,46 @@ void PairLJCutCoulDebyeOMP::eval(int iifrom, int iito, ThrData * const thr)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
-
- if (rsq < cut_coulsq[itype][jtype]) {
- r = sqrt(rsq);
- rinv = 1.0/r;
- screening = exp(-kappa*r);
- forcecoul = qqrd2e * qtmp*q[j] * screening * (kappa + rinv);
- forcecoul *= factor_coul;
- } else forcecoul = 0.0;
-
- if (rsq < cut_ljsq[itype][jtype]) {
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- forcelj *= factor_lj;
- } else forcelj = 0.0;
-
- fpair = (forcecoul + forcelj) * r2inv;
-
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (EFLAG) {
- if (rsq < cut_coulsq[itype][jtype])
- ecoul = factor_coul * qqrd2e * qtmp*q[j] * rinv * screening;
- else ecoul = 0.0;
- if (rsq < cut_ljsq[itype][jtype]) {
- evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
- offset[itype][jtype];
- evdwl *= factor_lj;
- } else evdwl = 0.0;
- }
-
- if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
- evdwl,ecoul,fpair,delx,dely,delz,thr);
+ r2inv = 1.0/rsq;
+
+ if (rsq < cut_coulsq[itype][jtype]) {
+ r = sqrt(rsq);
+ rinv = 1.0/r;
+ screening = exp(-kappa*r);
+ forcecoul = qqrd2e * qtmp*q[j] * screening * (kappa + rinv);
+ forcecoul *= factor_coul;
+ } else forcecoul = 0.0;
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ forcelj *= factor_lj;
+ } else forcelj = 0.0;
+
+ fpair = (forcecoul + forcelj) * r2inv;
+
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (EFLAG) {
+ if (rsq < cut_coulsq[itype][jtype])
+ ecoul = factor_coul * qqrd2e * qtmp*q[j] * rinv * screening;
+ else ecoul = 0.0;
+ if (rsq < cut_ljsq[itype][jtype]) {
+ evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
+ offset[itype][jtype];
+ evdwl *= factor_lj;
+ } else evdwl = 0.0;
+ }
+
+ if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
+ evdwl,ecoul,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_lj_cut_coul_debye_omp.h b/src/USER-OMP/pair_lj_cut_coul_debye_omp.h
index e2205cb7cef1f696866704f3e772ae018c5ac014..b327fc665fda97223a4526ba90d1e376867e579f 100644
--- a/src/USER-OMP/pair_lj_cut_coul_debye_omp.h
+++ b/src/USER-OMP/pair_lj_cut_coul_debye_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_lj_cut_coul_long_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_long_omp.cpp
index 5f9b80ac803d6da06332b268a09b29bb9be10a36..19639ac731c2bd2cbd83f24b6c84a32b414f6077 100644
--- a/src/USER-OMP/pair_lj_cut_coul_long_omp.cpp
+++ b/src/USER-OMP/pair_lj_cut_coul_long_omp.cpp
@@ -65,11 +65,11 @@ void PairLJCutCoulLongOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -135,71 +135,71 @@ void PairLJCutCoulLongOMP::eval(int iifrom, int iito, ThrData * const thr)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
-
- if (rsq < cut_coulsq) {
- if (!ncoultablebits || rsq <= tabinnersq) {
- r = sqrt(rsq);
- grij = g_ewald * r;
- expm2 = exp(-grij*grij);
- t = 1.0 / (1.0 + EWALD_P*grij);
- erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
- prefactor = qqrd2e * qtmp*q[j]/r;
- forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
- if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
- } else {
- union_int_float_t rsq_lookup;
- rsq_lookup.f = rsq;
- itable = rsq_lookup.i & ncoulmask;
- itable >>= ncoulshiftbits;
- fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
- table = ftable[itable] + fraction*dftable[itable];
- forcecoul = qtmp*q[j] * table;
- if (factor_coul < 1.0) {
- table = ctable[itable] + fraction*dctable[itable];
- prefactor = qtmp*q[j] * table;
- forcecoul -= (1.0-factor_coul)*prefactor;
- }
- }
- } else forcecoul = 0.0;
-
- if (rsq < cut_ljsq[itype][jtype]) {
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- forcelj *= factor_lj;
- } else forcelj = 0.0;
-
- fpair = (forcecoul + forcelj) * r2inv;
-
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (EFLAG) {
- if (rsq < cut_coulsq) {
- if (!ncoultablebits || rsq <= tabinnersq)
- ecoul = prefactor*erfc;
- else {
- table = etable[itable] + fraction*detable[itable];
- ecoul = qtmp*q[j] * table;
- }
- if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
- } else ecoul = 0.0;
-
- if (rsq < cut_ljsq[itype][jtype]) {
- evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
- offset[itype][jtype];
- evdwl *= factor_lj;
- } else evdwl = 0.0;
- }
-
- if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
- evdwl,ecoul,fpair,delx,dely,delz,thr);
+ r2inv = 1.0/rsq;
+
+ if (rsq < cut_coulsq) {
+ if (!ncoultablebits || rsq <= tabinnersq) {
+ r = sqrt(rsq);
+ grij = g_ewald * r;
+ expm2 = exp(-grij*grij);
+ t = 1.0 / (1.0 + EWALD_P*grij);
+ erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
+ prefactor = qqrd2e * qtmp*q[j]/r;
+ forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
+ if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
+ } else {
+ union_int_float_t rsq_lookup;
+ rsq_lookup.f = rsq;
+ itable = rsq_lookup.i & ncoulmask;
+ itable >>= ncoulshiftbits;
+ fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
+ table = ftable[itable] + fraction*dftable[itable];
+ forcecoul = qtmp*q[j] * table;
+ if (factor_coul < 1.0) {
+ table = ctable[itable] + fraction*dctable[itable];
+ prefactor = qtmp*q[j] * table;
+ forcecoul -= (1.0-factor_coul)*prefactor;
+ }
+ }
+ } else forcecoul = 0.0;
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ forcelj *= factor_lj;
+ } else forcelj = 0.0;
+
+ fpair = (forcecoul + forcelj) * r2inv;
+
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (EFLAG) {
+ if (rsq < cut_coulsq) {
+ if (!ncoultablebits || rsq <= tabinnersq)
+ ecoul = prefactor*erfc;
+ else {
+ table = etable[itable] + fraction*detable[itable];
+ ecoul = qtmp*q[j] * table;
+ }
+ if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
+ } else ecoul = 0.0;
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
+ offset[itype][jtype];
+ evdwl *= factor_lj;
+ } else evdwl = 0.0;
+ }
+
+ if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
+ evdwl,ecoul,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_lj_cut_coul_long_omp.h b/src/USER-OMP/pair_lj_cut_coul_long_omp.h
index a907959ae3b518b598a50b41eab9a9128f986303..cea3271af0513138e8d63b84353a44a24f6ba9c4 100644
--- a/src/USER-OMP/pair_lj_cut_coul_long_omp.h
+++ b/src/USER-OMP/pair_lj_cut_coul_long_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_lj_cut_coul_long_tip4p_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_long_tip4p_omp.cpp
index 3e03fa6b9763764c9556a38acae2310ef603c1ce..e11d7769f687885bc27417fc7cbc719d99d19aaf 100644
--- a/src/USER-OMP/pair_lj_cut_coul_long_tip4p_omp.cpp
+++ b/src/USER-OMP/pair_lj_cut_coul_long_tip4p_omp.cpp
@@ -119,25 +119,25 @@ void PairLJCutCoulLongTIP4POMP::compute(int eflag, int vflag)
if (!ncoultablebits) {
if (evflag) {
if (eflag) {
- if (vflag) eval<1,1,1,1>(ifrom, ito, thr);
- else eval<1,1,1,0>(ifrom, ito, thr);
+ if (vflag) eval<1,1,1,1>(ifrom, ito, thr);
+ else eval<1,1,1,0>(ifrom, ito, thr);
} else {
- if (vflag) eval<1,1,0,1>(ifrom, ito, thr);
- else eval<1,1,0,0>(ifrom, ito, thr);
+ if (vflag) eval<1,1,0,1>(ifrom, ito, thr);
+ else eval<1,1,0,0>(ifrom, ito, thr);
}
} else eval<1,0,0,0>(ifrom, ito, thr);
} else {
if (evflag) {
if (eflag) {
- if (vflag) eval<0,1,1,1>(ifrom, ito, thr);
- else eval<0,1,1,0>(ifrom, ito, thr);
+ if (vflag) eval<0,1,1,1>(ifrom, ito, thr);
+ else eval<0,1,1,0>(ifrom, ito, thr);
} else {
- if (vflag) eval<0,1,0,1>(ifrom, ito, thr);
- else eval<0,1,0,0>(ifrom, ito, thr);
+ if (vflag) eval<0,1,0,1>(ifrom, ito, thr);
+ else eval<0,1,0,0>(ifrom, ito, thr);
}
} else eval<0,0,0,0>(ifrom, ito, thr);
}
-
+
reduce_thr(this, eflag, vflag, thr);
} // end of omp parallel region
@@ -214,26 +214,26 @@ void PairLJCutCoulLongTIP4POMP::eval(int iifrom, int iito, ThrData * const thr)
// LJ interaction based on true rsq
if (rsq < cut_ljsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- forcelj *= factor_lj * r2inv;
-
- fxtmp += delx*forcelj;
- fytmp += dely*forcelj;
- fztmp += delz*forcelj;
- f[j][0] -= delx*forcelj;
- f[j][1] -= dely*forcelj;
- f[j][2] -= delz*forcelj;
-
- if (EFLAG) {
- evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
- offset[itype][jtype];
- evdwl *= factor_lj;
- } else evdwl = 0.0;
-
- if (EVFLAG) ev_tally_thr(this,i,j,nlocal, /* newton_pair = */ 1,
- evdwl,0.0,forcelj,delx,dely,delz,thr);
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ forcelj *= factor_lj * r2inv;
+
+ fxtmp += delx*forcelj;
+ fytmp += dely*forcelj;
+ fztmp += delz*forcelj;
+ f[j][0] -= delx*forcelj;
+ f[j][1] -= dely*forcelj;
+ f[j][2] -= delz*forcelj;
+
+ if (EFLAG) {
+ evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
+ offset[itype][jtype];
+ evdwl *= factor_lj;
+ } else evdwl = 0.0;
+
+ if (EVFLAG) ev_tally_thr(this,i,j,nlocal, /* newton_pair = */ 1,
+ evdwl,0.0,forcelj,delx,dely,delz,thr);
}
// adjust rsq and delxyz for off-site O charge(s),
@@ -241,213 +241,213 @@ void PairLJCutCoulLongTIP4POMP::eval(int iifrom, int iito, ThrData * const thr)
if (rsq < cut_coulsqplus) {
- if (itype == typeO || jtype == typeO) {
- x2 = mpos[j];
- jH1 = h1idx[j];
- jH2 = h2idx[j];
-
- if (check_error_thr((jtype == typeO && ( jH1 < 0 || jH2 < 0 )),
- tid, FLERR,"TIP4P hydrogen is missing"))
- return;
-
- delx = x1[0] - x2[0];
- dely = x1[1] - x2[1];
- delz = x1[2] - x2[2];
- rsq = delx*delx + dely*dely + delz*delz;
- }
-
- // Coulombic interaction based on modified rsq
-
- if (rsq < cut_coulsq) {
- r2inv = 1 / rsq;
- if (CTABLE || rsq <= tabinnersq) {
- r = sqrt(rsq);
- grij = g_ewald * r;
- expm2 = exp(-grij*grij);
- t = 1.0 / (1.0 + EWALD_P*grij);
- erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
- prefactor = qqrd2e * qtmp*q[j]/r;
- forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
- if (factor_coul < 1.0) {
- forcecoul -= (1.0-factor_coul)*prefactor;
- }
- } else {
- union_int_float_t rsq_lookup;
- rsq_lookup.f = rsq;
- itable = rsq_lookup.i & ncoulmask;
- itable >>= ncoulshiftbits;
- fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
- table = ftable[itable] + fraction*dftable[itable];
- forcecoul = qtmp*q[j] * table;
- if (factor_coul < 1.0) {
- table = ctable[itable] + fraction*dctable[itable];
- prefactor = qtmp*q[j] * table;
- forcecoul -= (1.0-factor_coul)*prefactor;
- }
- }
-
- cforce = forcecoul * r2inv;
-
- // if i,j are not O atoms, force is applied directly
- // if i or j are O atoms, force is on fictitious atom & partitioned
- // force partitioning due to Feenstra, J Comp Chem, 20, 786 (1999)
- // f_f = fictitious force, fO = f_f (1 - 2 alpha), fH = alpha f_f
- // preserves total force and torque on water molecule
- // virial = sum(r x F) where each water's atoms are near xi and xj
- // vlist stores 2,4,6 atoms whose forces contribute to virial
-
- n = 0;
-
- if (itype != typeO) {
- fxtmp += delx * cforce;
- fytmp += dely * cforce;
- fztmp += delz * cforce;
-
- if (VFLAG) {
- v[0] = x[i][0] * delx * cforce;
- v[1] = x[i][1] * dely * cforce;
- v[2] = x[i][2] * delz * cforce;
- v[3] = x[i][0] * dely * cforce;
- v[4] = x[i][0] * delz * cforce;
- v[5] = x[i][1] * delz * cforce;
- vlist[n++] = i;
- }
-
- } else {
-
- fdx = delx*cforce;
- fdy = dely*cforce;
- fdz = delz*cforce;
-
- delxOM = x[i][0] - x1[0];
- delyOM = x[i][1] - x1[1];
- delzOM = x[i][2] - x1[2];
-
- ddotf = (delxOM * fdx + delyOM * fdy + delzOM * fdz) /
- (qdist*qdist);
-
- f1x = alpha * (fdx - ddotf * delxOM);
- f1y = alpha * (fdy - ddotf * delyOM);
- f1z = alpha * (fdz - ddotf * delzOM);
-
- fOx = fdx - f1x;
- fOy = fdy - f1y;
- fOz = fdz - f1z;
-
- fHx = 0.5 * f1x;
- fHy = 0.5 * f1y;
- fHz = 0.5 * f1z;
-
- fxtmp += fOx;
- fytmp += fOy;
- fztmp += fOz;
-
- f[iH1][0] += fHx;
- f[iH1][1] += fHy;
- f[iH1][2] += fHz;
-
- f[iH2][0] += fHx;
- f[iH2][1] += fHy;
- f[iH2][2] += fHz;
-
- if (VFLAG) {
- domain->closest_image(x[i],x[iH1],xH1);
- domain->closest_image(x[i],x[iH2],xH2);
-
- v[0] = x[i][0]*fOx + xH1[0]*fHx + xH2[0]*fHx;
- v[1] = x[i][1]*fOy + xH1[1]*fHy + xH2[1]*fHy;
- v[2] = x[i][2]*fOz + xH1[2]*fHz + xH2[2]*fHz;
- v[3] = x[i][0]*fOy + xH1[0]*fHy + xH2[0]*fHy;
- v[4] = x[i][0]*fOz + xH1[0]*fHz + xH2[0]*fHz;
- v[5] = x[i][1]*fOz + xH1[1]*fHz + xH2[1]*fHz;
-
- vlist[n++] = i;
- vlist[n++] = iH1;
- vlist[n++] = iH2;
- }
- }
-
- if (jtype != typeO) {
- f[j][0] -= delx * cforce;
- f[j][1] -= dely * cforce;
- f[j][2] -= delz * cforce;
-
- if (VFLAG) {
- v[0] -= x[j][0] * delx * cforce;
- v[1] -= x[j][1] * dely * cforce;
- v[2] -= x[j][2] * delz * cforce;
- v[3] -= x[j][0] * dely * cforce;
- v[4] -= x[j][0] * delz * cforce;
- v[5] -= x[j][1] * delz * cforce;
- vlist[n++] = j;
- }
-
- } else {
-
- fdx = -delx*cforce;
- fdy = -dely*cforce;
- fdz = -delz*cforce;
-
- delxOM = x[j][0] - x2[0];
- delyOM = x[j][1] - x2[1];
- delzOM = x[j][2] - x2[2];
-
- ddotf = (delxOM * fdx + delyOM * fdy + delzOM * fdz) /
- (qdist*qdist);
-
- f1x = alpha * (fdx - ddotf * delxOM);
- f1y = alpha * (fdy - ddotf * delyOM);
- f1z = alpha * (fdz - ddotf * delzOM);
-
- fOx = fdx - f1x;
- fOy = fdy - f1y;
- fOz = fdz - f1z;
-
- fHx = 0.5 * f1x;
- fHy = 0.5 * f1y;
- fHz = 0.5 * f1z;
-
- f[j][0] += fOx;
- f[j][1] += fOy;
- f[j][2] += fOz;
-
- f[jH1][0] += fHx;
- f[jH1][1] += fHy;
- f[jH1][2] += fHz;
-
- f[jH2][0] += fHx;
- f[jH2][1] += fHy;
- f[jH2][2] += fHz;
-
- if (VFLAG) {
- domain->closest_image(x[j],x[jH1],xH1);
- domain->closest_image(x[j],x[jH2],xH2);
-
- v[0] += x[j][0]*fOx + xH1[0]*fHx + xH2[0]*fHx;
- v[1] += x[j][1]*fOy + xH1[1]*fHy + xH2[1]*fHy;
- v[2] += x[j][2]*fOz + xH1[2]*fHz + xH2[2]*fHz;
- v[3] += x[j][0]*fOy + xH1[0]*fHy + xH2[0]*fHy;
- v[4] += x[j][0]*fOz + xH1[0]*fHz + xH2[0]*fHz;
- v[5] += x[j][1]*fOz + xH1[1]*fHz + xH2[1]*fHz;
-
- vlist[n++] = j;
- vlist[n++] = jH1;
- vlist[n++] = jH2;
- }
- }
-
- if (EFLAG) {
- if (CTABLE || rsq <= tabinnersq)
- ecoul = prefactor*erfc;
- else {
- table = etable[itable] + fraction*detable[itable];
- ecoul = qtmp*q[j] * table;
- }
- if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
- } else ecoul = 0.0;
-
- if (EVFLAG) ev_tally_list_thr(this,n,vlist,ecoul,v,thr);
- }
+ if (itype == typeO || jtype == typeO) {
+ x2 = mpos[j];
+ jH1 = h1idx[j];
+ jH2 = h2idx[j];
+
+ if (check_error_thr((jtype == typeO && ( jH1 < 0 || jH2 < 0 )),
+ tid, FLERR,"TIP4P hydrogen is missing"))
+ return;
+
+ delx = x1[0] - x2[0];
+ dely = x1[1] - x2[1];
+ delz = x1[2] - x2[2];
+ rsq = delx*delx + dely*dely + delz*delz;
+ }
+
+ // Coulombic interaction based on modified rsq
+
+ if (rsq < cut_coulsq) {
+ r2inv = 1 / rsq;
+ if (CTABLE || rsq <= tabinnersq) {
+ r = sqrt(rsq);
+ grij = g_ewald * r;
+ expm2 = exp(-grij*grij);
+ t = 1.0 / (1.0 + EWALD_P*grij);
+ erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
+ prefactor = qqrd2e * qtmp*q[j]/r;
+ forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
+ if (factor_coul < 1.0) {
+ forcecoul -= (1.0-factor_coul)*prefactor;
+ }
+ } else {
+ union_int_float_t rsq_lookup;
+ rsq_lookup.f = rsq;
+ itable = rsq_lookup.i & ncoulmask;
+ itable >>= ncoulshiftbits;
+ fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
+ table = ftable[itable] + fraction*dftable[itable];
+ forcecoul = qtmp*q[j] * table;
+ if (factor_coul < 1.0) {
+ table = ctable[itable] + fraction*dctable[itable];
+ prefactor = qtmp*q[j] * table;
+ forcecoul -= (1.0-factor_coul)*prefactor;
+ }
+ }
+
+ cforce = forcecoul * r2inv;
+
+ // if i,j are not O atoms, force is applied directly
+ // if i or j are O atoms, force is on fictitious atom & partitioned
+ // force partitioning due to Feenstra, J Comp Chem, 20, 786 (1999)
+ // f_f = fictitious force, fO = f_f (1 - 2 alpha), fH = alpha f_f
+ // preserves total force and torque on water molecule
+ // virial = sum(r x F) where each water's atoms are near xi and xj
+ // vlist stores 2,4,6 atoms whose forces contribute to virial
+
+ n = 0;
+
+ if (itype != typeO) {
+ fxtmp += delx * cforce;
+ fytmp += dely * cforce;
+ fztmp += delz * cforce;
+
+ if (VFLAG) {
+ v[0] = x[i][0] * delx * cforce;
+ v[1] = x[i][1] * dely * cforce;
+ v[2] = x[i][2] * delz * cforce;
+ v[3] = x[i][0] * dely * cforce;
+ v[4] = x[i][0] * delz * cforce;
+ v[5] = x[i][1] * delz * cforce;
+ vlist[n++] = i;
+ }
+
+ } else {
+
+ fdx = delx*cforce;
+ fdy = dely*cforce;
+ fdz = delz*cforce;
+
+ delxOM = x[i][0] - x1[0];
+ delyOM = x[i][1] - x1[1];
+ delzOM = x[i][2] - x1[2];
+
+ ddotf = (delxOM * fdx + delyOM * fdy + delzOM * fdz) /
+ (qdist*qdist);
+
+ f1x = alpha * (fdx - ddotf * delxOM);
+ f1y = alpha * (fdy - ddotf * delyOM);
+ f1z = alpha * (fdz - ddotf * delzOM);
+
+ fOx = fdx - f1x;
+ fOy = fdy - f1y;
+ fOz = fdz - f1z;
+
+ fHx = 0.5 * f1x;
+ fHy = 0.5 * f1y;
+ fHz = 0.5 * f1z;
+
+ fxtmp += fOx;
+ fytmp += fOy;
+ fztmp += fOz;
+
+ f[iH1][0] += fHx;
+ f[iH1][1] += fHy;
+ f[iH1][2] += fHz;
+
+ f[iH2][0] += fHx;
+ f[iH2][1] += fHy;
+ f[iH2][2] += fHz;
+
+ if (VFLAG) {
+ domain->closest_image(x[i],x[iH1],xH1);
+ domain->closest_image(x[i],x[iH2],xH2);
+
+ v[0] = x[i][0]*fOx + xH1[0]*fHx + xH2[0]*fHx;
+ v[1] = x[i][1]*fOy + xH1[1]*fHy + xH2[1]*fHy;
+ v[2] = x[i][2]*fOz + xH1[2]*fHz + xH2[2]*fHz;
+ v[3] = x[i][0]*fOy + xH1[0]*fHy + xH2[0]*fHy;
+ v[4] = x[i][0]*fOz + xH1[0]*fHz + xH2[0]*fHz;
+ v[5] = x[i][1]*fOz + xH1[1]*fHz + xH2[1]*fHz;
+
+ vlist[n++] = i;
+ vlist[n++] = iH1;
+ vlist[n++] = iH2;
+ }
+ }
+
+ if (jtype != typeO) {
+ f[j][0] -= delx * cforce;
+ f[j][1] -= dely * cforce;
+ f[j][2] -= delz * cforce;
+
+ if (VFLAG) {
+ v[0] -= x[j][0] * delx * cforce;
+ v[1] -= x[j][1] * dely * cforce;
+ v[2] -= x[j][2] * delz * cforce;
+ v[3] -= x[j][0] * dely * cforce;
+ v[4] -= x[j][0] * delz * cforce;
+ v[5] -= x[j][1] * delz * cforce;
+ vlist[n++] = j;
+ }
+
+ } else {
+
+ fdx = -delx*cforce;
+ fdy = -dely*cforce;
+ fdz = -delz*cforce;
+
+ delxOM = x[j][0] - x2[0];
+ delyOM = x[j][1] - x2[1];
+ delzOM = x[j][2] - x2[2];
+
+ ddotf = (delxOM * fdx + delyOM * fdy + delzOM * fdz) /
+ (qdist*qdist);
+
+ f1x = alpha * (fdx - ddotf * delxOM);
+ f1y = alpha * (fdy - ddotf * delyOM);
+ f1z = alpha * (fdz - ddotf * delzOM);
+
+ fOx = fdx - f1x;
+ fOy = fdy - f1y;
+ fOz = fdz - f1z;
+
+ fHx = 0.5 * f1x;
+ fHy = 0.5 * f1y;
+ fHz = 0.5 * f1z;
+
+ f[j][0] += fOx;
+ f[j][1] += fOy;
+ f[j][2] += fOz;
+
+ f[jH1][0] += fHx;
+ f[jH1][1] += fHy;
+ f[jH1][2] += fHz;
+
+ f[jH2][0] += fHx;
+ f[jH2][1] += fHy;
+ f[jH2][2] += fHz;
+
+ if (VFLAG) {
+ domain->closest_image(x[j],x[jH1],xH1);
+ domain->closest_image(x[j],x[jH2],xH2);
+
+ v[0] += x[j][0]*fOx + xH1[0]*fHx + xH2[0]*fHx;
+ v[1] += x[j][1]*fOy + xH1[1]*fHy + xH2[1]*fHy;
+ v[2] += x[j][2]*fOz + xH1[2]*fHz + xH2[2]*fHz;
+ v[3] += x[j][0]*fOy + xH1[0]*fHy + xH2[0]*fHy;
+ v[4] += x[j][0]*fOz + xH1[0]*fHz + xH2[0]*fHz;
+ v[5] += x[j][1]*fOz + xH1[1]*fHz + xH2[1]*fHz;
+
+ vlist[n++] = j;
+ vlist[n++] = jH1;
+ vlist[n++] = jH2;
+ }
+ }
+
+ if (EFLAG) {
+ if (CTABLE || rsq <= tabinnersq)
+ ecoul = prefactor*erfc;
+ else {
+ table = etable[itable] + fraction*detable[itable];
+ ecoul = qtmp*q[j] * table;
+ }
+ if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
+ } else ecoul = 0.0;
+
+ if (EVFLAG) ev_tally_list_thr(this,n,vlist,ecoul,v,thr);
+ }
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_lj_cut_coul_long_tip4p_omp.h b/src/USER-OMP/pair_lj_cut_coul_long_tip4p_omp.h
index 37743abf142886a5d04cfa30f39877b705687a67..4610e1f23e3f0b302c101fcef770d05333f69d8d 100644
--- a/src/USER-OMP/pair_lj_cut_coul_long_tip4p_omp.h
+++ b/src/USER-OMP/pair_lj_cut_coul_long_tip4p_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_lj_cut_coul_pppm_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_pppm_omp.cpp
index bc767958bb9952bbcf06a600be6fe306bcd28483..093f8d0216e3cbf150b2eda0ee02a3ae54298eee 100644
--- a/src/USER-OMP/pair_lj_cut_coul_pppm_omp.cpp
+++ b/src/USER-OMP/pair_lj_cut_coul_pppm_omp.cpp
@@ -90,19 +90,19 @@ void PairLJCutCoulPPPMOMP::compute(int eflag, int vflag)
kspace->compute_proxy(eflag,vflag);
} else {
if (evflag) {
- if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
- } else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
- }
+ if (eflag) {
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
+ } else {
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
+ }
} else {
- if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
- else eval<0,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
+ else eval<0,0,0>(ifrom, ito, thr);
}
}
-
+
sync_threads();
reduce_thr(this, eflag, vflag, thr, nproxy);
} // end of omp parallel region
@@ -162,71 +162,71 @@ void PairLJCutCoulPPPMOMP::eval(int iifrom, int iito, ThrData * const thr)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
-
- if (rsq < cut_coulsq) {
- if (!ncoultablebits || rsq <= tabinnersq) {
- r = sqrt(rsq);
- grij = g_ewald * r;
- expm2 = exp(-grij*grij);
- t = 1.0 / (1.0 + EWALD_P*grij);
- erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
- prefactor = qqrd2e * qtmp*q[j]/r;
- forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
- if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
- } else {
- union_int_float_t rsq_lookup;
- rsq_lookup.f = rsq;
- itable = rsq_lookup.i & ncoulmask;
- itable >>= ncoulshiftbits;
- fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
- table = ftable[itable] + fraction*dftable[itable];
- forcecoul = qtmp*q[j] * table;
- if (factor_coul < 1.0) {
- table = ctable[itable] + fraction*dctable[itable];
- prefactor = qtmp*q[j] * table;
- forcecoul -= (1.0-factor_coul)*prefactor;
- }
- }
- } else forcecoul = 0.0;
-
- if (rsq < cut_ljsq[itype][jtype]) {
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- forcelj *= factor_lj;
- } else forcelj = 0.0;
-
- fpair = (forcecoul + forcelj) * r2inv;
-
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (EFLAG) {
- if (rsq < cut_coulsq) {
- if (!ncoultablebits || rsq <= tabinnersq)
- ecoul = prefactor*erfc;
- else {
- table = etable[itable] + fraction*detable[itable];
- ecoul = qtmp*q[j] * table;
- }
- if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
- } else ecoul = 0.0;
-
- if (rsq < cut_ljsq[itype][jtype]) {
- evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
- offset[itype][jtype];
- evdwl *= factor_lj;
- } else evdwl = 0.0;
- }
-
- if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
- evdwl,ecoul,fpair,delx,dely,delz,thr);
+ r2inv = 1.0/rsq;
+
+ if (rsq < cut_coulsq) {
+ if (!ncoultablebits || rsq <= tabinnersq) {
+ r = sqrt(rsq);
+ grij = g_ewald * r;
+ expm2 = exp(-grij*grij);
+ t = 1.0 / (1.0 + EWALD_P*grij);
+ erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
+ prefactor = qqrd2e * qtmp*q[j]/r;
+ forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
+ if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
+ } else {
+ union_int_float_t rsq_lookup;
+ rsq_lookup.f = rsq;
+ itable = rsq_lookup.i & ncoulmask;
+ itable >>= ncoulshiftbits;
+ fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
+ table = ftable[itable] + fraction*dftable[itable];
+ forcecoul = qtmp*q[j] * table;
+ if (factor_coul < 1.0) {
+ table = ctable[itable] + fraction*dctable[itable];
+ prefactor = qtmp*q[j] * table;
+ forcecoul -= (1.0-factor_coul)*prefactor;
+ }
+ }
+ } else forcecoul = 0.0;
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ forcelj *= factor_lj;
+ } else forcelj = 0.0;
+
+ fpair = (forcecoul + forcelj) * r2inv;
+
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (EFLAG) {
+ if (rsq < cut_coulsq) {
+ if (!ncoultablebits || rsq <= tabinnersq)
+ ecoul = prefactor*erfc;
+ else {
+ table = etable[itable] + fraction*detable[itable];
+ ecoul = qtmp*q[j] * table;
+ }
+ if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
+ } else ecoul = 0.0;
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
+ offset[itype][jtype];
+ evdwl *= factor_lj;
+ } else evdwl = 0.0;
+ }
+
+ if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
+ evdwl,ecoul,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_lj_cut_coul_pppm_omp.h b/src/USER-OMP/pair_lj_cut_coul_pppm_omp.h
index 010b7818b22f4a763a6038e9605fcea74269a6ba..092996a21f4c8a5753d6094e299c2479c6a2d290 100644
--- a/src/USER-OMP/pair_lj_cut_coul_pppm_omp.h
+++ b/src/USER-OMP/pair_lj_cut_coul_pppm_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_lj_cut_coul_pppm_tip4p_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_pppm_tip4p_omp.cpp
index eb780621cb38efb2b1034f9aeb831bb2621c10f4..63c4658347c4c6e7eb34074908d73ac4039c70f8 100644
--- a/src/USER-OMP/pair_lj_cut_coul_pppm_tip4p_omp.cpp
+++ b/src/USER-OMP/pair_lj_cut_coul_pppm_tip4p_omp.cpp
@@ -46,7 +46,7 @@ PairLJCutCoulPPPMTIP4POMP::PairLJCutCoulPPPMTIP4POMP(LAMMPS *lmp) :
suffix_flag |= Suffix::OMP;
respa_enable = 0;
nproxy=1;
-
+
kspace = NULL;
// for caching m-shift corrected positions
@@ -138,25 +138,25 @@ void PairLJCutCoulPPPMTIP4POMP::compute(int eflag, int vflag)
kspace->compute_proxy(eflag,vflag);
} else {
if (!ncoultablebits) {
- if (evflag) {
- if (eflag) {
- if (vflag) eval<1,1,1,1>(ifrom, ito, thr);
- else eval<1,1,1,0>(ifrom, ito, thr);
- } else {
- if (vflag) eval<1,1,0,1>(ifrom, ito, thr);
- else eval<1,1,0,0>(ifrom, ito, thr);
- }
- } else eval<1,0,0,0>(ifrom, ito, thr);
+ if (evflag) {
+ if (eflag) {
+ if (vflag) eval<1,1,1,1>(ifrom, ito, thr);
+ else eval<1,1,1,0>(ifrom, ito, thr);
+ } else {
+ if (vflag) eval<1,1,0,1>(ifrom, ito, thr);
+ else eval<1,1,0,0>(ifrom, ito, thr);
+ }
+ } else eval<1,0,0,0>(ifrom, ito, thr);
} else {
- if (evflag) {
- if (eflag) {
- if (vflag) eval<0,1,1,1>(ifrom, ito, thr);
- else eval<0,1,1,0>(ifrom, ito, thr);
- } else {
- if (vflag) eval<0,1,0,1>(ifrom, ito, thr);
- else eval<0,1,0,0>(ifrom, ito, thr);
- }
- } else eval<0,0,0,0>(ifrom, ito, thr);
+ if (evflag) {
+ if (eflag) {
+ if (vflag) eval<0,1,1,1>(ifrom, ito, thr);
+ else eval<0,1,1,0>(ifrom, ito, thr);
+ } else {
+ if (vflag) eval<0,1,0,1>(ifrom, ito, thr);
+ else eval<0,1,0,0>(ifrom, ito, thr);
+ }
+ } else eval<0,0,0,0>(ifrom, ito, thr);
}
}
@@ -236,26 +236,26 @@ void PairLJCutCoulPPPMTIP4POMP::eval(int iifrom, int iito, ThrData * const thr)
// LJ interaction based on true rsq
if (rsq < cut_ljsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- forcelj *= factor_lj * r2inv;
-
- fxtmp += delx*forcelj;
- fytmp += dely*forcelj;
- fztmp += delz*forcelj;
- f[j][0] -= delx*forcelj;
- f[j][1] -= dely*forcelj;
- f[j][2] -= delz*forcelj;
-
- if (EFLAG) {
- evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
- offset[itype][jtype];
- evdwl *= factor_lj;
- } else evdwl = 0.0;
-
- if (EVFLAG) ev_tally_thr(this,i,j,nlocal, /* newton_pair = */ 1,
- evdwl,0.0,forcelj,delx,dely,delz,thr);
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ forcelj *= factor_lj * r2inv;
+
+ fxtmp += delx*forcelj;
+ fytmp += dely*forcelj;
+ fztmp += delz*forcelj;
+ f[j][0] -= delx*forcelj;
+ f[j][1] -= dely*forcelj;
+ f[j][2] -= delz*forcelj;
+
+ if (EFLAG) {
+ evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
+ offset[itype][jtype];
+ evdwl *= factor_lj;
+ } else evdwl = 0.0;
+
+ if (EVFLAG) ev_tally_thr(this,i,j,nlocal, /* newton_pair = */ 1,
+ evdwl,0.0,forcelj,delx,dely,delz,thr);
}
// adjust rsq and delxyz for off-site O charge(s),
@@ -263,213 +263,213 @@ void PairLJCutCoulPPPMTIP4POMP::eval(int iifrom, int iito, ThrData * const thr)
if (rsq < cut_coulsqplus) {
- if (itype == typeO || jtype == typeO) {
- x2 = mpos[j];
- jH1 = h1idx[j];
- jH2 = h2idx[j];
-
- if (check_error_thr((jtype == typeO && ( jH1 < 0 || jH2 < 0 )),
- tid, FLERR,"TIP4P hydrogen is missing"))
- return;
-
- delx = x1[0] - x2[0];
- dely = x1[1] - x2[1];
- delz = x1[2] - x2[2];
- rsq = delx*delx + dely*dely + delz*delz;
- }
-
- // Coulombic interaction based on modified rsq
-
- if (rsq < cut_coulsq) {
- r2inv = 1 / rsq;
- if (CTABLE || rsq <= tabinnersq) {
- r = sqrt(rsq);
- grij = g_ewald * r;
- expm2 = exp(-grij*grij);
- t = 1.0 / (1.0 + EWALD_P*grij);
- erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
- prefactor = qqrd2e * qtmp*q[j]/r;
- forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
- if (factor_coul < 1.0) {
- forcecoul -= (1.0-factor_coul)*prefactor;
- }
- } else {
- union_int_float_t rsq_lookup;
- rsq_lookup.f = rsq;
- itable = rsq_lookup.i & ncoulmask;
- itable >>= ncoulshiftbits;
- fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
- table = ftable[itable] + fraction*dftable[itable];
- forcecoul = qtmp*q[j] * table;
- if (factor_coul < 1.0) {
- table = ctable[itable] + fraction*dctable[itable];
- prefactor = qtmp*q[j] * table;
- forcecoul -= (1.0-factor_coul)*prefactor;
- }
- }
-
- cforce = forcecoul * r2inv;
-
- // if i,j are not O atoms, force is applied directly
- // if i or j are O atoms, force is on fictitious atom & partitioned
- // force partitioning due to Feenstra, J Comp Chem, 20, 786 (1999)
- // f_f = fictitious force, fO = f_f (1 - 2 alpha), fH = alpha f_f
- // preserves total force and torque on water molecule
- // virial = sum(r x F) where each water's atoms are near xi and xj
- // vlist stores 2,4,6 atoms whose forces contribute to virial
-
- n = 0;
-
- if (itype != typeO) {
- fxtmp += delx * cforce;
- fytmp += dely * cforce;
- fztmp += delz * cforce;
-
- if (VFLAG) {
- v[0] = x[i][0] * delx * cforce;
- v[1] = x[i][1] * dely * cforce;
- v[2] = x[i][2] * delz * cforce;
- v[3] = x[i][0] * dely * cforce;
- v[4] = x[i][0] * delz * cforce;
- v[5] = x[i][1] * delz * cforce;
- vlist[n++] = i;
- }
-
- } else {
-
- fdx = delx*cforce;
- fdy = dely*cforce;
- fdz = delz*cforce;
-
- delxOM = x[i][0] - x1[0];
- delyOM = x[i][1] - x1[1];
- delzOM = x[i][2] - x1[2];
-
- ddotf = (delxOM * fdx + delyOM * fdy + delzOM * fdz) /
- (qdist*qdist);
-
- f1x = alpha * (fdx - ddotf * delxOM);
- f1y = alpha * (fdy - ddotf * delyOM);
- f1z = alpha * (fdz - ddotf * delzOM);
-
- fOx = fdx - f1x;
- fOy = fdy - f1y;
- fOz = fdz - f1z;
-
- fHx = 0.5 * f1x;
- fHy = 0.5 * f1y;
- fHz = 0.5 * f1z;
-
- fxtmp += fOx;
- fytmp += fOy;
- fztmp += fOz;
-
- f[iH1][0] += fHx;
- f[iH1][1] += fHy;
- f[iH1][2] += fHz;
-
- f[iH2][0] += fHx;
- f[iH2][1] += fHy;
- f[iH2][2] += fHz;
-
- if (VFLAG) {
- domain->closest_image(x[i],x[iH1],xH1);
- domain->closest_image(x[i],x[iH2],xH2);
-
- v[0] = x[i][0]*fOx + xH1[0]*fHx + xH2[0]*fHx;
- v[1] = x[i][1]*fOy + xH1[1]*fHy + xH2[1]*fHy;
- v[2] = x[i][2]*fOz + xH1[2]*fHz + xH2[2]*fHz;
- v[3] = x[i][0]*fOy + xH1[0]*fHy + xH2[0]*fHy;
- v[4] = x[i][0]*fOz + xH1[0]*fHz + xH2[0]*fHz;
- v[5] = x[i][1]*fOz + xH1[1]*fHz + xH2[1]*fHz;
-
- vlist[n++] = i;
- vlist[n++] = iH1;
- vlist[n++] = iH2;
- }
- }
-
- if (jtype != typeO) {
- f[j][0] -= delx * cforce;
- f[j][1] -= dely * cforce;
- f[j][2] -= delz * cforce;
-
- if (VFLAG) {
- v[0] -= x[j][0] * delx * cforce;
- v[1] -= x[j][1] * dely * cforce;
- v[2] -= x[j][2] * delz * cforce;
- v[3] -= x[j][0] * dely * cforce;
- v[4] -= x[j][0] * delz * cforce;
- v[5] -= x[j][1] * delz * cforce;
- vlist[n++] = j;
- }
-
- } else {
-
- fdx = -delx*cforce;
- fdy = -dely*cforce;
- fdz = -delz*cforce;
-
- delxOM = x[j][0] - x2[0];
- delyOM = x[j][1] - x2[1];
- delzOM = x[j][2] - x2[2];
-
- ddotf = (delxOM * fdx + delyOM * fdy + delzOM * fdz) /
- (qdist*qdist);
-
- f1x = alpha * (fdx - ddotf * delxOM);
- f1y = alpha * (fdy - ddotf * delyOM);
- f1z = alpha * (fdz - ddotf * delzOM);
-
- fOx = fdx - f1x;
- fOy = fdy - f1y;
- fOz = fdz - f1z;
-
- fHx = 0.5 * f1x;
- fHy = 0.5 * f1y;
- fHz = 0.5 * f1z;
-
- f[j][0] += fOx;
- f[j][1] += fOy;
- f[j][2] += fOz;
-
- f[jH1][0] += fHx;
- f[jH1][1] += fHy;
- f[jH1][2] += fHz;
-
- f[jH2][0] += fHx;
- f[jH2][1] += fHy;
- f[jH2][2] += fHz;
-
- if (VFLAG) {
- domain->closest_image(x[j],x[jH1],xH1);
- domain->closest_image(x[j],x[jH2],xH2);
-
- v[0] += x[j][0]*fOx + xH1[0]*fHx + xH2[0]*fHx;
- v[1] += x[j][1]*fOy + xH1[1]*fHy + xH2[1]*fHy;
- v[2] += x[j][2]*fOz + xH1[2]*fHz + xH2[2]*fHz;
- v[3] += x[j][0]*fOy + xH1[0]*fHy + xH2[0]*fHy;
- v[4] += x[j][0]*fOz + xH1[0]*fHz + xH2[0]*fHz;
- v[5] += x[j][1]*fOz + xH1[1]*fHz + xH2[1]*fHz;
-
- vlist[n++] = j;
- vlist[n++] = jH1;
- vlist[n++] = jH2;
- }
- }
-
- if (EFLAG) {
- if (CTABLE || rsq <= tabinnersq)
- ecoul = prefactor*erfc;
- else {
- table = etable[itable] + fraction*detable[itable];
- ecoul = qtmp*q[j] * table;
- }
- if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
- } else ecoul = 0.0;
-
- if (EVFLAG) ev_tally_list_thr(this,n,vlist,ecoul,v,thr);
- }
+ if (itype == typeO || jtype == typeO) {
+ x2 = mpos[j];
+ jH1 = h1idx[j];
+ jH2 = h2idx[j];
+
+ if (check_error_thr((jtype == typeO && ( jH1 < 0 || jH2 < 0 )),
+ tid, FLERR,"TIP4P hydrogen is missing"))
+ return;
+
+ delx = x1[0] - x2[0];
+ dely = x1[1] - x2[1];
+ delz = x1[2] - x2[2];
+ rsq = delx*delx + dely*dely + delz*delz;
+ }
+
+ // Coulombic interaction based on modified rsq
+
+ if (rsq < cut_coulsq) {
+ r2inv = 1 / rsq;
+ if (CTABLE || rsq <= tabinnersq) {
+ r = sqrt(rsq);
+ grij = g_ewald * r;
+ expm2 = exp(-grij*grij);
+ t = 1.0 / (1.0 + EWALD_P*grij);
+ erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
+ prefactor = qqrd2e * qtmp*q[j]/r;
+ forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
+ if (factor_coul < 1.0) {
+ forcecoul -= (1.0-factor_coul)*prefactor;
+ }
+ } else {
+ union_int_float_t rsq_lookup;
+ rsq_lookup.f = rsq;
+ itable = rsq_lookup.i & ncoulmask;
+ itable >>= ncoulshiftbits;
+ fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
+ table = ftable[itable] + fraction*dftable[itable];
+ forcecoul = qtmp*q[j] * table;
+ if (factor_coul < 1.0) {
+ table = ctable[itable] + fraction*dctable[itable];
+ prefactor = qtmp*q[j] * table;
+ forcecoul -= (1.0-factor_coul)*prefactor;
+ }
+ }
+
+ cforce = forcecoul * r2inv;
+
+ // if i,j are not O atoms, force is applied directly
+ // if i or j are O atoms, force is on fictitious atom & partitioned
+ // force partitioning due to Feenstra, J Comp Chem, 20, 786 (1999)
+ // f_f = fictitious force, fO = f_f (1 - 2 alpha), fH = alpha f_f
+ // preserves total force and torque on water molecule
+ // virial = sum(r x F) where each water's atoms are near xi and xj
+ // vlist stores 2,4,6 atoms whose forces contribute to virial
+
+ n = 0;
+
+ if (itype != typeO) {
+ fxtmp += delx * cforce;
+ fytmp += dely * cforce;
+ fztmp += delz * cforce;
+
+ if (VFLAG) {
+ v[0] = x[i][0] * delx * cforce;
+ v[1] = x[i][1] * dely * cforce;
+ v[2] = x[i][2] * delz * cforce;
+ v[3] = x[i][0] * dely * cforce;
+ v[4] = x[i][0] * delz * cforce;
+ v[5] = x[i][1] * delz * cforce;
+ vlist[n++] = i;
+ }
+
+ } else {
+
+ fdx = delx*cforce;
+ fdy = dely*cforce;
+ fdz = delz*cforce;
+
+ delxOM = x[i][0] - x1[0];
+ delyOM = x[i][1] - x1[1];
+ delzOM = x[i][2] - x1[2];
+
+ ddotf = (delxOM * fdx + delyOM * fdy + delzOM * fdz) /
+ (qdist*qdist);
+
+ f1x = alpha * (fdx - ddotf * delxOM);
+ f1y = alpha * (fdy - ddotf * delyOM);
+ f1z = alpha * (fdz - ddotf * delzOM);
+
+ fOx = fdx - f1x;
+ fOy = fdy - f1y;
+ fOz = fdz - f1z;
+
+ fHx = 0.5 * f1x;
+ fHy = 0.5 * f1y;
+ fHz = 0.5 * f1z;
+
+ fxtmp += fOx;
+ fytmp += fOy;
+ fztmp += fOz;
+
+ f[iH1][0] += fHx;
+ f[iH1][1] += fHy;
+ f[iH1][2] += fHz;
+
+ f[iH2][0] += fHx;
+ f[iH2][1] += fHy;
+ f[iH2][2] += fHz;
+
+ if (VFLAG) {
+ domain->closest_image(x[i],x[iH1],xH1);
+ domain->closest_image(x[i],x[iH2],xH2);
+
+ v[0] = x[i][0]*fOx + xH1[0]*fHx + xH2[0]*fHx;
+ v[1] = x[i][1]*fOy + xH1[1]*fHy + xH2[1]*fHy;
+ v[2] = x[i][2]*fOz + xH1[2]*fHz + xH2[2]*fHz;
+ v[3] = x[i][0]*fOy + xH1[0]*fHy + xH2[0]*fHy;
+ v[4] = x[i][0]*fOz + xH1[0]*fHz + xH2[0]*fHz;
+ v[5] = x[i][1]*fOz + xH1[1]*fHz + xH2[1]*fHz;
+
+ vlist[n++] = i;
+ vlist[n++] = iH1;
+ vlist[n++] = iH2;
+ }
+ }
+
+ if (jtype != typeO) {
+ f[j][0] -= delx * cforce;
+ f[j][1] -= dely * cforce;
+ f[j][2] -= delz * cforce;
+
+ if (VFLAG) {
+ v[0] -= x[j][0] * delx * cforce;
+ v[1] -= x[j][1] * dely * cforce;
+ v[2] -= x[j][2] * delz * cforce;
+ v[3] -= x[j][0] * dely * cforce;
+ v[4] -= x[j][0] * delz * cforce;
+ v[5] -= x[j][1] * delz * cforce;
+ vlist[n++] = j;
+ }
+
+ } else {
+
+ fdx = -delx*cforce;
+ fdy = -dely*cforce;
+ fdz = -delz*cforce;
+
+ delxOM = x[j][0] - x2[0];
+ delyOM = x[j][1] - x2[1];
+ delzOM = x[j][2] - x2[2];
+
+ ddotf = (delxOM * fdx + delyOM * fdy + delzOM * fdz) /
+ (qdist*qdist);
+
+ f1x = alpha * (fdx - ddotf * delxOM);
+ f1y = alpha * (fdy - ddotf * delyOM);
+ f1z = alpha * (fdz - ddotf * delzOM);
+
+ fOx = fdx - f1x;
+ fOy = fdy - f1y;
+ fOz = fdz - f1z;
+
+ fHx = 0.5 * f1x;
+ fHy = 0.5 * f1y;
+ fHz = 0.5 * f1z;
+
+ f[j][0] += fOx;
+ f[j][1] += fOy;
+ f[j][2] += fOz;
+
+ f[jH1][0] += fHx;
+ f[jH1][1] += fHy;
+ f[jH1][2] += fHz;
+
+ f[jH2][0] += fHx;
+ f[jH2][1] += fHy;
+ f[jH2][2] += fHz;
+
+ if (VFLAG) {
+ domain->closest_image(x[j],x[jH1],xH1);
+ domain->closest_image(x[j],x[jH2],xH2);
+
+ v[0] += x[j][0]*fOx + xH1[0]*fHx + xH2[0]*fHx;
+ v[1] += x[j][1]*fOy + xH1[1]*fHy + xH2[1]*fHy;
+ v[2] += x[j][2]*fOz + xH1[2]*fHz + xH2[2]*fHz;
+ v[3] += x[j][0]*fOy + xH1[0]*fHy + xH2[0]*fHy;
+ v[4] += x[j][0]*fOz + xH1[0]*fHz + xH2[0]*fHz;
+ v[5] += x[j][1]*fOz + xH1[1]*fHz + xH2[1]*fHz;
+
+ vlist[n++] = j;
+ vlist[n++] = jH1;
+ vlist[n++] = jH2;
+ }
+ }
+
+ if (EFLAG) {
+ if (CTABLE || rsq <= tabinnersq)
+ ecoul = prefactor*erfc;
+ else {
+ table = etable[itable] + fraction*detable[itable];
+ ecoul = qtmp*q[j] * table;
+ }
+ if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
+ } else ecoul = 0.0;
+
+ if (EVFLAG) ev_tally_list_thr(this,n,vlist,ecoul,v,thr);
+ }
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_lj_cut_coul_pppm_tip4p_omp.h b/src/USER-OMP/pair_lj_cut_coul_pppm_tip4p_omp.h
index 4596369324b619eec2d1a169e07fcb8461b7e3b0..6811b09738069dded15d0e4587d997835c128bd6 100644
--- a/src/USER-OMP/pair_lj_cut_coul_pppm_tip4p_omp.h
+++ b/src/USER-OMP/pair_lj_cut_coul_pppm_tip4p_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_lj_cut_omp.cpp b/src/USER-OMP/pair_lj_cut_omp.cpp
index f8d3b1f8ac4a39890cce764f2b180e1e88c3ee56..83e5244add465a48316ebb2a74fa04df6152436f 100644
--- a/src/USER-OMP/pair_lj_cut_omp.cpp
+++ b/src/USER-OMP/pair_lj_cut_omp.cpp
@@ -57,11 +57,11 @@ void PairLJCutOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -118,28 +118,28 @@ void PairLJCutOMP::eval(int iifrom, int iito, ThrData * const thr)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- fpair = factor_lj*forcelj*r2inv;
-
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (EFLAG) {
- evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype])
- - offset[itype][jtype];
- evdwl *= factor_lj;
- }
-
- if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
- evdwl,0.0,fpair,delx,dely,delz,thr);
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ fpair = factor_lj*forcelj*r2inv;
+
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (EFLAG) {
+ evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype])
+ - offset[itype][jtype];
+ evdwl *= factor_lj;
+ }
+
+ if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
+ evdwl,0.0,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_lj_cut_omp.h b/src/USER-OMP/pair_lj_cut_omp.h
index f97996e4807f2165407c8acd0ec93aec3ae8834d..419b0693b19abd7137bfa8b4d425a3c6e6585c49 100644
--- a/src/USER-OMP/pair_lj_cut_omp.h
+++ b/src/USER-OMP/pair_lj_cut_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_lj_expand_omp.cpp b/src/USER-OMP/pair_lj_expand_omp.cpp
index 5d64d0d0e68e1501a4889b714138c3c7cb1d47d7..936c55c827074a42b72a91f5319bd5794d0dda95 100644
--- a/src/USER-OMP/pair_lj_expand_omp.cpp
+++ b/src/USER-OMP/pair_lj_expand_omp.cpp
@@ -56,11 +56,11 @@ void PairLJExpandOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -118,31 +118,31 @@ void PairLJExpandOMP::eval(int iifrom, int iito, ThrData * const thr)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r = sqrt(rsq);
- rshift = r - shift[itype][jtype];
- rshiftsq = rshift*rshift;
- r2inv = 1.0/rshiftsq;
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- fpair = factor_lj*forcelj/rshift/r;
-
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (EFLAG) {
- evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype])
- - offset[itype][jtype];
- evdwl *= factor_lj;
- }
-
- if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
- evdwl,0.0,fpair,delx,dely,delz,thr);
+ r = sqrt(rsq);
+ rshift = r - shift[itype][jtype];
+ rshiftsq = rshift*rshift;
+ r2inv = 1.0/rshiftsq;
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ fpair = factor_lj*forcelj/rshift/r;
+
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (EFLAG) {
+ evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype])
+ - offset[itype][jtype];
+ evdwl *= factor_lj;
+ }
+
+ if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
+ evdwl,0.0,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_lj_expand_omp.h b/src/USER-OMP/pair_lj_expand_omp.h
index 9ff8d3080a7ca516cbbfcb5b95e830b863f07551..53728ead6d1877c05c7b814ca7ef1884f2d597a0 100644
--- a/src/USER-OMP/pair_lj_expand_omp.h
+++ b/src/USER-OMP/pair_lj_expand_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp b/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp
index bf3e2046d7b03f0e139f35771a79f5c23dc96f31..4df4d334e75a3dd6cdb0313bf88de4842d9bd2b5 100644
--- a/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp
+++ b/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp
@@ -56,11 +56,11 @@ void PairLJGromacsCoulGromacsOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -125,70 +125,70 @@ void PairLJGromacsCoulGromacsOMP::eval(int iifrom, int iito, ThrData * const thr
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
+ r2inv = 1.0/rsq;
- // skip if qi or qj = 0.0 since this potential may be used as
- // coarse-grain model with many uncharged atoms
+ // skip if qi or qj = 0.0 since this potential may be used as
+ // coarse-grain model with many uncharged atoms
- if (rsq < cut_coulsq && qtmp != 0.0 && q[j] != 0.0) {
- forcecoul = qqrd2e * qtmp*q[j]*sqrt(r2inv);
+ if (rsq < cut_coulsq && qtmp != 0.0 && q[j] != 0.0) {
+ forcecoul = qqrd2e * qtmp*q[j]*sqrt(r2inv);
if (rsq > cut_coul_innersq) {
- r = sqrt(rsq);
- tc = r - cut_coul_inner;
+ r = sqrt(rsq);
+ tc = r - cut_coul_inner;
fswitchcoul = qqrd2e * qtmp*q[j]*r*tc*tc*(coulsw1 + coulsw2*tc);
forcecoul += fswitchcoul;
}
- forcecoul *= factor_coul;
- } else forcecoul = 0.0;
+ forcecoul *= factor_coul;
+ } else forcecoul = 0.0;
- if (rsq < cut_ljsq) {
- r6inv = r2inv*r2inv*r2inv;
- jtype = type[j];
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ if (rsq < cut_ljsq) {
+ r6inv = r2inv*r2inv*r2inv;
+ jtype = type[j];
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
if (rsq > cut_lj_innersq) {
- r = sqrt(rsq);
- tlj = r - cut_lj_inner;
- fswitch = r*tlj*tlj*(ljsw1[itype][jtype] +
- ljsw2[itype][jtype]*tlj);
- forcelj += fswitch;
+ r = sqrt(rsq);
+ tlj = r - cut_lj_inner;
+ fswitch = r*tlj*tlj*(ljsw1[itype][jtype] +
+ ljsw2[itype][jtype]*tlj);
+ forcelj += fswitch;
}
- forcelj *= factor_lj;
- } else forcelj = 0.0;
-
- fpair = (forcecoul + forcelj) * r2inv;
-
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (EFLAG) {
- if (rsq < cut_coulsq) {
- ecoul = qqrd2e * qtmp*q[j] * (sqrt(r2inv) - coulsw5);
+ forcelj *= factor_lj;
+ } else forcelj = 0.0;
+
+ fpair = (forcecoul + forcelj) * r2inv;
+
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (EFLAG) {
+ if (rsq < cut_coulsq) {
+ ecoul = qqrd2e * qtmp*q[j] * (sqrt(r2inv) - coulsw5);
if (rsq > cut_coul_innersq) {
ecoulswitch = tc*tc*tc * (coulsw3 + coulsw4*tc);
ecoul += qqrd2e*qtmp*q[j]*ecoulswitch;
}
- ecoul *= factor_coul;
- } else ecoul = 0.0;
- if (rsq < cut_ljsq) {
- evdwl = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
- evdwl += ljsw5[itype][jtype];
+ ecoul *= factor_coul;
+ } else ecoul = 0.0;
+ if (rsq < cut_ljsq) {
+ evdwl = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
+ evdwl += ljsw5[itype][jtype];
if (rsq > cut_lj_innersq) {
- eswitch = tlj*tlj*tlj *
- (ljsw3[itype][jtype] + ljsw4[itype][jtype]*tlj);
+ eswitch = tlj*tlj*tlj *
+ (ljsw3[itype][jtype] + ljsw4[itype][jtype]*tlj);
evdwl += eswitch;
}
- evdwl *= factor_lj;
- } else evdwl = 0.0;
- }
-
- if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
- evdwl,ecoul,fpair,delx,dely,delz,thr);
+ evdwl *= factor_lj;
+ } else evdwl = 0.0;
+ }
+
+ if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
+ evdwl,ecoul,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.h b/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.h
index ee506c2c4a6f2ce55eb26880be6184ed4ee00c4f..353e4d673de1bd20ab8a6ee86df3df1d8074d532 100644
--- a/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.h
+++ b/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_lj_gromacs_omp.cpp b/src/USER-OMP/pair_lj_gromacs_omp.cpp
index 457dc233ce8b18aadaa28bbf402e0d157c6fa32a..ce97ad2d1d5ac8185cbda412ffcae4376bb6a946 100644
--- a/src/USER-OMP/pair_lj_gromacs_omp.cpp
+++ b/src/USER-OMP/pair_lj_gromacs_omp.cpp
@@ -56,11 +56,11 @@ void PairLJGromacsOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -118,39 +118,39 @@ void PairLJGromacsOMP::eval(int iifrom, int iito, ThrData * const thr)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
if (rsq > cut_inner_sq[itype][jtype]) {
- r = sqrt(rsq);
- t = r - cut_inner[itype][jtype];
- fswitch = r*t*t*(ljsw1[itype][jtype] + ljsw2[itype][jtype]*t);
- forcelj += fswitch;
+ r = sqrt(rsq);
+ t = r - cut_inner[itype][jtype];
+ fswitch = r*t*t*(ljsw1[itype][jtype] + ljsw2[itype][jtype]*t);
+ forcelj += fswitch;
}
- fpair = factor_lj*forcelj*r2inv;
+ fpair = factor_lj*forcelj*r2inv;
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
- if (EFLAG) {
- evdwl = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
- evdwl += ljsw5[itype][jtype];
+ if (EFLAG) {
+ evdwl = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
+ evdwl += ljsw5[itype][jtype];
if (rsq > cut_inner_sq[itype][jtype]) {
eswitch = t*t*t*(ljsw3[itype][jtype] + ljsw4[itype][jtype]*t);
evdwl += eswitch;
}
- evdwl *= factor_lj;
- }
+ evdwl *= factor_lj;
+ }
- if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
- evdwl,0.0,fpair,delx,dely,delz,thr);
+ if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
+ evdwl,0.0,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_lj_gromacs_omp.h b/src/USER-OMP/pair_lj_gromacs_omp.h
index 8e0f4bd2810507a4f81935240be669782a19b061..3669d1b219f9431b8e1a7a872783dd1003ae2851 100644
--- a/src/USER-OMP/pair_lj_gromacs_omp.h
+++ b/src/USER-OMP/pair_lj_gromacs_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp b/src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp
index 6632f4fc472e73aced7e3db480ef829d151adb2c..aa4e432a7812592ce526b5cb53f7a041e7bb93ca 100644
--- a/src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp
+++ b/src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp
@@ -58,11 +58,11 @@ void PairLJSDKCoulLongOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval_thr<1,1,1>(ifrom, ito, thr);
- else eval_thr<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval_thr<1,1,1>(ifrom, ito, thr);
+ else eval_thr<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval_thr<1,0,1>(ifrom, ito, thr);
- else eval_thr<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval_thr<1,0,1>(ifrom, ito, thr);
+ else eval_thr<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval_thr<0,0,1>(ifrom, ito, thr);
@@ -122,100 +122,100 @@ void PairLJSDKCoulLongOMP::eval_thr(int iifrom, int iito, ThrData * const thr)
const int jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- const double r2inv = 1.0/rsq;
- const int ljt = lj_type[itype][jtype];
-
- if (rsq < cut_coulsq) {
- if (!ncoultablebits || rsq <= tabinnersq) {
- const double A1 = 0.254829592;
- const double A2 = -0.284496736;
- const double A3 = 1.421413741;
- const double A4 = -1.453152027;
- const double A5 = 1.061405429;
- const double EWALD_F = 1.12837917;
- const double INV_EWALD_P = 1.0/0.3275911;
-
- const double r = sqrt(rsq);
- const double grij = g_ewald * r;
- const double expm2 = exp(-grij*grij);
- const double t = INV_EWALD_P / (INV_EWALD_P + grij);
- const double erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
- const double prefactor = qqrd2e * qtmp*q[j]/r;
- forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
- if (EFLAG) ecoul = prefactor*erfc;
- if (sbindex) {
- const double adjust = (1.0-special_coul[sbindex])*prefactor;
- forcecoul -= adjust;
- if (EFLAG) ecoul -= adjust;
- }
- } else {
- union_int_float_t rsq_lookup;
- rsq_lookup.f = rsq;
- const int itable = (rsq_lookup.i & ncoulmask) >> ncoulshiftbits;
- const double fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
- const double table = ftable[itable] + fraction*dftable[itable];
- forcecoul = qtmp*q[j] * table;
- if (EFLAG) ecoul = qtmp*q[j] * (etable[itable] + fraction*detable[itable]);
- if (sbindex) {
- const double table2 = ctable[itable] + fraction*dctable[itable];
- const double prefactor = qtmp*q[j] * table2;
- const double adjust = (1.0-special_coul[sbindex])*prefactor;
- forcecoul -= adjust;
- if (EFLAG) ecoul -= adjust;
- }
- }
- }
-
- if (rsq < cut_ljsq[itype][jtype]) {
-
- if (ljt == LJ12_4) {
- const double r4inv=r2inv*r2inv;
- forcelj = r4inv*(lj1[itype][jtype]*r4inv*r4inv
- - lj2[itype][jtype]);
-
- if (EFLAG)
- evdwl = r4inv*(lj3[itype][jtype]*r4inv*r4inv
- - lj4[itype][jtype]) - offset[itype][jtype];
-
- } else if (ljt == LJ9_6) {
- const double r3inv = r2inv*sqrt(r2inv);
- const double r6inv = r3inv*r3inv;
- forcelj = r6inv*(lj1[itype][jtype]*r3inv
- - lj2[itype][jtype]);
- if (EFLAG)
- evdwl = r6inv*(lj3[itype][jtype]*r3inv
- - lj4[itype][jtype]) - offset[itype][jtype];
-
- } else if (ljt == LJ12_6) {
- const double r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv*(lj1[itype][jtype]*r6inv
- - lj2[itype][jtype]);
- if (EFLAG)
- evdwl = r6inv*(lj3[itype][jtype]*r6inv
- - lj4[itype][jtype]) - offset[itype][jtype];
- }
-
- if (sbindex) {
- const double factor_lj = special_lj[sbindex];
- forcelj *= factor_lj;
- if (EFLAG) evdwl *= factor_lj;
- }
-
- }
-
- const double fpair = (forcecoul + forcelj) * r2inv;
-
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
- evdwl,ecoul,fpair,delx,dely,delz,thr);
+ const double r2inv = 1.0/rsq;
+ const int ljt = lj_type[itype][jtype];
+
+ if (rsq < cut_coulsq) {
+ if (!ncoultablebits || rsq <= tabinnersq) {
+ const double A1 = 0.254829592;
+ const double A2 = -0.284496736;
+ const double A3 = 1.421413741;
+ const double A4 = -1.453152027;
+ const double A5 = 1.061405429;
+ const double EWALD_F = 1.12837917;
+ const double INV_EWALD_P = 1.0/0.3275911;
+
+ const double r = sqrt(rsq);
+ const double grij = g_ewald * r;
+ const double expm2 = exp(-grij*grij);
+ const double t = INV_EWALD_P / (INV_EWALD_P + grij);
+ const double erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
+ const double prefactor = qqrd2e * qtmp*q[j]/r;
+ forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
+ if (EFLAG) ecoul = prefactor*erfc;
+ if (sbindex) {
+ const double adjust = (1.0-special_coul[sbindex])*prefactor;
+ forcecoul -= adjust;
+ if (EFLAG) ecoul -= adjust;
+ }
+ } else {
+ union_int_float_t rsq_lookup;
+ rsq_lookup.f = rsq;
+ const int itable = (rsq_lookup.i & ncoulmask) >> ncoulshiftbits;
+ const double fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
+ const double table = ftable[itable] + fraction*dftable[itable];
+ forcecoul = qtmp*q[j] * table;
+ if (EFLAG) ecoul = qtmp*q[j] * (etable[itable] + fraction*detable[itable]);
+ if (sbindex) {
+ const double table2 = ctable[itable] + fraction*dctable[itable];
+ const double prefactor = qtmp*q[j] * table2;
+ const double adjust = (1.0-special_coul[sbindex])*prefactor;
+ forcecoul -= adjust;
+ if (EFLAG) ecoul -= adjust;
+ }
+ }
+ }
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+
+ if (ljt == LJ12_4) {
+ const double r4inv=r2inv*r2inv;
+ forcelj = r4inv*(lj1[itype][jtype]*r4inv*r4inv
+ - lj2[itype][jtype]);
+
+ if (EFLAG)
+ evdwl = r4inv*(lj3[itype][jtype]*r4inv*r4inv
+ - lj4[itype][jtype]) - offset[itype][jtype];
+
+ } else if (ljt == LJ9_6) {
+ const double r3inv = r2inv*sqrt(r2inv);
+ const double r6inv = r3inv*r3inv;
+ forcelj = r6inv*(lj1[itype][jtype]*r3inv
+ - lj2[itype][jtype]);
+ if (EFLAG)
+ evdwl = r6inv*(lj3[itype][jtype]*r3inv
+ - lj4[itype][jtype]) - offset[itype][jtype];
+
+ } else if (ljt == LJ12_6) {
+ const double r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv*(lj1[itype][jtype]*r6inv
+ - lj2[itype][jtype]);
+ if (EFLAG)
+ evdwl = r6inv*(lj3[itype][jtype]*r6inv
+ - lj4[itype][jtype]) - offset[itype][jtype];
+ }
+
+ if (sbindex) {
+ const double factor_lj = special_lj[sbindex];
+ forcelj *= factor_lj;
+ if (EFLAG) evdwl *= factor_lj;
+ }
+
+ }
+
+ const double fpair = (forcecoul + forcelj) * r2inv;
+
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
+ evdwl,ecoul,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_lj_sdk_coul_long_omp.h b/src/USER-OMP/pair_lj_sdk_coul_long_omp.h
index 01912535b1d4282dcd81049fe7623fac7444f212..a615efb5071899529063bbe780899732c3aff2b5 100644
--- a/src/USER-OMP/pair_lj_sdk_coul_long_omp.h
+++ b/src/USER-OMP/pair_lj_sdk_coul_long_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_lj_sdk_omp.cpp b/src/USER-OMP/pair_lj_sdk_omp.cpp
index 127ff41c86886eb97f7d404ae057423f2e34dce0..63b1a8c171f9e79eba2a9f19e934d0794fcc7499 100644
--- a/src/USER-OMP/pair_lj_sdk_omp.cpp
+++ b/src/USER-OMP/pair_lj_sdk_omp.cpp
@@ -60,11 +60,11 @@ void PairLJSDKOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval_thr<1,1,1>(ifrom, ito, thr);
- else eval_thr<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval_thr<1,1,1>(ifrom, ito, thr);
+ else eval_thr<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval_thr<1,0,1>(ifrom, ito, thr);
- else eval_thr<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval_thr<1,0,1>(ifrom, ito, thr);
+ else eval_thr<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval_thr<0,0,1>(ifrom, ito, thr);
@@ -123,50 +123,50 @@ void PairLJSDKOMP::eval_thr(int iifrom, int iito, ThrData * const thr)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- const int ljt = lj_type[itype][jtype];
-
- if (ljt == LJ12_4) {
- const double r4inv=r2inv*r2inv;
- forcelj = r4inv*(lj1[itype][jtype]*r4inv*r4inv
- - lj2[itype][jtype]);
-
- if (EFLAG)
- evdwl = r4inv*(lj3[itype][jtype]*r4inv*r4inv
- - lj4[itype][jtype]) - offset[itype][jtype];
-
- } else if (ljt == LJ9_6) {
- const double r3inv = r2inv*sqrt(r2inv);
- const double r6inv = r3inv*r3inv;
- forcelj = r6inv*(lj1[itype][jtype]*r3inv
- - lj2[itype][jtype]);
- if (EFLAG)
- evdwl = r6inv*(lj3[itype][jtype]*r3inv
- - lj4[itype][jtype]) - offset[itype][jtype];
-
- } else if (ljt == LJ12_6) {
- const double r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv*(lj1[itype][jtype]*r6inv
- - lj2[itype][jtype]);
- if (EFLAG)
- evdwl = r6inv*(lj3[itype][jtype]*r6inv
- - lj4[itype][jtype]) - offset[itype][jtype];
- } else continue;
-
- fpair = factor_lj*forcelj*r2inv;
-
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (EFLAG) evdwl *= factor_lj;
- if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
- evdwl,0.0,fpair,delx,dely,delz,thr);
+ r2inv = 1.0/rsq;
+ const int ljt = lj_type[itype][jtype];
+
+ if (ljt == LJ12_4) {
+ const double r4inv=r2inv*r2inv;
+ forcelj = r4inv*(lj1[itype][jtype]*r4inv*r4inv
+ - lj2[itype][jtype]);
+
+ if (EFLAG)
+ evdwl = r4inv*(lj3[itype][jtype]*r4inv*r4inv
+ - lj4[itype][jtype]) - offset[itype][jtype];
+
+ } else if (ljt == LJ9_6) {
+ const double r3inv = r2inv*sqrt(r2inv);
+ const double r6inv = r3inv*r3inv;
+ forcelj = r6inv*(lj1[itype][jtype]*r3inv
+ - lj2[itype][jtype]);
+ if (EFLAG)
+ evdwl = r6inv*(lj3[itype][jtype]*r3inv
+ - lj4[itype][jtype]) - offset[itype][jtype];
+
+ } else if (ljt == LJ12_6) {
+ const double r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv*(lj1[itype][jtype]*r6inv
+ - lj2[itype][jtype]);
+ if (EFLAG)
+ evdwl = r6inv*(lj3[itype][jtype]*r6inv
+ - lj4[itype][jtype]) - offset[itype][jtype];
+ } else continue;
+
+ fpair = factor_lj*forcelj*r2inv;
+
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (EFLAG) evdwl *= factor_lj;
+ if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
+ evdwl,0.0,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_lj_sdk_omp.h b/src/USER-OMP/pair_lj_sdk_omp.h
index f2c9e5ff1fd6521b476f50fcf3bd8d0903d7d615..c3837fb683c0b71d6378b6234c36074406b73f12 100644
--- a/src/USER-OMP/pair_lj_sdk_omp.h
+++ b/src/USER-OMP/pair_lj_sdk_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_lj_sf_omp.cpp b/src/USER-OMP/pair_lj_sf_omp.cpp
index b2314e13be01bc2d21a6af86d1b64c3b88adf43c..5c14e2913119206f99815571023fb56a521354d9 100644
--- a/src/USER-OMP/pair_lj_sf_omp.cpp
+++ b/src/USER-OMP/pair_lj_sf_omp.cpp
@@ -56,11 +56,11 @@ void PairLJShiftedForceOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -117,31 +117,31 @@ void PairLJShiftedForceOMP::eval(int iifrom, int iito, ThrData * const thr)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
- t = sqrt(r2inv*cutsq[itype][jtype]);
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]) -
- t*foffset[itype][jtype];
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- fpair = factor_lj*forcelj*r2inv;
-
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (EFLAG) {
- evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) +
- (t-1.0)*foffset[itype][jtype] - offset[itype][jtype];
- evdwl *= factor_lj;
- }
-
- if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
- evdwl,0.0,fpair,delx,dely,delz,thr);
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
+ t = sqrt(r2inv*cutsq[itype][jtype]);
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]) -
+ t*foffset[itype][jtype];
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ fpair = factor_lj*forcelj*r2inv;
+
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (EFLAG) {
+ evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) +
+ (t-1.0)*foffset[itype][jtype] - offset[itype][jtype];
+ evdwl *= factor_lj;
+ }
+
+ if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
+ evdwl,0.0,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_lj_sf_omp.h b/src/USER-OMP/pair_lj_sf_omp.h
index c73c8f746b855c26d4d7af8a0c478f305948a120..92db973b3de96031a1c17c5c0470fea1f9e0670a 100644
--- a/src/USER-OMP/pair_lj_sf_omp.h
+++ b/src/USER-OMP/pair_lj_sf_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_lj_smooth_linear_omp.cpp b/src/USER-OMP/pair_lj_smooth_linear_omp.cpp
index 8fd4a259ed332d839554b431fbb6135893f38eea..a8f3ad8daa587edfccdea8cc72da1c8bf7ac5a02 100644
--- a/src/USER-OMP/pair_lj_smooth_linear_omp.cpp
+++ b/src/USER-OMP/pair_lj_smooth_linear_omp.cpp
@@ -56,11 +56,11 @@ void PairLJSmoothLinearOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -118,32 +118,32 @@ void PairLJSmoothLinearOMP::eval(int iifrom, int iito, ThrData * const thr)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
rinv = sqrt(r2inv);
- forcelj = r6inv*(lj1[itype][jtype]*r6inv-lj2[itype][jtype]);
- forcelj = rinv*forcelj - dljcut[itype][jtype];
-
- fpair = factor_lj*forcelj*rinv;
-
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (EFLAG) {
+ forcelj = r6inv*(lj1[itype][jtype]*r6inv-lj2[itype][jtype]);
+ forcelj = rinv*forcelj - dljcut[itype][jtype];
+
+ fpair = factor_lj*forcelj*rinv;
+
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (EFLAG) {
r = sqrt(rsq);
- evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
+ evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
evdwl = evdwl - ljcut[itype][jtype]
- + (r-cut[itype][jtype])*dljcut[itype][jtype];
- }
+ + (r-cut[itype][jtype])*dljcut[itype][jtype];
+ }
- if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
- evdwl,0.0,fpair,delx,dely,delz,thr);
+ if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
+ evdwl,0.0,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_lj_smooth_linear_omp.h b/src/USER-OMP/pair_lj_smooth_linear_omp.h
index 1c3b861ca01e3437174f18af22b0403d1eab217d..940c0ea707e36ed460be359a86d5d175c6272015 100644
--- a/src/USER-OMP/pair_lj_smooth_linear_omp.h
+++ b/src/USER-OMP/pair_lj_smooth_linear_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_lj_smooth_omp.cpp b/src/USER-OMP/pair_lj_smooth_omp.cpp
index 1595d077129545fa1246c37673dc679fd776fdc3..b1918c3fcd250ec0e83fe1b9d2969011ed38748a 100644
--- a/src/USER-OMP/pair_lj_smooth_omp.cpp
+++ b/src/USER-OMP/pair_lj_smooth_omp.cpp
@@ -56,11 +56,11 @@ void PairLJSmoothOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -118,43 +118,43 @@ void PairLJSmoothOMP::eval(int iifrom, int iito, ThrData * const thr)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- if (rsq < cut_inner_sq[itype][jtype]) {
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (lj1[itype][jtype]*r6inv-lj2[itype][jtype]);
- } else {
- r = sqrt(rsq);
- t = r - cut_inner[itype][jtype];
- tsq = t*t;
- fskin = ljsw1[itype][jtype] + ljsw2[itype][jtype]*t +
- ljsw3[itype][jtype]*tsq + ljsw4[itype][jtype]*tsq*t;
- forcelj = fskin*r;
- }
-
- fpair = factor_lj*forcelj*r2inv;
-
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (EFLAG) {
- if (rsq < cut_inner_sq[itype][jtype])
- evdwl = r6inv * (lj3[itype][jtype]*r6inv -
- lj4[itype][jtype]) - offset[itype][jtype];
- else
- evdwl = ljsw0[itype][jtype] - ljsw1[itype][jtype]*t -
- ljsw2[itype][jtype]*tsq/2.0 - ljsw3[itype][jtype]*tsq*t/3.0 -
- ljsw4[itype][jtype]*tsq*tsq/4.0 - offset[itype][jtype];
- evdwl *= factor_lj;
- }
-
- if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
- evdwl,0.0,fpair,delx,dely,delz,thr);
+ r2inv = 1.0/rsq;
+ if (rsq < cut_inner_sq[itype][jtype]) {
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv-lj2[itype][jtype]);
+ } else {
+ r = sqrt(rsq);
+ t = r - cut_inner[itype][jtype];
+ tsq = t*t;
+ fskin = ljsw1[itype][jtype] + ljsw2[itype][jtype]*t +
+ ljsw3[itype][jtype]*tsq + ljsw4[itype][jtype]*tsq*t;
+ forcelj = fskin*r;
+ }
+
+ fpair = factor_lj*forcelj*r2inv;
+
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (EFLAG) {
+ if (rsq < cut_inner_sq[itype][jtype])
+ evdwl = r6inv * (lj3[itype][jtype]*r6inv -
+ lj4[itype][jtype]) - offset[itype][jtype];
+ else
+ evdwl = ljsw0[itype][jtype] - ljsw1[itype][jtype]*t -
+ ljsw2[itype][jtype]*tsq/2.0 - ljsw3[itype][jtype]*tsq*t/3.0 -
+ ljsw4[itype][jtype]*tsq*tsq/4.0 - offset[itype][jtype];
+ evdwl *= factor_lj;
+ }
+
+ if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
+ evdwl,0.0,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_lj_smooth_omp.h b/src/USER-OMP/pair_lj_smooth_omp.h
index eb6eb92decaf544bf72338a1d9f556bb8c6eb453..0b47a792a480ab252145b4a05836eddd752efc49 100644
--- a/src/USER-OMP/pair_lj_smooth_omp.h
+++ b/src/USER-OMP/pair_lj_smooth_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_lubricate_omp.cpp b/src/USER-OMP/pair_lubricate_omp.cpp
index 00a81f345b357c2c820abbcdfa40490a95f12647..22090b297823dade7bb63ad148ae971995183dc8 100644
--- a/src/USER-OMP/pair_lubricate_omp.cpp
+++ b/src/USER-OMP/pair_lubricate_omp.cpp
@@ -51,7 +51,7 @@ PairLubricateOMP::PairLubricateOMP(LAMMPS *lmp) :
/* ---------------------------------------------------------------------- */
-PairLubricateOMP::~PairLubricateOMP()
+PairLubricateOMP::~PairLubricateOMP()
{}
/* ---------------------------------------------------------------------- */
@@ -66,7 +66,7 @@ void PairLubricateOMP::compute(int eflag, int vflag)
const int nthreads = comm->nthreads;
const int inum = list->inum;
-
+
// This section of code adjusts R0/RT0/RS0 if necessary due to changes
// in the volume fraction as a result of fix deform or moving walls
@@ -74,45 +74,45 @@ void PairLubricateOMP::compute(int eflag, int vflag)
if (flagVF) // Flag for volume fraction corrections
if (flagdeform || flagwall == 2){ // Possible changes in volume fraction
if (flagdeform && !flagwall)
- for (int j = 0; j < 3; j++)
- dims[j] = domain->prd[j];
+ for (int j = 0; j < 3; j++)
+ dims[j] = domain->prd[j];
else if (flagwall == 2 || (flagdeform && flagwall == 1)){
- double wallhi[3], walllo[3];
- for (int j = 0; j < 3; j++){
- wallhi[j] = domain->prd[j];
- walllo[j] = 0;
- }
- for (int m = 0; m < wallfix->nwall; m++){
- int dim = wallfix->wallwhich[m] / 2;
- int side = wallfix->wallwhich[m] % 2;
- if (wallfix->wallstyle[m] == VARIABLE){
- wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
- }
- else wallcoord = wallfix->coord0[m];
- if (side == 0) walllo[dim] = wallcoord;
- else wallhi[dim] = wallcoord;
- }
- for (int j = 0; j < 3; j++)
- dims[j] = wallhi[j] - walllo[j];
+ double wallhi[3], walllo[3];
+ for (int j = 0; j < 3; j++){
+ wallhi[j] = domain->prd[j];
+ walllo[j] = 0;
+ }
+ for (int m = 0; m < wallfix->nwall; m++){
+ int dim = wallfix->wallwhich[m] / 2;
+ int side = wallfix->wallwhich[m] % 2;
+ if (wallfix->wallstyle[m] == VARIABLE){
+ wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
+ }
+ else wallcoord = wallfix->coord0[m];
+ if (side == 0) walllo[dim] = wallcoord;
+ else wallhi[dim] = wallcoord;
+ }
+ for (int j = 0; j < 3; j++)
+ dims[j] = wallhi[j] - walllo[j];
}
double vol_T = dims[0]*dims[1]*dims[2];
double vol_f = vol_P/vol_T;
if (flaglog == 0) {
- R0 = 6*MY_PI*mu*rad*(1.0 + 2.16*vol_f);
- RT0 = 8*MY_PI*mu*pow(rad,3.0);
- RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3.0)*
- (1.0 + 3.33*vol_f + 2.80*vol_f*vol_f);
+ R0 = 6*MY_PI*mu*rad*(1.0 + 2.16*vol_f);
+ RT0 = 8*MY_PI*mu*pow(rad,3.0);
+ RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3.0)*
+ (1.0 + 3.33*vol_f + 2.80*vol_f*vol_f);
} else {
- R0 = 6*MY_PI*mu*rad*(1.0 + 2.725*vol_f - 6.583*vol_f*vol_f);
- RT0 = 8*MY_PI*mu*pow(rad,3.0)*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
- RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3.0)*
- (1.0 + 3.64*vol_f - 6.95*vol_f*vol_f);
+ R0 = 6*MY_PI*mu*rad*(1.0 + 2.725*vol_f - 6.583*vol_f*vol_f);
+ RT0 = 8*MY_PI*mu*pow(rad,3.0)*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
+ RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3.0)*
+ (1.0 + 3.64*vol_f - 6.95*vol_f*vol_f);
}
}
-
+
// end of R0 adjustment code
-
+
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(eflag,vflag)
@@ -126,19 +126,19 @@ void PairLubricateOMP::compute(int eflag, int vflag)
if (flaglog) {
if (evflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
- } else {
+ } else {
if (evflag) {
- if (force->newton_pair) eval<0,1,1>(ifrom, ito, thr);
- else eval<0,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<0,1,1>(ifrom, ito, thr);
+ else eval<0,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
- else eval<0,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
+ else eval<0,0,0>(ifrom, ito, thr);
}
}
@@ -153,7 +153,7 @@ void PairLubricateOMP::eval(int iifrom, int iito, ThrData * const thr)
double xtmp,ytmp,ztmp,delx,dely,delz,fx,fy,fz,tx,ty,tz;
double rsq,r,h_sep,radi;
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3;
- double vt1,vt2,vt3,wt1,wt2,wt3,wdotn;
+ double vt1,vt2,vt3,wt1,wt2,wt3,wdotn;
double vRS0;
double vi[3],vj[3],wi[3],wj[3],xl[3];
double a_sq,a_sh,a_pu;
@@ -195,10 +195,10 @@ void PairLubricateOMP::eval(int iifrom, int iito, ThrData * const thr)
i = ilist[ii];
itype = type[i];
radi = radius[i];
-
+
domain->x2lamda(x[i],lamda);
- vstream[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
- h_rate[4]*lamda[2] + h_ratelo[0];
+ vstream[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
+ h_rate[4]*lamda[2] + h_ratelo[0];
vstream[1] = h_rate[1]*lamda[1] + h_rate[3]*lamda[2] + h_ratelo[1];
vstream[2] = h_rate[2]*lamda[2] + h_ratelo[2];
v[i][0] -= vstream[0];
@@ -214,7 +214,7 @@ void PairLubricateOMP::eval(int iifrom, int iito, ThrData * const thr)
Ef[0][0] = h_rate[0]/domain->xprd;
Ef[1][1] = h_rate[1]/domain->yprd;
- Ef[2][2] = h_rate[2]/domain->zprd;
+ Ef[2][2] = h_rate[2]/domain->zprd;
Ef[0][1] = Ef[1][0] = 0.5 * h_rate[5]/domain->yprd;
Ef[0][2] = Ef[2][0] = 0.5 * h_rate[4]/domain->zprd;
Ef[1][2] = Ef[2][1] = 0.5 * h_rate[3]/domain->zprd;
@@ -244,29 +244,29 @@ void PairLubricateOMP::eval(int iifrom, int iito, ThrData * const thr)
radi = radius[i];
jlist = firstneigh[i];
jnum = numneigh[i];
-
+
// angular velocity
wi[0] = omega[i][0];
wi[1] = omega[i][1];
- wi[2] = omega[i][2];
-
+ wi[2] = omega[i][2];
+
// FLD contribution to force and torque due to isotropic terms
// FLD contribution to stress from isotropic RS0
if (flagfld) {
f[i][0] -= vxmu2f*R0*v[i][0];
f[i][1] -= vxmu2f*R0*v[i][1];
- f[i][2] -= vxmu2f*R0*v[i][2];
+ f[i][2] -= vxmu2f*R0*v[i][2];
torque[i][0] -= vxmu2f*RT0*wi[0];
torque[i][1] -= vxmu2f*RT0*wi[1];
- torque[i][2] -= vxmu2f*RT0*wi[2];
+ torque[i][2] -= vxmu2f*RT0*wi[2];
if (shearing && vflag_either) {
- vRS0 = -vxmu2f * RS0;
- v_tally_tensor(i,i,nlocal,NEWTON_PAIR,
- vRS0*Ef[0][0],vRS0*Ef[1][1],vRS0*Ef[2][2],
- vRS0*Ef[0][1],vRS0*Ef[0][2],vRS0*Ef[1][2]);
+ vRS0 = -vxmu2f * RS0;
+ v_tally_tensor(i,i,nlocal,NEWTON_PAIR,
+ vRS0*Ef[0][0],vRS0*Ef[1][1],vRS0*Ef[2][2],
+ vRS0*Ef[0][1],vRS0*Ef[0][2],vRS0*Ef[1][2]);
}
}
@@ -283,20 +283,20 @@ void PairLubricateOMP::eval(int iifrom, int iito, ThrData * const thr)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r = sqrt(rsq);
-
+ r = sqrt(rsq);
+
// angular momentum = I*omega = 2/5 * M*R^2 * omega
-
- wj[0] = omega[j][0];
- wj[1] = omega[j][1];
- wj[2] = omega[j][2];
+
+ wj[0] = omega[j][0];
+ wj[1] = omega[j][1];
+ wj[2] = omega[j][2];
// xl = point of closest approach on particle i from its center
xl[0] = -delx/r*radi;
xl[1] = -dely/r*radi;
xl[2] = -delz/r*radi;
-
+
// velocity at the point of closest approach on both particles
// v = v + omega_cross_xl - Ef.xl
@@ -304,41 +304,41 @@ void PairLubricateOMP::eval(int iifrom, int iito, ThrData * const thr)
vi[0] = v[i][0] + (wi[1]*xl[2] - wi[2]*xl[1])
- (Ef[0][0]*xl[0] + Ef[0][1]*xl[1] + Ef[0][2]*xl[2]);
-
+
vi[1] = v[i][1] + (wi[2]*xl[0] - wi[0]*xl[2])
- (Ef[1][0]*xl[0] + Ef[1][1]*xl[1] + Ef[1][2]*xl[2]);
-
+
vi[2] = v[i][2] + (wi[0]*xl[1] - wi[1]*xl[0])
- (Ef[2][0]*xl[0] + Ef[2][1]*xl[1] + Ef[2][2]*xl[2]);
-
+
// particle j
vj[0] = v[j][0] - (wj[1]*xl[2] - wj[2]*xl[1])
+ (Ef[0][0]*xl[0] + Ef[0][1]*xl[1] + Ef[0][2]*xl[2]);
-
+
vj[1] = v[j][1] - (wj[2]*xl[0] - wj[0]*xl[2])
+ (Ef[1][0]*xl[0] + Ef[1][1]*xl[1] + Ef[1][2]*xl[2]);
-
+
vj[2] = v[j][2] - (wj[0]*xl[1] - wj[1]*xl[0])
+ (Ef[2][0]*xl[0] + Ef[2][1]*xl[1] + Ef[2][2]*xl[2]);
-
+
// scalar resistances XA and YA
h_sep = r - 2.0*radi;
-
+
// check for overlaps
if (h_sep < 0.0) overlaps++;
-
+
// if less than the minimum gap use the minimum gap instead
if (r < cut_inner[itype][jtype])
- h_sep = cut_inner[itype][jtype] - 2.0*radi;
-
+ h_sep = cut_inner[itype][jtype] - 2.0*radi;
+
// scale h_sep by radi
h_sep = h_sep/radi;
-
+
// scalar resistances
if (FLAGLOG) {
@@ -347,14 +347,14 @@ void PairLubricateOMP::eval(int iifrom, int iito, ThrData * const thr)
a_pu = 8.0*MY_PI*mu*pow(radi,3.0)*(3.0/160.0*log(1.0/h_sep));
} else
a_sq = 6.0*MY_PI*mu*radi*(1.0/4.0/h_sep);
-
+
// relative velocity at the point of closest approach
- // includes fluid velocity
+ // includes fluid velocity
vr1 = vi[0] - vj[0];
vr2 = vi[1] - vj[1];
vr3 = vi[2] - vj[2];
-
+
// normal component (vr.n)n
vnnr = (vr1*delx + vr2*dely + vr3*delz)/r;
@@ -379,7 +379,7 @@ void PairLubricateOMP::eval(int iifrom, int iito, ThrData * const thr)
if (FLAGLOG) {
fx = fx + a_sh*vt1;
fy = fy + a_sh*vt2;
- fz = fz + a_sh*vt3;
+ fz = fz + a_sh*vt3;
}
// scale forces for appropriate units
@@ -387,65 +387,65 @@ void PairLubricateOMP::eval(int iifrom, int iito, ThrData * const thr)
fx *= vxmu2f;
fy *= vxmu2f;
fz *= vxmu2f;
-
+
// add to total force
f[i][0] -= fx;
f[i][1] -= fy;
- f[i][2] -= fz;
-
+ f[i][2] -= fz;
+
if (NEWTON_PAIR || j < nlocal) {
f[j][0] += fx;
f[j][1] += fy;
- f[j][2] += fz;
+ f[j][2] += fz;
}
-
+
// torque due to this force
if (FLAGLOG) {
tx = xl[1]*fz - xl[2]*fy;
ty = xl[2]*fx - xl[0]*fz;
- tz = xl[0]*fy - xl[1]*fx;
-
+ tz = xl[0]*fy - xl[1]*fx;
+
torque[i][0] -= vxmu2f*tx;
torque[i][1] -= vxmu2f*ty;
- torque[i][2] -= vxmu2f*tz;
-
+ torque[i][2] -= vxmu2f*tz;
+
if (NEWTON_PAIR || j < nlocal) {
torque[j][0] -= vxmu2f*tx;
torque[j][1] -= vxmu2f*ty;
torque[j][2] -= vxmu2f*tz;
}
-
+
// torque due to a_pu
- wdotn = ((wi[0]-wj[0])*delx + (wi[1]-wj[1])*dely +
- (wi[2]-wj[2])*delz)/r;
+ wdotn = ((wi[0]-wj[0])*delx + (wi[1]-wj[1])*dely +
+ (wi[2]-wj[2])*delz)/r;
wt1 = (wi[0]-wj[0]) - wdotn*delx/r;
wt2 = (wi[1]-wj[1]) - wdotn*dely/r;
wt3 = (wi[2]-wj[2]) - wdotn*delz/r;
-
+
tx = a_pu*wt1;
ty = a_pu*wt2;
tz = a_pu*wt3;
-
+
torque[i][0] -= vxmu2f*tx;
torque[i][1] -= vxmu2f*ty;
- torque[i][2] -= vxmu2f*tz;
-
+ torque[i][2] -= vxmu2f*tz;
+
if (NEWTON_PAIR || j < nlocal) {
torque[j][0] += vxmu2f*tx;
torque[j][1] += vxmu2f*ty;
torque[j][2] += vxmu2f*tz;
}
- }
+ }
if (EVFLAG) ev_tally_xyz_thr(this,i,j,nlocal,NEWTON_PAIR,0.0,0.0,
- -fx,-fy,-fz,delx,dely,delz,thr);
+ -fx,-fy,-fz,delx,dely,delz,thr);
}
}
}
-
+
// restore streaming component of velocity, omega, angmom
if (shearing) {
@@ -456,10 +456,10 @@ void PairLubricateOMP::eval(int iifrom, int iito, ThrData * const thr)
i = ilist[ii];
itype = type[i];
radi = radius[i];
-
+
domain->x2lamda(x[i],lamda);
- vstream[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
- h_rate[4]*lamda[2] + h_ratelo[0];
+ vstream[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
+ h_rate[4]*lamda[2] + h_ratelo[0];
vstream[1] = h_rate[1]*lamda[1] + h_rate[3]*lamda[2] + h_ratelo[1];
vstream[2] = h_rate[2]*lamda[2] + h_ratelo[2];
v[i][0] += vstream[0];
diff --git a/src/USER-OMP/pair_lubricate_omp.h b/src/USER-OMP/pair_lubricate_omp.h
index 045421e566f336913e6b367bc5c21c30d51daf21..b35dc5d563efd6675fede2e27207a6e2b68add27 100644
--- a/src/USER-OMP/pair_lubricate_omp.h
+++ b/src/USER-OMP/pair_lubricate_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_lubricate_poly_omp.cpp b/src/USER-OMP/pair_lubricate_poly_omp.cpp
index 306c3f9bdf1d8d38b3afe7c612a49c4633447807..26339b774920fe426d2b614163df6799fe56b88d 100644
--- a/src/USER-OMP/pair_lubricate_poly_omp.cpp
+++ b/src/USER-OMP/pair_lubricate_poly_omp.cpp
@@ -52,7 +52,7 @@ PairLubricatePolyOMP::PairLubricatePolyOMP(LAMMPS *lmp) :
/* ---------------------------------------------------------------------- */
-PairLubricatePolyOMP::~PairLubricatePolyOMP()
+PairLubricatePolyOMP::~PairLubricatePolyOMP()
{}
/* ---------------------------------------------------------------------- */
@@ -75,41 +75,41 @@ void PairLubricatePolyOMP::compute(int eflag, int vflag)
if (flagVF) // Flag for volume fraction corrections
if (flagdeform || flagwall == 2){ // Possible changes in volume fraction
if (flagdeform && !flagwall)
- for (int j = 0; j < 3; j++)
- dims[j] = domain->prd[j];
+ for (int j = 0; j < 3; j++)
+ dims[j] = domain->prd[j];
else if (flagwall == 2 || (flagdeform && flagwall == 1)){
- double wallhi[3], walllo[3];
- for (int j = 0; j < 3; j++){
- wallhi[j] = domain->prd[j];
- walllo[j] = 0;
- }
- for (int m = 0; m < wallfix->nwall; m++){
- int dim = wallfix->wallwhich[m] / 2;
- int side = wallfix->wallwhich[m] % 2;
- if (wallfix->wallstyle[m] == VARIABLE){
- wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
- }
- else wallcoord = wallfix->coord0[m];
- if (side == 0) walllo[dim] = wallcoord;
- else wallhi[dim] = wallcoord;
- }
- for (int j = 0; j < 3; j++)
- dims[j] = wallhi[j] - walllo[j];
+ double wallhi[3], walllo[3];
+ for (int j = 0; j < 3; j++){
+ wallhi[j] = domain->prd[j];
+ walllo[j] = 0;
+ }
+ for (int m = 0; m < wallfix->nwall; m++){
+ int dim = wallfix->wallwhich[m] / 2;
+ int side = wallfix->wallwhich[m] % 2;
+ if (wallfix->wallstyle[m] == VARIABLE){
+ wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
+ }
+ else wallcoord = wallfix->coord0[m];
+ if (side == 0) walllo[dim] = wallcoord;
+ else wallhi[dim] = wallcoord;
+ }
+ for (int j = 0; j < 3; j++)
+ dims[j] = wallhi[j] - walllo[j];
}
double vol_T = dims[0]*dims[1]*dims[2];
double vol_f = vol_P/vol_T;
if (flaglog == 0) {
- R0 = 6*MY_PI*mu*(1.0 + 2.16*vol_f);
- RT0 = 8*MY_PI*mu;
- RS0 = 20.0/3.0*MY_PI*mu*(1.0 + 3.33*vol_f + 2.80*vol_f*vol_f);
+ R0 = 6*MY_PI*mu*(1.0 + 2.16*vol_f);
+ RT0 = 8*MY_PI*mu;
+ RS0 = 20.0/3.0*MY_PI*mu*(1.0 + 3.33*vol_f + 2.80*vol_f*vol_f);
} else {
- R0 = 6*MY_PI*mu*(1.0 + 2.725*vol_f - 6.583*vol_f*vol_f);
- RT0 = 8*MY_PI*mu*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
- RS0 = 20.0/3.0*MY_PI*mu*(1.0 + 3.64*vol_f - 6.95*vol_f*vol_f);
+ R0 = 6*MY_PI*mu*(1.0 + 2.725*vol_f - 6.583*vol_f*vol_f);
+ RT0 = 8*MY_PI*mu*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
+ RS0 = 20.0/3.0*MY_PI*mu*(1.0 + 3.64*vol_f - 6.95*vol_f*vol_f);
}
}
- // end of R0 adjustment code
+ // end of R0 adjustment code
#if defined(_OPENMP)
@@ -124,23 +124,23 @@ void PairLubricatePolyOMP::compute(int eflag, int vflag)
if (flaglog) {
if (shearing) {
- if (evflag)
- eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (evflag)
+ eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (evflag)
- eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (evflag)
+ eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
- } else {
+ } else {
if (shearing) {
- if (evflag)
- eval<0,1,1>(ifrom, ito, thr);
- else eval<0,1,0>(ifrom, ito, thr);
+ if (evflag)
+ eval<0,1,1>(ifrom, ito, thr);
+ else eval<0,1,0>(ifrom, ito, thr);
} else {
- if (evflag)
- eval<0,0,1>(ifrom, ito, thr);
- else eval<0,0,0>(ifrom, ito, thr);
+ if (evflag)
+ eval<0,0,1>(ifrom, ito, thr);
+ else eval<0,0,0>(ifrom, ito, thr);
}
}
@@ -155,7 +155,7 @@ void PairLubricatePolyOMP::eval(int iifrom, int iito, ThrData * const thr)
double xtmp,ytmp,ztmp,delx,dely,delz,fx,fy,fz,tx,ty,tz;
double rsq,r,h_sep,beta0,beta1,radi,radj;
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3;
- double vt1,vt2,vt3,wt1,wt2,wt3,wdotn;
+ double vt1,vt2,vt3,wt1,wt2,wt3,wdotn;
double vRS0;
double vi[3],vj[3],wi[3],wj[3],xl[3],jl[3];
double a_sq,a_sh,a_pu;
@@ -198,8 +198,8 @@ void PairLubricatePolyOMP::eval(int iifrom, int iito, ThrData * const thr)
itype = type[i];
radi = radius[i];
domain->x2lamda(x[i],lamda);
- vstream[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
- h_rate[4]*lamda[2] + h_ratelo[0];
+ vstream[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
+ h_rate[4]*lamda[2] + h_ratelo[0];
vstream[1] = h_rate[1]*lamda[1] + h_rate[3]*lamda[2] + h_ratelo[1];
vstream[2] = h_rate[2]*lamda[2] + h_ratelo[2];
v[i][0] -= vstream[0];
@@ -215,7 +215,7 @@ void PairLubricatePolyOMP::eval(int iifrom, int iito, ThrData * const thr)
Ef[0][0] = h_rate[0]/domain->xprd;
Ef[1][1] = h_rate[1]/domain->yprd;
- Ef[2][2] = h_rate[2]/domain->zprd;
+ Ef[2][2] = h_rate[2]/domain->zprd;
Ef[0][1] = Ef[1][0] = 0.5 * h_rate[5]/domain->yprd;
Ef[0][2] = Ef[2][0] = 0.5 * h_rate[4]/domain->zprd;
Ef[1][2] = Ef[2][1] = 0.5 * h_rate[3]/domain->zprd;
@@ -245,13 +245,13 @@ void PairLubricatePolyOMP::eval(int iifrom, int iito, ThrData * const thr)
radi = radius[i];
jlist = firstneigh[i];
jnum = numneigh[i];
-
+
// angular velocity
wi[0] = omega[i][0];
wi[1] = omega[i][1];
- wi[2] = omega[i][2];
-
+ wi[2] = omega[i][2];
+
// FLD contribution to force and torque due to isotropic terms
// FLD contribution to stress from isotropic RS0
@@ -262,13 +262,13 @@ void PairLubricatePolyOMP::eval(int iifrom, int iito, ThrData * const thr)
const double rad3 = radi*radi*radi;
torque[i][0] -= vxmu2f*RT0*rad3*wi[0];
torque[i][1] -= vxmu2f*RT0*rad3*wi[1];
- torque[i][2] -= vxmu2f*RT0*rad3*wi[2];
-
+ torque[i][2] -= vxmu2f*RT0*rad3*wi[2];
+
if (SHEARING && vflag_either) {
- vRS0 = -vxmu2f * RS0*rad3;
- v_tally_tensor(i,i,nlocal,/* newton_pair */ 0,
- vRS0*Ef[0][0],vRS0*Ef[1][1],vRS0*Ef[2][2],
- vRS0*Ef[0][1],vRS0*Ef[0][2],vRS0*Ef[1][2]);
+ vRS0 = -vxmu2f * RS0*rad3;
+ v_tally_tensor(i,i,nlocal,/* newton_pair */ 0,
+ vRS0*Ef[0][0],vRS0*Ef[1][1],vRS0*Ef[2][2],
+ vRS0*Ef[0][1],vRS0*Ef[0][2],vRS0*Ef[1][2]);
}
}
@@ -286,13 +286,13 @@ void PairLubricatePolyOMP::eval(int iifrom, int iito, ThrData * const thr)
radj = atom->radius[j];
if (rsq < cutsq[itype][jtype]) {
- r = sqrt(rsq);
-
+ r = sqrt(rsq);
+
// angular momentum = I*omega = 2/5 * M*R^2 * omega
- wj[0] = omega[j][0];
- wj[1] = omega[j][1];
- wj[2] = omega[j][2];
+ wj[0] = omega[j][0];
+ wj[1] = omega[j][1];
+ wj[2] = omega[j][2];
// xl = point of closest approach on particle i from its center
@@ -302,7 +302,7 @@ void PairLubricatePolyOMP::eval(int iifrom, int iito, ThrData * const thr)
jl[0] = -delx/r*radj;
jl[1] = -dely/r*radj;
jl[2] = -delz/r*radj;
-
+
// velocity at the point of closest approach on both particles
// v = v + omega_cross_xl - Ef.xl
@@ -310,71 +310,71 @@ void PairLubricatePolyOMP::eval(int iifrom, int iito, ThrData * const thr)
vi[0] = v[i][0] + (wi[1]*xl[2] - wi[2]*xl[1])
- (Ef[0][0]*xl[0] + Ef[0][1]*xl[1] + Ef[0][2]*xl[2]);
-
+
vi[1] = v[i][1] + (wi[2]*xl[0] - wi[0]*xl[2])
- (Ef[1][0]*xl[0] + Ef[1][1]*xl[1] + Ef[1][2]*xl[2]);
-
+
vi[2] = v[i][2] + (wi[0]*xl[1] - wi[1]*xl[0])
- (Ef[2][0]*xl[0] + Ef[2][1]*xl[1] + Ef[2][2]*xl[2]);
-
+
// particle j
vj[0] = v[j][0] - (wj[1]*jl[2] - wj[2]*jl[1])
+ (Ef[0][0]*jl[0] + Ef[0][1]*jl[1] + Ef[0][2]*jl[2]);
-
+
vj[1] = v[j][1] - (wj[2]*jl[0] - wj[0]*jl[2])
+ (Ef[1][0]*jl[0] + Ef[1][1]*jl[1] + Ef[1][2]*jl[2]);
-
+
vj[2] = v[j][2] - (wj[0]*jl[1] - wj[1]*jl[0])
+ (Ef[2][0]*jl[0] + Ef[2][1]*jl[1] + Ef[2][2]*jl[2]);
-
+
// scalar resistances XA and YA
h_sep = r - radi-radj;
-
+
// check for overlaps
if (h_sep < 0.0) overlaps++;
-
+
// if less than the minimum gap use the minimum gap instead
if (r < cut_inner[itype][jtype])
- h_sep = cut_inner[itype][jtype] - radi-radj;
-
+ h_sep = cut_inner[itype][jtype] - radi-radj;
+
// scale h_sep by radi
h_sep = h_sep/radi;
beta0 = radj/radi;
beta1 = 1.0 + beta0;
-
+
// scalar resistances
if (FLAGLOG) {
- a_sq = beta0*beta0/beta1/beta1/h_sep +
- (1.0+7.0*beta0+beta0*beta0)/5.0/pow(beta1,3.0)*log(1.0/h_sep);
- a_sq += (1.0+18.0*beta0-29.0*beta0*beta0+18.0 *
- pow(beta0,3.0)+pow(beta0,4.0))/21.0/pow(beta1,4.0) *
- h_sep*log(1.0/h_sep);
+ a_sq = beta0*beta0/beta1/beta1/h_sep +
+ (1.0+7.0*beta0+beta0*beta0)/5.0/pow(beta1,3.0)*log(1.0/h_sep);
+ a_sq += (1.0+18.0*beta0-29.0*beta0*beta0+18.0 *
+ pow(beta0,3.0)+pow(beta0,4.0))/21.0/pow(beta1,4.0) *
+ h_sep*log(1.0/h_sep);
a_sq *= 6.0*MY_PI*mu*radi;
- a_sh = 4.0*beta0*(2.0+beta0+2.0*beta0*beta0)/15.0/pow(beta1,3.0) *
- log(1.0/h_sep);
- a_sh += 4.0*(16.0-45.0*beta0+58.0*beta0*beta0-45.0*pow(beta0,3.0) +
- 16.0*pow(beta0,4.0))/375.0/pow(beta1,4.0) *
- h_sep*log(1.0/h_sep);
+ a_sh = 4.0*beta0*(2.0+beta0+2.0*beta0*beta0)/15.0/pow(beta1,3.0) *
+ log(1.0/h_sep);
+ a_sh += 4.0*(16.0-45.0*beta0+58.0*beta0*beta0-45.0*pow(beta0,3.0) +
+ 16.0*pow(beta0,4.0))/375.0/pow(beta1,4.0) *
+ h_sep*log(1.0/h_sep);
a_sh *= 6.0*MY_PI*mu*radi;
a_pu = beta0*(4.0+beta0)/10.0/beta1/beta1*log(1.0/h_sep);
- a_pu += (32.0-33.0*beta0+83.0*beta0*beta0+43.0 *
- pow(beta0,3.0))/250.0/pow(beta1,3.0)*h_sep*log(1.0/h_sep);
+ a_pu += (32.0-33.0*beta0+83.0*beta0*beta0+43.0 *
+ pow(beta0,3.0))/250.0/pow(beta1,3.0)*h_sep*log(1.0/h_sep);
a_pu *= 8.0*MY_PI*mu*pow(radi,3.0);
} else a_sq = 6.0*MY_PI*mu*radi*(beta0*beta0/beta1/beta1/h_sep);
-
+
// relative velocity at the point of closest approach
- // includes fluid velocity
+ // includes fluid velocity
vr1 = vi[0] - vj[0];
vr2 = vi[1] - vj[1];
vr3 = vi[2] - vj[2];
-
+
// normal component (vr.n)n
vnnr = (vr1*delx + vr2*dely + vr3*delz)/r;
@@ -399,7 +399,7 @@ void PairLubricatePolyOMP::eval(int iifrom, int iito, ThrData * const thr)
if (FLAGLOG) {
fx = fx + a_sh*vt1;
fy = fy + a_sh*vt2;
- fz = fz + a_sh*vt3;
+ fz = fz + a_sh*vt3;
}
// scale forces for appropriate units
@@ -407,48 +407,48 @@ void PairLubricatePolyOMP::eval(int iifrom, int iito, ThrData * const thr)
fx *= vxmu2f;
fy *= vxmu2f;
fz *= vxmu2f;
-
+
// add to total force
f[i][0] -= fx;
f[i][1] -= fy;
- f[i][2] -= fz;
-
+ f[i][2] -= fz;
+
// torque due to this force
if (FLAGLOG) {
tx = xl[1]*fz - xl[2]*fy;
ty = xl[2]*fx - xl[0]*fz;
- tz = xl[0]*fy - xl[1]*fx;
-
+ tz = xl[0]*fy - xl[1]*fx;
+
torque[i][0] -= vxmu2f*tx;
torque[i][1] -= vxmu2f*ty;
- torque[i][2] -= vxmu2f*tz;
+ torque[i][2] -= vxmu2f*tz;
// torque due to a_pu
- wdotn = ((wi[0]-wj[0])*delx + (wi[1]-wj[1])*dely +
- (wi[2]-wj[2])*delz)/r;
+ wdotn = ((wi[0]-wj[0])*delx + (wi[1]-wj[1])*dely +
+ (wi[2]-wj[2])*delz)/r;
wt1 = (wi[0]-wj[0]) - wdotn*delx/r;
wt2 = (wi[1]-wj[1]) - wdotn*dely/r;
wt3 = (wi[2]-wj[2]) - wdotn*delz/r;
-
+
tx = a_pu*wt1;
ty = a_pu*wt2;
tz = a_pu*wt3;
-
+
torque[i][0] -= vxmu2f*tx;
torque[i][1] -= vxmu2f*ty;
- torque[i][2] -= vxmu2f*tz;
+ torque[i][2] -= vxmu2f*tz;
- }
+ }
if (EVFLAG) ev_tally_xyz(i,nlocal,nlocal, /* newton_pair */ 0,
- 0.0,0.0,-fx,-fy,-fz,delx,dely,delz);
+ 0.0,0.0,-fx,-fy,-fz,delx,dely,delz);
}
}
}
-
+
// restore streaming component of velocity, omega, angmom
if (SHEARING) {
@@ -459,10 +459,10 @@ void PairLubricatePolyOMP::eval(int iifrom, int iito, ThrData * const thr)
i = ilist[ii];
itype = type[i];
radi = radius[i];
-
+
domain->x2lamda(x[i],lamda);
- vstream[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
- h_rate[4]*lamda[2] + h_ratelo[0];
+ vstream[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
+ h_rate[4]*lamda[2] + h_ratelo[0];
vstream[1] = h_rate[1]*lamda[1] + h_rate[3]*lamda[2] + h_ratelo[1];
vstream[2] = h_rate[2]*lamda[2] + h_ratelo[2];
v[i][0] += vstream[0];
diff --git a/src/USER-OMP/pair_lubricate_poly_omp.h b/src/USER-OMP/pair_lubricate_poly_omp.h
index 8e44d94093fca55641c7a945dbf28c2f722a76e0..e9984ce0d487160490080b6706386899d3c8ce05 100644
--- a/src/USER-OMP/pair_lubricate_poly_omp.h
+++ b/src/USER-OMP/pair_lubricate_poly_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_meam_spline_omp.cpp b/src/USER-OMP/pair_meam_spline_omp.cpp
index 33dfcd466cfa6550a035beb1520537bc80f6b037..cf9a6c5bc9fe6788225b3af7692bdac4d8756b4a 100644
--- a/src/USER-OMP/pair_meam_spline_omp.cpp
+++ b/src/USER-OMP/pair_meam_spline_omp.cpp
@@ -67,14 +67,14 @@ void PairMEAMSplineOMP::compute(int eflag, int vflag)
loop_setup_thr(ifrom, ito, tid, inum, nthreads);
ThrData *thr = fix->get_thr(tid);
ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
-
+
thr->init_eam(nall,Uprime_values);
if (evflag) {
if (eflag) {
- eval<1,1>(ifrom, ito, thr);
+ eval<1,1>(ifrom, ito, thr);
} else {
- eval<1,0>(ifrom, ito, thr);
+ eval<1,0>(ifrom, ito, thr);
}
} else {
eval<0,0>(ifrom, ito, thr);
@@ -90,7 +90,7 @@ void PairMEAMSplineOMP::eval(int iifrom, int iito, ThrData * const thr)
const int* const ilist_full = listfull->ilist;
const int* const numneigh_full = listfull->numneigh;
const int* const * const firstneigh_full = listfull->firstneigh;
-
+
// Determine the maximum number of neighbors a single atom has.
int myMaxNeighbors = 0;
for(int ii = iifrom; ii < iito; ii++) {
@@ -133,27 +133,27 @@ void PairMEAMSplineOMP::eval(int iifrom, int iito, ThrData * const thr)
const double rij_sq = jdelx*jdelx + jdely*jdely + jdelz*jdelz;
if (rij_sq < cutforcesq) {
- const double rij = sqrt(rij_sq);
- double partial_sum = 0;
-
- nextTwoBodyInfo->tag = j;
- nextTwoBodyInfo->r = rij;
- nextTwoBodyInfo->f = f.eval(rij, nextTwoBodyInfo->fprime);
- nextTwoBodyInfo->del[0] = jdelx / rij;
- nextTwoBodyInfo->del[1] = jdely / rij;
- nextTwoBodyInfo->del[2] = jdelz / rij;
-
- for(int kk = 0; kk < numBonds; kk++) {
- const MEAM2Body& bondk = myTwoBodyInfo[kk];
- double cos_theta = (nextTwoBodyInfo->del[0]*bondk.del[0] + nextTwoBodyInfo->del[1]*bondk.del[1] + nextTwoBodyInfo->del[2]*bondk.del[2]);
- partial_sum += bondk.f * g.eval(cos_theta);
- }
-
- rho_value += nextTwoBodyInfo->f * partial_sum;
- rho_value += rho.eval(rij);
-
- numBonds++;
- nextTwoBodyInfo++;
+ const double rij = sqrt(rij_sq);
+ double partial_sum = 0;
+
+ nextTwoBodyInfo->tag = j;
+ nextTwoBodyInfo->r = rij;
+ nextTwoBodyInfo->f = f.eval(rij, nextTwoBodyInfo->fprime);
+ nextTwoBodyInfo->del[0] = jdelx / rij;
+ nextTwoBodyInfo->del[1] = jdely / rij;
+ nextTwoBodyInfo->del[2] = jdelz / rij;
+
+ for(int kk = 0; kk < numBonds; kk++) {
+ const MEAM2Body& bondk = myTwoBodyInfo[kk];
+ double cos_theta = (nextTwoBodyInfo->del[0]*bondk.del[0] + nextTwoBodyInfo->del[1]*bondk.del[1] + nextTwoBodyInfo->del[2]*bondk.del[2]);
+ partial_sum += bondk.f * g.eval(cos_theta);
+ }
+
+ rho_value += nextTwoBodyInfo->f * partial_sum;
+ rho_value += rho.eval(rij);
+
+ numBonds++;
+ nextTwoBodyInfo++;
}
}
@@ -181,55 +181,55 @@ void PairMEAMSplineOMP::eval(int iifrom, int iito, ThrData * const thr)
MEAM2Body const* bondk = myTwoBodyInfo;
for(int kk = 0; kk < jj; kk++, ++bondk) {
- const double rik = bondk->r;
-
- const double cos_theta = (bondj.del[0]*bondk->del[0] + bondj.del[1]*bondk->del[1] + bondj.del[2]*bondk->del[2]);
- double g_prime;
- double g_value = g.eval(cos_theta, g_prime);
- const double f_rik_prime = bondk->fprime;
- const double f_rik = bondk->f;
-
- double fij = -Uprime_i * g_value * f_rik * f_rij_prime;
- double fik = -Uprime_i * g_value * f_rij * f_rik_prime;
-
- const double prefactor = Uprime_i * f_rij * f_rik * g_prime;
- const double prefactor_ij = prefactor / rij;
- const double prefactor_ik = prefactor / rik;
- fij += prefactor_ij * cos_theta;
- fik += prefactor_ik * cos_theta;
-
- double fj[3], fk[3];
-
- fj[0] = bondj.del[0] * fij - bondk->del[0] * prefactor_ij;
- fj[1] = bondj.del[1] * fij - bondk->del[1] * prefactor_ij;
- fj[2] = bondj.del[2] * fij - bondk->del[2] * prefactor_ij;
- forces_j[0] += fj[0];
- forces_j[1] += fj[1];
- forces_j[2] += fj[2];
-
- fk[0] = bondk->del[0] * fik - bondj.del[0] * prefactor_ik;
- fk[1] = bondk->del[1] * fik - bondj.del[1] * prefactor_ik;
- fk[2] = bondk->del[2] * fik - bondj.del[2] * prefactor_ik;
- forces_i[0] -= fk[0];
- forces_i[1] -= fk[1];
- forces_i[2] -= fk[2];
-
- const int k = bondk->tag;
- forces[k][0] += fk[0];
- forces[k][1] += fk[1];
- forces[k][2] += fk[2];
-
- if(EVFLAG) {
- double delta_ij[3];
- double delta_ik[3];
- delta_ij[0] = bondj.del[0] * rij;
- delta_ij[1] = bondj.del[1] * rij;
- delta_ij[2] = bondj.del[2] * rij;
- delta_ik[0] = bondk->del[0] * rik;
- delta_ik[1] = bondk->del[1] * rik;
- delta_ik[2] = bondk->del[2] * rik;
- ev_tally3_thr(this,i,j,k,0.0,0.0,fj,fk,delta_ij,delta_ik,thr);
- }
+ const double rik = bondk->r;
+
+ const double cos_theta = (bondj.del[0]*bondk->del[0] + bondj.del[1]*bondk->del[1] + bondj.del[2]*bondk->del[2]);
+ double g_prime;
+ double g_value = g.eval(cos_theta, g_prime);
+ const double f_rik_prime = bondk->fprime;
+ const double f_rik = bondk->f;
+
+ double fij = -Uprime_i * g_value * f_rik * f_rij_prime;
+ double fik = -Uprime_i * g_value * f_rij * f_rik_prime;
+
+ const double prefactor = Uprime_i * f_rij * f_rik * g_prime;
+ const double prefactor_ij = prefactor / rij;
+ const double prefactor_ik = prefactor / rik;
+ fij += prefactor_ij * cos_theta;
+ fik += prefactor_ik * cos_theta;
+
+ double fj[3], fk[3];
+
+ fj[0] = bondj.del[0] * fij - bondk->del[0] * prefactor_ij;
+ fj[1] = bondj.del[1] * fij - bondk->del[1] * prefactor_ij;
+ fj[2] = bondj.del[2] * fij - bondk->del[2] * prefactor_ij;
+ forces_j[0] += fj[0];
+ forces_j[1] += fj[1];
+ forces_j[2] += fj[2];
+
+ fk[0] = bondk->del[0] * fik - bondj.del[0] * prefactor_ik;
+ fk[1] = bondk->del[1] * fik - bondj.del[1] * prefactor_ik;
+ fk[2] = bondk->del[2] * fik - bondj.del[2] * prefactor_ik;
+ forces_i[0] -= fk[0];
+ forces_i[1] -= fk[1];
+ forces_i[2] -= fk[2];
+
+ const int k = bondk->tag;
+ forces[k][0] += fk[0];
+ forces[k][1] += fk[1];
+ forces[k][2] += fk[2];
+
+ if(EVFLAG) {
+ double delta_ij[3];
+ double delta_ik[3];
+ delta_ij[0] = bondj.del[0] * rij;
+ delta_ij[1] = bondj.del[1] * rij;
+ delta_ij[2] = bondj.del[2] * rij;
+ delta_ik[0] = bondk->del[0] * rik;
+ delta_ik[1] = bondk->del[1] * rik;
+ delta_ik[2] = bondk->del[2] * rik;
+ ev_tally3_thr(this,i,j,k,0.0,0.0,fj,fk,delta_ij,delta_ik,thr);
+ }
}
forces[i][0] -= forces_j[0];
@@ -247,7 +247,7 @@ void PairMEAMSplineOMP::eval(int iifrom, int iito, ThrData * const thr)
delete[] myTwoBodyInfo;
- sync_threads();
+ sync_threads();
// reduce per thread density
data_reduce_thr(Uprime_values, nall, nthreads, 1, tid);
@@ -287,27 +287,27 @@ void PairMEAMSplineOMP::eval(int iifrom, int iito, ThrData * const thr)
double rij_sq = jdel[0]*jdel[0] + jdel[1]*jdel[1] + jdel[2]*jdel[2];
if(rij_sq < cutforcesq) {
- double rij = sqrt(rij_sq);
-
- double rho_prime;
- rho.eval(rij, rho_prime);
- double fpair = rho_prime * (Uprime_values[i] + Uprime_values[j]);
-
- double pair_pot_deriv;
- double pair_pot = phi.eval(rij, pair_pot_deriv);
- fpair += pair_pot_deriv;
-
- // Divide by r_ij to get forces from gradient.
- fpair /= rij;
-
- forces[i][0] += jdel[0]*fpair;
- forces[i][1] += jdel[1]*fpair;
- forces[i][2] += jdel[2]*fpair;
- forces[j][0] -= jdel[0]*fpair;
- forces[j][1] -= jdel[1]*fpair;
- forces[j][2] -= jdel[2]*fpair;
- if (EVFLAG) ev_tally_thr(this,i,j,nlocal, 1 /* newton_pair */,
- pair_pot,0.0,-fpair,jdel[0],jdel[1],jdel[2],thr);
+ double rij = sqrt(rij_sq);
+
+ double rho_prime;
+ rho.eval(rij, rho_prime);
+ double fpair = rho_prime * (Uprime_values[i] + Uprime_values[j]);
+
+ double pair_pot_deriv;
+ double pair_pot = phi.eval(rij, pair_pot_deriv);
+ fpair += pair_pot_deriv;
+
+ // Divide by r_ij to get forces from gradient.
+ fpair /= rij;
+
+ forces[i][0] += jdel[0]*fpair;
+ forces[i][1] += jdel[1]*fpair;
+ forces[i][2] += jdel[2]*fpair;
+ forces[j][0] -= jdel[0]*fpair;
+ forces[j][1] -= jdel[1]*fpair;
+ forces[j][2] -= jdel[2]*fpair;
+ if (EVFLAG) ev_tally_thr(this,i,j,nlocal, 1 /* newton_pair */,
+ pair_pot,0.0,-fpair,jdel[0],jdel[1],jdel[2],thr);
}
}
}
diff --git a/src/USER-OMP/pair_meam_spline_omp.h b/src/USER-OMP/pair_meam_spline_omp.h
index c8f92ce74c6cd7692dd1a0acd43bd00d3dc7187a..2fd169609f27641efe794fc1b3e226e19c8d6164 100644
--- a/src/USER-OMP/pair_meam_spline_omp.h
+++ b/src/USER-OMP/pair_meam_spline_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_morse_omp.cpp b/src/USER-OMP/pair_morse_omp.cpp
index 18a3fe495014595d6f7401d4a33bde43f1af70ff..d1b0d56cfd238543b970a8a4e5917aa105523809 100644
--- a/src/USER-OMP/pair_morse_omp.cpp
+++ b/src/USER-OMP/pair_morse_omp.cpp
@@ -56,11 +56,11 @@ void PairMorseOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -117,28 +117,28 @@ void PairMorseOMP::eval(int iifrom, int iito, ThrData * const thr)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r = sqrt(rsq);
- dr = r - r0[itype][jtype];
- dexp = exp(-alpha[itype][jtype] * dr);
- fpair = factor_lj * morse1[itype][jtype] * (dexp*dexp - dexp) / r;
-
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (EFLAG) {
- evdwl = d0[itype][jtype] * (dexp*dexp - 2.0*dexp) -
- offset[itype][jtype];
- evdwl *= factor_lj;
- }
-
- if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
- evdwl,0.0,fpair,delx,dely,delz,thr);
+ r = sqrt(rsq);
+ dr = r - r0[itype][jtype];
+ dexp = exp(-alpha[itype][jtype] * dr);
+ fpair = factor_lj * morse1[itype][jtype] * (dexp*dexp - dexp) / r;
+
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (EFLAG) {
+ evdwl = d0[itype][jtype] * (dexp*dexp - 2.0*dexp) -
+ offset[itype][jtype];
+ evdwl *= factor_lj;
+ }
+
+ if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
+ evdwl,0.0,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_morse_omp.h b/src/USER-OMP/pair_morse_omp.h
index a20aad6716cfaddce3a16a68253e83fa1daff6be..40797e25022362c945696d5c1498f1608c5cd5f5 100644
--- a/src/USER-OMP/pair_morse_omp.h
+++ b/src/USER-OMP/pair_morse_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_peri_lps_omp.cpp b/src/USER-OMP/pair_peri_lps_omp.cpp
index ef6de8777f6c37ba69a1075c4134cd5450f56eff..d61f71aa061f597df0c39e0767375539c2dfd291 100644
--- a/src/USER-OMP/pair_peri_lps_omp.cpp
+++ b/src/USER-OMP/pair_peri_lps_omp.cpp
@@ -56,8 +56,8 @@ void PairPeriLPSOMP::compute(int eflag, int vflag)
// grow bond forces array if necessary
if (atom->nmax > nmax) {
- memory->destroy(s0_new);
- memory->destroy(theta);
+ memory->destroy(s0_new);
+ memory->destroy(theta);
nmax = atom->nmax;
memory->create(s0_new,nmax,"pair:s0_new");
memory->create(theta,nmax,"pair:theta");
@@ -75,11 +75,11 @@ void PairPeriLPSOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -163,7 +163,7 @@ void PairPeriLPSOMP::eval(int iifrom, int iito, ThrData * const thr)
if (periodic) domain->minimum_image(delx0,dely0,delz0);
rsq0 = delx0*delx0 + dely0*dely0 + delz0*delz0;
jtype = type[j];
-
+
r = sqrt(rsq);
// short-range interaction distance based on initial particle position
@@ -179,27 +179,27 @@ void PairPeriLPSOMP::eval(int iifrom, int iito, ThrData * const thr)
dr = r - d_ij;
// kshort based upon short-range force constant
- // of the bond-based theory used in PMB model
+ // of the bond-based theory used in PMB model
double kshort = (15.0 * 18.0 * bulkmodulus[itype][itype]) /
- (MY_PI * cutsq[itype][jtype] * cutsq[itype][jtype]);
+ (MY_PI * cutsq[itype][jtype] * cutsq[itype][jtype]);
rk = (kshort * vfrac[j]) * (dr / cut[itype][jtype]);
if (r > 0.0) fpair = -(rk/r);
else fpair = 0.0;
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
if (EFLAG) evdwl = 0.5*rk*dr;
- if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,evdwl,0.0,
- fpair*vfrac[i],delx,dely,delz,thr);
+ if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,evdwl,0.0,
+ fpair*vfrac[i],delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
@@ -216,7 +216,7 @@ void PairPeriLPSOMP::eval(int iifrom, int iito, ThrData * const thr)
const int idelta = 1 + nlocal/comm->nthreads;
iifrom = thr->get_tid()*idelta;
iito = ((iifrom + idelta) > nlocal) ? nlocal : (iifrom + idelta);
-#else
+#else
iifrom = 0;
iito = nlocal;
#endif
@@ -231,7 +231,7 @@ void PairPeriLPSOMP::eval(int iifrom, int iito, ThrData * const thr)
#if defined(_OPENMP)
#pragma omp master
#endif
- { // communicate dilatation (theta) of each particle
+ { // communicate dilatation (theta) of each particle
comm->forward_comm_pair(this);
// communicate weighted volume (wvolume) upon every reneighbor
if (neighbor->ago == 0)
@@ -242,10 +242,10 @@ void PairPeriLPSOMP::eval(int iifrom, int iito, ThrData * const thr)
// Volume-dependent part of the energy
if (EFLAG) {
- for (i = iifrom; i < iito; i++) {
+ for (i = iifrom; i < iito; i++) {
itype = type[i];
e_tally_thr(this, i, i, nlocal, NEWTON_PAIR,
- 0.5 * bulkmodulus[itype][itype] * (theta[i] * theta[i]), 0.0, thr);
+ 0.5 * bulkmodulus[itype][itype] * (theta[i] * theta[i]), 0.0, thr);
}
}
@@ -261,9 +261,9 @@ void PairPeriLPSOMP::eval(int iifrom, int iito, ThrData * const thr)
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
- xtmp0 = x0[i][0];
- ytmp0 = x0[i][1];
- ztmp0 = x0[i][2];
+ xtmp0 = x0[i][0];
+ ytmp0 = x0[i][1];
+ ztmp0 = x0[i][2];
itype = type[i];
jnum = npartner[i];
first = true;
@@ -286,10 +286,10 @@ void PairPeriLPSOMP::eval(int iifrom, int iito, ThrData * const thr)
delz = ztmp - x[j][2];
if (periodic) domain->minimum_image(delx,dely,delz);
rsq = delx*delx + dely*dely + delz*delz;
- delx0 = xtmp0 - x0[j][0];
- dely0 = ytmp0 - x0[j][1];
- delz0 = ztmp0 - x0[j][2];
- if (periodic) domain->minimum_image(delx0,dely0,delz0);
+ delx0 = xtmp0 - x0[j][0];
+ dely0 = ytmp0 - x0[j][1];
+ delz0 = ztmp0 - x0[j][2];
+ if (periodic) domain->minimum_image(delx0,dely0,delz0);
jtype = type[j];
delta = cut[itype][jtype];
r = sqrt(rsq);
@@ -302,18 +302,18 @@ void PairPeriLPSOMP::eval(int iifrom, int iito, ThrData * const thr)
// scale vfrac[j] if particle j near the horizon
if ((fabs(r0[i][jj] - delta)) <= half_lc)
- vfrac_scale = (-1.0/(2*half_lc))*(r0[i][jj]) +
- (1.0 + ((delta - half_lc)/(2*half_lc) ) );
+ vfrac_scale = (-1.0/(2*half_lc))*(r0[i][jj]) +
+ (1.0 + ((delta - half_lc)/(2*half_lc) ) );
else vfrac_scale = 1.0;
omega_plus = influence_function(-1.0*delx0,-1.0*dely0,-1.0*delz0);
omega_minus = influence_function(delx0,dely0,delz0);
- rk = ( (3.0 * bulkmodulus[itype][itype]) -
- (5.0 * shearmodulus[itype][itype]) ) * vfrac[j] * vfrac_scale *
- ( (omega_plus * theta[i] / wvolume[i]) +
- ( omega_minus * theta[j] / wvolume[j] ) ) * r0[i][jj];
+ rk = ( (3.0 * bulkmodulus[itype][itype]) -
+ (5.0 * shearmodulus[itype][itype]) ) * vfrac[j] * vfrac_scale *
+ ( (omega_plus * theta[i] / wvolume[i]) +
+ ( omega_minus * theta[j] / wvolume[j] ) ) * r0[i][jj];
rk += 15.0 * ( shearmodulus[itype][itype] * vfrac[j] * vfrac_scale ) *
- ( (omega_plus / wvolume[i]) + (omega_minus / wvolume[j]) ) * dr;
+ ( (omega_plus / wvolume[i]) + (omega_minus / wvolume[j]) ) * dr;
if (r > 0.0) fbond = -(rk/r);
else fbond = 0.0;
@@ -322,14 +322,14 @@ void PairPeriLPSOMP::eval(int iifrom, int iito, ThrData * const thr)
f[i][1] += dely*fbond;
f[i][2] += delz*fbond;
- // since I-J is double counted, set newton off & use 1/2 factor and I,I
+ // since I-J is double counted, set newton off & use 1/2 factor and I,I
double deviatoric_extension = dr - (theta[i]* r0[i][jj] / 3.0);
- if (EFLAG) evdwl = 0.5 * 15 * (shearmodulus[itype][itype]/wvolume[i]) *
- omega_plus*(deviatoric_extension * deviatoric_extension) *
- vfrac[j] * vfrac_scale;
+ if (EFLAG) evdwl = 0.5 * 15 * (shearmodulus[itype][itype]/wvolume[i]) *
+ omega_plus*(deviatoric_extension * deviatoric_extension) *
+ vfrac[j] * vfrac_scale;
if (EVFLAG) ev_tally_thr(this,i,i,nlocal,0,0.5*evdwl,0.0,
- 0.5*fbond*vfrac[i],delx,dely,delz,thr);
+ 0.5*fbond*vfrac[i],delx,dely,delz,thr);
// find stretch in bond I-J and break if necessary
// use s0 from previous timestep
@@ -370,7 +370,7 @@ void PairPeriLPSOMP::compute_dilatation_thr(int ifrom, int ito)
double **x0 = atom->x0;
double *vfrac = atom->vfrac;
double vfrac_scale = 1.0;
-
+
double lc = domain->lattice->xlattice;
double half_lc = 0.5*lc;
@@ -431,11 +431,11 @@ void PairPeriLPSOMP::compute_dilatation_thr(int ifrom, int ito)
else vfrac_scale = 1.0;
theta[i] += influence_function(delx0, dely0, delz0) * r0[i][jj] * dr *
- vfrac[j] * vfrac_scale;
+ vfrac[j] * vfrac_scale;
}
// if wvolume[i] is zero, then particle i has no bonds
- // therefore, the dilatation is set to
+ // therefore, the dilatation is set to
if (wvolume[i] != 0.0) theta[i] = (3.0/wvolume[i]) * theta[i];
else theta[i] = 0;
@@ -451,4 +451,3 @@ double PairPeriLPSOMP::memory_usage()
return bytes;
}
-
diff --git a/src/USER-OMP/pair_peri_lps_omp.h b/src/USER-OMP/pair_peri_lps_omp.h
index f234a4109814c9fde416069ebb369622e47be35c..aedb51472ee23f411555653149baeaac1ba0670c 100644
--- a/src/USER-OMP/pair_peri_lps_omp.h
+++ b/src/USER-OMP/pair_peri_lps_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_peri_pmb_omp.cpp b/src/USER-OMP/pair_peri_pmb_omp.cpp
index 36e4d1a16e45ba5327958a01b187e3b9bd97ee5c..404f1d56954610d158f544b03dd9fae599e76ce4 100644
--- a/src/USER-OMP/pair_peri_pmb_omp.cpp
+++ b/src/USER-OMP/pair_peri_pmb_omp.cpp
@@ -71,11 +71,11 @@ void PairPeriPMBOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -158,7 +158,7 @@ void PairPeriPMBOMP::eval(int iifrom, int iito, ThrData * const thr)
if (periodic) domain->minimum_image(delx0,dely0,delz0);
rsq0 = delx0*delx0 + dely0*dely0 + delz0*delz0;
jtype = type[j];
-
+
r = sqrt(rsq);
// short-range interaction distance based on initial particle position
@@ -173,23 +173,23 @@ void PairPeriPMBOMP::eval(int iifrom, int iito, ThrData * const thr)
if (r < d_ij) {
dr = r - d_ij;
- rk = (15.0 * kspring[itype][jtype] * vfrac[j]) *
- (dr / cut[itype][jtype]);
+ rk = (15.0 * kspring[itype][jtype] * vfrac[j]) *
+ (dr / cut[itype][jtype]);
if (r > 0.0) fpair = -(rk/r);
else fpair = 0.0;
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
if (EFLAG) evdwl = 0.5*rk*dr;
- if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,evdwl,0.0,
- fpair*vfrac[i],delx,dely,delz,thr);
+ if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,evdwl,0.0,
+ fpair*vfrac[i],delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
@@ -206,7 +206,7 @@ void PairPeriPMBOMP::eval(int iifrom, int iito, ThrData * const thr)
const int idelta = 1 + nlocal/comm->nthreads;
iifrom = thr->get_tid()*idelta;
iito = ((iifrom + idelta) > nlocal) ? nlocal : (iifrom + idelta);
-#else
+#else
iifrom = 0;
iito = nlocal;
#endif
@@ -234,8 +234,8 @@ void PairPeriPMBOMP::eval(int iifrom, int iito, ThrData * const thr)
// check if lost a partner without first breaking bond
if (j < 0) {
- partner[i][jj] = 0;
- continue;
+ partner[i][jj] = 0;
+ continue;
}
// compute force density, add to PD equation of motion
@@ -257,8 +257,8 @@ void PairPeriPMBOMP::eval(int iifrom, int iito, ThrData * const thr)
// scale vfrac[j] if particle j near the horizon
if ((fabs(r0[i][jj] - delta)) <= half_lc)
- vfrac_scale = (-1.0/(2*half_lc))*(r0[i][jj]) +
- (1.0 + ((delta - half_lc)/(2*half_lc) ) );
+ vfrac_scale = (-1.0/(2*half_lc))*(r0[i][jj]) +
+ (1.0 + ((delta - half_lc)/(2*half_lc) ) );
else vfrac_scale = 1.0;
stretch = dr / r0[i][jj];
@@ -270,12 +270,12 @@ void PairPeriPMBOMP::eval(int iifrom, int iito, ThrData * const thr)
f[i][1] += dely*fbond;
f[i][2] += delz*fbond;
- // since I-J is double counted, set newton off & use 1/2 factor and I,I
+ // since I-J is double counted, set newton off & use 1/2 factor and I,I
if (EFLAG) evdwl = 0.5*rk*dr;
- if (EVFLAG)
- ev_tally_thr(this,i,i,nlocal,0,0.5*evdwl,0.0,
- 0.5*fbond*vfrac[i],delx,dely,delz,thr);
+ if (EVFLAG)
+ ev_tally_thr(this,i,i,nlocal,0,0.5*evdwl,0.0,
+ 0.5*fbond*vfrac[i],delx,dely,delz,thr);
// find stretch in bond I-J and break if necessary
// use s0 from previous timestep
@@ -285,9 +285,9 @@ void PairPeriPMBOMP::eval(int iifrom, int iito, ThrData * const thr)
// update s0 for next timestep
if (first)
- s0_new[i] = s00[itype][jtype] - (alpha[itype][jtype] * stretch);
+ s0_new[i] = s00[itype][jtype] - (alpha[itype][jtype] * stretch);
else
- s0_new[i] = MAX(s0_new[i],s00[itype][jtype] - (alpha[itype][jtype] * stretch));
+ s0_new[i] = MAX(s0_new[i],s00[itype][jtype] - (alpha[itype][jtype] * stretch));
first = false;
}
@@ -297,7 +297,7 @@ void PairPeriPMBOMP::eval(int iifrom, int iito, ThrData * const thr)
// store new s0 (in parallel)
if (iifrom < nlocal)
- for (i = iifrom; i < iito; i++) s0[i] = s0_new[i];
+ for (i = iifrom; i < iito; i++) s0[i] = s0_new[i];
}
/* ---------------------------------------------------------------------- */
diff --git a/src/USER-OMP/pair_peri_pmb_omp.h b/src/USER-OMP/pair_peri_pmb_omp.h
index 8a7fc091d9aa7df290ee1246f0928ae9cf0803de..cb2d83250ee05ea13994bb05aa7e3f3172548ae4 100644
--- a/src/USER-OMP/pair_peri_pmb_omp.h
+++ b/src/USER-OMP/pair_peri_pmb_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_rebo_omp.cpp b/src/USER-OMP/pair_rebo_omp.cpp
index 70b5c4e8ae111fe1a2bca7620144b57eff679978..9a1ce8e11bf1d14874f4e18e553f1e6ba7c933a5 100644
--- a/src/USER-OMP/pair_rebo_omp.cpp
+++ b/src/USER-OMP/pair_rebo_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_rebo_omp.h b/src/USER-OMP/pair_rebo_omp.h
index 4606e56ae1c6d538bd26605ba13aa9b7c8c0b1f7..685c5d26a0939c46052e10307029eed53d7ff803 100644
--- a/src/USER-OMP/pair_rebo_omp.h
+++ b/src/USER-OMP/pair_rebo_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_resquared_omp.cpp b/src/USER-OMP/pair_resquared_omp.cpp
index 8decc2d6c5d4e5879ab0d6e7031aef4ad12dd8c2..de052023009807e29731de21f88d8ce86bc96a9c 100644
--- a/src/USER-OMP/pair_resquared_omp.cpp
+++ b/src/USER-OMP/pair_resquared_omp.cpp
@@ -58,11 +58,11 @@ void PairRESquaredOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -126,7 +126,7 @@ void PairRESquaredOMP::eval(int iifrom, int iito, ThrData * const thr)
// compute if less than cutoff
if (rsq < cutsq[itype][jtype]) {
- fforce[0] = fforce[1] = fforce[2] = 0.0;
+ fforce[0] = fforce[1] = fforce[2] = 0.0;
switch (form[itype][jtype]) {
@@ -178,9 +178,9 @@ void PairRESquaredOMP::eval(int iifrom, int iito, ThrData * const thr)
fforce[0] *= factor_lj;
fforce[1] *= factor_lj;
fforce[2] *= factor_lj;
- fxtmp += fforce[0];
- fytmp += fforce[1];
- fztmp += fforce[2];
+ fxtmp += fforce[0];
+ fytmp += fforce[1];
+ fztmp += fforce[2];
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= fforce[0];
@@ -190,9 +190,9 @@ void PairRESquaredOMP::eval(int iifrom, int iito, ThrData * const thr)
if (EFLAG) evdwl = factor_lj*one_eng;
- if (EVFLAG) ev_tally_xyz_thr(this,i,j,nlocal,NEWTON_PAIR,
- evdwl,0.0,fforce[0],fforce[1],fforce[2],
- -r12[0],-r12[1],-r12[2],thr);
+ if (EVFLAG) ev_tally_xyz_thr(this,i,j,nlocal,NEWTON_PAIR,
+ evdwl,0.0,fforce[0],fforce[1],fforce[2],
+ -r12[0],-r12[1],-r12[2],thr);
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_resquared_omp.h b/src/USER-OMP/pair_resquared_omp.h
index 53a6e2e28f059e7a76449c325bdce7601a5a574c..cc2a59d74a1b054cbab31dbfc5d433ddff76c1ad 100644
--- a/src/USER-OMP/pair_resquared_omp.h
+++ b/src/USER-OMP/pair_resquared_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_soft_omp.cpp b/src/USER-OMP/pair_soft_omp.cpp
index f0c9e60df2f3ea0e7ad27440b95170678b1caa15..51a43be28c49fe916f59e28dde30c54033cbeb65 100644
--- a/src/USER-OMP/pair_soft_omp.cpp
+++ b/src/USER-OMP/pair_soft_omp.cpp
@@ -60,11 +60,11 @@ void PairSoftOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -121,26 +121,26 @@ void PairSoftOMP::eval(int iifrom, int iito, ThrData * const thr)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r = sqrt(rsq);
- arg = MY_PI/cut[itype][jtype];
- if (r > SMALL) fpair = factor_lj * prefactor[itype][jtype] *
- sin(arg*r) * arg/r;
- else fpair = 0.0;
-
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (EFLAG)
- evdwl = factor_lj * prefactor[itype][jtype] * (1.0+cos(arg*r));
-
- if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
- evdwl,0.0,fpair,delx,dely,delz,thr);
+ r = sqrt(rsq);
+ arg = MY_PI/cut[itype][jtype];
+ if (r > SMALL) fpair = factor_lj * prefactor[itype][jtype] *
+ sin(arg*r) * arg/r;
+ else fpair = 0.0;
+
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (EFLAG)
+ evdwl = factor_lj * prefactor[itype][jtype] * (1.0+cos(arg*r));
+
+ if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
+ evdwl,0.0,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_soft_omp.h b/src/USER-OMP/pair_soft_omp.h
index 1698089521794aee7dccc30e32d7ee85b77d38d4..74958208eddb1e604af9b2b7a4690c12609f2a22 100644
--- a/src/USER-OMP/pair_soft_omp.h
+++ b/src/USER-OMP/pair_soft_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_sw_omp.cpp b/src/USER-OMP/pair_sw_omp.cpp
index 1da1450ad06d95e80d44864bd351adc4e9756cfe..6bac2420e1834c9d1557ca552e5d520346f276fe 100644
--- a/src/USER-OMP/pair_sw_omp.cpp
+++ b/src/USER-OMP/pair_sw_omp.cpp
@@ -56,9 +56,9 @@ void PairSWOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- eval<1,1>(ifrom, ito, thr);
+ eval<1,1>(ifrom, ito, thr);
} else {
- eval<1,0>(ifrom, ito, thr);
+ eval<1,0>(ifrom, ito, thr);
}
} else eval<0,0>(ifrom, ito, thr);
@@ -113,13 +113,13 @@ void PairSWOMP::eval(int iifrom, int iito, ThrData * const thr)
jtag = tag[j];
if (itag > jtag) {
- if ((itag+jtag) % 2 == 0) continue;
+ if ((itag+jtag) % 2 == 0) continue;
} else if (itag < jtag) {
- if ((itag+jtag) % 2 == 1) continue;
+ if ((itag+jtag) % 2 == 1) continue;
} else {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
- if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
+ if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
}
jtype = map[type[j]];
@@ -142,7 +142,7 @@ void PairSWOMP::eval(int iifrom, int iito, ThrData * const thr)
f[j][2] -= delz*fpair;
if (EVFLAG) ev_tally_thr(this,i,j,nlocal,/* newton_pair */ 1,
- evdwl,0.0,fpair,delx,dely,delz,thr);
+ evdwl,0.0,fpair,delx,dely,delz,thr);
}
jnumm1 = jnum - 1;
@@ -162,32 +162,32 @@ void PairSWOMP::eval(int iifrom, int iito, ThrData * const thr)
fjxtmp = fjytmp = fjztmp = 0.0;
for (kk = jj+1; kk < jnum; kk++) {
- k = jlist[kk];
- k &= NEIGHMASK;
- ktype = map[type[k]];
- ikparam = elem2param[itype][ktype][ktype];
- ijkparam = elem2param[itype][jtype][ktype];
-
- delr2[0] = x[k][0] - xtmp;
- delr2[1] = x[k][1] - ytmp;
- delr2[2] = x[k][2] - ztmp;
- rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
- if (rsq2 > params[ikparam].cutsq) continue;
-
- threebody(¶ms[ijparam],¶ms[ikparam],¶ms[ijkparam],
- rsq1,rsq2,delr1,delr2,fj,fk,EFLAG,evdwl);
-
- fxtmp -= fj[0] + fk[0];
- fytmp -= fj[1] + fk[1];
- fztmp -= fj[2] + fk[2];
- fjxtmp += fj[0];
- fjytmp += fj[1];
- fjztmp += fj[2];
- f[k][0] += fk[0];
- f[k][1] += fk[1];
- f[k][2] += fk[2];
-
- if (EVFLAG) ev_tally3_thr(this,i,j,k,evdwl,0.0,fj,fk,delr1,delr2,thr);
+ k = jlist[kk];
+ k &= NEIGHMASK;
+ ktype = map[type[k]];
+ ikparam = elem2param[itype][ktype][ktype];
+ ijkparam = elem2param[itype][jtype][ktype];
+
+ delr2[0] = x[k][0] - xtmp;
+ delr2[1] = x[k][1] - ytmp;
+ delr2[2] = x[k][2] - ztmp;
+ rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
+ if (rsq2 > params[ikparam].cutsq) continue;
+
+ threebody(¶ms[ijparam],¶ms[ikparam],¶ms[ijkparam],
+ rsq1,rsq2,delr1,delr2,fj,fk,EFLAG,evdwl);
+
+ fxtmp -= fj[0] + fk[0];
+ fytmp -= fj[1] + fk[1];
+ fztmp -= fj[2] + fk[2];
+ fjxtmp += fj[0];
+ fjytmp += fj[1];
+ fjztmp += fj[2];
+ f[k][0] += fk[0];
+ f[k][1] += fk[1];
+ f[k][2] += fk[2];
+
+ if (EVFLAG) ev_tally3_thr(this,i,j,k,evdwl,0.0,fj,fk,delr1,delr2,thr);
}
f[j][0] += fjxtmp;
f[j][1] += fjytmp;
diff --git a/src/USER-OMP/pair_sw_omp.h b/src/USER-OMP/pair_sw_omp.h
index c4af86007a3bd76648bc698d22be535fa4dc8d28..a99edba46e63791d46a70859dce0157d9462592e 100644
--- a/src/USER-OMP/pair_sw_omp.h
+++ b/src/USER-OMP/pair_sw_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_table_omp.cpp b/src/USER-OMP/pair_table_omp.cpp
index 5c6b7717f7efb7c794e0325a40a23980ff8cfbaa..ee2e447a56cc1e65d646864002e807d849086852 100644
--- a/src/USER-OMP/pair_table_omp.cpp
+++ b/src/USER-OMP/pair_table_omp.cpp
@@ -57,11 +57,11 @@ void PairTableOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -80,7 +80,7 @@ void PairTableOMP::eval(int iifrom, int iito, ThrData * const thr)
double rsq,factor_lj,fraction,value,a,b;
int *ilist,*jlist,*numneigh,**firstneigh;
Table *tb;
-
+
union_int_float_t rsq_lookup;
int tlm1 = tablength - 1;
@@ -123,75 +123,75 @@ void PairTableOMP::eval(int iifrom, int iito, ThrData * const thr)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- tb = &tables[tabindex[itype][jtype]];
-
- if (check_error_thr((rsq < tb->innersq),tid,
- FLERR,"Pair distance < table inner cutoff"))
- return;
-
- if (tabstyle == LOOKUP) {
- itable = static_cast<int> ((rsq - tb->innersq) * tb->invdelta);
-
- if (check_error_thr((itable >= tlm1),tid,
- FLERR,"Pair distance > table outer cutoff"))
- return;
-
- fpair = factor_lj * tb->f[itable];
- } else if (tabstyle == LINEAR) {
- itable = static_cast<int> ((rsq - tb->innersq) * tb->invdelta);
-
- if (check_error_thr((itable >= tlm1),tid,
- FLERR,"Pair distance > table outer cutoff"))
- return;
-
- fraction = (rsq - tb->rsq[itable]) * tb->invdelta;
- value = tb->f[itable] + fraction*tb->df[itable];
- fpair = factor_lj * value;
- } else if (tabstyle == SPLINE) {
- itable = static_cast<int> ((rsq - tb->innersq) * tb->invdelta);
-
- if (check_error_thr((itable >= tlm1),tid,
- FLERR,"Pair distance > table outer cutoff"))
- return;
-
- b = (rsq - tb->rsq[itable]) * tb->invdelta;
- a = 1.0 - b;
- value = a * tb->f[itable] + b * tb->f[itable+1] +
- ((a*a*a-a)*tb->f2[itable] + (b*b*b-b)*tb->f2[itable+1]) *
+ tb = &tables[tabindex[itype][jtype]];
+
+ if (check_error_thr((rsq < tb->innersq),tid,
+ FLERR,"Pair distance < table inner cutoff"))
+ return;
+
+ if (tabstyle == LOOKUP) {
+ itable = static_cast<int> ((rsq - tb->innersq) * tb->invdelta);
+
+ if (check_error_thr((itable >= tlm1),tid,
+ FLERR,"Pair distance > table outer cutoff"))
+ return;
+
+ fpair = factor_lj * tb->f[itable];
+ } else if (tabstyle == LINEAR) {
+ itable = static_cast<int> ((rsq - tb->innersq) * tb->invdelta);
+
+ if (check_error_thr((itable >= tlm1),tid,
+ FLERR,"Pair distance > table outer cutoff"))
+ return;
+
+ fraction = (rsq - tb->rsq[itable]) * tb->invdelta;
+ value = tb->f[itable] + fraction*tb->df[itable];
+ fpair = factor_lj * value;
+ } else if (tabstyle == SPLINE) {
+ itable = static_cast<int> ((rsq - tb->innersq) * tb->invdelta);
+
+ if (check_error_thr((itable >= tlm1),tid,
+ FLERR,"Pair distance > table outer cutoff"))
+ return;
+
+ b = (rsq - tb->rsq[itable]) * tb->invdelta;
+ a = 1.0 - b;
+ value = a * tb->f[itable] + b * tb->f[itable+1] +
+ ((a*a*a-a)*tb->f2[itable] + (b*b*b-b)*tb->f2[itable+1]) *
tb->deltasq6;
- fpair = factor_lj * value;
- } else {
- rsq_lookup.f = rsq;
- itable = rsq_lookup.i & tb->nmask;
- itable >>= tb->nshiftbits;
- fraction = (rsq_lookup.f - tb->rsq[itable]) * tb->drsq[itable];
- value = tb->f[itable] + fraction*tb->df[itable];
- fpair = factor_lj * value;
- }
-
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (EFLAG) {
- if (tabstyle == LOOKUP)
- evdwl = tb->e[itable];
- else if (tabstyle == LINEAR || tabstyle == BITMAP)
- evdwl = tb->e[itable] + fraction*tb->de[itable];
- else
- evdwl = a * tb->e[itable] + b * tb->e[itable+1] +
- ((a*a*a-a)*tb->e2[itable] + (b*b*b-b)*tb->e2[itable+1]) *
- tb->deltasq6;
- evdwl *= factor_lj;
- }
-
- if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
- evdwl,0.0,fpair,delx,dely,delz,thr);
+ fpair = factor_lj * value;
+ } else {
+ rsq_lookup.f = rsq;
+ itable = rsq_lookup.i & tb->nmask;
+ itable >>= tb->nshiftbits;
+ fraction = (rsq_lookup.f - tb->rsq[itable]) * tb->drsq[itable];
+ value = tb->f[itable] + fraction*tb->df[itable];
+ fpair = factor_lj * value;
+ }
+
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (EFLAG) {
+ if (tabstyle == LOOKUP)
+ evdwl = tb->e[itable];
+ else if (tabstyle == LINEAR || tabstyle == BITMAP)
+ evdwl = tb->e[itable] + fraction*tb->de[itable];
+ else
+ evdwl = a * tb->e[itable] + b * tb->e[itable+1] +
+ ((a*a*a-a)*tb->e2[itable] + (b*b*b-b)*tb->e2[itable+1]) *
+ tb->deltasq6;
+ evdwl *= factor_lj;
+ }
+
+ if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
+ evdwl,0.0,fpair,delx,dely,delz,thr);
}
}
diff --git a/src/USER-OMP/pair_table_omp.h b/src/USER-OMP/pair_table_omp.h
index 974149b9ac35cc92776126a6d4a9a2be9d1274d3..dbc0b8e5b91d51ea7ef710f468953597a2fec222 100644
--- a/src/USER-OMP/pair_table_omp.h
+++ b/src/USER-OMP/pair_table_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_tersoff_omp.cpp b/src/USER-OMP/pair_tersoff_omp.cpp
index c725d64253daf107d7e4d647c2ce90d3cd310c13..573ed92ba36a829fb5634746e9bd0c63f3f1d8e6 100644
--- a/src/USER-OMP/pair_tersoff_omp.cpp
+++ b/src/USER-OMP/pair_tersoff_omp.cpp
@@ -56,11 +56,11 @@ void PairTersoffOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (vflag_atom) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (vflag_atom) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (vflag_atom) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (vflag_atom) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else eval<0,0,0>(ifrom, ito, thr);
@@ -116,13 +116,13 @@ void PairTersoffOMP::eval(int iifrom, int iito, ThrData * const thr)
jtag = tag[j];
if (itag > jtag) {
- if ((itag+jtag) % 2 == 0) continue;
+ if ((itag+jtag) % 2 == 0) continue;
} else if (itag < jtag) {
- if ((itag+jtag) % 2 == 1) continue;
+ if ((itag+jtag) % 2 == 1) continue;
} else {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
- if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
+ if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
}
jtype = map[type[j]];
@@ -145,7 +145,7 @@ void PairTersoffOMP::eval(int iifrom, int iito, ThrData * const thr)
f[j][2] -= delz*fpair;
if (EVFLAG) ev_tally_thr(this,i,j,nlocal,/* newton_pair */ 1,
- evdwl,0.0,fpair,delx,dely,delz,thr);
+ evdwl,0.0,fpair,delx,dely,delz,thr);
}
// three-body interactions
@@ -170,19 +170,19 @@ void PairTersoffOMP::eval(int iifrom, int iito, ThrData * const thr)
zeta_ij = 0.0;
for (kk = 0; kk < jnum; kk++) {
- if (jj == kk) continue;
- k = jlist[kk];
- k &= NEIGHMASK;
- ktype = map[type[k]];
- iparam_ijk = elem2param[itype][jtype][ktype];
-
- delr2[0] = x[k][0] - xtmp;
- delr2[1] = x[k][1] - ytmp;
- delr2[2] = x[k][2] - ztmp;
- rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
- if (rsq2 > params[iparam_ijk].cutsq) continue;
-
- zeta_ij += zeta(¶ms[iparam_ijk],rsq1,rsq2,delr1,delr2);
+ if (jj == kk) continue;
+ k = jlist[kk];
+ k &= NEIGHMASK;
+ ktype = map[type[k]];
+ iparam_ijk = elem2param[itype][jtype][ktype];
+
+ delr2[0] = x[k][0] - xtmp;
+ delr2[1] = x[k][1] - ytmp;
+ delr2[2] = x[k][2] - ztmp;
+ rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
+ if (rsq2 > params[iparam_ijk].cutsq) continue;
+
+ zeta_ij += zeta(¶ms[iparam_ijk],rsq1,rsq2,delr1,delr2);
}
// pairwise force due to zeta
@@ -197,37 +197,37 @@ void PairTersoffOMP::eval(int iifrom, int iito, ThrData * const thr)
fjztmp -= delr1[2]*fpair;
if (EVFLAG) ev_tally_thr(this,i,j,nlocal,/* newton_pair */ 1,evdwl,0.0,
- -fpair,-delr1[0],-delr1[1],-delr1[2],thr);
+ -fpair,-delr1[0],-delr1[1],-delr1[2],thr);
// attractive term via loop over k
for (kk = 0; kk < jnum; kk++) {
- if (jj == kk) continue;
- k = jlist[kk];
- k &= NEIGHMASK;
- ktype = map[type[k]];
- iparam_ijk = elem2param[itype][jtype][ktype];
-
- delr2[0] = x[k][0] - xtmp;
- delr2[1] = x[k][1] - ytmp;
- delr2[2] = x[k][2] - ztmp;
- rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
- if (rsq2 > params[iparam_ijk].cutsq) continue;
-
- attractive(¶ms[iparam_ijk],prefactor,
- rsq1,rsq2,delr1,delr2,fi,fj,fk);
-
- fxtmp += fi[0];
- fytmp += fi[1];
- fztmp += fi[2];
- fjxtmp += fj[0];
- fjytmp += fj[1];
- fjztmp += fj[2];
- f[k][0] += fk[0];
- f[k][1] += fk[1];
- f[k][2] += fk[2];
-
- if (VFLAG_ATOM) v_tally3_thr(i,j,k,fj,fk,delr1,delr2,thr);
+ if (jj == kk) continue;
+ k = jlist[kk];
+ k &= NEIGHMASK;
+ ktype = map[type[k]];
+ iparam_ijk = elem2param[itype][jtype][ktype];
+
+ delr2[0] = x[k][0] - xtmp;
+ delr2[1] = x[k][1] - ytmp;
+ delr2[2] = x[k][2] - ztmp;
+ rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
+ if (rsq2 > params[iparam_ijk].cutsq) continue;
+
+ attractive(¶ms[iparam_ijk],prefactor,
+ rsq1,rsq2,delr1,delr2,fi,fj,fk);
+
+ fxtmp += fi[0];
+ fytmp += fi[1];
+ fztmp += fi[2];
+ fjxtmp += fj[0];
+ fjytmp += fj[1];
+ fjztmp += fj[2];
+ f[k][0] += fk[0];
+ f[k][1] += fk[1];
+ f[k][2] += fk[2];
+
+ if (VFLAG_ATOM) v_tally3_thr(i,j,k,fj,fk,delr1,delr2,thr);
}
f[j][0] += fjxtmp;
f[j][1] += fjytmp;
diff --git a/src/USER-OMP/pair_tersoff_table_omp.cpp b/src/USER-OMP/pair_tersoff_table_omp.cpp
index 5deb5525ff8fa7ddd0a2a14ee50e2f6c0393c35a..4560975b11b94c7db311b893f533a9d2e8b085be 100644
--- a/src/USER-OMP/pair_tersoff_table_omp.cpp
+++ b/src/USER-OMP/pair_tersoff_table_omp.cpp
@@ -89,7 +89,7 @@ void PairTersoffTableOMP::eval(int iifrom, int iito, ThrData * const thr)
double invR_ij, invR_ik, cosTeta;
double repulsivePotential, attractivePotential;
double exponentRepulsivePotential, exponentAttractivePotential,interpolTMP,interpolDeltaX,interpolY1;
- double interpolY2, cutoffFunctionIJ, attractiveExponential, repulsiveExponential, cutoffFunctionDerivedIJ,zeta;
+ double interpolY2, cutoffFunctionIJ, attractiveExponential, repulsiveExponential, cutoffFunctionDerivedIJ,zeta;
double gtetaFunctionIJK,gtetaFunctionDerivedIJK,cutoffFunctionIK;
double cutoffFunctionDerivedIK,factor_force3_ij,factor_1_force3_ik;
double factor_2_force3_ik,betaZetaPowerIJK,betaZetaPowerDerivedIJK,factor_force_tot;
@@ -123,9 +123,9 @@ void PairTersoffTableOMP::eval(int iifrom, int iito, ThrData * const thr)
jnum = numneigh[i];
if (check_error_thr((jnum > leadingDimensionInteractionList), tid,
- FLERR,"Too many neighbors for interaction list.\n"
- "Check your system or increase 'leadingDimension"
- "InteractionList'"))
+ FLERR,"Too many neighbors for interaction list.\n"
+ "Check your system or increase 'leadingDimension"
+ "InteractionList'"))
return;
// Pre-calculate gteta and cutoff function
@@ -149,11 +149,11 @@ void PairTersoffTableOMP::eval(int iifrom, int iito, ThrData * const thr)
r_ij = sqrt(r_ij);
invR_ij = 1.0 / r_ij;
-
+
directorCos_ij_x = invR_ij * dr_ij[0];
directorCos_ij_y = invR_ij * dr_ij[1];
directorCos_ij_z = invR_ij * dr_ij[2];
-
+
// preCutoffFunction
interpolDeltaX = r_ij - GRIDSTART;
interpolTMP = (interpolDeltaX * GRIDDENSITY_FCUTOFF);
@@ -168,47 +168,47 @@ void PairTersoffTableOMP::eval(int iifrom, int iito, ThrData * const thr)
for (int neighbor_k = neighbor_j + 1; neighbor_k < jnum; neighbor_k++) {
- double dr_ik[3], r_ik;
-
- k = jlist[neighbor_k];
- k &= NEIGHMASK;
- ktype = map[type[k]];
- ikparam = elem2param[itype][ktype][ktype];
- ijkparam = elem2param[itype][jtype][ktype];
-
- dr_ik[0] = xtmp -x[k][0];
- dr_ik[1] = ytmp -x[k][1];
- dr_ik[2] = ztmp -x[k][2];
- r_ik = dr_ik[0]*dr_ik[0] + dr_ik[1]*dr_ik[1] + dr_ik[2]*dr_ik[2];
-
- if (r_ik > params[ikparam].cutsq) continue;
-
- r_ik = sqrt(r_ik);
-
- invR_ik = 1.0 / r_ik;
-
- directorCos_ik_x = invR_ik * dr_ik[0];
- directorCos_ik_y = invR_ik * dr_ik[1];
- directorCos_ik_z = invR_ik * dr_ik[2];
-
- cosTeta = directorCos_ij_x * directorCos_ik_x + directorCos_ij_y * directorCos_ik_y + directorCos_ij_z * directorCos_ik_z;
-
- // preGtetaFunction
- interpolDeltaX=cosTeta+1.0;
- interpolTMP = (interpolDeltaX * GRIDDENSITY_GTETA);
- interpolIDX = (int) interpolTMP;
- interpolY1 = gtetaFunction[itype][interpolIDX];
- interpolY2 = gtetaFunction[itype][interpolIDX+1];
- gtetaFunction_temp = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
- // preGtetaFunctionDerived
- interpolY1 = gtetaFunctionDerived[itype][interpolIDX];
- interpolY2 = gtetaFunctionDerived[itype][interpolIDX+1];
- gtetaFunctionDerived_temp = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
-
- preGtetaFunction[neighbor_j][neighbor_k]=params[ijkparam].gamma*gtetaFunction_temp;
- preGtetaFunctionDerived[neighbor_j][neighbor_k]=params[ijkparam].gamma*gtetaFunctionDerived_temp;
- preGtetaFunction[neighbor_k][neighbor_j]=params[ijkparam].gamma*gtetaFunction_temp;
- preGtetaFunctionDerived[neighbor_k][neighbor_j]=params[ijkparam].gamma*gtetaFunctionDerived_temp;
+ double dr_ik[3], r_ik;
+
+ k = jlist[neighbor_k];
+ k &= NEIGHMASK;
+ ktype = map[type[k]];
+ ikparam = elem2param[itype][ktype][ktype];
+ ijkparam = elem2param[itype][jtype][ktype];
+
+ dr_ik[0] = xtmp -x[k][0];
+ dr_ik[1] = ytmp -x[k][1];
+ dr_ik[2] = ztmp -x[k][2];
+ r_ik = dr_ik[0]*dr_ik[0] + dr_ik[1]*dr_ik[1] + dr_ik[2]*dr_ik[2];
+
+ if (r_ik > params[ikparam].cutsq) continue;
+
+ r_ik = sqrt(r_ik);
+
+ invR_ik = 1.0 / r_ik;
+
+ directorCos_ik_x = invR_ik * dr_ik[0];
+ directorCos_ik_y = invR_ik * dr_ik[1];
+ directorCos_ik_z = invR_ik * dr_ik[2];
+
+ cosTeta = directorCos_ij_x * directorCos_ik_x + directorCos_ij_y * directorCos_ik_y + directorCos_ij_z * directorCos_ik_z;
+
+ // preGtetaFunction
+ interpolDeltaX=cosTeta+1.0;
+ interpolTMP = (interpolDeltaX * GRIDDENSITY_GTETA);
+ interpolIDX = (int) interpolTMP;
+ interpolY1 = gtetaFunction[itype][interpolIDX];
+ interpolY2 = gtetaFunction[itype][interpolIDX+1];
+ gtetaFunction_temp = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
+ // preGtetaFunctionDerived
+ interpolY1 = gtetaFunctionDerived[itype][interpolIDX];
+ interpolY2 = gtetaFunctionDerived[itype][interpolIDX+1];
+ gtetaFunctionDerived_temp = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
+
+ preGtetaFunction[neighbor_j][neighbor_k]=params[ijkparam].gamma*gtetaFunction_temp;
+ preGtetaFunctionDerived[neighbor_j][neighbor_k]=params[ijkparam].gamma*gtetaFunctionDerived_temp;
+ preGtetaFunction[neighbor_k][neighbor_j]=params[ijkparam].gamma*gtetaFunction_temp;
+ preGtetaFunctionDerived[neighbor_k][neighbor_j]=params[ijkparam].gamma*gtetaFunctionDerived_temp;
} // loop on K
@@ -235,7 +235,7 @@ void PairTersoffTableOMP::eval(int iifrom, int iito, ThrData * const thr)
r_ij = sqrt(r_ij);
invR_ij = 1.0 / r_ij;
-
+
directorCos_ij_x = invR_ij * dr_ij[0];
directorCos_ij_y = invR_ij * dr_ij[1];
directorCos_ij_z = invR_ij * dr_ij[2];
@@ -265,72 +265,72 @@ void PairTersoffTableOMP::eval(int iifrom, int iito, ThrData * const thr)
cutoffFunctionDerivedIJ = preCutoffFunctionDerived[neighbor_j];
zeta = 0.0;
-
+
// first loop over neighbours of atom i except j - part 1/2
for (int neighbor_k = 0; neighbor_k < neighbor_j; neighbor_k++) {
- double dr_ik[3], r_ik;
-
- k = jlist[neighbor_k];
- k &= NEIGHMASK;
- ktype = map[type[k]];
- ikparam = elem2param[itype][ktype][ktype];
- ijkparam = elem2param[itype][jtype][ktype];
-
- dr_ik[0] = xtmp -x[k][0];
- dr_ik[1] = ytmp -x[k][1];
- dr_ik[2] = ztmp -x[k][2];
- r_ik = dr_ik[0]*dr_ik[0] + dr_ik[1]*dr_ik[1] + dr_ik[2]*dr_ik[2];
-
- if (r_ik > params[ikparam].cutsq) continue;
-
- r_ik = sqrt(r_ik);
-
- invR_ik = 1.0 / r_ik;
-
- directorCos_ik_x = invR_ik * r_ik_x;
- directorCos_ik_y = invR_ik * r_ik_y;
- directorCos_ik_z = invR_ik * r_ik_z;
-
- gtetaFunctionIJK = preGtetaFunction[neighbor_j][neighbor_k];
-
- cutoffFunctionIK = preCutoffFunction[neighbor_k];
-
- zeta += cutoffFunctionIK * gtetaFunctionIJK;
-
+ double dr_ik[3], r_ik;
+
+ k = jlist[neighbor_k];
+ k &= NEIGHMASK;
+ ktype = map[type[k]];
+ ikparam = elem2param[itype][ktype][ktype];
+ ijkparam = elem2param[itype][jtype][ktype];
+
+ dr_ik[0] = xtmp -x[k][0];
+ dr_ik[1] = ytmp -x[k][1];
+ dr_ik[2] = ztmp -x[k][2];
+ r_ik = dr_ik[0]*dr_ik[0] + dr_ik[1]*dr_ik[1] + dr_ik[2]*dr_ik[2];
+
+ if (r_ik > params[ikparam].cutsq) continue;
+
+ r_ik = sqrt(r_ik);
+
+ invR_ik = 1.0 / r_ik;
+
+ directorCos_ik_x = invR_ik * r_ik_x;
+ directorCos_ik_y = invR_ik * r_ik_y;
+ directorCos_ik_z = invR_ik * r_ik_z;
+
+ gtetaFunctionIJK = preGtetaFunction[neighbor_j][neighbor_k];
+
+ cutoffFunctionIK = preCutoffFunction[neighbor_k];
+
+ zeta += cutoffFunctionIK * gtetaFunctionIJK;
+
}
// first loop over neighbours of atom i except j - part 2/2
for (int neighbor_k = neighbor_j+1; neighbor_k < jnum; neighbor_k++) {
- double dr_ik[3], r_ik;
-
- k = jlist[neighbor_k];
- k &= NEIGHMASK;
- ktype = map[type[k]];
- ikparam = elem2param[itype][ktype][ktype];
- ijkparam = elem2param[itype][jtype][ktype];
-
- dr_ik[0] = xtmp -x[k][0];
- dr_ik[1] = ytmp -x[k][1];
- dr_ik[2] = ztmp -x[k][2];
- r_ik = dr_ik[0]*dr_ik[0] + dr_ik[1]*dr_ik[1] + dr_ik[2]*dr_ik[2];
-
- if (r_ik > params[ikparam].cutsq) continue;
-
- r_ik = sqrt(r_ik);
- invR_ik = 1.0 / r_ik;
-
- directorCos_ik_x = invR_ik * dr_ik[0];
- directorCos_ik_y = invR_ik * dr_ik[1];
- directorCos_ik_z = invR_ik * dr_ik[2];
-
- gtetaFunctionIJK = preGtetaFunction[neighbor_j][neighbor_k];
-
- cutoffFunctionIK = preCutoffFunction[neighbor_k];
-
- zeta += cutoffFunctionIK * gtetaFunctionIJK;
+ double dr_ik[3], r_ik;
+
+ k = jlist[neighbor_k];
+ k &= NEIGHMASK;
+ ktype = map[type[k]];
+ ikparam = elem2param[itype][ktype][ktype];
+ ijkparam = elem2param[itype][jtype][ktype];
+
+ dr_ik[0] = xtmp -x[k][0];
+ dr_ik[1] = ytmp -x[k][1];
+ dr_ik[2] = ztmp -x[k][2];
+ r_ik = dr_ik[0]*dr_ik[0] + dr_ik[1]*dr_ik[1] + dr_ik[2]*dr_ik[2];
+
+ if (r_ik > params[ikparam].cutsq) continue;
+
+ r_ik = sqrt(r_ik);
+ invR_ik = 1.0 / r_ik;
+
+ directorCos_ik_x = invR_ik * dr_ik[0];
+ directorCos_ik_y = invR_ik * dr_ik[1];
+ directorCos_ik_z = invR_ik * dr_ik[2];
+
+ gtetaFunctionIJK = preGtetaFunction[neighbor_j][neighbor_k];
+
+ cutoffFunctionIK = preCutoffFunction[neighbor_k];
+
+ zeta += cutoffFunctionIK * gtetaFunctionIJK;
}
-
- // betaZetaPowerIJK
+
+ // betaZetaPowerIJK
interpolDeltaX= params[ijparam].beta * zeta;
interpolTMP = (interpolDeltaX * GRIDDENSITY_BIJ);
interpolIDX = (int) interpolTMP;
@@ -358,145 +358,145 @@ void PairTersoffTableOMP::eval(int iifrom, int iito, ThrData * const thr)
fztmp -= f_ij[2];
// potential energy
- evdwl = cutoffFunctionIJ * repulsivePotential
- + cutoffFunctionIJ * attractivePotential * betaZetaPowerIJK;
+ evdwl = cutoffFunctionIJ * repulsivePotential
+ + cutoffFunctionIJ * attractivePotential * betaZetaPowerIJK;
if (EVFLAG) ev_tally_thr(this,i, j, nlocal, /* newton_pair */ 1, 0.5 * evdwl, 0.0,
- -factor_force_ij*invR_ij, dr_ij[0], dr_ij[1], dr_ij[2],thr);
+ -factor_force_ij*invR_ij, dr_ij[0], dr_ij[1], dr_ij[2],thr);
factor_force_tot= 0.5*cutoffFunctionIJ*attractivePotential*betaZetaPowerDerivedIJK;
// second loop over neighbours of atom i except j, forces and virial only - part 1/2
for (int neighbor_k = 0; neighbor_k < neighbor_j; neighbor_k++) {
- double dr_ik[3], r_ik, f_ik[3];
-
- k = jlist[neighbor_k];
- k &= NEIGHMASK;
- ktype = map[type[k]];
- ikparam = elem2param[itype][ktype][ktype];
- ijkparam = elem2param[itype][jtype][ktype];
-
- dr_ik[0] = xtmp -x[k][0];
- dr_ik[1] = ytmp -x[k][1];
- dr_ik[2] = ztmp -x[k][2];
- r_ik = dr_ik[0]*dr_ik[0] + dr_ik[1]*dr_ik[1] + dr_ik[2]*dr_ik[2];
-
- if (r_ik > params[ikparam].cutsq) continue;
-
- r_ik = sqrt(r_ik);
- invR_ik = 1.0 / r_ik;
-
- directorCos_ik_x = invR_ik * dr_ik[0];
- directorCos_ik_y = invR_ik * dr_ik[1];
- directorCos_ik_z = invR_ik * dr_ik[2];
-
- cosTeta = directorCos_ij_x * directorCos_ik_x + directorCos_ij_y * directorCos_ik_y
- + directorCos_ij_z * directorCos_ik_z;
-
- gtetaFunctionIJK = preGtetaFunction[neighbor_j][neighbor_k];
-
- gtetaFunctionDerivedIJK = preGtetaFunctionDerived[neighbor_j][neighbor_k];
-
- cutoffFunctionIK = preCutoffFunction[neighbor_k];
-
- cutoffFunctionDerivedIK = preCutoffFunctionDerived[neighbor_k];
-
- factor_force3_ij= cutoffFunctionIK * gtetaFunctionDerivedIJK * invR_ij *factor_force_tot;
-
- f_ij[0] = factor_force3_ij * (directorCos_ij_x*cosTeta - directorCos_ik_x);
- f_ij[1] = factor_force3_ij * (directorCos_ij_y*cosTeta - directorCos_ik_y);
- f_ij[2] = factor_force3_ij * (directorCos_ij_z*cosTeta - directorCos_ik_z);
-
- factor_1_force3_ik = (cutoffFunctionIK * gtetaFunctionDerivedIJK * invR_ik)*factor_force_tot;
- factor_2_force3_ik = -(cutoffFunctionDerivedIK * gtetaFunctionIJK)*factor_force_tot;
-
- f_ik[0] = factor_1_force3_ik * (directorCos_ik_x*cosTeta - directorCos_ij_x)
- + factor_2_force3_ik * directorCos_ik_x;
- f_ik[1] = factor_1_force3_ik * (directorCos_ik_y*cosTeta - directorCos_ij_y)
- + factor_2_force3_ik * directorCos_ik_y;
- f_ik[2] = factor_1_force3_ik * (directorCos_ik_z*cosTeta - directorCos_ij_z)
- + factor_2_force3_ik * directorCos_ik_z;
-
- f[j][0] -= f_ij[0];
- f[j][1] -= f_ij[1];
- f[j][2] -= f_ij[2];
-
- f[k][0] -= f_ik[0];
- f[k][1] -= f_ik[1];
- f[k][2] -= f_ik[2];
-
- fxtmp += f_ij[0] + f_ik[0];
- fytmp += f_ij[1] + f_ik[1];
- fztmp += f_ij[2] + f_ik[2];
-
- if (VFLAG_ATOM) v_tally3_thr(i,j,k,f_ij,f_ik,dr_ij,dr_ik,thr);
+ double dr_ik[3], r_ik, f_ik[3];
+
+ k = jlist[neighbor_k];
+ k &= NEIGHMASK;
+ ktype = map[type[k]];
+ ikparam = elem2param[itype][ktype][ktype];
+ ijkparam = elem2param[itype][jtype][ktype];
+
+ dr_ik[0] = xtmp -x[k][0];
+ dr_ik[1] = ytmp -x[k][1];
+ dr_ik[2] = ztmp -x[k][2];
+ r_ik = dr_ik[0]*dr_ik[0] + dr_ik[1]*dr_ik[1] + dr_ik[2]*dr_ik[2];
+
+ if (r_ik > params[ikparam].cutsq) continue;
+
+ r_ik = sqrt(r_ik);
+ invR_ik = 1.0 / r_ik;
+
+ directorCos_ik_x = invR_ik * dr_ik[0];
+ directorCos_ik_y = invR_ik * dr_ik[1];
+ directorCos_ik_z = invR_ik * dr_ik[2];
+
+ cosTeta = directorCos_ij_x * directorCos_ik_x + directorCos_ij_y * directorCos_ik_y
+ + directorCos_ij_z * directorCos_ik_z;
+
+ gtetaFunctionIJK = preGtetaFunction[neighbor_j][neighbor_k];
+
+ gtetaFunctionDerivedIJK = preGtetaFunctionDerived[neighbor_j][neighbor_k];
+
+ cutoffFunctionIK = preCutoffFunction[neighbor_k];
+
+ cutoffFunctionDerivedIK = preCutoffFunctionDerived[neighbor_k];
+
+ factor_force3_ij= cutoffFunctionIK * gtetaFunctionDerivedIJK * invR_ij *factor_force_tot;
+
+ f_ij[0] = factor_force3_ij * (directorCos_ij_x*cosTeta - directorCos_ik_x);
+ f_ij[1] = factor_force3_ij * (directorCos_ij_y*cosTeta - directorCos_ik_y);
+ f_ij[2] = factor_force3_ij * (directorCos_ij_z*cosTeta - directorCos_ik_z);
+
+ factor_1_force3_ik = (cutoffFunctionIK * gtetaFunctionDerivedIJK * invR_ik)*factor_force_tot;
+ factor_2_force3_ik = -(cutoffFunctionDerivedIK * gtetaFunctionIJK)*factor_force_tot;
+
+ f_ik[0] = factor_1_force3_ik * (directorCos_ik_x*cosTeta - directorCos_ij_x)
+ + factor_2_force3_ik * directorCos_ik_x;
+ f_ik[1] = factor_1_force3_ik * (directorCos_ik_y*cosTeta - directorCos_ij_y)
+ + factor_2_force3_ik * directorCos_ik_y;
+ f_ik[2] = factor_1_force3_ik * (directorCos_ik_z*cosTeta - directorCos_ij_z)
+ + factor_2_force3_ik * directorCos_ik_z;
+
+ f[j][0] -= f_ij[0];
+ f[j][1] -= f_ij[1];
+ f[j][2] -= f_ij[2];
+
+ f[k][0] -= f_ik[0];
+ f[k][1] -= f_ik[1];
+ f[k][2] -= f_ik[2];
+
+ fxtmp += f_ij[0] + f_ik[0];
+ fytmp += f_ij[1] + f_ik[1];
+ fztmp += f_ij[2] + f_ik[2];
+
+ if (VFLAG_ATOM) v_tally3_thr(i,j,k,f_ij,f_ik,dr_ij,dr_ik,thr);
}
-
+
// second loop over neighbours of atom i except j, forces and virial only - part 2/2
for (int neighbor_k = neighbor_j+1; neighbor_k < jnum; neighbor_k++) {
- double dr_ik[3], r_ik, f_ik[3];
-
- k = jlist[neighbor_k];
- k &= NEIGHMASK;
- ktype = map[type[k]];
- ikparam = elem2param[itype][ktype][ktype];
- ijkparam = elem2param[itype][jtype][ktype];
-
- dr_ik[0] = xtmp -x[k][0];
- dr_ik[1] = ytmp -x[k][1];
- dr_ik[2] = ztmp -x[k][2];
- r_ik = dr_ik[0]*dr_ik[0] + dr_ik[1]*dr_ik[1] + dr_ik[2]*dr_ik[2];
-
- if (r_ik > params[ikparam].cutsq) continue;
-
- r_ik = sqrt(r_ik);
- invR_ik = 1.0 / r_ik;
-
- directorCos_ik_x = invR_ik * dr_ik[0];
- directorCos_ik_y = invR_ik * dr_ik[1];
- directorCos_ik_z = invR_ik * dr_ik[2];
-
- cosTeta = directorCos_ij_x * directorCos_ik_x + directorCos_ij_y * directorCos_ik_y
- + directorCos_ij_z * directorCos_ik_z;
-
- gtetaFunctionIJK = preGtetaFunction[neighbor_j][neighbor_k];
-
- gtetaFunctionDerivedIJK = preGtetaFunctionDerived[neighbor_j][neighbor_k];
-
- cutoffFunctionIK = preCutoffFunction[neighbor_k];
-
- cutoffFunctionDerivedIK = preCutoffFunctionDerived[neighbor_k];
-
- factor_force3_ij= cutoffFunctionIK * gtetaFunctionDerivedIJK * invR_ij *factor_force_tot;
-
- f_ij[0] = factor_force3_ij * (directorCos_ij_x*cosTeta - directorCos_ik_x);
- f_ij[1] = factor_force3_ij * (directorCos_ij_y*cosTeta - directorCos_ik_y);
- f_ij[2] = factor_force3_ij * (directorCos_ij_z*cosTeta - directorCos_ik_z);
-
- factor_1_force3_ik = (cutoffFunctionIK * gtetaFunctionDerivedIJK * invR_ik)*factor_force_tot;
- factor_2_force3_ik = -(cutoffFunctionDerivedIK * gtetaFunctionIJK)*factor_force_tot;
-
- f_ik[0] = factor_1_force3_ik * (directorCos_ik_x*cosTeta - directorCos_ij_x)
- + factor_2_force3_ik * directorCos_ik_x;
- f_ik[1] = factor_1_force3_ik * (directorCos_ik_y*cosTeta - directorCos_ij_y)
- + factor_2_force3_ik * directorCos_ik_y;
- f_ik[2] = factor_1_force3_ik * (directorCos_ik_z*cosTeta - directorCos_ij_z)
- + factor_2_force3_ik * directorCos_ik_z;
-
- f[j][0] -= f_ij[0];
- f[j][1] -= f_ij[1];
- f[j][2] -= f_ij[2];
-
- f[k][0] -= f_ik[0];
- f[k][1] -= f_ik[1];
- f[k][2] -= f_ik[2];
-
- fxtmp += f_ij[0] + f_ik[0];
- fytmp += f_ij[1] + f_ik[1];
- fztmp += f_ij[2] + f_ik[2];
-
- if (VFLAG_ATOM) v_tally3_thr(i,j,k,f_ij,f_ik,dr_ij,dr_ik,thr);
-
+ double dr_ik[3], r_ik, f_ik[3];
+
+ k = jlist[neighbor_k];
+ k &= NEIGHMASK;
+ ktype = map[type[k]];
+ ikparam = elem2param[itype][ktype][ktype];
+ ijkparam = elem2param[itype][jtype][ktype];
+
+ dr_ik[0] = xtmp -x[k][0];
+ dr_ik[1] = ytmp -x[k][1];
+ dr_ik[2] = ztmp -x[k][2];
+ r_ik = dr_ik[0]*dr_ik[0] + dr_ik[1]*dr_ik[1] + dr_ik[2]*dr_ik[2];
+
+ if (r_ik > params[ikparam].cutsq) continue;
+
+ r_ik = sqrt(r_ik);
+ invR_ik = 1.0 / r_ik;
+
+ directorCos_ik_x = invR_ik * dr_ik[0];
+ directorCos_ik_y = invR_ik * dr_ik[1];
+ directorCos_ik_z = invR_ik * dr_ik[2];
+
+ cosTeta = directorCos_ij_x * directorCos_ik_x + directorCos_ij_y * directorCos_ik_y
+ + directorCos_ij_z * directorCos_ik_z;
+
+ gtetaFunctionIJK = preGtetaFunction[neighbor_j][neighbor_k];
+
+ gtetaFunctionDerivedIJK = preGtetaFunctionDerived[neighbor_j][neighbor_k];
+
+ cutoffFunctionIK = preCutoffFunction[neighbor_k];
+
+ cutoffFunctionDerivedIK = preCutoffFunctionDerived[neighbor_k];
+
+ factor_force3_ij= cutoffFunctionIK * gtetaFunctionDerivedIJK * invR_ij *factor_force_tot;
+
+ f_ij[0] = factor_force3_ij * (directorCos_ij_x*cosTeta - directorCos_ik_x);
+ f_ij[1] = factor_force3_ij * (directorCos_ij_y*cosTeta - directorCos_ik_y);
+ f_ij[2] = factor_force3_ij * (directorCos_ij_z*cosTeta - directorCos_ik_z);
+
+ factor_1_force3_ik = (cutoffFunctionIK * gtetaFunctionDerivedIJK * invR_ik)*factor_force_tot;
+ factor_2_force3_ik = -(cutoffFunctionDerivedIK * gtetaFunctionIJK)*factor_force_tot;
+
+ f_ik[0] = factor_1_force3_ik * (directorCos_ik_x*cosTeta - directorCos_ij_x)
+ + factor_2_force3_ik * directorCos_ik_x;
+ f_ik[1] = factor_1_force3_ik * (directorCos_ik_y*cosTeta - directorCos_ij_y)
+ + factor_2_force3_ik * directorCos_ik_y;
+ f_ik[2] = factor_1_force3_ik * (directorCos_ik_z*cosTeta - directorCos_ij_z)
+ + factor_2_force3_ik * directorCos_ik_z;
+
+ f[j][0] -= f_ij[0];
+ f[j][1] -= f_ij[1];
+ f[j][2] -= f_ij[2];
+
+ f[k][0] -= f_ik[0];
+ f[k][1] -= f_ik[1];
+ f[k][2] -= f_ik[2];
+
+ fxtmp += f_ij[0] + f_ik[0];
+ fytmp += f_ij[1] + f_ik[1];
+ fztmp += f_ij[2] + f_ik[2];
+
+ if (VFLAG_ATOM) v_tally3_thr(i,j,k,f_ij,f_ik,dr_ij,dr_ik,thr);
+
}
} // loop on J
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_tersoff_zbl_omp.cpp b/src/USER-OMP/pair_tersoff_zbl_omp.cpp
index 74e77d5444b108d192e8d16a9feb429da8f84b98..f143312e0a4542cd6cce17e2b9fecaefe2fb3d77 100644
--- a/src/USER-OMP/pair_tersoff_zbl_omp.cpp
+++ b/src/USER-OMP/pair_tersoff_zbl_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -111,8 +111,8 @@ void PairTersoffZBLOMP::read_file(char *file)
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fp);
if (ptr == NULL) {
- eof = 1;
- fclose(fp);
+ eof = 1;
+ fclose(fp);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
@@ -133,8 +133,8 @@ void PairTersoffZBLOMP::read_file(char *file)
if (comm->me == 0) {
ptr = fgets(&line[n],MAXLINE-n,fp);
if (ptr == NULL) {
- eof = 1;
- fclose(fp);
+ eof = 1;
+ fclose(fp);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
@@ -173,7 +173,7 @@ void PairTersoffZBLOMP::read_file(char *file)
if (nparams == maxparam) {
maxparam += DELTA;
params = (Param *) memory->srealloc(params,maxparam*sizeof(Param),
- "pair:params");
+ "pair:params");
}
params[nparams].ielement = ielement;
@@ -203,18 +203,18 @@ void PairTersoffZBLOMP::read_file(char *file)
params[nparams].powermint = int(params[nparams].powerm);
if (
- params[nparams].lam3 < 0.0 || params[nparams].c < 0.0 ||
- params[nparams].d < 0.0 || params[nparams].powern < 0.0 ||
- params[nparams].beta < 0.0 || params[nparams].lam2 < 0.0 ||
- params[nparams].bigb < 0.0 || params[nparams].bigr < 0.0 ||
- params[nparams].bigd < 0.0 ||
- params[nparams].bigd > params[nparams].bigr ||
- params[nparams].lam3 < 0.0 || params[nparams].biga < 0.0 ||
- params[nparams].powerm - params[nparams].powermint != 0.0 ||
+ params[nparams].lam3 < 0.0 || params[nparams].c < 0.0 ||
+ params[nparams].d < 0.0 || params[nparams].powern < 0.0 ||
+ params[nparams].beta < 0.0 || params[nparams].lam2 < 0.0 ||
+ params[nparams].bigb < 0.0 || params[nparams].bigr < 0.0 ||
+ params[nparams].bigd < 0.0 ||
+ params[nparams].bigd > params[nparams].bigr ||
+ params[nparams].lam3 < 0.0 || params[nparams].biga < 0.0 ||
+ params[nparams].powerm - params[nparams].powermint != 0.0 ||
(params[nparams].powermint != 3 && params[nparams].powermint != 1) ||
- params[nparams].gamma < 0.0 ||
- params[nparams].Z_i < 1.0 || params[nparams].Z_j < 1.0 ||
- params[nparams].ZBLcut < 0.0 || params[nparams].ZBLexpscale < 0.0)
+ params[nparams].gamma < 0.0 ||
+ params[nparams].Z_i < 1.0 || params[nparams].Z_j < 1.0 ||
+ params[nparams].ZBLcut < 0.0 || params[nparams].ZBLexpscale < 0.0)
error->all(FLERR,"Illegal Tersoff parameter");
nparams++;
@@ -226,21 +226,21 @@ void PairTersoffZBLOMP::read_file(char *file)
/* ---------------------------------------------------------------------- */
void PairTersoffZBLOMP::force_zeta(Param *param, double rsq, double zeta_ij,
- double &fforce, double &prefactor,
- int eflag, double &eng)
+ double &fforce, double &prefactor,
+ int eflag, double &eng)
{
double r,fa,fa_d,bij;
r = sqrt(rsq);
fa = (r > param->bigr + param->bigd) ? 0.0 :
- -param->bigb * exp(-param->lam2 * r) * ters_fc(r,param) *
+ -param->bigb * exp(-param->lam2 * r) * ters_fc(r,param) *
F_fermi(r,param->ZBLexpscale,param->ZBLcut);
fa_d = (r > param->bigr + param->bigd) ? 0.0 :
param->bigb * exp(-param->lam2 * r) *
- (param->lam2 * ters_fc(r,param) *
- F_fermi(r,param->ZBLexpscale,param->ZBLcut) -
+ (param->lam2 * ters_fc(r,param) *
+ F_fermi(r,param->ZBLexpscale,param->ZBLcut) -
ters_fc_d(r,param) * F_fermi(r,param->ZBLexpscale,param->ZBLcut)
- ters_fc(r,param) * F_fermi_d(r,param->ZBLexpscale,param->ZBLcut));
@@ -253,7 +253,7 @@ void PairTersoffZBLOMP::force_zeta(Param *param, double rsq, double zeta_ij,
/* ---------------------------------------------------------------------- */
void PairTersoffZBLOMP::repulsive(Param *param, double rsq, double &fforce,
- int eflag, double &eng)
+ int eflag, double &eng)
{
double r,tmp_fc,tmp_fc_d,tmp_exp;
@@ -265,32 +265,31 @@ void PairTersoffZBLOMP::repulsive(Param *param, double rsq, double &fforce,
tmp_exp = exp(-param->lam1 * r);
double fforce_ters = param->biga * tmp_exp * (tmp_fc_d - tmp_fc*param->lam1);
double eng_ters = tmp_fc * param->biga * tmp_exp;
-
+
// ZBL repulsive portion
double esq = pow(global_e,2.0);
- double a_ij = (0.8854*global_a_0) /
+ double a_ij = (0.8854*global_a_0) /
(pow(param->Z_i,0.23) + pow(param->Z_j,0.23));
double premult = (param->Z_i * param->Z_j * esq)/(4.0*MY_PI*global_epsilon_0);
double r_ov_a = r/a_ij;
- double phi = 0.1818*exp(-3.2*r_ov_a) + 0.5099*exp(-0.9423*r_ov_a) +
+ double phi = 0.1818*exp(-3.2*r_ov_a) + 0.5099*exp(-0.9423*r_ov_a) +
0.2802*exp(-0.4029*r_ov_a) + 0.02817*exp(-0.2016*r_ov_a);
- double dphi = (1.0/a_ij) * (-3.2*0.1818*exp(-3.2*r_ov_a) -
- 0.9423*0.5099*exp(-0.9423*r_ov_a) -
- 0.4029*0.2802*exp(-0.4029*r_ov_a) -
- 0.2016*0.02817*exp(-0.2016*r_ov_a));
+ double dphi = (1.0/a_ij) * (-3.2*0.1818*exp(-3.2*r_ov_a) -
+ 0.9423*0.5099*exp(-0.9423*r_ov_a) -
+ 0.4029*0.2802*exp(-0.4029*r_ov_a) -
+ 0.2016*0.02817*exp(-0.2016*r_ov_a));
double fforce_ZBL = premult*-pow(r,-2.0)* phi + premult*pow(r,-1.0)*dphi;
double eng_ZBL = premult*(1.0/r)*phi;
-
+
// combine two parts with smoothing by Fermi-like function
fforce = -(-F_fermi_d(r,param->ZBLexpscale,param->ZBLcut) * eng_ZBL +
- (1.0 - F_fermi(r,param->ZBLexpscale,param->ZBLcut))*fforce_ZBL +
- F_fermi_d(r,param->ZBLexpscale,param->ZBLcut)*eng_ters +
- F_fermi(r,param->ZBLexpscale,param->ZBLcut)*fforce_ters) / r;
-
+ (1.0 - F_fermi(r,param->ZBLexpscale,param->ZBLcut))*fforce_ZBL +
+ F_fermi_d(r,param->ZBLexpscale,param->ZBLcut)*eng_ters +
+ F_fermi(r,param->ZBLexpscale,param->ZBLcut)*fforce_ters) / r;
+
if (eflag)
eng = (1.0 - F_fermi(r,param->ZBLexpscale,param->ZBLcut))*eng_ZBL +
F_fermi(r,param->ZBLexpscale,param->ZBLcut)*eng_ters;
}
-
diff --git a/src/USER-OMP/pair_tersoff_zbl_omp.h b/src/USER-OMP/pair_tersoff_zbl_omp.h
index 84d6ef1135794af4ac3636edc9bd595e7375663e..32d7b6b4c49a8e628c718acbea6b0eab0050eaf3 100644
--- a/src/USER-OMP/pair_tersoff_zbl_omp.h
+++ b/src/USER-OMP/pair_tersoff_zbl_omp.h
@@ -29,9 +29,9 @@ class PairTersoffZBLOMP : public PairTersoffOMP {
virtual ~PairTersoffZBLOMP() {}
protected:
- double global_a_0; // Bohr radius for Coulomb repulsion
- double global_epsilon_0; // permittivity of vacuum for Coulomb repulsion
- double global_e; // proton charge (negative of electron charge)
+ double global_a_0; // Bohr radius for Coulomb repulsion
+ double global_epsilon_0; // permittivity of vacuum for Coulomb repulsion
+ double global_e; // proton charge (negative of electron charge)
virtual void read_file(char *);
virtual void repulsive(Param *, double, double &, int, double &);
diff --git a/src/USER-OMP/pair_tri_lj_omp.cpp b/src/USER-OMP/pair_tri_lj_omp.cpp
index eedbc570afcbcff4f21b0b76188013647d284815..16dce231babfdcecc33c226442820b89cb054a55 100644
--- a/src/USER-OMP/pair_tri_lj_omp.cpp
+++ b/src/USER-OMP/pair_tri_lj_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -71,16 +71,16 @@ void PairTriLJOMP::compute(int eflag, int vflag)
// until we find a good way to multi-thread it.
for (int i = 0; i < nall; ++i) {
double dc1[3],dc2[3],dc3[3],p[3][3];
-
+
if (tri[i] >= 0) {
if (dnum[i] == 0) {
- MathExtra::quat_to_mat(bonus[tri[i]].quat,p);
- MathExtra::matvec(p,bonus[tri[i]].c1,dc1);
- MathExtra::matvec(p,bonus[tri[i]].c2,dc2);
- MathExtra::matvec(p,bonus[tri[i]].c3,dc3);
- dfirst[i] = ndiscrete;
- discretize(i,sigma[type[i]][type[i]],dc1,dc2,dc3);
- dnum[i] = ndiscrete - dfirst[i];
+ MathExtra::quat_to_mat(bonus[tri[i]].quat,p);
+ MathExtra::matvec(p,bonus[tri[i]].c1,dc1);
+ MathExtra::matvec(p,bonus[tri[i]].c2,dc2);
+ MathExtra::matvec(p,bonus[tri[i]].c3,dc3);
+ dfirst[i] = ndiscrete;
+ discretize(i,sigma[type[i]][type[i]],dc1,dc2,dc3);
+ dnum[i] = ndiscrete - dfirst[i];
}
}
}
@@ -97,11 +97,11 @@ void PairTriLJOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -155,247 +155,247 @@ void PairTriLJOMP::eval(int iifrom, int iito, ThrData * const thr)
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
-
+
if (rsq >= cutsq[itype][jtype]) continue;
-
+
// tri/tri interactions = NxN particles
// c1,c2,c3 = corner pts of triangle I or J
-
+
evdwl = 0.0;
if (tri[i] >= 0 && tri[j] >= 0) {
- npi = dnum[i];
- ifirst = dfirst[i];
- npj = dnum[j];
- jfirst = dfirst[j];
-
- fi[0]=fi[1]=fi[2]=fj[0]=fj[1]=fj[2]=0.0;
- ti[0]=ti[1]=ti[2]=tj[0]=tj[1]=tj[2]=0.0;
-
- for (ni = 0; ni < npi; ni++) {
- dxi = discrete[ifirst+ni].dx;
- dyi = discrete[ifirst+ni].dy;
- dzi = discrete[ifirst+ni].dz;
-
- for (nj = 0; nj < npj; nj++) {
- dxj = discrete[jfirst+nj].dx;
- dyj = discrete[jfirst+nj].dy;
- dzj = discrete[jfirst+nj].dz;
-
- xi[0] = x[i][0] + dxi;
- xi[1] = x[i][1] + dyi;
- xi[2] = x[i][2] + dzi;
- xj[0] = x[j][0] + dxj;
- xj[1] = x[j][1] + dyj;
- xj[2] = x[j][2] + dzj;
-
- delx = xi[0] - xj[0];
- dely = xi[1] - xj[1];
- delz = xi[2] - xj[2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- sig = 0.5 * (discrete[ifirst+ni].sigma+discrete[jfirst+nj].sigma);
- sig3 = sig*sig*sig;
- term2 = 24.0*epsilon[itype][jtype] * sig3*sig3;
- term1 = 2.0 * term2 * sig3*sig3;
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (term1*r6inv - term2);
- fpair = forcelj*r2inv;
-
- if (EFLAG) evdwl += r6inv*(term1/12.0*r6inv-term2/6.0);
-
- fi[0] += delx*fpair;
- fi[1] += dely*fpair;
- fi[2] += delz*fpair;
- ti[0] += fpair*(dyi*delz - dzi*dely);
- ti[1] += fpair*(dzi*delx - dxi*delz);
- ti[2] += fpair*(dxi*dely - dyi*delx);
-
- if (NEWTON_PAIR || j < nlocal) {
- fj[0] -= delx*fpair;
- fj[1] -= dely*fpair;
- fj[2] -= delz*fpair;
- tj[0] -= fpair*(dyj*delz - dzj*dely);
- tj[1] -= fpair*(dzj*delx - dxj*delz);
- tj[2] -= fpair*(dxj*dely - dyj*delx);
- }
- }
- }
-
- f[i][0] += fi[0];
- f[i][1] += fi[1];
- f[i][2] += fi[2];
- f[j][0] += fj[0];
- f[j][1] += fj[1];
- f[j][2] += fj[2];
- torque[i][0] += ti[0];
- torque[i][1] += ti[1];
- torque[i][2] += ti[2];
- torque[j][0] += tj[0];
- torque[j][1] += tj[1];
- torque[j][2] += tj[2];
-
- // tri/particle interaction = Nx1 particles
- // c1,c2,c3 = corner pts of triangle I
+ npi = dnum[i];
+ ifirst = dfirst[i];
+ npj = dnum[j];
+ jfirst = dfirst[j];
+
+ fi[0]=fi[1]=fi[2]=fj[0]=fj[1]=fj[2]=0.0;
+ ti[0]=ti[1]=ti[2]=tj[0]=tj[1]=tj[2]=0.0;
+
+ for (ni = 0; ni < npi; ni++) {
+ dxi = discrete[ifirst+ni].dx;
+ dyi = discrete[ifirst+ni].dy;
+ dzi = discrete[ifirst+ni].dz;
+
+ for (nj = 0; nj < npj; nj++) {
+ dxj = discrete[jfirst+nj].dx;
+ dyj = discrete[jfirst+nj].dy;
+ dzj = discrete[jfirst+nj].dz;
+
+ xi[0] = x[i][0] + dxi;
+ xi[1] = x[i][1] + dyi;
+ xi[2] = x[i][2] + dzi;
+ xj[0] = x[j][0] + dxj;
+ xj[1] = x[j][1] + dyj;
+ xj[2] = x[j][2] + dzj;
+
+ delx = xi[0] - xj[0];
+ dely = xi[1] - xj[1];
+ delz = xi[2] - xj[2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ sig = 0.5 * (discrete[ifirst+ni].sigma+discrete[jfirst+nj].sigma);
+ sig3 = sig*sig*sig;
+ term2 = 24.0*epsilon[itype][jtype] * sig3*sig3;
+ term1 = 2.0 * term2 * sig3*sig3;
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (term1*r6inv - term2);
+ fpair = forcelj*r2inv;
+
+ if (EFLAG) evdwl += r6inv*(term1/12.0*r6inv-term2/6.0);
+
+ fi[0] += delx*fpair;
+ fi[1] += dely*fpair;
+ fi[2] += delz*fpair;
+ ti[0] += fpair*(dyi*delz - dzi*dely);
+ ti[1] += fpair*(dzi*delx - dxi*delz);
+ ti[2] += fpair*(dxi*dely - dyi*delx);
+
+ if (NEWTON_PAIR || j < nlocal) {
+ fj[0] -= delx*fpair;
+ fj[1] -= dely*fpair;
+ fj[2] -= delz*fpair;
+ tj[0] -= fpair*(dyj*delz - dzj*dely);
+ tj[1] -= fpair*(dzj*delx - dxj*delz);
+ tj[2] -= fpair*(dxj*dely - dyj*delx);
+ }
+ }
+ }
+
+ f[i][0] += fi[0];
+ f[i][1] += fi[1];
+ f[i][2] += fi[2];
+ f[j][0] += fj[0];
+ f[j][1] += fj[1];
+ f[j][2] += fj[2];
+ torque[i][0] += ti[0];
+ torque[i][1] += ti[1];
+ torque[i][2] += ti[2];
+ torque[j][0] += tj[0];
+ torque[j][1] += tj[1];
+ torque[j][2] += tj[2];
+
+ // tri/particle interaction = Nx1 particles
+ // c1,c2,c3 = corner pts of triangle I
} else if (tri[i] >= 0) {
- npi = dnum[i];
- ifirst = dfirst[i];
-
- fi[0]=fi[1]=fi[2]=fj[0]=fj[1]=fj[2]=0.0;
- ti[0]=ti[1]=ti[2]=tj[0]=tj[1]=tj[2]=0.0;
-
- for (ni = 0; ni < npi; ni++) {
- dxi = discrete[ifirst+ni].dx;
- dyi = discrete[ifirst+ni].dy;
- dzi = discrete[ifirst+ni].dz;
-
- xi[0] = x[i][0] + dxi;
- xi[1] = x[i][1] + dyi;
- xi[2] = x[i][2] + dzi;
- xj[0] = x[j][0];
- xj[1] = x[j][1];
- xj[2] = x[j][2];
-
- delx = xi[0] - xj[0];
- dely = xi[1] - xj[1];
- delz = xi[2] - xj[2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- sig = 0.5 * (discrete[ifirst+ni].sigma+sigma[jtype][jtype]);
- sig3 = sig*sig*sig;
- term2 = 24.0*epsilon[itype][jtype] * sig3*sig3;
- term1 = 2.0 * term2 * sig3*sig3;
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (term1*r6inv - term2);
- fpair = forcelj*r2inv;
-
- if (EFLAG) evdwl += r6inv*(term1/12.0*r6inv-term2/6.0);
-
- fi[0] += delx*fpair;
- fi[1] += dely*fpair;
- fi[2] += delz*fpair;
- ti[0] += fpair*(dyi*delz - dzi*dely);
- ti[1] += fpair*(dzi*delx - dxi*delz);
- ti[2] += fpair*(dxi*dely - dyi*delx);
-
- if (NEWTON_PAIR || j < nlocal) {
- fj[0] -= delx*fpair;
- fj[1] -= dely*fpair;
- fj[2] -= delz*fpair;
- tj[0] -= fpair*(dyj*delz - dzj*dely);
- tj[1] -= fpair*(dzj*delx - dxj*delz);
- tj[2] -= fpair*(dxj*dely - dyj*delx);
- }
- }
-
- f[i][0] += fi[0];
- f[i][1] += fi[1];
- f[i][2] += fi[2];
- f[j][0] += fj[0];
- f[j][1] += fj[1];
- f[j][2] += fj[2];
- torque[i][0] += ti[0];
- torque[i][1] += ti[1];
- torque[i][2] += ti[2];
- torque[j][0] += tj[0];
- torque[j][1] += tj[1];
- torque[j][2] += tj[2];
-
- // particle/tri interaction = Nx1 particles
- // c1,c2,c3 = corner pts of triangle J
+ npi = dnum[i];
+ ifirst = dfirst[i];
+
+ fi[0]=fi[1]=fi[2]=fj[0]=fj[1]=fj[2]=0.0;
+ ti[0]=ti[1]=ti[2]=tj[0]=tj[1]=tj[2]=0.0;
+
+ for (ni = 0; ni < npi; ni++) {
+ dxi = discrete[ifirst+ni].dx;
+ dyi = discrete[ifirst+ni].dy;
+ dzi = discrete[ifirst+ni].dz;
+
+ xi[0] = x[i][0] + dxi;
+ xi[1] = x[i][1] + dyi;
+ xi[2] = x[i][2] + dzi;
+ xj[0] = x[j][0];
+ xj[1] = x[j][1];
+ xj[2] = x[j][2];
+
+ delx = xi[0] - xj[0];
+ dely = xi[1] - xj[1];
+ delz = xi[2] - xj[2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ sig = 0.5 * (discrete[ifirst+ni].sigma+sigma[jtype][jtype]);
+ sig3 = sig*sig*sig;
+ term2 = 24.0*epsilon[itype][jtype] * sig3*sig3;
+ term1 = 2.0 * term2 * sig3*sig3;
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (term1*r6inv - term2);
+ fpair = forcelj*r2inv;
+
+ if (EFLAG) evdwl += r6inv*(term1/12.0*r6inv-term2/6.0);
+
+ fi[0] += delx*fpair;
+ fi[1] += dely*fpair;
+ fi[2] += delz*fpair;
+ ti[0] += fpair*(dyi*delz - dzi*dely);
+ ti[1] += fpair*(dzi*delx - dxi*delz);
+ ti[2] += fpair*(dxi*dely - dyi*delx);
+
+ if (NEWTON_PAIR || j < nlocal) {
+ fj[0] -= delx*fpair;
+ fj[1] -= dely*fpair;
+ fj[2] -= delz*fpair;
+ tj[0] -= fpair*(dyj*delz - dzj*dely);
+ tj[1] -= fpair*(dzj*delx - dxj*delz);
+ tj[2] -= fpair*(dxj*dely - dyj*delx);
+ }
+ }
+
+ f[i][0] += fi[0];
+ f[i][1] += fi[1];
+ f[i][2] += fi[2];
+ f[j][0] += fj[0];
+ f[j][1] += fj[1];
+ f[j][2] += fj[2];
+ torque[i][0] += ti[0];
+ torque[i][1] += ti[1];
+ torque[i][2] += ti[2];
+ torque[j][0] += tj[0];
+ torque[j][1] += tj[1];
+ torque[j][2] += tj[2];
+
+ // particle/tri interaction = Nx1 particles
+ // c1,c2,c3 = corner pts of triangle J
} else if (tri[j] >= 0) {
- npj = dnum[j];
- jfirst = dfirst[j];
-
- fi[0]=fi[1]=fi[2]=fj[0]=fj[1]=fj[2]=0.0;
- ti[0]=ti[1]=ti[2]=tj[0]=tj[1]=tj[2]=0.0;
-
- for (nj = 0; nj < npj; nj++) {
- dxj = discrete[jfirst+nj].dx;
- dyj = discrete[jfirst+nj].dy;
- dzj = discrete[jfirst+nj].dz;
-
- xi[0] = x[i][0];
- xi[1] = x[i][1];
- xi[2] = x[i][2];
- xj[0] = x[j][0] + dxj;
- xj[1] = x[j][1] + dyj;
- xj[2] = x[j][2] + dzj;
-
- delx = xi[0] - xj[0];
- dely = xi[1] - xj[1];
- delz = xi[2] - xj[2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- sig = 0.5 * (sigma[itype][itype]+discrete[jfirst+nj].sigma);
- sig3 = sig*sig*sig;
- term2 = 24.0*epsilon[itype][jtype] * sig3*sig3;
- term1 = 2.0 * term2 * sig3*sig3;
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (term1*r6inv - term2);
- fpair = forcelj*r2inv;
-
- if (EFLAG) evdwl += r6inv*(term1/12.0*r6inv-term2/6.0);
-
- if (EFLAG) evdwl += r6inv*(term1/12.0*r6inv-term2/6.0);
-
- fi[0] += delx*fpair;
- fi[1] += dely*fpair;
- fi[2] += delz*fpair;
- ti[0] += fpair*(dyi*delz - dzi*dely);
- ti[1] += fpair*(dzi*delx - dxi*delz);
- ti[2] += fpair*(dxi*dely - dyi*delx);
-
- if (NEWTON_PAIR || j < nlocal) {
- fj[0] -= delx*fpair;
- fj[1] -= dely*fpair;
- fj[2] -= delz*fpair;
- tj[0] -= fpair*(dyj*delz - dzj*dely);
- tj[1] -= fpair*(dzj*delx - dxj*delz);
- tj[2] -= fpair*(dxj*dely - dyj*delx);
- }
- }
-
- f[i][0] += fi[0];
- f[i][1] += fi[1];
- f[i][2] += fi[2];
- f[j][0] += fj[0];
- f[j][1] += fj[1];
- f[j][2] += fj[2];
- torque[i][0] += ti[0];
- torque[i][1] += ti[1];
- torque[i][2] += ti[2];
- torque[j][0] += tj[0];
- torque[j][1] += tj[1];
- torque[j][2] += tj[2];
-
- // particle/particle interaction = 1x1 particles
+ npj = dnum[j];
+ jfirst = dfirst[j];
+
+ fi[0]=fi[1]=fi[2]=fj[0]=fj[1]=fj[2]=0.0;
+ ti[0]=ti[1]=ti[2]=tj[0]=tj[1]=tj[2]=0.0;
+
+ for (nj = 0; nj < npj; nj++) {
+ dxj = discrete[jfirst+nj].dx;
+ dyj = discrete[jfirst+nj].dy;
+ dzj = discrete[jfirst+nj].dz;
+
+ xi[0] = x[i][0];
+ xi[1] = x[i][1];
+ xi[2] = x[i][2];
+ xj[0] = x[j][0] + dxj;
+ xj[1] = x[j][1] + dyj;
+ xj[2] = x[j][2] + dzj;
+
+ delx = xi[0] - xj[0];
+ dely = xi[1] - xj[1];
+ delz = xi[2] - xj[2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ sig = 0.5 * (sigma[itype][itype]+discrete[jfirst+nj].sigma);
+ sig3 = sig*sig*sig;
+ term2 = 24.0*epsilon[itype][jtype] * sig3*sig3;
+ term1 = 2.0 * term2 * sig3*sig3;
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (term1*r6inv - term2);
+ fpair = forcelj*r2inv;
+
+ if (EFLAG) evdwl += r6inv*(term1/12.0*r6inv-term2/6.0);
+
+ if (EFLAG) evdwl += r6inv*(term1/12.0*r6inv-term2/6.0);
+
+ fi[0] += delx*fpair;
+ fi[1] += dely*fpair;
+ fi[2] += delz*fpair;
+ ti[0] += fpair*(dyi*delz - dzi*dely);
+ ti[1] += fpair*(dzi*delx - dxi*delz);
+ ti[2] += fpair*(dxi*dely - dyi*delx);
+
+ if (NEWTON_PAIR || j < nlocal) {
+ fj[0] -= delx*fpair;
+ fj[1] -= dely*fpair;
+ fj[2] -= delz*fpair;
+ tj[0] -= fpair*(dyj*delz - dzj*dely);
+ tj[1] -= fpair*(dzj*delx - dxj*delz);
+ tj[2] -= fpair*(dxj*dely - dyj*delx);
+ }
+ }
+
+ f[i][0] += fi[0];
+ f[i][1] += fi[1];
+ f[i][2] += fi[2];
+ f[j][0] += fj[0];
+ f[j][1] += fj[1];
+ f[j][2] += fj[2];
+ torque[i][0] += ti[0];
+ torque[i][1] += ti[1];
+ torque[i][2] += ti[2];
+ torque[j][0] += tj[0];
+ torque[j][1] += tj[1];
+ torque[j][2] += tj[2];
+
+ // particle/particle interaction = 1x1 particles
} else {
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- fpair = forcelj*r2inv;
-
- if (EFLAG)
- evdwl += r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ fpair = forcelj*r2inv;
+
+ if (EFLAG)
+ evdwl += r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
}
if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
- evdwl,0.0,fpair,delx,dely,delz,thr);
+ evdwl,0.0,fpair,delx,dely,delz,thr);
}
}
}
diff --git a/src/USER-OMP/pair_tri_lj_omp.h b/src/USER-OMP/pair_tri_lj_omp.h
index d21c562a80a96fac2ab3dccc1693e0971b8f2b2b..7c66fdcf44d1f4d200f9caf620eecf251c23321f 100644
--- a/src/USER-OMP/pair_tri_lj_omp.h
+++ b/src/USER-OMP/pair_tri_lj_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_yukawa_colloid_omp.cpp b/src/USER-OMP/pair_yukawa_colloid_omp.cpp
index 101f69f1dc5130731965ec1cbcf247544a165acd..e66d1bb2bf8309c61bd4cbb6066dd13c3260a627 100644
--- a/src/USER-OMP/pair_yukawa_colloid_omp.cpp
+++ b/src/USER-OMP/pair_yukawa_colloid_omp.cpp
@@ -56,11 +56,11 @@ void PairYukawaColloidOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -120,28 +120,28 @@ void PairYukawaColloidOMP::eval(int iifrom, int iito, ThrData * const thr)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r = sqrt(rsq);
- rinv = 1.0/r;
- screening = exp(-kappa*(r-(radi+radj)));
- forceyukawa = a[itype][jtype] * screening;
-
- fpair = factor*forceyukawa * rinv;
-
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (EFLAG) {
- evdwl = a[itype][jtype]/kappa * screening - offset[itype][jtype];
- evdwl *= factor;
- }
- if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
- evdwl,0.0,fpair,delx,dely,delz,thr);
+ r = sqrt(rsq);
+ rinv = 1.0/r;
+ screening = exp(-kappa*(r-(radi+radj)));
+ forceyukawa = a[itype][jtype] * screening;
+
+ fpair = factor*forceyukawa * rinv;
+
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (EFLAG) {
+ evdwl = a[itype][jtype]/kappa * screening - offset[itype][jtype];
+ evdwl *= factor;
+ }
+ if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
+ evdwl,0.0,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_yukawa_colloid_omp.h b/src/USER-OMP/pair_yukawa_colloid_omp.h
index c424e9eff354c7974c8f32230e6000525c50eb3e..b0ef483b5bc62d7f28d5a50e1d1ea50ace24866d 100644
--- a/src/USER-OMP/pair_yukawa_colloid_omp.h
+++ b/src/USER-OMP/pair_yukawa_colloid_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pair_yukawa_omp.cpp b/src/USER-OMP/pair_yukawa_omp.cpp
index c7fa20e814d87f08403bed9ba4c7377dae054260..3028901a9ea5067e2f8b0a0d1aac341a3bded776 100644
--- a/src/USER-OMP/pair_yukawa_omp.cpp
+++ b/src/USER-OMP/pair_yukawa_omp.cpp
@@ -56,11 +56,11 @@ void PairYukawaOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
- if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
- else eval<1,1,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+ else eval<1,1,0>(ifrom, ito, thr);
} else {
- if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
- else eval<1,0,0>(ifrom, ito, thr);
+ if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+ else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
@@ -117,30 +117,30 @@ void PairYukawaOMP::eval(int iifrom, int iito, ThrData * const thr)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- r = sqrt(rsq);
- rinv = 1.0/r;
- screening = exp(-kappa*r);
- forceyukawa = a[itype][jtype] * screening * (kappa + rinv);
-
- fpair = factor*forceyukawa * r2inv;
-
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
- if (NEWTON_PAIR || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (EFLAG) {
- evdwl = a[itype][jtype] * screening * rinv - offset[itype][jtype];
- evdwl *= factor;
- }
-
- if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
- evdwl,0.0,fpair,delx,dely,delz,thr);
+ r2inv = 1.0/rsq;
+ r = sqrt(rsq);
+ rinv = 1.0/r;
+ screening = exp(-kappa*r);
+ forceyukawa = a[itype][jtype] * screening * (kappa + rinv);
+
+ fpair = factor*forceyukawa * r2inv;
+
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+ if (NEWTON_PAIR || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (EFLAG) {
+ evdwl = a[itype][jtype] * screening * rinv - offset[itype][jtype];
+ evdwl *= factor;
+ }
+
+ if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
+ evdwl,0.0,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
diff --git a/src/USER-OMP/pair_yukawa_omp.h b/src/USER-OMP/pair_yukawa_omp.h
index 99abc569fa207274d9d8ea8ce2261d8f2d8b98b4..d9db21347450054a27289782a0454a2cc7b2188b 100644
--- a/src/USER-OMP/pair_yukawa_omp.h
+++ b/src/USER-OMP/pair_yukawa_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pppm_cg_omp.cpp b/src/USER-OMP/pppm_cg_omp.cpp
index 47708f9829e9871d647d26565d1b90aaa303a27d..51fc048b3b6cd2456c550ac8be3f69f26481880e 100644
--- a/src/USER-OMP/pppm_cg_omp.cpp
+++ b/src/USER-OMP/pppm_cg_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -48,7 +48,7 @@ PPPMCGOMP::PPPMCGOMP(LAMMPS *lmp, int narg, char **arg) :
}
/* ----------------------------------------------------------------------
- allocate memory that depends on # of K-vectors and order
+ allocate memory that depends on # of K-vectors and order
------------------------------------------------------------------------- */
void PPPMCGOMP::allocate()
@@ -78,7 +78,7 @@ void PPPMCGOMP::allocate()
// reallocate density brick, so it fits our needs
memory->destroy3d_offset(density_brick,nzlo_out,nylo_out,nxlo_out);
memory->create3d_offset(density_brick,nzlo_out,nzend,nylo_out,nyhi_out,
- nxlo_out,nxhi_out,"pppm:density_brick");
+ nxlo_out,nxhi_out,"pppm:density_brick");
}
// NOTE: special version of reduce_data for FFT_SCALAR data type.
@@ -102,12 +102,12 @@ static void data_reduce_fft(FFT_SCALAR *dall, int nall, int nthreads, int ndim,
const int ito = ((ifrom + idelta) > nvals) ? nvals : (ifrom + idelta);
// this if protects against having more threads than atoms
- if (ifrom < nall) {
+ if (ifrom < nall) {
for (int m = ifrom; m < ito; ++m) {
- for (int n = 1; n < nthreads; ++n) {
- dall[m] += dall[n*nvals + m];
- dall[n*nvals + m] = 0.0;
- }
+ for (int n = 1; n < nthreads; ++n) {
+ dall[m] += dall[n*nvals + m];
+ dall[n*nvals + m] = 0.0;
+ }
}
}
}
@@ -118,7 +118,7 @@ static void data_reduce_fft(FFT_SCALAR *dall, int nall, int nthreads, int ndim,
}
/* ----------------------------------------------------------------------
- free memory that depends on # of K-vectors and order
+ free memory that depends on # of K-vectors and order
------------------------------------------------------------------------- */
void PPPMCGOMP::deallocate()
@@ -132,7 +132,7 @@ void PPPMCGOMP::deallocate()
}
/* ----------------------------------------------------------------------
- adjust PPPMCG coeffs, called initially and whenever volume has changed
+ adjust PPPMCG coeffs, called initially and whenever volume has changed
------------------------------------------------------------------------- */
void PPPMCGOMP::setup()
@@ -152,7 +152,7 @@ void PPPMCGOMP::setup()
const double zprd = prd[2];
const double zprd_slab = zprd*slab_volfactor;
volume = xprd * yprd * zprd_slab;
-
+
delxinv = nx_pppm/xprd;
delyinv = ny_pppm/yprd;
delzinv = nz_pppm/zprd_slab;
@@ -190,36 +190,36 @@ void PPPMCGOMP::setup()
for (k = nzlo_fft; k <= nzhi_fft; k++) {
for (j = nylo_fft; j <= nyhi_fft; j++) {
for (i = nxlo_fft; i <= nxhi_fft; i++) {
- sqk = fkx[i]*fkx[i] + fky[j]*fky[j] + fkz[k]*fkz[k];
- if (sqk == 0.0) {
- vg[n][0] = 0.0;
- vg[n][1] = 0.0;
- vg[n][2] = 0.0;
- vg[n][3] = 0.0;
- vg[n][4] = 0.0;
- vg[n][5] = 0.0;
- } else {
- vterm = -2.0 * (1.0/sqk + 0.25/(g_ewald*g_ewald));
- vg[n][0] = 1.0 + vterm*fkx[i]*fkx[i];
- vg[n][1] = 1.0 + vterm*fky[j]*fky[j];
- vg[n][2] = 1.0 + vterm*fkz[k]*fkz[k];
- vg[n][3] = vterm*fkx[i]*fky[j];
- vg[n][4] = vterm*fkx[i]*fkz[k];
- vg[n][5] = vterm*fky[j]*fkz[k];
- }
- n++;
+ sqk = fkx[i]*fkx[i] + fky[j]*fky[j] + fkz[k]*fkz[k];
+ if (sqk == 0.0) {
+ vg[n][0] = 0.0;
+ vg[n][1] = 0.0;
+ vg[n][2] = 0.0;
+ vg[n][3] = 0.0;
+ vg[n][4] = 0.0;
+ vg[n][5] = 0.0;
+ } else {
+ vterm = -2.0 * (1.0/sqk + 0.25/(g_ewald*g_ewald));
+ vg[n][0] = 1.0 + vterm*fkx[i]*fkx[i];
+ vg[n][1] = 1.0 + vterm*fky[j]*fky[j];
+ vg[n][2] = 1.0 + vterm*fkz[k]*fkz[k];
+ vg[n][3] = vterm*fkx[i]*fky[j];
+ vg[n][4] = vterm*fkx[i]*fkz[k];
+ vg[n][5] = vterm*fky[j]*fkz[k];
+ }
+ n++;
}
}
}
// modified (Hockney-Eastwood) Coulomb Green's function
- const int nbx = static_cast<int> ((g_ewald*xprd/(MY_PI*nx_pppm)) *
- pow(-log(EPS_HOC),0.25));
- const int nby = static_cast<int> ((g_ewald*yprd/(MY_PI*ny_pppm)) *
- pow(-log(EPS_HOC),0.25));
- const int nbz = static_cast<int> ((g_ewald*zprd_slab/(MY_PI*nz_pppm)) *
- pow(-log(EPS_HOC),0.25));
+ const int nbx = static_cast<int> ((g_ewald*xprd/(MY_PI*nx_pppm)) *
+ pow(-log(EPS_HOC),0.25));
+ const int nby = static_cast<int> ((g_ewald*yprd/(MY_PI*ny_pppm)) *
+ pow(-log(EPS_HOC),0.25));
+ const int nbz = static_cast<int> ((g_ewald*zprd_slab/(MY_PI*nz_pppm)) *
+ pow(-log(EPS_HOC),0.25));
const double form = 1.0;
@@ -233,80 +233,80 @@ void PPPMCGOMP::setup()
double sum1,dot1,dot2;
double numerator,denominator;
const double gew2 = -4.0*g_ewald*g_ewald;
-
+
const int nnx = nxhi_fft-nxlo_fft+1;
const int nny = nyhi_fft-nylo_fft+1;
-
+
loop_setup_thr(nnfrom, nnto, tid, nfft, comm->nthreads);
-
+
for (m = nzlo_fft; m <= nzhi_fft; m++) {
-
+
const double fkzm = fkz[m];
snz = sin(0.5*fkzm*zprd_slab/nz_pppm);
snz *= snz;
for (l = nylo_fft; l <= nyhi_fft; l++) {
- const double fkyl = fky[l];
- sny = sin(0.5*fkyl*yprd/ny_pppm);
- sny *= sny;
+ const double fkyl = fky[l];
+ sny = sin(0.5*fkyl*yprd/ny_pppm);
+ sny *= sny;
+
+ for (k = nxlo_fft; k <= nxhi_fft; k++) {
- for (k = nxlo_fft; k <= nxhi_fft; k++) {
+ /* only compute the part designated to this thread */
+ nn = k-nxlo_fft + nnx*(l-nylo_fft + nny*(m-nzlo_fft));
+ if ((nn < nnfrom) || (nn >=nnto)) continue;
- /* only compute the part designated to this thread */
- nn = k-nxlo_fft + nnx*(l-nylo_fft + nny*(m-nzlo_fft));
- if ((nn < nnfrom) || (nn >=nnto)) continue;
+ const double fkxk = fkx[k];
+ snx = sin(0.5*fkxk*xprd/nx_pppm);
+ snx *= snx;
- const double fkxk = fkx[k];
- snx = sin(0.5*fkxk*xprd/nx_pppm);
- snx *= snx;
-
- sqk = fkxk*fkxk + fkyl*fkyl + fkzm*fkzm;
+ sqk = fkxk*fkxk + fkyl*fkyl + fkzm*fkzm;
- if (sqk != 0.0) {
- numerator = form*MY_4PI/sqk;
- denominator = gf_denom(snx,sny,snz);
+ if (sqk != 0.0) {
+ numerator = form*MY_4PI/sqk;
+ denominator = gf_denom(snx,sny,snz);
const double dorder = static_cast<double>(order);
- sum1 = 0.0;
- for (nx = -nbx; nx <= nbx; nx++) {
- qx = fkxk + unitkx*nx_pppm*nx;
- sx = exp(qx*qx/gew2);
- wx = 1.0;
- argx = 0.5*qx*xprd/nx_pppm;
- if (argx != 0.0) wx = pow(sin(argx)/argx,dorder);
- wx *=wx;
-
- for (ny = -nby; ny <= nby; ny++) {
- qy = fkyl + unitky*ny_pppm*ny;
- sy = exp(qy*qy/gew2);
- wy = 1.0;
- argy = 0.5*qy*yprd/ny_pppm;
- if (argy != 0.0) wy = pow(sin(argy)/argy,dorder);
- wy *= wy;
-
- for (nz = -nbz; nz <= nbz; nz++) {
- qz = fkzm + unitkz*nz_pppm*nz;
- sz = exp(qz*qz/gew2);
- wz = 1.0;
- argz = 0.5*qz*zprd_slab/nz_pppm;
- if (argz != 0.0) wz = pow(sin(argz)/argz,dorder);
- wz *= wz;
-
- dot1 = fkxk*qx + fkyl*qy + fkzm*qz;
- dot2 = qx*qx+qy*qy+qz*qz;
- sum1 += (dot1/dot2) * sx*sy*sz * wx*wy*wz;
- }
- }
- }
- greensfn[nn] = numerator*sum1/denominator;
- } else greensfn[nn] = 0.0;
- }
+ sum1 = 0.0;
+ for (nx = -nbx; nx <= nbx; nx++) {
+ qx = fkxk + unitkx*nx_pppm*nx;
+ sx = exp(qx*qx/gew2);
+ wx = 1.0;
+ argx = 0.5*qx*xprd/nx_pppm;
+ if (argx != 0.0) wx = pow(sin(argx)/argx,dorder);
+ wx *=wx;
+
+ for (ny = -nby; ny <= nby; ny++) {
+ qy = fkyl + unitky*ny_pppm*ny;
+ sy = exp(qy*qy/gew2);
+ wy = 1.0;
+ argy = 0.5*qy*yprd/ny_pppm;
+ if (argy != 0.0) wy = pow(sin(argy)/argy,dorder);
+ wy *= wy;
+
+ for (nz = -nbz; nz <= nbz; nz++) {
+ qz = fkzm + unitkz*nz_pppm*nz;
+ sz = exp(qz*qz/gew2);
+ wz = 1.0;
+ argz = 0.5*qz*zprd_slab/nz_pppm;
+ if (argz != 0.0) wz = pow(sin(argz)/argz,dorder);
+ wz *= wz;
+
+ dot1 = fkxk*qx + fkyl*qy + fkzm*qz;
+ dot2 = qx*qx+qy*qy+qz*qz;
+ sum1 += (dot1/dot2) * sx*sy*sz * wx*wy*wz;
+ }
+ }
+ }
+ greensfn[nn] = numerator*sum1/denominator;
+ } else greensfn[nn] = 0.0;
+ }
}
}
}
}
/* ----------------------------------------------------------------------
- run the regular toplevel compute method from plain PPPPMCG
+ run the regular toplevel compute method from plain PPPPMCG
which will have individual methods replaced by our threaded
versions and then call the obligatory force reduction.
------------------------------------------------------------------------- */
@@ -334,7 +334,7 @@ void PPPMCGOMP::compute(int eflag, int vflag)
create discretized "density" on section of global grid due to my particles
density(x,y,z) = charge "density" at grid points of my 3d brick
(nxlo:nxhi,nylo:nyhi,nzlo:nzhi) is extent of my brick (including ghosts)
- in global grid
+ in global grid
------------------------------------------------------------------------- */
void PPPMCGOMP::make_rho()
@@ -346,7 +346,7 @@ void PPPMCGOMP::make_rho()
#if defined(_OPENMP)
#pragma omp parallel default(none)
#endif
- {
+ {
#if defined(_OPENMP)
// each thread works on a fixed chunk of atoms.
const int tid = omp_get_thread_num();
@@ -379,30 +379,30 @@ void PPPMCGOMP::make_rho()
// this if protects against having more threads than charged local atoms
if (ifrom < num_charged) {
for (j = ifrom; j < ito; j++) {
- i = is_charged[j];
-
- nx = part2grid[i][0];
- ny = part2grid[i][1];
- nz = part2grid[i][2];
- dx = nx+shiftone - (x[i][0]-boxlo[0])*delxinv;
- dy = ny+shiftone - (x[i][1]-boxlo[1])*delyinv;
- dz = nz+shiftone - (x[i][2]-boxlo[2])*delzinv;
-
- compute_rho1d_thr(r1d,dx,dy,dz);
-
- z0 = delvolinv * q[i];
- for (n = nlower; n <= nupper; n++) {
- mz = n+nz;
- y0 = z0*r1d[2][n];
- for (m = nlower; m <= nupper; m++) {
- my = m+ny;
- x0 = y0*r1d[1][m];
- for (l = nlower; l <= nupper; l++) {
- mx = l+nx;
- db[mz][my][mx] += x0*r1d[0][l];
- }
- }
- }
+ i = is_charged[j];
+
+ nx = part2grid[i][0];
+ ny = part2grid[i][1];
+ nz = part2grid[i][2];
+ dx = nx+shiftone - (x[i][0]-boxlo[0])*delxinv;
+ dy = ny+shiftone - (x[i][1]-boxlo[1])*delyinv;
+ dz = nz+shiftone - (x[i][2]-boxlo[2])*delzinv;
+
+ compute_rho1d_thr(r1d,dx,dy,dz);
+
+ z0 = delvolinv * q[i];
+ for (n = nlower; n <= nupper; n++) {
+ mz = n+nz;
+ y0 = z0*r1d[2][n];
+ for (m = nlower; m <= nupper; m++) {
+ my = m+ny;
+ x0 = y0*r1d[1][m];
+ for (l = nlower; l <= nupper; l++) {
+ mx = l+nx;
+ db[mz][my][mx] += x0*r1d[0][l];
+ }
+ }
+ }
}
}
#if defined(_OPENMP)
@@ -415,7 +415,7 @@ void PPPMCGOMP::make_rho()
}
/* ----------------------------------------------------------------------
- interpolate from grid to get electric field & force on my particles
+ interpolate from grid to get electric field & force on my particles
------------------------------------------------------------------------- */
void PPPMCGOMP::fieldforce()
@@ -434,7 +434,7 @@ void PPPMCGOMP::fieldforce()
#if defined(_OPENMP)
#pragma omp parallel default(none)
#endif
- {
+ {
#if defined(_OPENMP)
// each thread works on a fixed chunk of atoms.
const int tid = omp_get_thread_num();
@@ -450,47 +450,47 @@ void PPPMCGOMP::fieldforce()
ThrData *thr = fix->get_thr(tid);
double * const * const f = thr->get_f();
FFT_SCALAR * const * const r1d = static_cast<FFT_SCALAR **>(thr->get_rho1d());
-
+
int i,j,l,m,n,nx,ny,nz,mx,my,mz;
FFT_SCALAR dx,dy,dz,x0,y0,z0;
FFT_SCALAR ekx,eky,ekz;
// this if protects against having more threads than charged local atoms
- if (ifrom < num_charged) {
+ if (ifrom < num_charged) {
for (j = ifrom; j < ito; j++) {
- i = is_charged[j];
-
- nx = part2grid[i][0];
- ny = part2grid[i][1];
- nz = part2grid[i][2];
- dx = nx+shiftone - (x[i][0]-boxlo[0])*delxinv;
- dy = ny+shiftone - (x[i][1]-boxlo[1])*delyinv;
- dz = nz+shiftone - (x[i][2]-boxlo[2])*delzinv;
-
- compute_rho1d_thr(r1d,dx,dy,dz);
-
- ekx = eky = ekz = ZEROF;
- for (n = nlower; n <= nupper; n++) {
- mz = n+nz;
- z0 = r1d[2][n];
- for (m = nlower; m <= nupper; m++) {
- my = m+ny;
- y0 = z0*r1d[1][m];
- for (l = nlower; l <= nupper; l++) {
- mx = l+nx;
- x0 = y0*r1d[0][l];
- ekx -= x0*vdx_brick[mz][my][mx];
- eky -= x0*vdy_brick[mz][my][mx];
- ekz -= x0*vdz_brick[mz][my][mx];
- }
- }
- }
-
- // convert E-field to force
- const double qfactor = qqrd2e*scale*q[i];
- f[i][0] += qfactor*ekx;
- f[i][1] += qfactor*eky;
- f[i][2] += qfactor*ekz;
+ i = is_charged[j];
+
+ nx = part2grid[i][0];
+ ny = part2grid[i][1];
+ nz = part2grid[i][2];
+ dx = nx+shiftone - (x[i][0]-boxlo[0])*delxinv;
+ dy = ny+shiftone - (x[i][1]-boxlo[1])*delyinv;
+ dz = nz+shiftone - (x[i][2]-boxlo[2])*delzinv;
+
+ compute_rho1d_thr(r1d,dx,dy,dz);
+
+ ekx = eky = ekz = ZEROF;
+ for (n = nlower; n <= nupper; n++) {
+ mz = n+nz;
+ z0 = r1d[2][n];
+ for (m = nlower; m <= nupper; m++) {
+ my = m+ny;
+ y0 = z0*r1d[1][m];
+ for (l = nlower; l <= nupper; l++) {
+ mx = l+nx;
+ x0 = y0*r1d[0][l];
+ ekx -= x0*vdx_brick[mz][my][mx];
+ eky -= x0*vdy_brick[mz][my][mx];
+ ekz -= x0*vdz_brick[mz][my][mx];
+ }
+ }
+ }
+
+ // convert E-field to force
+ const double qfactor = qqrd2e*scale*q[i];
+ f[i][0] += qfactor*ekx;
+ f[i][1] += qfactor*eky;
+ f[i][2] += qfactor*ekz;
}
}
}
@@ -537,49 +537,49 @@ void PPPMCGOMP::fieldforce_peratom()
// this if protects against having more threads than charged local atoms
if (ifrom < num_charged) {
for (j = ifrom; j < ito; j++) {
- i = is_charged[j];
-
- nx = part2grid[i][0];
- ny = part2grid[i][1];
- nz = part2grid[i][2];
- dx = nx+shiftone - (x[i][0]-boxlo[0])*delxinv;
- dy = ny+shiftone - (x[i][1]-boxlo[1])*delyinv;
- dz = nz+shiftone - (x[i][2]-boxlo[2])*delzinv;
-
- compute_rho1d_thr(r1d,dx,dy,dz);
-
- u = v0 = v1 = v2 = v3 = v4 = v5 = ZEROF;
- for (n = nlower; n <= nupper; n++) {
- mz = n+nz;
- z0 = r1d[2][n];
- for (m = nlower; m <= nupper; m++) {
- my = m+ny;
- y0 = z0*r1d[1][m];
- for (l = nlower; l <= nupper; l++) {
- mx = l+nx;
- x0 = y0*r1d[0][l];
- if (eflag_atom) u += x0*u_brick[mz][my][mx];
- if (vflag_atom) {
- v0 += x0*v0_brick[mz][my][mx];
- v1 += x0*v1_brick[mz][my][mx];
- v2 += x0*v2_brick[mz][my][mx];
- v3 += x0*v3_brick[mz][my][mx];
- v4 += x0*v4_brick[mz][my][mx];
- v5 += x0*v5_brick[mz][my][mx];
- }
- }
- }
- }
-
- if (eflag_atom) eatom[i] += q[i]*u;
- if (vflag_atom) {
- vatom[i][0] += v0;
- vatom[i][1] += v1;
- vatom[i][2] += v2;
- vatom[i][3] += v3;
- vatom[i][4] += v4;
- vatom[i][5] += v5;
- }
+ i = is_charged[j];
+
+ nx = part2grid[i][0];
+ ny = part2grid[i][1];
+ nz = part2grid[i][2];
+ dx = nx+shiftone - (x[i][0]-boxlo[0])*delxinv;
+ dy = ny+shiftone - (x[i][1]-boxlo[1])*delyinv;
+ dz = nz+shiftone - (x[i][2]-boxlo[2])*delzinv;
+
+ compute_rho1d_thr(r1d,dx,dy,dz);
+
+ u = v0 = v1 = v2 = v3 = v4 = v5 = ZEROF;
+ for (n = nlower; n <= nupper; n++) {
+ mz = n+nz;
+ z0 = r1d[2][n];
+ for (m = nlower; m <= nupper; m++) {
+ my = m+ny;
+ y0 = z0*r1d[1][m];
+ for (l = nlower; l <= nupper; l++) {
+ mx = l+nx;
+ x0 = y0*r1d[0][l];
+ if (eflag_atom) u += x0*u_brick[mz][my][mx];
+ if (vflag_atom) {
+ v0 += x0*v0_brick[mz][my][mx];
+ v1 += x0*v1_brick[mz][my][mx];
+ v2 += x0*v2_brick[mz][my][mx];
+ v3 += x0*v3_brick[mz][my][mx];
+ v4 += x0*v4_brick[mz][my][mx];
+ v5 += x0*v5_brick[mz][my][mx];
+ }
+ }
+ }
+ }
+
+ if (eflag_atom) eatom[i] += q[i]*u;
+ if (vflag_atom) {
+ vatom[i][0] += v0;
+ vatom[i][1] += v1;
+ vatom[i][2] += v2;
+ vatom[i][3] += v3;
+ vatom[i][4] += v4;
+ vatom[i][5] += v5;
+ }
}
}
}
@@ -587,10 +587,10 @@ void PPPMCGOMP::fieldforce_peratom()
/* ----------------------------------------------------------------------
charge assignment into rho1d
- dx,dy,dz = distance of particle from "lower left" grid point
+ dx,dy,dz = distance of particle from "lower left" grid point
------------------------------------------------------------------------- */
void PPPMCGOMP::compute_rho1d_thr(FFT_SCALAR * const * const r1d, const FFT_SCALAR &dx,
- const FFT_SCALAR &dy, const FFT_SCALAR &dz)
+ const FFT_SCALAR &dy, const FFT_SCALAR &dz)
{
int k,l;
FFT_SCALAR r1,r2,r3;
@@ -608,4 +608,3 @@ void PPPMCGOMP::compute_rho1d_thr(FFT_SCALAR * const * const r1d, const FFT_SCAL
r1d[2][k] = r3;
}
}
-
diff --git a/src/USER-OMP/pppm_cg_omp.h b/src/USER-OMP/pppm_cg_omp.h
index 598c5522a64642b20e51fed2f7fe829c673b0bdc..10a9d35f29e445ae4c36bb4ee48f0af5a54b0d9f 100644
--- a/src/USER-OMP/pppm_cg_omp.h
+++ b/src/USER-OMP/pppm_cg_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -40,7 +40,7 @@ namespace LAMMPS_NS {
virtual void make_rho();
void compute_rho1d_thr(FFT_SCALAR * const * const, const FFT_SCALAR &,
- const FFT_SCALAR &, const FFT_SCALAR &);
+ const FFT_SCALAR &, const FFT_SCALAR &);
// void compute_rho_coeff();
// void slabcorr(int);
diff --git a/src/USER-OMP/pppm_omp.cpp b/src/USER-OMP/pppm_omp.cpp
index 24308de5346323caec7ae3ddc85f19c265fed98e..5c400b6f48a83a1626b3926efb6b86479deb0f6e 100644
--- a/src/USER-OMP/pppm_omp.cpp
+++ b/src/USER-OMP/pppm_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -49,7 +49,7 @@ PPPMOMP::PPPMOMP(LAMMPS *lmp, int narg, char **arg) :
}
/* ----------------------------------------------------------------------
- allocate memory that depends on # of K-vectors and order
+ allocate memory that depends on # of K-vectors and order
------------------------------------------------------------------------- */
void PPPMOMP::allocate()
@@ -79,7 +79,7 @@ void PPPMOMP::allocate()
// reallocate density brick, so it fits our needs
memory->destroy3d_offset(density_brick,nzlo_out,nylo_out,nxlo_out);
memory->create3d_offset(density_brick,nzlo_out,nzend,nylo_out,nyhi_out,
- nxlo_out,nxhi_out,"pppm:density_brick");
+ nxlo_out,nxhi_out,"pppm:density_brick");
}
// NOTE: special version of reduce_data for FFT_SCALAR data type.
@@ -103,12 +103,12 @@ static void data_reduce_fft(FFT_SCALAR *dall, int nall, int nthreads, int ndim,
const int ito = ((ifrom + idelta) > nvals) ? nvals : (ifrom + idelta);
// this if protects against having more threads than atoms
- if (ifrom < nall) {
+ if (ifrom < nall) {
for (int m = ifrom; m < ito; ++m) {
- for (int n = 1; n < nthreads; ++n) {
- dall[m] += dall[n*nvals + m];
- dall[n*nvals + m] = 0.0;
- }
+ for (int n = 1; n < nthreads; ++n) {
+ dall[m] += dall[n*nvals + m];
+ dall[n*nvals + m] = 0.0;
+ }
}
}
}
@@ -119,7 +119,7 @@ static void data_reduce_fft(FFT_SCALAR *dall, int nall, int nthreads, int ndim,
}
/* ----------------------------------------------------------------------
- free memory that depends on # of K-vectors and order
+ free memory that depends on # of K-vectors and order
------------------------------------------------------------------------- */
void PPPMOMP::deallocate()
@@ -133,7 +133,7 @@ void PPPMOMP::deallocate()
}
/* ----------------------------------------------------------------------
- adjust PPPM coeffs, called initially and whenever volume has changed
+ adjust PPPM coeffs, called initially and whenever volume has changed
------------------------------------------------------------------------- */
void PPPMOMP::setup()
@@ -153,7 +153,7 @@ void PPPMOMP::setup()
const double zprd = prd[2];
const double zprd_slab = zprd*slab_volfactor;
volume = xprd * yprd * zprd_slab;
-
+
delxinv = nx_pppm/xprd;
delyinv = ny_pppm/yprd;
delzinv = nz_pppm/zprd_slab;
@@ -191,36 +191,36 @@ void PPPMOMP::setup()
for (k = nzlo_fft; k <= nzhi_fft; k++) {
for (j = nylo_fft; j <= nyhi_fft; j++) {
for (i = nxlo_fft; i <= nxhi_fft; i++) {
- sqk = fkx[i]*fkx[i] + fky[j]*fky[j] + fkz[k]*fkz[k];
- if (sqk == 0.0) {
- vg[n][0] = 0.0;
- vg[n][1] = 0.0;
- vg[n][2] = 0.0;
- vg[n][3] = 0.0;
- vg[n][4] = 0.0;
- vg[n][5] = 0.0;
- } else {
- vterm = -2.0 * (1.0/sqk + 0.25/(g_ewald*g_ewald));
- vg[n][0] = 1.0 + vterm*fkx[i]*fkx[i];
- vg[n][1] = 1.0 + vterm*fky[j]*fky[j];
- vg[n][2] = 1.0 + vterm*fkz[k]*fkz[k];
- vg[n][3] = vterm*fkx[i]*fky[j];
- vg[n][4] = vterm*fkx[i]*fkz[k];
- vg[n][5] = vterm*fky[j]*fkz[k];
- }
- n++;
+ sqk = fkx[i]*fkx[i] + fky[j]*fky[j] + fkz[k]*fkz[k];
+ if (sqk == 0.0) {
+ vg[n][0] = 0.0;
+ vg[n][1] = 0.0;
+ vg[n][2] = 0.0;
+ vg[n][3] = 0.0;
+ vg[n][4] = 0.0;
+ vg[n][5] = 0.0;
+ } else {
+ vterm = -2.0 * (1.0/sqk + 0.25/(g_ewald*g_ewald));
+ vg[n][0] = 1.0 + vterm*fkx[i]*fkx[i];
+ vg[n][1] = 1.0 + vterm*fky[j]*fky[j];
+ vg[n][2] = 1.0 + vterm*fkz[k]*fkz[k];
+ vg[n][3] = vterm*fkx[i]*fky[j];
+ vg[n][4] = vterm*fkx[i]*fkz[k];
+ vg[n][5] = vterm*fky[j]*fkz[k];
+ }
+ n++;
}
}
}
// modified (Hockney-Eastwood) Coulomb Green's function
- const int nbx = static_cast<int> ((g_ewald*xprd/(MY_PI*nx_pppm)) *
- pow(-log(EPS_HOC),0.25));
- const int nby = static_cast<int> ((g_ewald*yprd/(MY_PI*ny_pppm)) *
- pow(-log(EPS_HOC),0.25));
- const int nbz = static_cast<int> ((g_ewald*zprd_slab/(MY_PI*nz_pppm)) *
- pow(-log(EPS_HOC),0.25));
+ const int nbx = static_cast<int> ((g_ewald*xprd/(MY_PI*nx_pppm)) *
+ pow(-log(EPS_HOC),0.25));
+ const int nby = static_cast<int> ((g_ewald*yprd/(MY_PI*ny_pppm)) *
+ pow(-log(EPS_HOC),0.25));
+ const int nbz = static_cast<int> ((g_ewald*zprd_slab/(MY_PI*nz_pppm)) *
+ pow(-log(EPS_HOC),0.25));
const double form = 1.0;
@@ -234,80 +234,80 @@ void PPPMOMP::setup()
double sum1,dot1,dot2;
double numerator,denominator;
const double gew2 = -4.0*g_ewald*g_ewald;
-
+
const int nnx = nxhi_fft-nxlo_fft+1;
const int nny = nyhi_fft-nylo_fft+1;
-
+
loop_setup_thr(nnfrom, nnto, tid, nfft, comm->nthreads);
-
+
for (m = nzlo_fft; m <= nzhi_fft; m++) {
-
+
const double fkzm = fkz[m];
snz = sin(0.5*fkzm*zprd_slab/nz_pppm);
snz *= snz;
for (l = nylo_fft; l <= nyhi_fft; l++) {
- const double fkyl = fky[l];
- sny = sin(0.5*fkyl*yprd/ny_pppm);
- sny *= sny;
-
- for (k = nxlo_fft; k <= nxhi_fft; k++) {
-
- /* only compute the part designated to this thread */
- nn = k-nxlo_fft + nnx*(l-nylo_fft + nny*(m-nzlo_fft));
- if ((nn < nnfrom) || (nn >=nnto)) continue;
-
- const double fkxk = fkx[k];
- snx = sin(0.5*fkxk*xprd/nx_pppm);
- snx *= snx;
-
- sqk = fkxk*fkxk + fkyl*fkyl + fkzm*fkzm;
-
- if (sqk != 0.0) {
- numerator = form*MY_4PI/sqk;
- denominator = gf_denom(snx,sny,snz);
- sum1 = 0.0;
- const double dorder = static_cast<double>(order);
- for (nx = -nbx; nx <= nbx; nx++) {
- qx = fkxk + unitkx*nx_pppm*nx;
- sx = exp(qx*qx/gew2);
- wx = 1.0;
- argx = 0.5*qx*xprd/nx_pppm;
- if (argx != 0.0) wx = pow(sin(argx)/argx,dorder);
- wx *=wx;
-
- for (ny = -nby; ny <= nby; ny++) {
- qy = fkyl + unitky*ny_pppm*ny;
- sy = exp(qy*qy/gew2);
- wy = 1.0;
- argy = 0.5*qy*yprd/ny_pppm;
- if (argy != 0.0) wy = pow(sin(argy)/argy,dorder);
- wy *= wy;
-
- for (nz = -nbz; nz <= nbz; nz++) {
- qz = fkzm + unitkz*nz_pppm*nz;
- sz = exp(qz*qz/gew2);
- wz = 1.0;
- argz = 0.5*qz*zprd_slab/nz_pppm;
- if (argz != 0.0) wz = pow(sin(argz)/argz,dorder);
- wz *= wz;
-
- dot1 = fkxk*qx + fkyl*qy + fkzm*qz;
- dot2 = qx*qx+qy*qy+qz*qz;
- sum1 += (dot1/dot2) * sx*sy*sz * wx*wy*wz;
- }
- }
- }
- greensfn[nn] = numerator*sum1/denominator;
- } else greensfn[nn] = 0.0;
- }
+ const double fkyl = fky[l];
+ sny = sin(0.5*fkyl*yprd/ny_pppm);
+ sny *= sny;
+
+ for (k = nxlo_fft; k <= nxhi_fft; k++) {
+
+ /* only compute the part designated to this thread */
+ nn = k-nxlo_fft + nnx*(l-nylo_fft + nny*(m-nzlo_fft));
+ if ((nn < nnfrom) || (nn >=nnto)) continue;
+
+ const double fkxk = fkx[k];
+ snx = sin(0.5*fkxk*xprd/nx_pppm);
+ snx *= snx;
+
+ sqk = fkxk*fkxk + fkyl*fkyl + fkzm*fkzm;
+
+ if (sqk != 0.0) {
+ numerator = form*MY_4PI/sqk;
+ denominator = gf_denom(snx,sny,snz);
+ sum1 = 0.0;
+ const double dorder = static_cast<double>(order);
+ for (nx = -nbx; nx <= nbx; nx++) {
+ qx = fkxk + unitkx*nx_pppm*nx;
+ sx = exp(qx*qx/gew2);
+ wx = 1.0;
+ argx = 0.5*qx*xprd/nx_pppm;
+ if (argx != 0.0) wx = pow(sin(argx)/argx,dorder);
+ wx *=wx;
+
+ for (ny = -nby; ny <= nby; ny++) {
+ qy = fkyl + unitky*ny_pppm*ny;
+ sy = exp(qy*qy/gew2);
+ wy = 1.0;
+ argy = 0.5*qy*yprd/ny_pppm;
+ if (argy != 0.0) wy = pow(sin(argy)/argy,dorder);
+ wy *= wy;
+
+ for (nz = -nbz; nz <= nbz; nz++) {
+ qz = fkzm + unitkz*nz_pppm*nz;
+ sz = exp(qz*qz/gew2);
+ wz = 1.0;
+ argz = 0.5*qz*zprd_slab/nz_pppm;
+ if (argz != 0.0) wz = pow(sin(argz)/argz,dorder);
+ wz *= wz;
+
+ dot1 = fkxk*qx + fkyl*qy + fkzm*qz;
+ dot2 = qx*qx+qy*qy+qz*qz;
+ sum1 += (dot1/dot2) * sx*sy*sz * wx*wy*wz;
+ }
+ }
+ }
+ greensfn[nn] = numerator*sum1/denominator;
+ } else greensfn[nn] = 0.0;
+ }
}
}
}
}
/* ----------------------------------------------------------------------
- run the regular toplevel compute method from plain PPPPM
+ run the regular toplevel compute method from plain PPPPM
which will have individual methods replaced by our threaded
versions and then call the obligatory force reduction.
------------------------------------------------------------------------- */
@@ -335,7 +335,7 @@ void PPPMOMP::compute(int eflag, int vflag)
create discretized "density" on section of global grid due to my particles
density(x,y,z) = charge "density" at grid points of my 3d brick
(nxlo:nxhi,nylo:nyhi,nzlo:nzhi) is extent of my brick (including ghosts)
- in global grid
+ in global grid
------------------------------------------------------------------------- */
void PPPMOMP::make_rho()
@@ -348,7 +348,7 @@ void PPPMOMP::make_rho()
#if defined(_OPENMP)
#pragma omp parallel default(none)
#endif
- {
+ {
#if defined(_OPENMP)
// each thread works on a fixed chunk of atoms.
const int tid = omp_get_thread_num();
@@ -377,33 +377,33 @@ void PPPMOMP::make_rho()
// (nx,ny,nz) = global coords of grid pt to "lower left" of charge
// (dx,dy,dz) = distance to "lower left" grid pt
// (mx,my,mz) = global coords of moving stencil pt
-
+
// this if protects against having more threads than local atoms
- if (ifrom < nlocal) {
+ if (ifrom < nlocal) {
for (int i = ifrom; i < ito; i++) {
- nx = part2grid[i][0];
- ny = part2grid[i][1];
- nz = part2grid[i][2];
- dx = nx+shiftone - (x[i][0]-boxlo[0])*delxinv;
- dy = ny+shiftone - (x[i][1]-boxlo[1])*delyinv;
- dz = nz+shiftone - (x[i][2]-boxlo[2])*delzinv;
-
- compute_rho1d_thr(r1d,dx,dy,dz);
-
- z0 = delvolinv * q[i];
- for (n = nlower; n <= nupper; n++) {
- mz = n+nz;
- y0 = z0*r1d[2][n];
- for (m = nlower; m <= nupper; m++) {
- my = m+ny;
- x0 = y0*r1d[1][m];
- for (l = nlower; l <= nupper; l++) {
- mx = l+nx;
- db[mz][my][mx] += x0*r1d[0][l];
- }
- }
- }
+ nx = part2grid[i][0];
+ ny = part2grid[i][1];
+ nz = part2grid[i][2];
+ dx = nx+shiftone - (x[i][0]-boxlo[0])*delxinv;
+ dy = ny+shiftone - (x[i][1]-boxlo[1])*delyinv;
+ dz = nz+shiftone - (x[i][2]-boxlo[2])*delzinv;
+
+ compute_rho1d_thr(r1d,dx,dy,dz);
+
+ z0 = delvolinv * q[i];
+ for (n = nlower; n <= nupper; n++) {
+ mz = n+nz;
+ y0 = z0*r1d[2][n];
+ for (m = nlower; m <= nupper; m++) {
+ my = m+ny;
+ x0 = y0*r1d[1][m];
+ for (l = nlower; l <= nupper; l++) {
+ mx = l+nx;
+ db[mz][my][mx] += x0*r1d[0][l];
+ }
+ }
+ }
}
}
#if defined(_OPENMP)
@@ -416,7 +416,7 @@ void PPPMOMP::make_rho()
}
/* ----------------------------------------------------------------------
- interpolate from grid to get electric field & force on my particles
+ interpolate from grid to get electric field & force on my particles
------------------------------------------------------------------------- */
void PPPMOMP::fieldforce()
@@ -436,7 +436,7 @@ void PPPMOMP::fieldforce()
#if defined(_OPENMP)
#pragma omp parallel default(none)
#endif
- {
+ {
#if defined(_OPENMP)
// each thread works on a fixed chunk of atoms.
const int tid = omp_get_thread_num();
@@ -452,46 +452,46 @@ void PPPMOMP::fieldforce()
ThrData *thr = fix->get_thr(tid);
double * const * const f = thr->get_f();
FFT_SCALAR * const * const r1d = static_cast<FFT_SCALAR **>(thr->get_rho1d());
-
+
int l,m,n,nx,ny,nz,mx,my,mz;
FFT_SCALAR dx,dy,dz,x0,y0,z0;
FFT_SCALAR ekx,eky,ekz;
// this if protects against having more threads than local atoms
- if (ifrom < nlocal) {
+ if (ifrom < nlocal) {
for (int i = ifrom; i < ito; i++) {
- nx = part2grid[i][0];
- ny = part2grid[i][1];
- nz = part2grid[i][2];
- dx = nx+shiftone - (x[i][0]-boxlo[0])*delxinv;
- dy = ny+shiftone - (x[i][1]-boxlo[1])*delyinv;
- dz = nz+shiftone - (x[i][2]-boxlo[2])*delzinv;
-
- compute_rho1d_thr(r1d,dx,dy,dz);
-
- ekx = eky = ekz = ZEROF;
- for (n = nlower; n <= nupper; n++) {
- mz = n+nz;
- z0 = r1d[2][n];
- for (m = nlower; m <= nupper; m++) {
- my = m+ny;
- y0 = z0*r1d[1][m];
- for (l = nlower; l <= nupper; l++) {
- mx = l+nx;
- x0 = y0*r1d[0][l];
- ekx -= x0*vdx_brick[mz][my][mx];
- eky -= x0*vdy_brick[mz][my][mx];
- ekz -= x0*vdz_brick[mz][my][mx];
- }
- }
- }
-
- // convert E-field to force
- const double qfactor = qqrd2e*scale*q[i];
- f[i][0] += qfactor*ekx;
- f[i][1] += qfactor*eky;
- f[i][2] += qfactor*ekz;
+ nx = part2grid[i][0];
+ ny = part2grid[i][1];
+ nz = part2grid[i][2];
+ dx = nx+shiftone - (x[i][0]-boxlo[0])*delxinv;
+ dy = ny+shiftone - (x[i][1]-boxlo[1])*delyinv;
+ dz = nz+shiftone - (x[i][2]-boxlo[2])*delzinv;
+
+ compute_rho1d_thr(r1d,dx,dy,dz);
+
+ ekx = eky = ekz = ZEROF;
+ for (n = nlower; n <= nupper; n++) {
+ mz = n+nz;
+ z0 = r1d[2][n];
+ for (m = nlower; m <= nupper; m++) {
+ my = m+ny;
+ y0 = z0*r1d[1][m];
+ for (l = nlower; l <= nupper; l++) {
+ mx = l+nx;
+ x0 = y0*r1d[0][l];
+ ekx -= x0*vdx_brick[mz][my][mx];
+ eky -= x0*vdy_brick[mz][my][mx];
+ ekz -= x0*vdz_brick[mz][my][mx];
+ }
+ }
+ }
+
+ // convert E-field to force
+ const double qfactor = qqrd2e*scale*q[i];
+ f[i][0] += qfactor*ekx;
+ f[i][1] += qfactor*eky;
+ f[i][2] += qfactor*ekz;
}
}
}
@@ -540,47 +540,47 @@ void PPPMOMP::fieldforce_peratom()
if (ifrom < nlocal) {
for (int i = ifrom; i < ito; i++) {
- nx = part2grid[i][0];
- ny = part2grid[i][1];
- nz = part2grid[i][2];
- dx = nx+shiftone - (x[i][0]-boxlo[0])*delxinv;
- dy = ny+shiftone - (x[i][1]-boxlo[1])*delyinv;
- dz = nz+shiftone - (x[i][2]-boxlo[2])*delzinv;
-
- compute_rho1d_thr(r1d,dx,dy,dz);
-
- u = v0 = v1 = v2 = v3 = v4 = v5 = ZEROF;
- for (n = nlower; n <= nupper; n++) {
- mz = n+nz;
- z0 = r1d[2][n];
- for (m = nlower; m <= nupper; m++) {
- my = m+ny;
- y0 = z0*r1d[1][m];
- for (l = nlower; l <= nupper; l++) {
- mx = l+nx;
- x0 = y0*r1d[0][l];
- if (eflag_atom) u += x0*u_brick[mz][my][mx];
- if (vflag_atom) {
- v0 += x0*v0_brick[mz][my][mx];
- v1 += x0*v1_brick[mz][my][mx];
- v2 += x0*v2_brick[mz][my][mx];
- v3 += x0*v3_brick[mz][my][mx];
- v4 += x0*v4_brick[mz][my][mx];
- v5 += x0*v5_brick[mz][my][mx];
- }
- }
- }
- }
-
- if (eflag_atom) eatom[i] += q[i]*u;
- if (vflag_atom) {
- vatom[i][0] += v0;
- vatom[i][1] += v1;
- vatom[i][2] += v2;
- vatom[i][3] += v3;
- vatom[i][4] += v4;
- vatom[i][5] += v5;
- }
+ nx = part2grid[i][0];
+ ny = part2grid[i][1];
+ nz = part2grid[i][2];
+ dx = nx+shiftone - (x[i][0]-boxlo[0])*delxinv;
+ dy = ny+shiftone - (x[i][1]-boxlo[1])*delyinv;
+ dz = nz+shiftone - (x[i][2]-boxlo[2])*delzinv;
+
+ compute_rho1d_thr(r1d,dx,dy,dz);
+
+ u = v0 = v1 = v2 = v3 = v4 = v5 = ZEROF;
+ for (n = nlower; n <= nupper; n++) {
+ mz = n+nz;
+ z0 = r1d[2][n];
+ for (m = nlower; m <= nupper; m++) {
+ my = m+ny;
+ y0 = z0*r1d[1][m];
+ for (l = nlower; l <= nupper; l++) {
+ mx = l+nx;
+ x0 = y0*r1d[0][l];
+ if (eflag_atom) u += x0*u_brick[mz][my][mx];
+ if (vflag_atom) {
+ v0 += x0*v0_brick[mz][my][mx];
+ v1 += x0*v1_brick[mz][my][mx];
+ v2 += x0*v2_brick[mz][my][mx];
+ v3 += x0*v3_brick[mz][my][mx];
+ v4 += x0*v4_brick[mz][my][mx];
+ v5 += x0*v5_brick[mz][my][mx];
+ }
+ }
+ }
+ }
+
+ if (eflag_atom) eatom[i] += q[i]*u;
+ if (vflag_atom) {
+ vatom[i][0] += v0;
+ vatom[i][1] += v1;
+ vatom[i][2] += v2;
+ vatom[i][3] += v3;
+ vatom[i][4] += v4;
+ vatom[i][5] += v5;
+ }
}
}
}
@@ -588,10 +588,10 @@ void PPPMOMP::fieldforce_peratom()
/* ----------------------------------------------------------------------
charge assignment into rho1d
- dx,dy,dz = distance of particle from "lower left" grid point
+ dx,dy,dz = distance of particle from "lower left" grid point
------------------------------------------------------------------------- */
void PPPMOMP::compute_rho1d_thr(FFT_SCALAR * const * const r1d, const FFT_SCALAR &dx,
- const FFT_SCALAR &dy, const FFT_SCALAR &dz)
+ const FFT_SCALAR &dy, const FFT_SCALAR &dz)
{
int k,l;
FFT_SCALAR r1,r2,r3;
diff --git a/src/USER-OMP/pppm_omp.h b/src/USER-OMP/pppm_omp.h
index 93caa6ed6e20c2e5244edff04c819be358dc6021..b3c069844cc348f8b63fe2de03e78d2d0fb8f284 100644
--- a/src/USER-OMP/pppm_omp.h
+++ b/src/USER-OMP/pppm_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -40,7 +40,7 @@ namespace LAMMPS_NS {
virtual void make_rho();
void compute_rho1d_thr(FFT_SCALAR * const * const, const FFT_SCALAR &,
- const FFT_SCALAR &, const FFT_SCALAR &);
+ const FFT_SCALAR &, const FFT_SCALAR &);
// void compute_rho_coeff();
// void slabcorr(int);
diff --git a/src/USER-OMP/pppm_proxy.cpp b/src/USER-OMP/pppm_proxy.cpp
index 4e8112060f2ea4d0ee93abc056ca90cb56d0b687..25c2158a089de71d7208ae69e89064aa9fefaeb0 100644
--- a/src/USER-OMP/pppm_proxy.cpp
+++ b/src/USER-OMP/pppm_proxy.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -62,4 +62,3 @@ void PPPMProxy::compute_proxy(int eflag, int vflag)
setup_proxy();
PPPM::compute(eflag,vflag);
}
-
diff --git a/src/USER-OMP/pppm_proxy.h b/src/USER-OMP/pppm_proxy.h
index 505efe2e81eb7922d50032815775e671ad42a8fa..110abfc9daf3e2f07d505b5c9ca8f601bf990044 100644
--- a/src/USER-OMP/pppm_proxy.h
+++ b/src/USER-OMP/pppm_proxy.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/pppm_tip4p_omp.cpp b/src/USER-OMP/pppm_tip4p_omp.cpp
index 219b1b203035a5074b9336b9851875a4bc4e03c9..e59275239b71cc865d538c30ce07dcf24fa15f69 100644
--- a/src/USER-OMP/pppm_tip4p_omp.cpp
+++ b/src/USER-OMP/pppm_tip4p_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -71,12 +71,12 @@ static void data_reduce_fft(FFT_SCALAR *dall, int nall, int nthreads, int ndim,
const int ito = ((ifrom + idelta) > nvals) ? nvals : (ifrom + idelta);
// this if protects against having more threads than atoms
- if (ifrom < nall) {
+ if (ifrom < nall) {
for (int m = ifrom; m < ito; ++m) {
- for (int n = 1; n < nthreads; ++n) {
- dall[m] += dall[n*nvals + m];
- dall[n*nvals + m] = 0.0;
- }
+ for (int n = 1; n < nthreads; ++n) {
+ dall[m] += dall[n*nvals + m];
+ dall[n*nvals + m] = 0.0;
+ }
}
}
}
@@ -101,7 +101,7 @@ void PPPMTIP4POMP::init()
/* ----------------------------------------------------------------------
find center grid pt for each of my particles
check that full stencil for the particle will fit in my 3d brick
- store central grid pt indices in part2grid array
+ store central grid pt indices in part2grid array
------------------------------------------------------------------------- */
void PPPMTIP4POMP::particle_map()
@@ -119,7 +119,7 @@ void PPPMTIP4POMP::particle_map()
double xM[3];
if (type[i] == typeO) {
- find_M(i,iH1,iH2,xM);
+ find_M(i,iH1,iH2,xM);
} else {
xM[0] = x[i][0];
xM[1] = x[i][1];
@@ -141,8 +141,8 @@ void PPPMTIP4POMP::particle_map()
// check that entire stencil around nx,ny,nz will fit in my 3d brick
if (nx+nlower < nxlo_out || nx+nupper > nxhi_out ||
- ny+nlower < nylo_out || ny+nupper > nyhi_out ||
- nz+nlower < nzlo_out || nz+nupper > nzhi_out) flag++;
+ ny+nlower < nylo_out || ny+nupper > nyhi_out ||
+ nz+nlower < nzlo_out || nz+nupper > nzhi_out) flag++;
}
int flag_all;
@@ -154,7 +154,7 @@ void PPPMTIP4POMP::particle_map()
create discretized "density" on section of global grid due to my particles
density(x,y,z) = charge "density" at grid points of my 3d brick
(nxlo:nxhi,nylo:nyhi,nzlo:nzhi) is extent of my brick (including ghosts)
- in global grid
+ in global grid
------------------------------------------------------------------------- */
void PPPMTIP4POMP::make_rho()
@@ -168,7 +168,7 @@ void PPPMTIP4POMP::make_rho()
#if defined(_OPENMP)
#pragma omp parallel default(none)
#endif
- {
+ {
#if defined(_OPENMP)
// each thread works on a fixed chunk of atoms.
const int tid = omp_get_thread_num();
@@ -198,41 +198,41 @@ void PPPMTIP4POMP::make_rho()
// (nx,ny,nz) = global coords of grid pt to "lower left" of charge
// (dx,dy,dz) = distance to "lower left" grid pt
// (mx,my,mz) = global coords of moving stencil pt
-
+
// this if protects against having more threads than local atoms
- if (ifrom < nlocal) {
+ if (ifrom < nlocal) {
for (int i = ifrom; i < ito; i++) {
- if (type[i] == typeO) {
- find_M(i,iH1,iH2,xM);
- } else {
- xM[0] = x[i][0];
- xM[1] = x[i][1];
- xM[2] = x[i][2];
- }
-
- nx = part2grid[i][0];
- ny = part2grid[i][1];
- nz = part2grid[i][2];
- dx = nx+shiftone - (xM[0]-boxlo[0])*delxinv;
- dy = ny+shiftone - (xM[1]-boxlo[1])*delyinv;
- dz = nz+shiftone - (xM[2]-boxlo[2])*delzinv;
-
- compute_rho1d_thr(r1d,dx,dy,dz);
-
- z0 = delvolinv * q[i];
- for (n = nlower; n <= nupper; n++) {
- mz = n+nz;
- y0 = z0*r1d[2][n];
- for (m = nlower; m <= nupper; m++) {
- my = m+ny;
- x0 = y0*r1d[1][m];
- for (l = nlower; l <= nupper; l++) {
- mx = l+nx;
- db[mz][my][mx] += x0*r1d[0][l];
- }
- }
- }
+ if (type[i] == typeO) {
+ find_M(i,iH1,iH2,xM);
+ } else {
+ xM[0] = x[i][0];
+ xM[1] = x[i][1];
+ xM[2] = x[i][2];
+ }
+
+ nx = part2grid[i][0];
+ ny = part2grid[i][1];
+ nz = part2grid[i][2];
+ dx = nx+shiftone - (xM[0]-boxlo[0])*delxinv;
+ dy = ny+shiftone - (xM[1]-boxlo[1])*delyinv;
+ dz = nz+shiftone - (xM[2]-boxlo[2])*delzinv;
+
+ compute_rho1d_thr(r1d,dx,dy,dz);
+
+ z0 = delvolinv * q[i];
+ for (n = nlower; n <= nupper; n++) {
+ mz = n+nz;
+ y0 = z0*r1d[2][n];
+ for (m = nlower; m <= nupper; m++) {
+ my = m+ny;
+ x0 = y0*r1d[1][m];
+ for (l = nlower; l <= nupper; l++) {
+ mx = l+nx;
+ db[mz][my][mx] += x0*r1d[0][l];
+ }
+ }
+ }
}
}
#if defined(_OPENMP)
@@ -245,7 +245,7 @@ void PPPMTIP4POMP::make_rho()
}
/* ----------------------------------------------------------------------
- interpolate from grid to get electric field & force on my particles
+ interpolate from grid to get electric field & force on my particles
------------------------------------------------------------------------- */
void PPPMTIP4POMP::fieldforce()
@@ -266,7 +266,7 @@ void PPPMTIP4POMP::fieldforce()
#if defined(_OPENMP)
#pragma omp parallel default(none)
#endif
- {
+ {
#if defined(_OPENMP)
// each thread works on a fixed chunk of atoms.
const int tid = omp_get_thread_num();
@@ -282,7 +282,7 @@ void PPPMTIP4POMP::fieldforce()
ThrData *thr = fix->get_thr(tid);
double * const * const f = thr->get_f();
FFT_SCALAR * const * const r1d = static_cast<FFT_SCALAR **>(thr->get_rho1d());
-
+
int l,m,n,nx,ny,nz,mx,my,mz;
FFT_SCALAR dx,dy,dz,x0,y0,z0;
FFT_SCALAR ekx,eky,ekz;
@@ -291,79 +291,79 @@ void PPPMTIP4POMP::fieldforce()
double ddotf, rOMx, rOMy, rOMz, f1x, f1y, f1z;
// this if protects against having more threads than local atoms
- if (ifrom < nlocal) {
+ if (ifrom < nlocal) {
for (int i = ifrom; i < ito; i++) {
- if (type[i] == typeO) {
- find_M(i,iH1,iH2,xM);
- } else {
- xM[0] = x[i][0];
- xM[1] = x[i][1];
- xM[2] = x[i][2];
- }
-
- nx = part2grid[i][0];
- ny = part2grid[i][1];
- nz = part2grid[i][2];
- dx = nx+shiftone - (xM[0]-boxlo[0])*delxinv;
- dy = ny+shiftone - (xM[1]-boxlo[1])*delyinv;
- dz = nz+shiftone - (xM[2]-boxlo[2])*delzinv;
-
- compute_rho1d_thr(r1d,dx,dy,dz);
-
- ekx = eky = ekz = ZEROF;
- for (n = nlower; n <= nupper; n++) {
- mz = n+nz;
- z0 = r1d[2][n];
- for (m = nlower; m <= nupper; m++) {
- my = m+ny;
- y0 = z0*r1d[1][m];
- for (l = nlower; l <= nupper; l++) {
- mx = l+nx;
- x0 = y0*r1d[0][l];
- ekx -= x0*vdx_brick[mz][my][mx];
- eky -= x0*vdy_brick[mz][my][mx];
- ekz -= x0*vdz_brick[mz][my][mx];
- }
- }
- }
-
- // convert E-field to force
- const double qfactor = qqrd2e*scale*q[i];
-
- if (type[i] != typeO) {
- f[i][0] += qfactor*ekx;
- f[i][1] += qfactor*eky;
- f[i][2] += qfactor*ekz;
-
- } else {
- fx = qfactor * ekx;
- fy = qfactor * eky;
- fz = qfactor * ekz;
- find_M(i,iH1,iH2,xM);
-
- rOMx = xM[0] - x[i][0];
- rOMy = xM[1] - x[i][1];
- rOMz = xM[2] - x[i][2];
-
- ddotf = (rOMx * fx + rOMy * fy + rOMz * fz) / (qdist * qdist);
-
- f1x = ddotf * rOMx;
- f1y = ddotf * rOMy;
- f1z = ddotf * rOMz;
-
- f[i][0] += fx - alpha * (fx - f1x);
- f[i][1] += fy - alpha * (fy - f1y);
- f[i][2] += fz - alpha * (fz - f1z);
-
- f[iH1][0] += 0.5*alpha*(fx - f1x);
- f[iH1][1] += 0.5*alpha*(fy - f1y);
- f[iH1][2] += 0.5*alpha*(fz - f1z);
-
- f[iH2][0] += 0.5*alpha*(fx - f1x);
- f[iH2][1] += 0.5*alpha*(fy - f1y);
- f[iH2][2] += 0.5*alpha*(fz - f1z);
- }
+ if (type[i] == typeO) {
+ find_M(i,iH1,iH2,xM);
+ } else {
+ xM[0] = x[i][0];
+ xM[1] = x[i][1];
+ xM[2] = x[i][2];
+ }
+
+ nx = part2grid[i][0];
+ ny = part2grid[i][1];
+ nz = part2grid[i][2];
+ dx = nx+shiftone - (xM[0]-boxlo[0])*delxinv;
+ dy = ny+shiftone - (xM[1]-boxlo[1])*delyinv;
+ dz = nz+shiftone - (xM[2]-boxlo[2])*delzinv;
+
+ compute_rho1d_thr(r1d,dx,dy,dz);
+
+ ekx = eky = ekz = ZEROF;
+ for (n = nlower; n <= nupper; n++) {
+ mz = n+nz;
+ z0 = r1d[2][n];
+ for (m = nlower; m <= nupper; m++) {
+ my = m+ny;
+ y0 = z0*r1d[1][m];
+ for (l = nlower; l <= nupper; l++) {
+ mx = l+nx;
+ x0 = y0*r1d[0][l];
+ ekx -= x0*vdx_brick[mz][my][mx];
+ eky -= x0*vdy_brick[mz][my][mx];
+ ekz -= x0*vdz_brick[mz][my][mx];
+ }
+ }
+ }
+
+ // convert E-field to force
+ const double qfactor = qqrd2e*scale*q[i];
+
+ if (type[i] != typeO) {
+ f[i][0] += qfactor*ekx;
+ f[i][1] += qfactor*eky;
+ f[i][2] += qfactor*ekz;
+
+ } else {
+ fx = qfactor * ekx;
+ fy = qfactor * eky;
+ fz = qfactor * ekz;
+ find_M(i,iH1,iH2,xM);
+
+ rOMx = xM[0] - x[i][0];
+ rOMy = xM[1] - x[i][1];
+ rOMz = xM[2] - x[i][2];
+
+ ddotf = (rOMx * fx + rOMy * fy + rOMz * fz) / (qdist * qdist);
+
+ f1x = ddotf * rOMx;
+ f1y = ddotf * rOMy;
+ f1z = ddotf * rOMz;
+
+ f[i][0] += fx - alpha * (fx - f1x);
+ f[i][1] += fy - alpha * (fy - f1y);
+ f[i][2] += fz - alpha * (fz - f1z);
+
+ f[iH1][0] += 0.5*alpha*(fx - f1x);
+ f[iH1][1] += 0.5*alpha*(fy - f1y);
+ f[iH1][2] += 0.5*alpha*(fz - f1z);
+
+ f[iH2][0] += 0.5*alpha*(fx - f1x);
+ f[iH2][1] += 0.5*alpha*(fy - f1y);
+ f[iH2][2] += 0.5*alpha*(fz - f1z);
+ }
}
}
}
@@ -384,7 +384,7 @@ void PPPMTIP4POMP::find_M(int i, int &iH1, int &iH2, double *xM)
if (atom->type[iH1] != typeH || atom->type[iH2] != typeH)
error->one(FLERR,"TIP4P hydrogen has incorrect atom type");
- const double * const * const x = atom->x;
+ const double * const * const x = atom->x;
double delx1 = x[iH1][0] - x[i][0];
double dely1 = x[iH1][1] - x[i][1];
diff --git a/src/USER-OMP/pppm_tip4p_omp.h b/src/USER-OMP/pppm_tip4p_omp.h
index 33e5b0f224453f9ef2f45924c35c1cffc6a85a58..11801ccb35ef464a201a17f6031de7b3c7a6f1de 100644
--- a/src/USER-OMP/pppm_tip4p_omp.h
+++ b/src/USER-OMP/pppm_tip4p_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -29,14 +29,14 @@ class PPPMTIP4POMP : public PPPMOMP {
PPPMTIP4POMP(class LAMMPS *, int, char **);
virtual ~PPPMTIP4POMP () {};
virtual void init();
-
+
protected:
virtual void particle_map();
virtual void fieldforce();
virtual void make_rho();
private:
- void find_M(int, int &, int &, double *);
+ void find_M(int, int &, int &, double *);
// void slabcorr(int);
diff --git a/src/USER-OMP/pppm_tip4p_proxy.cpp b/src/USER-OMP/pppm_tip4p_proxy.cpp
index 367b51e48d56ac5322604d9ad96bbb5ed2be33ca..db851dec5b554d3804c8b73d9b34ba14d2aca88b 100644
--- a/src/USER-OMP/pppm_tip4p_proxy.cpp
+++ b/src/USER-OMP/pppm_tip4p_proxy.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -62,4 +62,3 @@ void PPPMTIP4PProxy::compute_proxy(int eflag, int vflag)
setup_proxy();
PPPMTIP4P::compute(eflag,vflag);
}
-
diff --git a/src/USER-OMP/pppm_tip4p_proxy.h b/src/USER-OMP/pppm_tip4p_proxy.h
index fee06800ffc543ac8397f9b3dbea45a953f66834..0a670d8b6314b211f80a49d37faae30a21986eec 100644
--- a/src/USER-OMP/pppm_tip4p_proxy.h
+++ b/src/USER-OMP/pppm_tip4p_proxy.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/thr_data.cpp b/src/USER-OMP/thr_data.cpp
index bc3d6d635b4209a2300e5aa2bfe71c6a9cf25840..cebed27721dd2c83cea58da8a0fdc74e3d7764fd 100644
--- a/src/USER-OMP/thr_data.cpp
+++ b/src/USER-OMP/thr_data.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -24,10 +24,10 @@
using namespace LAMMPS_NS;
-ThrData::ThrData(int tid)
+ThrData::ThrData(int tid)
: _f(NULL), _torque(NULL), _erforce(NULL), _de(NULL), _drho(NULL), _mu(NULL),
_lambda(NULL), _rhoB(NULL), _D_values(NULL), _rho(NULL), _fp(NULL),
- _rho1d(NULL), _tid(tid)
+ _rho1d(NULL), _tid(tid)
{
// nothing else to do here.
}
@@ -44,7 +44,7 @@ void ThrData::check_tid(int tid)
/* ---------------------------------------------------------------------- */
void ThrData::init_force(int nall, double **f, double **torque,
- double *erforce, double *de, double *drho)
+ double *erforce, double *de, double *drho)
{
eng_vdwl=eng_coul=eng_bond=eng_angle=eng_dihed=eng_imprp=eng_kspce=0.0;
memset(virial_pair,0,6*sizeof(double));
@@ -184,7 +184,7 @@ void ThrData::virial_fdotr_compute(double **x, int nlocal, int nghost, int nfirs
/* ---------------------------------------------------------------------- */
-double ThrData::memory_usage()
+double ThrData::memory_usage()
{
double bytes = (7 + 6*6) * sizeof(double);
bytes += 2 * sizeof(double*);
@@ -215,12 +215,12 @@ void LAMMPS_NS::data_reduce_thr(double *dall, int nall, int nthreads, int ndim,
const int ito = ((ifrom + idelta) > nvals) ? nvals : (ifrom + idelta);
// this if protects against having more threads than atoms
- if (ifrom < nvals) {
+ if (ifrom < nvals) {
for (int m = ifrom; m < ito; ++m) {
- for (int n = 1; n < nthreads; ++n) {
- dall[m] += dall[n*nvals + m];
- dall[n*nvals + m] = 0.0;
- }
+ for (int n = 1; n < nthreads; ++n) {
+ dall[m] += dall[n*nvals + m];
+ dall[n*nvals + m] = 0.0;
+ }
}
}
}
@@ -229,4 +229,3 @@ void LAMMPS_NS::data_reduce_thr(double *dall, int nall, int nthreads, int ndim,
return;
#endif
}
-
diff --git a/src/USER-OMP/thr_data.h b/src/USER-OMP/thr_data.h
index f2f8da061422f17023b1472608bf5fe3e29d47f3..6345a203c7c09b0cbd7dd3cdaed2639c38edaa0b 100644
--- a/src/USER-OMP/thr_data.h
+++ b/src/USER-OMP/thr_data.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -50,7 +50,7 @@ class ThrData {
// setup and erase per atom arrays
void init_adp(int, double *, double **, double **); // ADP (+ EAM)
void init_cdeam(int, double *, double *, double *); // CDEAM (+ EAM)
- void init_eam(int, double *); // EAM
+ void init_eam(int, double *); // EAM
void init_eim(int, double *, double *); // EIM (+ EAM)
void init_pppm(void *r1d) { _rho1d = r1d; };
@@ -76,7 +76,7 @@ class ThrData {
double virial_bond[6]; // virial contribution from bonds
double virial_angle[6]; // virial contribution from angles
double virial_dihed[6]; // virial contribution from dihedrals
- double virial_imprp[6]; // virial contribution from impropers
+ double virial_imprp[6]; // virial contribution from impropers
double virial_kspce[6]; // virial contribution from kspace
double *eatom_pair;
double *eatom_bond;
diff --git a/src/USER-OMP/thr_omp.cpp b/src/USER-OMP/thr_omp.cpp
index f916c519d233921f437b5e66c0223f6da49ae5a5..c41c2bc72dbb2a07a934b14d852e67ae77137707 100644
--- a/src/USER-OMP/thr_omp.cpp
+++ b/src/USER-OMP/thr_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -64,21 +64,21 @@ ThrOMP::~ThrOMP()
---------------------------------------------------------------------- */
void ThrOMP::ev_setup_thr(int eflag, int vflag, int nall, double *eatom,
- double **vatom, ThrData *thr)
+ double **vatom, ThrData *thr)
{
const int tid = thr->get_tid();
if (tid == 0) thr_error = 0;
-
+
if (thr_style & THR_PAIR) {
if (eflag & 2) {
thr->eatom_pair = eatom + tid*nall;
if (nall > 0)
- memset(&(thr->eatom_pair[0]),0,nall*sizeof(double));
+ memset(&(thr->eatom_pair[0]),0,nall*sizeof(double));
}
if (vflag & 4) {
thr->vatom_pair = vatom + tid*nall;
if (nall > 0)
- memset(&(thr->vatom_pair[0][0]),0,nall*6*sizeof(double));
+ memset(&(thr->vatom_pair[0][0]),0,nall*6*sizeof(double));
}
}
@@ -86,12 +86,12 @@ void ThrOMP::ev_setup_thr(int eflag, int vflag, int nall, double *eatom,
if (eflag & 2) {
thr->eatom_bond = eatom + tid*nall;
if (nall > 0)
- memset(&(thr->eatom_bond[0]),0,nall*sizeof(double));
+ memset(&(thr->eatom_bond[0]),0,nall*sizeof(double));
}
if (vflag & 4) {
thr->vatom_bond = vatom + tid*nall;
if (nall > 0)
- memset(&(thr->vatom_bond[0][0]),0,nall*6*sizeof(double));
+ memset(&(thr->vatom_bond[0][0]),0,nall*6*sizeof(double));
}
}
@@ -99,12 +99,12 @@ void ThrOMP::ev_setup_thr(int eflag, int vflag, int nall, double *eatom,
if (eflag & 2) {
thr->eatom_angle = eatom + tid*nall;
if (nall > 0)
- memset(&(thr->eatom_angle[0]),0,nall*sizeof(double));
+ memset(&(thr->eatom_angle[0]),0,nall*sizeof(double));
}
if (vflag & 4) {
thr->vatom_angle = vatom + tid*nall;
if (nall > 0)
- memset(&(thr->vatom_angle[0][0]),0,nall*6*sizeof(double));
+ memset(&(thr->vatom_angle[0][0]),0,nall*6*sizeof(double));
}
}
@@ -112,12 +112,12 @@ void ThrOMP::ev_setup_thr(int eflag, int vflag, int nall, double *eatom,
if (eflag & 2) {
thr->eatom_dihed = eatom + tid*nall;
if (nall > 0)
- memset(&(thr->eatom_dihed[0]),0,nall*sizeof(double));
+ memset(&(thr->eatom_dihed[0]),0,nall*sizeof(double));
}
if (vflag & 4) {
thr->vatom_dihed = vatom + tid*nall;
if (nall > 0)
- memset(&(thr->vatom_dihed[0][0]),0,nall*6*sizeof(double));
+ memset(&(thr->vatom_dihed[0][0]),0,nall*6*sizeof(double));
}
}
@@ -125,12 +125,12 @@ void ThrOMP::ev_setup_thr(int eflag, int vflag, int nall, double *eatom,
if (eflag & 2) {
thr->eatom_imprp = eatom + tid*nall;
if (nall > 0)
- memset(&(thr->eatom_imprp[0]),0,nall*sizeof(double));
+ memset(&(thr->eatom_imprp[0]),0,nall*sizeof(double));
}
if (vflag & 4) {
thr->vatom_imprp = vatom + tid*nall;
if (nall > 0)
- memset(&(thr->vatom_imprp[0][0]),0,nall*6*sizeof(double));
+ memset(&(thr->vatom_imprp[0][0]),0,nall*6*sizeof(double));
}
}
@@ -147,7 +147,7 @@ void ThrOMP::ev_setup_thr(int eflag, int vflag, int nall, double *eatom,
---------------------------------------------------------------------- */
void ThrOMP::reduce_thr(void *style, const int eflag, const int vflag,
- ThrData *const thr, const int nproxy)
+ ThrData *const thr, const int nproxy)
{
const int nlocal = lmp->atom->nlocal;
const int nghost = lmp->atom->nghost;
@@ -155,7 +155,7 @@ void ThrOMP::reduce_thr(void *style, const int eflag, const int vflag,
const int nfirst = lmp->atom->nfirst;
const int nthreads = lmp->comm->nthreads;
const int evflag = eflag | vflag;
-
+
const int tid = thr->get_tid();
double **f = lmp->atom->f;
double **x = lmp->atom->x;
@@ -173,18 +173,18 @@ void ThrOMP::reduce_thr(void *style, const int eflag, const int vflag,
if (pair->vflag_fdotr) {
if (style == fix->last_pair_hybrid) {
- // pair_style hybrid will compute fdotr for us
- // but we first need to reduce the forces
- data_reduce_thr(&(f[0][0]), nall, nthreads, 3, tid);
- need_force_reduce = 0;
+ // pair_style hybrid will compute fdotr for us
+ // but we first need to reduce the forces
+ data_reduce_thr(&(f[0][0]), nall, nthreads, 3, tid);
+ need_force_reduce = 0;
}
// this is a non-hybrid pair style. compute per thread fdotr
if (fix->last_pair_hybrid == NULL) {
- if (lmp->neighbor->includegroup == 0)
- thr->virial_fdotr_compute(x, nlocal, nghost, -1);
- else
- thr->virial_fdotr_compute(x, nlocal, nghost, nfirst);
+ if (lmp->neighbor->includegroup == 0)
+ thr->virial_fdotr_compute(x, nlocal, nghost, -1);
+ else
+ thr->virial_fdotr_compute(x, nlocal, nghost, nfirst);
}
}
@@ -193,23 +193,23 @@ void ThrOMP::reduce_thr(void *style, const int eflag, const int vflag,
#pragma omp critical
#endif
{
- if (eflag & 1) {
- pair->eng_vdwl += thr->eng_vdwl;
- pair->eng_coul += thr->eng_coul;
- thr->eng_vdwl = 0.0;
- thr->eng_coul = 0.0;
- }
- if (vflag & 3)
- for (int i=0; i < 6; ++i) {
- pair->virial[i] += thr->virial_pair[i];
- thr->virial_pair[i] = 0.0;
- }
+ if (eflag & 1) {
+ pair->eng_vdwl += thr->eng_vdwl;
+ pair->eng_coul += thr->eng_coul;
+ thr->eng_vdwl = 0.0;
+ thr->eng_coul = 0.0;
+ }
+ if (vflag & 3)
+ for (int i=0; i < 6; ++i) {
+ pair->virial[i] += thr->virial_pair[i];
+ thr->virial_pair[i] = 0.0;
+ }
}
if (eflag & 2) {
- data_reduce_thr(&(pair->eatom[0]), nall, nthreads, 1, tid);
+ data_reduce_thr(&(pair->eatom[0]), nall, nthreads, 1, tid);
}
if (vflag & 4) {
- data_reduce_thr(&(pair->vatom[0][0]), nall, nthreads, 6, tid);
+ data_reduce_thr(&(pair->vatom[0][0]), nall, nthreads, 6, tid);
}
}
}
@@ -221,56 +221,56 @@ void ThrOMP::reduce_thr(void *style, const int eflag, const int vflag,
if (tid >= nproxy && pair->vflag_fdotr) {
if (fix->last_pair_hybrid) {
- if (tid == nproxy)
- lmp->error->all(FLERR,
- "Cannot use hybrid pair style with kspace proxy");
- else return;
+ if (tid == nproxy)
+ lmp->error->all(FLERR,
+ "Cannot use hybrid pair style with kspace proxy");
+ else return;
}
// this is a non-hybrid pair style. compute per thread fdotr
if (fix->last_pair_hybrid == NULL) {
- if (lmp->neighbor->includegroup == 0)
- thr->virial_fdotr_compute(x, nlocal, nghost, -1);
- else
- thr->virial_fdotr_compute(x, nlocal, nghost, nfirst);
+ if (lmp->neighbor->includegroup == 0)
+ thr->virial_fdotr_compute(x, nlocal, nghost, -1);
+ else
+ thr->virial_fdotr_compute(x, nlocal, nghost, nfirst);
}
}
-
+
if (evflag) {
#if defined(_OPENMP)
#pragma omp critical
#endif
{
- if (tid < nproxy) {
- // nothing to collect for kspace proxy threads
- // just reset pair accumulators to 0.0.
- if (eflag & 1) {
- thr->eng_vdwl = 0.0;
- thr->eng_coul = 0.0;
- }
- if (vflag & 3)
- for (int i=0; i < 6; ++i) {
- thr->virial_pair[i] = 0.0;
- }
- } else {
- if (eflag & 1) {
- pair->eng_vdwl += thr->eng_vdwl;
- pair->eng_coul += thr->eng_coul;
- thr->eng_vdwl = 0.0;
- thr->eng_coul = 0.0;
- }
- if (vflag & 3)
- for (int i=0; i < 6; ++i) {
- pair->virial[i] += thr->virial_pair[i];
- thr->virial_pair[i] = 0.0;
- }
- }
+ if (tid < nproxy) {
+ // nothing to collect for kspace proxy threads
+ // just reset pair accumulators to 0.0.
+ if (eflag & 1) {
+ thr->eng_vdwl = 0.0;
+ thr->eng_coul = 0.0;
+ }
+ if (vflag & 3)
+ for (int i=0; i < 6; ++i) {
+ thr->virial_pair[i] = 0.0;
+ }
+ } else {
+ if (eflag & 1) {
+ pair->eng_vdwl += thr->eng_vdwl;
+ pair->eng_coul += thr->eng_coul;
+ thr->eng_vdwl = 0.0;
+ thr->eng_coul = 0.0;
+ }
+ if (vflag & 3)
+ for (int i=0; i < 6; ++i) {
+ pair->virial[i] += thr->virial_pair[i];
+ thr->virial_pair[i] = 0.0;
+ }
+ }
}
if (eflag & 2) {
- data_reduce_thr(&(pair->eatom[0]), nall, nthreads, 1, tid);
+ data_reduce_thr(&(pair->eatom[0]), nall, nthreads, 1, tid);
}
if (vflag & 4) {
- data_reduce_thr(&(pair->vatom[0][0]), nall, nthreads, 6, tid);
+ data_reduce_thr(&(pair->vatom[0][0]), nall, nthreads, 6, tid);
}
}
}
@@ -284,24 +284,24 @@ void ThrOMP::reduce_thr(void *style, const int eflag, const int vflag,
#pragma omp critical
#endif
{
- if (eflag & 1) {
- bond->energy += thr->eng_bond;
- thr->eng_bond = 0.0;
- }
-
- if (vflag & 3) {
- for (int i=0; i < 6; ++i) {
- bond->virial[i] += thr->virial_bond[i];
- thr->virial_bond[i] = 0.0;
- }
- }
-
- if (eflag & 2) {
- data_reduce_thr(&(bond->eatom[0]), nall, nthreads, 1, tid);
- }
- if (vflag & 4) {
- data_reduce_thr(&(bond->vatom[0][0]), nall, nthreads, 6, tid);
- }
+ if (eflag & 1) {
+ bond->energy += thr->eng_bond;
+ thr->eng_bond = 0.0;
+ }
+
+ if (vflag & 3) {
+ for (int i=0; i < 6; ++i) {
+ bond->virial[i] += thr->virial_bond[i];
+ thr->virial_bond[i] = 0.0;
+ }
+ }
+
+ if (eflag & 2) {
+ data_reduce_thr(&(bond->eatom[0]), nall, nthreads, 1, tid);
+ }
+ if (vflag & 4) {
+ data_reduce_thr(&(bond->vatom[0][0]), nall, nthreads, 6, tid);
+ }
}
}
break;
@@ -314,54 +314,54 @@ void ThrOMP::reduce_thr(void *style, const int eflag, const int vflag,
#pragma omp critical
#endif
{
- if (eflag & 1) {
- angle->energy += thr->eng_angle;
- thr->eng_angle = 0.0;
- }
-
- if (vflag & 3) {
- for (int i=0; i < 6; ++i) {
- angle->virial[i] += thr->virial_angle[i];
- thr->virial_angle[i] = 0.0;
- }
- }
-
- if (eflag & 2) {
- data_reduce_thr(&(angle->eatom[0]), nall, nthreads, 1, tid);
- }
- if (vflag & 4) {
- data_reduce_thr(&(angle->vatom[0][0]), nall, nthreads, 6, tid);
- }
+ if (eflag & 1) {
+ angle->energy += thr->eng_angle;
+ thr->eng_angle = 0.0;
+ }
+
+ if (vflag & 3) {
+ for (int i=0; i < 6; ++i) {
+ angle->virial[i] += thr->virial_angle[i];
+ thr->virial_angle[i] = 0.0;
+ }
+ }
+
+ if (eflag & 2) {
+ data_reduce_thr(&(angle->eatom[0]), nall, nthreads, 1, tid);
+ }
+ if (vflag & 4) {
+ data_reduce_thr(&(angle->vatom[0][0]), nall, nthreads, 6, tid);
+ }
}
}
break;
case THR_DIHEDRAL:
-
+
if (evflag) {
Dihedral * const dihedral = lmp->force->dihedral;
#if defined(_OPENMP)
#pragma omp critical
#endif
{
- if (eflag & 1) {
- dihedral->energy += thr->eng_dihed;
- thr->eng_dihed = 0.0;
- }
-
- if (vflag & 3) {
- for (int i=0; i < 6; ++i) {
- dihedral->virial[i] += thr->virial_dihed[i];
- thr->virial_dihed[i] = 0.0;
- }
- }
-
- if (eflag & 2) {
- data_reduce_thr(&(dihedral->eatom[0]), nall, nthreads, 1, tid);
- }
- if (vflag & 4) {
- data_reduce_thr(&(dihedral->vatom[0][0]), nall, nthreads, 6, tid);
- }
+ if (eflag & 1) {
+ dihedral->energy += thr->eng_dihed;
+ thr->eng_dihed = 0.0;
+ }
+
+ if (vflag & 3) {
+ for (int i=0; i < 6; ++i) {
+ dihedral->virial[i] += thr->virial_dihed[i];
+ thr->virial_dihed[i] = 0.0;
+ }
+ }
+
+ if (eflag & 2) {
+ data_reduce_thr(&(dihedral->eatom[0]), nall, nthreads, 1, tid);
+ }
+ if (vflag & 4) {
+ data_reduce_thr(&(dihedral->vatom[0][0]), nall, nthreads, 6, tid);
+ }
}
}
break;
@@ -375,32 +375,32 @@ void ThrOMP::reduce_thr(void *style, const int eflag, const int vflag,
#pragma omp critical
#endif
{
- if (eflag & 1) {
- dihedral->energy += thr->eng_dihed;
- pair->eng_vdwl += thr->eng_vdwl;
- pair->eng_coul += thr->eng_coul;
- thr->eng_dihed = 0.0;
- thr->eng_vdwl = 0.0;
- thr->eng_coul = 0.0;
- }
-
- if (vflag & 3) {
- for (int i=0; i < 6; ++i) {
- dihedral->virial[i] += thr->virial_dihed[i];
- pair->virial[i] += thr->virial_pair[i];
- thr->virial_dihed[i] = 0.0;
- thr->virial_pair[i] = 0.0;
- }
- }
-
- if (eflag & 2) {
- data_reduce_thr(&(dihedral->eatom[0]), nall, nthreads, 1, tid);
- data_reduce_thr(&(pair->eatom[0]), nall, nthreads, 1, tid);
- }
- if (vflag & 4) {
- data_reduce_thr(&(dihedral->vatom[0][0]), nall, nthreads, 6, tid);
- data_reduce_thr(&(pair->vatom[0][0]), nall, nthreads, 6, tid);
- }
+ if (eflag & 1) {
+ dihedral->energy += thr->eng_dihed;
+ pair->eng_vdwl += thr->eng_vdwl;
+ pair->eng_coul += thr->eng_coul;
+ thr->eng_dihed = 0.0;
+ thr->eng_vdwl = 0.0;
+ thr->eng_coul = 0.0;
+ }
+
+ if (vflag & 3) {
+ for (int i=0; i < 6; ++i) {
+ dihedral->virial[i] += thr->virial_dihed[i];
+ pair->virial[i] += thr->virial_pair[i];
+ thr->virial_dihed[i] = 0.0;
+ thr->virial_pair[i] = 0.0;
+ }
+ }
+
+ if (eflag & 2) {
+ data_reduce_thr(&(dihedral->eatom[0]), nall, nthreads, 1, tid);
+ data_reduce_thr(&(pair->eatom[0]), nall, nthreads, 1, tid);
+ }
+ if (vflag & 4) {
+ data_reduce_thr(&(dihedral->vatom[0][0]), nall, nthreads, 6, tid);
+ data_reduce_thr(&(pair->vatom[0][0]), nall, nthreads, 6, tid);
+ }
}
}
break;
@@ -413,24 +413,24 @@ void ThrOMP::reduce_thr(void *style, const int eflag, const int vflag,
#pragma omp critical
#endif
{
- if (eflag & 1) {
- improper->energy += thr->eng_imprp;
- thr->eng_imprp = 0.0;
- }
-
- if (vflag & 3) {
- for (int i=0; i < 6; ++i) {
- improper->virial[i] += thr->virial_imprp[i];
- thr->virial_imprp[i] = 0.0;
- }
- }
-
- if (eflag & 2) {
- data_reduce_thr(&(improper->eatom[0]), nall, nthreads, 1, tid);
- }
- if (vflag & 4) {
- data_reduce_thr(&(improper->vatom[0][0]), nall, nthreads, 6, tid);
- }
+ if (eflag & 1) {
+ improper->energy += thr->eng_imprp;
+ thr->eng_imprp = 0.0;
+ }
+
+ if (vflag & 3) {
+ for (int i=0; i < 6; ++i) {
+ improper->virial[i] += thr->virial_imprp[i];
+ thr->virial_imprp[i] = 0.0;
+ }
+ }
+
+ if (eflag & 2) {
+ data_reduce_thr(&(improper->eatom[0]), nall, nthreads, 1, tid);
+ }
+ if (vflag & 4) {
+ data_reduce_thr(&(improper->vatom[0][0]), nall, nthreads, 6, tid);
+ }
}
}
break;
@@ -444,7 +444,7 @@ void ThrOMP::reduce_thr(void *style, const int eflag, const int vflag,
printf("tid:%d unhandled thr_style case %d\n", tid, thr_style);
break;
}
-
+
if (style == fix->last_omp_style) {
if (need_force_reduce)
data_reduce_thr(&(f[0][0]), nall, nthreads, 3, tid);
@@ -458,9 +458,9 @@ void ThrOMP::reduce_thr(void *style, const int eflag, const int vflag,
tally eng_vdwl and eng_coul into per thread global and per-atom accumulators
------------------------------------------------------------------------- */
-void ThrOMP::e_tally_thr(Pair * const pair, const int i, const int j,
- const int nlocal, const int newton_pair,
- const double evdwl, const double ecoul, ThrData * const thr)
+void ThrOMP::e_tally_thr(Pair * const pair, const int i, const int j,
+ const int nlocal, const int newton_pair,
+ const double evdwl, const double ecoul, ThrData * const thr)
{
if (pair->eflag_global) {
if (newton_pair) {
@@ -470,12 +470,12 @@ void ThrOMP::e_tally_thr(Pair * const pair, const int i, const int j,
const double evdwlhalf = 0.5*evdwl;
const double ecoulhalf = 0.5*ecoul;
if (i < nlocal) {
- thr->eng_vdwl += evdwlhalf;
- thr->eng_coul += ecoulhalf;
+ thr->eng_vdwl += evdwlhalf;
+ thr->eng_coul += ecoulhalf;
}
if (j < nlocal) {
- thr->eng_vdwl += evdwlhalf;
- thr->eng_coul += ecoulhalf;
+ thr->eng_vdwl += evdwlhalf;
+ thr->eng_coul += ecoulhalf;
}
}
}
@@ -487,7 +487,7 @@ void ThrOMP::e_tally_thr(Pair * const pair, const int i, const int j,
}
/* helper functions */
-static void v_tally(double * const vout, const double * const vin)
+static void v_tally(double * const vout, const double * const vin)
{
vout[0] += vin[0];
vout[1] += vin[1];
@@ -497,7 +497,7 @@ static void v_tally(double * const vout, const double * const vin)
vout[5] += vin[5];
}
-static void v_tally(double * const vout, const double scale, const double * const vin)
+static void v_tally(double * const vout, const double scale, const double * const vin)
{
vout[0] += scale*vin[0];
vout[1] += scale*vin[1];
@@ -510,9 +510,9 @@ static void v_tally(double * const vout, const double scale, const double * cons
/* ----------------------------------------------------------------------
tally virial into per thread global and per-atom accumulators
------------------------------------------------------------------------- */
-void ThrOMP::v_tally_thr(Pair * const pair, const int i, const int j,
- const int nlocal, const int newton_pair,
- const double * const v, ThrData * const thr)
+void ThrOMP::v_tally_thr(Pair * const pair, const int i, const int j,
+ const int nlocal, const int newton_pair,
+ const double * const v, ThrData * const thr)
{
if (pair->vflag_global) {
double * const va = thr->virial_pair;
@@ -542,9 +542,9 @@ void ThrOMP::v_tally_thr(Pair * const pair, const int i, const int j,
------------------------------------------------------------------------- */
void ThrOMP::ev_tally_thr(Pair * const pair, const int i, const int j, const int nlocal,
- const int newton_pair, const double evdwl, const double ecoul,
- const double fpair, const double delx, const double dely,
- const double delz, ThrData * const thr)
+ const int newton_pair, const double evdwl, const double ecoul,
+ const double fpair, const double delx, const double dely,
+ const double delz, ThrData * const thr)
{
if (pair->eflag_either)
@@ -569,11 +569,11 @@ void ThrOMP::ev_tally_thr(Pair * const pair, const int i, const int j, const int
------------------------------------------------------------------------- */
void ThrOMP::ev_tally_xyz_thr(Pair * const pair, const int i, const int j,
- const int nlocal, const int newton_pair,
- const double evdwl, const double ecoul,
- const double fx, const double fy, const double fz,
- const double delx, const double dely, const double delz,
- ThrData * const thr)
+ const int nlocal, const int newton_pair,
+ const double evdwl, const double ecoul,
+ const double fx, const double fy, const double fz,
+ const double delx, const double dely, const double delz,
+ ThrData * const thr)
{
if (pair->eflag_either)
@@ -599,10 +599,10 @@ void ThrOMP::ev_tally_xyz_thr(Pair * const pair, const int i, const int j,
------------------------------------------------------------------------- */
void ThrOMP::ev_tally3_thr(Pair * const pair, const int i, const int j, const int k,
- const double evdwl, const double ecoul,
- const double * const fj, const double * const fk,
- const double * const drji, const double * const drki,
- ThrData * const thr)
+ const double evdwl, const double ecoul,
+ const double * const fj, const double * const fk,
+ const double * const drji, const double * const drki,
+ ThrData * const thr)
{
if (pair->eflag_either) {
if (pair->eflag_global) {
@@ -626,7 +626,7 @@ void ThrOMP::ev_tally3_thr(Pair * const pair, const int i, const int j, const in
v[3] = drji[0]*fj[1] + drki[0]*fk[1];
v[4] = drji[0]*fj[2] + drki[0]*fk[2];
v[5] = drji[1]*fj[2] + drki[1]*fk[2];
-
+
if (pair->vflag_global) v_tally(thr->virial_pair,v);
if (pair->vflag_atom) {
@@ -643,11 +643,11 @@ void ThrOMP::ev_tally3_thr(Pair * const pair, const int i, const int j, const in
------------------------------------------------------------------------- */
void ThrOMP::ev_tally4_thr(Pair * const pair, const int i, const int j,
- const int k, const int m, const double evdwl,
- const double * const fi, const double * const fj,
- const double * const fk, const double * const drim,
- const double * const drjm, const double * const drkm,
- ThrData * const thr)
+ const int k, const int m, const double evdwl,
+ const double * const fi, const double * const fj,
+ const double * const fk, const double * const drim,
+ const double * const drjm, const double * const drkm,
+ ThrData * const thr)
{
double v[6];
@@ -669,7 +669,7 @@ void ThrOMP::ev_tally4_thr(Pair * const pair, const int i, const int j,
v[3] = 0.25 * (drim[0]*fi[1] + drjm[0]*fj[1] + drkm[0]*fk[1]);
v[4] = 0.25 * (drim[0]*fi[2] + drjm[0]*fj[2] + drkm[0]*fk[2]);
v[5] = 0.25 * (drim[1]*fi[2] + drjm[1]*fj[2] + drkm[1]*fk[2]);
-
+
v_tally(thr->vatom_pair[i],v);
v_tally(thr->vatom_pair[j],v);
v_tally(thr->vatom_pair[k],v);
@@ -684,8 +684,8 @@ void ThrOMP::ev_tally4_thr(Pair * const pair, const int i, const int j,
------------------------------------------------------------------------- */
void ThrOMP::ev_tally_list_thr(Pair * const pair, const int n,
- const int * const list, const double ecoul,
- const double * const v, ThrData * const thr)
+ const int * const list, const double ecoul,
+ const double * const v, ThrData * const thr)
{
if (pair->eflag_either) {
if (pair->eflag_global) thr->eng_coul += ecoul;
@@ -711,8 +711,8 @@ void ThrOMP::ev_tally_list_thr(Pair * const pair, const int n,
vtmp[5] = s * v[5];
for (int i = 0; i < n; i++) {
- const int j = list[i];
- v_tally(thr->vatom_pair[j],vtmp);
+ const int j = list[i];
+ v_tally(thr->vatom_pair[j],vtmp);
}
}
}
@@ -723,27 +723,27 @@ void ThrOMP::ev_tally_list_thr(Pair * const pair, const int n,
------------------------------------------------------------------------- */
void ThrOMP::ev_tally_thr(Bond * const bond, const int i, const int j, const int nlocal,
- const int newton_bond, const double ebond, const double fbond,
- const double delx, const double dely, const double delz,
- ThrData * const thr)
+ const int newton_bond, const double ebond, const double fbond,
+ const double delx, const double dely, const double delz,
+ ThrData * const thr)
{
if (bond->eflag_either) {
const double ebondhalf = 0.5*ebond;
if (newton_bond) {
if (bond->eflag_global)
- thr->eng_bond += ebond;
+ thr->eng_bond += ebond;
if (bond->eflag_atom) {
- thr->eatom_bond[i] += ebondhalf;
- thr->eatom_bond[j] += ebondhalf;
+ thr->eatom_bond[i] += ebondhalf;
+ thr->eatom_bond[j] += ebondhalf;
}
} else {
if (bond->eflag_global) {
- if (i < nlocal) thr->eng_bond += ebondhalf;
- if (j < nlocal) thr->eng_bond += ebondhalf;
+ if (i < nlocal) thr->eng_bond += ebondhalf;
+ if (j < nlocal) thr->eng_bond += ebondhalf;
}
if (bond->eflag_atom) {
- if (i < nlocal) thr->eatom_bond[i] += ebondhalf;
- if (j < nlocal) thr->eatom_bond[j] += ebondhalf;
+ if (i < nlocal) thr->eatom_bond[i] += ebondhalf;
+ if (j < nlocal) thr->eatom_bond[j] += ebondhalf;
}
}
}
@@ -760,12 +760,12 @@ void ThrOMP::ev_tally_thr(Bond * const bond, const int i, const int j, const int
if (bond->vflag_global) {
if (newton_bond)
- v_tally(thr->virial_bond,v);
+ v_tally(thr->virial_bond,v);
else {
- if (i < nlocal)
- v_tally(thr->virial_bond,0.5,v);
- if (j < nlocal)
- v_tally(thr->virial_bond,0.5,v);
+ if (i < nlocal)
+ v_tally(thr->virial_bond,0.5,v);
+ if (j < nlocal)
+ v_tally(thr->virial_bond,0.5,v);
}
}
@@ -778,13 +778,13 @@ void ThrOMP::ev_tally_thr(Bond * const bond, const int i, const int j, const int
v[5] *= 0.5;
if (newton_bond) {
- v_tally(thr->vatom_bond[i],v);
- v_tally(thr->vatom_bond[j],v);
+ v_tally(thr->vatom_bond[i],v);
+ v_tally(thr->vatom_bond[j],v);
} else {
- if (j < nlocal)
- v_tally(thr->vatom_bond[i],v);
- if (j < nlocal)
- v_tally(thr->vatom_bond[j],v);
+ if (j < nlocal)
+ v_tally(thr->vatom_bond[i],v);
+ if (j < nlocal)
+ v_tally(thr->vatom_bond[j],v);
}
}
}
@@ -796,32 +796,32 @@ void ThrOMP::ev_tally_thr(Bond * const bond, const int i, const int j, const int
------------------------------------------------------------------------- */
void ThrOMP::ev_tally_thr(Angle * const angle, const int i, const int j, const int k,
- const int nlocal, const int newton_bond, const double eangle,
- const double * const f1, const double * const f3,
- const double delx1, const double dely1, const double delz1,
- const double delx2, const double dely2, const double delz2,
- ThrData * const thr)
+ const int nlocal, const int newton_bond, const double eangle,
+ const double * const f1, const double * const f3,
+ const double delx1, const double dely1, const double delz1,
+ const double delx2, const double dely2, const double delz2,
+ ThrData * const thr)
{
if (angle->eflag_either) {
const double eanglethird = THIRD*eangle;
if (newton_bond) {
if (angle->eflag_global)
- thr->eng_angle += eangle;
+ thr->eng_angle += eangle;
if (angle->eflag_atom) {
- thr->eatom_angle[i] += eanglethird;
- thr->eatom_angle[j] += eanglethird;
- thr->eatom_angle[k] += eanglethird;
+ thr->eatom_angle[i] += eanglethird;
+ thr->eatom_angle[j] += eanglethird;
+ thr->eatom_angle[k] += eanglethird;
}
} else {
if (angle->eflag_global) {
- if (i < nlocal) thr->eng_angle += eanglethird;
- if (j < nlocal) thr->eng_angle += eanglethird;
- if (k < nlocal) thr->eng_angle += eanglethird;
+ if (i < nlocal) thr->eng_angle += eanglethird;
+ if (j < nlocal) thr->eng_angle += eanglethird;
+ if (k < nlocal) thr->eng_angle += eanglethird;
}
if (angle->eflag_atom) {
- if (i < nlocal) thr->eatom_angle[i] += eanglethird;
- if (j < nlocal) thr->eatom_angle[j] += eanglethird;
- if (k < nlocal) thr->eatom_angle[k] += eanglethird;
+ if (i < nlocal) thr->eatom_angle[i] += eanglethird;
+ if (j < nlocal) thr->eatom_angle[j] += eanglethird;
+ if (k < nlocal) thr->eatom_angle[k] += eanglethird;
}
}
}
@@ -838,13 +838,13 @@ void ThrOMP::ev_tally_thr(Angle * const angle, const int i, const int j, const i
if (angle->vflag_global) {
if (newton_bond) {
- v_tally(thr->virial_angle,v);
+ v_tally(thr->virial_angle,v);
} else {
- int cnt = 0;
- if (i < nlocal) ++cnt;
- if (j < nlocal) ++cnt;
- if (k < nlocal) ++cnt;
- v_tally(thr->virial_angle,cnt*THIRD,v);
+ int cnt = 0;
+ if (i < nlocal) ++cnt;
+ if (j < nlocal) ++cnt;
+ if (k < nlocal) ++cnt;
+ v_tally(thr->virial_angle,cnt*THIRD,v);
}
}
@@ -857,13 +857,13 @@ void ThrOMP::ev_tally_thr(Angle * const angle, const int i, const int j, const i
v[5] *= THIRD;
if (newton_bond) {
- v_tally(thr->vatom_angle[i],v);
- v_tally(thr->vatom_angle[j],v);
- v_tally(thr->vatom_angle[k],v);
+ v_tally(thr->vatom_angle[i],v);
+ v_tally(thr->vatom_angle[j],v);
+ v_tally(thr->vatom_angle[k],v);
} else {
- if (j < nlocal) v_tally(thr->vatom_angle[i],v);
- if (j < nlocal) v_tally(thr->vatom_angle[j],v);
- if (k < nlocal) v_tally(thr->vatom_angle[k],v);
+ if (j < nlocal) v_tally(thr->vatom_angle[i],v);
+ if (j < nlocal) v_tally(thr->vatom_angle[j],v);
+ if (k < nlocal) v_tally(thr->vatom_angle[k],v);
}
}
}
@@ -874,10 +874,10 @@ void ThrOMP::ev_tally_thr(Angle * const angle, const int i, const int j, const i
------------------------------------------------------------------------- */
void ThrOMP::ev_tally13_thr(Angle * const angle, const int i1, const int i3,
- const int nlocal, const int newton_bond,
- const double epair, const double fpair,
- const double delx, const double dely,
- const double delz, ThrData * const thr)
+ const int nlocal, const int newton_bond,
+ const double epair, const double fpair,
+ const double delx, const double dely,
+ const double delz, ThrData * const thr)
{
if (angle->eflag_either) {
@@ -885,9 +885,9 @@ void ThrOMP::ev_tally13_thr(Angle * const angle, const int i1, const int i3,
if (angle->eflag_global) {
if (newton_bond || i1 < nlocal)
- thr->eng_angle += epairhalf;
+ thr->eng_angle += epairhalf;
if (newton_bond || i3 < nlocal)
- thr->eng_angle += epairhalf;
+ thr->eng_angle += epairhalf;
}
if (angle->eflag_atom) {
@@ -895,7 +895,7 @@ void ThrOMP::ev_tally13_thr(Angle * const angle, const int i1, const int i3,
if (newton_bond || i3 < nlocal) thr->eatom_angle[i3] += epairhalf;
}
}
-
+
if (angle->vflag_either) {
double v[6];
v[0] = delx*delx*fpair;
@@ -913,15 +913,15 @@ void ThrOMP::ev_tally13_thr(Angle * const angle, const int i1, const int i3,
if (angle->vflag_atom) {
if (newton_bond || i1 < nlocal) {
- double * const va = thr->vatom_angle[i1];
- v_tally(va,0.5,v);
+ double * const va = thr->vatom_angle[i1];
+ v_tally(va,0.5,v);
}
if (newton_bond || i3 < nlocal) {
- double * const va = thr->vatom_angle[i3];
- v_tally(va,0.5,v);
+ double * const va = thr->vatom_angle[i3];
+ v_tally(va,0.5,v);
}
}
- }
+ }
}
@@ -929,45 +929,45 @@ void ThrOMP::ev_tally13_thr(Angle * const angle, const int i1, const int i3,
tally energy and virial into global and per-atom accumulators
virial = r1F1 + r2F2 + r3F3 + r4F4 = (r1-r2) F1 + (r3-r2) F3 + (r4-r2) F4
= (r1-r2) F1 + (r3-r2) F3 + (r4-r3 + r3-r2) F4
- = vb1*f1 + vb2*f3 + (vb3+vb2)*f4
+ = vb1*f1 + vb2*f3 + (vb3+vb2)*f4
------------------------------------------------------------------------- */
void ThrOMP::ev_tally_thr(Dihedral * const dihed, const int i1, const int i2,
- const int i3, const int i4, const int nlocal,
- const int newton_bond, const double edihedral,
- const double * const f1, const double * const f3,
- const double * const f4, const double vb1x,
- const double vb1y, const double vb1z, const double vb2x,
- const double vb2y, const double vb2z, const double vb3x,
- const double vb3y, const double vb3z, ThrData * const thr)
+ const int i3, const int i4, const int nlocal,
+ const int newton_bond, const double edihedral,
+ const double * const f1, const double * const f3,
+ const double * const f4, const double vb1x,
+ const double vb1y, const double vb1z, const double vb2x,
+ const double vb2y, const double vb2z, const double vb3x,
+ const double vb3y, const double vb3z, ThrData * const thr)
{
if (dihed->eflag_either) {
if (dihed->eflag_global) {
if (newton_bond) {
- thr->eng_dihed += edihedral;
+ thr->eng_dihed += edihedral;
} else {
- const double edihedralquarter = 0.25*edihedral;
- int cnt = 0;
- if (i1 < nlocal) ++cnt;
- if (i2 < nlocal) ++cnt;
- if (i3 < nlocal) ++cnt;
- if (i4 < nlocal) ++cnt;
- thr->eng_dihed += static_cast<double>(cnt)*edihedralquarter;
+ const double edihedralquarter = 0.25*edihedral;
+ int cnt = 0;
+ if (i1 < nlocal) ++cnt;
+ if (i2 < nlocal) ++cnt;
+ if (i3 < nlocal) ++cnt;
+ if (i4 < nlocal) ++cnt;
+ thr->eng_dihed += static_cast<double>(cnt)*edihedralquarter;
}
}
if (dihed->eflag_atom) {
const double edihedralquarter = 0.25*edihedral;
if (newton_bond) {
- thr->eatom_dihed[i1] += edihedralquarter;
- thr->eatom_dihed[i2] += edihedralquarter;
- thr->eatom_dihed[i3] += edihedralquarter;
- thr->eatom_dihed[i4] += edihedralquarter;
+ thr->eatom_dihed[i1] += edihedralquarter;
+ thr->eatom_dihed[i2] += edihedralquarter;
+ thr->eatom_dihed[i3] += edihedralquarter;
+ thr->eatom_dihed[i4] += edihedralquarter;
} else {
- if (i1 < nlocal) thr->eatom_dihed[i1] += edihedralquarter;
- if (i2 < nlocal) thr->eatom_dihed[i2] += edihedralquarter;
- if (i3 < nlocal) thr->eatom_dihed[i3] += edihedralquarter;
- if (i4 < nlocal) thr->eatom_dihed[i4] += edihedralquarter;
+ if (i1 < nlocal) thr->eatom_dihed[i1] += edihedralquarter;
+ if (i2 < nlocal) thr->eatom_dihed[i2] += edihedralquarter;
+ if (i3 < nlocal) thr->eatom_dihed[i3] += edihedralquarter;
+ if (i4 < nlocal) thr->eatom_dihed[i4] += edihedralquarter;
}
}
}
@@ -983,14 +983,14 @@ void ThrOMP::ev_tally_thr(Dihedral * const dihed, const int i1, const int i2,
if (dihed->vflag_global) {
if (newton_bond) {
- v_tally(thr->virial_dihed,v);
+ v_tally(thr->virial_dihed,v);
} else {
- int cnt = 0;
- if (i1 < nlocal) ++cnt;
- if (i2 < nlocal) ++cnt;
- if (i3 < nlocal) ++cnt;
- if (i4 < nlocal) ++cnt;
- v_tally(thr->virial_dihed,0.25*static_cast<double>(cnt),v);
+ int cnt = 0;
+ if (i1 < nlocal) ++cnt;
+ if (i2 < nlocal) ++cnt;
+ if (i3 < nlocal) ++cnt;
+ if (i4 < nlocal) ++cnt;
+ v_tally(thr->virial_dihed,0.25*static_cast<double>(cnt),v);
}
}
@@ -1000,18 +1000,18 @@ void ThrOMP::ev_tally_thr(Dihedral * const dihed, const int i1, const int i2,
v[3] *= 0.25;
v[4] *= 0.25;
v[5] *= 0.25;
-
+
if (dihed->vflag_atom) {
if (newton_bond) {
- v_tally(thr->vatom_dihed[i1],v);
- v_tally(thr->vatom_dihed[i2],v);
- v_tally(thr->vatom_dihed[i3],v);
- v_tally(thr->vatom_dihed[i4],v);
+ v_tally(thr->vatom_dihed[i1],v);
+ v_tally(thr->vatom_dihed[i2],v);
+ v_tally(thr->vatom_dihed[i3],v);
+ v_tally(thr->vatom_dihed[i4],v);
} else {
- if (i1 < nlocal) v_tally(thr->vatom_dihed[i1],v);
- if (i2 < nlocal) v_tally(thr->vatom_dihed[i2],v);
- if (i3 < nlocal) v_tally(thr->vatom_dihed[i3],v);
- if (i4 < nlocal) v_tally(thr->vatom_dihed[i4],v);
+ if (i1 < nlocal) v_tally(thr->vatom_dihed[i1],v);
+ if (i2 < nlocal) v_tally(thr->vatom_dihed[i2],v);
+ if (i3 < nlocal) v_tally(thr->vatom_dihed[i3],v);
+ if (i4 < nlocal) v_tally(thr->vatom_dihed[i4],v);
}
}
}
@@ -1021,45 +1021,45 @@ void ThrOMP::ev_tally_thr(Dihedral * const dihed, const int i1, const int i2,
tally energy and virial into global and per-atom accumulators
virial = r1F1 + r2F2 + r3F3 + r4F4 = (r1-r2) F1 + (r3-r2) F3 + (r4-r2) F4
= (r1-r2) F1 + (r3-r2) F3 + (r4-r3 + r3-r2) F4
- = vb1*f1 + vb2*f3 + (vb3+vb2)*f4
+ = vb1*f1 + vb2*f3 + (vb3+vb2)*f4
------------------------------------------------------------------------- */
void ThrOMP::ev_tally_thr(Improper * const imprp, const int i1, const int i2,
- const int i3, const int i4, const int nlocal,
- const int newton_bond, const double eimproper,
- const double * const f1, const double * const f3,
- const double * const f4, const double vb1x,
- const double vb1y, const double vb1z, const double vb2x,
- const double vb2y, const double vb2z, const double vb3x,
- const double vb3y, const double vb3z, ThrData * const thr)
+ const int i3, const int i4, const int nlocal,
+ const int newton_bond, const double eimproper,
+ const double * const f1, const double * const f3,
+ const double * const f4, const double vb1x,
+ const double vb1y, const double vb1z, const double vb2x,
+ const double vb2y, const double vb2z, const double vb3x,
+ const double vb3y, const double vb3z, ThrData * const thr)
{
if (imprp->eflag_either) {
if (imprp->eflag_global) {
if (newton_bond) {
- thr->eng_imprp += eimproper;
+ thr->eng_imprp += eimproper;
} else {
- const double eimproperquarter = 0.25*eimproper;
- int cnt = 0;
- if (i1 < nlocal) ++cnt;
- if (i2 < nlocal) ++cnt;
- if (i3 < nlocal) ++cnt;
- if (i4 < nlocal) ++cnt;
- thr->eng_imprp += static_cast<double>(cnt)*eimproperquarter;
+ const double eimproperquarter = 0.25*eimproper;
+ int cnt = 0;
+ if (i1 < nlocal) ++cnt;
+ if (i2 < nlocal) ++cnt;
+ if (i3 < nlocal) ++cnt;
+ if (i4 < nlocal) ++cnt;
+ thr->eng_imprp += static_cast<double>(cnt)*eimproperquarter;
}
}
if (imprp->eflag_atom) {
const double eimproperquarter = 0.25*eimproper;
if (newton_bond) {
- thr->eatom_imprp[i1] += eimproperquarter;
- thr->eatom_imprp[i2] += eimproperquarter;
- thr->eatom_imprp[i3] += eimproperquarter;
- thr->eatom_imprp[i4] += eimproperquarter;
+ thr->eatom_imprp[i1] += eimproperquarter;
+ thr->eatom_imprp[i2] += eimproperquarter;
+ thr->eatom_imprp[i3] += eimproperquarter;
+ thr->eatom_imprp[i4] += eimproperquarter;
} else {
- if (i1 < nlocal) thr->eatom_imprp[i1] += eimproperquarter;
- if (i2 < nlocal) thr->eatom_imprp[i2] += eimproperquarter;
- if (i3 < nlocal) thr->eatom_imprp[i3] += eimproperquarter;
- if (i4 < nlocal) thr->eatom_imprp[i4] += eimproperquarter;
+ if (i1 < nlocal) thr->eatom_imprp[i1] += eimproperquarter;
+ if (i2 < nlocal) thr->eatom_imprp[i2] += eimproperquarter;
+ if (i3 < nlocal) thr->eatom_imprp[i3] += eimproperquarter;
+ if (i4 < nlocal) thr->eatom_imprp[i4] += eimproperquarter;
}
}
}
@@ -1075,14 +1075,14 @@ void ThrOMP::ev_tally_thr(Improper * const imprp, const int i1, const int i2,
if (imprp->vflag_global) {
if (newton_bond) {
- v_tally(thr->virial_imprp,v);
+ v_tally(thr->virial_imprp,v);
} else {
- int cnt = 0;
- if (i1 < nlocal) ++cnt;
- if (i2 < nlocal) ++cnt;
- if (i3 < nlocal) ++cnt;
- if (i4 < nlocal) ++cnt;
- v_tally(thr->virial_imprp,0.25*static_cast<double>(cnt),v);
+ int cnt = 0;
+ if (i1 < nlocal) ++cnt;
+ if (i2 < nlocal) ++cnt;
+ if (i3 < nlocal) ++cnt;
+ if (i4 < nlocal) ++cnt;
+ v_tally(thr->virial_imprp,0.25*static_cast<double>(cnt),v);
}
}
@@ -1092,18 +1092,18 @@ void ThrOMP::ev_tally_thr(Improper * const imprp, const int i1, const int i2,
v[3] *= 0.25;
v[4] *= 0.25;
v[5] *= 0.25;
-
+
if (imprp->vflag_atom) {
if (newton_bond) {
- v_tally(thr->vatom_imprp[i1],v);
- v_tally(thr->vatom_imprp[i2],v);
- v_tally(thr->vatom_imprp[i3],v);
- v_tally(thr->vatom_imprp[i4],v);
+ v_tally(thr->vatom_imprp[i1],v);
+ v_tally(thr->vatom_imprp[i2],v);
+ v_tally(thr->vatom_imprp[i3],v);
+ v_tally(thr->vatom_imprp[i4],v);
} else {
- if (i1 < nlocal) v_tally(thr->vatom_imprp[i1],v);
- if (i2 < nlocal) v_tally(thr->vatom_imprp[i2],v);
- if (i3 < nlocal) v_tally(thr->vatom_imprp[i3],v);
- if (i4 < nlocal) v_tally(thr->vatom_imprp[i4],v);
+ if (i1 < nlocal) v_tally(thr->vatom_imprp[i1],v);
+ if (i2 < nlocal) v_tally(thr->vatom_imprp[i2],v);
+ if (i3 < nlocal) v_tally(thr->vatom_imprp[i3],v);
+ if (i4 < nlocal) v_tally(thr->vatom_imprp[i4],v);
}
}
}
@@ -1116,10 +1116,10 @@ void ThrOMP::ev_tally_thr(Improper * const imprp, const int i1, const int i2,
------------------------------------------------------------------------- */
void ThrOMP::v_tally2_thr(const int i, const int j, const double fpair,
- const double * const drij, ThrData * const thr)
+ const double * const drij, ThrData * const thr)
{
double v[6];
-
+
v[0] = 0.5 * drij[0]*drij[0]*fpair;
v[1] = 0.5 * drij[1]*drij[1]*fpair;
v[2] = 0.5 * drij[2]*drij[2]*fpair;
@@ -1137,12 +1137,12 @@ void ThrOMP::v_tally2_thr(const int i, const int j, const double fpair,
------------------------------------------------------------------------- */
void ThrOMP::v_tally3_thr(const int i, const int j, const int k,
- const double * const fi, const double * const fj,
- const double * const drik, const double * const drjk,
- ThrData * const thr)
+ const double * const fi, const double * const fj,
+ const double * const drik, const double * const drjk,
+ ThrData * const thr)
{
double v[6];
-
+
v[0] = THIRD * (drik[0]*fi[0] + drjk[0]*fj[0]);
v[1] = THIRD * (drik[1]*fi[1] + drjk[1]*fj[1]);
v[2] = THIRD * (drik[2]*fi[2] + drjk[2]*fj[2]);
@@ -1161,10 +1161,10 @@ void ThrOMP::v_tally3_thr(const int i, const int j, const int k,
------------------------------------------------------------------------- */
void ThrOMP::v_tally4_thr(const int i, const int j, const int k, const int m,
- const double * const fi, const double * const fj,
- const double * const fk, const double * const drim,
- const double * const drjm, const double * const drkm,
- ThrData * const thr)
+ const double * const fi, const double * const fj,
+ const double * const fk, const double * const drim,
+ const double * const drjm, const double * const drkm,
+ ThrData * const thr)
{
double v[6];
@@ -1183,9 +1183,9 @@ void ThrOMP::v_tally4_thr(const int i, const int j, const int k, const int m,
/* ---------------------------------------------------------------------- */
-double ThrOMP::memory_usage_thr()
+double ThrOMP::memory_usage_thr()
{
double bytes=0.0;
-
+
return bytes;
}
diff --git a/src/USER-OMP/thr_omp.h b/src/USER-OMP/thr_omp.h
index 72fc330cb4884cb2d0067bf383523bd2e5e6df54..19e50031f8eee87154abe8b77032894a7b952877 100644
--- a/src/USER-OMP/thr_omp.h
+++ b/src/USER-OMP/thr_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -57,21 +57,21 @@ class ThrOMP {
};
enum {THR_NONE=0,THR_PAIR=1,THR_BOND=1<<1,THR_ANGLE=1<<2,
- THR_DIHEDRAL=1<<3,THR_IMPROPER=1<<4,THR_KSPACE=1<<5,
- THR_CHARMM=1<<6,THR_PROXY=1<<7,THR_HYBRID=1<<8,THR_FIX=1<<9};
+ THR_DIHEDRAL=1<<3,THR_IMPROPER=1<<4,THR_KSPACE=1<<5,
+ THR_CHARMM=1<<6,THR_PROXY=1<<7,THR_HYBRID=1<<8,THR_FIX=1<<9};
protected:
// extra ev_tally setup work for threaded styles
void ev_setup_thr(int, int, int, double *, double **, ThrData *);
// compute global per thread virial contribution from per-thread force
- void virial_fdotr_compute_thr(double * const, const double * const * const,
- const double * const * const,
- const int, const int, const int);
+ void virial_fdotr_compute_thr(double * const, const double * const * const,
+ const double * const * const,
+ const int, const int, const int);
// reduce per thread data as needed
void reduce_thr(void * const style, const int eflag, const int vflag,
- ThrData * const thr, const int nproxy=0);
+ ThrData * const thr, const int nproxy=0);
// thread safe variant error abort support.
// signals an error condition in any thread by making
@@ -82,7 +82,7 @@ class ThrOMP {
// use return value to jump/return to end of threaded region.
bool check_error_thr(const bool cond, const int tid, const char *fname,
- const int line, const char *errmsg) {
+ const int line, const char *errmsg) {
if (cond) {
#if defined(_OPENMP)
#pragma omp atomic
@@ -92,8 +92,8 @@ class ThrOMP {
else lmp->error->one(fname,line,errmsg);
} else {
if (thr_error > 0) {
- if (tid == 0) lmp->error->one(fname,line,errmsg);
- else return true;
+ if (tid == 0) lmp->error->one(fname,line,errmsg);
+ else return true;
} else return false;
}
return false;
@@ -106,68 +106,68 @@ class ThrOMP {
// Pair
void e_tally_thr(Pair * const, const int, const int, const int,
- const int, const double, const double, ThrData * const);
+ const int, const double, const double, ThrData * const);
void v_tally_thr(Pair * const, const int, const int, const int,
- const int, const double * const, ThrData * const);
+ const int, const double * const, ThrData * const);
void ev_tally_thr(Pair * const, const int, const int, const int, const int,
- const double, const double, const double, const double,
- const double, const double, ThrData * const);
+ const double, const double, const double, const double,
+ const double, const double, ThrData * const);
void ev_tally_xyz_thr(Pair * const, const int, const int, const int,
- const int, const double, const double, const double,
- const double, const double, const double,
- const double, const double, ThrData * const);
+ const int, const double, const double, const double,
+ const double, const double, const double,
+ const double, const double, ThrData * const);
void ev_tally3_thr(Pair * const, const int, const int, const int, const double,
- const double, const double * const, const double * const,
- const double * const, const double * const, ThrData * const);
+ const double, const double * const, const double * const,
+ const double * const, const double * const, ThrData * const);
void ev_tally4_thr(Pair * const, const int, const int, const int, const int,
- const double, const double * const, const double * const,
- const double * const, const double * const, const double * const,
- const double * const, ThrData * const);
+ const double, const double * const, const double * const,
+ const double * const, const double * const, const double * const,
+ const double * const, ThrData * const);
// Bond
void ev_tally_thr(Bond * const, const int, const int, const int, const int,
- const double, const double, const double, const double,
- const double, ThrData * const);
+ const double, const double, const double, const double,
+ const double, ThrData * const);
// Angle
void ev_tally_thr(Angle * const, const int, const int, const int, const int, const int,
- const double, const double * const, const double * const,
- const double, const double, const double, const double, const double,
- const double, ThrData * const thr);
+ const double, const double * const, const double * const,
+ const double, const double, const double, const double, const double,
+ const double, ThrData * const thr);
void ev_tally13_thr(Angle * const, const int, const int, const int, const int,
- const double, const double, const double, const double,
- const double, ThrData * const thr);
+ const double, const double, const double, const double,
+ const double, ThrData * const thr);
// Dihedral
void ev_tally_thr(Dihedral * const, const int, const int, const int, const int, const int,
- const int, const double, const double * const, const double * const,
- const double * const, const double, const double, const double,
- const double, const double, const double, const double, const double,
- const double, ThrData * const);
+ const int, const double, const double * const, const double * const,
+ const double * const, const double, const double, const double,
+ const double, const double, const double, const double, const double,
+ const double, ThrData * const);
// Improper
void ev_tally_thr(Improper * const, const int, const int, const int, const int, const int,
- const int, const double, const double * const, const double * const,
- const double * const, const double, const double, const double,
- const double, const double, const double, const double, const double,
- const double, ThrData * const);
+ const int, const double, const double * const, const double * const,
+ const double * const, const double, const double, const double,
+ const double, const double, const double, const double, const double,
+ const double, ThrData * const);
// style independent versions
void v_tally2_thr(const int, const int, const double, const double * const, ThrData * const);
void v_tally3_thr(const int, const int, const int, const double * const, const double * const,
- const double * const, const double * const, ThrData * const);
+ const double * const, const double * const, ThrData * const);
void v_tally4_thr(const int, const int, const int, const int, const double * const,
- const double * const, const double * const, const double * const,
- const double * const, const double * const, ThrData * const);
+ const double * const, const double * const, const double * const,
+ const double * const, const double * const, ThrData * const);
void ev_tally_list_thr(Pair * const, const int, const int * const,
- const double , const double * const , ThrData * const);
+ const double , const double * const , ThrData * const);
};
// set loop range thread id, and force array offset for threaded runs.
static inline void loop_setup_thr(int &ifrom, int &ito, int &tid,
- int inum, int nthreads, int nproxy=0)
+ int inum, int nthreads, int nproxy=0)
{
#if defined(_OPENMP)
tid = omp_get_thread_num();
diff --git a/src/USER-REAXC/fix_qeq_reax.cpp b/src/USER-REAXC/fix_qeq_reax.cpp
index cde118fa33f99408ea0634075e8bf293b75184d3..b61c14900287abc18c5c82c2c8edb7ea951c917e 100644
--- a/src/USER-REAXC/fix_qeq_reax.cpp
+++ b/src/USER-REAXC/fix_qeq_reax.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -53,11 +53,11 @@ using namespace FixConst;
/* ---------------------------------------------------------------------- */
-FixQEqReax::FixQEqReax(LAMMPS *lmp, int narg, char **arg) :
+FixQEqReax::FixQEqReax(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
- if (narg != 8) error->all(FLERR,"Illegal fix qeq/reax command");
-
+ if (narg != 8) error->all(FLERR,"Illegal fix qeq/reax command");
+
nevery = atoi(arg[3]);
swa = atof(arg[4]);
swb = atof(arg[5]);
@@ -73,7 +73,7 @@ FixQEqReax::FixQEqReax(LAMMPS *lmp, int narg, char **arg) :
s = NULL;
t = NULL;
nprev = 5;
-
+
Hdia_inv = NULL;
b_s = NULL;
b_t = NULL;
@@ -111,7 +111,7 @@ FixQEqReax::FixQEqReax(LAMMPS *lmp, int narg, char **arg) :
FixQEqReax::~FixQEqReax()
{
// unregister callbacks to this fix from Atom class
-
+
atom->delete_callback(id,0);
memory->destroy(s_hist);
@@ -153,7 +153,7 @@ void FixQEqReax::pertype_parameters(char *arg)
gamma = (double *) pair->extract("gamma",tmp);
if (chi == NULL || eta == NULL || gamma == NULL)
error->all(FLERR,
- "Fix qeq/reax could not extract params from pair reax/c");
+ "Fix qeq/reax could not extract params from pair reax/c");
return;
}
@@ -171,11 +171,11 @@ void FixQEqReax::pertype_parameters(char *arg)
if (comm->me == 0) {
if ((pf = fopen(arg,"r")) == NULL)
error->one(FLERR,"Fix qeq/reax parameter file could not be found");
-
+
for (i = 1; i <= ntypes && !feof(pf); i++) {
fscanf(pf,"%d %lg %lg %lg",&itype,&v1,&v2,&v3);
if (itype < 1 || itype > ntypes)
- error->one(FLERR,"Fix qeq/reax invalid atom type in param file");
+ error->one(FLERR,"Fix qeq/reax invalid atom type in param file");
chi[itype] = v1;
eta[itype] = v2;
gamma[itype] = v3;
@@ -255,7 +255,7 @@ void FixQEqReax::allocate_matrix()
m += list->numneigh[i];
}
m_cap = MAX( (int)(m * SAFE_ZONE), MIN_CAP * MIN_NBRS );
-
+
H.n = n_cap;
H.m = m_cap;
memory->create(H.firstnbr,n_cap,"qeq:H.firstnbr");
@@ -271,7 +271,7 @@ void FixQEqReax::deallocate_matrix()
memory->destroy( H.firstnbr );
memory->destroy( H.numnbrs );
memory->destroy( H.jlist );
- memory->destroy( H.val );
+ memory->destroy( H.val );
}
/* ---------------------------------------------------------------------- */
@@ -287,7 +287,7 @@ void FixQEqReax::reallocate_matrix()
void FixQEqReax::init()
{
if (!atom->q_flag) error->all(FLERR,"Fix qeq/reax requires atom attribute q");
-
+
// need a half neighbor list w/ Newton off
// built whenever re-neighboring occurs
@@ -319,7 +319,7 @@ void FixQEqReax::init_shielding()
ntypes = atom->ntypes;
memory->create(shld,ntypes+1,ntypes+1,"qeq:shileding");
-
+
for( i = 1; i <= ntypes; ++i )
for( j = 1; j <= ntypes; ++j )
shld[i][j] = pow( gamma[i] * gamma[j], -1.5 );
@@ -351,7 +351,7 @@ void FixQEqReax::init_taper()
Tap[2] =-210.0 * (swa3*swb2 + swa2*swb3) / d7;
Tap[1] = 140.0 * swa3 * swb3 / d7;
Tap[0] = (-35.0*swa3*swb2*swb2 + 21.0*swa2*swb3*swb2 +
- 7.0*swa*swb3*swb3 + swb3*swb3*swb ) / d7;
+ 7.0*swa*swb3*swb3 + swb3*swb3*swb ) / d7;
}
/* ---------------------------------------------------------------------- */
@@ -364,7 +364,7 @@ void FixQEqReax::setup_pre_force(int vflag)
allocate_matrix();
pre_force(vflag);
-}
+}
/* ---------------------------------------------------------------------- */
@@ -372,14 +372,14 @@ void FixQEqReax::setup_pre_force_respa(int vflag, int ilevel)
{
if (ilevel < nlevels_respa-1) return;
setup_pre_force(vflag);
-}
+}
/* ---------------------------------------------------------------------- */
void FixQEqReax::min_setup_pre_force(int vflag)
{
setup_pre_force(vflag);
-}
+}
/* ---------------------------------------------------------------------- */
@@ -387,7 +387,7 @@ void FixQEqReax::init_storage()
{
N = atom->nlocal + atom->nghost;
for( int i = 0; i < N; i++ ) {
- Hdia_inv[i] = 1. / eta[atom->type[i]];
+ Hdia_inv[i] = 1. / eta[atom->type[i]];
b_s[i] = -chi[atom->type[i]];
b_t[i] = -1.0;
b_prc[i] = 0;
@@ -412,9 +412,9 @@ void FixQEqReax::pre_force(int vflag)
if( atom->nmax > nmax ) reallocate_storage();
if( n > n_cap*DANGER_ZONE || m_fill > m_cap*DANGER_ZONE )
reallocate_matrix();
-
+
init_matvec();
- matvecs = CG(b_s, s); // CG on s - parallel
+ matvecs = CG(b_s, s); // CG on s - parallel
matvecs += CG(b_t, t); // CG on t - parallel
calculate_Q();
@@ -456,7 +456,7 @@ void FixQEqReax::init_matvec()
//t[i] = 2 * t_hist[i][0] - t_hist[i][1];
/* quadratic extrapolation for s & t from previous solutions */
- //s[i] = s_hist[i][2] + 3 * ( s_hist[i][0] - s_hist[i][1] );
+ //s[i] = s_hist[i][2] + 3 * ( s_hist[i][0] - s_hist[i][1] );
t[i] = t_hist[i][2] + 3 * ( t_hist[i][0] - t_hist[i][1] );
/* cubic extrapolation for s & t from previous solutions */
@@ -488,7 +488,7 @@ void FixQEqReax::compute_H()
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// fill in the H matrix
m_fill = 0;
r_sqr = 0;
@@ -497,20 +497,20 @@ void FixQEqReax::compute_H()
jlist = firstneigh[i];
jnum = numneigh[i];
H.firstnbr[i] = m_fill;
-
+
for( jj = 0; jj < jnum; jj++ ) {
j = jlist[jj];
-
+
dx = x[j][0] - x[i][0];
dy = x[j][1] - x[i][1];
dz = x[j][2] - x[i][2];
r_sqr = SQR(dx) + SQR(dy) + SQR(dz);
-
+
flag = 0;
if (r_sqr <= SQR(swb)) {
if (j < n) flag = 1;
else if (tag[i] < tag[j]) flag = 1;
- else if (tag[i] == tag[j]) {
+ else if (tag[i] == tag[j]) {
if (dz > SMALL) flag = 1;
else if (fabs(dz) < SMALL) {
if (dy > SMALL) flag = 1;
@@ -519,21 +519,21 @@ void FixQEqReax::compute_H()
}
}
}
-
+
if( flag ) {
- H.jlist[m_fill] = j;
- H.val[m_fill] = calculate_H( sqrt(r_sqr), shld[type[i]][type[j]] );
- m_fill++;
+ H.jlist[m_fill] = j;
+ H.val[m_fill] = calculate_H( sqrt(r_sqr), shld[type[i]][type[j]] );
+ m_fill++;
}
}
-
+
H.numnbrs[i] = m_fill - H.firstnbr[i];
}
if (m_fill >= H.m) {
char str[128];
sprintf(str,"H matrix size has been exceeded: m_fill=%d H.m=%d\n",
- m_fill, H.m );
+ m_fill, H.m );
error->warning(FLERR,str);
error->all(FLERR,"Fix qeq/reax has insufficient QEq matrix size");
}
@@ -583,21 +583,21 @@ int FixQEqReax::CG( double *b, double *x )
comm->forward_comm_fix(this); //Dist_vector( d );
sparse_matvec( &H, d, q );
comm->reverse_comm_fix(this); //Coll_vector( q );
-
+
tmp = parallel_dot( d, q, n );
alpha = sig_new / tmp;
// comm->me, i, parallel_norm( d, n ), parallel_norm( q, n ), tmp );
-
+
vector_add( x, alpha, d, n );
vector_add( r, -alpha, q, n );
-
+
// pre-conditioning
for( j = 0; j < n; ++j )
p[j] = r[j] * Hdia_inv[j];
-
+
sig_old = sig_new;
sig_new = parallel_dot( r, p, n );
-
+
beta = sig_new / sig_old;
vector_sum( d, 1., p, beta, d, n );
@@ -619,7 +619,7 @@ void FixQEqReax::sparse_matvec( sparse_matrix *A, double *x, double *b )
b[i] = eta[ atom->type[i] ] * x[i];
for( i = n; i < N; ++i )
b[i] = 0;
-
+
for( i = 0; i < n; ++i ) {
for( itr_j=A->firstnbr[i]; itr_j<A->firstnbr[i]+A->numnbrs[i]; itr_j++) {
j = A->jlist[itr_j];
@@ -640,10 +640,10 @@ void FixQEqReax::calculate_Q()
s_sum = parallel_vector_acc( s, n );
t_sum = parallel_vector_acc( t, n);
u = s_sum / t_sum;
-
+
for( i = 0; i < n; ++i ) {
q[i] = s[i] - u * t[i];
-
+
/* backup s & t */
for( k = 4; k > 0; --k ) {
s_hist[i][k] = s_hist[i][k-1];
@@ -659,12 +659,12 @@ void FixQEqReax::calculate_Q()
/* ---------------------------------------------------------------------- */
-int FixQEqReax::pack_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+int FixQEqReax::pack_comm(int n, int *list, double *buf,
+ int pbc_flag, int *pbc)
{
int m;
- if( pack_flag == 1)
+ if( pack_flag == 1)
for(m = 0; m < n; m++) buf[m] = d[list[m]];
else if( pack_flag == 2 )
for(m = 0; m < n; m++) buf[m] = s[list[m]];
@@ -675,23 +675,23 @@ int FixQEqReax::pack_comm(int n, int *list, double *buf,
return 1;
}
-
+
/* ---------------------------------------------------------------------- */
void FixQEqReax::unpack_comm(int n, int first, double *buf)
{
int i, m;
-
- if( pack_flag == 1)
+
+ if( pack_flag == 1)
for(m = 0, i = first; m < n; m++, i++) d[i] = buf[m];
- else if( pack_flag == 2)
+ else if( pack_flag == 2)
for(m = 0, i = first; m < n; m++, i++) s[i] = buf[m];
- else if( pack_flag == 3)
+ else if( pack_flag == 3)
for(m = 0, i = first; m < n; m++, i++) t[i] = buf[m];
- else if( pack_flag == 4)
+ else if( pack_flag == 4)
for(m = 0, i = first; m < n; m++, i++) atom->q[i] = buf[m];
}
-
+
/* ---------------------------------------------------------------------- */
int FixQEqReax::pack_reverse_comm(int n, int first, double *buf)
@@ -700,7 +700,7 @@ int FixQEqReax::pack_reverse_comm(int n, int first, double *buf)
for(m = 0, i = first; m < n; m++, i++) buf[m] = q[i];
return 1;
}
-
+
/* ---------------------------------------------------------------------- */
void FixQEqReax::unpack_reverse_comm(int n, int *list, double *buf)
@@ -720,7 +720,7 @@ double FixQEqReax::memory_usage()
bytes += atom->nmax*11 * sizeof(double); // storage
bytes += n_cap*2 * sizeof(int); // matrix...
bytes += m_cap * sizeof(int);
- bytes += m_cap * sizeof(double);
+ bytes += m_cap * sizeof(double);
return bytes;
}
@@ -823,7 +823,7 @@ double FixQEqReax::parallel_vector_acc( double *v, int n )
double FixQEqReax::norm( double* v1, int k )
{
double ret = 0;
-
+
for( --k; k>=0; --k )
ret += ( v1[k] * v1[k] );
@@ -832,8 +832,8 @@ double FixQEqReax::norm( double* v1, int k )
/* ---------------------------------------------------------------------- */
-void FixQEqReax::vector_sum( double* dest, double c, double* v,
- double d, double* y, int k )
+void FixQEqReax::vector_sum( double* dest, double c, double* v,
+ double d, double* y, int k )
{
for( --k; k>=0; --k )
dest[k] = c * v[k] + d * y[k];
@@ -852,7 +852,7 @@ void FixQEqReax::vector_scale( double* dest, double c, double* v, int k )
double FixQEqReax::dot( double* v1, double* v2, int k )
{
double ret = 0;
-
+
for( --k; k>=0; --k )
ret += v1[k] * v2[k];
diff --git a/src/USER-REAXC/fix_qeq_reax.h b/src/USER-REAXC/fix_qeq_reax.h
index 9bab44179b246be02e32e38d7c8f3d133840f7e7..b6f55976e391905b8a43ddcbb54fdab65d9f6ae4 100644
--- a/src/USER-REAXC/fix_qeq_reax.h
+++ b/src/USER-REAXC/fix_qeq_reax.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -72,7 +72,7 @@ class FixQEqReax : public Fix {
// fictitious charges
double *s, *t;
- double **s_hist, **t_hist;
+ double **s_hist, **t_hist;
int nprev;
typedef struct{
@@ -92,11 +92,11 @@ class FixQEqReax : public Fix {
double *p, *q, *r, *d;
//GMRES storage
- //double *g,*y;
+ //double *g,*y;
//double **v;
//double **h;
//double *hc, *hs;
-
+
void pertype_parameters(char*);
void init_shielding();
void init_taper();
@@ -106,17 +106,17 @@ class FixQEqReax : public Fix {
void allocate_matrix();
void deallocate_matrix();
void reallocate_matrix();
-
+
void init_matvec();
void init_H();
void compute_H();
double calculate_H(double,double);
void calculate_Q();
-
+
int CG(double*,double*);
//int GMRES(double*,double*);
void sparse_matvec(sparse_matrix*,double*,double*);
-
+
int pack_comm(int, int *, double *, int, int *);
void unpack_comm(int, int, double *);
int pack_reverse_comm(int, int, double *);
diff --git a/src/USER-REAXC/fix_reax_c.cpp b/src/USER-REAXC/fix_reax_c.cpp
index 8ec7165ffdbdc3e5a13070f7818e0d4e36cc76b8..ebaa652ad1f5abd6c16a45d0ef2ff94fc9a87223 100644
--- a/src/USER-REAXC/fix_reax_c.cpp
+++ b/src/USER-REAXC/fix_reax_c.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -36,17 +36,17 @@ using namespace FixConst;
/* ---------------------------------------------------------------------- */
-FixReaxC::FixReaxC(LAMMPS *lmp,int narg, char **arg) :
+FixReaxC::FixReaxC(LAMMPS *lmp,int narg, char **arg) :
Fix(lmp, narg, arg)
{
// perform initial allocation of atom-based arrays
// register with atom class
-
+
num_bonds = NULL;
num_hbonds = NULL;
grow_arrays(atom->nmax);
atom->add_callback(0);
-
+
// initialize arrays to MIN so atom migration is OK the 1st time
int nlocal = atom->nlocal;
@@ -136,7 +136,7 @@ int FixReaxC::unpack_exchange(int nlocal, double *buf)
/* ---------------------------------------------------------------------- */
int FixReaxC::pack_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
diff --git a/src/USER-REAXC/fix_reax_c.h b/src/USER-REAXC/fix_reax_c.h
index c54636ef51d422547428dde4f6085680077e55cb..8676f90f8b87c9061c5136f609adbdf903cc9170 100644
--- a/src/USER-REAXC/fix_reax_c.h
+++ b/src/USER-REAXC/fix_reax_c.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -36,7 +36,7 @@ namespace LAMMPS_NS {
class FixReaxC : public Fix {
friend class PairReaxC;
-
+
public:
FixReaxC(class LAMMPS *,int, char **);
~FixReaxC();
diff --git a/src/USER-REAXC/fix_reaxc_bonds.cpp b/src/USER-REAXC/fix_reaxc_bonds.cpp
index bc4505b904253e658b8729aaebd3e653729e12c7..a4f11018f4583e4bf43e98c7770b19063df87997 100644
--- a/src/USER-REAXC/fix_reaxc_bonds.cpp
+++ b/src/USER-REAXC/fix_reaxc_bonds.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -54,7 +54,7 @@ FixReaxCBonds::FixReaxCBonds(LAMMPS *lmp, int narg, char **arg) :
nevery = atoi(arg[3]);
nrepeat = atoi(arg[4]);
global_freq = nfreq = atoi(arg[5]);
-
+
if (nevery <= 0 || nrepeat <= 0 || nfreq <= 0)
error->all(FLERR,"Illegal fix reax/c/bonds command");
if (nfreq % nevery || (nrepeat-1)*nevery >= nfreq)
@@ -117,7 +117,7 @@ void FixReaxCBonds::init()
{
reaxc = (PairReaxC *) force->pair_match("reax/c",1);
if (reaxc == NULL) error->all(FLERR,"Cannot use fix reax/c/bonds without "
- "pair_style reax/c");
+ "pair_style reax/c");
if (nvalid < update->ntimestep) {
irepeat = 0;
@@ -157,7 +157,7 @@ void FixReaxCBonds::Output_ReaxC_Bonds(bigint ntimestep, FILE *fp)
for (i = 0; i < nmax; i++) {
sbo[i] = nlp[i] = avq[i] = 0.0;
for (j = 0; j < MAXBOND; j++) {
- tmpid[i][j] = 0;
+ tmpid[i][j] = 0;
tmpabo[i][j] = 0.0;
}
}
@@ -218,14 +218,14 @@ void FixReaxCBonds::GatherBond( reax_system *system, reax_list *lists)
bo_tmp = bo_ij->bo_data.BO;
if (bo_tmp > bo_cut) {
- here:;
- if (jtag != tmpid[i][nj] && tmpid[i][nj] != 0) {
- nj ++;
- if (nj > MAXBOND) error->all(FLERR,"Increase MAXBOND value");
- goto here;
- }
- tmpid[i][nj] = jtag;
- tmpabo[i][nj] += bo_tmp;
+ here:;
+ if (jtag != tmpid[i][nj] && tmpid[i][nj] != 0) {
+ nj ++;
+ if (nj > MAXBOND) error->all(FLERR,"Increase MAXBOND value");
+ goto here;
+ }
+ tmpid[i][nj] = jtag;
+ tmpabo[i][nj] += bo_tmp;
nj ++;
}
@@ -239,7 +239,7 @@ void FixReaxCBonds::GatherBond( reax_system *system, reax_list *lists)
/* ---------------------------------------------------------------------- */
void FixReaxCBonds::FindBond( reax_system *system, reax_list *lists,
- int &numbonds)
+ int &numbonds)
{
int *ilist, i, ii, inum;
int j, pj, nj, jtag, jtype;
@@ -268,9 +268,9 @@ void FixReaxCBonds::FindBond( reax_system *system, reax_list *lists,
for (j = 0; j < MAXBOND; j++){
if (tmpabo[i][j] > bo_cut) {
- neighid[i][nj] = tmpid[i][j];
- abo[i][nj] = tmpabo[i][j];
- nj ++;
+ neighid[i][nj] = tmpid[i][j];
+ abo[i][nj] = tmpabo[i][j];
+ nj ++;
}
}
numneigh[i] = nj;
@@ -280,8 +280,8 @@ void FixReaxCBonds::FindBond( reax_system *system, reax_list *lists,
/* ---------------------------------------------------------------------- */
-void FixReaxCBonds::PassBuffer( reax_system *system, double *buf,
- int &nbuf_local)
+void FixReaxCBonds::PassBuffer( reax_system *system, double *buf,
+ int &nbuf_local)
{
int i, j, k, jtag, numbonds;
int nlocal = atom->nlocal;
@@ -297,7 +297,7 @@ void FixReaxCBonds::PassBuffer( reax_system *system, double *buf,
buf[j+4] = numneigh[i];
numbonds = nint(buf[j+4]);
- for (k = 5; k < 5+numbonds; k++) {
+ for (k = 5; k < 5+numbonds; k++) {
buf[j+k] = neighid[i][k-5];
}
j += (5+numbonds);
@@ -306,7 +306,7 @@ void FixReaxCBonds::PassBuffer( reax_system *system, double *buf,
else buf[j] = atom->molecule[i];
j ++;
- for (k = 0; k < numbonds; k++) {
+ for (k = 0; k < numbonds; k++) {
buf[j+k] = abo[i][k];
}
j += (1+numbonds);
@@ -316,8 +316,8 @@ void FixReaxCBonds::PassBuffer( reax_system *system, double *buf,
/* ---------------------------------------------------------------------- */
-void FixReaxCBonds::RecvBuffer( reax_system *system, double *buf,
- int nbuf, int nbuf_local, int natoms, int maxnum)
+void FixReaxCBonds::RecvBuffer( reax_system *system, double *buf,
+ int nbuf, int nbuf_local, int natoms, int maxnum)
{
int i, j, k, l, itype, jtype, itag, jtag;
int inode, nlocal_tmp, numbonds, molid;
@@ -329,13 +329,13 @@ void FixReaxCBonds::RecvBuffer( reax_system *system, double *buf,
MPI_Request irequest, irequest2;
MPI_Status istatus;
- if (me == 0 ){
+ if (me == 0 ){
fprintf(fp,"# Timestep " BIGINT_FORMAT " \n",ntimestep);
fprintf(fp,"# \n");
fprintf(fp,"# Number of particles %d \n",natoms);
fprintf(fp,"# \n");
fprintf(fp,"# Max number of bonds per atom %d with "
- "coarse bond order cutoff %5.3f \n",maxnum,cutof3);
+ "coarse bond order cutoff %5.3f \n",maxnum,cutof3);
fprintf(fp,"# Particle connection table and bond orders \n");
fprintf(fp,"# id type nb id_1...id_nb mol bo_1...bo_nb abo nlp q \n");
}
@@ -344,38 +344,38 @@ void FixReaxCBonds::RecvBuffer( reax_system *system, double *buf,
if (me == 0) {
for (inode = 0; inode < nprocs; inode ++) {
if (inode == 0) {
- nlocal_tmp = nlocal;
+ nlocal_tmp = nlocal;
} else {
- MPI_Irecv(&buf[0],nbuf,MPI_DOUBLE,inode,0,world,&irequest);
+ MPI_Irecv(&buf[0],nbuf,MPI_DOUBLE,inode,0,world,&irequest);
MPI_Wait(&irequest,&istatus);
- nlocal_tmp = nint(buf[0]);
+ nlocal_tmp = nint(buf[0]);
}
j = 2;
for (i = 0; i < nlocal_tmp; i ++) {
- itag = nint(buf[j-1]);
- itype = nint(buf[j+0]);
- sbotmp = buf[j+1];
- nlptmp = buf[j+2];
- avqtmp = buf[j+3];
- numbonds = nint(buf[j+4]);
+ itag = nint(buf[j-1]);
+ itype = nint(buf[j+0]);
+ sbotmp = buf[j+1];
+ nlptmp = buf[j+2];
+ avqtmp = buf[j+3];
+ numbonds = nint(buf[j+4]);
- fprintf(fp," %d %d %d",itag,itype,numbonds);
+ fprintf(fp," %d %d %d",itag,itype,numbonds);
- for (k = 5; k < 5+numbonds; k++) {
+ for (k = 5; k < 5+numbonds; k++) {
jtag = nint(buf[j+k]);
- fprintf(fp," %d",jtag);
- }
- j += (5+numbonds);
-
- fprintf(fp," %d",nint(buf[j]));
- j ++;
-
- for (k = 0; k < numbonds; k++) {
- abotmp = buf[j+k];
- fprintf(fp,"%14.3f",abotmp);
- }
- j += (1+numbonds);
- fprintf(fp,"%14.3f%14.3f%14.3f\n",sbotmp,nlptmp,avqtmp);
+ fprintf(fp," %d",jtag);
+ }
+ j += (5+numbonds);
+
+ fprintf(fp," %d",nint(buf[j]));
+ j ++;
+
+ for (k = 0; k < numbonds; k++) {
+ abotmp = buf[j+k];
+ fprintf(fp,"%14.3f",abotmp);
+ }
+ j += (1+numbonds);
+ fprintf(fp,"%14.3f%14.3f%14.3f\n",sbotmp,nlptmp,avqtmp);
}
}
} else {
@@ -455,4 +455,3 @@ double FixReaxCBonds::memory_usage()
return bytes;
}
-
diff --git a/src/USER-REAXC/fix_reaxc_bonds.h b/src/USER-REAXC/fix_reaxc_bonds.h
index 94c8806cad17659f9b05f2609348b860f5cc47ff..e58a5766abe44f817ec71e757b8fa0cf6042c64f 100644
--- a/src/USER-REAXC/fix_reaxc_bonds.h
+++ b/src/USER-REAXC/fix_reaxc_bonds.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-REAXC/pair_reax_c.cpp b/src/USER-REAXC/pair_reax_c.cpp
index a9921e4fc7ef75922b3989442a9cb28e2ab5498c..2195132a0ffc0f95356bfd74377d230886a402f3 100644
--- a/src/USER-REAXC/pair_reax_c.cpp
+++ b/src/USER-REAXC/pair_reax_c.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -62,13 +62,13 @@ PairReaxC::PairReaxC(LAMMPS *lmp) : Pair(lmp)
system = (reax_system *)
memory->smalloc(sizeof(reax_system),"reax:system");
- control = (control_params *)
+ control = (control_params *)
memory->smalloc(sizeof(control_params),"reax:control");
data = (simulation_data *)
memory->smalloc(sizeof(simulation_data),"reax:data");
workspace = (storage *)
memory->smalloc(sizeof(storage),"reax:storage");
- lists = (reax_list *)
+ lists = (reax_list *)
memory->smalloc(LIST_N * sizeof(reax_list),"reax:lists");
out_control = (output_controls *)
memory->smalloc(sizeof(output_controls),"reax:out_control");
@@ -128,7 +128,7 @@ PairReaxC::~PairReaxC()
DeAllocate_System( system );
}
//fprintf( stderr, "4\n" );
-
+
memory->destroy( system );
memory->destroy( control );
memory->destroy( data );
@@ -190,7 +190,7 @@ void PairReaxC::settings(int narg, char **arg)
control->hbond_cut = 7.50;
control->thb_cut = 0.001;
control->thb_cutsq = 0.00001;
-
+
out_control->write_steps = 0;
out_control->traj_method = 0;
strcpy( out_control->traj_title, "default_title" );
@@ -246,7 +246,7 @@ void PairReaxC::coeff( int nargs, char **args )
// read ffield file
Read_Force_Field(args[2], &(system->reax_param), control);
-
+
// read args that map atom types to elements in potential file
// map[i] = which element the Ith atom type is, -1 if NULL
@@ -276,7 +276,7 @@ void PairReaxC::coeff( int nargs, char **args )
setflag[i][j] = 1;
count++;
}
-
+
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
@@ -290,7 +290,7 @@ void PairReaxC::init_style( )
int iqeq;
for (iqeq = 0; iqeq < modify->nfix; iqeq++)
if (strcmp(modify->fix[iqeq]->style,"qeq/reax") == 0) break;
- if (iqeq == modify->nfix && qeqflag == 1)
+ if (iqeq == modify->nfix && qeqflag == 1)
error->all(FLERR,"Pair reax/c requires use of fix qeq/reax");
system->n = atom->nlocal; // my atoms
@@ -299,8 +299,8 @@ void PairReaxC::init_style( )
system->wsize = comm->nprocs;
system->big_box.V = 0;
- system->big_box.box_norms[0] = 0;
- system->big_box.box_norms[1] = 0;
+ system->big_box.box_norms[0] = 0;
+ system->big_box.box_norms[1] = 0;
system->big_box.box_norms[2] = 0;
if (atom->tag_enable == 0)
@@ -344,7 +344,7 @@ void PairReaxC::setup( )
if (setup_flag == 0) {
setup_flag = 1;
-
+
int *num_bonds = fix_reax->num_bonds;
int *num_hbonds = fix_reax->num_hbonds;
@@ -359,15 +359,15 @@ void PairReaxC::setup( )
PreAllocate_Space( system, control, workspace, world );
write_reax_atoms();
-
+
int num_nbrs = estimate_reax_lists();
- if(!Make_List(system->total_cap, num_nbrs, TYP_FAR_NEIGHBOR,
- lists+FAR_NBRS, world))
+ if(!Make_List(system->total_cap, num_nbrs, TYP_FAR_NEIGHBOR,
+ lists+FAR_NBRS, world))
error->all(FLERR,"Pair reax/c problem in far neighbor list");
-
+
write_reax_lists();
- Initialize( system, control, data, workspace, &lists, out_control,
- mpi_data, world );
+ Initialize( system, control, data, workspace, &lists, out_control,
+ mpi_data, world );
for( int k = 0; k < system->N; ++k ) {
num_bonds[k] = system->my_atoms[k].num_bonds;
num_hbonds[k] = system->my_atoms[k].num_hbonds;
@@ -383,7 +383,7 @@ void PairReaxC::setup( )
for(int k = oldN; k < system->N; ++k)
Set_End_Index( k, Start_Index( k, lists+BONDS ), lists+BONDS );
-
+
// check if I need to shrink/extend my data-structs
ReAllocate( system, control, data, workspace, &lists, mpi_data );
@@ -417,9 +417,9 @@ void PairReaxC::compute(int eflag, int vflag)
/* if ((eflag_atom || vflag_atom) && firstwarn) {
firstwarn = 0;
- if (comm->me == 0)
+ if (comm->me == 0)
error->warning(FLERR,"Pair reax/c cannot yet compute "
- "per-atom energy or stress");
+ "per-atom energy or stress");
} */
if (vflag_global) control->virial = 1;
@@ -430,15 +430,15 @@ void PairReaxC::compute(int eflag, int vflag)
system->bigN = static_cast<int> (atom->natoms); // all atoms in the system
system->big_box.V = 0;
- system->big_box.box_norms[0] = 0;
- system->big_box.box_norms[1] = 0;
+ system->big_box.box_norms[0] = 0;
+ system->big_box.box_norms[1] = 0;
system->big_box.box_norms[2] = 0;
if( comm->me == 0 ) t_start = MPI_Wtime();
// setup data structures
setup();
-
+
Reset( system, control, data, workspace, &lists, world );
workspace->realloc.num_far = write_reax_lists();
// timing for filling in the reax lists
@@ -481,7 +481,7 @@ void PairReaxC::compute(int eflag, int vflag)
// Store the different parts of the energy
// in a list for output by compute pair command
- pvector[0] = data->my_en.e_bond;
+ pvector[0] = data->my_en.e_bond;
pvector[1] = data->my_en.e_ov + data->my_en.e_un;
pvector[2] = data->my_en.e_lp;
pvector[3] = 0.0;
@@ -512,11 +512,11 @@ void PairReaxC::compute(int eflag, int vflag)
Output_Results( system, control, data, &lists, out_control, mpi_data );
- if(fixbond_flag)
- fixbond( system, control, data, &lists, out_control, mpi_data );
+ if(fixbond_flag)
+ fixbond( system, control, data, &lists, out_control, mpi_data );
- if(fixspecies_flag)
- fixspecies( system, control, data, &lists, out_control, mpi_data );
+ if(fixspecies_flag)
+ fixspecies( system, control, data, &lists, out_control, mpi_data );
}
@@ -526,7 +526,7 @@ void PairReaxC::write_reax_atoms()
{
int *num_bonds = fix_reax->num_bonds;
int *num_hbonds = fix_reax->num_hbonds;
-
+
for( int i = 0; i < system->N; ++i ){
system->my_atoms[i].orig_id = atom->tag[i];
system->my_atoms[i].type = map[atom->type[i]];
@@ -551,8 +551,8 @@ void PairReaxC::get_distance( rvec xj, rvec xi, double *d_sqr, rvec *dvec )
/* ---------------------------------------------------------------------- */
-void PairReaxC::set_far_nbr( far_neighbor_data *fdest,
- int j, double d, rvec dvec )
+void PairReaxC::set_far_nbr( far_neighbor_data *fdest,
+ int j, double d, rvec dvec )
{
fdest->nbr = j;
fdest->d = d;
@@ -599,36 +599,36 @@ int PairReaxC::estimate_reax_lists()
j &= NEIGHMASK;
get_distance( x[j], x[i], &d_sqr, &dvec );
dist[j] = sqrt(d_sqr);
-
+
if( dist[j] <= control->nonb_cut )
- ++num_nbrs;
+ ++num_nbrs;
}
// compute the nbrs among ghost atoms
for( itr_j = 0; itr_j < numneigh[i]; ++itr_j ){
j = jlist[itr_j];
j &= NEIGHMASK;
-
- if( j >= nlocal && !marked[j] &&
- dist[j] <= (control->vlist_cut - control->bond_cut) ){
- marked[j] = 1;
- ++num_marked;
-
- for( itr_g = 0; itr_g < numneigh[i]; ++itr_g ){
- g = jlist[itr_g];
- g &= NEIGHMASK;
-
- if( g >= nlocal && !marked[g] ){
- get_distance( x[g], x[j], &g_d_sqr, &g_dvec );
- //g_dvec[0] = x[g][0] - x[j][0];
- //g_dvec[1] = x[g][1] - x[j][1];
- //g_dvec[2] = x[g][2] - x[j][2];
- //g_d_sqr = SQR(g_dvec[0]) + SQR(g_dvec[1]) + SQR(g_dvec[2]);
-
- if( g_d_sqr <= SQR(control->bond_cut) )
- ++num_nbrs;
- }
- }
+
+ if( j >= nlocal && !marked[j] &&
+ dist[j] <= (control->vlist_cut - control->bond_cut) ){
+ marked[j] = 1;
+ ++num_marked;
+
+ for( itr_g = 0; itr_g < numneigh[i]; ++itr_g ){
+ g = jlist[itr_g];
+ g &= NEIGHMASK;
+
+ if( g >= nlocal && !marked[g] ){
+ get_distance( x[g], x[j], &g_d_sqr, &g_dvec );
+ //g_dvec[0] = x[g][0] - x[j][0];
+ //g_dvec[1] = x[g][1] - x[j][1];
+ //g_dvec[2] = x[g][2] - x[j][2];
+ //g_d_sqr = SQR(g_dvec[0]) + SQR(g_dvec[1]) + SQR(g_dvec[2]);
+
+ if( g_d_sqr <= SQR(control->bond_cut) )
+ ++num_nbrs;
+ }
+ }
}
}
}
@@ -637,15 +637,15 @@ int PairReaxC::estimate_reax_lists()
if( !marked[i] ) {
marked[i] = 1;
++num_marked;
-
+
for( j = i+1; j < system->N; ++j )
- if( !marked[j] ) {
- get_distance( x[j], x[i], &d_sqr, &dvec );
- if( d_sqr <= SQR(control->bond_cut) )
- ++num_nbrs;
- }
+ if( !marked[j] ) {
+ get_distance( x[j], x[i], &d_sqr, &dvec );
+ if( d_sqr <= SQR(control->bond_cut) )
+ ++num_nbrs;
+ }
}
-
+
free( marked );
free( dist );
@@ -676,7 +676,7 @@ int PairReaxC::write_reax_lists()
far_nbrs = lists + FAR_NBRS;
far_list = far_nbrs->select.far_nbr_list;
- num_nbrs = 0;
+ num_nbrs = 0;
marked = (int*) calloc( system->N, sizeof(int) );
dist = (double*) calloc( system->N, sizeof(double) );
@@ -693,8 +693,8 @@ int PairReaxC::write_reax_lists()
dist[j] = sqrt( d_sqr );
if( dist[j] <= control->nonb_cut ){
- set_far_nbr( &far_list[num_nbrs], j, dist[j], dvec );
- ++num_nbrs;
+ set_far_nbr( &far_list[num_nbrs], j, dist[j], dvec );
+ ++num_nbrs;
}
}
Set_End_Index( i, num_nbrs, far_nbrs );
@@ -704,27 +704,27 @@ int PairReaxC::write_reax_lists()
j = jlist[itr_j];
j &= NEIGHMASK;
- if( j >= nlocal && !marked[j] &&
- dist[j] <= (control->vlist_cut - control->bond_cut) ){
- marked[j] = 1;
- Set_Start_Index( j, num_nbrs, far_nbrs );
-
- for( itr_g = 0; itr_g < numneigh[i]; ++itr_g ){
- g = jlist[itr_g];
- g &= NEIGHMASK;
-
- if( g >= nlocal && !marked[g] ){
- get_distance( x[g], x[j], &g_d_sqr, &g_dvec );
-
- if( g_d_sqr <= SQR(control->bond_cut) ){
- g_d = sqrt( g_d_sqr );
-
- set_far_nbr( &far_list[num_nbrs], g, g_d, g_dvec );
- ++num_nbrs;
- }
- }
- }
- Set_End_Index( j, num_nbrs, far_nbrs );
+ if( j >= nlocal && !marked[j] &&
+ dist[j] <= (control->vlist_cut - control->bond_cut) ){
+ marked[j] = 1;
+ Set_Start_Index( j, num_nbrs, far_nbrs );
+
+ for( itr_g = 0; itr_g < numneigh[i]; ++itr_g ){
+ g = jlist[itr_g];
+ g &= NEIGHMASK;
+
+ if( g >= nlocal && !marked[g] ){
+ get_distance( x[g], x[j], &g_d_sqr, &g_dvec );
+
+ if( g_d_sqr <= SQR(control->bond_cut) ){
+ g_d = sqrt( g_d_sqr );
+
+ set_far_nbr( &far_list[num_nbrs], g, g_d, g_dvec );
+ ++num_nbrs;
+ }
+ }
+ }
+ Set_End_Index( j, num_nbrs, far_nbrs );
}
}
}
@@ -733,27 +733,27 @@ int PairReaxC::write_reax_lists()
if( !marked[i] ) {
marked[i] = 1;
Set_Start_Index( i, num_nbrs, far_nbrs );
-
+
for( j = i+1; j < system->N; ++j )
- if( !marked[j] ) {
- get_distance( x[j], x[i], &d_sqr, &dvec );
- if( d_sqr <= SQR(control->bond_cut) ) {
- set_far_nbr( &far_list[num_nbrs], j, sqrt(d_sqr), dvec );
- ++num_nbrs;
- }
- }
+ if( !marked[j] ) {
+ get_distance( x[j], x[i], &d_sqr, &dvec );
+ if( d_sqr <= SQR(control->bond_cut) ) {
+ set_far_nbr( &far_list[num_nbrs], j, sqrt(d_sqr), dvec );
+ ++num_nbrs;
+ }
+ }
Set_End_Index( i, num_nbrs, far_nbrs );
}
-
+
free( marked );
free( dist );
-
+
return num_nbrs;
}
-
+
/* ---------------------------------------------------------------------- */
-
+
void PairReaxC::read_reax_forces()
{
for( int i = 0; i < system->N; ++i ) {
diff --git a/src/USER-REAXC/pair_reax_c.h b/src/USER-REAXC/pair_reax_c.h
index cfd9e35937fe9e9c1ce2e47c64931b77ec1f2dd2..111074ac889e4c7c09361e5eb2ed7736499a27e9 100644
--- a/src/USER-REAXC/pair_reax_c.h
+++ b/src/USER-REAXC/pair_reax_c.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -59,7 +59,7 @@ class PairReaxC : public Pair {
double cutmax;
int *map;
class FixReaxC *fix_reax;
-
+
double *chi,*eta,*gamma;
int qeqflag;
int setup_flag;
@@ -74,7 +74,7 @@ class PairReaxC : public Pair {
void read_reax_forces();
void setup();
};
-
+
}
#endif
diff --git a/src/USER-REAXC/reaxc_allocate.cpp b/src/USER-REAXC/reaxc_allocate.cpp
index f8387a4524be22b6e2fdafb83bf9ec132349082b..039b2a00cb64d9c519f0382dc958daec6b54e750 100644
--- a/src/USER-REAXC/reaxc_allocate.cpp
+++ b/src/USER-REAXC/reaxc_allocate.cpp
@@ -14,12 +14,12 @@
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -41,11 +41,11 @@
/* allocate space for my_atoms
- important: we cannot know the exact number of atoms that will fall into a
- process's box throughout the whole simulation. therefore
+ important: we cannot know the exact number of atoms that will fall into a
+ process's box throughout the whole simulation. therefore
we need to make upper bound estimates for various data structures */
-int PreAllocate_Space( reax_system *system, control_params *control,
- storage *workspace, MPI_Comm comm )
+int PreAllocate_Space( reax_system *system, control_params *control,
+ storage *workspace, MPI_Comm comm )
{
int i;
@@ -53,27 +53,27 @@ int PreAllocate_Space( reax_system *system, control_params *control,
system->local_cap = MAX( (int)(system->n * SAFE_ZONE), MIN_CAP );
system->total_cap = MAX( (int)(system->N * SAFE_ZONE), MIN_CAP );
#if defined(DEBUG)
- fprintf( stderr, "p%d: local_cap=%d total_cap=%d\n",
- system->my_rank, system->local_cap, system->total_cap );
+ fprintf( stderr, "p%d: local_cap=%d total_cap=%d\n",
+ system->my_rank, system->local_cap, system->total_cap );
#endif
- system->my_atoms = (reax_atom*)
+ system->my_atoms = (reax_atom*)
scalloc( system->total_cap, sizeof(reax_atom), "my_atoms", comm );
-
+
/* space for keeping restriction info, if any */
// not yet implemented in the parallel version!!!
// if( control->restrict_bonds ) {
- // workspace->restricted = (int*)
+ // workspace->restricted = (int*)
// scalloc( system->local_cap, sizeof(int), "restricted_atoms", comm );
-
- // workspace->restricted_list = (int**)
+
+ // workspace->restricted_list = (int**)
// scalloc( system->local_cap, sizeof(int*), "restricted_list", comm );
-
+
// for( i = 0; i < system->local_cap; ++i )
- // workspace->restricted_list[i] = (int*)
- // scalloc( MAX_RESTRICT, sizeof(int), "restricted_list[i]", comm );
+ // workspace->restricted_list[i] = (int*)
+ // scalloc( MAX_RESTRICT, sizeof(int), "restricted_list[i]", comm );
// }
-
+
return SUCCESS;
}
@@ -99,16 +99,16 @@ inline void reax_atom_Copy( reax_atom *dest, reax_atom *src )
void Copy_Atom_List( reax_atom *dest, reax_atom *src, int n )
{
int i;
-
+
for( i = 0; i < n; ++i )
memcpy( dest+i, src+i, sizeof(reax_atom) );
}
-int Allocate_System( reax_system *system, int local_cap, int total_cap,
- char *msg )
+int Allocate_System( reax_system *system, int local_cap, int total_cap,
+ char *msg )
{
- system->my_atoms = (reax_atom*)
+ system->my_atoms = (reax_atom*)
realloc( system->my_atoms, total_cap*sizeof(reax_atom) );
return SUCCESS;
@@ -123,7 +123,7 @@ void DeAllocate_System( reax_system *system )
// dealloocate the atom list
sfree( system->my_atoms, "system->my_atoms" );
-
+
// deallocate the ffield parameters storage
ff_params = &(system->reax_param);
ntypes = ff_params->num_atom_types;
@@ -133,7 +133,7 @@ void DeAllocate_System( reax_system *system )
for( i = 0; i < ntypes; ++i ) {
for( j = 0; j < ntypes; ++j ) {
for( k = 0; k < ntypes; ++k ) {
- sfree( ff_params->fbp[i][j][k], "ff:fbp[i,j,k]" );
+ sfree( ff_params->fbp[i][j][k], "ff:fbp[i,j,k]" );
}
sfree( ff_params->fbp[i][j], "ff:fbp[i,j]" );
sfree( ff_params->thbp[i][j], "ff:thbp[i,j]" );
@@ -159,7 +159,7 @@ void DeAllocate_Workspace( control_params *control, storage *workspace )
if( !workspace->allocated )
return;
-
+
workspace->allocated = 0;
/* communication storage */
@@ -279,10 +279,10 @@ void DeAllocate_Workspace( control_params *control, storage *workspace )
}
-int Allocate_Workspace( reax_system *system, control_params *control,
- storage *workspace, int local_cap, int total_cap,
- MPI_Comm comm, char *msg )
-{
+int Allocate_Workspace( reax_system *system, control_params *control,
+ storage *workspace, int local_cap, int total_cap,
+ MPI_Comm comm, char *msg )
+{
int i, total_real, total_rvec, local_int, local_real, local_rvec;
workspace->allocated = 1;
@@ -292,7 +292,7 @@ int Allocate_Workspace( reax_system *system, control_params *control,
local_real = local_cap * sizeof(real);
local_rvec = local_cap * sizeof(rvec);
- /* communication storage */
+ /* communication storage */
for( i = 0; i < MAX_NBRS; ++i ) {
workspace->tmp_dbl[i] = (real*)
scalloc( total_cap, sizeof(real), "tmp_dbl", comm );
@@ -303,7 +303,7 @@ int Allocate_Workspace( reax_system *system, control_params *control,
}
/* bond order related storage */
- workspace->within_bond_box = (int*)
+ workspace->within_bond_box = (int*)
scalloc( total_cap, sizeof(int), "skin", comm );
workspace->total_bond_order = (real*) smalloc( total_real, "total_bo", comm );
workspace->Deltap = (real*) smalloc( total_real, "Deltap", comm );
@@ -311,10 +311,10 @@ int Allocate_Workspace( reax_system *system, control_params *control,
workspace->dDeltap_self = (rvec*) smalloc( total_rvec, "dDeltap_self", comm );
workspace->Delta = (real*) smalloc( total_real, "Delta", comm );
workspace->Delta_lp = (real*) smalloc( total_real, "Delta_lp", comm );
- workspace->Delta_lp_temp = (real*)
+ workspace->Delta_lp_temp = (real*)
smalloc( total_real, "Delta_lp_temp", comm );
workspace->dDelta_lp = (real*) smalloc( total_real, "dDelta_lp", comm );
- workspace->dDelta_lp_temp = (real*)
+ workspace->dDelta_lp_temp = (real*)
smalloc( total_real, "dDelta_lp_temp", comm );
workspace->Delta_e = (real*) smalloc( total_real, "Delta_e", comm );
workspace->Delta_boc = (real*) smalloc( total_real, "Delta_boc", comm );
@@ -323,14 +323,14 @@ int Allocate_Workspace( reax_system *system, control_params *control,
workspace->nlp_temp = (real*) smalloc( total_real, "nlp_temp", comm );
workspace->Clp = (real*) smalloc( total_real, "Clp", comm );
workspace->vlpex = (real*) smalloc( total_real, "vlpex", comm );
- workspace->bond_mark = (int*)
+ workspace->bond_mark = (int*)
scalloc( total_cap, sizeof(int), "bond_mark", comm );
- workspace->done_after = (int*)
+ workspace->done_after = (int*)
scalloc( total_cap, sizeof(int), "done_after", comm );
// fprintf( stderr, "p%d: bond order storage\n", system->my_rank );
/* QEq storage */
- workspace->Hdia_inv = (real*)
+ workspace->Hdia_inv = (real*)
scalloc( total_cap, sizeof(real), "Hdia_inv", comm );
workspace->b_s = (real*) scalloc( total_cap, sizeof(real), "b_s", comm );
workspace->b_t = (real*) scalloc( total_cap, sizeof(real), "b_t", comm );
@@ -338,11 +338,11 @@ int Allocate_Workspace( reax_system *system, control_params *control,
workspace->b_prm = (real*) scalloc( total_cap, sizeof(real), "b_prm", comm );
workspace->s = (real*) scalloc( total_cap, sizeof(real), "s", comm );
workspace->t = (real*) scalloc( total_cap, sizeof(real), "t", comm );
- workspace->droptol = (real*)
+ workspace->droptol = (real*)
scalloc( total_cap, sizeof(real), "droptol", comm );
workspace->b = (rvec2*) scalloc( total_cap, sizeof(rvec2), "b", comm );
workspace->x = (rvec2*) scalloc( total_cap, sizeof(rvec2), "x", comm );
-
+
/* GMRES storage */
workspace->y = (real*) scalloc( RESTART+1, sizeof(real), "y", comm );
workspace->z = (real*) scalloc( RESTART+1, sizeof(real), "z", comm );
@@ -351,7 +351,7 @@ int Allocate_Workspace( reax_system *system, control_params *control,
workspace->hs = (real*) scalloc( RESTART+1, sizeof(real), "hs", comm );
workspace->hc = (real*) scalloc( RESTART+1, sizeof(real), "hc", comm );
workspace->v = (real**) scalloc( RESTART+1, sizeof(real*), "v", comm );
-
+
for( i = 0; i < RESTART+1; ++i ) {
workspace->h[i] = (real*) scalloc( RESTART+1, sizeof(real), "h[i]", comm );
workspace->v[i] = (real*) scalloc( total_cap, sizeof(real), "v[i]", comm );
@@ -374,20 +374,20 @@ int Allocate_Workspace( reax_system *system, control_params *control,
// not yet implemented in the parallel version!!!
// if( control->molecular_analysis || control->diffusion_coef ) {
// workspace->mark = (int*) scalloc( local_cap, sizeof(int), "mark", comm );
- // workspace->old_mark = (int*)
+ // workspace->old_mark = (int*)
// scalloc( local_cap, sizeof(int), "old_mark", comm );
// }
- // else
+ // else
// workspace->mark = workspace->old_mark = NULL;
// if( control->diffusion_coef )
- // workspace->x_old = (rvec*)
+ // workspace->x_old = (rvec*)
// scalloc( local_cap, sizeof(rvec), "x_old", comm );
// else workspace->x_old = NULL;
-
+
// /* force related storage */
workspace->f = (rvec*) scalloc( total_cap, sizeof(rvec), "f", comm );
- workspace->CdDelta = (real*)
+ workspace->CdDelta = (real*)
scalloc( total_cap, sizeof(real), "CdDelta", comm );
#ifdef TEST_FORCES
@@ -408,13 +408,13 @@ int Allocate_Workspace( reax_system *system, control_params *control,
workspace->f_tot =(rvec*) smalloc( total_rvec, "f_tot", comm );
if( system->my_rank == MASTER_NODE ) {
- workspace->rcounts = (int*)
+ workspace->rcounts = (int*)
smalloc( system->wsize*sizeof(int), "rcount", comm );
- workspace->displs = (int*)
+ workspace->displs = (int*)
smalloc( system->wsize*sizeof(int), "displs", comm );
- workspace->id_all = (int*)
+ workspace->id_all = (int*)
smalloc( system->bigN*sizeof(int), "id_all", comm );
- workspace->f_all = (rvec*)
+ workspace->f_all = (rvec*)
smalloc( system->bigN*sizeof(rvec), "f_all", comm );
}
else{
@@ -430,7 +430,7 @@ int Allocate_Workspace( reax_system *system, control_params *control,
void Reallocate_Neighbor_List( reax_list *far_nbrs, int n, int num_intrs,
- MPI_Comm comm )
+ MPI_Comm comm )
{
Delete_List( far_nbrs, comm );
if(!Make_List( n, num_intrs, TYP_FAR_NEIGHBOR, far_nbrs, comm )){
@@ -444,14 +444,14 @@ int Allocate_Matrix( sparse_matrix **pH, int cap, int m, MPI_Comm comm )
{
sparse_matrix *H;
- *pH = (sparse_matrix*)
+ *pH = (sparse_matrix*)
smalloc( sizeof(sparse_matrix), "sparse_matrix", comm );
H = *pH;
H->cap = cap;
H->m = m;
- H->start = (int*) smalloc( sizeof(int) * cap, "matrix_start", comm );
+ H->start = (int*) smalloc( sizeof(int) * cap, "matrix_start", comm );
H->end = (int*) smalloc( sizeof(int) * cap, "matrix_end", comm );
- H->entries = (sparse_matrix_entry*)
+ H->entries = (sparse_matrix_entry*)
smalloc( sizeof(sparse_matrix_entry)*m, "matrix_entries", comm );
return SUCCESS;
@@ -467,8 +467,8 @@ void Deallocate_Matrix( sparse_matrix *H )
}
-int Reallocate_Matrix( sparse_matrix **H, int n, int m, char *name,
- MPI_Comm comm )
+int Reallocate_Matrix( sparse_matrix **H, int n, int m, char *name,
+ MPI_Comm comm )
{
Deallocate_Matrix( *H );
if( !Allocate_Matrix( H, n, m, comm ) ) {
@@ -478,15 +478,15 @@ int Reallocate_Matrix( sparse_matrix **H, int n, int m, char *name,
#if defined(DEBUG_FOCUS)
fprintf( stderr, "reallocating %s matrix, n = %d, m = %d\n", name, n, m );
- fprintf( stderr, "memory allocated: %s = %dMB\n",
- name, (int)(m * sizeof(sparse_matrix_entry) / (1024*1024)) );
+ fprintf( stderr, "memory allocated: %s = %dMB\n",
+ name, (int)(m * sizeof(sparse_matrix_entry) / (1024*1024)) );
#endif
return SUCCESS;
}
-int Reallocate_HBonds_List( reax_system *system, reax_list *hbonds,
- MPI_Comm comm )
+int Reallocate_HBonds_List( reax_system *system, reax_list *hbonds,
+ MPI_Comm comm )
{
int i, id, total_hbonds;
@@ -497,9 +497,9 @@ int Reallocate_HBonds_List( reax_system *system, reax_list *hbonds,
// system->my_atoms[i].num_hbonds = MAX(Num_Entries(id,hbonds)*SAFER_ZONE,
// MIN_HBONDS);
total_hbonds += system->my_atoms[i].num_hbonds;
- }
+ }
total_hbonds = (int)(MAX( total_hbonds*SAFER_ZONE, MIN_CAP*MIN_HBONDS ));
-
+
Delete_List( hbonds, comm );
if( !Make_List( system->Hcap, total_hbonds, TYP_HBOND, hbonds, comm ) ) {
fprintf( stderr, "not enough space for hbonds list. terminating!\n" );
@@ -511,7 +511,7 @@ int Reallocate_HBonds_List( reax_system *system, reax_list *hbonds,
int Reallocate_Bonds_List( reax_system *system, reax_list *bonds,
- int *total_bonds, int *est_3body, MPI_Comm comm )
+ int *total_bonds, int *est_3body, MPI_Comm comm )
{
int i;
@@ -524,7 +524,7 @@ int Reallocate_Bonds_List( reax_system *system, reax_list *bonds,
*total_bonds += system->my_atoms[i].num_bonds;
}
*total_bonds = (int)(MAX( *total_bonds * SAFE_ZONE, MIN_CAP*MIN_BONDS ));
-
+
Delete_List( bonds, comm );
if(!Make_List(system->total_cap, *total_bonds, TYP_BOND, bonds, comm)) {
fprintf( stderr, "not enough space for bonds list. terminating!\n" );
@@ -544,7 +544,7 @@ int Estimate_GCell_Population( reax_system* system, MPI_Comm comm )
grid_cell *gc;
simulation_box *big_box, *my_ext_box;
reax_atom *atoms;
-
+
big_box = &(system->big_box);
my_ext_box = &(system->my_ext_box);
g = &(system->my_grid);
@@ -557,43 +557,43 @@ int Estimate_GCell_Population( reax_system* system, MPI_Comm comm )
// atoms[l].x[d] += big_box->box_norms[d];
//else if( atoms[l].x[d] >= big_box->max[d] )
// atoms[l].x[d] -= big_box->box_norms[d];
-
+
c[d] = (int)((atoms[l].x[d]-my_ext_box->min[d])*g->inv_len[d]);
-
+
if( c[d] >= g->native_end[d] )
- c[d] = g->native_end[d] - 1;
+ c[d] = g->native_end[d] - 1;
else if( c[d] < g->native_str[d] )
- c[d] = g->native_str[d];
+ c[d] = g->native_str[d];
}
#if defined(DEBUG)
- fprintf( stderr, "p%d bin_my_atoms: l:%d - atom%d @ %.5f %.5f %.5f" \
- "--> cell: %d %d %d\n",
- system->my_rank, l, atoms[l].orig_id,
- atoms[l].x[0], atoms[l].x[1], atoms[l].x[2],
- c[0], c[1], c[2] );
+ fprintf( stderr, "p%d bin_my_atoms: l:%d - atom%d @ %.5f %.5f %.5f" \
+ "--> cell: %d %d %d\n",
+ system->my_rank, l, atoms[l].orig_id,
+ atoms[l].x[0], atoms[l].x[1], atoms[l].x[2],
+ c[0], c[1], c[2] );
#endif
gc = &( g->cells[c[0]][c[1]][c[2]] );
gc->top++;
}
-
+
max_atoms = 0;
for( i = 0; i < g->ncells[0]; i++ )
for( j = 0; j < g->ncells[1]; j++ )
for( k = 0; k < g->ncells[2]; k++ ) {
- gc = &(g->cells[i][j][k]);
- if( max_atoms < gc->top )
- max_atoms = gc->top;
+ gc = &(g->cells[i][j][k]);
+ if( max_atoms < gc->top )
+ max_atoms = gc->top;
#if defined(DEBUG)
- fprintf( stderr, "p%d gc[%d,%d,%d]->top=%d\n",
- system->my_rank, i, j, k, gc->top );
+ fprintf( stderr, "p%d gc[%d,%d,%d]->top=%d\n",
+ system->my_rank, i, j, k, gc->top );
#endif
}
- my_max = (int)(MAX(max_atoms*SAFE_ZONE, MIN_GCELL_POPL));
+ my_max = (int)(MAX(max_atoms*SAFE_ZONE, MIN_GCELL_POPL));
MPI_Allreduce( &my_max, &all_max, 1, MPI_INT, MPI_MAX, comm );
#if defined(DEBUG)
- fprintf( stderr, "p%d max_atoms=%d, my_max=%d, all_max=%d\n",
- system->my_rank, max_atoms, my_max, all_max );
+ fprintf( stderr, "p%d max_atoms=%d, my_max=%d, all_max=%d\n",
+ system->my_rank, max_atoms, my_max, all_max );
#endif
return all_max;
@@ -605,7 +605,7 @@ void Allocate_Grid( reax_system *system, MPI_Comm comm )
int i, j, k, l;
grid *g;
grid_cell *gc;
-
+
g = &( system->my_grid );
/* allocate gcell reordering space */
@@ -613,29 +613,29 @@ void Allocate_Grid( reax_system *system, MPI_Comm comm )
/* allocate the gcells for the new grid */
g->max_nbrs = (2*g->vlist_span[0]+1)*(2*g->vlist_span[1]+1)*
- (2*g->vlist_span[2]+1)+3;
+ (2*g->vlist_span[2]+1)+3;
- g->cells = (grid_cell***)
+ g->cells = (grid_cell***)
scalloc( g->ncells[0], sizeof(grid_cell**), "gcells", comm );
for( i = 0; i < g->ncells[0]; i++ ) {
- g->cells[i] = (grid_cell**)
+ g->cells[i] = (grid_cell**)
scalloc( g->ncells[1], sizeof(grid_cell*),"gcells[i]", comm );
-
- for( j = 0; j < g->ncells[1]; ++j ) {
- g->cells[i][j] = (grid_cell*)
- scalloc( g->ncells[2], sizeof(grid_cell), "gcells[i][j]", comm );
+
+ for( j = 0; j < g->ncells[1]; ++j ) {
+ g->cells[i][j] = (grid_cell*)
+ scalloc( g->ncells[2], sizeof(grid_cell), "gcells[i][j]", comm );
for( k = 0; k < g->ncells[2]; k++ ) {
- gc = &(g->cells[i][j][k]);
- gc->top = gc->mark = gc->str = gc->end = 0;
- gc->nbrs = (grid_cell**)
- scalloc( g->max_nbrs, sizeof(grid_cell*), "g:nbrs", comm );
- gc->nbrs_x = (ivec*)
- scalloc( g->max_nbrs, sizeof(ivec), "g:nbrs_x", comm );
- gc->nbrs_cp = (rvec*)
- scalloc( g->max_nbrs, sizeof(rvec), "g:nbrs_cp", comm );
- for( l = 0; l < g->max_nbrs; ++l )
- gc->nbrs[l] = NULL;
+ gc = &(g->cells[i][j][k]);
+ gc->top = gc->mark = gc->str = gc->end = 0;
+ gc->nbrs = (grid_cell**)
+ scalloc( g->max_nbrs, sizeof(grid_cell*), "g:nbrs", comm );
+ gc->nbrs_x = (ivec*)
+ scalloc( g->max_nbrs, sizeof(ivec), "g:nbrs_x", comm );
+ gc->nbrs_cp = (rvec*)
+ scalloc( g->max_nbrs, sizeof(rvec), "g:nbrs_cp", comm );
+ for( l = 0; l < g->max_nbrs; ++l )
+ gc->nbrs[l] = NULL;
}
}
}
@@ -644,21 +644,21 @@ void Allocate_Grid( reax_system *system, MPI_Comm comm )
g->max_atoms = Estimate_GCell_Population( system, comm );
/* space for storing atom id's is required only for native cells */
for( i = g->native_str[0]; i < g->native_end[0]; ++i )
- for( j = g->native_str[1]; j < g->native_end[1]; ++j )
+ for( j = g->native_str[1]; j < g->native_end[1]; ++j )
for( k = g->native_str[2]; k < g->native_end[2]; ++k )
- g->cells[i][j][k].atoms = (int*) scalloc( g->max_atoms, sizeof(int),
- "g:atoms", comm );
+ g->cells[i][j][k].atoms = (int*) scalloc( g->max_atoms, sizeof(int),
+ "g:atoms", comm );
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d-allocated %dx%dx%d grid: nbrs=%d atoms=%d space=%dMB\n",
- system->my_rank, g->ncells[0], g->ncells[1], g->ncells[2],
- g->max_nbrs, g->max_atoms,
- (int)
- ((g->total*sizeof(grid_cell)+g->total*g->max_nbrs*sizeof(int*) +
- g->total*g->max_nbrs*sizeof(rvec) +
- (g->native_end[0]-g->native_str[0])*
- (g->native_end[1]-g->native_str[1])*
- (g->native_end[2]-g->native_str[2])*g->max_atoms*sizeof(int))/
- (1024*1024)) );
+ system->my_rank, g->ncells[0], g->ncells[1], g->ncells[2],
+ g->max_nbrs, g->max_atoms,
+ (int)
+ ((g->total*sizeof(grid_cell)+g->total*g->max_nbrs*sizeof(int*) +
+ g->total*g->max_nbrs*sizeof(rvec) +
+ (g->native_end[0]-g->native_str[0])*
+ (g->native_end[1]-g->native_str[1])*
+ (g->native_end[2]-g->native_str[2])*g->max_atoms*sizeof(int))/
+ (1024*1024)) );
#endif
}
@@ -674,12 +674,12 @@ void Deallocate_Grid( grid *g )
for( i = 0; i < g->ncells[0]; i++ ) {
for( j = 0; j < g->ncells[1]; j++ ) {
for( k = 0; k < g->ncells[2]; k++ ) {
- gc = &(g->cells[i][j][k]);
- sfree( gc->nbrs, "g:nbrs" );
- sfree( gc->nbrs_x, "g:nbrs_x" );
- sfree( gc->nbrs_cp, "g:nbrs_cp" );
- if(gc->atoms != NULL )
- sfree( gc->atoms, "g:atoms" );
+ gc = &(g->cells[i][j][k]);
+ sfree( gc->nbrs, "g:nbrs" );
+ sfree( gc->nbrs_x, "g:nbrs_x" );
+ sfree( gc->nbrs_cp, "g:nbrs_cp" );
+ if(gc->atoms != NULL )
+ sfree( gc->atoms, "g:atoms" );
}
sfree( g->cells[i][j], "g:cells[i][j]" );
}
@@ -694,12 +694,12 @@ void Deallocate_Grid( grid *g )
1- transfer an atom who has moved into other proc's domain (mpi_atom)
2- exchange boundary atoms (boundary_atom)
3- update position info for boundary atoms (mpi_rvec)
-
+
the largest space by far is required for the 2nd comm operation above.
- buffers are void*, type cast to the correct pointer type to access
+ buffers are void*, type cast to the correct pointer type to access
the allocated buffers */
-int Allocate_MPI_Buffers( mpi_datatypes *mpi_data, int est_recv,
- neighbor_proc *my_nbrs, char *msg )
+int Allocate_MPI_Buffers( mpi_datatypes *mpi_data, int est_recv,
+ neighbor_proc *my_nbrs, char *msg )
{
int i;
mpi_out_data *mpi_buf;
@@ -708,22 +708,22 @@ int Allocate_MPI_Buffers( mpi_datatypes *mpi_data, int est_recv,
comm = mpi_data->world;
/* in buffers */
- mpi_data->in1_buffer = (void*)
+ mpi_data->in1_buffer = (void*)
scalloc( est_recv, sizeof(boundary_atom), "in1_buffer", comm );
- mpi_data->in2_buffer = (void*)
+ mpi_data->in2_buffer = (void*)
scalloc( est_recv, sizeof(boundary_atom), "in2_buffer", comm );
-
+
/* out buffers */
for( i = 0; i < MAX_NBRS; ++i ) {
mpi_buf = &( mpi_data->out_buffers[i] );
/* allocate storage for the neighbor processor i */
- mpi_buf->index = (int*)
+ mpi_buf->index = (int*)
scalloc( my_nbrs[i].est_send, sizeof(int), "mpibuf:index", comm );
- mpi_buf->out_atoms = (void*)
- scalloc( my_nbrs[i].est_send, sizeof(boundary_atom), "mpibuf:out_atoms",
- comm );
+ mpi_buf->out_atoms = (void*)
+ scalloc( my_nbrs[i].est_send, sizeof(boundary_atom), "mpibuf:out_atoms",
+ comm );
}
-
+
return SUCCESS;
}
@@ -744,9 +744,9 @@ void Deallocate_MPI_Buffers( mpi_datatypes *mpi_data )
}
-void ReAllocate( reax_system *system, control_params *control,
- simulation_data *data, storage *workspace, reax_list **lists,
- mpi_datatypes *mpi_data )
+void ReAllocate( reax_system *system, control_params *control,
+ simulation_data *data, storage *workspace, reax_list **lists,
+ mpi_datatypes *mpi_data )
{
int i, j, k, p;
int num_bonds, est_3body, nflag, Nflag, Hflag, mpi_flag, ret, total_send;
@@ -766,22 +766,22 @@ void ReAllocate( reax_system *system, control_params *control,
#if defined(DEBUG)
fprintf( stderr, "p%d@reallocate: n: %d, N: %d, numH: %d\n",
- system->my_rank, system->n, system->N, system->numH );
+ system->my_rank, system->n, system->N, system->numH );
fprintf( stderr, "p%d@reallocate: local_cap: %d, total_cap: %d, Hcap: %d\n",
- system->my_rank, system->local_cap, system->total_cap,
- system->Hcap);
- fprintf( stderr, "p%d: realloc.num_far: %d\n",
- system->my_rank, realloc->num_far );
- fprintf( stderr, "p%d: realloc.H: %d, realloc.Htop: %d\n",
- system->my_rank, realloc->H, realloc->Htop );
- fprintf( stderr, "p%d: realloc.Hbonds: %d, realloc.num_hbonds: %d\n",
- system->my_rank, realloc->hbonds, realloc->num_hbonds );
- fprintf( stderr, "p%d: realloc.bonds: %d, num_bonds: %d\n",
- system->my_rank, realloc->bonds, realloc->num_bonds );
- fprintf( stderr, "p%d: realloc.num_3body: %d\n",
- system->my_rank, realloc->num_3body );
+ system->my_rank, system->local_cap, system->total_cap,
+ system->Hcap);
+ fprintf( stderr, "p%d: realloc.num_far: %d\n",
+ system->my_rank, realloc->num_far );
+ fprintf( stderr, "p%d: realloc.H: %d, realloc.Htop: %d\n",
+ system->my_rank, realloc->H, realloc->Htop );
+ fprintf( stderr, "p%d: realloc.Hbonds: %d, realloc.num_hbonds: %d\n",
+ system->my_rank, realloc->hbonds, realloc->num_hbonds );
+ fprintf( stderr, "p%d: realloc.bonds: %d, num_bonds: %d\n",
+ system->my_rank, realloc->bonds, realloc->num_bonds );
+ fprintf( stderr, "p%d: realloc.num_3body: %d\n",
+ system->my_rank, realloc->num_3body );
#endif
-
+
// IMPORTANT: LOOSE ZONES CHECKS ARE DISABLED FOR NOW BY &&'ing with 0!!!
nflag = 0;
if( system->n >= DANGER_ZONE * system->local_cap ||
@@ -801,25 +801,25 @@ void ReAllocate( reax_system *system, control_params *control,
/* system */
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d: reallocating system and workspace -"\
- "n=%d N=%d local_cap=%d total_cap=%d\n",
- system->my_rank, system->n, system->N,
- system->local_cap, system->total_cap );
+ "n=%d N=%d local_cap=%d total_cap=%d\n",
+ system->my_rank, system->n, system->N,
+ system->local_cap, system->total_cap );
#endif
ret = Allocate_System( system, system->local_cap, system->total_cap, msg );
if( ret != SUCCESS ) {
fprintf( stderr, "not enough space for atom_list: total_cap=%d",
- system->total_cap );
+ system->total_cap );
fprintf( stderr, "terminating...\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
-
+
/* workspace */
DeAllocate_Workspace( control, workspace );
- ret = Allocate_Workspace( system, control, workspace, system->local_cap,
- system->total_cap, comm, msg );
+ ret = Allocate_Workspace( system, control, workspace, system->local_cap,
+ system->total_cap, comm, msg );
if( ret != SUCCESS ) {
fprintf( stderr, "no space for workspace: local_cap=%d total_cap=%d",
- system->local_cap, system->total_cap );
+ system->local_cap, system->total_cap );
fprintf( stderr, "terminating...\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
@@ -833,19 +833,19 @@ void ReAllocate( reax_system *system, control_params *control,
if( Nflag || realloc->num_far >= far_nbrs->num_intrs * DANGER_ZONE ) {
if( realloc->num_far > far_nbrs->num_intrs ) {
- fprintf( stderr, "step%d-ran out of space on far_nbrs: top=%d, max=%d",
- data->step, realloc->num_far, far_nbrs->num_intrs );
- MPI_Abort( comm, INSUFFICIENT_MEMORY );
+ fprintf( stderr, "step%d-ran out of space on far_nbrs: top=%d, max=%d",
+ data->step, realloc->num_far, far_nbrs->num_intrs );
+ MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
- newsize = static_cast<int>
- (MAX( realloc->num_far*SAFE_ZONE, MIN_CAP*MIN_NBRS ));
+ newsize = static_cast<int>
+ (MAX( realloc->num_far*SAFE_ZONE, MIN_CAP*MIN_NBRS ));
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "p%d: reallocating far_nbrs: num_fars=%d, space=%dMB\n",
- system->my_rank, (int)(realloc->num_far*SAFE_ZONE),
- (newsize*sizeof(far_neighbor_data)/(1024*1024)) );
+ fprintf( stderr, "p%d: reallocating far_nbrs: num_fars=%d, space=%dMB\n",
+ system->my_rank, (int)(realloc->num_far*SAFE_ZONE),
+ (newsize*sizeof(far_neighbor_data)/(1024*1024)) );
#endif
-
+
Reallocate_Neighbor_List( far_nbrs, system->total_cap, newsize, comm );
realloc->num_far = 0;
}
@@ -856,22 +856,22 @@ void ReAllocate( reax_system *system, control_params *control,
H = workspace->H;
if( nflag || realloc->Htop >= H->m * DANGER_ZONE ) {
if( realloc->Htop > H->m ) {
- fprintf( stderr,
- "step%d - ran out of space on H matrix: Htop=%d, max = %d",
- data->step, realloc->Htop, H->m );
+ fprintf( stderr,
+ "step%d - ran out of space on H matrix: Htop=%d, max = %d",
+ data->step, realloc->Htop, H->m );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "p%d: reallocating H matrix: Htop=%d, space=%dMB\n",
- system->my_rank, (int)(realloc->Htop*SAFE_ZONE),
- (int)(realloc->Htop * SAFE_ZONE * sizeof(sparse_matrix_entry) /
- (1024*1024)) );
+ fprintf( stderr, "p%d: reallocating H matrix: Htop=%d, space=%dMB\n",
+ system->my_rank, (int)(realloc->Htop*SAFE_ZONE),
+ (int)(realloc->Htop * SAFE_ZONE * sizeof(sparse_matrix_entry) /
+ (1024*1024)) );
#endif
- newsize = static_cast<int>
- (MAX( realloc->Htop*SAFE_ZONE, MIN_CAP*MIN_NBRS ));
- Reallocate_Matrix( &(workspace->H), system->local_cap,
- newsize, "H", comm );
+ newsize = static_cast<int>
+ (MAX( realloc->Htop*SAFE_ZONE, MIN_CAP*MIN_NBRS ));
+ Reallocate_Matrix( &(workspace->H), system->local_cap,
+ newsize, "H", comm );
//Deallocate_Matrix( workspace->L );
//Deallocate_Matrix( workspace->U );
workspace->L = NULL;
@@ -881,10 +881,10 @@ void ReAllocate( reax_system *system, control_params *control,
#endif /*PURE_REAX*/
/* hydrogen bonds list */
- if( control->hbond_cut > 0 ) {
+ if( control->hbond_cut > 0 ) {
Hflag = 0;
- if( system->numH >= DANGER_ZONE * system->Hcap ||
- (0 && system->numH <= LOOSE_ZONE * system->Hcap) ) {
+ if( system->numH >= DANGER_ZONE * system->Hcap ||
+ (0 && system->numH <= LOOSE_ZONE * system->Hcap) ) {
Hflag = 1;
system->Hcap = int(MAX( system->numH * SAFER_ZONE, MIN_CAP ));
}
@@ -894,7 +894,7 @@ void ReAllocate( reax_system *system, control_params *control,
realloc->hbonds = 0;
#if defined(DEBUG_FOCUS)
fprintf(stderr, "p%d: reallocating hbonds: total_hbonds=%d space=%dMB\n",
- system->my_rank, ret, (int)(ret*sizeof(hbond_data)/(1024*1024)));
+ system->my_rank, ret, (int)(ret*sizeof(hbond_data)/(1024*1024)));
#endif
}
}
@@ -902,14 +902,14 @@ void ReAllocate( reax_system *system, control_params *control,
/* bonds list */
num_bonds = est_3body = -1;
if( Nflag || realloc->bonds ){
- Reallocate_Bonds_List( system, (*lists)+BONDS, &num_bonds,
- &est_3body, comm );
+ Reallocate_Bonds_List( system, (*lists)+BONDS, &num_bonds,
+ &est_3body, comm );
realloc->bonds = 0;
realloc->num_3body = MAX( realloc->num_3body, est_3body );
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "p%d: reallocating bonds: total_bonds=%d, space=%dMB\n",
- system->my_rank, num_bonds,
- (int)(num_bonds*sizeof(bond_data)/(1024*1024)) );
+ fprintf( stderr, "p%d: reallocating bonds: total_bonds=%d, space=%dMB\n",
+ system->my_rank, num_bonds,
+ (int)(num_bonds*sizeof(bond_data)/(1024*1024)) );
#endif
}
@@ -917,19 +917,19 @@ void ReAllocate( reax_system *system, control_params *control,
if( realloc->num_3body > 0 ) {
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d: reallocating 3body list: num_3body=%d, space=%dMB\n",
- system->my_rank, realloc->num_3body,
- (int)(realloc->num_3body * sizeof(three_body_interaction_data) /
- (1024*1024)) );
+ system->my_rank, realloc->num_3body,
+ (int)(realloc->num_3body * sizeof(three_body_interaction_data) /
+ (1024*1024)) );
#endif
Delete_List( (*lists)+THREE_BODIES, comm );
-
+
if( num_bonds == -1 )
num_bonds = ((*lists)+BONDS)->num_intrs;
realloc->num_3body = (int)(MAX(realloc->num_3body*SAFE_ZONE, MIN_3BODIES));
- if( !Make_List( num_bonds, realloc->num_3body, TYP_THREE_BODY,
- (*lists)+THREE_BODIES, comm ) ) {
+ if( !Make_List( num_bonds, realloc->num_3body, TYP_THREE_BODY,
+ (*lists)+THREE_BODIES, comm ) ) {
fprintf( stderr, "Problem in initializing angles list. Terminating!\n" );
MPI_Abort( comm, CANNOT_INITIALIZE );
}
@@ -944,22 +944,22 @@ void ReAllocate( reax_system *system, control_params *control,
#endif
for( i = g->native_str[0]; i < g->native_end[0]; i++ )
for( j = g->native_str[1]; j < g->native_end[1]; j++ )
- for( k = g->native_str[2]; k < g->native_end[2]; k++ ) {
- // reallocate g->atoms
- sfree( g->cells[i][j][k].atoms, "g:atoms" );
- g->cells[i][j][k].atoms = (int*)
- scalloc( realloc->gcell_atoms, sizeof(int), "g:atoms", comm);
- }
+ for( k = g->native_str[2]; k < g->native_end[2]; k++ ) {
+ // reallocate g->atoms
+ sfree( g->cells[i][j][k].atoms, "g:atoms" );
+ g->cells[i][j][k].atoms = (int*)
+ scalloc( realloc->gcell_atoms, sizeof(int), "g:atoms", comm);
+ }
realloc->gcell_atoms = -1;
}
/* mpi buffers */
- // we have to be at a renbring step -
+ // we have to be at a renbring step -
// to ensure correct values at mpi_buffers for update_boundary_positions
if( !renbr )
mpi_flag = 0;
// check whether in_buffer capacity is enough
- else if( system->max_recved >= system->est_recv * 0.90 )
+ else if( system->max_recved >= system->est_recv * 0.90 )
mpi_flag = 1;
else {
// otherwise check individual outgoing buffers
@@ -968,8 +968,8 @@ void ReAllocate( reax_system *system, control_params *control,
nbr_pr = &( system->my_nbrs[p] );
nbr_data = &( mpi_data->out_buffers[p] );
if( nbr_data->cnt >= nbr_pr->est_send * 0.90 ) {
- mpi_flag = 1;
- break;
+ mpi_flag = 1;
+ break;
}
}
}
@@ -977,14 +977,14 @@ void ReAllocate( reax_system *system, control_params *control,
if( mpi_flag ) {
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d: reallocating mpi_buf: old_recv=%d\n",
- system->my_rank, system->est_recv );
- for( p = 0; p < MAX_NBRS; ++p )
- fprintf( stderr, "p%d: nbr%d old_send=%d\n",
- system->my_rank, p, system->my_nbrs[p].est_send );
+ system->my_rank, system->est_recv );
+ for( p = 0; p < MAX_NBRS; ++p )
+ fprintf( stderr, "p%d: nbr%d old_send=%d\n",
+ system->my_rank, p, system->my_nbrs[p].est_send );
#endif
/* update mpi buffer estimates based on last comm */
system->est_recv = MAX( system->max_recved*SAFER_ZONE, MIN_SEND );
- system->est_trans =
+ system->est_trans =
(system->est_recv * sizeof(boundary_atom)) / sizeof(mpi_atom);
total_send = 0;
for( p = 0; p < MAX_NBRS; ++p ) {
@@ -995,18 +995,18 @@ void ReAllocate( reax_system *system, control_params *control,
}
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d: reallocating mpi_buf: recv=%d send=%d total=%dMB\n",
- system->my_rank, system->est_recv, total_send,
- (int)((system->est_recv+total_send)*sizeof(boundary_atom)/
- (1024*1024)));
- for( p = 0; p < MAX_NBRS; ++p )
- fprintf( stderr, "p%d: nbr%d new_send=%d\n",
- system->my_rank, p, system->my_nbrs[p].est_send );
+ system->my_rank, system->est_recv, total_send,
+ (int)((system->est_recv+total_send)*sizeof(boundary_atom)/
+ (1024*1024)));
+ for( p = 0; p < MAX_NBRS; ++p )
+ fprintf( stderr, "p%d: nbr%d new_send=%d\n",
+ system->my_rank, p, system->my_nbrs[p].est_send );
#endif
/* reallocate mpi buffers */
Deallocate_MPI_Buffers( mpi_data );
- ret = Allocate_MPI_Buffers( mpi_data, system->est_recv,
- system->my_nbrs, msg );
+ ret = Allocate_MPI_Buffers( mpi_data, system->est_recv,
+ system->my_nbrs, msg );
if( ret != SUCCESS ) {
fprintf( stderr, "%s", msg );
fprintf( stderr, "terminating...\n" );
@@ -1015,9 +1015,9 @@ void ReAllocate( reax_system *system, control_params *control,
}
#endif /*PURE_REAX*/
-#if defined(DEBUG_FOCUS)
- fprintf( stderr, "p%d @ step%d: reallocate done\n",
- system->my_rank, data->step );
+#if defined(DEBUG_FOCUS)
+ fprintf( stderr, "p%d @ step%d: reallocate done\n",
+ system->my_rank, data->step );
MPI_Barrier( comm );
#endif
}
diff --git a/src/USER-REAXC/reaxc_allocate.h b/src/USER-REAXC/reaxc_allocate.h
index e3d9049c5723b0c7373d5d9e0e0898d42ac6c9fa..0ad5f1a7104c09f216b899253e66a7b4b7313cd4 100644
--- a/src/USER-REAXC/reaxc_allocate.h
+++ b/src/USER-REAXC/reaxc_allocate.h
@@ -14,12 +14,12 @@
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -34,8 +34,8 @@ void reax_atom_Copy( reax_atom*, reax_atom* );
int Allocate_System( reax_system*, int, int, char* );
void DeAllocate_System( reax_system* );
-int Allocate_Workspace( reax_system*, control_params*, storage*,
- int, int, MPI_Comm, char* );
+int Allocate_Workspace( reax_system*, control_params*, storage*,
+ int, int, MPI_Comm, char* );
void DeAllocate_Workspace( control_params*, storage* );
void Allocate_Grid( reax_system*, MPI_Comm );
@@ -49,6 +49,6 @@ int Allocate_HBond_List( int, int, int*, int*, reax_list* );
int Allocate_Bond_List( int, int*, reax_list* );
-void ReAllocate( reax_system*, control_params*, simulation_data*, storage*,
- reax_list**, mpi_datatypes* );
+void ReAllocate( reax_system*, control_params*, simulation_data*, storage*,
+ reax_list**, mpi_datatypes* );
#endif
diff --git a/src/USER-REAXC/reaxc_basic_comm.cpp b/src/USER-REAXC/reaxc_basic_comm.cpp
index 1a0452ed97e3ae90f48eed629e1f8e65c5b83129..bd7b857d6d95e581f626f36457b86a9fadee34a3 100644
--- a/src/USER-REAXC/reaxc_basic_comm.cpp
+++ b/src/USER-REAXC/reaxc_basic_comm.cpp
@@ -14,12 +14,12 @@
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -67,8 +67,8 @@ void rvec2_packer( void *dummy, mpi_out_data *out_buf )
}
-void Dist( reax_system* system, mpi_datatypes *mpi_data,
- void *buf, MPI_Datatype type, int scale, dist_packer pack )
+void Dist( reax_system* system, mpi_datatypes *mpi_data,
+ void *buf, MPI_Datatype type, int scale, dist_packer pack )
{
int d;
mpi_out_data *out_bufs;
@@ -87,27 +87,27 @@ void Dist( reax_system* system, mpi_datatypes *mpi_data,
/* initiate recvs */
nbr1 = &(system->my_nbrs[2*d]);
if( nbr1->atoms_cnt )
- MPI_Irecv( buf + nbr1->atoms_str*scale, nbr1->atoms_cnt, type,
- nbr1->rank, 2*d+1,comm, &req1 );
-
+ MPI_Irecv( buf + nbr1->atoms_str*scale, nbr1->atoms_cnt, type,
+ nbr1->rank, 2*d+1,comm, &req1 );
+
nbr2 = &(system->my_nbrs[2*d+1]);
if( nbr2->atoms_cnt )
- MPI_Irecv( buf + nbr2->atoms_str*scale, nbr2->atoms_cnt, type,
- nbr2->rank, 2*d, comm, &req2 );
+ MPI_Irecv( buf + nbr2->atoms_str*scale, nbr2->atoms_cnt, type,
+ nbr2->rank, 2*d, comm, &req2 );
/* send both messages in dimension d */
if( out_bufs[2*d].cnt ) {
pack( buf, out_bufs + (2*d) );
- MPI_Send( out_bufs[2*d].out_atoms, out_bufs[2*d].cnt, type,
- nbr1->rank, 2*d, comm );
+ MPI_Send( out_bufs[2*d].out_atoms, out_bufs[2*d].cnt, type,
+ nbr1->rank, 2*d, comm );
}
-
+
if( out_bufs[2*d+1].cnt ) {
pack( buf, out_bufs + (2*d+1) );
- MPI_Send( out_bufs[2*d+1].out_atoms, out_bufs[2*d+1].cnt, type,
- nbr2->rank, 2*d+1, comm );
+ MPI_Send( out_bufs[2*d+1].out_atoms, out_bufs[2*d+1].cnt, type,
+ nbr2->rank, 2*d+1, comm );
}
-
+
if( nbr1->atoms_cnt ) MPI_Wait( &req1, &stat1 );
if( nbr2->atoms_cnt ) MPI_Wait( &req2, &stat2 );
}
@@ -123,7 +123,7 @@ void real_unpacker( void *dummy_in, void *dummy_buf, mpi_out_data *out_buf )
int i;
real *in = (real*) dummy_in;
real *buf = (real*) dummy_buf;
-
+
for( i = 0; i < out_buf->cnt; ++i )
buf[ out_buf->index[i] ] += in[i];
}
@@ -138,8 +138,8 @@ void rvec_unpacker( void *dummy_in, void *dummy_buf, mpi_out_data *out_buf )
for( i = 0; i < out_buf->cnt; ++i ) {
rvec_Add( buf[ out_buf->index[i] ], in[i] );
#if defined(DEBUG)
- fprintf( stderr, "rvec_unpacker: cnt=%d i =%d index[i]=%d\n",
- out_buf->cnt, i, out_buf->index[i] );
+ fprintf( stderr, "rvec_unpacker: cnt=%d i =%d index[i]=%d\n",
+ out_buf->cnt, i, out_buf->index[i] );
#endif
}
}
@@ -158,8 +158,8 @@ void rvec2_unpacker( void *dummy_in, void *dummy_buf, mpi_out_data *out_buf )
}
-void Coll( reax_system* system, mpi_datatypes *mpi_data,
- void *buf, MPI_Datatype type, int scale, coll_unpacker unpack )
+void Coll( reax_system* system, mpi_datatypes *mpi_data,
+ void *buf, MPI_Datatype type, int scale, coll_unpacker unpack )
{
int d;
void *in1, *in2;
@@ -189,27 +189,27 @@ void Coll( reax_system* system, mpi_datatypes *mpi_data,
/* send both messages in dimension d */
if( nbr1->atoms_cnt )
- MPI_Send( buf + nbr1->atoms_str*scale, nbr1->atoms_cnt, type,
- nbr1->rank, 2*d, comm );
-
+ MPI_Send( buf + nbr1->atoms_str*scale, nbr1->atoms_cnt, type,
+ nbr1->rank, 2*d, comm );
+
if( nbr2->atoms_cnt )
- MPI_Send( buf + nbr2->atoms_str*scale, nbr2->atoms_cnt, type,
- nbr2->rank, 2*d+1, comm );
+ MPI_Send( buf + nbr2->atoms_str*scale, nbr2->atoms_cnt, type,
+ nbr2->rank, 2*d+1, comm );
#if defined(DEBUG)
- fprintf( stderr, "p%d coll[%d] nbr1: str=%d cnt=%d recv=%d\n",
- system->my_rank, d, nbr1->atoms_str, nbr1->atoms_cnt,
- out_bufs[2*d].cnt );
- fprintf( stderr, "p%d coll[%d] nbr2: str=%d cnt=%d recv=%d\n",
- system->my_rank, d, nbr2->atoms_str, nbr2->atoms_cnt,
- out_bufs[2*d+1].cnt );
+ fprintf( stderr, "p%d coll[%d] nbr1: str=%d cnt=%d recv=%d\n",
+ system->my_rank, d, nbr1->atoms_str, nbr1->atoms_cnt,
+ out_bufs[2*d].cnt );
+ fprintf( stderr, "p%d coll[%d] nbr2: str=%d cnt=%d recv=%d\n",
+ system->my_rank, d, nbr2->atoms_str, nbr2->atoms_cnt,
+ out_bufs[2*d+1].cnt );
#endif
if( out_bufs[2*d].cnt ) {
MPI_Wait( &req1, &stat1 );
unpack( in1, buf, out_bufs + (2*d) );
}
-
+
if( out_bufs[2*d+1].cnt ) {
MPI_Wait( &req2, &stat2 );
unpack( in2, buf, out_bufs + (2*d+1) );
@@ -272,14 +272,14 @@ real Parallel_Vector_Acc( real *v, int n, MPI_Comm comm )
/*****************************************************************************/
#if defined(TEST_FORCES)
-void Coll_ids_at_Master( reax_system *system, storage *workspace,
- mpi_datatypes *mpi_data )
+void Coll_ids_at_Master( reax_system *system, storage *workspace,
+ mpi_datatypes *mpi_data )
{
int i;
int *id_list;
- MPI_Gather( &system->n, 1, MPI_INT, workspace->rcounts, 1, MPI_INT,
- MASTER_NODE, mpi_data->world );
+ MPI_Gather( &system->n, 1, MPI_INT, workspace->rcounts, 1, MPI_INT,
+ MASTER_NODE, mpi_data->world );
if( system->my_rank == MASTER_NODE ){
workspace->displs[0] = 0;
@@ -290,10 +290,10 @@ void Coll_ids_at_Master( reax_system *system, storage *workspace,
id_list = (int*) malloc( system->n * sizeof(int) );
for( i = 0; i < system->n; ++i )
id_list[i] = system->my_atoms[i].orig_id;
-
- MPI_Gatherv( id_list, system->n, MPI_INT,
- workspace->id_all, workspace->rcounts, workspace->displs,
- MPI_INT, MASTER_NODE, mpi_data->world );
+
+ MPI_Gatherv( id_list, system->n, MPI_INT,
+ workspace->id_all, workspace->rcounts, workspace->displs,
+ MPI_INT, MASTER_NODE, mpi_data->world );
free( id_list );
@@ -306,12 +306,12 @@ void Coll_ids_at_Master( reax_system *system, storage *workspace,
}
-void Coll_rvecs_at_Master( reax_system *system, storage *workspace,
- mpi_datatypes *mpi_data, rvec* v )
+void Coll_rvecs_at_Master( reax_system *system, storage *workspace,
+ mpi_datatypes *mpi_data, rvec* v )
{
- MPI_Gatherv( v, system->n, mpi_data->mpi_rvec,
- workspace->f_all, workspace->rcounts, workspace->displs,
- mpi_data->mpi_rvec, MASTER_NODE, mpi_data->world );
+ MPI_Gatherv( v, system->n, mpi_data->mpi_rvec,
+ workspace->f_all, workspace->rcounts, workspace->displs,
+ mpi_data->mpi_rvec, MASTER_NODE, mpi_data->world );
}
#endif
diff --git a/src/USER-REAXC/reaxc_basic_comm.h b/src/USER-REAXC/reaxc_basic_comm.h
index de9f7a5316e15048594841a6d6a2d942a346a5d7..95cfe11b4961e0da27e39571283a3f61249ad655 100644
--- a/src/USER-REAXC/reaxc_basic_comm.h
+++ b/src/USER-REAXC/reaxc_basic_comm.h
@@ -14,12 +14,12 @@
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -37,8 +37,8 @@ void Dist(reax_system*, mpi_datatypes*, void*, MPI_Datatype, int, dist_packer);
void real_unpacker( void*, void*, mpi_out_data* );
void rvec_unpacker( void*, void*, mpi_out_data* );
void rvec2_unpacker( void*, void*, mpi_out_data* );
-void Coll( reax_system*, mpi_datatypes*, void*, MPI_Datatype,
- int, coll_unpacker );
+void Coll( reax_system*, mpi_datatypes*, void*, MPI_Datatype,
+ int, coll_unpacker );
real Parallel_Norm( real*, int, MPI_Comm );
real Parallel_Dot( real*, real*, int, MPI_Comm );
diff --git a/src/USER-REAXC/reaxc_bond_orders.cpp b/src/USER-REAXC/reaxc_bond_orders.cpp
index 19ede46cea5167f3fd02e2879a6564c7a650a330..297fb8fbfc02f1f6794ff1b73eea439a92f7e917 100644
--- a/src/USER-REAXC/reaxc_bond_orders.cpp
+++ b/src/USER-REAXC/reaxc_bond_orders.cpp
@@ -14,12 +14,12 @@
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -38,25 +38,25 @@
#endif
#ifdef TEST_FORCES
-void Get_dBO( reax_system *system, reax_list **lists,
- int i, int pj, real C, rvec *v )
+void Get_dBO( reax_system *system, reax_list **lists,
+ int i, int pj, real C, rvec *v )
{
reax_list *bonds = (*lists) + BONDS;
reax_list *dBOs = (*lists) + DBOS;
int start_pj, end_pj, k;
-
+
pj = bonds->select.bond_list[pj].dbond_index;
start_pj = Start_Index(pj, dBOs);
end_pj = End_Index(pj, dBOs);
for( k = start_pj; k < end_pj; ++k )
- rvec_Scale( v[dBOs->select.dbo_list[k].wrt],
- C, dBOs->select.dbo_list[k].dBO );
+ rvec_Scale( v[dBOs->select.dbo_list[k].wrt],
+ C, dBOs->select.dbo_list[k].dBO );
}
-void Get_dBOpinpi2( reax_system *system, reax_list **lists,
- int i, int pj, real Cpi, real Cpi2, rvec *vpi, rvec *vpi2 )
+void Get_dBOpinpi2( reax_system *system, reax_list **lists,
+ int i, int pj, real Cpi, real Cpi2, rvec *vpi, rvec *vpi2 )
{
reax_list *bonds = (*lists) + BONDS;
reax_list *dBOs = (*lists) + DBOS;
@@ -76,8 +76,8 @@ void Get_dBOpinpi2( reax_system *system, reax_list **lists,
}
-void Add_dBO( reax_system *system, reax_list **lists,
- int i, int pj, real C, rvec *v )
+void Add_dBO( reax_system *system, reax_list **lists,
+ int i, int pj, real C, rvec *v )
{
reax_list *bonds = (*lists) + BONDS;
reax_list *dBOs = (*lists) + DBOS;
@@ -89,14 +89,14 @@ void Add_dBO( reax_system *system, reax_list **lists,
//fprintf( stderr, "i=%d j=%d start=%d end=%d\n", i, pj, start_pj, end_pj );
for( k = start_pj; k < end_pj; ++k )
- rvec_ScaledAdd( v[dBOs->select.dbo_list[k].wrt],
- C, dBOs->select.dbo_list[k].dBO );
+ rvec_ScaledAdd( v[dBOs->select.dbo_list[k].wrt],
+ C, dBOs->select.dbo_list[k].dBO );
}
-void Add_dBOpinpi2( reax_system *system, reax_list **lists,
- int i, int pj, real Cpi, real Cpi2, rvec *vpi, rvec *vpi2 )
+void Add_dBOpinpi2( reax_system *system, reax_list **lists,
+ int i, int pj, real Cpi, real Cpi2, rvec *vpi, rvec *vpi2 )
{
reax_list *bonds = (*lists) + BONDS;
reax_list *dBOs = (*lists) + DBOS;
@@ -116,8 +116,8 @@ void Add_dBOpinpi2( reax_system *system, reax_list **lists,
}
-void Add_dBO_to_Forces( reax_system *system, reax_list **lists,
- int i, int pj, real C )
+void Add_dBO_to_Forces( reax_system *system, reax_list **lists,
+ int i, int pj, real C )
{
reax_list *bonds = (*lists) + BONDS;
reax_list *dBOs = (*lists) + DBOS;
@@ -128,13 +128,13 @@ void Add_dBO_to_Forces( reax_system *system, reax_list **lists,
end_pj = End_Index(pj, dBOs);
for( k = start_pj; k < end_pj; ++k )
- rvec_ScaledAdd( system->my_atoms[dBOs->select.dbo_list[k].wrt].f,
- C, dBOs->select.dbo_list[k].dBO );
+ rvec_ScaledAdd( system->my_atoms[dBOs->select.dbo_list[k].wrt].f,
+ C, dBOs->select.dbo_list[k].dBO );
}
-void Add_dBOpinpi2_to_Forces( reax_system *system, reax_list **lists,
- int i, int pj, real Cpi, real Cpi2 )
+void Add_dBOpinpi2_to_Forces( reax_system *system, reax_list **lists,
+ int i, int pj, real Cpi, real Cpi2 )
{
reax_list *bonds = (*lists) + BONDS;
reax_list *dBOs = (*lists) + DBOS;
@@ -162,13 +162,13 @@ void Add_dDelta( reax_system *system, reax_list **lists, int i, real C, rvec *v
int k;
for( k = start; k < end; ++k )
- rvec_ScaledAdd( v[dDeltas->select.dDelta_list[k].wrt],
- C, dDeltas->select.dDelta_list[k].dVal );
+ rvec_ScaledAdd( v[dDeltas->select.dDelta_list[k].wrt],
+ C, dDeltas->select.dDelta_list[k].dVal );
}
-void Add_dDelta_to_Forces( reax_system *system, reax_list **lists,
- int i, real C )
+void Add_dDelta_to_Forces( reax_system *system, reax_list **lists,
+ int i, real C )
{
reax_list *dDeltas = &((*lists)[DDELTAS]);
int start = Start_Index(i, dDeltas);
@@ -176,14 +176,14 @@ void Add_dDelta_to_Forces( reax_system *system, reax_list **lists,
int k;
for( k = start; k < end; ++k )
- rvec_ScaledAdd( system->my_atoms[dDeltas->select.dDelta_list[k].wrt].f,
- C, dDeltas->select.dDelta_list[k].dVal );
+ rvec_ScaledAdd( system->my_atoms[dDeltas->select.dDelta_list[k].wrt].f,
+ C, dDeltas->select.dDelta_list[k].dVal );
}
-void Calculate_dBO( int i, int pj,
- storage *workspace, reax_list **lists, int *top )
+void Calculate_dBO( int i, int pj,
+ storage *workspace, reax_list **lists, int *top )
{
/* Initializations */
reax_list *bonds, *dBOs;
@@ -191,7 +191,7 @@ void Calculate_dBO( int i, int pj,
bond_data *nbr_l, *nbr_k;
bond_order_data *bo_ij;
dbond_data *top_dbo;
-
+
// rvec due_j[1000], due_i[1000];
// rvec due_j_pi[1000], due_i_pi[1000];
@@ -218,77 +218,77 @@ void Calculate_dBO( int i, int pj,
for( ; l < end_j && bonds->select.bond_list[l].nbr < nbr_k->nbr; ++l ) {
/* These are the neighbors of j which are not in the nbr_list of i
- Note that they might also include i! */
+ Note that they might also include i! */
nbr_l = &(bonds->select.bond_list[l]);
top_dbo->wrt = nbr_l->nbr;
-
- //rvec_ScaledAdd( due_j[top_dbo->wrt],
- // -bo_ij->BO * bo_ij->A2_ji, nbr_l->bo_data.dBOp );
-
+
+ //rvec_ScaledAdd( due_j[top_dbo->wrt],
+ // -bo_ij->BO * bo_ij->A2_ji, nbr_l->bo_data.dBOp );
+
/*3rd, dBO*/
rvec_Scale( top_dbo->dBO, -bo_ij->C3dbo, nbr_l->bo_data.dBOp );
/*4th, dBOpi*/
rvec_Scale( top_dbo->dBOpi, -bo_ij->C4dbopi, nbr_l->bo_data.dBOp );
/*4th, dBOpp*/
rvec_Scale( top_dbo->dBOpi2, -bo_ij->C4dbopi2, nbr_l->bo_data.dBOp );
-
+
if( nbr_l->nbr == i ) {
- /* do the adjustments on i */
- //rvec_ScaledAdd( due_i[i], bo_ij->A0_ij+bo_ij->BO*bo_ij->A1_ij,
- // bo_ij->dBOp ); /*1st, dBO*/
- //rvec_ScaledAdd( due_i[i], bo_ij->BO * bo_ij->A2_ij,
- // workspace->dDeltap_self[i] ); /*2nd, dBO*/
-
- /*1st, dBO*/
- rvec_ScaledAdd( top_dbo->dBO, bo_ij->C1dbo, bo_ij->dBOp );
- /*2nd, dBO*/
- rvec_ScaledAdd( top_dbo->dBO,
- bo_ij->C2dbo, workspace->dDeltap_self[i] );
-
- /*1st, dBOpi*/
- rvec_ScaledAdd(top_dbo->dBOpi,bo_ij->C1dbopi,bo_ij->dln_BOp_pi );
- /*2nd, dBOpi*/
- rvec_ScaledAdd( top_dbo->dBOpi, bo_ij->C2dbopi, bo_ij->dBOp );
- /*3rd, dBOpi*/
- rvec_ScaledAdd( top_dbo->dBOpi,
- bo_ij->C3dbopi, workspace->dDeltap_self[i] );
-
- /*1st, dBO_p*/
- rvec_ScaledAdd( top_dbo->dBOpi2,
- bo_ij->C1dbopi2, bo_ij->dln_BOp_pi2 );
- /*2nd, dBO_p*/
- rvec_ScaledAdd( top_dbo->dBOpi2, bo_ij->C2dbopi2, bo_ij->dBOp );
- /*3rd, dBO_p*/
- rvec_ScaledAdd( top_dbo->dBOpi2,
- bo_ij->C3dbopi2, workspace->dDeltap_self[i] );
+ /* do the adjustments on i */
+ //rvec_ScaledAdd( due_i[i], bo_ij->A0_ij+bo_ij->BO*bo_ij->A1_ij,
+ // bo_ij->dBOp ); /*1st, dBO*/
+ //rvec_ScaledAdd( due_i[i], bo_ij->BO * bo_ij->A2_ij,
+ // workspace->dDeltap_self[i] ); /*2nd, dBO*/
+
+ /*1st, dBO*/
+ rvec_ScaledAdd( top_dbo->dBO, bo_ij->C1dbo, bo_ij->dBOp );
+ /*2nd, dBO*/
+ rvec_ScaledAdd( top_dbo->dBO,
+ bo_ij->C2dbo, workspace->dDeltap_self[i] );
+
+ /*1st, dBOpi*/
+ rvec_ScaledAdd(top_dbo->dBOpi,bo_ij->C1dbopi,bo_ij->dln_BOp_pi );
+ /*2nd, dBOpi*/
+ rvec_ScaledAdd( top_dbo->dBOpi, bo_ij->C2dbopi, bo_ij->dBOp );
+ /*3rd, dBOpi*/
+ rvec_ScaledAdd( top_dbo->dBOpi,
+ bo_ij->C3dbopi, workspace->dDeltap_self[i] );
+
+ /*1st, dBO_p*/
+ rvec_ScaledAdd( top_dbo->dBOpi2,
+ bo_ij->C1dbopi2, bo_ij->dln_BOp_pi2 );
+ /*2nd, dBO_p*/
+ rvec_ScaledAdd( top_dbo->dBOpi2, bo_ij->C2dbopi2, bo_ij->dBOp );
+ /*3rd, dBO_p*/
+ rvec_ScaledAdd( top_dbo->dBOpi2,
+ bo_ij->C3dbopi2, workspace->dDeltap_self[i] );
}
//rvec_Add( workspace->dDelta[nbr_l->nbr], top_dbo->dBO );
++(*top), ++top_dbo;
}
-
- /* Now we are processing neighbor k of i. */
+
+ /* Now we are processing neighbor k of i. */
top_dbo->wrt = nbr_k->nbr;
-
+
//2nd, dBO
- //rvec_ScaledAdd( due_i[top_dbo->wrt],
+ //rvec_ScaledAdd( due_i[top_dbo->wrt],
// -bo_ij->BO * bo_ij->A2_ij, nbr_k->bo_data.dBOp );
-
+
/*2nd, dBO*/
rvec_Scale( top_dbo->dBO, -bo_ij->C2dbo, nbr_k->bo_data.dBOp );
/*3rd, dBOpi*/
rvec_Scale( top_dbo->dBOpi, -bo_ij->C3dbopi, nbr_k->bo_data.dBOp );
/*3rd, dBOpp*/
rvec_Scale( top_dbo->dBOpi2, -bo_ij->C3dbopi2, nbr_k->bo_data.dBOp );
-
+
if( l < end_j && bonds->select.bond_list[l].nbr == nbr_k->nbr ) {
/* This is a common neighbor of i and j. */
nbr_l = &(bonds->select.bond_list[l]);
/*3rd, dBO*/
- //rvec_ScaledAdd( due_j[top_dbo->wrt],
+ //rvec_ScaledAdd( due_j[top_dbo->wrt],
// -bo_ij->BO * bo_ij->A2_ji, nbr_l->bo_data.dBOp );
-
+
/*3rd, dBO*/
rvec_ScaledAdd( top_dbo->dBO, -bo_ij->C3dbo, nbr_l->bo_data.dBOp );
/*4th, dBOpi*/
@@ -297,13 +297,13 @@ void Calculate_dBO( int i, int pj,
rvec_ScaledAdd(top_dbo->dBOpi2,-bo_ij->C4dbopi2,nbr_l->bo_data.dBOp);
++l;
}
- else if( k == pj ) {
+ else if( k == pj ) {
/* This negihbor is j. */
- //rvec_ScaledAdd( due_j[j], -(bo_ij->A0_ij+bo_ij->BO*bo_ij->A1_ij),
+ //rvec_ScaledAdd( due_j[j], -(bo_ij->A0_ij+bo_ij->BO*bo_ij->A1_ij),
// bo_ij->dBOp ); /*1st, dBO*/
- //rvec_ScaledAdd( due_j[j], bo_ij->BO * bo_ij->A2_ji,
+ //rvec_ScaledAdd( due_j[j], bo_ij->BO * bo_ij->A2_ji,
// workspace->dDeltap_self[j] ); /*3rd, dBO*/
-
+
/*1st, dBO*/
rvec_ScaledAdd( top_dbo->dBO, -bo_ij->C1dbo, bo_ij->dBOp );
/*3rd, dBO*/
@@ -314,16 +314,16 @@ void Calculate_dBO( int i, int pj,
/*2nd, dBOpi*/
rvec_ScaledAdd( top_dbo->dBOpi, -bo_ij->C2dbopi, bo_ij->dBOp );
/*4th, dBOpi*/
- rvec_ScaledAdd( top_dbo->dBOpi,
- bo_ij->C4dbopi, workspace->dDeltap_self[j] );
+ rvec_ScaledAdd( top_dbo->dBOpi,
+ bo_ij->C4dbopi, workspace->dDeltap_self[j] );
/*1st, dBOpi2*/
rvec_ScaledAdd(top_dbo->dBOpi2,-bo_ij->C1dbopi2,bo_ij->dln_BOp_pi2);
/*2nd, dBOpi2*/
rvec_ScaledAdd(top_dbo->dBOpi2,-bo_ij->C2dbopi2,bo_ij->dBOp );
/*4th, dBOpi2*/
- rvec_ScaledAdd(top_dbo->dBOpi2, bo_ij->C4dbopi2,
- workspace->dDeltap_self[j] );
+ rvec_ScaledAdd(top_dbo->dBOpi2, bo_ij->C4dbopi2,
+ workspace->dDeltap_self[j] );
}
// rvec_Add( workspace->dDelta[nbr_k->nbr], top_dbo->dBO );
@@ -337,10 +337,10 @@ void Calculate_dBO( int i, int pj,
top_dbo->wrt = nbr_l->nbr;
// fprintf( stdout, "\tl: %d nbr:%d\n", l, nbr_l->nbr+1 );
-
- // rvec_ScaledAdd( due_j[top_dbo->wrt],
- // -bo_ij->BO * bo_ij->A2_ji, nbr_l->bo_data.dBOp );
-
+
+ // rvec_ScaledAdd( due_j[top_dbo->wrt],
+ // -bo_ij->BO * bo_ij->A2_ji, nbr_l->bo_data.dBOp );
+
/*3rd, dBO*/
rvec_Scale( top_dbo->dBO, -bo_ij->C3dbo, nbr_l->bo_data.dBOp );
/*4th, dBOpi*/
@@ -350,32 +350,32 @@ void Calculate_dBO( int i, int pj,
if( nbr_l->nbr == i )
{
- /* do the adjustments on i */
- //rvec_ScaledAdd( due_i[i], bo_ij->A0_ij + bo_ij->BO * bo_ij->A1_ij,
- // bo_ij->dBOp ); /*1st, dBO*/
- //rvec_ScaledAdd( due_i[i], bo_ij->BO * bo_ij->A2_ij,
- // workspace->dDeltap_self[i] ); /*2nd, dBO*/
-
- /*1st, dBO*/
- rvec_ScaledAdd( top_dbo->dBO, bo_ij->C1dbo, bo_ij->dBOp );
- /*2nd, dBO*/
- rvec_ScaledAdd(top_dbo->dBO,bo_ij->C2dbo,workspace->dDeltap_self[i]);
-
- /*1st, dBO_p*/
- rvec_ScaledAdd( top_dbo->dBOpi, bo_ij->C1dbopi, bo_ij->dln_BOp_pi );
- /*2nd, dBOpi*/
- rvec_ScaledAdd( top_dbo->dBOpi, bo_ij->C2dbopi, bo_ij->dBOp );
- /*3rd,dBOpi*/
- rvec_ScaledAdd( top_dbo->dBOpi,
- bo_ij->C3dbopi, workspace->dDeltap_self[i] );
-
- /*1st, dBO_p*/
- rvec_ScaledAdd(top_dbo->dBOpi2, bo_ij->C1dbopi2, bo_ij->dln_BOp_pi2);
- /*2nd, dBO_p*/
- rvec_ScaledAdd(top_dbo->dBOpi2, bo_ij->C2dbopi2, bo_ij->dBOp);
- /*3rd,dBO_p*/
- rvec_ScaledAdd(top_dbo->dBOpi2,
- bo_ij->C3dbopi2, workspace->dDeltap_self[i]);
+ /* do the adjustments on i */
+ //rvec_ScaledAdd( due_i[i], bo_ij->A0_ij + bo_ij->BO * bo_ij->A1_ij,
+ // bo_ij->dBOp ); /*1st, dBO*/
+ //rvec_ScaledAdd( due_i[i], bo_ij->BO * bo_ij->A2_ij,
+ // workspace->dDeltap_self[i] ); /*2nd, dBO*/
+
+ /*1st, dBO*/
+ rvec_ScaledAdd( top_dbo->dBO, bo_ij->C1dbo, bo_ij->dBOp );
+ /*2nd, dBO*/
+ rvec_ScaledAdd(top_dbo->dBO,bo_ij->C2dbo,workspace->dDeltap_self[i]);
+
+ /*1st, dBO_p*/
+ rvec_ScaledAdd( top_dbo->dBOpi, bo_ij->C1dbopi, bo_ij->dln_BOp_pi );
+ /*2nd, dBOpi*/
+ rvec_ScaledAdd( top_dbo->dBOpi, bo_ij->C2dbopi, bo_ij->dBOp );
+ /*3rd,dBOpi*/
+ rvec_ScaledAdd( top_dbo->dBOpi,
+ bo_ij->C3dbopi, workspace->dDeltap_self[i] );
+
+ /*1st, dBO_p*/
+ rvec_ScaledAdd(top_dbo->dBOpi2, bo_ij->C1dbopi2, bo_ij->dln_BOp_pi2);
+ /*2nd, dBO_p*/
+ rvec_ScaledAdd(top_dbo->dBOpi2, bo_ij->C2dbopi2, bo_ij->dBOp);
+ /*3rd,dBO_p*/
+ rvec_ScaledAdd(top_dbo->dBOpi2,
+ bo_ij->C3dbopi2, workspace->dDeltap_self[i]);
}
// rvec_Add( workspace->dDelta[nbr_l->nbr], top_dbo->dBO );
@@ -383,25 +383,25 @@ void Calculate_dBO( int i, int pj,
}
// for( k = 0; k < 21; ++k ){
- // fprintf( stderr, "%d %d %d, due_i:[%g %g %g]\n",
+ // fprintf( stderr, "%d %d %d, due_i:[%g %g %g]\n",
// i+1, j+1, k+1, due_i[k][0], due_i[k][1], due_i[k][2] );
- // fprintf( stderr, "%d %d %d, due_j:[%g %g %g]\n",
+ // fprintf( stderr, "%d %d %d, due_j:[%g %g %g]\n",
// i+1, j+1, k+1, due_j[k][0], due_j[k][1], due_j[k][2] );
}
#endif
-void Add_dBond_to_Forces_NPT( int i, int pj, simulation_data *data,
- storage *workspace, reax_list **lists )
+void Add_dBond_to_Forces_NPT( int i, int pj, simulation_data *data,
+ storage *workspace, reax_list **lists )
{
reax_list *bonds = (*lists) + BONDS;
bond_data *nbr_j, *nbr_k;
- bond_order_data *bo_ij, *bo_ji;
+ bond_order_data *bo_ij, *bo_ji;
dbond_coefficients coef;
rvec temp, ext_press;
ivec rel_box;
int pk, k, j;
-
+
/* Initializations */
nbr_j = &(bonds->select.bond_list[pj]);
j = nbr_j->nbr;
@@ -425,8 +425,8 @@ void Add_dBond_to_Forces_NPT( int i, int pj, simulation_data *data,
coef.C1dDelta = bo_ij->C1dbo * (workspace->CdDelta[i]+workspace->CdDelta[j]);
coef.C2dDelta = bo_ij->C2dbo * (workspace->CdDelta[i]+workspace->CdDelta[j]);
coef.C3dDelta = bo_ij->C3dbo * (workspace->CdDelta[i]+workspace->CdDelta[j]);
-
-
+
+
/************************************
* forces related to atom i *
* first neighbors of atom i *
@@ -449,9 +449,9 @@ void Add_dBond_to_Forces_NPT( int i, int pj, simulation_data *data,
/* if( !ivec_isZero( nbr_k->rel_box ) )
fprintf( stderr, "%3d %3d %3d: dvec[%10.6f %10.6f %10.6f]"
"ext[%3d %3d %3d] f[%10.6f %10.6f %10.6f]\n",
- i+1, system->my_atoms[i].x[0],
- system->my_atoms[i].x[1], system->my_atoms[i].x[2],
- j+1, k+1, system->my_atoms[k].x[0],
+ i+1, system->my_atoms[i].x[0],
+ system->my_atoms[i].x[1], system->my_atoms[i].x[2],
+ j+1, k+1, system->my_atoms[k].x[0],
system->my_atoms[k].x[1], system->my_atoms[k].x[2],
nbr_k->dvec[0], nbr_k->dvec[1], nbr_k->dvec[2],
nbr_k->rel_box[0], nbr_k->rel_box[1], nbr_k->rel_box[2],
@@ -466,26 +466,26 @@ void Add_dBond_to_Forces_NPT( int i, int pj, simulation_data *data,
rvec_ScaledAdd( temp, coef.C1dbopi, bo_ij->dln_BOp_pi ); /*1st,dBOpi*/
rvec_ScaledAdd( temp, coef.C2dbopi, bo_ij->dBOp ); /*2nd,dBOpi*/
rvec_ScaledAdd( temp, coef.C3dbopi, workspace->dDeltap_self[i]);/*3rd,dBOpi*/
-
+
rvec_ScaledAdd( temp, coef.C1dbopi2, bo_ij->dln_BOp_pi2 ); /*1st,dBO_pi2*/
rvec_ScaledAdd( temp, coef.C2dbopi2, bo_ij->dBOp ); /*2nd,dBO_pi2*/
rvec_ScaledAdd( temp, coef.C3dbopi2, workspace->dDeltap_self[i] );/*3rd*/
-
+
/* force */
rvec_Add( workspace->f[i], temp );
/* ext pressure due to i is dropped, counting force on j will be enough */
/******************************************************
- * forces and pressure related to atom j *
+ * forces and pressure related to atom j *
* first neighbors of atom j *
******************************************************/
for( pk = Start_Index(j, bonds); pk < End_Index(j, bonds); ++pk ) {
nbr_k = &(bonds->select.bond_list[pk]);
k = nbr_k->nbr;
-
+
rvec_Scale( temp, -coef.C3dbo, nbr_k->bo_data.dBOp ); /*3rd,dBO*/
- rvec_ScaledAdd( temp, -coef.C3dDelta, nbr_k->bo_data.dBOp);/*dDelta*/
+ rvec_ScaledAdd( temp, -coef.C3dDelta, nbr_k->bo_data.dBOp);/*dDelta*/
rvec_ScaledAdd( temp, -coef.C4dbopi, nbr_k->bo_data.dBOp); /*4th,dBOpi*/
rvec_ScaledAdd( temp, -coef.C4dbopi2, nbr_k->bo_data.dBOp);/*4th,dBOpi2*/
@@ -496,30 +496,30 @@ void Add_dBond_to_Forces_NPT( int i, int pj, simulation_data *data,
ivec_Sum( rel_box, nbr_k->rel_box, nbr_j->rel_box ); //rel_box(k, i)
rvec_iMultiply( ext_press, rel_box, temp );
rvec_Add( data->my_ext_press, ext_press );
-
+
/* if( !ivec_isZero( rel_box ) )
- fprintf( stderr, "%3d %3d %3d: dvec[%10.6f %10.6f %10.6f]"
- "ext[%3d %3d %3d] f[%10.6f %10.6f %10.6f]\n",
- i+1, j+1, system->my_atoms[j].x[0],
- system->my_atoms[j].x[1], system->my_atoms[j].x[2],
- k+1, system->my_atoms[k].x[0],
- system->my_atoms[k].x[1], system->my_atoms[k].x[2],
- nbr_k->dvec[0], nbr_k->dvec[1], nbr_k->dvec[2],
- rel_box[0], rel_box[1], rel_box[2],
- temp[0], temp[1], temp[2] ); */
+ fprintf( stderr, "%3d %3d %3d: dvec[%10.6f %10.6f %10.6f]"
+ "ext[%3d %3d %3d] f[%10.6f %10.6f %10.6f]\n",
+ i+1, j+1, system->my_atoms[j].x[0],
+ system->my_atoms[j].x[1], system->my_atoms[j].x[2],
+ k+1, system->my_atoms[k].x[0],
+ system->my_atoms[k].x[1], system->my_atoms[k].x[2],
+ nbr_k->dvec[0], nbr_k->dvec[1], nbr_k->dvec[2],
+ rel_box[0], rel_box[1], rel_box[2],
+ temp[0], temp[1], temp[2] ); */
}
}
-
+
/* then atom j itself */
rvec_Scale( temp, -coef.C1dbo, bo_ij->dBOp ); /*1st, dBO*/
rvec_ScaledAdd( temp, coef.C3dbo, workspace->dDeltap_self[j] ); /*2nd, dBO*/
rvec_ScaledAdd( temp, -coef.C1dDelta, bo_ij->dBOp ); /*1st, dBO*/
rvec_ScaledAdd( temp, coef.C3dDelta, workspace->dDeltap_self[j]);/*2nd, dBO*/
-
+
rvec_ScaledAdd( temp, -coef.C1dbopi, bo_ij->dln_BOp_pi ); /*1st,dBOpi*/
rvec_ScaledAdd( temp, -coef.C2dbopi, bo_ij->dBOp ); /*2nd,dBOpi*/
rvec_ScaledAdd( temp, coef.C4dbopi, workspace->dDeltap_self[j]);/*3rd,dBOpi*/
-
+
rvec_ScaledAdd( temp, -coef.C1dbopi2, bo_ij->dln_BOp_pi2 ); /*1st,dBOpi2*/
rvec_ScaledAdd( temp, -coef.C2dbopi2, bo_ij->dBOp ); /*2nd,dBOpi2*/
rvec_ScaledAdd( temp,coef.C4dbopi2,workspace->dDeltap_self[j]);/*3rd,dBOpi2*/
@@ -531,11 +531,11 @@ void Add_dBond_to_Forces_NPT( int i, int pj, simulation_data *data,
rvec_Add( data->my_ext_press, ext_press );
/* if( !ivec_isZero( nbr_j->rel_box ) )
- fprintf( stderr, "%3d %3d %3d: dvec[%10.6f %10.6f %10.6f]"
+ fprintf( stderr, "%3d %3d %3d: dvec[%10.6f %10.6f %10.6f]"
"ext[%3d %3d %3d] f[%10.6f %10.6f %10.6f]\n",
- i+1, system->my_atoms[i].x[0], system->my_atoms[i].x[1],
- system->my_atoms[i].x[2],
- j+1,system->my_atoms[j].x[0], system->my_atoms[j].x[1],
+ i+1, system->my_atoms[i].x[0], system->my_atoms[i].x[1],
+ system->my_atoms[i].x[2],
+ j+1,system->my_atoms[j].x[0], system->my_atoms[j].x[1],
system->my_atoms[j].x[2],
j+1, nbr_j->dvec[0], nbr_j->dvec[1], nbr_j->dvec[2],
nbr_j->rel_box[0], nbr_j->rel_box[1], nbr_j->rel_box[2],
@@ -544,12 +544,12 @@ void Add_dBond_to_Forces_NPT( int i, int pj, simulation_data *data,
-void Add_dBond_to_Forces( reax_system *system, int i, int pj,
- storage *workspace, reax_list **lists )
+void Add_dBond_to_Forces( reax_system *system, int i, int pj,
+ storage *workspace, reax_list **lists )
{
reax_list *bonds = (*lists) + BONDS;
bond_data *nbr_j, *nbr_k;
- bond_order_data *bo_ij, *bo_ji;
+ bond_order_data *bo_ij, *bo_ji;
dbond_coefficients coef;
int pk, k, j;
@@ -557,7 +557,7 @@ void Add_dBond_to_Forces( reax_system *system, int i, int pj,
real f_scaler;
rvec fi_tmp, fj_tmp, fk_tmp, delij, delji, delki, delkj, temp;
- /* Initializations */
+ /* Initializations */
nbr_j = &(bonds->select.bond_list[pj]);
j = nbr_j->nbr;
bo_ij = &(nbr_j->bo_data);
@@ -580,17 +580,17 @@ void Add_dBond_to_Forces( reax_system *system, int i, int pj,
coef.C1dDelta = bo_ij->C1dbo * (workspace->CdDelta[i]+workspace->CdDelta[j]);
coef.C2dDelta = bo_ij->C2dbo * (workspace->CdDelta[i]+workspace->CdDelta[j]);
coef.C3dDelta = bo_ij->C3dbo * (workspace->CdDelta[i]+workspace->CdDelta[j]);
-
+
// forces on i
- rvec_Scale( temp, coef.C1dbo, bo_ij->dBOp );
- rvec_ScaledAdd( temp, coef.C2dbo, workspace->dDeltap_self[i] );
- rvec_ScaledAdd( temp, coef.C1dDelta, bo_ij->dBOp );
+ rvec_Scale( temp, coef.C1dbo, bo_ij->dBOp );
+ rvec_ScaledAdd( temp, coef.C2dbo, workspace->dDeltap_self[i] );
+ rvec_ScaledAdd( temp, coef.C1dDelta, bo_ij->dBOp );
rvec_ScaledAdd( temp, coef.C2dDelta, workspace->dDeltap_self[i] );
- rvec_ScaledAdd( temp, coef.C1dbopi, bo_ij->dln_BOp_pi );
- rvec_ScaledAdd( temp, coef.C2dbopi, bo_ij->dBOp );
+ rvec_ScaledAdd( temp, coef.C1dbopi, bo_ij->dln_BOp_pi );
+ rvec_ScaledAdd( temp, coef.C2dbopi, bo_ij->dBOp );
rvec_ScaledAdd( temp, coef.C3dbopi, workspace->dDeltap_self[i]);
- rvec_ScaledAdd( temp, coef.C1dbopi2, bo_ij->dln_BOp_pi2 );
- rvec_ScaledAdd( temp, coef.C2dbopi2, bo_ij->dBOp );
+ rvec_ScaledAdd( temp, coef.C1dbopi2, bo_ij->dln_BOp_pi2 );
+ rvec_ScaledAdd( temp, coef.C2dbopi2, bo_ij->dBOp );
rvec_ScaledAdd( temp, coef.C3dbopi2, workspace->dDeltap_self[i] );
rvec_Add( workspace->f[i], temp );
@@ -601,15 +601,15 @@ void Add_dBond_to_Forces( reax_system *system, int i, int pj,
}
// forces on j
- rvec_Scale( temp, -coef.C1dbo, bo_ij->dBOp );
- rvec_ScaledAdd( temp, coef.C3dbo, workspace->dDeltap_self[j] );
- rvec_ScaledAdd( temp, -coef.C1dDelta, bo_ij->dBOp );
+ rvec_Scale( temp, -coef.C1dbo, bo_ij->dBOp );
+ rvec_ScaledAdd( temp, coef.C3dbo, workspace->dDeltap_self[j] );
+ rvec_ScaledAdd( temp, -coef.C1dDelta, bo_ij->dBOp );
rvec_ScaledAdd( temp, coef.C3dDelta, workspace->dDeltap_self[j]);
- rvec_ScaledAdd( temp, -coef.C1dbopi, bo_ij->dln_BOp_pi );
- rvec_ScaledAdd( temp, -coef.C2dbopi, bo_ij->dBOp );
+ rvec_ScaledAdd( temp, -coef.C1dbopi, bo_ij->dln_BOp_pi );
+ rvec_ScaledAdd( temp, -coef.C2dbopi, bo_ij->dBOp );
rvec_ScaledAdd( temp, coef.C4dbopi, workspace->dDeltap_self[j]);
- rvec_ScaledAdd( temp, -coef.C1dbopi2, bo_ij->dln_BOp_pi2 );
- rvec_ScaledAdd( temp, -coef.C2dbopi2, bo_ij->dBOp );
+ rvec_ScaledAdd( temp, -coef.C1dbopi2, bo_ij->dln_BOp_pi2 );
+ rvec_ScaledAdd( temp, -coef.C2dbopi2, bo_ij->dBOp );
rvec_ScaledAdd( temp, coef.C4dbopi2, workspace->dDeltap_self[j]);
rvec_Add( workspace->f[j], temp );
@@ -618,15 +618,15 @@ void Add_dBond_to_Forces( reax_system *system, int i, int pj,
rvec_ScaledSum( delji, 1., system->my_atoms[j].x,-1., system->my_atoms[i].x );
system->pair_ptr->v_tally(j,fj_tmp,delji);
}
-
+
// forces on k: i neighbor
for( pk = Start_Index(i, bonds); pk < End_Index(i, bonds); ++pk ) {
nbr_k = &(bonds->select.bond_list[pk]);
k = nbr_k->nbr;
- rvec_Scale( temp, -coef.C2dbo, nbr_k->bo_data.dBOp);
+ rvec_Scale( temp, -coef.C2dbo, nbr_k->bo_data.dBOp);
rvec_ScaledAdd( temp, -coef.C2dDelta, nbr_k->bo_data.dBOp);
- rvec_ScaledAdd( temp, -coef.C3dbopi, nbr_k->bo_data.dBOp);
+ rvec_ScaledAdd( temp, -coef.C3dbopi, nbr_k->bo_data.dBOp);
rvec_ScaledAdd( temp, -coef.C3dbopi2, nbr_k->bo_data.dBOp);
rvec_Add( workspace->f[k], temp );
@@ -638,15 +638,15 @@ void Add_dBond_to_Forces( reax_system *system, int i, int pj,
system->pair_ptr->v_tally(k,fk_tmp,delkj);
}
}
-
+
// forces on k: j neighbor
for( pk = Start_Index(j, bonds); pk < End_Index(j, bonds); ++pk ) {
nbr_k = &(bonds->select.bond_list[pk]);
k = nbr_k->nbr;
-
+
rvec_Scale( temp, -coef.C3dbo, nbr_k->bo_data.dBOp );
rvec_ScaledAdd( temp, -coef.C3dDelta, nbr_k->bo_data.dBOp);
- rvec_ScaledAdd( temp, -coef.C4dbopi, nbr_k->bo_data.dBOp);
+ rvec_ScaledAdd( temp, -coef.C4dbopi, nbr_k->bo_data.dBOp);
rvec_ScaledAdd( temp, -coef.C4dbopi2, nbr_k->bo_data.dBOp);
rvec_Add( workspace->f[k], temp );
@@ -658,14 +658,14 @@ void Add_dBond_to_Forces( reax_system *system, int i, int pj,
system->pair_ptr->v_tally(k,fk_tmp,delkj);
}
}
-
+
}
-int BOp( storage *workspace, reax_list *bonds, real bo_cut,
- int i, int btop_i, far_neighbor_data *nbr_pj,
- single_body_parameters *sbp_i, single_body_parameters *sbp_j,
- two_body_parameters *twbp ) {
+int BOp( storage *workspace, reax_list *bonds, real bo_cut,
+ int i, int btop_i, far_neighbor_data *nbr_pj,
+ single_body_parameters *sbp_i, single_body_parameters *sbp_j,
+ two_body_parameters *twbp ) {
int j, btop_j;
real r2, C12, C34, C56;
real Cln_BOp_s, Cln_BOp_pi, Cln_BOp_pi2;
@@ -675,34 +675,34 @@ int BOp( storage *workspace, reax_list *bonds, real bo_cut,
j = nbr_pj->nbr;
r2 = SQR(nbr_pj->d);
-
+
if( sbp_i->r_s > 0.0 && sbp_j->r_s > 0.0 ) {
C12 = twbp->p_bo1 * pow( nbr_pj->d / twbp->r_s, twbp->p_bo2 );
BO_s = (1.0 + bo_cut) * exp( C12 );
}
else BO_s = C12 = 0.0;
-
+
if( sbp_i->r_pi > 0.0 && sbp_j->r_pi > 0.0 ) {
C34 = twbp->p_bo3 * pow( nbr_pj->d / twbp->r_p, twbp->p_bo4 );
BO_pi = exp( C34 );
}
else BO_pi = C34 = 0.0;
-
+
if( sbp_i->r_pi_pi > 0.0 && sbp_j->r_pi_pi > 0.0 ) {
- C56 = twbp->p_bo5 * pow( nbr_pj->d / twbp->r_pp, twbp->p_bo6 );
+ C56 = twbp->p_bo5 * pow( nbr_pj->d / twbp->r_pp, twbp->p_bo6 );
BO_pi2= exp( C56 );
}
else BO_pi2 = C56 = 0.0;
-
+
/* Initially BO values are the uncorrected ones, page 1 */
BO = BO_s + BO_pi + BO_pi2;
-
+
if( BO >= bo_cut ) {
/****** bonds i-j and j-i ******/
ibond = &( bonds->select.bond_list[btop_i] );
btop_j = End_Index( j, bonds );
jbond = &(bonds->select.bond_list[btop_j]);
-
+
ibond->nbr = j;
jbond->nbr = i;
ibond->d = nbr_pj->d;
@@ -716,40 +716,40 @@ int BOp( storage *workspace, reax_list *bonds, real bo_cut,
ibond->sym_index = btop_j;
jbond->sym_index = btop_i;
Set_End_Index( j, btop_j+1, bonds );
-
+
bo_ij = &( ibond->bo_data );
bo_ji = &( jbond->bo_data );
bo_ji->BO = bo_ij->BO = BO;
bo_ji->BO_s = bo_ij->BO_s = BO_s;
bo_ji->BO_pi = bo_ij->BO_pi = BO_pi;
bo_ji->BO_pi2 = bo_ij->BO_pi2 = BO_pi2;
-
+
/* Bond Order page2-3, derivative of total bond order prime */
Cln_BOp_s = twbp->p_bo2 * C12 / r2;
Cln_BOp_pi = twbp->p_bo4 * C34 / r2;
Cln_BOp_pi2 = twbp->p_bo6 * C56 / r2;
-
- /* Only dln_BOp_xx wrt. dr_i is stored here, note that
+
+ /* Only dln_BOp_xx wrt. dr_i is stored here, note that
dln_BOp_xx/dr_i = -dln_BOp_xx/dr_j and all others are 0 */
rvec_Scale(bo_ij->dln_BOp_s,-bo_ij->BO_s*Cln_BOp_s,ibond->dvec);
rvec_Scale(bo_ij->dln_BOp_pi,-bo_ij->BO_pi*Cln_BOp_pi,ibond->dvec);
rvec_Scale(bo_ij->dln_BOp_pi2,
- -bo_ij->BO_pi2*Cln_BOp_pi2,ibond->dvec);
+ -bo_ij->BO_pi2*Cln_BOp_pi2,ibond->dvec);
rvec_Scale(bo_ji->dln_BOp_s, -1., bo_ij->dln_BOp_s);
rvec_Scale(bo_ji->dln_BOp_pi, -1., bo_ij->dln_BOp_pi );
rvec_Scale(bo_ji->dln_BOp_pi2, -1., bo_ij->dln_BOp_pi2 );
-
- /* Only dBOp wrt. dr_i is stored here, note that
+
+ /* Only dBOp wrt. dr_i is stored here, note that
dBOp/dr_i = -dBOp/dr_j and all others are 0 */
- rvec_Scale( bo_ij->dBOp,
- -(bo_ij->BO_s * Cln_BOp_s +
- bo_ij->BO_pi * Cln_BOp_pi +
- bo_ij->BO_pi2 * Cln_BOp_pi2), ibond->dvec );
+ rvec_Scale( bo_ij->dBOp,
+ -(bo_ij->BO_s * Cln_BOp_s +
+ bo_ij->BO_pi * Cln_BOp_pi +
+ bo_ij->BO_pi2 * Cln_BOp_pi2), ibond->dvec );
rvec_Scale( bo_ji->dBOp, -1., bo_ij->dBOp );
-
+
rvec_Add( workspace->dDeltap_self[i], bo_ij->dBOp );
rvec_Add( workspace->dDeltap_self[j], bo_ji->dBOp );
-
+
bo_ij->BO_s -= bo_cut;
bo_ij->BO -= bo_cut;
bo_ji->BO_s -= bo_cut;
@@ -758,58 +758,58 @@ int BOp( storage *workspace, reax_list *bonds, real bo_cut,
workspace->total_bond_order[j] += bo_ji->BO; //currently total_BOp
bo_ij->Cdbo = bo_ij->Cdbopi = bo_ij->Cdbopi2 = 0.0;
bo_ji->Cdbo = bo_ji->Cdbopi = bo_ji->Cdbopi2 = 0.0;
-
+
/*fprintf( stderr, "%d %d %g %g %g\n",
i+1, j+1, bo_ij->BO, bo_ij->BO_pi, bo_ij->BO_pi2 );*/
-
- /*fprintf( stderr, "Cln_BOp_s: %f, pbo2: %f, C12:%f\n",
+
+ /*fprintf( stderr, "Cln_BOp_s: %f, pbo2: %f, C12:%f\n",
Cln_BOp_s, twbp->p_bo2, C12 );
- fprintf( stderr, "Cln_BOp_pi: %f, pbo4: %f, C34:%f\n",
+ fprintf( stderr, "Cln_BOp_pi: %f, pbo4: %f, C34:%f\n",
Cln_BOp_pi, twbp->p_bo4, C34 );
fprintf( stderr, "Cln_BOp_pi2: %f, pbo6: %f, C56:%f\n",
Cln_BOp_pi2, twbp->p_bo6, C56 );*/
/*fprintf(stderr, "pbo1: %f, pbo2:%f\n", twbp->p_bo1, twbp->p_bo2);
fprintf(stderr, "pbo3: %f, pbo4:%f\n", twbp->p_bo3, twbp->p_bo4);
fprintf(stderr, "pbo5: %f, pbo6:%f\n", twbp->p_bo5, twbp->p_bo6);
- fprintf( stderr, "r_s: %f, r_p: %f, r_pp: %f\n",
+ fprintf( stderr, "r_s: %f, r_p: %f, r_pp: %f\n",
twbp->r_s, twbp->r_p, twbp->r_pp );
fprintf( stderr, "C12: %g, C34:%g, C56:%g\n", C12, C34, C56 );*/
-
+
/*fprintf( stderr, "\tfactors: %g %g %g\n",
- -(bo_ij->BO_s * Cln_BOp_s + bo_ij->BO_pi * Cln_BOp_pi +
+ -(bo_ij->BO_s * Cln_BOp_s + bo_ij->BO_pi * Cln_BOp_pi +
bo_ij->BO_pi2 * Cln_BOp_pp),
-bo_ij->BO_pi * Cln_BOp_pi, -bo_ij->BO_pi2 * Cln_BOp_pi2 );*/
- /*fprintf( stderr, "dBOpi:\t[%g, %g, %g]\n",
+ /*fprintf( stderr, "dBOpi:\t[%g, %g, %g]\n",
bo_ij->dBOp[0], bo_ij->dBOp[1], bo_ij->dBOp[2] );
- fprintf( stderr, "dBOpi:\t[%g, %g, %g]\n",
- bo_ij->dln_BOp_pi[0], bo_ij->dln_BOp_pi[1],
+ fprintf( stderr, "dBOpi:\t[%g, %g, %g]\n",
+ bo_ij->dln_BOp_pi[0], bo_ij->dln_BOp_pi[1],
bo_ij->dln_BOp_pi[2] );
fprintf( stderr, "dBOpi2:\t[%g, %g, %g]\n\n",
- bo_ij->dln_BOp_pi2[0], bo_ij->dln_BOp_pi2[1],
+ bo_ij->dln_BOp_pi2[0], bo_ij->dln_BOp_pi2[1],
bo_ij->dln_BOp_pi2[2] );*/
return 1;
}
-
+
return 0;
}
-
+
int compare_bonds( const void *p1, const void *p2 )
{
return ((bond_data *)p1)->nbr - ((bond_data *)p2)->nbr;
}
-
-void BO( reax_system *system, control_params *control, simulation_data *data,
- storage *workspace, reax_list **lists, output_controls *out_control )
+
+void BO( reax_system *system, control_params *control, simulation_data *data,
+ storage *workspace, reax_list **lists, output_controls *out_control )
{
int i, j, pj, type_i, type_j;
int start_i, end_i, sym_index, num_bonds;
real val_i, Deltap_i, Deltap_boc_i;
real val_j, Deltap_j, Deltap_boc_j;
real f1, f2, f3, f4, f5, f4f5, exp_f4, exp_f5;
- real exp_p1i, exp_p2i, exp_p1j, exp_p2j;
+ real exp_p1i, exp_p2i, exp_p1j, exp_p2j;
real temp, u1_ij, u1_ji, Cf1A_ij, Cf1B_ij, Cf1_ij, Cf1_ji;
real Cf45_ij, Cf45_ji, p_lp1; //u_ij, u_ji
real A0_ij, A1_ij, A2_ij, A2_ji, A3_ij, A3_ji;
@@ -830,7 +830,7 @@ void BO( reax_system *system, control_params *control, simulation_data *data,
dBOs = (*lists) + DBOS;
//for( i = 0; i < system->N; ++i )
- // qsort( &(bonds->select.bond_list[Start_Index(i, bonds)]),
+ // qsort( &(bonds->select.bond_list[Start_Index(i, bonds)]),
// Num_Entries(i, bonds), sizeof(bond_data), compare_bonds );
#endif
@@ -843,10 +843,10 @@ void BO( reax_system *system, control_params *control, simulation_data *data,
type_i = system->my_atoms[i].type;
sbp_i = &(system->reax_param.sbp[type_i]);
workspace->Deltap[i] = workspace->total_bond_order[i] - sbp_i->valency;
- workspace->Deltap_boc[i] =
+ workspace->Deltap_boc[i] =
workspace->total_bond_order[i] - sbp_i->valency_val;
-
- //fprintf( stdout, "%d(%d) %24.15f\n",
+
+ //fprintf( stdout, "%d(%d) %24.15f\n",
// i, workspace->bond_mark[i], workspace->total_bond_order[i] );
workspace->total_bond_order[i] = 0;
}
@@ -871,227 +871,227 @@ void BO( reax_system *system, control_params *control, simulation_data *data,
// fprintf( stderr, "\tj:%d - ubo: %8.3f\n", j+1, bo_ij->BO );
if( i < j || workspace->bond_mark[j] > 3 ) {
- twbp = &( system->reax_param.tbp[type_i][type_j] );
+ twbp = &( system->reax_param.tbp[type_i][type_j] );
#ifdef TEST_FORCES
- Set_Start_Index( pj, top_dbo, dBOs );
- /* fprintf( stderr, "%6d%6d%12.6f%12.6f%12.6f\n",
- workspace->reverse_map[i], workspace->reverse_map[j],
- twbp->ovc, twbp->v13cor, bo_ij->BO ); */
+ Set_Start_Index( pj, top_dbo, dBOs );
+ /* fprintf( stderr, "%6d%6d%12.6f%12.6f%12.6f\n",
+ workspace->reverse_map[i], workspace->reverse_map[j],
+ twbp->ovc, twbp->v13cor, bo_ij->BO ); */
#endif
- if( twbp->ovc < 0.001 && twbp->v13cor < 0.001 ) {
- /* There is no correction to bond orders nor to derivatives
- of bond order prime! So we leave bond orders unchanged and
- set derivative of bond order coefficients such that
- dBO = dBOp & dBOxx = dBOxxp in Add_dBO_to_Forces */
- bo_ij->C1dbo = 1.000000;
- bo_ij->C2dbo = 0.000000;
- bo_ij->C3dbo = 0.000000;
-
- bo_ij->C1dbopi = bo_ij->BO_pi;
- bo_ij->C2dbopi = 0.000000;
- bo_ij->C3dbopi = 0.000000;
- bo_ij->C4dbopi = 0.000000;
-
- bo_ij->C1dbopi2 = bo_ij->BO_pi2;
- bo_ij->C2dbopi2 = 0.000000;
- bo_ij->C3dbopi2 = 0.000000;
- bo_ij->C4dbopi2 = 0.000000;
+ if( twbp->ovc < 0.001 && twbp->v13cor < 0.001 ) {
+ /* There is no correction to bond orders nor to derivatives
+ of bond order prime! So we leave bond orders unchanged and
+ set derivative of bond order coefficients such that
+ dBO = dBOp & dBOxx = dBOxxp in Add_dBO_to_Forces */
+ bo_ij->C1dbo = 1.000000;
+ bo_ij->C2dbo = 0.000000;
+ bo_ij->C3dbo = 0.000000;
+
+ bo_ij->C1dbopi = bo_ij->BO_pi;
+ bo_ij->C2dbopi = 0.000000;
+ bo_ij->C3dbopi = 0.000000;
+ bo_ij->C4dbopi = 0.000000;
+
+ bo_ij->C1dbopi2 = bo_ij->BO_pi2;
+ bo_ij->C2dbopi2 = 0.000000;
+ bo_ij->C3dbopi2 = 0.000000;
+ bo_ij->C4dbopi2 = 0.000000;
#ifdef TEST_FORCES
- pdbo = &(dBOs->select.dbo_list[ top_dbo ]);
-
- // compute dBO_ij/dr_i
- pdbo->wrt = i;
- rvec_Copy( pdbo->dBO, bo_ij->dBOp );
- rvec_Scale( pdbo->dBOpi, bo_ij->BO_pi, bo_ij->dln_BOp_pi );
- rvec_Scale( pdbo->dBOpi2, bo_ij->BO_pi2, bo_ij->dln_BOp_pi2);
-
- // compute dBO_ij/dr_j
- pdbo++;
- pdbo->wrt = j;
- rvec_Scale( pdbo->dBO, -1.0, bo_ij->dBOp );
- rvec_Scale( pdbo->dBOpi, -bo_ij->BO_pi, bo_ij->dln_BOp_pi );
- rvec_Scale(pdbo->dBOpi2, -bo_ij->BO_pi2, bo_ij->dln_BOp_pi2);
-
- top_dbo += 2;
+ pdbo = &(dBOs->select.dbo_list[ top_dbo ]);
+
+ // compute dBO_ij/dr_i
+ pdbo->wrt = i;
+ rvec_Copy( pdbo->dBO, bo_ij->dBOp );
+ rvec_Scale( pdbo->dBOpi, bo_ij->BO_pi, bo_ij->dln_BOp_pi );
+ rvec_Scale( pdbo->dBOpi2, bo_ij->BO_pi2, bo_ij->dln_BOp_pi2);
+
+ // compute dBO_ij/dr_j
+ pdbo++;
+ pdbo->wrt = j;
+ rvec_Scale( pdbo->dBO, -1.0, bo_ij->dBOp );
+ rvec_Scale( pdbo->dBOpi, -bo_ij->BO_pi, bo_ij->dln_BOp_pi );
+ rvec_Scale(pdbo->dBOpi2, -bo_ij->BO_pi2, bo_ij->dln_BOp_pi2);
+
+ top_dbo += 2;
#endif
- }
- else {
- val_j = system->reax_param.sbp[type_j].valency;
- Deltap_j = workspace->Deltap[j];
- Deltap_boc_j = workspace->Deltap_boc[j];
-
- /* on page 1 */
- if( twbp->ovc >= 0.001 ) {
- /* Correction for overcoordination */
- exp_p1i = exp( -p_boc1 * Deltap_i );
- exp_p2i = exp( -p_boc2 * Deltap_i );
- exp_p1j = exp( -p_boc1 * Deltap_j );
- exp_p2j = exp( -p_boc2 * Deltap_j );
-
- f2 = exp_p1i + exp_p1j;
- f3 = -1.0 / p_boc2 * log( 0.5 * ( exp_p2i + exp_p2j ) );
- f1 = 0.5 * ( ( val_i + f2 )/( val_i + f2 + f3 ) +
- ( val_j + f2 )/( val_j + f2 + f3 ) );
-
- /*fprintf( stderr,"%d %d\t%g %g j:%g %g p_boc:%g %g\n"
- "\tf:%g %g %g, exp:%g %g %g %g\n",
- i+1, j+1,
- val_i, Deltap_i, val_j, Deltap_j, p_boc1, p_boc2,
- f1, f2, f3, exp_p1i, exp_p2i, exp_p1j, exp_p2j );*/
-
- /* Now come the derivates */
- /* Bond Order pages 5-7, derivative of f1 */
- temp = f2 + f3;
- u1_ij = val_i + temp;
- u1_ji = val_j + temp;
- Cf1A_ij = 0.5 * f3 * (1.0 / SQR( u1_ij ) +
- 1.0 / SQR( u1_ji ));
- Cf1B_ij = -0.5 * (( u1_ij - f3 ) / SQR( u1_ij ) +
- ( u1_ji - f3 ) / SQR( u1_ji ));
-
- //Cf1_ij = -Cf1A_ij * p_boc1 * exp_p1i +
- // Cf1B_ij * exp_p2i / ( exp_p2i + exp_p2j );
- Cf1_ij = 0.50 * ( -p_boc1 * exp_p1i / u1_ij -
- ((val_i+f2) / SQR(u1_ij)) *
- ( -p_boc1 * exp_p1i +
- exp_p2i / ( exp_p2i + exp_p2j ) ) +
- -p_boc1 * exp_p1i / u1_ji -
- ((val_j+f2) / SQR(u1_ji)) *
- ( -p_boc1 * exp_p1i +
- exp_p2i / ( exp_p2i + exp_p2j ) ));
-
-
- Cf1_ji = -Cf1A_ij * p_boc1 * exp_p1j +
- Cf1B_ij * exp_p2j / ( exp_p2i + exp_p2j );
-
- //fprintf( stderr, "\tCf1:%g %g\n", Cf1_ij, Cf1_ji );
- }
- else {
- /* No overcoordination correction! */
- f1 = 1.0;
- Cf1_ij = Cf1_ji = 0.0;
- }
-
- if( twbp->v13cor >= 0.001 ) {
- /* Correction for 1-3 bond orders */
- exp_f4 =exp(-(twbp->p_boc4 * SQR( bo_ij->BO ) -
- Deltap_boc_i) * twbp->p_boc3 + twbp->p_boc5);
- exp_f5 =exp(-(twbp->p_boc4 * SQR( bo_ij->BO ) -
- Deltap_boc_j) * twbp->p_boc3 + twbp->p_boc5);
-
- f4 = 1. / (1. + exp_f4);
- f5 = 1. / (1. + exp_f5);
- f4f5 = f4 * f5;
-
- /* Bond Order pages 8-9, derivative of f4 and f5 */
- /*temp = twbp->p_boc5 -
- twbp->p_boc3 * twbp->p_boc4 * SQR( bo_ij->BO );
- u_ij = temp + twbp->p_boc3 * Deltap_boc_i;
- u_ji = temp + twbp->p_boc3 * Deltap_boc_j;
- Cf45_ij = Cf45( u_ij, u_ji ) / f4f5;
- Cf45_ji = Cf45( u_ji, u_ij ) / f4f5;*/
- Cf45_ij = -f4 * exp_f4;
- Cf45_ji = -f5 * exp_f5;
- }
- else {
- f4 = f5 = f4f5 = 1.0;
- Cf45_ij = Cf45_ji = 0.0;
- }
-
- /* Bond Order page 10, derivative of total bond order */
- A0_ij = f1 * f4f5;
- A1_ij = -2 * twbp->p_boc3 * twbp->p_boc4 * bo_ij->BO *
- (Cf45_ij + Cf45_ji);
- A2_ij = Cf1_ij / f1 + twbp->p_boc3 * Cf45_ij;
- A2_ji = Cf1_ji / f1 + twbp->p_boc3 * Cf45_ji;
- A3_ij = A2_ij + Cf1_ij / f1;
- A3_ji = A2_ji + Cf1_ji / f1;
-
- /*fprintf( stderr, "\tBO: %f, A0: %f, A1: %f"
- "A2_ij: %f A2_ji: %f, A3_ij: %f, A3_ji: %f\n",
- bo_ij->BO,
- A0_ij, A1_ij, A2_ij, A2_ji, A3_ij, A3_ji );*/
-
-
- /* find corrected bond orders and their derivative coef */
- bo_ij->BO = bo_ij->BO * A0_ij;
- bo_ij->BO_pi = bo_ij->BO_pi * A0_ij *f1;
- bo_ij->BO_pi2= bo_ij->BO_pi2* A0_ij *f1;
- bo_ij->BO_s = bo_ij->BO - ( bo_ij->BO_pi + bo_ij->BO_pi2 );
-
- bo_ij->C1dbo = A0_ij + bo_ij->BO * A1_ij;
- bo_ij->C2dbo = bo_ij->BO * A2_ij;
- bo_ij->C3dbo = bo_ij->BO * A2_ji;
-
- bo_ij->C1dbopi = f1*f1*f4*f5;
- bo_ij->C2dbopi = bo_ij->BO_pi * A1_ij;
- bo_ij->C3dbopi = bo_ij->BO_pi * A3_ij;
- bo_ij->C4dbopi = bo_ij->BO_pi * A3_ji;
-
- bo_ij->C1dbopi2 = f1*f1*f4*f5;
- bo_ij->C2dbopi2 = bo_ij->BO_pi2 * A1_ij;
- bo_ij->C3dbopi2 = bo_ij->BO_pi2 * A3_ij;
- bo_ij->C4dbopi2 = bo_ij->BO_pi2 * A3_ji;
+ }
+ else {
+ val_j = system->reax_param.sbp[type_j].valency;
+ Deltap_j = workspace->Deltap[j];
+ Deltap_boc_j = workspace->Deltap_boc[j];
+
+ /* on page 1 */
+ if( twbp->ovc >= 0.001 ) {
+ /* Correction for overcoordination */
+ exp_p1i = exp( -p_boc1 * Deltap_i );
+ exp_p2i = exp( -p_boc2 * Deltap_i );
+ exp_p1j = exp( -p_boc1 * Deltap_j );
+ exp_p2j = exp( -p_boc2 * Deltap_j );
+
+ f2 = exp_p1i + exp_p1j;
+ f3 = -1.0 / p_boc2 * log( 0.5 * ( exp_p2i + exp_p2j ) );
+ f1 = 0.5 * ( ( val_i + f2 )/( val_i + f2 + f3 ) +
+ ( val_j + f2 )/( val_j + f2 + f3 ) );
+
+ /*fprintf( stderr,"%d %d\t%g %g j:%g %g p_boc:%g %g\n"
+ "\tf:%g %g %g, exp:%g %g %g %g\n",
+ i+1, j+1,
+ val_i, Deltap_i, val_j, Deltap_j, p_boc1, p_boc2,
+ f1, f2, f3, exp_p1i, exp_p2i, exp_p1j, exp_p2j );*/
+
+ /* Now come the derivates */
+ /* Bond Order pages 5-7, derivative of f1 */
+ temp = f2 + f3;
+ u1_ij = val_i + temp;
+ u1_ji = val_j + temp;
+ Cf1A_ij = 0.5 * f3 * (1.0 / SQR( u1_ij ) +
+ 1.0 / SQR( u1_ji ));
+ Cf1B_ij = -0.5 * (( u1_ij - f3 ) / SQR( u1_ij ) +
+ ( u1_ji - f3 ) / SQR( u1_ji ));
+
+ //Cf1_ij = -Cf1A_ij * p_boc1 * exp_p1i +
+ // Cf1B_ij * exp_p2i / ( exp_p2i + exp_p2j );
+ Cf1_ij = 0.50 * ( -p_boc1 * exp_p1i / u1_ij -
+ ((val_i+f2) / SQR(u1_ij)) *
+ ( -p_boc1 * exp_p1i +
+ exp_p2i / ( exp_p2i + exp_p2j ) ) +
+ -p_boc1 * exp_p1i / u1_ji -
+ ((val_j+f2) / SQR(u1_ji)) *
+ ( -p_boc1 * exp_p1i +
+ exp_p2i / ( exp_p2i + exp_p2j ) ));
+
+
+ Cf1_ji = -Cf1A_ij * p_boc1 * exp_p1j +
+ Cf1B_ij * exp_p2j / ( exp_p2i + exp_p2j );
+
+ //fprintf( stderr, "\tCf1:%g %g\n", Cf1_ij, Cf1_ji );
+ }
+ else {
+ /* No overcoordination correction! */
+ f1 = 1.0;
+ Cf1_ij = Cf1_ji = 0.0;
+ }
+
+ if( twbp->v13cor >= 0.001 ) {
+ /* Correction for 1-3 bond orders */
+ exp_f4 =exp(-(twbp->p_boc4 * SQR( bo_ij->BO ) -
+ Deltap_boc_i) * twbp->p_boc3 + twbp->p_boc5);
+ exp_f5 =exp(-(twbp->p_boc4 * SQR( bo_ij->BO ) -
+ Deltap_boc_j) * twbp->p_boc3 + twbp->p_boc5);
+
+ f4 = 1. / (1. + exp_f4);
+ f5 = 1. / (1. + exp_f5);
+ f4f5 = f4 * f5;
+
+ /* Bond Order pages 8-9, derivative of f4 and f5 */
+ /*temp = twbp->p_boc5 -
+ twbp->p_boc3 * twbp->p_boc4 * SQR( bo_ij->BO );
+ u_ij = temp + twbp->p_boc3 * Deltap_boc_i;
+ u_ji = temp + twbp->p_boc3 * Deltap_boc_j;
+ Cf45_ij = Cf45( u_ij, u_ji ) / f4f5;
+ Cf45_ji = Cf45( u_ji, u_ij ) / f4f5;*/
+ Cf45_ij = -f4 * exp_f4;
+ Cf45_ji = -f5 * exp_f5;
+ }
+ else {
+ f4 = f5 = f4f5 = 1.0;
+ Cf45_ij = Cf45_ji = 0.0;
+ }
+
+ /* Bond Order page 10, derivative of total bond order */
+ A0_ij = f1 * f4f5;
+ A1_ij = -2 * twbp->p_boc3 * twbp->p_boc4 * bo_ij->BO *
+ (Cf45_ij + Cf45_ji);
+ A2_ij = Cf1_ij / f1 + twbp->p_boc3 * Cf45_ij;
+ A2_ji = Cf1_ji / f1 + twbp->p_boc3 * Cf45_ji;
+ A3_ij = A2_ij + Cf1_ij / f1;
+ A3_ji = A2_ji + Cf1_ji / f1;
+
+ /*fprintf( stderr, "\tBO: %f, A0: %f, A1: %f"
+ "A2_ij: %f A2_ji: %f, A3_ij: %f, A3_ji: %f\n",
+ bo_ij->BO,
+ A0_ij, A1_ij, A2_ij, A2_ji, A3_ij, A3_ji );*/
+
+
+ /* find corrected bond orders and their derivative coef */
+ bo_ij->BO = bo_ij->BO * A0_ij;
+ bo_ij->BO_pi = bo_ij->BO_pi * A0_ij *f1;
+ bo_ij->BO_pi2= bo_ij->BO_pi2* A0_ij *f1;
+ bo_ij->BO_s = bo_ij->BO - ( bo_ij->BO_pi + bo_ij->BO_pi2 );
+
+ bo_ij->C1dbo = A0_ij + bo_ij->BO * A1_ij;
+ bo_ij->C2dbo = bo_ij->BO * A2_ij;
+ bo_ij->C3dbo = bo_ij->BO * A2_ji;
+
+ bo_ij->C1dbopi = f1*f1*f4*f5;
+ bo_ij->C2dbopi = bo_ij->BO_pi * A1_ij;
+ bo_ij->C3dbopi = bo_ij->BO_pi * A3_ij;
+ bo_ij->C4dbopi = bo_ij->BO_pi * A3_ji;
+
+ bo_ij->C1dbopi2 = f1*f1*f4*f5;
+ bo_ij->C2dbopi2 = bo_ij->BO_pi2 * A1_ij;
+ bo_ij->C3dbopi2 = bo_ij->BO_pi2 * A3_ij;
+ bo_ij->C4dbopi2 = bo_ij->BO_pi2 * A3_ji;
#ifdef TEST_FORCES
- Calculate_dBO( i, pj, workspace, lists, &top_dbo );
+ Calculate_dBO( i, pj, workspace, lists, &top_dbo );
#endif
- }
-
- /* neglect bonds that are < 1e-10 */
- if( bo_ij->BO < 1e-10 )
- bo_ij->BO = 0.0;
- if( bo_ij->BO_s < 1e-10 )
- bo_ij->BO_s = 0.0;
- if( bo_ij->BO_pi < 1e-10 )
- bo_ij->BO_pi = 0.0;
- if( bo_ij->BO_pi2 < 1e-10 )
- bo_ij->BO_pi2 = 0.0;
-
- workspace->total_bond_order[i] += bo_ij->BO; //now keeps total_BO
-
-
- /* fprintf( stderr, "%d %d\t%g %g %g %g\n"
- "Cdbo:\t%g %g %g\n"
- "Cdbopi:\t%g %g %g %g\n"
- "Cdbopi2:%g %g %g %g\n\n",
- i+1, j+1,
- bonds->select.bond_list[ pj ].d,
- bo_ij->BO,bo_ij->BO_pi, bo_ij->BO_pi2,
- bo_ij->C1dbo, bo_ij->C2dbo, bo_ij->C3dbo,
- bo_ij->C1dbopi, bo_ij->C2dbopi,
- bo_ij->C3dbopi, bo_ij->C4dbopi,
- bo_ij->C1dbopi2,bo_ij->C2dbopi2,
- bo_ij->C3dbopi2, bo_ij->C4dbopi2 ); */
-
- /* fprintf( stderr, "%d %d BO:%f BO_s:%f BO_pi:%f BO_pi2:%f\n",
- i+1,j+1,bo_ij->BO,bo_ij->BO_s,bo_ij->BO_pi,bo_ij->BO_pi2 );*/
+ }
+
+ /* neglect bonds that are < 1e-10 */
+ if( bo_ij->BO < 1e-10 )
+ bo_ij->BO = 0.0;
+ if( bo_ij->BO_s < 1e-10 )
+ bo_ij->BO_s = 0.0;
+ if( bo_ij->BO_pi < 1e-10 )
+ bo_ij->BO_pi = 0.0;
+ if( bo_ij->BO_pi2 < 1e-10 )
+ bo_ij->BO_pi2 = 0.0;
+
+ workspace->total_bond_order[i] += bo_ij->BO; //now keeps total_BO
+
+
+ /* fprintf( stderr, "%d %d\t%g %g %g %g\n"
+ "Cdbo:\t%g %g %g\n"
+ "Cdbopi:\t%g %g %g %g\n"
+ "Cdbopi2:%g %g %g %g\n\n",
+ i+1, j+1,
+ bonds->select.bond_list[ pj ].d,
+ bo_ij->BO,bo_ij->BO_pi, bo_ij->BO_pi2,
+ bo_ij->C1dbo, bo_ij->C2dbo, bo_ij->C3dbo,
+ bo_ij->C1dbopi, bo_ij->C2dbopi,
+ bo_ij->C3dbopi, bo_ij->C4dbopi,
+ bo_ij->C1dbopi2,bo_ij->C2dbopi2,
+ bo_ij->C3dbopi2, bo_ij->C4dbopi2 ); */
+
+ /* fprintf( stderr, "%d %d BO:%f BO_s:%f BO_pi:%f BO_pi2:%f\n",
+ i+1,j+1,bo_ij->BO,bo_ij->BO_s,bo_ij->BO_pi,bo_ij->BO_pi2 );*/
#ifdef TEST_FORCES
- Set_End_Index( pj, top_dbo, dBOs );
- Add_dBO( system, lists, i, pj, 1.0, workspace->dDelta );
+ Set_End_Index( pj, top_dbo, dBOs );
+ Add_dBO( system, lists, i, pj, 1.0, workspace->dDelta );
#endif
}
else {
- /* We only need to update bond orders from bo_ji
- everything else is set in uncorrected_bo calculations */
- sym_index = bonds->select.bond_list[pj].sym_index;
- bo_ji = &(bonds->select.bond_list[ sym_index ].bo_data);
- bo_ij->BO = bo_ji->BO;
- bo_ij->BO_s = bo_ji->BO_s;
- bo_ij->BO_pi = bo_ji->BO_pi;
- bo_ij->BO_pi2 = bo_ji->BO_pi2;
-
- workspace->total_bond_order[i] += bo_ij->BO;// now keeps total_BO
+ /* We only need to update bond orders from bo_ji
+ everything else is set in uncorrected_bo calculations */
+ sym_index = bonds->select.bond_list[pj].sym_index;
+ bo_ji = &(bonds->select.bond_list[ sym_index ].bo_data);
+ bo_ij->BO = bo_ji->BO;
+ bo_ij->BO_s = bo_ji->BO_s;
+ bo_ij->BO_pi = bo_ji->BO_pi;
+ bo_ij->BO_pi2 = bo_ji->BO_pi2;
+
+ workspace->total_bond_order[i] += bo_ij->BO;// now keeps total_BO
#ifdef TEST_FORCES
- Add_dBO( system, lists, j, sym_index, 1.0, workspace->dDelta );
+ Add_dBO( system, lists, j, sym_index, 1.0, workspace->dDelta );
#endif
- }
+ }
}
-#ifdef TEST_FORCES
+#ifdef TEST_FORCES
// fprintf( stderr, "dDelta computations\nj:" );
Set_Start_Index( i, top_dDelta, dDeltas );
ptop_dDelta = &( dDeltas->select.dDelta_list[top_dDelta] );
@@ -1101,22 +1101,22 @@ void BO( reax_system *system, control_params *control, simulation_data *data,
// fprintf( stderr, "%d ", j );
if( !rvec_isZero( workspace->dDelta[j] ) ) {
- ptop_dDelta->wrt = j;
- rvec_Copy( ptop_dDelta->dVal, workspace->dDelta[j] );
- rvec_MakeZero( workspace->dDelta[j] );
- ++top_dDelta, ++ptop_dDelta;
+ ptop_dDelta->wrt = j;
+ rvec_Copy( ptop_dDelta->dVal, workspace->dDelta[j] );
+ rvec_MakeZero( workspace->dDelta[j] );
+ ++top_dDelta, ++ptop_dDelta;
}
-
+
start_j = Start_Index(j, bonds);
- end_j = End_Index(j, bonds);
+ end_j = End_Index(j, bonds);
for( pk = start_j; pk < end_j; ++pk ) {
- k = bonds->select.bond_list[pk].nbr;
- if( !rvec_isZero( workspace->dDelta[k] ) ) {
- ptop_dDelta->wrt = k;
- rvec_Copy( ptop_dDelta->dVal, workspace->dDelta[k] );
- rvec_MakeZero( workspace->dDelta[k] );
- ++top_dDelta, ++ptop_dDelta;
- }
+ k = bonds->select.bond_list[pk].nbr;
+ if( !rvec_isZero( workspace->dDelta[k] ) ) {
+ ptop_dDelta->wrt = k;
+ rvec_Copy( ptop_dDelta->dVal, workspace->dDelta[k] );
+ rvec_MakeZero( workspace->dDelta[k] );
+ ++top_dDelta, ++ptop_dDelta;
+ }
}
}
@@ -1125,8 +1125,8 @@ void BO( reax_system *system, control_params *control, simulation_data *data,
/*for(pj = Start_Index(i,dDeltas); pj < End_Index(i,dDeltas); ++pj)
fprintf( stdout, "dDel: %d %d [%g %g %g]\n",
i+1, dDeltas->select.dDelta_list[pj].wrt+1,
- dDeltas->select.dDelta_list[pj].dVal[0],
- dDeltas->select.dDelta_list[pj].dVal[1],
+ dDeltas->select.dDelta_list[pj].dVal[0],
+ dDeltas->select.dDelta_list[pj].dVal[1],
dDeltas->select.dDelta_list[pj].dVal[2] );*/
#endif
}
@@ -1143,7 +1143,7 @@ void BO( reax_system *system, control_params *control, simulation_data *data,
for( j = 0; j < system->N; ++j ){
type_j = system->my_atoms[j].type;
sbp_j = &(system->reax_param.sbp[ type_j ]);
-
+
workspace->Delta[j] = workspace->total_bond_order[j] - sbp_j->valency;
workspace->Delta_e[j] = workspace->total_bond_order[j] - sbp_j->valency_e;
workspace->Delta_boc[j] = workspace->total_bond_order[j] -
@@ -1151,8 +1151,8 @@ void BO( reax_system *system, control_params *control, simulation_data *data,
workspace->Delta_val[j] = workspace->total_bond_order[j] -
sbp_j->valency_val;
- workspace->vlpex[j] = workspace->Delta_e[j] -
- 2.0 * (int)(workspace->Delta_e[j]/2.0);
+ workspace->vlpex[j] = workspace->Delta_e[j] -
+ 2.0 * (int)(workspace->Delta_e[j]/2.0);
explp1 = exp(-p_lp1 * SQR(2.0 + workspace->vlpex[j]));
workspace->nlp[j] = explp1 - (int)(workspace->Delta_e[j] / 2.0);
workspace->Delta_lp[j] = sbp_j->nlp_opt - workspace->nlp[j];
@@ -1179,7 +1179,7 @@ void BO( reax_system *system, control_params *control, simulation_data *data,
//workspace->nlp[j], system->reaxprm.sbp[type_j].nlp_opt,
//workspace->Delta_lp[j], workspace->Clp[j], workspace->dDelta_lp[j] );
- //fprintf( stdout, "%d(%d) %24.15f\n",
+ //fprintf( stdout, "%d(%d) %24.15f\n",
// j, workspace->bond_mark[j], workspace->total_bond_order[j] );
}
@@ -1204,15 +1204,15 @@ int Locate_Symmetric_Bond( reax_list *bonds, int i, int j )
int mid_nbr;
while( (mid_nbr = bonds->select.bond_list[mid].nbr) != j ) {
- /*fprintf( stderr, "\tstart: %d end: %d mid: %d\n",
+ /*fprintf( stderr, "\tstart: %d end: %d mid: %d\n",
start, end, mid );*/
if( mid_nbr < j )
start = mid+1;
else end = mid - 1;
-
+
mid = (start + end) / 2;
}
-
+
return mid;
}
diff --git a/src/USER-REAXC/reaxc_bond_orders.h b/src/USER-REAXC/reaxc_bond_orders.h
index 8ca9b8b2374d9e0407686047edda30eb2bd34367..0912a936d6d7e5c56474093bf2d21073b3add147 100644
--- a/src/USER-REAXC/reaxc_bond_orders.h
+++ b/src/USER-REAXC/reaxc_bond_orders.h
@@ -14,12 +14,12 @@
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -38,26 +38,26 @@ typedef struct{
#ifdef TEST_FORCES
void Get_dBO( reax_system*, reax_list**, int, int, real, rvec* );
-void Get_dBOpinpi2( reax_system*, reax_list**,
- int, int, real, real, rvec*, rvec* );
+void Get_dBOpinpi2( reax_system*, reax_list**,
+ int, int, real, real, rvec*, rvec* );
void Add_dBO( reax_system*, reax_list**, int, int, real, rvec* );
-void Add_dBOpinpi2( reax_system*, reax_list**,
- int, int, real, real, rvec*, rvec* );
+void Add_dBOpinpi2( reax_system*, reax_list**,
+ int, int, real, real, rvec*, rvec* );
void Add_dBO_to_Forces( reax_system*, reax_list**, int, int, real );
-void Add_dBOpinpi2_to_Forces( reax_system*, reax_list**,
- int, int, real, real );
+void Add_dBOpinpi2_to_Forces( reax_system*, reax_list**,
+ int, int, real, real );
void Add_dDelta( reax_system*, reax_list**, int, real, rvec* );
void Add_dDelta_to_Forces( reax_system *, reax_list**, int, real );
#endif
void Add_dBond_to_Forces( reax_system*, int, int, storage*, reax_list** );
-void Add_dBond_to_Forces_NPT( int, int, simulation_data*,
- storage*, reax_list** );
+void Add_dBond_to_Forces_NPT( int, int, simulation_data*,
+ storage*, reax_list** );
int BOp(storage*, reax_list*, real, int, int, far_neighbor_data*,
- single_body_parameters*, single_body_parameters*, two_body_parameters*);
+ single_body_parameters*, single_body_parameters*, two_body_parameters*);
void BO( reax_system*, control_params*, simulation_data*,
- storage*, reax_list**, output_controls* );
+ storage*, reax_list**, output_controls* );
#endif
diff --git a/src/USER-REAXC/reaxc_bonds.cpp b/src/USER-REAXC/reaxc_bonds.cpp
index 44185279926a679ad171630c1839e2338874ff00..45b493237fda1da680952f5de61fa690a5e472d8 100644
--- a/src/USER-REAXC/reaxc_bonds.cpp
+++ b/src/USER-REAXC/reaxc_bonds.cpp
@@ -14,12 +14,12 @@
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -40,9 +40,9 @@
#endif
-void Bonds( reax_system *system, control_params *control,
- simulation_data *data, storage *workspace, reax_list **lists,
- output_controls *out_control )
+void Bonds( reax_system *system, control_params *control,
+ simulation_data *data, storage *workspace, reax_list **lists,
+ output_controls *out_control )
{
int i, j, pj, natoms;
int start_i, end_i;
@@ -70,91 +70,91 @@ void Bonds( reax_system *system, control_params *control,
for( pj = start_i; pj < end_i; ++pj ) {
j = bonds->select.bond_list[pj].nbr;
-
+
if( system->my_atoms[i].orig_id <= system->my_atoms[j].orig_id ) {
- /* set the pointers */
- type_i = system->my_atoms[i].type;
- type_j = system->my_atoms[j].type;
- sbp_i = &( system->reax_param.sbp[type_i] );
- sbp_j = &( system->reax_param.sbp[type_j] );
- twbp = &( system->reax_param.tbp[type_i][type_j] );
- bo_ij = &( bonds->select.bond_list[pj].bo_data );
-
- /* calculate the constants */
- pow_BOs_be2 = pow( bo_ij->BO_s, twbp->p_be2 );
- exp_be12 = exp( twbp->p_be1 * ( 1.0 - pow_BOs_be2 ) );
- CEbo = -twbp->De_s * exp_be12 *
- ( 1.0 - twbp->p_be1 * twbp->p_be2 * pow_BOs_be2 );
-
- /* calculate the Bond Energy */
- data->my_en.e_bond += ebond =
- -twbp->De_s * bo_ij->BO_s * exp_be12
- -twbp->De_p * bo_ij->BO_pi
- -twbp->De_pp * bo_ij->BO_pi2;
-
- /* tally into per-atom energy */
+ /* set the pointers */
+ type_i = system->my_atoms[i].type;
+ type_j = system->my_atoms[j].type;
+ sbp_i = &( system->reax_param.sbp[type_i] );
+ sbp_j = &( system->reax_param.sbp[type_j] );
+ twbp = &( system->reax_param.tbp[type_i][type_j] );
+ bo_ij = &( bonds->select.bond_list[pj].bo_data );
+
+ /* calculate the constants */
+ pow_BOs_be2 = pow( bo_ij->BO_s, twbp->p_be2 );
+ exp_be12 = exp( twbp->p_be1 * ( 1.0 - pow_BOs_be2 ) );
+ CEbo = -twbp->De_s * exp_be12 *
+ ( 1.0 - twbp->p_be1 * twbp->p_be2 * pow_BOs_be2 );
+
+ /* calculate the Bond Energy */
+ data->my_en.e_bond += ebond =
+ -twbp->De_s * bo_ij->BO_s * exp_be12
+ -twbp->De_p * bo_ij->BO_pi
+ -twbp->De_pp * bo_ij->BO_pi2;
+
+ /* tally into per-atom energy */
if( system->pair_ptr->evflag)
system->pair_ptr->ev_tally(i,j,natoms,1,ebond,0.0,0.0,0.0,0.0,0.0);
-
- /* calculate derivatives of Bond Orders */
- bo_ij->Cdbo += CEbo;
- bo_ij->Cdbopi -= (CEbo + twbp->De_p);
- bo_ij->Cdbopi2 -= (CEbo + twbp->De_pp);
-
+
+ /* calculate derivatives of Bond Orders */
+ bo_ij->Cdbo += CEbo;
+ bo_ij->Cdbopi -= (CEbo + twbp->De_p);
+ bo_ij->Cdbopi2 -= (CEbo + twbp->De_pp);
+
#ifdef TEST_ENERGY
- //fprintf( out_control->ebond, "%6d%6d%24.15e%24.15e%24.15e\n",
- fprintf( out_control->ebond, "%6d%6d%12.4f%12.4f%12.4f\n",
- system->my_atoms[i].orig_id,
- system->my_atoms[j].orig_id,
- bo_ij->BO, ebond, data->my_en.e_bond );
+ //fprintf( out_control->ebond, "%6d%6d%24.15e%24.15e%24.15e\n",
+ fprintf( out_control->ebond, "%6d%6d%12.4f%12.4f%12.4f\n",
+ system->my_atoms[i].orig_id,
+ system->my_atoms[j].orig_id,
+ bo_ij->BO, ebond, data->my_en.e_bond );
#endif
#ifdef TEST_FORCES
- Add_dBO( system, lists, i, pj, CEbo, workspace->f_be );
- Add_dBOpinpi2( system, lists, i, pj,
- -(CEbo + twbp->De_p), -(CEbo + twbp->De_pp),
- workspace->f_be, workspace->f_be );
+ Add_dBO( system, lists, i, pj, CEbo, workspace->f_be );
+ Add_dBOpinpi2( system, lists, i, pj,
+ -(CEbo + twbp->De_p), -(CEbo + twbp->De_pp),
+ workspace->f_be, workspace->f_be );
#endif
- /* Stabilisation terminal triple bond */
- if( bo_ij->BO >= 1.00 ) {
- if( gp37 == 2 ||
- (sbp_i->mass == 12.0000 && sbp_j->mass == 15.9990) ||
- (sbp_j->mass == 12.0000 && sbp_i->mass == 15.9990) ) {
- exphu = exp( -gp7 * SQR(bo_ij->BO - 2.50) );
- exphua1 = exp(-gp3 * (workspace->total_bond_order[i]-bo_ij->BO));
- exphub1 = exp(-gp3 * (workspace->total_bond_order[j]-bo_ij->BO));
- exphuov = exp(gp4 * (workspace->Delta[i] + workspace->Delta[j]));
- hulpov = 1.0 / (1.0 + 25.0 * exphuov);
-
- estriph = gp10 * exphu * hulpov * (exphua1 + exphub1);
- data->my_en.e_bond += estriph;
-
- decobdbo = gp10 * exphu * hulpov * (exphua1 + exphub1) *
- ( gp3 - 2.0 * gp7 * (bo_ij->BO-2.50) );
- decobdboua = -gp10 * exphu * hulpov *
- (gp3*exphua1 + 25.0*gp4*exphuov*hulpov*(exphua1+exphub1));
- decobdboub = -gp10 * exphu * hulpov *
- (gp3*exphub1 + 25.0*gp4*exphuov*hulpov*(exphua1+exphub1));
-
- /* tally into per-atom energy */
- if( system->pair_ptr->evflag)
- system->pair_ptr->ev_tally(i,j,natoms,1,estriph,0.0,0.0,0.0,0.0,0.0);
-
- bo_ij->Cdbo += decobdbo;
- workspace->CdDelta[i] += decobdboua;
- workspace->CdDelta[j] += decobdboub;
+ /* Stabilisation terminal triple bond */
+ if( bo_ij->BO >= 1.00 ) {
+ if( gp37 == 2 ||
+ (sbp_i->mass == 12.0000 && sbp_j->mass == 15.9990) ||
+ (sbp_j->mass == 12.0000 && sbp_i->mass == 15.9990) ) {
+ exphu = exp( -gp7 * SQR(bo_ij->BO - 2.50) );
+ exphua1 = exp(-gp3 * (workspace->total_bond_order[i]-bo_ij->BO));
+ exphub1 = exp(-gp3 * (workspace->total_bond_order[j]-bo_ij->BO));
+ exphuov = exp(gp4 * (workspace->Delta[i] + workspace->Delta[j]));
+ hulpov = 1.0 / (1.0 + 25.0 * exphuov);
+
+ estriph = gp10 * exphu * hulpov * (exphua1 + exphub1);
+ data->my_en.e_bond += estriph;
+
+ decobdbo = gp10 * exphu * hulpov * (exphua1 + exphub1) *
+ ( gp3 - 2.0 * gp7 * (bo_ij->BO-2.50) );
+ decobdboua = -gp10 * exphu * hulpov *
+ (gp3*exphua1 + 25.0*gp4*exphuov*hulpov*(exphua1+exphub1));
+ decobdboub = -gp10 * exphu * hulpov *
+ (gp3*exphub1 + 25.0*gp4*exphuov*hulpov*(exphua1+exphub1));
+
+ /* tally into per-atom energy */
+ if( system->pair_ptr->evflag)
+ system->pair_ptr->ev_tally(i,j,natoms,1,estriph,0.0,0.0,0.0,0.0,0.0);
+
+ bo_ij->Cdbo += decobdbo;
+ workspace->CdDelta[i] += decobdboua;
+ workspace->CdDelta[j] += decobdboub;
#ifdef TEST_ENERGY
- //fprintf( out_control->ebond,
- // "%6d%6d%24.15e%24.15e%24.15e%24.15e\n",
- // system->my_atoms[i].orig_id, system->my_atoms[j].orig_id,
- // estriph, decobdbo, decobdboua, decobdboub );
+ //fprintf( out_control->ebond,
+ // "%6d%6d%24.15e%24.15e%24.15e%24.15e\n",
+ // system->my_atoms[i].orig_id, system->my_atoms[j].orig_id,
+ // estriph, decobdbo, decobdboua, decobdboub );
#endif
#ifdef TEST_FORCES
- Add_dBO( system, lists, i, pj, decobdbo, workspace->f_be );
- Add_dDelta( system, lists, i, decobdboua, workspace->f_be );
- Add_dDelta( system, lists, j, decobdboub, workspace->f_be );
+ Add_dBO( system, lists, i, pj, decobdbo, workspace->f_be );
+ Add_dDelta( system, lists, i, decobdboua, workspace->f_be );
+ Add_dDelta( system, lists, j, decobdboub, workspace->f_be );
#endif
- }
- }
+ }
+ }
}
}
}
diff --git a/src/USER-REAXC/reaxc_bonds.h b/src/USER-REAXC/reaxc_bonds.h
index 5a911cb21a7f5e1d23160adab18842ec1e8ea507..a4a1fb0b44eadbf396da8a4f4cfec0267a86c071 100644
--- a/src/USER-REAXC/reaxc_bonds.h
+++ b/src/USER-REAXC/reaxc_bonds.h
@@ -14,12 +14,12 @@
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -29,6 +29,6 @@
#include "reaxc_types.h"
-void Bonds( reax_system*, control_params*, simulation_data*,
- storage*, reax_list**, output_controls* );
+void Bonds( reax_system*, control_params*, simulation_data*,
+ storage*, reax_list**, output_controls* );
#endif
diff --git a/src/USER-REAXC/reaxc_control.cpp b/src/USER-REAXC/reaxc_control.cpp
index 3a2585744a94f397696f823cda1d1419dd84bc9e..40690175041fab50e48a37be33b7ab6832a50087 100644
--- a/src/USER-REAXC/reaxc_control.cpp
+++ b/src/USER-REAXC/reaxc_control.cpp
@@ -14,12 +14,12 @@
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -34,8 +34,8 @@
#endif
-char Read_Control_File( char *control_file, control_params* control,
- output_controls *out_control )
+char Read_Control_File( char *control_file, control_params* control,
+ output_controls *out_control )
{
FILE *fp;
char *s, **tmp;
@@ -131,7 +131,7 @@ char Read_Control_File( char *control_file, control_params* control,
ival = atoi(tmp[1]);
control->ensemble = ival;
if( ival == iNPT || ival ==sNPT || ival == NPT )
- control->virial = 1;
+ control->virial = 1;
}
else if( strcmp(tmp[0], "nsteps") == 0 ) {
ival = atoi(tmp[1]);
@@ -150,7 +150,7 @@ char Read_Control_File( char *control_file, control_params* control,
control->procs_by_dim[2] = ival;
control->nprocs = control->procs_by_dim[0]*control->procs_by_dim[1]*
- control->procs_by_dim[2];
+ control->procs_by_dim[2];
}
//else if( strcmp(tmp[0], "restart") == 0 ) {
// ival = atoi(tmp[1]);
@@ -203,15 +203,15 @@ char Read_Control_File( char *control_file, control_params* control,
val = atof(tmp[1]);
control->bond_cut = val;
}
- else if( strcmp(tmp[0], "bond_graph_cutoff") == 0 ) {
+ else if( strcmp(tmp[0], "bond_graph_cutoff") == 0 ) {
val = atof(tmp[1]);
control->bg_cut = val;
}
- else if( strcmp(tmp[0], "thb_cutoff") == 0 ) {
+ else if( strcmp(tmp[0], "thb_cutoff") == 0 ) {
val = atof(tmp[1]);
control->thb_cut = val;
}
- else if( strcmp(tmp[0], "thb_cutoff_sq") == 0 ) {
+ else if( strcmp(tmp[0], "thb_cutoff_sq") == 0 ) {
val = atof(tmp[1]);
control->thb_cutsq = val;
}
@@ -246,16 +246,16 @@ char Read_Control_File( char *control_file, control_params* control,
else if( strcmp(tmp[0], "temp_init") == 0 ) {
val = atof(tmp[1]);
control->T_init = val;
-
+
if( control->T_init < 0.1 )
- control->T_init = 0.1;
+ control->T_init = 0.1;
}
else if( strcmp(tmp[0], "temp_final") == 0 ) {
val = atof(tmp[1]);
control->T_final = val;
-
+
if( control->T_final < 0.1 )
- control->T_final = 0.1;
+ control->T_final = 0.1;
}
else if( strcmp(tmp[0], "t_mass") == 0 ) {
val = atof(tmp[1]);
@@ -275,30 +275,30 @@ char Read_Control_File( char *control_file, control_params* control,
}
else if( strcmp(tmp[0], "pressure") == 0 ) {
if( control->ensemble == iNPT ) {
- control->P[0] = control->P[1] = control->P[2] = atof(tmp[1]);
+ control->P[0] = control->P[1] = control->P[2] = atof(tmp[1]);
}
else if( control->ensemble == sNPT ) {
- control->P[0] = atof(tmp[1]);
- control->P[1] = atof(tmp[2]);
- control->P[2] = atof(tmp[3]);
+ control->P[0] = atof(tmp[1]);
+ control->P[1] = atof(tmp[2]);
+ control->P[2] = atof(tmp[3]);
}
}
else if( strcmp(tmp[0], "p_mass") == 0 ) {
// convert p_mass from fs to ps
if( control->ensemble == iNPT ) {
- control->Tau_P[0] = control->Tau_P[1] = control->Tau_P[2] =
- atof(tmp[1]) * 1.e-3;
+ control->Tau_P[0] = control->Tau_P[1] = control->Tau_P[2] =
+ atof(tmp[1]) * 1.e-3;
}
else if( control->ensemble == sNPT ) {
- control->Tau_P[0] = atof(tmp[1]) * 1.e-3;
- control->Tau_P[1] = atof(tmp[2]) * 1.e-3;
- control->Tau_P[2] = atof(tmp[3]) * 1.e-3;
+ control->Tau_P[0] = atof(tmp[1]) * 1.e-3;
+ control->Tau_P[1] = atof(tmp[2]) * 1.e-3;
+ control->Tau_P[2] = atof(tmp[3]) * 1.e-3;
}
}
else if( strcmp(tmp[0], "pt_mass") == 0 ) {
val = atof(tmp[1]);
- control->Tau_PT[0] = control->Tau_PT[1] = control->Tau_PT[2] =
- val * 1.e-3; // convert pt_mass from fs to ps
+ control->Tau_PT[0] = control->Tau_PT[1] = control->Tau_PT[2] =
+ val * 1.e-3; // convert pt_mass from fs to ps
}
else if( strcmp(tmp[0], "compress") == 0 ) {
val = atof(tmp[1]);
@@ -307,7 +307,7 @@ char Read_Control_File( char *control_file, control_params* control,
else if( strcmp(tmp[0], "press_mode") == 0 ) {
ival = atoi(tmp[1]);
control->press_mode = ival;
- }
+ }
else if( strcmp(tmp[0], "geo_format") == 0 ) {
ival = atoi( tmp[1] );
control->geo_format = ival;
@@ -351,10 +351,10 @@ char Read_Control_File( char *control_file, control_params* control,
ival = atoi(tmp[1]);
control->molecular_analysis = ival;
}
- else if( strcmp(tmp[0], "ignore") == 0 ) {
+ else if( strcmp(tmp[0], "ignore") == 0 ) {
control->num_ignored = atoi(tmp[1]);
for( i = 0; i < control->num_ignored; ++i )
- control->ignore[atoi(tmp[i+2])] = 1;
+ control->ignore[atoi(tmp[i+2])] = 1;
}
else if( strcmp(tmp[0], "dipole_anal") == 0 ) {
ival = atoi(tmp[1]);
diff --git a/src/USER-REAXC/reaxc_control.h b/src/USER-REAXC/reaxc_control.h
index f453ed5e606ad6a8b684bd1910734599af03187e..b2b455d6b8feca32c8bdfedf4d20454b2f8f2998 100644
--- a/src/USER-REAXC/reaxc_control.h
+++ b/src/USER-REAXC/reaxc_control.h
@@ -14,12 +14,12 @@
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
diff --git a/src/USER-REAXC/reaxc_defs.h b/src/USER-REAXC/reaxc_defs.h
index 1cc3106bbd653198b4cd17e65ddc05cb2c965fb3..33eb8dc170b9fda9ba547f58a43073a0013b91af 100644
--- a/src/USER-REAXC/reaxc_defs.h
+++ b/src/USER-REAXC/reaxc_defs.h
@@ -14,12 +14,12 @@
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -64,7 +64,7 @@
#define CAL_to_JOULES 4.184000 // CALories --> JOULES
#define JOULES_to_CAL 1/4.184000 // JOULES --> CALories
#define AMU_to_GRAM 1.6605e-24
-#define ANG_to_CM 1e-8
+#define ANG_to_CM 1e-8
#define AVOGNR 6.0221367e23
#define P_CONV 1e-24 * AVOGNR * JOULES_to_CAL
@@ -79,7 +79,7 @@
#define MAX_ATOM_TYPES 25
#define NUM_INTRS 10
-#define ALMOST_ZERO 1e-10
+#define ALMOST_ZERO 1e-10
#define NEG_INF -1e10
#define NO_BOND 1e-3 // 0.001
#define HB_THRESHOLD 1e-2 // 0.01
@@ -122,30 +122,30 @@ enum restart_formats { WRITE_ASCII, WRITE_BINARY, RF_N };
enum ensembles { NVE, bNVT, nhNVT, sNPT, iNPT, NPT, ens_N };
-enum lists { BONDS, OLD_BONDS, THREE_BODIES,
- HBONDS, FAR_NBRS, DBOS, DDELTAS, LIST_N };
+enum lists { BONDS, OLD_BONDS, THREE_BODIES,
+ HBONDS, FAR_NBRS, DBOS, DDELTAS, LIST_N };
-enum interactions { TYP_VOID, TYP_BOND, TYP_THREE_BODY,
- TYP_HBOND, TYP_FAR_NEIGHBOR, TYP_DBO, TYP_DDELTA, TYP_N };
+enum interactions { TYP_VOID, TYP_BOND, TYP_THREE_BODY,
+ TYP_HBOND, TYP_FAR_NEIGHBOR, TYP_DBO, TYP_DDELTA, TYP_N };
enum message_tags { INIT, UPDATE, BNDRY, UPDATE_BNDRY,
- EXC_VEC1, EXC_VEC2, DIST_RVEC2, COLL_RVEC2,
- DIST_RVECS, COLL_RVECS, INIT_DESCS, ATOM_LINES,
- BOND_LINES, ANGLE_LINES, RESTART_ATOMS, TAGS_N };
+ EXC_VEC1, EXC_VEC2, DIST_RVEC2, COLL_RVEC2,
+ DIST_RVECS, COLL_RVECS, INIT_DESCS, ATOM_LINES,
+ BOND_LINES, ANGLE_LINES, RESTART_ATOMS, TAGS_N };
-enum errors { FILE_NOT_FOUND = -10, UNKNOWN_ATOM_TYPE = -11,
- CANNOT_OPEN_FILE = -12, CANNOT_INITIALIZE = -13,
- INSUFFICIENT_MEMORY = -14, UNKNOWN_OPTION = -15,
- INVALID_INPUT = -16, INVALID_GEO = -17 };
+enum errors { FILE_NOT_FOUND = -10, UNKNOWN_ATOM_TYPE = -11,
+ CANNOT_OPEN_FILE = -12, CANNOT_INITIALIZE = -13,
+ INSUFFICIENT_MEMORY = -14, UNKNOWN_OPTION = -15,
+ INVALID_INPUT = -16, INVALID_GEO = -17 };
enum exchanges { NONE, NEAR_EXCH, FULL_EXCH };
-enum gcell_types { NO_NBRS=0, NEAR_ONLY=1, HBOND_ONLY=2, FAR_ONLY=4,
- NEAR_HBOND=3, NEAR_FAR=5, HBOND_FAR=6, FULL_NBRS=7,
- NATIVE=8 };
+enum gcell_types { NO_NBRS=0, NEAR_ONLY=1, HBOND_ONLY=2, FAR_ONLY=4,
+ NEAR_HBOND=3, NEAR_FAR=5, HBOND_FAR=6, FULL_NBRS=7,
+ NATIVE=8 };
-enum atoms { C_ATOM = 0, H_ATOM = 1, O_ATOM = 2, N_ATOM = 3,
- S_ATOM = 4, SI_ATOM = 5, GE_ATOM = 6, X_ATOM = 7 };
+enum atoms { C_ATOM = 0, H_ATOM = 1, O_ATOM = 2, N_ATOM = 3,
+ S_ATOM = 4, SI_ATOM = 5, GE_ATOM = 6, X_ATOM = 7 };
enum traj_methods { REG_TRAJ, MPI_TRAJ, TF_N };
diff --git a/src/USER-REAXC/reaxc_ffield.cpp b/src/USER-REAXC/reaxc_ffield.cpp
index 0230e611b9d09b6e489539bb3b359231ba7557a4..7d587ddb2769f611ed70b6b94f901471b3859de8 100644
--- a/src/USER-REAXC/reaxc_ffield.cpp
+++ b/src/USER-REAXC/reaxc_ffield.cpp
@@ -14,12 +14,12 @@
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -35,8 +35,8 @@
#endif
-char Read_Force_Field( char *ffield_file, reax_interaction *reax,
- control_params *control )
+char Read_Force_Field( char *ffield_file, reax_interaction *reax,
+ control_params *control )
{
FILE *fp;
char *s;
@@ -55,7 +55,7 @@ char Read_Force_Field( char *ffield_file, reax_interaction *reax,
fprintf( stderr, "error opening the force filed file! terminating...\n" );
MPI_Abort( comm, FILE_NOT_FOUND );
}
-
+
s = (char*) malloc(sizeof(char)*MAX_LINE);
tmp = (char**) malloc(sizeof(char*)*MAX_TOKENS);
for (i=0; i < MAX_TOKENS; i++)
@@ -80,17 +80,17 @@ char Read_Force_Field( char *ffield_file, reax_interaction *reax,
reax->gp.n_global = n;
reax->gp.l = (real*) malloc(sizeof(real)*n);
- /* see reax_types.h for mapping between l[i] and the lambdas used in ff */
+ /* see reax_types.h for mapping between l[i] and the lambdas used in ff */
for (i=0; i < n; i++) {
fgets(s,MAX_LINE,fp);
c = Tokenize(s,&tmp);
-
+
val = (real) atof(tmp[0]);
reax->gp.l[i] = val;
}
control->bo_cut = 0.01 * reax->gp.l[29];
- control->nonb_low = reax->gp.l[11];
+ control->nonb_low = reax->gp.l[11];
control->nonb_cut = reax->gp.l[12];
/* next line is number of atom types and some comments */
@@ -104,78 +104,78 @@ char Read_Force_Field( char *ffield_file, reax_interaction *reax,
fgets(s,MAX_LINE,fp);
/* Allocating structures in reax_interaction */
- reax->sbp = (single_body_parameters*)
- scalloc( reax->num_atom_types, sizeof(single_body_parameters), "sbp",
- comm );
- reax->tbp = (two_body_parameters**)
+ reax->sbp = (single_body_parameters*)
+ scalloc( reax->num_atom_types, sizeof(single_body_parameters), "sbp",
+ comm );
+ reax->tbp = (two_body_parameters**)
scalloc( reax->num_atom_types, sizeof(two_body_parameters*), "tbp", comm );
- reax->thbp= (three_body_header***)
+ reax->thbp= (three_body_header***)
scalloc( reax->num_atom_types, sizeof(three_body_header**), "thbp", comm );
- reax->hbp = (hbond_parameters***)
+ reax->hbp = (hbond_parameters***)
scalloc( reax->num_atom_types, sizeof(hbond_parameters**), "hbp", comm );
- reax->fbp = (four_body_header****)
+ reax->fbp = (four_body_header****)
scalloc( reax->num_atom_types, sizeof(four_body_header***), "fbp", comm );
- tor_flag = (char****)
+ tor_flag = (char****)
scalloc( reax->num_atom_types, sizeof(char***), "tor_flag", comm );
-
+
for( i = 0; i < reax->num_atom_types; i++ ) {
- reax->tbp[i] = (two_body_parameters*)
- scalloc( reax->num_atom_types, sizeof(two_body_parameters), "tbp[i]",
- comm );
- reax->thbp[i]= (three_body_header**)
- scalloc( reax->num_atom_types, sizeof(three_body_header*), "thbp[i]",
- comm );
- reax->hbp[i] = (hbond_parameters**)
- scalloc( reax->num_atom_types, sizeof(hbond_parameters*), "hbp[i]",
- comm );
- reax->fbp[i] = (four_body_header***)
- scalloc( reax->num_atom_types, sizeof(four_body_header**), "fbp[i]",
- comm );
- tor_flag[i] = (char***)
+ reax->tbp[i] = (two_body_parameters*)
+ scalloc( reax->num_atom_types, sizeof(two_body_parameters), "tbp[i]",
+ comm );
+ reax->thbp[i]= (three_body_header**)
+ scalloc( reax->num_atom_types, sizeof(three_body_header*), "thbp[i]",
+ comm );
+ reax->hbp[i] = (hbond_parameters**)
+ scalloc( reax->num_atom_types, sizeof(hbond_parameters*), "hbp[i]",
+ comm );
+ reax->fbp[i] = (four_body_header***)
+ scalloc( reax->num_atom_types, sizeof(four_body_header**), "fbp[i]",
+ comm );
+ tor_flag[i] = (char***)
scalloc( reax->num_atom_types, sizeof(char**), "tor_flag[i]", comm );
-
+
for( j = 0; j < reax->num_atom_types; j++ ) {
- reax->thbp[i][j]= (three_body_header*)
- scalloc( reax->num_atom_types, sizeof(three_body_header), "thbp[i,j]",
- comm );
- reax->hbp[i][j] = (hbond_parameters*)
- scalloc( reax->num_atom_types, sizeof(hbond_parameters), "hbp[i,j]",
- comm );
- reax->fbp[i][j] = (four_body_header**)
- scalloc( reax->num_atom_types, sizeof(four_body_header*), "fbp[i,j]",
- comm );
- tor_flag[i][j] = (char**)
- scalloc( reax->num_atom_types, sizeof(char*), "tor_flag[i,j]", comm );
-
+ reax->thbp[i][j]= (three_body_header*)
+ scalloc( reax->num_atom_types, sizeof(three_body_header), "thbp[i,j]",
+ comm );
+ reax->hbp[i][j] = (hbond_parameters*)
+ scalloc( reax->num_atom_types, sizeof(hbond_parameters), "hbp[i,j]",
+ comm );
+ reax->fbp[i][j] = (four_body_header**)
+ scalloc( reax->num_atom_types, sizeof(four_body_header*), "fbp[i,j]",
+ comm );
+ tor_flag[i][j] = (char**)
+ scalloc( reax->num_atom_types, sizeof(char*), "tor_flag[i,j]", comm );
+
for (k=0; k < reax->num_atom_types; k++) {
- reax->fbp[i][j][k] = (four_body_header*)
- scalloc( reax->num_atom_types, sizeof(four_body_header), "fbp[i,j,k]",
- comm );
- tor_flag[i][j][k] = (char*)
- scalloc( reax->num_atom_types, sizeof(char), "tor_flag[i,j,k]",
- comm );
+ reax->fbp[i][j][k] = (four_body_header*)
+ scalloc( reax->num_atom_types, sizeof(four_body_header), "fbp[i,j,k]",
+ comm );
+ tor_flag[i][j][k] = (char*)
+ scalloc( reax->num_atom_types, sizeof(char), "tor_flag[i,j,k]",
+ comm );
}
}
}
- // vdWaals type: 1: Shielded Morse, no inner-wall
- // 2: inner wall, no shielding
+ // vdWaals type: 1: Shielded Morse, no inner-wall
+ // 2: inner wall, no shielding
// 3: inner wall+shielding
reax->gp.vdw_type = 0;
-
+
/* reading single atom parameters */
- /* there are 4 or 5 lines of each single atom parameters in ff files,
- depending on using lgvdw or not. These parameters later determine
+ /* there are 4 or 5 lines of each single atom parameters in ff files,
+ depending on using lgvdw or not. These parameters later determine
some of the pair and triplet parameters using combination rules. */
for( i = 0; i < reax->num_atom_types; i++ ) {
/* line one */
fgets( s, MAX_LINE, fp );
c = Tokenize( s, &tmp );
-
+
for( j = 0; j < (int)(strlen(tmp[0])); ++j )
reax->sbp[i].name[j] = toupper( tmp[0][j] );
-
+
val = atof(tmp[1]); reax->sbp[i].r_s = val;
val = atof(tmp[2]); reax->sbp[i].valency = val;
val = atof(tmp[3]); reax->sbp[i].mass = val;
@@ -189,29 +189,29 @@ char Read_Force_Field( char *ffield_file, reax_interaction *reax,
/* line two */
fgets( s, MAX_LINE, fp );
c = Tokenize( s, &tmp );
-
+
val = atof(tmp[0]); reax->sbp[i].alpha = val;
val = atof(tmp[1]); reax->sbp[i].gamma_w = val;
val = atof(tmp[2]); reax->sbp[i].valency_boc= val;
val = atof(tmp[3]); reax->sbp[i].p_ovun5 = val;
- val = atof(tmp[4]);
+ val = atof(tmp[4]);
val = atof(tmp[5]); reax->sbp[i].chi = val;
val = atof(tmp[6]); reax->sbp[i].eta = 2.0 * val;
val = atof(tmp[7]); reax->sbp[i].p_hbond = (int) val;
-
+
/* line 3 */
fgets( s, MAX_LINE, fp );
c = Tokenize( s, &tmp );
-
+
val = atof(tmp[0]); reax->sbp[i].r_pi_pi = val;
val = atof(tmp[1]); reax->sbp[i].p_lp2 = val;
- val = atof(tmp[2]);
+ val = atof(tmp[2]);
val = atof(tmp[3]); reax->sbp[i].b_o_131 = val;
val = atof(tmp[4]); reax->sbp[i].b_o_132 = val;
val = atof(tmp[5]); reax->sbp[i].b_o_133 = val;
- val = atof(tmp[6]);
- val = atof(tmp[7]);
-
+ val = atof(tmp[6]);
+ val = atof(tmp[7]);
+
/* line 4 */
fgets( s, MAX_LINE, fp );
c = Tokenize( s, &tmp );
@@ -224,7 +224,7 @@ char Read_Force_Field( char *ffield_file, reax_interaction *reax,
val = atof(tmp[0]); reax->sbp[i].p_ovun2 = val;
val = atof(tmp[1]); reax->sbp[i].p_val3 = val;
- val = atof(tmp[2]);
+ val = atof(tmp[2]);
val = atof(tmp[3]); reax->sbp[i].valency_val= val;
val = atof(tmp[4]); reax->sbp[i].p_val5 = val;
val = atof(tmp[5]); reax->sbp[i].rcore2 = val;
@@ -242,74 +242,74 @@ char Read_Force_Field( char *ffield_file, reax_interaction *reax,
MPI_Abort( comm, FILE_NOT_FOUND );
}
- val = atof(tmp[0]); reax->sbp[i].lgcij = val;
- val = atof(tmp[1]); reax->sbp[i].lgre = val;
+ val = atof(tmp[0]); reax->sbp[i].lgcij = val;
+ val = atof(tmp[1]); reax->sbp[i].lgre = val;
}
if( reax->sbp[i].rcore2>0.01 && reax->sbp[i].acore2>0.01 ){ // Inner-wall
if( reax->sbp[i].gamma_w>0.5 ){ // Shielding vdWaals
- if( reax->gp.vdw_type != 0 && reax->gp.vdw_type != 3 ) {
- if (errorflag)
- fprintf( stderr, "Warning: inconsistent vdWaals-parameters\n" \
- "Force field parameters for element %s\n" \
- "indicate inner wall+shielding, but earlier\n" \
- "atoms indicate different vdWaals-method.\n" \
- "This may cause division-by-zero errors.\n" \
- "Keeping vdWaals-setting for earlier atoms.\n",
- reax->sbp[i].name );
- errorflag = 0;
- }
- else{
- reax->gp.vdw_type = 3;
+ if( reax->gp.vdw_type != 0 && reax->gp.vdw_type != 3 ) {
+ if (errorflag)
+ fprintf( stderr, "Warning: inconsistent vdWaals-parameters\n" \
+ "Force field parameters for element %s\n" \
+ "indicate inner wall+shielding, but earlier\n" \
+ "atoms indicate different vdWaals-method.\n" \
+ "This may cause division-by-zero errors.\n" \
+ "Keeping vdWaals-setting for earlier atoms.\n",
+ reax->sbp[i].name );
+ errorflag = 0;
+ }
+ else{
+ reax->gp.vdw_type = 3;
#if defined(DEBUG)
- fprintf( stderr, "vdWaals type for element %s: Shielding+inner-wall",
- reax->sbp[i].name );
+ fprintf( stderr, "vdWaals type for element %s: Shielding+inner-wall",
+ reax->sbp[i].name );
#endif
- }
+ }
}
else { // No shielding vdWaals parameters present
- if( reax->gp.vdw_type != 0 && reax->gp.vdw_type != 2 )
- fprintf( stderr, "Warning: inconsistent vdWaals-parameters\n" \
- "Force field parameters for element %s\n" \
- "indicate inner wall without shielding, but earlier\n" \
- "atoms indicate different vdWaals-method.\n" \
- "This may cause division-by-zero errors.\n" \
- "Keeping vdWaals-setting for earlier atoms.\n",
- reax->sbp[i].name );
- else{
- reax->gp.vdw_type = 2;
+ if( reax->gp.vdw_type != 0 && reax->gp.vdw_type != 2 )
+ fprintf( stderr, "Warning: inconsistent vdWaals-parameters\n" \
+ "Force field parameters for element %s\n" \
+ "indicate inner wall without shielding, but earlier\n" \
+ "atoms indicate different vdWaals-method.\n" \
+ "This may cause division-by-zero errors.\n" \
+ "Keeping vdWaals-setting for earlier atoms.\n",
+ reax->sbp[i].name );
+ else{
+ reax->gp.vdw_type = 2;
#if defined(DEBUG)
- fprintf( stderr,"vdWaals type for element%s: No Shielding,inner-wall",
- reax->sbp[i].name );
+ fprintf( stderr,"vdWaals type for element%s: No Shielding,inner-wall",
+ reax->sbp[i].name );
#endif
- }
+ }
}
}
else{ // No Inner wall parameters present
if( reax->sbp[i].gamma_w>0.5 ){ // Shielding vdWaals
- if( reax->gp.vdw_type != 0 && reax->gp.vdw_type != 1 )
- fprintf( stderr, "Warning: inconsistent vdWaals-parameters\n" \
- "Force field parameters for element %s\n" \
- "indicate shielding without inner wall, but earlier\n" \
- "atoms indicate different vdWaals-method.\n" \
- "This may cause division-by-zero errors.\n" \
- "Keeping vdWaals-setting for earlier atoms.\n",
- reax->sbp[i].name );
- else{
- reax->gp.vdw_type = 1;
+ if( reax->gp.vdw_type != 0 && reax->gp.vdw_type != 1 )
+ fprintf( stderr, "Warning: inconsistent vdWaals-parameters\n" \
+ "Force field parameters for element %s\n" \
+ "indicate shielding without inner wall, but earlier\n" \
+ "atoms indicate different vdWaals-method.\n" \
+ "This may cause division-by-zero errors.\n" \
+ "Keeping vdWaals-setting for earlier atoms.\n",
+ reax->sbp[i].name );
+ else{
+ reax->gp.vdw_type = 1;
#if defined(DEBUG)
- fprintf( stderr,"vdWaals type for element%s: Shielding,no inner-wall",
- reax->sbp[i].name );
+ fprintf( stderr,"vdWaals type for element%s: Shielding,no inner-wall",
+ reax->sbp[i].name );
#endif
- }
+ }
}
else{
- fprintf( stderr, "Error: inconsistent vdWaals-parameters\n"\
- "No shielding or inner-wall set for element %s\n",
- reax->sbp[i].name );
- MPI_Abort( comm, INVALID_INPUT );
+ fprintf( stderr, "Error: inconsistent vdWaals-parameters\n"\
+ "No shielding or inner-wall set for element %s\n",
+ reax->sbp[i].name );
+ MPI_Abort( comm, INVALID_INPUT );
}
- }
+ }
}
#if defined(DEBUG)
@@ -319,9 +319,9 @@ char Read_Force_Field( char *ffield_file, reax_interaction *reax,
/* Equate vval3 to valf for first-row elements (25/10/2004) */
for( i = 0; i < reax->num_atom_types; i++ )
if( reax->sbp[i].mass < 21 &&
- reax->sbp[i].valency_val != reax->sbp[i].valency_boc ){
+ reax->sbp[i].valency_val != reax->sbp[i].valency_boc ){
fprintf( stderr, "Warning: changed valency_val to valency_boc for %s\n",
- reax->sbp[i].name );
+ reax->sbp[i].name );
reax->sbp[i].valency_val = reax->sbp[i].valency_boc;
}
@@ -333,12 +333,12 @@ char Read_Force_Field( char *ffield_file, reax_interaction *reax,
/* a line of comments */
fgets(s,MAX_LINE,fp);
-
+
for (i=0; i < l; i++) {
/* line 1 */
fgets(s,MAX_LINE,fp);
c=Tokenize(s,&tmp);
-
+
j = atoi(tmp[0]) - 1;
k = atoi(tmp[1]) - 1;
@@ -356,7 +356,7 @@ char Read_Force_Field( char *ffield_file, reax_interaction *reax,
reax->tbp[k][j].p_bo5 = val;
val = atof(tmp[7]); reax->tbp[j][k].v13cor = val;
reax->tbp[k][j].v13cor = val;
-
+
val = atof(tmp[8]); reax->tbp[j][k].p_bo6 = val;
reax->tbp[k][j].p_bo6 = val;
val = atof(tmp[9]); reax->tbp[j][k].p_ovun1 = val;
@@ -372,118 +372,118 @@ char Read_Force_Field( char *ffield_file, reax_interaction *reax,
reax->tbp[k][j].p_bo3 = val;
val = atof(tmp[2]); reax->tbp[j][k].p_bo4 = val;
reax->tbp[k][j].p_bo4 = val;
- val = atof(tmp[3]);
-
+ val = atof(tmp[3]);
+
val = atof(tmp[4]); reax->tbp[j][k].p_bo1 = val;
reax->tbp[k][j].p_bo1 = val;
val = atof(tmp[5]); reax->tbp[j][k].p_bo2 = val;
reax->tbp[k][j].p_bo2 = val;
val = atof(tmp[6]); reax->tbp[j][k].ovc = val;
reax->tbp[k][j].ovc = val;
-
- val = atof(tmp[7]);
+
+ val = atof(tmp[7]);
}
}
/* calculating combination rules and filling up remaining fields. */
-
+
for (i=0; i < reax->num_atom_types; i++)
for (j=i; j < reax->num_atom_types; j++) {
reax->tbp[i][j].r_s = 0.5 *
- (reax->sbp[i].r_s + reax->sbp[j].r_s);
+ (reax->sbp[i].r_s + reax->sbp[j].r_s);
reax->tbp[j][i].r_s = 0.5 *
- (reax->sbp[j].r_s + reax->sbp[i].r_s);
+ (reax->sbp[j].r_s + reax->sbp[i].r_s);
reax->tbp[i][j].r_p = 0.5 *
- (reax->sbp[i].r_pi + reax->sbp[j].r_pi);
+ (reax->sbp[i].r_pi + reax->sbp[j].r_pi);
reax->tbp[j][i].r_p = 0.5 *
- (reax->sbp[j].r_pi + reax->sbp[i].r_pi);
+ (reax->sbp[j].r_pi + reax->sbp[i].r_pi);
reax->tbp[i][j].r_pp = 0.5 *
- (reax->sbp[i].r_pi_pi + reax->sbp[j].r_pi_pi);
+ (reax->sbp[i].r_pi_pi + reax->sbp[j].r_pi_pi);
reax->tbp[j][i].r_pp = 0.5 *
- (reax->sbp[j].r_pi_pi + reax->sbp[i].r_pi_pi);
-
-
- reax->tbp[i][j].p_boc3 =
- sqrt(reax->sbp[i].b_o_132 *
- reax->sbp[j].b_o_132);
- reax->tbp[j][i].p_boc3 =
- sqrt(reax->sbp[j].b_o_132 *
- reax->sbp[i].b_o_132);
-
- reax->tbp[i][j].p_boc4 =
- sqrt(reax->sbp[i].b_o_131 *
- reax->sbp[j].b_o_131);
- reax->tbp[j][i].p_boc4 =
- sqrt(reax->sbp[j].b_o_131 *
- reax->sbp[i].b_o_131);
-
- reax->tbp[i][j].p_boc5 =
- sqrt(reax->sbp[i].b_o_133 *
- reax->sbp[j].b_o_133);
- reax->tbp[j][i].p_boc5 =
- sqrt(reax->sbp[j].b_o_133 *
- reax->sbp[i].b_o_133);
-
-
- reax->tbp[i][j].D =
- sqrt(reax->sbp[i].epsilon *
- reax->sbp[j].epsilon);
-
- reax->tbp[j][i].D =
- sqrt(reax->sbp[j].epsilon *
- reax->sbp[i].epsilon);
-
- reax->tbp[i][j].alpha =
- sqrt(reax->sbp[i].alpha *
- reax->sbp[j].alpha);
-
- reax->tbp[j][i].alpha =
- sqrt(reax->sbp[j].alpha *
- reax->sbp[i].alpha);
-
- reax->tbp[i][j].r_vdW =
- 2.0 * sqrt(reax->sbp[i].r_vdw * reax->sbp[j].r_vdw);
+ (reax->sbp[j].r_pi_pi + reax->sbp[i].r_pi_pi);
+
+
+ reax->tbp[i][j].p_boc3 =
+ sqrt(reax->sbp[i].b_o_132 *
+ reax->sbp[j].b_o_132);
+ reax->tbp[j][i].p_boc3 =
+ sqrt(reax->sbp[j].b_o_132 *
+ reax->sbp[i].b_o_132);
+
+ reax->tbp[i][j].p_boc4 =
+ sqrt(reax->sbp[i].b_o_131 *
+ reax->sbp[j].b_o_131);
+ reax->tbp[j][i].p_boc4 =
+ sqrt(reax->sbp[j].b_o_131 *
+ reax->sbp[i].b_o_131);
+
+ reax->tbp[i][j].p_boc5 =
+ sqrt(reax->sbp[i].b_o_133 *
+ reax->sbp[j].b_o_133);
+ reax->tbp[j][i].p_boc5 =
+ sqrt(reax->sbp[j].b_o_133 *
+ reax->sbp[i].b_o_133);
+
+
+ reax->tbp[i][j].D =
+ sqrt(reax->sbp[i].epsilon *
+ reax->sbp[j].epsilon);
+
+ reax->tbp[j][i].D =
+ sqrt(reax->sbp[j].epsilon *
+ reax->sbp[i].epsilon);
+
+ reax->tbp[i][j].alpha =
+ sqrt(reax->sbp[i].alpha *
+ reax->sbp[j].alpha);
+
+ reax->tbp[j][i].alpha =
+ sqrt(reax->sbp[j].alpha *
+ reax->sbp[i].alpha);
+
+ reax->tbp[i][j].r_vdW =
+ 2.0 * sqrt(reax->sbp[i].r_vdw * reax->sbp[j].r_vdw);
reax->tbp[j][i].r_vdW =
- 2.0 * sqrt(reax->sbp[j].r_vdw * reax->sbp[i].r_vdw);
+ 2.0 * sqrt(reax->sbp[j].r_vdw * reax->sbp[i].r_vdw);
reax->tbp[i][j].gamma_w =
- sqrt(reax->sbp[i].gamma_w *
- reax->sbp[j].gamma_w);
+ sqrt(reax->sbp[i].gamma_w *
+ reax->sbp[j].gamma_w);
reax->tbp[j][i].gamma_w =
- sqrt(reax->sbp[j].gamma_w *
- reax->sbp[i].gamma_w);
+ sqrt(reax->sbp[j].gamma_w *
+ reax->sbp[i].gamma_w);
reax->tbp[i][j].gamma =
- pow(reax->sbp[i].gamma *
- reax->sbp[j].gamma,-1.5);
+ pow(reax->sbp[i].gamma *
+ reax->sbp[j].gamma,-1.5);
reax->tbp[j][i].gamma =
- pow(reax->sbp[j].gamma *
- reax->sbp[i].gamma,-1.5);
+ pow(reax->sbp[j].gamma *
+ reax->sbp[i].gamma,-1.5);
// additions for additional vdWaals interaction types - inner core
-
+
reax->tbp[i][j].rcore = reax->tbp[j][i].rcore =
- sqrt( reax->sbp[i].rcore2 * reax->sbp[j].rcore2 );
+ sqrt( reax->sbp[i].rcore2 * reax->sbp[j].rcore2 );
reax->tbp[i][j].ecore = reax->tbp[j][i].ecore =
- sqrt( reax->sbp[i].ecore2 * reax->sbp[j].ecore2 );
+ sqrt( reax->sbp[i].ecore2 * reax->sbp[j].ecore2 );
reax->tbp[i][j].acore = reax->tbp[j][i].acore =
- sqrt( reax->sbp[i].acore2 * reax->sbp[j].acore2 );
+ sqrt( reax->sbp[i].acore2 * reax->sbp[j].acore2 );
- // additions for additional vdWalls interaction types lg correction
+ // additions for additional vdWalls interaction types lg correction
reax->tbp[i][j].lgcij = reax->tbp[j][i].lgcij =
- sqrt( reax->sbp[i].lgcij * reax->sbp[j].lgcij );
+ sqrt( reax->sbp[i].lgcij * reax->sbp[j].lgcij );
- reax->tbp[i][j].lgre = reax->tbp[j][i].lgre = 2.0 *
+ reax->tbp[i][j].lgre = reax->tbp[j][i].lgre = 2.0 *
sqrt( reax->sbp[i].lgre*reax->sbp[j].lgre );
-
+
}
@@ -493,114 +493,114 @@ char Read_Force_Field( char *ffield_file, reax_interaction *reax,
fgets(s,MAX_LINE,fp);
c=Tokenize(s,&tmp);
l = atoi(tmp[0]);
-
+
for (i=0; i < l; i++) {
fgets(s,MAX_LINE,fp);
c=Tokenize(s,&tmp);
-
+
j = atoi(tmp[0]) - 1;
k = atoi(tmp[1]) - 1;
- if (j < reax->num_atom_types && k < reax->num_atom_types) {
- val = atof(tmp[2]);
+ if (j < reax->num_atom_types && k < reax->num_atom_types) {
+ val = atof(tmp[2]);
if (val > 0.0) {
- reax->tbp[j][k].D = val;
- reax->tbp[k][j].D = val;
+ reax->tbp[j][k].D = val;
+ reax->tbp[k][j].D = val;
}
- val = atof(tmp[3]);
+ val = atof(tmp[3]);
if (val > 0.0) {
- reax->tbp[j][k].r_vdW = 2 * val;
- reax->tbp[k][j].r_vdW = 2 * val;
+ reax->tbp[j][k].r_vdW = 2 * val;
+ reax->tbp[k][j].r_vdW = 2 * val;
}
- val = atof(tmp[4]);
+ val = atof(tmp[4]);
if (val > 0.0) {
- reax->tbp[j][k].alpha = val;
- reax->tbp[k][j].alpha = val;
+ reax->tbp[j][k].alpha = val;
+ reax->tbp[k][j].alpha = val;
}
- val = atof(tmp[5]);
+ val = atof(tmp[5]);
if (val > 0.0) {
- reax->tbp[j][k].r_s = val;
- reax->tbp[k][j].r_s = val;
+ reax->tbp[j][k].r_s = val;
+ reax->tbp[k][j].r_s = val;
}
- val = atof(tmp[6]);
+ val = atof(tmp[6]);
if (val > 0.0) {
- reax->tbp[j][k].r_p = val;
- reax->tbp[k][j].r_p = val;
+ reax->tbp[j][k].r_p = val;
+ reax->tbp[k][j].r_p = val;
}
- val = atof(tmp[7]);
+ val = atof(tmp[7]);
if (val > 0.0) {
- reax->tbp[j][k].r_pp = val;
- reax->tbp[k][j].r_pp = val;
+ reax->tbp[j][k].r_pp = val;
+ reax->tbp[k][j].r_pp = val;
}
- val = atof(tmp[8]);
+ val = atof(tmp[8]);
if (val >= 0.0) {
- reax->tbp[j][k].lgcij = val;
- reax->tbp[k][j].lgcij = val;
+ reax->tbp[j][k].lgcij = val;
+ reax->tbp[k][j].lgcij = val;
}
}
}
-
- /* 3-body parameters -
+
+ /* 3-body parameters -
supports multi-well potentials (upto MAX_3BODY_PARAM in mytypes.h) */
/* clear entries first */
for( i = 0; i < reax->num_atom_types; ++i )
for( j = 0; j < reax->num_atom_types; ++j )
for( k = 0; k < reax->num_atom_types; ++k )
- reax->thbp[i][j][k].cnt = 0;
+ reax->thbp[i][j][k].cnt = 0;
- /* next line is number of 3-body params and some comments */
+ /* next line is number of 3-body params and some comments */
fgets( s, MAX_LINE, fp );
c = Tokenize( s, &tmp );
l = atoi( tmp[0] );
-
+
for( i = 0; i < l; i++ ) {
fgets(s,MAX_LINE,fp);
c=Tokenize(s,&tmp);
-
+
j = atoi(tmp[0]) - 1;
k = atoi(tmp[1]) - 1;
m = atoi(tmp[2]) - 1;
- if (j < reax->num_atom_types && k < reax->num_atom_types &&
- m < reax->num_atom_types) {
+ if (j < reax->num_atom_types && k < reax->num_atom_types &&
+ m < reax->num_atom_types) {
cnt = reax->thbp[j][k][m].cnt;
reax->thbp[j][k][m].cnt++;
reax->thbp[m][k][j].cnt++;
- val = atof(tmp[3]);
+ val = atof(tmp[3]);
reax->thbp[j][k][m].prm[cnt].theta_00 = val;
reax->thbp[m][k][j].prm[cnt].theta_00 = val;
- val = atof(tmp[4]);
+ val = atof(tmp[4]);
reax->thbp[j][k][m].prm[cnt].p_val1 = val;
reax->thbp[m][k][j].prm[cnt].p_val1 = val;
- val = atof(tmp[5]);
+ val = atof(tmp[5]);
reax->thbp[j][k][m].prm[cnt].p_val2 = val;
reax->thbp[m][k][j].prm[cnt].p_val2 = val;
- val = atof(tmp[6]);
+ val = atof(tmp[6]);
reax->thbp[j][k][m].prm[cnt].p_coa1 = val;
reax->thbp[m][k][j].prm[cnt].p_coa1 = val;
- val = atof(tmp[7]);
+ val = atof(tmp[7]);
reax->thbp[j][k][m].prm[cnt].p_val7 = val;
reax->thbp[m][k][j].prm[cnt].p_val7 = val;
- val = atof(tmp[8]);
+ val = atof(tmp[8]);
reax->thbp[j][k][m].prm[cnt].p_pen1 = val;
reax->thbp[m][k][j].prm[cnt].p_pen1 = val;
- val = atof(tmp[9]);
+ val = atof(tmp[9]);
reax->thbp[j][k][m].prm[cnt].p_val4 = val;
- reax->thbp[m][k][j].prm[cnt].p_val4 = val;
+ reax->thbp[m][k][j].prm[cnt].p_val4 = val;
}
}
@@ -610,17 +610,17 @@ char Read_Force_Field( char *ffield_file, reax_interaction *reax,
position. However, explicit X-Y-Z-W takes precedence over the
default description.
supports multi-well potentials (upto MAX_4BODY_PARAM in mytypes.h)
- IMPORTANT: for now, directions on how to read multi-entries from ffield
+ IMPORTANT: for now, directions on how to read multi-entries from ffield
is not clear */
-
+
/* clear all entries first */
for( i = 0; i < reax->num_atom_types; ++i )
for( j = 0; j < reax->num_atom_types; ++j )
for( k = 0; k < reax->num_atom_types; ++k )
- for( m = 0; m < reax->num_atom_types; ++m ) {
- reax->fbp[i][j][k][m].cnt = 0;
- tor_flag[i][j][k][m] = 0;
- }
+ for( m = 0; m < reax->num_atom_types; ++m ) {
+ reax->fbp[i][j][k][m].cnt = 0;
+ tor_flag[i][j][k][m] = 0;
+ }
/* next line is number of 4-body params and some comments */
fgets( s, MAX_LINE, fp );
@@ -630,73 +630,73 @@ char Read_Force_Field( char *ffield_file, reax_interaction *reax,
for( i = 0; i < l; i++ ) {
fgets( s, MAX_LINE, fp );
c = Tokenize( s, &tmp );
-
+
j = atoi(tmp[0]) - 1;
k = atoi(tmp[1]) - 1;
m = atoi(tmp[2]) - 1;
n = atoi(tmp[3]) - 1;
-
+
if (j >= 0 && n >= 0) { // this means the entry is not in compact form
- if (j < reax->num_atom_types && k < reax->num_atom_types &&
- m < reax->num_atom_types && n < reax->num_atom_types) {
- /* these flags ensure that this entry take precedence
- over the compact form entries */
- tor_flag[j][k][m][n] = 1;
- tor_flag[n][m][k][j] = 1;
-
- reax->fbp[j][k][m][n].cnt = 1;
- reax->fbp[n][m][k][j].cnt = 1;
- /* cnt = reax->fbp[j][k][m][n].cnt;
- reax->fbp[j][k][m][n].cnt++;
- reax->fbp[n][m][k][j].cnt++; */
-
- val = atof(tmp[4]);
- reax->fbp[j][k][m][n].prm[0].V1 = val;
- reax->fbp[n][m][k][j].prm[0].V1 = val;
-
- val = atof(tmp[5]);
- reax->fbp[j][k][m][n].prm[0].V2 = val;
- reax->fbp[n][m][k][j].prm[0].V2 = val;
-
- val = atof(tmp[6]);
- reax->fbp[j][k][m][n].prm[0].V3 = val;
- reax->fbp[n][m][k][j].prm[0].V3 = val;
-
- val = atof(tmp[7]);
- reax->fbp[j][k][m][n].prm[0].p_tor1 = val;
- reax->fbp[n][m][k][j].prm[0].p_tor1 = val;
-
- val = atof(tmp[8]);
- reax->fbp[j][k][m][n].prm[0].p_cot1 = val;
- reax->fbp[n][m][k][j].prm[0].p_cot1 = val;
+ if (j < reax->num_atom_types && k < reax->num_atom_types &&
+ m < reax->num_atom_types && n < reax->num_atom_types) {
+ /* these flags ensure that this entry take precedence
+ over the compact form entries */
+ tor_flag[j][k][m][n] = 1;
+ tor_flag[n][m][k][j] = 1;
+
+ reax->fbp[j][k][m][n].cnt = 1;
+ reax->fbp[n][m][k][j].cnt = 1;
+ /* cnt = reax->fbp[j][k][m][n].cnt;
+ reax->fbp[j][k][m][n].cnt++;
+ reax->fbp[n][m][k][j].cnt++; */
+
+ val = atof(tmp[4]);
+ reax->fbp[j][k][m][n].prm[0].V1 = val;
+ reax->fbp[n][m][k][j].prm[0].V1 = val;
+
+ val = atof(tmp[5]);
+ reax->fbp[j][k][m][n].prm[0].V2 = val;
+ reax->fbp[n][m][k][j].prm[0].V2 = val;
+
+ val = atof(tmp[6]);
+ reax->fbp[j][k][m][n].prm[0].V3 = val;
+ reax->fbp[n][m][k][j].prm[0].V3 = val;
+
+ val = atof(tmp[7]);
+ reax->fbp[j][k][m][n].prm[0].p_tor1 = val;
+ reax->fbp[n][m][k][j].prm[0].p_tor1 = val;
+
+ val = atof(tmp[8]);
+ reax->fbp[j][k][m][n].prm[0].p_cot1 = val;
+ reax->fbp[n][m][k][j].prm[0].p_cot1 = val;
}
- }
+ }
else { /* This means the entry is of the form 0-X-Y-0 */
if( k < reax->num_atom_types && m < reax->num_atom_types )
- for( p = 0; p < reax->num_atom_types; p++ )
- for( o = 0; o < reax->num_atom_types; o++ ) {
- reax->fbp[p][k][m][o].cnt = 1;
- reax->fbp[o][m][k][p].cnt = 1;
- /* cnt = reax->fbp[p][k][m][o].cnt;
- reax->fbp[p][k][m][o].cnt++;
- reax->fbp[o][m][k][p].cnt++; */
-
- if (tor_flag[p][k][m][o] == 0) {
- reax->fbp[p][k][m][o].prm[0].V1 = atof(tmp[4]);
- reax->fbp[p][k][m][o].prm[0].V2 = atof(tmp[5]);
- reax->fbp[p][k][m][o].prm[0].V3 = atof(tmp[6]);
- reax->fbp[p][k][m][o].prm[0].p_tor1 = atof(tmp[7]);
- reax->fbp[p][k][m][o].prm[0].p_cot1 = atof(tmp[8]);
- }
-
- if (tor_flag[o][m][k][p] == 0) {
- reax->fbp[o][m][k][p].prm[0].V1 = atof(tmp[4]);
- reax->fbp[o][m][k][p].prm[0].V2 = atof(tmp[5]);
- reax->fbp[o][m][k][p].prm[0].V3 = atof(tmp[6]);
- reax->fbp[o][m][k][p].prm[0].p_tor1 = atof(tmp[7]);
- reax->fbp[o][m][k][p].prm[0].p_cot1 = atof(tmp[8]);
- }
- }
+ for( p = 0; p < reax->num_atom_types; p++ )
+ for( o = 0; o < reax->num_atom_types; o++ ) {
+ reax->fbp[p][k][m][o].cnt = 1;
+ reax->fbp[o][m][k][p].cnt = 1;
+ /* cnt = reax->fbp[p][k][m][o].cnt;
+ reax->fbp[p][k][m][o].cnt++;
+ reax->fbp[o][m][k][p].cnt++; */
+
+ if (tor_flag[p][k][m][o] == 0) {
+ reax->fbp[p][k][m][o].prm[0].V1 = atof(tmp[4]);
+ reax->fbp[p][k][m][o].prm[0].V2 = atof(tmp[5]);
+ reax->fbp[p][k][m][o].prm[0].V3 = atof(tmp[6]);
+ reax->fbp[p][k][m][o].prm[0].p_tor1 = atof(tmp[7]);
+ reax->fbp[p][k][m][o].prm[0].p_cot1 = atof(tmp[8]);
+ }
+
+ if (tor_flag[o][m][k][p] == 0) {
+ reax->fbp[o][m][k][p].prm[0].V1 = atof(tmp[4]);
+ reax->fbp[o][m][k][p].prm[0].V2 = atof(tmp[5]);
+ reax->fbp[o][m][k][p].prm[0].V3 = atof(tmp[6]);
+ reax->fbp[o][m][k][p].prm[0].p_tor1 = atof(tmp[7]);
+ reax->fbp[o][m][k][p].prm[0].p_cot1 = atof(tmp[8]);
+ }
+ }
}
}
@@ -710,28 +710,28 @@ char Read_Force_Field( char *ffield_file, reax_interaction *reax,
for( i = 0; i < l; i++ ) {
fgets( s, MAX_LINE, fp );
c = Tokenize( s, &tmp );
-
+
j = atoi(tmp[0]) - 1;
k = atoi(tmp[1]) - 1;
m = atoi(tmp[2]) - 1;
if( j < reax->num_atom_types && m < reax->num_atom_types ) {
- val = atof(tmp[3]);
+ val = atof(tmp[3]);
reax->hbp[j][k][m].r0_hb = val;
- val = atof(tmp[4]);
+ val = atof(tmp[4]);
reax->hbp[j][k][m].p_hb1 = val;
- val = atof(tmp[5]);
+ val = atof(tmp[5]);
reax->hbp[j][k][m].p_hb2 = val;
- val = atof(tmp[6]);
+ val = atof(tmp[6]);
reax->hbp[j][k][m].p_hb3 = val;
}
}
-
+
/* deallocate helper storage */
for( i = 0; i < MAX_TOKENS; i++ )
free( tmp[i] );
@@ -743,7 +743,7 @@ char Read_Force_Field( char *ffield_file, reax_interaction *reax,
for( i = 0; i < reax->num_atom_types; i++ ) {
for( j = 0; j < reax->num_atom_types; j++ ) {
for( k = 0; k < reax->num_atom_types; k++ ) {
- free( tor_flag[i][j][k] );
+ free( tor_flag[i][j][k] );
}
free( tor_flag[i][j] );
}
@@ -758,6 +758,6 @@ char Read_Force_Field( char *ffield_file, reax_interaction *reax,
#if defined(DEBUG_FOCUS)
fprintf( stderr, "force field read\n" );
#endif
-
+
return SUCCESS;
}
diff --git a/src/USER-REAXC/reaxc_ffield.h b/src/USER-REAXC/reaxc_ffield.h
index b4632b63793739e67aa560035a8cb85179169ac8..6ccc94d7d08e70f20415e8de14ac0ff89c4aaeb3 100644
--- a/src/USER-REAXC/reaxc_ffield.h
+++ b/src/USER-REAXC/reaxc_ffield.h
@@ -14,12 +14,12 @@
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
diff --git a/src/USER-REAXC/reaxc_forces.cpp b/src/USER-REAXC/reaxc_forces.cpp
index fa20fba10923980cd37ce75e67ef4cccc64621b7..578f25e89521d3cfd431bb900ea32314a88f4a2f 100644
--- a/src/USER-REAXC/reaxc_forces.cpp
+++ b/src/USER-REAXC/reaxc_forces.cpp
@@ -14,12 +14,12 @@
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -60,15 +60,15 @@
interaction_function Interaction_Functions[NUM_INTRS];
-void Dummy_Interaction( reax_system *system, control_params *control,
- simulation_data *data, storage *workspace,
- reax_list **lists, output_controls *out_control )
+void Dummy_Interaction( reax_system *system, control_params *control,
+ simulation_data *data, storage *workspace,
+ reax_list **lists, output_controls *out_control )
{
}
void Init_Force_Functions( control_params *control )
-{
+{
Interaction_Functions[0] = BO;
Interaction_Functions[1] = Bonds; //Dummy_Interaction;
Interaction_Functions[2] = Atom_Energy; //Dummy_Interaction;
@@ -84,17 +84,17 @@ void Init_Force_Functions( control_params *control )
}
-void Compute_Bonded_Forces( reax_system *system, control_params *control,
- simulation_data *data, storage *workspace,
- reax_list **lists, output_controls *out_control,
- MPI_Comm comm )
+void Compute_Bonded_Forces( reax_system *system, control_params *control,
+ simulation_data *data, storage *workspace,
+ reax_list **lists, output_controls *out_control,
+ MPI_Comm comm )
{
int i;
/* Mark beginning of a new timestep in bonded energy files */
#if defined(TEST_ENERGY)
Debug_Marker_Bonded( out_control, data->step );
-#endif
+#endif
/* Implement all force calls as function pointers */
for( i = 0; i < NUM_INTRS; i++ ) {
@@ -102,8 +102,8 @@ void Compute_Bonded_Forces( reax_system *system, control_params *control,
fprintf( stderr, "p%d: starting f%d\n", system->my_rank, i );
MPI_Barrier( comm );
#endif
- (Interaction_Functions[i])( system, control, data, workspace,
- lists, out_control );
+ (Interaction_Functions[i])( system, control, data, workspace,
+ lists, out_control );
#if defined(DEBUG)
fprintf( stderr, "p%d: f%d done\n", system->my_rank, i );
MPI_Barrier( comm );
@@ -112,10 +112,10 @@ void Compute_Bonded_Forces( reax_system *system, control_params *control,
}
-void Compute_NonBonded_Forces( reax_system *system, control_params *control,
- simulation_data *data, storage *workspace,
- reax_list **lists, output_controls *out_control,
- MPI_Comm comm )
+void Compute_NonBonded_Forces( reax_system *system, control_params *control,
+ simulation_data *data, storage *workspace,
+ reax_list **lists, output_controls *out_control,
+ MPI_Comm comm )
{
/* Mark beginning of a new timestep in nonbonded energy files */
#if defined(TEST_ENERGY)
@@ -124,12 +124,12 @@ void Compute_NonBonded_Forces( reax_system *system, control_params *control,
/* van der Waals and Coulomb interactions */
if( control->tabulate == 0 )
- vdW_Coulomb_Energy( system, control, data, workspace,
- lists, out_control );
+ vdW_Coulomb_Energy( system, control, data, workspace,
+ lists, out_control );
else
- Tabulated_vdW_Coulomb_Energy( system, control, data, workspace,
- lists, out_control );
-
+ Tabulated_vdW_Coulomb_Energy( system, control, data, workspace,
+ lists, out_control );
+
#if defined(DEBUG)
fprintf( stderr, "p%d: nonbonded forces done\n", system->my_rank );
MPI_Barrier( comm );
@@ -138,12 +138,12 @@ void Compute_NonBonded_Forces( reax_system *system, control_params *control,
-/* this version of Compute_Total_Force computes forces from
- coefficients accumulated by all interaction functions.
+/* this version of Compute_Total_Force computes forces from
+ coefficients accumulated by all interaction functions.
Saves enormous time & space! */
-void Compute_Total_Force( reax_system *system, control_params *control,
- simulation_data *data, storage *workspace,
- reax_list **lists, mpi_datatypes *mpi_data )
+void Compute_Total_Force( reax_system *system, control_params *control,
+ simulation_data *data, storage *workspace,
+ reax_list **lists, mpi_datatypes *mpi_data )
{
int i, pj;
reax_list *bonds = (*lists) + BONDS;
@@ -151,20 +151,20 @@ void Compute_Total_Force( reax_system *system, control_params *control,
for( i = 0; i < system->N; ++i )
for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj )
if( i < bonds->select.bond_list[pj].nbr ) {
- if( control->virial == 0 )
- Add_dBond_to_Forces( system, i, pj, workspace, lists );
- else
- Add_dBond_to_Forces_NPT( i, pj, data, workspace, lists );
+ if( control->virial == 0 )
+ Add_dBond_to_Forces( system, i, pj, workspace, lists );
+ else
+ Add_dBond_to_Forces_NPT( i, pj, data, workspace, lists );
}
//Print_Total_Force( system, data, workspace );
#if defined(PURE_REAX)
- /* now all forces are computed to their partially-final values
- based on the neighbors information each processor has had.
+ /* now all forces are computed to their partially-final values
+ based on the neighbors information each processor has had.
final values of force on each atom needs to be computed by adding up
all partially-final pieces */
- Coll( system, mpi_data, workspace->f, mpi_data->mpi_rvec,
- sizeof(rvec)/sizeof(void), rvec_unpacker );
+ Coll( system, mpi_data, workspace->f, mpi_data->mpi_rvec,
+ sizeof(rvec)/sizeof(void), rvec_unpacker );
for( i = 0; i < system->n; ++i )
rvec_Copy( system->my_atoms[i].f, workspace->f[i] );
@@ -187,7 +187,7 @@ void Compute_Total_Force( reax_system *system, control_params *control,
}
void Validate_Lists( reax_system *system, storage *workspace, reax_list **lists,
- int step, int n, int N, int numH, MPI_Comm comm )
+ int step, int n, int N, int numH, MPI_Comm comm )
{
int i, comp, Hindex;
reax_list *bonds, *hbonds;
@@ -197,22 +197,22 @@ void Validate_Lists( reax_system *system, storage *workspace, reax_list **lists,
/* bond list */
if( N > 0 ) {
bonds = *lists + BONDS;
-
+
for( i = 0; i < N; ++i ) {
// if( i < n ) - we need to update ghost estimates for delayed nbrings
system->my_atoms[i].num_bonds = MAX(Num_Entries(i,bonds)*2, MIN_BONDS);
-
+
//if( End_Index(i, bonds) >= Start_Index(i+1, bonds)-2 )
//workspace->realloc.bonds = 1;
-
+
if( i < N-1 )
- comp = Start_Index(i+1, bonds);
+ comp = Start_Index(i+1, bonds);
else comp = bonds->num_intrs;
-
+
if( End_Index(i, bonds) > comp ) {
- fprintf( stderr, "step%d-bondchk failed: i=%d end(i)=%d str(i+1)=%d\n",
- step, i, End_Index(i,bonds), comp );
- MPI_Abort( comm, INSUFFICIENT_MEMORY );
+ fprintf( stderr, "step%d-bondchk failed: i=%d end(i)=%d str(i+1)=%d\n",
+ step, i, End_Index(i,bonds), comp );
+ MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
}
}
@@ -221,26 +221,26 @@ void Validate_Lists( reax_system *system, storage *workspace, reax_list **lists,
/* hbonds list */
if( numH > 0 ) {
hbonds = *lists + HBONDS;
-
+
for( i = 0; i < n; ++i ) {
Hindex = system->my_atoms[i].Hindex;
if( Hindex > -1 ) {
- system->my_atoms[i].num_hbonds =
- (int)(MAX( Num_Entries(Hindex, hbonds)*SAFER_ZONE, MIN_HBONDS ));
-
- //if( Num_Entries(i, hbonds) >=
- //(Start_Index(i+1,hbonds)-Start_Index(i,hbonds))*0.90/*DANGER_ZONE*/){
- // workspace->realloc.hbonds = 1;
-
- if( Hindex < numH-1 )
- comp = Start_Index(Hindex+1, hbonds);
- else comp = hbonds->num_intrs;
-
- if( End_Index(Hindex, hbonds) > comp ) {
- fprintf(stderr,"step%d-hbondchk failed: H=%d end(H)=%d str(H+1)=%d\n",
- step, Hindex, End_Index(Hindex,hbonds), comp );
- MPI_Abort( comm, INSUFFICIENT_MEMORY );
- }
+ system->my_atoms[i].num_hbonds =
+ (int)(MAX( Num_Entries(Hindex, hbonds)*SAFER_ZONE, MIN_HBONDS ));
+
+ //if( Num_Entries(i, hbonds) >=
+ //(Start_Index(i+1,hbonds)-Start_Index(i,hbonds))*0.90/*DANGER_ZONE*/){
+ // workspace->realloc.hbonds = 1;
+
+ if( Hindex < numH-1 )
+ comp = Start_Index(Hindex+1, hbonds);
+ else comp = hbonds->num_intrs;
+
+ if( End_Index(Hindex, hbonds) > comp ) {
+ fprintf(stderr,"step%d-hbondchk failed: H=%d end(H)=%d str(H+1)=%d\n",
+ step, Hindex, End_Index(Hindex,hbonds), comp );
+ MPI_Abort( comm, INSUFFICIENT_MEMORY );
+ }
}
}
}
@@ -257,8 +257,8 @@ real Compute_H( real r, real gamma, real *ctap )
taper = taper * r + ctap[3];
taper = taper * r + ctap[2];
taper = taper * r + ctap[1];
- taper = taper * r + ctap[0];
-
+ taper = taper * r + ctap[0];
+
dr3gamij_1 = ( r*r*r + gamma );
dr3gamij_3 = pow( dr3gamij_1 , 0.33333333333333 );
return taper * EV_to_KCALpMOL / dr3gamij_3;
@@ -273,24 +273,24 @@ real Compute_tabH( real r_ij, int ti, int tj )
tmin = MIN( ti, tj );
tmax = MAX( ti, tj );
- t = &( LR[tmin][tmax] );
+ t = &( LR[tmin][tmax] );
/* cubic spline interpolation */
r = (int)(r_ij * t->inv_dx);
if( r == 0 ) ++r;
base = (real)(r+1) * t->dx;
dif = r_ij - base;
- val = ((t->ele[r].d*dif + t->ele[r].c)*dif + t->ele[r].b)*dif +
+ val = ((t->ele[r].d*dif + t->ele[r].c)*dif + t->ele[r].b)*dif +
t->ele[r].a;
val *= EV_to_KCALpMOL / C_ele;
-
+
return val;
}
-void Init_Forces( reax_system *system, control_params *control,
- simulation_data *data, storage *workspace, reax_list **lists,
- output_controls *out_control, MPI_Comm comm ) {
+void Init_Forces( reax_system *system, control_params *control,
+ simulation_data *data, storage *workspace, reax_list **lists,
+ output_controls *out_control, MPI_Comm comm ) {
int i, j, pj;
int start_i, end_i;
int type_i, type_j;
@@ -323,7 +323,7 @@ void Init_Forces( reax_system *system, control_params *control,
num_hbonds = 0;
btop_i = btop_j = 0;
renbr = (data->step-data->prev_steps) % control->reneighbor == 0;
-
+
for( i = 0; i < system->N; ++i ) {
atom_i = &(system->my_atoms[i]);
type_i = atom_i->type;
@@ -331,7 +331,7 @@ void Init_Forces( reax_system *system, control_params *control,
end_i = End_Index(i, far_nbrs);
btop_i = End_Index( i, bonds );
sbp_i = &(system->reax_param.sbp[type_i]);
-
+
if( i < system->n ) {
local = 1;
cutoff = control->nonb_cut;
@@ -350,12 +350,12 @@ void Init_Forces( reax_system *system, control_params *control,
++Htop;
if( control->hbond_cut > 0 ) {
- ihb = sbp_i->p_hbond;
- if( ihb == 1 )
- ihb_top = End_Index( atom_i->Hindex, hbonds );
- else ihb_top = -1;
+ ihb = sbp_i->p_hbond;
+ if( ihb == 1 )
+ ihb_top = End_Index( atom_i->Hindex, hbonds );
+ else ihb_top = -1;
}
- }
+ }
/* update i-j distance - check if j is within cutoff */
for( pj = start_i; pj < end_i; ++pj ) {
@@ -363,91 +363,91 @@ void Init_Forces( reax_system *system, control_params *control,
j = nbr_pj->nbr;
atom_j = &(system->my_atoms[j]);
//fprintf( stderr, "%d%d i=%d x_i: %f %f %f,j=%d x_j: %f %f %f, d=%f\n",
- // MIN(atom_i->orig_id, atom_j->orig_id),
- // MAX(atom_i->orig_id, atom_j->orig_id),
- // i, atom_i->x[0], atom_i->x[1], atom_i->x[2],
- // j, atom_j->x[0], atom_j->x[1], atom_j->x[2], nbr_pj->d );
- if( renbr ) {
- if(nbr_pj->d <= cutoff)
- flag = 1;
- else flag = 0;
+ // MIN(atom_i->orig_id, atom_j->orig_id),
+ // MAX(atom_i->orig_id, atom_j->orig_id),
+ // i, atom_i->x[0], atom_i->x[1], atom_i->x[2],
+ // j, atom_j->x[0], atom_j->x[1], atom_j->x[2], nbr_pj->d );
+ if( renbr ) {
+ if(nbr_pj->d <= cutoff)
+ flag = 1;
+ else flag = 0;
}
else{
- nbr_pj->dvec[0] = atom_j->x[0] - atom_i->x[0];
- nbr_pj->dvec[1] = atom_j->x[1] - atom_i->x[1];
- nbr_pj->dvec[2] = atom_j->x[2] - atom_i->x[2];
- nbr_pj->d = rvec_Norm_Sqr( nbr_pj->dvec );
- if( nbr_pj->d <= SQR(cutoff) ) {
- nbr_pj->d = sqrt(nbr_pj->d);
- flag = 1;
- }
- else {
- flag = 0;
- }
+ nbr_pj->dvec[0] = atom_j->x[0] - atom_i->x[0];
+ nbr_pj->dvec[1] = atom_j->x[1] - atom_i->x[1];
+ nbr_pj->dvec[2] = atom_j->x[2] - atom_i->x[2];
+ nbr_pj->d = rvec_Norm_Sqr( nbr_pj->dvec );
+ if( nbr_pj->d <= SQR(cutoff) ) {
+ nbr_pj->d = sqrt(nbr_pj->d);
+ flag = 1;
+ }
+ else {
+ flag = 0;
+ }
}
-
- if( flag ){
- type_j = atom_j->type;
- r_ij = nbr_pj->d;
- sbp_j = &(system->reax_param.sbp[type_j]);
- twbp = &(system->reax_param.tbp[type_i][type_j]);
-
- if( local ) {
- /* H matrix entry */
- if( j < system->n || atom_i->orig_id < atom_j->orig_id ) {//tryQEq||1
- H->entries[Htop].j = j;
- //fprintf( stdout, "%d%d %d %d\n",
- // MIN(atom_i->orig_id, atom_j->orig_id),
- // MAX(atom_i->orig_id, atom_j->orig_id),
- // MIN(atom_i->orig_id, atom_j->orig_id),
- // MAX(atom_i->orig_id, atom_j->orig_id) );
- if( control->tabulate == 0 )
- H->entries[Htop].val = Compute_H(r_ij,twbp->gamma,workspace->Tap);
- else H->entries[Htop].val = Compute_tabH(r_ij, type_i, type_j);
- ++Htop;
- }
-
- /* hydrogen bond lists */
- if( control->hbond_cut > 0 && (ihb==1 || ihb==2) &&
- nbr_pj->d <= control->hbond_cut ) {
- // fprintf( stderr, "%d %d\n", atom1, atom2 );
- jhb = sbp_j->p_hbond;
- if( ihb == 1 && jhb == 2 ) {
- hbonds->select.hbond_list[ihb_top].nbr = j;
- hbonds->select.hbond_list[ihb_top].scl = 1;
- hbonds->select.hbond_list[ihb_top].ptr = nbr_pj;
- ++ihb_top;
- ++num_hbonds;
- }
- else if( j < system->n && ihb == 2 && jhb == 1 ) {
- jhb_top = End_Index( atom_j->Hindex, hbonds );
- hbonds->select.hbond_list[jhb_top].nbr = i;
- hbonds->select.hbond_list[jhb_top].scl = -1;
- hbonds->select.hbond_list[jhb_top].ptr = nbr_pj;
- Set_End_Index( atom_j->Hindex, jhb_top+1, hbonds );
- ++num_hbonds;
- }
- }
- }
-
- /* uncorrected bond orders */
- if( //(workspace->bond_mark[i] < 3 || workspace->bond_mark[j] < 3) &&
- nbr_pj->d <= control->bond_cut &&
- BOp( workspace, bonds, control->bo_cut,
- i , btop_i, nbr_pj, sbp_i, sbp_j, twbp ) ) {
- num_bonds += 2;
- ++btop_i;
-
- if( workspace->bond_mark[j] > workspace->bond_mark[i] + 1 )
- workspace->bond_mark[j] = workspace->bond_mark[i] + 1;
- else if( workspace->bond_mark[i] > workspace->bond_mark[j] + 1 ) {
- workspace->bond_mark[i] = workspace->bond_mark[j] + 1;
- //if( workspace->bond_mark[i] == 1000 )
- // workspace->done_after[i] = pj;
- }
- //fprintf( stdout, "%d%d - %d(%d) %d(%d)\n",
- // i , j, i, workspace->bond_mark[i], j, workspace->bond_mark[j] );
- }
+
+ if( flag ){
+ type_j = atom_j->type;
+ r_ij = nbr_pj->d;
+ sbp_j = &(system->reax_param.sbp[type_j]);
+ twbp = &(system->reax_param.tbp[type_i][type_j]);
+
+ if( local ) {
+ /* H matrix entry */
+ if( j < system->n || atom_i->orig_id < atom_j->orig_id ) {//tryQEq||1
+ H->entries[Htop].j = j;
+ //fprintf( stdout, "%d%d %d %d\n",
+ // MIN(atom_i->orig_id, atom_j->orig_id),
+ // MAX(atom_i->orig_id, atom_j->orig_id),
+ // MIN(atom_i->orig_id, atom_j->orig_id),
+ // MAX(atom_i->orig_id, atom_j->orig_id) );
+ if( control->tabulate == 0 )
+ H->entries[Htop].val = Compute_H(r_ij,twbp->gamma,workspace->Tap);
+ else H->entries[Htop].val = Compute_tabH(r_ij, type_i, type_j);
+ ++Htop;
+ }
+
+ /* hydrogen bond lists */
+ if( control->hbond_cut > 0 && (ihb==1 || ihb==2) &&
+ nbr_pj->d <= control->hbond_cut ) {
+ // fprintf( stderr, "%d %d\n", atom1, atom2 );
+ jhb = sbp_j->p_hbond;
+ if( ihb == 1 && jhb == 2 ) {
+ hbonds->select.hbond_list[ihb_top].nbr = j;
+ hbonds->select.hbond_list[ihb_top].scl = 1;
+ hbonds->select.hbond_list[ihb_top].ptr = nbr_pj;
+ ++ihb_top;
+ ++num_hbonds;
+ }
+ else if( j < system->n && ihb == 2 && jhb == 1 ) {
+ jhb_top = End_Index( atom_j->Hindex, hbonds );
+ hbonds->select.hbond_list[jhb_top].nbr = i;
+ hbonds->select.hbond_list[jhb_top].scl = -1;
+ hbonds->select.hbond_list[jhb_top].ptr = nbr_pj;
+ Set_End_Index( atom_j->Hindex, jhb_top+1, hbonds );
+ ++num_hbonds;
+ }
+ }
+ }
+
+ /* uncorrected bond orders */
+ if( //(workspace->bond_mark[i] < 3 || workspace->bond_mark[j] < 3) &&
+ nbr_pj->d <= control->bond_cut &&
+ BOp( workspace, bonds, control->bo_cut,
+ i , btop_i, nbr_pj, sbp_i, sbp_j, twbp ) ) {
+ num_bonds += 2;
+ ++btop_i;
+
+ if( workspace->bond_mark[j] > workspace->bond_mark[i] + 1 )
+ workspace->bond_mark[j] = workspace->bond_mark[i] + 1;
+ else if( workspace->bond_mark[i] > workspace->bond_mark[j] + 1 ) {
+ workspace->bond_mark[i] = workspace->bond_mark[j] + 1;
+ //if( workspace->bond_mark[i] == 1000 )
+ // workspace->done_after[i] = pj;
+ }
+ //fprintf( stdout, "%d%d - %d(%d) %d(%d)\n",
+ // i , j, i, workspace->bond_mark[i], j, workspace->bond_mark[j] );
+ }
}
}
@@ -455,90 +455,90 @@ void Init_Forces( reax_system *system, control_params *control,
if( local ) {
H->end[i] = Htop;
if( ihb == 1 )
- Set_End_Index( atom_i->Hindex, ihb_top, hbonds );
+ Set_End_Index( atom_i->Hindex, ihb_top, hbonds );
}
}
//fprintf( stderr, "after the first init loop\n" );
- /*for( i = system->n; i < system->N; ++i )
+ /*for( i = system->n; i < system->N; ++i )
if( workspace->bond_mark[i] > 3 ) {
start_i = Start_Index(i, bonds);
end_i = End_Index(i, bonds);
num_bonds -= (end_i - start_i);
- Set_End_Index(i, start_i, bonds );
+ Set_End_Index(i, start_i, bonds );
}*/
/*for( i = system->n; i < system->N; ++i ) {
start_i = Start_Index(i, far_nbrs);
end_i = workspace->done_after[i];
-
+
if( workspace->bond_mark[i] >= 2 && start_i < end_i ) {
atom_i = &(system->my_atoms[i]);
type_i = atom_i->type;
btop_i = End_Index( i, bonds );
sbp_i = &(system->reax_param.sbp[type_i]);
-
+
for( pj = start_i; pj < end_i; ++pj ) {
- nbr_pj = &( far_nbrs->select.far_nbr_list[pj] );
- j = nbr_pj->nbr;
-
- if( workspace->bond_mark[j] >= 2 && nbr_pj->d <= control->bond_cut ) {
- atom_j = &(system->my_atoms[j]);
- type_j = atom_j->type;
- sbp_j = &(system->reax_param.sbp[type_j]);
- twbp = &(system->reax_param.tbp[type_i][type_j]);
-
- if( BOp( workspace, bonds, control->bo_cut,
- i , btop_i, nbr_pj, sbp_i, sbp_j, twbp ) ) {
- num_bonds += 2;
- ++btop_i;
-
- if( workspace->bond_mark[j] > workspace->bond_mark[i] + 1 )
- workspace->bond_mark[j] = workspace->bond_mark[i] + 1;
- else if( workspace->bond_mark[i] > workspace->bond_mark[j] + 1 )
- workspace->bond_mark[i] = workspace->bond_mark[j] + 1;
-
- //fprintf( stdout, "%d%d - %d(%d) %d(%d) new\n",
- // i , j, i, workspace->bond_mark[i], j, workspace->bond_mark[j] );
- }
- }
+ nbr_pj = &( far_nbrs->select.far_nbr_list[pj] );
+ j = nbr_pj->nbr;
+
+ if( workspace->bond_mark[j] >= 2 && nbr_pj->d <= control->bond_cut ) {
+ atom_j = &(system->my_atoms[j]);
+ type_j = atom_j->type;
+ sbp_j = &(system->reax_param.sbp[type_j]);
+ twbp = &(system->reax_param.tbp[type_i][type_j]);
+
+ if( BOp( workspace, bonds, control->bo_cut,
+ i , btop_i, nbr_pj, sbp_i, sbp_j, twbp ) ) {
+ num_bonds += 2;
+ ++btop_i;
+
+ if( workspace->bond_mark[j] > workspace->bond_mark[i] + 1 )
+ workspace->bond_mark[j] = workspace->bond_mark[i] + 1;
+ else if( workspace->bond_mark[i] > workspace->bond_mark[j] + 1 )
+ workspace->bond_mark[i] = workspace->bond_mark[j] + 1;
+
+ //fprintf( stdout, "%d%d - %d(%d) %d(%d) new\n",
+ // i , j, i, workspace->bond_mark[i], j, workspace->bond_mark[j] );
+ }
+ }
}
Set_End_Index( i, btop_i, bonds );
}
}*/
-
+
workspace->realloc.Htop = Htop;
workspace->realloc.num_bonds = num_bonds;
workspace->realloc.num_hbonds = num_hbonds;
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "p%d @ step%d: Htop = %d num_bonds = %d num_hbonds = %d\n",
- system->my_rank, data->step, Htop, num_bonds, num_hbonds );
+ fprintf( stderr, "p%d @ step%d: Htop = %d num_bonds = %d num_hbonds = %d\n",
+ system->my_rank, data->step, Htop, num_bonds, num_hbonds );
MPI_Barrier( comm );
#endif
#if defined( DEBUG )
- Print_Bonds( system, bonds, "debugbonds.out" );
- Print_Bond_List2( system, bonds, "pbonds.out" );
+ Print_Bonds( system, bonds, "debugbonds.out" );
+ Print_Bond_List2( system, bonds, "pbonds.out" );
Print_Sparse_Matrix( system, H );
for( i = 0; i < H->n; ++i )
for( j = H->start[i]; j < H->end[i]; ++j )
- fprintf( stderr, "%d %d %.15e\n",
- MIN(system->my_atoms[i].orig_id,
- system->my_atoms[H->entries[j].j].orig_id),
- MAX(system->my_atoms[i].orig_id,
- system->my_atoms[H->entries[j].j].orig_id),
- H->entries[j].val );
+ fprintf( stderr, "%d %d %.15e\n",
+ MIN(system->my_atoms[i].orig_id,
+ system->my_atoms[H->entries[j].j].orig_id),
+ MAX(system->my_atoms[i].orig_id,
+ system->my_atoms[H->entries[j].j].orig_id),
+ H->entries[j].val );
#endif
- Validate_Lists( system, workspace, lists, data->step,
- system->n, system->N, system->numH, comm );
+ Validate_Lists( system, workspace, lists, data->step,
+ system->n, system->N, system->numH, comm );
}
-void Init_Forces_noQEq( reax_system *system, control_params *control,
- simulation_data *data, storage *workspace,
- reax_list **lists, output_controls *out_control,
- MPI_Comm comm ) {
+void Init_Forces_noQEq( reax_system *system, control_params *control,
+ simulation_data *data, storage *workspace,
+ reax_list **lists, output_controls *out_control,
+ MPI_Comm comm ) {
int i, j, pj;
int start_i, end_i;
int type_i, type_j;
@@ -567,7 +567,7 @@ void Init_Forces_noQEq( reax_system *system, control_params *control,
num_hbonds = 0;
btop_i = btop_j = 0;
renbr = (data->step-data->prev_steps) % control->reneighbor == 0;
-
+
for( i = 0; i < system->N; ++i ) {
atom_i = &(system->my_atoms[i]);
type_i = atom_i->type;
@@ -575,7 +575,7 @@ void Init_Forces_noQEq( reax_system *system, control_params *control,
end_i = End_Index(i, far_nbrs);
btop_i = End_Index( i, bonds );
sbp_i = &(system->reax_param.sbp[type_i]);
-
+
if( i < system->n ) {
local = 1;
cutoff = MAX( control->hbond_cut, control->bond_cut );
@@ -590,7 +590,7 @@ void Init_Forces_noQEq( reax_system *system, control_params *control,
if( local && control->hbond_cut > 0 ) {
ihb = sbp_i->p_hbond;
if( ihb == 1 )
- ihb_top = End_Index( atom_i->Hindex, hbonds );
+ ihb_top = End_Index( atom_i->Hindex, hbonds );
else ihb_top = -1;
}
@@ -599,75 +599,75 @@ void Init_Forces_noQEq( reax_system *system, control_params *control,
nbr_pj = &( far_nbrs->select.far_nbr_list[pj] );
j = nbr_pj->nbr;
atom_j = &(system->my_atoms[j]);
-
- if( renbr ) {
- if( nbr_pj->d <= cutoff )
- flag = 1;
- else flag = 0;
+
+ if( renbr ) {
+ if( nbr_pj->d <= cutoff )
+ flag = 1;
+ else flag = 0;
}
else{
- nbr_pj->dvec[0] = atom_j->x[0] - atom_i->x[0];
- nbr_pj->dvec[1] = atom_j->x[1] - atom_i->x[1];
- nbr_pj->dvec[2] = atom_j->x[2] - atom_i->x[2];
- nbr_pj->d = rvec_Norm_Sqr( nbr_pj->dvec );
- if( nbr_pj->d <= SQR(cutoff) ) {
- nbr_pj->d = sqrt(nbr_pj->d);
- flag = 1;
- }
- else {
- flag = 0;
- }
+ nbr_pj->dvec[0] = atom_j->x[0] - atom_i->x[0];
+ nbr_pj->dvec[1] = atom_j->x[1] - atom_i->x[1];
+ nbr_pj->dvec[2] = atom_j->x[2] - atom_i->x[2];
+ nbr_pj->d = rvec_Norm_Sqr( nbr_pj->dvec );
+ if( nbr_pj->d <= SQR(cutoff) ) {
+ nbr_pj->d = sqrt(nbr_pj->d);
+ flag = 1;
+ }
+ else {
+ flag = 0;
+ }
}
-
+
if( flag ) {
- type_j = atom_j->type;
- r_ij = nbr_pj->d;
- sbp_j = &(system->reax_param.sbp[type_j]);
- twbp = &(system->reax_param.tbp[type_i][type_j]);
-
- if( local ) {
- /* hydrogen bond lists */
- if( control->hbond_cut > 0 && (ihb==1 || ihb==2) &&
- nbr_pj->d <= control->hbond_cut ) {
- // fprintf( stderr, "%d %d\n", atom1, atom2 );
- jhb = sbp_j->p_hbond;
- if( ihb == 1 && jhb == 2 ) {
- hbonds->select.hbond_list[ihb_top].nbr = j;
- hbonds->select.hbond_list[ihb_top].scl = 1;
- hbonds->select.hbond_list[ihb_top].ptr = nbr_pj;
- ++ihb_top;
- ++num_hbonds;
- }
- else if( j < system->n && ihb == 2 && jhb == 1 ) {
- jhb_top = End_Index( atom_j->Hindex, hbonds );
- hbonds->select.hbond_list[jhb_top].nbr = i;
- hbonds->select.hbond_list[jhb_top].scl = -1;
- hbonds->select.hbond_list[jhb_top].ptr = nbr_pj;
- Set_End_Index( atom_j->Hindex, jhb_top+1, hbonds );
- ++num_hbonds;
- }
- }
- }
-
-
- /* uncorrected bond orders */
- if( //(workspace->bond_mark[i] < 3 || workspace->bond_mark[j] < 3) &&
- nbr_pj->d <= control->bond_cut &&
- BOp( workspace, bonds, control->bo_cut,
- i , btop_i, nbr_pj, sbp_i, sbp_j, twbp ) ) {
- num_bonds += 2;
- ++btop_i;
-
- if( workspace->bond_mark[j] > workspace->bond_mark[i] + 1 )
- workspace->bond_mark[j] = workspace->bond_mark[i] + 1;
- else if( workspace->bond_mark[i] > workspace->bond_mark[j] + 1 ) {
- workspace->bond_mark[i] = workspace->bond_mark[j] + 1;
- //if( workspace->bond_mark[i] == 1000 )
- // workspace->done_after[i] = pj;
- }
- //fprintf( stdout, "%d%d - %d(%d) %d(%d)\n",
- // i , j, i, workspace->bond_mark[i], j, workspace->bond_mark[j] );
- }
+ type_j = atom_j->type;
+ r_ij = nbr_pj->d;
+ sbp_j = &(system->reax_param.sbp[type_j]);
+ twbp = &(system->reax_param.tbp[type_i][type_j]);
+
+ if( local ) {
+ /* hydrogen bond lists */
+ if( control->hbond_cut > 0 && (ihb==1 || ihb==2) &&
+ nbr_pj->d <= control->hbond_cut ) {
+ // fprintf( stderr, "%d %d\n", atom1, atom2 );
+ jhb = sbp_j->p_hbond;
+ if( ihb == 1 && jhb == 2 ) {
+ hbonds->select.hbond_list[ihb_top].nbr = j;
+ hbonds->select.hbond_list[ihb_top].scl = 1;
+ hbonds->select.hbond_list[ihb_top].ptr = nbr_pj;
+ ++ihb_top;
+ ++num_hbonds;
+ }
+ else if( j < system->n && ihb == 2 && jhb == 1 ) {
+ jhb_top = End_Index( atom_j->Hindex, hbonds );
+ hbonds->select.hbond_list[jhb_top].nbr = i;
+ hbonds->select.hbond_list[jhb_top].scl = -1;
+ hbonds->select.hbond_list[jhb_top].ptr = nbr_pj;
+ Set_End_Index( atom_j->Hindex, jhb_top+1, hbonds );
+ ++num_hbonds;
+ }
+ }
+ }
+
+
+ /* uncorrected bond orders */
+ if( //(workspace->bond_mark[i] < 3 || workspace->bond_mark[j] < 3) &&
+ nbr_pj->d <= control->bond_cut &&
+ BOp( workspace, bonds, control->bo_cut,
+ i , btop_i, nbr_pj, sbp_i, sbp_j, twbp ) ) {
+ num_bonds += 2;
+ ++btop_i;
+
+ if( workspace->bond_mark[j] > workspace->bond_mark[i] + 1 )
+ workspace->bond_mark[j] = workspace->bond_mark[i] + 1;
+ else if( workspace->bond_mark[i] > workspace->bond_mark[j] + 1 ) {
+ workspace->bond_mark[i] = workspace->bond_mark[j] + 1;
+ //if( workspace->bond_mark[i] == 1000 )
+ // workspace->done_after[i] = pj;
+ }
+ //fprintf( stdout, "%d%d - %d(%d) %d(%d)\n",
+ // i , j, i, workspace->bond_mark[i], j, workspace->bond_mark[j] );
+ }
}
}
@@ -676,35 +676,35 @@ void Init_Forces_noQEq( reax_system *system, control_params *control,
Set_End_Index( atom_i->Hindex, ihb_top, hbonds );
}
- /*for( i = system->n; i < system->N; ++i )
+ /*for( i = system->n; i < system->N; ++i )
if( workspace->bond_mark[i] > 3 ) {
start_i = Start_Index(i, bonds);
end_i = End_Index(i, bonds);
num_bonds -= (end_i - start_i);
- Set_End_Index(i, start_i, bonds );
+ Set_End_Index(i, start_i, bonds );
}*/
-
+
workspace->realloc.num_bonds = num_bonds;
workspace->realloc.num_hbonds = num_hbonds;
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "p%d @ step%d: num_bonds = %d num_hbonds = %d\n",
- system->my_rank, data->step, num_bonds, num_hbonds );
+ fprintf( stderr, "p%d @ step%d: num_bonds = %d num_hbonds = %d\n",
+ system->my_rank, data->step, num_bonds, num_hbonds );
MPI_Barrier( comm );
#endif
#if defined( DEBUG )
- Print_Bonds( system, bonds, "debugbonds.out" );
- Print_Bond_List2( system, bonds, "pbonds.out" );
+ Print_Bonds( system, bonds, "debugbonds.out" );
+ Print_Bond_List2( system, bonds, "pbonds.out" );
#endif
- Validate_Lists( system, workspace, lists, data->step,
- system->n, system->N, system->numH, comm );
+ Validate_Lists( system, workspace, lists, data->step,
+ system->n, system->N, system->numH, comm );
}
-void Estimate_Storages( reax_system *system, control_params *control,
- reax_list **lists, int *Htop, int *hb_top,
- int *bond_top, int *num_3body, MPI_Comm comm )
+void Estimate_Storages( reax_system *system, control_params *control,
+ reax_list **lists, int *Htop, int *hb_top,
+ int *bond_top, int *num_3body, MPI_Comm comm )
{
int i, j, pj;
int start_i, end_i;
@@ -733,7 +733,7 @@ void Estimate_Storages( reax_system *system, control_params *control,
start_i = Start_Index(i, far_nbrs);
end_i = End_Index(i, far_nbrs);
sbp_i = &(system->reax_param.sbp[type_i]);
-
+
if( i < system->n ) {
local = 1;
cutoff = control->nonb_cut;
@@ -745,63 +745,63 @@ void Estimate_Storages( reax_system *system, control_params *control,
cutoff = control->bond_cut;
ihb = -1;
}
-
+
for( pj = start_i; pj < end_i; ++pj ) {
nbr_pj = &( far_nbrs->select.far_nbr_list[pj] );
j = nbr_pj->nbr;
atom_j = &(system->my_atoms[j]);
if(nbr_pj->d <= cutoff) {
- type_j = system->my_atoms[j].type;
- r_ij = nbr_pj->d;
- sbp_j = &(system->reax_param.sbp[type_j]);
- twbp = &(system->reax_param.tbp[type_i][type_j]);
-
- if( local ) {
- if( j < system->n || atom_i->orig_id < atom_j->orig_id ) //tryQEq ||1
- ++(*Htop);
-
- /* hydrogen bond lists */
- if( control->hbond_cut > 0.1 && (ihb==1 || ihb==2) &&
- nbr_pj->d <= control->hbond_cut ) {
- jhb = sbp_j->p_hbond;
- if( ihb == 1 && jhb == 2 )
- ++hb_top[i];
- else if( j < system->n && ihb == 2 && jhb == 1 )
- ++hb_top[j];
- }
- }
-
- /* uncorrected bond orders */
- if( nbr_pj->d <= control->bond_cut ) {
- r2 = SQR(r_ij);
-
- if( sbp_i->r_s > 0.0 && sbp_j->r_s > 0.0) {
- C12 = twbp->p_bo1 * pow( r_ij / twbp->r_s, twbp->p_bo2 );
- BO_s = (1.0 + control->bo_cut) * exp( C12 );
- }
- else BO_s = C12 = 0.0;
-
- if( sbp_i->r_pi > 0.0 && sbp_j->r_pi > 0.0) {
- C34 = twbp->p_bo3 * pow( r_ij / twbp->r_p, twbp->p_bo4 );
- BO_pi = exp( C34 );
- }
- else BO_pi = C34 = 0.0;
-
- if( sbp_i->r_pi_pi > 0.0 && sbp_j->r_pi_pi > 0.0) {
- C56 = twbp->p_bo5 * pow( r_ij / twbp->r_pp, twbp->p_bo6 );
- BO_pi2= exp( C56 );
- }
- else BO_pi2 = C56 = 0.0;
-
- /* Initially BO values are the uncorrected ones, page 1 */
- BO = BO_s + BO_pi + BO_pi2;
-
- if( BO >= control->bo_cut ) {
- ++bond_top[i];
- ++bond_top[j];
- }
- }
+ type_j = system->my_atoms[j].type;
+ r_ij = nbr_pj->d;
+ sbp_j = &(system->reax_param.sbp[type_j]);
+ twbp = &(system->reax_param.tbp[type_i][type_j]);
+
+ if( local ) {
+ if( j < system->n || atom_i->orig_id < atom_j->orig_id ) //tryQEq ||1
+ ++(*Htop);
+
+ /* hydrogen bond lists */
+ if( control->hbond_cut > 0.1 && (ihb==1 || ihb==2) &&
+ nbr_pj->d <= control->hbond_cut ) {
+ jhb = sbp_j->p_hbond;
+ if( ihb == 1 && jhb == 2 )
+ ++hb_top[i];
+ else if( j < system->n && ihb == 2 && jhb == 1 )
+ ++hb_top[j];
+ }
+ }
+
+ /* uncorrected bond orders */
+ if( nbr_pj->d <= control->bond_cut ) {
+ r2 = SQR(r_ij);
+
+ if( sbp_i->r_s > 0.0 && sbp_j->r_s > 0.0) {
+ C12 = twbp->p_bo1 * pow( r_ij / twbp->r_s, twbp->p_bo2 );
+ BO_s = (1.0 + control->bo_cut) * exp( C12 );
+ }
+ else BO_s = C12 = 0.0;
+
+ if( sbp_i->r_pi > 0.0 && sbp_j->r_pi > 0.0) {
+ C34 = twbp->p_bo3 * pow( r_ij / twbp->r_p, twbp->p_bo4 );
+ BO_pi = exp( C34 );
+ }
+ else BO_pi = C34 = 0.0;
+
+ if( sbp_i->r_pi_pi > 0.0 && sbp_j->r_pi_pi > 0.0) {
+ C56 = twbp->p_bo5 * pow( r_ij / twbp->r_pp, twbp->p_bo6 );
+ BO_pi2= exp( C56 );
+ }
+ else BO_pi2 = C56 = 0.0;
+
+ /* Initially BO values are the uncorrected ones, page 1 */
+ BO = BO_s + BO_pi + BO_pi2;
+
+ if( BO >= control->bo_cut ) {
+ ++bond_top[i];
+ ++bond_top[j];
+ }
+ }
}
}
}
@@ -818,17 +818,17 @@ void Estimate_Storages( reax_system *system, control_params *control,
}
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "p%d @ estimate storages: Htop = %d, num_3body = %d\n",
- system->my_rank, *Htop, *num_3body );
+ fprintf( stderr, "p%d @ estimate storages: Htop = %d, num_3body = %d\n",
+ system->my_rank, *Htop, *num_3body );
MPI_Barrier( comm );
#endif
}
-void Compute_Forces( reax_system *system, control_params *control,
- simulation_data *data, storage *workspace,
- reax_list **lists, output_controls *out_control,
- mpi_datatypes *mpi_data )
+void Compute_Forces( reax_system *system, control_params *control,
+ simulation_data *data, storage *workspace,
+ reax_list **lists, output_controls *out_control,
+ mpi_datatypes *mpi_data )
{
MPI_Comm comm;
int qeq_flag;
@@ -853,8 +853,8 @@ void Compute_Forces( reax_system *system, control_params *control,
if( qeq_flag )
Init_Forces( system, control, data, workspace, lists, out_control, comm );
else
- Init_Forces_noQEq( system, control, data, workspace,
- lists, out_control, comm );
+ Init_Forces_noQEq( system, control, data, workspace,
+ lists, out_control, comm );
#if defined(LOG_PERFORMANCE)
//MPI_Barrier( mpi_data->world );
@@ -864,8 +864,8 @@ void Compute_Forces( reax_system *system, control_params *control,
/********* bonded interactions ************/
- Compute_Bonded_Forces( system, control, data, workspace,
- lists, out_control, mpi_data->world );
+ Compute_Bonded_Forces( system, control, data, workspace,
+ lists, out_control, mpi_data->world );
#if defined(LOG_PERFORMANCE)
//MPI_Barrier( mpi_data->world );
@@ -873,8 +873,8 @@ void Compute_Forces( reax_system *system, control_params *control,
Update_Timing_Info( &t_start, &(data->timing.bonded) );
#endif
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "p%d @ step%d: completed bonded\n",
- system->my_rank, data->step );
+ fprintf( stderr, "p%d @ step%d: completed bonded\n",
+ system->my_rank, data->step );
MPI_Barrier( mpi_data->world );
#endif
@@ -886,7 +886,7 @@ void Compute_Forces( reax_system *system, control_params *control,
#if defined(LOG_PERFORMANCE)
//MPI_Barrier( mpi_data->world );
- if( system->my_rank == MASTER_NODE )
+ if( system->my_rank == MASTER_NODE )
Update_Timing_Info( &t_start, &(data->timing.qEq) );
#endif
#if defined(DEBUG_FOCUS)
@@ -897,8 +897,8 @@ void Compute_Forces( reax_system *system, control_params *control,
/********* nonbonded interactions ************/
- Compute_NonBonded_Forces( system, control, data, workspace,
- lists, out_control, mpi_data->world );
+ Compute_NonBonded_Forces( system, control, data, workspace,
+ lists, out_control, mpi_data->world );
#if defined(LOG_PERFORMANCE)
//MPI_Barrier( mpi_data->world );
@@ -906,8 +906,8 @@ void Compute_Forces( reax_system *system, control_params *control,
Update_Timing_Info( &t_start, &(data->timing.nonb) );
#endif
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "p%d @ step%d: nonbonded forces completed\n",
- system->my_rank, data->step );
+ fprintf( stderr, "p%d @ step%d: nonbonded forces completed\n",
+ system->my_rank, data->step );
MPI_Barrier( mpi_data->world );
#endif
@@ -921,14 +921,14 @@ void Compute_Forces( reax_system *system, control_params *control,
Update_Timing_Info( &t_start, &(data->timing.bonded) );
#endif
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "p%d @ step%d: total forces computed\n",
- system->my_rank, data->step );
+ fprintf( stderr, "p%d @ step%d: total forces computed\n",
+ system->my_rank, data->step );
//Print_Total_Force( system, data, workspace );
MPI_Barrier( mpi_data->world );
#endif
#if defined(TEST_FORCES)
- Print_Force_Files( system, control, data, workspace,
- lists, out_control, mpi_data );
+ Print_Force_Files( system, control, data, workspace,
+ lists, out_control, mpi_data );
#endif
}
diff --git a/src/USER-REAXC/reaxc_forces.h b/src/USER-REAXC/reaxc_forces.h
index fe97a7121c89246e0123a0a8261a41aaed3bbf44..6c839a7023a1f794616e21549420fef5e1250dce 100644
--- a/src/USER-REAXC/reaxc_forces.h
+++ b/src/USER-REAXC/reaxc_forces.h
@@ -14,12 +14,12 @@
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -33,8 +33,8 @@
extern interaction_function Interaction_Functions[NUM_INTRS];
void Init_Force_Functions( control_params* );
-void Compute_Forces( reax_system*, control_params*, simulation_data*,
- storage*, reax_list**, output_controls*, mpi_datatypes* );
-void Estimate_Storages( reax_system*, control_params*, reax_list**,
- int*, int*, int*, int*, MPI_Comm );
+void Compute_Forces( reax_system*, control_params*, simulation_data*,
+ storage*, reax_list**, output_controls*, mpi_datatypes* );
+void Estimate_Storages( reax_system*, control_params*, reax_list**,
+ int*, int*, int*, int*, MPI_Comm );
#endif
diff --git a/src/USER-REAXC/reaxc_hydrogen_bonds.cpp b/src/USER-REAXC/reaxc_hydrogen_bonds.cpp
index d9d40267b7c3ec71f9fec2f31dc5b8bfd51fc013..12a929d3b822f4ed9a676abcbe14ffe78bd6982b 100644
--- a/src/USER-REAXC/reaxc_hydrogen_bonds.cpp
+++ b/src/USER-REAXC/reaxc_hydrogen_bonds.cpp
@@ -14,12 +14,12 @@
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -40,9 +40,9 @@
#endif
-void Hydrogen_Bonds( reax_system *system, control_params *control,
- simulation_data *data, storage *workspace,
- reax_list **lists, output_controls *out_control )
+void Hydrogen_Bonds( reax_system *system, control_params *control,
+ simulation_data *data, storage *workspace,
+ reax_list **lists, output_controls *out_control )
{
int i, j, k, pi, pk;
int type_i, type_j, type_k;
@@ -75,7 +75,7 @@ void Hydrogen_Bonds( reax_system *system, control_params *control,
/* loops below discover the Hydrogen bonds between i-j-k triplets.
here j is H atom and there has to be some bond between i and j.
Hydrogen bond is between j and k.
- so in this function i->X, j->H, k->Z when we map
+ so in this function i->X, j->H, k->Z when we map
variables onto the ones in the handout.*/
for( j = 0; j < system->n; ++j )
/* j has to be of type H */
@@ -86,157 +86,157 @@ void Hydrogen_Bonds( reax_system *system, control_params *control,
end_j = End_Index(j, bonds);
hb_start_j = Start_Index( system->my_atoms[j].Hindex, hbonds );
hb_end_j = End_Index( system->my_atoms[j].Hindex, hbonds );
-
+
top = 0;
for( pi = start_j; pi < end_j; ++pi ) {
- pbond_ij = &( bond_list[pi] );
- i = pbond_ij->nbr;
- bo_ij = &(pbond_ij->bo_data);
- type_i = system->my_atoms[i].type;
-
- if( system->reax_param.sbp[type_i].p_hbond == 2 &&
- bo_ij->BO >= HB_THRESHOLD )
- hblist[top++] = pi;
+ pbond_ij = &( bond_list[pi] );
+ i = pbond_ij->nbr;
+ bo_ij = &(pbond_ij->bo_data);
+ type_i = system->my_atoms[i].type;
+
+ if( system->reax_param.sbp[type_i].p_hbond == 2 &&
+ bo_ij->BO >= HB_THRESHOLD )
+ hblist[top++] = pi;
}
-
- // fprintf( stderr, "j: %d, top: %d, hb_start_j: %d, hb_end_j:%d\n",
+
+ // fprintf( stderr, "j: %d, top: %d, hb_start_j: %d, hb_end_j:%d\n",
// j, top, hb_start_j, hb_end_j );
-
+
for( pk = hb_start_j; pk < hb_end_j; ++pk ) {
- /* set k's varibles */
- k = hbond_list[pk].nbr;
- type_k = system->my_atoms[k].type;
- nbr_jk = hbond_list[pk].ptr;
- r_jk = nbr_jk->d;
- rvec_Scale( dvec_jk, hbond_list[pk].scl, nbr_jk->dvec );
-
- for( itr = 0; itr < top; ++itr ) {
- pi = hblist[itr];
- pbond_ij = &( bonds->select.bond_list[pi] );
- i = pbond_ij->nbr;
-
- if( system->my_atoms[i].orig_id != system->my_atoms[k].orig_id ) {
- bo_ij = &(pbond_ij->bo_data);
- type_i = system->my_atoms[i].type;
- r_ij = pbond_ij->d;
- hbp = &(system->reax_param.hbp[ type_i ][ type_j ][ type_k ]);
- ++num_hb_intrs;
-
- Calculate_Theta( pbond_ij->dvec, pbond_ij->d, dvec_jk, r_jk,
- &theta, &cos_theta );
- /* the derivative of cos(theta) */
- Calculate_dCos_Theta( pbond_ij->dvec, pbond_ij->d, dvec_jk, r_jk,
- &dcos_theta_di, &dcos_theta_dj,
- &dcos_theta_dk );
-
- /* hyrogen bond energy*/
- sin_theta2 = sin( theta/2.0 );
- sin_xhz4 = SQR(sin_theta2);
- sin_xhz4 *= sin_xhz4;
- cos_xhz1 = ( 1.0 - cos_theta );
- exp_hb2 = exp( -hbp->p_hb2 * bo_ij->BO );
- exp_hb3 = exp( -hbp->p_hb3 * ( hbp->r0_hb / r_jk +
- r_jk / hbp->r0_hb - 2.0 ) );
-
- data->my_en.e_hb += e_hb =
- hbp->p_hb1 * (1.0 - exp_hb2) * exp_hb3 * sin_xhz4;
-
- CEhb1 = hbp->p_hb1 * hbp->p_hb2 * exp_hb2 * exp_hb3 * sin_xhz4;
- CEhb2 = -hbp->p_hb1/2.0 * (1.0 - exp_hb2) * exp_hb3 * cos_xhz1;
- CEhb3 = -hbp->p_hb3 *
- (-hbp->r0_hb / SQR(r_jk) + 1.0 / hbp->r0_hb) * e_hb;
-
- /*fprintf( stdout,
- "%6d%6d%6d%12.6f%12.6f%12.6f%12.6f%12.6f%12.6f%12.6f%12.6f%12.6f\n",
- system->my_atoms[i].orig_id, system->my_atoms[j].orig_id,
- system->my_atoms[k].orig_id,
- r_jk, theta, hbp->p_hb1, exp_hb2, hbp->p_hb3, hbp->r0_hb,
- exp_hb3, sin_xhz4, e_hb ); */
-
- /* hydrogen bond forces */
- bo_ij->Cdbo += CEhb1; // dbo term
-
- if( control->virial == 0 ) {
- // dcos terms
- rvec_ScaledAdd( workspace->f[i], +CEhb2, dcos_theta_di );
- rvec_ScaledAdd( workspace->f[j], +CEhb2, dcos_theta_dj );
- rvec_ScaledAdd( workspace->f[k], +CEhb2, dcos_theta_dk );
- // dr terms
- rvec_ScaledAdd( workspace->f[j], -CEhb3/r_jk, dvec_jk );
- rvec_ScaledAdd( workspace->f[k], +CEhb3/r_jk, dvec_jk );
- }
- else {
- /* for pressure coupling, terms that are not related to bond order
- derivatives are added directly into pressure vector/tensor */
- rvec_Scale( force, +CEhb2, dcos_theta_di ); // dcos terms
- rvec_Add( workspace->f[i], force );
- rvec_iMultiply( ext_press, pbond_ij->rel_box, force );
- rvec_ScaledAdd( data->my_ext_press, 1.0, ext_press );
-
- rvec_ScaledAdd( workspace->f[j], +CEhb2, dcos_theta_dj );
-
- ivec_Scale( rel_jk, hbond_list[pk].scl, nbr_jk->rel_box );
- rvec_Scale( force, +CEhb2, dcos_theta_dk );
- rvec_Add( workspace->f[k], force );
- rvec_iMultiply( ext_press, rel_jk, force );
- rvec_ScaledAdd( data->my_ext_press, 1.0, ext_press );
- // dr terms
- rvec_ScaledAdd( workspace->f[j], -CEhb3/r_jk, dvec_jk );
-
- rvec_Scale( force, CEhb3/r_jk, dvec_jk );
- rvec_Add( workspace->f[k], force );
- rvec_iMultiply( ext_press, rel_jk, force );
- rvec_ScaledAdd( data->my_ext_press, 1.0, ext_press );
- }
-
- /* tally into per-atom virials */
- if (system->pair_ptr->vflag_atom || system->pair_ptr->evflag) {
- rvec_ScaledSum( delij, 1., system->my_atoms[i].x,
- -1., system->my_atoms[j].x );
- rvec_ScaledSum( delkj, 1., system->my_atoms[k].x,
- -1., system->my_atoms[j].x );
-
- rvec_Scale(fi_tmp, CEhb2, dcos_theta_di);
- rvec_Scale(fk_tmp, CEhb2, dcos_theta_dk);
- rvec_ScaledAdd(fk_tmp, CEhb3/r_jk, dvec_jk);
+ /* set k's varibles */
+ k = hbond_list[pk].nbr;
+ type_k = system->my_atoms[k].type;
+ nbr_jk = hbond_list[pk].ptr;
+ r_jk = nbr_jk->d;
+ rvec_Scale( dvec_jk, hbond_list[pk].scl, nbr_jk->dvec );
+
+ for( itr = 0; itr < top; ++itr ) {
+ pi = hblist[itr];
+ pbond_ij = &( bonds->select.bond_list[pi] );
+ i = pbond_ij->nbr;
+
+ if( system->my_atoms[i].orig_id != system->my_atoms[k].orig_id ) {
+ bo_ij = &(pbond_ij->bo_data);
+ type_i = system->my_atoms[i].type;
+ r_ij = pbond_ij->d;
+ hbp = &(system->reax_param.hbp[ type_i ][ type_j ][ type_k ]);
+ ++num_hb_intrs;
+
+ Calculate_Theta( pbond_ij->dvec, pbond_ij->d, dvec_jk, r_jk,
+ &theta, &cos_theta );
+ /* the derivative of cos(theta) */
+ Calculate_dCos_Theta( pbond_ij->dvec, pbond_ij->d, dvec_jk, r_jk,
+ &dcos_theta_di, &dcos_theta_dj,
+ &dcos_theta_dk );
+
+ /* hyrogen bond energy*/
+ sin_theta2 = sin( theta/2.0 );
+ sin_xhz4 = SQR(sin_theta2);
+ sin_xhz4 *= sin_xhz4;
+ cos_xhz1 = ( 1.0 - cos_theta );
+ exp_hb2 = exp( -hbp->p_hb2 * bo_ij->BO );
+ exp_hb3 = exp( -hbp->p_hb3 * ( hbp->r0_hb / r_jk +
+ r_jk / hbp->r0_hb - 2.0 ) );
+
+ data->my_en.e_hb += e_hb =
+ hbp->p_hb1 * (1.0 - exp_hb2) * exp_hb3 * sin_xhz4;
+
+ CEhb1 = hbp->p_hb1 * hbp->p_hb2 * exp_hb2 * exp_hb3 * sin_xhz4;
+ CEhb2 = -hbp->p_hb1/2.0 * (1.0 - exp_hb2) * exp_hb3 * cos_xhz1;
+ CEhb3 = -hbp->p_hb3 *
+ (-hbp->r0_hb / SQR(r_jk) + 1.0 / hbp->r0_hb) * e_hb;
+
+ /*fprintf( stdout,
+ "%6d%6d%6d%12.6f%12.6f%12.6f%12.6f%12.6f%12.6f%12.6f%12.6f%12.6f\n",
+ system->my_atoms[i].orig_id, system->my_atoms[j].orig_id,
+ system->my_atoms[k].orig_id,
+ r_jk, theta, hbp->p_hb1, exp_hb2, hbp->p_hb3, hbp->r0_hb,
+ exp_hb3, sin_xhz4, e_hb ); */
+
+ /* hydrogen bond forces */
+ bo_ij->Cdbo += CEhb1; // dbo term
+
+ if( control->virial == 0 ) {
+ // dcos terms
+ rvec_ScaledAdd( workspace->f[i], +CEhb2, dcos_theta_di );
+ rvec_ScaledAdd( workspace->f[j], +CEhb2, dcos_theta_dj );
+ rvec_ScaledAdd( workspace->f[k], +CEhb2, dcos_theta_dk );
+ // dr terms
+ rvec_ScaledAdd( workspace->f[j], -CEhb3/r_jk, dvec_jk );
+ rvec_ScaledAdd( workspace->f[k], +CEhb3/r_jk, dvec_jk );
+ }
+ else {
+ /* for pressure coupling, terms that are not related to bond order
+ derivatives are added directly into pressure vector/tensor */
+ rvec_Scale( force, +CEhb2, dcos_theta_di ); // dcos terms
+ rvec_Add( workspace->f[i], force );
+ rvec_iMultiply( ext_press, pbond_ij->rel_box, force );
+ rvec_ScaledAdd( data->my_ext_press, 1.0, ext_press );
+
+ rvec_ScaledAdd( workspace->f[j], +CEhb2, dcos_theta_dj );
+
+ ivec_Scale( rel_jk, hbond_list[pk].scl, nbr_jk->rel_box );
+ rvec_Scale( force, +CEhb2, dcos_theta_dk );
+ rvec_Add( workspace->f[k], force );
+ rvec_iMultiply( ext_press, rel_jk, force );
+ rvec_ScaledAdd( data->my_ext_press, 1.0, ext_press );
+ // dr terms
+ rvec_ScaledAdd( workspace->f[j], -CEhb3/r_jk, dvec_jk );
+
+ rvec_Scale( force, CEhb3/r_jk, dvec_jk );
+ rvec_Add( workspace->f[k], force );
+ rvec_iMultiply( ext_press, rel_jk, force );
+ rvec_ScaledAdd( data->my_ext_press, 1.0, ext_press );
+ }
+
+ /* tally into per-atom virials */
+ if (system->pair_ptr->vflag_atom || system->pair_ptr->evflag) {
+ rvec_ScaledSum( delij, 1., system->my_atoms[i].x,
+ -1., system->my_atoms[j].x );
+ rvec_ScaledSum( delkj, 1., system->my_atoms[k].x,
+ -1., system->my_atoms[j].x );
+
+ rvec_Scale(fi_tmp, CEhb2, dcos_theta_di);
+ rvec_Scale(fk_tmp, CEhb2, dcos_theta_dk);
+ rvec_ScaledAdd(fk_tmp, CEhb3/r_jk, dvec_jk);
system->pair_ptr->ev_tally3(i,j,k,e_hb,0.0,fi_tmp,fk_tmp,delij,delkj);
- }
+ }
#ifdef TEST_ENERGY
- /* fprintf( out_control->ehb,
- "%24.15e%24.15e%24.15e\n%24.15e%24.15e%24.15e\n%24.15e%24.15e%24.15e\n",
- dcos_theta_di[0], dcos_theta_di[1], dcos_theta_di[2],
- dcos_theta_dj[0], dcos_theta_dj[1], dcos_theta_dj[2],
- dcos_theta_dk[0], dcos_theta_dk[1], dcos_theta_dk[2]);
- fprintf( out_control->ehb, "%24.15e%24.15e%24.15e\n",
- CEhb1, CEhb2, CEhb3 ); */
- fprintf( out_control->ehb,
- //"%6d%6d%6d%24.15e%24.15e%24.15e%24.15e%24.15e\n",
- "%6d%6d%6d%12.4f%12.4f%12.4f%12.4f%12.4f\n",
- system->my_atoms[i].orig_id, system->my_atoms[j].orig_id,
- system->my_atoms[k].orig_id,
- r_jk, theta, bo_ij->BO, e_hb, data->my_en.e_hb );
+ /* fprintf( out_control->ehb,
+ "%24.15e%24.15e%24.15e\n%24.15e%24.15e%24.15e\n%24.15e%24.15e%24.15e\n",
+ dcos_theta_di[0], dcos_theta_di[1], dcos_theta_di[2],
+ dcos_theta_dj[0], dcos_theta_dj[1], dcos_theta_dj[2],
+ dcos_theta_dk[0], dcos_theta_dk[1], dcos_theta_dk[2]);
+ fprintf( out_control->ehb, "%24.15e%24.15e%24.15e\n",
+ CEhb1, CEhb2, CEhb3 ); */
+ fprintf( out_control->ehb,
+ //"%6d%6d%6d%24.15e%24.15e%24.15e%24.15e%24.15e\n",
+ "%6d%6d%6d%12.4f%12.4f%12.4f%12.4f%12.4f\n",
+ system->my_atoms[i].orig_id, system->my_atoms[j].orig_id,
+ system->my_atoms[k].orig_id,
+ r_jk, theta, bo_ij->BO, e_hb, data->my_en.e_hb );
#endif
#ifdef TEST_FORCES
- Add_dBO( system, lists, j, pi, +CEhb1, workspace->f_hb ); //dbo term
- // dcos terms
- rvec_ScaledAdd( workspace->f_hb[i], +CEhb2, dcos_theta_di );
- rvec_ScaledAdd( workspace->f_hb[j], +CEhb2, dcos_theta_dj );
- rvec_ScaledAdd( workspace->f_hb[k], +CEhb2, dcos_theta_dk );
- // dr terms
- rvec_ScaledAdd( workspace->f_hb[j], -CEhb3/r_jk, dvec_jk );
- rvec_ScaledAdd( workspace->f_hb[k], +CEhb3/r_jk, dvec_jk );
+ Add_dBO( system, lists, j, pi, +CEhb1, workspace->f_hb ); //dbo term
+ // dcos terms
+ rvec_ScaledAdd( workspace->f_hb[i], +CEhb2, dcos_theta_di );
+ rvec_ScaledAdd( workspace->f_hb[j], +CEhb2, dcos_theta_dj );
+ rvec_ScaledAdd( workspace->f_hb[k], +CEhb2, dcos_theta_dk );
+ // dr terms
+ rvec_ScaledAdd( workspace->f_hb[j], -CEhb3/r_jk, dvec_jk );
+ rvec_ScaledAdd( workspace->f_hb[k], +CEhb3/r_jk, dvec_jk );
#endif
- }
- }
+ }
+ }
}
}
#if defined(DEBUG)
fprintf( stderr, "Number of hydrogen bonds: %d\n", num_hb_intrs );
fprintf( stderr, "Hydrogen Bond Energy: %g\n", data->my_en.e_hb );
- fprintf( stderr, "hydbonds: ext_press (%24.15e %24.15e %24.15e)\n",
- data->ext_press[0], data->ext_press[1], data->ext_press[2] );
+ fprintf( stderr, "hydbonds: ext_press (%24.15e %24.15e %24.15e)\n",
+ data->ext_press[0], data->ext_press[1], data->ext_press[2] );
#endif
}
diff --git a/src/USER-REAXC/reaxc_hydrogen_bonds.h b/src/USER-REAXC/reaxc_hydrogen_bonds.h
index f25b669440f5d23e7fd1a0f952acf722b26b91b2..04d3d26d5c08dc8cc1fa2db0b87c4183252551ee 100644
--- a/src/USER-REAXC/reaxc_hydrogen_bonds.h
+++ b/src/USER-REAXC/reaxc_hydrogen_bonds.h
@@ -14,12 +14,12 @@
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -30,6 +30,6 @@
#include "reaxc_types.h"
void Hydrogen_Bonds( reax_system*, control_params*, simulation_data*,
- storage*, reax_list**, output_controls* );
+ storage*, reax_list**, output_controls* );
#endif
diff --git a/src/USER-REAXC/reaxc_init_md.cpp b/src/USER-REAXC/reaxc_init_md.cpp
index 55d0f143486f9e6cfcdd20867e773e06b9f78c02..14e0a575add3c4e39b67ed78ce4a9b17c2b160dd 100644
--- a/src/USER-REAXC/reaxc_init_md.cpp
+++ b/src/USER-REAXC/reaxc_init_md.cpp
@@ -14,12 +14,12 @@
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -58,13 +58,13 @@
#if defined(PURE_REAX)
/************************ initialize system ************************/
-int Reposition_Atoms( reax_system *system, control_params *control,
- simulation_data *data, mpi_datatypes *mpi_data,
- char *msg )
+int Reposition_Atoms( reax_system *system, control_params *control,
+ simulation_data *data, mpi_datatypes *mpi_data,
+ char *msg )
{
int i;
rvec dx;
-
+
/* reposition atoms */
if( control->reposition_atoms == 0 ) { //fit atoms to periodic box
rvec_MakeZero( dx );
@@ -80,7 +80,7 @@ int Reposition_Atoms( reax_system *system, control_params *control,
strcpy( msg, "reposition_atoms: invalid option" );
return FAILURE;
}
-
+
for( i = 0; i < system->n; ++i )
// Inc_on_T3_Gen( system->my_atoms[i].x, dx, &(system->big_box) );
rvec_Add( system->my_atoms[i].x, dx );
@@ -94,47 +94,47 @@ void Generate_Initial_Velocities( reax_system *system, real T )
{
int i;
real m, scale, norm;
-
-
+
+
if( T <= 0.1 ) {
for( i = 0; i < system->n; i++ )
rvec_MakeZero( system->my_atoms[i].v );
}
else {
Randomize();
-
+
for( i = 0; i < system->n; i++ ) {
rvec_Random( system->my_atoms[i].v );
-
+
norm = rvec_Norm_Sqr( system->my_atoms[i].v );
m = system->reax_param.sbp[ system->my_atoms[i].type ].mass;
scale = sqrt( m * norm / (3.0 * K_B * T) );
-
+
rvec_Scale( system->my_atoms[i].v, 1./scale, system->my_atoms[i].v );
-
- // fprintf( stderr, "v = %f %f %f\n",
- // system->my_atoms[i].v[0],
- // system->my_atoms[i].v[1],
- // system->my_atoms[i].v[2] );
-
+
+ // fprintf( stderr, "v = %f %f %f\n",
+ // system->my_atoms[i].v[0],
+ // system->my_atoms[i].v[1],
+ // system->my_atoms[i].v[2] );
+
// fprintf( stderr, "scale = %f\n", scale );
- // fprintf( stderr, "v = %f %f %f\n",
- // system->my_atoms[i].v[0],
- // system->my_atoms[i].v[1],
+ // fprintf( stderr, "v = %f %f %f\n",
+ // system->my_atoms[i].v[0],
+ // system->my_atoms[i].v[1],
// system->my_atoms[i].v[2] );
}
}
}
-int Init_System( reax_system *system, control_params *control,
- simulation_data *data, storage *workspace,
- mpi_datatypes *mpi_data, char *msg )
+int Init_System( reax_system *system, control_params *control,
+ simulation_data *data, storage *workspace,
+ mpi_datatypes *mpi_data, char *msg )
{
int i;
reax_atom *atom;
int nrecv[MAX_NBRS];
-
+
Setup_New_Grid( system, control, mpi_data->world );
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d GRID:\n", system->my_rank );
@@ -147,7 +147,7 @@ int Init_System( reax_system *system, control_params *control,
for( i = 0; i < MAX_NBRS; ++i ) nrecv[i] = 0;
system->max_recved = 0;
system->N = SendRecv( system, mpi_data, mpi_data->boundary_atom_type, nrecv,
- Estimate_Boundary_Atoms, Unpack_Estimate_Message, 1 );
+ Estimate_Boundary_Atoms, Unpack_Estimate_Message, 1 );
system->total_cap = MAX( (int)(system->N * SAFE_ZONE), MIN_CAP );
Bin_Boundary_Atoms( system );
@@ -157,44 +157,44 @@ int Init_System( reax_system *system, control_params *control,
for( i = 0; i < system->n; ++i ) {
atom = &(system->my_atoms[i]);
if( system->reax_param.sbp[ atom->type ].p_hbond == 1 )
- atom->Hindex = system->numH++;
+ atom->Hindex = system->numH++;
else atom->Hindex = -1;
}
system->Hcap = MAX( system->numH * SAFER_ZONE, MIN_CAP );
- //Allocate_System( system, system->local_cap, system->total_cap, msg );
+ //Allocate_System( system, system->local_cap, system->total_cap, msg );
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "p%d: n=%d local_cap=%d\n",
- system->my_rank, system->n, system->local_cap );
- fprintf( stderr, "p%d: N=%d total_cap=%d\n",
- system->my_rank, system->N, system->total_cap );
- fprintf( stderr, "p%d: numH=%d H_cap=%d\n",
- system->my_rank, system->numH, system->Hcap );
-#endif
-
+ fprintf( stderr, "p%d: n=%d local_cap=%d\n",
+ system->my_rank, system->n, system->local_cap );
+ fprintf( stderr, "p%d: N=%d total_cap=%d\n",
+ system->my_rank, system->N, system->total_cap );
+ fprintf( stderr, "p%d: numH=%d H_cap=%d\n",
+ system->my_rank, system->numH, system->Hcap );
+#endif
+
// if( Reposition_Atoms( system, control, data, mpi_data, msg ) == FAILURE )
// return FAILURE;
-
+
/* initialize velocities so that desired init T can be attained */
- if( !control->restart || (control->restart && control->random_vel) )
+ if( !control->restart || (control->restart && control->random_vel) )
Generate_Initial_Velocities( system, control->T_init );
-
+
return SUCCESS;
}
/************************ initialize simulation data ************************/
-int Init_Simulation_Data( reax_system *system, control_params *control,
- simulation_data *data, mpi_datatypes *mpi_data,
- char *msg )
+int Init_Simulation_Data( reax_system *system, control_params *control,
+ simulation_data *data, mpi_datatypes *mpi_data,
+ char *msg )
{
Reset_Simulation_Data( data, control->virial );
- if( !control->restart )
+ if( !control->restart )
data->step = data->prev_steps = 0;
Compute_Total_Mass( system, data, mpi_data->comm_mesh3D );
- Compute_Center_of_Mass( system, data, mpi_data, mpi_data->comm_mesh3D );
+ Compute_Center_of_Mass( system, data, mpi_data, mpi_data->comm_mesh3D );
Compute_Kinetic_Energy( system, data, mpi_data->comm_mesh3D );
switch( control->ensemble ){
@@ -202,62 +202,62 @@ int Init_Simulation_Data( reax_system *system, control_params *control,
data->N_f = 3 * system->bigN;
Evolve = Velocity_Verlet_NVE;
break;
-
+
case bNVT:
data->N_f = 3 * system->bigN + 1;
Evolve = Velocity_Verlet_Berendsen_NVT;
break;
-
+
case nhNVT:
fprintf( stderr, "WARNING: Nose-Hoover NVT is still under testing.\n" );
//return FAILURE;
- data->N_f = 3 * system->bigN + 1;
+ data->N_f = 3 * system->bigN + 1;
Evolve = Velocity_Verlet_Nose_Hoover_NVT_Klein;
if( !control->restart || (control->restart && control->random_vel) ) {
- data->therm.G_xi = control->Tau_T *
- (2.0 * data->sys_en.e_kin - data->N_f * K_B * control->T );
+ data->therm.G_xi = control->Tau_T *
+ (2.0 * data->sys_en.e_kin - data->N_f * K_B * control->T );
data->therm.v_xi = data->therm.G_xi * control->dt;
data->therm.v_xi_old = 0;
data->therm.xi = 0;
}
break;
-
+
case sNPT: /* Semi-Isotropic NPT */
data->N_f = 3 * system->bigN + 4;
Evolve = Velocity_Verlet_Berendsen_NPT;
if( !control->restart )
Reset_Pressures( data );
break;
-
+
case iNPT: /* Isotropic NPT */
data->N_f = 3 * system->bigN + 2;
Evolve = Velocity_Verlet_Berendsen_NPT;
if( !control->restart )
Reset_Pressures( data );
break;
-
+
case NPT: /* Anisotropic NPT */
strcpy( msg, "init_simulation_data: option not yet implemented" );
return FAILURE;
-
+
data->N_f = 3 * system->bigN + 9;
Evolve = Velocity_Verlet_Berendsen_NPT;
/*if( !control->restart ) {
- data->therm.G_xi = control->Tau_T *
+ data->therm.G_xi = control->Tau_T *
(2.0 * data->my_en.e_Kin - data->N_f * K_B * control->T );
data->therm.v_xi = data->therm.G_xi * control->dt;
data->iso_bar.eps = 0.33333 * log(system->box.volume);
- data->inv_W = 1.0 /
+ data->inv_W = 1.0 /
( data->N_f * K_B * control->T * SQR(control->Tau_P) );
Compute_Pressure( system, control, data, out_control );
}*/
break;
-
+
default:
strcpy( msg, "init_simulation_data: ensemble not recognized" );
return FAILURE;
}
-
+
/* initialize the timer(s) */
MPI_Barrier( mpi_data->world ); // wait for everyone to come here
if( system->my_rank == MASTER_NODE ) {
@@ -266,7 +266,7 @@ int Init_Simulation_Data( reax_system *system, control_params *control,
Reset_Timing( &data->timing );
#endif
}
-
+
#if defined(DEBUG)
fprintf( stderr, "data->N_f: %8.3f\n", data->N_f );
@@ -283,33 +283,33 @@ int Init_System( reax_system *system, control_params *control, char *msg )
/* determine the local and total capacity */
system->local_cap = MAX( (int)(system->n * SAFE_ZONE), MIN_CAP );
system->total_cap = MAX( (int)(system->N * SAFE_ZONE), MIN_CAP );
-
+
/* estimate numH and Hcap */
system->numH = 0;
if( control->hbond_cut > 0 )
for( i = 0; i < system->n; ++i ) {
atom = &(system->my_atoms[i]);
if( system->reax_param.sbp[ atom->type ].p_hbond == 1 )
- atom->Hindex = system->numH++;
+ atom->Hindex = system->numH++;
else atom->Hindex = -1;
}
system->Hcap = (int)(MAX( system->numH * SAFER_ZONE, MIN_CAP ));
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "p%d: n=%d local_cap=%d\n",
- system->my_rank, system->n, system->local_cap );
- fprintf( stderr, "p%d: N=%d total_cap=%d\n",
- system->my_rank, system->N, system->total_cap );
- fprintf( stderr, "p%d: numH=%d H_cap=%d\n",
- system->my_rank, system->numH, system->Hcap );
+ fprintf( stderr, "p%d: n=%d local_cap=%d\n",
+ system->my_rank, system->n, system->local_cap );
+ fprintf( stderr, "p%d: N=%d total_cap=%d\n",
+ system->my_rank, system->N, system->total_cap );
+ fprintf( stderr, "p%d: numH=%d H_cap=%d\n",
+ system->my_rank, system->numH, system->Hcap );
#endif
return SUCCESS;
}
-int Init_Simulation_Data( reax_system *system, control_params *control,
- simulation_data *data, char *msg )
+int Init_Simulation_Data( reax_system *system, control_params *control,
+ simulation_data *data, char *msg )
{
Reset_Simulation_Data( data, control->virial );
@@ -321,7 +321,7 @@ int Init_Simulation_Data( reax_system *system, control_params *control,
#endif
}
- //if( !control->restart )
+ //if( !control->restart )
data->step = data->prev_steps = 0;
return SUCCESS;
@@ -343,7 +343,7 @@ void Init_Taper( control_params *control, storage *workspace, MPI_Comm comm )
if( fabs( swa ) > 0.01 )
fprintf( stderr, "Warning: non-zero lower Taper-radius cutoff\n" );
-
+
if( swb < 0 ) {
fprintf( stderr, "Negative upper Taper-radius cutoff\n" );
MPI_Abort( comm, INVALID_INPUT );
@@ -365,18 +365,18 @@ void Init_Taper( control_params *control, storage *workspace, MPI_Comm comm )
workspace->Tap[3] = 140.0 * (swa3*swb + 3.0*swa2*swb2 + swa*swb3 ) / d7;
workspace->Tap[2] =-210.0 * (swa3*swb2 + swa2*swb3) / d7;
workspace->Tap[1] = 140.0 * swa3 * swb3 / d7;
- workspace->Tap[0] = (-35.0*swa3*swb2*swb2 + 21.0*swa2*swb3*swb2 +
- 7.0*swa*swb3*swb3 + swb3*swb3*swb ) / d7;
+ workspace->Tap[0] = (-35.0*swa3*swb2*swb2 + 21.0*swa2*swb3*swb2 +
+ 7.0*swa*swb3*swb3 + swb3*swb3*swb ) / d7;
}
-int Init_Workspace( reax_system *system, control_params *control,
- storage *workspace, MPI_Comm comm, char *msg )
-{
+int Init_Workspace( reax_system *system, control_params *control,
+ storage *workspace, MPI_Comm comm, char *msg )
+{
int ret;
-
- ret = Allocate_Workspace( system, control, workspace,
- system->local_cap, system->total_cap, comm, msg );
+
+ ret = Allocate_Workspace( system, control, workspace,
+ system->local_cap, system->total_cap, comm, msg );
if( ret != SUCCESS )
return ret;
@@ -391,8 +391,8 @@ int Init_Workspace( reax_system *system, control_params *control,
/************** setup communication data structures **************/
-int Init_MPI_Datatypes( reax_system *system, storage *workspace,
- mpi_datatypes *mpi_data, MPI_Comm comm, char *msg )
+int Init_MPI_Datatypes( reax_system *system, storage *workspace,
+ mpi_datatypes *mpi_data, MPI_Comm comm, char *msg )
{
#if defined(PURE_REAX)
int i, block[11];
@@ -414,7 +414,7 @@ int Init_MPI_Datatypes( reax_system *system, storage *workspace,
mpi_data->in1_buffer = NULL;
mpi_data->in2_buffer = NULL;
- /* mpi_atom - [orig_id, imprt_id, type, num_bonds, num_hbonds, name,
+ /* mpi_atom - [orig_id, imprt_id, type, num_bonds, num_hbonds, name,
x, v, f_old, s, t] */
block[0] = block[1] = block[2] = block[3] = block[4] = 1;
block[5] = 8;
@@ -431,8 +431,8 @@ int Init_MPI_Datatypes( reax_system *system, storage *workspace,
MPI_Address( &(sample.v[0]), disp + 7 );
MPI_Address( &(sample.f_old[0]), disp + 8 );
MPI_Address( &(sample.s[0]), disp + 9 );
- MPI_Address( &(sample.t[0]), disp + 10 );
-
+ MPI_Address( &(sample.t[0]), disp + 10 );
+
base = (MPI_Aint)(&(sample));
for( i = 0; i < 11; ++i ) disp[i] -= base;
@@ -446,14 +446,14 @@ int Init_MPI_Datatypes( reax_system *system, storage *workspace,
/* boundary_atom - [orig_id, imprt_id, type, num_bonds, num_hbonds, x] */
block[0] = block[1] = block[2] = block[3] = block[4] = 1;
block[5] = 3;
-
+
MPI_Address( &(b_sample.orig_id), disp + 0 );
MPI_Address( &(b_sample.imprt_id), disp + 1 );
MPI_Address( &(b_sample.type), disp + 2 );
MPI_Address( &(b_sample.num_bonds), disp + 3 );
MPI_Address( &(b_sample.num_hbonds), disp + 4 );
MPI_Address( &(b_sample.x[0]), disp + 5 );
-
+
base = (MPI_Aint)(&(b_sample));
for( i = 0; i < 6; ++i ) disp[i] -= base;
@@ -483,20 +483,20 @@ int Init_MPI_Datatypes( reax_system *system, storage *workspace,
/* restart_atom - [orig_id, type, name[8], x, v] */
block[0] = block[1] = 1 ;
- block[2] = 8;
+ block[2] = 8;
block[3] = block[4] = 3;
-
+
MPI_Address( &(r_sample.orig_id), disp + 0 );
MPI_Address( &(r_sample.type), disp + 1 );
MPI_Address( &(r_sample.name), disp + 2 );
MPI_Address( &(r_sample.x[0]), disp + 3 );
MPI_Address( &(r_sample.v[0]), disp + 4 );
-
+
base = (MPI_Aint)(&(r_sample));
for( i = 0; i < 5; ++i ) disp[i] -= base;
type[0] = type[1] = MPI_INT;
- type[2] = MPI_CHAR;
+ type[2] = MPI_CHAR;
type[3] = type[4] = MPI_DOUBLE;
MPI_Type_struct( 5, block, disp, type, &(mpi_data->restart_atom_type) );
@@ -509,44 +509,44 @@ int Init_MPI_Datatypes( reax_system *system, storage *workspace,
/********************** allocate lists *************************/
#if defined(PURE_REAX)
-int Init_Lists( reax_system *system, control_params *control,
- simulation_data *data, storage *workspace, reax_list **lists,
- mpi_datatypes *mpi_data, char *msg )
+int Init_Lists( reax_system *system, control_params *control,
+ simulation_data *data, storage *workspace, reax_list **lists,
+ mpi_datatypes *mpi_data, char *msg )
{
int i, num_nbrs;
int total_hbonds, total_bonds, bond_cap, num_3body, cap_3body, Htop;
int *hb_top, *bond_top;
MPI_Comm comm;
-
+
comm = mpi_data->world;
//for( i = 0; i < MAX_NBRS; ++i ) nrecv[i] = system->my_nbrs[i].est_recv;
//system->N = SendRecv( system, mpi_data, mpi_data->boundary_atom_type, nrecv,
- // Sort_Boundary_Atoms, Unpack_Exchange_Message, 1 );
+ // Sort_Boundary_Atoms, Unpack_Exchange_Message, 1 );
num_nbrs = Estimate_NumNeighbors( system, lists );
- if(!Make_List( system->total_cap, num_nbrs, TYP_FAR_NEIGHBOR,
- *lists+FAR_NBRS, comm )){
+ if(!Make_List( system->total_cap, num_nbrs, TYP_FAR_NEIGHBOR,
+ *lists+FAR_NBRS, comm )){
fprintf(stderr, "Problem in initializing far nbrs list. Terminating!\n");
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d: allocated far_nbrs: num_far=%d, space=%dMB\n",
- system->my_rank, num_nbrs,
- (int)(num_nbrs*sizeof(far_neighbor_data)/(1024*1024)) );
+ system->my_rank, num_nbrs,
+ (int)(num_nbrs*sizeof(far_neighbor_data)/(1024*1024)) );
#endif
Generate_Neighbor_Lists( system, data, workspace, lists );
bond_top = (int*) calloc( system->total_cap, sizeof(int) );
hb_top = (int*) calloc( system->local_cap, sizeof(int) );
Estimate_Storages( system, control, lists,
- &Htop, hb_top, bond_top, &num_3body, comm );
-
+ &Htop, hb_top, bond_top, &num_3body, comm );
+
Allocate_Matrix( &(workspace->H), system->local_cap, Htop, comm );
workspace->L = NULL;
workspace->U = NULL;
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "p%d: allocated H matrix: Htop=%d, space=%dMB\n",
- system->my_rank, Htop,
- (int)(Htop * sizeof(sparse_matrix_entry) / (1024*1024)) );
+ fprintf( stderr, "p%d: allocated H matrix: Htop=%d, space=%dMB\n",
+ system->my_rank, Htop,
+ (int)(Htop * sizeof(sparse_matrix_entry) / (1024*1024)) );
#endif
if( control->hbond_cut > 0 ) {
@@ -558,18 +558,18 @@ int Init_Lists( reax_system *system, control_params *control,
}
total_hbonds = MAX( total_hbonds*SAFER_ZONE, MIN_CAP*MIN_HBONDS );
- if( !Make_List( system->Hcap, total_hbonds, TYP_HBOND,
- *lists+HBONDS, comm ) ) {
+ if( !Make_List( system->Hcap, total_hbonds, TYP_HBOND,
+ *lists+HBONDS, comm ) ) {
fprintf( stderr, "not enough space for hbonds list. terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
- }
+ }
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "p%d: allocated hbonds: total_hbonds=%d, space=%dMB\n",
- system->my_rank, total_hbonds,
- (int)(total_hbonds*sizeof(hbond_data)/(1024*1024)) );
+ fprintf( stderr, "p%d: allocated hbonds: total_hbonds=%d, space=%dMB\n",
+ system->my_rank, total_hbonds,
+ (int)(total_hbonds*sizeof(hbond_data)/(1024*1024)) );
#endif
}
-
+
/* bonds list */
//Allocate_Bond_List( system->N, bond_top, (*lists)+BONDS );
//num_bonds = bond_top[system->N-1];
@@ -579,48 +579,48 @@ int Init_Lists( reax_system *system, control_params *control,
total_bonds += bond_top[i];
}
bond_cap = MAX( total_bonds*SAFE_ZONE, MIN_CAP*MIN_BONDS );
-
- if( !Make_List( system->total_cap, bond_cap, TYP_BOND,
- *lists+BONDS, comm ) ) {
+
+ if( !Make_List( system->total_cap, bond_cap, TYP_BOND,
+ *lists+BONDS, comm ) ) {
fprintf( stderr, "not enough space for bonds list. terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "p%d: allocated bonds: total_bonds=%d, space=%dMB\n",
- system->my_rank, bond_cap,
- (int)(bond_cap*sizeof(bond_data)/(1024*1024)) );
+ fprintf( stderr, "p%d: allocated bonds: total_bonds=%d, space=%dMB\n",
+ system->my_rank, bond_cap,
+ (int)(bond_cap*sizeof(bond_data)/(1024*1024)) );
#endif
/* 3bodies list */
cap_3body = MAX( num_3body*SAFE_ZONE, MIN_3BODIES );
- if( !Make_List( bond_cap, cap_3body, TYP_THREE_BODY,
- *lists+THREE_BODIES, comm ) ){
+ if( !Make_List( bond_cap, cap_3body, TYP_THREE_BODY,
+ *lists+THREE_BODIES, comm ) ){
fprintf( stderr, "Problem in initializing angles list. Terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "p%d: allocated 3-body list: num_3body=%d, space=%dMB\n",
- system->my_rank, cap_3body,
- (int)(cap_3body*sizeof(three_body_interaction_data)/(1024*1024)) );
+ fprintf( stderr, "p%d: allocated 3-body list: num_3body=%d, space=%dMB\n",
+ system->my_rank, cap_3body,
+ (int)(cap_3body*sizeof(three_body_interaction_data)/(1024*1024)) );
#endif
#if defined(TEST_FORCES)
- if( !Make_List( system->total_cap, bond_cap*8, TYP_DDELTA,
- *lists+DDELTAS, comm ) ) {
+ if( !Make_List( system->total_cap, bond_cap*8, TYP_DDELTA,
+ *lists+DDELTAS, comm ) ) {
fprintf( stderr, "Problem in initializing dDelta list. Terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
- fprintf( stderr, "p%d: allocated dDelta list: num_ddelta=%d space=%ldMB\n",
- system->my_rank, bond_cap*30,
- bond_cap*8*sizeof(dDelta_data)/(1024*1024) );
+ fprintf( stderr, "p%d: allocated dDelta list: num_ddelta=%d space=%ldMB\n",
+ system->my_rank, bond_cap*30,
+ bond_cap*8*sizeof(dDelta_data)/(1024*1024) );
if( !Make_List( bond_cap, bond_cap*50, TYP_DBO, *lists+DBOS, comm ) ) {
fprintf( stderr, "Problem in initializing dBO list. Terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
- fprintf( stderr, "p%d: allocated dbond list: num_dbonds=%d space=%ldMB\n",
- system->my_rank, bond_cap*MAX_BONDS*3,
- bond_cap*MAX_BONDS*3*sizeof(dbond_data)/(1024*1024) );
+ fprintf( stderr, "p%d: allocated dbond list: num_dbonds=%d space=%ldMB\n",
+ system->my_rank, bond_cap*MAX_BONDS*3,
+ bond_cap*MAX_BONDS*3*sizeof(dbond_data)/(1024*1024) );
#endif
free( hb_top );
@@ -629,22 +629,22 @@ int Init_Lists( reax_system *system, control_params *control,
return SUCCESS;
}
#elif defined(LAMMPS_REAX)
-int Init_Lists( reax_system *system, control_params *control,
- simulation_data *data, storage *workspace, reax_list **lists,
- mpi_datatypes *mpi_data, char *msg )
+int Init_Lists( reax_system *system, control_params *control,
+ simulation_data *data, storage *workspace, reax_list **lists,
+ mpi_datatypes *mpi_data, char *msg )
{
int i, num_nbrs;
int total_hbonds, total_bonds, bond_cap, num_3body, cap_3body, Htop;
int *hb_top, *bond_top;
int nrecv[MAX_NBRS];
MPI_Comm comm;
-
+
comm = mpi_data->world;
bond_top = (int*) calloc( system->total_cap, sizeof(int) );
hb_top = (int*) calloc( system->local_cap, sizeof(int) );
Estimate_Storages( system, control, lists,
- &Htop, hb_top, bond_top, &num_3body, comm );
-
+ &Htop, hb_top, bond_top, &num_3body, comm );
+
if( control->hbond_cut > 0 ) {
/* init H indexes */
total_hbonds = 0;
@@ -654,18 +654,18 @@ int Init_Lists( reax_system *system, control_params *control,
}
total_hbonds = (int)(MAX( total_hbonds*SAFER_ZONE, MIN_CAP*MIN_HBONDS ));
- if( !Make_List( system->Hcap, total_hbonds, TYP_HBOND,
- *lists+HBONDS, comm ) ) {
+ if( !Make_List( system->Hcap, total_hbonds, TYP_HBOND,
+ *lists+HBONDS, comm ) ) {
fprintf( stderr, "not enough space for hbonds list. terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
- }
+ }
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "p%d: allocated hbonds: total_hbonds=%d, space=%dMB\n",
- system->my_rank, total_hbonds,
- (int)(total_hbonds*sizeof(hbond_data)/(1024*1024)) );
+ fprintf( stderr, "p%d: allocated hbonds: total_hbonds=%d, space=%dMB\n",
+ system->my_rank, total_hbonds,
+ (int)(total_hbonds*sizeof(hbond_data)/(1024*1024)) );
#endif
}
-
+
/* bonds list */
//Allocate_Bond_List( system->N, bond_top, (*lists)+BONDS );
//num_bonds = bond_top[system->N-1];
@@ -675,48 +675,48 @@ int Init_Lists( reax_system *system, control_params *control,
total_bonds += bond_top[i];
}
bond_cap = (int)(MAX( total_bonds*SAFE_ZONE, MIN_CAP*MIN_BONDS ));
-
- if( !Make_List( system->total_cap, bond_cap, TYP_BOND,
- *lists+BONDS, comm ) ) {
+
+ if( !Make_List( system->total_cap, bond_cap, TYP_BOND,
+ *lists+BONDS, comm ) ) {
fprintf( stderr, "not enough space for bonds list. terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "p%d: allocated bonds: total_bonds=%d, space=%dMB\n",
- system->my_rank, bond_cap,
- (int)(bond_cap*sizeof(bond_data)/(1024*1024)) );
+ fprintf( stderr, "p%d: allocated bonds: total_bonds=%d, space=%dMB\n",
+ system->my_rank, bond_cap,
+ (int)(bond_cap*sizeof(bond_data)/(1024*1024)) );
#endif
/* 3bodies list */
cap_3body = (int)(MAX( num_3body*SAFE_ZONE, MIN_3BODIES ));
- if( !Make_List( bond_cap, cap_3body, TYP_THREE_BODY,
- *lists+THREE_BODIES, comm ) ){
+ if( !Make_List( bond_cap, cap_3body, TYP_THREE_BODY,
+ *lists+THREE_BODIES, comm ) ){
fprintf( stderr, "Problem in initializing angles list. Terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "p%d: allocated 3-body list: num_3body=%d, space=%dMB\n",
- system->my_rank, cap_3body,
- (int)(cap_3body*sizeof(three_body_interaction_data)/(1024*1024)) );
+ fprintf( stderr, "p%d: allocated 3-body list: num_3body=%d, space=%dMB\n",
+ system->my_rank, cap_3body,
+ (int)(cap_3body*sizeof(three_body_interaction_data)/(1024*1024)) );
#endif
#if defined(TEST_FORCES)
- if( !Make_List( system->total_cap, bond_cap*8, TYP_DDELTA,
- *lists+DDELTAS, comm ) ) {
+ if( !Make_List( system->total_cap, bond_cap*8, TYP_DDELTA,
+ *lists+DDELTAS, comm ) ) {
fprintf( stderr, "Problem in initializing dDelta list. Terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
- fprintf( stderr, "p%d: allocated dDelta list: num_ddelta=%d space=%ldMB\n",
- system->my_rank, bond_cap*30,
- bond_cap*8*sizeof(dDelta_data)/(1024*1024) );
+ fprintf( stderr, "p%d: allocated dDelta list: num_ddelta=%d space=%ldMB\n",
+ system->my_rank, bond_cap*30,
+ bond_cap*8*sizeof(dDelta_data)/(1024*1024) );
if( !Make_List( bond_cap, bond_cap*50, TYP_DBO, (*lists)+DBOS, comm ) ) {
fprintf( stderr, "Problem in initializing dBO list. Terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
- fprintf( stderr, "p%d: allocated dbond list: num_dbonds=%d space=%ldMB\n",
- system->my_rank, bond_cap*MAX_BONDS*3,
- bond_cap*MAX_BONDS*3*sizeof(dbond_data)/(1024*1024) );
+ fprintf( stderr, "p%d: allocated dbond list: num_dbonds=%d space=%ldMB\n",
+ system->my_rank, bond_cap*MAX_BONDS*3,
+ bond_cap*MAX_BONDS*3*sizeof(dbond_data)/(1024*1024) );
#endif
free( hb_top );
@@ -729,19 +729,19 @@ int Init_Lists( reax_system *system, control_params *control,
#if defined(PURE_REAX)
-void Initialize( reax_system *system, control_params *control,
- simulation_data *data, storage *workspace,
- reax_list **lists, output_controls *out_control,
- mpi_datatypes *mpi_data )
+void Initialize( reax_system *system, control_params *control,
+ simulation_data *data, storage *workspace,
+ reax_list **lists, output_controls *out_control,
+ mpi_datatypes *mpi_data )
{
char msg[MAX_STR];
if( Init_MPI_Datatypes( system, workspace, mpi_data, MPI_COMM_WORLD, msg ) ==
FAILURE ) {
fprintf( stderr, "p%d: init_mpi_datatypes: could not create datatypes\n",
- system->my_rank );
+ system->my_rank );
fprintf( stderr, "p%d: mpi_data couldn't be initialized! terminating.\n",
- system->my_rank );
+ system->my_rank );
MPI_Abort( mpi_data->world, CANNOT_INITIALIZE );
}
#if defined(DEBUG)
@@ -749,9 +749,9 @@ void Initialize( reax_system *system, control_params *control,
#endif
if( Init_System(system, control, data, workspace, mpi_data, msg) == FAILURE ){
- fprintf( stderr, "p%d: %s\n", system->my_rank, msg );
+ fprintf( stderr, "p%d: %s\n", system->my_rank, msg );
fprintf( stderr, "p%d: system could not be initialized! terminating.\n",
- system->my_rank );
+ system->my_rank );
MPI_Abort( mpi_data->world, CANNOT_INITIALIZE );
}
#if defined(DEBUG)
@@ -759,32 +759,32 @@ void Initialize( reax_system *system, control_params *control,
#endif
if( Init_Simulation_Data(system, control, data, mpi_data, msg) == FAILURE ) {
- fprintf( stderr, "p%d: %s\n", system->my_rank, msg );
+ fprintf( stderr, "p%d: %s\n", system->my_rank, msg );
fprintf( stderr, "p%d: sim_data couldn't be initialized! terminating.\n",
- system->my_rank );
+ system->my_rank );
MPI_Abort( mpi_data->world, CANNOT_INITIALIZE );
}
#if defined(DEBUG)
fprintf( stderr, "p%d: initialized simulation data\n", system->my_rank );
#endif
- if( Init_Workspace( system, control, workspace, mpi_data->world, msg ) ==
+ if( Init_Workspace( system, control, workspace, mpi_data->world, msg ) ==
FAILURE ) {
- fprintf( stderr, "p%d:init_workspace: not enough memory\n",
- system->my_rank );
+ fprintf( stderr, "p%d:init_workspace: not enough memory\n",
+ system->my_rank );
fprintf( stderr, "p%d:workspace couldn't be initialized! terminating.\n",
- system->my_rank );
+ system->my_rank );
MPI_Abort( mpi_data->world, CANNOT_INITIALIZE );
}
#if defined(DEBUG)
fprintf( stderr, "p%d: initialized workspace\n", system->my_rank );
#endif
-
- if( Init_Lists( system, control, data, workspace, lists, mpi_data, msg ) ==
+
+ if( Init_Lists( system, control, data, workspace, lists, mpi_data, msg ) ==
FAILURE ) {
fprintf( stderr, "p%d: %s\n", system->my_rank, msg );
fprintf( stderr, "p%d: system could not be initialized! terminating.\n",
- system->my_rank );
+ system->my_rank );
MPI_Abort( mpi_data->world, CANNOT_INITIALIZE );
}
#if defined(DEBUG)
@@ -793,8 +793,8 @@ void Initialize( reax_system *system, control_params *control,
if(Init_Output_Files(system,control,out_control,mpi_data,msg) == FAILURE) {
fprintf( stderr, "p%d: %s\n", system->my_rank, msg );
- fprintf( stderr, "p%d: could not open output files! terminating...\n",
- system->my_rank );
+ fprintf( stderr, "p%d: could not open output files! terminating...\n",
+ system->my_rank );
MPI_Abort( mpi_data->world, CANNOT_INITIALIZE );
}
#if defined(DEBUG)
@@ -805,7 +805,7 @@ void Initialize( reax_system *system, control_params *control,
if( Init_Lookup_Tables(system,control,workspace,mpi_data,msg) == FAILURE ) {
fprintf( stderr, "p%d: %s\n", system->my_rank, msg );
fprintf( stderr, "p%d: couldn't create lookup table! terminating.\n",
- system->my_rank );
+ system->my_rank );
MPI_Abort( mpi_data->world, CANNOT_INITIALIZE );
}
#if defined(DEBUG)
@@ -817,36 +817,36 @@ void Initialize( reax_system *system, control_params *control,
#if defined(DEBUG)
fprintf( stderr, "p%d: initialized force functions\n", system->my_rank );
#endif
- /*#ifdef TEST_FORCES
+ /*#ifdef TEST_FORCES
Init_Force_Test_Functions();
fprintf(stderr,"p%d: initialized force test functions\n",system->my_rank);
#endif */
}
#elif defined(LAMMPS_REAX)
-void Initialize( reax_system *system, control_params *control,
- simulation_data *data, storage *workspace,
- reax_list **lists, output_controls *out_control,
- mpi_datatypes *mpi_data, MPI_Comm comm )
+void Initialize( reax_system *system, control_params *control,
+ simulation_data *data, storage *workspace,
+ reax_list **lists, output_controls *out_control,
+ mpi_datatypes *mpi_data, MPI_Comm comm )
{
char msg[MAX_STR];
if( Init_MPI_Datatypes(system, workspace, mpi_data, comm, msg) == FAILURE ) {
fprintf( stderr, "p%d: init_mpi_datatypes: could not create datatypes\n",
- system->my_rank );
+ system->my_rank );
fprintf( stderr, "p%d: mpi_data couldn't be initialized! terminating.\n",
- system->my_rank );
+ system->my_rank );
MPI_Abort( mpi_data->world, CANNOT_INITIALIZE );
}
#if defined(DEBUG)
fprintf( stderr, "p%d: initialized mpi datatypes\n", system->my_rank );
#endif
-
+
if( Init_System(system, control, msg) == FAILURE ){
- fprintf( stderr, "p%d: %s\n", system->my_rank, msg );
+ fprintf( stderr, "p%d: %s\n", system->my_rank, msg );
fprintf( stderr, "p%d: system could not be initialized! terminating.\n",
- system->my_rank );
+ system->my_rank );
MPI_Abort( mpi_data->world, CANNOT_INITIALIZE );
}
#if defined(DEBUG)
@@ -854,32 +854,32 @@ void Initialize( reax_system *system, control_params *control,
#endif
if( Init_Simulation_Data( system, control, data, msg ) == FAILURE ) {
- fprintf( stderr, "p%d: %s\n", system->my_rank, msg );
+ fprintf( stderr, "p%d: %s\n", system->my_rank, msg );
fprintf( stderr, "p%d: sim_data couldn't be initialized! terminating.\n",
- system->my_rank );
+ system->my_rank );
MPI_Abort( mpi_data->world, CANNOT_INITIALIZE );
}
#if defined(DEBUG)
fprintf( stderr, "p%d: initialized simulation data\n", system->my_rank );
#endif
- if( Init_Workspace( system, control, workspace, mpi_data->world, msg ) ==
+ if( Init_Workspace( system, control, workspace, mpi_data->world, msg ) ==
FAILURE ) {
- fprintf( stderr, "p%d:init_workspace: not enough memory\n",
- system->my_rank );
+ fprintf( stderr, "p%d:init_workspace: not enough memory\n",
+ system->my_rank );
fprintf( stderr, "p%d:workspace couldn't be initialized! terminating.\n",
- system->my_rank );
+ system->my_rank );
MPI_Abort( mpi_data->world, CANNOT_INITIALIZE );
}
#if defined(DEBUG)
fprintf( stderr, "p%d: initialized workspace\n", system->my_rank );
#endif
- if( Init_Lists( system, control, data, workspace, lists, mpi_data, msg ) ==
+ if( Init_Lists( system, control, data, workspace, lists, mpi_data, msg ) ==
FAILURE ) {
fprintf( stderr, "p%d: %s\n", system->my_rank, msg );
fprintf( stderr, "p%d: system could not be initialized! terminating.\n",
- system->my_rank );
+ system->my_rank );
MPI_Abort( mpi_data->world, CANNOT_INITIALIZE );
}
#if defined(DEBUG)
@@ -888,8 +888,8 @@ void Initialize( reax_system *system, control_params *control,
if( Init_Output_Files(system,control,out_control,mpi_data,msg)== FAILURE) {
fprintf( stderr, "p%d: %s\n", system->my_rank, msg );
- fprintf( stderr, "p%d: could not open output files! terminating...\n",
- system->my_rank );
+ fprintf( stderr, "p%d: could not open output files! terminating...\n",
+ system->my_rank );
MPI_Abort( mpi_data->world, CANNOT_INITIALIZE );
}
#if defined(DEBUG)
@@ -900,7 +900,7 @@ void Initialize( reax_system *system, control_params *control,
if( Init_Lookup_Tables( system, control, workspace, mpi_data, msg ) == FAILURE ) {
fprintf( stderr, "p%d: %s\n", system->my_rank, msg );
fprintf( stderr, "p%d: couldn't create lookup table! terminating.\n",
- system->my_rank );
+ system->my_rank );
MPI_Abort( mpi_data->world, CANNOT_INITIALIZE );
}
#if defined(DEBUG)
@@ -913,7 +913,7 @@ void Initialize( reax_system *system, control_params *control,
#if defined(DEBUG)
fprintf( stderr, "p%d: initialized force functions\n", system->my_rank );
#endif
- /*#if defined(TEST_FORCES)
+ /*#if defined(TEST_FORCES)
Init_Force_Test_Functions();
fprintf(stderr,"p%d: initialized force test functions\n",system->my_rank);
#endif*/
diff --git a/src/USER-REAXC/reaxc_init_md.h b/src/USER-REAXC/reaxc_init_md.h
index 26990dfdec3ff66d5c4b818685e99480eb10dcba..ddaf587a4fea28bbfcb9a270861e502cfb9fa60f 100644
--- a/src/USER-REAXC/reaxc_init_md.h
+++ b/src/USER-REAXC/reaxc_init_md.h
@@ -14,12 +14,12 @@
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -31,10 +31,10 @@
#if defined(PURE_REAX)
void Initialize( reax_system*, control_params*, simulation_data*,
- storage*, reax_list**, output_controls*, mpi_datatypes* );
+ storage*, reax_list**, output_controls*, mpi_datatypes* );
#elif defined(LAMMPS_REAX)
-void Initialize( reax_system*, control_params*, simulation_data*, storage*,
- reax_list**, output_controls*, mpi_datatypes*, MPI_Comm );
+void Initialize( reax_system*, control_params*, simulation_data*, storage*,
+ reax_list**, output_controls*, mpi_datatypes*, MPI_Comm );
#endif
#endif
diff --git a/src/USER-REAXC/reaxc_io_tools.cpp b/src/USER-REAXC/reaxc_io_tools.cpp
index 9024b9b3d82792db62d35da6ce30e2976fe26e8e..65466724eb0ce500fcc4b05ae5d3537e65c05811 100644
--- a/src/USER-REAXC/reaxc_io_tools.cpp
+++ b/src/USER-REAXC/reaxc_io_tools.cpp
@@ -14,12 +14,12 @@
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -49,9 +49,9 @@
print_interaction Print_Interactions[NUM_INTRS];
/************************ initialize output controls ************************/
-int Init_Output_Files( reax_system *system, control_params *control,
- output_controls *out_control, mpi_datatypes *mpi_data,
- char *msg )
+int Init_Output_Files( reax_system *system, control_params *control,
+ output_controls *out_control, mpi_datatypes *mpi_data,
+ char *msg )
{
char temp[MAX_STR];
int ret;
@@ -70,19 +70,19 @@ int Init_Output_Files( reax_system *system, control_params *control,
sprintf( temp, "%s.out", control->sim_name );
if( (out_control->out = fopen( temp, "w" )) != NULL ) {
#if !defined(DEBUG) && !defined(DEBUG_FOCUS)
- fprintf( out_control->out, "%-6s%14s%14s%14s%11s%13s%13s\n",
- "step", "total energy", "potential", "kinetic",
- "T(K)", "V(A^3)", "P(Gpa)" );
+ fprintf( out_control->out, "%-6s%14s%14s%14s%11s%13s%13s\n",
+ "step", "total energy", "potential", "kinetic",
+ "T(K)", "V(A^3)", "P(Gpa)" );
#else
- fprintf( out_control->out, "%-6s%24s%24s%24s%13s%16s%13s\n",
- "step", "total energy", "potential", "kinetic",
- "T(K)", "V(A^3)", "P(GPa)" );
+ fprintf( out_control->out, "%-6s%24s%24s%24s%13s%16s%13s\n",
+ "step", "total energy", "potential", "kinetic",
+ "T(K)", "V(A^3)", "P(GPa)" );
#endif
- fflush( out_control->out );
+ fflush( out_control->out );
}
else {
- strcpy( msg, "init_out_controls: .out file could not be opened\n" );
- return FAILURE;
+ strcpy( msg, "init_out_controls: .out file could not be opened\n" );
+ return FAILURE;
}
#endif
@@ -90,55 +90,55 @@ int Init_Output_Files( reax_system *system, control_params *control,
sprintf( temp, "%s.pot", control->sim_name );
if( (out_control->pot = fopen( temp, "w" )) != NULL ) {
#if !defined(DEBUG) && !defined(DEBUG_FOCUS)
- fprintf( out_control->pot,
- "%-6s%14s%14s%14s%14s%14s%14s%14s%14s%14s%14s%14s\n",
- "step", "ebond", "eatom", "elp",
- "eang", "ecoa", "ehb", "etor", "econj",
- "evdw","ecoul", "epol" );
+ fprintf( out_control->pot,
+ "%-6s%14s%14s%14s%14s%14s%14s%14s%14s%14s%14s%14s\n",
+ "step", "ebond", "eatom", "elp",
+ "eang", "ecoa", "ehb", "etor", "econj",
+ "evdw","ecoul", "epol" );
#else
- fprintf( out_control->pot,
- "%-6s%24s%24s%24s%24s%24s%24s%24s%24s%24s%24s%24s\n",
- "step", "ebond", "eatom", "elp",
- "eang", "ecoa", "ehb", "etor", "econj",
- "evdw","ecoul", "epol" );
+ fprintf( out_control->pot,
+ "%-6s%24s%24s%24s%24s%24s%24s%24s%24s%24s%24s%24s\n",
+ "step", "ebond", "eatom", "elp",
+ "eang", "ecoa", "ehb", "etor", "econj",
+ "evdw","ecoul", "epol" );
#endif
- fflush( out_control->pot );
+ fflush( out_control->pot );
}
else {
- strcpy( msg, "init_out_controls: .pot file could not be opened\n" );
- return FAILURE;
+ strcpy( msg, "init_out_controls: .pot file could not be opened\n" );
+ return FAILURE;
}
-
+
/* init log file */
#if defined(LOG_PERFORMANCE)
sprintf( temp, "%s.log", control->sim_name );
if( (out_control->log = fopen( temp, "w" )) != NULL ) {
- fprintf( out_control->log, "%6s%8s%8s%8s%8s%8s%8s%8s%8s\n",
- "step", "total", "comm", "nbrs", "init", "bonded", "nonb",
- "qeq", "matvecs" );
- fflush( out_control->log );
+ fprintf( out_control->log, "%6s%8s%8s%8s%8s%8s%8s%8s%8s\n",
+ "step", "total", "comm", "nbrs", "init", "bonded", "nonb",
+ "qeq", "matvecs" );
+ fflush( out_control->log );
}
else {
- strcpy( msg, "init_out_controls: .log file could not be opened\n" );
- return FAILURE;
+ strcpy( msg, "init_out_controls: .log file could not be opened\n" );
+ return FAILURE;
}
#endif
}
/* init pressure file */
if( control->ensemble == NPT ||
- control->ensemble == iNPT ||
- control->ensemble == sNPT ) {
+ control->ensemble == iNPT ||
+ control->ensemble == sNPT ) {
sprintf( temp, "%s.prs", control->sim_name );
if( (out_control->prs = fopen( temp, "w" )) != NULL ) {
- fprintf(out_control->prs,"%8s%13s%13s%13s%13s%13s%13s%13s\n",
- "step", "Pint/norm[x]", "Pint/norm[y]", "Pint/norm[z]",
- "Pext/Ptot[x]", "Pext/Ptot[y]", "Pext/Ptot[z]", "Pkin/V" );
- fflush( out_control->prs );
+ fprintf(out_control->prs,"%8s%13s%13s%13s%13s%13s%13s%13s\n",
+ "step", "Pint/norm[x]", "Pint/norm[y]", "Pint/norm[z]",
+ "Pext/Ptot[x]", "Pext/Ptot[y]", "Pext/Ptot[z]", "Pkin/V" );
+ fflush( out_control->prs );
}
else {
- strcpy(msg,"init_out_controls: .prs file couldn't be opened\n");
- return FAILURE;
+ strcpy(msg,"init_out_controls: .prs file couldn't be opened\n");
+ return FAILURE;
}
}
@@ -147,28 +147,28 @@ int Init_Output_Files( reax_system *system, control_params *control,
// if( control->dipole_anal ) {
// sprintf( temp, "%s.dpl", control->sim_name );
// if( (out_control->dpl = fopen( temp, "w" )) != NULL ) {
- // fprintf( out_control->dpl, "%6s%20s%30s",
- // "step", "molecule count", "avg dipole moment norm" );
- // fflush( out_control->dpl );
+ // fprintf( out_control->dpl, "%6s%20s%30s",
+ // "step", "molecule count", "avg dipole moment norm" );
+ // fflush( out_control->dpl );
// }
// else {
- // strcpy(msg, "init_out_controls: .dpl file couldn't be opened\n");
- // return FAILURE;
+ // strcpy(msg, "init_out_controls: .dpl file couldn't be opened\n");
+ // return FAILURE;
// }
// }
-
+
/* init diffusion coef analysis file */
// not yet implemented in the parallel version!!!
// if( control->diffusion_coef ) {
// sprintf( temp, "%s.drft", control->sim_name );
// if( (out_control->drft = fopen( temp, "w" )) != NULL ) {
- // fprintf( out_control->drft, "%7s%20s%20s\n",
- // "step", "type count", "avg disp^2" );
- // fflush( out_control->drft );
+ // fprintf( out_control->drft, "%7s%20s%20s\n",
+ // "step", "type count", "avg disp^2" );
+ // fflush( out_control->drft );
// }
// else {
- // strcpy(msg,"init_out_controls: .drft file couldn't be opened\n");
- // return FAILURE;
+ // strcpy(msg,"init_out_controls: .drft file couldn't be opened\n");
+ // return FAILURE;
// }
// }
}
@@ -176,14 +176,14 @@ int Init_Output_Files( reax_system *system, control_params *control,
/* init molecular analysis file */
/* proc0 opens this file and shares it with everyone.
- then all processors write into it in a round-robin
+ then all processors write into it in a round-robin
fashion controlled by their rank */
/*if( control->molecular_analysis ) {
if( system->my_rank == MASTER_NODE ) {
sprintf( temp, "%s.mol", control->sim_name );
if( (out_control->mol = fopen( temp, "w" )) == NULL ) {
- strcpy(msg,"init_out_controls: .mol file could not be opened\n");
- return FAILURE;
+ strcpy(msg,"init_out_controls: .mol file could not be opened\n");
+ return FAILURE;
}
}
@@ -208,14 +208,14 @@ int Init_Output_Files( reax_system *system, control_params *control,
/* open overcoordination energy file */
sprintf( temp, "%s.eov.%d", control->sim_name, system->my_rank );
- if( (out_control->eov = fopen( temp, "w" )) == NULL ) {
+ if( (out_control->eov = fopen( temp, "w" )) == NULL ) {
strcpy(msg,"Init_Out_Files: .eov file couldn't be opened\n");
return FAILURE;
}
/* open undercoordination energy file */
sprintf( temp, "%s.eun.%d", control->sim_name, system->my_rank );
- if( (out_control->eun = fopen( temp, "w" )) == NULL ) {
+ if( (out_control->eun = fopen( temp, "w" )) == NULL ) {
strcpy(msg,"Init_Out_Files: .eun file couldn't be opened\n");
return FAILURE;
}
@@ -257,7 +257,7 @@ int Init_Output_Files( reax_system *system, control_params *control,
/* open hydrogen bond energy file */
sprintf( temp, "%s.ehb.%d", control->sim_name, system->my_rank );
- if( (out_control->ehb = fopen( temp, "w" )) == NULL ) {
+ if( (out_control->ehb = fopen( temp, "w" )) == NULL ) {
strcpy(msg,"Init_Out_Files: .ehb file couldn't be opened\n");
return FAILURE;
}
@@ -285,7 +285,7 @@ int Init_Output_Files( reax_system *system, control_params *control,
strcpy(msg,"Init_Out_Files: .fbo file couldn't be opened\n");
return FAILURE;
}
-
+
/* open bond orders derivatives file */
sprintf( temp, "%s.fdbo.%d", control->sim_name, system->my_rank );
if( (out_control->fdbo = fopen( temp, "w" )) == NULL ) {
@@ -308,7 +308,7 @@ int Init_Output_Files( reax_system *system, control_params *control,
strcpy(msg,"Init_Out_Files: .flp file couldn't be opened\n");
return FAILURE;
}
-
+
/* open overcoordination forces file */
sprintf( temp, "%s.fov", control->sim_name );
if( (out_control->fov = fopen( temp, "w" )) == NULL ) {
@@ -321,7 +321,7 @@ int Init_Output_Files( reax_system *system, control_params *control,
if( (out_control->fun = fopen( temp, "w" )) == NULL ) {
strcpy(msg,"Init_Out_Files: .fun file couldn't be opened\n");
return FAILURE;
- }
+ }
/* open angle forces file */
sprintf( temp, "%s.fang", control->sim_name );
@@ -336,14 +336,14 @@ int Init_Output_Files( reax_system *system, control_params *control,
strcpy(msg,"Init_Out_Files: .fcoa file couldn't be opened\n");
return FAILURE;
}
-
+
/* open penalty forces file */
sprintf( temp, "%s.fpen", control->sim_name );
if( (out_control->fpen = fopen( temp, "w" )) == NULL ) {
strcpy(msg,"Init_Out_Files: .fpen file couldn't be opened\n");
return FAILURE;
}
-
+
/* open torsion forces file */
sprintf( temp, "%s.ftor", control->sim_name );
if( (out_control->ftor = fopen( temp, "w" )) == NULL ) {
@@ -360,11 +360,11 @@ int Init_Output_Files( reax_system *system, control_params *control,
/* open hydrogen bond forces file */
sprintf( temp, "%s.fhb", control->sim_name );
- if( (out_control->fhb = fopen( temp, "w" )) == NULL ) {
+ if( (out_control->fhb = fopen( temp, "w" )) == NULL ) {
strcpy(msg,"Init_Out_Files: .fhb file couldn't be opened\n");
return FAILURE;
}
-
+
/* open vdw forces file */
sprintf( temp, "%s.fvdw", control->sim_name );
if( (out_control->fvdw = fopen( temp, "w" )) == NULL ) {
@@ -378,7 +378,7 @@ int Init_Output_Files( reax_system *system, control_params *control,
strcpy(msg,"Init_Out_Files: .fele file couldn't be opened\n");
return FAILURE;
}
-
+
/* open total force file */
sprintf( temp, "%s.ftot", control->sim_name );
if( (out_control->ftot = fopen( temp, "w" )) == NULL ) {
@@ -425,8 +425,8 @@ int Init_Output_Files( reax_system *system, control_params *control,
/************************ close output files ************************/
-int Close_Output_Files( reax_system *system, control_params *control,
- output_controls *out_control, mpi_datatypes *mpi_data )
+int Close_Output_Files( reax_system *system, control_params *control,
+ output_controls *out_control, mpi_datatypes *mpi_data )
{
if( out_control->write_steps > 0 )
End_Traj( system->my_rank, out_control );
@@ -443,7 +443,7 @@ int Close_Output_Files( reax_system *system, control_params *control,
}
if( control->ensemble == NPT || control->ensemble == iNPT ||
- control->ensemble == sNPT )
+ control->ensemble == sNPT )
fclose( out_control->prs );
// not yet implemented in the parallel version
@@ -451,7 +451,7 @@ int Close_Output_Files( reax_system *system, control_params *control,
//if( control->diffusion_coef ) fclose( out_control->drft );
//if( control->molecular_analysis ) fclose( out_control->mol );
}
-
+
#ifdef TEST_ENERGY
fclose( out_control->ebond );
fclose( out_control->elp );
@@ -472,7 +472,7 @@ int Close_Output_Files( reax_system *system, control_params *control,
fclose( out_control->fdbo );
if( system->my_rank == MASTER_NODE ) {
- fclose( out_control->fbond );
+ fclose( out_control->fbond );
fclose( out_control->flp );
fclose( out_control->fov );
fclose( out_control->fun );
@@ -507,12 +507,12 @@ void Print_Box( simulation_box* box, char *name, FILE *out )
// int i, j;
fprintf( out, "%s:\n", name );
- fprintf( out, "\tmin[%8.3f %8.3f %8.3f]\n",
- box->min[0], box->min[1], box->min[2] );
+ fprintf( out, "\tmin[%8.3f %8.3f %8.3f]\n",
+ box->min[0], box->min[1], box->min[2] );
fprintf( out, "\tmax[%8.3f %8.3f %8.3f]\n",
- box->max[0], box->max[1], box->max[2] );
- fprintf( out, "\tdims[%8.3f%8.3f%8.3f]\n",
- box->box_norms[0], box->box_norms[1], box->box_norms[2] );
+ box->max[0], box->max[1], box->max[2] );
+ fprintf( out, "\tdims[%8.3f%8.3f%8.3f]\n",
+ box->box_norms[0], box->box_norms[1], box->box_norms[2] );
// fprintf( out, "box: {" );
// for( i = 0; i < 3; ++i )
@@ -529,7 +529,7 @@ void Print_Box( simulation_box* box, char *name, FILE *out )
// {
// fprintf( out, "{" );
// for( j = 0; j < 3; ++j )
- // fprintf( out, "%8.3f ", box->trans[i][j] );
+ // fprintf( out, "%8.3f ", box->trans[i][j] );
// fprintf( out, "}" );
// }
// fprintf( out, "}\n" );
@@ -539,7 +539,7 @@ void Print_Box( simulation_box* box, char *name, FILE *out )
// {
// fprintf( out, "{" );
// for( j = 0; j < 3; ++j )
- // fprintf( out, "%8.3f ", box->trans_inv[i][j] );
+ // fprintf( out, "%8.3f ", box->trans_inv[i][j] );
// fprintf( out, "}" );
// }
// fprintf( out, "}\n" );
@@ -551,43 +551,43 @@ void Print_Grid( grid* g, FILE *out )
{
int x, y, z, gc_type;
ivec gc_str;
- char gcell_type_text[10][12] =
- { "NO_NBRS", "NEAR_ONLY", "HBOND_ONLY", "FAR_ONLY",
+ char gcell_type_text[10][12] =
+ { "NO_NBRS", "NEAR_ONLY", "HBOND_ONLY", "FAR_ONLY",
"NEAR_HBOND", "NEAR_FAR", "HBOND_FAR", "FULL_NBRS", "NATIVE" };
fprintf( out, "\tnumber of grid cells: %d %d %d\n",
- g->ncells[0], g->ncells[1], g->ncells[2] );
- fprintf( out, "\tgcell lengths: %8.3f %8.3f %8.3f\n",
- g->cell_len[0], g->cell_len[1], g->cell_len[2] );
+ g->ncells[0], g->ncells[1], g->ncells[2] );
+ fprintf( out, "\tgcell lengths: %8.3f %8.3f %8.3f\n",
+ g->cell_len[0], g->cell_len[1], g->cell_len[2] );
fprintf( out, "\tinverses of gcell lengths: %8.3f %8.3f %8.3f\n",
- g->inv_len[0], g->inv_len[1], g->inv_len[2] );
+ g->inv_len[0], g->inv_len[1], g->inv_len[2] );
fprintf( out, "\t---------------------------------\n" );
fprintf( out, "\tnumber of native gcells: %d %d %d\n",
- g->native_cells[0], g->native_cells[1], g->native_cells[2] );
+ g->native_cells[0], g->native_cells[1], g->native_cells[2] );
fprintf( out, "\tnative gcell span: %d-%d %d-%d %d-%d\n",
- g->native_str[0], g->native_end[0],
- g->native_str[1], g->native_end[1],
- g->native_str[2], g->native_end[2] );
+ g->native_str[0], g->native_end[0],
+ g->native_str[1], g->native_end[1],
+ g->native_str[2], g->native_end[2] );
fprintf( out, "\t---------------------------------\n" );
fprintf( out, "\tvlist gcell stretch: %d %d %d\n",
- g->vlist_span[0], g->vlist_span[1], g->vlist_span[2] );
+ g->vlist_span[0], g->vlist_span[1], g->vlist_span[2] );
fprintf( out, "\tnonbonded nbrs gcell stretch: %d %d %d\n",
- g->nonb_span[0], g->nonb_span[1], g->nonb_span[2] );
+ g->nonb_span[0], g->nonb_span[1], g->nonb_span[2] );
fprintf( out, "\tbonded nbrs gcell stretch: %d %d %d\n",
- g->bond_span[0], g->bond_span[1], g->bond_span[2] );
+ g->bond_span[0], g->bond_span[1], g->bond_span[2] );
fprintf( out, "\t---------------------------------\n" );
fprintf( out, "\tghost gcell span: %d %d %d\n",
- g->ghost_span[0], g->ghost_span[1], g->ghost_span[2] );
+ g->ghost_span[0], g->ghost_span[1], g->ghost_span[2] );
fprintf( out, "\tnonbonded ghost gcell span: %d %d %d\n",
- g->ghost_nonb_span[0],g->ghost_nonb_span[1],g->ghost_nonb_span[2]);
+ g->ghost_nonb_span[0],g->ghost_nonb_span[1],g->ghost_nonb_span[2]);
fprintf(out, "\thbonded ghost gcell span: %d %d %d\n",
- g->ghost_hbond_span[0],g->ghost_hbond_span[1],g->ghost_hbond_span[2]);
+ g->ghost_hbond_span[0],g->ghost_hbond_span[1],g->ghost_hbond_span[2]);
fprintf( out, "\tbonded ghost gcell span: %d %d %d\n",
- g->ghost_bond_span[0],g->ghost_bond_span[1],g->ghost_bond_span[2]);
+ g->ghost_bond_span[0],g->ghost_bond_span[1],g->ghost_bond_span[2]);
//fprintf(out, "\t---------------------------------\n" );
//fprintf(out, "\tmax number of gcells at the boundary: %d\n", g->gcell_cap);
fprintf( out, "\t---------------------------------\n" );
-
+
fprintf( stderr, "GCELL MARKS:\n" );
gc_type = g->cells[0][0][0].type;
ivec_MakeZero( gc_str );
@@ -596,19 +596,19 @@ void Print_Grid( grid* g, FILE *out )
for( x = 0; x < g->ncells[0]; ++x )
for( y = 0; y < g->ncells[1]; ++y )
for( z = 0; z < g->ncells[2]; ++z )
- if( g->cells[x][y][z].type != gc_type ){
- fprintf( stderr,
- "\tgcells from(%2d %2d %2d) to (%2d %2d %2d): %d - %s\n",
- gc_str[0], gc_str[1], gc_str[2], x, y, z,
- gc_type, gcell_type_text[gc_type] );
- gc_type = g->cells[x][y][z].type;
- gc_str[0] = x;
- gc_str[1] = y;
- gc_str[2] = z;
- }
+ if( g->cells[x][y][z].type != gc_type ){
+ fprintf( stderr,
+ "\tgcells from(%2d %2d %2d) to (%2d %2d %2d): %d - %s\n",
+ gc_str[0], gc_str[1], gc_str[2], x, y, z,
+ gc_type, gcell_type_text[gc_type] );
+ gc_type = g->cells[x][y][z].type;
+ gc_str[0] = x;
+ gc_str[1] = y;
+ gc_str[2] = z;
+ }
fprintf( stderr, "\tgcells from(%2d %2d %2d) to (%2d %2d %2d): %d - %s\n",
- gc_str[0], gc_str[1], gc_str[2], x, y, z,
- gc_type, gcell_type_text[gc_type] );
+ gc_str[0], gc_str[1], gc_str[2], x, y, z,
+ gc_type, gcell_type_text[gc_type] );
fprintf( out, "-------------------------------------\n" );
}
@@ -625,32 +625,32 @@ void Print_GCell_Exchange_Bounds( int my_rank, neighbor_proc *my_nbrs )
sprintf( fname, "gcell_exchange_bounds%d", my_rank );
f = fopen( fname, "w" );
-
+
/* loop over neighbor processes */
for( r[0] = -1; r[0] <= 1; ++r[0])
for( r[1] = -1; r[1] <= 1; ++r[1] )
- for( r[2] = -1; r[2] <= 1; ++r[2] )
- if( r[0]!=0 || r[1]!=0 || r[2]!=0 ) {
- nbr_pr = &(my_nbrs[nbr]);
-
- fprintf( f, "p%-2d GCELL BOUNDARIES with r(%2d %2d %2d):\n",
- my_rank, r[0], r[1], r[2] );
-
- fprintf( f, "\tsend_type %s: send(%d %d %d) to (%d %d %d)\n",
- exch[nbr_pr->send_type],
- nbr_pr->str_send[0], nbr_pr->str_send[1],
- nbr_pr->str_send[2],
- nbr_pr->end_send[0], nbr_pr->end_send[1],
- nbr_pr->end_send[2] );
-
- fprintf( f, "\trecv_type %s: recv(%d %d %d) to (%d %d %d)\n",
- exch[nbr_pr->recv_type],
- nbr_pr->str_recv[0], nbr_pr->str_recv[1],
- nbr_pr->str_recv[2],
- nbr_pr->end_recv[0], nbr_pr->end_recv[1],
- nbr_pr->end_recv[2] );
- }
-
+ for( r[2] = -1; r[2] <= 1; ++r[2] )
+ if( r[0]!=0 || r[1]!=0 || r[2]!=0 ) {
+ nbr_pr = &(my_nbrs[nbr]);
+
+ fprintf( f, "p%-2d GCELL BOUNDARIES with r(%2d %2d %2d):\n",
+ my_rank, r[0], r[1], r[2] );
+
+ fprintf( f, "\tsend_type %s: send(%d %d %d) to (%d %d %d)\n",
+ exch[nbr_pr->send_type],
+ nbr_pr->str_send[0], nbr_pr->str_send[1],
+ nbr_pr->str_send[2],
+ nbr_pr->end_send[0], nbr_pr->end_send[1],
+ nbr_pr->end_send[2] );
+
+ fprintf( f, "\trecv_type %s: recv(%d %d %d) to (%d %d %d)\n",
+ exch[nbr_pr->recv_type],
+ nbr_pr->str_recv[0], nbr_pr->str_recv[1],
+ nbr_pr->str_recv[2],
+ nbr_pr->end_recv[0], nbr_pr->end_recv[1],
+ nbr_pr->end_recv[2] );
+ }
+
fclose(f);
}
@@ -663,8 +663,8 @@ void Print_Native_GCells( reax_system *system )
FILE *f;
grid *g;
grid_cell *gc;
- char gcell_type_text[10][12] =
- { "NO_NBRS", "NEAR_ONLY", "HBOND_ONLY", "FAR_ONLY",
+ char gcell_type_text[10][12] =
+ { "NO_NBRS", "NEAR_ONLY", "HBOND_ONLY", "FAR_ONLY",
"NEAR_HBOND", "NEAR_FAR", "HBOND_FAR", "FULL_NBRS", "NATIVE" };
sprintf( fname, "native_gcells.%d", system->my_rank );
@@ -674,19 +674,19 @@ void Print_Native_GCells( reax_system *system )
for( i = g->native_str[0]; i < g->native_end[0]; i++ )
for( j = g->native_str[1]; j < g->native_end[1]; j++ )
for( k = g->native_str[2]; k < g->native_end[2]; k++ )
- {
- gc = &( g->cells[i][j][k] );
+ {
+ gc = &( g->cells[i][j][k] );
- fprintf( f, "p%d gcell(%2d %2d %2d) of type %d(%s)\n",
- system->my_rank, i, j, k,
- gc->type, gcell_type_text[gc->type] );
+ fprintf( f, "p%d gcell(%2d %2d %2d) of type %d(%s)\n",
+ system->my_rank, i, j, k,
+ gc->type, gcell_type_text[gc->type] );
- fprintf( f, "\tatom list start: %d, end: %d\n\t", gc->str, gc->end );
+ fprintf( f, "\tatom list start: %d, end: %d\n\t", gc->str, gc->end );
- for( l = gc->str; l < gc->end; ++l )
- fprintf( f, "%5d", system->my_atoms[l].orig_id );
- fprintf( f, "\n" );
- }
+ for( l = gc->str; l < gc->end; ++l )
+ fprintf( f, "%5d", system->my_atoms[l].orig_id );
+ fprintf( f, "\n" );
+ }
fclose(f);
}
@@ -700,8 +700,8 @@ void Print_All_GCells( reax_system *system )
FILE *f;
grid *g;
grid_cell *gc;
- char gcell_type_text[10][12] =
- { "NO_NBRS", "NEAR_ONLY", "HBOND_ONLY", "FAR_ONLY",
+ char gcell_type_text[10][12] =
+ { "NO_NBRS", "NEAR_ONLY", "HBOND_ONLY", "FAR_ONLY",
"NEAR_HBOND", "NEAR_FAR", "HBOND_FAR", "FULL_NBRS", "NATIVE" };
sprintf( fname, "all_gcells.%d", system->my_rank );
@@ -711,19 +711,19 @@ void Print_All_GCells( reax_system *system )
for( i = 0; i < g->ncells[0]; i++ )
for( j = 0; j < g->ncells[1]; j++ )
for( k = 0; k < g->ncells[2]; k++ )
- {
- gc = &( g->cells[i][j][k] );
+ {
+ gc = &( g->cells[i][j][k] );
- fprintf( f, "p%d gcell(%2d %2d %2d) of type %d(%s)\n",
- system->my_rank, i, j, k,
- gc->type, gcell_type_text[gc->type] );
+ fprintf( f, "p%d gcell(%2d %2d %2d) of type %d(%s)\n",
+ system->my_rank, i, j, k,
+ gc->type, gcell_type_text[gc->type] );
- fprintf( f, "\tatom list start: %d, end: %d\n\t", gc->str, gc->end );
-
- for( l = gc->str; l < gc->end; ++l )
- fprintf( f, "%5d", system->my_atoms[l].orig_id );
- fprintf( f, "\n" );
- }
+ fprintf( f, "\tatom list start: %d, end: %d\n\t", gc->str, gc->end );
+
+ for( l = gc->str; l < gc->end; ++l )
+ fprintf( f, "%5d", system->my_atoms[l].orig_id );
+ fprintf( f, "\n" );
+ }
fclose(f);
}
@@ -748,11 +748,11 @@ void Print_My_Atoms( reax_system *system )
for( i = 0; i < system->n; ++i )
fprintf( fh, "p%-2d %-5d %2d %24.15e%24.15e%24.15e\n",
- system->my_rank,
- system->my_atoms[i].orig_id, system->my_atoms[i].type,
- system->my_atoms[i].x[0],
- system->my_atoms[i].x[1],
- system->my_atoms[i].x[2] );
+ system->my_rank,
+ system->my_atoms[i].orig_id, system->my_atoms[i].type,
+ system->my_atoms[i].x[0],
+ system->my_atoms[i].x[1],
+ system->my_atoms[i].x[2] );
fclose( fh );
}
@@ -776,21 +776,21 @@ void Print_My_Ext_Atoms( reax_system *system )
for( i = 0; i < system->N; ++i )
fprintf( fh, "p%-2d %-5d imprt%-5d %2d %24.15e%24.15e%24.15e\n",
- system->my_rank, system->my_atoms[i].orig_id,
- system->my_atoms[i].imprt_id, system->my_atoms[i].type,
- system->my_atoms[i].x[0],
- system->my_atoms[i].x[1],
- system->my_atoms[i].x[2] );
+ system->my_rank, system->my_atoms[i].orig_id,
+ system->my_atoms[i].imprt_id, system->my_atoms[i].type,
+ system->my_atoms[i].x[0],
+ system->my_atoms[i].x[1],
+ system->my_atoms[i].x[2] );
fclose( fh );
}
-void Print_Far_Neighbors( reax_system *system, reax_list **lists,
- control_params *control )
+void Print_Far_Neighbors( reax_system *system, reax_list **lists,
+ control_params *control )
{
char fname[100];
- int i, j, id_i, id_j, nbr, natoms;
+ int i, j, id_i, id_j, nbr, natoms;
FILE *fout;
reax_list *far_nbrs;
@@ -807,19 +807,19 @@ void Print_Far_Neighbors( reax_system *system, reax_list **lists,
id_j = system->my_atoms[nbr].orig_id;
fprintf( fout, "%6d%6d%24.15e%24.15e%24.15e%24.15e\n",
- id_i, id_j, far_nbrs->select.far_nbr_list[j].d,
- far_nbrs->select.far_nbr_list[j].dvec[0],
- far_nbrs->select.far_nbr_list[j].dvec[1],
- far_nbrs->select.far_nbr_list[j].dvec[2] );
-
+ id_i, id_j, far_nbrs->select.far_nbr_list[j].d,
+ far_nbrs->select.far_nbr_list[j].dvec[0],
+ far_nbrs->select.far_nbr_list[j].dvec[1],
+ far_nbrs->select.far_nbr_list[j].dvec[2] );
+
fprintf( fout, "%6d%6d%24.15e%24.15e%24.15e%24.15e\n",
- id_j, id_i, far_nbrs->select.far_nbr_list[j].d,
- -far_nbrs->select.far_nbr_list[j].dvec[0],
- -far_nbrs->select.far_nbr_list[j].dvec[1],
- -far_nbrs->select.far_nbr_list[j].dvec[2] );
+ id_j, id_i, far_nbrs->select.far_nbr_list[j].d,
+ -far_nbrs->select.far_nbr_list[j].dvec[0],
+ -far_nbrs->select.far_nbr_list[j].dvec[1],
+ -far_nbrs->select.far_nbr_list[j].dvec[2] );
}
}
-
+
fclose( fout );
}
@@ -830,10 +830,10 @@ void Print_Sparse_Matrix( reax_system *system, sparse_matrix *A )
for( i = 0; i < A->n; ++i )
for( j = A->start[i]; j < A->end[i]; ++j )
- fprintf( stderr, "%d %d %.15e\n",
- system->my_atoms[i].orig_id,
- system->my_atoms[A->entries[j].j].orig_id,
- A->entries[j].val );
+ fprintf( stderr, "%d %d %.15e\n",
+ system->my_atoms[i].orig_id,
+ system->my_atoms[A->entries[j].j].orig_id,
+ A->entries[j].val );
}
@@ -844,10 +844,10 @@ void Print_Sparse_Matrix2( reax_system *system, sparse_matrix *A, char *fname )
for( i = 0; i < A->n; ++i )
for( j = A->start[i]; j < A->end[i]; ++j )
- fprintf( f, "%d %d %.15e\n",
- system->my_atoms[i].orig_id,
- system->my_atoms[A->entries[j].j].orig_id,
- A->entries[j].val );
+ fprintf( f, "%d %d %.15e\n",
+ system->my_atoms[i].orig_id,
+ system->my_atoms[A->entries[j].j].orig_id,
+ A->entries[j].val );
fclose(f);
}
@@ -863,11 +863,11 @@ void Print_Symmetric_Sparse(reax_system *system, sparse_matrix *A, char *fname)
ai = &(system->my_atoms[i]);
for( j = A->start[i]; j < A->end[i]; ++j ) {
aj = &(system->my_atoms[A->entries[j].j]);
- fprintf( f, "%d %d %.15e\n",
- ai->renumber, aj->renumber, A->entries[j].val );
+ fprintf( f, "%d %d %.15e\n",
+ ai->renumber, aj->renumber, A->entries[j].val );
if( A->entries[j].j < system->n && ai->renumber != aj->renumber )
- fprintf( f, "%d %d %.15e\n",
- aj->renumber, ai->renumber, A->entries[j].val );
+ fprintf( f, "%d %d %.15e\n",
+ aj->renumber, ai->renumber, A->entries[j].val );
}
}
@@ -875,8 +875,8 @@ void Print_Symmetric_Sparse(reax_system *system, sparse_matrix *A, char *fname)
}
-void Print_Linear_System( reax_system *system, control_params *control,
- storage *workspace, int step )
+void Print_Linear_System( reax_system *system, control_params *control,
+ storage *workspace, int step )
{
int i, j;
char fname[100];
@@ -889,35 +889,35 @@ void Print_Linear_System( reax_system *system, control_params *control,
out = fopen( fname, "w" );
for( i = 0; i < system->n; i++ ) {
ai = &(system->my_atoms[i]);
- fprintf( out, "%6d%2d%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e\n",
- ai->renumber, ai->type, ai->x[0], ai->x[1], ai->x[2],
- workspace->s[i], workspace->b_s[i],
- workspace->t[i], workspace->b_t[i] );
+ fprintf( out, "%6d%2d%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e\n",
+ ai->renumber, ai->type, ai->x[0], ai->x[1], ai->x[2],
+ workspace->s[i], workspace->b_s[i],
+ workspace->t[i], workspace->b_t[i] );
}
fclose( out );
-
+
// print QEq coef matrix
sprintf( fname, "%s.p%dH%d", control->sim_name, system->my_rank, step );
Print_Symmetric_Sparse( system, workspace->H, fname );
-
+
// print the incomplete H matrix
/*sprintf( fname, "%s.p%dHinc%d", control->sim_name, system->my_rank, step );
out = fopen( fname, "w" );
H = workspace->H;
for( i = 0; i < H->n; ++i ) {
ai = &(system->my_atoms[i]);
- for( j = H->start[i]; j < H->end[i]; ++j )
+ for( j = H->start[i]; j < H->end[i]; ++j )
if( H->entries[j].j < system->n ) {
- aj = &(system->my_atoms[H->entries[j].j]);
- fprintf( out, "%d %d %.15e\n",
- ai->orig_id, aj->orig_id, H->entries[j].val );
- if( ai->orig_id != aj->orig_id )
- fprintf( out, "%d %d %.15e\n",
- aj->orig_id, ai->orig_id, H->entries[j].val );
+ aj = &(system->my_atoms[H->entries[j].j]);
+ fprintf( out, "%d %d %.15e\n",
+ ai->orig_id, aj->orig_id, H->entries[j].val );
+ if( ai->orig_id != aj->orig_id )
+ fprintf( out, "%d %d %.15e\n",
+ aj->orig_id, ai->orig_id, H->entries[j].val );
}
}
fclose( out );*/
-
+
// print the L from incomplete cholesky decomposition
/*sprintf( fname, "%s.p%dL%d", control->sim_name, system->my_rank, step );
Print_Sparse_Matrix2( system, workspace->L, fname );*/
@@ -934,8 +934,8 @@ void Print_LinSys_Soln( reax_system *system, real *x, real *b_prm, real *b )
fout = fopen( fname, "w" );
for( i = 0; i < system->n; ++i )
- fprintf( fout, "%6d%10.4f%10.4f%10.4f\n",
- system->my_atoms[i].orig_id, x[i], b_prm[i], b[i] );
+ fprintf( fout, "%6d%10.4f%10.4f%10.4f\n",
+ system->my_atoms[i].orig_id, x[i], b_prm[i], b[i] );
fclose( fout );
}
@@ -951,11 +951,11 @@ void Print_Charges( reax_system *system )
fout = fopen( fname, "w" );
for( i = 0; i < system->n; ++i )
- fprintf( fout, "%6d %10.7f %10.7f %10.7f\n",
- system->my_atoms[i].orig_id,
- system->my_atoms[i].s[0],
- system->my_atoms[i].t[0],
- system->my_atoms[i].q );
+ fprintf( fout, "%6d %10.7f %10.7f %10.7f\n",
+ system->my_atoms[i].orig_id,
+ system->my_atoms[i].s[0],
+ system->my_atoms[i].t[0],
+ system->my_atoms[i].q );
fclose( fout );
}
@@ -973,22 +973,22 @@ void Print_Bonds( reax_system *system, reax_list *bonds, char *fname )
pbond = &(bonds->select.bond_list[pj]);
bo_ij = &(pbond->bo_data);
j = pbond->nbr;
- //fprintf( f, "%6d%6d%23.15e%23.15e%23.15e%23.15e%23.15e\n",
- // system->my_atoms[i].orig_id, system->my_atoms[j].orig_id,
+ //fprintf( f, "%6d%6d%23.15e%23.15e%23.15e%23.15e%23.15e\n",
+ // system->my_atoms[i].orig_id, system->my_atoms[j].orig_id,
// pbond->d, bo_ij->BO, bo_ij->BO_s, bo_ij->BO_pi, bo_ij->BO_pi2 );
- fprintf( f, "%8d%8d %24.15f %24.15f\n",
- i, j,//system->my_atoms[i].orig_id, system->my_atoms[j].orig_id,
- pbond->d, bo_ij->BO );
+ fprintf( f, "%8d%8d %24.15f %24.15f\n",
+ i, j,//system->my_atoms[i].orig_id, system->my_atoms[j].orig_id,
+ pbond->d, bo_ij->BO );
}
fclose(f);
}
-int fn_qsort_intcmp( const void *a, const void *b )
-{
- return( *(int *)a - *(int *)b );
-}
+int fn_qsort_intcmp( const void *a, const void *b )
+{
+ return( *(int *)a - *(int *)b );
+}
void Print_Bond_List2( reax_system *system, reax_list *bonds, char *fname )
{
@@ -1002,12 +1002,12 @@ void Print_Bond_List2( reax_system *system, reax_list *bonds, char *fname )
id_i = system->my_atoms[i].orig_id;
fprintf( f, "%6d:", id_i);
for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj ) {
- nbr = bonds->select.bond_list[pj].nbr;
+ nbr = bonds->select.bond_list[pj].nbr;
id_j = system->my_atoms[nbr].orig_id;
- if( id_i < id_j )
- temp[num++] = id_j;
+ if( id_i < id_j )
+ temp[num++] = id_j;
}
-
+
qsort(&temp, num, sizeof(int), fn_qsort_intcmp);
for(j=0; j < num; j++)
fprintf(f, "%6d", temp[j] );
@@ -1016,8 +1016,8 @@ void Print_Bond_List2( reax_system *system, reax_list *bonds, char *fname )
}
-void Print_Total_Force( reax_system *system, simulation_data *data,
- storage *workspace )
+void Print_Total_Force( reax_system *system, simulation_data *data,
+ storage *workspace )
{
int i;
@@ -1025,15 +1025,15 @@ void Print_Total_Force( reax_system *system, simulation_data *data,
fprintf( stderr, "%6s\t%-38s\n", "atom", "atom.f[0,1,2]");
for( i = 0; i < system->N; ++i )
- fprintf( stderr, "%6d %f %f %f\n",
- //"%6d%24.15e%24.15e%24.15e\n",
- system->my_atoms[i].orig_id,
- workspace->f[i][0], workspace->f[i][1], workspace->f[i][2] );
+ fprintf( stderr, "%6d %f %f %f\n",
+ //"%6d%24.15e%24.15e%24.15e\n",
+ system->my_atoms[i].orig_id,
+ workspace->f[i][0], workspace->f[i][1], workspace->f[i][2] );
}
-void fixbond( reax_system *system, control_params *control,
- simulation_data *data, reax_list **lists,
- output_controls *out_control, mpi_datatypes *mpi_data )
+void fixbond( reax_system *system, control_params *control,
+ simulation_data *data, reax_list **lists,
+ output_controls *out_control, mpi_datatypes *mpi_data )
{
// count the number of bonds around each atom, for fix reax/c/bond
int i, j, pj, my_bonds_0, i_id, j_id;
@@ -1051,9 +1051,9 @@ void fixbond( reax_system *system, control_params *control,
j_id = system->my_atoms[j].orig_id;
BO_tmp = bonds->select.bond_list[pj].bo_data.BO;
if( i_id != j_id && BO_tmp >= control->bg_cut ) {
- ++my_bonds_0;
- system->my_atoms[i].nbr_id[my_bonds_0] = j_id;
- system->my_atoms[i].nbr_bo[my_bonds_0] = BO_tmp;
+ ++my_bonds_0;
+ system->my_atoms[i].nbr_id[my_bonds_0] = j_id;
+ system->my_atoms[i].nbr_bo[my_bonds_0] = BO_tmp;
}
}
my_bonds_max = MAX(my_bonds_0, my_bonds_max);
@@ -1063,9 +1063,9 @@ void fixbond( reax_system *system, control_params *control,
}
-void fixspecies( reax_system *system, control_params *control,
- simulation_data *data, reax_list **lists,
- output_controls *out_control, mpi_datatypes *mpi_data )
+void fixspecies( reax_system *system, control_params *control,
+ simulation_data *data, reax_list **lists,
+ output_controls *out_control, mpi_datatypes *mpi_data )
{
// count the number of bonds around each atom, for fix reax/c/bond
int i, j, pj, my_bonds_0, i_id, j_id;
@@ -1083,9 +1083,9 @@ void fixspecies( reax_system *system, control_params *control,
j_id = system->my_atoms[j].orig_id;
BO_tmp = bonds->select.bond_list[pj].bo_data.BO;
if( i_id != j_id && BO_tmp >= control->bg_cut ) {
- ++my_bonds_0;
- system->my_atoms[i].nbr_id[my_bonds_0] = j_id;
- system->my_atoms[i].nbr_bo[my_bonds_0] = BO_tmp;
+ ++my_bonds_0;
+ system->my_atoms[i].nbr_id[my_bonds_0] = j_id;
+ system->my_atoms[i].nbr_bo[my_bonds_0] = BO_tmp;
}
}
my_bonds_max = MAX(my_bonds_0, my_bonds_max);
@@ -1095,114 +1095,114 @@ void fixspecies( reax_system *system, control_params *control,
}
-void Output_Results( reax_system *system, control_params *control,
- simulation_data *data, reax_list **lists,
- output_controls *out_control, mpi_datatypes *mpi_data )
+void Output_Results( reax_system *system, control_params *control,
+ simulation_data *data, reax_list **lists,
+ output_controls *out_control, mpi_datatypes *mpi_data )
{
#if defined(LOG_PERFORMANCE)
real t_elapsed, denom;
#endif
- if((out_control->energy_update_freq > 0 &&
+ if((out_control->energy_update_freq > 0 &&
data->step%out_control->energy_update_freq == 0) ||
- (out_control->write_steps > 0 &&
+ (out_control->write_steps > 0 &&
data->step%out_control->write_steps == 0)){
/* update system-wide energies */
Compute_System_Energy( system, data, mpi_data->world );
-
+
/* output energies */
- if( system->my_rank == MASTER_NODE &&
- out_control->energy_update_freq > 0 &&
- data->step % out_control->energy_update_freq == 0 ) {
+ if( system->my_rank == MASTER_NODE &&
+ out_control->energy_update_freq > 0 &&
+ data->step % out_control->energy_update_freq == 0 ) {
#if !defined(DEBUG) && !defined(DEBUG_FOCUS)
#if defined(PURE_REAX)
- fprintf( out_control->out,
- "%-6d%14.2f%14.2f%14.2f%11.2f%13.2f%13.5f\n",
- data->step, data->sys_en.e_tot, data->sys_en.e_pot,
- E_CONV * data->sys_en.e_kin, data->therm.T,
- system->big_box.V, data->iso_bar.P );
+ fprintf( out_control->out,
+ "%-6d%14.2f%14.2f%14.2f%11.2f%13.2f%13.5f\n",
+ data->step, data->sys_en.e_tot, data->sys_en.e_pot,
+ E_CONV * data->sys_en.e_kin, data->therm.T,
+ system->big_box.V, data->iso_bar.P );
fflush( out_control->out );
#endif
- fprintf( out_control->pot,
- "%-6d%14.2f%14.2f%14.2f%14.2f%14.2f%14.2f%14.2f%14.2f%14.2f%14.2f%14.2f\n",
- data->step,
- data->sys_en.e_bond,
- data->sys_en.e_ov + data->sys_en.e_un, data->sys_en.e_lp,
- data->sys_en.e_ang + data->sys_en.e_pen, data->sys_en.e_coa,
- data->sys_en.e_hb,
- data->sys_en.e_tor, data->sys_en.e_con,
- data->sys_en.e_vdW, data->sys_en.e_ele, data->sys_en.e_pol);
+ fprintf( out_control->pot,
+ "%-6d%14.2f%14.2f%14.2f%14.2f%14.2f%14.2f%14.2f%14.2f%14.2f%14.2f%14.2f\n",
+ data->step,
+ data->sys_en.e_bond,
+ data->sys_en.e_ov + data->sys_en.e_un, data->sys_en.e_lp,
+ data->sys_en.e_ang + data->sys_en.e_pen, data->sys_en.e_coa,
+ data->sys_en.e_hb,
+ data->sys_en.e_tor, data->sys_en.e_con,
+ data->sys_en.e_vdW, data->sys_en.e_ele, data->sys_en.e_pol);
fflush( out_control->pot );
#else
#if defined(PURE_REAX)
- fprintf( out_control->out,
- "%-6d%24.15e%24.15e%24.15e%13.5f%16.5f%13.5f\n",
- data->step, data->sys_en.e_tot, data->sys_en.e_pot,
- E_CONV * data->sys_en.e_kin, data->therm.T,
- system->big_box.V, data->iso_bar.P );
+ fprintf( out_control->out,
+ "%-6d%24.15e%24.15e%24.15e%13.5f%16.5f%13.5f\n",
+ data->step, data->sys_en.e_tot, data->sys_en.e_pot,
+ E_CONV * data->sys_en.e_kin, data->therm.T,
+ system->big_box.V, data->iso_bar.P );
fflush( out_control->out );
#endif
- fprintf( out_control->pot,
- "%-6d%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e\n",
- data->step,
- data->sys_en.e_bond,
- data->sys_en.e_ov + data->sys_en.e_un, data->sys_en.e_lp,
- data->sys_en.e_ang + data->sys_en.e_pen, data->sys_en.e_coa,
- data->sys_en.e_hb,
- data->sys_en.e_tor, data->sys_en.e_con,
- data->sys_en.e_vdW, data->sys_en.e_ele, data->sys_en.e_pol);
+ fprintf( out_control->pot,
+ "%-6d%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e\n",
+ data->step,
+ data->sys_en.e_bond,
+ data->sys_en.e_ov + data->sys_en.e_un, data->sys_en.e_lp,
+ data->sys_en.e_ang + data->sys_en.e_pen, data->sys_en.e_coa,
+ data->sys_en.e_hb,
+ data->sys_en.e_tor, data->sys_en.e_con,
+ data->sys_en.e_vdW, data->sys_en.e_ele, data->sys_en.e_pol);
fflush( out_control->pot );
#endif //DEBUG
-
+
#if defined(LOG_PERFORMANCE)
t_elapsed = Get_Timing_Info( data->timing.total );
if( data->step - data->prev_steps > 0 )
- denom = 1.0 / out_control->energy_update_freq;
+ denom = 1.0 / out_control->energy_update_freq;
else denom = 1;
-
+
fprintf( out_control->log, "%6d%8.3f%8.3f%8.3f%8.3f%8.3f%8.3f%8.3f%6d\n",
- data->step,
- t_elapsed * denom,
- data->timing.comm * denom,
- data->timing.nbrs * denom,
- data->timing.init_forces * denom,
- data->timing.bonded * denom,
- data->timing.nonb * denom,
- data->timing.qEq * denom,
- (int)((data->timing.s_matvecs+data->timing.t_matvecs)*denom) );
-
+ data->step,
+ t_elapsed * denom,
+ data->timing.comm * denom,
+ data->timing.nbrs * denom,
+ data->timing.init_forces * denom,
+ data->timing.bonded * denom,
+ data->timing.nonb * denom,
+ data->timing.qEq * denom,
+ (int)((data->timing.s_matvecs+data->timing.t_matvecs)*denom) );
+
Reset_Timing( &(data->timing) );
fflush( out_control->log );
#endif //LOG_PERFORMANCE
-
+
if( control->virial ){
- fprintf( out_control->prs,
- "%8d%13.6f%13.6f%13.6f%13.6f%13.6f%13.6f%13.6f\n",
- data->step,
- data->int_press[0], data->int_press[1], data->int_press[2],
- data->ext_press[0], data->ext_press[1], data->ext_press[2],
- data->kin_press );
-
- fprintf( out_control->prs,
- "%8s%13.6f%13.6f%13.6f%13.6f%13.6f%13.6f%13.6f\n",
- "",system->big_box.box_norms[0], system->big_box.box_norms[1],
- system->big_box.box_norms[2],
- data->tot_press[0], data->tot_press[1], data->tot_press[2],
- system->big_box.V );
-
- fflush( out_control->prs);
+ fprintf( out_control->prs,
+ "%8d%13.6f%13.6f%13.6f%13.6f%13.6f%13.6f%13.6f\n",
+ data->step,
+ data->int_press[0], data->int_press[1], data->int_press[2],
+ data->ext_press[0], data->ext_press[1], data->ext_press[2],
+ data->kin_press );
+
+ fprintf( out_control->prs,
+ "%8s%13.6f%13.6f%13.6f%13.6f%13.6f%13.6f%13.6f\n",
+ "",system->big_box.box_norms[0], system->big_box.box_norms[1],
+ system->big_box.box_norms[2],
+ data->tot_press[0], data->tot_press[1], data->tot_press[2],
+ system->big_box.V );
+
+ fflush( out_control->prs);
}
}
-
+
/* write current frame */
- if( out_control->write_steps > 0 &&
- (data->step-data->prev_steps) % out_control->write_steps == 0 ) {
+ if( out_control->write_steps > 0 &&
+ (data->step-data->prev_steps) % out_control->write_steps == 0 ) {
Append_Frame( system, control, data, lists, out_control, mpi_data );
}
}
-
+
#if defined(DEBUG)
fprintf( stderr, "output_results... done\n" );
#endif
@@ -1212,40 +1212,40 @@ void Output_Results( reax_system *system, control_params *control,
#ifdef TEST_ENERGY
void Debug_Marker_Bonded( output_controls *out_control, int step )
{
- fprintf( out_control->ebond, "step: %d\n%6s%6s%12s%12s%12s\n",
- step, "atom1", "atom2", "bo", "ebond", "total" );
- fprintf( out_control->elp, "step: %d\n%6s%12s%12s%12s\n",
- step, "atom", "nlp", "elp", "total" );
- fprintf( out_control->eov, "step: %d\n%6s%12s%12s\n",
- step, "atom", "eov", "total" );
- fprintf( out_control->eun, "step: %d\n%6s%12s%12s\n",
- step, "atom", "eun", "total" );
- fprintf( out_control->eval, "step: %d\n%6s%6s%6s%12s%12s%12s%12s%12s%12s\n",
- step, "atom1", "atom2", "atom3", "angle", "theta0",
- "bo(12)", "bo(23)", "eval", "total" );
- fprintf( out_control->epen, "step: %d\n%6s%6s%6s%12s%12s%12s%12s%12s\n",
- step, "atom1", "atom2", "atom3", "angle", "bo(12)", "bo(23)",
- "epen", "total" );
- fprintf( out_control->ecoa, "step: %d\n%6s%6s%6s%12s%12s%12s%12s%12s\n",
- step, "atom1", "atom2", "atom3", "angle", "bo(12)", "bo(23)",
- "ecoa", "total" );
- fprintf( out_control->ehb, "step: %d\n%6s%6s%6s%12s%12s%12s%12s%12s\n",
- step, "atom1", "atom2", "atom3", "r(23)", "angle", "bo(12)",
- "ehb", "total" );
- fprintf( out_control->etor, "step: %d\n%6s%6s%6s%6s%12s%12s%12s%12s\n",
- step, "atom1", "atom2", "atom3", "atom4", "phi", "bo(23)",
- "etor", "total" );
+ fprintf( out_control->ebond, "step: %d\n%6s%6s%12s%12s%12s\n",
+ step, "atom1", "atom2", "bo", "ebond", "total" );
+ fprintf( out_control->elp, "step: %d\n%6s%12s%12s%12s\n",
+ step, "atom", "nlp", "elp", "total" );
+ fprintf( out_control->eov, "step: %d\n%6s%12s%12s\n",
+ step, "atom", "eov", "total" );
+ fprintf( out_control->eun, "step: %d\n%6s%12s%12s\n",
+ step, "atom", "eun", "total" );
+ fprintf( out_control->eval, "step: %d\n%6s%6s%6s%12s%12s%12s%12s%12s%12s\n",
+ step, "atom1", "atom2", "atom3", "angle", "theta0",
+ "bo(12)", "bo(23)", "eval", "total" );
+ fprintf( out_control->epen, "step: %d\n%6s%6s%6s%12s%12s%12s%12s%12s\n",
+ step, "atom1", "atom2", "atom3", "angle", "bo(12)", "bo(23)",
+ "epen", "total" );
+ fprintf( out_control->ecoa, "step: %d\n%6s%6s%6s%12s%12s%12s%12s%12s\n",
+ step, "atom1", "atom2", "atom3", "angle", "bo(12)", "bo(23)",
+ "ecoa", "total" );
+ fprintf( out_control->ehb, "step: %d\n%6s%6s%6s%12s%12s%12s%12s%12s\n",
+ step, "atom1", "atom2", "atom3", "r(23)", "angle", "bo(12)",
+ "ehb", "total" );
+ fprintf( out_control->etor, "step: %d\n%6s%6s%6s%6s%12s%12s%12s%12s\n",
+ step, "atom1", "atom2", "atom3", "atom4", "phi", "bo(23)",
+ "etor", "total" );
fprintf( out_control->econ,"step:%d\n%6s%6s%6s%6s%12s%12s%12s%12s%12s%12s\n",
- step, "atom1", "atom2", "atom3", "atom4",
- "phi", "bo(12)", "bo(23)", "bo(34)", "econ", "total" );
+ step, "atom1", "atom2", "atom3", "atom4",
+ "phi", "bo(12)", "bo(23)", "bo(34)", "econ", "total" );
}
void Debug_Marker_Nonbonded( output_controls *out_control, int step )
{
fprintf( out_control->evdw, "step: %d\n%6s%6s%12s%12s%12s\n",
- step, "atom1", "atom2", "r12", "evdw", "total" );
+ step, "atom1", "atom2", "r12", "evdw", "total" );
fprintf( out_control->ecou, "step: %d\n%6s%6s%12s%12s%12s%12s%12s\n",
- step, "atom1", "atom2", "r12", "q1", "q2", "ecou", "total" );
+ step, "atom1", "atom2", "r12", "q1", "q2", "ecou", "total" );
}
#endif
@@ -1253,16 +1253,16 @@ void Debug_Marker_Nonbonded( output_controls *out_control, int step )
#ifdef TEST_FORCES
void Dummy_Printer( reax_system *system, control_params *control,
- simulation_data *data, storage *workspace,
- reax_list **lists, output_controls *out_control )
+ simulation_data *data, storage *workspace,
+ reax_list **lists, output_controls *out_control )
{
}
-void Print_Bond_Orders( reax_system *system, control_params *control,
- simulation_data *data, storage *workspace,
- reax_list **lists, output_controls *out_control )
+void Print_Bond_Orders( reax_system *system, control_params *control,
+ simulation_data *data, storage *workspace,
+ reax_list **lists, output_controls *out_control )
{
int i, pj, pk;
bond_order_data *bo_ij;
@@ -1272,50 +1272,50 @@ void Print_Bond_Orders( reax_system *system, control_params *control,
/* bond orders */
fprintf( out_control->fbo, "step: %d\n", data->step );
- fprintf( out_control->fbo, "%6s%6s%12s%12s%12s%12s%12s\n",
- "atom1", "atom2", "r_ij", "total_bo", "bo_s", "bo_p", "bo_pp" );
-
+ fprintf( out_control->fbo, "%6s%6s%12s%12s%12s%12s%12s\n",
+ "atom1", "atom2", "r_ij", "total_bo", "bo_s", "bo_p", "bo_pp" );
+
for( i = 0; i < system->N; ++i )
for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj ) {
- bo_ij = &(bonds->select.bond_list[pj].bo_data);
- fprintf( out_control->fbo,
- "%6d%6d%24.15e%24.15e%24.15e%24.15e%24.15e\n",
- system->my_atoms[i].orig_id,
- system->my_atoms[bonds->select.bond_list[pj].nbr].orig_id,
- bonds->select.bond_list[pj].d,
- bo_ij->BO, bo_ij->BO_s, bo_ij->BO_pi, bo_ij->BO_pi2 );
+ bo_ij = &(bonds->select.bond_list[pj].bo_data);
+ fprintf( out_control->fbo,
+ "%6d%6d%24.15e%24.15e%24.15e%24.15e%24.15e\n",
+ system->my_atoms[i].orig_id,
+ system->my_atoms[bonds->select.bond_list[pj].nbr].orig_id,
+ bonds->select.bond_list[pj].d,
+ bo_ij->BO, bo_ij->BO_s, bo_ij->BO_pi, bo_ij->BO_pi2 );
}
/* derivatives of bond orders */
fprintf( out_control->fdbo, "step: %d\n", data->step );
- fprintf( out_control->fdbo, "%6s%6s%6s%24s%24s%24s\n",
- "atom1", "atom2", "atom2", "dBO", "dBOpi", "dBOpi2" );
+ fprintf( out_control->fdbo, "%6s%6s%6s%24s%24s%24s\n",
+ "atom1", "atom2", "atom2", "dBO", "dBOpi", "dBOpi2" );
for( i = 0; i < system->N; ++i )
for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj ) {
- /* fprintf( out_control->fdbo, "%6d %6d\tstart: %6d\tend: %6d\n",
- system->my_atoms[i].orig_id,
- system->my_atoms[bonds->select.bond_list[pj].nbr].orig_id,
- Start_Index( pj, dBOs ), End_Index( pj, dBOs ) ); */
+ /* fprintf( out_control->fdbo, "%6d %6d\tstart: %6d\tend: %6d\n",
+ system->my_atoms[i].orig_id,
+ system->my_atoms[bonds->select.bond_list[pj].nbr].orig_id,
+ Start_Index( pj, dBOs ), End_Index( pj, dBOs ) ); */
for( pk = Start_Index(pj, dBOs); pk < End_Index(pj, dBOs); ++pk ) {
- dbo_k = &(dBOs->select.dbo_list[pk]);
- fprintf( out_control->fdbo, "%6d%6d%6d%24.15e%24.15e%24.15e\n",
- system->my_atoms[i].orig_id,
- system->my_atoms[bonds->select.bond_list[pj].nbr].orig_id,
- system->my_atoms[dbo_k->wrt].orig_id,
- dbo_k->dBO[0], dbo_k->dBO[1], dbo_k->dBO[2] );
-
- fprintf( out_control->fdbo, "%6d%6d%6d%24.15e%24.15e%24.15e\n",
- system->my_atoms[i].orig_id,
- system->my_atoms[bonds->select.bond_list[pj].nbr].orig_id,
- system->my_atoms[dbo_k->wrt].orig_id,
- dbo_k->dBOpi[0], dbo_k->dBOpi[1], dbo_k->dBOpi[2] );
-
- fprintf( out_control->fdbo, "%6d%6d%6d%24.15e%24.15e%24.15e\n",
- system->my_atoms[i].orig_id,
- system->my_atoms[bonds->select.bond_list[pj].nbr].orig_id,
- system->my_atoms[dbo_k->wrt].orig_id,
- dbo_k->dBOpi2[0], dbo_k->dBOpi2[1], dbo_k->dBOpi2[2] );
+ dbo_k = &(dBOs->select.dbo_list[pk]);
+ fprintf( out_control->fdbo, "%6d%6d%6d%24.15e%24.15e%24.15e\n",
+ system->my_atoms[i].orig_id,
+ system->my_atoms[bonds->select.bond_list[pj].nbr].orig_id,
+ system->my_atoms[dbo_k->wrt].orig_id,
+ dbo_k->dBO[0], dbo_k->dBO[1], dbo_k->dBO[2] );
+
+ fprintf( out_control->fdbo, "%6d%6d%6d%24.15e%24.15e%24.15e\n",
+ system->my_atoms[i].orig_id,
+ system->my_atoms[bonds->select.bond_list[pj].nbr].orig_id,
+ system->my_atoms[dbo_k->wrt].orig_id,
+ dbo_k->dBOpi[0], dbo_k->dBOpi[1], dbo_k->dBOpi[2] );
+
+ fprintf( out_control->fdbo, "%6d%6d%6d%24.15e%24.15e%24.15e\n",
+ system->my_atoms[i].orig_id,
+ system->my_atoms[bonds->select.bond_list[pj].nbr].orig_id,
+ system->my_atoms[dbo_k->wrt].orig_id,
+ dbo_k->dBOpi2[0], dbo_k->dBOpi2[1], dbo_k->dBOpi2[2] );
}
}
}
@@ -1327,20 +1327,20 @@ void Print_Forces( FILE *f, storage *workspace, int N, int step )
fprintf( f, "step: %d\n", step );
for( i = 0; i < N; ++i )
- //fprintf( f, "%6d %23.15e %23.15e %23.15e\n",
- //fprintf( f, "%6d%12.6f%12.6f%12.6f\n",
- fprintf( f, "%6d %19.9e %19.9e %19.9e\n",
- workspace->id_all[i], workspace->f_all[i][0],
- workspace->f_all[i][1], workspace->f_all[i][2] );
+ //fprintf( f, "%6d %23.15e %23.15e %23.15e\n",
+ //fprintf( f, "%6d%12.6f%12.6f%12.6f\n",
+ fprintf( f, "%6d %19.9e %19.9e %19.9e\n",
+ workspace->id_all[i], workspace->f_all[i][0],
+ workspace->f_all[i][1], workspace->f_all[i][2] );
}
-void Print_Force_Files( reax_system *system, control_params *control,
- simulation_data *data, storage *workspace,
- reax_list **lists, output_controls *out_control,
- mpi_datatypes *mpi_data )
+void Print_Force_Files( reax_system *system, control_params *control,
+ simulation_data *data, storage *workspace,
+ reax_list **lists, output_controls *out_control,
+ mpi_datatypes *mpi_data )
{
- int i, d;
+ int i, d;
Coll_ids_at_Master( system, workspace, mpi_data );
@@ -1400,12 +1400,12 @@ void Print_Force_Files( reax_system *system, control_params *control,
for( i = 0; i < system->n; ++i ) {
for( d = 0; d < 3; ++d )
- workspace->f_tot[i][d] = workspace->f_be[i][d] +
- workspace->f_lp[i][d]+workspace->f_ov[i][d]+workspace->f_un[i][d] +
- workspace->f_ang[i][d]+workspace->f_pen[i][d]+workspace->f_coa[i][d] +
- workspace->f_tor[i][d]+workspace->f_con[i][d] +
- workspace->f_vdw[i][d]+workspace->f_ele[i][d] +
- workspace->f_hb[i][d];
+ workspace->f_tot[i][d] = workspace->f_be[i][d] +
+ workspace->f_lp[i][d]+workspace->f_ov[i][d]+workspace->f_un[i][d] +
+ workspace->f_ang[i][d]+workspace->f_pen[i][d]+workspace->f_coa[i][d] +
+ workspace->f_tor[i][d]+workspace->f_con[i][d] +
+ workspace->f_vdw[i][d]+workspace->f_ele[i][d] +
+ workspace->f_hb[i][d];
}
Coll_rvecs_at_Master( system, workspace, mpi_data, workspace->f_tot );
@@ -1415,13 +1415,13 @@ void Print_Force_Files( reax_system *system, control_params *control,
#endif
-#if defined(TEST_FORCES) || defined(TEST_ENERGY)
+#if defined(TEST_FORCES) || defined(TEST_ENERGY)
-void Print_Far_Neighbors_List( reax_system *system, reax_list **lists,
- control_params *control, simulation_data *data,
- output_controls *out_control )
+void Print_Far_Neighbors_List( reax_system *system, reax_list **lists,
+ control_params *control, simulation_data *data,
+ output_controls *out_control )
{
- int i, j, id_i, id_j, nbr, natoms;
+ int i, j, id_i, id_j, nbr, natoms;
int num=0;
int temp[500];
reax_list *far_nbrs;
@@ -1436,13 +1436,13 @@ void Print_Far_Neighbors_List( reax_system *system, reax_list **lists,
id_i = system->my_atoms[i].orig_id;
fprintf( out_control->flist, "%6d:",id_i);
num=0;
-
+
for( j = Start_Index(i,far_nbrs); j < End_Index(i,far_nbrs); ++j ) {
nbr = far_nbrs->select.far_nbr_list[j].nbr;
id_j = system->my_atoms[nbr].orig_id;
temp[num++] = id_j;
}
-
+
qsort(&temp, num, sizeof(int), fn_qsort_intcmp);
for(j=0; j < num; j++)
fprintf(out_control->flist, "%6d",temp[j]);
@@ -1450,9 +1450,9 @@ void Print_Far_Neighbors_List( reax_system *system, reax_list **lists,
}
}
-void Print_Bond_List( reax_system *system, control_params *control,
- simulation_data *data, reax_list **lists,
- output_controls *out_control)
+void Print_Bond_List( reax_system *system, control_params *control,
+ simulation_data *data, reax_list **lists,
+ output_controls *out_control)
{
int i,j, id_i, id_j, nbr, pj;
reax_list *bonds = (*lists) + BONDS;
@@ -1469,12 +1469,12 @@ void Print_Bond_List( reax_system *system, control_params *control,
id_i = system->my_atoms[i].orig_id;
fprintf( out_control->blist, "%6d:", id_i);
for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj ) {
- nbr = bonds->select.bond_list[pj].nbr;
+ nbr = bonds->select.bond_list[pj].nbr;
id_j = system->my_atoms[nbr].orig_id;
- if( id_i < id_j )
- temp[num++] = id_j;
+ if( id_i < id_j )
+ temp[num++] = id_j;
}
-
+
qsort(&temp, num, sizeof(int), fn_qsort_intcmp);
for(j=0; j < num; j++)
fprintf(out_control->blist, "%6d",temp[j]);
@@ -1492,226 +1492,226 @@ void Print_Init_Atoms( reax_system *system, storage *workspace )
int i;
fprintf( stderr, "p%d had %d atoms\n",
- system->my_rank, workspace->init_cnt );
+ system->my_rank, workspace->init_cnt );
for( i = 0; i < workspace->init_cnt; ++i )
fprintf( stderr, "p%d, atom%d: %d %s %8.3f %8.3f %8.3f\n",
- system->my_rank, i,
- workspace->init_atoms[i].type, workspace->init_atoms[i].name,
- workspace->init_atoms[i].x[0],
- workspace->init_atoms[i].x[1],
- workspace->init_atoms[i].x[2] );
+ system->my_rank, i,
+ workspace->init_atoms[i].type, workspace->init_atoms[i].name,
+ workspace->init_atoms[i].x[0],
+ workspace->init_atoms[i].x[1],
+ workspace->init_atoms[i].x[2] );
}
#endif //OLD_VERSION
-/*void Print_Bond_Forces( reax_system *system, control_params *control,
- simulation_data *data, storage *workspace,
- reax_list **lists, output_controls *out_control )
+/*void Print_Bond_Forces( reax_system *system, control_params *control,
+ simulation_data *data, storage *workspace,
+ reax_list **lists, output_controls *out_control )
{
int i;
fprintf( out_control->fbond, "step: %d\n", data->step );
- fprintf( out_control->fbond, "%6s%24s%24s%24s\n",
- "atom", "f_be[0]", "f_be[1]", "f_be[2]" );
-
+ fprintf( out_control->fbond, "%6s%24s%24s%24s\n",
+ "atom", "f_be[0]", "f_be[1]", "f_be[2]" );
+
for( i = 0; i < system->bigN; ++i )
fprintf(out_control->fbond, "%6d%24.15e%24.15e%24.15e\n",
- system->my_atoms[i].orig_id,
- workspace->f_all[i][0], workspace->f_all[i][1],
- workspace->f_all[i][2]);
+ system->my_atoms[i].orig_id,
+ workspace->f_all[i][0], workspace->f_all[i][1],
+ workspace->f_all[i][2]);
}
-void Print_LonePair_Forces( reax_system *system, control_params *control,
- simulation_data *data, storage *workspace,
- reax_list **lists, output_controls *out_control )
+void Print_LonePair_Forces( reax_system *system, control_params *control,
+ simulation_data *data, storage *workspace,
+ reax_list **lists, output_controls *out_control )
{
int i;
fprintf( out_control->flp, "step: %d\n", data->step );
fprintf( out_control->flp, "%6s%24s\n", "atom", "f_lonepair" );
-
+
for( i = 0; i < system->bigN; ++i )
fprintf(out_control->flp, "%6d%24.15e%24.15e%24.15e\n",
- system->my_atoms[i].orig_id,
- workspace->f_all[i][0], workspace->f_all[i][1],
- workspace->f_all[i][2]);
+ system->my_atoms[i].orig_id,
+ workspace->f_all[i][0], workspace->f_all[i][1],
+ workspace->f_all[i][2]);
}
void Print_OverCoor_Forces( reax_system *system, control_params *control,
- simulation_data *data, storage *workspace,
- reax_list **lists, output_controls *out_control )
+ simulation_data *data, storage *workspace,
+ reax_list **lists, output_controls *out_control )
{
int i;
fprintf( out_control->fov, "step: %d\n", data->step );
- fprintf( out_control->fov, "%6s%-38s%-38s%-38s\n",
- "atom","f_over[0]", "f_over[1]", "f_over[2]" );
-
+ fprintf( out_control->fov, "%6s%-38s%-38s%-38s\n",
+ "atom","f_over[0]", "f_over[1]", "f_over[2]" );
+
for( i = 0; i < system->bigN; ++i )
- fprintf( out_control->fov,
- "%6d %24.15e%24.15e%24.15e 0 0 0\n",
- system->my_atoms[i].orig_id,
- workspace->f_all[i][0], workspace->f_all[i][1],
- workspace->f_all[i][2] );
+ fprintf( out_control->fov,
+ "%6d %24.15e%24.15e%24.15e 0 0 0\n",
+ system->my_atoms[i].orig_id,
+ workspace->f_all[i][0], workspace->f_all[i][1],
+ workspace->f_all[i][2] );
}
void Print_UnderCoor_Forces( reax_system *system, control_params *control,
- simulation_data *data, storage *workspace,
- reax_list **lists, output_controls *out_control )
+ simulation_data *data, storage *workspace,
+ reax_list **lists, output_controls *out_control )
{
int i;
fprintf( out_control->fun, "step: %d\n", data->step );
- fprintf( out_control->fun, "%6s%-38s%-38s%-38s\n",
- "atom","f_under[0]", "f_under[1]", "f_under[2]" );
-
+ fprintf( out_control->fun, "%6s%-38s%-38s%-38s\n",
+ "atom","f_under[0]", "f_under[1]", "f_under[2]" );
+
for( i = 0; i < system->bigN; ++i )
- fprintf( out_control->fun,
- "%6d %24.15e%24.15e%24.15e 0 0 0\n",
- system->my_atoms[i].orig_id,
- workspace->f_all[i][0], workspace->f_all[i][1],
- workspace->f_all[i][2] );
+ fprintf( out_control->fun,
+ "%6d %24.15e%24.15e%24.15e 0 0 0\n",
+ system->my_atoms[i].orig_id,
+ workspace->f_all[i][0], workspace->f_all[i][1],
+ workspace->f_all[i][2] );
}
-void Print_ValAngle_Forces( reax_system *system, control_params *control,
- simulation_data *data, storage *workspace,
- reax_list **lists, output_controls *out_control )
+void Print_ValAngle_Forces( reax_system *system, control_params *control,
+ simulation_data *data, storage *workspace,
+ reax_list **lists, output_controls *out_control )
{
int j;
fprintf( out_control->f3body, "step: %d\n", data->step );
- fprintf( out_control->f3body, "%6s%-37s%-37s%-37s%-38s\n",
- "atom", "3-body total", "f_ang", "f_pen", "f_coa" );
-
+ fprintf( out_control->f3body, "%6s%-37s%-37s%-37s%-38s\n",
+ "atom", "3-body total", "f_ang", "f_pen", "f_coa" );
+
for( j = 0; j < system->N; ++j ){
if( rvec_isZero(workspace->f_pen[j]) && rvec_isZero(workspace->f_coa[j]) )
- fprintf( out_control->f3body,
- "%6d %24.15e%24.15e%24.15e 0 0 0 0 0 0\n",
- system->my_atoms[j].orig_id,
- workspace->f_ang[j][0], workspace->f_ang[j][1],
- workspace->f_ang[j][2] );
+ fprintf( out_control->f3body,
+ "%6d %24.15e%24.15e%24.15e 0 0 0 0 0 0\n",
+ system->my_atoms[j].orig_id,
+ workspace->f_ang[j][0], workspace->f_ang[j][1],
+ workspace->f_ang[j][2] );
else if( rvec_isZero(workspace->f_coa[j]) )
- fprintf( out_control->f3body,
- "%6d %24.15e%24.15e%24.15e %24.15e%24.15e%24.15e " \
- "%24.15e%24.15e%24.15e\n",
- system->my_atoms[j].orig_id,
- workspace->f_ang[j][0] + workspace->f_pen[j][0],
- workspace->f_ang[j][1] + workspace->f_pen[j][1],
- workspace->f_ang[j][2] + workspace->f_pen[j][2],
- workspace->f_ang[j][0], workspace->f_ang[j][1],
- workspace->f_ang[j][2],
- workspace->f_pen[j][0], workspace->f_pen[j][1],
- workspace->f_pen[j][2] );
+ fprintf( out_control->f3body,
+ "%6d %24.15e%24.15e%24.15e %24.15e%24.15e%24.15e " \
+ "%24.15e%24.15e%24.15e\n",
+ system->my_atoms[j].orig_id,
+ workspace->f_ang[j][0] + workspace->f_pen[j][0],
+ workspace->f_ang[j][1] + workspace->f_pen[j][1],
+ workspace->f_ang[j][2] + workspace->f_pen[j][2],
+ workspace->f_ang[j][0], workspace->f_ang[j][1],
+ workspace->f_ang[j][2],
+ workspace->f_pen[j][0], workspace->f_pen[j][1],
+ workspace->f_pen[j][2] );
else{
fprintf( out_control->f3body, "%6d %24.15e%24.15e%24.15e ",
- system->my_atoms[j].orig_id,
- workspace->f_ang[j][0] + workspace->f_pen[j][0] +
- workspace->f_coa[j][0],
- workspace->f_ang[j][1] + workspace->f_pen[j][1] +
- workspace->f_coa[j][1],
- workspace->f_ang[j][2] + workspace->f_pen[j][2] +
- workspace->f_coa[j][2] );
-
- fprintf( out_control->f3body,
- "%24.15e%24.15e%24.15e %24.15e%24.15e%24.15e "\
- "%24.15e%24.15e%24.15e\n",
- workspace->f_ang[j][0], workspace->f_ang[j][1],
- workspace->f_ang[j][2],
- workspace->f_pen[j][0], workspace->f_pen[j][1],
- workspace->f_pen[j][2],
- workspace->f_coa[j][0], workspace->f_coa[j][1],
- workspace->f_coa[j][2] );
- }
+ system->my_atoms[j].orig_id,
+ workspace->f_ang[j][0] + workspace->f_pen[j][0] +
+ workspace->f_coa[j][0],
+ workspace->f_ang[j][1] + workspace->f_pen[j][1] +
+ workspace->f_coa[j][1],
+ workspace->f_ang[j][2] + workspace->f_pen[j][2] +
+ workspace->f_coa[j][2] );
+
+ fprintf( out_control->f3body,
+ "%24.15e%24.15e%24.15e %24.15e%24.15e%24.15e "\
+ "%24.15e%24.15e%24.15e\n",
+ workspace->f_ang[j][0], workspace->f_ang[j][1],
+ workspace->f_ang[j][2],
+ workspace->f_pen[j][0], workspace->f_pen[j][1],
+ workspace->f_pen[j][2],
+ workspace->f_coa[j][0], workspace->f_coa[j][1],
+ workspace->f_coa[j][2] );
+ }
}
}
-void Print_Hydrogen_Bond_Forces( reax_system *system, control_params *control,
- simulation_data *data, storage *workspace,
- reax_list **lists, output_controls *out_control)
+void Print_Hydrogen_Bond_Forces( reax_system *system, control_params *control,
+ simulation_data *data, storage *workspace,
+ reax_list **lists, output_controls *out_control)
{
int j;
fprintf( out_control->fhb, "step: %d\n", data->step );
fprintf( out_control->fhb, "%6s\t%-38s\n", "atom", "f_hb[0,1,2]" );
-
+
for( j = 0; j < system->N; ++j )
fprintf(out_control->fhb, "%6d%24.15e%24.15e%24.15e\n",
- system->my_atoms[j].orig_id,
- workspace->f_hb[j][0],
- workspace->f_hb[j][1],
- workspace->f_hb[j][2] );
+ system->my_atoms[j].orig_id,
+ workspace->f_hb[j][0],
+ workspace->f_hb[j][1],
+ workspace->f_hb[j][2] );
}
-void Print_Four_Body_Forces( reax_system *system, control_params *control,
- simulation_data *data, storage *workspace,
- reax_list **lists, output_controls *out_control )
+void Print_Four_Body_Forces( reax_system *system, control_params *control,
+ simulation_data *data, storage *workspace,
+ reax_list **lists, output_controls *out_control )
{
int j;
fprintf( out_control->f4body, "step: %d\n", data->step );
- fprintf( out_control->f4body, "%6s\t%-38s%-38s%-38s\n",
- "atom", "4-body total", "f_tor", "f_con" );
+ fprintf( out_control->f4body, "%6s\t%-38s%-38s%-38s\n",
+ "atom", "4-body total", "f_tor", "f_con" );
for( j = 0; j < system->N; ++j ){
if( !rvec_isZero( workspace->f_con[j] ) )
- fprintf( out_control->f4body,
- "%6d %24.15e%24.15e%24.15e %24.15e%24.15e%24.15e "\
- "%24.15e%24.15e%24.15e\n",
- system->my_atoms[j].orig_id,
- workspace->f_tor[j][0] + workspace->f_con[j][0],
- workspace->f_tor[j][1] + workspace->f_con[j][1],
- workspace->f_tor[j][2] + workspace->f_con[j][2],
- workspace->f_tor[j][0], workspace->f_tor[j][1],
- workspace->f_tor[j][2],
- workspace->f_con[j][0], workspace->f_con[j][1],
- workspace->f_con[j][2] );
+ fprintf( out_control->f4body,
+ "%6d %24.15e%24.15e%24.15e %24.15e%24.15e%24.15e "\
+ "%24.15e%24.15e%24.15e\n",
+ system->my_atoms[j].orig_id,
+ workspace->f_tor[j][0] + workspace->f_con[j][0],
+ workspace->f_tor[j][1] + workspace->f_con[j][1],
+ workspace->f_tor[j][2] + workspace->f_con[j][2],
+ workspace->f_tor[j][0], workspace->f_tor[j][1],
+ workspace->f_tor[j][2],
+ workspace->f_con[j][0], workspace->f_con[j][1],
+ workspace->f_con[j][2] );
else
- fprintf( out_control->f4body,
- "%6d %24.15e%24.15e%24.15e 0 0 0\n",
- system->my_atoms[j].orig_id, workspace->f_tor[j][0],
- workspace->f_tor[j][1], workspace->f_tor[j][2] );
+ fprintf( out_control->f4body,
+ "%6d %24.15e%24.15e%24.15e 0 0 0\n",
+ system->my_atoms[j].orig_id, workspace->f_tor[j][0],
+ workspace->f_tor[j][1], workspace->f_tor[j][2] );
}
}
-void Print_vdW_Coulomb_Forces( reax_system *system, control_params *control,
- simulation_data *data, storage *workspace,
- reax_list **lists, output_controls *out_control )
+void Print_vdW_Coulomb_Forces( reax_system *system, control_params *control,
+ simulation_data *data, storage *workspace,
+ reax_list **lists, output_controls *out_control )
{
int i;
return;
fprintf( out_control->fnonb, "step: %d\n", data->step );
- fprintf( out_control->fnonb, "%6s\t%-38s%-38s%-38s\n",
- "atom", "nonbonded_total[0,1,2]", "f_vdw[0,1,2]", "f_ele[0,1,2]" );
+ fprintf( out_control->fnonb, "%6s\t%-38s%-38s%-38s\n",
+ "atom", "nonbonded_total[0,1,2]", "f_vdw[0,1,2]", "f_ele[0,1,2]" );
for( i = 0; i < system->N; ++i )
- fprintf( out_control->fnonb,
- "%6d%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e\n",
- system->my_atoms[i].orig_id,
- workspace->f_vdw[i][0] + workspace->f_ele[i][0],
- workspace->f_vdw[i][1] + workspace->f_ele[i][1],
- workspace->f_vdw[i][2] + workspace->f_ele[i][2],
- workspace->f_vdw[i][0],
- workspace->f_vdw[i][1],
- workspace->f_vdw[i][2],
- workspace->f_ele[i][0],
- workspace->f_ele[i][1],
- workspace->f_ele[i][2] );
+ fprintf( out_control->fnonb,
+ "%6d%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e\n",
+ system->my_atoms[i].orig_id,
+ workspace->f_vdw[i][0] + workspace->f_ele[i][0],
+ workspace->f_vdw[i][1] + workspace->f_ele[i][1],
+ workspace->f_vdw[i][2] + workspace->f_ele[i][2],
+ workspace->f_vdw[i][0],
+ workspace->f_vdw[i][1],
+ workspace->f_vdw[i][2],
+ workspace->f_ele[i][0],
+ workspace->f_ele[i][1],
+ workspace->f_ele[i][2] );
}
-void Print_Total_Force( reax_system *system, control_params *control,
- simulation_data *data, storage *workspace,
- reax_list **lists, output_controls *out_control )
+void Print_Total_Force( reax_system *system, control_params *control,
+ simulation_data *data, storage *workspace,
+ reax_list **lists, output_controls *out_control )
{
int i;
@@ -1721,50 +1721,50 @@ void Print_Total_Force( reax_system *system, control_params *control,
fprintf( out_control->ftot, "%6s\t%-38s\n", "atom", "atom.f[0,1,2]");
for( i = 0; i < system->n; ++i )
- fprintf( out_control->ftot, "%6d%24.15e%24.15e%24.15e\n",
- system->my_atoms[i].orig_id,
- system->my_atoms[i].f[0],
- system->my_atoms[i].f[1],
- system->my_atoms[i].f[2] );
+ fprintf( out_control->ftot, "%6d%24.15e%24.15e%24.15e\n",
+ system->my_atoms[i].orig_id,
+ system->my_atoms[i].f[0],
+ system->my_atoms[i].f[1],
+ system->my_atoms[i].f[2] );
}
-void Compare_Total_Forces( reax_system *system, control_params *control,
- simulation_data *data, storage *workspace,
- reax_list **lists, output_controls *out_control )
+void Compare_Total_Forces( reax_system *system, control_params *control,
+ simulation_data *data, storage *workspace,
+ reax_list **lists, output_controls *out_control )
{
int i;
return;
fprintf( out_control->ftot2, "step: %d\n", data->step );
- fprintf( out_control->ftot2, "%6s\t%-38s%-38s\n",
- "atom", "f_total[0,1,2]", "test_force_total[0,1,2]" );
+ fprintf( out_control->ftot2, "%6s\t%-38s%-38s\n",
+ "atom", "f_total[0,1,2]", "test_force_total[0,1,2]" );
for( i = 0; i < system->N; ++i )
- fprintf( out_control->ftot2, "%6d%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e\n",
- system->my_atoms[i].orig_id,
- system->my_atoms[i].f[0],
- system->my_atoms[i].f[1],
- system->my_atoms[i].f[2],
- workspace->f_be[i][0] + workspace->f_lp[i][0] +
- workspace->f_ov[i][0] + workspace->f_un[i][0] +
- workspace->f_ang[i][0]+ workspace->f_pen[i][0]+
- workspace->f_coa[i][0]+ + workspace->f_hb[i][0] +
- workspace->f_tor[i][0] + workspace->f_con[i][0] +
- workspace->f_vdw[i][0] + workspace->f_ele[i][0],
- workspace->f_be[i][1] + workspace->f_lp[i][1] +
- workspace->f_ov[i][1] + workspace->f_un[i][1] +
- workspace->f_ang[i][1]+ workspace->f_pen[i][1]+
- workspace->f_coa[i][1]+ + workspace->f_hb[i][1] +
- workspace->f_tor[i][1] + workspace->f_con[i][1] +
- workspace->f_vdw[i][1] + workspace->f_ele[i][1],
- workspace->f_be[i][2] + workspace->f_lp[i][2] +
- workspace->f_ov[i][2] + workspace->f_un[i][2] +
- workspace->f_ang[i][2]+ workspace->f_pen[i][2] +
- workspace->f_coa[i][2]+ + workspace->f_hb[i][2] +
- workspace->f_tor[i][2] + workspace->f_con[i][2] +
- workspace->f_vdw[i][2] + workspace->f_ele[i][2] );
+ fprintf( out_control->ftot2, "%6d%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e\n",
+ system->my_atoms[i].orig_id,
+ system->my_atoms[i].f[0],
+ system->my_atoms[i].f[1],
+ system->my_atoms[i].f[2],
+ workspace->f_be[i][0] + workspace->f_lp[i][0] +
+ workspace->f_ov[i][0] + workspace->f_un[i][0] +
+ workspace->f_ang[i][0]+ workspace->f_pen[i][0]+
+ workspace->f_coa[i][0]+ + workspace->f_hb[i][0] +
+ workspace->f_tor[i][0] + workspace->f_con[i][0] +
+ workspace->f_vdw[i][0] + workspace->f_ele[i][0],
+ workspace->f_be[i][1] + workspace->f_lp[i][1] +
+ workspace->f_ov[i][1] + workspace->f_un[i][1] +
+ workspace->f_ang[i][1]+ workspace->f_pen[i][1]+
+ workspace->f_coa[i][1]+ + workspace->f_hb[i][1] +
+ workspace->f_tor[i][1] + workspace->f_con[i][1] +
+ workspace->f_vdw[i][1] + workspace->f_ele[i][1],
+ workspace->f_be[i][2] + workspace->f_lp[i][2] +
+ workspace->f_ov[i][2] + workspace->f_un[i][2] +
+ workspace->f_ang[i][2]+ workspace->f_pen[i][2] +
+ workspace->f_coa[i][2]+ + workspace->f_hb[i][2] +
+ workspace->f_tor[i][2] + workspace->f_con[i][2] +
+ workspace->f_vdw[i][2] + workspace->f_ele[i][2] );
}*/
/*void Init_Force_Test_Functions( )
diff --git a/src/USER-REAXC/reaxc_io_tools.h b/src/USER-REAXC/reaxc_io_tools.h
index 5b775bd78be114638c3bbc9107a19549634a9bd2..72847731aab258f502aad47a551ffe2fb4d652d0 100644
--- a/src/USER-REAXC/reaxc_io_tools.h
+++ b/src/USER-REAXC/reaxc_io_tools.h
@@ -14,12 +14,12 @@
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -29,10 +29,10 @@
#include "reaxc_types.h"
-int Init_Output_Files( reax_system*, control_params*,
- output_controls*, mpi_datatypes*, char* );
-int Close_Output_Files( reax_system*, control_params*,
- output_controls*, mpi_datatypes* );
+int Init_Output_Files( reax_system*, control_params*,
+ output_controls*, mpi_datatypes*, char* );
+int Close_Output_Files( reax_system*, control_params*,
+ output_controls*, mpi_datatypes* );
void Print_Box( simulation_box*, char*, FILE* );
@@ -54,63 +54,63 @@ void Print_Charges( reax_system* );
void Print_Bonds( reax_system*, reax_list*, char* );
void Print_Bond_List2( reax_system*, reax_list*, char* );
void Print_Total_Force( reax_system*, simulation_data*, storage* );
-void Output_Results( reax_system*, control_params*, simulation_data*,
- reax_list**, output_controls*, mpi_datatypes* );
-void fixbond( reax_system*, control_params*, simulation_data*,
- reax_list**, output_controls*, mpi_datatypes* );
-void fixspecies( reax_system*, control_params*, simulation_data*,
- reax_list**, output_controls*, mpi_datatypes* );
-
-#if defined(DEBUG_FOCUS) || defined(TEST_FORCES) || defined(TEST_ENERGY)
+void Output_Results( reax_system*, control_params*, simulation_data*,
+ reax_list**, output_controls*, mpi_datatypes* );
+void fixbond( reax_system*, control_params*, simulation_data*,
+ reax_list**, output_controls*, mpi_datatypes* );
+void fixspecies( reax_system*, control_params*, simulation_data*,
+ reax_list**, output_controls*, mpi_datatypes* );
+
+#if defined(DEBUG_FOCUS) || defined(TEST_FORCES) || defined(TEST_ENERGY)
void Debug_Marker_Bonded( output_controls*, int );
void Debug_Marker_Nonbonded( output_controls*, int );
-void Print_Near_Neighbors_List( reax_system*, reax_list**, control_params*,
- simulation_data*, output_controls* );
-void Print_Far_Neighbors_List( reax_system*, reax_list**, control_params*,
- simulation_data*, output_controls* );
-void Print_Bond_List( reax_system*, control_params*, simulation_data*,
- reax_list**, output_controls* );
-/*void Dummy_Printer( reax_system*, control_params*, simulation_data*,
- storage*, reax_list**, output_controls* );
-void Print_Bond_Orders( reax_system*, control_params*, simulation_data*,
- storage*, reax_list**, output_controls* );
-void Print_Bond_Forces( reax_system*, control_params*, simulation_data*,
- storage*, reax_list**, output_controls* );
-void Print_LonePair_Forces( reax_system*, control_params*, simulation_data*,
- storage*, reax_list**, output_controls* );
-void Print_OverUnderCoor_Forces( reax_system*, control_params*,
- simulation_data*, storage*, reax_list**,
- output_controls* );
-void Print_Three_Body_Forces( reax_system*, control_params*, simulation_data*,
- storage*, reax_list**, output_controls* );
-void Print_Hydrogen_Bond_Forces( reax_system*, control_params*,
- simulation_data*, storage*, reax_list**,
- output_controls* );
-void Print_Four_Body_Forces( reax_system*, control_params*, simulation_data*,
- storage*, reax_list**, output_controls* );
-void Print_vdW_Coulomb_Forces( reax_system*, control_params*,
- simulation_data*, storage*, reax_list**,
- output_controls* );
-void Print_Total_Force( reax_system*, control_params*, simulation_data*,
- storage*, reax_list**, output_controls* );
-void Compare_Total_Forces( reax_system*, control_params*, simulation_data*,
+void Print_Near_Neighbors_List( reax_system*, reax_list**, control_params*,
+ simulation_data*, output_controls* );
+void Print_Far_Neighbors_List( reax_system*, reax_list**, control_params*,
+ simulation_data*, output_controls* );
+void Print_Bond_List( reax_system*, control_params*, simulation_data*,
+ reax_list**, output_controls* );
+/*void Dummy_Printer( reax_system*, control_params*, simulation_data*,
+ storage*, reax_list**, output_controls* );
+void Print_Bond_Orders( reax_system*, control_params*, simulation_data*,
+ storage*, reax_list**, output_controls* );
+void Print_Bond_Forces( reax_system*, control_params*, simulation_data*,
+ storage*, reax_list**, output_controls* );
+void Print_LonePair_Forces( reax_system*, control_params*, simulation_data*,
+ storage*, reax_list**, output_controls* );
+void Print_OverUnderCoor_Forces( reax_system*, control_params*,
+ simulation_data*, storage*, reax_list**,
+ output_controls* );
+void Print_Three_Body_Forces( reax_system*, control_params*, simulation_data*,
+ storage*, reax_list**, output_controls* );
+void Print_Hydrogen_Bond_Forces( reax_system*, control_params*,
+ simulation_data*, storage*, reax_list**,
+ output_controls* );
+void Print_Four_Body_Forces( reax_system*, control_params*, simulation_data*,
+ storage*, reax_list**, output_controls* );
+void Print_vdW_Coulomb_Forces( reax_system*, control_params*,
+ simulation_data*, storage*, reax_list**,
+ output_controls* );
+void Print_Total_Force( reax_system*, control_params*, simulation_data*,
+ storage*, reax_list**, output_controls* );
+void Compare_Total_Forces( reax_system*, control_params*, simulation_data*,
storage*, reax_list**, output_controls* );*/
//void Print_Total_Force( reax_system*, control_params* );
-void Print_Force_Files( reax_system*, control_params*, simulation_data*,
- storage*, reax_list**, output_controls*,
- mpi_datatypes * );
+void Print_Force_Files( reax_system*, control_params*, simulation_data*,
+ storage*, reax_list**, output_controls*,
+ mpi_datatypes * );
//void Init_Force_Test_Functions( );
-int fn_qsort_intcmp( const void *, const void * );
+int fn_qsort_intcmp( const void *, const void * );
-void Print_Far_Neighbors_List( reax_system*, reax_list**, control_params*,
- simulation_data*, output_controls* );
+void Print_Far_Neighbors_List( reax_system*, reax_list**, control_params*,
+ simulation_data*, output_controls* );
void Print_Near_Neighbors_List( reax_system*, reax_list**, control_params*,
- simulation_data*, output_controls* );
+ simulation_data*, output_controls* );
-void Print_Bond_List( reax_system*, control_params*, simulation_data*,
- reax_list**, output_controls*);
+void Print_Bond_List( reax_system*, control_params*, simulation_data*,
+ reax_list**, output_controls*);
#endif
#endif
diff --git a/src/USER-REAXC/reaxc_list.cpp b/src/USER-REAXC/reaxc_list.cpp
index 6eab487af04cffbb43402c2934817fd129ac65c8..9a6ee51b1f014fb355116bf866db119eab7b99bc 100644
--- a/src/USER-REAXC/reaxc_list.cpp
+++ b/src/USER-REAXC/reaxc_list.cpp
@@ -14,12 +14,12 @@
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -38,10 +38,10 @@
int Make_List(int n, int num_intrs, int type, reax_list *l, MPI_Comm comm)
{
l->allocated = 1;
-
+
l->n = n;
l->num_intrs = num_intrs;
-
+
l->index = (int*) smalloc( n * sizeof(int), "list:index", comm );
l->end_index = (int*) smalloc( n * sizeof(int), "list:end_index", comm );
@@ -54,38 +54,38 @@ int Make_List(int n, int num_intrs, int type, reax_list *l, MPI_Comm comm)
case TYP_VOID:
l->select.v = (void*) smalloc(l->num_intrs * sizeof(void*), "list:v", comm);
break;
-
+
case TYP_THREE_BODY:
- l->select.three_body_list = (three_body_interaction_data*)
- smalloc( l->num_intrs * sizeof(three_body_interaction_data),
- "list:three_bodies", comm );
+ l->select.three_body_list = (three_body_interaction_data*)
+ smalloc( l->num_intrs * sizeof(three_body_interaction_data),
+ "list:three_bodies", comm );
break;
-
+
case TYP_BOND:
- l->select.bond_list = (bond_data*)
+ l->select.bond_list = (bond_data*)
smalloc( l->num_intrs * sizeof(bond_data), "list:bonds", comm );
break;
-
+
case TYP_DBO:
- l->select.dbo_list = (dbond_data*)
+ l->select.dbo_list = (dbond_data*)
smalloc( l->num_intrs * sizeof(dbond_data), "list:dbonds", comm );
break;
-
+
case TYP_DDELTA:
- l->select.dDelta_list = (dDelta_data*)
+ l->select.dDelta_list = (dDelta_data*)
smalloc( l->num_intrs * sizeof(dDelta_data), "list:dDeltas", comm );
break;
-
+
case TYP_FAR_NEIGHBOR:
- l->select.far_nbr_list = (far_neighbor_data*)
+ l->select.far_nbr_list = (far_neighbor_data*)
smalloc(l->num_intrs * sizeof(far_neighbor_data), "list:far_nbrs", comm);
break;
-
+
case TYP_HBOND:
l->select.hbond_list = (hbond_data*)
smalloc( l->num_intrs * sizeof(hbond_data), "list:hbonds", comm );
- break;
-
+ break;
+
default:
fprintf( stderr, "ERROR: no %d list type defined!\n", l->type );
MPI_Abort( comm, INVALID_INPUT );
@@ -103,7 +103,7 @@ void Delete_List( reax_list *l, MPI_Comm comm )
sfree( l->index, "list:index" );
sfree( l->end_index, "list:end_index" );
-
+
switch(l->type) {
case TYP_VOID:
sfree( l->select.v, "list:v" );
diff --git a/src/USER-REAXC/reaxc_list.h b/src/USER-REAXC/reaxc_list.h
index 39ca1b973e02de4c43fec85df5cba132f94debd9..ab7fbce19cad33beb18706d2074bac19d395074e 100644
--- a/src/USER-REAXC/reaxc_list.h
+++ b/src/USER-REAXC/reaxc_list.h
@@ -14,12 +14,12 @@
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
diff --git a/src/USER-REAXC/reaxc_lookup.cpp b/src/USER-REAXC/reaxc_lookup.cpp
index 9f6396fdfb09f2f6000e01059445adcd327b37db..aa7b069afaac0049d843660f5b7d38ce48d15122 100644
--- a/src/USER-REAXC/reaxc_lookup.cpp
+++ b/src/USER-REAXC/reaxc_lookup.cpp
@@ -14,12 +14,12 @@
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -38,20 +38,20 @@
LR_lookup_table **LR;
/* Fills solution into x. Warning: will modify c and d! */
-void Tridiagonal_Solve( const real *a, const real *b,
- real *c, real *d, real *x, unsigned int n){
+void Tridiagonal_Solve( const real *a, const real *b,
+ real *c, real *d, real *x, unsigned int n){
int i;
real id;
-
+
/* Modify the coefficients. */
- c[0] /= b[0]; /* Division by zero risk. */
- d[0] /= b[0]; /* Division by zero would imply a singular matrix. */
+ c[0] /= b[0]; /* Division by zero risk. */
+ d[0] /= b[0]; /* Division by zero would imply a singular matrix. */
for(i = 1; i < n; i++){
id = (b[i] - c[i-1] * a[i]); /* Division by zero risk. */
- c[i] /= id; /* Last value calculated is redundant. */
+ c[i] /= id; /* Last value calculated is redundant. */
d[i] = (d[i] - d[i-1] * a[i])/id;
}
-
+
/* Now back substitute. */
x[n - 1] = d[n - 1];
for(i = n - 2; i >= 0; i--)
@@ -59,9 +59,9 @@ void Tridiagonal_Solve( const real *a, const real *b,
}
-void Natural_Cubic_Spline( const real *h, const real *f,
- cubic_spline_coef *coef, unsigned int n,
- MPI_Comm comm )
+void Natural_Cubic_Spline( const real *h, const real *f,
+ cubic_spline_coef *coef, unsigned int n,
+ MPI_Comm comm )
{
int i;
real *a, *b, *c, *d, *v;
@@ -80,7 +80,7 @@ void Natural_Cubic_Spline( const real *h, const real *f,
b[0] = b[n-1] = 0;
for( i = 1; i < n-1; ++i )
- b[i] = 2 * (h[i-1] + h[i]);
+ b[i] = 2 * (h[i-1] + h[i]);
c[0] = c[n-2] = c[n-1] = 0;
for( i = 1; i < n-2; ++i )
@@ -89,11 +89,11 @@ void Natural_Cubic_Spline( const real *h, const real *f,
d[0] = d[n-1] = 0;
for( i = 1; i < n-1; ++i )
d[i] = 6 * ((f[i+1]-f[i])/h[i] - (f[i]-f[i-1])/h[i-1]);
-
+
v[0] = 0;
v[n-1] = 0;
Tridiagonal_Solve( &(a[1]), &(b[1]), &(c[1]), &(d[1]), &(v[1]), n-2 );
-
+
for( i = 1; i < n; ++i ){
coef[i-1].d = (v[i] - v[i-1]) / (6*h[i-1]);
coef[i-1].c = v[i]/2;
@@ -111,8 +111,8 @@ void Natural_Cubic_Spline( const real *h, const real *f,
void Complete_Cubic_Spline( const real *h, const real *f, real v0, real vlast,
- cubic_spline_coef *coef, unsigned int n,
- MPI_Comm comm )
+ cubic_spline_coef *coef, unsigned int n,
+ MPI_Comm comm )
{
int i;
real *a, *b, *c, *d, *v;
@@ -131,13 +131,13 @@ void Complete_Cubic_Spline( const real *h, const real *f, real v0, real vlast,
b[0] = 2*h[0];
for( i = 1; i < n; ++i )
- b[i] = 2 * (h[i-1] + h[i]);
+ b[i] = 2 * (h[i-1] + h[i]);
c[n-1] = 0;
for( i = 0; i < n-1; ++i )
c[i] = h[i];
- d[0] = 6 * (f[1]-f[0])/h[0] - 6 * v0;
+ d[0] = 6 * (f[1]-f[0])/h[0] - 6 * v0;
d[n-1] = 6 * vlast - 6 * (f[n-1]-f[n-2]/h[n-2]);
for( i = 1; i < n-1; ++i )
d[i] = 6 * ((f[i+1]-f[i])/h[i] - (f[i]-f[i-1])/h[i-1]);
@@ -169,12 +169,12 @@ void LR_Lookup( LR_lookup_table *t, real r, LR_data *y )
base = (real)(i+1) * t->dx;
dif = r - base;
- y->e_vdW = ((t->vdW[i].d*dif + t->vdW[i].c)*dif + t->vdW[i].b)*dif +
+ y->e_vdW = ((t->vdW[i].d*dif + t->vdW[i].c)*dif + t->vdW[i].b)*dif +
t->vdW[i].a;
- y->CEvd = ((t->CEvd[i].d*dif + t->CEvd[i].c)*dif +
- t->CEvd[i].b)*dif + t->CEvd[i].a;
+ y->CEvd = ((t->CEvd[i].d*dif + t->CEvd[i].c)*dif +
+ t->CEvd[i].b)*dif + t->CEvd[i].a;
- y->e_ele = ((t->ele[i].d*dif + t->ele[i].c)*dif + t->ele[i].b)*dif +
+ y->e_ele = ((t->ele[i].d*dif + t->ele[i].c)*dif + t->ele[i].b)*dif +
t->ele[i].a;
y->CEclmb = ((t->CEclmb[i].d*dif + t->CEclmb[i].c)*dif + t->CEclmb[i].b)*dif +
t->CEclmb[i].a;
@@ -183,8 +183,8 @@ void LR_Lookup( LR_lookup_table *t, real r, LR_data *y )
}
-int Init_Lookup_Tables( reax_system *system, control_params *control,
- storage *workspace, mpi_datatypes *mpi_data, char *msg )
+int Init_Lookup_Tables( reax_system *system, control_params *control,
+ storage *workspace, mpi_datatypes *mpi_data, char *msg )
{
int i, j, r;
int num_atom_types;
@@ -203,25 +203,25 @@ int Init_Lookup_Tables( reax_system *system, control_params *control,
num_atom_types = system->reax_param.num_atom_types;
dr = control->nonb_cut / control->tabulate;
- h = (real*)
+ h = (real*)
smalloc( (control->tabulate+2) * sizeof(real), "lookup:h", comm );
- fh = (real*)
+ fh = (real*)
smalloc( (control->tabulate+2) * sizeof(real), "lookup:fh", comm );
- fvdw = (real*)
+ fvdw = (real*)
smalloc( (control->tabulate+2) * sizeof(real), "lookup:fvdw", comm );
- fCEvd = (real*)
+ fCEvd = (real*)
smalloc( (control->tabulate+2) * sizeof(real), "lookup:fCEvd", comm );
- fele = (real*)
+ fele = (real*)
smalloc( (control->tabulate+2) * sizeof(real), "lookup:fele", comm );
- fCEclmb = (real*)
+ fCEclmb = (real*)
smalloc( (control->tabulate+2) * sizeof(real), "lookup:fCEclmb", comm );
-
- /* allocate Long-Range LookUp Table space based on
+
+ /* allocate Long-Range LookUp Table space based on
number of atom types in the ffield file */
- LR = (LR_lookup_table**)
+ LR = (LR_lookup_table**)
scalloc( num_atom_types, sizeof(LR_lookup_table*), "lookup:LR", comm );
for( i = 0; i < num_atom_types; ++i )
- LR[i] = (LR_lookup_table*)
+ LR[i] = (LR_lookup_table*)
scalloc( num_atom_types, sizeof(LR_lookup_table), "lookup:LR[i]", comm );
/* most atom types in ffield file will not exist in the current
@@ -232,8 +232,8 @@ int Init_Lookup_Tables( reax_system *system, control_params *control,
for( i = 0; i < system->n; ++i )
existing_types[ system->my_atoms[i].type ] = 1;
- MPI_Allreduce( existing_types, aggregated, MAX_ATOM_TYPES,
- MPI_INT, MPI_SUM, mpi_data->world );
+ MPI_Allreduce( existing_types, aggregated, MAX_ATOM_TYPES,
+ MPI_INT, MPI_SUM, mpi_data->world );
/* fill in the lookup table entries for existing atom types.
only lower half should be enough. */
@@ -241,75 +241,75 @@ int Init_Lookup_Tables( reax_system *system, control_params *control,
if( aggregated[i] )
//for( j = 0; j < num_atom_types; ++j )
for( j = i; j < num_atom_types; ++j )
- if( aggregated[j] ) {
- LR[i][j].xmin = 0;
- LR[i][j].xmax = control->nonb_cut;
- LR[i][j].n = control->tabulate + 2;
- LR[i][j].dx = dr;
- LR[i][j].inv_dx = control->tabulate / control->nonb_cut;
- LR[i][j].y = (LR_data*)
- smalloc( LR[i][j].n * sizeof(LR_data), "lookup:LR[i,j].y", comm );
- LR[i][j].H = (cubic_spline_coef*)
- smalloc( LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].H" ,
- comm );
- LR[i][j].vdW = (cubic_spline_coef*)
- smalloc( LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].vdW",
- comm);
- LR[i][j].CEvd = (cubic_spline_coef*)
- smalloc( LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].CEvd",
- comm);
- LR[i][j].ele = (cubic_spline_coef*)
- smalloc( LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].ele",
- comm );
- LR[i][j].CEclmb = (cubic_spline_coef*)
- smalloc( LR[i][j].n*sizeof(cubic_spline_coef),
- "lookup:LR[i,j].CEclmb", comm );
-
- for( r = 1; r <= control->tabulate; ++r ) {
- LR_vdW_Coulomb( system, workspace, control, i, j, r * dr, &(LR[i][j].y[r]) );
- h[r] = LR[i][j].dx;
- fh[r] = LR[i][j].y[r].H;
- fvdw[r] = LR[i][j].y[r].e_vdW;
- fCEvd[r] = LR[i][j].y[r].CEvd;
- fele[r] = LR[i][j].y[r].e_ele;
- fCEclmb[r] = LR[i][j].y[r].CEclmb;
- }
-
- // init the start-end points
- h[r] = LR[i][j].dx;
- v0_vdw = LR[i][j].y[1].CEvd;
- v0_ele = LR[i][j].y[1].CEclmb;
- fh[r] = fh[r-1];
- fvdw[r] = fvdw[r-1];
- fCEvd[r] = fCEvd[r-1];
- fele[r] = fele[r-1];
- fCEclmb[r] = fCEclmb[r-1];
- vlast_vdw = fCEvd[r-1];
- vlast_ele = fele[r-1];
-
- Natural_Cubic_Spline( &h[1], &fh[1],
- &(LR[i][j].H[1]), control->tabulate+1, comm );
-
- Complete_Cubic_Spline( &h[1], &fvdw[1], v0_vdw, vlast_vdw,
- &(LR[i][j].vdW[1]), control->tabulate+1,
- comm );
-
- Natural_Cubic_Spline( &h[1], &fCEvd[1],
- &(LR[i][j].CEvd[1]), control->tabulate+1,
- comm );
-
- Complete_Cubic_Spline( &h[1], &fele[1], v0_ele, vlast_ele,
- &(LR[i][j].ele[1]), control->tabulate+1,
- comm );
-
- Natural_Cubic_Spline( &h[1], &fCEclmb[1],
- &(LR[i][j].CEclmb[1]), control->tabulate+1,
- comm );
- }
- else{
- LR[i][j].n = 0;
- }
-
+ if( aggregated[j] ) {
+ LR[i][j].xmin = 0;
+ LR[i][j].xmax = control->nonb_cut;
+ LR[i][j].n = control->tabulate + 2;
+ LR[i][j].dx = dr;
+ LR[i][j].inv_dx = control->tabulate / control->nonb_cut;
+ LR[i][j].y = (LR_data*)
+ smalloc( LR[i][j].n * sizeof(LR_data), "lookup:LR[i,j].y", comm );
+ LR[i][j].H = (cubic_spline_coef*)
+ smalloc( LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].H" ,
+ comm );
+ LR[i][j].vdW = (cubic_spline_coef*)
+ smalloc( LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].vdW",
+ comm);
+ LR[i][j].CEvd = (cubic_spline_coef*)
+ smalloc( LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].CEvd",
+ comm);
+ LR[i][j].ele = (cubic_spline_coef*)
+ smalloc( LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].ele",
+ comm );
+ LR[i][j].CEclmb = (cubic_spline_coef*)
+ smalloc( LR[i][j].n*sizeof(cubic_spline_coef),
+ "lookup:LR[i,j].CEclmb", comm );
+
+ for( r = 1; r <= control->tabulate; ++r ) {
+ LR_vdW_Coulomb( system, workspace, control, i, j, r * dr, &(LR[i][j].y[r]) );
+ h[r] = LR[i][j].dx;
+ fh[r] = LR[i][j].y[r].H;
+ fvdw[r] = LR[i][j].y[r].e_vdW;
+ fCEvd[r] = LR[i][j].y[r].CEvd;
+ fele[r] = LR[i][j].y[r].e_ele;
+ fCEclmb[r] = LR[i][j].y[r].CEclmb;
+ }
+
+ // init the start-end points
+ h[r] = LR[i][j].dx;
+ v0_vdw = LR[i][j].y[1].CEvd;
+ v0_ele = LR[i][j].y[1].CEclmb;
+ fh[r] = fh[r-1];
+ fvdw[r] = fvdw[r-1];
+ fCEvd[r] = fCEvd[r-1];
+ fele[r] = fele[r-1];
+ fCEclmb[r] = fCEclmb[r-1];
+ vlast_vdw = fCEvd[r-1];
+ vlast_ele = fele[r-1];
+
+ Natural_Cubic_Spline( &h[1], &fh[1],
+ &(LR[i][j].H[1]), control->tabulate+1, comm );
+
+ Complete_Cubic_Spline( &h[1], &fvdw[1], v0_vdw, vlast_vdw,
+ &(LR[i][j].vdW[1]), control->tabulate+1,
+ comm );
+
+ Natural_Cubic_Spline( &h[1], &fCEvd[1],
+ &(LR[i][j].CEvd[1]), control->tabulate+1,
+ comm );
+
+ Complete_Cubic_Spline( &h[1], &fele[1], v0_ele, vlast_ele,
+ &(LR[i][j].ele[1]), control->tabulate+1,
+ comm );
+
+ Natural_Cubic_Spline( &h[1], &fCEclmb[1],
+ &(LR[i][j].CEclmb[1]), control->tabulate+1,
+ comm );
+ }
+ else{
+ LR[i][j].n = 0;
+ }
+
free(h);
free(fh);
free(fvdw);
@@ -331,12 +331,12 @@ void Deallocate_Lookup_Tables( reax_system *system )
for( i = 0; i < ntypes; ++i ) {
for( j = i; j < ntypes; ++j )
if( LR[i][j].n ) {
- sfree( LR[i][j].y, "LR[i,j].y" );
- sfree( LR[i][j].H, "LR[i,j].H" );
- sfree( LR[i][j].vdW, "LR[i,j].vdW" );
- sfree( LR[i][j].CEvd, "LR[i,j].CEvd" );
- sfree( LR[i][j].ele, "LR[i,j].ele" );
- sfree( LR[i][j].CEclmb, "LR[i,j].CEclmb" );
+ sfree( LR[i][j].y, "LR[i,j].y" );
+ sfree( LR[i][j].H, "LR[i,j].H" );
+ sfree( LR[i][j].vdW, "LR[i,j].vdW" );
+ sfree( LR[i][j].CEvd, "LR[i,j].CEvd" );
+ sfree( LR[i][j].ele, "LR[i,j].ele" );
+ sfree( LR[i][j].CEclmb, "LR[i,j].CEclmb" );
}
sfree( LR[i], "LR[i]" );
}
diff --git a/src/USER-REAXC/reaxc_lookup.h b/src/USER-REAXC/reaxc_lookup.h
index 437f26bc77f48c1132a445203bd6d9b93ed04b7a..79c734c63cadd4403198a74e590f3cf0fcb52616 100644
--- a/src/USER-REAXC/reaxc_lookup.h
+++ b/src/USER-REAXC/reaxc_lookup.h
@@ -14,12 +14,12 @@
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -29,8 +29,8 @@
#include "reaxc_types.h"
-int Init_Lookup_Tables( reax_system*, control_params*, storage*,
- mpi_datatypes*, char* );
+int Init_Lookup_Tables( reax_system*, control_params*, storage*,
+ mpi_datatypes*, char* );
void Deallocate_Lookup_Tables( reax_system* );
diff --git a/src/USER-REAXC/reaxc_multi_body.cpp b/src/USER-REAXC/reaxc_multi_body.cpp
index 7cac68865b36d1453cca4a7d700741cb09a44923..4932a79b998e1b625ca27b341d40008fb996d607 100644
--- a/src/USER-REAXC/reaxc_multi_body.cpp
+++ b/src/USER-REAXC/reaxc_multi_body.cpp
@@ -14,12 +14,12 @@
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -38,9 +38,9 @@
#endif
-void Atom_Energy( reax_system *system, control_params *control,
- simulation_data *data, storage *workspace, reax_list **lists,
- output_controls *out_control )
+void Atom_Energy( reax_system *system, control_params *control,
+ simulation_data *data, storage *workspace, reax_list **lists,
+ output_controls *out_control )
{
int i, j, pj, type_i, type_j;
real Delta_lpcorr, dfvl;
@@ -58,7 +58,7 @@ void Atom_Energy( reax_system *system, control_params *control,
single_body_parameters *sbp_i, *sbp_j;
two_body_parameters *twbp;
bond_data *pbond;
- bond_order_data *bo_ij;
+ bond_order_data *bo_ij;
reax_list *bonds = (*lists) + BONDS;
/* Initialize parameters */
@@ -76,19 +76,19 @@ void Atom_Energy( reax_system *system, control_params *control,
sbp_i = &(system->reax_param.sbp[ type_i ]);
/* lone-pair Energy */
- p_lp2 = sbp_i->p_lp2;
+ p_lp2 = sbp_i->p_lp2;
expvd2 = exp( -75 * workspace->Delta_lp[i] );
inv_expvd2 = 1. / (1. + expvd2 );
-
+
/* calculate the energy */
- data->my_en.e_lp += e_lp =
+ data->my_en.e_lp += e_lp =
p_lp2 * workspace->Delta_lp[i] * inv_expvd2;
-
- dElp = p_lp2 * inv_expvd2 +
+
+ dElp = p_lp2 * inv_expvd2 +
75 * p_lp2 * workspace->Delta_lp[i] * expvd2 * SQR(inv_expvd2);
CElp = dElp * workspace->dDelta_lp[i];
- workspace->CdDelta[i] += CElp; // lp - 1st term
+ workspace->CdDelta[i] += CElp; // lp - 1st term
/* tally into per-atom energy */
if( system->pair_ptr->evflag)
@@ -96,11 +96,11 @@ void Atom_Energy( reax_system *system, control_params *control,
#ifdef TEST_ENERGY
// fprintf( out_control->elp, "%24.15e%24.15e%24.15e%24.15e\n",
-// p_lp2, workspace->Delta_lp_temp[i], expvd2, dElp );
+// p_lp2, workspace->Delta_lp_temp[i], expvd2, dElp );
// fprintf( out_control->elp, "%6d%24.15e%24.15e%24.15e\n",
fprintf( out_control->elp, "%6d%12.4f%12.4f%12.4f\n",
- system->my_atoms[i].orig_id, workspace->nlp[i],
- e_lp, data->my_en.e_lp );
+ system->my_atoms[i].orig_id, workspace->nlp[i],
+ e_lp, data->my_en.e_lp );
#endif
#ifdef TEST_FORCES
Add_dDelta( system, lists, i, CElp, workspace->f_lp ); // lp - 1st term
@@ -109,39 +109,39 @@ void Atom_Energy( reax_system *system, control_params *control,
/* correction for C2 */
if( p_lp3 > 0.001 && !strcmp(system->reax_param.sbp[type_i].name, "C") )
for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj ) {
- j = bonds->select.bond_list[pj].nbr;
- type_j = system->my_atoms[j].type;
-
- if( !strcmp( system->reax_param.sbp[type_j].name, "C" ) ) {
- twbp = &( system->reax_param.tbp[type_i][type_j]);
- bo_ij = &( bonds->select.bond_list[pj].bo_data );
- Di = workspace->Delta[i];
- vov3 = bo_ij->BO - Di - 0.040*pow(Di, 4.);
-
- if( vov3 > 3. ) {
- data->my_en.e_lp += e_lph = p_lp3 * SQR(vov3-3.0);
-
- deahu2dbo = 2.*p_lp3*(vov3 - 3.);
- deahu2dsbo = 2.*p_lp3*(vov3 - 3.)*(-1. - 0.16*pow(Di, 3.));
-
- bo_ij->Cdbo += deahu2dbo;
- workspace->CdDelta[i] += deahu2dsbo;
-
- /* tally into per-atom energy */
- if( system->pair_ptr->evflag)
+ j = bonds->select.bond_list[pj].nbr;
+ type_j = system->my_atoms[j].type;
+
+ if( !strcmp( system->reax_param.sbp[type_j].name, "C" ) ) {
+ twbp = &( system->reax_param.tbp[type_i][type_j]);
+ bo_ij = &( bonds->select.bond_list[pj].bo_data );
+ Di = workspace->Delta[i];
+ vov3 = bo_ij->BO - Di - 0.040*pow(Di, 4.);
+
+ if( vov3 > 3. ) {
+ data->my_en.e_lp += e_lph = p_lp3 * SQR(vov3-3.0);
+
+ deahu2dbo = 2.*p_lp3*(vov3 - 3.);
+ deahu2dsbo = 2.*p_lp3*(vov3 - 3.)*(-1. - 0.16*pow(Di, 3.));
+
+ bo_ij->Cdbo += deahu2dbo;
+ workspace->CdDelta[i] += deahu2dsbo;
+
+ /* tally into per-atom energy */
+ if( system->pair_ptr->evflag)
system->pair_ptr->ev_tally(i,j,system->n,1,e_lph,0.0,0.0,0.0,0.0,0.0);
-
+
#ifdef TEST_ENERGY
- fprintf(out_control->elp,"C2cor%6d%6d%12.6f%12.6f%12.6f\n",
- system->my_atoms[i].orig_id, system->my_atoms[j].orig_id,
- e_lph, deahu2dbo, deahu2dsbo );
+ fprintf(out_control->elp,"C2cor%6d%6d%12.6f%12.6f%12.6f\n",
+ system->my_atoms[i].orig_id, system->my_atoms[j].orig_id,
+ e_lph, deahu2dbo, deahu2dsbo );
#endif
#ifdef TEST_FORCES
- Add_dBO(system, lists, i, pj, deahu2dbo, workspace->f_lp);
- Add_dDelta(system, lists, i, deahu2dsbo, workspace->f_lp);
+ Add_dBO(system, lists, i, pj, deahu2dbo, workspace->f_lp);
+ Add_dDelta(system, lists, i, deahu2dsbo, workspace->f_lp);
#endif
- }
- }
+ }
+ }
}
}
@@ -151,41 +151,41 @@ void Atom_Energy( reax_system *system, control_params *control,
sbp_i = &(system->reax_param.sbp[ type_i ]);
/* over-coordination energy */
- if( sbp_i->mass > 21.0 )
+ if( sbp_i->mass > 21.0 )
dfvl = 0.0;
else dfvl = 1.0; // only for 1st-row elements
-
+
p_ovun2 = sbp_i->p_ovun2;
sum_ovun1 = sum_ovun2 = 0;
for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj ) {
- j = bonds->select.bond_list[pj].nbr;
- type_j = system->my_atoms[j].type;
- bo_ij = &(bonds->select.bond_list[pj].bo_data);
- sbp_j = &(system->reax_param.sbp[ type_j ]);
- twbp = &(system->reax_param.tbp[ type_i ][ type_j ]);
-
- sum_ovun1 += twbp->p_ovun1 * twbp->De_s * bo_ij->BO;
- sum_ovun2 += (workspace->Delta[j] - dfvl*workspace->Delta_lp_temp[j])*
- ( bo_ij->BO_pi + bo_ij->BO_pi2 );
-
- /*fprintf( stdout, "%4d%4d%12.6f%12.6f%12.6f\n",
- i+1, j+1,
- dfvl * workspace->Delta_lp_temp[j],
- sbp_j->nlp_opt,
+ j = bonds->select.bond_list[pj].nbr;
+ type_j = system->my_atoms[j].type;
+ bo_ij = &(bonds->select.bond_list[pj].bo_data);
+ sbp_j = &(system->reax_param.sbp[ type_j ]);
+ twbp = &(system->reax_param.tbp[ type_i ][ type_j ]);
+
+ sum_ovun1 += twbp->p_ovun1 * twbp->De_s * bo_ij->BO;
+ sum_ovun2 += (workspace->Delta[j] - dfvl*workspace->Delta_lp_temp[j])*
+ ( bo_ij->BO_pi + bo_ij->BO_pi2 );
+
+ /*fprintf( stdout, "%4d%4d%12.6f%12.6f%12.6f\n",
+ i+1, j+1,
+ dfvl * workspace->Delta_lp_temp[j],
+ sbp_j->nlp_opt,
workspace->nlp_temp[j] );*/
}
exp_ovun1 = p_ovun3 * exp( p_ovun4 * sum_ovun2 );
inv_exp_ovun1 = 1.0 / (1 + exp_ovun1);
- Delta_lpcorr = workspace->Delta[i] -
+ Delta_lpcorr = workspace->Delta[i] -
(dfvl * workspace->Delta_lp_temp[i]) * inv_exp_ovun1;
-
+
exp_ovun2 = exp( p_ovun2 * Delta_lpcorr );
inv_exp_ovun2 = 1.0 / (1.0 + exp_ovun2);
-
+
DlpVi = 1.0 / (Delta_lpcorr + sbp_i->valency + 1e-8);
CEover1 = Delta_lpcorr * DlpVi * inv_exp_ovun2;
-
+
data->my_en.e_ov += e_ov = sum_ovun1 * CEover1;
CEover2 = sum_ovun1 * DlpVi * inv_exp_ovun2 *
@@ -193,14 +193,14 @@ void Atom_Energy( reax_system *system, control_params *control,
CEover3 = CEover2 * (1.0 - dfvl * workspace->dDelta_lp[i] * inv_exp_ovun1 );
- CEover4 = CEover2 * (dfvl * workspace->Delta_lp_temp[i]) *
+ CEover4 = CEover2 * (dfvl * workspace->Delta_lp_temp[i]) *
p_ovun4 * exp_ovun1 * SQR(inv_exp_ovun1);
-
+
/* under-coordination potential */
p_ovun2 = sbp_i->p_ovun2;
p_ovun5 = sbp_i->p_ovun5;
-
+
exp_ovun2n = 1.0 / exp_ovun2;
exp_ovun6 = exp( p_ovun6 * Delta_lpcorr );
exp_ovun8 = p_ovun7 * exp(p_ovun8 * sum_ovun2);
@@ -209,15 +209,15 @@ void Atom_Energy( reax_system *system, control_params *control,
data->my_en.e_un += e_un =
-p_ovun5 * (1.0 - exp_ovun6) * inv_exp_ovun2n * inv_exp_ovun8;
-
- CEunder1 = inv_exp_ovun2n *
+
+ CEunder1 = inv_exp_ovun2n *
( p_ovun5 * p_ovun6 * exp_ovun6 * inv_exp_ovun8 +
- p_ovun2 * e_un * exp_ovun2n );
+ p_ovun2 * e_un * exp_ovun2n );
CEunder2 = -e_un * p_ovun8 * exp_ovun8 * inv_exp_ovun8;
CEunder3 = CEunder1 * (1.0 - dfvl*workspace->dDelta_lp[i]*inv_exp_ovun1);
- CEunder4 = CEunder1 * (dfvl*workspace->Delta_lp_temp[i]) *
+ CEunder4 = CEunder1 * (dfvl*workspace->Delta_lp_temp[i]) *
p_ovun4 * exp_ovun1 * SQR(inv_exp_ovun1) + CEunder2;
-
+
/* tally into per-atom energy */
if( system->pair_ptr->evflag) {
eng_tmp = e_ov + e_un;
@@ -233,97 +233,97 @@ void Atom_Energy( reax_system *system, control_params *control,
Add_dDelta( system, lists, i, CEover3, workspace->f_ov ); // OvCoor 2nd
Add_dDelta( system, lists, i, CEunder3, workspace->f_un ); // UnCoor 1st
#endif
-
+
for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj ) {
pbond = &(bonds->select.bond_list[pj]);
j = pbond->nbr;
bo_ij = &(pbond->bo_data);
twbp = &(system->reax_param.tbp[ system->my_atoms[i].type ]
- [system->my_atoms[pbond->nbr].type]);
+ [system->my_atoms[pbond->nbr].type]);
- bo_ij->Cdbo += CEover1 * twbp->p_ovun1 * twbp->De_s;// OvCoor-1st
- workspace->CdDelta[j] += CEover4 * (1.0 - dfvl*workspace->dDelta_lp[j]) *
- (bo_ij->BO_pi + bo_ij->BO_pi2); // OvCoor-3a
- bo_ij->Cdbopi += CEover4 *
- (workspace->Delta[j] - dfvl*workspace->Delta_lp_temp[j]); // OvCoor-3b
- bo_ij->Cdbopi2 += CEover4 *
- (workspace->Delta[j] - dfvl*workspace->Delta_lp_temp[j]); // OvCoor-3b
+ bo_ij->Cdbo += CEover1 * twbp->p_ovun1 * twbp->De_s;// OvCoor-1st
+ workspace->CdDelta[j] += CEover4 * (1.0 - dfvl*workspace->dDelta_lp[j]) *
+ (bo_ij->BO_pi + bo_ij->BO_pi2); // OvCoor-3a
+ bo_ij->Cdbopi += CEover4 *
+ (workspace->Delta[j] - dfvl*workspace->Delta_lp_temp[j]); // OvCoor-3b
+ bo_ij->Cdbopi2 += CEover4 *
+ (workspace->Delta[j] - dfvl*workspace->Delta_lp_temp[j]); // OvCoor-3b
workspace->CdDelta[j] += CEunder4 * (1.0 - dfvl*workspace->dDelta_lp[j]) *
- (bo_ij->BO_pi + bo_ij->BO_pi2); // UnCoor - 2a
- bo_ij->Cdbopi += CEunder4 *
- (workspace->Delta[j] - dfvl*workspace->Delta_lp_temp[j]); // UnCoor-2b
- bo_ij->Cdbopi2 += CEunder4 *
- (workspace->Delta[j] - dfvl*workspace->Delta_lp_temp[j]); // UnCoor-2b
+ (bo_ij->BO_pi + bo_ij->BO_pi2); // UnCoor - 2a
+ bo_ij->Cdbopi += CEunder4 *
+ (workspace->Delta[j] - dfvl*workspace->Delta_lp_temp[j]); // UnCoor-2b
+ bo_ij->Cdbopi2 += CEunder4 *
+ (workspace->Delta[j] - dfvl*workspace->Delta_lp_temp[j]); // UnCoor-2b
#ifdef TEST_ENERGY
-/* fprintf( out_control->eov, "%6d%12.6f\n",
- workspace->reverse_map[j],
- // CEover1 * twbp->p_ovun1 * twbp->De_s, CEover3,
- CEover4 * (1.0 - workspace->dDelta_lp[j]) *
- (bo_ij->BO_pi + bo_ij->BO_pi2)
-*/// /*CEover4 * (workspace->Delta[j]-workspace->Delta_lp[j])*/);
-// fprintf( out_control->eov, "%6d%12.6f\n",
-// fprintf( out_control->eov, "%6d%24.15e\n",
-// system->my_atoms[j].orig_id,
- // CEover1 * twbp->p_ovun1 * twbp->De_s, CEover3,
-// CEover4 * (1.0 - workspace->dDelta_lp[j]) *
-// (bo_ij->BO_pi + bo_ij->BO_pi2)
-// /*CEover4 * (workspace->Delta[j]-workspace->Delta_lp[j])*/);
-
- // CEunder4 * (1.0 - workspace->dDelta_lp[j]) *
- // (bo_ij->BO_pi + bo_ij->BO_pi2),
- // CEunder4 * (workspace->Delta[j] - workspace->Delta_lp[j]) );
+/* fprintf( out_control->eov, "%6d%12.6f\n",
+ workspace->reverse_map[j],
+ // CEover1 * twbp->p_ovun1 * twbp->De_s, CEover3,
+ CEover4 * (1.0 - workspace->dDelta_lp[j]) *
+ (bo_ij->BO_pi + bo_ij->BO_pi2)
+*/// /*CEover4 * (workspace->Delta[j]-workspace->Delta_lp[j])*/);
+// fprintf( out_control->eov, "%6d%12.6f\n",
+// fprintf( out_control->eov, "%6d%24.15e\n",
+// system->my_atoms[j].orig_id,
+ // CEover1 * twbp->p_ovun1 * twbp->De_s, CEover3,
+// CEover4 * (1.0 - workspace->dDelta_lp[j]) *
+// (bo_ij->BO_pi + bo_ij->BO_pi2)
+// /*CEover4 * (workspace->Delta[j]-workspace->Delta_lp[j])*/);
+
+ // CEunder4 * (1.0 - workspace->dDelta_lp[j]) *
+ // (bo_ij->BO_pi + bo_ij->BO_pi2),
+ // CEunder4 * (workspace->Delta[j] - workspace->Delta_lp[j]) );
#endif
#ifdef TEST_FORCES
Add_dBO( system, lists, i, pj, CEover1 * twbp->p_ovun1 * twbp->De_s,
- workspace->f_ov ); // OvCoor - 1st term
+ workspace->f_ov ); // OvCoor - 1st term
Add_dDelta( system, lists, j,
- CEover4 * (1.0 - dfvl*workspace->dDelta_lp[j]) *
- (bo_ij->BO_pi + bo_ij->BO_pi2),
- workspace->f_ov ); // OvCoor - 3a
+ CEover4 * (1.0 - dfvl*workspace->dDelta_lp[j]) *
+ (bo_ij->BO_pi + bo_ij->BO_pi2),
+ workspace->f_ov ); // OvCoor - 3a
- Add_dBOpinpi2( system, lists, i, pj,
- CEover4 * (workspace->Delta[j] -
- dfvl * workspace->Delta_lp_temp[j]),
- CEover4 * (workspace->Delta[j] -
- dfvl * workspace->Delta_lp_temp[j]),
- workspace->f_ov, workspace->f_ov ); // OvCoor - 3b
+ Add_dBOpinpi2( system, lists, i, pj,
+ CEover4 * (workspace->Delta[j] -
+ dfvl * workspace->Delta_lp_temp[j]),
+ CEover4 * (workspace->Delta[j] -
+ dfvl * workspace->Delta_lp_temp[j]),
+ workspace->f_ov, workspace->f_ov ); // OvCoor - 3b
Add_dDelta( system, lists, j,
- CEunder4 * (1.0 - dfvl*workspace->dDelta_lp[j]) *
- (bo_ij->BO_pi + bo_ij->BO_pi2),
- workspace->f_un ); // UnCoor - 2a
-
- Add_dBOpinpi2( system, lists, i, pj,
- CEunder4 * (workspace->Delta[j] -
- dfvl * workspace->Delta_lp_temp[j]),
- CEunder4 * (workspace->Delta[j] -
- dfvl * workspace->Delta_lp_temp[j]),
- workspace->f_un, workspace->f_un ); // UnCoor - 2b
+ CEunder4 * (1.0 - dfvl*workspace->dDelta_lp[j]) *
+ (bo_ij->BO_pi + bo_ij->BO_pi2),
+ workspace->f_un ); // UnCoor - 2a
+
+ Add_dBOpinpi2( system, lists, i, pj,
+ CEunder4 * (workspace->Delta[j] -
+ dfvl * workspace->Delta_lp_temp[j]),
+ CEunder4 * (workspace->Delta[j] -
+ dfvl * workspace->Delta_lp_temp[j]),
+ workspace->f_un, workspace->f_un ); // UnCoor - 2b
#endif
}
#ifdef TEST_ENERGY
//fprintf( out_control->elp, "%6d%24.15e%24.15e%24.15e\n",
//fprintf( out_control->elp, "%6d%12.4f%12.4f%12.4f\n",
- // system->my_atoms[i].orig_id, workspace->nlp[i],
+ // system->my_atoms[i].orig_id, workspace->nlp[i],
// e_lp, data->my_en.e_lp );
-
- //fprintf( out_control->eov, "%6d%24.15e%24.15e\n",
- fprintf( out_control->eov, "%6d%12.4f%12.4f\n",
- system->my_atoms[i].orig_id,
- e_ov, data->my_en.e_ov + data->my_en.e_un );
-
- //fprintf( out_control->eun, "%6d%24.15e%24.15e\n",
- fprintf( out_control->eun, "%6d%12.4f%12.4f\n",
- system->my_atoms[i].orig_id,
- e_un, data->my_en.e_ov + data->my_en.e_un );
+
+ //fprintf( out_control->eov, "%6d%24.15e%24.15e\n",
+ fprintf( out_control->eov, "%6d%12.4f%12.4f\n",
+ system->my_atoms[i].orig_id,
+ e_ov, data->my_en.e_ov + data->my_en.e_un );
+
+ //fprintf( out_control->eun, "%6d%24.15e%24.15e\n",
+ fprintf( out_control->eun, "%6d%12.4f%12.4f\n",
+ system->my_atoms[i].orig_id,
+ e_un, data->my_en.e_ov + data->my_en.e_un );
#endif
}
}
diff --git a/src/USER-REAXC/reaxc_multi_body.h b/src/USER-REAXC/reaxc_multi_body.h
index ba43b31a6d8e9cb8caa7f30b79cb97a976243e17..a17c9f484ee22fc4ed6937ca5513025174dc8f87 100644
--- a/src/USER-REAXC/reaxc_multi_body.h
+++ b/src/USER-REAXC/reaxc_multi_body.h
@@ -14,12 +14,12 @@
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -30,7 +30,6 @@
#include "reaxc_types.h"
void Atom_Energy( reax_system*, control_params*, simulation_data*,
- storage*, reax_list**, output_controls* );
+ storage*, reax_list**, output_controls* );
#endif
-
diff --git a/src/USER-REAXC/reaxc_nonbonded.cpp b/src/USER-REAXC/reaxc_nonbonded.cpp
index 1fec8b5912de6064affbfc2065cad1a5cf155c37..bbaac67d3e6d183264d7294cec178366ae4ef0dd 100644
--- a/src/USER-REAXC/reaxc_nonbonded.cpp
+++ b/src/USER-REAXC/reaxc_nonbonded.cpp
@@ -14,12 +14,12 @@
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -38,9 +38,9 @@
#include "reaxc_vector.h"
#endif
-void vdW_Coulomb_Energy( reax_system *system, control_params *control,
- simulation_data *data, storage *workspace,
- reax_list **lists, output_controls *out_control )
+void vdW_Coulomb_Energy( reax_system *system, control_params *control,
+ simulation_data *data, storage *workspace,
+ reax_list **lists, output_controls *out_control )
{
int i, j, pj, natoms;
int start_i, end_i, orig_i, orig_j, flag;
@@ -83,25 +83,25 @@ void vdW_Coulomb_Energy( reax_system *system, control_params *control,
if( nbr_pj->d <= control->nonb_cut && (j < natoms || orig_i < orig_j) ) {
#elif defined(LAMMPS_REAX)
flag = 0;
- if(nbr_pj->d <= control->nonb_cut) {
- if (j < natoms) flag = 1;
- else if (orig_i < orig_j) flag = 1;
- else if (orig_i == orig_j) {
- if (nbr_pj->dvec[2] > SMALL) flag = 1;
- else if (fabs(nbr_pj->dvec[2]) < SMALL) {
- if (nbr_pj->dvec[1] > SMALL) flag = 1;
- else if (fabs(nbr_pj->dvec[1]) < SMALL && nbr_pj->dvec[0] > SMALL)
- flag = 1;
- }
- }
+ if(nbr_pj->d <= control->nonb_cut) {
+ if (j < natoms) flag = 1;
+ else if (orig_i < orig_j) flag = 1;
+ else if (orig_i == orig_j) {
+ if (nbr_pj->dvec[2] > SMALL) flag = 1;
+ else if (fabs(nbr_pj->dvec[2]) < SMALL) {
+ if (nbr_pj->dvec[1] > SMALL) flag = 1;
+ else if (fabs(nbr_pj->dvec[1]) < SMALL && nbr_pj->dvec[0] > SMALL)
+ flag = 1;
+ }
+ }
}
-
+
if (flag) {
#endif
r_ij = nbr_pj->d;
twbp = &(system->reax_param.tbp[ system->my_atoms[i].type ]
- [ system->my_atoms[j].type ]);
+ [ system->my_atoms[j].type ]);
/* Calculate Taper and its derivative */
// Tap = nbr_pj->Tap; -- precomputed during compte_H
@@ -112,7 +112,7 @@ void vdW_Coulomb_Energy( reax_system *system, control_params *control,
Tap = Tap * r_ij + workspace->Tap[2];
Tap = Tap * r_ij + workspace->Tap[1];
Tap = Tap * r_ij + workspace->Tap[0];
-
+
dTap = 7*workspace->Tap[7] * r_ij + 6*workspace->Tap[6];
dTap = dTap * r_ij + 5*workspace->Tap[5];
dTap = dTap * r_ij + 4*workspace->Tap[4];
@@ -122,119 +122,119 @@ void vdW_Coulomb_Energy( reax_system *system, control_params *control,
/*vdWaals Calculations*/
if(system->reax_param.gp.vdw_type==1 || system->reax_param.gp.vdw_type==3)
- { // shielding
- powr_vdW1 = pow(r_ij, p_vdW1);
- powgi_vdW1 = pow( 1.0 / twbp->gamma_w, p_vdW1);
-
- fn13 = pow( powr_vdW1 + powgi_vdW1, p_vdW1i );
- exp1 = exp( twbp->alpha * (1.0 - fn13 / twbp->r_vdW) );
- exp2 = exp( 0.5 * twbp->alpha * (1.0 - fn13 / twbp->r_vdW) );
-
- e_vdW = twbp->D * (exp1 - 2.0 * exp2);
- data->my_en.e_vdW += Tap * e_vdW;
-
- dfn13 = pow( powr_vdW1 + powgi_vdW1, p_vdW1i - 1.0) *
- pow(r_ij, p_vdW1 - 2.0);
-
- CEvd = dTap * e_vdW -
- Tap * twbp->D * (twbp->alpha / twbp->r_vdW) * (exp1 - exp2) * dfn13;
- }
+ { // shielding
+ powr_vdW1 = pow(r_ij, p_vdW1);
+ powgi_vdW1 = pow( 1.0 / twbp->gamma_w, p_vdW1);
+
+ fn13 = pow( powr_vdW1 + powgi_vdW1, p_vdW1i );
+ exp1 = exp( twbp->alpha * (1.0 - fn13 / twbp->r_vdW) );
+ exp2 = exp( 0.5 * twbp->alpha * (1.0 - fn13 / twbp->r_vdW) );
+
+ e_vdW = twbp->D * (exp1 - 2.0 * exp2);
+ data->my_en.e_vdW += Tap * e_vdW;
+
+ dfn13 = pow( powr_vdW1 + powgi_vdW1, p_vdW1i - 1.0) *
+ pow(r_ij, p_vdW1 - 2.0);
+
+ CEvd = dTap * e_vdW -
+ Tap * twbp->D * (twbp->alpha / twbp->r_vdW) * (exp1 - exp2) * dfn13;
+ }
else{ // no shielding
- exp1 = exp( twbp->alpha * (1.0 - r_ij / twbp->r_vdW) );
- exp2 = exp( 0.5 * twbp->alpha * (1.0 - r_ij / twbp->r_vdW) );
-
- e_vdW = twbp->D * (exp1 - 2.0 * exp2);
- data->my_en.e_vdW += Tap * e_vdW;
-
- CEvd = dTap * e_vdW -
- Tap * twbp->D * (twbp->alpha / twbp->r_vdW) * (exp1 - exp2) / r_ij;
+ exp1 = exp( twbp->alpha * (1.0 - r_ij / twbp->r_vdW) );
+ exp2 = exp( 0.5 * twbp->alpha * (1.0 - r_ij / twbp->r_vdW) );
+
+ e_vdW = twbp->D * (exp1 - 2.0 * exp2);
+ data->my_en.e_vdW += Tap * e_vdW;
+
+ CEvd = dTap * e_vdW -
+ Tap * twbp->D * (twbp->alpha / twbp->r_vdW) * (exp1 - exp2) / r_ij;
}
if(system->reax_param.gp.vdw_type==2 || system->reax_param.gp.vdw_type==3)
- { // innner wall
- e_core = twbp->ecore * exp(twbp->acore * (1.0-(r_ij/twbp->rcore)));
- data->my_en.e_vdW += Tap * e_core;
+ { // innner wall
+ e_core = twbp->ecore * exp(twbp->acore * (1.0-(r_ij/twbp->rcore)));
+ data->my_en.e_vdW += Tap * e_core;
- de_core = -(twbp->acore/twbp->rcore) * e_core;
- CEvd += dTap * e_core + Tap * de_core / r_ij;
+ de_core = -(twbp->acore/twbp->rcore) * e_core;
+ CEvd += dTap * e_core + Tap * de_core / r_ij;
// lg correction, only if lgvdw is yes
- if (control->lgflag) {
- r_ij5 = pow( r_ij, 5.0 );
+ if (control->lgflag) {
+ r_ij5 = pow( r_ij, 5.0 );
r_ij6 = pow( r_ij, 6.0 );
re6 = pow( twbp->lgre, 6.0 );
- e_lg = -(twbp->lgcij/( r_ij6 + re6 ));
+ e_lg = -(twbp->lgcij/( r_ij6 + re6 ));
data->my_en.e_vdW += Tap * e_lg;
de_lg = -6.0 * e_lg * r_ij5 / ( r_ij6 + re6 ) ;
CEvd += dTap * e_lg + Tap * de_lg / r_ij;
- }
+ }
- }
+ }
/*Coulomb Calculations*/
dr3gamij_1 = ( r_ij * r_ij * r_ij + twbp->gamma );
dr3gamij_3 = pow( dr3gamij_1 , 0.33333333333333 );
tmp = Tap / dr3gamij_3;
- data->my_en.e_ele += e_ele =
- C_ele * system->my_atoms[i].q * system->my_atoms[j].q * tmp;
-
- CEclmb = C_ele * system->my_atoms[i].q * system->my_atoms[j].q *
- ( dTap - Tap * r_ij / dr3gamij_1 ) / dr3gamij_3;
+ data->my_en.e_ele += e_ele =
+ C_ele * system->my_atoms[i].q * system->my_atoms[j].q * tmp;
+
+ CEclmb = C_ele * system->my_atoms[i].q * system->my_atoms[j].q *
+ ( dTap - Tap * r_ij / dr3gamij_1 ) / dr3gamij_3;
/* tally into per-atom energy */
if( system->pair_ptr->evflag || system->pair_ptr->vflag_atom) {
pe_vdw = Tap * (e_vdW + e_core + e_lg);
- rvec_ScaledSum( delij, 1., system->my_atoms[i].x,
- -1., system->my_atoms[j].x );
- f_tmp = -(CEvd + CEclmb);
+ rvec_ScaledSum( delij, 1., system->my_atoms[i].x,
+ -1., system->my_atoms[j].x );
+ f_tmp = -(CEvd + CEclmb);
system->pair_ptr->ev_tally(i,j,natoms,1,pe_vdw,e_ele,
- f_tmp,delij[0],delij[1],delij[2]);
- }
+ f_tmp,delij[0],delij[1],delij[2]);
+ }
/* fprintf(stderr, "%5d %5d %10.6f %10.6f\n",
MIN( system->my_atoms[i].orig_id, system->my_atoms[j].orig_id ),
- MAX( system->my_atoms[i].orig_id, system->my_atoms[j].orig_id ),
- CEvd, CEclmb ); */
+ MAX( system->my_atoms[i].orig_id, system->my_atoms[j].orig_id ),
+ CEvd, CEclmb ); */
if( control->virial == 0 ) {
- rvec_ScaledAdd( workspace->f[i], -(CEvd + CEclmb), nbr_pj->dvec );
- rvec_ScaledAdd( workspace->f[j], +(CEvd + CEclmb), nbr_pj->dvec );
+ rvec_ScaledAdd( workspace->f[i], -(CEvd + CEclmb), nbr_pj->dvec );
+ rvec_ScaledAdd( workspace->f[j], +(CEvd + CEclmb), nbr_pj->dvec );
}
else { /* NPT, iNPT or sNPT */
- /* for pressure coupling, terms not related to bond order
- derivatives are added directly into pressure vector/tensor */
- rvec_Scale( temp, CEvd + CEclmb, nbr_pj->dvec );
-
- rvec_ScaledAdd( workspace->f[i], -1., temp );
- rvec_Add( workspace->f[j], temp );
-
- rvec_iMultiply( ext_press, nbr_pj->rel_box, temp );
- rvec_Add( data->my_ext_press, ext_press );
-
- /* fprintf( stderr, "nonbonded(%d,%d): rel_box (%f %f %f)
- force(%f %f %f) ext_press (%12.6f %12.6f %12.6f)\n",
- i, j, nbr_pj->rel_box[0], nbr_pj->rel_box[1], nbr_pj->rel_box[2],
- temp[0], temp[1], temp[2],
- data->ext_press[0], data->ext_press[1], data->ext_press[2] ); */
+ /* for pressure coupling, terms not related to bond order
+ derivatives are added directly into pressure vector/tensor */
+ rvec_Scale( temp, CEvd + CEclmb, nbr_pj->dvec );
+
+ rvec_ScaledAdd( workspace->f[i], -1., temp );
+ rvec_Add( workspace->f[j], temp );
+
+ rvec_iMultiply( ext_press, nbr_pj->rel_box, temp );
+ rvec_Add( data->my_ext_press, ext_press );
+
+ /* fprintf( stderr, "nonbonded(%d,%d): rel_box (%f %f %f)
+ force(%f %f %f) ext_press (%12.6f %12.6f %12.6f)\n",
+ i, j, nbr_pj->rel_box[0], nbr_pj->rel_box[1], nbr_pj->rel_box[2],
+ temp[0], temp[1], temp[2],
+ data->ext_press[0], data->ext_press[1], data->ext_press[2] ); */
}
-
+
#ifdef TEST_ENERGY
- // fprintf( out_control->evdw,
- // "%12.9f%12.9f%12.9f%12.9f%12.9f%12.9f%12.9f%12.9f\n",
+ // fprintf( out_control->evdw,
+ // "%12.9f%12.9f%12.9f%12.9f%12.9f%12.9f%12.9f%12.9f\n",
// workspace->Tap[7],workspace->Tap[6],workspace->Tap[5],
- // workspace->Tap[4],workspace->Tap[3],workspace->Tap[2],
+ // workspace->Tap[4],workspace->Tap[3],workspace->Tap[2],
// workspace->Tap[1], Tap );
//fprintf( out_control->evdw, "%6d%6d%24.15e%24.15e%24.15e\n",
fprintf( out_control->evdw, "%6d%6d%12.4f%12.4f%12.4f\n",
- system->my_atoms[i].orig_id, system->my_atoms[j].orig_id,
- r_ij, e_vdW, data->my_en.e_vdW );
+ system->my_atoms[i].orig_id, system->my_atoms[j].orig_id,
+ r_ij, e_vdW, data->my_en.e_vdW );
//fprintf(out_control->ecou,"%6d%6d%24.15e%24.15e%24.15e%24.15e%24.15e\n",
fprintf( out_control->ecou, "%6d%6d%12.4f%12.4f%12.4f%12.4f%12.4f\n",
- system->my_atoms[i].orig_id, system->my_atoms[j].orig_id,
- r_ij, system->my_atoms[i].q, system->my_atoms[j].q,
- e_ele, data->my_en.e_ele );
+ system->my_atoms[i].orig_id, system->my_atoms[j].orig_id,
+ r_ij, system->my_atoms[i].q, system->my_atoms[j].q,
+ e_ele, data->my_en.e_ele );
#endif
#ifdef TEST_FORCES
rvec_ScaledAdd( workspace->f_vdw[i], -CEvd, nbr_pj->dvec );
@@ -247,8 +247,8 @@ void vdW_Coulomb_Energy( reax_system *system, control_params *control,
}
#if defined(DEBUG)
- fprintf( stderr, "nonbonded: ext_press (%12.6f %12.6f %12.6f)\n",
- data->ext_press[0], data->ext_press[1], data->ext_press[2] );
+ fprintf( stderr, "nonbonded: ext_press (%12.6f %12.6f %12.6f)\n",
+ data->ext_press[0], data->ext_press[1], data->ext_press[2] );
MPI_Barrier( MPI_COMM_WORLD );
#endif
@@ -257,10 +257,10 @@ void vdW_Coulomb_Energy( reax_system *system, control_params *control,
-void Tabulated_vdW_Coulomb_Energy( reax_system *system,control_params *control,
- simulation_data *data, storage *workspace,
- reax_list **lists,
- output_controls *out_control )
+void Tabulated_vdW_Coulomb_Energy( reax_system *system,control_params *control,
+ simulation_data *data, storage *workspace,
+ reax_list **lists,
+ output_controls *out_control )
{
int i, j, pj, r, natoms, steps, update_freq, update_energies;
int type_i, type_j, tmin, tmax;
@@ -297,19 +297,19 @@ void Tabulated_vdW_Coulomb_Energy( reax_system *system,control_params *control,
if( nbr_pj->d <= control->nonb_cut && (j < natoms || orig_i < orig_j) ) {
#elif defined(LAMMPS_REAX)
flag = 0;
- if(nbr_pj->d <= control->nonb_cut) {
- if (j < natoms) flag = 1;
- else if (orig_i < orig_j) flag = 1;
- else if (orig_i == orig_j) {
- if (nbr_pj->dvec[2] > SMALL) flag = 1;
- else if (fabs(nbr_pj->dvec[2]) < SMALL) {
- if (nbr_pj->dvec[1] > SMALL) flag = 1;
- else if (fabs(nbr_pj->dvec[1]) < SMALL && nbr_pj->dvec[0] > SMALL)
- flag = 1;
- }
- }
+ if(nbr_pj->d <= control->nonb_cut) {
+ if (j < natoms) flag = 1;
+ else if (orig_i < orig_j) flag = 1;
+ else if (orig_i == orig_j) {
+ if (nbr_pj->dvec[2] > SMALL) flag = 1;
+ else if (fabs(nbr_pj->dvec[2]) < SMALL) {
+ if (nbr_pj->dvec[1] > SMALL) flag = 1;
+ else if (fabs(nbr_pj->dvec[1]) < SMALL && nbr_pj->dvec[0] > SMALL)
+ flag = 1;
+ }
+ }
}
-
+
if (flag) {
#endif
j = nbr_pj->nbr;
@@ -318,8 +318,8 @@ void Tabulated_vdW_Coulomb_Energy( reax_system *system,control_params *control,
r_ij = nbr_pj->d;
tmin = MIN( type_i, type_j );
tmax = MAX( type_i, type_j );
- t = &( LR[tmin][tmax] );
- //t = &( LR[type_i][type_j] );
+ t = &( LR[tmin][tmax] );
+ //t = &( LR[type_i][type_j] );
/* Cubic Spline Interpolation */
r = (int)(r_ij * t->inv_dx);
@@ -327,62 +327,62 @@ void Tabulated_vdW_Coulomb_Energy( reax_system *system,control_params *control,
base = (real)(r+1) * t->dx;
dif = r_ij - base;
//fprintf(stderr, "r: %f, i: %d, base: %f, dif: %f\n", r, i, base, dif);
-
+
if( update_energies ) {
- e_vdW = ((t->vdW[r].d*dif + t->vdW[r].c)*dif + t->vdW[r].b)*dif +
- t->vdW[r].a;
-
- e_ele = ((t->ele[r].d*dif + t->ele[r].c)*dif + t->ele[r].b)*dif +
- t->ele[r].a;
- e_ele *= system->my_atoms[i].q * system->my_atoms[j].q;
-
- data->my_en.e_vdW += e_vdW;
- data->my_en.e_ele += e_ele;
- }
-
- CEvd = ((t->CEvd[r].d*dif + t->CEvd[r].c)*dif + t->CEvd[r].b)*dif +
- t->CEvd[r].a;
-
- CEclmb = ((t->CEclmb[r].d*dif+t->CEclmb[r].c)*dif+t->CEclmb[r].b)*dif +
- t->CEclmb[r].a;
+ e_vdW = ((t->vdW[r].d*dif + t->vdW[r].c)*dif + t->vdW[r].b)*dif +
+ t->vdW[r].a;
+
+ e_ele = ((t->ele[r].d*dif + t->ele[r].c)*dif + t->ele[r].b)*dif +
+ t->ele[r].a;
+ e_ele *= system->my_atoms[i].q * system->my_atoms[j].q;
+
+ data->my_en.e_vdW += e_vdW;
+ data->my_en.e_ele += e_ele;
+ }
+
+ CEvd = ((t->CEvd[r].d*dif + t->CEvd[r].c)*dif + t->CEvd[r].b)*dif +
+ t->CEvd[r].a;
+
+ CEclmb = ((t->CEclmb[r].d*dif+t->CEclmb[r].c)*dif+t->CEclmb[r].b)*dif +
+ t->CEclmb[r].a;
CEclmb *= system->my_atoms[i].q * system->my_atoms[j].q;
/* tally into per-atom energy */
if( system->pair_ptr->evflag || system->pair_ptr->vflag_atom) {
- rvec_ScaledSum( delij, 1., system->my_atoms[i].x,
- -1., system->my_atoms[j].x );
- f_tmp = -(CEvd + CEclmb);
+ rvec_ScaledSum( delij, 1., system->my_atoms[i].x,
+ -1., system->my_atoms[j].x );
+ f_tmp = -(CEvd + CEclmb);
system->pair_ptr->ev_tally(i,j,natoms,1,e_vdW,e_ele,
- f_tmp,delij[0],delij[1],delij[2]);
- }
+ f_tmp,delij[0],delij[1],delij[2]);
+ }
if( control->virial == 0 ) {
- rvec_ScaledAdd( workspace->f[i], -(CEvd + CEclmb), nbr_pj->dvec );
- rvec_ScaledAdd( workspace->f[j], +(CEvd + CEclmb), nbr_pj->dvec );
+ rvec_ScaledAdd( workspace->f[i], -(CEvd + CEclmb), nbr_pj->dvec );
+ rvec_ScaledAdd( workspace->f[j], +(CEvd + CEclmb), nbr_pj->dvec );
}
else { // NPT, iNPT or sNPT
- /* for pressure coupling, terms not related to bond order derivatives
- are added directly into pressure vector/tensor */
- rvec_Scale( temp, CEvd + CEclmb, nbr_pj->dvec );
-
- rvec_ScaledAdd( workspace->f[i], -1., temp );
- rvec_Add( workspace->f[j], temp );
-
- rvec_iMultiply( ext_press, nbr_pj->rel_box, temp );
- rvec_Add( data->my_ext_press, ext_press );
+ /* for pressure coupling, terms not related to bond order derivatives
+ are added directly into pressure vector/tensor */
+ rvec_Scale( temp, CEvd + CEclmb, nbr_pj->dvec );
+
+ rvec_ScaledAdd( workspace->f[i], -1., temp );
+ rvec_Add( workspace->f[j], temp );
+
+ rvec_iMultiply( ext_press, nbr_pj->rel_box, temp );
+ rvec_Add( data->my_ext_press, ext_press );
}
#ifdef TEST_ENERGY
//fprintf( out_control->evdw, "%6d%6d%24.15e%24.15e%24.15e\n",
fprintf( out_control->evdw, "%6d%6d%12.4f%12.4f%12.4f\n",
- system->my_atoms[i].orig_id, system->my_atoms[j].orig_id,
- r_ij, e_vdW, data->my_en.e_vdW );
+ system->my_atoms[i].orig_id, system->my_atoms[j].orig_id,
+ r_ij, e_vdW, data->my_en.e_vdW );
//fprintf(out_control->ecou,"%6d%6d%24.15e%24.15e%24.15e%24.15e%24.15e\n",
fprintf( out_control->ecou, "%6d%6d%12.4f%12.4f%12.4f%12.4f%12.4f\n",
- system->my_atoms[i].orig_id, system->my_atoms[j].orig_id,
- r_ij, system->my_atoms[i].q, system->my_atoms[j].q,
- e_ele, data->my_en.e_ele );
+ system->my_atoms[i].orig_id, system->my_atoms[j].orig_id,
+ r_ij, system->my_atoms[i].q, system->my_atoms[j].q,
+ e_ele, data->my_en.e_ele );
#endif
#ifdef TEST_FORCES
rvec_ScaledAdd( workspace->f_vdw[i], -CEvd, nbr_pj->dvec );
@@ -408,19 +408,19 @@ void Compute_Polarization_Energy( reax_system *system, simulation_data *data )
for( i = 0; i < system->n; i++ ) {
q = system->my_atoms[i].q;
type_i = system->my_atoms[i].type;
-
- en_tmp = KCALpMOL_to_EV * (system->reax_param.sbp[type_i].chi * q +
- (system->reax_param.sbp[type_i].eta / 2.) * SQR(q));
+
+ en_tmp = KCALpMOL_to_EV * (system->reax_param.sbp[type_i].chi * q +
+ (system->reax_param.sbp[type_i].eta / 2.) * SQR(q));
data->my_en.e_pol += en_tmp;
/* tally into per-atom energy */
- if( system->pair_ptr->evflag)
+ if( system->pair_ptr->evflag)
system->pair_ptr->ev_tally(i,i,system->n,1,0.0,en_tmp,0.0,0.0,0.0,0.0);
}
}
-void LR_vdW_Coulomb( reax_system *system, storage *workspace,
- control_params *control, int i, int j, real r_ij, LR_data *lr )
+void LR_vdW_Coulomb( reax_system *system, storage *workspace,
+ control_params *control, int i, int j, real r_ij, LR_data *lr )
{
real p_vdW1 = system->reax_param.gp.l[28];
real p_vdW1i = 1.0 / p_vdW1;
@@ -445,7 +445,7 @@ void LR_vdW_Coulomb( reax_system *system, storage *workspace,
Tap = Tap * r_ij + workspace->Tap[2];
Tap = Tap * r_ij + workspace->Tap[1];
Tap = Tap * r_ij + workspace->Tap[0];
-
+
dTap = 7*workspace->Tap[7] * r_ij + 6*workspace->Tap[6];
dTap = dTap * r_ij + 5*workspace->Tap[5];
dTap = dTap * r_ij + 4*workspace->Tap[4];
@@ -458,22 +458,22 @@ void LR_vdW_Coulomb( reax_system *system, storage *workspace,
{ // shielding
powr_vdW1 = pow(r_ij, p_vdW1);
powgi_vdW1 = pow( 1.0 / twbp->gamma_w, p_vdW1);
-
+
fn13 = pow( powr_vdW1 + powgi_vdW1, p_vdW1i );
exp1 = exp( twbp->alpha * (1.0 - fn13 / twbp->r_vdW) );
exp2 = exp( 0.5 * twbp->alpha * (1.0 - fn13 / twbp->r_vdW) );
lr->e_vdW = Tap * twbp->D * (exp1 - 2.0 * exp2);
-
+
dfn13 = pow( powr_vdW1 + powgi_vdW1, p_vdW1i-1.0) * pow(r_ij, p_vdW1-2.0);
-
- lr->CEvd = dTap * twbp->D * (exp1 - 2.0 * exp2) -
- Tap * twbp->D * (twbp->alpha / twbp->r_vdW) * (exp1 - exp2) * dfn13;
+
+ lr->CEvd = dTap * twbp->D * (exp1 - 2.0 * exp2) -
+ Tap * twbp->D * (twbp->alpha / twbp->r_vdW) * (exp1 - exp2) * dfn13;
}
else{ // no shielding
exp1 = exp( twbp->alpha * (1.0 - r_ij / twbp->r_vdW) );
exp2 = exp( 0.5 * twbp->alpha * (1.0 - r_ij / twbp->r_vdW) );
-
+
lr->e_vdW = Tap * twbp->D * (exp1 - 2.0 * exp2);
lr->CEvd = dTap * twbp->D * (exp1 - 2.0 * exp2) -
Tap * twbp->D * (twbp->alpha / twbp->r_vdW) * (exp1 - exp2) / r_ij;
@@ -483,16 +483,16 @@ void LR_vdW_Coulomb( reax_system *system, storage *workspace,
{ // innner wall
e_core = twbp->ecore * exp(twbp->acore * (1.0-(r_ij/twbp->rcore)));
lr->e_vdW += Tap * e_core;
-
+
de_core = -(twbp->acore/twbp->rcore) * e_core;
lr->CEvd += dTap * e_core + Tap * de_core / r_ij;
// lg correction, only if lgvdw is yes
if (control->lgflag) {
- r_ij5 = pow( r_ij, 5.0 );
+ r_ij5 = pow( r_ij, 5.0 );
r_ij6 = pow( r_ij, 6.0 );
re6 = pow( twbp->lgre, 6.0 );
- e_lg = -(twbp->lgcij/( r_ij6 + re6 ));
+ e_lg = -(twbp->lgcij/( r_ij6 + re6 ));
lr->e_vdW += Tap * e_lg;
de_lg = -6.0 * e_lg * r_ij5 / ( r_ij6 + re6 ) ;
@@ -501,7 +501,7 @@ void LR_vdW_Coulomb( reax_system *system, storage *workspace,
}
-
+
/* Coulomb calculations */
dr3gamij_1 = ( r_ij * r_ij * r_ij + twbp->gamma );
dr3gamij_3 = pow( dr3gamij_1 , 0.33333333333333 );
@@ -511,10 +511,10 @@ void LR_vdW_Coulomb( reax_system *system, storage *workspace,
lr->e_ele = C_ele * tmp;
// fprintf( stderr,
// "i:%d(%d), j:%d(%d), gamma:%f, Tap:%f, dr3gamij_3:%f, qi: %f, qj: %f\n",
- // i, system->my_atoms[i].type, j, system->my_atoms[j].type,
- // twbp->gamma, Tap, dr3gamij_3,
+ // i, system->my_atoms[i].type, j, system->my_atoms[j].type,
+ // twbp->gamma, Tap, dr3gamij_3,
// system->my_atoms[i].q, system->my_atoms[j].q );
-
+
lr->CEclmb = C_ele * ( dTap - Tap * r_ij / dr3gamij_1 ) / dr3gamij_3;
// fprintf( stdout, "%d %d\t%g\t%g %g\t%g %g\t%g %g\n",
// i+1, j+1, r_ij, e_vdW, CEvd * r_ij,
diff --git a/src/USER-REAXC/reaxc_nonbonded.h b/src/USER-REAXC/reaxc_nonbonded.h
index e5cd8e3eb188d768718b7d6322bc105f97888050..ecb07494c6e0d6746fa725d9d2d26c090f2e19fa 100644
--- a/src/USER-REAXC/reaxc_nonbonded.h
+++ b/src/USER-REAXC/reaxc_nonbonded.h
@@ -14,12 +14,12 @@
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -30,14 +30,14 @@
#include "reaxc_types.h"
void vdW_Coulomb_Energy( reax_system*, control_params*, simulation_data*,
- storage*, reax_list**, output_controls* );
+ storage*, reax_list**, output_controls* );
-void Tabulated_vdW_Coulomb_Energy( reax_system*, control_params*,
- simulation_data*, storage*,
- reax_list**, output_controls* );
+void Tabulated_vdW_Coulomb_Energy( reax_system*, control_params*,
+ simulation_data*, storage*,
+ reax_list**, output_controls* );
void Compute_Polarization_Energy( reax_system*, simulation_data* );
void LR_vdW_Coulomb( reax_system*, storage*, control_params*,
- int, int, real, LR_data* );
+ int, int, real, LR_data* );
#endif
diff --git a/src/USER-REAXC/reaxc_reset_tools.cpp b/src/USER-REAXC/reaxc_reset_tools.cpp
index 234104c19044ee452cc216252262bf8edc366c0a..d57296a1c130afaaffb13aa67547f398b689223a 100644
--- a/src/USER-REAXC/reaxc_reset_tools.cpp
+++ b/src/USER-REAXC/reaxc_reset_tools.cpp
@@ -14,12 +14,12 @@
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -48,7 +48,7 @@ void Reset_Atoms( reax_system* system, control_params *control )
for( i = 0; i < system->n; ++i ) {
atom = &(system->my_atoms[i]);
if( system->reax_param.sbp[ atom->type ].p_hbond == 1 )
- atom->Hindex = system->numH++;
+ atom->Hindex = system->numH++;
else atom->Hindex = -1;
}
}
@@ -86,7 +86,7 @@ void Reset_Pressures( simulation_data *data )
{
data->flex_bar.P_scalar = 0;
rtensor_MakeZero( data->flex_bar.P );
-
+
data->iso_bar.P = 0;
rvec_MakeZero( data->int_press );
rvec_MakeZero( data->my_ext_press );
@@ -156,11 +156,11 @@ void Reset_Grid( grid *g )
int i, j, k;
for( i = 0; i < g->ncells[0]; i++ )
- for( j = 0; j < g->ncells[1]; j++ )
+ for( j = 0; j < g->ncells[1]; j++ )
for( k = 0; k < g->ncells[2]; k++ ) {
- g->cells[i][j][k].top = 0;
- g->cells[i][j][k].str = 0;
- g->cells[i][j][k].end = 0;
+ g->cells[i][j][k].top = 0;
+ g->cells[i][j][k].str = 0;
+ g->cells[i][j][k].end = 0;
}
}
@@ -175,8 +175,8 @@ void Reset_Out_Buffers( mpi_out_data *out_buf, int n )
void Reset_Neighbor_Lists( reax_system *system, control_params *control,
- storage *workspace, reax_list **lists,
- MPI_Comm comm )
+ storage *workspace, reax_list **lists,
+ MPI_Comm comm )
{
int i, total_bonds, Hindex, total_hbonds;
reax_list *bonds, *hbonds;
@@ -197,10 +197,10 @@ void Reset_Neighbor_Lists( reax_system *system, control_params *control,
if( total_bonds >= bonds->num_intrs * DANGER_ZONE ) {
workspace->realloc.bonds = 1;
if( total_bonds >= bonds->num_intrs ) {
- fprintf(stderr,
- "p%d: not enough space for bonds! total=%d allocated=%d\n",
- system->my_rank, total_bonds, bonds->num_intrs );
- MPI_Abort( comm, INSUFFICIENT_MEMORY );
+ fprintf(stderr,
+ "p%d: not enough space for bonds! total=%d allocated=%d\n",
+ system->my_rank, total_bonds, bonds->num_intrs );
+ MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
}
}
@@ -209,28 +209,28 @@ void Reset_Neighbor_Lists( reax_system *system, control_params *control,
// system->my_rank, hbonds->n, hbonds->num_intrs, workspace->num_H );
// MPI_Barrier( comm );
/* hbonds list */
- if( control->hbond_cut > 0 && system->numH > 0 ) {
+ if( control->hbond_cut > 0 && system->numH > 0 ) {
hbonds = (*lists) + HBONDS;
total_hbonds = 0;
-
+
/* reset start-end indexes */
for( i = 0; i < system->n; ++i ) {
Hindex = system->my_atoms[i].Hindex;
if( Hindex > -1 ) {
- Set_Start_Index( Hindex, total_hbonds, hbonds );
- Set_End_Index( Hindex, total_hbonds, hbonds );
- total_hbonds += system->my_atoms[i].num_hbonds;
+ Set_Start_Index( Hindex, total_hbonds, hbonds );
+ Set_End_Index( Hindex, total_hbonds, hbonds );
+ total_hbonds += system->my_atoms[i].num_hbonds;
}
}
-
+
/* is reallocation needed? */
if( total_hbonds >= hbonds->num_intrs * 0.90/*DANGER_ZONE*/ ) {
workspace->realloc.hbonds = 1;
if( total_hbonds >= hbonds->num_intrs ) {
- fprintf(stderr,
- "p%d: not enough space for hbonds! total=%d allocated=%d\n",
- system->my_rank, total_hbonds, hbonds->num_intrs );
- MPI_Abort( comm, INSUFFICIENT_MEMORY );
+ fprintf(stderr,
+ "p%d: not enough space for hbonds! total=%d allocated=%d\n",
+ system->my_rank, total_hbonds, hbonds->num_intrs );
+ MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
}
}
@@ -240,20 +240,19 @@ void Reset_Neighbor_Lists( reax_system *system, control_params *control,
void Reset( reax_system *system, control_params *control, simulation_data *data,
- storage *workspace, reax_list **lists, MPI_Comm comm )
+ storage *workspace, reax_list **lists, MPI_Comm comm )
{
Reset_Atoms( system, control );
-
+
Reset_Simulation_Data( data, control->virial );
- Reset_Workspace( system, workspace );
+ Reset_Workspace( system, workspace );
Reset_Neighbor_Lists( system, control, workspace, lists, comm );
-#if defined(DEBUG_FOCUS)
+#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d @ step%d: reset done\n", system->my_rank, data->step );
MPI_Barrier( comm );
#endif
}
-
diff --git a/src/USER-REAXC/reaxc_reset_tools.h b/src/USER-REAXC/reaxc_reset_tools.h
index 1662813a5c62387b61f1a8677daa414b8641d002..adc562735cfe76987bc44e0c72d6dc1d6fc39178 100644
--- a/src/USER-REAXC/reaxc_reset_tools.h
+++ b/src/USER-REAXC/reaxc_reset_tools.h
@@ -14,12 +14,12 @@
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -35,10 +35,10 @@ void Reset_Timing( reax_timing* );
void Reset_Workspace( reax_system*, storage* );
void Reset_Grid( grid* );
void Reset_Out_Buffers( mpi_out_data*, int );
-void Reset_Neighbor_Lists( reax_system*, control_params*, storage*,
- reax_list**, MPI_Comm );
+void Reset_Neighbor_Lists( reax_system*, control_params*, storage*,
+ reax_list**, MPI_Comm );
void Reset( reax_system*, control_params*, simulation_data*, storage*,
- reax_list**, MPI_Comm );
+ reax_list**, MPI_Comm );
#ifdef TEST_FORCES
void Reset_Test_Forces( reax_system*, storage* );
#endif
diff --git a/src/USER-REAXC/reaxc_system_props.cpp b/src/USER-REAXC/reaxc_system_props.cpp
index f708d9cac3c8c11ec58eb1c11c754d1fceb11675..0410b625a95dcc3b774d8f4f57fae198ff5ec539 100644
--- a/src/USER-REAXC/reaxc_system_props.cpp
+++ b/src/USER-REAXC/reaxc_system_props.cpp
@@ -14,12 +14,12 @@
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -40,25 +40,25 @@ void Temperature_Control( control_params *control, simulation_data *data )
{
real tmp;
- if( control->T_mode == 1 ) {// step-wise temperature control
+ if( control->T_mode == 1 ) {// step-wise temperature control
if((data->step-data->prev_steps) % ((int)(control->T_freq/control->dt))==0){
if( fabs( control->T - control->T_final ) >= fabs( control->T_rate ) )
- control->T += control->T_rate;
- else control->T = control->T_final;
+ control->T += control->T_rate;
+ else control->T = control->T_final;
}
}
else if( control->T_mode == 2 ) { // constant slope control
tmp = control->T_rate * control->dt / control->T_freq;
-
+
if( fabs( control->T - control->T_final ) >= fabs( tmp ) )
- control->T += tmp;
+ control->T += tmp;
}
}
-void Compute_Kinetic_Energy( reax_system* system, simulation_data* data,
- MPI_Comm comm )
+void Compute_Kinetic_Energy( reax_system* system, simulation_data* data,
+ MPI_Comm comm )
{
int i;
rvec p;
@@ -70,27 +70,27 @@ void Compute_Kinetic_Energy( reax_system* system, simulation_data* data,
for( i = 0; i < system->n; i++ ) {
m = system->reax_param.sbp[system->my_atoms[i].type].mass;
-
+
rvec_Scale( p, m, system->my_atoms[i].v );
data->my_en.e_kin += 0.5 * rvec_Dot( p, system->my_atoms[i].v );
}
-
- MPI_Allreduce( &data->my_en.e_kin, &data->sys_en.e_kin,
- 1, MPI_DOUBLE, MPI_SUM, comm );
+
+ MPI_Allreduce( &data->my_en.e_kin, &data->sys_en.e_kin,
+ 1, MPI_DOUBLE, MPI_SUM, comm );
data->therm.T = (2. * data->sys_en.e_kin) / (data->N_f * K_B);
// avoid T being an absolute zero, might cause F.P.E!
- if( fabs(data->therm.T) < ALMOST_ZERO )
+ if( fabs(data->therm.T) < ALMOST_ZERO )
data->therm.T = ALMOST_ZERO;
}
-void Compute_System_Energy( reax_system *system, simulation_data *data,
- MPI_Comm comm )
+void Compute_System_Energy( reax_system *system, simulation_data *data,
+ MPI_Comm comm )
{
real my_en[15], sys_en[15];
-
+
my_en[0] = data->my_en.e_bond;
my_en[1] = data->my_en.e_ov;
my_en[2] = data->my_en.e_un;
@@ -107,13 +107,13 @@ void Compute_System_Energy( reax_system *system, simulation_data *data,
my_en[13] = data->my_en.e_kin;
MPI_Reduce( my_en, sys_en, 14, MPI_DOUBLE, MPI_SUM, MASTER_NODE, comm );
- data->my_en.e_pot = data->my_en.e_bond +
+ data->my_en.e_pot = data->my_en.e_bond +
data->my_en.e_ov + data->my_en.e_un + data->my_en.e_lp +
- data->my_en.e_ang + data->my_en.e_pen + data->my_en.e_coa +
- data->my_en.e_hb +
- data->my_en.e_tor + data->my_en.e_con +
+ data->my_en.e_ang + data->my_en.e_pen + data->my_en.e_coa +
+ data->my_en.e_hb +
+ data->my_en.e_tor + data->my_en.e_con +
data->my_en.e_vdW + data->my_en.e_ele + data->my_en.e_pol;
-
+
data->my_en.e_tot = data->my_en.e_pot + E_CONV * data->my_en.e_kin;
if( system->my_rank == MASTER_NODE ) {
@@ -132,24 +132,24 @@ void Compute_System_Energy( reax_system *system, simulation_data *data,
data->sys_en.e_pol = sys_en[12];
data->sys_en.e_kin = sys_en[13];
- data->sys_en.e_pot = data->sys_en.e_bond +
+ data->sys_en.e_pot = data->sys_en.e_bond +
data->sys_en.e_ov + data->sys_en.e_un + data->sys_en.e_lp +
- data->sys_en.e_ang + data->sys_en.e_pen + data->sys_en.e_coa +
- data->sys_en.e_hb +
- data->sys_en.e_tor + data->sys_en.e_con +
+ data->sys_en.e_ang + data->sys_en.e_pen + data->sys_en.e_coa +
+ data->sys_en.e_hb +
+ data->sys_en.e_tor + data->sys_en.e_con +
data->sys_en.e_vdW + data->sys_en.e_ele + data->sys_en.e_pol;
-
+
data->sys_en.e_tot = data->sys_en.e_pot + E_CONV * data->sys_en.e_kin;
}
}
-void Compute_Total_Mass( reax_system *system, simulation_data *data,
- MPI_Comm comm )
+void Compute_Total_Mass( reax_system *system, simulation_data *data,
+ MPI_Comm comm )
{
int i;
real tmp;
-
+
tmp = 0;
for( i = 0; i < system->n; i++ )
tmp += system->reax_param.sbp[ system->my_atoms[i].type ].mass;
@@ -161,8 +161,8 @@ void Compute_Total_Mass( reax_system *system, simulation_data *data,
-void Compute_Center_of_Mass( reax_system *system, simulation_data *data,
- mpi_datatypes *mpi_data, MPI_Comm comm )
+void Compute_Center_of_Mass( reax_system *system, simulation_data *data,
+ mpi_datatypes *mpi_data, MPI_Comm comm )
{
int i;
real m, det; //xx, xy, xz, yy, yz, zz;
@@ -182,11 +182,11 @@ void Compute_Center_of_Mass( reax_system *system, simulation_data *data,
rvec_ScaledAdd( my_xcm, m, system->my_atoms[i].x );
rvec_ScaledAdd( my_vcm, m, system->my_atoms[i].v );
-
+
rvec_Cross( tvec, system->my_atoms[i].x, system->my_atoms[i].v );
rvec_ScaledAdd( my_amcm, m, tvec );
}
-
+
MPI_Allreduce( my_xcm, data->xcm, 3, MPI_DOUBLE, MPI_SUM, comm );
MPI_Allreduce( my_vcm, data->vcm, 3, MPI_DOUBLE, MPI_SUM, comm );
MPI_Allreduce( my_amcm, data->amcm, 3, MPI_DOUBLE, MPI_SUM, comm );
@@ -211,9 +211,9 @@ void Compute_Center_of_Mass( reax_system *system, simulation_data *data,
tmp_mat[2]/*my_xz*/ += diff[0] * diff[2] * m;
tmp_mat[3]/*my_yy*/ += diff[1] * diff[1] * m;
tmp_mat[4]/*my_yz*/ += diff[1] * diff[2] * m;
- tmp_mat[5]/*my_zz*/ += diff[2] * diff[2] * m;
+ tmp_mat[5]/*my_zz*/ += diff[2] * diff[2] * m;
}
-
+
MPI_Reduce( tmp_mat, tot_mat, 6, MPI_DOUBLE, MPI_SUM, MASTER_NODE, comm );
if( system->my_rank == MASTER_NODE ) {
@@ -223,15 +223,15 @@ void Compute_Center_of_Mass( reax_system *system, simulation_data *data,
mat[1][1] = tot_mat[0] + tot_mat[5]; // xx + zz;
mat[2][1] = mat[1][2] = -tot_mat[4]; // -yz;
mat[2][2] = tot_mat[0] + tot_mat[3]; // xx + yy;
-
+
/* invert the inertial tensor */
- det = ( mat[0][0] * mat[1][1] * mat[2][2] +
- mat[0][1] * mat[1][2] * mat[2][0] +
- mat[0][2] * mat[1][0] * mat[2][1] ) -
- ( mat[0][0] * mat[1][2] * mat[2][1] +
- mat[0][1] * mat[1][0] * mat[2][2] +
- mat[0][2] * mat[1][1] * mat[2][0] );
-
+ det = ( mat[0][0] * mat[1][1] * mat[2][2] +
+ mat[0][1] * mat[1][2] * mat[2][0] +
+ mat[0][2] * mat[1][0] * mat[2][1] ) -
+ ( mat[0][0] * mat[1][2] * mat[2][1] +
+ mat[0][1] * mat[1][0] * mat[2][2] +
+ mat[0][2] * mat[1][1] * mat[2][0] );
+
inv[0][0] = mat[1][1] * mat[2][2] - mat[1][2] * mat[2][1];
inv[0][1] = mat[0][2] * mat[2][1] - mat[0][1] * mat[2][2];
inv[0][2] = mat[0][1] * mat[1][2] - mat[0][2] * mat[1][1];
@@ -241,7 +241,7 @@ void Compute_Center_of_Mass( reax_system *system, simulation_data *data,
inv[2][0] = mat[1][0] * mat[2][1] - mat[2][0] * mat[1][1];
inv[2][1] = mat[2][0] * mat[0][1] - mat[0][0] * mat[2][1];
inv[2][2] = mat[0][0] * mat[1][1] - mat[1][0] * mat[0][1];
-
+
if( det > ALMOST_ZERO )
rtensor_Scale( inv, 1./det, inv );
else rtensor_MakeZero( inv );
@@ -256,22 +256,22 @@ void Compute_Center_of_Mass( reax_system *system, simulation_data *data,
data->erot_cm = 0.5 * E_CONV * rvec_Dot( data->avcm, data->amcm );
#if defined(DEBUG)
- fprintf( stderr, "xcm: %24.15e %24.15e %24.15e\n",
- data->xcm[0], data->xcm[1], data->xcm[2] );
- fprintf( stderr, "vcm: %24.15e %24.15e %24.15e\n",
- data->vcm[0], data->vcm[1], data->vcm[2] );
- fprintf( stderr, "amcm: %24.15e %24.15e %24.15e\n",
- data->amcm[0], data->amcm[1], data->amcm[2] );
+ fprintf( stderr, "xcm: %24.15e %24.15e %24.15e\n",
+ data->xcm[0], data->xcm[1], data->xcm[2] );
+ fprintf( stderr, "vcm: %24.15e %24.15e %24.15e\n",
+ data->vcm[0], data->vcm[1], data->vcm[2] );
+ fprintf( stderr, "amcm: %24.15e %24.15e %24.15e\n",
+ data->amcm[0], data->amcm[1], data->amcm[2] );
/* fprintf( stderr, "mat: %f %f %f\n %f %f %f\n %f %f %f\n",
- mat[0][0], mat[0][1], mat[0][2],
- mat[1][0], mat[1][1], mat[1][2],
+ mat[0][0], mat[0][1], mat[0][2],
+ mat[1][0], mat[1][1], mat[1][2],
mat[2][0], mat[2][1], mat[2][2] );
fprintf( stderr, "inv: %g %g %g\n %g %g %g\n %g %g %g\n",
- inv[0][0], inv[0][1], inv[0][2],
- inv[1][0], inv[1][1], inv[1][2],
+ inv[0][0], inv[0][1], inv[0][2],
+ inv[1][0], inv[1][1], inv[1][2],
inv[2][0], inv[2][1], inv[2][2] ); */
- fprintf( stderr, "avcm: %24.15e %24.15e %24.15e\n",
- data->avcm[0], data->avcm[1], data->avcm[2] );
+ fprintf( stderr, "avcm: %24.15e %24.15e %24.15e\n",
+ data->avcm[0], data->avcm[1], data->avcm[2] );
#endif
}
@@ -280,13 +280,13 @@ void Compute_Center_of_Mass( reax_system *system, simulation_data *data,
/* IMPORTANT: This function assumes that current kinetic energy
* the system is already computed
*
- * IMPORTANT: In Klein's paper, it is stated that a dU/dV term needs
- * to be added when there are long-range interactions or long-range
+ * IMPORTANT: In Klein's paper, it is stated that a dU/dV term needs
+ * to be added when there are long-range interactions or long-range
* corrections to short-range interactions present.
- * We may want to add that for more accuracy.
+ * We may want to add that for more accuracy.
*/
-void Compute_Pressure(reax_system* system, control_params *control,
- simulation_data* data, mpi_datatypes *mpi_data)
+void Compute_Pressure(reax_system* system, control_params *control,
+ simulation_data* data, mpi_datatypes *mpi_data)
{
int i;
reax_atom *p_atom;
@@ -300,76 +300,76 @@ void Compute_Pressure(reax_system* system, control_params *control,
if( control->press_mode == 0 || control->press_mode == 2 ) {
for( i = 0; i < system->n; ++i ) {
p_atom = &( system->my_atoms[i] );
-
+
/* transform x into unitbox coordinates */
Transform_to_UnitBox( p_atom->x, big_box, 1, tx );
-
+
/* this atom's contribution to internal pressure */
rvec_Multiply( tmp, p_atom->f, tx );
rvec_Add( int_press, tmp );
-
+
#if defined(DEBUG)
- fprintf( stderr, "%8d%8.2f%8.2f%8.2f",
- i+1, p_atom->x[0], p_atom->x[1], p_atom->x[2] );
- fprintf( stderr, "%8.2f%8.2f%8.2f",
- p_atom->f[0], p_atom->f[1], p_atom->f[2] );
- fprintf( stderr, "%8.2f%8.2f%8.2f\n",
- int_press[0], int_press[1], int_press[2] );
+ fprintf( stderr, "%8d%8.2f%8.2f%8.2f",
+ i+1, p_atom->x[0], p_atom->x[1], p_atom->x[2] );
+ fprintf( stderr, "%8.2f%8.2f%8.2f",
+ p_atom->f[0], p_atom->f[1], p_atom->f[2] );
+ fprintf( stderr, "%8.2f%8.2f%8.2f\n",
+ int_press[0], int_press[1], int_press[2] );
#endif
}
}
/* sum up internal and external pressure */
-#if defined(DEBUG)
+#if defined(DEBUG)
fprintf(stderr,"p%d:p_int(%10.5f %10.5f %10.5f)p_ext(%10.5f %10.5f %10.5f)\n",
- system->my_rank, int_press[0], int_press[1], int_press[2],
- data->my_ext_press[0], data->my_ext_press[1], data->my_ext_press[2] );
+ system->my_rank, int_press[0], int_press[1], int_press[2],
+ data->my_ext_press[0], data->my_ext_press[1], data->my_ext_press[2] );
#endif
- MPI_Allreduce( int_press, data->int_press,
- 3, MPI_DOUBLE, MPI_SUM, mpi_data->comm_mesh3D );
- MPI_Allreduce( data->my_ext_press, data->ext_press,
- 3, MPI_DOUBLE, MPI_SUM, mpi_data->comm_mesh3D );
-#if defined(DEBUG)
- fprintf( stderr, "p%d: %10.5f %10.5f %10.5f\n",
- system->my_rank,
- data->int_press[0], data->int_press[1], data->int_press[2] );
- fprintf( stderr, "p%d: %10.5f %10.5f %10.5f\n",
- system->my_rank,
- data->ext_press[0], data->ext_press[1], data->ext_press[2] );
+ MPI_Allreduce( int_press, data->int_press,
+ 3, MPI_DOUBLE, MPI_SUM, mpi_data->comm_mesh3D );
+ MPI_Allreduce( data->my_ext_press, data->ext_press,
+ 3, MPI_DOUBLE, MPI_SUM, mpi_data->comm_mesh3D );
+#if defined(DEBUG)
+ fprintf( stderr, "p%d: %10.5f %10.5f %10.5f\n",
+ system->my_rank,
+ data->int_press[0], data->int_press[1], data->int_press[2] );
+ fprintf( stderr, "p%d: %10.5f %10.5f %10.5f\n",
+ system->my_rank,
+ data->ext_press[0], data->ext_press[1], data->ext_press[2] );
#endif
/* kinetic contribution */
data->kin_press = 2.*(E_CONV*data->sys_en.e_kin) / (3.*big_box->V*P_CONV);
- /* Calculate total pressure in each direction */
- data->tot_press[0] = data->kin_press -
- (( data->int_press[0] + data->ext_press[0] ) /
+ /* Calculate total pressure in each direction */
+ data->tot_press[0] = data->kin_press -
+ (( data->int_press[0] + data->ext_press[0] ) /
( big_box->box_norms[1] * big_box->box_norms[2] * P_CONV ));
- data->tot_press[1] = data->kin_press -
- (( data->int_press[1] + data->ext_press[1] ) /
+ data->tot_press[1] = data->kin_press -
+ (( data->int_press[1] + data->ext_press[1] ) /
( big_box->box_norms[0] * big_box->box_norms[2] * P_CONV ));
- data->tot_press[2] = data->kin_press -
- (( data->int_press[2] + data->ext_press[2] ) /
+ data->tot_press[2] = data->kin_press -
+ (( data->int_press[2] + data->ext_press[2] ) /
( big_box->box_norms[0] * big_box->box_norms[1] * P_CONV ));
/* Average pressure for the whole box */
- data->iso_bar.P =
+ data->iso_bar.P =
( data->tot_press[0] + data->tot_press[1] + data->tot_press[2] ) / 3.;
}
/*
-void Compute_Pressure_Isotropic_Klein( reax_system* system,
- simulation_data* data )
+void Compute_Pressure_Isotropic_Klein( reax_system* system,
+ simulation_data* data )
{
int i;
reax_atom *p_atom;
rvec dx;
- // IMPORTANT: This function assumes that current kinetic energy and
+ // IMPORTANT: This function assumes that current kinetic energy and
// the center of mass of the system is already computed before.
data->iso_bar.P = 2.0 * data->my_en.e_kin;
@@ -378,11 +378,11 @@ void Compute_Pressure_Isotropic_Klein( reax_system* system,
rvec_ScaledSum(dx,1.0,p_atom->x,-1.0,data->xcm);
data->iso_bar.P += ( -F_CONV * rvec_Dot(p_atom->f, dx) );
}
-
+
data->iso_bar.P /= (3.0 * system->my_box.V);
-
- // IMPORTANT: In Klein's paper, it is stated that a dU/dV term needs
- // to be added when there are long-range interactions or long-range
+
+ // IMPORTANT: In Klein's paper, it is stated that a dU/dV term needs
+ // to be added when there are long-range interactions or long-range
// corrections to short-range interactions present.
// We may want to add that for more accuracy.
}
@@ -395,22 +395,22 @@ void Compute_Pressure( reax_system* system, simulation_data* data )
rtensor temp;
rtensor_MakeZero( data->flex_bar.P );
-
+
for( i = 0; i < system->N; ++i ) {
p_atom = &( system->my_atoms[i] );
-
+
// Distance_on_T3_Gen( data->rcm, p_atom->x, &(system->my_box), &dx );
-
+
rvec_OuterProduct( temp, p_atom->v, p_atom->v );
- rtensor_ScaledAdd( data->flex_bar.P,
- system->reax_param.sbp[ p_atom->type ].mass, temp );
-
+ rtensor_ScaledAdd( data->flex_bar.P,
+ system->reax_param.sbp[ p_atom->type ].mass, temp );
+
// rvec_OuterProduct(temp,workspace->virial_forces[i],p_atom->x); //dx);
rtensor_ScaledAdd( data->flex_bar.P, -F_CONV, temp );
}
-
+
rtensor_Scale( data->flex_bar.P, 1.0 / system->my_box.V, data->flex_bar.P );
-
+
data->iso_bar.P = rtensor_Trace( data->flex_bar.P ) / 3.0;
}
*/
diff --git a/src/USER-REAXC/reaxc_system_props.h b/src/USER-REAXC/reaxc_system_props.h
index fb1cc40e605c4cab543430ed9c6045701269c4d8..544b051dce5d1a39895394fc7cdb973629e6a15f 100644
--- a/src/USER-REAXC/reaxc_system_props.h
+++ b/src/USER-REAXC/reaxc_system_props.h
@@ -14,12 +14,12 @@
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -37,10 +37,10 @@ void Compute_System_Energy( reax_system*, simulation_data*, MPI_Comm );
void Compute_Total_Mass( reax_system*, simulation_data*, MPI_Comm );
-void Compute_Center_of_Mass( reax_system*, simulation_data*,
- mpi_datatypes*, MPI_Comm );
+void Compute_Center_of_Mass( reax_system*, simulation_data*,
+ mpi_datatypes*, MPI_Comm );
-void Compute_Pressure( reax_system*, control_params*,
- simulation_data*, mpi_datatypes* );
+void Compute_Pressure( reax_system*, control_params*,
+ simulation_data*, mpi_datatypes* );
//void Compute_Pressure( reax_system*, simulation_data* );
#endif
diff --git a/src/USER-REAXC/reaxc_tool_box.cpp b/src/USER-REAXC/reaxc_tool_box.cpp
index 1846500e0587275cd7bdba8fa640684ba6c7b3ef..bee7bb6efe5ecb06c5689aae49f6abc4761bd773 100644
--- a/src/USER-REAXC/reaxc_tool_box.cpp
+++ b/src/USER-REAXC/reaxc_tool_box.cpp
@@ -14,12 +14,12 @@
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -42,22 +42,22 @@ int SumScan( int n, int me, int root, MPI_Comm comm )
if( me == root ) {
MPI_Comm_size( comm, &wsize );
nbuf = (int *) calloc( wsize, sizeof(int) );
-
+
MPI_Gather( &n, 1, MPI_INT, nbuf, 1, MPI_INT, root, comm );
-
+
for( i = 0; i < wsize-1; ++i ) {
nbuf[i+1] += nbuf[i];
}
-
+
MPI_Scatter( nbuf, 1, MPI_INT, &my_order, 1, MPI_INT, root, comm );
-
+
free( nbuf );
}
else {
MPI_Gather( &n, 1, MPI_INT, nbuf, 1, MPI_INT, root, comm );
MPI_Scatter( nbuf, 1, MPI_INT, &my_order, 1, MPI_INT, root, comm );
}
-
+
return my_order;
}
@@ -72,7 +72,7 @@ void SumScanB( int n, int me, int wsize, int root, MPI_Comm comm, int *nbuf )
for( i = 0; i < wsize-1; ++i )
nbuf[i+1] += nbuf[i];
}
-
+
MPI_Bcast( nbuf, wsize, MPI_INT, root, comm );
}
#endif
@@ -85,12 +85,12 @@ void Transform( rvec x1, simulation_box *box, char flag, rvec x2 )
real tmp;
// printf(">x1: (%lf, %lf, %lf)\n",x1[0],x1[1],x1[2]);
-
+
if (flag > 0) {
for (i=0; i < 3; i++) {
tmp = 0.0;
for (j=0; j < 3; j++)
- tmp += box->trans[i][j]*x1[j];
+ tmp += box->trans[i][j]*x1[j];
x2[i] = tmp;
}
}
@@ -98,18 +98,18 @@ void Transform( rvec x1, simulation_box *box, char flag, rvec x2 )
for (i=0; i < 3; i++) {
tmp = 0.0;
for (j=0; j < 3; j++)
- tmp += box->trans_inv[i][j]*x1[j];
+ tmp += box->trans_inv[i][j]*x1[j];
x2[i] = tmp;
}
}
- // printf(">x2: (%lf, %lf, %lf)\n", x2[0], x2[1], x2[2]);
+ // printf(">x2: (%lf, %lf, %lf)\n", x2[0], x2[1], x2[2]);
}
void Transform_to_UnitBox( rvec x1, simulation_box *box, char flag, rvec x2 )
{
Transform( x1, box, flag, x2 );
-
+
x2[0] /= box->box_norms[0];
x2[1] /= box->box_norms[1];
x2[2] /= box->box_norms[2];
@@ -122,21 +122,21 @@ void Fit_to_Periodic_Box( simulation_box *box, rvec *p )
int i;
for( i = 0; i < 3; ++i ) {
- if( (*p)[i] < box->min[i] ) {
+ if( (*p)[i] < box->min[i] ) {
/* handle lower coords */
while( (*p)[i] < box->min[i] )
- (*p)[i] += box->box_norms[i];
+ (*p)[i] += box->box_norms[i];
}
else if( (*p)[i] >= box->max[i] ) {
/* handle higher coords */
while( (*p)[i] >= box->max[i] )
- (*p)[i] -= box->box_norms[i];
+ (*p)[i] -= box->box_norms[i];
}
}
}
#if defined(PURE_REAX)
-/* determine the touch point, tp, of a box to
+/* determine the touch point, tp, of a box to
its neighbor denoted by the relative coordinate rl */
inline void Box_Touch_Point( simulation_box *box, ivec rl, rvec tp )
{
@@ -156,8 +156,8 @@ inline void Box_Touch_Point( simulation_box *box, ivec rl, rvec tp )
/* assumes orthogonal box */
inline int is_Inside_Box( simulation_box *box, rvec p )
{
- if( p[0] < box->min[0] || p[0] >= box->max[0] ||
- p[1] < box->min[1] || p[1] >= box->max[1] ||
+ if( p[0] < box->min[0] || p[0] >= box->max[0] ||
+ p[1] < box->min[1] || p[1] >= box->max[1] ||
p[2] < box->min[2] || p[2] >= box->max[2] )
return 0;
@@ -173,11 +173,11 @@ inline int iown_midpoint( simulation_box *box, rvec p1, rvec p2 )
midp[1] = (p1[1] + p2[1]) / 2;
midp[2] = (p1[2] + p2[2]) / 2;
- if( midp[0] < box->min[0] || midp[0] >= box->max[0] ||
- midp[1] < box->min[1] || midp[1] >= box->max[1] ||
+ if( midp[0] < box->min[0] || midp[0] >= box->max[0] ||
+ midp[1] < box->min[1] || midp[1] >= box->max[1] ||
midp[2] < box->min[2] || midp[2] >= box->max[2] )
return 0;
-
+
return 1;
}
@@ -185,13 +185,13 @@ inline int iown_midpoint( simulation_box *box, rvec p1, rvec p2 )
/**************** from grid.c ****************/
/* finds the closest point of grid cell cj to ci.
- no need to consider periodic boundary conditions as in the serial case
+ no need to consider periodic boundary conditions as in the serial case
because the box of a process is not periodic in itself */
inline void GridCell_Closest_Point( grid_cell *gci, grid_cell *gcj,
- ivec ci, ivec cj, rvec cp )
+ ivec ci, ivec cj, rvec cp )
{
int d;
-
+
for( d = 0; d < 3; d++ )
if( cj[d] > ci[d] )
cp[d] = gcj->min[d];
@@ -206,7 +206,7 @@ inline void GridCell_Closest_Point( grid_cell *gci, grid_cell *gcj,
inline void GridCell_to_Box_Points( grid_cell *gc, ivec rl, rvec cp, rvec fp )
{
int d;
-
+
for( d = 0; d < 3; ++d )
if( rl[d] == -1 ) {
cp[d] = gc->min[d];
@@ -218,7 +218,7 @@ inline void GridCell_to_Box_Points( grid_cell *gc, ivec rl, rvec cp, rvec fp )
else{
cp[d] = gc->max[d];
fp[d] = gc->min[d];
- }
+ }
}
@@ -269,12 +269,12 @@ int is_Valid_Serial( storage *workspace, int serial )
{
// if( workspace->map_serials[ serial ] < 0 )
// {
- // fprintf( stderr, "CONECT line includes invalid pdb serial number %d.\n",
+ // fprintf( stderr, "CONECT line includes invalid pdb serial number %d.\n",
// serial );
// fprintf( stderr, "Please correct the input file.Terminating...\n" );
// MPI_Abort( MPI_COMM_WORLD, INVALID_INPUT );
// }
-
+
return SUCCESS;
}
@@ -283,11 +283,11 @@ int is_Valid_Serial( storage *workspace, int serial )
int Check_Input_Range( int val, int lo, int hi, char *message, MPI_Comm comm )
{
if( val < lo || val > hi ) {
- fprintf( stderr, "%s\nInput %d - Out of range %d-%d. Terminating...\n",
- message, val, lo, hi );
+ fprintf( stderr, "%s\nInput %d - Out of range %d-%d. Terminating...\n",
+ message, val, lo, hi );
MPI_Abort( comm, INVALID_INPUT );
}
-
+
return 1;
}
@@ -297,7 +297,7 @@ void Trim_Spaces( char *element )
int i, j;
for( i = 0; element[i] == ' '; ++i ); // skip initial space chars
-
+
for( j = i; j < (int)(strlen(element)) && element[j] != ' '; ++j )
element[j-i] = toupper( element[j] ); // make uppercase, offset to 0
element[j-i] = 0; // finalize the string
@@ -307,7 +307,7 @@ void Trim_Spaces( char *element )
/************ from system_props.c *************/
struct timeval tim;
real t_end;
-
+
real Get_Time( )
{
gettimeofday(&tim, NULL );
@@ -316,7 +316,7 @@ real Get_Time( )
real Get_Timing_Info( real t_start )
-{
+{
gettimeofday(&tim, NULL );
t_end = tim.tv_sec + (tim.tv_usec / 1000000.0);
return (t_end - t_start);
@@ -343,7 +343,7 @@ int Get_Atom_Type( reax_interaction *reax_param, char *s, MPI_Comm comm )
fprintf( stderr, "Unknown atom type %s. Terminating...\n", s );
MPI_Abort( comm, UNKNOWN_ATOM_TYPE );
-
+
return -1;
}
@@ -393,7 +393,7 @@ int Tokenize( char* s, char*** tok )
int count=0;
strncpy( test, s, MAX_LINE );
-
+
for( word = strtok(test, sep); word; word = strtok(NULL, sep) ) {
strncpy( (*tok)[count], word, MAX_LINE );
count++;
@@ -411,15 +411,15 @@ void *smalloc( long n, char *name, MPI_Comm comm )
if( n <= 0 ) {
fprintf( stderr, "WARNING: trying to allocate %ld bytes for array %s. ",
- n, name );
+ n, name );
fprintf( stderr, "returning NULL.\n" );
return NULL;
}
ptr = malloc( n );
if( ptr == NULL ) {
- fprintf( stderr, "ERROR: failed to allocate %ld bytes for array %s",
- n, name );
+ fprintf( stderr, "ERROR: failed to allocate %ld bytes for array %s",
+ n, name );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
@@ -434,22 +434,22 @@ void *scalloc( int n, int size, char *name, MPI_Comm comm )
if( n <= 0 ) {
fprintf( stderr, "WARNING: trying to allocate %d elements for array %s. ",
- n, name );
+ n, name );
fprintf( stderr, "returning NULL.\n" );
return NULL;
}
if( size <= 0 ) {
fprintf( stderr, "WARNING: elements size for array %s is %d. ",
- name, size );
+ name, size );
fprintf( stderr, "returning NULL.\n" );
return NULL;
}
ptr = calloc( n, size );
if( ptr == NULL ) {
- fprintf( stderr, "ERROR: failed to allocate %d bytes for array %s",
- n*size, name );
+ fprintf( stderr, "ERROR: failed to allocate %d bytes for array %s",
+ n*size, name );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
@@ -462,11 +462,10 @@ void sfree( void *ptr, char *name )
{
if( ptr == NULL ) {
fprintf( stderr, "WARNING: trying to free the already NULL pointer %s!\n",
- name );
+ name );
return;
}
-
+
free( ptr );
ptr = NULL;
}
-
diff --git a/src/USER-REAXC/reaxc_tool_box.h b/src/USER-REAXC/reaxc_tool_box.h
index b6666abe4f605592e0a1d0e0852e79a3bc0b068e..b9e1f4a8db7550669d9a35b177045aa2cfaa8d66 100644
--- a/src/USER-REAXC/reaxc_tool_box.h
+++ b/src/USER-REAXC/reaxc_tool_box.h
@@ -14,12 +14,12 @@
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
diff --git a/src/USER-REAXC/reaxc_torsion_angles.cpp b/src/USER-REAXC/reaxc_torsion_angles.cpp
index 9b3258d8b61b3df3214b343b5352140331f8a0b7..1cbcc5892a8d3ca833ff28b5057d6dd3ee3d0aab 100644
--- a/src/USER-REAXC/reaxc_torsion_angles.cpp
+++ b/src/USER-REAXC/reaxc_torsion_angles.cpp
@@ -14,12 +14,12 @@
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -42,14 +42,14 @@
#define MIN_SINE 1e-10
real Calculate_Omega( rvec dvec_ij, real r_ij,
- rvec dvec_jk, real r_jk,
- rvec dvec_kl, real r_kl,
- rvec dvec_li, real r_li,
- three_body_interaction_data *p_ijk,
- three_body_interaction_data *p_jkl,
- rvec dcos_omega_di, rvec dcos_omega_dj,
- rvec dcos_omega_dk, rvec dcos_omega_dl,
- output_controls *out_control )
+ rvec dvec_jk, real r_jk,
+ rvec dvec_kl, real r_kl,
+ rvec dvec_li, real r_li,
+ three_body_interaction_data *p_ijk,
+ three_body_interaction_data *p_jkl,
+ rvec dcos_omega_di, rvec dcos_omega_dj,
+ rvec dcos_omega_dk, rvec dcos_omega_dl,
+ output_controls *out_control )
{
real unnorm_cos_omega, unnorm_sin_omega, omega;
real sin_ijk, cos_ijk, sin_jkl, cos_jkl;
@@ -63,13 +63,13 @@ real Calculate_Omega( rvec dvec_ij, real r_ij,
cos_jkl = cos( p_jkl->theta );
/* omega */
- unnorm_cos_omega = -rvec_Dot(dvec_ij, dvec_jk) * rvec_Dot(dvec_jk, dvec_kl) +
+ unnorm_cos_omega = -rvec_Dot(dvec_ij, dvec_jk) * rvec_Dot(dvec_jk, dvec_kl) +
SQR( r_jk ) * rvec_Dot( dvec_ij, dvec_kl );
rvec_Cross( cross_jk_kl, dvec_jk, dvec_kl );
unnorm_sin_omega = -r_jk * rvec_Dot( dvec_ij, cross_jk_kl );
- omega = atan2( unnorm_sin_omega, unnorm_cos_omega );
+ omega = atan2( unnorm_sin_omega, unnorm_cos_omega );
/* derivatives */
@@ -91,16 +91,16 @@ real Calculate_Omega( rvec dvec_ij, real r_ij,
poem = 2.0 * r_ij * r_kl * sin_ijk * sin_jkl;
if( poem < 1e-20 ) poem = 1e-20;
- tel = SQR( r_ij ) + SQR( r_jk ) + SQR( r_kl ) - SQR( r_li ) -
- 2.0 * ( r_ij * r_jk * cos_ijk - r_ij * r_kl * cos_ijk * cos_jkl +
- r_jk * r_kl * cos_jkl );
-
+ tel = SQR( r_ij ) + SQR( r_jk ) + SQR( r_kl ) - SQR( r_li ) -
+ 2.0 * ( r_ij * r_jk * cos_ijk - r_ij * r_kl * cos_ijk * cos_jkl +
+ r_jk * r_kl * cos_jkl );
+
arg = tel / poem;
if( arg > 1.0 ) arg = 1.0;
if( arg < -1.0 ) arg = -1.0;
- /* fprintf( out_control->etor,
+ /* fprintf( out_control->etor,
"%12.6f%12.6f%12.6f%12.6f%12.6f%12.6f%12.6f%12.6f%12.6f\n",
htra, htrb, htrc, hthd, hthe, hnra, hnrc, hnhd, hnhe );
fprintf( out_control->etor, "%12.6f%12.6f%12.6f\n",
@@ -114,10 +114,10 @@ real Calculate_Omega( rvec dvec_ij, real r_ij,
fprintf( out_control->etor, "%12.6f%12.6f%12.6f\n",
poem, tel, arg ); */
/* fprintf( out_control->etor, "%12.6f%12.6f%12.6f\n",
- -p_ijk->dcos_dk[0]/sin_ijk, -p_ijk->dcos_dk[1]/sin_ijk,
+ -p_ijk->dcos_dk[0]/sin_ijk, -p_ijk->dcos_dk[1]/sin_ijk,
-p_ijk->dcos_dk[2]/sin_ijk );
fprintf( out_control->etor, "%12.6f%12.6f%12.6f\n",
- -p_jkl->dcos_dk[0]/sin_jkl, -p_jkl->dcos_dk[1]/sin_jkl,
+ -p_jkl->dcos_dk[0]/sin_jkl, -p_jkl->dcos_dk[1]/sin_jkl,
-p_jkl->dcos_dk[2]/sin_jkl );*/
if( sin_ijk >= 0 && sin_ijk <= MIN_SINE ) sin_ijk = MIN_SINE;
@@ -131,15 +131,15 @@ real Calculate_Omega( rvec dvec_ij, real r_ij,
rvec_Scale( dcos_omega_di, 2.0 / poem, dcos_omega_di );
// dcos_omega_dj
- rvec_ScaledSum( dcos_omega_dj,-(htra-arg*hnra)/r_ij, dvec_ij,
- -htrb / r_jk, dvec_jk );
+ rvec_ScaledSum( dcos_omega_dj,-(htra-arg*hnra)/r_ij, dvec_ij,
+ -htrb / r_jk, dvec_jk );
rvec_ScaledAdd( dcos_omega_dj,-(hthd-arg*hnhd)/sin_ijk, p_ijk->dcos_dj );
rvec_ScaledAdd( dcos_omega_dj,-(hthe-arg*hnhe)/sin_jkl, p_jkl->dcos_di );
rvec_Scale( dcos_omega_dj, 2.0 / poem, dcos_omega_dj );
// dcos_omega_dk
- rvec_ScaledSum( dcos_omega_dk,-(htrc-arg*hnrc)/r_kl, dvec_kl,
- htrb / r_jk, dvec_jk );
+ rvec_ScaledSum( dcos_omega_dk,-(htrc-arg*hnrc)/r_kl, dvec_kl,
+ htrb / r_jk, dvec_jk );
rvec_ScaledAdd( dcos_omega_dk,-(hthd-arg*hnhd)/sin_ijk, p_ijk->dcos_di );
rvec_ScaledAdd( dcos_omega_dk,-(hthe-arg*hnhe)/sin_jkl, p_jkl->dcos_dj );
rvec_Scale( dcos_omega_dk, 2.0 / poem, dcos_omega_dk );
@@ -149,14 +149,14 @@ real Calculate_Omega( rvec dvec_ij, real r_ij,
rvec_ScaledAdd( dcos_omega_dl,-(hthe-arg*hnhe)/sin_jkl, p_jkl->dcos_dk );
rvec_Scale( dcos_omega_dl, 2.0 / poem, dcos_omega_dl );
- return omega;
+ return omega;
}
-void Torsion_Angles( reax_system *system, control_params *control,
- simulation_data *data, storage *workspace,
- reax_list **lists, output_controls *out_control )
+void Torsion_Angles( reax_system *system, control_params *control,
+ simulation_data *data, storage *workspace,
+ reax_list **lists, output_controls *out_control )
{
int i, j, k, l, pi, pj, pk, pl, pij, plk, natoms;
int type_i, type_j, type_k, type_l;
@@ -215,418 +215,418 @@ void Torsion_Angles( reax_system *system, control_params *control,
Delta_j = workspace->Delta_boc[j];
start_j = Start_Index(j, bonds);
end_j = End_Index(j, bonds);
-
+
for( pk = start_j; pk < end_j; ++pk ) {
pbond_jk = &( bonds->select.bond_list[pk] );
k = pbond_jk->nbr;
bo_jk = &( pbond_jk->bo_data );
BOA_jk = bo_jk->BO - control->thb_cut;
-
+
/* see if there are any 3-body interactions involving j&k
- where j is the central atom. Otherwise there is no point in
- trying to form a 4-body interaction out of this neighborhood */
- if( system->my_atoms[j].orig_id < system->my_atoms[k].orig_id &&
- bo_jk->BO > control->thb_cut/*0*/ && Num_Entries(pk, thb_intrs) ) {
- start_k = Start_Index(k, bonds);
- end_k = End_Index(k, bonds);
- pj = pbond_jk->sym_index; // pj points to j on k's list
-
- /* do the same check as above:
- are there any 3-body interactions involving k&j
- where k is the central atom */
- if( Num_Entries(pj, thb_intrs) ) {
- type_k = system->my_atoms[k].type;
- Delta_k = workspace->Delta_boc[k];
- r_jk = pbond_jk->d;
-
- start_pk = Start_Index(pk, thb_intrs );
- end_pk = End_Index(pk, thb_intrs );
- start_pj = Start_Index(pj, thb_intrs );
- end_pj = End_Index(pj, thb_intrs );
-
- exp_tor2_jk = exp( -p_tor2 * BOA_jk );
- exp_cot2_jk = exp( -p_cot2 * SQR(BOA_jk - 1.5) );
- exp_tor3_DjDk = exp( -p_tor3 * (Delta_j + Delta_k) );
- exp_tor4_DjDk = exp( p_tor4 * (Delta_j + Delta_k) );
- exp_tor34_inv = 1.0 / (1.0 + exp_tor3_DjDk + exp_tor4_DjDk);
- f11_DjDk = (2.0 + exp_tor3_DjDk) * exp_tor34_inv;
-
-
- /* pick i up from j-k interaction where j is the central atom */
- for( pi = start_pk; pi < end_pk; ++pi ) {
- p_ijk = &( thb_intrs->select.three_body_list[pi] );
- pij = p_ijk->pthb; // pij is pointer to i on j's bond_list
- pbond_ij = &( bonds->select.bond_list[pij] );
- bo_ij = &( pbond_ij->bo_data );
-
-
- if( bo_ij->BO > control->thb_cut/*0*/ ) {
- i = p_ijk->thb;
- type_i = system->my_atoms[i].type;
- r_ij = pbond_ij->d;
- BOA_ij = bo_ij->BO - control->thb_cut;
-
- theta_ijk = p_ijk->theta;
- sin_ijk = sin( theta_ijk );
- cos_ijk = cos( theta_ijk );
- //tan_ijk_i = 1. / tan( theta_ijk );
- if( sin_ijk >= 0 && sin_ijk <= MIN_SINE )
- tan_ijk_i = cos_ijk / MIN_SINE;
- else if( sin_ijk <= 0 && sin_ijk >= -MIN_SINE )
- tan_ijk_i = cos_ijk / -MIN_SINE;
- else tan_ijk_i = cos_ijk / sin_ijk;
-
- exp_tor2_ij = exp( -p_tor2 * BOA_ij );
- exp_cot2_ij = exp( -p_cot2 * SQR(BOA_ij -1.5) );
-
-
- /* pick l up from j-k interaction where k is the central atom */
- for( pl = start_pj; pl < end_pj; ++pl ) {
- p_jkl = &( thb_intrs->select.three_body_list[pl] );
- l = p_jkl->thb;
- plk = p_jkl->pthb; //pointer to l on k's bond_list!
- pbond_kl = &( bonds->select.bond_list[plk] );
- bo_kl = &( pbond_kl->bo_data );
- type_l = system->my_atoms[l].type;
- fbh = &(system->reax_param.fbp[type_i][type_j]
- [type_k][type_l]);
- fbp = &(system->reax_param.fbp[type_i][type_j]
- [type_k][type_l].prm[0]);
-
-
- if( i != l && fbh->cnt &&
- bo_kl->BO > control->thb_cut/*0*/ &&
- bo_ij->BO * bo_jk->BO * bo_kl->BO > control->thb_cut/*0*/ ){
- ++num_frb_intrs;
- r_kl = pbond_kl->d;
- BOA_kl = bo_kl->BO - control->thb_cut;
-
- theta_jkl = p_jkl->theta;
- sin_jkl = sin( theta_jkl );
- cos_jkl = cos( theta_jkl );
- //tan_jkl_i = 1. / tan( theta_jkl );
- if( sin_jkl >= 0 && sin_jkl <= MIN_SINE )
- tan_jkl_i = cos_jkl / MIN_SINE;
- else if( sin_jkl <= 0 && sin_jkl >= -MIN_SINE )
- tan_jkl_i = cos_jkl / -MIN_SINE;
- else tan_jkl_i = cos_jkl /sin_jkl;
-
- rvec_ScaledSum( dvec_li, 1., system->my_atoms[i].x,
- -1., system->my_atoms[l].x );
- r_li = rvec_Norm( dvec_li );
-
-
- /* omega and its derivative */
- omega = Calculate_Omega( pbond_ij->dvec, r_ij,
- pbond_jk->dvec, r_jk,
- pbond_kl->dvec, r_kl,
- dvec_li, r_li,
- p_ijk, p_jkl,
- dcos_omega_di, dcos_omega_dj,
- dcos_omega_dk, dcos_omega_dl,
- out_control );
-
- cos_omega = cos( omega );
- cos2omega = cos( 2. * omega );
- cos3omega = cos( 3. * omega );
- /* end omega calculations */
-
- /* torsion energy */
- exp_tor1 = exp( fbp->p_tor1 *
- SQR(2.0 - bo_jk->BO_pi - f11_DjDk) );
- exp_tor2_kl = exp( -p_tor2 * BOA_kl );
- exp_cot2_kl = exp( -p_cot2 * SQR(BOA_kl - 1.5) );
- fn10 = (1.0 - exp_tor2_ij) * (1.0 - exp_tor2_jk) *
- (1.0 - exp_tor2_kl);
-
- CV = 0.5 * ( fbp->V1 * (1.0 + cos_omega) +
- fbp->V2 * exp_tor1 * (1.0 - cos2omega) +
- fbp->V3 * (1.0 + cos3omega) );
-
- data->my_en.e_tor += e_tor = fn10 * sin_ijk * sin_jkl * CV;
-
- dfn11 = (-p_tor3 * exp_tor3_DjDk +
- (p_tor3 * exp_tor3_DjDk - p_tor4 * exp_tor4_DjDk) *
- (2.0 + exp_tor3_DjDk) * exp_tor34_inv) *
- exp_tor34_inv;
-
- CEtors1 = sin_ijk * sin_jkl * CV;
-
- CEtors2 = -fn10 * 2.0 * fbp->p_tor1 * fbp->V2 * exp_tor1 *
- (2.0 - bo_jk->BO_pi - f11_DjDk) * (1.0 - SQR(cos_omega)) *
- sin_ijk * sin_jkl;
- CEtors3 = CEtors2 * dfn11;
-
- CEtors4 = CEtors1 * p_tor2 * exp_tor2_ij *
- (1.0 - exp_tor2_jk) * (1.0 - exp_tor2_kl);
- CEtors5 = CEtors1 * p_tor2 *
- (1.0 - exp_tor2_ij) * exp_tor2_jk * (1.0 - exp_tor2_kl);
- CEtors6 = CEtors1 * p_tor2 *
- (1.0 - exp_tor2_ij) * (1.0 - exp_tor2_jk) * exp_tor2_kl;
-
- cmn = -fn10 * CV;
- CEtors7 = cmn * sin_jkl * tan_ijk_i;
- CEtors8 = cmn * sin_ijk * tan_jkl_i;
-
- CEtors9 = fn10 * sin_ijk * sin_jkl *
- (0.5 * fbp->V1 - 2.0 * fbp->V2 * exp_tor1 * cos_omega +
- 1.5 * fbp->V3 * (cos2omega + 2.0 * SQR(cos_omega)));
- /* end of torsion energy */
-
-
- /* 4-body conjugation energy */
- fn12 = exp_cot2_ij * exp_cot2_jk * exp_cot2_kl;
- data->my_en.e_con += e_con =
- fbp->p_cot1 * fn12 *
- (1.0 + (SQR(cos_omega) - 1.0) * sin_ijk * sin_jkl);
-
- Cconj = -2.0 * fn12 * fbp->p_cot1 * p_cot2 *
- (1.0 + (SQR(cos_omega) - 1.0) * sin_ijk * sin_jkl);
-
- CEconj1 = Cconj * (BOA_ij - 1.5e0);
- CEconj2 = Cconj * (BOA_jk - 1.5e0);
- CEconj3 = Cconj * (BOA_kl - 1.5e0);
-
- CEconj4 = -fbp->p_cot1 * fn12 *
- (SQR(cos_omega) - 1.0) * sin_jkl * tan_ijk_i;
- CEconj5 = -fbp->p_cot1 * fn12 *
- (SQR(cos_omega) - 1.0) * sin_ijk * tan_jkl_i;
- CEconj6 = 2.0 * fbp->p_cot1 * fn12 *
- cos_omega * sin_ijk * sin_jkl;
- /* end 4-body conjugation energy */
-
- /* forces */
- bo_jk->Cdbopi += CEtors2;
- workspace->CdDelta[j] += CEtors3;
- workspace->CdDelta[k] += CEtors3;
- bo_ij->Cdbo += (CEtors4 + CEconj1);
- bo_jk->Cdbo += (CEtors5 + CEconj2);
- bo_kl->Cdbo += (CEtors6 + CEconj3);
-
- if( control->virial == 0 ) {
- /* dcos_theta_ijk */
- rvec_ScaledAdd( workspace->f[i],
- CEtors7 + CEconj4, p_ijk->dcos_dk );
- rvec_ScaledAdd( workspace->f[j],
- CEtors7 + CEconj4, p_ijk->dcos_dj );
- rvec_ScaledAdd( workspace->f[k],
- CEtors7 + CEconj4, p_ijk->dcos_di );
-
- /* dcos_theta_jkl */
- rvec_ScaledAdd( workspace->f[j],
- CEtors8 + CEconj5, p_jkl->dcos_di );
- rvec_ScaledAdd( workspace->f[k],
- CEtors8 + CEconj5, p_jkl->dcos_dj );
- rvec_ScaledAdd( workspace->f[l],
- CEtors8 + CEconj5, p_jkl->dcos_dk );
-
- /* dcos_omega */
- rvec_ScaledAdd( workspace->f[i],
- CEtors9 + CEconj6, dcos_omega_di );
- rvec_ScaledAdd( workspace->f[j],
- CEtors9 + CEconj6, dcos_omega_dj );
- rvec_ScaledAdd( workspace->f[k],
- CEtors9 + CEconj6, dcos_omega_dk );
- rvec_ScaledAdd( workspace->f[l],
- CEtors9 + CEconj6, dcos_omega_dl );
- }
- else {
- ivec_Sum(rel_box_jl, pbond_jk->rel_box, pbond_kl->rel_box);
-
- /* dcos_theta_ijk */
- rvec_Scale( force, CEtors7 + CEconj4, p_ijk->dcos_dk );
- rvec_Add( workspace->f[i], force );
- rvec_iMultiply( ext_press, pbond_ij->rel_box, force );
- rvec_Add( data->my_ext_press, ext_press );
-
- rvec_ScaledAdd( workspace->f[j],
- CEtors7 + CEconj4, p_ijk->dcos_dj );
-
- rvec_Scale( force, CEtors7 + CEconj4, p_ijk->dcos_di );
- rvec_Add( workspace->f[k], force );
- rvec_iMultiply( ext_press, pbond_jk->rel_box, force );
- rvec_Add( data->my_ext_press, ext_press );
-
-
- /* dcos_theta_jkl */
- rvec_ScaledAdd( workspace->f[j],
- CEtors8 + CEconj5, p_jkl->dcos_di );
-
- rvec_Scale( force, CEtors8 + CEconj5, p_jkl->dcos_dj );
- rvec_Add( workspace->f[k], force );
- rvec_iMultiply( ext_press, pbond_jk->rel_box, force );
- rvec_Add( data->my_ext_press, ext_press );
-
- rvec_Scale( force, CEtors8 + CEconj5, p_jkl->dcos_dk );
- rvec_Add( workspace->f[l], force );
- rvec_iMultiply( ext_press, rel_box_jl, force );
- rvec_Add( data->my_ext_press, ext_press );
-
-
- /* dcos_omega */
- rvec_Scale( force, CEtors9 + CEconj6, dcos_omega_di );
- rvec_Add( workspace->f[i], force );
- rvec_iMultiply( ext_press, pbond_ij->rel_box, force );
- rvec_Add( data->my_ext_press, ext_press );
-
- rvec_ScaledAdd( workspace->f[j],
- CEtors9 + CEconj6, dcos_omega_dj );
-
- rvec_Scale( force, CEtors9 + CEconj6, dcos_omega_dk );
- rvec_Add( workspace->f[k], force );
- rvec_iMultiply( ext_press, pbond_jk->rel_box, force );
- rvec_Add( data->my_ext_press, ext_press );
-
- rvec_Scale( force, CEtors9 + CEconj6, dcos_omega_dl );
- rvec_Add( workspace->f[l], force );
- rvec_iMultiply( ext_press, rel_box_jl, force );
- rvec_Add( data->my_ext_press, ext_press );
- }
-
- /* tally into per-atom virials */
- if( system->pair_ptr->vflag_atom || system->pair_ptr->evflag) {
-
- // acquire vectors
- rvec_ScaledSum( delil, 1., system->my_atoms[l].x,
- -1., system->my_atoms[i].x );
- rvec_ScaledSum( deljl, 1., system->my_atoms[l].x,
- -1., system->my_atoms[j].x );
- rvec_ScaledSum( delkl, 1., system->my_atoms[l].x,
- -1., system->my_atoms[k].x );
- // dcos_theta_ijk
- rvec_Scale( fi_tmp, CEtors7 + CEconj4, p_ijk->dcos_dk );
- rvec_Scale( fj_tmp, CEtors7 + CEconj4, p_ijk->dcos_dj );
- rvec_Scale( fk_tmp, CEtors7 + CEconj4, p_ijk->dcos_di );
-
- // dcos_theta_jkl
- rvec_ScaledAdd( fj_tmp, CEtors8 + CEconj5, p_jkl->dcos_di );
- rvec_ScaledAdd( fk_tmp, CEtors8 + CEconj5, p_jkl->dcos_dj );
-
- // dcos_omega
- rvec_ScaledAdd( fi_tmp, CEtors9 + CEconj6, dcos_omega_di );
- rvec_ScaledAdd( fj_tmp, CEtors9 + CEconj6, dcos_omega_dj );
- rvec_ScaledAdd( fk_tmp, CEtors9 + CEconj6, dcos_omega_dk );
-
- // tally
- eng_tmp = e_tor + e_con;
- if( system->pair_ptr->evflag)
- system->pair_ptr->ev_tally(j,k,natoms,1,eng_tmp,0.0,0.0,0.0,0.0,0.0);
- if( system->pair_ptr->vflag_atom)
- system->pair_ptr->v_tally4(i,j,k,l,fi_tmp,fj_tmp,fk_tmp,delil,deljl,delkl);
- }
-
+ where j is the central atom. Otherwise there is no point in
+ trying to form a 4-body interaction out of this neighborhood */
+ if( system->my_atoms[j].orig_id < system->my_atoms[k].orig_id &&
+ bo_jk->BO > control->thb_cut/*0*/ && Num_Entries(pk, thb_intrs) ) {
+ start_k = Start_Index(k, bonds);
+ end_k = End_Index(k, bonds);
+ pj = pbond_jk->sym_index; // pj points to j on k's list
+
+ /* do the same check as above:
+ are there any 3-body interactions involving k&j
+ where k is the central atom */
+ if( Num_Entries(pj, thb_intrs) ) {
+ type_k = system->my_atoms[k].type;
+ Delta_k = workspace->Delta_boc[k];
+ r_jk = pbond_jk->d;
+
+ start_pk = Start_Index(pk, thb_intrs );
+ end_pk = End_Index(pk, thb_intrs );
+ start_pj = Start_Index(pj, thb_intrs );
+ end_pj = End_Index(pj, thb_intrs );
+
+ exp_tor2_jk = exp( -p_tor2 * BOA_jk );
+ exp_cot2_jk = exp( -p_cot2 * SQR(BOA_jk - 1.5) );
+ exp_tor3_DjDk = exp( -p_tor3 * (Delta_j + Delta_k) );
+ exp_tor4_DjDk = exp( p_tor4 * (Delta_j + Delta_k) );
+ exp_tor34_inv = 1.0 / (1.0 + exp_tor3_DjDk + exp_tor4_DjDk);
+ f11_DjDk = (2.0 + exp_tor3_DjDk) * exp_tor34_inv;
+
+
+ /* pick i up from j-k interaction where j is the central atom */
+ for( pi = start_pk; pi < end_pk; ++pi ) {
+ p_ijk = &( thb_intrs->select.three_body_list[pi] );
+ pij = p_ijk->pthb; // pij is pointer to i on j's bond_list
+ pbond_ij = &( bonds->select.bond_list[pij] );
+ bo_ij = &( pbond_ij->bo_data );
+
+
+ if( bo_ij->BO > control->thb_cut/*0*/ ) {
+ i = p_ijk->thb;
+ type_i = system->my_atoms[i].type;
+ r_ij = pbond_ij->d;
+ BOA_ij = bo_ij->BO - control->thb_cut;
+
+ theta_ijk = p_ijk->theta;
+ sin_ijk = sin( theta_ijk );
+ cos_ijk = cos( theta_ijk );
+ //tan_ijk_i = 1. / tan( theta_ijk );
+ if( sin_ijk >= 0 && sin_ijk <= MIN_SINE )
+ tan_ijk_i = cos_ijk / MIN_SINE;
+ else if( sin_ijk <= 0 && sin_ijk >= -MIN_SINE )
+ tan_ijk_i = cos_ijk / -MIN_SINE;
+ else tan_ijk_i = cos_ijk / sin_ijk;
+
+ exp_tor2_ij = exp( -p_tor2 * BOA_ij );
+ exp_cot2_ij = exp( -p_cot2 * SQR(BOA_ij -1.5) );
+
+
+ /* pick l up from j-k interaction where k is the central atom */
+ for( pl = start_pj; pl < end_pj; ++pl ) {
+ p_jkl = &( thb_intrs->select.three_body_list[pl] );
+ l = p_jkl->thb;
+ plk = p_jkl->pthb; //pointer to l on k's bond_list!
+ pbond_kl = &( bonds->select.bond_list[plk] );
+ bo_kl = &( pbond_kl->bo_data );
+ type_l = system->my_atoms[l].type;
+ fbh = &(system->reax_param.fbp[type_i][type_j]
+ [type_k][type_l]);
+ fbp = &(system->reax_param.fbp[type_i][type_j]
+ [type_k][type_l].prm[0]);
+
+
+ if( i != l && fbh->cnt &&
+ bo_kl->BO > control->thb_cut/*0*/ &&
+ bo_ij->BO * bo_jk->BO * bo_kl->BO > control->thb_cut/*0*/ ){
+ ++num_frb_intrs;
+ r_kl = pbond_kl->d;
+ BOA_kl = bo_kl->BO - control->thb_cut;
+
+ theta_jkl = p_jkl->theta;
+ sin_jkl = sin( theta_jkl );
+ cos_jkl = cos( theta_jkl );
+ //tan_jkl_i = 1. / tan( theta_jkl );
+ if( sin_jkl >= 0 && sin_jkl <= MIN_SINE )
+ tan_jkl_i = cos_jkl / MIN_SINE;
+ else if( sin_jkl <= 0 && sin_jkl >= -MIN_SINE )
+ tan_jkl_i = cos_jkl / -MIN_SINE;
+ else tan_jkl_i = cos_jkl /sin_jkl;
+
+ rvec_ScaledSum( dvec_li, 1., system->my_atoms[i].x,
+ -1., system->my_atoms[l].x );
+ r_li = rvec_Norm( dvec_li );
+
+
+ /* omega and its derivative */
+ omega = Calculate_Omega( pbond_ij->dvec, r_ij,
+ pbond_jk->dvec, r_jk,
+ pbond_kl->dvec, r_kl,
+ dvec_li, r_li,
+ p_ijk, p_jkl,
+ dcos_omega_di, dcos_omega_dj,
+ dcos_omega_dk, dcos_omega_dl,
+ out_control );
+
+ cos_omega = cos( omega );
+ cos2omega = cos( 2. * omega );
+ cos3omega = cos( 3. * omega );
+ /* end omega calculations */
+
+ /* torsion energy */
+ exp_tor1 = exp( fbp->p_tor1 *
+ SQR(2.0 - bo_jk->BO_pi - f11_DjDk) );
+ exp_tor2_kl = exp( -p_tor2 * BOA_kl );
+ exp_cot2_kl = exp( -p_cot2 * SQR(BOA_kl - 1.5) );
+ fn10 = (1.0 - exp_tor2_ij) * (1.0 - exp_tor2_jk) *
+ (1.0 - exp_tor2_kl);
+
+ CV = 0.5 * ( fbp->V1 * (1.0 + cos_omega) +
+ fbp->V2 * exp_tor1 * (1.0 - cos2omega) +
+ fbp->V3 * (1.0 + cos3omega) );
+
+ data->my_en.e_tor += e_tor = fn10 * sin_ijk * sin_jkl * CV;
+
+ dfn11 = (-p_tor3 * exp_tor3_DjDk +
+ (p_tor3 * exp_tor3_DjDk - p_tor4 * exp_tor4_DjDk) *
+ (2.0 + exp_tor3_DjDk) * exp_tor34_inv) *
+ exp_tor34_inv;
+
+ CEtors1 = sin_ijk * sin_jkl * CV;
+
+ CEtors2 = -fn10 * 2.0 * fbp->p_tor1 * fbp->V2 * exp_tor1 *
+ (2.0 - bo_jk->BO_pi - f11_DjDk) * (1.0 - SQR(cos_omega)) *
+ sin_ijk * sin_jkl;
+ CEtors3 = CEtors2 * dfn11;
+
+ CEtors4 = CEtors1 * p_tor2 * exp_tor2_ij *
+ (1.0 - exp_tor2_jk) * (1.0 - exp_tor2_kl);
+ CEtors5 = CEtors1 * p_tor2 *
+ (1.0 - exp_tor2_ij) * exp_tor2_jk * (1.0 - exp_tor2_kl);
+ CEtors6 = CEtors1 * p_tor2 *
+ (1.0 - exp_tor2_ij) * (1.0 - exp_tor2_jk) * exp_tor2_kl;
+
+ cmn = -fn10 * CV;
+ CEtors7 = cmn * sin_jkl * tan_ijk_i;
+ CEtors8 = cmn * sin_ijk * tan_jkl_i;
+
+ CEtors9 = fn10 * sin_ijk * sin_jkl *
+ (0.5 * fbp->V1 - 2.0 * fbp->V2 * exp_tor1 * cos_omega +
+ 1.5 * fbp->V3 * (cos2omega + 2.0 * SQR(cos_omega)));
+ /* end of torsion energy */
+
+
+ /* 4-body conjugation energy */
+ fn12 = exp_cot2_ij * exp_cot2_jk * exp_cot2_kl;
+ data->my_en.e_con += e_con =
+ fbp->p_cot1 * fn12 *
+ (1.0 + (SQR(cos_omega) - 1.0) * sin_ijk * sin_jkl);
+
+ Cconj = -2.0 * fn12 * fbp->p_cot1 * p_cot2 *
+ (1.0 + (SQR(cos_omega) - 1.0) * sin_ijk * sin_jkl);
+
+ CEconj1 = Cconj * (BOA_ij - 1.5e0);
+ CEconj2 = Cconj * (BOA_jk - 1.5e0);
+ CEconj3 = Cconj * (BOA_kl - 1.5e0);
+
+ CEconj4 = -fbp->p_cot1 * fn12 *
+ (SQR(cos_omega) - 1.0) * sin_jkl * tan_ijk_i;
+ CEconj5 = -fbp->p_cot1 * fn12 *
+ (SQR(cos_omega) - 1.0) * sin_ijk * tan_jkl_i;
+ CEconj6 = 2.0 * fbp->p_cot1 * fn12 *
+ cos_omega * sin_ijk * sin_jkl;
+ /* end 4-body conjugation energy */
+
+ /* forces */
+ bo_jk->Cdbopi += CEtors2;
+ workspace->CdDelta[j] += CEtors3;
+ workspace->CdDelta[k] += CEtors3;
+ bo_ij->Cdbo += (CEtors4 + CEconj1);
+ bo_jk->Cdbo += (CEtors5 + CEconj2);
+ bo_kl->Cdbo += (CEtors6 + CEconj3);
+
+ if( control->virial == 0 ) {
+ /* dcos_theta_ijk */
+ rvec_ScaledAdd( workspace->f[i],
+ CEtors7 + CEconj4, p_ijk->dcos_dk );
+ rvec_ScaledAdd( workspace->f[j],
+ CEtors7 + CEconj4, p_ijk->dcos_dj );
+ rvec_ScaledAdd( workspace->f[k],
+ CEtors7 + CEconj4, p_ijk->dcos_di );
+
+ /* dcos_theta_jkl */
+ rvec_ScaledAdd( workspace->f[j],
+ CEtors8 + CEconj5, p_jkl->dcos_di );
+ rvec_ScaledAdd( workspace->f[k],
+ CEtors8 + CEconj5, p_jkl->dcos_dj );
+ rvec_ScaledAdd( workspace->f[l],
+ CEtors8 + CEconj5, p_jkl->dcos_dk );
+
+ /* dcos_omega */
+ rvec_ScaledAdd( workspace->f[i],
+ CEtors9 + CEconj6, dcos_omega_di );
+ rvec_ScaledAdd( workspace->f[j],
+ CEtors9 + CEconj6, dcos_omega_dj );
+ rvec_ScaledAdd( workspace->f[k],
+ CEtors9 + CEconj6, dcos_omega_dk );
+ rvec_ScaledAdd( workspace->f[l],
+ CEtors9 + CEconj6, dcos_omega_dl );
+ }
+ else {
+ ivec_Sum(rel_box_jl, pbond_jk->rel_box, pbond_kl->rel_box);
+
+ /* dcos_theta_ijk */
+ rvec_Scale( force, CEtors7 + CEconj4, p_ijk->dcos_dk );
+ rvec_Add( workspace->f[i], force );
+ rvec_iMultiply( ext_press, pbond_ij->rel_box, force );
+ rvec_Add( data->my_ext_press, ext_press );
+
+ rvec_ScaledAdd( workspace->f[j],
+ CEtors7 + CEconj4, p_ijk->dcos_dj );
+
+ rvec_Scale( force, CEtors7 + CEconj4, p_ijk->dcos_di );
+ rvec_Add( workspace->f[k], force );
+ rvec_iMultiply( ext_press, pbond_jk->rel_box, force );
+ rvec_Add( data->my_ext_press, ext_press );
+
+
+ /* dcos_theta_jkl */
+ rvec_ScaledAdd( workspace->f[j],
+ CEtors8 + CEconj5, p_jkl->dcos_di );
+
+ rvec_Scale( force, CEtors8 + CEconj5, p_jkl->dcos_dj );
+ rvec_Add( workspace->f[k], force );
+ rvec_iMultiply( ext_press, pbond_jk->rel_box, force );
+ rvec_Add( data->my_ext_press, ext_press );
+
+ rvec_Scale( force, CEtors8 + CEconj5, p_jkl->dcos_dk );
+ rvec_Add( workspace->f[l], force );
+ rvec_iMultiply( ext_press, rel_box_jl, force );
+ rvec_Add( data->my_ext_press, ext_press );
+
+
+ /* dcos_omega */
+ rvec_Scale( force, CEtors9 + CEconj6, dcos_omega_di );
+ rvec_Add( workspace->f[i], force );
+ rvec_iMultiply( ext_press, pbond_ij->rel_box, force );
+ rvec_Add( data->my_ext_press, ext_press );
+
+ rvec_ScaledAdd( workspace->f[j],
+ CEtors9 + CEconj6, dcos_omega_dj );
+
+ rvec_Scale( force, CEtors9 + CEconj6, dcos_omega_dk );
+ rvec_Add( workspace->f[k], force );
+ rvec_iMultiply( ext_press, pbond_jk->rel_box, force );
+ rvec_Add( data->my_ext_press, ext_press );
+
+ rvec_Scale( force, CEtors9 + CEconj6, dcos_omega_dl );
+ rvec_Add( workspace->f[l], force );
+ rvec_iMultiply( ext_press, rel_box_jl, force );
+ rvec_Add( data->my_ext_press, ext_press );
+ }
+
+ /* tally into per-atom virials */
+ if( system->pair_ptr->vflag_atom || system->pair_ptr->evflag) {
+
+ // acquire vectors
+ rvec_ScaledSum( delil, 1., system->my_atoms[l].x,
+ -1., system->my_atoms[i].x );
+ rvec_ScaledSum( deljl, 1., system->my_atoms[l].x,
+ -1., system->my_atoms[j].x );
+ rvec_ScaledSum( delkl, 1., system->my_atoms[l].x,
+ -1., system->my_atoms[k].x );
+ // dcos_theta_ijk
+ rvec_Scale( fi_tmp, CEtors7 + CEconj4, p_ijk->dcos_dk );
+ rvec_Scale( fj_tmp, CEtors7 + CEconj4, p_ijk->dcos_dj );
+ rvec_Scale( fk_tmp, CEtors7 + CEconj4, p_ijk->dcos_di );
+
+ // dcos_theta_jkl
+ rvec_ScaledAdd( fj_tmp, CEtors8 + CEconj5, p_jkl->dcos_di );
+ rvec_ScaledAdd( fk_tmp, CEtors8 + CEconj5, p_jkl->dcos_dj );
+
+ // dcos_omega
+ rvec_ScaledAdd( fi_tmp, CEtors9 + CEconj6, dcos_omega_di );
+ rvec_ScaledAdd( fj_tmp, CEtors9 + CEconj6, dcos_omega_dj );
+ rvec_ScaledAdd( fk_tmp, CEtors9 + CEconj6, dcos_omega_dk );
+
+ // tally
+ eng_tmp = e_tor + e_con;
+ if( system->pair_ptr->evflag)
+ system->pair_ptr->ev_tally(j,k,natoms,1,eng_tmp,0.0,0.0,0.0,0.0,0.0);
+ if( system->pair_ptr->vflag_atom)
+ system->pair_ptr->v_tally4(i,j,k,l,fi_tmp,fj_tmp,fk_tmp,delil,deljl,delkl);
+ }
+
#ifdef TEST_ENERGY
- /* fprintf( out_control->etor,
- "%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f\n",
- r_ij, r_jk, r_kl, cos_ijk, cos_jkl, sin_ijk, sin_jkl );
- fprintf( out_control->etor, "%12.8f\n", dfn11 ); */
- /* fprintf( out_control->etor,
- "%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f\n",
- CEtors2, CEtors3, CEtors4, CEtors5, CEtors6,
- CEtors7, CEtors8, CEtors9 ); */
- /* fprintf( out_control->etor,
- "%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f\n",
- htra, htrb, htrc, hthd, hthe, hnra, hnrc, hnhd, hnhe ); */
- /* fprintf( out_control->etor,
- "%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f\n",
- CEconj1, CEconj2, CEconj3, CEconj4, CEconj5, CEconj6 ); */
-
- /* fprintf( out_control->etor, "%12.6f%12.6f%12.6f%12.6f\n",
- fbp->V1, fbp->V2, fbp->V3, fbp->p_tor1 );*/
-
- fprintf(out_control->etor,
- //"%6d%6d%6d%6d%24.15e%24.15e%24.15e%24.15e\n",
- "%6d%6d%6d%6d%12.4f%12.4f%12.4f%12.4f\n",
- system->my_atoms[i].orig_id,system->my_atoms[j].orig_id,
- system->my_atoms[k].orig_id,system->my_atoms[l].orig_id,
- RAD2DEG(omega), BOA_jk, e_tor, data->my_en.e_tor );
-
- fprintf(out_control->econ,
- //"%6d%6d%6d%6d%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e\n",
- "%6d%6d%6d%6d%12.4f%12.4f%12.4f%12.4f%12.4f%12.4f\n",
- system->my_atoms[i].orig_id,system->my_atoms[j].orig_id,
- system->my_atoms[k].orig_id,system->my_atoms[l].orig_id,
- RAD2DEG(omega), BOA_ij, BOA_jk, BOA_kl,
- e_con, data->my_en.e_con );
+ /* fprintf( out_control->etor,
+ "%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f\n",
+ r_ij, r_jk, r_kl, cos_ijk, cos_jkl, sin_ijk, sin_jkl );
+ fprintf( out_control->etor, "%12.8f\n", dfn11 ); */
+ /* fprintf( out_control->etor,
+ "%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f\n",
+ CEtors2, CEtors3, CEtors4, CEtors5, CEtors6,
+ CEtors7, CEtors8, CEtors9 ); */
+ /* fprintf( out_control->etor,
+ "%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f\n",
+ htra, htrb, htrc, hthd, hthe, hnra, hnrc, hnhd, hnhe ); */
+ /* fprintf( out_control->etor,
+ "%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f\n",
+ CEconj1, CEconj2, CEconj3, CEconj4, CEconj5, CEconj6 ); */
+
+ /* fprintf( out_control->etor, "%12.6f%12.6f%12.6f%12.6f\n",
+ fbp->V1, fbp->V2, fbp->V3, fbp->p_tor1 );*/
+
+ fprintf(out_control->etor,
+ //"%6d%6d%6d%6d%24.15e%24.15e%24.15e%24.15e\n",
+ "%6d%6d%6d%6d%12.4f%12.4f%12.4f%12.4f\n",
+ system->my_atoms[i].orig_id,system->my_atoms[j].orig_id,
+ system->my_atoms[k].orig_id,system->my_atoms[l].orig_id,
+ RAD2DEG(omega), BOA_jk, e_tor, data->my_en.e_tor );
+
+ fprintf(out_control->econ,
+ //"%6d%6d%6d%6d%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e\n",
+ "%6d%6d%6d%6d%12.4f%12.4f%12.4f%12.4f%12.4f%12.4f\n",
+ system->my_atoms[i].orig_id,system->my_atoms[j].orig_id,
+ system->my_atoms[k].orig_id,system->my_atoms[l].orig_id,
+ RAD2DEG(omega), BOA_ij, BOA_jk, BOA_kl,
+ e_con, data->my_en.e_con );
#endif
-
+
#ifdef TEST_FORCES
- /* Torsion Forces */
- Add_dBOpinpi2( system, lists, j, pk, CEtors2, 0.0,
- workspace->f_tor, workspace->f_tor );
- Add_dDelta( system, lists, j, CEtors3, workspace->f_tor );
- Add_dDelta( system, lists, k, CEtors3, workspace->f_tor );
- Add_dBO( system, lists, j, pij, CEtors4, workspace->f_tor );
- Add_dBO( system, lists, j, pk, CEtors5, workspace->f_tor );
- Add_dBO( system, lists, k, plk, CEtors6, workspace->f_tor );
-
- rvec_ScaledAdd( workspace->f_tor[i],
- CEtors7, p_ijk->dcos_dk );
- rvec_ScaledAdd( workspace->f_tor[j],
- CEtors7, p_ijk->dcos_dj );
- rvec_ScaledAdd( workspace->f_tor[k],
- CEtors7, p_ijk->dcos_di );
-
- rvec_ScaledAdd( workspace->f_tor[j],
- CEtors8, p_jkl->dcos_di );
- rvec_ScaledAdd( workspace->f_tor[k],
- CEtors8, p_jkl->dcos_dj );
- rvec_ScaledAdd( workspace->f_tor[l],
- CEtors8, p_jkl->dcos_dk );
-
- rvec_ScaledAdd( workspace->f_tor[i],
- CEtors9, dcos_omega_di );
- rvec_ScaledAdd( workspace->f_tor[j],
- CEtors9, dcos_omega_dj );
- rvec_ScaledAdd( workspace->f_tor[k],
- CEtors9, dcos_omega_dk );
- rvec_ScaledAdd( workspace->f_tor[l],
- CEtors9, dcos_omega_dl );
-
- /* Conjugation Forces */
- Add_dBO( system, lists, j, pij, CEconj1, workspace->f_con );
- Add_dBO( system, lists, j, pk, CEconj2, workspace->f_con );
- Add_dBO( system, lists, k, plk, CEconj3, workspace->f_con );
-
- rvec_ScaledAdd( workspace->f_con[i],
- CEconj4, p_ijk->dcos_dk );
- rvec_ScaledAdd( workspace->f_con[j],
- CEconj4, p_ijk->dcos_dj );
- rvec_ScaledAdd( workspace->f_con[k],
- CEconj4, p_ijk->dcos_di );
-
- rvec_ScaledAdd( workspace->f_con[j],
- CEconj5, p_jkl->dcos_di );
- rvec_ScaledAdd( workspace->f_con[k],
- CEconj5, p_jkl->dcos_dj );
- rvec_ScaledAdd( workspace->f_con[l],
- CEconj5, p_jkl->dcos_dk );
-
- rvec_ScaledAdd( workspace->f_con[i],
- CEconj6, dcos_omega_di );
- rvec_ScaledAdd( workspace->f_con[j],
- CEconj6, dcos_omega_dj );
- rvec_ScaledAdd( workspace->f_con[k],
- CEconj6, dcos_omega_dk );
- rvec_ScaledAdd( workspace->f_con[l],
- CEconj6, dcos_omega_dl );
+ /* Torsion Forces */
+ Add_dBOpinpi2( system, lists, j, pk, CEtors2, 0.0,
+ workspace->f_tor, workspace->f_tor );
+ Add_dDelta( system, lists, j, CEtors3, workspace->f_tor );
+ Add_dDelta( system, lists, k, CEtors3, workspace->f_tor );
+ Add_dBO( system, lists, j, pij, CEtors4, workspace->f_tor );
+ Add_dBO( system, lists, j, pk, CEtors5, workspace->f_tor );
+ Add_dBO( system, lists, k, plk, CEtors6, workspace->f_tor );
+
+ rvec_ScaledAdd( workspace->f_tor[i],
+ CEtors7, p_ijk->dcos_dk );
+ rvec_ScaledAdd( workspace->f_tor[j],
+ CEtors7, p_ijk->dcos_dj );
+ rvec_ScaledAdd( workspace->f_tor[k],
+ CEtors7, p_ijk->dcos_di );
+
+ rvec_ScaledAdd( workspace->f_tor[j],
+ CEtors8, p_jkl->dcos_di );
+ rvec_ScaledAdd( workspace->f_tor[k],
+ CEtors8, p_jkl->dcos_dj );
+ rvec_ScaledAdd( workspace->f_tor[l],
+ CEtors8, p_jkl->dcos_dk );
+
+ rvec_ScaledAdd( workspace->f_tor[i],
+ CEtors9, dcos_omega_di );
+ rvec_ScaledAdd( workspace->f_tor[j],
+ CEtors9, dcos_omega_dj );
+ rvec_ScaledAdd( workspace->f_tor[k],
+ CEtors9, dcos_omega_dk );
+ rvec_ScaledAdd( workspace->f_tor[l],
+ CEtors9, dcos_omega_dl );
+
+ /* Conjugation Forces */
+ Add_dBO( system, lists, j, pij, CEconj1, workspace->f_con );
+ Add_dBO( system, lists, j, pk, CEconj2, workspace->f_con );
+ Add_dBO( system, lists, k, plk, CEconj3, workspace->f_con );
+
+ rvec_ScaledAdd( workspace->f_con[i],
+ CEconj4, p_ijk->dcos_dk );
+ rvec_ScaledAdd( workspace->f_con[j],
+ CEconj4, p_ijk->dcos_dj );
+ rvec_ScaledAdd( workspace->f_con[k],
+ CEconj4, p_ijk->dcos_di );
+
+ rvec_ScaledAdd( workspace->f_con[j],
+ CEconj5, p_jkl->dcos_di );
+ rvec_ScaledAdd( workspace->f_con[k],
+ CEconj5, p_jkl->dcos_dj );
+ rvec_ScaledAdd( workspace->f_con[l],
+ CEconj5, p_jkl->dcos_dk );
+
+ rvec_ScaledAdd( workspace->f_con[i],
+ CEconj6, dcos_omega_di );
+ rvec_ScaledAdd( workspace->f_con[j],
+ CEconj6, dcos_omega_dj );
+ rvec_ScaledAdd( workspace->f_con[k],
+ CEconj6, dcos_omega_dk );
+ rvec_ScaledAdd( workspace->f_con[l],
+ CEconj6, dcos_omega_dl );
#endif
- } // pl check ends
- } // pl loop ends
- } // pi check ends
- } // pi loop ends
- } // k-j neighbor check ends
+ } // pl check ends
+ } // pl loop ends
+ } // pi check ends
+ } // pi loop ends
+ } // k-j neighbor check ends
} // j<k && j-k neighbor check ends
} // pk loop ends
} // j loop
-
+
#if defined(DEBUG)
fprintf( stderr, "Number of torsion angles: %d\n", num_frb_intrs );
- fprintf( stderr, "Torsion Energy: %g\t Conjugation Energy: %g\n",
- data->my_en.e_tor, data->my_en.e_con );
+ fprintf( stderr, "Torsion Energy: %g\t Conjugation Energy: %g\n",
+ data->my_en.e_tor, data->my_en.e_con );
fprintf( stderr, "4body: ext_press (%12.6f %12.6f %12.6f)\n",
- data->ext_press[0], data->ext_press[1], data->ext_press[2] );
+ data->ext_press[0], data->ext_press[1], data->ext_press[2] );
#endif
}
diff --git a/src/USER-REAXC/reaxc_torsion_angles.h b/src/USER-REAXC/reaxc_torsion_angles.h
index a34ef7709e6d7651c2238bb2af2f6245aaafa4cd..755e8c65325ced98e9c00b22895087276e65f9f3 100644
--- a/src/USER-REAXC/reaxc_torsion_angles.h
+++ b/src/USER-REAXC/reaxc_torsion_angles.h
@@ -14,12 +14,12 @@
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -30,6 +30,6 @@
#include "reaxc_types.h"
void Torsion_Angles( reax_system*, control_params*, simulation_data*,
- storage*, reax_list**, output_controls* );
+ storage*, reax_list**, output_controls* );
#endif
diff --git a/src/USER-REAXC/reaxc_traj.cpp b/src/USER-REAXC/reaxc_traj.cpp
index 88a35c7354fb9887a7c33766f676ec89a54d1ede..8fbd26217fc5c8a154faa36a99a69a5b1f23aab5 100644
--- a/src/USER-REAXC/reaxc_traj.cpp
+++ b/src/USER-REAXC/reaxc_traj.cpp
@@ -14,12 +14,12 @@
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -38,7 +38,7 @@
#if defined(PURE_REAX)
int Set_My_Trajectory_View( MPI_File trj, int offset, MPI_Datatype etype,
- MPI_Comm comm, int my_rank, int my_n, int big_n )
+ MPI_Comm comm, int my_rank, int my_n, int big_n )
{
int my_disp;
int length[3];
@@ -70,83 +70,83 @@ int Set_My_Trajectory_View( MPI_File trj, int offset, MPI_Datatype etype,
MPI_Type_commit( &view );
MPI_File_set_view( trj, offset, etype, view, "native", MPI_INFO_NULL );
-
+
return my_disp;
}
#endif
-int Reallocate_Output_Buffer( output_controls *out_control, int req_space,
- MPI_Comm comm )
+int Reallocate_Output_Buffer( output_controls *out_control, int req_space,
+ MPI_Comm comm )
{
- if( out_control->buffer_len > 0 )
+ if( out_control->buffer_len > 0 )
free( out_control->buffer );
out_control->buffer_len = (int)(req_space*SAFE_ZONE);
out_control->buffer = (char*) malloc(out_control->buffer_len*sizeof(char));
if( out_control->buffer == NULL ) {
- fprintf( stderr,
- "insufficient memory for required buffer size %d. terminating!\n",
- (int) (req_space*SAFE_ZONE) );
+ fprintf( stderr,
+ "insufficient memory for required buffer size %d. terminating!\n",
+ (int) (req_space*SAFE_ZONE) );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
-
+
return SUCCESS;
}
-void Write_Skip_Line( output_controls *out_control, mpi_datatypes *mpi_data,
- int my_rank, int skip, int num_section )
+void Write_Skip_Line( output_controls *out_control, mpi_datatypes *mpi_data,
+ int my_rank, int skip, int num_section )
{
#if defined(PURE_REAX)
MPI_Status status;
if( out_control->traj_method == MPI_TRAJ ) {
- MPI_File_set_view( out_control->trj, out_control->trj_offset,
- mpi_data->header_line, mpi_data->header_line,
- "native", MPI_INFO_NULL );
+ MPI_File_set_view( out_control->trj, out_control->trj_offset,
+ mpi_data->header_line, mpi_data->header_line,
+ "native", MPI_INFO_NULL );
if( my_rank == MASTER_NODE ) {
- sprintf( out_control->line, INT2_LINE, "chars_to_skip_section:",
- skip, num_section );
- MPI_File_write( out_control->trj, out_control->line, 1,
- mpi_data->header_line, &status );
+ sprintf( out_control->line, INT2_LINE, "chars_to_skip_section:",
+ skip, num_section );
+ MPI_File_write( out_control->trj, out_control->line, 1,
+ mpi_data->header_line, &status );
}
out_control->trj_offset += HEADER_LINE_LEN;
}
else {
if( my_rank == MASTER_NODE )
- fprintf( out_control->strj, INT2_LINE,
- "chars_to_skip_section:", skip, num_section );
+ fprintf( out_control->strj, INT2_LINE,
+ "chars_to_skip_section:", skip, num_section );
}
#elif defined(LAMMPS_REAX)
if( my_rank == MASTER_NODE )
- fprintf( out_control->strj, INT2_LINE,
- "chars_to_skip_section:", skip, num_section );
+ fprintf( out_control->strj, INT2_LINE,
+ "chars_to_skip_section:", skip, num_section );
#endif
}
-int Write_Header( reax_system *system, control_params *control,
- output_controls *out_control, mpi_datatypes *mpi_data )
+int Write_Header( reax_system *system, control_params *control,
+ output_controls *out_control, mpi_datatypes *mpi_data )
{
int num_hdr_lines, my_hdr_lines, buffer_req;
MPI_Status status;
- char ensembles[ens_N][25] = { "NVE", "NVT", "fully flexible NPT",
- "semi isotropic NPT", "isotropic NPT" };
- char reposition[3][25] = { "fit to periodic box", "CoM to center of box",
- "CoM to origin" };
+ char ensembles[ens_N][25] = { "NVE", "NVT", "fully flexible NPT",
+ "semi isotropic NPT", "isotropic NPT" };
+ char reposition[3][25] = { "fit to periodic box", "CoM to center of box",
+ "CoM to origin" };
char t_regime[3][25] = { "T-coupling only", "step-wise", "constant slope" };
char traj_methods[TF_N][10] = { "custom", "xyz" };
- char atom_formats[8][40] = { "none", "invalid", "invalid", "invalid",
- "xyz_q",
- "xyz_q_fxfyfz",
- "xyz_q_vxvyvz",
- "detailed_atom_info" };
- char bond_formats[3][30] = { "none",
- "basic_bond_info",
- "detailed_bond_info" };
+ char atom_formats[8][40] = { "none", "invalid", "invalid", "invalid",
+ "xyz_q",
+ "xyz_q_fxfyfz",
+ "xyz_q_vxvyvz",
+ "detailed_atom_info" };
+ char bond_formats[3][30] = { "none",
+ "basic_bond_info",
+ "detailed_bond_info" };
char angle_formats[2][30] = { "none", "basic_angle_info" };
/* set header lengths */
@@ -161,172 +161,172 @@ int Write_Header( reax_system *system, control_params *control,
/* clear the contents of line & buffer */
out_control->line[0] = 0;
out_control->buffer[0] = 0;
-
+
/* to skip the header */
- sprintf( out_control->line, INT_LINE, "chars_to_skip_header:",
- (num_hdr_lines-1) * HEADER_LINE_LEN );
+ sprintf( out_control->line, INT_LINE, "chars_to_skip_header:",
+ (num_hdr_lines-1) * HEADER_LINE_LEN );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
+
/* general simulation info */
- sprintf( out_control->line, STR_LINE, "simulation_name:",
- out_control->traj_title );
+ sprintf( out_control->line, STR_LINE, "simulation_name:",
+ out_control->traj_title );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
+
sprintf( out_control->line, INT_LINE, "number_of_atoms:", system->bigN );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
- sprintf( out_control->line, STR_LINE, "ensemble_type:",
- ensembles[ control->ensemble ] );
+
+ sprintf( out_control->line, STR_LINE, "ensemble_type:",
+ ensembles[ control->ensemble ] );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
- sprintf( out_control->line, INT_LINE, "number_of_steps:",
- control->nsteps );
+
+ sprintf( out_control->line, INT_LINE, "number_of_steps:",
+ control->nsteps );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
- sprintf( out_control->line, REAL_LINE, "timestep_length_(in_fs):",
- control->dt * 1000 );
+
+ sprintf( out_control->line, REAL_LINE, "timestep_length_(in_fs):",
+ control->dt * 1000 );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
+
/* restart info */
- sprintf( out_control->line, STR_LINE, "is_this_a_restart?:",
- (control->restart ? "yes" : "no") );
+ sprintf( out_control->line, STR_LINE, "is_this_a_restart?:",
+ (control->restart ? "yes" : "no") );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
- //sprintf( out_control->line, STR_LINE, "restarted_from_file:",
+
+ //sprintf( out_control->line, STR_LINE, "restarted_from_file:",
// (control->restart ? control->restart_from : "NA") );
//strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
- //sprintf( out_control->line, STR_LINE, "kept_restart_velocities?:",
+
+ //sprintf( out_control->line, STR_LINE, "kept_restart_velocities?:",
// (control->restart ? (control->random_vel ? "no":"yes"):"NA") );
//strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
- sprintf( out_control->line, STR_LINE, "write_restart_files?:",
- ((out_control->restart_freq > 0) ? "yes" : "no") );
+
+ sprintf( out_control->line, STR_LINE, "write_restart_files?:",
+ ((out_control->restart_freq > 0) ? "yes" : "no") );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
- sprintf( out_control->line, INT_LINE, "frequency_to_write_restarts:",
- out_control->restart_freq );
+
+ sprintf( out_control->line, INT_LINE, "frequency_to_write_restarts:",
+ out_control->restart_freq );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
+
/* preferences */
- sprintf( out_control->line, STR_LINE, "tabulate_long_range_intrs?:",
- (control->tabulate ? "yes" : "no") );
+ sprintf( out_control->line, STR_LINE, "tabulate_long_range_intrs?:",
+ (control->tabulate ? "yes" : "no") );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
+
sprintf( out_control->line, INT_LINE, "table_size:", control->tabulate );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
- sprintf( out_control->line, STR_LINE, "restrict_bonds?:",
- (control->restrict_bonds ? "yes" : "no") );
+
+ sprintf( out_control->line, STR_LINE, "restrict_bonds?:",
+ (control->restrict_bonds ? "yes" : "no") );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
+
sprintf( out_control->line, INT_LINE, "bond_restriction_length:",
- control->restrict_bonds );
+ control->restrict_bonds );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
- sprintf( out_control->line, STR_LINE, "reposition_atoms?:",
- reposition[control->reposition_atoms] );
+
+ sprintf( out_control->line, STR_LINE, "reposition_atoms?:",
+ reposition[control->reposition_atoms] );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
- sprintf( out_control->line, INT_LINE, "remove_CoM_velocity?:",
- (control->ensemble==NVE) ? 0 : control->remove_CoM_vel);
+
+ sprintf( out_control->line, INT_LINE, "remove_CoM_velocity?:",
+ (control->ensemble==NVE) ? 0 : control->remove_CoM_vel);
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
-
+
+
/* cut-off values */
- sprintf( out_control->line, REAL_LINE, "bonded_intr_dist_cutoff:",
- control->bond_cut );
+ sprintf( out_control->line, REAL_LINE, "bonded_intr_dist_cutoff:",
+ control->bond_cut );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
- sprintf( out_control->line, REAL_LINE, "nonbonded_intr_dist_cutoff:",
- control->nonb_cut );
+
+ sprintf( out_control->line, REAL_LINE, "nonbonded_intr_dist_cutoff:",
+ control->nonb_cut );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
- sprintf( out_control->line, REAL_LINE, "hbond_dist_cutoff:",
- control->hbond_cut );
+
+ sprintf( out_control->line, REAL_LINE, "hbond_dist_cutoff:",
+ control->hbond_cut );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
- sprintf( out_control->line, REAL_LINE, "reax_bond_threshold:",
- control->bo_cut );
+
+ sprintf( out_control->line, REAL_LINE, "reax_bond_threshold:",
+ control->bo_cut );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
- sprintf( out_control->line, REAL_LINE, "physical_bond_threshold:",
- control->bg_cut );
+
+ sprintf( out_control->line, REAL_LINE, "physical_bond_threshold:",
+ control->bg_cut );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
- sprintf( out_control->line, REAL_LINE, "valence_angle_threshold:",
- control->thb_cut );
+
+ sprintf( out_control->line, REAL_LINE, "valence_angle_threshold:",
+ control->thb_cut );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
+
sprintf( out_control->line, SCI_LINE, "QEq_tolerance:", control->q_err );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
+
/* temperature controls */
sprintf( out_control->line, REAL_LINE, "initial_temperature:",
- control->T_init );
+ control->T_init );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
- sprintf( out_control->line, REAL_LINE, "target_temperature:",
- control->T_final );
+
+ sprintf( out_control->line, REAL_LINE, "target_temperature:",
+ control->T_final );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
- sprintf( out_control->line, REAL_LINE, "thermal_inertia:",
- control->Tau_T );
+
+ sprintf( out_control->line, REAL_LINE, "thermal_inertia:",
+ control->Tau_T );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
- sprintf( out_control->line, STR_LINE, "temperature_regime:",
- t_regime[ control->T_mode ] );
+
+ sprintf( out_control->line, STR_LINE, "temperature_regime:",
+ t_regime[ control->T_mode ] );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
- sprintf( out_control->line, REAL_LINE, "temperature_change_rate_(K/ps):",
- control->T_rate / control->T_freq );
+
+ sprintf( out_control->line, REAL_LINE, "temperature_change_rate_(K/ps):",
+ control->T_rate / control->T_freq );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
+
/* pressure controls */
- sprintf( out_control->line, REAL3_LINE, "target_pressure_(GPa):",
- control->P[0], control->P[1], control->P[2] );
+ sprintf( out_control->line, REAL3_LINE, "target_pressure_(GPa):",
+ control->P[0], control->P[1], control->P[2] );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
- sprintf( out_control->line, REAL3_LINE, "virial_inertia:",
- control->Tau_P[0], control->Tau_P[1], control->Tau_P[2] );
+
+ sprintf( out_control->line, REAL3_LINE, "virial_inertia:",
+ control->Tau_P[0], control->Tau_P[1], control->Tau_P[2] );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
+
/* trajectory */
- sprintf( out_control->line, INT_LINE, "energy_dumping_freq:",
- out_control->energy_update_freq );
+ sprintf( out_control->line, INT_LINE, "energy_dumping_freq:",
+ out_control->energy_update_freq );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
- sprintf( out_control->line, INT_LINE, "trajectory_dumping_freq:",
- out_control->write_steps );
+
+ sprintf( out_control->line, INT_LINE, "trajectory_dumping_freq:",
+ out_control->write_steps );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
- sprintf( out_control->line, STR_LINE, "compress_trajectory_output?:",
- (out_control->traj_compress ? "yes" : "no") );
+
+ sprintf( out_control->line, STR_LINE, "compress_trajectory_output?:",
+ (out_control->traj_compress ? "yes" : "no") );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
- sprintf( out_control->line, STR_LINE, "trajectory_format:",
- traj_methods[ out_control->traj_method ] );
+
+ sprintf( out_control->line, STR_LINE, "trajectory_format:",
+ traj_methods[ out_control->traj_method ] );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
- sprintf( out_control->line, STR_LINE, "atom_info:",
- atom_formats[ out_control->atom_info ] );
+
+ sprintf( out_control->line, STR_LINE, "atom_info:",
+ atom_formats[ out_control->atom_info ] );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
- sprintf( out_control->line, STR_LINE, "bond_info:",
- bond_formats[ out_control->bond_info ] );
+
+ sprintf( out_control->line, STR_LINE, "bond_info:",
+ bond_formats[ out_control->bond_info ] );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
- sprintf( out_control->line, STR_LINE, "angle_info:",
- angle_formats[ out_control->angle_info ] );
+
+ sprintf( out_control->line, STR_LINE, "angle_info:",
+ angle_formats[ out_control->angle_info ] );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
+
/* analysis */
- //sprintf( out_control->line, STR_LINE, "molecular_analysis:",
+ //sprintf( out_control->line, STR_LINE, "molecular_analysis:",
// (control->molec_anal ? "yes" : "no") );
//strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
- sprintf( out_control->line, INT_LINE, "molecular_analysis_frequency:",
- control->molecular_analysis );
+
+ sprintf( out_control->line, INT_LINE, "molecular_analysis_frequency:",
+ control->molecular_analysis );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
}
@@ -334,12 +334,12 @@ int Write_Header( reax_system *system, control_params *control,
#if defined(PURE_REAX)
if( out_control->traj_method == MPI_TRAJ ) {
out_control->trj_offset = 0;
- Set_My_Trajectory_View( out_control->trj,
- out_control->trj_offset, mpi_data->header_line,
- mpi_data->world, system->my_rank,
- my_hdr_lines, num_hdr_lines );
- MPI_File_write_all( out_control->trj, out_control->buffer,
- num_hdr_lines, mpi_data->header_line, &status );
+ Set_My_Trajectory_View( out_control->trj,
+ out_control->trj_offset, mpi_data->header_line,
+ mpi_data->world, system->my_rank,
+ my_hdr_lines, num_hdr_lines );
+ MPI_File_write_all( out_control->trj, out_control->buffer,
+ num_hdr_lines, mpi_data->header_line, &status );
out_control->trj_offset = (num_hdr_lines) * HEADER_LINE_LEN;
}
else {
@@ -350,13 +350,13 @@ int Write_Header( reax_system *system, control_params *control,
if( system->my_rank == MASTER_NODE )
fprintf( out_control->strj, "%s", out_control->buffer );
#endif
-
+
return SUCCESS;
}
int Write_Init_Desc( reax_system *system, control_params *control,
- output_controls *out_control, mpi_datatypes *mpi_data )
+ output_controls *out_control, mpi_datatypes *mpi_data )
{
int i, me, np, cnt, buffer_len, buffer_req;
reax_atom *p_atom;
@@ -367,9 +367,9 @@ int Write_Init_Desc( reax_system *system, control_params *control,
np = system->wsize;
/* skip info */
- Write_Skip_Line( out_control, mpi_data, me,
- system->bigN * INIT_DESC_LEN, system->bigN );
-
+ Write_Skip_Line( out_control, mpi_data, me,
+ system->bigN * INIT_DESC_LEN, system->bigN );
+
if( out_control->traj_method == REG_TRAJ && me == MASTER_NODE )
buffer_req = system->bigN * INIT_DESC_LEN + 1;
else buffer_req = system->n * INIT_DESC_LEN + 1;
@@ -381,51 +381,51 @@ int Write_Init_Desc( reax_system *system, control_params *control,
out_control->buffer[0] = 0;
for( i = 0; i < system->n; ++i ) {
p_atom = &( system->my_atoms[i] );
- sprintf( out_control->line, INIT_DESC,
- p_atom->orig_id, p_atom->type, p_atom->name,
- system->reax_param.sbp[ p_atom->type ].mass );
- strncpy( out_control->buffer + i*INIT_DESC_LEN,
- out_control->line, INIT_DESC_LEN+1 );
+ sprintf( out_control->line, INIT_DESC,
+ p_atom->orig_id, p_atom->type, p_atom->name,
+ system->reax_param.sbp[ p_atom->type ].mass );
+ strncpy( out_control->buffer + i*INIT_DESC_LEN,
+ out_control->line, INIT_DESC_LEN+1 );
}
#if defined(PURE_REAX)
if( out_control->traj_method == MPI_TRAJ ) {
- Set_My_Trajectory_View( out_control->trj, out_control->trj_offset,
- mpi_data->init_desc_line, mpi_data->world,
- me, system->n, system->bigN );
- MPI_File_write( out_control->trj, out_control->buffer, system->n,
- mpi_data->init_desc_line, &status );
+ Set_My_Trajectory_View( out_control->trj, out_control->trj_offset,
+ mpi_data->init_desc_line, mpi_data->world,
+ me, system->n, system->bigN );
+ MPI_File_write( out_control->trj, out_control->buffer, system->n,
+ mpi_data->init_desc_line, &status );
out_control->trj_offset += system->bigN * INIT_DESC_LEN;
}
else{
if( me != MASTER_NODE )
- MPI_Send( out_control->buffer, buffer_req-1, MPI_CHAR, MASTER_NODE,
- np * INIT_DESCS + me, mpi_data->world );
+ MPI_Send( out_control->buffer, buffer_req-1, MPI_CHAR, MASTER_NODE,
+ np * INIT_DESCS + me, mpi_data->world );
else{
buffer_len = system->n * INIT_DESC_LEN;
for( i = 0; i < np; ++i )
- if( i != MASTER_NODE ) {
- MPI_Recv( out_control->buffer + buffer_len, buffer_req - buffer_len,
- MPI_CHAR, i, np*INIT_DESCS+i, mpi_data->world, &status );
- MPI_Get_count( &status, MPI_CHAR, &cnt );
- buffer_len += cnt;
- }
+ if( i != MASTER_NODE ) {
+ MPI_Recv( out_control->buffer + buffer_len, buffer_req - buffer_len,
+ MPI_CHAR, i, np*INIT_DESCS+i, mpi_data->world, &status );
+ MPI_Get_count( &status, MPI_CHAR, &cnt );
+ buffer_len += cnt;
+ }
out_control->buffer[buffer_len] = 0;
fprintf( out_control->strj, "%s", out_control->buffer );
}
}
#elif defined(LAMMPS_REAX)
if( me != MASTER_NODE )
- MPI_Send( out_control->buffer, buffer_req-1, MPI_CHAR, MASTER_NODE,
- np * INIT_DESCS + me, mpi_data->world );
+ MPI_Send( out_control->buffer, buffer_req-1, MPI_CHAR, MASTER_NODE,
+ np * INIT_DESCS + me, mpi_data->world );
else{
buffer_len = system->n * INIT_DESC_LEN;
for( i = 0; i < np; ++i )
if( i != MASTER_NODE ) {
- MPI_Recv( out_control->buffer + buffer_len, buffer_req - buffer_len,
- MPI_CHAR, i, np*INIT_DESCS+i, mpi_data->world, &status );
- MPI_Get_count( &status, MPI_CHAR, &cnt );
- buffer_len += cnt;
+ MPI_Recv( out_control->buffer + buffer_len, buffer_req - buffer_len,
+ MPI_CHAR, i, np*INIT_DESCS+i, mpi_data->world, &status );
+ MPI_Get_count( &status, MPI_CHAR, &cnt );
+ buffer_len += cnt;
}
out_control->buffer[buffer_len] = 0;
fprintf( out_control->strj, "%s", out_control->buffer );
@@ -436,14 +436,14 @@ int Write_Init_Desc( reax_system *system, control_params *control,
}
-int Init_Traj( reax_system *system, control_params *control,
- output_controls *out_control, mpi_datatypes *mpi_data,
- char *msg )
+int Init_Traj( reax_system *system, control_params *control,
+ output_controls *out_control, mpi_datatypes *mpi_data,
+ char *msg )
{
char fname[MAX_STR];
- int atom_line_len[ NR_OPT_ATOM ] = { 0, 0, 0, 0,
- ATOM_BASIC_LEN, ATOM_wV_LEN,
- ATOM_wF_LEN, ATOM_FULL_LEN };
+ int atom_line_len[ NR_OPT_ATOM ] = { 0, 0, 0, 0,
+ ATOM_BASIC_LEN, ATOM_wV_LEN,
+ ATOM_wF_LEN, ATOM_FULL_LEN };
int bond_line_len[ NR_OPT_BOND ] = { 0, BOND_BASIC_LEN, BOND_FULL_LEN };
int angle_line_len[ NR_OPT_ANGLE ] = { 0, ANGLE_BASIC_LEN };
@@ -459,19 +459,19 @@ int Init_Traj( reax_system *system, control_params *control,
/* angles? */
out_control->angle_line_len = angle_line_len[ out_control->angle_info ];
out_control->write_angles = ( out_control->angle_line_len ? 1 : 0 );
-
+
/* allocate line & buffer space */
out_control->line = (char*) calloc( MAX_TRJ_LINE_LEN + 1, sizeof(char) );
out_control->buffer_len = 0;
out_control->buffer = NULL;
-
- /* fprintf( stderr, "p%d: init_traj: atom_line_len = %d " \
- "bond_line_len = %d, angle_line_len = %d\n" \
- "max_line = %d, max_buffer_size = %d\n",
- system->my_rank, out_control->atom_line_len,
+
+ /* fprintf( stderr, "p%d: init_traj: atom_line_len = %d " \
+ "bond_line_len = %d, angle_line_len = %d\n" \
+ "max_line = %d, max_buffer_size = %d\n",
+ system->my_rank, out_control->atom_line_len,
out_control->bond_line_len, out_control->angle_line_len,
MAX_TRJ_LINE_LEN, MAX_TRJ_BUFFER_SIZE ); */
-
+
/* write trajectory header and atom info, if applicable */
#if defined(PURE_REAX)
if( out_control->traj_method == MPI_TRAJ ) {
@@ -479,15 +479,15 @@ int Init_Traj( reax_system *system, control_params *control,
if( system->my_rank == MASTER_NODE ) {
MPI_File_delete( fname, MPI_INFO_NULL );
}
-
+
/* open a fresh trajectory file */
- if( MPI_File_open( mpi_data->world, fname,
- MPI_MODE_CREATE | MPI_MODE_WRONLY, MPI_INFO_NULL,
- &(out_control->trj) ) ) {
+ if( MPI_File_open( mpi_data->world, fname,
+ MPI_MODE_CREATE | MPI_MODE_WRONLY, MPI_INFO_NULL,
+ &(out_control->trj) ) ) {
strcpy( msg, "init_traj: unable to open trajectory file" );
return FAILURE;
}
-
+
/* build the mpi structs for trajectory */
/* header_line */
MPI_Type_contiguous( HEADER_LINE_LEN, MPI_CHAR, &(mpi_data->header_line) );
@@ -496,16 +496,16 @@ int Init_Traj( reax_system *system, control_params *control,
MPI_Type_contiguous( INIT_DESC_LEN, MPI_CHAR, &(mpi_data->init_desc_line) );
MPI_Type_commit( &(mpi_data->init_desc_line) );
/* atom */
- MPI_Type_contiguous( out_control->atom_line_len, MPI_CHAR,
- &(mpi_data->atom_line) );
+ MPI_Type_contiguous( out_control->atom_line_len, MPI_CHAR,
+ &(mpi_data->atom_line) );
MPI_Type_commit( &(mpi_data->atom_line) );
/* bonds */
- MPI_Type_contiguous( out_control->bond_line_len, MPI_CHAR,
- &(mpi_data->bond_line) );
+ MPI_Type_contiguous( out_control->bond_line_len, MPI_CHAR,
+ &(mpi_data->bond_line) );
MPI_Type_commit( &(mpi_data->bond_line) );
/* angles */
- MPI_Type_contiguous( out_control->angle_line_len, MPI_CHAR,
- &(mpi_data->angle_line) );
+ MPI_Type_contiguous( out_control->angle_line_len, MPI_CHAR,
+ &(mpi_data->angle_line) );
MPI_Type_commit( &(mpi_data->angle_line) );
}
else if( out_control->traj_method == REG_TRAJ) {
@@ -513,7 +513,7 @@ int Init_Traj( reax_system *system, control_params *control,
out_control->strj = fopen( fname, "w" );
}
else {
- strcpy( msg, "init_traj: unknown trajectory option" );
+ strcpy( msg, "init_traj: unknown trajectory option" );
return FAILURE;
}
#elif defined(LAMMPS_REAX)
@@ -522,7 +522,7 @@ int Init_Traj( reax_system *system, control_params *control,
out_control->strj = fopen( fname, "w" );
}
else {
- strcpy( msg, "init_traj: unknown trajectory option" );
+ strcpy( msg, "init_traj: unknown trajectory option" );
return FAILURE;
}
#endif
@@ -539,14 +539,14 @@ int Init_Traj( reax_system *system, control_params *control,
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d: atom descriptions written\n", system->my_rank );
#endif
-
+
return SUCCESS;
}
-int Write_Frame_Header( reax_system *system, control_params *control,
- simulation_data *data, output_controls *out_control,
- mpi_datatypes *mpi_data )
+int Write_Frame_Header( reax_system *system, control_params *control,
+ simulation_data *data, output_controls *out_control,
+ mpi_datatypes *mpi_data )
{
int me, num_frm_hdr_lines, my_frm_hdr_lines, buffer_req;
MPI_Status status;
@@ -557,7 +557,7 @@ int Write_Frame_Header( reax_system *system, control_params *control,
my_frm_hdr_lines = num_frm_hdr_lines * ( me == MASTER_NODE );
buffer_req = my_frm_hdr_lines * HEADER_LINE_LEN;
if( buffer_req > out_control->buffer_len * DANGER_ZONE )
- Reallocate_Output_Buffer( out_control, buffer_req, mpi_data->world );
+ Reallocate_Output_Buffer( out_control, buffer_req, mpi_data->world );
/* only the master node writes into trajectory header */
if( me == MASTER_NODE ) {
@@ -566,111 +566,111 @@ int Write_Frame_Header( reax_system *system, control_params *control,
out_control->buffer[0] = 0;
/* skip info */
- sprintf( out_control->line, INT_LINE, "chars_to_skip_frame_header:",
- (num_frm_hdr_lines - 1) * HEADER_LINE_LEN );
+ sprintf( out_control->line, INT_LINE, "chars_to_skip_frame_header:",
+ (num_frm_hdr_lines - 1) * HEADER_LINE_LEN );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
/* step & time */
sprintf( out_control->line, INT_LINE, "step:", data->step );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
- sprintf( out_control->line, REAL_LINE, "time_in_ps:",
- data->step * control->dt );
+
+ sprintf( out_control->line, REAL_LINE, "time_in_ps:",
+ data->step * control->dt );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
-
+
+
/* box info */
sprintf( out_control->line, REAL_LINE, "volume:", system->big_box.V );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
- sprintf( out_control->line, REAL3_LINE, "box_dimensions:",
- system->big_box.box_norms[0],
- system->big_box.box_norms[1],
- system->big_box.box_norms[2] );
+
+ sprintf( out_control->line, REAL3_LINE, "box_dimensions:",
+ system->big_box.box_norms[0],
+ system->big_box.box_norms[1],
+ system->big_box.box_norms[2] );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
- sprintf( out_control->line, REAL3_LINE,
- "coordinate_angles:", 90.0, 90.0, 90.0 );
+
+ sprintf( out_control->line, REAL3_LINE,
+ "coordinate_angles:", 90.0, 90.0, 90.0 );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
-
+
+
/* system T and P */
sprintf( out_control->line, REAL_LINE, "temperature:", data->therm.T );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
- sprintf( out_control->line, REAL_LINE, "pressure:",
- (control->ensemble==iNPT) ?
- data->iso_bar.P : data->flex_bar.P_scalar );
+
+ sprintf( out_control->line, REAL_LINE, "pressure:",
+ (control->ensemble==iNPT) ?
+ data->iso_bar.P : data->flex_bar.P_scalar );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
-
+
+
/* energies */
- sprintf( out_control->line, REAL_LINE, "total_energy:",
- data->sys_en.e_tot );
+ sprintf( out_control->line, REAL_LINE, "total_energy:",
+ data->sys_en.e_tot );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
- sprintf( out_control->line, REAL_LINE, "total_kinetic:",
- data->sys_en.e_kin );
+
+ sprintf( out_control->line, REAL_LINE, "total_kinetic:",
+ data->sys_en.e_kin );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
- sprintf( out_control->line, REAL_LINE, "total_potential:",
- data->sys_en.e_pot );
+
+ sprintf( out_control->line, REAL_LINE, "total_potential:",
+ data->sys_en.e_pot );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
- sprintf( out_control->line, REAL_LINE, "bond_energy:",
- data->sys_en.e_bond );
+
+ sprintf( out_control->line, REAL_LINE, "bond_energy:",
+ data->sys_en.e_bond );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
- sprintf( out_control->line, REAL_LINE, "atom_energy:",
- data->sys_en.e_ov + data->sys_en.e_un );
+
+ sprintf( out_control->line, REAL_LINE, "atom_energy:",
+ data->sys_en.e_ov + data->sys_en.e_un );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
- sprintf( out_control->line, REAL_LINE, "lone_pair_energy:",
- data->sys_en.e_lp );
+
+ sprintf( out_control->line, REAL_LINE, "lone_pair_energy:",
+ data->sys_en.e_lp );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
- sprintf( out_control->line, REAL_LINE, "valence_angle_energy:",
- data->sys_en.e_ang + data->sys_en.e_pen );
+
+ sprintf( out_control->line, REAL_LINE, "valence_angle_energy:",
+ data->sys_en.e_ang + data->sys_en.e_pen );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
- sprintf( out_control->line, REAL_LINE, "3-body_conjugation:",
- data->sys_en.e_coa );
+
+ sprintf( out_control->line, REAL_LINE, "3-body_conjugation:",
+ data->sys_en.e_coa );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
- sprintf( out_control->line, REAL_LINE, "hydrogen_bond_energy:",
- data->sys_en.e_hb );
+
+ sprintf( out_control->line, REAL_LINE, "hydrogen_bond_energy:",
+ data->sys_en.e_hb );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
- sprintf( out_control->line, REAL_LINE, "torsion_angle_energy:",
- data->sys_en.e_tor );
+
+ sprintf( out_control->line, REAL_LINE, "torsion_angle_energy:",
+ data->sys_en.e_tor );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
- sprintf( out_control->line, REAL_LINE, "4-body_conjugation:",
- data->sys_en.e_con );
+
+ sprintf( out_control->line, REAL_LINE, "4-body_conjugation:",
+ data->sys_en.e_con );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
- sprintf( out_control->line, REAL_LINE, "vdWaals_energy:",
- data->sys_en.e_vdW );
+
+ sprintf( out_control->line, REAL_LINE, "vdWaals_energy:",
+ data->sys_en.e_vdW );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
- sprintf( out_control->line, REAL_LINE, "electrostatics_energy:",
- data->sys_en.e_ele );
+
+ sprintf( out_control->line, REAL_LINE, "electrostatics_energy:",
+ data->sys_en.e_ele );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
-
- sprintf( out_control->line, REAL_LINE, "polarization_energy:",
- data->sys_en.e_pol );
+
+ sprintf( out_control->line, REAL_LINE, "polarization_energy:",
+ data->sys_en.e_pol );
strncat( out_control->buffer, out_control->line, HEADER_LINE_LEN+1 );
}
/* dump out the buffer */
#if defined(PURE_REAX)
- if( out_control->traj_method == MPI_TRAJ ) {
- Set_My_Trajectory_View( out_control->trj, out_control->trj_offset,
- mpi_data->header_line, mpi_data->world,
- me, my_frm_hdr_lines, num_frm_hdr_lines );
-
+ if( out_control->traj_method == MPI_TRAJ ) {
+ Set_My_Trajectory_View( out_control->trj, out_control->trj_offset,
+ mpi_data->header_line, mpi_data->world,
+ me, my_frm_hdr_lines, num_frm_hdr_lines );
+
MPI_File_write_all(out_control->trj, out_control->buffer, my_frm_hdr_lines,
- mpi_data->header_line, &status);
+ mpi_data->header_line, &status);
out_control->trj_offset += (num_frm_hdr_lines) * HEADER_LINE_LEN;
}
else {
@@ -688,7 +688,7 @@ int Write_Frame_Header( reax_system *system, control_params *control,
int Write_Atoms( reax_system *system, control_params *control,
- output_controls *out_control, mpi_datatypes *mpi_data )
+ output_controls *out_control, mpi_datatypes *mpi_data )
{
int i, me, np, line_len, buffer_len, buffer_req, cnt;
MPI_Status status;
@@ -698,8 +698,8 @@ int Write_Atoms( reax_system *system, control_params *control,
np = system->wsize;
line_len = out_control->atom_line_len;
- Write_Skip_Line( out_control, mpi_data, me,
- system->bigN*line_len, system->bigN );
+ Write_Skip_Line( out_control, mpi_data, me,
+ system->bigN*line_len, system->bigN );
if( out_control->traj_method == REG_TRAJ && me == MASTER_NODE )
buffer_req = system->bigN * line_len + 1;
@@ -715,30 +715,30 @@ int Write_Atoms( reax_system *system, control_params *control,
p_atom = &( system->my_atoms[i] );
switch( out_control->atom_info ) {
- case OPT_ATOM_BASIC:
- sprintf( out_control->line, ATOM_BASIC,
- p_atom->orig_id, p_atom->x[0], p_atom->x[1], p_atom->x[2],
- p_atom->q );
+ case OPT_ATOM_BASIC:
+ sprintf( out_control->line, ATOM_BASIC,
+ p_atom->orig_id, p_atom->x[0], p_atom->x[1], p_atom->x[2],
+ p_atom->q );
break;
case OPT_ATOM_wF:
- sprintf( out_control->line, ATOM_wF,
- p_atom->orig_id, p_atom->x[0], p_atom->x[1], p_atom->x[2],
- p_atom->f[0], p_atom->f[1], p_atom->f[2], p_atom->q );
+ sprintf( out_control->line, ATOM_wF,
+ p_atom->orig_id, p_atom->x[0], p_atom->x[1], p_atom->x[2],
+ p_atom->f[0], p_atom->f[1], p_atom->f[2], p_atom->q );
break;
case OPT_ATOM_wV:
- sprintf( out_control->line, ATOM_wV,
- p_atom->orig_id, p_atom->x[0], p_atom->x[1], p_atom->x[2],
- p_atom->v[0], p_atom->v[1], p_atom->v[2], p_atom->q );
+ sprintf( out_control->line, ATOM_wV,
+ p_atom->orig_id, p_atom->x[0], p_atom->x[1], p_atom->x[2],
+ p_atom->v[0], p_atom->v[1], p_atom->v[2], p_atom->q );
break;
case OPT_ATOM_FULL:
sprintf( out_control->line, ATOM_FULL,
- p_atom->orig_id, p_atom->x[0], p_atom->x[1], p_atom->x[2],
- p_atom->v[0], p_atom->v[1], p_atom->v[2],
- p_atom->f[0], p_atom->f[1], p_atom->f[2], p_atom->q );
+ p_atom->orig_id, p_atom->x[0], p_atom->x[1], p_atom->x[2],
+ p_atom->v[0], p_atom->v[1], p_atom->v[2],
+ p_atom->f[0], p_atom->f[1], p_atom->f[2], p_atom->q );
break;
default:
- fprintf( stderr,
- "write_traj_atoms: unknown atom trajectroy format!\n");
+ fprintf( stderr,
+ "write_traj_atoms: unknown atom trajectroy format!\n");
MPI_Abort( mpi_data->world, UNKNOWN_OPTION );
}
@@ -747,56 +747,56 @@ int Write_Atoms( reax_system *system, control_params *control,
#if defined(PURE_REAX)
if( out_control->traj_method == MPI_TRAJ ) {
- Set_My_Trajectory_View( out_control->trj, out_control->trj_offset,
- mpi_data->atom_line, mpi_data->world,
- me, system->n, system->bigN );
- MPI_File_write( out_control->trj, out_control->buffer, system->n,
- mpi_data->atom_line, &status );
+ Set_My_Trajectory_View( out_control->trj, out_control->trj_offset,
+ mpi_data->atom_line, mpi_data->world,
+ me, system->n, system->bigN );
+ MPI_File_write( out_control->trj, out_control->buffer, system->n,
+ mpi_data->atom_line, &status );
out_control->trj_offset += (system->bigN) * out_control->atom_line_len;
}
else{
if( me != MASTER_NODE )
- MPI_Send( out_control->buffer, buffer_req-1, MPI_CHAR, MASTER_NODE,
- np*ATOM_LINES+me, mpi_data->world );
+ MPI_Send( out_control->buffer, buffer_req-1, MPI_CHAR, MASTER_NODE,
+ np*ATOM_LINES+me, mpi_data->world );
else{
buffer_len = system->n * line_len;
for( i = 0; i < np; ++i )
- if( i != MASTER_NODE ) {
- MPI_Recv( out_control->buffer + buffer_len, buffer_req - buffer_len,
- MPI_CHAR, i, np*ATOM_LINES+i, mpi_data->world, &status );
- MPI_Get_count( &status, MPI_CHAR, &cnt );
- buffer_len += cnt;
- }
+ if( i != MASTER_NODE ) {
+ MPI_Recv( out_control->buffer + buffer_len, buffer_req - buffer_len,
+ MPI_CHAR, i, np*ATOM_LINES+i, mpi_data->world, &status );
+ MPI_Get_count( &status, MPI_CHAR, &cnt );
+ buffer_len += cnt;
+ }
out_control->buffer[buffer_len] = 0;
fprintf( out_control->strj, "%s", out_control->buffer );
- }
+ }
}
#elif defined(LAMMPS_REAX)
if( me != MASTER_NODE )
- MPI_Send( out_control->buffer, buffer_req-1, MPI_CHAR, MASTER_NODE,
- np*ATOM_LINES+me, mpi_data->world );
+ MPI_Send( out_control->buffer, buffer_req-1, MPI_CHAR, MASTER_NODE,
+ np*ATOM_LINES+me, mpi_data->world );
else{
buffer_len = system->n * line_len;
for( i = 0; i < np; ++i )
if( i != MASTER_NODE ) {
- MPI_Recv( out_control->buffer + buffer_len, buffer_req - buffer_len,
- MPI_CHAR, i, np*ATOM_LINES+i, mpi_data->world, &status );
- MPI_Get_count( &status, MPI_CHAR, &cnt );
- buffer_len += cnt;
+ MPI_Recv( out_control->buffer + buffer_len, buffer_req - buffer_len,
+ MPI_CHAR, i, np*ATOM_LINES+i, mpi_data->world, &status );
+ MPI_Get_count( &status, MPI_CHAR, &cnt );
+ buffer_len += cnt;
}
out_control->buffer[buffer_len] = 0;
fprintf( out_control->strj, "%s", out_control->buffer );
}
#endif
-
+
return SUCCESS;
}
-int Write_Bonds(reax_system *system, control_params *control, reax_list *bonds,
- output_controls *out_control, mpi_datatypes *mpi_data)
+int Write_Bonds(reax_system *system, control_params *control, reax_list *bonds,
+ output_controls *out_control, mpi_datatypes *mpi_data)
{
- int i, j, pj, me, np;
+ int i, j, pj, me, np;
int my_bonds, num_bonds;
int line_len, buffer_len, buffer_req, cnt;
MPI_Status status;
@@ -804,16 +804,16 @@ int Write_Bonds(reax_system *system, control_params *control, reax_list *bonds,
me = system->my_rank;
np = system->wsize;
- line_len = out_control->bond_line_len;
+ line_len = out_control->bond_line_len;
/* count the number of bonds I will write */
my_bonds = 0;
for( i=0; i < system->n; ++i )
for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj ) {
j = bonds->select.bond_list[pj].nbr;
- if( system->my_atoms[i].orig_id <= system->my_atoms[j].orig_id &&
- bonds->select.bond_list[pj].bo_data.BO >= control->bg_cut )
- ++my_bonds;
+ if( system->my_atoms[i].orig_id <= system->my_atoms[j].orig_id &&
+ bonds->select.bond_list[pj].bo_data.BO >= control->bg_cut )
+ ++my_bonds;
}
/* allreduce - total number of bonds */
@@ -827,7 +827,7 @@ int Write_Bonds(reax_system *system, control_params *control, reax_list *bonds,
if( buffer_req > out_control->buffer_len * DANGER_ZONE )
Reallocate_Output_Buffer( out_control, buffer_req, mpi_data->world );
-
+
/* fill in the buffer */
out_control->line[0] = 0;
out_control->buffer[0] = 0;
@@ -837,28 +837,28 @@ int Write_Bonds(reax_system *system, control_params *control, reax_list *bonds,
for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj ) {
bo_ij = &( bonds->select.bond_list[pj] );
j = bo_ij->nbr;
-
- if( system->my_atoms[i].orig_id <= system->my_atoms[j].orig_id &&
- bo_ij->bo_data.BO >= control->bg_cut ) {
- switch( out_control->bond_info ) {
- case OPT_BOND_BASIC:
- sprintf( out_control->line, BOND_BASIC,
- system->my_atoms[i].orig_id, system->my_atoms[j].orig_id,
- bo_ij->d, bo_ij->bo_data.BO );
- break;
- case OPT_BOND_FULL:
- sprintf( out_control->line, BOND_FULL,
- system->my_atoms[i].orig_id, system->my_atoms[j].orig_id,
- bo_ij->d, bo_ij->bo_data.BO, bo_ij->bo_data.BO_s,
- bo_ij->bo_data.BO_pi, bo_ij->bo_data.BO_pi2 );
- break;
- default:
- fprintf(stderr, "write_traj_bonds: FATAL! invalid bond_info option");
- MPI_Abort( mpi_data->world, UNKNOWN_OPTION );
- }
- strncpy( out_control->buffer + my_bonds*line_len,
- out_control->line, line_len+1 );
- ++my_bonds;
+
+ if( system->my_atoms[i].orig_id <= system->my_atoms[j].orig_id &&
+ bo_ij->bo_data.BO >= control->bg_cut ) {
+ switch( out_control->bond_info ) {
+ case OPT_BOND_BASIC:
+ sprintf( out_control->line, BOND_BASIC,
+ system->my_atoms[i].orig_id, system->my_atoms[j].orig_id,
+ bo_ij->d, bo_ij->bo_data.BO );
+ break;
+ case OPT_BOND_FULL:
+ sprintf( out_control->line, BOND_FULL,
+ system->my_atoms[i].orig_id, system->my_atoms[j].orig_id,
+ bo_ij->d, bo_ij->bo_data.BO, bo_ij->bo_data.BO_s,
+ bo_ij->bo_data.BO_pi, bo_ij->bo_data.BO_pi2 );
+ break;
+ default:
+ fprintf(stderr, "write_traj_bonds: FATAL! invalid bond_info option");
+ MPI_Abort( mpi_data->world, UNKNOWN_OPTION );
+ }
+ strncpy( out_control->buffer + my_bonds*line_len,
+ out_control->line, line_len+1 );
+ ++my_bonds;
}
}
}
@@ -866,66 +866,66 @@ int Write_Bonds(reax_system *system, control_params *control, reax_list *bonds,
#if defined(PURE_REAX)
if( out_control->traj_method == MPI_TRAJ ) {
- Set_My_Trajectory_View( out_control->trj, out_control->trj_offset,
- mpi_data->bond_line, mpi_data->world,
- me, my_bonds, num_bonds );
- MPI_File_write( out_control->trj, out_control->buffer, my_bonds,
- mpi_data->bond_line, &status );
+ Set_My_Trajectory_View( out_control->trj, out_control->trj_offset,
+ mpi_data->bond_line, mpi_data->world,
+ me, my_bonds, num_bonds );
+ MPI_File_write( out_control->trj, out_control->buffer, my_bonds,
+ mpi_data->bond_line, &status );
out_control->trj_offset += num_bonds * line_len;
}
else{
if( me != MASTER_NODE )
- MPI_Send( out_control->buffer, buffer_req-1, MPI_CHAR, MASTER_NODE,
- np*BOND_LINES+me, mpi_data->world );
+ MPI_Send( out_control->buffer, buffer_req-1, MPI_CHAR, MASTER_NODE,
+ np*BOND_LINES+me, mpi_data->world );
else{
buffer_len = my_bonds * line_len;
for( i = 0; i < np; ++i )
- if( i != MASTER_NODE ) {
- MPI_Recv( out_control->buffer + buffer_len, buffer_req - buffer_len,
- MPI_CHAR, i, np*BOND_LINES+i, mpi_data->world, &status );
- MPI_Get_count( &status, MPI_CHAR, &cnt );
- buffer_len += cnt;
- }
+ if( i != MASTER_NODE ) {
+ MPI_Recv( out_control->buffer + buffer_len, buffer_req - buffer_len,
+ MPI_CHAR, i, np*BOND_LINES+i, mpi_data->world, &status );
+ MPI_Get_count( &status, MPI_CHAR, &cnt );
+ buffer_len += cnt;
+ }
out_control->buffer[buffer_len] = 0;
fprintf( out_control->strj, "%s", out_control->buffer );
- }
+ }
}
#elif defined(LAMMPS_REAX)
if( me != MASTER_NODE )
- MPI_Send( out_control->buffer, buffer_req-1, MPI_CHAR, MASTER_NODE,
- np*BOND_LINES+me, mpi_data->world );
+ MPI_Send( out_control->buffer, buffer_req-1, MPI_CHAR, MASTER_NODE,
+ np*BOND_LINES+me, mpi_data->world );
else{
buffer_len = my_bonds * line_len;
for( i = 0; i < np; ++i )
if( i != MASTER_NODE ) {
- MPI_Recv( out_control->buffer + buffer_len, buffer_req - buffer_len,
- MPI_CHAR, i, np*BOND_LINES+i, mpi_data->world, &status );
- MPI_Get_count( &status, MPI_CHAR, &cnt );
- buffer_len += cnt;
+ MPI_Recv( out_control->buffer + buffer_len, buffer_req - buffer_len,
+ MPI_CHAR, i, np*BOND_LINES+i, mpi_data->world, &status );
+ MPI_Get_count( &status, MPI_CHAR, &cnt );
+ buffer_len += cnt;
}
out_control->buffer[buffer_len] = 0;
fprintf( out_control->strj, "%s", out_control->buffer );
- }
+ }
#endif
-
+
return SUCCESS;
}
-int Write_Angles( reax_system *system, control_params *control,
- reax_list *bonds, reax_list *thb_intrs,
- output_controls *out_control, mpi_datatypes *mpi_data )
+int Write_Angles( reax_system *system, control_params *control,
+ reax_list *bonds, reax_list *thb_intrs,
+ output_controls *out_control, mpi_datatypes *mpi_data )
{
int i, j, k, pi, pk, me, np;
int my_angles, num_angles;
int line_len, buffer_len, buffer_req, cnt;
- bond_data *bo_ij, *bo_jk;
+ bond_data *bo_ij, *bo_jk;
three_body_interaction_data *angle_ijk;
MPI_Status status;
-
+
me = system->my_rank;
np = system->wsize;
- line_len = out_control->angle_line_len;
+ line_len = out_control->angle_line_len;
/* count the number of valence angles I will output */
my_angles = 0;
@@ -933,18 +933,18 @@ int Write_Angles( reax_system *system, control_params *control,
for( pi = Start_Index(j, bonds); pi < End_Index(j, bonds); ++pi ) {
bo_ij = &(bonds->select.bond_list[pi]);
i = bo_ij->nbr;
-
+
if( bo_ij->bo_data.BO >= control->bg_cut ) // physical j&i bond
- for( pk = Start_Index( pi, thb_intrs );
- pk < End_Index( pi, thb_intrs ); ++pk ) {
- angle_ijk = &(thb_intrs->select.three_body_list[pk]);
- k = angle_ijk->thb;
- bo_jk = &(bonds->select.bond_list[ angle_ijk->pthb ]);
-
- if( system->my_atoms[i].orig_id < system->my_atoms[k].orig_id &&
- bo_jk->bo_data.BO >= control->bg_cut ) // physical j&k bond
- ++my_angles;
- }
+ for( pk = Start_Index( pi, thb_intrs );
+ pk < End_Index( pi, thb_intrs ); ++pk ) {
+ angle_ijk = &(thb_intrs->select.three_body_list[pk]);
+ k = angle_ijk->thb;
+ bo_jk = &(bonds->select.bond_list[ angle_ijk->pthb ]);
+
+ if( system->my_atoms[i].orig_id < system->my_atoms[k].orig_id &&
+ bo_jk->bo_data.BO >= control->bg_cut ) // physical j&k bond
+ ++my_angles;
+ }
}
/* total number of valences */
MPI_Allreduce(&my_angles, &num_angles, 1, MPI_INT, MPI_SUM, mpi_data->world);
@@ -966,78 +966,78 @@ int Write_Angles( reax_system *system, control_params *control,
for( pi = Start_Index(j, bonds); pi < End_Index(j, bonds); ++pi ) {
bo_ij = &(bonds->select.bond_list[pi]);
i = bo_ij->nbr;
-
+
if( bo_ij->bo_data.BO >= control->bg_cut ) // physical j&i bond
- for( pk = Start_Index( pi, thb_intrs );
- pk < End_Index( pi, thb_intrs ); ++pk ) {
- angle_ijk = &(thb_intrs->select.three_body_list[pk]);
- k = angle_ijk->thb;
- bo_jk = &(bonds->select.bond_list[ angle_ijk->pthb ]);
-
- if( system->my_atoms[i].orig_id < system->my_atoms[k].orig_id &&
- bo_jk->bo_data.BO >= control->bg_cut ) { // physical j&k bond
- sprintf( out_control->line, ANGLE_BASIC,
- system->my_atoms[i].orig_id, system->my_atoms[j].orig_id,
- system->my_atoms[k].orig_id, RAD2DEG( angle_ijk->theta ) );
-
- strncpy( out_control->buffer + my_angles*line_len,
- out_control->line, line_len+1 );
- ++my_angles;
- }
- }
+ for( pk = Start_Index( pi, thb_intrs );
+ pk < End_Index( pi, thb_intrs ); ++pk ) {
+ angle_ijk = &(thb_intrs->select.three_body_list[pk]);
+ k = angle_ijk->thb;
+ bo_jk = &(bonds->select.bond_list[ angle_ijk->pthb ]);
+
+ if( system->my_atoms[i].orig_id < system->my_atoms[k].orig_id &&
+ bo_jk->bo_data.BO >= control->bg_cut ) { // physical j&k bond
+ sprintf( out_control->line, ANGLE_BASIC,
+ system->my_atoms[i].orig_id, system->my_atoms[j].orig_id,
+ system->my_atoms[k].orig_id, RAD2DEG( angle_ijk->theta ) );
+
+ strncpy( out_control->buffer + my_angles*line_len,
+ out_control->line, line_len+1 );
+ ++my_angles;
+ }
+ }
}
#if defined(PURE_REAX)
if( out_control->traj_method == MPI_TRAJ ){
- Set_My_Trajectory_View( out_control->trj, out_control->trj_offset,
- mpi_data->angle_line, mpi_data->world,
- me, my_angles, num_angles );
- MPI_File_write( out_control->trj, out_control->buffer, my_angles,
- mpi_data->angle_line, &status );
+ Set_My_Trajectory_View( out_control->trj, out_control->trj_offset,
+ mpi_data->angle_line, mpi_data->world,
+ me, my_angles, num_angles );
+ MPI_File_write( out_control->trj, out_control->buffer, my_angles,
+ mpi_data->angle_line, &status );
out_control->trj_offset += num_angles * line_len;
}
else{
if( me != MASTER_NODE )
- MPI_Send( out_control->buffer, buffer_req-1, MPI_CHAR, MASTER_NODE,
- np*ANGLE_LINES+me, mpi_data->world );
+ MPI_Send( out_control->buffer, buffer_req-1, MPI_CHAR, MASTER_NODE,
+ np*ANGLE_LINES+me, mpi_data->world );
else{
buffer_len = my_angles * line_len;
for( i = 0; i < np; ++i )
- if( i != MASTER_NODE ) {
- MPI_Recv( out_control->buffer + buffer_len, buffer_req - buffer_len,
- MPI_CHAR, i, np*ANGLE_LINES+i, mpi_data->world, &status );
- MPI_Get_count( &status, MPI_CHAR, &cnt );
- buffer_len += cnt;
- }
+ if( i != MASTER_NODE ) {
+ MPI_Recv( out_control->buffer + buffer_len, buffer_req - buffer_len,
+ MPI_CHAR, i, np*ANGLE_LINES+i, mpi_data->world, &status );
+ MPI_Get_count( &status, MPI_CHAR, &cnt );
+ buffer_len += cnt;
+ }
out_control->buffer[buffer_len] = 0;
fprintf( out_control->strj, "%s", out_control->buffer );
}
}
#elif defined(LAMMPS_REAX)
if( me != MASTER_NODE )
- MPI_Send( out_control->buffer, buffer_req-1, MPI_CHAR, MASTER_NODE,
- np*ANGLE_LINES+me, mpi_data->world );
+ MPI_Send( out_control->buffer, buffer_req-1, MPI_CHAR, MASTER_NODE,
+ np*ANGLE_LINES+me, mpi_data->world );
else{
buffer_len = my_angles * line_len;
for( i = 0; i < np; ++i )
if( i != MASTER_NODE ) {
- MPI_Recv( out_control->buffer + buffer_len, buffer_req - buffer_len,
- MPI_CHAR, i, np*ANGLE_LINES+i, mpi_data->world, &status );
- MPI_Get_count( &status, MPI_CHAR, &cnt );
- buffer_len += cnt;
+ MPI_Recv( out_control->buffer + buffer_len, buffer_req - buffer_len,
+ MPI_CHAR, i, np*ANGLE_LINES+i, mpi_data->world, &status );
+ MPI_Get_count( &status, MPI_CHAR, &cnt );
+ buffer_len += cnt;
}
out_control->buffer[buffer_len] = 0;
fprintf( out_control->strj, "%s", out_control->buffer );
}
#endif
-
+
return SUCCESS;
}
-int Append_Frame( reax_system *system, control_params *control,
- simulation_data *data, reax_list **lists,
- output_controls *out_control, mpi_datatypes *mpi_data )
+int Append_Frame( reax_system *system, control_params *control,
+ simulation_data *data, reax_list **lists,
+ output_controls *out_control, mpi_datatypes *mpi_data )
{
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d: appending frame %d\n", system->my_rank, data->step );
@@ -1051,8 +1051,8 @@ int Append_Frame( reax_system *system, control_params *control,
Write_Bonds( system, control, (*lists + BONDS), out_control, mpi_data );
if( out_control->write_angles )
- Write_Angles( system, control, (*lists + BONDS), (*lists + THREE_BODIES),
- out_control, mpi_data );
+ Write_Angles( system, control, (*lists + BONDS), (*lists + THREE_BODIES),
+ out_control, mpi_data );
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d: appended frame %d\n", system->my_rank, data->step );
#endif
@@ -1071,10 +1071,10 @@ int End_Traj( int my_rank, output_controls *out_control )
#elif defined(LAMMPS_REAX)
if( my_rank == MASTER_NODE )
fclose( out_control->strj );
-#endif
+#endif
free( out_control->buffer );
free( out_control->line );
-
+
return SUCCESS;
}
diff --git a/src/USER-REAXC/reaxc_traj.h b/src/USER-REAXC/reaxc_traj.h
index 074e65df28b9021dd99c2273c85d420eaab08c87..e00341e5e19a579c5205fe376dc64cae39ec5793 100644
--- a/src/USER-REAXC/reaxc_traj.h
+++ b/src/USER-REAXC/reaxc_traj.h
@@ -14,12 +14,12 @@
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -72,11 +72,11 @@ enum BOND_LINE_OPTS { OPT_NOBOND, OPT_BOND_BASIC, OPT_BOND_FULL, NR_OPT_BOND };
enum ANGLE_LINE_OPTS { OPT_NOANGLE, OPT_ANGLE_BASIC, NR_OPT_ANGLE };
-int Init_Traj( reax_system*, control_params*, output_controls*,
- mpi_datatypes*, char* );
+int Init_Traj( reax_system*, control_params*, output_controls*,
+ mpi_datatypes*, char* );
int End_Traj( int, output_controls* );
-int Append_Frame( reax_system*, control_params*, simulation_data*,
- reax_list**, output_controls*, mpi_datatypes* );
+int Append_Frame( reax_system*, control_params*, simulation_data*,
+ reax_list**, output_controls*, mpi_datatypes* );
#endif
diff --git a/src/USER-REAXC/reaxc_types.h b/src/USER-REAXC/reaxc_types.h
index 69f74a1b2c59b3a48ff5a0d59b926a29cf2a7a19..90feca2dd471aee62ac64d463bdae80dd1278ba9 100644
--- a/src/USER-REAXC/reaxc_types.h
+++ b/src/USER-REAXC/reaxc_types.h
@@ -14,12 +14,12 @@
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -52,12 +52,12 @@
//#define MIDPOINT_BOUNDARIES
#define REAX_MAX_STR 1024
-#define REAX_MAX_NBRS 6
+#define REAX_MAX_NBRS 6
#define REAX_MAX_3BODY_PARAM 5
#define REAX_MAX_4BODY_PARAM 5
#define REAX_MAX_ATOM_TYPES 25
#define REAX_MAX_MOLECULE_SIZE 20
-#define MAX_BOND 20 // same as reaxc_defs.h
+#define MAX_BOND 20 // same as reaxc_defs.h
/********************** TYPE DEFINITIONS ********************/
typedef int ivec[3];
@@ -87,12 +87,12 @@ typedef struct
int type;
int num_bonds;
int num_hbonds;
- //int pad; // pad to 8-byte address boundary
+ //int pad; // pad to 8-byte address boundary
char name[8];
- rvec x; // position
- rvec v; // velocity
- rvec f_old; // old force
- rvec4 s, t; // for calculating q
+ rvec x; // position
+ rvec v; // velocity
+ rvec f_old; // old force
+ rvec4 s, t; // for calculating q
} mpi_atom;
@@ -102,9 +102,9 @@ typedef struct
int imprt_id;
int type;
int num_bonds;
- int num_hbonds;
+ int num_hbonds;
//int pad;
- rvec x; // position
+ rvec x; // position
} boundary_atom;
@@ -157,7 +157,7 @@ typedef struct
/* Global params mapping */
-/*
+/*
l[0] = p_boc1
l[1] = p_boc2
l[2] = p_coa2
@@ -200,7 +200,7 @@ l[38] = p_coa3
*/
typedef struct
-{
+{
int n_global;
real* l;
int vdw_type;
@@ -222,7 +222,7 @@ typedef struct
real r_pi;
real valency_e;
real nlp_opt;
-
+
/* Line two in field file */
real alpha;
real gamma_w;
@@ -238,7 +238,7 @@ typedef struct
real b_o_131;
real b_o_132;
real b_o_133;
-
+
/* Line four in the field file */
real p_ovun2;
real p_val3;
@@ -353,24 +353,24 @@ typedef struct
int type;
char name[8];
- rvec x; // position
- rvec v; // velocity
- rvec f; // force
+ rvec x; // position
+ rvec v; // velocity
+ rvec f; // force
rvec f_old;
- real q; // charge
- rvec4 s; // they take part in
- rvec4 t; // computing q
+ real q; // charge
+ rvec4 s; // they take part in
+ rvec4 t; // computing q
int Hindex;
int num_bonds;
int num_hbonds;
int renumber;
- int numbonds; // true number of bonds around atoms
- int nbr_id[MAX_BOND]; // ids of neighbors around atoms
- double nbr_bo[MAX_BOND]; // BO values of bond between i and nbr
- double sum_bo, no_lp; // sum of BO values and no. of lone pairs
+ int numbonds; // true number of bonds around atoms
+ int nbr_id[MAX_BOND]; // ids of neighbors around atoms
+ double nbr_bo[MAX_BOND]; // BO values of bond between i and nbr
+ double sum_bo, no_lp; // sum of BO values and no. of lone pairs
} reax_atom;
@@ -379,7 +379,7 @@ typedef struct
{
real V;
rvec min, max, box_norms;
-
+
rtensor box, box_inv;
rtensor trans, trans_inv;
rtensor g;
@@ -403,7 +403,7 @@ struct grid_cell
ivec* nbrs_x;
rvec* nbrs_cp;
};
-
+
typedef struct grid_cell grid_cell;
@@ -412,7 +412,7 @@ typedef struct
int total, max_atoms, max_nbrs;
ivec ncells;
rvec cell_len;
- rvec inv_len;
+ rvec inv_len;
ivec bond_span;
ivec nonb_span;
@@ -501,10 +501,10 @@ typedef struct
ivec procs_by_dim;
/* ensemble values:
0 : NVE
- 1 : bNVT (Berendsen)
+ 1 : bNVT (Berendsen)
2 : nhNVT (Nose-Hoover)
3 : sNPT (Parrinello-Rehman-Nose-Hoover) semiisotropic
- 4 : iNPT (Parrinello-Rehman-Nose-Hoover) isotropic
+ 4 : iNPT (Parrinello-Rehman-Nose-Hoover) isotropic
5 : NPT (Parrinello-Rehman-Nose-Hoover) Anisotropic*/
int ensemble;
int nsteps;
@@ -516,7 +516,7 @@ typedef struct
int remove_CoM_vel;
int random_vel;
int reposition_atoms;
-
+
int reneighbor;
real vlist_cut;
real bond_cut;
@@ -534,14 +534,14 @@ typedef struct
int qeq_freq;
real q_err;
int refactor;
- real droptol;
+ real droptol;
real T_init, T_final, T;
real Tau_T;
int T_mode;
real T_rate, T_freq;
-
- int virial;
+
+ int virial;
rvec P, Tau_P, Tau_PT;
int press_mode;
real compressibility;
@@ -587,7 +587,7 @@ typedef struct
{
rtensor P;
real P_scalar;
-
+
real eps;
real v_eps;
real v_eps_old;
@@ -622,22 +622,22 @@ typedef struct
typedef struct
{
real e_tot;
- real e_kin; // Total kinetic energy
+ real e_kin; // Total kinetic energy
real e_pot;
- real e_bond; // Total bond energy
- real e_ov; // Total over coordination
- real e_un; // Total under coordination energy
- real e_lp; // Total under coordination energy
- real e_ang; // Total valance angle energy
- real e_pen; // Total penalty energy
- real e_coa; // Total three body conjgation energy
- real e_hb; // Total Hydrogen bond energy
- real e_tor; // Total torsional energy
- real e_con; // Total four body conjugation energy
- real e_vdW; // Total van der Waals energy
- real e_ele; // Total electrostatics energy
- real e_pol; // Polarization energy
+ real e_bond; // Total bond energy
+ real e_ov; // Total over coordination
+ real e_un; // Total under coordination energy
+ real e_lp; // Total under coordination energy
+ real e_ang; // Total valance angle energy
+ real e_pen; // Total penalty energy
+ real e_coa; // Total three body conjgation energy
+ real e_hb; // Total Hydrogen bond energy
+ real e_tor; // Total torsional energy
+ real e_con; // Total four body conjugation energy
+ real e_vdW; // Total van der Waals energy
+ real e_ele; // Total electrostatics energy
+ real e_pol; // Polarization energy
} energy_data;
typedef struct
@@ -646,27 +646,27 @@ typedef struct
int prev_steps;
real time;
- real M; // Total Mass
- real inv_M; // 1 / Total Mass
+ real M; // Total Mass
+ real inv_M; // 1 / Total Mass
- rvec xcm; // Center of mass
- rvec vcm; // Center of mass velocity
- rvec fcm; // Center of mass force
- rvec amcm; // Angular momentum of CoM
- rvec avcm; // Angular velocity of CoM
- real etran_cm; // Translational kinetic energy of CoM
- real erot_cm; // Rotational kinetic energy of CoM
+ rvec xcm; // Center of mass
+ rvec vcm; // Center of mass velocity
+ rvec fcm; // Center of mass force
+ rvec amcm; // Angular momentum of CoM
+ rvec avcm; // Angular velocity of CoM
+ real etran_cm; // Translational kinetic energy of CoM
+ real erot_cm; // Rotational kinetic energy of CoM
- rtensor kinetic; // Kinetic energy tensor
- rtensor virial; // Hydrodynamic virial
+ rtensor kinetic; // Kinetic energy tensor
+ rtensor virial; // Hydrodynamic virial
energy_data my_en;
energy_data sys_en;
- real N_f; //Number of degrees of freedom
+ real N_f; //Number of degrees of freedom
rvec t_scale;
rtensor p_scale;
- thermostat therm; // Used in Nose_Hoover method
+ thermostat therm; // Used in Nose_Hoover method
isotropic_barostat iso_bar;
flexible_barostat flex_bar;
real inv_W;
@@ -677,13 +677,13 @@ typedef struct
rvec ext_press;
rvec tot_press;
- reax_timing timing;
+ reax_timing timing;
} simulation_data;
typedef struct{
int thb;
- int pthb; // pointer to the third body on the central atom's nbrlist
+ int pthb; // pointer to the third body on the central atom's nbrlist
real theta, cos_theta;
rvec dcos_di, dcos_dj, dcos_dk;
} three_body_interaction_data;
@@ -748,7 +748,7 @@ typedef struct {
} sparse_matrix;
-typedef struct {
+typedef struct {
int num_far;
int H, Htop;
int hbonds, num_hbonds;
@@ -782,7 +782,7 @@ typedef struct
real *Hdia_inv, *b_s, *b_t, *b_prc, *b_prm, *s, *t;
real *droptol;
rvec2 *b, *x;
-
+
/* GMRES storage */
real *y, *z, *g;
real *hc, *hs;
@@ -796,16 +796,16 @@ typedef struct
/* storage for analysis */
int *mark, *old_mark;
rvec *x_old;
-
+
/* storage space for bond restrictions */
int *restricted;
- int **restricted_list;
+ int **restricted_list;
/* integrator */
rvec *v_const;
/* force calculations */
- real *CdDelta; // coefficient of dDelta
+ real *CdDelta; // coefficient of dDelta
rvec *f;
#ifdef TEST_FORCES
rvec *f_ele;
@@ -822,7 +822,7 @@ typedef struct
rvec *f_tor;
rvec *f_con;
rvec *f_tot;
- rvec *dDelta; // calculated on the fly in bond_orders.c together with bo'
+ rvec *dDelta; // calculated on the fly in bond_orders.c together with bo'
int *rcounts;
int *displs;
@@ -940,7 +940,7 @@ typedef struct
int atom_count;
int atom_list[REAX_MAX_MOLECULE_SIZE];
int mtypes[REAX_MAX_ATOM_TYPES];
-} molecule;
+} molecule;
typedef struct
@@ -975,20 +975,20 @@ typedef struct
extern LR_lookup_table **LR;
/* function pointer defs */
-typedef void (*evolve_function)(reax_system*, control_params*,
- simulation_data*, storage*, reax_list**,
- output_controls*, mpi_datatypes* );
+typedef void (*evolve_function)(reax_system*, control_params*,
+ simulation_data*, storage*, reax_list**,
+ output_controls*, mpi_datatypes* );
#if defined(PURE_REAX)
evolve_function Evolve;
#endif
-typedef void (*interaction_function) (reax_system*, control_params*,
- simulation_data*, storage*,
- reax_list**, output_controls*);
+typedef void (*interaction_function) (reax_system*, control_params*,
+ simulation_data*, storage*,
+ reax_list**, output_controls*);
-typedef void (*print_interaction)(reax_system*, control_params*,
- simulation_data*, storage*,
- reax_list**, output_controls*);
+typedef void (*print_interaction)(reax_system*, control_params*,
+ simulation_data*, storage*,
+ reax_list**, output_controls*);
typedef real (*lookup_function)(real);
diff --git a/src/USER-REAXC/reaxc_valence_angles.cpp b/src/USER-REAXC/reaxc_valence_angles.cpp
index 6eee1548a19ace455c4ef3d493ce2b79543df05b..5049fb769fdb3d3122c90767f9c78b932400afb5 100644
--- a/src/USER-REAXC/reaxc_valence_angles.cpp
+++ b/src/USER-REAXC/reaxc_valence_angles.cpp
@@ -14,12 +14,12 @@
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -39,22 +39,22 @@
/* calculates the theta angle between i-j-k */
-void Calculate_Theta( rvec dvec_ji, real d_ji, rvec dvec_jk, real d_jk,
- real *theta, real *cos_theta )
+void Calculate_Theta( rvec dvec_ji, real d_ji, rvec dvec_jk, real d_jk,
+ real *theta, real *cos_theta )
{
(*cos_theta) = Dot( dvec_ji, dvec_jk, 3 ) / ( d_ji * d_jk );
if( *cos_theta > 1. ) *cos_theta = 1.0;
if( *cos_theta < -1. ) *cos_theta = -1.0;
-
+
(*theta) = acos( *cos_theta );
}
/* calculates the derivative of the cosine of the angle between i-j-k */
-void Calculate_dCos_Theta( rvec dvec_ji, real d_ji, rvec dvec_jk, real d_jk,
- rvec* dcos_theta_di,
- rvec* dcos_theta_dj,
- rvec* dcos_theta_dk )
+void Calculate_dCos_Theta( rvec dvec_ji, real d_ji, rvec dvec_jk, real d_jk,
+ rvec* dcos_theta_di,
+ rvec* dcos_theta_dj,
+ rvec* dcos_theta_dk )
{
int t;
real sqr_d_ji = SQR(d_ji);
@@ -65,21 +65,21 @@ void Calculate_dCos_Theta( rvec dvec_ji, real d_ji, rvec dvec_jk, real d_jk,
real Cdot_inv3 = dot_dvecs * inv_dists3;
for( t = 0; t < 3; ++t ) {
- (*dcos_theta_di)[t] = dvec_jk[t] * inv_dists -
+ (*dcos_theta_di)[t] = dvec_jk[t] * inv_dists -
Cdot_inv3 * sqr_d_jk * dvec_ji[t];
(*dcos_theta_dj)[t] = -(dvec_jk[t] + dvec_ji[t]) * inv_dists +
Cdot_inv3 * ( sqr_d_jk * dvec_ji[t] + sqr_d_ji * dvec_jk[t] );
- (*dcos_theta_dk)[t] = dvec_ji[t] * inv_dists -
+ (*dcos_theta_dk)[t] = dvec_ji[t] * inv_dists -
Cdot_inv3 * sqr_d_ji * dvec_jk[t];
}
}
-/* this is a 3-body interaction in which the main role is
+/* this is a 3-body interaction in which the main role is
played by j which sits in the middle of the other two. */
-void Valence_Angles( reax_system *system, control_params *control,
- simulation_data *data, storage *workspace,
- reax_list **lists, output_controls *out_control )
+void Valence_Angles( reax_system *system, control_params *control,
+ simulation_data *data, storage *workspace,
+ reax_list **lists, output_controls *out_control )
{
int i, j, pi, k, pk, t;
int type_i, type_j, type_k;
@@ -125,26 +125,26 @@ void Valence_Angles( reax_system *system, control_params *control,
p_val10 = system->reax_param.gp.l[17];
num_thb_intrs = 0;
-
- for( j = 0; j < system->N; ++j ) { // Ray: the first one with system->N
+
+ for( j = 0; j < system->N; ++j ) { // Ray: the first one with system->N
// fprintf( out_control->eval, "j: %d\n", j );
type_j = system->my_atoms[j].type;
start_j = Start_Index(j, bonds);
end_j = End_Index(j, bonds);
-
+
p_val3 = system->reax_param.sbp[ type_j ].p_val3;
p_val5 = system->reax_param.sbp[ type_j ].p_val5;
-
+
SBOp = 0, prod_SBO = 1;
for( t = start_j; t < end_j; ++t ) {
bo_jt = &(bonds->select.bond_list[t].bo_data);
SBOp += (bo_jt->BO_pi + bo_jt->BO_pi2);
temp = SQR( bo_jt->BO );
- temp *= temp;
+ temp *= temp;
temp *= temp;
prod_SBO *= exp( -temp );
}
-
+
/* modifications to match Adri's code - 09/01/09 */
if( workspace->vlpex[j] >= 0 ){
vlpadj = 0;
@@ -157,388 +157,388 @@ void Valence_Angles( reax_system *system, control_params *control,
SBO = SBOp + (1 - prod_SBO) * (-workspace->Delta_boc[j] - p_val8 * vlpadj);
dSBO1 = -8 * prod_SBO * ( workspace->Delta_boc[j] + p_val8 * vlpadj );
-
+
if( SBO <= 0 )
SBO2 = 0, CSBO2 = 0;
else if( SBO > 0 && SBO <= 1 ) {
- SBO2 = pow( SBO, p_val9 );
- CSBO2 = p_val9 * pow( SBO, p_val9 - 1 );
+ SBO2 = pow( SBO, p_val9 );
+ CSBO2 = p_val9 * pow( SBO, p_val9 - 1 );
}
else if( SBO > 1 && SBO < 2 ) {
SBO2 = 2 - pow( 2-SBO, p_val9 );
CSBO2 = p_val9 * pow( 2 - SBO, p_val9 - 1 );
}
- else
- SBO2 = 2, CSBO2 = 0;
-
- expval6 = exp( p_val6 * workspace->Delta_boc[j] );
-
+ else
+ SBO2 = 2, CSBO2 = 0;
+
+ expval6 = exp( p_val6 * workspace->Delta_boc[j] );
+
for( pi = start_j; pi < end_j; ++pi ) {
Set_Start_Index( pi, num_thb_intrs, thb_intrs );
pbond_ij = &(bonds->select.bond_list[pi]);
bo_ij = &(pbond_ij->bo_data);
BOA_ij = bo_ij->BO - control->thb_cut;
-
-
- if( BOA_ij/*bo_ij->BO*/ > 0.0 &&
- ( j < system->n || pbond_ij->nbr < system->n ) ) {
- i = pbond_ij->nbr;
- r_ij = pbond_ij->d;
- type_i = system->my_atoms[i].type;
- // fprintf( out_control->eval, "i: %d\n", i );
-
-
- /* first copy 3-body intrs from previously computed ones where i>k.
- in the second for-loop below,
- we compute only new 3-body intrs where i < k */
- for( pk = start_j; pk < pi; ++pk ) {
- // fprintf( out_control->eval, "pk: %d\n", pk );
- start_pk = Start_Index( pk, thb_intrs );
- end_pk = End_Index( pk, thb_intrs );
-
- for( t = start_pk; t < end_pk; ++t )
- if( thb_intrs->select.three_body_list[t].thb == i ) {
- p_ijk = &(thb_intrs->select.three_body_list[num_thb_intrs] );
- p_kji = &(thb_intrs->select.three_body_list[t]);
-
- p_ijk->thb = bonds->select.bond_list[pk].nbr;
- p_ijk->pthb = pk;
- p_ijk->theta = p_kji->theta;
- rvec_Copy( p_ijk->dcos_di, p_kji->dcos_dk );
- rvec_Copy( p_ijk->dcos_dj, p_kji->dcos_dj );
- rvec_Copy( p_ijk->dcos_dk, p_kji->dcos_di );
-
- ++num_thb_intrs;
- break;
- }
- }
-
-
- /* and this is the second for loop mentioned above */
- for( pk = pi+1; pk < end_j; ++pk ) {
- pbond_jk = &(bonds->select.bond_list[pk]);
- bo_jk = &(pbond_jk->bo_data);
- BOA_jk = bo_jk->BO - control->thb_cut;
- k = pbond_jk->nbr;
- type_k = system->my_atoms[k].type;
- p_ijk = &( thb_intrs->select.three_body_list[num_thb_intrs] );
-
- Calculate_Theta( pbond_ij->dvec, pbond_ij->d,
- pbond_jk->dvec, pbond_jk->d,
- &theta, &cos_theta );
-
- Calculate_dCos_Theta( pbond_ij->dvec, pbond_ij->d,
- pbond_jk->dvec, pbond_jk->d,
- &(p_ijk->dcos_di), &(p_ijk->dcos_dj),
- &(p_ijk->dcos_dk) );
- p_ijk->thb = k;
- p_ijk->pthb = pk;
- p_ijk->theta = theta;
-
- sin_theta = sin( theta );
- if( sin_theta < 1.0e-5 )
- sin_theta = 1.0e-5;
-
- ++num_thb_intrs;
-
-
- if( (j < system->n) && (BOA_jk > 0.0) &&
- (bo_ij->BO > control->thb_cut) &&
- (bo_jk->BO > control->thb_cut) &&
+
+
+ if( BOA_ij/*bo_ij->BO*/ > 0.0 &&
+ ( j < system->n || pbond_ij->nbr < system->n ) ) {
+ i = pbond_ij->nbr;
+ r_ij = pbond_ij->d;
+ type_i = system->my_atoms[i].type;
+ // fprintf( out_control->eval, "i: %d\n", i );
+
+
+ /* first copy 3-body intrs from previously computed ones where i>k.
+ in the second for-loop below,
+ we compute only new 3-body intrs where i < k */
+ for( pk = start_j; pk < pi; ++pk ) {
+ // fprintf( out_control->eval, "pk: %d\n", pk );
+ start_pk = Start_Index( pk, thb_intrs );
+ end_pk = End_Index( pk, thb_intrs );
+
+ for( t = start_pk; t < end_pk; ++t )
+ if( thb_intrs->select.three_body_list[t].thb == i ) {
+ p_ijk = &(thb_intrs->select.three_body_list[num_thb_intrs] );
+ p_kji = &(thb_intrs->select.three_body_list[t]);
+
+ p_ijk->thb = bonds->select.bond_list[pk].nbr;
+ p_ijk->pthb = pk;
+ p_ijk->theta = p_kji->theta;
+ rvec_Copy( p_ijk->dcos_di, p_kji->dcos_dk );
+ rvec_Copy( p_ijk->dcos_dj, p_kji->dcos_dj );
+ rvec_Copy( p_ijk->dcos_dk, p_kji->dcos_di );
+
+ ++num_thb_intrs;
+ break;
+ }
+ }
+
+
+ /* and this is the second for loop mentioned above */
+ for( pk = pi+1; pk < end_j; ++pk ) {
+ pbond_jk = &(bonds->select.bond_list[pk]);
+ bo_jk = &(pbond_jk->bo_data);
+ BOA_jk = bo_jk->BO - control->thb_cut;
+ k = pbond_jk->nbr;
+ type_k = system->my_atoms[k].type;
+ p_ijk = &( thb_intrs->select.three_body_list[num_thb_intrs] );
+
+ Calculate_Theta( pbond_ij->dvec, pbond_ij->d,
+ pbond_jk->dvec, pbond_jk->d,
+ &theta, &cos_theta );
+
+ Calculate_dCos_Theta( pbond_ij->dvec, pbond_ij->d,
+ pbond_jk->dvec, pbond_jk->d,
+ &(p_ijk->dcos_di), &(p_ijk->dcos_dj),
+ &(p_ijk->dcos_dk) );
+ p_ijk->thb = k;
+ p_ijk->pthb = pk;
+ p_ijk->theta = theta;
+
+ sin_theta = sin( theta );
+ if( sin_theta < 1.0e-5 )
+ sin_theta = 1.0e-5;
+
+ ++num_thb_intrs;
+
+
+ if( (j < system->n) && (BOA_jk > 0.0) &&
+ (bo_ij->BO > control->thb_cut) &&
+ (bo_jk->BO > control->thb_cut) &&
(bo_ij->BO * bo_jk->BO > control->thb_cutsq) ) {
- r_jk = pbond_jk->d;
- thbh = &( system->reax_param.thbp[ type_i ][ type_j ][ type_k ] );
-
- /* if( system->my_atoms[i].orig_id < system->my_atoms[k].orig_id )
- fprintf( fval, "%6d %6d %6d %7.3f %7.3f %7.3f\n",
- system->my_atoms[i].orig_id,
- system->my_atoms[j].orig_id,
- system->my_atoms[k].orig_id,
- bo_ij->BO, bo_jk->BO, p_ijk->theta );
- else
- fprintf( fval, "%6d %6d %6d %7.3f %7.3f %7.3f\n",
- system->my_atoms[k].orig_id,
- system->my_atoms[j].orig_id,
- system->my_atoms[i].orig_id,
- bo_jk->BO, bo_ij->BO, p_ijk->theta ); */
-
- for( cnt = 0; cnt < thbh->cnt; ++cnt ) {
- // fprintf( out_control->eval, "%6d%6d%6d -- exists in thbp\n",
- // i+1, j+1, k+1 );
-
- if( fabs(thbh->prm[cnt].p_val1) > 0.001 ) {
- thbp = &( thbh->prm[cnt] );
-
- /* ANGLE ENERGY */
- p_val1 = thbp->p_val1;
- p_val2 = thbp->p_val2;
- p_val4 = thbp->p_val4;
- p_val7 = thbp->p_val7;
- theta_00 = thbp->theta_00;
-
- exp3ij = exp( -p_val3 * pow( BOA_ij, p_val4 ) );
- f7_ij = 1.0 - exp3ij;
- Cf7ij = p_val3 * p_val4 * pow( BOA_ij, p_val4 - 1.0 ) * exp3ij;
-
- exp3jk = exp( -p_val3 * pow( BOA_jk, p_val4 ) );
- f7_jk = 1.0 - exp3jk;
- Cf7jk = p_val3 * p_val4 * pow( BOA_jk, p_val4 - 1.0 ) * exp3jk;
-
- expval7 = exp( -p_val7 * workspace->Delta_boc[j] );
- trm8 = 1.0 + expval6 + expval7;
- f8_Dj = p_val5 - ( (p_val5 - 1.0) * (2.0 + expval6) / trm8 );
- Cf8j = ( (1.0 - p_val5) / SQR(trm8) ) *
- ( p_val6 * expval6 * trm8 -
- (2.0 + expval6) * ( p_val6*expval6 - p_val7*expval7 ) );
-
- theta_0 = 180.0 - theta_00 * (1.0 -
- exp(-p_val10 * (2.0 - SBO2)));
- theta_0 = DEG2RAD( theta_0 );
-
- expval2theta = exp( -p_val2 * SQR(theta_0 - theta) );
- if( p_val1 >= 0 )
- expval12theta = p_val1 * (1.0 - expval2theta);
- else // To avoid linear Me-H-Me angles (6/6/06)
- expval12theta = p_val1 * -expval2theta;
-
- CEval1 = Cf7ij * f7_jk * f8_Dj * expval12theta;
- CEval2 = Cf7jk * f7_ij * f8_Dj * expval12theta;
- CEval3 = Cf8j * f7_ij * f7_jk * expval12theta;
- CEval4 = -2.0 * p_val1 * p_val2 * f7_ij * f7_jk * f8_Dj *
- expval2theta * (theta_0 - theta);
-
- Ctheta_0 = p_val10 * DEG2RAD(theta_00) *
- exp( -p_val10 * (2.0 - SBO2) );
-
- CEval5 = -CEval4 * Ctheta_0 * CSBO2;
- CEval6 = CEval5 * dSBO1;
- CEval7 = CEval5 * dSBO2;
- CEval8 = -CEval4 / sin_theta;
-
- data->my_en.e_ang += e_ang =
- f7_ij * f7_jk * f8_Dj * expval12theta;
- /* END ANGLE ENERGY*/
-
-
- /* PENALTY ENERGY */
- p_pen1 = thbp->p_pen1;
- p_pen2 = system->reax_param.gp.l[19];
- p_pen3 = system->reax_param.gp.l[20];
- p_pen4 = system->reax_param.gp.l[21];
-
- exp_pen2ij = exp( -p_pen2 * SQR( BOA_ij - 2.0 ) );
- exp_pen2jk = exp( -p_pen2 * SQR( BOA_jk - 2.0 ) );
- exp_pen3 = exp( -p_pen3 * workspace->Delta[j] );
- exp_pen4 = exp( p_pen4 * workspace->Delta[j] );
- trm_pen34 = 1.0 + exp_pen3 + exp_pen4;
- f9_Dj = ( 2.0 + exp_pen3 ) / trm_pen34;
- Cf9j = ( -p_pen3 * exp_pen3 * trm_pen34 -
- (2.0 + exp_pen3) * ( -p_pen3 * exp_pen3 +
- p_pen4 * exp_pen4 ) ) /
- SQR( trm_pen34 );
-
- data->my_en.e_pen += e_pen =
- p_pen1 * f9_Dj * exp_pen2ij * exp_pen2jk;
-
- CEpen1 = e_pen * Cf9j / f9_Dj;
- temp = -2.0 * p_pen2 * e_pen;
- CEpen2 = temp * (BOA_ij - 2.0);
- CEpen3 = temp * (BOA_jk - 2.0);
- /* END PENALTY ENERGY */
-
-
- /* COALITION ENERGY */
- p_coa1 = thbp->p_coa1;
- p_coa2 = system->reax_param.gp.l[2];
- p_coa3 = system->reax_param.gp.l[38];
- p_coa4 = system->reax_param.gp.l[30];
-
- exp_coa2 = exp( p_coa2 * workspace->Delta_val[j] );
- data->my_en.e_coa += e_coa =
- p_coa1 / (1. + exp_coa2) *
- exp( -p_coa3 * SQR(workspace->total_bond_order[i]-BOA_ij) ) *
- exp( -p_coa3 * SQR(workspace->total_bond_order[k]-BOA_jk) ) *
- exp( -p_coa4 * SQR(BOA_ij - 1.5) ) *
- exp( -p_coa4 * SQR(BOA_jk - 1.5) );
-
- CEcoa1 = -2 * p_coa4 * (BOA_ij - 1.5) * e_coa;
- CEcoa2 = -2 * p_coa4 * (BOA_jk - 1.5) * e_coa;
- CEcoa3 = -p_coa2 * exp_coa2 * e_coa / (1 + exp_coa2);
- CEcoa4 = -2 * p_coa3 *
- (workspace->total_bond_order[i]-BOA_ij) * e_coa;
- CEcoa5 = -2 * p_coa3 *
- (workspace->total_bond_order[k]-BOA_jk) * e_coa;
- /* END COALITION ENERGY */
-
-
- /* FORCES */
- bo_ij->Cdbo += (CEval1 + CEpen2 + (CEcoa1 - CEcoa4));
- bo_jk->Cdbo += (CEval2 + CEpen3 + (CEcoa2 - CEcoa5));
- workspace->CdDelta[j] += ((CEval3 + CEval7) + CEpen1 + CEcoa3);
- workspace->CdDelta[i] += CEcoa4;
- workspace->CdDelta[k] += CEcoa5;
-
- for( t = start_j; t < end_j; ++t ) {
- pbond_jt = &( bonds->select.bond_list[t] );
- bo_jt = &(pbond_jt->bo_data);
- temp_bo_jt = bo_jt->BO;
- temp = CUBE( temp_bo_jt );
- pBOjt7 = temp * temp * temp_bo_jt;
-
- // fprintf( out_control->eval, "%6d%12.8f\n",
- // workspace->reverse_map[bonds->select.bond_list[t].nbr],
- // (CEval6 * pBOjt7) );
-
- bo_jt->Cdbo += (CEval6 * pBOjt7);
- bo_jt->Cdbopi += CEval5;
- bo_jt->Cdbopi2 += CEval5;
- }
-
- if( control->virial == 0 ) {
- rvec_ScaledAdd( workspace->f[i], CEval8, p_ijk->dcos_di );
- rvec_ScaledAdd( workspace->f[j], CEval8, p_ijk->dcos_dj );
- rvec_ScaledAdd( workspace->f[k], CEval8, p_ijk->dcos_dk );
- }
- else {
- /* terms not related to bond order derivatives are
- added directly into forces and pressure vector/tensor */
- rvec_Scale( force, CEval8, p_ijk->dcos_di );
- rvec_Add( workspace->f[i], force );
- rvec_iMultiply( ext_press, pbond_ij->rel_box, force );
- rvec_Add( data->my_ext_press, ext_press );
-
- rvec_ScaledAdd( workspace->f[j], CEval8, p_ijk->dcos_dj );
-
- rvec_Scale( force, CEval8, p_ijk->dcos_dk );
- rvec_Add( workspace->f[k], force );
- rvec_iMultiply( ext_press, pbond_jk->rel_box, force );
- rvec_Add( data->my_ext_press, ext_press );
- }
-
- /* tally into per-atom virials */
- if( system->pair_ptr->vflag_atom || system->pair_ptr->evflag) {
-
- /* Acquire vectors */
- rvec_ScaledSum( delij, 1., system->my_atoms[i].x,
- -1., system->my_atoms[j].x );
- rvec_ScaledSum( delkj, 1., system->my_atoms[k].x,
- -1., system->my_atoms[j].x );
-
- rvec_Scale( fi_tmp, -CEval8, p_ijk->dcos_di );
- rvec_Scale( fj_tmp, -CEval8, p_ijk->dcos_dj );
- rvec_Scale( fk_tmp, -CEval8, p_ijk->dcos_dk );
-
- eng_tmp = e_ang + e_pen + e_coa;
-
- if( system->pair_ptr->evflag)
- system->pair_ptr->ev_tally(j,j,system->N,1,eng_tmp,0.0,0.0,0.0,0.0,0.0);
- if( system->pair_ptr->vflag_atom)
- system->pair_ptr->v_tally3(i,j,k,fi_tmp,fk_tmp,delij,delkj);
- }
-
+ r_jk = pbond_jk->d;
+ thbh = &( system->reax_param.thbp[ type_i ][ type_j ][ type_k ] );
+
+ /* if( system->my_atoms[i].orig_id < system->my_atoms[k].orig_id )
+ fprintf( fval, "%6d %6d %6d %7.3f %7.3f %7.3f\n",
+ system->my_atoms[i].orig_id,
+ system->my_atoms[j].orig_id,
+ system->my_atoms[k].orig_id,
+ bo_ij->BO, bo_jk->BO, p_ijk->theta );
+ else
+ fprintf( fval, "%6d %6d %6d %7.3f %7.3f %7.3f\n",
+ system->my_atoms[k].orig_id,
+ system->my_atoms[j].orig_id,
+ system->my_atoms[i].orig_id,
+ bo_jk->BO, bo_ij->BO, p_ijk->theta ); */
+
+ for( cnt = 0; cnt < thbh->cnt; ++cnt ) {
+ // fprintf( out_control->eval, "%6d%6d%6d -- exists in thbp\n",
+ // i+1, j+1, k+1 );
+
+ if( fabs(thbh->prm[cnt].p_val1) > 0.001 ) {
+ thbp = &( thbh->prm[cnt] );
+
+ /* ANGLE ENERGY */
+ p_val1 = thbp->p_val1;
+ p_val2 = thbp->p_val2;
+ p_val4 = thbp->p_val4;
+ p_val7 = thbp->p_val7;
+ theta_00 = thbp->theta_00;
+
+ exp3ij = exp( -p_val3 * pow( BOA_ij, p_val4 ) );
+ f7_ij = 1.0 - exp3ij;
+ Cf7ij = p_val3 * p_val4 * pow( BOA_ij, p_val4 - 1.0 ) * exp3ij;
+
+ exp3jk = exp( -p_val3 * pow( BOA_jk, p_val4 ) );
+ f7_jk = 1.0 - exp3jk;
+ Cf7jk = p_val3 * p_val4 * pow( BOA_jk, p_val4 - 1.0 ) * exp3jk;
+
+ expval7 = exp( -p_val7 * workspace->Delta_boc[j] );
+ trm8 = 1.0 + expval6 + expval7;
+ f8_Dj = p_val5 - ( (p_val5 - 1.0) * (2.0 + expval6) / trm8 );
+ Cf8j = ( (1.0 - p_val5) / SQR(trm8) ) *
+ ( p_val6 * expval6 * trm8 -
+ (2.0 + expval6) * ( p_val6*expval6 - p_val7*expval7 ) );
+
+ theta_0 = 180.0 - theta_00 * (1.0 -
+ exp(-p_val10 * (2.0 - SBO2)));
+ theta_0 = DEG2RAD( theta_0 );
+
+ expval2theta = exp( -p_val2 * SQR(theta_0 - theta) );
+ if( p_val1 >= 0 )
+ expval12theta = p_val1 * (1.0 - expval2theta);
+ else // To avoid linear Me-H-Me angles (6/6/06)
+ expval12theta = p_val1 * -expval2theta;
+
+ CEval1 = Cf7ij * f7_jk * f8_Dj * expval12theta;
+ CEval2 = Cf7jk * f7_ij * f8_Dj * expval12theta;
+ CEval3 = Cf8j * f7_ij * f7_jk * expval12theta;
+ CEval4 = -2.0 * p_val1 * p_val2 * f7_ij * f7_jk * f8_Dj *
+ expval2theta * (theta_0 - theta);
+
+ Ctheta_0 = p_val10 * DEG2RAD(theta_00) *
+ exp( -p_val10 * (2.0 - SBO2) );
+
+ CEval5 = -CEval4 * Ctheta_0 * CSBO2;
+ CEval6 = CEval5 * dSBO1;
+ CEval7 = CEval5 * dSBO2;
+ CEval8 = -CEval4 / sin_theta;
+
+ data->my_en.e_ang += e_ang =
+ f7_ij * f7_jk * f8_Dj * expval12theta;
+ /* END ANGLE ENERGY*/
+
+
+ /* PENALTY ENERGY */
+ p_pen1 = thbp->p_pen1;
+ p_pen2 = system->reax_param.gp.l[19];
+ p_pen3 = system->reax_param.gp.l[20];
+ p_pen4 = system->reax_param.gp.l[21];
+
+ exp_pen2ij = exp( -p_pen2 * SQR( BOA_ij - 2.0 ) );
+ exp_pen2jk = exp( -p_pen2 * SQR( BOA_jk - 2.0 ) );
+ exp_pen3 = exp( -p_pen3 * workspace->Delta[j] );
+ exp_pen4 = exp( p_pen4 * workspace->Delta[j] );
+ trm_pen34 = 1.0 + exp_pen3 + exp_pen4;
+ f9_Dj = ( 2.0 + exp_pen3 ) / trm_pen34;
+ Cf9j = ( -p_pen3 * exp_pen3 * trm_pen34 -
+ (2.0 + exp_pen3) * ( -p_pen3 * exp_pen3 +
+ p_pen4 * exp_pen4 ) ) /
+ SQR( trm_pen34 );
+
+ data->my_en.e_pen += e_pen =
+ p_pen1 * f9_Dj * exp_pen2ij * exp_pen2jk;
+
+ CEpen1 = e_pen * Cf9j / f9_Dj;
+ temp = -2.0 * p_pen2 * e_pen;
+ CEpen2 = temp * (BOA_ij - 2.0);
+ CEpen3 = temp * (BOA_jk - 2.0);
+ /* END PENALTY ENERGY */
+
+
+ /* COALITION ENERGY */
+ p_coa1 = thbp->p_coa1;
+ p_coa2 = system->reax_param.gp.l[2];
+ p_coa3 = system->reax_param.gp.l[38];
+ p_coa4 = system->reax_param.gp.l[30];
+
+ exp_coa2 = exp( p_coa2 * workspace->Delta_val[j] );
+ data->my_en.e_coa += e_coa =
+ p_coa1 / (1. + exp_coa2) *
+ exp( -p_coa3 * SQR(workspace->total_bond_order[i]-BOA_ij) ) *
+ exp( -p_coa3 * SQR(workspace->total_bond_order[k]-BOA_jk) ) *
+ exp( -p_coa4 * SQR(BOA_ij - 1.5) ) *
+ exp( -p_coa4 * SQR(BOA_jk - 1.5) );
+
+ CEcoa1 = -2 * p_coa4 * (BOA_ij - 1.5) * e_coa;
+ CEcoa2 = -2 * p_coa4 * (BOA_jk - 1.5) * e_coa;
+ CEcoa3 = -p_coa2 * exp_coa2 * e_coa / (1 + exp_coa2);
+ CEcoa4 = -2 * p_coa3 *
+ (workspace->total_bond_order[i]-BOA_ij) * e_coa;
+ CEcoa5 = -2 * p_coa3 *
+ (workspace->total_bond_order[k]-BOA_jk) * e_coa;
+ /* END COALITION ENERGY */
+
+
+ /* FORCES */
+ bo_ij->Cdbo += (CEval1 + CEpen2 + (CEcoa1 - CEcoa4));
+ bo_jk->Cdbo += (CEval2 + CEpen3 + (CEcoa2 - CEcoa5));
+ workspace->CdDelta[j] += ((CEval3 + CEval7) + CEpen1 + CEcoa3);
+ workspace->CdDelta[i] += CEcoa4;
+ workspace->CdDelta[k] += CEcoa5;
+
+ for( t = start_j; t < end_j; ++t ) {
+ pbond_jt = &( bonds->select.bond_list[t] );
+ bo_jt = &(pbond_jt->bo_data);
+ temp_bo_jt = bo_jt->BO;
+ temp = CUBE( temp_bo_jt );
+ pBOjt7 = temp * temp * temp_bo_jt;
+
+ // fprintf( out_control->eval, "%6d%12.8f\n",
+ // workspace->reverse_map[bonds->select.bond_list[t].nbr],
+ // (CEval6 * pBOjt7) );
+
+ bo_jt->Cdbo += (CEval6 * pBOjt7);
+ bo_jt->Cdbopi += CEval5;
+ bo_jt->Cdbopi2 += CEval5;
+ }
+
+ if( control->virial == 0 ) {
+ rvec_ScaledAdd( workspace->f[i], CEval8, p_ijk->dcos_di );
+ rvec_ScaledAdd( workspace->f[j], CEval8, p_ijk->dcos_dj );
+ rvec_ScaledAdd( workspace->f[k], CEval8, p_ijk->dcos_dk );
+ }
+ else {
+ /* terms not related to bond order derivatives are
+ added directly into forces and pressure vector/tensor */
+ rvec_Scale( force, CEval8, p_ijk->dcos_di );
+ rvec_Add( workspace->f[i], force );
+ rvec_iMultiply( ext_press, pbond_ij->rel_box, force );
+ rvec_Add( data->my_ext_press, ext_press );
+
+ rvec_ScaledAdd( workspace->f[j], CEval8, p_ijk->dcos_dj );
+
+ rvec_Scale( force, CEval8, p_ijk->dcos_dk );
+ rvec_Add( workspace->f[k], force );
+ rvec_iMultiply( ext_press, pbond_jk->rel_box, force );
+ rvec_Add( data->my_ext_press, ext_press );
+ }
+
+ /* tally into per-atom virials */
+ if( system->pair_ptr->vflag_atom || system->pair_ptr->evflag) {
+
+ /* Acquire vectors */
+ rvec_ScaledSum( delij, 1., system->my_atoms[i].x,
+ -1., system->my_atoms[j].x );
+ rvec_ScaledSum( delkj, 1., system->my_atoms[k].x,
+ -1., system->my_atoms[j].x );
+
+ rvec_Scale( fi_tmp, -CEval8, p_ijk->dcos_di );
+ rvec_Scale( fj_tmp, -CEval8, p_ijk->dcos_dj );
+ rvec_Scale( fk_tmp, -CEval8, p_ijk->dcos_dk );
+
+ eng_tmp = e_ang + e_pen + e_coa;
+
+ if( system->pair_ptr->evflag)
+ system->pair_ptr->ev_tally(j,j,system->N,1,eng_tmp,0.0,0.0,0.0,0.0,0.0);
+ if( system->pair_ptr->vflag_atom)
+ system->pair_ptr->v_tally3(i,j,k,fi_tmp,fk_tmp,delij,delkj);
+ }
+
#ifdef TEST_ENERGY
- /*fprintf( out_control->eval, "%12.8f%12.8f%12.8f%12.8f\n",
- p_val3, p_val4, BOA_ij, BOA_jk );
- fprintf(out_control->eval, "%13.8f%13.8f%13.8f%13.8f%13.8f\n",
- workspace->Delta_e[j], workspace->vlpex[j],
- dSBO1, dSBO2, vlpadj );
- fprintf( out_control->eval, "%12.8f%12.8f%12.8f%12.8f\n",
- f7_ij, f7_jk, f8_Dj, expval12theta );
- fprintf( out_control->eval,
- "%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f\n",
- CEval1, CEval2, CEval3, CEval4,
- CEval5, CEval6, CEval7, CEval8 );
-
- fprintf( out_control->eval,
- "%12.8f%12.8f%12.8f\n%12.8f%12.8f%12.8f\n%12.8f%12.8f%12.8f\n",
- p_ijk->dcos_di[0]/sin_theta, p_ijk->dcos_di[1]/sin_theta,
- p_ijk->dcos_di[2]/sin_theta,
- p_ijk->dcos_dj[0]/sin_theta, p_ijk->dcos_dj[1]/sin_theta,
- p_ijk->dcos_dj[2]/sin_theta,
- p_ijk->dcos_dk[0]/sin_theta, p_ijk->dcos_dk[1]/sin_theta,
- p_ijk->dcos_dk[2]/sin_theta);
-
- fprintf( out_control->eval,
- "%6d%6d%6d%15.8f%15.8f\n",
- system->my_atoms[i].orig_id,
- system->my_atoms[j].orig_id,
- system->my_atoms[k].orig_id,
- RAD2DEG(theta), e_ang );*/
-
- fprintf( out_control->eval,
- //"%6d%6d%6d%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e\n",
- "%6d%6d%6d%12.4f%12.4f%12.4f%12.4f%12.4f%12.4f\n",
- system->my_atoms[i].orig_id,
- system->my_atoms[j].orig_id,
- system->my_atoms[k].orig_id,
- RAD2DEG(theta), theta_0, BOA_ij, BOA_jk,
- e_ang, data->my_en.e_ang );
-
- fprintf( out_control->epen,
- //"%6d%6d%6d%24.15e%24.15e%24.15e%24.15e%24.15e\n",
- "%6d%6d%6d%12.4f%12.4f%12.4f%12.4f%12.4f\n",
- system->my_atoms[i].orig_id,
- system->my_atoms[j].orig_id,
- system->my_atoms[k].orig_id,
- RAD2DEG(theta), BOA_ij, BOA_jk, e_pen,
- data->my_en.e_pen );
-
- fprintf( out_control->ecoa,
- //"%6d%6d%6d%24.15e%24.15e%24.15e%24.15e%24.15e\n",
- "%6d%6d%6d%12.4f%12.4f%12.4f%12.4f%12.4f\n",
- system->my_atoms[i].orig_id,
- system->my_atoms[j].orig_id,
- system->my_atoms[k].orig_id,
- RAD2DEG(theta), BOA_ij, BOA_jk,
- e_coa, data->my_en.e_coa );
+ /*fprintf( out_control->eval, "%12.8f%12.8f%12.8f%12.8f\n",
+ p_val3, p_val4, BOA_ij, BOA_jk );
+ fprintf(out_control->eval, "%13.8f%13.8f%13.8f%13.8f%13.8f\n",
+ workspace->Delta_e[j], workspace->vlpex[j],
+ dSBO1, dSBO2, vlpadj );
+ fprintf( out_control->eval, "%12.8f%12.8f%12.8f%12.8f\n",
+ f7_ij, f7_jk, f8_Dj, expval12theta );
+ fprintf( out_control->eval,
+ "%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f\n",
+ CEval1, CEval2, CEval3, CEval4,
+ CEval5, CEval6, CEval7, CEval8 );
+
+ fprintf( out_control->eval,
+ "%12.8f%12.8f%12.8f\n%12.8f%12.8f%12.8f\n%12.8f%12.8f%12.8f\n",
+ p_ijk->dcos_di[0]/sin_theta, p_ijk->dcos_di[1]/sin_theta,
+ p_ijk->dcos_di[2]/sin_theta,
+ p_ijk->dcos_dj[0]/sin_theta, p_ijk->dcos_dj[1]/sin_theta,
+ p_ijk->dcos_dj[2]/sin_theta,
+ p_ijk->dcos_dk[0]/sin_theta, p_ijk->dcos_dk[1]/sin_theta,
+ p_ijk->dcos_dk[2]/sin_theta);
+
+ fprintf( out_control->eval,
+ "%6d%6d%6d%15.8f%15.8f\n",
+ system->my_atoms[i].orig_id,
+ system->my_atoms[j].orig_id,
+ system->my_atoms[k].orig_id,
+ RAD2DEG(theta), e_ang );*/
+
+ fprintf( out_control->eval,
+ //"%6d%6d%6d%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e\n",
+ "%6d%6d%6d%12.4f%12.4f%12.4f%12.4f%12.4f%12.4f\n",
+ system->my_atoms[i].orig_id,
+ system->my_atoms[j].orig_id,
+ system->my_atoms[k].orig_id,
+ RAD2DEG(theta), theta_0, BOA_ij, BOA_jk,
+ e_ang, data->my_en.e_ang );
+
+ fprintf( out_control->epen,
+ //"%6d%6d%6d%24.15e%24.15e%24.15e%24.15e%24.15e\n",
+ "%6d%6d%6d%12.4f%12.4f%12.4f%12.4f%12.4f\n",
+ system->my_atoms[i].orig_id,
+ system->my_atoms[j].orig_id,
+ system->my_atoms[k].orig_id,
+ RAD2DEG(theta), BOA_ij, BOA_jk, e_pen,
+ data->my_en.e_pen );
+
+ fprintf( out_control->ecoa,
+ //"%6d%6d%6d%24.15e%24.15e%24.15e%24.15e%24.15e\n",
+ "%6d%6d%6d%12.4f%12.4f%12.4f%12.4f%12.4f\n",
+ system->my_atoms[i].orig_id,
+ system->my_atoms[j].orig_id,
+ system->my_atoms[k].orig_id,
+ RAD2DEG(theta), BOA_ij, BOA_jk,
+ e_coa, data->my_en.e_coa );
#endif
#ifdef TEST_FORCES /* angle forces */
- Add_dBO( system, lists, j, pi, CEval1, workspace->f_ang );
- Add_dBO( system, lists, j, pk, CEval2, workspace->f_ang );
- Add_dDelta( system, lists, j,
- CEval3 + CEval7, workspace->f_ang );
-
- for( t = start_j; t < end_j; ++t ) {
- pbond_jt = &( bonds->select.bond_list[t] );
- bo_jt = &(pbond_jt->bo_data);
- temp_bo_jt = bo_jt->BO;
- temp = CUBE( temp_bo_jt );
- pBOjt7 = temp * temp * temp_bo_jt;
-
- Add_dBO( system, lists, j, t, pBOjt7 * CEval6,
- workspace->f_ang );
- Add_dBOpinpi2( system, lists, j, t, CEval5, CEval5,
- workspace->f_ang, workspace->f_ang );
- }
-
- rvec_ScaledAdd( workspace->f_ang[i], CEval8, p_ijk->dcos_di );
- rvec_ScaledAdd( workspace->f_ang[j], CEval8, p_ijk->dcos_dj );
- rvec_ScaledAdd( workspace->f_ang[k], CEval8, p_ijk->dcos_dk );
- /* end angle forces */
-
- /* penalty forces */
- Add_dDelta( system, lists, j, CEpen1, workspace->f_pen );
- Add_dBO( system, lists, j, pi, CEpen2, workspace->f_pen );
- Add_dBO( system, lists, j, pk, CEpen3, workspace->f_pen );
- /* end penalty forces */
-
- /* coalition forces */
- Add_dBO( system, lists, j, pi, CEcoa1 - CEcoa4,
- workspace->f_coa );
- Add_dBO( system, lists, j, pk, CEcoa2 - CEcoa5,
- workspace->f_coa );
- Add_dDelta( system, lists, j, CEcoa3, workspace->f_coa );
- Add_dDelta( system, lists, i, CEcoa4, workspace->f_coa );
- Add_dDelta( system, lists, k, CEcoa5, workspace->f_coa );
- /* end coalition forces */
+ Add_dBO( system, lists, j, pi, CEval1, workspace->f_ang );
+ Add_dBO( system, lists, j, pk, CEval2, workspace->f_ang );
+ Add_dDelta( system, lists, j,
+ CEval3 + CEval7, workspace->f_ang );
+
+ for( t = start_j; t < end_j; ++t ) {
+ pbond_jt = &( bonds->select.bond_list[t] );
+ bo_jt = &(pbond_jt->bo_data);
+ temp_bo_jt = bo_jt->BO;
+ temp = CUBE( temp_bo_jt );
+ pBOjt7 = temp * temp * temp_bo_jt;
+
+ Add_dBO( system, lists, j, t, pBOjt7 * CEval6,
+ workspace->f_ang );
+ Add_dBOpinpi2( system, lists, j, t, CEval5, CEval5,
+ workspace->f_ang, workspace->f_ang );
+ }
+
+ rvec_ScaledAdd( workspace->f_ang[i], CEval8, p_ijk->dcos_di );
+ rvec_ScaledAdd( workspace->f_ang[j], CEval8, p_ijk->dcos_dj );
+ rvec_ScaledAdd( workspace->f_ang[k], CEval8, p_ijk->dcos_dk );
+ /* end angle forces */
+
+ /* penalty forces */
+ Add_dDelta( system, lists, j, CEpen1, workspace->f_pen );
+ Add_dBO( system, lists, j, pi, CEpen2, workspace->f_pen );
+ Add_dBO( system, lists, j, pk, CEpen3, workspace->f_pen );
+ /* end penalty forces */
+
+ /* coalition forces */
+ Add_dBO( system, lists, j, pi, CEcoa1 - CEcoa4,
+ workspace->f_coa );
+ Add_dBO( system, lists, j, pk, CEcoa2 - CEcoa5,
+ workspace->f_coa );
+ Add_dDelta( system, lists, j, CEcoa3, workspace->f_coa );
+ Add_dDelta( system, lists, i, CEcoa4, workspace->f_coa );
+ Add_dDelta( system, lists, k, CEcoa5, workspace->f_coa );
+ /* end coalition forces */
#endif
- }
- }
- }
- }
+ }
+ }
+ }
+ }
}
-
+
Set_End_Index(pi, num_thb_intrs, thb_intrs );
}
}
@@ -547,20 +547,20 @@ void Valence_Angles( reax_system *system, control_params *control,
workspace->realloc.num_3body = num_thb_intrs;
if( num_thb_intrs > thb_intrs->num_intrs ) {
fprintf( stderr, "step%d-ran out of space on angle_list: top=%d, max=%d",
- data->step, num_thb_intrs, thb_intrs->num_intrs );
+ data->step, num_thb_intrs, thb_intrs->num_intrs );
MPI_Abort( MPI_COMM_WORLD, INSUFFICIENT_MEMORY );
}
}
- //fprintf( stderr,"%d: Number of angle interactions: %d\n",
- // data->step, num_thb_intrs );
-
+ //fprintf( stderr,"%d: Number of angle interactions: %d\n",
+ // data->step, num_thb_intrs );
+
#if defined(DEBUG)
fprintf( stderr, "Number of angle interactions: %d\n", num_thb_intrs );
- fprintf( stderr,
- "Angle Energy: %g\t Penalty Energy: %g\t Coalition Energy: %g\t\n",
- data->my_en.e_ang, data->my_en.e_pen, data->my_en.e_coa );
-
- fprintf( stderr, "3body: ext_press (%12.6f %12.6f %12.6f)\n",
- data->ext_press[0], data->ext_press[1], data->ext_press[2] );
+ fprintf( stderr,
+ "Angle Energy: %g\t Penalty Energy: %g\t Coalition Energy: %g\t\n",
+ data->my_en.e_ang, data->my_en.e_pen, data->my_en.e_coa );
+
+ fprintf( stderr, "3body: ext_press (%12.6f %12.6f %12.6f)\n",
+ data->ext_press[0], data->ext_press[1], data->ext_press[2] );
#endif
}
diff --git a/src/USER-REAXC/reaxc_valence_angles.h b/src/USER-REAXC/reaxc_valence_angles.h
index 21cb5ec4510c8bc9d53accbc44751ce0d78a2440..d7b79d7fc7f8af1beea0b995e76203ee23651c99 100644
--- a/src/USER-REAXC/reaxc_valence_angles.h
+++ b/src/USER-REAXC/reaxc_valence_angles.h
@@ -14,12 +14,12 @@
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -30,10 +30,10 @@
#include "reaxc_types.h"
void Valence_Angles( reax_system*, control_params*, simulation_data*,
- storage*, reax_list**, output_controls* );
+ storage*, reax_list**, output_controls* );
void Calculate_Theta( rvec, real, rvec, real, real*, real* );
-
+
void Calculate_dCos_Theta( rvec, real, rvec, real, rvec*, rvec*, rvec* );
-
+
#endif
diff --git a/src/USER-REAXC/reaxc_vector.cpp b/src/USER-REAXC/reaxc_vector.cpp
index df4a546d8d2ff524039c77dec3b7f7b3381912cf..1008eabe3444b4309afecc45551e5cb5eacaa430 100644
--- a/src/USER-REAXC/reaxc_vector.cpp
+++ b/src/USER-REAXC/reaxc_vector.cpp
@@ -1,6 +1,6 @@
/*----------------------------------------------------------------------
PuReMD - Purdue ReaxFF Molecular Dynamics Program
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, hmaktulga@lbl.gov
Joseph Fogarty, jcfogart@mail.usf.edu
@@ -9,17 +9,17 @@
Please cite the related publication:
H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama,
- "Parallel Reactive Molecular Dynamics: Numerical Methods and
+ "Parallel Reactive Molecular Dynamics: Numerical Methods and
Algorithmic Techniques", Parallel Computing, in press.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -37,7 +37,7 @@ int Vector_isZero( real* v, int k )
for( --k; k>=0; --k )
if( fabs( v[k] ) > ALMOST_ZERO )
return 0;
-
+
return 1;
}
@@ -80,7 +80,7 @@ void Vector_Add( real* dest, real c, real* v, int k )
real Dot( real* v1, real* v2, int k )
{
real ret = 0;
-
+
for( --k; k>=0; --k )
ret += v1[k] * v2[k];
@@ -91,7 +91,7 @@ real Dot( real* v1, real* v2, int k )
real Norm( real* v1, int k )
{
real ret = 0;
-
+
for( --k; k>=0; --k )
ret += SQR( v1[k] );
@@ -143,7 +143,7 @@ void rvec_Sum( rvec ret, rvec v1 ,rvec v2 )
void rvec_ScaledSum( rvec ret, real c1, rvec v1 ,real c2, rvec v2 )
{
- ret[0] = c1 * v1[0] + c2 * v2[0];
+ ret[0] = c1 * v1[0] + c2 * v2[0];
ret[1] = c1 * v1[1] + c2 * v2[1];
ret[2] = c1 * v1[2] + c2 * v2[2];
}
@@ -233,8 +233,8 @@ real rvec_Norm( rvec v )
int rvec_isZero( rvec v )
{
- if( fabs(v[0]) > ALMOST_ZERO ||
- fabs(v[1]) > ALMOST_ZERO ||
+ if( fabs(v[0]) > ALMOST_ZERO ||
+ fabs(v[1]) > ALMOST_ZERO ||
fabs(v[2]) > ALMOST_ZERO )
return 0;
return 1;
@@ -264,31 +264,31 @@ void rtensor_Multiply( rtensor ret, rtensor m1, rtensor m2 )
rtensor temp;
// check if the result matrix is the same as one of m1, m2.
- // if so, we cannot modify the contents of m1 or m2, so
+ // if so, we cannot modify the contents of m1 or m2, so
// we have to use a temp matrix.
if( ret == m1 || ret == m2 )
{
for( i = 0; i < 3; ++i )
- for( j = 0; j < 3; ++j )
- {
- temp[i][j] = 0;
- for( k = 0; k < 3; ++k )
- temp[i][j] += m1[i][k] * m2[k][j];
- }
-
+ for( j = 0; j < 3; ++j )
+ {
+ temp[i][j] = 0;
+ for( k = 0; k < 3; ++k )
+ temp[i][j] += m1[i][k] * m2[k][j];
+ }
+
for( i = 0; i < 3; ++i )
- for( j = 0; j < 3; ++j )
- ret[i][j] = temp[i][j];
+ for( j = 0; j < 3; ++j )
+ ret[i][j] = temp[i][j];
}
else
{
for( i = 0; i < 3; ++i )
- for( j = 0; j < 3; ++j )
- {
- ret[i][j] = 0;
- for( k = 0; k < 3; ++k )
- ret[i][j] += m1[i][k] * m2[k][j];
- }
+ for( j = 0; j < 3; ++j )
+ {
+ ret[i][j] = 0;
+ for( k = 0; k < 3; ++k )
+ ret[i][j] += m1[i][k] * m2[k][j];
+ }
}
}
@@ -298,20 +298,20 @@ void rtensor_MatVec( rvec ret, rtensor m, rvec v )
int i;
rvec temp;
- // if ret is the same vector as v, we cannot modify the
+ // if ret is the same vector as v, we cannot modify the
// contents of v until all computation is finished.
if( ret == v )
{
for( i = 0; i < 3; ++i )
- temp[i] = m[i][0] * v[0] + m[i][1] * v[1] + m[i][2] * v[2];
+ temp[i] = m[i][0] * v[0] + m[i][1] * v[1] + m[i][2] * v[2];
for( i = 0; i < 3; ++i )
- ret[i] = temp[i];
+ ret[i] = temp[i];
}
else
{
for( i = 0; i < 3; ++i )
- ret[i] = m[i][0] * v[0] + m[i][1] * v[1] + m[i][2] * v[2];
+ ret[i] = m[i][0] * v[0] + m[i][1] * v[1] + m[i][2] * v[2];
}
}
@@ -356,8 +356,8 @@ void rtensor_Sum( rtensor ret, rtensor t1, rtensor t2 )
}
-void rtensor_ScaledSum( rtensor ret, real c1, rtensor t1,
- real c2, rtensor t2 )
+void rtensor_ScaledSum( rtensor ret, real c1, rtensor t1,
+ real c2, rtensor t2 )
{
int i, j;
@@ -423,7 +423,7 @@ void Print_rTensor(FILE* fp, rtensor t)
{
fprintf(fp,"[");
for (j=0; j < 3; j++)
- fprintf(fp,"%8.3f,\t",t[i][j]);
+ fprintf(fp,"%8.3f,\t",t[i][j]);
fprintf(fp,"]\n");
}
}
@@ -520,4 +520,3 @@ void ivec_Max3( ivec res, ivec v1, ivec v2, ivec v3 )
res[1] = MAX3( v1[1], v2[1], v3[1] );
res[2] = MAX3( v1[2], v2[2], v3[2] );
}
-
diff --git a/src/USER-REAXC/reaxc_vector.h b/src/USER-REAXC/reaxc_vector.h
index 2d43cc057cc686a4bfeb61d40c7b2c48f1c4562f..a33e249bcdb73bdcc02b04965be74d1d011e5c87 100644
--- a/src/USER-REAXC/reaxc_vector.h
+++ b/src/USER-REAXC/reaxc_vector.h
@@ -14,12 +14,12 @@
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
diff --git a/src/USER-SPH/atom_vec_meso.cpp b/src/USER-SPH/atom_vec_meso.cpp
index 792355007b13d4ca2959b76353fb5b94bea049af..4bf403daecf1992473e88cc00d3be81db3dbaa06 100644
--- a/src/USER-SPH/atom_vec_meso.cpp
+++ b/src/USER-SPH/atom_vec_meso.cpp
@@ -28,24 +28,24 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
AtomVecMeso::AtomVecMeso(LAMMPS *lmp, int narg, char **arg) :
- AtomVec(lmp, narg, arg) {
- molecular = 0;
- mass_type = 1;
-
- comm_x_only = 0; // we communicate not only x forward but also vest ...
- comm_f_only = 0; // we also communicate de and drho in reverse direction
- size_forward = 8; // 3 + rho + e + vest[3], that means we may only communicate 5 in hybrid
- size_reverse = 5; // 3 + drho + de
- size_border = 12; // 6 + rho + e + vest[3] + cv
- size_velocity = 3;
- size_data_atom = 8;
- size_data_vel = 4;
- xcol_data = 6;
-
- atom->e_flag = 1;
- atom->rho_flag = 1;
- atom->cv_flag = 1;
- atom->vest_flag = 1;
+ AtomVec(lmp, narg, arg) {
+ molecular = 0;
+ mass_type = 1;
+
+ comm_x_only = 0; // we communicate not only x forward but also vest ...
+ comm_f_only = 0; // we also communicate de and drho in reverse direction
+ size_forward = 8; // 3 + rho + e + vest[3], that means we may only communicate 5 in hybrid
+ size_reverse = 5; // 3 + drho + de
+ size_border = 12; // 6 + rho + e + vest[3] + cv
+ size_velocity = 3;
+ size_data_atom = 8;
+ size_data_vel = 4;
+ xcol_data = 6;
+
+ atom->e_flag = 1;
+ atom->rho_flag = 1;
+ atom->cv_flag = 1;
+ atom->vest_flag = 1;
}
/* ----------------------------------------------------------------------
@@ -55,32 +55,32 @@ AtomVecMeso::AtomVecMeso(LAMMPS *lmp, int narg, char **arg) :
------------------------------------------------------------------------- */
void AtomVecMeso::grow(int n) {
- if (n == 0)
- nmax += DELTA;
- else
- nmax = n;
- atom->nmax = nmax;
- if (nmax < 0 || nmax > MAXSMALLINT)
- error->one(FLERR,"Per-processor system is too big");
-
- tag = memory->grow(atom->tag, nmax, "atom:tag");
- type = memory->grow(atom->type, nmax, "atom:type");
- mask = memory->grow(atom->mask, nmax, "atom:mask");
- image = memory->grow(atom->image, nmax, "atom:image");
- x = memory->grow(atom->x, nmax, 3, "atom:x");
- v = memory->grow(atom->v, nmax, 3, "atom:v");
- f = memory->grow(atom->f, nmax*comm->nthreads, 3, "atom:f");
-
- rho = memory->grow(atom->rho, nmax, "atom:rho");
- drho = memory->grow(atom->drho, nmax*comm->nthreads, "atom:drho");
- e = memory->grow(atom->e, nmax, "atom:e");
- de = memory->grow(atom->de, nmax*comm->nthreads, "atom:de");
- vest = memory->grow(atom->vest, nmax, 3, "atom:vest");
- cv = memory->grow(atom->cv, nmax, "atom:cv");
-
- if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
- modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
+ if (n == 0)
+ nmax += DELTA;
+ else
+ nmax = n;
+ atom->nmax = nmax;
+ if (nmax < 0 || nmax > MAXSMALLINT)
+ error->one(FLERR,"Per-processor system is too big");
+
+ tag = memory->grow(atom->tag, nmax, "atom:tag");
+ type = memory->grow(atom->type, nmax, "atom:type");
+ mask = memory->grow(atom->mask, nmax, "atom:mask");
+ image = memory->grow(atom->image, nmax, "atom:image");
+ x = memory->grow(atom->x, nmax, 3, "atom:x");
+ v = memory->grow(atom->v, nmax, 3, "atom:v");
+ f = memory->grow(atom->f, nmax*comm->nthreads, 3, "atom:f");
+
+ rho = memory->grow(atom->rho, nmax, "atom:rho");
+ drho = memory->grow(atom->drho, nmax*comm->nthreads, "atom:drho");
+ e = memory->grow(atom->e, nmax, "atom:e");
+ de = memory->grow(atom->de, nmax*comm->nthreads, "atom:de");
+ vest = memory->grow(atom->vest, nmax, 3, "atom:vest");
+ cv = memory->grow(atom->cv, nmax, "atom:cv");
+
+ if (atom->nextra_grow)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
}
/* ----------------------------------------------------------------------
@@ -88,495 +88,495 @@ void AtomVecMeso::grow(int n) {
------------------------------------------------------------------------- */
void AtomVecMeso::grow_reset() {
- tag = atom->tag;
- type = atom->type;
- mask = atom->mask;
- image = atom->image;
- x = atom->x;
- v = atom->v;
- f = atom->f;
- rho = atom->rho;
- drho = atom->drho;
- e = atom->e;
- de = atom->de;
- vest = atom->vest;
- cv = atom->cv;
+ tag = atom->tag;
+ type = atom->type;
+ mask = atom->mask;
+ image = atom->image;
+ x = atom->x;
+ v = atom->v;
+ f = atom->f;
+ rho = atom->rho;
+ drho = atom->drho;
+ e = atom->e;
+ de = atom->de;
+ vest = atom->vest;
+ cv = atom->cv;
}
/* ---------------------------------------------------------------------- */
void AtomVecMeso::copy(int i, int j, int delflag) {
- //printf("in AtomVecMeso::copy\n");
- tag[j] = tag[i];
- type[j] = type[i];
- mask[j] = mask[i];
- image[j] = image[i];
- x[j][0] = x[i][0];
- x[j][1] = x[i][1];
- x[j][2] = x[i][2];
- v[j][0] = v[i][0];
- v[j][1] = v[i][1];
- v[j][2] = v[i][2];
-
- rho[j] = rho[i];
- drho[j] = drho[i];
- e[j] = e[i];
- de[j] = de[i];
- cv[j] = cv[i];
- vest[j][0] = vest[i][0];
- vest[j][1] = vest[i][1];
- vest[j][2] = vest[i][2];
-
- if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
- modify->fix[atom->extra_grow[iextra]]->copy_arrays(i, j);
+ //printf("in AtomVecMeso::copy\n");
+ tag[j] = tag[i];
+ type[j] = type[i];
+ mask[j] = mask[i];
+ image[j] = image[i];
+ x[j][0] = x[i][0];
+ x[j][1] = x[i][1];
+ x[j][2] = x[i][2];
+ v[j][0] = v[i][0];
+ v[j][1] = v[i][1];
+ v[j][2] = v[i][2];
+
+ rho[j] = rho[i];
+ drho[j] = drho[i];
+ e[j] = e[i];
+ de[j] = de[i];
+ cv[j] = cv[i];
+ vest[j][0] = vest[i][0];
+ vest[j][1] = vest[i][1];
+ vest[j][2] = vest[i][2];
+
+ if (atom->nextra_grow)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ modify->fix[atom->extra_grow[iextra]]->copy_arrays(i, j);
}
/* ---------------------------------------------------------------------- */
int AtomVecMeso::pack_comm_hybrid(int n, int *list, double *buf) {
- //printf("in AtomVecMeso::pack_comm_hybrid\n");
- int i, j, m;
-
- m = 0;
- for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = rho[j];
- buf[m++] = e[j];
- buf[m++] = vest[j][0];
- buf[m++] = vest[j][1];
- buf[m++] = vest[j][2];
- }
- return m;
+ //printf("in AtomVecMeso::pack_comm_hybrid\n");
+ int i, j, m;
+
+ m = 0;
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = rho[j];
+ buf[m++] = e[j];
+ buf[m++] = vest[j][0];
+ buf[m++] = vest[j][1];
+ buf[m++] = vest[j][2];
+ }
+ return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecMeso::unpack_comm_hybrid(int n, int first, double *buf) {
- //printf("in AtomVecMeso::unpack_comm_hybrid\n");
- int i, m, last;
-
- m = 0;
- last = first + n;
- for (i = first; i < last; i++) {
- rho[i] = buf[m++];
- e[i] = buf[m++];
- vest[i][0] = buf[m++];
- vest[i][1] = buf[m++];
- vest[i][2] = buf[m++];
- }
- return m;
+ //printf("in AtomVecMeso::unpack_comm_hybrid\n");
+ int i, m, last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ rho[i] = buf[m++];
+ e[i] = buf[m++];
+ vest[i][0] = buf[m++];
+ vest[i][1] = buf[m++];
+ vest[i][2] = buf[m++];
+ }
+ return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecMeso::pack_border_hybrid(int n, int *list, double *buf) {
- //printf("in AtomVecMeso::pack_border_hybrid\n");
- int i, j, m;
-
- m = 0;
- for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = rho[j];
- buf[m++] = e[j];
- buf[m++] = vest[j][0];
- buf[m++] = vest[j][1];
- buf[m++] = vest[j][2];
- }
- return m;
+ //printf("in AtomVecMeso::pack_border_hybrid\n");
+ int i, j, m;
+
+ m = 0;
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = rho[j];
+ buf[m++] = e[j];
+ buf[m++] = vest[j][0];
+ buf[m++] = vest[j][1];
+ buf[m++] = vest[j][2];
+ }
+ return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecMeso::unpack_border_hybrid(int n, int first, double *buf) {
- //printf("in AtomVecMeso::unpack_border_hybrid\n");
- int i, m, last;
-
- m = 0;
- last = first + n;
- for (i = first; i < last; i++) {
- rho[i] = buf[m++];
- e[i] = buf[m++];
- vest[i][0] = buf[m++];
- vest[i][1] = buf[m++];
- vest[i][2] = buf[m++];
- }
- return m;
+ //printf("in AtomVecMeso::unpack_border_hybrid\n");
+ int i, m, last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ rho[i] = buf[m++];
+ e[i] = buf[m++];
+ vest[i][0] = buf[m++];
+ vest[i][1] = buf[m++];
+ vest[i][2] = buf[m++];
+ }
+ return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecMeso::pack_reverse_hybrid(int n, int first, double *buf) {
- //printf("in AtomVecMeso::pack_reverse_hybrid\n");
- int i, m, last;
-
- m = 0;
- last = first + n;
- for (i = first; i < last; i++) {
- buf[m++] = drho[i];
- buf[m++] = de[i];
- }
- return m;
+ //printf("in AtomVecMeso::pack_reverse_hybrid\n");
+ int i, m, last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ buf[m++] = drho[i];
+ buf[m++] = de[i];
+ }
+ return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecMeso::unpack_reverse_hybrid(int n, int *list, double *buf) {
- //printf("in AtomVecMeso::unpack_reverse_hybrid\n");
- int i, j, m;
-
- m = 0;
- for (i = 0; i < n; i++) {
- j = list[i];
- drho[j] += buf[m++];
- de[j] += buf[m++];
- }
- return m;
+ //printf("in AtomVecMeso::unpack_reverse_hybrid\n");
+ int i, j, m;
+
+ m = 0;
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ drho[j] += buf[m++];
+ de[j] += buf[m++];
+ }
+ return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecMeso::pack_comm(int n, int *list, double *buf, int pbc_flag,
- int *pbc) {
- //printf("in AtomVecMeso::pack_comm\n");
- int i, j, m;
- double dx, dy, dz;
-
- m = 0;
- if (pbc_flag == 0) {
- for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0];
- buf[m++] = x[j][1];
- buf[m++] = x[j][2];
- buf[m++] = rho[j];
- buf[m++] = e[j];
- buf[m++] = vest[j][0];
- buf[m++] = vest[j][1];
- buf[m++] = vest[j][2];
- }
- } else {
- if (domain->triclinic == 0) {
- dx = pbc[0] * domain->xprd;
- dy = pbc[1] * domain->yprd;
- dz = pbc[2] * domain->zprd;
- } else {
- dx = pbc[0] * domain->xprd + pbc[5] * domain->xy + pbc[4] * domain->xz;
- dy = pbc[1] * domain->yprd + pbc[3] * domain->yz;
- dz = pbc[2] * domain->zprd;
- }
- for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = rho[j];
- buf[m++] = e[j];
- buf[m++] = vest[j][0];
- buf[m++] = vest[j][1];
- buf[m++] = vest[j][2];
- }
- }
- return m;
+ int *pbc) {
+ //printf("in AtomVecMeso::pack_comm\n");
+ int i, j, m;
+ double dx, dy, dz;
+
+ m = 0;
+ if (pbc_flag == 0) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = x[j][0];
+ buf[m++] = x[j][1];
+ buf[m++] = x[j][2];
+ buf[m++] = rho[j];
+ buf[m++] = e[j];
+ buf[m++] = vest[j][0];
+ buf[m++] = vest[j][1];
+ buf[m++] = vest[j][2];
+ }
+ } else {
+ if (domain->triclinic == 0) {
+ dx = pbc[0] * domain->xprd;
+ dy = pbc[1] * domain->yprd;
+ dz = pbc[2] * domain->zprd;
+ } else {
+ dx = pbc[0] * domain->xprd + pbc[5] * domain->xy + pbc[4] * domain->xz;
+ dy = pbc[1] * domain->yprd + pbc[3] * domain->yz;
+ dz = pbc[2] * domain->zprd;
+ }
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = rho[j];
+ buf[m++] = e[j];
+ buf[m++] = vest[j][0];
+ buf[m++] = vest[j][1];
+ buf[m++] = vest[j][2];
+ }
+ }
+ return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecMeso::pack_comm_vel(int n, int *list, double *buf, int pbc_flag,
- int *pbc) {
- //printf("in AtomVecMeso::pack_comm_vel\n");
- int i, j, m;
- double dx, dy, dz;
-
- m = 0;
- if (pbc_flag == 0) {
- for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0];
- buf[m++] = x[j][1];
- buf[m++] = x[j][2];
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
- buf[m++] = rho[j];
- buf[m++] = e[j];
- buf[m++] = vest[j][0];
- buf[m++] = vest[j][1];
- buf[m++] = vest[j][2];
- }
- } else {
- if (domain->triclinic == 0) {
- dx = pbc[0] * domain->xprd;
- dy = pbc[1] * domain->yprd;
- dz = pbc[2] * domain->zprd;
- } else {
- dx = pbc[0] * domain->xprd + pbc[5] * domain->xy + pbc[4] * domain->xz;
- dy = pbc[1] * domain->yprd + pbc[3] * domain->yz;
- dz = pbc[2] * domain->zprd;
- }
- for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
- buf[m++] = rho[j];
- buf[m++] = e[j];
- buf[m++] = vest[j][0];
- buf[m++] = vest[j][1];
- buf[m++] = vest[j][2];
- }
- }
- return m;
+ int *pbc) {
+ //printf("in AtomVecMeso::pack_comm_vel\n");
+ int i, j, m;
+ double dx, dy, dz;
+
+ m = 0;
+ if (pbc_flag == 0) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = x[j][0];
+ buf[m++] = x[j][1];
+ buf[m++] = x[j][2];
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
+ buf[m++] = rho[j];
+ buf[m++] = e[j];
+ buf[m++] = vest[j][0];
+ buf[m++] = vest[j][1];
+ buf[m++] = vest[j][2];
+ }
+ } else {
+ if (domain->triclinic == 0) {
+ dx = pbc[0] * domain->xprd;
+ dy = pbc[1] * domain->yprd;
+ dz = pbc[2] * domain->zprd;
+ } else {
+ dx = pbc[0] * domain->xprd + pbc[5] * domain->xy + pbc[4] * domain->xz;
+ dy = pbc[1] * domain->yprd + pbc[3] * domain->yz;
+ dz = pbc[2] * domain->zprd;
+ }
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
+ buf[m++] = rho[j];
+ buf[m++] = e[j];
+ buf[m++] = vest[j][0];
+ buf[m++] = vest[j][1];
+ buf[m++] = vest[j][2];
+ }
+ }
+ return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecMeso::unpack_comm(int n, int first, double *buf) {
- //printf("in AtomVecMeso::unpack_comm\n");
- int i, m, last;
-
- m = 0;
- last = first + n;
- for (i = first; i < last; i++) {
- x[i][0] = buf[m++];
- x[i][1] = buf[m++];
- x[i][2] = buf[m++];
- rho[i] = buf[m++];
- e[i] = buf[m++];
- vest[i][0] = buf[m++];
- vest[i][1] = buf[m++];
- vest[i][2] = buf[m++];
- }
+ //printf("in AtomVecMeso::unpack_comm\n");
+ int i, m, last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ x[i][0] = buf[m++];
+ x[i][1] = buf[m++];
+ x[i][2] = buf[m++];
+ rho[i] = buf[m++];
+ e[i] = buf[m++];
+ vest[i][0] = buf[m++];
+ vest[i][1] = buf[m++];
+ vest[i][2] = buf[m++];
+ }
}
/* ---------------------------------------------------------------------- */
void AtomVecMeso::unpack_comm_vel(int n, int first, double *buf) {
- //printf("in AtomVecMeso::unpack_comm_vel\n");
- int i, m, last;
-
- m = 0;
- last = first + n;
- for (i = first; i < last; i++) {
- x[i][0] = buf[m++];
- x[i][1] = buf[m++];
- x[i][2] = buf[m++];
- v[i][0] = buf[m++];
- v[i][1] = buf[m++];
- v[i][2] = buf[m++];
- rho[i] = buf[m++];
- e[i] = buf[m++];
- vest[i][0] = buf[m++];
- vest[i][1] = buf[m++];
- vest[i][2] = buf[m++];
- }
+ //printf("in AtomVecMeso::unpack_comm_vel\n");
+ int i, m, last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ x[i][0] = buf[m++];
+ x[i][1] = buf[m++];
+ x[i][2] = buf[m++];
+ v[i][0] = buf[m++];
+ v[i][1] = buf[m++];
+ v[i][2] = buf[m++];
+ rho[i] = buf[m++];
+ e[i] = buf[m++];
+ vest[i][0] = buf[m++];
+ vest[i][1] = buf[m++];
+ vest[i][2] = buf[m++];
+ }
}
/* ---------------------------------------------------------------------- */
int AtomVecMeso::pack_reverse(int n, int first, double *buf) {
- //printf("in AtomVecMeso::pack_reverse\n");
- int i, m, last;
-
- m = 0;
- last = first + n;
- for (i = first; i < last; i++) {
- buf[m++] = f[i][0];
- buf[m++] = f[i][1];
- buf[m++] = f[i][2];
- buf[m++] = drho[i];
- buf[m++] = de[i];
- }
- return m;
+ //printf("in AtomVecMeso::pack_reverse\n");
+ int i, m, last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ buf[m++] = f[i][0];
+ buf[m++] = f[i][1];
+ buf[m++] = f[i][2];
+ buf[m++] = drho[i];
+ buf[m++] = de[i];
+ }
+ return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecMeso::unpack_reverse(int n, int *list, double *buf) {
- //printf("in AtomVecMeso::unpack_reverse\n");
- int i, j, m;
-
- m = 0;
- for (i = 0; i < n; i++) {
- j = list[i];
- f[j][0] += buf[m++];
- f[j][1] += buf[m++];
- f[j][2] += buf[m++];
- drho[j] += buf[m++];
- de[j] += buf[m++];
- }
+ //printf("in AtomVecMeso::unpack_reverse\n");
+ int i, j, m;
+
+ m = 0;
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ f[j][0] += buf[m++];
+ f[j][1] += buf[m++];
+ f[j][2] += buf[m++];
+ drho[j] += buf[m++];
+ de[j] += buf[m++];
+ }
}
/* ---------------------------------------------------------------------- */
int AtomVecMeso::pack_border(int n, int *list, double *buf, int pbc_flag,
- int *pbc) {
- //printf("in AtomVecMeso::pack_border\n");
- int i, j, m;
- double dx, dy, dz;
-
- m = 0;
- if (pbc_flag == 0) {
- for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0];
- buf[m++] = x[j][1];
- buf[m++] = x[j][2];
- buf[m++] = tag[j];
- buf[m++] = type[j];
- buf[m++] = mask[j];
- buf[m++] = rho[j];
- buf[m++] = e[j];
- buf[m++] = cv[j];
- buf[m++] = vest[j][0];
- buf[m++] = vest[j][1];
- buf[m++] = vest[j][2];
- }
- } else {
- if (domain->triclinic == 0) {
- dx = pbc[0] * domain->xprd;
- dy = pbc[1] * domain->yprd;
- dz = pbc[2] * domain->zprd;
- } else {
- dx = pbc[0];
- dy = pbc[1];
- dz = pbc[2];
- }
- for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = tag[j];
- buf[m++] = type[j];
- buf[m++] = mask[j];
- buf[m++] = rho[j];
- buf[m++] = e[j];
- buf[m++] = cv[j];
- buf[m++] = vest[j][0];
- buf[m++] = vest[j][1];
- buf[m++] = vest[j][2];
- }
- }
- return m;
+ int *pbc) {
+ //printf("in AtomVecMeso::pack_border\n");
+ int i, j, m;
+ double dx, dy, dz;
+
+ m = 0;
+ if (pbc_flag == 0) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = x[j][0];
+ buf[m++] = x[j][1];
+ buf[m++] = x[j][2];
+ buf[m++] = tag[j];
+ buf[m++] = type[j];
+ buf[m++] = mask[j];
+ buf[m++] = rho[j];
+ buf[m++] = e[j];
+ buf[m++] = cv[j];
+ buf[m++] = vest[j][0];
+ buf[m++] = vest[j][1];
+ buf[m++] = vest[j][2];
+ }
+ } else {
+ if (domain->triclinic == 0) {
+ dx = pbc[0] * domain->xprd;
+ dy = pbc[1] * domain->yprd;
+ dz = pbc[2] * domain->zprd;
+ } else {
+ dx = pbc[0];
+ dy = pbc[1];
+ dz = pbc[2];
+ }
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = tag[j];
+ buf[m++] = type[j];
+ buf[m++] = mask[j];
+ buf[m++] = rho[j];
+ buf[m++] = e[j];
+ buf[m++] = cv[j];
+ buf[m++] = vest[j][0];
+ buf[m++] = vest[j][1];
+ buf[m++] = vest[j][2];
+ }
+ }
+ return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecMeso::pack_border_vel(int n, int *list, double *buf, int pbc_flag,
- int *pbc) {
- //printf("in AtomVecMeso::pack_border_vel\n");
- int i, j, m;
- double dx, dy, dz;
-
- m = 0;
- if (pbc_flag == 0) {
- for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0];
- buf[m++] = x[j][1];
- buf[m++] = x[j][2];
- buf[m++] = tag[j];
- buf[m++] = type[j];
- buf[m++] = mask[j];
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
- buf[m++] = rho[j];
- buf[m++] = e[j];
- buf[m++] = cv[j];
- buf[m++] = vest[j][0];
- buf[m++] = vest[j][1];
- buf[m++] = vest[j][2];
- }
- } else {
- if (domain->triclinic == 0) {
- dx = pbc[0] * domain->xprd;
- dy = pbc[1] * domain->yprd;
- dz = pbc[2] * domain->zprd;
- } else {
- dx = pbc[0];
- dy = pbc[1];
- dz = pbc[2];
- }
- for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = tag[j];
- buf[m++] = type[j];
- buf[m++] = mask[j];
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
- buf[m++] = rho[j];
- buf[m++] = e[j];
- buf[m++] = cv[j];
- buf[m++] = vest[j][0];
- buf[m++] = vest[j][1];
- buf[m++] = vest[j][2];
- }
- }
- return m;
+ int *pbc) {
+ //printf("in AtomVecMeso::pack_border_vel\n");
+ int i, j, m;
+ double dx, dy, dz;
+
+ m = 0;
+ if (pbc_flag == 0) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = x[j][0];
+ buf[m++] = x[j][1];
+ buf[m++] = x[j][2];
+ buf[m++] = tag[j];
+ buf[m++] = type[j];
+ buf[m++] = mask[j];
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
+ buf[m++] = rho[j];
+ buf[m++] = e[j];
+ buf[m++] = cv[j];
+ buf[m++] = vest[j][0];
+ buf[m++] = vest[j][1];
+ buf[m++] = vest[j][2];
+ }
+ } else {
+ if (domain->triclinic == 0) {
+ dx = pbc[0] * domain->xprd;
+ dy = pbc[1] * domain->yprd;
+ dz = pbc[2] * domain->zprd;
+ } else {
+ dx = pbc[0];
+ dy = pbc[1];
+ dz = pbc[2];
+ }
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = tag[j];
+ buf[m++] = type[j];
+ buf[m++] = mask[j];
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
+ buf[m++] = rho[j];
+ buf[m++] = e[j];
+ buf[m++] = cv[j];
+ buf[m++] = vest[j][0];
+ buf[m++] = vest[j][1];
+ buf[m++] = vest[j][2];
+ }
+ }
+ return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecMeso::unpack_border(int n, int first, double *buf) {
- //printf("in AtomVecMeso::unpack_border\n");
- int i, m, last;
-
- m = 0;
- last = first + n;
- for (i = first; i < last; i++) {
- if (i == nmax)
- grow(0);
- x[i][0] = buf[m++];
- x[i][1] = buf[m++];
- x[i][2] = buf[m++];
- tag[i] = static_cast<int> (buf[m++]);
- type[i] = static_cast<int> (buf[m++]);
- mask[i] = static_cast<int> (buf[m++]);
- rho[i] = buf[m++];
- e[i] = buf[m++];
- cv[i] = buf[m++];
- vest[i][0] = buf[m++];
- vest[i][1] = buf[m++];
- vest[i][2] = buf[m++];
- }
+ //printf("in AtomVecMeso::unpack_border\n");
+ int i, m, last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ if (i == nmax)
+ grow(0);
+ x[i][0] = buf[m++];
+ x[i][1] = buf[m++];
+ x[i][2] = buf[m++];
+ tag[i] = static_cast<int> (buf[m++]);
+ type[i] = static_cast<int> (buf[m++]);
+ mask[i] = static_cast<int> (buf[m++]);
+ rho[i] = buf[m++];
+ e[i] = buf[m++];
+ cv[i] = buf[m++];
+ vest[i][0] = buf[m++];
+ vest[i][1] = buf[m++];
+ vest[i][2] = buf[m++];
+ }
}
/* ---------------------------------------------------------------------- */
void AtomVecMeso::unpack_border_vel(int n, int first, double *buf) {
- //printf("in AtomVecMeso::unpack_border_vel\n");
- int i, m, last;
-
- m = 0;
- last = first + n;
- for (i = first; i < last; i++) {
- if (i == nmax)
- grow(0);
- x[i][0] = buf[m++];
- x[i][1] = buf[m++];
- x[i][2] = buf[m++];
- tag[i] = static_cast<int> (buf[m++]);
- type[i] = static_cast<int> (buf[m++]);
- mask[i] = static_cast<int> (buf[m++]);
- v[i][0] = buf[m++];
- v[i][1] = buf[m++];
- v[i][2] = buf[m++];
- rho[i] = buf[m++];
- e[i] = buf[m++];
- cv[i] = buf[m++];
- vest[i][0] = buf[m++];
- vest[i][1] = buf[m++];
- vest[i][2] = buf[m++];
- }
+ //printf("in AtomVecMeso::unpack_border_vel\n");
+ int i, m, last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ if (i == nmax)
+ grow(0);
+ x[i][0] = buf[m++];
+ x[i][1] = buf[m++];
+ x[i][2] = buf[m++];
+ tag[i] = static_cast<int> (buf[m++]);
+ type[i] = static_cast<int> (buf[m++]);
+ mask[i] = static_cast<int> (buf[m++]);
+ v[i][0] = buf[m++];
+ v[i][1] = buf[m++];
+ v[i][2] = buf[m++];
+ rho[i] = buf[m++];
+ e[i] = buf[m++];
+ cv[i] = buf[m++];
+ vest[i][0] = buf[m++];
+ vest[i][1] = buf[m++];
+ vest[i][2] = buf[m++];
+ }
}
/* ----------------------------------------------------------------------
@@ -585,66 +585,66 @@ void AtomVecMeso::unpack_border_vel(int n, int first, double *buf) {
------------------------------------------------------------------------- */
int AtomVecMeso::pack_exchange(int i, double *buf) {
- //printf("in AtomVecMeso::pack_exchange\n");
- int m = 1;
- buf[m++] = x[i][0];
- buf[m++] = x[i][1];
- buf[m++] = x[i][2];
- buf[m++] = v[i][0];
- buf[m++] = v[i][1];
- buf[m++] = v[i][2];
- buf[m++] = tag[i];
- buf[m++] = type[i];
- buf[m++] = mask[i];
- buf[m++] = image[i];
- buf[m++] = rho[i];
- buf[m++] = e[i];
- buf[m++] = cv[i];
- buf[m++] = vest[i][0];
- buf[m++] = vest[i][1];
- buf[m++] = vest[i][2];
-
- if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
- m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i, &buf[m]);
-
- buf[0] = m;
- return m;
+ //printf("in AtomVecMeso::pack_exchange\n");
+ int m = 1;
+ buf[m++] = x[i][0];
+ buf[m++] = x[i][1];
+ buf[m++] = x[i][2];
+ buf[m++] = v[i][0];
+ buf[m++] = v[i][1];
+ buf[m++] = v[i][2];
+ buf[m++] = tag[i];
+ buf[m++] = type[i];
+ buf[m++] = mask[i];
+ buf[m++] = image[i];
+ buf[m++] = rho[i];
+ buf[m++] = e[i];
+ buf[m++] = cv[i];
+ buf[m++] = vest[i][0];
+ buf[m++] = vest[i][1];
+ buf[m++] = vest[i][2];
+
+ if (atom->nextra_grow)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i, &buf[m]);
+
+ buf[0] = m;
+ return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecMeso::unpack_exchange(double *buf) {
- //printf("in AtomVecMeso::unpack_exchange\n");
- int nlocal = atom->nlocal;
- if (nlocal == nmax)
- grow(0);
-
- int m = 1;
- x[nlocal][0] = buf[m++];
- x[nlocal][1] = buf[m++];
- x[nlocal][2] = buf[m++];
- v[nlocal][0] = buf[m++];
- v[nlocal][1] = buf[m++];
- v[nlocal][2] = buf[m++];
- tag[nlocal] = static_cast<int> (buf[m++]);
- type[nlocal] = static_cast<int> (buf[m++]);
- mask[nlocal] = static_cast<int> (buf[m++]);
- image[nlocal] = static_cast<int> (buf[m++]);
- rho[nlocal] = buf[m++];
- e[nlocal] = buf[m++];
- cv[nlocal] = buf[m++];
- vest[nlocal][0] = buf[m++];
- vest[nlocal][1] = buf[m++];
- vest[nlocal][2] = buf[m++];
-
- if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
- m += modify->fix[atom->extra_grow[iextra]]-> unpack_exchange(nlocal,
- &buf[m]);
-
- atom->nlocal++;
- return m;
+ //printf("in AtomVecMeso::unpack_exchange\n");
+ int nlocal = atom->nlocal;
+ if (nlocal == nmax)
+ grow(0);
+
+ int m = 1;
+ x[nlocal][0] = buf[m++];
+ x[nlocal][1] = buf[m++];
+ x[nlocal][2] = buf[m++];
+ v[nlocal][0] = buf[m++];
+ v[nlocal][1] = buf[m++];
+ v[nlocal][2] = buf[m++];
+ tag[nlocal] = static_cast<int> (buf[m++]);
+ type[nlocal] = static_cast<int> (buf[m++]);
+ mask[nlocal] = static_cast<int> (buf[m++]);
+ image[nlocal] = static_cast<int> (buf[m++]);
+ rho[nlocal] = buf[m++];
+ e[nlocal] = buf[m++];
+ cv[nlocal] = buf[m++];
+ vest[nlocal][0] = buf[m++];
+ vest[nlocal][1] = buf[m++];
+ vest[nlocal][2] = buf[m++];
+
+ if (atom->nextra_grow)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ m += modify->fix[atom->extra_grow[iextra]]-> unpack_exchange(nlocal,
+ &buf[m]);
+
+ atom->nlocal++;
+ return m;
}
/* ----------------------------------------------------------------------
@@ -653,17 +653,17 @@ int AtomVecMeso::unpack_exchange(double *buf) {
------------------------------------------------------------------------- */
int AtomVecMeso::size_restart() {
- int i;
+ int i;
- int nlocal = atom->nlocal;
- int n = 17 * nlocal; // 11 + rho + e + cv + vest[3]
+ int nlocal = atom->nlocal;
+ int n = 17 * nlocal; // 11 + rho + e + cv + vest[3]
- if (atom->nextra_restart)
- for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
- for (i = 0; i < nlocal; i++)
- n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
+ if (atom->nextra_restart)
+ for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
+ for (i = 0; i < nlocal; i++)
+ n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
- return n;
+ return n;
}
/* ----------------------------------------------------------------------
@@ -673,30 +673,30 @@ int AtomVecMeso::size_restart() {
------------------------------------------------------------------------- */
int AtomVecMeso::pack_restart(int i, double *buf) {
- int m = 1;
- buf[m++] = x[i][0];
- buf[m++] = x[i][1];
- buf[m++] = x[i][2];
- buf[m++] = tag[i];
- buf[m++] = type[i];
- buf[m++] = mask[i];
- buf[m++] = image[i];
- buf[m++] = v[i][0];
- buf[m++] = v[i][1];
- buf[m++] = v[i][2];
- buf[m++] = rho[i];
- buf[m++] = e[i];
- buf[m++] = cv[i];
- buf[m++] = vest[i][0];
- buf[m++] = vest[i][1];
- buf[m++] = vest[i][2];
-
- if (atom->nextra_restart)
- for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
- m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i, &buf[m]);
-
- buf[0] = m;
- return m;
+ int m = 1;
+ buf[m++] = x[i][0];
+ buf[m++] = x[i][1];
+ buf[m++] = x[i][2];
+ buf[m++] = tag[i];
+ buf[m++] = type[i];
+ buf[m++] = mask[i];
+ buf[m++] = image[i];
+ buf[m++] = v[i][0];
+ buf[m++] = v[i][1];
+ buf[m++] = v[i][2];
+ buf[m++] = rho[i];
+ buf[m++] = e[i];
+ buf[m++] = cv[i];
+ buf[m++] = vest[i][0];
+ buf[m++] = vest[i][1];
+ buf[m++] = vest[i][2];
+
+ if (atom->nextra_restart)
+ for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
+ m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i, &buf[m]);
+
+ buf[0] = m;
+ return m;
}
/* ----------------------------------------------------------------------
@@ -704,40 +704,40 @@ int AtomVecMeso::pack_restart(int i, double *buf) {
------------------------------------------------------------------------- */
int AtomVecMeso::unpack_restart(double *buf) {
- int nlocal = atom->nlocal;
- if (nlocal == nmax) {
- grow(0);
- if (atom->nextra_store)
- memory->grow(atom->extra, nmax, atom->nextra_store, "atom:extra");
- }
-
- int m = 1;
- x[nlocal][0] = buf[m++];
- x[nlocal][1] = buf[m++];
- x[nlocal][2] = buf[m++];
- tag[nlocal] = static_cast<int> (buf[m++]);
- type[nlocal] = static_cast<int> (buf[m++]);
- mask[nlocal] = static_cast<int> (buf[m++]);
- image[nlocal] = static_cast<int> (buf[m++]);
- v[nlocal][0] = buf[m++];
- v[nlocal][1] = buf[m++];
- v[nlocal][2] = buf[m++];
- rho[nlocal] = buf[m++];
- e[nlocal] = buf[m++];
- cv[nlocal] = buf[m++];
- vest[nlocal][0] = buf[m++];
- vest[nlocal][1] = buf[m++];
- vest[nlocal][2] = buf[m++];
-
- double **extra = atom->extra;
- if (atom->nextra_store) {
- int size = static_cast<int> (buf[0]) - m;
- for (int i = 0; i < size; i++)
- extra[nlocal][i] = buf[m++];
- }
-
- atom->nlocal++;
- return m;
+ int nlocal = atom->nlocal;
+ if (nlocal == nmax) {
+ grow(0);
+ if (atom->nextra_store)
+ memory->grow(atom->extra, nmax, atom->nextra_store, "atom:extra");
+ }
+
+ int m = 1;
+ x[nlocal][0] = buf[m++];
+ x[nlocal][1] = buf[m++];
+ x[nlocal][2] = buf[m++];
+ tag[nlocal] = static_cast<int> (buf[m++]);
+ type[nlocal] = static_cast<int> (buf[m++]);
+ mask[nlocal] = static_cast<int> (buf[m++]);
+ image[nlocal] = static_cast<int> (buf[m++]);
+ v[nlocal][0] = buf[m++];
+ v[nlocal][1] = buf[m++];
+ v[nlocal][2] = buf[m++];
+ rho[nlocal] = buf[m++];
+ e[nlocal] = buf[m++];
+ cv[nlocal] = buf[m++];
+ vest[nlocal][0] = buf[m++];
+ vest[nlocal][1] = buf[m++];
+ vest[nlocal][2] = buf[m++];
+
+ double **extra = atom->extra;
+ if (atom->nextra_store) {
+ int size = static_cast<int> (buf[0]) - m;
+ for (int i = 0; i < size; i++)
+ extra[nlocal][i] = buf[m++];
+ }
+
+ atom->nlocal++;
+ return m;
}
/* ----------------------------------------------------------------------
@@ -746,30 +746,30 @@ int AtomVecMeso::unpack_restart(double *buf) {
------------------------------------------------------------------------- */
void AtomVecMeso::create_atom(int itype, double *coord) {
- int nlocal = atom->nlocal;
- if (nlocal == nmax)
- grow(0);
-
- tag[nlocal] = 0;
- type[nlocal] = itype;
- x[nlocal][0] = coord[0];
- x[nlocal][1] = coord[1];
- x[nlocal][2] = coord[2];
- mask[nlocal] = 1;
- image[nlocal] = (512 << 20) | (512 << 10) | 512;
- v[nlocal][0] = 0.0;
- v[nlocal][1] = 0.0;
- v[nlocal][2] = 0.0;
- rho[nlocal] = 0.0;
- e[nlocal] = 0.0;
- cv[nlocal] = 1.0;
- vest[nlocal][0] = 0.0;
- vest[nlocal][1] = 0.0;
- vest[nlocal][2] = 0.0;
- de[nlocal] = 0.0;
- drho[nlocal] = 0.0;
-
- atom->nlocal++;
+ int nlocal = atom->nlocal;
+ if (nlocal == nmax)
+ grow(0);
+
+ tag[nlocal] = 0;
+ type[nlocal] = itype;
+ x[nlocal][0] = coord[0];
+ x[nlocal][1] = coord[1];
+ x[nlocal][2] = coord[2];
+ mask[nlocal] = 1;
+ image[nlocal] = (512 << 20) | (512 << 10) | 512;
+ v[nlocal][0] = 0.0;
+ v[nlocal][1] = 0.0;
+ v[nlocal][2] = 0.0;
+ rho[nlocal] = 0.0;
+ e[nlocal] = 0.0;
+ cv[nlocal] = 1.0;
+ vest[nlocal][0] = 0.0;
+ vest[nlocal][1] = 0.0;
+ vest[nlocal][2] = 0.0;
+ de[nlocal] = 0.0;
+ drho[nlocal] = 0.0;
+
+ atom->nlocal++;
}
/* ----------------------------------------------------------------------
@@ -778,43 +778,43 @@ void AtomVecMeso::create_atom(int itype, double *coord) {
------------------------------------------------------------------------- */
void AtomVecMeso::data_atom(double *coord, int imagetmp, char **values) {
- int nlocal = atom->nlocal;
- if (nlocal == nmax)
- grow(0);
+ int nlocal = atom->nlocal;
+ if (nlocal == nmax)
+ grow(0);
- tag[nlocal] = atoi(values[0]);
- if (tag[nlocal] <= 0)
- error->one(FLERR,"Invalid atom ID in Atoms section of data file");
+ tag[nlocal] = atoi(values[0]);
+ if (tag[nlocal] <= 0)
+ error->one(FLERR,"Invalid atom ID in Atoms section of data file");
- type[nlocal] = atoi(values[1]);
- if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
- error->one(FLERR,"Invalid atom type in Atoms section of data file");
+ type[nlocal] = atoi(values[1]);
+ if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
+ error->one(FLERR,"Invalid atom type in Atoms section of data file");
- rho[nlocal] = atof(values[2]);
- e[nlocal] = atof(values[3]);
- cv[nlocal] = atof(values[4]);
+ rho[nlocal] = atof(values[2]);
+ e[nlocal] = atof(values[3]);
+ cv[nlocal] = atof(values[4]);
- x[nlocal][0] = coord[0];
- x[nlocal][1] = coord[1];
- x[nlocal][2] = coord[2];
+ x[nlocal][0] = coord[0];
+ x[nlocal][1] = coord[1];
+ x[nlocal][2] = coord[2];
- //printf("rho=%f, e=%f, cv=%f, x=%f\n", rho[nlocal], e[nlocal], cv[nlocal], x[nlocal][0]);
+ //printf("rho=%f, e=%f, cv=%f, x=%f\n", rho[nlocal], e[nlocal], cv[nlocal], x[nlocal][0]);
- image[nlocal] = imagetmp;
+ image[nlocal] = imagetmp;
- mask[nlocal] = 1;
- v[nlocal][0] = 0.0;
- v[nlocal][1] = 0.0;
- v[nlocal][2] = 0.0;
+ mask[nlocal] = 1;
+ v[nlocal][0] = 0.0;
+ v[nlocal][1] = 0.0;
+ v[nlocal][2] = 0.0;
- vest[nlocal][0] = 0.0;
- vest[nlocal][1] = 0.0;
- vest[nlocal][2] = 0.0;
+ vest[nlocal][0] = 0.0;
+ vest[nlocal][1] = 0.0;
+ vest[nlocal][2] = 0.0;
- de[nlocal] = 0.0;
- drho[nlocal] = 0.0;
+ de[nlocal] = 0.0;
+ drho[nlocal] = 0.0;
- atom->nlocal++;
+ atom->nlocal++;
}
/* ----------------------------------------------------------------------
@@ -824,11 +824,11 @@ void AtomVecMeso::data_atom(double *coord, int imagetmp, char **values) {
int AtomVecMeso::data_atom_hybrid(int nlocal, char **values) {
- rho[nlocal] = atof(values[0]);
- e[nlocal] = atof(values[1]);
- cv[nlocal] = atof(values[2]);
+ rho[nlocal] = atof(values[0]);
+ e[nlocal] = atof(values[1]);
+ cv[nlocal] = atof(values[2]);
- return 3;
+ return 3;
}
/* ----------------------------------------------------------------------
@@ -836,34 +836,34 @@ int AtomVecMeso::data_atom_hybrid(int nlocal, char **values) {
------------------------------------------------------------------------- */
bigint AtomVecMeso::memory_usage() {
- bigint bytes = 0;
-
- if (atom->memcheck("tag"))
- bytes += memory->usage(tag, nmax);
- if (atom->memcheck("type"))
- bytes += memory->usage(type, nmax);
- if (atom->memcheck("mask"))
- bytes += memory->usage(mask, nmax);
- if (atom->memcheck("image"))
- bytes += memory->usage(image, nmax);
- if (atom->memcheck("x"))
- bytes += memory->usage(x, nmax, 3);
- if (atom->memcheck("v"))
- bytes += memory->usage(v, nmax, 3);
- if (atom->memcheck("f"))
- bytes += memory->usage(f, nmax*comm->nthreads, 3);
- if (atom->memcheck("rho"))
- bytes += memory->usage(rho, nmax);
- if (atom->memcheck("drho"))
- bytes += memory->usage(drho, nmax*comm->nthreads);
- if (atom->memcheck("e"))
- bytes += memory->usage(e, nmax);
- if (atom->memcheck("de"))
- bytes += memory->usage(de, nmax*comm->nthreads);
- if (atom->memcheck("cv"))
- bytes += memory->usage(cv, nmax);
- if (atom->memcheck("vest"))
- bytes += memory->usage(vest, nmax);
-
- return bytes;
+ bigint bytes = 0;
+
+ if (atom->memcheck("tag"))
+ bytes += memory->usage(tag, nmax);
+ if (atom->memcheck("type"))
+ bytes += memory->usage(type, nmax);
+ if (atom->memcheck("mask"))
+ bytes += memory->usage(mask, nmax);
+ if (atom->memcheck("image"))
+ bytes += memory->usage(image, nmax);
+ if (atom->memcheck("x"))
+ bytes += memory->usage(x, nmax, 3);
+ if (atom->memcheck("v"))
+ bytes += memory->usage(v, nmax, 3);
+ if (atom->memcheck("f"))
+ bytes += memory->usage(f, nmax*comm->nthreads, 3);
+ if (atom->memcheck("rho"))
+ bytes += memory->usage(rho, nmax);
+ if (atom->memcheck("drho"))
+ bytes += memory->usage(drho, nmax*comm->nthreads);
+ if (atom->memcheck("e"))
+ bytes += memory->usage(e, nmax);
+ if (atom->memcheck("de"))
+ bytes += memory->usage(de, nmax*comm->nthreads);
+ if (atom->memcheck("cv"))
+ bytes += memory->usage(cv, nmax);
+ if (atom->memcheck("vest"))
+ bytes += memory->usage(vest, nmax);
+
+ return bytes;
}
diff --git a/src/USER-SPH/atom_vec_meso.h b/src/USER-SPH/atom_vec_meso.h
index b187198c095ffe79911cdb91f4abe3e3895b05ea..eeb3bb456e29b774f02b10b2d044e322ff831d83 100644
--- a/src/USER-SPH/atom_vec_meso.h
+++ b/src/USER-SPH/atom_vec_meso.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-SPH/compute_meso_e_atom.cpp b/src/USER-SPH/compute_meso_e_atom.cpp
index 4ee0dce518e5c91dcbc813eeffde7c308564141d..0446d948c4b3f0483d622015f97b2508cb2acd12 100644
--- a/src/USER-SPH/compute_meso_e_atom.cpp
+++ b/src/USER-SPH/compute_meso_e_atom.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -78,10 +78,10 @@ void ComputeMesoEAtom::compute_peratom()
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
- evector[i] = e[i];
+ evector[i] = e[i];
}
else {
- evector[i] = 0.0;
+ evector[i] = 0.0;
}
}
}
diff --git a/src/USER-SPH/compute_meso_e_atom.h b/src/USER-SPH/compute_meso_e_atom.h
index 07fc01c9209741013aa277e5aaf98f02881d8ae8..d3a896bafd4c7d87a5180a317fdcdb8bcf0f55b3 100644
--- a/src/USER-SPH/compute_meso_e_atom.h
+++ b/src/USER-SPH/compute_meso_e_atom.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-SPH/compute_meso_rho_atom.cpp b/src/USER-SPH/compute_meso_rho_atom.cpp
index 465bbfe164e22e0f8ebe660f670e902705ba772c..e1db2185445e9859f5f421fce04c3282ea32ec33 100644
--- a/src/USER-SPH/compute_meso_rho_atom.cpp
+++ b/src/USER-SPH/compute_meso_rho_atom.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -80,10 +80,10 @@ void ComputeMesoRhoAtom::compute_peratom()
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
- rhoVector[i] = rho[i];
+ rhoVector[i] = rho[i];
}
else {
- rhoVector[i] = 0.0;
+ rhoVector[i] = 0.0;
}
}
}
diff --git a/src/USER-SPH/compute_meso_rho_atom.h b/src/USER-SPH/compute_meso_rho_atom.h
index e1100a2f8188eb47a0fe1774bd711cbb59486ae5..6c51593b2ed3d7b24ace8b35c263e5f61d3e6ba4 100644
--- a/src/USER-SPH/compute_meso_rho_atom.h
+++ b/src/USER-SPH/compute_meso_rho_atom.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-SPH/compute_meso_t_atom.cpp b/src/USER-SPH/compute_meso_t_atom.cpp
index 5d4f1177bad747d41428f15c9175c507ad0f3028..98b0c88f5579fcb791c3d7ade16950c09c44b7ef 100644
--- a/src/USER-SPH/compute_meso_t_atom.cpp
+++ b/src/USER-SPH/compute_meso_t_atom.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -30,7 +30,7 @@ ComputeMesoTAtom::ComputeMesoTAtom(LAMMPS *lmp, int narg, char **arg) :
{
if (narg != 3) error->all(FLERR,"Number of arguments for compute meso_t/atom command != 3");
if ((atom->e_flag != 1) || (atom->cv_flag != 1))
- error->all(FLERR,"compute meso_e/atom command requires atom_style with both energy and heat capacity (e.g. meso)");
+ error->all(FLERR,"compute meso_e/atom command requires atom_style with both energy and heat capacity (e.g. meso)");
peratom_flag = 1;
size_peratom_cols = 0;
@@ -80,12 +80,12 @@ void ComputeMesoTAtom::compute_peratom()
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
- if (cv[i] > 0.0) {
- tvector[i] = e[i] / cv[i];
- }
+ if (cv[i] > 0.0) {
+ tvector[i] = e[i] / cv[i];
+ }
}
else {
- tvector[i] = 0.0;
+ tvector[i] = 0.0;
}
}
}
diff --git a/src/USER-SPH/compute_meso_t_atom.h b/src/USER-SPH/compute_meso_t_atom.h
index 279d749f877d0774b881bd43c3c028c38d0bec1e..6b8c618e0f3676594d3c571661c79f8dbdf0a8a9 100644
--- a/src/USER-SPH/compute_meso_t_atom.h
+++ b/src/USER-SPH/compute_meso_t_atom.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-SPH/fix_meso.cpp b/src/USER-SPH/fix_meso.cpp
index ffb69a8c80cd6ed67db52c96764bee3c168f30a0..53e7b66b65df4b74635f43402bafba4edc51150f 100644
--- a/src/USER-SPH/fix_meso.cpp
+++ b/src/USER-SPH/fix_meso.cpp
@@ -165,4 +165,3 @@ void FixMeso::reset_dt() {
dtv = update->dt;
dtf = 0.5 * update->dt * force->ftm2v;
}
-
diff --git a/src/USER-SPH/fix_meso.h b/src/USER-SPH/fix_meso.h
index eee5ee1d45f8885e188dbca8482af5afd97a8f89..f9fcb5a8938f02d9d2a251abb2891bef09f06375 100644
--- a/src/USER-SPH/fix_meso.h
+++ b/src/USER-SPH/fix_meso.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-SPH/fix_meso_stationary.cpp b/src/USER-SPH/fix_meso_stationary.cpp
index f12297f072d6205bd150855501dcfa2f71c8b11d..101b2639f154cff416b79d76f691d652dd83864f 100644
--- a/src/USER-SPH/fix_meso_stationary.cpp
+++ b/src/USER-SPH/fix_meso_stationary.cpp
@@ -120,4 +120,3 @@ void FixMesoStationary::reset_dt() {
dtv = update->dt;
dtf = 0.5 * update->dt * force->ftm2v;
}
-
diff --git a/src/USER-SPH/fix_meso_stationary.h b/src/USER-SPH/fix_meso_stationary.h
index 08869d2105ee5191e3d8233022bf089f257f42c8..6cc83f9e93259fd6b12401cdc066eafca6f94789 100644
--- a/src/USER-SPH/fix_meso_stationary.h
+++ b/src/USER-SPH/fix_meso_stationary.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-SPH/pair_sph_heatconduction.h b/src/USER-SPH/pair_sph_heatconduction.h
index 81402fda2e76b64885dffe3f91ba3e2a14618d2e..95b4e845ae59fbcb75c6125da32ddf8a514a9e39 100644
--- a/src/USER-SPH/pair_sph_heatconduction.h
+++ b/src/USER-SPH/pair_sph_heatconduction.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-SPH/pair_sph_idealgas.h b/src/USER-SPH/pair_sph_idealgas.h
index 540789afebe4456ed3aacd588c3c15714fdf31d9..e9d2e9a8b3ec8d72cd328bcf3c236bd4e2f42b41 100644
--- a/src/USER-SPH/pair_sph_idealgas.h
+++ b/src/USER-SPH/pair_sph_idealgas.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-SPH/pair_sph_lj.h b/src/USER-SPH/pair_sph_lj.h
index 244ee044a5784f3287bc48e581768b89f3135426..cb8f8c745a642c87429a2a3d9e045bf674381242 100644
--- a/src/USER-SPH/pair_sph_lj.h
+++ b/src/USER-SPH/pair_sph_lj.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-SPH/pair_sph_rhosum.cpp b/src/USER-SPH/pair_sph_rhosum.cpp
index 3985297dd8532101b899054fc52616049346bef8..4e1a1e52da2a9f21bc4dd004e9de870f63650146 100644
--- a/src/USER-SPH/pair_sph_rhosum.cpp
+++ b/src/USER-SPH/pair_sph_rhosum.cpp
@@ -311,4 +311,3 @@ void PairSPHRhoSum::unpack_comm(int n, int first, double *buf) {
for (i = first; i < last; i++)
rho[i] = buf[m++];
}
-
diff --git a/src/USER-SPH/pair_sph_rhosum.h b/src/USER-SPH/pair_sph_rhosum.h
index 227cdef95c4e4b5c25806014419840e9cc6dac97..57639ff37865fad7b14e25a2f52854a904f1a299 100644
--- a/src/USER-SPH/pair_sph_rhosum.h
+++ b/src/USER-SPH/pair_sph_rhosum.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-SPH/pair_sph_taitwater.h b/src/USER-SPH/pair_sph_taitwater.h
index de081aa5445f3d0b949cbce737bd21e1c8387ad5..6e90aac537b1f7fb9ccf118278f79972a677940f 100644
--- a/src/USER-SPH/pair_sph_taitwater.h
+++ b/src/USER-SPH/pair_sph_taitwater.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-SPH/pair_sph_taitwater_morris.h b/src/USER-SPH/pair_sph_taitwater_morris.h
index 5390d73f087b8ab10c68f0104ae5a16f68f15c28..05568b12d64e78cb894fee6c67f45e3d8f9ae6d7 100644
--- a/src/USER-SPH/pair_sph_taitwater_morris.h
+++ b/src/USER-SPH/pair_sph_taitwater_morris.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/XTC/dump_xtc.cpp b/src/XTC/dump_xtc.cpp
index d003a1c20fb913a6a6b9786f362ae2a4da4c973d..2ff16b38816090ca9d6b310f0d3f1183df33481a 100644
--- a/src/XTC/dump_xtc.cpp
+++ b/src/XTC/dump_xtc.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -14,12 +14,12 @@
/* ----------------------------------------------------------------------
Contributing authors: Naveen Michaud-Agrawal (Johns Hopkins U)
open-source XDR routines from
- Frans van Hoesel (http://md.chem.rug.nl/hoesel)
- are included in this file
+ Frans van Hoesel (http://md.chem.rug.nl/hoesel)
+ are included in this file
Axel Kohlmeyer (Temple U)
port to platforms without XDR support
added support for unwrapped trajectories
- support for groups
+ support for groups
------------------------------------------------------------------------- */
#include "math.h"
@@ -68,7 +68,7 @@ DumpXTC::DumpXTC(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg)
// allocate global array for atom coords
bigint n = group->count(igroup);
- if (n > MAXSMALLINT/3/sizeof(float))
+ if (n > MAXSMALLINT/3/sizeof(float))
error->all(FLERR,"Too many atoms for dump xtc");
natoms = static_cast<int> (n);
@@ -210,29 +210,29 @@ void DumpXTC::pack(int *ids)
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- int ix = (image[i] & 1023) - 512;
- int iy = (image[i] >> 10 & 1023) - 512;
- int iz = (image[i] >> 20) - 512;
-
- if (domain->triclinic) {
- buf[m++] = sfactor * (x[i][0] + ix * xprd + iy * xy + iz * xz);
- buf[m++] = sfactor * (x[i][1] + iy * yprd + iz * yz);
- buf[m++] = sfactor * (x[i][2] + iz * zprd);
- } else {
- buf[m++] = sfactor * (x[i][0] + ix * xprd);
- buf[m++] = sfactor * (x[i][1] + iy * yprd);
- buf[m++] = sfactor * (x[i][2] + iz * zprd);
- }
- ids[n++] = tag[i];
+ int ix = (image[i] & 1023) - 512;
+ int iy = (image[i] >> 10 & 1023) - 512;
+ int iz = (image[i] >> 20) - 512;
+
+ if (domain->triclinic) {
+ buf[m++] = sfactor * (x[i][0] + ix * xprd + iy * xy + iz * xz);
+ buf[m++] = sfactor * (x[i][1] + iy * yprd + iz * yz);
+ buf[m++] = sfactor * (x[i][2] + iz * zprd);
+ } else {
+ buf[m++] = sfactor * (x[i][0] + ix * xprd);
+ buf[m++] = sfactor * (x[i][1] + iy * yprd);
+ buf[m++] = sfactor * (x[i][2] + iz * zprd);
+ }
+ ids[n++] = tag[i];
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- buf[m++] = sfactor*x[i][0];
- buf[m++] = sfactor*x[i][1];
- buf[m++] = sfactor*x[i][2];
- ids[n++] = tag[i];
+ buf[m++] = sfactor*x[i][0];
+ buf[m++] = sfactor*x[i][1];
+ buf[m++] = sfactor*x[i][2];
+ ids[n++] = tag[i];
}
}
}
@@ -273,10 +273,10 @@ int DumpXTC::modify_param(int narg, char **arg)
} else if (strcmp(arg[0],"precision") == 0) {
if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
precision = atof(arg[1]);
- if ((fabs(precision-10.0) > EPS) && (fabs(precision-100.0) > EPS) &&
- (fabs(precision-1000.0) > EPS) && (fabs(precision-10000.0) > EPS) &&
- (fabs(precision-100000.0) > EPS) &&
- (fabs(precision-1000000.0) > EPS))
+ if ((fabs(precision-10.0) > EPS) && (fabs(precision-100.0) > EPS) &&
+ (fabs(precision-1000.0) > EPS) && (fabs(precision-10000.0) > EPS) &&
+ (fabs(precision-100000.0) > EPS) &&
+ (fabs(precision-1000000.0) > EPS))
error->all(FLERR,"Illegal dump_modify command");
return 2;
}
@@ -310,32 +310,32 @@ void DumpXTC::write_frame()
/*____________________________________________________________________________
|
| Below are the routines to be used by C programmers. Use the 'normal'
- | xdr routines to write integers, floats, etc (see man xdr)
+ | xdr routines to write integers, floats, etc (see man xdr)
|
| int xdropen(XDR *xdrs, const char *filename, const char *type)
- | This will open the file with the given filename and the
- | given mode. You should pass it an allocated XDR struct
- | in xdrs, to be used in all other calls to xdr routines.
- | Mode is 'w' to create, or update an file, and for all
- | other values of mode the file is opened for reading.
- | You need to call xdrclose to flush the output and close
- | the file.
+ | This will open the file with the given filename and the
+ | given mode. You should pass it an allocated XDR struct
+ | in xdrs, to be used in all other calls to xdr routines.
+ | Mode is 'w' to create, or update an file, and for all
+ | other values of mode the file is opened for reading.
+ | You need to call xdrclose to flush the output and close
+ | the file.
|
- | Note that you should not use xdrstdio_create, which
- | comes with the standard xdr library.
+ | Note that you should not use xdrstdio_create, which
+ | comes with the standard xdr library.
|
| int xdrclose(XDR *xdrs)
- | Flush the data to the file, and close the file;
- | You should not use xdr_destroy (which comes standard
- | with the xdr libraries).
- |
+ | Flush the data to the file, and close the file;
+ | You should not use xdr_destroy (which comes standard
+ | with the xdr libraries).
+ |
| int xdr3dfcoord(XDR *xdrs, float *fp, int *size, float *precision)
- | This is \fInot\fR a standard xdr routine. I named it this
- | way, because it invites people to use the other xdr
- | routines.
+ | This is \fInot\fR a standard xdr routine. I named it this
+ | way, because it invites people to use the other xdr
+ | routines.
|
- | (c) 1995 Frans van Hoesel, hoesel@chem.rug.nl
-*/
+ | (c) 1995 Frans van Hoesel, hoesel@chem.rug.nl
+*/
#define MAXID 20
static FILE *xdrfiles[MAXID];
@@ -362,9 +362,9 @@ static int magicints[] = {
80, 101, 128, 161, 203, 256, 322, 406, 512, 645,
812, 1024, 1290, 1625, 2048, 2580, 3250, 4096, 5060, 6501,
8192, 10321, 13003, 16384, 20642, 26007, 32768, 41285, 52015, 65536,
- 82570, 104031, 131072, 165140, 208063, 262144, 330280, 416127,
+ 82570, 104031, 131072, 165140, 208063, 262144, 330280, 416127,
524287, 660561,
- 832255, 1048576, 1321122, 1664510, 2097152, 2642245, 3329021,
+ 832255, 1048576, 1321122, 1664510, 2097152, 2642245, 3329021,
4194304, 5284491, 6658042,
8388607, 10568983, 13316085, 16777216 };
@@ -388,7 +388,7 @@ int xdropen(XDR *xdrs, const char *filename, const char *type)
static int init_done = 0;
enum xdr_op lmode;
int xdrid;
-
+
if (init_done == 0) {
for (xdrid = 1; xdrid < MAXID; xdrid++) {
xdridptr[xdrid] = NULL;
@@ -440,24 +440,24 @@ int xdropen(XDR *xdrs, const char *filename, const char *type)
| done by xdr_destroy).
|
*/
-
+
int xdrclose(XDR *xdrs)
{
int xdrid;
-
+
if (xdrs == NULL) {
fprintf(stderr, "xdrclose: passed a NULL pointer\n");
exit(1);
}
for (xdrid = 1; xdrid < MAXID; xdrid++) {
if (xdridptr[xdrid] == xdrs) {
-
+
xdr_destroy(xdrs);
fclose(xdrfiles[xdrid]);
xdridptr[xdrid] = NULL;
return 1;
}
- }
+ }
fprintf(stderr, "xdrclose: no such open xdr file\n");
exit(1);
return 1;
@@ -493,7 +493,7 @@ static void sendbits(int buf[], int num_of_bits, int num)
unsigned int cnt, lastbyte;
int lastbits;
unsigned char * cbuf;
-
+
cbuf = ((unsigned char *)buf) + 3 * sizeof(*buf);
cnt = (unsigned int) buf[0];
lastbits = buf[1];
@@ -531,7 +531,7 @@ static int sizeofint(const int size)
{
unsigned int num = 1;
int num_of_bits = 0;
-
+
while (size >= num && num_of_bits < 32) {
num_of_bits++;
num <<= 1;
@@ -558,7 +558,7 @@ static int sizeofints( const int num_of_ints, unsigned int sizes[])
num_of_bytes = 1;
bytes[0] = 1;
num_of_bits = 0;
- for (i=0; i < num_of_ints; i++) {
+ for (i=0; i < num_of_ints; i++) {
tmp = 0;
for (bytecnt = 0; bytecnt < num_of_bytes; bytecnt++) {
tmp = bytes[bytecnt] * sizes[i] + tmp;
@@ -582,10 +582,10 @@ static int sizeofints( const int num_of_ints, unsigned int sizes[])
/*____________________________________________________________________________
|
- | sendints - send a small set of small integers in compressed
+ | sendints - send a small set of small integers in compressed
|
| this routine is used internally by xdr3dfcoord, to send a set of
- | small integers to the buffer.
+ | small integers to the buffer.
| Multiplication with fixed (specified maximum ) sizes is used to get
| to one big, multibyte integer. Allthough the routine could be
| modified to handle sizes bigger than 16777216, or more than just
@@ -594,27 +594,27 @@ static int sizeofints( const int num_of_ints, unsigned int sizes[])
| or the byte buffer (32 bytes) is unchecked and causes bad results.
|
*/
-
+
static void sendints(int buf[], const int num_of_ints, const int num_of_bits,
- unsigned int sizes[], unsigned int nums[])
+ unsigned int sizes[], unsigned int nums[])
{
int i;
unsigned int bytes[32], num_of_bytes, bytecnt, tmp;
-
+
tmp = nums[0];
num_of_bytes = 0;
do {
bytes[num_of_bytes++] = tmp & 0xff;
tmp >>= 8;
} while (tmp != 0);
-
+
for (i = 1; i < num_of_ints; i++) {
if (nums[i] >= sizes[i]) {
fprintf(stderr,"major breakdown in sendints num %d doesn't "
- "match size %d\n", nums[i], sizes[i]);
+ "match size %d\n", nums[i], sizes[i]);
exit(1);
}
- /* use one step multiply */
+ /* use one step multiply */
tmp = nums[i];
for (bytecnt = 0; bytecnt < num_of_bytes; bytecnt++) {
tmp = bytes[bytecnt] * sizes[i] + tmp;
@@ -643,7 +643,7 @@ static void sendints(int buf[], const int num_of_ints, const int num_of_bits,
/*___________________________________________________________________________
|
| receivebits - decode number from buf using specified number of bits
- |
+ |
| extract the number of bits from the array buf and construct an integer
| from it. Return that value.
|
@@ -651,16 +651,16 @@ static void sendints(int buf[], const int num_of_ints, const int num_of_bits,
static int receivebits(int buf[], int num_of_bits)
{
- int cnt, num;
+ int cnt, num;
unsigned int lastbits, lastbyte;
unsigned char * cbuf;
int mask = (1 << num_of_bits) -1;
-
+
cbuf = ((unsigned char *)buf) + 3 * sizeof(*buf);
cnt = buf[0];
lastbits = (unsigned int) buf[1];
lastbyte = (unsigned int) buf[2];
-
+
num = 0;
while (num_of_bits >= 8) {
lastbyte = ( lastbyte << 8 ) | cbuf[cnt++];
@@ -679,7 +679,7 @@ static int receivebits(int buf[], int num_of_bits)
buf[0] = cnt;
buf[1] = lastbits;
buf[2] = lastbyte;
- return num;
+ return num;
}
/*____________________________________________________________________________
@@ -694,11 +694,11 @@ static int receivebits(int buf[], int num_of_bits)
*/
static void receiveints(int buf[], const int num_of_ints, int num_of_bits,
- unsigned int sizes[], int nums[])
+ unsigned int sizes[], int nums[])
{
int bytes[32];
int i, j, num_of_bytes, p, num;
-
+
bytes[1] = bytes[2] = bytes[3] = 0;
num_of_bytes = 0;
while (num_of_bits > 8) {
@@ -720,7 +720,7 @@ static void receiveints(int buf[], const int num_of_ints, int num_of_bits,
}
nums[0] = bytes[0] | (bytes[1] << 8) | (bytes[2] << 16) | (bytes[3] << 24);
}
-
+
/*____________________________________________________________________________
|
| xdr3dfcoord - read or write compressed 3d coordinates to xdr file.
@@ -747,11 +747,11 @@ static void receiveints(int buf[], const int num_of_ints, int num_of_bits,
| it shouldn't harm in the general case.
|
*/
-
+
int xdr3dfcoord(XDR *xdrs, float *fp, int *size, float *precision)
{
static int oldsize;
-
+
int minint[3], maxint[3], mindiff, *lip, diff;
int lint1, lint2, lint3, oldlint1, oldlint2, oldlint3, smallidx;
int minidx, maxidx;
@@ -761,12 +761,12 @@ int xdr3dfcoord(XDR *xdrs, float *fp, int *size, float *precision)
float *lfp, lf;
int tmp, *thiscoord, prevcoord[3];
unsigned int tmpcoord[30];
-
+
int bufsize, xdrid, lsize;
unsigned int bitsize;
float inv_precision;
int errval = 1;
-
+
/* find out if xdrs is opened for reading or for writing */
xdrid = 0;
while (xdridptr[xdrid] != xdrs) {
@@ -777,9 +777,9 @@ int xdr3dfcoord(XDR *xdrs, float *fp, int *size, float *precision)
}
}
if (xdrmodes[xdrid] == 'w') {
-
+
/* xdrs is open for writing */
-
+
if (xdr_int(xdrs, size) == 0)
return 0;
size3 = *size * 3;
@@ -788,34 +788,34 @@ int xdr3dfcoord(XDR *xdrs, float *fp, int *size, float *precision)
*/
if (*size <= 9 ) {
return (xdr_vector(xdrs, (char *) fp, size3, sizeof(*fp),
- (xdrproc_t)xdr_float));
+ (xdrproc_t)xdr_float));
}
-
+
xdr_float(xdrs, precision);
if (ip == NULL) {
ip = (int *) malloc(size3 * sizeof(*ip));
if (ip == NULL) {
- fprintf(stderr,"malloc failed\n");
- exit(1);
+ fprintf(stderr,"malloc failed\n");
+ exit(1);
}
bufsize = (int) (size3 * 1.2);
buf = (int *) malloc(bufsize * sizeof(*buf));
if (buf == NULL) {
- fprintf(stderr,"malloc failed\n");
- exit(1);
+ fprintf(stderr,"malloc failed\n");
+ exit(1);
}
oldsize = *size;
} else if (*size > oldsize) {
ip = (int *) realloc(ip, size3 * sizeof(*ip));
if (ip == NULL) {
- fprintf(stderr,"malloc failed\n");
- exit(1);
+ fprintf(stderr,"malloc failed\n");
+ exit(1);
}
bufsize = (int) (size3 * 1.2);
buf = (int *) realloc(buf, bufsize * sizeof(*buf));
if (buf == NULL) {
- fprintf(stderr,"malloc failed\n");
- exit(1);
+ fprintf(stderr,"malloc failed\n");
+ exit(1);
}
oldsize = *size;
}
@@ -831,12 +831,12 @@ int xdr3dfcoord(XDR *xdrs, float *fp, int *size, float *precision)
while(lfp < fp + size3 ) {
/* find nearest integer */
if (*lfp >= 0.0)
- lf = *lfp * *precision + 0.5;
+ lf = *lfp * *precision + 0.5;
else
- lf = *lfp * *precision - 0.5;
+ lf = *lfp * *precision - 0.5;
if (fabs(lf) > MAXABS) {
- /* scaling would cause overflow */
- errval = 0;
+ /* scaling would cause overflow */
+ errval = 0;
}
lint1 = (int) lf;
if (lint1 < minint[0]) minint[0] = lint1;
@@ -844,12 +844,12 @@ int xdr3dfcoord(XDR *xdrs, float *fp, int *size, float *precision)
*lip++ = lint1;
lfp++;
if (*lfp >= 0.0)
- lf = *lfp * *precision + 0.5;
+ lf = *lfp * *precision + 0.5;
else
- lf = *lfp * *precision - 0.5;
+ lf = *lfp * *precision - 0.5;
if (fabs(lf) > MAXABS) {
- /* scaling would cause overflow */
- errval = 0;
+ /* scaling would cause overflow */
+ errval = 0;
}
lint2 = (int) lf;
if (lint2 < minint[1]) minint[1] = lint2;
@@ -857,12 +857,12 @@ int xdr3dfcoord(XDR *xdrs, float *fp, int *size, float *precision)
*lip++ = lint2;
lfp++;
if (*lfp >= 0.0)
- lf = *lfp * *precision + 0.5;
+ lf = *lfp * *precision + 0.5;
else
- lf = *lfp * *precision - 0.5;
+ lf = *lfp * *precision - 0.5;
if (fabs(lf) > MAXABS) {
- /* scaling would cause overflow */
- errval = 0;
+ /* scaling would cause overflow */
+ errval = 0;
}
lint3 = (int) lf;
if (lint3 < minint[2]) minint[2] = lint3;
@@ -871,7 +871,7 @@ int xdr3dfcoord(XDR *xdrs, float *fp, int *size, float *precision)
lfp++;
diff = abs(oldlint1-lint1)+abs(oldlint2-lint2)+abs(oldlint3-lint3);
if (diff < mindiff && lfp > fp + 3)
- mindiff = diff;
+ mindiff = diff;
oldlint1 = lint1;
oldlint2 = lint2;
oldlint3 = lint3;
@@ -879,14 +879,14 @@ int xdr3dfcoord(XDR *xdrs, float *fp, int *size, float *precision)
xdr_int(xdrs, &(minint[0]));
xdr_int(xdrs, &(minint[1]));
xdr_int(xdrs, &(minint[2]));
-
+
xdr_int(xdrs, &(maxint[0]));
xdr_int(xdrs, &(maxint[1]));
xdr_int(xdrs, &(maxint[2]));
-
+
if ((float)maxint[0] - (float)minint[0] >= MAXABS ||
- (float)maxint[1] - (float)minint[1] >= MAXABS ||
- (float)maxint[2] - (float)minint[2] >= MAXABS) {
+ (float)maxint[1] - (float)minint[1] >= MAXABS ||
+ (float)maxint[2] - (float)minint[2] >= MAXABS) {
/* turning value in unsigned by subtracting minint
* would cause overflow
*/
@@ -895,7 +895,7 @@ int xdr3dfcoord(XDR *xdrs, float *fp, int *size, float *precision)
sizeint[0] = maxint[0] - minint[0]+1;
sizeint[1] = maxint[1] - minint[1]+1;
sizeint[2] = maxint[2] - minint[2]+1;
-
+
/* check if one of the sizes is to big to be multiplied */
if ((sizeint[0] | sizeint[1] | sizeint[2] ) > 0xffffff) {
bitsizeint[0] = sizeofint(sizeint[0]);
@@ -923,160 +923,160 @@ int xdr3dfcoord(XDR *xdrs, float *fp, int *size, float *precision)
is_small = 0;
thiscoord = (int *)(luip) + i * 3;
if (smallidx < maxidx && i >= 1 &&
- abs(thiscoord[0] - prevcoord[0]) < larger &&
- abs(thiscoord[1] - prevcoord[1]) < larger &&
- abs(thiscoord[2] - prevcoord[2]) < larger) {
- is_smaller = 1;
+ abs(thiscoord[0] - prevcoord[0]) < larger &&
+ abs(thiscoord[1] - prevcoord[1]) < larger &&
+ abs(thiscoord[2] - prevcoord[2]) < larger) {
+ is_smaller = 1;
} else if (smallidx > minidx) {
- is_smaller = -1;
+ is_smaller = -1;
} else {
- is_smaller = 0;
+ is_smaller = 0;
}
if (i + 1 < *size) {
- if (abs(thiscoord[0] - thiscoord[3]) < small &&
- abs(thiscoord[1] - thiscoord[4]) < small &&
- abs(thiscoord[2] - thiscoord[5]) < small) {
- /* interchange first with second atom for better
- * compression of water molecules
- */
- tmp = thiscoord[0]; thiscoord[0] = thiscoord[3];
- thiscoord[3] = tmp;
- tmp = thiscoord[1]; thiscoord[1] = thiscoord[4];
- thiscoord[4] = tmp;
- tmp = thiscoord[2]; thiscoord[2] = thiscoord[5];
- thiscoord[5] = tmp;
- is_small = 1;
- }
-
+ if (abs(thiscoord[0] - thiscoord[3]) < small &&
+ abs(thiscoord[1] - thiscoord[4]) < small &&
+ abs(thiscoord[2] - thiscoord[5]) < small) {
+ /* interchange first with second atom for better
+ * compression of water molecules
+ */
+ tmp = thiscoord[0]; thiscoord[0] = thiscoord[3];
+ thiscoord[3] = tmp;
+ tmp = thiscoord[1]; thiscoord[1] = thiscoord[4];
+ thiscoord[4] = tmp;
+ tmp = thiscoord[2]; thiscoord[2] = thiscoord[5];
+ thiscoord[5] = tmp;
+ is_small = 1;
+ }
+
}
tmpcoord[0] = thiscoord[0] - minint[0];
tmpcoord[1] = thiscoord[1] - minint[1];
tmpcoord[2] = thiscoord[2] - minint[2];
if (bitsize == 0) {
- sendbits(buf, bitsizeint[0], tmpcoord[0]);
- sendbits(buf, bitsizeint[1], tmpcoord[1]);
- sendbits(buf, bitsizeint[2], tmpcoord[2]);
+ sendbits(buf, bitsizeint[0], tmpcoord[0]);
+ sendbits(buf, bitsizeint[1], tmpcoord[1]);
+ sendbits(buf, bitsizeint[2], tmpcoord[2]);
} else {
- sendints(buf, 3, bitsize, sizeint, tmpcoord);
+ sendints(buf, 3, bitsize, sizeint, tmpcoord);
}
prevcoord[0] = thiscoord[0];
prevcoord[1] = thiscoord[1];
prevcoord[2] = thiscoord[2];
thiscoord = thiscoord + 3;
i++;
-
+
run = 0;
if (is_small == 0 && is_smaller == -1)
- is_smaller = 0;
+ is_smaller = 0;
while (is_small && run < 8*3) {
- if (is_smaller == -1 && (SQR(thiscoord[0] - prevcoord[0]) +
- SQR(thiscoord[1] - prevcoord[1]) +
- SQR(thiscoord[2] - prevcoord[2]) >=
- smaller * smaller)) {
- is_smaller = 0;
- }
-
- tmpcoord[run++] = thiscoord[0] - prevcoord[0] + small;
- tmpcoord[run++] = thiscoord[1] - prevcoord[1] + small;
- tmpcoord[run++] = thiscoord[2] - prevcoord[2] + small;
-
- prevcoord[0] = thiscoord[0];
- prevcoord[1] = thiscoord[1];
- prevcoord[2] = thiscoord[2];
-
- i++;
- thiscoord = thiscoord + 3;
- is_small = 0;
- if (i < *size &&
- abs(thiscoord[0] - prevcoord[0]) < small &&
- abs(thiscoord[1] - prevcoord[1]) < small &&
- abs(thiscoord[2] - prevcoord[2]) < small) {
- is_small = 1;
- }
+ if (is_smaller == -1 && (SQR(thiscoord[0] - prevcoord[0]) +
+ SQR(thiscoord[1] - prevcoord[1]) +
+ SQR(thiscoord[2] - prevcoord[2]) >=
+ smaller * smaller)) {
+ is_smaller = 0;
+ }
+
+ tmpcoord[run++] = thiscoord[0] - prevcoord[0] + small;
+ tmpcoord[run++] = thiscoord[1] - prevcoord[1] + small;
+ tmpcoord[run++] = thiscoord[2] - prevcoord[2] + small;
+
+ prevcoord[0] = thiscoord[0];
+ prevcoord[1] = thiscoord[1];
+ prevcoord[2] = thiscoord[2];
+
+ i++;
+ thiscoord = thiscoord + 3;
+ is_small = 0;
+ if (i < *size &&
+ abs(thiscoord[0] - prevcoord[0]) < small &&
+ abs(thiscoord[1] - prevcoord[1]) < small &&
+ abs(thiscoord[2] - prevcoord[2]) < small) {
+ is_small = 1;
+ }
}
if (run != prevrun || is_smaller != 0) {
- prevrun = run;
- sendbits(buf, 1, 1); /* flag the change in run-length */
- sendbits(buf, 5, run+is_smaller+1);
+ prevrun = run;
+ sendbits(buf, 1, 1); /* flag the change in run-length */
+ sendbits(buf, 5, run+is_smaller+1);
} else {
- sendbits(buf, 1, 0); /* flag the fact that runlength did not change */
+ sendbits(buf, 1, 0); /* flag the fact that runlength did not change */
}
for (k=0; k < run; k+=3) {
- sendints(buf, 3, smallidx, sizesmall, &tmpcoord[k]);
+ sendints(buf, 3, smallidx, sizesmall, &tmpcoord[k]);
}
if (is_smaller != 0) {
- smallidx += is_smaller;
- if (is_smaller < 0) {
- small = smaller;
- smaller = magicints[smallidx-1] / 2;
- } else {
- smaller = small;
- small = magicints[smallidx] / 2;
- }
- sizesmall[0] = sizesmall[1] = sizesmall[2] = magicints[smallidx];
+ smallidx += is_smaller;
+ if (is_smaller < 0) {
+ small = smaller;
+ smaller = magicints[smallidx-1] / 2;
+ } else {
+ smaller = small;
+ small = magicints[smallidx] / 2;
+ }
+ sizesmall[0] = sizesmall[1] = sizesmall[2] = magicints[smallidx];
}
}
if (buf[1] != 0) buf[0]++;;
xdr_int(xdrs, &(buf[0])); /* buf[0] holds the length in bytes */
return errval * (xdr_opaque(xdrs, (caddr_t)&(buf[3]), (u_int)buf[0]));
} else {
-
+
/* xdrs is open for reading */
-
- if (xdr_int(xdrs, &lsize) == 0)
+
+ if (xdr_int(xdrs, &lsize) == 0)
return 0;
if (*size != 0 && lsize != *size) {
fprintf(stderr, "wrong number of coordinates in xdr3dfcoor; "
- "%d arg vs %d in file", *size, lsize);
+ "%d arg vs %d in file", *size, lsize);
}
*size = lsize;
size3 = *size * 3;
if (*size <= 9) {
return (xdr_vector(xdrs, (char *) fp, size3, sizeof(*fp),
- (xdrproc_t)xdr_float));
+ (xdrproc_t)xdr_float));
}
xdr_float(xdrs, precision);
if (ip == NULL) {
ip = (int *) malloc(size3 * sizeof(*ip));
if (ip == NULL) {
- fprintf(stderr,"malloc failed\n");
- exit(1);
+ fprintf(stderr,"malloc failed\n");
+ exit(1);
}
bufsize = (int) (size3 * 1.2);
buf = (int *) malloc(bufsize * sizeof(*buf));
if (buf == NULL) {
- fprintf(stderr,"malloc failed\n");
- exit(1);
+ fprintf(stderr,"malloc failed\n");
+ exit(1);
}
oldsize = *size;
} else if (*size > oldsize) {
ip = (int *)realloc(ip, size3 * sizeof(*ip));
if (ip == NULL) {
- fprintf(stderr,"malloc failed\n");
- exit(1);
+ fprintf(stderr,"malloc failed\n");
+ exit(1);
}
bufsize = (int) (size3 * 1.2);
buf = (int *)realloc(buf, bufsize * sizeof(*buf));
if (buf == NULL) {
- fprintf(stderr,"malloc failed\n");
- exit(1);
+ fprintf(stderr,"malloc failed\n");
+ exit(1);
}
oldsize = *size;
}
buf[0] = buf[1] = buf[2] = 0;
-
+
xdr_int(xdrs, &(minint[0]));
xdr_int(xdrs, &(minint[1]));
xdr_int(xdrs, &(minint[2]));
-
+
xdr_int(xdrs, &(maxint[0]));
xdr_int(xdrs, &(maxint[1]));
xdr_int(xdrs, &(maxint[2]));
-
+
sizeint[0] = maxint[0] - minint[0]+1;
sizeint[1] = maxint[1] - minint[1]+1;
sizeint[2] = maxint[2] - minint[2]+1;
-
+
/* check if one of the sizes is to big to be multiplied */
if ((sizeint[0] | sizeint[1] | sizeint[2] ) > 0xffffff) {
bitsizeint[0] = sizeofint(sizeint[0]);
@@ -1086,7 +1086,7 @@ int xdr3dfcoord(XDR *xdrs, float *fp, int *size, float *precision)
} else {
bitsize = sizeofints(3, sizeint);
}
-
+
xdr_int(xdrs, &smallidx);
maxidx = MYMIN(LASTIDX, smallidx + 8) ;
minidx = maxidx - 8; /* often this equal smallidx */
@@ -1094,15 +1094,15 @@ int xdr3dfcoord(XDR *xdrs, float *fp, int *size, float *precision)
small = magicints[smallidx] / 2;
sizesmall[0] = sizesmall[1] = sizesmall[2] = magicints[smallidx] ;
larger = magicints[maxidx];
-
+
/* buf[0] holds the length in bytes */
-
+
if (xdr_int(xdrs, &(buf[0])) == 0)
return 0;
if (xdr_opaque(xdrs, (caddr_t)&(buf[3]), (u_int)buf[0]) == 0)
return 0;
buf[0] = buf[1] = buf[2] = 0;
-
+
lfp = fp;
inv_precision = 1.0 / * precision;
run = 0;
@@ -1110,79 +1110,79 @@ int xdr3dfcoord(XDR *xdrs, float *fp, int *size, float *precision)
lip = ip;
while ( i < lsize ) {
thiscoord = (int *)(lip) + i * 3;
-
+
if (bitsize == 0) {
- thiscoord[0] = receivebits(buf, bitsizeint[0]);
- thiscoord[1] = receivebits(buf, bitsizeint[1]);
- thiscoord[2] = receivebits(buf, bitsizeint[2]);
+ thiscoord[0] = receivebits(buf, bitsizeint[0]);
+ thiscoord[1] = receivebits(buf, bitsizeint[1]);
+ thiscoord[2] = receivebits(buf, bitsizeint[2]);
} else {
- receiveints(buf, 3, bitsize, sizeint, thiscoord);
+ receiveints(buf, 3, bitsize, sizeint, thiscoord);
}
-
+
i++;
thiscoord[0] += minint[0];
thiscoord[1] += minint[1];
thiscoord[2] += minint[2];
-
+
prevcoord[0] = thiscoord[0];
prevcoord[1] = thiscoord[1];
prevcoord[2] = thiscoord[2];
-
-
+
+
flag = receivebits(buf, 1);
is_smaller = 0;
if (flag == 1) {
- run = receivebits(buf, 5);
- is_smaller = run % 3;
- run -= is_smaller;
- is_smaller--;
+ run = receivebits(buf, 5);
+ is_smaller = run % 3;
+ run -= is_smaller;
+ is_smaller--;
}
if (run > 0) {
- thiscoord += 3;
- for (k = 0; k < run; k+=3) {
- receiveints(buf, 3, smallidx, sizesmall, thiscoord);
- i++;
- thiscoord[0] += prevcoord[0] - small;
- thiscoord[1] += prevcoord[1] - small;
- thiscoord[2] += prevcoord[2] - small;
- if (k == 0) {
- /* interchange first with second atom for better
- * compression of water molecules
- */
- tmp = thiscoord[0]; thiscoord[0] = prevcoord[0];
- prevcoord[0] = tmp;
- tmp = thiscoord[1]; thiscoord[1] = prevcoord[1];
- prevcoord[1] = tmp;
- tmp = thiscoord[2]; thiscoord[2] = prevcoord[2];
- prevcoord[2] = tmp;
- *lfp++ = prevcoord[0] * inv_precision;
- *lfp++ = prevcoord[1] * inv_precision;
- *lfp++ = prevcoord[2] * inv_precision;
- } else {
- prevcoord[0] = thiscoord[0];
- prevcoord[1] = thiscoord[1];
- prevcoord[2] = thiscoord[2];
- }
- *lfp++ = thiscoord[0] * inv_precision;
- *lfp++ = thiscoord[1] * inv_precision;
- *lfp++ = thiscoord[2] * inv_precision;
- }
+ thiscoord += 3;
+ for (k = 0; k < run; k+=3) {
+ receiveints(buf, 3, smallidx, sizesmall, thiscoord);
+ i++;
+ thiscoord[0] += prevcoord[0] - small;
+ thiscoord[1] += prevcoord[1] - small;
+ thiscoord[2] += prevcoord[2] - small;
+ if (k == 0) {
+ /* interchange first with second atom for better
+ * compression of water molecules
+ */
+ tmp = thiscoord[0]; thiscoord[0] = prevcoord[0];
+ prevcoord[0] = tmp;
+ tmp = thiscoord[1]; thiscoord[1] = prevcoord[1];
+ prevcoord[1] = tmp;
+ tmp = thiscoord[2]; thiscoord[2] = prevcoord[2];
+ prevcoord[2] = tmp;
+ *lfp++ = prevcoord[0] * inv_precision;
+ *lfp++ = prevcoord[1] * inv_precision;
+ *lfp++ = prevcoord[2] * inv_precision;
+ } else {
+ prevcoord[0] = thiscoord[0];
+ prevcoord[1] = thiscoord[1];
+ prevcoord[2] = thiscoord[2];
+ }
+ *lfp++ = thiscoord[0] * inv_precision;
+ *lfp++ = thiscoord[1] * inv_precision;
+ *lfp++ = thiscoord[2] * inv_precision;
+ }
} else {
- *lfp++ = thiscoord[0] * inv_precision;
- *lfp++ = thiscoord[1] * inv_precision;
- *lfp++ = thiscoord[2] * inv_precision;
+ *lfp++ = thiscoord[0] * inv_precision;
+ *lfp++ = thiscoord[1] * inv_precision;
+ *lfp++ = thiscoord[2] * inv_precision;
}
smallidx += is_smaller;
if (is_smaller < 0) {
- small = smaller;
- if (smallidx > FIRSTIDX) {
- smaller = magicints[smallidx - 1] /2;
- } else {
- smaller = 0;
- }
+ small = smaller;
+ if (smallidx > FIRSTIDX) {
+ smaller = magicints[smallidx - 1] /2;
+ } else {
+ smaller = 0;
+ }
} else if (is_smaller > 0) {
- smaller = small;
- small = magicints[smallidx] / 2;
+ smaller = small;
+ small = magicints[smallidx] / 2;
}
sizesmall[0] = sizesmall[1] = sizesmall[2] = magicints[smallidx] ;
}
diff --git a/src/XTC/dump_xtc.h b/src/XTC/dump_xtc.h
index e0a113e09da4d3579e9fa00d5cda85821ba06798..8d7d89df467aacd49a61a2547395bc84680b3372 100644
--- a/src/XTC/dump_xtc.h
+++ b/src/XTC/dump_xtc.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -35,7 +35,7 @@ class DumpXTC : public Dump {
public:
DumpXTC(class LAMMPS *, int, char**);
~DumpXTC();
-
+
private:
int natoms,ntotal;
int nevery_save;
diff --git a/src/XTC/xdr_compat.cpp b/src/XTC/xdr_compat.cpp
index cacedb77051c26bbb8c8688a677fb6236fda0e60..12bc777b90674bf5b7df6e3d005c46389a804a32 100644
--- a/src/XTC/xdr_compat.cpp
+++ b/src/XTC/xdr_compat.cpp
@@ -8,15 +8,15 @@
/* This file is needed for systems, that do not provide XDR support
* in their system libraries. It was written for windows, but will
* most probably work on other platforms too. better make sure you
- * test that the xtc files produced are ok before using it.
+ * test that the xtc files produced are ok before using it.
*
- * It is also needed on BG/L and Cray XT3/XT4 as we don't have
+ * It is also needed on BG/L and Cray XT3/XT4 as we don't have
* XDR support in the lightweight kernel runtimes either.
*
- * This file contains the definitions for Sun External Data
+ * This file contains the definitions for Sun External Data
* Representation (XDR) headers and routines.
*
- * Although the rest of LAMPPS is GPL, you can copy and use the XDR
+ * Although the rest of LAMPPS is GPL, you can copy and use the XDR
* routines in any way you want as long as you obey Sun's license:
*
* Sun RPC is a product of Sun Microsystems, Inc. and is provided for
@@ -45,7 +45,7 @@
* Sun Microsystems, Inc.
* 2550 Garcia Avenue
* Mountain View, California 94043
- */
+ */
#ifdef __cplusplus
extern "C" {
@@ -62,10 +62,10 @@ static xdr_uint32_t xdr_swapbytes(xdr_uint32_t x)
int i;
char *px=(char *)&x;
char *py=(char *)&y;
-
+
for(i=0;i<4;i++)
py[i]=px[3-i];
-
+
return y;
}
@@ -132,11 +132,11 @@ xdr_int (XDR *xdrs, int *ip)
case XDR_DECODE:
if (!xdr_getint32 (xdrs, &l))
- {
- return FALSE;
- }
+ {
+ return FALSE;
+ }
*ip = (int) l;
-
+
case XDR_FREE:
return TRUE;
}
@@ -160,11 +160,11 @@ xdr_u_int (XDR *xdrs, unsigned int *up)
case XDR_DECODE:
if (!xdr_getuint32 (xdrs, &l))
- {
- return FALSE;
- }
+ {
+ return FALSE;
+ }
*up = (unsigned int) l;
-
+
case XDR_FREE:
return TRUE;
}
@@ -190,9 +190,9 @@ xdr_short (XDR *xdrs, short *sp)
case XDR_DECODE:
if (!xdr_getint32 (xdrs, &l))
- {
- return FALSE;
- }
+ {
+ return FALSE;
+ }
*sp = (short) l;
return TRUE;
@@ -219,10 +219,10 @@ xdr_u_short (XDR *xdrs, unsigned short *usp)
case XDR_DECODE:
if (!xdr_getuint32 (xdrs, &l))
- {
- return FALSE;
- }
- *usp = (unsigned short) l;
+ {
+ return FALSE;
+ }
+ *usp = (unsigned short) l;
return TRUE;
case XDR_FREE:
@@ -272,8 +272,8 @@ xdr_u_char (XDR *xdrs, unsigned char *cp)
bool_t
xdr_bool (XDR *xdrs, int *bp)
{
-#define XDR_FALSE ((xdr_int32_t) 0)
-#define XDR_TRUE ((xdr_int32_t) 1)
+#define XDR_FALSE ((xdr_int32_t) 0)
+#define XDR_TRUE ((xdr_int32_t) 1)
xdr_int32_t lb;
@@ -285,9 +285,9 @@ xdr_bool (XDR *xdrs, int *bp)
case XDR_DECODE:
if (!xdr_getint32 (xdrs, &lb))
- {
- return FALSE;
- }
+ {
+ return FALSE;
+ }
*bp = (lb == XDR_FALSE) ? FALSE : TRUE;
return TRUE;
@@ -329,20 +329,20 @@ xdr_opaque (XDR *xdrs, char *cp, unsigned int cnt)
{
case XDR_DECODE:
if (!xdr_getbytes (xdrs, cp, cnt))
- {
- return FALSE;
- }
+ {
+ return FALSE;
+ }
if (rndup == 0)
- return TRUE;
+ return TRUE;
return xdr_getbytes (xdrs, (char *)crud, rndup);
case XDR_ENCODE:
if (!xdr_putbytes (xdrs, cp, cnt))
- {
- return FALSE;
- }
+ {
+ return FALSE;
+ }
if (rndup == 0)
- return TRUE;
+ return TRUE;
return xdr_putbytes (xdrs, xdr_zero, rndup);
case XDR_FREE:
@@ -363,7 +363,7 @@ xdr_opaque (XDR *xdrs, char *cp, unsigned int cnt)
bool_t
xdr_string (XDR *xdrs, char **cpp, unsigned int maxsize)
{
- char *sp = *cpp; /* sp is the actual string pointer */
+ char *sp = *cpp; /* sp is the actual string pointer */
unsigned int size = 0;
unsigned int nodesize = 0;
@@ -374,19 +374,19 @@ xdr_string (XDR *xdrs, char **cpp, unsigned int maxsize)
{
case XDR_FREE:
if (sp == NULL)
- {
- return TRUE; /* already free */
- }
+ {
+ return TRUE; /* already free */
+ }
/* fall through... */
case XDR_ENCODE:
if (sp == NULL)
- return FALSE;
+ return FALSE;
size = strlen (sp);
break;
case XDR_DECODE:
break;
}
-
+
if (!xdr_u_int (xdrs, &size))
{
return FALSE;
@@ -404,16 +404,16 @@ xdr_string (XDR *xdrs, char **cpp, unsigned int maxsize)
{
case XDR_DECODE:
if (nodesize == 0)
- {
- return TRUE;
- }
+ {
+ return TRUE;
+ }
if (sp == NULL)
- *cpp = sp = (char *) malloc (nodesize);
+ *cpp = sp = (char *) malloc (nodesize);
if (sp == NULL)
- {
- (void) fputs ("xdr_string: out of memory\n", stderr);
- return FALSE;
- }
+ {
+ (void) fputs ("xdr_string: out of memory\n", stderr);
+ return FALSE;
+ }
sp[size] = 0;
/* fall into ... */
@@ -435,28 +435,28 @@ xdr_string (XDR *xdrs, char **cpp, unsigned int maxsize)
bool_t
xdr_float(XDR *xdrs, float *fp)
{
- xdr_int32_t tmp;
-
- switch (xdrs->x_op) {
+ xdr_int32_t tmp;
+
+ switch (xdrs->x_op) {
- case XDR_ENCODE:
- tmp = *(xdr_int32_t *)fp;
- return (xdr_putint32(xdrs, &tmp));
+ case XDR_ENCODE:
+ tmp = *(xdr_int32_t *)fp;
+ return (xdr_putint32(xdrs, &tmp));
- break;
+ break;
- case XDR_DECODE:
- if (xdr_getint32(xdrs, &tmp)) {
- *(xdr_int32_t *)fp = tmp;
- return (TRUE);
- }
+ case XDR_DECODE:
+ if (xdr_getint32(xdrs, &tmp)) {
+ *(xdr_int32_t *)fp = tmp;
+ return (TRUE);
+ }
- break;
+ break;
- case XDR_FREE:
- return (TRUE);
- }
- return (FALSE);
+ case XDR_FREE:
+ return (TRUE);
+ }
+ return (FALSE);
}
@@ -475,53 +475,53 @@ xdr_double(XDR *xdrs, double *dp)
if(LSW<0) {
double x=0.987654321; /* Just a number */
- /* Possible representations in IEEE double precision:
+ /* Possible representations in IEEE double precision:
* (S=small endian, B=big endian)
- *
+ *
* Byte order, Word order, Hex
- * S S b8 56 0e 3c dd 9a ef 3f
+ * S S b8 56 0e 3c dd 9a ef 3f
* B S 3c 0e 56 b8 3f ef 9a dd
* S B dd 9a ef 3f b8 56 0e 3c
* B B 3f ef 9a dd 3c 0e 56 b8
- */
-
+ */
+
unsigned char ix = *((char *)&x);
-
+
if(ix==0xdd || ix==0x3f)
LSW=1; /* Big endian word order */
else if(ix==0xb8 || ix==0x3c)
LSW=0; /* Small endian word order */
else { /* Catch strange errors */
printf("Error when detecting floating-point word order.\n"
- "Do you have a non-IEEE system?\n"
- "If possible, use the XDR libraries provided with your system,\n"
- "instead of the Gromacs fallback XDR source.\n");
+ "Do you have a non-IEEE system?\n"
+ "If possible, use the XDR libraries provided with your system,\n"
+ "instead of the Gromacs fallback XDR source.\n");
exit(0);
}
- }
-
+ }
+
switch (xdrs->x_op) {
-
+
case XDR_ENCODE:
ip = (int *)dp;
tmp[0] = ip[!LSW];
tmp[1] = ip[LSW];
return (xdr_putint32(xdrs, tmp) &&
- xdr_putint32(xdrs, tmp+1));
-
+ xdr_putint32(xdrs, tmp+1));
+
break;
-
+
case XDR_DECODE:
ip = (int *)dp;
if (xdr_getint32(xdrs, tmp+!LSW) &&
- xdr_getint32(xdrs, tmp+LSW)) {
- ip[0] = tmp[0];
- ip[1] = tmp[1];
- return (TRUE);
+ xdr_getint32(xdrs, tmp+LSW)) {
+ ip[0] = tmp[0];
+ ip[1] = tmp[1];
+ return (TRUE);
}
break;
-
+
case XDR_FREE:
return (TRUE);
}
@@ -542,10 +542,10 @@ xdr_double(XDR *xdrs, double *dp)
* > xdr_elem: routine to XDR each element
*/
bool_t
-xdr_vector (XDR *xdrs, char *basep, unsigned int nelem,
+xdr_vector (XDR *xdrs, char *basep, unsigned int nelem,
unsigned int elemsize, xdrproc_t xdr_elem)
{
-#define LASTUNSIGNED ((unsigned int)0-1)
+#define LASTUNSIGNED ((unsigned int)0-1)
unsigned int i;
char *elptr;
@@ -553,9 +553,9 @@ xdr_vector (XDR *xdrs, char *basep, unsigned int nelem,
for (i = 0; i < nelem; i++)
{
if (!(*xdr_elem) (xdrs, elptr, LASTUNSIGNED))
- {
- return FALSE;
- }
+ {
+ return FALSE;
+ }
elptr += elemsize;
}
return TRUE;
@@ -580,16 +580,16 @@ static bool_t xdrstdio_putuint32 (XDR *, xdr_uint32_t *);
*/
static const struct xdr_ops xdrstdio_ops =
{
- xdrstdio_getbytes, /* deserialize counted bytes */
- xdrstdio_putbytes, /* serialize counted bytes */
- xdrstdio_getpos, /* get offset in the stream */
- xdrstdio_setpos, /* set offset in the stream */
- xdrstdio_inline, /* prime stream for inline macros */
- xdrstdio_destroy, /* destroy stream */
- xdrstdio_getint32, /* deserialize a int */
- xdrstdio_putint32, /* serialize a int */
- xdrstdio_getuint32, /* deserialize a int */
- xdrstdio_putuint32 /* serialize a int */
+ xdrstdio_getbytes, /* deserialize counted bytes */
+ xdrstdio_putbytes, /* serialize counted bytes */
+ xdrstdio_getpos, /* get offset in the stream */
+ xdrstdio_setpos, /* set offset in the stream */
+ xdrstdio_inline, /* prime stream for inline macros */
+ xdrstdio_destroy, /* destroy stream */
+ xdrstdio_getint32, /* deserialize a int */
+ xdrstdio_putint32, /* serialize a int */
+ xdrstdio_getuint32, /* deserialize a int */
+ xdrstdio_putuint32 /* serialize a int */
};
/*
@@ -625,7 +625,7 @@ static bool_t
xdrstdio_getbytes (XDR *xdrs, char *addr, unsigned int len)
{
if ((len != 0) && (fread (addr, (int) len, 1,
- (FILE *) xdrs->x_private) != 1))
+ (FILE *) xdrs->x_private) != 1))
return FALSE;
return TRUE;
}
@@ -634,7 +634,7 @@ static bool_t
xdrstdio_putbytes (XDR *xdrs, char *addr, unsigned int len)
{
if ((len != 0) && (fwrite (addr, (int) len, 1,
- (FILE *) xdrs->x_private) != 1))
+ (FILE *) xdrs->x_private) != 1))
return FALSE;
return TRUE;
}
@@ -691,30 +691,30 @@ xdrstdio_putint32 (XDR *xdrs, xdr_int32_t *ip)
static bool_t
xdrstdio_getuint32 (XDR *xdrs, xdr_uint32_t *ip)
{
- xdr_uint32_t mycopy;
-
- if (fread ((char *) &mycopy, 4, 1, (FILE *) xdrs->x_private) != 1)
- return FALSE;
- *ip = xdr_ntohl (mycopy);
- return TRUE;
+ xdr_uint32_t mycopy;
+
+ if (fread ((char *) &mycopy, 4, 1, (FILE *) xdrs->x_private) != 1)
+ return FALSE;
+ *ip = xdr_ntohl (mycopy);
+ return TRUE;
}
static bool_t
xdrstdio_putuint32 (XDR *xdrs, xdr_uint32_t *ip)
{
- xdr_uint32_t mycopy = xdr_htonl (*ip);
-
- ip = &mycopy;
- if (fwrite ((char *) ip, 4, 1, (FILE *) xdrs->x_private) != 1)
- return FALSE;
- return TRUE;
+ xdr_uint32_t mycopy = xdr_htonl (*ip);
+
+ ip = &mycopy;
+ if (fwrite ((char *) ip, 4, 1, (FILE *) xdrs->x_private) != 1)
+ return FALSE;
+ return TRUE;
}
#ifdef __cplusplus
}
#endif
-#else
+#else
/* satisfy compilers that do not like to compile empty files. */
static void i_am_a_dummy_subroutine(void) {
return;
diff --git a/src/XTC/xdr_compat.h b/src/XTC/xdr_compat.h
index cb9be939915eea513f61a64462ff655b429f6140..d1946ef0af99c31d2b797abd0045e2235f99af2f 100644
--- a/src/XTC/xdr_compat.h
+++ b/src/XTC/xdr_compat.h
@@ -13,15 +13,15 @@ extern "C" {
* This file is needed for systems, that do not provide XDR support
* in their system libraries. It was written for windows, but will
* most probably work on other platforms too. better make sure you
- * test that the xtc files produced are ok before using it.
+ * test that the xtc files produced are ok before using it.
*
* It is also needed on BG/L, BG/P and Cray XT3/XT4/XT5 as we don't
* have XDR support in the lightweight kernel runtimes either.
*
- * This file contains the definitions for Sun External Data
+ * This file contains the definitions for Sun External Data
* Representation (XDR) headers and routines.
*
- * Although the rest of LAMPPS is GPL, you can copy and use the XDR
+ * Although the rest of LAMPPS is GPL, you can copy and use the XDR
* routines in any way you want as long as you obey Sun's license:
* Sun RPC is a product of Sun Microsystems, Inc. and is provided for
* unrestricted use provided that this legend is included on all tape
@@ -49,12 +49,12 @@ extern "C" {
* Sun Microsystems, Inc.
* 2550 Garcia Avenue
* Mountain View, California 94043
- */
+ */
/*
* Xdr operations. XDR_ENCODE causes the type to be encoded into the
* stream. XDR_DECODE causes the type to be extracted from the stream.
- * XDR_FREE can be used to release the space allocated by an
+ * XDR_FREE can be used to release the space allocated by an
* XDR_DECODE request.
*/
@@ -65,7 +65,7 @@ typedef char * caddr_t;
typedef unsigned int u_int;
#endif
-/*
+/*
* Aninteger type that is 32 bits wide. Check if int,
* long or short is 32 bits and die if none of them is :-)
*/
@@ -95,7 +95,7 @@ enum xdr_op {
# define TRUE (1)
#endif
-#define BYTES_PER_XDR_UNIT (4)
+#define BYTES_PER_XDR_UNIT (4)
/* Macro to round up to units of 4. */
#define XDR_RNDUP(x) (((x) + BYTES_PER_XDR_UNIT - 1) & ~(BYTES_PER_XDR_UNIT - 1))
@@ -110,36 +110,36 @@ enum xdr_op {
typedef struct XDR XDR;
struct XDR
{
- enum xdr_op x_op; /* operation; fast additional param */
+ enum xdr_op x_op; /* operation; fast additional param */
struct xdr_ops *x_ops;
- char *x_public; /* users' data */
- char *x_private; /* pointer to private data */
- char *x_base; /* private used for position info */
- int x_handy; /* extra private word */
+ char *x_public; /* users' data */
+ char *x_private; /* pointer to private data */
+ char *x_base; /* private used for position info */
+ int x_handy; /* extra private word */
};
struct xdr_ops
{
- bool_t (*x_getbytes) (XDR *__xdrs, char *__addr, unsigned int __len);
- /* get some bytes from " */
- bool_t (*x_putbytes) (XDR *__xdrs, char *__addr, unsigned int __len);
- /* put some bytes to " */
- unsigned int (*x_getpostn) (XDR *__xdrs);
- /* returns bytes off from beginning */
- bool_t (*x_setpostn) (XDR *__xdrs, unsigned int __pos);
- /* lets you reposition the stream */
- xdr_int32_t *(*x_inline) (XDR *__xdrs, int __len);
- /* buf quick ptr to buffered data */
- void (*x_destroy) (XDR *__xdrs);
- /* free privates of this xdr_stream */
- bool_t (*x_getint32) (XDR *__xdrs, xdr_int32_t *__ip);
- /* get a int from underlying stream */
- bool_t (*x_putint32) (XDR *__xdrs, xdr_int32_t *__ip);
- /* put a int to " */
- bool_t (*x_getuint32) (XDR *__xdrs, xdr_uint32_t *__ip);
- /* get a unsigned int from underlying stream */
- bool_t (*x_putuint32) (XDR *__xdrs, xdr_uint32_t *__ip);
- /* put a int to " */
+ bool_t (*x_getbytes) (XDR *__xdrs, char *__addr, unsigned int __len);
+ /* get some bytes from " */
+ bool_t (*x_putbytes) (XDR *__xdrs, char *__addr, unsigned int __len);
+ /* put some bytes to " */
+ unsigned int (*x_getpostn) (XDR *__xdrs);
+ /* returns bytes off from beginning */
+ bool_t (*x_setpostn) (XDR *__xdrs, unsigned int __pos);
+ /* lets you reposition the stream */
+ xdr_int32_t *(*x_inline) (XDR *__xdrs, int __len);
+ /* buf quick ptr to buffered data */
+ void (*x_destroy) (XDR *__xdrs);
+ /* free privates of this xdr_stream */
+ bool_t (*x_getint32) (XDR *__xdrs, xdr_int32_t *__ip);
+ /* get a int from underlying stream */
+ bool_t (*x_putint32) (XDR *__xdrs, xdr_int32_t *__ip);
+ /* put a int to " */
+ bool_t (*x_getuint32) (XDR *__xdrs, xdr_uint32_t *__ip);
+ /* get a unsigned int from underlying stream */
+ bool_t (*x_putuint32) (XDR *__xdrs, xdr_uint32_t *__ip);
+ /* put a int to " */
};
/*
@@ -177,26 +177,26 @@ typedef bool_t (*xdrproc_t) (XDR *, void *,...);
#define xdr_putuint32(xdrs, uint32p) \
(*(xdrs)->x_ops->x_putuint32)(xdrs, uint32p)
-#define xdr_getbytes(xdrs, addr, len) \
- (*(xdrs)->x_ops->x_getbytes)(xdrs, addr, len)
+#define xdr_getbytes(xdrs, addr, len) \
+ (*(xdrs)->x_ops->x_getbytes)(xdrs, addr, len)
-#define xdr_putbytes(xdrs, addr, len) \
- (*(xdrs)->x_ops->x_putbytes)(xdrs, addr, len)
+#define xdr_putbytes(xdrs, addr, len) \
+ (*(xdrs)->x_ops->x_putbytes)(xdrs, addr, len)
-#define xdr_getpos(xdrs) \
- (*(xdrs)->x_ops->x_getpostn)(xdrs)
+#define xdr_getpos(xdrs) \
+ (*(xdrs)->x_ops->x_getpostn)(xdrs)
-#define xdr_setpos(xdrs, pos) \
- (*(xdrs)->x_ops->x_setpostn)(xdrs, pos)
+#define xdr_setpos(xdrs, pos) \
+ (*(xdrs)->x_ops->x_setpostn)(xdrs, pos)
-#define xdr_inline(xdrs, len) \
- (*(xdrs)->x_ops->x_inline)(xdrs, len)
+#define xdr_inline(xdrs, len) \
+ (*(xdrs)->x_ops->x_inline)(xdrs, len)
-#define xdr_destroy(xdrs) \
- do { \
- if ((xdrs)->x_ops->x_destroy) \
- (*(xdrs)->x_ops->x_destroy)(xdrs); \
- } while (0)
+#define xdr_destroy(xdrs) \
+ do { \
+ if ((xdrs)->x_ops->x_destroy) \
+ (*(xdrs)->x_ops->x_destroy)(xdrs); \
+ } while (0)
extern bool_t xdr_int (XDR *__xdrs, int *__ip);
@@ -209,7 +209,7 @@ extern bool_t xdr_string (XDR *__xdrs, char **__cpp, unsigned int __maxsize);
extern bool_t xdr_char (XDR *__xdrs, char *__cp);
extern bool_t xdr_u_char (XDR *__xdrs, unsigned char *__cp);
extern bool_t xdr_vector (XDR *__xdrs, char *__basep, unsigned int __nelem,
- unsigned int __elemsize, xdrproc_t __xdr_elem);
+ unsigned int __elemsize, xdrproc_t __xdr_elem);
extern bool_t xdr_float (XDR *__xdrs, float *__fp);
extern bool_t xdr_double (XDR *__xdrs, double *__dp);
extern void xdrstdio_create (XDR *__xdrs, FILE *__file, enum xdr_op __xop);
@@ -223,4 +223,3 @@ extern void xdr_free (xdrproc_t __proc, char *__objp);
#endif /* XDR_COMPAT_H */
-
diff --git a/src/accelerator_cuda.h b/src/accelerator_cuda.h
index 307a045caeb14044eefe0518c7348afdd221f239..1f4f863533b2904e0a6021de54f46a7c98fa08c2 100644
--- a/src/accelerator_cuda.h
+++ b/src/accelerator_cuda.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -41,7 +41,7 @@ class Cuda {
public:
int cuda_exists;
int oncpu;
-
+
Cuda(class LAMMPS *) {cuda_exists = 0;}
~Cuda() {}
void accelerator(int, char **) {}
@@ -73,7 +73,7 @@ class ModifyCuda : public Modify {
ModifyCuda(class LAMMPS *lmp) : Modify(lmp) {}
~ModifyCuda() {}
};
-
+
class VerletCuda : public Verlet {
public:
VerletCuda(class LAMMPS *lmp, int narg, char **arg) : Verlet(lmp,narg,arg) {}
diff --git a/src/accelerator_omp.h b/src/accelerator_omp.h
index 5ad4277b93d280038cda12921b6283b0e9fdce46..89db35cae2a1f8973346613a8ce2a83d9bfddc21 100644
--- a/src/accelerator_omp.h
+++ b/src/accelerator_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/angle.cpp b/src/angle.cpp
index 526bfa646eb0aa2f0930a109c41bb6b664266754..9d9ee2fc916ba3170dfc429ad723129aaf0b3e6b 100644
--- a/src/angle.cpp
+++ b/src/angle.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -77,7 +77,7 @@ void Angle::ev_setup(int eflag, int vflag)
vflag_either = vflag;
vflag_global = vflag % 4;
vflag_atom = vflag / 4;
-
+
// reallocate per-atom arrays if necessary
if (eflag_atom && atom->nmax > maxeatom) {
@@ -120,9 +120,9 @@ void Angle::ev_setup(int eflag, int vflag)
------------------------------------------------------------------------- */
void Angle::ev_tally(int i, int j, int k, int nlocal, int newton_bond,
- double eangle, double *f1, double *f3,
- double delx1, double dely1, double delz1,
- double delx2, double dely2, double delz2)
+ double eangle, double *f1, double *f3,
+ double delx1, double dely1, double delz1,
+ double delx2, double dely2, double delz2)
{
double eanglethird,v[6];
@@ -130,10 +130,10 @@ void Angle::ev_tally(int i, int j, int k, int nlocal, int newton_bond,
if (eflag_global) {
if (newton_bond) energy += eangle;
else {
- eanglethird = THIRD*eangle;
- if (i < nlocal) energy += eanglethird;
- if (j < nlocal) energy += eanglethird;
- if (k < nlocal) energy += eanglethird;
+ eanglethird = THIRD*eangle;
+ if (i < nlocal) energy += eanglethird;
+ if (j < nlocal) energy += eanglethird;
+ if (k < nlocal) energy += eanglethird;
}
}
if (eflag_atom) {
@@ -154,64 +154,64 @@ void Angle::ev_tally(int i, int j, int k, int nlocal, int newton_bond,
if (vflag_global) {
if (newton_bond) {
- virial[0] += v[0];
- virial[1] += v[1];
- virial[2] += v[2];
- virial[3] += v[3];
- virial[4] += v[4];
- virial[5] += v[5];
+ virial[0] += v[0];
+ virial[1] += v[1];
+ virial[2] += v[2];
+ virial[3] += v[3];
+ virial[4] += v[4];
+ virial[5] += v[5];
} else {
- if (i < nlocal) {
- virial[0] += THIRD*v[0];
- virial[1] += THIRD*v[1];
- virial[2] += THIRD*v[2];
- virial[3] += THIRD*v[3];
- virial[4] += THIRD*v[4];
- virial[5] += THIRD*v[5];
- }
- if (j < nlocal) {
- virial[0] += THIRD*v[0];
- virial[1] += THIRD*v[1];
- virial[2] += THIRD*v[2];
- virial[3] += THIRD*v[3];
- virial[4] += THIRD*v[4];
- virial[5] += THIRD*v[5];
- }
- if (k < nlocal) {
- virial[0] += THIRD*v[0];
- virial[1] += THIRD*v[1];
- virial[2] += THIRD*v[2];
- virial[3] += THIRD*v[3];
- virial[4] += THIRD*v[4];
- virial[5] += THIRD*v[5];
- }
+ if (i < nlocal) {
+ virial[0] += THIRD*v[0];
+ virial[1] += THIRD*v[1];
+ virial[2] += THIRD*v[2];
+ virial[3] += THIRD*v[3];
+ virial[4] += THIRD*v[4];
+ virial[5] += THIRD*v[5];
+ }
+ if (j < nlocal) {
+ virial[0] += THIRD*v[0];
+ virial[1] += THIRD*v[1];
+ virial[2] += THIRD*v[2];
+ virial[3] += THIRD*v[3];
+ virial[4] += THIRD*v[4];
+ virial[5] += THIRD*v[5];
+ }
+ if (k < nlocal) {
+ virial[0] += THIRD*v[0];
+ virial[1] += THIRD*v[1];
+ virial[2] += THIRD*v[2];
+ virial[3] += THIRD*v[3];
+ virial[4] += THIRD*v[4];
+ virial[5] += THIRD*v[5];
+ }
}
}
if (vflag_atom) {
if (newton_bond || i < nlocal) {
- vatom[i][0] += THIRD*v[0];
- vatom[i][1] += THIRD*v[1];
- vatom[i][2] += THIRD*v[2];
- vatom[i][3] += THIRD*v[3];
- vatom[i][4] += THIRD*v[4];
- vatom[i][5] += THIRD*v[5];
+ vatom[i][0] += THIRD*v[0];
+ vatom[i][1] += THIRD*v[1];
+ vatom[i][2] += THIRD*v[2];
+ vatom[i][3] += THIRD*v[3];
+ vatom[i][4] += THIRD*v[4];
+ vatom[i][5] += THIRD*v[5];
}
if (newton_bond || j < nlocal) {
- vatom[j][0] += THIRD*v[0];
- vatom[j][1] += THIRD*v[1];
- vatom[j][2] += THIRD*v[2];
- vatom[j][3] += THIRD*v[3];
- vatom[j][4] += THIRD*v[4];
- vatom[j][5] += THIRD*v[5];
+ vatom[j][0] += THIRD*v[0];
+ vatom[j][1] += THIRD*v[1];
+ vatom[j][2] += THIRD*v[2];
+ vatom[j][3] += THIRD*v[3];
+ vatom[j][4] += THIRD*v[4];
+ vatom[j][5] += THIRD*v[5];
}
if (newton_bond || k < nlocal) {
- vatom[k][0] += THIRD*v[0];
- vatom[k][1] += THIRD*v[1];
- vatom[k][2] += THIRD*v[2];
- vatom[k][3] += THIRD*v[3];
- vatom[k][4] += THIRD*v[4];
- vatom[k][5] += THIRD*v[5];
+ vatom[k][0] += THIRD*v[0];
+ vatom[k][1] += THIRD*v[1];
+ vatom[k][2] += THIRD*v[2];
+ vatom[k][3] += THIRD*v[3];
+ vatom[k][4] += THIRD*v[4];
+ vatom[k][5] += THIRD*v[5];
}
}
}
diff --git a/src/angle.h b/src/angle.h
index a94846b0e85c9ce7701bf3761c0669d8bcf9ed56..e46ae2f470c5de36080e69d79d4377e8fbb0cbde 100644
--- a/src/angle.h
+++ b/src/angle.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -52,7 +52,7 @@ class Angle : protected Pointers {
void ev_setup(int, int);
void ev_tally(int, int, int, int, int, double, double *, double *,
- double, double, double, double, double, double);
+ double, double, double, double, double, double);
};
}
diff --git a/src/atom.cpp b/src/atom.cpp
index 4a68a7e0f6c0c58886e2574cb221baa545af1a71..7d4564359cd5d66966755eeb4a3f840b9f1f2e68 100644
--- a/src/atom.cpp
+++ b/src/atom.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -135,14 +135,14 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
map_style = 0;
map_tag_max = 0;
map_nhash = 0;
-
+
nprimes = 38;
primes = new int[nprimes];
int plist[] = {5041,10007,20011,30011,40009,50021,60013,70001,80021,
- 90001,100003,110017,120011,130003,140009,150001,160001,
- 170003,180001,190027,200003,210011,220009,230003,240007,
- 250007,260003,270001,280001,290011,300007,310019,320009,
- 330017,340007,350003,362881,3628801};
+ 90001,100003,110017,120011,130003,140009,150001,160001,
+ 170003,180001,190027,200003,210011,220009,230003,240007,
+ 250007,260003,270001,280001,290011,300007,310019,320009,
+ 330017,340007,350003,362881,3628801};
for (int i = 0; i < nprimes; i++) primes[i] = plist[i];
// default atom style = atomic
@@ -264,7 +264,7 @@ void Atom::create_avec(const char *style, int narg, char **arg, char *suffix)
sphere_flag = ellipsoid_flag = line_flag = tri_flag = 0;
peri_flag = electron_flag = 0;
-
+
molecule_flag = q_flag = mu_flag = 0;
rmass_flag = radius_flag = omega_flag = torque_flag = angmom_flag = 0;
vfrac_flag = spin_flag = eradius_flag = ervel_flag = erforce_flag = 0;
@@ -295,7 +295,7 @@ void Atom::create_avec(const char *style, int narg, char **arg, char *suffix)
------------------------------------------------------------------------- */
AtomVec *Atom::new_avec(const char *style, int narg, char **arg,
- char *suffix, int &sflag)
+ char *suffix, int &sflag)
{
if (suffix && lmp->suffix_enable) {
sflag = 1;
@@ -379,7 +379,7 @@ AtomVec *Atom::style_match(const char *style)
AtomVecHybrid *avec_hybrid = (AtomVecHybrid *) avec;
for (int i = 0; i < avec_hybrid->nstyles; i++)
if (strcmp(avec_hybrid->keywords[i],style) == 0)
- return avec_hybrid->styles[i];
+ return avec_hybrid->styles[i];
}
return NULL;
}
@@ -401,20 +401,20 @@ void Atom::modify_params(int narg, char **arg)
if (strcmp(arg[iarg+1],"array") == 0) map_style = 1;
else if (strcmp(arg[iarg+1],"hash") == 0) map_style = 2;
else error->all(FLERR,"Illegal atom_modify command");
- if (domain->box_exist)
- error->all(FLERR,
- "Atom_modify map command after simulation box is defined");
+ if (domain->box_exist)
+ error->all(FLERR,
+ "Atom_modify map command after simulation box is defined");
iarg += 2;
} else if (strcmp(arg[iarg],"first") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal atom_modify command");
if (strcmp(arg[iarg+1],"all") == 0) {
- delete [] firstgroupname;
- firstgroupname = NULL;
+ delete [] firstgroupname;
+ firstgroupname = NULL;
} else {
- int n = strlen(arg[iarg+1]) + 1;
- firstgroupname = new char[n];
- strcpy(firstgroupname,arg[iarg+1]);
- sortfreq = 0;
+ int n = strlen(arg[iarg+1]) + 1;
+ firstgroupname = new char[n];
+ strcpy(firstgroupname,arg[iarg+1]);
+ sortfreq = 0;
}
iarg += 2;
} else if (strcmp(arg[iarg],"sort") == 0) {
@@ -422,10 +422,10 @@ void Atom::modify_params(int narg, char **arg)
sortfreq = atoi(arg[iarg+1]);
userbinsize = atof(arg[iarg+2]);
if (sortfreq < 0 || userbinsize < 0.0)
- error->all(FLERR,"Illegal atom_modify command");
- if (sortfreq >= 0 && firstgroupname)
- error->all(FLERR,"Atom_modify sort and first options "
- "cannot be used together");
+ error->all(FLERR,"Illegal atom_modify command");
+ if (sortfreq >= 0 && firstgroupname)
+ error->all(FLERR,"Atom_modify sort and first options "
+ "cannot be used together");
iarg += 3;
} else error->all(FLERR,"Illegal atom_modify command");
}
@@ -515,18 +515,18 @@ void Atom::map_clear()
ibucket = global % map_nbucket;
index = map_bucket[ibucket];
while (index > -1) {
- if (map_hash[index].global == global) break;
- previous = index;
- index = map_hash[index].next;
+ if (map_hash[index].global == global) break;
+ previous = index;
+ index = map_hash[index].next;
}
if (index == -1) continue;
// delete the hash entry and add it to free list
// special logic if entry is 1st in the bucket
-
+
if (previous == -1) map_bucket[ibucket] = map_hash[index].next;
else map_hash[previous].next = map_hash[index].next;
-
+
map_hash[index].next = map_free;
map_free = index;
map_nused--;
@@ -538,7 +538,7 @@ void Atom::map_clear()
set global -> local map for all of my own and ghost atoms
loop in reverse order so that nearby images take precedence over far ones
and owned atoms take precedence over images
- this enables valid lookups of bond topology atoms
+ this enables valid lookups of bond topology atoms
for hash table option:
if hash table too small, re-init
global ID may already be in table if image atom was set
@@ -565,13 +565,13 @@ void Atom::map_set()
ibucket = global % map_nbucket;
index = map_bucket[ibucket];
while (index > -1) {
- if (map_hash[index].global == global) break;
- previous = index;
- index = map_hash[index].next;
+ if (map_hash[index].global == global) break;
+ previous = index;
+ index = map_hash[index].next;
}
if (index > -1) {
- map_hash[index].local = i;
- continue;
+ map_hash[index].local = i;
+ continue;
}
// take one entry from free list
@@ -603,7 +603,7 @@ void Atom::map_one(int global, int local)
else {
// search for key
// if found it, just overwrite local value with index
-
+
int previous = -1;
int ibucket = global % map_nbucket;
int index = map_bucket[ibucket];
@@ -616,11 +616,11 @@ void Atom::map_one(int global, int local)
map_hash[index].local = local;
return;
}
-
+
// take one entry from free list
// add the new global/local pair as entry at end of bucket list
// special logic if this entry is 1st in bucket
-
+
index = map_free;
map_free = map_hash[map_free].next;
if (previous == -1) map_bucket[ibucket] = index;
@@ -708,7 +708,7 @@ int Atom::tag_consecutive()
{
int idmin = MAXTAGINT;
int idmax = 0;
-
+
for (int i = 0; i < nlocal; i++) {
idmin = MIN(idmin,tag[i]);
idmax = MAX(idmax,tag[i]);
@@ -826,18 +826,18 @@ void Atom::data_atoms(int n, char *buf)
next = strchr(buf,'\n');
values[0] = strtok(buf," \t\n\r\f");
- if (values[0] == NULL)
+ if (values[0] == NULL)
error->all(FLERR,"Incorrect atom format in data file");
for (m = 1; m < nwords; m++) {
values[m] = strtok(NULL," \t\n\r\f");
- if (values[m] == NULL)
- error->all(FLERR,"Incorrect atom format in data file");
+ if (values[m] == NULL)
+ error->all(FLERR,"Incorrect atom format in data file");
}
if (imageflag)
imagedata = ((atoi(values[iptr+2]) + 512 & 1023) << 20) |
- ((atoi(values[iptr+1]) + 512 & 1023) << 10) |
- (atoi(values[iptr]) + 512 & 1023);
+ ((atoi(values[iptr+1]) + 512 & 1023) << 10) |
+ (atoi(values[iptr]) + 512 & 1023);
else imagedata = (512 << 20) | (512 << 10) | 512;
xdata[0] = atof(values[xptr]);
@@ -850,8 +850,8 @@ void Atom::data_atoms(int n, char *buf)
} else coord = xdata;
if (coord[0] >= sublo[0] && coord[0] < subhi[0] &&
- coord[1] >= sublo[1] && coord[1] < subhi[1] &&
- coord[2] >= sublo[2] && coord[2] < subhi[2])
+ coord[1] >= sublo[1] && coord[1] < subhi[1] &&
+ coord[2] >= sublo[2] && coord[2] < subhi[2])
avec->data_atom(xdata,imagedata,values);
buf = next + 1;
@@ -964,8 +964,8 @@ void Atom::data_bonds(int n, char *buf)
next = strchr(buf,'\n');
*next = '\0';
sscanf(buf,"%d %d %d %d",&tmp,&itype,&atom1,&atom2);
- if (atom1 <= 0 || atom1 > map_tag_max ||
- atom2 <= 0 || atom2 > map_tag_max)
+ if (atom1 <= 0 || atom1 > map_tag_max ||
+ atom2 <= 0 || atom2 > map_tag_max)
error->one(FLERR,"Invalid atom ID in Bonds section of data file");
if (itype <= 0 || itype > nbondtypes)
error->one(FLERR,"Invalid bond type in Bonds section of data file");
@@ -976,9 +976,9 @@ void Atom::data_bonds(int n, char *buf)
}
if (newton_bond == 0) {
if ((m = map(atom2)) >= 0) {
- bond_type[m][num_bond[m]] = itype;
- bond_atom[m][num_bond[m]] = atom1;
- num_bond[m]++;
+ bond_type[m][num_bond[m]] = itype;
+ bond_atom[m][num_bond[m]] = atom1;
+ num_bond[m]++;
}
}
buf = next + 1;
@@ -999,9 +999,9 @@ void Atom::data_angles(int n, char *buf)
next = strchr(buf,'\n');
*next = '\0';
sscanf(buf,"%d %d %d %d %d",&tmp,&itype,&atom1,&atom2,&atom3);
- if (atom1 <= 0 || atom1 > map_tag_max ||
- atom2 <= 0 || atom2 > map_tag_max ||
- atom3 <= 0 || atom3 > map_tag_max)
+ if (atom1 <= 0 || atom1 > map_tag_max ||
+ atom2 <= 0 || atom2 > map_tag_max ||
+ atom3 <= 0 || atom3 > map_tag_max)
error->one(FLERR,"Invalid atom ID in Angles section of data file");
if (itype <= 0 || itype > nangletypes)
error->one(FLERR,"Invalid angle type in Angles section of data file");
@@ -1014,18 +1014,18 @@ void Atom::data_angles(int n, char *buf)
}
if (newton_bond == 0) {
if ((m = map(atom1)) >= 0) {
- angle_type[m][num_angle[m]] = itype;
- angle_atom1[m][num_angle[m]] = atom1;
- angle_atom2[m][num_angle[m]] = atom2;
- angle_atom3[m][num_angle[m]] = atom3;
- num_angle[m]++;
+ angle_type[m][num_angle[m]] = itype;
+ angle_atom1[m][num_angle[m]] = atom1;
+ angle_atom2[m][num_angle[m]] = atom2;
+ angle_atom3[m][num_angle[m]] = atom3;
+ num_angle[m]++;
}
if ((m = map(atom3)) >= 0) {
- angle_type[m][num_angle[m]] = itype;
- angle_atom1[m][num_angle[m]] = atom1;
- angle_atom2[m][num_angle[m]] = atom2;
- angle_atom3[m][num_angle[m]] = atom3;
- num_angle[m]++;
+ angle_type[m][num_angle[m]] = itype;
+ angle_atom1[m][num_angle[m]] = atom1;
+ angle_atom2[m][num_angle[m]] = atom2;
+ angle_atom3[m][num_angle[m]] = atom3;
+ num_angle[m]++;
}
}
buf = next + 1;
@@ -1046,14 +1046,14 @@ void Atom::data_dihedrals(int n, char *buf)
next = strchr(buf,'\n');
*next = '\0';
sscanf(buf,"%d %d %d %d %d %d",&tmp,&itype,&atom1,&atom2,&atom3,&atom4);
- if (atom1 <= 0 || atom1 > map_tag_max ||
- atom2 <= 0 || atom2 > map_tag_max ||
- atom3 <= 0 || atom3 > map_tag_max ||
- atom4 <= 0 || atom4 > map_tag_max)
+ if (atom1 <= 0 || atom1 > map_tag_max ||
+ atom2 <= 0 || atom2 > map_tag_max ||
+ atom3 <= 0 || atom3 > map_tag_max ||
+ atom4 <= 0 || atom4 > map_tag_max)
error->one(FLERR,"Invalid atom ID in Dihedrals section of data file");
if (itype <= 0 || itype > ndihedraltypes)
error->one(FLERR,
- "Invalid dihedral type in Dihedrals section of data file");
+ "Invalid dihedral type in Dihedrals section of data file");
if ((m = map(atom2)) >= 0) {
dihedral_type[m][num_dihedral[m]] = itype;
dihedral_atom1[m][num_dihedral[m]] = atom1;
@@ -1064,28 +1064,28 @@ void Atom::data_dihedrals(int n, char *buf)
}
if (newton_bond == 0) {
if ((m = map(atom1)) >= 0) {
- dihedral_type[m][num_dihedral[m]] = itype;
- dihedral_atom1[m][num_dihedral[m]] = atom1;
- dihedral_atom2[m][num_dihedral[m]] = atom2;
- dihedral_atom3[m][num_dihedral[m]] = atom3;
- dihedral_atom4[m][num_dihedral[m]] = atom4;
- num_dihedral[m]++;
+ dihedral_type[m][num_dihedral[m]] = itype;
+ dihedral_atom1[m][num_dihedral[m]] = atom1;
+ dihedral_atom2[m][num_dihedral[m]] = atom2;
+ dihedral_atom3[m][num_dihedral[m]] = atom3;
+ dihedral_atom4[m][num_dihedral[m]] = atom4;
+ num_dihedral[m]++;
}
if ((m = map(atom3)) >= 0) {
- dihedral_type[m][num_dihedral[m]] = itype;
- dihedral_atom1[m][num_dihedral[m]] = atom1;
- dihedral_atom2[m][num_dihedral[m]] = atom2;
- dihedral_atom3[m][num_dihedral[m]] = atom3;
- dihedral_atom4[m][num_dihedral[m]] = atom4;
- num_dihedral[m]++;
+ dihedral_type[m][num_dihedral[m]] = itype;
+ dihedral_atom1[m][num_dihedral[m]] = atom1;
+ dihedral_atom2[m][num_dihedral[m]] = atom2;
+ dihedral_atom3[m][num_dihedral[m]] = atom3;
+ dihedral_atom4[m][num_dihedral[m]] = atom4;
+ num_dihedral[m]++;
}
if ((m = map(atom4)) >= 0) {
- dihedral_type[m][num_dihedral[m]] = itype;
- dihedral_atom1[m][num_dihedral[m]] = atom1;
- dihedral_atom2[m][num_dihedral[m]] = atom2;
- dihedral_atom3[m][num_dihedral[m]] = atom3;
- dihedral_atom4[m][num_dihedral[m]] = atom4;
- num_dihedral[m]++;
+ dihedral_type[m][num_dihedral[m]] = itype;
+ dihedral_atom1[m][num_dihedral[m]] = atom1;
+ dihedral_atom2[m][num_dihedral[m]] = atom2;
+ dihedral_atom3[m][num_dihedral[m]] = atom3;
+ dihedral_atom4[m][num_dihedral[m]] = atom4;
+ num_dihedral[m]++;
}
}
buf = next + 1;
@@ -1106,14 +1106,14 @@ void Atom::data_impropers(int n, char *buf)
next = strchr(buf,'\n');
*next = '\0';
sscanf(buf,"%d %d %d %d %d %d",&tmp,&itype,&atom1,&atom2,&atom3,&atom4);
- if (atom1 <= 0 || atom1 > map_tag_max ||
- atom2 <= 0 || atom2 > map_tag_max ||
- atom3 <= 0 || atom3 > map_tag_max ||
- atom4 <= 0 || atom4 > map_tag_max)
+ if (atom1 <= 0 || atom1 > map_tag_max ||
+ atom2 <= 0 || atom2 > map_tag_max ||
+ atom3 <= 0 || atom3 > map_tag_max ||
+ atom4 <= 0 || atom4 > map_tag_max)
error->one(FLERR,"Invalid atom ID in Impropers section of data file");
if (itype <= 0 || itype > nimpropertypes)
error->one(FLERR,
- "Invalid improper type in Impropers section of data file");
+ "Invalid improper type in Impropers section of data file");
if ((m = map(atom2)) >= 0) {
improper_type[m][num_improper[m]] = itype;
improper_atom1[m][num_improper[m]] = atom1;
@@ -1124,28 +1124,28 @@ void Atom::data_impropers(int n, char *buf)
}
if (newton_bond == 0) {
if ((m = map(atom1)) >= 0) {
- improper_type[m][num_improper[m]] = itype;
- improper_atom1[m][num_improper[m]] = atom1;
- improper_atom2[m][num_improper[m]] = atom2;
- improper_atom3[m][num_improper[m]] = atom3;
- improper_atom4[m][num_improper[m]] = atom4;
- num_improper[m]++;
+ improper_type[m][num_improper[m]] = itype;
+ improper_atom1[m][num_improper[m]] = atom1;
+ improper_atom2[m][num_improper[m]] = atom2;
+ improper_atom3[m][num_improper[m]] = atom3;
+ improper_atom4[m][num_improper[m]] = atom4;
+ num_improper[m]++;
}
if ((m = map(atom3)) >= 0) {
- improper_type[m][num_improper[m]] = itype;
- improper_atom1[m][num_improper[m]] = atom1;
- improper_atom2[m][num_improper[m]] = atom2;
- improper_atom3[m][num_improper[m]] = atom3;
- improper_atom4[m][num_improper[m]] = atom4;
- num_improper[m]++;
+ improper_type[m][num_improper[m]] = itype;
+ improper_atom1[m][num_improper[m]] = atom1;
+ improper_atom2[m][num_improper[m]] = atom2;
+ improper_atom3[m][num_improper[m]] = atom3;
+ improper_atom4[m][num_improper[m]] = atom4;
+ num_improper[m]++;
}
if ((m = map(atom4)) >= 0) {
- improper_type[m][num_improper[m]] = itype;
- improper_atom1[m][num_improper[m]] = atom1;
- improper_atom2[m][num_improper[m]] = atom2;
- improper_atom3[m][num_improper[m]] = atom3;
- improper_atom4[m][num_improper[m]] = atom4;
- num_improper[m]++;
+ improper_type[m][num_improper[m]] = itype;
+ improper_atom1[m][num_improper[m]] = atom1;
+ improper_atom2[m][num_improper[m]] = atom2;
+ improper_atom3[m][num_improper[m]] = atom3;
+ improper_atom4[m][num_improper[m]] = atom4;
+ num_improper[m]++;
}
}
buf = next + 1;
@@ -1180,7 +1180,7 @@ void Atom::set_mass(const char *str)
int n = sscanf(str,"%d %lg",&itype,&mass_one);
if (n != 2) error->all(FLERR,"Invalid mass line in data file");
- if (itype < 1 || itype > ntypes)
+ if (itype < 1 || itype > ntypes)
error->all(FLERR,"Invalid type for mass set");
mass[itype] = mass_one;
@@ -1197,7 +1197,7 @@ void Atom::set_mass(const char *str)
void Atom::set_mass(int itype, double value)
{
if (mass == NULL) error->all(FLERR,"Cannot set mass for this atom style");
- if (itype < 1 || itype > ntypes)
+ if (itype < 1 || itype > ntypes)
error->all(FLERR,"Invalid type for mass set");
mass[itype] = value;
@@ -1281,7 +1281,7 @@ int Atom::radius_consistency(int itype, double &rad)
------------------------------------------------------------------------- */
int Atom::shape_consistency(int itype,
- double &shapex, double &shapey, double &shapez)
+ double &shapex, double &shapey, double &shapez)
{
double zero[3] = {0.0, 0.0, 0.0};
double one[3] = {-1.0, -1.0, -1.0};
@@ -1435,7 +1435,7 @@ void Atom::sort()
while (permute[empty] != i) {
avec->copy(permute[empty],empty,0);
empty = current[empty] = permute[empty];
- }
+ }
avec->copy(nlocal,empty,0);
current[empty] = permute[empty];
}
@@ -1471,13 +1471,13 @@ void Atom::setup_sort_bins()
else if (!lmp->cuda) binsize = 0.5 * neighbor->cutneighmax;
else {
if (domain->dimension == 3) {
- double vol = (domain->boxhi[0]-domain->boxlo[0]) *
- (domain->boxhi[1]-domain->boxlo[1]) *
- (domain->boxhi[2]-domain->boxlo[2]);
+ double vol = (domain->boxhi[0]-domain->boxlo[0]) *
+ (domain->boxhi[1]-domain->boxlo[1]) *
+ (domain->boxhi[2]-domain->boxlo[2]);
binsize = pow(1.0*CUDA_CHUNK/natoms*vol,1.0/3.0);
} else {
- double area = (domain->boxhi[0]-domain->boxlo[0]) *
- (domain->boxhi[1]-domain->boxlo[1]);
+ double area = (domain->boxhi[0]-domain->boxlo[0]) *
+ (domain->boxhi[1]-domain->boxlo[1]);
binsize = pow(1.0*CUDA_CHUNK/natoms*area,1.0/2.0);
}
}
@@ -1487,7 +1487,7 @@ void Atom::setup_sort_bins()
// nbin xyz = local bins
// bbox lo/hi = bounding box of my sub-domain
-
+
if (domain->triclinic)
domain->bbox(domain->sublo_lamda,domain->subhi_lamda,bboxlo,bboxhi);
else {
@@ -1498,12 +1498,12 @@ void Atom::setup_sort_bins()
bboxhi[1] = domain->subhi[1];
bboxhi[2] = domain->subhi[2];
}
-
+
nbinx = static_cast<int> ((bboxhi[0]-bboxlo[0]) * bininv);
nbiny = static_cast<int> ((bboxhi[1]-bboxlo[1]) * bininv);
nbinz = static_cast<int> ((bboxhi[2]-bboxlo[2]) * bininv);
if (domain->dimension == 2) nbinz = 1;
-
+
if (nbinx == 0) nbinx = 1;
if (nbiny == 0) nbiny = 1;
if (nbinz == 0) nbinz = 1;
@@ -1512,7 +1512,7 @@ void Atom::setup_sort_bins()
bininvy = nbiny / (bboxhi[1]-bboxlo[1]);
bininvz = nbinz / (bboxhi[2]-bboxlo[2]);
- if (1.0*nbinx*nbiny*nbinz > INT_MAX)
+ if (1.0*nbinx*nbiny*nbinz > INT_MAX)
error->one(FLERR,"Too many atom sorting bins");
nbins = nbinx*nbiny*nbinz;
@@ -1670,7 +1670,7 @@ int Atom::memcheck(const char *str)
strcpy(padded," ");
strcat(padded,str);
strcat(padded," ");
-
+
if (strstr(memstr,padded)) {
delete [] padded;
return 0;
diff --git a/src/atom.h b/src/atom.h
index 111761884b0cfb14fc8327e64c62cb77131c4213..9a93e620d1fa84efc68c332df962a0c1565a4cc4 100644
--- a/src/atom.h
+++ b/src/atom.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -94,7 +94,7 @@ class Atom : protected Pointers {
int cs_flag,csforce_flag,vforce_flag,ervelforce_flag,etag_flag;
int rho_flag,e_flag,cv_flag,vest_flag;
- // extra peratom info in restart file destined for fix & diag
+ // extra peratom info in restart file destined for fix & diag
double **extra;
@@ -173,7 +173,7 @@ class Atom : protected Pointers {
// functions for global to local ID mapping
// map lookup function inlined for efficiency
-
+
inline int map(int global) {
if (map_style == 1) return map_array[global];
else return map_find_hash(global);
diff --git a/src/atom_vec.cpp b/src/atom_vec.cpp
index 0d415692ec88568e1f50a99aab7a5f592f85fd94..e33fb007bc43917751aa4f59651b821acaf22afb 100644
--- a/src/atom_vec.cpp
+++ b/src/atom_vec.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/atom_vec.h b/src/atom_vec.h
index b0d9d85451026068ac2c0c3d8899cedd6cff9aab..b05d4bf4ca11ccdc0bea9cc70c1cc4f6f1174528 100644
--- a/src/atom_vec.h
+++ b/src/atom_vec.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -29,7 +29,7 @@ class AtomVec : protected Pointers {
int comm_x_only; // 1 if only exchange x in forward comm
int comm_f_only; // 1 if only exchange f in reverse comm
- int size_forward; // # of values per atom in comm
+ int size_forward; // # of values per atom in comm
int size_reverse; // # in reverse comm
int size_border; // # in border comm
int size_velocity; // # of velocity based quantities
diff --git a/src/atom_vec_atomic.cpp b/src/atom_vec_atomic.cpp
index 61f8681dde6ab8408f8476cee6e8c7dbd3819c34..080a32c23eba9e2221dda9d920b795a665f80d2e 100644
--- a/src/atom_vec_atomic.cpp
+++ b/src/atom_vec_atomic.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -46,7 +46,7 @@ AtomVecAtomic::AtomVecAtomic(LAMMPS *lmp, int narg, char **arg) :
/* ----------------------------------------------------------------------
grow atom arrays
n = 0 grows arrays by DELTA
- n > 0 allocates arrays to size n
+ n > 0 allocates arrays to size n
------------------------------------------------------------------------- */
void AtomVecAtomic::grow(int n)
@@ -66,7 +66,7 @@ void AtomVecAtomic::grow(int n)
f = memory->grow(atom->f,nmax*comm->nthreads,3,"atom:f");
if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
}
@@ -99,14 +99,14 @@ void AtomVecAtomic::copy(int i, int j, int delflag)
v[j][2] = v[i][2];
if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j);
}
/* ---------------------------------------------------------------------- */
int AtomVecAtomic::pack_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
@@ -142,7 +142,7 @@ int AtomVecAtomic::pack_comm(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
int AtomVecAtomic::pack_comm_vel(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz,dvx,dvy,dvz;
@@ -170,32 +170,32 @@ int AtomVecAtomic::pack_comm_vel(int n, int *list, double *buf,
}
if (!deform_vremap) {
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
}
} else {
dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
dvz = pbc[2]*h_rate[2];
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- if (mask[i] & deform_groupbit) {
- buf[m++] = v[j][0] + dvx;
- buf[m++] = v[j][1] + dvy;
- buf[m++] = v[j][2] + dvz;
- } else {
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
- }
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ if (mask[i] & deform_groupbit) {
+ buf[m++] = v[j][0] + dvx;
+ buf[m++] = v[j][1] + dvy;
+ buf[m++] = v[j][2] + dvz;
+ } else {
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
+ }
}
}
}
@@ -269,7 +269,7 @@ void AtomVecAtomic::unpack_reverse(int n, int *list, double *buf)
/* ---------------------------------------------------------------------- */
int AtomVecAtomic::pack_border(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
@@ -311,7 +311,7 @@ int AtomVecAtomic::pack_border(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
int AtomVecAtomic::pack_border_vel(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz,dvx,dvy,dvz;
@@ -342,38 +342,38 @@ int AtomVecAtomic::pack_border_vel(int n, int *list, double *buf,
}
if (!deform_vremap) {
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = tag[j];
- buf[m++] = type[j];
- buf[m++] = mask[j];
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = tag[j];
+ buf[m++] = type[j];
+ buf[m++] = mask[j];
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
}
} else {
dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
dvz = pbc[2]*h_rate[2];
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = tag[j];
- buf[m++] = type[j];
- buf[m++] = mask[j];
- if (mask[i] & deform_groupbit) {
- buf[m++] = v[j][0] + dvx;
- buf[m++] = v[j][1] + dvy;
- buf[m++] = v[j][2] + dvz;
- } else {
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
- }
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = tag[j];
+ buf[m++] = type[j];
+ buf[m++] = mask[j];
+ if (mask[i] & deform_groupbit) {
+ buf[m++] = v[j][0] + dvx;
+ buf[m++] = v[j][1] + dvy;
+ buf[m++] = v[j][2] + dvz;
+ } else {
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
+ }
}
}
}
@@ -423,7 +423,7 @@ void AtomVecAtomic::unpack_border_vel(int n, int first, double *buf)
/* ----------------------------------------------------------------------
pack data for atom I for sending to another proc
- xyz must be 1st 3 values, so comm::exchange() can test on them
+ xyz must be 1st 3 values, so comm::exchange() can test on them
------------------------------------------------------------------------- */
int AtomVecAtomic::pack_exchange(int i, double *buf)
@@ -441,7 +441,7 @@ int AtomVecAtomic::pack_exchange(int i, double *buf)
buf[m++] = image[i];
if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]);
buf[0] = m;
@@ -468,9 +468,9 @@ int AtomVecAtomic::unpack_exchange(double *buf)
image[nlocal] = static_cast<int> (buf[m++]);
if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->
- unpack_exchange(nlocal,&buf[m]);
+ unpack_exchange(nlocal,&buf[m]);
atom->nlocal++;
return m;
@@ -489,9 +489,9 @@ int AtomVecAtomic::size_restart()
int n = 11 * nlocal;
if (atom->nextra_restart)
- for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
for (i = 0; i < nlocal; i++)
- n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
+ n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
return n;
}
@@ -499,7 +499,7 @@ int AtomVecAtomic::size_restart()
/* ----------------------------------------------------------------------
pack atom I's data for restart file including extra quantities
xyz must be 1st 3 values, so that read_restart can test on them
- molecular types may be negative, but write as positive
+ molecular types may be negative, but write as positive
------------------------------------------------------------------------- */
int AtomVecAtomic::pack_restart(int i, double *buf)
@@ -517,7 +517,7 @@ int AtomVecAtomic::pack_restart(int i, double *buf)
buf[m++] = v[i][2];
if (atom->nextra_restart)
- for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]);
buf[0] = m;
@@ -616,7 +616,7 @@ void AtomVecAtomic::data_atom(double *coord, int imagetmp, char **values)
}
/* ----------------------------------------------------------------------
- return # of bytes of allocated memory
+ return # of bytes of allocated memory
------------------------------------------------------------------------- */
bigint AtomVecAtomic::memory_usage()
diff --git a/src/atom_vec_atomic.h b/src/atom_vec_atomic.h
index 4503b50a74c3f345147200722ee38bfca3c2786d..d7aa50c214fc9ed15be0273d1671ef1785e93da3 100644
--- a/src/atom_vec_atomic.h
+++ b/src/atom_vec_atomic.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/atom_vec_charge.cpp b/src/atom_vec_charge.cpp
index 41a8f122822aaac8a5d7886611d6e060fadf8ed2..b9ec7a185111120eaca4e08af8f49fb4be39ed39 100644
--- a/src/atom_vec_charge.cpp
+++ b/src/atom_vec_charge.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -27,7 +27,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-AtomVecCharge::AtomVecCharge(LAMMPS *lmp, int narg, char **arg) :
+AtomVecCharge::AtomVecCharge(LAMMPS *lmp, int narg, char **arg) :
AtomVec(lmp, narg, arg)
{
molecular = 0;
@@ -48,7 +48,7 @@ AtomVecCharge::AtomVecCharge(LAMMPS *lmp, int narg, char **arg) :
/* ----------------------------------------------------------------------
grow atom arrays
n = 0 grows arrays by DELTA
- n > 0 allocates arrays to size n
+ n > 0 allocates arrays to size n
------------------------------------------------------------------------- */
void AtomVecCharge::grow(int n)
@@ -70,7 +70,7 @@ void AtomVecCharge::grow(int n)
q = memory->grow(atom->q,nmax,"atom:q");
if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
}
@@ -106,14 +106,14 @@ void AtomVecCharge::copy(int i, int j, int delflag)
q[j] = q[i];
if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j);
}
/* ---------------------------------------------------------------------- */
int AtomVecCharge::pack_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
@@ -149,7 +149,7 @@ int AtomVecCharge::pack_comm(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
int AtomVecCharge::pack_comm_vel(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz,dvx,dvy,dvz;
@@ -177,32 +177,32 @@ int AtomVecCharge::pack_comm_vel(int n, int *list, double *buf,
}
if (!deform_vremap) {
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
}
} else {
dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
dvz = pbc[2]*h_rate[2];
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- if (mask[i] & deform_groupbit) {
- buf[m++] = v[j][0] + dvx;
- buf[m++] = v[j][1] + dvy;
- buf[m++] = v[j][2] + dvz;
- } else {
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
- }
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ if (mask[i] & deform_groupbit) {
+ buf[m++] = v[j][0] + dvx;
+ buf[m++] = v[j][1] + dvy;
+ buf[m++] = v[j][2] + dvz;
+ } else {
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
+ }
}
}
}
@@ -276,7 +276,7 @@ void AtomVecCharge::unpack_reverse(int n, int *list, double *buf)
/* ---------------------------------------------------------------------- */
int AtomVecCharge::pack_border(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
@@ -320,7 +320,7 @@ int AtomVecCharge::pack_border(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
int AtomVecCharge::pack_border_vel(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz,dvx,dvy,dvz;
@@ -352,40 +352,40 @@ int AtomVecCharge::pack_border_vel(int n, int *list, double *buf,
}
if (!deform_vremap) {
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = tag[j];
- buf[m++] = type[j];
- buf[m++] = mask[j];
- buf[m++] = q[j];
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = tag[j];
+ buf[m++] = type[j];
+ buf[m++] = mask[j];
+ buf[m++] = q[j];
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
}
} else {
dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
dvz = pbc[2]*h_rate[2];
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = tag[j];
- buf[m++] = type[j];
- buf[m++] = mask[j];
- buf[m++] = q[j];
- if (mask[i] & deform_groupbit) {
- buf[m++] = v[j][0] + dvx;
- buf[m++] = v[j][1] + dvy;
- buf[m++] = v[j][2] + dvz;
- } else {
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
- }
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = tag[j];
+ buf[m++] = type[j];
+ buf[m++] = mask[j];
+ buf[m++] = q[j];
+ if (mask[i] & deform_groupbit) {
+ buf[m++] = v[j][0] + dvx;
+ buf[m++] = v[j][1] + dvy;
+ buf[m++] = v[j][2] + dvz;
+ } else {
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
+ }
}
}
}
@@ -464,7 +464,7 @@ int AtomVecCharge::unpack_border_hybrid(int n, int first, double *buf)
/* ----------------------------------------------------------------------
pack data for atom I for sending to another proc
- xyz must be 1st 3 values, so comm::exchange() can test on them
+ xyz must be 1st 3 values, so comm::exchange() can test on them
------------------------------------------------------------------------- */
int AtomVecCharge::pack_exchange(int i, double *buf)
@@ -484,7 +484,7 @@ int AtomVecCharge::pack_exchange(int i, double *buf)
buf[m++] = q[i];
if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]);
buf[0] = m;
@@ -513,9 +513,9 @@ int AtomVecCharge::unpack_exchange(double *buf)
q[nlocal] = buf[m++];
if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->
- unpack_exchange(nlocal,&buf[m]);
+ unpack_exchange(nlocal,&buf[m]);
atom->nlocal++;
return m;
@@ -534,9 +534,9 @@ int AtomVecCharge::size_restart()
int n = 12 * nlocal;
if (atom->nextra_restart)
- for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
for (i = 0; i < nlocal; i++)
- n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
+ n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
return n;
}
@@ -544,7 +544,7 @@ int AtomVecCharge::size_restart()
/* ----------------------------------------------------------------------
pack atom I's data for restart file including extra quantities
xyz must be 1st 3 values, so that read_restart can test on them
- molecular types may be negative, but write as positive
+ molecular types may be negative, but write as positive
------------------------------------------------------------------------- */
int AtomVecCharge::pack_restart(int i, double *buf)
@@ -564,7 +564,7 @@ int AtomVecCharge::pack_restart(int i, double *buf)
buf[m++] = q[i];
if (atom->nextra_restart)
- for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]);
buf[0] = m;
@@ -681,7 +681,7 @@ int AtomVecCharge::data_atom_hybrid(int nlocal, char **values)
}
/* ----------------------------------------------------------------------
- return # of bytes of allocated memory
+ return # of bytes of allocated memory
------------------------------------------------------------------------- */
bigint AtomVecCharge::memory_usage()
diff --git a/src/atom_vec_charge.h b/src/atom_vec_charge.h
index d2b6b75189befb3a7f7b5c9043af2e6666d96cc8..bc658a2073b4f7b81cb4141d3ba95ec9e6e3219c 100644
--- a/src/atom_vec_charge.h
+++ b/src/atom_vec_charge.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/atom_vec_ellipsoid.cpp b/src/atom_vec_ellipsoid.cpp
index ceaab905d7b897ef997c8c015261179532a6a92f..fc0396ec60bd5776bf97aa278310202b25d16c2b 100755
--- a/src/atom_vec_ellipsoid.cpp
+++ b/src/atom_vec_ellipsoid.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -120,7 +120,7 @@ void AtomVecEllipsoid::grow_bonus()
error->one(FLERR,"Per-processor system is too big");
bonus = (Bonus *) memory->srealloc(bonus,nmax_bonus*sizeof(Bonus),
- "atom:bonus");
+ "atom:bonus");
}
/* ----------------------------------------------------------------------
@@ -189,8 +189,8 @@ void AtomVecEllipsoid::clear_bonus()
this may create or delete entry in bonus data
------------------------------------------------------------------------- */
-void AtomVecEllipsoid::set_shape(int i,
- double shapex, double shapey, double shapez)
+void AtomVecEllipsoid::set_shape(int i,
+ double shapex, double shapey, double shapez)
{
if (ellipsoid[i] < 0) {
if (shapex == 0.0 && shapey == 0.0 && shapez == 0.0) return;
@@ -221,7 +221,7 @@ void AtomVecEllipsoid::set_shape(int i,
/* ---------------------------------------------------------------------- */
int AtomVecEllipsoid::pack_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
@@ -235,11 +235,11 @@ int AtomVecEllipsoid::pack_comm(int n, int *list, double *buf,
buf[m++] = x[j][1];
buf[m++] = x[j][2];
if (ellipsoid[j] >= 0) {
- quat = bonus[ellipsoid[j]].quat;
- buf[m++] = quat[0];
- buf[m++] = quat[1];
- buf[m++] = quat[2];
- buf[m++] = quat[3];
+ quat = bonus[ellipsoid[j]].quat;
+ buf[m++] = quat[0];
+ buf[m++] = quat[1];
+ buf[m++] = quat[2];
+ buf[m++] = quat[3];
}
}
} else {
@@ -258,11 +258,11 @@ int AtomVecEllipsoid::pack_comm(int n, int *list, double *buf,
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
if (ellipsoid[j] >= 0) {
- quat = bonus[ellipsoid[j]].quat;
- buf[m++] = quat[0];
- buf[m++] = quat[1];
- buf[m++] = quat[2];
- buf[m++] = quat[3];
+ quat = bonus[ellipsoid[j]].quat;
+ buf[m++] = quat[0];
+ buf[m++] = quat[1];
+ buf[m++] = quat[2];
+ buf[m++] = quat[3];
}
}
}
@@ -272,7 +272,7 @@ int AtomVecEllipsoid::pack_comm(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
int AtomVecEllipsoid::pack_comm_vel(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz,dvx,dvy,dvz;
@@ -286,11 +286,11 @@ int AtomVecEllipsoid::pack_comm_vel(int n, int *list, double *buf,
buf[m++] = x[j][1];
buf[m++] = x[j][2];
if (ellipsoid[j] >= 0) {
- quat = bonus[ellipsoid[j]].quat;
- buf[m++] = quat[0];
- buf[m++] = quat[1];
- buf[m++] = quat[2];
- buf[m++] = quat[3];
+ quat = bonus[ellipsoid[j]].quat;
+ buf[m++] = quat[0];
+ buf[m++] = quat[1];
+ buf[m++] = quat[2];
+ buf[m++] = quat[3];
}
buf[m++] = v[j][0];
buf[m++] = v[j][1];
@@ -311,52 +311,52 @@ int AtomVecEllipsoid::pack_comm_vel(int n, int *list, double *buf,
}
if (!deform_vremap) {
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- if (ellipsoid[j] >= 0) {
- quat = bonus[ellipsoid[j]].quat;
- buf[m++] = quat[0];
- buf[m++] = quat[1];
- buf[m++] = quat[2];
- buf[m++] = quat[3];
- }
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
- buf[m++] = angmom[j][0];
- buf[m++] = angmom[j][1];
- buf[m++] = angmom[j][2];
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ if (ellipsoid[j] >= 0) {
+ quat = bonus[ellipsoid[j]].quat;
+ buf[m++] = quat[0];
+ buf[m++] = quat[1];
+ buf[m++] = quat[2];
+ buf[m++] = quat[3];
+ }
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
+ buf[m++] = angmom[j][0];
+ buf[m++] = angmom[j][1];
+ buf[m++] = angmom[j][2];
}
} else {
dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
dvz = pbc[2]*h_rate[2];
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- if (ellipsoid[j] >= 0) {
- quat = bonus[ellipsoid[j]].quat;
- buf[m++] = quat[0];
- buf[m++] = quat[1];
- buf[m++] = quat[2];
- buf[m++] = quat[3];
- }
- if (mask[i] & deform_groupbit) {
- buf[m++] = v[j][0] + dvx;
- buf[m++] = v[j][1] + dvy;
- buf[m++] = v[j][2] + dvz;
- } else {
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
- }
- buf[m++] = angmom[j][0];
- buf[m++] = angmom[j][1];
- buf[m++] = angmom[j][2];
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ if (ellipsoid[j] >= 0) {
+ quat = bonus[ellipsoid[j]].quat;
+ buf[m++] = quat[0];
+ buf[m++] = quat[1];
+ buf[m++] = quat[2];
+ buf[m++] = quat[3];
+ }
+ if (mask[i] & deform_groupbit) {
+ buf[m++] = v[j][0] + dvx;
+ buf[m++] = v[j][1] + dvy;
+ buf[m++] = v[j][2] + dvz;
+ } else {
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
+ }
+ buf[m++] = angmom[j][0];
+ buf[m++] = angmom[j][1];
+ buf[m++] = angmom[j][2];
}
}
}
@@ -529,7 +529,7 @@ int AtomVecEllipsoid::unpack_reverse_hybrid(int n, int *list, double *buf)
/* ---------------------------------------------------------------------- */
int AtomVecEllipsoid::pack_border(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
@@ -547,16 +547,16 @@ int AtomVecEllipsoid::pack_border(int n, int *list, double *buf,
buf[m++] = mask[j];
if (ellipsoid[j] < 0) buf[m++] = 0;
else {
- buf[m++] = 1;
- shape = bonus[ellipsoid[j]].shape;
- quat = bonus[ellipsoid[j]].quat;
- buf[m++] = shape[0];
- buf[m++] = shape[1];
- buf[m++] = shape[2];
- buf[m++] = quat[0];
- buf[m++] = quat[1];
- buf[m++] = quat[2];
- buf[m++] = quat[3];
+ buf[m++] = 1;
+ shape = bonus[ellipsoid[j]].shape;
+ quat = bonus[ellipsoid[j]].quat;
+ buf[m++] = shape[0];
+ buf[m++] = shape[1];
+ buf[m++] = shape[2];
+ buf[m++] = quat[0];
+ buf[m++] = quat[1];
+ buf[m++] = quat[2];
+ buf[m++] = quat[3];
}
}
} else {
@@ -579,16 +579,16 @@ int AtomVecEllipsoid::pack_border(int n, int *list, double *buf,
buf[m++] = mask[j];
if (ellipsoid[j] < 0) buf[m++] = 0;
else {
- buf[m++] = 1;
- shape = bonus[ellipsoid[j]].shape;
- quat = bonus[ellipsoid[j]].quat;
- buf[m++] = shape[0];
- buf[m++] = shape[1];
- buf[m++] = shape[2];
- buf[m++] = quat[0];
- buf[m++] = quat[1];
- buf[m++] = quat[2];
- buf[m++] = quat[3];
+ buf[m++] = 1;
+ shape = bonus[ellipsoid[j]].shape;
+ quat = bonus[ellipsoid[j]].quat;
+ buf[m++] = shape[0];
+ buf[m++] = shape[1];
+ buf[m++] = shape[2];
+ buf[m++] = quat[0];
+ buf[m++] = quat[1];
+ buf[m++] = quat[2];
+ buf[m++] = quat[3];
}
}
}
@@ -598,7 +598,7 @@ int AtomVecEllipsoid::pack_border(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
int AtomVecEllipsoid::pack_border_vel(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz,dvx,dvy,dvz;
@@ -616,16 +616,16 @@ int AtomVecEllipsoid::pack_border_vel(int n, int *list, double *buf,
buf[m++] = mask[j];
if (ellipsoid[j] < 0) buf[m++] = 0;
else {
- buf[m++] = 1;
- shape = bonus[ellipsoid[j]].shape;
- quat = bonus[ellipsoid[j]].quat;
- buf[m++] = shape[0];
- buf[m++] = shape[1];
- buf[m++] = shape[2];
- buf[m++] = quat[0];
- buf[m++] = quat[1];
- buf[m++] = quat[2];
- buf[m++] = quat[3];
+ buf[m++] = 1;
+ shape = bonus[ellipsoid[j]].shape;
+ quat = bonus[ellipsoid[j]].quat;
+ buf[m++] = shape[0];
+ buf[m++] = shape[1];
+ buf[m++] = shape[2];
+ buf[m++] = quat[0];
+ buf[m++] = quat[1];
+ buf[m++] = quat[2];
+ buf[m++] = quat[3];
}
buf[m++] = v[j][0];
buf[m++] = v[j][1];
@@ -646,69 +646,69 @@ int AtomVecEllipsoid::pack_border_vel(int n, int *list, double *buf,
}
if (!deform_vremap) {
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = tag[j];
- buf[m++] = type[j];
- buf[m++] = mask[j];
- if (ellipsoid[j] < 0) buf[m++] = 0;
- else {
- buf[m++] = 1;
- quat = bonus[ellipsoid[j]].quat;
- buf[m++] = shape[0];
- buf[m++] = shape[1];
- buf[m++] = shape[2];
- buf[m++] = quat[0];
- buf[m++] = quat[1];
- buf[m++] = quat[2];
- buf[m++] = quat[3];
- }
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
- buf[m++] = angmom[j][0];
- buf[m++] = angmom[j][1];
- buf[m++] = angmom[j][2];
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = tag[j];
+ buf[m++] = type[j];
+ buf[m++] = mask[j];
+ if (ellipsoid[j] < 0) buf[m++] = 0;
+ else {
+ buf[m++] = 1;
+ quat = bonus[ellipsoid[j]].quat;
+ buf[m++] = shape[0];
+ buf[m++] = shape[1];
+ buf[m++] = shape[2];
+ buf[m++] = quat[0];
+ buf[m++] = quat[1];
+ buf[m++] = quat[2];
+ buf[m++] = quat[3];
+ }
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
+ buf[m++] = angmom[j][0];
+ buf[m++] = angmom[j][1];
+ buf[m++] = angmom[j][2];
}
} else {
dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
dvz = pbc[2]*h_rate[2];
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = tag[j];
- buf[m++] = type[j];
- buf[m++] = mask[j];
- if (ellipsoid[j] < 0) buf[m++] = 0;
- else {
- buf[m++] = 1;
- shape = bonus[ellipsoid[j]].shape;
- quat = bonus[ellipsoid[j]].quat;
- buf[m++] = shape[0];
- buf[m++] = shape[1];
- buf[m++] = shape[2];
- buf[m++] = quat[0];
- buf[m++] = quat[1];
- buf[m++] = quat[2];
- buf[m++] = quat[3];
- }
- if (mask[i] & deform_groupbit) {
- buf[m++] = v[j][0] + dvx;
- buf[m++] = v[j][1] + dvy;
- buf[m++] = v[j][2] + dvz;
- } else {
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
- }
- buf[m++] = angmom[j][0];
- buf[m++] = angmom[j][1];
- buf[m++] = angmom[j][2];
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = tag[j];
+ buf[m++] = type[j];
+ buf[m++] = mask[j];
+ if (ellipsoid[j] < 0) buf[m++] = 0;
+ else {
+ buf[m++] = 1;
+ shape = bonus[ellipsoid[j]].shape;
+ quat = bonus[ellipsoid[j]].quat;
+ buf[m++] = shape[0];
+ buf[m++] = shape[1];
+ buf[m++] = shape[2];
+ buf[m++] = quat[0];
+ buf[m++] = quat[1];
+ buf[m++] = quat[2];
+ buf[m++] = quat[3];
+ }
+ if (mask[i] & deform_groupbit) {
+ buf[m++] = v[j][0] + dvx;
+ buf[m++] = v[j][1] + dvy;
+ buf[m++] = v[j][2] + dvz;
+ } else {
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
+ }
+ buf[m++] = angmom[j][0];
+ buf[m++] = angmom[j][1];
+ buf[m++] = angmom[j][2];
}
}
}
@@ -893,7 +893,7 @@ int AtomVecEllipsoid::pack_exchange(int i, double *buf)
buf[m++] = quat[2];
buf[m++] = quat[3];
}
-
+
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]);
@@ -946,7 +946,7 @@ int AtomVecEllipsoid::unpack_exchange(double *buf)
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->
- unpack_exchange(nlocal,&buf[m]);
+ unpack_exchange(nlocal,&buf[m]);
atom->nlocal++;
return m;
@@ -970,7 +970,7 @@ int AtomVecEllipsoid::size_restart()
if (atom->nextra_restart)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
for (i = 0; i < nlocal; i++)
- n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
+ n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
return n;
}
@@ -1030,7 +1030,7 @@ int AtomVecEllipsoid::unpack_restart(double *buf)
int nlocal = atom->nlocal;
if (nlocal == nmax) {
grow(0);
- if (atom->nextra_store)
+ if (atom->nextra_store)
memory->grow(atom->extra,nmax,atom->nextra_store,"atom:extra");
}
@@ -1067,7 +1067,7 @@ int AtomVecEllipsoid::unpack_restart(double *buf)
bonus[nlocal_bonus].ilocal = nlocal;
ellipsoid[nlocal] = nlocal_bonus++;
}
-
+
double **extra = atom->extra;
if (atom->nextra_store) {
int size = static_cast<int> (buf[0]) - m;
@@ -1098,7 +1098,7 @@ void AtomVecEllipsoid::create_atom(int itype, double *coord)
v[nlocal][0] = 0.0;
v[nlocal][1] = 0.0;
v[nlocal][2] = 0.0;
-
+
rmass[nlocal] = 1.0;
angmom[nlocal][0] = 0.0;
angmom[nlocal][1] = 0.0;
@@ -1232,7 +1232,7 @@ int AtomVecEllipsoid::data_vel_hybrid(int m, char **values)
}
/* ----------------------------------------------------------------------
- return # of bytes of allocated memory
+ return # of bytes of allocated memory
------------------------------------------------------------------------- */
bigint AtomVecEllipsoid::memory_usage()
@@ -1251,7 +1251,7 @@ bigint AtomVecEllipsoid::memory_usage()
if (atom->memcheck("angmom")) bytes += memory->usage(angmom,nmax,3);
if (atom->memcheck("torque")) bytes += memory->usage(torque,nmax*comm->nthreads,3);
if (atom->memcheck("ellipsoid")) bytes += memory->usage(ellipsoid,nmax);
-
+
bytes += nmax_bonus*sizeof(Bonus);
return bytes;
diff --git a/src/atom_vec_ellipsoid.h b/src/atom_vec_ellipsoid.h
index 2e2e13fbbbbbc90184b05f2fac730f94867c5c75..65966819d6c8452d182e868fec1855a5e57e3d0e 100755
--- a/src/atom_vec_ellipsoid.h
+++ b/src/atom_vec_ellipsoid.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/atom_vec_hybrid.cpp b/src/atom_vec_hybrid.cpp
index 2f0f51699dcd29a2029f647c3eb1f2d23a94dc41..fc93450c86ebc112622ae7a0231caf515f792789 100644
--- a/src/atom_vec_hybrid.cpp
+++ b/src/atom_vec_hybrid.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -42,9 +42,9 @@ AtomVecHybrid::AtomVecHybrid(LAMMPS *lmp, int narg, char **arg) :
for (i = 0; i < narg; i++) {
for (k = 0; k < i; k++)
- if (strcmp(arg[i],keywords[k]) == 0)
- error->all(FLERR,"Atom style hybrid cannot use same atom style twice");
- if (strcmp(arg[i],"hybrid") == 0)
+ if (strcmp(arg[i],keywords[k]) == 0)
+ error->all(FLERR,"Atom style hybrid cannot use same atom style twice");
+ if (strcmp(arg[i],"hybrid") == 0)
error->all(FLERR,"Atom style hybrid cannot have hybrid as an argument");
styles[i] = atom->new_avec(arg[i],0,NULL,NULL,dummy);
keywords[i] = new char[strlen(arg[i])+1];
@@ -108,7 +108,7 @@ void AtomVecHybrid::init()
/* ----------------------------------------------------------------------
grow atom arrays
n = 0 grows arrays by DELTA
- n > 0 allocates arrays to size n
+ n > 0 allocates arrays to size n
------------------------------------------------------------------------- */
void AtomVecHybrid::grow(int n)
@@ -134,7 +134,7 @@ void AtomVecHybrid::grow(int n)
grow_reset();
if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
}
@@ -164,7 +164,7 @@ void AtomVecHybrid::copy(int i, int j, int delflag)
atom->nextra_grow = tmp;
if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j);
}
@@ -178,7 +178,7 @@ void AtomVecHybrid::clear_bonus()
/* ---------------------------------------------------------------------- */
int AtomVecHybrid::pack_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,k,m;
double dx,dy,dz;
@@ -220,7 +220,7 @@ int AtomVecHybrid::pack_comm(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
int AtomVecHybrid::pack_comm_vel(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,k,m;
double dx,dy,dz,dvx,dvy,dvz;
@@ -238,14 +238,14 @@ int AtomVecHybrid::pack_comm_vel(int n, int *list, double *buf,
buf[m++] = v[j][1];
buf[m++] = v[j][2];
if (omega_flag) {
- buf[m++] = omega[j][0];
- buf[m++] = omega[j][1];
- buf[m++] = omega[j][2];
+ buf[m++] = omega[j][0];
+ buf[m++] = omega[j][1];
+ buf[m++] = omega[j][2];
}
if (angmom_flag) {
- buf[m++] = angmom[j][0];
- buf[m++] = angmom[j][1];
- buf[m++] = angmom[j][2];
+ buf[m++] = angmom[j][0];
+ buf[m++] = angmom[j][1];
+ buf[m++] = angmom[j][2];
}
}
} else {
@@ -260,52 +260,52 @@ int AtomVecHybrid::pack_comm_vel(int n, int *list, double *buf,
}
if (!deform_vremap) {
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
- if (omega_flag) {
- buf[m++] = omega[j][0];
- buf[m++] = omega[j][1];
- buf[m++] = omega[j][2];
- }
- if (angmom_flag) {
- buf[m++] = angmom[j][0];
- buf[m++] = angmom[j][1];
- buf[m++] = angmom[j][2];
- }
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
+ if (omega_flag) {
+ buf[m++] = omega[j][0];
+ buf[m++] = omega[j][1];
+ buf[m++] = omega[j][2];
+ }
+ if (angmom_flag) {
+ buf[m++] = angmom[j][0];
+ buf[m++] = angmom[j][1];
+ buf[m++] = angmom[j][2];
+ }
}
} else {
dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
dvz = pbc[2]*h_rate[2];
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- if (mask[i] & deform_groupbit) {
- buf[m++] = v[j][0] + dvx;
- buf[m++] = v[j][1] + dvy;
- buf[m++] = v[j][2] + dvz;
- } else {
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
- }
- if (omega_flag) {
- buf[m++] = omega[j][0];
- buf[m++] = omega[j][1];
- buf[m++] = omega[j][2];
- }
- if (angmom_flag) {
- buf[m++] = angmom[j][0];
- buf[m++] = angmom[j][1];
- buf[m++] = angmom[j][2];
- }
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ if (mask[i] & deform_groupbit) {
+ buf[m++] = v[j][0] + dvx;
+ buf[m++] = v[j][1] + dvy;
+ buf[m++] = v[j][2] + dvz;
+ } else {
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
+ }
+ if (omega_flag) {
+ buf[m++] = omega[j][0];
+ buf[m++] = omega[j][1];
+ buf[m++] = omega[j][2];
+ }
+ if (angmom_flag) {
+ buf[m++] = angmom[j][0];
+ buf[m++] = angmom[j][1];
+ buf[m++] = angmom[j][2];
+ }
}
}
}
@@ -418,7 +418,7 @@ void AtomVecHybrid::unpack_reverse(int n, int *list, double *buf)
/* ---------------------------------------------------------------------- */
int AtomVecHybrid::pack_border(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,k,m;
double dx,dy,dz;
@@ -466,7 +466,7 @@ int AtomVecHybrid::pack_border(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
int AtomVecHybrid::pack_border_vel(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,k,m;
double dx,dy,dz,dvx,dvy,dvz;
@@ -487,14 +487,14 @@ int AtomVecHybrid::pack_border_vel(int n, int *list, double *buf,
buf[m++] = v[j][1];
buf[m++] = v[j][2];
if (omega_flag) {
- buf[m++] = omega[j][0];
- buf[m++] = omega[j][1];
- buf[m++] = omega[j][2];
+ buf[m++] = omega[j][0];
+ buf[m++] = omega[j][1];
+ buf[m++] = omega[j][2];
}
if (angmom_flag) {
- buf[m++] = angmom[j][0];
- buf[m++] = angmom[j][1];
- buf[m++] = angmom[j][2];
+ buf[m++] = angmom[j][0];
+ buf[m++] = angmom[j][1];
+ buf[m++] = angmom[j][2];
}
}
} else {
@@ -509,58 +509,58 @@ int AtomVecHybrid::pack_border_vel(int n, int *list, double *buf,
}
if (!deform_vremap) {
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = tag[j];
- buf[m++] = type[j];
- buf[m++] = mask[j];
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
- if (omega_flag) {
- buf[m++] = omega[j][0];
- buf[m++] = omega[j][1];
- buf[m++] = omega[j][2];
- }
- if (angmom_flag) {
- buf[m++] = angmom[j][0];
- buf[m++] = angmom[j][1];
- buf[m++] = angmom[j][2];
- }
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = tag[j];
+ buf[m++] = type[j];
+ buf[m++] = mask[j];
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
+ if (omega_flag) {
+ buf[m++] = omega[j][0];
+ buf[m++] = omega[j][1];
+ buf[m++] = omega[j][2];
+ }
+ if (angmom_flag) {
+ buf[m++] = angmom[j][0];
+ buf[m++] = angmom[j][1];
+ buf[m++] = angmom[j][2];
+ }
}
} else {
dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
dvz = pbc[2]*h_rate[2];
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = tag[j];
- buf[m++] = type[j];
- buf[m++] = mask[j];
- if (mask[i] & deform_groupbit) {
- buf[m++] = v[j][0] + dvx;
- buf[m++] = v[j][1] + dvy;
- buf[m++] = v[j][2] + dvz;
- } else {
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
- }
- if (omega_flag) {
- buf[m++] = omega[j][0];
- buf[m++] = omega[j][1];
- buf[m++] = omega[j][2];
- }
- if (angmom_flag) {
- buf[m++] = angmom[j][0];
- buf[m++] = angmom[j][1];
- buf[m++] = angmom[j][2];
- }
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = tag[j];
+ buf[m++] = type[j];
+ buf[m++] = mask[j];
+ if (mask[i] & deform_groupbit) {
+ buf[m++] = v[j][0] + dvx;
+ buf[m++] = v[j][1] + dvy;
+ buf[m++] = v[j][2] + dvz;
+ } else {
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
+ }
+ if (omega_flag) {
+ buf[m++] = omega[j][0];
+ buf[m++] = omega[j][1];
+ buf[m++] = omega[j][2];
+ }
+ if (angmom_flag) {
+ buf[m++] = angmom[j][0];
+ buf[m++] = angmom[j][1];
+ buf[m++] = angmom[j][2];
+ }
}
}
}
@@ -649,13 +649,13 @@ int AtomVecHybrid::pack_exchange(int i, double *buf)
atom->nextra_grow = 0;
m = 0;
- for (k = 0; k < nstyles; k++)
+ for (k = 0; k < nstyles; k++)
m += styles[k]->pack_exchange(i,&buf[m]);
atom->nextra_grow = tmp;
if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]);
buf[0] = m;
@@ -687,9 +687,9 @@ int AtomVecHybrid::unpack_exchange(double *buf)
atom->nextra_grow = tmp;
if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->
- unpack_exchange(nlocal,&buf[m]);
+ unpack_exchange(nlocal,&buf[m]);
atom->nlocal++;
return m;
@@ -713,9 +713,9 @@ int AtomVecHybrid::size_restart()
int nlocal = atom->nlocal;
if (atom->nextra_restart)
- for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
for (int i = 0; i < nlocal; i++)
- n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
+ n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
return n;
}
@@ -738,7 +738,7 @@ int AtomVecHybrid::pack_restart(int i, double *buf)
atom->nextra_restart = tmp;
if (atom->nextra_restart)
- for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]);
buf[0] = m;
@@ -840,7 +840,7 @@ void AtomVecHybrid::data_atom(double *coord, int imagetmp, char **values)
// each sub-style parses sub-style specific values
int m = 5;
- for (int k = 0; k < nstyles; k++)
+ for (int k = 0; k < nstyles; k++)
m += styles[k]->data_atom_hybrid(nlocal,&values[m]);
atom->nlocal++;
@@ -859,7 +859,7 @@ void AtomVecHybrid::data_vel(int m, char **values)
// each sub-style parses sub-style specific values
int n = 3;
- for (int k = 0; k < nstyles; k++)
+ for (int k = 0; k < nstyles; k++)
n += styles[k]->data_vel_hybrid(m,&values[n]);
}
diff --git a/src/atom_vec_hybrid.h b/src/atom_vec_hybrid.h
index 4f2f2d1851d435de85b7fa49042b341a0bb77b3e..ea1d1ff2343221b7eee98f152f43c647f654e290 100644
--- a/src/atom_vec_hybrid.h
+++ b/src/atom_vec_hybrid.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/atom_vec_line.cpp b/src/atom_vec_line.cpp
index 550f2b3249df57f894abf842eeec8d11118d8fcd..55997b990be0e8edffc196ad86ec533bed32cabc 100644
--- a/src/atom_vec_line.cpp
+++ b/src/atom_vec_line.cpp
@@ -129,7 +129,7 @@ void AtomVecLine::grow_bonus()
error->one(FLERR,"Per-processor system is too big");
bonus = (Bonus *) memory->srealloc(bonus,nmax_bonus*sizeof(Bonus),
- "atom:bonus");
+ "atom:bonus");
}
/* ----------------------------------------------------------------------
@@ -199,7 +199,7 @@ void AtomVecLine::clear_bonus()
this may create or delete entry in bonus data
------------------------------------------------------------------------- */
-void AtomVecLine::set_length(int i, double value)
+void AtomVecLine::set_length(int i, double value)
{
if (line[i] < 0) {
if (value == 0.0) return;
@@ -218,7 +218,7 @@ void AtomVecLine::set_length(int i, double value)
/* ---------------------------------------------------------------------- */
int AtomVecLine::pack_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
@@ -257,7 +257,7 @@ int AtomVecLine::pack_comm(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
int AtomVecLine::pack_comm_vel(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz,dvx,dvy,dvz;
@@ -289,40 +289,40 @@ int AtomVecLine::pack_comm_vel(int n, int *list, double *buf,
}
if (!deform_vremap) {
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- if (line[j] >= 0) buf[m++] = bonus[line[j]].theta;
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
- buf[m++] = omega[j][0];
- buf[m++] = omega[j][1];
- buf[m++] = omega[j][2];
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ if (line[j] >= 0) buf[m++] = bonus[line[j]].theta;
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
+ buf[m++] = omega[j][0];
+ buf[m++] = omega[j][1];
+ buf[m++] = omega[j][2];
}
} else {
dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
dvz = pbc[2]*h_rate[2];
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- if (line[j] >= 0) buf[m++] = bonus[line[j]].theta;
- if (mask[i] & deform_groupbit) {
- buf[m++] = v[j][0] + dvx;
- buf[m++] = v[j][1] + dvy;
- buf[m++] = v[j][2] + dvz;
- } else {
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
- }
- buf[m++] = omega[j][0];
- buf[m++] = omega[j][1];
- buf[m++] = omega[j][2];
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ if (line[j] >= 0) buf[m++] = bonus[line[j]].theta;
+ if (mask[i] & deform_groupbit) {
+ buf[m++] = v[j][0] + dvx;
+ buf[m++] = v[j][1] + dvy;
+ buf[m++] = v[j][2] + dvz;
+ } else {
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
+ }
+ buf[m++] = omega[j][0];
+ buf[m++] = omega[j][1];
+ buf[m++] = omega[j][2];
}
}
}
@@ -467,7 +467,7 @@ int AtomVecLine::unpack_reverse_hybrid(int n, int *list, double *buf)
/* ---------------------------------------------------------------------- */
int AtomVecLine::pack_border(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
@@ -485,9 +485,9 @@ int AtomVecLine::pack_border(int n, int *list, double *buf,
buf[m++] = molecule[j];
if (line[j] < 0) buf[m++] = 0;
else {
- buf[m++] = 1;
- buf[m++] = bonus[line[j]].length;
- buf[m++] = bonus[line[j]].theta;
+ buf[m++] = 1;
+ buf[m++] = bonus[line[j]].length;
+ buf[m++] = bonus[line[j]].theta;
}
}
} else {
@@ -511,9 +511,9 @@ int AtomVecLine::pack_border(int n, int *list, double *buf,
buf[m++] = molecule[j];
if (line[j] < 0) buf[m++] = 0;
else {
- buf[m++] = 1;
- buf[m++] = bonus[line[j]].length;
- buf[m++] = bonus[line[j]].theta;
+ buf[m++] = 1;
+ buf[m++] = bonus[line[j]].length;
+ buf[m++] = bonus[line[j]].theta;
}
}
}
@@ -523,7 +523,7 @@ int AtomVecLine::pack_border(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
int AtomVecLine::pack_border_vel(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz,dvx,dvy,dvz;
@@ -541,9 +541,9 @@ int AtomVecLine::pack_border_vel(int n, int *list, double *buf,
buf[m++] = molecule[j];
if (line[j] < 0) buf[m++] = 0;
else {
- buf[m++] = 1;
- buf[m++] = bonus[line[j]].length;
- buf[m++] = bonus[line[j]].theta;
+ buf[m++] = 1;
+ buf[m++] = bonus[line[j]].length;
+ buf[m++] = bonus[line[j]].theta;
}
buf[m++] = v[j][0];
buf[m++] = v[j][1];
@@ -564,58 +564,58 @@ int AtomVecLine::pack_border_vel(int n, int *list, double *buf,
}
if (!deform_vremap) {
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = tag[j];
- buf[m++] = type[j];
- buf[m++] = mask[j];
- buf[m++] = molecule[j];
- if (line[j] < 0) buf[m++] = 0;
- else {
- buf[m++] = 1;
- buf[m++] = bonus[line[j]].length;
- buf[m++] = bonus[line[j]].theta;
- }
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
- buf[m++] = omega[j][0];
- buf[m++] = omega[j][1];
- buf[m++] = omega[j][2];
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = tag[j];
+ buf[m++] = type[j];
+ buf[m++] = mask[j];
+ buf[m++] = molecule[j];
+ if (line[j] < 0) buf[m++] = 0;
+ else {
+ buf[m++] = 1;
+ buf[m++] = bonus[line[j]].length;
+ buf[m++] = bonus[line[j]].theta;
+ }
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
+ buf[m++] = omega[j][0];
+ buf[m++] = omega[j][1];
+ buf[m++] = omega[j][2];
}
} else {
dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
dvz = pbc[2]*h_rate[2];
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = tag[j];
- buf[m++] = type[j];
- buf[m++] = mask[j];
- buf[m++] = molecule[j];
- if (line[j] < 0) buf[m++] = 0;
- else {
- buf[m++] = 1;
- buf[m++] = bonus[line[j]].length;
- buf[m++] = bonus[line[j]].theta;
- }
- if (mask[i] & deform_groupbit) {
- buf[m++] = v[j][0] + dvx;
- buf[m++] = v[j][1] + dvy;
- buf[m++] = v[j][2] + dvz;
- } else {
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
- }
- buf[m++] = omega[j][0];
- buf[m++] = omega[j][1];
- buf[m++] = omega[j][2];
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = tag[j];
+ buf[m++] = type[j];
+ buf[m++] = mask[j];
+ buf[m++] = molecule[j];
+ if (line[j] < 0) buf[m++] = 0;
+ else {
+ buf[m++] = 1;
+ buf[m++] = bonus[line[j]].length;
+ buf[m++] = bonus[line[j]].theta;
+ }
+ if (mask[i] & deform_groupbit) {
+ buf[m++] = v[j][0] + dvx;
+ buf[m++] = v[j][1] + dvy;
+ buf[m++] = v[j][2] + dvz;
+ } else {
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
+ }
+ buf[m++] = omega[j][0];
+ buf[m++] = omega[j][1];
+ buf[m++] = omega[j][2];
}
}
}
@@ -737,7 +737,7 @@ int AtomVecLine::unpack_border_hybrid(int n, int first, double *buf)
/* ----------------------------------------------------------------------
pack data for atom I for sending to another proc
- xyz must be 1st 3 values, so comm::exchange() can test on them
+ xyz must be 1st 3 values, so comm::exchange() can test on them
------------------------------------------------------------------------- */
int AtomVecLine::pack_exchange(int i, double *buf)
@@ -769,7 +769,7 @@ int AtomVecLine::pack_exchange(int i, double *buf)
}
if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]);
buf[0] = m;
@@ -812,9 +812,9 @@ int AtomVecLine::unpack_exchange(double *buf)
}
if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->
- unpack_exchange(nlocal,&buf[m]);
+ unpack_exchange(nlocal,&buf[m]);
atom->nlocal++;
return m;
@@ -836,9 +836,9 @@ int AtomVecLine::size_restart()
else n += 17;
if (atom->nextra_restart)
- for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
for (i = 0; i < nlocal; i++)
- n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
+ n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
return n;
}
@@ -846,7 +846,7 @@ int AtomVecLine::size_restart()
/* ----------------------------------------------------------------------
pack atom I's data for restart file including extra quantities
xyz must be 1st 3 values, so that read_restart can test on them
- molecular types may be negative, but write as positive
+ molecular types may be negative, but write as positive
------------------------------------------------------------------------- */
int AtomVecLine::pack_restart(int i, double *buf)
@@ -878,7 +878,7 @@ int AtomVecLine::pack_restart(int i, double *buf)
}
if (atom->nextra_restart)
- for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]);
buf[0] = m;
@@ -1104,7 +1104,7 @@ int AtomVecLine::data_vel_hybrid(int m, char **values)
}
/* ----------------------------------------------------------------------
- return # of bytes of allocated memory
+ return # of bytes of allocated memory
------------------------------------------------------------------------- */
bigint AtomVecLine::memory_usage()
@@ -1141,20 +1141,20 @@ void AtomVecLine::consistency_check(int n, char *str)
int iflag = 0;
int count = 0;
for (int i = 0; i < n; i++) {
-
+
if (line[i] >= 0) {
count++;
if (line[i] >= nlocal_bonus) iflag++;
if (bonus[line[i]].ilocal != i) iflag++;
//if (comm->me == 1 && update->ntimestep == 873)
- // printf("CCHK %s: %d %d: %d %d: %d %d\n",
+ // printf("CCHK %s: %d %d: %d %d: %d %d\n",
// str,i,n,line[i],nlocal_bonus,bonus[line[i]].ilocal,iflag);
}
}
if (iflag) {
printf("BAD vecline ptrs: %s: %d %d: %d\n",str,comm->me,
- update->ntimestep,iflag);
+ update->ntimestep,iflag);
MPI_Abort(world,1);
}
diff --git a/src/atom_vec_line.h b/src/atom_vec_line.h
index 38b7aee79b05f3c7db1702445903bb4ee4b3677a..b37bb667717eec0f908b04c8eb9c671952df5ccf 100644
--- a/src/atom_vec_line.h
+++ b/src/atom_vec_line.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/atom_vec_sphere.cpp b/src/atom_vec_sphere.cpp
index 5630fa6bac2c4445c348f30303605e7e3723091c..f77a7e091b437ffbecc933be96c7ef07a6d2012b 100644
--- a/src/atom_vec_sphere.cpp
+++ b/src/atom_vec_sphere.cpp
@@ -49,7 +49,7 @@ AtomVecSphere::AtomVecSphere(LAMMPS *lmp, int narg, char **arg) :
xcol_data = 5;
atom->sphere_flag = 1;
- atom->radius_flag = atom->rmass_flag = atom->omega_flag =
+ atom->radius_flag = atom->rmass_flag = atom->omega_flag =
atom->torque_flag = 1;
}
@@ -70,7 +70,7 @@ void AtomVecSphere::init()
FixAdapt *fix = (FixAdapt *) modify->fix[i];
if (fix->diamflag) {
radvary = 1;
- comm_x_only = 0;
+ comm_x_only = 0;
size_forward = 5;
}
}
@@ -152,7 +152,7 @@ void AtomVecSphere::copy(int i, int j, int delflag)
/* ---------------------------------------------------------------------- */
int AtomVecSphere::pack_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
@@ -161,26 +161,26 @@ int AtomVecSphere::pack_comm(int n, int *list, double *buf,
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0];
- buf[m++] = x[j][1];
- buf[m++] = x[j][2];
+ j = list[i];
+ buf[m++] = x[j][0];
+ buf[m++] = x[j][1];
+ buf[m++] = x[j][2];
}
} else {
if (domain->triclinic == 0) {
- dx = pbc[0]*domain->xprd;
- dy = pbc[1]*domain->yprd;
- dz = pbc[2]*domain->zprd;
+ dx = pbc[0]*domain->xprd;
+ dy = pbc[1]*domain->yprd;
+ dz = pbc[2]*domain->zprd;
} else {
- dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
- dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
- dz = pbc[2]*domain->zprd;
+ dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
+ dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
+ dz = pbc[2]*domain->zprd;
}
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
}
}
@@ -188,30 +188,30 @@ int AtomVecSphere::pack_comm(int n, int *list, double *buf,
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0];
- buf[m++] = x[j][1];
- buf[m++] = x[j][2];
- buf[m++] = radius[j];
- buf[m++] = rmass[j];
+ j = list[i];
+ buf[m++] = x[j][0];
+ buf[m++] = x[j][1];
+ buf[m++] = x[j][2];
+ buf[m++] = radius[j];
+ buf[m++] = rmass[j];
}
} else {
if (domain->triclinic == 0) {
- dx = pbc[0]*domain->xprd;
- dy = pbc[1]*domain->yprd;
- dz = pbc[2]*domain->zprd;
+ dx = pbc[0]*domain->xprd;
+ dy = pbc[1]*domain->yprd;
+ dz = pbc[2]*domain->zprd;
} else {
- dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
- dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
- dz = pbc[2]*domain->zprd;
+ dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
+ dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
+ dz = pbc[2]*domain->zprd;
}
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = radius[j];
- buf[m++] = rmass[j];
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = radius[j];
+ buf[m++] = rmass[j];
}
}
}
@@ -222,7 +222,7 @@ int AtomVecSphere::pack_comm(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
int AtomVecSphere::pack_comm_vel(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz,dvx,dvy,dvz;
@@ -231,62 +231,62 @@ int AtomVecSphere::pack_comm_vel(int n, int *list, double *buf,
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0];
- buf[m++] = x[j][1];
- buf[m++] = x[j][2];
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
- buf[m++] = omega[j][0];
- buf[m++] = omega[j][1];
- buf[m++] = omega[j][2];
+ j = list[i];
+ buf[m++] = x[j][0];
+ buf[m++] = x[j][1];
+ buf[m++] = x[j][2];
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
+ buf[m++] = omega[j][0];
+ buf[m++] = omega[j][1];
+ buf[m++] = omega[j][2];
}
} else {
if (domain->triclinic == 0) {
- dx = pbc[0]*domain->xprd;
- dy = pbc[1]*domain->yprd;
- dz = pbc[2]*domain->zprd;
+ dx = pbc[0]*domain->xprd;
+ dy = pbc[1]*domain->yprd;
+ dz = pbc[2]*domain->zprd;
} else {
- dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
- dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
- dz = pbc[2]*domain->zprd;
+ dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
+ dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
+ dz = pbc[2]*domain->zprd;
}
if (!deform_vremap) {
- for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
- buf[m++] = omega[j][0];
- buf[m++] = omega[j][1];
- buf[m++] = omega[j][2];
- }
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
+ buf[m++] = omega[j][0];
+ buf[m++] = omega[j][1];
+ buf[m++] = omega[j][2];
+ }
} else {
- dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
- dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
- dvz = pbc[2]*h_rate[2];
- for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- if (mask[i] & deform_groupbit) {
- buf[m++] = v[j][0] + dvx;
- buf[m++] = v[j][1] + dvy;
- buf[m++] = v[j][2] + dvz;
- } else {
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
- }
- buf[m++] = omega[j][0];
- buf[m++] = omega[j][1];
- buf[m++] = omega[j][2];
- }
+ dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
+ dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
+ dvz = pbc[2]*h_rate[2];
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ if (mask[i] & deform_groupbit) {
+ buf[m++] = v[j][0] + dvx;
+ buf[m++] = v[j][1] + dvy;
+ buf[m++] = v[j][2] + dvz;
+ } else {
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
+ }
+ buf[m++] = omega[j][0];
+ buf[m++] = omega[j][1];
+ buf[m++] = omega[j][2];
+ }
}
}
@@ -294,68 +294,68 @@ int AtomVecSphere::pack_comm_vel(int n, int *list, double *buf,
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0];
- buf[m++] = x[j][1];
- buf[m++] = x[j][2];
- buf[m++] = radius[j];
- buf[m++] = rmass[j];
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
- buf[m++] = omega[j][0];
- buf[m++] = omega[j][1];
- buf[m++] = omega[j][2];
+ j = list[i];
+ buf[m++] = x[j][0];
+ buf[m++] = x[j][1];
+ buf[m++] = x[j][2];
+ buf[m++] = radius[j];
+ buf[m++] = rmass[j];
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
+ buf[m++] = omega[j][0];
+ buf[m++] = omega[j][1];
+ buf[m++] = omega[j][2];
}
} else {
if (domain->triclinic == 0) {
- dx = pbc[0]*domain->xprd;
- dy = pbc[1]*domain->yprd;
- dz = pbc[2]*domain->zprd;
+ dx = pbc[0]*domain->xprd;
+ dy = pbc[1]*domain->yprd;
+ dz = pbc[2]*domain->zprd;
} else {
- dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
- dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
- dz = pbc[2]*domain->zprd;
+ dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
+ dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
+ dz = pbc[2]*domain->zprd;
}
if (!deform_vremap) {
- for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = radius[j];
- buf[m++] = rmass[j];
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
- buf[m++] = omega[j][0];
- buf[m++] = omega[j][1];
- buf[m++] = omega[j][2];
- }
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = radius[j];
+ buf[m++] = rmass[j];
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
+ buf[m++] = omega[j][0];
+ buf[m++] = omega[j][1];
+ buf[m++] = omega[j][2];
+ }
} else {
- dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
- dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
- dvz = pbc[2]*h_rate[2];
- for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = radius[j];
- buf[m++] = rmass[j];
- if (mask[i] & deform_groupbit) {
- buf[m++] = v[j][0] + dvx;
- buf[m++] = v[j][1] + dvy;
- buf[m++] = v[j][2] + dvz;
- } else {
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
- }
- buf[m++] = omega[j][0];
- buf[m++] = omega[j][1];
- buf[m++] = omega[j][2];
- }
+ dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
+ dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
+ dvz = pbc[2]*h_rate[2];
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = radius[j];
+ buf[m++] = rmass[j];
+ if (mask[i] & deform_groupbit) {
+ buf[m++] = v[j][0] + dvx;
+ buf[m++] = v[j][1] + dvy;
+ buf[m++] = v[j][2] + dvz;
+ } else {
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
+ }
+ buf[m++] = omega[j][0];
+ buf[m++] = omega[j][1];
+ buf[m++] = omega[j][2];
+ }
}
}
}
@@ -535,7 +535,7 @@ int AtomVecSphere::unpack_reverse_hybrid(int n, int *list, double *buf)
/* ---------------------------------------------------------------------- */
int AtomVecSphere::pack_border(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
@@ -581,7 +581,7 @@ int AtomVecSphere::pack_border(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
int AtomVecSphere::pack_border_vel(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz,dvx,dvy,dvz;
@@ -617,48 +617,48 @@ int AtomVecSphere::pack_border_vel(int n, int *list, double *buf,
}
if (!deform_vremap) {
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = tag[j];
- buf[m++] = type[j];
- buf[m++] = mask[j];
- buf[m++] = radius[j];
- buf[m++] = rmass[j];
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
- buf[m++] = omega[j][0];
- buf[m++] = omega[j][1];
- buf[m++] = omega[j][2];
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = tag[j];
+ buf[m++] = type[j];
+ buf[m++] = mask[j];
+ buf[m++] = radius[j];
+ buf[m++] = rmass[j];
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
+ buf[m++] = omega[j][0];
+ buf[m++] = omega[j][1];
+ buf[m++] = omega[j][2];
}
} else {
dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
dvz = pbc[2]*h_rate[2];
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = tag[j];
- buf[m++] = type[j];
- buf[m++] = mask[j];
- buf[m++] = radius[j];
- buf[m++] = rmass[j];
- if (mask[i] & deform_groupbit) {
- buf[m++] = v[j][0] + dvx;
- buf[m++] = v[j][1] + dvy;
- buf[m++] = v[j][2] + dvz;
- } else {
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
- }
- buf[m++] = omega[j][0];
- buf[m++] = omega[j][1];
- buf[m++] = omega[j][2];
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = tag[j];
+ buf[m++] = type[j];
+ buf[m++] = mask[j];
+ buf[m++] = radius[j];
+ buf[m++] = rmass[j];
+ if (mask[i] & deform_groupbit) {
+ buf[m++] = v[j][0] + dvx;
+ buf[m++] = v[j][1] + dvy;
+ buf[m++] = v[j][2] + dvz;
+ } else {
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
+ }
+ buf[m++] = omega[j][0];
+ buf[m++] = omega[j][1];
+ buf[m++] = omega[j][2];
}
}
}
@@ -746,7 +746,7 @@ int AtomVecSphere::unpack_border_hybrid(int n, int first, double *buf)
/* ----------------------------------------------------------------------
pack data for atom I for sending to another proc
- xyz must be 1st 3 values, so comm::exchange() can test on them
+ xyz must be 1st 3 values, so comm::exchange() can test on them
------------------------------------------------------------------------- */
int AtomVecSphere::pack_exchange(int i, double *buf)
@@ -770,7 +770,7 @@ int AtomVecSphere::pack_exchange(int i, double *buf)
buf[m++] = omega[i][2];
if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]);
buf[0] = m;
@@ -803,9 +803,9 @@ int AtomVecSphere::unpack_exchange(double *buf)
omega[nlocal][2] = buf[m++];
if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->
- unpack_exchange(nlocal,&buf[m]);
+ unpack_exchange(nlocal,&buf[m]);
atom->nlocal++;
return m;
@@ -824,9 +824,9 @@ int AtomVecSphere::size_restart()
int n = 16 * nlocal;
if (atom->nextra_restart)
- for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
for (i = 0; i < nlocal; i++)
- n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
+ n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
return n;
}
@@ -834,7 +834,7 @@ int AtomVecSphere::size_restart()
/* ----------------------------------------------------------------------
pack atom I's data for restart file including extra quantities
xyz must be 1st 3 values, so that read_restart can test on them
- molecular types may be negative, but write as positive
+ molecular types may be negative, but write as positive
------------------------------------------------------------------------- */
int AtomVecSphere::pack_restart(int i, double *buf)
@@ -858,7 +858,7 @@ int AtomVecSphere::pack_restart(int i, double *buf)
buf[m++] = omega[i][2];
if (atom->nextra_restart)
- for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]);
buf[0] = m;
@@ -963,7 +963,7 @@ void AtomVecSphere::data_atom(double *coord, int imagetmp, char **values)
error->one(FLERR,"Invalid density in Atoms section of data file");
if (radius[nlocal] == 0.0) rmass[nlocal] = density;
- else
+ else
rmass[nlocal] = 4.0*MY_PI/3.0 *
radius[nlocal]*radius[nlocal]*radius[nlocal] * density;
@@ -1000,7 +1000,7 @@ int AtomVecSphere::data_atom_hybrid(int nlocal, char **values)
error->one(FLERR,"Invalid density in Atoms section of data file");
if (radius[nlocal] == 0.0) rmass[nlocal] = density;
- else
+ else
rmass[nlocal] = 4.0*MY_PI/3.0 *
radius[nlocal]*radius[nlocal]*radius[nlocal] * density;
@@ -1034,7 +1034,7 @@ int AtomVecSphere::data_vel_hybrid(int m, char **values)
}
/* ----------------------------------------------------------------------
- return # of bytes of allocated memory
+ return # of bytes of allocated memory
------------------------------------------------------------------------- */
bigint AtomVecSphere::memory_usage()
diff --git a/src/atom_vec_sphere.h b/src/atom_vec_sphere.h
index 1df8aaa2da5840a3240ce299c2f1669c08729d8d..3ee23e9dc4d00231fabc8f29569a0be6ce2c5022 100644
--- a/src/atom_vec_sphere.h
+++ b/src/atom_vec_sphere.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/atom_vec_tri.cpp b/src/atom_vec_tri.cpp
index 0ad878a30831c735c2fd87d9f76a652d632eea4d..283718ef94926d3fbd87fa8f552102e004757ecd 100644
--- a/src/atom_vec_tri.cpp
+++ b/src/atom_vec_tri.cpp
@@ -130,7 +130,7 @@ void AtomVecTri::grow_bonus()
error->one(FLERR,"Per-processor system is too big");
bonus = (Bonus *) memory->srealloc(bonus,nmax_bonus*sizeof(Bonus),
- "atom:bonus");
+ "atom:bonus");
}
/* ----------------------------------------------------------------------
@@ -256,7 +256,7 @@ void AtomVecTri::set_equilateral(int i, double size)
/* ---------------------------------------------------------------------- */
int AtomVecTri::pack_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
@@ -270,11 +270,11 @@ int AtomVecTri::pack_comm(int n, int *list, double *buf,
buf[m++] = x[j][1];
buf[m++] = x[j][2];
if (tri[j] >= 0) {
- quat = bonus[tri[j]].quat;
- buf[m++] = quat[0];
- buf[m++] = quat[1];
- buf[m++] = quat[2];
- buf[m++] = quat[3];
+ quat = bonus[tri[j]].quat;
+ buf[m++] = quat[0];
+ buf[m++] = quat[1];
+ buf[m++] = quat[2];
+ buf[m++] = quat[3];
}
}
} else {
@@ -293,11 +293,11 @@ int AtomVecTri::pack_comm(int n, int *list, double *buf,
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
if (tri[j] >= 0) {
- quat = bonus[tri[j]].quat;
- buf[m++] = quat[0];
- buf[m++] = quat[1];
- buf[m++] = quat[2];
- buf[m++] = quat[3];
+ quat = bonus[tri[j]].quat;
+ buf[m++] = quat[0];
+ buf[m++] = quat[1];
+ buf[m++] = quat[2];
+ buf[m++] = quat[3];
}
}
}
@@ -308,7 +308,7 @@ int AtomVecTri::pack_comm(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
int AtomVecTri::pack_comm_vel(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz,dvx,dvy,dvz;
@@ -322,11 +322,11 @@ int AtomVecTri::pack_comm_vel(int n, int *list, double *buf,
buf[m++] = x[j][1];
buf[m++] = x[j][2];
if (tri[j] >= 0) {
- quat = bonus[tri[j]].quat;
- buf[m++] = quat[0];
- buf[m++] = quat[1];
- buf[m++] = quat[2];
- buf[m++] = quat[3];
+ quat = bonus[tri[j]].quat;
+ buf[m++] = quat[0];
+ buf[m++] = quat[1];
+ buf[m++] = quat[2];
+ buf[m++] = quat[3];
}
buf[m++] = v[j][0];
buf[m++] = v[j][1];
@@ -347,52 +347,52 @@ int AtomVecTri::pack_comm_vel(int n, int *list, double *buf,
}
if (!deform_vremap) {
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- if (tri[j] >= 0) {
- quat = bonus[tri[j]].quat;
- buf[m++] = quat[0];
- buf[m++] = quat[1];
- buf[m++] = quat[2];
- buf[m++] = quat[3];
- }
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
- buf[m++] = angmom[j][0];
- buf[m++] = angmom[j][1];
- buf[m++] = angmom[j][2];
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ if (tri[j] >= 0) {
+ quat = bonus[tri[j]].quat;
+ buf[m++] = quat[0];
+ buf[m++] = quat[1];
+ buf[m++] = quat[2];
+ buf[m++] = quat[3];
+ }
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
+ buf[m++] = angmom[j][0];
+ buf[m++] = angmom[j][1];
+ buf[m++] = angmom[j][2];
}
} else {
dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
dvz = pbc[2]*h_rate[2];
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- if (tri[j] >= 0) {
- quat = bonus[tri[j]].quat;
- buf[m++] = quat[0];
- buf[m++] = quat[1];
- buf[m++] = quat[2];
- buf[m++] = quat[3];
- }
- if (mask[i] & deform_groupbit) {
- buf[m++] = v[j][0] + dvx;
- buf[m++] = v[j][1] + dvy;
- buf[m++] = v[j][2] + dvz;
- } else {
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
- }
- buf[m++] = angmom[j][0];
- buf[m++] = angmom[j][1];
- buf[m++] = angmom[j][2];
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ if (tri[j] >= 0) {
+ quat = bonus[tri[j]].quat;
+ buf[m++] = quat[0];
+ buf[m++] = quat[1];
+ buf[m++] = quat[2];
+ buf[m++] = quat[3];
+ }
+ if (mask[i] & deform_groupbit) {
+ buf[m++] = v[j][0] + dvx;
+ buf[m++] = v[j][1] + dvy;
+ buf[m++] = v[j][2] + dvz;
+ } else {
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
+ }
+ buf[m++] = angmom[j][0];
+ buf[m++] = angmom[j][1];
+ buf[m++] = angmom[j][2];
}
}
}
@@ -565,7 +565,7 @@ int AtomVecTri::unpack_reverse_hybrid(int n, int *list, double *buf)
/* ---------------------------------------------------------------------- */
int AtomVecTri::pack_border(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
@@ -584,28 +584,28 @@ int AtomVecTri::pack_border(int n, int *list, double *buf,
buf[m++] = molecule[j];
if (tri[j] < 0) buf[m++] = 0;
else {
- buf[m++] = 1;
- quat = bonus[tri[j]].quat;
- c1 = bonus[tri[j]].c1;
- c2 = bonus[tri[j]].c2;
- c3 = bonus[tri[j]].c3;
- inertia = bonus[tri[j]].inertia;
- buf[m++] = quat[0];
- buf[m++] = quat[1];
- buf[m++] = quat[2];
- buf[m++] = quat[3];
- buf[m++] = c1[0];
- buf[m++] = c1[1];
- buf[m++] = c1[2];
- buf[m++] = c2[0];
- buf[m++] = c2[1];
- buf[m++] = c2[2];
- buf[m++] = c3[0];
- buf[m++] = c3[1];
- buf[m++] = c3[2];
- buf[m++] = inertia[0];
- buf[m++] = inertia[1];
- buf[m++] = inertia[2];
+ buf[m++] = 1;
+ quat = bonus[tri[j]].quat;
+ c1 = bonus[tri[j]].c1;
+ c2 = bonus[tri[j]].c2;
+ c3 = bonus[tri[j]].c3;
+ inertia = bonus[tri[j]].inertia;
+ buf[m++] = quat[0];
+ buf[m++] = quat[1];
+ buf[m++] = quat[2];
+ buf[m++] = quat[3];
+ buf[m++] = c1[0];
+ buf[m++] = c1[1];
+ buf[m++] = c1[2];
+ buf[m++] = c2[0];
+ buf[m++] = c2[1];
+ buf[m++] = c2[2];
+ buf[m++] = c3[0];
+ buf[m++] = c3[1];
+ buf[m++] = c3[2];
+ buf[m++] = inertia[0];
+ buf[m++] = inertia[1];
+ buf[m++] = inertia[2];
}
}
} else {
@@ -629,28 +629,28 @@ int AtomVecTri::pack_border(int n, int *list, double *buf,
buf[m++] = molecule[j];
if (tri[j] < 0) buf[m++] = 0;
else {
- buf[m++] = 1;
- quat = bonus[tri[j]].quat;
- c1 = bonus[tri[j]].c1;
- c2 = bonus[tri[j]].c2;
- c3 = bonus[tri[j]].c3;
- inertia = bonus[tri[j]].inertia;
- buf[m++] = quat[0];
- buf[m++] = quat[1];
- buf[m++] = quat[2];
- buf[m++] = quat[3];
- buf[m++] = c1[0];
- buf[m++] = c1[1];
- buf[m++] = c1[2];
- buf[m++] = c2[0];
- buf[m++] = c2[1];
- buf[m++] = c2[2];
- buf[m++] = c3[0];
- buf[m++] = c3[1];
- buf[m++] = c3[2];
- buf[m++] = inertia[0];
- buf[m++] = inertia[1];
- buf[m++] = inertia[2];
+ buf[m++] = 1;
+ quat = bonus[tri[j]].quat;
+ c1 = bonus[tri[j]].c1;
+ c2 = bonus[tri[j]].c2;
+ c3 = bonus[tri[j]].c3;
+ inertia = bonus[tri[j]].inertia;
+ buf[m++] = quat[0];
+ buf[m++] = quat[1];
+ buf[m++] = quat[2];
+ buf[m++] = quat[3];
+ buf[m++] = c1[0];
+ buf[m++] = c1[1];
+ buf[m++] = c1[2];
+ buf[m++] = c2[0];
+ buf[m++] = c2[1];
+ buf[m++] = c2[2];
+ buf[m++] = c3[0];
+ buf[m++] = c3[1];
+ buf[m++] = c3[2];
+ buf[m++] = inertia[0];
+ buf[m++] = inertia[1];
+ buf[m++] = inertia[2];
}
}
}
@@ -660,7 +660,7 @@ int AtomVecTri::pack_border(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
int AtomVecTri::pack_border_vel(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz,dvx,dvy,dvz;
@@ -679,28 +679,28 @@ int AtomVecTri::pack_border_vel(int n, int *list, double *buf,
buf[m++] = molecule[j];
if (tri[j] < 0) buf[m++] = 0;
else {
- buf[m++] = 1;
- quat = bonus[tri[j]].quat;
- c1 = bonus[tri[j]].c1;
- c2 = bonus[tri[j]].c2;
- c3 = bonus[tri[j]].c3;
- inertia = bonus[tri[j]].inertia;
- buf[m++] = quat[0];
- buf[m++] = quat[1];
- buf[m++] = quat[2];
- buf[m++] = quat[3];
- buf[m++] = c1[0];
- buf[m++] = c1[1];
- buf[m++] = c1[2];
- buf[m++] = c2[0];
- buf[m++] = c2[1];
- buf[m++] = c2[2];
- buf[m++] = c3[0];
- buf[m++] = c3[1];
- buf[m++] = c3[2];
- buf[m++] = inertia[0];
- buf[m++] = inertia[1];
- buf[m++] = inertia[2];
+ buf[m++] = 1;
+ quat = bonus[tri[j]].quat;
+ c1 = bonus[tri[j]].c1;
+ c2 = bonus[tri[j]].c2;
+ c3 = bonus[tri[j]].c3;
+ inertia = bonus[tri[j]].inertia;
+ buf[m++] = quat[0];
+ buf[m++] = quat[1];
+ buf[m++] = quat[2];
+ buf[m++] = quat[3];
+ buf[m++] = c1[0];
+ buf[m++] = c1[1];
+ buf[m++] = c1[2];
+ buf[m++] = c2[0];
+ buf[m++] = c2[1];
+ buf[m++] = c2[2];
+ buf[m++] = c3[0];
+ buf[m++] = c3[1];
+ buf[m++] = c3[2];
+ buf[m++] = inertia[0];
+ buf[m++] = inertia[1];
+ buf[m++] = inertia[2];
}
buf[m++] = v[j][0];
buf[m++] = v[j][1];
@@ -721,96 +721,96 @@ int AtomVecTri::pack_border_vel(int n, int *list, double *buf,
}
if (!deform_vremap) {
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = tag[j];
- buf[m++] = type[j];
- buf[m++] = mask[j];
- buf[m++] = molecule[j];
- if (tri[j] < 0) buf[m++] = 0;
- else {
- buf[m++] = 1;
- quat = bonus[tri[j]].quat;
- c1 = bonus[tri[j]].c1;
- c2 = bonus[tri[j]].c2;
- c3 = bonus[tri[j]].c3;
- inertia = bonus[tri[j]].inertia;
- buf[m++] = quat[0];
- buf[m++] = quat[1];
- buf[m++] = quat[2];
- buf[m++] = quat[3];
- buf[m++] = c1[0];
- buf[m++] = c1[1];
- buf[m++] = c1[2];
- buf[m++] = c2[0];
- buf[m++] = c2[1];
- buf[m++] = c2[2];
- buf[m++] = c3[0];
- buf[m++] = c3[1];
- buf[m++] = c3[2];
- buf[m++] = inertia[0];
- buf[m++] = inertia[1];
- buf[m++] = inertia[2];
- }
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
- buf[m++] = angmom[j][0];
- buf[m++] = angmom[j][1];
- buf[m++] = angmom[j][2];
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = tag[j];
+ buf[m++] = type[j];
+ buf[m++] = mask[j];
+ buf[m++] = molecule[j];
+ if (tri[j] < 0) buf[m++] = 0;
+ else {
+ buf[m++] = 1;
+ quat = bonus[tri[j]].quat;
+ c1 = bonus[tri[j]].c1;
+ c2 = bonus[tri[j]].c2;
+ c3 = bonus[tri[j]].c3;
+ inertia = bonus[tri[j]].inertia;
+ buf[m++] = quat[0];
+ buf[m++] = quat[1];
+ buf[m++] = quat[2];
+ buf[m++] = quat[3];
+ buf[m++] = c1[0];
+ buf[m++] = c1[1];
+ buf[m++] = c1[2];
+ buf[m++] = c2[0];
+ buf[m++] = c2[1];
+ buf[m++] = c2[2];
+ buf[m++] = c3[0];
+ buf[m++] = c3[1];
+ buf[m++] = c3[2];
+ buf[m++] = inertia[0];
+ buf[m++] = inertia[1];
+ buf[m++] = inertia[2];
+ }
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
+ buf[m++] = angmom[j][0];
+ buf[m++] = angmom[j][1];
+ buf[m++] = angmom[j][2];
}
} else {
dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
dvz = pbc[2]*h_rate[2];
for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = tag[j];
- buf[m++] = type[j];
- buf[m++] = mask[j];
- buf[m++] = molecule[j];
- if (tri[j] < 0) buf[m++] = 0;
- else {
- buf[m++] = 1;
- quat = bonus[tri[j]].quat;
- c1 = bonus[tri[j]].c1;
- c2 = bonus[tri[j]].c2;
- c3 = bonus[tri[j]].c3;
- inertia = bonus[tri[j]].inertia;
- buf[m++] = quat[0];
- buf[m++] = quat[1];
- buf[m++] = quat[2];
- buf[m++] = quat[3];
- buf[m++] = c1[0];
- buf[m++] = c1[1];
- buf[m++] = c1[2];
- buf[m++] = c2[0];
- buf[m++] = c2[1];
- buf[m++] = c2[2];
- buf[m++] = c3[0];
- buf[m++] = c3[1];
- buf[m++] = c3[2];
- buf[m++] = inertia[0];
- buf[m++] = inertia[1];
- buf[m++] = inertia[2];
- }
- if (mask[i] & deform_groupbit) {
- buf[m++] = v[j][0] + dvx;
- buf[m++] = v[j][1] + dvy;
- buf[m++] = v[j][2] + dvz;
- } else {
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2];
- }
- buf[m++] = angmom[j][0];
- buf[m++] = angmom[j][1];
- buf[m++] = angmom[j][2];
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = tag[j];
+ buf[m++] = type[j];
+ buf[m++] = mask[j];
+ buf[m++] = molecule[j];
+ if (tri[j] < 0) buf[m++] = 0;
+ else {
+ buf[m++] = 1;
+ quat = bonus[tri[j]].quat;
+ c1 = bonus[tri[j]].c1;
+ c2 = bonus[tri[j]].c2;
+ c3 = bonus[tri[j]].c3;
+ inertia = bonus[tri[j]].inertia;
+ buf[m++] = quat[0];
+ buf[m++] = quat[1];
+ buf[m++] = quat[2];
+ buf[m++] = quat[3];
+ buf[m++] = c1[0];
+ buf[m++] = c1[1];
+ buf[m++] = c1[2];
+ buf[m++] = c2[0];
+ buf[m++] = c2[1];
+ buf[m++] = c2[2];
+ buf[m++] = c3[0];
+ buf[m++] = c3[1];
+ buf[m++] = c3[2];
+ buf[m++] = inertia[0];
+ buf[m++] = inertia[1];
+ buf[m++] = inertia[2];
+ }
+ if (mask[i] & deform_groupbit) {
+ buf[m++] = v[j][0] + dvx;
+ buf[m++] = v[j][1] + dvy;
+ buf[m++] = v[j][2] + dvz;
+ } else {
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
+ }
+ buf[m++] = angmom[j][0];
+ buf[m++] = angmom[j][1];
+ buf[m++] = angmom[j][2];
}
}
}
@@ -1012,7 +1012,7 @@ int AtomVecTri::unpack_border_hybrid(int n, int first, double *buf)
/* ----------------------------------------------------------------------
pack data for atom I for sending to another proc
- xyz must be 1st 3 values, so comm::exchange() can test on them
+ xyz must be 1st 3 values, so comm::exchange() can test on them
------------------------------------------------------------------------- */
int AtomVecTri::pack_exchange(int i, double *buf)
@@ -1063,7 +1063,7 @@ int AtomVecTri::pack_exchange(int i, double *buf)
}
if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]);
buf[0] = m;
@@ -1125,9 +1125,9 @@ int AtomVecTri::unpack_exchange(double *buf)
}
if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->
- unpack_exchange(nlocal,&buf[m]);
+ unpack_exchange(nlocal,&buf[m]);
atom->nlocal++;
return m;
@@ -1149,9 +1149,9 @@ int AtomVecTri::size_restart()
else n += 17;
if (atom->nextra_restart)
- for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
for (i = 0; i < nlocal; i++)
- n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
+ n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
return n;
}
@@ -1159,7 +1159,7 @@ int AtomVecTri::size_restart()
/* ----------------------------------------------------------------------
pack atom I's data for restart file including extra quantities
xyz must be 1st 3 values, so that read_restart can test on them
- molecular types may be negative, but write as positive
+ molecular types may be negative, but write as positive
------------------------------------------------------------------------- */
int AtomVecTri::pack_restart(int i, double *buf)
@@ -1210,7 +1210,7 @@ int AtomVecTri::pack_restart(int i, double *buf)
}
if (atom->nextra_restart)
- for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
+ for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]);
buf[0] = m;
@@ -1469,7 +1469,7 @@ void AtomVecTri::data_atom_bonus(int m, char **values)
int ierror = MathExtra::jacobi(tensor,bonus[nlocal_bonus].inertia,evectors);
if (ierror) error->one(FLERR,"Insufficient Jacobi rotations for triangle");
-
+
double ex_space[3],ey_space[3],ez_space[3];
ex_space[0] = evectors[0][0];
ex_space[1] = evectors[1][0];
@@ -1488,7 +1488,7 @@ void AtomVecTri::data_atom_bonus(int m, char **values)
if (MathExtra::dot3(norm,ez_space) < 0.0) MathExtra::negate3(ez_space);
// create initial quaternion
-
+
MathExtra::exyz_to_q(ex_space,ey_space,ez_space,bonus[nlocal_bonus].quat);
// bonus c1,c2,c3 = displacement of c1,c2,c3 from centroid
@@ -1497,13 +1497,13 @@ void AtomVecTri::data_atom_bonus(int m, char **values)
double disp[3];
MathExtra::sub3(c1,centroid,disp);
MathExtra::transpose_matvec(ex_space,ey_space,ez_space,
- disp,bonus[nlocal_bonus].c1);
+ disp,bonus[nlocal_bonus].c1);
MathExtra::sub3(c2,centroid,disp);
MathExtra::transpose_matvec(ex_space,ey_space,ez_space,
- disp,bonus[nlocal_bonus].c2);
+ disp,bonus[nlocal_bonus].c2);
MathExtra::sub3(c3,centroid,disp);
MathExtra::transpose_matvec(ex_space,ey_space,ez_space,
- disp,bonus[nlocal_bonus].c3);
+ disp,bonus[nlocal_bonus].c3);
bonus[nlocal_bonus].ilocal = m;
tri[m] = nlocal_bonus++;
@@ -1536,7 +1536,7 @@ int AtomVecTri::data_vel_hybrid(int m, char **values)
}
/* ----------------------------------------------------------------------
- return # of bytes of allocated memory
+ return # of bytes of allocated memory
------------------------------------------------------------------------- */
bigint AtomVecTri::memory_usage()
diff --git a/src/atom_vec_tri.h b/src/atom_vec_tri.h
index 10a0743bd51b8a8d6320a0d53c326c9b405c3a04..f481c8f072bb4307ed0e46fa2873b9e427ac3478 100644
--- a/src/atom_vec_tri.h
+++ b/src/atom_vec_tri.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/balance.cpp b/src/balance.cpp
index 1af18c5c1b62f9acf2f559b1b1311f52b75ae80f..502794cf69a4e2d2bb479154dab9070f6c742c75 100644
--- a/src/balance.cpp
+++ b/src/balance.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -102,61 +102,61 @@ void Balance::command(int narg, char **arg)
if (strcmp(arg[iarg],"x") == 0) {
if (xflag == DYNAMIC) error->all(FLERR,"Illegal balance command");
if (strcmp(arg[iarg+1],"uniform") == 0) {
- if (iarg+2 > narg) error->all(FLERR,"Illegal balance command");
- xflag = UNIFORM;
- iarg += 2;
+ if (iarg+2 > narg) error->all(FLERR,"Illegal balance command");
+ xflag = UNIFORM;
+ iarg += 2;
} else {
- if (1 + procgrid[0]-1 > narg)
- error->all(FLERR,"Illegal balance command");
- xflag = USER;
- delete [] user_xsplit;
- user_xsplit = new double[procgrid[0]+1];
- user_xsplit[0] = 0.0;
- iarg++;
- for (int i = 1; i < procgrid[0]; i++)
- user_xsplit[i] = force->numeric(arg[iarg++]);
- user_xsplit[procgrid[0]] = 1.0;
+ if (1 + procgrid[0]-1 > narg)
+ error->all(FLERR,"Illegal balance command");
+ xflag = USER;
+ delete [] user_xsplit;
+ user_xsplit = new double[procgrid[0]+1];
+ user_xsplit[0] = 0.0;
+ iarg++;
+ for (int i = 1; i < procgrid[0]; i++)
+ user_xsplit[i] = force->numeric(arg[iarg++]);
+ user_xsplit[procgrid[0]] = 1.0;
}
} else if (strcmp(arg[iarg],"y") == 0) {
if (yflag == DYNAMIC) error->all(FLERR,"Illegal balance command");
if (strcmp(arg[iarg+1],"uniform") == 0) {
- if (iarg+2 > narg) error->all(FLERR,"Illegal balance command");
- yflag = UNIFORM;
- iarg += 2;
+ if (iarg+2 > narg) error->all(FLERR,"Illegal balance command");
+ yflag = UNIFORM;
+ iarg += 2;
} else {
- if (1 + procgrid[1]-1 > narg)
- error->all(FLERR,"Illegal balance command");
- yflag = USER;
- delete [] user_ysplit;
- user_ysplit = new double[procgrid[1]+1];
- user_ysplit[0] = 0.0;
- iarg++;
- for (int i = 1; i < procgrid[1]; i++)
- user_ysplit[i] = force->numeric(arg[iarg++]);
- user_ysplit[procgrid[1]] = 1.0;
+ if (1 + procgrid[1]-1 > narg)
+ error->all(FLERR,"Illegal balance command");
+ yflag = USER;
+ delete [] user_ysplit;
+ user_ysplit = new double[procgrid[1]+1];
+ user_ysplit[0] = 0.0;
+ iarg++;
+ for (int i = 1; i < procgrid[1]; i++)
+ user_ysplit[i] = force->numeric(arg[iarg++]);
+ user_ysplit[procgrid[1]] = 1.0;
}
} else if (strcmp(arg[iarg],"z") == 0) {
if (zflag == DYNAMIC) error->all(FLERR,"Illegal balance command");
if (strcmp(arg[iarg+1],"uniform") == 0) {
- if (iarg+2 > narg) error->all(FLERR,"Illegal balance command");
- zflag = UNIFORM;
- iarg += 2;
+ if (iarg+2 > narg) error->all(FLERR,"Illegal balance command");
+ zflag = UNIFORM;
+ iarg += 2;
} else {
- if (1 + procgrid[2]-1 > narg)
- error->all(FLERR,"Illegal balance command");
- zflag = USER;
- delete [] user_zsplit;
- user_zsplit = new double[procgrid[2]+1];
- user_zsplit[0] = 0.0;
- iarg++;
- for (int i = 1; i < procgrid[2]; i++)
- user_zsplit[i] = force->numeric(arg[iarg++]);
- user_zsplit[procgrid[2]] = 1.0;
+ if (1 + procgrid[2]-1 > narg)
+ error->all(FLERR,"Illegal balance command");
+ zflag = USER;
+ delete [] user_zsplit;
+ user_zsplit = new double[procgrid[2]+1];
+ user_zsplit[0] = 0.0;
+ iarg++;
+ for (int i = 1; i < procgrid[2]; i++)
+ user_zsplit[i] = force->numeric(arg[iarg++]);
+ user_zsplit[procgrid[2]] = 1.0;
}
} else if (strcmp(arg[iarg],"dynamic") == 0) {
if (xflag != NONE || yflag != NONE || zflag != NONE)
- error->all(FLERR,"Illegal balance command");
+ error->all(FLERR,"Illegal balance command");
if (iarg+5 > narg) error->all(FLERR,"Illegal balance command");
dflag = 1;
xflag = yflag = DYNAMIC;
@@ -164,7 +164,7 @@ void Balance::command(int narg, char **arg)
nrepeat = atoi(arg[iarg+1]);
niter = atoi(arg[iarg+2]);
if (nrepeat <= 0 || niter <= 0)
- error->all(FLERR,"Illegal balance command");
+ error->all(FLERR,"Illegal balance command");
int n = strlen(arg[iarg+3]) + 1;
bstr = new char[n];
strcpy(bstr,arg[iarg+3]);
@@ -182,23 +182,23 @@ void Balance::command(int narg, char **arg)
if (xflag == USER)
for (int i = 1; i <= procgrid[0]; i++)
- if (user_xsplit[i-1] >= user_xsplit[i])
- error->all(FLERR,"Illegal balance command");
+ if (user_xsplit[i-1] >= user_xsplit[i])
+ error->all(FLERR,"Illegal balance command");
if (yflag == USER)
for (int i = 1; i <= procgrid[1]; i++)
- if (user_ysplit[i-1] >= user_ysplit[i])
- error->all(FLERR,"Illegal balance command");
+ if (user_ysplit[i-1] >= user_ysplit[i])
+ error->all(FLERR,"Illegal balance command");
if (zflag == USER)
for (int i = 1; i <= procgrid[2]; i++)
- if (user_zsplit[i-1] >= user_zsplit[i])
- error->all(FLERR,"Illegal balance command");
+ if (user_zsplit[i-1] >= user_zsplit[i])
+ error->all(FLERR,"Illegal balance command");
if (dflag) {
for (int i = 0; i < strlen(bstr); i++) {
- if (bstr[i] != 'x' && bstr[i] != 'y' && bstr[i] != 'z')
- error->all(FLERR,"Balance dynamic string is invalid");
- if (bstr[i] == 'z' && dimension == 2)
- error->all(FLERR,"Balance dynamic string is invalid for 2d simulation");
+ if (bstr[i] != 'x' && bstr[i] != 'y' && bstr[i] != 'z')
+ error->all(FLERR,"Balance dynamic string is invalid");
+ if (bstr[i] == 'z' && dimension == 2)
+ error->all(FLERR,"Balance dynamic string is invalid for 2d simulation");
}
}
@@ -227,19 +227,19 @@ void Balance::command(int narg, char **arg)
// explicit setting of sub-domain sizes
if (xflag == UNIFORM) {
- for (int i = 0; i < procgrid[0]; i++)
+ for (int i = 0; i < procgrid[0]; i++)
comm->xsplit[i] = i * 1.0/procgrid[0];
comm->xsplit[procgrid[0]] = 1.0;
}
if (yflag == UNIFORM) {
- for (int i = 0; i < procgrid[1]; i++)
+ for (int i = 0; i < procgrid[1]; i++)
comm->ysplit[i] = i * 1.0/procgrid[1];
comm->ysplit[procgrid[1]] = 1.0;
}
if (zflag == UNIFORM) {
- for (int i = 0; i < procgrid[2]; i++)
+ for (int i = 0; i < procgrid[2]; i++)
comm->zsplit[i] = i * 1.0/procgrid[2];
comm->zsplit[procgrid[2]] = 1.0;
}
@@ -276,7 +276,7 @@ void Balance::command(int narg, char **arg)
} else {
if (dimension == 3) {
if (xflag == UNIFORM && yflag == UNIFORM && zflag == UNIFORM)
- comm->uniform = 1;
+ comm->uniform = 1;
} else {
if (xflag == UNIFORM && yflag == UNIFORM) comm->uniform = 1;
}
@@ -302,8 +302,8 @@ void Balance::command(int narg, char **arg)
MPI_Allreduce(&nblocal,&natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);
if (natoms != atom->natoms) {
char str[128];
- sprintf(str,"Lost atoms via balance: original " BIGINT_FORMAT
- " current " BIGINT_FORMAT,atom->natoms,natoms);
+ sprintf(str,"Lost atoms via balance: original " BIGINT_FORMAT
+ " current " BIGINT_FORMAT,atom->natoms,natoms);
error->all(FLERR,str);
}
@@ -316,16 +316,16 @@ void Balance::command(int narg, char **arg)
if (screen) {
fprintf(screen," iteration count = %d\n",count);
fprintf(screen," initial/final max atoms/proc = %d %d\n",
- maxinit,maxfinal);
+ maxinit,maxfinal);
fprintf(screen," initial/final imbalance factor = %g %g\n",
- imbinit,imbfinal);
+ imbinit,imbfinal);
}
if (logfile) {
fprintf(logfile," iteration count = %d\n",count);
fprintf(logfile," initial/final max atoms/proc = %d %d\n",
- maxinit,maxfinal);
+ maxinit,maxfinal);
fprintf(logfile," initial/final imbalance factor = %g %g\n",
- imbinit,imbfinal);
+ imbinit,imbfinal);
}
}
@@ -333,29 +333,29 @@ void Balance::command(int narg, char **arg)
if (screen) {
fprintf(screen," x cuts:");
for (int i = 0; i <= comm->procgrid[0]; i++)
- fprintf(screen," %g",comm->xsplit[i]);
+ fprintf(screen," %g",comm->xsplit[i]);
fprintf(screen,"\n");
fprintf(screen," y cuts:");
for (int i = 0; i <= comm->procgrid[1]; i++)
- fprintf(screen," %g",comm->ysplit[i]);
+ fprintf(screen," %g",comm->ysplit[i]);
fprintf(screen,"\n");
fprintf(screen," z cuts:");
for (int i = 0; i <= comm->procgrid[2]; i++)
- fprintf(screen," %g",comm->zsplit[i]);
+ fprintf(screen," %g",comm->zsplit[i]);
fprintf(screen,"\n");
}
if (logfile) {
fprintf(logfile," x cuts:");
for (int i = 0; i <= comm->procgrid[0]; i++)
- fprintf(logfile," %g",comm->xsplit[i]);
+ fprintf(logfile," %g",comm->xsplit[i]);
fprintf(logfile,"\n");
fprintf(logfile," y cuts:");
for (int i = 0; i <= comm->procgrid[1]; i++)
- fprintf(logfile," %g",comm->ysplit[i]);
+ fprintf(logfile," %g",comm->ysplit[i]);
fprintf(logfile,"\n");
fprintf(logfile," z cuts:");
for (int i = 0; i <= comm->procgrid[2]; i++)
- fprintf(logfile," %g",comm->zsplit[i]);
+ fprintf(logfile," %g",comm->zsplit[i]);
fprintf(logfile,"\n");
}
}
@@ -427,7 +427,7 @@ void Balance::dynamic_setup(char *str)
if (str[i] == 'y') ops[i] = Y;
if (str[i] == 'z') ops[i] = Z;
}
-
+
splits[0] = comm->xsplit;
splits[1] = comm->ysplit;
splits[2] = comm->zsplit;
@@ -452,7 +452,7 @@ void Balance::dynamic_setup(char *str)
------------------------------------------------------------------------- */
void Balance::dynamic_setup(int nrepeat_in, int niter_in,
- char *str, double thresh_in)
+ char *str, double thresh_in)
{
nrepeat = nrepeat_in;
niter = niter_in;
@@ -480,12 +480,12 @@ int Balance::dynamic_once()
for (int irepeat = 0; irepeat < nrepeat; irepeat++) {
for (i = 0; i < nops; i++) {
for (m = 0; m < niter; m++) {
- stats(ops[i],procgrid[ops[i]],splits[ops[i]],counts[ops[i]]);
- adjust(procgrid[ops[i]],counts[ops[i]],splits[ops[i]]);
- count++;
+ stats(ops[i],procgrid[ops[i]],splits[ops[i]],counts[ops[i]]);
+ adjust(procgrid[ops[i]],counts[ops[i]],splits[ops[i]]);
+ count++;
#ifdef BALANCE_DEBUG
- dumpout(-1);
+ dumpout(-1);
#endif
}
imbfactor = imbalance_splits(max);
@@ -523,12 +523,12 @@ int Balance::dynamic()
for (int irepeat = 0; irepeat < nrepeat; irepeat++) {
for (i = 0; i < nops; i++) {
for (m = 0; m < niter; m++) {
- stats(ops[i],procgrid[ops[i]],splits[ops[i]],counts[ops[i]]);
- adjust(procgrid[ops[i]],counts[ops[i]],splits[ops[i]]);
- count++;
+ stats(ops[i],procgrid[ops[i]],splits[ops[i]],counts[ops[i]]);
+ adjust(procgrid[ops[i]],counts[ops[i]],splits[ops[i]]);
+ count++;
#ifdef BALANCE_DEBUG
- dumpout(-1);
+ dumpout(-1);
#endif
}
imbfactor = imbalance_splits(max);
@@ -632,27 +632,27 @@ void Balance::adjust(int n, bigint *count, double *split)
if (mycount > leftcount && mycount > rightcount) {
if (mycount-MAX(leftcount,rightcount) >= fabs(leftcount-rightcount)) {
- if (leftcount <= rightcount) {
- targetleft = damp *
- (rightcount-leftcount + (mycount-rightcount)/3.0);
- targetright = damp * (mycount-rightcount)/3.0;
- cuts[i] = split[i] + targetleft/rho;
- cuts[i+1] = split[i+1] - targetright/rho;
- } else {
- targetleft = damp * (mycount-leftcount)/3.0;
- targetright = damp *
- (leftcount-rightcount + (mycount-leftcount)/3.0);
- cuts[i] = split[i] + targetleft/rho;
- cuts[i+1] = split[i+1] - targetright/rho;
- }
+ if (leftcount <= rightcount) {
+ targetleft = damp *
+ (rightcount-leftcount + (mycount-rightcount)/3.0);
+ targetright = damp * (mycount-rightcount)/3.0;
+ cuts[i] = split[i] + targetleft/rho;
+ cuts[i+1] = split[i+1] - targetright/rho;
+ } else {
+ targetleft = damp * (mycount-leftcount)/3.0;
+ targetright = damp *
+ (leftcount-rightcount + (mycount-leftcount)/3.0);
+ cuts[i] = split[i] + targetleft/rho;
+ cuts[i+1] = split[i+1] - targetright/rho;
+ }
} else if (leftcount < rightcount) {
- target = damp * 0.5*(mycount-leftcount);
- cuts[i] = split[i] + target/rho;
- cuts[i+1] = split[i+1];
+ target = damp * 0.5*(mycount-leftcount);
+ cuts[i] = split[i] + target/rho;
+ cuts[i+1] = split[i+1];
} else if (rightcount < leftcount) {
- target = damp * 0.5*(mycount-rightcount);
- cuts[i+1] = split[i+1] - target/rho;
- cuts[i] = split[i];
+ target = damp * 0.5*(mycount-rightcount);
+ cuts[i+1] = split[i+1] - target/rho;
+ cuts[i] = split[i];
}
// middle slice has more atoms than only left or right slice
@@ -743,32 +743,32 @@ void Balance::dumpout(bigint tstamp)
if (domain->dimension == 2) {
int m = 0;
for (int j = 0; j < comm->procgrid[1]; j++)
- for (int i = 0; i < comm->procgrid[0]; i++) {
- int c1 = j*nx + i + 1;
- int c2 = c1 + 1;
- int c3 = c2 + nx;
- int c4 = c3 - 1;
- fprintf(fp,"%d %d %d %d %d %d\n",m+1,m+1,c1,c2,c3,c4);
- m++;
- }
+ for (int i = 0; i < comm->procgrid[0]; i++) {
+ int c1 = j*nx + i + 1;
+ int c2 = c1 + 1;
+ int c3 = c2 + nx;
+ int c4 = c3 - 1;
+ fprintf(fp,"%d %d %d %d %d %d\n",m+1,m+1,c1,c2,c3,c4);
+ m++;
+ }
} else {
int m = 0;
for (int k = 0; k < comm->procgrid[2]; k++)
- for (int j = 0; j < comm->procgrid[1]; j++)
- for (int i = 0; i < comm->procgrid[0]; i++) {
- int c1 = k*ny*nx + j*nx + i + 1;
- int c2 = c1 + 1;
- int c3 = c2 + nx;
- int c4 = c3 - 1;
- int c5 = c1 + ny*nx;
- int c6 = c2 + ny*nx;
- int c7 = c3 + ny*nx;
- int c8 = c4 + ny*nx;
- fprintf(fp,"%d %d %d %d %d %d %d %d %d %d\n",
- m+1,m+1,c1,c2,c3,c4,c5,c6,c7,c8);
- m++;
- }
+ for (int j = 0; j < comm->procgrid[1]; j++)
+ for (int i = 0; i < comm->procgrid[0]; i++) {
+ int c1 = k*ny*nx + j*nx + i + 1;
+ int c2 = c1 + 1;
+ int c3 = c2 + nx;
+ int c4 = c3 - 1;
+ int c5 = c1 + ny*nx;
+ int c6 = c2 + ny*nx;
+ int c7 = c3 + ny*nx;
+ int c8 = c4 + ny*nx;
+ fprintf(fp,"%d %d %d %d %d %d %d %d %d %d\n",
+ m+1,m+1,c1,c2,c3,c4,c5,c6,c7,c8);
+ m++;
+ }
}
}
@@ -787,9 +787,9 @@ void Balance::dumpout(bigint tstamp)
fprintf(fp,"ITEM: TIMESTEP\n");
fprintf(fp,"%ld\n",tstep);
fprintf(fp,"ITEM: NUMBER OF NODES\n");
- if (domain->dimension == 2)
+ if (domain->dimension == 2)
fprintf(fp,"%d\n",nx*ny);
- else
+ else
fprintf(fp,"%d\n",nx*ny*nz);
fprintf(fp,"ITEM: BOX BOUNDS\n");
fprintf(fp,"%g %g\n",boxlo[0],boxhi[0]);
@@ -801,22 +801,22 @@ void Balance::dumpout(bigint tstamp)
int m = 0;
for (int j = 0; j < ny; j++)
for (int i = 0; i < nx; i++) {
- fprintf(fp,"%d %d %g %g %g\n",m+1,1,
- boxlo[0] + prd[0]*comm->xsplit[i],
- boxlo[1] + prd[1]*comm->ysplit[j],
- 0.0);
- m++;
+ fprintf(fp,"%d %d %g %g %g\n",m+1,1,
+ boxlo[0] + prd[0]*comm->xsplit[i],
+ boxlo[1] + prd[1]*comm->ysplit[j],
+ 0.0);
+ m++;
}
} else {
int m = 0;
for (int k = 0; k < nz; k++)
for (int j = 0; j < ny; j++)
- for (int i = 0; i < nx; i++) {
- fprintf(fp,"%d %d %g %g %g\n",m+1,1,
- boxlo[0] + prd[0]*comm->xsplit[i],
- boxlo[1] + prd[1]*comm->ysplit[j],
- boxlo[2] + prd[2]*comm->zsplit[j]);
- m++;
+ for (int i = 0; i < nx; i++) {
+ fprintf(fp,"%d %d %g %g %g\n",m+1,1,
+ boxlo[0] + prd[0]*comm->xsplit[i],
+ boxlo[1] + prd[1]*comm->ysplit[j],
+ boxlo[2] + prd[2]*comm->zsplit[j]);
+ m++;
}
}
}
diff --git a/src/balance.h b/src/balance.h
index f2a3376b408f183d5da11dbd13c88e55fce863b8..68c1ba1e8b0dcccb1ff3435a6f164270189f0c9d 100644
--- a/src/balance.h
+++ b/src/balance.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/bond.cpp b/src/bond.cpp
index 14138ab38d51095da404512eaf68c4982af738e9..a054cac4959c66f1c61a5c48170f8e92e077a053 100644
--- a/src/bond.cpp
+++ b/src/bond.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -77,7 +77,7 @@ void Bond::ev_setup(int eflag, int vflag)
vflag_either = vflag;
vflag_global = vflag % 4;
vflag_atom = vflag / 4;
-
+
// reallocate per-atom arrays if necessary
if (eflag_atom && atom->nmax > maxeatom) {
@@ -119,8 +119,8 @@ void Bond::ev_setup(int eflag, int vflag)
------------------------------------------------------------------------- */
void Bond::ev_tally(int i, int j, int nlocal, int newton_bond,
- double ebond, double fbond,
- double delx, double dely, double delz)
+ double ebond, double fbond,
+ double delx, double dely, double delz)
{
double ebondhalf,v[6];
@@ -128,9 +128,9 @@ void Bond::ev_tally(int i, int j, int nlocal, int newton_bond,
if (eflag_global) {
if (newton_bond) energy += ebond;
else {
- ebondhalf = 0.5*ebond;
- if (i < nlocal) energy += ebondhalf;
- if (j < nlocal) energy += ebondhalf;
+ ebondhalf = 0.5*ebond;
+ if (i < nlocal) energy += ebondhalf;
+ if (j < nlocal) energy += ebondhalf;
}
}
if (eflag_atom) {
@@ -150,48 +150,48 @@ void Bond::ev_tally(int i, int j, int nlocal, int newton_bond,
if (vflag_global) {
if (newton_bond) {
- virial[0] += v[0];
- virial[1] += v[1];
- virial[2] += v[2];
- virial[3] += v[3];
- virial[4] += v[4];
- virial[5] += v[5];
+ virial[0] += v[0];
+ virial[1] += v[1];
+ virial[2] += v[2];
+ virial[3] += v[3];
+ virial[4] += v[4];
+ virial[5] += v[5];
} else {
- if (i < nlocal) {
- virial[0] += 0.5*v[0];
- virial[1] += 0.5*v[1];
- virial[2] += 0.5*v[2];
- virial[3] += 0.5*v[3];
- virial[4] += 0.5*v[4];
- virial[5] += 0.5*v[5];
- }
- if (j < nlocal) {
- virial[0] += 0.5*v[0];
- virial[1] += 0.5*v[1];
- virial[2] += 0.5*v[2];
- virial[3] += 0.5*v[3];
- virial[4] += 0.5*v[4];
- virial[5] += 0.5*v[5];
- }
+ if (i < nlocal) {
+ virial[0] += 0.5*v[0];
+ virial[1] += 0.5*v[1];
+ virial[2] += 0.5*v[2];
+ virial[3] += 0.5*v[3];
+ virial[4] += 0.5*v[4];
+ virial[5] += 0.5*v[5];
+ }
+ if (j < nlocal) {
+ virial[0] += 0.5*v[0];
+ virial[1] += 0.5*v[1];
+ virial[2] += 0.5*v[2];
+ virial[3] += 0.5*v[3];
+ virial[4] += 0.5*v[4];
+ virial[5] += 0.5*v[5];
+ }
}
}
if (vflag_atom) {
if (newton_bond || i < nlocal) {
- vatom[i][0] += 0.5*v[0];
- vatom[i][1] += 0.5*v[1];
- vatom[i][2] += 0.5*v[2];
- vatom[i][3] += 0.5*v[3];
- vatom[i][4] += 0.5*v[4];
- vatom[i][5] += 0.5*v[5];
+ vatom[i][0] += 0.5*v[0];
+ vatom[i][1] += 0.5*v[1];
+ vatom[i][2] += 0.5*v[2];
+ vatom[i][3] += 0.5*v[3];
+ vatom[i][4] += 0.5*v[4];
+ vatom[i][5] += 0.5*v[5];
}
if (newton_bond || j < nlocal) {
- vatom[j][0] += 0.5*v[0];
- vatom[j][1] += 0.5*v[1];
- vatom[j][2] += 0.5*v[2];
- vatom[j][3] += 0.5*v[3];
- vatom[j][4] += 0.5*v[4];
- vatom[j][5] += 0.5*v[5];
+ vatom[j][0] += 0.5*v[0];
+ vatom[j][1] += 0.5*v[1];
+ vatom[j][2] += 0.5*v[2];
+ vatom[j][3] += 0.5*v[3];
+ vatom[j][4] += 0.5*v[4];
+ vatom[j][5] += 0.5*v[5];
}
}
}
diff --git a/src/bond.h b/src/bond.h
index 7c055d4174f57a9c7fe935d45889880c4fd8e98d..e2a977d5a89df7bf30d7b49f5b9d1d9302d5c463 100644
--- a/src/bond.h
+++ b/src/bond.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/bond_hybrid.cpp b/src/bond_hybrid.cpp
index c85c15b02ac6cb402dd47236fb228cb7b022d533..1d853b7fecc6c3893068478b47de4b0052442de5 100644
--- a/src/bond_hybrid.cpp
+++ b/src/bond_hybrid.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -80,9 +80,9 @@ void BondHybrid::compute(int eflag, int vflag)
}
for (m = 0; m < nstyles; m++) {
if (nbondlist[m] > maxbond[m]) {
- memory->destroy(bondlist[m]);
- maxbond[m] = nbondlist[m] + EXTRA;
- memory->create(bondlist[m],maxbond[m],3,"bond_hybrid:bondlist");
+ memory->destroy(bondlist[m]);
+ maxbond[m] = nbondlist[m] + EXTRA;
+ memory->create(bondlist[m],maxbond[m],3,"bond_hybrid:bondlist");
}
nbondlist[m] = 0;
}
@@ -96,7 +96,7 @@ void BondHybrid::compute(int eflag, int vflag)
nbondlist[m]++;
}
}
-
+
// call each sub-style's compute function
// set neighbor->bondlist to sub-style bondlist before call
// accumulate sub-style global/peratom energy/virial in hybrid
@@ -124,8 +124,8 @@ void BondHybrid::compute(int eflag, int vflag)
if (force->newton_bond) n += atom->nghost;
double **vatom_substyle = styles[m]->vatom;
for (i = 0; i < n; i++)
- for (j = 0; j < 6; j++)
- vatom[i][j] += vatom_substyle[i][j];
+ for (j = 0; j < 6; j++)
+ vatom[i][j] += vatom_substyle[i][j];
}
}
@@ -212,11 +212,11 @@ void BondHybrid::settings(int narg, char **arg)
while (i < narg) {
for (m = 0; m < nstyles; m++)
- if (strcmp(arg[i],keywords[m]) == 0)
- error->all(FLERR,"Bond style hybrid cannot use same pair style twice");
- if (strcmp(arg[i],"hybrid") == 0)
+ if (strcmp(arg[i],keywords[m]) == 0)
+ error->all(FLERR,"Bond style hybrid cannot use same pair style twice");
+ if (strcmp(arg[i],"hybrid") == 0)
error->all(FLERR,"Bond style hybrid cannot have hybrid as an argument");
- if (strcmp(arg[i],"none") == 0)
+ if (strcmp(arg[i],"none") == 0)
error->all(FLERR,"Bond style hybrid cannot have none as an argument");
styles[nstyles] = force->new_bond(arg[i],lmp->suffix,dummy);
keywords[nstyles] = new char[strlen(arg[i])+1];
@@ -277,17 +277,17 @@ void BondHybrid::coeff(int narg, char **arg)
void BondHybrid::init_style()
{
- for (int m = 0; m < nstyles; m++)
+ for (int m = 0; m < nstyles; m++)
if (styles[m]) styles[m]->init_style();
}
/* ----------------------------------------------------------------------
- return an equilbrium bond length
+ return an equilbrium bond length
------------------------------------------------------------------------- */
double BondHybrid::equilibrium_distance(int i)
{
- if (map[i] < 0)
+ if (map[i] < 0)
error->one(FLERR,"Invoked bond equil distance on bond style none");
return styles[map[i]]->equilibrium_distance(i);
}
diff --git a/src/bond_hybrid.h b/src/bond_hybrid.h
index 058524161eba5d08d81c102d4b1710b7319af011..57c82b0e637050774273185803a241a10fe11452 100644
--- a/src/bond_hybrid.h
+++ b/src/bond_hybrid.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -51,7 +51,7 @@ class BondHybrid : public Bond {
int *nbondlist; // # of bonds in sub-style bondlists
int *maxbond; // max # of bonds sub-style lists can store
int ***bondlist; // bondlist for each sub-style
-
+
void allocate();
};
diff --git a/src/change_box.cpp b/src/change_box.cpp
index 84f7e773da3608df85ef90f102ed177c83884fbc..ddce444e1b8b92d12404b9a2e6785e99f30cc0a7 100644
--- a/src/change_box.cpp
+++ b/src/change_box.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -44,12 +44,12 @@ void ChangeBox::command(int narg, char **arg)
{
int i;
- if (domain->box_exist == 0)
+ if (domain->box_exist == 0)
error->all(FLERR,"Change_box command before simulation box is defined");
if (narg < 2) error->all(FLERR,"Illegal change_box command");
- if (modify->nfix_restart_peratom)
+ if (modify->nfix_restart_peratom)
error->all(FLERR,"Cannot change_box after "
- "reading restart file with per-atom info");
+ "reading restart file with per-atom info");
if (comm->me == 0 && screen) fprintf(screen,"Changing box ...\n");
@@ -72,7 +72,7 @@ void ChangeBox::command(int narg, char **arg)
int iarg = 1;
while (iarg < narg) {
if (strcmp(arg[iarg],"x") == 0 || strcmp(arg[iarg],"y") == 0 ||
- strcmp(arg[iarg],"z") == 0) {
+ strcmp(arg[iarg],"z") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal change_box command");
ops[nops].style = XYZ;
if (strcmp(arg[iarg],"x") == 0) ops[nops].dim = X;
@@ -80,45 +80,45 @@ void ChangeBox::command(int narg, char **arg)
else if (strcmp(arg[iarg],"z") == 0) ops[nops].dim = Z;
if (dimension == 2 && ops[nops].dim == Z)
- error->all(FLERR,"Cannot change_box in z dimension for 2d simulation");
+ error->all(FLERR,"Cannot change_box in z dimension for 2d simulation");
if (strcmp(arg[iarg+1],"final") == 0) {
- if (iarg+4 > narg) error->all(FLERR,"Illegal change_box command");
- ops[nops].flavor = FINAL;
- ops[nops].flo = atof(arg[iarg+2]);
- ops[nops].fhi = atof(arg[iarg+3]);
- ops[nops].vdim1 = ops[nops].vdim2 = -1;
- nops++;
- iarg += 4;
+ if (iarg+4 > narg) error->all(FLERR,"Illegal change_box command");
+ ops[nops].flavor = FINAL;
+ ops[nops].flo = atof(arg[iarg+2]);
+ ops[nops].fhi = atof(arg[iarg+3]);
+ ops[nops].vdim1 = ops[nops].vdim2 = -1;
+ nops++;
+ iarg += 4;
} else if (strcmp(arg[iarg+1],"delta") == 0) {
- if (iarg+4 > narg) error->all(FLERR,"Illegal change_box command");
- ops[nops].flavor = DELTA;
- ops[nops].dlo = atof(arg[iarg+2]);
- ops[nops].dhi = atof(arg[iarg+3]);
- ops[nops].vdim1 = ops[nops].vdim2 = -1;
- nops++;
- iarg += 4;
+ if (iarg+4 > narg) error->all(FLERR,"Illegal change_box command");
+ ops[nops].flavor = DELTA;
+ ops[nops].dlo = atof(arg[iarg+2]);
+ ops[nops].dhi = atof(arg[iarg+3]);
+ ops[nops].vdim1 = ops[nops].vdim2 = -1;
+ nops++;
+ iarg += 4;
} else if (strcmp(arg[iarg+1],"scale") == 0) {
- if (iarg+3 > narg) error->all(FLERR,"Illegal change_box command");
- ops[nops].flavor = SCALE;
- ops[nops].scale = atof(arg[iarg+2]);
- ops[nops].vdim1 = ops[nops].vdim2 = -1;
- nops++;
- iarg += 3;
+ if (iarg+3 > narg) error->all(FLERR,"Illegal change_box command");
+ ops[nops].flavor = SCALE;
+ ops[nops].scale = atof(arg[iarg+2]);
+ ops[nops].vdim1 = ops[nops].vdim2 = -1;
+ nops++;
+ iarg += 3;
} else if (strcmp(arg[iarg+1],"volume") == 0) {
- if (nops == 0 || ops[nops-1].style != XYZ ||
- ops[nops].dim == ops[nops-1].dim)
- error->all(FLERR,"Change_box volume used incorrectly");
- if (ops[nops-1].vdim2 >= 0)
- error->all(FLERR,"Change_box volume used incorrectly");
- else if (ops[nops-1].vdim1 >= 0) ops[nops-1].vdim2 = ops[nops].dim;
- else ops[nops-1].vdim1 = ops[nops].dim;
- iarg += 2;
+ if (nops == 0 || ops[nops-1].style != XYZ ||
+ ops[nops].dim == ops[nops-1].dim)
+ error->all(FLERR,"Change_box volume used incorrectly");
+ if (ops[nops-1].vdim2 >= 0)
+ error->all(FLERR,"Change_box volume used incorrectly");
+ else if (ops[nops-1].vdim1 >= 0) ops[nops-1].vdim2 = ops[nops].dim;
+ else ops[nops-1].vdim1 = ops[nops].dim;
+ iarg += 2;
} else error->all(FLERR,"Illegal change_box command");
} else if (strcmp(arg[iarg],"xy") == 0 || strcmp(arg[iarg],"xz") == 0 ||
- strcmp(arg[iarg],"yz") == 0) {
+ strcmp(arg[iarg],"yz") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal change_box command");
ops[nops].style = TILT;
if (strcmp(arg[iarg],"xy") == 0) ops[nops].dim = XY;
@@ -126,20 +126,20 @@ void ChangeBox::command(int narg, char **arg)
else if (strcmp(arg[iarg],"yz") == 0) ops[nops].dim = YZ;
if (dimension == 2 && (ops[nops].dim == XZ || ops[nops].dim == YZ))
- error->all(FLERR,"Cannot change_box in xz or yz for 2d simulation");
+ error->all(FLERR,"Cannot change_box in xz or yz for 2d simulation");
if (strcmp(arg[iarg+1],"final") == 0) {
- if (iarg+3 > narg) error->all(FLERR,"Illegal change_box command");
- ops[nops].flavor = FINAL;
- ops[nops].ftilt = atof(arg[iarg+2]);
- nops++;
- iarg += 3;
+ if (iarg+3 > narg) error->all(FLERR,"Illegal change_box command");
+ ops[nops].flavor = FINAL;
+ ops[nops].ftilt = atof(arg[iarg+2]);
+ nops++;
+ iarg += 3;
} else if (strcmp(arg[iarg+1],"delta") == 0) {
- if (iarg+3 > narg) error->all(FLERR,"Illegal change_box command");
- ops[nops].flavor = DELTA;
- ops[nops].dtilt = atof(arg[iarg+2]);
- nops++;
- iarg += 3;
+ if (iarg+3 > narg) error->all(FLERR,"Illegal change_box command");
+ ops[nops].flavor = DELTA;
+ ops[nops].dtilt = atof(arg[iarg+2]);
+ nops++;
+ iarg += 3;
} else error->all(FLERR,"Illegal change_box command");
} else if (strcmp(arg[iarg],"boundary") == 0) {
@@ -216,85 +216,85 @@ void ChangeBox::command(int narg, char **arg)
else volume = domain->xprd * domain->yprd * domain->zprd;
if (ops[i].flavor == FINAL) {
- domain->boxlo[ops[i].dim] = scale[ops[i].dim]*ops[i].flo;
- domain->boxhi[ops[i].dim] = scale[ops[i].dim]*ops[i].fhi;
- if (ops[i].vdim1 >= 0)
- volume_preserve(ops[i].vdim1,ops[i].vdim2,volume);
- domain->set_initial_box();
- domain->set_global_box();
- domain->set_local_box();
- domain->print_box(" ");
+ domain->boxlo[ops[i].dim] = scale[ops[i].dim]*ops[i].flo;
+ domain->boxhi[ops[i].dim] = scale[ops[i].dim]*ops[i].fhi;
+ if (ops[i].vdim1 >= 0)
+ volume_preserve(ops[i].vdim1,ops[i].vdim2,volume);
+ domain->set_initial_box();
+ domain->set_global_box();
+ domain->set_local_box();
+ domain->print_box(" ");
} else if (ops[i].flavor == DELTA) {
- domain->boxlo[ops[i].dim] += scale[ops[i].dim]*ops[i].dlo;
- domain->boxhi[ops[i].dim] += scale[ops[i].dim]*ops[i].dhi;
- if (ops[i].vdim1 >= 0)
- volume_preserve(ops[i].vdim1,ops[i].vdim2,volume);
- domain->set_initial_box();
- domain->set_global_box();
- domain->set_local_box();
- domain->print_box(" ");
+ domain->boxlo[ops[i].dim] += scale[ops[i].dim]*ops[i].dlo;
+ domain->boxhi[ops[i].dim] += scale[ops[i].dim]*ops[i].dhi;
+ if (ops[i].vdim1 >= 0)
+ volume_preserve(ops[i].vdim1,ops[i].vdim2,volume);
+ domain->set_initial_box();
+ domain->set_global_box();
+ domain->set_local_box();
+ domain->print_box(" ");
} else if (ops[i].flavor == SCALE) {
- double mid = 0.5 *
- (domain->boxlo[ops[i].dim] + domain->boxhi[ops[i].dim]);
- double delta = domain->boxlo[ops[i].dim] - mid;
- domain->boxlo[ops[i].dim] = mid + ops[i].scale*delta;
- delta = domain->boxhi[ops[i].dim] - mid;
- domain->boxhi[ops[i].dim] = mid + ops[i].scale*delta;
- if (ops[i].vdim1 >= 0)
- volume_preserve(ops[i].vdim1,ops[i].vdim2,volume);
- domain->set_initial_box();
- domain->set_global_box();
- domain->set_local_box();
- domain->print_box(" ");
+ double mid = 0.5 *
+ (domain->boxlo[ops[i].dim] + domain->boxhi[ops[i].dim]);
+ double delta = domain->boxlo[ops[i].dim] - mid;
+ domain->boxlo[ops[i].dim] = mid + ops[i].scale*delta;
+ delta = domain->boxhi[ops[i].dim] - mid;
+ domain->boxhi[ops[i].dim] = mid + ops[i].scale*delta;
+ if (ops[i].vdim1 >= 0)
+ volume_preserve(ops[i].vdim1,ops[i].vdim2,volume);
+ domain->set_initial_box();
+ domain->set_global_box();
+ domain->set_local_box();
+ domain->print_box(" ");
}
} else if (ops[i].style == TILT) {
if (domain->triclinic == 0)
- error->all(FLERR,"Cannot change box tilt factors for orthogonal box");
-
+ error->all(FLERR,"Cannot change box tilt factors for orthogonal box");
+
if (ops[i].flavor == FINAL) {
- if (ops[i].dim == XY) domain->xy = scale[X]*ops[i].ftilt;
- else if (ops[i].dim == XZ) domain->xz = scale[X]*ops[i].ftilt;
- else if (ops[i].dim == YZ) domain->yz = scale[Y]*ops[i].ftilt;
- domain->set_initial_box();
- domain->set_global_box();
- domain->set_local_box();
- domain->print_box(" ");
+ if (ops[i].dim == XY) domain->xy = scale[X]*ops[i].ftilt;
+ else if (ops[i].dim == XZ) domain->xz = scale[X]*ops[i].ftilt;
+ else if (ops[i].dim == YZ) domain->yz = scale[Y]*ops[i].ftilt;
+ domain->set_initial_box();
+ domain->set_global_box();
+ domain->set_local_box();
+ domain->print_box(" ");
} else if (ops[i].flavor == DELTA) {
- if (ops[i].dim == XY) domain->xy += scale[X]*ops[i].dtilt;
- else if (ops[i].dim == XZ) domain->xz += scale[X]*ops[i].dtilt;
- else if (ops[i].dim == YZ) domain->yz += scale[Y]*ops[i].dtilt;
- domain->set_initial_box();
- domain->set_global_box();
- domain->set_local_box();
- domain->print_box(" ");
+ if (ops[i].dim == XY) domain->xy += scale[X]*ops[i].dtilt;
+ else if (ops[i].dim == XZ) domain->xz += scale[X]*ops[i].dtilt;
+ else if (ops[i].dim == YZ) domain->yz += scale[Y]*ops[i].dtilt;
+ domain->set_initial_box();
+ domain->set_global_box();
+ domain->set_local_box();
+ domain->print_box(" ");
}
} else if (ops[i].style == BOUNDARY) {
domain->set_boundary(3,&arg[ops[i].boundindex],1);
if (domain->dimension == 2 && domain->zperiodic == 0)
- error->all(FLERR,
- "Cannot change box z boundary to "
- "nonperiodic for a 2d simulation");
+ error->all(FLERR,
+ "Cannot change box z boundary to "
+ "nonperiodic for a 2d simulation");
domain->set_initial_box();
domain->set_global_box();
domain->set_local_box();
-
+
} else if (ops[i].style == ORTHO) {
if (domain->xy != 0.0 || domain->yz != 0.0 || domain->xz != 0.0)
- error->all(FLERR,
- "Cannot change box to orthogonal when tilt is non-zero");
+ error->all(FLERR,
+ "Cannot change box to orthogonal when tilt is non-zero");
if (output->ndump)
- error->all(FLERR,
- "Cannot change box ortho/triclinic with dumps defined");
+ error->all(FLERR,
+ "Cannot change box ortho/triclinic with dumps defined");
for (int i = 0; i < modify->nfix; i++)
- if (modify->fix[i]->no_change_box)
- error->all(FLERR,
- "Cannot change box ortho/triclinic with "
- "certain fixes defined");
+ if (modify->fix[i]->no_change_box)
+ error->all(FLERR,
+ "Cannot change box ortho/triclinic with "
+ "certain fixes defined");
domain->triclinic = 0;
domain->set_initial_box();
domain->set_global_box();
@@ -303,13 +303,13 @@ void ChangeBox::command(int narg, char **arg)
} else if (ops[i].style == TRICLINIC) {
if (output->ndump)
- error->all(FLERR,
- "Cannot change box ortho/triclinic with dumps defined");
+ error->all(FLERR,
+ "Cannot change box ortho/triclinic with dumps defined");
for (int i = 0; i < modify->nfix; i++)
- if (modify->fix[i]->no_change_box)
- error->all(FLERR,
- "Cannot change box ortho/triclinic with "
- "certain fixes defined");
+ if (modify->fix[i]->no_change_box)
+ error->all(FLERR,
+ "Cannot change box ortho/triclinic with "
+ "certain fixes defined");
domain->triclinic = 1;
domain->set_lamda_box();
domain->set_initial_box();
@@ -329,14 +329,14 @@ void ChangeBox::command(int narg, char **arg)
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
-
+
for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit)
- domain->x2lamda(x[i],x[i],boxlo,h_inv);
-
+ if (mask[i] & groupbit)
+ domain->x2lamda(x[i],x[i],boxlo,h_inv);
+
for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit)
- domain->lamda2x(x[i],x[i]);
+ if (mask[i] & groupbit)
+ domain->lamda2x(x[i],x[i]);
save_box_state();
}
@@ -374,8 +374,8 @@ void ChangeBox::command(int narg, char **arg)
MPI_Allreduce(&nblocal,&natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);
if (natoms != atom->natoms && comm->me == 0) {
char str[128];
- sprintf(str,"Lost atoms via change_box: original " BIGINT_FORMAT
- " current " BIGINT_FORMAT,atom->natoms,natoms);
+ sprintf(str,"Lost atoms via change_box: original " BIGINT_FORMAT
+ " current " BIGINT_FORMAT,atom->natoms,natoms);
error->warning(FLERR,str);
}
}
diff --git a/src/change_box.h b/src/change_box.h
index 10c3810aa49eac24acea25e59386283061d97ca6..4592cf7031d65817ca65d4ce7fc5567a96a73fbb 100644
--- a/src/change_box.h
+++ b/src/change_box.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/comm.cpp b/src/comm.cpp
index 49ba0cad7154f1cde9f94be70729bdc3e3511023..69d096e873a6af08747a6729e2da9db36ec7bd02 100644
--- a/src/comm.cpp
+++ b/src/comm.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -57,7 +57,7 @@ enum{ONELEVEL,TWOLEVEL,NUMA,CUSTOM};
enum{CART,CARTREORDER,XYZ};
/* ----------------------------------------------------------------------
- setup MPI and allocate buffer space
+ setup MPI and allocate buffer space
------------------------------------------------------------------------- */
Comm::Comm(LAMMPS *lmp) : Pointers(lmp)
@@ -162,11 +162,11 @@ void Comm::set_proc_grid()
MPI_Status status;
if (me == 0) {
MPI_Recv(other_procgrid,3,MPI_INT,
- universe->root_proc[recv_from_partition],0,
- universe->uworld,&status);
+ universe->root_proc[recv_from_partition],0,
+ universe->uworld,&status);
MPI_Recv(other_coregrid,3,MPI_INT,
- universe->root_proc[recv_from_partition],0,
- universe->uworld,&status);
+ universe->root_proc[recv_from_partition],0,
+ universe->uworld,&status);
}
MPI_Bcast(other_procgrid,3,MPI_INT,0,world);
MPI_Bcast(other_coregrid,3,MPI_INT,0,world);
@@ -181,12 +181,12 @@ void Comm::set_proc_grid()
if (gridflag == ONELEVEL) {
pmap->onelevel_grid(nprocs,user_procgrid,procgrid,
- otherflag,other_style,other_procgrid,other_coregrid);
+ otherflag,other_style,other_procgrid,other_coregrid);
} else if (gridflag == TWOLEVEL) {
pmap->twolevel_grid(nprocs,user_procgrid,procgrid,
- ncores,user_coregrid,coregrid,
- otherflag,other_style,other_procgrid,other_coregrid);
+ ncores,user_coregrid,coregrid,
+ otherflag,other_style,other_procgrid,other_coregrid);
} else if (gridflag == NUMA) {
pmap->numa_grid(nprocs,user_procgrid,procgrid,coregrid);
@@ -207,7 +207,7 @@ void Comm::set_proc_grid()
if (grid2proc) memory->destroy(grid2proc);
memory->create(grid2proc,procgrid[0],procgrid[1],procgrid[2],
- "comm:grid2proc");
+ "comm:grid2proc");
// map processor IDs to 3d processor grid
// produces myloc, procneigh, grid2proc
@@ -227,7 +227,7 @@ void Comm::set_proc_grid()
pmap->cart_map(1,procgrid,ncores,coregrid,myloc,procneigh,grid2proc);
else if (mapflag == XYZ)
pmap->xyz_map(xyz,procgrid,ncores,coregrid,myloc,procneigh,grid2proc);
-
+
} else if (gridflag == NUMA) {
pmap->numa_map(0,coregrid,myloc,procneigh,grid2proc);
@@ -240,17 +240,17 @@ void Comm::set_proc_grid()
if (me == 0) {
if (screen) {
fprintf(screen," %d by %d by %d MPI processor grid\n",
- procgrid[0],procgrid[1],procgrid[2]);
- if (gridflag == NUMA || gridflag == TWOLEVEL)
- fprintf(screen," %d by %d by %d core grid within node\n",
- coregrid[0],coregrid[1],coregrid[2]);
+ procgrid[0],procgrid[1],procgrid[2]);
+ if (gridflag == NUMA || gridflag == TWOLEVEL)
+ fprintf(screen," %d by %d by %d core grid within node\n",
+ coregrid[0],coregrid[1],coregrid[2]);
}
if (logfile) {
fprintf(logfile," %d by %d by %d MPI processor grid\n",
- procgrid[0],procgrid[1],procgrid[2]);
- if (gridflag == NUMA || gridflag == TWOLEVEL)
- fprintf(logfile," %d by %d by %d core grid within node\n",
- coregrid[0],coregrid[1],coregrid[2]);
+ procgrid[0],procgrid[1],procgrid[2]);
+ if (gridflag == NUMA || gridflag == TWOLEVEL)
+ fprintf(logfile," %d by %d by %d core grid within node\n",
+ coregrid[0],coregrid[1],coregrid[2]);
}
}
@@ -288,11 +288,11 @@ void Comm::set_proc_grid()
if (send_to_partition >= 0) {
if (me == 0) {
MPI_Send(procgrid,3,MPI_INT,
- universe->root_proc[send_to_partition],0,
- universe->uworld);
+ universe->root_proc[send_to_partition],0,
+ universe->uworld);
MPI_Send(coregrid,3,MPI_INT,
- universe->root_proc[send_to_partition],0,
- universe->uworld);
+ universe->root_proc[send_to_partition],0,
+ universe->uworld);
}
}
}
@@ -383,7 +383,7 @@ void Comm::setup()
int i;
int ntypes = atom->ntypes;
double *prd,*sublo,*subhi;
-
+
double cut = MAX(neighbor->cutneighmax,cutghostuser);
if (triclinic == 0) {
@@ -395,8 +395,8 @@ void Comm::setup()
if (style == MULTI) {
double *cuttype = neighbor->cuttype;
for (i = 1; i <= ntypes; i++)
- cutghostmulti[i][0] = cutghostmulti[i][1] = cutghostmulti[i][2] =
- cuttype[i];
+ cutghostmulti[i][0] = cutghostmulti[i][1] = cutghostmulti[i][2] =
+ cuttype[i];
}
} else {
@@ -415,9 +415,9 @@ void Comm::setup()
if (style == MULTI) {
double *cuttype = neighbor->cuttype;
for (i = 1; i <= ntypes; i++) {
- cutghostmulti[i][0] = cuttype[i] * length0;
- cutghostmulti[i][1] = cuttype[i] * length1;
- cutghostmulti[i][2] = cuttype[i] * length2;
+ cutghostmulti[i][0] = cuttype[i] * length0;
+ cutghostmulti[i][1] = cuttype[i] * length1;
+ cutghostmulti[i][2] = cuttype[i] * length2;
}
}
}
@@ -460,8 +460,8 @@ void Comm::setup()
right = myloc[0] + 1;
if (right == procgrid[0]) right = 0;
sendneed[0][1] = MIN(maxneed[0],right);
- } else recvneed[0][0] = recvneed[0][1] =
- sendneed[0][0] = sendneed[0][1] = maxneed[0];
+ } else recvneed[0][0] = recvneed[0][1] =
+ sendneed[0][0] = sendneed[0][1] = maxneed[0];
if (!periodicity[1]) {
recvneed[1][0] = MIN(maxneed[1],myloc[1]);
@@ -472,8 +472,8 @@ void Comm::setup()
right = myloc[1] + 1;
if (right == procgrid[1]) right = 0;
sendneed[1][1] = MIN(maxneed[1],right);
- } else recvneed[1][0] = recvneed[1][1] =
- sendneed[1][0] = sendneed[1][1] = maxneed[1];
+ } else recvneed[1][0] = recvneed[1][1] =
+ sendneed[1][0] = sendneed[1][1] = maxneed[1];
if (!periodicity[2]) {
recvneed[2][0] = MIN(maxneed[2],myloc[2]);
@@ -484,8 +484,8 @@ void Comm::setup()
right = myloc[2] + 1;
if (right == procgrid[2]) right = 0;
sendneed[2][1] = MIN(maxneed[2],right);
- } else recvneed[2][0] = recvneed[2][1] =
- sendneed[2][0] = sendneed[2][1] = maxneed[2];
+ } else recvneed[2][0] = recvneed[2][1] =
+ sendneed[2][0] = sendneed[2][1] = maxneed[2];
} else {
recvneed[0][0] = updown(0,0,myloc[0],prd[0],periodicity[0],xsplit);
@@ -506,7 +506,7 @@ void Comm::setup()
if (right == procgrid[1]) right = 0;
sendneed[1][1] = updown(1,0,right,prd[1],periodicity[1],ysplit);
- if (domain->dimension == 3) {
+ if (domain->dimension == 3) {
recvneed[2][0] = updown(2,0,myloc[2],prd[2],periodicity[2],zsplit);
recvneed[2][1] = updown(2,1,myloc[2],prd[2],periodicity[2],zsplit);
left = myloc[2] - 1;
@@ -515,8 +515,8 @@ void Comm::setup()
right = myloc[2] + 1;
if (right == procgrid[2]) right = 0;
sendneed[2][1] = updown(2,0,right,prd[2],periodicity[2],zsplit);
- } else recvneed[2][0] = recvneed[2][1] =
- sendneed[2][0] = sendneed[2][1] = 0;
+ } else recvneed[2][0] = recvneed[2][1] =
+ sendneed[2][0] = sendneed[2][1] = 0;
int all[6];
MPI_Allreduce(&recvneed[0][0],all,6,MPI_INT,MPI_MAX,world);
@@ -554,55 +554,55 @@ void Comm::setup()
for (ineed = 0; ineed < 2*maxneed[dim]; ineed++) {
pbc_flag[iswap] = 0;
pbc[iswap][0] = pbc[iswap][1] = pbc[iswap][2] =
- pbc[iswap][3] = pbc[iswap][4] = pbc[iswap][5] = 0;
-
+ pbc[iswap][3] = pbc[iswap][4] = pbc[iswap][5] = 0;
+
if (ineed % 2 == 0) {
- sendproc[iswap] = procneigh[dim][0];
- recvproc[iswap] = procneigh[dim][1];
- if (style == SINGLE) {
- if (ineed < 2) slablo[iswap] = -BIG;
- else slablo[iswap] = 0.5 * (sublo[dim] + subhi[dim]);
- slabhi[iswap] = sublo[dim] + cutghost[dim];
- } else {
- for (i = 1; i <= ntypes; i++) {
- if (ineed < 2) multilo[iswap][i] = -BIG;
- else multilo[iswap][i] = 0.5 * (sublo[dim] + subhi[dim]);
- multihi[iswap][i] = sublo[dim] + cutghostmulti[i][dim];
- }
- }
- if (myloc[dim] == 0) {
- pbc_flag[iswap] = 1;
- pbc[iswap][dim] = 1;
- if (triclinic) {
- if (dim == 1) pbc[iswap][5] = 1;
- else if (dim == 2) pbc[iswap][4] = pbc[iswap][3] = 1;
- }
- }
-
+ sendproc[iswap] = procneigh[dim][0];
+ recvproc[iswap] = procneigh[dim][1];
+ if (style == SINGLE) {
+ if (ineed < 2) slablo[iswap] = -BIG;
+ else slablo[iswap] = 0.5 * (sublo[dim] + subhi[dim]);
+ slabhi[iswap] = sublo[dim] + cutghost[dim];
+ } else {
+ for (i = 1; i <= ntypes; i++) {
+ if (ineed < 2) multilo[iswap][i] = -BIG;
+ else multilo[iswap][i] = 0.5 * (sublo[dim] + subhi[dim]);
+ multihi[iswap][i] = sublo[dim] + cutghostmulti[i][dim];
+ }
+ }
+ if (myloc[dim] == 0) {
+ pbc_flag[iswap] = 1;
+ pbc[iswap][dim] = 1;
+ if (triclinic) {
+ if (dim == 1) pbc[iswap][5] = 1;
+ else if (dim == 2) pbc[iswap][4] = pbc[iswap][3] = 1;
+ }
+ }
+
} else {
- sendproc[iswap] = procneigh[dim][1];
- recvproc[iswap] = procneigh[dim][0];
- if (style == SINGLE) {
- slablo[iswap] = subhi[dim] - cutghost[dim];
- if (ineed < 2) slabhi[iswap] = BIG;
- else slabhi[iswap] = 0.5 * (sublo[dim] + subhi[dim]);
- } else {
- for (i = 1; i <= ntypes; i++) {
- multilo[iswap][i] = subhi[dim] - cutghostmulti[i][dim];
- if (ineed < 2) multihi[iswap][i] = BIG;
- else multihi[iswap][i] = 0.5 * (sublo[dim] + subhi[dim]);
- }
- }
- if (myloc[dim] == procgrid[dim]-1) {
- pbc_flag[iswap] = 1;
- pbc[iswap][dim] = -1;
- if (triclinic) {
- if (dim == 1) pbc[iswap][5] = -1;
- else if (dim == 2) pbc[iswap][4] = pbc[iswap][3] = -1;
- }
- }
+ sendproc[iswap] = procneigh[dim][1];
+ recvproc[iswap] = procneigh[dim][0];
+ if (style == SINGLE) {
+ slablo[iswap] = subhi[dim] - cutghost[dim];
+ if (ineed < 2) slabhi[iswap] = BIG;
+ else slabhi[iswap] = 0.5 * (sublo[dim] + subhi[dim]);
+ } else {
+ for (i = 1; i <= ntypes; i++) {
+ multilo[iswap][i] = subhi[dim] - cutghostmulti[i][dim];
+ if (ineed < 2) multihi[iswap][i] = BIG;
+ else multihi[iswap][i] = 0.5 * (sublo[dim] + subhi[dim]);
+ }
+ }
+ if (myloc[dim] == procgrid[dim]-1) {
+ pbc_flag[iswap] = 1;
+ pbc[iswap][dim] = -1;
+ if (triclinic) {
+ if (dim == 1) pbc[iswap][5] = -1;
+ else if (dim == 2) pbc[iswap][4] = pbc[iswap][3] = -1;
+ }
+ }
}
-
+
iswap++;
}
}
@@ -617,8 +617,8 @@ void Comm::setup()
return how many procs away are needed to encompass cutghost away from loc
------------------------------------------------------------------------- */
-int Comm::updown(int dim, int dir, int loc,
- double prd, int periodicity, double *split)
+int Comm::updown(int dim, int dir, int loc,
+ double prd, int periodicity, double *split)
{
int index,count;
double frac,delta;
@@ -630,8 +630,8 @@ int Comm::updown(int dim, int dir, int loc,
count = 0;
while (delta < frac) {
if (index < 0) {
- if (!periodicity) break;
- index = procgrid[dim] - 1;
+ if (!periodicity) break;
+ index = procgrid[dim] - 1;
}
count++;
delta += split[index+1] - split[index];
@@ -645,8 +645,8 @@ int Comm::updown(int dim, int dir, int loc,
count = 0;
while (delta < frac) {
if (index >= procgrid[dim]) {
- if (!periodicity) break;
- index = 0;
+ if (!periodicity) break;
+ index = 0;
}
count++;
delta += split[index+1] - split[index];
@@ -655,7 +655,7 @@ int Comm::updown(int dim, int dir, int loc,
}
return count;
-}
+}
/* ----------------------------------------------------------------------
forward communication of atom coords every timestep
@@ -678,59 +678,59 @@ void Comm::forward_comm(int dummy)
for (int iswap = 0; iswap < nswap; iswap++) {
if (sendproc[iswap] != me) {
if (comm_x_only) {
- if (size_forward_recv[iswap]) buf = x[firstrecv[iswap]];
- else buf = NULL;
- if (size_forward_recv[iswap])
- MPI_Irecv(buf,size_forward_recv[iswap],MPI_DOUBLE,
- recvproc[iswap],0,world,&request);
- n = avec->pack_comm(sendnum[iswap],sendlist[iswap],
- buf_send,pbc_flag[iswap],pbc[iswap]);
- if (n) MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap],0,world);
- if (size_forward_recv[iswap]) MPI_Wait(&request,&status);
+ if (size_forward_recv[iswap]) buf = x[firstrecv[iswap]];
+ else buf = NULL;
+ if (size_forward_recv[iswap])
+ MPI_Irecv(buf,size_forward_recv[iswap],MPI_DOUBLE,
+ recvproc[iswap],0,world,&request);
+ n = avec->pack_comm(sendnum[iswap],sendlist[iswap],
+ buf_send,pbc_flag[iswap],pbc[iswap]);
+ if (n) MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap],0,world);
+ if (size_forward_recv[iswap]) MPI_Wait(&request,&status);
} else if (ghost_velocity) {
- if (size_forward_recv[iswap])
- MPI_Irecv(buf_recv,size_forward_recv[iswap],MPI_DOUBLE,
- recvproc[iswap],0,world,&request);
- n = avec->pack_comm_vel(sendnum[iswap],sendlist[iswap],
- buf_send,pbc_flag[iswap],pbc[iswap]);
- if (n) MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap],0,world);
- if (size_forward_recv[iswap]) MPI_Wait(&request,&status);
- avec->unpack_comm_vel(recvnum[iswap],firstrecv[iswap],buf_recv);
+ if (size_forward_recv[iswap])
+ MPI_Irecv(buf_recv,size_forward_recv[iswap],MPI_DOUBLE,
+ recvproc[iswap],0,world,&request);
+ n = avec->pack_comm_vel(sendnum[iswap],sendlist[iswap],
+ buf_send,pbc_flag[iswap],pbc[iswap]);
+ if (n) MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap],0,world);
+ if (size_forward_recv[iswap]) MPI_Wait(&request,&status);
+ avec->unpack_comm_vel(recvnum[iswap],firstrecv[iswap],buf_recv);
} else {
- if (size_forward_recv[iswap])
- MPI_Irecv(buf_recv,size_forward_recv[iswap],MPI_DOUBLE,
- recvproc[iswap],0,world,&request);
- n = avec->pack_comm(sendnum[iswap],sendlist[iswap],
- buf_send,pbc_flag[iswap],pbc[iswap]);
- if (n) MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap],0,world);
- if (size_forward_recv[iswap]) MPI_Wait(&request,&status);
- avec->unpack_comm(recvnum[iswap],firstrecv[iswap],buf_recv);
+ if (size_forward_recv[iswap])
+ MPI_Irecv(buf_recv,size_forward_recv[iswap],MPI_DOUBLE,
+ recvproc[iswap],0,world,&request);
+ n = avec->pack_comm(sendnum[iswap],sendlist[iswap],
+ buf_send,pbc_flag[iswap],pbc[iswap]);
+ if (n) MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap],0,world);
+ if (size_forward_recv[iswap]) MPI_Wait(&request,&status);
+ avec->unpack_comm(recvnum[iswap],firstrecv[iswap],buf_recv);
}
} else {
if (comm_x_only) {
- if (sendnum[iswap])
- n = avec->pack_comm(sendnum[iswap],sendlist[iswap],
- x[firstrecv[iswap]],pbc_flag[iswap],
- pbc[iswap]);
+ if (sendnum[iswap])
+ n = avec->pack_comm(sendnum[iswap],sendlist[iswap],
+ x[firstrecv[iswap]],pbc_flag[iswap],
+ pbc[iswap]);
} else if (ghost_velocity) {
- n = avec->pack_comm_vel(sendnum[iswap],sendlist[iswap],
- buf_send,pbc_flag[iswap],pbc[iswap]);
- avec->unpack_comm_vel(recvnum[iswap],firstrecv[iswap],buf_send);
+ n = avec->pack_comm_vel(sendnum[iswap],sendlist[iswap],
+ buf_send,pbc_flag[iswap],pbc[iswap]);
+ avec->unpack_comm_vel(recvnum[iswap],firstrecv[iswap],buf_send);
} else {
- n = avec->pack_comm(sendnum[iswap],sendlist[iswap],
- buf_send,pbc_flag[iswap],pbc[iswap]);
- avec->unpack_comm(recvnum[iswap],firstrecv[iswap],buf_send);
+ n = avec->pack_comm(sendnum[iswap],sendlist[iswap],
+ buf_send,pbc_flag[iswap],pbc[iswap]);
+ avec->unpack_comm(recvnum[iswap],firstrecv[iswap],buf_send);
}
}
}
}
/* ----------------------------------------------------------------------
- reverse communication of forces on atoms every timestep
+ reverse communication of forces on atoms every timestep
other per-atom attributes may also be sent via pack/unpack routines
------------------------------------------------------------------------- */
-
+
void Comm::reverse_comm()
{
int n;
@@ -747,33 +747,33 @@ void Comm::reverse_comm()
for (int iswap = nswap-1; iswap >= 0; iswap--) {
if (sendproc[iswap] != me) {
if (comm_f_only) {
- if (size_reverse_recv[iswap])
- MPI_Irecv(buf_recv,size_reverse_recv[iswap],MPI_DOUBLE,
- sendproc[iswap],0,world,&request);
- if (size_reverse_send[iswap]) buf = f[firstrecv[iswap]];
- else buf = NULL;
- if (size_reverse_send[iswap])
- MPI_Send(buf,size_reverse_send[iswap],MPI_DOUBLE,
- recvproc[iswap],0,world);
- if (size_reverse_recv[iswap]) MPI_Wait(&request,&status);
+ if (size_reverse_recv[iswap])
+ MPI_Irecv(buf_recv,size_reverse_recv[iswap],MPI_DOUBLE,
+ sendproc[iswap],0,world,&request);
+ if (size_reverse_send[iswap]) buf = f[firstrecv[iswap]];
+ else buf = NULL;
+ if (size_reverse_send[iswap])
+ MPI_Send(buf,size_reverse_send[iswap],MPI_DOUBLE,
+ recvproc[iswap],0,world);
+ if (size_reverse_recv[iswap]) MPI_Wait(&request,&status);
} else {
- if (size_reverse_recv[iswap])
- MPI_Irecv(buf_recv,size_reverse_recv[iswap],MPI_DOUBLE,
- sendproc[iswap],0,world,&request);
- n = avec->pack_reverse(recvnum[iswap],firstrecv[iswap],buf_send);
- if (n) MPI_Send(buf_send,n,MPI_DOUBLE,recvproc[iswap],0,world);
- if (size_reverse_recv[iswap]) MPI_Wait(&request,&status);
+ if (size_reverse_recv[iswap])
+ MPI_Irecv(buf_recv,size_reverse_recv[iswap],MPI_DOUBLE,
+ sendproc[iswap],0,world,&request);
+ n = avec->pack_reverse(recvnum[iswap],firstrecv[iswap],buf_send);
+ if (n) MPI_Send(buf_send,n,MPI_DOUBLE,recvproc[iswap],0,world);
+ if (size_reverse_recv[iswap]) MPI_Wait(&request,&status);
}
avec->unpack_reverse(sendnum[iswap],sendlist[iswap],buf_recv);
} else {
if (comm_f_only) {
- if (sendnum[iswap])
- avec->unpack_reverse(sendnum[iswap],sendlist[iswap],
- f[firstrecv[iswap]]);
+ if (sendnum[iswap])
+ avec->unpack_reverse(sendnum[iswap],sendlist[iswap],
+ f[firstrecv[iswap]]);
} else {
- n = avec->pack_reverse(recvnum[iswap],firstrecv[iswap],buf_send);
- avec->unpack_reverse(sendnum[iswap],sendlist[iswap],buf_send);
+ n = avec->pack_reverse(recvnum[iswap],firstrecv[iswap],buf_send);
+ avec->unpack_reverse(sendnum[iswap],sendlist[iswap],buf_send);
}
}
}
@@ -801,7 +801,7 @@ void Comm::exchange()
AtomVec *avec = atom->avec;
// clear global->local map for owned and ghost atoms
- // b/c atoms migrate to new procs in exchange() and
+ // b/c atoms migrate to new procs in exchange() and
// new ghosts are created in borders()
// map_set() is done at end of borders()
@@ -832,10 +832,10 @@ void Comm::exchange()
while (i < nlocal) {
if (x[i][dim] < lo || x[i][dim] >= hi) {
- if (nsend > maxsend) grow_send(nsend,1);
- nsend += avec->pack_exchange(i,&buf_send[nsend]);
- avec->copy(nlocal-1,i,1);
- nlocal--;
+ if (nsend > maxsend) grow_send(nsend,1);
+ nsend += avec->pack_exchange(i,&buf_send[nsend]);
+ avec->copy(nlocal-1,i,1);
+ nlocal--;
} else i++;
}
atom->nlocal = nlocal;
@@ -851,27 +851,27 @@ void Comm::exchange()
} else {
MPI_Sendrecv(&nsend,1,MPI_INT,procneigh[dim][0],0,
- &nrecv1,1,MPI_INT,procneigh[dim][1],0,world,&status);
+ &nrecv1,1,MPI_INT,procneigh[dim][1],0,world,&status);
nrecv = nrecv1;
if (procgrid[dim] > 2) {
- MPI_Sendrecv(&nsend,1,MPI_INT,procneigh[dim][1],0,
- &nrecv2,1,MPI_INT,procneigh[dim][0],0,world,&status);
- nrecv += nrecv2;
+ MPI_Sendrecv(&nsend,1,MPI_INT,procneigh[dim][1],0,
+ &nrecv2,1,MPI_INT,procneigh[dim][0],0,world,&status);
+ nrecv += nrecv2;
}
if (nrecv > maxrecv) grow_recv(nrecv);
-
+
MPI_Irecv(buf_recv,nrecv1,MPI_DOUBLE,procneigh[dim][1],0,
- world,&request);
+ world,&request);
MPI_Send(buf_send,nsend,MPI_DOUBLE,procneigh[dim][0],0,world);
MPI_Wait(&request,&status);
-
+
if (procgrid[dim] > 2) {
- MPI_Irecv(&buf_recv[nrecv1],nrecv2,MPI_DOUBLE,procneigh[dim][0],0,
- world,&request);
- MPI_Send(buf_send,nsend,MPI_DOUBLE,procneigh[dim][1],0,world);
- MPI_Wait(&request,&status);
+ MPI_Irecv(&buf_recv[nrecv1],nrecv2,MPI_DOUBLE,procneigh[dim][0],0,
+ world,&request);
+ MPI_Send(buf_send,nsend,MPI_DOUBLE,procneigh[dim][1],0,world);
+ MPI_Wait(&request,&status);
}
-
+
buf = buf_recv;
}
@@ -934,16 +934,16 @@ void Comm::borders()
x = atom->x;
if (style == SINGLE) {
- lo = slablo[iswap];
- hi = slabhi[iswap];
+ lo = slablo[iswap];
+ hi = slabhi[iswap];
} else {
- type = atom->type;
- mlo = multilo[iswap];
- mhi = multihi[iswap];
+ type = atom->type;
+ mlo = multilo[iswap];
+ mhi = multihi[iswap];
}
if (ineed % 2 == 0) {
- nfirst = nlast;
- nlast = atom->nlocal + atom->nghost;
+ nfirst = nlast;
+ nlast = atom->nlocal + atom->nghost;
}
nsend = 0;
@@ -961,92 +961,92 @@ void Comm::borders()
// on these sends, break loop in two: owned (in group) and ghost
if (sendflag) {
- if (!bordergroup || ineed >= 2) {
- if (style == SINGLE) {
- for (i = nfirst; i < nlast; i++)
- if (x[i][dim] >= lo && x[i][dim] <= hi) {
- if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend);
- sendlist[iswap][nsend++] = i;
- }
- } else {
- for (i = nfirst; i < nlast; i++) {
- itype = type[i];
- if (x[i][dim] >= mlo[itype] && x[i][dim] <= mhi[itype]) {
- if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend);
- sendlist[iswap][nsend++] = i;
- }
- }
- }
-
- } else {
- if (style == SINGLE) {
- ngroup = atom->nfirst;
- for (i = 0; i < ngroup; i++)
- if (x[i][dim] >= lo && x[i][dim] <= hi) {
- if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend);
- sendlist[iswap][nsend++] = i;
- }
- for (i = atom->nlocal; i < nlast; i++)
- if (x[i][dim] >= lo && x[i][dim] <= hi) {
- if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend);
- sendlist[iswap][nsend++] = i;
- }
- } else {
- ngroup = atom->nfirst;
- for (i = 0; i < ngroup; i++) {
- itype = type[i];
- if (x[i][dim] >= mlo[itype] && x[i][dim] <= mhi[itype]) {
- if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend);
- sendlist[iswap][nsend++] = i;
- }
- }
- for (i = atom->nlocal; i < nlast; i++) {
- itype = type[i];
- if (x[i][dim] >= mlo[itype] && x[i][dim] <= mhi[itype]) {
- if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend);
- sendlist[iswap][nsend++] = i;
- }
- }
- }
- }
+ if (!bordergroup || ineed >= 2) {
+ if (style == SINGLE) {
+ for (i = nfirst; i < nlast; i++)
+ if (x[i][dim] >= lo && x[i][dim] <= hi) {
+ if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend);
+ sendlist[iswap][nsend++] = i;
+ }
+ } else {
+ for (i = nfirst; i < nlast; i++) {
+ itype = type[i];
+ if (x[i][dim] >= mlo[itype] && x[i][dim] <= mhi[itype]) {
+ if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend);
+ sendlist[iswap][nsend++] = i;
+ }
+ }
+ }
+
+ } else {
+ if (style == SINGLE) {
+ ngroup = atom->nfirst;
+ for (i = 0; i < ngroup; i++)
+ if (x[i][dim] >= lo && x[i][dim] <= hi) {
+ if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend);
+ sendlist[iswap][nsend++] = i;
+ }
+ for (i = atom->nlocal; i < nlast; i++)
+ if (x[i][dim] >= lo && x[i][dim] <= hi) {
+ if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend);
+ sendlist[iswap][nsend++] = i;
+ }
+ } else {
+ ngroup = atom->nfirst;
+ for (i = 0; i < ngroup; i++) {
+ itype = type[i];
+ if (x[i][dim] >= mlo[itype] && x[i][dim] <= mhi[itype]) {
+ if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend);
+ sendlist[iswap][nsend++] = i;
+ }
+ }
+ for (i = atom->nlocal; i < nlast; i++) {
+ itype = type[i];
+ if (x[i][dim] >= mlo[itype] && x[i][dim] <= mhi[itype]) {
+ if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend);
+ sendlist[iswap][nsend++] = i;
+ }
+ }
+ }
+ }
}
// pack up list of border atoms
if (nsend*size_border > maxsend)
- grow_send(nsend*size_border,0);
+ grow_send(nsend*size_border,0);
if (ghost_velocity)
- n = avec->pack_border_vel(nsend,sendlist[iswap],buf_send,
- pbc_flag[iswap],pbc[iswap]);
+ n = avec->pack_border_vel(nsend,sendlist[iswap],buf_send,
+ pbc_flag[iswap],pbc[iswap]);
else
- n = avec->pack_border(nsend,sendlist[iswap],buf_send,
- pbc_flag[iswap],pbc[iswap]);
-
+ n = avec->pack_border(nsend,sendlist[iswap],buf_send,
+ pbc_flag[iswap],pbc[iswap]);
+
// swap atoms with other proc
// no MPI calls except SendRecv if nsend/nrecv = 0
// put incoming ghosts at end of my atom arrays
// if swapping with self, simply copy, no messages
if (sendproc[iswap] != me) {
- MPI_Sendrecv(&nsend,1,MPI_INT,sendproc[iswap],0,
- &nrecv,1,MPI_INT,recvproc[iswap],0,world,&status);
- if (nrecv*size_border > maxrecv) grow_recv(nrecv*size_border);
- if (nrecv) MPI_Irecv(buf_recv,nrecv*size_border,MPI_DOUBLE,
- recvproc[iswap],0,world,&request);
- if (n) MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap],0,world);
- if (nrecv) MPI_Wait(&request,&status);
- buf = buf_recv;
+ MPI_Sendrecv(&nsend,1,MPI_INT,sendproc[iswap],0,
+ &nrecv,1,MPI_INT,recvproc[iswap],0,world,&status);
+ if (nrecv*size_border > maxrecv) grow_recv(nrecv*size_border);
+ if (nrecv) MPI_Irecv(buf_recv,nrecv*size_border,MPI_DOUBLE,
+ recvproc[iswap],0,world,&request);
+ if (n) MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap],0,world);
+ if (nrecv) MPI_Wait(&request,&status);
+ buf = buf_recv;
} else {
- nrecv = nsend;
- buf = buf_send;
+ nrecv = nsend;
+ buf = buf_send;
}
// unpack buffer
if (ghost_velocity)
- avec->unpack_border_vel(nrecv,atom->nlocal+atom->nghost,buf);
+ avec->unpack_border_vel(nrecv,atom->nlocal+atom->nghost,buf);
else
- avec->unpack_border(nrecv,atom->nlocal+atom->nghost,buf);
+ avec->unpack_border(nrecv,atom->nlocal+atom->nghost,buf);
// set all pointers & counters
@@ -1091,17 +1091,17 @@ void Comm::forward_comm_pair(Pair *pair)
// pack buffer
n = pair->pack_comm(sendnum[iswap],sendlist[iswap],
- buf_send,pbc_flag[iswap],pbc[iswap]);
+ buf_send,pbc_flag[iswap],pbc[iswap]);
// exchange with another proc
// if self, set recv buffer to send buffer
if (sendproc[iswap] != me) {
if (recvnum[iswap])
- MPI_Irecv(buf_recv,n*recvnum[iswap],MPI_DOUBLE,recvproc[iswap],0,
- world,&request);
+ MPI_Irecv(buf_recv,n*recvnum[iswap],MPI_DOUBLE,recvproc[iswap],0,
+ world,&request);
if (sendnum[iswap])
- MPI_Send(buf_send,n*sendnum[iswap],MPI_DOUBLE,sendproc[iswap],0,world);
+ MPI_Send(buf_send,n*sendnum[iswap],MPI_DOUBLE,sendproc[iswap],0,world);
if (recvnum[iswap]) MPI_Wait(&request,&status);
buf = buf_recv;
} else buf = buf_send;
@@ -1129,15 +1129,15 @@ void Comm::reverse_comm_pair(Pair *pair)
n = pair->pack_reverse_comm(recvnum[iswap],firstrecv[iswap],buf_send);
- // exchange with another proc
+ // exchange with another proc
// if self, set recv buffer to send buffer
if (sendproc[iswap] != me) {
- if (sendnum[iswap])
- MPI_Irecv(buf_recv,n*sendnum[iswap],MPI_DOUBLE,sendproc[iswap],0,
- world,&request);
+ if (sendnum[iswap])
+ MPI_Irecv(buf_recv,n*sendnum[iswap],MPI_DOUBLE,sendproc[iswap],0,
+ world,&request);
if (recvnum[iswap])
- MPI_Send(buf_send,n*recvnum[iswap],MPI_DOUBLE,recvproc[iswap],0,world);
+ MPI_Send(buf_send,n*recvnum[iswap],MPI_DOUBLE,recvproc[iswap],0,world);
if (sendnum[iswap]) MPI_Wait(&request,&status);
buf = buf_recv;
} else buf = buf_send;
@@ -1164,17 +1164,17 @@ void Comm::forward_comm_fix(Fix *fix)
// pack buffer
n = fix->pack_comm(sendnum[iswap],sendlist[iswap],
- buf_send,pbc_flag[iswap],pbc[iswap]);
+ buf_send,pbc_flag[iswap],pbc[iswap]);
// exchange with another proc
// if self, set recv buffer to send buffer
if (sendproc[iswap] != me) {
- if (recvnum[iswap])
- MPI_Irecv(buf_recv,n*recvnum[iswap],MPI_DOUBLE,recvproc[iswap],0,
- world,&request);
- if (sendnum[iswap])
- MPI_Send(buf_send,n*sendnum[iswap],MPI_DOUBLE,sendproc[iswap],0,world);
+ if (recvnum[iswap])
+ MPI_Irecv(buf_recv,n*recvnum[iswap],MPI_DOUBLE,recvproc[iswap],0,
+ world,&request);
+ if (sendnum[iswap])
+ MPI_Send(buf_send,n*sendnum[iswap],MPI_DOUBLE,sendproc[iswap],0,world);
if (recvnum[iswap]) MPI_Wait(&request,&status);
buf = buf_recv;
} else buf = buf_send;
@@ -1202,15 +1202,15 @@ void Comm::reverse_comm_fix(Fix *fix)
n = fix->pack_reverse_comm(recvnum[iswap],firstrecv[iswap],buf_send);
- // exchange with another proc
+ // exchange with another proc
// if self, set recv buffer to send buffer
if (sendproc[iswap] != me) {
- if (sendnum[iswap])
- MPI_Irecv(buf_recv,n*sendnum[iswap],MPI_DOUBLE,sendproc[iswap],0,
- world,&request);
- if (recvnum[iswap])
- MPI_Send(buf_send,n*recvnum[iswap],MPI_DOUBLE,recvproc[iswap],0,world);
+ if (sendnum[iswap])
+ MPI_Irecv(buf_recv,n*sendnum[iswap],MPI_DOUBLE,sendproc[iswap],0,
+ world,&request);
+ if (recvnum[iswap])
+ MPI_Send(buf_send,n*recvnum[iswap],MPI_DOUBLE,recvproc[iswap],0,world);
if (sendnum[iswap]) MPI_Wait(&request,&status);
buf = buf_recv;
} else buf = buf_send;
@@ -1237,17 +1237,17 @@ void Comm::forward_comm_compute(Compute *compute)
// pack buffer
n = compute->pack_comm(sendnum[iswap],sendlist[iswap],
- buf_send,pbc_flag[iswap],pbc[iswap]);
+ buf_send,pbc_flag[iswap],pbc[iswap]);
// exchange with another proc
// if self, set recv buffer to send buffer
if (sendproc[iswap] != me) {
- if (recvnum[iswap])
- MPI_Irecv(buf_recv,n*recvnum[iswap],MPI_DOUBLE,recvproc[iswap],0,
- world,&request);
- if (sendnum[iswap])
- MPI_Send(buf_send,n*sendnum[iswap],MPI_DOUBLE,sendproc[iswap],0,world);
+ if (recvnum[iswap])
+ MPI_Irecv(buf_recv,n*recvnum[iswap],MPI_DOUBLE,recvproc[iswap],0,
+ world,&request);
+ if (sendnum[iswap])
+ MPI_Send(buf_send,n*sendnum[iswap],MPI_DOUBLE,sendproc[iswap],0,world);
if (recvnum[iswap]) MPI_Wait(&request,&status);
buf = buf_recv;
} else buf = buf_send;
@@ -1275,15 +1275,15 @@ void Comm::reverse_comm_compute(Compute *compute)
n = compute->pack_reverse_comm(recvnum[iswap],firstrecv[iswap],buf_send);
- // exchange with another proc
+ // exchange with another proc
// if self, set recv buffer to send buffer
if (sendproc[iswap] != me) {
- if (sendnum[iswap])
- MPI_Irecv(buf_recv,n*sendnum[iswap],MPI_DOUBLE,sendproc[iswap],0,
- world,&request);
- if (recvnum[iswap])
- MPI_Send(buf_send,n*recvnum[iswap],MPI_DOUBLE,recvproc[iswap],0,world);
+ if (sendnum[iswap])
+ MPI_Irecv(buf_recv,n*sendnum[iswap],MPI_DOUBLE,sendproc[iswap],0,
+ world,&request);
+ if (recvnum[iswap])
+ MPI_Send(buf_send,n*recvnum[iswap],MPI_DOUBLE,recvproc[iswap],0,world);
if (sendnum[iswap]) MPI_Wait(&request,&status);
buf = buf_recv;
} else buf = buf_send;
@@ -1310,17 +1310,17 @@ void Comm::forward_comm_dump(Dump *dump)
// pack buffer
n = dump->pack_comm(sendnum[iswap],sendlist[iswap],
- buf_send,pbc_flag[iswap],pbc[iswap]);
+ buf_send,pbc_flag[iswap],pbc[iswap]);
// exchange with another proc
// if self, set recv buffer to send buffer
if (sendproc[iswap] != me) {
- if (recvnum[iswap])
- MPI_Irecv(buf_recv,n*recvnum[iswap],MPI_DOUBLE,recvproc[iswap],0,
- world,&request);
- if (sendnum[iswap])
- MPI_Send(buf_send,n*sendnum[iswap],MPI_DOUBLE,sendproc[iswap],0,world);
+ if (recvnum[iswap])
+ MPI_Irecv(buf_recv,n*recvnum[iswap],MPI_DOUBLE,recvproc[iswap],0,
+ world,&request);
+ if (sendnum[iswap])
+ MPI_Send(buf_send,n*sendnum[iswap],MPI_DOUBLE,sendproc[iswap],0,world);
if (recvnum[iswap]) MPI_Wait(&request,&status);
buf = buf_recv;
} else buf = buf_send;
@@ -1348,15 +1348,15 @@ void Comm::reverse_comm_dump(Dump *dump)
n = dump->pack_reverse_comm(recvnum[iswap],firstrecv[iswap],buf_send);
- // exchange with another proc
+ // exchange with another proc
// if self, set recv buffer to send buffer
if (sendproc[iswap] != me) {
- if (sendnum[iswap])
- MPI_Irecv(buf_recv,n*sendnum[iswap],MPI_DOUBLE,sendproc[iswap],0,
- world,&request);
- if (recvnum[iswap])
- MPI_Send(buf_send,n*recvnum[iswap],MPI_DOUBLE,recvproc[iswap],0,world);
+ if (sendnum[iswap])
+ MPI_Irecv(buf_recv,n*sendnum[iswap],MPI_DOUBLE,sendproc[iswap],0,
+ world,&request);
+ if (recvnum[iswap])
+ MPI_Send(buf_send,n*recvnum[iswap],MPI_DOUBLE,recvproc[iswap],0,world);
if (sendnum[iswap]) MPI_Wait(&request,&status);
buf = buf_recv;
} else buf = buf_send;
@@ -1368,7 +1368,7 @@ void Comm::reverse_comm_dump(Dump *dump)
}
/* ----------------------------------------------------------------------
- realloc the size of the send buffer as needed with BUFFACTOR & BUFEXTRA
+ realloc the size of the send buffer as needed with BUFFACTOR & BUFEXTRA
if flag = 1, realloc
if flag = 0, don't need to realloc with copy, just free/malloc
------------------------------------------------------------------------- */
@@ -1385,7 +1385,7 @@ void Comm::grow_send(int n, int flag)
}
/* ----------------------------------------------------------------------
- free/malloc the size of the recv buffer as needed with BUFFACTOR
+ free/malloc the size of the recv buffer as needed with BUFFACTOR
------------------------------------------------------------------------- */
void Comm::grow_recv(int n)
@@ -1396,7 +1396,7 @@ void Comm::grow_recv(int n)
}
/* ----------------------------------------------------------------------
- realloc the size of the iswap sendlist as needed with BUFFACTOR
+ realloc the size of the iswap sendlist as needed with BUFFACTOR
------------------------------------------------------------------------- */
void Comm::grow_list(int iswap, int n)
@@ -1406,7 +1406,7 @@ void Comm::grow_list(int iswap, int n)
}
/* ----------------------------------------------------------------------
- realloc the buffers needed for swaps
+ realloc the buffers needed for swaps
------------------------------------------------------------------------- */
void Comm::grow_swap(int n)
@@ -1429,7 +1429,7 @@ void Comm::grow_swap(int n)
}
/* ----------------------------------------------------------------------
- allocation of swap info
+ allocation of swap info
------------------------------------------------------------------------- */
void Comm::allocate_swap(int n)
@@ -1459,7 +1459,7 @@ void Comm::allocate_multi(int n)
}
/* ----------------------------------------------------------------------
- free memory for swaps
+ free memory for swaps
------------------------------------------------------------------------- */
void Comm::free_swap()
@@ -1507,16 +1507,16 @@ void Comm::set(int narg, char **arg)
if (iarg+2 > narg) error->all(FLERR,"Illegal communicate command");
bordergroup = group->find(arg[iarg+1]);
if (bordergroup < 0)
- error->all(FLERR,"Invalid group in communicate command");
- if (bordergroup && (atom->firstgroupname == NULL ||
- strcmp(arg[iarg+1],atom->firstgroupname) != 0))
- error->all(FLERR,"Communicate group != atom_modify first group");
+ error->all(FLERR,"Invalid group in communicate command");
+ if (bordergroup && (atom->firstgroupname == NULL ||
+ strcmp(arg[iarg+1],atom->firstgroupname) != 0))
+ error->all(FLERR,"Communicate group != atom_modify first group");
iarg += 2;
} else if (strcmp(arg[iarg],"cutoff") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal communicate command");
cutghostuser = atof(arg[iarg+1]);
- if (cutghostuser < 0.0)
- error->all(FLERR,"Invalid cutoff in communicate command");
+ if (cutghostuser < 0.0)
+ error->all(FLERR,"Invalid cutoff in communicate command");
iarg += 2;
} else if (strcmp(arg[iarg],"vel") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal communicate command");
@@ -1544,7 +1544,7 @@ void Comm::set_processors(int narg, char **arg)
if (strcmp(arg[2],"*") == 0) user_procgrid[2] = 0;
else user_procgrid[2] = atoi(arg[2]);
- if (user_procgrid[0] < 0 || user_procgrid[1] < 0 || user_procgrid[2] < 0)
+ if (user_procgrid[0] < 0 || user_procgrid[1] < 0 || user_procgrid[2] < 0)
error->all(FLERR,"Illegal processors command");
int p = user_procgrid[0]*user_procgrid[1]*user_procgrid[2];
@@ -1557,36 +1557,36 @@ void Comm::set_processors(int narg, char **arg)
if (iarg+2 > narg) error->all(FLERR,"Illegal processors command");
if (strcmp(arg[iarg+1],"onelevel") == 0) {
- gridflag = ONELEVEL;
-
+ gridflag = ONELEVEL;
+
} else if (strcmp(arg[iarg+1],"twolevel") == 0) {
- if (iarg+6 > narg) error->all(FLERR,"Illegal processors command");
- gridflag = TWOLEVEL;
-
- ncores = atoi(arg[iarg+2]);
- if (strcmp(arg[iarg+3],"*") == 0) user_coregrid[0] = 0;
- else user_coregrid[0] = atoi(arg[iarg+3]);
- if (strcmp(arg[iarg+4],"*") == 0) user_coregrid[1] = 0;
- else user_coregrid[1] = atoi(arg[iarg+4]);
- if (strcmp(arg[iarg+5],"*") == 0) user_coregrid[2] = 0;
- else user_coregrid[2] = atoi(arg[iarg+5]);
-
- if (ncores <= 0 || user_coregrid[0] < 0 ||
- user_coregrid[1] < 0 || user_coregrid[2] < 0)
- error->all(FLERR,"Illegal processors command");
- iarg += 4;
-
+ if (iarg+6 > narg) error->all(FLERR,"Illegal processors command");
+ gridflag = TWOLEVEL;
+
+ ncores = atoi(arg[iarg+2]);
+ if (strcmp(arg[iarg+3],"*") == 0) user_coregrid[0] = 0;
+ else user_coregrid[0] = atoi(arg[iarg+3]);
+ if (strcmp(arg[iarg+4],"*") == 0) user_coregrid[1] = 0;
+ else user_coregrid[1] = atoi(arg[iarg+4]);
+ if (strcmp(arg[iarg+5],"*") == 0) user_coregrid[2] = 0;
+ else user_coregrid[2] = atoi(arg[iarg+5]);
+
+ if (ncores <= 0 || user_coregrid[0] < 0 ||
+ user_coregrid[1] < 0 || user_coregrid[2] < 0)
+ error->all(FLERR,"Illegal processors command");
+ iarg += 4;
+
} else if (strcmp(arg[iarg+1],"numa") == 0) {
- gridflag = NUMA;
-
+ gridflag = NUMA;
+
} else if (strcmp(arg[iarg],"custom") == 0) {
- if (iarg+3 > narg) error->all(FLERR,"Illegal processors command");
- gridflag = CUSTOM;
- delete [] customfile;
- int n = strlen(arg[iarg+2]) + 1;
- customfile = new char[n];
- strcpy(customfile,arg[iarg+2]);
- iarg += 1;
+ if (iarg+3 > narg) error->all(FLERR,"Illegal processors command");
+ gridflag = CUSTOM;
+ delete [] customfile;
+ int n = strlen(arg[iarg+2]) + 1;
+ customfile = new char[n];
+ strcpy(customfile,arg[iarg+2]);
+ iarg += 1;
} else error->all(FLERR,"Illegal processors command");
iarg += 2;
@@ -1596,49 +1596,49 @@ void Comm::set_processors(int narg, char **arg)
if (strcmp(arg[iarg+1],"cart") == 0) mapflag = CART;
else if (strcmp(arg[iarg+1],"cart/reorder") == 0) mapflag = CARTREORDER;
else if (strcmp(arg[iarg+1],"xyz") == 0 ||
- strcmp(arg[iarg+1],"xzy") == 0 ||
- strcmp(arg[iarg+1],"yxz") == 0 ||
- strcmp(arg[iarg+1],"yzx") == 0 ||
- strcmp(arg[iarg+1],"zxy") == 0 ||
- strcmp(arg[iarg+1],"zyx") == 0) {
- mapflag = XYZ;
- strcpy(xyz,arg[iarg+1]);
+ strcmp(arg[iarg+1],"xzy") == 0 ||
+ strcmp(arg[iarg+1],"yxz") == 0 ||
+ strcmp(arg[iarg+1],"yzx") == 0 ||
+ strcmp(arg[iarg+1],"zxy") == 0 ||
+ strcmp(arg[iarg+1],"zyx") == 0) {
+ mapflag = XYZ;
+ strcpy(xyz,arg[iarg+1]);
} else error->all(FLERR,"Illegal processors command");
iarg += 2;
} else if (strcmp(arg[iarg],"part") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal processors command");
if (universe->nworlds == 1)
- error->all(FLERR,
- "Cannot use processors part command "
- "without using partitions");
+ error->all(FLERR,
+ "Cannot use processors part command "
+ "without using partitions");
int isend = atoi(arg[iarg+1]);
int irecv = atoi(arg[iarg+2]);
if (isend < 1 || isend > universe->nworlds ||
- irecv < 1 || irecv > universe->nworlds || isend == irecv)
- error->all(FLERR,"Invalid partitions in processors part command");
+ irecv < 1 || irecv > universe->nworlds || isend == irecv)
+ error->all(FLERR,"Invalid partitions in processors part command");
if (isend-1 == universe->iworld) {
- if (send_to_partition >= 0)
- error->all(FLERR,
- "Sending partition in processors part command "
- "is already a sender");
- send_to_partition = irecv-1;
+ if (send_to_partition >= 0)
+ error->all(FLERR,
+ "Sending partition in processors part command "
+ "is already a sender");
+ send_to_partition = irecv-1;
}
if (irecv-1 == universe->iworld) {
- if (recv_from_partition >= 0)
- error->all(FLERR,
- "Receiving partition in processors part command "
- "is already a receiver");
- recv_from_partition = isend-1;
+ if (recv_from_partition >= 0)
+ error->all(FLERR,
+ "Receiving partition in processors part command "
+ "is already a receiver");
+ recv_from_partition = isend-1;
}
// only receiver has otherflag dependency
if (strcmp(arg[iarg+3],"multiple") == 0) {
- if (universe->iworld == irecv-1) {
- otherflag = 1;
- other_style = MULTIPLE;
- }
+ if (universe->iworld == irecv-1) {
+ otherflag = 1;
+ other_style = MULTIPLE;
+ }
} else error->all(FLERR,"Illegal processors command");
iarg += 4;
@@ -1659,17 +1659,17 @@ void Comm::set_processors(int narg, char **arg)
error->all(FLERR,"Processors grid numa and map style are incompatible");
if (otherflag && (gridflag == NUMA || gridflag == CUSTOM))
error->all(FLERR,
- "Processors part option and grid style are incompatible");
+ "Processors part option and grid style are incompatible");
}
/* ----------------------------------------------------------------------
- return # of bytes of allocated memory
+ return # of bytes of allocated memory
------------------------------------------------------------------------- */
bigint Comm::memory_usage()
{
bigint bytes = 0;
- for (int i = 0; i < nswap; i++)
+ for (int i = 0; i < nswap; i++)
bytes += memory->usage(sendlist[i],maxsendlist[i]);
bytes += memory->usage(buf_send,maxsend+BUFEXTRA);
bytes += memory->usage(buf_recv,maxrecv);
diff --git a/src/comm.h b/src/comm.h
index a285e80ef5b68b14c2773fbf3b3b21a8efba650e..0557ccbc792024c4c1bbf653fa734f65a49b0947 100644
--- a/src/comm.h
+++ b/src/comm.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -109,7 +109,7 @@ class Comm : protected Pointers {
double *buf_recv; // recv buffer for all comm
int maxsend,maxrecv; // current size of send/recv buffer
int maxforward,maxreverse; // max # of datums in forward/reverse comm
-
+
int updown(int, int, int, double, int, double *);
// compare cutoff to procs
virtual void grow_send(int,int); // reallocate send buffer
diff --git a/src/compute.cpp b/src/compute.cpp
index b33fe7595e18ecbffdf52298838de905d4f1422e..9261dee769180eba119a4dff5aa23bee5e2234cd 100644
--- a/src/compute.cpp
+++ b/src/compute.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -45,7 +45,7 @@ Compute::Compute(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
for (int i = 0; i < n-1; i++)
if (!isalnum(id[i]) && id[i] != '_')
error->all(FLERR,
- "Compute ID must be alphanumeric or underscore characters");
+ "Compute ID must be alphanumeric or underscore characters");
igroup = group->find(arg[1]);
if (igroup == -1) error->all(FLERR,"Could not find compute group ID");
@@ -77,7 +77,7 @@ Compute::Compute(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
dynamic = 0;
// setup list of timesteps
-
+
ntime = maxtime = 0;
tlist = NULL;
@@ -139,7 +139,7 @@ void Compute::reset_extra_dof()
void Compute::reset_extra_compute_fix(const char *)
{
error->all(FLERR,
- "Compute does not allow an extra compute or fix to be reset");
+ "Compute does not allow an extra compute or fix to be reset");
}
/* ----------------------------------------------------------------------
@@ -206,7 +206,7 @@ void Compute::clearstep()
set molmap to NULL if molecule IDs include all in range from 1 to Ncount
else: molecule IDs range from idlo to idhi
set molmap to vector of length idhi-idlo+1
- molmap[id-idlo] = index from 0 to Ncount-1
+ molmap[id-idlo] = index from 0 to Ncount-1
return idlo and idhi
------------------------------------------------------------------------- */
@@ -238,7 +238,7 @@ int Compute::molecules_in_group(int &idlo, int &idhi)
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall && comm->me == 0)
error->warning(FLERR,"Atom with molecule ID = 0 included in "
- "compute molecule group");
+ "compute molecule group");
MPI_Allreduce(&lo,&idlo,1,MPI_INT,MPI_MIN,world);
MPI_Allreduce(&hi,&idhi,1,MPI_INT,MPI_MAX,world);
diff --git a/src/compute.h b/src/compute.h
index e8f185ee24b43288ecf6d5a52d77b0bb1c0cef3d..734a1eefb2f4b10b0976a2d13e27c48f16472128 100644
--- a/src/compute.h
+++ b/src/compute.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/compute_angle_local.cpp b/src/compute_angle_local.cpp
index d19b7e71aacb31130c600ee920b88d6f10ac72ad..3ed2a0cb88e8fdfe7e41789934caf8d9994df74c 100644
--- a/src/compute_angle_local.cpp
+++ b/src/compute_angle_local.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -72,7 +72,7 @@ ComputeAngleLocal::~ComputeAngleLocal()
void ComputeAngleLocal::init()
{
- if (force->angle == NULL)
+ if (force->angle == NULL)
error->all(FLERR,"No angle style is defined for compute angle/local");
// do initial memory allocation so that memory_usage() is correct
@@ -148,38 +148,38 @@ int ComputeAngleLocal::compute_angles(int flag)
if (angle_type[atom2][i] == 0) continue;
if (flag) {
- if (tflag >= 0) {
- delx1 = x[atom1][0] - x[atom2][0];
- dely1 = x[atom1][1] - x[atom2][1];
- delz1 = x[atom1][2] - x[atom2][2];
- domain->minimum_image(delx1,dely1,delz1);
-
- rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
- r1 = sqrt(rsq1);
-
- delx2 = x[atom3][0] - x[atom2][0];
- dely2 = x[atom3][1] - x[atom2][1];
- delz2 = x[atom3][2] - x[atom2][2];
- domain->minimum_image(delx2,dely2,delz2);
-
- rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
- r2 = sqrt(rsq2);
-
- // c = cosine of angle
-
- c = delx1*delx2 + dely1*dely2 + delz1*delz2;
- c /= r1*r2;
- if (c > 1.0) c = 1.0;
- if (c < -1.0) c = -1.0;
- tbuf[n] = 180.0*acos(c)/MY_PI;
- }
-
- if (eflag >= 0) {
- if (angle_type[atom2][i] > 0)
- ebuf[n] = angle->single(angle_type[atom2][i],atom1,atom2,atom3);
- else ebuf[n] = 0.0;
- }
- n += nvalues;
+ if (tflag >= 0) {
+ delx1 = x[atom1][0] - x[atom2][0];
+ dely1 = x[atom1][1] - x[atom2][1];
+ delz1 = x[atom1][2] - x[atom2][2];
+ domain->minimum_image(delx1,dely1,delz1);
+
+ rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
+ r1 = sqrt(rsq1);
+
+ delx2 = x[atom3][0] - x[atom2][0];
+ dely2 = x[atom3][1] - x[atom2][1];
+ delz2 = x[atom3][2] - x[atom2][2];
+ domain->minimum_image(delx2,dely2,delz2);
+
+ rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
+ r2 = sqrt(rsq2);
+
+ // c = cosine of angle
+
+ c = delx1*delx2 + dely1*dely2 + delz1*delz2;
+ c /= r1*r2;
+ if (c > 1.0) c = 1.0;
+ if (c < -1.0) c = -1.0;
+ tbuf[n] = 180.0*acos(c)/MY_PI;
+ }
+
+ if (eflag >= 0) {
+ if (angle_type[atom2][i] > 0)
+ ebuf[n] = angle->single(angle_type[atom2][i],atom1,atom2,atom3);
+ else ebuf[n] = 0.0;
+ }
+ n += nvalues;
}
m++;
diff --git a/src/compute_angle_local.h b/src/compute_angle_local.h
index 77858a418dd03abab24c7fe2023ef257f169538b..d70be21253e38614fb3eae61df41bde45ca02c6c 100644
--- a/src/compute_angle_local.h
+++ b/src/compute_angle_local.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/compute_atom_molecule.cpp b/src/compute_atom_molecule.cpp
index 2bb6f7a5108330018a489e8d1d3266c5ec8c9f9c..5538980ab692339436ad4f2785892cd02625977f 100644
--- a/src/compute_atom_molecule.cpp
+++ b/src/compute_atom_molecule.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -51,9 +51,9 @@ ComputeAtomMolecule(LAMMPS *lmp, int narg, char **arg) :
int iarg = 3;
while (iarg < narg) {
- if (strncmp(arg[iarg],"c_",2) == 0 ||
- strncmp(arg[iarg],"f_",2) == 0 ||
- strncmp(arg[iarg],"v_",2) == 0) {
+ if (strncmp(arg[iarg],"c_",2) == 0 ||
+ strncmp(arg[iarg],"f_",2) == 0 ||
+ strncmp(arg[iarg],"v_",2) == 0) {
if (arg[iarg][0] == 'c') which[nvalues] = COMPUTE;
else if (arg[iarg][0] == 'f') which[nvalues] = FIX;
else if (arg[iarg][0] == 'v') which[nvalues] = VARIABLE;
@@ -64,10 +64,10 @@ ComputeAtomMolecule(LAMMPS *lmp, int narg, char **arg) :
char *ptr = strchr(suffix,'[');
if (ptr) {
- if (suffix[strlen(suffix)-1] != ']')
- error->all(FLERR,"Illegal compute reduce command");
- argindex[nvalues] = atoi(ptr+1);
- *ptr = '\0';
+ if (suffix[strlen(suffix)-1] != ']')
+ error->all(FLERR,"Illegal compute reduce command");
+ argindex[nvalues] = atoi(ptr+1);
+ *ptr = '\0';
} else argindex[nvalues] = 0;
n = strlen(suffix) + 1;
@@ -86,47 +86,47 @@ ComputeAtomMolecule(LAMMPS *lmp, int narg, char **arg) :
if (which[i] == COMPUTE) {
int icompute = modify->find_compute(ids[i]);
if (icompute < 0)
- error->all(FLERR,"Compute ID for compute atom/molecule does not exist");
+ error->all(FLERR,"Compute ID for compute atom/molecule does not exist");
if (modify->compute[icompute]->peratom_flag == 0)
- error->all(FLERR,"Compute atom/molecule compute does not "
- "calculate per-atom values");
- if (argindex[i] == 0 &&
- modify->compute[icompute]->size_peratom_cols != 0)
- error->all(FLERR,"Compute atom/molecule compute does not "
- "calculate a per-atom vector");
+ error->all(FLERR,"Compute atom/molecule compute does not "
+ "calculate per-atom values");
+ if (argindex[i] == 0 &&
+ modify->compute[icompute]->size_peratom_cols != 0)
+ error->all(FLERR,"Compute atom/molecule compute does not "
+ "calculate a per-atom vector");
if (argindex[i] && modify->compute[icompute]->size_peratom_cols == 0)
- error->all(FLERR,"Compute atom/molecule compute does not "
- "calculate a per-atom array");
- if (argindex[i] &&
- argindex[i] > modify->compute[icompute]->size_peratom_cols)
- error->all(FLERR,"Compute atom/molecule compute array is "
- "accessed out-of-range");
+ error->all(FLERR,"Compute atom/molecule compute does not "
+ "calculate a per-atom array");
+ if (argindex[i] &&
+ argindex[i] > modify->compute[icompute]->size_peratom_cols)
+ error->all(FLERR,"Compute atom/molecule compute array is "
+ "accessed out-of-range");
} else if (which[i] == FIX) {
int ifix = modify->find_fix(ids[i]);
if (ifix < 0)
- error->all(FLERR,"Fix ID for compute atom/molecule does not exist");
+ error->all(FLERR,"Fix ID for compute atom/molecule does not exist");
if (modify->fix[ifix]->peratom_flag)
- error->all(FLERR,"Compute atom/molecule fix does not "
- "calculate per-atom values");
- if (argindex[i] == 0 &&
- modify->fix[ifix]->size_peratom_cols != 0)
- error->all(FLERR,"Compute atom/molecule fix does not "
- "calculate a per-atom vector");
+ error->all(FLERR,"Compute atom/molecule fix does not "
+ "calculate per-atom values");
+ if (argindex[i] == 0 &&
+ modify->fix[ifix]->size_peratom_cols != 0)
+ error->all(FLERR,"Compute atom/molecule fix does not "
+ "calculate a per-atom vector");
if (argindex[i] && modify->fix[ifix]->size_peratom_cols == 0)
- error->all(FLERR,"Compute atom/molecule fix does not "
- "calculate a per-atom array");
- if (argindex[i] &&
- argindex[i] > modify->fix[ifix]->size_peratom_cols)
- error->all(FLERR,"Compute atom/molecule fix array is accessed out-of-range");
+ error->all(FLERR,"Compute atom/molecule fix does not "
+ "calculate a per-atom array");
+ if (argindex[i] &&
+ argindex[i] > modify->fix[ifix]->size_peratom_cols)
+ error->all(FLERR,"Compute atom/molecule fix array is accessed out-of-range");
} else if (which[i] == VARIABLE) {
int ivariable = input->variable->find(ids[i]);
if (ivariable < 0)
- error->all(FLERR,"Variable name for compute atom/molecule does not exist");
+ error->all(FLERR,"Variable name for compute atom/molecule does not exist");
if (input->variable->atomstyle(ivariable) == 0)
- error->all(FLERR,"Compute atom/molecule variable is not "
- "atom-style variable");
+ error->all(FLERR,"Compute atom/molecule variable is not "
+ "atom-style variable");
}
}
@@ -187,19 +187,19 @@ void ComputeAtomMolecule::init()
if (which[m] == COMPUTE) {
int icompute = modify->find_compute(ids[m]);
if (icompute < 0)
- error->all(FLERR,"Compute ID for compute atom/molecule does not exist");
+ error->all(FLERR,"Compute ID for compute atom/molecule does not exist");
value2index[m] = icompute;
-
+
} else if (which[m] == FIX) {
int ifix = modify->find_fix(ids[m]);
- if (ifix < 0)
- error->all(FLERR,"Fix ID for compute atom/molecule does not exist");
+ if (ifix < 0)
+ error->all(FLERR,"Fix ID for compute atom/molecule does not exist");
value2index[m] = ifix;
} else if (which[m] == VARIABLE) {
int ivariable = input->variable->find(ids[m]);
- if (ivariable < 0)
- error->all(FLERR,"Variable name for compute atom/molecule does not exist");
+ if (ivariable < 0)
+ error->all(FLERR,"Variable name for compute atom/molecule does not exist");
value2index[m] = ivariable;
} else value2index[m] = -1;
@@ -255,17 +255,17 @@ void ComputeAtomMolecule::compute_array()
j = 0;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
- imol = molecule[i];
- if (molmap) imol = molmap[imol-idlo];
- else imol--;
- aone[imol][m] += peratom[j];
+ imol = molecule[i];
+ if (molmap) imol = molmap[imol-idlo];
+ else imol--;
+ aone[imol][m] += peratom[j];
}
j += nstride;
}
}
MPI_Allreduce(&aone[0][0],&array[0][0],nvalues*nmolecules,
- MPI_DOUBLE,MPI_SUM,world);
+ MPI_DOUBLE,MPI_SUM,world);
}
/* ----------------------------------------------------------------------
@@ -283,7 +283,7 @@ void ComputeAtomMolecule::compute_one(int m)
if (which[m] == COMPUTE) {
Compute *compute = modify->compute[vidx];
-
+
if (!(compute->invoked_flag & INVOKED_PERATOM)) {
compute->compute_peratom();
compute->invoked_flag |= INVOKED_PERATOM;
@@ -302,7 +302,7 @@ void ComputeAtomMolecule::compute_one(int m)
} else if (which[m] == FIX) {
if (update->ntimestep % modify->fix[vidx]->peratom_freq)
error->all(FLERR,"Fix used in compute atom/molecule not computed "
- "at compatible time");
+ "at compatible time");
Fix *fix = modify->fix[vidx];
if (aidx == 0) {
@@ -312,7 +312,7 @@ void ComputeAtomMolecule::compute_one(int m)
peratom = &fix->array_atom[0][aidx-1];
nstride = fix->size_array_cols;
}
-
+
// evaluate atom-style variable
} else if (which[m] == VARIABLE) {
diff --git a/src/compute_atom_molecule.h b/src/compute_atom_molecule.h
index 7e87ca7a2acf8089f99f94c1c8021ff73b73f4a7..769f58d5ec5c538b7095e15a2aeb4f829f0730e1 100644
--- a/src/compute_atom_molecule.h
+++ b/src/compute_atom_molecule.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/compute_bond_local.cpp b/src/compute_bond_local.cpp
index 76feec4209cea4b1c0d5cb8a9655b1ce959a978f..2ffea3556cc5719c7273b52bc96d9ddacdc98db3 100644
--- a/src/compute_bond_local.cpp
+++ b/src/compute_bond_local.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -70,7 +70,7 @@ ComputeBondLocal::~ComputeBondLocal()
void ComputeBondLocal::init()
{
- if (force->bond == NULL)
+ if (force->bond == NULL)
error->all(FLERR,"No bond style is defined for compute bond/local");
// do initial memory allocation so that memory_usage() is correct
@@ -142,18 +142,18 @@ int ComputeBondLocal::compute_bonds(int flag)
if (bond_type[atom1][i] == 0) continue;
if (flag) {
- delx = x[atom1][0] - x[atom2][0];
- dely = x[atom1][1] - x[atom2][1];
- delz = x[atom1][2] - x[atom2][2];
- domain->minimum_image(delx,dely,delz);
- rsq = delx*delx + dely*dely + delz*delz;
- if (dflag >= 0) dbuf[n] = sqrt(rsq);
- if (eflag >= 0) {
- if (bond_type[atom1][i] > 0)
- ebuf[n] = bond->single(bond_type[atom1][i],rsq,atom1,atom2);
- else ebuf[n] = 0.0;
- }
- n += nvalues;
+ delx = x[atom1][0] - x[atom2][0];
+ dely = x[atom1][1] - x[atom2][1];
+ delz = x[atom1][2] - x[atom2][2];
+ domain->minimum_image(delx,dely,delz);
+ rsq = delx*delx + dely*dely + delz*delz;
+ if (dflag >= 0) dbuf[n] = sqrt(rsq);
+ if (eflag >= 0) {
+ if (bond_type[atom1][i] > 0)
+ ebuf[n] = bond->single(bond_type[atom1][i],rsq,atom1,atom2);
+ else ebuf[n] = 0.0;
+ }
+ n += nvalues;
}
m++;
diff --git a/src/compute_bond_local.h b/src/compute_bond_local.h
index 902cd6bac220c4cea72152c2a90d71b92779edfa..9bb680be4f95ef336e43db0c8166716b8fd3a474 100644
--- a/src/compute_bond_local.h
+++ b/src/compute_bond_local.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/compute_centro_atom.cpp b/src/compute_centro_atom.cpp
index 68478955c8cfc6196b49b71b831d9869e9945177..f5fad86bd2c2641d2a557b1b6a2d8677dfa8bd5b 100644
--- a/src/compute_centro_atom.cpp
+++ b/src/compute_centro_atom.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -38,7 +38,7 @@ ComputeCentroAtom::ComputeCentroAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 4) error->all(FLERR,"Illegal compute centro/atom command");
-
+
if (strcmp(arg[3],"fcc") == 0) nnn = 12;
else if (strcmp(arg[3],"bcc") == 0) nnn = 8;
else nnn = atoi(arg[3]);
@@ -69,7 +69,7 @@ ComputeCentroAtom::~ComputeCentroAtom()
void ComputeCentroAtom::init()
{
- if (force->pair == NULL)
+ if (force->pair == NULL)
error->all(FLERR,"Compute centro/atom requires a pair style be defined");
int count = 0;
@@ -148,11 +148,11 @@ void ComputeCentroAtom::compute_peratom()
// insure distsq and nearest arrays are long enough
if (jnum > maxneigh) {
- memory->destroy(distsq);
- memory->destroy(nearest);
- maxneigh = jnum;
- memory->create(distsq,maxneigh,"centro/atom:distsq");
- memory->create(nearest,maxneigh,"centro/atom:nearest");
+ memory->destroy(distsq);
+ memory->destroy(nearest);
+ maxneigh = jnum;
+ memory->create(distsq,maxneigh,"centro/atom:distsq");
+ memory->create(nearest,maxneigh,"centro/atom:nearest");
}
// loop over list of all neighbors within force cutoff
@@ -161,24 +161,24 @@ void ComputeCentroAtom::compute_peratom()
n = 0;
for (jj = 0; jj < jnum; jj++) {
- j = jlist[jj];
- j &= NEIGHMASK;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
- if (rsq < cutsq) {
- distsq[n] = rsq;
- nearest[n++] = j;
- }
+ j = jlist[jj];
+ j &= NEIGHMASK;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+ if (rsq < cutsq) {
+ distsq[n] = rsq;
+ nearest[n++] = j;
+ }
}
// if not nnn neighbors, centro = 0.0
if (n < nnn) {
- centro[i] = 0.0;
- continue;
+ centro[i] = 0.0;
+ continue;
}
// store nnn nearest neighs in 1st nnn locations of distsq and nearest
@@ -190,14 +190,14 @@ void ComputeCentroAtom::compute_peratom()
n = 0;
for (j = 0; j < nnn; j++) {
- jj = nearest[j];
- for (k = j+1; k < nnn; k++) {
- kk = nearest[k];
- delx = x[jj][0] + x[kk][0] - 2.0*xtmp;
- dely = x[jj][1] + x[kk][1] - 2.0*ytmp;
- delz = x[jj][2] + x[kk][2] - 2.0*ztmp;
- pairs[n++] = delx*delx + dely*dely + delz*delz;
- }
+ jj = nearest[j];
+ for (k = j+1; k < nnn; k++) {
+ kk = nearest[k];
+ delx = x[jj][0] + x[kk][0] - 2.0*xtmp;
+ dely = x[jj][1] + x[kk][1] - 2.0*ytmp;
+ delz = x[jj][2] + x[kk][2] - 2.0*ztmp;
+ pairs[n++] = delx*delx + dely*dely + delz*delz;
+ }
}
// store nhalf smallest pair distances in 1st nhalf locations of pairs
@@ -235,29 +235,29 @@ void ComputeCentroAtom::select(int k, int n, double *arr)
for (;;) {
if (ir <= l+1) {
if (ir == l+1 && arr[ir] < arr[l]) {
- SWAP(arr[l],arr[ir])
+ SWAP(arr[l],arr[ir])
}
return;
} else {
mid=(l+ir) >> 1;
SWAP(arr[mid],arr[l+1])
if (arr[l] > arr[ir]) {
- SWAP(arr[l],arr[ir])
+ SWAP(arr[l],arr[ir])
}
if (arr[l+1] > arr[ir]) {
- SWAP(arr[l+1],arr[ir])
+ SWAP(arr[l+1],arr[ir])
}
if (arr[l] > arr[l+1]) {
- SWAP(arr[l],arr[l+1])
+ SWAP(arr[l],arr[l+1])
}
i = l+1;
j = ir;
a = arr[l+1];
for (;;) {
- do i++; while (arr[i] < a);
- do j--; while (arr[j] > a);
- if (j < i) break;
- SWAP(arr[i],arr[j])
+ do i++; while (arr[i] < a);
+ do j--; while (arr[j] > a);
+ if (j < i) break;
+ SWAP(arr[i],arr[j])
}
arr[l+1] = arr[j];
arr[j] = a;
@@ -281,8 +281,8 @@ void ComputeCentroAtom::select2(int k, int n, double *arr, int *iarr)
for (;;) {
if (ir <= l+1) {
if (ir == l+1 && arr[ir] < arr[l]) {
- SWAP(arr[l],arr[ir])
- ISWAP(iarr[l],iarr[ir])
+ SWAP(arr[l],arr[ir])
+ ISWAP(iarr[l],iarr[ir])
}
return;
} else {
@@ -290,27 +290,27 @@ void ComputeCentroAtom::select2(int k, int n, double *arr, int *iarr)
SWAP(arr[mid],arr[l+1])
ISWAP(iarr[mid],iarr[l+1])
if (arr[l] > arr[ir]) {
- SWAP(arr[l],arr[ir])
- ISWAP(iarr[l],iarr[ir])
+ SWAP(arr[l],arr[ir])
+ ISWAP(iarr[l],iarr[ir])
}
if (arr[l+1] > arr[ir]) {
- SWAP(arr[l+1],arr[ir])
- ISWAP(iarr[l+1],iarr[ir])
+ SWAP(arr[l+1],arr[ir])
+ ISWAP(iarr[l+1],iarr[ir])
}
if (arr[l] > arr[l+1]) {
- SWAP(arr[l],arr[l+1])
- ISWAP(iarr[l],iarr[l+1])
+ SWAP(arr[l],arr[l+1])
+ ISWAP(iarr[l],iarr[l+1])
}
i = l+1;
j = ir;
a = arr[l+1];
ia = iarr[l+1];
for (;;) {
- do i++; while (arr[i] < a);
- do j--; while (arr[j] > a);
- if (j < i) break;
- SWAP(arr[i],arr[j])
- ISWAP(iarr[i],iarr[j])
+ do i++; while (arr[i] < a);
+ do j--; while (arr[j] > a);
+ if (j < i) break;
+ SWAP(arr[i],arr[j])
+ ISWAP(iarr[i],iarr[j])
}
arr[l+1] = arr[j];
arr[j] = a;
diff --git a/src/compute_centro_atom.h b/src/compute_centro_atom.h
index 51a9a192115f47b80209b383ec7100457d715807..a292911e369f0da0b4cac2c787ce812371b7fc5b 100644
--- a/src/compute_centro_atom.h
+++ b/src/compute_centro_atom.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/compute_cluster_atom.cpp b/src/compute_cluster_atom.cpp
index 9b8036ad2963cf29ff220959c16de23f15390a64..5911b5a88d4468216d84fc2d8fcea534f2896efb 100644
--- a/src/compute_cluster_atom.cpp
+++ b/src/compute_cluster_atom.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -60,9 +60,9 @@ void ComputeClusterAtom::init()
{
if (atom->tag_enable == 0)
error->all(FLERR,"Cannot use compute cluster/atom unless atoms have IDs");
- if (force->pair == NULL)
+ if (force->pair == NULL)
error->all(FLERR,"Compute cluster/atom requires a pair style be defined");
- if (sqrt(cutsq) > force->pair->cutforce)
+ if (sqrt(cutsq) > force->pair->cutforce)
error->all(FLERR,"Compute cluster/atom cutoff is longer than pairwise cutoff");
// need an occasional full neighbor list
@@ -146,38 +146,38 @@ void ComputeClusterAtom::compute_peratom()
while (1) {
done = 1;
for (ii = 0; ii < inum; ii++) {
- i = ilist[ii];
- if (!(mask[i] & groupbit)) continue;
-
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- jlist = firstneigh[i];
- jnum = numneigh[i];
-
- n = 0;
- for (jj = 0; jj < jnum; jj++) {
- j = jlist[jj];
- j &= NEIGHMASK;
- if (!(mask[j] & groupbit)) continue;
- if (clusterID[i] == clusterID[j]) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
- if (rsq < cutsq) {
- clusterID[i] = clusterID[j] = MIN(clusterID[i],clusterID[j]);
- done = 0;
- }
- }
+ i = ilist[ii];
+ if (!(mask[i] & groupbit)) continue;
+
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+
+ n = 0;
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
+ j &= NEIGHMASK;
+ if (!(mask[j] & groupbit)) continue;
+ if (clusterID[i] == clusterID[j]) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+ if (rsq < cutsq) {
+ clusterID[i] = clusterID[j] = MIN(clusterID[i],clusterID[j]);
+ done = 0;
+ }
+ }
}
if (!done) change = 1;
if (done) break;
}
-
+
// stop if all procs are done
-
+
MPI_Allreduce(&change,&anychange,1,MPI_INT,MPI_MAX,world);
if (!anychange) break;
}
@@ -185,8 +185,8 @@ void ComputeClusterAtom::compute_peratom()
/* ---------------------------------------------------------------------- */
-int ComputeClusterAtom::pack_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+int ComputeClusterAtom::pack_comm(int n, int *list, double *buf,
+ int pbc_flag, int *pbc)
{
int i,j,m;
diff --git a/src/compute_cluster_atom.h b/src/compute_cluster_atom.h
index 510d9bf126c4ac24bc6f2096c8d69592fbcee53b..a88c61b45f19fa7c62b1ff4af68f2f85ccc1f690 100644
--- a/src/compute_cluster_atom.h
+++ b/src/compute_cluster_atom.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/compute_cna_atom.cpp b/src/compute_cna_atom.cpp
index 5df5b68919f679ad3a100d505188585b09e8bc80..5b274a33d3eaccc7a933f3c62d55072760034e2e 100644
--- a/src/compute_cna_atom.cpp
+++ b/src/compute_cna_atom.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -72,17 +72,17 @@ ComputeCNAAtom::~ComputeCNAAtom()
void ComputeCNAAtom::init()
{
- if (force->pair == NULL)
+ if (force->pair == NULL)
error->all(FLERR,"Compute cna/atom requires a pair style be defined");
- if (sqrt(cutsq) > force->pair->cutforce)
+ if (sqrt(cutsq) > force->pair->cutforce)
error->all(FLERR,"Compute cna/atom cutoff is longer than pairwise cutoff");
// cannot use neighbor->cutneighmax b/c neighbor has not yet been init
- if (2.0*sqrt(cutsq) > force->pair->cutforce + neighbor->skin &&
+ if (2.0*sqrt(cutsq) > force->pair->cutforce + neighbor->skin &&
comm->me == 0)
error->warning(FLERR,"Compute cna/atom cutoff may be too large to find "
- "ghost atom neighbors");
+ "ghost atom neighbors");
int count = 0;
for (int i = 0; i < modify->ncompute; i++)
@@ -148,7 +148,7 @@ void ComputeCNAAtom::compute_peratom()
// nearest[] = atom indices of nearest neighbors, up to MAXNEAR
// do this for all atoms, not just compute group
// since CNA calculation requires neighbors of neighbors
-
+
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
@@ -172,11 +172,11 @@ void ComputeCNAAtom::compute_peratom()
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cutsq) {
- if (n < MAXNEAR) nearest[i][n++] = j;
- else {
- nerror++;
- break;
- }
+ if (n < MAXNEAR) nearest[i][n++] = j;
+ else {
+ nerror++;
+ break;
+ }
}
}
nnearest[i] = n;
@@ -224,52 +224,52 @@ void ComputeCNAAtom::compute_peratom()
// in latter case, must exclude J from I's neighbor list
if (j < nlocal) {
- firstflag = 1;
- ncommon = 0;
- for (inear = 0; inear < nnearest[i]; inear++)
- for (jnear = 0; jnear < nnearest[j]; jnear++)
- if (nearest[i][inear] == nearest[j][jnear]) {
- if (ncommon < MAXCOMMON) common[ncommon++] = nearest[i][inear];
- else if (firstflag) {
- nerror++;
- firstflag = 0;
- }
- }
+ firstflag = 1;
+ ncommon = 0;
+ for (inear = 0; inear < nnearest[i]; inear++)
+ for (jnear = 0; jnear < nnearest[j]; jnear++)
+ if (nearest[i][inear] == nearest[j][jnear]) {
+ if (ncommon < MAXCOMMON) common[ncommon++] = nearest[i][inear];
+ else if (firstflag) {
+ nerror++;
+ firstflag = 0;
+ }
+ }
} else {
- xtmp = x[j][0];
- ytmp = x[j][1];
- ztmp = x[j][2];
- jlist = firstneigh[i];
- jnum = numneigh[i];
-
- n = 0;
- for (kk = 0; kk < jnum; kk++) {
- k = jlist[kk];
- k &= NEIGHMASK;
- if (k == j) continue;
-
- delx = xtmp - x[k][0];
- dely = ytmp - x[k][1];
- delz = ztmp - x[k][2];
- rsq = delx*delx + dely*dely + delz*delz;
- if (rsq < cutsq) {
- if (n < MAXNEAR) onenearest[n++] = k;
- else break;
- }
- }
-
- firstflag = 1;
- ncommon = 0;
- for (inear = 0; inear < nnearest[i]; inear++)
- for (jnear = 0; jnear < n; jnear++)
- if (nearest[i][inear] == onenearest[jnear]) {
- if (ncommon < MAXCOMMON) common[ncommon++] = nearest[i][inear];
- else if (firstflag) {
- nerror++;
- firstflag = 0;
- }
- }
+ xtmp = x[j][0];
+ ytmp = x[j][1];
+ ztmp = x[j][2];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+
+ n = 0;
+ for (kk = 0; kk < jnum; kk++) {
+ k = jlist[kk];
+ k &= NEIGHMASK;
+ if (k == j) continue;
+
+ delx = xtmp - x[k][0];
+ dely = ytmp - x[k][1];
+ delz = ztmp - x[k][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+ if (rsq < cutsq) {
+ if (n < MAXNEAR) onenearest[n++] = k;
+ else break;
+ }
+ }
+
+ firstflag = 1;
+ ncommon = 0;
+ for (inear = 0; inear < nnearest[i]; inear++)
+ for (jnear = 0; jnear < n; jnear++)
+ if (nearest[i][inear] == onenearest[jnear]) {
+ if (ncommon < MAXCOMMON) common[ncommon++] = nearest[i][inear];
+ else if (firstflag) {
+ nerror++;
+ firstflag = 0;
+ }
+ }
}
cna[m][NCOMMON] = ncommon;
@@ -282,22 +282,22 @@ void ComputeCNAAtom::compute_peratom()
nbonds = 0;
for (jj = 0; jj < ncommon; jj++) {
- j = common[jj];
- xtmp = x[j][0];
- ytmp = x[j][1];
- ztmp = x[j][2];
- for (kk = jj+1; kk < ncommon; kk++) {
- k = common[kk];
- delx = xtmp - x[k][0];
- dely = ytmp - x[k][1];
- delz = ztmp - x[k][2];
- rsq = delx*delx + dely*dely + delz*delz;
- if (rsq < cutsq) {
- nbonds++;
- bonds[jj]++;
- bonds[kk]++;
- }
- }
+ j = common[jj];
+ xtmp = x[j][0];
+ ytmp = x[j][1];
+ ztmp = x[j][2];
+ for (kk = jj+1; kk < ncommon; kk++) {
+ k = common[kk];
+ delx = xtmp - x[k][0];
+ dely = ytmp - x[k][1];
+ delz = ztmp - x[k][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+ if (rsq < cutsq) {
+ nbonds++;
+ bonds[jj]++;
+ bonds[kk]++;
+ }
+ }
}
cna[m][NBOND] = nbonds;
@@ -305,9 +305,9 @@ void ComputeCNAAtom::compute_peratom()
maxbonds = 0;
minbonds = MAXCOMMON;
for (n = 0; n < ncommon; n++) {
- maxbonds = MAX(bonds[n],maxbonds);
- minbonds = MIN(bonds[n],minbonds);
- }
+ maxbonds = MAX(bonds[n],maxbonds);
+ minbonds = MIN(bonds[n],minbonds);
+ }
cna[m][MAXBOND] = maxbonds;
cna[m][MINBOND] = minbonds;
}
@@ -319,26 +319,26 @@ void ComputeCNAAtom::compute_peratom()
if (nnearest[i] == 12) {
for (inear = 0; inear < 12; inear++) {
- cj = cna[inear][NCOMMON];
- ck = cna[inear][NBOND];
- cl = cna[inear][MAXBOND];
- cm = cna[inear][MINBOND];
- if (cj == 4 && ck == 2 && cl == 1 && cm == 1) nfcc++;
- else if (cj == 4 && ck == 2 && cl == 2 && cm == 0) nhcp++;
- else if (cj == 5 && ck == 5 && cl == 2 && cm == 2) nico++;
+ cj = cna[inear][NCOMMON];
+ ck = cna[inear][NBOND];
+ cl = cna[inear][MAXBOND];
+ cm = cna[inear][MINBOND];
+ if (cj == 4 && ck == 2 && cl == 1 && cm == 1) nfcc++;
+ else if (cj == 4 && ck == 2 && cl == 2 && cm == 0) nhcp++;
+ else if (cj == 5 && ck == 5 && cl == 2 && cm == 2) nico++;
}
if (nfcc == 12) pattern[i] = FCC;
else if (nfcc == 6 && nhcp == 6) pattern[i] = HCP;
else if (nico == 12) pattern[i] = ICOS;
-
+
} else if (nnearest[i] == 14) {
for (inear = 0; inear < 14; inear++) {
- cj = cna[inear][NCOMMON];
- ck = cna[inear][NBOND];
- cl = cna[inear][MAXBOND];
- cm = cna[inear][MINBOND];
- if (cj == 4 && ck == 4 && cl == 2 && cm == 2) nbcc4++;
- else if (cj == 6 && ck == 6 && cl == 2 && cm == 2) nbcc6++;
+ cj = cna[inear][NCOMMON];
+ ck = cna[inear][NBOND];
+ cl = cna[inear][MAXBOND];
+ cm = cna[inear][MINBOND];
+ if (cj == 4 && ck == 4 && cl == 2 && cm == 2) nbcc4++;
+ else if (cj == 6 && ck == 6 && cl == 2 && cm == 2) nbcc6++;
}
if (nbcc4 == 6 && nbcc6 == 8) pattern[i] = BCC;
}
diff --git a/src/compute_cna_atom.h b/src/compute_cna_atom.h
index 3913480dcaaa5869ae77aa8a46bfeed5570e09ed..fdb6c25702678687204bf842484a021cf9da7190 100644
--- a/src/compute_cna_atom.h
+++ b/src/compute_cna_atom.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/compute_com.cpp b/src/compute_com.cpp
index d0f4296c42dad68d364e1fe44ef9a7322885b89e..e086210322481cacf70c0fb240b47748b50e63e1 100644
--- a/src/compute_com.cpp
+++ b/src/compute_com.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/compute_com.h b/src/compute_com.h
index 7f4cb82a956f949621468d28402c2d0519c294a0..6fe46ab6ab18377e73633609687aba300fd3d3fb 100644
--- a/src/compute_com.h
+++ b/src/compute_com.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/compute_com_molecule.cpp b/src/compute_com_molecule.cpp
index ad3ba957bd97c66aed0b760cb7bd451f6f8beb50..2b52919f80f4787234ce862b8e8a7db5c7c6c8e7 100644
--- a/src/compute_com_molecule.cpp
+++ b/src/compute_com_molecule.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -133,7 +133,7 @@ void ComputeCOMMolecule::compute_array()
}
MPI_Allreduce(&com[0][0],&comall[0][0],3*nmolecules,
- MPI_DOUBLE,MPI_SUM,world);
+ MPI_DOUBLE,MPI_SUM,world);
for (i = 0; i < nmolecules; i++) {
comall[i][0] /= masstotal[i];
comall[i][1] /= masstotal[i];
diff --git a/src/compute_com_molecule.h b/src/compute_com_molecule.h
index 80dee0303030d2d9a765052b162c0f4e27a00ab1..a4f941c52aa8e563503d46a8c1cea7dbd15ed25f 100644
--- a/src/compute_com_molecule.h
+++ b/src/compute_com_molecule.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/compute_coord_atom.cpp b/src/compute_coord_atom.cpp
index a7296ba08802290fb5e52e90ff868289c7331886..01a533e201d05ab911c8d51235b39b216ff083eb 100644
--- a/src/compute_coord_atom.cpp
+++ b/src/compute_coord_atom.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -57,11 +57,11 @@ ComputeCoordAtom::~ComputeCoordAtom()
void ComputeCoordAtom::init()
{
- if (force->pair == NULL)
+ if (force->pair == NULL)
error->all(FLERR,"Compute coord/atom requires a pair style be defined");
- if (sqrt(cutsq) > force->pair->cutforce)
+ if (sqrt(cutsq) > force->pair->cutforce)
error->all(FLERR,
- "Compute coord/atom cutoff is longer than pairwise cutoff");
+ "Compute coord/atom cutoff is longer than pairwise cutoff");
// need an occasional full neighbor list
@@ -131,14 +131,14 @@ void ComputeCoordAtom::compute_peratom()
n = 0;
for (jj = 0; jj < jnum; jj++) {
- j = jlist[jj];
- j &= NEIGHMASK;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
- if (rsq < cutsq) n++;
+ j = jlist[jj];
+ j &= NEIGHMASK;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+ if (rsq < cutsq) n++;
}
coordination[i] = n;
diff --git a/src/compute_coord_atom.h b/src/compute_coord_atom.h
index b9b7af64c34bbac6c03c8e02464eb028bacb9311..1b97a5dab13bc0c57ef942dab0ad673d9e591187 100644
--- a/src/compute_coord_atom.h
+++ b/src/compute_coord_atom.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/compute_dihedral_local.cpp b/src/compute_dihedral_local.cpp
index 10cac6f6070537917899447581ee6dfd15891caa..36feeca32ebfa0b414e5b12341be7823b8dce920 100644
--- a/src/compute_dihedral_local.cpp
+++ b/src/compute_dihedral_local.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -72,7 +72,7 @@ ComputeDihedralLocal::~ComputeDihedralLocal()
void ComputeDihedralLocal::init()
{
- if (force->dihedral == NULL)
+ if (force->dihedral == NULL)
error->all(FLERR,"No dihedral style is defined for compute dihedral/local");
// do initial memory allocation so that memory_usage() is correct
@@ -144,55 +144,55 @@ int ComputeDihedralLocal::compute_dihedrals(int flag)
if (flag) {
- // phi calculation from dihedral style harmonic
-
- if (pflag >= 0) {
- vb1x = x[atom1][0] - x[atom2][0];
- vb1y = x[atom1][1] - x[atom2][1];
- vb1z = x[atom1][2] - x[atom2][2];
- domain->minimum_image(vb1x,vb1y,vb1z);
-
- vb2x = x[atom3][0] - x[atom2][0];
- vb2y = x[atom3][1] - x[atom2][1];
- vb2z = x[atom3][2] - x[atom2][2];
- domain->minimum_image(vb2x,vb2y,vb2z);
-
- vb2xm = -vb2x;
- vb2ym = -vb2y;
- vb2zm = -vb2z;
- domain->minimum_image(vb2xm,vb2ym,vb2zm);
-
- vb3x = x[atom4][0] - x[atom3][0];
- vb3y = x[atom4][1] - x[atom3][1];
- vb3z = x[atom4][2] - x[atom3][2];
- domain->minimum_image(vb3x,vb3y,vb3z);
-
- ax = vb1y*vb2zm - vb1z*vb2ym;
- ay = vb1z*vb2xm - vb1x*vb2zm;
- az = vb1x*vb2ym - vb1y*vb2xm;
- bx = vb3y*vb2zm - vb3z*vb2ym;
- by = vb3z*vb2xm - vb3x*vb2zm;
- bz = vb3x*vb2ym - vb3y*vb2xm;
-
- rasq = ax*ax + ay*ay + az*az;
- rbsq = bx*bx + by*by + bz*bz;
- rgsq = vb2xm*vb2xm + vb2ym*vb2ym + vb2zm*vb2zm;
- rg = sqrt(rgsq);
-
- rginv = ra2inv = rb2inv = 0.0;
- if (rg > 0) rginv = 1.0/rg;
- if (rasq > 0) ra2inv = 1.0/rasq;
- if (rbsq > 0) rb2inv = 1.0/rbsq;
- rabinv = sqrt(ra2inv*rb2inv);
-
- c = (ax*bx + ay*by + az*bz)*rabinv;
- s = rg*rabinv*(ax*vb3x + ay*vb3y + az*vb3z);
-
- if (c > 1.0) c = 1.0;
- if (c < -1.0) c = -1.0;
- pbuf[n] = 180.0*atan2(s,c)/MY_PI;
- }
- n += nvalues;
+ // phi calculation from dihedral style harmonic
+
+ if (pflag >= 0) {
+ vb1x = x[atom1][0] - x[atom2][0];
+ vb1y = x[atom1][1] - x[atom2][1];
+ vb1z = x[atom1][2] - x[atom2][2];
+ domain->minimum_image(vb1x,vb1y,vb1z);
+
+ vb2x = x[atom3][0] - x[atom2][0];
+ vb2y = x[atom3][1] - x[atom2][1];
+ vb2z = x[atom3][2] - x[atom2][2];
+ domain->minimum_image(vb2x,vb2y,vb2z);
+
+ vb2xm = -vb2x;
+ vb2ym = -vb2y;
+ vb2zm = -vb2z;
+ domain->minimum_image(vb2xm,vb2ym,vb2zm);
+
+ vb3x = x[atom4][0] - x[atom3][0];
+ vb3y = x[atom4][1] - x[atom3][1];
+ vb3z = x[atom4][2] - x[atom3][2];
+ domain->minimum_image(vb3x,vb3y,vb3z);
+
+ ax = vb1y*vb2zm - vb1z*vb2ym;
+ ay = vb1z*vb2xm - vb1x*vb2zm;
+ az = vb1x*vb2ym - vb1y*vb2xm;
+ bx = vb3y*vb2zm - vb3z*vb2ym;
+ by = vb3z*vb2xm - vb3x*vb2zm;
+ bz = vb3x*vb2ym - vb3y*vb2xm;
+
+ rasq = ax*ax + ay*ay + az*az;
+ rbsq = bx*bx + by*by + bz*bz;
+ rgsq = vb2xm*vb2xm + vb2ym*vb2ym + vb2zm*vb2zm;
+ rg = sqrt(rgsq);
+
+ rginv = ra2inv = rb2inv = 0.0;
+ if (rg > 0) rginv = 1.0/rg;
+ if (rasq > 0) ra2inv = 1.0/rasq;
+ if (rbsq > 0) rb2inv = 1.0/rbsq;
+ rabinv = sqrt(ra2inv*rb2inv);
+
+ c = (ax*bx + ay*by + az*bz)*rabinv;
+ s = rg*rabinv*(ax*vb3x + ay*vb3y + az*vb3z);
+
+ if (c > 1.0) c = 1.0;
+ if (c < -1.0) c = -1.0;
+ pbuf[n] = 180.0*atan2(s,c)/MY_PI;
+ }
+ n += nvalues;
}
m++;
diff --git a/src/compute_dihedral_local.h b/src/compute_dihedral_local.h
index 3aaadb154a21414b9e10c74995e733d78340c8d8..82326bdf88eecf592c85cb1a61c9df3f654185c6 100644
--- a/src/compute_dihedral_local.h
+++ b/src/compute_dihedral_local.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/compute_displace_atom.cpp b/src/compute_displace_atom.cpp
index 59370ea831cda6562d2543f08014b1ec2850af46..f34e74c91b898542ef0b29fd8321d91bc3afce54 100644
--- a/src/compute_displace_atom.cpp
+++ b/src/compute_displace_atom.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -118,34 +118,34 @@ void ComputeDisplaceAtom::compute_peratom()
if (domain->triclinic == 0) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- xbox = (image[i] & 1023) - 512;
- ybox = (image[i] >> 10 & 1023) - 512;
- zbox = (image[i] >> 20) - 512;
- dx = x[i][0] + xbox*xprd - xoriginal[i][0];
- dy = x[i][1] + ybox*yprd - xoriginal[i][1];
- dz = x[i][2] + zbox*zprd - xoriginal[i][2];
- displace[i][0] = dx;
- displace[i][1] = dy;
- displace[i][2] = dz;
- displace[i][3] = sqrt(dx*dx + dy*dy + dz*dz);
+ xbox = (image[i] & 1023) - 512;
+ ybox = (image[i] >> 10 & 1023) - 512;
+ zbox = (image[i] >> 20) - 512;
+ dx = x[i][0] + xbox*xprd - xoriginal[i][0];
+ dy = x[i][1] + ybox*yprd - xoriginal[i][1];
+ dz = x[i][2] + zbox*zprd - xoriginal[i][2];
+ displace[i][0] = dx;
+ displace[i][1] = dy;
+ displace[i][2] = dz;
+ displace[i][3] = sqrt(dx*dx + dy*dy + dz*dz);
} else displace[i][0] = displace[i][1] =
- displace[i][2] = displace[i][3] = 0.0;
+ displace[i][2] = displace[i][3] = 0.0;
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- xbox = (image[i] & 1023) - 512;
- ybox = (image[i] >> 10 & 1023) - 512;
- zbox = (image[i] >> 20) - 512;
- dx = x[i][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox - xoriginal[i][0];
- dy = x[i][1] + h[1]*ybox + h[3]*zbox - xoriginal[i][1];
- dz = x[i][2] + h[2]*zbox - xoriginal[i][2];
- displace[i][0] = dx;
- displace[i][1] = dy;
- displace[i][2] = dz;
- displace[i][3] = sqrt(dx*dx + dy*dy + dz*dz);
+ xbox = (image[i] & 1023) - 512;
+ ybox = (image[i] >> 10 & 1023) - 512;
+ zbox = (image[i] >> 20) - 512;
+ dx = x[i][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox - xoriginal[i][0];
+ dy = x[i][1] + h[1]*ybox + h[3]*zbox - xoriginal[i][1];
+ dz = x[i][2] + h[2]*zbox - xoriginal[i][2];
+ displace[i][0] = dx;
+ displace[i][1] = dy;
+ displace[i][2] = dz;
+ displace[i][3] = sqrt(dx*dx + dy*dy + dz*dz);
} else displace[i][0] = displace[i][1] =
- displace[i][2] = displace[i][3] = 0.0;
+ displace[i][2] = displace[i][3] = 0.0;
}
}
diff --git a/src/compute_displace_atom.h b/src/compute_displace_atom.h
index ba8c8b8f043e480ea82487005e9b088575759d18..74e41cce4531eab1ec2a950b38ead81e3e2942af 100644
--- a/src/compute_displace_atom.h
+++ b/src/compute_displace_atom.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/compute_erotate_sphere.cpp b/src/compute_erotate_sphere.cpp
index 47bee40890486ad930ca4ee50cd29b5794958fc6..f0ba88cda6257e1bc2fdb69141b3189eda37f7c5 100644
--- a/src/compute_erotate_sphere.cpp
+++ b/src/compute_erotate_sphere.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -37,7 +37,7 @@ ComputeERotateSphere::ComputeERotateSphere(LAMMPS *lmp, int narg, char **arg) :
// error check
- if (!atom->sphere_flag)
+ if (!atom->sphere_flag)
error->all(FLERR,"Compute erotate/sphere requires atom style sphere");
}
@@ -64,10 +64,10 @@ double ComputeERotateSphere::compute_scalar()
// point particles will not contribute due to radius = 0
double erotate = 0.0;
- for (int i = 0; i < nlocal; i++)
+ for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
- erotate += (omega[i][0]*omega[i][0] + omega[i][1]*omega[i][1] +
- omega[i][2]*omega[i][2]) * radius[i]*radius[i]*rmass[i];
+ erotate += (omega[i][0]*omega[i][0] + omega[i][1]*omega[i][1] +
+ omega[i][2]*omega[i][2]) * radius[i]*radius[i]*rmass[i];
MPI_Allreduce(&erotate,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
scalar *= pfactor;
diff --git a/src/compute_erotate_sphere.h b/src/compute_erotate_sphere.h
index 6194b689ec8e9e0e255bd1c8f50e5527a40acadd..815a6655835a4d98a0588ab9b0741d25ed203863 100644
--- a/src/compute_erotate_sphere.h
+++ b/src/compute_erotate_sphere.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/compute_group_group.cpp b/src/compute_group_group.cpp
index 7981676cb3dc31f36f2530037fa90267dde011c6..069738e74db4d3bb927b1dddb5a33480a3f75fa0 100644
--- a/src/compute_group_group.cpp
+++ b/src/compute_group_group.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -41,7 +41,7 @@ using namespace MathConst;
/* ---------------------------------------------------------------------- */
-ComputeGroupGroup::ComputeGroupGroup(LAMMPS *lmp, int narg, char **arg) :
+ComputeGroupGroup::ComputeGroupGroup(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg < 4) error->all(FLERR,"Illegal compute group/group command");
@@ -56,7 +56,7 @@ ComputeGroupGroup::ComputeGroupGroup(LAMMPS *lmp, int narg, char **arg) :
strcpy(group2,arg[3]);
jgroup = group->find(group2);
- if (jgroup == -1)
+ if (jgroup == -1)
error->all(FLERR,"Compute group/group group ID does not exist");
jgroupbit = group->bitmask[jgroup];
@@ -68,21 +68,21 @@ ComputeGroupGroup::ComputeGroupGroup(LAMMPS *lmp, int narg, char **arg) :
while (iarg < narg) {
if (strcmp(arg[iarg],"pair") == 0) {
if (iarg+2 > narg)
- error->all(FLERR,"Illegal compute group/group command");
+ error->all(FLERR,"Illegal compute group/group command");
if (strcmp(arg[iarg+1],"yes") == 0) pairflag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) pairflag = 0;
else error->all(FLERR,"Illegal compute group/group command");
iarg += 2;
} else if (strcmp(arg[iarg],"kspace") == 0) {
if (iarg+2 > narg)
- error->all(FLERR,"Illegal compute group/group command");
+ error->all(FLERR,"Illegal compute group/group command");
if (strcmp(arg[iarg+1],"yes") == 0) kspaceflag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) kspaceflag = 0;
else error->all(FLERR,"Illegal compute group/group command");
iarg += 2;
} else if (strcmp(arg[iarg],"boundary") == 0) {
if (iarg+2 > narg)
- error->all(FLERR,"Illegal compute group/group command");
+ error->all(FLERR,"Illegal compute group/group command");
if (strcmp(arg[iarg+1],"yes") == 0) boundaryflag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) boundaryflag = 0;
else error->all(FLERR,"Illegal compute group/group command");
@@ -124,26 +124,26 @@ void ComputeGroupGroup::init()
pair = force->pair;
cutsq = force->pair->cutsq;
} else pair = NULL;
-
+
if (kspaceflag) kspace = force->kspace;
else kspace = NULL;
-
+
// compute Kspace correction terms
-
+
if (kspaceflag) {
kspace_correction();
if (fabs(e_correction) > SMALL && comm->me == 0) {
char str[128];
sprintf(str,"Both groups in compute group/group have a net charge; "
- "the Kspace boundary correction to energy will be non-zero");
+ "the Kspace boundary correction to energy will be non-zero");
error->warning(FLERR,str);
}
}
-
+
// recheck that group 2 has not been deleted
jgroup = group->find(group2);
- if (jgroup == -1)
+ if (jgroup == -1)
error->all(FLERR,"Compute group/group group ID does not exist");
jgroupbit = group->bitmask[jgroup];
@@ -252,35 +252,35 @@ void ComputeGroupGroup::pair_contribution()
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- eng = pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
-
- // energy only computed once so tally full amount
- // force tally is jgroup acting on igroup
-
- if (newton_pair || j < nlocal) {
- one[0] += eng;
- if (othergroupbit == jgroupbit) {
- one[1] += delx*fpair;
- one[2] += dely*fpair;
- one[3] += delz*fpair;
- }
- if (othergroupbit == groupbit) {
- one[1] -= delx*fpair;
- one[2] -= dely*fpair;
- one[3] -= delz*fpair;
- }
-
- // energy computed twice so tally half amount
- // only tally force if I own igroup atom
-
- } else {
- one[0] += 0.5*eng;
- if (othergroupbit == jgroupbit) {
- one[1] += delx*fpair;
- one[2] += dely*fpair;
- one[3] += delz*fpair;
- }
- }
+ eng = pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
+
+ // energy only computed once so tally full amount
+ // force tally is jgroup acting on igroup
+
+ if (newton_pair || j < nlocal) {
+ one[0] += eng;
+ if (othergroupbit == jgroupbit) {
+ one[1] += delx*fpair;
+ one[2] += dely*fpair;
+ one[3] += delz*fpair;
+ }
+ if (othergroupbit == groupbit) {
+ one[1] -= delx*fpair;
+ one[2] -= dely*fpair;
+ one[3] -= delz*fpair;
+ }
+
+ // energy computed twice so tally half amount
+ // only tally force if I own igroup atom
+
+ } else {
+ one[0] += 0.5*eng;
+ if (othergroupbit == jgroupbit) {
+ one[1] += delx*fpair;
+ one[2] += dely*fpair;
+ one[3] += delz*fpair;
+ }
+ }
}
}
}
@@ -297,23 +297,23 @@ void ComputeGroupGroup::kspace_contribution()
{
double *vector_kspace = force->kspace->f2group;
- force->kspace->compute_group_group(groupbit,jgroupbit,0);
+ force->kspace->compute_group_group(groupbit,jgroupbit,0);
scalar += force->kspace->e2group;
vector[0] += vector_kspace[0];
vector[1] += vector_kspace[1];
vector[2] += vector_kspace[2];
-
+
// compute extra B <--> A Kspace interaction so energy matches
// real-space style of compute group-group
// add extra Kspace term to energy
-
- force->kspace->compute_group_group(groupbit,jgroupbit,1);
+
+ force->kspace->compute_group_group(groupbit,jgroupbit,1);
scalar += force->kspace->e2group;
-
+
// self energy correction term
-
+
scalar -= e_self;
-
+
// k=0 boundary correction term
if (boundaryflag) {
@@ -330,63 +330,63 @@ void ComputeGroupGroup::kspace_contribution()
void ComputeGroupGroup::kspace_correction()
{
- // total charge of groups A & B, needed for correction term
-
+ // total charge of groups A & B, needed for correction term
+
double qsqsum_group,qsum_A,qsum_B;
qsqsum_group = qsum_A = qsum_B = 0.0;
-
+
double *q = atom->q;
int *mask = atom->mask;
int groupbit_A = groupbit;
int groupbit_B = jgroupbit;
-
+
for (int i = 0; i < atom->nlocal; i++) {
if ((mask[i] & groupbit_A) && (mask[i] & groupbit_B))
qsqsum_group += q[i]*q[i];
if (mask[i] & groupbit_A) qsum_A += q[i];
if (mask[i] & groupbit_B) qsum_B += q[i];
}
-
+
double tmp;
MPI_Allreduce(&qsqsum_group,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
qsqsum_group = tmp;
-
+
MPI_Allreduce(&qsum_A,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
qsum_A = tmp;
-
+
MPI_Allreduce(&qsum_B,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
qsum_B = tmp;
-
+
double g_ewald = force->kspace->g_ewald;
-
+
double scale = 1.0;
const double qscale = force->qqrd2e * scale;
-
+
// self-energy correction
-
+
e_self = qscale * g_ewald*qsqsum_group/MY_PIS;
e_correction = qsum_A*qsum_B;
-
+
// Extra BA terms
-
+
qsum_A = qsum_B = 0.0;
-
+
for (int i = 0; i < atom->nlocal; i++) {
if ((mask[i] & groupbit_A) && (mask[i] & groupbit_B))
- continue;
-
- if (mask[i] & groupbit_A) qsum_A += q[i];
+ continue;
+
+ if (mask[i] & groupbit_A) qsum_A += q[i];
if (mask[i] & groupbit_B) qsum_B += q[i];
}
-
+
MPI_Allreduce(&qsum_A,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
qsum_A = tmp;
-
+
MPI_Allreduce(&qsum_B,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
qsum_B = tmp;
-
+
// k=0 energy correction term (still need to divide by volume above)
-
+
e_correction += qsum_A*qsum_B;
- e_correction *= qscale * MY_PI2 / (g_ewald*g_ewald);
+ e_correction *= qscale * MY_PI2 / (g_ewald*g_ewald);
}
diff --git a/src/compute_group_group.h b/src/compute_group_group.h
index 850532ef42a066776c24626f7416a5d19ec8db4e..27eb7487fbf572a729acfc80c4a645da2f2ecc82 100644
--- a/src/compute_group_group.h
+++ b/src/compute_group_group.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/compute_gyration.cpp b/src/compute_gyration.cpp
index f192ea3d69d9d03309690f85de5a04e615e794d2..6eb38b059c60ceec58b3cf6b7f59e48384b5ab0a 100644
--- a/src/compute_gyration.cpp
+++ b/src/compute_gyration.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/compute_gyration.h b/src/compute_gyration.h
index 9ecab47eefade26c95729b95bd3cc571f858b346..fec374ea98a4ba100e2895d86dcd93bb70cf3c4d 100644
--- a/src/compute_gyration.h
+++ b/src/compute_gyration.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/compute_gyration_molecule.cpp b/src/compute_gyration_molecule.cpp
index dd96079d2196b0a2f4a40f685ee6a18012a20f61..cb1b2c33f5097f6085b5ad71bcf2d42b4a623789 100644
--- a/src/compute_gyration_molecule.cpp
+++ b/src/compute_gyration_molecule.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -23,8 +23,8 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-ComputeGyrationMolecule::ComputeGyrationMolecule(LAMMPS *lmp,
- int narg, char **arg) :
+ComputeGyrationMolecule::ComputeGyrationMolecule(LAMMPS *lmp,
+ int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 3) error->all(FLERR,"Illegal compute gyration/molecule command");
@@ -138,7 +138,7 @@ void ComputeGyrationMolecule::compute_vector()
}
MPI_Allreduce(&com[0][0],&comall[0][0],3*nmolecules,
- MPI_DOUBLE,MPI_SUM,world);
+ MPI_DOUBLE,MPI_SUM,world);
for (i = 0; i < nmolecules; i++) {
comall[i][0] /= masstotal[i];
comall[i][1] /= masstotal[i];
diff --git a/src/compute_gyration_molecule.h b/src/compute_gyration_molecule.h
index 952feb2110dde6633310aa00009344f7ee21e8b1..8c30321d89f7791c3915bc10969664b2e3c9fff4 100644
--- a/src/compute_gyration_molecule.h
+++ b/src/compute_gyration_molecule.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/compute_heat_flux.cpp b/src/compute_heat_flux.cpp
index a575eaf5e7ae3cfe5c589990d73533947bac704c..335304ef9d50d648e144d211c5009781dd7d9420 100644
--- a/src/compute_heat_flux.cpp
+++ b/src/compute_heat_flux.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -32,7 +32,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-ComputeHeatFlux::ComputeHeatFlux(LAMMPS *lmp, int narg, char **arg) :
+ComputeHeatFlux::ComputeHeatFlux(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 6) error->all(FLERR,"Illegal compute heat/flux command");
@@ -67,7 +67,7 @@ ComputeHeatFlux::ComputeHeatFlux(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,"Compute heat/flux compute ID does not compute pe/atom");
if (modify->compute[istress]->pressatomflag == 0)
error->all(FLERR,
- "Compute heat/flux compute ID does not compute stress/atom");
+ "Compute heat/flux compute ID does not compute stress/atom");
vector = new double[6];
}
@@ -75,7 +75,7 @@ ComputeHeatFlux::ComputeHeatFlux(LAMMPS *lmp, int narg, char **arg) :
/* ---------------------------------------------------------------------- */
ComputeHeatFlux::~ComputeHeatFlux()
-{
+{
delete [] id_ke;
delete [] id_pe;
delete [] id_stress;
@@ -106,7 +106,7 @@ void ComputeHeatFlux::compute_vector()
invoked_vector = update->ntimestep;
// invoke 3 computes if they haven't been already
-
+
if (!(c_ke->invoked_flag & INVOKED_PERATOM)) {
c_ke->compute_peratom();
c_ke->invoked_flag |= INVOKED_PERATOM;
@@ -137,20 +137,20 @@ void ComputeHeatFlux::compute_vector()
double jv[3] = {0.0,0.0,0.0};
double eng;
- for (int i = 0; i < nlocal; i++) {
+ for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
eng = pe[i] + ke[i];
- jc[0] += eng*v[i][0];
+ jc[0] += eng*v[i][0];
jc[1] += eng*v[i][1];
jc[2] += eng*v[i][2];
- jv[0] -= stress[i][0]*v[i][0] + stress[i][3]*v[i][1] +
- stress[i][4]*v[i][2];
- jv[1] -= stress[i][3]*v[i][0] + stress[i][1]*v[i][1] +
- stress[i][5]*v[i][2];
- jv[2] -= stress[i][4]*v[i][0] + stress[i][5]*v[i][1] +
- stress[i][2]*v[i][2];
+ jv[0] -= stress[i][0]*v[i][0] + stress[i][3]*v[i][1] +
+ stress[i][4]*v[i][2];
+ jv[1] -= stress[i][3]*v[i][0] + stress[i][1]*v[i][1] +
+ stress[i][5]*v[i][2];
+ jv[2] -= stress[i][4]*v[i][0] + stress[i][5]*v[i][1] +
+ stress[i][2]*v[i][2];
}
- }
+ }
// convert jv from stress*volume to energy units via nktv2p factor
@@ -162,7 +162,7 @@ void ComputeHeatFlux::compute_vector()
// sum across all procs
// 1st 3 terms are total heat flux
// 2nd 3 terms are just conductive portion
-
+
double data[6] = {jc[0]+jv[0],jc[1]+jv[1],jc[2]+jv[2],jc[0],jc[1],jc[2]};
MPI_Allreduce(data,vector,6,MPI_DOUBLE,MPI_SUM,world);
}
diff --git a/src/compute_heat_flux.h b/src/compute_heat_flux.h
index 26c5a9e778317ee032c2985822800b096d01ef78..865411776c6c7ea0fd7df8f726dac6bac96473c6 100644
--- a/src/compute_heat_flux.h
+++ b/src/compute_heat_flux.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/compute_improper_local.cpp b/src/compute_improper_local.cpp
index 3285f2561c3d54dde1bc1affc4e53eb762b45c3d..708b27d6f3f03a2e83ef8a6a4cfd1ed919ae9e33 100644
--- a/src/compute_improper_local.cpp
+++ b/src/compute_improper_local.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -73,7 +73,7 @@ ComputeImproperLocal::~ComputeImproperLocal()
void ComputeImproperLocal::init()
{
- if (force->improper == NULL)
+ if (force->improper == NULL)
error->all(FLERR,"No improper style is defined for compute improper/local");
// do initial memory allocation so that memory_usage() is correct
@@ -145,52 +145,52 @@ int ComputeImproperLocal::compute_impropers(int flag)
if (flag) {
- // chi calculation from improper style harmonic
-
- if (cflag >= 0) {
- vb1x = x[atom1][0] - x[atom2][0];
- vb1y = x[atom1][1] - x[atom2][1];
- vb1z = x[atom1][2] - x[atom2][2];
- domain->minimum_image(vb1x,vb1y,vb1z);
-
- vb2x = x[atom3][0] - x[atom2][0];
- vb2y = x[atom3][1] - x[atom2][1];
- vb2z = x[atom3][2] - x[atom2][2];
- domain->minimum_image(vb2x,vb2y,vb2z);
-
- vb3x = x[atom4][0] - x[atom3][0];
- vb3y = x[atom4][1] - x[atom3][1];
- vb3z = x[atom4][2] - x[atom3][2];
- domain->minimum_image(vb3x,vb3y,vb3z);
-
- ss1 = 1.0 / (vb1x*vb1x + vb1y*vb1y + vb1z*vb1z);
- ss2 = 1.0 / (vb2x*vb2x + vb2y*vb2y + vb2z*vb2z);
- ss3 = 1.0 / (vb3x*vb3x + vb3y*vb3y + vb3z*vb3z);
-
- r1 = sqrt(ss1);
- r2 = sqrt(ss2);
- r3 = sqrt(ss3);
-
- c0 = (vb1x * vb3x + vb1y * vb3y + vb1z * vb3z) * r1 * r3;
- c1 = (vb1x * vb2x + vb1y * vb2y + vb1z * vb2z) * r1 * r2;
- c2 = -(vb3x * vb2x + vb3y * vb2y + vb3z * vb2z) * r3 * r2;
-
- s1 = 1.0 - c1*c1;
- if (s1 < SMALL) s1 = SMALL;
- s1 = 1.0 / s1;
-
- s2 = 1.0 - c2*c2;
- if (s2 < SMALL) s2 = SMALL;
- s2 = 1.0 / s2;
-
- s12 = sqrt(s1*s2);
- c = (c1*c2 + c0) * s12;
-
- if (c > 1.0) c = 1.0;
- if (c < -1.0) c = -1.0;
- cbuf[n] = 180.0*acos(c)/MY_PI;
- }
- n += nvalues;
+ // chi calculation from improper style harmonic
+
+ if (cflag >= 0) {
+ vb1x = x[atom1][0] - x[atom2][0];
+ vb1y = x[atom1][1] - x[atom2][1];
+ vb1z = x[atom1][2] - x[atom2][2];
+ domain->minimum_image(vb1x,vb1y,vb1z);
+
+ vb2x = x[atom3][0] - x[atom2][0];
+ vb2y = x[atom3][1] - x[atom2][1];
+ vb2z = x[atom3][2] - x[atom2][2];
+ domain->minimum_image(vb2x,vb2y,vb2z);
+
+ vb3x = x[atom4][0] - x[atom3][0];
+ vb3y = x[atom4][1] - x[atom3][1];
+ vb3z = x[atom4][2] - x[atom3][2];
+ domain->minimum_image(vb3x,vb3y,vb3z);
+
+ ss1 = 1.0 / (vb1x*vb1x + vb1y*vb1y + vb1z*vb1z);
+ ss2 = 1.0 / (vb2x*vb2x + vb2y*vb2y + vb2z*vb2z);
+ ss3 = 1.0 / (vb3x*vb3x + vb3y*vb3y + vb3z*vb3z);
+
+ r1 = sqrt(ss1);
+ r2 = sqrt(ss2);
+ r3 = sqrt(ss3);
+
+ c0 = (vb1x * vb3x + vb1y * vb3y + vb1z * vb3z) * r1 * r3;
+ c1 = (vb1x * vb2x + vb1y * vb2y + vb1z * vb2z) * r1 * r2;
+ c2 = -(vb3x * vb2x + vb3y * vb2y + vb3z * vb2z) * r3 * r2;
+
+ s1 = 1.0 - c1*c1;
+ if (s1 < SMALL) s1 = SMALL;
+ s1 = 1.0 / s1;
+
+ s2 = 1.0 - c2*c2;
+ if (s2 < SMALL) s2 = SMALL;
+ s2 = 1.0 / s2;
+
+ s12 = sqrt(s1*s2);
+ c = (c1*c2 + c0) * s12;
+
+ if (c > 1.0) c = 1.0;
+ if (c < -1.0) c = -1.0;
+ cbuf[n] = 180.0*acos(c)/MY_PI;
+ }
+ n += nvalues;
}
m++;
diff --git a/src/compute_improper_local.h b/src/compute_improper_local.h
index 60028bdb84056af89fc502399a47fc23f24a29c2..57fe7886eb223db09ad3984b10e60993a379ab58 100644
--- a/src/compute_improper_local.h
+++ b/src/compute_improper_local.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/compute_ke.cpp b/src/compute_ke.cpp
index 629f1488e1b6767a228d997f67c0d8864aadabfa..3efd6983250a3ca922921928e77f5fe8c89ac082 100644
--- a/src/compute_ke.cpp
+++ b/src/compute_ke.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -56,14 +56,14 @@ double ComputeKE::compute_scalar()
double ke = 0.0;
if (rmass) {
- for (int i = 0; i < nlocal; i++)
+ for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
- ke += rmass[i] * (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]);
+ ke += rmass[i] * (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]);
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
- ke += mass[type[i]] *
- (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]);
+ ke += mass[type[i]] *
+ (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]);
}
MPI_Allreduce(&ke,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
diff --git a/src/compute_ke.h b/src/compute_ke.h
index 7bb4b4cfa5bb63260423272a3bba184aa4ceedf2..5dbfeb3081be3ab4de70721c150208a3abb9967e 100644
--- a/src/compute_ke.h
+++ b/src/compute_ke.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/compute_ke_atom.cpp b/src/compute_ke_atom.cpp
index 6d9d45268f4562eca48b1486a88a6f36287351dc..5709c428374be4f9e0468207a804878ddfe767ed 100644
--- a/src/compute_ke_atom.cpp
+++ b/src/compute_ke_atom.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -83,16 +83,16 @@ void ComputeKEAtom::compute_peratom()
if (rmass)
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
- ke[i] = 0.5 * mvv2e * rmass[i] *
- (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]);
+ ke[i] = 0.5 * mvv2e * rmass[i] *
+ (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]);
} else ke[i] = 0.0;
}
else
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
- ke[i] = 0.5 * mvv2e * mass[type[i]] *
- (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]);
+ ke[i] = 0.5 * mvv2e * mass[type[i]] *
+ (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]);
} else ke[i] = 0.0;
}
}
diff --git a/src/compute_ke_atom.h b/src/compute_ke_atom.h
index 9a1265402b900d88e2c7f54f97c44f5bfa341f1c..3c815ed1c32eb693c4ef83223a5d5a894cca57ba 100644
--- a/src/compute_ke_atom.h
+++ b/src/compute_ke_atom.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/compute_msd.cpp b/src/compute_msd.cpp
index bf2d00332e69e3c2c9a05cc01ea11fffe1a70cfb..9941abe42a1328e5ca34239e3a350e97a0f4e28c 100644
--- a/src/compute_msd.cpp
+++ b/src/compute_msd.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -140,7 +140,7 @@ void ComputeMSD::compute_vector()
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
-
+
double dx,dy,dz;
int xbox,ybox,zbox;
@@ -150,32 +150,32 @@ void ComputeMSD::compute_vector()
if (domain->triclinic == 0) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- xbox = (image[i] & 1023) - 512;
- ybox = (image[i] >> 10 & 1023) - 512;
- zbox = (image[i] >> 20) - 512;
- dx = x[i][0] + xbox*xprd - cm[0] - xoriginal[i][0];
- dy = x[i][1] + ybox*yprd - cm[1] - xoriginal[i][1];
- dz = x[i][2] + zbox*zprd - cm[2] - xoriginal[i][2];
- msd[0] += dx*dx;
- msd[1] += dy*dy;
- msd[2] += dz*dz;
- msd[3] += dx*dx + dy*dy + dz*dz;
+ xbox = (image[i] & 1023) - 512;
+ ybox = (image[i] >> 10 & 1023) - 512;
+ zbox = (image[i] >> 20) - 512;
+ dx = x[i][0] + xbox*xprd - cm[0] - xoriginal[i][0];
+ dy = x[i][1] + ybox*yprd - cm[1] - xoriginal[i][1];
+ dz = x[i][2] + zbox*zprd - cm[2] - xoriginal[i][2];
+ msd[0] += dx*dx;
+ msd[1] += dy*dy;
+ msd[2] += dz*dz;
+ msd[3] += dx*dx + dy*dy + dz*dz;
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- xbox = (image[i] & 1023) - 512;
- ybox = (image[i] >> 10 & 1023) - 512;
- zbox = (image[i] >> 20) - 512;
- dx = x[i][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox -
- cm[0] - xoriginal[i][0];
- dy = x[i][1] + h[1]*ybox + h[3]*zbox - cm[1] - xoriginal[i][1];
- dz = x[i][2] + h[2]*zbox - cm[2] - xoriginal[i][2];
- msd[0] += dx*dx;
- msd[1] += dy*dy;
- msd[2] += dz*dz;
- msd[3] += dx*dx + dy*dy + dz*dz;
+ xbox = (image[i] & 1023) - 512;
+ ybox = (image[i] >> 10 & 1023) - 512;
+ zbox = (image[i] >> 20) - 512;
+ dx = x[i][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox -
+ cm[0] - xoriginal[i][0];
+ dy = x[i][1] + h[1]*ybox + h[3]*zbox - cm[1] - xoriginal[i][1];
+ dz = x[i][2] + h[2]*zbox - cm[2] - xoriginal[i][2];
+ msd[0] += dx*dx;
+ msd[1] += dy*dy;
+ msd[2] += dz*dz;
+ msd[3] += dx*dx + dy*dy + dz*dz;
}
}
diff --git a/src/compute_msd.h b/src/compute_msd.h
index f4cc93d50275ea6f882910094a89f5420dbca8cb..d2a35a4d62290b871c967b366d860565539557be 100644
--- a/src/compute_msd.h
+++ b/src/compute_msd.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/compute_msd_molecule.cpp b/src/compute_msd_molecule.cpp
index de8d2f63c5883a48307f7cdd41b83aecac277b81..bd4e9960fb49162cf50c259dfda26ab70d39dc29 100644
--- a/src/compute_msd_molecule.cpp
+++ b/src/compute_msd_molecule.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -150,7 +150,7 @@ void ComputeMSDMolecule::compute_array()
}
MPI_Allreduce(&com[0][0],&comall[0][0],3*nmolecules,
- MPI_DOUBLE,MPI_SUM,world);
+ MPI_DOUBLE,MPI_SUM,world);
for (i = 0; i < nmolecules; i++) {
comall[i][0] /= masstotal[i];
comall[i][1] /= masstotal[i];
diff --git a/src/compute_msd_molecule.h b/src/compute_msd_molecule.h
index 3c1a59f6e2e00115c013052b6da101ea0faa295e..b4c5bd53a19e3c6e410783836da5ab4aba96ca3b 100644
--- a/src/compute_msd_molecule.h
+++ b/src/compute_msd_molecule.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/compute_pair.cpp b/src/compute_pair.cpp
index 60c723b952f2d1cf9146818d0fd6a297e1a7be71..8c7fa0cef3660e5210088fff03c5d1afb67c86d1 100644
--- a/src/compute_pair.cpp
+++ b/src/compute_pair.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -25,7 +25,7 @@ enum{EPAIR,EVDWL,ECOUL};
/* ---------------------------------------------------------------------- */
-ComputePair::ComputePair(LAMMPS *lmp, int narg, char **arg) :
+ComputePair::ComputePair(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg < 4 || narg > 5) error->all(FLERR,"Illegal compute pair command");
@@ -56,7 +56,7 @@ ComputePair::ComputePair(LAMMPS *lmp, int narg, char **arg) :
pair = force->pair_match(pstyle,1);
}
- if (!pair)
+ if (!pair)
error->all(FLERR,"Unrecognized pair style in compute pair command");
npair = pair->nextra;
@@ -85,7 +85,7 @@ void ComputePair::init()
// recheck for pair style in case it has been deleted
pair = force->pair_match(pstyle,1);
- if (!pair)
+ if (!pair)
error->all(FLERR,"Unrecognized pair style in compute pair command");
}
diff --git a/src/compute_pair.h b/src/compute_pair.h
index ff37eb6e048d2b30e03a585b533fd2742a268fad..880d02cbd223b2dab6bf83baf2ee256346121816 100644
--- a/src/compute_pair.h
+++ b/src/compute_pair.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/compute_pair_local.cpp b/src/compute_pair_local.cpp
index a33232db1b4291d54bb0b5d659b0515f3155cdb2..4215584e4e19101f3bedcf3b243c12eed3f91606 100644
--- a/src/compute_pair_local.cpp
+++ b/src/compute_pair_local.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -58,7 +58,7 @@ ComputePairLocal::ComputePairLocal(LAMMPS *lmp, int narg, char **arg) :
else if (arg[iarg][0] == 'p') {
int n = atoi(&arg[iarg][1]);
if (n <= 0) error->all(FLERR,
- "Invalid keyword in compute pair/local command");
+ "Invalid keyword in compute pair/local command");
pstyle[nvalues] = PN;
pindex[nvalues++] = n-1;
} else error->all(FLERR,"Invalid keyword in compute pair/local command");
@@ -89,7 +89,7 @@ ComputePairLocal::~ComputePairLocal()
void ComputePairLocal::init()
{
- if (singleflag && force->pair == NULL)
+ if (singleflag && force->pair == NULL)
error->all(FLERR,"No pair style is defined for compute pair/local");
if (singleflag && force->pair->single_enable == 0)
error->all(FLERR,"Pair style does not support compute pair/local");
@@ -97,7 +97,7 @@ void ComputePairLocal::init()
for (int i = 0; i < nvalues; i++)
if (pstyle[i] == PN && pindex[i] >= force->pair->single_extra)
error->all(FLERR,"Pair style does not have extra field"
- " requested by compute pair/local");
+ " requested by compute pair/local");
// need an occasional half neighbor list
@@ -195,39 +195,39 @@ int ComputePairLocal::compute_pairs(int flag)
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq >= cutsq[itype][jtype]) continue;
-
+
if (flag) {
- if (singleflag)
- eng = pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
-
- if (nvalues == 1) ptr = &vector[m];
- else ptr = array[m];
-
- for (n = 0; n < nvalues; n++) {
- switch (pstyle[n]) {
- case DIST:
- ptr[n] = sqrt(rsq);
- break;
- case ENG:
- ptr[n] = eng;
- break;
- case FORCE:
- ptr[n] = sqrt(rsq)*fpair;
- break;
- case FX:
- ptr[n] = delx*fpair;
- break;
- case FY:
- ptr[n] = dely*fpair;
- break;
- case FZ:
- ptr[n] = delz*fpair;
- break;
- case PN:
- ptr[n] = pair->svector[pindex[n]];
- break;
- }
- }
+ if (singleflag)
+ eng = pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
+
+ if (nvalues == 1) ptr = &vector[m];
+ else ptr = array[m];
+
+ for (n = 0; n < nvalues; n++) {
+ switch (pstyle[n]) {
+ case DIST:
+ ptr[n] = sqrt(rsq);
+ break;
+ case ENG:
+ ptr[n] = eng;
+ break;
+ case FORCE:
+ ptr[n] = sqrt(rsq)*fpair;
+ break;
+ case FX:
+ ptr[n] = delx*fpair;
+ break;
+ case FY:
+ ptr[n] = dely*fpair;
+ break;
+ case FZ:
+ ptr[n] = delz*fpair;
+ break;
+ case PN:
+ ptr[n] = pair->svector[pindex[n]];
+ break;
+ }
+ }
}
m++;
diff --git a/src/compute_pair_local.h b/src/compute_pair_local.h
index d9ed87d9470fa2634845dd4de15846fb3dc07bd1..82851861c48599bc2f90e687940fc9908661b951 100644
--- a/src/compute_pair_local.h
+++ b/src/compute_pair_local.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -37,7 +37,7 @@ class ComputePairLocal : public Compute {
int nvalues,dflag,eflag,fflag;
int ncount;
- int *pstyle; // style of each requested output
+ int *pstyle; // style of each requested output
int *pindex; // for pI, index of the output (0 to M-1)
int singleflag;
diff --git a/src/compute_pe.cpp b/src/compute_pe.cpp
index 75ec66dfd6fff0bd3c992a52c0b944823ac335f1..aaa87d820424376a74a7a8e3bd9dbe4f5ac6b3fe 100644
--- a/src/compute_pe.cpp
+++ b/src/compute_pe.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -31,7 +31,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-ComputePE::ComputePE(LAMMPS *lmp, int narg, char **arg) :
+ComputePE::ComputePE(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg < 3) error->all(FLERR,"Illegal compute pe command");
diff --git a/src/compute_pe.h b/src/compute_pe.h
index e4a45a485cda2f911d03ca806ab4263b6e0b9421..88a2b63790c17568b5dd529cc31ccc303286c50a 100644
--- a/src/compute_pe.h
+++ b/src/compute_pe.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/compute_pe_atom.cpp b/src/compute_pe_atom.cpp
index c16349402ce6db3521745708464c08b30950e2d4..91bdb9120cfdcab11ed3b750713d12a73191c15a 100755
--- a/src/compute_pe_atom.cpp
+++ b/src/compute_pe_atom.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -30,7 +30,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-ComputePEAtom::ComputePEAtom(LAMMPS *lmp, int narg, char **arg) :
+ComputePEAtom::ComputePEAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg < 3) error->all(FLERR,"Illegal compute pe/atom command");
@@ -111,7 +111,7 @@ void ComputePEAtom::compute_peratom()
for (i = 0; i < ntotal; i++) energy[i] = 0.0;
// add in per-atom contributions from each force
-
+
if (pairflag && force->pair) {
double *eatom = force->pair->eatom;
for (i = 0; i < npair; i++) energy[i] += eatom[i];
diff --git a/src/compute_pe_atom.h b/src/compute_pe_atom.h
index 6feaa4af4a50111e134bdbc3df38c32c77f524c4..986e16fcd20fcd4c5fbeaf57eb23653ca2617e89 100755
--- a/src/compute_pe_atom.h
+++ b/src/compute_pe_atom.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/compute_pressure.cpp b/src/compute_pressure.cpp
index 1870882a18933ec0b13441d59c2c19d6b5125290..95a66af51f1a4434ba3ecc932d29351c22301ab7 100644
--- a/src/compute_pressure.cpp
+++ b/src/compute_pressure.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -54,11 +54,11 @@ ComputePressure::ComputePressure(LAMMPS *lmp, int narg, char **arg) :
strcpy(id_temp,arg[3]);
int icompute = modify->find_compute(id_temp);
- if (icompute < 0)
+ if (icompute < 0)
error->all(FLERR,"Could not find compute pressure temperature ID");
if (modify->compute[icompute]->tempflag == 0)
error->all(FLERR,
- "Compute pressure temperature ID does not compute temperature");
+ "Compute pressure temperature ID does not compute temperature");
// process optional args
@@ -83,9 +83,9 @@ ComputePressure::ComputePressure(LAMMPS *lmp, int narg, char **arg) :
else if (strcmp(arg[iarg],"kspace") == 0) kspaceflag = 1;
else if (strcmp(arg[iarg],"fix") == 0) fixflag = 1;
else if (strcmp(arg[iarg],"virial") == 0) {
- pairflag = 1;
- bondflag = angleflag = dihedralflag = improperflag = 1;
- kspaceflag = fixflag = 1;
+ pairflag = 1;
+ bondflag = angleflag = dihedralflag = improperflag = 1;
+ kspaceflag = fixflag = 1;
} else error->all(FLERR,"Illegal compute pressure command");
iarg++;
}
@@ -117,7 +117,7 @@ void ComputePressure::init()
// fixes could have changed or compute_modify could have changed it
int icompute = modify->find_compute(id_temp);
- if (icompute < 0)
+ if (icompute < 0)
error->all(FLERR,"Could not find compute pressure temperature ID");
temperature = modify->compute[icompute];
@@ -149,8 +149,8 @@ void ComputePressure::init()
vptr[nvirial++] = force->improper->virial;
if (fixflag)
for (int i = 0; i < modify->nfix; i++)
- if (modify->fix[i]->virial_flag)
- vptr[nvirial++] = modify->fix[i]->virial;
+ if (modify->fix[i]->virial_flag)
+ vptr[nvirial++] = modify->fix[i]->virial;
}
// flag Kspace contribution separately, since not summed across procs
@@ -182,16 +182,16 @@ double ComputePressure::compute_scalar()
inv_volume = 1.0 / (domain->xprd * domain->yprd * domain->zprd);
virial_compute(3,3);
if (keflag)
- scalar = (temperature->dof * boltz * t +
- virial[0] + virial[1] + virial[2]) / 3.0 * inv_volume * nktv2p;
+ scalar = (temperature->dof * boltz * t +
+ virial[0] + virial[1] + virial[2]) / 3.0 * inv_volume * nktv2p;
else
scalar = (virial[0] + virial[1] + virial[2]) / 3.0 * inv_volume * nktv2p;
} else {
inv_volume = 1.0 / (domain->xprd * domain->yprd);
virial_compute(2,2);
if (keflag)
- scalar = (temperature->dof * boltz * t +
- virial[0] + virial[1]) / 2.0 * inv_volume * nktv2p;
+ scalar = (temperature->dof * boltz * t +
+ virial[0] + virial[1]) / 2.0 * inv_volume * nktv2p;
else
scalar = (virial[0] + virial[1]) / 2.0 * inv_volume * nktv2p;
}
@@ -224,10 +224,10 @@ void ComputePressure::compute_vector()
virial_compute(6,3);
if (keflag) {
for (int i = 0; i < 6; i++)
- vector[i] = (ke_tensor[i] + virial[i]) * inv_volume * nktv2p;
+ vector[i] = (ke_tensor[i] + virial[i]) * inv_volume * nktv2p;
} else
for (int i = 0; i < 6; i++)
- vector[i] = virial[i] * inv_volume * nktv2p;
+ vector[i] = virial[i] * inv_volume * nktv2p;
} else {
inv_volume = 1.0 / (domain->xprd * domain->yprd);
virial_compute(4,2);
diff --git a/src/compute_pressure.h b/src/compute_pressure.h
index ab5948114100993e983b2da03506d69f0bfdc49e..8056a1bfaad199497fc3e13c16ef59cb3ea635a3 100644
--- a/src/compute_pressure.h
+++ b/src/compute_pressure.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/compute_property_atom.cpp b/src/compute_property_atom.cpp
index 80efd8a5bf815799df8c120f44c966133ce3908e..4336c890a9f0b2df435d46c057c730f9f79e6a0f 100644
--- a/src/compute_property_atom.cpp
+++ b/src/compute_property_atom.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -51,8 +51,8 @@ ComputePropertyAtom::ComputePropertyAtom(LAMMPS *lmp, int narg, char **arg) :
pack_choice[i] = &ComputePropertyAtom::pack_id;
} else if (strcmp(arg[iarg],"mol") == 0) {
if (!atom->molecule_flag)
- error->all(FLERR,"Compute property/atom for "
- "atom property that isn't allocated");
+ error->all(FLERR,"Compute property/atom for "
+ "atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_molecule;
} else if (strcmp(arg[iarg],"type") == 0) {
pack_choice[i] = &ComputePropertyAtom::pack_type;
@@ -66,28 +66,28 @@ ComputePropertyAtom::ComputePropertyAtom(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"z") == 0) {
pack_choice[i] = &ComputePropertyAtom::pack_z;
} else if (strcmp(arg[iarg],"xs") == 0) {
- if (domain->triclinic)
- pack_choice[i] = &ComputePropertyAtom::pack_xs_triclinic;
+ if (domain->triclinic)
+ pack_choice[i] = &ComputePropertyAtom::pack_xs_triclinic;
else pack_choice[i] = &ComputePropertyAtom::pack_xs;
} else if (strcmp(arg[iarg],"ys") == 0) {
- if (domain->triclinic)
- pack_choice[i] = &ComputePropertyAtom::pack_ys_triclinic;
+ if (domain->triclinic)
+ pack_choice[i] = &ComputePropertyAtom::pack_ys_triclinic;
else pack_choice[i] = &ComputePropertyAtom::pack_ys;
} else if (strcmp(arg[iarg],"zs") == 0) {
- if (domain->triclinic)
- pack_choice[i] = &ComputePropertyAtom::pack_zs_triclinic;
+ if (domain->triclinic)
+ pack_choice[i] = &ComputePropertyAtom::pack_zs_triclinic;
else pack_choice[i] = &ComputePropertyAtom::pack_zs;
} else if (strcmp(arg[iarg],"xu") == 0) {
- if (domain->triclinic)
- pack_choice[i] = &ComputePropertyAtom::pack_xu_triclinic;
+ if (domain->triclinic)
+ pack_choice[i] = &ComputePropertyAtom::pack_xu_triclinic;
else pack_choice[i] = &ComputePropertyAtom::pack_xu;
} else if (strcmp(arg[iarg],"yu") == 0) {
- if (domain->triclinic)
- pack_choice[i] = &ComputePropertyAtom::pack_yu_triclinic;
+ if (domain->triclinic)
+ pack_choice[i] = &ComputePropertyAtom::pack_yu_triclinic;
else pack_choice[i] = &ComputePropertyAtom::pack_yu;
} else if (strcmp(arg[iarg],"zu") == 0) {
- if (domain->triclinic)
- pack_choice[i] = &ComputePropertyAtom::pack_zu_triclinic;
+ if (domain->triclinic)
+ pack_choice[i] = &ComputePropertyAtom::pack_zu_triclinic;
else pack_choice[i] = &ComputePropertyAtom::pack_zu;
} else if (strcmp(arg[iarg],"ix") == 0) {
pack_choice[i] = &ComputePropertyAtom::pack_ix;
@@ -111,218 +111,218 @@ ComputePropertyAtom::ComputePropertyAtom(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"q") == 0) {
if (!atom->q_flag)
- error->all(FLERR,"Compute property/atom for "
- "atom property that isn't allocated");
+ error->all(FLERR,"Compute property/atom for "
+ "atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_q;
} else if (strcmp(arg[iarg],"mux") == 0) {
if (!atom->mu_flag)
- error->all(FLERR,"Compute property/atom for "
- "atom property that isn't allocated");
+ error->all(FLERR,"Compute property/atom for "
+ "atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_mux;
} else if (strcmp(arg[iarg],"muy") == 0) {
if (!atom->mu_flag)
- error->all(FLERR,"Compute property/atom for "
- "atom property that isn't allocated");
+ error->all(FLERR,"Compute property/atom for "
+ "atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_muy;
} else if (strcmp(arg[iarg],"muz") == 0) {
if (!atom->mu_flag)
- error->all(FLERR,"Compute property/atom for "
- "atom property that isn't allocated");
+ error->all(FLERR,"Compute property/atom for "
+ "atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_muz;
} else if (strcmp(arg[iarg],"mu") == 0) {
if (!atom->mu_flag)
- error->all(FLERR,"Compute property/atom for "
- "atom property that isn't allocated");
+ error->all(FLERR,"Compute property/atom for "
+ "atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_mu;
} else if (strcmp(arg[iarg],"radius") == 0) {
if (!atom->radius_flag)
- error->all(FLERR,"Compute property/atom for "
- "atom property that isn't allocated");
+ error->all(FLERR,"Compute property/atom for "
+ "atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_radius;
} else if (strcmp(arg[iarg],"diameter") == 0) {
if (!atom->radius_flag)
- error->all(FLERR,"Compute property/atom for "
- "atom property that isn't allocated");
+ error->all(FLERR,"Compute property/atom for "
+ "atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_diameter;
} else if (strcmp(arg[iarg],"omegax") == 0) {
if (!atom->omega_flag)
- error->all(FLERR,"Compute property/atom for "
- "atom property that isn't allocated");
+ error->all(FLERR,"Compute property/atom for "
+ "atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_omegax;
} else if (strcmp(arg[iarg],"omegay") == 0) {
if (!atom->omega_flag)
- error->all(FLERR,"Compute property/atom for "
- "atom property that isn't allocated");
+ error->all(FLERR,"Compute property/atom for "
+ "atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_omegay;
} else if (strcmp(arg[iarg],"omegaz") == 0) {
if (!atom->omega_flag)
- error->all(FLERR,"Compute property/atom for "
- "atom property that isn't allocated");
+ error->all(FLERR,"Compute property/atom for "
+ "atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_omegaz;
} else if (strcmp(arg[iarg],"angmomx") == 0) {
if (!atom->angmom_flag)
- error->all(FLERR,"Compute property/atom for "
- "atom property that isn't allocated");
+ error->all(FLERR,"Compute property/atom for "
+ "atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_angmomx;
} else if (strcmp(arg[iarg],"angmomy") == 0) {
if (!atom->angmom_flag)
- error->all(FLERR,"Compute property/atom for "
- "atom property that isn't allocated");
+ error->all(FLERR,"Compute property/atom for "
+ "atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_angmomy;
} else if (strcmp(arg[iarg],"angmomz") == 0) {
if (!atom->angmom_flag)
- error->all(FLERR,"Compute property/atom for "
- "atom property that isn't allocated");
+ error->all(FLERR,"Compute property/atom for "
+ "atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_angmomz;
} else if (strcmp(arg[iarg],"shapex") == 0) {
avec_ellipsoid = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
if (!avec_ellipsoid) error->all(FLERR,"Compute property/atom for "
- "atom property that isn't allocated");
+ "atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_shapex;
} else if (strcmp(arg[iarg],"shapey") == 0) {
avec_ellipsoid = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
if (!avec_ellipsoid) error->all(FLERR,"Compute property/atom for "
- "atom property that isn't allocated");
+ "atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_shapey;
} else if (strcmp(arg[iarg],"shapez") == 0) {
avec_ellipsoid = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
if (!avec_ellipsoid) error->all(FLERR,"Compute property/atom for "
- "atom property that isn't allocated");
+ "atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_shapez;
} else if (strcmp(arg[iarg],"quatw") == 0) {
avec_ellipsoid = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
if (!avec_ellipsoid) error->all(FLERR,"Compute property/atom for "
- "atom property that isn't allocated");
+ "atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_quatw;
} else if (strcmp(arg[iarg],"quati") == 0) {
avec_ellipsoid = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
if (!avec_ellipsoid) error->all(FLERR,"Compute property/atom for "
- "atom property that isn't allocated");
+ "atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_quati;
} else if (strcmp(arg[iarg],"quatj") == 0) {
avec_ellipsoid = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
if (!avec_ellipsoid) error->all(FLERR,"Compute property/atom for "
- "atom property that isn't allocated");
+ "atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_quatj;
} else if (strcmp(arg[iarg],"quatk") == 0) {
avec_ellipsoid = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
if (!avec_ellipsoid) error->all(FLERR,"Compute property/atom for "
- "atom property that isn't allocated");
+ "atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_quatk;
} else if (strcmp(arg[iarg],"tqx") == 0) {
if (!atom->torque_flag)
- error->all(FLERR,"Compute property/atom for "
- "atom property that isn't allocated");
+ error->all(FLERR,"Compute property/atom for "
+ "atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_tqx;
} else if (strcmp(arg[iarg],"tqy") == 0) {
if (!atom->torque_flag)
- error->all(FLERR,"Compute property/atom for "
- "atom property that isn't allocated");
+ error->all(FLERR,"Compute property/atom for "
+ "atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_tqy;
} else if (strcmp(arg[iarg],"tqz") == 0) {
if (!atom->torque_flag)
- error->all(FLERR,"Compute property/atom for "
- "atom property that isn't allocated");
+ error->all(FLERR,"Compute property/atom for "
+ "atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_tqz;
} else if (strcmp(arg[iarg],"spin") == 0) {
if (!atom->spin_flag)
- error->all(FLERR,"Compute property/atom for "
- "atom property that isn't allocated");
+ error->all(FLERR,"Compute property/atom for "
+ "atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_spin;
} else if (strcmp(arg[iarg],"eradius") == 0) {
if (!atom->eradius_flag)
- error->all(FLERR,"Compute property/atom for "
- "atom property that isn't allocated");
+ error->all(FLERR,"Compute property/atom for "
+ "atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_eradius;
} else if (strcmp(arg[iarg],"ervel") == 0) {
if (!atom->ervel_flag)
- error->all(FLERR,"Compute property/atom for "
- "atom property that isn't allocated");
+ error->all(FLERR,"Compute property/atom for "
+ "atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_ervel;
} else if (strcmp(arg[iarg],"erforce") == 0) {
if (!atom->erforce_flag)
- error->all(FLERR,"Compute property/atom for "
- "atom property that isn't allocated");
+ error->all(FLERR,"Compute property/atom for "
+ "atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_erforce;
} else if (strcmp(arg[iarg],"end1x") == 0) {
avec_line = (AtomVecLine *) atom->style_match("line");
if (!avec_line) error->all(FLERR,"Compute property/atom for "
- "atom property that isn't allocated");
+ "atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_end1x;
} else if (strcmp(arg[iarg],"end1y") == 0) {
avec_line = (AtomVecLine *) atom->style_match("line");
if (!avec_line) error->all(FLERR,"Compute property/atom for "
- "atom property that isn't allocated");
+ "atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_end1y;
} else if (strcmp(arg[iarg],"end1z") == 0) {
avec_line = (AtomVecLine *) atom->style_match("line");
if (!avec_line) error->all(FLERR,"Compute property/atom for "
- "atom property that isn't allocated");
+ "atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_end1z;
} else if (strcmp(arg[iarg],"end2x") == 0) {
avec_line = (AtomVecLine *) atom->style_match("line");
if (!avec_line) error->all(FLERR,"Compute property/atom for "
- "atom property that isn't allocated");
+ "atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_end2x;
} else if (strcmp(arg[iarg],"end2y") == 0) {
avec_line = (AtomVecLine *) atom->style_match("line");
if (!avec_line) error->all(FLERR,"Compute property/atom for "
- "atom property that isn't allocated");
+ "atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_end2y;
} else if (strcmp(arg[iarg],"end2z") == 0) {
avec_line = (AtomVecLine *) atom->style_match("line");
if (!avec_line) error->all(FLERR,"Compute property/atom for "
- "atom property that isn't allocated");
+ "atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_end2z;
} else if (strcmp(arg[iarg],"corner1x") == 0) {
avec_tri = (AtomVecTri *) atom->style_match("tri");
if (!avec_tri) error->all(FLERR,"Compute property/atom for "
- "atom property that isn't allocated");
+ "atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_corner1x;
} else if (strcmp(arg[iarg],"corner1y") == 0) {
avec_tri = (AtomVecTri *) atom->style_match("tri");
if (!avec_tri) error->all(FLERR,"Compute property/atom for "
- "atom property that isn't allocated");
+ "atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_corner1y;
} else if (strcmp(arg[iarg],"corner1z") == 0) {
avec_tri = (AtomVecTri *) atom->style_match("tri");
if (!avec_tri) error->all(FLERR,"Compute property/atom for "
- "atom property that isn't allocated");
+ "atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_corner1z;
} else if (strcmp(arg[iarg],"corner2x") == 0) {
avec_tri = (AtomVecTri *) atom->style_match("tri");
if (!avec_tri) error->all(FLERR,"Compute property/atom for "
- "atom property that isn't allocated");
+ "atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_corner2x;
} else if (strcmp(arg[iarg],"corner2y") == 0) {
avec_tri = (AtomVecTri *) atom->style_match("tri");
if (!avec_tri) error->all(FLERR,"Compute property/atom for "
- "atom property that isn't allocated");
+ "atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_corner2y;
} else if (strcmp(arg[iarg],"corner2z") == 0) {
avec_tri = (AtomVecTri *) atom->style_match("tri");
if (!avec_tri) error->all(FLERR,"Compute property/atom for "
- "atom property that isn't allocated");
+ "atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_corner2z;
} else if (strcmp(arg[iarg],"corner3x") == 0) {
avec_tri = (AtomVecTri *) atom->style_match("tri");
if (!avec_tri) error->all(FLERR,"Compute property/atom for "
- "atom property that isn't allocated");
+ "atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_corner3x;
} else if (strcmp(arg[iarg],"corner3y") == 0) {
avec_tri = (AtomVecTri *) atom->style_match("tri");
if (!avec_tri) error->all(FLERR,"Compute property/atom for "
- "atom property that isn't allocated");
+ "atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_corner3y;
} else if (strcmp(arg[iarg],"corner3z") == 0) {
avec_tri = (AtomVecTri *) atom->style_match("tri");
if (!avec_tri) error->all(FLERR,"Compute property/atom for "
- "atom property that isn't allocated");
+ "atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_corner3z;
} else error->all(FLERR,"Invalid keyword in compute property/atom command");
@@ -572,9 +572,9 @@ void ComputePropertyAtom::pack_xs_triclinic(int n)
double *h_inv = domain->h_inv;
for (int i = 0; i < nlocal; i++) {
- if (mask[i] & groupbit)
- buf[n] = h_inv[0]*(x[i][0]-boxlo[0]) +
- h_inv[5]*(x[i][1]-boxlo[1]) + h_inv[4]*(x[i][2]-boxlo[2]);
+ if (mask[i] & groupbit)
+ buf[n] = h_inv[0]*(x[i][0]-boxlo[0]) +
+ h_inv[5]*(x[i][1]-boxlo[1]) + h_inv[4]*(x[i][2]-boxlo[2]);
else buf[n] = 0.0;
n += nvalues;
}
@@ -630,7 +630,7 @@ void ComputePropertyAtom::pack_xu(int n)
double xprd = domain->xprd;
for (int i = 0; i < nlocal; i++) {
- if (mask[i] & groupbit)
+ if (mask[i] & groupbit)
buf[n] = x[i][0] + ((image[i] & 1023) - 512) * xprd;
else buf[n] = 0.0;
n += nvalues;
diff --git a/src/compute_property_atom.h b/src/compute_property_atom.h
index 41f17b46f5333459bbe1af0a2b827b4f6f418ba4..3e43bc9303d66d8a884d849f4f189612d9a35b83 100644
--- a/src/compute_property_atom.h
+++ b/src/compute_property_atom.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/compute_property_local.cpp b/src/compute_property_local.cpp
index 48ab145d8c83d948642aa85bc1f3ce5217d892f7..b8e6f1e5a7161a88946adaae6a541ccf1fdb61be 100644
--- a/src/compute_property_local.cpp
+++ b/src/compute_property_local.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -52,113 +52,113 @@ ComputePropertyLocal::ComputePropertyLocal(LAMMPS *lmp, int narg, char **arg) :
if (strcmp(arg[iarg],"natom1") == 0) {
pack_choice[i] = &ComputePropertyLocal::pack_patom1;
- if (kindflag != NONE && kindflag != NEIGH)
- error->all(FLERR,"Compute property/local cannot use these inputs together");
+ if (kindflag != NONE && kindflag != NEIGH)
+ error->all(FLERR,"Compute property/local cannot use these inputs together");
kindflag = NEIGH;
} else if (strcmp(arg[iarg],"natom2") == 0) {
pack_choice[i] = &ComputePropertyLocal::pack_patom2;
- if (kindflag != NONE && kindflag != NEIGH)
- error->all(FLERR,"Compute property/local cannot use these inputs together");
+ if (kindflag != NONE && kindflag != NEIGH)
+ error->all(FLERR,"Compute property/local cannot use these inputs together");
kindflag = NEIGH;
} else if (strcmp(arg[iarg],"patom1") == 0) {
pack_choice[i] = &ComputePropertyLocal::pack_patom1;
- if (kindflag != NONE && kindflag != PAIR)
- error->all(FLERR,"Compute property/local cannot use these inputs together");
+ if (kindflag != NONE && kindflag != PAIR)
+ error->all(FLERR,"Compute property/local cannot use these inputs together");
kindflag = PAIR;
} else if (strcmp(arg[iarg],"patom2") == 0) {
pack_choice[i] = &ComputePropertyLocal::pack_patom2;
- if (kindflag != NONE && kindflag != PAIR)
- error->all(FLERR,"Compute property/local cannot use these inputs together");
+ if (kindflag != NONE && kindflag != PAIR)
+ error->all(FLERR,"Compute property/local cannot use these inputs together");
kindflag = PAIR;
} else if (strcmp(arg[iarg],"batom1") == 0) {
pack_choice[i] = &ComputePropertyLocal::pack_batom1;
- if (kindflag != NONE && kindflag != BOND)
- error->all(FLERR,"Compute property/local cannot use these inputs together");
+ if (kindflag != NONE && kindflag != BOND)
+ error->all(FLERR,"Compute property/local cannot use these inputs together");
kindflag = BOND;
} else if (strcmp(arg[iarg],"batom2") == 0) {
pack_choice[i] = &ComputePropertyLocal::pack_batom2;
- if (kindflag != NONE && kindflag != BOND)
- error->all(FLERR,"Compute property/local cannot use these inputs together");
+ if (kindflag != NONE && kindflag != BOND)
+ error->all(FLERR,"Compute property/local cannot use these inputs together");
kindflag = BOND;
} else if (strcmp(arg[iarg],"btype") == 0) {
pack_choice[i] = &ComputePropertyLocal::pack_btype;
- if (kindflag != NONE && kindflag != BOND)
- error->all(FLERR,"Compute property/local cannot use these inputs together");
+ if (kindflag != NONE && kindflag != BOND)
+ error->all(FLERR,"Compute property/local cannot use these inputs together");
kindflag = BOND;
} else if (strcmp(arg[iarg],"aatom1") == 0) {
pack_choice[i] = &ComputePropertyLocal::pack_aatom1;
- if (kindflag != NONE && kindflag != ANGLE)
- error->all(FLERR,"Compute property/local cannot use these inputs together");
+ if (kindflag != NONE && kindflag != ANGLE)
+ error->all(FLERR,"Compute property/local cannot use these inputs together");
kindflag = ANGLE;
} else if (strcmp(arg[iarg],"aatom2") == 0) {
pack_choice[i] = &ComputePropertyLocal::pack_aatom2;
- if (kindflag != NONE && kindflag != ANGLE)
- error->all(FLERR,"Compute property/local cannot use these inputs together");
+ if (kindflag != NONE && kindflag != ANGLE)
+ error->all(FLERR,"Compute property/local cannot use these inputs together");
kindflag = ANGLE;
} else if (strcmp(arg[iarg],"aatom3") == 0) {
pack_choice[i] = &ComputePropertyLocal::pack_aatom3;
- if (kindflag != NONE && kindflag != ANGLE)
- error->all(FLERR,"Compute property/local cannot use these inputs together");
+ if (kindflag != NONE && kindflag != ANGLE)
+ error->all(FLERR,"Compute property/local cannot use these inputs together");
kindflag = ANGLE;
} else if (strcmp(arg[iarg],"atype") == 0) {
pack_choice[i] = &ComputePropertyLocal::pack_atype;
- if (kindflag != NONE && kindflag != ANGLE)
- error->all(FLERR,"Compute property/local cannot use these inputs together");
+ if (kindflag != NONE && kindflag != ANGLE)
+ error->all(FLERR,"Compute property/local cannot use these inputs together");
kindflag = ANGLE;
} else if (strcmp(arg[iarg],"datom1") == 0) {
pack_choice[i] = &ComputePropertyLocal::pack_datom1;
- if (kindflag != NONE && kindflag != DIHEDRAL)
- error->all(FLERR,"Compute property/local cannot use these inputs together");
+ if (kindflag != NONE && kindflag != DIHEDRAL)
+ error->all(FLERR,"Compute property/local cannot use these inputs together");
kindflag = DIHEDRAL;
} else if (strcmp(arg[iarg],"datom2") == 0) {
pack_choice[i] = &ComputePropertyLocal::pack_datom2;
- if (kindflag != NONE && kindflag != DIHEDRAL)
- error->all(FLERR,"Compute property/local cannot use these inputs together");
+ if (kindflag != NONE && kindflag != DIHEDRAL)
+ error->all(FLERR,"Compute property/local cannot use these inputs together");
kindflag = DIHEDRAL;
} else if (strcmp(arg[iarg],"datom3") == 0) {
pack_choice[i] = &ComputePropertyLocal::pack_datom3;
- if (kindflag != NONE && kindflag != DIHEDRAL)
- error->all(FLERR,"Compute property/local cannot use these inputs together");
+ if (kindflag != NONE && kindflag != DIHEDRAL)
+ error->all(FLERR,"Compute property/local cannot use these inputs together");
kindflag = DIHEDRAL;
} else if (strcmp(arg[iarg],"datom4") == 0) {
pack_choice[i] = &ComputePropertyLocal::pack_datom4;
- if (kindflag != NONE && kindflag != DIHEDRAL)
- error->all(FLERR,"Compute property/local cannot use these inputs together");
+ if (kindflag != NONE && kindflag != DIHEDRAL)
+ error->all(FLERR,"Compute property/local cannot use these inputs together");
kindflag = DIHEDRAL;
} else if (strcmp(arg[iarg],"dtype") == 0) {
pack_choice[i] = &ComputePropertyLocal::pack_dtype;
- if (kindflag != NONE && kindflag != DIHEDRAL)
- error->all(FLERR,"Compute property/local cannot use these inputs together");
+ if (kindflag != NONE && kindflag != DIHEDRAL)
+ error->all(FLERR,"Compute property/local cannot use these inputs together");
kindflag = DIHEDRAL;
} else if (strcmp(arg[iarg],"iatom1") == 0) {
pack_choice[i] = &ComputePropertyLocal::pack_iatom1;
- if (kindflag != NONE && kindflag != IMPROPER)
- error->all(FLERR,"Compute property/local cannot use these inputs together");
+ if (kindflag != NONE && kindflag != IMPROPER)
+ error->all(FLERR,"Compute property/local cannot use these inputs together");
kindflag = IMPROPER;
} else if (strcmp(arg[iarg],"iatom2") == 0) {
pack_choice[i] = &ComputePropertyLocal::pack_iatom2;
- if (kindflag != NONE && kindflag != IMPROPER)
- error->all(FLERR,"Compute property/local cannot use these inputs together");
+ if (kindflag != NONE && kindflag != IMPROPER)
+ error->all(FLERR,"Compute property/local cannot use these inputs together");
kindflag = IMPROPER;
} else if (strcmp(arg[iarg],"iatom3") == 0) {
pack_choice[i] = &ComputePropertyLocal::pack_iatom3;
- if (kindflag != NONE && kindflag != IMPROPER)
- error->all(FLERR,"Compute property/local cannot use these inputs together");
+ if (kindflag != NONE && kindflag != IMPROPER)
+ error->all(FLERR,"Compute property/local cannot use these inputs together");
kindflag = IMPROPER;
} else if (strcmp(arg[iarg],"iatom4") == 0) {
pack_choice[i] = &ComputePropertyLocal::pack_iatom4;
- if (kindflag != NONE && kindflag != IMPROPER)
- error->all(FLERR,"Compute property/local cannot use these inputs together");
+ if (kindflag != NONE && kindflag != IMPROPER)
+ error->all(FLERR,"Compute property/local cannot use these inputs together");
kindflag = IMPROPER;
} else if (strcmp(arg[iarg],"itype") == 0) {
pack_choice[i] = &ComputePropertyLocal::pack_itype;
- if (kindflag != NONE && kindflag != IMPROPER)
- error->all(FLERR,"Compute property/local cannot use these inputs together");
+ if (kindflag != NONE && kindflag != IMPROPER)
+ error->all(FLERR,"Compute property/local cannot use these inputs together");
kindflag = IMPROPER;
} else error->all(FLERR,"Invalid keyword in compute property/local command");
@@ -196,7 +196,7 @@ ComputePropertyLocal::~ComputePropertyLocal()
void ComputePropertyLocal::init()
{
if (kindflag == NEIGH || kindflag == PAIR) {
- if (force->pair == NULL)
+ if (force->pair == NULL)
error->all(FLERR,"No pair style is defined for compute property/local");
if (force->pair->single_enable == 0)
error->all(FLERR,"Pair style does not support compute property/local");
@@ -333,8 +333,8 @@ int ComputePropertyLocal::count_pairs(int allflag, int forceflag)
if (forceflag && rsq >= cutsq[itype][jtype]) continue;
if (allflag) {
- indices[m][0] = tag[i];
- indices[m][1] = tag[j];
+ indices[m][0] = tag[i];
+ indices[m][1] = tag[j];
}
m++;
}
@@ -374,8 +374,8 @@ int ComputePropertyLocal::count_bonds(int flag)
if (bond_type[atom1][i] == 0) continue;
if (flag) {
- indices[m][0] = atom1;
- indices[m][1] = i;
+ indices[m][0] = atom1;
+ indices[m][1] = i;
}
m++;
}
@@ -418,8 +418,8 @@ int ComputePropertyLocal::count_angles(int flag)
if (angle_type[atom2][i] == 0) continue;
if (flag) {
- indices[m][0] = atom2;
- indices[m][1] = i;
+ indices[m][0] = atom2;
+ indices[m][1] = i;
}
m++;
}
@@ -461,8 +461,8 @@ int ComputePropertyLocal::count_dihedrals(int flag)
if (atom4 < 0 || !(mask[atom4] & groupbit)) continue;
if (flag) {
- indices[m][0] = atom2;
- indices[m][1] = i;
+ indices[m][0] = atom2;
+ indices[m][1] = i;
}
m++;
}
@@ -504,8 +504,8 @@ int ComputePropertyLocal::count_impropers(int flag)
if (atom4 < 0 || !(mask[atom4] & groupbit)) continue;
if (flag) {
- indices[m][0] = atom2;
- indices[m][1] = i;
+ indices[m][0] = atom2;
+ indices[m][1] = i;
}
m++;
}
diff --git a/src/compute_property_local.h b/src/compute_property_local.h
index d7a2d6a61227c6bf6e318fe8375217e5f64d0f56..eab19768f6d25d434c3af68c3d4b2e9274dbb705 100644
--- a/src/compute_property_local.h
+++ b/src/compute_property_local.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/compute_property_molecule.cpp b/src/compute_property_molecule.cpp
index 65ec20ef03aa946b86a01c3a73d2214cf5ad500c..c0bcafc9ea6a2660080495916c0c3c873b5379e6 100644
--- a/src/compute_property_molecule.cpp
+++ b/src/compute_property_molecule.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -65,7 +65,7 @@ ComputePropertyMolecule(LAMMPS *lmp, int narg, char **arg) :
size_array_cols = nvalues;
extarray = 0;
}
-
+
// fill vector or array with molecule values
if (nvalues == 1) {
diff --git a/src/compute_property_molecule.h b/src/compute_property_molecule.h
index 9c79e93bc89128b067dd31e13dbb1ccf3a850c6c..0c5ae68df08c2b515af08bdfbb208e39da165ee7 100644
--- a/src/compute_property_molecule.h
+++ b/src/compute_property_molecule.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/compute_rdf.cpp b/src/compute_rdf.cpp
index 31776f94731c25480b29a93d6a50aec6e642a12f..7511e1b5c3097d1c7451e0478d679d5e8300b592 100644
--- a/src/compute_rdf.cpp
+++ b/src/compute_rdf.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -73,7 +73,7 @@ ComputeRDF::ComputeRDF(LAMMPS *lmp, int narg, char **arg) :
force->bounds(arg[iarg],atom->ntypes,ilo[npairs],ihi[npairs]);
force->bounds(arg[iarg+1],atom->ntypes,jlo[npairs],jhi[npairs]);
if (ilo[npairs] > ihi[npairs] || jlo[npairs] > jhi[npairs])
- error->all(FLERR,"Illegal compute rdf command");
+ error->all(FLERR,"Illegal compute rdf command");
npairs++;
iarg += 2;
}
@@ -87,7 +87,7 @@ ComputeRDF::ComputeRDF(LAMMPS *lmp, int narg, char **arg) :
for (int m = 0; m < npairs; m++)
for (i = ilo[m]; i <= ihi[m]; i++)
for (j = jlo[m]; j <= jhi[m]; j++)
- rdfpair[nrdfpair[i][j]++][i][j] = m;
+ rdfpair[nrdfpair[i][j]++][i][j] = m;
memory->create(hist,npairs,nbin,"rdf:hist");
memory->create(histall,npairs,nbin,"rdf:histall");
@@ -250,12 +250,12 @@ void ComputeRDF::compute_array()
if (ibin >= nbin) continue;
if (ipair)
- for (ihisto = 0; ihisto < ipair; ihisto++)
- hist[rdfpair[ihisto][itype][jtype]][ibin] += 1.0;
+ for (ihisto = 0; ihisto < ipair; ihisto++)
+ hist[rdfpair[ihisto][itype][jtype]][ibin] += 1.0;
if (newton_pair || j < nlocal) {
- if (jpair)
- for (ihisto = 0; ihisto < jpair; ihisto++)
- hist[rdfpair[ihisto][jtype][itype]][ibin] += 1.0;
+ if (jpair)
+ for (ihisto = 0; ihisto < jpair; ihisto++)
+ hist[rdfpair[ihisto][jtype][itype]][ibin] += 1.0;
}
}
}
@@ -276,16 +276,16 @@ void ComputeRDF::compute_array()
for (m = 0; m < npairs; m++) {
ncoord = 0.0;
for (ibin = 0; ibin < nbin; ibin++) {
- rlower = ibin*delr;
- rupper = (ibin+1)*delr;
- nideal = constant *
- (rupper*rupper*rupper - rlower*rlower*rlower) * jcount[m];
- if (icount[m]*nideal != 0.0)
- gr = histall[m][ibin] / (icount[m]*nideal);
- else gr = 0.0;
- ncoord += gr*nideal;
- array[ibin][1+2*m] = gr;
- array[ibin][2+2*m] = ncoord;
+ rlower = ibin*delr;
+ rupper = (ibin+1)*delr;
+ nideal = constant *
+ (rupper*rupper*rupper - rlower*rlower*rlower) * jcount[m];
+ if (icount[m]*nideal != 0.0)
+ gr = histall[m][ibin] / (icount[m]*nideal);
+ else gr = 0.0;
+ ncoord += gr*nideal;
+ array[ibin][1+2*m] = gr;
+ array[ibin][2+2*m] = ncoord;
}
}
@@ -295,15 +295,15 @@ void ComputeRDF::compute_array()
for (m = 0; m < npairs; m++) {
ncoord = 0.0;
for (ibin = 0; ibin < nbin; ibin++) {
- rlower = ibin*delr;
- rupper = (ibin+1)*delr;
- nideal = constant * (rupper*rupper - rlower*rlower) * jcount[m];
- if (icount[m]*nideal != 0.0)
- gr = histall[m][ibin] / (icount[m]*nideal);
- else gr = 0.0;
- ncoord += gr*nideal;
- array[ibin][1+2*m] = gr;
- array[ibin][2+2*m] = ncoord;
+ rlower = ibin*delr;
+ rupper = (ibin+1)*delr;
+ nideal = constant * (rupper*rupper - rlower*rlower) * jcount[m];
+ if (icount[m]*nideal != 0.0)
+ gr = histall[m][ibin] / (icount[m]*nideal);
+ else gr = 0.0;
+ ncoord += gr*nideal;
+ array[ibin][1+2*m] = gr;
+ array[ibin][2+2*m] = ncoord;
}
}
}
diff --git a/src/compute_rdf.h b/src/compute_rdf.h
index 5255abdc5203fb58e702edd0684981e0e4cb103d..8436593c9dfecc681fd669716903c432f555ba4e 100644
--- a/src/compute_rdf.h
+++ b/src/compute_rdf.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -35,14 +35,14 @@ class ComputeRDF : public Compute {
private:
int first;
- int nbin; // # of rdf bins
- int npairs; // # of rdf pairs
- double delr,delrinv; // bin width and its inverse
- int ***rdfpair; // map 2 type pair to rdf pair for each histo
+ int nbin; // # of rdf bins
+ int npairs; // # of rdf pairs
+ double delr,delrinv; // bin width and its inverse
+ int ***rdfpair; // map 2 type pair to rdf pair for each histo
int **nrdfpair; // # of histograms for each type pair
int *ilo,*ihi,*jlo,*jhi;
- double **hist; // histogram bins
- double **histall; // summed histogram bins across all procs
+ double **hist; // histogram bins
+ double **histall; // summed histogram bins across all procs
int *typecount;
int *icount,*jcount;
diff --git a/src/compute_reduce.cpp b/src/compute_reduce.cpp
index 816e551f98ca3ab7f54b048a6ddc133639c9d4c9..645dbac73844addcfafa05582c3d64fb62292810 100644
--- a/src/compute_reduce.cpp
+++ b/src/compute_reduce.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -112,9 +112,9 @@ ComputeReduce::ComputeReduce(LAMMPS *lmp, int narg, char **arg) :
which[nvalues] = F;
argindex[nvalues++] = 2;
- } else if (strncmp(arg[iarg],"c_",2) == 0 ||
- strncmp(arg[iarg],"f_",2) == 0 ||
- strncmp(arg[iarg],"v_",2) == 0) {
+ } else if (strncmp(arg[iarg],"c_",2) == 0 ||
+ strncmp(arg[iarg],"f_",2) == 0 ||
+ strncmp(arg[iarg],"v_",2) == 0) {
if (arg[iarg][0] == 'c') which[nvalues] = COMPUTE;
else if (arg[iarg][0] == 'f') which[nvalues] = FIX;
else if (arg[iarg][0] == 'v') which[nvalues] = VARIABLE;
@@ -125,10 +125,10 @@ ComputeReduce::ComputeReduce(LAMMPS *lmp, int narg, char **arg) :
char *ptr = strchr(suffix,'[');
if (ptr) {
- if (suffix[strlen(suffix)-1] != ']')
- error->all(FLERR,"Illegal compute reduce command");
- argindex[nvalues] = atoi(ptr+1);
- *ptr = '\0';
+ if (suffix[strlen(suffix)-1] != ']')
+ error->all(FLERR,"Illegal compute reduce command");
+ argindex[nvalues] = atoi(ptr+1);
+ *ptr = '\0';
} else argindex[nvalues] = 0;
n = strlen(suffix) + 1;
@@ -151,14 +151,14 @@ ComputeReduce::ComputeReduce(LAMMPS *lmp, int narg, char **arg) :
if (strcmp(arg[iarg],"replace") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal compute reduce command");
if (mode != MINN && mode != MAXX)
- error->all(FLERR,"Compute reduce replace requires min or max mode");
+ error->all(FLERR,"Compute reduce replace requires min or max mode");
int col1 = atoi(arg[iarg+1]) - 1;
int col2 = atoi(arg[iarg+2]) - 1;
if (col1 < 0 || col1 >= nvalues || col2 < 0 || col2 >= nvalues)
- error->all(FLERR,"Illegal compute reduce command");
- if (col1 == col2) error->all(FLERR,"Illegal compute reduce command");
+ error->all(FLERR,"Illegal compute reduce command");
+ if (col1 == col2) error->all(FLERR,"Illegal compute reduce command");
if (replace[col1] >= 0 || replace[col2] >= 0)
- error->all(FLERR,"Invalid replace values in compute reduce");
+ error->all(FLERR,"Invalid replace values in compute reduce");
replace[col1] = col2;
iarg += 3;
} else error->all(FLERR,"Illegal compute reduce command");
@@ -183,69 +183,69 @@ ComputeReduce::ComputeReduce(LAMMPS *lmp, int narg, char **arg) :
else if (which[i] == COMPUTE) {
int icompute = modify->find_compute(ids[i]);
if (icompute < 0)
- error->all(FLERR,"Compute ID for compute reduce does not exist");
+ error->all(FLERR,"Compute ID for compute reduce does not exist");
if (modify->compute[icompute]->peratom_flag) {
- flavor[i] = PERATOM;
- if (argindex[i] == 0 &&
- modify->compute[icompute]->size_peratom_cols != 0)
- error->all(FLERR,"Compute reduce compute does not "
- "calculate a per-atom vector");
- if (argindex[i] && modify->compute[icompute]->size_peratom_cols == 0)
- error->all(FLERR,"Compute reduce compute does not "
- "calculate a per-atom array");
- if (argindex[i] &&
- argindex[i] > modify->compute[icompute]->size_peratom_cols)
- error->all(FLERR,"Compute reduce compute array is accessed out-of-range");
+ flavor[i] = PERATOM;
+ if (argindex[i] == 0 &&
+ modify->compute[icompute]->size_peratom_cols != 0)
+ error->all(FLERR,"Compute reduce compute does not "
+ "calculate a per-atom vector");
+ if (argindex[i] && modify->compute[icompute]->size_peratom_cols == 0)
+ error->all(FLERR,"Compute reduce compute does not "
+ "calculate a per-atom array");
+ if (argindex[i] &&
+ argindex[i] > modify->compute[icompute]->size_peratom_cols)
+ error->all(FLERR,"Compute reduce compute array is accessed out-of-range");
} else if (modify->compute[icompute]->local_flag) {
- flavor[i] = LOCAL;
- if (argindex[i] == 0 &&
- modify->compute[icompute]->size_local_cols != 0)
- error->all(FLERR,"Compute reduce compute does not "
- "calculate a local vector");
- if (argindex[i] && modify->compute[icompute]->size_local_cols == 0)
- error->all(FLERR,"Compute reduce compute does not "
- "calculate a local array");
- if (argindex[i] &&
- argindex[i] > modify->compute[icompute]->size_local_cols)
- error->all(FLERR,"Compute reduce compute array is accessed out-of-range");
+ flavor[i] = LOCAL;
+ if (argindex[i] == 0 &&
+ modify->compute[icompute]->size_local_cols != 0)
+ error->all(FLERR,"Compute reduce compute does not "
+ "calculate a local vector");
+ if (argindex[i] && modify->compute[icompute]->size_local_cols == 0)
+ error->all(FLERR,"Compute reduce compute does not "
+ "calculate a local array");
+ if (argindex[i] &&
+ argindex[i] > modify->compute[icompute]->size_local_cols)
+ error->all(FLERR,"Compute reduce compute array is accessed out-of-range");
} else error->all(FLERR,"Compute reduce compute calculates global values");
} else if (which[i] == FIX) {
int ifix = modify->find_fix(ids[i]);
if (ifix < 0)
- error->all(FLERR,"Fix ID for compute reduce does not exist");
+ error->all(FLERR,"Fix ID for compute reduce does not exist");
if (modify->fix[ifix]->peratom_flag) {
- flavor[i] = PERATOM;
- if (argindex[i] == 0 &&
- modify->fix[ifix]->size_peratom_cols != 0)
- error->all(FLERR,"Compute reduce fix does not "
- "calculate a per-atom vector");
- if (argindex[i] && modify->fix[ifix]->size_peratom_cols == 0)
- error->all(FLERR,"Compute reduce fix does not "
- "calculate a per-atom array");
- if (argindex[i] &&
- argindex[i] > modify->fix[ifix]->size_peratom_cols)
- error->all(FLERR,"Compute reduce fix array is accessed out-of-range");
+ flavor[i] = PERATOM;
+ if (argindex[i] == 0 &&
+ modify->fix[ifix]->size_peratom_cols != 0)
+ error->all(FLERR,"Compute reduce fix does not "
+ "calculate a per-atom vector");
+ if (argindex[i] && modify->fix[ifix]->size_peratom_cols == 0)
+ error->all(FLERR,"Compute reduce fix does not "
+ "calculate a per-atom array");
+ if (argindex[i] &&
+ argindex[i] > modify->fix[ifix]->size_peratom_cols)
+ error->all(FLERR,"Compute reduce fix array is accessed out-of-range");
} else if (modify->fix[ifix]->local_flag) {
- flavor[i] = LOCAL;
- if (argindex[i] == 0 &&
- modify->fix[ifix]->size_local_cols != 0)
- error->all(FLERR,"Compute reduce fix does not "
- "calculate a local vector");
- if (argindex[i] && modify->fix[ifix]->size_local_cols == 0)
- error->all(FLERR,"Compute reduce fix does not "
- "calculate a local array");
- if (argindex[i] &&
- argindex[i] > modify->fix[ifix]->size_local_cols)
- error->all(FLERR,"Compute reduce fix array is accessed out-of-range");
+ flavor[i] = LOCAL;
+ if (argindex[i] == 0 &&
+ modify->fix[ifix]->size_local_cols != 0)
+ error->all(FLERR,"Compute reduce fix does not "
+ "calculate a local vector");
+ if (argindex[i] && modify->fix[ifix]->size_local_cols == 0)
+ error->all(FLERR,"Compute reduce fix does not "
+ "calculate a local array");
+ if (argindex[i] &&
+ argindex[i] > modify->fix[ifix]->size_local_cols)
+ error->all(FLERR,"Compute reduce fix array is accessed out-of-range");
} else error->all(FLERR,"Compute reduce fix calculates global values");
} else if (which[i] == VARIABLE) {
int ivariable = input->variable->find(ids[i]);
if (ivariable < 0)
- error->all(FLERR,"Variable name for compute reduce does not exist");
+ error->all(FLERR,"Variable name for compute reduce does not exist");
if (input->variable->atomstyle(ivariable) == 0)
- error->all(FLERR,"Compute reduce variable is not atom-style variable");
+ error->all(FLERR,"Compute reduce variable is not atom-style variable");
flavor[i] = PERATOM;
}
}
@@ -304,19 +304,19 @@ void ComputeReduce::init()
if (which[m] == COMPUTE) {
int icompute = modify->find_compute(ids[m]);
if (icompute < 0)
- error->all(FLERR,"Compute ID for compute reduce does not exist");
+ error->all(FLERR,"Compute ID for compute reduce does not exist");
value2index[m] = icompute;
-
+
} else if (which[m] == FIX) {
int ifix = modify->find_fix(ids[m]);
- if (ifix < 0)
- error->all(FLERR,"Fix ID for compute reduce does not exist");
+ if (ifix < 0)
+ error->all(FLERR,"Fix ID for compute reduce does not exist");
value2index[m] = ifix;
} else if (which[m] == VARIABLE) {
int ivariable = input->variable->find(ids[m]);
- if (ivariable < 0)
- error->all(FLERR,"Variable name for compute reduce does not exist");
+ if (ivariable < 0)
+ error->all(FLERR,"Variable name for compute reduce does not exist");
value2index[m] = ivariable;
} else value2index[m] = -1;
@@ -373,45 +373,45 @@ void ComputeReduce::compute_vector()
} else if (mode == MINN) {
if (!replace) {
for (int m = 0; m < nvalues; m++)
- MPI_Allreduce(&onevec[m],&vector[m],1,MPI_DOUBLE,MPI_MIN,world);
+ MPI_Allreduce(&onevec[m],&vector[m],1,MPI_DOUBLE,MPI_MIN,world);
} else {
for (int m = 0; m < nvalues; m++)
- if (replace[m] < 0) {
- pairme.value = onevec[m];
- pairme.proc = me;
- MPI_Allreduce(&pairme,&pairall,1,MPI_DOUBLE_INT,MPI_MINLOC,world);
- vector[m] = pairall.value;
- owner[m] = pairall.proc;
- }
+ if (replace[m] < 0) {
+ pairme.value = onevec[m];
+ pairme.proc = me;
+ MPI_Allreduce(&pairme,&pairall,1,MPI_DOUBLE_INT,MPI_MINLOC,world);
+ vector[m] = pairall.value;
+ owner[m] = pairall.proc;
+ }
for (int m = 0; m < nvalues; m++)
- if (replace[m] >= 0) {
- if (me == owner[replace[m]])
- vector[m] = compute_one(m,indices[replace[m]]);
- MPI_Bcast(&vector[m],1,MPI_DOUBLE,owner[replace[m]],world);
- }
+ if (replace[m] >= 0) {
+ if (me == owner[replace[m]])
+ vector[m] = compute_one(m,indices[replace[m]]);
+ MPI_Bcast(&vector[m],1,MPI_DOUBLE,owner[replace[m]],world);
+ }
}
} else if (mode == MAXX) {
if (!replace) {
for (int m = 0; m < nvalues; m++)
- MPI_Allreduce(&onevec[m],&vector[m],1,MPI_DOUBLE,MPI_MAX,world);
+ MPI_Allreduce(&onevec[m],&vector[m],1,MPI_DOUBLE,MPI_MAX,world);
} else {
for (int m = 0; m < nvalues; m++)
- if (replace[m] < 0) {
- pairme.value = onevec[m];
- pairme.proc = me;
- MPI_Allreduce(&pairme,&pairall,1,MPI_DOUBLE_INT,MPI_MAXLOC,world);
- vector[m] = pairall.value;
- owner[m] = pairall.proc;
- }
+ if (replace[m] < 0) {
+ pairme.value = onevec[m];
+ pairme.proc = me;
+ MPI_Allreduce(&pairme,&pairall,1,MPI_DOUBLE_INT,MPI_MAXLOC,world);
+ vector[m] = pairall.value;
+ owner[m] = pairall.proc;
+ }
for (int m = 0; m < nvalues; m++)
- if (replace[m] >= 0) {
- if (me == owner[replace[m]])
- vector[m] = compute_one(m,indices[replace[m]]);
- MPI_Bcast(&vector[m],1,MPI_DOUBLE,owner[replace[m]],world);
- }
+ if (replace[m] >= 0) {
+ if (me == owner[replace[m]])
+ vector[m] = compute_one(m,indices[replace[m]]);
+ MPI_Bcast(&vector[m],1,MPI_DOUBLE,owner[replace[m]],world);
+ }
}
} else if (mode == AVE) {
@@ -457,70 +457,70 @@ double ComputeReduce::compute_one(int m, int flag)
double **x = atom->x;
if (flag < 0) {
for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit) combine(one,x[i][aidx],i);
+ if (mask[i] & groupbit) combine(one,x[i][aidx],i);
} else one = x[flag][aidx];
} else if (which[m] == V) {
double **v = atom->v;
if (flag < 0) {
for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit) combine(one,v[i][aidx],i);
+ if (mask[i] & groupbit) combine(one,v[i][aidx],i);
} else one = v[flag][aidx];
} else if (which[m] == F) {
double **f = atom->f;
if (flag < 0) {
for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit) combine(one,f[i][aidx],i);
+ if (mask[i] & groupbit) combine(one,f[i][aidx],i);
} else one = f[flag][aidx];
-
+
// invoke compute if not previously invoked
} else if (which[m] == COMPUTE) {
Compute *compute = modify->compute[vidx];
-
+
if (flavor[m] == PERATOM) {
if (!(compute->invoked_flag & INVOKED_PERATOM)) {
- compute->compute_peratom();
- compute->invoked_flag |= INVOKED_PERATOM;
+ compute->compute_peratom();
+ compute->invoked_flag |= INVOKED_PERATOM;
}
if (aidx == 0) {
- double *comp_vec = compute->vector_atom;
- int n = nlocal;
- if (flag < 0) {
- for (i = 0; i < n; i++)
- if (mask[i] & groupbit) combine(one,comp_vec[i],i);
- } else one = comp_vec[flag];
+ double *comp_vec = compute->vector_atom;
+ int n = nlocal;
+ if (flag < 0) {
+ for (i = 0; i < n; i++)
+ if (mask[i] & groupbit) combine(one,comp_vec[i],i);
+ } else one = comp_vec[flag];
} else {
- double **carray_atom = compute->array_atom;
- int n = nlocal;
- int aidxm1 = aidx - 1;
- if (flag < 0) {
- for (i = 0; i < n; i++)
- if (mask[i] & groupbit) combine(one,carray_atom[i][aidxm1],i);
- } else one = carray_atom[flag][aidxm1];
+ double **carray_atom = compute->array_atom;
+ int n = nlocal;
+ int aidxm1 = aidx - 1;
+ if (flag < 0) {
+ for (i = 0; i < n; i++)
+ if (mask[i] & groupbit) combine(one,carray_atom[i][aidxm1],i);
+ } else one = carray_atom[flag][aidxm1];
}
} else if (flavor[m] == LOCAL) {
if (!(compute->invoked_flag & INVOKED_LOCAL)) {
- compute->compute_local();
- compute->invoked_flag |= INVOKED_LOCAL;
+ compute->compute_local();
+ compute->invoked_flag |= INVOKED_LOCAL;
}
if (aidx == 0) {
- double *comp_vec = compute->vector_local;
- int n = compute->size_local_rows;
- if (flag < 0)
- for (i = 0; i < n; i++)
- combine(one,comp_vec[i],i);
- else one = comp_vec[flag];
+ double *comp_vec = compute->vector_local;
+ int n = compute->size_local_rows;
+ if (flag < 0)
+ for (i = 0; i < n; i++)
+ combine(one,comp_vec[i],i);
+ else one = comp_vec[flag];
} else {
- double **carray_local = compute->array_local;
- int n = compute->size_local_rows;
- int aidxm1 = aidx - 1;
- if (flag < 0)
- for (i = 0; i < n; i++)
- combine(one,carray_local[i][aidxm1],i);
- else one = carray_local[flag][aidxm1];
+ double **carray_local = compute->array_local;
+ int n = compute->size_local_rows;
+ int aidxm1 = aidx - 1;
+ if (flag < 0)
+ for (i = 0; i < n; i++)
+ combine(one,carray_local[i][aidxm1],i);
+ else one = carray_local[flag][aidxm1];
}
}
@@ -533,40 +533,40 @@ double ComputeReduce::compute_one(int m, int flag)
if (flavor[m] == PERATOM) {
if (aidx == 0) {
- double *fix_vector = fix->vector_atom;
- int n = nlocal;
- if (flag < 0) {
- for (i = 0; i < n; i++)
- if (mask[i] & groupbit) combine(one,fix_vector[i],i);
- } else one = fix_vector[flag];
+ double *fix_vector = fix->vector_atom;
+ int n = nlocal;
+ if (flag < 0) {
+ for (i = 0; i < n; i++)
+ if (mask[i] & groupbit) combine(one,fix_vector[i],i);
+ } else one = fix_vector[flag];
} else {
- double **fix_array = fix->array_atom;
- int aidxm1 = aidx - 1;
- if (flag < 0) {
- for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit) combine(one,fix_array[i][aidxm1],i);
- } else one = fix_array[flag][aidxm1];
+ double **fix_array = fix->array_atom;
+ int aidxm1 = aidx - 1;
+ if (flag < 0) {
+ for (i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit) combine(one,fix_array[i][aidxm1],i);
+ } else one = fix_array[flag][aidxm1];
}
} else if (flavor[m] == LOCAL) {
if (aidx == 0) {
- double *fix_vector = fix->vector_local;
- int n = fix->size_local_rows;
- if (flag < 0)
- for (i = 0; i < n; i++)
- combine(one,fix_vector[i],i);
- else one = fix_vector[flag];
+ double *fix_vector = fix->vector_local;
+ int n = fix->size_local_rows;
+ if (flag < 0)
+ for (i = 0; i < n; i++)
+ combine(one,fix_vector[i],i);
+ else one = fix_vector[flag];
} else {
- double **fix_array = fix->array_local;
- int n = fix->size_local_rows;
- int aidxm1 = aidx - 1;
- if (flag < 0)
- for (i = 0; i < n; i++)
- combine(one,fix_array[i][aidxm1],i);
- else one = fix_array[flag][aidxm1];
+ double **fix_array = fix->array_local;
+ int n = fix->size_local_rows;
+ int aidxm1 = aidx - 1;
+ if (flag < 0)
+ for (i = 0; i < n; i++)
+ combine(one,fix_array[i][aidxm1],i);
+ else one = fix_array[flag][aidxm1];
}
}
-
+
// evaluate atom-style variable
} else if (which[m] == VARIABLE) {
@@ -579,7 +579,7 @@ double ComputeReduce::compute_one(int m, int flag)
input->variable->compute_atom(vidx,igroup,varatom,1,0);
if (flag < 0) {
for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit) combine(one,varatom[i],i);
+ if (mask[i] & groupbit) combine(one,varatom[i],i);
} else one = varatom[flag];
}
diff --git a/src/compute_reduce.h b/src/compute_reduce.h
index 90621ac2839b6686da41c0a6d7cac8f8305d2018..b0195d982f14ee9fb8c62c1938602e4e6dadfc5b 100644
--- a/src/compute_reduce.h
+++ b/src/compute_reduce.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/compute_reduce_region.cpp b/src/compute_reduce_region.cpp
index 648b90e1d87dc12e2c0a485e3ebe908c586816df..3f54dd5bbed0b6d5ac1c5ae1f296f3fa5f38485e 100644
--- a/src/compute_reduce_region.cpp
+++ b/src/compute_reduce_region.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -80,24 +80,24 @@ double ComputeReduceRegion::compute_one(int m, int flag)
if (which[m] == X) {
if (flag < 0) {
for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]))
- combine(one,x[i][j],i);
+ if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]))
+ combine(one,x[i][j],i);
} else one = x[flag][j];
} else if (which[m] == V) {
double **v = atom->v;
if (flag < 0) {
for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]))
- combine(one,v[i][j],i);
+ if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]))
+ combine(one,v[i][j],i);
} else one = v[flag][j];
} else if (which[m] == F) {
double **f = atom->f;
if (flag < 0) {
for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]))
- combine(one,f[i][j],i);
+ if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]))
+ combine(one,f[i][j],i);
} else one = f[flag][j];
-
+
// invoke compute if not previously invoked
} else if (which[m] == COMPUTE) {
@@ -105,50 +105,50 @@ double ComputeReduceRegion::compute_one(int m, int flag)
if (flavor[m] == PERATOM) {
if (!(compute->invoked_flag & INVOKED_PERATOM)) {
- compute->compute_peratom();
- compute->invoked_flag |= INVOKED_PERATOM;
+ compute->compute_peratom();
+ compute->invoked_flag |= INVOKED_PERATOM;
}
if (j == 0) {
- double *compute_vector = compute->vector_atom;
- int n = nlocal;
- if (flag < 0) {
- for (i = 0; i < n; i++)
- if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]))
- combine(one,compute_vector[i],i);
- } else one = compute_vector[flag];
+ double *compute_vector = compute->vector_atom;
+ int n = nlocal;
+ if (flag < 0) {
+ for (i = 0; i < n; i++)
+ if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]))
+ combine(one,compute_vector[i],i);
+ } else one = compute_vector[flag];
} else {
- double **compute_array = compute->array_atom;
- int n = nlocal;
- int jm1 = j - 1;
- if (flag < 0) {
- for (i = 0; i < n; i++)
- if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]))
- combine(one,compute_array[i][jm1],i);
- } else one = compute_array[flag][jm1];
+ double **compute_array = compute->array_atom;
+ int n = nlocal;
+ int jm1 = j - 1;
+ if (flag < 0) {
+ for (i = 0; i < n; i++)
+ if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]))
+ combine(one,compute_array[i][jm1],i);
+ } else one = compute_array[flag][jm1];
}
} else if (flavor[m] == LOCAL) {
if (!(compute->invoked_flag & INVOKED_LOCAL)) {
- compute->compute_local();
- compute->invoked_flag |= INVOKED_LOCAL;
+ compute->compute_local();
+ compute->invoked_flag |= INVOKED_LOCAL;
}
if (j == 0) {
- double *compute_vector = compute->vector_local;
- int n = compute->size_local_rows;
- if (flag < 0)
- for (i = 0; i < n; i++)
- combine(one,compute_vector[i],i);
- else one = compute_vector[flag];
+ double *compute_vector = compute->vector_local;
+ int n = compute->size_local_rows;
+ if (flag < 0)
+ for (i = 0; i < n; i++)
+ combine(one,compute_vector[i],i);
+ else one = compute_vector[flag];
} else {
- double **compute_array = compute->array_local;
- int n = compute->size_local_rows;
- int jm1 = j - 1;
- if (flag < 0)
- for (i = 0; i < n; i++)
- combine(one,compute_array[i][jm1],i);
- else one = compute_array[flag][jm1];
+ double **compute_array = compute->array_local;
+ int n = compute->size_local_rows;
+ int jm1 = j - 1;
+ if (flag < 0)
+ for (i = 0; i < n; i++)
+ combine(one,compute_array[i][jm1],i);
+ else one = compute_array[flag][jm1];
}
}
@@ -161,42 +161,42 @@ double ComputeReduceRegion::compute_one(int m, int flag)
if (flavor[m] == PERATOM) {
if (j == 0) {
- double *fix_vector = fix->vector_atom;
- int n = nlocal;
- if (flag < 0) {
- for (i = 0; i < n; i++)
- if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]))
- combine(one,fix_vector[i],i);
- } else one = fix_vector[flag];
+ double *fix_vector = fix->vector_atom;
+ int n = nlocal;
+ if (flag < 0) {
+ for (i = 0; i < n; i++)
+ if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]))
+ combine(one,fix_vector[i],i);
+ } else one = fix_vector[flag];
} else {
- double **fix_array = fix->array_atom;
- int jm1 = j - 1;
- if (flag < 0) {
- for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]))
- combine(one,fix_array[i][jm1],i);
- } else one = fix_array[flag][jm1];
+ double **fix_array = fix->array_atom;
+ int jm1 = j - 1;
+ if (flag < 0) {
+ for (i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]))
+ combine(one,fix_array[i][jm1],i);
+ } else one = fix_array[flag][jm1];
}
} else if (flavor[m] == LOCAL) {
if (j == 0) {
- double *fix_vector = fix->vector_local;
- int n = fix->size_local_rows;
- if (flag < 0)
- for (i = 0; i < n; i++)
- combine(one,fix_vector[i],i);
- else one = fix_vector[flag];
+ double *fix_vector = fix->vector_local;
+ int n = fix->size_local_rows;
+ if (flag < 0)
+ for (i = 0; i < n; i++)
+ combine(one,fix_vector[i],i);
+ else one = fix_vector[flag];
} else {
- double **fix_array = fix->array_local;
- int n = fix->size_local_rows;
- int jm1 = j - 1;
- if (flag < 0)
- for (i = 0; i < n; i++)
- combine(one,fix_array[i][jm1],i);
- else one = fix_array[flag][jm1];
+ double **fix_array = fix->array_local;
+ int n = fix->size_local_rows;
+ int jm1 = j - 1;
+ if (flag < 0)
+ for (i = 0; i < n; i++)
+ combine(one,fix_array[i][jm1],i);
+ else one = fix_array[flag][jm1];
}
}
-
+
// evaluate atom-style variable
} else if (which[m] == VARIABLE) {
@@ -209,8 +209,8 @@ double ComputeReduceRegion::compute_one(int m, int flag)
input->variable->compute_atom(n,igroup,varatom,1,0);
if (flag < 0) {
for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]))
- combine(one,varatom[i],i);
+ if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]))
+ combine(one,varatom[i],i);
} else one = varatom[flag];
}
diff --git a/src/compute_reduce_region.h b/src/compute_reduce_region.h
index d27c9f4f811cdb6016ade2d691bd28596a01c5f5..bba46383f4882a8229bfdf20d0b296b74dacfd1c 100644
--- a/src/compute_reduce_region.h
+++ b/src/compute_reduce_region.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/compute_slice.cpp b/src/compute_slice.cpp
index 85e92304992ded897a308dd5f8bcf399a1905893..76763dc50f223bc15fc9edb8a8a799996b7a1518 100644
--- a/src/compute_slice.cpp
+++ b/src/compute_slice.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -53,8 +53,8 @@ ComputeSlice::ComputeSlice(LAMMPS *lmp, int narg, char **arg) :
nvalues = 0;
for (int iarg = 6; iarg < narg; iarg++) {
- if (strncmp(arg[iarg],"c_",2) == 0 ||
- strncmp(arg[iarg],"f_",2) == 0) {
+ if (strncmp(arg[iarg],"c_",2) == 0 ||
+ strncmp(arg[iarg],"f_",2) == 0) {
if (arg[iarg][0] == 'c') which[nvalues] = COMPUTE;
else if (arg[iarg][0] == 'f') which[nvalues] = FIX;
@@ -64,10 +64,10 @@ ComputeSlice::ComputeSlice(LAMMPS *lmp, int narg, char **arg) :
char *ptr = strchr(suffix,'[');
if (ptr) {
- if (suffix[strlen(suffix)-1] != ']')
- error->all(FLERR,"Illegal compute slice command");
- argindex[nvalues] = atoi(ptr+1);
- *ptr = '\0';
+ if (suffix[strlen(suffix)-1] != ']')
+ error->all(FLERR,"Illegal compute slice command");
+ argindex[nvalues] = atoi(ptr+1);
+ *ptr = '\0';
} else argindex[nvalues] = 0;
n = strlen(suffix) + 1;
@@ -85,39 +85,39 @@ ComputeSlice::ComputeSlice(LAMMPS *lmp, int narg, char **arg) :
if (which[i] == COMPUTE) {
int icompute = modify->find_compute(ids[i]);
if (icompute < 0)
- error->all(FLERR,"Compute ID for compute slice does not exist");
+ error->all(FLERR,"Compute ID for compute slice does not exist");
if (modify->compute[icompute]->vector_flag) {
- if (argindex[i])
- error->all(FLERR,"Compute slice compute does not calculate a global array");
- if (nstop > modify->compute[icompute]->size_vector)
- error->all(FLERR,"Compute slice compute vector is accessed out-of-range");
+ if (argindex[i])
+ error->all(FLERR,"Compute slice compute does not calculate a global array");
+ if (nstop > modify->compute[icompute]->size_vector)
+ error->all(FLERR,"Compute slice compute vector is accessed out-of-range");
} else if (modify->compute[icompute]->array_flag) {
- if (argindex[i] == 0)
- error->all(FLERR,"Compute slice compute does not calculate a global vector");
- if (argindex[i] > modify->compute[icompute]->size_array_cols)
- error->all(FLERR,"Compute slice compute array is accessed out-of-range");
- if (nstop > modify->compute[icompute]->size_array_rows)
- error->all(FLERR,"Compute slice compute array is accessed out-of-range");
+ if (argindex[i] == 0)
+ error->all(FLERR,"Compute slice compute does not calculate a global vector");
+ if (argindex[i] > modify->compute[icompute]->size_array_cols)
+ error->all(FLERR,"Compute slice compute array is accessed out-of-range");
+ if (nstop > modify->compute[icompute]->size_array_rows)
+ error->all(FLERR,"Compute slice compute array is accessed out-of-range");
} else error->all(FLERR,"Compute slice compute does not calculate "
- "global vector or array");
+ "global vector or array");
} else if (which[i] == FIX) {
int ifix = modify->find_fix(ids[i]);
if (ifix < 0)
- error->all(FLERR,"Fix ID for compute slice does not exist");
+ error->all(FLERR,"Fix ID for compute slice does not exist");
if (modify->fix[ifix]->vector_flag) {
- if (argindex[i])
- error->all(FLERR,"Compute slice fix does not calculate a global array");
- if (nstop > modify->fix[ifix]->size_vector)
- error->all(FLERR,"Compute slice fix vector is accessed out-of-range");
+ if (argindex[i])
+ error->all(FLERR,"Compute slice fix does not calculate a global array");
+ if (nstop > modify->fix[ifix]->size_vector)
+ error->all(FLERR,"Compute slice fix vector is accessed out-of-range");
} else if (modify->fix[ifix]->array_flag) {
- if (argindex[i] == 0)
- error->all(FLERR,"Compute slice fix does not calculate a global vector");
- if (argindex[i] > modify->fix[ifix]->size_array_cols)
- error->all(FLERR,"Compute slice fix array is accessed out-of-range");
- if (nstop > modify->fix[ifix]->size_array_rows)
- error->all(FLERR,"Compute slice fix array is accessed out-of-range");
+ if (argindex[i] == 0)
+ error->all(FLERR,"Compute slice fix does not calculate a global vector");
+ if (argindex[i] > modify->fix[ifix]->size_array_cols)
+ error->all(FLERR,"Compute slice fix array is accessed out-of-range");
+ if (nstop > modify->fix[ifix]->size_array_rows)
+ error->all(FLERR,"Compute slice fix array is accessed out-of-range");
} else error->all(FLERR,"Compute slice fix does not calculate "
- "global vector or array");
+ "global vector or array");
}
}
@@ -137,24 +137,24 @@ ComputeSlice::ComputeSlice(LAMMPS *lmp, int narg, char **arg) :
if (which[0] == COMPUTE) {
int icompute = modify->find_compute(ids[0]);
if (argindex[0] == 0) {
- extvector = modify->compute[icompute]->extvector;
- if (modify->compute[icompute]->extvector == -1) {
- extlist = new int[size_vector];
- int j = 0;
- for (int i = nstart; i < nstop; i += nskip)
- extlist[j++] = modify->compute[icompute]->extlist[i-1];
- }
+ extvector = modify->compute[icompute]->extvector;
+ if (modify->compute[icompute]->extvector == -1) {
+ extlist = new int[size_vector];
+ int j = 0;
+ for (int i = nstart; i < nstop; i += nskip)
+ extlist[j++] = modify->compute[icompute]->extlist[i-1];
+ }
} else extvector = modify->compute[icompute]->extarray;
} else if (which[0] == FIX) {
int ifix = modify->find_fix(ids[0]);
if (argindex[0] == 0) {
- extvector = modify->fix[ifix]->extvector;
- if (modify->fix[ifix]->extvector == -1) {
- extlist = new int[size_vector];
- int j = 0;
- for (int i = nstart; i < nstop; i += nskip)
- extlist[j++] = modify->fix[ifix]->extlist[i-1];
- }
+ extvector = modify->fix[ifix]->extvector;
+ if (modify->fix[ifix]->extvector == -1) {
+ extlist = new int[size_vector];
+ int j = 0;
+ for (int i = nstart; i < nstop; i += nskip)
+ extlist[j++] = modify->fix[ifix]->extlist[i-1];
+ }
} else extvector = modify->fix[ifix]->extarray;
}
@@ -167,27 +167,27 @@ ComputeSlice::ComputeSlice(LAMMPS *lmp, int narg, char **arg) :
extarray = 0;
for (int i = 0; i < nvalues; i++) {
if (which[i] == COMPUTE) {
- int icompute = modify->find_compute(ids[i]);
- if (argindex[i] == 0) {
- if (modify->compute[icompute]->extvector == 1) extarray = 1;
- if (modify->compute[icompute]->extvector == -1) {
- for (int j = 0; j < modify->compute[icompute]->size_vector; j++)
- if (modify->compute[icompute]->extlist[j]) extarray = 1;
- }
- } else {
- if (modify->compute[icompute]->extarray) extarray = 1;
- }
+ int icompute = modify->find_compute(ids[i]);
+ if (argindex[i] == 0) {
+ if (modify->compute[icompute]->extvector == 1) extarray = 1;
+ if (modify->compute[icompute]->extvector == -1) {
+ for (int j = 0; j < modify->compute[icompute]->size_vector; j++)
+ if (modify->compute[icompute]->extlist[j]) extarray = 1;
+ }
+ } else {
+ if (modify->compute[icompute]->extarray) extarray = 1;
+ }
} else if (which[i] == FIX) {
- int ifix = modify->find_fix(ids[i]);
- if (argindex[i] == 0) {
- if (modify->fix[ifix]->extvector == 1) extarray = 1;
- if (modify->fix[ifix]->extvector == -1) {
- for (int j = 0; j < modify->fix[ifix]->size_vector; j++)
- if (modify->fix[ifix]->extlist[j]) extarray = 1;
- }
- } else {
- if (modify->fix[ifix]->extarray) extarray = 1;
- }
+ int ifix = modify->find_fix(ids[i]);
+ if (argindex[i] == 0) {
+ if (modify->fix[ifix]->extvector == 1) extarray = 1;
+ if (modify->fix[ifix]->extvector == -1) {
+ for (int j = 0; j < modify->fix[ifix]->size_vector; j++)
+ if (modify->fix[ifix]->extlist[j]) extarray = 1;
+ }
+ } else {
+ if (modify->fix[ifix]->extarray) extarray = 1;
+ }
}
}
}
@@ -217,12 +217,12 @@ void ComputeSlice::init()
if (which[m] == COMPUTE) {
int icompute = modify->find_compute(ids[m]);
if (icompute < 0)
- error->all(FLERR,"Compute ID for compute slice does not exist");
+ error->all(FLERR,"Compute ID for compute slice does not exist");
value2index[m] = icompute;
} else if (which[m] == FIX) {
int ifix = modify->find_fix(ids[m]);
- if (ifix < 0)
- error->all(FLERR,"Fix ID for compute slice does not exist");
+ if (ifix < 0)
+ error->all(FLERR,"Fix ID for compute slice does not exist");
value2index[m] = ifix;
}
}
@@ -263,32 +263,32 @@ void ComputeSlice::extract_one(int m, double *vec, int stride)
if (argindex[m] == 0) {
if (!(compute->invoked_flag & INVOKED_VECTOR)) {
- compute->compute_vector();
- compute->invoked_flag |= INVOKED_VECTOR;
+ compute->compute_vector();
+ compute->invoked_flag |= INVOKED_VECTOR;
}
double *cvector = compute->vector;
j = 0;
for (i = nstart; i < nstop; i += nskip) {
- vec[j] = cvector[i-1];
- j += stride;
+ vec[j] = cvector[i-1];
+ j += stride;
}
-
+
} else {
if (!(compute->invoked_flag & INVOKED_ARRAY)) {
- compute->compute_array();
- compute->invoked_flag |= INVOKED_ARRAY;
+ compute->compute_array();
+ compute->invoked_flag |= INVOKED_ARRAY;
}
double **carray = compute->array;
int icol = argindex[m]-1;
j = 0;
for (i = nstart; i < nstop; i += nskip) {
- vec[j] = carray[i-1][icol];
- j += stride;
+ vec[j] = carray[i-1][icol];
+ j += stride;
}
}
// access fix fields, check if fix frequency is a match
-
+
} else if (which[m] == FIX) {
if (update->ntimestep % modify->fix[value2index[m]]->global_freq)
error->all(FLERR,"Fix used in compute slice not computed at compatible time");
@@ -297,15 +297,15 @@ void ComputeSlice::extract_one(int m, double *vec, int stride)
if (argindex[m] == 0) {
j = 0;
for (i = nstart; i < nstop; i += nskip) {
- vec[j] = fix->compute_vector(i-1);
- j += stride;
+ vec[j] = fix->compute_vector(i-1);
+ j += stride;
}
} else {
int icol = argindex[m]-1;
j = 0;
for (i = nstart; i < nstop; i += nskip) {
- vec[j] = fix->compute_array(i-1,icol);
- j += stride;
+ vec[j] = fix->compute_array(i-1,icol);
+ j += stride;
}
}
}
diff --git a/src/compute_slice.h b/src/compute_slice.h
index e837fa945b28ae415e62572bd7e0272fd34329dc..b112d72a3a6fc9f02d270f9513fb3172be2cd304 100644
--- a/src/compute_slice.h
+++ b/src/compute_slice.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/compute_stress_atom.cpp b/src/compute_stress_atom.cpp
index f64069870045973ea38c1ab0ef4dbc3de7df740b..d18d264e795513e4a0c0262ffdc0e71f6177c52b 100644
--- a/src/compute_stress_atom.cpp
+++ b/src/compute_stress_atom.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -33,7 +33,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-ComputeStressAtom::ComputeStressAtom(LAMMPS *lmp, int narg, char **arg) :
+ComputeStressAtom::ComputeStressAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg < 3) error->all(FLERR,"Illegal compute stress/atom command");
@@ -67,9 +67,9 @@ ComputeStressAtom::ComputeStressAtom(LAMMPS *lmp, int narg, char **arg) :
else if (strcmp(arg[iarg],"kspace") == 0) kspaceflag = 1;
else if (strcmp(arg[iarg],"fix") == 0) fixflag = 1;
else if (strcmp(arg[iarg],"virial") == 0) {
- pairflag = 1;
- bondflag = angleflag = dihedralflag = improperflag = 1;
- kspaceflag = fixflag = 1;
+ pairflag = 1;
+ bondflag = angleflag = dihedralflag = improperflag = 1;
+ kspaceflag = fixflag = 1;
} else error->all(FLERR,"Illegal compute stress/atom command");
iarg++;
}
@@ -132,35 +132,35 @@ void ComputeStressAtom::compute_peratom()
double **vatom = force->pair->vatom;
for (i = 0; i < npair; i++)
for (j = 0; j < 6; j++)
- stress[i][j] += vatom[i][j];
+ stress[i][j] += vatom[i][j];
}
if (bondflag && force->bond) {
double **vatom = force->bond->vatom;
for (i = 0; i < nbond; i++)
for (j = 0; j < 6; j++)
- stress[i][j] += vatom[i][j];
+ stress[i][j] += vatom[i][j];
}
if (angleflag && force->angle) {
double **vatom = force->angle->vatom;
for (i = 0; i < nbond; i++)
for (j = 0; j < 6; j++)
- stress[i][j] += vatom[i][j];
+ stress[i][j] += vatom[i][j];
}
if (dihedralflag && force->dihedral) {
double **vatom = force->dihedral->vatom;
for (i = 0; i < nbond; i++)
for (j = 0; j < 6; j++)
- stress[i][j] += vatom[i][j];
+ stress[i][j] += vatom[i][j];
}
if (improperflag && force->improper) {
double **vatom = force->improper->vatom;
for (i = 0; i < nbond; i++)
for (j = 0; j < 6; j++)
- stress[i][j] += vatom[i][j];
+ stress[i][j] += vatom[i][j];
}
// add in per-atom contributions from relevant fixes
@@ -168,10 +168,10 @@ void ComputeStressAtom::compute_peratom()
if (fixflag) {
for (int ifix = 0; ifix < modify->nfix; ifix++)
if (modify->fix[ifix]->virial_flag) {
- double **vatom = modify->fix[ifix]->vatom;
- for (i = 0; i < nlocal; i++)
- for (j = 0; j < 6; j++)
- stress[i][j] += vatom[i][j];
+ double **vatom = modify->fix[ifix]->vatom;
+ for (i = 0; i < nlocal; i++)
+ for (j = 0; j < 6; j++)
+ stress[i][j] += vatom[i][j];
}
}
@@ -185,7 +185,7 @@ void ComputeStressAtom::compute_peratom()
double **vatom = force->kspace->vatom;
for (i = 0; i < nlocal; i++)
for (j = 0; j < 6; j++)
- stress[i][j] += vatom[i][j];
+ stress[i][j] += vatom[i][j];
}
// zero virial of atoms not in group
@@ -215,27 +215,27 @@ void ComputeStressAtom::compute_peratom()
if (rmass) {
for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit) {
- onemass = mvv2e * rmass[i];
- stress[i][0] += onemass*v[i][0]*v[i][0];
- stress[i][1] += onemass*v[i][1]*v[i][1];
- stress[i][2] += onemass*v[i][2]*v[i][2];
- stress[i][3] += onemass*v[i][0]*v[i][1];
- stress[i][4] += onemass*v[i][0]*v[i][2];
- stress[i][5] += onemass*v[i][1]*v[i][2];
- }
+ if (mask[i] & groupbit) {
+ onemass = mvv2e * rmass[i];
+ stress[i][0] += onemass*v[i][0]*v[i][0];
+ stress[i][1] += onemass*v[i][1]*v[i][1];
+ stress[i][2] += onemass*v[i][2]*v[i][2];
+ stress[i][3] += onemass*v[i][0]*v[i][1];
+ stress[i][4] += onemass*v[i][0]*v[i][2];
+ stress[i][5] += onemass*v[i][1]*v[i][2];
+ }
} else {
for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit) {
- onemass = mvv2e * mass[type[i]];
- stress[i][0] += onemass*v[i][0]*v[i][0];
- stress[i][1] += onemass*v[i][1]*v[i][1];
- stress[i][2] += onemass*v[i][2]*v[i][2];
- stress[i][3] += onemass*v[i][0]*v[i][1];
- stress[i][4] += onemass*v[i][0]*v[i][2];
- stress[i][5] += onemass*v[i][1]*v[i][2];
- }
+ if (mask[i] & groupbit) {
+ onemass = mvv2e * mass[type[i]];
+ stress[i][0] += onemass*v[i][0]*v[i][0];
+ stress[i][1] += onemass*v[i][1]*v[i][1];
+ stress[i][2] += onemass*v[i][2]*v[i][2];
+ stress[i][3] += onemass*v[i][0]*v[i][1];
+ stress[i][4] += onemass*v[i][0]*v[i][2];
+ stress[i][5] += onemass*v[i][1]*v[i][2];
+ }
}
}
diff --git a/src/compute_stress_atom.h b/src/compute_stress_atom.h
index 5665b875b1b94e5d799bd8853ce0bf6e4e58ca99..4592689b2a6fb60401f4cfaab2d1e5dafc7bfd15 100644
--- a/src/compute_stress_atom.h
+++ b/src/compute_stress_atom.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/compute_temp.cpp b/src/compute_temp.cpp
index ab63a8c9f644fe399494e1705ecfd532c3e916b4..0ce6b285ff9bc6ee32bc8629e706797574883ace 100644
--- a/src/compute_temp.cpp
+++ b/src/compute_temp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -27,7 +27,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-ComputeTemp::ComputeTemp(LAMMPS *lmp, int narg, char **arg) :
+ComputeTemp::ComputeTemp(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 3) error->all(FLERR,"Illegal compute temp command");
@@ -87,12 +87,12 @@ double ComputeTemp::compute_scalar()
if (rmass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
- t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) * rmass[i];
+ t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) * rmass[i];
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
- t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
- mass[type[i]];
+ t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
+ mass[type[i]];
}
MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
diff --git a/src/compute_temp.h b/src/compute_temp.h
index 7e201f87121aad30a68f76bab5067ce96e6b280c..79533e9764dc8f0568ae02fb2941ebb803b2302d 100644
--- a/src/compute_temp.h
+++ b/src/compute_temp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/compute_temp_com.cpp b/src/compute_temp_com.cpp
index d344d3d2148ef9164d66f78ef897f51c9a02ac6a..6bf71d6cb10d2a42676432b4d479e713826ae92e 100644
--- a/src/compute_temp_com.cpp
+++ b/src/compute_temp_com.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -29,7 +29,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-ComputeTempCOM::ComputeTempCOM(LAMMPS *lmp, int narg, char **arg) :
+ComputeTempCOM::ComputeTempCOM(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 3) error->all(FLERR,"Illegal compute temp command");
@@ -100,11 +100,11 @@ double ComputeTempCOM::compute_scalar()
vthermal[1] = v[i][1] - vbias[1];
vthermal[2] = v[i][2] - vbias[2];
if (rmass)
- t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] +
- vthermal[2]*vthermal[2]) * rmass[i];
+ t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] +
+ vthermal[2]*vthermal[2]) * rmass[i];
else
- t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] +
- vthermal[2]*vthermal[2]) * mass[type[i]];
+ t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] +
+ vthermal[2]*vthermal[2]) * mass[type[i]];
}
MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
diff --git a/src/compute_temp_com.h b/src/compute_temp_com.h
index 364ed57d9f800d7c58c09b99868d72fb9073b771..8a93cbc9f679402e1d8d9c8c28e5f42ee73132d3 100644
--- a/src/compute_temp_com.h
+++ b/src/compute_temp_com.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/compute_temp_deform.cpp b/src/compute_temp_deform.cpp
index 87fcb02eae469a5e729e74b36b42e8e52a8feccd..48e3a488f48ef09c4ae635530c2db166ab2f2b33 100644
--- a/src/compute_temp_deform.cpp
+++ b/src/compute_temp_deform.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -76,10 +76,10 @@ void ComputeTempDeform::init()
for (i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"deform") == 0) {
- if (((FixDeform *) modify->fix[i])->remapflag == X_REMAP &&
- comm->me == 0)
- error->warning(FLERR,"Using compute temp/deform with inconsistent "
- "fix deform remap option");
+ if (((FixDeform *) modify->fix[i])->remapflag == X_REMAP &&
+ comm->me == 0)
+ error->warning(FLERR,"Using compute temp/deform with inconsistent "
+ "fix deform remap option");
break;
}
if (i == modify->nfix && comm->me == 0)
@@ -125,19 +125,19 @@ double ComputeTempDeform::compute_scalar()
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
domain->x2lamda(x[i],lamda);
- vstream[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
- h_rate[4]*lamda[2] + h_ratelo[0];
+ vstream[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
+ h_rate[4]*lamda[2] + h_ratelo[0];
vstream[1] = h_rate[1]*lamda[1] + h_rate[3]*lamda[2] + h_ratelo[1];
vstream[2] = h_rate[2]*lamda[2] + h_ratelo[2];
vthermal[0] = v[i][0] - vstream[0];
vthermal[1] = v[i][1] - vstream[1];
vthermal[2] = v[i][2] - vstream[2];
if (rmass)
- t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] +
- vthermal[2]*vthermal[2]) * rmass[i];
+ t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] +
+ vthermal[2]*vthermal[2]) * rmass[i];
else
- t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] +
- vthermal[2]*vthermal[2]) * mass[type[i]];
+ t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] +
+ vthermal[2]*vthermal[2]) * mass[type[i]];
}
MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
@@ -171,8 +171,8 @@ void ComputeTempDeform::compute_vector()
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
domain->x2lamda(x[i],lamda);
- vstream[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
- h_rate[4]*lamda[2] + h_ratelo[0];
+ vstream[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
+ h_rate[4]*lamda[2] + h_ratelo[0];
vstream[1] = h_rate[1]*lamda[1] + h_rate[3]*lamda[2] + h_ratelo[1];
vstream[2] = h_rate[2]*lamda[2] + h_ratelo[2];
vthermal[0] = v[i][0] - vstream[0];
@@ -202,9 +202,9 @@ void ComputeTempDeform::remove_bias(int i, double *v)
double lamda[3];
double *h_rate = domain->h_rate;
double *h_ratelo = domain->h_ratelo;
-
+
domain->x2lamda(atom->x[i],lamda);
- vbias[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
+ vbias[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
h_rate[4]*lamda[2] + h_ratelo[0];
vbias[1] = h_rate[1]*lamda[1] + h_rate[3]*lamda[2] + h_ratelo[1];
vbias[2] = h_rate[2]*lamda[2] + h_ratelo[2];
@@ -236,8 +236,8 @@ void ComputeTempDeform::remove_bias_all()
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
domain->x2lamda(atom->x[i],lamda);
- vbiasall[i][0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
- h_rate[4]*lamda[2] + h_ratelo[0];
+ vbiasall[i][0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
+ h_rate[4]*lamda[2] + h_ratelo[0];
vbiasall[i][1] = h_rate[1]*lamda[1] + h_rate[3]*lamda[2] + h_ratelo[1];
vbiasall[i][2] = h_rate[2]*lamda[2] + h_ratelo[2];
v[i][0] -= vbiasall[i][0];
diff --git a/src/compute_temp_deform.h b/src/compute_temp_deform.h
index fd18cce16f03145d5ff41d8804dc6cd8cffb400a..c7afaa97deefacacc3934ccc380974c500e99e88 100644
--- a/src/compute_temp_deform.h
+++ b/src/compute_temp_deform.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/compute_temp_partial.cpp b/src/compute_temp_partial.cpp
index bfb2088e5608b3c4b4aa32b005a6b3abf79a2914..31a55671dde5bca5362ff3a4ca9109cc5a3fe2c5 100644
--- a/src/compute_temp_partial.cpp
+++ b/src/compute_temp_partial.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -28,7 +28,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-ComputeTempPartial::ComputeTempPartial(LAMMPS *lmp, int narg, char **arg) :
+ComputeTempPartial::ComputeTempPartial(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 6) error->all(FLERR,"Illegal compute temp/partial command");
@@ -110,13 +110,13 @@ double ComputeTempPartial::compute_scalar()
if (rmass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
- t += (xflag*v[i][0]*v[i][0] + yflag*v[i][1]*v[i][1] +
- zflag*v[i][2]*v[i][2]) * rmass[i];
+ t += (xflag*v[i][0]*v[i][0] + yflag*v[i][1]*v[i][1] +
+ zflag*v[i][2]*v[i][2]) * rmass[i];
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
- t += (xflag*v[i][0]*v[i][0] + yflag*v[i][1]*v[i][1] +
- zflag*v[i][2]*v[i][2]) * mass[type[i]];
+ t += (xflag*v[i][0]*v[i][0] + yflag*v[i][1]*v[i][1] +
+ zflag*v[i][2]*v[i][2]) * mass[type[i]];
}
MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
@@ -198,22 +198,22 @@ void ComputeTempPartial::remove_bias_all()
if (!xflag) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- vbiasall[i][0] = v[i][0];
- v[i][0] = 0.0;
+ vbiasall[i][0] = v[i][0];
+ v[i][0] = 0.0;
}
}
if (!yflag) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- vbiasall[i][1] = v[i][1];
- v[i][1] = 0.0;
+ vbiasall[i][1] = v[i][1];
+ v[i][1] = 0.0;
}
}
if (!zflag) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- vbiasall[i][2] = v[i][2];
- v[i][2] = 0.0;
+ vbiasall[i][2] = v[i][2];
+ v[i][2] = 0.0;
}
}
}
@@ -244,17 +244,17 @@ void ComputeTempPartial::restore_bias_all()
if (!xflag) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
- v[i][0] += vbiasall[i][0];
+ v[i][0] += vbiasall[i][0];
}
if (!yflag) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
- v[i][1] += vbiasall[i][1];
+ v[i][1] += vbiasall[i][1];
}
if (!zflag) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
- v[i][2] += vbiasall[i][2];
+ v[i][2] += vbiasall[i][2];
}
}
diff --git a/src/compute_temp_partial.h b/src/compute_temp_partial.h
index 6302d28e216bb4be2835a6b8b9e04251c18bb1a2..97ac60541e7b5dc8dfa2280b079b9aa2daa02559 100644
--- a/src/compute_temp_partial.h
+++ b/src/compute_temp_partial.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/compute_temp_profile.cpp b/src/compute_temp_profile.cpp
index a242aba339e1626bcefd9fac7c29f04983a32749..dfd609c6c5b2754cf9692f138b141e99e92b4039 100644
--- a/src/compute_temp_profile.cpp
+++ b/src/compute_temp_profile.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -29,7 +29,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-ComputeTempProfile::ComputeTempProfile(LAMMPS *lmp, int narg, char **arg) :
+ComputeTempProfile::ComputeTempProfile(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg < 7) error->all(FLERR,"Illegal compute temp/profile command");
@@ -96,7 +96,7 @@ ComputeTempProfile::ComputeTempProfile(LAMMPS *lmp, int narg, char **arg) :
memory->create(vbin,nbins,ncount+1,"temp/profile:vbin");
memory->create(binave,nbins,ncount+1,"temp/profile:binave");
-
+
maxatom = 0;
bin = NULL;
@@ -186,11 +186,11 @@ double ComputeTempProfile::compute_scalar()
else vthermal[2] = v[i][2];
if (rmass)
- t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] +
- vthermal[2]*vthermal[2]) * rmass[i];
+ t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] +
+ vthermal[2]*vthermal[2]) * rmass[i];
else
- t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] +
- vthermal[2]*vthermal[2]) * mass[type[i]];
+ t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] +
+ vthermal[2]*vthermal[2]) * mass[type[i]];
}
MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
@@ -286,16 +286,16 @@ void ComputeTempProfile::remove_bias_all()
if (mask[i] & groupbit) {
ibin = bin[i];
if (xflag) {
- vbiasall[i][0] = binave[ibin][ivx];
- v[i][0] -= vbiasall[i][0];
+ vbiasall[i][0] = binave[ibin][ivx];
+ v[i][0] -= vbiasall[i][0];
}
if (yflag) {
- vbiasall[i][1] = binave[ibin][ivy];
- v[i][1] -= vbiasall[i][1];
+ vbiasall[i][1] = binave[ibin][ivy];
+ v[i][1] -= vbiasall[i][1];
}
if (zflag) {
- vbiasall[i][2] = binave[ibin][ivz];
- v[i][2] -= vbiasall[i][2];
+ vbiasall[i][2] = binave[ibin][ivz];
+ v[i][2] -= vbiasall[i][2];
}
}
}
@@ -326,17 +326,17 @@ void ComputeTempProfile::restore_bias_all()
if (xflag) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
- v[i][0] += vbiasall[i][0];
+ v[i][0] += vbiasall[i][0];
}
if (yflag) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
- v[i][1] += vbiasall[i][1];
+ v[i][1] += vbiasall[i][1];
}
if (zflag) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
- v[i][2] += vbiasall[i][2];
+ v[i][2] += vbiasall[i][2];
}
}
@@ -381,7 +381,7 @@ void ComputeTempProfile::bin_average()
for (i = 0; i < nbins; i++)
if (binave[i][ncount] > 0.0)
for (j = 0; j < ncount; j++)
- binave[i][j] /= binave[i][ncount];
+ binave[i][j] /= binave[i][ncount];
}
/* ----------------------------------------------------------------------
@@ -424,38 +424,38 @@ void ComputeTempProfile::bin_assign()
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (nbinx > 1) {
- coord = x[i][0];
- if (periodicity[0]) {
- if (coord < boxlo[0]) coord += prd[0];
- if (coord >= boxhi[0]) coord -= prd[0];
- }
- ibinx = static_cast<int> ((coord - boxlo[0]) * invdelta[0]);
- ibinx = MAX(ibinx,0);
- ibinx = MIN(ibinx,nbinx-1);
+ coord = x[i][0];
+ if (periodicity[0]) {
+ if (coord < boxlo[0]) coord += prd[0];
+ if (coord >= boxhi[0]) coord -= prd[0];
+ }
+ ibinx = static_cast<int> ((coord - boxlo[0]) * invdelta[0]);
+ ibinx = MAX(ibinx,0);
+ ibinx = MIN(ibinx,nbinx-1);
} else ibinx = 0;
-
+
if (nbiny > 1) {
- coord = x[i][1];
- if (periodicity[1]) {
- if (coord < boxlo[1]) coord += prd[1];
- if (coord >= boxhi[1]) coord -= prd[1];
- }
- ibiny = static_cast<int> ((coord - boxlo[1]) * invdelta[1]);
- ibiny = MAX(ibiny,0);
- ibiny = MIN(ibiny,nbiny-1);
+ coord = x[i][1];
+ if (periodicity[1]) {
+ if (coord < boxlo[1]) coord += prd[1];
+ if (coord >= boxhi[1]) coord -= prd[1];
+ }
+ ibiny = static_cast<int> ((coord - boxlo[1]) * invdelta[1]);
+ ibiny = MAX(ibiny,0);
+ ibiny = MIN(ibiny,nbiny-1);
} else ibiny = 0;
-
+
if (nbinz > 1) {
- coord = x[i][2];
- if (periodicity[2]) {
- if (coord < boxlo[2]) coord += prd[2];
- if (coord >= boxhi[2]) coord -= prd[2];
- }
- ibinz = static_cast<int> ((coord - boxlo[2]) * invdelta[2]);
- ibinz = MAX(ibinz,0);
- ibinz = MIN(ibinz,nbinz-1);
+ coord = x[i][2];
+ if (periodicity[2]) {
+ if (coord < boxlo[2]) coord += prd[2];
+ if (coord >= boxhi[2]) coord -= prd[2];
+ }
+ ibinz = static_cast<int> ((coord - boxlo[2]) * invdelta[2]);
+ ibinz = MAX(ibinz,0);
+ ibinz = MIN(ibinz,nbinz-1);
} else ibinz = 0;
-
+
bin[i] = nbinx*nbiny*ibinz + nbinx*ibiny + ibinx;
}
diff --git a/src/compute_temp_profile.h b/src/compute_temp_profile.h
index 3dc8583a6b768465839d1b87faab1fd384a1262f..6fa423d5db497dad52a8885a3a436e5af0a546f4 100644
--- a/src/compute_temp_profile.h
+++ b/src/compute_temp_profile.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -53,7 +53,7 @@ class ComputeTempProfile : public Compute {
int maxatom;
int *bin;
double **vbin,**binave;
-
+
void dof_compute();
void bin_average();
void bin_setup();
diff --git a/src/compute_temp_ramp.cpp b/src/compute_temp_ramp.cpp
index 135a3eea6db834e78ae4457621c8e7919e0e861f..a28bcc89950f952a4e5bcc49a97fccb1390713a4 100644
--- a/src/compute_temp_ramp.cpp
+++ b/src/compute_temp_ramp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -30,7 +30,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-ComputeTempRamp::ComputeTempRamp(LAMMPS *lmp, int narg, char **arg) :
+ComputeTempRamp::ComputeTempRamp(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg < 9) error->all(FLERR,"Illegal compute temp command");
@@ -166,11 +166,11 @@ double ComputeTempRamp::compute_scalar()
vthermal[2] = v[i][2];
vthermal[v_dim] -= vramp;
if (rmass)
- t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] +
- vthermal[2]*vthermal[2]) * rmass[i];
+ t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] +
+ vthermal[2]*vthermal[2]) * rmass[i];
else
- t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] +
- vthermal[2]*vthermal[2]) * mass[type[i]];
+ t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] +
+ vthermal[2]*vthermal[2]) * mass[type[i]];
}
MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
diff --git a/src/compute_temp_ramp.h b/src/compute_temp_ramp.h
index c3933467843b38b96994427a362a772f9e823d9e..b470011dd79f14f56828b29f72576637f3da555c 100644
--- a/src/compute_temp_ramp.h
+++ b/src/compute_temp_ramp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/compute_temp_region.cpp b/src/compute_temp_region.cpp
index 964f162d9fc66d3ce5efa13ea03d3888ac4d0e15..ba74fc0077393cfa15b83d90baf2efd0b42ce259 100644
--- a/src/compute_temp_region.cpp
+++ b/src/compute_temp_region.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -27,13 +27,13 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-ComputeTempRegion::ComputeTempRegion(LAMMPS *lmp, int narg, char **arg) :
+ComputeTempRegion::ComputeTempRegion(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 4) error->all(FLERR,"Illegal compute temp/region command");
iregion = domain->find_region(arg[3]);
- if (iregion == -1)
+ if (iregion == -1)
error->all(FLERR,"Region ID for compute temp/region does not exist");
int n = strlen(arg[3]) + 1;
idregion = new char[n];
@@ -103,15 +103,15 @@ double ComputeTempRegion::compute_scalar()
if (rmass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
- count++;
- t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) * rmass[i];
+ count++;
+ t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) * rmass[i];
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
- count++;
- t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
- mass[type[i]];
+ count++;
+ t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
+ mass[type[i]];
}
}
@@ -194,18 +194,18 @@ void ComputeTempRegion::remove_bias_all()
maxbias = atom->nmax;
memory->create(vbiasall,maxbias,3,"temp/region:vbiasall");
}
-
+
Region *region = domain->regions[iregion];
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (region->match(x[i][0],x[i][1],x[i][2]))
- vbiasall[i][0] = vbiasall[i][1] = vbiasall[i][2] = 0.0;
+ vbiasall[i][0] = vbiasall[i][1] = vbiasall[i][2] = 0.0;
else {
- vbiasall[i][0] = v[i][0];
- vbiasall[i][1] = v[i][1];
- vbiasall[i][2] = v[i][2];
- v[i][0] = v[i][1] = v[i][2] = 0.0;
+ vbiasall[i][0] = v[i][0];
+ vbiasall[i][1] = v[i][1];
+ vbiasall[i][2] = v[i][2];
+ v[i][0] = v[i][1] = v[i][2] = 0.0;
}
}
}
diff --git a/src/compute_temp_region.h b/src/compute_temp_region.h
index e0df3a8f623a998d4f351f94f42faf52c9151809..ce1df7a0416dade3c8b193fab7d9884704d0a4c6 100644
--- a/src/compute_temp_region.h
+++ b/src/compute_temp_region.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/compute_temp_sphere.cpp b/src/compute_temp_sphere.cpp
index c4db2f5987ab9c1e4fbe7473419026dd17337557..2c4b4c420d5d59bb0df950ae7720c1db55a2e9f1 100644
--- a/src/compute_temp_sphere.cpp
+++ b/src/compute_temp_sphere.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -32,7 +32,7 @@ enum{ROTATE,ALL};
/* ---------------------------------------------------------------------- */
-ComputeTempSphere::ComputeTempSphere(LAMMPS *lmp, int narg, char **arg) :
+ComputeTempSphere::ComputeTempSphere(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg < 3) error->all(FLERR,"Illegal compute temp/sphere command");
@@ -46,20 +46,20 @@ ComputeTempSphere::ComputeTempSphere(LAMMPS *lmp, int narg, char **arg) :
tempbias = 0;
id_bias = NULL;
mode = ALL;
-
+
int iarg = 3;
while (iarg < narg) {
if (strcmp(arg[iarg],"bias") == 0) {
- if (iarg+2 > narg)
- error->all(FLERR,"Illegal compute temp/sphere command");
+ if (iarg+2 > narg)
+ error->all(FLERR,"Illegal compute temp/sphere command");
tempbias = 1;
int n = strlen(arg[iarg+1]) + 1;
id_bias = new char[n];
strcpy(id_bias,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"dof") == 0) {
- if (iarg+2 > narg)
- error->all(FLERR,"Illegal compute temp/sphere command");
+ if (iarg+2 > narg)
+ error->all(FLERR,"Illegal compute temp/sphere command");
if (strcmp(arg[iarg+1],"rotate") == 0) mode = ROTATE;
else if (strcmp(arg[iarg+1],"all") == 0) mode = ALL;
else error->all(FLERR,"Illegal compute temp/sphere command");
@@ -71,7 +71,7 @@ ComputeTempSphere::ComputeTempSphere(LAMMPS *lmp, int narg, char **arg) :
// error checks
- if (!atom->sphere_flag)
+ if (!atom->sphere_flag)
error->all(FLERR,"Compute temp/sphere requires atom style sphere");
}
@@ -89,7 +89,7 @@ void ComputeTempSphere::init()
{
if (tempbias) {
int i = modify->find_compute(id_bias);
- if (i < 0)
+ if (i < 0)
error->all(FLERR,"Could not find compute ID for temperature bias");
tbias = modify->compute[i];
if (tbias->tempflag == 0)
@@ -129,22 +129,22 @@ void ComputeTempSphere::dof_compute()
if (domain->dimension == 3) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- if (radius[i] == 0.0) {
- if (mode == ALL) count += 3;
- } else {
- if (mode == ALL) count += 6;
- else count += 3;
- }
+ if (radius[i] == 0.0) {
+ if (mode == ALL) count += 3;
+ } else {
+ if (mode == ALL) count += 6;
+ else count += 3;
+ }
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- if (radius[i] == 0.0) {
- if (mode == ALL) count += 2;
- } else {
- if (mode == ALL) count += 3;
- else count += 1;
- }
+ if (radius[i] == 0.0) {
+ if (mode == ALL) count += 2;
+ } else {
+ if (mode == ALL) count += 3;
+ else count += 1;
+ }
}
}
@@ -166,28 +166,28 @@ void ComputeTempSphere::dof_compute()
count = 0;
if (domain->dimension == 3) {
for (int i = 0; i < nlocal; i++)
- if (mask[i] & groupbit) {
- if (tbias->dof_remove(i)) {
- if (radius[i] == 0.0) {
- if (mode == ALL) count += 3;
- } else {
- if (mode == ALL) count += 6;
- else count += 3;
- }
- }
- }
+ if (mask[i] & groupbit) {
+ if (tbias->dof_remove(i)) {
+ if (radius[i] == 0.0) {
+ if (mode == ALL) count += 3;
+ } else {
+ if (mode == ALL) count += 6;
+ else count += 3;
+ }
+ }
+ }
} else {
for (int i = 0; i < nlocal; i++)
- if (mask[i] & groupbit) {
- if (tbias->dof_remove(i)) {
- if (radius[i] == 0.0) {
- if (mode == ALL) count += 2;
- } else {
- if (mode == ALL) count += 3;
- else count += 1;
- }
- }
- }
+ if (mask[i] & groupbit) {
+ if (tbias->dof_remove(i)) {
+ if (radius[i] == 0.0) {
+ if (mode == ALL) count += 2;
+ } else {
+ if (mode == ALL) count += 3;
+ else count += 1;
+ }
+ }
+ }
}
MPI_Allreduce(&count,&count_all,1,MPI_INT,MPI_SUM,world);
@@ -224,15 +224,15 @@ double ComputeTempSphere::compute_scalar()
if (mode == ALL) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) * rmass[i];
- t += (omega[i][0]*omega[i][0] + omega[i][1]*omega[i][1] +
- omega[i][2]*omega[i][2]) * INERTIA*rmass[i]*radius[i]*radius[i];
+ t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) * rmass[i];
+ t += (omega[i][0]*omega[i][0] + omega[i][1]*omega[i][1] +
+ omega[i][2]*omega[i][2]) * INERTIA*rmass[i]*radius[i]*radius[i];
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
- t += (omega[i][0]*omega[i][0] + omega[i][1]*omega[i][1] +
- omega[i][2]*omega[i][2]) * INERTIA*rmass[i]*radius[i]*radius[i];
+ t += (omega[i][0]*omega[i][0] + omega[i][1]*omega[i][1] +
+ omega[i][2]*omega[i][2]) * INERTIA*rmass[i]*radius[i]*radius[i];
}
if (tempbias) tbias->restore_bias_all();
@@ -269,35 +269,35 @@ void ComputeTempSphere::compute_vector()
if (mode == ALL) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- massone = rmass[i];
- t[0] += massone * v[i][0]*v[i][0];
- t[1] += massone * v[i][1]*v[i][1];
- t[2] += massone * v[i][2]*v[i][2];
- t[3] += massone * v[i][0]*v[i][1];
- t[4] += massone * v[i][0]*v[i][2];
- t[5] += massone * v[i][1]*v[i][2];
-
- inertiaone = INERTIA*rmass[i]*radius[i]*radius[i];
- t[0] += inertiaone * omega[i][0]*omega[i][0];
- t[1] += inertiaone * omega[i][1]*omega[i][1];
- t[2] += inertiaone * omega[i][2]*omega[i][2];
- t[3] += inertiaone * omega[i][0]*omega[i][1];
- t[4] += inertiaone * omega[i][0]*omega[i][2];
- t[5] += inertiaone * omega[i][1]*omega[i][2];
+ massone = rmass[i];
+ t[0] += massone * v[i][0]*v[i][0];
+ t[1] += massone * v[i][1]*v[i][1];
+ t[2] += massone * v[i][2]*v[i][2];
+ t[3] += massone * v[i][0]*v[i][1];
+ t[4] += massone * v[i][0]*v[i][2];
+ t[5] += massone * v[i][1]*v[i][2];
+
+ inertiaone = INERTIA*rmass[i]*radius[i]*radius[i];
+ t[0] += inertiaone * omega[i][0]*omega[i][0];
+ t[1] += inertiaone * omega[i][1]*omega[i][1];
+ t[2] += inertiaone * omega[i][2]*omega[i][2];
+ t[3] += inertiaone * omega[i][0]*omega[i][1];
+ t[4] += inertiaone * omega[i][0]*omega[i][2];
+ t[5] += inertiaone * omega[i][1]*omega[i][2];
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- inertiaone = INERTIA*rmass[i]*radius[i]*radius[i];
- t[0] += inertiaone * omega[i][0]*omega[i][0];
- t[1] += inertiaone * omega[i][1]*omega[i][1];
- t[2] += inertiaone * omega[i][2]*omega[i][2];
- t[3] += inertiaone * omega[i][0]*omega[i][1];
- t[4] += inertiaone * omega[i][0]*omega[i][2];
- t[5] += inertiaone * omega[i][1]*omega[i][2];
+ inertiaone = INERTIA*rmass[i]*radius[i]*radius[i];
+ t[0] += inertiaone * omega[i][0]*omega[i][0];
+ t[1] += inertiaone * omega[i][1]*omega[i][1];
+ t[2] += inertiaone * omega[i][2]*omega[i][2];
+ t[3] += inertiaone * omega[i][0]*omega[i][1];
+ t[4] += inertiaone * omega[i][0]*omega[i][2];
+ t[5] += inertiaone * omega[i][1]*omega[i][2];
}
}
-
+
if (tempbias) tbias->restore_bias_all();
MPI_Allreduce(t,vector,6,MPI_DOUBLE,MPI_SUM,world);
diff --git a/src/compute_temp_sphere.h b/src/compute_temp_sphere.h
index 47241bd29a0d7ea6214a8ec19d46d5e28a5427f4..3b5916f2789f4263454346e8b817a316aa3d9de1 100644
--- a/src/compute_temp_sphere.h
+++ b/src/compute_temp_sphere.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/compute_ti.cpp b/src/compute_ti.cpp
index 035fb35767d47d80a098aaac877f0a85bb54294d..749a169c45d024b8c1f7bc558e27ced0c569d220 100644
--- a/src/compute_ti.cpp
+++ b/src/compute_ti.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -34,9 +34,9 @@ enum{PAIR,TAIL,KSPACE};
/* ---------------------------------------------------------------------- */
-ComputeTI::ComputeTI(LAMMPS *lmp, int narg, char **arg) :
- Compute(lmp, narg, arg)
-{
+ComputeTI::ComputeTI(LAMMPS *lmp, int narg, char **arg) :
+ Compute(lmp, narg, arg)
+{
if (narg < 4) error->all(FLERR,"Illegal compute ti command");
peflag = 1;
@@ -58,7 +58,7 @@ ComputeTI::ComputeTI(LAMMPS *lmp, int narg, char **arg) :
pstyle = new char*[nterms];
for (int m = 0; m < nterms; m++) pstyle[m] = NULL;
-
+
// parse keywords
nterms = 0;
@@ -121,7 +121,7 @@ void ComputeTI::init()
if (ivar1[m] < 0 || ivar2 < 0)
error->all(FLERR,"Variable name for compute ti does not exist");
if (!input->variable->equalstyle(ivar1[m]) ||
- !input->variable->equalstyle(ivar2[m]))
+ !input->variable->equalstyle(ivar2[m]))
error->all(FLERR,"Variable for compute ti is invalid style");
if (which[m] == PAIR) {
@@ -129,13 +129,13 @@ void ComputeTI::init()
if (pptr[m] == NULL) error->all(FLERR,"Compute ti pair style does not exist");
} else if (which[m] == TAIL) {
- if (force->pair == NULL || force->pair->tail_flag == 0)
- error->all(FLERR,"Compute ti tail when pair style does not "
- "compute tail corrections");
+ if (force->pair == NULL || force->pair->tail_flag == 0)
+ error->all(FLERR,"Compute ti tail when pair style does not "
+ "compute tail corrections");
} else if (which[m] == KSPACE) {
- if (force->kspace == NULL)
- error->all(FLERR,"Compute ti kspace style does not exist");
+ if (force->kspace == NULL)
+ error->all(FLERR,"Compute ti kspace style does not exist");
}
}
}
diff --git a/src/compute_ti.h b/src/compute_ti.h
index 56d04ea8bd8905a5eeccdc91f3769e2dc268dc63..79179018aeb7370a328330c56361425c7844ec14 100644
--- a/src/compute_ti.h
+++ b/src/compute_ti.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -23,9 +23,9 @@ ComputeStyle(ti,ComputeTI)
#include "compute.h"
namespace LAMMPS_NS {
-
+
class ComputeTI : public Compute {
- public:
+ public:
ComputeTI(class LAMMPS *, int, char **);
~ComputeTI();
void init();
diff --git a/src/create_atoms.cpp b/src/create_atoms.cpp
index ef1dd7f7a88a4c2a32abd9473ed3fde5c9ff7aa8..9cb7de3344b20f7bbdda3b0b056053ad40aeaf70 100644
--- a/src/create_atoms.cpp
+++ b/src/create_atoms.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -41,17 +41,17 @@ CreateAtoms::CreateAtoms(LAMMPS *lmp) : Pointers(lmp) {}
void CreateAtoms::command(int narg, char **arg)
{
- if (domain->box_exist == 0)
+ if (domain->box_exist == 0)
error->all(FLERR,"Create_atoms command before simulation box is defined");
- if (modify->nfix_restart_peratom)
+ if (modify->nfix_restart_peratom)
error->all(FLERR,"Cannot create_atoms after "
- "reading restart file with per-atom info");
+ "reading restart file with per-atom info");
// parse arguments
if (narg < 2) error->all(FLERR,"Illegal create_atoms command");
itype = atoi(arg[0]);
- if (itype <= 0 || itype > atom->ntypes)
+ if (itype <= 0 || itype > atom->ntypes)
error->all(FLERR,"Invalid atom type in create_atoms command");
int iarg;
@@ -63,7 +63,7 @@ void CreateAtoms::command(int narg, char **arg)
if (narg < 3) error->all(FLERR,"Illegal create_atoms command");
nregion = domain->find_region(arg[2]);
if (nregion == -1) error->all(FLERR,
- "Create_atoms region ID does not exist");
+ "Create_atoms region ID does not exist");
iarg = 3;;
} else if (strcmp(arg[1],"single") == 0) {
style = SINGLE;
@@ -81,7 +81,7 @@ void CreateAtoms::command(int narg, char **arg)
else {
nregion = domain->find_region(arg[4]);
if (nregion == -1) error->all(FLERR,
- "Create_atoms region ID does not exist");
+ "Create_atoms region ID does not exist");
}
iarg = 5;
} else error->all(FLERR,"Illegal create_atoms command");
@@ -101,12 +101,12 @@ void CreateAtoms::command(int narg, char **arg)
if (strcmp(arg[iarg],"basis") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal create_atoms command");
if (domain->lattice == NULL)
- error->all(FLERR,"Cannot create atoms with undefined lattice");
+ error->all(FLERR,"Cannot create atoms with undefined lattice");
int ibasis = atoi(arg[iarg+1]);
itype = atoi(arg[iarg+2]);
- if (ibasis <= 0 || ibasis > nbasis ||
- itype <= 0 || itype > atom->ntypes)
- error->all(FLERR,"Illegal create_atoms command");
+ if (ibasis <= 0 || ibasis > nbasis ||
+ itype <= 0 || itype > atom->ntypes)
+ error->all(FLERR,"Illegal create_atoms command");
basistype[ibasis-1] = itype;
iarg += 3;
} else if (strcmp(arg[iarg],"remap") == 0) {
@@ -209,7 +209,7 @@ void CreateAtoms::command(int narg, char **arg)
Fix *fix = modify->fix[m];
if (fix->create_attribute)
for (int i = nlocal_previous; i < nlocal; i++)
- fix->set_arrays(i);
+ fix->set_arrays(i);
}
// clean up
@@ -228,10 +228,10 @@ void CreateAtoms::command(int narg, char **arg)
if (comm->me == 0) {
if (screen)
fprintf(screen,"Created " BIGINT_FORMAT " atoms\n",
- atom->natoms-natoms_previous);
+ atom->natoms-natoms_previous);
if (logfile)
fprintf(logfile,"Created " BIGINT_FORMAT " atoms\n",
- atom->natoms-natoms_previous);
+ atom->natoms-natoms_previous);
}
// reset simulation now that more atoms are defined
@@ -345,15 +345,15 @@ void CreateAtoms::add_random()
if (domain->dimension == 2) xone[2] = zmid;
valid = 1;
- if (nregion >= 0 &&
- domain->regions[nregion]->match(xone[0],xone[1],xone[2]) == 0)
- valid = 0;
+ if (nregion >= 0 &&
+ domain->regions[nregion]->match(xone[0],xone[1],xone[2]) == 0)
+ valid = 0;
if (triclinic) {
- domain->x2lamda(xone,lamda);
- coord = lamda;
- if (coord[0] < boxlo[0] || coord[0] >= boxhi[0] ||
- coord[1] < boxlo[1] || coord[1] >= boxhi[1] ||
- coord[2] < boxlo[2] || coord[2] >= boxhi[2]) valid = 0;
+ domain->x2lamda(xone,lamda);
+ coord = lamda;
+ if (coord[0] < boxlo[0] || coord[0] >= boxhi[0] ||
+ coord[1] < boxlo[1] || coord[1] >= boxhi[1] ||
+ coord[2] < boxlo[2] || coord[2] >= boxhi[2]) valid = 0;
} else coord = xone;
if (valid) break;
@@ -362,11 +362,11 @@ void CreateAtoms::add_random()
// if triclinic, coord is now in lamda units
if (coord[0] >= sublo[0] && coord[0] < subhi[0] &&
- coord[1] >= sublo[1] && coord[1] < subhi[1] &&
- coord[2] >= sublo[2] && coord[2] < subhi[2])
+ coord[1] >= sublo[1] && coord[1] < subhi[1] &&
+ coord[2] >= sublo[2] && coord[2] < subhi[2])
atom->avec->create_atom(itype,xone);
}
-
+
// clean-up
delete random;
@@ -396,21 +396,21 @@ void CreateAtoms::add_lattice()
xmax = ymax = zmax = -BIG;
domain->lattice->bbox(1,bboxlo[0],bboxlo[1],bboxlo[2],
- xmin,ymin,zmin,xmax,ymax,zmax);
+ xmin,ymin,zmin,xmax,ymax,zmax);
domain->lattice->bbox(1,bboxhi[0],bboxlo[1],bboxlo[2],
- xmin,ymin,zmin,xmax,ymax,zmax);
+ xmin,ymin,zmin,xmax,ymax,zmax);
domain->lattice->bbox(1,bboxlo[0],bboxhi[1],bboxlo[2],
- xmin,ymin,zmin,xmax,ymax,zmax);
+ xmin,ymin,zmin,xmax,ymax,zmax);
domain->lattice->bbox(1,bboxhi[0],bboxhi[1],bboxlo[2],
- xmin,ymin,zmin,xmax,ymax,zmax);
+ xmin,ymin,zmin,xmax,ymax,zmax);
domain->lattice->bbox(1,bboxlo[0],bboxlo[1],bboxhi[2],
- xmin,ymin,zmin,xmax,ymax,zmax);
+ xmin,ymin,zmin,xmax,ymax,zmax);
domain->lattice->bbox(1,bboxhi[0],bboxlo[1],bboxhi[2],
- xmin,ymin,zmin,xmax,ymax,zmax);
+ xmin,ymin,zmin,xmax,ymax,zmax);
domain->lattice->bbox(1,bboxlo[0],bboxhi[1],bboxhi[2],
- xmin,ymin,zmin,xmax,ymax,zmax);
+ xmin,ymin,zmin,xmax,ymax,zmax);
domain->lattice->bbox(1,bboxhi[0],bboxhi[1],bboxhi[2],
- xmin,ymin,zmin,xmax,ymax,zmax);
+ xmin,ymin,zmin,xmax,ymax,zmax);
// ilo:ihi,jlo:jhi,klo:khi = loop bounds for lattice overlap of my subbox
// overlap = any part of a unit cell (face,edge,pt) in common with my subbox
@@ -436,7 +436,7 @@ void CreateAtoms::add_lattice()
// iterate on 3d periodic lattice of unit cells using loop bounds
// iterate on nbasis atoms in each unit cell
// convert lattice coords to box coords
- // add atom if it meets all criteria
+ // add atom if it meets all criteria
double **basis = domain->lattice->basis;
double x[3],lamda[3];
@@ -446,34 +446,34 @@ void CreateAtoms::add_lattice()
for (k = klo; k <= khi; k++)
for (j = jlo; j <= jhi; j++)
for (i = ilo; i <= ihi; i++)
- for (m = 0; m < nbasis; m++) {
+ for (m = 0; m < nbasis; m++) {
- x[0] = i + basis[m][0];
- x[1] = j + basis[m][1];
- x[2] = k + basis[m][2];
+ x[0] = i + basis[m][0];
+ x[1] = j + basis[m][1];
+ x[2] = k + basis[m][2];
- // convert from lattice coords to box coords
+ // convert from lattice coords to box coords
- domain->lattice->lattice2box(x[0],x[1],x[2]);
+ domain->lattice->lattice2box(x[0],x[1],x[2]);
- // if a region was specified, test if atom is in it
+ // if a region was specified, test if atom is in it
- if (style == REGION)
- if (!domain->regions[nregion]->match(x[0],x[1],x[2])) continue;
+ if (style == REGION)
+ if (!domain->regions[nregion]->match(x[0],x[1],x[2])) continue;
- // test if atom is in my subbox
+ // test if atom is in my subbox
- if (triclinic) {
- domain->x2lamda(x,lamda);
- coord = lamda;
- } else coord = x;
+ if (triclinic) {
+ domain->x2lamda(x,lamda);
+ coord = lamda;
+ } else coord = x;
- if (coord[0] < sublo[0] || coord[0] >= subhi[0] ||
- coord[1] < sublo[1] || coord[1] >= subhi[1] ||
- coord[2] < sublo[2] || coord[2] >= subhi[2]) continue;
+ if (coord[0] < sublo[0] || coord[0] >= subhi[0] ||
+ coord[1] < sublo[1] || coord[1] >= subhi[1] ||
+ coord[2] < sublo[2] || coord[2] >= subhi[2]) continue;
- // add the atom to my list of atoms
+ // add the atom to my list of atoms
- atom->avec->create_atom(basistype[m],x);
- }
+ atom->avec->create_atom(basistype[m],x);
+ }
}
diff --git a/src/create_atoms.h b/src/create_atoms.h
index 708abfb3522295829f3912a409440d55b8302b92..f68c0d4993aa7aad6b8400c4c7638d23d1aa4dae 100644
--- a/src/create_atoms.h
+++ b/src/create_atoms.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/create_box.cpp b/src/create_box.cpp
index be437d0729f459014aac3ac960111df71a8d6985..b8d53494199fce40e736806d3bd3e28d53e17236 100644
--- a/src/create_box.cpp
+++ b/src/create_box.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -35,7 +35,7 @@ void CreateBox::command(int narg, char **arg)
{
if (narg != 2) error->all(FLERR,"Illegal create_box command");
- if (domain->box_exist)
+ if (domain->box_exist)
error->all(FLERR,"Cannot create_box after simulation box is defined");
if (domain->dimension == 2 && domain->zperiodic == 0)
error->all(FLERR,"Cannot run 2d simulation with nonperiodic Z dimension");
diff --git a/src/create_box.h b/src/create_box.h
index 974e1db2d294aaf8aa8aee229d8960bf5183da68..39d89536c8509091ab290ee154f3b6ff2520ab31 100644
--- a/src/create_box.h
+++ b/src/create_box.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/delete_atoms.cpp b/src/delete_atoms.cpp
index 48a4fa68944b43ef9ed23b9b1011fa6b3dde9173..dc70d8557c0abe13519f21df846359298bfc23f5 100644
--- a/src/delete_atoms.cpp
+++ b/src/delete_atoms.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -38,7 +38,7 @@ DeleteAtoms::DeleteAtoms(LAMMPS *lmp) : Pointers(lmp) {}
void DeleteAtoms::command(int narg, char **arg)
{
- if (domain->box_exist == 0)
+ if (domain->box_exist == 0)
error->all(FLERR,"Delete_atoms command before simulation box is defined");
if (narg < 1) error->all(FLERR,"Illegal delete_atoms command");
if (atom->tag_enable == 0)
@@ -101,12 +101,12 @@ void DeleteAtoms::command(int narg, char **arg)
bigint ndelete = natoms_previous - atom->natoms;
if (comm->me == 0) {
- if (screen) fprintf(screen,"Deleted " BIGINT_FORMAT
- " atoms, new total = " BIGINT_FORMAT "\n",
- ndelete,atom->natoms);
- if (logfile) fprintf(logfile,"Deleted " BIGINT_FORMAT
- " atoms, new total = " BIGINT_FORMAT "\n",
- ndelete,atom->natoms);
+ if (screen) fprintf(screen,"Deleted " BIGINT_FORMAT
+ " atoms, new total = " BIGINT_FORMAT "\n",
+ ndelete,atom->natoms);
+ if (logfile) fprintf(logfile,"Deleted " BIGINT_FORMAT
+ " atoms, new total = " BIGINT_FORMAT "\n",
+ ndelete,atom->natoms);
}
}
@@ -124,7 +124,7 @@ void DeleteAtoms::delete_group(int narg, char **arg)
options(narg-2,&arg[2]);
// allocate and initialize deletion list
-
+
int nlocal = atom->nlocal;
memory->create(dlist,nlocal,"delete_atoms:dlist");
for (int i = 0; i < nlocal; i++) dlist[i] = 0;
@@ -143,13 +143,13 @@ void DeleteAtoms::delete_group(int narg, char **arg)
void DeleteAtoms::delete_region(int narg, char **arg)
{
if (narg < 2) error->all(FLERR,"Illegal delete_atoms command");
-
+
int iregion = domain->find_region(arg[1]);
if (iregion == -1) error->all(FLERR,"Could not find delete_atoms region ID");
options(narg-2,&arg[2]);
// allocate and initialize deletion list
-
+
int nlocal = atom->nlocal;
memory->create(dlist,nlocal,"delete_atoms:dlist");
for (int i = 0; i < nlocal; i++) dlist[i] = 0;
@@ -170,7 +170,7 @@ void DeleteAtoms::delete_region(int narg, char **arg)
void DeleteAtoms::delete_overlap(int narg, char **arg)
{
if (narg < 4) error->all(FLERR,"Illegal delete_atoms command");
-
+
// read args
double cut = atof(arg[1]);
@@ -199,7 +199,7 @@ void DeleteAtoms::delete_overlap(int narg, char **arg)
// init entire system since comm->borders and neighbor->build is done
// comm::init needs neighbor::init needs pair::init needs kspace::init, etc
-
+
lmp->init();
// error check on cutoff
@@ -207,7 +207,7 @@ void DeleteAtoms::delete_overlap(int narg, char **arg)
if (force->pair == NULL)
error->all(FLERR,"Delete_atoms requires a pair style be defined");
- if (cut > neighbor->cutneighmax)
+ if (cut > neighbor->cutneighmax)
error->all(FLERR,"Delete_atoms cutoff > neighbor cutoff");
// setup domain, communication and neighboring
@@ -228,7 +228,7 @@ void DeleteAtoms::delete_overlap(int narg, char **arg)
// allocate and initialize deletion list
// must be after exchange potentially changes nlocal
-
+
int nlocal = atom->nlocal;
memory->create(dlist,nlocal,"delete_atoms:dlist");
for (int i = 0; i < nlocal; i++) dlist[i] = 0;
@@ -298,9 +298,9 @@ void DeleteAtoms::delete_overlap(int narg, char **arg)
// test on tags of I,J insures that only I or J is deleted
if (j < nlocal) {
- if (dlist[j]) continue;
+ if (dlist[j]) continue;
} else if ((mask[i] & group2bit) && (mask[j] & group1bit)) {
- if (tag[i] > tag[j]) continue;
+ if (tag[i] > tag[j]) continue;
}
dlist[i] = 1;
@@ -310,7 +310,7 @@ void DeleteAtoms::delete_overlap(int narg, char **arg)
}
/* ----------------------------------------------------------------------
- create porosity by deleting atoms in a specified region
+ create porosity by deleting atoms in a specified region
------------------------------------------------------------------------- */
void DeleteAtoms::delete_porosity(int narg, char **arg)
@@ -327,7 +327,7 @@ void DeleteAtoms::delete_porosity(int narg, char **arg)
RanMars *random = new RanMars(lmp,seed + comm->me);
// allocate and initialize deletion list
-
+
int nlocal = atom->nlocal;
memory->create(dlist,nlocal,"delete_atoms:dlist");
for (int i = 0; i < nlocal; i++) dlist[i] = 0;
diff --git a/src/delete_atoms.h b/src/delete_atoms.h
index 365c7507d92dd00f0efcb607a014a9cc526ed1d0..a1d8104e8893206ae0b6911cee38a5c6543465bd 100644
--- a/src/delete_atoms.h
+++ b/src/delete_atoms.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/delete_bonds.cpp b/src/delete_bonds.cpp
index 1910e1203f815d3fe3d61a98bab3cc0d3666aeb0..6699ab7478326781a799600888c2b6e5d80fe81b 100644
--- a/src/delete_bonds.cpp
+++ b/src/delete_bonds.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -37,7 +37,7 @@ DeleteBonds::DeleteBonds(LAMMPS *lmp) : Pointers(lmp) {}
void DeleteBonds::command(int narg, char **arg)
{
- if (domain->box_exist == 0)
+ if (domain->box_exist == 0)
error->all(FLERR,"Delete_bonds command before simulation box is defined");
if (atom->natoms == 0)
error->all(FLERR,"Delete_bonds command with no atoms existing");
@@ -59,7 +59,7 @@ void DeleteBonds::command(int narg, char **arg)
int igroup = group->find(arg[0]);
if (igroup == -1) error->all(FLERR,"Cannot find delete_bonds group ID");
int groupbit = group->bitmask[igroup];
-
+
// set style and which = type value
int style;
@@ -131,26 +131,26 @@ void DeleteBonds::command(int narg, char **arg)
for (i = 0; i < nlocal; i++) {
for (m = 0; m < num_bond[i]; m++) {
- atom1 = atom->map(atom->bond_atom[i][m]);
- if (atom1 == -1) error->one(FLERR,"Bond atom missing in delete_bonds");
- consider = 0;
- if (!any_flag && mask[i] & groupbit && mask[atom1] & groupbit)
- consider = 1;
- if (any_flag && (mask[i] & groupbit || mask[atom1] & groupbit))
- consider = 1;
- if (consider) {
- flag = 0;
- if (style == MULTI) flag = 1;
- if (style == ATOM &&
- (type[i] == which || type[atom1] == which)) flag = 1;
- if (style == BOND && (bond_type[i][m] == which)) flag = 1;
- if (flag) {
- if (undo_flag == 0 && bond_type[i][m] > 0)
- bond_type[i][m] = -bond_type[i][m];
- if (undo_flag == 1 && bond_type[i][m] < 0)
- bond_type[i][m] = -bond_type[i][m];
- }
- }
+ atom1 = atom->map(atom->bond_atom[i][m]);
+ if (atom1 == -1) error->one(FLERR,"Bond atom missing in delete_bonds");
+ consider = 0;
+ if (!any_flag && mask[i] & groupbit && mask[atom1] & groupbit)
+ consider = 1;
+ if (any_flag && (mask[i] & groupbit || mask[atom1] & groupbit))
+ consider = 1;
+ if (consider) {
+ flag = 0;
+ if (style == MULTI) flag = 1;
+ if (style == ATOM &&
+ (type[i] == which || type[atom1] == which)) flag = 1;
+ if (style == BOND && (bond_type[i][m] == which)) flag = 1;
+ if (flag) {
+ if (undo_flag == 0 && bond_type[i][m] > 0)
+ bond_type[i][m] = -bond_type[i][m];
+ if (undo_flag == 1 && bond_type[i][m] < 0)
+ bond_type[i][m] = -bond_type[i][m];
+ }
+ }
}
}
}
@@ -161,30 +161,30 @@ void DeleteBonds::command(int narg, char **arg)
for (i = 0; i < nlocal; i++) {
for (m = 0; m < num_angle[i]; m++) {
- atom1 = atom->map(atom->angle_atom1[i][m]);
- atom2 = atom->map(atom->angle_atom2[i][m]);
- atom3 = atom->map(atom->angle_atom3[i][m]);
- if (atom1 == -1 || atom2 == -1 || atom3 == -1)
- error->one(FLERR,"Angle atom missing in delete_bonds");
- consider = 0;
- if (!any_flag && mask[atom1] & groupbit && mask[atom2] & groupbit &&
- mask[atom3] & groupbit) consider = 1;
- if (any_flag && (mask[atom1] & groupbit || mask[atom2] & groupbit ||
- mask[atom3] & groupbit)) consider = 1;
- if (consider) {
- flag = 0;
- if (style == MULTI) flag = 1;
- if (style == ATOM &&
- (type[atom1] == which || type[atom2] == which ||
- type[atom3] == which)) flag = 1;
- if (style == ANGLE && (angle_type[i][m] == which)) flag = 1;
- if (flag) {
- if (undo_flag == 0 && angle_type[i][m] > 0)
- angle_type[i][m] = -angle_type[i][m];
- if (undo_flag == 1 && angle_type[i][m] < 0)
- angle_type[i][m] = -angle_type[i][m];
- }
- }
+ atom1 = atom->map(atom->angle_atom1[i][m]);
+ atom2 = atom->map(atom->angle_atom2[i][m]);
+ atom3 = atom->map(atom->angle_atom3[i][m]);
+ if (atom1 == -1 || atom2 == -1 || atom3 == -1)
+ error->one(FLERR,"Angle atom missing in delete_bonds");
+ consider = 0;
+ if (!any_flag && mask[atom1] & groupbit && mask[atom2] & groupbit &&
+ mask[atom3] & groupbit) consider = 1;
+ if (any_flag && (mask[atom1] & groupbit || mask[atom2] & groupbit ||
+ mask[atom3] & groupbit)) consider = 1;
+ if (consider) {
+ flag = 0;
+ if (style == MULTI) flag = 1;
+ if (style == ATOM &&
+ (type[atom1] == which || type[atom2] == which ||
+ type[atom3] == which)) flag = 1;
+ if (style == ANGLE && (angle_type[i][m] == which)) flag = 1;
+ if (flag) {
+ if (undo_flag == 0 && angle_type[i][m] > 0)
+ angle_type[i][m] = -angle_type[i][m];
+ if (undo_flag == 1 && angle_type[i][m] < 0)
+ angle_type[i][m] = -angle_type[i][m];
+ }
+ }
}
}
}
@@ -195,32 +195,32 @@ void DeleteBonds::command(int narg, char **arg)
for (i = 0; i < nlocal; i++) {
for (m = 0; m < num_dihedral[i]; m++) {
- atom1 = atom->map(atom->dihedral_atom1[i][m]);
- atom2 = atom->map(atom->dihedral_atom2[i][m]);
- atom3 = atom->map(atom->dihedral_atom3[i][m]);
- atom4 = atom->map(atom->dihedral_atom4[i][m]);
- if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1)
- error->one(FLERR,"Dihedral atom missing in delete_bonds");
- consider = 0;
- if (!any_flag && mask[atom1] & groupbit && mask[atom2] & groupbit &&
- mask[atom3] & groupbit && mask[atom4] & groupbit) consider = 1;
- if (any_flag && (mask[atom1] & groupbit || mask[atom2] & groupbit ||
- mask[atom3] & groupbit || mask[atom4] & groupbit))
- consider = 1;
- if (consider) {
- flag = 0;
- if (style == MULTI) flag = 1;
- if (style == ATOM &&
- (type[atom1] == which || type[atom2] == which ||
- type[atom3] == which || type[atom4] == which)) flag = 1;
- if (style == DIHEDRAL && (dihedral_type[i][m] == which)) flag = 1;
- if (flag) {
- if (undo_flag == 0 && dihedral_type[i][m] > 0)
- dihedral_type[i][m] = -dihedral_type[i][m];
- if (undo_flag == 1 && dihedral_type[i][m] < 0)
- dihedral_type[i][m] = -dihedral_type[i][m];
- }
- }
+ atom1 = atom->map(atom->dihedral_atom1[i][m]);
+ atom2 = atom->map(atom->dihedral_atom2[i][m]);
+ atom3 = atom->map(atom->dihedral_atom3[i][m]);
+ atom4 = atom->map(atom->dihedral_atom4[i][m]);
+ if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1)
+ error->one(FLERR,"Dihedral atom missing in delete_bonds");
+ consider = 0;
+ if (!any_flag && mask[atom1] & groupbit && mask[atom2] & groupbit &&
+ mask[atom3] & groupbit && mask[atom4] & groupbit) consider = 1;
+ if (any_flag && (mask[atom1] & groupbit || mask[atom2] & groupbit ||
+ mask[atom3] & groupbit || mask[atom4] & groupbit))
+ consider = 1;
+ if (consider) {
+ flag = 0;
+ if (style == MULTI) flag = 1;
+ if (style == ATOM &&
+ (type[atom1] == which || type[atom2] == which ||
+ type[atom3] == which || type[atom4] == which)) flag = 1;
+ if (style == DIHEDRAL && (dihedral_type[i][m] == which)) flag = 1;
+ if (flag) {
+ if (undo_flag == 0 && dihedral_type[i][m] > 0)
+ dihedral_type[i][m] = -dihedral_type[i][m];
+ if (undo_flag == 1 && dihedral_type[i][m] < 0)
+ dihedral_type[i][m] = -dihedral_type[i][m];
+ }
+ }
}
}
}
@@ -231,32 +231,32 @@ void DeleteBonds::command(int narg, char **arg)
for (i = 0; i < nlocal; i++) {
for (m = 0; m < num_improper[i]; m++) {
- atom1 = atom->map(atom->improper_atom1[i][m]);
- atom2 = atom->map(atom->improper_atom2[i][m]);
- atom3 = atom->map(atom->improper_atom3[i][m]);
- atom4 = atom->map(atom->improper_atom4[i][m]);
- if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1)
- error->one(FLERR,"Improper atom missing in delete_bonds");
- consider = 0;
- if (!any_flag && mask[atom1] & groupbit && mask[atom2] & groupbit &&
- mask[atom3] & groupbit && mask[atom4] & groupbit) consider = 1;
- if (any_flag && (mask[atom1] & groupbit || mask[atom2] & groupbit ||
- mask[atom3] & groupbit || mask[atom4] & groupbit))
- consider = 1;
- if (consider) {
- flag = 0;
- if (style == MULTI) flag = 1;
- if (style == ATOM &&
- (type[atom1] == which || type[atom2] == which ||
- type[atom3] == which || type[atom4] == which)) flag = 1;
- if (style == IMPROPER && (improper_type[i][m] == which)) flag = 1;
- if (flag) {
- if (undo_flag == 0 && improper_type[i][m] > 0)
- improper_type[i][m] = -improper_type[i][m];
- if (undo_flag == 1 && improper_type[i][m] < 0)
- improper_type[i][m] = -improper_type[i][m];
- }
- }
+ atom1 = atom->map(atom->improper_atom1[i][m]);
+ atom2 = atom->map(atom->improper_atom2[i][m]);
+ atom3 = atom->map(atom->improper_atom3[i][m]);
+ atom4 = atom->map(atom->improper_atom4[i][m]);
+ if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1)
+ error->one(FLERR,"Improper atom missing in delete_bonds");
+ consider = 0;
+ if (!any_flag && mask[atom1] & groupbit && mask[atom2] & groupbit &&
+ mask[atom3] & groupbit && mask[atom4] & groupbit) consider = 1;
+ if (any_flag && (mask[atom1] & groupbit || mask[atom2] & groupbit ||
+ mask[atom3] & groupbit || mask[atom4] & groupbit))
+ consider = 1;
+ if (consider) {
+ flag = 0;
+ if (style == MULTI) flag = 1;
+ if (style == ATOM &&
+ (type[atom1] == which || type[atom2] == which ||
+ type[atom3] == which || type[atom4] == which)) flag = 1;
+ if (style == IMPROPER && (improper_type[i][m] == which)) flag = 1;
+ if (flag) {
+ if (undo_flag == 0 && improper_type[i][m] > 0)
+ improper_type[i][m] = -improper_type[i][m];
+ if (undo_flag == 1 && improper_type[i][m] < 0)
+ improper_type[i][m] = -improper_type[i][m];
+ }
+ }
}
}
}
@@ -268,88 +268,88 @@ void DeleteBonds::command(int narg, char **arg)
if (atom->avec->bonds_allow) {
for (i = 0; i < nlocal; i++) {
- m = 0;
- while (m < atom->num_bond[i]) {
- if (atom->bond_type[i][m] <= 0) {
- atom1 = atom->map(atom->bond_atom[i][m]);
- if (mask[i] & groupbit && mask[atom1] & groupbit) {
- n = atom->num_bond[i];
- atom->bond_type[i][m] = atom->bond_type[i][n-1];
- atom->bond_atom[i][m] = atom->bond_atom[i][n-1];
- atom->num_bond[i]--;
- } else m++;
- } else m++;
- }
+ m = 0;
+ while (m < atom->num_bond[i]) {
+ if (atom->bond_type[i][m] <= 0) {
+ atom1 = atom->map(atom->bond_atom[i][m]);
+ if (mask[i] & groupbit && mask[atom1] & groupbit) {
+ n = atom->num_bond[i];
+ atom->bond_type[i][m] = atom->bond_type[i][n-1];
+ atom->bond_atom[i][m] = atom->bond_atom[i][n-1];
+ atom->num_bond[i]--;
+ } else m++;
+ } else m++;
+ }
}
}
if (atom->avec->angles_allow) {
for (i = 0; i < nlocal; i++) {
- m = 0;
- while (m < atom->num_angle[i]) {
- if (atom->angle_type[i][m] <= 0) {
- atom1 = atom->map(atom->angle_atom1[i][m]);
- atom2 = atom->map(atom->angle_atom2[i][m]);
- atom3 = atom->map(atom->angle_atom3[i][m]);
- if (mask[atom1] & groupbit && mask[atom2] & groupbit &&
- mask[atom3] & groupbit) {
- n = atom->num_angle[i];
- atom->angle_type[i][m] = atom->angle_type[i][n-1];
- atom->angle_atom1[i][m] = atom->angle_atom1[i][n-1];
- atom->angle_atom2[i][m] = atom->angle_atom2[i][n-1];
- atom->angle_atom3[i][m] = atom->angle_atom3[i][n-1];
- atom->num_angle[i]--;
- } else m++;
- } else m++;
- }
+ m = 0;
+ while (m < atom->num_angle[i]) {
+ if (atom->angle_type[i][m] <= 0) {
+ atom1 = atom->map(atom->angle_atom1[i][m]);
+ atom2 = atom->map(atom->angle_atom2[i][m]);
+ atom3 = atom->map(atom->angle_atom3[i][m]);
+ if (mask[atom1] & groupbit && mask[atom2] & groupbit &&
+ mask[atom3] & groupbit) {
+ n = atom->num_angle[i];
+ atom->angle_type[i][m] = atom->angle_type[i][n-1];
+ atom->angle_atom1[i][m] = atom->angle_atom1[i][n-1];
+ atom->angle_atom2[i][m] = atom->angle_atom2[i][n-1];
+ atom->angle_atom3[i][m] = atom->angle_atom3[i][n-1];
+ atom->num_angle[i]--;
+ } else m++;
+ } else m++;
+ }
}
}
if (atom->avec->dihedrals_allow) {
for (i = 0; i < nlocal; i++) {
- m = 0;
- while (m < atom->num_dihedral[i]) {
- if (atom->dihedral_type[i][m] <= 0) {
- atom1 = atom->map(atom->dihedral_atom1[i][m]);
- atom2 = atom->map(atom->dihedral_atom2[i][m]);
- atom3 = atom->map(atom->dihedral_atom3[i][m]);
- atom4 = atom->map(atom->dihedral_atom4[i][m]);
- if (mask[atom1] & groupbit && mask[atom2] & groupbit &&
- mask[atom3] & groupbit && mask[atom4] & groupbit) {
- n = atom->num_dihedral[i];
- atom->dihedral_type[i][m] = atom->dihedral_type[i][n-1];
- atom->dihedral_atom1[i][m] = atom->dihedral_atom1[i][n-1];
- atom->dihedral_atom2[i][m] = atom->dihedral_atom2[i][n-1];
- atom->dihedral_atom3[i][m] = atom->dihedral_atom3[i][n-1];
- atom->dihedral_atom4[i][m] = atom->dihedral_atom4[i][n-1];
- atom->num_dihedral[i]--;
- } else m++;
- } else m++;
- }
+ m = 0;
+ while (m < atom->num_dihedral[i]) {
+ if (atom->dihedral_type[i][m] <= 0) {
+ atom1 = atom->map(atom->dihedral_atom1[i][m]);
+ atom2 = atom->map(atom->dihedral_atom2[i][m]);
+ atom3 = atom->map(atom->dihedral_atom3[i][m]);
+ atom4 = atom->map(atom->dihedral_atom4[i][m]);
+ if (mask[atom1] & groupbit && mask[atom2] & groupbit &&
+ mask[atom3] & groupbit && mask[atom4] & groupbit) {
+ n = atom->num_dihedral[i];
+ atom->dihedral_type[i][m] = atom->dihedral_type[i][n-1];
+ atom->dihedral_atom1[i][m] = atom->dihedral_atom1[i][n-1];
+ atom->dihedral_atom2[i][m] = atom->dihedral_atom2[i][n-1];
+ atom->dihedral_atom3[i][m] = atom->dihedral_atom3[i][n-1];
+ atom->dihedral_atom4[i][m] = atom->dihedral_atom4[i][n-1];
+ atom->num_dihedral[i]--;
+ } else m++;
+ } else m++;
+ }
}
}
if (atom->avec->impropers_allow) {
for (i = 0; i < nlocal; i++) {
- m = 0;
- while (m < atom->num_improper[i]) {
- if (atom->improper_type[i][m] <= 0) {
- atom1 = atom->map(atom->improper_atom1[i][m]);
- atom2 = atom->map(atom->improper_atom2[i][m]);
- atom3 = atom->map(atom->improper_atom3[i][m]);
- atom4 = atom->map(atom->improper_atom4[i][m]);
- if (mask[atom1] & groupbit && mask[atom2] & groupbit &&
- mask[atom3] & groupbit && mask[atom4] & groupbit) {
- n = atom->num_improper[i];
- atom->improper_type[i][m] = atom->improper_type[i][n-1];
- atom->improper_atom1[i][m] = atom->improper_atom1[i][n-1];
- atom->improper_atom2[i][m] = atom->improper_atom2[i][n-1];
- atom->improper_atom3[i][m] = atom->improper_atom3[i][n-1];
- atom->improper_atom4[i][m] = atom->improper_atom4[i][n-1];
- atom->num_improper[i]--;
- } else m++;
- } else m++;
- }
+ m = 0;
+ while (m < atom->num_improper[i]) {
+ if (atom->improper_type[i][m] <= 0) {
+ atom1 = atom->map(atom->improper_atom1[i][m]);
+ atom2 = atom->map(atom->improper_atom2[i][m]);
+ atom3 = atom->map(atom->improper_atom3[i][m]);
+ atom4 = atom->map(atom->improper_atom4[i][m]);
+ if (mask[atom1] & groupbit && mask[atom2] & groupbit &&
+ mask[atom3] & groupbit && mask[atom4] & groupbit) {
+ n = atom->num_improper[i];
+ atom->improper_type[i][m] = atom->improper_type[i][n-1];
+ atom->improper_atom1[i][m] = atom->improper_atom1[i][n-1];
+ atom->improper_atom2[i][m] = atom->improper_atom2[i][n-1];
+ atom->improper_atom3[i][m] = atom->improper_atom3[i][n-1];
+ atom->improper_atom4[i][m] = atom->improper_atom4[i][n-1];
+ atom->num_improper[i]--;
+ } else m++;
+ } else m++;
+ }
}
}
@@ -363,7 +363,7 @@ void DeleteBonds::command(int narg, char **arg)
bigint nbonds = 0;
for (i = 0; i < nlocal; i++) nbonds += atom->num_bond[i];
MPI_Allreduce(&nbonds,&atom->nbonds,1,MPI_LMP_BIGINT,
- MPI_SUM,world);
+ MPI_SUM,world);
if (force->newton_bond == 0) atom->nbonds /= 2;
}
@@ -371,7 +371,7 @@ void DeleteBonds::command(int narg, char **arg)
bigint nangles = 0;
for (i = 0; i < nlocal; i++) nangles += atom->num_angle[i];
MPI_Allreduce(&nangles,&atom->nangles,1,MPI_LMP_BIGINT,
- MPI_SUM,world);
+ MPI_SUM,world);
if (force->newton_bond == 0) atom->nangles /= 3;
}
@@ -379,7 +379,7 @@ void DeleteBonds::command(int narg, char **arg)
bigint ndihedrals = 0;
for (i = 0; i < nlocal; i++) ndihedrals += atom->num_dihedral[i];
MPI_Allreduce(&ndihedrals,&atom->ndihedrals,
- 1,MPI_LMP_BIGINT,MPI_SUM,world);
+ 1,MPI_LMP_BIGINT,MPI_SUM,world);
if (force->newton_bond == 0) atom->ndihedrals /= 4;
}
@@ -387,7 +387,7 @@ void DeleteBonds::command(int narg, char **arg)
bigint nimpropers = 0;
for (i = 0; i < nlocal; i++) nimpropers += atom->num_improper[i];
MPI_Allreduce(&nimpropers,&atom->nimpropers,
- 1,MPI_LMP_BIGINT,MPI_SUM,world);
+ 1,MPI_LMP_BIGINT,MPI_SUM,world);
if (force->newton_bond == 0) atom->nimpropers /= 4;
}
@@ -405,8 +405,8 @@ void DeleteBonds::command(int narg, char **arg)
bond_on = bond_off = 0;
for (i = 0; i < nlocal; i++)
for (m = 0; m < atom->num_bond[i]; m++)
- if (atom->bond_type[i][m] > 0) bond_on++;
- else bond_off++;
+ if (atom->bond_type[i][m] > 0) bond_on++;
+ else bond_off++;
MPI_Allreduce(&bond_on,&tmp,1,MPI_LMP_BIGINT,MPI_SUM,world);
bond_on = tmp;
MPI_Allreduce(&bond_off,&tmp,1,MPI_LMP_BIGINT,MPI_SUM,world);
@@ -421,8 +421,8 @@ void DeleteBonds::command(int narg, char **arg)
angle_on = angle_off = 0;
for (i = 0; i < nlocal; i++)
for (m = 0; m < atom->num_angle[i]; m++)
- if (atom->angle_type[i][m] > 0) angle_on++;
- else angle_off++;
+ if (atom->angle_type[i][m] > 0) angle_on++;
+ else angle_off++;
MPI_Allreduce(&angle_on,&tmp,1,MPI_LMP_BIGINT,MPI_SUM,world);
angle_on = tmp;
MPI_Allreduce(&angle_off,&tmp,1,MPI_LMP_BIGINT,MPI_SUM,world);
@@ -437,8 +437,8 @@ void DeleteBonds::command(int narg, char **arg)
dihedral_on = dihedral_off = 0;
for (i = 0; i < nlocal; i++)
for (m = 0; m < atom->num_dihedral[i]; m++)
- if (atom->dihedral_type[i][m] > 0) dihedral_on++;
- else dihedral_off++;
+ if (atom->dihedral_type[i][m] > 0) dihedral_on++;
+ else dihedral_off++;
MPI_Allreduce(&dihedral_on,&tmp,1,MPI_LMP_BIGINT,MPI_SUM,world);
dihedral_on = tmp;
MPI_Allreduce(&dihedral_off,&tmp,1,MPI_LMP_BIGINT,MPI_SUM,world);
@@ -453,8 +453,8 @@ void DeleteBonds::command(int narg, char **arg)
improper_on = improper_off = 0;
for (i = 0; i < nlocal; i++)
for (m = 0; m < atom->num_improper[i]; m++)
- if (atom->improper_type[i][m] > 0) improper_on++;
- else improper_off++;
+ if (atom->improper_type[i][m] > 0) improper_on++;
+ else improper_off++;
MPI_Allreduce(&improper_on,&tmp,1,MPI_LMP_BIGINT,MPI_SUM,world);
improper_on = tmp;
MPI_Allreduce(&improper_off,&tmp,1,MPI_LMP_BIGINT,MPI_SUM,world);
@@ -468,47 +468,47 @@ void DeleteBonds::command(int narg, char **arg)
if (comm->me == 0) {
if (atom->avec->bonds_allow) {
if (screen) fprintf(screen,
- " " BIGINT_FORMAT " total bonds, " BIGINT_FORMAT
- " turned on, " BIGINT_FORMAT " turned off\n",
- atom->nbonds,bond_on,bond_off);
+ " " BIGINT_FORMAT " total bonds, " BIGINT_FORMAT
+ " turned on, " BIGINT_FORMAT " turned off\n",
+ atom->nbonds,bond_on,bond_off);
if (logfile) fprintf(logfile,
- " " BIGINT_FORMAT " total bonds, " BIGINT_FORMAT
- " turned on, " BIGINT_FORMAT " turned off\n",
- atom->nbonds,bond_on,bond_off);
+ " " BIGINT_FORMAT " total bonds, " BIGINT_FORMAT
+ " turned on, " BIGINT_FORMAT " turned off\n",
+ atom->nbonds,bond_on,bond_off);
}
if (atom->avec->angles_allow) {
if (screen) fprintf(screen,
- " " BIGINT_FORMAT " total angles, " BIGINT_FORMAT
- " turned on, " BIGINT_FORMAT " turned off\n",
- atom->nangles,angle_on,angle_off);
+ " " BIGINT_FORMAT " total angles, " BIGINT_FORMAT
+ " turned on, " BIGINT_FORMAT " turned off\n",
+ atom->nangles,angle_on,angle_off);
if (logfile) fprintf(logfile,
- " " BIGINT_FORMAT " total angles, " BIGINT_FORMAT
- " turned on, " BIGINT_FORMAT " turned off\n",
- atom->nangles,angle_on,angle_off);
+ " " BIGINT_FORMAT " total angles, " BIGINT_FORMAT
+ " turned on, " BIGINT_FORMAT " turned off\n",
+ atom->nangles,angle_on,angle_off);
}
if (atom->avec->dihedrals_allow) {
if (screen) fprintf(screen,
- " " BIGINT_FORMAT " total dihedrals, "
- BIGINT_FORMAT " turned on, " BIGINT_FORMAT
- " turned off\n",
- atom->ndihedrals,dihedral_on,dihedral_off);
+ " " BIGINT_FORMAT " total dihedrals, "
+ BIGINT_FORMAT " turned on, " BIGINT_FORMAT
+ " turned off\n",
+ atom->ndihedrals,dihedral_on,dihedral_off);
if (logfile) fprintf(logfile,
- " " BIGINT_FORMAT " total dihedrals, "
- BIGINT_FORMAT " turned on, " BIGINT_FORMAT
- " turned off\n",
- atom->ndihedrals,dihedral_on,dihedral_off);
+ " " BIGINT_FORMAT " total dihedrals, "
+ BIGINT_FORMAT " turned on, " BIGINT_FORMAT
+ " turned off\n",
+ atom->ndihedrals,dihedral_on,dihedral_off);
}
if (atom->avec->impropers_allow) {
if (screen) fprintf(screen,
- " " BIGINT_FORMAT " total impropers, "
- BIGINT_FORMAT " turned on, " BIGINT_FORMAT
- " turned off\n",
- atom->nimpropers,improper_on,improper_off);
+ " " BIGINT_FORMAT " total impropers, "
+ BIGINT_FORMAT " turned on, " BIGINT_FORMAT
+ " turned off\n",
+ atom->nimpropers,improper_on,improper_off);
if (logfile) fprintf(logfile,
- " " BIGINT_FORMAT " total impropers, "
- BIGINT_FORMAT " turned on, " BIGINT_FORMAT
- " turned off\n",
- atom->nimpropers,improper_on,improper_off);
+ " " BIGINT_FORMAT " total impropers, "
+ BIGINT_FORMAT " turned on, " BIGINT_FORMAT
+ " turned off\n",
+ atom->nimpropers,improper_on,improper_off);
}
}
diff --git a/src/delete_bonds.h b/src/delete_bonds.h
index 39ce872e7f3ab01caf34a372c30c188eb606f119..50260c59a7213ee6252a5bdb9e695546f1f5b6ae 100644
--- a/src/delete_bonds.h
+++ b/src/delete_bonds.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/dihedral.cpp b/src/dihedral.cpp
index 80a029b94c9efb0075012e4203943ca325a97024..2e2ae9cc616569acfb773dda54ca2802b504253c 100644
--- a/src/dihedral.cpp
+++ b/src/dihedral.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -77,7 +77,7 @@ void Dihedral::ev_setup(int eflag, int vflag)
vflag_either = vflag;
vflag_global = vflag % 4;
vflag_atom = vflag / 4;
-
+
// reallocate per-atom arrays if necessary
if (eflag_atom && atom->nmax > maxeatom) {
@@ -118,15 +118,15 @@ void Dihedral::ev_setup(int eflag, int vflag)
tally energy and virial into global and per-atom accumulators
virial = r1F1 + r2F2 + r3F3 + r4F4 = (r1-r2) F1 + (r3-r2) F3 + (r4-r2) F4
= (r1-r2) F1 + (r3-r2) F3 + (r4-r3 + r3-r2) F4
- = vb1*f1 + vb2*f3 + (vb3+vb2)*f4
+ = vb1*f1 + vb2*f3 + (vb3+vb2)*f4
------------------------------------------------------------------------- */
void Dihedral::ev_tally(int i1, int i2, int i3, int i4,
- int nlocal, int newton_bond,
- double edihedral, double *f1, double *f3, double *f4,
- double vb1x, double vb1y, double vb1z,
- double vb2x, double vb2y, double vb2z,
- double vb3x, double vb3y, double vb3z)
+ int nlocal, int newton_bond,
+ double edihedral, double *f1, double *f3, double *f4,
+ double vb1x, double vb1y, double vb1z,
+ double vb2x, double vb2y, double vb2z,
+ double vb3x, double vb3y, double vb3z)
{
double edihedralquarter,v[6];
@@ -134,11 +134,11 @@ void Dihedral::ev_tally(int i1, int i2, int i3, int i4,
if (eflag_global) {
if (newton_bond) energy += edihedral;
else {
- edihedralquarter = 0.25*edihedral;
- if (i1 < nlocal) energy += edihedralquarter;
- if (i2 < nlocal) energy += edihedralquarter;
- if (i3 < nlocal) energy += edihedralquarter;
- if (i4 < nlocal) energy += edihedralquarter;
+ edihedralquarter = 0.25*edihedral;
+ if (i1 < nlocal) energy += edihedralquarter;
+ if (i2 < nlocal) energy += edihedralquarter;
+ if (i3 < nlocal) energy += edihedralquarter;
+ if (i4 < nlocal) energy += edihedralquarter;
}
}
if (eflag_atom) {
@@ -160,80 +160,80 @@ void Dihedral::ev_tally(int i1, int i2, int i3, int i4,
if (vflag_global) {
if (newton_bond) {
- virial[0] += v[0];
- virial[1] += v[1];
- virial[2] += v[2];
- virial[3] += v[3];
- virial[4] += v[4];
- virial[5] += v[5];
+ virial[0] += v[0];
+ virial[1] += v[1];
+ virial[2] += v[2];
+ virial[3] += v[3];
+ virial[4] += v[4];
+ virial[5] += v[5];
} else {
- if (i1 < nlocal) {
- virial[0] += 0.25*v[0];
- virial[1] += 0.25*v[1];
- virial[2] += 0.25*v[2];
- virial[3] += 0.25*v[3];
- virial[4] += 0.25*v[4];
- virial[5] += 0.25*v[5];
- }
- if (i2 < nlocal) {
- virial[0] += 0.25*v[0];
- virial[1] += 0.25*v[1];
- virial[2] += 0.25*v[2];
- virial[3] += 0.25*v[3];
- virial[4] += 0.25*v[4];
- virial[5] += 0.25*v[5];
- }
- if (i3 < nlocal) {
- virial[0] += 0.25*v[0];
- virial[1] += 0.25*v[1];
- virial[2] += 0.25*v[2];
- virial[3] += 0.25*v[3];
- virial[4] += 0.25*v[4];
- virial[5] += 0.25*v[5];
- }
- if (i4 < nlocal) {
- virial[0] += 0.25*v[0];
- virial[1] += 0.25*v[1];
- virial[2] += 0.25*v[2];
- virial[3] += 0.25*v[3];
- virial[4] += 0.25*v[4];
- virial[5] += 0.25*v[5];
- }
+ if (i1 < nlocal) {
+ virial[0] += 0.25*v[0];
+ virial[1] += 0.25*v[1];
+ virial[2] += 0.25*v[2];
+ virial[3] += 0.25*v[3];
+ virial[4] += 0.25*v[4];
+ virial[5] += 0.25*v[5];
+ }
+ if (i2 < nlocal) {
+ virial[0] += 0.25*v[0];
+ virial[1] += 0.25*v[1];
+ virial[2] += 0.25*v[2];
+ virial[3] += 0.25*v[3];
+ virial[4] += 0.25*v[4];
+ virial[5] += 0.25*v[5];
+ }
+ if (i3 < nlocal) {
+ virial[0] += 0.25*v[0];
+ virial[1] += 0.25*v[1];
+ virial[2] += 0.25*v[2];
+ virial[3] += 0.25*v[3];
+ virial[4] += 0.25*v[4];
+ virial[5] += 0.25*v[5];
+ }
+ if (i4 < nlocal) {
+ virial[0] += 0.25*v[0];
+ virial[1] += 0.25*v[1];
+ virial[2] += 0.25*v[2];
+ virial[3] += 0.25*v[3];
+ virial[4] += 0.25*v[4];
+ virial[5] += 0.25*v[5];
+ }
}
}
if (vflag_atom) {
if (newton_bond || i1 < nlocal) {
- vatom[i1][0] += 0.25*v[0];
- vatom[i1][1] += 0.25*v[1];
- vatom[i1][2] += 0.25*v[2];
- vatom[i1][3] += 0.25*v[3];
- vatom[i1][4] += 0.25*v[4];
- vatom[i1][5] += 0.25*v[5];
+ vatom[i1][0] += 0.25*v[0];
+ vatom[i1][1] += 0.25*v[1];
+ vatom[i1][2] += 0.25*v[2];
+ vatom[i1][3] += 0.25*v[3];
+ vatom[i1][4] += 0.25*v[4];
+ vatom[i1][5] += 0.25*v[5];
}
if (newton_bond || i2 < nlocal) {
- vatom[i2][0] += 0.25*v[0];
- vatom[i2][1] += 0.25*v[1];
- vatom[i2][2] += 0.25*v[2];
- vatom[i2][3] += 0.25*v[3];
- vatom[i2][4] += 0.25*v[4];
- vatom[i2][5] += 0.25*v[5];
+ vatom[i2][0] += 0.25*v[0];
+ vatom[i2][1] += 0.25*v[1];
+ vatom[i2][2] += 0.25*v[2];
+ vatom[i2][3] += 0.25*v[3];
+ vatom[i2][4] += 0.25*v[4];
+ vatom[i2][5] += 0.25*v[5];
}
if (newton_bond || i3 < nlocal) {
- vatom[i3][0] += 0.25*v[0];
- vatom[i3][1] += 0.25*v[1];
- vatom[i3][2] += 0.25*v[2];
- vatom[i3][3] += 0.25*v[3];
- vatom[i3][4] += 0.25*v[4];
- vatom[i3][5] += 0.25*v[5];
+ vatom[i3][0] += 0.25*v[0];
+ vatom[i3][1] += 0.25*v[1];
+ vatom[i3][2] += 0.25*v[2];
+ vatom[i3][3] += 0.25*v[3];
+ vatom[i3][4] += 0.25*v[4];
+ vatom[i3][5] += 0.25*v[5];
}
if (newton_bond || i4 < nlocal) {
- vatom[i4][0] += 0.25*v[0];
- vatom[i4][1] += 0.25*v[1];
- vatom[i4][2] += 0.25*v[2];
- vatom[i4][3] += 0.25*v[3];
- vatom[i4][4] += 0.25*v[4];
- vatom[i4][5] += 0.25*v[5];
+ vatom[i4][0] += 0.25*v[0];
+ vatom[i4][1] += 0.25*v[1];
+ vatom[i4][2] += 0.25*v[2];
+ vatom[i4][3] += 0.25*v[3];
+ vatom[i4][4] += 0.25*v[4];
+ vatom[i4][5] += 0.25*v[5];
}
}
}
diff --git a/src/dihedral.h b/src/dihedral.h
index 0abb3afeba48fd447ee459b62930367f765af5e4..87fae227a83ae4b3c7a4969d7712dc266f69f1cc 100644
--- a/src/dihedral.h
+++ b/src/dihedral.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -50,8 +50,8 @@ class Dihedral : protected Pointers {
void ev_setup(int, int);
void ev_tally(int, int, int, int, int, int, double,
- double *, double *, double *, double, double, double,
- double, double, double, double, double, double);
+ double *, double *, double *, double, double, double,
+ double, double, double, double, double, double);
};
}
diff --git a/src/displace_atoms.cpp b/src/displace_atoms.cpp
index a46547078b236fae6a2ae8e9c07d597e1f3f5893..8e2a49320e39993caa52267d9a9082099a2d75f0 100644
--- a/src/displace_atoms.cpp
+++ b/src/displace_atoms.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -40,12 +40,12 @@ void DisplaceAtoms::command(int narg, char **arg)
{
int i;
- if (domain->box_exist == 0)
+ if (domain->box_exist == 0)
error->all(FLERR,"Displace_atoms command before simulation box is defined");
if (narg < 2) error->all(FLERR,"Illegal displace_atoms command");
- if (modify->nfix_restart_peratom)
+ if (modify->nfix_restart_peratom)
error->all(FLERR,"Cannot displace_atoms after "
- "reading restart file with per-atom info");
+ "reading restart file with per-atom info");
if (comm->me == 0 && screen) fprintf(screen,"Displacing atoms ...\n");
@@ -98,15 +98,15 @@ void DisplaceAtoms::command(int narg, char **arg)
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
- x[i][0] += delx;
- x[i][1] += dely;
- x[i][2] += delz;
+ x[i][0] += delx;
+ x[i][1] += dely;
+ x[i][2] += delz;
}
}
}
// move atoms in ramped fashion
-
+
if (style == RAMP) {
int d_dim;
@@ -153,18 +153,18 @@ void DisplaceAtoms::command(int narg, char **arg)
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
- fraction = (x[i][coord_dim] - coord_lo) / (coord_hi - coord_lo);
- fraction = MAX(fraction,0.0);
- fraction = MIN(fraction,1.0);
- dramp = d_lo + fraction*(d_hi - d_lo);
- x[i][d_dim] += dramp;
+ fraction = (x[i][coord_dim] - coord_lo) / (coord_hi - coord_lo);
+ fraction = MAX(fraction,0.0);
+ fraction = MIN(fraction,1.0);
+ dramp = d_lo + fraction*(d_hi - d_lo);
+ x[i][d_dim] += dramp;
}
}
}
// move atoms randomly
// makes atom result independent of what proc owns it via random->reset()
-
+
if (style == RANDOM) {
RanPark *random = new RanPark(lmp,1);
@@ -180,10 +180,10 @@ void DisplaceAtoms::command(int narg, char **arg)
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
- random->reset(seed,x[i]);
- x[i][0] += dx * 2.0*(random->uniform()-0.5);
- x[i][1] += dy * 2.0*(random->uniform()-0.5);
- x[i][2] += dz * 2.0*(random->uniform()-0.5);
+ random->reset(seed,x[i]);
+ x[i][0] += dx * 2.0*(random->uniform()-0.5);
+ x[i][1] += dy * 2.0*(random->uniform()-0.5);
+ x[i][2] += dz * 2.0*(random->uniform()-0.5);
}
}
@@ -213,14 +213,14 @@ void DisplaceAtoms::command(int narg, char **arg)
MPI_Allreduce(&nblocal,&natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);
if (natoms != atom->natoms && comm->me == 0) {
char str[128];
- sprintf(str,"Lost atoms via displace_atoms: original " BIGINT_FORMAT
- " current " BIGINT_FORMAT,atom->natoms,natoms);
+ sprintf(str,"Lost atoms via displace_atoms: original " BIGINT_FORMAT
+ " current " BIGINT_FORMAT,atom->natoms,natoms);
error->warning(FLERR,str);
}
}
/* ----------------------------------------------------------------------
- parse optional parameters at end of displace_atoms input line
+ parse optional parameters at end of displace_atoms input line
------------------------------------------------------------------------- */
void DisplaceAtoms::options(int narg, char **arg)
diff --git a/src/displace_atoms.h b/src/displace_atoms.h
index cd4601021840e974605fbba98b2e1d47abaca634..cfab30cec8784e212c788db299bc88917f93f764 100644
--- a/src/displace_atoms.h
+++ b/src/displace_atoms.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/domain.cpp b/src/domain.cpp
index 71c220dd07cb1934a73479ca3a968e9baf8bfba8..96f3772c212c0591e021bc4872b43d72387bcd5a 100644
--- a/src/domain.cpp
+++ b/src/domain.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -45,7 +45,7 @@ using namespace MathConst;
enum{NO_REMAP,X_REMAP,V_REMAP}; // same as fix_deform.cpp
/* ----------------------------------------------------------------------
- default is periodic
+ default is periodic
------------------------------------------------------------------------- */
Domain::Domain(LAMMPS *lmp) : Pointers(lmp)
@@ -70,10 +70,10 @@ Domain::Domain(LAMMPS *lmp) : Pointers(lmp)
h[3] = h[4] = h[5] = 0.0;
h_inv[3] = h_inv[4] = h_inv[5] = 0.0;
- h_rate[0] = h_rate[1] = h_rate[2] =
+ h_rate[0] = h_rate[1] = h_rate[2] =
h_rate[3] = h_rate[4] = h_rate[5] = 0.0;
h_ratelo[0] = h_ratelo[1] = h_ratelo[2] = 0.0;
-
+
prd_lamda[0] = prd_lamda[1] = prd_lamda[2] = 1.0;
prd_half_lamda[0] = prd_half_lamda[1] = prd_half_lamda[2] = 0.5;
boxlo_lamda[0] = boxlo_lamda[1] = boxlo_lamda[2] = 0.0;
@@ -112,8 +112,8 @@ void Domain::init()
if (strcmp(modify->fix[i]->style,"deform") == 0) {
deform_flag = 1;
if (((FixDeform *) modify->fix[i])->remapflag == V_REMAP) {
- deform_vremap = 1;
- deform_groupbit = modify->fix[i]->groupbit;
+ deform_vremap = 1;
+ deform_groupbit = modify->fix[i]->groupbit;
}
}
@@ -201,7 +201,7 @@ void Domain::set_global_box()
h_inv[3] = -h[3] / (h[1]*h[2]);
h_inv[4] = (h[3]*h[5] - h[1]*h[4]) / (h[0]*h[1]*h[2]);
h_inv[5] = -h[5] / (h[0]*h[1]);
-
+
boxlo_bound[0] = MIN(boxlo[0],boxlo[0]+xy);
boxlo_bound[0] = MIN(boxlo_bound[0],boxlo_bound[0]+xz);
boxlo_bound[1] = MIN(boxlo[1],boxlo[1]+yz);
@@ -290,7 +290,7 @@ void Domain::reset_box()
double **x = atom->x;
int nlocal = atom->nlocal;
-
+
for (int i = 0; i < nlocal; i++) {
extent[0][0] = MIN(extent[0][0],x[i][0]);
extent[0][1] = MAX(extent[0][1],x[i][0]);
@@ -322,67 +322,67 @@ void Domain::reset_box()
if (triclinic == 0) {
if (xperiodic == 0) {
- if (boundary[0][0] == 2) boxlo[0] = -all[0][0] - small[0];
- else if (boundary[0][0] == 3)
- boxlo[0] = MIN(-all[0][0]-small[0],minxlo);
- if (boundary[0][1] == 2) boxhi[0] = all[0][1] + small[0];
- else if (boundary[0][1] == 3) boxhi[0] = MAX(all[0][1]+small[0],minxhi);
- if (boxlo[0] > boxhi[0]) error->all(FLERR,"Illegal simulation box");
+ if (boundary[0][0] == 2) boxlo[0] = -all[0][0] - small[0];
+ else if (boundary[0][0] == 3)
+ boxlo[0] = MIN(-all[0][0]-small[0],minxlo);
+ if (boundary[0][1] == 2) boxhi[0] = all[0][1] + small[0];
+ else if (boundary[0][1] == 3) boxhi[0] = MAX(all[0][1]+small[0],minxhi);
+ if (boxlo[0] > boxhi[0]) error->all(FLERR,"Illegal simulation box");
}
if (yperiodic == 0) {
- if (boundary[1][0] == 2) boxlo[1] = -all[1][0] - small[1];
- else if (boundary[1][0] == 3)
- boxlo[1] = MIN(-all[1][0]-small[1],minylo);
- if (boundary[1][1] == 2) boxhi[1] = all[1][1] + small[1];
- else if (boundary[1][1] == 3) boxhi[1] = MAX(all[1][1]+small[1],minyhi);
- if (boxlo[1] > boxhi[1]) error->all(FLERR,"Illegal simulation box");
+ if (boundary[1][0] == 2) boxlo[1] = -all[1][0] - small[1];
+ else if (boundary[1][0] == 3)
+ boxlo[1] = MIN(-all[1][0]-small[1],minylo);
+ if (boundary[1][1] == 2) boxhi[1] = all[1][1] + small[1];
+ else if (boundary[1][1] == 3) boxhi[1] = MAX(all[1][1]+small[1],minyhi);
+ if (boxlo[1] > boxhi[1]) error->all(FLERR,"Illegal simulation box");
}
if (zperiodic == 0) {
- if (boundary[2][0] == 2) boxlo[2] = -all[2][0] - small[2];
- else if (boundary[2][0] == 3)
- boxlo[2] = MIN(-all[2][0]-small[2],minzlo);
- if (boundary[2][1] == 2) boxhi[2] = all[2][1] + small[2];
- else if (boundary[2][1] == 3) boxhi[2] = MAX(all[2][1]+small[2],minzhi);
- if (boxlo[2] > boxhi[2]) error->all(FLERR,"Illegal simulation box");
+ if (boundary[2][0] == 2) boxlo[2] = -all[2][0] - small[2];
+ else if (boundary[2][0] == 3)
+ boxlo[2] = MIN(-all[2][0]-small[2],minzlo);
+ if (boundary[2][1] == 2) boxhi[2] = all[2][1] + small[2];
+ else if (boundary[2][1] == 3) boxhi[2] = MAX(all[2][1]+small[2],minzhi);
+ if (boxlo[2] > boxhi[2]) error->all(FLERR,"Illegal simulation box");
}
} else {
double lo[3],hi[3];
if (xperiodic == 0) {
- lo[0] = -all[0][0]; lo[1] = 0.0; lo[2] = 0.0;
- lamda2x(lo,lo);
- hi[0] = all[0][1]; hi[1] = 0.0; hi[2] = 0.0;
- lamda2x(hi,hi);
- if (boundary[0][0] == 2) boxlo[0] = lo[0] - small[0];
- else if (boundary[0][0] == 3) boxlo[0] = MIN(lo[0]-small[0],minxlo);
- if (boundary[0][1] == 2) boxhi[0] = hi[0] + small[0];
- else if (boundary[0][1] == 3) boxhi[0] = MAX(hi[0]+small[0],minxhi);
- if (boxlo[0] > boxhi[0]) error->all(FLERR,"Illegal simulation box");
+ lo[0] = -all[0][0]; lo[1] = 0.0; lo[2] = 0.0;
+ lamda2x(lo,lo);
+ hi[0] = all[0][1]; hi[1] = 0.0; hi[2] = 0.0;
+ lamda2x(hi,hi);
+ if (boundary[0][0] == 2) boxlo[0] = lo[0] - small[0];
+ else if (boundary[0][0] == 3) boxlo[0] = MIN(lo[0]-small[0],minxlo);
+ if (boundary[0][1] == 2) boxhi[0] = hi[0] + small[0];
+ else if (boundary[0][1] == 3) boxhi[0] = MAX(hi[0]+small[0],minxhi);
+ if (boxlo[0] > boxhi[0]) error->all(FLERR,"Illegal simulation box");
}
if (yperiodic == 0) {
- lo[0] = 0.0; lo[1] = -all[1][0]; lo[2] = 0.0;
- lamda2x(lo,lo);
- hi[0] = 0.0; hi[1] = all[1][1]; hi[2] = 0.0;
- lamda2x(hi,hi);
- if (boundary[1][0] == 2) boxlo[1] = lo[1] - small[1];
- else if (boundary[1][0] == 3) boxlo[1] = MIN(lo[1]-small[1],minylo);
- if (boundary[1][1] == 2) boxhi[1] = hi[1] + small[1];
- else if (boundary[1][1] == 3) boxhi[1] = MAX(hi[1]+small[1],minyhi);
- if (boxlo[1] > boxhi[1]) error->all(FLERR,"Illegal simulation box");
- //xy *= (boxhi[1]-boxlo[1]) / yprd;
+ lo[0] = 0.0; lo[1] = -all[1][0]; lo[2] = 0.0;
+ lamda2x(lo,lo);
+ hi[0] = 0.0; hi[1] = all[1][1]; hi[2] = 0.0;
+ lamda2x(hi,hi);
+ if (boundary[1][0] == 2) boxlo[1] = lo[1] - small[1];
+ else if (boundary[1][0] == 3) boxlo[1] = MIN(lo[1]-small[1],minylo);
+ if (boundary[1][1] == 2) boxhi[1] = hi[1] + small[1];
+ else if (boundary[1][1] == 3) boxhi[1] = MAX(hi[1]+small[1],minyhi);
+ if (boxlo[1] > boxhi[1]) error->all(FLERR,"Illegal simulation box");
+ //xy *= (boxhi[1]-boxlo[1]) / yprd;
}
if (zperiodic == 0) {
- lo[0] = 0.0; lo[1] = 0.0; lo[2] = -all[2][0];
- lamda2x(lo,lo);
- hi[0] = 0.0; hi[1] = 0.0; hi[2] = all[2][1];
- lamda2x(hi,hi);
- if (boundary[2][0] == 2) boxlo[2] = lo[2] - small[2];
- else if (boundary[2][0] == 3) boxlo[2] = MIN(lo[2]-small[2],minzlo);
- if (boundary[2][1] == 2) boxhi[2] = hi[2] + small[2];
- else if (boundary[2][1] == 3) boxhi[2] = MAX(hi[2]+small[2],minzhi);
- if (boxlo[2] > boxhi[2]) error->all(FLERR,"Illegal simulation box");
- //xz *= (boxhi[2]-boxlo[2]) / xprd;
- //yz *= (boxhi[2]-boxlo[2]) / yprd;
+ lo[0] = 0.0; lo[1] = 0.0; lo[2] = -all[2][0];
+ lamda2x(lo,lo);
+ hi[0] = 0.0; hi[1] = 0.0; hi[2] = all[2][1];
+ lamda2x(hi,hi);
+ if (boundary[2][0] == 2) boxlo[2] = lo[2] - small[2];
+ else if (boundary[2][0] == 3) boxlo[2] = MIN(lo[2]-small[2],minzlo);
+ if (boundary[2][1] == 2) boxhi[2] = hi[2] + small[2];
+ else if (boundary[2][1] == 3) boxhi[2] = MAX(hi[2]+small[2],minzhi);
+ if (boxlo[2] > boxhi[2]) error->all(FLERR,"Illegal simulation box");
+ //xz *= (boxhi[2]-boxlo[2]) / xprd;
+ //yz *= (boxhi[2]-boxlo[2]) / yprd;
}
}
}
@@ -435,81 +435,81 @@ void Domain::pbc()
for (i = 0; i < nlocal; i++) {
if (xperiodic) {
if (x[i][0] < lo[0]) {
- x[i][0] += period[0];
- if (deform_vremap && mask[i] & deform_groupbit) v[i][0] += h_rate[0];
- idim = image[i] & 1023;
+ x[i][0] += period[0];
+ if (deform_vremap && mask[i] & deform_groupbit) v[i][0] += h_rate[0];
+ idim = image[i] & 1023;
otherdims = image[i] ^ idim;
- idim--;
- idim &= 1023;
- image[i] = otherdims | idim;
+ idim--;
+ idim &= 1023;
+ image[i] = otherdims | idim;
}
if (x[i][0] >= hi[0]) {
- x[i][0] -= period[0];
- x[i][0] = MAX(x[i][0],lo[0]);
- if (deform_vremap && mask[i] & deform_groupbit) v[i][0] -= h_rate[0];
- idim = image[i] & 1023;
- otherdims = image[i] ^ idim;
- idim++;
- idim &= 1023;
- image[i] = otherdims | idim;
+ x[i][0] -= period[0];
+ x[i][0] = MAX(x[i][0],lo[0]);
+ if (deform_vremap && mask[i] & deform_groupbit) v[i][0] -= h_rate[0];
+ idim = image[i] & 1023;
+ otherdims = image[i] ^ idim;
+ idim++;
+ idim &= 1023;
+ image[i] = otherdims | idim;
}
}
if (yperiodic) {
if (x[i][1] < lo[1]) {
- x[i][1] += period[1];
- if (deform_vremap && mask[i] & deform_groupbit) {
- v[i][0] += h_rate[5];
- v[i][1] += h_rate[1];
- }
- idim = (image[i] >> 10) & 1023;
+ x[i][1] += period[1];
+ if (deform_vremap && mask[i] & deform_groupbit) {
+ v[i][0] += h_rate[5];
+ v[i][1] += h_rate[1];
+ }
+ idim = (image[i] >> 10) & 1023;
otherdims = image[i] ^ (idim << 10);
- idim--;
- idim &= 1023;
- image[i] = otherdims | (idim << 10);
+ idim--;
+ idim &= 1023;
+ image[i] = otherdims | (idim << 10);
}
if (x[i][1] >= hi[1]) {
- x[i][1] -= period[1];
- x[i][1] = MAX(x[i][1],lo[1]);
- if (deform_vremap && mask[i] & deform_groupbit) {
- v[i][0] -= h_rate[5];
- v[i][1] -= h_rate[1];
- }
- idim = (image[i] >> 10) & 1023;
+ x[i][1] -= period[1];
+ x[i][1] = MAX(x[i][1],lo[1]);
+ if (deform_vremap && mask[i] & deform_groupbit) {
+ v[i][0] -= h_rate[5];
+ v[i][1] -= h_rate[1];
+ }
+ idim = (image[i] >> 10) & 1023;
otherdims = image[i] ^ (idim << 10);
- idim++;
- idim &= 1023;
- image[i] = otherdims | (idim << 10);
+ idim++;
+ idim &= 1023;
+ image[i] = otherdims | (idim << 10);
}
}
if (zperiodic) {
if (x[i][2] < lo[2]) {
- x[i][2] += period[2];
- if (deform_vremap && mask[i] & deform_groupbit) {
- v[i][0] += h_rate[4];
- v[i][1] += h_rate[3];
- v[i][2] += h_rate[2];
- }
- idim = image[i] >> 20;
+ x[i][2] += period[2];
+ if (deform_vremap && mask[i] & deform_groupbit) {
+ v[i][0] += h_rate[4];
+ v[i][1] += h_rate[3];
+ v[i][2] += h_rate[2];
+ }
+ idim = image[i] >> 20;
otherdims = image[i] ^ (idim << 20);
- idim--;
- idim &= 1023;
- image[i] = otherdims | (idim << 20);
+ idim--;
+ idim &= 1023;
+ image[i] = otherdims | (idim << 20);
}
if (x[i][2] >= hi[2]) {
- x[i][2] -= period[2];
- x[i][2] = MAX(x[i][2],lo[2]);
- if (deform_vremap && mask[i] & deform_groupbit) {
- v[i][0] -= h_rate[4];
- v[i][1] -= h_rate[3];
- v[i][2] -= h_rate[2];
- }
- idim = image[i] >> 20;
+ x[i][2] -= period[2];
+ x[i][2] = MAX(x[i][2],lo[2]);
+ if (deform_vremap && mask[i] & deform_groupbit) {
+ v[i][0] -= h_rate[4];
+ v[i][1] -= h_rate[3];
+ v[i][2] -= h_rate[2];
+ }
+ idim = image[i] >> 20;
otherdims = image[i] ^ (idim << 20);
- idim++;
- idim &= 1023;
- image[i] = otherdims | (idim << 20);
+ idim++;
+ idim &= 1023;
+ image[i] = otherdims | (idim << 20);
}
}
}
@@ -530,7 +530,7 @@ int Domain::minimum_image_check(double dx, double dy, double dz)
/* ----------------------------------------------------------------------
minimum image convention
- use 1/2 of box size as test
+ use 1/2 of box size as test
for triclinic, also add/subtract tilt factors in other dims as needed
------------------------------------------------------------------------- */
@@ -539,52 +539,52 @@ void Domain::minimum_image(double &dx, double &dy, double &dz)
if (triclinic == 0) {
if (xperiodic) {
if (fabs(dx) > xprd_half) {
- if (dx < 0.0) dx += xprd;
- else dx -= xprd;
+ if (dx < 0.0) dx += xprd;
+ else dx -= xprd;
}
}
if (yperiodic) {
if (fabs(dy) > yprd_half) {
- if (dy < 0.0) dy += yprd;
- else dy -= yprd;
+ if (dy < 0.0) dy += yprd;
+ else dy -= yprd;
}
}
if (zperiodic) {
if (fabs(dz) > zprd_half) {
- if (dz < 0.0) dz += zprd;
- else dz -= zprd;
+ if (dz < 0.0) dz += zprd;
+ else dz -= zprd;
}
}
} else {
if (zperiodic) {
if (fabs(dz) > zprd_half) {
- if (dz < 0.0) {
- dz += zprd;
- dy += yz;
- dx += xz;
- } else {
- dz -= zprd;
- dy -= yz;
- dx -= xz;
- }
+ if (dz < 0.0) {
+ dz += zprd;
+ dy += yz;
+ dx += xz;
+ } else {
+ dz -= zprd;
+ dy -= yz;
+ dx -= xz;
+ }
}
}
if (yperiodic) {
if (fabs(dy) > yprd_half) {
- if (dy < 0.0) {
- dy += yprd;
- dx += xy;
- } else {
- dy -= yprd;
- dx -= xy;
- }
+ if (dy < 0.0) {
+ dy += yprd;
+ dx += xy;
+ } else {
+ dy -= yprd;
+ dx -= xy;
+ }
}
}
if (xperiodic) {
if (fabs(dx) > xprd_half) {
- if (dx < 0.0) dx += xprd;
- else dx -= xprd;
+ if (dx < 0.0) dx += xprd;
+ else dx -= xprd;
}
}
}
@@ -601,52 +601,52 @@ void Domain::minimum_image(double *delta)
if (triclinic == 0) {
if (xperiodic) {
if (fabs(delta[0]) > xprd_half) {
- if (delta[0] < 0.0) delta[0] += xprd;
- else delta[0] -= xprd;
+ if (delta[0] < 0.0) delta[0] += xprd;
+ else delta[0] -= xprd;
}
}
if (yperiodic) {
if (fabs(delta[1]) > yprd_half) {
- if (delta[1] < 0.0) delta[1] += yprd;
- else delta[1] -= yprd;
+ if (delta[1] < 0.0) delta[1] += yprd;
+ else delta[1] -= yprd;
}
}
if (zperiodic) {
if (fabs(delta[2]) > zprd_half) {
- if (delta[2] < 0.0) delta[2] += zprd;
- else delta[2] -= zprd;
+ if (delta[2] < 0.0) delta[2] += zprd;
+ else delta[2] -= zprd;
}
}
} else {
if (zperiodic) {
if (fabs(delta[2]) > zprd_half) {
- if (delta[2] < 0.0) {
- delta[2] += zprd;
- delta[1] += yz;
- delta[0] += xz;
- } else {
- delta[2] -= zprd;
- delta[1] -= yz;
- delta[0] -= xz;
- }
+ if (delta[2] < 0.0) {
+ delta[2] += zprd;
+ delta[1] += yz;
+ delta[0] += xz;
+ } else {
+ delta[2] -= zprd;
+ delta[1] -= yz;
+ delta[0] -= xz;
+ }
}
}
if (yperiodic) {
if (fabs(delta[1]) > yprd_half) {
- if (delta[1] < 0.0) {
- delta[1] += yprd;
- delta[0] += xy;
- } else {
- delta[1] -= yprd;
- delta[0] -= xy;
- }
+ if (delta[1] < 0.0) {
+ delta[1] += yprd;
+ delta[0] += xy;
+ } else {
+ delta[1] -= yprd;
+ delta[0] -= xy;
+ }
}
}
if (xperiodic) {
if (fabs(delta[0]) > xprd_half) {
- if (delta[0] < 0.0) delta[0] += xprd;
- else delta[0] -= xprd;
+ if (delta[0] < 0.0) delta[0] += xprd;
+ else delta[0] -= xprd;
}
}
}
@@ -658,7 +658,7 @@ void Domain::minimum_image(double *delta)
------------------------------------------------------------------------- */
void Domain::closest_image(const double * const xi, const double * const xj,
- double * const xjimage)
+ double * const xjimage)
{
double dx = xj[0] - xi[0];
double dy = xj[1] - xi[1];
@@ -667,86 +667,86 @@ void Domain::closest_image(const double * const xi, const double * const xj,
if (triclinic == 0) {
if (xperiodic) {
if (dx < 0.0) {
- while (dx < 0.0) dx += xprd;
- if (dx > xprd_half) dx -= xprd;
+ while (dx < 0.0) dx += xprd;
+ if (dx > xprd_half) dx -= xprd;
} else {
- while (dx > 0.0) dx -= xprd;
- if (dx < -xprd_half) dx += xprd;
+ while (dx > 0.0) dx -= xprd;
+ if (dx < -xprd_half) dx += xprd;
}
}
if (yperiodic) {
if (dy < 0.0) {
- while (dy < 0.0) dy += yprd;
- if (dy > yprd_half) dy -= yprd;
+ while (dy < 0.0) dy += yprd;
+ if (dy > yprd_half) dy -= yprd;
} else {
- while (dy > 0.0) dy -= yprd;
- if (dy < -yprd_half) dy += yprd;
+ while (dy > 0.0) dy -= yprd;
+ if (dy < -yprd_half) dy += yprd;
}
}
if (zperiodic) {
if (dz < 0.0) {
- while (dz < 0.0) dz += zprd;
- if (dz > zprd_half) dz -= zprd;
+ while (dz < 0.0) dz += zprd;
+ if (dz > zprd_half) dz -= zprd;
} else {
- while (dz > 0.0) dz -= zprd;
- if (dz < -zprd_half) dz += zprd;
+ while (dz > 0.0) dz -= zprd;
+ if (dz < -zprd_half) dz += zprd;
}
}
} else {
if (zperiodic) {
if (dz < 0.0) {
- while (dz < 0.0) {
- dz += zprd;
- dy += yz;
- dx += xz;
- }
- if (dz > zprd_half) {
- dz -= zprd;
- dy -= yz;
- dx -= xz;
- }
+ while (dz < 0.0) {
+ dz += zprd;
+ dy += yz;
+ dx += xz;
+ }
+ if (dz > zprd_half) {
+ dz -= zprd;
+ dy -= yz;
+ dx -= xz;
+ }
} else {
- while (dz > 0.0) {
- dz -= zprd;
- dy -= yz;
- dx -= xz;
- }
- if (dz < -zprd_half) {
- dz += zprd;
- dy += yz;
- dx += xz;
- }
+ while (dz > 0.0) {
+ dz -= zprd;
+ dy -= yz;
+ dx -= xz;
+ }
+ if (dz < -zprd_half) {
+ dz += zprd;
+ dy += yz;
+ dx += xz;
+ }
}
}
if (yperiodic) {
if (dy < 0.0) {
- while (dy < 0.0) {
- dy += yprd;
- dx += xy;
- }
- if (dy > yprd_half) {
- dy -= yprd;
- dx -= xy;
- }
+ while (dy < 0.0) {
+ dy += yprd;
+ dx += xy;
+ }
+ if (dy > yprd_half) {
+ dy -= yprd;
+ dx -= xy;
+ }
} else {
- while (dy > 0.0) {
- dy -= yprd;
- dx -= xy;
- }
- if (dy < -yprd_half) {
- dy += yprd;
- dx += xy;
- }
+ while (dy > 0.0) {
+ dy -= yprd;
+ dx -= xy;
+ }
+ if (dy < -yprd_half) {
+ dy += yprd;
+ dx += xy;
+ }
}
}
if (xperiodic) {
if (dx < 0.0) {
- while (dx < 0.0) dx += xprd;
- if (dx > xprd_half) dx -= xprd;
+ while (dx < 0.0) dx += xprd;
+ if (dx > xprd_half) dx -= xprd;
} else {
- while (dx > 0.0) dx -= xprd;
- if (dx < -xprd_half) dx += xprd;
+ while (dx > 0.0) dx -= xprd;
+ if (dx < -xprd_half) dx += xprd;
}
}
}
@@ -1041,7 +1041,7 @@ void Domain::image_flip(int m, int n, int p)
int *image = atom->image;
int nlocal = atom->nlocal;
- for (int i = 0; i < nlocal; i++) {
+ for (int i = 0; i < nlocal; i++) {
int xbox = (image[i] & 1023) - 512;
int ybox = (image[i] >> 10 & 1023) - 512;
int zbox = (image[i] >> 20) - 512;
@@ -1088,7 +1088,7 @@ void Domain::add_region(int narg, char **arg)
if (nregion == maxregion) {
maxregion += DELTA;
- regions = (Region **)
+ regions = (Region **)
memory->srealloc(regions,maxregion*sizeof(Region *),"domain:regions");
}
@@ -1158,14 +1158,14 @@ void Domain::set_boundary(int narg, char **arg, int flag)
else if (c == 's') boundary[idim][iside] = 2;
else if (c == 'm') boundary[idim][iside] = 3;
else {
- if (flag == 0) error->all(FLERR,"Illegal boundary command");
- if (flag == 1) error->all(FLERR,"Illegal change_box command");
+ if (flag == 0) error->all(FLERR,"Illegal boundary command");
+ if (flag == 1) error->all(FLERR,"Illegal change_box command");
}
}
for (int idim = 0; idim < 3; idim++)
if ((boundary[idim][0] == 0 && boundary[idim][1]) ||
- (boundary[idim][0] && boundary[idim][1] == 0))
+ (boundary[idim][0] && boundary[idim][1] == 0))
error->all(FLERR,"Both sides of boundary must be periodic");
if (boundary[0][0] == 0) xperiodic = 1;
@@ -1183,8 +1183,8 @@ void Domain::set_boundary(int narg, char **arg, int flag)
if (xperiodic == 0 || yperiodic == 0 || zperiodic == 0) {
nonperiodic = 1;
if (boundary[0][0] >= 2 || boundary[0][1] >= 2 ||
- boundary[1][0] >= 2 || boundary[1][1] >= 2 ||
- boundary[2][0] >= 2 || boundary[2][1] >= 2) nonperiodic = 2;
+ boundary[1][0] >= 2 || boundary[1][1] >= 2 ||
+ boundary[2][0] >= 2 || boundary[2][1] >= 2) nonperiodic = 2;
}
}
@@ -1197,26 +1197,26 @@ void Domain::print_box(const char *str)
if (comm->me == 0) {
if (screen) {
if (triclinic == 0)
- fprintf(screen,"%sorthogonal box = (%g %g %g) to (%g %g %g)\n",
- str,boxlo[0],boxlo[1],boxlo[2],boxhi[0],boxhi[1],boxhi[2]);
+ fprintf(screen,"%sorthogonal box = (%g %g %g) to (%g %g %g)\n",
+ str,boxlo[0],boxlo[1],boxlo[2],boxhi[0],boxhi[1],boxhi[2]);
else {
- char *format = (char *)
- "%striclinic box = (%g %g %g) to (%g %g %g) with tilt (%g %g %g)\n";
- fprintf(screen,format,
- str,boxlo[0],boxlo[1],boxlo[2],boxhi[0],boxhi[1],boxhi[2],
- xy,xz,yz);
+ char *format = (char *)
+ "%striclinic box = (%g %g %g) to (%g %g %g) with tilt (%g %g %g)\n";
+ fprintf(screen,format,
+ str,boxlo[0],boxlo[1],boxlo[2],boxhi[0],boxhi[1],boxhi[2],
+ xy,xz,yz);
}
}
if (logfile) {
if (triclinic == 0)
- fprintf(logfile,"%sorthogonal box = (%g %g %g) to (%g %g %g)\n",
- str,boxlo[0],boxlo[1],boxlo[2],boxhi[0],boxhi[1],boxhi[2]);
+ fprintf(logfile,"%sorthogonal box = (%g %g %g) to (%g %g %g)\n",
+ str,boxlo[0],boxlo[1],boxlo[2],boxhi[0],boxhi[1],boxhi[2]);
else {
- char *format = (char *)
- "%striclinic box = (%g %g %g) to (%g %g %g) with tilt (%g %g %g)\n";
- fprintf(logfile,format,
- str,boxlo[0],boxlo[1],boxlo[2],boxhi[0],boxhi[1],boxhi[2],
- xy,xz,yz);
+ char *format = (char *)
+ "%striclinic box = (%g %g %g) to (%g %g %g) with tilt (%g %g %g)\n";
+ fprintf(logfile,format,
+ str,boxlo[0],boxlo[1],boxlo[2],boxhi[0],boxhi[1],boxhi[2],
+ xy,xz,yz);
}
}
}
@@ -1251,7 +1251,7 @@ void Domain::lamda2x(int n)
{
double **x = atom->x;
- for (int i = 0; i < n; i++) {
+ for (int i = 0; i < n; i++) {
x[i][0] = h[0]*x[i][0] + h[5]*x[i][1] + h[4]*x[i][2] + boxlo[0];
x[i][1] = h[1]*x[i][1] + h[3]*x[i][2] + boxlo[1];
x[i][2] = h[2]*x[i][2] + boxlo[2];
@@ -1268,7 +1268,7 @@ void Domain::x2lamda(int n)
double delta[3];
double **x = atom->x;
- for (int i = 0; i < n; i++) {
+ for (int i = 0; i < n; i++) {
delta[0] = x[i][0] - boxlo[0];
delta[1] = x[i][1] - boxlo[1];
delta[2] = x[i][2] - boxlo[2];
@@ -1318,7 +1318,7 @@ void Domain::x2lamda(double *x, double *lamda)
------------------------------------------------------------------------- */
void Domain::x2lamda(double *x, double *lamda,
- double *my_boxlo, double *my_h_inv)
+ double *my_boxlo, double *my_h_inv)
{
double delta[3];
delta[0] = x[0] - my_boxlo[0];
diff --git a/src/domain.h b/src/domain.h
index a449449d580a6b437339d0f5da7bbcb6ba6fb998..592290807107fb7dcbf4db6ce0c60f274493f0de 100644
--- a/src/domain.h
+++ b/src/domain.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -34,7 +34,7 @@ class Domain : protected Pointers {
// 2 = shrink-wrap non-periodic
// 3 = shrink-wrap non-per w/ min
- int triclinic; // 0 = orthog box, 1 = triclinic
+ int triclinic; // 0 = orthog box, 1 = triclinic
// orthogonal box
double xprd,yprd,zprd; // global box dimensions
@@ -70,7 +70,7 @@ class Domain : protected Pointers {
// triclinic box
double xy,xz,yz; // 3 tilt factors
- double h[6],h_inv[6]; // shape matrix in Voigt notation
+ double h[6],h_inv[6]; // shape matrix in Voigt notation
double h_rate[6],h_ratelo[3]; // rate of box size/shape change
int box_change; // 1 if box bounds ever change, 0 if fixed
@@ -96,8 +96,8 @@ class Domain : protected Pointers {
int minimum_image_check(double, double, double);
void minimum_image(double &, double &, double &);
void minimum_image(double *);
- void closest_image(const double * const, const double * const,
- double * const);
+ void closest_image(const double * const, const double * const,
+ double * const);
void remap(double *, int &);
void remap(double *);
void remap_near(double *, double *);
diff --git a/src/dump.cpp b/src/dump.cpp
index f5dcea53c3edfc98430702d838d0fb6f1f6dfc81..7c7f2cd3a2d4b516ba4a8962fb5a02632958a156 100644
--- a/src/dump.cpp
+++ b/src/dump.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -191,32 +191,32 @@ void Dump::init()
int min = IBIG;
int max = 0;
for (int i = 0; i < nlocal; i++)
- if (mask[i] & groupbit) {
- min = MIN(min,tag[i]);
- max = MAX(max,tag[i]);
- }
+ if (mask[i] & groupbit) {
+ min = MIN(min,tag[i]);
+ max = MAX(max,tag[i]);
+ }
int minall,maxall;
MPI_Allreduce(&min,&minall,1,MPI_INT,MPI_MIN,world);
MPI_Allreduce(&max,&maxall,1,MPI_INT,MPI_MAX,world);
int isize = static_cast<int> (size);
if (maxall-minall+1 == isize) {
- reorderflag = 1;
- double range = maxall-minall + EPSILON;
- idlo = static_cast<int> (range*me/nprocs + minall);
- int idhi = static_cast<int> (range*(me+1)/nprocs + minall);
-
- int lom1 = static_cast<int> ((idlo-1-minall)/range * nprocs);
- int lo = static_cast<int> ((idlo-minall)/range * nprocs);
- int him1 = static_cast<int> ((idhi-1-minall)/range * nprocs);
- int hi = static_cast<int> ((idhi-minall)/range * nprocs);
- if (me && me == lom1) idlo--;
- else if (me && me != lo) idlo++;
- if (me+1 == him1) idhi--;
- else if (me+1 != hi) idhi++;
-
- nme_reorder = idhi-idlo;
- ntotal_reorder = isize;
+ reorderflag = 1;
+ double range = maxall-minall + EPSILON;
+ idlo = static_cast<int> (range*me/nprocs + minall);
+ int idhi = static_cast<int> (range*(me+1)/nprocs + minall);
+
+ int lom1 = static_cast<int> ((idlo-1-minall)/range * nprocs);
+ int lo = static_cast<int> ((idlo-minall)/range * nprocs);
+ int him1 = static_cast<int> ((idhi-1-minall)/range * nprocs);
+ int hi = static_cast<int> ((idhi-minall)/range * nprocs);
+ if (me && me == lom1) idlo--;
+ else if (me && me != lo) idlo++;
+ if (me+1 == him1) idhi--;
+ else if (me+1 != hi) idhi++;
+
+ nme_reorder = idhi-idlo;
+ ntotal_reorder = isize;
}
}
}
@@ -309,7 +309,7 @@ void Dump::write()
else pack(NULL);
if (sort_flag) sort();
- // multiproc = 1 = each proc writes own data to own file
+ // multiproc = 1 = each proc writes own data to own file
// multiproc = 0 = all procs write to one file thru proc 0
// proc 0 pings each proc, receives it's data, writes to file
// all other procs wait for ping, send their data to proc 0
@@ -322,18 +322,18 @@ void Dump::write()
if (me == 0) {
for (int iproc = 0; iproc < nprocs; iproc++) {
- if (iproc) {
- MPI_Irecv(buf,maxbuf*size_one,MPI_DOUBLE,iproc,0,world,&request);
- MPI_Send(&tmp,0,MPI_INT,iproc,0,world);
- MPI_Wait(&request,&status);
- MPI_Get_count(&status,MPI_DOUBLE,&nlines);
- nlines /= size_one;
- } else nlines = nme;
-
- write_data(nlines,buf);
+ if (iproc) {
+ MPI_Irecv(buf,maxbuf*size_one,MPI_DOUBLE,iproc,0,world,&request);
+ MPI_Send(&tmp,0,MPI_INT,iproc,0,world);
+ MPI_Wait(&request,&status);
+ MPI_Get_count(&status,MPI_DOUBLE,&nlines);
+ nlines /= size_one;
+ } else nlines = nme;
+
+ write_data(nlines,buf);
}
if (flush_flag) fflush(fp);
-
+
} else {
MPI_Recv(&tmp,0,MPI_INT,0,0,world,&status);
MPI_Rsend(buf,nme*size_one,MPI_DOUBLE,0,0,world);
@@ -374,9 +374,9 @@ void Dump::openfile()
filecurrent = new char[strlen(filename) + 16];
char *ptr = strchr(filename,'*');
*ptr = '\0';
- if (padflag == 0)
+ if (padflag == 0)
sprintf(filecurrent,"%s" BIGINT_FORMAT "%s",
- filename,update->ntimestep,ptr+1);
+ filename,update->ntimestep,ptr+1);
else {
char bif[8],pad[16];
strcpy(bif,BIGINT_FORMAT);
@@ -433,8 +433,8 @@ void Dump::sort()
memory->destroy(index);
memory->create(index,maxsort,"dump:index");
if (sortcol == 0) {
- memory->destroy(idsort);
- memory->create(idsort,maxsort,"dump:idsort");
+ memory->destroy(idsort);
+ memory->create(idsort,maxsort,"dump:idsort");
}
}
@@ -449,7 +449,7 @@ void Dump::sort()
}
// if multiple procs, exchange datums between procs via irregular
-
+
} else {
// grow proclist if necessary
@@ -459,32 +459,32 @@ void Dump::sort()
memory->destroy(proclist);
memory->create(proclist,maxproc,"dump:proclist");
}
-
+
// proclist[i] = which proc Ith datum will be sent to
if (sortcol == 0) {
int min = IBIG;
int max = 0;
for (i = 0; i < nme; i++) {
- min = MIN(min,ids[i]);
- max = MAX(max,ids[i]);
+ min = MIN(min,ids[i]);
+ max = MAX(max,ids[i]);
}
int minall,maxall;
MPI_Allreduce(&min,&minall,1,MPI_INT,MPI_MIN,world);
MPI_Allreduce(&max,&maxall,1,MPI_INT,MPI_MAX,world);
double range = maxall-minall + EPSILON;
for (i = 0; i < nme; i++) {
- iproc = static_cast<int> ((ids[i]-minall)/range * nprocs);
- proclist[i] = iproc;
+ iproc = static_cast<int> ((ids[i]-minall)/range * nprocs);
+ proclist[i] = iproc;
}
} else {
double min = BIG;
double max = -BIG;
for (i = 0; i < nme; i++) {
- value = buf[i*size_one + sortcolm1];
- min = MIN(min,value);
- max = MAX(max,value);
+ value = buf[i*size_one + sortcolm1];
+ min = MIN(min,value);
+ max = MAX(max,value);
}
double minall,maxall;
MPI_Allreduce(&min,&minall,1,MPI_DOUBLE,MPI_MIN,world);
@@ -492,9 +492,9 @@ void Dump::sort()
double range = maxall-minall + EPSILON*(maxall-minall);
if (range == 0.0) range = EPSILON;
for (i = 0; i < nme; i++) {
- value = buf[i*size_one + sortcolm1];
- iproc = static_cast<int> ((value-minall)/range * nprocs);
- proclist[i] = iproc;
+ value = buf[i*size_one + sortcolm1];
+ iproc = static_cast<int> ((value-minall)/range * nprocs);
+ proclist[i] = iproc;
}
}
@@ -511,14 +511,14 @@ void Dump::sort()
memory->destroy(index);
memory->create(index,maxsort,"dump:index");
if (sortcol == 0) {
- memory->destroy(idsort);
- memory->create(idsort,maxsort,"dump:idsort");
+ memory->destroy(idsort);
+ memory->create(idsort,maxsort,"dump:idsort");
}
}
-
+
irregular->exchange_data((char *) buf,size_one*sizeof(double),
- (char *) bufsort);
- if (sortcol == 0)
+ (char *) bufsort);
+ if (sortcol == 0)
irregular->exchange_data((char *) ids,sizeof(int),(char *) idsort);
irregular->destroy_data();
}
@@ -537,7 +537,7 @@ void Dump::sort()
if (reorderflag)
for (i = 0; i < nme; i++)
- index[idsort[i]-idlo] = i;
+ index[idsort[i]-idlo] = i;
}
if (!reorderflag) {
@@ -562,7 +562,7 @@ void Dump::sort()
}
// copy data from bufsort to buf using index
-
+
int nbytes = size_one*sizeof(double);
for (i = 0; i < nme; i++)
memcpy(&buf[i*size_one],&bufsort[index[i]*size_one],nbytes);
@@ -649,17 +649,17 @@ void Dump::modify_params(int narg, char **arg)
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
int idump;
for (idump = 0; idump < output->ndump; idump++)
- if (strcmp(id,output->dump[idump]->id) == 0) break;
+ if (strcmp(id,output->dump[idump]->id) == 0) break;
int n;
if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) {
- delete [] output->var_dump[idump];
- n = strlen(&arg[iarg+1][2]) + 1;
- output->var_dump[idump] = new char[n];
- strcpy(output->var_dump[idump],&arg[iarg+1][2]);
- n = 0;
+ delete [] output->var_dump[idump];
+ n = strlen(&arg[iarg+1][2]) + 1;
+ output->var_dump[idump] = new char[n];
+ strcpy(output->var_dump[idump],&arg[iarg+1][2]);
+ n = 0;
} else {
- n = atoi(arg[iarg+1]);
- if (n <= 0) error->all(FLERR,"Illegal dump_modify command");
+ n = atoi(arg[iarg+1]);
+ if (n <= 0) error->all(FLERR,"Illegal dump_modify command");
}
output->every_dump[idump] = n;
iarg += 2;
@@ -680,9 +680,9 @@ void Dump::modify_params(int narg, char **arg)
delete [] format_user;
format_user = NULL;
if (strcmp(arg[iarg+1],"none")) {
- int n = strlen(arg[iarg+1]) + 1;
- format_user = new char[n];
- strcpy(format_user,arg[iarg+1]);
+ int n = strlen(arg[iarg+1]) + 1;
+ format_user = new char[n];
+ strcpy(format_user,arg[iarg+1]);
}
iarg += 2;
} else if (strcmp(arg[iarg],"pad") == 0) {
@@ -694,19 +694,19 @@ void Dump::modify_params(int narg, char **arg)
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
if (strcmp(arg[iarg+1],"off") == 0) sort_flag = 0;
else if (strcmp(arg[iarg+1],"id") == 0) {
- sort_flag = 1;
- sortcol = 0;
- sortorder = ASCEND;
+ sort_flag = 1;
+ sortcol = 0;
+ sortorder = ASCEND;
} else {
- sort_flag = 1;
- sortcol = atoi(arg[iarg+1]);
- sortorder = ASCEND;
- if (sortcol == 0) error->all(FLERR,"Illegal dump_modify command");
- if (sortcol < 0) {
- sortorder = DESCEND;
- sortcol = -sortcol;
- }
- sortcolm1 = sortcol - 1;
+ sort_flag = 1;
+ sortcol = atoi(arg[iarg+1]);
+ sortorder = ASCEND;
+ if (sortcol == 0) error->all(FLERR,"Illegal dump_modify command");
+ if (sortcol < 0) {
+ sortorder = DESCEND;
+ sortcol = -sortcol;
+ }
+ sortcolm1 = sortcol - 1;
}
iarg += 2;
} else {
diff --git a/src/dump.h b/src/dump.h
index 852202544a216864e7c211f93ed7413f46ed2da2..b54705aa930be1380ed2b60d25ca0accebb1c6a0 100644
--- a/src/dump.h
+++ b/src/dump.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/dump_atom.cpp b/src/dump_atom.cpp
index fa951c8fcf47076f67eab2bbce92cacec25a5439..42ddf8f1965247c31412814db3cb9a971cc5e22d 100644
--- a/src/dump_atom.cpp
+++ b/src/dump_atom.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -269,7 +269,7 @@ void DumpAtom::pack_scale_noimage(int *ids)
double invxprd = 1.0/domain->xprd;
double invyprd = 1.0/domain->yprd;
double invzprd = 1.0/domain->zprd;
-
+
m = n = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
@@ -326,7 +326,7 @@ void DumpAtom::pack_scale_noimage_triclinic(int *ids)
int nlocal = atom->nlocal;
double lamda[3];
-
+
m = n = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
@@ -408,9 +408,9 @@ void DumpAtom::write_image(int n, double *mybuf)
int m = 0;
for (int i = 0; i < n; i++) {
fprintf(fp,format,
- static_cast<int> (mybuf[m]), static_cast<int> (mybuf[m+1]),
- mybuf[m+2],mybuf[m+3],mybuf[m+4], static_cast<int> (mybuf[m+5]),
- static_cast<int> (mybuf[m+6]), static_cast<int> (mybuf[m+7]));
+ static_cast<int> (mybuf[m]), static_cast<int> (mybuf[m+1]),
+ mybuf[m+2],mybuf[m+3],mybuf[m+4], static_cast<int> (mybuf[m+5]),
+ static_cast<int> (mybuf[m+6]), static_cast<int> (mybuf[m+7]));
m += size_one;
}
}
@@ -422,8 +422,8 @@ void DumpAtom::write_noimage(int n, double *mybuf)
int m = 0;
for (int i = 0; i < n; i++) {
fprintf(fp,format,
- static_cast<int> (mybuf[m]), static_cast<int> (mybuf[m+1]),
- mybuf[m+2],mybuf[m+3],mybuf[m+4]);
+ static_cast<int> (mybuf[m]), static_cast<int> (mybuf[m+1]),
+ mybuf[m+2],mybuf[m+3],mybuf[m+4]);
m += size_one;
}
}
diff --git a/src/dump_atom.h b/src/dump_atom.h
index 54a57784dcdf689a3f28532650dc668c275a4fd8..c792f8c0ab2e414d58fcbe093c7a25973ddcc7ae 100644
--- a/src/dump_atom.h
+++ b/src/dump_atom.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/dump_cfg.cpp b/src/dump_cfg.cpp
index 940e34549fe118ea28d99f8bda426450f9b36c21..3792ee5c57a1756af1b0213c76659e5b71eb1b41 100755
--- a/src/dump_cfg.cpp
+++ b/src/dump_cfg.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -15,7 +15,7 @@
Contributing author: Liang Wan (Chinese Academy of Sciences)
------------------------------------------------------------------------- */
-#include "math.h"
+#include "math.h"
#include "stdlib.h"
#include "string.h"
#include "dump_cfg.h"
@@ -43,11 +43,11 @@ DumpCFG::DumpCFG(LAMMPS *lmp, int narg, char **arg) :
{
if (narg < 10 ||
strcmp(arg[5],"id") != 0 || strcmp(arg[6],"type") != 0 ||
- (strcmp(arg[7],"xs") != 0 && strcmp(arg[7],"xsu") != 0) ||
+ (strcmp(arg[7],"xs") != 0 && strcmp(arg[7],"xsu") != 0) ||
(strcmp(arg[8],"ys") != 0 && strcmp(arg[8],"ysu") != 0) ||
(strcmp(arg[9],"zs") != 0 && strcmp(arg[9],"zsu") != 0))
error->all(FLERR,"Dump cfg arguments must start with "
- "'id type xs ys zs' or 'id type xsu ysu zsu'");
+ "'id type xs ys zs' or 'id type xsu ysu zsu'");
if (strcmp(arg[7],"xs") == 0)
if (strcmp(arg[8],"ysu") == 0 || strcmp(arg[9],"zsu") == 0)
@@ -56,7 +56,7 @@ DumpCFG::DumpCFG(LAMMPS *lmp, int narg, char **arg) :
else if (strcmp(arg[8],"ys") == 0 || strcmp(arg[9],"zs") == 0)
error->all(FLERR,"Dump cfg arguments can not mix xs|ys|zs with xsu|ysu|zsu");
else unwrapflag = 1;
-
+
// arrays for data rearrangement
rbuf = NULL;
@@ -71,25 +71,25 @@ DumpCFG::DumpCFG(LAMMPS *lmp, int narg, char **arg) :
int i = 0;
for (int iarg = 10; iarg < narg; iarg++, i++) {
if (strncmp(arg[iarg],"c_",2) == 0 ||
- strncmp(arg[iarg],"f_",2) == 0 ||
- strncmp(arg[iarg],"v_",2) == 0) {
+ strncmp(arg[iarg],"f_",2) == 0 ||
+ strncmp(arg[iarg],"v_",2) == 0) {
int n = strlen(arg[iarg]);
char *suffix = new char[n];
strcpy(suffix,&arg[iarg][2]);
char *ptr = strchr(suffix,'[');
if (ptr) {
- if (suffix[strlen(suffix)-1] != ']')
- error->all(FLERR,"Invalid keyword in dump cfg command");
- *ptr = '\0';
- *(ptr+2) = '\0';
- auxname[i] = new char[strlen(suffix) + 3];
- strcpy(auxname[i],suffix);
- strcat(auxname[i],"_");
- strcat(auxname[i],ptr+1);
+ if (suffix[strlen(suffix)-1] != ']')
+ error->all(FLERR,"Invalid keyword in dump cfg command");
+ *ptr = '\0';
+ *(ptr+2) = '\0';
+ auxname[i] = new char[strlen(suffix) + 3];
+ strcpy(auxname[i],suffix);
+ strcat(auxname[i],"_");
+ strcat(auxname[i],ptr+1);
} else {
- auxname[i] = new char[strlen(suffix) + 1];
- strcpy(auxname[i],suffix);
+ auxname[i] = new char[strlen(suffix) + 1];
+ strcpy(auxname[i],suffix);
}
delete [] suffix;
@@ -128,7 +128,7 @@ void DumpCFG::write_header(bigint n)
{
// special handling for atom style peri
// use average volume of particles to scale particles to mimic C atoms
- // scale box dimension to sc lattice for C with sigma = 1.44 Angstroms
+ // scale box dimension to sc lattice for C with sigma = 1.44 Angstroms
// special handling for unwrapped coordinates
double scale;
@@ -137,12 +137,12 @@ void DumpCFG::write_header(bigint n)
double vone = 0.0;
for (int i = 0; i < nlocal; i++) vone += atom->vfrac[i];
double vave;
- MPI_Allreduce(&vone,&vave,1,MPI_DOUBLE,MPI_SUM,world);
- if (atom->natoms) vave /= atom->natoms;
- if (vave > 0.0) scale = 1.44 / pow(vave,1.0/3.0);
+ MPI_Allreduce(&vone,&vave,1,MPI_DOUBLE,MPI_SUM,world);
+ if (atom->natoms) vave /= atom->natoms;
+ if (vave > 0.0) scale = 1.44 / pow(vave,1.0/3.0);
} else if (unwrapflag == 1) scale = UNWRAPEXPAND;
else scale = 1.0;
-
+
if (me == 0 || multiproc) {
char str[64];
sprintf(str,"Number of particles = %s\n",BIGINT_FORMAT);
@@ -198,46 +198,46 @@ void DumpCFG::write_data(int n, double *mybuf)
}
// write data lines in rbuf to file after transfer is done
-
+
double unwrap_coord;
if (nlines == nchosen) {
for (itype = 1; itype <= ntypes; itype++) {
for (i = 0; i < nchosen; i++)
- if (rbuf[i][1] == itype) break;
+ if (rbuf[i][1] == itype) break;
if (i < nchosen) {
- if (rmass) fprintf(fp,"%g\n",rmass[i]);
- else fprintf(fp,"%g\n",mass[itype]);
- fprintf(fp,"%s\n",typenames[itype]);
- for (; i < nchosen; i++) {
- if (rbuf[i][1] == itype) {
- if (unwrapflag == 0)
- for (j = 2; j < size_one; j++) {
- if (vtype[j] == INT)
- fprintf(fp,vformat[j],static_cast<int> (rbuf[i][j]));
- else fprintf(fp,vformat[j],rbuf[i][j]);
- }
- else {
-
- // Unwrapped scaled coordinates are shifted to
- // center of expanded box, to prevent
- // rewrapping by AtomEye. Dividing by
- // expansion factor restores correct
- // interatomic distances.
-
- for (j = 2; j < 5; j++) {
- unwrap_coord = (rbuf[i][j] - 0.5)/UNWRAPEXPAND + 0.5;
- fprintf(fp,vformat[j],unwrap_coord);
- }
- for (j = 5; j < size_one; j++) {
- if (vtype[j] == INT)
- fprintf(fp,vformat[j],static_cast<int> (rbuf[i][j]));
- else fprintf(fp,vformat[j],rbuf[i][j]);
- }
- }
- fprintf(fp,"\n");
- }
- }
+ if (rmass) fprintf(fp,"%g\n",rmass[i]);
+ else fprintf(fp,"%g\n",mass[itype]);
+ fprintf(fp,"%s\n",typenames[itype]);
+ for (; i < nchosen; i++) {
+ if (rbuf[i][1] == itype) {
+ if (unwrapflag == 0)
+ for (j = 2; j < size_one; j++) {
+ if (vtype[j] == INT)
+ fprintf(fp,vformat[j],static_cast<int> (rbuf[i][j]));
+ else fprintf(fp,vformat[j],rbuf[i][j]);
+ }
+ else {
+
+ // Unwrapped scaled coordinates are shifted to
+ // center of expanded box, to prevent
+ // rewrapping by AtomEye. Dividing by
+ // expansion factor restores correct
+ // interatomic distances.
+
+ for (j = 2; j < 5; j++) {
+ unwrap_coord = (rbuf[i][j] - 0.5)/UNWRAPEXPAND + 0.5;
+ fprintf(fp,vformat[j],unwrap_coord);
+ }
+ for (j = 5; j < size_one; j++) {
+ if (vtype[j] == INT)
+ fprintf(fp,vformat[j],static_cast<int> (rbuf[i][j]));
+ else fprintf(fp,vformat[j],rbuf[i][j]);
+ }
+ }
+ fprintf(fp,"\n");
+ }
+ }
}
}
nlines = 0;
diff --git a/src/dump_cfg.h b/src/dump_cfg.h
index 576448a695f82b43e3ffe4a48d672f756cd9f3a3..654582b1c6c0222d771385a5a482a5dd1393489b 100755
--- a/src/dump_cfg.h
+++ b/src/dump_cfg.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/dump_custom.cpp b/src/dump_custom.cpp
index c5ed749f082984c5b8dc3dac16a5efe2fd13bab5..32c51d5e3425bdabca3947ebd54ab2d6def1e290 100644
--- a/src/dump_custom.cpp
+++ b/src/dump_custom.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -256,7 +256,7 @@ void DumpCustom::init_style()
int ivariable;
for (int i = 0; i < nvariable; i++) {
ivariable = input->variable->find(id_variable[i]);
- if (ivariable < 0)
+ if (ivariable < 0)
error->all(FLERR,"Could not find dump custom variable name");
variable[i] = ivariable;
}
@@ -265,7 +265,7 @@ void DumpCustom::init_style()
if (iregion >= 0) {
iregion = domain->find_region(idregion);
- if (iregion == -1)
+ if (iregion == -1)
error->all(FLERR,"Region ID for dump custom does not exist");
}
@@ -387,8 +387,8 @@ int DumpCustom::count()
if (ncompute) {
for (i = 0; i < ncompute; i++)
if (!(compute[i]->invoked_flag & INVOKED_PERATOM)) {
- compute[i]->compute_peratom();
- compute[i]->invoked_flag |= INVOKED_PERATOM;
+ compute[i]->compute_peratom();
+ compute[i]->invoked_flag |= INVOKED_PERATOM;
}
}
@@ -397,7 +397,7 @@ int DumpCustom::count()
if (nvariable)
for (i = 0; i < nvariable; i++)
input->variable->compute_atom(variable[i],igroup,vbuf[i],1,0);
-
+
// choose all local atoms for output
for (i = 0; i < nlocal; i++) choose[i] = 1;
@@ -408,7 +408,7 @@ int DumpCustom::count()
int *mask = atom->mask;
for (i = 0; i < nlocal; i++)
if (!(mask[i] & groupbit))
- choose[i] = 0;
+ choose[i] = 0;
}
// un-choose if not in region
@@ -417,8 +417,8 @@ int DumpCustom::count()
Region *region = domain->regions[iregion];
double **x = atom->x;
for (i = 0; i < nlocal; i++)
- if (choose[i] && region->match(x[i][0],x[i][1],x[i][2]) == 0)
- choose[i] = 0;
+ if (choose[i] && region->match(x[i][0],x[i][1],x[i][2]) == 0)
+ choose[i] = 0;
}
// un-choose if any threshhold criterion isn't met
@@ -428,424 +428,424 @@ int DumpCustom::count()
double value;
int nstride;
int nlocal = atom->nlocal;
-
+
for (int ithresh = 0; ithresh < nthresh; ithresh++) {
// customize by adding to if statement
if (thresh_array[ithresh] == ID) {
- int *tag = atom->tag;
- for (i = 0; i < nlocal; i++) dchoose[i] = tag[i];
- ptr = dchoose;
- nstride = 1;
+ int *tag = atom->tag;
+ for (i = 0; i < nlocal; i++) dchoose[i] = tag[i];
+ ptr = dchoose;
+ nstride = 1;
} else if (thresh_array[ithresh] == MOL) {
- if (!atom->molecule_flag)
- error->all(FLERR,
- "Threshhold for an atom property that isn't allocated");
- int *molecule = atom->molecule;
- for (i = 0; i < nlocal; i++) dchoose[i] = molecule[i];
- ptr = dchoose;
- nstride = 1;
+ if (!atom->molecule_flag)
+ error->all(FLERR,
+ "Threshhold for an atom property that isn't allocated");
+ int *molecule = atom->molecule;
+ for (i = 0; i < nlocal; i++) dchoose[i] = molecule[i];
+ ptr = dchoose;
+ nstride = 1;
} else if (thresh_array[ithresh] == TYPE) {
- int *type = atom->type;
- for (i = 0; i < nlocal; i++) dchoose[i] = type[i];
- ptr = dchoose;
- nstride = 1;
+ int *type = atom->type;
+ for (i = 0; i < nlocal; i++) dchoose[i] = type[i];
+ ptr = dchoose;
+ nstride = 1;
} else if (thresh_array[ithresh] == ELEMENT) {
- int *type = atom->type;
- for (i = 0; i < nlocal; i++) dchoose[i] = type[i];
- ptr = dchoose;
- nstride = 1;
+ int *type = atom->type;
+ for (i = 0; i < nlocal; i++) dchoose[i] = type[i];
+ ptr = dchoose;
+ nstride = 1;
} else if (thresh_array[ithresh] == MASS) {
- if (atom->rmass) {
- ptr = atom->rmass;
- nstride = 1;
- } else {
- double *mass = atom->mass;
- int *type = atom->type;
- for (i = 0; i < nlocal; i++) dchoose[i] = mass[type[i]];
- ptr = dchoose;
- nstride = 1;
- }
+ if (atom->rmass) {
+ ptr = atom->rmass;
+ nstride = 1;
+ } else {
+ double *mass = atom->mass;
+ int *type = atom->type;
+ for (i = 0; i < nlocal; i++) dchoose[i] = mass[type[i]];
+ ptr = dchoose;
+ nstride = 1;
+ }
} else if (thresh_array[ithresh] == X) {
- ptr = &atom->x[0][0];
- nstride = 3;
+ ptr = &atom->x[0][0];
+ nstride = 3;
} else if (thresh_array[ithresh] == Y) {
- ptr = &atom->x[0][1];
- nstride = 3;
+ ptr = &atom->x[0][1];
+ nstride = 3;
} else if (thresh_array[ithresh] == Z) {
- ptr = &atom->x[0][2];
- nstride = 3;
+ ptr = &atom->x[0][2];
+ nstride = 3;
} else if (thresh_array[ithresh] == XS) {
double **x = atom->x;
- double boxxlo = domain->boxlo[0];
- double invxprd = 1.0/domain->xprd;
- for (i = 0; i < nlocal; i++)
- dchoose[i] = (x[i][0] - boxxlo) * invxprd;
- ptr = dchoose;
- nstride = 1;
+ double boxxlo = domain->boxlo[0];
+ double invxprd = 1.0/domain->xprd;
+ for (i = 0; i < nlocal; i++)
+ dchoose[i] = (x[i][0] - boxxlo) * invxprd;
+ ptr = dchoose;
+ nstride = 1;
} else if (thresh_array[ithresh] == YS) {
double **x = atom->x;
- double boxylo = domain->boxlo[1];
- double invyprd = 1.0/domain->yprd;
- for (i = 0; i < nlocal; i++)
- dchoose[i] = (x[i][1] - boxylo) * invyprd;
- ptr = dchoose;
- nstride = 1;
+ double boxylo = domain->boxlo[1];
+ double invyprd = 1.0/domain->yprd;
+ for (i = 0; i < nlocal; i++)
+ dchoose[i] = (x[i][1] - boxylo) * invyprd;
+ ptr = dchoose;
+ nstride = 1;
} else if (thresh_array[ithresh] == ZS) {
double **x = atom->x;
- double boxzlo = domain->boxlo[2];
- double invzprd = 1.0/domain->zprd;
- for (i = 0; i < nlocal; i++)
- dchoose[i] = (x[i][2] - boxzlo) * invzprd;
- ptr = dchoose;
- nstride = 1;
+ double boxzlo = domain->boxlo[2];
+ double invzprd = 1.0/domain->zprd;
+ for (i = 0; i < nlocal; i++)
+ dchoose[i] = (x[i][2] - boxzlo) * invzprd;
+ ptr = dchoose;
+ nstride = 1;
} else if (thresh_array[ithresh] == XSTRI) {
double **x = atom->x;
- double *boxlo = domain->boxlo;
- double *h_inv = domain->h_inv;
- for (i = 0; i < nlocal; i++)
- dchoose[i] = h_inv[0]*(x[i][0]-boxlo[0]) +
- h_inv[5]*(x[i][1]-boxlo[1]) + h_inv[4]*(x[i][2]-boxlo[2]);
- ptr = dchoose;
- nstride = 1;
+ double *boxlo = domain->boxlo;
+ double *h_inv = domain->h_inv;
+ for (i = 0; i < nlocal; i++)
+ dchoose[i] = h_inv[0]*(x[i][0]-boxlo[0]) +
+ h_inv[5]*(x[i][1]-boxlo[1]) + h_inv[4]*(x[i][2]-boxlo[2]);
+ ptr = dchoose;
+ nstride = 1;
} else if (thresh_array[ithresh] == YSTRI) {
double **x = atom->x;
- double *boxlo = domain->boxlo;
- double *h_inv = domain->h_inv;
- for (i = 0; i < nlocal; i++)
- dchoose[i] = h_inv[1]*(x[i][1]-boxlo[1]) +
- h_inv[3]*(x[i][2]-boxlo[2]);
- ptr = dchoose;
- nstride = 1;
+ double *boxlo = domain->boxlo;
+ double *h_inv = domain->h_inv;
+ for (i = 0; i < nlocal; i++)
+ dchoose[i] = h_inv[1]*(x[i][1]-boxlo[1]) +
+ h_inv[3]*(x[i][2]-boxlo[2]);
+ ptr = dchoose;
+ nstride = 1;
} else if (thresh_array[ithresh] == ZSTRI) {
double **x = atom->x;
- double *boxlo = domain->boxlo;
- double *h_inv = domain->h_inv;
- for (i = 0; i < nlocal; i++)
- dchoose[i] = h_inv[2]*(x[i][2]-boxlo[2]);
- ptr = dchoose;
- nstride = 1;
+ double *boxlo = domain->boxlo;
+ double *h_inv = domain->h_inv;
+ for (i = 0; i < nlocal; i++)
+ dchoose[i] = h_inv[2]*(x[i][2]-boxlo[2]);
+ ptr = dchoose;
+ nstride = 1;
} else if (thresh_array[ithresh] == XU) {
double **x = atom->x;
- int *image = atom->image;
- double xprd = domain->xprd;
- for (i = 0; i < nlocal; i++)
- dchoose[i] = x[i][0] + ((image[i] & 1023) - 512) * xprd;
- ptr = dchoose;
- nstride = 1;
+ int *image = atom->image;
+ double xprd = domain->xprd;
+ for (i = 0; i < nlocal; i++)
+ dchoose[i] = x[i][0] + ((image[i] & 1023) - 512) * xprd;
+ ptr = dchoose;
+ nstride = 1;
} else if (thresh_array[ithresh] == YU) {
double **x = atom->x;
- int *image = atom->image;
- double yprd = domain->yprd;
- for (i = 0; i < nlocal; i++)
- dchoose[i] = x[i][1] + ((image[i] >> 10 & 1023) - 512) * yprd;
- ptr = dchoose;
- nstride = 1;
+ int *image = atom->image;
+ double yprd = domain->yprd;
+ for (i = 0; i < nlocal; i++)
+ dchoose[i] = x[i][1] + ((image[i] >> 10 & 1023) - 512) * yprd;
+ ptr = dchoose;
+ nstride = 1;
} else if (thresh_array[ithresh] == ZU) {
double **x = atom->x;
- int *image = atom->image;
- double zprd = domain->zprd;
- for (i = 0; i < nlocal; i++)
- dchoose[i] = x[i][2] + ((image[i] >> 20) - 512) * zprd;
- ptr = dchoose;
- nstride = 1;
+ int *image = atom->image;
+ double zprd = domain->zprd;
+ for (i = 0; i < nlocal; i++)
+ dchoose[i] = x[i][2] + ((image[i] >> 20) - 512) * zprd;
+ ptr = dchoose;
+ nstride = 1;
} else if (thresh_array[ithresh] == XUTRI) {
double **x = atom->x;
- int *image = atom->image;
- double *h = domain->h;
- int xbox,ybox,zbox;
- for (i = 0; i < nlocal; i++) {
- xbox = (image[i] & 1023) - 512;
- ybox = (image[i] >> 10 & 1023) - 512;
- zbox = (image[i] >> 20) - 512;
- dchoose[i] = x[i][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox;
- }
- ptr = dchoose;
- nstride = 1;
+ int *image = atom->image;
+ double *h = domain->h;
+ int xbox,ybox,zbox;
+ for (i = 0; i < nlocal; i++) {
+ xbox = (image[i] & 1023) - 512;
+ ybox = (image[i] >> 10 & 1023) - 512;
+ zbox = (image[i] >> 20) - 512;
+ dchoose[i] = x[i][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox;
+ }
+ ptr = dchoose;
+ nstride = 1;
} else if (thresh_array[ithresh] == YUTRI) {
double **x = atom->x;
- int *image = atom->image;
- double *h = domain->h;
- int ybox,zbox;
- for (i = 0; i < nlocal; i++) {
- ybox = (image[i] >> 10 & 1023) - 512;
- zbox = (image[i] >> 20) - 512;
- dchoose[i] = x[i][1] + h[1]*ybox + h[3]*zbox;
- }
- ptr = dchoose;
- nstride = 1;
+ int *image = atom->image;
+ double *h = domain->h;
+ int ybox,zbox;
+ for (i = 0; i < nlocal; i++) {
+ ybox = (image[i] >> 10 & 1023) - 512;
+ zbox = (image[i] >> 20) - 512;
+ dchoose[i] = x[i][1] + h[1]*ybox + h[3]*zbox;
+ }
+ ptr = dchoose;
+ nstride = 1;
} else if (thresh_array[ithresh] == ZUTRI) {
double **x = atom->x;
- int *image = atom->image;
- double *h = domain->h;
- int zbox;
- for (i = 0; i < nlocal; i++) {
- zbox = (image[i] >> 20) - 512;
- dchoose[i] = x[i][2] + h[2]*zbox;
- }
- ptr = dchoose;
- nstride = 1;
+ int *image = atom->image;
+ double *h = domain->h;
+ int zbox;
+ for (i = 0; i < nlocal; i++) {
+ zbox = (image[i] >> 20) - 512;
+ dchoose[i] = x[i][2] + h[2]*zbox;
+ }
+ ptr = dchoose;
+ nstride = 1;
} else if (thresh_array[ithresh] == XSU) {
double **x = atom->x;
- int *image = atom->image;
- double boxxlo = domain->boxlo[0];
- double invxprd = 1.0/domain->xprd;
- for (i = 0; i < nlocal; i++)
- dchoose[i] = (x[i][0] - boxxlo) * invxprd + (image[i] & 1023) - 512;
- ptr = dchoose;
- nstride = 1;
+ int *image = atom->image;
+ double boxxlo = domain->boxlo[0];
+ double invxprd = 1.0/domain->xprd;
+ for (i = 0; i < nlocal; i++)
+ dchoose[i] = (x[i][0] - boxxlo) * invxprd + (image[i] & 1023) - 512;
+ ptr = dchoose;
+ nstride = 1;
} else if (thresh_array[ithresh] == YSU) {
double **x = atom->x;
- int *image = atom->image;
- double boxylo = domain->boxlo[1];
- double invyprd = 1.0/domain->yprd;
- for (i = 0; i < nlocal; i++)
- dchoose[i] =
- (x[i][1] - boxylo) * invyprd + (image[i] >> 10 & 1023) - 512;
- ptr = dchoose;
- nstride = 1;
+ int *image = atom->image;
+ double boxylo = domain->boxlo[1];
+ double invyprd = 1.0/domain->yprd;
+ for (i = 0; i < nlocal; i++)
+ dchoose[i] =
+ (x[i][1] - boxylo) * invyprd + (image[i] >> 10 & 1023) - 512;
+ ptr = dchoose;
+ nstride = 1;
} else if (thresh_array[ithresh] == ZSU) {
double **x = atom->x;
- int *image = atom->image;
- double boxzlo = domain->boxlo[2];
- double invzprd = 1.0/domain->zprd;
- for (i = 0; i < nlocal; i++)
- dchoose[i] = (x[i][2] - boxzlo) * invzprd + (image[i] >> 20) - 512;
- ptr = dchoose;
- nstride = 1;
+ int *image = atom->image;
+ double boxzlo = domain->boxlo[2];
+ double invzprd = 1.0/domain->zprd;
+ for (i = 0; i < nlocal; i++)
+ dchoose[i] = (x[i][2] - boxzlo) * invzprd + (image[i] >> 20) - 512;
+ ptr = dchoose;
+ nstride = 1;
} else if (thresh_array[ithresh] == XSUTRI) {
double **x = atom->x;
- int *image = atom->image;
- double *boxlo = domain->boxlo;
- double *h_inv = domain->h_inv;
- for (i = 0; i < nlocal; i++)
- dchoose[i] = h_inv[0]*(x[i][0]-boxlo[0]) +
- h_inv[5]*(x[i][1]-boxlo[1]) +
- h_inv[4]*(x[i][2]-boxlo[2]) +
- (image[i] & 1023) - 512;
- ptr = dchoose;
- nstride = 1;
+ int *image = atom->image;
+ double *boxlo = domain->boxlo;
+ double *h_inv = domain->h_inv;
+ for (i = 0; i < nlocal; i++)
+ dchoose[i] = h_inv[0]*(x[i][0]-boxlo[0]) +
+ h_inv[5]*(x[i][1]-boxlo[1]) +
+ h_inv[4]*(x[i][2]-boxlo[2]) +
+ (image[i] & 1023) - 512;
+ ptr = dchoose;
+ nstride = 1;
} else if (thresh_array[ithresh] == YSUTRI) {
double **x = atom->x;
- int *image = atom->image;
- double *boxlo = domain->boxlo;
- double *h_inv = domain->h_inv;
- for (i = 0; i < nlocal; i++)
- dchoose[i] = h_inv[1]*(x[i][1]-boxlo[1]) +
- h_inv[3]*(x[i][2]-boxlo[2]) +
- (image[i] >> 10 & 1023) - 512;
- ptr = dchoose;
- nstride = 1;
+ int *image = atom->image;
+ double *boxlo = domain->boxlo;
+ double *h_inv = domain->h_inv;
+ for (i = 0; i < nlocal; i++)
+ dchoose[i] = h_inv[1]*(x[i][1]-boxlo[1]) +
+ h_inv[3]*(x[i][2]-boxlo[2]) +
+ (image[i] >> 10 & 1023) - 512;
+ ptr = dchoose;
+ nstride = 1;
} else if (thresh_array[ithresh] == ZSUTRI) {
double **x = atom->x;
- int *image = atom->image;
- double *boxlo = domain->boxlo;
- double *h_inv = domain->h_inv;
- for (i = 0; i < nlocal; i++)
- dchoose[i] = h_inv[2]*(x[i][2]-boxlo[2]) +
- (image[i] >> 20) - 512;
- ptr = dchoose;
- nstride = 1;
+ int *image = atom->image;
+ double *boxlo = domain->boxlo;
+ double *h_inv = domain->h_inv;
+ for (i = 0; i < nlocal; i++)
+ dchoose[i] = h_inv[2]*(x[i][2]-boxlo[2]) +
+ (image[i] >> 20) - 512;
+ ptr = dchoose;
+ nstride = 1;
} else if (thresh_array[ithresh] == IX) {
- int *image = atom->image;
- for (i = 0; i < nlocal; i++)
- dchoose[i] = (image[i] & 1023) - 512;
- ptr = dchoose;
- nstride = 1;
+ int *image = atom->image;
+ for (i = 0; i < nlocal; i++)
+ dchoose[i] = (image[i] & 1023) - 512;
+ ptr = dchoose;
+ nstride = 1;
} else if (thresh_array[ithresh] == IY) {
- int *image = atom->image;
- for (i = 0; i < nlocal; i++)
- dchoose[i] = (image[i] >> 10 & 1023) - 512;
- ptr = dchoose;
- nstride = 1;
+ int *image = atom->image;
+ for (i = 0; i < nlocal; i++)
+ dchoose[i] = (image[i] >> 10 & 1023) - 512;
+ ptr = dchoose;
+ nstride = 1;
} else if (thresh_array[ithresh] == IZ) {
- int *image = atom->image;
- for (i = 0; i < nlocal; i++)
- dchoose[i] = (image[i] >> 20) - 512;
- ptr = dchoose;
- nstride = 1;
+ int *image = atom->image;
+ for (i = 0; i < nlocal; i++)
+ dchoose[i] = (image[i] >> 20) - 512;
+ ptr = dchoose;
+ nstride = 1;
} else if (thresh_array[ithresh] == VX) {
- ptr = &atom->v[0][0];
- nstride = 3;
+ ptr = &atom->v[0][0];
+ nstride = 3;
} else if (thresh_array[ithresh] == VY) {
- ptr = &atom->v[0][1];
- nstride = 3;
+ ptr = &atom->v[0][1];
+ nstride = 3;
} else if (thresh_array[ithresh] == VZ) {
- ptr = &atom->v[0][2];
- nstride = 3;
+ ptr = &atom->v[0][2];
+ nstride = 3;
} else if (thresh_array[ithresh] == FX) {
- ptr = &atom->f[0][0];
- nstride = 3;
+ ptr = &atom->f[0][0];
+ nstride = 3;
} else if (thresh_array[ithresh] == FY) {
- ptr = &atom->f[0][1];
- nstride = 3;
+ ptr = &atom->f[0][1];
+ nstride = 3;
} else if (thresh_array[ithresh] == FZ) {
- ptr = &atom->f[0][2];
- nstride = 3;
+ ptr = &atom->f[0][2];
+ nstride = 3;
} else if (thresh_array[ithresh] == Q) {
- if (!atom->q_flag)
- error->all(FLERR,
- "Threshhold for an atom property that isn't allocated");
- ptr = atom->q;
- nstride = 1;
+ if (!atom->q_flag)
+ error->all(FLERR,
+ "Threshhold for an atom property that isn't allocated");
+ ptr = atom->q;
+ nstride = 1;
} else if (thresh_array[ithresh] == MUX) {
- if (!atom->mu_flag)
- error->all(FLERR,
- "Threshhold for an atom property that isn't allocated");
- ptr = &atom->mu[0][0];
- nstride = 4;
+ if (!atom->mu_flag)
+ error->all(FLERR,
+ "Threshhold for an atom property that isn't allocated");
+ ptr = &atom->mu[0][0];
+ nstride = 4;
} else if (thresh_array[ithresh] == MUY) {
- if (!atom->mu_flag)
- error->all(FLERR,
- "Threshhold for an atom property that isn't allocated");
- ptr = &atom->mu[0][1];
- nstride = 4;
+ if (!atom->mu_flag)
+ error->all(FLERR,
+ "Threshhold for an atom property that isn't allocated");
+ ptr = &atom->mu[0][1];
+ nstride = 4;
} else if (thresh_array[ithresh] == MUZ) {
- if (!atom->mu_flag)
- error->all(FLERR,
- "Threshhold for an atom property that isn't allocated");
- ptr = &atom->mu[0][2];
- nstride = 4;
+ if (!atom->mu_flag)
+ error->all(FLERR,
+ "Threshhold for an atom property that isn't allocated");
+ ptr = &atom->mu[0][2];
+ nstride = 4;
} else if (thresh_array[ithresh] == MU) {
- if (!atom->mu_flag)
- error->all(FLERR,
- "Threshhold for an atom property that isn't allocated");
- ptr = &atom->mu[0][3];
- nstride = 4;
+ if (!atom->mu_flag)
+ error->all(FLERR,
+ "Threshhold for an atom property that isn't allocated");
+ ptr = &atom->mu[0][3];
+ nstride = 4;
} else if (thresh_array[ithresh] == RADIUS) {
- if (!atom->radius_flag)
- error->all(FLERR,
- "Threshhold for an atom property that isn't allocated");
- ptr = atom->radius;
- nstride = 1;
+ if (!atom->radius_flag)
+ error->all(FLERR,
+ "Threshhold for an atom property that isn't allocated");
+ ptr = atom->radius;
+ nstride = 1;
} else if (thresh_array[ithresh] == DIAMETER) {
- if (!atom->radius_flag)
- error->all(FLERR,
- "Threshhold for an atom property that isn't allocated");
- double *radius = atom->radius;
- for (i = 0; i < nlocal; i++) dchoose[i] = 2.0*radius[i];
- ptr = dchoose;
- nstride = 1;
+ if (!atom->radius_flag)
+ error->all(FLERR,
+ "Threshhold for an atom property that isn't allocated");
+ double *radius = atom->radius;
+ for (i = 0; i < nlocal; i++) dchoose[i] = 2.0*radius[i];
+ ptr = dchoose;
+ nstride = 1;
} else if (thresh_array[ithresh] == OMEGAX) {
- if (!atom->omega_flag)
- error->all(FLERR,
- "Threshhold for an atom property that isn't allocated");
- ptr = &atom->omega[0][0];
- nstride = 3;
+ if (!atom->omega_flag)
+ error->all(FLERR,
+ "Threshhold for an atom property that isn't allocated");
+ ptr = &atom->omega[0][0];
+ nstride = 3;
} else if (thresh_array[ithresh] == OMEGAY) {
- if (!atom->omega_flag)
- error->all(FLERR,
- "Threshhold for an atom property that isn't allocated");
- ptr = &atom->omega[0][1];
- nstride = 3;
+ if (!atom->omega_flag)
+ error->all(FLERR,
+ "Threshhold for an atom property that isn't allocated");
+ ptr = &atom->omega[0][1];
+ nstride = 3;
} else if (thresh_array[ithresh] == OMEGAZ) {
- if (!atom->omega_flag)
- error->all(FLERR,
- "Threshhold for an atom property that isn't allocated");
- ptr = &atom->omega[0][2];
- nstride = 3;
+ if (!atom->omega_flag)
+ error->all(FLERR,
+ "Threshhold for an atom property that isn't allocated");
+ ptr = &atom->omega[0][2];
+ nstride = 3;
} else if (thresh_array[ithresh] == ANGMOMX) {
- if (!atom->angmom_flag)
- error->all(FLERR,
- "Threshhold for an atom property that isn't allocated");
- ptr = &atom->angmom[0][0];
- nstride = 3;
+ if (!atom->angmom_flag)
+ error->all(FLERR,
+ "Threshhold for an atom property that isn't allocated");
+ ptr = &atom->angmom[0][0];
+ nstride = 3;
} else if (thresh_array[ithresh] == ANGMOMY) {
- if (!atom->angmom_flag)
- error->all(FLERR,
- "Threshhold for an atom property that isn't allocated");
- ptr = &atom->angmom[0][1];
- nstride = 3;
+ if (!atom->angmom_flag)
+ error->all(FLERR,
+ "Threshhold for an atom property that isn't allocated");
+ ptr = &atom->angmom[0][1];
+ nstride = 3;
} else if (thresh_array[ithresh] == ANGMOMZ) {
- if (!atom->angmom_flag)
- error->all(FLERR,
- "Threshhold for an atom property that isn't allocated");
- ptr = &atom->angmom[0][2];
- nstride = 3;
+ if (!atom->angmom_flag)
+ error->all(FLERR,
+ "Threshhold for an atom property that isn't allocated");
+ ptr = &atom->angmom[0][2];
+ nstride = 3;
} else if (thresh_array[ithresh] == TQX) {
- if (!atom->torque_flag)
- error->all(FLERR,
- "Threshhold for an atom property that isn't allocated");
- ptr = &atom->torque[0][0];
- nstride = 3;
+ if (!atom->torque_flag)
+ error->all(FLERR,
+ "Threshhold for an atom property that isn't allocated");
+ ptr = &atom->torque[0][0];
+ nstride = 3;
} else if (thresh_array[ithresh] == TQY) {
- if (!atom->torque_flag)
- error->all(FLERR,
- "Threshhold for an atom property that isn't allocated");
- ptr = &atom->torque[0][1];
- nstride = 3;
+ if (!atom->torque_flag)
+ error->all(FLERR,
+ "Threshhold for an atom property that isn't allocated");
+ ptr = &atom->torque[0][1];
+ nstride = 3;
} else if (thresh_array[ithresh] == TQZ) {
- if (!atom->torque_flag)
- error->all(FLERR,
- "Threshhold for an atom property that isn't allocated");
- ptr = &atom->torque[0][2];
- nstride = 3;
+ if (!atom->torque_flag)
+ error->all(FLERR,
+ "Threshhold for an atom property that isn't allocated");
+ ptr = &atom->torque[0][2];
+ nstride = 3;
} else if (thresh_array[ithresh] == SPIN) {
- if (!atom->spin_flag)
- error->all(FLERR,
- "Threshhold for an atom property that isn't allocated");
+ if (!atom->spin_flag)
+ error->all(FLERR,
+ "Threshhold for an atom property that isn't allocated");
int *spin = atom->spin;
for (i = 0; i < nlocal; i++) dchoose[i] = spin[i];
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == ERADIUS) {
- if (!atom->eradius_flag)
- error->all(FLERR,
- "Threshhold for an atom property that isn't allocated");
+ if (!atom->eradius_flag)
+ error->all(FLERR,
+ "Threshhold for an atom property that isn't allocated");
ptr = atom->eradius;
nstride = 1;
} else if (thresh_array[ithresh] == ERVEL) {
- if (!atom->ervel_flag)
- error->all(FLERR,
- "Threshhold for an atom property that isn't allocated");
+ if (!atom->ervel_flag)
+ error->all(FLERR,
+ "Threshhold for an atom property that isn't allocated");
ptr = atom->ervel;
nstride = 1;
} else if (thresh_array[ithresh] == ERFORCE) {
- if (!atom->erforce_flag)
- error->all(FLERR,
- "Threshhold for an atom property that isn't allocated");
+ if (!atom->erforce_flag)
+ error->all(FLERR,
+ "Threshhold for an atom property that isn't allocated");
ptr = atom->erforce;
- nstride = 1;
+ nstride = 1;
} else if (thresh_array[ithresh] == COMPUTE) {
- i = nfield + ithresh;
- if (argindex[i] == 0) {
- ptr = compute[field2index[i]]->vector_atom;
- nstride = 1;
- } else {
- ptr = &compute[field2index[i]]->array_atom[0][argindex[i]-1];
- nstride = compute[field2index[i]]->size_peratom_cols;
- }
+ i = nfield + ithresh;
+ if (argindex[i] == 0) {
+ ptr = compute[field2index[i]]->vector_atom;
+ nstride = 1;
+ } else {
+ ptr = &compute[field2index[i]]->array_atom[0][argindex[i]-1];
+ nstride = compute[field2index[i]]->size_peratom_cols;
+ }
} else if (thresh_array[ithresh] == FIX) {
- i = nfield + ithresh;
- if (argindex[i] == 0) {
- ptr = fix[field2index[i]]->vector_atom;
- nstride = 1;
- } else {
- ptr = &fix[field2index[i]]->array_atom[0][argindex[i]-1];
- nstride = fix[field2index[i]]->size_peratom_cols;
- }
+ i = nfield + ithresh;
+ if (argindex[i] == 0) {
+ ptr = fix[field2index[i]]->vector_atom;
+ nstride = 1;
+ } else {
+ ptr = &fix[field2index[i]]->array_atom[0][argindex[i]-1];
+ nstride = fix[field2index[i]]->size_peratom_cols;
+ }
} else if (thresh_array[ithresh] == VARIABLE) {
- i = nfield + ithresh;
- ptr = vbuf[field2index[i]];
- nstride = 1;
+ i = nfield + ithresh;
+ ptr = vbuf[field2index[i]];
+ nstride = 1;
}
// unselect atoms that don't meet threshhold criterion
@@ -853,23 +853,23 @@ int DumpCustom::count()
value = thresh_value[ithresh];
if (thresh_op[ithresh] == LT) {
- for (i = 0; i < nlocal; i++, ptr += nstride)
- if (choose[i] && *ptr >= value) choose[i] = 0;
+ for (i = 0; i < nlocal; i++, ptr += nstride)
+ if (choose[i] && *ptr >= value) choose[i] = 0;
} else if (thresh_op[ithresh] == LE) {
- for (i = 0; i < nlocal; i++, ptr += nstride)
- if (choose[i] && *ptr > value) choose[i] = 0;
+ for (i = 0; i < nlocal; i++, ptr += nstride)
+ if (choose[i] && *ptr > value) choose[i] = 0;
} else if (thresh_op[ithresh] == GT) {
- for (i = 0; i < nlocal; i++, ptr += nstride)
- if (choose[i] && *ptr <= value) choose[i] = 0;
+ for (i = 0; i < nlocal; i++, ptr += nstride)
+ if (choose[i] && *ptr <= value) choose[i] = 0;
} else if (thresh_op[ithresh] == GE) {
- for (i = 0; i < nlocal; i++, ptr += nstride)
- if (choose[i] && *ptr < value) choose[i] = 0;
+ for (i = 0; i < nlocal; i++, ptr += nstride)
+ if (choose[i] && *ptr < value) choose[i] = 0;
} else if (thresh_op[ithresh] == EQ) {
- for (i = 0; i < nlocal; i++, ptr += nstride)
- if (choose[i] && *ptr != value) choose[i] = 0;
+ for (i = 0; i < nlocal; i++, ptr += nstride)
+ if (choose[i] && *ptr != value) choose[i] = 0;
} else if (thresh_op[ithresh] == NEQ) {
- for (i = 0; i < nlocal; i++, ptr += nstride)
- if (choose[i] && *ptr == value) choose[i] = 0;
+ for (i = 0; i < nlocal; i++, ptr += nstride)
+ if (choose[i] && *ptr == value) choose[i] = 0;
}
}
}
@@ -924,8 +924,8 @@ void DumpCustom::write_text(int n, double *mybuf)
for (j = 0; j < size_one; j++) {
if (vtype[j] == INT) fprintf(fp,vformat[j],static_cast<int> (mybuf[m]));
else if (vtype[j] == DOUBLE) fprintf(fp,vformat[j],mybuf[m]);
- else if (vtype[j] == STRING)
- fprintf(fp,vformat[j],typenames[(int) mybuf[m]]);
+ else if (vtype[j] == STRING)
+ fprintf(fp,vformat[j],typenames[(int) mybuf[m]]);
m++;
}
fprintf(fp,"\n");
@@ -947,7 +947,7 @@ int DumpCustom::parse_fields(int narg, char **arg)
vtype[i] = INT;
} else if (strcmp(arg[iarg],"mol") == 0) {
if (!atom->molecule_flag)
- error->all(FLERR,"Dumping an atom property that isn't allocated");
+ error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[i] = &DumpCustom::pack_molecule;
vtype[i] = INT;
} else if (strcmp(arg[iarg],"type") == 0) {
@@ -1036,83 +1036,83 @@ int DumpCustom::parse_fields(int narg, char **arg)
} else if (strcmp(arg[iarg],"q") == 0) {
if (!atom->q_flag)
- error->all(FLERR,"Dumping an atom property that isn't allocated");
+ error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[i] = &DumpCustom::pack_q;
vtype[i] = DOUBLE;
} else if (strcmp(arg[iarg],"mux") == 0) {
if (!atom->mu_flag)
- error->all(FLERR,"Dumping an atom property that isn't allocated");
+ error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[i] = &DumpCustom::pack_mux;
vtype[i] = DOUBLE;
} else if (strcmp(arg[iarg],"muy") == 0) {
if (!atom->mu_flag)
- error->all(FLERR,"Dumping an atom property that isn't allocated");
+ error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[i] = &DumpCustom::pack_muy;
vtype[i] = DOUBLE;
} else if (strcmp(arg[iarg],"muz") == 0) {
if (!atom->mu_flag)
- error->all(FLERR,"Dumping an atom property that isn't allocated");
+ error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[i] = &DumpCustom::pack_muz;
vtype[i] = DOUBLE;
} else if (strcmp(arg[iarg],"mu") == 0) {
if (!atom->mu_flag)
- error->all(FLERR,"Dumping an atom property that isn't allocated");
+ error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[i] = &DumpCustom::pack_mu;
vtype[i] = DOUBLE;
} else if (strcmp(arg[iarg],"radius") == 0) {
if (!atom->radius_flag)
- error->all(FLERR,"Dumping an atom property that isn't allocated");
+ error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[i] = &DumpCustom::pack_radius;
vtype[i] = DOUBLE;
} else if (strcmp(arg[iarg],"diameter") == 0) {
if (!atom->radius_flag)
- error->all(FLERR,"Dumping an atom property that isn't allocated");
+ error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[i] = &DumpCustom::pack_diameter;
vtype[i] = DOUBLE;
} else if (strcmp(arg[iarg],"omegax") == 0) {
if (!atom->omega_flag)
- error->all(FLERR,"Dumping an atom property that isn't allocated");
+ error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[i] = &DumpCustom::pack_omegax;
vtype[i] = DOUBLE;
} else if (strcmp(arg[iarg],"omegay") == 0) {
if (!atom->omega_flag)
- error->all(FLERR,"Dumping an atom property that isn't allocated");
+ error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[i] = &DumpCustom::pack_omegay;
vtype[i] = DOUBLE;
} else if (strcmp(arg[iarg],"omegaz") == 0) {
if (!atom->omega_flag)
- error->all(FLERR,"Dumping an atom property that isn't allocated");
+ error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[i] = &DumpCustom::pack_omegaz;
vtype[i] = DOUBLE;
} else if (strcmp(arg[iarg],"angmomx") == 0) {
if (!atom->angmom_flag)
- error->all(FLERR,"Dumping an atom property that isn't allocated");
+ error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[i] = &DumpCustom::pack_angmomx;
vtype[i] = DOUBLE;
} else if (strcmp(arg[iarg],"angmomy") == 0) {
if (!atom->angmom_flag)
- error->all(FLERR,"Dumping an atom property that isn't allocated");
+ error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[i] = &DumpCustom::pack_angmomy;
vtype[i] = DOUBLE;
} else if (strcmp(arg[iarg],"angmomz") == 0) {
if (!atom->angmom_flag)
- error->all(FLERR,"Dumping an atom property that isn't allocated");
+ error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[i] = &DumpCustom::pack_angmomz;
vtype[i] = DOUBLE;
} else if (strcmp(arg[iarg],"tqx") == 0) {
if (!atom->torque_flag)
- error->all(FLERR,"Dumping an atom property that isn't allocated");
+ error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[i] = &DumpCustom::pack_tqx;
vtype[i] = DOUBLE;
} else if (strcmp(arg[iarg],"tqy") == 0) {
if (!atom->torque_flag)
- error->all(FLERR,"Dumping an atom property that isn't allocated");
+ error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[i] = &DumpCustom::pack_tqy;
vtype[i] = DOUBLE;
} else if (strcmp(arg[iarg],"tqz") == 0) {
if (!atom->torque_flag)
- error->all(FLERR,"Dumping an atom property that isn't allocated");
+ error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[i] = &DumpCustom::pack_tqz;
vtype[i] = DOUBLE;
@@ -1150,27 +1150,27 @@ int DumpCustom::parse_fields(int narg, char **arg)
char *ptr = strchr(suffix,'[');
if (ptr) {
- if (suffix[strlen(suffix)-1] != ']')
- error->all(FLERR,"Invalid attribute in dump custom command");
- argindex[i] = atoi(ptr+1);
- *ptr = '\0';
+ if (suffix[strlen(suffix)-1] != ']')
+ error->all(FLERR,"Invalid attribute in dump custom command");
+ argindex[i] = atoi(ptr+1);
+ *ptr = '\0';
} else argindex[i] = 0;
n = modify->find_compute(suffix);
if (n < 0) error->all(FLERR,"Could not find dump custom compute ID");
if (modify->compute[n]->peratom_flag == 0)
- error->all(FLERR,"Dump custom compute does not compute per-atom info");
+ error->all(FLERR,"Dump custom compute does not compute per-atom info");
if (argindex[i] == 0 && modify->compute[n]->size_peratom_cols > 0)
- error->all(FLERR,"Dump custom compute does not calculate per-atom vector");
+ error->all(FLERR,"Dump custom compute does not calculate per-atom vector");
if (argindex[i] > 0 && modify->compute[n]->size_peratom_cols == 0)
- error->all(FLERR,"Dump custom compute does not calculate per-atom array");
- if (argindex[i] > 0 &&
- argindex[i] > modify->compute[n]->size_peratom_cols)
- error->all(FLERR,"Dump custom compute vector is accessed out-of-range");
+ error->all(FLERR,"Dump custom compute does not calculate per-atom array");
+ if (argindex[i] > 0 &&
+ argindex[i] > modify->compute[n]->size_peratom_cols)
+ error->all(FLERR,"Dump custom compute vector is accessed out-of-range");
field2index[i] = add_compute(suffix);
delete [] suffix;
-
+
// fix value = f_ID
// if no trailing [], then arg is set to 0, else arg is between []
@@ -1184,23 +1184,23 @@ int DumpCustom::parse_fields(int narg, char **arg)
char *ptr = strchr(suffix,'[');
if (ptr) {
- if (suffix[strlen(suffix)-1] != ']')
- error->all(FLERR,"Invalid attribute in dump custom command");
- argindex[i] = atoi(ptr+1);
- *ptr = '\0';
+ if (suffix[strlen(suffix)-1] != ']')
+ error->all(FLERR,"Invalid attribute in dump custom command");
+ argindex[i] = atoi(ptr+1);
+ *ptr = '\0';
} else argindex[i] = 0;
n = modify->find_fix(suffix);
if (n < 0) error->all(FLERR,"Could not find dump custom fix ID");
if (modify->fix[n]->peratom_flag == 0)
- error->all(FLERR,"Dump custom fix does not compute per-atom info");
+ error->all(FLERR,"Dump custom fix does not compute per-atom info");
if (argindex[i] == 0 && modify->fix[n]->size_peratom_cols > 0)
- error->all(FLERR,"Dump custom fix does not compute per-atom vector");
+ error->all(FLERR,"Dump custom fix does not compute per-atom vector");
if (argindex[i] > 0 && modify->fix[n]->size_peratom_cols == 0)
- error->all(FLERR,"Dump custom fix does not compute per-atom array");
- if (argindex[i] > 0 &&
- argindex[i] > modify->fix[n]->size_peratom_cols)
- error->all(FLERR,"Dump custom fix vector is accessed out-of-range");
+ error->all(FLERR,"Dump custom fix does not compute per-atom array");
+ if (argindex[i] > 0 &&
+ argindex[i] > modify->fix[n]->size_peratom_cols)
+ error->all(FLERR,"Dump custom fix vector is accessed out-of-range");
field2index[i] = add_fix(suffix);
delete [] suffix;
@@ -1220,7 +1220,7 @@ int DumpCustom::parse_fields(int narg, char **arg)
n = input->variable->find(suffix);
if (n < 0) error->all(FLERR,"Could not find dump custom variable name");
if (input->variable->atomstyle(n) == 0)
- error->all(FLERR,"Dump custom variable is not atom-style variable");
+ error->all(FLERR,"Dump custom variable is not atom-style variable");
field2index[i] = add_variable(suffix);
delete [] suffix;
@@ -1243,7 +1243,7 @@ int DumpCustom::add_compute(char *id)
for (icompute = 0; icompute < ncompute; icompute++)
if (strcmp(id,id_compute[icompute]) == 0) break;
if (icompute < ncompute) return icompute;
-
+
id_compute = (char **)
memory->srealloc(id_compute,(ncompute+1)*sizeof(char *),"dump:id_compute");
delete [] compute;
@@ -1268,7 +1268,7 @@ int DumpCustom::add_fix(char *id)
for (ifix = 0; ifix < nfix; ifix++)
if (strcmp(id,id_fix[ifix]) == 0) break;
if (ifix < nfix) return ifix;
-
+
id_fix = (char **)
memory->srealloc(id_fix,(nfix+1)*sizeof(char *),"dump:id_fix");
delete [] fix;
@@ -1293,10 +1293,10 @@ int DumpCustom::add_variable(char *id)
for (ivariable = 0; ivariable < nvariable; ivariable++)
if (strcmp(id,id_variable[ivariable]) == 0) break;
if (ivariable < nvariable) return ivariable;
-
+
id_variable = (char **)
memory->srealloc(id_variable,(nvariable+1)*sizeof(char *),
- "dump:id_variable");
+ "dump:id_variable");
delete [] variable;
variable = new int[nvariable+1];
delete [] vbuf;
@@ -1319,8 +1319,8 @@ int DumpCustom::modify_param(int narg, char **arg)
if (strcmp(arg[1],"none") == 0) iregion = -1;
else {
iregion = domain->find_region(arg[1]);
- if (iregion == -1)
- error->all(FLERR,"Dump_modify region ID does not exist");
+ if (iregion == -1)
+ error->all(FLERR,"Dump_modify region ID does not exist");
int n = strlen(arg[1]) + 1;
idregion = new char[n];
strcpy(idregion,arg[1]);
@@ -1351,28 +1351,28 @@ int DumpCustom::modify_param(int narg, char **arg)
if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
if (strcmp(arg[1],"none") == 0) {
if (nthresh) {
- memory->destroy(thresh_array);
- memory->destroy(thresh_op);
- memory->destroy(thresh_value);
- thresh_array = NULL;
- thresh_op = NULL;
- thresh_value = NULL;
+ memory->destroy(thresh_array);
+ memory->destroy(thresh_op);
+ memory->destroy(thresh_value);
+ thresh_array = NULL;
+ thresh_op = NULL;
+ thresh_value = NULL;
}
nthresh = 0;
return 2;
}
if (narg < 4) error->all(FLERR,"Illegal dump_modify command");
-
+
// grow threshhold arrays
-
+
memory->grow(thresh_array,nthresh+1,"dump:thresh_array");
memory->grow(thresh_op,(nthresh+1),"dump:thresh_op");
memory->grow(thresh_value,(nthresh+1),"dump:thresh_value");
// set attribute type of threshhold
// customize by adding to if statement
-
+
if (strcmp(arg[1],"id") == 0) thresh_array[nthresh] = ID;
else if (strcmp(arg[1],"mol") == 0) thresh_array[nthresh] = MOL;
else if (strcmp(arg[1],"type") == 0) thresh_array[nthresh] = TYPE;
@@ -1465,32 +1465,32 @@ int DumpCustom::modify_param(int narg, char **arg)
int n = strlen(arg[1]);
char *suffix = new char[n];
strcpy(suffix,&arg[1][2]);
-
+
char *ptr = strchr(suffix,'[');
if (ptr) {
- if (suffix[strlen(suffix)-1] != ']')
- error->all(FLERR,"Invalid attribute in dump modify command");
- argindex[nfield+nthresh] = atoi(ptr+1);
- *ptr = '\0';
+ if (suffix[strlen(suffix)-1] != ']')
+ error->all(FLERR,"Invalid attribute in dump modify command");
+ argindex[nfield+nthresh] = atoi(ptr+1);
+ *ptr = '\0';
} else argindex[nfield+nthresh] = 0;
-
+
n = modify->find_compute(suffix);
if (n < 0) error->all(FLERR,"Could not find dump modify compute ID");
if (modify->compute[n]->peratom_flag == 0)
- error->all(FLERR,
- "Dump modify compute ID does not compute per-atom info");
- if (argindex[nfield+nthresh] == 0 &&
- modify->compute[n]->size_peratom_cols > 0)
- error->all(FLERR,
- "Dump modify compute ID does not compute per-atom vector");
- if (argindex[nfield+nthresh] > 0 &&
- modify->compute[n]->size_peratom_cols == 0)
- error->all(FLERR,
- "Dump modify compute ID does not compute per-atom array");
- if (argindex[nfield+nthresh] > 0 &&
- argindex[nfield+nthresh] > modify->compute[n]->size_peratom_cols)
- error->all(FLERR,"Dump modify compute ID vector is not large enough");
+ error->all(FLERR,
+ "Dump modify compute ID does not compute per-atom info");
+ if (argindex[nfield+nthresh] == 0 &&
+ modify->compute[n]->size_peratom_cols > 0)
+ error->all(FLERR,
+ "Dump modify compute ID does not compute per-atom vector");
+ if (argindex[nfield+nthresh] > 0 &&
+ modify->compute[n]->size_peratom_cols == 0)
+ error->all(FLERR,
+ "Dump modify compute ID does not compute per-atom array");
+ if (argindex[nfield+nthresh] > 0 &&
+ argindex[nfield+nthresh] > modify->compute[n]->size_peratom_cols)
+ error->all(FLERR,"Dump modify compute ID vector is not large enough");
field2index[nfield+nthresh] = add_compute(suffix);
delete [] suffix;
@@ -1506,29 +1506,29 @@ int DumpCustom::modify_param(int narg, char **arg)
int n = strlen(arg[1]);
char *suffix = new char[n];
strcpy(suffix,&arg[1][2]);
-
+
char *ptr = strchr(suffix,'[');
if (ptr) {
- if (suffix[strlen(suffix)-1] != ']')
- error->all(FLERR,"Invalid attribute in dump modify command");
- argindex[nfield+nthresh] = atoi(ptr+1);
- *ptr = '\0';
+ if (suffix[strlen(suffix)-1] != ']')
+ error->all(FLERR,"Invalid attribute in dump modify command");
+ argindex[nfield+nthresh] = atoi(ptr+1);
+ *ptr = '\0';
} else argindex[nfield+nthresh] = 0;
-
+
n = modify->find_fix(suffix);
if (n < 0) error->all(FLERR,"Could not find dump modify fix ID");
if (modify->fix[n]->peratom_flag == 0)
- error->all(FLERR,"Dump modify fix ID does not compute per-atom info");
- if (argindex[nfield+nthresh] == 0 &&
- modify->fix[n]->size_peratom_cols > 0)
- error->all(FLERR,"Dump modify fix ID does not compute per-atom vector");
- if (argindex[nfield+nthresh] > 0 &&
- modify->fix[n]->size_peratom_cols == 0)
- error->all(FLERR,"Dump modify fix ID does not compute per-atom array");
- if (argindex[nfield+nthresh] > 0 &&
- argindex[nfield+nthresh] > modify->fix[n]->size_peratom_cols)
- error->all(FLERR,"Dump modify fix ID vector is not large enough");
+ error->all(FLERR,"Dump modify fix ID does not compute per-atom info");
+ if (argindex[nfield+nthresh] == 0 &&
+ modify->fix[n]->size_peratom_cols > 0)
+ error->all(FLERR,"Dump modify fix ID does not compute per-atom vector");
+ if (argindex[nfield+nthresh] > 0 &&
+ modify->fix[n]->size_peratom_cols == 0)
+ error->all(FLERR,"Dump modify fix ID does not compute per-atom array");
+ if (argindex[nfield+nthresh] > 0 &&
+ argindex[nfield+nthresh] > modify->fix[n]->size_peratom_cols)
+ error->all(FLERR,"Dump modify fix ID vector is not large enough");
field2index[nfield+nthresh] = add_fix(suffix);
delete [] suffix;
@@ -1543,13 +1543,13 @@ int DumpCustom::modify_param(int narg, char **arg)
int n = strlen(arg[1]);
char *suffix = new char[n];
strcpy(suffix,&arg[1][2]);
-
+
argindex[nfield+nthresh] = 0;
-
+
n = input->variable->find(suffix);
if (n < 0) error->all(FLERR,"Could not find dump modify variable name");
if (input->variable->atomstyle(n) == 0)
- error->all(FLERR,"Dump modify variable is not atom-style variable");
+ error->all(FLERR,"Dump modify variable is not atom-style variable");
field2index[nfield+nthresh] = add_variable(suffix);
delete [] suffix;
@@ -1803,7 +1803,7 @@ void DumpCustom::pack_xs_triclinic(int n)
for (int i = 0; i < nchoose; i++) {
j = clist[i];
- buf[n] = h_inv[0]*(x[j][0]-boxlo[0]) + h_inv[5]*(x[j][1]-boxlo[1]) +
+ buf[n] = h_inv[0]*(x[j][0]-boxlo[0]) + h_inv[5]*(x[j][1]-boxlo[1]) +
h_inv[4]*(x[j][2]-boxlo[2]);
n += size_one;
}
@@ -2019,7 +2019,7 @@ void DumpCustom::pack_xsu_triclinic(int n)
for (int i = 0; i < nchoose; i++) {
j = clist[i];
- buf[n] = h_inv[0]*(x[j][0]-boxlo[0]) + h_inv[5]*(x[j][1]-boxlo[1]) +
+ buf[n] = h_inv[0]*(x[j][0]-boxlo[0]) + h_inv[5]*(x[j][1]-boxlo[1]) +
h_inv[4]*(x[j][2]-boxlo[2]) + (image[j] & 1023) - 512;
n += size_one;
}
@@ -2367,7 +2367,7 @@ void DumpCustom::pack_tqz(int n)
void DumpCustom::pack_spin(int n)
{
int *spin = atom->spin;
-
+
for (int i = 0; i < nchoose; i++) {
buf[n] = spin[clist[i]];
n += size_one;
diff --git a/src/dump_custom.h b/src/dump_custom.h
index 1679aaf1256f7f064c900dc86fe1cfefe9097d42..00b5bb4dab9fd518653ac5d01beab7fc6038dd18 100644
--- a/src/dump_custom.h
+++ b/src/dump_custom.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -70,7 +70,7 @@ class DumpCustom : public Dump {
double **vbuf; // local storage for variable evaluation
int ntypes; // # of atom types
- char **typenames; // array of element names for each type
+ char **typenames; // array of element names for each type
// private methods
diff --git a/src/dump_dcd.cpp b/src/dump_dcd.cpp
index 6512229735f0ce44e6d0de460fe0f2c44c8a5a41..a758f1a6e853acd5e3a1c72e6d8b169fbcbec58f 100644
--- a/src/dump_dcd.cpp
+++ b/src/dump_dcd.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -64,7 +64,7 @@ DumpDCD::DumpDCD(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg)
unwrap_flag = 0;
format_default = NULL;
-
+
// allocate global array for atom coords
bigint n = group->count(igroup);
@@ -162,11 +162,11 @@ void DumpDCD::write_header(bigint n)
dim[5] = domain->zprd;
dim[1] = dim[3] = dim[4] = 0.0;
}
-
+
if (me == 0) {
uint32_t out_integer = 48;
fwrite_int32(fp,out_integer);
- fwrite(dim,out_integer,1,fp);
+ fwrite(dim,out_integer,1,fp);
fwrite_int32(fp,out_integer);
if (flush_flag) fflush(fp);
}
@@ -195,30 +195,30 @@ void DumpDCD::pack(int *ids)
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
- int ix = (image[i] & 1023) - 512;
- int iy = (image[i] >> 10 & 1023) - 512;
- int iz = (image[i] >> 20) - 512;
-
- if (domain->triclinic) {
- buf[m++] = x[i][0] + ix * xprd + iy * xy + iz * xz;
- buf[m++] = x[i][1] + iy * yprd + iz * yz;
- buf[m++] = x[i][2] + iz * zprd;
- } else {
- buf[m++] = x[i][0] + ix * xprd;
- buf[m++] = x[i][1] + iy * yprd;
- buf[m++] = x[i][2] + iz * zprd;
- }
- ids[n++] = tag[i];
+ int ix = (image[i] & 1023) - 512;
+ int iy = (image[i] >> 10 & 1023) - 512;
+ int iz = (image[i] >> 20) - 512;
+
+ if (domain->triclinic) {
+ buf[m++] = x[i][0] + ix * xprd + iy * xy + iz * xz;
+ buf[m++] = x[i][1] + iy * yprd + iz * yz;
+ buf[m++] = x[i][2] + iz * zprd;
+ } else {
+ buf[m++] = x[i][0] + ix * xprd;
+ buf[m++] = x[i][1] + iy * yprd;
+ buf[m++] = x[i][2] + iz * zprd;
+ }
+ ids[n++] = tag[i];
}
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- buf[m++] = x[i][0];
- buf[m++] = x[i][1];
- buf[m++] = x[i][2];
- ids[n++] = tag[i];
+ buf[m++] = x[i][0];
+ buf[m++] = x[i][1];
+ buf[m++] = x[i][2];
+ ids[n++] = tag[i];
}
}
}
@@ -286,7 +286,7 @@ void DumpDCD::write_frame()
fwrite_int32(fp,out_integer);
fwrite(zf,out_integer,1,fp);
fwrite_int32(fp,out_integer);
-
+
// update NFILE and NSTEP fields in DCD header
nframes++;
@@ -319,7 +319,7 @@ void DumpDCD::write_dcd_header(const char *remarks)
fwrite_int32(fp,ntimestep); // START = timestep of first snapshot
fwrite_int32(fp,nevery_save); // SKIP = interval between snapshots
fwrite_int32(fp,ntimestep); // NSTEP = timestep of last snapshot
- fwrite_int32(fp,0); // NAMD writes NSTEP or ISTART
+ fwrite_int32(fp,0); // NAMD writes NSTEP or ISTART
fwrite_int32(fp,0);
fwrite_int32(fp,0);
fwrite_int32(fp,0);
diff --git a/src/dump_dcd.h b/src/dump_dcd.h
index 6915068579b205424c4249d59be8b3957eac2d49..a5b88f3cafc3fdc30586504e42ee000a18ea57e5 100644
--- a/src/dump_dcd.h
+++ b/src/dump_dcd.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/dump_image.cpp b/src/dump_image.cpp
index d30db48a3411451dea8a2682882b78c0b4bfc628..c06b35e6c2a1a637535e192185341169707b90a2 100644
--- a/src/dump_image.cpp
+++ b/src/dump_image.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -42,7 +42,7 @@ enum{NO,YES};
/* ---------------------------------------------------------------------- */
-DumpImage::DumpImage(LAMMPS *lmp, int narg, char **arg) :
+DumpImage::DumpImage(LAMMPS *lmp, int narg, char **arg) :
DumpCustom(lmp, narg, arg)
{
if (binary || multiproc) error->all(FLERR,"Invalid dump image filename");
@@ -127,16 +127,16 @@ DumpImage::DumpImage(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"bond") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal dump image command");
if (atom->nbondtypes == 0)
- error->all(FLERR,"Dump image bond not allowed with no bond types");
+ error->all(FLERR,"Dump image bond not allowed with no bond types");
bondflag = YES;
if (strcmp(arg[iarg+1],"none") == 0) bondflag = NO;
else if (strcmp(arg[iarg+1],"atom") == 0) bcolor = ATOM;
else if (strcmp(arg[iarg+1],"type") == 0) bcolor = TYPE;
else error->all(FLERR,"Illegal dump image command");
if (!islower(arg[iarg+2][0])) {
- bdiam = NUMERIC;
- bdiamvalue = atof(arg[iarg+2]);
- if (bdiamvalue <= 0.0) error->all(FLERR,"Illegal dump image command");
+ bdiam = NUMERIC;
+ bdiamvalue = atof(arg[iarg+2]);
+ if (bdiamvalue <= 0.0) error->all(FLERR,"Illegal dump image command");
} else if (strcmp(arg[iarg+2],"atom") == 0) bdiam = ATOM;
else if (strcmp(arg[iarg+2],"type") == 0) bdiam = TYPE;
else if (strcmp(arg[iarg+2],"none") == 0) bondflag = NO;
@@ -147,8 +147,8 @@ DumpImage::DumpImage(LAMMPS *lmp, int narg, char **arg) :
if (iarg+3 > narg) error->all(FLERR,"Illegal dump image command");
int width = atoi(arg[iarg+1]);
int height = atoi(arg[iarg+2]);
- if (width <= 0 || height <= 0)
- error->all(FLERR,"Illegal dump image command");
+ if (width <= 0 || height <= 0)
+ error->all(FLERR,"Illegal dump image command");
image->width = width;
image->height = height;
iarg += 3;
@@ -156,24 +156,24 @@ DumpImage::DumpImage(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"view") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal dump image command");
if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) {
- int n = strlen(&arg[iarg+1][2]) + 1;
- thetastr = new char[n];
- strcpy(thetastr,&arg[iarg+1][2]);
+ int n = strlen(&arg[iarg+1][2]) + 1;
+ thetastr = new char[n];
+ strcpy(thetastr,&arg[iarg+1][2]);
} else {
- double theta = atof(arg[iarg+1]);
- if (theta < 0.0 || theta > 180.0)
- error->all(FLERR,"Invalid dump image theta value");
- theta *= MY_PI/180.0;
- image->theta = theta;
+ double theta = atof(arg[iarg+1]);
+ if (theta < 0.0 || theta > 180.0)
+ error->all(FLERR,"Invalid dump image theta value");
+ theta *= MY_PI/180.0;
+ image->theta = theta;
}
if (strstr(arg[iarg+2],"v_") == arg[iarg+2]) {
- int n = strlen(&arg[iarg+2][2]) + 1;
- phistr = new char[n];
- strcpy(phistr,&arg[iarg+2][2]);
+ int n = strlen(&arg[iarg+2][2]) + 1;
+ phistr = new char[n];
+ strcpy(phistr,&arg[iarg+2][2]);
} else {
- double phi = atof(arg[iarg+2]);
- phi *= MY_PI/180.0;
- image->phi = phi;
+ double phi = atof(arg[iarg+2]);
+ phi *= MY_PI/180.0;
+ image->phi = phi;
}
iarg += 3;
@@ -183,54 +183,54 @@ DumpImage::DumpImage(LAMMPS *lmp, int narg, char **arg) :
else if (strcmp(arg[iarg+1],"d") == 0) cflag = DYNAMIC;
else error->all(FLERR,"Illegal dump image command");
if (strstr(arg[iarg+2],"v_") == arg[iarg+2]) {
- int n = strlen(&arg[iarg+2][2]) + 1;
- cxstr = new char[n];
- strcpy(cxstr,&arg[iarg+2][2]);
- cflag = DYNAMIC;
+ int n = strlen(&arg[iarg+2][2]) + 1;
+ cxstr = new char[n];
+ strcpy(cxstr,&arg[iarg+2][2]);
+ cflag = DYNAMIC;
} else cx = atof(arg[iarg+2]);
if (strstr(arg[iarg+3],"v_") == arg[iarg+3]) {
- int n = strlen(&arg[iarg+3][2]) + 1;
- cystr = new char[n];
- strcpy(cystr,&arg[iarg+3][2]);
- cflag = DYNAMIC;
+ int n = strlen(&arg[iarg+3][2]) + 1;
+ cystr = new char[n];
+ strcpy(cystr,&arg[iarg+3][2]);
+ cflag = DYNAMIC;
} else cy = atof(arg[iarg+3]);
if (strstr(arg[iarg+4],"v_") == arg[iarg+4]) {
- int n = strlen(&arg[iarg+4][2]) + 1;
- czstr = new char[n];
- strcpy(czstr,&arg[iarg+4][2]);
- cflag = DYNAMIC;
+ int n = strlen(&arg[iarg+4][2]) + 1;
+ czstr = new char[n];
+ strcpy(czstr,&arg[iarg+4][2]);
+ cflag = DYNAMIC;
} else cz = atof(arg[iarg+4]);
iarg += 5;
} else if (strcmp(arg[iarg],"up") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal dump image command");
if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) {
- int n = strlen(&arg[iarg+1][2]) + 1;
- upxstr = new char[n];
- strcpy(upxstr,&arg[iarg+1][2]);
+ int n = strlen(&arg[iarg+1][2]) + 1;
+ upxstr = new char[n];
+ strcpy(upxstr,&arg[iarg+1][2]);
} else image->up[0] = atof(arg[iarg+1]);
if (strstr(arg[iarg+2],"v_") == arg[iarg+2]) {
- int n = strlen(&arg[iarg+2][2]) + 1;
- upystr = new char[n];
- strcpy(upystr,&arg[iarg+2][2]);
+ int n = strlen(&arg[iarg+2][2]) + 1;
+ upystr = new char[n];
+ strcpy(upystr,&arg[iarg+2][2]);
} else image->up[1] = atof(arg[iarg+2]);
if (strstr(arg[iarg+3],"v_") == arg[iarg+3]) {
- int n = strlen(&arg[iarg+3][2]) + 1;
- upzstr = new char[n];
- strcpy(upzstr,&arg[iarg+3][2]);
+ int n = strlen(&arg[iarg+3][2]) + 1;
+ upzstr = new char[n];
+ strcpy(upzstr,&arg[iarg+3][2]);
} else image->up[2] = atof(arg[iarg+3]);
iarg += 4;
} else if (strcmp(arg[iarg],"zoom") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump image command");
if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) {
- int n = strlen(&arg[iarg+1][2]) + 1;
- zoomstr = new char[n];
- strcpy(zoomstr,&arg[iarg+1][2]);
+ int n = strlen(&arg[iarg+1][2]) + 1;
+ zoomstr = new char[n];
+ strcpy(zoomstr,&arg[iarg+1][2]);
} else {
- double zoom = atof(arg[iarg+1]);
- if (zoom <= 0.0) error->all(FLERR,"Illegal dump image command");
- image->zoom = zoom;
+ double zoom = atof(arg[iarg+1]);
+ if (zoom <= 0.0) error->all(FLERR,"Illegal dump image command");
+ image->zoom = zoom;
}
iarg += 2;
@@ -238,13 +238,13 @@ DumpImage::DumpImage(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,"Dump image persp option is not yet supported");
if (iarg+2 > narg) error->all(FLERR,"Illegal dump image command");
if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) {
- int n = strlen(&arg[iarg+1][2]) + 1;
- perspstr = new char[n];
- strcpy(perspstr,&arg[iarg+1][2]);
+ int n = strlen(&arg[iarg+1][2]) + 1;
+ perspstr = new char[n];
+ strcpy(perspstr,&arg[iarg+1][2]);
} else {
- double persp = atof(arg[iarg+1]);
- if (persp < 0.0) error->all(FLERR,"Illegal dump image command");
- image->persp = persp;
+ double persp = atof(arg[iarg+1]);
+ if (persp < 0.0) error->all(FLERR,"Illegal dump image command");
+ image->persp = persp;
}
iarg += 2;
@@ -265,14 +265,14 @@ DumpImage::DumpImage(LAMMPS *lmp, int narg, char **arg) :
axeslen = atof(arg[iarg+2]);
axesdiam = atof(arg[iarg+3]);
if (axeslen < 0.0 || axesdiam < 0.0)
- error->all(FLERR,"Illegal dump image command");
+ error->all(FLERR,"Illegal dump image command");
iarg += 4;
} else if (strcmp(arg[iarg],"shiny") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump image command");
double shiny = atof(arg[iarg+1]);
if (shiny < 0.0 || shiny > 1.0)
- error->all(FLERR,"Illegal dump image command");
+ error->all(FLERR,"Illegal dump image command");
image->shiny = shiny;
iarg += 2;
@@ -286,7 +286,7 @@ DumpImage::DumpImage(LAMMPS *lmp, int narg, char **arg) :
image->seed = seed;
double ssaoint = atof(arg[iarg+3]);
if (ssaoint < 0.0 || ssaoint > 1.0)
- error->all(FLERR,"Illegal dump image command");
+ error->all(FLERR,"Illegal dump image command");
image->ssaoint = ssaoint;
iarg += 4;
@@ -341,7 +341,7 @@ DumpImage::DumpImage(LAMMPS *lmp, int narg, char **arg) :
// viewflag = DYNAMIC if any view parameter is dynamic
viewflag = STATIC;
- if (thetastr || phistr || cflag == DYNAMIC ||
+ if (thetastr || phistr || cflag == DYNAMIC ||
upxstr || upystr || upzstr || zoomstr || perspstr) viewflag = DYNAMIC;
box_bounds();
@@ -372,7 +372,7 @@ DumpImage::~DumpImage()
void DumpImage::init_style()
{
- if (multifile == 0)
+ if (multifile == 0)
error->all(FLERR,"Dump image requires one snapshot per file");
if (sort_flag) error->all(FLERR,"Dump image cannot perform sorting");
@@ -382,70 +382,70 @@ void DumpImage::init_style()
if (thetastr) {
thetavar = input->variable->find(thetastr);
- if (thetavar < 0)
+ if (thetavar < 0)
error->all(FLERR,"Variable name for dump image theta does not exist");
if (!input->variable->equalstyle(thetavar))
error->all(FLERR,"Variable for dump image theta is invalid style");
}
if (phistr) {
phivar = input->variable->find(phistr);
- if (phivar < 0)
+ if (phivar < 0)
error->all(FLERR,"Variable name for dump image phi does not exist");
if (!input->variable->equalstyle(phivar))
error->all(FLERR,"Variable for dump image phi is invalid style");
}
if (cxstr) {
cxvar = input->variable->find(cxstr);
- if (cxvar < 0)
+ if (cxvar < 0)
error->all(FLERR,"Variable name for dump image center does not exist");
if (!input->variable->equalstyle(cxvar))
error->all(FLERR,"Variable for dump image center is invalid style");
}
if (cystr) {
cyvar = input->variable->find(cystr);
- if (cyvar < 0)
+ if (cyvar < 0)
error->all(FLERR,"Variable name for dump image center does not exist");
if (!input->variable->equalstyle(cyvar))
error->all(FLERR,"Variable for dump image center is invalid style");
}
if (czstr) {
czvar = input->variable->find(czstr);
- if (czvar < 0)
+ if (czvar < 0)
error->all(FLERR,"Variable name for dump image center does not exist");
if (!input->variable->equalstyle(czvar))
error->all(FLERR,"Variable for dump image center is invalid style");
}
if (upxstr) {
upxvar = input->variable->find(upxstr);
- if (upxvar < 0)
+ if (upxvar < 0)
error->all(FLERR,"Variable name for dump image center does not exist");
if (!input->variable->equalstyle(upxvar))
error->all(FLERR,"Variable for dump image center is invalid style");
}
if (upystr) {
upyvar = input->variable->find(upystr);
- if (upyvar < 0)
+ if (upyvar < 0)
error->all(FLERR,"Variable name for dump image center does not exist");
if (!input->variable->equalstyle(upyvar))
error->all(FLERR,"Variable for dump image center is invalid style");
}
if (upzstr) {
upzvar = input->variable->find(upzstr);
- if (upzvar < 0)
+ if (upzvar < 0)
error->all(FLERR,"Variable name for dump image center does not exist");
if (!input->variable->equalstyle(upzvar))
error->all(FLERR,"Variable for dump image center is invalid style");
}
if (zoomstr) {
zoomvar = input->variable->find(zoomstr);
- if (zoomvar < 0)
+ if (zoomvar < 0)
error->all(FLERR,"Variable name for dump image zoom does not exist");
if (!input->variable->equalstyle(zoomvar))
error->all(FLERR,"Variable for dump image zoom is invalid style");
}
if (perspstr) {
perspvar = input->variable->find(perspstr);
- if (perspvar < 0)
+ if (perspvar < 0)
error->all(FLERR,"Variable name for dump image persp does not exist");
if (!input->variable->equalstyle(perspvar))
error->all(FLERR,"Variable for dump image persp is invalid style");
@@ -457,7 +457,7 @@ void DumpImage::init_style()
for (int i = 1; i <= ntypes; i++) {
colorelement[i] = image->element2color(typenames[i]);
if (colorelement[i] == NULL)
- error->all(FLERR,"Invalid dump image element name");
+ error->all(FLERR,"Invalid dump image element name");
}
}
@@ -465,7 +465,7 @@ void DumpImage::init_style()
for (int i = 1; i <= ntypes; i++) {
diamelement[i] = image->element2diam(typenames[i]);
if (diamelement[i] == 0.0)
- error->all(FLERR,"Invalid dump image element name");
+ error->all(FLERR,"Invalid dump image element name");
}
}
}
@@ -488,7 +488,7 @@ void DumpImage::write()
// pack buf with x,y,z,color,diameter
// set minmax color range if using color map
// create my portion of image for my particles
-
+
nme = count();
if (nme > maxbuf) {
@@ -602,7 +602,7 @@ void DumpImage::view_params()
/* ----------------------------------------------------------------------
create image for atoms on this proc
- every pixel has depth
+ every pixel has depth
------------------------------------------------------------------------- */
void DumpImage::create_image()
@@ -620,27 +620,27 @@ void DumpImage::create_image()
m = 0;
for (i = 0; i < nchoose; i++) {
j = clist[i];
-
+
if (acolor == TYPE) {
- itype = static_cast<int> (buf[m]);
- color = colortype[itype];
+ itype = static_cast<int> (buf[m]);
+ color = colortype[itype];
} else if (acolor == ELEMENT) {
- itype = static_cast<int> (buf[m]);
- color = colorelement[itype];
+ itype = static_cast<int> (buf[m]);
+ color = colorelement[itype];
} else if (acolor == ATTRIBUTE) {
- color = image->value2color(buf[m]);
+ color = image->value2color(buf[m]);
}
if (adiam == NUMERIC) {
- diameter = adiamvalue;
+ diameter = adiamvalue;
} else if (adiam == TYPE) {
- itype = static_cast<int> (buf[m+1]);
- diameter = diamtype[itype];
+ itype = static_cast<int> (buf[m+1]);
+ diameter = diamtype[itype];
} else if (adiam == ELEMENT) {
- itype = static_cast<int> (buf[m+1]);
- diameter = diamelement[itype];
+ itype = static_cast<int> (buf[m+1]);
+ diameter = diamelement[itype];
} else if (adiam == ATTRIBUTE) {
- diameter = buf[m+1];
+ diameter = buf[m+1];
}
image->draw_sphere(x[j],color,diameter);
@@ -671,18 +671,18 @@ void DumpImage::create_image()
if (comm_forward == 3) {
if (nall > maxbufcopy) {
- maxbufcopy = atom->nmax;
- memory->destroy(bufcopy);
- memory->create(bufcopy,maxbufcopy,2,"dump:bufcopy");
+ maxbufcopy = atom->nmax;
+ memory->destroy(bufcopy);
+ memory->create(bufcopy,maxbufcopy,2,"dump:bufcopy");
}
for (i = 0; i < nlocal; i++) bufcopy[i][0] = bufcopy[i][1] = 0.0;
m = 0;
for (i = 0; i < nchoose; i++) {
- j = clist[i];
- bufcopy[j][0] = buf[m];
- bufcopy[j][1] = buf[m+1];
- m += size_one;
+ j = clist[i];
+ bufcopy[j][0] = buf[m];
+ bufcopy[j][1] = buf[m+1];
+ m += size_one;
}
}
@@ -691,69 +691,69 @@ void DumpImage::create_image()
for (i = 0; i < nchoose; i++) {
atom1 = clist[i];
for (m = 0; m < num_bond[atom1]; m++) {
- atom2 = atom->map(bond_atom[atom1][m]);
- if (atom2 < 0 || !choose[atom2]) continue;
- if (newton_bond == 0 && tag[atom1] > tag[atom2]) continue;
- if (bond_type[atom1][m] == 0) continue;
-
- if (bcolor == ATOM) {
- if (acolor == TYPE) {
- color1 = colortype[type[atom1]];
- color2 = colortype[type[atom2]];
- } else if (acolor == ELEMENT) {
- color1 = colorelement[type[atom1]];
- color2 = colorelement[type[atom2]];
- } else if (acolor == ATTRIBUTE) {
- color1 = image->value2color(bufcopy[atom1][0]);
- color2 = image->value2color(bufcopy[atom2][0]);
- }
- } else if (bcolor == TYPE) {
- itype = bond_type[atom1][m];
- if (itype < 0) itype = -itype;
- color = bcolortype[itype];
- }
-
- if (bdiam == NUMERIC) {
- diameter = bdiamvalue;
- } else if (bdiam == ATOM) {
- if (adiam == NUMERIC) {
- diameter = adiamvalue;
- } else if (adiam == TYPE) {
- diameter = MIN(diamtype[type[atom1]],diamtype[type[atom1]]);
- } else if (adiam == ELEMENT) {
- diameter = MIN(diamelement[type[atom1]],diamelement[type[atom1]]);
- } else if (adiam == ATTRIBUTE) {
- diameter = MIN(bufcopy[atom1][1],bufcopy[atom2][1]);
- }
- } else if (bdiam == TYPE) {
- itype = bond_type[atom1][m];
- if (itype < 0) itype = -itype;
- diameter = bdiamtype[itype];
- }
-
- // draw cylinder in 2 pieces if bcolor = ATOM
- // or bond crosses periodic boundary
-
- delx = x[atom2][0] - x[atom1][0];
- dely = x[atom2][1] - x[atom1][1];
- delz = x[atom2][2] - x[atom1][2];
-
- if (bcolor == ATOM || domain->minimum_image_check(delx,dely,delz)) {
- domain->minimum_image(delx,dely,delz);
- xmid[0] = x[atom1][0] + 0.5*delx;
- xmid[1] = x[atom1][1] + 0.5*dely;
- xmid[2] = x[atom1][2] + 0.5*delz;
- if (bcolor == ATOM)
- image->draw_cylinder(x[atom1],xmid,color1,diameter,3);
- else image->draw_cylinder(x[atom1],xmid,color,diameter,3);
- xmid[0] = x[atom2][0] - 0.5*delx;
- xmid[1] = x[atom2][1] - 0.5*dely;
- xmid[2] = x[atom2][2] - 0.5*delz;
- if (bcolor == ATOM)
- image->draw_cylinder(xmid,x[atom2],color2,diameter,3);
- else image->draw_cylinder(xmid,x[atom2],color,diameter,3);
-
- } else image->draw_cylinder(x[atom1],x[atom2],color,diameter,3);
+ atom2 = atom->map(bond_atom[atom1][m]);
+ if (atom2 < 0 || !choose[atom2]) continue;
+ if (newton_bond == 0 && tag[atom1] > tag[atom2]) continue;
+ if (bond_type[atom1][m] == 0) continue;
+
+ if (bcolor == ATOM) {
+ if (acolor == TYPE) {
+ color1 = colortype[type[atom1]];
+ color2 = colortype[type[atom2]];
+ } else if (acolor == ELEMENT) {
+ color1 = colorelement[type[atom1]];
+ color2 = colorelement[type[atom2]];
+ } else if (acolor == ATTRIBUTE) {
+ color1 = image->value2color(bufcopy[atom1][0]);
+ color2 = image->value2color(bufcopy[atom2][0]);
+ }
+ } else if (bcolor == TYPE) {
+ itype = bond_type[atom1][m];
+ if (itype < 0) itype = -itype;
+ color = bcolortype[itype];
+ }
+
+ if (bdiam == NUMERIC) {
+ diameter = bdiamvalue;
+ } else if (bdiam == ATOM) {
+ if (adiam == NUMERIC) {
+ diameter = adiamvalue;
+ } else if (adiam == TYPE) {
+ diameter = MIN(diamtype[type[atom1]],diamtype[type[atom1]]);
+ } else if (adiam == ELEMENT) {
+ diameter = MIN(diamelement[type[atom1]],diamelement[type[atom1]]);
+ } else if (adiam == ATTRIBUTE) {
+ diameter = MIN(bufcopy[atom1][1],bufcopy[atom2][1]);
+ }
+ } else if (bdiam == TYPE) {
+ itype = bond_type[atom1][m];
+ if (itype < 0) itype = -itype;
+ diameter = bdiamtype[itype];
+ }
+
+ // draw cylinder in 2 pieces if bcolor = ATOM
+ // or bond crosses periodic boundary
+
+ delx = x[atom2][0] - x[atom1][0];
+ dely = x[atom2][1] - x[atom1][1];
+ delz = x[atom2][2] - x[atom1][2];
+
+ if (bcolor == ATOM || domain->minimum_image_check(delx,dely,delz)) {
+ domain->minimum_image(delx,dely,delz);
+ xmid[0] = x[atom1][0] + 0.5*delx;
+ xmid[1] = x[atom1][1] + 0.5*dely;
+ xmid[2] = x[atom1][2] + 0.5*delz;
+ if (bcolor == ATOM)
+ image->draw_cylinder(x[atom1],xmid,color1,diameter,3);
+ else image->draw_cylinder(x[atom1],xmid,color,diameter,3);
+ xmid[0] = x[atom2][0] - 0.5*delx;
+ xmid[1] = x[atom2][1] - 0.5*dely;
+ xmid[2] = x[atom2][2] - 0.5*delz;
+ if (bcolor == ATOM)
+ image->draw_cylinder(xmid,x[atom2],color2,diameter,3);
+ else image->draw_cylinder(xmid,x[atom2],color,diameter,3);
+
+ } else image->draw_cylinder(x[atom1],x[atom2],color,diameter,3);
}
}
}
@@ -803,17 +803,17 @@ void DumpImage::create_image()
} else {
domain->box_corners();
boxcorners = domain->corners;
- axes[0][0] = boxcorners[0][0];
- axes[0][1] = boxcorners[0][1];
+ axes[0][0] = boxcorners[0][0];
+ axes[0][1] = boxcorners[0][1];
axes[0][2] = boxcorners[0][2];
- axes[1][0] = boxcorners[1][0];
- axes[1][1] = boxcorners[1][1];
+ axes[1][0] = boxcorners[1][0];
+ axes[1][1] = boxcorners[1][1];
axes[1][2] = boxcorners[1][2];
- axes[2][0] = boxcorners[2][0];
- axes[2][1] = boxcorners[2][1];
+ axes[2][0] = boxcorners[2][0];
+ axes[2][1] = boxcorners[2][1];
axes[2][2] = boxcorners[2][2];
- axes[3][0] = boxcorners[4][0];
- axes[3][1] = boxcorners[4][1];
+ axes[3][0] = boxcorners[4][0];
+ axes[3][1] = boxcorners[4][1];
axes[3][2] = boxcorners[4][2];
}
@@ -917,7 +917,7 @@ int DumpImage::modify_param(int narg, char **arg)
for (int i = nlo; i <= nhi; i++) {
colortype[i] = image->color2rgb(ptrs[m%ncount]);
if (colortype[i] == NULL)
- error->all(FLERR,"Invalid color in dump_modify command");
+ error->all(FLERR,"Invalid color in dump_modify command");
m++;
}
@@ -970,21 +970,21 @@ int DumpImage::modify_param(int narg, char **arg)
ptrs[ncount++] = strtok(arg[2],"/");
while (ptrs[ncount++] = strtok(NULL,"/"));
ncount--;
-
+
// assign each of ncount colors in round-robin fashion to types
-
+
int m = 0;
for (int i = nlo; i <= nhi; i++) {
bcolortype[i] = image->color2rgb(ptrs[m%ncount]);
if (bcolortype[i] == NULL)
- error->all(FLERR,"Invalid color in dump_modify command");
+ error->all(FLERR,"Invalid color in dump_modify command");
m++;
}
-
+
delete [] ptrs;
return 3;
}
-
+
if (strcmp(arg[0],"bdiam") == 0) {
if (narg < 3) error->all(FLERR,"Illegal dump_modify command");
if (atom->nbondtypes == 0)
@@ -1010,7 +1010,7 @@ int DumpImage::modify_param(int narg, char **arg)
if (strcmp(arg[0],"boxcolor") == 0) {
if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
image->boxcolor = image->color2rgb(arg[1]);
- if (image->boxcolor == NULL)
+ if (image->boxcolor == NULL)
error->all(FLERR,"Invalid color in dump_modify command");
return 2;
}
diff --git a/src/dump_image.h b/src/dump_image.h
index fe9ad7f13c16f59c401d6805dc59292344a99a58..f8ea748d9329b2b3dfa43b89161b7a8a5b7a1534 100644
--- a/src/dump_image.h
+++ b/src/dump_image.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/dump_local.cpp b/src/dump_local.cpp
index f44781194a4bc594cc8428a2d9b0778bfa3367e0..331ee1e4d41b14de05925c9cc6feb01891d43f04 100644
--- a/src/dump_local.cpp
+++ b/src/dump_local.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -32,7 +32,7 @@ enum{INT,DOUBLE};
/* ---------------------------------------------------------------------- */
-DumpLocal::DumpLocal(LAMMPS *lmp, int narg, char **arg) :
+DumpLocal::DumpLocal(LAMMPS *lmp, int narg, char **arg) :
Dump(lmp, narg, arg)
{
if (narg == 5) error->all(FLERR,"No dump local arguments specified");
@@ -209,8 +209,8 @@ int DumpLocal::count()
if (ncompute) {
for (i = 0; i < ncompute; i++) {
if (!(compute[i]->invoked_flag & INVOKED_LOCAL)) {
- compute[i]->compute_local();
- compute[i]->invoked_flag |= INVOKED_LOCAL;
+ compute[i]->compute_local();
+ compute[i]->invoked_flag |= INVOKED_LOCAL;
}
}
}
@@ -289,27 +289,27 @@ void DumpLocal::parse_fields(int narg, char **arg)
char *ptr = strchr(suffix,'[');
if (ptr) {
- if (suffix[strlen(suffix)-1] != ']')
- error->all(FLERR,"Invalid attribute in dump local command");
- argindex[i] = atoi(ptr+1);
- *ptr = '\0';
+ if (suffix[strlen(suffix)-1] != ']')
+ error->all(FLERR,"Invalid attribute in dump local command");
+ argindex[i] = atoi(ptr+1);
+ *ptr = '\0';
} else argindex[i] = 0;
n = modify->find_compute(suffix);
if (n < 0) error->all(FLERR,"Could not find dump local compute ID");
if (modify->compute[n]->local_flag == 0)
- error->all(FLERR,"Dump local compute does not compute local info");
+ error->all(FLERR,"Dump local compute does not compute local info");
if (argindex[i] == 0 && modify->compute[n]->size_local_cols > 0)
- error->all(FLERR,"Dump local compute does not calculate local vector");
+ error->all(FLERR,"Dump local compute does not calculate local vector");
if (argindex[i] > 0 && modify->compute[n]->size_local_cols == 0)
- error->all(FLERR,"Dump local compute does not calculate local array");
- if (argindex[i] > 0 &&
- argindex[i] > modify->compute[n]->size_local_cols)
- error->all(FLERR,"Dump local compute vector is accessed out-of-range");
+ error->all(FLERR,"Dump local compute does not calculate local array");
+ if (argindex[i] > 0 &&
+ argindex[i] > modify->compute[n]->size_local_cols)
+ error->all(FLERR,"Dump local compute vector is accessed out-of-range");
field2index[i] = add_compute(suffix);
delete [] suffix;
-
+
// fix value = f_ID
// if no trailing [], then arg is set to 0, else arg is between []
@@ -324,23 +324,23 @@ void DumpLocal::parse_fields(int narg, char **arg)
char *ptr = strchr(suffix,'[');
if (ptr) {
- if (suffix[strlen(suffix)-1] != ']')
- error->all(FLERR,"Invalid attribute in dump local command");
- argindex[i] = atoi(ptr+1);
- *ptr = '\0';
+ if (suffix[strlen(suffix)-1] != ']')
+ error->all(FLERR,"Invalid attribute in dump local command");
+ argindex[i] = atoi(ptr+1);
+ *ptr = '\0';
} else argindex[i] = 0;
n = modify->find_fix(suffix);
if (n < 0) error->all(FLERR,"Could not find dump local fix ID");
if (modify->fix[n]->local_flag == 0)
- error->all(FLERR,"Dump local fix does not compute local info");
+ error->all(FLERR,"Dump local fix does not compute local info");
if (argindex[i] == 0 && modify->fix[n]->size_local_cols > 0)
- error->all(FLERR,"Dump local fix does not compute local vector");
+ error->all(FLERR,"Dump local fix does not compute local vector");
if (argindex[i] > 0 && modify->fix[n]->size_local_cols == 0)
- error->all(FLERR,"Dump local fix does not compute local array");
- if (argindex[i] > 0 &&
- argindex[i] > modify->fix[n]->size_local_cols)
- error->all(FLERR,"Dump local fix vector is accessed out-of-range");
+ error->all(FLERR,"Dump local fix does not compute local array");
+ if (argindex[i] > 0 &&
+ argindex[i] > modify->fix[n]->size_local_cols)
+ error->all(FLERR,"Dump local fix vector is accessed out-of-range");
field2index[i] = add_fix(suffix);
delete [] suffix;
@@ -364,7 +364,7 @@ int DumpLocal::add_compute(char *id)
for (icompute = 0; icompute < ncompute; icompute++)
if (strcmp(id,id_compute[icompute]) == 0) break;
if (icompute < ncompute) return icompute;
-
+
id_compute = (char **)
memory->srealloc(id_compute,(ncompute+1)*sizeof(char *),"dump:id_compute");
delete [] compute;
@@ -389,7 +389,7 @@ int DumpLocal::add_fix(char *id)
for (ifix = 0; ifix < nfix; ifix++)
if (strcmp(id,id_fix[ifix]) == 0) break;
if (ifix < nfix) return ifix;
-
+
id_fix = (char **)
memory->srealloc(id_fix,(nfix+1)*sizeof(char *),"dump:id_fix");
delete [] fix;
diff --git a/src/dump_local.h b/src/dump_local.h
index 8fe10ca136b723d2c013821b27a1c2e8e0a27f3f..75ea54c8e351df54c5d1f7d4ee7bc7aaa39667db 100644
--- a/src/dump_local.h
+++ b/src/dump_local.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/dump_xyz.cpp b/src/dump_xyz.cpp
index 8d9cd6b15163f801d8ff06d24822ac5bf318175c..65504b6798823fc0920186e7374e7368bdc82d5e 100644
--- a/src/dump_xyz.cpp
+++ b/src/dump_xyz.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -98,7 +98,7 @@ int DumpXYZ::modify_param(int narg, char **arg)
if (typenames) {
for (int i = 1; i <= ntypes; i++)
- delete [] typenames[i];
+ delete [] typenames[i];
delete [] typenames;
typenames = NULL;
@@ -158,8 +158,8 @@ void DumpXYZ::write_data(int n, double *mybuf)
int m = 0;
for (int i = 0; i < n; i++) {
fprintf(fp,format,
- typenames[static_cast<int> (mybuf[m+1])],
- mybuf[m+2],mybuf[m+3],mybuf[m+4]);
+ typenames[static_cast<int> (mybuf[m+1])],
+ mybuf[m+2],mybuf[m+3],mybuf[m+4]);
m += size_one;
}
}
diff --git a/src/dump_xyz.h b/src/dump_xyz.h
index 4824ed6df426d87c9a15b10e9e462704d28a231c..eab50b8215fdaa3745ca818ed944ad40d522f4b8 100644
--- a/src/dump_xyz.h
+++ b/src/dump_xyz.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/error.cpp b/src/error.cpp
index 3686ab3ecfaacb954bdb488f42bc3a4584ecca01..6c4fb2e06296e7aa9100e97ee797eba617ae9028 100644
--- a/src/error.cpp
+++ b/src/error.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -35,9 +35,9 @@ void Error::universe_all(const char *file, int line, const char *str)
if (universe->me == 0) {
if (universe->uscreen) fprintf(universe->uscreen,
- "ERROR: %s (%s:%d)\n",str,file,line);
+ "ERROR: %s (%s:%d)\n",str,file,line);
if (universe->ulogfile) fprintf(universe->ulogfile,
- "ERROR: %s (%s:%d)\n",str,file,line);
+ "ERROR: %s (%s:%d)\n",str,file,line);
}
if (output) delete output;
@@ -60,7 +60,7 @@ void Error::universe_one(const char *file, int line, const char *str)
{
if (universe->uscreen)
fprintf(universe->uscreen,"ERROR on proc %d: %s (%s:%d)\n",
- universe->me,str,file,line);
+ universe->me,str,file,line);
MPI_Abort(universe->uworld,1);
}
@@ -95,7 +95,7 @@ void Error::all(const char *file, int line, const char *str)
/* ----------------------------------------------------------------------
called by one proc in world
write to world screen only if non-NULL on this proc
- always write to universe screen
+ always write to universe screen
forces abort of entire world (and universe) if any proc in world calls
------------------------------------------------------------------------- */
@@ -104,24 +104,24 @@ void Error::one(const char *file, int line, const char *str)
int me;
MPI_Comm_rank(world,&me);
if (screen) fprintf(screen,"ERROR on proc %d: %s (%s:%d)\n",
- me,str,file,line);
+ me,str,file,line);
if (universe->nworlds > 1)
if (universe->uscreen)
fprintf(universe->uscreen,"ERROR on proc %d: %s (%s:%d)\n",
- universe->me,str,file,line);
+ universe->me,str,file,line);
MPI_Abort(world,1);
}
/* ----------------------------------------------------------------------
called by one proc in world
- only write to screen if non-NULL on this proc since could be file
+ only write to screen if non-NULL on this proc since could be file
------------------------------------------------------------------------- */
void Error::warning(const char *file, int line, const char *str, int logflag)
{
if (screen) fprintf(screen,"WARNING: %s (%s:%d)\n",str,file,line);
if (logflag && logfile) fprintf(logfile,"WARNING: %s (%s:%d)\n",
- str,file,line);
+ str,file,line);
}
/* ----------------------------------------------------------------------
diff --git a/src/error.h b/src/error.h
index 66d83feccf892952321dd2165699e62e83baa246..8a70a691f01564ae016ca9bd5759de4fe345f9ce 100644
--- a/src/error.h
+++ b/src/error.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/finish.cpp b/src/finish.cpp
index 3ca6f4888fb4f472451ef1bd4265fe462e3784c6..3c063aefc51a949b6b7aed83ef2ac0aad366abda 100644
--- a/src/finish.cpp
+++ b/src/finish.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -54,7 +54,7 @@ void Finish::end(int flag)
bigint nblocal = atom->nlocal;
MPI_Allreduce(&nblocal,&atom->natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);
-
+
// choose flavors of statistical output
// flag determines caller
// flag = 0 = just loop summary
@@ -70,9 +70,9 @@ void Finish::end(int flag)
if (update->whichflag == 2) minflag = 1;
timeflag = histoflag = 1;
neighflag = 1;
- if (update->whichflag == 1 &&
- strcmp(update->integrate_style,"verlet/split") == 0 &&
- universe->iworld == 1) neighflag = 0;
+ if (update->whichflag == 1 &&
+ strcmp(update->integrate_style,"verlet/split") == 0 &&
+ universe->iworld == 1) neighflag = 0;
if (force->kspace && force->kspace_match("pppm",0)) fftflag = 1;
}
if (flag == 2) prdflag = histoflag = neighflag = 1;
@@ -82,40 +82,40 @@ void Finish::end(int flag)
if (loopflag) {
time_other = timer->array[TIME_LOOP] -
- (timer->array[TIME_PAIR] + timer->array[TIME_BOND] +
+ (timer->array[TIME_PAIR] + timer->array[TIME_BOND] +
timer->array[TIME_KSPACE] + timer->array[TIME_NEIGHBOR] +
timer->array[TIME_COMM] + timer->array[TIME_OUTPUT]);
-
+
time_loop = timer->array[TIME_LOOP];
MPI_Allreduce(&time_loop,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time_loop = tmp/nprocs;
// overall loop time
-#if defined(_OPENMP)
+#if defined(_OPENMP)
if (me == 0) {
int ntasks = nprocs * comm->nthreads;
if (screen) fprintf(screen,
- "Loop time of %g on %d procs (%d MPI x %d OpenMP) "
- "for %d steps with " BIGINT_FORMAT " atoms\n",
- time_loop,ntasks,nprocs,comm->nthreads,
- update->nsteps,atom->natoms);
+ "Loop time of %g on %d procs (%d MPI x %d OpenMP) "
+ "for %d steps with " BIGINT_FORMAT " atoms\n",
+ time_loop,ntasks,nprocs,comm->nthreads,
+ update->nsteps,atom->natoms);
if (logfile) fprintf(logfile,
- "Loop time of %g on %d procs (%d MPI x %d OpenMP) "
- "for %d steps with " BIGINT_FORMAT " atoms\n",
- time_loop,ntasks,nprocs,comm->nthreads,
- update->nsteps,atom->natoms);
+ "Loop time of %g on %d procs (%d MPI x %d OpenMP) "
+ "for %d steps with " BIGINT_FORMAT " atoms\n",
+ time_loop,ntasks,nprocs,comm->nthreads,
+ update->nsteps,atom->natoms);
}
#else
if (me == 0) {
if (screen) fprintf(screen,
- "Loop time of %g on %d procs for %d steps with "
- BIGINT_FORMAT " atoms\n",
- time_loop,nprocs,update->nsteps,atom->natoms);
+ "Loop time of %g on %d procs for %d steps with "
+ BIGINT_FORMAT " atoms\n",
+ time_loop,nprocs,update->nsteps,atom->natoms);
if (logfile) fprintf(logfile,
- "Loop time of %g on %d procs for %d steps with "
- BIGINT_FORMAT " atoms\n",
- time_loop,nprocs,update->nsteps,atom->natoms);
+ "Loop time of %g on %d procs for %d steps with "
+ BIGINT_FORMAT " atoms\n",
+ time_loop,nprocs,update->nsteps,atom->natoms);
}
#endif
@@ -132,44 +132,44 @@ void Finish::end(int flag)
if (me == 0) {
if (screen) {
- fprintf(screen,"Minimization stats:\n");
- fprintf(screen," Stopping criterion = %s\n",
- update->minimize->stopstr);
- fprintf(screen," Energy initial, next-to-last, final = \n"
- " %18.12g %18.12g %18.12g\n",
- update->minimize->einitial,update->minimize->eprevious,
- update->minimize->efinal);
- fprintf(screen," Force two-norm initial, final = %g %g\n",
- update->minimize->fnorm2_init,update->minimize->fnorm2_final);
- fprintf(screen," Force max component initial, final = %g %g\n",
- update->minimize->fnorminf_init,
- update->minimize->fnorminf_final);
- fprintf(screen," Final line search alpha, max atom move = %g %g\n",
- update->minimize->alpha_final,
- update->minimize->alpha_final*
- update->minimize->fnorminf_final);
- fprintf(screen," Iterations, force evaluations = %d %d\n",
- update->minimize->niter,update->minimize->neval);
+ fprintf(screen,"Minimization stats:\n");
+ fprintf(screen," Stopping criterion = %s\n",
+ update->minimize->stopstr);
+ fprintf(screen," Energy initial, next-to-last, final = \n"
+ " %18.12g %18.12g %18.12g\n",
+ update->minimize->einitial,update->minimize->eprevious,
+ update->minimize->efinal);
+ fprintf(screen," Force two-norm initial, final = %g %g\n",
+ update->minimize->fnorm2_init,update->minimize->fnorm2_final);
+ fprintf(screen," Force max component initial, final = %g %g\n",
+ update->minimize->fnorminf_init,
+ update->minimize->fnorminf_final);
+ fprintf(screen," Final line search alpha, max atom move = %g %g\n",
+ update->minimize->alpha_final,
+ update->minimize->alpha_final*
+ update->minimize->fnorminf_final);
+ fprintf(screen," Iterations, force evaluations = %d %d\n",
+ update->minimize->niter,update->minimize->neval);
}
if (logfile) {
- fprintf(logfile,"Minimization stats:\n");
- fprintf(logfile," Stopping criterion = %s\n",
- update->minimize->stopstr);
- fprintf(logfile," Energy initial, next-to-last, final = \n"
- " %18.12g %18.12g %18.12g\n",
- update->minimize->einitial,update->minimize->eprevious,
- update->minimize->efinal);
- fprintf(logfile," Force two-norm initial, final = %g %g\n",
- update->minimize->fnorm2_init,update->minimize->fnorm2_final);
- fprintf(logfile," Force max component initial, final = %g %g\n",
- update->minimize->fnorminf_init,
- update->minimize->fnorminf_final);
- fprintf(logfile," Final line search alpha, max atom move = %g %g\n",
- update->minimize->alpha_final,
- update->minimize->alpha_final*
- update->minimize->fnorminf_final);
- fprintf(logfile," Iterations, force evaluations = %d %d\n",
- update->minimize->niter,update->minimize->neval);
+ fprintf(logfile,"Minimization stats:\n");
+ fprintf(logfile," Stopping criterion = %s\n",
+ update->minimize->stopstr);
+ fprintf(logfile," Energy initial, next-to-last, final = \n"
+ " %18.12g %18.12g %18.12g\n",
+ update->minimize->einitial,update->minimize->eprevious,
+ update->minimize->efinal);
+ fprintf(logfile," Force two-norm initial, final = %g %g\n",
+ update->minimize->fnorm2_init,update->minimize->fnorm2_final);
+ fprintf(logfile," Force max component initial, final = %g %g\n",
+ update->minimize->fnorminf_init,
+ update->minimize->fnorminf_final);
+ fprintf(logfile," Final line search alpha, max atom move = %g %g\n",
+ update->minimize->alpha_final,
+ update->minimize->alpha_final*
+ update->minimize->fnorminf_final);
+ fprintf(logfile," Iterations, force evaluations = %d %d\n",
+ update->minimize->niter,update->minimize->neval);
}
}
}
@@ -189,48 +189,48 @@ void Finish::end(int flag)
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time = tmp/nprocs;
if (me == 0) {
- if (screen)
- fprintf(screen," Dephase time (%%) = %g (%g)\n",
- time,time/time_loop*100.0);
- if (logfile)
- fprintf(logfile," Dephase time (%%) = %g (%g)\n",
- time,time/time_loop*100.0);
+ if (screen)
+ fprintf(screen," Dephase time (%%) = %g (%g)\n",
+ time,time/time_loop*100.0);
+ if (logfile)
+ fprintf(logfile," Dephase time (%%) = %g (%g)\n",
+ time,time/time_loop*100.0);
}
time = timer->array[TIME_BOND];
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time = tmp/nprocs;
if (me == 0) {
- if (screen)
- fprintf(screen," Dynamics time (%%) = %g (%g)\n",
- time,time/time_loop*100.0);
- if (logfile)
- fprintf(logfile," Dynamics time (%%) = %g (%g)\n",
- time,time/time_loop*100.0);
+ if (screen)
+ fprintf(screen," Dynamics time (%%) = %g (%g)\n",
+ time,time/time_loop*100.0);
+ if (logfile)
+ fprintf(logfile," Dynamics time (%%) = %g (%g)\n",
+ time,time/time_loop*100.0);
}
time = timer->array[TIME_KSPACE];
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time = tmp/nprocs;
if (me == 0) {
- if (screen)
- fprintf(screen," Quench time (%%) = %g (%g)\n",
- time,time/time_loop*100.0);
- if (logfile)
- fprintf(logfile," Quench time (%%) = %g (%g)\n",
- time,time/time_loop*100.0);
+ if (screen)
+ fprintf(screen," Quench time (%%) = %g (%g)\n",
+ time,time/time_loop*100.0);
+ if (logfile)
+ fprintf(logfile," Quench time (%%) = %g (%g)\n",
+ time,time/time_loop*100.0);
}
time = time_other;
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time = tmp/nprocs;
if (me == 0) {
- if (screen)
- fprintf(screen," Other time (%%) = %g (%g)\n",
- time,time/time_loop*100.0);
- if (logfile)
- fprintf(logfile," Other time (%%) = %g (%g)\n",
- time,time/time_loop*100.0);
+ if (screen)
+ fprintf(screen," Other time (%%) = %g (%g)\n",
+ time,time/time_loop*100.0);
+ if (logfile)
+ fprintf(logfile," Other time (%%) = %g (%g)\n",
+ time,time/time_loop*100.0);
}
}
@@ -249,36 +249,36 @@ void Finish::end(int flag)
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time = tmp/nprocs;
if (me == 0) {
- if (screen)
- fprintf(screen," NEB time (%%) = %g (%g)\n",
- time,time/time_loop*100.0);
- if (logfile)
- fprintf(logfile," NEB time (%%) = %g (%g)\n",
- time,time/time_loop*100.0);
+ if (screen)
+ fprintf(screen," NEB time (%%) = %g (%g)\n",
+ time,time/time_loop*100.0);
+ if (logfile)
+ fprintf(logfile," NEB time (%%) = %g (%g)\n",
+ time,time/time_loop*100.0);
}
time = timer->array[TIME_BOND];
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time = tmp/nprocs;
if (me == 0) {
- if (screen)
- fprintf(screen," Dynamics time (%%) = %g (%g)\n",
- time,time/time_loop*100.0);
- if (logfile)
- fprintf(logfile," Dynamics time (%%) = %g (%g)\n",
- time,time/time_loop*100.0);
+ if (screen)
+ fprintf(screen," Dynamics time (%%) = %g (%g)\n",
+ time,time/time_loop*100.0);
+ if (logfile)
+ fprintf(logfile," Dynamics time (%%) = %g (%g)\n",
+ time,time/time_loop*100.0);
}
time = timer->array[TIME_KSPACE];
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time = tmp/nprocs;
if (me == 0) {
- if (screen)
- fprintf(screen," Quench time (%%) = %g (%g)\n",
- time,time/time_loop*100.0);
- if (logfile)
- fprintf(logfile," Quench time (%%) = %g (%g)\n",
- time,time/time_loop*100.0);
+ if (screen)
+ fprintf(screen," Quench time (%%) = %g (%g)\n",
+ time,time/time_loop*100.0);
+ if (logfile)
+ fprintf(logfile," Quench time (%%) = %g (%g)\n",
+ time,time/time_loop*100.0);
}
@@ -286,12 +286,12 @@ void Finish::end(int flag)
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time = tmp/nprocs;
if (me == 0) {
- if (screen)
- fprintf(screen," Comm time (%%) = %g (%g)\n",
- time,time/time_loop*100.0);
- if (logfile)
- fprintf(logfile," Comm time (%%) = %g (%g)\n",
- time,time/time_loop*100.0);
+ if (screen)
+ fprintf(screen," Comm time (%%) = %g (%g)\n",
+ time,time/time_loop*100.0);
+ if (logfile)
+ fprintf(logfile," Comm time (%%) = %g (%g)\n",
+ time,time/time_loop*100.0);
}
@@ -299,24 +299,24 @@ void Finish::end(int flag)
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time = tmp/nprocs;
if (me == 0) {
- if (screen)
- fprintf(screen," Output time (%%) = %g (%g)\n",
- time,time/time_loop*100.0);
- if (logfile)
- fprintf(logfile," Output time (%%) = %g (%g)\n",
- time,time/time_loop*100.0);
+ if (screen)
+ fprintf(screen," Output time (%%) = %g (%g)\n",
+ time,time/time_loop*100.0);
+ if (logfile)
+ fprintf(logfile," Output time (%%) = %g (%g)\n",
+ time,time/time_loop*100.0);
}
time = time_other;
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time = tmp/nprocs;
if (me == 0) {
- if (screen)
- fprintf(screen," Other time (%%) = %g (%g)\n",
- time,time/time_loop*100.0);
- if (logfile)
- fprintf(logfile," Other time (%%) = %g (%g)\n",
- time,time/time_loop*100.0);
+ if (screen)
+ fprintf(screen," Other time (%%) = %g (%g)\n",
+ time,time/time_loop*100.0);
+ if (logfile)
+ fprintf(logfile," Other time (%%) = %g (%g)\n",
+ time,time/time_loop*100.0);
}
}
@@ -332,12 +332,12 @@ void Finish::end(int flag)
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time = tmp/nprocs;
if (me == 0) {
- if (screen)
- fprintf(screen,"Pair time (%%) = %g (%g)\n",
- time,time/time_loop*100.0);
- if (logfile)
- fprintf(logfile,"Pair time (%%) = %g (%g)\n",
- time,time/time_loop*100.0);
+ if (screen)
+ fprintf(screen,"Pair time (%%) = %g (%g)\n",
+ time,time/time_loop*100.0);
+ if (logfile)
+ fprintf(logfile,"Pair time (%%) = %g (%g)\n",
+ time,time/time_loop*100.0);
}
if (atom->molecular) {
@@ -345,78 +345,78 @@ void Finish::end(int flag)
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time = tmp/nprocs;
if (me == 0) {
- if (screen)
- fprintf(screen,"Bond time (%%) = %g (%g)\n",
- time,time/time_loop*100.0);
- if (logfile)
- fprintf(logfile,"Bond time (%%) = %g (%g)\n",
- time,time/time_loop*100.0);
+ if (screen)
+ fprintf(screen,"Bond time (%%) = %g (%g)\n",
+ time,time/time_loop*100.0);
+ if (logfile)
+ fprintf(logfile,"Bond time (%%) = %g (%g)\n",
+ time,time/time_loop*100.0);
}
}
-
+
if (force->kspace) {
time = timer->array[TIME_KSPACE];
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time = tmp/nprocs;
if (me == 0) {
- if (screen)
- fprintf(screen,"Kspce time (%%) = %g (%g)\n",
- time,time/time_loop*100.0);
- if (logfile)
- fprintf(logfile,"Kspce time (%%) = %g (%g)\n",
- time,time/time_loop*100.0);
+ if (screen)
+ fprintf(screen,"Kspce time (%%) = %g (%g)\n",
+ time,time/time_loop*100.0);
+ if (logfile)
+ fprintf(logfile,"Kspce time (%%) = %g (%g)\n",
+ time,time/time_loop*100.0);
}
}
-
+
time = timer->array[TIME_NEIGHBOR];
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time = tmp/nprocs;
if (me == 0) {
- if (screen)
- fprintf(screen,"Neigh time (%%) = %g (%g)\n",
- time,time/time_loop*100.0);
- if (logfile)
- fprintf(logfile,"Neigh time (%%) = %g (%g)\n",
- time,time/time_loop*100.0);
- }
-
+ if (screen)
+ fprintf(screen,"Neigh time (%%) = %g (%g)\n",
+ time,time/time_loop*100.0);
+ if (logfile)
+ fprintf(logfile,"Neigh time (%%) = %g (%g)\n",
+ time,time/time_loop*100.0);
+ }
+
time = timer->array[TIME_COMM];
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time = tmp/nprocs;
if (me == 0) {
- if (screen)
- fprintf(screen,"Comm time (%%) = %g (%g)\n",
- time,time/time_loop*100.0);
- if (logfile)
- fprintf(logfile,"Comm time (%%) = %g (%g)\n",
- time,time/time_loop*100.0);
- }
-
+ if (screen)
+ fprintf(screen,"Comm time (%%) = %g (%g)\n",
+ time,time/time_loop*100.0);
+ if (logfile)
+ fprintf(logfile,"Comm time (%%) = %g (%g)\n",
+ time,time/time_loop*100.0);
+ }
+
time = timer->array[TIME_OUTPUT];
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time = tmp/nprocs;
if (me == 0) {
- if (screen)
- fprintf(screen,"Outpt time (%%) = %g (%g)\n",
- time,time/time_loop*100.0);
- if (logfile)
- fprintf(logfile,"Outpt time (%%) = %g (%g)\n",
- time,time/time_loop*100.0);
- }
-
+ if (screen)
+ fprintf(screen,"Outpt time (%%) = %g (%g)\n",
+ time,time/time_loop*100.0);
+ if (logfile)
+ fprintf(logfile,"Outpt time (%%) = %g (%g)\n",
+ time,time/time_loop*100.0);
+ }
+
time = time_other;
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time = tmp/nprocs;
if (me == 0) {
- if (screen)
- fprintf(screen,"Other time (%%) = %g (%g)\n",
- time,time/time_loop*100.0);
- if (logfile)
- fprintf(logfile,"Other time (%%) = %g (%g)\n",
- time,time/time_loop*100.0);
+ if (screen)
+ fprintf(screen,"Other time (%%) = %g (%g)\n",
+ time,time/time_loop*100.0);
+ if (logfile)
+ fprintf(logfile,"Other time (%%) = %g (%g)\n",
+ time,time/time_loop*100.0);
}
}
-
+
// FFT timing statistics
// time3d,time1d = total time during run for 3d and 1d FFTs
// time_kspace may be 0.0 if another partition is doing Kspace
@@ -432,15 +432,15 @@ void Finish::end(int flag)
int nsample = 5;
double time3d,time1d;
force->kspace->timing(nsample,time3d,time1d);
-
+
time3d = nsteps * time3d / nsample;
MPI_Allreduce(&time3d,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time3d = tmp/nprocs;
-
+
time1d = nsteps * time1d / nsample;
MPI_Allreduce(&time1d,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time1d = tmp/nprocs;
-
+
double time_kspace = timer->array[TIME_KSPACE];
MPI_Allreduce(&time_kspace,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time_kspace = tmp/nprocs;
@@ -459,12 +459,12 @@ void Finish::end(int flag)
if (me == 0) {
if (screen) {
- fprintf(screen,"FFT time (%% of Kspce) = %g (%g)\n",time3d,fraction);
- fprintf(screen,"FFT Gflps 3d (1d only) = %g %g\n",flop3,flop1);
+ fprintf(screen,"FFT time (%% of Kspce) = %g (%g)\n",time3d,fraction);
+ fprintf(screen,"FFT Gflps 3d (1d only) = %g %g\n",flop3,flop1);
}
if (logfile) {
- fprintf(logfile,"FFT time (%% of Kspce) = %g (%g)\n",time3d,fraction);
- fprintf(logfile,"FFT Gflps 3d (1d only) = %g %g\n",flop3,flop1);
+ fprintf(logfile,"FFT time (%% of Kspce) = %g (%g)\n",time3d,fraction);
+ fprintf(logfile,"FFT Gflps 3d (1d only) = %g %g\n",flop3,flop1);
}
}
}
@@ -479,46 +479,46 @@ void Finish::end(int flag)
stats(1,&tmp,&ave,&max,&min,10,histo);
if (me == 0) {
if (screen) {
- fprintf(screen,"Nlocal: %g ave %g max %g min\n",ave,max,min);
- fprintf(screen,"Histogram:");
- for (i = 0; i < 10; i++) fprintf(screen," %d",histo[i]);
- fprintf(screen,"\n");
+ fprintf(screen,"Nlocal: %g ave %g max %g min\n",ave,max,min);
+ fprintf(screen,"Histogram:");
+ for (i = 0; i < 10; i++) fprintf(screen," %d",histo[i]);
+ fprintf(screen,"\n");
}
if (logfile) {
- fprintf(logfile,"Nlocal: %g ave %g max %g min\n",ave,max,min);
- fprintf(logfile,"Histogram:");
- for (i = 0; i < 10; i++) fprintf(logfile," %d",histo[i]);
- fprintf(logfile,"\n");
+ fprintf(logfile,"Nlocal: %g ave %g max %g min\n",ave,max,min);
+ fprintf(logfile,"Histogram:");
+ for (i = 0; i < 10; i++) fprintf(logfile," %d",histo[i]);
+ fprintf(logfile,"\n");
}
}
-
+
tmp = atom->nghost;
stats(1,&tmp,&ave,&max,&min,10,histo);
if (me == 0) {
if (screen) {
- fprintf(screen,"Nghost: %g ave %g max %g min\n",ave,max,min);
- fprintf(screen,"Histogram:");
- for (i = 0; i < 10; i++) fprintf(screen," %d",histo[i]);
- fprintf(screen,"\n");
+ fprintf(screen,"Nghost: %g ave %g max %g min\n",ave,max,min);
+ fprintf(screen,"Histogram:");
+ for (i = 0; i < 10; i++) fprintf(screen," %d",histo[i]);
+ fprintf(screen,"\n");
}
if (logfile) {
- fprintf(logfile,"Nghost: %g ave %g max %g min\n",ave,max,min);
- fprintf(logfile,"Histogram:");
- for (i = 0; i < 10; i++) fprintf(logfile," %d",histo[i]);
- fprintf(logfile,"\n");
+ fprintf(logfile,"Nghost: %g ave %g max %g min\n",ave,max,min);
+ fprintf(logfile,"Histogram:");
+ for (i = 0; i < 10; i++) fprintf(logfile," %d",histo[i]);
+ fprintf(logfile,"\n");
}
}
-
+
// find a non-skip neighbor list containing half the pairwise interactions
// count neighbors in that list for stats purposes
-
+
for (m = 0; m < neighbor->old_nrequest; m++)
- if ((neighbor->old_requests[m]->half ||
- neighbor->old_requests[m]->gran ||
- neighbor->old_requests[m]->respaouter ||
- neighbor->old_requests[m]->half_from_full) &&
- neighbor->old_requests[m]->skip == 0 &&
- neighbor->lists[m]->numneigh) break;
+ if ((neighbor->old_requests[m]->half ||
+ neighbor->old_requests[m]->gran ||
+ neighbor->old_requests[m]->respaouter ||
+ neighbor->old_requests[m]->half_from_full) &&
+ neighbor->old_requests[m]->skip == 0 &&
+ neighbor->lists[m]->numneigh) break;
nneigh = 0;
if (m < neighbor->old_nrequest) {
@@ -526,58 +526,58 @@ void Finish::end(int flag)
int *ilist = neighbor->lists[m]->ilist;
int *numneigh = neighbor->lists[m]->numneigh;
for (i = 0; i < inum; i++)
- nneigh += numneigh[ilist[i]];
+ nneigh += numneigh[ilist[i]];
}
-
+
tmp = nneigh;
stats(1,&tmp,&ave,&max,&min,10,histo);
if (me == 0) {
if (screen) {
- fprintf(screen,"Neighs: %g ave %g max %g min\n",ave,max,min);
- fprintf(screen,"Histogram:");
- for (i = 0; i < 10; i++) fprintf(screen," %d",histo[i]);
- fprintf(screen,"\n");
+ fprintf(screen,"Neighs: %g ave %g max %g min\n",ave,max,min);
+ fprintf(screen,"Histogram:");
+ for (i = 0; i < 10; i++) fprintf(screen," %d",histo[i]);
+ fprintf(screen,"\n");
}
if (logfile) {
- fprintf(logfile,"Neighs: %g ave %g max %g min\n",ave,max,min);
- fprintf(logfile,"Histogram:");
- for (i = 0; i < 10; i++) fprintf(logfile," %d",histo[i]);
- fprintf(logfile,"\n");
+ fprintf(logfile,"Neighs: %g ave %g max %g min\n",ave,max,min);
+ fprintf(logfile,"Histogram:");
+ for (i = 0; i < 10; i++) fprintf(logfile," %d",histo[i]);
+ fprintf(logfile,"\n");
}
}
-
+
// find a non-skip neighbor list containing full pairwise interactions
// count neighbors in that list for stats purposes
for (m = 0; m < neighbor->old_nrequest; m++)
if (neighbor->old_requests[m]->full &&
- neighbor->old_requests[m]->skip == 0) break;
-
+ neighbor->old_requests[m]->skip == 0) break;
+
nneighfull = 0;
if (m < neighbor->old_nrequest) {
if (neighbor->lists[m]->numneigh > 0) {
- int inum = neighbor->lists[m]->inum;
- int *ilist = neighbor->lists[m]->ilist;
- int *numneigh = neighbor->lists[m]->numneigh;
- for (i = 0; i < inum; i++)
- nneighfull += numneigh[ilist[i]];
+ int inum = neighbor->lists[m]->inum;
+ int *ilist = neighbor->lists[m]->ilist;
+ int *numneigh = neighbor->lists[m]->numneigh;
+ for (i = 0; i < inum; i++)
+ nneighfull += numneigh[ilist[i]];
}
tmp = nneighfull;
stats(1,&tmp,&ave,&max,&min,10,histo);
if (me == 0) {
- if (screen) {
- fprintf(screen,"FullNghs: %g ave %g max %g min\n",ave,max,min);
- fprintf(screen,"Histogram:");
- for (i = 0; i < 10; i++) fprintf(screen," %d",histo[i]);
- fprintf(screen,"\n");
- }
- if (logfile) {
- fprintf(logfile,"FullNghs: %g ave %g max %g min\n",ave,max,min);
- fprintf(logfile,"Histogram:");
- for (i = 0; i < 10; i++) fprintf(logfile," %d",histo[i]);
- fprintf(logfile,"\n");
- }
+ if (screen) {
+ fprintf(screen,"FullNghs: %g ave %g max %g min\n",ave,max,min);
+ fprintf(screen,"Histogram:");
+ for (i = 0; i < 10; i++) fprintf(screen," %d",histo[i]);
+ fprintf(screen,"\n");
+ }
+ if (logfile) {
+ fprintf(logfile,"FullNghs: %g ave %g max %g min\n",ave,max,min);
+ fprintf(logfile,"Histogram:");
+ for (i = 0; i < 10; i++) fprintf(logfile," %d",histo[i]);
+ fprintf(logfile,"\n");
+ }
}
}
}
@@ -587,11 +587,11 @@ void Finish::end(int flag)
if (screen) fprintf(screen,"\n");
if (logfile) fprintf(logfile,"\n");
}
-
+
tmp = MAX(nneigh,nneighfull);
double nall;
MPI_Allreduce(&tmp,&nall,1,MPI_DOUBLE,MPI_SUM,world);
-
+
int nspec;
double nspec_all;
if (atom->molecular) {
@@ -601,45 +601,45 @@ void Finish::end(int flag)
tmp = nspec;
MPI_Allreduce(&tmp,&nspec_all,1,MPI_DOUBLE,MPI_SUM,world);
}
-
+
if (me == 0) {
if (screen) {
- if (nall < 2.0e9)
- fprintf(screen,
- "Total # of neighbors = %d\n",static_cast<int> (nall));
- else fprintf(screen,"Total # of neighbors = %g\n",nall);
- if (atom->natoms > 0)
- fprintf(screen,"Ave neighs/atom = %g\n",nall/atom->natoms);
- if (atom->molecular && atom->natoms > 0)
- fprintf(screen,"Ave special neighs/atom = %g\n",
- nspec_all/atom->natoms);
- fprintf(screen,"Neighbor list builds = %d\n",neighbor->ncalls);
- fprintf(screen,"Dangerous builds = %d\n",neighbor->ndanger);
+ if (nall < 2.0e9)
+ fprintf(screen,
+ "Total # of neighbors = %d\n",static_cast<int> (nall));
+ else fprintf(screen,"Total # of neighbors = %g\n",nall);
+ if (atom->natoms > 0)
+ fprintf(screen,"Ave neighs/atom = %g\n",nall/atom->natoms);
+ if (atom->molecular && atom->natoms > 0)
+ fprintf(screen,"Ave special neighs/atom = %g\n",
+ nspec_all/atom->natoms);
+ fprintf(screen,"Neighbor list builds = %d\n",neighbor->ncalls);
+ fprintf(screen,"Dangerous builds = %d\n",neighbor->ndanger);
}
if (logfile) {
- if (nall < 2.0e9)
- fprintf(logfile,
- "Total # of neighbors = %d\n",static_cast<int> (nall));
- else fprintf(logfile,"Total # of neighbors = %g\n",nall);
- if (atom->natoms > 0)
- fprintf(logfile,"Ave neighs/atom = %g\n",nall/atom->natoms);
- if (atom->molecular && atom->natoms > 0)
- fprintf(logfile,"Ave special neighs/atom = %g\n",
- nspec_all/atom->natoms);
- fprintf(logfile,"Neighbor list builds = %d\n",neighbor->ncalls);
- fprintf(logfile,"Dangerous builds = %d\n",neighbor->ndanger);
+ if (nall < 2.0e9)
+ fprintf(logfile,
+ "Total # of neighbors = %d\n",static_cast<int> (nall));
+ else fprintf(logfile,"Total # of neighbors = %g\n",nall);
+ if (atom->natoms > 0)
+ fprintf(logfile,"Ave neighs/atom = %g\n",nall/atom->natoms);
+ if (atom->molecular && atom->natoms > 0)
+ fprintf(logfile,"Ave special neighs/atom = %g\n",
+ nspec_all/atom->natoms);
+ fprintf(logfile,"Neighbor list builds = %d\n",neighbor->ncalls);
+ fprintf(logfile,"Dangerous builds = %d\n",neighbor->ndanger);
}
}
}
-
+
if (logfile) fflush(logfile);
}
/* ---------------------------------------------------------------------- */
-void Finish::stats(int n, double *data,
- double *pave, double *pmax, double *pmin,
- int nhisto, int *histo)
+void Finish::stats(int n, double *data,
+ double *pave, double *pmax, double *pmin,
+ int nhisto, int *histo)
{
int i,m;
int *histotmp;
diff --git a/src/finish.h b/src/finish.h
index 09c28f975ec9e69ae4a83789a664585b8fc8861d..9036aef3b9a7f3a175bab18dd673abf8ef4ba2ec 100644
--- a/src/finish.h
+++ b/src/finish.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix.cpp b/src/fix.cpp
index 5f19d75dca8c1ff612e03c5e440ad3e5f66db72d..50b30869d478c16a410c064bb8fd97ca75d21f94 100644
--- a/src/fix.cpp
+++ b/src/fix.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -119,7 +119,7 @@ void Fix::v_setup(int vflag)
vflag_atom = vflag / 4;
// reallocate per-atom array if necessary
-
+
if (vflag_atom && atom->nlocal > maxvatom) {
maxvatom = atom->nmax;
memory->destroy(vatom);
diff --git a/src/fix.h b/src/fix.h
index 25ee41b58776767a389c80cd9baa74ef0b8ec8c6..4214ba355b7df82d6820fce93c976c7188d3c274 100644
--- a/src/fix.h
+++ b/src/fix.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_adapt.cpp b/src/fix_adapt.cpp
index 380eb8c8e55f0ffc3cb89a20bd4f651e93d87852..e8af253f6a4a772dcd5da0cfcae17fb83005489c 100644
--- a/src/fix_adapt.cpp
+++ b/src/fix_adapt.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -84,13 +84,13 @@ FixAdapt::FixAdapt(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
adapt[nadapt].pparam = new char[n];
strcpy(adapt[nadapt].pparam,arg[iarg+2]);
force->bounds(arg[iarg+3],atom->ntypes,
- adapt[nadapt].ilo,adapt[nadapt].ihi);
+ adapt[nadapt].ilo,adapt[nadapt].ihi);
force->bounds(arg[iarg+4],atom->ntypes,
- adapt[nadapt].jlo,adapt[nadapt].jhi);
+ adapt[nadapt].jlo,adapt[nadapt].jhi);
if (strstr(arg[iarg+5],"v_") == arg[iarg+5]) {
- n = strlen(&arg[iarg+5][2]) + 1;
- adapt[nadapt].var = new char[n];
- strcpy(adapt[nadapt].var,&arg[iarg+5][2]);
+ n = strlen(&arg[iarg+5][2]) + 1;
+ adapt[nadapt].var = new char[n];
+ strcpy(adapt[nadapt].var,&arg[iarg+5][2]);
} else error->all(FLERR,"Illegal fix adapt command");
nadapt++;
iarg += 6;
@@ -98,9 +98,9 @@ FixAdapt::FixAdapt(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
if (iarg+2 > narg) error->all(FLERR,"Illegal fix adapt command");
adapt[nadapt].which = KSPACE;
if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) {
- int n = strlen(&arg[iarg+1][2]) + 1;
- adapt[nadapt].var = new char[n];
- strcpy(adapt[nadapt].var,&arg[iarg+1][2]);
+ int n = strlen(&arg[iarg+1][2]) + 1;
+ adapt[nadapt].var = new char[n];
+ strcpy(adapt[nadapt].var,&arg[iarg+1][2]);
} else error->all(FLERR,"Illegal fix adapt command");
nadapt++;
iarg += 2;
@@ -108,13 +108,13 @@ FixAdapt::FixAdapt(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
if (iarg+3 > narg) error->all(FLERR,"Illegal fix adapt command");
adapt[nadapt].which = ATOM;
if (strcmp(arg[iarg+1],"diameter") == 0) {
- adapt[nadapt].aparam = DIAMETER;
- diamflag = 1;
+ adapt[nadapt].aparam = DIAMETER;
+ diamflag = 1;
} else error->all(FLERR,"Illegal fix adapt command");
if (strstr(arg[iarg+2],"v_") == arg[iarg+2]) {
- int n = strlen(&arg[iarg+2][2]) + 1;
- adapt[nadapt].var = new char[n];
- strcpy(adapt[nadapt].var,&arg[iarg+2][2]);
+ int n = strlen(&arg[iarg+2][2]) + 1;
+ adapt[nadapt].var = new char[n];
+ strcpy(adapt[nadapt].var,&arg[iarg+2][2]);
} else error->all(FLERR,"Illegal fix adapt command");
nadapt++;
iarg += 3;
@@ -205,28 +205,28 @@ void FixAdapt::init()
ad->pdim = 2;
if (ad->pdim == 0) ad->scalar = (double *) ptr;
if (ad->pdim == 2) ad->array = (double **) ptr;
-
+
// if pair hybrid, test that ilo,ihi,jlo,jhi are valid for sub-style
if (ad->pdim == 2 && (strcmp(force->pair_style,"hybrid") == 0 ||
- strcmp(force->pair_style,"hybrid/overlay") == 0)) {
- PairHybrid *pair = (PairHybrid *) force->pair;
- for (i = ad->ilo; i <= ad->ihi; i++)
- for (j = MAX(ad->jlo,i); j <= ad->jhi; j++)
- if (!pair->check_ijtype(i,j,ad->pstyle))
- error->all(FLERR,"Fix adapt type pair range is not valid for "
- "pair hybrid sub-style");
+ strcmp(force->pair_style,"hybrid/overlay") == 0)) {
+ PairHybrid *pair = (PairHybrid *) force->pair;
+ for (i = ad->ilo; i <= ad->ihi; i++)
+ for (j = MAX(ad->jlo,i); j <= ad->jhi; j++)
+ if (!pair->check_ijtype(i,j,ad->pstyle))
+ error->all(FLERR,"Fix adapt type pair range is not valid for "
+ "pair hybrid sub-style");
}
} else if (ad->which == KSPACE) {
- if (force->kspace == NULL)
- error->all(FLERR,"Fix adapt kspace style does not exist");
+ if (force->kspace == NULL)
+ error->all(FLERR,"Fix adapt kspace style does not exist");
kspace_scale = (double *) force->kspace->extract("scale");
} else if (ad->which == ATOM) {
if (ad->aparam == DIAMETER) {
- if (!atom->radius_flag)
- error->all(FLERR,"Fix adapt requires atom attribute diameter");
+ if (!atom->radius_flag)
+ error->all(FLERR,"Fix adapt requires atom attribute diameter");
}
}
}
@@ -237,8 +237,8 @@ void FixAdapt::init()
Adapt *ad = &adapt[m];
if (ad->which == PAIR && ad->pdim == 2) {
for (i = ad->ilo; i <= ad->ihi; i++)
- for (j = MAX(ad->jlo,i); j <= ad->jhi; j++)
- ad->array_orig[i][j] = ad->array[i][j];
+ for (j = MAX(ad->jlo,i); j <= ad->jhi; j++)
+ ad->array_orig[i][j] = ad->array[i][j];
}
}
}
@@ -281,22 +281,22 @@ void FixAdapt::change_settings()
for (int m = 0; m < nadapt; m++) {
Adapt *ad = &adapt[m];
double value = input->variable->compute_equal(ad->ivar);
-
+
// set global scalar or type pair array values
if (ad->which == PAIR) {
if (ad->pdim == 0) {
- if (scaleflag) *ad->scalar = value * ad->scalar_orig;
- else *ad->scalar = value;
+ if (scaleflag) *ad->scalar = value * ad->scalar_orig;
+ else *ad->scalar = value;
} else if (ad->pdim == 2) {
- if (scaleflag)
- for (i = ad->ilo; i <= ad->ihi; i++)
- for (j = MAX(ad->jlo,i); j <= ad->jhi; j++)
- ad->array[i][j] = value*ad->array_orig[i][j];
- else
- for (i = ad->ilo; i <= ad->ihi; i++)
- for (j = MAX(ad->jlo,i); j <= ad->jhi; j++)
- ad->array[i][j] = value;
+ if (scaleflag)
+ for (i = ad->ilo; i <= ad->ihi; i++)
+ for (j = MAX(ad->jlo,i); j <= ad->jhi; j++)
+ ad->array[i][j] = value*ad->array_orig[i][j];
+ else
+ for (i = ad->ilo; i <= ad->ihi; i++)
+ for (j = MAX(ad->jlo,i); j <= ad->jhi; j++)
+ ad->array[i][j] = value;
}
// set kspace scale factor
@@ -310,29 +310,29 @@ void FixAdapt::change_settings()
// also scale rmass to new value
if (ad->aparam == DIAMETER) {
- int mflag = 0;
- if (atom->rmass_flag) mflag = 1;
- double density;
-
- double *radius = atom->radius;
- double *rmass = atom->rmass;
- int *mask = atom->mask;
- int nlocal = atom->nlocal;
-
- if (mflag == 0) {
- for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit)
- radius[i] = 0.5*value;
- } else {
- for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit) {
- density = rmass[i] / (4.0*MY_PI/3.0 *
- radius[i]*radius[i]*radius[i]);
- radius[i] = 0.5*value;
- rmass[i] = 4.0*MY_PI/3.0 *
- radius[i]*radius[i]*radius[i] * density;
- }
- }
+ int mflag = 0;
+ if (atom->rmass_flag) mflag = 1;
+ double density;
+
+ double *radius = atom->radius;
+ double *rmass = atom->rmass;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+
+ if (mflag == 0) {
+ for (i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit)
+ radius[i] = 0.5*value;
+ } else {
+ for (i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit) {
+ density = rmass[i] / (4.0*MY_PI/3.0 *
+ radius[i]*radius[i]*radius[i]);
+ radius[i] = 0.5*value;
+ rmass[i] = 4.0*MY_PI/3.0 *
+ radius[i]*radius[i]*radius[i] * density;
+ }
+ }
}
}
}
@@ -357,9 +357,9 @@ void FixAdapt::restore_settings()
if (ad->which == PAIR) {
if (ad->pdim == 0) *ad->scalar = ad->scalar_orig;
else if (ad->pdim == 2) {
- for (int i = ad->ilo; i <= ad->ihi; i++)
- for (int j = MAX(ad->jlo,i); j <= ad->jhi; j++)
- ad->array[i][j] = ad->array_orig[i][j];
+ for (int i = ad->ilo; i <= ad->ihi; i++)
+ for (int j = MAX(ad->jlo,i); j <= ad->jhi; j++)
+ ad->array[i][j] = ad->array_orig[i][j];
}
} else if (ad->which == KSPACE) {
diff --git a/src/fix_adapt.h b/src/fix_adapt.h
index 2fb9987cd6527636b64fb60261f14fcb359fb22e..658932c96adaf0b86ec57a1b14930c6220be8617 100644
--- a/src/fix_adapt.h
+++ b/src/fix_adapt.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_addforce.cpp b/src/fix_addforce.cpp
index f86a4f847c6333280faa66d0cec6908104495adb..cb1e7ca1aa76fc157f98a6d21a4b74a575864fad 100644
--- a/src/fix_addforce.cpp
+++ b/src/fix_addforce.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -83,7 +83,7 @@ FixAddForce::FixAddForce(LAMMPS *lmp, int narg, char **arg) :
if (iarg+2 > narg) error->all(FLERR,"Illegal fix addforce command");
iregion = domain->find_region(arg[iarg+1]);
if (iregion == -1)
- error->all(FLERR,"Region ID for fix addforce does not exist");
+ error->all(FLERR,"Region ID for fix addforce does not exist");
int n = strlen(arg[iarg+1]) + 1;
idregion = new char[n];
strcpy(idregion,arg[iarg+1]);
@@ -91,9 +91,9 @@ FixAddForce::FixAddForce(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"energy") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix addforce command");
if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) {
- int n = strlen(&arg[iarg+1][2]) + 1;
- estr = new char[n];
- strcpy(estr,&arg[iarg+1][2]);
+ int n = strlen(&arg[iarg+1][2]) + 1;
+ estr = new char[n];
+ strcpy(estr,&arg[iarg+1][2]);
} else error->all(FLERR,"Illegal fix addforce command");
iarg += 2;
} else error->all(FLERR,"Illegal fix addforce command");
@@ -138,7 +138,7 @@ void FixAddForce::init()
if (xstr) {
xvar = input->variable->find(xstr);
- if (xvar < 0)
+ if (xvar < 0)
error->all(FLERR,"Variable name for fix addforce does not exist");
if (input->variable->equalstyle(xvar)) xstyle = EQUAL;
else if (input->variable->atomstyle(xvar)) xstyle = ATOM;
@@ -146,7 +146,7 @@ void FixAddForce::init()
}
if (ystr) {
yvar = input->variable->find(ystr);
- if (yvar < 0)
+ if (yvar < 0)
error->all(FLERR,"Variable name for fix addforce does not exist");
if (input->variable->equalstyle(yvar)) ystyle = EQUAL;
else if (input->variable->atomstyle(yvar)) ystyle = ATOM;
@@ -154,7 +154,7 @@ void FixAddForce::init()
}
if (zstr) {
zvar = input->variable->find(zstr);
- if (zvar < 0)
+ if (zvar < 0)
error->all(FLERR,"Variable name for fix addforce does not exist");
if (input->variable->equalstyle(zvar)) zstyle = EQUAL;
else if (input->variable->atomstyle(zvar)) zstyle = ATOM;
@@ -162,7 +162,7 @@ void FixAddForce::init()
}
if (estr) {
evar = input->variable->find(estr);
- if (evar < 0)
+ if (evar < 0)
error->all(FLERR,"Variable name for fix addforce does not exist");
if (input->variable->atomstyle(evar)) estyle = ATOM;
else error->all(FLERR,"Variable for fix addforce is invalid style");
@@ -176,7 +176,7 @@ void FixAddForce::init()
error->all(FLERR,"Region ID for fix addforce does not exist");
}
- if (xstyle == ATOM || ystyle == ATOM || zstyle == ATOM)
+ if (xstyle == ATOM || ystyle == ATOM || zstyle == ATOM)
varflag = ATOM;
else if (xstyle == EQUAL || ystyle == EQUAL || zstyle == EQUAL)
varflag = EQUAL;
@@ -184,8 +184,8 @@ void FixAddForce::init()
if (varflag == CONSTANT && estyle != NONE)
error->all(FLERR,"Cannot use variable energy with "
- "constant force in fix addforce");
- if ((varflag == EQUAL || varflag == ATOM) &&
+ "constant force in fix addforce");
+ if ((varflag == EQUAL || varflag == ATOM) &&
update->whichflag == 2 && estyle == NONE)
error->all(FLERR,"Must use variable energy with fix addforce");
@@ -249,22 +249,22 @@ void FixAddForce::post_force(int vflag)
if (varflag == CONSTANT) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- if (iregion >= 0 &&
- !domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2]))
- continue;
-
- xbox = (image[i] & 1023) - 512;
- ybox = (image[i] >> 10 & 1023) - 512;
- zbox = (image[i] >> 20) - 512;
- foriginal[0] -= xvalue * (x[i][0]+xbox*xprd) +
- yvalue * (x[i][1]+ybox*yprd) + zvalue * (x[i][2]+zbox*zprd);
-
- foriginal[1] += f[i][0];
- foriginal[2] += f[i][1];
- foriginal[3] += f[i][2];
- f[i][0] += xvalue;
- f[i][1] += yvalue;
- f[i][2] += zvalue;
+ if (iregion >= 0 &&
+ !domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2]))
+ continue;
+
+ xbox = (image[i] & 1023) - 512;
+ ybox = (image[i] >> 10 & 1023) - 512;
+ zbox = (image[i] >> 20) - 512;
+ foriginal[0] -= xvalue * (x[i][0]+xbox*xprd) +
+ yvalue * (x[i][1]+ybox*yprd) + zvalue * (x[i][2]+zbox*zprd);
+
+ foriginal[1] += f[i][0];
+ foriginal[2] += f[i][1];
+ foriginal[3] += f[i][2];
+ f[i][0] += xvalue;
+ f[i][1] += yvalue;
+ f[i][2] += zvalue;
}
// variable force, wrap with clear/add
@@ -279,7 +279,7 @@ void FixAddForce::post_force(int vflag)
else if (xstyle == ATOM && sforce)
input->variable->compute_atom(xvar,igroup,&sforce[0][0],4,0);
if (ystyle == EQUAL) yvalue = input->variable->compute_equal(yvar);
- else if (ystyle == ATOM && sforce)
+ else if (ystyle == ATOM && sforce)
input->variable->compute_atom(yvar,igroup,&sforce[0][1],4,0);
if (zstyle == EQUAL) zvalue = input->variable->compute_equal(zvar);
else if (zstyle == ATOM && sforce)
@@ -291,20 +291,20 @@ void FixAddForce::post_force(int vflag)
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- if (iregion >= 0 &&
- !domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2]))
- continue;
-
- if (estyle == ATOM) foriginal[0] += sforce[i][3];
- foriginal[1] += f[i][0];
- foriginal[2] += f[i][1];
- foriginal[3] += f[i][2];
- if (xstyle == ATOM) f[i][0] += sforce[i][0];
- else if (xstyle) f[i][0] += xvalue;
- if (ystyle == ATOM) f[i][1] += sforce[i][1];
- else if (ystyle) f[i][1] += yvalue;
- if (zstyle == ATOM) f[i][2] += sforce[i][2];
- else if (zstyle) f[i][2] += zvalue;
+ if (iregion >= 0 &&
+ !domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2]))
+ continue;
+
+ if (estyle == ATOM) foriginal[0] += sforce[i][3];
+ foriginal[1] += f[i][0];
+ foriginal[2] += f[i][1];
+ foriginal[3] += f[i][2];
+ if (xstyle == ATOM) f[i][0] += sforce[i][0];
+ else if (xstyle) f[i][0] += xvalue;
+ if (ystyle == ATOM) f[i][1] += sforce[i][1];
+ else if (ystyle) f[i][1] += yvalue;
+ if (zstyle == ATOM) f[i][2] += sforce[i][2];
+ else if (zstyle) f[i][2] += zvalue;
}
}
}
diff --git a/src/fix_addforce.h b/src/fix_addforce.h
index a8c283369ba126b4a5f4f8187e72f77bdd171ee7..b4ca9839d72e9e77b0bfa21ebe7d81c23823e794 100644
--- a/src/fix_addforce.h
+++ b/src/fix_addforce.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_ave_atom.cpp b/src/fix_ave_atom.cpp
index 66622684bc7c4dc8531ad4f2fedf3d23531d31b5..561a9039040c5d027b08da4ba1dff625a77e9e93 100644
--- a/src/fix_ave_atom.cpp
+++ b/src/fix_ave_atom.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -86,9 +86,9 @@ FixAveAtom::FixAveAtom(LAMMPS *lmp, int narg, char **arg) :
which[nvalues] = F;
argindex[nvalues++] = 2;
- } else if (strncmp(arg[iarg],"c_",2) == 0 ||
- strncmp(arg[iarg],"f_",2) == 0 ||
- strncmp(arg[iarg],"v_",2) == 0) {
+ } else if (strncmp(arg[iarg],"c_",2) == 0 ||
+ strncmp(arg[iarg],"f_",2) == 0 ||
+ strncmp(arg[iarg],"v_",2) == 0) {
if (arg[iarg][0] == 'c') which[nvalues] = COMPUTE;
else if (arg[iarg][0] == 'f') which[nvalues] = FIX;
else if (arg[iarg][0] == 'v') which[nvalues] = VARIABLE;
@@ -99,10 +99,10 @@ FixAveAtom::FixAveAtom(LAMMPS *lmp, int narg, char **arg) :
char *ptr = strchr(suffix,'[');
if (ptr) {
- if (suffix[strlen(suffix)-1] != ']')
- error->all(FLERR,"Illegal fix ave/atom command");
- argindex[nvalues] = atoi(ptr+1);
- *ptr = '\0';
+ if (suffix[strlen(suffix)-1] != ']')
+ error->all(FLERR,"Illegal fix ave/atom command");
+ argindex[nvalues] = atoi(ptr+1);
+ *ptr = '\0';
} else argindex[nvalues] = 0;
n = strlen(suffix) + 1;
@@ -128,41 +128,41 @@ FixAveAtom::FixAveAtom(LAMMPS *lmp, int narg, char **arg) :
if (which[i] == COMPUTE) {
int icompute = modify->find_compute(ids[i]);
if (icompute < 0)
- error->all(FLERR,"Compute ID for fix ave/atom does not exist");
+ error->all(FLERR,"Compute ID for fix ave/atom does not exist");
if (modify->compute[icompute]->peratom_flag == 0)
- error->all(FLERR,"Fix ave/atom compute does not calculate per-atom values");
- if (argindex[i] == 0 &&
- modify->compute[icompute]->size_peratom_cols != 0)
- error->all(FLERR,"Fix ave/atom compute does not "
- "calculate a per-atom vector");
+ error->all(FLERR,"Fix ave/atom compute does not calculate per-atom values");
+ if (argindex[i] == 0 &&
+ modify->compute[icompute]->size_peratom_cols != 0)
+ error->all(FLERR,"Fix ave/atom compute does not "
+ "calculate a per-atom vector");
if (argindex[i] && modify->compute[icompute]->size_peratom_cols == 0)
- error->all(FLERR,"Fix ave/atom compute does not "
- "calculate a per-atom array");
- if (argindex[i] &&
- argindex[i] > modify->compute[icompute]->size_peratom_cols)
- error->all(FLERR,"Fix ave/atom compute array is accessed out-of-range");
+ error->all(FLERR,"Fix ave/atom compute does not "
+ "calculate a per-atom array");
+ if (argindex[i] &&
+ argindex[i] > modify->compute[icompute]->size_peratom_cols)
+ error->all(FLERR,"Fix ave/atom compute array is accessed out-of-range");
} else if (which[i] == FIX) {
int ifix = modify->find_fix(ids[i]);
if (ifix < 0)
- error->all(FLERR,"Fix ID for fix ave/atom does not exist");
+ error->all(FLERR,"Fix ID for fix ave/atom does not exist");
if (modify->fix[ifix]->peratom_flag == 0)
- error->all(FLERR,"Fix ave/atom fix does not calculate per-atom values");
+ error->all(FLERR,"Fix ave/atom fix does not calculate per-atom values");
if (argindex[i] == 0 && modify->fix[ifix]->size_peratom_cols != 0)
- error->all(FLERR,"Fix ave/atom fix does not calculate a per-atom vector");
+ error->all(FLERR,"Fix ave/atom fix does not calculate a per-atom vector");
if (argindex[i] && modify->fix[ifix]->size_peratom_cols == 0)
- error->all(FLERR,"Fix ave/atom fix does not calculate a per-atom array");
+ error->all(FLERR,"Fix ave/atom fix does not calculate a per-atom array");
if (argindex[i] && argindex[i] > modify->fix[ifix]->size_peratom_cols)
- error->all(FLERR,"Fix ave/atom fix array is accessed out-of-range");
+ error->all(FLERR,"Fix ave/atom fix array is accessed out-of-range");
if (nevery % modify->fix[ifix]->peratom_freq)
- error->all(FLERR,"Fix for fix ave/atom not computed at compatible time");
+ error->all(FLERR,"Fix for fix ave/atom not computed at compatible time");
} else if (which[i] == VARIABLE) {
int ivariable = input->variable->find(ids[i]);
if (ivariable < 0)
- error->all(FLERR,"Variable name for fix ave/atom does not exist");
+ error->all(FLERR,"Variable name for fix ave/atom does not exist");
if (input->variable->atomstyle(ivariable) == 0)
- error->all(FLERR,"Fix ave/atom variable is not atom-style variable");
+ error->all(FLERR,"Fix ave/atom variable is not atom-style variable");
}
}
@@ -186,7 +186,7 @@ FixAveAtom::FixAveAtom(LAMMPS *lmp, int narg, char **arg) :
for (int i = 0; i < nlocal; i++)
for (int m = 0; m < nvalues; m++)
array[i][m] = 0.0;
-
+
// nvalid = next step on which end_of_step does something
// add nvalid to all computes that store invocation times
// since don't know a priori which are invoked by this fix
@@ -202,7 +202,7 @@ FixAveAtom::FixAveAtom(LAMMPS *lmp, int narg, char **arg) :
FixAveAtom::~FixAveAtom()
{
// unregister callback to this fix from Atom class
-
+
atom->delete_callback(id,0);
delete [] which;
@@ -233,19 +233,19 @@ void FixAveAtom::init()
if (which[m] == COMPUTE) {
int icompute = modify->find_compute(ids[m]);
if (icompute < 0)
- error->all(FLERR,"Compute ID for fix ave/atom does not exist");
+ error->all(FLERR,"Compute ID for fix ave/atom does not exist");
value2index[m] = icompute;
-
+
} else if (which[m] == FIX) {
int ifix = modify->find_fix(ids[m]);
- if (ifix < 0)
- error->all(FLERR,"Fix ID for fix ave/atom does not exist");
+ if (ifix < 0)
+ error->all(FLERR,"Fix ID for fix ave/atom does not exist");
value2index[m] = ifix;
} else if (which[m] == VARIABLE) {
int ivariable = input->variable->find(ids[m]);
- if (ivariable < 0)
- error->all(FLERR,"Variable name for fix ave/atom does not exist");
+ if (ivariable < 0)
+ error->all(FLERR,"Variable name for fix ave/atom does not exist");
value2index[m] = ivariable;
} else value2index[m] = -1;
@@ -287,8 +287,8 @@ void FixAveAtom::end_of_step()
if (irepeat == 0)
for (i = 0; i < nlocal; i++)
for (m = 0; m < nvalues; m++)
- array[i][m] = 0.0;
-
+ array[i][m] = 0.0;
+
// accumulate results of attributes,computes,fixes,variables to local copy
// compute/fix/variable may invoke computes so wrap with clear/add
@@ -303,50 +303,50 @@ void FixAveAtom::end_of_step()
if (which[m] == X) {
double **x = atom->x;
for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit) array[i][m] += x[i][j];
+ if (mask[i] & groupbit) array[i][m] += x[i][j];
} else if (which[m] == V) {
double **v = atom->v;
for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit) array[i][m] += v[i][j];
+ if (mask[i] & groupbit) array[i][m] += v[i][j];
} else if (which[m] == F) {
double **f = atom->f;
for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit) array[i][m] += f[i][j];
+ if (mask[i] & groupbit) array[i][m] += f[i][j];
// invoke compute if not previously invoked
} else if (which[m] == COMPUTE) {
Compute *compute = modify->compute[n];
if (!(compute->invoked_flag & INVOKED_PERATOM)) {
- compute->compute_peratom();
- compute->invoked_flag |= INVOKED_PERATOM;
+ compute->compute_peratom();
+ compute->invoked_flag |= INVOKED_PERATOM;
}
if (j == 0) {
- double *compute_vector = compute->vector_atom;
- for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit) array[i][m] += compute_vector[i];
+ double *compute_vector = compute->vector_atom;
+ for (i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit) array[i][m] += compute_vector[i];
} else {
- int jm1 = j - 1;
- double **compute_array = compute->array_atom;
- for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit) array[i][m] += compute_array[i][jm1];
+ int jm1 = j - 1;
+ double **compute_array = compute->array_atom;
+ for (i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit) array[i][m] += compute_array[i][jm1];
}
// access fix fields, guaranteed to be ready
} else if (which[m] == FIX) {
if (j == 0) {
- double *fix_vector = modify->fix[n]->vector_atom;
- for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit) array[i][m] += fix_vector[i];
+ double *fix_vector = modify->fix[n]->vector_atom;
+ for (i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit) array[i][m] += fix_vector[i];
} else {
- int jm1 = j - 1;
- double **fix_array = modify->fix[n]->array_atom;
- for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit) array[i][m] += fix_array[i][jm1];
+ int jm1 = j - 1;
+ double **fix_array = modify->fix[n]->array_atom;
+ for (i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit) array[i][m] += fix_array[i][jm1];
}
// evaluate atom-style variable
diff --git a/src/fix_ave_atom.h b/src/fix_ave_atom.h
index 10bfb34fade93f6bd51d53611d83d64ac33cf2aa..67d760660a7e73efff24f62c4e05e99ceb7c07b5 100644
--- a/src/fix_ave_atom.h
+++ b/src/fix_ave_atom.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_ave_correlate.cpp b/src/fix_ave_correlate.cpp
index 390ce63f5455d316fe3a11312c41313609ecd54d..a08f537bd4f5800cfba7191e3abc16f624671fa1 100644
--- a/src/fix_ave_correlate.cpp
+++ b/src/fix_ave_correlate.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -65,9 +65,9 @@ FixAveCorrelate::FixAveCorrelate(LAMMPS * lmp, int narg, char **arg):
int iarg = 6;
while (iarg < narg) {
- if (strncmp(arg[iarg],"c_",2) == 0 ||
- strncmp(arg[iarg],"f_",2) == 0 ||
- strncmp(arg[iarg],"v_",2) == 0) {
+ if (strncmp(arg[iarg],"c_",2) == 0 ||
+ strncmp(arg[iarg],"f_",2) == 0 ||
+ strncmp(arg[iarg],"v_",2) == 0) {
if (arg[iarg][0] == 'c') which[nvalues] = COMPUTE;
else if (arg[iarg][0] == 'f') which[nvalues] = FIX;
else if (arg[iarg][0] == 'v') which[nvalues] = VARIABLE;
@@ -78,10 +78,10 @@ FixAveCorrelate::FixAveCorrelate(LAMMPS * lmp, int narg, char **arg):
char *ptr = strchr(suffix,'[');
if (ptr) {
- if (suffix[strlen(suffix)-1] != ']')
- error->all(FLERR,"Illegal fix ave/correlate command");
- argindex[nvalues] = atoi(ptr+1);
- *ptr = '\0';
+ if (suffix[strlen(suffix)-1] != ']')
+ error->all(FLERR,"Illegal fix ave/correlate command");
+ argindex[nvalues] = atoi(ptr+1);
+ *ptr = '\0';
} else argindex[nvalues] = 0;
n = strlen(suffix) + 1;
@@ -133,12 +133,12 @@ FixAveCorrelate::FixAveCorrelate(LAMMPS * lmp, int narg, char **arg):
} else if (strcmp(arg[iarg],"file") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/correlate command");
if (me == 0) {
- fp = fopen(arg[iarg+1],"w");
- if (fp == NULL) {
- char str[128];
- sprintf(str,"Cannot open fix ave/correlate file %s",arg[iarg+1]);
- error->one(FLERR,str);
- }
+ fp = fopen(arg[iarg+1],"w");
+ if (fp == NULL) {
+ char str[128];
+ sprintf(str,"Cannot open fix ave/correlate file %s",arg[iarg+1]);
+ error->one(FLERR,str);
+ }
}
iarg += 2;
} else if (strcmp(arg[iarg],"title1") == 0) {
@@ -179,39 +179,39 @@ FixAveCorrelate::FixAveCorrelate(LAMMPS * lmp, int narg, char **arg):
if (which[i] == COMPUTE) {
int icompute = modify->find_compute(ids[i]);
if (icompute < 0)
- error->all(FLERR,"Compute ID for fix ave/correlate does not exist");
+ error->all(FLERR,"Compute ID for fix ave/correlate does not exist");
if (argindex[i] == 0 && modify->compute[icompute]->scalar_flag == 0)
- error->all(FLERR,
- "Fix ave/correlate compute does not calculate a scalar");
+ error->all(FLERR,
+ "Fix ave/correlate compute does not calculate a scalar");
if (argindex[i] && modify->compute[icompute]->vector_flag == 0)
- error->all(FLERR,
- "Fix ave/correlate compute does not calculate a vector");
+ error->all(FLERR,
+ "Fix ave/correlate compute does not calculate a vector");
if (argindex[i] && argindex[i] > modify->compute[icompute]->size_vector)
- error->all(FLERR,"Fix ave/correlate compute vector "
- "is accessed out-of-range");
+ error->all(FLERR,"Fix ave/correlate compute vector "
+ "is accessed out-of-range");
} else if (which[i] == FIX) {
int ifix = modify->find_fix(ids[i]);
if (ifix < 0)
- error->all(FLERR,"Fix ID for fix ave/correlate does not exist");
+ error->all(FLERR,"Fix ID for fix ave/correlate does not exist");
if (argindex[i] == 0 && modify->fix[ifix]->scalar_flag == 0)
- error->all(FLERR,"Fix ave/correlate fix does not calculate a scalar");
+ error->all(FLERR,"Fix ave/correlate fix does not calculate a scalar");
if (argindex[i] && modify->fix[ifix]->vector_flag == 0)
- error->all(FLERR,"Fix ave/correlate fix does not calculate a vector");
+ error->all(FLERR,"Fix ave/correlate fix does not calculate a vector");
if (argindex[i] && argindex[i] > modify->fix[ifix]->size_vector)
- error->all(FLERR,
- "Fix ave/correlate fix vector is accessed out-of-range");
+ error->all(FLERR,
+ "Fix ave/correlate fix vector is accessed out-of-range");
if (nevery % modify->fix[ifix]->global_freq)
- error->all(FLERR,"Fix for fix ave/correlate "
- "not computed at compatible time");
+ error->all(FLERR,"Fix for fix ave/correlate "
+ "not computed at compatible time");
} else if (which[i] == VARIABLE) {
int ivariable = input->variable->find(ids[i]);
if (ivariable < 0)
- error->all(FLERR,"Variable name for fix ave/correlate does not exist");
+ error->all(FLERR,"Variable name for fix ave/correlate does not exist");
if (input->variable->equalstyle(ivariable) == 0)
- error->all(FLERR,
- "Fix ave/correlate variable is not equal-style variable");
+ error->all(FLERR,
+ "Fix ave/correlate variable is not equal-style variable");
}
}
@@ -233,28 +233,28 @@ FixAveCorrelate::FixAveCorrelate(LAMMPS * lmp, int narg, char **arg):
else {
fprintf(fp,"# Index TimeDelta Ncount");
if (type == AUTO)
- for (int i = 0; i < nvalues; i++)
- fprintf(fp," %s*%s",arg[6+i],arg[6+i]);
+ for (int i = 0; i < nvalues; i++)
+ fprintf(fp," %s*%s",arg[6+i],arg[6+i]);
else if (type == UPPER)
- for (int i = 0; i < nvalues; i++)
- for (int j = i+1; j < nvalues; j++)
- fprintf(fp," %s*%s",arg[6+i],arg[6+j]);
- else if (type == LOWER)
- for (int i = 0; i < nvalues; i++)
- for (int j = 0; j < i-1; j++)
- fprintf(fp," %s*%s",arg[6+i],arg[6+j]);
+ for (int i = 0; i < nvalues; i++)
+ for (int j = i+1; j < nvalues; j++)
+ fprintf(fp," %s*%s",arg[6+i],arg[6+j]);
+ else if (type == LOWER)
+ for (int i = 0; i < nvalues; i++)
+ for (int j = 0; j < i-1; j++)
+ fprintf(fp," %s*%s",arg[6+i],arg[6+j]);
else if (type == AUTOUPPER)
- for (int i = 0; i < nvalues; i++)
- for (int j = i; j < nvalues; j++)
- fprintf(fp," %s*%s",arg[6+i],arg[6+j]);
- else if (type == AUTOLOWER)
- for (int i = 0; i < nvalues; i++)
- for (int j = 0; j < i; j++)
- fprintf(fp," %s*%s",arg[6+i],arg[6+j]);
+ for (int i = 0; i < nvalues; i++)
+ for (int j = i; j < nvalues; j++)
+ fprintf(fp," %s*%s",arg[6+i],arg[6+j]);
+ else if (type == AUTOLOWER)
+ for (int i = 0; i < nvalues; i++)
+ for (int j = 0; j < i; j++)
+ fprintf(fp," %s*%s",arg[6+i],arg[6+j]);
else if (type == FULL)
- for (int i = 0; i < nvalues; i++)
- for (int j = 0; j < nvalues; j++)
- fprintf(fp," %s*%s",arg[6+i],arg[6+j]);
+ for (int i = 0; i < nvalues; i++)
+ for (int j = 0; j < nvalues; j++)
+ fprintf(fp," %s*%s",arg[6+i],arg[6+j]);
fprintf(fp,"\n");
}
}
@@ -262,7 +262,7 @@ FixAveCorrelate::FixAveCorrelate(LAMMPS * lmp, int narg, char **arg):
delete [] title1;
delete [] title2;
delete [] title3;
-
+
// allocate and initialize memory for averaging
// set count and corr to zero since they accumulate
// also set save versions to zero in case accessed via compute_array()
@@ -337,19 +337,19 @@ void FixAveCorrelate::init()
if (which[i] == COMPUTE) {
int icompute = modify->find_compute(ids[i]);
if (icompute < 0)
- error->all(FLERR,"Compute ID for fix ave/correlate does not exist");
+ error->all(FLERR,"Compute ID for fix ave/correlate does not exist");
value2index[i] = icompute;
} else if (which[i] == FIX) {
int ifix = modify->find_fix(ids[i]);
- if (ifix < 0)
- error->all(FLERR,"Fix ID for fix ave/correlate does not exist");
+ if (ifix < 0)
+ error->all(FLERR,"Fix ID for fix ave/correlate does not exist");
value2index[i] = ifix;
} else if (which[i] == VARIABLE) {
int ivariable = input->variable->find(ids[i]);
- if (ivariable < 0)
- error->all(FLERR,"Variable name for fix ave/correlate does not exist");
+ if (ivariable < 0)
+ error->all(FLERR,"Variable name for fix ave/correlate does not exist");
value2index[i] = ivariable;
}
}
@@ -398,39 +398,39 @@ void FixAveCorrelate::end_of_step()
for (i = 0; i < nvalues; i++) {
m = value2index[i];
-
+
// invoke compute if not previously invoked
-
+
if (which[i] == COMPUTE) {
Compute *compute = modify->compute[m];
-
+
if (argindex[i] == 0) {
- if (!(compute->invoked_flag & INVOKED_SCALAR)) {
- compute->compute_scalar();
- compute->invoked_flag |= INVOKED_SCALAR;
- }
- scalar = compute->scalar;
+ if (!(compute->invoked_flag & INVOKED_SCALAR)) {
+ compute->compute_scalar();
+ compute->invoked_flag |= INVOKED_SCALAR;
+ }
+ scalar = compute->scalar;
} else {
- if (!(compute->invoked_flag & INVOKED_VECTOR)) {
- compute->compute_vector();
- compute->invoked_flag |= INVOKED_VECTOR;
- }
- scalar = compute->vector[argindex[i]-1];
+ if (!(compute->invoked_flag & INVOKED_VECTOR)) {
+ compute->compute_vector();
+ compute->invoked_flag |= INVOKED_VECTOR;
+ }
+ scalar = compute->vector[argindex[i]-1];
}
-
+
// access fix fields, guaranteed to be ready
-
+
} else if (which[i] == FIX) {
- if (argindex[i] == 0)
- scalar = modify->fix[m]->compute_scalar();
+ if (argindex[i] == 0)
+ scalar = modify->fix[m]->compute_scalar();
else
- scalar = modify->fix[m]->compute_vector(argindex[i]-1);
-
+ scalar = modify->fix[m]->compute_vector(argindex[i]-1);
+
// evaluate equal-style variable
-
+
} else if (which[i] == VARIABLE)
scalar = input->variable->compute_equal(m);
-
+
values[lastindex][i] = scalar;
}
@@ -457,10 +457,10 @@ void FixAveCorrelate::end_of_step()
save_count[i] = count[i];
if (count[i])
for (j = 0; j < npair; j++)
- save_corr[i][j] = prefactor*corr[i][j]/count[i];
+ save_corr[i][j] = prefactor*corr[i][j]/count[i];
else
for (j = 0; j < npair; j++)
- save_corr[i][j] = 0.0;
+ save_corr[i][j] = 0.0;
}
// output to file
@@ -470,11 +470,11 @@ void FixAveCorrelate::end_of_step()
for (i = 0; i < nrepeat; i++) {
fprintf(fp,"%d %d %d",i+1,i*nevery,count[i]);
if (count[i])
- for (j = 0; j < npair; j++)
- fprintf(fp," %g",prefactor*corr[i][j]/count[i]);
+ for (j = 0; j < npair; j++)
+ fprintf(fp," %g",prefactor*corr[i][j]/count[i]);
else
- for (j = 0; j < npair; j++)
- fprintf(fp," 0.0");
+ for (j = 0; j < npair; j++)
+ fprintf(fp," 0.0");
fprintf(fp,"\n");
}
fflush(fp);
@@ -487,7 +487,7 @@ void FixAveCorrelate::end_of_step()
for (i = 0; i < nrepeat; i++) {
count[i] = 0;
for (j = 0; j < npair; j++)
- corr[i][j] = 0.0;
+ corr[i][j] = 0.0;
}
nsample = 1;
accumulate();
@@ -509,7 +509,7 @@ void FixAveCorrelate::accumulate()
for (k = 0; k < nsample; k++) {
ipair = 0;
for (i = 0; i < nvalues; i++) {
- corr[k][ipair++] += values[m][i]*values[n][i];
+ corr[k][ipair++] += values[m][i]*values[n][i];
}
m--;
if (m < 0) m = nrepeat-1;
@@ -519,8 +519,8 @@ void FixAveCorrelate::accumulate()
for (k = 0; k < nsample; k++) {
ipair = 0;
for (i = 0; i < nvalues; i++)
- for (j = i+1; j < nvalues; j++)
- corr[k][ipair++] += values[m][i]*values[n][j];
+ for (j = i+1; j < nvalues; j++)
+ corr[k][ipair++] += values[m][i]*values[n][j];
m--;
if (m < 0) m = nrepeat-1;
}
@@ -529,8 +529,8 @@ void FixAveCorrelate::accumulate()
for (k = 0; k < nsample; k++) {
ipair = 0;
for (i = 0; i < nvalues; i++)
- for (j = 0; j < i-1; j++)
- corr[k][ipair++] += values[m][i]*values[n][j];
+ for (j = 0; j < i-1; j++)
+ corr[k][ipair++] += values[m][i]*values[n][j];
m--;
if (m < 0) m = nrepeat-1;
}
@@ -539,8 +539,8 @@ void FixAveCorrelate::accumulate()
for (k = 0; k < nsample; k++) {
ipair = 0;
for (i = 0; i < nvalues; i++)
- for (j = i; j < nvalues; j++)
- corr[k][ipair++] += values[m][i]*values[n][j];
+ for (j = i; j < nvalues; j++)
+ corr[k][ipair++] += values[m][i]*values[n][j];
m--;
if (m < 0) m = nrepeat-1;
}
@@ -549,8 +549,8 @@ void FixAveCorrelate::accumulate()
for (k = 0; k < nsample; k++) {
ipair = 0;
for (i = 0; i < nvalues; i++)
- for (j = 0; j < i; j++)
- corr[k][ipair++] += values[m][i]*values[n][j];
+ for (j = 0; j < i; j++)
+ corr[k][ipair++] += values[m][i]*values[n][j];
m--;
if (m < 0) m = nrepeat-1;
}
@@ -559,8 +559,8 @@ void FixAveCorrelate::accumulate()
for (k = 0; k < nsample; k++) {
ipair = 0;
for (i = 0; i < nvalues; i++)
- for (j = 0; j < nvalues; j++)
- corr[k][ipair++] += values[m][i]*values[n][j];
+ for (j = 0; j < nvalues; j++)
+ corr[k][ipair++] += values[m][i]*values[n][j];
m--;
if (m < 0) m = nrepeat-1;
}
diff --git a/src/fix_ave_correlate.h b/src/fix_ave_correlate.h
index cae02b83e46726259e69ecafe50ee51d27b93cd6..b54a68c908ed10f8dcd00f6f27c80b055db3310d 100644
--- a/src/fix_ave_correlate.h
+++ b/src/fix_ave_correlate.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -57,7 +57,7 @@ class FixAveCorrelate : public Fix {
int *save_count; // saved values at Nfreq for output via compute_array()
double **save_corr;
-
+
void accumulate();
bigint nextvalid();
};
diff --git a/src/fix_ave_histo.cpp b/src/fix_ave_histo.cpp
index 7dd5a1f6d71f0705015a2f3351730a001fdad7a0..05d5a4343179e2288d848acdbffaf7a4bd7d0bf9 100644
--- a/src/fix_ave_histo.cpp
+++ b/src/fix_ave_histo.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -74,17 +74,17 @@ FixAveHisto::FixAveHisto(LAMMPS *lmp, int narg, char **arg) :
int iarg = 9;
while (iarg < narg) {
if (strcmp(arg[iarg],"x") == 0 ||
- strcmp(arg[iarg],"y") == 0 ||
- strcmp(arg[iarg],"z") == 0 ||
- strcmp(arg[iarg],"vx") == 0 ||
- strcmp(arg[iarg],"vy") == 0 ||
- strcmp(arg[iarg],"vz") == 0 ||
- strcmp(arg[iarg],"fx") == 0 ||
- strcmp(arg[iarg],"fy") == 0 ||
- strcmp(arg[iarg],"fz") == 0 ||
- strncmp(arg[iarg],"c_",2) == 0 ||
- strncmp(arg[iarg],"f_",2) == 0 ||
- strncmp(arg[iarg],"v_",2) == 0) {
+ strcmp(arg[iarg],"y") == 0 ||
+ strcmp(arg[iarg],"z") == 0 ||
+ strcmp(arg[iarg],"vx") == 0 ||
+ strcmp(arg[iarg],"vy") == 0 ||
+ strcmp(arg[iarg],"vz") == 0 ||
+ strcmp(arg[iarg],"fx") == 0 ||
+ strcmp(arg[iarg],"fy") == 0 ||
+ strcmp(arg[iarg],"fz") == 0 ||
+ strncmp(arg[iarg],"c_",2) == 0 ||
+ strncmp(arg[iarg],"f_",2) == 0 ||
+ strncmp(arg[iarg],"v_",2) == 0) {
nvalues++;
iarg++;
} else break;
@@ -162,9 +162,9 @@ FixAveHisto::FixAveHisto(LAMMPS *lmp, int narg, char **arg) :
nvalues++;
iarg++;
- } else if ((strncmp(arg[iarg],"c_",2) == 0) ||
- (strncmp(arg[iarg],"f_",2) == 0) ||
- (strncmp(arg[iarg],"v_",2) == 0)) {
+ } else if ((strncmp(arg[iarg],"c_",2) == 0) ||
+ (strncmp(arg[iarg],"f_",2) == 0) ||
+ (strncmp(arg[iarg],"v_",2) == 0)) {
if (arg[iarg][0] == 'c') which[nvalues] = COMPUTE;
else if (arg[iarg][0] == 'f') which[nvalues] = FIX;
else if (arg[iarg][0] == 'v') which[nvalues] = VARIABLE;
@@ -175,10 +175,10 @@ FixAveHisto::FixAveHisto(LAMMPS *lmp, int narg, char **arg) :
char *ptr = strchr(suffix,'[');
if (ptr) {
- if (suffix[strlen(suffix)-1] != ']')
- error->all(FLERR,"Illegal fix ave/histo command");
- argindex[nvalues] = atoi(ptr+1);
- *ptr = '\0';
+ if (suffix[strlen(suffix)-1] != ']')
+ error->all(FLERR,"Illegal fix ave/histo command");
+ argindex[nvalues] = atoi(ptr+1);
+ *ptr = '\0';
} else argindex[nvalues] = 0;
n = strlen(suffix) + 1;
@@ -186,45 +186,45 @@ FixAveHisto::FixAveHisto(LAMMPS *lmp, int narg, char **arg) :
strcpy(ids[nvalues],suffix);
delete [] suffix;
- if (mode == VECTOR && which[nvalues] == COMPUTE &&
- argindex[nvalues] == 0) {
- int icompute = modify->find_compute(ids[nvalues]);
- if (icompute < 0)
- error->all(FLERR,"Compute ID for fix ave/histo does not exist");
- if (modify->compute[icompute]->array_flag) {
- int ncols = modify->compute[icompute]->size_array_cols;
- maxvalues += ncols-1;
- allocate_values(maxvalues);
- argindex[nvalues] = 1;
- for (int icol = 1; icol < ncols; icol++) {
- which[nvalues+icol] = which[nvalues];
- argindex[nvalues+icol] = icol+1;
- n = strlen(ids[nvalues]) + 1;
- ids[nvalues+icol] = new char[n];
- strcpy(ids[nvalues+icol],ids[nvalues]);
- }
- nvalues += ncols-1;
- }
-
- } else if (mode == VECTOR && which[nvalues] == FIX &&
- argindex[nvalues] == 0) {
- int ifix = modify->find_fix(ids[nvalues]);
- if (ifix < 0)
- error->all(FLERR,"Fix ID for fix ave/histo does not exist");
- if (modify->fix[ifix]->array_flag) {
- int ncols = modify->fix[ifix]->size_array_cols;
- maxvalues += ncols-1;
- allocate_values(maxvalues);
- argindex[nvalues] = 1;
- for (int icol = 1; icol < ncols; icol++) {
- which[nvalues+icol] = which[nvalues];
- argindex[nvalues+icol] = icol+1;
- n = strlen(ids[nvalues]) + 1;
- ids[nvalues+icol] = new char[n];
- strcpy(ids[nvalues+icol],ids[nvalues]);
- }
- nvalues += ncols-1;
- }
+ if (mode == VECTOR && which[nvalues] == COMPUTE &&
+ argindex[nvalues] == 0) {
+ int icompute = modify->find_compute(ids[nvalues]);
+ if (icompute < 0)
+ error->all(FLERR,"Compute ID for fix ave/histo does not exist");
+ if (modify->compute[icompute]->array_flag) {
+ int ncols = modify->compute[icompute]->size_array_cols;
+ maxvalues += ncols-1;
+ allocate_values(maxvalues);
+ argindex[nvalues] = 1;
+ for (int icol = 1; icol < ncols; icol++) {
+ which[nvalues+icol] = which[nvalues];
+ argindex[nvalues+icol] = icol+1;
+ n = strlen(ids[nvalues]) + 1;
+ ids[nvalues+icol] = new char[n];
+ strcpy(ids[nvalues+icol],ids[nvalues]);
+ }
+ nvalues += ncols-1;
+ }
+
+ } else if (mode == VECTOR && which[nvalues] == FIX &&
+ argindex[nvalues] == 0) {
+ int ifix = modify->find_fix(ids[nvalues]);
+ if (ifix < 0)
+ error->all(FLERR,"Fix ID for fix ave/histo does not exist");
+ if (modify->fix[ifix]->array_flag) {
+ int ncols = modify->fix[ifix]->size_array_cols;
+ maxvalues += ncols-1;
+ allocate_values(maxvalues);
+ argindex[nvalues] = 1;
+ for (int icol = 1; icol < ncols; icol++) {
+ which[nvalues+icol] = which[nvalues];
+ argindex[nvalues+icol] = icol+1;
+ n = strlen(ids[nvalues]) + 1;
+ ids[nvalues+icol] = new char[n];
+ strcpy(ids[nvalues+icol],ids[nvalues]);
+ }
+ nvalues += ncols-1;
+ }
}
nvalues++;
@@ -249,14 +249,14 @@ FixAveHisto::FixAveHisto(LAMMPS *lmp, int narg, char **arg) :
else if (which[i] == COMPUTE) {
Compute *compute = modify->compute[modify->find_compute(ids[0])];
if (compute->scalar_flag || compute->vector_flag || compute->array_flag)
- kindflag = GLOBAL;
+ kindflag = GLOBAL;
else if (compute->peratom_flag) kindflag = PERATOM;
else if (compute->local_flag) kindflag = LOCAL;
else error->all(FLERR,"Fix ave/histo input is invalid compute");
} else if (which[i] == FIX) {
Fix *fix = modify->fix[modify->find_fix(ids[0])];
if (fix->scalar_flag || fix->vector_flag || fix->array_flag)
- kindflag = GLOBAL;
+ kindflag = GLOBAL;
else if (fix->peratom_flag) kindflag = PERATOM;
else if (fix->local_flag) kindflag = LOCAL;
else error->all(FLERR,"Fix ave/histo input is invalid fix");
@@ -271,7 +271,7 @@ FixAveHisto::FixAveHisto(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,"Fix ave/histo inputs are not all global, peratom, or local");
}
- if (kind == PERATOM && mode == SCALAR)
+ if (kind == PERATOM && mode == SCALAR)
error->all(FLERR,"Fix ave/histo cannot input per-atom values in scalar mode");
if (kind == LOCAL && mode == SCALAR)
error->all(FLERR,"Fix ave/histo cannot input local values in scalar mode");
@@ -280,133 +280,133 @@ FixAveHisto::FixAveHisto(LAMMPS *lmp, int narg, char **arg) :
if (which[i] == COMPUTE && kind == GLOBAL && mode == SCALAR) {
int icompute = modify->find_compute(ids[i]);
if (icompute < 0)
- error->all(FLERR,"Compute ID for fix ave/histo does not exist");
+ error->all(FLERR,"Compute ID for fix ave/histo does not exist");
if (argindex[i] == 0 && modify->compute[icompute]->scalar_flag == 0)
- error->all(FLERR,"Fix ave/histo compute does not calculate a global scalar");
+ error->all(FLERR,"Fix ave/histo compute does not calculate a global scalar");
if (argindex[i] && modify->compute[icompute]->vector_flag == 0)
- error->all(FLERR,"Fix ave/histo compute does not calculate a global vector");
+ error->all(FLERR,"Fix ave/histo compute does not calculate a global vector");
if (argindex[i] && argindex[i] > modify->compute[icompute]->size_vector)
- error->all(FLERR,"Fix ave/histo compute vector is accessed out-of-range");
+ error->all(FLERR,"Fix ave/histo compute vector is accessed out-of-range");
} else if (which[i] == COMPUTE && kind == GLOBAL && mode == VECTOR) {
int icompute = modify->find_compute(ids[i]);
if (icompute < 0)
- error->all(FLERR,"Compute ID for fix ave/histo does not exist");
+ error->all(FLERR,"Compute ID for fix ave/histo does not exist");
if (argindex[i] == 0 && modify->compute[icompute]->vector_flag == 0)
- error->all(FLERR,"Fix ave/histo compute does not calculate a global vector");
+ error->all(FLERR,"Fix ave/histo compute does not calculate a global vector");
if (argindex[i] && modify->compute[icompute]->array_flag == 0)
- error->all(FLERR,"Fix ave/histo compute does not calculate a global array");
- if (argindex[i] &&
- argindex[i] > modify->compute[icompute]->size_array_cols)
- error->all(FLERR,"Fix ave/histo compute array is accessed out-of-range");
+ error->all(FLERR,"Fix ave/histo compute does not calculate a global array");
+ if (argindex[i] &&
+ argindex[i] > modify->compute[icompute]->size_array_cols)
+ error->all(FLERR,"Fix ave/histo compute array is accessed out-of-range");
} else if (which[i] == COMPUTE && kind == PERATOM) {
int icompute = modify->find_compute(ids[i]);
if (icompute < 0)
- error->all(FLERR,"Compute ID for fix ave/histo does not exist");
+ error->all(FLERR,"Compute ID for fix ave/histo does not exist");
if (modify->compute[icompute]->peratom_flag == 0)
- error->all(FLERR,"Fix ave/histo compute does not calculate per-atom values");
- if (argindex[i] == 0 &&
- modify->compute[icompute]->size_peratom_cols != 0)
- error->all(FLERR,"Fix ave/histo compute does not "
- "calculate a per-atom vector");
+ error->all(FLERR,"Fix ave/histo compute does not calculate per-atom values");
+ if (argindex[i] == 0 &&
+ modify->compute[icompute]->size_peratom_cols != 0)
+ error->all(FLERR,"Fix ave/histo compute does not "
+ "calculate a per-atom vector");
if (argindex[i] && modify->compute[icompute]->size_peratom_cols == 0)
- error->all(FLERR,"Fix ave/histo compute does not "
- "calculate a per-atom array");
- if (argindex[i] &&
- argindex[i] > modify->compute[icompute]->size_peratom_cols)
- error->all(FLERR,"Fix ave/histo compute array is accessed out-of-range");
+ error->all(FLERR,"Fix ave/histo compute does not "
+ "calculate a per-atom array");
+ if (argindex[i] &&
+ argindex[i] > modify->compute[icompute]->size_peratom_cols)
+ error->all(FLERR,"Fix ave/histo compute array is accessed out-of-range");
} else if (which[i] == COMPUTE && kind == LOCAL) {
int icompute = modify->find_compute(ids[i]);
if (icompute < 0)
- error->all(FLERR,"Compute ID for fix ave/histo does not exist");
+ error->all(FLERR,"Compute ID for fix ave/histo does not exist");
if (modify->compute[icompute]->local_flag == 0)
- error->all(FLERR,"Fix ave/histo compute does not calculate local values");
- if (argindex[i] == 0 &&
- modify->compute[icompute]->size_local_cols != 0)
- error->all(FLERR,"Fix ave/histo compute does not "
- "calculate a local vector");
+ error->all(FLERR,"Fix ave/histo compute does not calculate local values");
+ if (argindex[i] == 0 &&
+ modify->compute[icompute]->size_local_cols != 0)
+ error->all(FLERR,"Fix ave/histo compute does not "
+ "calculate a local vector");
if (argindex[i] && modify->compute[icompute]->size_local_cols == 0)
- error->all(FLERR,"Fix ave/histo compute does not "
- "calculate a local array");
- if (argindex[i] &&
- argindex[i] > modify->compute[icompute]->size_local_cols)
- error->all(FLERR,"Fix ave/histo compute array is accessed out-of-range");
+ error->all(FLERR,"Fix ave/histo compute does not "
+ "calculate a local array");
+ if (argindex[i] &&
+ argindex[i] > modify->compute[icompute]->size_local_cols)
+ error->all(FLERR,"Fix ave/histo compute array is accessed out-of-range");
} else if (which[i] == FIX && kind == GLOBAL && mode == SCALAR) {
int ifix = modify->find_fix(ids[i]);
if (ifix < 0)
- error->all(FLERR,"Fix ID for fix ave/histo does not exist");
+ error->all(FLERR,"Fix ID for fix ave/histo does not exist");
if (argindex[i] == 0 && modify->fix[ifix]->scalar_flag == 0)
- error->all(FLERR,"Fix ave/histo fix does not calculate a global scalar");
+ error->all(FLERR,"Fix ave/histo fix does not calculate a global scalar");
if (argindex[i] && modify->fix[ifix]->vector_flag == 0)
- error->all(FLERR,"Fix ave/histo fix does not calculate a global vector");
+ error->all(FLERR,"Fix ave/histo fix does not calculate a global vector");
if (argindex[i] && argindex[i] > modify->fix[ifix]->size_vector)
- error->all(FLERR,"Fix ave/histo fix vector is accessed out-of-range");
+ error->all(FLERR,"Fix ave/histo fix vector is accessed out-of-range");
if (nevery % modify->fix[ifix]->global_freq)
- error->all(FLERR,"Fix for fix ave/histo not computed at compatible time");
+ error->all(FLERR,"Fix for fix ave/histo not computed at compatible time");
} else if (which[i] == FIX && kind == GLOBAL && mode == VECTOR) {
int ifix = modify->find_fix(ids[i]);
if (ifix < 0)
- error->all(FLERR,"Fix ID for fix ave/histo does not exist");
+ error->all(FLERR,"Fix ID for fix ave/histo does not exist");
if (argindex[i] == 0 && modify->fix[ifix]->vector_flag == 0)
- error->all(FLERR,"Fix ave/histo fix does not calculate a global vector");
+ error->all(FLERR,"Fix ave/histo fix does not calculate a global vector");
if (argindex[i] && modify->fix[ifix]->array_flag == 0)
- error->all(FLERR,"Fix ave/histo fix does not calculate a global array");
+ error->all(FLERR,"Fix ave/histo fix does not calculate a global array");
if (argindex[i] && argindex[i] > modify->fix[ifix]->size_array_cols)
- error->all(FLERR,"Fix ave/histo fix array is accessed out-of-range");
+ error->all(FLERR,"Fix ave/histo fix array is accessed out-of-range");
if (nevery % modify->fix[ifix]->global_freq)
- error->all(FLERR,"Fix for fix ave/histo not computed at compatible time");
+ error->all(FLERR,"Fix for fix ave/histo not computed at compatible time");
} else if (which[i] == FIX && kind == PERATOM) {
int ifix = modify->find_fix(ids[i]);
if (ifix < 0)
- error->all(FLERR,"Fix ID for fix ave/histo does not exist");
+ error->all(FLERR,"Fix ID for fix ave/histo does not exist");
if (modify->fix[ifix]->peratom_flag == 0)
- error->all(FLERR,"Fix ave/histo fix does not calculate per-atom values");
- if (argindex[i] == 0 &&
- modify->fix[ifix]->size_peratom_cols != 0)
- error->all(FLERR,"Fix ave/histo fix does not "
- "calculate a per-atom vector");
+ error->all(FLERR,"Fix ave/histo fix does not calculate per-atom values");
+ if (argindex[i] == 0 &&
+ modify->fix[ifix]->size_peratom_cols != 0)
+ error->all(FLERR,"Fix ave/histo fix does not "
+ "calculate a per-atom vector");
if (argindex[i] && modify->fix[ifix]->size_peratom_cols == 0)
- error->all(FLERR,"Fix ave/histo fix does not "
- "calculate a per-atom array");
- if (argindex[i] &&
- argindex[i] > modify->fix[ifix]->size_peratom_cols)
- error->all(FLERR,"Fix ave/histo fix array is accessed out-of-range");
+ error->all(FLERR,"Fix ave/histo fix does not "
+ "calculate a per-atom array");
+ if (argindex[i] &&
+ argindex[i] > modify->fix[ifix]->size_peratom_cols)
+ error->all(FLERR,"Fix ave/histo fix array is accessed out-of-range");
if (nevery % modify->fix[ifix]->global_freq)
- error->all(FLERR,"Fix for fix ave/histo not computed at compatible time");
+ error->all(FLERR,"Fix for fix ave/histo not computed at compatible time");
} else if (which[i] == FIX && kind == LOCAL) {
int ifix = modify->find_fix(ids[i]);
if (ifix < 0)
- error->all(FLERR,"Fix ID for fix ave/histo does not exist");
+ error->all(FLERR,"Fix ID for fix ave/histo does not exist");
if (modify->fix[ifix]->local_flag == 0)
- error->all(FLERR,"Fix ave/histo fix does not calculate local values");
- if (argindex[i] == 0 &&
- modify->fix[ifix]->size_local_cols != 0)
- error->all(FLERR,"Fix ave/histo fix does not "
- "calculate a local vector");
+ error->all(FLERR,"Fix ave/histo fix does not calculate local values");
+ if (argindex[i] == 0 &&
+ modify->fix[ifix]->size_local_cols != 0)
+ error->all(FLERR,"Fix ave/histo fix does not "
+ "calculate a local vector");
if (argindex[i] && modify->fix[ifix]->size_local_cols == 0)
- error->all(FLERR,"Fix ave/histo fix does not "
- "calculate a local array");
- if (argindex[i] &&
- argindex[i] > modify->fix[ifix]->size_local_cols)
- error->all(FLERR,"Fix ave/histo fix array is accessed out-of-range");
+ error->all(FLERR,"Fix ave/histo fix does not "
+ "calculate a local array");
+ if (argindex[i] &&
+ argindex[i] > modify->fix[ifix]->size_local_cols)
+ error->all(FLERR,"Fix ave/histo fix array is accessed out-of-range");
if (nevery % modify->fix[ifix]->global_freq)
- error->all(FLERR,"Fix for fix ave/histo not computed at compatible time");
+ error->all(FLERR,"Fix for fix ave/histo not computed at compatible time");
} else if (which[i] == VARIABLE && kind == GLOBAL) {
int ivariable = input->variable->find(ids[i]);
if (ivariable < 0)
- error->all(FLERR,"Variable name for fix ave/histo does not exist");
+ error->all(FLERR,"Variable name for fix ave/histo does not exist");
} else if (which[i] == VARIABLE && kind == PERATOM) {
int ivariable = input->variable->find(ids[i]);
if (ivariable < 0)
- error->all(FLERR,"Variable name for fix ave/histo does not exist");
+ error->all(FLERR,"Variable name for fix ave/histo does not exist");
}
}
@@ -417,7 +417,7 @@ FixAveHisto::FixAveHisto(LAMMPS *lmp, int narg, char **arg) :
else fprintf(fp,"# Histogrammed data for fix %s\n",id);
if (title2) fprintf(fp,"%s\n",title2);
else fprintf(fp,"# TimeStep Number-of-bins "
- "Total-counts Missing-counts Min-value Max-value\n");
+ "Total-counts Missing-counts Min-value Max-value\n");
if (title3) fprintf(fp,"%s\n",title3);
else fprintf(fp,"# Bin Coord Count Count/Total\n");
}
@@ -521,19 +521,19 @@ void FixAveHisto::init()
if (which[i] == COMPUTE) {
int icompute = modify->find_compute(ids[i]);
if (icompute < 0)
- error->all(FLERR,"Compute ID for fix ave/histo does not exist");
+ error->all(FLERR,"Compute ID for fix ave/histo does not exist");
value2index[i] = icompute;
} else if (which[i] == FIX) {
int ifix = modify->find_fix(ids[i]);
- if (ifix < 0)
- error->all(FLERR,"Fix ID for fix ave/histo does not exist");
+ if (ifix < 0)
+ error->all(FLERR,"Fix ID for fix ave/histo does not exist");
value2index[i] = ifix;
} else if (which[i] == VARIABLE) {
int ivariable = input->variable->find(ids[i]);
- if (ivariable < 0)
- error->all(FLERR,"Variable name for fix ave/histo does not exist");
+ if (ivariable < 0)
+ error->all(FLERR,"Variable name for fix ave/histo does not exist");
value2index[i] = ivariable;
}
}
@@ -595,103 +595,103 @@ void FixAveHisto::end_of_step()
bin_atoms(&atom->f[0][j],3);
// invoke compute if not previously invoked
-
+
if (which[i] == COMPUTE) {
Compute *compute = modify->compute[m];
if (kind == GLOBAL && mode == SCALAR) {
- if (j == 0) {
- if (!(compute->invoked_flag & INVOKED_SCALAR)) {
- compute->compute_scalar();
- compute->invoked_flag |= INVOKED_SCALAR;
- }
- bin_one(compute->scalar);
- } else {
- if (!(compute->invoked_flag & INVOKED_VECTOR)) {
- compute->compute_vector();
- compute->invoked_flag |= INVOKED_VECTOR;
- }
- bin_one(compute->vector[j-1]);
- }
+ if (j == 0) {
+ if (!(compute->invoked_flag & INVOKED_SCALAR)) {
+ compute->compute_scalar();
+ compute->invoked_flag |= INVOKED_SCALAR;
+ }
+ bin_one(compute->scalar);
+ } else {
+ if (!(compute->invoked_flag & INVOKED_VECTOR)) {
+ compute->compute_vector();
+ compute->invoked_flag |= INVOKED_VECTOR;
+ }
+ bin_one(compute->vector[j-1]);
+ }
} else if (kind == GLOBAL && mode == VECTOR) {
- if (j == 0) {
- if (!(compute->invoked_flag & INVOKED_VECTOR)) {
- compute->compute_vector();
- compute->invoked_flag |= INVOKED_VECTOR;
- }
- bin_vector(compute->size_vector,compute->vector,1);
- } else {
- if (!(compute->invoked_flag & INVOKED_ARRAY)) {
- compute->compute_array();
- compute->invoked_flag |= INVOKED_ARRAY;
- }
- bin_vector(compute->size_array_rows,&compute->array[0][j-1],
- compute->size_array_cols);
- }
+ if (j == 0) {
+ if (!(compute->invoked_flag & INVOKED_VECTOR)) {
+ compute->compute_vector();
+ compute->invoked_flag |= INVOKED_VECTOR;
+ }
+ bin_vector(compute->size_vector,compute->vector,1);
+ } else {
+ if (!(compute->invoked_flag & INVOKED_ARRAY)) {
+ compute->compute_array();
+ compute->invoked_flag |= INVOKED_ARRAY;
+ }
+ bin_vector(compute->size_array_rows,&compute->array[0][j-1],
+ compute->size_array_cols);
+ }
} else if (kind == PERATOM) {
- if (!(compute->invoked_flag & INVOKED_PERATOM)) {
- compute->compute_peratom();
- compute->invoked_flag |= INVOKED_PERATOM;
- }
- if (j == 0)
- bin_atoms(compute->vector_atom,1);
- else
- bin_atoms(compute->array_atom[j-1],
- compute->size_peratom_cols);
+ if (!(compute->invoked_flag & INVOKED_PERATOM)) {
+ compute->compute_peratom();
+ compute->invoked_flag |= INVOKED_PERATOM;
+ }
+ if (j == 0)
+ bin_atoms(compute->vector_atom,1);
+ else
+ bin_atoms(compute->array_atom[j-1],
+ compute->size_peratom_cols);
} else if (kind == LOCAL) {
- if (!(compute->invoked_flag & INVOKED_LOCAL)) {
- compute->compute_local();
- compute->invoked_flag |= INVOKED_LOCAL;
- }
- if (j == 0)
- bin_vector(compute->size_local_rows,compute->vector_local,1);
- else
- bin_vector(compute->size_local_rows,&compute->array_local[0][j-1],
- compute->size_local_cols);
+ if (!(compute->invoked_flag & INVOKED_LOCAL)) {
+ compute->compute_local();
+ compute->invoked_flag |= INVOKED_LOCAL;
+ }
+ if (j == 0)
+ bin_vector(compute->size_local_rows,compute->vector_local,1);
+ else
+ bin_vector(compute->size_local_rows,&compute->array_local[0][j-1],
+ compute->size_local_cols);
}
// access fix fields, guaranteed to be ready
-
+
} else if (which[i] == FIX) {
Fix *fix = modify->fix[m];
if (kind == GLOBAL && mode == SCALAR) {
- if (j == 0) bin_one(fix->compute_scalar());
- else bin_one(fix->compute_vector(j-1));
+ if (j == 0) bin_one(fix->compute_scalar());
+ else bin_one(fix->compute_vector(j-1));
} else if (kind == GLOBAL && mode == VECTOR) {
- if (j == 0) {
- int n = fix->size_vector;
- for (i = 0; i < n; i++) bin_one(fix->compute_vector(i));
- } else {
- int n = fix->size_vector;
- for (i = 0; i < n; i++) bin_one(fix->compute_array(i,j-1));
- }
+ if (j == 0) {
+ int n = fix->size_vector;
+ for (i = 0; i < n; i++) bin_one(fix->compute_vector(i));
+ } else {
+ int n = fix->size_vector;
+ for (i = 0; i < n; i++) bin_one(fix->compute_array(i,j-1));
+ }
} else if (kind == PERATOM) {
- if (j == 0) bin_atoms(fix->vector_atom,1);
- else bin_atoms(fix->array_atom[j-1],fix->size_peratom_cols);
+ if (j == 0) bin_atoms(fix->vector_atom,1);
+ else bin_atoms(fix->array_atom[j-1],fix->size_peratom_cols);
} else if (kind == LOCAL) {
- if (j == 0) bin_vector(fix->size_local_rows,fix->vector_local,1);
- else
- bin_vector(fix->size_local_rows,&fix->array_local[0][j-1],
- fix->size_local_cols);
+ if (j == 0) bin_vector(fix->size_local_rows,fix->vector_local,1);
+ else
+ bin_vector(fix->size_local_rows,&fix->array_local[0][j-1],
+ fix->size_local_cols);
}
// evaluate equal-style variable
-
+
} else if (which[i] == VARIABLE && kind == GLOBAL) {
bin_one(input->variable->compute_equal(m));
} else if (which[i] == VARIABLE && kind == PERATOM) {
if (atom->nlocal > maxatom) {
- memory->destroy(vector);
- maxatom = atom->nmax;
- memory->create(vector,maxatom,"ave/histo:vector");
+ memory->destroy(vector);
+ maxatom = atom->nmax;
+ memory->create(vector,maxatom,"ave/histo:vector");
}
input->variable->compute_atom(m,igroup,vector,1,0);
bin_atoms(vector,1);
@@ -737,14 +737,14 @@ void FixAveHisto::end_of_step()
stats_total[2] = stats[2];
stats_total[3] = stats[3];
for (i = 0; i < nbins; i++) bin_total[i] = bin[i];
-
+
} else if (ave == RUNNING) {
stats_total[0] += stats[0];
stats_total[1] += stats[1];
stats_total[2] = MIN(stats_total[2],stats[2]);
stats_total[3] = MAX(stats_total[3],stats[3]);
for (i = 0; i < nbins; i++) bin_total[i] += bin[i];
-
+
} else if (ave == WINDOW) {
stats_total[0] += stats[0];
if (window_limit) stats_total[0] -= stats_list[iwindow][0];
@@ -752,25 +752,25 @@ void FixAveHisto::end_of_step()
stats_total[1] += stats[1];
if (window_limit) stats_total[1] -= stats_list[iwindow][1];
stats_list[iwindow][1] = stats[1];
-
+
if (window_limit) m = nwindow;
else m = iwindow+1;
-
+
stats_list[iwindow][2] = stats[2];
stats_total[2] = stats_list[0][2];
- for (i = 1; i < m; i++)
+ for (i = 1; i < m; i++)
stats_total[2] = MIN(stats_total[2],stats_list[i][2]);
stats_list[iwindow][3] = stats[3];
stats_total[3] = stats_list[0][3];
- for (i = 1; i < m; i++)
+ for (i = 1; i < m; i++)
stats_total[3] = MAX(stats_total[3],stats_list[i][3]);
-
+
for (i = 0; i < nbins; i++) {
bin_total[i] += bin[i];
if (window_limit) bin_total[i] -= bin_list[iwindow][i];
bin_list[iwindow][i] = bin[i];
}
-
+
iwindow++;
if (iwindow == nwindow) {
iwindow = 0;
@@ -782,14 +782,14 @@ void FixAveHisto::end_of_step()
if (fp && me == 0) {
fprintf(fp,BIGINT_FORMAT " %d %g %g %g %g\n",ntimestep,nbins,
- stats_total[0],stats_total[1],stats_total[2],stats_total[3]);
+ stats_total[0],stats_total[1],stats_total[2],stats_total[3]);
if (stats_total[0] != 0.0)
for (i = 0; i < nbins; i++)
- fprintf(fp,"%d %g %g %g\n",
- i+1,coord[i],bin_total[i],bin_total[i]/stats_total[0]);
+ fprintf(fp,"%d %g %g %g\n",
+ i+1,coord[i],bin_total[i],bin_total[i]/stats_total[0]);
else
for (i = 0; i < nbins; i++)
- fprintf(fp,"%d %g %g %g\n",i+1,coord[i],0.0,0.0);
+ fprintf(fp,"%d %g %g %g\n",i+1,coord[i],0.0,0.0);
fflush(fp);
}
}
@@ -898,12 +898,12 @@ void FixAveHisto::options(int narg, char **arg)
if (strcmp(arg[iarg],"file") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/histo command");
if (me == 0) {
- fp = fopen(arg[iarg+1],"w");
- if (fp == NULL) {
- char str[128];
- sprintf(str,"Cannot open fix ave/histo file %s",arg[iarg+1]);
- error->one(FLERR,str);
- }
+ fp = fopen(arg[iarg+1],"w");
+ if (fp == NULL) {
+ char str[128];
+ sprintf(str,"Cannot open fix ave/histo file %s",arg[iarg+1]);
+ error->one(FLERR,str);
+ }
}
iarg += 2;
} else if (strcmp(arg[iarg],"ave") == 0) {
@@ -913,9 +913,9 @@ void FixAveHisto::options(int narg, char **arg)
else if (strcmp(arg[iarg+1],"window") == 0) ave = WINDOW;
else error->all(FLERR,"Illegal fix ave/histo command");
if (ave == WINDOW) {
- if (iarg+3 > narg) error->all(FLERR,"Illegal fix ave/histo command");
- nwindow = atoi(arg[iarg+2]);
- if (nwindow <= 0) error->all(FLERR,"Illegal fix ave/histo command");
+ if (iarg+3 > narg) error->all(FLERR,"Illegal fix ave/histo command");
+ nwindow = atoi(arg[iarg+2]);
+ if (nwindow <= 0) error->all(FLERR,"Illegal fix ave/histo command");
}
iarg += 2;
if (ave == WINDOW) iarg++;
diff --git a/src/fix_ave_histo.h b/src/fix_ave_histo.h
index 4316bd72e73a6effd1aa111535d7875cb78561fc..106224b3d24d6376e19bed06daf5da4f4c145e37 100644
--- a/src/fix_ave_histo.h
+++ b/src/fix_ave_histo.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_ave_spatial.cpp b/src/fix_ave_spatial.cpp
index 51e91a47f3b5e10cd6c13909a1b24dd8e449e6f0..35624863bf6fd5c1ed2c270a1b2c237c32ca57e1 100644
--- a/src/fix_ave_spatial.cpp
+++ b/src/fix_ave_spatial.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -86,7 +86,7 @@ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
if (!ndim) error->all(FLERR,"Illegal fix ave/spatial command");
if (ndim == 2 && dim[0] == dim[1])
error->all(FLERR,"Same dimension twice in fix ave/spatial");
- if (ndim == 3 && (dim[0] == dim[1] || dim[1] == dim[2] || dim[0] == dim[2]))
+ if (ndim == 3 && (dim[0] == dim[1] || dim[1] == dim[2] || dim[0] == dim[2]))
error->all(FLERR,"Same dimension twice in fix ave/spatial");
// parse values until one isn't recognized
@@ -127,9 +127,9 @@ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
which[nvalues] = DENSITY_MASS;
argindex[nvalues++] = 0;
- } else if (strncmp(arg[iarg],"c_",2) == 0 ||
- strncmp(arg[iarg],"f_",2) == 0 ||
- strncmp(arg[iarg],"v_",2) == 0) {
+ } else if (strncmp(arg[iarg],"c_",2) == 0 ||
+ strncmp(arg[iarg],"f_",2) == 0 ||
+ strncmp(arg[iarg],"v_",2) == 0) {
if (arg[iarg][0] == 'c') which[nvalues] = COMPUTE;
else if (arg[iarg][0] == 'f') which[nvalues] = FIX;
else if (arg[iarg][0] == 'v') which[nvalues] = VARIABLE;
@@ -140,10 +140,10 @@ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
char *ptr = strchr(suffix,'[');
if (ptr) {
- if (suffix[strlen(suffix)-1] != ']')
- error->all(FLERR,"Illegal fix ave/spatial command");
- argindex[nvalues] = atoi(ptr+1);
- *ptr = '\0';
+ if (suffix[strlen(suffix)-1] != ']')
+ error->all(FLERR,"Illegal fix ave/spatial command");
+ argindex[nvalues] = atoi(ptr+1);
+ *ptr = '\0';
} else argindex[nvalues] = 0;
n = strlen(suffix) + 1;
@@ -187,8 +187,8 @@ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"region") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/spatial command");
iregion = domain->find_region(arg[iarg+1]);
- if (iregion == -1)
- error->all(FLERR,"Region ID for fix ave/spatial does not exist");
+ if (iregion == -1)
+ error->all(FLERR,"Region ID for fix ave/spatial does not exist");
int n = strlen(arg[iarg+1]) + 1;
idregion = new char[n];
strcpy(idregion,arg[iarg+1]);
@@ -197,12 +197,12 @@ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"file") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/spatial command");
if (me == 0) {
- fp = fopen(arg[iarg+1],"w");
- if (fp == NULL) {
- char str[128];
- sprintf(str,"Cannot open fix ave/spatial file %s",arg[iarg+1]);
- error->one(FLERR,str);
- }
+ fp = fopen(arg[iarg+1],"w");
+ if (fp == NULL) {
+ char str[128];
+ sprintf(str,"Cannot open fix ave/spatial file %s",arg[iarg+1]);
+ error->one(FLERR,str);
+ }
}
iarg += 2;
} else if (strcmp(arg[iarg],"ave") == 0) {
@@ -212,9 +212,9 @@ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
else if (strcmp(arg[iarg+1],"window") == 0) ave = WINDOW;
else error->all(FLERR,"Illegal fix ave/spatial command");
if (ave == WINDOW) {
- if (iarg+3 > narg) error->all(FLERR,"Illegal fix ave/spatial command");
- nwindow = atoi(arg[iarg+2]);
- if (nwindow <= 0) error->all(FLERR,"Illegal fix ave/spatial command");
+ if (iarg+3 > narg) error->all(FLERR,"Illegal fix ave/spatial command");
+ nwindow = atoi(arg[iarg+2]);
+ if (nwindow <= 0) error->all(FLERR,"Illegal fix ave/spatial command");
}
iarg += 2;
if (ave == WINDOW) iarg++;
@@ -249,52 +249,52 @@ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
if (nfreq % nevery || (nrepeat-1)*nevery >= nfreq)
error->all(FLERR,"Illegal fix ave/spatial command");
if (delta[0] <= 0.0) error->all(FLERR,"Illegal fix ave/spatial command");
- if (ndim >= 2 && delta[1] <= 0.0)
+ if (ndim >= 2 && delta[1] <= 0.0)
error->all(FLERR,"Illegal fix ave/spatial command");
- if (ndim == 3 && delta[2] <= 0.0)
+ if (ndim == 3 && delta[2] <= 0.0)
error->all(FLERR,"Illegal fix ave/spatial command");
for (int i = 0; i < nvalues; i++) {
if (which[i] == COMPUTE) {
int icompute = modify->find_compute(ids[i]);
if (icompute < 0)
- error->all(FLERR,"Compute ID for fix ave/spatial does not exist");
+ error->all(FLERR,"Compute ID for fix ave/spatial does not exist");
if (modify->compute[icompute]->peratom_flag == 0)
- error->all(FLERR,"Fix ave/spatial compute does not "
- "calculate per-atom values");
- if (argindex[i] == 0 &&
- modify->compute[icompute]->size_peratom_cols != 0)
- error->all(FLERR,"Fix ave/spatial compute does not "
- "calculate a per-atom vector");
+ error->all(FLERR,"Fix ave/spatial compute does not "
+ "calculate per-atom values");
+ if (argindex[i] == 0 &&
+ modify->compute[icompute]->size_peratom_cols != 0)
+ error->all(FLERR,"Fix ave/spatial compute does not "
+ "calculate a per-atom vector");
if (argindex[i] && modify->compute[icompute]->size_peratom_cols == 0)
- error->all(FLERR,"Fix ave/spatial compute does not "
- "calculate a per-atom array");
- if (argindex[i] &&
- argindex[i] > modify->compute[icompute]->size_peratom_cols)
- error->all(FLERR,
- "Fix ave/spatial compute vector is accessed out-of-range");
+ error->all(FLERR,"Fix ave/spatial compute does not "
+ "calculate a per-atom array");
+ if (argindex[i] &&
+ argindex[i] > modify->compute[icompute]->size_peratom_cols)
+ error->all(FLERR,
+ "Fix ave/spatial compute vector is accessed out-of-range");
} else if (which[i] == FIX) {
int ifix = modify->find_fix(ids[i]);
if (ifix < 0)
- error->all(FLERR,"Fix ID for fix ave/spatial does not exist");
+ error->all(FLERR,"Fix ID for fix ave/spatial does not exist");
if (modify->fix[ifix]->peratom_flag == 0)
- error->all(FLERR,
- "Fix ave/spatial fix does not calculate per-atom values");
+ error->all(FLERR,
+ "Fix ave/spatial fix does not calculate per-atom values");
if (argindex[i] && modify->fix[ifix]->size_peratom_cols != 0)
- error->all(FLERR,
- "Fix ave/spatial fix does not calculate a per-atom vector");
+ error->all(FLERR,
+ "Fix ave/spatial fix does not calculate a per-atom vector");
if (argindex[i] && modify->fix[ifix]->size_peratom_cols == 0)
- error->all(FLERR,
- "Fix ave/spatial fix does not calculate a per-atom array");
+ error->all(FLERR,
+ "Fix ave/spatial fix does not calculate a per-atom array");
if (argindex[i] && argindex[i] > modify->fix[ifix]->size_peratom_cols)
- error->all(FLERR,"Fix ave/spatial fix vector is accessed out-of-range");
+ error->all(FLERR,"Fix ave/spatial fix vector is accessed out-of-range");
} else if (which[i] == VARIABLE) {
int ivariable = input->variable->find(ids[i]);
if (ivariable < 0)
- error->all(FLERR,"Variable name for fix ave/spatial does not exist");
+ error->all(FLERR,"Variable name for fix ave/spatial does not exist");
if (input->variable->atomstyle(ivariable) == 0)
- error->all(FLERR,"Fix ave/spatial variable is not atom-style variable");
+ error->all(FLERR,"Fix ave/spatial variable is not atom-style variable");
}
}
@@ -303,7 +303,7 @@ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
if (fp && me == 0) {
if (title1) fprintf(fp,"%s\n",title1);
else fprintf(fp,"# Spatial-averaged data for fix %s and group %s\n",
- id,arg[1]);
+ id,arg[1]);
if (title2) fprintf(fp,"%s\n",title2);
else fprintf(fp,"# Timestep Number-of-bins\n");
if (title3) fprintf(fp,"%s\n",title3);
@@ -332,7 +332,7 @@ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
int triclinic = domain->triclinic;
if (triclinic == 1 && scaleflag != REDUCED)
error->all(FLERR,
- "Fix ave/spatial for triclinic boxes requires units reduced");
+ "Fix ave/spatial for triclinic boxes requires units reduced");
if (scaleflag == LATTICE && domain->lattice == NULL)
error->all(FLERR,"Use of fix ave/spatial with undefined lattice");
@@ -449,23 +449,23 @@ void FixAveSpatial::init()
if (which[m] == COMPUTE) {
int icompute = modify->find_compute(ids[m]);
if (icompute < 0)
- error->all(FLERR,"Compute ID for fix ave/spatial does not exist");
+ error->all(FLERR,"Compute ID for fix ave/spatial does not exist");
value2index[m] = icompute;
-
+
} else if (which[m] == FIX) {
int ifix = modify->find_fix(ids[m]);
- if (ifix < 0)
- error->all(FLERR,"Fix ID for fix ave/spatial does not exist");
+ if (ifix < 0)
+ error->all(FLERR,"Fix ID for fix ave/spatial does not exist");
value2index[m] = ifix;
if (nevery % modify->fix[ifix]->peratom_freq)
- error->all(FLERR,
- "Fix for fix ave/spatial not computed at compatible time");
+ error->all(FLERR,
+ "Fix for fix ave/spatial not computed at compatible time");
} else if (which[m] == VARIABLE) {
int ivariable = input->variable->find(ids[m]);
- if (ivariable < 0)
- error->all(FLERR,"Variable name for fix ave/spatial does not exist");
+ if (ivariable < 0)
+ error->all(FLERR,"Variable name for fix ave/spatial does not exist");
value2index[m] = ivariable;
} else value2index[m] = -1;
@@ -553,15 +553,15 @@ void FixAveSpatial::end_of_step()
double **attribute;
if (which[m] == V) attribute = atom->v;
else attribute = atom->f;
-
+
if (regionflag == 0) {
- for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit)
- values_one[bin[i]][m] += attribute[i][j];
+ for (i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit)
+ values_one[bin[i]][m] += attribute[i][j];
} else {
- for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]))
- values_one[bin[i]][m] += attribute[i][j];
+ for (i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]))
+ values_one[bin[i]][m] += attribute[i][j];
}
// DENSITY_NUMBER adds 1 to values
@@ -569,13 +569,13 @@ void FixAveSpatial::end_of_step()
} else if (which[m] == DENSITY_NUMBER) {
if (regionflag == 0) {
- for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit)
- values_one[bin[i]][m] += 1.0;
+ for (i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit)
+ values_one[bin[i]][m] += 1.0;
} else {
- for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]))
- values_one[bin[i]][m] += 1.0;
+ for (i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]))
+ values_one[bin[i]][m] += 1.0;
}
// DENSITY_MASS adds mass to values
@@ -586,17 +586,17 @@ void FixAveSpatial::end_of_step()
double *rmass = atom->rmass;
if (regionflag == 0) {
- for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit) {
- if (rmass) values_one[bin[i]][m] += rmass[i];
- else values_one[bin[i]][m] += mass[type[i]];
- }
+ for (i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit) {
+ if (rmass) values_one[bin[i]][m] += rmass[i];
+ else values_one[bin[i]][m] += mass[type[i]];
+ }
} else {
- for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
- if (rmass) values_one[bin[i]][m] += rmass[i];
- else values_one[bin[i]][m] += mass[type[i]];
- }
+ for (i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
+ if (rmass) values_one[bin[i]][m] += rmass[i];
+ else values_one[bin[i]][m] += mass[type[i]];
+ }
}
// COMPUTE adds its scalar or vector component to values
@@ -605,25 +605,25 @@ void FixAveSpatial::end_of_step()
} else if (which[m] == COMPUTE) {
Compute *compute = modify->compute[n];
if (!(compute->invoked_flag & INVOKED_PERATOM)) {
- compute->compute_peratom();
- compute->invoked_flag |= INVOKED_PERATOM;
+ compute->compute_peratom();
+ compute->invoked_flag |= INVOKED_PERATOM;
}
double *vector = compute->vector_atom;
double **array = compute->array_atom;
int jm1 = j - 1;
if (regionflag == 0) {
- for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit) {
- if (j == 0) values_one[bin[i]][m] += vector[i];
- else values_one[bin[i]][m] += array[i][jm1];
- }
+ for (i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit) {
+ if (j == 0) values_one[bin[i]][m] += vector[i];
+ else values_one[bin[i]][m] += array[i][jm1];
+ }
} else {
- for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
- if (j == 0) values_one[bin[i]][m] += vector[i];
- else values_one[bin[i]][m] += array[i][jm1];
- }
+ for (i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
+ if (j == 0) values_one[bin[i]][m] += vector[i];
+ else values_one[bin[i]][m] += array[i][jm1];
+ }
}
// FIX adds its scalar or vector component to values
@@ -635,17 +635,17 @@ void FixAveSpatial::end_of_step()
int jm1 = j - 1;
if (regionflag == 0) {
- for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit) {
- if (j == 0) values_one[bin[i]][m] += vector[i];
- else values_one[bin[i]][m] += array[i][jm1];
- }
+ for (i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit) {
+ if (j == 0) values_one[bin[i]][m] += vector[i];
+ else values_one[bin[i]][m] += array[i][jm1];
+ }
} else {
- for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
- if (j == 0) values_one[bin[i]][m] += vector[i];
- else values_one[bin[i]][m] += array[i][jm1];
- }
+ for (i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
+ if (j == 0) values_one[bin[i]][m] += vector[i];
+ else values_one[bin[i]][m] += array[i][jm1];
+ }
}
// VARIABLE adds its per-atom quantities to values
@@ -653,21 +653,21 @@ void FixAveSpatial::end_of_step()
} else if (which[m] == VARIABLE) {
if (nlocal > maxvar) {
- maxvar = atom->nmax;
- memory->destroy(varatom);
- memory->create(varatom,maxvar,"ave/spatial:varatom");
+ maxvar = atom->nmax;
+ memory->destroy(varatom);
+ memory->create(varatom,maxvar,"ave/spatial:varatom");
}
input->variable->compute_atom(n,igroup,varatom,1,0);
if (regionflag == 0) {
- for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit)
- values_one[bin[i]][m] += varatom[i];
+ for (i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit)
+ values_one[bin[i]][m] += varatom[i];
} else {
- for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]))
- values_one[bin[i]][m] += varatom[i];
+ for (i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]))
+ values_one[bin[i]][m] += varatom[i];
}
}
}
@@ -681,17 +681,17 @@ void FixAveSpatial::end_of_step()
for (m = 0; m < nbins; m++) {
count_many[m] += count_one[m];
for (j = 0; j < nvalues; j++)
- values_many[m][j] += values_one[m][j];
+ values_many[m][j] += values_one[m][j];
}
} else {
MPI_Allreduce(count_one,count_many,nbins,MPI_DOUBLE,MPI_SUM,world);
for (m = 0; m < nbins; m++) {
if (count_many[m] > 0.0)
- for (j = 0; j < nvalues; j++) {
- if (which[j] == DENSITY_NUMBER || which[j] == DENSITY_MASS)
- values_many[m][j] += values_one[m][j];
- else values_many[m][j] += values_one[m][j]/count_many[m];
- }
+ for (j = 0; j < nvalues; j++) {
+ if (which[j] == DENSITY_NUMBER || which[j] == DENSITY_MASS)
+ values_many[m][j] += values_one[m][j];
+ else values_many[m][j] += values_one[m][j]/count_many[m];
+ }
count_sum[m] += count_many[m];
}
}
@@ -721,21 +721,21 @@ void FixAveSpatial::end_of_step()
if (normflag == ALL) {
MPI_Allreduce(count_many,count_sum,nbins,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(&values_many[0][0],&values_sum[0][0],nbins*nvalues,
- MPI_DOUBLE,MPI_SUM,world);
+ MPI_DOUBLE,MPI_SUM,world);
for (m = 0; m < nbins; m++) {
if (count_sum[m] > 0.0)
- for (j = 0; j < nvalues; j++)
- if (which[j] == DENSITY_NUMBER) values_sum[m][j] /= repeat;
- else if (which[j] == DENSITY_MASS) values_sum[m][j] *= mv2d/repeat;
- else values_sum[m][j] /= count_sum[m];
+ for (j = 0; j < nvalues; j++)
+ if (which[j] == DENSITY_NUMBER) values_sum[m][j] /= repeat;
+ else if (which[j] == DENSITY_MASS) values_sum[m][j] *= mv2d/repeat;
+ else values_sum[m][j] /= count_sum[m];
count_sum[m] /= repeat;
}
} else {
MPI_Allreduce(&values_many[0][0],&values_sum[0][0],nbins*nvalues,
- MPI_DOUBLE,MPI_SUM,world);
+ MPI_DOUBLE,MPI_SUM,world);
for (m = 0; m < nbins; m++) {
for (j = 0; j < nvalues; j++)
- values_sum[m][j] /= repeat;
+ values_sum[m][j] /= repeat;
count_sum[m] /= repeat;
}
}
@@ -745,7 +745,7 @@ void FixAveSpatial::end_of_step()
for (j = 0; j < nvalues; j++)
if (which[j] == DENSITY_NUMBER || which[j] == DENSITY_MASS)
for (m = 0; m < nbins; m++)
- values_sum[m][j] /= bin_volume;
+ values_sum[m][j] /= bin_volume;
// if ave = ONE, only single Nfreq timestep value is needed
// if ave = RUNNING, combine with all previous Nfreq timestep values
@@ -753,8 +753,8 @@ void FixAveSpatial::end_of_step()
if (ave == ONE) {
for (m = 0; m < nbins; m++) {
- for (i = 0; i < nvalues; i++)
- values_total[m][i] = values_sum[m][i];
+ for (i = 0; i < nvalues; i++)
+ values_total[m][i] = values_sum[m][i];
count_total[m] = count_sum[m];
}
norm = 1;
@@ -762,7 +762,7 @@ void FixAveSpatial::end_of_step()
} else if (ave == RUNNING) {
for (m = 0; m < nbins; m++) {
for (i = 0; i < nvalues; i++)
- values_total[m][i] += values_sum[m][i];
+ values_total[m][i] += values_sum[m][i];
count_total[m] += count_sum[m];
}
norm++;
@@ -770,9 +770,9 @@ void FixAveSpatial::end_of_step()
} else if (ave == WINDOW) {
for (m = 0; m < nbins; m++) {
for (i = 0; i < nvalues; i++) {
- values_total[m][i] += values_sum[m][i];
- if (window_limit) values_total[m][i] -= values_list[iwindow][m][i];
- values_list[iwindow][m][i] = values_sum[m][i];
+ values_total[m][i] += values_sum[m][i];
+ if (window_limit) values_total[m][i] -= values_list[iwindow][m][i];
+ values_list[iwindow][m][i] = values_sum[m][i];
}
count_total[m] += count_sum[m];
if (window_limit) count_total[m] -= count_list[iwindow][m];
@@ -789,32 +789,32 @@ void FixAveSpatial::end_of_step()
}
// output result to file
-
+
if (fp && me == 0) {
fprintf(fp,BIGINT_FORMAT " %d\n",ntimestep,nbins);
if (ndim == 1)
for (m = 0; m < nbins; m++) {
- fprintf(fp," %d %g %g",m+1,coord[m][0],
- count_total[m]/norm);
- for (i = 0; i < nvalues; i++)
- fprintf(fp," %g",values_total[m][i]/norm);
- fprintf(fp,"\n");
+ fprintf(fp," %d %g %g",m+1,coord[m][0],
+ count_total[m]/norm);
+ for (i = 0; i < nvalues; i++)
+ fprintf(fp," %g",values_total[m][i]/norm);
+ fprintf(fp,"\n");
}
else if (ndim == 2)
for (m = 0; m < nbins; m++) {
- fprintf(fp," %d %g %g %g",m+1,coord[m][0],coord[m][1],
- count_total[m]/norm);
- for (i = 0; i < nvalues; i++)
- fprintf(fp," %g",values_total[m][i]/norm);
- fprintf(fp,"\n");
+ fprintf(fp," %d %g %g %g",m+1,coord[m][0],coord[m][1],
+ count_total[m]/norm);
+ for (i = 0; i < nvalues; i++)
+ fprintf(fp," %g",values_total[m][i]/norm);
+ fprintf(fp,"\n");
}
else
for (m = 0; m < nbins; m++) {
- fprintf(fp," %d %g %g %g %g",m+1,coord[m][0],coord[m][1],coord[m][2],
- count_total[m]/norm);
- for (i = 0; i < nvalues; i++)
- fprintf(fp," %g",values_total[m][i]/norm);
- fprintf(fp,"\n");
+ fprintf(fp," %d %g %g %g %g",m+1,coord[m][0],coord[m][1],coord[m][2],
+ count_total[m]/norm);
+ for (i = 0; i < nvalues; i++)
+ fprintf(fp," %g",values_total[m][i]/norm);
+ fprintf(fp,"\n");
}
fflush(fp);
@@ -854,9 +854,9 @@ void FixAveSpatial::setup_bins()
for (m = 0; m < ndim; m++) {
if (originflag[m] == LOWER) origin[m] = boxlo[dim[m]];
else if (originflag[m] == UPPER) origin[m] = boxhi[dim[m]];
- else if (originflag[m] == CENTER)
+ else if (originflag[m] == CENTER)
origin[m] = 0.5 * (boxlo[dim[m]] + boxhi[dim[m]]);
-
+
if (origin[m] < boxlo[dim[m]]) {
n = static_cast<int> ((boxlo[dim[m]] - origin[m]) * invdelta[m]);
lo = origin[m] + n*delta[m];
@@ -873,7 +873,7 @@ void FixAveSpatial::setup_bins()
n = static_cast<int> ((origin[m] - boxhi[dim[m]]) * invdelta[m]);
hi = origin[m] - n*delta[m];
}
-
+
offset[m] = lo;
nlayers[m] = static_cast<int> ((hi-lo) * invdelta[m] + 0.5);
nbins *= nlayers[m];
@@ -888,19 +888,19 @@ void FixAveSpatial::setup_bins()
memory->grow(count_many,nbins,"ave/spatial:count_many");
memory->grow(count_sum,nbins,"ave/spatial:count_sum");
memory->grow(count_total,nbins,"ave/spatial:count_total");
-
+
memory->grow(coord,nbins,ndim,"ave/spatial:coord");
memory->grow(values_one,nbins,nvalues,"ave/spatial:values_one");
memory->grow(values_many,nbins,nvalues,"ave/spatial:values_many");
memory->grow(values_sum,nbins,nvalues,"ave/spatial:values_sum");
memory->grow(values_total,nbins,nvalues,"ave/spatial:values_total");
-
+
// only allocate count and values list for ave = WINDOW
-
+
if (ave == WINDOW) {
memory->create(count_list,nwindow,nbins,"ave/spatial:count_list");
memory->create(values_list,nwindow,nbins,nvalues,
- "ave/spatial:values_list");
+ "ave/spatial:values_list");
}
// reinitialize regrown count/values total since they accumulate
@@ -921,9 +921,9 @@ void FixAveSpatial::setup_bins()
for (i = 0; i < nlayers[0]; i++) {
coord1 = offset[0] + (i+0.5)*delta[0];
for (j = 0; j < nlayers[1]; j++) {
- coord[m][0] = coord1;
- coord[m][1] = offset[1] + (j+0.5)*delta[1];
- m++;
+ coord[m][0] = coord1;
+ coord[m][1] = offset[1] + (j+0.5)*delta[1];
+ m++;
}
}
} else if (ndim == 3) {
@@ -931,13 +931,13 @@ void FixAveSpatial::setup_bins()
for (i = 0; i < nlayers[0]; i++) {
coord1 = offset[0] + (i+0.5)*delta[0];
for (j = 0; j < nlayers[1]; j++) {
- coord2 = offset[1] + (j+0.5)*delta[1];
- for (k = 0; k < nlayers[2]; k++) {
- coord[m][0] = coord1;
- coord[m][1] = coord2;
- coord[m][2] = offset[2] + (k+0.5)*delta[2];
- m++;
- }
+ coord2 = offset[1] + (j+0.5)*delta[1];
+ for (k = 0; k < nlayers[2]; k++) {
+ coord[m][0] = coord1;
+ coord[m][1] = coord2;
+ coord[m][2] = offset[2] + (k+0.5)*delta[2];
+ m++;
+ }
}
}
}
@@ -981,35 +981,35 @@ void FixAveSpatial::atom2bin1d()
if (scaleflag == REDUCED) domain->x2lamda(nlocal);
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- xremap = x[i][idim];
- if (periodicity) {
- if (xremap < boxlo[idim]) xremap += prd[idim];
- if (xremap >= boxhi[idim]) xremap -= prd[idim];
- }
- ibin = static_cast<int> ((xremap - offset[0]) * invdelta[0]);
- ibin = MAX(ibin,0);
- ibin = MIN(ibin,nlayerm1);
- bin[i] = ibin;
- count_one[ibin] += 1.0;
+ xremap = x[i][idim];
+ if (periodicity) {
+ if (xremap < boxlo[idim]) xremap += prd[idim];
+ if (xremap >= boxhi[idim]) xremap -= prd[idim];
+ }
+ ibin = static_cast<int> ((xremap - offset[0]) * invdelta[0]);
+ ibin = MAX(ibin,0);
+ ibin = MIN(ibin,nlayerm1);
+ bin[i] = ibin;
+ count_one[ibin] += 1.0;
}
if (scaleflag == REDUCED) domain->lamda2x(nlocal);
} else {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
- if (scaleflag == REDUCED) {
- domain->x2lamda(x[i],lamda);
- xremap = lamda[idim];
- } else xremap = x[i][idim];
- if (periodicity) {
- if (xremap < boxlo[idim]) xremap += prd[idim];
- if (xremap >= boxhi[idim]) xremap -= prd[idim];
- }
- ibin = static_cast<int> ((xremap - offset[0]) * invdelta[0]);
- ibin = MAX(ibin,0);
- ibin = MIN(ibin,nlayerm1);
- bin[i] = ibin;
- count_one[ibin] += 1.0;
+ if (scaleflag == REDUCED) {
+ domain->x2lamda(x[i],lamda);
+ xremap = lamda[idim];
+ } else xremap = x[i][idim];
+ if (periodicity) {
+ if (xremap < boxlo[idim]) xremap += prd[idim];
+ if (xremap >= boxhi[idim]) xremap -= prd[idim];
+ }
+ ibin = static_cast<int> ((xremap - offset[0]) * invdelta[0]);
+ ibin = MAX(ibin,0);
+ ibin = MIN(ibin,nlayerm1);
+ bin[i] = ibin;
+ count_one[ibin] += 1.0;
}
}
}
@@ -1054,61 +1054,61 @@ void FixAveSpatial::atom2bin2d()
if (scaleflag == REDUCED) domain->x2lamda(nlocal);
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- xremap = x[i][idim];
- if (periodicity[idim]) {
- if (xremap < boxlo[idim]) xremap += prd[idim];
- if (xremap >= boxhi[idim]) xremap -= prd[idim];
- }
- i1bin = static_cast<int> ((xremap - offset[0]) * invdelta[0]);
- i1bin = MAX(i1bin,0);
- i1bin = MIN(i1bin,nlayer1m1);
-
- yremap = x[i][jdim];
- if (periodicity[jdim]) {
- if (yremap < boxlo[jdim]) yremap += prd[jdim];
- if (yremap >= boxhi[jdim]) yremap -= prd[jdim];
- }
- i2bin = static_cast<int> ((yremap - offset[1]) * invdelta[1]);
- i2bin = MAX(i2bin,0);
- i2bin = MIN(i2bin,nlayer2m1);
-
- ibin = i1bin*nlayers[1] + i2bin;
- bin[i] = ibin;
- count_one[ibin] += 1.0;
+ xremap = x[i][idim];
+ if (periodicity[idim]) {
+ if (xremap < boxlo[idim]) xremap += prd[idim];
+ if (xremap >= boxhi[idim]) xremap -= prd[idim];
+ }
+ i1bin = static_cast<int> ((xremap - offset[0]) * invdelta[0]);
+ i1bin = MAX(i1bin,0);
+ i1bin = MIN(i1bin,nlayer1m1);
+
+ yremap = x[i][jdim];
+ if (periodicity[jdim]) {
+ if (yremap < boxlo[jdim]) yremap += prd[jdim];
+ if (yremap >= boxhi[jdim]) yremap -= prd[jdim];
+ }
+ i2bin = static_cast<int> ((yremap - offset[1]) * invdelta[1]);
+ i2bin = MAX(i2bin,0);
+ i2bin = MIN(i2bin,nlayer2m1);
+
+ ibin = i1bin*nlayers[1] + i2bin;
+ bin[i] = ibin;
+ count_one[ibin] += 1.0;
}
if (scaleflag == REDUCED) domain->lamda2x(nlocal);
} else {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
- if (scaleflag == REDUCED) {
- domain->x2lamda(x[i],lamda);
- xremap = lamda[idim];
- yremap = lamda[jdim];
- } else {
- xremap = x[i][idim];
- yremap = x[i][jdim];
- }
-
- if (periodicity[idim]) {
- if (xremap < boxlo[idim]) xremap += prd[idim];
- if (xremap >= boxhi[idim]) xremap -= prd[idim];
- }
- i1bin = static_cast<int> ((xremap - offset[0]) * invdelta[0]);
- i1bin = MAX(i1bin,0);
- i1bin = MIN(i1bin,nlayer1m1-1);
-
- if (periodicity[jdim]) {
- if (yremap < boxlo[jdim]) yremap += prd[jdim];
- if (yremap >= boxhi[jdim]) yremap -= prd[jdim];
- }
- i2bin = static_cast<int> ((yremap - offset[1]) * invdelta[1]);
- i2bin = MAX(i2bin,0);
- i2bin = MIN(i2bin,nlayer2m1-1);
-
- ibin = i1bin*nlayers[1] + i2bin;
- bin[i] = ibin;
- count_one[ibin] += 1.0;
+ if (scaleflag == REDUCED) {
+ domain->x2lamda(x[i],lamda);
+ xremap = lamda[idim];
+ yremap = lamda[jdim];
+ } else {
+ xremap = x[i][idim];
+ yremap = x[i][jdim];
+ }
+
+ if (periodicity[idim]) {
+ if (xremap < boxlo[idim]) xremap += prd[idim];
+ if (xremap >= boxhi[idim]) xremap -= prd[idim];
+ }
+ i1bin = static_cast<int> ((xremap - offset[0]) * invdelta[0]);
+ i1bin = MAX(i1bin,0);
+ i1bin = MIN(i1bin,nlayer1m1-1);
+
+ if (periodicity[jdim]) {
+ if (yremap < boxlo[jdim]) yremap += prd[jdim];
+ if (yremap >= boxhi[jdim]) yremap -= prd[jdim];
+ }
+ i2bin = static_cast<int> ((yremap - offset[1]) * invdelta[1]);
+ i2bin = MAX(i2bin,0);
+ i2bin = MIN(i2bin,nlayer2m1-1);
+
+ ibin = i1bin*nlayers[1] + i2bin;
+ bin[i] = ibin;
+ count_one[ibin] += 1.0;
}
}
}
@@ -1155,80 +1155,80 @@ void FixAveSpatial::atom2bin3d()
if (scaleflag == REDUCED) domain->x2lamda(nlocal);
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- xremap = x[i][idim];
- if (periodicity[idim]) {
- if (xremap < boxlo[idim]) xremap += prd[idim];
- if (xremap >= boxhi[idim]) xremap -= prd[idim];
- }
- i1bin = static_cast<int> ((xremap - offset[0]) * invdelta[0]);
- i1bin = MAX(i1bin,0);
- i1bin = MIN(i1bin,nlayer1m1);
-
- yremap = x[i][jdim];
- if (periodicity[jdim]) {
- if (yremap < boxlo[jdim]) yremap += prd[jdim];
- if (yremap >= boxhi[jdim]) yremap -= prd[jdim];
- }
- i2bin = static_cast<int> ((yremap - offset[1]) * invdelta[1]);
- i2bin = MAX(i2bin,0);
- i2bin = MIN(i2bin,nlayer2m1);
-
- zremap = x[i][kdim];
- if (periodicity[kdim]) {
- if (zremap < boxlo[kdim]) yremap += prd[kdim];
- if (zremap >= boxhi[kdim]) yremap -= prd[kdim];
- }
- i3bin = static_cast<int> ((zremap - offset[2]) * invdelta[2]);
- i3bin = MAX(i3bin,0);
- i3bin = MIN(i3bin,nlayer3m1);
-
- ibin = i1bin*nlayers[1]*nlayers[2] + i2bin*nlayers[2] + i3bin;
- bin[i] = ibin;
- count_one[ibin] += 1.0;
+ xremap = x[i][idim];
+ if (periodicity[idim]) {
+ if (xremap < boxlo[idim]) xremap += prd[idim];
+ if (xremap >= boxhi[idim]) xremap -= prd[idim];
+ }
+ i1bin = static_cast<int> ((xremap - offset[0]) * invdelta[0]);
+ i1bin = MAX(i1bin,0);
+ i1bin = MIN(i1bin,nlayer1m1);
+
+ yremap = x[i][jdim];
+ if (periodicity[jdim]) {
+ if (yremap < boxlo[jdim]) yremap += prd[jdim];
+ if (yremap >= boxhi[jdim]) yremap -= prd[jdim];
+ }
+ i2bin = static_cast<int> ((yremap - offset[1]) * invdelta[1]);
+ i2bin = MAX(i2bin,0);
+ i2bin = MIN(i2bin,nlayer2m1);
+
+ zremap = x[i][kdim];
+ if (periodicity[kdim]) {
+ if (zremap < boxlo[kdim]) yremap += prd[kdim];
+ if (zremap >= boxhi[kdim]) yremap -= prd[kdim];
+ }
+ i3bin = static_cast<int> ((zremap - offset[2]) * invdelta[2]);
+ i3bin = MAX(i3bin,0);
+ i3bin = MIN(i3bin,nlayer3m1);
+
+ ibin = i1bin*nlayers[1]*nlayers[2] + i2bin*nlayers[2] + i3bin;
+ bin[i] = ibin;
+ count_one[ibin] += 1.0;
}
if (scaleflag == REDUCED) domain->lamda2x(nlocal);
} else {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
- if (scaleflag == REDUCED) {
- domain->x2lamda(x[i],lamda);
- xremap = lamda[idim];
- yremap = lamda[jdim];
- zremap = lamda[kdim];
- } else {
- xremap = x[i][idim];
- yremap = x[i][jdim];
- zremap = x[i][kdim];
- }
-
- if (periodicity[idim]) {
- if (xremap < boxlo[idim]) xremap += prd[idim];
- if (xremap >= boxhi[idim]) xremap -= prd[idim];
- }
- i1bin = static_cast<int> ((xremap - offset[0]) * invdelta[0]);
- i1bin = MAX(i1bin,0);
- i1bin = MIN(i1bin,nlayer1m1);
-
- if (periodicity[jdim]) {
- if (yremap < boxlo[jdim]) yremap += prd[jdim];
- if (yremap >= boxhi[jdim]) yremap -= prd[jdim];
- }
- i2bin = static_cast<int> ((yremap - offset[1]) * invdelta[1]);
- i2bin = MAX(i2bin,0);
- i2bin = MIN(i2bin,nlayer2m1);
-
- if (periodicity[kdim]) {
- if (zremap < boxlo[kdim]) yremap += prd[kdim];
- if (zremap >= boxhi[kdim]) yremap -= prd[kdim];
- }
- i3bin = static_cast<int> ((zremap - offset[2]) * invdelta[2]);
- i3bin = MAX(i3bin,0);
- i3bin = MIN(i3bin,nlayer3m1);
-
- ibin = i1bin*nlayers[1]*nlayers[2] + i2bin*nlayers[2] + i3bin;
- bin[i] = ibin;
- count_one[ibin] += 1.0;
+ if (scaleflag == REDUCED) {
+ domain->x2lamda(x[i],lamda);
+ xremap = lamda[idim];
+ yremap = lamda[jdim];
+ zremap = lamda[kdim];
+ } else {
+ xremap = x[i][idim];
+ yremap = x[i][jdim];
+ zremap = x[i][kdim];
+ }
+
+ if (periodicity[idim]) {
+ if (xremap < boxlo[idim]) xremap += prd[idim];
+ if (xremap >= boxhi[idim]) xremap -= prd[idim];
+ }
+ i1bin = static_cast<int> ((xremap - offset[0]) * invdelta[0]);
+ i1bin = MAX(i1bin,0);
+ i1bin = MIN(i1bin,nlayer1m1);
+
+ if (periodicity[jdim]) {
+ if (yremap < boxlo[jdim]) yremap += prd[jdim];
+ if (yremap >= boxhi[jdim]) yremap -= prd[jdim];
+ }
+ i2bin = static_cast<int> ((yremap - offset[1]) * invdelta[1]);
+ i2bin = MAX(i2bin,0);
+ i2bin = MIN(i2bin,nlayer2m1);
+
+ if (periodicity[kdim]) {
+ if (zremap < boxlo[kdim]) yremap += prd[kdim];
+ if (zremap >= boxhi[kdim]) yremap -= prd[kdim];
+ }
+ i3bin = static_cast<int> ((zremap - offset[2]) * invdelta[2]);
+ i3bin = MAX(i3bin,0);
+ i3bin = MIN(i3bin,nlayer3m1);
+
+ ibin = i1bin*nlayers[1]*nlayers[2] + i2bin*nlayers[2] + i3bin;
+ bin[i] = ibin;
+ count_one[ibin] += 1.0;
}
}
}
diff --git a/src/fix_ave_spatial.h b/src/fix_ave_spatial.h
index ece55f48fc50e96da0d6d3f84e978280874fb4b6..fb0420a7d61f5488c5f5ecb5d69bd35e3e7bf3f9 100644
--- a/src/fix_ave_spatial.h
+++ b/src/fix_ave_spatial.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -54,7 +54,7 @@ class FixAveSpatial : public Fix {
int dim[3],originflag[3],nlayers[3];
double origin[3],delta[3];
- double offset[3],invdelta[3];
+ double offset[3],invdelta[3];
int maxvar;
double *varatom;
diff --git a/src/fix_ave_time.cpp b/src/fix_ave_time.cpp
index 12e779cc6477386d369ad79e251cc61dd23be9c4..b113c0163bd8e3e5c6e9ec38ccf764aff67a529b 100644
--- a/src/fix_ave_time.cpp
+++ b/src/fix_ave_time.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -61,9 +61,9 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
int iarg = 6;
while (iarg < narg) {
- if ((strncmp(arg[iarg],"c_",2) == 0) ||
- (strncmp(arg[iarg],"f_",2) == 0) ||
- (strncmp(arg[iarg],"v_",2) == 0)) {
+ if ((strncmp(arg[iarg],"c_",2) == 0) ||
+ (strncmp(arg[iarg],"f_",2) == 0) ||
+ (strncmp(arg[iarg],"v_",2) == 0)) {
nvalues++;
iarg++;
} else break;
@@ -84,9 +84,9 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
iarg = 6;
while (iarg < narg) {
- if (strncmp(arg[iarg],"c_",2) == 0 ||
- strncmp(arg[iarg],"f_",2) == 0 ||
- strncmp(arg[iarg],"v_",2) == 0) {
+ if (strncmp(arg[iarg],"c_",2) == 0 ||
+ strncmp(arg[iarg],"f_",2) == 0 ||
+ strncmp(arg[iarg],"v_",2) == 0) {
if (arg[iarg][0] == 'c') which[nvalues] = COMPUTE;
else if (arg[iarg][0] == 'f') which[nvalues] = FIX;
else if (arg[iarg][0] == 'v') which[nvalues] = VARIABLE;
@@ -97,10 +97,10 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
char *ptr = strchr(suffix,'[');
if (ptr) {
- if (suffix[strlen(suffix)-1] != ']')
- error->all(FLERR,"Illegal fix ave/time command");
- argindex[nvalues] = atoi(ptr+1);
- *ptr = '\0';
+ if (suffix[strlen(suffix)-1] != ']')
+ error->all(FLERR,"Illegal fix ave/time command");
+ argindex[nvalues] = atoi(ptr+1);
+ *ptr = '\0';
} else argindex[nvalues] = 0;
n = strlen(suffix) + 1;
@@ -108,45 +108,45 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
strcpy(ids[nvalues],suffix);
delete [] suffix;
- if (mode == VECTOR && which[nvalues] == COMPUTE &&
- argindex[nvalues] == 0) {
- int icompute = modify->find_compute(ids[nvalues]);
- if (icompute < 0)
- error->all(FLERR,"Compute ID for fix ave/time does not exist");
- if (modify->compute[icompute]->array_flag) {
- int ncols = modify->compute[icompute]->size_array_cols;
- maxvalues += ncols-1;
- allocate_values(maxvalues);
- argindex[nvalues] = 1;
- for (int icol = 1; icol < ncols; icol++) {
- which[nvalues+icol] = which[nvalues];
- argindex[nvalues+icol] = icol+1;
- n = strlen(ids[nvalues]) + 1;
- ids[nvalues+icol] = new char[n];
- strcpy(ids[nvalues+icol],ids[nvalues]);
- }
- nvalues += ncols-1;
- }
-
- } else if (mode == VECTOR && which[nvalues] == FIX &&
- argindex[nvalues] == 0) {
- int ifix = modify->find_fix(ids[nvalues]);
- if (ifix < 0)
- error->all(FLERR,"Fix ID for fix ave/time does not exist");
- if (modify->fix[ifix]->array_flag) {
- int ncols = modify->fix[ifix]->size_array_cols;
- maxvalues += ncols-1;
- allocate_values(maxvalues);
- argindex[nvalues] = 1;
- for (int icol = 1; icol < ncols; icol++) {
- which[nvalues+icol] = which[nvalues];
- argindex[nvalues+icol] = icol+1;
- n = strlen(ids[nvalues]) + 1;
- ids[nvalues+icol] = new char[n];
- strcpy(ids[nvalues+icol],ids[nvalues]);
- }
- nvalues += ncols-1;
- }
+ if (mode == VECTOR && which[nvalues] == COMPUTE &&
+ argindex[nvalues] == 0) {
+ int icompute = modify->find_compute(ids[nvalues]);
+ if (icompute < 0)
+ error->all(FLERR,"Compute ID for fix ave/time does not exist");
+ if (modify->compute[icompute]->array_flag) {
+ int ncols = modify->compute[icompute]->size_array_cols;
+ maxvalues += ncols-1;
+ allocate_values(maxvalues);
+ argindex[nvalues] = 1;
+ for (int icol = 1; icol < ncols; icol++) {
+ which[nvalues+icol] = which[nvalues];
+ argindex[nvalues+icol] = icol+1;
+ n = strlen(ids[nvalues]) + 1;
+ ids[nvalues+icol] = new char[n];
+ strcpy(ids[nvalues+icol],ids[nvalues]);
+ }
+ nvalues += ncols-1;
+ }
+
+ } else if (mode == VECTOR && which[nvalues] == FIX &&
+ argindex[nvalues] == 0) {
+ int ifix = modify->find_fix(ids[nvalues]);
+ if (ifix < 0)
+ error->all(FLERR,"Fix ID for fix ave/time does not exist");
+ if (modify->fix[ifix]->array_flag) {
+ int ncols = modify->fix[ifix]->size_array_cols;
+ maxvalues += ncols-1;
+ allocate_values(maxvalues);
+ argindex[nvalues] = 1;
+ for (int icol = 1; icol < ncols; icol++) {
+ which[nvalues+icol] = which[nvalues];
+ argindex[nvalues+icol] = icol+1;
+ n = strlen(ids[nvalues]) + 1;
+ ids[nvalues+icol] = new char[n];
+ strcpy(ids[nvalues+icol],ids[nvalues]);
+ }
+ nvalues += ncols-1;
+ }
}
nvalues++;
@@ -175,60 +175,60 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
if (which[i] == COMPUTE && mode == SCALAR) {
int icompute = modify->find_compute(ids[i]);
if (icompute < 0)
- error->all(FLERR,"Compute ID for fix ave/time does not exist");
+ error->all(FLERR,"Compute ID for fix ave/time does not exist");
if (argindex[i] == 0 && modify->compute[icompute]->scalar_flag == 0)
- error->all(FLERR,"Fix ave/time compute does not calculate a scalar");
+ error->all(FLERR,"Fix ave/time compute does not calculate a scalar");
if (argindex[i] && modify->compute[icompute]->vector_flag == 0)
- error->all(FLERR,"Fix ave/time compute does not calculate a vector");
+ error->all(FLERR,"Fix ave/time compute does not calculate a vector");
if (argindex[i] && argindex[i] > modify->compute[icompute]->size_vector)
- error->all(FLERR,"Fix ave/time compute vector is accessed out-of-range");
+ error->all(FLERR,"Fix ave/time compute vector is accessed out-of-range");
} else if (which[i] == COMPUTE && mode == VECTOR) {
int icompute = modify->find_compute(ids[i]);
if (icompute < 0)
- error->all(FLERR,"Compute ID for fix ave/time does not exist");
+ error->all(FLERR,"Compute ID for fix ave/time does not exist");
if (argindex[i] == 0 && modify->compute[icompute]->vector_flag == 0)
- error->all(FLERR,"Fix ave/time compute does not calculate a vector");
+ error->all(FLERR,"Fix ave/time compute does not calculate a vector");
if (argindex[i] && modify->compute[icompute]->array_flag == 0)
- error->all(FLERR,"Fix ave/time compute does not calculate an array");
- if (argindex[i] &&
- argindex[i] > modify->compute[icompute]->size_array_cols)
- error->all(FLERR,"Fix ave/time compute array is accessed out-of-range");
+ error->all(FLERR,"Fix ave/time compute does not calculate an array");
+ if (argindex[i] &&
+ argindex[i] > modify->compute[icompute]->size_array_cols)
+ error->all(FLERR,"Fix ave/time compute array is accessed out-of-range");
} else if (which[i] == FIX && mode == SCALAR) {
int ifix = modify->find_fix(ids[i]);
if (ifix < 0)
- error->all(FLERR,"Fix ID for fix ave/time does not exist");
+ error->all(FLERR,"Fix ID for fix ave/time does not exist");
if (argindex[i] == 0 && modify->fix[ifix]->scalar_flag == 0)
- error->all(FLERR,"Fix ave/time fix does not calculate a scalar");
+ error->all(FLERR,"Fix ave/time fix does not calculate a scalar");
if (argindex[i] && modify->fix[ifix]->vector_flag == 0)
- error->all(FLERR,"Fix ave/time fix does not calculate a vector");
+ error->all(FLERR,"Fix ave/time fix does not calculate a vector");
if (argindex[i] && argindex[i] > modify->fix[ifix]->size_vector)
- error->all(FLERR,"Fix ave/time fix vector is accessed out-of-range");
+ error->all(FLERR,"Fix ave/time fix vector is accessed out-of-range");
if (nevery % modify->fix[ifix]->global_freq)
- error->all(FLERR,"Fix for fix ave/time not computed at compatible time");
+ error->all(FLERR,"Fix for fix ave/time not computed at compatible time");
} else if (which[i] == FIX && mode == VECTOR) {
int ifix = modify->find_fix(ids[i]);
if (ifix < 0)
- error->all(FLERR,"Fix ID for fix ave/time does not exist");
+ error->all(FLERR,"Fix ID for fix ave/time does not exist");
if (argindex[i] == 0 && modify->fix[ifix]->vector_flag == 0)
- error->all(FLERR,"Fix ave/time fix does not calculate a vector");
+ error->all(FLERR,"Fix ave/time fix does not calculate a vector");
if (argindex[i] && modify->fix[ifix]->array_flag == 0)
- error->all(FLERR,"Fix ave/time fix does not calculate an array");
+ error->all(FLERR,"Fix ave/time fix does not calculate an array");
if (argindex[i] && argindex[i] > modify->fix[ifix]->size_array_cols)
- error->all(FLERR,"Fix ave/time fix array is accessed out-of-range");
+ error->all(FLERR,"Fix ave/time fix array is accessed out-of-range");
if (nevery % modify->fix[ifix]->global_freq)
- error->all(FLERR,"Fix for fix ave/time not computed at compatible time");
+ error->all(FLERR,"Fix for fix ave/time not computed at compatible time");
} else if (which[i] == VARIABLE) {
int ivariable = input->variable->find(ids[i]);
if (ivariable < 0)
- error->all(FLERR,"Variable name for fix ave/time does not exist");
+ error->all(FLERR,"Variable name for fix ave/time does not exist");
if (input->variable->equalstyle(ivariable) == 0)
- error->all(FLERR,"Fix ave/time variable is not equal-style variable");
+ error->all(FLERR,"Fix ave/time variable is not equal-style variable");
if (mode == VECTOR)
- error->all(FLERR,"Fix ave/time cannot use variable with vector mode");
+ error->all(FLERR,"Fix ave/time cannot use variable with vector mode");
}
}
@@ -240,17 +240,17 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
for (int i = 0; i < nvalues; i++) {
if (which[i] == COMPUTE) {
- int icompute = modify->find_compute(ids[i]);
- if (argindex[i] == 0) length = modify->compute[icompute]->size_vector;
- else length = modify->compute[icompute]->size_array_rows;
+ int icompute = modify->find_compute(ids[i]);
+ if (argindex[i] == 0) length = modify->compute[icompute]->size_vector;
+ else length = modify->compute[icompute]->size_array_rows;
} else if (which[i] == FIX) {
- int ifix = modify->find_fix(ids[i]);
- if (argindex[i] == 0) length = modify->fix[ifix]->size_vector;
- else length = modify->fix[ifix]->size_array_rows;
+ int ifix = modify->find_fix(ids[i]);
+ if (argindex[i] == 0) length = modify->fix[ifix]->size_vector;
+ else length = modify->fix[ifix]->size_array_rows;
}
if (i == 0) nrows = length;
else if (length != nrows)
- error->all(FLERR,"Fix ave/time columns are inconsistent lengths");
+ error->all(FLERR,"Fix ave/time columns are inconsistent lengths");
}
column = new double[nrows];
@@ -273,10 +273,10 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
else if (mode == VECTOR) {
fprintf(fp,"# Row");
for (int i = 0; i < nvalues; i++) {
- if (which[i] == COMPUTE) fprintf(fp," c_%s",ids[i]);
- else if (which[i] == FIX) fprintf(fp," f_%s",ids[i]);
- else if (which[i] == VARIABLE) fprintf(fp," v_%s",ids[i]);
- if (argindex[i]) fprintf(fp,"[%d]",argindex[i]);
+ if (which[i] == COMPUTE) fprintf(fp," c_%s",ids[i]);
+ else if (which[i] == FIX) fprintf(fp," f_%s",ids[i]);
+ else if (which[i] == VARIABLE) fprintf(fp," v_%s",ids[i]);
+ if (argindex[i]) fprintf(fp,"[%d]",argindex[i]);
}
fprintf(fp,"\n");
}
@@ -292,7 +292,7 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
vector_list = NULL;
array = array_total = NULL;
array_list = NULL;
-
+
if (mode == SCALAR) {
vector = new double[nvalues];
vector_total = new double[nvalues];
@@ -309,43 +309,43 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
// SCALAR mode produces either a scalar or vector
// VECTOR mode produces either a vector or array
// intensive/extensive flags set by compute,fix,variable that produces value
-
+
extlist = NULL;
if (mode == SCALAR) {
if (nvalues == 1) {
scalar_flag = 1;
if (which[0] == COMPUTE) {
- Compute *compute = modify->compute[modify->find_compute(ids[0])];
- if (argindex[0] == 0) extscalar = compute->extscalar;
- else if (compute->extvector >= 0) extscalar = compute->extvector;
- else extscalar = compute->extlist[argindex[0]-1];
+ Compute *compute = modify->compute[modify->find_compute(ids[0])];
+ if (argindex[0] == 0) extscalar = compute->extscalar;
+ else if (compute->extvector >= 0) extscalar = compute->extvector;
+ else extscalar = compute->extlist[argindex[0]-1];
} else if (which[0] == FIX) {
- Fix *fix = modify->fix[modify->find_fix(ids[0])];
- if (argindex[0] == 0) extscalar = fix->extscalar;
- else if (fix->extvector >= 0) extscalar = fix->extvector;
- else extscalar = fix->extlist[argindex[0]-1];
+ Fix *fix = modify->fix[modify->find_fix(ids[0])];
+ if (argindex[0] == 0) extscalar = fix->extscalar;
+ else if (fix->extvector >= 0) extscalar = fix->extvector;
+ else extscalar = fix->extlist[argindex[0]-1];
} else if (which[0] == VARIABLE)
- extscalar = 0;
-
+ extscalar = 0;
+
} else {
vector_flag = 1;
size_vector = nvalues;
extvector = -1;
extlist = new int[nvalues];
for (int i = 0; i < nvalues; i++) {
- if (which[i] == COMPUTE) {
- Compute *compute = modify->compute[modify->find_compute(ids[i])];
- if (argindex[i] == 0) extlist[i] = compute->extscalar;
- else if (compute->extvector >= 0) extlist[i] = compute->extvector;
- else extlist[i] = compute->extlist[argindex[i]-1];
- } else if (which[i] == FIX) {
- Fix *fix = modify->fix[modify->find_fix(ids[i])];
- if (argindex[i] == 0) extlist[i] = fix->extscalar;
- else if (fix->extvector >= 0) extlist[i] = fix->extvector;
- else extlist[i] = fix->extlist[argindex[i]-1];
- } else if (which[i] == VARIABLE)
- extlist[i] = 0;
+ if (which[i] == COMPUTE) {
+ Compute *compute = modify->compute[modify->find_compute(ids[i])];
+ if (argindex[i] == 0) extlist[i] = compute->extscalar;
+ else if (compute->extvector >= 0) extlist[i] = compute->extvector;
+ else extlist[i] = compute->extlist[argindex[i]-1];
+ } else if (which[i] == FIX) {
+ Fix *fix = modify->fix[modify->find_fix(ids[i])];
+ if (argindex[i] == 0) extlist[i] = fix->extscalar;
+ else if (fix->extvector >= 0) extlist[i] = fix->extvector;
+ else extlist[i] = fix->extlist[argindex[i]-1];
+ } else if (which[i] == VARIABLE)
+ extlist[i] = 0;
}
}
@@ -354,23 +354,23 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
vector_flag = 1;
size_vector = nrows;
if (which[0] == COMPUTE) {
- Compute *compute = modify->compute[modify->find_compute(ids[0])];
- if (argindex[0] == 0) {
- extvector = compute->extvector;
- if (extvector == -1) {
- extlist = new int[nrows];
- for (int i = 0; i < nrows; i++) extlist[i] = compute->extlist[i];
- }
- } else extvector = compute->extarray;
+ Compute *compute = modify->compute[modify->find_compute(ids[0])];
+ if (argindex[0] == 0) {
+ extvector = compute->extvector;
+ if (extvector == -1) {
+ extlist = new int[nrows];
+ for (int i = 0; i < nrows; i++) extlist[i] = compute->extlist[i];
+ }
+ } else extvector = compute->extarray;
} else if (which[0] == FIX) {
- Fix *fix = modify->fix[modify->find_fix(ids[0])];
- if (argindex[0] == 0) {
- extvector = fix->extvector;
- if (extvector == -1) {
- extlist = new int[nrows];
- for (int i = 0; i < nrows; i++) extlist[i] = fix->extlist[i];
- }
- } else extvector = fix->extarray;
+ Fix *fix = modify->fix[modify->find_fix(ids[0])];
+ if (argindex[0] == 0) {
+ extvector = fix->extvector;
+ if (extvector == -1) {
+ extlist = new int[nrows];
+ for (int i = 0; i < nrows; i++) extlist[i] = fix->extlist[i];
+ }
+ } else extvector = fix->extarray;
}
} else {
@@ -379,22 +379,22 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
size_array_cols = nvalues;
int value;
for (int i = 0; i < nvalues; i++) {
- if (which[i] == COMPUTE) {
- Compute *compute = modify->compute[modify->find_compute(ids[i])];
- if (argindex[i] == 0) value = compute->extvector;
- else value = compute->extarray;
- } else if (which[i] == FIX) {
- Fix *fix = modify->fix[modify->find_fix(ids[i])];
- if (argindex[i] == 0) value = fix->extvector;
- else value = fix->extarray;
- }
- if (value == -1)
- error->all(FLERR,"Fix ave/time cannot set output array "
- "intensive/extensive from these inputs");
- if (i == 0) extarray = value;
- else if (value != extarray)
- error->all(FLERR,"Fix ave/time cannot set output array "
- "intensive/extensive from these inputs");
+ if (which[i] == COMPUTE) {
+ Compute *compute = modify->compute[modify->find_compute(ids[i])];
+ if (argindex[i] == 0) value = compute->extvector;
+ else value = compute->extarray;
+ } else if (which[i] == FIX) {
+ Fix *fix = modify->fix[modify->find_fix(ids[i])];
+ if (argindex[i] == 0) value = fix->extvector;
+ else value = fix->extarray;
+ }
+ if (value == -1)
+ error->all(FLERR,"Fix ave/time cannot set output array "
+ "intensive/extensive from these inputs");
+ if (i == 0) extarray = value;
+ else if (value != extarray)
+ error->all(FLERR,"Fix ave/time cannot set output array "
+ "intensive/extensive from these inputs");
}
}
}
@@ -463,19 +463,19 @@ void FixAveTime::init()
if (which[i] == COMPUTE) {
int icompute = modify->find_compute(ids[i]);
if (icompute < 0)
- error->all(FLERR,"Compute ID for fix ave/time does not exist");
+ error->all(FLERR,"Compute ID for fix ave/time does not exist");
value2index[i] = icompute;
} else if (which[i] == FIX) {
int ifix = modify->find_fix(ids[i]);
- if (ifix < 0)
- error->all(FLERR,"Fix ID for fix ave/time does not exist");
+ if (ifix < 0)
+ error->all(FLERR,"Fix ID for fix ave/time does not exist");
value2index[i] = ifix;
} else if (which[i] == VARIABLE) {
int ivariable = input->variable->find(ids[i]);
- if (ivariable < 0)
- error->all(FLERR,"Variable name for fix ave/time does not exist");
+ if (ivariable < 0)
+ error->all(FLERR,"Variable name for fix ave/time does not exist");
value2index[i] = ivariable;
}
}
@@ -530,41 +530,41 @@ void FixAveTime::invoke_scalar(bigint ntimestep)
for (i = 0; i < nvalues; i++) {
m = value2index[i];
-
+
// invoke compute if not previously invoked
-
+
if (which[i] == COMPUTE) {
Compute *compute = modify->compute[m];
-
+
if (argindex[i] == 0) {
- if (!(compute->invoked_flag & INVOKED_SCALAR)) {
- compute->compute_scalar();
- compute->invoked_flag |= INVOKED_SCALAR;
- }
- scalar = compute->scalar;
+ if (!(compute->invoked_flag & INVOKED_SCALAR)) {
+ compute->compute_scalar();
+ compute->invoked_flag |= INVOKED_SCALAR;
+ }
+ scalar = compute->scalar;
} else {
- if (!(compute->invoked_flag & INVOKED_VECTOR)) {
- compute->compute_vector();
- compute->invoked_flag |= INVOKED_VECTOR;
- }
- scalar = compute->vector[argindex[i]-1];
+ if (!(compute->invoked_flag & INVOKED_VECTOR)) {
+ compute->compute_vector();
+ compute->invoked_flag |= INVOKED_VECTOR;
+ }
+ scalar = compute->vector[argindex[i]-1];
}
-
+
// access fix fields, guaranteed to be ready
-
+
} else if (which[i] == FIX) {
- if (argindex[i] == 0)
- scalar = modify->fix[m]->compute_scalar();
+ if (argindex[i] == 0)
+ scalar = modify->fix[m]->compute_scalar();
else
- scalar = modify->fix[m]->compute_vector(argindex[i]-1);
-
+ scalar = modify->fix[m]->compute_vector(argindex[i]-1);
+
// evaluate equal-style variable
-
+
} else if (which[i] == VARIABLE)
scalar = input->variable->compute_equal(m);
-
+
// add value to vector or just set directly if offcol is set
-
+
if (offcol[i]) vector[i] = scalar;
else vector[i] += scalar;
}
@@ -596,18 +596,18 @@ void FixAveTime::invoke_scalar(bigint ntimestep)
if (ave == ONE) {
for (i = 0; i < nvalues; i++) vector_total[i] = vector[i];
norm = 1;
-
+
} else if (ave == RUNNING) {
for (i = 0; i < nvalues; i++) vector_total[i] += vector[i];
norm++;
-
+
} else if (ave == WINDOW) {
for (i = 0; i < nvalues; i++) {
vector_total[i] += vector[i];
if (window_limit) vector_total[i] -= vector_list[iwindow][i];
vector_list[iwindow][i] = vector[i];
}
-
+
iwindow++;
if (iwindow == nwindow) {
iwindow = 0;
@@ -616,7 +616,7 @@ void FixAveTime::invoke_scalar(bigint ntimestep)
if (window_limit) norm = nwindow;
else norm = iwindow;
}
-
+
// insure any columns with offcol set are effectively set to last value
for (i = 0; i < nvalues; i++)
@@ -637,114 +637,114 @@ void FixAveTime::invoke_scalar(bigint ntimestep)
void FixAveTime::invoke_vector(bigint ntimestep)
{
int i,j,m;
-
+
// zero if first step
if (irepeat == 0)
for (i = 0; i < nrows; i++)
for (j = 0; j < nvalues; j++) array[i][j] = 0.0;
-
+
// accumulate results of computes,fixes,variables to local copy
// compute/fix/variable may invoke computes so wrap with clear/add
-
+
modify->clearstep_compute();
-
+
for (j = 0; j < nvalues; j++) {
m = value2index[j];
-
+
// invoke compute if not previously invoked
-
+
if (which[j] == COMPUTE) {
Compute *compute = modify->compute[m];
-
+
if (argindex[j] == 0) {
- if (!(compute->invoked_flag & INVOKED_VECTOR)) {
- compute->compute_vector();
- compute->invoked_flag |= INVOKED_VECTOR;
- }
- double *cvector = compute->vector;
- for (i = 0; i < nrows; i++)
- column[i] = cvector[i];
-
+ if (!(compute->invoked_flag & INVOKED_VECTOR)) {
+ compute->compute_vector();
+ compute->invoked_flag |= INVOKED_VECTOR;
+ }
+ double *cvector = compute->vector;
+ for (i = 0; i < nrows; i++)
+ column[i] = cvector[i];
+
} else {
- if (!(compute->invoked_flag & INVOKED_ARRAY)) {
- compute->compute_array();
- compute->invoked_flag |= INVOKED_ARRAY;
- }
- double **carray = compute->array;
- int icol = argindex[j]-1;
- for (i = 0; i < nrows; i++)
- column[i] = carray[i][icol];
+ if (!(compute->invoked_flag & INVOKED_ARRAY)) {
+ compute->compute_array();
+ compute->invoked_flag |= INVOKED_ARRAY;
+ }
+ double **carray = compute->array;
+ int icol = argindex[j]-1;
+ for (i = 0; i < nrows; i++)
+ column[i] = carray[i][icol];
}
-
+
// access fix fields, guaranteed to be ready
-
+
} else if (which[j] == FIX) {
Fix *fix = modify->fix[m];
if (argindex[j] == 0)
- for (i = 0; i < nrows; i++)
- column[i] = fix->compute_vector(i);
+ for (i = 0; i < nrows; i++)
+ column[i] = fix->compute_vector(i);
else {
- int icol = argindex[j]-1;
- for (i = 0; i < nrows; i++)
- column[i] = fix->compute_array(i,icol);
+ int icol = argindex[j]-1;
+ for (i = 0; i < nrows; i++)
+ column[i] = fix->compute_array(i,icol);
}
}
-
+
// add columns of values to array or just set directly if offcol is set
-
+
if (offcol[j]) {
for (i = 0; i < nrows; i++)
- array[i][j] = column[i];
+ array[i][j] = column[i];
} else {
for (i = 0; i < nrows; i++)
- array[i][j] += column[i];
+ array[i][j] += column[i];
}
}
-
+
// done if irepeat < nrepeat
// else reset irepeat and nvalid
-
+
irepeat++;
if (irepeat < nrepeat) {
nvalid += nevery;
modify->addstep_compute(nvalid);
return;
}
-
+
irepeat = 0;
nvalid = ntimestep+nfreq - (nrepeat-1)*nevery;
modify->addstep_compute(nvalid);
-
+
// average the final result for the Nfreq timestep
-
+
double repeat = nrepeat;
for (i = 0; i < nrows; i++)
for (j = 0; j < nvalues; j++)
if (offcol[j] == 0) array[i][j] /= repeat;
-
+
// if ave = ONE, only single Nfreq timestep value is needed
// if ave = RUNNING, combine with all previous Nfreq timestep values
// if ave = WINDOW, combine with nwindow most recent Nfreq timestep values
-
+
if (ave == ONE) {
for (i = 0; i < nrows; i++)
for (j = 0; j < nvalues; j++) array_total[i][j] = array[i][j];
norm = 1;
-
+
} else if (ave == RUNNING) {
for (i = 0; i < nrows; i++)
for (j = 0; j < nvalues; j++) array_total[i][j] += array[i][j];
norm++;
-
+
} else if (ave == WINDOW) {
for (i = 0; i < nrows; i++)
for (j = 0; j < nvalues; j++) {
- array_total[i][j] += array[i][j];
- if (window_limit) array_total[i][j] -= array_list[iwindow][i][j];
- array_list[iwindow][i][j] = array[i][j];
+ array_total[i][j] += array[i][j];
+ if (window_limit) array_total[i][j] -= array_list[iwindow][i][j];
+ array_list[iwindow][i][j] = array[i][j];
}
-
+
iwindow++;
if (iwindow == nwindow) {
iwindow = 0;
@@ -753,15 +753,15 @@ void FixAveTime::invoke_vector(bigint ntimestep)
if (window_limit) norm = nwindow;
else norm = iwindow;
}
-
+
// insure any columns with offcol set are effectively set to last value
-
+
for (i = 0; i < nrows; i++)
for (j = 0; j < nvalues; j++)
if (offcol[j]) array_total[i][j] = norm*array[i][j];
-
+
// output result to file
-
+
if (fp && me == 0) {
fprintf(fp,BIGINT_FORMAT " %d\n",ntimestep,nrows);
for (i = 0; i < nrows; i++) {
@@ -831,12 +831,12 @@ void FixAveTime::options(int narg, char **arg)
if (strcmp(arg[iarg],"file") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/time command");
if (me == 0) {
- fp = fopen(arg[iarg+1],"w");
- if (fp == NULL) {
- char str[128];
- sprintf(str,"Cannot open fix ave/time file %s",arg[iarg+1]);
- error->one(FLERR,str);
- }
+ fp = fopen(arg[iarg+1],"w");
+ if (fp == NULL) {
+ char str[128];
+ sprintf(str,"Cannot open fix ave/time file %s",arg[iarg+1]);
+ error->one(FLERR,str);
+ }
}
iarg += 2;
} else if (strcmp(arg[iarg],"ave") == 0) {
@@ -846,9 +846,9 @@ void FixAveTime::options(int narg, char **arg)
else if (strcmp(arg[iarg+1],"window") == 0) ave = WINDOW;
else error->all(FLERR,"Illegal fix ave/time command");
if (ave == WINDOW) {
- if (iarg+3 > narg) error->all(FLERR,"Illegal fix ave/time command");
- nwindow = atoi(arg[iarg+2]);
- if (nwindow <= 0) error->all(FLERR,"Illegal fix ave/time command");
+ if (iarg+3 > narg) error->all(FLERR,"Illegal fix ave/time command");
+ nwindow = atoi(arg[iarg+2]);
+ if (nwindow <= 0) error->all(FLERR,"Illegal fix ave/time command");
}
iarg += 2;
if (ave == WINDOW) iarg++;
diff --git a/src/fix_ave_time.h b/src/fix_ave_time.h
index 0423bee3e292c83002727ea4cd2bd9899b1bc17e..2493f98e76ac7ef863629c9792cdc163c205c249 100644
--- a/src/fix_ave_time.h
+++ b/src/fix_ave_time.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_aveforce.cpp b/src/fix_aveforce.cpp
index 274820a0e3ad374412cf945d358acfd94eff3c49..7fa07b299ffa858b49582771a2b7131ba49c7cb6 100644
--- a/src/fix_aveforce.cpp
+++ b/src/fix_aveforce.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -86,7 +86,7 @@ FixAveForce::FixAveForce(LAMMPS *lmp, int narg, char **arg) :
if (iarg+2 > narg) error->all(FLERR,"Illegal fix aveforce command");
iregion = domain->find_region(arg[iarg+1]);
if (iregion == -1)
- error->all(FLERR,"Region ID for fix aveforce does not exist");
+ error->all(FLERR,"Region ID for fix aveforce does not exist");
int n = strlen(arg[iarg+1]) + 1;
idregion = new char[n];
strcpy(idregion,arg[iarg+1]);
@@ -95,7 +95,7 @@ FixAveForce::FixAveForce(LAMMPS *lmp, int narg, char **arg) :
}
- foriginal_all[0] = foriginal_all[1] =
+ foriginal_all[0] = foriginal_all[1] =
foriginal_all[2] = foriginal_all[3] = 0.0;
}
@@ -196,9 +196,9 @@ void FixAveForce::post_force(int vflag)
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- if (iregion >= 0 &&
+ if (iregion >= 0 &&
!domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2]))
- continue;
+ continue;
foriginal[0] += f[i][0];
foriginal[1] += f[i][1];
@@ -233,9 +233,9 @@ void FixAveForce::post_force(int vflag)
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- if (iregion >= 0 &&
+ if (iregion >= 0 &&
!domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2]))
- continue;
+ continue;
if (xstyle) f[i][0] = fave[0];
if (ystyle) f[i][1] = fave[1];
@@ -262,14 +262,14 @@ void FixAveForce::post_force_respa(int vflag, int ilevel, int iloop)
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- if (iregion >= 0 &&
- !domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2]))
- continue;
-
- foriginal[0] += f[i][0];
- foriginal[1] += f[i][1];
- foriginal[2] += f[i][2];
- foriginal[3] += 1.0;
+ if (iregion >= 0 &&
+ !domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2]))
+ continue;
+
+ foriginal[0] += f[i][0];
+ foriginal[1] += f[i][1];
+ foriginal[2] += f[i][2];
+ foriginal[3] += 1.0;
}
MPI_Allreduce(foriginal,foriginal_all,4,MPI_DOUBLE,MPI_SUM,world);
@@ -284,13 +284,13 @@ void FixAveForce::post_force_respa(int vflag, int ilevel, int iloop)
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- if (iregion >= 0 &&
- !domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2]))
- continue;
+ if (iregion >= 0 &&
+ !domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2]))
+ continue;
- if (xstyle) f[i][0] = fave[0];
- if (ystyle) f[i][1] = fave[1];
- if (zstyle) f[i][2] = fave[2];
+ if (xstyle) f[i][0] = fave[0];
+ if (ystyle) f[i][1] = fave[1];
+ if (zstyle) f[i][2] = fave[2];
}
}
}
diff --git a/src/fix_aveforce.h b/src/fix_aveforce.h
index f4bda6d9103b138d377b1caf2a88373aa5df1626..ba5aa3764097cdc040686684e5d161073b44bf07 100644
--- a/src/fix_aveforce.h
+++ b/src/fix_aveforce.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_box_relax.cpp b/src/fix_box_relax.cpp
index 24891ee950c5659a4ced13e5a6d7a0dbf00b57a5..b40284acef50ed641fdecd931b34aa03b3c6bf7e 100644
--- a/src/fix_box_relax.cpp
+++ b/src/fix_box_relax.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -59,9 +59,9 @@ FixBoxRelax::FixBoxRelax(LAMMPS *lmp, int narg, char **arg) :
deviatoric_flag = 0;
nreset_h0 = 0;
- p_target[0] = p_target[1] = p_target[2] =
+ p_target[0] = p_target[1] = p_target[2] =
p_target[3] = p_target[4] = p_target[5] = 0.0;
- p_flag[0] = p_flag[1] = p_flag[2] =
+ p_flag[0] = p_flag[1] = p_flag[2] =
p_flag[3] = p_flag[4] = p_flag[5] = 0;
// process keywords
@@ -77,18 +77,18 @@ FixBoxRelax::FixBoxRelax(LAMMPS *lmp, int narg, char **arg) :
p_target[0] = p_target[1] = p_target[2] = atof(arg[iarg+1]);
p_flag[0] = p_flag[1] = p_flag[2] = 1;
if (dimension == 2) {
- p_target[2] = 0.0;
- p_flag[2] = 0;
+ p_target[2] = 0.0;
+ p_flag[2] = 0;
}
- iarg += 2;
+ iarg += 2;
} else if (strcmp(arg[iarg],"aniso") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix box/relax command");
pcouple = NONE;
p_target[0] = p_target[1] = p_target[2] = atof(arg[iarg+1]);
p_flag[0] = p_flag[1] = p_flag[2] = 1;
if (dimension == 2) {
- p_target[2] = 0.0;
- p_flag[2] = 0;
+ p_target[2] = 0.0;
+ p_flag[2] = 0;
}
iarg += 2;
} else if (strcmp(arg[iarg],"tri") == 0) {
@@ -99,8 +99,8 @@ FixBoxRelax::FixBoxRelax(LAMMPS *lmp, int narg, char **arg) :
p_target[3] = p_target[4] = p_target[5] = 0.0;
p_flag[3] = p_flag[4] = p_flag[5] = 1;
if (dimension == 2) {
- p_target[2] = p_target[3] = p_target[4] = 0.0;
- p_flag[2] = p_flag[3] = p_flag[4] = 0;
+ p_target[2] = p_target[3] = p_target[4] = 0.0;
+ p_flag[2] = p_flag[3] = p_flag[4] = 0;
}
iarg += 2;
@@ -109,44 +109,44 @@ FixBoxRelax::FixBoxRelax(LAMMPS *lmp, int narg, char **arg) :
p_target[0] = atof(arg[iarg+1]);
p_flag[0] = 1;
deviatoric_flag = 1;
- iarg += 2;
+ iarg += 2;
} else if (strcmp(arg[iarg],"y") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix box/relax command");
p_target[1] = atof(arg[iarg+1]);
p_flag[1] = 1;
deviatoric_flag = 1;
- iarg += 2;
+ iarg += 2;
} else if (strcmp(arg[iarg],"z") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix box/relax command");
p_target[2] = atof(arg[iarg+1]);
p_flag[2] = 1;
deviatoric_flag = 1;
- iarg += 2;
+ iarg += 2;
if (dimension == 2)
- error->all(FLERR,"Invalid fix box/relax command for a 2d simulation");
+ error->all(FLERR,"Invalid fix box/relax command for a 2d simulation");
} else if (strcmp(arg[iarg],"yz") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix box/relax command");
p_target[3] = atof(arg[iarg+1]);
p_flag[3] = 1;
deviatoric_flag = 1;
- iarg += 2;
+ iarg += 2;
if (dimension == 2)
- error->all(FLERR,"Invalid fix box/relax command for a 2d simulation");
+ error->all(FLERR,"Invalid fix box/relax command for a 2d simulation");
} else if (strcmp(arg[iarg],"xz") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix box/relax command");
p_target[4] = atof(arg[iarg+1]);
p_flag[4] = 1;
deviatoric_flag = 1;
- iarg += 2;
+ iarg += 2;
if (dimension == 2)
- error->all(FLERR,"Invalid fix box/relax command for a 2d simulation");
+ error->all(FLERR,"Invalid fix box/relax command for a 2d simulation");
} else if (strcmp(arg[iarg],"xy") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix box/relax command");
p_target[5] = atof(arg[iarg+1]);
p_flag[5] = 1;
deviatoric_flag = 1;
- iarg += 2;
+ iarg += 2;
} else if (strcmp(arg[iarg],"couple") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix box/relax command");
@@ -211,17 +211,17 @@ FixBoxRelax::FixBoxRelax(LAMMPS *lmp, int narg, char **arg) :
if (p_flag[3] && domain->zperiodic == 0)
error->all(FLERR,
- "Cannot use fix box/relax on a 2nd non-periodic dimension");
+ "Cannot use fix box/relax on a 2nd non-periodic dimension");
if (p_flag[4] && domain->zperiodic == 0)
error->all(FLERR,
- "Cannot use fix box/relax on a 2nd non-periodic dimension");
+ "Cannot use fix box/relax on a 2nd non-periodic dimension");
if (p_flag[5] && domain->yperiodic == 0)
error->all(FLERR,
- "Cannot use fix box/relax on a 2nd non-periodic dimension");
+ "Cannot use fix box/relax on a 2nd non-periodic dimension");
- if (!domain->triclinic && (p_flag[3] || p_flag[4] || p_flag[5]))
+ if (!domain->triclinic && (p_flag[3] || p_flag[4] || p_flag[5]))
error->all(FLERR,"Can not specify Pxy/Pxz/Pyz in "
- "fix box/relax with non-triclinic box");
+ "fix box/relax with non-triclinic box");
if (pcouple == XYZ && dimension == 3 &&
(p_target[0] != p_target[1] || p_target[0] != p_target[2]))
@@ -319,12 +319,12 @@ void FixBoxRelax::init()
// set temperature and pressure ptrs
int icompute = modify->find_compute(id_temp);
- if (icompute < 0)
+ if (icompute < 0)
error->all(FLERR,"Temperature ID for fix box/relax does not exist");
temperature = modify->compute[icompute];
icompute = modify->find_compute(id_press);
- if (icompute < 0)
+ if (icompute < 0)
error->all(FLERR,"Pressure ID for fix box/relax does not exist");
pressure = modify->compute[icompute];
@@ -415,11 +415,11 @@ double FixBoxRelax::min_energy(double *fextra)
if (pstyle == TRICLINIC) {
fextra[3] = fextra[4] = fextra[5] = 0.0;
if (p_flag[3])
- fextra[3] = pv2e*p_current[3]*scaley*yprdinit*scalex*xprdinit*yprdinit;
- if (p_flag[4])
- fextra[4] = pv2e*p_current[4]*scalex*xprdinit*scaley*yprdinit*xprdinit;
- if (p_flag[5])
- fextra[5] = pv2e*p_current[5]*scalex*xprdinit*scalez*zprdinit*xprdinit;
+ fextra[3] = pv2e*p_current[3]*scaley*yprdinit*scalex*xprdinit*yprdinit;
+ if (p_flag[4])
+ fextra[4] = pv2e*p_current[4]*scalex*xprdinit*scaley*yprdinit*xprdinit;
+ if (p_flag[5])
+ fextra[5] = pv2e*p_current[5]*scalex*xprdinit*scalez*zprdinit*xprdinit;
}
if (deviatoric_flag) {
@@ -428,9 +428,9 @@ double FixBoxRelax::min_energy(double *fextra)
if (p_flag[1]) fextra[1] -= fdev[1]*yprdinit;
if (p_flag[2]) fextra[2] -= fdev[2]*zprdinit;
if (pstyle == TRICLINIC) {
- if (p_flag[3]) fextra[3] -= fdev[3]*yprdinit;
- if (p_flag[4]) fextra[4] -= fdev[4]*xprdinit;
- if (p_flag[5]) fextra[5] -= fdev[5]*xprdinit;
+ if (p_flag[3]) fextra[3] -= fdev[3]*yprdinit;
+ if (p_flag[4]) fextra[4] -= fdev[4]*xprdinit;
+ if (p_flag[5]) fextra[5] -= fdev[5]*xprdinit;
}
eng += compute_strain_energy();
@@ -586,7 +586,7 @@ void FixBoxRelax::remap()
{
int i,n;
double ctr;
-
+
// ctr = geometric center of box in a dimension
// rescale simulation box from linesearch starting point
// scale atom coords for all atoms or only for fix group atoms
@@ -601,7 +601,7 @@ void FixBoxRelax::remap()
else {
for (i = 0; i < n; i++)
if (mask[i] & groupbit)
- domain->x2lamda(x[i],x[i]);
+ domain->x2lamda(x[i],x[i]);
}
if (nrigid)
@@ -618,7 +618,7 @@ void FixBoxRelax::remap()
domain->boxlo[i] = currentBoxLo0 + (currentBoxLo0-ctr)*ds[i]/s0[i];
domain->boxhi[i] = currentBoxHi0 + (currentBoxHi0-ctr)*ds[i]/s0[i];
if (domain->boxlo[i] >= domain->boxhi[i])
- error->all(FLERR,"Fix box/relax generated negative box length");
+ error->all(FLERR,"Fix box/relax generated negative box length");
}
if (pstyle == TRICLINIC) {
@@ -636,7 +636,7 @@ void FixBoxRelax::remap()
else {
for (i = 0; i < n; i++)
if (mask[i] & groupbit)
- domain->lamda2x(x[i],x[i]);
+ domain->lamda2x(x[i],x[i]);
}
if (nrigid)
@@ -673,8 +673,8 @@ void FixBoxRelax::couple()
p_current[2] = tensor[2];
}
- // switch order from xy-xz-yz to Voigt
-
+ // switch order from xy-xz-yz to Voigt
+
if (pstyle == TRICLINIC) {
p_current[3] = tensor[5];
p_current[4] = tensor[4];
@@ -698,20 +698,20 @@ int FixBoxRelax::modify_param(int narg, char **arg)
strcpy(id_temp,arg[1]);
int icompute = modify->find_compute(arg[1]);
- if (icompute < 0)
+ if (icompute < 0)
error->all(FLERR,"Could not find fix_modify temperature ID");
temperature = modify->compute[icompute];
if (temperature->tempflag == 0)
error->all(FLERR,
- "Fix_modify temperature ID does not compute temperature");
+ "Fix_modify temperature ID does not compute temperature");
if (temperature->igroup != 0 && comm->me == 0)
error->warning(FLERR,"Temperature for fix modify is not for group all");
// reset id_temp of pressure to new temperature ID
-
+
icompute = modify->find_compute(id_press);
- if (icompute < 0)
+ if (icompute < 0)
error->all(FLERR,"Pressure ID for fix modify does not exist");
modify->compute[icompute]->reset_extra_compute_fix(id_temp);
@@ -769,7 +769,7 @@ void FixBoxRelax::compute_sigma()
h0_inv[3] = domain->h_inv[3];
h0_inv[4] = domain->h_inv[4];
h0_inv[5] = domain->h_inv[5];
-
+
htmp[0][0] = h0[0];
htmp[1][1] = h0[1];
htmp[2][2] = h0[2];
@@ -835,26 +835,26 @@ void FixBoxRelax::compute_sigma()
double FixBoxRelax::compute_strain_energy()
{
- // compute strain energy = 0.5*Tr(sigma*h*h^t) in energy units
+ // compute strain energy = 0.5*Tr(sigma*h*h^t) in energy units
double* h = domain->h;
double d0,d1,d2;
if (dimension == 3) {
- d0 =
+ d0 =
sigma[0]*(h[0]*h[0]+h[5]*h[5]+h[4]*h[4]) +
sigma[5]*( h[1]*h[5]+h[3]*h[4]) +
sigma[4]*( h[2]*h[4]);
- d1 =
+ d1 =
sigma[5]*( h[5]*h[1]+h[4]*h[3]) +
sigma[1]*( h[1]*h[1]+h[3]*h[3]) +
sigma[3]*( h[2]*h[3]);
- d2 =
+ d2 =
sigma[4]*( h[4]*h[2]) +
sigma[3]*( h[3]*h[2]) +
sigma[2]*( h[2]*h[2]);
} else {
- d0 = sigma[0]*(h[0]*h[0]+h[5]*h[5]) + sigma[5]*h[1]*h[5];
+ d0 = sigma[0]*(h[0]*h[0]+h[5]*h[5]) + sigma[5]*h[1]*h[5];
d1 = sigma[5]*h[5]*h[1] + sigma[1]*h[1]*h[1];
d2 = 0.0;
}
@@ -870,7 +870,7 @@ double FixBoxRelax::compute_strain_energy()
void FixBoxRelax::compute_deviatoric()
{
double* h = domain->h;
-
+
// [ 0 5 4 ] [ 0 5 4 ] [ 0 5 4 ]
// [ 5 1 3 ] = [ - 1 3 ] [ 5 1 3 ]
// [ 4 3 2 ] [ - - 2 ] [ 4 3 2 ]
diff --git a/src/fix_box_relax.h b/src/fix_box_relax.h
index 53caf18ef31019daad3a82cb1efebeabac3ea4d2..566beb1fd9882aad8b85474c06554b667c20b1f6 100644
--- a/src/fix_box_relax.h
+++ b/src/fix_box_relax.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -67,7 +67,7 @@ class FixBoxRelax : public Fix {
int *rfix;
double sigma[6]; // scaled target stress
- double utsigma[3]; // weighting for upper-tri elements
+ double utsigma[3]; // weighting for upper-tri elements
// of modified sigma
int sigmamod_flag; // 1 if modified sigma to be used
double fdev[6]; // Deviatoric force on cell
diff --git a/src/fix_deform.cpp b/src/fix_deform.cpp
index 2c9edcf7de02f045dac41a46cea304ddd6a11574..56a24723d2c3ef9876661138f7daa679aff863f2 100644
--- a/src/fix_deform.cpp
+++ b/src/fix_deform.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -59,11 +59,11 @@ FixDeform::FixDeform(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
// set defaults
set = new Set[6];
- set[0].style = set[1].style = set[2].style =
+ set[0].style = set[1].style = set[2].style =
set[3].style = set[4].style = set[5].style = NONE;
- set[0].hstr = set[1].hstr = set[2].hstr =
+ set[0].hstr = set[1].hstr = set[2].hstr =
set[3].hstr = set[4].hstr = set[5].hstr = NULL;
- set[0].hratestr = set[1].hratestr = set[2].hratestr =
+ set[0].hratestr = set[1].hratestr = set[2].hratestr =
set[3].hratestr = set[4].hratestr = set[5].hratestr = NULL;
// parse arguments
@@ -73,9 +73,9 @@ FixDeform::FixDeform(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
int index;
int iarg = 4;
while (iarg < narg) {
- if (strcmp(arg[iarg],"x") == 0 ||
- strcmp(arg[iarg],"y") == 0 ||
- strcmp(arg[iarg],"z") == 0) {
+ if (strcmp(arg[iarg],"x") == 0 ||
+ strcmp(arg[iarg],"y") == 0 ||
+ strcmp(arg[iarg],"z") == 0) {
if (strcmp(arg[iarg],"x") == 0) index = 0;
else if (strcmp(arg[iarg],"y") == 0) index = 1;
@@ -83,126 +83,126 @@ FixDeform::FixDeform(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
if (iarg+2 > narg) error->all(FLERR,"Illegal fix deform command");
if (strcmp(arg[iarg+1],"final") == 0) {
- if (iarg+4 > narg) error->all(FLERR,"Illegal fix deform command");
- set[index].style = FINAL;
- set[index].flo = atof(arg[iarg+2]);
- set[index].fhi = atof(arg[iarg+3]);
- iarg += 4;
+ if (iarg+4 > narg) error->all(FLERR,"Illegal fix deform command");
+ set[index].style = FINAL;
+ set[index].flo = atof(arg[iarg+2]);
+ set[index].fhi = atof(arg[iarg+3]);
+ iarg += 4;
} else if (strcmp(arg[iarg+1],"delta") == 0) {
- if (iarg+4 > narg) error->all(FLERR,"Illegal fix deform command");
- set[index].style = DELTA;
- set[index].dlo = atof(arg[iarg+2]);
- set[index].dhi = atof(arg[iarg+3]);
- iarg += 4;
+ if (iarg+4 > narg) error->all(FLERR,"Illegal fix deform command");
+ set[index].style = DELTA;
+ set[index].dlo = atof(arg[iarg+2]);
+ set[index].dhi = atof(arg[iarg+3]);
+ iarg += 4;
} else if (strcmp(arg[iarg+1],"scale") == 0) {
- if (iarg+3 > narg) error->all(FLERR,"Illegal fix deform command");
- set[index].style = SCALE;
- set[index].scale = atof(arg[iarg+2]);
- iarg += 3;
+ if (iarg+3 > narg) error->all(FLERR,"Illegal fix deform command");
+ set[index].style = SCALE;
+ set[index].scale = atof(arg[iarg+2]);
+ iarg += 3;
} else if (strcmp(arg[iarg+1],"vel") == 0) {
- if (iarg+3 > narg) error->all(FLERR,"Illegal fix deform command");
- set[index].style = VEL;
- set[index].vel = atof(arg[iarg+2]);
- iarg += 3;
+ if (iarg+3 > narg) error->all(FLERR,"Illegal fix deform command");
+ set[index].style = VEL;
+ set[index].vel = atof(arg[iarg+2]);
+ iarg += 3;
} else if (strcmp(arg[iarg+1],"erate") == 0) {
- if (iarg+3 > narg) error->all(FLERR,"Illegal fix deform command");
- set[index].style = ERATE;
- set[index].rate = atof(arg[iarg+2]);
- iarg += 3;
+ if (iarg+3 > narg) error->all(FLERR,"Illegal fix deform command");
+ set[index].style = ERATE;
+ set[index].rate = atof(arg[iarg+2]);
+ iarg += 3;
} else if (strcmp(arg[iarg+1],"trate") == 0) {
- if (iarg+3 > narg) error->all(FLERR,"Illegal fix deform command");
- set[index].style = TRATE;
- set[index].rate = atof(arg[iarg+2]);
- iarg += 3;
+ if (iarg+3 > narg) error->all(FLERR,"Illegal fix deform command");
+ set[index].style = TRATE;
+ set[index].rate = atof(arg[iarg+2]);
+ iarg += 3;
} else if (strcmp(arg[iarg+1],"volume") == 0) {
- set[index].style = VOLUME;
- iarg += 2;
+ set[index].style = VOLUME;
+ iarg += 2;
} else if (strcmp(arg[iarg+1],"wiggle") == 0) {
- if (iarg+4 > narg) error->all(FLERR,"Illegal fix deform command");
- set[index].style = WIGGLE;
- set[index].amplitude = atof(arg[iarg+2]);
- set[index].tperiod = atof(arg[iarg+3]);
- if (set[index].tperiod <= 0.0)
- error->all(FLERR,"Illegal fix deform command");
- iarg += 4;
+ if (iarg+4 > narg) error->all(FLERR,"Illegal fix deform command");
+ set[index].style = WIGGLE;
+ set[index].amplitude = atof(arg[iarg+2]);
+ set[index].tperiod = atof(arg[iarg+3]);
+ if (set[index].tperiod <= 0.0)
+ error->all(FLERR,"Illegal fix deform command");
+ iarg += 4;
} else if (strcmp(arg[iarg+1],"variable") == 0) {
- if (iarg+4 > narg) error->all(FLERR,"Illegal fix deform command");
- set[index].style = VARIABLE;
- if (strstr(arg[iarg+2],"v_") != arg[iarg+2])
- error->all(FLERR,"Illegal fix deform command");
- if (strstr(arg[iarg+3],"v_") != arg[iarg+3])
- error->all(FLERR,"Illegal fix deform command");
- delete [] set[index].hstr;
- delete [] set[index].hratestr;
- int n = strlen(&arg[iarg+2][2]) + 1;
- set[index].hstr = new char[n];
- strcpy(set[index].hstr,&arg[iarg+2][2]);
- n = strlen(&arg[iarg+3][2]) + 1;
- set[index].hratestr = new char[n];
- strcpy(set[index].hratestr,&arg[iarg+3][2]);
- iarg += 4;
+ if (iarg+4 > narg) error->all(FLERR,"Illegal fix deform command");
+ set[index].style = VARIABLE;
+ if (strstr(arg[iarg+2],"v_") != arg[iarg+2])
+ error->all(FLERR,"Illegal fix deform command");
+ if (strstr(arg[iarg+3],"v_") != arg[iarg+3])
+ error->all(FLERR,"Illegal fix deform command");
+ delete [] set[index].hstr;
+ delete [] set[index].hratestr;
+ int n = strlen(&arg[iarg+2][2]) + 1;
+ set[index].hstr = new char[n];
+ strcpy(set[index].hstr,&arg[iarg+2][2]);
+ n = strlen(&arg[iarg+3][2]) + 1;
+ set[index].hratestr = new char[n];
+ strcpy(set[index].hratestr,&arg[iarg+3][2]);
+ iarg += 4;
} else error->all(FLERR,"Illegal fix deform command");
-
- } else if (strcmp(arg[iarg],"xy") == 0 ||
- strcmp(arg[iarg],"xz") == 0 ||
- strcmp(arg[iarg],"yz") == 0) {
+
+ } else if (strcmp(arg[iarg],"xy") == 0 ||
+ strcmp(arg[iarg],"xz") == 0 ||
+ strcmp(arg[iarg],"yz") == 0) {
if (triclinic == 0)
- error->all(FLERR,"Fix deform tilt factors require triclinic box");
+ error->all(FLERR,"Fix deform tilt factors require triclinic box");
if (strcmp(arg[iarg],"xy") == 0) index = 5;
else if (strcmp(arg[iarg],"xz") == 0) index = 4;
else if (strcmp(arg[iarg],"yz") == 0) index = 3;
if (iarg+2 > narg) error->all(FLERR,"Illegal fix deform command");
if (strcmp(arg[iarg+1],"final") == 0) {
- if (iarg+3 > narg) error->all(FLERR,"Illegal fix deform command");
- set[index].style = FINAL;
- set[index].ftilt = atof(arg[iarg+2]);
- iarg += 3;
+ if (iarg+3 > narg) error->all(FLERR,"Illegal fix deform command");
+ set[index].style = FINAL;
+ set[index].ftilt = atof(arg[iarg+2]);
+ iarg += 3;
} else if (strcmp(arg[iarg+1],"delta") == 0) {
- if (iarg+3 > narg) error->all(FLERR,"Illegal fix deform command");
- set[index].style = DELTA;
- set[index].dtilt = atof(arg[iarg+2]);
- iarg += 3;
+ if (iarg+3 > narg) error->all(FLERR,"Illegal fix deform command");
+ set[index].style = DELTA;
+ set[index].dtilt = atof(arg[iarg+2]);
+ iarg += 3;
} else if (strcmp(arg[iarg+1],"vel") == 0) {
- if (iarg+3 > narg) error->all(FLERR,"Illegal fix deform command");
- set[index].style = VEL;
- set[index].vel = atof(arg[iarg+2]);
- iarg += 3;
+ if (iarg+3 > narg) error->all(FLERR,"Illegal fix deform command");
+ set[index].style = VEL;
+ set[index].vel = atof(arg[iarg+2]);
+ iarg += 3;
} else if (strcmp(arg[iarg+1],"erate") == 0) {
- if (iarg+3 > narg) error->all(FLERR,"Illegal fix deform command");
- set[index].style = ERATE;
- set[index].rate = atof(arg[iarg+2]);
- iarg += 3;
+ if (iarg+3 > narg) error->all(FLERR,"Illegal fix deform command");
+ set[index].style = ERATE;
+ set[index].rate = atof(arg[iarg+2]);
+ iarg += 3;
} else if (strcmp(arg[iarg+1],"trate") == 0) {
- if (iarg+3 > narg) error->all(FLERR,"Illegal fix deform command");
- set[index].style = TRATE;
- set[index].rate = atof(arg[iarg+2]);
- iarg += 3;
+ if (iarg+3 > narg) error->all(FLERR,"Illegal fix deform command");
+ set[index].style = TRATE;
+ set[index].rate = atof(arg[iarg+2]);
+ iarg += 3;
} else if (strcmp(arg[iarg+1],"wiggle") == 0) {
- if (iarg+4 > narg) error->all(FLERR,"Illegal fix deform command");
- set[index].style = WIGGLE;
- set[index].amplitude = atof(arg[iarg+2]);
- set[index].tperiod = atof(arg[iarg+3]);
- if (set[index].tperiod <= 0.0)
- error->all(FLERR,"Illegal fix deform command");
- iarg += 4;
+ if (iarg+4 > narg) error->all(FLERR,"Illegal fix deform command");
+ set[index].style = WIGGLE;
+ set[index].amplitude = atof(arg[iarg+2]);
+ set[index].tperiod = atof(arg[iarg+3]);
+ if (set[index].tperiod <= 0.0)
+ error->all(FLERR,"Illegal fix deform command");
+ iarg += 4;
} else if (strcmp(arg[iarg+1],"variable") == 0) {
- if (iarg+4 > narg) error->all(FLERR,"Illegal fix deform command");
- set[index].style = VARIABLE;
- if (strstr(arg[iarg+2],"v_") != arg[iarg+2])
- error->all(FLERR,"Illegal fix deform command");
- if (strstr(arg[iarg+3],"v_") != arg[iarg+3])
- error->all(FLERR,"Illegal fix deform command");
- delete [] set[index].hstr;
- delete [] set[index].hratestr;
- int n = strlen(&arg[iarg+2][2]) + 1;
- set[index].hstr = new char[n];
- strcpy(set[index].hstr,&arg[iarg+2][2]);
- n = strlen(&arg[iarg+3][2]) + 1;
- set[index].hratestr = new char[n];
- strcpy(set[index].hratestr,&arg[iarg+3][2]);
- iarg += 4;
+ if (iarg+4 > narg) error->all(FLERR,"Illegal fix deform command");
+ set[index].style = VARIABLE;
+ if (strstr(arg[iarg+2],"v_") != arg[iarg+2])
+ error->all(FLERR,"Illegal fix deform command");
+ if (strstr(arg[iarg+3],"v_") != arg[iarg+3])
+ error->all(FLERR,"Illegal fix deform command");
+ delete [] set[index].hstr;
+ delete [] set[index].hratestr;
+ int n = strlen(&arg[iarg+2][2]) + 1;
+ set[index].hstr = new char[n];
+ strcpy(set[index].hstr,&arg[iarg+2][2]);
+ n = strlen(&arg[iarg+3][2]) + 1;
+ set[index].hratestr = new char[n];
+ strcpy(set[index].hratestr,&arg[iarg+3][2]);
+ iarg += 4;
} else error->all(FLERR,"Illegal fix deform command");
} else break;
@@ -226,26 +226,26 @@ FixDeform::FixDeform(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
// no tensile deformation on shrink-wrapped dims
// b/c shrink wrap will change box-length
- if (set[0].style &&
+ if (set[0].style &&
(domain->boundary[0][0] >= 2 || domain->boundary[0][1] >= 2))
error->all(FLERR,"Cannot use fix deform on a shrink-wrapped boundary");
- if (set[1].style &&
+ if (set[1].style &&
(domain->boundary[1][0] >= 2 || domain->boundary[1][1] >= 2))
error->all(FLERR,"Cannot use fix deform on a shrink-wrapped boundary");
- if (set[2].style &&
+ if (set[2].style &&
(domain->boundary[2][0] >= 2 || domain->boundary[2][1] >= 2))
error->all(FLERR,"Cannot use fix deform on a shrink-wrapped boundary");
// no tilt deformation on shrink-wrapped 2nd dim
// b/c shrink wrap will change tilt factor in domain::reset_box()
- if (set[3].style &&
+ if (set[3].style &&
(domain->boundary[2][0] >= 2 || domain->boundary[2][1] >= 2))
error->all(FLERR,"Cannot use fix deform tilt on a shrink-wrapped 2nd dim");
- if (set[4].style &&
+ if (set[4].style &&
(domain->boundary[2][0] >= 2 || domain->boundary[2][1] >= 2))
error->all(FLERR,"Cannot use fix deform tilt on a shrink-wrapped 2nd dim");
- if (set[4].style &&
+ if (set[4].style &&
(domain->boundary[1][0] >= 2 || domain->boundary[1][1] >= 2))
error->all(FLERR,"Cannot use fix deform tilt on a shrink-wrapped 2nd dim");
@@ -253,8 +253,8 @@ FixDeform::FixDeform(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
int flag = 0;
for (int i = 0; i < 6; i++)
- if (set[i].style == FINAL || set[i].style == DELTA ||
- set[i].style == VEL || set[i].style == WIGGLE) flag = 1;
+ if (set[i].style == FINAL || set[i].style == DELTA ||
+ set[i].style == VEL || set[i].style == WIGGLE) flag = 1;
if (flag && scaleflag && domain->lattice == NULL)
error->all(FLERR,"Use of fix deform with undefined lattice");
@@ -304,25 +304,25 @@ FixDeform::FixDeform(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
if (set[other1].style == NONE) {
if (set[other2].style == NONE || set[other2].style == VOLUME)
- error->all(FLERR,"Fix deform volume setting is invalid");
+ error->all(FLERR,"Fix deform volume setting is invalid");
set[i].substyle = ONE_FROM_ONE;
set[i].fixed = other1;
set[i].dynamic1 = other2;
} else if (set[other2].style == NONE) {
if (set[other1].style == NONE || set[other1].style == VOLUME)
- error->all(FLERR,"Fix deform volume setting is invalid");
+ error->all(FLERR,"Fix deform volume setting is invalid");
set[i].substyle = ONE_FROM_ONE;
set[i].fixed = other2;
set[i].dynamic1 = other1;
} else if (set[other1].style == VOLUME) {
if (set[other2].style == NONE || set[other2].style == VOLUME)
- error->all(FLERR,"Fix deform volume setting is invalid");
+ error->all(FLERR,"Fix deform volume setting is invalid");
set[i].substyle = TWO_FROM_ONE;
set[i].fixed = other1;
set[i].dynamic1 = other2;
} else if (set[other2].style == VOLUME) {
if (set[other1].style == NONE || set[other1].style == VOLUME)
- error->all(FLERR,"Fix deform volume setting is invalid");
+ error->all(FLERR,"Fix deform volume setting is invalid");
set[i].substyle = TWO_FROM_ONE;
set[i].fixed = other2;
set[i].dynamic1 = other1;
@@ -360,7 +360,7 @@ FixDeform::FixDeform(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
nrigid = 0;
rfix = NULL;
flip = 0;
-
+
if (force_reneighbor) irregular = new Irregular(lmp);
else irregular = NULL;
@@ -385,7 +385,7 @@ FixDeform::~FixDeform()
double *h_rate = domain->h_rate;
double *h_ratelo = domain->h_ratelo;
- h_rate[0] = h_rate[1] = h_rate[2] =
+ h_rate[0] = h_rate[1] = h_rate[2] =
h_rate[3] = h_rate[4] = h_rate[5] = 0.0;
h_ratelo[0] = h_ratelo[1] = h_ratelo[2] = 0.0;
}
@@ -426,12 +426,12 @@ void FixDeform::init()
for (int i = 0; i < 6; i++) {
if (set[i].style != VARIABLE) continue;
set[i].hvar = input->variable->find(set[i].hstr);
- if (set[i].hvar < 0)
+ if (set[i].hvar < 0)
error->all(FLERR,"Variable name for fix deform does not exist");
if (!input->variable->equalstyle(set[i].hvar))
error->all(FLERR,"Variable for fix deform is invalid style");
set[i].hratevar = input->variable->find(set[i].hratestr);
- if (set[i].hratevar < 0)
+ if (set[i].hratevar < 0)
error->all(FLERR,"Variable name for fix deform does not exist");
if (!input->variable->equalstyle(set[i].hratevar))
error->all(FLERR,"Variable for fix deform is invalid style");
@@ -461,30 +461,30 @@ void FixDeform::init()
set[i].lo_stop = set[i].lo_start + set[i].dlo;
set[i].hi_stop = set[i].hi_start + set[i].dhi;
} else if (set[i].style == SCALE) {
- set[i].lo_stop = 0.5*(set[i].lo_start+set[i].hi_start) -
- 0.5*set[i].scale*(set[i].hi_start-set[i].lo_start);
- set[i].hi_stop = 0.5*(set[i].lo_start+set[i].hi_start) +
- 0.5*set[i].scale*(set[i].hi_start-set[i].lo_start);
+ set[i].lo_stop = 0.5*(set[i].lo_start+set[i].hi_start) -
+ 0.5*set[i].scale*(set[i].hi_start-set[i].lo_start);
+ set[i].hi_stop = 0.5*(set[i].lo_start+set[i].hi_start) +
+ 0.5*set[i].scale*(set[i].hi_start-set[i].lo_start);
} else if (set[i].style == VEL) {
set[i].lo_stop = set[i].lo_start - 0.5*delt*set[i].vel;
set[i].hi_stop = set[i].hi_start + 0.5*delt*set[i].vel;
} else if (set[i].style == ERATE) {
- set[i].lo_stop = set[i].lo_start -
- 0.5*delt*set[i].rate * (set[i].hi_start-set[i].lo_start);
- set[i].hi_stop = set[i].hi_start +
- 0.5*delt*set[i].rate * (set[i].hi_start-set[i].lo_start);
+ set[i].lo_stop = set[i].lo_start -
+ 0.5*delt*set[i].rate * (set[i].hi_start-set[i].lo_start);
+ set[i].hi_stop = set[i].hi_start +
+ 0.5*delt*set[i].rate * (set[i].hi_start-set[i].lo_start);
if (set[i].hi_stop <= set[i].lo_stop)
- error->all(FLERR,"Final box dimension due to fix deform is < 0.0");
+ error->all(FLERR,"Final box dimension due to fix deform is < 0.0");
} else if (set[i].style == TRATE) {
- set[i].lo_stop = 0.5*(set[i].lo_start+set[i].hi_start) -
- 0.5*((set[i].hi_start-set[i].lo_start) * exp(set[i].rate*delt));
- set[i].hi_stop = 0.5*(set[i].lo_start+set[i].hi_start) +
- 0.5*((set[i].hi_start-set[i].lo_start) * exp(set[i].rate*delt));
+ set[i].lo_stop = 0.5*(set[i].lo_start+set[i].hi_start) -
+ 0.5*((set[i].hi_start-set[i].lo_start) * exp(set[i].rate*delt));
+ set[i].hi_stop = 0.5*(set[i].lo_start+set[i].hi_start) +
+ 0.5*((set[i].hi_start-set[i].lo_start) * exp(set[i].rate*delt));
} else if (set[i].style == WIGGLE) {
set[i].lo_stop = set[i].lo_start -
- 0.5*set[i].amplitude * sin(TWOPI*delt/set[i].tperiod);
+ 0.5*set[i].amplitude * sin(TWOPI*delt/set[i].tperiod);
set[i].hi_stop = set[i].hi_start +
- 0.5*set[i].amplitude * sin(TWOPI*delt/set[i].tperiod);
+ 0.5*set[i].amplitude * sin(TWOPI*delt/set[i].tperiod);
}
}
@@ -502,52 +502,52 @@ void FixDeform::init()
} else if (set[i].style == VEL) {
set[i].tilt_stop = set[i].tilt_start + delt*set[i].vel;
} else if (set[i].style == ERATE) {
- if (i == 3) set[i].tilt_stop = set[i].tilt_start +
- delt*set[i].rate * (set[2].hi_start-set[2].lo_start);
- if (i == 4) set[i].tilt_stop = set[i].tilt_start +
- delt*set[i].rate * (set[2].hi_start-set[2].lo_start);
- if (i == 5) set[i].tilt_stop = set[i].tilt_start +
- delt*set[i].rate * (set[1].hi_start-set[1].lo_start);
+ if (i == 3) set[i].tilt_stop = set[i].tilt_start +
+ delt*set[i].rate * (set[2].hi_start-set[2].lo_start);
+ if (i == 4) set[i].tilt_stop = set[i].tilt_start +
+ delt*set[i].rate * (set[2].hi_start-set[2].lo_start);
+ if (i == 5) set[i].tilt_stop = set[i].tilt_start +
+ delt*set[i].rate * (set[1].hi_start-set[1].lo_start);
} else if (set[i].style == TRATE) {
set[i].tilt_stop = set[i].tilt_start * exp(set[i].rate*delt);
} else if (set[i].style == WIGGLE) {
set[i].tilt_stop = set[i].tilt_start +
- set[i].amplitude * sin(TWOPI*delt/set[i].tperiod);
+ set[i].amplitude * sin(TWOPI*delt/set[i].tperiod);
// compute min/max for WIGGLE = extrema tilt factor will ever reach
if (set[i].amplitude >= 0.0) {
- if (delt < 0.25*set[i].tperiod) {
- set[i].tilt_min = set[i].tilt_start;
- set[i].tilt_max = set[i].tilt_start +
- set[i].amplitude*sin(TWOPI*delt/set[i].tperiod);
- } else if (delt < 0.5*set[i].tperiod) {
- set[i].tilt_min = set[i].tilt_start;
- set[i].tilt_max = set[i].tilt_start + set[i].amplitude;
- } else if (delt < 0.75*set[i].tperiod) {
- set[i].tilt_min = set[i].tilt_start -
- set[i].amplitude*sin(TWOPI*delt/set[i].tperiod);
- set[i].tilt_max = set[i].tilt_start + set[i].amplitude;
- } else {
- set[i].tilt_min = set[i].tilt_start - set[i].amplitude;
- set[i].tilt_max = set[i].tilt_start + set[i].amplitude;
- }
+ if (delt < 0.25*set[i].tperiod) {
+ set[i].tilt_min = set[i].tilt_start;
+ set[i].tilt_max = set[i].tilt_start +
+ set[i].amplitude*sin(TWOPI*delt/set[i].tperiod);
+ } else if (delt < 0.5*set[i].tperiod) {
+ set[i].tilt_min = set[i].tilt_start;
+ set[i].tilt_max = set[i].tilt_start + set[i].amplitude;
+ } else if (delt < 0.75*set[i].tperiod) {
+ set[i].tilt_min = set[i].tilt_start -
+ set[i].amplitude*sin(TWOPI*delt/set[i].tperiod);
+ set[i].tilt_max = set[i].tilt_start + set[i].amplitude;
+ } else {
+ set[i].tilt_min = set[i].tilt_start - set[i].amplitude;
+ set[i].tilt_max = set[i].tilt_start + set[i].amplitude;
+ }
} else {
- if (delt < 0.25*set[i].tperiod) {
- set[i].tilt_min = set[i].tilt_start -
- set[i].amplitude*sin(TWOPI*delt/set[i].tperiod);
- set[i].tilt_max = set[i].tilt_start;
- } else if (delt < 0.5*set[i].tperiod) {
- set[i].tilt_min = set[i].tilt_start - set[i].amplitude;
- set[i].tilt_max = set[i].tilt_start;
- } else if (delt < 0.75*set[i].tperiod) {
- set[i].tilt_min = set[i].tilt_start - set[i].amplitude;
- set[i].tilt_max = set[i].tilt_start +
- set[i].amplitude*sin(TWOPI*delt/set[i].tperiod);
- } else {
- set[i].tilt_min = set[i].tilt_start - set[i].amplitude;
- set[i].tilt_max = set[i].tilt_start + set[i].amplitude;
- }
+ if (delt < 0.25*set[i].tperiod) {
+ set[i].tilt_min = set[i].tilt_start -
+ set[i].amplitude*sin(TWOPI*delt/set[i].tperiod);
+ set[i].tilt_max = set[i].tilt_start;
+ } else if (delt < 0.5*set[i].tperiod) {
+ set[i].tilt_min = set[i].tilt_start - set[i].amplitude;
+ set[i].tilt_max = set[i].tilt_start;
+ } else if (delt < 0.75*set[i].tperiod) {
+ set[i].tilt_min = set[i].tilt_start - set[i].amplitude;
+ set[i].tilt_max = set[i].tilt_start +
+ set[i].amplitude*sin(TWOPI*delt/set[i].tperiod);
+ } else {
+ set[i].tilt_min = set[i].tilt_start - set[i].amplitude;
+ set[i].tilt_max = set[i].tilt_start + set[i].amplitude;
+ }
}
}
}
@@ -576,10 +576,10 @@ void FixDeform::init()
hi = set[3].tilt_max;
} else lo = hi = set[3].tilt_stop;
if (lo/(set[1].hi_start-set[1].lo_start) < -0.5 ||
- hi/(set[1].hi_start-set[1].lo_start) > 0.5) flag = 1;
+ hi/(set[1].hi_start-set[1].lo_start) > 0.5) flag = 1;
if (set[1].style) {
if (lo/(set[1].hi_stop-set[1].lo_stop) < -0.5 ||
- hi/(set[1].hi_stop-set[1].lo_stop) > 0.5) flag = 1;
+ hi/(set[1].hi_stop-set[1].lo_stop) > 0.5) flag = 1;
}
if (flag) error->all(FLERR,"Fix deform is changing yz too much with xy");
}
@@ -594,12 +594,12 @@ void FixDeform::init()
for (int i = 0; i < 3; i++) {
h_rate[i] = h_ratelo[i] = 0.0;
if (set[i].style == FINAL || set[i].style == DELTA ||
- set[i].style == SCALE || set[i].style == VEL ||
- set[i].style == ERATE) {
+ set[i].style == SCALE || set[i].style == VEL ||
+ set[i].style == ERATE) {
double dlo_dt,dhi_dt;
if (delt != 0.0) {
- dlo_dt = (set[i].lo_stop - set[i].lo_start) / delt;
- dhi_dt = (set[i].hi_stop - set[i].hi_start) / delt;
+ dlo_dt = (set[i].lo_stop - set[i].lo_start) / delt;
+ dhi_dt = (set[i].hi_stop - set[i].hi_start) / delt;
} else dlo_dt = dhi_dt = 0.0;
h_rate[i] = dhi_dt - dlo_dt;
h_ratelo[i] = dlo_dt;
@@ -608,13 +608,13 @@ void FixDeform::init()
for (int i = 3; i < 6; i++) {
h_rate[i] = 0.0;
- if (set[i].style == FINAL || set[i].style == DELTA ||
- set[i].style == VEL || set[i].style == ERATE) {
+ if (set[i].style == FINAL || set[i].style == DELTA ||
+ set[i].style == VEL || set[i].style == ERATE) {
if (delt != 0.0)
- h_rate[i] = (set[i].tilt_stop - set[i].tilt_start) / delt;
+ h_rate[i] = (set[i].tilt_stop - set[i].tilt_start) / delt;
else h_rate[i] = 0.0;
}
- }
+ }
// detect if any rigid fixes exist so rigid bodies can be rescaled
// rfix[] = indices to each fix rigid
@@ -693,20 +693,20 @@ void FixDeform::end_of_step()
set[i].hi_target = domain->boxhi[i];
} else if (set[i].style == TRATE) {
double delt = (update->ntimestep - update->beginstep) * update->dt;
- set[i].lo_target = 0.5*(set[i].lo_start+set[i].hi_start) -
- 0.5*((set[i].hi_start-set[i].lo_start) * exp(set[i].rate*delt));
- set[i].hi_target = 0.5*(set[i].lo_start+set[i].hi_start) +
- 0.5*((set[i].hi_start-set[i].lo_start) * exp(set[i].rate*delt));
+ set[i].lo_target = 0.5*(set[i].lo_start+set[i].hi_start) -
+ 0.5*((set[i].hi_start-set[i].lo_start) * exp(set[i].rate*delt));
+ set[i].hi_target = 0.5*(set[i].lo_start+set[i].hi_start) +
+ 0.5*((set[i].hi_start-set[i].lo_start) * exp(set[i].rate*delt));
h_rate[i] = set[i].rate * domain->h[i];
h_ratelo[i] = -0.5*h_rate[i];
} else if (set[i].style == WIGGLE) {
double delt = (update->ntimestep - update->beginstep) * update->dt;
set[i].lo_target = set[i].lo_start -
- 0.5*set[i].amplitude * sin(TWOPI*delt/set[i].tperiod);
+ 0.5*set[i].amplitude * sin(TWOPI*delt/set[i].tperiod);
set[i].hi_target = set[i].hi_start +
- 0.5*set[i].amplitude * sin(TWOPI*delt/set[i].tperiod);
- h_rate[i] = TWOPI/set[i].tperiod * set[i].amplitude *
- cos(TWOPI*delt/set[i].tperiod);
+ 0.5*set[i].amplitude * sin(TWOPI*delt/set[i].tperiod);
+ h_rate[i] = TWOPI/set[i].tperiod * set[i].amplitude *
+ cos(TWOPI*delt/set[i].tperiod);
h_ratelo[i] = -0.5*h_rate[i];
} else if (set[i].style == VARIABLE) {
double del = input->variable->compute_equal(set[i].hvar);
@@ -715,10 +715,10 @@ void FixDeform::end_of_step()
h_rate[i] = input->variable->compute_equal(set[i].hratevar);
h_ratelo[i] = -0.5*h_rate[i];
} else if (set[i].style != VOLUME) {
- set[i].lo_target = set[i].lo_start +
- delta*(set[i].lo_stop - set[i].lo_start);
- set[i].hi_target = set[i].hi_start +
- delta*(set[i].hi_stop - set[i].hi_start);
+ set[i].lo_target = set[i].lo_start +
+ delta*(set[i].lo_stop - set[i].lo_start);
+ set[i].hi_target = set[i].hi_start +
+ delta*(set[i].hi_stop - set[i].hi_start);
}
}
@@ -730,45 +730,45 @@ void FixDeform::end_of_step()
if (set[i].substyle == ONE_FROM_ONE) {
set[i].lo_target = 0.5*(set[i].lo_start+set[i].hi_start) -
- 0.5*(set[i].vol_start /
- (set[set[i].dynamic1].hi_target -
- set[set[i].dynamic1].lo_target) /
- (set[set[i].fixed].hi_start-set[set[i].fixed].lo_start));
+ 0.5*(set[i].vol_start /
+ (set[set[i].dynamic1].hi_target -
+ set[set[i].dynamic1].lo_target) /
+ (set[set[i].fixed].hi_start-set[set[i].fixed].lo_start));
set[i].hi_target = 0.5*(set[i].lo_start+set[i].hi_start) +
- 0.5*(set[i].vol_start /
- (set[set[i].dynamic1].hi_target -
- set[set[i].dynamic1].lo_target) /
- (set[set[i].fixed].hi_start-set[set[i].fixed].lo_start));
+ 0.5*(set[i].vol_start /
+ (set[set[i].dynamic1].hi_target -
+ set[set[i].dynamic1].lo_target) /
+ (set[set[i].fixed].hi_start-set[set[i].fixed].lo_start));
} else if (set[i].substyle == ONE_FROM_TWO) {
set[i].lo_target = 0.5*(set[i].lo_start+set[i].hi_start) -
- 0.5*(set[i].vol_start /
- (set[set[i].dynamic1].hi_target -
- set[set[i].dynamic1].lo_target) /
- (set[set[i].dynamic2].hi_target -
- set[set[i].dynamic2].lo_target));
+ 0.5*(set[i].vol_start /
+ (set[set[i].dynamic1].hi_target -
+ set[set[i].dynamic1].lo_target) /
+ (set[set[i].dynamic2].hi_target -
+ set[set[i].dynamic2].lo_target));
set[i].hi_target = 0.5*(set[i].lo_start+set[i].hi_start) +
- 0.5*(set[i].vol_start /
- (set[set[i].dynamic1].hi_target -
- set[set[i].dynamic1].lo_target) /
- (set[set[i].dynamic2].hi_target -
- set[set[i].dynamic2].lo_target));
-
+ 0.5*(set[i].vol_start /
+ (set[set[i].dynamic1].hi_target -
+ set[set[i].dynamic1].lo_target) /
+ (set[set[i].dynamic2].hi_target -
+ set[set[i].dynamic2].lo_target));
+
} else if (set[i].substyle == TWO_FROM_ONE) {
set[i].lo_target = 0.5*(set[i].lo_start+set[i].hi_start) -
- 0.5*sqrt(set[i].vol_start /
- (set[set[i].dynamic1].hi_target -
- set[set[i].dynamic1].lo_target) /
- (set[set[i].fixed].hi_start -
- set[set[i].fixed].lo_start) *
- (set[i].hi_start - set[i].lo_start));
+ 0.5*sqrt(set[i].vol_start /
+ (set[set[i].dynamic1].hi_target -
+ set[set[i].dynamic1].lo_target) /
+ (set[set[i].fixed].hi_start -
+ set[set[i].fixed].lo_start) *
+ (set[i].hi_start - set[i].lo_start));
set[i].hi_target = 0.5*(set[i].lo_start+set[i].hi_start) +
- 0.5*sqrt(set[i].vol_start /
- (set[set[i].dynamic1].hi_target -
- set[set[i].dynamic1].lo_target) /
- (set[set[i].fixed].hi_start -
- set[set[i].fixed].lo_start) *
- (set[i].hi_start - set[i].lo_start));
+ 0.5*sqrt(set[i].vol_start /
+ (set[set[i].dynamic1].hi_target -
+ set[set[i].dynamic1].lo_target) /
+ (set[set[i].fixed].hi_start -
+ set[set[i].fixed].lo_start) *
+ (set[i].hi_start - set[i].lo_start));
}
}
@@ -784,26 +784,26 @@ void FixDeform::end_of_step()
for (i = 3; i < 6; i++) {
if (set[i].style == NONE) {
- if (i == 5) set[i].tilt_target = domain->xy;
- else if (i == 4) set[i].tilt_target = domain->xz;
- else if (i == 3) set[i].tilt_target = domain->yz;
+ if (i == 5) set[i].tilt_target = domain->xy;
+ else if (i == 4) set[i].tilt_target = domain->xz;
+ else if (i == 3) set[i].tilt_target = domain->yz;
} else if (set[i].style == TRATE) {
- double delt = (update->ntimestep - update->beginstep) * update->dt;
- set[i].tilt_target = set[i].tilt_start * exp(set[i].rate*delt);
- h_rate[i] = set[i].rate * domain->h[i];
+ double delt = (update->ntimestep - update->beginstep) * update->dt;
+ set[i].tilt_target = set[i].tilt_start * exp(set[i].rate*delt);
+ h_rate[i] = set[i].rate * domain->h[i];
} else if (set[i].style == WIGGLE) {
- double delt = (update->ntimestep - update->beginstep) * update->dt;
- set[i].tilt_target = set[i].tilt_start +
- set[i].amplitude * sin(TWOPI*delt/set[i].tperiod);
- h_rate[i] = TWOPI/set[i].tperiod * set[i].amplitude *
- cos(TWOPI*delt/set[i].tperiod);
+ double delt = (update->ntimestep - update->beginstep) * update->dt;
+ set[i].tilt_target = set[i].tilt_start +
+ set[i].amplitude * sin(TWOPI*delt/set[i].tperiod);
+ h_rate[i] = TWOPI/set[i].tperiod * set[i].amplitude *
+ cos(TWOPI*delt/set[i].tperiod);
} else if (set[i].style == VARIABLE) {
- double delta_tilt = input->variable->compute_equal(set[i].hvar);
- set[i].tilt_target = set[i].tilt_start + delta_tilt;
- h_rate[i] = input->variable->compute_equal(set[i].hratevar);
+ double delta_tilt = input->variable->compute_equal(set[i].hvar);
+ set[i].tilt_target = set[i].tilt_start + delta_tilt;
+ h_rate[i] = input->variable->compute_equal(set[i].hratevar);
} else {
- set[i].tilt_target = set[i].tilt_start +
- delta*(set[i].tilt_stop - set[i].tilt_start);
+ set[i].tilt_target = set[i].tilt_start +
+ delta*(set[i].tilt_stop - set[i].tilt_start);
}
// tilt_target can be large positive or large negative value
@@ -818,12 +818,12 @@ void FixDeform::end_of_step()
double current = h[i]/h[idenom];
while (set[i].tilt_target/denom - current > 0.0)
- set[i].tilt_target -= denom;
+ set[i].tilt_target -= denom;
while (set[i].tilt_target/denom - current < 0.0)
- set[i].tilt_target += denom;
- if (fabs(set[i].tilt_target/denom - 1.0 - current) <
- fabs(set[i].tilt_target/denom - current))
- set[i].tilt_target -= denom;
+ set[i].tilt_target += denom;
+ if (fabs(set[i].tilt_target/denom - 1.0 - current) <
+ fabs(set[i].tilt_target/denom - current))
+ set[i].tilt_target -= denom;
}
}
@@ -843,46 +843,46 @@ void FixDeform::end_of_step()
double yprd = set[1].hi_target - set[1].lo_target;
double xprdinv = 1.0 / xprd;
double yprdinv = 1.0 / yprd;
- if (set[3].tilt_target*yprdinv < -0.5 ||
- set[3].tilt_target*yprdinv > 0.5 ||
- set[4].tilt_target*xprdinv < -0.5 ||
- set[4].tilt_target*xprdinv > 0.5 ||
- set[5].tilt_target*xprdinv < -0.5 ||
- set[5].tilt_target*xprdinv > 0.5) {
+ if (set[3].tilt_target*yprdinv < -0.5 ||
+ set[3].tilt_target*yprdinv > 0.5 ||
+ set[4].tilt_target*xprdinv < -0.5 ||
+ set[4].tilt_target*xprdinv > 0.5 ||
+ set[5].tilt_target*xprdinv < -0.5 ||
+ set[5].tilt_target*xprdinv > 0.5) {
set[3].tilt_flip = set[3].tilt_target;
set[4].tilt_flip = set[4].tilt_target;
set[5].tilt_flip = set[5].tilt_target;
-
+
flipxy = flipxz = flipyz = 0;
if (domain->yperiodic) {
- if (set[3].tilt_flip*yprdinv < -0.5) {
- set[3].tilt_flip += yprd;
- set[4].tilt_flip += set[5].tilt_flip;
- flipyz = 1;
- } else if (set[3].tilt_flip*yprdinv > 0.5) {
- set[3].tilt_flip -= yprd;
- set[4].tilt_flip -= set[5].tilt_flip;
- flipyz = -1;
- }
+ if (set[3].tilt_flip*yprdinv < -0.5) {
+ set[3].tilt_flip += yprd;
+ set[4].tilt_flip += set[5].tilt_flip;
+ flipyz = 1;
+ } else if (set[3].tilt_flip*yprdinv > 0.5) {
+ set[3].tilt_flip -= yprd;
+ set[4].tilt_flip -= set[5].tilt_flip;
+ flipyz = -1;
+ }
}
if (domain->xperiodic) {
- if (set[4].tilt_flip*xprdinv < -0.5) {
- set[4].tilt_flip += xprd;
- flipxz = 1;
- }
- if (set[4].tilt_flip*xprdinv > 0.5) {
- set[4].tilt_flip -= xprd;
- flipxz = -1;
- }
- if (set[5].tilt_flip*xprdinv < -0.5) {
- set[5].tilt_flip += xprd;
- flipxy = 1;
- }
- if (set[5].tilt_flip*xprdinv > 0.5) {
- set[5].tilt_flip -= xprd;
- flipxy = -1;
- }
+ if (set[4].tilt_flip*xprdinv < -0.5) {
+ set[4].tilt_flip += xprd;
+ flipxz = 1;
+ }
+ if (set[4].tilt_flip*xprdinv > 0.5) {
+ set[4].tilt_flip -= xprd;
+ flipxz = -1;
+ }
+ if (set[5].tilt_flip*xprdinv < -0.5) {
+ set[5].tilt_flip += xprd;
+ flipxy = 1;
+ }
+ if (set[5].tilt_flip*xprdinv > 0.5) {
+ set[5].tilt_flip -= xprd;
+ flipxy = -1;
+ }
}
flip = 0;
@@ -900,11 +900,11 @@ void FixDeform::end_of_step()
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
- domain->x2lamda(x[i],x[i]);
+ domain->x2lamda(x[i],x[i]);
if (nrigid)
for (i = 0; i < nrigid; i++)
- modify->fix[rfix[i]]->deform(0);
+ modify->fix[rfix[i]]->deform(0);
}
// reset global and local box to new size/shape
@@ -940,11 +940,11 @@ void FixDeform::end_of_step()
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
- domain->lamda2x(x[i],x[i]);
+ domain->lamda2x(x[i],x[i]);
if (nrigid)
for (i = 0; i < nrigid; i++)
- modify->fix[rfix[i]]->deform(1);
+ modify->fix[rfix[i]]->deform(1);
}
// redo KSpace coeffs since box has changed
diff --git a/src/fix_deform.h b/src/fix_deform.h
index 33a86b375b1087a050891afdc92cd61a077e3876..d4ee95be977d3502b9a866ffb02c5853cf670d45 100644
--- a/src/fix_deform.h
+++ b/src/fix_deform.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_deposit.cpp b/src/fix_deposit.cpp
index b3f403a8d4128b94edc71cb8cac5098a89ffeb66..106b293d421aca1424d2fef2387a29e2ce55017d 100644
--- a/src/fix_deposit.cpp
+++ b/src/fix_deposit.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -84,14 +84,14 @@ FixDeposit::FixDeposit(LAMMPS *lmp, int narg, char **arg) :
zhi = domain->regions[iregion]->extent_zhi;
if (domain->triclinic == 0) {
- if (xlo < domain->boxlo[0] || xhi > domain->boxhi[0] ||
- ylo < domain->boxlo[1] || yhi > domain->boxhi[1] ||
- zlo < domain->boxlo[2] || zhi > domain->boxhi[2])
+ if (xlo < domain->boxlo[0] || xhi > domain->boxhi[0] ||
+ ylo < domain->boxlo[1] || yhi > domain->boxhi[1] ||
+ zlo < domain->boxlo[2] || zhi > domain->boxhi[2])
error->all(FLERR,"Deposition region extends outside simulation box");
} else {
- if (xlo < domain->boxlo_bound[0] || xhi > domain->boxhi_bound[0] ||
- ylo < domain->boxlo_bound[1] || yhi > domain->boxhi_bound[1] ||
- zlo < domain->boxlo_bound[2] || zhi > domain->boxhi_bound[2])
+ if (xlo < domain->boxlo_bound[0] || xhi > domain->boxhi_bound[0] ||
+ ylo < domain->boxlo_bound[1] || yhi > domain->boxhi_bound[1] ||
+ zlo < domain->boxlo_bound[2] || zhi > domain->boxhi_bound[2])
error->all(FLERR,"Deposition region extends outside simulation box");
}
@@ -167,7 +167,7 @@ void FixDeposit::init()
// set index and check validity of region
iregion = domain->find_region(idregion);
- if (iregion == -1)
+ if (iregion == -1)
error->all(FLERR,"Region ID for fix deposit does not exist");
}
@@ -235,34 +235,34 @@ void FixDeposit::pre_exchange()
double max,maxall,delx,dely,delz,rsq;
if (domain->dimension == 2) {
- dim = 1;
- max = domain->boxlo[1];
+ dim = 1;
+ max = domain->boxlo[1];
} else {
- dim = 2;
- max = domain->boxlo[2];
+ dim = 2;
+ max = domain->boxlo[2];
}
double **x = atom->x;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
- if (localflag) {
- delx = coord[0] - x[i][0];
- dely = coord[1] - x[i][1];
- delz = 0.0;
- domain->minimum_image(delx,dely,delz);
- if (domain->dimension == 2) rsq = delx*delx;
- else rsq = delx*delx + dely*dely;
- if (rsq > deltasq) continue;
- }
- if (x[i][dim] > max) max = x[i][dim];
+ if (localflag) {
+ delx = coord[0] - x[i][0];
+ dely = coord[1] - x[i][1];
+ delz = 0.0;
+ domain->minimum_image(delx,dely,delz);
+ if (domain->dimension == 2) rsq = delx*delx;
+ else rsq = delx*delx + dely*dely;
+ if (rsq > deltasq) continue;
+ }
+ if (x[i][dim] > max) max = x[i][dim];
}
MPI_Allreduce(&max,&maxall,1,MPI_DOUBLE,MPI_MAX,world);
if (domain->dimension == 2)
- coord[1] = maxall + lo + random->uniform()*(hi-lo);
+ coord[1] = maxall + lo + random->uniform()*(hi-lo);
else
- coord[2] = maxall + lo + random->uniform()*(hi-lo);
- }
+ coord[2] = maxall + lo + random->uniform()*(hi-lo);
+ }
// now have final coord
// if distance to any atom is less than near, try again
@@ -297,10 +297,10 @@ void FixDeposit::pre_exchange()
delz = tz - coord[2];
double rsq = delx*delx + dely*dely + delz*delz;
if (rsq > 0.0) {
- double rinv = sqrt(1.0/rsq);
- vxtmp = delx*rinv*vel;
- vytmp = dely*rinv*vel;
- vztmp = delz*rinv*vel;
+ double rinv = sqrt(1.0/rsq);
+ vxtmp = delx*rinv*vel;
+ vytmp = dely*rinv*vel;
+ vztmp = delz*rinv*vel;
}
}
@@ -308,7 +308,7 @@ void FixDeposit::pre_exchange()
// if so, add to my list via create_atom()
// initialize info about the atoms
// set group mask to "all" plus fix group
-
+
if (domain->triclinic) {
domain->x2lamda(coord,lamda);
newcoord = lamda;
@@ -316,15 +316,15 @@ void FixDeposit::pre_exchange()
flag = 0;
if (newcoord[0] >= sublo[0] && newcoord[0] < subhi[0] &&
- newcoord[1] >= sublo[1] && newcoord[1] < subhi[1] &&
- newcoord[2] >= sublo[2] && newcoord[2] < subhi[2]) flag = 1;
+ newcoord[1] >= sublo[1] && newcoord[1] < subhi[1] &&
+ newcoord[2] >= sublo[2] && newcoord[2] < subhi[2]) flag = 1;
else if (domain->dimension == 3 && newcoord[2] >= domain->boxhi[2] &&
- comm->myloc[2] == comm->procgrid[2]-1 &&
- newcoord[0] >= sublo[0] && newcoord[0] < subhi[0] &&
- newcoord[1] >= sublo[1] && newcoord[1] < subhi[1]) flag = 1;
+ comm->myloc[2] == comm->procgrid[2]-1 &&
+ newcoord[0] >= sublo[0] && newcoord[0] < subhi[0] &&
+ newcoord[1] >= sublo[1] && newcoord[1] < subhi[1]) flag = 1;
else if (domain->dimension == 2 && newcoord[1] >= domain->boxhi[1] &&
- comm->myloc[1] == comm->procgrid[1]-1 &&
- newcoord[0] >= sublo[0] && newcoord[0] < subhi[0]) flag = 1;
+ comm->myloc[1] == comm->procgrid[1]-1 &&
+ newcoord[0] >= sublo[0] && newcoord[0] < subhi[0]) flag = 1;
if (flag) {
atom->avec->create_atom(ntype,coord);
@@ -335,7 +335,7 @@ void FixDeposit::pre_exchange()
atom->v[m][1] = vytmp;
atom->v[m][2] = vztmp;
for (j = 0; j < nfix; j++)
- if (fix[j]->create_attribute) fix[j]->set_arrays(m);
+ if (fix[j]->create_attribute) fix[j]->set_arrays(m);
}
MPI_Allreduce(&flag,&success,1,MPI_INT,MPI_MAX,world);
break;
@@ -356,9 +356,9 @@ void FixDeposit::pre_exchange()
if (atom->tag_enable) {
atom->tag_extend();
if (atom->map_style) {
- atom->nghost = 0;
- atom->map_init();
- atom->map_set();
+ atom->nghost = 0;
+ atom->map_init();
+ atom->map_set();
}
}
}
@@ -372,7 +372,7 @@ void FixDeposit::pre_exchange()
}
/* ----------------------------------------------------------------------
- parse optional parameters at end of input line
+ parse optional parameters at end of input line
------------------------------------------------------------------------- */
void FixDeposit::options(int narg, char **arg)
@@ -385,7 +385,7 @@ void FixDeposit::options(int narg, char **arg)
if (iarg+2 > narg) error->all(FLERR,"Illegal fix deposit command");
iregion = domain->find_region(arg[iarg+1]);
if (iregion == -1)
- error->all(FLERR,"Region ID for fix deposit does not exist");
+ error->all(FLERR,"Region ID for fix deposit does not exist");
int n = strlen(arg[iarg+1]) + 1;
idregion = new char[n];
strcpy(idregion,arg[iarg+1]);
@@ -451,7 +451,7 @@ void FixDeposit::options(int narg, char **arg)
}
/* ----------------------------------------------------------------------
- pack entire state of Fix into one write
+ pack entire state of Fix into one write
------------------------------------------------------------------------- */
void FixDeposit::write_restart(FILE *fp)
@@ -471,7 +471,7 @@ void FixDeposit::write_restart(FILE *fp)
}
/* ----------------------------------------------------------------------
- use state info from restart file to restart the Fix
+ use state info from restart file to restart the Fix
------------------------------------------------------------------------- */
void FixDeposit::restart(char *buf)
diff --git a/src/fix_deposit.h b/src/fix_deposit.h
index 0b1f4b802885ed8b268dd2f0fcf9ef3b027d3475..b379d4db493b68b478174219be10393b9e3c7ea4 100644
--- a/src/fix_deposit.h
+++ b/src/fix_deposit.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_drag.cpp b/src/fix_drag.cpp
index 30c886ae7124a8ccb34ea81264576a253b0ac13f..0abdf0d3d2670355b1bf2e9de48868fc5758e62c 100644
--- a/src/fix_drag.cpp
+++ b/src/fix_drag.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -97,7 +97,7 @@ void FixDrag::post_force(int vflag)
ftotal[0] = ftotal[1] = ftotal[2] = 0.0;
force_flag = 0;
-
+
double dx,dy,dz,r,prefactor,fx,fy,fz;
for (int i = 0; i < nlocal; i++)
@@ -111,16 +111,16 @@ void FixDrag::post_force(int vflag)
domain->minimum_image(dx,dy,dz);
r = sqrt(dx*dx + dy*dy + dz*dz);
if (r > delta) {
- prefactor = f_mag/r;
- fx = prefactor*dx;
- fy = prefactor*dy;
- fz = prefactor*dz;
- f[i][0] -= fx;
- f[i][1] -= fy;
- f[i][2] -= fz;
- ftotal[0] -= fx;
- ftotal[1] -= fy;
- ftotal[2] -= fz;
+ prefactor = f_mag/r;
+ fx = prefactor*dx;
+ fy = prefactor*dy;
+ fz = prefactor*dz;
+ f[i][0] -= fx;
+ f[i][1] -= fy;
+ f[i][2] -= fz;
+ ftotal[0] -= fx;
+ ftotal[1] -= fy;
+ ftotal[2] -= fz;
}
}
}
diff --git a/src/fix_drag.h b/src/fix_drag.h
index 49df06e9bb3ba40acccd1039d8798d0101726355..e6b05d8039ec889db0af1da85d1ad24da2c30ea1 100644
--- a/src/fix_drag.h
+++ b/src/fix_drag.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_dt_reset.cpp b/src/fix_dt_reset.cpp
index b0a95a61005b2cffb84ad826e249f869178a46ab..60e9e0b44969885ddbfaf25f00c2c40f43001a84 100644
--- a/src/fix_dt_reset.cpp
+++ b/src/fix_dt_reset.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -43,7 +43,7 @@ FixDtReset::FixDtReset(LAMMPS *lmp, int narg, char **arg) :
// set time_depend, else elapsed time accumulation can be messed up
- time_depend = 1;
+ time_depend = 1;
scalar_flag = 1;
vector_flag = 1;
size_vector = 2;
@@ -116,9 +116,9 @@ void FixDtReset::init()
for (int i = 0; i < output->ndump; i++)
if ((strcmp(output->dump[i]->style,"dcd") == 0 ||
- strcmp(output->dump[i]->style,"xtc") == 0) && comm->me == 0)
+ strcmp(output->dump[i]->style,"xtc") == 0) && comm->me == 0)
error->warning(FLERR,
- "Dump dcd/xtc timestamp may be wrong with fix dt/reset");
+ "Dump dcd/xtc timestamp may be wrong with fix dt/reset");
ftm2v = force->ftm2v;
dt = update->dt;
@@ -183,7 +183,7 @@ void FixDtReset::end_of_step()
if (minbound) dt = MAX(dt,tmin);
if (maxbound) dt = MIN(dt,tmax);
-
+
// if timestep didn't change, just return
// else reset update->dt and other classes that depend on it
// rRESPA, pair style, fixes
diff --git a/src/fix_dt_reset.h b/src/fix_dt_reset.h
index 5198afa820bb2a4bd9e522f52b0375dbc938c30e..4679163291d8c4e233e0ec2c21627d979d1d91b6 100644
--- a/src/fix_dt_reset.h
+++ b/src/fix_dt_reset.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_efield.cpp b/src/fix_efield.cpp
index ac953950f19d19317d1687b11934eb94dbcc1194..d6e7158528bc5f02419db5d02e18fc1b6850ddca 100644
--- a/src/fix_efield.cpp
+++ b/src/fix_efield.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -106,7 +106,7 @@ void FixEfield::init()
if (xstr) {
xvar = input->variable->find(xstr);
if (xvar < 0) error->all(FLERR,
- "Variable name for fix efield does not exist");
+ "Variable name for fix efield does not exist");
if (input->variable->equalstyle(xvar)) xstyle = EQUAL;
else if (input->variable->atomstyle(xvar)) xstyle = ATOM;
else error->all(FLERR,"Variable for fix efield is invalid style");
@@ -114,7 +114,7 @@ void FixEfield::init()
if (ystr) {
yvar = input->variable->find(ystr);
if (yvar < 0) error->all(FLERR,
- "Variable name for fix efield does not exist");
+ "Variable name for fix efield does not exist");
if (input->variable->equalstyle(yvar)) ystyle = EQUAL;
else if (input->variable->atomstyle(yvar)) ystyle = ATOM;
else error->all(FLERR,"Variable for fix efield is invalid style");
@@ -122,7 +122,7 @@ void FixEfield::init()
if (zstr) {
zvar = input->variable->find(zstr);
if (zvar < 0) error->all(FLERR,
- "Variable name for fix efield does not exist");
+ "Variable name for fix efield does not exist");
if (input->variable->equalstyle(zvar)) zstyle = EQUAL;
else if (input->variable->atomstyle(zvar)) zstyle = ATOM;
else error->all(FLERR,"Variable for fix efield is invalid style");
@@ -173,9 +173,9 @@ void FixEfield::post_force(int vflag)
if (varflag == CONSTANT) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- f[i][0] += q[i]*ex;
- f[i][1] += q[i]*ey;
- f[i][2] += q[i]*ez;
+ f[i][0] += q[i]*ex;
+ f[i][1] += q[i]*ey;
+ f[i][2] += q[i]*ez;
}
// variable efield, wrap with clear/add
@@ -198,12 +198,12 @@ void FixEfield::post_force(int vflag)
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- if (xstyle == ATOM) f[i][0] += qe2f * q[i]*efield[i][0];
- else f[i][0] += q[i]*ex;
- if (ystyle == ATOM) f[i][1] += qe2f * q[i]*efield[i][1];
- else f[i][1] += q[i]*ey;
- if (zstyle == ATOM) f[i][2] += qe2f * q[i]*efield[i][2];
- else f[i][2] += q[i]*ez;
+ if (xstyle == ATOM) f[i][0] += qe2f * q[i]*efield[i][0];
+ else f[i][0] += q[i]*ex;
+ if (ystyle == ATOM) f[i][1] += qe2f * q[i]*efield[i][1];
+ else f[i][1] += q[i]*ey;
+ if (zstyle == ATOM) f[i][2] += qe2f * q[i]*efield[i][2];
+ else f[i][2] += q[i]*ez;
}
}
}
diff --git a/src/fix_efield.h b/src/fix_efield.h
index ba70cbae54a8cf64c399a1e296403cb06fc40c52..dabda61b412640ca9436a187d0fbef9bc0989bef 100644
--- a/src/fix_efield.h
+++ b/src/fix_efield.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_enforce2d.cpp b/src/fix_enforce2d.cpp
index d6f02b0188ed07bbf8c71a58ab4df44e9ead163d..ed169d36e57f2d1e7c3df98ffe980f0605ecb32a 100644
--- a/src/fix_enforce2d.cpp
+++ b/src/fix_enforce2d.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -94,8 +94,8 @@ void FixEnforce2D::post_force(int vflag)
double **omega = atom->omega;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- omega[i][0] = 0.0;
- omega[i][1] = 0.0;
+ omega[i][0] = 0.0;
+ omega[i][1] = 0.0;
}
}
@@ -103,8 +103,8 @@ void FixEnforce2D::post_force(int vflag)
double **angmom = atom->angmom;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- angmom[i][0] = 0.0;
- angmom[i][1] = 0.0;
+ angmom[i][0] = 0.0;
+ angmom[i][1] = 0.0;
}
}
@@ -112,8 +112,8 @@ void FixEnforce2D::post_force(int vflag)
double **torque = atom->torque;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- torque[i][0] = 0.0;
- torque[i][1] = 0.0;
+ torque[i][0] = 0.0;
+ torque[i][1] = 0.0;
}
}
}
diff --git a/src/fix_enforce2d.h b/src/fix_enforce2d.h
index d1df796dfc7bfc4a64a587d192fad30a360d5e71..f3f56dbb920c0bd0ed7a6257d89178f53533d88a 100644
--- a/src/fix_enforce2d.h
+++ b/src/fix_enforce2d.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_evaporate.cpp b/src/fix_evaporate.cpp
index eee0418b8422450fec75758c82ad2a547f4773f7..7eb5093d3fe5ecb005996924b87f548f53c2edde 100644
--- a/src/fix_evaporate.cpp
+++ b/src/fix_evaporate.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -143,17 +143,17 @@ void FixEvaporate::init()
int flag = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
- if (molecule[i]) flag = 1;
+ if (molecule[i]) flag = 1;
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall && comm->me == 0)
error->warning(FLERR,
- "Fix evaporate may delete atom with non-zero molecule ID");
+ "Fix evaporate may delete atom with non-zero molecule ID");
}
if (molflag && atom->molecule_flag == 0)
error->all(FLERR,
- "Fix evaporate molecule requires atom attribute molecule");
+ "Fix evaporate molecule requires atom attribute molecule");
}
/* ----------------------------------------------------------------------
@@ -193,7 +193,7 @@ void FixEvaporate::pre_exchange()
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2]))
- list[ncount++] = i;
+ list[ncount++] = i;
int nall,nbefore;
MPI_Allreduce(&ncount,&nall,1,MPI_INT,MPI_SUM,world);
@@ -217,10 +217,10 @@ void FixEvaporate::pre_exchange()
iwhichglobal = static_cast<int> (nall*random->uniform());
if (iwhichglobal < nbefore) nbefore--;
else if (iwhichglobal < nbefore + ncount) {
- iwhichlocal = iwhichglobal - nbefore;
- mark[list[iwhichlocal]] = 1;
- list[iwhichlocal] = list[ncount-1];
- ncount--;
+ iwhichlocal = iwhichglobal - nbefore;
+ mark[list[iwhichlocal]] = 1;
+ list[iwhichlocal] = list[ncount-1];
+ ncount--;
}
ndel++;
nall--;
@@ -245,10 +245,10 @@ void FixEvaporate::pre_exchange()
iwhichglobal = static_cast<int> (nall*random->uniform());
if (iwhichglobal >= nbefore && iwhichglobal < nbefore + ncount) {
- iwhichlocal = iwhichglobal - nbefore;
- iatom = list[iwhichlocal];
- imolecule = molecule[iatom];
- me = comm->me;
+ iwhichlocal = iwhichglobal - nbefore;
+ iatom = list[iwhichlocal];
+ imolecule = molecule[iatom];
+ me = comm->me;
} else me = -1;
// bcast mol ID to delete all atoms from
@@ -260,60 +260,60 @@ void FixEvaporate::pre_exchange()
MPI_Bcast(&imolecule,1,MPI_INT,proc,world);
ndelone = 0;
for (i = 0; i < nlocal; i++) {
- if (imolecule && molecule[i] == imolecule) {
- mark[i] = 1;
- ndelone++;
-
- if (atom->avec->bonds_allow) {
- if (force->newton_bond) ndeltopo[0] += atom->num_bond[i];
- else {
- for (j = 0; j < atom->num_bond[i]; j++) {
- if (tag[i] < atom->bond_atom[i][j]) ndeltopo[0]++;
- }
- }
- }
- if (atom->avec->angles_allow) {
- if (force->newton_bond) ndeltopo[1] += atom->num_angle[i];
- else {
- for (j = 0; j < atom->num_angle[i]; j++) {
- m = atom->map(atom->angle_atom2[i][j]);
- if (m >= 0 && m < nlocal) ndeltopo[1]++;
- }
- }
- }
- if (atom->avec->dihedrals_allow) {
- if (force->newton_bond) ndeltopo[2] += atom->num_dihedral[i];
- else {
- for (j = 0; j < atom->num_dihedral[i]; j++) {
- m = atom->map(atom->dihedral_atom2[i][j]);
- if (m >= 0 && m < nlocal) ndeltopo[2]++;
- }
- }
- }
- if (atom->avec->impropers_allow) {
- if (force->newton_bond) ndeltopo[3] += atom->num_improper[i];
- else {
- for (j = 0; j < atom->num_improper[i]; j++) {
- m = atom->map(atom->improper_atom2[i][j]);
- if (m >= 0 && m < nlocal) ndeltopo[3]++;
- }
- }
- }
-
- } else if (me == proc && i == iatom) {
- mark[i] = 1;
- ndelone++;
- }
+ if (imolecule && molecule[i] == imolecule) {
+ mark[i] = 1;
+ ndelone++;
+
+ if (atom->avec->bonds_allow) {
+ if (force->newton_bond) ndeltopo[0] += atom->num_bond[i];
+ else {
+ for (j = 0; j < atom->num_bond[i]; j++) {
+ if (tag[i] < atom->bond_atom[i][j]) ndeltopo[0]++;
+ }
+ }
+ }
+ if (atom->avec->angles_allow) {
+ if (force->newton_bond) ndeltopo[1] += atom->num_angle[i];
+ else {
+ for (j = 0; j < atom->num_angle[i]; j++) {
+ m = atom->map(atom->angle_atom2[i][j]);
+ if (m >= 0 && m < nlocal) ndeltopo[1]++;
+ }
+ }
+ }
+ if (atom->avec->dihedrals_allow) {
+ if (force->newton_bond) ndeltopo[2] += atom->num_dihedral[i];
+ else {
+ for (j = 0; j < atom->num_dihedral[i]; j++) {
+ m = atom->map(atom->dihedral_atom2[i][j]);
+ if (m >= 0 && m < nlocal) ndeltopo[2]++;
+ }
+ }
+ }
+ if (atom->avec->impropers_allow) {
+ if (force->newton_bond) ndeltopo[3] += atom->num_improper[i];
+ else {
+ for (j = 0; j < atom->num_improper[i]; j++) {
+ m = atom->map(atom->improper_atom2[i][j]);
+ if (m >= 0 && m < nlocal) ndeltopo[3]++;
+ }
+ }
+ }
+
+ } else if (me == proc && i == iatom) {
+ mark[i] = 1;
+ ndelone++;
+ }
}
// remove any atoms marked for deletion from my eligible list
i = 0;
while (i < ncount) {
- if (mark[list[i]]) {
- list[i] = list[ncount-1];
- ncount--;
- } else i++;
+ if (mark[list[i]]) {
+ list[i] = list[ncount-1];
+ ncount--;
+ } else i++;
}
// update ndel,ncount,nall,nbefore
@@ -330,9 +330,9 @@ void FixEvaporate::pre_exchange()
// delete my marked atoms
// loop in reverse order to avoid copying marked atoms
-
+
AtomVec *avec = atom->avec;
-
+
for (i = nlocal-1; i >= 0; i--) {
if (mark[i]) {
avec->copy(atom->nlocal-1,i,1);
@@ -361,7 +361,7 @@ void FixEvaporate::pre_exchange()
}
// statistics
-
+
ndeleted += ndel;
next_reneighbor = update->ntimestep + nevery;
}
diff --git a/src/fix_evaporate.h b/src/fix_evaporate.h
index 065e92d7020f124e210271794b3be11bca0519f1..f59558103a30b725bba8f6170ca774c41e9124c5 100644
--- a/src/fix_evaporate.h
+++ b/src/fix_evaporate.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_external.cpp b/src/fix_external.cpp
index 85cd2f6505b9b3c3319be21b6d164a33a09366f0..0e787d078ddea6aa71699f3834e75b58aa407756 100644
--- a/src/fix_external.cpp
+++ b/src/fix_external.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -56,7 +56,7 @@ int FixExternal::setmask()
void FixExternal::init()
{
- if (callback == NULL)
+ if (callback == NULL)
error->all(FLERR,"Fix external callback function not set");
}
@@ -88,7 +88,7 @@ void FixExternal::post_force(int vflag)
// it will fill fexternal with forces
(this->callback)(ptr_caller,update->ntimestep,
- atom->nlocal,atom->tag,atom->x,fexternal);
+ atom->nlocal,atom->tag,atom->x,fexternal);
// add forces from fexternal to atoms in group
diff --git a/src/fix_external.h b/src/fix_external.h
index 8cd798a72f75056dd16934d941d8addad742829c..8dce882216affa6e1467389ce7720ef404e27172 100644
--- a/src/fix_external.h
+++ b/src/fix_external.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_gravity.cpp b/src/fix_gravity.cpp
index f03ded78c78410bc80214c2c0c968114996e0cc1..bc72f5b11338663d18989bd1b61a5968be6c8b70 100644
--- a/src/fix_gravity.cpp
+++ b/src/fix_gravity.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -167,57 +167,57 @@ void FixGravity::init()
if (mstr) {
mvar = input->variable->find(mstr);
- if (mvar < 0)
+ if (mvar < 0)
error->all(FLERR,"Variable name for fix gravity does not exist");
if (!input->variable->equalstyle(mvar))
error->all(FLERR,"Variable for fix gravity is invalid style");
}
if (vstr) {
vvar = input->variable->find(vstr);
- if (vvar < 0)
+ if (vvar < 0)
error->all(FLERR,"Variable name for fix gravity does not exist");
if (!input->variable->equalstyle(vvar))
error->all(FLERR,"Variable for fix gravity is invalid style");
}
if (pstr) {
pvar = input->variable->find(pstr);
- if (pvar < 0)
+ if (pvar < 0)
error->all(FLERR,"Variable name for fix gravity does not exist");
if (!input->variable->equalstyle(pvar))
error->all(FLERR,"Variable for fix gravity is invalid style");
}
if (tstr) {
tvar = input->variable->find(tstr);
- if (tvar < 0)
+ if (tvar < 0)
error->all(FLERR,"Variable name for fix gravity does not exist");
if (!input->variable->equalstyle(tvar))
error->all(FLERR,"Variable for fix gravity is invalid style");
}
if (xstr) {
xvar = input->variable->find(xstr);
- if (xvar < 0)
+ if (xvar < 0)
error->all(FLERR,"Variable name for fix gravity does not exist");
if (!input->variable->equalstyle(xvar))
error->all(FLERR,"Variable for fix gravity is invalid style");
}
if (ystr) {
yvar = input->variable->find(ystr);
- if (yvar < 0)
+ if (yvar < 0)
error->all(FLERR,"Variable name for fix gravity does not exist");
if (!input->variable->equalstyle(yvar))
error->all(FLERR,"Variable for fix gravity is invalid style");
}
if (zstr) {
zvar = input->variable->find(zstr);
- if (zvar < 0)
+ if (zvar < 0)
error->all(FLERR,"Variable name for fix gravity does not exist");
if (!input->variable->equalstyle(zvar))
error->all(FLERR,"Variable for fix gravity is invalid style");
}
varflag = CONSTANT;
- if (mstyle != CONSTANT || vstyle != CONSTANT || pstyle != CONSTANT ||
- tstyle != CONSTANT || xstyle != CONSTANT || ystyle != CONSTANT ||
+ if (mstyle != CONSTANT || vstyle != CONSTANT || pstyle != CONSTANT ||
+ tstyle != CONSTANT || xstyle != CONSTANT || ystyle != CONSTANT ||
zstyle != CONSTANT) varflag = EQUAL;
// set gravity components once and for all
@@ -273,20 +273,20 @@ void FixGravity::post_force(int vflag)
if (rmass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- massone = rmass[i];
- f[i][0] += massone*xacc;
- f[i][1] += massone*yacc;
- f[i][2] += massone*zacc;
- egrav -= massone * (xacc*x[i][0] + yacc*x[i][1] + zacc*x[i][2]);
+ massone = rmass[i];
+ f[i][0] += massone*xacc;
+ f[i][1] += massone*yacc;
+ f[i][2] += massone*zacc;
+ egrav -= massone * (xacc*x[i][0] + yacc*x[i][1] + zacc*x[i][2]);
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- massone = mass[type[i]];
- f[i][0] += massone*xacc;
- f[i][1] += massone*yacc;
- f[i][2] += massone*zacc;
- egrav -= massone * (xacc*x[i][0] + yacc*x[i][1] + zacc*x[i][2]);
+ massone = mass[type[i]];
+ f[i][0] += massone*xacc;
+ f[i][1] += massone*yacc;
+ f[i][2] += massone*zacc;
+ egrav -= massone * (xacc*x[i][0] + yacc*x[i][1] + zacc*x[i][2]);
}
}
}
diff --git a/src/fix_gravity.h b/src/fix_gravity.h
index 410f0440934f97e01765ff95b744909a7d5bc11c..fedab3b14b7b47e5a3cb9e0ba517657108d8abf4 100644
--- a/src/fix_gravity.h
+++ b/src/fix_gravity.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_heat.cpp b/src/fix_heat.cpp
index 275b306eb0bbccca996f39fdb7422ae423d1db91..52ec746b200192e816b73f3ffca0c7e2c2f11037 100644
--- a/src/fix_heat.cpp
+++ b/src/fix_heat.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -55,8 +55,8 @@ FixHeat::FixHeat(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
if (strcmp(arg[iarg],"region") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix heat command");
iregion = domain->find_region(arg[iarg+1]);
- if (iregion == -1)
- error->all(FLERR,"Region ID for fix heat does not exist");
+ if (iregion == -1)
+ error->all(FLERR,"Region ID for fix heat does not exist");
int n = strlen(arg[iarg+1]) + 1;
idregion = new char[n];
strcpy(idregion,arg[iarg+1]);
@@ -91,13 +91,13 @@ void FixHeat::init()
if (iregion >= 0) {
iregion = domain->find_region(idregion);
- if (iregion == -1)
+ if (iregion == -1)
error->all(FLERR,"Region ID for fix heat does not exist");
}
// cannot have 0 atoms in group
- if (group->count(igroup) == 0)
+ if (group->count(igroup) == 0)
error->all(FLERR,"Fix heat group has no atoms");
masstotal = group->mass(igroup);
}
@@ -105,12 +105,12 @@ void FixHeat::init()
/* ---------------------------------------------------------------------- */
void FixHeat::end_of_step()
-{
+{
double heat,ke;
double vsub[3],vcm[3];
Region *region = NULL;
if (iregion >= 0) region = domain->regions[iregion];
-
+
if (iregion < 0) {
heat = heat_input*nevery*update->dt*force->ftm2v;
ke = group->ke(igroup)*force->ftm2v;
@@ -140,16 +140,16 @@ void FixHeat::end_of_step()
if (iregion < 0) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- v[i][0] = scale*v[i][0] - vsub[0];
- v[i][1] = scale*v[i][1] - vsub[1];
- v[i][2] = scale*v[i][2] - vsub[2];
+ v[i][0] = scale*v[i][0] - vsub[0];
+ v[i][1] = scale*v[i][1] - vsub[1];
+ v[i][2] = scale*v[i][2] - vsub[2];
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
- v[i][0] = scale*v[i][0] - vsub[0];
- v[i][1] = scale*v[i][1] - vsub[1];
- v[i][2] = scale*v[i][2] - vsub[2];
+ v[i][0] = scale*v[i][0] - vsub[0];
+ v[i][1] = scale*v[i][1] - vsub[1];
+ v[i][2] = scale*v[i][2] - vsub[2];
}
}
}
diff --git a/src/fix_heat.h b/src/fix_heat.h
index 045c486490449f45978d34d149e9bc6d9f7a3de4..83551e6637c97f49b8f76a1fb0e6e0aec65df259 100644
--- a/src/fix_heat.h
+++ b/src/fix_heat.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_indent.cpp b/src/fix_indent.cpp
index a0fdceed38fe0d1b6199d902aa7efe8b3322917c..6f4700c2adf362015d7bf84eb968a4476833c66d 100644
--- a/src/fix_indent.cpp
+++ b/src/fix_indent.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -119,35 +119,35 @@ void FixIndent::init()
{
if (xstr) {
xvar = input->variable->find(xstr);
- if (xvar < 0)
+ if (xvar < 0)
error->all(FLERR,"Variable name for fix indent does not exist");
if (!input->variable->equalstyle(xvar))
error->all(FLERR,"Variable for fix indent is invalid style");
}
if (ystr) {
yvar = input->variable->find(ystr);
- if (yvar < 0)
+ if (yvar < 0)
error->all(FLERR,"Variable name for fix indent does not exist");
if (!input->variable->equalstyle(yvar))
error->all(FLERR,"Variable for fix indent is not equal style");
}
if (zstr) {
zvar = input->variable->find(zstr);
- if (zvar < 0)
+ if (zvar < 0)
error->all(FLERR,"Variable name for fix indent does not exist");
if (!input->variable->equalstyle(zvar))
error->all(FLERR,"Variable for fix indent is not equal style");
}
if (rstr) {
rvar = input->variable->find(rstr);
- if (rvar < 0)
+ if (rvar < 0)
error->all(FLERR,"Variable name for fix indent does not exist");
if (!input->variable->equalstyle(rvar))
error->all(FLERR,"Variable for fix indent is not equal style");
}
if (pstr) {
pvar = input->variable->find(pstr);
- if (pvar < 0)
+ if (pvar < 0)
error->all(FLERR,"Variable name for fix indent does not exist");
if (!input->variable->equalstyle(pvar))
error->all(FLERR,"Variable for fix indent is not equal style");
@@ -183,7 +183,7 @@ void FixIndent::post_force(int vflag)
{
// indenter values, 0 = energy, 1-3 = force components
// wrap variable evaluations with clear/add
-
+
if (varflag) modify->clearstep_compute();
indenter_flag = 0;
@@ -218,29 +218,29 @@ void FixIndent::post_force(int vflag)
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- delx = x[i][0] - ctr[0];
- dely = x[i][1] - ctr[1];
- delz = x[i][2] - ctr[2];
- domain->minimum_image(delx,dely,delz);
- r = sqrt(delx*delx + dely*dely + delz*delz);
- if (side == OUTSIDE) {
- dr = r - radius;
- fmag = k*dr*dr;
- } else {
- dr = radius - r;
- fmag = -k*dr*dr;
- }
- if (dr >= 0.0) continue;
- fx = delx*fmag/r;
- fy = dely*fmag/r;
- fz = delz*fmag/r;
- f[i][0] += fx;
- f[i][1] += fy;
- f[i][2] += fz;
- indenter[0] -= k3 * dr*dr*dr;
- indenter[1] -= fx;
- indenter[2] -= fy;
- indenter[3] -= fz;
+ delx = x[i][0] - ctr[0];
+ dely = x[i][1] - ctr[1];
+ delz = x[i][2] - ctr[2];
+ domain->minimum_image(delx,dely,delz);
+ r = sqrt(delx*delx + dely*dely + delz*delz);
+ if (side == OUTSIDE) {
+ dr = r - radius;
+ fmag = k*dr*dr;
+ } else {
+ dr = radius - r;
+ fmag = -k*dr*dr;
+ }
+ if (dr >= 0.0) continue;
+ fx = delx*fmag/r;
+ fy = dely*fmag/r;
+ fz = delz*fmag/r;
+ f[i][0] += fx;
+ f[i][1] += fy;
+ f[i][2] += fz;
+ indenter[0] -= k3 * dr*dr*dr;
+ indenter[1] -= fx;
+ indenter[2] -= fy;
+ indenter[3] -= fz;
}
// cylindrical indenter
@@ -250,7 +250,7 @@ void FixIndent::post_force(int vflag)
// ctr = current indenter axis
// remap into periodic box
// 3rd coord is just near box for remap(), since isn't used
-
+
double ctr[3];
if (cdim == 0) {
ctr[0] = domain->boxlo[0];
@@ -281,44 +281,44 @@ void FixIndent::post_force(int vflag)
double **f = atom->f;
int *mask = atom->mask;
int nlocal = atom->nlocal;
-
+
double delx,dely,delz,r,dr,fmag,fx,fy,fz;
-
+
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- if (cdim == 0) {
- delx = 0;
- dely = x[i][1] - ctr[1];
- delz = x[i][2] - ctr[2];
- } else if (cdim == 1) {
- delx = x[i][0] - ctr[0];
- dely = 0;
- delz = x[i][2] - ctr[2];
- } else {
- delx = x[i][0] - ctr[0];
- dely = x[i][1] - ctr[1];
- delz = 0;
- }
- domain->minimum_image(delx,dely,delz);
- r = sqrt(delx*delx + dely*dely + delz*delz);
- if (side == OUTSIDE) {
- dr = r - radius;
- fmag = k*dr*dr;
- } else {
- dr = radius - r;
- fmag = -k*dr*dr;
- }
- if (dr >= 0.0) continue;
- fx = delx*fmag/r;
- fy = dely*fmag/r;
- fz = delz*fmag/r;
- f[i][0] += fx;
- f[i][1] += fy;
- f[i][2] += fz;
- indenter[0] -= k3 * dr*dr*dr;
- indenter[1] -= fx;
- indenter[2] -= fy;
- indenter[3] -= fz;
+ if (cdim == 0) {
+ delx = 0;
+ dely = x[i][1] - ctr[1];
+ delz = x[i][2] - ctr[2];
+ } else if (cdim == 1) {
+ delx = x[i][0] - ctr[0];
+ dely = 0;
+ delz = x[i][2] - ctr[2];
+ } else {
+ delx = x[i][0] - ctr[0];
+ dely = x[i][1] - ctr[1];
+ delz = 0;
+ }
+ domain->minimum_image(delx,dely,delz);
+ r = sqrt(delx*delx + dely*dely + delz*delz);
+ if (side == OUTSIDE) {
+ dr = r - radius;
+ fmag = k*dr*dr;
+ } else {
+ dr = radius - r;
+ fmag = -k*dr*dr;
+ }
+ if (dr >= 0.0) continue;
+ fx = delx*fmag/r;
+ fy = dely*fmag/r;
+ fz = delz*fmag/r;
+ f[i][0] += fx;
+ f[i][1] += fy;
+ f[i][2] += fz;
+ indenter[0] -= k3 * dr*dr*dr;
+ indenter[1] -= fx;
+ indenter[2] -= fy;
+ indenter[3] -= fz;
}
// planar indenter
@@ -326,26 +326,26 @@ void FixIndent::post_force(int vflag)
} else {
// plane = current plane position
-
+
double plane;
if (pstr) plane = input->variable->compute_equal(pvar);
else plane = pvalue;
-
+
double **x = atom->x;
double **f = atom->f;
int *mask = atom->mask;
int nlocal = atom->nlocal;
-
+
double dr,fatom;
-
+
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- dr = planeside * (plane - x[i][cdim]);
- if (dr >= 0.0) continue;
- fatom = -planeside * k*dr*dr;
- f[i][cdim] += fatom;
- indenter[0] -= k3 * dr*dr*dr;
- indenter[cdim+1] -= fatom;
+ dr = planeside * (plane - x[i][cdim]);
+ if (dr >= 0.0) continue;
+ fatom = -planeside * k*dr*dr;
+ f[i][cdim] += fatom;
+ indenter[0] -= k3 * dr*dr*dr;
+ indenter[cdim+1] -= fatom;
}
}
@@ -397,7 +397,7 @@ double FixIndent::compute_vector(int n)
}
/* ----------------------------------------------------------------------
- parse optional parameters at end of input line
+ parse optional parameters at end of input line
------------------------------------------------------------------------- */
void FixIndent::options(int narg, char **arg)
@@ -416,24 +416,24 @@ void FixIndent::options(int narg, char **arg)
if (iarg+5 > narg) error->all(FLERR,"Illegal fix indent command");
if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) {
- int n = strlen(&arg[iarg+1][2]) + 1;
- xstr = new char[n];
- strcpy(xstr,&arg[iarg+1][2]);
+ int n = strlen(&arg[iarg+1][2]) + 1;
+ xstr = new char[n];
+ strcpy(xstr,&arg[iarg+1][2]);
} else xvalue = atof(arg[iarg+1]);
if (strstr(arg[iarg+2],"v_") == arg[iarg+2]) {
- int n = strlen(&arg[iarg+2][2]) + 1;
- ystr = new char[n];
- strcpy(ystr,&arg[iarg+2][2]);
+ int n = strlen(&arg[iarg+2][2]) + 1;
+ ystr = new char[n];
+ strcpy(ystr,&arg[iarg+2][2]);
} else yvalue = atof(arg[iarg+2]);
if (strstr(arg[iarg+3],"v_") == arg[iarg+3]) {
- int n = strlen(&arg[iarg+3][2]) + 1;
- zstr = new char[n];
- strcpy(zstr,&arg[iarg+3][2]);
+ int n = strlen(&arg[iarg+3][2]) + 1;
+ zstr = new char[n];
+ strcpy(zstr,&arg[iarg+3][2]);
} else zvalue = atof(arg[iarg+3]);
if (strstr(arg[iarg+4],"v_") == arg[iarg+4]) {
- int n = strlen(&arg[iarg+4][2]) + 1;
- rstr = new char[n];
- strcpy(rstr,&arg[iarg+4][2]);
+ int n = strlen(&arg[iarg+4][2]) + 1;
+ rstr = new char[n];
+ strcpy(rstr,&arg[iarg+4][2]);
} else rvalue = atof(arg[iarg+4]);
istyle = SPHERE;
@@ -443,47 +443,47 @@ void FixIndent::options(int narg, char **arg)
if (iarg+5 > narg) error->all(FLERR,"Illegal fix indent command");
if (strcmp(arg[iarg+1],"x") == 0) {
- cdim = 0;
- if (strstr(arg[iarg+2],"v_") == arg[iarg+2]) {
- int n = strlen(&arg[iarg+2][2]) + 1;
- ystr = new char[n];
- strcpy(ystr,&arg[iarg+2][2]);
- } else yvalue = atof(arg[iarg+2]);
- if (strstr(arg[iarg+3],"v_") == arg[iarg+3]) {
- int n = strlen(&arg[iarg+3][2]) + 1;
- zstr = new char[n];
- strcpy(zstr,&arg[iarg+3][2]);
- } else zvalue = atof(arg[iarg+3]);
+ cdim = 0;
+ if (strstr(arg[iarg+2],"v_") == arg[iarg+2]) {
+ int n = strlen(&arg[iarg+2][2]) + 1;
+ ystr = new char[n];
+ strcpy(ystr,&arg[iarg+2][2]);
+ } else yvalue = atof(arg[iarg+2]);
+ if (strstr(arg[iarg+3],"v_") == arg[iarg+3]) {
+ int n = strlen(&arg[iarg+3][2]) + 1;
+ zstr = new char[n];
+ strcpy(zstr,&arg[iarg+3][2]);
+ } else zvalue = atof(arg[iarg+3]);
} else if (strcmp(arg[iarg+1],"y") == 0) {
- cdim = 1;
- if (strstr(arg[iarg+2],"v_") == arg[iarg+2]) {
- int n = strlen(&arg[iarg+2][2]) + 1;
- xstr = new char[n];
- strcpy(xstr,&arg[iarg+2][2]);
- } else xvalue = atof(arg[iarg+2]);
- if (strstr(arg[iarg+3],"v_") == arg[iarg+3]) {
- int n = strlen(&arg[iarg+3][2]) + 1;
- zstr = new char[n];
- strcpy(zstr,&arg[iarg+3][2]);
- } else zvalue = atof(arg[iarg+3]);
+ cdim = 1;
+ if (strstr(arg[iarg+2],"v_") == arg[iarg+2]) {
+ int n = strlen(&arg[iarg+2][2]) + 1;
+ xstr = new char[n];
+ strcpy(xstr,&arg[iarg+2][2]);
+ } else xvalue = atof(arg[iarg+2]);
+ if (strstr(arg[iarg+3],"v_") == arg[iarg+3]) {
+ int n = strlen(&arg[iarg+3][2]) + 1;
+ zstr = new char[n];
+ strcpy(zstr,&arg[iarg+3][2]);
+ } else zvalue = atof(arg[iarg+3]);
} else if (strcmp(arg[iarg+1],"z") == 0) {
- cdim = 2;
- if (strstr(arg[iarg+2],"v_") == arg[iarg+2]) {
- int n = strlen(&arg[iarg+2][2]) + 1;
- xstr = new char[n];
- strcpy(xstr,&arg[iarg+2][2]);
- } else xvalue = atof(arg[iarg+2]);
- if (strstr(arg[iarg+3],"v_") == arg[iarg+3]) {
- int n = strlen(&arg[iarg+3][2]) + 1;
- ystr = new char[n];
- strcpy(ystr,&arg[iarg+3][2]);
- } else yvalue = atof(arg[iarg+3]);
+ cdim = 2;
+ if (strstr(arg[iarg+2],"v_") == arg[iarg+2]) {
+ int n = strlen(&arg[iarg+2][2]) + 1;
+ xstr = new char[n];
+ strcpy(xstr,&arg[iarg+2][2]);
+ } else xvalue = atof(arg[iarg+2]);
+ if (strstr(arg[iarg+3],"v_") == arg[iarg+3]) {
+ int n = strlen(&arg[iarg+3][2]) + 1;
+ ystr = new char[n];
+ strcpy(ystr,&arg[iarg+3][2]);
+ } else yvalue = atof(arg[iarg+3]);
} else error->all(FLERR,"Illegal fix indent command");
if (strstr(arg[iarg+4],"v_") == arg[iarg+4]) {
- int n = strlen(&arg[iarg+4][2]) + 1;
- rstr = new char[n];
- strcpy(rstr,&arg[iarg+4][2]);
+ int n = strlen(&arg[iarg+4][2]) + 1;
+ rstr = new char[n];
+ strcpy(rstr,&arg[iarg+4][2]);
} else rvalue = atof(arg[iarg+4]);
istyle = CYLINDER;
@@ -497,9 +497,9 @@ void FixIndent::options(int narg, char **arg)
else error->all(FLERR,"Illegal fix indent command");
if (strstr(arg[iarg+2],"v_") == arg[iarg+2]) {
- int n = strlen(&arg[iarg+2][2]) + 1;
- pstr = new char[n];
- strcpy(pstr,&arg[iarg+2][2]);
+ int n = strlen(&arg[iarg+2][2]) + 1;
+ pstr = new char[n];
+ strcpy(pstr,&arg[iarg+2][2]);
} else pvalue = atof(arg[iarg+2]);
if (strcmp(arg[iarg+3],"lo") == 0) planeside = -1;
diff --git a/src/fix_indent.h b/src/fix_indent.h
index af7efadd35e5ef6a4df1d01d5e2142191bc3c691..6e0bad8ec8ed8f08468a9f95340fb768e293ded6 100644
--- a/src/fix_indent.h
+++ b/src/fix_indent.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_langevin.cpp b/src/fix_langevin.cpp
index 9387a07a6db07932f193890249cf2c09800bb809..98f827dfdd0ff38bbc5309680da508a5785beefe 100644
--- a/src/fix_langevin.cpp
+++ b/src/fix_langevin.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -86,7 +86,7 @@ FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) :
gfactor1 = new double[atom->ntypes+1];
gfactor2 = new double[atom->ntypes+1];
ratio = new double[atom->ntypes+1];
-
+
// optional args
for (int i = 1; i <= atom->ntypes; i++) ratio[i] = 1.0;
@@ -113,7 +113,7 @@ FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) :
int itype = atoi(arg[iarg+1]);
double scale = atof(arg[iarg+2]);
if (itype <= 0 || itype > atom->ntypes)
- error->all(FLERR,"Illegal fix langevin command");
+ error->all(FLERR,"Illegal fix langevin command");
ratio[itype] = scale;
iarg += 3;
} else if (strcmp(arg[iarg],"tally") == 0) {
@@ -135,7 +135,7 @@ FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) :
if (aflag) {
avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
- if (!avec)
+ if (!avec)
error->all(FLERR,"Fix langevin angmom requires atom style ellipsoid");
}
@@ -192,7 +192,7 @@ void FixLangevin::init()
if (tstr) {
tvar = input->variable->find(tstr);
- if (tvar < 0)
+ if (tvar < 0)
error->all(FLERR,"Variable name for fix langevin does not exist");
if (input->variable->equalstyle(tvar)) tstyle = EQUAL;
else if (input->variable->atomstyle(tvar)) tstyle = ATOM;
@@ -208,8 +208,8 @@ void FixLangevin::init()
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
- if (radius[i] == 0.0)
- error->one(FLERR,"Fix langevin omega requires extended particles");
+ if (radius[i] == 0.0)
+ error->one(FLERR,"Fix langevin omega requires extended particles");
}
if (aflag) {
@@ -219,8 +219,8 @@ void FixLangevin::init()
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
- if (ellipsoid[i] < 0)
- error->one(FLERR,"Fix langevin angmom requires extended particles");
+ if (ellipsoid[i] < 0)
+ error->one(FLERR,"Fix langevin angmom requires extended particles");
}
// set force prefactors
@@ -228,9 +228,9 @@ void FixLangevin::init()
if (!atom->rmass) {
for (int i = 1; i <= atom->ntypes; i++) {
gfactor1[i] = -atom->mass[i] / t_period / force->ftm2v;
- gfactor2[i] = sqrt(atom->mass[i]) *
- sqrt(24.0*force->boltz/t_period/update->dt/force->mvv2e) /
- force->ftm2v;
+ gfactor2[i] = sqrt(atom->mass[i]) *
+ sqrt(24.0*force->boltz/t_period/update->dt/force->mvv2e) /
+ force->ftm2v;
gfactor1[i] *= 1.0/ratio[i];
gfactor2[i] *= 1.0/sqrt(ratio[i]);
}
@@ -299,20 +299,20 @@ void FixLangevin::post_force_no_tally()
if (tstyle == EQUAL) {
t_target = input->variable->compute_equal(tvar);
if (t_target < 0.0)
- error->one(FLERR,"Fix langevin variable returned negative temperature");
+ error->one(FLERR,"Fix langevin variable returned negative temperature");
tsqrt = sqrt(t_target);
} else {
if (nlocal > maxatom2) {
- maxatom2 = atom->nmax;
- memory->destroy(tforce);
- memory->create(tforce,maxatom2,"langevin:tforce");
+ maxatom2 = atom->nmax;
+ memory->destroy(tforce);
+ memory->create(tforce,maxatom2,"langevin:tforce");
}
input->variable->compute_atom(tvar,igroup,tforce,1,0);
for (int i = 0; i < nlocal; i++)
- if (mask[i] & groupbit)
- if (tforce[i] < 0.0)
- error->one(FLERR,
- "Fix langevin variable returned negative temperature");
+ if (mask[i] & groupbit)
+ if (tforce[i] < 0.0)
+ error->one(FLERR,
+ "Fix langevin variable returned negative temperature");
}
modify->addstep_compute(update->ntimestep + 1);
}
@@ -325,7 +325,7 @@ void FixLangevin::post_force_no_tally()
// and added force has extra term not multiplied by v = 0
// for ZEROFLAG:
// sum random force over all atoms in group
- // subtract sum/count from each atom in group
+ // subtract sum/count from each atom in group
double fran[3],fsum[3],fsumall[3];
fsum[0] = fsum[1] = fsum[2] = 0.0;
@@ -335,103 +335,103 @@ void FixLangevin::post_force_no_tally()
double dt = update->dt;
double mvv2e = force->mvv2e;
double ftm2v = force->ftm2v;
-
+
if (zeroflag) {
count = group->count(igroup);
if (count == 0)
error->all(FLERR,"Cannot zero Langevin force of 0 atoms");
}
-
+
if (rmass) {
if (which == NOBIAS) {
for (int i = 0; i < nlocal; i++) {
- if (mask[i] & groupbit) {
- if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
- gamma1 = -rmass[i] / t_period / ftm2v;
- gamma2 = sqrt(rmass[i]) * sqrt(24.0*boltz/t_period/dt/mvv2e) / ftm2v;
- gamma1 *= 1.0/ratio[type[i]];
- gamma2 *= 1.0/sqrt(ratio[type[i]]) * tsqrt;
- fran[0] = gamma2*(random->uniform()-0.5);
- fran[1] = gamma2*(random->uniform()-0.5);
- fran[2] = gamma2*(random->uniform()-0.5);
- f[i][0] += gamma1*v[i][0] + fran[0];
- f[i][1] += gamma1*v[i][1] + fran[1];
- f[i][2] += gamma1*v[i][2] + fran[2];
- fsum[0] += fran[0];
- fsum[1] += fran[1];
- fsum[2] += fran[2];
- }
+ if (mask[i] & groupbit) {
+ if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
+ gamma1 = -rmass[i] / t_period / ftm2v;
+ gamma2 = sqrt(rmass[i]) * sqrt(24.0*boltz/t_period/dt/mvv2e) / ftm2v;
+ gamma1 *= 1.0/ratio[type[i]];
+ gamma2 *= 1.0/sqrt(ratio[type[i]]) * tsqrt;
+ fran[0] = gamma2*(random->uniform()-0.5);
+ fran[1] = gamma2*(random->uniform()-0.5);
+ fran[2] = gamma2*(random->uniform()-0.5);
+ f[i][0] += gamma1*v[i][0] + fran[0];
+ f[i][1] += gamma1*v[i][1] + fran[1];
+ f[i][2] += gamma1*v[i][2] + fran[2];
+ fsum[0] += fran[0];
+ fsum[1] += fran[1];
+ fsum[2] += fran[2];
+ }
}
} else if (which == BIAS) {
temperature->compute_scalar();
for (int i = 0; i < nlocal; i++) {
- if (mask[i] & groupbit) {
- if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
- gamma1 = -rmass[i] / t_period / ftm2v;
- gamma2 = sqrt(rmass[i]) * sqrt(24.0*boltz/t_period/dt/mvv2e) / ftm2v;
- gamma1 *= 1.0/ratio[type[i]];
- gamma2 *= 1.0/sqrt(ratio[type[i]]) * tsqrt;
- temperature->remove_bias(i,v[i]);
- fran[0] = gamma2*(random->uniform()-0.5);
- fran[1] = gamma2*(random->uniform()-0.5);
- fran[2] = gamma2*(random->uniform()-0.5);
- if (v[i][0] != 0.0)
- f[i][0] += gamma1*v[i][0] + fran[0];
- if (v[i][1] != 0.0)
- f[i][1] += gamma1*v[i][1] + fran[1];
- if (v[i][2] != 0.0)
- f[i][2] += gamma1*v[i][2] + fran[2];
- fsum[0] += fran[0];
- fsum[1] += fran[1];
- fsum[2] += fran[2];
- temperature->restore_bias(i,v[i]);
- }
+ if (mask[i] & groupbit) {
+ if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
+ gamma1 = -rmass[i] / t_period / ftm2v;
+ gamma2 = sqrt(rmass[i]) * sqrt(24.0*boltz/t_period/dt/mvv2e) / ftm2v;
+ gamma1 *= 1.0/ratio[type[i]];
+ gamma2 *= 1.0/sqrt(ratio[type[i]]) * tsqrt;
+ temperature->remove_bias(i,v[i]);
+ fran[0] = gamma2*(random->uniform()-0.5);
+ fran[1] = gamma2*(random->uniform()-0.5);
+ fran[2] = gamma2*(random->uniform()-0.5);
+ if (v[i][0] != 0.0)
+ f[i][0] += gamma1*v[i][0] + fran[0];
+ if (v[i][1] != 0.0)
+ f[i][1] += gamma1*v[i][1] + fran[1];
+ if (v[i][2] != 0.0)
+ f[i][2] += gamma1*v[i][2] + fran[2];
+ fsum[0] += fran[0];
+ fsum[1] += fran[1];
+ fsum[2] += fran[2];
+ temperature->restore_bias(i,v[i]);
+ }
}
}
} else {
-
+
if (which == NOBIAS) {
for (int i = 0; i < nlocal; i++) {
- if (mask[i] & groupbit) {
- if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
- gamma1 = gfactor1[type[i]];
- gamma2 = gfactor2[type[i]] * tsqrt;
- fran[0] = gamma2*(random->uniform()-0.5);
- fran[1] = gamma2*(random->uniform()-0.5);
- fran[2] = gamma2*(random->uniform()-0.5);
- f[i][0] += gamma1*v[i][0] + fran[0];
- f[i][1] += gamma1*v[i][1] + fran[1];
- f[i][2] += gamma1*v[i][2] + fran[2];
- fsum[0] += fran[0];
- fsum[1] += fran[1];
- fsum[2] += fran[2];
- }
+ if (mask[i] & groupbit) {
+ if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
+ gamma1 = gfactor1[type[i]];
+ gamma2 = gfactor2[type[i]] * tsqrt;
+ fran[0] = gamma2*(random->uniform()-0.5);
+ fran[1] = gamma2*(random->uniform()-0.5);
+ fran[2] = gamma2*(random->uniform()-0.5);
+ f[i][0] += gamma1*v[i][0] + fran[0];
+ f[i][1] += gamma1*v[i][1] + fran[1];
+ f[i][2] += gamma1*v[i][2] + fran[2];
+ fsum[0] += fran[0];
+ fsum[1] += fran[1];
+ fsum[2] += fran[2];
+ }
}
} else if (which == BIAS) {
temperature->compute_scalar();
for (int i = 0; i < nlocal; i++) {
- if (mask[i] & groupbit) {
- if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
- gamma1 = gfactor1[type[i]];
- gamma2 = gfactor2[type[i]] * tsqrt;
- temperature->remove_bias(i,v[i]);
- fran[0] = gamma2*(random->uniform()-0.5);
- fran[1] = gamma2*(random->uniform()-0.5);
- fran[2] = gamma2*(random->uniform()-0.5);
- if (v[i][0] != 0.0)
- f[i][0] += gamma1*v[i][0] + fran[0];
- if (v[i][1] != 0.0)
- f[i][1] += gamma1*v[i][1] + fran[1];
- if (v[i][2] != 0.0)
- f[i][2] += gamma1*v[i][2] + fran[2];
- fsum[0] += fran[0];
- fsum[1] += fran[1];
- fsum[2] += fran[2];
- temperature->restore_bias(i,v[i]);
- }
+ if (mask[i] & groupbit) {
+ if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
+ gamma1 = gfactor1[type[i]];
+ gamma2 = gfactor2[type[i]] * tsqrt;
+ temperature->remove_bias(i,v[i]);
+ fran[0] = gamma2*(random->uniform()-0.5);
+ fran[1] = gamma2*(random->uniform()-0.5);
+ fran[2] = gamma2*(random->uniform()-0.5);
+ if (v[i][0] != 0.0)
+ f[i][0] += gamma1*v[i][0] + fran[0];
+ if (v[i][1] != 0.0)
+ f[i][1] += gamma1*v[i][1] + fran[1];
+ if (v[i][2] != 0.0)
+ f[i][2] += gamma1*v[i][2] + fran[2];
+ fsum[0] += fran[0];
+ fsum[1] += fran[1];
+ fsum[2] += fran[2];
+ temperature->restore_bias(i,v[i]);
+ }
}
}
}
@@ -445,9 +445,9 @@ void FixLangevin::post_force_no_tally()
fsumall[2] /= count;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
- f[i][0] -= fsumall[0];
- f[i][1] -= fsumall[1];
- f[i][2] -= fsumall[2];
+ f[i][0] -= fsumall[0];
+ f[i][1] -= fsumall[1];
+ f[i][2] -= fsumall[2];
}
}
}
@@ -494,20 +494,20 @@ void FixLangevin::post_force_tally()
if (tstyle == EQUAL) {
t_target = input->variable->compute_equal(tvar);
if (t_target < 0.0)
- error->one(FLERR,"Fix langevin variable returned negative temperature");
+ error->one(FLERR,"Fix langevin variable returned negative temperature");
tsqrt = sqrt(t_target);
} else {
if (nlocal > maxatom2) {
- maxatom2 = atom->nmax;
- memory->destroy(tforce);
- memory->create(tforce,maxatom2,"langevin:tforce");
+ maxatom2 = atom->nmax;
+ memory->destroy(tforce);
+ memory->create(tforce,maxatom2,"langevin:tforce");
}
input->variable->compute_atom(tvar,igroup,tforce,1,0);
for (int i = 0; i < nlocal; i++)
- if (mask[i] & groupbit)
- if (tforce[i] < 0.0)
- error->one(FLERR,
- "Fix langevin variable returned negative temperature");
+ if (mask[i] & groupbit)
+ if (tforce[i] < 0.0)
+ error->one(FLERR,
+ "Fix langevin variable returned negative temperature");
}
modify->addstep_compute(update->ntimestep + 1);
}
@@ -527,80 +527,80 @@ void FixLangevin::post_force_tally()
if (rmass) {
if (which == NOBIAS) {
for (int i = 0; i < nlocal; i++) {
- if (mask[i] & groupbit) {
- if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
- gamma1 = -rmass[i] / t_period / ftm2v;
- gamma2 = sqrt(rmass[i]) * sqrt(24.0*boltz/t_period/dt/mvv2e) / ftm2v;
- gamma1 *= 1.0/ratio[type[i]];
- gamma2 *= 1.0/sqrt(ratio[type[i]]) * tsqrt;
- flangevin[i][0] = gamma1*v[i][0] + gamma2*(random->uniform()-0.5);
- flangevin[i][1] = gamma1*v[i][1] + gamma2*(random->uniform()-0.5);
- flangevin[i][2] = gamma1*v[i][2] + gamma2*(random->uniform()-0.5);
- f[i][0] += flangevin[i][0];
- f[i][1] += flangevin[i][1];
- f[i][2] += flangevin[i][2];
- }
+ if (mask[i] & groupbit) {
+ if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
+ gamma1 = -rmass[i] / t_period / ftm2v;
+ gamma2 = sqrt(rmass[i]) * sqrt(24.0*boltz/t_period/dt/mvv2e) / ftm2v;
+ gamma1 *= 1.0/ratio[type[i]];
+ gamma2 *= 1.0/sqrt(ratio[type[i]]) * tsqrt;
+ flangevin[i][0] = gamma1*v[i][0] + gamma2*(random->uniform()-0.5);
+ flangevin[i][1] = gamma1*v[i][1] + gamma2*(random->uniform()-0.5);
+ flangevin[i][2] = gamma1*v[i][2] + gamma2*(random->uniform()-0.5);
+ f[i][0] += flangevin[i][0];
+ f[i][1] += flangevin[i][1];
+ f[i][2] += flangevin[i][2];
+ }
}
} else if (which == BIAS) {
temperature->compute_scalar();
for (int i = 0; i < nlocal; i++) {
- if (mask[i] & groupbit) {
- if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
- gamma1 = -rmass[i] / t_period / ftm2v;
- gamma2 = sqrt(rmass[i]) * sqrt(24.0*boltz/t_period/dt/mvv2e) / ftm2v;
- gamma1 *= 1.0/ratio[type[i]];
- gamma2 *= 1.0/sqrt(ratio[type[i]]) * tsqrt;
- temperature->remove_bias(i,v[i]);
- flangevin[i][0] = gamma1*v[i][0] + gamma2*(random->uniform()-0.5);
- flangevin[i][1] = gamma1*v[i][1] + gamma2*(random->uniform()-0.5);
- flangevin[i][2] = gamma1*v[i][2] + gamma2*(random->uniform()-0.5);
- if (v[i][0] != 0.0) f[i][0] += flangevin[i][0];
- else flangevin[i][0] = 0;
- if (v[i][1] != 0.0) f[i][1] += flangevin[i][1];
- else flangevin[i][1] = 0;
- if (v[i][2] != 0.0) f[i][2] += flangevin[i][2];
- else flangevin[i][2] = 0;
- temperature->restore_bias(i,v[i]);
- }
+ if (mask[i] & groupbit) {
+ if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
+ gamma1 = -rmass[i] / t_period / ftm2v;
+ gamma2 = sqrt(rmass[i]) * sqrt(24.0*boltz/t_period/dt/mvv2e) / ftm2v;
+ gamma1 *= 1.0/ratio[type[i]];
+ gamma2 *= 1.0/sqrt(ratio[type[i]]) * tsqrt;
+ temperature->remove_bias(i,v[i]);
+ flangevin[i][0] = gamma1*v[i][0] + gamma2*(random->uniform()-0.5);
+ flangevin[i][1] = gamma1*v[i][1] + gamma2*(random->uniform()-0.5);
+ flangevin[i][2] = gamma1*v[i][2] + gamma2*(random->uniform()-0.5);
+ if (v[i][0] != 0.0) f[i][0] += flangevin[i][0];
+ else flangevin[i][0] = 0;
+ if (v[i][1] != 0.0) f[i][1] += flangevin[i][1];
+ else flangevin[i][1] = 0;
+ if (v[i][2] != 0.0) f[i][2] += flangevin[i][2];
+ else flangevin[i][2] = 0;
+ temperature->restore_bias(i,v[i]);
+ }
}
}
} else {
if (which == NOBIAS) {
for (int i = 0; i < nlocal; i++) {
- if (mask[i] & groupbit) {
- if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
- gamma1 = gfactor1[type[i]];
- gamma2 = gfactor2[type[i]] * tsqrt;
- flangevin[i][0] = gamma1*v[i][0] + gamma2*(random->uniform()-0.5);
- flangevin[i][1] = gamma1*v[i][1] + gamma2*(random->uniform()-0.5);
- flangevin[i][2] = gamma1*v[i][2] + gamma2*(random->uniform()-0.5);
- f[i][0] += flangevin[i][0];
- f[i][1] += flangevin[i][1];
- f[i][2] += flangevin[i][2];
- }
+ if (mask[i] & groupbit) {
+ if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
+ gamma1 = gfactor1[type[i]];
+ gamma2 = gfactor2[type[i]] * tsqrt;
+ flangevin[i][0] = gamma1*v[i][0] + gamma2*(random->uniform()-0.5);
+ flangevin[i][1] = gamma1*v[i][1] + gamma2*(random->uniform()-0.5);
+ flangevin[i][2] = gamma1*v[i][2] + gamma2*(random->uniform()-0.5);
+ f[i][0] += flangevin[i][0];
+ f[i][1] += flangevin[i][1];
+ f[i][2] += flangevin[i][2];
+ }
}
} else if (which == BIAS) {
temperature->compute_scalar();
for (int i = 0; i < nlocal; i++) {
- if (mask[i] & groupbit) {
- if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
- gamma1 = gfactor1[type[i]];
- gamma2 = gfactor2[type[i]] * tsqrt;
- temperature->remove_bias(i,v[i]);
- flangevin[i][0] = gamma1*v[i][0] + gamma2*(random->uniform()-0.5);
- flangevin[i][1] = gamma1*v[i][1] + gamma2*(random->uniform()-0.5);
- flangevin[i][2] = gamma1*v[i][2] + gamma2*(random->uniform()-0.5);
- if (v[i][0] != 0.0) f[i][0] += flangevin[i][0];
- else flangevin[i][0] = 0.0;
- if (v[i][1] != 0.0) f[i][1] += flangevin[i][1];
- else flangevin[i][1] = 0.0;
- if (v[i][2] != 0.0) f[i][2] += flangevin[i][2];
- else flangevin[i][2] = 0.0;
- temperature->restore_bias(i,v[i]);
- }
+ if (mask[i] & groupbit) {
+ if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
+ gamma1 = gfactor1[type[i]];
+ gamma2 = gfactor2[type[i]] * tsqrt;
+ temperature->remove_bias(i,v[i]);
+ flangevin[i][0] = gamma1*v[i][0] + gamma2*(random->uniform()-0.5);
+ flangevin[i][1] = gamma1*v[i][1] + gamma2*(random->uniform()-0.5);
+ flangevin[i][2] = gamma1*v[i][2] + gamma2*(random->uniform()-0.5);
+ if (v[i][0] != 0.0) f[i][0] += flangevin[i][0];
+ else flangevin[i][0] = 0.0;
+ if (v[i][1] != 0.0) f[i][1] += flangevin[i][1];
+ else flangevin[i][1] = 0.0;
+ if (v[i][2] != 0.0) f[i][2] += flangevin[i][2];
+ else flangevin[i][2] = 0.0;
+ temperature->restore_bias(i,v[i]);
+ }
}
}
}
@@ -686,7 +686,7 @@ void FixLangevin::angmom_thermostat()
inertia[2] = EINERTIA*rmass[i] * (shape[0]*shape[0]+shape[1]*shape[1]);
quat = bonus[ellipsoid[i]].quat;
MathExtra::mq_to_omega(angmom[i],quat,inertia,omega);
-
+
if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
gamma1 = -1.0 / t_period / ftm2v;
gamma2 = sqrt(24.0*boltz/t_period/dt/mvv2e) / ftm2v;
@@ -712,14 +712,14 @@ void FixLangevin::end_of_step()
double **v = atom->v;
int *mask = atom->mask;
- int nlocal = atom->nlocal;
+ int nlocal = atom->nlocal;
energy_onestep = 0.0;
-
+
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
- energy_onestep += flangevin[i][0]*v[i][0] + flangevin[i][1]*v[i][1] +
- flangevin[i][2]*v[i][2];
+ energy_onestep += flangevin[i][0]*v[i][0] + flangevin[i][1]*v[i][1] +
+ flangevin[i][2]*v[i][2];
energy += energy_onestep*update->dt;
}
@@ -737,9 +737,9 @@ void FixLangevin::reset_dt()
{
if (atom->mass) {
for (int i = 1; i <= atom->ntypes; i++) {
- gfactor2[i] = sqrt(atom->mass[i]) *
- sqrt(24.0*force->boltz/t_period/update->dt/force->mvv2e) /
- force->ftm2v;
+ gfactor2[i] = sqrt(atom->mass[i]) *
+ sqrt(24.0*force->boltz/t_period/update->dt/force->mvv2e) /
+ force->ftm2v;
gfactor2[i] *= 1.0/sqrt(ratio[i]);
}
}
@@ -757,13 +757,13 @@ int FixLangevin::modify_param(int narg, char **arg)
strcpy(id_temp,arg[1]);
int icompute = modify->find_compute(id_temp);
- if (icompute < 0)
+ if (icompute < 0)
error->all(FLERR,"Could not find fix_modify temperature ID");
temperature = modify->compute[icompute];
if (temperature->tempflag == 0)
error->all(FLERR,
- "Fix_modify temperature ID does not compute temperature");
+ "Fix_modify temperature ID does not compute temperature");
if (temperature->igroup != igroup && comm->me == 0)
error->warning(FLERR,"Group for fix_modify temp != fix group");
return 2;
@@ -781,21 +781,21 @@ double FixLangevin::compute_scalar()
double **v = atom->v;
int *mask = atom->mask;
- int nlocal = atom->nlocal;
+ int nlocal = atom->nlocal;
if (update->ntimestep == update->beginstep) {
energy_onestep = 0.0;
- for (int i = 0; i < nlocal; i++)
- if (mask[i] & groupbit)
- energy_onestep += flangevin[i][0]*v[i][0] + flangevin[i][1]*v[i][1] +
- flangevin[i][2]*v[i][2];
+ for (int i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit)
+ energy_onestep += flangevin[i][0]*v[i][0] + flangevin[i][1]*v[i][1] +
+ flangevin[i][2]*v[i][2];
energy = 0.5*energy_onestep*update->dt;
}
double energy_me = energy - 0.5*energy_onestep*update->dt;
- double energy_all;
- MPI_Allreduce(&energy_me,&energy_all,1,MPI_DOUBLE,MPI_SUM,world);
+ double energy_all;
+ MPI_Allreduce(&energy_me,&energy_all,1,MPI_DOUBLE,MPI_SUM,world);
return -energy_all;
}
@@ -808,7 +808,7 @@ void *FixLangevin::extract(const char *str, int &dim)
dim=0;
if (strcmp(str,"t_target") == 0) {
return &t_target;
- }
+ }
return NULL;
}
diff --git a/src/fix_langevin.h b/src/fix_langevin.h
index 790f81dc08e204b5a585bb4b3df94417f2507738..69c144ce7bd34a46df8351542d86a2ddff015bf7 100644
--- a/src/fix_langevin.h
+++ b/src/fix_langevin.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_lineforce.cpp b/src/fix_lineforce.cpp
index 5da729f84fb29522cd57cdab179827ccc3e991b9..a778ac13c51d017e887af20ad70fade17347787f 100644
--- a/src/fix_lineforce.cpp
+++ b/src/fix_lineforce.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_lineforce.h b/src/fix_lineforce.h
index ddcff234629df82abde7d87ab775789f70ef75eb..2e367333f17cd11a8da633a6088bac200bc64e25 100644
--- a/src/fix_lineforce.h
+++ b/src/fix_lineforce.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_minimize.cpp b/src/fix_minimize.cpp
index c0c61098d5420b0ed2b98156ee010b7f991b1bae..26e2d7efc0872a10f2895f81a77a192c386cd07f 100644
--- a/src/fix_minimize.cpp
+++ b/src/fix_minimize.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -110,7 +110,7 @@ void FixMinimize::reset_coords()
{
box_swap();
domain->set_global_box();
-
+
double **x = atom->x;
double *x0 = vectors[0];
int nlocal = atom->nlocal;
@@ -127,7 +127,7 @@ void FixMinimize::reset_coords()
if (dz != dz0) x0[n+2] = x[i][2] - dz;
n += 3;
}
-
+
box_swap();
domain->set_global_box();
}
@@ -162,7 +162,7 @@ void FixMinimize::box_swap()
}
/* ----------------------------------------------------------------------
- memory usage of local atom-based arrays
+ memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double FixMinimize::memory_usage()
@@ -174,7 +174,7 @@ double FixMinimize::memory_usage()
}
/* ----------------------------------------------------------------------
- allocate local atom-based arrays
+ allocate local atom-based arrays
------------------------------------------------------------------------- */
void FixMinimize::grow_arrays(int nmax)
@@ -184,7 +184,7 @@ void FixMinimize::grow_arrays(int nmax)
}
/* ----------------------------------------------------------------------
- copy values within local atom-based arrays
+ copy values within local atom-based arrays
------------------------------------------------------------------------- */
void FixMinimize::copy_arrays(int i, int j)
@@ -200,7 +200,7 @@ void FixMinimize::copy_arrays(int i, int j)
}
/* ----------------------------------------------------------------------
- pack values in local atom-based arrays for exchange with another proc
+ pack values in local atom-based arrays for exchange with another proc
------------------------------------------------------------------------- */
int FixMinimize::pack_exchange(int i, double *buf)
@@ -217,7 +217,7 @@ int FixMinimize::pack_exchange(int i, double *buf)
}
/* ----------------------------------------------------------------------
- unpack values in local atom-based arrays from exchange with another proc
+ unpack values in local atom-based arrays from exchange with another proc
------------------------------------------------------------------------- */
int FixMinimize::unpack_exchange(int nlocal, double *buf)
diff --git a/src/fix_minimize.h b/src/fix_minimize.h
index 8cb96ea25baa2d6cf11f53bfd0e2c845bc0c5b9f..e4b1634b8446380b26d47f53cc2f972843c9525b 100644
--- a/src/fix_minimize.h
+++ b/src/fix_minimize.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_momentum.cpp b/src/fix_momentum.cpp
index a2067a516de67228260e2f36072a2c3ba4334bd3..590a55dbc078eca2a5e298aca1a7ed16abe3bf32 100644
--- a/src/fix_momentum.cpp
+++ b/src/fix_momentum.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -56,8 +56,8 @@ FixMomentum::FixMomentum(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,"Illegal fix momentum command");
if (linear)
- if (xflag < 0 || xflag > 1 || yflag < 0 || yflag > 1 ||
- zflag < 0 || zflag > 1) error->all(FLERR,"Illegal fix momentum command");
+ if (xflag < 0 || xflag > 1 || yflag < 0 || yflag > 1 ||
+ zflag < 0 || zflag > 1) error->all(FLERR,"Illegal fix momentum command");
// cannot have 0 atoms in group
@@ -91,16 +91,16 @@ void FixMomentum::end_of_step()
// adjust velocities by vcm to zero linear momentum
// only adjust a component if flag is set
-
+
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
-
+
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- if (xflag) v[i][0] -= vcm[0];
- if (yflag) v[i][1] -= vcm[1];
- if (zflag) v[i][2] -= vcm[2];
+ if (xflag) v[i][0] -= vcm[0];
+ if (yflag) v[i][1] -= vcm[1];
+ if (zflag) v[i][2] -= vcm[2];
}
}
@@ -110,7 +110,7 @@ void FixMomentum::end_of_step()
group->angmom(igroup,xcm,angmom);
group->inertia(igroup,xcm,inertia);
group->omega(angmom,inertia,omega);
-
+
// adjust velocities to zero omega
// vnew_i = v_i - w x r_i
// must use unwrapped coords to compute r_i correctly
@@ -129,15 +129,15 @@ void FixMomentum::end_of_step()
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- xbox = (image[i] & 1023) - 512;
- ybox = (image[i] >> 10 & 1023) - 512;
- zbox = (image[i] >> 20) - 512;
- dx = (x[i][0] + xbox*xprd) - xcm[0];
- dy = (x[i][1] + ybox*yprd) - xcm[1];
- dz = (x[i][2] + zbox*zprd) - xcm[2];
- v[i][0] -= omega[1]*dz - omega[2]*dy;
- v[i][1] -= omega[2]*dx - omega[0]*dz;
- v[i][2] -= omega[0]*dy - omega[1]*dx;
+ xbox = (image[i] & 1023) - 512;
+ ybox = (image[i] >> 10 & 1023) - 512;
+ zbox = (image[i] >> 20) - 512;
+ dx = (x[i][0] + xbox*xprd) - xcm[0];
+ dy = (x[i][1] + ybox*yprd) - xcm[1];
+ dz = (x[i][2] + zbox*zprd) - xcm[2];
+ v[i][0] -= omega[1]*dz - omega[2]*dy;
+ v[i][1] -= omega[2]*dx - omega[0]*dz;
+ v[i][2] -= omega[0]*dy - omega[1]*dx;
}
}
}
diff --git a/src/fix_momentum.h b/src/fix_momentum.h
index a15d98b6017115a5850360f59a5a19709e56cbd9..c647b184224f0b337bdfcf4ec6019501dc2098c1 100644
--- a/src/fix_momentum.h
+++ b/src/fix_momentum.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_move.cpp b/src/fix_move.cpp
index ff938a5e2846b2ad9fc8fca792d5c13b089e8724..0740fdf4feffbdf1edf23ef59e2bc2f443774d2f 100644
--- a/src/fix_move.cpp
+++ b/src/fix_move.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -151,7 +151,7 @@ FixMove::FixMove(LAMMPS *lmp, int narg, char **arg) :
vzvarstr = new char[n];
strcpy(vzvarstr,&arg[9][2]);
} else error->all(FLERR,"Illegal fix move command");
-
+
} else error->all(FLERR,"Illegal fix move command");
// optional args
@@ -177,10 +177,10 @@ FixMove::FixMove(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,"Fix move cannot set wiggle z motion for 2d problem");
if (mstyle == ROTATE && (axis[0] != 0.0 || axis[1] != 0.0))
error->all(FLERR,
- "Fix move cannot rotate aroung non z-axis for 2d problem");
+ "Fix move cannot rotate aroung non z-axis for 2d problem");
if (mstyle == VARIABLE && (zvarstr || vzvarstr))
error->all(FLERR,
- "Fix move cannot define z or vz variable for 2d problem");
+ "Fix move cannot define z or vz variable for 2d problem");
}
if (atom->angmom_flag && comm->me == 0)
@@ -190,7 +190,7 @@ FixMove::FixMove(LAMMPS *lmp, int narg, char **arg) :
// setup scaling and apply scaling factors to velocity & amplitude
- if ((mstyle == LINEAR || mstyle == WIGGLE || mstyle == ROTATE) &&
+ if ((mstyle == LINEAR || mstyle == WIGGLE || mstyle == ROTATE) &&
scaleflag) {
if (domain->lattice == NULL)
error->all(FLERR,"Use of fix move with undefined lattice");
@@ -226,7 +226,7 @@ FixMove::FixMove(LAMMPS *lmp, int narg, char **arg) :
if (mstyle == ROTATE) {
double len = sqrt(axis[0]*axis[0] + axis[1]*axis[1] + axis[2]*axis[2]);
- if (len == 0.0)
+ if (len == 0.0)
error->all(FLERR,"Fix move cannot have 0 length rotation vector");
runit[0] = axis[0]/len;
runit[1] = axis[1]/len;
@@ -236,7 +236,7 @@ FixMove::FixMove(LAMMPS *lmp, int narg, char **arg) :
// set omega_flag if particles store omega
omega_flag = atom->omega_flag;
-
+
// perform initial allocation of atom-based array
// register with Atom class
@@ -268,7 +268,7 @@ FixMove::FixMove(LAMMPS *lmp, int narg, char **arg) :
FixMove::~FixMove()
{
// unregister callbacks to this fix from Atom class
-
+
atom->delete_callback(id,0);
atom->delete_callback(id,1);
@@ -312,7 +312,7 @@ void FixMove::init()
if (xvarstr) {
xvar = input->variable->find(xvarstr);
if (xvar < 0) error->all(FLERR,
- "Variable name for fix move does not exist");
+ "Variable name for fix move does not exist");
if (input->variable->equalstyle(xvar)) xvarstyle = EQUAL;
else if (input->variable->atomstyle(xvar)) xvarstyle = ATOM;
else error->all(FLERR,"Variable for fix move is invalid style");
@@ -320,7 +320,7 @@ void FixMove::init()
if (yvarstr) {
yvar = input->variable->find(yvarstr);
if (yvar < 0) error->all(FLERR,
- "Variable name for fix move does not exist");
+ "Variable name for fix move does not exist");
if (input->variable->equalstyle(yvar)) yvarstyle = EQUAL;
else if (input->variable->atomstyle(yvar)) yvarstyle = ATOM;
else error->all(FLERR,"Variable for fix move is invalid style");
@@ -328,7 +328,7 @@ void FixMove::init()
if (zvarstr) {
zvar = input->variable->find(zvarstr);
if (zvar < 0) error->all(FLERR,
- "Variable name for fix move does not exist");
+ "Variable name for fix move does not exist");
if (input->variable->equalstyle(zvar)) zvarstyle = EQUAL;
else if (input->variable->atomstyle(zvar)) zvarstyle = ATOM;
else error->all(FLERR,"Variable for fix move is invalid style");
@@ -336,7 +336,7 @@ void FixMove::init()
if (vxvarstr) {
vxvar = input->variable->find(vxvarstr);
if (vxvar < 0) error->all(FLERR,
- "Variable name for fix move does not exist");
+ "Variable name for fix move does not exist");
if (input->variable->equalstyle(vxvar)) vxvarstyle = EQUAL;
else if (input->variable->atomstyle(vxvar)) vxvarstyle = ATOM;
else error->all(FLERR,"Variable for fix move is invalid style");
@@ -344,7 +344,7 @@ void FixMove::init()
if (vyvarstr) {
vyvar = input->variable->find(vyvarstr);
if (vyvar < 0) error->all(FLERR,
- "Variable name for fix move does not exist");
+ "Variable name for fix move does not exist");
if (input->variable->equalstyle(vyvar)) vyvarstyle = EQUAL;
else if (input->variable->atomstyle(vyvar)) vyvarstyle = ATOM;
else error->all(FLERR,"Variable for fix move is invalid style");
@@ -352,7 +352,7 @@ void FixMove::init()
if (vzvarstr) {
vzvar = input->variable->find(vzvarstr);
if (vzvar < 0) error->all(FLERR,
- "Variable name for fix move does not exist");
+ "Variable name for fix move does not exist");
if (input->variable->equalstyle(vzvar)) vzvarstyle = EQUAL;
else if (input->variable->atomstyle(vzvar)) vzvarstyle = ATOM;
else error->all(FLERR,"Variable for fix move is invalid style");
@@ -398,50 +398,50 @@ void FixMove::initial_integrate(int vflag)
if (mstyle == LINEAR) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
- xold[0] = x[i][0];
- xold[1] = x[i][1];
- xold[2] = x[i][2];
-
- if (vxflag) {
- v[i][0] = vx;
- x[i][0] = xoriginal[i][0] + vx*delta;
- } else if (rmass) {
- dtfm = dtf / rmass[i];
- v[i][0] += dtfm * f[i][0];
- x[i][0] += dtv * v[i][0];
- } else {
- dtfm = dtf / mass[type[i]];
- v[i][0] += dtfm * f[i][0];
- x[i][0] += dtv * v[i][0];
- }
-
- if (vyflag) {
- v[i][1] = vy;
- x[i][1] = xoriginal[i][1] + vy*delta;
- } else if (rmass) {
- dtfm = dtf / rmass[i];
- v[i][1] += dtfm * f[i][1];
- x[i][1] += dtv * v[i][1];
- } else {
- dtfm = dtf / mass[type[i]];
- v[i][1] += dtfm * f[i][1];
- x[i][1] += dtv * v[i][1];
- }
-
- if (vzflag) {
- v[i][2] = vz;
- x[i][2] = xoriginal[i][2] + vz*delta;
- } else if (rmass) {
- dtfm = dtf / rmass[i];
- v[i][2] += dtfm * f[i][2];
- x[i][2] += dtv * v[i][2];
- } else {
- dtfm = dtf / mass[type[i]];
- v[i][2] += dtfm * f[i][2];
- x[i][2] += dtv * v[i][2];
- }
-
- domain->remap_near(x[i],xold);
+ xold[0] = x[i][0];
+ xold[1] = x[i][1];
+ xold[2] = x[i][2];
+
+ if (vxflag) {
+ v[i][0] = vx;
+ x[i][0] = xoriginal[i][0] + vx*delta;
+ } else if (rmass) {
+ dtfm = dtf / rmass[i];
+ v[i][0] += dtfm * f[i][0];
+ x[i][0] += dtv * v[i][0];
+ } else {
+ dtfm = dtf / mass[type[i]];
+ v[i][0] += dtfm * f[i][0];
+ x[i][0] += dtv * v[i][0];
+ }
+
+ if (vyflag) {
+ v[i][1] = vy;
+ x[i][1] = xoriginal[i][1] + vy*delta;
+ } else if (rmass) {
+ dtfm = dtf / rmass[i];
+ v[i][1] += dtfm * f[i][1];
+ x[i][1] += dtv * v[i][1];
+ } else {
+ dtfm = dtf / mass[type[i]];
+ v[i][1] += dtfm * f[i][1];
+ x[i][1] += dtv * v[i][1];
+ }
+
+ if (vzflag) {
+ v[i][2] = vz;
+ x[i][2] = xoriginal[i][2] + vz*delta;
+ } else if (rmass) {
+ dtfm = dtf / rmass[i];
+ v[i][2] += dtfm * f[i][2];
+ x[i][2] += dtv * v[i][2];
+ } else {
+ dtfm = dtf / mass[type[i]];
+ v[i][2] += dtfm * f[i][2];
+ x[i][2] += dtv * v[i][2];
+ }
+
+ domain->remap_near(x[i],xold);
}
}
@@ -454,50 +454,50 @@ void FixMove::initial_integrate(int vflag)
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
- xold[0] = x[i][0];
- xold[1] = x[i][1];
- xold[2] = x[i][2];
-
- if (axflag) {
- v[i][0] = ax*omega_rotate*cosine;
- x[i][0] = xoriginal[i][0] + ax*sine;
- } else if (rmass) {
- dtfm = dtf / rmass[i];
- v[i][0] += dtfm * f[i][0];
- x[i][0] += dtv * v[i][0];
- } else {
- dtfm = dtf / mass[type[i]];
- v[i][0] += dtfm * f[i][0];
- x[i][0] += dtv * v[i][0];
- }
-
- if (ayflag) {
- v[i][1] = ay*omega_rotate*cosine;
- x[i][1] = xoriginal[i][1] + ay*sine;
- } else if (rmass) {
- dtfm = dtf / rmass[i];
- v[i][1] += dtfm * f[i][1];
- x[i][1] += dtv * v[i][1];
- } else {
- dtfm = dtf / mass[type[i]];
- v[i][1] += dtfm * f[i][1];
- x[i][1] += dtv * v[i][1];
- }
-
- if (azflag) {
- v[i][2] = az*omega_rotate*cosine;
- x[i][2] = xoriginal[i][2] + az*sine;
- } else if (rmass) {
- dtfm = dtf / rmass[i];
- v[i][2] += dtfm * f[i][2];
- x[i][2] += dtv * v[i][2];
- } else {
- dtfm = dtf / mass[type[i]];
- v[i][2] += dtfm * f[i][2];
- x[i][2] += dtv * v[i][2];
- }
-
- domain->remap_near(x[i],xold);
+ xold[0] = x[i][0];
+ xold[1] = x[i][1];
+ xold[2] = x[i][2];
+
+ if (axflag) {
+ v[i][0] = ax*omega_rotate*cosine;
+ x[i][0] = xoriginal[i][0] + ax*sine;
+ } else if (rmass) {
+ dtfm = dtf / rmass[i];
+ v[i][0] += dtfm * f[i][0];
+ x[i][0] += dtv * v[i][0];
+ } else {
+ dtfm = dtf / mass[type[i]];
+ v[i][0] += dtfm * f[i][0];
+ x[i][0] += dtv * v[i][0];
+ }
+
+ if (ayflag) {
+ v[i][1] = ay*omega_rotate*cosine;
+ x[i][1] = xoriginal[i][1] + ay*sine;
+ } else if (rmass) {
+ dtfm = dtf / rmass[i];
+ v[i][1] += dtfm * f[i][1];
+ x[i][1] += dtv * v[i][1];
+ } else {
+ dtfm = dtf / mass[type[i]];
+ v[i][1] += dtfm * f[i][1];
+ x[i][1] += dtv * v[i][1];
+ }
+
+ if (azflag) {
+ v[i][2] = az*omega_rotate*cosine;
+ x[i][2] = xoriginal[i][2] + az*sine;
+ } else if (rmass) {
+ dtfm = dtf / rmass[i];
+ v[i][2] += dtfm * f[i][2];
+ x[i][2] += dtv * v[i][2];
+ } else {
+ dtfm = dtf / mass[type[i]];
+ v[i][2] += dtfm * f[i][2];
+ x[i][2] += dtv * v[i][2];
+ }
+
+ domain->remap_near(x[i],xold);
}
}
@@ -522,40 +522,40 @@ void FixMove::initial_integrate(int vflag)
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
- xold[0] = x[i][0];
- xold[1] = x[i][1];
- xold[2] = x[i][2];
-
- d[0] = xoriginal[i][0] - point[0];
- d[1] = xoriginal[i][1] - point[1];
- d[2] = xoriginal[i][2] - point[2];
- ddotr = d[0]*runit[0] + d[1]*runit[1] + d[2]*runit[2];
- c[0] = ddotr*runit[0];
- c[1] = ddotr*runit[1];
- c[2] = ddotr*runit[2];
- a[0] = d[0] - c[0];
- a[1] = d[1] - c[1];
- a[2] = d[2] - c[2];
- b[0] = runit[1]*a[2] - runit[2]*a[1];
- b[1] = runit[2]*a[0] - runit[0]*a[2];
- b[2] = runit[0]*a[1] - runit[1]*a[0];
- disp[0] = a[0]*cosine + b[0]*sine;
- disp[1] = a[1]*cosine + b[1]*sine;
- disp[2] = a[2]*cosine + b[2]*sine;
-
- x[i][0] = point[0] + c[0] + disp[0];
- x[i][1] = point[1] + c[1] + disp[1];
- x[i][2] = point[2] + c[2] + disp[2];
- v[i][0] = omega_rotate * (runit[1]*disp[2] - runit[2]*disp[1]);
- v[i][1] = omega_rotate * (runit[2]*disp[0] - runit[0]*disp[2]);
- v[i][2] = omega_rotate * (runit[0]*disp[1] - runit[1]*disp[0]);
- if (omega_flag) {
- omega[i][0] = omega_rotate*runit[0];
- omega[i][1] = omega_rotate*runit[1];
- omega[i][2] = omega_rotate*runit[2];
- }
-
- domain->remap_near(x[i],xold);
+ xold[0] = x[i][0];
+ xold[1] = x[i][1];
+ xold[2] = x[i][2];
+
+ d[0] = xoriginal[i][0] - point[0];
+ d[1] = xoriginal[i][1] - point[1];
+ d[2] = xoriginal[i][2] - point[2];
+ ddotr = d[0]*runit[0] + d[1]*runit[1] + d[2]*runit[2];
+ c[0] = ddotr*runit[0];
+ c[1] = ddotr*runit[1];
+ c[2] = ddotr*runit[2];
+ a[0] = d[0] - c[0];
+ a[1] = d[1] - c[1];
+ a[2] = d[2] - c[2];
+ b[0] = runit[1]*a[2] - runit[2]*a[1];
+ b[1] = runit[2]*a[0] - runit[0]*a[2];
+ b[2] = runit[0]*a[1] - runit[1]*a[0];
+ disp[0] = a[0]*cosine + b[0]*sine;
+ disp[1] = a[1]*cosine + b[1]*sine;
+ disp[2] = a[2]*cosine + b[2]*sine;
+
+ x[i][0] = point[0] + c[0] + disp[0];
+ x[i][1] = point[1] + c[1] + disp[1];
+ x[i][2] = point[2] + c[2] + disp[2];
+ v[i][0] = omega_rotate * (runit[1]*disp[2] - runit[2]*disp[1]);
+ v[i][1] = omega_rotate * (runit[2]*disp[0] - runit[0]*disp[2]);
+ v[i][2] = omega_rotate * (runit[0]*disp[1] - runit[1]*disp[0]);
+ if (omega_flag) {
+ omega[i][0] = omega_rotate*runit[0];
+ omega[i][1] = omega_rotate*runit[1];
+ omega[i][2] = omega_rotate*runit[2];
+ }
+
+ domain->remap_near(x[i],xold);
}
}
@@ -568,12 +568,12 @@ void FixMove::initial_integrate(int vflag)
if ((displaceflag || velocityflag) && nlocal > maxatom) {
maxatom = atom->nmax;
if (displaceflag) {
- memory->destroy(displace);
- memory->create(displace,maxatom,3,"move:displace");
+ memory->destroy(displace);
+ memory->create(displace,maxatom,3,"move:displace");
}
if (velocityflag) {
- memory->destroy(velocity);
- memory->create(velocity,maxatom,3,"move:velocity");
+ memory->destroy(velocity);
+ memory->create(velocity,maxatom,3,"move:velocity");
}
}
@@ -584,32 +584,32 @@ void FixMove::initial_integrate(int vflag)
if (xvarstr) {
if (xvarstyle == EQUAL) dx = input->variable->compute_equal(xvar);
else if (displace)
- input->variable->compute_atom(xvar,igroup,&displace[0][0],3,0);
+ input->variable->compute_atom(xvar,igroup,&displace[0][0],3,0);
}
if (yvarstr) {
if (yvarstyle == EQUAL) dy = input->variable->compute_equal(yvar);
else if (displace)
- input->variable->compute_atom(yvar,igroup,&displace[0][1],3,0);
+ input->variable->compute_atom(yvar,igroup,&displace[0][1],3,0);
}
if (zvarstr) {
if (zvarstyle == EQUAL) dz = input->variable->compute_equal(zvar);
else if (displace)
- input->variable->compute_atom(zvar,igroup,&displace[0][2],3,0);
+ input->variable->compute_atom(zvar,igroup,&displace[0][2],3,0);
}
if (vxvarstr) {
if (vxvarstyle == EQUAL) vx = input->variable->compute_equal(vxvar);
else if (velocity)
- input->variable->compute_atom(vxvar,igroup,&velocity[0][0],3,0);
+ input->variable->compute_atom(vxvar,igroup,&velocity[0][0],3,0);
}
if (vyvarstr) {
if (vyvarstyle == EQUAL) vy = input->variable->compute_equal(vyvar);
else if (velocity)
- input->variable->compute_atom(vyvar,igroup,&velocity[0][1],3,0);
+ input->variable->compute_atom(vyvar,igroup,&velocity[0][1],3,0);
}
if (vzvarstr) {
if (vzvarstyle == EQUAL) vz = input->variable->compute_equal(vzvar);
else if (velocity)
- input->variable->compute_atom(vzvar,igroup,&velocity[0][2],3,0);
+ input->variable->compute_atom(vzvar,igroup,&velocity[0][2],3,0);
}
modify->addstep_compute(update->ntimestep + 1);
@@ -618,101 +618,101 @@ void FixMove::initial_integrate(int vflag)
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
- xold[0] = x[i][0];
- xold[1] = x[i][1];
- xold[2] = x[i][2];
-
- if (xvarstr && vxvarstr) {
- if (vxvarstyle == EQUAL) v[i][0] = vx;
- else v[i][0] = velocity[i][0];
- if (xvarstyle == EQUAL) x[i][0] = xoriginal[i][0] + dx;
- else x[i][0] = xoriginal[i][0] + displace[i][0];
- } else if (xvarstr) {
- if (xvarstyle == EQUAL) x[i][0] = xoriginal[i][0] + dx;
- else x[i][0] = xoriginal[i][0] + displace[i][0];
- } else if (vxvarstr) {
- if (vxvarstyle == EQUAL) v[i][0] = vx;
- else v[i][0] = velocity[i][0];
- if (rmass) {
- dtfm = dtf / rmass[i];
- x[i][0] += dtv * v[i][0];
- } else {
- dtfm = dtf / mass[type[i]];
- x[i][0] += dtv * v[i][0];
- }
- } else {
- if (rmass) {
- dtfm = dtf / rmass[i];
- v[i][0] += dtfm * f[i][0];
- x[i][0] += dtv * v[i][0];
- } else {
- dtfm = dtf / mass[type[i]];
- v[i][0] += dtfm * f[i][0];
- x[i][0] += dtv * v[i][0];
- }
- }
-
- if (yvarstr && vyvarstr) {
- if (vyvarstyle == EQUAL) v[i][1] = vy;
- else v[i][1] = velocity[i][1];
- if (yvarstyle == EQUAL) x[i][1] = xoriginal[i][1] + dy;
- else x[i][1] = xoriginal[i][1] + displace[i][1];
- } else if (yvarstr) {
- if (yvarstyle == EQUAL) x[i][1] = xoriginal[i][1] + dy;
- else x[i][1] = xoriginal[i][1] + displace[i][1];
- } else if (vyvarstr) {
- if (vyvarstyle == EQUAL) v[i][1] = vy;
- else v[i][1] = velocity[i][1];
- if (rmass) {
- dtfm = dtf / rmass[i];
- x[i][1] += dtv * v[i][1];
- } else {
- dtfm = dtf / mass[type[i]];
- x[i][1] += dtv * v[i][1];
- }
- } else {
- if (rmass) {
- dtfm = dtf / rmass[i];
- v[i][1] += dtfm * f[i][1];
- x[i][1] += dtv * v[i][1];
- } else {
- dtfm = dtf / mass[type[i]];
- v[i][1] += dtfm * f[i][1];
- x[i][1] += dtv * v[i][1];
- }
- }
-
- if (zvarstr && vzvarstr) {
- if (vzvarstyle == EQUAL) v[i][2] = vz;
- else v[i][2] = velocity[i][2];
- if (zvarstyle == EQUAL) x[i][2] = xoriginal[i][2] + dz;
- else x[i][2] = xoriginal[i][2] + displace[i][2];
- } else if (zvarstr) {
- if (zvarstyle == EQUAL) x[i][2] = xoriginal[i][2] + dz;
- else x[i][2] = xoriginal[i][2] + displace[i][2];
- } else if (vzvarstr) {
- if (vzvarstyle == EQUAL) v[i][2] = vz;
- else v[i][2] = velocity[i][2];
- if (rmass) {
- dtfm = dtf / rmass[i];
- x[i][2] += dtv * v[i][2];
- } else {
- dtfm = dtf / mass[type[i]];
- x[i][2] += dtv * v[i][2];
- }
- } else {
- if (rmass) {
- dtfm = dtf / rmass[i];
- v[i][2] += dtfm * f[i][2];
- x[i][2] += dtv * v[i][2];
- } else {
- dtfm = dtf / mass[type[i]];
- v[i][2] += dtfm * f[i][2];
- x[i][2] += dtv * v[i][2];
- }
- }
-
- domain->remap_near(x[i],xold);
+ xold[0] = x[i][0];
+ xold[1] = x[i][1];
+ xold[2] = x[i][2];
+
+ if (xvarstr && vxvarstr) {
+ if (vxvarstyle == EQUAL) v[i][0] = vx;
+ else v[i][0] = velocity[i][0];
+ if (xvarstyle == EQUAL) x[i][0] = xoriginal[i][0] + dx;
+ else x[i][0] = xoriginal[i][0] + displace[i][0];
+ } else if (xvarstr) {
+ if (xvarstyle == EQUAL) x[i][0] = xoriginal[i][0] + dx;
+ else x[i][0] = xoriginal[i][0] + displace[i][0];
+ } else if (vxvarstr) {
+ if (vxvarstyle == EQUAL) v[i][0] = vx;
+ else v[i][0] = velocity[i][0];
+ if (rmass) {
+ dtfm = dtf / rmass[i];
+ x[i][0] += dtv * v[i][0];
+ } else {
+ dtfm = dtf / mass[type[i]];
+ x[i][0] += dtv * v[i][0];
+ }
+ } else {
+ if (rmass) {
+ dtfm = dtf / rmass[i];
+ v[i][0] += dtfm * f[i][0];
+ x[i][0] += dtv * v[i][0];
+ } else {
+ dtfm = dtf / mass[type[i]];
+ v[i][0] += dtfm * f[i][0];
+ x[i][0] += dtv * v[i][0];
+ }
+ }
+
+ if (yvarstr && vyvarstr) {
+ if (vyvarstyle == EQUAL) v[i][1] = vy;
+ else v[i][1] = velocity[i][1];
+ if (yvarstyle == EQUAL) x[i][1] = xoriginal[i][1] + dy;
+ else x[i][1] = xoriginal[i][1] + displace[i][1];
+ } else if (yvarstr) {
+ if (yvarstyle == EQUAL) x[i][1] = xoriginal[i][1] + dy;
+ else x[i][1] = xoriginal[i][1] + displace[i][1];
+ } else if (vyvarstr) {
+ if (vyvarstyle == EQUAL) v[i][1] = vy;
+ else v[i][1] = velocity[i][1];
+ if (rmass) {
+ dtfm = dtf / rmass[i];
+ x[i][1] += dtv * v[i][1];
+ } else {
+ dtfm = dtf / mass[type[i]];
+ x[i][1] += dtv * v[i][1];
+ }
+ } else {
+ if (rmass) {
+ dtfm = dtf / rmass[i];
+ v[i][1] += dtfm * f[i][1];
+ x[i][1] += dtv * v[i][1];
+ } else {
+ dtfm = dtf / mass[type[i]];
+ v[i][1] += dtfm * f[i][1];
+ x[i][1] += dtv * v[i][1];
+ }
+ }
+
+ if (zvarstr && vzvarstr) {
+ if (vzvarstyle == EQUAL) v[i][2] = vz;
+ else v[i][2] = velocity[i][2];
+ if (zvarstyle == EQUAL) x[i][2] = xoriginal[i][2] + dz;
+ else x[i][2] = xoriginal[i][2] + displace[i][2];
+ } else if (zvarstr) {
+ if (zvarstyle == EQUAL) x[i][2] = xoriginal[i][2] + dz;
+ else x[i][2] = xoriginal[i][2] + displace[i][2];
+ } else if (vzvarstr) {
+ if (vzvarstyle == EQUAL) v[i][2] = vz;
+ else v[i][2] = velocity[i][2];
+ if (rmass) {
+ dtfm = dtf / rmass[i];
+ x[i][2] += dtv * v[i][2];
+ } else {
+ dtfm = dtf / mass[type[i]];
+ x[i][2] += dtv * v[i][2];
+ }
+ } else {
+ if (rmass) {
+ dtfm = dtf / rmass[i];
+ v[i][2] += dtfm * f[i][2];
+ x[i][2] += dtv * v[i][2];
+ } else {
+ dtfm = dtf / mass[type[i]];
+ v[i][2] += dtfm * f[i][2];
+ x[i][2] += dtv * v[i][2];
+ }
+ }
+
+ domain->remap_near(x[i],xold);
}
}
}
@@ -755,31 +755,31 @@ void FixMove::final_integrate()
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (xflag)
- if (rmass) {
- dtfm = dtf / rmass[i];
- v[i][0] += dtfm * f[i][0];
- } else {
- dtfm = dtf / mass[type[i]];
- v[i][0] += dtfm * f[i][0];
- }
-
+ if (rmass) {
+ dtfm = dtf / rmass[i];
+ v[i][0] += dtfm * f[i][0];
+ } else {
+ dtfm = dtf / mass[type[i]];
+ v[i][0] += dtfm * f[i][0];
+ }
+
if (yflag)
- if (rmass) {
- dtfm = dtf / rmass[i];
- v[i][1] += dtfm * f[i][1];
- } else {
- dtfm = dtf / mass[type[i]];
- v[i][1] += dtfm * f[i][1];
- }
-
+ if (rmass) {
+ dtfm = dtf / rmass[i];
+ v[i][1] += dtfm * f[i][1];
+ } else {
+ dtfm = dtf / mass[type[i]];
+ v[i][1] += dtfm * f[i][1];
+ }
+
if (zflag)
- if (rmass) {
- dtfm = dtf / rmass[i];
- v[i][2] += dtfm * f[i][2];
- } else {
- dtfm = dtf / mass[type[i]];
- v[i][2] += dtfm * f[i][2];
- }
+ if (rmass) {
+ dtfm = dtf / rmass[i];
+ v[i][2] += dtfm * f[i][2];
+ } else {
+ dtfm = dtf / mass[type[i]];
+ v[i][2] += dtfm * f[i][2];
+ }
}
}
}
@@ -814,7 +814,7 @@ double FixMove::memory_usage()
}
/* ----------------------------------------------------------------------
- pack entire state of Fix into one write
+ pack entire state of Fix into one write
------------------------------------------------------------------------- */
void FixMove::write_restart(FILE *fp)
@@ -831,7 +831,7 @@ void FixMove::write_restart(FILE *fp)
}
/* ----------------------------------------------------------------------
- use state info from restart file to restart the Fix
+ use state info from restart file to restart the Fix
------------------------------------------------------------------------- */
void FixMove::restart(char *buf)
@@ -917,7 +917,7 @@ void FixMove::set_arrays(int i)
c[0] = ddotr*runit[0];
c[1] = ddotr*runit[1];
c[2] = ddotr*runit[2];
-
+
a[0] = d[0] - c[0];
a[1] = d[1] - c[1];
a[2] = d[2] - c[2];
@@ -927,7 +927,7 @@ void FixMove::set_arrays(int i)
disp[0] = a[0]*cosine + b[0]*sine;
disp[1] = a[1]*cosine + b[1]*sine;
disp[2] = a[2]*cosine + b[2]*sine;
-
+
xoriginal[i][0] = point[0] + c[0] + disp[0];
xoriginal[i][1] = point[1] + c[1] + disp[1];
xoriginal[i][2] = point[2] + c[2] + disp[2];
diff --git a/src/fix_move.h b/src/fix_move.h
index 632839340ec44f7946a99809bda0b2d8ee4b93e1..118a617ecd4bb9b428217fb3318f231dae1587b8 100644
--- a/src/fix_move.h
+++ b/src/fix_move.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_nh.cpp b/src/fix_nh.cpp
index 1e4a4de236066608bac686d51cf7f398d1425ec7..6548045ff4f80aa983bc2aded882e6951d2d75b4 100644
--- a/src/fix_nh.cpp
+++ b/src/fix_nh.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -46,7 +46,7 @@ enum{NONE,XYZ,XY,YZ,XZ};
enum{ISO,ANISO,TRICLINIC};
/* ----------------------------------------------------------------------
- NVT,NPH,NPT integrators for improved Nose-Hoover equations of motion
+ NVT,NPH,NPT integrators for improved Nose-Hoover equations of motion
---------------------------------------------------------------------- */
FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
@@ -93,7 +93,7 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
fixedpoint[1] = 0.5*(domain->boxlo[1]+domain->boxhi[1]);
fixedpoint[2] = 0.5*(domain->boxlo[2]+domain->boxhi[2]);
- // used by FixNVTSllod to preserve non-default value
+ // used by FixNVTSllod to preserve non-default value
mtchain_default_flag = 1;
@@ -119,8 +119,8 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
t_stop = atof(arg[iarg+2]);
t_period = atof(arg[iarg+3]);
if (t_start < 0.0 || t_stop <= 0.0)
- error->all(FLERR,
- "Target temperature for fix nvt/npt/nph cannot be 0.0");
+ error->all(FLERR,
+ "Target temperature for fix nvt/npt/nph cannot be 0.0");
iarg += 4;
} else if (strcmp(arg[iarg],"iso") == 0) {
@@ -131,10 +131,10 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
p_period[0] = p_period[1] = p_period[2] = atof(arg[iarg+3]);
p_flag[0] = p_flag[1] = p_flag[2] = 1;
if (dimension == 2) {
- p_start[2] = p_stop[2] = p_period[2] = 0.0;
- p_flag[2] = 0;
+ p_start[2] = p_stop[2] = p_period[2] = 0.0;
+ p_flag[2] = 0;
}
- iarg += 4;
+ iarg += 4;
} else if (strcmp(arg[iarg],"aniso") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
pcouple = NONE;
@@ -143,8 +143,8 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
p_period[0] = p_period[1] = p_period[2] = atof(arg[iarg+3]);
p_flag[0] = p_flag[1] = p_flag[2] = 1;
if (dimension == 2) {
- p_start[2] = p_stop[2] = p_period[2] = 0.0;
- p_flag[2] = 0;
+ p_start[2] = p_stop[2] = p_period[2] = 0.0;
+ p_flag[2] = 0;
}
iarg += 4;
} else if (strcmp(arg[iarg],"tri") == 0) {
@@ -160,12 +160,12 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
p_period[3] = p_period[4] = p_period[5] = atof(arg[iarg+3]);
p_flag[3] = p_flag[4] = p_flag[5] = 1;
if (dimension == 2) {
- p_start[2] = p_stop[2] = p_period[2] = 0.0;
- p_flag[2] = 0;
- p_start[3] = p_stop[3] = p_period[3] = 0.0;
- p_flag[3] = 0;
- p_start[4] = p_stop[4] = p_period[4] = 0.0;
- p_flag[4] = 0;
+ p_start[2] = p_stop[2] = p_period[2] = 0.0;
+ p_flag[2] = 0;
+ p_start[3] = p_stop[3] = p_period[3] = 0.0;
+ p_flag[3] = 0;
+ p_start[4] = p_stop[4] = p_period[4] = 0.0;
+ p_flag[4] = 0;
}
iarg += 4;
} else if (strcmp(arg[iarg],"x") == 0) {
@@ -175,7 +175,7 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
p_period[0] = atof(arg[iarg+3]);
p_flag[0] = 1;
deviatoric_flag = 1;
- iarg += 4;
+ iarg += 4;
} else if (strcmp(arg[iarg],"y") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
p_start[1] = atof(arg[iarg+1]);
@@ -183,7 +183,7 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
p_period[1] = atof(arg[iarg+3]);
p_flag[1] = 1;
deviatoric_flag = 1;
- iarg += 4;
+ iarg += 4;
} else if (strcmp(arg[iarg],"z") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
p_start[2] = atof(arg[iarg+1]);
@@ -191,9 +191,9 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
p_period[2] = atof(arg[iarg+3]);
p_flag[2] = 1;
deviatoric_flag = 1;
- iarg += 4;
+ iarg += 4;
if (dimension == 2)
- error->all(FLERR,"Invalid fix nvt/npt/nph command for a 2d simulation");
+ error->all(FLERR,"Invalid fix nvt/npt/nph command for a 2d simulation");
} else if (strcmp(arg[iarg],"yz") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
@@ -203,9 +203,9 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
p_period[3] = atof(arg[iarg+3]);
p_flag[3] = 1;
deviatoric_flag = 1;
- iarg += 4;
+ iarg += 4;
if (dimension == 2)
- error->all(FLERR,"Invalid fix nvt/npt/nph command for a 2d simulation");
+ error->all(FLERR,"Invalid fix nvt/npt/nph command for a 2d simulation");
} else if (strcmp(arg[iarg],"xz") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
scalexz = 0;
@@ -214,9 +214,9 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
p_period[4] = atof(arg[iarg+3]);
p_flag[4] = 1;
deviatoric_flag = 1;
- iarg += 4;
+ iarg += 4;
if (dimension == 2)
- error->all(FLERR,"Invalid fix nvt/npt/nph command for a 2d simulation");
+ error->all(FLERR,"Invalid fix nvt/npt/nph command for a 2d simulation");
} else if (strcmp(arg[iarg],"xy") == 0) {
scalexy = 0;
if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
@@ -225,7 +225,7 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
p_period[5] = atof(arg[iarg+3]);
p_flag[5] = 1;
deviatoric_flag = 1;
- iarg += 4;
+ iarg += 4;
} else if (strcmp(arg[iarg],"couple") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
@@ -246,21 +246,21 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
if (strcmp(arg[iarg+1],"all") == 0) allremap = 1;
else {
- allremap = 0;
- delete [] id_dilate;
- int n = strlen(arg[iarg+2]) + 1;
- id_dilate = new char[n];
- strcpy(id_dilate,arg[iarg+2]);
- int idilate = group->find(id_dilate);
- if (idilate == -1)
- error->all(FLERR,"Fix nvt/npt/nph dilate group ID does not exist");
+ allremap = 0;
+ delete [] id_dilate;
+ int n = strlen(arg[iarg+2]) + 1;
+ id_dilate = new char[n];
+ strcpy(id_dilate,arg[iarg+2]);
+ int idilate = group->find(id_dilate);
+ if (idilate == -1)
+ error->all(FLERR,"Fix nvt/npt/nph dilate group ID does not exist");
}
iarg += 2;
} else if (strcmp(arg[iarg],"tchain") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
mtchain = atoi(arg[iarg+1]);
- // used by FixNVTSllod to preserve non-default value
+ // used by FixNVTSllod to preserve non-default value
mtchain_default_flag = 0;
if (mtchain < 1) error->all(FLERR,"Illegal fix nvt/npt/nph command");
iarg += 2;
@@ -350,66 +350,66 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
if (p_flag[3] && domain->zperiodic == 0)
error->all(FLERR,
- "Cannot use fix nvt/npt/nph on a 2nd non-periodic dimension");
+ "Cannot use fix nvt/npt/nph on a 2nd non-periodic dimension");
if (p_flag[4] && domain->zperiodic == 0)
error->all(FLERR,
- "Cannot use fix nvt/npt/nph on a 2nd non-periodic dimension");
+ "Cannot use fix nvt/npt/nph on a 2nd non-periodic dimension");
if (p_flag[5] && domain->yperiodic == 0)
error->all(FLERR,
- "Cannot use fix nvt/npt/nph on a 2nd non-periodic dimension");
+ "Cannot use fix nvt/npt/nph on a 2nd non-periodic dimension");
if (scaleyz == 1 && domain->zperiodic == 0)
error->all(FLERR,"Cannot use fix nvt/npt/nph "
- "with yz dynamics when z is non-periodic dimension");
+ "with yz dynamics when z is non-periodic dimension");
if (scalexz == 1 && domain->zperiodic == 0)
error->all(FLERR,"Cannot use fix nvt/npt/nph "
- "with xz dynamics when z is non-periodic dimension");
+ "with xz dynamics when z is non-periodic dimension");
if (scalexy == 1 && domain->yperiodic == 0)
error->all(FLERR,"Cannot use fix nvt/npt/nph "
- "with xy dynamics when y is non-periodic dimension");
+ "with xy dynamics when y is non-periodic dimension");
if (p_flag[3] && scaleyz == 1)
error->all(FLERR,"Cannot use fix nvt/npt/nph with "
- "both yz dynamics and yz scaling");
+ "both yz dynamics and yz scaling");
if (p_flag[4] && scalexz == 1)
error->all(FLERR,"Cannot use fix nvt/npt/nph with "
- "both xz dynamics and xz scaling");
+ "both xz dynamics and xz scaling");
if (p_flag[5] && scalexy == 1)
error->all(FLERR,"Cannot use fix nvt/npt/nph with "
- "both xy dynamics and xy scaling");
+ "both xy dynamics and xy scaling");
- if (!domain->triclinic && (p_flag[3] || p_flag[4] || p_flag[5]))
+ if (!domain->triclinic && (p_flag[3] || p_flag[4] || p_flag[5]))
error->all(FLERR,"Can not specify Pxy/Pxz/Pyz in "
- "fix nvt/npt/nph with non-triclinic box");
+ "fix nvt/npt/nph with non-triclinic box");
if (pcouple == XYZ && dimension == 3 &&
- (p_start[0] != p_start[1] || p_start[0] != p_start[2] ||
- p_stop[0] != p_stop[1] || p_stop[0] != p_stop[2] ||
+ (p_start[0] != p_start[1] || p_start[0] != p_start[2] ||
+ p_stop[0] != p_stop[1] || p_stop[0] != p_stop[2] ||
p_period[0] != p_period[1] || p_period[0] != p_period[2]))
error->all(FLERR,"Invalid fix nvt/npt/nph pressure settings");
if (pcouple == XYZ && dimension == 2 &&
- (p_start[0] != p_start[1] || p_stop[0] != p_stop[1] ||
+ (p_start[0] != p_start[1] || p_stop[0] != p_stop[1] ||
p_period[0] != p_period[1]))
error->all(FLERR,"Invalid fix nvt/npt/nph pressure settings");
- if (pcouple == XY &&
- (p_start[0] != p_start[1] || p_stop[0] != p_stop[1] ||
+ if (pcouple == XY &&
+ (p_start[0] != p_start[1] || p_stop[0] != p_stop[1] ||
p_period[0] != p_period[1]))
error->all(FLERR,"Invalid fix nvt/npt/nph pressure settings");
- if (pcouple == YZ &&
+ if (pcouple == YZ &&
(p_start[1] != p_start[2] || p_stop[1] != p_stop[2] ||
p_period[1] != p_period[2]))
error->all(FLERR,"Invalid fix nvt/npt/nph pressure settings");
- if (pcouple == XZ &&
+ if (pcouple == XZ &&
(p_start[0] != p_start[2] || p_stop[0] != p_stop[2] ||
p_period[0] != p_period[2]))
error->all(FLERR,"Invalid fix nvt/npt/nph pressure settings");
- if ((tstat_flag && t_period <= 0.0) ||
- (p_flag[0] && p_period[0] <= 0.0) ||
- (p_flag[1] && p_period[1] <= 0.0) ||
+ if ((tstat_flag && t_period <= 0.0) ||
+ (p_flag[0] && p_period[0] <= 0.0) ||
+ (p_flag[1] && p_period[1] <= 0.0) ||
(p_flag[2] && p_period[2] <= 0.0) ||
- (p_flag[3] && p_period[3] <= 0.0) ||
- (p_flag[4] && p_period[4] <= 0.0) ||
+ (p_flag[3] && p_period[3] <= 0.0) ||
+ (p_flag[4] && p_period[4] <= 0.0) ||
(p_flag[5] && p_period[5] <= 0.0))
error->all(FLERR,"Fix nvt/npt/nph damping parameters must be > 0.0");
@@ -483,7 +483,7 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
if (pstyle == ISO) size_vector += 2*2*1;
else if (pstyle == ANISO) size_vector += 2*2*3;
else if (pstyle == TRICLINIC) size_vector += 2*2*6;
-
+
if (mpchain) {
int ich;
etap = new double[mpchain];
@@ -494,8 +494,8 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
etap_dot[mpchain] = 0.0;
etap_dotdot = new double[mpchain];
for (ich = 0; ich < mpchain; ich++) {
- etap[ich] = etap_dot[ich] =
- etap_dotdot[ich] = 0.0;
+ etap[ich] = etap_dot[ich] =
+ etap_dotdot[ich] = 0.0;
}
etap_mass = new double[mpchain];
size_vector += 2*2*mpchain;
@@ -515,9 +515,9 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
vol0 = t0 = 0.0;
}
-
+
/* ---------------------------------------------------------------------- */
-
+
FixNH::~FixNH()
{
delete [] id_dilate;
@@ -571,28 +571,28 @@ void FixNH::init()
if (allremap == 0) {
int idilate = group->find(id_dilate);
- if (idilate == -1)
- error->all(FLERR,"Fix nvt/npt/nph dilate group ID does not exist");
+ if (idilate == -1)
+ error->all(FLERR,"Fix nvt/npt/nph dilate group ID does not exist");
dilate_group_bit = group->bitmask[idilate];
}
-
+
// ensure no conflict with fix deform
if (pstat_flag)
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"deform") == 0) {
- int *dimflag = ((FixDeform *) modify->fix[i])->dimflag;
- if ((p_flag[0] && dimflag[0]) || (p_flag[1] && dimflag[1]) ||
- (p_flag[2] && dimflag[2]) || (p_flag[3] && dimflag[3]) ||
- (p_flag[4] && dimflag[4]) || (p_flag[5] && dimflag[5]))
- error->all(FLERR,"Cannot use fix npt and fix deform on "
- "same component of stress tensor");
+ int *dimflag = ((FixDeform *) modify->fix[i])->dimflag;
+ if ((p_flag[0] && dimflag[0]) || (p_flag[1] && dimflag[1]) ||
+ (p_flag[2] && dimflag[2]) || (p_flag[3] && dimflag[3]) ||
+ (p_flag[4] && dimflag[4]) || (p_flag[5] && dimflag[5]))
+ error->all(FLERR,"Cannot use fix npt and fix deform on "
+ "same component of stress tensor");
}
// set temperature and pressure ptrs
int icompute = modify->find_compute(id_temp);
- if (icompute < 0)
+ if (icompute < 0)
error->all(FLERR,"Temperature ID for fix nvt/nph/npt does not exist");
temperature = modify->compute[icompute];
@@ -601,7 +601,7 @@ void FixNH::init()
if (pstat_flag) {
icompute = modify->find_compute(id_press);
- if (icompute < 0)
+ if (icompute < 0)
error->all(FLERR,"Pressure ID for fix npt/nph does not exist");
pressure = modify->compute[icompute];
}
@@ -677,7 +677,7 @@ void FixNH::init()
}
/* ----------------------------------------------------------------------
- compute T,P before integrator starts
+ compute T,P before integrator starts
------------------------------------------------------------------------- */
void FixNH::setup(int vflag)
@@ -687,7 +687,7 @@ void FixNH::setup(int vflag)
tdof = temperature->dof;
// t_target is needed by NPH and NPT in compute_scalar()
- // If no thermostat or using fix nphug,
+ // If no thermostat or using fix nphug,
// t_target must be defined by other means.
if (tstat_flag && strcmp(style,"nphug") != 0) {
@@ -703,8 +703,8 @@ void FixNH::setup(int vflag)
if (t0 == 0.0) {
t0 = temperature->compute_scalar();
if (t0 == 0.0) {
- if (strcmp(update->unit_style,"lj") == 0) t0 = 1.0;
- else t0 = 300.0;
+ if (strcmp(update->unit_style,"lj") == 0) t0 = 1.0;
+ else t0 = 300.0;
}
}
t_target = t0;
@@ -728,7 +728,7 @@ void FixNH::setup(int vflag)
eta_mass[ich] = boltz * t_target / (t_freq*t_freq);
for (int ich = 1; ich < mtchain; ich++) {
eta_dotdot[ich] = (eta_mass[ich-1]*eta_dot[ich-1]*eta_dot[ich-1] -
- boltz * t_target) / eta_mass[ich];
+ boltz * t_target) / eta_mass[ich];
}
}
@@ -740,11 +740,11 @@ void FixNH::setup(int vflag)
for (int i = 0; i < 3; i++)
if (p_flag[i])
- omega_mass[i] = nkt/(p_freq[i]*p_freq[i]);
+ omega_mass[i] = nkt/(p_freq[i]*p_freq[i]);
if (pstyle == TRICLINIC) {
for (int i = 3; i < 6; i++)
- if (p_flag[i]) omega_mass[i] = nkt/(p_freq[i]*p_freq[i]);
+ if (p_flag[i]) omega_mass[i] = nkt/(p_freq[i]*p_freq[i]);
}
// masses and initial forces on barostat thermostat variables
@@ -752,18 +752,18 @@ void FixNH::setup(int vflag)
if (mpchain) {
etap_mass[0] = boltz * t_target / (p_freq_max*p_freq_max);
for (int ich = 1; ich < mpchain; ich++)
- etap_mass[ich] = boltz * t_target / (p_freq_max*p_freq_max);
+ etap_mass[ich] = boltz * t_target / (p_freq_max*p_freq_max);
for (int ich = 1; ich < mpchain; ich++)
- etap_dotdot[ich] =
- (etap_mass[ich-1]*etap_dot[ich-1]*etap_dot[ich-1] -
- boltz * t_target) / etap_mass[ich];
+ etap_dotdot[ich] =
+ (etap_mass[ich-1]*etap_dot[ich-1]*etap_dot[ich-1] -
+ boltz * t_target) / etap_mass[ich];
}
}
}
/* ----------------------------------------------------------------------
- 1st half of Verlet update
+ 1st half of Verlet update
------------------------------------------------------------------------- */
void FixNH::initial_integrate(int vflag)
@@ -819,7 +819,7 @@ void FixNH::initial_integrate(int vflag)
}
/* ----------------------------------------------------------------------
- 2nd half of Verlet update
+ 2nd half of Verlet update
------------------------------------------------------------------------- */
void FixNH::final_integrate()
@@ -865,7 +865,7 @@ void FixNH::initial_integrate_respa(int vflag, int ilevel, int iloop)
if (ilevel == nlevels_respa-1) {
// update eta_press_dot
-
+
if (pstat_flag && mpchain) nhc_press_integrate();
// update eta_dot
@@ -881,16 +881,16 @@ void FixNH::initial_integrate_respa(int vflag, int ilevel, int iloop)
if (pstat_flag) {
if (pstyle == ISO) {
- temperature->compute_scalar();
- pressure->compute_scalar();
+ temperature->compute_scalar();
+ pressure->compute_scalar();
} else {
- temperature->compute_vector();
- pressure->compute_vector();
+ temperature->compute_vector();
+ pressure->compute_vector();
}
couple();
pressure->addstep(update->ntimestep+1);
}
-
+
if (pstat_flag) {
compute_press_target();
nh_omega_dot();
@@ -910,10 +910,10 @@ void FixNH::initial_integrate_respa(int vflag, int ilevel, int iloop)
if (pstat_flag) remap();
}
- // if barostat, redo KSpace coeffs at outermost level,
+ // if barostat, redo KSpace coeffs at outermost level,
// since volume has changed
- if (ilevel == nlevels_respa-1 && kspace_flag && pstat_flag)
+ if (ilevel == nlevels_respa-1 && kspace_flag && pstat_flag)
force->kspace->setup();
}
@@ -961,9 +961,9 @@ void FixNH::couple()
p_current[1] = tensor[1];
p_current[2] = tensor[2];
}
-
- // switch order from xy-xz-yz to Voigt
-
+
+ // switch order from xy-xz-yz to Voigt
+
if (pstyle == TRICLINIC) {
p_current[3] = tensor[5];
p_current[4] = tensor[4];
@@ -998,7 +998,7 @@ void FixNH::remap()
else {
for (i = 0; i < nlocal; i++)
if (mask[i] & dilate_group_bit)
- domain->x2lamda(x[i],x[i]);
+ domain->x2lamda(x[i],x[i]);
}
if (nrigid)
@@ -1008,16 +1008,16 @@ void FixNH::remap()
// reset global and local box to new size/shape
// this operation corresponds to applying the
- // translate and scale operations
+ // translate and scale operations
// corresponding to the solution of the following ODE:
//
// h_dot = omega_dot * h
//
// where h_dot, omega_dot and h are all upper-triangular
- // 3x3 tensors. In Voigt notation, the elements of the
+ // 3x3 tensors. In Voigt notation, the elements of the
// RHS product tensor are:
// h_dot = [0*0, 1*1, 2*2, 1*3+3*2, 0*4+5*3+4*2, 0*5+5*1]
- //
+ //
// Ordering of operations preserves time symmetry.
double dto2 = dto/2.0;
@@ -1031,28 +1031,28 @@ void FixNH::remap()
if (p_flag[4]) {
expfac = exp(dto8*omega_dot[0]);
h[4] *= expfac;
- h[4] += dto4*(omega_dot[5]*h[3]+omega_dot[4]*h[2]);
+ h[4] += dto4*(omega_dot[5]*h[3]+omega_dot[4]*h[2]);
h[4] *= expfac;
}
if (p_flag[3]) {
expfac = exp(dto4*omega_dot[1]);
h[3] *= expfac;
- h[3] += dto2*(omega_dot[3]*h[2]);
+ h[3] += dto2*(omega_dot[3]*h[2]);
h[3] *= expfac;
}
if (p_flag[5]) {
expfac = exp(dto4*omega_dot[0]);
h[5] *= expfac;
- h[5] += dto2*(omega_dot[5]*h[1]);
+ h[5] += dto2*(omega_dot[5]*h[1]);
h[5] *= expfac;
}
if (p_flag[4]) {
expfac = exp(dto8*omega_dot[0]);
h[4] *= expfac;
- h[4] += dto4*(omega_dot[5]*h[3]+omega_dot[4]*h[2]);
+ h[4] += dto4*(omega_dot[5]*h[3]+omega_dot[4]*h[2]);
h[4] *= expfac;
}
}
@@ -1094,28 +1094,28 @@ void FixNH::remap()
if (p_flag[4]) {
expfac = exp(dto8*omega_dot[0]);
h[4] *= expfac;
- h[4] += dto4*(omega_dot[5]*h[3]+omega_dot[4]*h[2]);
+ h[4] += dto4*(omega_dot[5]*h[3]+omega_dot[4]*h[2]);
h[4] *= expfac;
}
if (p_flag[3]) {
expfac = exp(dto4*omega_dot[1]);
h[3] *= expfac;
- h[3] += dto2*(omega_dot[3]*h[2]);
+ h[3] += dto2*(omega_dot[3]*h[2]);
h[3] *= expfac;
}
if (p_flag[5]) {
expfac = exp(dto4*omega_dot[0]);
h[5] *= expfac;
- h[5] += dto2*(omega_dot[5]*h[1]);
+ h[5] += dto2*(omega_dot[5]*h[1]);
h[5] *= expfac;
}
if (p_flag[4]) {
expfac = exp(dto8*omega_dot[0]);
h[4] *= expfac;
- h[4] += dto4*(omega_dot[5]*h[3]+omega_dot[4]*h[2]);
+ h[4] += dto4*(omega_dot[5]*h[3]+omega_dot[4]*h[2]);
h[4] *= expfac;
}
@@ -1127,14 +1127,14 @@ void FixNH::remap()
// tilt factor to cell length ratio can not exceed TILTMAX in one step
- if (domain->yz < -TILTMAX*domain->yprd ||
+ if (domain->yz < -TILTMAX*domain->yprd ||
domain->yz > TILTMAX*domain->yprd ||
- domain->xz < -TILTMAX*domain->xprd ||
+ domain->xz < -TILTMAX*domain->xprd ||
domain->xz > TILTMAX*domain->xprd ||
- domain->xy < -TILTMAX*domain->xprd ||
+ domain->xy < -TILTMAX*domain->xprd ||
domain->xy > TILTMAX*domain->xprd)
error->all(FLERR,"Fix npt/nph has tilted box too far in one step - "
- "periodic cell is too far from equilibrium state");
+ "periodic cell is too far from equilibrium state");
domain->set_global_box();
domain->set_local_box();
@@ -1145,7 +1145,7 @@ void FixNH::remap()
else {
for (i = 0; i < nlocal; i++)
if (mask[i] & dilate_group_bit)
- domain->lamda2x(x[i],x[i]);
+ domain->lamda2x(x[i],x[i]);
}
if (nrigid)
@@ -1154,7 +1154,7 @@ void FixNH::remap()
}
/* ----------------------------------------------------------------------
- pack entire state of Fix into one write
+ pack entire state of Fix into one write
------------------------------------------------------------------------- */
void FixNH::write_restart(FILE *fp)
@@ -1192,7 +1192,7 @@ int FixNH::size_restart_global()
}
/* ----------------------------------------------------------------------
- pack restart data
+ pack restart data
------------------------------------------------------------------------- */
int FixNH::pack_restart_data(double *list)
@@ -1227,9 +1227,9 @@ int FixNH::pack_restart_data(double *list)
list[n++] = mpchain;
if (mpchain) {
for (int ich = 0; ich < mpchain; ich++)
- list[n++] = etap[ich];
+ list[n++] = etap[ich];
for (int ich = 0; ich < mpchain; ich++)
- list[n++] = etap_dot[ich];
+ list[n++] = etap_dot[ich];
}
list[n++] = deviatoric_flag;
@@ -1247,7 +1247,7 @@ int FixNH::pack_restart_data(double *list)
}
/* ----------------------------------------------------------------------
- use state info from restart file to restart the Fix
+ use state info from restart file to restart the Fix
------------------------------------------------------------------------- */
void FixNH::restart(char *buf)
@@ -1259,9 +1259,9 @@ void FixNH::restart(char *buf)
int m = static_cast<int> (list[n++]);
if (tstat_flag && m == mtchain) {
for (int ich = 0; ich < mtchain; ich++)
- eta[ich] = list[n++];
+ eta[ich] = list[n++];
for (int ich = 0; ich < mtchain; ich++)
- eta_dot[ich] = list[n++];
+ eta_dot[ich] = list[n++];
} else n += 2*m;
}
flag = static_cast<int> (list[n++]);
@@ -1283,9 +1283,9 @@ void FixNH::restart(char *buf)
int m = static_cast<int> (list[n++]);
if (pstat_flag && m == mpchain) {
for (int ich = 0; ich < mpchain; ich++)
- etap[ich] = list[n++];
+ etap[ich] = list[n++];
for (int ich = 0; ich < mpchain; ich++)
- etap_dot[ich] = list[n++];
+ etap_dot[ich] = list[n++];
} else n+=2*m;
flag = static_cast<int> (list[n++]);
if (flag) {
@@ -1315,13 +1315,13 @@ int FixNH::modify_param(int narg, char **arg)
strcpy(id_temp,arg[1]);
int icompute = modify->find_compute(arg[1]);
- if (icompute < 0)
+ if (icompute < 0)
error->all(FLERR,"Could not find fix_modify temperature ID");
temperature = modify->compute[icompute];
if (temperature->tempflag == 0)
error->all(FLERR,
- "Fix_modify temperature ID does not compute temperature");
+ "Fix_modify temperature ID does not compute temperature");
if (temperature->igroup != 0 && comm->me == 0)
error->warning(FLERR,"Temperature for fix modify is not for group all");
@@ -1329,8 +1329,8 @@ int FixNH::modify_param(int narg, char **arg)
if (pstat_flag) {
icompute = modify->find_compute(id_press);
- if (icompute < 0)
- error->all(FLERR,"Pressure ID for fix modify does not exist");
+ if (icompute < 0)
+ error->all(FLERR,"Pressure ID for fix modify does not exist");
modify->compute[icompute]->reset_extra_compute_fix(id_temp);
}
@@ -1382,7 +1382,7 @@ double FixNH::compute_scalar()
// M = mtchain
// p_eta_k = Q_k*eta_dot[k-1]
// Q_1 = L*k*T/t_freq^2
- // Q_k = k*T/t_freq^2, k > 1
+ // Q_k = k*T/t_freq^2, k > 1
if (tstat_flag) {
energy += ke_target * eta[0] + 0.5*eta_mass[0]*eta_dot[0]*eta_dot[0];
@@ -1398,16 +1398,16 @@ double FixNH::compute_scalar()
// W = N*k*T/p_freq^2
// sum is over barostatted dimensions
- if (pstat_flag) {
+ if (pstat_flag) {
for (i = 0; i < 3; i++)
if (p_flag[i])
- energy += 0.5*omega_dot[i]*omega_dot[i]*omega_mass[i] +
- p_hydro*(volume-vol0) / (pdim*nktv2p);
+ energy += 0.5*omega_dot[i]*omega_dot[i]*omega_mass[i] +
+ p_hydro*(volume-vol0) / (pdim*nktv2p);
if (pstyle == TRICLINIC) {
for (i = 3; i < 6; i++)
- if (p_flag[i])
- energy += 0.5*omega_dot[i]*omega_dot[i]*omega_mass[i];
+ if (p_flag[i])
+ energy += 0.5*omega_dot[i]*omega_dot[i]*omega_mass[i];
}
// extra contributions from thermostat chain for barostat
@@ -1415,8 +1415,8 @@ double FixNH::compute_scalar()
if (mpchain) {
energy += lkt_press * etap[0] + 0.5*etap_mass[0]*etap_dot[0]*etap_dot[0];
for (ich = 1; ich < mpchain; ich++)
- energy += kt * etap[ich] +
- 0.5*etap_mass[ich]*etap_dot[ich]*etap_dot[ich];
+ energy += kt * etap[ich] +
+ 0.5*etap_mass[ich]*etap_dot[ich]*etap_dot[ich];
}
// extra contribution from strain energy
@@ -1442,7 +1442,7 @@ double FixNH::compute_vector(int n)
{
int ilen;
- if (tstat_flag) {
+ if (tstat_flag) {
ilen = mtchain;
if (n < ilen) return eta[n];
n -= ilen;
@@ -1451,7 +1451,7 @@ double FixNH::compute_vector(int n)
n -= ilen;
}
- if (pstat_flag) {
+ if (pstat_flag) {
if (pstyle == ISO) {
ilen = 1;
if (n < ilen) return omega[n];
@@ -1465,7 +1465,7 @@ double FixNH::compute_vector(int n)
if (n < ilen) return omega[n];
n -= ilen;
}
-
+
if (pstyle == ISO) {
ilen = 1;
if (n < ilen) return omega_dot[n];
@@ -1479,7 +1479,7 @@ double FixNH::compute_vector(int n)
if (n < ilen) return omega_dot[n];
n -= ilen;
}
-
+
if (mpchain) {
ilen = mpchain;
if (n < ilen) return etap[n];
@@ -1497,88 +1497,88 @@ double FixNH::compute_vector(int n)
if (dimension == 3) volume = domain->xprd * domain->yprd * domain->zprd;
else volume = domain->xprd * domain->yprd;
- if (tstat_flag) {
+ if (tstat_flag) {
ilen = mtchain;
- if (n < ilen) {
+ if (n < ilen) {
ich = n;
if (ich == 0)
- return ke_target * eta[0];
+ return ke_target * eta[0];
else
- return kt * eta[ich];
+ return kt * eta[ich];
}
n -= ilen;
ilen = mtchain;
if (n < ilen) {
ich = n;
if (ich == 0)
- return 0.5*eta_mass[0]*eta_dot[0]*eta_dot[0];
+ return 0.5*eta_mass[0]*eta_dot[0]*eta_dot[0];
else
- return 0.5*eta_mass[ich]*eta_dot[ich]*eta_dot[ich];
+ return 0.5*eta_mass[ich]*eta_dot[ich]*eta_dot[ich];
}
n -= ilen;
}
- if (pstat_flag) {
+ if (pstat_flag) {
if (pstyle == ISO) {
ilen = 1;
- if (n < ilen)
- return p_hydro*(volume-vol0) / nktv2p;
+ if (n < ilen)
+ return p_hydro*(volume-vol0) / nktv2p;
n -= ilen;
} else if (pstyle == ANISO) {
ilen = 3;
- if (n < ilen)
- if (p_flag[n])
- return p_hydro*(volume-vol0) / (pdim*nktv2p);
- else
- return 0.0;
+ if (n < ilen)
+ if (p_flag[n])
+ return p_hydro*(volume-vol0) / (pdim*nktv2p);
+ else
+ return 0.0;
n -= ilen;
} else {
ilen = 6;
if (n < ilen)
- if (n > 2) return 0.0;
- else if (p_flag[n])
- return p_hydro*(volume-vol0) / (pdim*nktv2p);
- else
- return 0.0;
+ if (n > 2) return 0.0;
+ else if (p_flag[n])
+ return p_hydro*(volume-vol0) / (pdim*nktv2p);
+ else
+ return 0.0;
n -= ilen;
}
-
+
if (pstyle == ISO) {
ilen = 1;
- if (n < ilen)
- return pdim*0.5*omega_dot[n]*omega_dot[n]*omega_mass[n];
+ if (n < ilen)
+ return pdim*0.5*omega_dot[n]*omega_dot[n]*omega_mass[n];
n -= ilen;
} else if (pstyle == ANISO) {
ilen = 3;
- if (n < ilen)
- if (p_flag[n])
- return 0.5*omega_dot[n]*omega_dot[n]*omega_mass[n];
- else return 0.0;
+ if (n < ilen)
+ if (p_flag[n])
+ return 0.5*omega_dot[n]*omega_dot[n]*omega_mass[n];
+ else return 0.0;
n -= ilen;
} else {
ilen = 6;
if (n < ilen)
- if (p_flag[n])
- return 0.5*omega_dot[n]*omega_dot[n]*omega_mass[n];
- else return 0.0;
+ if (p_flag[n])
+ return 0.5*omega_dot[n]*omega_dot[n]*omega_mass[n];
+ else return 0.0;
n -= ilen;
}
-
+
if (mpchain) {
ilen = mpchain;
if (n < ilen) {
- ich = n;
- if (ich == 0) return lkt_press * etap[0];
- else return kt * etap[ich];
+ ich = n;
+ if (ich == 0) return lkt_press * etap[0];
+ else return kt * etap[ich];
}
n -= ilen;
ilen = mpchain;
if (n < ilen) {
- ich = n;
- if (ich == 0)
- return 0.5*etap_mass[0]*etap_dot[0]*etap_dot[0];
- else
- return 0.5*etap_mass[ich]*etap_dot[ich]*etap_dot[ich];
+ ich = n;
+ if (ich == 0)
+ return 0.5*etap_mass[0]*etap_dot[0]*etap_dot[0];
+ else
+ return 0.5*etap_mass[ich]*etap_dot[ich]*etap_dot[ich];
}
n -= ilen;
}
@@ -1586,7 +1586,7 @@ double FixNH::compute_vector(int n)
if (deviatoric_flag) {
ilen = 1;
if (n < ilen)
- return compute_strain_energy();
+ return compute_strain_energy();
n -= ilen;
}
}
@@ -1613,13 +1613,13 @@ void FixNH::reset_dt()
dto = dthalf;
// If using respa, then remap is performed in innermost level
-
+
if (strstr(update->integrate_style,"respa"))
dto = 0.5*step_respa[0];
if (pstat_flag)
pdrag_factor = 1.0 - (update->dt * p_freq_max * drag / nc_pchain);
-
+
if (tstat_flag)
tdrag_factor = 1.0 - (update->dt * t_freq * drag / nc_tchain);
}
@@ -1633,7 +1633,7 @@ void *FixNH::extract(const char *str, int &dim)
dim=0;
if (strcmp(str,"t_target") == 0) {
return &t_target;
- }
+ }
return NULL;
}
@@ -1649,7 +1649,7 @@ void FixNH::nhc_temp_integrate()
// Update masses, to preserve initial freq, if flag set
- if (eta_mass_flag) {
+ if (eta_mass_flag) {
eta_mass[0] = tdof * boltz * t_target / (t_freq*t_freq);
for (int ich = 1; ich < mtchain; ich++)
eta_mass[ich] = boltz * t_target / (t_freq*t_freq);
@@ -1675,12 +1675,12 @@ void FixNH::nhc_temp_integrate()
eta_dot[0] += eta_dotdot[0] * ncfac*dt4;
eta_dot[0] *= tdrag_factor;
eta_dot[0] *= expfac;
-
+
factor_eta = exp(-ncfac*dthalf*eta_dot[0]);
nh_v_temp();
// rescale temperature due to velocity scaling
- // should not be necessary to explicitly recompute the temperature
+ // should not be necessary to explicitly recompute the temperature
t_current *= factor_eta*factor_eta;
kecurrent = tdof * boltz * t_current;
@@ -1691,16 +1691,16 @@ void FixNH::nhc_temp_integrate()
for (ich = 0; ich < mtchain; ich++)
eta[ich] += ncfac*dthalf*eta_dot[ich];
-
+
eta_dot[0] *= expfac;
eta_dot[0] += eta_dotdot[0] * ncfac*dt4;
eta_dot[0] *= expfac;
-
+
for (ich = 1; ich < mtchain; ich++) {
expfac = exp(-ncfac*dt8*eta_dot[ich+1]);
eta_dot[ich] *= expfac;
- eta_dotdot[ich] = (eta_mass[ich-1]*eta_dot[ich-1]*eta_dot[ich-1]
- - boltz * t_target)/eta_mass[ich];
+ eta_dotdot[ich] = (eta_mass[ich-1]*eta_dot[ich-1]*eta_dot[ich-1]
+ - boltz * t_target)/eta_mass[ich];
eta_dot[ich] += eta_dotdot[ich] * ncfac*dt4;
eta_dot[ich] *= expfac;
}
@@ -1721,27 +1721,27 @@ void FixNH::nhc_press_integrate()
// Update masses, to preserve initial freq, if flag set
- if (omega_mass_flag) {
+ if (omega_mass_flag) {
double nkt = atom->natoms * kt;
for (int i = 0; i < 3; i++)
if (p_flag[i])
- omega_mass[i] = nkt/(p_freq[i]*p_freq[i]);
+ omega_mass[i] = nkt/(p_freq[i]*p_freq[i]);
if (pstyle == TRICLINIC) {
for (int i = 3; i < 6; i++)
- if (p_flag[i]) omega_mass[i] = nkt/(p_freq[i]*p_freq[i]);
+ if (p_flag[i]) omega_mass[i] = nkt/(p_freq[i]*p_freq[i]);
}
}
- if (etap_mass_flag) {
+ if (etap_mass_flag) {
if (mpchain) {
etap_mass[0] = boltz * t_target / (p_freq_max*p_freq_max);
for (int ich = 1; ich < mpchain; ich++)
- etap_mass[ich] = boltz * t_target / (p_freq_max*p_freq_max);
+ etap_mass[ich] = boltz * t_target / (p_freq_max*p_freq_max);
for (int ich = 1; ich < mpchain; ich++)
- etap_dotdot[ich] =
- (etap_mass[ich-1]*etap_dot[ich-1]*etap_dot[ich-1] -
- boltz * t_target) / etap_mass[ich];
+ etap_dotdot[ich] =
+ (etap_mass[ich-1]*etap_dot[ich-1]*etap_dot[ich-1] -
+ boltz * t_target) / etap_mass[ich];
}
}
@@ -1750,7 +1750,7 @@ void FixNH::nhc_press_integrate()
if (p_flag[i]) kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i];
if (pstyle == TRICLINIC) {
- for (i = 3; i < 6; i++)
+ for (i = 3; i < 6; i++)
if (p_flag[i]) kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i];
}
@@ -1766,46 +1766,46 @@ void FixNH::nhc_press_integrate()
etap_dot[ich] *= pdrag_factor;
etap_dot[ich] *= expfac;
}
-
+
expfac = exp(-ncfac*dt8*etap_dot[1]);
etap_dot[0] *= expfac;
etap_dot[0] += etap_dotdot[0] * ncfac*dt4;
etap_dot[0] *= pdrag_factor;
etap_dot[0] *= expfac;
-
+
for (ich = 0; ich < mpchain; ich++)
etap[ich] += ncfac*dthalf*etap_dot[ich];
-
+
factor_etap = exp(-ncfac*dthalf*etap_dot[0]);
for (i = 0; i < 3; i++)
if (p_flag[i]) omega_dot[i] *= factor_etap;
-
+
if (pstyle == TRICLINIC) {
for (i = 3; i < 6; i++)
- if (p_flag[i]) omega_dot[i] *= factor_etap;
+ if (p_flag[i]) omega_dot[i] *= factor_etap;
}
-
+
kecurrent = 0.0;
for (i = 0; i < 3; i++)
if (p_flag[i]) kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i];
-
+
if (pstyle == TRICLINIC) {
- for (i = 3; i < 6; i++)
- if (p_flag[i]) kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i];
+ for (i = 3; i < 6; i++)
+ if (p_flag[i]) kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i];
}
-
+
etap_dotdot[0] = (kecurrent - lkt_press)/etap_mass[0];
-
+
etap_dot[0] *= expfac;
etap_dot[0] += etap_dotdot[0] * ncfac*dt4;
etap_dot[0] *= expfac;
-
+
for (ich = 1; ich < mpchain; ich++) {
expfac = exp(-ncfac*dt8*etap_dot[ich+1]);
etap_dot[ich] *= expfac;
- etap_dotdot[ich] =
- (etap_mass[ich-1]*etap_dot[ich-1]*etap_dot[ich-1] - boltz*t_target) /
- etap_mass[ich];
+ etap_dotdot[ich] =
+ (etap_mass[ich-1]*etap_dot[ich-1]*etap_dot[ich-1] - boltz*t_target) /
+ etap_mass[ich];
etap_dot[ich] += etap_dotdot[ich] * ncfac*dt4;
etap_dot[ich] *= expfac;
}
@@ -1831,33 +1831,33 @@ void FixNH::nh_v_press()
if (which == NOBIAS) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
- v[i][0] *= factor[0];
- v[i][1] *= factor[1];
- v[i][2] *= factor[2];
- if (pstyle == TRICLINIC) {
- v[i][0] += -dthalf*(v[i][1]*omega_dot[5] + v[i][2]*omega_dot[4]);
- v[i][1] += -dthalf*v[i][2]*omega_dot[3];
- }
- v[i][0] *= factor[0];
- v[i][1] *= factor[1];
- v[i][2] *= factor[2];
+ v[i][0] *= factor[0];
+ v[i][1] *= factor[1];
+ v[i][2] *= factor[2];
+ if (pstyle == TRICLINIC) {
+ v[i][0] += -dthalf*(v[i][1]*omega_dot[5] + v[i][2]*omega_dot[4]);
+ v[i][1] += -dthalf*v[i][2]*omega_dot[3];
+ }
+ v[i][0] *= factor[0];
+ v[i][1] *= factor[1];
+ v[i][2] *= factor[2];
}
}
} else if (which == BIAS) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
- temperature->remove_bias(i,v[i]);
- v[i][0] *= factor[0];
- v[i][1] *= factor[1];
- v[i][2] *= factor[2];
- if (pstyle == TRICLINIC) {
- v[i][0] += -dthalf*(v[i][1]*omega_dot[5] + v[i][2]*omega_dot[4]);
- v[i][1] += -dthalf*v[i][2]*omega_dot[3];
- }
- v[i][0] *= factor[0];
- v[i][1] *= factor[1];
- v[i][2] *= factor[2];
- temperature->restore_bias(i,v[i]);
+ temperature->remove_bias(i,v[i]);
+ v[i][0] *= factor[0];
+ v[i][1] *= factor[1];
+ v[i][2] *= factor[2];
+ if (pstyle == TRICLINIC) {
+ v[i][0] += -dthalf*(v[i][1]*omega_dot[5] + v[i][2]*omega_dot[4]);
+ v[i][1] += -dthalf*v[i][2]*omega_dot[3];
+ }
+ v[i][0] *= factor[0];
+ v[i][1] *= factor[1];
+ v[i][2] *= factor[2];
+ temperature->restore_bias(i,v[i]);
}
}
}
@@ -1882,19 +1882,19 @@ void FixNH::nve_v()
if (rmass) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
- dtfm = dtf / rmass[i];
- v[i][0] += dtfm*f[i][0];
- v[i][1] += dtfm*f[i][1];
- v[i][2] += dtfm*f[i][2];
+ dtfm = dtf / rmass[i];
+ v[i][0] += dtfm*f[i][0];
+ v[i][1] += dtfm*f[i][1];
+ v[i][2] += dtfm*f[i][2];
}
}
} else {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
- dtfm = dtf / mass[type[i]];
- v[i][0] += dtfm*f[i][0];
- v[i][1] += dtfm*f[i][1];
- v[i][2] += dtfm*f[i][2];
+ dtfm = dtf / mass[type[i]];
+ v[i][0] += dtfm*f[i][0];
+ v[i][1] += dtfm*f[i][1];
+ v[i][2] += dtfm*f[i][2];
}
}
}
@@ -1937,24 +1937,24 @@ void FixNH::nh_v_temp()
if (which == NOBIAS) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
- v[i][0] *= factor_eta;
- v[i][1] *= factor_eta;
- v[i][2] *= factor_eta;
+ v[i][0] *= factor_eta;
+ v[i][1] *= factor_eta;
+ v[i][2] *= factor_eta;
}
}
} else if (which == BIAS) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
- temperature->remove_bias(i,v[i]);
- v[i][0] *= factor_eta;
- v[i][1] *= factor_eta;
- v[i][2] *= factor_eta;
- temperature->restore_bias(i,v[i]);
+ temperature->remove_bias(i,v[i]);
+ v[i][0] *= factor_eta;
+ v[i][1] *= factor_eta;
+ v[i][2] *= factor_eta;
+ temperature->restore_bias(i,v[i]);
}
}
}
}
-
+
/* ----------------------------------------------------------------------
compute sigma tensor
needed whenever p_target or h0_inv changes
@@ -1962,7 +1962,7 @@ void FixNH::nh_v_temp()
void FixNH::compute_sigma()
{
- // if nreset_h0 > 0, reset vol0 and h0_inv
+ // if nreset_h0 > 0, reset vol0 and h0_inv
// every nreset_h0 timesteps
if (nreset_h0 > 0) {
@@ -1981,37 +1981,37 @@ void FixNH::compute_sigma()
// generate upper-triangular half of
// sigma = vol0*h0inv*(p_target-p_hydro)*h0inv^t
- // units of sigma are are PV/L^2 e.g. atm.A
+ // units of sigma are are PV/L^2 e.g. atm.A
//
// [ 0 5 4 ] [ 0 5 4 ] [ 0 5 4 ] [ 0 - - ]
// [ 5 1 3 ] = [ - 1 3 ] [ 5 1 3 ] [ 5 1 - ]
// [ 4 3 2 ] [ - - 2 ] [ 4 3 2 ] [ 4 3 2 ]
- sigma[0] =
+ sigma[0] =
vol0*(h0_inv[0]*((p_target[0]-p_hydro)*h0_inv[0] +
- p_target[5]*h0_inv[5]+p_target[4]*h0_inv[4]) +
- h0_inv[5]*(p_target[5]*h0_inv[0] +
- (p_target[1]-p_hydro)*h0_inv[5]+p_target[3]*h0_inv[4]) +
- h0_inv[4]*(p_target[4]*h0_inv[0]+p_target[3]*h0_inv[5] +
- (p_target[2]-p_hydro)*h0_inv[4]));
- sigma[1] =
+ p_target[5]*h0_inv[5]+p_target[4]*h0_inv[4]) +
+ h0_inv[5]*(p_target[5]*h0_inv[0] +
+ (p_target[1]-p_hydro)*h0_inv[5]+p_target[3]*h0_inv[4]) +
+ h0_inv[4]*(p_target[4]*h0_inv[0]+p_target[3]*h0_inv[5] +
+ (p_target[2]-p_hydro)*h0_inv[4]));
+ sigma[1] =
vol0*(h0_inv[1]*((p_target[1]-p_hydro)*h0_inv[1] +
- p_target[3]*h0_inv[3]) +
- h0_inv[3]*(p_target[3]*h0_inv[1] +
- (p_target[2]-p_hydro)*h0_inv[3]));
- sigma[2] =
+ p_target[3]*h0_inv[3]) +
+ h0_inv[3]*(p_target[3]*h0_inv[1] +
+ (p_target[2]-p_hydro)*h0_inv[3]));
+ sigma[2] =
vol0*(h0_inv[2]*((p_target[2]-p_hydro)*h0_inv[2]));
- sigma[3] =
+ sigma[3] =
vol0*(h0_inv[1]*(p_target[3]*h0_inv[2]) +
- h0_inv[3]*((p_target[2]-p_hydro)*h0_inv[2]));
- sigma[4] =
+ h0_inv[3]*((p_target[2]-p_hydro)*h0_inv[2]));
+ sigma[4] =
vol0*(h0_inv[0]*(p_target[4]*h0_inv[2]) +
- h0_inv[5]*(p_target[3]*h0_inv[2]) +
- h0_inv[4]*((p_target[2]-p_hydro)*h0_inv[2]));
- sigma[5] =
+ h0_inv[5]*(p_target[3]*h0_inv[2]) +
+ h0_inv[4]*((p_target[2]-p_hydro)*h0_inv[2]));
+ sigma[5] =
vol0*(h0_inv[0]*(p_target[5]*h0_inv[1]+p_target[4]*h0_inv[3]) +
- h0_inv[5]*((p_target[1]-p_hydro)*h0_inv[1]+p_target[3]*h0_inv[3]) +
- h0_inv[4]*(p_target[3]*h0_inv[1]+(p_target[2]-p_hydro)*h0_inv[3]));
+ h0_inv[5]*((p_target[1]-p_hydro)*h0_inv[1]+p_target[3]*h0_inv[3]) +
+ h0_inv[4]*(p_target[3]*h0_inv[1]+(p_target[2]-p_hydro)*h0_inv[3]));
}
/* ----------------------------------------------------------------------
@@ -2020,20 +2020,20 @@ void FixNH::compute_sigma()
double FixNH::compute_strain_energy()
{
- // compute strain energy = 0.5*Tr(sigma*h*h^t) in energy units
+ // compute strain energy = 0.5*Tr(sigma*h*h^t) in energy units
double* h = domain->h;
double d0,d1,d2;
- d0 =
+ d0 =
sigma[0]*(h[0]*h[0]+h[5]*h[5]+h[4]*h[4]) +
sigma[5]*( h[1]*h[5]+h[3]*h[4]) +
sigma[4]*( h[2]*h[4]);
- d1 =
+ d1 =
sigma[5]*( h[5]*h[1]+h[4]*h[3]) +
sigma[1]*( h[1]*h[1]+h[3]*h[3]) +
sigma[3]*( h[2]*h[3]);
- d2 =
+ d2 =
sigma[4]*( h[4]*h[2]) +
sigma[3]*( h[3]*h[2]) +
sigma[2]*( h[2]*h[2]);
@@ -2049,30 +2049,30 @@ double FixNH::compute_strain_energy()
void FixNH::compute_deviatoric()
{
// generate upper-triangular part of h*sigma*h^t
- // units of fdev are are PV, e.g. atm*A^3
+ // units of fdev are are PV, e.g. atm*A^3
// [ 0 5 4 ] [ 0 5 4 ] [ 0 5 4 ] [ 0 - - ]
// [ 5 1 3 ] = [ - 1 3 ] [ 5 1 3 ] [ 5 1 - ]
// [ 4 3 2 ] [ - - 2 ] [ 4 3 2 ] [ 4 3 2 ]
-
+
double* h = domain->h;
-
- fdev[0] =
+
+ fdev[0] =
h[0]*(sigma[0]*h[0]+sigma[5]*h[5]+sigma[4]*h[4]) +
h[5]*(sigma[5]*h[0]+sigma[1]*h[5]+sigma[3]*h[4]) +
h[4]*(sigma[4]*h[0]+sigma[3]*h[5]+sigma[2]*h[4]);
- fdev[1] =
+ fdev[1] =
h[1]*( sigma[1]*h[1]+sigma[3]*h[3]) +
h[3]*( sigma[3]*h[1]+sigma[2]*h[3]);
- fdev[2] =
+ fdev[2] =
h[2]*( sigma[2]*h[2]);
- fdev[3] =
+ fdev[3] =
h[1]*( sigma[3]*h[2]) +
h[3]*( sigma[2]*h[2]);
- fdev[4] =
+ fdev[4] =
h[0]*( sigma[4]*h[2]) +
h[5]*( sigma[3]*h[2]) +
h[4]*( sigma[2]*h[2]);
- fdev[5] =
+ fdev[5] =
h[0]*( sigma[5]*h[1]+sigma[4]*h[3]) +
h[5]*( sigma[1]*h[1]+sigma[3]*h[3]) +
h[4]*( sigma[3]*h[1]+sigma[2]*h[3]);
@@ -2088,7 +2088,7 @@ void FixNH::compute_temp_target()
if (update->endstep > update->beginstep)
delta /= update->endstep - update->beginstep;
else delta = 0.0;
-
+
t_target = t_start + delta * (t_stop-t_start);
ke_target = tdof * boltz * t_target;
}
@@ -2103,7 +2103,7 @@ void FixNH::compute_press_target()
if (update->endstep > update->beginstep)
delta /= update->endstep - update->beginstep;
else delta = 0.0;
-
+
p_hydro = 0.0;
for (int i = 0; i < 3; i++)
if (p_flag[i]) {
@@ -2136,21 +2136,21 @@ void FixNH::nh_omega_dot()
mtk_term1 = 0.0;
if (mtk_flag)
- if (pstyle == ISO) {
+ if (pstyle == ISO) {
mtk_term1 = tdof * boltz * t_current;
mtk_term1 /= pdim * atom->natoms;
} else {
double *mvv_current = temperature->vector;
for (int i = 0; i < 3; i++)
- if (p_flag[i])
- mtk_term1 += mvv_current[i];
+ if (p_flag[i])
+ mtk_term1 += mvv_current[i];
mtk_term1 /= pdim * atom->natoms;
}
-
+
for (int i = 0; i < 3; i++)
if (p_flag[i]) {
f_omega = (p_current[i]-p_hydro)*volume /
- (omega_mass[i] * nktv2p) + mtk_term1 / omega_mass[i];
+ (omega_mass[i] * nktv2p) + mtk_term1 / omega_mass[i];
if (deviatoric_flag) f_omega -= fdev[i]/(omega_mass[i] * nktv2p);
omega_dot[i] += f_omega*dthalf;
omega_dot[i] *= pdrag_factor;
@@ -2160,20 +2160,20 @@ void FixNH::nh_omega_dot()
if (mtk_flag) {
for (int i = 0; i < 3; i++)
if (p_flag[i])
- mtk_term2 += omega_dot[i];
+ mtk_term2 += omega_dot[i];
mtk_term2 /= pdim * atom->natoms;
}
if (pstyle == TRICLINIC) {
for (int i = 3; i < 6; i++) {
if (p_flag[i]) {
- f_omega = p_current[i]*volume/(omega_mass[i] * nktv2p);
- if (deviatoric_flag)
- f_omega -= fdev[i]/(omega_mass[i] * nktv2p);
- omega_dot[i] += f_omega*dthalf;
- omega_dot[i] *= pdrag_factor;
+ f_omega = p_current[i]*volume/(omega_mass[i] * nktv2p);
+ if (deviatoric_flag)
+ f_omega -= fdev[i]/(omega_mass[i] * nktv2p);
+ omega_dot[i] += f_omega*dthalf;
+ omega_dot[i] *= pdrag_factor;
}
- }
+ }
}
}
diff --git a/src/fix_nh.h b/src/fix_nh.h
index e87b6958987bcbd41d586081290eeffe304c9a3d..819260c1d118bceea5b3d315db4aecae6b827c6e 100644
--- a/src/fix_nh.h
+++ b/src/fix_nh.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -45,7 +45,7 @@ class FixNH : public Fix {
double dtv,dtf,dthalf,dt4,dt8,dto;
double boltz,nktv2p,tdof;
double vol0; // reference volume
- double t0; // reference temperature
+ double t0; // reference temperature
// used for barostat mass
double t_start,t_stop;
double t_current,t_target,ke_target;
@@ -81,14 +81,14 @@ class FixNH : public Fix {
double *eta_dotdot;
double *eta_mass;
int mtchain; // length of chain
- int mtchain_default_flag; // 1 = mtchain is default
-
+ int mtchain_default_flag; // 1 = mtchain is default
+
double *etap; // chain thermostat for barostat
double *etap_dot;
double *etap_dotdot;
double *etap_mass;
int mpchain; // length of chain
-
+
int mtk_flag; // 0 if using Hoover barostat
int pdim; // number of barostatted dims
double p_freq_max; // maximum barostat frequency
@@ -109,9 +109,9 @@ class FixNH : public Fix {
int omega_mass_flag; // 1 if omega_mass updated, 0 if not.
int etap_mass_flag; // 1 if etap_mass updated, 0 if not.
- int scaleyz; // 1 if yz scaled with lz
- int scalexz; // 1 if xz scaled with lz
- int scalexy; // 1 if xy scaled with ly
+ int scaleyz; // 1 if yz scaled with lz
+ int scalexz; // 1 if xz scaled with lz
+ int scalexy; // 1 if xy scaled with ly
double fixedpoint[3]; // Location of dilation fixed-point
diff --git a/src/fix_nh_sphere.cpp b/src/fix_nh_sphere.cpp
index 53805080974208a355d0ba15e187f56107926363..c6a09f29546382576b5a14b9359a02daff2bea57 100644
--- a/src/fix_nh_sphere.cpp
+++ b/src/fix_nh_sphere.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -50,7 +50,7 @@ void FixNHSphere::init()
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (radius[i] == 0.0)
- error->one(FLERR,"Fix nvt/sphere requires extended particles");
+ error->one(FLERR,"Fix nvt/sphere requires extended particles");
FixNH::init();
}
@@ -106,7 +106,7 @@ void FixNHSphere::nh_v_temp()
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
- for (int i = 0; i < nlocal; i++) {
+ for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
omega[i][0] *= factor_eta;
omega[i][1] *= factor_eta;
diff --git a/src/fix_nh_sphere.h b/src/fix_nh_sphere.h
index ed360a23c87c94a7c0a94cba24b5e0d39330a97f..126f04005458e80f646f2e4733c583425ae570bd 100644
--- a/src/fix_nh_sphere.h
+++ b/src/fix_nh_sphere.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_nph.cpp b/src/fix_nph.cpp
index b9e0f9e2238c955883d6e7de49b7f172adaa83b8..419a6980a02e5d8fda090cb54f329970cdb68a54 100644
--- a/src/fix_nph.cpp
+++ b/src/fix_nph.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -38,7 +38,7 @@ FixNPH::FixNPH(LAMMPS *lmp, int narg, char **arg) :
id_temp = new char[n];
strcpy(id_temp,id);
strcat(id_temp,"_temp");
-
+
char **newarg = new char*[3];
newarg[0] = id_temp;
newarg[1] = (char *) "all";
@@ -56,7 +56,7 @@ FixNPH::FixNPH(LAMMPS *lmp, int narg, char **arg) :
id_press = new char[n];
strcpy(id_press,id);
strcat(id_press,"_press");
-
+
newarg = new char*[4];
newarg[0] = id_press;
newarg[1] = (char *) "all";
diff --git a/src/fix_nph.h b/src/fix_nph.h
index a42d7f087c049f5ed7486b95b8a803a55ade4e8e..c9ff742dc8c16d3f12ef726617653192bcc1769c 100644
--- a/src/fix_nph.h
+++ b/src/fix_nph.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_nph_sphere.cpp b/src/fix_nph_sphere.cpp
index cdc7801cf51d84b5e52822a3bd66c85febaf5c0b..2c87e6b34f33559f689505a0db7db2a2fe55327c 100644
--- a/src/fix_nph_sphere.cpp
+++ b/src/fix_nph_sphere.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -38,7 +38,7 @@ FixNPHSphere::FixNPHSphere(LAMMPS *lmp, int narg, char **arg) :
id_temp = new char[n];
strcpy(id_temp,id);
strcat(id_temp,"_temp");
-
+
char **newarg = new char*[3];
newarg[0] = id_temp;
newarg[1] = (char *) "all";
@@ -56,7 +56,7 @@ FixNPHSphere::FixNPHSphere(LAMMPS *lmp, int narg, char **arg) :
id_press = new char[n];
strcpy(id_press,id);
strcat(id_press,"_press");
-
+
newarg = new char*[4];
newarg[0] = id_press;
newarg[1] = (char *) "all";
diff --git a/src/fix_nph_sphere.h b/src/fix_nph_sphere.h
index db8d5d743e57b35a236b9f6005becf1b078c30a5..dd75f6b3fd4e35ce8a4dd34caa533fd00ca17c41 100644
--- a/src/fix_nph_sphere.h
+++ b/src/fix_nph_sphere.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_npt.cpp b/src/fix_npt.cpp
index a412bc9c6fc457dd782ae93532fb7b48426bdbf4..cf83ded491fa2a1f2ebe00bf406c3fe457a9d8c5 100644
--- a/src/fix_npt.cpp
+++ b/src/fix_npt.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -38,7 +38,7 @@ FixNPT::FixNPT(LAMMPS *lmp, int narg, char **arg) :
id_temp = new char[n];
strcpy(id_temp,id);
strcat(id_temp,"_temp");
-
+
char **newarg = new char*[3];
newarg[0] = id_temp;
newarg[1] = (char *) "all";
@@ -56,7 +56,7 @@ FixNPT::FixNPT(LAMMPS *lmp, int narg, char **arg) :
id_press = new char[n];
strcpy(id_press,id);
strcat(id_press,"_press");
-
+
newarg = new char*[4];
newarg[0] = id_press;
newarg[1] = (char *) "all";
diff --git a/src/fix_npt.h b/src/fix_npt.h
index 6cdd1b37c0ef0deb5038e8a17bf42e9b88281a9f..75d6c26f29dea8aeffb4b7668584984dda520713 100644
--- a/src/fix_npt.h
+++ b/src/fix_npt.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_npt_sphere.cpp b/src/fix_npt_sphere.cpp
index 4fafcccbb5d90367e824f68512d91bd1c0428ee0..81c0e3c799b524625ff7be7bbe1299a407bfee17 100644
--- a/src/fix_npt_sphere.cpp
+++ b/src/fix_npt_sphere.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -38,7 +38,7 @@ FixNPTSphere::FixNPTSphere(LAMMPS *lmp, int narg, char **arg) :
id_temp = new char[n];
strcpy(id_temp,id);
strcat(id_temp,"_temp");
-
+
char **newarg = new char*[3];
newarg[0] = id_temp;
newarg[1] = (char *) "all";
@@ -56,7 +56,7 @@ FixNPTSphere::FixNPTSphere(LAMMPS *lmp, int narg, char **arg) :
id_press = new char[n];
strcpy(id_press,id);
strcat(id_press,"_press");
-
+
newarg = new char*[4];
newarg[0] = id_press;
newarg[1] = (char *) "all";
diff --git a/src/fix_npt_sphere.h b/src/fix_npt_sphere.h
index efcd47b2ad4914ba4a7df4b34a69194a8d9fe794..06522716cd7f699f6fc4c2b7de92f5f9cc7fcf5e 100644
--- a/src/fix_npt_sphere.h
+++ b/src/fix_npt_sphere.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_nve.cpp b/src/fix_nve.cpp
index cf4044ab07c4bb57ebc587d4fd948949130fb771..d1431a4e8de5dc5f172bfc2bef6ec1f7a8dd8667 100644
--- a/src/fix_nve.cpp
+++ b/src/fix_nve.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -80,25 +80,25 @@ void FixNVE::initial_integrate(int vflag)
if (rmass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- dtfm = dtf / rmass[i];
- v[i][0] += dtfm * f[i][0];
- v[i][1] += dtfm * f[i][1];
- v[i][2] += dtfm * f[i][2];
- x[i][0] += dtv * v[i][0];
- x[i][1] += dtv * v[i][1];
- x[i][2] += dtv * v[i][2];
+ dtfm = dtf / rmass[i];
+ v[i][0] += dtfm * f[i][0];
+ v[i][1] += dtfm * f[i][1];
+ v[i][2] += dtfm * f[i][2];
+ x[i][0] += dtv * v[i][0];
+ x[i][1] += dtv * v[i][1];
+ x[i][2] += dtv * v[i][2];
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- dtfm = dtf / mass[type[i]];
- v[i][0] += dtfm * f[i][0];
- v[i][1] += dtfm * f[i][1];
- v[i][2] += dtfm * f[i][2];
- x[i][0] += dtv * v[i][0];
- x[i][1] += dtv * v[i][1];
- x[i][2] += dtv * v[i][2];
+ dtfm = dtf / mass[type[i]];
+ v[i][0] += dtfm * f[i][0];
+ v[i][1] += dtfm * f[i][1];
+ v[i][2] += dtfm * f[i][2];
+ x[i][0] += dtv * v[i][0];
+ x[i][1] += dtv * v[i][1];
+ x[i][2] += dtv * v[i][2];
}
}
}
@@ -123,19 +123,19 @@ void FixNVE::final_integrate()
if (rmass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- dtfm = dtf / rmass[i];
- v[i][0] += dtfm * f[i][0];
- v[i][1] += dtfm * f[i][1];
- v[i][2] += dtfm * f[i][2];
+ dtfm = dtf / rmass[i];
+ v[i][0] += dtfm * f[i][0];
+ v[i][1] += dtfm * f[i][1];
+ v[i][2] += dtfm * f[i][2];
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- dtfm = dtf / mass[type[i]];
- v[i][0] += dtfm * f[i][0];
- v[i][1] += dtfm * f[i][1];
- v[i][2] += dtfm * f[i][2];
+ dtfm = dtf / mass[type[i]];
+ v[i][0] += dtfm * f[i][0];
+ v[i][1] += dtfm * f[i][1];
+ v[i][2] += dtfm * f[i][2];
}
}
}
diff --git a/src/fix_nve.h b/src/fix_nve.h
index 838f79b995bc7b09eb3c6805772850f002aae4ab..9e8dd06fbda65a7f2966c3c2802023dd1315a6e8 100644
--- a/src/fix_nve.h
+++ b/src/fix_nve.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_nve_limit.cpp b/src/fix_nve_limit.cpp
index 8a47113f3c8a3359c51fb29489dc94399ba681a0..13cf5580025b264e360b402f57683d023d63dc41 100644
--- a/src/fix_nve_limit.cpp
+++ b/src/fix_nve_limit.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -88,46 +88,46 @@ void FixNVELimit::initial_integrate(int vflag)
if (rmass) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
- dtfm = dtf / rmass[i];
- v[i][0] += dtfm * f[i][0];
- v[i][1] += dtfm * f[i][1];
- v[i][2] += dtfm * f[i][2];
-
- vsq = v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2];
- if (vsq > vlimitsq) {
- ncount++;
- scale = sqrt(vlimitsq/vsq);
- v[i][0] *= scale;
- v[i][1] *= scale;
- v[i][2] *= scale;
- }
-
- x[i][0] += dtv * v[i][0];
- x[i][1] += dtv * v[i][1];
- x[i][2] += dtv * v[i][2];
+ dtfm = dtf / rmass[i];
+ v[i][0] += dtfm * f[i][0];
+ v[i][1] += dtfm * f[i][1];
+ v[i][2] += dtfm * f[i][2];
+
+ vsq = v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2];
+ if (vsq > vlimitsq) {
+ ncount++;
+ scale = sqrt(vlimitsq/vsq);
+ v[i][0] *= scale;
+ v[i][1] *= scale;
+ v[i][2] *= scale;
+ }
+
+ x[i][0] += dtv * v[i][0];
+ x[i][1] += dtv * v[i][1];
+ x[i][2] += dtv * v[i][2];
}
}
} else {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
- dtfm = dtf / mass[type[i]];
- v[i][0] += dtfm * f[i][0];
- v[i][1] += dtfm * f[i][1];
- v[i][2] += dtfm * f[i][2];
-
- vsq = v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2];
- if (vsq > vlimitsq) {
- ncount++;
- scale = sqrt(vlimitsq/vsq);
- v[i][0] *= scale;
- v[i][1] *= scale;
- v[i][2] *= scale;
- }
-
- x[i][0] += dtv * v[i][0];
- x[i][1] += dtv * v[i][1];
- x[i][2] += dtv * v[i][2];
+ dtfm = dtf / mass[type[i]];
+ v[i][0] += dtfm * f[i][0];
+ v[i][1] += dtfm * f[i][1];
+ v[i][2] += dtfm * f[i][2];
+
+ vsq = v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2];
+ if (vsq > vlimitsq) {
+ ncount++;
+ scale = sqrt(vlimitsq/vsq);
+ v[i][0] *= scale;
+ v[i][1] *= scale;
+ v[i][2] *= scale;
+ }
+
+ x[i][0] += dtv * v[i][0];
+ x[i][1] += dtv * v[i][1];
+ x[i][2] += dtv * v[i][2];
}
}
}
@@ -151,38 +151,38 @@ void FixNVELimit::final_integrate()
if (rmass) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
- dtfm = dtf / rmass[i];
- v[i][0] += dtfm * f[i][0];
- v[i][1] += dtfm * f[i][1];
- v[i][2] += dtfm * f[i][2];
-
- vsq = v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2];
- if (vsq > vlimitsq) {
- ncount++;
- scale = sqrt(vlimitsq/vsq);
- v[i][0] *= scale;
- v[i][1] *= scale;
- v[i][2] *= scale;
- }
+ dtfm = dtf / rmass[i];
+ v[i][0] += dtfm * f[i][0];
+ v[i][1] += dtfm * f[i][1];
+ v[i][2] += dtfm * f[i][2];
+
+ vsq = v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2];
+ if (vsq > vlimitsq) {
+ ncount++;
+ scale = sqrt(vlimitsq/vsq);
+ v[i][0] *= scale;
+ v[i][1] *= scale;
+ v[i][2] *= scale;
+ }
}
}
} else {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
- dtfm = dtf / mass[type[i]];
- v[i][0] += dtfm * f[i][0];
- v[i][1] += dtfm * f[i][1];
- v[i][2] += dtfm * f[i][2];
-
- vsq = v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2];
- if (vsq > vlimitsq) {
- ncount++;
- scale = sqrt(vlimitsq/vsq);
- v[i][0] *= scale;
- v[i][1] *= scale;
- v[i][2] *= scale;
- }
+ dtfm = dtf / mass[type[i]];
+ v[i][0] += dtfm * f[i][0];
+ v[i][1] += dtfm * f[i][1];
+ v[i][2] += dtfm * f[i][2];
+
+ vsq = v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2];
+ if (vsq > vlimitsq) {
+ ncount++;
+ scale = sqrt(vlimitsq/vsq);
+ v[i][0] *= scale;
+ v[i][1] *= scale;
+ v[i][2] *= scale;
+ }
}
}
}
diff --git a/src/fix_nve_limit.h b/src/fix_nve_limit.h
index 68927155d71e91256f154debe3e3fe5c5b0ad854..0ab45afaad050149cba8143ccf0eda020c9337e3 100644
--- a/src/fix_nve_limit.h
+++ b/src/fix_nve_limit.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_nve_noforce.cpp b/src/fix_nve_noforce.cpp
index ffffd0123561df13e5ac20f14d723be0cbeddd06..e373e00b197997aeacb10a30252737da10a5d46c 100644
--- a/src/fix_nve_noforce.cpp
+++ b/src/fix_nve_noforce.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_nve_noforce.h b/src/fix_nve_noforce.h
index 29d198564a3a3e1d63aa4f382e76c3f2c73cacfd..92452f7b1a5dd3215b9290e493cdb098ed9c7250 100644
--- a/src/fix_nve_noforce.h
+++ b/src/fix_nve_noforce.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_nve_sphere.cpp b/src/fix_nve_sphere.cpp
index a3d270155f1908c598827467bb958c3c54aea646..0ad787a27f6d7c451a1103a51d819af3f6adc604 100644
--- a/src/fix_nve_sphere.cpp
+++ b/src/fix_nve_sphere.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -76,7 +76,7 @@ void FixNVESphere::init()
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (radius[i] == 0.0)
- error->one(FLERR,"Fix nve/sphere requires extended particles");
+ error->one(FLERR,"Fix nve/sphere requires extended particles");
}
/* ---------------------------------------------------------------------- */
@@ -113,7 +113,7 @@ void FixNVESphere::initial_integrate(int vflag)
x[i][0] += dtv * v[i][0];
x[i][1] += dtv * v[i][1];
x[i][2] += dtv * v[i][2];
-
+
dtirotate = dtfrotate / (radius[i]*radius[i]*rmass[i]);
omega[i][0] += dtirotate * torque[i][0];
omega[i][1] += dtirotate * torque[i][1];
@@ -129,16 +129,16 @@ void FixNVESphere::initial_integrate(int vflag)
double **mu = atom->mu;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
- if (mu[i][3] > 0.0) {
- g[0] = mu[i][0] + dtv * (omega[i][1]*mu[i][2]-omega[i][2]*mu[i][1]);
- g[1] = mu[i][1] + dtv * (omega[i][2]*mu[i][0]-omega[i][0]*mu[i][2]);
- g[2] = mu[i][2] + dtv * (omega[i][0]*mu[i][1]-omega[i][1]*mu[i][0]);
- msq = g[0]*g[0] + g[1]*g[1] + g[2]*g[2];
- scale = mu[i][3]/sqrt(msq);
- mu[i][0] = g[0]*scale;
- mu[i][1] = g[1]*scale;
- mu[i][2] = g[2]*scale;
- }
+ if (mu[i][3] > 0.0) {
+ g[0] = mu[i][0] + dtv * (omega[i][1]*mu[i][2]-omega[i][2]*mu[i][1]);
+ g[1] = mu[i][1] + dtv * (omega[i][2]*mu[i][0]-omega[i][0]*mu[i][2]);
+ g[2] = mu[i][2] + dtv * (omega[i][0]*mu[i][1]-omega[i][1]*mu[i][0]);
+ msq = g[0]*g[0] + g[1]*g[1] + g[2]*g[2];
+ scale = mu[i][3]/sqrt(msq);
+ mu[i][0] = g[0]*scale;
+ mu[i][1] = g[1]*scale;
+ mu[i][2] = g[2]*scale;
+ }
}
}
@@ -171,7 +171,7 @@ void FixNVESphere::final_integrate()
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
-
+
dtirotate = dtfrotate / (radius[i]*radius[i]*rmass[i]);
omega[i][0] += dtirotate * torque[i][0];
omega[i][1] += dtirotate * torque[i][1];
diff --git a/src/fix_nve_sphere.h b/src/fix_nve_sphere.h
index 4fbb0bfcced225c434e5c88d80b3caac33a3834b..1938b0f855c7eebd4921e9d8bca3d7e6a6003af0 100644
--- a/src/fix_nve_sphere.h
+++ b/src/fix_nve_sphere.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_nvt.cpp b/src/fix_nvt.cpp
index c7d7f054e8fedd804da784e8df8f7663b726a53a..839b7ce0a3b3d0651239db49a68361eb90a4dcca 100644
--- a/src/fix_nvt.cpp
+++ b/src/fix_nvt.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -37,7 +37,7 @@ FixNVT::FixNVT(LAMMPS *lmp, int narg, char **arg) :
id_temp = new char[n];
strcpy(id_temp,id);
strcat(id_temp,"_temp");
-
+
char **newarg = new char*[3];
newarg[0] = id_temp;
newarg[1] = group->names[igroup];
diff --git a/src/fix_nvt.h b/src/fix_nvt.h
index e0aa289a473add59d3979d2477e21604477e684e..3f2df5f72f90ceefffd0c32f55693fac9a69443d 100644
--- a/src/fix_nvt.h
+++ b/src/fix_nvt.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_nvt_sllod.cpp b/src/fix_nvt_sllod.cpp
index a18787f17765d0b3dbd8634bf601eb538f0c79ec..460ba7a39399a59c1e9f2ffd4b0dbc96015bbbef 100644
--- a/src/fix_nvt_sllod.cpp
+++ b/src/fix_nvt_sllod.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -55,7 +55,7 @@ FixNVTSllod::FixNVTSllod(LAMMPS *lmp, int narg, char **arg) :
id_temp = new char[n];
strcpy(id_temp,id);
strcat(id_temp,"_temp");
-
+
char **newarg = new char*[3];
newarg[0] = id_temp;
newarg[1] = group->names[igroup];
@@ -84,8 +84,8 @@ void FixNVTSllod::init()
for (i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"deform") == 0) {
if (((FixDeform *) modify->fix[i])->remapflag != V_REMAP)
- error->all(FLERR,"Using fix nvt/sllod with inconsistent fix deform "
- "remap option");
+ error->all(FLERR,"Using fix nvt/sllod with inconsistent fix deform "
+ "remap option");
break;
}
if (i == modify->nfix)
diff --git a/src/fix_nvt_sllod.h b/src/fix_nvt_sllod.h
index a95065f8b7f263c2df36e34537a0276316f1c847..77911b0b89a0317421ed8741cff49967edea7f2f 100644
--- a/src/fix_nvt_sllod.h
+++ b/src/fix_nvt_sllod.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_nvt_sphere.cpp b/src/fix_nvt_sphere.cpp
index b90fc23ffc3e8975937610cfb1f82ae71202e0c2..58dbbb782c6f953a717a12683e397c9e494b468e 100644
--- a/src/fix_nvt_sphere.cpp
+++ b/src/fix_nvt_sphere.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -37,7 +37,7 @@ FixNVTSphere::FixNVTSphere(LAMMPS *lmp, int narg, char **arg) :
id_temp = new char[n];
strcpy(id_temp,id);
strcat(id_temp,"_temp");
-
+
char **newarg = new char*[3];
newarg[0] = id_temp;
newarg[1] = group->names[igroup];
diff --git a/src/fix_nvt_sphere.h b/src/fix_nvt_sphere.h
index daf1cc9225ce51a32f6a4ac44bb466875a7599cd..15eaeff1155ebc0f33708e7208480f69a64c177b 100644
--- a/src/fix_nvt_sphere.h
+++ b/src/fix_nvt_sphere.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_orient_fcc.cpp b/src/fix_orient_fcc.cpp
index e9f4c8fbdeb6e08f8c23b7ba4a60b83cf9cfd119..5f8193c10f58cdda4108ae76dde39d5e5e4c9391 100644
--- a/src/fix_orient_fcc.cpp
+++ b/src/fix_orient_fcc.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -50,7 +50,7 @@ FixOrientFCC::FixOrientFCC(LAMMPS *lmp, int narg, char **arg) :
scalar_flag = 1;
global_freq = 1;
extscalar = 1;
-
+
peratom_flag = 1;
size_peratom_cols = 2;
peratom_freq = 1;
@@ -297,27 +297,27 @@ void FixOrientFCC::post_force(int vflag)
rsq = dx*dx + dy*dy + dz*dz;
if (rsq < cutsq) {
- sort[nsort].id = j;
- sort[nsort].rsq = rsq;
- sort[nsort].delta[0] = dx;
- sort[nsort].delta[1] = dy;
- sort[nsort].delta[2] = dz;
- if (use_xismooth) {
- xismooth = (xicutoffsq - 2.0*rsq/(a*a)) / (xicutoffsq - 1.0);
- sort[nsort].xismooth = 1.0 - fabs(1.0-xismooth);
- }
- nsort++;
+ sort[nsort].id = j;
+ sort[nsort].rsq = rsq;
+ sort[nsort].delta[0] = dx;
+ sort[nsort].delta[1] = dy;
+ sort[nsort].delta[2] = dz;
+ if (use_xismooth) {
+ xismooth = (xicutoffsq - 2.0*rsq/(a*a)) / (xicutoffsq - 1.0);
+ sort[nsort].xismooth = 1.0 - fabs(1.0-xismooth);
+ }
+ nsort++;
}
}
// sort neighbors by rsq distance
// no need to sort if nsort <= 12
-
+
if (nsort > 12) qsort(sort,nsort,sizeof(Sort),compare);
// copy up to 12 nearest neighbors into nbr data structure
// operate on delta vector via find_best_ref() to compute dxi
-
+
n = MIN(12,nsort);
nbr[i].n = n;
if (n == 0) continue;
@@ -353,9 +353,9 @@ void FixOrientFCC::post_force(int vflag)
}
added_energy += edelta;
}
-
+
if (maxcount) delete [] sort;
-
+
// communicate to acquire nbr data for ghost atoms
comm->forward_comm_fix(this);
@@ -372,12 +372,12 @@ void FixOrientFCC::post_force(int vflag)
for (j = 0; j < n; j++) {
dxiptr = &nbr[i].dxi[j][0];
if (use_xismooth) {
- xismooth = nbr[i].xismooth[j];
+ xismooth = nbr[i].xismooth[j];
f[i][0] += duxi * dxiptr[0] * xismooth;
f[i][1] += duxi * dxiptr[1] * xismooth;
f[i][2] += duxi * dxiptr[2] * xismooth;
} else {
- f[i][0] += duxi * dxiptr[0];
+ f[i][0] += duxi * dxiptr[0];
f[i][1] += duxi * dxiptr[1];
f[i][2] += duxi * dxiptr[2];
}
@@ -387,29 +387,29 @@ void FixOrientFCC::post_force(int vflag)
// if M is local atom, id_self will be local ID of atom I
// if M is ghost atom, id_self will be global ID of atom I
- m = nbr[i].id[j];
+ m = nbr[i].id[j];
if (m < nlocal) id_self = i;
else id_self = tag[i];
found_myself = false;
nn = nbr[m].n;
for (k = 0; k < nn; k++) {
- if (id_self == nbr[m].id[k]) {
- if (found_myself) error->one(FLERR,"Fix orient/fcc found self twice");
- found_myself = true;
- duxi_other = nbr[m].duxi;
- dxiptr = &nbr[m].dxi[k][0];
- if (use_xismooth) {
- xismooth = nbr[m].xismooth[k];
- f[i][0] -= duxi_other * dxiptr[0] * xismooth;
- f[i][1] -= duxi_other * dxiptr[1] * xismooth;
- f[i][2] -= duxi_other * dxiptr[2] * xismooth;
- } else {
- f[i][0] -= duxi_other * dxiptr[0];
- f[i][1] -= duxi_other * dxiptr[1];
- f[i][2] -= duxi_other * dxiptr[2];
- }
- }
+ if (id_self == nbr[m].id[k]) {
+ if (found_myself) error->one(FLERR,"Fix orient/fcc found self twice");
+ found_myself = true;
+ duxi_other = nbr[m].duxi;
+ dxiptr = &nbr[m].dxi[k][0];
+ if (use_xismooth) {
+ xismooth = nbr[m].xismooth[k];
+ f[i][0] -= duxi_other * dxiptr[0] * xismooth;
+ f[i][1] -= duxi_other * dxiptr[1] * xismooth;
+ f[i][2] -= duxi_other * dxiptr[2] * xismooth;
+ } else {
+ f[i][0] -= duxi_other * dxiptr[0];
+ f[i][1] -= duxi_other * dxiptr[1];
+ f[i][2] -= duxi_other * dxiptr[2];
+ }
+ }
}
}
}
@@ -425,21 +425,21 @@ void FixOrientFCC::post_force(int vflag)
MPI_Allreduce(&mincount,&min,1,MPI_INT,MPI_MIN,world);
MPI_Allreduce(&maxcount,&max,1,MPI_INT,MPI_MAX,world);
- if (me == 0) {
+ if (me == 0) {
if (screen) fprintf(screen,
- "orient step " BIGINT_FORMAT ": " BIGINT_FORMAT
- " atoms have %d neighbors\n",
- update->ntimestep,atom->natoms,total);
+ "orient step " BIGINT_FORMAT ": " BIGINT_FORMAT
+ " atoms have %d neighbors\n",
+ update->ntimestep,atom->natoms,total);
if (logfile) fprintf(logfile,
- "orient step " BIGINT_FORMAT ": " BIGINT_FORMAT
- " atoms have %d neighbors\n",
- update->ntimestep,atom->natoms,total);
+ "orient step " BIGINT_FORMAT ": " BIGINT_FORMAT
+ " atoms have %d neighbors\n",
+ update->ntimestep,atom->natoms,total);
if (screen)
- fprintf(screen," neighs: min = %d, max = %d, ave = %g\n",
- min,max,ave);
+ fprintf(screen," neighs: min = %d, max = %d, ave = %g\n",
+ min,max,ave);
if (logfile)
- fprintf(logfile," neighs: min = %d, max = %d, ave = %g\n",
- min,max,ave);
+ fprintf(logfile," neighs: min = %d, max = %d, ave = %g\n",
+ min,max,ave);
}
}
}
@@ -463,7 +463,7 @@ double FixOrientFCC::compute_scalar()
/* ---------------------------------------------------------------------- */
int FixOrientFCC::pack_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int i,j,k,id,num;
int *tag = atom->tag;
@@ -526,8 +526,8 @@ void FixOrientFCC::unpack_comm(int n, int first, double *buf)
/* ---------------------------------------------------------------------- */
-void FixOrientFCC::find_best_ref(double *displs, int which_crystal,
- double &xi_sq, double *dxi)
+void FixOrientFCC::find_best_ref(double *displs, int which_crystal,
+ double &xi_sq, double *dxi)
{
int i;
double dot,tmp;
@@ -557,8 +557,8 @@ void FixOrientFCC::find_best_ref(double *displs, int which_crystal,
if (xi_sq > 0.0) {
double xi = sqrt(xi_sq);
for (i = 0; i < 3; i++)
- dxi[i] = (best_sign * half_xi_chi_vec[which_crystal][best_i][i] -
- displs[i]) / xi;
+ dxi[i] = (best_sign * half_xi_chi_vec[which_crystal][best_i][i] -
+ displs[i]) / xi;
} else dxi[0] = dxi[1] = dxi[2] = 0.0;
}
@@ -581,7 +581,7 @@ int FixOrientFCC::compare(const void *pi, const void *pj)
}
/* ----------------------------------------------------------------------
- memory usage of local atom-based arrays
+ memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double FixOrientFCC::memory_usage()
diff --git a/src/fix_orient_fcc.h b/src/fix_orient_fcc.h
index d565ca47b320258cb6a8c477113f3e46dbb2b238..727be005396f4ea8daff8c4b45c1790b4ba6be58 100644
--- a/src/fix_orient_fcc.h
+++ b/src/fix_orient_fcc.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -36,7 +36,7 @@ class FixOrientFCC : public Fix {
double duxi; // d Energy / d order-parameter for atom
};
- struct Sort { // data structure for sorting to find 12 closest
+ struct Sort { // data structure for sorting to find 12 closest
int id; // ID of neighbor atom
double rsq; // distance between center and neighbor atom
double delta[3]; // displacement between center and neighbor atom
diff --git a/src/fix_planeforce.cpp b/src/fix_planeforce.cpp
index 43fe933c1c35d7343d18fa6f3057c307f88d3a91..7f12590cf4a2a87d1efc7526943cdaa551181804 100644
--- a/src/fix_planeforce.cpp
+++ b/src/fix_planeforce.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_planeforce.h b/src/fix_planeforce.h
index 78c66382da97a00e6dd1b572993f3c7000afc4fa..021078f07751896b5bd5aff081829f9c0f809bff 100644
--- a/src/fix_planeforce.h
+++ b/src/fix_planeforce.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_press_berendsen.cpp b/src/fix_press_berendsen.cpp
index f01e38bf3706d2e612bff2b6677a0177cfa1b56f..e9ffbdfb1cb9d2646fc0952b12e269cc83de2810 100644
--- a/src/fix_press_berendsen.cpp
+++ b/src/fix_press_berendsen.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -68,62 +68,62 @@ FixPressBerendsen::FixPressBerendsen(LAMMPS *lmp, int narg, char **arg) :
while (iarg < narg) {
if (strcmp(arg[iarg],"iso") == 0) {
- if (iarg+4 > narg)
- error->all(FLERR,"Illegal fix press/berendsen command");
+ if (iarg+4 > narg)
+ error->all(FLERR,"Illegal fix press/berendsen command");
pcouple = XYZ;
p_start[0] = p_start[1] = p_start[2] = atof(arg[iarg+1]);
p_stop[0] = p_stop[1] = p_stop[2] = atof(arg[iarg+2]);
p_period[0] = p_period[1] = p_period[2] = atof(arg[iarg+3]);
p_flag[0] = p_flag[1] = p_flag[2] = 1;
if (dimension == 2) {
- p_start[2] = p_stop[2] = p_period[2] = 0.0;
- p_flag[2] = 0;
+ p_start[2] = p_stop[2] = p_period[2] = 0.0;
+ p_flag[2] = 0;
}
- iarg += 4;
+ iarg += 4;
} else if (strcmp(arg[iarg],"aniso") == 0) {
- if (iarg+4 > narg)
- error->all(FLERR,"Illegal fix press/berendsen command");
+ if (iarg+4 > narg)
+ error->all(FLERR,"Illegal fix press/berendsen command");
pcouple = NONE;
p_start[0] = p_start[1] = p_start[2] = atof(arg[iarg+1]);
p_stop[0] = p_stop[1] = p_stop[2] = atof(arg[iarg+2]);
p_period[0] = p_period[1] = p_period[2] = atof(arg[iarg+3]);
p_flag[0] = p_flag[1] = p_flag[2] = 1;
if (dimension == 2) {
- p_start[2] = p_stop[2] = p_period[2] = 0.0;
- p_flag[2] = 0;
+ p_start[2] = p_stop[2] = p_period[2] = 0.0;
+ p_flag[2] = 0;
}
iarg += 4;
} else if (strcmp(arg[iarg],"x") == 0) {
if (iarg+4 > narg)
- error->all(FLERR,"Illegal fix press/berendsen command");
+ error->all(FLERR,"Illegal fix press/berendsen command");
p_start[0] = atof(arg[iarg+1]);
p_stop[0] = atof(arg[iarg+2]);
p_period[0] = atof(arg[iarg+3]);
p_flag[0] = 1;
- iarg += 4;
+ iarg += 4;
} else if (strcmp(arg[iarg],"y") == 0) {
if (iarg+4 > narg)
- error->all(FLERR,"Illegal fix press/berendsen command");
+ error->all(FLERR,"Illegal fix press/berendsen command");
p_start[1] = atof(arg[iarg+1]);
p_stop[1] = atof(arg[iarg+2]);
p_period[1] = atof(arg[iarg+3]);
p_flag[1] = 1;
- iarg += 4;
+ iarg += 4;
} else if (strcmp(arg[iarg],"z") == 0) {
- if (iarg+4 > narg)
- error->all(FLERR,"Illegal fix press/berendsen command");
+ if (iarg+4 > narg)
+ error->all(FLERR,"Illegal fix press/berendsen command");
p_start[2] = atof(arg[iarg+1]);
p_stop[2] = atof(arg[iarg+2]);
p_period[2] = atof(arg[iarg+3]);
p_flag[2] = 1;
- iarg += 4;
+ iarg += 4;
if (dimension == 2)
- error->all(FLERR,"Invalid fix press/berendsen for a 2d simulation");
+ error->all(FLERR,"Invalid fix press/berendsen for a 2d simulation");
} else if (strcmp(arg[iarg],"couple") == 0) {
- if (iarg+2 > narg)
- error->all(FLERR,"Illegal fix press/berendsen command");
+ if (iarg+2 > narg)
+ error->all(FLERR,"Illegal fix press/berendsen command");
if (strcmp(arg[iarg+1],"xyz") == 0) pcouple = XYZ;
else if (strcmp(arg[iarg+1],"xy") == 0) pcouple = XY;
else if (strcmp(arg[iarg+1],"yz") == 0) pcouple = YZ;
@@ -133,15 +133,15 @@ FixPressBerendsen::FixPressBerendsen(LAMMPS *lmp, int narg, char **arg) :
iarg += 2;
} else if (strcmp(arg[iarg],"modulus") == 0) {
- if (iarg+2 > narg)
- error->all(FLERR,"Illegal fix press/berendsen command");
+ if (iarg+2 > narg)
+ error->all(FLERR,"Illegal fix press/berendsen command");
bulkmodulus = atof(arg[iarg+1]);
- if (bulkmodulus <= 0.0)
- error->all(FLERR,"Illegal fix press/berendsen command");
+ if (bulkmodulus <= 0.0)
+ error->all(FLERR,"Illegal fix press/berendsen command");
iarg += 2;
} else if (strcmp(arg[iarg],"dilate") == 0) {
- if (iarg+2 > narg)
- error->all(FLERR,"Illegal fix press/berendsen command");
+ if (iarg+2 > narg)
+ error->all(FLERR,"Illegal fix press/berendsen command");
if (strcmp(arg[iarg+1],"all") == 0) allremap = 1;
else if (strcmp(arg[iarg+1],"partial") == 0) allremap = 0;
else error->all(FLERR,"Illegal fix press/berendsen command");
@@ -171,38 +171,38 @@ FixPressBerendsen::FixPressBerendsen(LAMMPS *lmp, int narg, char **arg) :
if (p_flag[0] && domain->xperiodic == 0)
error->all(FLERR,
- "Cannot use fix press/berendsen on a non-periodic dimension");
+ "Cannot use fix press/berendsen on a non-periodic dimension");
if (p_flag[1] && domain->yperiodic == 0)
error->all(FLERR,
- "Cannot use fix press/berendsen on a non-periodic dimension");
+ "Cannot use fix press/berendsen on a non-periodic dimension");
if (p_flag[2] && domain->zperiodic == 0)
error->all(FLERR,
- "Cannot use fix press/berendsen on a non-periodic dimension");
+ "Cannot use fix press/berendsen on a non-periodic dimension");
if (pcouple == XYZ && dimension == 3 &&
- (p_start[0] != p_start[1] || p_start[0] != p_start[2] ||
- p_stop[0] != p_stop[1] || p_stop[0] != p_stop[2] ||
+ (p_start[0] != p_start[1] || p_start[0] != p_start[2] ||
+ p_stop[0] != p_stop[1] || p_stop[0] != p_stop[2] ||
p_period[0] != p_period[1] || p_period[0] != p_period[2]))
error->all(FLERR,"Invalid fix press/berendsen pressure settings");
if (pcouple == XYZ && dimension == 2 &&
- (p_start[0] != p_start[1] || p_stop[0] != p_stop[1] ||
+ (p_start[0] != p_start[1] || p_stop[0] != p_stop[1] ||
p_period[0] != p_period[1]))
error->all(FLERR,"Invalid fix press/berendsen pressure settings");
- if (pcouple == XY &&
- (p_start[0] != p_start[1] || p_stop[0] != p_stop[1] ||
+ if (pcouple == XY &&
+ (p_start[0] != p_start[1] || p_stop[0] != p_stop[1] ||
p_period[0] != p_period[1]))
error->all(FLERR,"Invalid fix press/berendsen pressure settings");
- if (pcouple == YZ &&
+ if (pcouple == YZ &&
(p_start[1] != p_start[2] || p_stop[1] != p_stop[2] ||
p_period[1] != p_period[2]))
error->all(FLERR,"Invalid fix press/berendsen pressure settings");
- if (pcouple == XZ &&
+ if (pcouple == XZ &&
(p_start[0] != p_start[2] || p_stop[0] != p_stop[2] ||
p_period[0] != p_period[2]))
error->all(FLERR,"Invalid fix press/berendsen pressure settings");
- if ((p_flag[0] && p_period[0] <= 0.0) ||
- (p_flag[1] && p_period[1] <= 0.0) ||
+ if ((p_flag[0] && p_period[0] <= 0.0) ||
+ (p_flag[1] && p_period[1] <= 0.0) ||
(p_flag[2] && p_period[2] <= 0.0))
error->all(FLERR,"Fix press/berendsen damping parameters must be > 0.0");
@@ -279,7 +279,7 @@ int FixPressBerendsen::setmask()
void FixPressBerendsen::init()
{
- if (domain->triclinic)
+ if (domain->triclinic)
error->all(FLERR,"Cannot use fix press/berendsen with triclinic box");
// insure no conflict with fix deform
@@ -287,16 +287,16 @@ void FixPressBerendsen::init()
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"deform") == 0) {
int *dimflag = ((FixDeform *) modify->fix[i])->dimflag;
- if ((p_flag[0] && dimflag[0]) || (p_flag[1] && dimflag[1]) ||
- (p_flag[2] && dimflag[2]))
- error->all(FLERR,"Cannot use fix press/berendsen and "
- "fix deform on same component of stress tensor");
+ if ((p_flag[0] && dimflag[0]) || (p_flag[1] && dimflag[1]) ||
+ (p_flag[2] && dimflag[2]))
+ error->all(FLERR,"Cannot use fix press/berendsen and "
+ "fix deform on same component of stress tensor");
}
// set temperature and pressure ptrs
int icompute = modify->find_compute(id_temp);
- if (icompute < 0)
+ if (icompute < 0)
error->all(FLERR,"Temperature ID for fix press/berendsen does not exist");
temperature = modify->compute[icompute];
@@ -331,7 +331,7 @@ void FixPressBerendsen::init()
}
/* ----------------------------------------------------------------------
- compute T,P before integrator starts
+ compute T,P before integrator starts
------------------------------------------------------------------------- */
void FixPressBerendsen::setup(int vflag)
@@ -362,9 +362,9 @@ void FixPressBerendsen::end_of_step()
for (int i = 0; i < 3; i++) {
if (p_flag[i]) {
p_target[i] = p_start[i] + delta * (p_stop[i]-p_start[i]);
- dilation[i] =
- pow(1.0 - update->dt/p_period[i] *
- (p_target[i]-p_current[i])/bulkmodulus,1.0/3.0);
+ dilation[i] =
+ pow(1.0 - update->dt/p_period[i] *
+ (p_target[i]-p_current[i])/bulkmodulus,1.0/3.0);
}
}
@@ -430,7 +430,7 @@ void FixPressBerendsen::remap()
else {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
- domain->x2lamda(x[i],x[i]);
+ domain->x2lamda(x[i],x[i]);
}
if (nrigid)
@@ -458,7 +458,7 @@ void FixPressBerendsen::remap()
else {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
- domain->lamda2x(x[i],x[i]);
+ domain->lamda2x(x[i],x[i]);
}
if (nrigid)
@@ -491,9 +491,9 @@ int FixPressBerendsen::modify_param(int narg, char **arg)
error->warning(FLERR,"Temperature for NPT is not for group all");
// reset id_temp of pressure to new temperature ID
-
+
icompute = modify->find_compute(id_press);
- if (icompute < 0)
+ if (icompute < 0)
error->all(FLERR,"Pressure ID for fix press/berendsen does not exist");
modify->compute[icompute]->reset_extra_compute_fix(id_temp);
diff --git a/src/fix_press_berendsen.h b/src/fix_press_berendsen.h
index 2caf9ea61cc03b7c61b0f73ba07f87365c0a0fb2..e54e5d35b0953463c5bb661fbffe8bc6c45f13ca 100644
--- a/src/fix_press_berendsen.h
+++ b/src/fix_press_berendsen.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_print.cpp b/src/fix_print.cpp
index 7d2d5116a37259a7d6d3a78bf0952af15f24423f..d422e4b84316ab2f4e5b8d68b53c06fb788627d0 100644
--- a/src/fix_print.cpp
+++ b/src/fix_print.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -51,13 +51,13 @@ FixPrint::FixPrint(LAMMPS *lmp, int narg, char **arg) :
if (strcmp(arg[iarg],"file") == 0 || strcmp(arg[iarg],"append") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix print command");
if (me == 0) {
- if (strcmp(arg[iarg],"file") == 0) fp = fopen(arg[iarg+1],"w");
- else fp = fopen(arg[iarg+1],"a");
- if (fp == NULL) {
- char str[128];
- sprintf(str,"Cannot open fix print file %s",arg[iarg+1]);
- error->one(FLERR,str);
- }
+ if (strcmp(arg[iarg],"file") == 0) fp = fopen(arg[iarg+1],"w");
+ else fp = fopen(arg[iarg+1],"a");
+ if (fp == NULL) {
+ char str[128];
+ sprintf(str,"Cannot open fix print file %s",arg[iarg+1]);
+ error->one(FLERR,str);
+ }
}
iarg += 2;
} else if (strcmp(arg[iarg],"screen") == 0) {
diff --git a/src/fix_print.h b/src/fix_print.h
index c874d2dcde7ee06227fe72e15575aa003ebd57ac..35c18d78f213a36203682f37a993ffeaef6bd4d1 100644
--- a/src/fix_print.h
+++ b/src/fix_print.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_read_restart.cpp b/src/fix_read_restart.cpp
index e4d29a0a3be9ce3d67a82c98c76ed4e8d969e970..30ca3d3acb6b93c87001296c34ce7c877140669c 100644
--- a/src/fix_read_restart.cpp
+++ b/src/fix_read_restart.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -54,7 +54,7 @@ FixReadRestart::FixReadRestart(LAMMPS *lmp, int narg, char **arg) :
FixReadRestart::~FixReadRestart()
{
// unregister callback to this fix from Atom class
-
+
atom->delete_callback(id,0);
// delete locally stored arrays
diff --git a/src/fix_read_restart.h b/src/fix_read_restart.h
index 897fc468a97a569cb74231db1a63e4ae649897d7..4a97d60afd93ce4261888270f8f9a6207bc12236 100644
--- a/src/fix_read_restart.h
+++ b/src/fix_read_restart.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_recenter.cpp b/src/fix_recenter.cpp
index a93c1b7893016fa93086a96ee5fb63d4429920e4..dbdbb197448e25b235145e614f9b662f0ab78ba6 100644
--- a/src/fix_recenter.cpp
+++ b/src/fix_recenter.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_recenter.h b/src/fix_recenter.h
index ea78c09e3d6c17b70a36caaa9321fe492cfe27b5..9b0977787fd3b6ececd06ebf0db6cc69deee5c1d 100644
--- a/src/fix_recenter.h
+++ b/src/fix_recenter.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -66,7 +66,7 @@ Self-explanatory.
W: Fix recenter should come after all other integration fixes
-Other fixes may change the position of the center-of-mass, so
+Other fixes may change the position of the center-of-mass, so
fix recenter should come last.
*/
diff --git a/src/fix_respa.cpp b/src/fix_respa.cpp
index f2fd4d1756f18f57fd57ef0714d56a3d39a51843..3a4afb09c2c0edad9ed0c642600cdc72aa2100ad 100644
--- a/src/fix_respa.cpp
+++ b/src/fix_respa.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -58,7 +58,7 @@ int FixRespa::setmask()
}
/* ----------------------------------------------------------------------
- memory usage of local atom-based arrays
+ memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double FixRespa::memory_usage()
@@ -68,7 +68,7 @@ double FixRespa::memory_usage()
}
/* ----------------------------------------------------------------------
- allocate local atom-based arrays
+ allocate local atom-based arrays
------------------------------------------------------------------------- */
void FixRespa::grow_arrays(int nmax)
@@ -77,7 +77,7 @@ void FixRespa::grow_arrays(int nmax)
}
/* ----------------------------------------------------------------------
- copy values within local atom-based arrays
+ copy values within local atom-based arrays
------------------------------------------------------------------------- */
void FixRespa::copy_arrays(int i, int j)
@@ -90,7 +90,7 @@ void FixRespa::copy_arrays(int i, int j)
}
/* ----------------------------------------------------------------------
- pack values in local atom-based arrays for exchange with another proc
+ pack values in local atom-based arrays for exchange with another proc
------------------------------------------------------------------------- */
int FixRespa::pack_exchange(int i, double *buf)
@@ -105,7 +105,7 @@ int FixRespa::pack_exchange(int i, double *buf)
}
/* ----------------------------------------------------------------------
- unpack values in local atom-based arrays from exchange with another proc
+ unpack values in local atom-based arrays from exchange with another proc
------------------------------------------------------------------------- */
int FixRespa::unpack_exchange(int nlocal, double *buf)
diff --git a/src/fix_respa.h b/src/fix_respa.h
index 74f53f1a6c7d54dbcd55b73d2d91c6dc341c79da..8eb61940289666ee405098ee245e253467b96fc6 100644
--- a/src/fix_respa.h
+++ b/src/fix_respa.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_restrain.cpp b/src/fix_restrain.cpp
index b4af6c45e5f804d77937521c6938b946a9e5925b..1c2080a50e60dc6098901a4c82e4e421854730b1 100644
--- a/src/fix_restrain.cpp
+++ b/src/fix_restrain.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -114,7 +114,7 @@ FixRestrain::FixRestrain(LAMMPS *lmp, int narg, char **arg) :
// require atom map to lookup atom IDs
- if (atom->map_style == 0)
+ if (atom->map_style == 0)
error->all(FLERR,"Fix restrain requires an atom map, see atom_modify");
}
@@ -227,9 +227,9 @@ void FixRestrain::restrain_bond(int m)
if (i1 == -1) {
char str[128];
sprintf(str,
- "Restrain atoms %d %d missing on proc %d at step " BIGINT_FORMAT,
- ids[m][0],ids[m][1],
- comm->me,update->ntimestep);
+ "Restrain atoms %d %d missing on proc %d at step " BIGINT_FORMAT,
+ ids[m][0],ids[m][1],
+ comm->me,update->ntimestep);
error->one(FLERR,str);
}
} else {
@@ -237,38 +237,38 @@ void FixRestrain::restrain_bond(int m)
if (i1 == -1 || i2 == -1) {
char str[128];
sprintf(str,
- "Restrain atoms %d %d missing on proc %d at step " BIGINT_FORMAT,
- ids[m][0],ids[m][1],
- comm->me,update->ntimestep);
+ "Restrain atoms %d %d missing on proc %d at step " BIGINT_FORMAT,
+ ids[m][0],ids[m][1],
+ comm->me,update->ntimestep);
error->one(FLERR,str);
}
}
-
+
delx = x[i1][0] - x[i2][0];
dely = x[i1][1] - x[i2][1];
delz = x[i1][2] - x[i2][2];
domain->minimum_image(delx,dely,delz);
-
+
rsq = delx*delx + dely*dely + delz*delz;
r = sqrt(rsq);
dr = r - target[m];
rk = k * dr;
-
+
// force & energy
-
+
if (r > 0.0) fbond = -2.0*rk/r;
else fbond = 0.0;
-
+
energy = rk*dr;
-
+
// apply force to each of 2 atoms
-
+
if (newton_bond || i1 < nlocal) {
f[i1][0] += delx*fbond;
f[i1][1] += dely*fbond;
f[i1][2] += delz*fbond;
}
-
+
if (newton_bond || i2 < nlocal) {
f[i2][0] -= delx*fbond;
f[i2][1] -= dely*fbond;
@@ -303,97 +303,97 @@ void FixRestrain::restrain_angle(int m)
// newton_bond on: only processor owning i2 computes restraint
// newton_bond off: only processors owning any of i1-i3 computes restraint
-
+
if (newton_bond) {
if (i2 == -1 || i2 >= nlocal) return;
if (i1 == -1 || i3 == -1) {
char str[128];
sprintf(str,
- "Restrain atoms %d %d %d missing on proc %d at step "
- BIGINT_FORMAT,
- ids[m][0],ids[m][1],ids[m][2],
- comm->me,update->ntimestep);
+ "Restrain atoms %d %d %d missing on proc %d at step "
+ BIGINT_FORMAT,
+ ids[m][0],ids[m][1],ids[m][2],
+ comm->me,update->ntimestep);
error->one(FLERR,str);
}
} else {
if ((i1 == -1 || i1 >= nlocal) && (i2 == -1 || i2 >= nlocal) &&
- (i3 == -1 || i3 >= nlocal)) return;
+ (i3 == -1 || i3 >= nlocal)) return;
if (i1 == -1 || i2 == -1 || i3 == -1) {
char str[128];
sprintf(str,
- "Restrain atoms %d %d %d missing on proc %d at step "
- BIGINT_FORMAT,
- ids[m][0],ids[m][1],ids[m][2],
- comm->me,update->ntimestep);
+ "Restrain atoms %d %d %d missing on proc %d at step "
+ BIGINT_FORMAT,
+ ids[m][0],ids[m][1],ids[m][2],
+ comm->me,update->ntimestep);
error->one(FLERR,str);
}
}
-
+
// 1st bond
delx1 = x[i1][0] - x[i2][0];
dely1 = x[i1][1] - x[i2][1];
delz1 = x[i1][2] - x[i2][2];
domain->minimum_image(delx1,dely1,delz1);
-
+
rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
r1 = sqrt(rsq1);
-
+
// 2nd bond
-
+
delx2 = x[i3][0] - x[i2][0];
dely2 = x[i3][1] - x[i2][1];
delz2 = x[i3][2] - x[i2][2];
domain->minimum_image(delx2,dely2,delz2);
-
+
rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
r2 = sqrt(rsq2);
-
+
// angle (cos and sin)
-
+
c = delx1*delx2 + dely1*dely2 + delz1*delz2;
c /= r1*r2;
-
+
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
-
+
s = sqrt(1.0 - c*c);
if (s < SMALL) s = SMALL;
s = 1.0/s;
-
+
// force & energy
-
+
dtheta = acos(c) - target[m];
tk = k * dtheta;
-
+
energy = tk*dtheta;
-
+
a = -2.0 * tk * s;
a11 = a*c / rsq1;
a12 = -a / (r1*r2);
a22 = a*c / rsq2;
-
+
f1[0] = a11*delx1 + a12*delx2;
f1[1] = a11*dely1 + a12*dely2;
f1[2] = a11*delz1 + a12*delz2;
f3[0] = a22*delx2 + a12*delx1;
f3[1] = a22*dely2 + a12*dely1;
f3[2] = a22*delz2 + a12*delz1;
-
+
// apply force to each of 3 atoms
-
+
if (newton_bond || i1 < nlocal) {
f[i1][0] += f1[0];
f[i1][1] += f1[1];
f[i1][2] += f1[2];
}
-
+
if (newton_bond || i2 < nlocal) {
f[i2][0] -= f1[0] + f3[0];
f[i2][1] -= f1[1] + f3[1];
f[i2][2] -= f1[2] + f3[2];
}
-
+
if (newton_bond || i3 < nlocal) {
f[i3][0] += f3[0];
f[i3][1] += f3[1];
@@ -413,7 +413,7 @@ void FixRestrain::restrain_dihedral(int m)
double f1[3],f2[3],f3[3],f4[3];
double ax,ay,az,bx,by,bz,rasq,rbsq,rgsq,rg,rginv,ra2inv,rb2inv,rabinv;
double df,df1,ddf1,fg,hg,fga,hgb,gaa,gbb;
- double dtfx,dtfy,dtfz,dtgx,dtgy,dtgz,dthx,dthy,dthz;
+ double dtfx,dtfy,dtfz,dtgx,dtgy,dtgz,dthx,dthy,dthz;
double c,s,p,sx2,sy2,sz2;
double **x = atom->x;
@@ -438,22 +438,22 @@ void FixRestrain::restrain_dihedral(int m)
if (i1 == -1 || i3 == -1 || i4 == -1) {
char str[128];
sprintf(str,
- "Restrain atoms %d %d %d %d missing on proc %d at step "
- BIGINT_FORMAT,
- ids[m][0],ids[m][1],ids[m][2],ids[m][3],
- comm->me,update->ntimestep);
+ "Restrain atoms %d %d %d %d missing on proc %d at step "
+ BIGINT_FORMAT,
+ ids[m][0],ids[m][1],ids[m][2],ids[m][3],
+ comm->me,update->ntimestep);
error->one(FLERR,str);
}
} else {
if ((i1 == -1 || i1 >= nlocal) && (i2 == -1 || i2 >= nlocal) &&
- (i3 == -1 || i3 >= nlocal) && (i4 == -1 || i3 >= nlocal)) return;
+ (i3 == -1 || i3 >= nlocal) && (i4 == -1 || i3 >= nlocal)) return;
if (i1 == -1 || i2 == -1 || i3 == -1 || i4 == -1) {
char str[128];
sprintf(str,
- "Restrain atoms %d %d %d %d missing on proc %d at step "
- BIGINT_FORMAT,
- ids[m][0],ids[m][1],ids[m][2],ids[m][3],
- comm->me,update->ntimestep);
+ "Restrain atoms %d %d %d %d missing on proc %d at step "
+ BIGINT_FORMAT,
+ ids[m][0],ids[m][1],ids[m][2],ids[m][3],
+ comm->me,update->ntimestep);
error->one(FLERR,str);
}
}
@@ -464,96 +464,96 @@ void FixRestrain::restrain_dihedral(int m)
vb1y = x[i1][1] - x[i2][1];
vb1z = x[i1][2] - x[i2][2];
domain->minimum_image(vb1x,vb1y,vb1z);
-
+
// 2nd bond
-
+
vb2x = x[i3][0] - x[i2][0];
vb2y = x[i3][1] - x[i2][1];
vb2z = x[i3][2] - x[i2][2];
domain->minimum_image(vb2x,vb2y,vb2z);
-
+
vb2xm = -vb2x;
vb2ym = -vb2y;
vb2zm = -vb2z;
domain->minimum_image(vb2xm,vb2ym,vb2zm);
-
+
// 3rd bond
-
+
vb3x = x[i4][0] - x[i3][0];
vb3y = x[i4][1] - x[i3][1];
vb3z = x[i4][2] - x[i3][2];
domain->minimum_image(vb3x,vb3y,vb3z);
-
+
ax = vb1y*vb2zm - vb1z*vb2ym;
ay = vb1z*vb2xm - vb1x*vb2zm;
az = vb1x*vb2ym - vb1y*vb2xm;
bx = vb3y*vb2zm - vb3z*vb2ym;
by = vb3z*vb2xm - vb3x*vb2zm;
bz = vb3x*vb2ym - vb3y*vb2xm;
-
+
rasq = ax*ax + ay*ay + az*az;
rbsq = bx*bx + by*by + bz*bz;
rgsq = vb2xm*vb2xm + vb2ym*vb2ym + vb2zm*vb2zm;
rg = sqrt(rgsq);
-
+
rginv = ra2inv = rb2inv = 0.0;
if (rg > 0) rginv = 1.0/rg;
if (rasq > 0) ra2inv = 1.0/rasq;
if (rbsq > 0) rb2inv = 1.0/rbsq;
rabinv = sqrt(ra2inv*rb2inv);
-
+
c = (ax*bx + ay*by + az*bz)*rabinv;
s = rg*rabinv*(ax*vb3x + ay*vb3y + az*vb3z);
-
+
// error check
-
+
if (c > 1.0 + TOLERANCE || c < (-1.0 - TOLERANCE)) {
int me;
MPI_Comm_rank(world,&me);
if (screen) {
char str[128];
sprintf(str,"Restrain problem: %d " BIGINT_FORMAT " %d %d %d %d",
- me,update->ntimestep,
- atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
+ me,update->ntimestep,
+ atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
error->warning(FLERR,str);
fprintf(screen," 1st atom: %d %g %g %g\n",
- me,x[i1][0],x[i1][1],x[i1][2]);
+ me,x[i1][0],x[i1][1],x[i1][2]);
fprintf(screen," 2nd atom: %d %g %g %g\n",
- me,x[i2][0],x[i2][1],x[i2][2]);
+ me,x[i2][0],x[i2][1],x[i2][2]);
fprintf(screen," 3rd atom: %d %g %g %g\n",
- me,x[i3][0],x[i3][1],x[i3][2]);
+ me,x[i3][0],x[i3][1],x[i3][2]);
fprintf(screen," 4th atom: %d %g %g %g\n",
- me,x[i4][0],x[i4][1],x[i4][2]);
+ me,x[i4][0],x[i4][1],x[i4][2]);
}
}
-
+
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
-
+
mult = 1; // multiplicity
p = 1.0;
df1 = 0.0;
-
+
for (i = 0; i < mult; i++) {
ddf1 = p*c - df1*s;
df1 = p*s + df1*c;
p = ddf1;
}
-
+
p = p*cos_target[m] + df1*sin_target[m];
df1 = df1*cos_target[m] - ddf1*sin_target[m];
df1 *= -mult;
p += 1.0;
-
- energy = k * p;
-
+
+ energy = k * p;
+
fg = vb1x*vb2xm + vb1y*vb2ym + vb1z*vb2zm;
hg = vb3x*vb2xm + vb3y*vb2ym + vb3z*vb2zm;
fga = fg*ra2inv*rginv;
hgb = hg*rb2inv*rginv;
gaa = -ra2inv*rg;
gbb = rb2inv*rg;
-
+
dtfx = gaa*ax;
dtfy = gaa*ay;
dtfz = gaa*az;
@@ -563,49 +563,49 @@ void FixRestrain::restrain_dihedral(int m)
dthx = gbb*bx;
dthy = gbb*by;
dthz = gbb*bz;
-
+
df = -k * df1;
-
+
sx2 = df*dtgx;
sy2 = df*dtgy;
sz2 = df*dtgz;
-
+
f1[0] = df*dtfx;
f1[1] = df*dtfy;
f1[2] = df*dtfz;
-
+
f2[0] = sx2 - f1[0];
f2[1] = sy2 - f1[1];
f2[2] = sz2 - f1[2];
-
+
f4[0] = df*dthx;
f4[1] = df*dthy;
f4[2] = df*dthz;
-
+
f3[0] = -sx2 - f4[0];
f3[1] = -sy2 - f4[1];
f3[2] = -sz2 - f4[2];
-
+
// apply force to each of 4 atoms
-
+
if (newton_bond || i1 < nlocal) {
f[i1][0] += f1[0];
f[i1][1] += f1[1];
f[i1][2] += f1[2];
}
-
+
if (newton_bond || i2 < nlocal) {
f[i2][0] += f2[0];
f[i2][1] += f2[1];
f[i2][2] += f2[2];
}
-
+
if (newton_bond || i3 < nlocal) {
f[i3][0] += f3[0];
f[i3][1] += f3[1];
f[i3][2] += f3[2];
}
-
+
if (newton_bond || i4 < nlocal) {
f[i4][0] += f4[0];
f[i4][1] += f4[1];
diff --git a/src/fix_restrain.h b/src/fix_restrain.h
index c1093bbce9bde647108b03415153a687b2f9482d..a36f95cc507e4fb338c7d9d65271057fb8fcf808 100644
--- a/src/fix_restrain.h
+++ b/src/fix_restrain.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_rigid.cpp b/src/fix_rigid.cpp
index 795cd4956769981c83f675614b558a9d2381006e..7b5cc0099f88f6e17402a44ef8a394102d8311c7 100644
--- a/src/fix_rigid.cpp
+++ b/src/fix_rigid.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -156,8 +156,8 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
int *igroups = new int[nbody];
for (ibody = 0; ibody < nbody; ibody++) {
igroups[ibody] = group->find(arg[5+ibody]);
- if (igroups[ibody] == -1)
- error->all(FLERR,"Could not find fix rigid group ID");
+ if (igroups[ibody] == -1)
+ error->all(FLERR,"Could not find fix rigid group ID");
}
int *mask = atom->mask;
@@ -167,16 +167,16 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
for (i = 0; i < nlocal; i++) {
body[i] = -1;
if (mask[i] & groupbit)
- for (ibody = 0; ibody < nbody; ibody++)
- if (mask[i] & group->bitmask[igroups[ibody]]) {
- if (body[i] >= 0) flag = 1;
- body[i] = ibody;
- }
+ for (ibody = 0; ibody < nbody; ibody++)
+ if (mask[i] & group->bitmask[igroups[ibody]]) {
+ if (body[i] >= 0) flag = 1;
+ body[i] = ibody;
+ }
}
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
- if (flagall)
+ if (flagall)
error->all(FLERR,"One or more atoms belong to multiple rigid bodies");
delete [] igroups;
@@ -256,14 +256,14 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
else error->all(FLERR,"Illegal fix rigid command");
if (domain->dimension == 2 && zflag == 1.0)
- error->all(FLERR,"Fix rigid z force cannot be on for 2d simulation");
+ error->all(FLERR,"Fix rigid z force cannot be on for 2d simulation");
int count = 0;
for (int m = mlo; m <= mhi; m++) {
- fflag[m-1][0] = xflag;
- fflag[m-1][1] = yflag;
- fflag[m-1][2] = zflag;
- count++;
+ fflag[m-1][0] = xflag;
+ fflag[m-1][1] = yflag;
+ fflag[m-1][2] = zflag;
+ count++;
}
if (count == 0) error->all(FLERR,"Illegal fix rigid command");
@@ -287,14 +287,14 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
else error->all(FLERR,"Illegal fix rigid command");
if (domain->dimension == 2 && (xflag == 1.0 || yflag == 1.0))
- error->all(FLERR,"Fix rigid xy torque cannot be on for 2d simulation");
+ error->all(FLERR,"Fix rigid xy torque cannot be on for 2d simulation");
int count = 0;
for (int m = mlo; m <= mhi; m++) {
- tflag[m-1][0] = xflag;
- tflag[m-1][1] = yflag;
- tflag[m-1][2] = zflag;
- count++;
+ tflag[m-1][0] = xflag;
+ tflag[m-1][1] = yflag;
+ tflag[m-1][2] = zflag;
+ count++;
}
if (count == 0) error->all(FLERR,"Illegal fix rigid command");
@@ -303,21 +303,21 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"langevin") == 0) {
if (iarg+5 > narg) error->all(FLERR,"Illegal fix rigid command");
if (strcmp(style,"rigid") != 0 && strcmp(style,"rigid/nve") != 0)
- error->all(FLERR,"Illegal fix rigid command");
+ error->all(FLERR,"Illegal fix rigid command");
langflag = 1;
t_start = atof(arg[iarg+1]);
t_stop = atof(arg[iarg+2]);
t_period = atof(arg[iarg+3]);
seed = atoi(arg[iarg+4]);
- if (t_period <= 0.0)
- error->all(FLERR,"Fix rigid langevin period must be > 0.0");
+ if (t_period <= 0.0)
+ error->all(FLERR,"Fix rigid langevin period must be > 0.0");
if (seed <= 0) error->all(FLERR,"Illegal fix rigid command");
iarg += 5;
} else if (strcmp(arg[iarg],"temp") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix rigid command");
if (strcmp(style,"rigid/nvt") != 0 && strcmp(style,"rigid/npt") != 0)
- error->all(FLERR,"Illegal fix rigid command");
+ error->all(FLERR,"Illegal fix rigid command");
tempflag = 1;
t_start = atof(arg[iarg+1]);
t_stop = atof(arg[iarg+2]);
@@ -327,7 +327,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"press") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix rigid command");
if (strcmp(style,"rigid/npt") != 0)
- error->all(FLERR,"Illegal fix rigid command");
+ error->all(FLERR,"Illegal fix rigid command");
pressflag = 1;
p_start = atof(arg[iarg+1]);
p_stop = atof(arg[iarg+2]);
@@ -337,7 +337,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"tparam") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix rigid command");
if (strcmp(style,"rigid/nvt") != 0)
- error->all(FLERR,"Illegal fix rigid command");
+ error->all(FLERR,"Illegal fix rigid command");
t_chain = atoi(arg[iarg+1]);
t_iter = atoi(arg[iarg+2]);
t_order = atoi(arg[iarg+3]);
@@ -346,7 +346,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"pparam") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix rigid command");
if (strcmp(style,"rigid/npt") != 0)
- error->all(FLERR,"Illegal fix rigid command");
+ error->all(FLERR,"Illegal fix rigid command");
p_chain = atoi(arg[iarg+1]);
iarg += 2;
@@ -370,7 +370,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
// nrigid[n] = # of atoms in Nth rigid body
// error if one or zero atoms
-
+
int *ncount = new int[nbody];
for (ibody = 0; ibody < nbody; ibody++) ncount[ibody] = 0;
@@ -378,7 +378,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
for (i = 0; i < nlocal; i++)
if (body[i] >= 0) ncount[body[i]]++;
-
+
MPI_Allreduce(ncount,nrigid,nbody,MPI_INT,MPI_SUM,world);
delete [] ncount;
@@ -417,7 +417,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
int nsum = 0;
for (ibody = 0; ibody < nbody; ibody++) nsum += nrigid[ibody];
-
+
if (me == 0) {
if (screen) fprintf(screen,"%d rigid bodies with %d atoms\n",nbody,nsum);
if (logfile) fprintf(logfile,"%d rigid bodies with %d atoms\n",nbody,nsum);
@@ -431,17 +431,17 @@ FixRigid::~FixRigid()
// unregister callbacks to this fix from Atom class
atom->delete_callback(id,0);
-
+
delete random;
// delete locally stored arrays
-
+
memory->destroy(body);
memory->destroy(displace);
memory->destroy(eflags);
memory->destroy(orient);
memory->destroy(dorient);
-
+
// delete nbody-length arrays
memory->destroy(nrigid);
@@ -505,7 +505,7 @@ void FixRigid::init()
if (i < modify->nfix) {
for (int j = i; j < modify->nfix; j++)
if (strcmp(modify->fix[j]->style,"rigid") == 0)
- error->all(FLERR,"Rigid fix must come before NPT/NPH fix");
+ error->all(FLERR,"Rigid fix must come before NPT/NPH fix");
}
// timestep info
@@ -538,7 +538,7 @@ void FixRigid::init()
int *type = atom->type;
int nlocal = atom->nlocal;
- if (atom->radius_flag || atom->ellipsoid_flag || atom->line_flag ||
+ if (atom->radius_flag || atom->ellipsoid_flag || atom->line_flag ||
atom->tri_flag || atom->mu_flag) {
int flag = 0;
for (i = 0; i < nlocal; i++) {
@@ -572,27 +572,27 @@ void FixRigid::init()
// set to POINT or SPHERE or ELLIPSOID or LINE
if (radius && radius[i] > 0.0) {
- eflags[i] |= SPHERE;
- eflags[i] |= OMEGA;
- eflags[i] |= TORQUE;
+ eflags[i] |= SPHERE;
+ eflags[i] |= OMEGA;
+ eflags[i] |= TORQUE;
} else if (ellipsoid && ellipsoid[i] >= 0) {
- eflags[i] |= ELLIPSOID;
- eflags[i] |= ANGMOM;
- eflags[i] |= TORQUE;
+ eflags[i] |= ELLIPSOID;
+ eflags[i] |= ANGMOM;
+ eflags[i] |= TORQUE;
} else if (line && line[i] >= 0) {
- eflags[i] |= LINE;
- eflags[i] |= OMEGA;
- eflags[i] |= TORQUE;
+ eflags[i] |= LINE;
+ eflags[i] |= OMEGA;
+ eflags[i] |= TORQUE;
} else if (tri && tri[i] >= 0) {
- eflags[i] |= TRIANGLE;
- eflags[i] |= ANGMOM;
- eflags[i] |= TORQUE;
+ eflags[i] |= TRIANGLE;
+ eflags[i] |= ANGMOM;
+ eflags[i] |= TORQUE;
} else eflags[i] |= POINT;
// set DIPOLE if atom->mu and mu[3] > 0.0
if (atom->mu_flag && mu[i][3] > 0.0)
- eflags[i] |= DIPOLE;
+ eflags[i] |= DIPOLE;
}
}
@@ -601,7 +601,7 @@ void FixRigid::init()
double **x = atom->x;
int *image = atom->image;
-
+
int *periodicity = domain->periodicity;
double xprd = domain->xprd;
double yprd = domain->yprd;
@@ -614,7 +614,7 @@ void FixRigid::init()
for (i = 0; i < 6; i++) sum[ibody][i] = 0.0;
int xbox,ybox,zbox;
double massone,xunwrap,yunwrap,zunwrap;
-
+
for (i = 0; i < nlocal; i++) {
if (body[i] < 0) continue;
ibody = body[i];
@@ -626,9 +626,9 @@ void FixRigid::init()
else massone = mass[type[i]];
if ((xbox && !periodicity[0]) || (ybox && !periodicity[1]) ||
- (zbox && !periodicity[2]))
+ (zbox && !periodicity[2]))
error->one(FLERR,"Fix rigid atom has non-zero image flag "
- "in a non-periodic dimension");
+ "in a non-periodic dimension");
if (triclinic == 0) {
xunwrap = x[i][0] + xbox*xprd;
@@ -647,7 +647,7 @@ void FixRigid::init()
}
MPI_Allreduce(sum[0],all[0],6*nbody,MPI_DOUBLE,MPI_SUM,world);
-
+
for (ibody = 0; ibody < nbody; ibody++) {
masstotal[ibody] = all[ibody][3];
xcm[ibody][0] = all[ibody][0]/masstotal[ibody];
@@ -716,45 +716,45 @@ void FixRigid::init()
else massone = mass[type[i]];
if (eflags[i] & SPHERE) {
- sum[ibody][0] += SINERTIA*massone * radius[i]*radius[i];
- sum[ibody][1] += SINERTIA*massone * radius[i]*radius[i];
- sum[ibody][2] += SINERTIA*massone * radius[i]*radius[i];
+ sum[ibody][0] += SINERTIA*massone * radius[i]*radius[i];
+ sum[ibody][1] += SINERTIA*massone * radius[i]*radius[i];
+ sum[ibody][2] += SINERTIA*massone * radius[i]*radius[i];
} else if (eflags[i] & ELLIPSOID) {
- shape = ebonus[ellipsoid[i]].shape;
- quatatom = ebonus[ellipsoid[i]].quat;
- MathExtra::inertia_ellipsoid(shape,quatatom,massone,ivec);
- sum[ibody][0] += ivec[0];
- sum[ibody][1] += ivec[1];
- sum[ibody][2] += ivec[2];
- sum[ibody][3] += ivec[3];
- sum[ibody][4] += ivec[4];
- sum[ibody][5] += ivec[5];
+ shape = ebonus[ellipsoid[i]].shape;
+ quatatom = ebonus[ellipsoid[i]].quat;
+ MathExtra::inertia_ellipsoid(shape,quatatom,massone,ivec);
+ sum[ibody][0] += ivec[0];
+ sum[ibody][1] += ivec[1];
+ sum[ibody][2] += ivec[2];
+ sum[ibody][3] += ivec[3];
+ sum[ibody][4] += ivec[4];
+ sum[ibody][5] += ivec[5];
} else if (eflags[i] & LINE) {
- length = lbonus[line[i]].length;
- theta = lbonus[line[i]].theta;
- MathExtra::inertia_line(length,theta,massone,ivec);
- sum[ibody][0] += ivec[0];
- sum[ibody][1] += ivec[1];
- sum[ibody][2] += ivec[2];
- sum[ibody][3] += ivec[3];
- sum[ibody][4] += ivec[4];
- sum[ibody][5] += ivec[5];
+ length = lbonus[line[i]].length;
+ theta = lbonus[line[i]].theta;
+ MathExtra::inertia_line(length,theta,massone,ivec);
+ sum[ibody][0] += ivec[0];
+ sum[ibody][1] += ivec[1];
+ sum[ibody][2] += ivec[2];
+ sum[ibody][3] += ivec[3];
+ sum[ibody][4] += ivec[4];
+ sum[ibody][5] += ivec[5];
} else if (eflags[i] & TRIANGLE) {
- inertiaatom = tbonus[tri[i]].inertia;
- quatatom = tbonus[tri[i]].quat;
- MathExtra::inertia_triangle(inertiaatom,quatatom,massone,ivec);
- sum[ibody][0] += ivec[0];
- sum[ibody][1] += ivec[1];
- sum[ibody][2] += ivec[2];
- sum[ibody][3] += ivec[3];
- sum[ibody][4] += ivec[4];
- sum[ibody][5] += ivec[5];
+ inertiaatom = tbonus[tri[i]].inertia;
+ quatatom = tbonus[tri[i]].quat;
+ MathExtra::inertia_triangle(inertiaatom,quatatom,massone,ivec);
+ sum[ibody][0] += ivec[0];
+ sum[ibody][1] += ivec[1];
+ sum[ibody][2] += ivec[2];
+ sum[ibody][3] += ivec[3];
+ sum[ibody][4] += ivec[4];
+ sum[ibody][5] += ivec[5];
}
}
}
-
+
MPI_Allreduce(sum[0],all[0],6*nbody,MPI_DOUBLE,MPI_SUM,world);
-
+
// diagonalize inertia tensor for each body via Jacobi rotations
// inertia = 3 eigenvalues = principal moments of inertia
// evectors and exzy_space = 3 evectors = principal axes of rigid body
@@ -773,7 +773,7 @@ void FixRigid::init()
ierror = MathExtra::jacobi(tensor,inertia[ibody],evectors);
if (ierror) error->all(FLERR,
- "Insufficient Jacobi rotations for rigid body");
+ "Insufficient Jacobi rotations for rigid body");
ex_space[ibody][0] = evectors[0][0];
ex_space[ibody][1] = evectors[1][0];
@@ -786,11 +786,11 @@ void FixRigid::init()
ez_space[ibody][2] = evectors[2][2];
// if any principal moment < scaled EPSILON, set to 0.0
-
+
double max;
max = MAX(inertia[ibody][0],inertia[ibody][1]);
max = MAX(max,inertia[ibody][2]);
-
+
if (inertia[ibody][0] < EPSILON*max) inertia[ibody][0] = 0.0;
if (inertia[ibody][1] < EPSILON*max) inertia[ibody][1] = 0.0;
if (inertia[ibody][2] < EPSILON*max) inertia[ibody][2] = 0.0;
@@ -803,9 +803,9 @@ void FixRigid::init()
MathExtra::negate3(ez_space[ibody]);
// create initial quaternion
-
+
MathExtra::exyz_to_q(ex_space[ibody],ey_space[ibody],ez_space[ibody],
- quat[ibody]);
+ quat[ibody]);
}
// displace = initial atom coords in basis of principal axes
@@ -827,7 +827,7 @@ void FixRigid::init()
xbox = (image[i] & 1023) - 512;
ybox = (image[i] >> 10 & 1023) - 512;
zbox = (image[i] >> 20) - 512;
-
+
if (triclinic == 0) {
xunwrap = x[i][0] + xbox*xprd;
yunwrap = x[i][1] + ybox*yprd;
@@ -837,65 +837,65 @@ void FixRigid::init()
yunwrap = x[i][1] + ybox*yprd + zbox*yz;
zunwrap = x[i][2] + zbox*zprd;
}
-
+
delta[0] = xunwrap - xcm[ibody][0];
delta[1] = yunwrap - xcm[ibody][1];
delta[2] = zunwrap - xcm[ibody][2];
MathExtra::transpose_matvec(ex_space[ibody],ey_space[ibody],
- ez_space[ibody],delta,displace[i]);
+ ez_space[ibody],delta,displace[i]);
if (extended) {
if (eflags[i] & ELLIPSOID) {
- quatatom = ebonus[ellipsoid[i]].quat;
- MathExtra::qconjugate(quat[ibody],qc);
- MathExtra::quatquat(qc,quatatom,orient[i]);
- MathExtra::qnormalize(orient[i]);
+ quatatom = ebonus[ellipsoid[i]].quat;
+ MathExtra::qconjugate(quat[ibody],qc);
+ MathExtra::quatquat(qc,quatatom,orient[i]);
+ MathExtra::qnormalize(orient[i]);
} else if (eflags[i] & LINE) {
- if (quat[ibody][3] >= 0.0) theta_body = 2.0*acos(quat[ibody][0]);
- else theta_body = -2.0*acos(quat[ibody][0]);
- orient[i][0] = lbonus[line[i]].theta - theta_body;
- while (orient[i][0] <= MINUSPI) orient[i][0] += TWOPI;
- while (orient[i][0] > MY_PI) orient[i][0] -= TWOPI;
- if (orientflag == 4) orient[i][1] = orient[i][2] = orient[i][3] = 0.0;
+ if (quat[ibody][3] >= 0.0) theta_body = 2.0*acos(quat[ibody][0]);
+ else theta_body = -2.0*acos(quat[ibody][0]);
+ orient[i][0] = lbonus[line[i]].theta - theta_body;
+ while (orient[i][0] <= MINUSPI) orient[i][0] += TWOPI;
+ while (orient[i][0] > MY_PI) orient[i][0] -= TWOPI;
+ if (orientflag == 4) orient[i][1] = orient[i][2] = orient[i][3] = 0.0;
} else if (eflags[i] & TRIANGLE) {
- quatatom = tbonus[tri[i]].quat;
- MathExtra::qconjugate(quat[ibody],qc);
- MathExtra::quatquat(qc,quatatom,orient[i]);
- MathExtra::qnormalize(orient[i]);
+ quatatom = tbonus[tri[i]].quat;
+ MathExtra::qconjugate(quat[ibody],qc);
+ MathExtra::quatquat(qc,quatatom,orient[i]);
+ MathExtra::qnormalize(orient[i]);
} else if (orientflag == 4) {
- orient[i][0] = orient[i][1] = orient[i][2] = orient[i][3] = 0.0;
+ orient[i][0] = orient[i][1] = orient[i][2] = orient[i][3] = 0.0;
} else if (orientflag == 1)
- orient[i][0] = 0.0;
+ orient[i][0] = 0.0;
if (eflags[i] & DIPOLE) {
- MathExtra::transpose_matvec(ex_space[ibody],ey_space[ibody],
- ez_space[ibody],mu[i],dorient[i]);
- MathExtra::snormalize3(mu[i][3],dorient[i],dorient[i]);
+ MathExtra::transpose_matvec(ex_space[ibody],ey_space[ibody],
+ ez_space[ibody],mu[i],dorient[i]);
+ MathExtra::snormalize3(mu[i][3],dorient[i],dorient[i]);
} else if (dorientflag)
- dorient[i][0] = dorient[i][1] = dorient[i][2] = 0.0;
+ dorient[i][0] = dorient[i][1] = dorient[i][2] = 0.0;
}
}
-
+
// test for valid principal moments & axes
// recompute moments of inertia around new axes
// 3 diagonal moments should equal principal moments
// 3 off-diagonal moments should be 0.0
// extended particles may contribute extra terms to moments of inertia
-
+
for (ibody = 0; ibody < nbody; ibody++)
for (i = 0; i < 6; i++) sum[ibody][i] = 0.0;
-
+
for (i = 0; i < nlocal; i++) {
if (body[i] < 0) continue;
ibody = body[i];
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
- sum[ibody][0] += massone *
+ sum[ibody][0] += massone *
(displace[i][1]*displace[i][1] + displace[i][2]*displace[i][2]);
- sum[ibody][1] += massone *
+ sum[ibody][1] += massone *
(displace[i][0]*displace[i][0] + displace[i][2]*displace[i][2]);
- sum[ibody][2] += massone *
+ sum[ibody][2] += massone *
(displace[i][0]*displace[i][0] + displace[i][1]*displace[i][1]);
sum[ibody][3] -= massone * displace[i][1]*displace[i][2];
sum[ibody][4] -= massone * displace[i][0]*displace[i][2];
@@ -914,36 +914,36 @@ void FixRigid::init()
else massone = mass[type[i]];
if (eflags[i] & SPHERE) {
- sum[ibody][0] += SINERTIA*massone * radius[i]*radius[i];
- sum[ibody][1] += SINERTIA*massone * radius[i]*radius[i];
- sum[ibody][2] += SINERTIA*massone * radius[i]*radius[i];
+ sum[ibody][0] += SINERTIA*massone * radius[i]*radius[i];
+ sum[ibody][1] += SINERTIA*massone * radius[i]*radius[i];
+ sum[ibody][2] += SINERTIA*massone * radius[i]*radius[i];
} else if (eflags[i] & ELLIPSOID) {
- shape = ebonus[ellipsoid[i]].shape;
- MathExtra::inertia_ellipsoid(shape,orient[i],massone,ivec);
- sum[ibody][0] += ivec[0];
- sum[ibody][1] += ivec[1];
- sum[ibody][2] += ivec[2];
- sum[ibody][3] += ivec[3];
- sum[ibody][4] += ivec[4];
- sum[ibody][5] += ivec[5];
+ shape = ebonus[ellipsoid[i]].shape;
+ MathExtra::inertia_ellipsoid(shape,orient[i],massone,ivec);
+ sum[ibody][0] += ivec[0];
+ sum[ibody][1] += ivec[1];
+ sum[ibody][2] += ivec[2];
+ sum[ibody][3] += ivec[3];
+ sum[ibody][4] += ivec[4];
+ sum[ibody][5] += ivec[5];
} else if (eflags[i] & LINE) {
- length = lbonus[line[i]].length;
- MathExtra::inertia_line(length,orient[i][0],massone,ivec);
- sum[ibody][0] += ivec[0];
- sum[ibody][1] += ivec[1];
- sum[ibody][2] += ivec[2];
- sum[ibody][3] += ivec[3];
- sum[ibody][4] += ivec[4];
- sum[ibody][5] += ivec[5];
+ length = lbonus[line[i]].length;
+ MathExtra::inertia_line(length,orient[i][0],massone,ivec);
+ sum[ibody][0] += ivec[0];
+ sum[ibody][1] += ivec[1];
+ sum[ibody][2] += ivec[2];
+ sum[ibody][3] += ivec[3];
+ sum[ibody][4] += ivec[4];
+ sum[ibody][5] += ivec[5];
} else if (eflags[i] & TRIANGLE) {
- inertiaatom = tbonus[tri[i]].inertia;
- MathExtra::inertia_triangle(inertiaatom,orient[i],massone,ivec);
- sum[ibody][0] += ivec[0];
- sum[ibody][1] += ivec[1];
- sum[ibody][2] += ivec[2];
- sum[ibody][3] += ivec[3];
- sum[ibody][4] += ivec[4];
- sum[ibody][5] += ivec[5];
+ inertiaatom = tbonus[tri[i]].inertia;
+ MathExtra::inertia_triangle(inertiaatom,orient[i],massone,ivec);
+ sum[ibody][0] += ivec[0];
+ sum[ibody][1] += ivec[1];
+ sum[ibody][2] += ivec[2];
+ sum[ibody][3] += ivec[3];
+ sum[ibody][4] += ivec[4];
+ sum[ibody][5] += ivec[5];
}
}
}
@@ -954,29 +954,29 @@ void FixRigid::init()
for (ibody = 0; ibody < nbody; ibody++) {
if (inertia[ibody][0] == 0.0) {
if (fabs(all[ibody][0]) > TOLERANCE)
- error->all(FLERR,"Fix rigid: Bad principal moments");
+ error->all(FLERR,"Fix rigid: Bad principal moments");
} else {
- if (fabs((all[ibody][0]-inertia[ibody][0])/inertia[ibody][0]) >
- TOLERANCE) error->all(FLERR,"Fix rigid: Bad principal moments");
+ if (fabs((all[ibody][0]-inertia[ibody][0])/inertia[ibody][0]) >
+ TOLERANCE) error->all(FLERR,"Fix rigid: Bad principal moments");
}
if (inertia[ibody][1] == 0.0) {
if (fabs(all[ibody][1]) > TOLERANCE)
- error->all(FLERR,"Fix rigid: Bad principal moments");
+ error->all(FLERR,"Fix rigid: Bad principal moments");
} else {
- if (fabs((all[ibody][1]-inertia[ibody][1])/inertia[ibody][1]) >
- TOLERANCE) error->all(FLERR,"Fix rigid: Bad principal moments");
+ if (fabs((all[ibody][1]-inertia[ibody][1])/inertia[ibody][1]) >
+ TOLERANCE) error->all(FLERR,"Fix rigid: Bad principal moments");
}
if (inertia[ibody][2] == 0.0) {
if (fabs(all[ibody][2]) > TOLERANCE)
- error->all(FLERR,"Fix rigid: Bad principal moments");
+ error->all(FLERR,"Fix rigid: Bad principal moments");
} else {
- if (fabs((all[ibody][2]-inertia[ibody][2])/inertia[ibody][2]) >
- TOLERANCE) error->all(FLERR,"Fix rigid: Bad principal moments");
+ if (fabs((all[ibody][2]-inertia[ibody][2])/inertia[ibody][2]) >
+ TOLERANCE) error->all(FLERR,"Fix rigid: Bad principal moments");
}
norm = (inertia[ibody][0] + inertia[ibody][1] + inertia[ibody][2]) / 3.0;
- if (fabs(all[ibody][3]/norm) > TOLERANCE ||
- fabs(all[ibody][4]/norm) > TOLERANCE ||
- fabs(all[ibody][5]/norm) > TOLERANCE)
+ if (fabs(all[ibody][3]/norm) > TOLERANCE ||
+ fabs(all[ibody][4]/norm) > TOLERANCE ||
+ fabs(all[ibody][5]/norm) > TOLERANCE)
error->all(FLERR,"Fix rigid: Bad principal moments");
}
@@ -997,7 +997,7 @@ void FixRigid::setup(int vflag)
{
int i,n,ibody;
double massone,radone;
-
+
// vcm = velocity of center-of-mass of each rigid body
// fcm = force on center-of-mass of each rigid body
@@ -1010,7 +1010,7 @@ void FixRigid::setup(int vflag)
for (ibody = 0; ibody < nbody; ibody++)
for (i = 0; i < 6; i++) sum[ibody][i] = 0.0;
-
+
for (i = 0; i < nlocal; i++) {
if (body[i] < 0) continue;
ibody = body[i];
@@ -1024,7 +1024,7 @@ void FixRigid::setup(int vflag)
sum[ibody][4] += f[i][1];
sum[ibody][5] += f[i][2];
}
-
+
MPI_Allreduce(sum[0],all[0],6*nbody,MPI_DOUBLE,MPI_SUM,world);
for (ibody = 0; ibody < nbody; ibody++) {
@@ -1038,10 +1038,10 @@ void FixRigid::setup(int vflag)
// angmom = angular momentum of each rigid body
// torque = torque on each rigid body
-
+
int *image = atom->image;
double **x = atom->x;
-
+
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
@@ -1053,7 +1053,7 @@ void FixRigid::setup(int vflag)
for (i = 0; i < 6; i++) sum[ibody][i] = 0.0;
int xbox,ybox,zbox;
double xunwrap,yunwrap,zunwrap,dx,dy,dz;
-
+
for (i = 0; i < nlocal; i++) {
if (body[i] < 0) continue;
ibody = body[i];
@@ -1075,7 +1075,7 @@ void FixRigid::setup(int vflag)
dx = xunwrap - xcm[ibody][0];
dy = yunwrap - xcm[ibody][1];
dz = zunwrap - xcm[ibody][2];
-
+
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
@@ -1103,29 +1103,29 @@ void FixRigid::setup(int vflag)
ibody = body[i];
if (eflags[i] & OMEGA) {
- if (eflags[i] & SPHERE) {
- radone = radius[i];
- sum[ibody][0] += SINERTIA*rmass[i] * radone*radone * omega_one[i][0];
- sum[ibody][1] += SINERTIA*rmass[i] * radone*radone * omega_one[i][1];
- sum[ibody][2] += SINERTIA*rmass[i] * radone*radone * omega_one[i][2];
- } else if (eflags[i] & LINE) {
- radone = lbonus[line[i]].length;
- sum[ibody][2] += LINERTIA*rmass[i] * radone*radone * omega_one[i][2];
- }
+ if (eflags[i] & SPHERE) {
+ radone = radius[i];
+ sum[ibody][0] += SINERTIA*rmass[i] * radone*radone * omega_one[i][0];
+ sum[ibody][1] += SINERTIA*rmass[i] * radone*radone * omega_one[i][1];
+ sum[ibody][2] += SINERTIA*rmass[i] * radone*radone * omega_one[i][2];
+ } else if (eflags[i] & LINE) {
+ radone = lbonus[line[i]].length;
+ sum[ibody][2] += LINERTIA*rmass[i] * radone*radone * omega_one[i][2];
+ }
}
if (eflags[i] & ANGMOM) {
- sum[ibody][0] += angmom_one[i][0];
- sum[ibody][1] += angmom_one[i][1];
- sum[ibody][2] += angmom_one[i][2];
+ sum[ibody][0] += angmom_one[i][0];
+ sum[ibody][1] += angmom_one[i][1];
+ sum[ibody][2] += angmom_one[i][2];
}
if (eflags[i] & TORQUE) {
- sum[ibody][3] += torque_one[i][0];
- sum[ibody][4] += torque_one[i][1];
- sum[ibody][5] += torque_one[i][2];
+ sum[ibody][3] += torque_one[i][0];
+ sum[ibody][4] += torque_one[i][1];
+ sum[ibody][5] += torque_one[i][2];
}
}
}
-
+
MPI_Allreduce(sum[0],all[0],6*nbody,MPI_DOUBLE,MPI_SUM,world);
for (ibody = 0; ibody < nbody; ibody++) {
@@ -1153,7 +1153,7 @@ void FixRigid::setup(int vflag)
for (ibody = 0; ibody < nbody; ibody++)
MathExtra::angmom_to_omega(angmom[ibody],ex_space[ibody],ey_space[ibody],
- ez_space[ibody],inertia[ibody],omega[ibody]);
+ ez_space[ibody],inertia[ibody],omega[ibody]);
set_v();
// guesstimate virial as 2x the set_v contribution
@@ -1163,7 +1163,7 @@ void FixRigid::setup(int vflag)
if (vflag_atom) {
for (i = 0; i < nlocal; i++)
for (n = 0; n < 6; n++)
- vatom[i][n] *= 2.0;
+ vatom[i][n] *= 2.0;
}
}
@@ -1176,20 +1176,20 @@ void FixRigid::initial_integrate(int vflag)
for (int ibody = 0; ibody < nbody; ibody++) {
// update vcm by 1/2 step
-
+
dtfm = dtf / masstotal[ibody];
vcm[ibody][0] += dtfm * fcm[ibody][0] * fflag[ibody][0];
vcm[ibody][1] += dtfm * fcm[ibody][1] * fflag[ibody][1];
vcm[ibody][2] += dtfm * fcm[ibody][2] * fflag[ibody][2];
-
+
// update xcm by full step
-
+
xcm[ibody][0] += dtv * vcm[ibody][0];
xcm[ibody][1] += dtv * vcm[ibody][1];
xcm[ibody][2] += dtv * vcm[ibody][2];
-
+
// update angular momentum by 1/2 step
-
+
angmom[ibody][0] += dtf * torque[ibody][0] * tflag[ibody][0];
angmom[ibody][1] += dtf * torque[ibody][1] * tflag[ibody][1];
angmom[ibody][2] += dtf * torque[ibody][2] * tflag[ibody][2];
@@ -1200,11 +1200,11 @@ void FixRigid::initial_integrate(int vflag)
// update ex,ey,ez to reflect new quaternion
MathExtra::angmom_to_omega(angmom[ibody],ex_space[ibody],ey_space[ibody],
- ez_space[ibody],inertia[ibody],omega[ibody]);
+ ez_space[ibody],inertia[ibody],omega[ibody]);
MathExtra::richardson(quat[ibody],angmom[ibody],omega[ibody],
- inertia[ibody],dtq);
+ inertia[ibody],dtq);
MathExtra::q_to_exyz(quat[ibody],
- ex_space[ibody],ey_space[ibody],ez_space[ibody]);
+ ex_space[ibody],ey_space[ibody],ez_space[ibody]);
}
// virial setup before call to set_xv
@@ -1214,7 +1214,7 @@ void FixRigid::initial_integrate(int vflag)
// set coords/orient and velocity/rotation of atoms in rigid bodies
// from quarternion and omega
-
+
set_xv();
}
@@ -1239,23 +1239,23 @@ void FixRigid::post_force(int vflag)
double dt = update->dt;
double mvv2e = force->mvv2e;
double ftm2v = force->ftm2v;
-
+
for (int i = 0; i < nbody; i++) {
gamma1 = -masstotal[i] / t_period / ftm2v;
- gamma2 = sqrt(masstotal[i]) * tsqrt *
- sqrt(24.0*boltz/t_period/dt/mvv2e) / ftm2v;
+ gamma2 = sqrt(masstotal[i]) * tsqrt *
+ sqrt(24.0*boltz/t_period/dt/mvv2e) / ftm2v;
langextra[i][0] = gamma1*vcm[i][0] + gamma2*(random->uniform()-0.5);
langextra[i][1] = gamma1*vcm[i][1] + gamma2*(random->uniform()-0.5);
langextra[i][2] = gamma1*vcm[i][2] + gamma2*(random->uniform()-0.5);
gamma1 = -1.0 / t_period / ftm2v;
gamma2 = tsqrt * sqrt(24.0*boltz/t_period/dt/mvv2e) / ftm2v;
- langextra[i][3] = inertia[i][0]*gamma1*omega[i][0] +
- sqrt(inertia[i][0])*gamma2*(random->uniform()-0.5);
- langextra[i][4] = inertia[i][1]*gamma1*omega[i][1] +
- sqrt(inertia[i][1])*gamma2*(random->uniform()-0.5);
- langextra[i][5] = inertia[i][2]*gamma1*omega[i][2] +
- sqrt(inertia[i][2])*gamma2*(random->uniform()-0.5);
+ langextra[i][3] = inertia[i][0]*gamma1*omega[i][0] +
+ sqrt(inertia[i][0])*gamma2*(random->uniform()-0.5);
+ langextra[i][4] = inertia[i][1]*gamma1*omega[i][1] +
+ sqrt(inertia[i][1])*gamma2*(random->uniform()-0.5);
+ langextra[i][5] = inertia[i][2]*gamma1*omega[i][2] +
+ sqrt(inertia[i][2])*gamma2*(random->uniform()-0.5);
}
}
@@ -1270,12 +1270,12 @@ void FixRigid::final_integrate()
double dtfm,xy,xz,yz;
// sum over atoms to get force and torque on rigid body
-
+
int *image = atom->image;
double **x = atom->x;
double **f = atom->f;
int nlocal = atom->nlocal;
-
+
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
@@ -1289,7 +1289,7 @@ void FixRigid::final_integrate()
double xunwrap,yunwrap,zunwrap,dx,dy,dz;
for (ibody = 0; ibody < nbody; ibody++)
for (i = 0; i < 6; i++) sum[ibody][i] = 0.0;
-
+
for (i = 0; i < nlocal; i++) {
if (body[i] < 0) continue;
ibody = body[i];
@@ -1297,7 +1297,7 @@ void FixRigid::final_integrate()
sum[ibody][0] += f[i][0];
sum[ibody][1] += f[i][1];
sum[ibody][2] += f[i][2];
-
+
xbox = (image[i] & 1023) - 512;
ybox = (image[i] >> 10 & 1023) - 512;
zbox = (image[i] >> 20) - 512;
@@ -1315,7 +1315,7 @@ void FixRigid::final_integrate()
dx = xunwrap - xcm[ibody][0];
dy = yunwrap - xcm[ibody][1];
dz = zunwrap - xcm[ibody][2];
-
+
sum[ibody][3] += dy*f[i][2] - dz*f[i][1];
sum[ibody][4] += dz*f[i][0] - dx*f[i][2];
sum[ibody][5] += dx*f[i][1] - dy*f[i][0];
@@ -1331,15 +1331,15 @@ void FixRigid::final_integrate()
ibody = body[i];
if (eflags[i] & TORQUE) {
- sum[ibody][3] += torque_one[i][0];
- sum[ibody][4] += torque_one[i][1];
- sum[ibody][5] += torque_one[i][2];
+ sum[ibody][3] += torque_one[i][0];
+ sum[ibody][4] += torque_one[i][1];
+ sum[ibody][5] += torque_one[i][2];
}
}
}
MPI_Allreduce(sum[0],all[0],6*nbody,MPI_DOUBLE,MPI_SUM,world);
-
+
// update vcm and angmom
// include Langevin thermostat forces
// fflag,tflag = 0 for some dimensions in 2d
@@ -1353,20 +1353,20 @@ void FixRigid::final_integrate()
torque[ibody][2] = all[ibody][5] + langextra[ibody][5];
// update vcm by 1/2 step
-
+
dtfm = dtf / masstotal[ibody];
vcm[ibody][0] += dtfm * fcm[ibody][0] * fflag[ibody][0];
vcm[ibody][1] += dtfm * fcm[ibody][1] * fflag[ibody][1];
vcm[ibody][2] += dtfm * fcm[ibody][2] * fflag[ibody][2];
-
+
// update angular momentum by 1/2 step
-
+
angmom[ibody][0] += dtf * torque[ibody][0] * tflag[ibody][0];
angmom[ibody][1] += dtf * torque[ibody][1] * tflag[ibody][1];
angmom[ibody][2] += dtf * torque[ibody][2] * tflag[ibody][2];
MathExtra::angmom_to_omega(angmom[ibody],ex_space[ibody],ey_space[ibody],
- ez_space[ibody],inertia[ibody],omega[ibody]);
+ ez_space[ibody],inertia[ibody],omega[ibody]);
}
// set velocity/rotation of atoms in rigid bodies
@@ -1380,11 +1380,11 @@ void FixRigid::final_integrate()
see Miller paper cited in fix rigid/nvt and fix rigid/npt
------------------------------------------------------------------------- */
-void FixRigid::no_squish_rotate(int k, double *p, double *q,
- double *inertia, double dt)
+void FixRigid::no_squish_rotate(int k, double *p, double *q,
+ double *inertia, double dt)
{
double phi,c_phi,s_phi,kp[4],kq[4];
-
+
// apply permuation operator on p and q, get kp and kq
if (k == 1) {
@@ -1403,22 +1403,22 @@ void FixRigid::no_squish_rotate(int k, double *p, double *q,
kq[2] = -q[1]; kp[2] = -p[1];
kq[3] = q[0]; kp[3] = p[0];
}
-
+
// obtain phi, cosines and sines
-
+
phi = p[0]*kq[0] + p[1]*kq[1] + p[2]*kq[2] + p[3]*kq[3];
- if (fabs(inertia[k-1]) < 1e-6) phi *= 0.0;
+ if (fabs(inertia[k-1]) < 1e-6) phi *= 0.0;
else phi /= 4.0 * inertia[k-1];
c_phi = cos(dt * phi);
s_phi = sin(dt * phi);
-
+
// advance p and q
-
+
p[0] = c_phi*p[0] + s_phi*kp[0];
p[1] = c_phi*p[1] + s_phi*kp[1];
p[2] = c_phi*p[2] + s_phi*kp[2];
p[3] = c_phi*p[3] + s_phi*kp[3];
-
+
q[0] = c_phi*q[0] + s_phi*kq[0];
q[1] = c_phi*q[1] + s_phi*kq[1];
q[2] = c_phi*q[2] + s_phi*kq[2];
@@ -1464,7 +1464,7 @@ void FixRigid::pre_neighbor()
for (int ibody = 0; ibody < nbody; ibody++) {
original = imagebody[ibody];
domain->remap(xcm[ibody],imagebody[ibody]);
-
+
if (original == imagebody[ibody]) remapflag[ibody][3] = 0;
else {
oldimage = original & 1023;
@@ -1517,7 +1517,7 @@ void FixRigid::pre_neighbor()
}
/* ----------------------------------------------------------------------
- count # of degrees-of-freedom removed by fix_rigid for atoms in igroup
+ count # of degrees-of-freedom removed by fix_rigid for atoms in igroup
------------------------------------------------------------------------- */
int FixRigid::dof(int igroup)
@@ -1551,8 +1551,8 @@ int FixRigid::dof(int igroup)
int flag = 0;
for (int ibody = 0; ibody < nbody; ibody++) {
- if (nall[ibody]+mall[ibody] > 0 &&
- nall[ibody]+mall[ibody] != nrigid[ibody]) flag = 1;
+ if (nall[ibody]+mall[ibody] > 0 &&
+ nall[ibody]+mall[ibody] != nrigid[ibody]) flag = 1;
}
if (flag && me == 0)
error->warning(FLERR,"Computing temperature of portions of rigid bodies");
@@ -1572,14 +1572,14 @@ int FixRigid::dof(int igroup)
if (domain->dimension == 3) {
for (int ibody = 0; ibody < nbody; ibody++)
if (nall[ibody]+mall[ibody] == nrigid[ibody]) {
- n += 3*nall[ibody] + 6*mall[ibody] - 6;
- if (inertia[ibody][0] == 0.0 || inertia[ibody][1] == 0.0 ||
- inertia[ibody][2] == 0.0) n++;
+ n += 3*nall[ibody] + 6*mall[ibody] - 6;
+ if (inertia[ibody][0] == 0.0 || inertia[ibody][1] == 0.0 ||
+ inertia[ibody][2] == 0.0) n++;
}
} else if (domain->dimension == 2) {
for (int ibody = 0; ibody < nbody; ibody++)
if (nall[ibody]+mall[ibody] == nrigid[ibody])
- n += 2*nall[ibody] + 3*mall[ibody] - 3;
+ n += 2*nall[ibody] + 3*mall[ibody] - 3;
}
delete [] ncount;
@@ -1598,7 +1598,7 @@ int FixRigid::dof(int igroup)
void FixRigid::deform(int flag)
{
- if (flag == 0)
+ if (flag == 0)
for (int ibody = 0; ibody < nbody; ibody++)
domain->x2lamda(xcm[ibody],xcm[ibody]);
else
@@ -1625,11 +1625,11 @@ void FixRigid::set_xv()
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
- double *rmass = atom->rmass;
- double *mass = atom->mass;
+ double *rmass = atom->rmass;
+ double *mass = atom->mass;
int *type = atom->type;
int nlocal = atom->nlocal;
-
+
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
@@ -1641,7 +1641,7 @@ void FixRigid::set_xv()
}
// set x and v of each atom
-
+
for (int i = 0; i < nlocal; i++) {
if (body[i] < 0) continue;
ibody = body[i];
@@ -1654,13 +1654,13 @@ void FixRigid::set_xv()
if (evflag) {
if (triclinic == 0) {
- x0 = x[i][0] + xbox*xprd;
- x1 = x[i][1] + ybox*yprd;
- x2 = x[i][2] + zbox*zprd;
+ x0 = x[i][0] + xbox*xprd;
+ x1 = x[i][1] + ybox*yprd;
+ x2 = x[i][2] + zbox*zprd;
} else {
- x0 = x[i][0] + xbox*xprd + ybox*xy + zbox*xz;
- x1 = x[i][1] + ybox*yprd + zbox*yz;
- x2 = x[i][2] + zbox*zprd;
+ x0 = x[i][0] + xbox*xprd + ybox*xy + zbox*xz;
+ x1 = x[i][1] + ybox*yprd + zbox*yz;
+ x2 = x[i][2] + zbox*zprd;
}
v0 = v[i][0];
v1 = v[i][1];
@@ -1671,7 +1671,7 @@ void FixRigid::set_xv()
// v = vcm + omega around center-of-mass
MathExtra::matvec(ex_space[ibody],ey_space[ibody],
- ez_space[ibody],displace[i],x[i]);
+ ez_space[ibody],displace[i],x[i]);
v[i][0] = omega[ibody][1]*x[i][2] - omega[ibody][2]*x[i][1] +
vcm[ibody][0];
@@ -1705,7 +1705,7 @@ void FixRigid::set_xv()
else massone = mass[type[i]];
fc0 = massone*(v[i][0] - v0)/dtf - f[i][0];
fc1 = massone*(v[i][1] - v1)/dtf - f[i][1];
- fc2 = massone*(v[i][2] - v2)/dtf - f[i][2];
+ fc2 = massone*(v[i][2] - v2)/dtf - f[i][2];
vr[0] = 0.5*x0*fc0;
vr[1] = 0.5*x1*fc1;
@@ -1719,7 +1719,7 @@ void FixRigid::set_xv()
}
// set orientation, omega, angmom of each extended particle
-
+
if (extended) {
double theta_body,theta;
double *shape,*quatatom,*inertiaatom;
@@ -1742,43 +1742,43 @@ void FixRigid::set_xv()
ibody = body[i];
if (eflags[i] & SPHERE) {
- omega_one[i][0] = omega[ibody][0];
- omega_one[i][1] = omega[ibody][1];
- omega_one[i][2] = omega[ibody][2];
+ omega_one[i][0] = omega[ibody][0];
+ omega_one[i][1] = omega[ibody][1];
+ omega_one[i][2] = omega[ibody][2];
} else if (eflags[i] & ELLIPSOID) {
- shape = ebonus[ellipsoid[i]].shape;
- quatatom = ebonus[ellipsoid[i]].quat;
- MathExtra::quatquat(quat[ibody],orient[i],quatatom);
- MathExtra::qnormalize(quatatom);
- ione[0] = EINERTIA*rmass[i] * (shape[1]*shape[1] + shape[2]*shape[2]);
- ione[1] = EINERTIA*rmass[i] * (shape[0]*shape[0] + shape[2]*shape[2]);
- ione[2] = EINERTIA*rmass[i] * (shape[0]*shape[0] + shape[1]*shape[1]);
- MathExtra::q_to_exyz(quatatom,exone,eyone,ezone);
- MathExtra::omega_to_angmom(omega[ibody],exone,eyone,ezone,ione,
- angmom_one[i]);
+ shape = ebonus[ellipsoid[i]].shape;
+ quatatom = ebonus[ellipsoid[i]].quat;
+ MathExtra::quatquat(quat[ibody],orient[i],quatatom);
+ MathExtra::qnormalize(quatatom);
+ ione[0] = EINERTIA*rmass[i] * (shape[1]*shape[1] + shape[2]*shape[2]);
+ ione[1] = EINERTIA*rmass[i] * (shape[0]*shape[0] + shape[2]*shape[2]);
+ ione[2] = EINERTIA*rmass[i] * (shape[0]*shape[0] + shape[1]*shape[1]);
+ MathExtra::q_to_exyz(quatatom,exone,eyone,ezone);
+ MathExtra::omega_to_angmom(omega[ibody],exone,eyone,ezone,ione,
+ angmom_one[i]);
} else if (eflags[i] & LINE) {
- if (quat[ibody][3] >= 0.0) theta_body = 2.0*acos(quat[ibody][0]);
- else theta_body = -2.0*acos(quat[ibody][0]);
- theta = orient[i][0] + theta_body;
- while (theta <= MINUSPI) theta += TWOPI;
- while (theta > MY_PI) theta -= TWOPI;
- lbonus[line[i]].theta = theta;
- omega_one[i][0] = omega[ibody][0];
- omega_one[i][1] = omega[ibody][1];
- omega_one[i][2] = omega[ibody][2];
+ if (quat[ibody][3] >= 0.0) theta_body = 2.0*acos(quat[ibody][0]);
+ else theta_body = -2.0*acos(quat[ibody][0]);
+ theta = orient[i][0] + theta_body;
+ while (theta <= MINUSPI) theta += TWOPI;
+ while (theta > MY_PI) theta -= TWOPI;
+ lbonus[line[i]].theta = theta;
+ omega_one[i][0] = omega[ibody][0];
+ omega_one[i][1] = omega[ibody][1];
+ omega_one[i][2] = omega[ibody][2];
} else if (eflags[i] & TRIANGLE) {
- inertiaatom = tbonus[tri[i]].inertia;
- quatatom = tbonus[tri[i]].quat;
- MathExtra::quatquat(quat[ibody],orient[i],quatatom);
- MathExtra::qnormalize(quatatom);
- MathExtra::q_to_exyz(quatatom,exone,eyone,ezone);
- MathExtra::omega_to_angmom(omega[ibody],exone,eyone,ezone,
- inertiaatom,angmom_one[i]);
+ inertiaatom = tbonus[tri[i]].inertia;
+ quatatom = tbonus[tri[i]].quat;
+ MathExtra::quatquat(quat[ibody],orient[i],quatatom);
+ MathExtra::qnormalize(quatatom);
+ MathExtra::q_to_exyz(quatatom,exone,eyone,ezone);
+ MathExtra::omega_to_angmom(omega[ibody],exone,eyone,ezone,
+ inertiaatom,angmom_one[i]);
}
if (eflags[i] & DIPOLE) {
- MathExtra::quat_to_mat(quat[ibody],p);
- MathExtra::matvec(p,dorient[i],mu[i]);
- MathExtra::snormalize3(mu[i][3],mu[i],mu[i]);
+ MathExtra::quat_to_mat(quat[ibody],p);
+ MathExtra::matvec(p,dorient[i],mu[i]);
+ MathExtra::snormalize3(mu[i][3],mu[i],mu[i]);
}
}
}
@@ -1802,8 +1802,8 @@ void FixRigid::set_v()
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
- double *rmass = atom->rmass;
- double *mass = atom->mass;
+ double *rmass = atom->rmass;
+ double *mass = atom->mass;
int *type = atom->type;
int *image = atom->image;
int nlocal = atom->nlocal;
@@ -1824,7 +1824,7 @@ void FixRigid::set_v()
ibody = body[i];
MathExtra::matvec(ex_space[ibody],ey_space[ibody],
- ez_space[ibody],displace[i],delta);
+ ez_space[ibody],displace[i],delta);
// save old velocities for virial
@@ -1834,11 +1834,11 @@ void FixRigid::set_v()
v2 = v[i][2];
}
- v[i][0] = omega[ibody][1]*delta[2] - omega[ibody][2]*delta[1] +
+ v[i][0] = omega[ibody][1]*delta[2] - omega[ibody][2]*delta[1] +
vcm[ibody][0];
- v[i][1] = omega[ibody][2]*delta[0] - omega[ibody][0]*delta[2] +
+ v[i][1] = omega[ibody][2]*delta[0] - omega[ibody][0]*delta[2] +
vcm[ibody][1];
- v[i][2] = omega[ibody][0]*delta[1] - omega[ibody][1]*delta[0] +
+ v[i][2] = omega[ibody][0]*delta[1] - omega[ibody][1]*delta[0] +
vcm[ibody][2];
// virial = unwrapped coords dotted into body constraint force
@@ -1852,20 +1852,20 @@ void FixRigid::set_v()
else massone = mass[type[i]];
fc0 = massone*(v[i][0] - v0)/dtf - f[i][0];
fc1 = massone*(v[i][1] - v1)/dtf - f[i][1];
- fc2 = massone*(v[i][2] - v2)/dtf - f[i][2];
+ fc2 = massone*(v[i][2] - v2)/dtf - f[i][2];
xbox = (image[i] & 1023) - 512;
ybox = (image[i] >> 10 & 1023) - 512;
zbox = (image[i] >> 20) - 512;
if (triclinic == 0) {
- x0 = x[i][0] + xbox*xprd;
- x1 = x[i][1] + ybox*yprd;
- x2 = x[i][2] + zbox*zprd;
+ x0 = x[i][0] + xbox*xprd;
+ x1 = x[i][1] + ybox*yprd;
+ x2 = x[i][2] + zbox*zprd;
} else {
- x0 = x[i][0] + xbox*xprd + ybox*xy + zbox*xz;
- x1 = x[i][1] + ybox*yprd + zbox*yz;
- x2 = x[i][2] + zbox*zprd;
+ x0 = x[i][0] + xbox*xprd + ybox*xy + zbox*xz;
+ x1 = x[i][1] + ybox*yprd + zbox*yz;
+ x2 = x[i][2] + zbox*zprd;
}
vr[0] = 0.5*x0*fc0;
@@ -1880,7 +1880,7 @@ void FixRigid::set_v()
}
// set omega, angmom of each extended particle
-
+
if (extended) {
double *shape,*quatatom,*inertiaatom;
@@ -1898,35 +1898,35 @@ void FixRigid::set_v()
ibody = body[i];
if (eflags[i] & SPHERE) {
- omega_one[i][0] = omega[ibody][0];
- omega_one[i][1] = omega[ibody][1];
- omega_one[i][2] = omega[ibody][2];
+ omega_one[i][0] = omega[ibody][0];
+ omega_one[i][1] = omega[ibody][1];
+ omega_one[i][2] = omega[ibody][2];
} else if (eflags[i] & ELLIPSOID) {
- shape = ebonus[ellipsoid[i]].shape;
- quatatom = ebonus[ellipsoid[i]].quat;
- ione[0] = EINERTIA*rmass[i] * (shape[1]*shape[1] + shape[2]*shape[2]);
- ione[1] = EINERTIA*rmass[i] * (shape[0]*shape[0] + shape[2]*shape[2]);
- ione[2] = EINERTIA*rmass[i] * (shape[0]*shape[0] + shape[1]*shape[1]);
- MathExtra::q_to_exyz(quatatom,exone,eyone,ezone);
- MathExtra::omega_to_angmom(omega[ibody],exone,eyone,ezone,ione,
- angmom_one[i]);
+ shape = ebonus[ellipsoid[i]].shape;
+ quatatom = ebonus[ellipsoid[i]].quat;
+ ione[0] = EINERTIA*rmass[i] * (shape[1]*shape[1] + shape[2]*shape[2]);
+ ione[1] = EINERTIA*rmass[i] * (shape[0]*shape[0] + shape[2]*shape[2]);
+ ione[2] = EINERTIA*rmass[i] * (shape[0]*shape[0] + shape[1]*shape[1]);
+ MathExtra::q_to_exyz(quatatom,exone,eyone,ezone);
+ MathExtra::omega_to_angmom(omega[ibody],exone,eyone,ezone,ione,
+ angmom_one[i]);
} else if (eflags[i] & LINE) {
- omega_one[i][0] = omega[ibody][0];
- omega_one[i][1] = omega[ibody][1];
- omega_one[i][2] = omega[ibody][2];
+ omega_one[i][0] = omega[ibody][0];
+ omega_one[i][1] = omega[ibody][1];
+ omega_one[i][2] = omega[ibody][2];
} else if (eflags[i] & TRIANGLE) {
- inertiaatom = tbonus[tri[i]].inertia;
- quatatom = tbonus[tri[i]].quat;
- MathExtra::q_to_exyz(quatatom,exone,eyone,ezone);
- MathExtra::omega_to_angmom(omega[ibody],exone,eyone,ezone,
- inertiaatom,angmom_one[i]);
+ inertiaatom = tbonus[tri[i]].inertia;
+ quatatom = tbonus[tri[i]].quat;
+ MathExtra::q_to_exyz(quatatom,exone,eyone,ezone);
+ MathExtra::omega_to_angmom(omega[ibody],exone,eyone,ezone,
+ inertiaatom,angmom_one[i]);
}
}
}
}
/* ----------------------------------------------------------------------
- memory usage of local atom-based arrays
+ memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double FixRigid::memory_usage()
@@ -1941,10 +1941,10 @@ double FixRigid::memory_usage()
if (dorientflag) bytes = nmax*3 * sizeof(double);
}
return bytes;
-}
+}
/* ----------------------------------------------------------------------
- allocate local atom-based arrays
+ allocate local atom-based arrays
------------------------------------------------------------------------- */
void FixRigid::grow_arrays(int nmax)
@@ -1959,7 +1959,7 @@ void FixRigid::grow_arrays(int nmax)
}
/* ----------------------------------------------------------------------
- copy values within local atom-based arrays
+ copy values within local atom-based arrays
------------------------------------------------------------------------- */
void FixRigid::copy_arrays(int i, int j)
@@ -1993,7 +1993,7 @@ void FixRigid::set_arrays(int i)
}
/* ----------------------------------------------------------------------
- pack values in local atom-based arrays for exchange with another proc
+ pack values in local atom-based arrays for exchange with another proc
------------------------------------------------------------------------- */
int FixRigid::pack_exchange(int i, double *buf)
@@ -2017,7 +2017,7 @@ int FixRigid::pack_exchange(int i, double *buf)
}
/* ----------------------------------------------------------------------
- unpack values in local atom-based arrays from exchange with another proc
+ unpack values in local atom-based arrays from exchange with another proc
------------------------------------------------------------------------- */
int FixRigid::unpack_exchange(int nlocal, double *buf)
@@ -2061,12 +2061,12 @@ double FixRigid::compute_scalar()
double t = 0.0;
for (int i = 0; i < nbody; i++) {
- t += masstotal[i] * (fflag[i][0]*vcm[i][0]*vcm[i][0] +
- fflag[i][1]*vcm[i][1]*vcm[i][1] + \
- fflag[i][2]*vcm[i][2]*vcm[i][2]);
-
+ t += masstotal[i] * (fflag[i][0]*vcm[i][0]*vcm[i][0] +
+ fflag[i][1]*vcm[i][1]*vcm[i][1] + \
+ fflag[i][2]*vcm[i][2]*vcm[i][2]);
+
// wbody = angular velocity in body frame
-
+
MathExtra::quat_to_mat(quat[i],rot);
MathExtra::transpose_matvec(rot,angmom[i],wbody);
if (inertia[i][0] == 0.0) wbody[0] = 0.0;
@@ -2075,9 +2075,9 @@ double FixRigid::compute_scalar()
else wbody[1] /= inertia[i][1];
if (inertia[i][2] == 0.0) wbody[2] = 0.0;
else wbody[2] /= inertia[i][2];
-
+
t += tflag[i][0]*inertia[i][0]*wbody[0]*wbody[0] +
- tflag[i][1]*inertia[i][1]*wbody[1]*wbody[1] +
+ tflag[i][1]*inertia[i][1]*wbody[1]*wbody[1] +
tflag[i][2]*inertia[i][2]*wbody[2]*wbody[2];
}
@@ -2094,7 +2094,7 @@ void *FixRigid::extract(const char *str, int &dim)
dim=0;
if (strcmp(str,"t_target") == 0) {
return &t_target;
- }
+ }
return NULL;
}
diff --git a/src/fix_rigid.h b/src/fix_rigid.h
index 26fce86a7be2184a84cce7e1069cc2ba1df113d2..a50bb00f6dd3fcfe42a8bc37a07bf3d0409b839a 100644
--- a/src/fix_rigid.h
+++ b/src/fix_rigid.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_rigid_nve.cpp b/src/fix_rigid_nve.cpp
index 39af01b2f5fe1ff412b8b8217fbf16dab1d9acb1..cd04526d8966b45cdf951a15667e2df1f1f33cd1 100644
--- a/src/fix_rigid_nve.cpp
+++ b/src/fix_rigid_nve.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -14,7 +14,7 @@
/* ----------------------------------------------------------------------
Contributing author: Tony Sheh (U Michigan), Trung Dac Nguyen (U Michigan)
references: Kamberaj et al., J. Chem. Phys. 122, 224114 (2005)
- Miller et al., J Chem Phys. 116, 8649-8659
+ Miller et al., J Chem Phys. 116, 8649-8659
------------------------------------------------------------------------- */
#include "math.h"
@@ -40,7 +40,7 @@ using namespace FixConst;
FixRigidNVE::FixRigidNVE(LAMMPS *lmp, int narg, char **arg) :
FixRigid(lmp, narg, arg)
-{
+{
memory->create(conjqm,nbody,4,"rigid/nve:conjqm");
}
@@ -56,11 +56,11 @@ FixRigidNVE::~FixRigidNVE()
void FixRigidNVE::setup(int vflag)
{
FixRigid::setup(vflag);
-
+
double mbody[3];
for (int ibody = 0; ibody < nbody; ibody++) {
MathExtra::transpose_matvec(ex_space[ibody],ey_space[ibody],ez_space[ibody],
- angmom[ibody],mbody);
+ angmom[ibody],mbody);
MathExtra::quatvec(quat[ibody],mbody,conjqm[ibody]);
conjqm[ibody][0] *= 2.0;
conjqm[ibody][1] *= 2.0;
@@ -78,71 +78,71 @@ void FixRigidNVE::initial_integrate(int vflag)
{
double dtfm,mbody[3],tbody[3],fquat[4];
double dtf2 = dtf * 2.0;
-
+
for (int ibody = 0; ibody < nbody; ibody++) {
-
+
// step 1.1 - update vcm by 1/2 step
-
+
dtfm = dtf / masstotal[ibody];
vcm[ibody][0] += dtfm * fcm[ibody][0] * fflag[ibody][0];
vcm[ibody][1] += dtfm * fcm[ibody][1] * fflag[ibody][1];
vcm[ibody][2] += dtfm * fcm[ibody][2] * fflag[ibody][2];
-
+
// step 1.2 - update xcm by full step
-
+
xcm[ibody][0] += dtv * vcm[ibody][0];
xcm[ibody][1] += dtv * vcm[ibody][1];
xcm[ibody][2] += dtv * vcm[ibody][2];
-
+
// step 1.3 - apply torque (body coords) to quaternion momentum
-
+
torque[ibody][0] *= tflag[ibody][0];
torque[ibody][1] *= tflag[ibody][1];
torque[ibody][2] *= tflag[ibody][2];
-
+
MathExtra::transpose_matvec(ex_space[ibody],ey_space[ibody],ez_space[ibody],
- torque[ibody],tbody);
+ torque[ibody],tbody);
MathExtra::quatvec(quat[ibody],tbody,fquat);
-
+
conjqm[ibody][0] += dtf2 * fquat[0];
conjqm[ibody][1] += dtf2 * fquat[1];
conjqm[ibody][2] += dtf2 * fquat[2];
conjqm[ibody][3] += dtf2 * fquat[3];
-
+
// step 1.4 to 1.13 - use no_squish rotate to update p and q
-
+
no_squish_rotate(3,conjqm[ibody],quat[ibody],inertia[ibody],dtq);
no_squish_rotate(2,conjqm[ibody],quat[ibody],inertia[ibody],dtq);
no_squish_rotate(1,conjqm[ibody],quat[ibody],inertia[ibody],dtv);
no_squish_rotate(2,conjqm[ibody],quat[ibody],inertia[ibody],dtq);
no_squish_rotate(3,conjqm[ibody],quat[ibody],inertia[ibody],dtq);
-
+
// update exyz_space
// transform p back to angmom
// update angular velocity
-
+
MathExtra::q_to_exyz(quat[ibody],ex_space[ibody],ey_space[ibody],
- ez_space[ibody]);
+ ez_space[ibody]);
MathExtra::invquatvec(quat[ibody],conjqm[ibody],mbody);
MathExtra::matvec(ex_space[ibody],ey_space[ibody],ez_space[ibody],
- mbody,angmom[ibody]);
-
+ mbody,angmom[ibody]);
+
angmom[ibody][0] *= 0.5;
angmom[ibody][1] *= 0.5;
angmom[ibody][2] *= 0.5;
-
+
MathExtra::angmom_to_omega(angmom[ibody],ex_space[ibody],ey_space[ibody],
- ez_space[ibody],inertia[ibody],omega[ibody]);
+ ez_space[ibody],inertia[ibody],omega[ibody]);
}
-
+
// virial setup before call to set_xv
if (vflag) v_setup(vflag);
else evflag = 0;
-
+
// set coords/orient and velocity/rotation of atoms in rigid bodies
// from quarternion and omega
-
+
set_xv();
}
@@ -154,12 +154,12 @@ void FixRigidNVE::final_integrate()
double dtfm,xy,xz,yz;
// sum over atoms to get force and torque on rigid body
-
+
int *image = atom->image;
double **x = atom->x;
double **f = atom->f;
int nlocal = atom->nlocal;
-
+
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
@@ -173,7 +173,7 @@ void FixRigidNVE::final_integrate()
double xunwrap,yunwrap,zunwrap,dx,dy,dz;
for (ibody = 0; ibody < nbody; ibody++)
for (i = 0; i < 6; i++) sum[ibody][i] = 0.0;
-
+
for (i = 0; i < nlocal; i++) {
if (body[i] < 0) continue;
ibody = body[i];
@@ -181,7 +181,7 @@ void FixRigidNVE::final_integrate()
sum[ibody][0] += f[i][0];
sum[ibody][1] += f[i][1];
sum[ibody][2] += f[i][2];
-
+
xbox = (image[i] & 1023) - 512;
ybox = (image[i] >> 10 & 1023) - 512;
zbox = (image[i] >> 20) - 512;
@@ -199,12 +199,12 @@ void FixRigidNVE::final_integrate()
dx = xunwrap - xcm[ibody][0];
dy = yunwrap - xcm[ibody][1];
dz = zunwrap - xcm[ibody][2];
-
+
sum[ibody][3] += dy*f[i][2] - dz*f[i][1];
sum[ibody][4] += dz*f[i][0] - dx*f[i][2];
sum[ibody][5] += dx*f[i][1] - dy*f[i][0];
}
-
+
// extended particles add their torque to torque of body
if (extended) {
@@ -215,15 +215,15 @@ void FixRigidNVE::final_integrate()
ibody = body[i];
if (eflags[i] & TORQUE) {
- sum[ibody][3] += torque_one[i][0];
- sum[ibody][4] += torque_one[i][1];
- sum[ibody][5] += torque_one[i][2];
+ sum[ibody][3] += torque_one[i][0];
+ sum[ibody][4] += torque_one[i][1];
+ sum[ibody][5] += torque_one[i][2];
}
}
}
MPI_Allreduce(sum[0],all[0],6*nbody,MPI_DOUBLE,MPI_SUM,world);
-
+
// update vcm and angmom
// include Langevin thermostat forces
// fflag,tflag = 0 for some dimensions in 2d
@@ -240,40 +240,40 @@ void FixRigidNVE::final_integrate()
torque[ibody][2] = all[ibody][5] + langextra[ibody][5];
// update vcm by 1/2 step
-
+
dtfm = dtf / masstotal[ibody];
vcm[ibody][0] += dtfm * fcm[ibody][0] * fflag[ibody][0];
vcm[ibody][1] += dtfm * fcm[ibody][1] * fflag[ibody][1];
vcm[ibody][2] += dtfm * fcm[ibody][2] * fflag[ibody][2];
-
+
// update conjqm, then transform to angmom, set velocity again
// virial is already setup from initial_integrate
-
+
torque[ibody][0] *= tflag[ibody][0];
torque[ibody][1] *= tflag[ibody][1];
torque[ibody][2] *= tflag[ibody][2];
-
+
MathExtra::transpose_matvec(ex_space[ibody],ey_space[ibody],ez_space[ibody],
- torque[ibody],tbody);
+ torque[ibody],tbody);
MathExtra::quatvec(quat[ibody],tbody,fquat);
-
+
conjqm[ibody][0] += dtf2 * fquat[0];
conjqm[ibody][1] += dtf2 * fquat[1];
conjqm[ibody][2] += dtf2 * fquat[2];
conjqm[ibody][3] += dtf2 * fquat[3];
-
+
MathExtra::invquatvec(quat[ibody],conjqm[ibody],mbody);
MathExtra::matvec(ex_space[ibody],ey_space[ibody],ez_space[ibody],
- mbody,angmom[ibody]);
-
+ mbody,angmom[ibody]);
+
angmom[ibody][0] *= 0.5;
angmom[ibody][1] *= 0.5;
- angmom[ibody][2] *= 0.5;
-
+ angmom[ibody][2] *= 0.5;
+
MathExtra::angmom_to_omega(angmom[ibody],ex_space[ibody],ey_space[ibody],
- ez_space[ibody],inertia[ibody],omega[ibody]);
+ ez_space[ibody],inertia[ibody],omega[ibody]);
}
-
+
// set velocity/rotation of atoms in rigid bodies
// virial is already setup from initial_integrate
diff --git a/src/fix_rigid_nve.h b/src/fix_rigid_nve.h
index 3c30e6c5dfe68e32abca32fafaed2f17829a4bd3..ef7105bc83efb38ffb6b41c8f005a2eee7639251 100644
--- a/src/fix_rigid_nve.h
+++ b/src/fix_rigid_nve.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_rigid_nvt.cpp b/src/fix_rigid_nvt.cpp
index a6f1d07e03254d94c6239e325f8e753a18f060d0..a02ab54669de1a59523ffeeb1449d14cb623ea20 100644
--- a/src/fix_rigid_nvt.cpp
+++ b/src/fix_rigid_nvt.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -14,7 +14,7 @@
/* ----------------------------------------------------------------------
Contributing author: Tony Sheh (U Michigan), Trung Dac Nguyen (U Michigan)
references: Kamberaj et al., J. Chem. Phys. 122, 224114 (2005)
- Miller et al., J Chem Phys. 116, 8649-8659
+ Miller et al., J Chem Phys. 116, 8649-8659
------------------------------------------------------------------------- */
#include "math.h"
@@ -41,13 +41,13 @@ using namespace FixConst;
FixRigidNVT::FixRigidNVT(LAMMPS *lmp, int narg, char **arg) :
FixRigid(lmp, narg, arg)
-{
+{
// other settings are made by FixRigid parent
scalar_flag = 1;
restart_global = 1;
extscalar = 1;
-
+
// error checking
// convert input period to frequency
@@ -60,19 +60,19 @@ FixRigidNVT::FixRigidNVT(LAMMPS *lmp, int narg, char **arg) :
if (t_chain < 1) error->all(FLERR,"Illegal fix_modify command");
if (t_iter < 1) error->all(FLERR,"Illegal fix_modify command");
- if (t_order != 3 && t_order != 5)
- error->all(FLERR,"Fix_modify order must be 3 or 5");
-
+ if (t_order != 3 && t_order != 5)
+ error->all(FLERR,"Fix_modify order must be 3 or 5");
+
allocate_chain();
allocate_order();
memory->create(conjqm,nbody,4,"nve_rigid:conjqm");
-
+
// one-time initialize of thermostat variables
-
+
eta_t[0] = eta_r[0] = 0.0;
eta_dot_t[0] = eta_dot_r[0] = 0.0;
f_eta_t[0] = f_eta_r[0] = 0.0;
-
+
for (int i = 1; i < t_chain; i++) {
eta_t[i] = eta_r[i] = 0.0;
eta_dot_t[i] = eta_dot_r[i] = 0.0;
@@ -109,20 +109,20 @@ void FixRigidNVT::init()
FixRigid::init();
// initialize thermostats
- // set timesteps, constants
+ // set timesteps, constants
// store Yoshida-Suzuki integrator parameters
-
+
dtv = update->dt;
dtf = 0.5 * update->dt * force->ftm2v;
dtq = 0.5 * update->dt;
-
+
boltz = force->boltz;
nf_t = nf_r = domain->dimension * nbody;
-
+
for (int ibody = 0; ibody < nbody; ibody++)
for (int k = 0; k < domain->dimension; k++)
if (fabs(inertia[ibody][k]) < 1e-6) nf_r--;
-
+
// see Table 1 in Kamberaj et al
if (t_order == 3) {
@@ -136,9 +136,9 @@ void FixRigidNVT::init()
w[3] = w[0];
w[4] = w[0];
}
-
+
// initialize thermostat settings
-
+
t_target = t_start;
double kt = boltz * t_target;
double t_mass = kt / (t_freq*t_freq);
@@ -146,9 +146,9 @@ void FixRigidNVT::init()
q_r[0] = nf_r * t_mass;
for (int i = 1; i < t_chain; i++)
q_t[i] = q_r[i] = t_mass;
-
+
// initialize thermostat chain positions, velocites, forces
-
+
for (int i = 1; i < t_chain; i++) {
f_eta_t[i] = q_t[i-1] * eta_dot_t[i-1] * eta_dot_t[i-1] - kt;
f_eta_r[i] = q_r[i-1] * eta_dot_r[i-1] * eta_dot_r[i-1] - kt;
@@ -162,11 +162,11 @@ void FixRigidNVT::setup(int vflag)
FixRigid::setup(vflag);
t_target = t_start;
-
+
double mbody[3];
for (int ibody = 0; ibody < nbody; ibody++) {
MathExtra::transpose_matvec(ex_space[ibody],ey_space[ibody],ez_space[ibody],
- angmom[ibody],mbody);
+ angmom[ibody],mbody);
MathExtra::quatvec(quat[ibody],mbody,conjqm[ibody]);
conjqm[ibody][0] *= 2.0;
conjqm[ibody][1] *= 2.0;
@@ -185,23 +185,23 @@ void FixRigidNVT::initial_integrate(int vflag)
double tmp,akin_t,akin_r,scale_t,scale_r;
double dtfm,mbody[3],tbody[3],fquat[4];
double dtf2 = dtf * 2.0;
-
+
double delta = update->ntimestep - update->beginstep;
delta /= update->endstep - update->beginstep;
t_target = t_start + delta * (t_stop - t_start);
-
+
// intialize velocity scale for translation and rotation
-
+
akin_t = akin_r = 0.0;
tmp = -1.0 * dtq * eta_dot_t[0];
scale_t = exp(tmp);
tmp = -1.0 * dtq * eta_dot_r[0];
scale_r = exp(tmp);
-
+
for (int ibody = 0; ibody < nbody; ibody++) {
-
+
// step 1.1 - update vcm by 1/2 step
-
+
dtfm = dtf / masstotal[ibody];
vcm[ibody][0] += dtfm * fcm[ibody][0] * fflag[ibody][0];
vcm[ibody][1] += dtfm * fcm[ibody][1] * fflag[ibody][1];
@@ -209,27 +209,27 @@ void FixRigidNVT::initial_integrate(int vflag)
vcm[ibody][0] *= scale_t;
vcm[ibody][1] *= scale_t;
vcm[ibody][2] *= scale_t;
-
+
tmp = vcm[ibody][0]*vcm[ibody][0] + vcm[ibody][1]*vcm[ibody][1] +
vcm[ibody][2]*vcm[ibody][2];
akin_t += masstotal[ibody]*tmp;
-
+
// step 1.2 - update xcm by full step
-
+
xcm[ibody][0] += dtv * vcm[ibody][0];
xcm[ibody][1] += dtv * vcm[ibody][1];
xcm[ibody][2] += dtv * vcm[ibody][2];
-
+
torque[ibody][0] *= tflag[ibody][0];
torque[ibody][1] *= tflag[ibody][1];
torque[ibody][2] *= tflag[ibody][2];
-
+
// step 1.3 - apply torque (body coords) to quaternion momentum
MathExtra::transpose_matvec(ex_space[ibody],ey_space[ibody],ez_space[ibody],
- torque[ibody],tbody);
+ torque[ibody],tbody);
MathExtra::quatvec(quat[ibody],tbody,fquat);
-
+
conjqm[ibody][0] += dtf2 * fquat[0];
conjqm[ibody][1] += dtf2 * fquat[1];
conjqm[ibody][2] += dtf2 * fquat[2];
@@ -238,48 +238,48 @@ void FixRigidNVT::initial_integrate(int vflag)
conjqm[ibody][1] *= scale_r;
conjqm[ibody][2] *= scale_r;
conjqm[ibody][3] *= scale_r;
-
+
// step 1.4 to 1.8 - use no_squish rotate to update p (i.e. conjqm) and q
-
+
no_squish_rotate(3,conjqm[ibody],quat[ibody],inertia[ibody],dtq);
no_squish_rotate(2,conjqm[ibody],quat[ibody],inertia[ibody],dtq);
no_squish_rotate(1,conjqm[ibody],quat[ibody],inertia[ibody],dtv);
no_squish_rotate(2,conjqm[ibody],quat[ibody],inertia[ibody],dtq);
no_squish_rotate(3,conjqm[ibody],quat[ibody],inertia[ibody],dtq);
-
+
// update the exyz_space from new quaternion
// transform p back to angmom
// update angular velocity
-
+
MathExtra::q_to_exyz(quat[ibody],ex_space[ibody],ey_space[ibody],
- ez_space[ibody]);
+ ez_space[ibody]);
MathExtra::invquatvec(quat[ibody],conjqm[ibody],mbody);
MathExtra::matvec(ex_space[ibody],ey_space[ibody],ez_space[ibody],
- mbody,angmom[ibody]);
-
+ mbody,angmom[ibody]);
+
angmom[ibody][0] *= 0.5;
angmom[ibody][1] *= 0.5;
angmom[ibody][2] *= 0.5;
-
+
MathExtra::angmom_to_omega(angmom[ibody],ex_space[ibody],ey_space[ibody],
- ez_space[ibody],inertia[ibody],omega[ibody]);
-
- akin_r += angmom[ibody][0]*omega[ibody][0] +
+ ez_space[ibody],inertia[ibody],omega[ibody]);
+
+ akin_r += angmom[ibody][0]*omega[ibody][0] +
angmom[ibody][1]*omega[ibody][1] + angmom[ibody][2]*omega[ibody][2];
}
-
+
// update thermostat chains
-
+
update_nhcp(akin_t,akin_r);
-
+
// virial setup before call to set_xv
-
+
if (vflag) v_setup(vflag);
else evflag = 0;
-
+
// set coords/orient and velocity/rotation of atoms in rigid bodies
// from quarternion and omega
-
+
set_xv();
}
@@ -290,21 +290,21 @@ void FixRigidNVT::final_integrate()
int i,ibody;
double tmp,scale_t,scale_r;
double dtfm,xy,xz,yz;
-
+
// compute velocity scales for translation and rotation
-
+
tmp = -1.0 * dtq * eta_dot_t[0];
scale_t = exp(tmp);
tmp = -1.0 * dtq * eta_dot_r[0];
scale_r = exp(tmp);
// sum over atoms to get force and torque on rigid body
-
+
int *image = atom->image;
double **x = atom->x;
double **f = atom->f;
int nlocal = atom->nlocal;
-
+
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
@@ -318,15 +318,15 @@ void FixRigidNVT::final_integrate()
double xunwrap,yunwrap,zunwrap,dx,dy,dz;
for (ibody = 0; ibody < nbody; ibody++)
for (i = 0; i < 6; i++) sum[ibody][i] = 0.0;
-
+
for (i = 0; i < nlocal; i++) {
if (body[i] < 0) continue;
ibody = body[i];
-
+
sum[ibody][0] += f[i][0];
sum[ibody][1] += f[i][1];
sum[ibody][2] += f[i][2];
-
+
xbox = (image[i] & 1023) - 512;
ybox = (image[i] >> 10 & 1023) - 512;
zbox = (image[i] >> 20) - 512;
@@ -344,12 +344,12 @@ void FixRigidNVT::final_integrate()
dx = xunwrap - xcm[ibody][0];
dy = yunwrap - xcm[ibody][1];
dz = zunwrap - xcm[ibody][2];
-
+
sum[ibody][3] += dy*f[i][2] - dz*f[i][1];
sum[ibody][4] += dz*f[i][0] - dx*f[i][2];
sum[ibody][5] += dx*f[i][1] - dy*f[i][0];
}
-
+
// extended particles add their torque to torque of body
if (extended) {
@@ -360,18 +360,18 @@ void FixRigidNVT::final_integrate()
ibody = body[i];
if (eflags[i] & TORQUE) {
- sum[ibody][3] += torque_one[i][0];
- sum[ibody][4] += torque_one[i][1];
- sum[ibody][5] += torque_one[i][2];
+ sum[ibody][3] += torque_one[i][0];
+ sum[ibody][4] += torque_one[i][1];
+ sum[ibody][5] += torque_one[i][2];
}
}
}
MPI_Allreduce(sum[0],all[0],6*nbody,MPI_DOUBLE,MPI_SUM,world);
-
+
double mbody[3],tbody[3],fquat[4];
double dtf2 = dtf * 2.0;
-
+
for (ibody = 0; ibody < nbody; ibody++) {
fcm[ibody][0] = all[ibody][0];
fcm[ibody][1] = all[ibody][1];
@@ -381,7 +381,7 @@ void FixRigidNVT::final_integrate()
torque[ibody][2] = all[ibody][5];
// 2.5-2.6 update vcm by 1/2 step
-
+
dtfm = dtf / masstotal[ibody];
vcm[ibody][0] *= scale_t;
vcm[ibody][1] *= scale_t;
@@ -389,47 +389,47 @@ void FixRigidNVT::final_integrate()
vcm[ibody][0] += dtfm * fcm[ibody][0] * fflag[ibody][0];
vcm[ibody][1] += dtfm * fcm[ibody][1] * fflag[ibody][1];
vcm[ibody][2] += dtfm * fcm[ibody][2] * fflag[ibody][2];
-
+
// 2.1-2.4 update conjqm, angular momentum and angular velocity
- // apply body torque flags
-
+ // apply body torque flags
+
torque[ibody][0] *= tflag[ibody][0];
torque[ibody][1] *= tflag[ibody][1];
torque[ibody][2] *= tflag[ibody][2];
-
- // convert torque to the body frame
-
+
+ // convert torque to the body frame
+
MathExtra::transpose_matvec(ex_space[ibody],ey_space[ibody],ez_space[ibody],
- torque[ibody],tbody);
-
+ torque[ibody],tbody);
+
// compute "force" for quaternion
-
+
MathExtra::quatvec(quat[ibody],tbody,fquat);
-
+
// update the conjugate quaternion momentum (conjqm)
-
+
conjqm[ibody][0] = scale_r * conjqm[ibody][0] + dtf2 * fquat[0];
conjqm[ibody][1] = scale_r * conjqm[ibody][1] + dtf2 * fquat[1];
conjqm[ibody][2] = scale_r * conjqm[ibody][2] + dtf2 * fquat[2];
conjqm[ibody][3] = scale_r * conjqm[ibody][3] + dtf2 * fquat[3];
-
+
// compute angular momentum in the body frame
// then convert to the space-fixed frame
-
+
MathExtra::invquatvec(quat[ibody],conjqm[ibody],mbody);
MathExtra::matvec(ex_space[ibody],ey_space[ibody],ez_space[ibody],
- mbody,angmom[ibody]);
-
+ mbody,angmom[ibody]);
+
angmom[ibody][0] *= 0.5;
angmom[ibody][1] *= 0.5;
- angmom[ibody][2] *= 0.5;
-
+ angmom[ibody][2] *= 0.5;
+
// compute new angular velocity
-
+
MathExtra::angmom_to_omega(angmom[ibody],ex_space[ibody],ey_space[ibody],
- ez_space[ibody],inertia[ibody],omega[ibody]);
+ ez_space[ibody],inertia[ibody],omega[ibody]);
}
-
+
// set velocity/rotation of atoms in rigid bodies
// virial is already setup from initial_integrate
@@ -442,97 +442,97 @@ void FixRigidNVT::update_nhcp(double akin_t, double akin_r)
{
int i,j,k;
double kt,gfkt_t,gfkt_r,tmp,ms,s,s2;
-
+
kt = boltz * t_target;
gfkt_t = nf_t * kt;
gfkt_r = nf_r * kt;
-
+
akin_t *= force->mvv2e;
akin_r *= force->mvv2e;
-
+
// update thermostat masses
-
+
double t_mass = boltz * t_target / (t_freq * t_freq);
q_t[0] = nf_t * t_mass;
q_r[0] = nf_r * t_mass;
for (i = 1; i < t_chain; i++)
q_t[i] = q_r[i] = t_mass;
-
+
// update order/timestep dependent coefficients
-
+
for (i = 0; i < t_order; i++) {
wdti1[i] = w[i] * dtv / t_iter;
wdti2[i] = wdti1[i] / 2.0;
wdti4[i] = wdti1[i] / 4.0;
}
-
+
// update force of thermostats coupled to particles
-
+
f_eta_t[0] = (akin_t - gfkt_t) / q_t[0];
f_eta_r[0] = (akin_r - gfkt_r) / q_r[0];
-
+
// multiple timestep iteration
-
+
for (i = 0; i < t_iter; i++) {
for (j = 0; j < t_order; j++) {
-
+
// update thermostat velocities half step
-
+
eta_dot_t[t_chain-1] += wdti2[j] * f_eta_t[t_chain-1];
eta_dot_r[t_chain-1] += wdti2[j] * f_eta_r[t_chain-1];
-
+
for (k = 1; k < t_chain; k++) {
- tmp = wdti4[j] * eta_dot_t[t_chain-k];
- ms = maclaurin_series(tmp);
- s = exp(-1.0 * tmp);
- s2 = s * s;
- eta_dot_t[t_chain-k-1] = eta_dot_t[t_chain-k-1] * s2 +
- wdti2[j] * f_eta_t[t_chain-k-1] * s * ms;
-
- tmp = wdti4[j] * eta_dot_r[t_chain-k];
- ms = maclaurin_series(tmp);
- s = exp(-1.0 * tmp);
- s2 = s * s;
- eta_dot_r[t_chain-k-1] = eta_dot_r[t_chain-k-1] * s2 +
- wdti2[j] * f_eta_r[t_chain-k-1] * s * ms;
+ tmp = wdti4[j] * eta_dot_t[t_chain-k];
+ ms = maclaurin_series(tmp);
+ s = exp(-1.0 * tmp);
+ s2 = s * s;
+ eta_dot_t[t_chain-k-1] = eta_dot_t[t_chain-k-1] * s2 +
+ wdti2[j] * f_eta_t[t_chain-k-1] * s * ms;
+
+ tmp = wdti4[j] * eta_dot_r[t_chain-k];
+ ms = maclaurin_series(tmp);
+ s = exp(-1.0 * tmp);
+ s2 = s * s;
+ eta_dot_r[t_chain-k-1] = eta_dot_r[t_chain-k-1] * s2 +
+ wdti2[j] * f_eta_r[t_chain-k-1] * s * ms;
}
-
+
// update thermostat positions a full step
-
+
for (k = 0; k < t_chain; k++) {
- eta_t[k] += wdti1[j] * eta_dot_t[k];
- eta_r[k] += wdti1[j] * eta_dot_r[k];
+ eta_t[k] += wdti1[j] * eta_dot_t[k];
+ eta_r[k] += wdti1[j] * eta_dot_r[k];
}
-
- // update thermostat forces
-
+
+ // update thermostat forces
+
for (k = 1; k < t_chain; k++) {
- f_eta_t[k] = q_t[k-1] * eta_dot_t[k-1] * eta_dot_t[k-1] - kt;
- f_eta_t[k] /= q_t[k];
- f_eta_r[k] = q_r[k-1] * eta_dot_r[k-1] * eta_dot_r[k-1] - kt;
- f_eta_r[k] /= q_r[k];
+ f_eta_t[k] = q_t[k-1] * eta_dot_t[k-1] * eta_dot_t[k-1] - kt;
+ f_eta_t[k] /= q_t[k];
+ f_eta_r[k] = q_r[k-1] * eta_dot_r[k-1] * eta_dot_r[k-1] - kt;
+ f_eta_r[k] /= q_r[k];
}
-
+
// update thermostat velocities a full step
-
+
for (k = 0; k < t_chain-1; k++) {
- tmp = wdti4[j] * eta_dot_t[k+1];
- ms = maclaurin_series(tmp);
- s = exp(-1.0 * tmp);
- s2 = s * s;
- eta_dot_t[k] = eta_dot_t[k] * s2 + wdti2[j] * f_eta_t[k] * s * ms;
- tmp = q_t[k] * eta_dot_t[k] * eta_dot_t[k] - kt;
- f_eta_t[k+1] = tmp / q_t[k+1];
-
- tmp = wdti4[j] * eta_dot_r[k+1];
- ms = maclaurin_series(tmp);
- s = exp(-1.0 * tmp);
- s2 = s * s;
- eta_dot_r[k] = eta_dot_r[k] * s2 + wdti2[j] * f_eta_r[k] * s * ms;
- tmp = q_r[k] * eta_dot_r[k] * eta_dot_r[k] - kt;
- f_eta_r[k+1] = tmp / q_r[k+1];
+ tmp = wdti4[j] * eta_dot_t[k+1];
+ ms = maclaurin_series(tmp);
+ s = exp(-1.0 * tmp);
+ s2 = s * s;
+ eta_dot_t[k] = eta_dot_t[k] * s2 + wdti2[j] * f_eta_t[k] * s * ms;
+ tmp = q_t[k] * eta_dot_t[k] * eta_dot_t[k] - kt;
+ f_eta_t[k+1] = tmp / q_t[k+1];
+
+ tmp = wdti4[j] * eta_dot_r[k+1];
+ ms = maclaurin_series(tmp);
+ s = exp(-1.0 * tmp);
+ s2 = s * s;
+ eta_dot_r[k] = eta_dot_r[k] * s2 + wdti2[j] * f_eta_r[k] * s * ms;
+ tmp = q_r[k] * eta_dot_r[k] * eta_dot_r[k] - kt;
+ f_eta_r[k+1] = tmp / q_r[k+1];
}
-
+
eta_dot_t[t_chain-1] += wdti2[j] * f_eta_t[t_chain-1];
eta_dot_r[t_chain-1] += wdti2[j] * f_eta_r[t_chain-1];
}
@@ -540,7 +540,7 @@ void FixRigidNVT::update_nhcp(double akin_t, double akin_r)
}
/* ----------------------------------------------------------------------
- pack entire state of Fix into one write
+ pack entire state of Fix into one write
------------------------------------------------------------------------- */
void FixRigidNVT::write_restart(FILE *fp)
@@ -557,17 +557,17 @@ void FixRigidNVT::write_restart(FILE *fp)
list[n++] = f_eta_t[i];
list[n++] = f_eta_r[i];
}
-
+
if (comm->me == 0) {
int size = (1 + 6*t_chain)*sizeof(double);
fwrite(&size,sizeof(int),1,fp);
fwrite(list,sizeof(double),1+6*t_chain,fp);
}
-
+
delete list;
}
-/* ----------------------------------------------------------------------
+/* ----------------------------------------------------------------------
compute kinetic energy in the extended Hamiltonian
conserved quantity = sum of returned energy and potential energy
-----------------------------------------------------------------------*/
@@ -577,17 +577,17 @@ double FixRigidNVT::compute_scalar()
int i,k,ibody;
double kt = boltz * t_target;
double energy,ke_t,ke_q,tmp,Pkq[4];
-
+
// compute the kinetic parts of H_NVE in Kameraj et al (JCP 2005, pp 224114)
-
+
// translational kinetic energy
ke_t = 0.0;
for (ibody = 0; ibody < nbody; ibody++)
ke_t += 0.5 * masstotal[ibody] * (vcm[ibody][0]*vcm[ibody][0] +
- vcm[ibody][1]*vcm[ibody][1] +
- vcm[ibody][2]*vcm[ibody][2]);
-
+ vcm[ibody][1]*vcm[ibody][1] +
+ vcm[ibody][2]*vcm[ibody][2]);
+
// rotational kinetic energy
ke_q = 0.0;
@@ -607,45 +607,45 @@ double FixRigidNVT::compute_scalar()
Pkq[0] = -quat[ibody][3];
Pkq[1] = quat[ibody][2];
Pkq[2] = -quat[ibody][1];
- Pkq[3] = quat[ibody][0];
+ Pkq[3] = quat[ibody][0];
}
-
+
tmp = conjqm[ibody][0]*Pkq[0] + conjqm[ibody][1]*Pkq[1] +
- conjqm[ibody][2]*Pkq[2] + conjqm[ibody][3]*Pkq[3];
+ conjqm[ibody][2]*Pkq[2] + conjqm[ibody][3]*Pkq[3];
tmp *= tmp;
-
+
if (fabs(inertia[ibody][k-1]) < 1e-6) tmp = 0.0;
- else tmp /= (8.0 * inertia[ibody][k-1]);
+ else tmp /= (8.0 * inertia[ibody][k-1]);
ke_q += tmp;
}
}
-
+
energy = ke_t + ke_q;
-
+
// thermostat chain energy: from equation 12 in Kameraj et al (JCP 2005)
energy += kt * (nf_t * eta_t[0] + nf_r * eta_r[0]);
-
- for (i = 1; i < t_chain; i++)
+
+ for (i = 1; i < t_chain; i++)
energy += kt * (eta_t[i] + eta_r[i]);
-
+
for (i = 0; i < t_chain; i++) {
energy += 0.5 * q_t[i] * (eta_dot_t[i] * eta_dot_t[i]);
energy += 0.5 * q_r[i] * (eta_dot_r[i] * eta_dot_r[i]);
}
-
+
return energy;
}
/* ----------------------------------------------------------------------
- use state info from restart file to restart the Fix
+ use state info from restart file to restart the Fix
------------------------------------------------------------------------- */
void FixRigidNVT::restart(char *buf)
{
int n = 0;
double *list = (double *) buf;
-
+
int t_chain_prev = static_cast<int> (list[n++]);
if (t_chain_prev != t_chain)
error->all(FLERR,"Cannot restart fix rigid/nvt with different # of chains");
diff --git a/src/fix_rigid_nvt.h b/src/fix_rigid_nvt.h
index e65f281082dcc3ff4eb2e442a630c6758512fdad..9286e0fa02e3f159355b622fdb54aa7fcc9d1eb7 100644
--- a/src/fix_rigid_nvt.h
+++ b/src/fix_rigid_nvt.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -37,7 +37,7 @@ class FixRigidNVT : public FixRigid {
void write_restart(FILE *);
void restart(char *);
void reset_target(double);
-
+
private:
double **conjqm; // conjugate quaternion momentum
double boltz; // boltzman constant
diff --git a/src/fix_setforce.cpp b/src/fix_setforce.cpp
index ee843fbbcee432826ab515d97a745c6c8e07a577..6522e595793c9b4d43b0dc8fb8dde8e86d73af9e 100644
--- a/src/fix_setforce.cpp
+++ b/src/fix_setforce.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -86,7 +86,7 @@ FixSetForce::FixSetForce(LAMMPS *lmp, int narg, char **arg) :
if (iarg+2 > narg) error->all(FLERR,"Illegal fix setforce command");
iregion = domain->find_region(arg[iarg+1]);
if (iregion == -1)
- error->all(FLERR,"Region ID for fix setforce does not exist");
+ error->all(FLERR,"Region ID for fix setforce does not exist");
int n = strlen(arg[iarg+1]) + 1;
idregion = new char[n];
strcpy(idregion,arg[iarg+1]);
@@ -131,7 +131,7 @@ void FixSetForce::init()
if (xstr) {
xvar = input->variable->find(xstr);
- if (xvar < 0)
+ if (xvar < 0)
error->all(FLERR,"Variable name for fix setforce does not exist");
if (input->variable->equalstyle(xvar)) xstyle = EQUAL;
else if (input->variable->atomstyle(xvar)) xstyle = ATOM;
@@ -139,7 +139,7 @@ void FixSetForce::init()
}
if (ystr) {
yvar = input->variable->find(ystr);
- if (yvar < 0)
+ if (yvar < 0)
error->all(FLERR,"Variable name for fix setforce does not exist");
if (input->variable->equalstyle(yvar)) ystyle = EQUAL;
else if (input->variable->atomstyle(yvar)) ystyle = ATOM;
@@ -147,7 +147,7 @@ void FixSetForce::init()
}
if (zstr) {
zvar = input->variable->find(zstr);
- if (zvar < 0)
+ if (zvar < 0)
error->all(FLERR,"Variable name for fix setforce does not exist");
if (input->variable->equalstyle(zvar)) zstyle = EQUAL;
else if (input->variable->atomstyle(zvar)) zstyle = ATOM;
@@ -158,11 +158,11 @@ void FixSetForce::init()
if (iregion >= 0) {
iregion = domain->find_region(idregion);
- if (iregion == -1)
+ if (iregion == -1)
error->all(FLERR,"Region ID for fix setforce does not exist");
}
- if (xstyle == ATOM || ystyle == ATOM || zstyle == ATOM)
+ if (xstyle == ATOM || ystyle == ATOM || zstyle == ATOM)
varflag = ATOM;
else if (xstyle == EQUAL || ystyle == EQUAL || zstyle == EQUAL)
varflag = EQUAL;
@@ -183,7 +183,7 @@ void FixSetForce::init()
if (ystyle == CONSTANT && yvalue != 0.0) flag = 1;
if (zstyle == CONSTANT && zvalue != 0.0) flag = 1;
}
- if (flag)
+ if (flag)
error->all(FLERR,"Cannot use non-zero forces in an energy minimization");
}
@@ -231,16 +231,16 @@ void FixSetForce::post_force(int vflag)
if (varflag == CONSTANT) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- if (iregion >= 0 &&
- !domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2]))
- continue;
-
- foriginal[0] += f[i][0];
- foriginal[1] += f[i][1];
- foriginal[2] += f[i][2];
- if (xstyle) f[i][0] = xvalue;
- if (ystyle) f[i][1] = yvalue;
- if (zstyle) f[i][2] = zvalue;
+ if (iregion >= 0 &&
+ !domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2]))
+ continue;
+
+ foriginal[0] += f[i][0];
+ foriginal[1] += f[i][1];
+ foriginal[2] += f[i][2];
+ if (xstyle) f[i][0] = xvalue;
+ if (ystyle) f[i][1] = yvalue;
+ if (zstyle) f[i][2] = zvalue;
}
// variable force, wrap with clear/add
@@ -253,7 +253,7 @@ void FixSetForce::post_force(int vflag)
else if (xstyle == ATOM && sforce)
input->variable->compute_atom(xvar,igroup,&sforce[0][0],3,0);
if (ystyle == EQUAL) yvalue = input->variable->compute_equal(yvar);
- else if (ystyle == ATOM && sforce)
+ else if (ystyle == ATOM && sforce)
input->variable->compute_atom(yvar,igroup,&sforce[0][1],3,0);
if (zstyle == EQUAL) zvalue = input->variable->compute_equal(zvar);
else if (zstyle == ATOM && sforce)
@@ -263,19 +263,19 @@ void FixSetForce::post_force(int vflag)
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- if (iregion >= 0 &&
- !domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2]))
- continue;
-
- foriginal[0] += f[i][0];
- foriginal[1] += f[i][1];
- foriginal[2] += f[i][2];
- if (xstyle == ATOM) f[i][0] = sforce[i][0];
- else if (xstyle) f[i][0] = xvalue;
- if (ystyle == ATOM) f[i][1] = sforce[i][1];
- else if (ystyle) f[i][1] = yvalue;
- if (zstyle == ATOM) f[i][2] = sforce[i][2];
- else if (zstyle) f[i][2] = zvalue;
+ if (iregion >= 0 &&
+ !domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2]))
+ continue;
+
+ foriginal[0] += f[i][0];
+ foriginal[1] += f[i][1];
+ foriginal[2] += f[i][2];
+ if (xstyle == ATOM) f[i][0] = sforce[i][0];
+ else if (xstyle) f[i][0] = xvalue;
+ if (ystyle == ATOM) f[i][1] = sforce[i][1];
+ else if (ystyle) f[i][1] = yvalue;
+ if (zstyle == ATOM) f[i][2] = sforce[i][2];
+ else if (zstyle) f[i][2] = zvalue;
}
}
}
@@ -291,12 +291,12 @@ void FixSetForce::post_force_respa(int vflag, int ilevel, int iloop)
double **f = atom->f;
int *mask = atom->mask;
int nlocal = atom->nlocal;
-
+
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- if (xstyle) f[i][0] = 0.0;
- if (ystyle) f[i][1] = 0.0;
- if (zstyle) f[i][2] = 0.0;
+ if (xstyle) f[i][0] = 0.0;
+ if (ystyle) f[i][1] = 0.0;
+ if (zstyle) f[i][2] = 0.0;
}
}
}
diff --git a/src/fix_setforce.h b/src/fix_setforce.h
index 7221397fc9aba9925f4f4c5803aa5899e0bc6966..5ced70a473dce3f3f56946583ead1d3627b8e27f 100644
--- a/src/fix_setforce.h
+++ b/src/fix_setforce.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_shake.cpp b/src/fix_shake.cpp
index db40a67da69ff154f1df1d92130830261cc5662b..cb27eb3d7e79938f674432c1d6edd90f062038a3 100644
--- a/src/fix_shake.cpp
+++ b/src/fix_shake.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -107,20 +107,20 @@ FixShake::FixShake(LAMMPS *lmp, int narg, char **arg) :
} else if (mode == 'b') {
int i = atoi(arg[next]);
- if (i < 1 || i > atom->nbondtypes)
- error->all(FLERR,"Invalid bond type index for fix shake");
+ if (i < 1 || i > atom->nbondtypes)
+ error->all(FLERR,"Invalid bond type index for fix shake");
bond_flag[i] = 1;
} else if (mode == 'a') {
int i = atoi(arg[next]);
- if (i < 1 || i > atom->nangletypes)
- error->all(FLERR,"Invalid angle type index for fix shake");
+ if (i < 1 || i > atom->nangletypes)
+ error->all(FLERR,"Invalid angle type index for fix shake");
angle_flag[i] = 1;
} else if (mode == 't') {
int i = atoi(arg[next]);
- if (i < 1 || i > atom->ntypes)
- error->all(FLERR,"Invalid atom type index for fix shake");
+ if (i < 1 || i > atom->ntypes)
+ error->all(FLERR,"Invalid atom type index for fix shake");
type_flag[i] = 1;
} else if (mode == 'm') {
@@ -266,7 +266,7 @@ int FixShake::setmask()
/* ----------------------------------------------------------------------
set bond and angle distances
- this init must happen after force->bond and force->angle inits
+ this init must happen after force->bond and force->angle inits
------------------------------------------------------------------------- */
void FixShake::init()
@@ -296,7 +296,7 @@ void FixShake::init()
if (i < modify->nfix) {
for (int j = i; j < modify->nfix; j++)
if (strcmp(modify->fix[j]->style,"shake") == 0)
- error->all(FLERR,"Shake fix must come before NPT/NPH fix");
+ error->all(FLERR,"Shake fix must come before NPT/NPH fix");
}
// if rRESPA, find associated fix that must exist
@@ -315,7 +315,7 @@ void FixShake::init()
if (force->bond == NULL)
error->all(FLERR,"Bond potential must be defined for SHAKE");
- for (i = 1; i <= atom->nbondtypes; i++)
+ for (i = 1; i <= atom->nbondtypes; i++)
bond_distance[i] = force->bond->equilibrium_distance(i);
// set equilibrium angle distances
@@ -331,7 +331,7 @@ void FixShake::init()
// extract bond types for the 2 bonds in the cluster
// bond types must be same in all clusters of this angle type,
// else set error flag
-
+
flag = 0;
bond1_type = bond2_type = 0;
for (m = 0; m < nlocal; m++) {
@@ -340,46 +340,46 @@ void FixShake::init()
type1 = MIN(shake_type[m][0],shake_type[m][1]);
type2 = MAX(shake_type[m][0],shake_type[m][1]);
if (bond1_type > 0) {
- if (type1 != bond1_type || type2 != bond2_type) {
- flag = 1;
- break;
- }
+ if (type1 != bond1_type || type2 != bond2_type) {
+ flag = 1;
+ break;
+ }
}
bond1_type = type1;
bond2_type = type2;
}
// error check for any bond types that are not the same
-
+
MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_MAX,world);
if (flag_all) error->all(FLERR,"Shake angles have different bond types");
-
+
// insure all procs have bond types
-
+
MPI_Allreduce(&bond1_type,&flag_all,1,MPI_INT,MPI_MAX,world);
bond1_type = flag_all;
MPI_Allreduce(&bond2_type,&flag_all,1,MPI_INT,MPI_MAX,world);
bond2_type = flag_all;
-
+
// if bond types are 0, no SHAKE angles of this type exist
// just skip this angle
-
+
if (bond1_type == 0) {
angle_distance[i] = 0.0;
continue;
}
// compute the angle distance as a function of 2 bond distances
-
+
angle = force->angle->equilibrium_angle(i);
- rsq = 2.0*bond_distance[bond1_type]*bond_distance[bond2_type] *
+ rsq = 2.0*bond_distance[bond1_type]*bond_distance[bond2_type] *
(1.0-cos(angle));
angle_distance[i] = sqrt(rsq);
}
}
/* ----------------------------------------------------------------------
- SHAKE as pre-integrator constraint
+ SHAKE as pre-integrator constraint
------------------------------------------------------------------------- */
void FixShake::setup(int vflag)
@@ -417,7 +417,7 @@ void FixShake::setup(int vflag)
/* ----------------------------------------------------------------------
build list of SHAKE clusters to constrain
if one or more atoms in cluster are on this proc,
- this proc lists the cluster exactly once
+ this proc lists the cluster exactly once
------------------------------------------------------------------------- */
void FixShake::pre_neighbor()
@@ -450,53 +450,53 @@ void FixShake::pre_neighbor()
for (int i = 0; i < nlocal; i++)
if (shake_flag[i]) {
if (shake_flag[i] == 2) {
- atom1 = atom->map(shake_atom[i][0]);
- atom2 = atom->map(shake_atom[i][1]);
- if (atom1 == -1 || atom2 == -1) {
- char str[128];
- sprintf(str,
- "Shake atoms %d %d missing on proc %d at step " BIGINT_FORMAT,
- shake_atom[i][0],shake_atom[i][1],me,update->ntimestep);
- error->one(FLERR,str);
- }
- if (i <= atom1 && i <= atom2) list[nlist++] = i;
+ atom1 = atom->map(shake_atom[i][0]);
+ atom2 = atom->map(shake_atom[i][1]);
+ if (atom1 == -1 || atom2 == -1) {
+ char str[128];
+ sprintf(str,
+ "Shake atoms %d %d missing on proc %d at step " BIGINT_FORMAT,
+ shake_atom[i][0],shake_atom[i][1],me,update->ntimestep);
+ error->one(FLERR,str);
+ }
+ if (i <= atom1 && i <= atom2) list[nlist++] = i;
} else if (shake_flag[i] % 2 == 1) {
- atom1 = atom->map(shake_atom[i][0]);
- atom2 = atom->map(shake_atom[i][1]);
- atom3 = atom->map(shake_atom[i][2]);
- if (atom1 == -1 || atom2 == -1 || atom3 == -1) {
- char str[128];
- sprintf(str,
- "Shake atoms %d %d %d missing on proc %d at step "
- BIGINT_FORMAT,
- shake_atom[i][0],shake_atom[i][1],shake_atom[i][2],
- me,update->ntimestep);
- error->one(FLERR,str);
- }
- if (i <= atom1 && i <= atom2 && i <= atom3) list[nlist++] = i;
+ atom1 = atom->map(shake_atom[i][0]);
+ atom2 = atom->map(shake_atom[i][1]);
+ atom3 = atom->map(shake_atom[i][2]);
+ if (atom1 == -1 || atom2 == -1 || atom3 == -1) {
+ char str[128];
+ sprintf(str,
+ "Shake atoms %d %d %d missing on proc %d at step "
+ BIGINT_FORMAT,
+ shake_atom[i][0],shake_atom[i][1],shake_atom[i][2],
+ me,update->ntimestep);
+ error->one(FLERR,str);
+ }
+ if (i <= atom1 && i <= atom2 && i <= atom3) list[nlist++] = i;
} else {
- atom1 = atom->map(shake_atom[i][0]);
- atom2 = atom->map(shake_atom[i][1]);
- atom3 = atom->map(shake_atom[i][2]);
- atom4 = atom->map(shake_atom[i][3]);
- if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
- char str[128];
- sprintf(str,
- "Shake atoms %d %d %d %d missing on proc %d at step "
- BIGINT_FORMAT,
- shake_atom[i][0],shake_atom[i][1],
- shake_atom[i][2],shake_atom[i][3],
- me,update->ntimestep);
- error->one(FLERR,str);
- }
- if (i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)
- list[nlist++] = i;
+ atom1 = atom->map(shake_atom[i][0]);
+ atom2 = atom->map(shake_atom[i][1]);
+ atom3 = atom->map(shake_atom[i][2]);
+ atom4 = atom->map(shake_atom[i][3]);
+ if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
+ char str[128];
+ sprintf(str,
+ "Shake atoms %d %d %d %d missing on proc %d at step "
+ BIGINT_FORMAT,
+ shake_atom[i][0],shake_atom[i][1],
+ shake_atom[i][2],shake_atom[i][3],
+ me,update->ntimestep);
+ error->one(FLERR,str);
+ }
+ if (i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)
+ list[nlist++] = i;
}
}
}
/* ----------------------------------------------------------------------
- compute the force adjustment for SHAKE constraint
+ compute the force adjustment for SHAKE constraint
------------------------------------------------------------------------- */
void FixShake::post_force(int vflag)
@@ -566,7 +566,7 @@ void FixShake::post_force_respa(int vflag, int ilevel, int iloop)
}
/* ----------------------------------------------------------------------
- count # of degrees-of-freedom removed by SHAKE for atoms in igroup
+ count # of degrees-of-freedom removed by SHAKE for atoms in igroup
------------------------------------------------------------------------- */
int FixShake::dof(int igroup)
@@ -601,7 +601,7 @@ int FixShake::dof(int igroup)
only include atoms in fix group and those bonds/angles specified in input
test whether all clusters are valid
set shake_flag, shake_atom, shake_type values
- set bond,angle types negative so will be ignored in neighbor lists
+ set bond,angle types negative so will be ignored in neighbor lists
------------------------------------------------------------------------- */
void FixShake::find_clusters()
@@ -633,7 +633,7 @@ void FixShake::find_clusters()
// setup ring of procs
int next = me + 1;
- int prev = me -1;
+ int prev = me -1;
if (next == nprocs) next = 0;
if (prev < 0) prev = nprocs - 1;
@@ -700,19 +700,19 @@ void FixShake::find_clusters()
m = atom->map(partner_tag[i][j]);
if (m >= 0 && m < nlocal) {
- partner_mask[i][j] = mask[m];
- partner_type[i][j] = type[m];
- if (nmass) {
- if (rmass) massone = rmass[m];
- else massone = mass[type[m]];
- partner_massflag[i][j] = masscheck(massone);
- }
- n = bondfind(i,tag[i],partner_tag[i][j]);
- if (n >= 0) partner_bondtype[i][j] = bond_type[i][n];
- else {
- n = bondfind(m,tag[i],partner_tag[i][j]);
- if (n >= 0) partner_bondtype[i][j] = bond_type[m][n];
- }
+ partner_mask[i][j] = mask[m];
+ partner_type[i][j] = type[m];
+ if (nmass) {
+ if (rmass) massone = rmass[m];
+ else massone = mass[type[m]];
+ partner_massflag[i][j] = masscheck(massone);
+ }
+ n = bondfind(i,tag[i],partner_tag[i][j]);
+ if (n >= 0) partner_bondtype[i][j] = bond_type[i][n];
+ else {
+ n = bondfind(m,tag[i],partner_tag[i][j]);
+ if (n >= 0) partner_bondtype[i][j] = bond_type[m][n];
+ }
} else nbuf += nper;
}
}
@@ -729,15 +729,15 @@ void FixShake::find_clusters()
for (j = 0; j < npartner[i]; j++) {
m = atom->map(partner_tag[i][j]);
if (m < 0 || m >= nlocal) {
- buf[size] = tag[i];
- buf[size+1] = partner_tag[i][j];
- buf[size+2] = 0;
- buf[size+3] = 0;
- buf[size+4] = 0;
- n = bondfind(i,tag[i],partner_tag[i][j]);
- if (n >= 0) buf[size+5] = bond_type[i][n];
- else buf[size+5] = 0;
- size += nper;
+ buf[size] = tag[i];
+ buf[size+1] = partner_tag[i][j];
+ buf[size+2] = 0;
+ buf[size+3] = 0;
+ buf[size+4] = 0;
+ n = bondfind(i,tag[i],partner_tag[i][j]);
+ if (n >= 0) buf[size+5] = bond_type[i][n];
+ else buf[size+5] = 0;
+ size += nper;
}
}
}
@@ -754,17 +754,17 @@ void FixShake::find_clusters()
while (i < size) {
m = atom->map(buf[i+1]);
if (m >= 0 && m < nlocal) {
- buf[i+2] = mask[m];
- buf[i+3] = type[m];
- if (nmass) {
- if (rmass) massone = rmass[m];
- else massone = mass[type[m]];
- buf[i+4] = masscheck(massone);
- }
- if (buf[i+5] == 0) {
- n = bondfind(m,buf[i],buf[i+1]);
- if (n >= 0) buf[i+5] = bond_type[m][n];
- }
+ buf[i+2] = mask[m];
+ buf[i+3] = type[m];
+ if (nmass) {
+ if (rmass) massone = rmass[m];
+ else massone = mass[type[m]];
+ buf[i+4] = masscheck(massone);
+ }
+ if (buf[i+5] == 0) {
+ n = bondfind(m,buf[i],buf[i+1]);
+ if (n >= 0) buf[i+5] = bond_type[m][n];
+ }
}
i += nper;
}
@@ -837,29 +837,29 @@ void FixShake::find_clusters()
if (partner_bondtype[i][j] <= 0) continue;
if (bond_flag[partner_bondtype[i][j]]) {
- partner_shake[i][j] = 1;
- nshake[i]++;
- continue;
+ partner_shake[i][j] = 1;
+ nshake[i]++;
+ continue;
}
if (type_flag[type[i]] || type_flag[partner_type[i][j]]) {
- partner_shake[i][j] = 1;
- nshake[i]++;
- continue;
+ partner_shake[i][j] = 1;
+ nshake[i]++;
+ continue;
}
if (nmass) {
- if (partner_massflag[i][j]) {
- partner_shake[i][j] = 1;
- nshake[i]++;
- continue;
- } else {
- if (rmass) massone = rmass[i];
- else massone = mass[type[i]];
- if (masscheck(massone)) {
- partner_shake[i][j] = 1;
- nshake[i]++;
- continue;
- }
- }
+ if (partner_massflag[i][j]) {
+ partner_shake[i][j] = 1;
+ nshake[i]++;
+ continue;
+ } else {
+ if (rmass) massone = rmass[i];
+ else massone = mass[type[i]];
+ if (masscheck(massone)) {
+ partner_shake[i][j] = 1;
+ nshake[i]++;
+ continue;
+ }
+ }
}
}
}
@@ -882,7 +882,7 @@ void FixShake::find_clusters()
else nbuf += 3;
}
}
-
+
MPI_Allreduce(&nbuf,&nbufmax,1,MPI_INT,MPI_MAX,world);
buf = new int[nbufmax];
@@ -895,9 +895,9 @@ void FixShake::find_clusters()
for (j = 0; j < npartner[i]; j++) {
m = atom->map(partner_tag[i][j]);
if (m < 0 || m >= nlocal) {
- buf[size] = tag[i];
- buf[size+1] = partner_tag[i][j];
- size += 3;
+ buf[size] = tag[i];
+ buf[size+1] = partner_tag[i][j];
+ size += 3;
}
}
}
@@ -960,7 +960,7 @@ void FixShake::find_clusters()
// -----------------------------------------------------
// set SHAKE arrays that are stored with atoms & add angle constraints
// zero shake arrays for all owned atoms
- // if I am central atom set shake_flag & shake_atom & shake_type
+ // if I am central atom set shake_flag & shake_atom & shake_type
// for 2-atom clusters, I am central atom if my atom ID < partner ID
// for 3-atom clusters, test for angle constraint
// angle will be stored by this atom if it exists
@@ -987,12 +987,12 @@ void FixShake::find_clusters()
if (nshake[i] == 1) {
for (j = 0; j < npartner[i]; j++)
- if (partner_shake[i][j]) break;
+ if (partner_shake[i][j]) break;
if (partner_nshake[i][j] == 1 && tag[i] < partner_tag[i][j]) {
- shake_flag[i] = 2;
- shake_atom[i][0] = tag[i];
- shake_atom[i][1] = partner_tag[i][j];
- shake_type[i][0] = partner_bondtype[i][j];
+ shake_flag[i] = 2;
+ shake_atom[i][0] = tag[i];
+ shake_atom[i][1] = partner_tag[i][j];
+ shake_type[i][0] = partner_bondtype[i][j];
}
}
@@ -1000,12 +1000,12 @@ void FixShake::find_clusters()
shake_flag[i] = 1;
shake_atom[i][0] = tag[i];
for (j = 0; j < npartner[i]; j++)
- if (partner_shake[i][j]) {
- m = shake_flag[i];
- shake_atom[i][m] = partner_tag[i][j];
- shake_type[i][m-1] = partner_bondtype[i][j];
- shake_flag[i]++;
- }
+ if (partner_shake[i][j]) {
+ m = shake_flag[i];
+ shake_atom[i][m] = partner_tag[i][j];
+ shake_type[i][m-1] = partner_bondtype[i][j];
+ shake_flag[i]++;
+ }
}
if (nshake[i] == 2 && angles_allow) {
@@ -1013,8 +1013,8 @@ void FixShake::find_clusters()
if (n < 0) continue;
if (angle_type[i][n] < 0) continue;
if (angle_flag[angle_type[i][n]]) {
- shake_flag[i] = 1;
- shake_type[i][2] = angle_type[i][n];
+ shake_flag[i] = 1;
+ shake_type[i][2] = angle_type[i][n];
}
}
}
@@ -1036,14 +1036,14 @@ void FixShake::find_clusters()
if (partner_shake[i][j] == 0) continue;
m = atom->map(partner_tag[i][j]);
if (m >= 0 && m < nlocal) {
- shake_flag[m] = shake_flag[i];
- shake_atom[m][0] = shake_atom[i][0];
- shake_atom[m][1] = shake_atom[i][1];
- shake_atom[m][2] = shake_atom[i][2];
- shake_atom[m][3] = shake_atom[i][3];
- shake_type[m][0] = shake_type[i][0];
- shake_type[m][1] = shake_type[i][1];
- shake_type[m][2] = shake_type[i][2];
+ shake_flag[m] = shake_flag[i];
+ shake_atom[m][0] = shake_atom[i][0];
+ shake_atom[m][1] = shake_atom[i][1];
+ shake_atom[m][2] = shake_atom[i][2];
+ shake_atom[m][3] = shake_atom[i][3];
+ shake_type[m][0] = shake_type[i][0];
+ shake_type[m][1] = shake_type[i][1];
+ shake_type[m][2] = shake_type[i][2];
} else nbuf += 9;
}
}
@@ -1062,16 +1062,16 @@ void FixShake::find_clusters()
if (partner_shake[i][j] == 0) continue;
m = atom->map(partner_tag[i][j]);
if (m < 0 || m >= nlocal) {
- buf[size] = partner_tag[i][j];
- buf[size+1] = shake_flag[i];
- buf[size+2] = shake_atom[i][0];
- buf[size+3] = shake_atom[i][1];
- buf[size+4] = shake_atom[i][2];
- buf[size+5] = shake_atom[i][3];
- buf[size+6] = shake_type[i][0];
- buf[size+7] = shake_type[i][1];
- buf[size+8] = shake_type[i][2];
- size += 9;
+ buf[size] = partner_tag[i][j];
+ buf[size+1] = shake_flag[i];
+ buf[size+2] = shake_atom[i][0];
+ buf[size+3] = shake_atom[i][1];
+ buf[size+4] = shake_atom[i][2];
+ buf[size+5] = shake_atom[i][3];
+ buf[size+6] = shake_type[i][0];
+ buf[size+7] = shake_type[i][1];
+ buf[size+8] = shake_type[i][2];
+ size += 9;
}
}
}
@@ -1086,14 +1086,14 @@ void FixShake::find_clusters()
while (i < size) {
m = atom->map(buf[i]);
if (m >= 0 && m < nlocal) {
- shake_flag[m] = buf[i+1];
- shake_atom[m][0] = buf[i+2];
- shake_atom[m][1] = buf[i+3];
- shake_atom[m][2] = buf[i+4];
- shake_atom[m][3] = buf[i+5];
- shake_type[m][0] = buf[i+6];
- shake_type[m][1] = buf[i+7];
- shake_type[m][2] = buf[i+8];
+ shake_flag[m] = buf[i+1];
+ shake_atom[m][0] = buf[i+2];
+ shake_atom[m][1] = buf[i+3];
+ shake_atom[m][2] = buf[i+4];
+ shake_atom[m][3] = buf[i+5];
+ shake_type[m][0] = buf[i+6];
+ shake_type[m][1] = buf[i+7];
+ shake_type[m][2] = buf[i+8];
}
i += 9;
}
@@ -1209,29 +1209,29 @@ int FixShake::masscheck(double massone)
/* ----------------------------------------------------------------------
update the unconstrained position of each atom
only for SHAKE clusters, else set to 0.0
- assumes NVE update, seems to be accurate enough for NVT,NPT,NPH as well
+ assumes NVE update, seems to be accurate enough for NVT,NPT,NPH as well
------------------------------------------------------------------------- */
void FixShake::unconstrained_update()
{
double dtfmsq;
-
+
if (rmass) {
for (int i = 0; i < nlocal; i++) {
if (shake_flag[i]) {
- dtfmsq = dtfsq / rmass[i];
- xshake[i][0] = x[i][0] + dtv*v[i][0] + dtfmsq*f[i][0];
- xshake[i][1] = x[i][1] + dtv*v[i][1] + dtfmsq*f[i][1];
- xshake[i][2] = x[i][2] + dtv*v[i][2] + dtfmsq*f[i][2];
+ dtfmsq = dtfsq / rmass[i];
+ xshake[i][0] = x[i][0] + dtv*v[i][0] + dtfmsq*f[i][0];
+ xshake[i][1] = x[i][1] + dtv*v[i][1] + dtfmsq*f[i][1];
+ xshake[i][2] = x[i][2] + dtv*v[i][2] + dtfmsq*f[i][2];
} else xshake[i][2] = xshake[i][1] = xshake[i][0] = 0.0;
}
} else {
for (int i = 0; i < nlocal; i++) {
if (shake_flag[i]) {
- dtfmsq = dtfsq / mass[type[i]];
- xshake[i][0] = x[i][0] + dtv*v[i][0] + dtfmsq*f[i][0];
- xshake[i][1] = x[i][1] + dtv*v[i][1] + dtfmsq*f[i][1];
- xshake[i][2] = x[i][2] + dtv*v[i][2] + dtfmsq*f[i][2];
+ dtfmsq = dtfsq / mass[type[i]];
+ xshake[i][0] = x[i][0] + dtv*v[i][0] + dtfmsq*f[i][0];
+ xshake[i][1] = x[i][1] + dtv*v[i][1] + dtfmsq*f[i][1];
+ xshake[i][2] = x[i][2] + dtv*v[i][2] + dtfmsq*f[i][2];
} else xshake[i][2] = xshake[i][1] = xshake[i][0] = 0.0;
}
}
@@ -1240,7 +1240,7 @@ void FixShake::unconstrained_update()
/* ----------------------------------------------------------------------
update the unconstrained position of each atom in a rRESPA step
only for SHAKE clusters, else set to 0.0
- assumes NVE update, seems to be accurate enough for NVT,NPT,NPH as well
+ assumes NVE update, seems to be accurate enough for NVT,NPT,NPH as well
------------------------------------------------------------------------- */
void FixShake::unconstrained_update_respa(int ilevel)
@@ -1261,34 +1261,34 @@ void FixShake::unconstrained_update_respa(int ilevel)
if (rmass) {
for (int i = 0; i < nlocal; i++) {
if (shake_flag[i]) {
- invmass = 1.0 / rmass[i];
- dtfmsq = dtfsq * invmass;
- xshake[i][0] = x[i][0] + dtv*v[i][0] + dtfmsq*f[i][0];
- xshake[i][1] = x[i][1] + dtv*v[i][1] + dtfmsq*f[i][1];
- xshake[i][2] = x[i][2] + dtv*v[i][2] + dtfmsq*f[i][2];
- for (jlevel = 0; jlevel < ilevel; jlevel++) {
- dtfmsq = dtf_innerhalf * step_respa[jlevel] * invmass;
- xshake[i][0] += dtfmsq*f_level[i][jlevel][0];
- xshake[i][1] += dtfmsq*f_level[i][jlevel][1];
- xshake[i][2] += dtfmsq*f_level[i][jlevel][2];
- }
+ invmass = 1.0 / rmass[i];
+ dtfmsq = dtfsq * invmass;
+ xshake[i][0] = x[i][0] + dtv*v[i][0] + dtfmsq*f[i][0];
+ xshake[i][1] = x[i][1] + dtv*v[i][1] + dtfmsq*f[i][1];
+ xshake[i][2] = x[i][2] + dtv*v[i][2] + dtfmsq*f[i][2];
+ for (jlevel = 0; jlevel < ilevel; jlevel++) {
+ dtfmsq = dtf_innerhalf * step_respa[jlevel] * invmass;
+ xshake[i][0] += dtfmsq*f_level[i][jlevel][0];
+ xshake[i][1] += dtfmsq*f_level[i][jlevel][1];
+ xshake[i][2] += dtfmsq*f_level[i][jlevel][2];
+ }
} else xshake[i][2] = xshake[i][1] = xshake[i][0] = 0.0;
}
} else {
for (int i = 0; i < nlocal; i++) {
if (shake_flag[i]) {
- invmass = 1.0 / mass[type[i]];
- dtfmsq = dtfsq * invmass;
- xshake[i][0] = x[i][0] + dtv*v[i][0] + dtfmsq*f[i][0];
- xshake[i][1] = x[i][1] + dtv*v[i][1] + dtfmsq*f[i][1];
- xshake[i][2] = x[i][2] + dtv*v[i][2] + dtfmsq*f[i][2];
- for (jlevel = 0; jlevel < ilevel; jlevel++) {
- dtfmsq = dtf_innerhalf * step_respa[jlevel] * invmass;
- xshake[i][0] += dtfmsq*f_level[i][jlevel][0];
- xshake[i][1] += dtfmsq*f_level[i][jlevel][1];
- xshake[i][2] += dtfmsq*f_level[i][jlevel][2];
- }
+ invmass = 1.0 / mass[type[i]];
+ dtfmsq = dtfsq * invmass;
+ xshake[i][0] = x[i][0] + dtv*v[i][0] + dtfmsq*f[i][0];
+ xshake[i][1] = x[i][1] + dtv*v[i][1] + dtfmsq*f[i][1];
+ xshake[i][2] = x[i][2] + dtv*v[i][2] + dtfmsq*f[i][2];
+ for (jlevel = 0; jlevel < ilevel; jlevel++) {
+ dtfmsq = dtf_innerhalf * step_respa[jlevel] * invmass;
+ xshake[i][0] += dtfmsq*f_level[i][jlevel][0];
+ xshake[i][1] += dtfmsq*f_level[i][jlevel][1];
+ xshake[i][2] += dtfmsq*f_level[i][jlevel][2];
+ }
} else xshake[i][2] = xshake[i][1] = xshake[i][0] = 0.0;
}
}
@@ -1330,7 +1330,7 @@ void FixShake::shake2(int m)
double s01sq = s01[0]*s01[0] + s01[1]*s01[1] + s01[2]*s01[2];
// a,b,c = coeffs in quadratic equation for lamda
-
+
if (rmass) {
invmass0 = 1.0/rmass[i0];
invmass1 = 1.0/rmass[i1];
@@ -1470,7 +1470,7 @@ void FixShake::shake3(int m)
double determ = a11*a22 - a12*a21;
if (determ == 0.0) error->one(FLERR,"Shake determinant = 0.0");
double determinv = 1.0/determ;
-
+
double a11inv = a22*determinv;
double a12inv = -a12*determinv;
double a21inv = -a21*determinv;
@@ -1498,14 +1498,14 @@ void FixShake::shake3(int m)
double quad1,quad2,b1,b2,lamda01_new,lamda02_new;
while (!done && niter < max_iter) {
- quad1 = quad1_0101 * lamda01*lamda01 + quad1_0202 * lamda02*lamda02 +
+ quad1 = quad1_0101 * lamda01*lamda01 + quad1_0202 * lamda02*lamda02 +
quad1_0102 * lamda01*lamda02;
- quad2 = quad2_0101 * lamda01*lamda01 + quad2_0202 * lamda02*lamda02 +
+ quad2 = quad2_0101 * lamda01*lamda01 + quad2_0202 * lamda02*lamda02 +
quad2_0102 * lamda01*lamda02;
-
+
b1 = bond1*bond1 - s01sq - quad1;
b2 = bond2*bond2 - s02sq - quad2;
-
+
lamda01_new = a11inv*b1 + a12inv*b2;
lamda02_new = a21inv*b1 + a22inv*b2;
@@ -1657,14 +1657,14 @@ void FixShake::shake4(int m)
(s03[0]*r02[0] + s03[1]*r02[1] + s03[2]*r02[2]);
double a33 = 2.0 * (invmass0+invmass3) *
(s03[0]*r03[0] + s03[1]*r03[1] + s03[2]*r03[2]);
-
+
// inverse of matrix;
double determ = a11*a22*a33 + a12*a23*a31 + a13*a21*a32 -
a11*a23*a32 - a12*a21*a33 - a13*a22*a31;
if (determ == 0.0) error->one(FLERR,"Shake determinant = 0.0");
double determinv = 1.0/determ;
-
+
double a11inv = determinv * (a22*a33 - a23*a32);
double a12inv = -determinv * (a12*a33 - a13*a32);
double a13inv = determinv * (a12*a23 - a13*a22);
@@ -1713,23 +1713,23 @@ void FixShake::shake4(int m)
double quad1,quad2,quad3,b1,b2,b3,lamda01_new,lamda02_new,lamda03_new;
while (!done && niter < max_iter) {
- quad1 = quad1_0101 * lamda01*lamda01 +
+ quad1 = quad1_0101 * lamda01*lamda01 +
quad1_0202 * lamda02*lamda02 +
- quad1_0303 * lamda03*lamda03 +
+ quad1_0303 * lamda03*lamda03 +
quad1_0102 * lamda01*lamda02 +
quad1_0103 * lamda01*lamda03 +
quad1_0203 * lamda02*lamda03;
- quad2 = quad2_0101 * lamda01*lamda01 +
+ quad2 = quad2_0101 * lamda01*lamda01 +
quad2_0202 * lamda02*lamda02 +
- quad2_0303 * lamda03*lamda03 +
+ quad2_0303 * lamda03*lamda03 +
quad2_0102 * lamda01*lamda02 +
quad2_0103 * lamda01*lamda03 +
quad2_0203 * lamda02*lamda03;
- quad3 = quad3_0101 * lamda01*lamda01 +
+ quad3 = quad3_0101 * lamda01*lamda01 +
quad3_0202 * lamda02*lamda02 +
- quad3_0303 * lamda03*lamda03 +
+ quad3_0303 * lamda03*lamda03 +
quad3_0102 * lamda01*lamda02 +
quad3_0103 * lamda01*lamda03 +
quad3_0203 * lamda02*lamda03;
@@ -1737,7 +1737,7 @@ void FixShake::shake4(int m)
b1 = bond1*bond1 - s01sq - quad1;
b2 = bond2*bond2 - s02sq - quad2;
b3 = bond3*bond3 - s03sq - quad3;
-
+
lamda01_new = a11inv*b1 + a12inv*b2 + a13inv*b3;
lamda02_new = a21inv*b1 + a22inv*b2 + a23inv*b3;
lamda03_new = a31inv*b1 + a32inv*b2 + a33inv*b3;
@@ -1904,7 +1904,7 @@ void FixShake::shake3angle(int m)
a11*a23*a32 - a12*a21*a33 - a13*a22*a31;
if (determ == 0.0) error->one(FLERR,"Shake determinant = 0.0");
double determinv = 1.0/determ;
-
+
double a11inv = determinv * (a22*a33 - a23*a32);
double a12inv = -determinv * (a12*a33 - a13*a32);
double a13inv = determinv * (a12*a23 - a13*a22);
@@ -1953,23 +1953,23 @@ void FixShake::shake3angle(int m)
double quad1,quad2,quad3,b1,b2,b3,lamda01_new,lamda02_new,lamda12_new;
while (!done && niter < max_iter) {
- quad1 = quad1_0101 * lamda01*lamda01 +
+ quad1 = quad1_0101 * lamda01*lamda01 +
quad1_0202 * lamda02*lamda02 +
- quad1_1212 * lamda12*lamda12 +
+ quad1_1212 * lamda12*lamda12 +
quad1_0102 * lamda01*lamda02 +
quad1_0112 * lamda01*lamda12 +
quad1_0212 * lamda02*lamda12;
- quad2 = quad2_0101 * lamda01*lamda01 +
+ quad2 = quad2_0101 * lamda01*lamda01 +
quad2_0202 * lamda02*lamda02 +
- quad2_1212 * lamda12*lamda12 +
+ quad2_1212 * lamda12*lamda12 +
quad2_0102 * lamda01*lamda02 +
quad2_0112 * lamda01*lamda12 +
quad2_0212 * lamda02*lamda12;
-
- quad3 = quad3_0101 * lamda01*lamda01 +
+
+ quad3 = quad3_0101 * lamda01*lamda01 +
quad3_0202 * lamda02*lamda02 +
- quad3_1212 * lamda12*lamda12 +
+ quad3_1212 * lamda12*lamda12 +
quad3_0102 * lamda01*lamda02 +
quad3_0112 * lamda01*lamda12 +
quad3_0212 * lamda02*lamda12;
@@ -1977,7 +1977,7 @@ void FixShake::shake3angle(int m)
b1 = bond1*bond1 - s01sq - quad1;
b2 = bond2*bond2 - s02sq - quad2;
b3 = bond12*bond12 - s12sq - quad3;
-
+
lamda01_new = a11inv*b1 + a12inv*b2 + a13inv*b3;
lamda02_new = a21inv*b1 + a22inv*b2 + a23inv*b3;
lamda12_new = a31inv*b1 + a32inv*b2 + a33inv*b3;
@@ -2035,7 +2035,7 @@ void FixShake::shake3angle(int m)
}
/* ----------------------------------------------------------------------
- print-out bond & angle statistics
+ print-out bond & angle statistics
------------------------------------------------------------------------- */
void FixShake::stats()
@@ -2081,7 +2081,7 @@ void FixShake::stats()
delz = x[iatom][2] - x[jatom][2];
domain->minimum_image(delx,dely,delz);
r = sqrt(delx*delx + dely*dely + delz*delz);
-
+
m = shake_type[i][j-1];
b_count[m]++;
b_ave[m] += r;
@@ -2142,29 +2142,29 @@ void FixShake::stats()
if (screen) {
fprintf(screen,
- "SHAKE stats (type/ave/delta) on step " BIGINT_FORMAT "\n",
- update->ntimestep);
- for (i = 1; i < nb; i++)
- if (b_count_all[i])
- fprintf(screen," %d %g %g\n",i,
- b_ave_all[i]/b_count_all[i],b_max_all[i]-b_min_all[i]);
- for (i = 1; i < na; i++)
- if (a_count_all[i])
- fprintf(screen," %d %g %g\n",i,
- a_ave_all[i]/a_count_all[i],a_max_all[i]-a_min_all[i]);
+ "SHAKE stats (type/ave/delta) on step " BIGINT_FORMAT "\n",
+ update->ntimestep);
+ for (i = 1; i < nb; i++)
+ if (b_count_all[i])
+ fprintf(screen," %d %g %g\n",i,
+ b_ave_all[i]/b_count_all[i],b_max_all[i]-b_min_all[i]);
+ for (i = 1; i < na; i++)
+ if (a_count_all[i])
+ fprintf(screen," %d %g %g\n",i,
+ a_ave_all[i]/a_count_all[i],a_max_all[i]-a_min_all[i]);
}
if (logfile) {
fprintf(logfile,
- "SHAKE stats (type/ave/delta) on step " BIGINT_FORMAT "\n",
- update->ntimestep);
- for (i = 0; i < nb; i++)
- if (b_count_all[i])
- fprintf(logfile," %d %g %g\n",i,
- b_ave_all[i]/b_count_all[i],b_max_all[i]-b_min_all[i]);
- for (i = 0; i < na; i++)
- if (a_count_all[i])
- fprintf(logfile," %d %g %g\n",i,
- a_ave_all[i]/a_count_all[i],a_max_all[i]-a_min_all[i]);
+ "SHAKE stats (type/ave/delta) on step " BIGINT_FORMAT "\n",
+ update->ntimestep);
+ for (i = 0; i < nb; i++)
+ if (b_count_all[i])
+ fprintf(logfile," %d %g %g\n",i,
+ b_ave_all[i]/b_count_all[i],b_max_all[i]-b_min_all[i]);
+ for (i = 0; i < na; i++)
+ if (a_count_all[i])
+ fprintf(logfile," %d %g %g\n",i,
+ a_ave_all[i]/a_count_all[i],a_max_all[i]-a_min_all[i]);
}
}
@@ -2216,7 +2216,7 @@ int FixShake::anglefind(int i, int n1, int n2)
}
/* ----------------------------------------------------------------------
- memory usage of local atom-based arrays
+ memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double FixShake::memory_usage()
@@ -2231,7 +2231,7 @@ double FixShake::memory_usage()
}
/* ----------------------------------------------------------------------
- allocate local atom-based arrays
+ allocate local atom-based arrays
------------------------------------------------------------------------- */
void FixShake::grow_arrays(int nmax)
@@ -2244,7 +2244,7 @@ void FixShake::grow_arrays(int nmax)
}
/* ----------------------------------------------------------------------
- copy values within local atom-based arrays
+ copy values within local atom-based arrays
------------------------------------------------------------------------- */
void FixShake::copy_arrays(int i, int j)
@@ -2288,7 +2288,7 @@ void FixShake::set_arrays(int i)
}
/* ----------------------------------------------------------------------
- pack values in local atom-based arrays for exchange with another proc
+ pack values in local atom-based arrays for exchange with another proc
------------------------------------------------------------------------- */
int FixShake::pack_exchange(int i, double *buf)
@@ -2326,7 +2326,7 @@ int FixShake::pack_exchange(int i, double *buf)
}
/* ----------------------------------------------------------------------
- unpack values in local atom-based arrays from exchange with another proc
+ unpack values in local atom-based arrays from exchange with another proc
------------------------------------------------------------------------- */
int FixShake::unpack_exchange(int nlocal, double *buf)
diff --git a/src/fix_shake.h b/src/fix_shake.h
index a752357c06aca431bc4986c6631751aadd4a2509..e7db5b0794158b73b2c319ee85c5628ca40a3901 100644
--- a/src/fix_shake.h
+++ b/src/fix_shake.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_shear_history.cpp b/src/fix_shear_history.cpp
index b1ef95806fde2e53f56219810757282dd0b5de07..4f073ee6554bcc242a40c9f633521153d8e29c74 100644
--- a/src/fix_shear_history.cpp
+++ b/src/fix_shear_history.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -86,7 +86,7 @@ int FixShearHistory::setmask()
void FixShearHistory::init()
{
- if (atom->tag_enable == 0)
+ if (atom->tag_enable == 0)
error->all(FLERR,"Pair style granular with history requires atoms have IDs");
}
@@ -135,27 +135,27 @@ void FixShearHistory::pre_exchange()
for (jj = 0; jj < jnum; jj++) {
if (touch[jj]) {
- shear = &allshear[3*jj];
- j = jlist[jj];
- j &= NEIGHMASK;
- if (npartner[i] < MAXTOUCH) {
- m = npartner[i];
- partner[i][m] = tag[j];
- shearpartner[i][m][0] = shear[0];
- shearpartner[i][m][1] = shear[1];
- shearpartner[i][m][2] = shear[2];
- }
- npartner[i]++;
- if (j < nlocal) {
- if (npartner[j] < MAXTOUCH) {
- m = npartner[j];
- partner[j][m] = tag[i];
- shearpartner[j][m][0] = -shear[0];
- shearpartner[j][m][1] = -shear[1];
- shearpartner[j][m][2] = -shear[2];
- }
- npartner[j]++;
- }
+ shear = &allshear[3*jj];
+ j = jlist[jj];
+ j &= NEIGHMASK;
+ if (npartner[i] < MAXTOUCH) {
+ m = npartner[i];
+ partner[i][m] = tag[j];
+ shearpartner[i][m][0] = shear[0];
+ shearpartner[i][m][1] = shear[1];
+ shearpartner[i][m][2] = shear[2];
+ }
+ npartner[i]++;
+ if (j < nlocal) {
+ if (npartner[j] < MAXTOUCH) {
+ m = npartner[j];
+ partner[j][m] = tag[i];
+ shearpartner[j][m][0] = -shear[0];
+ shearpartner[j][m][1] = -shear[1];
+ shearpartner[j][m][2] = -shear[2];
+ }
+ npartner[j]++;
+ }
}
}
}
diff --git a/src/fix_shear_history.h b/src/fix_shear_history.h
index 259a560b50a650f9c33b60544fa72ee6c407c299..58e7bcfb2d0f1b1012755d0196adae626a8e2766 100644
--- a/src/fix_shear_history.h
+++ b/src/fix_shear_history.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_spring.cpp b/src/fix_spring.cpp
index 28a5b74a5e99ec6a8a94824e7fd8dbb1493bc99d..7b214074ca96a7abe9909e930b028d09924c2d09 100644
--- a/src/fix_spring.cpp
+++ b/src/fix_spring.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -71,10 +71,10 @@ FixSpring::FixSpring(LAMMPS *lmp, int narg, char **arg) :
group2 = new char[n];
strcpy(group2,arg[4]);
igroup2 = group->find(arg[4]);
- if (igroup2 == -1)
- error->all(FLERR,"Fix spring couple group ID does not exist");
- if (igroup2 == igroup)
- error->all(FLERR,"Two groups cannot be the same in fix spring couple");
+ if (igroup2 == -1)
+ error->all(FLERR,"Fix spring couple group ID does not exist");
+ if (igroup2 == igroup)
+ error->all(FLERR,"Two groups cannot be the same in fix spring couple");
group2bit = group->bitmask[igroup2];
k_spring = atof(arg[5]);
@@ -120,14 +120,14 @@ void FixSpring::init()
if (group2) {
igroup2 = group->find(group2);
- if (igroup2 == -1)
- error->all(FLERR,"Fix spring couple group ID does not exist");
+ if (igroup2 == -1)
+ error->all(FLERR,"Fix spring couple group ID does not exist");
group2bit = group->bitmask[igroup2];
}
masstotal = group->mass(igroup);
if (styleflag == COUPLE) masstotal2 = group->mass(igroup2);
-
+
if (strstr(update->integrate_style,"respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;
}
@@ -168,9 +168,9 @@ void FixSpring::spring_tether()
group->xcm(igroup,masstotal,xcm);
// fx,fy,fz = components of k * (r-r0) / masstotal
-
+
double dx,dy,dz,fx,fy,fz,r,dr;
-
+
dx = xcm[0] - xc;
dy = xcm[1] - yc;
dz = xcm[2] - zc;
@@ -188,7 +188,7 @@ void FixSpring::spring_tether()
ftotal[1] = -fy;
ftotal[2] = -fz;
ftotal[3] = sqrt(fx*fx + fy*fy + fz*fz);
- if (dr < 0.0) ftotal[3] = -ftotal[3];
+ if (dr < 0.0) ftotal[3] = -ftotal[3];
espring = 0.5*k_spring * dr*dr;
fx /= masstotal;
@@ -203,24 +203,24 @@ void FixSpring::spring_tether()
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
-
+
double massone;
if (rmass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- massone = rmass[i];
- f[i][0] -= fx*massone;
- f[i][1] -= fy*massone;
- f[i][2] -= fz*massone;
+ massone = rmass[i];
+ f[i][0] -= fx*massone;
+ f[i][1] -= fy*massone;
+ f[i][2] -= fz*massone;
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- massone = mass[type[i]];
- f[i][0] -= fx*massone;
- f[i][1] -= fy*massone;
- f[i][2] -= fz*massone;
+ massone = mass[type[i]];
+ f[i][0] -= fx*massone;
+ f[i][1] -= fy*massone;
+ f[i][2] -= fz*massone;
}
}
}
@@ -232,22 +232,22 @@ void FixSpring::spring_couple()
double xcm[3],xcm2[3];
group->xcm(igroup,masstotal,xcm);
group->xcm(igroup2,masstotal2,xcm2);
-
+
// fx,fy,fz = components of k * (r-r0) / masstotal
// fx2,fy2,fz2 = components of k * (r-r0) / masstotal2
-
+
double dx,dy,dz,fx,fy,fz,fx2,fy2,fz2,r,dr;
-
+
dx = xcm2[0] - xcm[0] - xc;
dy = xcm2[1] - xcm[1] - yc;
- dz = xcm2[2] - xcm[2] - zc;
+ dz = xcm2[2] - xcm[2] - zc;
if (!xflag) dx = 0.0;
if (!yflag) dy = 0.0;
if (!zflag) dz = 0.0;
r = sqrt(dx*dx + dy*dy + dz*dz);
r = MAX(r,SMALL);
dr = r - r0;
-
+
fx = k_spring*dx*dr/r;
fy = k_spring*dy*dr/r;
fz = k_spring*dz*dr/r;
@@ -255,7 +255,7 @@ void FixSpring::spring_couple()
ftotal[1] = fy;
ftotal[2] = fz;
ftotal[3] = sqrt(fx*fx + fy*fy + fz*fz);
- if (dr < 0.0) ftotal[3] = -ftotal[3];
+ if (dr < 0.0) ftotal[3] = -ftotal[3];
espring = 0.5*k_spring * dr*dr;
fx2 = fx/masstotal2;
@@ -278,33 +278,33 @@ void FixSpring::spring_couple()
double massone;
if (rmass) {
- for (int i = 0; i < nlocal; i++) {
+ for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
- massone = rmass[i];
- f[i][0] += fx*massone;
- f[i][1] += fy*massone;
- f[i][2] += fz*massone;
+ massone = rmass[i];
+ f[i][0] += fx*massone;
+ f[i][1] += fy*massone;
+ f[i][2] += fz*massone;
}
if (mask[i] & group2bit) {
- massone = rmass[i];
- f[i][0] -= fx2*massone;
- f[i][1] -= fy2*massone;
- f[i][2] -= fz2*massone;
+ massone = rmass[i];
+ f[i][0] -= fx2*massone;
+ f[i][1] -= fy2*massone;
+ f[i][2] -= fz2*massone;
}
}
} else {
- for (int i = 0; i < nlocal; i++) {
+ for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
- massone = mass[type[i]];
- f[i][0] += fx*massone;
- f[i][1] += fy*massone;
- f[i][2] += fz*massone;
+ massone = mass[type[i]];
+ f[i][0] += fx*massone;
+ f[i][1] += fy*massone;
+ f[i][2] += fz*massone;
}
if (mask[i] & group2bit) {
- massone = mass[type[i]];
- f[i][0] -= fx2*massone;
- f[i][1] -= fy2*massone;
- f[i][2] -= fz2*massone;
+ massone = mass[type[i]];
+ f[i][0] -= fx2*massone;
+ f[i][1] -= fy2*massone;
+ f[i][2] -= fz2*massone;
}
}
}
diff --git a/src/fix_spring.h b/src/fix_spring.h
index 92b5fb66733ac2fae68d860f60eb8c3a1d72df89..c1fe8ec499dcdf1de7828f294cbc0a298b7ae5ab 100644
--- a/src/fix_spring.h
+++ b/src/fix_spring.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_spring_rg.cpp b/src/fix_spring_rg.cpp
index c9c6322c6fa4bbcb08b156aa86645ddda74100b5..785fd40e3ee5d27a0e46ea793ad232686ca40bdb 100644
--- a/src/fix_spring_rg.cpp
+++ b/src/fix_spring_rg.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -108,12 +108,12 @@ void FixSpringRG::post_force(int vflag)
int *image = atom->image;
double *mass = atom->mass;
int nlocal = atom->nlocal;
-
+
double massfrac;
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
-
+
int xbox,ybox,zbox;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
diff --git a/src/fix_spring_rg.h b/src/fix_spring_rg.h
index 9abc90fbd4fb289925deac753173919ad99cf739..9ffe9d95837846a57420e2c81e95dff5b835f022 100644
--- a/src/fix_spring_rg.h
+++ b/src/fix_spring_rg.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_spring_self.cpp b/src/fix_spring_self.cpp
index 0b5378d4fed351e2ee1f8888a61b8724fd7c7a16..675a53e495c0ba27317455c95a360a56b20b8deb 100644
--- a/src/fix_spring_self.cpp
+++ b/src/fix_spring_self.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -72,7 +72,7 @@ FixSpringSelf::FixSpringSelf(LAMMPS *lmp, int narg, char **arg) :
atom->add_callback(1);
// xoriginal = initial unwrapped positions of atoms
-
+
double **x = atom->x;
int *mask = atom->mask;
int *image = atom->image;
diff --git a/src/fix_spring_self.h b/src/fix_spring_self.h
index e545b8fbf596b1854c2f872f0ae97f238897d7bf..aa6b546608de7c91e90762c74514af9b9527dbf1 100644
--- a/src/fix_spring_self.h
+++ b/src/fix_spring_self.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_store_force.cpp b/src/fix_store_force.cpp
index 20a0ea412cdee03c26bbd311707f0cbff85b9ac4..3f132be8f2b67d55bff4bedaf25fa8f9c77e614d 100644
--- a/src/fix_store_force.cpp
+++ b/src/fix_store_force.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_store_force.h b/src/fix_store_force.h
index cced61884db8168ab00805e2780a333f4779f395..f68ba8d17b21240322ad7ffe4db4fcc286f83a70 100644
--- a/src/fix_store_force.h
+++ b/src/fix_store_force.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_store_state.cpp b/src/fix_store_state.cpp
index 87f382b7db53bf621af433758f44b3bccaf215a1..1554bf51918fd07c732d8bdd7f57acc99ba1541a 100644
--- a/src/fix_store_state.cpp
+++ b/src/fix_store_state.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -66,7 +66,7 @@ FixStoreState::FixStoreState(LAMMPS *lmp, int narg, char **arg) :
pack_choice[nvalues++] = &FixStoreState::pack_id;
} else if (strcmp(arg[iarg],"mol") == 0) {
if (!atom->molecule_flag)
- error->all(FLERR,"Fix store/state for atom property that isn't allocated");
+ error->all(FLERR,"Fix store/state for atom property that isn't allocated");
pack_choice[nvalues++] = &FixStoreState::pack_molecule;
} else if (strcmp(arg[iarg],"type") == 0) {
pack_choice[nvalues++] = &FixStoreState::pack_type;
@@ -80,28 +80,28 @@ FixStoreState::FixStoreState(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"z") == 0) {
pack_choice[nvalues++] = &FixStoreState::pack_z;
} else if (strcmp(arg[iarg],"xs") == 0) {
- if (domain->triclinic)
- pack_choice[nvalues++] = &FixStoreState::pack_xs_triclinic;
+ if (domain->triclinic)
+ pack_choice[nvalues++] = &FixStoreState::pack_xs_triclinic;
else pack_choice[nvalues++] = &FixStoreState::pack_xs;
} else if (strcmp(arg[iarg],"ys") == 0) {
- if (domain->triclinic)
- pack_choice[nvalues++] = &FixStoreState::pack_ys_triclinic;
+ if (domain->triclinic)
+ pack_choice[nvalues++] = &FixStoreState::pack_ys_triclinic;
else pack_choice[nvalues++] = &FixStoreState::pack_ys;
} else if (strcmp(arg[iarg],"zs") == 0) {
- if (domain->triclinic)
- pack_choice[nvalues++] = &FixStoreState::pack_zs_triclinic;
+ if (domain->triclinic)
+ pack_choice[nvalues++] = &FixStoreState::pack_zs_triclinic;
else pack_choice[nvalues++] = &FixStoreState::pack_zs;
} else if (strcmp(arg[iarg],"xu") == 0) {
- if (domain->triclinic)
- pack_choice[nvalues++] = &FixStoreState::pack_xu_triclinic;
+ if (domain->triclinic)
+ pack_choice[nvalues++] = &FixStoreState::pack_xu_triclinic;
else pack_choice[nvalues++] = &FixStoreState::pack_xu;
} else if (strcmp(arg[iarg],"yu") == 0) {
- if (domain->triclinic)
- pack_choice[nvalues++] = &FixStoreState::pack_yu_triclinic;
+ if (domain->triclinic)
+ pack_choice[nvalues++] = &FixStoreState::pack_yu_triclinic;
else pack_choice[nvalues++] = &FixStoreState::pack_yu;
} else if (strcmp(arg[iarg],"zu") == 0) {
- if (domain->triclinic)
- pack_choice[nvalues++] = &FixStoreState::pack_zu_triclinic;
+ if (domain->triclinic)
+ pack_choice[nvalues++] = &FixStoreState::pack_zu_triclinic;
else pack_choice[nvalues++] = &FixStoreState::pack_zu;
} else if (strcmp(arg[iarg],"ix") == 0) {
pack_choice[nvalues++] = &FixStoreState::pack_ix;
@@ -125,65 +125,65 @@ FixStoreState::FixStoreState(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"q") == 0) {
if (!atom->q_flag)
- error->all(FLERR,"Fix store/state for atom property that isn't allocated");
+ error->all(FLERR,"Fix store/state for atom property that isn't allocated");
pack_choice[nvalues++] = &FixStoreState::pack_q;
} else if (strcmp(arg[iarg],"mux") == 0) {
if (!atom->mu_flag)
- error->all(FLERR,"Fix store/state for atom property that isn't allocated");
+ error->all(FLERR,"Fix store/state for atom property that isn't allocated");
pack_choice[nvalues++] = &FixStoreState::pack_mux;
} else if (strcmp(arg[iarg],"muy") == 0) {
if (!atom->mu_flag)
- error->all(FLERR,"Fix store/state for atom property that isn't allocated");
+ error->all(FLERR,"Fix store/state for atom property that isn't allocated");
pack_choice[nvalues++] = &FixStoreState::pack_muy;
} else if (strcmp(arg[iarg],"muz") == 0) {
if (!atom->mu_flag)
- error->all(FLERR,"Fix store/state for atom property that isn't allocated");
+ error->all(FLERR,"Fix store/state for atom property that isn't allocated");
pack_choice[nvalues++] = &FixStoreState::pack_muz;
} else if (strcmp(arg[iarg],"radius") == 0) {
if (!atom->radius_flag)
- error->all(FLERR,"Fix store/state for atom property that isn't allocated");
+ error->all(FLERR,"Fix store/state for atom property that isn't allocated");
pack_choice[nvalues++] = &FixStoreState::pack_radius;
} else if (strcmp(arg[iarg],"omegax") == 0) {
if (!atom->omega_flag)
- error->all(FLERR,"Fix store/state for atom property that isn't allocated");
+ error->all(FLERR,"Fix store/state for atom property that isn't allocated");
pack_choice[nvalues++] = &FixStoreState::pack_omegax;
} else if (strcmp(arg[iarg],"omegay") == 0) {
if (!atom->omega_flag)
- error->all(FLERR,"Fix store/state for atom property that isn't allocated");
+ error->all(FLERR,"Fix store/state for atom property that isn't allocated");
pack_choice[nvalues++] = &FixStoreState::pack_omegay;
} else if (strcmp(arg[iarg],"omegaz") == 0) {
if (!atom->omega_flag)
- error->all(FLERR,"Fix store/state for atom property that isn't allocated");
+ error->all(FLERR,"Fix store/state for atom property that isn't allocated");
pack_choice[nvalues++] = &FixStoreState::pack_omegaz;
} else if (strcmp(arg[iarg],"angmomx") == 0) {
if (!atom->angmom_flag)
- error->all(FLERR,"Fix store/state for atom property that isn't allocated");
+ error->all(FLERR,"Fix store/state for atom property that isn't allocated");
pack_choice[nvalues++] = &FixStoreState::pack_angmomx;
} else if (strcmp(arg[iarg],"angmomy") == 0) {
if (!atom->angmom_flag)
- error->all(FLERR,"Fix store/state for atom property that isn't allocated");
+ error->all(FLERR,"Fix store/state for atom property that isn't allocated");
pack_choice[nvalues++] = &FixStoreState::pack_angmomy;
} else if (strcmp(arg[iarg],"angmomz") == 0) {
if (!atom->angmom_flag)
- error->all(FLERR,"Fix store/state for atom property that isn't allocated");
+ error->all(FLERR,"Fix store/state for atom property that isn't allocated");
pack_choice[nvalues++] = &FixStoreState::pack_angmomz;
} else if (strcmp(arg[iarg],"tqx") == 0) {
if (!atom->torque_flag)
- error->all(FLERR,"Fix store/state for atom property that isn't allocated");
+ error->all(FLERR,"Fix store/state for atom property that isn't allocated");
pack_choice[nvalues++] = &FixStoreState::pack_tqx;
} else if (strcmp(arg[iarg],"tqy") == 0) {
if (!atom->torque_flag)
- error->all(FLERR,"Fix store/state for atom property that isn't allocated");
+ error->all(FLERR,"Fix store/state for atom property that isn't allocated");
pack_choice[nvalues++] = &FixStoreState::pack_tqy;
} else if (strcmp(arg[iarg],"tqz") == 0) {
if (!atom->torque_flag)
- error->all(FLERR,"Fix store/state for atom property that isn't allocated");
+ error->all(FLERR,"Fix store/state for atom property that isn't allocated");
pack_choice[nvalues++] = &FixStoreState::pack_tqz;
- } else if (strncmp(arg[iarg],"c_",2) == 0 ||
- strncmp(arg[iarg],"f_",2) == 0 ||
- strncmp(arg[iarg],"v_",2) == 0) {
+ } else if (strncmp(arg[iarg],"c_",2) == 0 ||
+ strncmp(arg[iarg],"f_",2) == 0 ||
+ strncmp(arg[iarg],"v_",2) == 0) {
cfv_any = 1;
if (arg[iarg][0] == 'c') which[nvalues] = COMPUTE;
else if (arg[iarg][0] == 'f') which[nvalues] = FIX;
@@ -195,10 +195,10 @@ FixStoreState::FixStoreState(LAMMPS *lmp, int narg, char **arg) :
char *ptr = strchr(suffix,'[');
if (ptr) {
- if (suffix[strlen(suffix)-1] != ']')
- error->all(FLERR,"Illegal fix store/state command");
- argindex[nvalues] = atoi(ptr+1);
- *ptr = '\0';
+ if (suffix[strlen(suffix)-1] != ']')
+ error->all(FLERR,"Illegal fix store/state command");
+ argindex[nvalues] = atoi(ptr+1);
+ *ptr = '\0';
} else argindex[nvalues] = 0;
n = strlen(suffix) + 1;
@@ -232,42 +232,42 @@ FixStoreState::FixStoreState(LAMMPS *lmp, int narg, char **arg) :
if (which[i] == COMPUTE) {
int icompute = modify->find_compute(ids[i]);
if (icompute < 0)
- error->all(FLERR,"Compute ID for fix store/state does not exist");
+ error->all(FLERR,"Compute ID for fix store/state does not exist");
if (modify->compute[icompute]->peratom_flag == 0)
- error->all(FLERR,"Fix store/state compute "
- "does not calculate per-atom values");
- if (argindex[i] == 0 &&
- modify->compute[icompute]->size_peratom_cols != 0)
- error->all(FLERR,"Fix store/state compute does not "
- "calculate a per-atom vector");
+ error->all(FLERR,"Fix store/state compute "
+ "does not calculate per-atom values");
+ if (argindex[i] == 0 &&
+ modify->compute[icompute]->size_peratom_cols != 0)
+ error->all(FLERR,"Fix store/state compute does not "
+ "calculate a per-atom vector");
if (argindex[i] && modify->compute[icompute]->size_peratom_cols == 0)
- error->all(FLERR,"Fix store/state compute does not "
- "calculate a per-atom array");
- if (argindex[i] &&
- argindex[i] > modify->compute[icompute]->size_peratom_cols)
- error->all(FLERR,"Fix store/state compute array is accessed out-of-range");
+ error->all(FLERR,"Fix store/state compute does not "
+ "calculate a per-atom array");
+ if (argindex[i] &&
+ argindex[i] > modify->compute[icompute]->size_peratom_cols)
+ error->all(FLERR,"Fix store/state compute array is accessed out-of-range");
} else if (which[i] == FIX) {
int ifix = modify->find_fix(ids[i]);
if (ifix < 0)
- error->all(FLERR,"Fix ID for fix store/state does not exist");
+ error->all(FLERR,"Fix ID for fix store/state does not exist");
if (modify->fix[ifix]->peratom_flag == 0)
- error->all(FLERR,"Fix store/state fix does not calculate per-atom values");
+ error->all(FLERR,"Fix store/state fix does not calculate per-atom values");
if (argindex[i] == 0 && modify->fix[ifix]->size_peratom_cols != 0)
- error->all(FLERR,"Fix store/state fix does not calculate a per-atom vector");
+ error->all(FLERR,"Fix store/state fix does not calculate a per-atom vector");
if (argindex[i] && modify->fix[ifix]->size_peratom_cols == 0)
- error->all(FLERR,"Fix store/state fix does not calculate a per-atom array");
+ error->all(FLERR,"Fix store/state fix does not calculate a per-atom array");
if (argindex[i] && argindex[i] > modify->fix[ifix]->size_peratom_cols)
- error->all(FLERR,"Fix store/state fix array is accessed out-of-range");
+ error->all(FLERR,"Fix store/state fix array is accessed out-of-range");
if (nevery % modify->fix[ifix]->peratom_freq)
- error->all(FLERR,"Fix for fix store/state not computed at compatible time");
+ error->all(FLERR,"Fix for fix store/state not computed at compatible time");
} else if (which[i] == VARIABLE) {
int ivariable = input->variable->find(ids[i]);
if (ivariable < 0)
- error->all(FLERR,"Variable name for fix store/state does not exist");
+ error->all(FLERR,"Variable name for fix store/state does not exist");
if (input->variable->atomstyle(ivariable) == 0)
- error->all(FLERR,"Fix store/state variable is not atom-style variable");
+ error->all(FLERR,"Fix store/state variable is not atom-style variable");
}
}
@@ -306,7 +306,7 @@ FixStoreState::FixStoreState(LAMMPS *lmp, int narg, char **arg) :
FixStoreState::~FixStoreState()
{
// unregister callbacks to this fix from Atom class
-
+
atom->delete_callback(id,0);
atom->delete_callback(id,1);
@@ -339,19 +339,19 @@ void FixStoreState::init()
if (which[m] == COMPUTE) {
int icompute = modify->find_compute(ids[m]);
if (icompute < 0)
- error->all(FLERR,"Compute ID for fix store/state does not exist");
+ error->all(FLERR,"Compute ID for fix store/state does not exist");
value2index[m] = icompute;
-
+
} else if (which[m] == FIX) {
int ifix = modify->find_fix(ids[m]);
- if (ifix < 0)
- error->all(FLERR,"Fix ID for fix store/state does not exist");
+ if (ifix < 0)
+ error->all(FLERR,"Fix ID for fix store/state does not exist");
value2index[m] = ifix;
} else if (which[m] == VARIABLE) {
int ivariable = input->variable->find(ids[m]);
- if (ivariable < 0)
- error->all(FLERR,"Variable name for fix store/state does not exist");
+ if (ivariable < 0)
+ error->all(FLERR,"Variable name for fix store/state does not exist");
value2index[m] = ivariable;
}
}
@@ -407,41 +407,41 @@ void FixStoreState::end_of_step()
// invoke compute if not previously invoked
if (which[m] == COMPUTE) {
- Compute *compute = modify->compute[n];
- if (!(compute->invoked_flag & INVOKED_PERATOM)) {
- compute->compute_peratom();
- compute->invoked_flag |= INVOKED_PERATOM;
- }
-
- if (j == 0) {
- double *compute_vector = compute->vector_atom;
- for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit) values[i][m] += compute_vector[i];
- } else {
- int jm1 = j - 1;
- double **compute_array = compute->array_atom;
- for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit) values[i][m] += compute_array[i][jm1];
- }
-
+ Compute *compute = modify->compute[n];
+ if (!(compute->invoked_flag & INVOKED_PERATOM)) {
+ compute->compute_peratom();
+ compute->invoked_flag |= INVOKED_PERATOM;
+ }
+
+ if (j == 0) {
+ double *compute_vector = compute->vector_atom;
+ for (i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit) values[i][m] += compute_vector[i];
+ } else {
+ int jm1 = j - 1;
+ double **compute_array = compute->array_atom;
+ for (i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit) values[i][m] += compute_array[i][jm1];
+ }
+
// access fix fields, guaranteed to be ready
-
+
} else if (which[m] == FIX) {
- if (j == 0) {
- double *fix_vector = modify->fix[n]->vector_atom;
- for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit) values[i][m] += fix_vector[i];
- } else {
- int jm1 = j - 1;
- double **fix_array = modify->fix[n]->array_atom;
- for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit) values[i][m] += fix_array[i][jm1];
- }
+ if (j == 0) {
+ double *fix_vector = modify->fix[n]->vector_atom;
+ for (i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit) values[i][m] += fix_vector[i];
+ } else {
+ int jm1 = j - 1;
+ double **fix_array = modify->fix[n]->array_atom;
+ for (i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit) values[i][m] += fix_array[i][jm1];
+ }
// evaluate atom-style variable
-
+
} else if (which[m] == VARIABLE)
- input->variable->compute_atom(n,igroup,&values[0][m],nvalues,0);
+ input->variable->compute_atom(n,igroup,&values[0][m],nvalues,0);
}
}
@@ -738,9 +738,9 @@ void FixStoreState::pack_xs_triclinic(int n)
double *h_inv = domain->h_inv;
for (int i = 0; i < nlocal; i++) {
- if (mask[i] & groupbit)
- vbuf[n] = h_inv[0]*(x[i][0]-boxlo[0]) +
- h_inv[5]*(x[i][1]-boxlo[1]) + h_inv[4]*(x[i][2]-boxlo[2]);
+ if (mask[i] & groupbit)
+ vbuf[n] = h_inv[0]*(x[i][0]-boxlo[0]) +
+ h_inv[5]*(x[i][1]-boxlo[1]) + h_inv[4]*(x[i][2]-boxlo[2]);
else vbuf[n] = 0.0;
n += nvalues;
}
diff --git a/src/fix_store_state.h b/src/fix_store_state.h
index 807c55af10c2032856109c2ba6af2628c89f919c..39eaf183a38c0a58e62da47adc670464024f44d5 100644
--- a/src/fix_store_state.h
+++ b/src/fix_store_state.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_temp_berendsen.cpp b/src/fix_temp_berendsen.cpp
index 9594ae1227061f1f90030fe2f09c3e5eb3fb53b1..4cd6599eec21d5dc907cef441ed78a216f833a43 100644
--- a/src/fix_temp_berendsen.cpp
+++ b/src/fix_temp_berendsen.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -63,7 +63,7 @@ FixTempBerendsen::FixTempBerendsen(LAMMPS *lmp, int narg, char **arg) :
// error checks
- if (t_period <= 0.0)
+ if (t_period <= 0.0)
error->all(FLERR,"Fix temp/berendsen period must be > 0.0");
// create a new compute temp style
@@ -115,7 +115,7 @@ void FixTempBerendsen::init()
if (tstr) {
tvar = input->variable->find(tstr);
- if (tvar < 0)
+ if (tvar < 0)
error->all(FLERR,"Variable name for fix temp/berendsen does not exist");
if (input->variable->equalstyle(tvar)) tstyle = EQUAL;
else error->all(FLERR,"Variable for fix temp/berendsen is invalid style");
@@ -137,7 +137,7 @@ void FixTempBerendsen::end_of_step()
double t_current = temperature->compute_scalar();
if (t_current == 0.0)
error->all(FLERR,
- "Computed temperature for fix temp/berendsen cannot be 0.0");
+ "Computed temperature for fix temp/berendsen cannot be 0.0");
double delta = update->ntimestep - update->beginstep;
delta /= update->endstep - update->beginstep;
@@ -152,7 +152,7 @@ void FixTempBerendsen::end_of_step()
t_target = input->variable->compute_equal(tvar);
if (t_target < 0.0)
error->one(FLERR,
- "Fix temp/berendsen variable returned negative temperature");
+ "Fix temp/berendsen variable returned negative temperature");
modify->addstep_compute(update->ntimestep + nevery);
}
@@ -172,19 +172,19 @@ void FixTempBerendsen::end_of_step()
if (which == NOBIAS) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
- v[i][0] *= lamda;
- v[i][1] *= lamda;
- v[i][2] *= lamda;
+ v[i][0] *= lamda;
+ v[i][1] *= lamda;
+ v[i][2] *= lamda;
}
}
} else {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
- temperature->remove_bias(i,v[i]);
- v[i][0] *= lamda;
- v[i][1] *= lamda;
- v[i][2] *= lamda;
- temperature->restore_bias(i,v[i]);
+ temperature->remove_bias(i,v[i]);
+ v[i][0] *= lamda;
+ v[i][1] *= lamda;
+ v[i][2] *= lamda;
+ temperature->restore_bias(i,v[i]);
}
}
}
@@ -206,13 +206,13 @@ int FixTempBerendsen::modify_param(int narg, char **arg)
strcpy(id_temp,arg[1]);
int icompute = modify->find_compute(id_temp);
- if (icompute < 0)
+ if (icompute < 0)
error->all(FLERR,"Could not find fix_modify temperature ID");
temperature = modify->compute[icompute];
if (temperature->tempflag == 0)
error->all(FLERR,
- "Fix_modify temperature ID does not compute temperature");
+ "Fix_modify temperature ID does not compute temperature");
if (temperature->igroup != igroup && comm->me == 0)
error->warning(FLERR,"Group for fix_modify temp != fix group");
return 2;
@@ -232,7 +232,7 @@ void FixTempBerendsen::reset_target(double t_new)
double FixTempBerendsen::compute_scalar()
{
return energy;
-}
+}
/* ----------------------------------------------------------------------
extract thermostat properties
@@ -243,6 +243,6 @@ void *FixTempBerendsen::extract(const char *str, int &dim)
dim=0;
if (strcmp(str,"t_target") == 0) {
return &t_target;
- }
+ }
return NULL;
}
diff --git a/src/fix_temp_berendsen.h b/src/fix_temp_berendsen.h
index 31ca302cbb5e991c3f494ff611ba4d223c80df83..8fa2d4a3ab2b4532530ad923a2bd7e8f0afd01d5 100644
--- a/src/fix_temp_berendsen.h
+++ b/src/fix_temp_berendsen.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_temp_rescale.cpp b/src/fix_temp_rescale.cpp
index bfa8194be0c31643550aa0296104b3a0363388b4..f28a25f6bc0169e6e3a21c921ca70cbde374b9d4 100644
--- a/src/fix_temp_rescale.cpp
+++ b/src/fix_temp_rescale.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -113,14 +113,14 @@ void FixTempRescale::init()
if (tstr) {
tvar = input->variable->find(tstr);
- if (tvar < 0)
+ if (tvar < 0)
error->all(FLERR,"Variable name for fix temp/rescale does not exist");
if (input->variable->equalstyle(tvar)) tstyle = EQUAL;
else error->all(FLERR,"Variable for fix temp/rescale is invalid style");
}
int icompute = modify->find_compute(id_temp);
- if (icompute < 0)
+ if (icompute < 0)
error->all(FLERR,"Temperature ID for fix temp/rescale does not exist");
temperature = modify->compute[icompute];
@@ -149,7 +149,7 @@ void FixTempRescale::end_of_step()
t_target = input->variable->compute_equal(tvar);
if (t_target < 0.0)
error->one(FLERR,
- "Fix temp/rescale variable returned negative temperature");
+ "Fix temp/rescale variable returned negative temperature");
modify->addstep_compute(update->ntimestep + nevery);
}
@@ -171,21 +171,21 @@ void FixTempRescale::end_of_step()
if (which == NOBIAS) {
for (int i = 0; i < nlocal; i++) {
- if (mask[i] & groupbit) {
- v[i][0] *= factor;
- v[i][1] *= factor;
- v[i][2] *= factor;
- }
+ if (mask[i] & groupbit) {
+ v[i][0] *= factor;
+ v[i][1] *= factor;
+ v[i][2] *= factor;
+ }
}
} else {
for (int i = 0; i < nlocal; i++) {
- if (mask[i] & groupbit) {
- temperature->remove_bias(i,v[i]);
- v[i][0] *= factor;
- v[i][1] *= factor;
- v[i][2] *= factor;
- temperature->restore_bias(i,v[i]);
- }
+ if (mask[i] & groupbit) {
+ temperature->remove_bias(i,v[i]);
+ v[i][0] *= factor;
+ v[i][1] *= factor;
+ v[i][2] *= factor;
+ temperature->restore_bias(i,v[i]);
+ }
}
}
}
@@ -207,13 +207,13 @@ int FixTempRescale::modify_param(int narg, char **arg)
strcpy(id_temp,arg[1]);
int icompute = modify->find_compute(id_temp);
- if (icompute < 0)
+ if (icompute < 0)
error->all(FLERR,"Could not find fix_modify temperature ID");
temperature = modify->compute[icompute];
if (temperature->tempflag == 0)
error->all(FLERR,
- "Fix_modify temperature ID does not compute temperature");
+ "Fix_modify temperature ID does not compute temperature");
if (temperature->igroup != igroup && comm->me == 0)
error->warning(FLERR,"Group for fix_modify temp != fix group");
return 2;
@@ -244,6 +244,6 @@ void *FixTempRescale::extract(const char *str, int &dim)
dim=0;
if (strcmp(str,"t_target") == 0) {
return &t_target;
- }
+ }
return NULL;
}
diff --git a/src/fix_temp_rescale.h b/src/fix_temp_rescale.h
index 1b8d0f8f5593668fe807bfa049639520f9e2f97a..3b4e4cb2c99e6e3395ea55a21da78d674e471979 100644
--- a/src/fix_temp_rescale.h
+++ b/src/fix_temp_rescale.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_thermal_conductivity.cpp b/src/fix_thermal_conductivity.cpp
index e3ec944e6d55e1445294e9bc82d0b38767cde09b..c1f4258a8f544e17c6f5c431c266e77d54d076ce 100644
--- a/src/fix_thermal_conductivity.cpp
+++ b/src/fix_thermal_conductivity.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -35,7 +35,7 @@ using namespace FixConst;
/* ---------------------------------------------------------------------- */
FixThermalConductivity::FixThermalConductivity(LAMMPS *lmp,
- int narg, char **arg) :
+ int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 6) error->all(FLERR,"Illegal fix thermal/conductivity command");
@@ -55,7 +55,7 @@ FixThermalConductivity::FixThermalConductivity(LAMMPS *lmp,
else error->all(FLERR,"Illegal fix thermal/conductivity command");
nbin = atoi(arg[5]);
- if (nbin % 2 || nbin <= 2)
+ if (nbin % 2 || nbin <= 2)
error->all(FLERR,"Illegal fix thermal/conductivity command");
// optional keywords
@@ -66,10 +66,10 @@ FixThermalConductivity::FixThermalConductivity(LAMMPS *lmp,
while (iarg < narg) {
if (strcmp(arg[iarg],"swap") == 0) {
if (iarg+2 > narg)
- error->all(FLERR,"Illegal fix thermal/conductivity command");
+ error->all(FLERR,"Illegal fix thermal/conductivity command");
nswap = atoi(arg[iarg+1]);
if (nswap <= 0)
- error->all(FLERR,"Fix thermal/conductivity swap value must be positive");
+ error->all(FLERR,"Fix thermal/conductivity swap value must be positive");
iarg += 2;
} else error->all(FLERR,"Illegal fix thermal/conductivity command");
}
@@ -184,39 +184,39 @@ void FixThermalConductivity::end_of_step()
else if (coord >= boxhi && periodicity) coord -= prd;
if (coord >= slablo_lo && coord < slablo_hi) {
- ke = v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2];
- if (rmass) ke *= 0.5*rmass[i];
- else ke *= 0.5*mass[type[i]];
- if (nlo < nswap || ke > ke_lo[nswap-1]) {
- for (insert = nlo-1; insert >= 0; insert--)
- if (ke < ke_lo[insert]) break;
- insert++;
- for (m = nlo-1; m >= insert; m--) {
- ke_lo[m+1] = ke_lo[m];
- index_lo[m+1] = index_lo[m];
- }
- ke_lo[insert] = ke;
- index_lo[insert] = i;
- if (nlo < nswap) nlo++;
- }
+ ke = v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2];
+ if (rmass) ke *= 0.5*rmass[i];
+ else ke *= 0.5*mass[type[i]];
+ if (nlo < nswap || ke > ke_lo[nswap-1]) {
+ for (insert = nlo-1; insert >= 0; insert--)
+ if (ke < ke_lo[insert]) break;
+ insert++;
+ for (m = nlo-1; m >= insert; m--) {
+ ke_lo[m+1] = ke_lo[m];
+ index_lo[m+1] = index_lo[m];
+ }
+ ke_lo[insert] = ke;
+ index_lo[insert] = i;
+ if (nlo < nswap) nlo++;
+ }
}
if (coord >= slabhi_lo && coord < slabhi_hi) {
- ke = v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2];
- if (rmass) ke *= 0.5*rmass[i];
- else ke *= 0.5*mass[type[i]];
- if (nhi < nswap || ke < ke_hi[nswap-1]) {
- for (insert = nhi-1; insert >= 0; insert--)
- if (ke > ke_hi[insert]) break;
- insert++;
- for (m = nhi-1; m >= insert; m--) {
- ke_hi[m+1] = ke_hi[m];
- index_hi[m+1] = index_hi[m];
- }
- ke_hi[insert] = ke;
- index_hi[insert] = i;
- if (nhi < nswap) nhi++;
- }
+ ke = v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2];
+ if (rmass) ke *= 0.5*rmass[i];
+ else ke *= 0.5*mass[type[i]];
+ if (nhi < nswap || ke < ke_hi[nswap-1]) {
+ for (insert = nhi-1; insert >= 0; insert--)
+ if (ke > ke_hi[insert]) break;
+ insert++;
+ for (m = nhi-1; m >= insert; m--) {
+ ke_hi[m+1] = ke_hi[m];
+ index_hi[m+1] = index_hi[m];
+ }
+ ke_hi[insert] = ke;
+ index_hi[insert] = i;
+ if (nhi < nswap) nhi++;
+ }
}
}
@@ -240,7 +240,7 @@ void FixThermalConductivity::end_of_step()
else mine[0].value = BIG;
if (ihi < nhi) mine[1].value = ke_hi[ihi];
else mine[1].value = BIG;
-
+
MPI_Allreduce(mine,all,2,MPI_DOUBLE_INT,MPI_MINLOC,world);
if (all[0].value == BIG || all[1].value == BIG) continue;
@@ -272,7 +272,7 @@ void FixThermalConductivity::end_of_step()
eswap -= rbuf[3] * (vcm[0] * (vcm[0] - rbuf[0]) +
vcm[1] * (vcm[1] - rbuf[1]) +
vcm[2] * (vcm[2] - rbuf[2]));
-
+
} else if (me == all[0].proc) {
j = index_lo[ilo++];
sbuf[0] = v[j][0];
@@ -281,7 +281,7 @@ void FixThermalConductivity::end_of_step()
if (rmass) sbuf[3] = rmass[j];
else sbuf[3] = mass[type[j]];
MPI_Sendrecv(sbuf,4,MPI_DOUBLE,all[1].proc,0,
- rbuf,4,MPI_DOUBLE,all[1].proc,0,world,&status);
+ rbuf,4,MPI_DOUBLE,all[1].proc,0,world,&status);
vcm[0] = (sbuf[3]*sbuf[0] + rbuf[3]*rbuf[0]) / (sbuf[3] + rbuf[3]);
vcm[1] = (sbuf[3]*sbuf[1] + rbuf[3]*rbuf[1]) / (sbuf[3] + rbuf[3]);
vcm[2] = (sbuf[3]*sbuf[2] + rbuf[3]*rbuf[2]) / (sbuf[3] + rbuf[3]);
@@ -300,7 +300,7 @@ void FixThermalConductivity::end_of_step()
if (rmass) sbuf[3] = rmass[j];
else sbuf[3] = mass[type[j]];
MPI_Sendrecv(sbuf,4,MPI_DOUBLE,all[0].proc,0,
- rbuf,4,MPI_DOUBLE,all[0].proc,0,world,&status);
+ rbuf,4,MPI_DOUBLE,all[0].proc,0,world,&status);
vcm[0] = (sbuf[3]*sbuf[0] + rbuf[3]*rbuf[0]) / (sbuf[3] + rbuf[3]);
vcm[1] = (sbuf[3]*sbuf[1] + rbuf[3]*rbuf[1]) / (sbuf[3] + rbuf[3]);
vcm[2] = (sbuf[3]*sbuf[2] + rbuf[3]*rbuf[2]) / (sbuf[3] + rbuf[3]);
diff --git a/src/fix_thermal_conductivity.h b/src/fix_thermal_conductivity.h
index 752876247745cdb377e135fb03ccf6c7ec29129f..22688bb7c0b4165ed5ce5530278d0de2b05c7ab8 100644
--- a/src/fix_thermal_conductivity.h
+++ b/src/fix_thermal_conductivity.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_tmd.cpp b/src/fix_tmd.cpp
index 5627802b7cc99164a22e1bf4280f694f23ec0768..1e5ec70e78123e4405a714c7fcf169623bd54b58 100644
--- a/src/fix_tmd.cpp
+++ b/src/fix_tmd.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -47,7 +47,7 @@ FixTMD::FixTMD(LAMMPS *lmp, int narg, char **arg) :
rho_stop = atof(arg[3]);
nfileevery = atoi(arg[5]);
- if (rho_stop < 0 || nfileevery < 0)
+ if (rho_stop < 0 || nfileevery < 0)
error->all(FLERR,"Illegal fix tmd command");
if (nfileevery && narg != 7) error->all(FLERR,"Illegal fix tmd command");
@@ -63,7 +63,7 @@ FixTMD::FixTMD(LAMMPS *lmp, int narg, char **arg) :
// make sure an atom map exists before reading in target coordinates
- if (atom->map_style == 0)
+ if (atom->map_style == 0)
error->all(FLERR,"Cannot use fix TMD unless atom map exists");
// read from arg[4] and store coordinates of final target in xf
@@ -77,12 +77,12 @@ FixTMD::FixTMD(LAMMPS *lmp, int narg, char **arg) :
if (me == 0) {
fp = fopen(arg[6],"w");
if (fp == NULL) {
- char str[128];
- sprintf(str,"Cannot open fix tmd file %s",arg[6]);
- error->one(FLERR,str);
+ char str[128];
+ sprintf(str,"Cannot open fix tmd file %s",arg[6]);
+ error->one(FLERR,str);
}
fprintf(fp,"%s %s\n","# Step rho_target rho_old gamma_back",
- "gamma_forward lambda work_lambda work_analytical");
+ "gamma_forward lambda work_lambda work_analytical");
}
}
@@ -236,7 +236,7 @@ void FixTMD::initial_integrate(int vflag)
b = 2.0*abetotal[1]/masstotal;
e = abetotal[2]/masstotal;
c = e - rho_old*rho_old;
- d = b*b - 4*a*c;
+ d = b*b - 4*a*c;
if (d < 0) d = 0;
if (b >= 0) gamma_max = (-b - sqrt(d))/(2*a);
@@ -245,7 +245,7 @@ void FixTMD::initial_integrate(int vflag)
if (a == 0.0) gamma_back = 0;
c = e - rho_target*rho_target;
- d = b*b - 4*a*c;
+ d = b*b - 4*a*c;
if (d < 0) d = 0;
if (b >= 0) gamma_max = (-b - sqrt(d))/(2*a);
else gamma_max = (-b + sqrt(d))/(2*a);
@@ -280,16 +280,16 @@ void FixTMD::initial_integrate(int vflag)
// stat write of mean constraint force based on previous time step constraint
- if (nfileevery && me == 0) {
- work_analytical +=
+ if (nfileevery && me == 0) {
+ work_analytical +=
(-frtotal - kttotal/dtv/dtf)*(rho_target - rho_old)/rho_old;
lambda = gamma_back*rho_old*masstotal/dtv/dtf;
work_lambda += lambda*(rho_target - rho_old);
- if (!(update->ntimestep % nfileevery) &&
- (previous_stat != update->ntimestep)) {
+ if (!(update->ntimestep % nfileevery) &&
+ (previous_stat != update->ntimestep)) {
fprintf(fp,
- BIGINT_FORMAT " %g %g %g %g %g %g %g\n",
- update->ntimestep,rho_target,rho_old,
+ BIGINT_FORMAT " %g %g %g %g %g %g %g\n",
+ update->ntimestep,rho_target,rho_old,
gamma_back,gamma_forward,lambda,work_lambda,work_analytical);
fflush(fp);
previous_stat = update->ntimestep;
@@ -428,9 +428,9 @@ void FixTMD::readfile(char *file)
if (me == 0) {
m = 0;
for (nlines = 0; nlines < CHUNK; nlines++) {
- ptr = fgets(&buffer[m],MAXLINE,fp);
- if (ptr == NULL) break;
- m += strlen(&buffer[m]);
+ ptr = fgets(&buffer[m],MAXLINE,fp);
+ if (ptr == NULL) break;
+ m += strlen(&buffer[m]);
}
if (ptr == NULL) eof = 1;
buffer[m++] = '\n';
@@ -447,54 +447,54 @@ void FixTMD::readfile(char *file)
*next = '\0';
if (firstline) {
- if (strstr(bufptr,"xlo xhi")) {
- double lo,hi;
- sscanf(bufptr,"%lg %lg",&lo,&hi);
- xprd = hi - lo;
- bufptr = next + 1;
- continue;
- } else if (strstr(bufptr,"ylo yhi")) {
- double lo,hi;
- sscanf(bufptr,"%lg %lg",&lo,&hi);
- yprd = hi - lo;
- bufptr = next + 1;
- continue;
- } else if (strstr(bufptr,"zlo zhi")) {
- double lo,hi;
- sscanf(bufptr,"%lg %lg",&lo,&hi);
- zprd = hi - lo;
- bufptr = next + 1;
- continue;
- } else if (atom->count_words(bufptr) == 4) {
- if (xprd >= 0.0 || yprd >= 0.0 || zprd >= 0.0)
- error->all(FLERR,"Incorrect format in TMD target file");
- imageflag = 0;
- firstline = 0;
- } else if (atom->count_words(bufptr) == 7) {
- if (xprd < 0.0 || yprd < 0.0 || zprd < 0.0)
- error->all(FLERR,"Incorrect format in TMD target file");
- imageflag = 1;
- firstline = 0;
- } else error->all(FLERR,"Incorrect format in TMD target file");
+ if (strstr(bufptr,"xlo xhi")) {
+ double lo,hi;
+ sscanf(bufptr,"%lg %lg",&lo,&hi);
+ xprd = hi - lo;
+ bufptr = next + 1;
+ continue;
+ } else if (strstr(bufptr,"ylo yhi")) {
+ double lo,hi;
+ sscanf(bufptr,"%lg %lg",&lo,&hi);
+ yprd = hi - lo;
+ bufptr = next + 1;
+ continue;
+ } else if (strstr(bufptr,"zlo zhi")) {
+ double lo,hi;
+ sscanf(bufptr,"%lg %lg",&lo,&hi);
+ zprd = hi - lo;
+ bufptr = next + 1;
+ continue;
+ } else if (atom->count_words(bufptr) == 4) {
+ if (xprd >= 0.0 || yprd >= 0.0 || zprd >= 0.0)
+ error->all(FLERR,"Incorrect format in TMD target file");
+ imageflag = 0;
+ firstline = 0;
+ } else if (atom->count_words(bufptr) == 7) {
+ if (xprd < 0.0 || yprd < 0.0 || zprd < 0.0)
+ error->all(FLERR,"Incorrect format in TMD target file");
+ imageflag = 1;
+ firstline = 0;
+ } else error->all(FLERR,"Incorrect format in TMD target file");
}
if (imageflag)
- sscanf(bufptr,"%d %lg %lg %lg %d %d %d",&tag,&x,&y,&z,&ix,&iy,&iz);
+ sscanf(bufptr,"%d %lg %lg %lg %d %d %d",&tag,&x,&y,&z,&ix,&iy,&iz);
else
- sscanf(bufptr,"%d %lg %lg %lg",&tag,&x,&y,&z);
+ sscanf(bufptr,"%d %lg %lg %lg",&tag,&x,&y,&z);
m = atom->map(tag);
if (m >= 0 && m < nlocal && mask[m] & groupbit) {
- if (imageflag) {
- xf[m][0] = x + ix*xprd;
- xf[m][1] = y + iy*yprd;
- xf[m][2] = z + iz*zprd;
- } else {
- xf[m][0] = x;
- xf[m][1] = y;
- xf[m][2] = z;
- }
- ncount++;
+ if (imageflag) {
+ xf[m][0] = x + ix*xprd;
+ xf[m][1] = y + iy*yprd;
+ xf[m][2] = z + iz*zprd;
+ } else {
+ xf[m][0] = x;
+ xf[m][1] = y;
+ xf[m][2] = z;
+ }
+ ncount++;
}
bufptr = next + 1;
diff --git a/src/fix_tmd.h b/src/fix_tmd.h
index 49768293e6f960164b14b34facc631e31a794fa8..4bfae04ecb57867ddd80a5168d40373ac50edd5c 100644
--- a/src/fix_tmd.h
+++ b/src/fix_tmd.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_ttm.cpp b/src/fix_ttm.cpp
index 8f5eecfc7aab8eb0df875a4c024d63c5f7a9c5fe..405842d6a42a60a957440be3bb7ba1cd7096ab03 100644
--- a/src/fix_ttm.cpp
+++ b/src/fix_ttm.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -89,9 +89,9 @@ FixTTM::FixTTM(LAMMPS *lmp, int narg, char **arg) :
// error check
if (seed <= 0) error->all(FLERR,"Invalid random number seed in fix ttm command");
- if (electronic_specific_heat <= 0.0)
+ if (electronic_specific_heat <= 0.0)
error->all(FLERR,"Fix ttm electronic_specific_heat must be > 0.0");
- if (electronic_density <= 0.0)
+ if (electronic_density <= 0.0)
error->all(FLERR,"Fix ttm electronic_density must be > 0.0");
if (electronic_thermal_conductivity < 0.0)
error->all(FLERR,"Fix ttm electronic_thermal_conductivity must be >= 0.0");
@@ -123,14 +123,14 @@ FixTTM::FixTTM(LAMMPS *lmp, int narg, char **arg) :
memory->create(sum_mass_vsq,nxnodes,nynodes,nznodes,"ttm:sum_mass_vsq");
memory->create(sum_vsq_all,nxnodes,nynodes,nznodes,"ttm:sum_vsq_all");
memory->create(sum_mass_vsq_all,nxnodes,nynodes,nznodes,
- "ttm:sum_mass_vsq_all");
+ "ttm:sum_mass_vsq_all");
memory->create(T_electron_old,nxnodes,nynodes,nznodes,"ttm:T_electron_old");
memory->create(T_electron,nxnodes,nynodes,nznodes,"ttm:T_electron");
memory->create(net_energy_transfer,nxnodes,nynodes,nznodes,
- "TTM:net_energy_transfer");
+ "TTM:net_energy_transfer");
memory->create(net_energy_transfer_all,nxnodes,nynodes,nznodes,
- "TTM:net_energy_transfer_all");
-
+ "TTM:net_energy_transfer_all");
+
flangevin = NULL;
grow_arrays(atom->nmax);
@@ -173,7 +173,7 @@ FixTTM::~FixTTM()
memory->destroy(T_electron);
memory->destroy(flangevin);
memory->destroy(net_energy_transfer);
- memory->destroy(net_energy_transfer_all);
+ memory->destroy(net_energy_transfer_all);
}
/* ---------------------------------------------------------------------- */
@@ -202,7 +202,7 @@ void FixTTM::init()
for (int i = 1; i <= atom->ntypes; i++) {
gfactor1[i] = - gamma_p / force->ftm2v;
- gfactor2[i] =
+ gfactor2[i] =
sqrt(24.0*force->boltz*gamma_p/update->dt/force->mvv2e) / force->ftm2v;
}
@@ -259,7 +259,7 @@ void FixTTM::post_force(int vflag)
while (iynode < 0) iynode += nynodes;
while (iznode < 0) iznode += nznodes;
- if (T_electron[ixnode][iynode][iznode] < 0)
+ if (T_electron[ixnode][iynode][iznode] < 0)
error->all(FLERR,"Electronic temperature dropped below zero");
double tsqrt = sqrt(T_electron[ixnode][iynode][iznode]);
@@ -318,7 +318,7 @@ void FixTTM::post_force_respa_setup(int vflag, int ilevel, int iloop)
void FixTTM::reset_dt()
{
for (int i = 1; i <= atom->ntypes; i++)
- gfactor2[i] =
+ gfactor2[i] =
sqrt(24.0*force->boltz*gamma_p/update->dt/force->mvv2e) / force->ftm2v;
}
@@ -370,12 +370,12 @@ void FixTTM::end_of_step()
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
-
+
for (int ixnode = 0; ixnode < nxnodes; ixnode++)
for (int iynode = 0; iynode < nynodes; iynode++)
for (int iznode = 0; iznode < nznodes; iznode++)
net_energy_transfer[ixnode][iynode][iznode] = 0;
-
+
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
double xscale = (x[i][0] - domain->boxlo[0])/domain->xprd;
@@ -390,14 +390,14 @@ void FixTTM::end_of_step()
while (ixnode < 0) ixnode += nxnodes;
while (iynode < 0) iynode += nynodes;
while (iznode < 0) iznode += nznodes;
- net_energy_transfer[ixnode][iynode][iznode] +=
- (flangevin[i][0]*v[i][0] + flangevin[i][1]*v[i][1] +
- flangevin[i][2]*v[i][2]);
+ net_energy_transfer[ixnode][iynode][iznode] +=
+ (flangevin[i][0]*v[i][0] + flangevin[i][1]*v[i][1] +
+ flangevin[i][2]*v[i][2]);
}
-
+
MPI_Allreduce(&net_energy_transfer[0][0][0],
- &net_energy_transfer_all[0][0][0],
- total_nnodes,MPI_DOUBLE,MPI_SUM,world);
+ &net_energy_transfer_all[0][0][0],
+ total_nnodes,MPI_DOUBLE,MPI_SUM,world);
double dx = domain->xprd/nxnodes;
double dy = domain->yprd/nynodes;
@@ -409,19 +409,19 @@ void FixTTM::end_of_step()
int num_inner_timesteps = 1;
double inner_dt = update->dt;
- double stability_criterion = 1.0 -
- 2.0*inner_dt/(electronic_specific_heat*electronic_density) *
+ double stability_criterion = 1.0 -
+ 2.0*inner_dt/(electronic_specific_heat*electronic_density) *
(electronic_thermal_conductivity*(1.0/dx/dx + 1.0/dy/dy + 1.0/dz/dz));
if (stability_criterion < 0.0) {
- inner_dt = 0.5*(electronic_specific_heat*electronic_density) /
+ inner_dt = 0.5*(electronic_specific_heat*electronic_density) /
(electronic_thermal_conductivity*(1.0/dx/dx + 1.0/dy/dy + 1.0/dz/dz));
num_inner_timesteps = static_cast<int>(update->dt/inner_dt) + 1;
inner_dt = update->dt/double(num_inner_timesteps);
- if (num_inner_timesteps > 1000000)
+ if (num_inner_timesteps > 1000000)
error->warning(FLERR,"Too many inner timesteps in fix ttm",0);
}
- for (int ith_inner_timestep = 0; ith_inner_timestep < num_inner_timesteps;
+ for (int ith_inner_timestep = 0; ith_inner_timestep < num_inner_timesteps;
ith_inner_timestep++) {
for (int ixnode = 0; ixnode < nxnodes; ixnode++)
@@ -429,7 +429,7 @@ void FixTTM::end_of_step()
for (int iznode = 0; iznode < nznodes; iznode++)
T_electron_old[ixnode][iynode][iznode] =
T_electron[ixnode][iynode][iznode];
-
+
// compute new electron T profile
for (int ixnode = 0; ixnode < nxnodes; ixnode++)
@@ -447,41 +447,41 @@ void FixTTM::end_of_step()
if (left_xnode == -1) left_xnode = nxnodes - 1;
if (left_ynode == -1) left_ynode = nynodes - 1;
if (left_znode == -1) left_znode = nznodes - 1;
- T_electron[ixnode][iynode][iznode] =
- T_electron_old[ixnode][iynode][iznode] +
- inner_dt/(electronic_specific_heat*electronic_density) *
+ T_electron[ixnode][iynode][iznode] =
+ T_electron_old[ixnode][iynode][iznode] +
+ inner_dt/(electronic_specific_heat*electronic_density) *
(electronic_thermal_conductivity *
- ((T_electron_old[right_xnode][iynode][iznode] +
- T_electron_old[left_xnode][iynode][iznode] -
+ ((T_electron_old[right_xnode][iynode][iznode] +
+ T_electron_old[left_xnode][iynode][iznode] -
2*T_electron_old[ixnode][iynode][iznode])/dx/dx +
- (T_electron_old[ixnode][right_ynode][iznode] +
- T_electron_old[ixnode][left_ynode][iznode] -
+ (T_electron_old[ixnode][right_ynode][iznode] +
+ T_electron_old[ixnode][left_ynode][iznode] -
2*T_electron_old[ixnode][iynode][iznode])/dy/dy +
- (T_electron_old[ixnode][iynode][right_znode] +
- T_electron_old[ixnode][iynode][left_znode] -
+ (T_electron_old[ixnode][iynode][right_znode] +
+ T_electron_old[ixnode][iynode][left_znode] -
2*T_electron_old[ixnode][iynode][iznode])/dz/dz) -
- (net_energy_transfer_all[ixnode][iynode][iznode])/del_vol);
+ (net_energy_transfer_all[ixnode][iynode][iznode])/del_vol);
}
}
// output nodal temperatures for current timestep
- if ((nfileevery) && !(update->ntimestep % nfileevery)) {
+ if ((nfileevery) && !(update->ntimestep % nfileevery)) {
// compute atomic Ta for each grid point
-
+
for (int ixnode = 0; ixnode < nxnodes; ixnode++)
for (int iynode = 0; iynode < nynodes; iynode++)
for (int iznode = 0; iznode < nznodes; iznode++) {
nsum[ixnode][iynode][iznode] = 0;
nsum_all[ixnode][iynode][iznode] = 0;
- sum_vsq[ixnode][iynode][iznode] = 0.0;
+ sum_vsq[ixnode][iynode][iznode] = 0.0;
sum_mass_vsq[ixnode][iynode][iznode] = 0.0;
sum_vsq_all[ixnode][iynode][iznode] = 0.0;
sum_mass_vsq_all[ixnode][iynode][iznode] = 0.0;
- }
+ }
- double massone;
+ double massone;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (rmass) massone = rmass[i];
@@ -503,14 +503,14 @@ void FixTTM::end_of_step()
sum_vsq[ixnode][iynode][iznode] += vsq;
sum_mass_vsq[ixnode][iynode][iznode] += massone*vsq;
}
-
+
MPI_Allreduce(&nsum[0][0][0],&nsum_all[0][0][0],total_nnodes,
MPI_INT,MPI_SUM,world);
MPI_Allreduce(&sum_vsq[0][0][0],&sum_vsq_all[0][0][0],total_nnodes,
MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(&sum_mass_vsq[0][0][0],&sum_mass_vsq_all[0][0][0],
total_nnodes,MPI_DOUBLE,MPI_SUM,world);
-
+
if (me == 0) {
fprintf(fp,BIGINT_FORMAT,update->ntimestep);
@@ -524,7 +524,7 @@ void FixTTM::end_of_step()
(3.0*force->boltz*nsum_all[ixnode][iynode][iznode]/force->mvv2e);
fprintf(fp," %f",T_a);
}
-
+
fprintf(fp,"\t");
for (int ixnode = 0; ixnode < nxnodes; ixnode++)
for (int iynode = 0; iynode < nynodes; iynode++)
@@ -549,10 +549,10 @@ double FixTTM::memory_usage()
/* ---------------------------------------------------------------------- */
-void FixTTM::grow_arrays(int ngrow)
+void FixTTM::grow_arrays(int ngrow)
{
- memory->grow(flangevin,ngrow,3,"TTM:flangevin");
+ memory->grow(flangevin,ngrow,3,"TTM:flangevin");
}
@@ -574,11 +574,11 @@ double FixTTM::compute_vector(int n)
for (int ixnode = 0; ixnode < nxnodes; ixnode++)
for (int iynode = 0; iynode < nynodes; iynode++)
for (int iznode = 0; iznode < nznodes; iznode++) {
- e_energy +=
- T_electron[ixnode][iynode][iznode]*electronic_specific_heat*
- electronic_density*del_vol;
- transfer_energy +=
- net_energy_transfer_all[ixnode][iynode][iznode]*update->dt;
+ e_energy +=
+ T_electron[ixnode][iynode][iznode]*electronic_specific_heat*
+ electronic_density*del_vol;
+ transfer_energy +=
+ net_energy_transfer_all[ixnode][iynode][iznode]*update->dt;
}
if (n == 0) return e_energy;
@@ -587,7 +587,7 @@ double FixTTM::compute_vector(int n)
}
/* ----------------------------------------------------------------------
- pack entire state of Fix into one write
+ pack entire state of Fix into one write
------------------------------------------------------------------------- */
void FixTTM::write_restart(FILE *fp)
@@ -597,12 +597,12 @@ void FixTTM::write_restart(FILE *fp)
int n = 0;
rlist[n++] = seed;
-
+
for (int ixnode = 0; ixnode < nxnodes; ixnode++)
for (int iynode = 0; iynode < nynodes; iynode++)
for (int iznode = 0; iznode < nznodes; iznode++)
rlist[n++] = T_electron[ixnode][iynode][iznode];
-
+
if (comm->me == 0) {
int size = n * sizeof(double);
fwrite(&size,sizeof(int),1,fp);
@@ -613,23 +613,23 @@ void FixTTM::write_restart(FILE *fp)
}
/* ----------------------------------------------------------------------
- use state info from restart file to restart the Fix
+ use state info from restart file to restart the Fix
------------------------------------------------------------------------- */
void FixTTM::restart(char *buf)
{
int n = 0;
double *rlist = (double *) buf;
-
+
// the seed must be changed from the initial seed
seed = static_cast<int> (0.5*rlist[n++]);
-
+
for (int ixnode = 0; ixnode < nxnodes; ixnode++)
for (int iynode = 0; iynode < nynodes; iynode++)
for (int iznode = 0; iznode < nznodes; iznode++)
T_electron[ixnode][iynode][iznode] = rlist[n++];
-
+
delete random;
random = new RanMars(lmp,seed+comm->me);
}
diff --git a/src/fix_ttm.h b/src/fix_ttm.h
index 6669e21d63b5bb77c7bac055289c7782459884c9..f8ed2e626b6cc23a4c04d68512c8c010378b2af8 100644
--- a/src/fix_ttm.h
+++ b/src/fix_ttm.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -44,7 +44,7 @@ class FixTTM : public Fix {
int size_restart(int);
int maxsize_restart();
double memory_usage();
- void grow_arrays(int);
+ void grow_arrays(int);
double compute_vector(int);
private:
@@ -58,7 +58,7 @@ class FixTTM : public Fix {
int ***nsum;
int ***nsum_all,***T_initial_set;
double *gfactor1,*gfactor2,*ratio;
- double **flangevin;
+ double **flangevin;
double ***T_electron,***T_electron_old;
double ***sum_vsq,***sum_mass_vsq;
double ***sum_vsq_all,***sum_mass_vsq_all;
diff --git a/src/fix_viscosity.cpp b/src/fix_viscosity.cpp
index e566a5057efe4012016944409253cd81a75618dd..24f0a911c5b7ad911cfd2c84526274e42d3bafab 100644
--- a/src/fix_viscosity.cpp
+++ b/src/fix_viscosity.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -79,7 +79,7 @@ FixViscosity::FixViscosity(LAMMPS *lmp, int narg, char **arg) :
if (strcmp(arg[iarg+1],"INF") == 0) vtarget = BIG;
else vtarget = atof(arg[iarg+1]);
if (vtarget <= 0.0)
- error->all(FLERR,"Fix viscosity vtarget value must be positive");
+ error->all(FLERR,"Fix viscosity vtarget value must be positive");
iarg += 2;
} else error->all(FLERR,"Illegal fix viscosity command");
}
@@ -192,37 +192,37 @@ void FixViscosity::end_of_step()
else if (coord >= boxhi && periodicity) coord -= prd;
if (coord >= slablo_lo && coord < slablo_hi) {
- if (v[i][vdim] < 0.0) continue;
- delta = fabs(v[i][vdim] - vtarget);
- if (npositive < nswap || delta < pos_delta[nswap-1]) {
- for (insert = npositive-1; insert >= 0; insert--)
- if (delta > pos_delta[insert]) break;
- insert++;
- for (m = npositive-1; m >= insert; m--) {
- pos_delta[m+1] = pos_delta[m];
- pos_index[m+1] = pos_index[m];
- }
- pos_delta[insert] = delta;
- pos_index[insert] = i;
- if (npositive < nswap) npositive++;
- }
+ if (v[i][vdim] < 0.0) continue;
+ delta = fabs(v[i][vdim] - vtarget);
+ if (npositive < nswap || delta < pos_delta[nswap-1]) {
+ for (insert = npositive-1; insert >= 0; insert--)
+ if (delta > pos_delta[insert]) break;
+ insert++;
+ for (m = npositive-1; m >= insert; m--) {
+ pos_delta[m+1] = pos_delta[m];
+ pos_index[m+1] = pos_index[m];
+ }
+ pos_delta[insert] = delta;
+ pos_index[insert] = i;
+ if (npositive < nswap) npositive++;
+ }
}
if (coord >= slabhi_lo && coord < slabhi_hi) {
- if (v[i][vdim] > 0.0) continue;
- delta = fabs(v[i][vdim] + vtarget);
- if (nnegative < nswap || delta < neg_delta[nswap-1]) {
- for (insert = nnegative-1; insert >= 0; insert--)
- if (delta > neg_delta[insert]) break;
- insert++;
- for (m = nnegative-1; m >= insert; m--) {
- neg_delta[m+1] = neg_delta[m];
- neg_index[m+1] = neg_index[m];
- }
- neg_delta[insert] = delta;
- neg_index[insert] = i;
- if (nnegative < nswap) nnegative++;
- }
+ if (v[i][vdim] > 0.0) continue;
+ delta = fabs(v[i][vdim] + vtarget);
+ if (nnegative < nswap || delta < neg_delta[nswap-1]) {
+ for (insert = nnegative-1; insert >= 0; insert--)
+ if (delta > neg_delta[insert]) break;
+ insert++;
+ for (m = nnegative-1; m >= insert; m--) {
+ neg_delta[m+1] = neg_delta[m];
+ neg_index[m+1] = neg_index[m];
+ }
+ neg_delta[insert] = delta;
+ neg_index[insert] = i;
+ if (nnegative < nswap) nnegative++;
+ }
}
}
@@ -249,7 +249,7 @@ void FixViscosity::end_of_step()
else mine[0].value = BIG;
if (inegative < nnegative) mine[1].value = neg_delta[inegative];
else mine[1].value = BIG;
-
+
MPI_Allreduce(mine,all,2,MPI_DOUBLE_INT,MPI_MINLOC,world);
if (all[0].value == BIG || all[1].value == BIG) continue;
@@ -267,14 +267,14 @@ void FixViscosity::end_of_step()
v[ineg][vdim] = 2.0 * vcm - sbuf[0];
v[ipos][vdim] = 2.0 * vcm - rbuf[0];
pswap += rbuf[1] * (vcm - rbuf[0]) - sbuf[1] * (vcm - sbuf[0]);
-
+
} else if (me == all[0].proc) {
ipos = pos_index[ipositive++];
sbuf[0] = v[ipos][vdim];
if (rmass) sbuf[1] = rmass[ipos];
else sbuf[1] = mass[type[ipos]];
MPI_Sendrecv(sbuf,2,MPI_DOUBLE,all[1].proc,0,
- rbuf,2,MPI_DOUBLE,all[1].proc,0,world,&status);
+ rbuf,2,MPI_DOUBLE,all[1].proc,0,world,&status);
vcm = (sbuf[1]*sbuf[0] + rbuf[1]*rbuf[0]) / (sbuf[1] + rbuf[1]);
v[ipos][vdim] = 2.0 * vcm - sbuf[0];
pswap += sbuf[1] * (vcm - sbuf[0]);
@@ -285,7 +285,7 @@ void FixViscosity::end_of_step()
if (rmass) sbuf[1] = rmass[ineg];
else sbuf[1] = mass[type[ineg]];
MPI_Sendrecv(sbuf,2,MPI_DOUBLE,all[0].proc,0,
- rbuf,2,MPI_DOUBLE,all[0].proc,0,world,&status);
+ rbuf,2,MPI_DOUBLE,all[0].proc,0,world,&status);
vcm = (sbuf[1]*sbuf[0] + rbuf[1]*rbuf[0]) / (sbuf[1] + rbuf[1]);
v[ineg][vdim] = 2.0 * vcm - sbuf[0];
pswap -= sbuf[1] * (vcm - sbuf[0]);
diff --git a/src/fix_viscosity.h b/src/fix_viscosity.h
index 46ae4727a389f845d1fdc8f9ee9133d9d3257ea2..6f694d4f9454af2cb9874e98a3769d76c7894979 100644
--- a/src/fix_viscosity.h
+++ b/src/fix_viscosity.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_viscous.cpp b/src/fix_viscous.cpp
index f54140db02bfcc919d997c90da39293b850bcd6d..f6a6f2d66ac4455fb5198d920f56b54b7a0d9b82 100644
--- a/src/fix_viscous.cpp
+++ b/src/fix_viscous.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -43,7 +43,7 @@ FixViscous::FixViscous(LAMMPS *lmp, int narg, char **arg) :
int itype = atoi(arg[iarg+1]);
double scale = atof(arg[iarg+2]);
if (itype <= 0 || itype > atom->ntypes)
- error->all(FLERR,"Illegal fix viscous command");
+ error->all(FLERR,"Illegal fix viscous command");
gamma[itype] = gamma_one * scale;
iarg += 3;
} else error->all(FLERR,"Illegal fix viscous command");
@@ -109,7 +109,7 @@ void FixViscous::post_force(int vflag)
int *mask = atom->mask;
int *type = atom->type;
int nlocal = atom->nlocal;
-
+
double drag;
for (int i = 0; i < nlocal; i++)
@@ -134,4 +134,3 @@ void FixViscous::min_post_force(int vflag)
{
post_force(vflag);
}
-
diff --git a/src/fix_viscous.h b/src/fix_viscous.h
index 06b67c1299fe311aec3ebbdf6281449ab5e8f2c9..437b93f2ccf2483b480b641e4832bb5aca5618ec 100644
--- a/src/fix_viscous.h
+++ b/src/fix_viscous.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_wall.cpp b/src/fix_wall.cpp
index 5a145a8b08f25e19e3fc20f67de36c89b2d4ad8c..7a031634c2bff4b20a0c12e5c234b27e1f09ba7f 100644
--- a/src/fix_wall.cpp
+++ b/src/fix_wall.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -51,8 +51,8 @@ FixWall::FixWall(LAMMPS *lmp, int narg, char **arg) :
int iarg = 3;
while (iarg < narg) {
if ((strcmp(arg[iarg],"xlo") == 0) || (strcmp(arg[iarg],"xhi") == 0) ||
- (strcmp(arg[iarg],"ylo") == 0) || (strcmp(arg[iarg],"yhi") == 0) ||
- (strcmp(arg[iarg],"zlo") == 0) || (strcmp(arg[iarg],"zhi") == 0)) {
+ (strcmp(arg[iarg],"ylo") == 0) || (strcmp(arg[iarg],"yhi") == 0) ||
+ (strcmp(arg[iarg],"zlo") == 0) || (strcmp(arg[iarg],"zhi") == 0)) {
if (iarg+5 > narg) error->all(FLERR,"Illegal fix wall command");
int newwall;
@@ -64,24 +64,24 @@ FixWall::FixWall(LAMMPS *lmp, int narg, char **arg) :
else if (strcmp(arg[iarg],"zhi") == 0) newwall = ZHI;
for (int m = 0; m < nwall; m++)
- if (newwall == wallwhich[m])
- error->all(FLERR,"Wall defined twice in fix wall command");
+ if (newwall == wallwhich[m])
+ error->all(FLERR,"Wall defined twice in fix wall command");
wallwhich[nwall] = newwall;
if (strcmp(arg[iarg+1],"EDGE") == 0) {
- wallstyle[nwall] = EDGE;
- int dim = wallwhich[nwall] / 2;
- int side = wallwhich[nwall] % 2;
- if (side == 0) coord0[nwall] = domain->boxlo[dim];
- else coord0[nwall] = domain->boxhi[dim];
+ wallstyle[nwall] = EDGE;
+ int dim = wallwhich[nwall] / 2;
+ int side = wallwhich[nwall] % 2;
+ if (side == 0) coord0[nwall] = domain->boxlo[dim];
+ else coord0[nwall] = domain->boxhi[dim];
} else if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) {
- wallstyle[nwall] = VARIABLE;
- int n = strlen(&arg[iarg+1][2]) + 1;
- varstr[nwall] = new char[n];
- strcpy(varstr[nwall],&arg[iarg+1][2]);
+ wallstyle[nwall] = VARIABLE;
+ int n = strlen(&arg[iarg+1][2]) + 1;
+ varstr[nwall] = new char[n];
+ strcpy(varstr[nwall],&arg[iarg+1][2]);
} else {
- wallstyle[nwall] = CONSTANT;
- coord0[nwall] = atof(arg[iarg+1]);
+ wallstyle[nwall] = CONSTANT;
+ coord0[nwall] = atof(arg[iarg+1]);
}
epsilon[nwall] = atof(arg[iarg+2]);
@@ -126,7 +126,7 @@ FixWall::FixWall(LAMMPS *lmp, int narg, char **arg) :
for (int m = 0; m < nwall; m++)
if ((wallwhich[m] == ZLO || wallwhich[m] == ZHI) && domain->dimension == 2)
error->all(FLERR,"Cannot use fix wall zlo/zhi for a 2d simulation");
-
+
// scale factors for CONSTANT and VARIABLE walls
int flag = 0;
diff --git a/src/fix_wall.h b/src/fix_wall.h
index 185edea237b328dbbb40f8ba930c98f11b2ac2f7..84f824b6e8365426758a6a56167988287ea4792a 100644
--- a/src/fix_wall.h
+++ b/src/fix_wall.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -35,7 +35,7 @@ class FixWall : public Fix {
virtual void precompute(int) = 0;
virtual void wall_particle(int, int, double) = 0;
-
+
int nwall;
int wallwhich[6];
double coord0[6];
@@ -43,7 +43,7 @@ class FixWall : public Fix {
int wallstyle[6];
int varindex[6];
char *varstr[6];
-
+
protected:
double epsilon[6],sigma[6],cutoff[6];
diff --git a/src/fix_wall_harmonic.cpp b/src/fix_wall_harmonic.cpp
index 48a32331b5b382f1d1a41d5babcdb67101adae0d..1766fa63c9b26ffdc248858231897d54c62af434 100644
--- a/src/fix_wall_harmonic.cpp
+++ b/src/fix_wall_harmonic.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -21,7 +21,7 @@ using namespace FixConst;
/* ---------------------------------------------------------------------- */
-FixWallHarmonic::FixWallHarmonic(LAMMPS *lmp, int narg, char **arg) :
+FixWallHarmonic::FixWallHarmonic(LAMMPS *lmp, int narg, char **arg) :
FixWall(lmp, narg, arg) {}
/* ----------------------------------------------------------------------
@@ -52,8 +52,8 @@ void FixWallHarmonic::wall_particle(int m, int which, double coord)
else delta = coord - x[i][dim];
if (delta >= cutoff[m]) continue;
if (delta <= 0.0) {
- onflag = 1;
- continue;
+ onflag = 1;
+ continue;
}
dr = cutoff[m]-delta;
fwall = side * 2.0*epsilon[m]*dr;
diff --git a/src/fix_wall_harmonic.h b/src/fix_wall_harmonic.h
index 23947b4e6b217a766672463839defce67248bcb4..d8d7b309d60ab368454c19084ac96d46979c31ce 100644
--- a/src/fix_wall_harmonic.h
+++ b/src/fix_wall_harmonic.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_wall_lj126.cpp b/src/fix_wall_lj126.cpp
index 4aa87e07cc605dc588a5543092126ac2f2061e52..c942a34acd052e6e3b58c877caf4e0b4a0cb516f 100644
--- a/src/fix_wall_lj126.cpp
+++ b/src/fix_wall_lj126.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -21,7 +21,7 @@ using namespace FixConst;
/* ---------------------------------------------------------------------- */
-FixWallLJ126::FixWallLJ126(LAMMPS *lmp, int narg, char **arg) :
+FixWallLJ126::FixWallLJ126(LAMMPS *lmp, int narg, char **arg) :
FixWall(lmp, narg, arg) {}
/* ---------------------------------------------------------------------- */
@@ -66,8 +66,8 @@ void FixWallLJ126::wall_particle(int m, int which, double coord)
else delta = coord - x[i][dim];
if (delta >= cutoff[m]) continue;
if (delta <= 0.0) {
- onflag = 1;
- continue;
+ onflag = 1;
+ continue;
}
rinv = 1.0/delta;
r2inv = rinv*rinv;
diff --git a/src/fix_wall_lj126.h b/src/fix_wall_lj126.h
index 37fb89446d6b088c659c74a2d2694049d1cd86c5..8455345708144285b8124c681870bb30853536af 100644
--- a/src/fix_wall_lj126.h
+++ b/src/fix_wall_lj126.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_wall_lj93.cpp b/src/fix_wall_lj93.cpp
index d2f92825e825d82377f9ba86ccecad1d9710df44..a4cd6b65164560969b4024143249c2c2c8ce469e 100644
--- a/src/fix_wall_lj93.cpp
+++ b/src/fix_wall_lj93.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -21,7 +21,7 @@ using namespace FixConst;
/* ---------------------------------------------------------------------- */
-FixWallLJ93::FixWallLJ93(LAMMPS *lmp, int narg, char **arg) :
+FixWallLJ93::FixWallLJ93(LAMMPS *lmp, int narg, char **arg) :
FixWall(lmp, narg, arg) {}
/* ---------------------------------------------------------------------- */
@@ -67,8 +67,8 @@ void FixWallLJ93::wall_particle(int m, int which, double coord)
else delta = coord - x[i][dim];
if (delta >= cutoff[m]) continue;
if (delta <= 0.0) {
- onflag = 1;
- continue;
+ onflag = 1;
+ continue;
}
rinv = 1.0/delta;
r2inv = rinv*rinv;
@@ -76,8 +76,8 @@ void FixWallLJ93::wall_particle(int m, int which, double coord)
r10inv = r4inv*r4inv*r2inv;
fwall = side * (coeff1[m]*r10inv - coeff2[m]*r4inv);
f[i][dim] -= fwall;
- ewall[0] += coeff3[m]*r4inv*r4inv*rinv -
- coeff4[m]*r2inv*rinv - offset[m];
+ ewall[0] += coeff3[m]*r4inv*r4inv*rinv -
+ coeff4[m]*r2inv*rinv - offset[m];
ewall[m+1] += fwall;
}
diff --git a/src/fix_wall_lj93.h b/src/fix_wall_lj93.h
index 30e2788c02dacdaff6c97191b987729c3ea29d82..a2ab52ba606d1b5f7b04436bfe7c6924843a4cd1 100644
--- a/src/fix_wall_lj93.h
+++ b/src/fix_wall_lj93.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_wall_reflect.cpp b/src/fix_wall_reflect.cpp
index ddca6887cce6f994ae489a85c6f4071cc2211347..a79333ad1436eee751e2afcc2cd1e26e5b58d7e4 100644
--- a/src/fix_wall_reflect.cpp
+++ b/src/fix_wall_reflect.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -45,8 +45,8 @@ FixWallReflect::FixWallReflect(LAMMPS *lmp, int narg, char **arg) :
int iarg = 3;
while (iarg < narg) {
if ((strcmp(arg[iarg],"xlo") == 0) || (strcmp(arg[iarg],"xhi") == 0) ||
- (strcmp(arg[iarg],"ylo") == 0) || (strcmp(arg[iarg],"yhi") == 0) ||
- (strcmp(arg[iarg],"zlo") == 0) || (strcmp(arg[iarg],"zhi") == 0)) {
+ (strcmp(arg[iarg],"ylo") == 0) || (strcmp(arg[iarg],"yhi") == 0) ||
+ (strcmp(arg[iarg],"zlo") == 0) || (strcmp(arg[iarg],"zhi") == 0)) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix wall/reflect command");
int newwall;
@@ -58,24 +58,24 @@ FixWallReflect::FixWallReflect(LAMMPS *lmp, int narg, char **arg) :
else if (strcmp(arg[iarg],"zhi") == 0) newwall = ZHI;
for (int m = 0; m < nwall; m++)
- if (newwall == wallwhich[m])
- error->all(FLERR,"Wall defined twice in fix wall/reflect command");
+ if (newwall == wallwhich[m])
+ error->all(FLERR,"Wall defined twice in fix wall/reflect command");
wallwhich[nwall] = newwall;
if (strcmp(arg[iarg+1],"EDGE") == 0) {
- wallstyle[nwall] = EDGE;
- int dim = wallwhich[nwall] / 2;
- int side = wallwhich[nwall] % 2;
- if (side == 0) coord0[nwall] = domain->boxlo[dim];
- else coord0[nwall] = domain->boxhi[dim];
+ wallstyle[nwall] = EDGE;
+ int dim = wallwhich[nwall] / 2;
+ int side = wallwhich[nwall] % 2;
+ if (side == 0) coord0[nwall] = domain->boxlo[dim];
+ else coord0[nwall] = domain->boxhi[dim];
} else if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) {
- wallstyle[nwall] = VARIABLE;
- int n = strlen(&arg[iarg+1][2]) + 1;
- varstr[nwall] = new char[n];
- strcpy(varstr[nwall],&arg[iarg+1][2]);
+ wallstyle[nwall] = VARIABLE;
+ int n = strlen(&arg[iarg+1][2]) + 1;
+ varstr[nwall] = new char[n];
+ strcpy(varstr[nwall],&arg[iarg+1][2]);
} else {
- wallstyle[nwall] = CONSTANT;
- coord0[nwall] = atof(arg[iarg+1]);
+ wallstyle[nwall] = CONSTANT;
+ coord0[nwall] = atof(arg[iarg+1]);
}
nwall++;
@@ -106,7 +106,7 @@ FixWallReflect::FixWallReflect(LAMMPS *lmp, int narg, char **arg) :
for (int m = 0; m < nwall; m++)
if ((wallwhich[m] == ZLO || wallwhich[m] == ZHI) && domain->dimension == 2)
error->all(FLERR,
- "Cannot use fix wall/reflect zlo/zhi for a 2d simulation");
+ "Cannot use fix wall/reflect zlo/zhi for a 2d simulation");
// scale factors for CONSTANT and VARIABLE walls
@@ -124,7 +124,7 @@ FixWallReflect::FixWallReflect(LAMMPS *lmp, int narg, char **arg) :
zscale = domain->lattice->zlattice;
}
else xscale = yscale = zscale = 1.0;
-
+
for (int m = 0; m < nwall; m++) {
if (wallstyle[m] != CONSTANT) continue;
if (wallwhich[m] < YLO) coord0[m] *= xscale;
@@ -175,9 +175,9 @@ void FixWallReflect::init()
for (int i = 0; i < modify->nfix; i++)
if (modify->fix[i]->rigid_flag) nrigid++;
- if (nrigid && comm->me == 0)
+ if (nrigid && comm->me == 0)
error->warning(FLERR,"Should not allow rigid bodies to bounce off "
- "relecting walls");
+ "relecting walls");
}
/* ---------------------------------------------------------------------- */
@@ -210,17 +210,17 @@ void FixWallReflect::post_integrate()
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- if (side == 0) {
- if (x[i][dim] < coord) {
- x[i][dim] = coord + (coord - x[i][dim]);
- v[i][dim] = -v[i][dim];
- }
- } else {
- if (x[i][dim] > coord) {
- x[i][dim] = coord - (x[i][dim] - coord);
- v[i][dim] = -v[i][dim];
- }
- }
+ if (side == 0) {
+ if (x[i][dim] < coord) {
+ x[i][dim] = coord + (coord - x[i][dim]);
+ v[i][dim] = -v[i][dim];
+ }
+ } else {
+ if (x[i][dim] > coord) {
+ x[i][dim] = coord - (x[i][dim] - coord);
+ v[i][dim] = -v[i][dim];
+ }
+ }
}
}
diff --git a/src/fix_wall_reflect.h b/src/fix_wall_reflect.h
index 475c4a33824298f5e9b5353f48ee60fae05bfabb..d1d345c5318778fe21224955131842d8bf21ce4b 100644
--- a/src/fix_wall_reflect.h
+++ b/src/fix_wall_reflect.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_wall_region.cpp b/src/fix_wall_region.cpp
index bd5b3ea98b587f79be6e4e27600858aaffc03d44..e4572e8fed42158b8534965f023ab2691baa5337 100644
--- a/src/fix_wall_region.cpp
+++ b/src/fix_wall_region.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -102,21 +102,21 @@ void FixWallRegion::init()
// insure all particles in group are extended particles
if (style == COLLOID) {
- if (!atom->sphere_flag)
+ if (!atom->sphere_flag)
error->all(FLERR,"Fix wall/region colloid requires atom style sphere");
double *radius = atom->radius;
int *mask = atom->mask;
int nlocal = atom->nlocal;
-
+
int flag = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
- if (radius[i] == 0.0) flag = 1;
-
+ if (radius[i] == 0.0) flag = 1;
+
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
- if (flagall)
+ if (flagall)
error->all(FLERR,"Fix wall/region colloid requires extended particles");
}
@@ -196,12 +196,12 @@ void FixWallRegion::post_force(int vflag)
// region->match() insures particle is in region or on surface, else error
// if returned contact dist r = 0, is on surface, also an error
// in COLLOID case, r <= radius is an error
-
+
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (!region->match(x[i][0],x[i][1],x[i][2])) {
- onflag = 1;
- continue;
+ onflag = 1;
+ continue;
}
if (style == COLLOID) tooclose = radius[i];
else tooclose = 0.0;
@@ -209,31 +209,31 @@ void FixWallRegion::post_force(int vflag)
n = region->surface(x[i][0],x[i][1],x[i][2],cutoff);
for (m = 0; m < n; m++) {
- if (region->contact[m].r <= tooclose) {
- onflag = 1;
- continue;
- } else rinv = 1.0/region->contact[m].r;
-
- if (style == LJ93) lj93(region->contact[m].r);
- else if (style == LJ126) lj126(region->contact[m].r);
- else if (style == COLLOID) colloid(region->contact[m].r,radius[i]);
- else harmonic(region->contact[m].r);
-
- ewall[0] += eng;
- fx = fwall * region->contact[m].delx * rinv;
- fy = fwall * region->contact[m].dely * rinv;
- fz = fwall * region->contact[m].delz * rinv;
- f[i][0] += fx;
- f[i][1] += fy;
- f[i][2] += fz;
- ewall[1] -= fx;
- ewall[2] -= fy;
- ewall[3] -= fz;
+ if (region->contact[m].r <= tooclose) {
+ onflag = 1;
+ continue;
+ } else rinv = 1.0/region->contact[m].r;
+
+ if (style == LJ93) lj93(region->contact[m].r);
+ else if (style == LJ126) lj126(region->contact[m].r);
+ else if (style == COLLOID) colloid(region->contact[m].r,radius[i]);
+ else harmonic(region->contact[m].r);
+
+ ewall[0] += eng;
+ fx = fwall * region->contact[m].delx * rinv;
+ fy = fwall * region->contact[m].dely * rinv;
+ fz = fwall * region->contact[m].delz * rinv;
+ f[i][0] += fx;
+ f[i][1] += fy;
+ f[i][2] += fz;
+ ewall[1] -= fx;
+ ewall[2] -= fy;
+ ewall[3] -= fz;
}
}
if (onflag) error->one(FLERR,"Particle on or inside surface of region "
- "used in fix wall/region");
+ "used in fix wall/region");
}
/* ---------------------------------------------------------------------- */
@@ -328,8 +328,8 @@ void FixWallRegion::colloid(double r, double rad)
double r4inv = r2inv*r2inv;
double r8inv = r4inv*r4inv;
fwall = coeff1*(rad8*rad + 27.0*rad4*rad2*rad*pow(r,2.0)
- + 63.0*rad4*rad*pow(r,4.0)
- + 21.0*rad2*rad*pow(r,6.0))*r8inv - new_coeff2*r2inv;
+ + 63.0*rad4*rad*pow(r,4.0)
+ + 21.0*rad2*rad*pow(r,6.0))*r8inv - new_coeff2*r2inv;
double r2 = 0.5*diam - r;
double rinv2 = 1.0/r2;
@@ -340,9 +340,9 @@ void FixWallRegion::colloid(double r, double rad)
double r2inv3 = rinv3*rinv3;
double r4inv3 = r2inv3*r2inv3;
eng = coeff3*((-3.5*diam+r)*r4inv2*r2inv2*rinv2
- + (3.5*diam+r)*r4inv3*r2inv3*rinv3) -
+ + (3.5*diam+r)*r4inv3*r2inv3*rinv3) -
coeff4*((-diam*r+r2*r3*(log(-r2)-log(r3)))*
- (-rinv2)*rinv3) - offset;
+ (-rinv2)*rinv3) - offset;
}
/* ----------------------------------------------------------------------
diff --git a/src/fix_wall_region.h b/src/fix_wall_region.h
index 15a667af6425fc5cd3944051e7996c438b900ac3..92d7b393d3df0554b0d8a1c1f7fe1a24d9862b21 100644
--- a/src/fix_wall_region.h
+++ b/src/fix_wall_region.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/force.cpp b/src/force.cpp
index 98a972dd71ae0f2df92235317b2bef92d147de0d..8170c874f8163e1690910533f5d110ea131ac04e 100644
--- a/src/force.cpp
+++ b/src/force.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -188,20 +188,20 @@ Pair *Force::pair_match(const char *word, int exact)
count = 0;
for (int i = 0; i < hybrid->nstyles; i++)
if ((exact && strcmp(hybrid->keywords[i],word) == 0) ||
- (!exact && strstr(hybrid->keywords[i],word))) {
- iwhich = i;
- count++;
+ (!exact && strstr(hybrid->keywords[i],word))) {
+ iwhich = i;
+ count++;
}
if (count == 1) return hybrid->styles[iwhich];
-
+
} else if (strstr(pair_style,"hybrid")) {
PairHybrid *hybrid = (PairHybrid *) pair;
count = 0;
for (int i = 0; i < hybrid->nstyles; i++)
if ((exact && strcmp(hybrid->keywords[i],word) == 0) ||
- (!exact && strstr(hybrid->keywords[i],word))) {
- iwhich = i;
- count++;
+ (!exact && strstr(hybrid->keywords[i],word))) {
+ iwhich = i;
+ count++;
}
if (count == 1) return hybrid->styles[iwhich];
}
@@ -469,7 +469,7 @@ Improper *Force::new_improper(const char *style, const char *suffix, int &sflag)
}
/* ----------------------------------------------------------------------
- new kspace style
+ new kspace style
------------------------------------------------------------------------- */
void Force::create_kspace(int narg, char **arg, const char *suffix)
@@ -544,7 +544,7 @@ KSpace *Force::kspace_match(const char *word, int exact)
}
/* ----------------------------------------------------------------------
- set special bond values
+ set special bond values
------------------------------------------------------------------------- */
void Force::set_special(int narg, char **arg)
@@ -628,7 +628,7 @@ void Force::set_special(int narg, char **arg)
for (int i = 1; i <= 3; i++)
if (special_lj[i] < 0.0 || special_lj[i] > 1.0 ||
- special_coul[i] < 0.0 || special_coul[i] > 1.0)
+ special_coul[i] < 0.0 || special_coul[i] > 1.0)
error->all(FLERR,"Illegal special_bonds command");
if (special_extra < 0) error->all(FLERR,"Illegal special_bonds command");
@@ -680,7 +680,7 @@ double Force::numeric(char *str)
if (str[i] == '-' || str[i] == '+' || str[i] == '.') continue;
if (str[i] == 'e' || str[i] == 'E') continue;
error->all(FLERR,"Expected floating point parameter in "
- "input script or data file");
+ "input script or data file");
}
return atof(str);
diff --git a/src/force.h b/src/force.h
index d219226e6e048a41a371f289c44ede3a5b608811..0a84cd869b07e3524a810b6678e26bcf3faafb86 100644
--- a/src/force.h
+++ b/src/force.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -34,7 +34,7 @@ class Force : protected Pointers {
double qqrd2e; // q^2/r to energy w/ dielectric constant
double e_mass; // electron mass
double hhmrr2e; // conversion of (hbar)^2/(mr^2) to energy
- double mvh2r; // conversion of mv/hbar to distance
+ double mvh2r; // conversion of mv/hbar to distance
// hbar = h/(2*pi)
double angstrom; // 1 angstrom in native units
double femtosecond; // 1 femtosecond in native units
@@ -78,7 +78,7 @@ class Force : protected Pointers {
void create_bond(const char *, const char *suffix = NULL);
class Bond *new_bond(const char *, const char *, int &);
- class Bond *bond_match(const char *);
+ class Bond *bond_match(const char *);
void create_angle(const char *, const char *suffix = NULL);
class Angle *new_angle(const char *, const char *, int &);
diff --git a/src/group.cpp b/src/group.cpp
index 7c52a5d368b49d8a907579328699029e9e07d47d..dfccc77f4605f5792e4ba09352135a2bcd679a24 100644
--- a/src/group.cpp
+++ b/src/group.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -82,7 +82,7 @@ void Group::assign(int narg, char **arg)
{
int i;
- if (domain->box_exist == 0)
+ if (domain->box_exist == 0)
error->all(FLERR,"Group command before simulation box is defined");
if (narg < 2) error->all(FLERR,"Illegal group command");
@@ -95,16 +95,16 @@ void Group::assign(int narg, char **arg)
if (igroup == 0) error->all(FLERR,"Cannot delete group all");
for (i = 0; i < modify->nfix; i++)
if (modify->fix[i]->igroup == igroup)
- error->all(FLERR,"Cannot delete group currently used by a fix");
+ error->all(FLERR,"Cannot delete group currently used by a fix");
for (i = 0; i < modify->ncompute; i++)
if (modify->compute[i]->igroup == igroup)
- error->all(FLERR,"Cannot delete group currently used by a compute");
+ error->all(FLERR,"Cannot delete group currently used by a compute");
for (i = 0; i < output->ndump; i++)
if (output->dump[i]->igroup == igroup)
- error->all(FLERR,"Cannot delete group currently used by a dump");
+ error->all(FLERR,"Cannot delete group currently used by a dump");
if (atom->firstgroupname && strcmp(arg[0],atom->firstgroupname) == 0)
error->all(FLERR,
- "Cannot delete group currently used by atom_modify first");
+ "Cannot delete group currently used by atom_modify first");
int *mask = atom->mask;
int nlocal = atom->nlocal;
@@ -136,7 +136,7 @@ void Group::assign(int narg, char **arg)
int *mask = atom->mask;
int nlocal = atom->nlocal;
int bit = bitmask[igroup];
-
+
// style = region
// add to group if atom is in region
// init all regions via domain->init() to insure region can perform match()
@@ -144,21 +144,21 @@ void Group::assign(int narg, char **arg)
if (strcmp(arg[1],"region") == 0) {
if (narg != 3) error->all(FLERR,"Illegal group command");
-
+
int iregion = domain->find_region(arg[2]);
if (iregion == -1) error->all(FLERR,"Group region ID does not exist");
domain->init();
for (i = 0; i < nlocal; i++)
if (domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2]))
- mask[i] |= bit;
+ mask[i] |= bit;
// style = logical condition
- } else if (narg >= 3 &&
- (strcmp(arg[2],"<") == 0 || strcmp(arg[2],">") == 0 ||
- strcmp(arg[2],"<=") == 0 || strcmp(arg[2],">=") == 0 ||
- strcmp(arg[2],"<>") == 0)) {
+ } else if (narg >= 3 &&
+ (strcmp(arg[2],"<") == 0 || strcmp(arg[2],">") == 0 ||
+ strcmp(arg[2],"<=") == 0 || strcmp(arg[2],">=") == 0 ||
+ strcmp(arg[2],"<>") == 0)) {
if (narg < 4 || narg > 5) error->all(FLERR,"Illegal group command");
int category,condition,bound1,bound2;
@@ -167,7 +167,7 @@ void Group::assign(int narg, char **arg)
else if (strcmp(arg[1],"molecule") == 0) category = MOLECULE;
else if (strcmp(arg[1],"id") == 0) category = ID;
else error->all(FLERR,"Illegal group command");
-
+
if (strcmp(arg[2],"<") == 0) condition = LT;
else if (strcmp(arg[2],"<=") == 0) condition = LE;
else if (strcmp(arg[2],">") == 0) condition = GT;
@@ -206,13 +206,13 @@ void Group::assign(int narg, char **arg)
for (i = 0; i < nlocal; i++) if (attribute[i] != bound1) mask[i] |= bit;
} else if (condition == BETWEEN) {
for (i = 0; i < nlocal; i++)
- if (attribute[i] >= bound1 && attribute[i] <= bound2) mask[i] |= bit;
+ if (attribute[i] >= bound1 && attribute[i] <= bound2) mask[i] |= bit;
}
// style = list of values
} else if (strcmp(arg[1],"type") == 0 || strcmp(arg[1],"molecule") == 0 ||
- strcmp(arg[1],"id") == 0) {
+ strcmp(arg[1],"id") == 0) {
if (narg < 3) error->all(FLERR,"Illegal group command");
@@ -224,7 +224,7 @@ void Group::assign(int narg, char **arg)
else if (strcmp(arg[1],"molecule") == 0) category = MOLECULE;
else if (strcmp(arg[1],"id") == 0) category = ID;
else error->all(FLERR,"Illegal group command");
-
+
length = narg - 2;
for (int iarg = 2; iarg < narg; iarg++) list[iarg-2] = atoi(arg[iarg]);
@@ -237,16 +237,16 @@ void Group::assign(int narg, char **arg)
for (int ilist = 0; ilist < length; ilist++)
for (i = 0; i < nlocal; i++)
- if (attribute[i] == list[ilist]) mask[i] |= bit;
+ if (attribute[i] == list[ilist]) mask[i] |= bit;
delete [] list;
-
+
// style = subtract
} else if (strcmp(arg[1],"subtract") == 0) {
if (narg < 4) error->all(FLERR,"Illegal group command");
-
+
int length = narg-2;
int *list = new int[length];
@@ -261,7 +261,7 @@ void Group::assign(int narg, char **arg)
int otherbit = bitmask[list[0]];
- for (i = 0; i < nlocal; i++)
+ for (i = 0; i < nlocal; i++)
if (mask[i] & otherbit) mask[i] |= bit;
// remove atoms if they are in any of the other groups
@@ -271,8 +271,8 @@ void Group::assign(int narg, char **arg)
for (int ilist = 1; ilist < length; ilist++) {
otherbit = bitmask[list[ilist]];
- for (i = 0; i < nlocal; i++)
- if (mask[i] & otherbit) mask[i] &= inverse;
+ for (i = 0; i < nlocal; i++)
+ if (mask[i] & otherbit) mask[i] &= inverse;
}
delete [] list;
@@ -282,7 +282,7 @@ void Group::assign(int narg, char **arg)
} else if (strcmp(arg[1],"union") == 0) {
if (narg < 3) error->all(FLERR,"Illegal group command");
-
+
int length = narg-2;
int *list = new int[length];
@@ -299,8 +299,8 @@ void Group::assign(int narg, char **arg)
for (int ilist = 0; ilist < length; ilist++) {
otherbit = bitmask[list[ilist]];
- for (i = 0; i < nlocal; i++)
- if (mask[i] & otherbit) mask[i] |= bit;
+ for (i = 0; i < nlocal; i++)
+ if (mask[i] & otherbit) mask[i] |= bit;
}
delete [] list;
@@ -310,7 +310,7 @@ void Group::assign(int narg, char **arg)
} else if (strcmp(arg[1],"intersect") == 0) {
if (narg < 4) error->all(FLERR,"Illegal group command");
-
+
int length = narg-2;
int *list = new int[length];
@@ -328,8 +328,8 @@ void Group::assign(int narg, char **arg)
for (i = 0; i < nlocal; i++) {
ok = 1;
for (ilist = 0; ilist < length; ilist++) {
- otherbit = bitmask[list[ilist]];
- if ((mask[i] & otherbit) == 0) ok = 0;
+ otherbit = bitmask[list[ilist]];
+ if ((mask[i] & otherbit) == 0) ok = 0;
}
if (ok) mask[i] |= bit;
}
@@ -356,7 +356,7 @@ void Group::assign(int narg, char **arg)
fprintf(logfile,"%.15g atoms in group %s\n",all,names[igroup]);
}
}
-
+
/* ----------------------------------------------------------------------
add flagged atoms to a new or existing group
------------------------------------------------------------------------- */
@@ -385,7 +385,7 @@ void Group::create(char *name, int *flag)
int nlocal = atom->nlocal;
int bit = bitmask[igroup];
- for (i = 0; i < nlocal; i++)
+ for (i = 0; i < nlocal; i++)
if (flag[i]) mask[i] |= bit;
}
@@ -575,11 +575,11 @@ double Group::mass(int igroup, int iregion)
if (rmass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]))
- one += rmass[i];
+ one += rmass[i];
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]))
- one += mass[type[i]];
+ one += mass[type[i]];
}
double all;
@@ -644,7 +644,7 @@ void Group::bounds(int igroup, double *minmax)
double extent[6];
extent[0] = extent[2] = extent[4] = BIG;
extent[1] = extent[3] = extent[5] = -BIG;
-
+
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
@@ -659,15 +659,15 @@ void Group::bounds(int igroup, double *minmax)
extent[5] = MAX(extent[5],x[i][2]);
}
}
-
+
// compute extent across all procs
// flip sign of MIN to do it in one Allreduce MAX
// set box by extent in shrink-wrapped dims
-
+
extent[0] = -extent[0];
extent[2] = -extent[2];
extent[4] = -extent[4];
-
+
MPI_Allreduce(extent,minmax,6,MPI_DOUBLE,MPI_MAX,world);
minmax[0] = -minmax[0];
@@ -688,7 +688,7 @@ void Group::bounds(int igroup, double *minmax, int iregion)
double extent[6];
extent[0] = extent[2] = extent[4] = BIG;
extent[1] = extent[3] = extent[5] = -BIG;
-
+
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
@@ -703,15 +703,15 @@ void Group::bounds(int igroup, double *minmax, int iregion)
extent[5] = MAX(extent[5],x[i][2]);
}
}
-
+
// compute extent across all procs
// flip sign of MIN to do it in one Allreduce MAX
// set box by extent in shrink-wrapped dims
-
+
extent[0] = -extent[0];
extent[2] = -extent[2];
extent[4] = -extent[4];
-
+
MPI_Allreduce(extent,minmax,6,MPI_DOUBLE,MPI_MAX,world);
minmax[0] = -minmax[0];
@@ -750,24 +750,24 @@ void Group::xcm(int igroup, double masstotal, double *cm)
if (rmass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- xbox = (image[i] & 1023) - 512;
- ybox = (image[i] >> 10 & 1023) - 512;
- zbox = (image[i] >> 20) - 512;
- massone = rmass[i];
- cmone[0] += (x[i][0] + xbox*xprd) * massone;
- cmone[1] += (x[i][1] + ybox*yprd) * massone;
- cmone[2] += (x[i][2] + zbox*zprd) * massone;
+ xbox = (image[i] & 1023) - 512;
+ ybox = (image[i] >> 10 & 1023) - 512;
+ zbox = (image[i] >> 20) - 512;
+ massone = rmass[i];
+ cmone[0] += (x[i][0] + xbox*xprd) * massone;
+ cmone[1] += (x[i][1] + ybox*yprd) * massone;
+ cmone[2] += (x[i][2] + zbox*zprd) * massone;
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- xbox = (image[i] & 1023) - 512;
- ybox = (image[i] >> 10 & 1023) - 512;
- zbox = (image[i] >> 20) - 512;
- massone = mass[type[i]];
- cmone[0] += (x[i][0] + xbox*xprd) * massone;
- cmone[1] += (x[i][1] + ybox*yprd) * massone;
- cmone[2] += (x[i][2] + zbox*zprd) * massone;
+ xbox = (image[i] & 1023) - 512;
+ ybox = (image[i] >> 10 & 1023) - 512;
+ zbox = (image[i] >> 20) - 512;
+ massone = mass[type[i]];
+ cmone[0] += (x[i][0] + xbox*xprd) * massone;
+ cmone[1] += (x[i][1] + ybox*yprd) * massone;
+ cmone[2] += (x[i][2] + zbox*zprd) * massone;
}
}
@@ -811,24 +811,24 @@ void Group::xcm(int igroup, double masstotal, double *cm, int iregion)
if (rmass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
- xbox = (image[i] & 1023) - 512;
- ybox = (image[i] >> 10 & 1023) - 512;
- zbox = (image[i] >> 20) - 512;
- massone = rmass[i];
- cmone[0] += (x[i][0] + xbox*xprd) * massone;
- cmone[1] += (x[i][1] + ybox*yprd) * massone;
- cmone[2] += (x[i][2] + zbox*zprd) * massone;
+ xbox = (image[i] & 1023) - 512;
+ ybox = (image[i] >> 10 & 1023) - 512;
+ zbox = (image[i] >> 20) - 512;
+ massone = rmass[i];
+ cmone[0] += (x[i][0] + xbox*xprd) * massone;
+ cmone[1] += (x[i][1] + ybox*yprd) * massone;
+ cmone[2] += (x[i][2] + zbox*zprd) * massone;
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
- xbox = (image[i] & 1023) - 512;
- ybox = (image[i] >> 10 & 1023) - 512;
- zbox = (image[i] >> 20) - 512;
- massone = mass[type[i]];
- cmone[0] += (x[i][0] + xbox*xprd) * massone;
- cmone[1] += (x[i][1] + ybox*yprd) * massone;
- cmone[2] += (x[i][2] + zbox*zprd) * massone;
+ xbox = (image[i] & 1023) - 512;
+ ybox = (image[i] >> 10 & 1023) - 512;
+ zbox = (image[i] >> 20) - 512;
+ massone = mass[type[i]];
+ cmone[0] += (x[i][0] + xbox*xprd) * massone;
+ cmone[1] += (x[i][1] + ybox*yprd) * massone;
+ cmone[2] += (x[i][2] + zbox*zprd) * massone;
}
}
@@ -863,18 +863,18 @@ void Group::vcm(int igroup, double masstotal, double *cm)
if (rmass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- massone = rmass[i];
- p[0] += v[i][0]*massone;
- p[1] += v[i][1]*massone;
- p[2] += v[i][2]*massone;
+ massone = rmass[i];
+ p[0] += v[i][0]*massone;
+ p[1] += v[i][1]*massone;
+ p[2] += v[i][2]*massone;
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- massone = mass[type[i]];
- p[0] += v[i][0]*massone;
- p[1] += v[i][1]*massone;
- p[2] += v[i][2]*massone;
+ massone = mass[type[i]];
+ p[0] += v[i][0]*massone;
+ p[1] += v[i][1]*massone;
+ p[2] += v[i][2]*massone;
}
}
@@ -911,18 +911,18 @@ void Group::vcm(int igroup, double masstotal, double *cm, int iregion)
if (rmass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
- massone = rmass[i];
- p[0] += v[i][0]*massone;
- p[1] += v[i][1]*massone;
- p[2] += v[i][2]*massone;
+ massone = rmass[i];
+ p[0] += v[i][0]*massone;
+ p[1] += v[i][1]*massone;
+ p[2] += v[i][2]*massone;
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
- massone = mass[type[i]];
- p[0] += v[i][0]*massone;
- p[1] += v[i][1]*massone;
- p[2] += v[i][2]*massone;
+ massone = mass[type[i]];
+ p[0] += v[i][0]*massone;
+ p[1] += v[i][1]*massone;
+ p[2] += v[i][2]*massone;
}
}
@@ -1006,15 +1006,15 @@ double Group::ke(int igroup)
if (rmass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
- one += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
- rmass[i];
+ one += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
+ rmass[i];
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
- one += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
- mass[type[i]];
+ one += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
+ mass[type[i]];
}
-
+
double all;
MPI_Allreduce(&one,&all,1,MPI_DOUBLE,MPI_SUM,world);
all *= 0.5 * force->mvv2e;
@@ -1043,15 +1043,15 @@ double Group::ke(int igroup, int iregion)
if (rmass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]))
- one += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
- rmass[i];
+ one += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
+ rmass[i];
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]))
- one += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
- mass[type[i]];
+ one += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
+ mass[type[i]];
}
-
+
double all;
MPI_Allreduce(&one,&all,1,MPI_DOUBLE,MPI_SUM,world);
all *= 0.5 * force->mvv2e;
@@ -1097,7 +1097,7 @@ double Group::gyration(int igroup, double masstotal, double *cm)
}
double rg_all;
MPI_Allreduce(&rg,&rg_all,1,MPI_DOUBLE,MPI_SUM,world);
-
+
if (masstotal > 0.0) return sqrt(rg_all/masstotal);
return 0.0;
}
@@ -1142,7 +1142,7 @@ double Group::gyration(int igroup, double masstotal, double *cm, int iregion)
}
double rg_all;
MPI_Allreduce(&rg,&rg_all,1,MPI_DOUBLE,MPI_SUM,world);
-
+
if (masstotal > 0.0) return sqrt(rg_all/masstotal);
return 0.0;
}
@@ -1447,22 +1447,22 @@ void Group::omega(double *angmom, double inertia[3][3], double *w)
inverse[2][1] = -(inertia[0][0]*inertia[2][1] - inertia[0][1]*inertia[2][0]);
inverse[2][2] = inertia[0][0]*inertia[1][1] - inertia[0][1]*inertia[1][0];
- double determinant = inertia[0][0]*inertia[1][1]*inertia[2][2] +
- inertia[0][1]*inertia[1][2]*inertia[2][0] +
- inertia[0][2]*inertia[1][0]*inertia[2][1] -
+ double determinant = inertia[0][0]*inertia[1][1]*inertia[2][2] +
+ inertia[0][1]*inertia[1][2]*inertia[2][0] +
+ inertia[0][2]*inertia[1][0]*inertia[2][1] -
inertia[0][0]*inertia[1][2]*inertia[2][1] -
- inertia[0][1]*inertia[1][0]*inertia[2][2] -
- inertia[2][0]*inertia[1][1]*inertia[0][2];
+ inertia[0][1]*inertia[1][0]*inertia[2][2] -
+ inertia[2][0]*inertia[1][1]*inertia[0][2];
if (determinant > 0.0)
for (int i = 0; i < 3; i++)
for (int j = 0; j < 3; j++)
- inverse[i][j] /= determinant;
+ inverse[i][j] /= determinant;
- w[0] = inverse[0][0]*angmom[0] + inverse[0][1]*angmom[1] +
+ w[0] = inverse[0][0]*angmom[0] + inverse[0][1]*angmom[1] +
inverse[0][2]*angmom[2];
- w[1] = inverse[1][0]*angmom[0] + inverse[1][1]*angmom[1] +
+ w[1] = inverse[1][0]*angmom[0] + inverse[1][1]*angmom[1] +
inverse[1][2]*angmom[2];
- w[2] = inverse[2][0]*angmom[0] + inverse[2][1]*angmom[1] +
+ w[2] = inverse[2][0]*angmom[0] + inverse[2][1]*angmom[1] +
inverse[2][2]*angmom[2];
}
diff --git a/src/group.h b/src/group.h
index 6c3ea74bcae5af22d9efaf8a1d6f612e7a0ee00b..6cb64a902d679b993bf981ca4b08be9eac057193 100644
--- a/src/group.h
+++ b/src/group.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -109,7 +109,7 @@ Self-explanatory.
E: Too many groups
-The maximum number of atom groups (including the "all" group) is
+The maximum number of atom groups (including the "all" group) is
given by MAX_GROUP in group.cpp and is 32.
E: Group region ID does not exist
diff --git a/src/image.cpp b/src/image.cpp
index 0792e70d5a00031eb21bbd04b6fd09aadc428436..5efe67b9f8150afbe9ec834a6f5e74f429a6832d 100644
--- a/src/image.cpp
+++ b/src/image.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -102,7 +102,7 @@ Image::Image(LAMMPS *lmp) : Pointers(lmp)
keyLightColor[2] = 0.9;
fillLightPhi = MY_PI/6.0; // 30 degrees
- fillLightTheta = 0;
+ fillLightTheta = 0;
fillLightColor[0] = 0.45;
fillLightColor[1] = 0.45;
fillLightColor[2] = 0.45;
@@ -115,7 +115,7 @@ Image::Image(LAMMPS *lmp) : Pointers(lmp)
// RNG for SSAO depth shading
- if (ssao) random = new RanMars(lmp,seed+me);
+ if (ssao) random = new RanMars(lmp,seed+me);
else random = NULL;
}
@@ -135,7 +135,7 @@ Image::~Image()
memory->destroy(surfacecopy);
memory->destroy(rgbcopy);
- delete random;
+ delete random;
}
/* ----------------------------------------------------------------------
@@ -161,7 +161,7 @@ void Image::buffers()
------------------------------------------------------------------------- */
void Image::view_params(double boxxlo, double boxxhi, double boxylo,
- double boxyhi, double boxzlo, double boxzhi)
+ double boxyhi, double boxzlo, double boxzhi)
{
// camDir points at the camera, view direction = -camDir
@@ -258,7 +258,7 @@ void Image::view_params(double boxxlo, double boxxhi, double boxylo,
ambientColor[1] = 0.5;
ambientColor[2] = 0.5;
}
-
+
// param for rasterizing spheres
tanPerPixel = -(maxdel / (double) height);
@@ -302,12 +302,12 @@ void Image::color_minmax(int n, double *buf, int stride)
} else if (mstyle == DISCRETE) {
for (int i = 0; i < nentry; i++) {
if (mentry[i].lo == MINVALUE) {
- if (mrange == ABSOLUTE) mentry[i].lvalue = locurrent;
- else mentry[i].lvalue = 0.0;
+ if (mrange == ABSOLUTE) mentry[i].lvalue = locurrent;
+ else mentry[i].lvalue = 0.0;
}
if (mentry[i].hi == MAXVALUE) {
- if (mrange == ABSOLUTE) mentry[i].hvalue = hicurrent;
- else mentry[i].hvalue = 1.0;
+ if (mrange == ABSOLUTE) mentry[i].hvalue = hicurrent;
+ else mentry[i].hvalue = 1.0;
}
}
}
@@ -354,14 +354,14 @@ void Image::merge()
MPI_Irecv(rgbcopy,npixels*3,MPI_BYTE,me+nhalf,0,world,&requests[0]);
MPI_Irecv(depthcopy,npixels,MPI_DOUBLE,me+nhalf,0,world,&requests[1]);
if (ssao)
- MPI_Irecv(surfacecopy,npixels*2,MPI_DOUBLE,
- me+nhalf,0,world,&requests[2]);
+ MPI_Irecv(surfacecopy,npixels*2,MPI_DOUBLE,
+ me+nhalf,0,world,&requests[2]);
if (ssao) MPI_Waitall(3,requests,statuses);
else MPI_Waitall(2,requests,statuses);
for (int i = 0; i < npixels; i++) {
- if (depthBuffer[i] < 0 || (depthcopy[i] >= 0 &&
- depthcopy[i] < depthBuffer[i])) {
+ if (depthBuffer[i] < 0 || (depthcopy[i] >= 0 &&
+ depthcopy[i] < depthBuffer[i])) {
depthBuffer[i] = depthcopy[i];
imageBuffer[i*3+0] = rgbcopy[i*3+0];
imageBuffer[i*3+1] = rgbcopy[i*3+1];
@@ -455,7 +455,7 @@ void Image::draw_sphere(double *x, double *surfaceColor, double diameter)
double radius = 0.5*diameter;
double radsq = radius*radius;
- double pixelWidth = (tanPerPixel > 0) ? tanPerPixel * dist :
+ double pixelWidth = (tanPerPixel > 0) ? tanPerPixel * dist :
-tanPerPixel / zoom;
double pixelRadiusFull = radius / pixelWidth;
int pixelRadius = static_cast<int> (pixelRadiusFull + 0.5) + 1;
@@ -479,9 +479,9 @@ void Image::draw_sphere(double *x, double *surfaceColor, double diameter)
surface[1] = ((iy - yc) - height_error) * pixelWidth;
surface[0] = ((ix - xc) - width_error) * pixelWidth;
projRad = surface[0]*surface[0] + surface[1]*surface[1];
-
+
// outside the sphere in the projected image
-
+
if (projRad > radsq) continue;
surface[2] = sqrt(radsq - projRad);
depth = dist - surface[2];
@@ -515,7 +515,7 @@ void Image::draw_cube(double *x, double *surfaceColor, double diameter)
double dist = MathExtra::dot3(camPos,camDir) - MathExtra::dot3(xlocal,camDir);
double radius = 0.5*diameter;
- double pixelWidth = (tanPerPixel > 0) ? tanPerPixel * dist :
+ double pixelWidth = (tanPerPixel > 0) ? tanPerPixel * dist :
-tanPerPixel / zoom;
double halfWidth = diameter;
@@ -537,7 +537,7 @@ void Image::draw_cube(double *x, double *surfaceColor, double diameter)
for (int iy = yc - pixelHalfWidth; iy <= yc + pixelHalfWidth; iy ++) {
for (int ix = xc - pixelHalfWidth; ix <= xc + pixelHalfWidth; ix ++) {
if (iy < 0 || iy >= height || ix < 0 || ix >= width) continue;
-
+
double sy = ((iy - yc) - height_error) * pixelWidth;
double sx = ((ix - xc) - width_error) * pixelWidth;
surface[0] = camRight[0] * sx + camUp[0] * sy;
@@ -565,32 +565,32 @@ void Image::draw_cube(double *x, double *surfaceColor, double diameter)
tdir[1] = camDir[1] * t;
tdir[2] = camDir[2] * t;
- bool xin = ((surface[0]+tdir[0]) >= -radius) &&
- ((surface[0]+tdir[0]) <= radius);
- bool yin = ((surface[1]+tdir[1]) >= -radius) &&
- ((surface[1]+tdir[1]) <= radius);
- bool zin = ((surface[2]+tdir[2]) >= -radius) &&
- ((surface[2]+tdir[2]) <= radius);
+ bool xin = ((surface[0]+tdir[0]) >= -radius) &&
+ ((surface[0]+tdir[0]) <= radius);
+ bool yin = ((surface[1]+tdir[1]) >= -radius) &&
+ ((surface[1]+tdir[1]) <= radius);
+ bool zin = ((surface[2]+tdir[2]) >= -radius) &&
+ ((surface[2]+tdir[2]) <= radius);
switch (dim) {
- case 0:
- if (yin & zin) {
- depth = dist - t;
- draw_pixel (ix, iy, depth, normal, surfaceColor);
- }
- break;
- case 1:
- if (xin & zin) {
- depth = dist - t;
- draw_pixel (ix, iy, depth, normal, surfaceColor);
- }
- break;
- case 2:
- if (xin & yin) {
- depth = dist - t;
- draw_pixel (ix, iy, depth, normal, surfaceColor);
- }
- break;
+ case 0:
+ if (yin & zin) {
+ depth = dist - t;
+ draw_pixel (ix, iy, depth, normal, surfaceColor);
+ }
+ break;
+ case 1:
+ if (xin & zin) {
+ depth = dist - t;
+ draw_pixel (ix, iy, depth, normal, surfaceColor);
+ }
+ break;
+ case 2:
+ if (xin & yin) {
+ depth = dist - t;
+ draw_pixel (ix, iy, depth, normal, surfaceColor);
+ }
+ break;
}
}
}
@@ -608,7 +608,7 @@ void Image::draw_cube(double *x, double *surfaceColor, double diameter)
------------------------------------------------------------------------- */
void Image::draw_cylinder(double *x, double *y,
- double *surfaceColor, double diameter, int sflag)
+ double *surfaceColor, double diameter, int sflag)
{
double surface[3], normal[3];
double mid[3],xaxis[3],yaxis[3],zaxis[3];
@@ -642,7 +642,7 @@ void Image::draw_cylinder(double *x, double *y,
double ymap = MathExtra::dot3(camUp,mid);
double dist = MathExtra::dot3(camPos,camDir) - MathExtra::dot3(mid,camDir);
- double pixelWidth = (tanPerPixel > 0) ? tanPerPixel * dist :
+ double pixelWidth = (tanPerPixel > 0) ? tanPerPixel * dist :
-tanPerPixel / zoom;
double xf = xmap / pixelWidth;
@@ -664,7 +664,7 @@ void Image::draw_cylinder(double *x, double *y,
if (zaxis[0] == camDir[0] && zaxis[1] == camDir[1] && zaxis[2] == camDir[2])
return;
- if (zaxis[0] == -camDir[0] && zaxis[1] == -camDir[1] &&
+ if (zaxis[0] == -camDir[0] && zaxis[1] == -camDir[1] &&
zaxis[2] == -camDir[2]) return;
MathExtra::cross3(zaxis,camDir,yaxis);
@@ -691,7 +691,7 @@ void Image::draw_cylinder(double *x, double *y,
for (int iy = yc - pixelHalfHeight; iy <= yc + pixelHalfHeight; iy ++) {
for (int ix = xc - pixelHalfWidth; ix <= xc + pixelHalfWidth; ix ++) {
if (iy < 0 || iy >= height || ix < 0 || ix >= width) continue;
-
+
double sy = ((iy - yc) - height_error) * pixelWidth;
double sx = ((ix - xc) - width_error) * pixelWidth;
surface[0] = camLRight[0] * sx + camLUp[0] * sy;
@@ -721,7 +721,7 @@ void Image::draw_cylinder(double *x, double *y,
normal[1] = surface[1] / radius;
normal[2] = 0.0;
- // in camera space
+ // in camera space
surface[0] = MathExtra::dot3 (normal, camLRight);
surface[1] = MathExtra::dot3 (normal, camLUp);
@@ -793,7 +793,7 @@ void Image::draw_triangle(double *x, double *y, double *z, double *surfaceColor)
double ymap = MathExtra::dot3(camUp,xlocal);
double dist = MathExtra::dot3(camPos,camDir) - MathExtra::dot3(xlocal,camDir);
- double pixelWidth = (tanPerPixel > 0) ? tanPerPixel * dist :
+ double pixelWidth = (tanPerPixel > 0) ? tanPerPixel * dist :
-tanPerPixel / zoom;
double xf = xmap / pixelWidth;
@@ -873,50 +873,50 @@ void Image::draw_triangle(double *x, double *y, double *z, double *surfaceColor)
/* ---------------------------------------------------------------------- */
-void Image::draw_pixel(int ix, int iy, double depth,
- double *surface, double *surfaceColor)
+void Image::draw_pixel(int ix, int iy, double depth,
+ double *surface, double *surfaceColor)
{
double diffuseKey,diffuseFill,diffuseBack,specularKey;
- if (depth < 0 || (depthBuffer[ix + iy*width] >= 0 &&
- depth >= depthBuffer[ix + iy*width])) return;
+ if (depth < 0 || (depthBuffer[ix + iy*width] >= 0 &&
+ depth >= depthBuffer[ix + iy*width])) return;
depthBuffer[ix + iy*width] = depth;
-
+
// store only the tangent relative to the camera normal (0,0,-1)
surfaceBuffer[0 + ix * 2 + iy*width * 2] = surface[1];
surfaceBuffer[1 + ix * 2 + iy*width * 2] = -surface[0];
-
+
diffuseKey = saturate(MathExtra::dot3(surface, keyLightDir));
diffuseFill = saturate(MathExtra::dot3(surface, fillLightDir));
diffuseBack = saturate(MathExtra::dot3(surface, backLightDir));
specularKey = pow(saturate(MathExtra::dot3(surface, keyHalfDir)),
- specularHardness) * specularIntensity;
-
+ specularHardness) * specularIntensity;
+
double c[3];
c[0] = surfaceColor[0] * ambientColor[0];
c[1] = surfaceColor[1] * ambientColor[1];
c[2] = surfaceColor[2] * ambientColor[2];
-
+
c[0] += surfaceColor[0] * keyLightColor[0] * diffuseKey;
c[1] += surfaceColor[1] * keyLightColor[1] * diffuseKey;
c[2] += surfaceColor[2] * keyLightColor[2] * diffuseKey;
-
+
c[0] += keyLightColor[0] * specularKey;
c[1] += keyLightColor[1] * specularKey;
c[2] += keyLightColor[2] * specularKey;
-
+
c[0] += surfaceColor[0] * fillLightColor[0] * diffuseFill;
c[1] += surfaceColor[1] * fillLightColor[1] * diffuseFill;
c[2] += surfaceColor[2] * fillLightColor[2] * diffuseFill;
-
+
c[0] += surfaceColor[0] * backLightColor[0] * diffuseBack;
c[1] += surfaceColor[1] * backLightColor[1] * diffuseBack;
c[2] += surfaceColor[2] * backLightColor[2] * diffuseBack;
-
+
c[0] = saturate(c[0]);
c[1] = saturate(c[1]);
c[2] = saturate(c[2]);
-
+
imageBuffer[0 + ix*3 + iy*width*3] = static_cast<int>(c[0] * 255.0);
imageBuffer[1 + ix*3 + iy*width*3] = static_cast<int>(c[1] * 255.0);
imageBuffer[2 + ix*3 + iy*width*3] = static_cast<int>(c[2] * 255.0);
@@ -932,8 +932,8 @@ void Image::compute_SSAO()
// typical neighborhood value for shading
- double pixelWidth = (tanPerPixel > 0) ? tanPerPixel :
- -tanPerPixel / zoom;
+ double pixelWidth = (tanPerPixel > 0) ? tanPerPixel :
+ -tanPerPixel / zoom;
int pixelRadius = (int) trunc (SSAORadius / pixelWidth + 0.5);
int x,y,s;
@@ -956,8 +956,8 @@ void Image::compute_SSAO()
double hy = sin(mytheta);
mytheta += delTheta;
- // multiply by z cross surface tangent
- // so that dot (aka cos) works here
+ // multiply by z cross surface tangent
+ // so that dot (aka cos) works here
double scaled_sin_t = sin_t * (hx*sy + hy*sx);
@@ -969,7 +969,7 @@ void Image::compute_SSAO()
if (ex < 0) { ex = 0; } if (ex >= width) { ex = width - 1; }
int ey = y + dy;
if (ey < 0) { ey = 0; } if (ey >= height) { ey = height - 1; }
- double delta;
+ double delta;
int small, large;
double lenIncr;
if (fabs(hx) > fabs(hy)) {
@@ -984,7 +984,7 @@ void Image::compute_SSAO()
lenIncr = sqrt (1 + delta * delta) * pixelWidth;
// initialize with one step
- // because the center point doesn't need testing
+ // because the center point doesn't need testing
int end = ex + ey * width;
int ind = index + small;
@@ -1005,8 +1005,8 @@ void Image::compute_SSAO()
// cdepth - depthBuffer B/C we want it in the negative z direction
- if (minPeak < 0 || (depthBuffer[ind] >= 0 &&
- depthBuffer[ind] < minPeak)) {
+ if (minPeak < 0 || (depthBuffer[ind] >= 0 &&
+ depthBuffer[ind] < minPeak)) {
minPeak = depthBuffer[ind];
peakLen = len;
}
@@ -1028,7 +1028,7 @@ void Image::compute_SSAO()
}
}
ao /= (double)SSAOSamples;
-
+
double c[3];
c[0] = (double) (*(unsigned char *) &imageBuffer[index * 3 + 0]);
c[1] = (double) (*(unsigned char *) &imageBuffer[index * 3 + 1]);
@@ -1045,7 +1045,7 @@ void Image::compute_SSAO()
/* ---------------------------------------------------------------------- */
-void Image::write_JPG(FILE *fp)
+void Image::write_JPG(FILE *fp)
{
#ifdef LAMMPS_JPEG
struct jpeg_compress_struct cinfo;
@@ -1065,7 +1065,7 @@ void Image::write_JPG(FILE *fp)
jpeg_start_compress(&cinfo, 1);
while (cinfo.next_scanline < cinfo.image_height) {
- row_pointer = (JSAMPROW)
+ row_pointer = (JSAMPROW)
&writeBuffer[(cinfo.image_height - 1 - cinfo.next_scanline) * 3 * width];
jpeg_write_scanlines(&cinfo,&row_pointer,1);
}
@@ -1077,7 +1077,7 @@ void Image::write_JPG(FILE *fp)
/* ---------------------------------------------------------------------- */
-void Image::write_PPM(FILE *fp)
+void Image::write_PPM(FILE *fp)
{
fprintf (fp,"P6\n%d %d\n255\n",width,height);
@@ -1085,9 +1085,9 @@ void Image::write_PPM(FILE *fp)
for (y = height-1; y >= 0; y --)
for (x = 0; x < width; x ++)
fprintf(fp,"%c%c%c",
- writeBuffer[0 + x*3 + y*width*3],
- writeBuffer[1 + x*3 + y*width*3],
- writeBuffer[2 + x*3 + y*width*3]);
+ writeBuffer[0 + x*3 + y*width*3],
+ writeBuffer[1 + x*3 + y*width*3],
+ writeBuffer[2 + x*3 + y*width*3]);
}
/* ----------------------------------------------------------------------
@@ -1126,7 +1126,7 @@ int Image::colormap(int narg, char **arg)
if (mbinsize <= 0.0) return 1;
mbinsizeinv = 1.0/mbinsize;
}
-
+
nentry = atoi(arg[4]);
if (nentry < 1) return 1;
mentry = new MapEntry[nentry];
@@ -1136,8 +1136,8 @@ int Image::colormap(int narg, char **arg)
if (mstyle == CONTINUOUS) {
if (n+2 > narg) return 1;
if (!islower(arg[n][0])) {
- mentry[i].single = NUMERIC;
- mentry[i].svalue = atof(arg[n]);
+ mentry[i].single = NUMERIC;
+ mentry[i].svalue = atof(arg[n]);
} else if (strcmp(arg[n],"min") == 0) mentry[i].single = MINVALUE;
else if (strcmp(arg[n],"max") == 0) mentry[i].single = MAXVALUE;
else return 1;
@@ -1146,14 +1146,14 @@ int Image::colormap(int narg, char **arg)
} else if (mstyle == DISCRETE) {
if (n+3 > narg) return 1;
if (!islower(arg[n][0])) {
- mentry[i].lo = NUMERIC;
- mentry[i].lvalue = atof(arg[n]);
+ mentry[i].lo = NUMERIC;
+ mentry[i].lvalue = atof(arg[n]);
} else if (strcmp(arg[n],"min") == 0) mentry[i].single = MINVALUE;
else if (strcmp(arg[n],"max") == 0) mentry[i].single = MAXVALUE;
else return 1;
if (!islower(arg[n+1][0])) {
- mentry[i].hi = NUMERIC;
- mentry[i].hvalue = atof(arg[n+1]);
+ mentry[i].hi = NUMERIC;
+ mentry[i].hvalue = atof(arg[n+1]);
} else if (strcmp(arg[n+1],"min") == 0) mentry[i].single = MINVALUE;
else if (strcmp(arg[n+1],"max") == 0) mentry[i].single = MAXVALUE;
else return 1;
@@ -1166,7 +1166,7 @@ int Image::colormap(int narg, char **arg)
}
if (mentry[i].color == NULL) return 1;
}
-
+
if (mstyle == CONTINUOUS) {
if (nentry < 2) return 1;
if (mentry[0].single != MINVALUE || mentry[nentry-1].single != MAXVALUE)
@@ -1180,7 +1180,7 @@ int Image::colormap(int narg, char **arg)
} else if (mstyle == SEQUENTIAL) {
if (nentry < 1) return 1;
}
-
+
return 0;
}
@@ -1197,7 +1197,7 @@ int Image::addcolor(char *name, double r, double g, double b)
if (strcmp(name,username[icolor]) == 0) break;
if (icolor == ncolors) {
- username = (char **)
+ username = (char **)
memory->srealloc(username,(ncolors+1)*sizeof(char *),"image:username");
memory->grow(userrgb,ncolors+1,3,"image:userrgb");
ncolors++;
@@ -1241,20 +1241,20 @@ double *Image::value2color(double value)
if (mstyle == CONTINUOUS) {
for (int i = 0; i < nentry-1; i++)
if (value >= mentry[i].svalue && value <= mentry[i+1].svalue) {
- double fraction = (value-mentry[i].svalue) /
- (mentry[i+1].svalue-mentry[i].svalue);
- interpolate[0] = mentry[i].color[0] +
- fraction*(mentry[i+1].color[0]-mentry[i].color[0]);
- interpolate[1] = mentry[i].color[1] +
- fraction*(mentry[i+1].color[1]-mentry[i].color[1]);
- interpolate[2] = mentry[i].color[2] +
- fraction*(mentry[i+1].color[2]-mentry[i].color[2]);
- return interpolate;
+ double fraction = (value-mentry[i].svalue) /
+ (mentry[i+1].svalue-mentry[i].svalue);
+ interpolate[0] = mentry[i].color[0] +
+ fraction*(mentry[i+1].color[0]-mentry[i].color[0]);
+ interpolate[1] = mentry[i].color[1] +
+ fraction*(mentry[i+1].color[1]-mentry[i].color[1]);
+ interpolate[2] = mentry[i].color[2] +
+ fraction*(mentry[i+1].color[2]-mentry[i].color[2]);
+ return interpolate;
}
} else if (mstyle == DISCRETE) {
for (int i = 0; i < nentry; i++)
if (value >= mentry[i].lvalue && value <= mentry[i].hvalue)
- return mentry[i].color;
+ return mentry[i].color;
} else {
int ibin = static_cast<int> ((value-lo) * mbinsizeinv);
return mentry[ibin%nentry].color;
@@ -1271,7 +1271,7 @@ double *Image::value2color(double value)
double *Image::color2rgb(const char *color, int index)
{
- static const char *name[NCOLORS] = {
+ static const char *name[NCOLORS] = {
"aliceblue",
"antiquewhite",
"aqua",
@@ -1583,7 +1583,7 @@ int Image::default_colors()
double *Image::element2color(char *element)
{
- static const char *name[NELEMENTS] = {
+ static const char *name[NELEMENTS] = {
"H", "He", "Li", "Be", "B", "C", "N", "O", "F", "Ne",
"Na", "Mg", "Al", "Si", "P", "S", "Cl", "Ar", "K", "Ca",
"Sc", "Ti", "V", "Cr", "Mn", "Fe", "Co", "Ni", "Cu", "Zn",
@@ -1722,7 +1722,7 @@ double *Image::element2color(char *element)
double Image::element2diam(char *element)
{
- static const char *name[NELEMENTS] = {
+ static const char *name[NELEMENTS] = {
"H", "He", "Li", "Be", "B", "C", "N", "O", "F", "Ne",
"Na", "Mg", "Al", "Si", "P", "S", "Cl", "Ar", "K", "Ca",
"Sc", "Ti", "V", "Cr", "Mn", "Fe", "Co", "Ni", "Cu", "Zn",
@@ -1754,4 +1754,3 @@ double Image::element2diam(char *element)
if (strcmp(element,name[i]) == 0) return diameter[i];
return 0.0;
}
-
diff --git a/src/image.h b/src/image.h
index 3474fcee9e9bed56cac736c67505fd2dea1a3fac..59d93607964dd12fb3b1f691670282baad6748f8 100644
--- a/src/image.h
+++ b/src/image.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -142,9 +142,9 @@ class Image : protected Pointers {
}
inline double distance(double* a, double* b) {
- return sqrt((a[0] - b[0]) * (a[0] - b[0]) +
- (a[1] - b[1]) * (a[1] - b[1]) +
- (a[2] - b[2]) * (a[2] - b[2]));
+ return sqrt((a[0] - b[0]) * (a[0] - b[0]) +
+ (a[1] - b[1]) * (a[1] - b[1]) +
+ (a[2] - b[2]) * (a[2] - b[2]));
}
};
diff --git a/src/improper.cpp b/src/improper.cpp
index 47ae5c69edb343701adce766ed8096842a49bdab..7225d34709cfa2e84de9ab1d381bb4ca9785d62a 100644
--- a/src/improper.cpp
+++ b/src/improper.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -73,7 +73,7 @@ void Improper::ev_setup(int eflag, int vflag)
vflag_either = vflag;
vflag_global = vflag % 4;
vflag_atom = vflag / 4;
-
+
// reallocate per-atom arrays if necessary
if (eflag_atom && atom->nmax > maxeatom) {
@@ -114,15 +114,15 @@ void Improper::ev_setup(int eflag, int vflag)
tally energy and virial into global and per-atom accumulators
virial = r1F1 + r2F2 + r3F3 + r4F4 = (r1-r2) F1 + (r3-r2) F3 + (r4-r2) F4
= (r1-r2) F1 + (r3-r2) F3 + (r4-r3 + r3-r2) F4
- = vb1*f1 + vb2*f3 + (vb3+vb2)*f4
+ = vb1*f1 + vb2*f3 + (vb3+vb2)*f4
------------------------------------------------------------------------- */
void Improper::ev_tally(int i1, int i2, int i3, int i4,
- int nlocal, int newton_bond,
- double eimproper, double *f1, double *f3, double *f4,
- double vb1x, double vb1y, double vb1z,
- double vb2x, double vb2y, double vb2z,
- double vb3x, double vb3y, double vb3z)
+ int nlocal, int newton_bond,
+ double eimproper, double *f1, double *f3, double *f4,
+ double vb1x, double vb1y, double vb1z,
+ double vb2x, double vb2y, double vb2z,
+ double vb3x, double vb3y, double vb3z)
{
double eimproperquarter,v[6];
@@ -130,11 +130,11 @@ void Improper::ev_tally(int i1, int i2, int i3, int i4,
if (eflag_global) {
if (newton_bond) energy += eimproper;
else {
- eimproperquarter = 0.25*eimproper;
- if (i1 < nlocal) energy += eimproperquarter;
- if (i2 < nlocal) energy += eimproperquarter;
- if (i3 < nlocal) energy += eimproperquarter;
- if (i4 < nlocal) energy += eimproperquarter;
+ eimproperquarter = 0.25*eimproper;
+ if (i1 < nlocal) energy += eimproperquarter;
+ if (i2 < nlocal) energy += eimproperquarter;
+ if (i3 < nlocal) energy += eimproperquarter;
+ if (i4 < nlocal) energy += eimproperquarter;
}
}
if (eflag_atom) {
@@ -156,80 +156,80 @@ void Improper::ev_tally(int i1, int i2, int i3, int i4,
if (vflag_global) {
if (newton_bond) {
- virial[0] += v[0];
- virial[1] += v[1];
- virial[2] += v[2];
- virial[3] += v[3];
- virial[4] += v[4];
- virial[5] += v[5];
+ virial[0] += v[0];
+ virial[1] += v[1];
+ virial[2] += v[2];
+ virial[3] += v[3];
+ virial[4] += v[4];
+ virial[5] += v[5];
} else {
- if (i1 < nlocal) {
- virial[0] += 0.25*v[0];
- virial[1] += 0.25*v[1];
- virial[2] += 0.25*v[2];
- virial[3] += 0.25*v[3];
- virial[4] += 0.25*v[4];
- virial[5] += 0.25*v[5];
- }
- if (i2 < nlocal) {
- virial[0] += 0.25*v[0];
- virial[1] += 0.25*v[1];
- virial[2] += 0.25*v[2];
- virial[3] += 0.25*v[3];
- virial[4] += 0.25*v[4];
- virial[5] += 0.25*v[5];
- }
- if (i3 < nlocal) {
- virial[0] += 0.25*v[0];
- virial[1] += 0.25*v[1];
- virial[2] += 0.25*v[2];
- virial[3] += 0.25*v[3];
- virial[4] += 0.25*v[4];
- virial[5] += 0.25*v[5];
- }
- if (i4 < nlocal) {
- virial[0] += 0.25*v[0];
- virial[1] += 0.25*v[1];
- virial[2] += 0.25*v[2];
- virial[3] += 0.25*v[3];
- virial[4] += 0.25*v[4];
- virial[5] += 0.25*v[5];
- }
+ if (i1 < nlocal) {
+ virial[0] += 0.25*v[0];
+ virial[1] += 0.25*v[1];
+ virial[2] += 0.25*v[2];
+ virial[3] += 0.25*v[3];
+ virial[4] += 0.25*v[4];
+ virial[5] += 0.25*v[5];
+ }
+ if (i2 < nlocal) {
+ virial[0] += 0.25*v[0];
+ virial[1] += 0.25*v[1];
+ virial[2] += 0.25*v[2];
+ virial[3] += 0.25*v[3];
+ virial[4] += 0.25*v[4];
+ virial[5] += 0.25*v[5];
+ }
+ if (i3 < nlocal) {
+ virial[0] += 0.25*v[0];
+ virial[1] += 0.25*v[1];
+ virial[2] += 0.25*v[2];
+ virial[3] += 0.25*v[3];
+ virial[4] += 0.25*v[4];
+ virial[5] += 0.25*v[5];
+ }
+ if (i4 < nlocal) {
+ virial[0] += 0.25*v[0];
+ virial[1] += 0.25*v[1];
+ virial[2] += 0.25*v[2];
+ virial[3] += 0.25*v[3];
+ virial[4] += 0.25*v[4];
+ virial[5] += 0.25*v[5];
+ }
}
}
if (vflag_atom) {
if (newton_bond || i1 < nlocal) {
- vatom[i1][0] += 0.25*v[0];
- vatom[i1][1] += 0.25*v[1];
- vatom[i1][2] += 0.25*v[2];
- vatom[i1][3] += 0.25*v[3];
- vatom[i1][4] += 0.25*v[4];
- vatom[i1][5] += 0.25*v[5];
+ vatom[i1][0] += 0.25*v[0];
+ vatom[i1][1] += 0.25*v[1];
+ vatom[i1][2] += 0.25*v[2];
+ vatom[i1][3] += 0.25*v[3];
+ vatom[i1][4] += 0.25*v[4];
+ vatom[i1][5] += 0.25*v[5];
}
if (newton_bond || i2 < nlocal) {
- vatom[i2][0] += 0.25*v[0];
- vatom[i2][1] += 0.25*v[1];
- vatom[i2][2] += 0.25*v[2];
- vatom[i2][3] += 0.25*v[3];
- vatom[i2][4] += 0.25*v[4];
- vatom[i2][5] += 0.25*v[5];
+ vatom[i2][0] += 0.25*v[0];
+ vatom[i2][1] += 0.25*v[1];
+ vatom[i2][2] += 0.25*v[2];
+ vatom[i2][3] += 0.25*v[3];
+ vatom[i2][4] += 0.25*v[4];
+ vatom[i2][5] += 0.25*v[5];
}
if (newton_bond || i3 < nlocal) {
- vatom[i3][0] += 0.25*v[0];
- vatom[i3][1] += 0.25*v[1];
- vatom[i3][2] += 0.25*v[2];
- vatom[i3][3] += 0.25*v[3];
- vatom[i3][4] += 0.25*v[4];
- vatom[i3][5] += 0.25*v[5];
+ vatom[i3][0] += 0.25*v[0];
+ vatom[i3][1] += 0.25*v[1];
+ vatom[i3][2] += 0.25*v[2];
+ vatom[i3][3] += 0.25*v[3];
+ vatom[i3][4] += 0.25*v[4];
+ vatom[i3][5] += 0.25*v[5];
}
if (newton_bond || i4 < nlocal) {
- vatom[i4][0] += 0.25*v[0];
- vatom[i4][1] += 0.25*v[1];
- vatom[i4][2] += 0.25*v[2];
- vatom[i4][3] += 0.25*v[3];
- vatom[i4][4] += 0.25*v[4];
- vatom[i4][5] += 0.25*v[5];
+ vatom[i4][0] += 0.25*v[0];
+ vatom[i4][1] += 0.25*v[1];
+ vatom[i4][2] += 0.25*v[2];
+ vatom[i4][3] += 0.25*v[3];
+ vatom[i4][4] += 0.25*v[4];
+ vatom[i4][5] += 0.25*v[5];
}
}
}
diff --git a/src/improper.h b/src/improper.h
index 56f38e7641d74ba4907b3a7e4a57cef5cbc461a9..dcf07035634eec812e71f27fd500e02c84a82a3b 100644
--- a/src/improper.h
+++ b/src/improper.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -49,8 +49,8 @@ class Improper : protected Pointers {
void ev_setup(int, int);
void ev_tally(int, int, int, int, int, int, double,
- double *, double *, double *, double, double, double,
- double, double, double, double, double, double);
+ double *, double *, double *, double, double, double,
+ double, double, double, double, double, double);
};
}
diff --git a/src/input.cpp b/src/input.cpp
index d506ddacc32c59495443a9ee1d00c25450cdb8e4..8eda9eab560add7880d278d7053182a51f2ca671 100644
--- a/src/input.cpp
+++ b/src/input.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -93,8 +93,8 @@ Input::Input(LAMMPS *lmp, int argc, char **argv) : Pointers(lmp)
while (jarg < argc && argv[jarg][0] != '-') jarg++;
variable->set(argv[iarg+1],jarg-iarg-2,&argv[iarg+2]);
iarg = jarg;
- } else if (strcmp(argv[iarg],"-echo") == 0 ||
- strcmp(argv[iarg],"-e") == 0) {
+ } else if (strcmp(argv[iarg],"-echo") == 0 ||
+ strcmp(argv[iarg],"-e") == 0) {
narg = 1;
char **tmp = arg; // trick echo() into using argv instead of arg
arg = &argv[iarg+1];
@@ -131,7 +131,7 @@ void Input::file()
int m,n;
while (1) {
-
+
// read a line from input script
// if line ends in continuation char '&', concatenate next line(s)
// n = length of line including str terminator, 0 if end of file
@@ -140,12 +140,12 @@ void Input::file()
if (me == 0) {
m = 0;
while (1) {
- if (fgets(&line[m],MAXLINE-m,infile) == NULL) n = 0;
- else n = strlen(line) + 1;
- if (n == 0) break;
- m = n-2;
- while (m >= 0 && isspace(line[m])) m--;
- if (m < 0 || line[m] != '&') break;
+ if (fgets(&line[m],MAXLINE-m,infile) == NULL) n = 0;
+ else n = strlen(line) + 1;
+ if (n == 0) break;
+ m = n-2;
+ while (m >= 0 && isspace(line[m])) m--;
+ if (m < 0 || line[m] != '&') break;
}
}
@@ -159,8 +159,8 @@ void Input::file()
if (n == 0) {
if (label_active) error->all(FLERR,"Label wasn't found in input script");
if (me == 0) {
- if (infile != stdin) fclose(infile);
- nfile--;
+ if (infile != stdin) fclose(infile);
+ nfile--;
}
MPI_Bcast(&nfile,1,MPI_INT,0,world);
if (nfile == 0) break;
@@ -181,7 +181,7 @@ void Input::file()
// echo the command unless scanning for label
if (me == 0 && label_active == 0) {
- if (echo_screen && screen) fprintf(screen,"%s",line);
+ if (echo_screen && screen) fprintf(screen,"%s",line);
if (echo_log && logfile) fprintf(logfile,"%s",line);
}
@@ -241,9 +241,9 @@ char *Input::one(const char *single)
strcpy(line,single);
// echo the command unless scanning for label
-
+
if (me == 0 && label_active == 0) {
- if (echo_screen && screen) fprintf(screen,"%s\n",line);
+ if (echo_screen && screen) fprintf(screen,"%s\n",line);
if (echo_log && logfile) fprintf(logfile,"%s\n",line);
}
@@ -383,17 +383,17 @@ void Input::substitute(char *str, int flag)
while (*ptr) {
if (*ptr == '$' && !quote) {
if (*(ptr+1) == '{') {
- var = ptr+2;
- int i = 0;
- while (var[i] != '\0' && var[i] != '}') i++;
- if (var[i] == '\0') error->one(FLERR,"Invalid variable name");
- var[i] = '\0';
- beyond = ptr + strlen(var) + 3;
+ var = ptr+2;
+ int i = 0;
+ while (var[i] != '\0' && var[i] != '}') i++;
+ if (var[i] == '\0') error->one(FLERR,"Invalid variable name");
+ var[i] = '\0';
+ beyond = ptr + strlen(var) + 3;
} else {
- var = ptr;
- var[0] = var[1];
- var[1] = '\0';
- beyond = ptr + strlen(var) + 1;
+ var = ptr;
+ var[0] = var[1];
+ var[1] = '\0';
+ beyond = ptr + strlen(var) + 1;
}
value = variable->retrieve(var);
if (value == NULL) error->one(FLERR,"Substitution for illegal variable");
@@ -401,16 +401,16 @@ void Input::substitute(char *str, int flag)
*ptr = '\0';
strcpy(work,str);
if (strlen(work)+strlen(value) >= MAXLINE)
- error->one(FLERR,"Input line too long after variable substitution");
+ error->one(FLERR,"Input line too long after variable substitution");
strcat(work,value);
if (strlen(work)+strlen(beyond) >= MAXLINE)
- error->one(FLERR,"Input line too long after variable substitution");
+ error->one(FLERR,"Input line too long after variable substitution");
strcat(work,beyond);
strcpy(str,work);
ptr += strlen(value);
if (flag && me == 0 && label_active == 0) {
- if (echo_screen && screen) fprintf(screen,"%s",str);
- if (echo_log && logfile) fprintf(logfile,"%s",str);
+ if (echo_screen && screen) fprintf(screen,"%s",str);
+ if (echo_log && logfile) fprintf(logfile,"%s",str);
}
continue;
}
@@ -507,7 +507,7 @@ int Input::execute_command()
#define COMMAND_CLASS
#define CommandStyle(key,Class) \
else if (strcmp(command,#key) == 0) { \
- Class key(lmp); \
+ Class key(lmp); \
key.command(narg,arg); \
return 0; \
}
@@ -578,8 +578,8 @@ void Input::ifthenelse()
int first = 2;
int iarg = first;
- while (iarg < narg &&
- (strcmp(arg[iarg],"elif") != 0 && strcmp(arg[iarg],"else") != 0))
+ while (iarg < narg &&
+ (strcmp(arg[iarg],"elif") != 0 && strcmp(arg[iarg],"else") != 0))
iarg++;
int last = iarg-1;
@@ -600,9 +600,9 @@ void Input::ifthenelse()
strcpy(commands[ncommands],arg[i]);
ncommands++;
}
-
+
for (int i = 0; i < ncommands; i++) one(commands[i]);
-
+
for (int i = 0; i < ncommands; i++) delete [] commands[i];
delete [] commands;
delete [] scopy;
@@ -635,8 +635,8 @@ void Input::ifthenelse()
}
iarg = first;
- while (iarg < narg &&
- (strcmp(arg[iarg],"elif") != 0 && strcmp(arg[iarg],"else") != 0))
+ while (iarg < narg &&
+ (strcmp(arg[iarg],"elif") != 0 && strcmp(arg[iarg],"else") != 0))
iarg++;
last = iarg-1;
@@ -654,11 +654,11 @@ void Input::ifthenelse()
strcpy(commands[ncommands],arg[i]);
ncommands++;
}
-
+
// execute the list of commands
-
+
for (int i = 0; i < ncommands; i++) one(commands[i]);
-
+
// clean up
for (int i = 0; i < ncommands; i++) delete [] commands[i];
@@ -678,7 +678,7 @@ void Input::include()
if (me == 0) {
if (nfile == maxfile) {
maxfile++;
- infiles = (FILE **)
+ infiles = (FILE **)
memory->srealloc(infiles,maxfile*sizeof(FILE *),"input:infiles");
}
infile = fopen(arg[0],"r");
@@ -708,9 +708,9 @@ void Input::jump()
if (infile != stdin) fclose(infile);
infile = fopen(arg[0],"r");
if (infile == NULL) {
- char str[128];
- sprintf(str,"Cannot open input script %s",arg[0]);
- error->one(FLERR,str);
+ char str[128];
+ sprintf(str,"Cannot open input script %s",arg[0]);
+ error->one(FLERR,str);
}
infiles[nfile-1] = infile;
}
@@ -745,9 +745,9 @@ void Input::log()
else {
logfile = fopen(arg[0],"w");
if (logfile == NULL) {
- char str[128];
- sprintf(str,"Cannot open logfile %s",arg[0]);
- error->one(FLERR,str);
+ char str[128];
+ sprintf(str,"Cannot open logfile %s",arg[0]);
+ error->one(FLERR,str);
}
}
if (universe->nworlds == 1) universe->ulogfile = logfile;
@@ -830,10 +830,10 @@ void Input::shell()
} else if (strcmp(arg[0],"mkdir") == 0) {
if (narg < 2) error->all(FLERR,"Illegal shell command");
-#if !defined(WINDOWS) && !defined(__MINGW32_VERSION)
+#if !defined(WINDOWS) && !defined(__MINGW32_VERSION)
if (me == 0)
for (int i = 1; i < narg; i++)
- mkdir(arg[i], S_IRWXU | S_IRGRP | S_IXGRP);
+ mkdir(arg[i], S_IRWXU | S_IRGRP | S_IXGRP);
#endif
} else if (strcmp(arg[0],"mv") == 0) {
@@ -884,9 +884,9 @@ void Input::angle_coeff()
{
if (domain->box_exist == 0)
error->all(FLERR,"Angle_coeff command before simulation box is defined");
- if (force->angle == NULL)
+ if (force->angle == NULL)
error->all(FLERR,"Angle_coeff command before angle_style is defined");
- if (atom->avec->angles_allow == 0)
+ if (atom->avec->angles_allow == 0)
error->all(FLERR,"Angle_coeff command when no angles allowed");
force->angle->coeff(narg,arg);
}
@@ -896,7 +896,7 @@ void Input::angle_coeff()
void Input::angle_style()
{
if (narg < 1) error->all(FLERR,"Illegal angle_style command");
- if (atom->avec->angles_allow == 0)
+ if (atom->avec->angles_allow == 0)
error->all(FLERR,"Angle_style command when no angles allowed");
force->create_angle(arg[0],lmp->suffix);
if (force->angle) force->angle->settings(narg-1,&arg[1]);
@@ -914,7 +914,7 @@ void Input::atom_modify()
void Input::atom_style()
{
if (narg < 1) error->all(FLERR,"Illegal atom_style command");
- if (domain->box_exist)
+ if (domain->box_exist)
error->all(FLERR,"Atom_style command after simulation box is defined");
atom->create_avec(arg[0],narg-1,&arg[1],lmp->suffix);
}
@@ -925,9 +925,9 @@ void Input::bond_coeff()
{
if (domain->box_exist == 0)
error->all(FLERR,"Bond_coeff command before simulation box is defined");
- if (force->bond == NULL)
+ if (force->bond == NULL)
error->all(FLERR,"Bond_coeff command before bond_style is defined");
- if (atom->avec->bonds_allow == 0)
+ if (atom->avec->bonds_allow == 0)
error->all(FLERR,"Bond_coeff command when no bonds allowed");
force->bond->coeff(narg,arg);
}
@@ -937,7 +937,7 @@ void Input::bond_coeff()
void Input::bond_style()
{
if (narg < 1) error->all(FLERR,"Illegal bond_style command");
- if (atom->avec->bonds_allow == 0)
+ if (atom->avec->bonds_allow == 0)
error->all(FLERR,"Bond_style command when no bonds allowed");
force->create_bond(arg[0],lmp->suffix);
if (force->bond) force->bond->settings(narg-1,&arg[1]);
@@ -987,9 +987,9 @@ void Input::dihedral_coeff()
{
if (domain->box_exist == 0)
error->all(FLERR,"Dihedral_coeff command before simulation box is defined");
- if (force->dihedral == NULL)
+ if (force->dihedral == NULL)
error->all(FLERR,"Dihedral_coeff command before dihedral_style is defined");
- if (atom->avec->dihedrals_allow == 0)
+ if (atom->avec->dihedrals_allow == 0)
error->all(FLERR,"Dihedral_coeff command when no dihedrals allowed");
force->dihedral->coeff(narg,arg);
}
@@ -999,7 +999,7 @@ void Input::dihedral_coeff()
void Input::dihedral_style()
{
if (narg < 1) error->all(FLERR,"Illegal dihedral_style command");
- if (atom->avec->dihedrals_allow == 0)
+ if (atom->avec->dihedrals_allow == 0)
error->all(FLERR,"Dihedral_style command when no dihedrals allowed");
force->create_dihedral(arg[0],lmp->suffix);
if (force->dihedral) force->dihedral->settings(narg-1,&arg[1]);
@@ -1010,7 +1010,7 @@ void Input::dihedral_style()
void Input::dimension()
{
if (narg != 1) error->all(FLERR,"Illegal dimension command");
- if (domain->box_exist)
+ if (domain->box_exist)
error->all(FLERR,"Dimension command after simulation box is defined");
domain->dimension = atoi(arg[0]);
if (domain->dimension != 2 && domain->dimension != 3)
@@ -1064,9 +1064,9 @@ void Input::improper_coeff()
{
if (domain->box_exist == 0)
error->all(FLERR,"Improper_coeff command before simulation box is defined");
- if (force->improper == NULL)
+ if (force->improper == NULL)
error->all(FLERR,"Improper_coeff command before improper_style is defined");
- if (atom->avec->impropers_allow == 0)
+ if (atom->avec->impropers_allow == 0)
error->all(FLERR,"Improper_coeff command when no impropers allowed");
force->improper->coeff(narg,arg);
}
@@ -1076,7 +1076,7 @@ void Input::improper_coeff()
void Input::improper_style()
{
if (narg < 1) error->all(FLERR,"Illegal improper_style command");
- if (atom->avec->impropers_allow == 0)
+ if (atom->avec->impropers_allow == 0)
error->all(FLERR,"Improper_style command when no impropers allowed");
force->create_improper(arg[0],lmp->suffix);
if (force->improper) force->improper->settings(narg-1,&arg[1]);
@@ -1086,7 +1086,7 @@ void Input::improper_style()
void Input::kspace_modify()
{
- if (force->kspace == NULL)
+ if (force->kspace == NULL)
error->all(FLERR,"KSpace style has not yet been set");
force->kspace->modify_params(narg,arg);
}
@@ -1167,11 +1167,11 @@ void Input::newton()
force->newton_pair = newton_pair;
if (newton_bond == 0) {
- if (domain->box_exist && force->newton_bond == 1)
+ if (domain->box_exist && force->newton_bond == 1)
error->all(FLERR,"Newton bond change after simulation box is defined");
force->newton_bond = 0;
} else {
- if (domain->box_exist && force->newton_bond == 0)
+ if (domain->box_exist && force->newton_bond == 0)
error->all(FLERR,"Newton bond change after simulation box is defined");
force->newton_bond = 1;
}
@@ -1184,7 +1184,7 @@ void Input::newton()
void Input::package()
{
- if (domain->box_exist)
+ if (domain->box_exist)
error->all(FLERR,"Package command after simulation box is defined");
if (narg < 1) error->all(FLERR,"Illegal package command");
@@ -1220,7 +1220,7 @@ void Input::pair_coeff()
{
if (domain->box_exist == 0)
error->all(FLERR,"Pair_coeff command before simulation box is defined");
- if (force->pair == NULL)
+ if (force->pair == NULL)
error->all(FLERR,"Pair_coeff command before pair_style is defined");
force->pair->coeff(narg,arg);
}
@@ -1229,7 +1229,7 @@ void Input::pair_coeff()
void Input::pair_modify()
{
- if (force->pair == NULL)
+ if (force->pair == NULL)
error->all(FLERR,"Pair_modify command before pair_style is defined");
force->pair->modify_params(narg,arg);
}
@@ -1254,7 +1254,7 @@ void Input::pair_style()
void Input::pair_write()
{
- if (force->pair == NULL)
+ if (force->pair == NULL)
error->all(FLERR,"Pair_write command before pair_style is defined");
force->pair->write_file(narg,arg);
}
@@ -1319,10 +1319,10 @@ void Input::special_bonds()
if (domain->box_exist && atom->molecular) {
if (lj2 != force->special_lj[2] || lj3 != force->special_lj[3] ||
- coul2 != force->special_coul[2] || coul3 != force->special_coul[3] ||
- angle != force->special_angle ||
- dihedral != force->special_dihedral ||
- extra != force->special_extra) {
+ coul2 != force->special_coul[2] || coul3 != force->special_coul[3] ||
+ angle != force->special_angle ||
+ dihedral != force->special_dihedral ||
+ extra != force->special_extra) {
Special special(lmp);
special.build();
}
@@ -1334,7 +1334,7 @@ void Input::special_bonds()
void Input::suffix()
{
if (narg != 1) error->all(FLERR,"Illegal suffix command");
-
+
if (strcmp(arg[0],"off") == 0) lmp->suffix_enable = 0;
else if (strcmp(arg[0],"on") == 0) lmp->suffix_enable = 1;
else {
@@ -1407,7 +1407,7 @@ void Input::unfix()
void Input::units()
{
if (narg != 1) error->all(FLERR,"Illegal units command");
- if (domain->box_exist)
+ if (domain->box_exist)
error->all(FLERR,"Units command after simulation box is defined");
update->set_units(arg[0]);
}
diff --git a/src/input.h b/src/input.h
index 1c83a01a5151a2c8cfa099db466e0e16fa09302d..ca1f0a56b38e2ef9c27aab396cb842fd8fc5f0a6 100644
--- a/src/input.h
+++ b/src/input.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/integrate.cpp b/src/integrate.cpp
index beef03c302510955c6d37105841a7be815a411ef..0a10ef22d250c4a86d59e79dfbaeeb1f6d259be0 100644
--- a/src/integrate.cpp
+++ b/src/integrate.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/integrate.h b/src/integrate.h
index bc5a43fd9e788c4a26ff928fd45057eb83d835f6..5b581859461c284c6ee397fa9c78ae7cdfb32eaa 100644
--- a/src/integrate.h
+++ b/src/integrate.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/irregular.cpp b/src/irregular.cpp
index f02c401acb89526e14b2b1c25b005c3ae996d35b..5e28aa554d622a1d7c92997087e91504ee452fc2 100644
--- a/src/irregular.cpp
+++ b/src/irregular.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -121,16 +121,16 @@ void Irregular::migrate_atoms()
int i = 0;
while (i < nlocal) {
if (x[i][0] < sublo[0] || x[i][0] >= subhi[0] ||
- x[i][1] < sublo[1] || x[i][1] >= subhi[1] ||
- x[i][2] < sublo[2] || x[i][2] >= subhi[2]) {
+ x[i][1] < sublo[1] || x[i][1] >= subhi[1] ||
+ x[i][2] < sublo[2] || x[i][2] >= subhi[2]) {
proclist[nsendatom] = coord2proc(x[i]);
if (proclist[nsendatom] != me) {
- if (nsend > maxsend) grow_send(nsend,1);
- sizes[nsendatom] = avec->pack_exchange(i,&buf_send[nsend]);
- nsend += sizes[nsendatom];
- nsendatom++;
- avec->copy(nlocal-1,i,1);
- nlocal--;
+ if (nsend > maxsend) grow_send(nsend,1);
+ sizes[nsendatom] = avec->pack_exchange(i,&buf_send[nsend]);
+ nsend += sizes[nsendatom];
+ nsendatom++;
+ avec->copy(nlocal-1,i,1);
+ nlocal--;
} else i++;
} else i++;
}
@@ -285,7 +285,7 @@ int Irregular::create_atom(int n, int *sizes, int *proclist)
delete [] count;
delete [] list;
-
+
// initialize plan
aplan->nsend = nsend;
@@ -322,7 +322,7 @@ void Irregular::exchange_atom(double *sendbuf, int *sizes, double *recvbuf)
offset = 0;
for (int irecv = 0; irecv < aplan->nrecv; irecv++) {
MPI_Irecv(&recvbuf[offset],aplan->length_recv[irecv],MPI_DOUBLE,
- aplan->proc_recv[irecv],0,world,&aplan->request[irecv]);
+ aplan->proc_recv[irecv],0,world,&aplan->request[irecv]);
offset += aplan->length_recv[irecv];
}
@@ -345,12 +345,12 @@ void Irregular::exchange_atom(double *sendbuf, int *sizes, double *recvbuf)
for (i = 0; i < num_send; i++) {
m = index_send[n++];
memcpy(&buf[offset],&sendbuf[aplan->offset_send[m]],
- sizes[m]*sizeof(double));
+ sizes[m]*sizeof(double));
offset += sizes[m];
}
MPI_Send(buf,aplan->length_send[isend],MPI_DOUBLE,
- aplan->proc_send[isend],0,world);
- }
+ aplan->proc_send[isend],0,world);
+ }
// free temporary send buffer
@@ -507,7 +507,7 @@ int Irregular::create_data(int n, int *proclist)
delete [] count;
delete [] list;
-
+
// initialize plan and return it
dplan->nsend = nsend;
@@ -544,7 +544,7 @@ void Irregular::exchange_data(char *sendbuf, int nbytes, char *recvbuf)
offset = dplan->num_self*nbytes;
for (int irecv = 0; irecv < dplan->nrecv; irecv++) {
MPI_Irecv(&recvbuf[offset],dplan->num_recv[irecv]*nbytes,MPI_CHAR,
- dplan->proc_recv[irecv],0,world,&dplan->request[irecv]);
+ dplan->proc_recv[irecv],0,world,&dplan->request[irecv]);
offset += dplan->num_recv[irecv]*nbytes;
}
@@ -568,8 +568,8 @@ void Irregular::exchange_data(char *sendbuf, int nbytes, char *recvbuf)
memcpy(&buf[i*nbytes],&sendbuf[m*nbytes],nbytes);
}
MPI_Send(buf,dplan->num_send[isend]*nbytes,MPI_CHAR,
- dplan->proc_send[isend],0,world);
- }
+ dplan->proc_send[isend],0,world);
+ }
// free temporary send buffer
@@ -622,8 +622,8 @@ int Irregular::coord2proc(double *x)
if (uniform) {
if (triclinic == 0) {
loc[0] = static_cast<int> (procgrid[0] * (x[0]-boxlo[0]) / prd[0]);
- loc[1] = static_cast<int> (procgrid[1] * (x[1]-boxlo[1]) / prd[1]);
- loc[2] = static_cast<int> (procgrid[2] * (x[2]-boxlo[2]) / prd[2]);
+ loc[1] = static_cast<int> (procgrid[1] * (x[1]-boxlo[1]) / prd[1]);
+ loc[2] = static_cast<int> (procgrid[2] * (x[2]-boxlo[2]) / prd[2]);
} else {
loc[0] = static_cast<int> (procgrid[0] * x[0]);
loc[1] = static_cast<int> (procgrid[1] * x[1]);
@@ -683,7 +683,7 @@ int Irregular::binary(double value, int n, double *vec)
}
/* ----------------------------------------------------------------------
- realloc the size of the send buffer as needed with BUFFACTOR & BUFEXTRA
+ realloc the size of the send buffer as needed with BUFFACTOR & BUFEXTRA
if flag = 1, realloc
if flag = 0, don't need to realloc with copy, just free/malloc
------------------------------------------------------------------------- */
@@ -700,7 +700,7 @@ void Irregular::grow_send(int n, int flag)
}
/* ----------------------------------------------------------------------
- free/malloc the size of the recv buffer as needed with BUFFACTOR
+ free/malloc the size of the recv buffer as needed with BUFFACTOR
------------------------------------------------------------------------- */
void Irregular::grow_recv(int n)
diff --git a/src/irregular.h b/src/irregular.h
index 1b1477872b999fade4dca71b79f2eab5108ee606..c3ebcea6c62b0213fdb3fb76ed5693c295f5a26a 100644
--- a/src/irregular.h
+++ b/src/irregular.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -36,7 +36,7 @@ class Irregular : protected Pointers {
double *xsplit,*ysplit,*zsplit; // ptrs to comm
int *procgrid; // ptr to comm
int ***grid2proc; // ptr to comm
- double *boxlo; // ptr to domain
+ double *boxlo; // ptr to domain
double *prd; // ptr to domain
int maxsend,maxrecv; // size of buffers in # of doubles
diff --git a/src/kspace.cpp b/src/kspace.cpp
index f6ec055520d7a7e6ea2c8c21b97f6139093661af..b0b345bdfcdc4edec720e02c73b10ab89f71fadd 100644
--- a/src/kspace.cpp
+++ b/src/kspace.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -42,8 +42,8 @@ KSpace::KSpace(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
suffix_flag = Suffix::NONE;
accuracy_absolute = -1.0;
- two_charge_force = force->qqr2e *
- (force->qelectron * force->qelectron) /
+ two_charge_force = force->qqr2e *
+ (force->qelectron * force->qelectron) /
(force->angstrom * force->angstrom);
maxeatom = maxvatom = 0;
@@ -64,8 +64,8 @@ KSpace::~KSpace()
void KSpace::compute_dummy(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
- else evflag = evflag_atom = eflag_global = vflag_global =
- eflag_atom = vflag_atom = 0;
+ else evflag = evflag_atom = eflag_global = vflag_global =
+ eflag_atom = vflag_atom = 0;
}
/* ----------------------------------------------------------------------
@@ -86,7 +86,7 @@ void KSpace::ev_setup(int eflag, int vflag)
vflag_either = vflag;
vflag_global = vflag % 4;
vflag_atom = vflag / 4;
-
+
if (eflag_atom || vflag_atom) evflag_atom = 1;
else evflag_atom = 0;
@@ -125,7 +125,7 @@ void KSpace::ev_setup(int eflag, int vflag)
}
/* ----------------------------------------------------------------------
- modify parameters of the KSpace style
+ modify parameters of the KSpace style
------------------------------------------------------------------------- */
void KSpace::modify_params(int narg, char **arg)
@@ -159,10 +159,10 @@ void KSpace::modify_params(int narg, char **arg)
slab_volfactor = atof(arg[iarg+1]);
iarg += 2;
if (slab_volfactor <= 1.0)
- error->all(FLERR,"Bad kspace_modify slab parameter");
- if (slab_volfactor < 2.0 && comm->me == 0)
- error->warning(FLERR,"Kspace_modify slab param < 2.0 may "
- "cause unphysical behavior");
+ error->all(FLERR,"Bad kspace_modify slab parameter");
+ if (slab_volfactor < 2.0 && comm->me == 0)
+ error->warning(FLERR,"Kspace_modify slab param < 2.0 may "
+ "cause unphysical behavior");
slabflag = 1;
} else if (strcmp(arg[iarg],"compute") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal kspace_modify command");
diff --git a/src/kspace.h b/src/kspace.h
index 851cad7dd30e1a7eb7bbf0ca527b0e0ec0c6dc1a..c5ea971d4d1a1f753be18656c6251907b1d680dd 100644
--- a/src/kspace.h
+++ b/src/kspace.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -56,7 +56,7 @@ class KSpace : protected Pointers {
int suffix_flag; // suffix compatibility flag
double scale;
double slab_volfactor;
-
+
double accuracy; // accuracy of KSpace solver (force units)
double accuracy_absolute; // user-specifed accuracy in force units
double accuracy_relative; // user-specified dimensionless accuracy
diff --git a/src/lammps.cpp b/src/lammps.cpp
index 3b188392c3ed5b489e920f036a0145e475c707a6..1202939a981a488e7779f57a8205c1de897bd1a1 100644
--- a/src/lammps.cpp
+++ b/src/lammps.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -78,87 +78,87 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
int iarg = 1;
while (iarg < narg) {
- if (strcmp(arg[iarg],"-partition") == 0 ||
- strcmp(arg[iarg],"-p") == 0) {
+ if (strcmp(arg[iarg],"-partition") == 0 ||
+ strcmp(arg[iarg],"-p") == 0) {
universe->existflag = 1;
- if (iarg+2 > narg)
- error->universe_all(FLERR,"Invalid command-line argument");
+ if (iarg+2 > narg)
+ error->universe_all(FLERR,"Invalid command-line argument");
iarg++;
while (iarg < narg && arg[iarg][0] != '-') {
- universe->add_world(arg[iarg]);
- iarg++;
+ universe->add_world(arg[iarg]);
+ iarg++;
}
- } else if (strcmp(arg[iarg],"-in") == 0 ||
- strcmp(arg[iarg],"-i") == 0) {
- if (iarg+2 > narg)
- error->universe_all(FLERR,"Invalid command-line argument");
+ } else if (strcmp(arg[iarg],"-in") == 0 ||
+ strcmp(arg[iarg],"-i") == 0) {
+ if (iarg+2 > narg)
+ error->universe_all(FLERR,"Invalid command-line argument");
inflag = iarg + 1;
iarg += 2;
- } else if (strcmp(arg[iarg],"-screen") == 0 ||
- strcmp(arg[iarg],"-sc") == 0) {
- if (iarg+2 > narg)
- error->universe_all(FLERR,"Invalid command-line argument");
+ } else if (strcmp(arg[iarg],"-screen") == 0 ||
+ strcmp(arg[iarg],"-sc") == 0) {
+ if (iarg+2 > narg)
+ error->universe_all(FLERR,"Invalid command-line argument");
screenflag = iarg + 1;
iarg += 2;
- } else if (strcmp(arg[iarg],"-log") == 0 ||
- strcmp(arg[iarg],"-l") == 0) {
- if (iarg+2 > narg)
- error->universe_all(FLERR,"Invalid command-line argument");
+ } else if (strcmp(arg[iarg],"-log") == 0 ||
+ strcmp(arg[iarg],"-l") == 0) {
+ if (iarg+2 > narg)
+ error->universe_all(FLERR,"Invalid command-line argument");
logflag = iarg + 1;
iarg += 2;
- } else if (strcmp(arg[iarg],"-var") == 0 ||
- strcmp(arg[iarg],"-v") == 0) {
- if (iarg+3 > narg)
- error->universe_all(FLERR,"Invalid command-line argument");
+ } else if (strcmp(arg[iarg],"-var") == 0 ||
+ strcmp(arg[iarg],"-v") == 0) {
+ if (iarg+3 > narg)
+ error->universe_all(FLERR,"Invalid command-line argument");
iarg += 3;
while (iarg < narg && arg[iarg][0] != '-') iarg++;
- } else if (strcmp(arg[iarg],"-echo") == 0 ||
- strcmp(arg[iarg],"-e") == 0) {
- if (iarg+2 > narg)
- error->universe_all(FLERR,"Invalid command-line argument");
+ } else if (strcmp(arg[iarg],"-echo") == 0 ||
+ strcmp(arg[iarg],"-e") == 0) {
+ if (iarg+2 > narg)
+ error->universe_all(FLERR,"Invalid command-line argument");
iarg += 2;
- } else if (strcmp(arg[iarg],"-pscreen") == 0 ||
- strcmp(arg[iarg],"-ps") == 0) {
- if (iarg+2 > narg)
+ } else if (strcmp(arg[iarg],"-pscreen") == 0 ||
+ strcmp(arg[iarg],"-ps") == 0) {
+ if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
partscreenflag = iarg + 1;
iarg += 2;
- } else if (strcmp(arg[iarg],"-plog") == 0 ||
- strcmp(arg[iarg],"-pl") == 0) {
- if (iarg+2 > narg)
+ } else if (strcmp(arg[iarg],"-plog") == 0 ||
+ strcmp(arg[iarg],"-pl") == 0) {
+ if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
partlogflag = iarg + 1;
iarg += 2;
- } else if (strcmp(arg[iarg],"-cuda") == 0 ||
- strcmp(arg[iarg],"-c") == 0) {
- if (iarg+2 > narg)
- error->universe_all(FLERR,"Invalid command-line argument");
+ } else if (strcmp(arg[iarg],"-cuda") == 0 ||
+ strcmp(arg[iarg],"-c") == 0) {
+ if (iarg+2 > narg)
+ error->universe_all(FLERR,"Invalid command-line argument");
if (strcmp(arg[iarg+1],"on") == 0) cudaflag = 1;
else if (strcmp(arg[iarg+1],"off") == 0) cudaflag = 0;
else error->universe_all(FLERR,"Invalid command-line argument");
iarg += 2;
- } else if (strcmp(arg[iarg],"-suffix") == 0 ||
- strcmp(arg[iarg],"-sf") == 0) {
- if (iarg+2 > narg)
- error->universe_all(FLERR,"Invalid command-line argument");
+ } else if (strcmp(arg[iarg],"-suffix") == 0 ||
+ strcmp(arg[iarg],"-sf") == 0) {
+ if (iarg+2 > narg)
+ error->universe_all(FLERR,"Invalid command-line argument");
delete [] suffix;
int n = strlen(arg[iarg+1]) + 1;
suffix = new char[n];
strcpy(suffix,arg[iarg+1]);
suffix_enable = 1;
iarg += 2;
- } else if (strcmp(arg[iarg],"-reorder") == 0 ||
- strcmp(arg[iarg],"-r") == 0) {
- if (iarg+3 > narg)
- error->universe_all(FLERR,"Invalid command-line argument");
+ } else if (strcmp(arg[iarg],"-reorder") == 0 ||
+ strcmp(arg[iarg],"-r") == 0) {
+ if (iarg+3 > narg)
+ error->universe_all(FLERR,"Invalid command-line argument");
if (universe->existflag)
- error->universe_all(FLERR,"Cannot use -reorder after -partition");
+ error->universe_all(FLERR,"Cannot use -reorder after -partition");
universe->reorder(arg[iarg+1],arg[iarg+2]);
iarg += 3;
- } else if (strcmp(arg[iarg],"-help") == 0 ||
- strcmp(arg[iarg],"-h") == 0) {
- if (iarg+1 > narg)
- error->universe_all(FLERR,"Invalid command-line argument");
+ } else if (strcmp(arg[iarg],"-help") == 0 ||
+ strcmp(arg[iarg],"-h") == 0) {
+ if (iarg+1 > narg)
+ error->universe_all(FLERR,"Invalid command-line argument");
helpflag = 1;
iarg += 1;
} else error->universe_all(FLERR,"Invalid command-line argument");
@@ -197,19 +197,19 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
universe->uscreen = NULL;
else {
universe->uscreen = fopen(arg[screenflag],"w");
- if (universe->uscreen == NULL)
- error->universe_one(FLERR,"Cannot open universe screen file");
+ if (universe->uscreen == NULL)
+ error->universe_one(FLERR,"Cannot open universe screen file");
}
if (logflag == 0) {
universe->ulogfile = fopen("log.lammps","w");
- if (universe->ulogfile == NULL)
- error->universe_one(FLERR,"Cannot open log.lammps");
+ if (universe->ulogfile == NULL)
+ error->universe_one(FLERR,"Cannot open log.lammps");
} else if (strcmp(arg[logflag],"none") == 0)
universe->ulogfile = NULL;
else {
universe->ulogfile = fopen(arg[logflag],"w");
- if (universe->ulogfile == NULL)
- error->universe_one(FLERR,"Cannot open universe log file");
+ if (universe->ulogfile == NULL)
+ error->universe_one(FLERR,"Cannot open universe log file");
}
}
@@ -234,9 +234,9 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
if (inflag == 0) infile = stdin;
else infile = fopen(arg[inflag],"r");
if (infile == NULL) {
- char str[128];
- sprintf(str,"Cannot open input script %s",arg[inflag]);
- error->one(FLERR,str);
+ char str[128];
+ sprintf(str,"Cannot open input script %s",arg[inflag]);
+ error->one(FLERR,str);
}
}
@@ -271,14 +271,14 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
if (screen == NULL) error->one(FLERR,"Cannot open screen file");
}
else if (strcmp(arg[partscreenflag],"none") == 0)
- screen = NULL;
+ screen = NULL;
else {
- char str[128];
- sprintf(str,"%s.%d",arg[partscreenflag],universe->iworld);
- screen = fopen(str,"w");
- if (screen == NULL) error->one(FLERR,"Cannot open screen file");
+ char str[128];
+ sprintf(str,"%s.%d",arg[partscreenflag],universe->iworld);
+ screen = fopen(str,"w");
+ if (screen == NULL) error->one(FLERR,"Cannot open screen file");
} else screen = NULL;
-
+
if (me == 0)
if (partlogflag == 0)
if (logflag == 0) {
@@ -295,46 +295,46 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
if (logfile == NULL) error->one(FLERR,"Cannot open logfile");
}
else if (strcmp(arg[partlogflag],"none") == 0)
- logfile = NULL;
+ logfile = NULL;
else {
- char str[128];
- sprintf(str,"%s.%d",arg[partlogflag],universe->iworld);
- logfile = fopen(str,"w");
- if (logfile == NULL) error->one(FLERR,"Cannot open logfile");
+ char str[128];
+ sprintf(str,"%s.%d",arg[partlogflag],universe->iworld);
+ logfile = fopen(str,"w");
+ if (logfile == NULL) error->one(FLERR,"Cannot open logfile");
} else logfile = NULL;
-
+
if (me == 0) {
infile = fopen(arg[inflag],"r");
if (infile == NULL) {
- char str[128];
- sprintf(str,"Cannot open input script %s",arg[inflag]);
- error->one(FLERR,str);
+ char str[128];
+ sprintf(str,"Cannot open input script %s",arg[inflag]);
+ error->one(FLERR,str);
}
} else infile = NULL;
-
+
// screen and logfile messages for universe and world
-
+
if (universe->me == 0) {
if (universe->uscreen) {
- fprintf(universe->uscreen,"LAMMPS (%s)\n",universe->version);
- fprintf(universe->uscreen,"Running on %d partitions of processors\n",
- universe->nworlds);
+ fprintf(universe->uscreen,"LAMMPS (%s)\n",universe->version);
+ fprintf(universe->uscreen,"Running on %d partitions of processors\n",
+ universe->nworlds);
}
if (universe->ulogfile) {
- fprintf(universe->ulogfile,"LAMMPS (%s)\n",universe->version);
- fprintf(universe->ulogfile,"Running on %d partitions of processors\n",
- universe->nworlds);
+ fprintf(universe->ulogfile,"LAMMPS (%s)\n",universe->version);
+ fprintf(universe->ulogfile,"Running on %d partitions of processors\n",
+ universe->nworlds);
}
}
-
+
if (me == 0) {
if (screen) {
- fprintf(screen,"LAMMPS (%s)\n",universe->version);
- fprintf(screen,"Processor partition = %d\n",universe->iworld);
+ fprintf(screen,"LAMMPS (%s)\n",universe->version);
+ fprintf(screen,"Processor partition = %d\n",universe->iworld);
}
if (logfile) {
- fprintf(logfile,"LAMMPS (%s)\n",universe->version);
- fprintf(logfile,"Processor partition = %d\n",universe->iworld);
+ fprintf(logfile,"LAMMPS (%s)\n",universe->version);
+ fprintf(logfile,"Processor partition = %d\n",universe->iworld);
}
}
}
@@ -352,11 +352,11 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
MPI_Type_size(MPI_LMP_TAGINT,&mpisize);
if (mpisize != sizeof(tagint))
error->all(FLERR,
- "MPI_LMP_TAGINT and tagint in lmptype.h are not compatible");
+ "MPI_LMP_TAGINT and tagint in lmptype.h are not compatible");
MPI_Type_size(MPI_LMP_BIGINT,&mpisize);
if (mpisize != sizeof(bigint))
error->all(FLERR,
- "MPI_LMP_BIGINT and bigint in lmptype.h are not compatible");
+ "MPI_LMP_BIGINT and bigint in lmptype.h are not compatible");
#ifdef LAMMPS_SMALLBIG
if (sizeof(smallint) != 4 || sizeof(tagint) != 4 || sizeof(bigint) != 8)
@@ -371,7 +371,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
error->all(FLERR,"Small, tag, big integers are not sized correctly");
#endif
- if (sizeof(tagint) == 8)
+ if (sizeof(tagint) == 8)
error->all(FLERR,"64-bit atom IDs are not yet supported");
// create CUDA class if USER-CUDA installed, unless explicitly switched off
@@ -390,7 +390,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
cuda = NULL;
}
}
-
+
int me;
MPI_Comm_rank(world,&me);
if (cuda && me == 0) error->message(FLERR,"USER-CUDA mode is enabled");
@@ -496,7 +496,7 @@ void LAMMPS::post_create()
void LAMMPS::init()
{
if (cuda) cuda->accelerator(0,NULL);
-
+
update->init();
force->init(); // pair must come after update due to minimizer
domain->init();
diff --git a/src/lammps.h b/src/lammps.h
index cfc00edb4bcd28f4a31049ae46b7c1660b79b5e4..9809dc508e5b7f64019fd79915878e94e02a32cc 100644
--- a/src/lammps.h
+++ b/src/lammps.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/lattice.cpp b/src/lattice.cpp
index 9157dfa273485ad669803ba14bd78c351236edec..5b8a5aed3485d6986fe5a921d5254a7bca466cfa 100644
--- a/src/lattice.cpp
+++ b/src/lattice.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -61,7 +61,7 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
int dimension = domain->dimension;
if (dimension == 2) {
if (style == SC || style == BCC || style == FCC || style == HCP ||
- style == DIAMOND)
+ style == DIAMOND)
error->all(FLERR,"Lattice style incompatible with simulation dimension");
}
if (dimension == 3) {
@@ -143,9 +143,9 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
origin[1] = atof(arg[iarg+2]);
origin[2] = atof(arg[iarg+3]);
if (origin[0] < 0.0 || origin[0] >= 1.0 ||
- origin[1] < 0.0 || origin[1] >= 1.0 ||
- origin[2] < 0.0 || origin[2] >= 1.0)
- error->all(FLERR,"Illegal lattice command");
+ origin[1] < 0.0 || origin[1] >= 1.0 ||
+ origin[2] < 0.0 || origin[2] >= 1.0)
+ error->all(FLERR,"Illegal lattice command");
iarg += 4;
} else if (strcmp(arg[iarg],"orient") == 0) {
@@ -174,27 +174,27 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
} else if (strcmp(arg[iarg],"a1") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal lattice command");
- if (style != CUSTOM)
- error->all(FLERR,
- "Invalid option in lattice command for non-custom style");
+ if (style != CUSTOM)
+ error->all(FLERR,
+ "Invalid option in lattice command for non-custom style");
a1[0] = atof(arg[iarg+1]);
a1[1] = atof(arg[iarg+2]);
a1[2] = atof(arg[iarg+3]);
iarg += 4;
} else if (strcmp(arg[iarg],"a2") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal lattice command");
- if (style != CUSTOM)
- error->all(FLERR,
- "Invalid option in lattice command for non-custom style");
+ if (style != CUSTOM)
+ error->all(FLERR,
+ "Invalid option in lattice command for non-custom style");
a2[0] = atof(arg[iarg+1]);
a2[1] = atof(arg[iarg+2]);
a2[2] = atof(arg[iarg+3]);
iarg += 4;
} else if (strcmp(arg[iarg],"a3") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal lattice command");
- if (style != CUSTOM)
- error->all(FLERR,
- "Invalid option in lattice command for non-custom style");
+ if (style != CUSTOM)
+ error->all(FLERR,
+ "Invalid option in lattice command for non-custom style");
a3[0] = atof(arg[iarg+1]);
a3[1] = atof(arg[iarg+2]);
a3[2] = atof(arg[iarg+3]);
@@ -202,14 +202,14 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
} else if (strcmp(arg[iarg],"basis") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal lattice command");
- if (style != CUSTOM)
- error->all(FLERR,
- "Invalid option in lattice command for non-custom style");
+ if (style != CUSTOM)
+ error->all(FLERR,
+ "Invalid option in lattice command for non-custom style");
double x = atof(arg[iarg+1]);
double y = atof(arg[iarg+2]);
double z = atof(arg[iarg+3]);
if (x < 0.0 || x >= 1.0 || y < 0.0 || y >= 1.0 || z < 0.0 || z >= 1.0)
- error->all(FLERR,"Illegal lattice command");
+ error->all(FLERR,"Illegal lattice command");
add_basis(x,y,z);
iarg += 4;
} else error->all(FLERR,"Illegal lattice command");
@@ -228,14 +228,14 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
if (dimension == 2) {
if (origin[2] != 0.0)
error->all(FLERR,
- "Lattice settings are not compatible with 2d simulation");
- if (orientx[2] != 0 || orienty[2] != 0 ||
- orientz[0] != 0 || orientz[1] != 0)
+ "Lattice settings are not compatible with 2d simulation");
+ if (orientx[2] != 0 || orienty[2] != 0 ||
+ orientz[0] != 0 || orientz[1] != 0)
error->all(FLERR,
- "Lattice settings are not compatible with 2d simulation");
+ "Lattice settings are not compatible with 2d simulation");
if (a1[2] != 0.0 || a2[2] != 0.0 || a3[0] != 0.0 || a3[1] != 0.0)
error->all(FLERR,
- "Lattice settings are not compatible with 2d simulation");
+ "Lattice settings are not compatible with 2d simulation");
}
if (spaceflag) {
@@ -293,10 +293,10 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
if (comm->me == 0) {
if (screen)
fprintf(screen,"Lattice spacing in x,y,z = %g %g %g\n",
- xlattice,ylattice,zlattice);
+ xlattice,ylattice,zlattice);
if (logfile)
fprintf(logfile,"Lattice spacing in x,y,z = %g %g %g\n",
- xlattice,ylattice,zlattice);
+ xlattice,ylattice,zlattice);
}
}
@@ -308,23 +308,23 @@ Lattice::~Lattice()
}
/* ----------------------------------------------------------------------
- check if 3 orientation vectors are mutually orthogonal
+ check if 3 orientation vectors are mutually orthogonal
------------------------------------------------------------------------- */
int Lattice::orthogonal()
{
- if (orientx[0]*orienty[0] + orientx[1]*orienty[1] +
+ if (orientx[0]*orienty[0] + orientx[1]*orienty[1] +
orientx[2]*orienty[2]) return 0;
- if (orienty[0]*orientz[0] + orienty[1]*orientz[1] +
+ if (orienty[0]*orientz[0] + orienty[1]*orientz[1] +
orienty[2]*orientz[2]) return 0;
- if (orientx[0]*orientz[0] + orientx[1]*orientz[1] +
+ if (orientx[0]*orientz[0] + orientx[1]*orientz[1] +
orientx[2]*orientz[2]) return 0;
return 1;
}
/* ----------------------------------------------------------------------
check righthandedness of orientation vectors
- x cross y must be in same direction as z
+ x cross y must be in same direction as z
------------------------------------------------------------------------- */
int Lattice::right_handed()
@@ -381,29 +381,29 @@ void Lattice::setup_transform()
primitive[0][1]*primitive[1][0]*primitive[2][2] -
primitive[0][2]*primitive[1][1]*primitive[2][0];
- if (determinant == 0.0)
+ if (determinant == 0.0)
error->all(FLERR,"Degenerate lattice primitive vectors");
- priminv[0][0] = (primitive[1][1]*primitive[2][2] -
- primitive[1][2]*primitive[2][1]) / determinant;
- priminv[1][0] = (primitive[1][2]*primitive[2][0] -
- primitive[1][0]*primitive[2][2]) / determinant;
- priminv[2][0] = (primitive[1][0]*primitive[2][1] -
- primitive[1][1]*primitive[2][0]) / determinant;
-
- priminv[0][1] = (primitive[0][2]*primitive[2][1] -
- primitive[0][1]*primitive[2][2]) / determinant;
- priminv[1][1] = (primitive[0][0]*primitive[2][2] -
- primitive[0][2]*primitive[2][0]) / determinant;
- priminv[2][1] = (primitive[0][1]*primitive[2][0] -
- primitive[0][0]*primitive[2][1]) / determinant;
-
- priminv[0][2] = (primitive[0][1]*primitive[1][2] -
- primitive[0][2]*primitive[1][1]) / determinant;
- priminv[1][2] = (primitive[0][2]*primitive[1][0] -
- primitive[0][0]*primitive[1][2]) / determinant;
- priminv[2][2] = (primitive[0][0]*primitive[1][1] -
- primitive[0][1]*primitive[1][0]) / determinant;
+ priminv[0][0] = (primitive[1][1]*primitive[2][2] -
+ primitive[1][2]*primitive[2][1]) / determinant;
+ priminv[1][0] = (primitive[1][2]*primitive[2][0] -
+ primitive[1][0]*primitive[2][2]) / determinant;
+ priminv[2][0] = (primitive[1][0]*primitive[2][1] -
+ primitive[1][1]*primitive[2][0]) / determinant;
+
+ priminv[0][1] = (primitive[0][2]*primitive[2][1] -
+ primitive[0][1]*primitive[2][2]) / determinant;
+ priminv[1][1] = (primitive[0][0]*primitive[2][2] -
+ primitive[0][2]*primitive[2][0]) / determinant;
+ priminv[2][1] = (primitive[0][1]*primitive[2][0] -
+ primitive[0][0]*primitive[2][1]) / determinant;
+
+ priminv[0][2] = (primitive[0][1]*primitive[1][2] -
+ primitive[0][2]*primitive[1][1]) / determinant;
+ priminv[1][2] = (primitive[0][2]*primitive[1][0] -
+ primitive[0][0]*primitive[1][2]) / determinant;
+ priminv[2][2] = (primitive[0][0]*primitive[1][1] -
+ primitive[0][1]*primitive[1][0]) / determinant;
// rotaterow = 3x3 matrix with normalized orient vectors as rows
@@ -420,11 +420,11 @@ void Lattice::setup_transform()
orienty[2]*orienty[2];
length = sqrt((double) lensq);
if (length == 0.0) error->all(FLERR,"Zero-length lattice orient vector");
-
+
rotaterow[1][0] = orienty[0] / length;
rotaterow[1][1] = orienty[1] / length;
rotaterow[1][2] = orienty[2] / length;
-
+
lensq = orientz[0]*orientz[0] + orientz[1]*orientz[1] +
orientz[2]*orientz[2];
length = sqrt((double) lensq);
@@ -549,12 +549,12 @@ void Lattice::cross(double *x, double *y, double *z)
/* ----------------------------------------------------------------------
convert x,y,z from lattice coords to box coords (flag = 0) or vice versa
- use new point to expand bounding box (min to max)
+ use new point to expand bounding box (min to max)
------------------------------------------------------------------------- */
void Lattice::bbox(int flag, double x, double y, double z,
- double &xmin, double &ymin, double &zmin,
- double &xmax, double &ymax, double &zmax)
+ double &xmin, double &ymin, double &zmin,
+ double &xmax, double &ymax, double &zmax)
{
if (flag == 0) lattice2box(x,y,z);
else box2lattice(x,y,z);
diff --git a/src/lattice.h b/src/lattice.h
index a293d835a0f80eba9a308a2f796ca780e87c5e7a..d1ba972fcd10d2dd16f56884328e3a1cdafdb839 100644
--- a/src/lattice.h
+++ b/src/lattice.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -32,7 +32,7 @@ class Lattice : protected Pointers {
void lattice2box(double &, double &, double &);
void box2lattice(double &, double &, double &);
void bbox(int, double, double, double,
- double &, double &, double &, double &, double &, double &);
+ double &, double &, double &, double &, double &, double &);
private:
double scale;
diff --git a/src/library.cpp b/src/library.cpp
index fd58515d29eaf84b0f78b359a4a9257e7306880c..6a861a60aa14aa6dd9718909baffe37b0e9d66a4 100644
--- a/src/library.cpp
+++ b/src/library.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -177,19 +177,19 @@ void *lammps_extract_compute(void *ptr, char *id, int style, int type)
if (type == 0) {
if (!compute->scalar_flag) return NULL;
if (compute->invoked_scalar != lmp->update->ntimestep)
- compute->compute_scalar();
+ compute->compute_scalar();
return (void *) &compute->scalar;
}
if (type == 1) {
if (!compute->vector_flag) return NULL;
if (compute->invoked_vector != lmp->update->ntimestep)
- compute->compute_vector();
+ compute->compute_vector();
return (void *) compute->vector;
}
if (type == 2) {
if (!compute->array_flag) return NULL;
if (compute->invoked_array != lmp->update->ntimestep)
- compute->compute_array();
+ compute->compute_array();
return (void *) compute->array;
}
}
@@ -198,12 +198,12 @@ void *lammps_extract_compute(void *ptr, char *id, int style, int type)
if (!compute->peratom_flag) return NULL;
if (type == 1) {
if (compute->invoked_peratom != lmp->update->ntimestep)
- compute->compute_peratom();
+ compute->compute_peratom();
return (void *) compute->vector_atom;
}
if (type == 2) {
if (compute->invoked_peratom != lmp->update->ntimestep)
- compute->compute_peratom();
+ compute->compute_peratom();
return (void *) compute->array_atom;
}
}
@@ -212,12 +212,12 @@ void *lammps_extract_compute(void *ptr, char *id, int style, int type)
if (!compute->local_flag) return NULL;
if (type == 1) {
if (compute->invoked_local != lmp->update->ntimestep)
- compute->compute_local();
+ compute->compute_local();
return (void *) compute->vector_local;
}
if (type == 2) {
if (compute->invoked_local != lmp->update->ntimestep)
- compute->compute_local();
+ compute->compute_local();
return (void *) compute->array_local;
}
}
@@ -234,7 +234,7 @@ void *lammps_extract_compute(void *ptr, char *id, int style, int type)
for global data, returns a pointer to a memory location
which is allocated by this function
which the caller can cast to a (double *) which points to the value
- for per-atom or local data, returns a pointer to the
+ for per-atom or local data, returns a pointer to the
fix's internal data structure for the entity
which the caller can cast to the proper data type
returns a NULL if id is not recognized or style/type not supported
@@ -249,7 +249,7 @@ void *lammps_extract_compute(void *ptr, char *id, int style, int type)
------------------------------------------------------------------------- */
void *lammps_extract_fix(void *ptr, char *id, int style, int type,
- int i, int j)
+ int i, int j)
{
LAMMPS *lmp = (LAMMPS *) ptr;
@@ -298,7 +298,7 @@ void *lammps_extract_fix(void *ptr, char *id, int style, int type,
for equal-style variable, returns a pointer to a memory location
which is allocated by this function
which the caller can cast to a (double *) which points to the value
- for atom-style variable, returns a pointer to the
+ for atom-style variable, returns a pointer to the
vector of per-atom values on each processor,
which the caller can cast to the proper data type
returns a NULL if name is not recognized or not equal-style or atom-style
diff --git a/src/library.h b/src/library.h
index 213a004c259389d015339adc02e3c27658a6b996..86882bda75f188f154209f09e9f23e4c00dae6c3 100644
--- a/src/library.h
+++ b/src/library.h
@@ -5,13 +5,13 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-/*
+/*
C or Fortran style library interface to LAMMPS
new LAMMPS-specific functions can be added
*/
diff --git a/src/lmptype.h b/src/lmptype.h
index 3e015a9aa866a42bd386c061c0813c8b7c902cfd..5eca877ec996acbfb83b6540ebe52b285e432bdb 100644
--- a/src/lmptype.h
+++ b/src/lmptype.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/lmpwindows.h b/src/lmpwindows.h
index 8cecf8a7e35fd18e9754fafed1cd35e20dc3272a..e4431547de58c81f787b652eaefc02dbdf83a3ff 100644
--- a/src/lmpwindows.h
+++ b/src/lmpwindows.h
@@ -17,7 +17,7 @@
#define pclose _pclose
#define __restrict__ __restrict
-// the following functions ared defined to get rid of
+// the following functions ared defined to get rid of
// 'ambiguous call to overloaded function' error in VSS for mismathched type arguments
#if defined(__MINGW32_VERSION)
diff --git a/src/main.cpp b/src/main.cpp
index 13b391e1219356a1cf828deb832a05eec2d970ea..471be9aa46e03ed574bde65d95daa0966945bc8f 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/math_const.h b/src/math_const.h
index 2d1cb3819f76f2c28bc9b7e367d422094c6e66ed..89437510e356d41c60cbe623cc0fa0d1ec27ad07 100644
--- a/src/math_const.h
+++ b/src/math_const.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/math_extra.cpp b/src/math_extra.cpp
index 32acc8ed082e1641b09e56c455ee1d22633b2236..1c9ff749e115e81ecdd32a937c6b3c2a7adaf8ff 100644
--- a/src/math_extra.cpp
+++ b/src/math_extra.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -79,7 +79,7 @@ int mldivide3(const double m[3][3], const double *v, double *ans)
}
if (aug[2][2] == 0.0) return 1;
-
+
// back substitution
ans[2] = aug[2][3]/aug[2][2];
@@ -102,7 +102,7 @@ int jacobi(double matrix[3][3], double *evalues, double evectors[3][3])
{
int i,j,k;
double tresh,theta,tau,t,sm,s,h,g,c,b[3],z[3];
-
+
for (i = 0; i < 3; i++) {
for (j = 0; j < 3; j++) evectors[i][j] = 0.0;
evectors[i][i] = 1.0;
@@ -111,48 +111,48 @@ int jacobi(double matrix[3][3], double *evalues, double evectors[3][3])
b[i] = evalues[i] = matrix[i][i];
z[i] = 0.0;
}
-
+
for (int iter = 1; iter <= MAXJACOBI; iter++) {
sm = 0.0;
for (i = 0; i < 2; i++)
for (j = i+1; j < 3; j++)
- sm += fabs(matrix[i][j]);
+ sm += fabs(matrix[i][j]);
if (sm == 0.0) return 0;
-
+
if (iter < 4) tresh = 0.2*sm/(3*3);
else tresh = 0.0;
-
+
for (i = 0; i < 2; i++) {
for (j = i+1; j < 3; j++) {
- g = 100.0*fabs(matrix[i][j]);
- if (iter > 4 && fabs(evalues[i])+g == fabs(evalues[i])
- && fabs(evalues[j])+g == fabs(evalues[j]))
- matrix[i][j] = 0.0;
- else if (fabs(matrix[i][j]) > tresh) {
- h = evalues[j]-evalues[i];
- if (fabs(h)+g == fabs(h)) t = (matrix[i][j])/h;
- else {
- theta = 0.5*h/(matrix[i][j]);
- t = 1.0/(fabs(theta)+sqrt(1.0+theta*theta));
- if (theta < 0.0) t = -t;
- }
- c = 1.0/sqrt(1.0+t*t);
- s = t*c;
- tau = s/(1.0+c);
- h = t*matrix[i][j];
- z[i] -= h;
- z[j] += h;
- evalues[i] -= h;
- evalues[j] += h;
- matrix[i][j] = 0.0;
- for (k = 0; k < i; k++) rotate(matrix,k,i,k,j,s,tau);
- for (k = i+1; k < j; k++) rotate(matrix,i,k,k,j,s,tau);
- for (k = j+1; k < 3; k++) rotate(matrix,i,k,j,k,s,tau);
- for (k = 0; k < 3; k++) rotate(evectors,k,i,k,j,s,tau);
- }
+ g = 100.0*fabs(matrix[i][j]);
+ if (iter > 4 && fabs(evalues[i])+g == fabs(evalues[i])
+ && fabs(evalues[j])+g == fabs(evalues[j]))
+ matrix[i][j] = 0.0;
+ else if (fabs(matrix[i][j]) > tresh) {
+ h = evalues[j]-evalues[i];
+ if (fabs(h)+g == fabs(h)) t = (matrix[i][j])/h;
+ else {
+ theta = 0.5*h/(matrix[i][j]);
+ t = 1.0/(fabs(theta)+sqrt(1.0+theta*theta));
+ if (theta < 0.0) t = -t;
+ }
+ c = 1.0/sqrt(1.0+t*t);
+ s = t*c;
+ tau = s/(1.0+c);
+ h = t*matrix[i][j];
+ z[i] -= h;
+ z[j] += h;
+ evalues[i] -= h;
+ evalues[j] += h;
+ matrix[i][j] = 0.0;
+ for (k = 0; k < i; k++) rotate(matrix,k,i,k,j,s,tau);
+ for (k = i+1; k < j; k++) rotate(matrix,i,k,k,j,s,tau);
+ for (k = j+1; k < 3; k++) rotate(matrix,i,k,j,k,s,tau);
+ for (k = 0; k < 3; k++) rotate(evectors,k,i,k,j,s,tau);
+ }
}
}
-
+
for (i = 0; i < 3; i++) {
evalues[i] = b[i] += z[i];
z[i] = 0.0;
@@ -166,7 +166,7 @@ int jacobi(double matrix[3][3], double *evalues, double evectors[3][3])
------------------------------------------------------------------------- */
void rotate(double matrix[3][3], int i, int j, int k, int l,
- double s, double tau)
+ double s, double tau)
{
double g = matrix[i][j];
double h = matrix[k][l];
@@ -238,7 +238,7 @@ void richardson(double *q, double *m, double *w, double *moments, double dtq)
------------------------------------------------------------------------- */
void angmom_to_omega(double *m, double *ex, double *ey, double *ez,
- double *idiag, double *w)
+ double *idiag, double *w)
{
double wbody[3];
@@ -288,7 +288,7 @@ void mq_to_omega(double *m, double *q, double *moments, double *w)
------------------------------------------------------------------------- */
void omega_to_angmom(double *w, double *ex, double *ey, double *ez,
- double *idiag, double *m)
+ double *idiag, double *m)
{
double mbody[3];
@@ -309,15 +309,15 @@ void omega_to_angmom(double *w, double *ex, double *ey, double *ez,
void exyz_to_q(double *ex, double *ey, double *ez, double *q)
{
// squares of quaternion components
-
+
double q0sq = 0.25 * (ex[0] + ey[1] + ez[2] + 1.0);
double q1sq = q0sq - 0.5 * (ey[1] + ez[2]);
double q2sq = q0sq - 0.5 * (ex[0] + ez[2]);
double q3sq = q0sq - 0.5 * (ex[0] + ey[1]);
-
+
// some component must be greater than 1/4 since they sum to 1
// compute other components from it
-
+
if (q0sq >= 0.25) {
q[0] = sqrt(q0sq);
q[1] = (ey[2] - ez[1]) / (4.0*q[0]);
@@ -354,11 +354,11 @@ void q_to_exyz(double *q, double *ex, double *ey, double *ez)
ex[0] = q[0]*q[0] + q[1]*q[1] - q[2]*q[2] - q[3]*q[3];
ex[1] = 2.0 * (q[1]*q[2] + q[0]*q[3]);
ex[2] = 2.0 * (q[1]*q[3] - q[0]*q[2]);
-
+
ey[0] = 2.0 * (q[1]*q[2] - q[0]*q[3]);
ey[1] = q[0]*q[0] - q[1]*q[1] + q[2]*q[2] - q[3]*q[3];
ey[2] = 2.0 * (q[2]*q[3] + q[0]*q[1]);
-
+
ez[0] = 2.0 * (q[1]*q[3] + q[0]*q[2]);
ez[1] = 2.0 * (q[2]*q[3] - q[0]*q[1]);
ez[2] = q[0]*q[0] - q[1]*q[1] - q[2]*q[2] + q[3]*q[3];
@@ -389,7 +389,7 @@ void quat_to_mat(const double *quat, double mat[3][3])
mat[1][0] = twoij+twokw;
mat[1][1] = w2-i2+j2-k2;
mat[1][2] = twojk-twoiw;
-
+
mat[2][0] = twoik-twojw;
mat[2][1] = twojk+twoiw;
mat[2][2] = w2-i2-j2+k2;
@@ -420,7 +420,7 @@ void quat_to_mat_trans(const double *quat, double mat[3][3])
mat[0][1] = twoij+twokw;
mat[1][1] = w2-i2+j2-k2;
mat[2][1] = twojk-twoiw;
-
+
mat[0][2] = twoik-twojw;
mat[1][2] = twojk+twoiw;
mat[2][2] = w2-i2-j2+k2;
@@ -434,7 +434,7 @@ void quat_to_mat_trans(const double *quat, double mat[3][3])
------------------------------------------------------------------------- */
void inertia_ellipsoid(double *radii, double *quat, double mass,
- double *inertia)
+ double *inertia)
{
double p[3][3],ptrans[3][3],itemp[3][3],tensor[3][3];
double idiag[3];
@@ -500,7 +500,7 @@ void inertia_line(double length, double theta, double mass, double *inertia)
------------------------------------------------------------------------- */
void inertia_triangle(double *v0, double *v1, double *v2,
- double mass, double *inertia)
+ double mass, double *inertia)
{
double s[3][3] = {{2.0, 1.0, 1.0}, {1.0, 2.0, 1.0}, {1.0, 1.0, 2.0}};
double v[3][3],sv[3][3],vtsv[3][3];
@@ -541,7 +541,7 @@ void inertia_triangle(double *v0, double *v1, double *v2,
------------------------------------------------------------------------- */
void inertia_triangle(double *idiag, double *quat, double mass,
- double *inertia)
+ double *inertia)
{
double p[3][3],ptrans[3][3],itemp[3][3],tensor[3][3];
diff --git a/src/math_extra.h b/src/math_extra.h
index c161b40f152716b6fc6181eb64fff8fe61943683..515e55f5f8b297fde581ea3b3be21d223ea77231 100755
--- a/src/math_extra.h
+++ b/src/math_extra.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -48,31 +48,31 @@ namespace MathExtra {
double ans[3][3]);
inline void times3(const double m[3][3], const double m2[3][3],
double ans[3][3]);
- inline void transpose_times3(const double mat1[3][3],
+ inline void transpose_times3(const double mat1[3][3],
+ const double mat2[3][3],
+ double ans[3][3]);
+ inline void times3_transpose(const double mat1[3][3],
const double mat2[3][3],
double ans[3][3]);
- inline void times3_transpose(const double mat1[3][3],
- const double mat2[3][3],
- double ans[3][3]);
inline void invert3(const double mat[3][3], double ans[3][3]);
inline void matvec(const double mat[3][3], const double*vec, double *ans);
inline void matvec(const double *ex, const double *ey, const double *ez,
- const double *vec, double *ans);
+ const double *vec, double *ans);
inline void transpose_matvec(const double mat[3][3], const double*vec,
- double *ans);
- inline void transpose_matvec(const double *ex, const double *ey,
- const double *ez, const double *v,
- double *ans);
+ double *ans);
+ inline void transpose_matvec(const double *ex, const double *ey,
+ const double *ez, const double *v,
+ double *ans);
inline void transpose_diag3(const double mat[3][3], const double*vec,
- double ans[3][3]);
+ double ans[3][3]);
inline void vecmat(const double *v, const double m[3][3], double *ans);
- inline void scalar_times3(const double f, double m[3][3]);
+ inline void scalar_times3(const double f, double m[3][3]);
void write3(const double mat[3][3]);
int mldivide3(const double mat[3][3], const double *vec, double *ans);
int jacobi(double matrix[3][3], double *evalues, double evectors[3][3]);
void rotate(double matrix[3][3], int i, int j, int k, int l,
- double s, double tau);
+ double s, double tau);
void richardson(double *q, double *m, double *w, double *moments, double dtq);
// shape matrix operations
@@ -93,9 +93,9 @@ namespace MathExtra {
double *quat);
void angmom_to_omega(double *m, double *ex, double *ey, double *ez,
- double *idiag, double *w);
+ double *idiag, double *w);
void omega_to_angmom(double *w, double *ex, double *ey, double *ez,
- double *idiag, double *m);
+ double *idiag, double *m);
void mq_to_omega(double *m, double *q, double *moments, double *w);
void exyz_to_q(double *ex, double *ey, double *ez, double *q);
void q_to_exyz(double *q, double *ex, double *ey, double *ez);
@@ -103,7 +103,7 @@ namespace MathExtra {
void quat_to_mat_trans(const double *quat, double mat[3][3]);
// rotation operations
-
+
inline void rotation_generator_x(const double m[3][3], double ans[3][3]);
inline void rotation_generator_y(const double m[3][3], double ans[3][3]);
inline void rotation_generator_z(const double m[3][3], double ans[3][3]);
@@ -111,13 +111,13 @@ namespace MathExtra {
// moment of inertia operations
void inertia_ellipsoid(double *shape, double *quat, double mass,
- double *inertia);
+ double *inertia);
void inertia_line(double length, double theta, double mass,
- double *inertia);
- void inertia_triangle(double *v0, double *v1, double *v2,
- double mass, double *inertia);
- void inertia_triangle(double *idiag, double *quat, double mass,
- double *inertia);
+ double *inertia);
+ void inertia_triangle(double *v0, double *v1, double *v2,
+ double mass, double *inertia);
+ void inertia_triangle(double *idiag, double *quat, double mass,
+ double *inertia);
}
/* ----------------------------------------------------------------------
@@ -244,8 +244,8 @@ void MathExtra::cross3(const double *v1, const double *v2, double *ans)
double MathExtra::det3(const double m[3][3])
{
- double ans = m[0][0]*m[1][1]*m[2][2] - m[0][0]*m[1][2]*m[2][1] -
- m[1][0]*m[0][1]*m[2][2] + m[1][0]*m[0][2]*m[2][1] +
+ double ans = m[0][0]*m[1][1]*m[2][2] - m[0][0]*m[1][2]*m[2][1] -
+ m[1][0]*m[0][1]*m[2][2] + m[1][0]*m[0][2]*m[2][1] +
m[2][0]*m[0][1]*m[1][2] - m[2][0]*m[0][2]*m[1][1];
return ans;
}
@@ -255,7 +255,7 @@ double MathExtra::det3(const double m[3][3])
------------------------------------------------------------------------- */
void MathExtra::diag_times3(const double *d, const double m[3][3],
- double ans[3][3])
+ double ans[3][3])
{
ans[0][0] = d[0]*m[0][0];
ans[0][1] = d[0]*m[0][1];
@@ -273,7 +273,7 @@ void MathExtra::diag_times3(const double *d, const double m[3][3],
------------------------------------------------------------------------- */
void MathExtra::plus3(const double m[3][3], const double m2[3][3],
- double ans[3][3])
+ double ans[3][3])
{
ans[0][0] = m[0][0]+m2[0][0];
ans[0][1] = m[0][1]+m2[0][1];
@@ -366,7 +366,7 @@ void MathExtra::invert3(const double m[3][3], double ans[3][3])
matrix times vector
------------------------------------------------------------------------- */
-void MathExtra::matvec(const double m[3][3], const double *v, double *ans)
+void MathExtra::matvec(const double m[3][3], const double *v, double *ans)
{
ans[0] = m[0][0]*v[0] + m[0][1]*v[1] + m[0][2]*v[2];
ans[1] = m[1][0]*v[0] + m[1][1]*v[1] + m[1][2]*v[2];
@@ -378,7 +378,7 @@ void MathExtra::matvec(const double m[3][3], const double *v, double *ans)
------------------------------------------------------------------------- */
void MathExtra::matvec(const double *ex, const double *ey, const double *ez,
- const double *v, double *ans)
+ const double *v, double *ans)
{
ans[0] = ex[0]*v[0] + ey[0]*v[1] + ez[0]*v[2];
ans[1] = ex[1]*v[0] + ey[1]*v[1] + ez[1]*v[2];
@@ -390,7 +390,7 @@ void MathExtra::matvec(const double *ex, const double *ey, const double *ez,
------------------------------------------------------------------------- */
void MathExtra::transpose_matvec(const double m[3][3], const double *v,
- double *ans)
+ double *ans)
{
ans[0] = m[0][0]*v[0] + m[1][0]*v[1] + m[2][0]*v[2];
ans[1] = m[0][1]*v[0] + m[1][1]*v[1] + m[2][1]*v[2];
@@ -401,9 +401,9 @@ void MathExtra::transpose_matvec(const double m[3][3], const double *v,
transposed matrix times vector
------------------------------------------------------------------------- */
-void MathExtra::transpose_matvec(const double *ex, const double *ey,
- const double *ez, const double *v,
- double *ans)
+void MathExtra::transpose_matvec(const double *ex, const double *ey,
+ const double *ez, const double *v,
+ double *ans)
{
ans[0] = ex[0]*v[0] + ex[1]*v[1] + ex[2]*v[2];
ans[1] = ey[0]*v[0] + ey[1]*v[1] + ey[2]*v[2];
@@ -414,8 +414,8 @@ void MathExtra::transpose_matvec(const double *ex, const double *ey,
transposed matrix times diagonal matrix
------------------------------------------------------------------------- */
-void MathExtra::transpose_diag3(const double m[3][3], const double *d,
- double ans[3][3])
+void MathExtra::transpose_diag3(const double m[3][3], const double *d,
+ double ans[3][3])
{
ans[0][0] = m[0][0]*d[0];
ans[0][1] = m[1][0]*d[1];
@@ -443,7 +443,7 @@ void MathExtra::vecmat(const double *v, const double m[3][3], double *ans)
matrix times scalar, in place
------------------------------------------------------------------------- */
-inline void MathExtra::scalar_times3(const double f, double m[3][3])
+inline void MathExtra::scalar_times3(const double f, double m[3][3])
{
m[0][0] *= f; m[0][1] *= f; m[0][2] *= f;
m[1][0] *= f; m[1][1] *= f; m[1][2] *= f;
@@ -536,7 +536,7 @@ void MathExtra::quatquat(double *a, double *b, double *c)
------------------------------------------------------------------------- */
void MathExtra::invquatvec(double *a, double *b, double *c)
-{
+{
c[0] = -a[1]*b[0] + a[0]*b[1] + a[3]*b[2] - a[2]*b[3];
c[1] = -a[2]*b[0] - a[3]*b[1] + a[0]*b[2] + a[1]*b[3];
c[2] = -a[3]*b[0] + a[2]*b[1] - a[1]*b[2] + a[0]*b[3];
@@ -548,7 +548,7 @@ void MathExtra::invquatvec(double *a, double *b, double *c)
------------------------------------------------------------------------- */
void MathExtra::axisangle_to_quat(const double *v, const double angle,
- double *quat)
+ double *quat)
{
double halfa = 0.5*angle;
double sina = sin(halfa);
diff --git a/src/memory.cpp b/src/memory.cpp
index f56b4bdcd3b70e9fb1877ab73e27d64977f5465d..b8f71016e037bf54bfdd7ec0b8e000935dac4d0a 100644
--- a/src/memory.cpp
+++ b/src/memory.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -24,7 +24,7 @@ using namespace LAMMPS_NS;
Memory::Memory(LAMMPS *lmp) : Pointers(lmp) {}
/* ----------------------------------------------------------------------
- safe malloc
+ safe malloc
------------------------------------------------------------------------- */
void *Memory::smalloc(bigint nbytes, const char *name)
@@ -41,14 +41,14 @@ void *Memory::smalloc(bigint nbytes, const char *name)
if (ptr == NULL) {
char str[128];
sprintf(str,"Failed to allocate " BIGINT_FORMAT " bytes for array %s",
- nbytes,name);
+ nbytes,name);
error->one(FLERR,str);
}
return ptr;
}
/* ----------------------------------------------------------------------
- safe realloc
+ safe realloc
------------------------------------------------------------------------- */
void *Memory::srealloc(void *ptr, bigint nbytes, const char *name)
@@ -62,14 +62,14 @@ void *Memory::srealloc(void *ptr, bigint nbytes, const char *name)
if (ptr == NULL) {
char str[128];
sprintf(str,"Failed to reallocate " BIGINT_FORMAT " bytes for array %s",
- nbytes,name);
+ nbytes,name);
error->one(FLERR,str);
}
return ptr;
}
/* ----------------------------------------------------------------------
- safe free
+ safe free
------------------------------------------------------------------------- */
void Memory::sfree(void *ptr)
diff --git a/src/memory.h b/src/memory.h
index aa1ec6e1972534f1d8bda40660a4abc04b51f00a..4a89a9cefaa42d320a23c3996d920304e3dc70e3 100644
--- a/src/memory.h
+++ b/src/memory.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -31,13 +31,13 @@ class Memory : protected Pointers {
/* ----------------------------------------------------------------------
create/grow/destroy vecs and multidim arrays with contiguous memory blocks
only use with primitive data types, e.g. 1d vec of ints, 2d array of doubles
- cannot use with pointers, e.g. 1d vec of int*, due to mismatched destroy
+ cannot use with pointers, e.g. 1d vec of int*, due to mismatched destroy
avoid use with non-primitive data types to avoid code bloat
for these other cases, use smalloc/srealloc/sfree directly
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
- create a 1d array
+ create a 1d array
------------------------------------------------------------------------- */
template <typename TYPE>
@@ -47,7 +47,7 @@ class Memory : protected Pointers {
array = (TYPE *) smalloc(nbytes,name);
return array;
}
-
+
template <typename TYPE>
TYPE **create(TYPE **&array, int n, const char *name) {fail(name);}
@@ -56,10 +56,10 @@ class Memory : protected Pointers {
------------------------------------------------------------------------- */
template <typename TYPE>
- TYPE *grow(TYPE *&array, int n, const char *name)
+ TYPE *grow(TYPE *&array, int n, const char *name)
{
if (array == NULL) return create(array,n,name);
-
+
bigint nbytes = ((bigint) sizeof(TYPE)) * n;
array = (TYPE *) srealloc(array,nbytes,name);
return array;
@@ -69,22 +69,22 @@ class Memory : protected Pointers {
TYPE **grow(TYPE **&array, int n, const char *name) {fail(name);}
/* ----------------------------------------------------------------------
- destroy a 1d array
+ destroy a 1d array
------------------------------------------------------------------------- */
template <typename TYPE>
- void destroy(TYPE *array)
+ void destroy(TYPE *array)
{
sfree(array);
}
/* ----------------------------------------------------------------------
- create a 1d array with index from nlo to nhi inclusive
+ create a 1d array with index from nlo to nhi inclusive
cannot grow it
------------------------------------------------------------------------- */
template <typename TYPE>
- TYPE *create1d_offset(TYPE *&array, int nlo, int nhi, const char *name)
+ TYPE *create1d_offset(TYPE *&array, int nlo, int nhi, const char *name)
{
bigint nbytes = ((bigint) sizeof(TYPE)) * (nhi-nlo+1);
array = (TYPE *) smalloc(nbytes,name);
@@ -97,31 +97,31 @@ class Memory : protected Pointers {
{fail(name);}
/* ----------------------------------------------------------------------
- destroy a 1d array with index offset
+ destroy a 1d array with index offset
------------------------------------------------------------------------- */
template <typename TYPE>
- void destroy1d_offset(TYPE *array, int offset)
+ void destroy1d_offset(TYPE *array, int offset)
{
if (array) sfree(&array[offset]);
}
/* ----------------------------------------------------------------------
- create a 2d array
+ create a 2d array
------------------------------------------------------------------------- */
template <typename TYPE>
- TYPE **create(TYPE **&array, int n1, int n2, const char *name)
+ TYPE **create(TYPE **&array, int n1, int n2, const char *name)
{
bigint nbytes = ((bigint) sizeof(TYPE)) * n1*n2;
TYPE *data = (TYPE *) smalloc(nbytes,name);
nbytes = ((bigint) sizeof(TYPE *)) * n1;
array = (TYPE **) smalloc(nbytes,name);
-
+
bigint n = 0;
for (int i = 0; i < n1; i++) {
- array[i] = &data[n];
- n += n2;
+ array[i] = &data[n];
+ n += n2;
}
return array;
}
@@ -136,19 +136,19 @@ class Memory : protected Pointers {
------------------------------------------------------------------------- */
template <typename TYPE>
- TYPE **grow(TYPE **&array, int n1, int n2, const char *name)
+ TYPE **grow(TYPE **&array, int n1, int n2, const char *name)
{
if (array == NULL) return create(array,n1,n2,name);
-
+
bigint nbytes = ((bigint) sizeof(TYPE)) * n1*n2;
TYPE *data = (TYPE *) srealloc(array[0],nbytes,name);
nbytes = ((bigint) sizeof(TYPE *)) * n1;
array = (TYPE **) srealloc(array,nbytes,name);
-
+
bigint n = 0;
for (int i = 0; i < n1; i++) {
- array[i] = &data[n];
- n += n2;
+ array[i] = &data[n];
+ n += n2;
}
return array;
}
@@ -158,7 +158,7 @@ class Memory : protected Pointers {
{fail(name);}
/* ----------------------------------------------------------------------
- destroy a 2d array
+ destroy a 2d array
------------------------------------------------------------------------- */
template <typename TYPE>
@@ -174,7 +174,7 @@ class Memory : protected Pointers {
------------------------------------------------------------------------- */
template <typename TYPE>
- TYPE **create_ragged(TYPE **&array, int n1, int *n2, const char *name)
+ TYPE **create_ragged(TYPE **&array, int n1, int *n2, const char *name)
{
bigint n2sum = 0;
for (int i = 0; i < n1; i++) n2sum += n2[i];
@@ -183,11 +183,11 @@ class Memory : protected Pointers {
TYPE *data = (TYPE *) smalloc(nbytes,name);
nbytes = ((bigint) sizeof(TYPE *)) * n1;
array = (TYPE **) smalloc(nbytes,name);
-
+
bigint n = 0;
for (int i = 0; i < n1; i++) {
- array[i] = &data[n];
- n += n2[i];
+ array[i] = &data[n];
+ n += n2[i];
}
return array;
}
@@ -197,13 +197,13 @@ class Memory : protected Pointers {
{fail(name);}
/* ----------------------------------------------------------------------
- create a 2d array with 2nd index from n2lo to n2hi inclusive
+ create a 2d array with 2nd index from n2lo to n2hi inclusive
cannot grow it
------------------------------------------------------------------------- */
template <typename TYPE>
TYPE **create2d_offset(TYPE **&array, int n1, int n2lo, int n2hi,
- const char *name)
+ const char *name)
{
int n2 = n2hi - n2lo + 1;
create(array,n1,n2,name);
@@ -213,10 +213,10 @@ class Memory : protected Pointers {
template <typename TYPE>
TYPE ***create2d_offset(TYPE ***&array, int n1, int n2lo, int n2hi,
- const char *name) {fail(name);}
+ const char *name) {fail(name);}
/* ----------------------------------------------------------------------
- destroy a 2d array with 2nd index offset
+ destroy a 2d array with 2nd index offset
------------------------------------------------------------------------- */
template <typename TYPE>
@@ -228,11 +228,11 @@ class Memory : protected Pointers {
}
/* ----------------------------------------------------------------------
- create a 3d array
+ create a 3d array
------------------------------------------------------------------------- */
template <typename TYPE>
- TYPE ***create(TYPE ***&array, int n1, int n2, int n3, const char *name)
+ TYPE ***create(TYPE ***&array, int n1, int n2, int n3, const char *name)
{
bigint nbytes = ((bigint) sizeof(TYPE)) * n1*n2*n3;
TYPE *data = (TYPE *) smalloc(nbytes,name);
@@ -240,23 +240,23 @@ class Memory : protected Pointers {
TYPE **plane = (TYPE **) smalloc(nbytes,name);
nbytes = ((bigint) sizeof(TYPE **)) * n1;
array = (TYPE ***) smalloc(nbytes,name);
-
+
int i,j;
bigint m;
bigint n = 0;
for (i = 0; i < n1; i++) {
- m = ((bigint) i) * n2;
- array[i] = &plane[m];
- for (j = 0; j < n2; j++) {
- plane[m+j] = &data[n];
- n += n3;
- }
+ m = ((bigint) i) * n2;
+ array[i] = &plane[m];
+ for (j = 0; j < n2; j++) {
+ plane[m+j] = &data[n];
+ n += n3;
+ }
}
return array;
}
template <typename TYPE>
- TYPE ****create(TYPE ****&array, int n1, int n2, int n3, const char *name)
+ TYPE ****create(TYPE ****&array, int n1, int n2, int n3, const char *name)
{fail(name);}
/* ----------------------------------------------------------------------
@@ -265,41 +265,41 @@ class Memory : protected Pointers {
------------------------------------------------------------------------- */
template <typename TYPE>
- TYPE ***grow(TYPE ***&array, int n1, int n2, int n3, const char *name)
+ TYPE ***grow(TYPE ***&array, int n1, int n2, int n3, const char *name)
{
if (array == NULL) return create(array,n1,n2,n3,name);
-
+
bigint nbytes = ((bigint) sizeof(TYPE)) * n1*n2*n3;
TYPE *data = (TYPE *) srealloc(array[0][0],nbytes,name);
nbytes = ((bigint) sizeof(TYPE *)) * n1*n2;
TYPE **plane = (TYPE **) srealloc(array[0],nbytes,name);
nbytes = ((bigint) sizeof(TYPE **)) * n1;
array = (TYPE ***) srealloc(array,nbytes,name);
-
+
int i,j;
bigint m;
bigint n = 0;
for (i = 0; i < n1; i++) {
- m = ((bigint) i) * n2;
- array[i] = &plane[m];
- for (j = 0; j < n2; j++) {
- plane[m+j] = &data[n];
- n += n3;
- }
+ m = ((bigint) i) * n2;
+ array[i] = &plane[m];
+ for (j = 0; j < n2; j++) {
+ plane[m+j] = &data[n];
+ n += n3;
+ }
}
return array;
}
template <typename TYPE>
- TYPE ****grow(TYPE ****&array, int n1, int n2, int n3, const char *name)
+ TYPE ****grow(TYPE ****&array, int n1, int n2, int n3, const char *name)
{fail(name);}
/* ----------------------------------------------------------------------
- destroy a 3d array
+ destroy a 3d array
------------------------------------------------------------------------- */
template <typename TYPE>
- void destroy(TYPE ***array)
+ void destroy(TYPE ***array)
{
if (array == NULL) return;
sfree(array[0][0]);
@@ -308,13 +308,13 @@ class Memory : protected Pointers {
}
/* ----------------------------------------------------------------------
- create a 3d array with 1st index from n1lo to n1hi inclusive
+ create a 3d array with 1st index from n1lo to n1hi inclusive
cannot grow it
------------------------------------------------------------------------- */
template <typename TYPE>
- TYPE ***create3d_offset(TYPE ***&array, int n1lo, int n1hi,
- int n2, int n3, const char *name)
+ TYPE ***create3d_offset(TYPE ***&array, int n1lo, int n1hi,
+ int n2, int n3, const char *name)
{
int n1 = n1hi - n1lo + 1;
create(array,n1,n2,n3,name);
@@ -323,12 +323,12 @@ class Memory : protected Pointers {
}
template <typename TYPE>
- TYPE ****create3d_offset(TYPE ****&array, int n1lo, int n1hi,
- int n2, int n3, const char *name)
+ TYPE ****create3d_offset(TYPE ****&array, int n1lo, int n1hi,
+ int n2, int n3, const char *name)
{fail(name);}
/* ----------------------------------------------------------------------
- free a 3d array with 1st index offset
+ free a 3d array with 1st index offset
------------------------------------------------------------------------- */
template <typename TYPE>
@@ -341,20 +341,20 @@ class Memory : protected Pointers {
create a 3d array with
1st index from n1lo to n1hi inclusive,
2nd index from n2lo to n2hi inclusive,
- 3rd index from n3lo to n3hi inclusive
+ 3rd index from n3lo to n3hi inclusive
cannot grow it
------------------------------------------------------------------------- */
template <typename TYPE>
- TYPE ***create3d_offset(TYPE ***&array, int n1lo, int n1hi,
- int n2lo, int n2hi, int n3lo, int n3hi,
- const char *name)
+ TYPE ***create3d_offset(TYPE ***&array, int n1lo, int n1hi,
+ int n2lo, int n2hi, int n3lo, int n3hi,
+ const char *name)
{
int n1 = n1hi - n1lo + 1;
int n2 = n2hi - n2lo + 1;
int n3 = n3hi - n3lo + 1;
create(array,n1,n2,n3,name);
-
+
bigint m = ((bigint) n1) * n2;
for (bigint i = 0; i < m; i++) array[0][i] -= n3lo;
for (int i = 0; i < n1; i++) array[i] -= n2lo;
@@ -363,18 +363,18 @@ class Memory : protected Pointers {
}
template <typename TYPE>
- TYPE ****create3d_offset(TYPE ****&array, int n1lo, int n1hi,
- int n2lo, int n2hi, int n3lo, int n3hi,
- const char *name)
+ TYPE ****create3d_offset(TYPE ****&array, int n1lo, int n1hi,
+ int n2lo, int n2hi, int n3lo, int n3hi,
+ const char *name)
{fail(name);}
/* ----------------------------------------------------------------------
- free a 3d array with all 3 indices offset
+ free a 3d array with all 3 indices offset
------------------------------------------------------------------------- */
template <typename TYPE>
- void destroy3d_offset(TYPE ***array,
- int n1_offset, int n2_offset, int n3_offset)
+ void destroy3d_offset(TYPE ***array,
+ int n1_offset, int n2_offset, int n3_offset)
{
if (array == NULL) return;
sfree(&array[n1_offset][n2_offset][n3_offset]);
@@ -383,12 +383,12 @@ class Memory : protected Pointers {
}
/* ----------------------------------------------------------------------
- create a 4d array
+ create a 4d array
------------------------------------------------------------------------- */
template <typename TYPE>
TYPE ****create(TYPE ****&array, int n1, int n2, int n3, int n4,
- const char *name)
+ const char *name)
{
bigint nbytes = ((bigint) sizeof(TYPE)) * n1*n2*n3*n4;
TYPE *data = (TYPE *) smalloc(nbytes,name);
@@ -398,34 +398,34 @@ class Memory : protected Pointers {
TYPE ***plane = (TYPE ***) smalloc(nbytes,name);
nbytes = ((bigint) sizeof(TYPE ***)) * n1;
array = (TYPE ****) smalloc(nbytes,name);
-
+
int i,j,k;
bigint m1,m2,m3;
bigint n = 0;
for (i = 0; i < n1; i++) {
- m2 = ((bigint) i) * n2;
- array[i] = &plane[m2];
- for (j = 0; j < n2; j++) {
- m1 = ((bigint) i) * n2 + j;
- m2 = ((bigint) i) * n2*n3 + j*n3;
- plane[m1] = &cube[m2];
- for (k = 0; k < n3; k++) {
- m1 = ((bigint) i) * n2*n3 + j*n3 + k;
- cube[m1] = &data[n];
- n += n4;
- }
- }
+ m2 = ((bigint) i) * n2;
+ array[i] = &plane[m2];
+ for (j = 0; j < n2; j++) {
+ m1 = ((bigint) i) * n2 + j;
+ m2 = ((bigint) i) * n2*n3 + j*n3;
+ plane[m1] = &cube[m2];
+ for (k = 0; k < n3; k++) {
+ m1 = ((bigint) i) * n2*n3 + j*n3 + k;
+ cube[m1] = &data[n];
+ n += n4;
+ }
+ }
}
return array;
}
template <typename TYPE>
TYPE *****create(TYPE *****&array, int n1, int n2, int n3, int n4,
- const char *name)
+ const char *name)
{fail(name);}
/* ----------------------------------------------------------------------
- destroy a 4d array
+ destroy a 4d array
------------------------------------------------------------------------- */
template <typename TYPE>
@@ -439,12 +439,12 @@ class Memory : protected Pointers {
}
/* ----------------------------------------------------------------------
- create a 5d array
+ create a 5d array
------------------------------------------------------------------------- */
template <typename TYPE>
TYPE *****create(TYPE *****&array, int n1, int n2, int n3, int n4,
- int n5, const char *name)
+ int n5, const char *name)
{
bigint nbytes = ((bigint) sizeof(TYPE)) * n1*n2*n3*n4*n5;
TYPE *data = (TYPE *) smalloc(nbytes,name);
@@ -456,41 +456,41 @@ class Memory : protected Pointers {
TYPE ****level2 = (TYPE ****) smalloc(nbytes,name);
nbytes = ((bigint) sizeof(TYPE ****)) * n1;
array = (TYPE *****) smalloc(nbytes,name);
-
+
int i,j,k,l;
bigint m1,m2,m3,m4,m5;
bigint n = 0;
for (i = 0; i < n1; i++) {
- m2 = ((bigint) i) * n2;
- array[i] = &level2[m2];
- for (j = 0; j < n2; j++) {
- m1 = ((bigint) i) * n2 + j;
- m2 = ((bigint) i) * n2*n3 + ((bigint) j) * n3;
- level2[m1] = &level3[m2];
- for (k = 0; k < n3; k++) {
- m1 = ((bigint) i) * n2*n3 + ((bigint) j) * n3 + k;
- m2 = ((bigint) i) * n2*n3*n4 +
- ((bigint) j) * n3*n4 + ((bigint) k) * n4;
- level3[m1] = &level4[m2];
- for (l = 0; l < n4; l++) {
- m1 = ((bigint) i) * n2*n3*n4 +
- ((bigint) j) * n3*n4 + ((bigint) k) * n4 + l;
- level4[m1] = &data[n];
- n += n5;
- }
- }
- }
+ m2 = ((bigint) i) * n2;
+ array[i] = &level2[m2];
+ for (j = 0; j < n2; j++) {
+ m1 = ((bigint) i) * n2 + j;
+ m2 = ((bigint) i) * n2*n3 + ((bigint) j) * n3;
+ level2[m1] = &level3[m2];
+ for (k = 0; k < n3; k++) {
+ m1 = ((bigint) i) * n2*n3 + ((bigint) j) * n3 + k;
+ m2 = ((bigint) i) * n2*n3*n4 +
+ ((bigint) j) * n3*n4 + ((bigint) k) * n4;
+ level3[m1] = &level4[m2];
+ for (l = 0; l < n4; l++) {
+ m1 = ((bigint) i) * n2*n3*n4 +
+ ((bigint) j) * n3*n4 + ((bigint) k) * n4 + l;
+ level4[m1] = &data[n];
+ n += n5;
+ }
+ }
+ }
}
return array;
}
template <typename TYPE>
TYPE ******create(TYPE ******&array, int n1, int n2, int n3, int n4,
- int n5, const char *name)
+ int n5, const char *name)
{fail(name);}
/* ----------------------------------------------------------------------
- destroy a 5d array
+ destroy a 5d array
------------------------------------------------------------------------- */
template <typename TYPE>
diff --git a/src/min.cpp b/src/min.cpp
index 945c1a2f51e4ef33e45cadcda64a89ecce8991fa..83468936cd99ddcf1ea7a032ea693161405a9992 100644
--- a/src/min.cpp
+++ b/src/min.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -167,11 +167,11 @@ void Min::init()
neigh_every = neighbor->every;
neigh_delay = neighbor->delay;
neigh_dist_check = neighbor->dist_check;
-
+
if (neigh_every != 1 || neigh_delay != 0 || neigh_dist_check != 1) {
- if (comm->me == 0)
+ if (comm->me == 0)
error->warning(FLERR,
- "Resetting reneighboring criteria during minimization");
+ "Resetting reneighboring criteria during minimization");
}
neighbor->every = 1;
@@ -238,10 +238,10 @@ void Min::setup()
if (nextra_global && searchflag == 0)
error->all(FLERR,
- "Cannot use a damped dynamics min style with fix box/relax");
+ "Cannot use a damped dynamics min style with fix box/relax");
if (nextra_atom && searchflag == 0)
error->all(FLERR,
- "Cannot use a damped dynamics min style with per-atom DOF");
+ "Cannot use a damped dynamics min style with per-atom DOF");
// atoms may have migrated in comm->exchange()
@@ -285,7 +285,7 @@ void Min::setup()
ecurrent = pe_compute->compute_scalar();
if (nextra_global) ecurrent += modify->min_energy(fextra);
if (output->thermo->normflag) ecurrent /= atom->natoms;
-
+
einitial = ecurrent;
fnorm2_init = sqrt(fnorm_sqr());
fnorminf_init = fnorm_inf();
@@ -357,7 +357,7 @@ void Min::setup_minimal(int flag)
ecurrent = pe_compute->compute_scalar();
if (nextra_global) ecurrent += modify->min_energy(fextra);
if (output->thermo->normflag) ecurrent /= atom->natoms;
-
+
einitial = ecurrent;
fnorm2_init = sqrt(fnorm_sqr());
fnorminf_init = fnorm_inf();
@@ -387,14 +387,14 @@ void Min::run(int n)
if (update->restrict_output == 0) {
for (int idump = 0; idump < output->ndump; idump++)
- output->next_dump[idump] = update->ntimestep;
+ output->next_dump[idump] = update->ntimestep;
output->next_dump_any = update->ntimestep;
if (output->restart_flag) {
- output->next_restart = update->ntimestep;
- if (output->restart_every_single)
- output->next_restart_single = update->ntimestep;
- if (output->restart_every_double)
- output->next_restart_double = update->ntimestep;
+ output->next_restart = update->ntimestep;
+ if (output->restart_every_single)
+ output->next_restart_single = update->ntimestep;
+ if (output->restart_every_double)
+ output->next_restart_double = update->ntimestep;
}
}
output->next_thermo = update->ntimestep;
@@ -410,7 +410,7 @@ void Min::run(int n)
void Min::cleanup()
{
// stats for Finish to print
-
+
efinal = ecurrent;
fnorm2_final = sqrt(fnorm_sqr());
fnorminf_final = fnorm_inf();
@@ -456,8 +456,8 @@ double Min::energy_force(int resetflag)
}
timer->stamp();
comm->exchange();
- if (atom->sortfreq > 0 &&
- update->ntimestep >= atom->nextsort) atom->sort();
+ if (atom->sortfreq > 0 &&
+ update->ntimestep >= atom->nextsort) atom->sort();
comm->borders();
if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
timer->stamp(TIME_COMM);
@@ -565,14 +565,14 @@ int Min::request(Pair *pair, int peratom, double maxvalue)
{
int n = nextra_atom + 1;
xextra_atom = (double **) memory->srealloc(xextra_atom,n*sizeof(double *),
- "min:xextra_atom");
+ "min:xextra_atom");
fextra_atom = (double **) memory->srealloc(fextra_atom,n*sizeof(double *),
- "min:fextra_atom");
+ "min:fextra_atom");
memory->grow(extra_peratom,n,"min:extra_peratom");
memory->grow(extra_nlen,n,"min:extra_nlen");
memory->grow(extra_max,n,"min:extra_max");
requestor = (Pair **) memory->srealloc(requestor,n*sizeof(Pair *),
- "min:requestor");
+ "min:requestor");
requestor[nextra_atom] = pair;
extra_peratom[nextra_atom] = peratom;
@@ -712,7 +712,7 @@ double Min::fnorm_sqr()
fatom = fextra_atom[m];
n = extra_nlen[m];
for (i = 0; i < n; i++)
- local_norm2_sqr += fatom[i]*fatom[i];
+ local_norm2_sqr += fatom[i]*fatom[i];
}
}
@@ -720,9 +720,9 @@ double Min::fnorm_sqr()
MPI_Allreduce(&local_norm2_sqr,&norm2_sqr,1,MPI_DOUBLE,MPI_SUM,world);
if (nextra_global)
- for (i = 0; i < nextra_global; i++)
+ for (i = 0; i < nextra_global; i++)
norm2_sqr += fextra[i]*fextra[i];
-
+
return norm2_sqr;
}
@@ -743,7 +743,7 @@ double Min::fnorm_inf()
fatom = fextra_atom[m];
n = extra_nlen[m];
for (i = 0; i < n; i++)
- local_norm_inf = MAX(fabs(fatom[i]),local_norm_inf);
+ local_norm_inf = MAX(fabs(fatom[i]),local_norm_inf);
}
}
@@ -751,7 +751,7 @@ double Min::fnorm_inf()
MPI_Allreduce(&local_norm_inf,&norm_inf,1,MPI_DOUBLE,MPI_MAX,world);
if (nextra_global)
- for (i = 0; i < nextra_global; i++)
+ for (i = 0; i < nextra_global; i++)
norm_inf = MAX(fabs(fextra[i]),norm_inf);
return norm_inf;
@@ -764,14 +764,14 @@ double Min::fnorm_inf()
char *Min::stopstrings(int n)
{
const char *strings[] = {"max iterations",
- "max force evaluations",
- "energy tolerance",
- "force tolerance",
- "search direction is not downhill",
- "linesearch alpha is zero",
- "forces are zero",
- "quadratic factors are zero",
- "trust region too small",
- "HFTN minimizer error"};
+ "max force evaluations",
+ "energy tolerance",
+ "force tolerance",
+ "search direction is not downhill",
+ "linesearch alpha is zero",
+ "forces are zero",
+ "quadratic factors are zero",
+ "trust region too small",
+ "HFTN minimizer error"};
return (char *) strings[n];
}
diff --git a/src/min.h b/src/min.h
index bb21df05807e5b28e689c0a3af498b848fd4a443..2ba3e5cb22b6c769221f688560c11da1d61f0e23 100644
--- a/src/min.h
+++ b/src/min.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/min_cg.cpp b/src/min_cg.cpp
index f2b1a666f54a25795e257a40cef634fcb2fc001e..a9887a6cec72325f5685cb968c014b53ab2e7fb0 100644
--- a/src/min_cg.cpp
+++ b/src/min_cg.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -73,7 +73,7 @@ int MinCG::iterate(int maxiter)
// line minimization along direction h from current atom->x
eprevious = ecurrent;
- fail = (this->*linemin)(ecurrent,alpha_final);
+ fail = (this->*linemin)(ecurrent,alpha_final);
if (fail) return fail;
// function evaluation criterion
@@ -82,8 +82,8 @@ int MinCG::iterate(int maxiter)
// energy tolerance criterion
- if (fabs(ecurrent-eprevious) <
- update->etol * 0.5*(fabs(ecurrent) + fabs(eprevious) + EPS_ENERGY))
+ if (fabs(ecurrent-eprevious) <
+ update->etol * 0.5*(fabs(ecurrent) + fabs(eprevious) + EPS_ENERGY))
return ETOL;
// force tolerance criterion
@@ -95,19 +95,19 @@ int MinCG::iterate(int maxiter)
}
if (nextra_atom)
for (m = 0; m < nextra_atom; m++) {
- fatom = fextra_atom[m];
- gatom = gextra_atom[m];
- n = extra_nlen[m];
- for (i = 0; i < n; i++) {
- dot[0] += fatom[i]*fatom[i];
- dot[1] += fatom[i]*gatom[i];
- }
+ fatom = fextra_atom[m];
+ gatom = gextra_atom[m];
+ n = extra_nlen[m];
+ for (i = 0; i < n; i++) {
+ dot[0] += fatom[i]*fatom[i];
+ dot[1] += fatom[i]*gatom[i];
+ }
}
MPI_Allreduce(dot,dotall,2,MPI_DOUBLE,MPI_SUM,world);
if (nextra_global)
for (i = 0; i < nextra_global; i++) {
- dotall[0] += fextra[i]*fextra[i];
- dotall[1] += fextra[i]*gextra[i];
+ dotall[0] += fextra[i]*fextra[i];
+ dotall[1] += fextra[i]*gextra[i];
}
if (dotall[0] < update->ftol*update->ftol) return FTOL;
@@ -127,19 +127,19 @@ int MinCG::iterate(int maxiter)
}
if (nextra_atom)
for (m = 0; m < nextra_atom; m++) {
- fatom = fextra_atom[m];
- gatom = gextra_atom[m];
- hatom = hextra_atom[m];
- n = extra_nlen[m];
- for (i = 0; i < n; i++) {
- gatom[i] = fatom[i];
- hatom[i] = gatom[i] + beta*hatom[i];
- }
+ fatom = fextra_atom[m];
+ gatom = gextra_atom[m];
+ hatom = hextra_atom[m];
+ n = extra_nlen[m];
+ for (i = 0; i < n; i++) {
+ gatom[i] = fatom[i];
+ hatom[i] = gatom[i] + beta*hatom[i];
+ }
}
if (nextra_global)
for (i = 0; i < nextra_global; i++) {
- gextra[i] = fextra[i];
- hextra[i] = gextra[i] + beta*hextra[i];
+ gextra[i] = fextra[i];
+ hextra[i] = gextra[i] + beta*hextra[i];
}
// reinitialize CG if new search direction h is not downhill
@@ -148,27 +148,27 @@ int MinCG::iterate(int maxiter)
for (i = 0; i < nvec; i++) dot[0] += g[i]*h[i];
if (nextra_atom)
for (m = 0; m < nextra_atom; m++) {
- gatom = gextra_atom[m];
- hatom = hextra_atom[m];
- n = extra_nlen[m];
- for (i = 0; i < n; i++) dot[0] += gatom[i]*hatom[i];
+ gatom = gextra_atom[m];
+ hatom = hextra_atom[m];
+ n = extra_nlen[m];
+ for (i = 0; i < n; i++) dot[0] += gatom[i]*hatom[i];
}
MPI_Allreduce(dot,dotall,1,MPI_DOUBLE,MPI_SUM,world);
if (nextra_global)
for (i = 0; i < nextra_global; i++)
- dotall[0] += gextra[i]*hextra[i];
+ dotall[0] += gextra[i]*hextra[i];
if (dotall[0] <= 0.0) {
for (i = 0; i < nvec; i++) h[i] = g[i];
if (nextra_atom)
- for (m = 0; m < nextra_atom; m++) {
- gatom = gextra_atom[m];
- hatom = hextra_atom[m];
- n = extra_nlen[m];
- for (i = 0; i < n; i++) hatom[i] = gatom[i];
- }
+ for (m = 0; m < nextra_atom; m++) {
+ gatom = gextra_atom[m];
+ hatom = hextra_atom[m];
+ n = extra_nlen[m];
+ for (i = 0; i < n; i++) hatom[i] = gatom[i];
+ }
if (nextra_global)
- for (i = 0; i < nextra_global; i++) hextra[i] = gextra[i];
+ for (i = 0; i < nextra_global; i++) hextra[i] = gextra[i];
}
// output for thermo, dump, restart files
diff --git a/src/min_cg.h b/src/min_cg.h
index 5588e4f3fb19c6705cc4fb46169be1a8bfd68b5f..6ac8901d2474ad07668d6f3aa945abd9a37615ce 100644
--- a/src/min_cg.h
+++ b/src/min_cg.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/min_fire.cpp b/src/min_fire.cpp
index c061eceedaf2c8e63479d71bb2c9fa8d0a3a342c..c8ade7dcb229880a05dbf8937f1939f197151ee4 100644
--- a/src/min_fire.cpp
+++ b/src/min_fire.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -123,42 +123,42 @@ int MinFire::iterate(int maxiter)
if (vdotfall > 0.0) {
vdotv = 0.0;
for (int i = 0; i < nlocal; i++)
- vdotv += v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2];
+ vdotv += v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2];
MPI_Allreduce(&vdotv,&vdotvall,1,MPI_DOUBLE,MPI_SUM,world);
// sum vdotv over replicas, if necessary
// this communicator would be invalid for multiprocess replicas
if (update->multireplica == 1) {
- vdotv = vdotvall;
- MPI_Allreduce(&vdotv,&vdotvall,1,MPI_DOUBLE,MPI_SUM,universe->uworld);
+ vdotv = vdotvall;
+ MPI_Allreduce(&vdotv,&vdotvall,1,MPI_DOUBLE,MPI_SUM,universe->uworld);
}
fdotf = 0.0;
for (int i = 0; i < nlocal; i++)
- fdotf += f[i][0]*f[i][0] + f[i][1]*f[i][1] + f[i][2]*f[i][2];
+ fdotf += f[i][0]*f[i][0] + f[i][1]*f[i][1] + f[i][2]*f[i][2];
MPI_Allreduce(&fdotf,&fdotfall,1,MPI_DOUBLE,MPI_SUM,world);
// sum fdotf over replicas, if necessary
// this communicator would be invalid for multiprocess replicas
-
+
if (update->multireplica == 1) {
- fdotf = fdotfall;
- MPI_Allreduce(&fdotf,&fdotfall,1,MPI_DOUBLE,MPI_SUM,universe->uworld);
+ fdotf = fdotfall;
+ MPI_Allreduce(&fdotf,&fdotfall,1,MPI_DOUBLE,MPI_SUM,universe->uworld);
}
scale1 = 1.0 - alpha;
if (fdotfall == 0.0) scale2 = 0.0;
else scale2 = alpha * sqrt(vdotvall/fdotfall);
for (int i = 0; i < nlocal; i++) {
- v[i][0] = scale1*v[i][0] + scale2*f[i][0];
- v[i][1] = scale1*v[i][1] + scale2*f[i][1];
- v[i][2] = scale1*v[i][2] + scale2*f[i][2];
+ v[i][0] = scale1*v[i][0] + scale2*f[i][0];
+ v[i][1] = scale1*v[i][1] + scale2*f[i][1];
+ v[i][2] = scale1*v[i][2] + scale2*f[i][2];
}
if (ntimestep - last_negative > DELAYSTEP) {
- dt = MIN(dt*DT_GROW,dtmax);
- alpha *= ALPHA_SHRINK;
+ dt = MIN(dt*DT_GROW,dtmax);
+ alpha *= ALPHA_SHRINK;
}
// else (v dot f) <= 0:
@@ -169,7 +169,7 @@ int MinFire::iterate(int maxiter)
dt *= DT_SHRINK;
alpha = ALPHA0;
for (int i = 0; i < nlocal; i++)
- v[i][0] = v[i][1] = v[i][2] = 0.0;
+ v[i][0] = v[i][1] = v[i][2] = 0.0;
}
// limit timestep so no particle moves further than dmax
@@ -198,29 +198,29 @@ int MinFire::iterate(int maxiter)
// Euler integration step
double **x = atom->x;
-
+
if (rmass) {
for (int i = 0; i < nlocal; i++) {
- dtfm = dtv / rmass[i];
- x[i][0] += dtv * v[i][0];
- x[i][1] += dtv * v[i][1];
- x[i][2] += dtv * v[i][2];
- v[i][0] += dtfm * f[i][0];
- v[i][1] += dtfm * f[i][1];
- v[i][2] += dtfm * f[i][2];
+ dtfm = dtv / rmass[i];
+ x[i][0] += dtv * v[i][0];
+ x[i][1] += dtv * v[i][1];
+ x[i][2] += dtv * v[i][2];
+ v[i][0] += dtfm * f[i][0];
+ v[i][1] += dtfm * f[i][1];
+ v[i][2] += dtfm * f[i][2];
}
} else {
for (int i = 0; i < nlocal; i++) {
- dtfm = dtv / mass[type[i]];
- x[i][0] += dtv * v[i][0];
- x[i][1] += dtv * v[i][1];
- x[i][2] += dtv * v[i][2];
- v[i][0] += dtfm * f[i][0];
- v[i][1] += dtfm * f[i][1];
- v[i][2] += dtfm * f[i][2];
+ dtfm = dtv / mass[type[i]];
+ x[i][0] += dtv * v[i][0];
+ x[i][1] += dtv * v[i][1];
+ x[i][2] += dtv * v[i][2];
+ v[i][0] += dtfm * f[i][0];
+ v[i][1] += dtfm * f[i][1];
+ v[i][2] += dtfm * f[i][2];
}
}
-
+
eprevious = ecurrent;
ecurrent = energy_force(0);
neval++;
@@ -231,16 +231,16 @@ int MinFire::iterate(int maxiter)
if (update->etol > 0.0 && ntimestep-last_negative > DELAYSTEP) {
if (update->multireplica == 0) {
- if (fabs(ecurrent-eprevious) <
- update->etol * 0.5*(fabs(ecurrent) + fabs(eprevious) + EPS_ENERGY))
- return ETOL;
+ if (fabs(ecurrent-eprevious) <
+ update->etol * 0.5*(fabs(ecurrent) + fabs(eprevious) + EPS_ENERGY))
+ return ETOL;
} else {
- if (fabs(ecurrent-eprevious) <
- update->etol * 0.5*(fabs(ecurrent) + fabs(eprevious) + EPS_ENERGY))
- flag = 0;
- else flag = 1;
- MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,universe->uworld);
- if (flagall == 0) return ETOL;
+ if (fabs(ecurrent-eprevious) <
+ update->etol * 0.5*(fabs(ecurrent) + fabs(eprevious) + EPS_ENERGY))
+ flag = 0;
+ else flag = 1;
+ MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,universe->uworld);
+ if (flagall == 0) return ETOL;
}
}
@@ -250,12 +250,12 @@ int MinFire::iterate(int maxiter)
if (update->ftol > 0.0) {
fdotf = fnorm_sqr();
if (update->multireplica == 0) {
- if (fdotf < update->ftol*update->ftol) return FTOL;
+ if (fdotf < update->ftol*update->ftol) return FTOL;
} else {
- if (fdotf < update->ftol*update->ftol) flag = 0;
- else flag = 1;
- MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,universe->uworld);
- if (flagall == 0) return FTOL;
+ if (fdotf < update->ftol*update->ftol) flag = 0;
+ else flag = 1;
+ MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,universe->uworld);
+ if (flagall == 0) return FTOL;
}
}
@@ -267,6 +267,6 @@ int MinFire::iterate(int maxiter)
timer->stamp(TIME_OUTPUT);
}
}
-
+
return MAXITER;
}
diff --git a/src/min_fire.h b/src/min_fire.h
index 926b1e6ecc1de84cec0711a95a53a87db8f585de..54867d6c6b7d4b3a1d2b8f52e8ce0b3825bc6746 100644
--- a/src/min_fire.h
+++ b/src/min_fire.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/min_hftn.cpp b/src/min_hftn.cpp
index 60e4890bd46a4b868f40ddfdf005a98855a5ba66..cb479343801cc4090c03257a7292009619442d26 100644
--- a/src/min_hftn.cpp
+++ b/src/min_hftn.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -81,9 +81,9 @@ MinHFTN::MinHFTN(LAMMPS *lmp) : Min(lmp)
_daExtraGlobal[i] = NULL;
for (int i = 0; i < NUM_HFTN_ATOM_BASED_VECTORS; i++)
_daExtraAtom[i] = NULL;
-
+
_fpPrint = NULL;
-
+
return;
}
@@ -99,7 +99,7 @@ MinHFTN::~MinHFTN (void)
for (int i = 0; i < NUM_HFTN_ATOM_BASED_VECTORS; i++)
if (_daExtraAtom[i] != NULL)
delete [] _daExtraAtom[i];
-
+
return;
}
@@ -121,7 +121,7 @@ void MinHFTN::init()
delete [] _daExtraAtom[i];
_daExtraAtom[i] = NULL;
}
-
+
return;
}
@@ -134,7 +134,7 @@ void MinHFTN::setup_style()
//---- ALLOCATE MEMORY FOR ATOMIC DEGREES OF FREEDOM.
for (int i = 0; i < NUM_HFTN_ATOM_BASED_VECTORS; i++)
fix_minimize->add_vector(3);
-
+
//---- ALLOCATE MEMORY FOR EXTRA GLOBAL DEGREES OF FREEDOM.
//---- THE FIX MODULE TAKES CARE OF THE FIRST VECTOR, X0 (XK).
if (nextra_global) {
@@ -146,13 +146,13 @@ void MinHFTN::setup_style()
if (nextra_atom) {
for (int i = 0; i < NUM_HFTN_ATOM_BASED_VECTORS; i++)
_daExtraAtom[i] = new double*[nextra_atom];
-
+
for (int m = 0; m < nextra_atom; m++) {
for (int i = 0; i < NUM_HFTN_ATOM_BASED_VECTORS; i++)
- fix_minimize->add_vector (extra_peratom[m]);
+ fix_minimize->add_vector (extra_peratom[m]);
}
}
-
+
return;
}
@@ -167,7 +167,7 @@ void MinHFTN::setup_style()
void MinHFTN::reset_vectors()
{
nvec = 3 * atom->nlocal;
-
+
//---- ATOMIC DEGREES OF FREEDOM.
if (nvec > 0) {
xvec = atom->x[0];
@@ -175,7 +175,7 @@ void MinHFTN::reset_vectors()
}
for (int i = 0; i < NUM_HFTN_ATOM_BASED_VECTORS; i++)
_daAVectors[i] = fix_minimize->request_vector (i);
-
+
//---- EXTRA PER-ATOM DEGREES OF FREEDOM.
if (nextra_atom) {
int n = NUM_HFTN_ATOM_BASED_VECTORS;
@@ -183,10 +183,10 @@ void MinHFTN::reset_vectors()
extra_nlen[m] = extra_peratom[m] * atom->nlocal;
requestor[m]->min_xf_pointers(m,&xextra_atom[m],&fextra_atom[m]);
for (int i = 0; i < NUM_HFTN_ATOM_BASED_VECTORS; i++)
- _daExtraAtom[i][m] = fix_minimize->request_vector (n++);
+ _daExtraAtom[i][m] = fix_minimize->request_vector (n++);
}
}
-
+
return;
}
@@ -201,22 +201,22 @@ int MinHFTN::iterate(int)
{
//---- TURN THIS ON TO GENERATE AN OPTIMIZATION PROGRESS FILE.
bool bPrintProgress = false;
-
+
if (bPrintProgress)
open_hftn_print_file_();
-
+
double dFinalEnergy = 0.0;
double dFinalFnorm2 = 0.0;
modify->min_clearstore();
int nStopCode = execute_hftn_ (bPrintProgress,
- einitial,
- fnorm2_init,
- dFinalEnergy,
- dFinalFnorm2);
+ einitial,
+ fnorm2_init,
+ dFinalEnergy,
+ dFinalFnorm2);
modify->min_clearstore();
if (bPrintProgress)
close_hftn_print_file_();
-
+
return( nStopCode );
}
@@ -234,20 +234,20 @@ int MinHFTN::iterate(int)
atom->f - forces evaluated at output x
------------------------------------------------------------------------- */
int MinHFTN::execute_hftn_(const bool bPrintProgress,
- const double dInitialEnergy,
- const double dInitialForce2,
- double & dFinalEnergy,
- double & dFinalForce2)
+ const double dInitialEnergy,
+ const double dInitialForce2,
+ double & dFinalEnergy,
+ double & dFinalForce2)
{
//---- DEFINE OUTPUTS PRINTED BY "Finish".
eprevious = dInitialEnergy;
alpha_final = 0.0;
dFinalEnergy = dInitialEnergy;
dFinalForce2 = dInitialForce2;
-
+
if (dInitialForce2 < update->ftol)
return( STOP_FORCE_TOL );
-
+
//---- SAVE ATOM POSITIONS BEFORE AN ITERATION.
fix_minimize->store_box();
for (int i = 0; i < nvec; i++)
@@ -258,295 +258,295 @@ int MinHFTN::execute_hftn_(const bool bPrintProgress,
double * xkAtom = _daExtraAtom[VEC_XK][m];
int n = extra_nlen[m];
for (int i = 0; i < n; i++)
- xkAtom[i] = xatom[i];
+ xkAtom[i] = xatom[i];
}
}
if (nextra_global)
modify->min_store();
-
+
double dXInf = calc_xinf_using_mpi_();
-
+
//---- FIND THE NUMBER OF UNKNOWNS.
int nLocalNumUnknowns = nvec + nextra_atom;
MPI_Allreduce (&nLocalNumUnknowns, &_nNumUnknowns,
- 1, MPI_INT, MPI_SUM, world);
-
+ 1, MPI_INT, MPI_SUM, world);
+
//---- INITIALIZE THE TRUST RADIUS BASED ON THE GRADIENT.
double dTrustRadius = 1.5 * dInitialForce2;
-
+
//---- TRUST RADIUS MUST KEEP STEPS FROM LETTING ATOMS MOVE SO FAR THEY
//---- VIOLATE PHYSICS OR JUMP BEYOND A PARALLEL PROCESSING DOMAIN.
//---- LINE SEARCH METHODS DO THIS BY RESTRICTING THE LARGEST CHANGE
//---- OF ANY ATOM'S COMPONENT TO dmax. AN EXACT CHECK IS MADE LATER,
//---- BUT THIS GUIDES DETERMINATION OF A MAX TRUST RADIUS.
double dMaxTrustRadius = dmax * sqrt((double) _nNumUnknowns);
-
+
dTrustRadius = MIN (dTrustRadius, dMaxTrustRadius);
double dLastNewtonStep2 = dMaxTrustRadius;
-
+
if (bPrintProgress)
hftn_print_line_ (false, -1, neval, dInitialEnergy, dInitialForce2,
- -1, dTrustRadius, 0.0, 0.0, 0.0);
-
+ -1, dTrustRadius, 0.0, 0.0, 0.0);
+
bool bHaveEvaluatedAtX = true;
double dCurrentEnergy = dInitialEnergy;
double dCurrentForce2 = dInitialForce2;
for (niter = 0; niter < update->nsteps; niter++) {
(update->ntimestep)++;
-
+
//---- CALL THE INNER LOOP TO GET THE NEXT TRUST REGION STEP.
-
+
double dCgForce2StopTol = MIN ((dCurrentForce2 / 2.0), 0.1 / (niter+1));
dCgForce2StopTol = MAX (dCgForce2StopTol, update->ftol);
-
+
double dNewEnergy;
double dNewForce2;
int nStepType;
double dStepLength2;
double dStepLengthInf;
if (compute_inner_cg_step_ (dTrustRadius,
- dCgForce2StopTol,
- update->max_eval,
- bHaveEvaluatedAtX,
- dCurrentEnergy, dCurrentForce2,
- dNewEnergy, dNewForce2,
- nStepType,
- dStepLength2, dStepLengthInf) == false) {
+ dCgForce2StopTol,
+ update->max_eval,
+ bHaveEvaluatedAtX,
+ dCurrentEnergy, dCurrentForce2,
+ dNewEnergy, dNewForce2,
+ nStepType,
+ dStepLength2, dStepLengthInf) == false) {
//---- THERE WAS AN ERROR. RESTORE TO LAST ACCEPTED STEP.
if (nextra_global)
- modify->min_step (0.0, _daExtraGlobal[VEC_CG_P]);
+ modify->min_step (0.0, _daExtraGlobal[VEC_CG_P]);
for (int i = 0; i < nvec; i++)
- xvec[i] = _daAVectors[VEC_XK][i];
+ xvec[i] = _daAVectors[VEC_XK][i];
if (nextra_atom) {
- for (int m = 0; m < nextra_atom; m++) {
- double * xatom = xextra_atom[m];
- double * xkAtom = _daExtraAtom[VEC_XK][m];
- int n = extra_nlen[m];
- for (int i = 0; i < n; i++)
- xatom[i] = xkAtom[i];
- requestor[m]->min_x_set(m);
- }
+ for (int m = 0; m < nextra_atom; m++) {
+ double * xatom = xextra_atom[m];
+ double * xkAtom = _daExtraAtom[VEC_XK][m];
+ int n = extra_nlen[m];
+ for (int i = 0; i < n; i++)
+ xatom[i] = xkAtom[i];
+ requestor[m]->min_x_set(m);
+ }
}
dFinalEnergy = energy_force (0);
neval++;
dFinalForce2 = sqrt (fnorm_sqr());
return( STOP_ERROR );
}
-
+
//---- STOP IF THE CURRENT POSITION WAS FOUND TO BE ALREADY GOOD ENOUGH.
//---- IN THIS CASE THE ENERGY AND FORCES ARE ALREADY COMPUTED.
if (nStepType == NO_CGSTEP_BECAUSE_F_TOL_SATISFIED) {
if (bPrintProgress)
- hftn_print_line_ (true, niter+1, neval, dNewEnergy, dNewForce2,
- nStepType, dTrustRadius, dStepLength2,
- 0.0, 0.0);
+ hftn_print_line_ (true, niter+1, neval, dNewEnergy, dNewForce2,
+ nStepType, dTrustRadius, dStepLength2,
+ 0.0, 0.0);
dFinalEnergy = dNewEnergy;
dFinalForce2 = dNewForce2;
return( STOP_FORCE_TOL );
}
-
+
//---- COMPUTE THE DIRECTIONAL DERIVATIVE H(x_k) p.
bool bUseForwardDiffs = (dCurrentForce2 > 1000.0 * sqrt (MACHINE_EPS));
evaluate_dir_der_ (bUseForwardDiffs,
- VEC_CG_P,
- VEC_CG_HD,
- true,
- dCurrentEnergy);
-
+ VEC_CG_P,
+ VEC_CG_HD,
+ true,
+ dCurrentEnergy);
+
//---- COMPUTE p^T grad(x_k) AND SAVE IT FOR PRED.
double dGradDotP = calc_grad_dot_v_using_mpi_ (VEC_CG_P);
-
+
//---- MOVE TO THE NEW POINT AND EVALUATE ENERGY AND FORCES.
//---- THIS IS THE PLACE WHERE energy_force IS ALLOWED TO RESET.
for (int i = 0; i < nvec; i++)
xvec[i] = _daAVectors[VEC_XK][i] + _daAVectors[VEC_CG_P][i];
if (nextra_atom) {
for (int m = 0; m < nextra_atom; m++) {
- double * xatom = xextra_atom[m];
- double * xkAtom = _daExtraAtom[VEC_XK][m];
- double * pAtom = _daExtraAtom[VEC_CG_P][m];
- int n = extra_nlen[m];
- for (int i = 0; i < n; i++)
- xatom[i] = xkAtom[i] + pAtom[i];
- requestor[m]->min_x_set(m);
+ double * xatom = xextra_atom[m];
+ double * xkAtom = _daExtraAtom[VEC_XK][m];
+ double * pAtom = _daExtraAtom[VEC_CG_P][m];
+ int n = extra_nlen[m];
+ for (int i = 0; i < n; i++)
+ xatom[i] = xkAtom[i] + pAtom[i];
+ requestor[m]->min_x_set(m);
}
}
if (nextra_global)
modify->min_step (1.0, _daExtraGlobal[VEC_CG_P]);
dNewEnergy = energy_force (1);
neval++;
-
+
dNewForce2 = sqrt (fnorm_sqr());
-
+
double dAred = dCurrentEnergy - dNewEnergy;
-
+
//---- STOP IF THE FORCE TOLERANCE IS MET.
if (dNewForce2 < update->ftol) {
if (bPrintProgress)
- hftn_print_line_ (true, niter+1, neval, dNewEnergy, dNewForce2,
- nStepType, dTrustRadius, dStepLength2,
- dAred, -1.0);
+ hftn_print_line_ (true, niter+1, neval, dNewEnergy, dNewForce2,
+ nStepType, dTrustRadius, dStepLength2,
+ dAred, -1.0);
//---- (IMPLICITLY ACCEPT THE LAST STEP TO THE NEW POINT.)
dFinalEnergy = dNewEnergy;
dFinalForce2 = dNewForce2;
return( STOP_FORCE_TOL );
}
-
+
//---- STOP IF THE ACTUAL ENERGY REDUCTION IS TINY.
if (nStepType != CGSTEP_TO_DMAX) {
double dMag = 0.5 * (fabs (dCurrentEnergy) + fabs (dNewEnergy));
dMag = MAX (dMag, MIN_ETOL_MAG);
if ( (fabs (dAred) < (update->etol * dMag))
- || (dStepLengthInf == 0.0) ) {
- if (bPrintProgress)
- hftn_print_line_ (true, niter+1, neval,
- dNewEnergy, dNewForce2,
- nStepType, dTrustRadius, dStepLength2,
- dAred, -1.0);
- //---- (IMPLICITLY ACCEPT THE LAST STEP TO THE NEW POINT.)
- dFinalEnergy = dNewEnergy;
- dFinalForce2 = dNewForce2;
- return( STOP_ENERGY_TOL );
+ || (dStepLengthInf == 0.0) ) {
+ if (bPrintProgress)
+ hftn_print_line_ (true, niter+1, neval,
+ dNewEnergy, dNewForce2,
+ nStepType, dTrustRadius, dStepLength2,
+ dAred, -1.0);
+ //---- (IMPLICITLY ACCEPT THE LAST STEP TO THE NEW POINT.)
+ dFinalEnergy = dNewEnergy;
+ dFinalForce2 = dNewForce2;
+ return( STOP_ENERGY_TOL );
}
}
-
+
//---- COMPUTE THE PREDICTED REDUCTION - p^T grad - 0.5 p^T Hp
double dPHP = calc_dot_prod_using_mpi_ (VEC_CG_P, VEC_CG_HD);
double dPred = - dGradDotP - (0.5 * dPHP);
-
+
//---- ACCEPT OR REJECT THE STEP PROPOSED BY THE INNER CG LOOP.
//---- WHEN NEAR A SOLUTION, THE FORCE NORM IS PROBABLY MORE ACCURATE,
//---- SO DON'T ACCEPT A STEP THAT REDUCES ENERGY SOME TINY AMOUNT
//---- WHILE INCREASING THE FORCE NORM.
bool bStepAccepted = (dAred > 0.0)
&& ( (dNewForce2 < dCurrentForce2)
- || (dCurrentForce2 > 1.0e-6));
+ || (dCurrentForce2 > 1.0e-6));
if (bStepAccepted) {
//---- THE STEP IS ACCEPTED.
if (bPrintProgress)
- hftn_print_line_ (true, niter+1, neval, dNewEnergy, dNewForce2,
- nStepType, dTrustRadius, dStepLength2,
- dAred, dPred);
-
+ hftn_print_line_ (true, niter+1, neval, dNewEnergy, dNewForce2,
+ nStepType, dTrustRadius, dStepLength2,
+ dAred, dPred);
+
fix_minimize->store_box();
modify->min_clearstore();
for (int i = 0; i < nvec; i++)
- _daAVectors[VEC_XK][i] = xvec[i];
+ _daAVectors[VEC_XK][i] = xvec[i];
if (nextra_atom) {
- for (int m = 0; m < nextra_atom; m++) {
- double * xatom = xextra_atom[m];
- double * xkAtom = _daExtraAtom[VEC_XK][m];
- int n = extra_nlen[m];
- for (int i = 0; i < n; i++)
- xkAtom[i] = xatom[i];
- }
+ for (int m = 0; m < nextra_atom; m++) {
+ double * xatom = xextra_atom[m];
+ double * xkAtom = _daExtraAtom[VEC_XK][m];
+ int n = extra_nlen[m];
+ for (int i = 0; i < n; i++)
+ xkAtom[i] = xatom[i];
+ }
}
if (nextra_global)
- modify->min_store();
-
+ modify->min_store();
+
if (niter > 0)
- eprevious = dCurrentEnergy;
+ eprevious = dCurrentEnergy;
dCurrentEnergy = dNewEnergy;
dCurrentForce2 = dNewForce2;
bHaveEvaluatedAtX = true;
-
+
if (nStepType == CGSTEP_NEWTON)
- dLastNewtonStep2 = dStepLength2;
-
+ dLastNewtonStep2 = dStepLength2;
+
//---- UPDATE THE TRUST REGION BASED ON AGREEMENT BETWEEN
//---- THE ACTUAL REDUCTION AND THE PREDICTED MODEL REDUCTION.
if ((dAred > 0.75 * dPred) && (dStepLength2 >= 0.99 * dTrustRadius))
- dTrustRadius = 2.0 * dTrustRadius;
+ dTrustRadius = 2.0 * dTrustRadius;
dTrustRadius = MIN (dTrustRadius, dMaxTrustRadius);
-
+
//---- DMAX VIOLATIONS TRUNCATE THE CG STEP WITHOUT COMPARISONS;
//---- BETTER TO ADJUST THE TRUST REGION SO DMAX STOPS HAPPENING.
if (nStepType == CGSTEP_TO_DMAX) {
- if (dStepLength2 <= MACHINE_EPS)
- dTrustRadius = 0.1 * dTrustRadius;
- else
- dTrustRadius = MIN (dTrustRadius, 2.0 * dStepLength2);
+ if (dStepLength2 <= MACHINE_EPS)
+ dTrustRadius = 0.1 * dTrustRadius;
+ else
+ dTrustRadius = MIN (dTrustRadius, 2.0 * dStepLength2);
}
}
else {
//---- THE STEP IS REJECTED.
if (bPrintProgress)
- hftn_print_line_ (false, niter+1, neval,
- dCurrentEnergy, dCurrentForce2,
- nStepType, dTrustRadius, dStepLength2,
- dAred, dPred);
-
+ hftn_print_line_ (false, niter+1, neval,
+ dCurrentEnergy, dCurrentForce2,
+ nStepType, dTrustRadius, dStepLength2,
+ dAred, dPred);
+
//---- RESTORE THE LAST X_K POSITION.
if (nextra_global)
- modify->min_step (0.0, _daExtraGlobal[VEC_CG_P]);
+ modify->min_step (0.0, _daExtraGlobal[VEC_CG_P]);
for (int i = 0; i < nvec; i++)
- xvec[i] = _daAVectors[VEC_XK][i];
+ xvec[i] = _daAVectors[VEC_XK][i];
if (nextra_atom) {
- for (int m = 0; m < nextra_atom; m++) {
- double * xatom = xextra_atom[m];
- double * xkAtom = _daExtraAtom[VEC_XK][m];
- int n = extra_nlen[m];
- for (int i = 0; i < n; i++)
- xatom[i] = xkAtom[i];
- requestor[m]->min_x_set(m);
- }
+ for (int m = 0; m < nextra_atom; m++) {
+ double * xatom = xextra_atom[m];
+ double * xkAtom = _daExtraAtom[VEC_XK][m];
+ int n = extra_nlen[m];
+ for (int i = 0; i < n; i++)
+ xatom[i] = xkAtom[i];
+ requestor[m]->min_x_set(m);
+ }
}
modify->min_clearstore();
bHaveEvaluatedAtX = false;
-
+
//---- UPDATE THE TRUST REGION.
//---- EXPERIMENTS INDICATE NEGATIVE CURVATURE CAN TAKE A BAD
//---- STEP A LONG WAY, SO BE MORE AGGRESSIVE IN THIS CASE.
//---- ALSO, IF NEAR A SOLUTION AND DONE WITH NEWTON STEPS,
//---- THEN REDUCE TO SOMETHING NEAR THE LAST GOOD NEWTON STEP.
if ((nStepType == CGSTEP_NEGATIVE_CURVATURE) && (-dAred > dPred))
- dTrustRadius = 0.10 * MIN (dTrustRadius, dStepLength2);
+ dTrustRadius = 0.10 * MIN (dTrustRadius, dStepLength2);
else if ( (nStepType == CGSTEP_TO_DMAX)
- && (dStepLength2 <= MACHINE_EPS))
- dTrustRadius = 0.10 * dTrustRadius;
+ && (dStepLength2 <= MACHINE_EPS))
+ dTrustRadius = 0.10 * dTrustRadius;
else if (-dAred > dPred)
- dTrustRadius = 0.20 * MIN (dTrustRadius, dStepLength2);
+ dTrustRadius = 0.20 * MIN (dTrustRadius, dStepLength2);
else
- dTrustRadius = 0.25 * MIN (dTrustRadius, dStepLength2);
-
+ dTrustRadius = 0.25 * MIN (dTrustRadius, dStepLength2);
+
if ( (nStepType != CGSTEP_NEWTON)
- && (dCurrentForce2 < sqrt (MACHINE_EPS)))
- dTrustRadius = MIN (dTrustRadius, 2.0 * dLastNewtonStep2);
-
+ && (dCurrentForce2 < sqrt (MACHINE_EPS)))
+ dTrustRadius = MIN (dTrustRadius, 2.0 * dLastNewtonStep2);
+
dLastNewtonStep2 = dMaxTrustRadius;
-
+
//---- STOP IF THE TRUST RADIUS IS TOO SMALL TO CONTINUE.
if ( (dTrustRadius <= 0.0)
- || (dTrustRadius <= MACHINE_EPS * MAX (1.0, dXInf))) {
- dFinalEnergy = dCurrentEnergy;
- dFinalForce2 = dCurrentForce2;
- return( STOP_TR_TOO_SMALL );
+ || (dTrustRadius <= MACHINE_EPS * MAX (1.0, dXInf))) {
+ dFinalEnergy = dCurrentEnergy;
+ dFinalForce2 = dCurrentForce2;
+ return( STOP_TR_TOO_SMALL );
}
}
-
+
//---- OUTPUT FOR thermo, dump, restart FILES.
if (output->next == update->ntimestep) {
//---- IF THE LAST STEP WAS REJECTED, THEN REEVALUATE ENERGY AND
//---- FORCES AT THE OLD POINT SO THE OUTPUT DOES NOT DISPLAY
//---- THE INCREASED ENERGY OF THE REJECTED STEP.
if (bStepAccepted == false) {
- dCurrentEnergy = energy_force (1);
- neval++;
+ dCurrentEnergy = energy_force (1);
+ neval++;
}
timer->stamp();
output->write (update->ntimestep);
timer->stamp (TIME_OUTPUT);
}
-
+
//---- RETURN IF NUMBER OF EVALUATIONS EXCEEDED.
if (neval >= update->max_eval) {
dFinalEnergy = dCurrentEnergy;
dFinalForce2 = dCurrentForce2;
return( STOP_MAX_FORCE_EVALS );
}
-
+
} //-- END for LOOP OVER niter
-
+
dFinalEnergy = dCurrentEnergy;
dFinalForce2 = dCurrentForce2;
return( STOP_MAX_ITER );
@@ -592,16 +592,16 @@ int MinHFTN::execute_hftn_(const bool bPrintProgress,
------------------------------------------------------------------------- */
bool MinHFTN::compute_inner_cg_step_(const double dTrustRadius,
- const double dForceTol,
- const int nMaxEvals,
- const bool bHaveEvalAtXin,
- const double dEnergyAtXin,
- const double dForce2AtXin,
- double & dEnergyAtXout,
- double & dForce2AtXout,
- int & nStepType,
- double & dStepLength2,
- double & dStepLengthInf)
+ const double dForceTol,
+ const int nMaxEvals,
+ const bool bHaveEvalAtXin,
+ const double dEnergyAtXin,
+ const double dForce2AtXin,
+ double & dEnergyAtXout,
+ double & dForce2AtXout,
+ int & nStepType,
+ double & dStepLength2,
+ double & dStepLengthInf)
{
//---- SET p_0 = 0.
if (nextra_global) {
@@ -615,11 +615,11 @@ bool MinHFTN::compute_inner_cg_step_(const double dTrustRadius,
double * pAtom = _daExtraAtom[VEC_CG_P][m];
int n = extra_nlen[m];
for (int i = 0; i < n; i++)
- pAtom[i] = 0.0;
+ pAtom[i] = 0.0;
}
}
double dPP = 0.0;
-
+
//---- OBTAIN THE ENERGY AND FORCES AT THE INPUT POSITION.
double dEnergyAtX = dEnergyAtXin;
double dForce2AtX = dForce2AtXin;
@@ -628,7 +628,7 @@ bool MinHFTN::compute_inner_cg_step_(const double dTrustRadius,
neval++;
dForce2AtX = sqrt (fnorm_sqr());
}
-
+
//---- RETURN IMMEDIATELY IF THE FORCE TOLERANCE IS ALREADY MET.
//---- THE STEP TYPE INFORMS THE CALLER THAT ENERGY AND FORCES HAVE
//---- BEEN EVALUATED.
@@ -640,7 +640,7 @@ bool MinHFTN::compute_inner_cg_step_(const double dTrustRadius,
dStepLengthInf = 0.0;
return( true );
}
-
+
//---- r_0 = -grad (FIRST SEARCH DIRECTION IS STEEPEST DESCENT)
//---- d_0 = r_0
//---- REMEMBER THAT FORCES = -GRADIENT.
@@ -661,14 +661,14 @@ bool MinHFTN::compute_inner_cg_step_(const double dTrustRadius,
double * dAtom = _daExtraAtom[VEC_CG_D][m];
int n = extra_nlen[m];
for (int i = 0; i < n; i++) {
- rAtom[i] = fatom[i];
- dAtom[i] = fatom[i];
+ rAtom[i] = fatom[i];
+ dAtom[i] = fatom[i];
}
}
}
double dRR = dForce2AtX * dForce2AtX;
double dR0norm2 = sqrt (dRR);
-
+
//---- LIMIT THE NUMBER OF INNER CG ITERATIONS.
//---- BASE IT ON THE NUMBER OF UNKNOWNS, OR MAXIMUM EVALUATIONS ASSUMING
//---- FORWARD DIFFERENCES ARE USED.
@@ -678,92 +678,92 @@ bool MinHFTN::compute_inner_cg_step_(const double dTrustRadius,
nLimit1 = MIN (_nNumUnknowns, 100);
int nLimit2 = (nMaxEvals - neval) / 2;
int nMaxInnerIters = MIN (nLimit1, nLimit2);
-
+
//---- FURTHER LIMIT ITERATIONS IF NEAR MACHINE ROUNDOFF.
//---- THE METHOD CAN WASTE A LOT EVALUATIONS WITH LITTLE PAYOFF PROSPECT.
if (dForce2AtX < (sqrt (MACHINE_EPS) * MAX (1.0, fabs (dEnergyAtX))) )
nMaxInnerIters = MIN (nMaxInnerIters, _nNumUnknowns / 20);
-
+
bool bUseForwardDiffs = (dForce2AtX > 1000.0 * sqrt (MACHINE_EPS));
-
+
//---- MAIN CG LOOP.
for (int nInnerIter = 0; nInnerIter < nMaxInnerIters; nInnerIter++) {
//---- COMPUTE HESSIAN-VECTOR PRODUCT: H(x_k) d_i.
double dDummyEnergy;
evaluate_dir_der_ (bUseForwardDiffs,
- VEC_CG_D,
- VEC_CG_HD,
- false,
- dDummyEnergy);
-
+ VEC_CG_D,
+ VEC_CG_HD,
+ false,
+ dDummyEnergy);
+
//---- CALCULATE d_i^T H d_i AND d_i^T d_i.
double dDHD;
double dDD;
calc_dhd_dd_using_mpi_ (dDHD, dDD);
-
+
//---- HANDLE NEGATIVE CURVATURE.
if (dDHD <= (MACHINE_EPS * dDD)) {
//---- PROJECT BOTH DIRECTIONS TO THE TRUST RADIUS AND DECIDE
//---- WHICH MAKES A BETTER PREDICTED REDUCTION.
//---- p_i^T H(x_k) d_i AND grad_i^T d_i.
-
+
double dPdotD = calc_dot_prod_using_mpi_ (VEC_CG_P, VEC_CG_D);
double dPdotHD = calc_dot_prod_using_mpi_ (VEC_CG_P, VEC_CG_HD);
-
+
//---- MOVE TO X_K AND COMPUTE ENERGY AND FORCES.
if (nextra_global)
- modify->min_step (0.0, _daExtraGlobal[VEC_CG_P]);
+ modify->min_step (0.0, _daExtraGlobal[VEC_CG_P]);
for (int i = 0; i < nvec; i++)
- xvec[i] = _daAVectors[VEC_XK][i];
+ xvec[i] = _daAVectors[VEC_XK][i];
if (nextra_atom) {
- for (int m = 0; m < nextra_atom; m++) {
- double * xatom = xextra_atom[m];
- double * xkAtom = _daExtraAtom[VEC_XK][m];
- int n = extra_nlen[m];
- for (int i = 0; i < n; i++)
- xatom[i] = xkAtom[i];
- requestor[m]->min_x_set(m);
- }
+ for (int m = 0; m < nextra_atom; m++) {
+ double * xatom = xextra_atom[m];
+ double * xkAtom = _daExtraAtom[VEC_XK][m];
+ int n = extra_nlen[m];
+ for (int i = 0; i < n; i++)
+ xatom[i] = xkAtom[i];
+ requestor[m]->min_x_set(m);
+ }
}
dEnergyAtX = energy_force (0);
neval++;
-
+
double dGradDotD = calc_grad_dot_v_using_mpi_ (VEC_CG_D);
-
+
double tau = compute_to_tr_ (dPP, dPdotD, dDD, dTrustRadius,
- true, dDHD, dPdotHD, dGradDotD);
-
+ true, dDHD, dPdotHD, dGradDotD);
+
//---- MOVE THE POINT.
if (nextra_global) {
- double * pGlobal = _daExtraGlobal[VEC_CG_P];
- double * dGlobal = _daExtraGlobal[VEC_CG_D];
- for (int i = 0; i < nextra_global; i++) {
- pGlobal[i] += tau * dGlobal[i];
- }
+ double * pGlobal = _daExtraGlobal[VEC_CG_P];
+ double * dGlobal = _daExtraGlobal[VEC_CG_D];
+ for (int i = 0; i < nextra_global; i++) {
+ pGlobal[i] += tau * dGlobal[i];
+ }
}
for (int i = 0; i < nvec; i++)
- _daAVectors[VEC_CG_P][i] += tau * _daAVectors[VEC_CG_D][i];
+ _daAVectors[VEC_CG_P][i] += tau * _daAVectors[VEC_CG_D][i];
if (nextra_atom) {
- for (int m = 0; m < nextra_atom; m++) {
- double * pAtom = _daExtraAtom[VEC_CG_P][m];
- double * dAtom = _daExtraAtom[VEC_CG_D][m];
- int n = extra_nlen[m];
- for (int i = 0; i < n; i++)
- pAtom[i] += tau * dAtom[i];
- }
+ for (int m = 0; m < nextra_atom; m++) {
+ double * pAtom = _daExtraAtom[VEC_CG_P][m];
+ double * dAtom = _daExtraAtom[VEC_CG_D][m];
+ int n = extra_nlen[m];
+ for (int i = 0; i < n; i++)
+ pAtom[i] += tau * dAtom[i];
+ }
}
-
+
nStepType = CGSTEP_NEGATIVE_CURVATURE;
calc_plengths_using_mpi_ (dStepLength2, dStepLengthInf);
return( true );
}
-
+
//---- COMPUTE THE OPTIMAL STEP LENGTH BASED ON THE QUADRATIC CG MODEL.
double dAlpha = dRR / dDHD;
-
+
//---- MIGHT WANT TO ENABLE THIS TO DEBUG INTERNAL CG STEPS.
//fprintf (_fpPrint, " alpha = %11.8f neval=%4d\n", dAlpha, neval);
-
+
//---- p_i+1 = p_i + alpha_i d_i
//---- (SAVE THE CURRENT p_i IN CASE THE STEP HAS TO BE SHORTENED.)
if (nextra_global) {
@@ -771,8 +771,8 @@ bool MinHFTN::compute_inner_cg_step_(const double dTrustRadius,
double * dGlobal = _daExtraGlobal[VEC_CG_D];
double * d1Global = _daExtraGlobal[VEC_DIF1];
for (int i = 0; i < nextra_global; i++) {
- d1Global[i] = pGlobal[i];
- pGlobal[i] += dAlpha * dGlobal[i];
+ d1Global[i] = pGlobal[i];
+ pGlobal[i] += dAlpha * dGlobal[i];
}
}
for (int i = 0; i < nvec; i++) {
@@ -781,24 +781,24 @@ bool MinHFTN::compute_inner_cg_step_(const double dTrustRadius,
}
if (nextra_atom) {
for (int m = 0; m < nextra_atom; m++) {
- double * pAtom = _daExtraAtom[VEC_CG_P][m];
- double * dAtom = _daExtraAtom[VEC_CG_D][m];
- double * d1Atom = _daExtraAtom[VEC_DIF1][m];
- int n = extra_nlen[m];
- for (int i = 0; i < n; i++) {
- d1Atom[i] = pAtom[i];
- pAtom[i] += dAlpha * dAtom[i];
- }
+ double * pAtom = _daExtraAtom[VEC_CG_P][m];
+ double * dAtom = _daExtraAtom[VEC_CG_D][m];
+ double * d1Atom = _daExtraAtom[VEC_DIF1][m];
+ int n = extra_nlen[m];
+ for (int i = 0; i < n; i++) {
+ d1Atom[i] = pAtom[i];
+ pAtom[i] += dAlpha * dAtom[i];
+ }
}
}
-
+
//---- COMPUTE VECTOR PRODUCTS p_i+1^T p_i+1 AND p_i^T d_i.
double dPnewDotPnew;
double dPoldDotD;
calc_ppnew_pdold_using_mpi_ (dPnewDotPnew, dPoldDotD);
-
+
nStepType = CGSTEP_UNDETERMINED;
-
+
//---- IF STEP LENGTH IS TOO LARGE, THEN REDUCE IT AND RETURN.
double tau;
if (step_exceeds_TR_ (dTrustRadius, dPP, dPoldDotD, dDD, tau)) {
@@ -813,36 +813,36 @@ bool MinHFTN::compute_inner_cg_step_(const double dTrustRadius,
calc_plengths_using_mpi_ (dStepLength2, dStepLengthInf);
return( true );
}
-
+
dStepLength2 = sqrt (dPnewDotPnew);
-
+
//---- r_i+1 = r_i - alpha * H d_i
if (nextra_global) {
double * rGlobal = _daExtraGlobal[VEC_CG_R];
double * hdGlobal = _daExtraGlobal[VEC_CG_HD];
for (int i = 0; i < nextra_global; i++)
- rGlobal[i] -= dAlpha * hdGlobal[i];
+ rGlobal[i] -= dAlpha * hdGlobal[i];
}
for (int i = 0; i < nvec; i++)
_daAVectors[VEC_CG_R][i] -= dAlpha * _daAVectors[VEC_CG_HD][i];
if (nextra_atom) {
for (int m = 0; m < nextra_atom; m++) {
- double * rAtom = _daExtraAtom[VEC_CG_R][m];
- double * hdAtom = _daExtraAtom[VEC_CG_HD][m];
- int n = extra_nlen[m];
- for (int i = 0; i < n; i++)
- rAtom[i] -= dAlpha * hdAtom[i];
+ double * rAtom = _daExtraAtom[VEC_CG_R][m];
+ double * hdAtom = _daExtraAtom[VEC_CG_HD][m];
+ int n = extra_nlen[m];
+ for (int i = 0; i < n; i++)
+ rAtom[i] -= dAlpha * hdAtom[i];
}
}
double dRnewDotRnew = calc_dot_prod_using_mpi_ (VEC_CG_R, VEC_CG_R);
-
+
//---- IF RESIDUAL IS SMALL ENOUGH, THEN RETURN THE CURRENT STEP.
if (sqrt (dRnewDotRnew) < dForceTol * dR0norm2) {
nStepType = CGSTEP_NEWTON;
calc_plengths_using_mpi_ (dStepLength2, dStepLengthInf);
return( true );
}
-
+
//---- beta = r_i+1^T r_i+1 / r_i^T r_i
//---- d_i+1 = r_i+1 + beta d_i
double dBeta = dRnewDotRnew / dRR;
@@ -850,29 +850,29 @@ bool MinHFTN::compute_inner_cg_step_(const double dTrustRadius,
double * rGlobal = _daExtraGlobal[VEC_CG_R];
double * dGlobal = _daExtraGlobal[VEC_CG_D];
for (int i = 0; i < nextra_global; i++)
- dGlobal[i] = rGlobal[i] + dBeta * dGlobal[i];
+ dGlobal[i] = rGlobal[i] + dBeta * dGlobal[i];
}
for (int i = 0; i < nvec; i++)
_daAVectors[VEC_CG_D][i] = _daAVectors[VEC_CG_R][i]
- + dBeta * _daAVectors[VEC_CG_D][i];
+ + dBeta * _daAVectors[VEC_CG_D][i];
if (nextra_atom) {
for (int m = 0; m < nextra_atom; m++) {
- double * rAtom = _daExtraAtom[VEC_CG_R][m];
- double * dAtom = _daExtraAtom[VEC_CG_D][m];
- int n = extra_nlen[m];
- for (int i = 0; i < n; i++)
- dAtom[i] = rAtom[i] + dBeta * dAtom[i];
+ double * rAtom = _daExtraAtom[VEC_CG_R][m];
+ double * dAtom = _daExtraAtom[VEC_CG_D][m];
+ int n = extra_nlen[m];
+ for (int i = 0; i < n; i++)
+ dAtom[i] = rAtom[i] + dBeta * dAtom[i];
}
}
-
+
//---- CONTINUE THE LOOP.
dRR = dRnewDotRnew;
dPP = dPnewDotPnew;
}
-
+
nStepType = CGSTEP_MAX_INNER_ITERS;
calc_plengths_using_mpi_ (dStepLength2, dStepLengthInf);
- return( true );
+ return( true );
}
/* ----------------------------------------------------------------------
@@ -884,24 +884,24 @@ double MinHFTN::calc_xinf_using_mpi_(void) const
double dXInfLocal = 0.0;
for (int i = 0; i < nvec; i++)
dXInfLocal = MAX(dXInfLocal,fabs(xvec[i]));
-
+
double dXInf;
MPI_Allreduce (&dXInfLocal, &dXInf, 1, MPI_DOUBLE, MPI_MAX, world);
-
+
if (nextra_atom) {
for (int m = 0; m < nextra_atom; m++) {
double * xatom = xextra_atom[m];
int n = extra_nlen[m];
double dXInfLocalExtra = 0.0;
for (int i = 0; i < n; i++)
- dXInfLocalExtra = MAX (dXInfLocalExtra, fabs (xatom[i]));
+ dXInfLocalExtra = MAX (dXInfLocalExtra, fabs (xatom[i]));
double dXInfExtra;
MPI_Allreduce (&dXInfLocalExtra, &dXInfExtra,
- 1, MPI_DOUBLE, MPI_MAX, world);
+ 1, MPI_DOUBLE, MPI_MAX, world);
dXInf = MAX (dXInf, dXInfExtra);
}
}
-
+
return( dXInf );
}
@@ -911,7 +911,7 @@ double MinHFTN::calc_xinf_using_mpi_(void) const
------------------------------------------------------------------------- */
double MinHFTN::calc_dot_prod_using_mpi_(const int nIx1,
- const int nIx2) const
+ const int nIx2) const
{
double dDotLocal = 0.0;
for (int i = 0; i < nvec; i++)
@@ -922,13 +922,13 @@ double MinHFTN::calc_dot_prod_using_mpi_(const int nIx1,
double * i2Atom = _daExtraAtom[nIx2][m];
int n = extra_nlen[m];
for (int i = 0; i < n; i++)
- dDotLocal += i1Atom[i] * i2Atom[i];
+ dDotLocal += i1Atom[i] * i2Atom[i];
}
}
-
+
double dDot;
MPI_Allreduce (&dDotLocal, &dDot, 1, MPI_DOUBLE, MPI_SUM, world);
-
+
if (nextra_global) {
for (int i = 0; i < nextra_global; i++) {
double * i1Global = _daExtraGlobal[nIx1];
@@ -936,7 +936,7 @@ double MinHFTN::calc_dot_prod_using_mpi_(const int nIx1,
dDot += i1Global[i] * i2Global[i];
}
}
-
+
return( dDot );
}
@@ -948,7 +948,7 @@ double MinHFTN::calc_grad_dot_v_using_mpi_(const int nIx) const
{
//---- ASSUME THAT FORCES HAVE BEEN EVALUATED AT DESIRED ATOM POSITIONS.
//---- REMEMBER THAT FORCES = -GRADIENT.
-
+
double dGradDotVLocal = 0.0;
for (int i = 0; i < nvec; i++)
dGradDotVLocal += - _daAVectors[nIx][i] * fvec[i];
@@ -958,20 +958,20 @@ double MinHFTN::calc_grad_dot_v_using_mpi_(const int nIx) const
double * iAtom = _daExtraAtom[nIx][m];
int n = extra_nlen[m];
for (int i = 0; i < n; i++)
- dGradDotVLocal += - iAtom[i] * fatom[i];
+ dGradDotVLocal += - iAtom[i] * fatom[i];
}
}
-
+
double dGradDotV;
MPI_Allreduce (&dGradDotVLocal, &dGradDotV, 1, MPI_DOUBLE, MPI_SUM, world);
-
+
if (nextra_global) {
for (int i = 0; i < nextra_global; i++) {
double * iGlobal = _daExtraGlobal[nIx];
dGradDotV += - iGlobal[i] * fextra[i];
}
}
-
+
return( dGradDotV );
}
@@ -980,7 +980,7 @@ double MinHFTN::calc_grad_dot_v_using_mpi_(const int nIx) const
------------------------------------------------------------------------- */
void MinHFTN::calc_dhd_dd_using_mpi_(double & dDHD,
- double & dDD) const
+ double & dDD) const
{
double dDHDLocal = 0.0;
double dDDLocal = 0.0;
@@ -994,18 +994,18 @@ void MinHFTN::calc_dhd_dd_using_mpi_(double & dDHD,
double * hdAtom = _daExtraAtom[VEC_CG_HD][m];
int n = extra_nlen[m];
for (int i = 0; i < n; i++) {
- dDHDLocal += dAtom[i] * hdAtom[i];
- dDDLocal += dAtom[i] * dAtom[i];
+ dDHDLocal += dAtom[i] * hdAtom[i];
+ dDDLocal += dAtom[i] * dAtom[i];
}
}
}
-
+
double daDotsLocal[2];
daDotsLocal[0] = dDHDLocal;
daDotsLocal[1] = dDDLocal;
double daDots[2];
MPI_Allreduce (daDotsLocal, daDots, 2, MPI_DOUBLE, MPI_SUM, world);
-
+
if (nextra_global) {
double * dGlobal = _daExtraGlobal[VEC_CG_D];
double * hdGlobal = _daExtraGlobal[VEC_CG_HD];
@@ -1016,7 +1016,7 @@ void MinHFTN::calc_dhd_dd_using_mpi_(double & dDHD,
}
dDHD = daDots[0];
dDD = daDots[1];
-
+
return;
}
@@ -1025,7 +1025,7 @@ void MinHFTN::calc_dhd_dd_using_mpi_(double & dDHD,
------------------------------------------------------------------------- */
void MinHFTN::calc_ppnew_pdold_using_mpi_(double & dPnewDotPnew,
- double & dPoldDotD) const
+ double & dPoldDotD) const
{
double dPnewDotPnewLocal = 0.0;
double dPoldDotDLocal = 0.0;
@@ -1042,18 +1042,18 @@ void MinHFTN::calc_ppnew_pdold_using_mpi_(double & dPnewDotPnew,
double * d1Atom = _daExtraAtom[VEC_DIF1][m];
int n = extra_nlen[m];
for (int i = 0; i < n; i++) {
- dPnewDotPnewLocal += pAtom[i] * pAtom[i];
- dPoldDotDLocal += d1Atom[i] * dAtom[i];
+ dPnewDotPnewLocal += pAtom[i] * pAtom[i];
+ dPoldDotDLocal += d1Atom[i] * dAtom[i];
}
}
}
-
+
double daDotsLocal[2];
daDotsLocal[0] = dPnewDotPnewLocal;
daDotsLocal[1] = dPoldDotDLocal;
double daDots[2];
MPI_Allreduce (daDotsLocal, daDots, 2, MPI_DOUBLE, MPI_SUM, world);
-
+
if (nextra_global) {
for (int i = 0; i < nextra_global; i++) {
double * dGlobal = _daExtraGlobal[VEC_CG_D];
@@ -1063,10 +1063,10 @@ void MinHFTN::calc_ppnew_pdold_using_mpi_(double & dPnewDotPnew,
daDots[1] += d1Global[i] * dGlobal[i];
}
}
-
+
dPnewDotPnew = daDots[0];
dPoldDotD = daDots[1];
-
+
return;
}
@@ -1075,7 +1075,7 @@ void MinHFTN::calc_ppnew_pdold_using_mpi_(double & dPnewDotPnew,
------------------------------------------------------------------------- */
void MinHFTN::calc_plengths_using_mpi_(double & dStepLength2,
- double & dStepLengthInf) const
+ double & dStepLengthInf) const
{
double dPPLocal = 0.0;
double dPInfLocal = 0.0;
@@ -1088,18 +1088,18 @@ void MinHFTN::calc_plengths_using_mpi_(double & dStepLength2,
double * pAtom = _daExtraAtom[VEC_CG_P][m];
int n = extra_nlen[m];
for (int i = 0; i < n; i++) {
- dPPLocal += pAtom[i] * pAtom[i];
- dPInfLocal = MAX (dPInfLocal, fabs (pAtom[i]));
+ dPPLocal += pAtom[i] * pAtom[i];
+ dPInfLocal = MAX (dPInfLocal, fabs (pAtom[i]));
}
}
}
-
+
double dPP;
MPI_Allreduce (&dPPLocal, &dPP, 1, MPI_DOUBLE, MPI_SUM, world);
-
+
double dPInf;
MPI_Allreduce (&dPInfLocal, &dPInf, 1, MPI_DOUBLE, MPI_MAX, world);
-
+
if (nextra_global) {
for (int i = 0; i < nextra_global; i++) {
double * pGlobal = _daExtraGlobal[VEC_CG_P];
@@ -1107,7 +1107,7 @@ void MinHFTN::calc_plengths_using_mpi_(double & dStepLength2,
dPInf = MAX (dPInf, fabs (pGlobal[i]));
}
}
-
+
dStepLength2 = sqrt (dPP);
dStepLengthInf = dPInf;
return;
@@ -1118,21 +1118,21 @@ void MinHFTN::calc_plengths_using_mpi_(double & dStepLength2,
------------------------------------------------------------------------- */
bool MinHFTN::step_exceeds_TR_(const double dTrustRadius,
- const double dPP,
- const double dPD,
- const double dDD,
- double & dTau) const
+ const double dPP,
+ const double dPD,
+ const double dDD,
+ double & dTau) const
{
double dPnewNorm2;
double dPnewNormInf;
calc_plengths_using_mpi_ (dPnewNorm2, dPnewNormInf);
-
+
if (dPnewNorm2 > dTrustRadius) {
dTau = compute_to_tr_ (dPP, dPD, dDD, dTrustRadius,
- false, 0.0, 0.0, 0.0);
+ false, 0.0, 0.0, 0.0);
return( true );
}
-
+
//---- STEP LENGTH IS NOT TOO LONG.
dTau = 0.0;
return( false );
@@ -1151,7 +1151,7 @@ bool MinHFTN::step_exceeds_TR_(const double dTrustRadius,
bool MinHFTN::step_exceeds_DMAX_(void) const
{
double dAlpha = dmax * sqrt((double) _nNumUnknowns);
-
+
double dPInfLocal = 0.0;
for (int i = 0; i < nvec; i++)
dPInfLocal = MAX (dPInfLocal, fabs (_daAVectors[VEC_CG_P][i]));
@@ -1161,22 +1161,22 @@ bool MinHFTN::step_exceeds_DMAX_(void) const
return( true );
if (dPInf > MACHINE_EPS)
dAlpha = MIN (dAlpha, dmax / dPInf);
-
+
if (nextra_atom) {
for (int m = 0; m < nextra_atom; m++) {
double * pAtom = _daExtraAtom[VEC_CG_P][m];
dPInfLocal = 0.0;
int n = extra_nlen[m];
for (int i = 0; i < n; i++)
- dPInfLocal = MAX (dPInfLocal, fabs (pAtom[i]));
+ dPInfLocal = MAX (dPInfLocal, fabs (pAtom[i]));
MPI_Allreduce (&dPInfLocal, &dPInf, 1, MPI_DOUBLE, MPI_MAX, world);
if (dPInf > extra_max[m])
- return( true );
+ return( true );
if (dPInf > MACHINE_EPS)
- dAlpha = MIN (dAlpha, extra_max[m] / dPInf);
+ dAlpha = MIN (dAlpha, extra_max[m] / dPInf);
}
}
-
+
if (nextra_global) {
//---- IF THE MAXIMUM DISTANCE THAT THE GLOBAL BOX CONSTRAINT WILL
//---- ALLOW IS SMALLER THAN THE PROPOSED DISTANCE, THEN THE STEP
@@ -1185,7 +1185,7 @@ bool MinHFTN::step_exceeds_DMAX_(void) const
if (dAlphaExtra < dAlpha)
return( true );
}
-
+
//---- STEP LENGTH IS NOT TOO LONG.
return( false );
}
@@ -1215,7 +1215,7 @@ void MinHFTN::adjust_step_to_tau_(const double tau)
double * d1Atom = _daExtraAtom[VEC_DIF1][m];
int n = extra_nlen[m];
for (int i = 0; i < n; i++)
- pAtom[i] = d1Atom[i] + (tau * dAtom[i]);
+ pAtom[i] = d1Atom[i] + (tau * dAtom[i]);
}
}
return;
@@ -1240,41 +1240,41 @@ void MinHFTN::adjust_step_to_tau_(const double tau)
------------------------------------------------------------------------- */
double MinHFTN::compute_to_tr_(const double dPP,
- const double dPD,
- const double dDD,
- const double dTrustRadius,
- const bool bConsiderBothRoots,
- const double dDHD,
- const double dPdotHD,
- const double dGradDotD) const
+ const double dPD,
+ const double dDD,
+ const double dTrustRadius,
+ const bool bConsiderBothRoots,
+ const double dDHD,
+ const double dPdotHD,
+ const double dGradDotD) const
{
//---- SOLVE A QUADRATIC EQUATION FOR TAU.
//---- THE COEFFICIENTS ARE SUCH THAT THERE ARE ALWAYS TWO REAL ROOTS,
//---- ONE POSITIVE AND ONE NEGATIVE.
-
+
//---- CHECK FOR ERRONEOUS DATA.
if ( (dDD <= 0.0) || (dPP < 0.0) || (dTrustRadius < 0.0)
- || (dTrustRadius * dTrustRadius < dPP) ) {
+ || (dTrustRadius * dTrustRadius < dPP) ) {
printf ("HFTN internal error - bad data given to compute_to_tr_()\n");
return( 0.0 );
}
-
+
double dTRsqrd = dTrustRadius * dTrustRadius;
double dDiscr = (dPD * dPD) - (dDD * (dPP - dTRsqrd));
dDiscr = MAX (0.0, dDiscr); //-- SHOULD NEVER BE NEGATIVE
dDiscr = sqrt (dDiscr);
-
+
double dRootPos = (-dPD + dDiscr) / dDD;
double dRootNeg = (-dPD - dDiscr) / dDD;
-
+
if (bConsiderBothRoots == false)
return( dRootPos );
-
+
//---- EVALUATE THE CG OBJECTIVE FUNCTION FOR EACH ROOT.
double dTmpTerm = dGradDotD + dPdotHD;
double dCgRedPos = (dRootPos * dTmpTerm) + (0.5 * dRootPos*dRootPos * dDHD);
double dCgRedNeg = (dRootNeg * dTmpTerm) + (0.5 * dRootNeg*dRootNeg * dDHD);
-
+
if ((-dCgRedPos) > (-dCgRedNeg))
return( dRootPos );
else
@@ -1286,7 +1286,7 @@ double MinHFTN::compute_to_tr_(const double dPP,
Compute the directional derivative using a finite difference approximation.
This is equivalent to the Hessian times direction vector p.
As a side effect, the method computes the energy and forces at x.
-
+
On input these must be defined:
atom->x - positions at x
atom->f - ignored
@@ -1300,7 +1300,7 @@ double MinHFTN::compute_to_tr_(const double dPP,
During processing these are modified:
VEC_DIF1
VEC_DIF2
-
+
@param[in] bUseForwardDiffs - if true use forward difference approximation,
else use central difference
@param[in] nIxDir - VEC_ index of the direction
@@ -1312,10 +1312,10 @@ double MinHFTN::compute_to_tr_(const double dPP,
------------------------------------------------------------------------- */
void MinHFTN::evaluate_dir_der_(const bool bUseForwardDiffs,
- const int nIxDir,
- const int nIxResult,
- const bool bEvaluateAtX,
- double & dNewEnergy)
+ const int nIxDir,
+ const int nIxResult,
+ const bool bEvaluateAtX,
+ double & dNewEnergy)
{
//---- COMPUTE THE MAGNITUDE OF THE DIRECTION VECTOR: |p|_2.
double dDirNorm2SqrdLocal = 0.0;
@@ -1327,12 +1327,12 @@ void MinHFTN::evaluate_dir_der_(const bool bUseForwardDiffs,
double * iAtom = _daExtraAtom[nIxDir][m];
int n = extra_nlen[m];
for (int i = 0; i < n; i++)
- dDirNorm2SqrdLocal += iAtom[i] * iAtom[i];
+ dDirNorm2SqrdLocal += iAtom[i] * iAtom[i];
}
}
double dDirNorm2Sqrd = 0.0;
MPI_Allreduce (&dDirNorm2SqrdLocal, &dDirNorm2Sqrd,
- 1, MPI_DOUBLE, MPI_SUM, world);
+ 1, MPI_DOUBLE, MPI_SUM, world);
if (nextra_global) {
for (int i = 0; i < nextra_global; i++) {
double * iGlobal = _daExtraGlobal[nIxDir];
@@ -1340,58 +1340,58 @@ void MinHFTN::evaluate_dir_der_(const bool bUseForwardDiffs,
}
}
double dDirNorm2 = sqrt (dDirNorm2Sqrd);
-
+
//---- IF THE STEP IS TOO SMALL, RETURN ZERO FOR THE DERIVATIVE.
if (dDirNorm2 == 0.0) {
for (int i = 0; i < nvec; i++)
_daAVectors[nIxResult][i] = 0.0;
if (nextra_atom) {
for (int m = 0; m < nextra_atom; m++) {
- double * iAtom = _daExtraAtom[nIxDir][m];
- int n = extra_nlen[m];
- for (int i = 0; i < n; i++)
- iAtom[i] = 0;
+ double * iAtom = _daExtraAtom[nIxDir][m];
+ int n = extra_nlen[m];
+ for (int i = 0; i < n; i++)
+ iAtom[i] = 0;
}
}
if (nextra_global) {
for (int i = 0; i < nextra_global; i++)
- _daExtraGlobal[nIxDir][i] = 0.0;
+ _daExtraGlobal[nIxDir][i] = 0.0;
}
-
+
if (bEvaluateAtX) {
dNewEnergy = energy_force (0);
neval++;
}
-
+
return;
}
-
+
//---- FORWARD DIFFERENCES ARE LESS ACCURATE THAN CENTRAL DIFFERENCES,
//---- BUT REQUIRE ONLY 2 ENERGY+FORCE EVALUATIONS VERSUS 3 EVALUATIONS.
//---- STORAGE REQUIREMENTS ARE THE SAME.
-
+
if (bUseForwardDiffs) {
//---- EQUATION IS FROM THE OLD LAMMPS VERSION, SAND98-8201.
double dEps = 2.0 * sqrt (1000.0 * MACHINE_EPS) / dDirNorm2;
-
+
//---- SAVE A COPY OF x.
fix_minimize->store_box();
for (int i = 0; i < nvec; i++)
_daAVectors[VEC_DIF1][i] = xvec[i];
if (nextra_atom) {
for (int m = 0; m < nextra_atom; m++) {
- double * xatom = xextra_atom[m];
- double * d1Atom = _daExtraAtom[VEC_DIF1][m];
- int n = extra_nlen[m];
- for (int i = 0; i < n; i++)
- d1Atom[i] = xatom[i];
+ double * xatom = xextra_atom[m];
+ double * d1Atom = _daExtraAtom[VEC_DIF1][m];
+ int n = extra_nlen[m];
+ for (int i = 0; i < n; i++)
+ d1Atom[i] = xatom[i];
}
}
if (nextra_global) {
modify->min_pushstore();
modify->min_store();
}
-
+
//---- EVALUATE FORCES AT x + eps*p.
if (nextra_global)
modify->min_step (dEps, _daExtraGlobal[nIxDir]);
@@ -1399,34 +1399,34 @@ void MinHFTN::evaluate_dir_der_(const bool bUseForwardDiffs,
xvec[i] += dEps * _daAVectors[nIxDir][i];
if (nextra_atom) {
for (int m = 0; m < nextra_atom; m++) {
- double * xatom = xextra_atom[m];
- double * iAtom = _daExtraAtom[nIxDir][m];
- int n = extra_nlen[m];
- for (int i = 0; i < n; i++)
- xatom[i] += dEps * iAtom[i];
- requestor[m]->min_x_set(m);
+ double * xatom = xextra_atom[m];
+ double * iAtom = _daExtraAtom[nIxDir][m];
+ int n = extra_nlen[m];
+ for (int i = 0; i < n; i++)
+ xatom[i] += dEps * iAtom[i];
+ requestor[m]->min_x_set(m);
}
}
energy_force (0);
neval++;
-
+
//---- STORE THE FORCE IN DIF2.
if (nextra_global) {
for (int i = 0; i < nextra_global; i++)
- _daExtraGlobal[VEC_DIF2][i] = fextra[i];
+ _daExtraGlobal[VEC_DIF2][i] = fextra[i];
}
for (int i = 0; i < nvec; i++)
_daAVectors[VEC_DIF2][i] = fvec[i];
if (nextra_atom) {
for (int m = 0; m < nextra_atom; m++) {
- double * fatom = fextra_atom[m];
- double * d2Atom = _daExtraAtom[VEC_DIF2][m];
- int n = extra_nlen[m];
- for (int i = 0; i < n; i++)
- d2Atom[i] = fatom[i];
+ double * fatom = fextra_atom[m];
+ double * d2Atom = _daExtraAtom[VEC_DIF2][m];
+ int n = extra_nlen[m];
+ for (int i = 0; i < n; i++)
+ d2Atom[i] = fatom[i];
}
}
-
+
//---- MOVE BACK TO x AND EVALUATE FORCES.
if (nextra_global) {
modify->min_step (0.0, _daExtraGlobal[VEC_DIF1]);
@@ -1436,59 +1436,59 @@ void MinHFTN::evaluate_dir_der_(const bool bUseForwardDiffs,
xvec[i] = _daAVectors[VEC_DIF1][i];
if (nextra_atom) {
for (int m = 0; m < nextra_atom; m++) {
- double * xatom = xextra_atom[m];
- double * d1Atom = _daExtraAtom[VEC_DIF1][m];
- int n = extra_nlen[m];
- for (int i = 0; i < n; i++)
- xatom[i] += d1Atom[i];
- requestor[m]->min_x_set(m);
+ double * xatom = xextra_atom[m];
+ double * d1Atom = _daExtraAtom[VEC_DIF1][m];
+ int n = extra_nlen[m];
+ for (int i = 0; i < n; i++)
+ xatom[i] += d1Atom[i];
+ requestor[m]->min_x_set(m);
}
}
dNewEnergy = energy_force (0);
neval++;
-
+
//---- COMPUTE THE DIFFERENCE VECTOR: [grad(x + eps*p) - grad(x)] / eps.
//---- REMEMBER THAT FORCES = -GRADIENT.
for (int i = 0; i < nvec; i++)
_daAVectors[nIxResult][i] = (fvec[i] - _daAVectors[VEC_DIF2][i]) / dEps;
if (nextra_atom) {
for (int m = 0; m < nextra_atom; m++) {
- double * iAtom = _daExtraAtom[nIxResult][m];
- double * d2Atom = _daExtraAtom[VEC_DIF2][m];
- int n = extra_nlen[m];
- for (int i = 0; i < n; i++)
- iAtom[i] = (fextra_atom[m][i] - d2Atom[i]) / dEps;
+ double * iAtom = _daExtraAtom[nIxResult][m];
+ double * d2Atom = _daExtraAtom[VEC_DIF2][m];
+ int n = extra_nlen[m];
+ for (int i = 0; i < n; i++)
+ iAtom[i] = (fextra_atom[m][i] - d2Atom[i]) / dEps;
}
}
if (nextra_global) {
for (int i = 0; i < nextra_global; i++)
- _daExtraGlobal[nIxResult][i]
- = (fextra[i] - _daExtraGlobal[VEC_DIF2][i]) / dEps;
+ _daExtraGlobal[nIxResult][i]
+ = (fextra[i] - _daExtraGlobal[VEC_DIF2][i]) / dEps;
}
}
-
+
else { //-- bUseForwardDiffs == false
//---- EQUATION IS FROM THE OLD LAMMPS VERSION, SAND98-8201.
double dEps = pow (3000.0 * MACHINE_EPS, 0.33333333) / dDirNorm2;
-
+
//---- SAVE A COPY OF x.
fix_minimize->store_box();
for (int i = 0; i < nvec; i++)
_daAVectors[VEC_DIF1][i] = xvec[i];
if (nextra_atom) {
for (int m = 0; m < nextra_atom; m++) {
- double * xatom = xextra_atom[m];
- double * d1Atom = _daExtraAtom[VEC_DIF1][m];
- int n = extra_nlen[m];
- for (int i = 0; i < n; i++)
- d1Atom[i] = xatom[i];
+ double * xatom = xextra_atom[m];
+ double * d1Atom = _daExtraAtom[VEC_DIF1][m];
+ int n = extra_nlen[m];
+ for (int i = 0; i < n; i++)
+ d1Atom[i] = xatom[i];
}
}
if (nextra_global) {
modify->min_pushstore();
modify->min_store();
}
-
+
//---- EVALUATE FORCES AT x + eps*p.
if (nextra_global)
modify->min_step (dEps, _daExtraGlobal[nIxDir]);
@@ -1496,54 +1496,54 @@ void MinHFTN::evaluate_dir_der_(const bool bUseForwardDiffs,
xvec[i] += dEps * _daAVectors[nIxDir][i];
if (nextra_atom) {
for (int m = 0; m < nextra_atom; m++) {
- double * xatom = xextra_atom[m];
- double * iAtom = _daExtraAtom[nIxDir][m];
- int n = extra_nlen[m];
- for (int i = 0; i < n; i++)
- xatom[i] += dEps * iAtom[i];
- requestor[m]->min_x_set(m);
+ double * xatom = xextra_atom[m];
+ double * iAtom = _daExtraAtom[nIxDir][m];
+ int n = extra_nlen[m];
+ for (int i = 0; i < n; i++)
+ xatom[i] += dEps * iAtom[i];
+ requestor[m]->min_x_set(m);
}
}
energy_force (0);
neval++;
-
+
//---- STORE THE FORCE IN DIF2.
if (nextra_global) {
for (int i = 0; i < nextra_global; i++)
- _daExtraGlobal[VEC_DIF2][i] = fextra[i];
+ _daExtraGlobal[VEC_DIF2][i] = fextra[i];
}
for (int i = 0; i < nvec; i++)
_daAVectors[VEC_DIF2][i] = fvec[i];
if (nextra_atom) {
for (int m = 0; m < nextra_atom; m++) {
- double * fatom = fextra_atom[m];
- double * d2Atom = _daExtraAtom[VEC_DIF2][m];
- int n = extra_nlen[m];
- for (int i = 0; i < n; i++)
- d2Atom[i] = fatom[i];
+ double * fatom = fextra_atom[m];
+ double * d2Atom = _daExtraAtom[VEC_DIF2][m];
+ int n = extra_nlen[m];
+ for (int i = 0; i < n; i++)
+ d2Atom[i] = fatom[i];
}
}
-
+
//---- EVALUATE FORCES AT x - eps*p.
if (nextra_global)
modify->min_step (-dEps, _daExtraGlobal[nIxDir]);
for (int i = 0; i < nvec; i++)
xvec[i] = _daAVectors[VEC_DIF1][i]
- - dEps * _daAVectors[nIxDir][i];
+ - dEps * _daAVectors[nIxDir][i];
if (nextra_atom) {
for (int m = 0; m < nextra_atom; m++) {
- double * xatom = xextra_atom[m];
- double * iAtom = _daExtraAtom[nIxDir][m];
- double * d1Atom = _daExtraAtom[VEC_DIF1][m];
- int n = extra_nlen[m];
- for (int i = 0; i < n; i++)
- xatom[i] = d1Atom[i] - dEps * iAtom[i];
- requestor[m]->min_x_set(m);
+ double * xatom = xextra_atom[m];
+ double * iAtom = _daExtraAtom[nIxDir][m];
+ double * d1Atom = _daExtraAtom[VEC_DIF1][m];
+ int n = extra_nlen[m];
+ for (int i = 0; i < n; i++)
+ xatom[i] = d1Atom[i] - dEps * iAtom[i];
+ requestor[m]->min_x_set(m);
}
}
energy_force (0);
neval++;
-
+
//---- COMPUTE THE DIFFERENCE VECTOR:
//---- [grad(x + eps*p) - grad(x - eps*p)] / 2*eps.
//---- REMEMBER THAT FORCES = -GRADIENT.
@@ -1551,45 +1551,45 @@ void MinHFTN::evaluate_dir_der_(const bool bUseForwardDiffs,
double * iGlobal = _daExtraGlobal[nIxResult];
double * d2Global = _daExtraGlobal[VEC_DIF2];
for (int i = 0; i < nextra_global; i++)
- iGlobal[i] = (fextra[i] - d2Global[i]) / (2.0 + dEps);
+ iGlobal[i] = (fextra[i] - d2Global[i]) / (2.0 + dEps);
}
for (int i = 0; i < nvec; i++)
- _daAVectors[nIxResult][i] =
- (fvec[i] - _daAVectors[VEC_DIF2][i]) / (2.0 * dEps);
+ _daAVectors[nIxResult][i] =
+ (fvec[i] - _daAVectors[VEC_DIF2][i]) / (2.0 * dEps);
if (nextra_atom) {
for (int m = 0; m < nextra_atom; m++) {
- double * fatom = fextra_atom[m];
- double * iAtom = _daExtraAtom[nIxResult][m];
- double * d2Atom = _daExtraAtom[VEC_DIF2][m];
- int n = extra_nlen[m];
- for (int i = 0; i < n; i++)
- iAtom[i] = (fatom[i] - d2Atom[i]) / (2.0 + dEps);
+ double * fatom = fextra_atom[m];
+ double * iAtom = _daExtraAtom[nIxResult][m];
+ double * d2Atom = _daExtraAtom[VEC_DIF2][m];
+ int n = extra_nlen[m];
+ for (int i = 0; i < n; i++)
+ iAtom[i] = (fatom[i] - d2Atom[i]) / (2.0 + dEps);
}
}
-
+
if (bEvaluateAtX) {
//---- EVALUATE FORCES AT x.
if (nextra_global) {
- modify->min_step (0.0, _daExtraGlobal[VEC_DIF1]);
- modify->min_popstore();
+ modify->min_step (0.0, _daExtraGlobal[VEC_DIF1]);
+ modify->min_popstore();
}
for (int i = 0; i < nvec; i++)
- xvec[i] = _daAVectors[VEC_DIF1][i];
+ xvec[i] = _daAVectors[VEC_DIF1][i];
if (nextra_atom) {
- for (int m = 0; m < nextra_atom; m++) {
- double * xatom = xextra_atom[m];
- double * d1Atom = _daExtraAtom[VEC_DIF1][m];
- int n = extra_nlen[m];
- for (int i = 0; i < n; i++)
- xatom[i] = d1Atom[i];
- requestor[m]->min_x_set(m);
- }
+ for (int m = 0; m < nextra_atom; m++) {
+ double * xatom = xextra_atom[m];
+ double * d1Atom = _daExtraAtom[VEC_DIF1][m];
+ int n = extra_nlen[m];
+ for (int i = 0; i < n; i++)
+ xatom[i] = d1Atom[i];
+ requestor[m]->min_x_set(m);
+ }
}
dNewEnergy = energy_force (0);
neval++;
}
}
-
+
return;
}
@@ -1601,7 +1601,7 @@ void MinHFTN::open_hftn_print_file_(void)
{
int nMyRank;
MPI_Comm_rank (world, &nMyRank);
-
+
char szTmp[50];
sprintf (szTmp, "progress_MinHFTN_%d.txt", nMyRank);
_fpPrint = fopen (szTmp, "w");
@@ -1610,9 +1610,9 @@ void MinHFTN::open_hftn_print_file_(void)
printf ("*** continuing...\n");
return;
}
-
+
fprintf (_fpPrint, " Iter Evals Energy |F|_2"
- " Step TR used |step|_2 ared pred\n");
+ " Step TR used |step|_2 ared pred\n");
return;
}
@@ -1625,15 +1625,15 @@ void MinHFTN::open_hftn_print_file_(void)
------------------------------------------------------------------------- */
void MinHFTN::hftn_print_line_(const bool bIsStepAccepted,
- const int nIteration,
- const int nTotalEvals,
- const double dEnergy,
- const double dForce2,
- const int nStepType,
- const double dTrustRadius,
- const double dStepLength2,
- const double dActualRed,
- const double dPredictedRed) const
+ const int nIteration,
+ const int nTotalEvals,
+ const double dEnergy,
+ const double dForce2,
+ const int nStepType,
+ const double dTrustRadius,
+ const double dStepLength2,
+ const double dActualRed,
+ const double dPredictedRed) const
{
const char sFormat1[]
= " %4d %5d %14.8f %11.5e\n";
@@ -1641,10 +1641,10 @@ void MinHFTN::hftn_print_line_(const bool bIsStepAccepted,
= " %4d %5d %14.8f %11.5e %3s %9.3e %8.2e %10.3e %10.3e\n";
const char sFormatR[]
= "r %4d %5d %14.8f %11.5e %3s %9.3e %8.2e %10.3e %10.3e\n";
-
+
if (_fpPrint == NULL)
return;
-
+
char sStepType[4];
if (nStepType == NO_CGSTEP_BECAUSE_F_TOL_SATISFIED)
strcpy (sStepType, " - ");
@@ -1660,24 +1660,24 @@ void MinHFTN::hftn_print_line_(const bool bIsStepAccepted,
strcpy (sStepType, "its");
else
strcpy (sStepType, "???");
-
+
if (nIteration == -1) {
fprintf (_fpPrint, sFormat1,
- 0, nTotalEvals, dEnergy, dForce2);
+ 0, nTotalEvals, dEnergy, dForce2);
}
else {
if (bIsStepAccepted)
fprintf (_fpPrint, sFormatA,
- nIteration, nTotalEvals, dEnergy, dForce2,
- sStepType, dTrustRadius, dStepLength2,
- dActualRed, dPredictedRed);
+ nIteration, nTotalEvals, dEnergy, dForce2,
+ sStepType, dTrustRadius, dStepLength2,
+ dActualRed, dPredictedRed);
else
fprintf (_fpPrint, sFormatR,
- nIteration, nTotalEvals, dEnergy, dForce2,
- sStepType, dTrustRadius, dStepLength2,
- dActualRed, dPredictedRed);
+ nIteration, nTotalEvals, dEnergy, dForce2,
+ sStepType, dTrustRadius, dStepLength2,
+ dActualRed, dPredictedRed);
}
-
+
fflush (_fpPrint);
return;
}
diff --git a/src/min_hftn.h b/src/min_hftn.h
index 42c181930ce1c104075d686955998581087110b9..9d9932572bf163df172960ebf82d0ef8c8bba148 100644
--- a/src/min_hftn.h
+++ b/src/min_hftn.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -39,7 +39,7 @@ namespace LAMMPS_NS
class MinHFTN : public Min
{
public:
-
+
MinHFTN (LAMMPS *);
~MinHFTN (void);
void init();
@@ -52,73 +52,73 @@ class MinHFTN : public Min
//---- ATOM-BASED STORAGE VECTORS.
double * _daAVectors[NUM_HFTN_ATOM_BASED_VECTORS];
double ** _daExtraAtom[NUM_HFTN_ATOM_BASED_VECTORS];
-
+
//---- GLOBAL DOF STORAGE. ELEMENT [0] IS X0 (XK), NOT USED IN THIS ARRAY.
double * _daExtraGlobal[NUM_HFTN_ATOM_BASED_VECTORS];
-
+
int _nNumUnknowns;
FILE * _fpPrint;
-
+
int execute_hftn_ (const bool bPrintProgress,
- const double dInitialEnergy,
- const double dInitialForce2,
- double & dFinalEnergy,
- double & dFinalForce2);
+ const double dInitialEnergy,
+ const double dInitialForce2,
+ double & dFinalEnergy,
+ double & dFinalForce2);
bool compute_inner_cg_step_ (const double dTrustRadius,
- const double dForceTol,
- const int nMaxEvals,
- const bool bHaveEvalAtXin,
- const double dEnergyAtXin,
- const double dForce2AtXin,
- double & dEnergyAtXout,
- double & dForce2AtXout,
- int & nStepType,
- double & dStepLength2,
- double & dStepLengthInf);
+ const double dForceTol,
+ const int nMaxEvals,
+ const bool bHaveEvalAtXin,
+ const double dEnergyAtXin,
+ const double dForce2AtXin,
+ double & dEnergyAtXout,
+ double & dForce2AtXout,
+ int & nStepType,
+ double & dStepLength2,
+ double & dStepLengthInf);
double calc_xinf_using_mpi_ (void) const;
double calc_dot_prod_using_mpi_ (const int nIx1,
- const int nIx2) const;
+ const int nIx2) const;
double calc_grad_dot_v_using_mpi_ (const int nIx) const;
void calc_dhd_dd_using_mpi_ (double & dDHD,
- double & dDD) const;
+ double & dDD) const;
void calc_ppnew_pdold_using_mpi_ (double & dPnewDotPnew,
- double & dPoldDotD) const;
+ double & dPoldDotD) const;
void calc_plengths_using_mpi_ (double & dStepLength2,
- double & dStepLengthInf) const;
+ double & dStepLengthInf) const;
bool step_exceeds_TR_ (const double dTrustRadius,
- const double dPP,
- const double dPD,
- const double dDD,
- double & dTau) const;
+ const double dPP,
+ const double dPD,
+ const double dDD,
+ double & dTau) const;
bool step_exceeds_DMAX_ (void) const;
void adjust_step_to_tau_ (const double tau);
double compute_to_tr_ (const double dPP,
- const double dPD,
- const double dDD,
- const double dTrustRadius,
- const bool bConsiderBothRoots,
- const double dDHD,
- const double dPdotHD,
- const double dGradDotD) const;
+ const double dPD,
+ const double dDD,
+ const double dTrustRadius,
+ const bool bConsiderBothRoots,
+ const double dDHD,
+ const double dPdotHD,
+ const double dGradDotD) const;
void evaluate_dir_der_ (const bool bUseForwardDiffs,
- const int nIxDir,
- const int nIxResult,
- const bool bEvaluateAtX,
- double & dNewEnergy);
+ const int nIxDir,
+ const int nIxResult,
+ const bool bEvaluateAtX,
+ double & dNewEnergy);
void open_hftn_print_file_ (void);
void hftn_print_line_ (const bool bIsStepAccepted,
- const int nIteration,
- const int nTotalEvals,
- const double dEnergy,
- const double dForce2,
- const int nStepType,
- const double dTrustRadius,
- const double dStepLength2,
- const double dActualRed,
- const double dPredictedRed) const;
+ const int nIteration,
+ const int nTotalEvals,
+ const double dEnergy,
+ const double dForce2,
+ const int nStepType,
+ const double dTrustRadius,
+ const double dStepLength2,
+ const double dActualRed,
+ const double dPredictedRed) const;
void close_hftn_print_file_ (void);
};
-
+
}
#endif
diff --git a/src/min_linesearch.cpp b/src/min_linesearch.cpp
index b50971a35b712d1f373c4bc183034241dfed6722..5ddf719ca9c71f97bb56bddd357d6cefa68bd7f0 100644
--- a/src/min_linesearch.cpp
+++ b/src/min_linesearch.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -267,8 +267,8 @@ int MinLineSearch::linemin_backtrack(double eoriginal, double &alpha)
de = ecurrent - eoriginal;
if (de <= de_ideal) {
if (nextra_global) {
- int itmp = modify->min_reset_ref();
- if (itmp) ecurrent = energy_force(1);
+ int itmp = modify->min_reset_ref();
+ if (itmp) ecurrent = energy_force(1);
}
return 0;
}
@@ -289,16 +289,16 @@ int MinLineSearch::linemin_backtrack(double eoriginal, double &alpha)
/* ----------------------------------------------------------------------
// linemin: quadratic line search (adapted from Dennis and Schnabel)
- // The objective function is approximated by a quadratic
- // function in alpha, for sufficiently small alpha.
+ // The objective function is approximated by a quadratic
+ // function in alpha, for sufficiently small alpha.
// This idea is the same as that used in the well-known secant
- // method. However, since the change in the objective function
- // (difference of two finite numbers) is not known as accurately
- // as the gradient (which is close to zero), all the expressions
- // are written in terms of gradients. In this way, we can converge
- // the LAMMPS forces much closer to zero.
+ // method. However, since the change in the objective function
+ // (difference of two finite numbers) is not known as accurately
+ // as the gradient (which is close to zero), all the expressions
+ // are written in terms of gradients. In this way, we can converge
+ // the LAMMPS forces much closer to zero.
//
- // We know E,Eprev,fh,fhprev. The Taylor series about alpha_prev
+ // We know E,Eprev,fh,fhprev. The Taylor series about alpha_prev
// truncated at the quadratic term is:
//
// E = Eprev - del_alpha*fhprev + (1/2)del_alpha^2*Hprev
@@ -317,7 +317,7 @@ int MinLineSearch::linemin_backtrack(double eoriginal, double &alpha)
//
// relerr = |(Esolve-E)/Eprev|
// = |1.0 - (0.5*del_alpha*(f+fprev)+E)/Eprev|
- //
+ //
// If this is accurate to within a reasonable tolerance, then
// we go ahead and use a secant step to fh = 0:
//
@@ -331,7 +331,7 @@ int MinLineSearch::linemin_quadratic(double eoriginal, double &alpha)
double fdothall,fdothme,hme,hmax,hmaxall;
double de_ideal,de;
double delfh,engprev,relerr,alphaprev,fhprev,ff,fh,alpha0;
- double dot[2],dotall[2];
+ double dot[2],dotall[2];
double *xatom,*x0atom,*fatom,*hatom;
double alphamax;
@@ -426,19 +426,19 @@ int MinLineSearch::linemin_quadratic(double eoriginal, double &alpha)
}
if (nextra_atom)
for (m = 0; m < nextra_atom; m++) {
- fatom = fextra_atom[m];
- hatom = hextra_atom[m];
- n = extra_nlen[m];
- for (i = 0; i < n; i++) {
- dot[0] += fatom[i]*fatom[i];
- dot[1] += fatom[i]*hatom[i];
- }
+ fatom = fextra_atom[m];
+ hatom = hextra_atom[m];
+ n = extra_nlen[m];
+ for (i = 0; i < n; i++) {
+ dot[0] += fatom[i]*fatom[i];
+ dot[1] += fatom[i]*hatom[i];
+ }
}
MPI_Allreduce(dot,dotall,2,MPI_DOUBLE,MPI_SUM,world);
if (nextra_global) {
for (i = 0; i < nextra_global; i++) {
- dotall[0] += fextra[i]*fextra[i];
- dotall[1] += fextra[i]*hextra[i];
+ dotall[0] += fextra[i]*fextra[i];
+ dotall[1] += fextra[i]*hextra[i];
}
}
ff = dotall[0];
@@ -466,11 +466,11 @@ int MinLineSearch::linemin_quadratic(double eoriginal, double &alpha)
if (relerr <= QUADRATIC_TOL && alpha0 > 0.0 && alpha0 < alphamax) {
ecurrent = alpha_step(alpha0,1);
if (ecurrent - eoriginal < EMACH) {
- if (nextra_global) {
- int itmp = modify->min_reset_ref();
- if (itmp) ecurrent = energy_force(1);
- }
- return 0;
+ if (nextra_global) {
+ int itmp = modify->min_reset_ref();
+ if (itmp) ecurrent = energy_force(1);
+ }
+ return 0;
}
}
@@ -481,8 +481,8 @@ int MinLineSearch::linemin_quadratic(double eoriginal, double &alpha)
if (de <= de_ideal) {
if (nextra_global) {
- int itmp = modify->min_reset_ref();
- if (itmp) ecurrent = energy_force(1);
+ int itmp = modify->min_reset_ref();
+ if (itmp) ecurrent = energy_force(1);
}
return 0;
}
@@ -509,76 +509,76 @@ int MinLineSearch::linemin_quadratic(double eoriginal, double &alpha)
/* ----------------------------------------------------------------------
-forcezero linesearch method - seeks a zero of force in a robust manner.
+forcezero linesearch method - seeks a zero of force in a robust manner.
(motivated by a line minimization routine of f77 DYNAMO code)
-central idea:
- In each linesearch we attempt to converge to a zero of force
+central idea:
+ In each linesearch we attempt to converge to a zero of force
(usual case) or reduces forces (worst case).
- Energy does not play any role in the search procedure,
+ Energy does not play any role in the search procedure,
except we ensure that it doesn't increase.
pseudo code:
i) Fix an alpha max:
- // also account for nextra atom & global
- alpha_max <= dmax/hmaxall
+ // also account for nextra atom & global
+ alpha_max <= dmax/hmaxall
ii) Initialize:
fhCurr = current_force.dot.search_direction
fhoriginal = fhCurr
// try decreasing the energy to 1/10 of initial
- alpha_init = 0.1*fabs(eoriginal)/fhCurr;
+ alpha_init = 0.1*fabs(eoriginal)/fhCurr;
// initial alpha is smaller than alpha_max
alpha_del = MIN(alpha_init, 0.5*alpha_max);
alpha = 0.0
iii) Loop:
backtrack = false
- alpha += alpha_del
- if (alpha > alpha_max):
- // we have done enough in the search space
- EXIT with success
+ alpha += alpha_del
+ if (alpha > alpha_max):
+ // we have done enough in the search space
+ EXIT with success
Step with the new alpha
- Compute:
- current energy and 'fhCurr'
- de = ecurrent - eprev
-
- // ZERO_ENERGY = 1e-12, is max allowed energy increase
- if (de > ZERO_ENERGY):
- bactrack = true
-
- // GRAD_TOL = 0.1
- if ( (not backtrack) && (fabs(fhCurr/fh0) <= GRAD_TOL) ):
- // forces sufficiently reduced without energy increase
- EXIT with success
-
- // projected force changed sign but didn't become small enough
- if ( fhCurr < 0):
- backtrack = true
-
- if (bactrack):
- // forces along search direction changed sign
- if (fhCurr < 0):
- Get alpha_del by solving for zero
+ Compute:
+ current energy and 'fhCurr'
+ de = ecurrent - eprev
+
+ // ZERO_ENERGY = 1e-12, is max allowed energy increase
+ if (de > ZERO_ENERGY):
+ bactrack = true
+
+ // GRAD_TOL = 0.1
+ if ( (not backtrack) && (fabs(fhCurr/fh0) <= GRAD_TOL) ):
+ // forces sufficiently reduced without energy increase
+ EXIT with success
+
+ // projected force changed sign but didn't become small enough
+ if ( fhCurr < 0):
+ backtrack = true
+
+ if (bactrack):
+ // forces along search direction changed sign
+ if (fhCurr < 0):
+ Get alpha_del by solving for zero
of force (1D Newton's Method)
- else:
- // force didn't change sign but only energy increased,
- // we overshot a minimum which is very close to a
+ else:
+ // force didn't change sign but only energy increased,
+ // we overshot a minimum which is very close to a
// maximum (or there is an inflection point)
- // New alpha_del should be much smaller
- // ALPHA_FACT = 0.1
- alpha_del *= ALPHA_FACT
+ // New alpha_del should be much smaller
+ // ALPHA_FACT = 0.1
+ alpha_del *= ALPHA_FACT
- // Check to see if new 'alpha_del' isn't too small
- if (alpha_del < MIN_ALPHA):
- EXIT with failure("linesearch alpha is zero")
+ // Check to see if new 'alpha_del' isn't too small
+ if (alpha_del < MIN_ALPHA):
+ EXIT with failure("linesearch alpha is zero")
- Undo the step of alpha.
+ Undo the step of alpha.
- // continue the loop with a new alpha_del
- else:
- Get new alpha_del by linearizing force and solving for its zero
+ // continue the loop with a new alpha_del
+ else:
+ Get new alpha_del by linearizing force and solving for its zero
---------------------------------------------------------------------- */
@@ -589,8 +589,8 @@ int MinLineSearch::linemin_forcezero(double eoriginal, double &alpha)
double de_ideal,de;
double *xatom,*x0atom,*fatom,*hatom;
- double alpha_max, alpha_init, alpha_del;
- // projection of: force on itself, current force on search direction,
+ double alpha_max, alpha_init, alpha_del;
+ // projection of: force on itself, current force on search direction,
double ffCurr, fhCurr;
// previous force on search direction, initial force on search direction
double fhPrev, fhoriginal;
@@ -620,13 +620,13 @@ int MinLineSearch::linemin_forcezero(double eoriginal, double &alpha)
fatom = fextra_atom[m];
hatom = hextra_atom[m];
n = extra_nlen[m];
- for (i = 0; i < n; i++)
- fdothme += fatom[i]*hatom[i];
+ for (i = 0; i < n; i++)
+ fdothme += fatom[i]*hatom[i];
}
MPI_Allreduce(&fdothme,&fdothall,1,MPI_DOUBLE,MPI_SUM,world);
if (nextra_global)
- for (i = 0; i < nextra_global; i++)
+ for (i = 0; i < nextra_global; i++)
fdothall += fextra[i]*hextra[i];
if (output->thermo->normflag) fdothall /= atom->natoms;
if (fdothall <= 0.0) return DOWNHILL;
@@ -636,13 +636,13 @@ int MinLineSearch::linemin_forcezero(double eoriginal, double &alpha)
// for extra per-atom dof, max amount = extra_max[]
// for extra global dof, max amount is set by fix
- // also insure alpha <= ALPHA_MAX else will have
+ // also insure alpha <= ALPHA_MAX else will have
// to backtrack from huge value when forces are tiny
// if all search dir components are already 0.0, exit with error
hme = 0.0;
- for (i = 0; i < nvec; i++)
+ for (i = 0; i < nvec; i++)
hme = MAX(hme,fabs(h[i]));
MPI_Allreduce(&hme,&hmaxall,1,MPI_DOUBLE,MPI_MAX,world);
@@ -682,12 +682,12 @@ int MinLineSearch::linemin_forcezero(double eoriginal, double &alpha)
if (nextra_global) modify->min_store();
- // initialize important variables before main linesearch loop
+ // initialize important variables before main linesearch loop
ffCurr = 0.0;
fhCurr = fdothall;
fhoriginal = fhCurr;
- engCurr = eoriginal;
+ engCurr = eoriginal;
// stores energy difference due to the current move
@@ -698,16 +698,16 @@ int MinLineSearch::linemin_forcezero(double eoriginal, double &alpha)
alpha_init = 0.1*fabs(eoriginal)/fdothall;
- // initialize aplha to 0.0
+ // initialize aplha to 0.0
alpha = 0.0;
-
- // compute increment to alpha, ensure that we
+
+ // compute increment to alpha, ensure that we
// don't take the largest allowed alpha
// first alpha that will actually apply
alpha_del = MIN(alpha_init,0.5*alpha_max);
-
+
// main linesearch loop
while (1) {
@@ -715,27 +715,27 @@ int MinLineSearch::linemin_forcezero(double eoriginal, double &alpha)
fhPrev = fhCurr;
engPrev = engCurr;
- // apply the increment to alpha, but first
+ // apply the increment to alpha, but first
// check whether we are still in allowed search space
alpha += alpha_del;
if (alpha > alpha_max) {
- // undo the increment
+ // undo the increment
- alpha -= alpha_del;
+ alpha -= alpha_del;
if (nextra_global) {
- int itmp = modify->min_reset_ref();
- if (itmp) ecurrent = energy_force(1);
+ int itmp = modify->min_reset_ref();
+ if (itmp) ecurrent = energy_force(1);
}
- // exit linesearch with success: have done
+ // exit linesearch with success: have done
// enough in allowed search space
return 0;
}
- // move the system
+ // move the system
// '1' updates coordinates of atoms which cross PBC
@@ -750,7 +750,7 @@ int MinLineSearch::linemin_forcezero(double eoriginal, double &alpha)
de = engCurr - engPrev;
- // if the function value increases measurably,
+ // if the function value increases measurably,
// then we have to reduce alpha
if (de >= ZERO_ENERGY)
@@ -761,8 +761,8 @@ int MinLineSearch::linemin_forcezero(double eoriginal, double &alpha)
if ((!backtrack) && (fabs(fhCurr/fhoriginal) <= GRAD_TOL)) {
if (nextra_global) {
- int itmp = modify->min_reset_ref();
- if (itmp) ecurrent = energy_force(1);
+ int itmp = modify->min_reset_ref();
+ if (itmp) ecurrent = energy_force(1);
}
// we are done
@@ -770,7 +770,7 @@ int MinLineSearch::linemin_forcezero(double eoriginal, double &alpha)
return 0;
}
- // check if the directional derivative changed sign
+ // check if the directional derivative changed sign
// but it's not small: we overshot the minima -- BACKTRACK
if (fhCurr < 0.0)
@@ -783,21 +783,21 @@ int MinLineSearch::linemin_forcezero(double eoriginal, double &alpha)
// move back
alpha -= alpha_del;
-
- // choose new alpha
- // if the force changed sign, linearize force and
+
+ // choose new alpha
+ // if the force changed sign, linearize force and
// solve for new alpha_del
if (fhCurr < 0.0)
- alpha_del *= fhPrev/(fhPrev - fhCurr);
+ alpha_del *= fhPrev/(fhPrev - fhCurr);
else
- // force didn't change sign but only energy increased,
- // we overshot a minimum which is very close to a maxima
+ // force didn't change sign but only energy increased,
+ // we overshot a minimum which is very close to a maxima
// (or there is an inflection point)
// new alpha_del should be much smaller
- alpha_del *= ALPHA_FACT;
+ alpha_del *= ALPHA_FACT;
// since we moved back ...
@@ -805,33 +805,33 @@ int MinLineSearch::linemin_forcezero(double eoriginal, double &alpha)
ecurrent = engCurr;
fhCurr = fhPrev;
- // if new move is too small then we have failed;
+ // if new move is too small then we have failed;
// exit with 'failed_linesearch'
if (hmaxall*alpha_del <= MIN_ALPHA_FAC) {
- // undo all line minization moves
+ // undo all line minization moves
- engCurr = alpha_step(0.0,1);
- ecurrent= engCurr;
- return ZEROALPHA;
+ engCurr = alpha_step(0.0,1);
+ ecurrent= engCurr;
+ return ZEROALPHA;
}
- } else {
+ } else {
+
+ // get a new alpha by linearizing force and start over
- // get a new alpha by linearizing force and start over
-
double boostFactor = LIMIT_BOOST;
-
- // avoids problems near an energy inflection point
-
+
+ // avoids problems near an energy inflection point
+
if (fhPrev > fhCurr)
- boostFactor = fhCurr/(fhPrev - fhCurr);
+ boostFactor = fhCurr/(fhPrev - fhCurr);
- // don't want to boost too much
+ // don't want to boost too much
- boostFactor = MIN(boostFactor, LIMIT_BOOST);
- alpha_del *= boostFactor;
+ boostFactor = MIN(boostFactor, LIMIT_BOOST);
+ alpha_del *= boostFactor;
}
}
}
@@ -855,7 +855,7 @@ double MinLineSearch::alpha_step(double alpha, int resetflag)
for (i = 0; i < n; i++) xatom[i] = x0atom[i];
requestor[m]->min_x_set(m);
}
-
+
// step forward along h
if (alpha > 0.0) {
@@ -863,11 +863,11 @@ double MinLineSearch::alpha_step(double alpha, int resetflag)
for (i = 0; i < nvec; i++) xvec[i] += alpha*h[i];
if (nextra_atom)
for (m = 0; m < nextra_atom; m++) {
- xatom = xextra_atom[m];
- hatom = hextra_atom[m];
- n = extra_nlen[m];
- for (i = 0; i < n; i++) xatom[i] += alpha*hatom[i];
- requestor[m]->min_x_set(m);
+ xatom = xextra_atom[m];
+ hatom = hextra_atom[m];
+ n = extra_nlen[m];
+ for (i = 0; i < n; i++) xatom[i] += alpha*hatom[i];
+ requestor[m]->min_x_set(m);
}
}
@@ -879,7 +879,7 @@ double MinLineSearch::alpha_step(double alpha, int resetflag)
/* ---------------------------------------------------------------------- */
-// compute projection of force on: itself and the search direction
+// compute projection of force on: itself and the search direction
double MinLineSearch::compute_dir_deriv(double &ff)
{
diff --git a/src/min_linesearch.h b/src/min_linesearch.h
index 55dbad17a62efd9a33f354f644ddadc00857d6c5..51e127750678695b0b3e2135126fac587f8522c2 100644
--- a/src/min_linesearch.h
+++ b/src/min_linesearch.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/min_quickmin.cpp b/src/min_quickmin.cpp
index 80479827da8bb0e9881acad64e5d179cada4d61b..ee6766af2f511d84f69d6edaf21cb09c7f347aaa 100644
--- a/src/min_quickmin.cpp
+++ b/src/min_quickmin.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -114,28 +114,28 @@ int MinQuickMin::iterate(int maxiter)
if (vdotfall < 0.0) {
last_negative = ntimestep;
for (int i = 0; i < nlocal; i++)
- v[i][0] = v[i][1] = v[i][2] = 0.0;
+ v[i][0] = v[i][1] = v[i][2] = 0.0;
} else {
fdotf = 0.0;
for (int i = 0; i < nlocal; i++)
- fdotf += f[i][0]*f[i][0] + f[i][1]*f[i][1] + f[i][2]*f[i][2];
+ fdotf += f[i][0]*f[i][0] + f[i][1]*f[i][1] + f[i][2]*f[i][2];
MPI_Allreduce(&fdotf,&fdotfall,1,MPI_DOUBLE,MPI_SUM,world);
// sum fdotf over replicas, if necessary
// this communicator would be invalid for multiprocess replicas
if (update->multireplica == 1) {
- fdotf = fdotfall;
- MPI_Allreduce(&fdotf,&fdotfall,1,MPI_DOUBLE,MPI_SUM,universe->uworld);
+ fdotf = fdotfall;
+ MPI_Allreduce(&fdotf,&fdotfall,1,MPI_DOUBLE,MPI_SUM,universe->uworld);
}
if (fdotfall == 0.0) scale = 0.0;
else scale = vdotfall/fdotfall;
for (int i = 0; i < nlocal; i++) {
- v[i][0] = scale * f[i][0];
- v[i][1] = scale * f[i][1];
- v[i][2] = scale * f[i][2];
+ v[i][0] = scale * f[i][0];
+ v[i][1] = scale * f[i][1];
+ v[i][2] = scale * f[i][2];
}
}
@@ -165,29 +165,29 @@ int MinQuickMin::iterate(int maxiter)
// Euler integration step
double **x = atom->x;
-
+
if (rmass) {
for (int i = 0; i < nlocal; i++) {
- dtfm = dtv / rmass[i];
- x[i][0] += dtv * v[i][0];
- x[i][1] += dtv * v[i][1];
- x[i][2] += dtv * v[i][2];
- v[i][0] += dtfm * f[i][0];
- v[i][1] += dtfm * f[i][1];
- v[i][2] += dtfm * f[i][2];
+ dtfm = dtv / rmass[i];
+ x[i][0] += dtv * v[i][0];
+ x[i][1] += dtv * v[i][1];
+ x[i][2] += dtv * v[i][2];
+ v[i][0] += dtfm * f[i][0];
+ v[i][1] += dtfm * f[i][1];
+ v[i][2] += dtfm * f[i][2];
}
} else {
for (int i = 0; i < nlocal; i++) {
- dtfm = dtv / mass[type[i]];
- x[i][0] += dtv * v[i][0];
- x[i][1] += dtv * v[i][1];
- x[i][2] += dtv * v[i][2];
- v[i][0] += dtfm * f[i][0];
- v[i][1] += dtfm * f[i][1];
- v[i][2] += dtfm * f[i][2];
+ dtfm = dtv / mass[type[i]];
+ x[i][0] += dtv * v[i][0];
+ x[i][1] += dtv * v[i][1];
+ x[i][2] += dtv * v[i][2];
+ v[i][0] += dtfm * f[i][0];
+ v[i][1] += dtfm * f[i][1];
+ v[i][2] += dtfm * f[i][2];
}
}
-
+
eprevious = ecurrent;
ecurrent = energy_force(0);
neval++;
@@ -198,16 +198,16 @@ int MinQuickMin::iterate(int maxiter)
if (update->etol > 0.0 && ntimestep-last_negative > DELAYSTEP) {
if (update->multireplica == 0) {
- if (fabs(ecurrent-eprevious) <
- update->etol * 0.5*(fabs(ecurrent) + fabs(eprevious) + EPS_ENERGY))
- return ETOL;
+ if (fabs(ecurrent-eprevious) <
+ update->etol * 0.5*(fabs(ecurrent) + fabs(eprevious) + EPS_ENERGY))
+ return ETOL;
} else {
- if (fabs(ecurrent-eprevious) <
- update->etol * 0.5*(fabs(ecurrent) + fabs(eprevious) + EPS_ENERGY))
- flag = 0;
- else flag = 1;
- MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,universe->uworld);
- if (flagall == 0) return ETOL;
+ if (fabs(ecurrent-eprevious) <
+ update->etol * 0.5*(fabs(ecurrent) + fabs(eprevious) + EPS_ENERGY))
+ flag = 0;
+ else flag = 1;
+ MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,universe->uworld);
+ if (flagall == 0) return ETOL;
}
}
@@ -217,12 +217,12 @@ int MinQuickMin::iterate(int maxiter)
if (update->ftol > 0.0) {
fdotf = fnorm_sqr();
if (update->multireplica == 0) {
- if (fdotf < update->ftol*update->ftol) return FTOL;
+ if (fdotf < update->ftol*update->ftol) return FTOL;
} else {
- if (fdotf < update->ftol*update->ftol) flag = 0;
- else flag = 1;
- MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,universe->uworld);
- if (flagall == 0) return FTOL;
+ if (fdotf < update->ftol*update->ftol) flag = 0;
+ else flag = 1;
+ MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,universe->uworld);
+ if (flagall == 0) return FTOL;
}
}
@@ -234,6 +234,6 @@ int MinQuickMin::iterate(int maxiter)
timer->stamp(TIME_OUTPUT);
}
}
-
+
return MAXITER;
}
diff --git a/src/min_quickmin.h b/src/min_quickmin.h
index a69c30f616bce7a8870e5bf8c9c08b7ad5e20ec1..bfb2af941ee45b1d4f97b43f445b8d2a1674fbc3 100644
--- a/src/min_quickmin.h
+++ b/src/min_quickmin.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/min_sd.cpp b/src/min_sd.cpp
index 02020f83dbfb80bf797e41211f749bf090243206..80cad3e1357127bf559d13a82ac60529e50f15d4 100644
--- a/src/min_sd.cpp
+++ b/src/min_sd.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -73,8 +73,8 @@ int MinSD::iterate(int maxiter)
// energy tolerance criterion
- if (fabs(ecurrent-eprevious) <
- update->etol * 0.5*(fabs(ecurrent) + fabs(eprevious) + EPS_ENERGY))
+ if (fabs(ecurrent-eprevious) <
+ update->etol * 0.5*(fabs(ecurrent) + fabs(eprevious) + EPS_ENERGY))
return ETOL;
// force tolerance criterion
@@ -87,10 +87,10 @@ int MinSD::iterate(int maxiter)
for (i = 0; i < nvec; i++) h[i] = fvec[i];
if (nextra_atom)
for (m = 0; m < nextra_atom; m++) {
- fatom = fextra_atom[m];
- hatom = hextra_atom[m];
- n = extra_nlen[m];
- for (i = 0; i < n; i++) hatom[i] = fatom[i];
+ fatom = fextra_atom[m];
+ hatom = hextra_atom[m];
+ n = extra_nlen[m];
+ for (i = 0; i < n; i++) hatom[i] = fatom[i];
}
if (nextra_global)
for (i = 0; i < nextra_global; i++) hextra[i] = fextra[i];
@@ -103,6 +103,6 @@ int MinSD::iterate(int maxiter)
timer->stamp(TIME_OUTPUT);
}
}
-
+
return MAXITER;
}
diff --git a/src/min_sd.h b/src/min_sd.h
index 75928b191c6f2d32feea287935522e48ed629a49..2104280729c3ef2888ccbd13ba29aec5b90f0e28 100644
--- a/src/min_sd.h
+++ b/src/min_sd.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/minimize.cpp b/src/minimize.cpp
index 4e3fc4da1e81e5a23ecc809abeae85460b9eccc2..98dfa6e55813d10db8b5f34b027e824dbef5f76d 100644
--- a/src/minimize.cpp
+++ b/src/minimize.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/minimize.h b/src/minimize.h
index 8a4fa36f482913eba26060f435514dfc4bcc9a7a..2f41291563130f64fb0f05fb3f1721797beeb865 100644
--- a/src/minimize.h
+++ b/src/minimize.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -50,7 +50,7 @@ or create_box command.
E: Too many iterations
-You must use a number of iterations that fit in a 32-bit integer
+You must use a number of iterations that fit in a 32-bit integer
for minimization.
*/
diff --git a/src/modify.cpp b/src/modify.cpp
index 9c19816821369c568c8114eae12bd4885ddb88b9..1dc6a04dd7cf0043ebf03216f4595fd5a7d325c3 100644
--- a/src/modify.cpp
+++ b/src/modify.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -56,7 +56,7 @@ Modify::Modify(LAMMPS *lmp) : Pointers(lmp)
list_initial_integrate_respa = list_post_integrate_respa = NULL;
list_pre_force_respa = list_post_force_respa = NULL;
list_final_integrate_respa = NULL;
- list_min_pre_exchange = list_min_pre_force =
+ list_min_pre_exchange = list_min_pre_force =
list_min_post_force = list_min_energy = NULL;
end_of_step_every = NULL;
@@ -139,15 +139,15 @@ void Modify::init()
list_init_thermo_energy(THERMO_ENERGY,n_thermo_energy,list_thermo_energy);
list_init(INITIAL_INTEGRATE_RESPA,
- n_initial_integrate_respa,list_initial_integrate_respa);
+ n_initial_integrate_respa,list_initial_integrate_respa);
list_init(POST_INTEGRATE_RESPA,
- n_post_integrate_respa,list_post_integrate_respa);
+ n_post_integrate_respa,list_post_integrate_respa);
list_init(POST_FORCE_RESPA,
- n_post_force_respa,list_post_force_respa);
+ n_post_force_respa,list_post_force_respa);
list_init(PRE_FORCE_RESPA,
- n_pre_force_respa,list_pre_force_respa);
+ n_pre_force_respa,list_pre_force_respa);
list_init(FINAL_INTEGRATE_RESPA,
- n_final_integrate_respa,list_final_integrate_respa);
+ n_final_integrate_respa,list_final_integrate_respa);
list_init(MIN_PRE_EXCHANGE,n_min_pre_exchange,list_min_pre_exchange);
list_init(MIN_PRE_FORCE,n_min_pre_force,list_min_pre_force);
@@ -214,7 +214,7 @@ void Modify::init()
MPI_Allreduce(&check,&checkall,1,MPI_INT,MPI_SUM,world);
if (comm->me == 0 && checkall)
error->warning(FLERR,
- "One or more atoms are time integrated more than once");
+ "One or more atoms are time integrated more than once");
}
/* ----------------------------------------------------------------------
@@ -669,13 +669,13 @@ void Modify::add_fix(int narg, char **arg, char *suffix)
for (int i = 0; i < nfix_restart_global; i++)
if (strcmp(id_restart_global[i],fix[ifix]->id) == 0 &&
- strcmp(style_restart_global[i],fix[ifix]->style) == 0) {
+ strcmp(style_restart_global[i],fix[ifix]->style) == 0) {
fix[ifix]->restart(state_restart_global[i]);
if (comm->me == 0) {
- char *str = (char *) ("Resetting global state of Fix %s Style %s "
- "from restart file info\n");
- if (screen) fprintf(screen,str,fix[ifix]->id,fix[ifix]->style);
- if (logfile) fprintf(logfile,str,fix[ifix]->id,fix[ifix]->style);
+ char *str = (char *) ("Resetting global state of Fix %s Style %s "
+ "from restart file info\n");
+ if (screen) fprintf(screen,str,fix[ifix]->id,fix[ifix]->style);
+ if (logfile) fprintf(logfile,str,fix[ifix]->id,fix[ifix]->style);
}
}
@@ -684,14 +684,14 @@ void Modify::add_fix(int narg, char **arg, char *suffix)
for (int i = 0; i < nfix_restart_peratom; i++)
if (strcmp(id_restart_peratom[i],fix[ifix]->id) == 0 &&
- strcmp(style_restart_peratom[i],fix[ifix]->style) == 0) {
+ strcmp(style_restart_peratom[i],fix[ifix]->style) == 0) {
for (int j = 0; j < atom->nlocal; j++)
- fix[ifix]->unpack_restart(j,index_restart_peratom[i]);
+ fix[ifix]->unpack_restart(j,index_restart_peratom[i]);
if (comm->me == 0) {
- char *str = (char *) ("Resetting per-atom state of Fix %s Style %s "
- "from restart file info\n");
- if (screen) fprintf(screen,str,fix[ifix]->id,fix[ifix]->style);
- if (logfile) fprintf(logfile,str,fix[ifix]->id,fix[ifix]->style);
+ char *str = (char *) ("Resetting per-atom state of Fix %s Style %s "
+ "from restart file info\n");
+ if (screen) fprintf(screen,str,fix[ifix]->id,fix[ifix]->style);
+ if (logfile) fprintf(logfile,str,fix[ifix]->id,fix[ifix]->style);
}
}
}
@@ -710,7 +710,7 @@ void Modify::modify_fix(int narg, char **arg)
for (ifix = 0; ifix < nfix; ifix++)
if (strcmp(arg[0],fix[ifix]->id) == 0) break;
if (ifix == nfix) error->all(FLERR,"Could not find fix_modify ID");
-
+
fix[ifix]->modify_params(narg-1,&arg[1]);
}
@@ -822,7 +822,7 @@ void Modify::modify_compute(int narg, char **arg)
for (icompute = 0; icompute < ncompute; icompute++)
if (strcmp(arg[0],compute[icompute]->id) == 0) break;
if (icompute == ncompute) error->all(FLERR,"Could not find compute_modify ID");
-
+
compute[icompute]->modify_params(narg-1,&arg[1]);
}
@@ -906,7 +906,7 @@ void Modify::write_restart(FILE *fp)
int me = comm->me;
int count = 0;
- for (int i = 0; i < nfix; i++)
+ for (int i = 0; i < nfix; i++)
if (fix[i]->restart_global) count++;
if (me == 0) fwrite(&count,sizeof(int),1,fp);
@@ -915,18 +915,18 @@ void Modify::write_restart(FILE *fp)
for (int i = 0; i < nfix; i++)
if (fix[i]->restart_global) {
if (me == 0) {
- n = strlen(fix[i]->id) + 1;
- fwrite(&n,sizeof(int),1,fp);
- fwrite(fix[i]->id,sizeof(char),n,fp);
- n = strlen(fix[i]->style) + 1;
- fwrite(&n,sizeof(int),1,fp);
- fwrite(fix[i]->style,sizeof(char),n,fp);
+ n = strlen(fix[i]->id) + 1;
+ fwrite(&n,sizeof(int),1,fp);
+ fwrite(fix[i]->id,sizeof(char),n,fp);
+ n = strlen(fix[i]->style) + 1;
+ fwrite(&n,sizeof(int),1,fp);
+ fwrite(fix[i]->style,sizeof(char),n,fp);
}
fix[i]->write_restart(fp);
}
count = 0;
- for (int i = 0; i < nfix; i++)
+ for (int i = 0; i < nfix; i++)
if (fix[i]->restart_peratom) count++;
if (me == 0) fwrite(&count,sizeof(int),1,fp);
@@ -934,14 +934,14 @@ void Modify::write_restart(FILE *fp)
for (int i = 0; i < nfix; i++)
if (fix[i]->restart_peratom) {
if (me == 0) {
- n = strlen(fix[i]->id) + 1;
- fwrite(&n,sizeof(int),1,fp);
- fwrite(fix[i]->id,sizeof(char),n,fp);
- n = strlen(fix[i]->style) + 1;
- fwrite(&n,sizeof(int),1,fp);
- fwrite(fix[i]->style,sizeof(char),n,fp);
- n = fix[i]->maxsize_restart();
- fwrite(&n,sizeof(int),1,fp);
+ n = strlen(fix[i]->id) + 1;
+ fwrite(&n,sizeof(int),1,fp);
+ fwrite(fix[i]->id,sizeof(char),n,fp);
+ n = strlen(fix[i]->style) + 1;
+ fwrite(&n,sizeof(int),1,fp);
+ fwrite(fix[i]->style,sizeof(char),n,fp);
+ n = fix[i]->maxsize_restart();
+ fwrite(&n,sizeof(int),1,fp);
}
}
}
@@ -1149,9 +1149,9 @@ void Modify::list_init_compute()
bigint Modify::memory_usage()
{
bigint bytes = 0;
- for (int i = 0; i < nfix; i++)
+ for (int i = 0; i < nfix; i++)
bytes += static_cast<bigint> (fix[i]->memory_usage());
- for (int i = 0; i < ncompute; i++)
+ for (int i = 0; i < ncompute; i++)
bytes += static_cast<bigint> (compute[i]->memory_usage());
return bytes;
}
diff --git a/src/modify.h b/src/modify.h
index c95f3f282c7c1e3b53485553f18286f6cf63fe59..9172f577d92785bf132c273c8d168c61cc2790a7 100644
--- a/src/modify.h
+++ b/src/modify.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/neigh_bond.cpp b/src/neigh_bond.cpp
index dd307bd67009216b78f3c1cd51d05a129c621049..df95e272cbafb00389ee437d6e2109992e75fa7e 100644
--- a/src/neigh_bond.cpp
+++ b/src/neigh_bond.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -41,21 +41,21 @@ void Neighbor::bond_all()
for (m = 0; m < num_bond[i]; m++) {
atom1 = atom->map(bond_atom[i][m]);
if (atom1 == -1) {
- char str[128];
- sprintf(str,
- "Bond atoms %d %d missing on proc %d at step " BIGINT_FORMAT,
- tag[i],bond_atom[i][m],me,update->ntimestep);
- error->one(FLERR,str);
+ char str[128];
+ sprintf(str,
+ "Bond atoms %d %d missing on proc %d at step " BIGINT_FORMAT,
+ tag[i],bond_atom[i][m],me,update->ntimestep);
+ error->one(FLERR,str);
}
if (newton_bond || i < atom1) {
- if (nbondlist == maxbond) {
- maxbond += BONDDELTA;
- memory->grow(bondlist,maxbond,3,"neighbor:bondlist");
- }
- bondlist[nbondlist][0] = i;
- bondlist[nbondlist][1] = atom1;
- bondlist[nbondlist][2] = bond_type[i][m];
- nbondlist++;
+ if (nbondlist == maxbond) {
+ maxbond += BONDDELTA;
+ memory->grow(bondlist,maxbond,3,"neighbor:bondlist");
+ }
+ bondlist[nbondlist][0] = i;
+ bondlist[nbondlist][1] = atom1;
+ bondlist[nbondlist][2] = bond_type[i][m];
+ nbondlist++;
}
}
}
@@ -80,21 +80,21 @@ void Neighbor::bond_partial()
if (bond_type[i][m] <= 0) continue;
atom1 = atom->map(bond_atom[i][m]);
if (atom1 == -1) {
- char str[128];
- sprintf(str,
- "Bond atoms %d %d missing on proc %d at step " BIGINT_FORMAT,
- tag[i],bond_atom[i][m],me,update->ntimestep);
- error->one(FLERR,str);
+ char str[128];
+ sprintf(str,
+ "Bond atoms %d %d missing on proc %d at step " BIGINT_FORMAT,
+ tag[i],bond_atom[i][m],me,update->ntimestep);
+ error->one(FLERR,str);
}
if (newton_bond || i < atom1) {
- if (nbondlist == maxbond) {
- maxbond += BONDDELTA;
- memory->grow(bondlist,maxbond,3,"neighbor:bondlist");
- }
- bondlist[nbondlist][0] = i;
- bondlist[nbondlist][1] = atom1;
- bondlist[nbondlist][2] = bond_type[i][m];
- nbondlist++;
+ if (nbondlist == maxbond) {
+ maxbond += BONDDELTA;
+ memory->grow(bondlist,maxbond,3,"neighbor:bondlist");
+ }
+ bondlist[nbondlist][0] = i;
+ bondlist[nbondlist][1] = atom1;
+ bondlist[nbondlist][2] = bond_type[i][m];
+ nbondlist++;
}
}
}
@@ -121,24 +121,24 @@ void Neighbor::angle_all()
atom2 = atom->map(angle_atom2[i][m]);
atom3 = atom->map(angle_atom3[i][m]);
if (atom1 == -1 || atom2 == -1 || atom3 == -1) {
- char str[128];
- sprintf(str,
- "Angle atoms %d %d %d missing on proc %d at step "
- BIGINT_FORMAT,
- angle_atom1[i][m],angle_atom2[i][m],angle_atom3[i][m],
- me,update->ntimestep);
- error->one(FLERR,str);
+ char str[128];
+ sprintf(str,
+ "Angle atoms %d %d %d missing on proc %d at step "
+ BIGINT_FORMAT,
+ angle_atom1[i][m],angle_atom2[i][m],angle_atom3[i][m],
+ me,update->ntimestep);
+ error->one(FLERR,str);
}
if (newton_bond || (i <= atom1 && i <= atom2 && i <= atom3)) {
- if (nanglelist == maxangle) {
- maxangle += BONDDELTA;
- memory->grow(anglelist,maxangle,4,"neighbor:anglelist");
- }
- anglelist[nanglelist][0] = atom1;
- anglelist[nanglelist][1] = atom2;
- anglelist[nanglelist][2] = atom3;
- anglelist[nanglelist][3] = angle_type[i][m];
- nanglelist++;
+ if (nanglelist == maxangle) {
+ maxangle += BONDDELTA;
+ memory->grow(anglelist,maxangle,4,"neighbor:anglelist");
+ }
+ anglelist[nanglelist][0] = atom1;
+ anglelist[nanglelist][1] = atom2;
+ anglelist[nanglelist][2] = atom3;
+ anglelist[nanglelist][3] = angle_type[i][m];
+ nanglelist++;
}
}
}
@@ -166,24 +166,24 @@ void Neighbor::angle_partial()
atom2 = atom->map(angle_atom2[i][m]);
atom3 = atom->map(angle_atom3[i][m]);
if (atom1 == -1 || atom2 == -1 || atom3 == -1) {
- char str[128];
- sprintf(str,
- "Angle atoms %d %d %d missing on proc %d at step "
- BIGINT_FORMAT,
- angle_atom1[i][m],angle_atom2[i][m],angle_atom3[i][m],
- me,update->ntimestep);
- error->one(FLERR,str);
+ char str[128];
+ sprintf(str,
+ "Angle atoms %d %d %d missing on proc %d at step "
+ BIGINT_FORMAT,
+ angle_atom1[i][m],angle_atom2[i][m],angle_atom3[i][m],
+ me,update->ntimestep);
+ error->one(FLERR,str);
}
if (newton_bond || (i <= atom1 && i <= atom2 && i <= atom3)) {
- if (nanglelist == maxangle) {
- maxangle += BONDDELTA;
- memory->grow(anglelist,maxangle,4,"neighbor:anglelist");
- }
- anglelist[nanglelist][0] = atom1;
- anglelist[nanglelist][1] = atom2;
- anglelist[nanglelist][2] = atom3;
- anglelist[nanglelist][3] = angle_type[i][m];
- nanglelist++;
+ if (nanglelist == maxangle) {
+ maxangle += BONDDELTA;
+ memory->grow(anglelist,maxangle,4,"neighbor:anglelist");
+ }
+ anglelist[nanglelist][0] = atom1;
+ anglelist[nanglelist][1] = atom2;
+ anglelist[nanglelist][2] = atom3;
+ anglelist[nanglelist][3] = angle_type[i][m];
+ nanglelist++;
}
}
}
@@ -212,27 +212,27 @@ void Neighbor::dihedral_all()
atom3 = atom->map(dihedral_atom3[i][m]);
atom4 = atom->map(dihedral_atom4[i][m]);
if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
- char str[128];
- sprintf(str,
- "Dihedral atoms %d %d %d %d missing on proc %d at step "
- BIGINT_FORMAT,
- dihedral_atom1[i][m],dihedral_atom2[i][m],
- dihedral_atom3[i][m],dihedral_atom4[i][m],
- me,update->ntimestep);
- error->one(FLERR,str);
+ char str[128];
+ sprintf(str,
+ "Dihedral atoms %d %d %d %d missing on proc %d at step "
+ BIGINT_FORMAT,
+ dihedral_atom1[i][m],dihedral_atom2[i][m],
+ dihedral_atom3[i][m],dihedral_atom4[i][m],
+ me,update->ntimestep);
+ error->one(FLERR,str);
}
- if (newton_bond ||
- (i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)) {
- if (ndihedrallist == maxdihedral) {
- maxdihedral += BONDDELTA;
- memory->grow(dihedrallist,maxdihedral,5,"neighbor:dihedrallist");
- }
- dihedrallist[ndihedrallist][0] = atom1;
- dihedrallist[ndihedrallist][1] = atom2;
- dihedrallist[ndihedrallist][2] = atom3;
- dihedrallist[ndihedrallist][3] = atom4;
- dihedrallist[ndihedrallist][4] = dihedral_type[i][m];
- ndihedrallist++;
+ if (newton_bond ||
+ (i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)) {
+ if (ndihedrallist == maxdihedral) {
+ maxdihedral += BONDDELTA;
+ memory->grow(dihedrallist,maxdihedral,5,"neighbor:dihedrallist");
+ }
+ dihedrallist[ndihedrallist][0] = atom1;
+ dihedrallist[ndihedrallist][1] = atom2;
+ dihedrallist[ndihedrallist][2] = atom3;
+ dihedrallist[ndihedrallist][3] = atom4;
+ dihedrallist[ndihedrallist][4] = dihedral_type[i][m];
+ ndihedrallist++;
}
}
}
@@ -262,27 +262,27 @@ void Neighbor::dihedral_partial()
atom3 = atom->map(dihedral_atom3[i][m]);
atom4 = atom->map(dihedral_atom4[i][m]);
if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
- char str[128];
- sprintf(str,
- "Dihedral atoms %d %d %d %d missing on proc %d at step "
- BIGINT_FORMAT,
- dihedral_atom1[i][m],dihedral_atom2[i][m],
- dihedral_atom3[i][m],dihedral_atom4[i][m],
- me,update->ntimestep);
- error->one(FLERR,str);
+ char str[128];
+ sprintf(str,
+ "Dihedral atoms %d %d %d %d missing on proc %d at step "
+ BIGINT_FORMAT,
+ dihedral_atom1[i][m],dihedral_atom2[i][m],
+ dihedral_atom3[i][m],dihedral_atom4[i][m],
+ me,update->ntimestep);
+ error->one(FLERR,str);
}
- if (newton_bond ||
- (i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)) {
- if (ndihedrallist == maxdihedral) {
- maxdihedral += BONDDELTA;
- memory->grow(dihedrallist,maxdihedral,5,"neighbor:dihedrallist");
- }
- dihedrallist[ndihedrallist][0] = atom1;
- dihedrallist[ndihedrallist][1] = atom2;
- dihedrallist[ndihedrallist][2] = atom3;
- dihedrallist[ndihedrallist][3] = atom4;
- dihedrallist[ndihedrallist][4] = dihedral_type[i][m];
- ndihedrallist++;
+ if (newton_bond ||
+ (i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)) {
+ if (ndihedrallist == maxdihedral) {
+ maxdihedral += BONDDELTA;
+ memory->grow(dihedrallist,maxdihedral,5,"neighbor:dihedrallist");
+ }
+ dihedrallist[ndihedrallist][0] = atom1;
+ dihedrallist[ndihedrallist][1] = atom2;
+ dihedrallist[ndihedrallist][2] = atom3;
+ dihedrallist[ndihedrallist][3] = atom4;
+ dihedrallist[ndihedrallist][4] = dihedral_type[i][m];
+ ndihedrallist++;
}
}
}
@@ -311,27 +311,27 @@ void Neighbor::improper_all()
atom3 = atom->map(improper_atom3[i][m]);
atom4 = atom->map(improper_atom4[i][m]);
if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
- char str[128];
- sprintf(str,
- "Improper atoms %d %d %d %d missing on proc %d at step "
- BIGINT_FORMAT,
- improper_atom1[i][m],improper_atom2[i][m],
- improper_atom3[i][m],improper_atom4[i][m],
- me,update->ntimestep);
- error->one(FLERR,str);
+ char str[128];
+ sprintf(str,
+ "Improper atoms %d %d %d %d missing on proc %d at step "
+ BIGINT_FORMAT,
+ improper_atom1[i][m],improper_atom2[i][m],
+ improper_atom3[i][m],improper_atom4[i][m],
+ me,update->ntimestep);
+ error->one(FLERR,str);
}
- if (newton_bond ||
- (i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)) {
- if (nimproperlist == maximproper) {
- maximproper += BONDDELTA;
- memory->grow(improperlist,maximproper,5,"neighbor:improperlist");
- }
- improperlist[nimproperlist][0] = atom1;
- improperlist[nimproperlist][1] = atom2;
- improperlist[nimproperlist][2] = atom3;
- improperlist[nimproperlist][3] = atom4;
- improperlist[nimproperlist][4] = improper_type[i][m];
- nimproperlist++;
+ if (newton_bond ||
+ (i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)) {
+ if (nimproperlist == maximproper) {
+ maximproper += BONDDELTA;
+ memory->grow(improperlist,maximproper,5,"neighbor:improperlist");
+ }
+ improperlist[nimproperlist][0] = atom1;
+ improperlist[nimproperlist][1] = atom2;
+ improperlist[nimproperlist][2] = atom3;
+ improperlist[nimproperlist][3] = atom4;
+ improperlist[nimproperlist][4] = improper_type[i][m];
+ nimproperlist++;
}
}
}
@@ -361,27 +361,27 @@ void Neighbor::improper_partial()
atom3 = atom->map(improper_atom3[i][m]);
atom4 = atom->map(improper_atom4[i][m]);
if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
- char str[128];
- sprintf(str,
- "Improper atoms %d %d %d %d missing on proc %d at step "
- BIGINT_FORMAT,
- improper_atom1[i][m],improper_atom2[i][m],
- improper_atom3[i][m],improper_atom4[i][m],
- me,update->ntimestep);
- error->one(FLERR,str);
+ char str[128];
+ sprintf(str,
+ "Improper atoms %d %d %d %d missing on proc %d at step "
+ BIGINT_FORMAT,
+ improper_atom1[i][m],improper_atom2[i][m],
+ improper_atom3[i][m],improper_atom4[i][m],
+ me,update->ntimestep);
+ error->one(FLERR,str);
}
- if (newton_bond ||
- (i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)) {
- if (nimproperlist == maximproper) {
- maximproper += BONDDELTA;
- memory->grow(improperlist,maximproper,5,"neighbor:improperlist");
- }
- improperlist[nimproperlist][0] = atom1;
- improperlist[nimproperlist][1] = atom2;
- improperlist[nimproperlist][2] = atom3;
- improperlist[nimproperlist][3] = atom4;
- improperlist[nimproperlist][4] = improper_type[i][m];
- nimproperlist++;
+ if (newton_bond ||
+ (i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)) {
+ if (nimproperlist == maximproper) {
+ maximproper += BONDDELTA;
+ memory->grow(improperlist,maximproper,5,"neighbor:improperlist");
+ }
+ improperlist[nimproperlist][0] = atom1;
+ improperlist[nimproperlist][1] = atom2;
+ improperlist[nimproperlist][2] = atom3;
+ improperlist[nimproperlist][3] = atom4;
+ improperlist[nimproperlist][4] = improper_type[i][m];
+ nimproperlist++;
}
}
}
diff --git a/src/neigh_bond.h b/src/neigh_bond.h
index a79fa16ef37ee9bafcf8b207b7c2b19f89dcaf1d..b9446c7c3c10beae964a564d09964c4aaef3e6c8 100644
--- a/src/neigh_bond.h
+++ b/src/neigh_bond.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/neigh_derive.cpp b/src/neigh_derive.cpp
index 7c83088b82c0d4283ae5755b86720eefc4d1d048..4bda3d71d08b49080e079c5944c128979a9aa05d 100644
--- a/src/neigh_derive.cpp
+++ b/src/neigh_derive.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -135,13 +135,13 @@ void Neighbor::half_from_full_newton(NeighList *list)
joriginal = jlist[jj];
j = joriginal & NEIGHMASK;
if (j < nlocal) {
- if (i > j) continue;
+ if (i > j) continue;
} else {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp) {
- if (x[j][1] < ytmp) continue;
- if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
- }
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp) {
+ if (x[j][1] < ytmp) continue;
+ if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
+ }
}
neighptr[n++] = joriginal;
}
@@ -289,9 +289,9 @@ void Neighbor::skip_from_granular(NeighList *list)
npnt = 0;
npage++;
if (npage == list->maxpage) {
- pages = list->add_pages();
- pages_touch = listgranhistory->add_pages();
- pages_shear = listgranhistory->dpages;
+ pages = list->add_pages();
+ pages_touch = listgranhistory->add_pages();
+ pages_shear = listgranhistory->dpages;
}
}
@@ -406,17 +406,17 @@ void Neighbor::skip_from_respa(NeighList *list)
npnt_inner = 0;
npage_inner++;
if (npage_inner == listinner->maxpage)
- pages_inner = listinner->add_pages();
+ pages_inner = listinner->add_pages();
}
neighptr_inner = &pages_inner[npage_inner][npnt_inner];
n_inner = 0;
if (respamiddle) {
if (pgsize - npnt_middle < oneatom) {
- npnt_middle = 0;
- npage_middle++;
- if (npage_middle == listmiddle->maxpage)
- pages_middle = listmiddle->add_pages();
+ npnt_middle = 0;
+ npage_middle++;
+ if (npage_middle == listmiddle->maxpage)
+ pages_middle = listmiddle->add_pages();
}
neighptr_middle = &pages_middle[npage_middle][npnt_middle];
n_middle = 0;
@@ -453,10 +453,10 @@ void Neighbor::skip_from_respa(NeighList *list)
jnum = numneigh_middle_skip[i];
for (jj = 0; jj < jnum; jj++) {
- joriginal = jlist[jj];
- j = joriginal & NEIGHMASK;
- if (ijskip[itype][type[j]]) continue;
- neighptr_middle[n_middle++] = joriginal;
+ joriginal = jlist[jj];
+ j = joriginal & NEIGHMASK;
+ if (ijskip[itype][type[j]]) continue;
+ neighptr_middle[n_middle++] = joriginal;
}
}
@@ -478,7 +478,7 @@ void Neighbor::skip_from_respa(NeighList *list)
numneigh_middle[i] = n_middle;
npnt_middle += n_middle;
if (n_middle > oneatom)
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
}
diff --git a/src/neigh_derive.h b/src/neigh_derive.h
index 2b9b9d420ce50142864964bbc1d8582eba7e3fee..5ad76c98afe51d02161934917d9b4f544c774258 100644
--- a/src/neigh_derive.h
+++ b/src/neigh_derive.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/neigh_full.cpp b/src/neigh_full.cpp
index 76e2888ae0018a196a39967af963e7b9ac2c6594..15ca926340ddc1dcc315cc3c874e695112a28de4 100644
--- a/src/neigh_full.cpp
+++ b/src/neigh_full.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -87,10 +87,10 @@ void Neighbor::full_nsq(NeighList *list)
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- which = find_special(special[i],nspecial[i],tag[j]);
- if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
+ if (molecular) {
+ which = find_special(special[i],nspecial[i],tag[j]);
+ if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
}
}
@@ -162,34 +162,34 @@ void Neighbor::full_nsq_ghost(NeighList *list)
if (i < nlocal) {
for (j = 0; j < nall; j++) {
- if (i == j) continue;
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- which = find_special(special[i],nspecial[i],tag[j]);
- if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
+ if (i == j) continue;
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ which = find_special(special[i],nspecial[i],tag[j]);
+ if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
}
} else {
for (j = 0; j < nall; j++) {
- if (i == j) continue;
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighghostsq[itype][jtype])
- neighptr[n++] = j;
+ if (i == j) continue;
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighghostsq[itype][jtype])
+ neighptr[n++] = j;
}
}
@@ -268,22 +268,22 @@ void Neighbor::full_bin(NeighList *list)
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- if (i == j) continue;
-
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- which = find_special(special[i],nspecial[i],tag[j]);
- if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
+ if (i == j) continue;
+
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ which = find_special(special[i],nspecial[i],tag[j]);
+ if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
}
}
@@ -365,49 +365,49 @@ void Neighbor::full_bin_ghost(NeighList *list)
if (i < nlocal) {
ibin = coord2bin(x[i]);
for (k = 0; k < nstencil; k++) {
- for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- if (i == j) continue;
-
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- which = find_special(special[i],nspecial[i],tag[j]);
- if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
- }
+ for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
+ if (i == j) continue;
+
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ which = find_special(special[i],nspecial[i],tag[j]);
+ if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
+ }
}
} else {
ibin = coord2bin(x[i],xbin,ybin,zbin);
for (k = 0; k < nstencil; k++) {
- xbin2 = xbin + stencilxyz[k][0];
- ybin2 = ybin + stencilxyz[k][1];
- zbin2 = zbin + stencilxyz[k][2];
- if (xbin2 < 0 || xbin2 >= mbinx ||
- ybin2 < 0 || ybin2 >= mbiny ||
- zbin2 < 0 || zbin2 >= mbinz) continue;
- for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- if (i == j) continue;
-
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighghostsq[itype][jtype])
- neighptr[n++] = j;
- }
+ xbin2 = xbin + stencilxyz[k][0];
+ ybin2 = ybin + stencilxyz[k][1];
+ zbin2 = zbin + stencilxyz[k][2];
+ if (xbin2 < 0 || xbin2 >= mbinx ||
+ ybin2 < 0 || ybin2 >= mbiny ||
+ zbin2 < 0 || zbin2 >= mbinz) continue;
+ for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
+ if (i == j) continue;
+
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighghostsq[itype][jtype])
+ neighptr[n++] = j;
+ }
}
}
@@ -493,23 +493,23 @@ void Neighbor::full_multi(NeighList *list)
ns = nstencil_multi[itype];
for (k = 0; k < ns; k++) {
for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
- jtype = type[j];
- if (cutsq[jtype] < distsq[k]) continue;
- if (i == j) continue;
-
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- which = find_special(special[i],nspecial[i],tag[j]);
- if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
+ jtype = type[j];
+ if (cutsq[jtype] < distsq[k]) continue;
+ if (i == j) continue;
+
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ which = find_special(special[i],nspecial[i],tag[j]);
+ if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
}
}
diff --git a/src/neigh_full.h b/src/neigh_full.h
index 2b9b9d420ce50142864964bbc1d8582eba7e3fee..5ad76c98afe51d02161934917d9b4f544c774258 100644
--- a/src/neigh_full.h
+++ b/src/neigh_full.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/neigh_gran.cpp b/src/neigh_gran.cpp
index 1c8f8338ab583776a6e3cb66b5f8a5bea3432cba..a5a70b2b40a357de3e9caef5d6dd0558aa47af48 100644
--- a/src/neigh_gran.cpp
+++ b/src/neigh_gran.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -84,11 +84,11 @@ void Neighbor::granular_nsq_no_newton(NeighList *list)
npnt = 0;
npage++;
if (npage == list->maxpage) {
- pages = list->add_pages();
- if (fix_history) {
- pages_touch = listgranhistory->add_pages();
- pages_shear = listgranhistory->dpages;
- }
+ pages = list->add_pages();
+ if (fix_history) {
+ pages_touch = listgranhistory->add_pages();
+ pages_shear = listgranhistory->dpages;
+ }
}
}
@@ -119,34 +119,34 @@ void Neighbor::granular_nsq_no_newton(NeighList *list)
cutsq = (radsum+skin) * (radsum+skin);
if (rsq <= cutsq) {
- neighptr[n] = j;
-
- if (fix_history) {
- if (rsq < radsum*radsum) {
- for (m = 0; m < npartner[i]; m++)
- if (partner[i][m] == tag[j]) break;
- if (m < npartner[i]) {
- touchptr[n] = 1;
- shearptr[nn++] = shearpartner[i][m][0];
- shearptr[nn++] = shearpartner[i][m][1];
- shearptr[nn++] = shearpartner[i][m][2];
- } else {
- touchptr[n] = 0;
- shearptr[nn++] = 0.0;
- shearptr[nn++] = 0.0;
- shearptr[nn++] = 0.0;
- }
- } else {
- touchptr[n] = 0;
- shearptr[nn++] = 0.0;
- shearptr[nn++] = 0.0;
- shearptr[nn++] = 0.0;
- }
- }
-
- n++;
+ neighptr[n] = j;
+
+ if (fix_history) {
+ if (rsq < radsum*radsum) {
+ for (m = 0; m < npartner[i]; m++)
+ if (partner[i][m] == tag[j]) break;
+ if (m < npartner[i]) {
+ touchptr[n] = 1;
+ shearptr[nn++] = shearpartner[i][m][0];
+ shearptr[nn++] = shearpartner[i][m][1];
+ shearptr[nn++] = shearpartner[i][m][2];
+ } else {
+ touchptr[n] = 0;
+ shearptr[nn++] = 0.0;
+ shearptr[nn++] = 0.0;
+ shearptr[nn++] = 0.0;
+ }
+ } else {
+ touchptr[n] = 0;
+ shearptr[nn++] = 0.0;
+ shearptr[nn++] = 0.0;
+ shearptr[nn++] = 0.0;
+ }
+ }
+
+ n++;
}
- }
+ }
ilist[inum++] = i;
firstneigh[i] = neighptr;
@@ -224,18 +224,18 @@ void Neighbor::granular_nsq_newton(NeighList *list)
if (includegroup && !(mask[j] & bitmask)) continue;
if (j >= nlocal) {
- jtag = tag[j];
- if (itag > jtag) {
- if ((itag+jtag) % 2 == 0) continue;
- } else if (itag < jtag) {
- if ((itag+jtag) % 2 == 1) continue;
- } else {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp) {
- if (x[j][1] < ytmp) continue;
- if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
- }
- }
+ jtag = tag[j];
+ if (itag > jtag) {
+ if ((itag+jtag) % 2 == 0) continue;
+ } else if (itag < jtag) {
+ if ((itag+jtag) % 2 == 1) continue;
+ } else {
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp) {
+ if (x[j][1] < ytmp) continue;
+ if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
+ }
+ }
}
if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
@@ -246,7 +246,7 @@ void Neighbor::granular_nsq_newton(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
radsum = radi + radius[j];
cutsq = (radsum+skin) * (radsum+skin);
-
+
if (rsq <= cutsq) neighptr[n++] = j;
}
@@ -330,11 +330,11 @@ void Neighbor::granular_bin_no_newton(NeighList *list)
npnt = 0;
npage++;
if (npage == list->maxpage) {
- pages = list->add_pages();
- if (fix_history) {
- pages_touch = listgranhistory->add_pages();
- pages_shear = listgranhistory->dpages;
- }
+ pages = list->add_pages();
+ if (fix_history) {
+ pages_touch = listgranhistory->add_pages();
+ pages_shear = listgranhistory->dpages;
+ }
}
}
@@ -359,44 +359,44 @@ void Neighbor::granular_bin_no_newton(NeighList *list)
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- if (j <= i) continue;
- if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
- radsum = radi + radius[j];
- cutsq = (radsum+skin) * (radsum+skin);
-
- if (rsq <= cutsq) {
- neighptr[n] = j;
-
- if (fix_history) {
- if (rsq < radsum*radsum) {
- for (m = 0; m < npartner[i]; m++)
- if (partner[i][m] == tag[j]) break;
- if (m < npartner[i]) {
- touchptr[n] = 1;
- shearptr[nn++] = shearpartner[i][m][0];
- shearptr[nn++] = shearpartner[i][m][1];
- shearptr[nn++] = shearpartner[i][m][2];
- } else {
- touchptr[n] = 0;
- shearptr[nn++] = 0.0;
- shearptr[nn++] = 0.0;
- shearptr[nn++] = 0.0;
- }
- } else {
- touchptr[n] = 0;
- shearptr[nn++] = 0.0;
- shearptr[nn++] = 0.0;
- shearptr[nn++] = 0.0;
- }
- }
-
- n++;
- }
+ if (j <= i) continue;
+ if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+ radsum = radi + radius[j];
+ cutsq = (radsum+skin) * (radsum+skin);
+
+ if (rsq <= cutsq) {
+ neighptr[n] = j;
+
+ if (fix_history) {
+ if (rsq < radsum*radsum) {
+ for (m = 0; m < npartner[i]; m++)
+ if (partner[i][m] == tag[j]) break;
+ if (m < npartner[i]) {
+ touchptr[n] = 1;
+ shearptr[nn++] = shearpartner[i][m][0];
+ shearptr[nn++] = shearpartner[i][m][1];
+ shearptr[nn++] = shearpartner[i][m][2];
+ } else {
+ touchptr[n] = 0;
+ shearptr[nn++] = 0.0;
+ shearptr[nn++] = 0.0;
+ shearptr[nn++] = 0.0;
+ }
+ } else {
+ touchptr[n] = 0;
+ shearptr[nn++] = 0.0;
+ shearptr[nn++] = 0.0;
+ shearptr[nn++] = 0.0;
+ }
+ }
+
+ n++;
+ }
}
}
@@ -477,11 +477,11 @@ void Neighbor::granular_bin_newton(NeighList *list)
for (j = bins[i]; j >= 0; j = bins[j]) {
if (j >= nlocal) {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp) {
- if (x[j][1] < ytmp) continue;
- if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
- }
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp) {
+ if (x[j][1] < ytmp) continue;
+ if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
+ }
}
if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
@@ -501,16 +501,16 @@ void Neighbor::granular_bin_newton(NeighList *list)
ibin = coord2bin(x[i]);
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
+ if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
- radsum = radi + radius[j];
- cutsq = (radsum+skin) * (radsum+skin);
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+ radsum = radi + radius[j];
+ cutsq = (radsum+skin) * (radsum+skin);
- if (rsq <= cutsq) neighptr[n++] = j;
+ if (rsq <= cutsq) neighptr[n++] = j;
}
}
@@ -590,25 +590,25 @@ void Neighbor::granular_bin_newton_tri(NeighList *list)
ibin = coord2bin(x[i]);
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp) {
- if (x[j][1] < ytmp) continue;
- if (x[j][1] == ytmp) {
- if (x[j][0] < xtmp) continue;
- if (x[j][0] == xtmp && j <= i) continue;
- }
- }
-
- if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
- radsum = radi + radius[j];
- cutsq = (radsum+skin) * (radsum+skin);
-
- if (rsq <= cutsq) neighptr[n++] = j;
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp) {
+ if (x[j][1] < ytmp) continue;
+ if (x[j][1] == ytmp) {
+ if (x[j][0] < xtmp) continue;
+ if (x[j][0] == xtmp && j <= i) continue;
+ }
+ }
+
+ if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+ radsum = radi + radius[j];
+ cutsq = (radsum+skin) * (radsum+skin);
+
+ if (rsq <= cutsq) neighptr[n++] = j;
}
}
diff --git a/src/neigh_gran.h b/src/neigh_gran.h
index 2b9b9d420ce50142864964bbc1d8582eba7e3fee..5ad76c98afe51d02161934917d9b4f544c774258 100644
--- a/src/neigh_gran.h
+++ b/src/neigh_gran.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/neigh_half_bin.cpp b/src/neigh_half_bin.cpp
index 45f84f9af41f54c95e8f4e59a9c6adaa896bc0a4..09a5ccab9238bd84ffb1d126b40b36d34946a64f 100644
--- a/src/neigh_half_bin.cpp
+++ b/src/neigh_half_bin.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -85,22 +85,22 @@ void Neighbor::half_bin_no_newton(NeighList *list)
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- if (j <= i) continue;
-
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- which = find_special(special[i],nspecial[i],tag[j]);
- if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
+ if (j <= i) continue;
+
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ which = find_special(special[i],nspecial[i],tag[j]);
+ if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
}
}
@@ -151,7 +151,7 @@ void Neighbor::half_bin_newton(NeighList *list)
int **pages = list->pages;
int nstencil = list->nstencil;
int *stencil = list->stencil;
-
+
int inum = 0;
int npage = 0;
int npnt = 0;
@@ -178,11 +178,11 @@ void Neighbor::half_bin_newton(NeighList *list)
for (j = bins[i]; j >= 0; j = bins[j]) {
if (j >= nlocal) {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp) {
- if (x[j][1] < ytmp) continue;
- if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
- }
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp) {
+ if (x[j][1] < ytmp) continue;
+ if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
+ }
}
jtype = type[j];
@@ -194,10 +194,10 @@ void Neighbor::half_bin_newton(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- which = find_special(special[i],nspecial[i],tag[j]);
- if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
+ if (molecular) {
+ which = find_special(special[i],nspecial[i],tag[j]);
+ if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
}
}
@@ -206,20 +206,20 @@ void Neighbor::half_bin_newton(NeighList *list)
ibin = coord2bin(x[i]);
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- which = find_special(special[i],nspecial[i],tag[j]);
- if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ which = find_special(special[i],nspecial[i],tag[j]);
+ if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
}
}
@@ -300,29 +300,29 @@ void Neighbor::half_bin_newton_tri(NeighList *list)
ibin = coord2bin(x[i]);
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp) {
- if (x[j][1] < ytmp) continue;
- if (x[j][1] == ytmp) {
- if (x[j][0] < xtmp) continue;
- if (x[j][0] == xtmp && j <= i) continue;
- }
- }
-
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- which = find_special(special[i],nspecial[i],tag[j]);
- if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp) {
+ if (x[j][1] < ytmp) continue;
+ if (x[j][1] == ytmp) {
+ if (x[j][0] < xtmp) continue;
+ if (x[j][0] == xtmp && j <= i) continue;
+ }
+ }
+
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ which = find_special(special[i],nspecial[i],tag[j]);
+ if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
}
}
diff --git a/src/neigh_half_bin.h b/src/neigh_half_bin.h
index 2b9b9d420ce50142864964bbc1d8582eba7e3fee..5ad76c98afe51d02161934917d9b4f544c774258 100644
--- a/src/neigh_half_bin.h
+++ b/src/neigh_half_bin.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/neigh_half_multi.cpp b/src/neigh_half_multi.cpp
index bc9404793cdf8f1eed1a74bb0c6ed26c00902b16..917699c44441f99bade7e1f35ee3f3927f0b58ff 100644
--- a/src/neigh_half_multi.cpp
+++ b/src/neigh_half_multi.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -92,23 +92,23 @@ void Neighbor::half_multi_no_newton(NeighList *list)
ns = nstencil_multi[itype];
for (k = 0; k < ns; k++) {
for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
- if (j <= i) continue;
- jtype = type[j];
- if (cutsq[jtype] < distsq[k]) continue;
-
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- which = find_special(special[i],nspecial[i],tag[j]);
- if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
+ if (j <= i) continue;
+ jtype = type[j];
+ if (cutsq[jtype] < distsq[k]) continue;
+
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ which = find_special(special[i],nspecial[i],tag[j]);
+ if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
}
}
@@ -189,11 +189,11 @@ void Neighbor::half_multi_newton(NeighList *list)
for (j = bins[i]; j >= 0; j = bins[j]) {
if (j >= nlocal) {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp) {
- if (x[j][1] < ytmp) continue;
- if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
- }
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp) {
+ if (x[j][1] < ytmp) continue;
+ if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
+ }
}
jtype = type[j];
@@ -205,10 +205,10 @@ void Neighbor::half_multi_newton(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- which = find_special(special[i],nspecial[i],tag[j]);
- if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
+ if (molecular) {
+ which = find_special(special[i],nspecial[i],tag[j]);
+ if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
}
}
@@ -222,22 +222,22 @@ void Neighbor::half_multi_newton(NeighList *list)
ns = nstencil_multi[itype];
for (k = 0; k < ns; k++) {
for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
- jtype = type[j];
- if (cutsq[jtype] < distsq[k]) continue;
-
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- which = find_special(special[i],nspecial[i],tag[j]);
- if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
+ jtype = type[j];
+ if (cutsq[jtype] < distsq[k]) continue;
+
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ which = find_special(special[i],nspecial[i],tag[j]);
+ if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
}
}
@@ -327,30 +327,30 @@ void Neighbor::half_multi_newton_tri(NeighList *list)
ns = nstencil_multi[itype];
for (k = 0; k < ns; k++) {
for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
- jtype = type[j];
- if (cutsq[jtype] < distsq[k]) continue;
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp) {
- if (x[j][1] < ytmp) continue;
- if (x[j][1] == ytmp) {
- if (x[j][0] < xtmp) continue;
- if (x[j][0] == xtmp && j <= i) continue;
- }
- }
-
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- which = find_special(special[i],nspecial[i],tag[j]);
- if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
- }
+ jtype = type[j];
+ if (cutsq[jtype] < distsq[k]) continue;
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp) {
+ if (x[j][1] < ytmp) continue;
+ if (x[j][1] == ytmp) {
+ if (x[j][0] < xtmp) continue;
+ if (x[j][0] == xtmp && j <= i) continue;
+ }
+ }
+
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ which = find_special(special[i],nspecial[i],tag[j]);
+ if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+ }
}
}
diff --git a/src/neigh_half_multi.h b/src/neigh_half_multi.h
index 2b9b9d420ce50142864964bbc1d8582eba7e3fee..5ad76c98afe51d02161934917d9b4f544c774258 100644
--- a/src/neigh_half_multi.h
+++ b/src/neigh_half_multi.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/neigh_half_nsq.cpp b/src/neigh_half_nsq.cpp
index c3361736efb03676986e4fb7e172b27716509559..22f0952d151e415422dfaa157ecf1b5a4a4aaa51 100644
--- a/src/neigh_half_nsq.cpp
+++ b/src/neigh_half_nsq.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -87,10 +87,10 @@ void Neighbor::half_nsq_no_newton(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- which = find_special(special[i],nspecial[i],tag[j]);
- if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
+ if (molecular) {
+ which = find_special(special[i],nspecial[i],tag[j]);
+ if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
}
}
@@ -168,18 +168,18 @@ void Neighbor::half_nsq_newton(NeighList *list)
if (includegroup && !(mask[j] & bitmask)) continue;
if (j >= nlocal) {
- jtag = tag[j];
- if (itag > jtag) {
- if ((itag+jtag) % 2 == 0) continue;
- } else if (itag < jtag) {
- if ((itag+jtag) % 2 == 1) continue;
- } else {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp) {
- if (x[j][1] < ytmp) continue;
- if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
- }
- }
+ jtag = tag[j];
+ if (itag > jtag) {
+ if ((itag+jtag) % 2 == 0) continue;
+ } else if (itag < jtag) {
+ if ((itag+jtag) % 2 == 1) continue;
+ } else {
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp) {
+ if (x[j][1] < ytmp) continue;
+ if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
+ }
+ }
}
jtype = type[j];
@@ -191,10 +191,10 @@ void Neighbor::half_nsq_newton(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- which = find_special(special[i],nspecial[i],tag[j]);
- if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
+ if (molecular) {
+ which = find_special(special[i],nspecial[i],tag[j]);
+ if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
}
}
diff --git a/src/neigh_half_nsq.h b/src/neigh_half_nsq.h
index 2b9b9d420ce50142864964bbc1d8582eba7e3fee..5ad76c98afe51d02161934917d9b4f544c774258 100644
--- a/src/neigh_half_nsq.h
+++ b/src/neigh_half_nsq.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/neigh_list.cpp b/src/neigh_list.cpp
index a70b626f7f67c3bd5b67825cf99514781fb07329..e294dcaf4831807414c48e26c9eaf8e03e3c15ee 100644
--- a/src/neigh_list.cpp
+++ b/src/neigh_list.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -123,11 +123,11 @@ void NeighList::grow(int nmax)
memory->create(ilist,maxatoms,"neighlist:ilist");
memory->create(numneigh,maxatoms,"neighlist:numneigh");
firstneigh = (int **) memory->smalloc(maxatoms*sizeof(int *),
- "neighlist:firstneigh");
+ "neighlist:firstneigh");
- if (dnum)
+ if (dnum)
firstdouble = (double **) memory->smalloc(maxatoms*sizeof(double *),
- "neighlist:firstdouble");
+ "neighlist:firstdouble");
}
/* ----------------------------------------------------------------------
@@ -145,8 +145,8 @@ void NeighList::stencil_allocate(int smax, int style)
memory->destroy(stencil);
memory->create(stencil,maxstencil,"neighlist:stencil");
if (ghostflag) {
- memory->destroy(stencilxyz);
- memory->create(stencilxyz,maxstencil,3,"neighlist:stencilxyz");
+ memory->destroy(stencilxyz);
+ memory->create(stencilxyz,maxstencil,3,"neighlist:stencilxyz");
}
}
@@ -157,20 +157,20 @@ void NeighList::stencil_allocate(int smax, int style)
stencil_multi = new int*[n+1];
distsq_multi = new double*[n+1];
for (i = 1; i <= n; i++) {
- nstencil_multi[i] = 0;
- stencil_multi[i] = NULL;
- distsq_multi[i] = NULL;
+ nstencil_multi[i] = 0;
+ stencil_multi[i] = NULL;
+ distsq_multi[i] = NULL;
}
}
if (smax > maxstencil_multi) {
maxstencil_multi = smax;
for (i = 1; i <= n; i++) {
- memory->destroy(stencil_multi[i]);
- memory->destroy(distsq_multi[i]);
- memory->create(stencil_multi[i],maxstencil_multi,
- "neighlist:stencil_multi");
- memory->create(distsq_multi[i],maxstencil_multi,
- "neighlist:distsq_multi");
+ memory->destroy(stencil_multi[i]);
+ memory->destroy(distsq_multi[i]);
+ memory->create(stencil_multi[i],maxstencil_multi,
+ "neighlist:stencil_multi");
+ memory->create(distsq_multi[i],maxstencil_multi,
+ "neighlist:distsq_multi");
}
}
}
@@ -185,13 +185,13 @@ int **NeighList::add_pages(int howmany)
int toppage = maxpage;
maxpage += howmany*PGDELTA;
- pages = (int **)
+ pages = (int **)
memory->srealloc(pages,maxpage*sizeof(int *),"neighlist:pages");
for (int i = toppage; i < maxpage; i++)
memory->create(pages[i],pgsize,"neighlist:pages[i]");
if (dnum) {
- dpages = (double **)
+ dpages = (double **)
memory->srealloc(dpages,maxpage*sizeof(double *),"neighlist:dpages");
for (int i = toppage; i < maxpage; i++)
memory->create(dpages[i],dnum*pgsize,"neighlist:dpages[i]");
diff --git a/src/neigh_list.h b/src/neigh_list.h
index a8857811a380dfce7adeed0ce895452b7db8743b..ddecb4bbf20d89182fc0322382259e805241cf93 100644
--- a/src/neigh_list.h
+++ b/src/neigh_list.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -52,7 +52,7 @@ class NeighList : protected Pointers {
// settings and pointers for related neighbor lists and fixes
NeighList *listgranhistory; // point at history list
- class FixShearHistory *fix_history; // fix that stores history info
+ class FixShearHistory *fix_history; // fix that stores history info
int respamiddle; // 1 if this respaouter has middle list
NeighList *listinner; // me = respaouter, point to respainner
diff --git a/src/neigh_request.cpp b/src/neigh_request.cpp
index 2146009a99039baee432133a0a235eac5fa1b216..da334da65e58ed16f642cad40a9578d89a4dd1c4 100644
--- a/src/neigh_request.cpp
+++ b/src/neigh_request.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -83,7 +83,7 @@ int NeighRequest::identical(NeighRequest *other)
if (requestor != other->requestor) same = 0;
if (id != other->id) same = 0;
-
+
if (pair != other->pair) same = 0;
if (fix != other->fix) same = 0;
if (compute != other->compute) same = 0;
@@ -156,7 +156,7 @@ int NeighRequest::same_skip(NeighRequest *other)
if (iskip[i] != other->iskip[i]) same = 0;
for (i = 1; i <= ntypes; i++)
for (j = 1; j <= ntypes; j++)
- if (ijskip[i][j] != other->ijskip[i][j]) same = 0;
+ if (ijskip[i][j] != other->ijskip[i][j]) same = 0;
}
return same;
diff --git a/src/neigh_request.h b/src/neigh_request.h
index e3dcc915a7bc0018864d9a0d148bdce8142a9125..f5947cf729b2000f1a8ea18dff9460f96186e0c9 100644
--- a/src/neigh_request.h
+++ b/src/neigh_request.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -40,7 +40,7 @@ class NeighRequest : protected Pointers {
int gran; // 1 if granular list
int granhistory; // 1 if granular history list
- int respainner; // 1 if a rRESPA inner list
+ int respainner; // 1 if a rRESPA inner list
int respamiddle; // 1 if a rRESPA middle list
int respaouter; // 1 if a rRESPA outer list
diff --git a/src/neigh_respa.cpp b/src/neigh_respa.cpp
index c71d3c583a3ebe68f76bc8749c535d532a700a01..6770b26a5176be618553737b94c39d846407efe2 100644
--- a/src/neigh_respa.cpp
+++ b/src/neigh_respa.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -96,17 +96,17 @@ void Neighbor::respa_nsq_no_newton(NeighList *list)
npnt_inner = 0;
npage_inner++;
if (npage_inner == listinner->maxpage)
- pages_inner = listinner->add_pages();
+ pages_inner = listinner->add_pages();
}
neighptr_inner = &pages_inner[npage_inner][npnt_inner];
n_inner = 0;
if (respamiddle) {
if (pgsize - npnt_middle < oneatom) {
- npnt_middle = 0;
- npage_middle++;
- if (npage_middle == listmiddle->maxpage)
- pages_middle = listmiddle->add_pages();
+ npnt_middle = 0;
+ npage_middle++;
+ if (npage_middle == listmiddle->maxpage)
+ pages_middle = listmiddle->add_pages();
}
neighptr_middle = &pages_middle[npage_middle][npnt_middle];
n_middle = 0;
@@ -130,20 +130,20 @@ void Neighbor::respa_nsq_no_newton(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- which = find_special(special[i],nspecial[i],tag[j]);
- if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
+ if (molecular) {
+ which = find_special(special[i],nspecial[i],tag[j]);
+ if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
if (rsq < cut_inner_sq) {
- if (which == 0) neighptr_inner[n_inner++] = j;
- else if (which > 0) neighptr_inner[n_inner++] = j ^ (which << SBBITS);
+ if (which == 0) neighptr_inner[n_inner++] = j;
+ else if (which > 0) neighptr_inner[n_inner++] = j ^ (which << SBBITS);
}
if (respamiddle && rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
- if (which == 0) neighptr_middle[n_middle++] = j;
- else if (which > 0)
- neighptr_middle[n_middle++] = j ^ (which << SBBITS);
+ if (which == 0) neighptr_middle[n_middle++] = j;
+ else if (which > 0)
+ neighptr_middle[n_middle++] = j ^ (which << SBBITS);
}
}
}
@@ -168,7 +168,7 @@ void Neighbor::respa_nsq_no_newton(NeighList *list)
numneigh_middle[i] = n_middle;
npnt_middle += n_middle;
if (n_middle > oneatom)
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
inum++;
@@ -257,17 +257,17 @@ void Neighbor::respa_nsq_newton(NeighList *list)
npnt_inner = 0;
npage_inner++;
if (npage_inner == listinner->maxpage)
- pages_inner = listinner->add_pages();
+ pages_inner = listinner->add_pages();
}
neighptr_inner = &pages_inner[npage_inner][npnt_inner];
n_inner = 0;
if (respamiddle) {
if (pgsize - npnt_middle < oneatom) {
- npnt_middle = 0;
- npage_middle++;
- if (npage_middle == listmiddle->maxpage)
- pages_middle = listmiddle->add_pages();
+ npnt_middle = 0;
+ npage_middle++;
+ if (npage_middle == listmiddle->maxpage)
+ pages_middle = listmiddle->add_pages();
}
neighptr_middle = &pages_middle[npage_middle][npnt_middle];
n_middle = 0;
@@ -285,18 +285,18 @@ void Neighbor::respa_nsq_newton(NeighList *list)
if (includegroup && !(mask[j] & bitmask)) continue;
if (j >= nlocal) {
- jtag = tag[j];
- if (itag > jtag) {
- if ((itag+jtag) % 2 == 0) continue;
- } else if (itag < jtag) {
- if ((itag+jtag) % 2 == 1) continue;
- } else {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp) {
- if (x[j][1] < ytmp) continue;
- if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
- }
- }
+ jtag = tag[j];
+ if (itag > jtag) {
+ if ((itag+jtag) % 2 == 0) continue;
+ } else if (itag < jtag) {
+ if ((itag+jtag) % 2 == 1) continue;
+ } else {
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp) {
+ if (x[j][1] < ytmp) continue;
+ if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
+ }
+ }
}
jtype = type[j];
@@ -308,21 +308,21 @@ void Neighbor::respa_nsq_newton(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- which = find_special(special[i],nspecial[i],tag[j]);
- if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
+ if (molecular) {
+ which = find_special(special[i],nspecial[i],tag[j]);
+ if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
if (rsq < cut_inner_sq) {
- if (which == 0) neighptr_inner[n_inner++] = j;
- else if (which > 0) neighptr_inner[n_inner++] = j ^ (which << SBBITS);
+ if (which == 0) neighptr_inner[n_inner++] = j;
+ else if (which > 0) neighptr_inner[n_inner++] = j ^ (which << SBBITS);
}
- if (respamiddle &&
- rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
- if (which == 0) neighptr_middle[n_middle++] = j;
- else if (which > 0)
- neighptr_middle[n_middle++] = j ^ (which << SBBITS);
+ if (respamiddle &&
+ rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
+ if (which == 0) neighptr_middle[n_middle++] = j;
+ else if (which > 0)
+ neighptr_middle[n_middle++] = j ^ (which << SBBITS);
}
}
}
@@ -347,7 +347,7 @@ void Neighbor::respa_nsq_newton(NeighList *list)
numneigh_middle[i] = n_middle;
npnt_middle += n_middle;
if (n_middle > oneatom)
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
inum++;
@@ -438,17 +438,17 @@ void Neighbor::respa_bin_no_newton(NeighList *list)
npnt_inner = 0;
npage_inner++;
if (npage_inner == listinner->maxpage)
- pages_inner = listinner->add_pages();
+ pages_inner = listinner->add_pages();
}
neighptr_inner = &pages_inner[npage_inner][npnt_inner];
n_inner = 0;
if (respamiddle) {
if (pgsize - npnt_middle < oneatom) {
- npnt_middle = 0;
- npage_middle++;
- if (npage_middle == listmiddle->maxpage)
- pages_middle = listmiddle->add_pages();
+ npnt_middle = 0;
+ npage_middle++;
+ if (npage_middle == listmiddle->maxpage)
+ pages_middle = listmiddle->add_pages();
}
neighptr_middle = &pages_middle[npage_middle][npnt_middle];
n_middle = 0;
@@ -467,35 +467,35 @@ void Neighbor::respa_bin_no_newton(NeighList *list)
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- if (j <= i) continue;
-
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- which = find_special(special[i],nspecial[i],tag[j]);
- if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
-
- if (rsq < cut_inner_sq) {
- if (which == 0) neighptr_inner[n_inner++] = j;
- else if (which > 0)
- neighptr_inner[n_inner++] = j ^ (which << SBBITS);
- }
-
- if (respamiddle &&
- rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
- if (which == 0) neighptr_middle[n_middle++] = j;
- else if (which > 0)
- neighptr_middle[n_middle++] = j ^ (which << SBBITS);
- }
- }
+ if (j <= i) continue;
+
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ which = find_special(special[i],nspecial[i],tag[j]);
+ if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+
+ if (rsq < cut_inner_sq) {
+ if (which == 0) neighptr_inner[n_inner++] = j;
+ else if (which > 0)
+ neighptr_inner[n_inner++] = j ^ (which << SBBITS);
+ }
+
+ if (respamiddle &&
+ rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
+ if (which == 0) neighptr_middle[n_middle++] = j;
+ else if (which > 0)
+ neighptr_middle[n_middle++] = j ^ (which << SBBITS);
+ }
+ }
}
}
@@ -519,7 +519,7 @@ void Neighbor::respa_bin_no_newton(NeighList *list)
numneigh_middle[i] = n_middle;
npnt_middle += n_middle;
if (n_middle > oneatom)
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
inum++;
@@ -529,7 +529,7 @@ void Neighbor::respa_bin_no_newton(NeighList *list)
listinner->inum = inum;
if (respamiddle) listmiddle->inum = inum;
}
-
+
/* ----------------------------------------------------------------------
multiple respa lists
binned neighbor list construction with full Newton's 3rd law
@@ -609,17 +609,17 @@ void Neighbor::respa_bin_newton(NeighList *list)
npnt_inner = 0;
npage_inner++;
if (npage_inner == listinner->maxpage)
- pages_inner = listinner->add_pages();
+ pages_inner = listinner->add_pages();
}
neighptr_inner = &pages_inner[npage_inner][npnt_inner];
n_inner = 0;
if (respamiddle) {
if (pgsize - npnt_middle < oneatom) {
- npnt_middle = 0;
- npage_middle++;
- if (npage_middle == listmiddle->maxpage)
- pages_middle = listmiddle->add_pages();
+ npnt_middle = 0;
+ npage_middle++;
+ if (npage_middle == listmiddle->maxpage)
+ pages_middle = listmiddle->add_pages();
}
neighptr_middle = &pages_middle[npage_middle][npnt_middle];
n_middle = 0;
@@ -636,11 +636,11 @@ void Neighbor::respa_bin_newton(NeighList *list)
for (j = bins[i]; j >= 0; j = bins[j]) {
if (j >= nlocal) {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp) {
- if (x[j][1] < ytmp) continue;
- if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
- }
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp) {
+ if (x[j][1] < ytmp) continue;
+ if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
+ }
}
jtype = type[j];
@@ -652,21 +652,21 @@ void Neighbor::respa_bin_newton(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- which = find_special(special[i],nspecial[i],tag[j]);
- if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
+ if (molecular) {
+ which = find_special(special[i],nspecial[i],tag[j]);
+ if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
if (rsq < cut_inner_sq) {
- if (which == 0) neighptr_inner[n_inner++] = j;
- else if (which > 0) neighptr_inner[n_inner++] = j ^ (which << SBBITS);
+ if (which == 0) neighptr_inner[n_inner++] = j;
+ else if (which > 0) neighptr_inner[n_inner++] = j ^ (which << SBBITS);
}
- if (respamiddle &&
- rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
- if (which == 0) neighptr_middle[n_middle++] = j;
- else if (which > 0)
- neighptr_middle[n_middle++] = j ^ (which << SBBITS);
+ if (respamiddle &&
+ rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
+ if (which == 0) neighptr_middle[n_middle++] = j;
+ else if (which > 0)
+ neighptr_middle[n_middle++] = j ^ (which << SBBITS);
}
}
}
@@ -676,33 +676,33 @@ void Neighbor::respa_bin_newton(NeighList *list)
ibin = coord2bin(x[i]);
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- which = find_special(special[i],nspecial[i],tag[j]);
- if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
-
- if (rsq < cut_inner_sq) {
- if (which == 0) neighptr_inner[n_inner++] = j;
- else if (which > 0)
- neighptr_inner[n_inner++] = j ^ (which << SBBITS);
- }
-
- if (respamiddle &&
- rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
- if (which == 0) neighptr_middle[n_middle++] = j;
- else if (which > 0)
- neighptr_middle[n_middle++] = j ^ (which << SBBITS);
- }
- }
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ which = find_special(special[i],nspecial[i],tag[j]);
+ if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+
+ if (rsq < cut_inner_sq) {
+ if (which == 0) neighptr_inner[n_inner++] = j;
+ else if (which > 0)
+ neighptr_inner[n_inner++] = j ^ (which << SBBITS);
+ }
+
+ if (respamiddle &&
+ rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
+ if (which == 0) neighptr_middle[n_middle++] = j;
+ else if (which > 0)
+ neighptr_middle[n_middle++] = j ^ (which << SBBITS);
+ }
+ }
}
}
@@ -726,7 +726,7 @@ void Neighbor::respa_bin_newton(NeighList *list)
numneigh_middle[i] = n_middle;
npnt_middle += n_middle;
if (n_middle > oneatom)
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
inum++;
@@ -816,17 +816,17 @@ void Neighbor::respa_bin_newton_tri(NeighList *list)
npnt_inner = 0;
npage_inner++;
if (npage_inner == listinner->maxpage)
- pages_inner = listinner->add_pages();
+ pages_inner = listinner->add_pages();
}
neighptr_inner = &pages_inner[npage_inner][npnt_inner];
n_inner = 0;
if (respamiddle) {
if (pgsize - npnt_middle < oneatom) {
- npnt_middle = 0;
- npage_middle++;
- if (npage_middle == listmiddle->maxpage)
- pages_middle = listmiddle->add_pages();
+ npnt_middle = 0;
+ npage_middle++;
+ if (npage_middle == listmiddle->maxpage)
+ pages_middle = listmiddle->add_pages();
}
neighptr_middle = &pages_middle[npage_middle][npnt_middle];
n_middle = 0;
@@ -846,42 +846,42 @@ void Neighbor::respa_bin_newton_tri(NeighList *list)
ibin = coord2bin(x[i]);
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp) {
- if (x[j][1] < ytmp) continue;
- if (x[j][1] == ytmp) {
- if (x[j][0] < xtmp) continue;
- if (x[j][0] == xtmp && j <= i) continue;
- }
- }
-
- jtype = type[j];
- if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) {
- which = find_special(special[i],nspecial[i],tag[j]);
- if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
-
- if (rsq < cut_inner_sq) {
- if (which == 0) neighptr_inner[n_inner++] = j;
- else if (which > 0)
- neighptr_inner[n_inner++] = j ^ (which << SBBITS);
- }
-
- if (respamiddle &&
- rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
- if (which == 0) neighptr_middle[n_middle++] = j;
- else if (which > 0)
- neighptr_middle[n_middle++] = j ^ (which << SBBITS);
- }
- }
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp) {
+ if (x[j][1] < ytmp) continue;
+ if (x[j][1] == ytmp) {
+ if (x[j][0] < xtmp) continue;
+ if (x[j][0] == xtmp && j <= i) continue;
+ }
+ }
+
+ jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq <= cutneighsq[itype][jtype]) {
+ if (molecular) {
+ which = find_special(special[i],nspecial[i],tag[j]);
+ if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
+ } else neighptr[n++] = j;
+
+ if (rsq < cut_inner_sq) {
+ if (which == 0) neighptr_inner[n_inner++] = j;
+ else if (which > 0)
+ neighptr_inner[n_inner++] = j ^ (which << SBBITS);
+ }
+
+ if (respamiddle &&
+ rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
+ if (which == 0) neighptr_middle[n_middle++] = j;
+ else if (which > 0)
+ neighptr_middle[n_middle++] = j ^ (which << SBBITS);
+ }
+ }
}
}
@@ -905,7 +905,7 @@ void Neighbor::respa_bin_newton_tri(NeighList *list)
numneigh_middle[i] = n_middle;
npnt_middle += n_middle;
if (n_middle > oneatom)
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
inum++;
diff --git a/src/neigh_respa.h b/src/neigh_respa.h
index 2b9b9d420ce50142864964bbc1d8582eba7e3fee..5ad76c98afe51d02161934917d9b4f544c774258 100644
--- a/src/neigh_respa.h
+++ b/src/neigh_respa.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/neigh_stencil.cpp b/src/neigh_stencil.cpp
index c72974a43e6208cb7ace82d109021a0950a2fead..34a5ddc305cbb71d78808d46531c4178dbd70999 100644
--- a/src/neigh_stencil.cpp
+++ b/src/neigh_stencil.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -45,7 +45,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
void Neighbor::stencil_half_bin_2d_no_newton(NeighList *list,
- int sx, int sy, int sz)
+ int sx, int sy, int sz)
{
int i,j;
int *stencil = list->stencil;
@@ -54,7 +54,7 @@ void Neighbor::stencil_half_bin_2d_no_newton(NeighList *list,
for (j = -sy; j <= sy; j++)
for (i = -sx; i <= sx; i++)
if (bin_distance(i,j,0) < cutneighmaxsq)
- stencil[nstencil++] = j*mbinx + i;
+ stencil[nstencil++] = j*mbinx + i;
list->nstencil = nstencil;
}
@@ -62,7 +62,7 @@ void Neighbor::stencil_half_bin_2d_no_newton(NeighList *list,
/* ---------------------------------------------------------------------- */
void Neighbor::stencil_half_bin_3d_no_newton(NeighList *list,
- int sx, int sy, int sz)
+ int sx, int sy, int sz)
{
int i,j,k;
int *stencil = list->stencil;
@@ -71,8 +71,8 @@ void Neighbor::stencil_half_bin_3d_no_newton(NeighList *list,
for (k = -sz; k <= sz; k++)
for (j = -sy; j <= sy; j++)
for (i = -sx; i <= sx; i++)
- if (bin_distance(i,j,k) < cutneighmaxsq)
- stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i;
+ if (bin_distance(i,j,k) < cutneighmaxsq)
+ stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i;
list->nstencil = nstencil;
}
@@ -80,7 +80,7 @@ void Neighbor::stencil_half_bin_3d_no_newton(NeighList *list,
/* ---------------------------------------------------------------------- */
void Neighbor::stencil_half_bin_2d_newton(NeighList *list,
- int sx, int sy, int sz)
+ int sx, int sy, int sz)
{
int i,j;
int *stencil = list->stencil;
@@ -89,8 +89,8 @@ void Neighbor::stencil_half_bin_2d_newton(NeighList *list,
for (j = 0; j <= sy; j++)
for (i = -sx; i <= sx; i++)
if (j > 0 || (j == 0 && i > 0))
- if (bin_distance(i,j,0) < cutneighmaxsq)
- stencil[nstencil++] = j*mbinx + i;
+ if (bin_distance(i,j,0) < cutneighmaxsq)
+ stencil[nstencil++] = j*mbinx + i;
list->nstencil = nstencil;
}
@@ -98,7 +98,7 @@ void Neighbor::stencil_half_bin_2d_newton(NeighList *list,
/* ---------------------------------------------------------------------- */
void Neighbor::stencil_half_bin_3d_newton(NeighList *list,
- int sx, int sy, int sz)
+ int sx, int sy, int sz)
{
int i,j,k;
int *stencil = list->stencil;
@@ -107,9 +107,9 @@ void Neighbor::stencil_half_bin_3d_newton(NeighList *list,
for (k = 0; k <= sz; k++)
for (j = -sy; j <= sy; j++)
for (i = -sx; i <= sx; i++)
- if (k > 0 || j > 0 || (j == 0 && i > 0))
- if (bin_distance(i,j,k) < cutneighmaxsq)
- stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i;
+ if (k > 0 || j > 0 || (j == 0 && i > 0))
+ if (bin_distance(i,j,k) < cutneighmaxsq)
+ stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i;
list->nstencil = nstencil;
}
@@ -117,7 +117,7 @@ void Neighbor::stencil_half_bin_3d_newton(NeighList *list,
/* ---------------------------------------------------------------------- */
void Neighbor::stencil_half_bin_2d_newton_tri(NeighList *list,
- int sx, int sy, int sz)
+ int sx, int sy, int sz)
{
int i,j;
int *stencil = list->stencil;
@@ -126,7 +126,7 @@ void Neighbor::stencil_half_bin_2d_newton_tri(NeighList *list,
for (j = 0; j <= sy; j++)
for (i = -sx; i <= sx; i++)
if (bin_distance(i,j,0) < cutneighmaxsq)
- stencil[nstencil++] = j*mbinx + i;
+ stencil[nstencil++] = j*mbinx + i;
list->nstencil = nstencil;
}
@@ -134,7 +134,7 @@ void Neighbor::stencil_half_bin_2d_newton_tri(NeighList *list,
/* ---------------------------------------------------------------------- */
void Neighbor::stencil_half_bin_3d_newton_tri(NeighList *list,
- int sx, int sy, int sz)
+ int sx, int sy, int sz)
{
int i,j,k;
int *stencil = list->stencil;
@@ -143,8 +143,8 @@ void Neighbor::stencil_half_bin_3d_newton_tri(NeighList *list,
for (k = 0; k <= sz; k++)
for (j = -sy; j <= sy; j++)
for (i = -sx; i <= sx; i++)
- if (bin_distance(i,j,k) < cutneighmaxsq)
- stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i;
+ if (bin_distance(i,j,k) < cutneighmaxsq)
+ stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i;
list->nstencil = nstencil;
}
@@ -152,7 +152,7 @@ void Neighbor::stencil_half_bin_3d_newton_tri(NeighList *list,
/* ---------------------------------------------------------------------- */
void Neighbor::stencil_half_multi_2d_no_newton(NeighList *list,
- int sx, int sy, int sz)
+ int sx, int sy, int sz)
{
int i,j,n;
double rsq,typesq;
@@ -171,11 +171,11 @@ void Neighbor::stencil_half_multi_2d_no_newton(NeighList *list,
n = 0;
for (j = -sy; j <= sy; j++)
for (i = -sx; i <= sx; i++) {
- rsq = bin_distance(i,j,0);
- if (rsq < typesq) {
- distsq[n] = rsq;
- s[n++] = j*mbinx + i;
- }
+ rsq = bin_distance(i,j,0);
+ if (rsq < typesq) {
+ distsq[n] = rsq;
+ s[n++] = j*mbinx + i;
+ }
}
nstencil_multi[itype] = n;
}
@@ -184,7 +184,7 @@ void Neighbor::stencil_half_multi_2d_no_newton(NeighList *list,
/* ---------------------------------------------------------------------- */
void Neighbor::stencil_half_multi_3d_no_newton(NeighList *list,
- int sx, int sy, int sz)
+ int sx, int sy, int sz)
{
int i,j,k,n;
double rsq,typesq;
@@ -203,13 +203,13 @@ void Neighbor::stencil_half_multi_3d_no_newton(NeighList *list,
n = 0;
for (k = -sz; k <= sz; k++)
for (j = -sy; j <= sy; j++)
- for (i = -sx; i <= sx; i++) {
- rsq = bin_distance(i,j,k);
- if (rsq < typesq) {
- distsq[n] = rsq;
- s[n++] = k*mbiny*mbinx + j*mbinx + i;
- }
- }
+ for (i = -sx; i <= sx; i++) {
+ rsq = bin_distance(i,j,k);
+ if (rsq < typesq) {
+ distsq[n] = rsq;
+ s[n++] = k*mbiny*mbinx + j*mbinx + i;
+ }
+ }
nstencil_multi[itype] = n;
}
}
@@ -217,7 +217,7 @@ void Neighbor::stencil_half_multi_3d_no_newton(NeighList *list,
/* ---------------------------------------------------------------------- */
void Neighbor::stencil_half_multi_2d_newton(NeighList *list,
- int sx, int sy, int sz)
+ int sx, int sy, int sz)
{
int i,j,n;
double rsq,typesq;
@@ -236,13 +236,13 @@ void Neighbor::stencil_half_multi_2d_newton(NeighList *list,
n = 0;
for (j = 0; j <= sy; j++)
for (i = -sx; i <= sx; i++)
- if (j > 0 || (j == 0 && i > 0)) {
- rsq = bin_distance(i,j,0);
- if (rsq < typesq) {
- distsq[n] = rsq;
- s[n++] = j*mbinx + i;
- }
- }
+ if (j > 0 || (j == 0 && i > 0)) {
+ rsq = bin_distance(i,j,0);
+ if (rsq < typesq) {
+ distsq[n] = rsq;
+ s[n++] = j*mbinx + i;
+ }
+ }
nstencil_multi[itype] = n;
}
}
@@ -250,7 +250,7 @@ void Neighbor::stencil_half_multi_2d_newton(NeighList *list,
/* ---------------------------------------------------------------------- */
void Neighbor::stencil_half_multi_3d_newton(NeighList *list,
- int sx, int sy, int sz)
+ int sx, int sy, int sz)
{
int i,j,k,n;
double rsq,typesq;
@@ -269,14 +269,14 @@ void Neighbor::stencil_half_multi_3d_newton(NeighList *list,
n = 0;
for (k = 0; k <= sz; k++)
for (j = -sy; j <= sy; j++)
- for (i = -sx; i <= sx; i++)
- if (k > 0 || j > 0 || (j == 0 && i > 0)) {
- rsq = bin_distance(i,j,k);
- if (rsq < typesq) {
- distsq[n] = rsq;
- s[n++] = k*mbiny*mbinx + j*mbinx + i;
- }
- }
+ for (i = -sx; i <= sx; i++)
+ if (k > 0 || j > 0 || (j == 0 && i > 0)) {
+ rsq = bin_distance(i,j,k);
+ if (rsq < typesq) {
+ distsq[n] = rsq;
+ s[n++] = k*mbiny*mbinx + j*mbinx + i;
+ }
+ }
nstencil_multi[itype] = n;
}
}
@@ -284,7 +284,7 @@ void Neighbor::stencil_half_multi_3d_newton(NeighList *list,
/* ---------------------------------------------------------------------- */
void Neighbor::stencil_half_multi_2d_newton_tri(NeighList *list,
- int sx, int sy, int sz)
+ int sx, int sy, int sz)
{
int i,j,n;
double rsq,typesq;
@@ -303,11 +303,11 @@ void Neighbor::stencil_half_multi_2d_newton_tri(NeighList *list,
n = 0;
for (j = 0; j <= sy; j++)
for (i = -sx; i <= sx; i++) {
- rsq = bin_distance(i,j,0);
- if (rsq < typesq) {
- distsq[n] = rsq;
- s[n++] = j*mbinx + i;
- }
+ rsq = bin_distance(i,j,0);
+ if (rsq < typesq) {
+ distsq[n] = rsq;
+ s[n++] = j*mbinx + i;
+ }
}
nstencil_multi[itype] = n;
}
@@ -317,7 +317,7 @@ void Neighbor::stencil_half_multi_2d_newton_tri(NeighList *list,
/* ---------------------------------------------------------------------- */
void Neighbor::stencil_half_multi_3d_newton_tri(NeighList *list,
- int sx, int sy, int sz)
+ int sx, int sy, int sz)
{
int i,j,k,n;
double rsq,typesq;
@@ -336,13 +336,13 @@ void Neighbor::stencil_half_multi_3d_newton_tri(NeighList *list,
n = 0;
for (k = 0; k <= sz; k++)
for (j = -sy; j <= sy; j++)
- for (i = -sx; i <= sx; i++) {
- rsq = bin_distance(i,j,k);
- if (rsq < typesq) {
- distsq[n] = rsq;
- s[n++] = k*mbiny*mbinx + j*mbinx + i;
- }
- }
+ for (i = -sx; i <= sx; i++) {
+ rsq = bin_distance(i,j,k);
+ if (rsq < typesq) {
+ distsq[n] = rsq;
+ s[n++] = k*mbiny*mbinx + j*mbinx + i;
+ }
+ }
nstencil_multi[itype] = n;
}
}
@@ -350,7 +350,7 @@ void Neighbor::stencil_half_multi_3d_newton_tri(NeighList *list,
/* ---------------------------------------------------------------------- */
void Neighbor::stencil_full_bin_2d(NeighList *list,
- int sx, int sy, int sz)
+ int sx, int sy, int sz)
{
int i,j;
int *stencil = list->stencil;
@@ -359,7 +359,7 @@ void Neighbor::stencil_full_bin_2d(NeighList *list,
for (j = -sy; j <= sy; j++)
for (i = -sx; i <= sx; i++)
if (bin_distance(i,j,0) < cutneighmaxsq)
- stencil[nstencil++] = j*mbinx + i;
+ stencil[nstencil++] = j*mbinx + i;
list->nstencil = nstencil;
}
@@ -367,7 +367,7 @@ void Neighbor::stencil_full_bin_2d(NeighList *list,
/* ---------------------------------------------------------------------- */
void Neighbor::stencil_full_ghost_bin_2d(NeighList *list,
- int sx, int sy, int sz)
+ int sx, int sy, int sz)
{
int i,j;
int *stencil = list->stencil;
@@ -377,10 +377,10 @@ void Neighbor::stencil_full_ghost_bin_2d(NeighList *list,
for (j = -sy; j <= sy; j++)
for (i = -sx; i <= sx; i++)
if (bin_distance(i,j,0) < cutneighmaxsq) {
- stencilxyz[nstencil][0] = i;
- stencilxyz[nstencil][1] = j;
- stencilxyz[nstencil][2] = 0;
- stencil[nstencil++] = j*mbinx + i;
+ stencilxyz[nstencil][0] = i;
+ stencilxyz[nstencil][1] = j;
+ stencilxyz[nstencil][2] = 0;
+ stencil[nstencil++] = j*mbinx + i;
}
list->nstencil = nstencil;
@@ -389,7 +389,7 @@ void Neighbor::stencil_full_ghost_bin_2d(NeighList *list,
/* ---------------------------------------------------------------------- */
void Neighbor::stencil_full_bin_3d(NeighList *list,
- int sx, int sy, int sz)
+ int sx, int sy, int sz)
{
int i,j,k;
int *stencil = list->stencil;
@@ -398,8 +398,8 @@ void Neighbor::stencil_full_bin_3d(NeighList *list,
for (k = -sz; k <= sz; k++)
for (j = -sy; j <= sy; j++)
for (i = -sx; i <= sx; i++)
- if (bin_distance(i,j,k) < cutneighmaxsq)
- stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i;
+ if (bin_distance(i,j,k) < cutneighmaxsq)
+ stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i;
list->nstencil = nstencil;
}
@@ -407,7 +407,7 @@ void Neighbor::stencil_full_bin_3d(NeighList *list,
/* ---------------------------------------------------------------------- */
void Neighbor::stencil_full_ghost_bin_3d(NeighList *list,
- int sx, int sy, int sz)
+ int sx, int sy, int sz)
{
int i,j,k;
int *stencil = list->stencil;
@@ -417,12 +417,12 @@ void Neighbor::stencil_full_ghost_bin_3d(NeighList *list,
for (k = -sz; k <= sz; k++)
for (j = -sy; j <= sy; j++)
for (i = -sx; i <= sx; i++)
- if (bin_distance(i,j,k) < cutneighmaxsq) {
- stencilxyz[nstencil][0] = i;
- stencilxyz[nstencil][1] = j;
- stencilxyz[nstencil][2] = k;
- stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i;
- }
+ if (bin_distance(i,j,k) < cutneighmaxsq) {
+ stencilxyz[nstencil][0] = i;
+ stencilxyz[nstencil][1] = j;
+ stencilxyz[nstencil][2] = k;
+ stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i;
+ }
list->nstencil = nstencil;
}
@@ -430,7 +430,7 @@ void Neighbor::stencil_full_ghost_bin_3d(NeighList *list,
/* ---------------------------------------------------------------------- */
void Neighbor::stencil_full_multi_2d(NeighList *list,
- int sx, int sy, int sz)
+ int sx, int sy, int sz)
{
int i,j,n;
double rsq,typesq;
@@ -449,11 +449,11 @@ void Neighbor::stencil_full_multi_2d(NeighList *list,
n = 0;
for (j = -sy; j <= sy; j++)
for (i = -sx; i <= sx; i++) {
- rsq = bin_distance(i,j,0);
- if (rsq < typesq) {
- distsq[n] = rsq;
- s[n++] = j*mbinx + i;
- }
+ rsq = bin_distance(i,j,0);
+ if (rsq < typesq) {
+ distsq[n] = rsq;
+ s[n++] = j*mbinx + i;
+ }
}
nstencil_multi[itype] = n;
}
@@ -462,7 +462,7 @@ void Neighbor::stencil_full_multi_2d(NeighList *list,
/* ---------------------------------------------------------------------- */
void Neighbor::stencil_full_multi_3d(NeighList *list,
- int sx, int sy, int sz)
+ int sx, int sy, int sz)
{
int i,j,k,n;
double rsq,typesq;
@@ -481,13 +481,13 @@ void Neighbor::stencil_full_multi_3d(NeighList *list,
n = 0;
for (k = -sz; k <= sz; k++)
for (j = -sy; j <= sy; j++)
- for (i = -sx; i <= sx; i++) {
- rsq = bin_distance(i,j,k);
- if (rsq < typesq) {
- distsq[n] = rsq;
- s[n++] = k*mbiny*mbinx + j*mbinx + i;
- }
- }
+ for (i = -sx; i <= sx; i++) {
+ rsq = bin_distance(i,j,k);
+ if (rsq < typesq) {
+ distsq[n] = rsq;
+ s[n++] = k*mbiny*mbinx + j*mbinx + i;
+ }
+ }
nstencil_multi[itype] = n;
}
}
diff --git a/src/neighbor.cpp b/src/neighbor.cpp
index 106b4f26b74d17bc9774394014571899ac13bd92..8c8183bf2dd248f5f49b26a1ecd441e087b92e67 100644
--- a/src/neighbor.cpp
+++ b/src/neighbor.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -219,10 +219,10 @@ void Neighbor::init()
triggersq = 0.25*skin*skin;
boxcheck = 0;
- if (domain->box_change && (domain->xperiodic || domain->yperiodic ||
- (dimension == 3 && domain->zperiodic)))
+ if (domain->box_change && (domain->xperiodic || domain->yperiodic ||
+ (dimension == 3 && domain->zperiodic)))
boxcheck = 1;
-
+
n = atom->ntypes;
if (cutneighsq == NULL) {
memory->create(cutneighsq,n+1,n+1,"neigh:cutneighsq");
@@ -251,8 +251,8 @@ void Neighbor::init()
cutneighmax = MAX(cutneighmax,cut);
if (force->pair && force->pair->ghostneigh) {
- cut = force->pair->cutghost[i][j] + skin;
- cutneighghostsq[i][j] = cut*cut;
+ cut = force->pair->cutghost[i][j] + skin;
+ cutneighghostsq[i][j] = cut*cut;
}
}
}
@@ -284,21 +284,21 @@ void Neighbor::init()
// flag = 2 otherwise or if KSpace solver is enabled
// pairwise portion of KSpace solver uses all 1-2,1-3,1-4 neighbors
- if (force->special_lj[1] == 0.0 && force->special_coul[1] == 0.0)
+ if (force->special_lj[1] == 0.0 && force->special_coul[1] == 0.0)
special_flag[1] = 0;
- else if (force->special_lj[1] == 1.0 && force->special_coul[1] == 1.0)
+ else if (force->special_lj[1] == 1.0 && force->special_coul[1] == 1.0)
special_flag[1] = 1;
else special_flag[1] = 2;
- if (force->special_lj[2] == 0.0 && force->special_coul[2] == 0.0)
+ if (force->special_lj[2] == 0.0 && force->special_coul[2] == 0.0)
special_flag[2] = 0;
- else if (force->special_lj[2] == 1.0 && force->special_coul[2] == 1.0)
+ else if (force->special_lj[2] == 1.0 && force->special_coul[2] == 1.0)
special_flag[2] = 1;
else special_flag[2] = 2;
- if (force->special_lj[3] == 0.0 && force->special_coul[3] == 0.0)
+ if (force->special_lj[3] == 0.0 && force->special_coul[3] == 0.0)
special_flag[3] = 0;
- else if (force->special_lj[3] == 1.0 && force->special_coul[3] == 1.0)
+ else if (force->special_lj[3] == 1.0 && force->special_coul[3] == 1.0)
special_flag[3] = 1;
else special_flag[3] = 2;
@@ -360,7 +360,7 @@ void Neighbor::init()
memory->create(bins,maxbin,"bins");
}
}
-
+
// exclusion lists for type, group, molecule settings from neigh_modify
n = atom->ntypes;
@@ -374,12 +374,12 @@ void Neighbor::init()
for (i = 1; i <= n; i++)
for (j = 1; j <= n; j++)
- ex_type[i][j] = 0;
+ ex_type[i][j] = 0;
for (i = 0; i < nex_type; i++) {
- if (ex1_type[i] <= 0 || ex1_type[i] > n ||
- ex2_type[i] <= 0 || ex2_type[i] > n)
- error->all(FLERR,"Invalid atom type in neighbor exclusion list");
+ if (ex1_type[i] <= 0 || ex1_type[i] > n ||
+ ex2_type[i] <= 0 || ex2_type[i] > n)
+ error->all(FLERR,"Invalid atom type in neighbor exclusion list");
ex_type[ex1_type[i]][ex2_type[i]] = 1;
ex_type[ex2_type[i]][ex1_type[i]] = 1;
}
@@ -451,14 +451,14 @@ void Neighbor::init()
lists[i]->dnum = requests[i]->dnum;
if (requests[i]->pair) {
- Pair *pair = (Pair *) requests[i]->requestor;
- pair->init_list(requests[i]->id,lists[i]);
+ Pair *pair = (Pair *) requests[i]->requestor;
+ pair->init_list(requests[i]->id,lists[i]);
} else if (requests[i]->fix) {
- Fix *fix = (Fix *) requests[i]->requestor;
- fix->init_list(requests[i]->id,lists[i]);
+ Fix *fix = (Fix *) requests[i]->requestor;
+ fix->init_list(requests[i]->id,lists[i]);
} else if (requests[i]->compute) {
- Compute *compute = (Compute *) requests[i]->requestor;
- compute->init_list(requests[i]->id,lists[i]);
+ Compute *compute = (Compute *) requests[i]->requestor;
+ compute->init_list(requests[i]->id,lists[i]);
}
}
@@ -487,68 +487,68 @@ void Neighbor::init()
for (i = 0; i < nlist; i++) {
if (requests[i]->copy)
- lists[i]->listcopy = lists[requests[i]->otherlist];
+ lists[i]->listcopy = lists[requests[i]->otherlist];
else if (requests[i]->skip) {
- lists[i]->listskip = lists[requests[i]->otherlist];
- lists[i]->copy_skip_info(requests[i]->iskip,requests[i]->ijskip);
+ lists[i]->listskip = lists[requests[i]->otherlist];
+ lists[i]->copy_skip_info(requests[i]->iskip,requests[i]->ijskip);
} else if (requests[i]->half_from_full)
- lists[i]->listfull = lists[i-1];
+ lists[i]->listfull = lists[i-1];
else if (requests[i]->granhistory) {
- lists[i-1]->listgranhistory = lists[i];
- for (int ifix = 0; ifix < modify->nfix; ifix++)
- if (strcmp(modify->fix[ifix]->style,"SHEAR_HISTORY") == 0)
- lists[i-1]->fix_history = (FixShearHistory *) modify->fix[ifix];
-
+ lists[i-1]->listgranhistory = lists[i];
+ for (int ifix = 0; ifix < modify->nfix; ifix++)
+ if (strcmp(modify->fix[ifix]->style,"SHEAR_HISTORY") == 0)
+ lists[i-1]->fix_history = (FixShearHistory *) modify->fix[ifix];
+
} else if (requests[i]->respaouter) {
- if (requests[i-1]->respainner) {
- lists[i]->respamiddle = 0;
- lists[i]->listinner = lists[i-1];
- } else {
- lists[i]->respamiddle = 1;
- lists[i]->listmiddle = lists[i-1];
- lists[i]->listinner = lists[i-2];
- }
+ if (requests[i-1]->respainner) {
+ lists[i]->respamiddle = 0;
+ lists[i]->listinner = lists[i-1];
+ } else {
+ lists[i]->respamiddle = 1;
+ lists[i]->listmiddle = lists[i-1];
+ lists[i]->listinner = lists[i-2];
+ }
} else if (requests[i]->pair && requests[i]->half) {
- for (j = 0; j < nlist; j++)
- if (requests[j]->full && requests[j]->occasional == 0 &&
- requests[j]->skip == 0) break;
- if (j < nlist) {
- requests[i]->half = 0;
- requests[i]->half_from_full = 1;
- lists[i]->listfull = lists[j];
- }
+ for (j = 0; j < nlist; j++)
+ if (requests[j]->full && requests[j]->occasional == 0 &&
+ requests[j]->skip == 0) break;
+ if (j < nlist) {
+ requests[i]->half = 0;
+ requests[i]->half_from_full = 1;
+ lists[i]->listfull = lists[j];
+ }
} else if (requests[i]->fix || requests[i]->compute) {
- for (j = 0; j < nlist; j++) {
- if (requests[i]->half && requests[j]->pair &&
- requests[j]->skip == 0 && requests[j]->half) break;
- if (requests[i]->full && requests[j]->pair &&
- requests[j]->skip == 0 && requests[j]->full) break;
- if (requests[i]->half && requests[j]->pair &&
- requests[j]->skip == 0 && requests[j]->respaouter) break;
- }
- if (j < nlist && requests[j]->cudable != requests[i]->cudable)
- j = nlist;
- if (j < nlist) {
- requests[i]->copy = 1;
- lists[i]->listcopy = lists[j];
- } else {
- for (j = 0; j < nlist; j++) {
- if (requests[i]->half && requests[j]->pair &&
- requests[j]->skip == 0 && requests[j]->full) break;
- }
- if (j < nlist && requests[j]->cudable != requests[i]->cudable)
- j = nlist;
- if (j < nlist) {
- requests[i]->half = 0;
- requests[i]->half_from_full = 1;
- lists[i]->listfull = lists[j];
- }
- }
+ for (j = 0; j < nlist; j++) {
+ if (requests[i]->half && requests[j]->pair &&
+ requests[j]->skip == 0 && requests[j]->half) break;
+ if (requests[i]->full && requests[j]->pair &&
+ requests[j]->skip == 0 && requests[j]->full) break;
+ if (requests[i]->half && requests[j]->pair &&
+ requests[j]->skip == 0 && requests[j]->respaouter) break;
+ }
+ if (j < nlist && requests[j]->cudable != requests[i]->cudable)
+ j = nlist;
+ if (j < nlist) {
+ requests[i]->copy = 1;
+ lists[i]->listcopy = lists[j];
+ } else {
+ for (j = 0; j < nlist; j++) {
+ if (requests[i]->half && requests[j]->pair &&
+ requests[j]->skip == 0 && requests[j]->full) break;
+ }
+ if (j < nlist && requests[j]->cudable != requests[i]->cudable)
+ j = nlist;
+ if (j < nlist) {
+ requests[i]->half = 0;
+ requests[i]->half_from_full = 1;
+ lists[i]->listfull = lists[j];
+ }
+ }
}
}
@@ -597,8 +597,8 @@ void Neighbor::init()
maxatom = atom->nmax;
for (i = 0; i < nlist; i++)
if (lists[i]->growflag) {
- lists[i]->grow(maxatom);
- lists[i]->add_pages();
+ lists[i]->grow(maxatom);
+ lists[i]->add_pages();
}
// setup 3 vectors of pairwise neighbor lists
@@ -619,9 +619,9 @@ void Neighbor::init()
for (i = 0; i < nlist; i++) {
if (lists[i]->buildflag) blist[nblist++] = i;
if (lists[i]->growflag && requests[i]->occasional == 0)
- glist[nglist++] = i;
+ glist[nglist++] = i;
if (lists[i]->stencilflag && requests[i]->occasional == 0)
- slist[nslist++] = i;
+ slist[nslist++] = i;
}
#ifdef NEIGH_LIST_DEBUG
@@ -639,21 +639,21 @@ void Neighbor::init()
while (!done) {
done = 1;
for (i = 0; i < nblist; i++) {
- NeighList *ptr = NULL;
- if (lists[blist[i]]->listfull) ptr = lists[blist[i]]->listfull;
- if (lists[blist[i]]->listcopy) ptr = lists[blist[i]]->listcopy;
- if (lists[blist[i]]->listskip) ptr = lists[blist[i]]->listskip;
- if (ptr == NULL) continue;
- for (m = 0; m < nlist; m++)
- if (ptr == lists[m]) break;
- for (j = 0; j < nblist; j++)
- if (m == blist[j]) break;
- if (j < i) continue;
- int tmp = blist[i];
- blist[i] = blist[j];
- blist[j] = tmp;
- done = 0;
- break;
+ NeighList *ptr = NULL;
+ if (lists[blist[i]]->listfull) ptr = lists[blist[i]]->listfull;
+ if (lists[blist[i]]->listcopy) ptr = lists[blist[i]]->listcopy;
+ if (lists[blist[i]]->listskip) ptr = lists[blist[i]]->listskip;
+ if (ptr == NULL) continue;
+ for (m = 0; m < nlist; m++)
+ if (ptr == lists[m]) break;
+ for (j = 0; j < nblist; j++)
+ if (m == blist[j]) break;
+ if (j < i) continue;
+ int tmp = blist[i];
+ blist[i] = blist[j];
+ blist[j] = tmp;
+ done = 0;
+ break;
}
}
@@ -664,7 +664,7 @@ void Neighbor::init()
// delete old requests
// copy current requests and style to old for next run
-
+
for (i = 0; i < old_nrequest; i++) delete old_requests[i];
memory->sfree(old_requests);
old_nrequest = nrequest;
@@ -693,15 +693,15 @@ void Neighbor::init()
if (atom->molecular && atom->ndihedrals && maxdihedral == 0) {
if (nprocs == 1) maxdihedral = atom->ndihedrals;
- else maxdihedral = static_cast<int>
- (LB_FACTOR * atom->ndihedrals / nprocs);
+ else maxdihedral = static_cast<int>
+ (LB_FACTOR * atom->ndihedrals / nprocs);
memory->create(dihedrallist,maxdihedral,5,"neigh:dihedrallist");
}
if (atom->molecular && atom->nimpropers && maximproper == 0) {
if (nprocs == 1) maximproper = atom->nimpropers;
else maximproper = static_cast<int>
- (LB_FACTOR * atom->nimpropers / nprocs);
+ (LB_FACTOR * atom->nimpropers / nprocs);
memory->create(improperlist,maximproper,5,"neigh:improperlist");
}
@@ -721,7 +721,7 @@ void Neighbor::init()
for (i = 0; i < atom->nlocal; i++) {
if (bond_off) break;
for (m = 0; m < atom->num_bond[i]; m++)
- if (atom->bond_type[i][m] <= 0) bond_off = 1;
+ if (atom->bond_type[i][m] <= 0) bond_off = 1;
}
}
@@ -729,7 +729,7 @@ void Neighbor::init()
for (i = 0; i < atom->nlocal; i++) {
if (angle_off) break;
for (m = 0; m < atom->num_angle[i]; m++)
- if (atom->angle_type[i][m] <= 0) angle_off = 1;
+ if (atom->angle_type[i][m] <= 0) angle_off = 1;
}
}
@@ -738,7 +738,7 @@ void Neighbor::init()
for (i = 0; i < atom->nlocal; i++) {
if (dihedral_off) break;
for (m = 0; m < atom->num_dihedral[i]; m++)
- if (atom->dihedral_type[i][m] <= 0) dihedral_off = 1;
+ if (atom->dihedral_type[i][m] <= 0) dihedral_off = 1;
}
}
@@ -747,7 +747,7 @@ void Neighbor::init()
for (i = 0; i < atom->nlocal; i++) {
if (improper_off) break;
for (m = 0; m < atom->num_improper[i]; m++)
- if (atom->improper_type[i][m] <= 0) improper_off = 1;
+ if (atom->improper_type[i][m] <= 0) improper_off = 1;
}
}
@@ -777,9 +777,9 @@ int Neighbor::request(void *requestor)
{
if (nrequest == maxrequest) {
maxrequest += RQDELTA;
- requests = (NeighRequest **)
+ requests = (NeighRequest **)
memory->srealloc(requests,maxrequest*sizeof(NeighRequest *),
- "neighbor:requests");
+ "neighbor:requests");
}
requests[nrequest] = new NeighRequest(lmp);
@@ -794,7 +794,7 @@ int Neighbor::request(void *requestor)
copy -> copy_from function
skip -> granular function if gran with granhistory,
respa function if respaouter,
- skip_from function for everything else
+ skip_from function for everything else
half_from_full, half, full, gran, respaouter ->
choose by newton and rq->newton and tri settings
style NSQ options = newton off, newton on
@@ -814,7 +814,7 @@ void Neighbor::choose_build(int index, NeighRequest *rq)
else if (rq->skip) {
if (rq->gran && lists[index]->listgranhistory)
- pb = &Neighbor::skip_from_granular;
+ pb = &Neighbor::skip_from_granular;
else if (rq->respaouter) pb = &Neighbor::skip_from_respa;
else pb = &Neighbor::skip_from;
@@ -824,74 +824,74 @@ void Neighbor::choose_build(int index, NeighRequest *rq)
} else if (rq->half) {
if (style == NSQ) {
- if (rq->newton == 0) {
- if (newton_pair == 0) pb = &Neighbor::half_nsq_no_newton;
- else if (newton_pair == 1) pb = &Neighbor::half_nsq_newton;
- } else if (rq->newton == 1) {
- pb = &Neighbor::half_nsq_newton;
- } else if (rq->newton == 2) {
- pb = &Neighbor::half_nsq_no_newton;
- }
+ if (rq->newton == 0) {
+ if (newton_pair == 0) pb = &Neighbor::half_nsq_no_newton;
+ else if (newton_pair == 1) pb = &Neighbor::half_nsq_newton;
+ } else if (rq->newton == 1) {
+ pb = &Neighbor::half_nsq_newton;
+ } else if (rq->newton == 2) {
+ pb = &Neighbor::half_nsq_no_newton;
+ }
} else if (style == BIN) {
- if (rq->newton == 0) {
- if (newton_pair == 0) pb = &Neighbor::half_bin_no_newton;
- else if (triclinic == 0) pb = &Neighbor::half_bin_newton;
- else if (triclinic == 1) pb = &Neighbor::half_bin_newton_tri;
- } else if (rq->newton == 1) {
- if (triclinic == 0) pb = &Neighbor::half_bin_newton;
- else if (triclinic == 1) pb = &Neighbor::half_bin_newton_tri;
- } else if (rq->newton == 2) pb = &Neighbor::half_bin_no_newton;
+ if (rq->newton == 0) {
+ if (newton_pair == 0) pb = &Neighbor::half_bin_no_newton;
+ else if (triclinic == 0) pb = &Neighbor::half_bin_newton;
+ else if (triclinic == 1) pb = &Neighbor::half_bin_newton_tri;
+ } else if (rq->newton == 1) {
+ if (triclinic == 0) pb = &Neighbor::half_bin_newton;
+ else if (triclinic == 1) pb = &Neighbor::half_bin_newton_tri;
+ } else if (rq->newton == 2) pb = &Neighbor::half_bin_no_newton;
} else if (style == MULTI) {
- if (rq->newton == 0) {
- if (newton_pair == 0) pb = &Neighbor::half_multi_no_newton;
- else if (triclinic == 0) pb = &Neighbor::half_multi_newton;
- else if (triclinic == 1) pb = &Neighbor::half_multi_newton_tri;
- } else if (rq->newton == 1) {
- if (triclinic == 0) pb = &Neighbor::half_multi_newton;
- else if (triclinic == 1) pb = &Neighbor::half_multi_newton_tri;
- } else if (rq->newton == 2) pb = &Neighbor::half_multi_no_newton;
+ if (rq->newton == 0) {
+ if (newton_pair == 0) pb = &Neighbor::half_multi_no_newton;
+ else if (triclinic == 0) pb = &Neighbor::half_multi_newton;
+ else if (triclinic == 1) pb = &Neighbor::half_multi_newton_tri;
+ } else if (rq->newton == 1) {
+ if (triclinic == 0) pb = &Neighbor::half_multi_newton;
+ else if (triclinic == 1) pb = &Neighbor::half_multi_newton_tri;
+ } else if (rq->newton == 2) pb = &Neighbor::half_multi_no_newton;
}
} else if (rq->full) {
if (style == NSQ) {
- if (rq->ghost == 0) pb = &Neighbor::full_nsq;
- else if (includegroup)
- error->all(FLERR,
- "Neighbor include group not allowed with ghost neighbors");
- else if (rq->ghost == 1) pb = &Neighbor::full_nsq_ghost;
+ if (rq->ghost == 0) pb = &Neighbor::full_nsq;
+ else if (includegroup)
+ error->all(FLERR,
+ "Neighbor include group not allowed with ghost neighbors");
+ else if (rq->ghost == 1) pb = &Neighbor::full_nsq_ghost;
} else if (style == BIN) {
- if (rq->ghost == 0) pb = &Neighbor::full_bin;
- else if (includegroup)
- error->all(FLERR,
- "Neighbor include group not allowed with ghost neighbors");
- else if (rq->ghost == 1) pb = &Neighbor::full_bin_ghost;
+ if (rq->ghost == 0) pb = &Neighbor::full_bin;
+ else if (includegroup)
+ error->all(FLERR,
+ "Neighbor include group not allowed with ghost neighbors");
+ else if (rq->ghost == 1) pb = &Neighbor::full_bin_ghost;
} else if (style == MULTI) {
- if (rq->ghost == 0) pb = &Neighbor::full_multi;
- else error->all(FLERR,
- "Neighbor multi not yet enabled for ghost neighbors");
+ if (rq->ghost == 0) pb = &Neighbor::full_multi;
+ else error->all(FLERR,
+ "Neighbor multi not yet enabled for ghost neighbors");
}
} else if (rq->gran) {
if (style == NSQ) {
- if (newton_pair == 0) pb = &Neighbor::granular_nsq_no_newton;
- else if (newton_pair == 1) pb = &Neighbor::granular_nsq_newton;
+ if (newton_pair == 0) pb = &Neighbor::granular_nsq_no_newton;
+ else if (newton_pair == 1) pb = &Neighbor::granular_nsq_newton;
} else if (style == BIN) {
- if (newton_pair == 0) pb = &Neighbor::granular_bin_no_newton;
- else if (triclinic == 0) pb = &Neighbor::granular_bin_newton;
- else if (triclinic == 1) pb = &Neighbor::granular_bin_newton_tri;
+ if (newton_pair == 0) pb = &Neighbor::granular_bin_no_newton;
+ else if (triclinic == 0) pb = &Neighbor::granular_bin_newton;
+ else if (triclinic == 1) pb = &Neighbor::granular_bin_newton_tri;
} else if (style == MULTI)
- error->all(FLERR,"Neighbor multi not yet enabled for granular");
+ error->all(FLERR,"Neighbor multi not yet enabled for granular");
} else if (rq->respaouter) {
if (style == NSQ) {
- if (newton_pair == 0) pb = &Neighbor::respa_nsq_no_newton;
- else if (newton_pair == 1) pb = &Neighbor::respa_nsq_newton;
+ if (newton_pair == 0) pb = &Neighbor::respa_nsq_no_newton;
+ else if (newton_pair == 1) pb = &Neighbor::respa_nsq_newton;
} else if (style == BIN) {
- if (newton_pair == 0) pb = &Neighbor::respa_bin_no_newton;
- else if (triclinic == 0) pb = &Neighbor::respa_bin_newton;
- else if (triclinic == 1) pb = &Neighbor::respa_bin_newton_tri;
+ if (newton_pair == 0) pb = &Neighbor::respa_bin_no_newton;
+ else if (triclinic == 0) pb = &Neighbor::respa_bin_newton;
+ else if (triclinic == 1) pb = &Neighbor::respa_bin_newton_tri;
} else if (style == MULTI)
- error->all(FLERR,"Neighbor multi not yet enabled for rRESPA");
+ error->all(FLERR,"Neighbor multi not yet enabled for rRESPA");
}
} else {
@@ -899,7 +899,7 @@ void Neighbor::choose_build(int index, NeighRequest *rq)
else if (rq->skip) {
if (rq->gran && lists[index]->listgranhistory)
- pb = &Neighbor::skip_from_granular;
+ pb = &Neighbor::skip_from_granular;
else if (rq->respaouter) pb = &Neighbor::skip_from_respa;
else pb = &Neighbor::skip_from;
@@ -909,74 +909,74 @@ void Neighbor::choose_build(int index, NeighRequest *rq)
} else if (rq->half) {
if (style == NSQ) {
- if (rq->newton == 0) {
- if (newton_pair == 0) pb = &Neighbor::half_nsq_no_newton_omp;
- else if (newton_pair == 1) pb = &Neighbor::half_nsq_newton_omp;
- } else if (rq->newton == 1) {
- pb = &Neighbor::half_nsq_newton_omp;
- } else if (rq->newton == 2) {
- pb = &Neighbor::half_nsq_no_newton_omp;
- }
+ if (rq->newton == 0) {
+ if (newton_pair == 0) pb = &Neighbor::half_nsq_no_newton_omp;
+ else if (newton_pair == 1) pb = &Neighbor::half_nsq_newton_omp;
+ } else if (rq->newton == 1) {
+ pb = &Neighbor::half_nsq_newton_omp;
+ } else if (rq->newton == 2) {
+ pb = &Neighbor::half_nsq_no_newton_omp;
+ }
} else if (style == BIN) {
- if (rq->newton == 0) {
- if (newton_pair == 0) pb = &Neighbor::half_bin_no_newton_omp;
- else if (triclinic == 0) pb = &Neighbor::half_bin_newton_omp;
- else if (triclinic == 1) pb = &Neighbor::half_bin_newton_tri_omp;
- } else if (rq->newton == 1) {
- if (triclinic == 0) pb = &Neighbor::half_bin_newton_omp;
- else if (triclinic == 1) pb = &Neighbor::half_bin_newton_tri_omp;
- } else if (rq->newton == 2) pb = &Neighbor::half_bin_no_newton_omp;
+ if (rq->newton == 0) {
+ if (newton_pair == 0) pb = &Neighbor::half_bin_no_newton_omp;
+ else if (triclinic == 0) pb = &Neighbor::half_bin_newton_omp;
+ else if (triclinic == 1) pb = &Neighbor::half_bin_newton_tri_omp;
+ } else if (rq->newton == 1) {
+ if (triclinic == 0) pb = &Neighbor::half_bin_newton_omp;
+ else if (triclinic == 1) pb = &Neighbor::half_bin_newton_tri_omp;
+ } else if (rq->newton == 2) pb = &Neighbor::half_bin_no_newton_omp;
} else if (style == MULTI) {
- if (rq->newton == 0) {
- if (newton_pair == 0) pb = &Neighbor::half_multi_no_newton_omp;
- else if (triclinic == 0) pb = &Neighbor::half_multi_newton_omp;
- else if (triclinic == 1) pb = &Neighbor::half_multi_newton_tri_omp;
- } else if (rq->newton == 1) {
- if (triclinic == 0) pb = &Neighbor::half_multi_newton_omp;
- else if (triclinic == 1) pb = &Neighbor::half_multi_newton_tri_omp;
- } else if (rq->newton == 2) pb = &Neighbor::half_multi_no_newton_omp;
+ if (rq->newton == 0) {
+ if (newton_pair == 0) pb = &Neighbor::half_multi_no_newton_omp;
+ else if (triclinic == 0) pb = &Neighbor::half_multi_newton_omp;
+ else if (triclinic == 1) pb = &Neighbor::half_multi_newton_tri_omp;
+ } else if (rq->newton == 1) {
+ if (triclinic == 0) pb = &Neighbor::half_multi_newton_omp;
+ else if (triclinic == 1) pb = &Neighbor::half_multi_newton_tri_omp;
+ } else if (rq->newton == 2) pb = &Neighbor::half_multi_no_newton_omp;
}
} else if (rq->full) {
if (style == NSQ) {
- if (rq->ghost == 0) pb = &Neighbor::full_nsq_omp;
- else if (includegroup)
- error->all(FLERR,
- "Neighbor include group not allowed with ghost neighbors");
- else if (rq->ghost == 1) pb = &Neighbor::full_nsq_ghost_omp;
+ if (rq->ghost == 0) pb = &Neighbor::full_nsq_omp;
+ else if (includegroup)
+ error->all(FLERR,
+ "Neighbor include group not allowed with ghost neighbors");
+ else if (rq->ghost == 1) pb = &Neighbor::full_nsq_ghost_omp;
} else if (style == BIN) {
- if (rq->ghost == 0) pb = &Neighbor::full_bin_omp;
- else if (includegroup)
- error->all(FLERR,
- "Neighbor include group not allowed with ghost neighbors");
- else if (rq->ghost == 1) pb = &Neighbor::full_bin_ghost_omp;
+ if (rq->ghost == 0) pb = &Neighbor::full_bin_omp;
+ else if (includegroup)
+ error->all(FLERR,
+ "Neighbor include group not allowed with ghost neighbors");
+ else if (rq->ghost == 1) pb = &Neighbor::full_bin_ghost_omp;
} else if (style == MULTI) {
- if (rq->ghost == 0) pb = &Neighbor::full_multi_omp;
- else error->all(FLERR,
- "Neighbor multi not yet enabled for ghost neighbors");
+ if (rq->ghost == 0) pb = &Neighbor::full_multi_omp;
+ else error->all(FLERR,
+ "Neighbor multi not yet enabled for ghost neighbors");
}
} else if (rq->gran) {
if (style == NSQ) {
- if (newton_pair == 0) pb = &Neighbor::granular_nsq_no_newton_omp;
- else if (newton_pair == 1) pb = &Neighbor::granular_nsq_newton_omp;
+ if (newton_pair == 0) pb = &Neighbor::granular_nsq_no_newton_omp;
+ else if (newton_pair == 1) pb = &Neighbor::granular_nsq_newton_omp;
} else if (style == BIN) {
- if (newton_pair == 0) pb = &Neighbor::granular_bin_no_newton_omp;
- else if (triclinic == 0) pb = &Neighbor::granular_bin_newton_omp;
- else if (triclinic == 1) pb = &Neighbor::granular_bin_newton_tri_omp;
+ if (newton_pair == 0) pb = &Neighbor::granular_bin_no_newton_omp;
+ else if (triclinic == 0) pb = &Neighbor::granular_bin_newton_omp;
+ else if (triclinic == 1) pb = &Neighbor::granular_bin_newton_tri_omp;
} else if (style == MULTI)
- error->all(FLERR,"Neighbor multi not yet enabled for granular");
+ error->all(FLERR,"Neighbor multi not yet enabled for granular");
} else if (rq->respaouter) {
if (style == NSQ) {
- if (newton_pair == 0) pb = &Neighbor::respa_nsq_no_newton_omp;
- else if (newton_pair == 1) pb = &Neighbor::respa_nsq_newton_omp;
+ if (newton_pair == 0) pb = &Neighbor::respa_nsq_no_newton_omp;
+ else if (newton_pair == 1) pb = &Neighbor::respa_nsq_newton_omp;
} else if (style == BIN) {
- if (newton_pair == 0) pb = &Neighbor::respa_bin_no_newton_omp;
- else if (triclinic == 0) pb = &Neighbor::respa_bin_newton_omp;
- else if (triclinic == 1) pb = &Neighbor::respa_bin_newton_tri_omp;
+ if (newton_pair == 0) pb = &Neighbor::respa_bin_no_newton_omp;
+ else if (triclinic == 0) pb = &Neighbor::respa_bin_newton_omp;
+ else if (triclinic == 1) pb = &Neighbor::respa_bin_newton_tri_omp;
} else if (style == MULTI)
- error->all(FLERR,"Neighbor multi not yet enabled for rRESPA");
+ error->all(FLERR,"Neighbor multi not yet enabled for rRESPA");
}
}
@@ -984,7 +984,7 @@ void Neighbor::choose_build(int index, NeighRequest *rq)
if (rq->ghost && !rq->full)
error->all(FLERR,
- "Neighbors of ghost atoms only allowed for full neighbor lists");
+ "Neighbors of ghost atoms only allowed for full neighbor lists");
pair_build[index] = pb;
}
@@ -1007,88 +1007,88 @@ void Neighbor::choose_stencil(int index, NeighRequest *rq)
else if (rq->half || rq->gran || rq->respaouter) {
if (style == BIN) {
if (rq->newton == 0) {
- if (newton_pair == 0) {
- if (dimension == 2)
- sc = &Neighbor::stencil_half_bin_2d_no_newton;
- else if (dimension == 3)
- sc = &Neighbor::stencil_half_bin_3d_no_newton;
- } else if (triclinic == 0) {
- if (dimension == 2)
- sc = &Neighbor::stencil_half_bin_2d_newton;
- else if (dimension == 3)
- sc = &Neighbor::stencil_half_bin_3d_newton;
- } else if (triclinic == 1) {
- if (dimension == 2)
- sc = &Neighbor::stencil_half_bin_2d_newton_tri;
- else if (dimension == 3)
- sc = &Neighbor::stencil_half_bin_3d_newton_tri;
- }
+ if (newton_pair == 0) {
+ if (dimension == 2)
+ sc = &Neighbor::stencil_half_bin_2d_no_newton;
+ else if (dimension == 3)
+ sc = &Neighbor::stencil_half_bin_3d_no_newton;
+ } else if (triclinic == 0) {
+ if (dimension == 2)
+ sc = &Neighbor::stencil_half_bin_2d_newton;
+ else if (dimension == 3)
+ sc = &Neighbor::stencil_half_bin_3d_newton;
+ } else if (triclinic == 1) {
+ if (dimension == 2)
+ sc = &Neighbor::stencil_half_bin_2d_newton_tri;
+ else if (dimension == 3)
+ sc = &Neighbor::stencil_half_bin_3d_newton_tri;
+ }
} else if (rq->newton == 1) {
- if (triclinic == 0) {
- if (dimension == 2)
- sc = &Neighbor::stencil_half_bin_2d_newton;
- else if (dimension == 3)
- sc = &Neighbor::stencil_half_bin_3d_newton;
- } else if (triclinic == 1) {
- if (dimension == 2)
- sc = &Neighbor::stencil_half_bin_2d_newton_tri;
- else if (dimension == 3)
- sc = &Neighbor::stencil_half_bin_3d_newton_tri;
- }
+ if (triclinic == 0) {
+ if (dimension == 2)
+ sc = &Neighbor::stencil_half_bin_2d_newton;
+ else if (dimension == 3)
+ sc = &Neighbor::stencil_half_bin_3d_newton;
+ } else if (triclinic == 1) {
+ if (dimension == 2)
+ sc = &Neighbor::stencil_half_bin_2d_newton_tri;
+ else if (dimension == 3)
+ sc = &Neighbor::stencil_half_bin_3d_newton_tri;
+ }
} else if (rq->newton == 2) {
- if (dimension == 2)
- sc = &Neighbor::stencil_half_bin_2d_no_newton;
- else if (dimension == 3)
- sc = &Neighbor::stencil_half_bin_3d_no_newton;
+ if (dimension == 2)
+ sc = &Neighbor::stencil_half_bin_2d_no_newton;
+ else if (dimension == 3)
+ sc = &Neighbor::stencil_half_bin_3d_no_newton;
}
} else if (style == MULTI) {
if (rq->newton == 0) {
- if (newton_pair == 0) {
- if (dimension == 2)
- sc = &Neighbor::stencil_half_multi_2d_no_newton;
- else if (dimension == 3)
- sc = &Neighbor::stencil_half_multi_3d_no_newton;
- } else if (triclinic == 0) {
- if (dimension == 2)
- sc = &Neighbor::stencil_half_multi_2d_newton;
- else if (dimension == 3)
- sc = &Neighbor::stencil_half_multi_3d_newton;
- } else if (triclinic == 1) {
- if (dimension == 2)
- sc = &Neighbor::stencil_half_multi_2d_newton_tri;
- else if (dimension == 3)
- sc = &Neighbor::stencil_half_multi_3d_newton_tri;
- }
+ if (newton_pair == 0) {
+ if (dimension == 2)
+ sc = &Neighbor::stencil_half_multi_2d_no_newton;
+ else if (dimension == 3)
+ sc = &Neighbor::stencil_half_multi_3d_no_newton;
+ } else if (triclinic == 0) {
+ if (dimension == 2)
+ sc = &Neighbor::stencil_half_multi_2d_newton;
+ else if (dimension == 3)
+ sc = &Neighbor::stencil_half_multi_3d_newton;
+ } else if (triclinic == 1) {
+ if (dimension == 2)
+ sc = &Neighbor::stencil_half_multi_2d_newton_tri;
+ else if (dimension == 3)
+ sc = &Neighbor::stencil_half_multi_3d_newton_tri;
+ }
} else if (rq->newton == 1) {
- if (triclinic == 0) {
- if (dimension == 2)
- sc = &Neighbor::stencil_half_multi_2d_newton;
- else if (dimension == 3)
- sc = &Neighbor::stencil_half_multi_3d_newton;
- } else if (triclinic == 1) {
- if (dimension == 2)
- sc = &Neighbor::stencil_half_multi_2d_newton_tri;
- else if (dimension == 3)
- sc = &Neighbor::stencil_half_multi_3d_newton_tri;
- }
+ if (triclinic == 0) {
+ if (dimension == 2)
+ sc = &Neighbor::stencil_half_multi_2d_newton;
+ else if (dimension == 3)
+ sc = &Neighbor::stencil_half_multi_3d_newton;
+ } else if (triclinic == 1) {
+ if (dimension == 2)
+ sc = &Neighbor::stencil_half_multi_2d_newton_tri;
+ else if (dimension == 3)
+ sc = &Neighbor::stencil_half_multi_3d_newton_tri;
+ }
} else if (rq->newton == 2) {
- if (dimension == 2)
- sc = &Neighbor::stencil_half_multi_2d_no_newton;
- else if (dimension == 3)
- sc = &Neighbor::stencil_half_multi_3d_no_newton;
+ if (dimension == 2)
+ sc = &Neighbor::stencil_half_multi_2d_no_newton;
+ else if (dimension == 3)
+ sc = &Neighbor::stencil_half_multi_3d_no_newton;
}
}
} else if (rq->full) {
if (style == BIN) {
if (dimension == 2) {
- if (rq->ghost) sc = &Neighbor::stencil_full_ghost_bin_2d;
- else sc = &Neighbor::stencil_full_bin_2d;
+ if (rq->ghost) sc = &Neighbor::stencil_full_ghost_bin_2d;
+ else sc = &Neighbor::stencil_full_bin_2d;
}
else if (dimension == 3) {
- if (rq->ghost) sc = &Neighbor::stencil_full_ghost_bin_3d;
- else sc = &Neighbor::stencil_full_bin_3d;
+ if (rq->ghost) sc = &Neighbor::stencil_full_ghost_bin_3d;
+ else sc = &Neighbor::stencil_full_bin_3d;
}
} else if (style == MULTI) {
if (dimension == 2) sc = &Neighbor::stencil_full_multi_2d;
@@ -1167,12 +1167,12 @@ int Neighbor::check_distance()
domain->box_corners();
delta1 = delta2 = 0.0;
for (int i = 0; i < 8; i++) {
- delx = corners[i][0] - corners_hold[i][0];
- dely = corners[i][1] - corners_hold[i][1];
- delz = corners[i][2] - corners_hold[i][2];
- delta = sqrt(delx*delx + dely*dely + delz*delz);
- if (delta > delta1) delta1 = delta;
- else if (delta > delta2) delta2 = delta;
+ delx = corners[i][0] - corners_hold[i][0];
+ dely = corners[i][1] - corners_hold[i][1];
+ delz = corners[i][2] - corners_hold[i][2];
+ delta = sqrt(delx*delx + dely*dely + delz*delz);
+ if (delta > delta1) delta1 = delta;
+ else if (delta > delta2) delta2 = delta;
}
delta = 0.5 * (skin - (delta1+delta2));
deltasq = delta*delta;
@@ -1228,20 +1228,20 @@ void Neighbor::build()
}
if (boxcheck) {
if (triclinic == 0) {
- boxlo_hold[0] = bboxlo[0];
- boxlo_hold[1] = bboxlo[1];
- boxlo_hold[2] = bboxlo[2];
- boxhi_hold[0] = bboxhi[0];
- boxhi_hold[1] = bboxhi[1];
- boxhi_hold[2] = bboxhi[2];
+ boxlo_hold[0] = bboxlo[0];
+ boxlo_hold[1] = bboxlo[1];
+ boxlo_hold[2] = bboxlo[2];
+ boxhi_hold[0] = bboxhi[0];
+ boxhi_hold[1] = bboxhi[1];
+ boxhi_hold[2] = bboxhi[2];
} else {
- domain->box_corners();
- corners = domain->corners;
- for (i = 0; i < 8; i++) {
- corners_hold[i][0] = corners[i][0];
- corners_hold[i][1] = corners[i][1];
- corners_hold[i][2] = corners[i][2];
- }
+ domain->box_corners();
+ corners = domain->corners;
+ for (i = 0; i < 8; i++) {
+ corners_hold[i][0] = corners[i][0];
+ corners_hold[i][1] = corners[i][1];
+ corners_hold[i][2] = corners[i][2];
+ }
}
}
}
@@ -1258,7 +1258,7 @@ void Neighbor::build()
maxatom = atom->nmax;
for (i = 0; i < nglist; i++) lists[glist[i]]->grow(maxatom);
}
-
+
// extend atom bin list if necessary
if (style != NSQ && atom->nmax > maxbin) {
@@ -1325,7 +1325,7 @@ void Neighbor::build_one(int i)
if (dist_check && update->whichflag) flag = check_distance();
if (flag && me == 0)
error->warning(FLERR,"Building an occasional neighobr list when "
- "atoms may have moved too far");
+ "atoms may have moved too far");
(this->*pair_build[i])(lists[i]);
}
@@ -1430,12 +1430,12 @@ void Neighbor::setup_bins()
bininvx = 1.0 / binsizex;
bininvy = 1.0 / binsizey;
bininvz = 1.0 / binsizez;
-
- if (binsize_optimal*bininvx > CUT2BIN_RATIO ||
- binsize_optimal*bininvy > CUT2BIN_RATIO ||
+
+ if (binsize_optimal*bininvx > CUT2BIN_RATIO ||
+ binsize_optimal*bininvy > CUT2BIN_RATIO ||
binsize_optimal*bininvz > CUT2BIN_RATIO)
error->all(FLERR,"Cannot use neighbor bins - box size << cutoff");
-
+
// mbinlo/hi = lowest and highest global bins my ghost atoms could be in
// coord = lowest and highest values of coords for my ghost atoms
// static_cast(-1.5) = -1, so subract additional -1
@@ -1534,7 +1534,7 @@ double Neighbor::bin_distance(int i, int j, int k)
if (k > 0) delz = (k-1)*binsizez;
else if (k == 0) delz = 0.0;
else delz = (k+1)*binsizez;
-
+
return (delx*delx + dely*dely + delz*delz);
}
@@ -1603,59 +1603,59 @@ void Neighbor::modify_params(int narg, char **arg)
if (iarg+2 > narg) error->all(FLERR,"Illegal neigh_modify command");
includegroup = group->find(arg[iarg+1]);
if (includegroup < 0)
- error->all(FLERR,"Invalid group ID in neigh_modify command");
+ error->all(FLERR,"Invalid group ID in neigh_modify command");
if (includegroup && (atom->firstgroupname == NULL ||
- strcmp(arg[iarg+1],atom->firstgroupname) != 0))
- error->all(FLERR,
- "Neigh_modify include group != atom_modify first group");
+ strcmp(arg[iarg+1],atom->firstgroupname) != 0))
+ error->all(FLERR,
+ "Neigh_modify include group != atom_modify first group");
iarg += 2;
} else if (strcmp(arg[iarg],"exclude") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal neigh_modify command");
if (strcmp(arg[iarg+1],"type") == 0) {
- if (iarg+4 > narg) error->all(FLERR,"Illegal neigh_modify command");
- if (nex_type == maxex_type) {
- maxex_type += EXDELTA;
- memory->grow(ex1_type,maxex_type,"neigh:ex1_type");
- memory->grow(ex2_type,maxex_type,"neigh:ex2_type");
- }
- ex1_type[nex_type] = atoi(arg[iarg+2]);
- ex2_type[nex_type] = atoi(arg[iarg+3]);
- nex_type++;
- iarg += 4;
+ if (iarg+4 > narg) error->all(FLERR,"Illegal neigh_modify command");
+ if (nex_type == maxex_type) {
+ maxex_type += EXDELTA;
+ memory->grow(ex1_type,maxex_type,"neigh:ex1_type");
+ memory->grow(ex2_type,maxex_type,"neigh:ex2_type");
+ }
+ ex1_type[nex_type] = atoi(arg[iarg+2]);
+ ex2_type[nex_type] = atoi(arg[iarg+3]);
+ nex_type++;
+ iarg += 4;
} else if (strcmp(arg[iarg+1],"group") == 0) {
- if (iarg+4 > narg) error->all(FLERR,"Illegal neigh_modify command");
- if (nex_group == maxex_group) {
- maxex_group += EXDELTA;
- memory->grow(ex1_group,maxex_group,"neigh:ex1_group");
- memory->grow(ex2_group,maxex_group,"neigh:ex2_group");
- }
- ex1_group[nex_group] = group->find(arg[iarg+2]);
- ex2_group[nex_group] = group->find(arg[iarg+3]);
- if (ex1_group[nex_group] == -1 || ex2_group[nex_group] == -1)
- error->all(FLERR,"Invalid group ID in neigh_modify command");
- nex_group++;
- iarg += 4;
+ if (iarg+4 > narg) error->all(FLERR,"Illegal neigh_modify command");
+ if (nex_group == maxex_group) {
+ maxex_group += EXDELTA;
+ memory->grow(ex1_group,maxex_group,"neigh:ex1_group");
+ memory->grow(ex2_group,maxex_group,"neigh:ex2_group");
+ }
+ ex1_group[nex_group] = group->find(arg[iarg+2]);
+ ex2_group[nex_group] = group->find(arg[iarg+3]);
+ if (ex1_group[nex_group] == -1 || ex2_group[nex_group] == -1)
+ error->all(FLERR,"Invalid group ID in neigh_modify command");
+ nex_group++;
+ iarg += 4;
} else if (strcmp(arg[iarg+1],"molecule") == 0) {
- if (iarg+3 > narg) error->all(FLERR,"Illegal neigh_modify command");
- if (atom->molecule_flag == 0)
- error->all(FLERR,"Neigh_modify exclude molecule "
- "requires atom attribute molecule");
- if (nex_mol == maxex_mol) {
- maxex_mol += EXDELTA;
- memory->grow(ex_mol_group,maxex_mol,"neigh:ex_mol_group");
- }
- ex_mol_group[nex_mol] = group->find(arg[iarg+2]);
- if (ex_mol_group[nex_mol] == -1)
- error->all(FLERR,"Invalid group ID in neigh_modify command");
- nex_mol++;
- iarg += 3;
+ if (iarg+3 > narg) error->all(FLERR,"Illegal neigh_modify command");
+ if (atom->molecule_flag == 0)
+ error->all(FLERR,"Neigh_modify exclude molecule "
+ "requires atom attribute molecule");
+ if (nex_mol == maxex_mol) {
+ maxex_mol += EXDELTA;
+ memory->grow(ex_mol_group,maxex_mol,"neigh:ex_mol_group");
+ }
+ ex_mol_group[nex_mol] = group->find(arg[iarg+2]);
+ if (ex_mol_group[nex_mol] == -1)
+ error->all(FLERR,"Invalid group ID in neigh_modify command");
+ nex_mol++;
+ iarg += 3;
} else if (strcmp(arg[iarg+1],"none") == 0) {
- nex_type = nex_group = nex_mol = 0;
- iarg += 2;
+ nex_type = nex_group = nex_mol = 0;
+ iarg += 2;
} else error->all(FLERR,"Illegal neigh_modify command");
} else error->all(FLERR,"Illegal neigh_modify command");
@@ -1684,9 +1684,9 @@ void Neighbor::bin_atoms()
int bitmask = group->bitmask[includegroup];
for (i = nall-1; i >= nlocal; i--) {
if (mask[i] & bitmask) {
- ibin = coord2bin(x[i]);
- bins[i] = binhead[ibin];
- binhead[ibin] = i;
+ ibin = coord2bin(x[i]);
+ bins[i] = binhead[ibin];
+ binhead[ibin] = i;
}
}
for (i = atom->nfirst-1; i >= 0; i--) {
@@ -1727,7 +1727,7 @@ int Neighbor::coord2bin(double *x)
ix = MIN(ix,nbinx-1);
} else
ix = static_cast<int> ((x[0]-bboxlo[0])*bininvx) - 1;
-
+
if (x[1] >= bboxhi[1])
iy = static_cast<int> ((x[1]-bboxhi[1])*bininvy) + nbiny;
else if (x[1] >= bboxlo[1]) {
@@ -1735,7 +1735,7 @@ int Neighbor::coord2bin(double *x)
iy = MIN(iy,nbiny-1);
} else
iy = static_cast<int> ((x[1]-bboxlo[1])*bininvy) - 1;
-
+
if (x[2] >= bboxhi[2])
iz = static_cast<int> ((x[2]-bboxhi[2])*bininvz) + nbinz;
else if (x[2] >= bboxlo[2]) {
@@ -1760,7 +1760,7 @@ int Neighbor::coord2bin(double *x, int &ix, int &iy, int &iz)
ix = MIN(ix,nbinx-1);
} else
ix = static_cast<int> ((x[0]-bboxlo[0])*bininvx) - 1;
-
+
if (x[1] >= bboxhi[1])
iy = static_cast<int> ((x[1]-bboxhi[1])*bininvy) + nbiny;
else if (x[1] >= bboxlo[1]) {
@@ -1768,7 +1768,7 @@ int Neighbor::coord2bin(double *x, int &ix, int &iy, int &iz)
iy = MIN(iy,nbiny-1);
} else
iy = static_cast<int> ((x[1]-bboxlo[1])*bininvy) - 1;
-
+
if (x[2] >= bboxhi[2])
iz = static_cast<int> ((x[2]-bboxhi[2])*bininvz) + nbinz;
else if (x[2] >= bboxlo[2]) {
@@ -1790,7 +1790,7 @@ int Neighbor::coord2bin(double *x, int &ix, int &iy, int &iz)
------------------------------------------------------------------------- */
int Neighbor::exclusion(int i, int j, int itype, int jtype,
- int *mask, int *molecule) const {
+ int *mask, int *molecule) const {
int m;
if (nex_type && ex_type[itype][jtype]) return 1;
@@ -1805,7 +1805,7 @@ int Neighbor::exclusion(int i, int j, int itype, int jtype,
if (nex_mol) {
for (m = 0; m < nex_mol; m++)
if (mask[i] & ex_mol_bit[m] && mask[j] & ex_mol_bit[m] &&
- molecule[i] == molecule[j]) return 1;
+ molecule[i] == molecule[j]) return 1;
}
return 0;
diff --git a/src/neighbor.h b/src/neighbor.h
index 36d80fb7e2ac52f33208ddf18bcafdcd4722531a..3cffa42bf83432a472e0f10d6ea43643f3bcf571 100644
--- a/src/neighbor.h
+++ b/src/neighbor.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -49,7 +49,7 @@ class Neighbor : protected Pointers {
int old_nrequest; // re-creation of pairwise neighbor lists
int old_triclinic;
class NeighRequest **old_requests;
-
+
int nlist; // pairwise neighbor lists
class NeighList **lists;
@@ -76,7 +76,7 @@ class Neighbor : protected Pointers {
void modify_params(int, char**); // modify parameters that control builds
bigint memory_usage();
int exclude_setting();
-
+
protected:
int me,nprocs;
@@ -129,7 +129,7 @@ class Neighbor : protected Pointers {
double (*corners)[3]; // ptr to 8 corners of triclinic box
double inner[2],middle[2]; // rRESPA cutoffs for extra lists
- double cut_inner_sq; // outer cutoff for inner neighbor list
+ double cut_inner_sq; // outer cutoff for inner neighbor list
double cut_middle_sq; // outer cutoff for middle neighbor list
double cut_middle_inside_sq; // inner cutoff for middle neighbor list
@@ -165,8 +165,8 @@ class Neighbor : protected Pointers {
int coord2bin(double *); // mapping atom coord to a bin
int coord2bin(double *, int &, int &, int&); // ditto
- int exclusion(int, int, int,
- int, int *, int *) const; // test for pair exclusion
+ int exclusion(int, int, int,
+ int, int *, int *) const; // test for pair exclusion
virtual void choose_build(int, class NeighRequest *);
void choose_stencil(int, class NeighRequest *);
@@ -269,27 +269,27 @@ class Neighbor : protected Pointers {
// if it is and special flag is 2 (otherwise), return 1,2,3
// for which level of neighbor it is (and which coeff it maps to)
- inline int find_special(const int *list, const int *nspecial,
- const int tag) const {
+ inline int find_special(const int *list, const int *nspecial,
+ const int tag) const {
const int n1 = nspecial[0];
const int n2 = nspecial[1];
const int n3 = nspecial[2];
for (int i = 0; i < n3; i++) {
if (list[i] == tag) {
- if (i < n1) {
- if (special_flag[1] == 0) return -1;
- else if (special_flag[1] == 1) return 0;
- else return 1;
- } else if (i < n2) {
- if (special_flag[2] == 0) return -1;
- else if (special_flag[2] == 1) return 0;
- else return 2;
- } else {
- if (special_flag[3] == 0) return -1;
- else if (special_flag[3] == 1) return 0;
- else return 3;
- }
+ if (i < n1) {
+ if (special_flag[1] == 0) return -1;
+ else if (special_flag[1] == 1) return 0;
+ else return 1;
+ } else if (i < n2) {
+ if (special_flag[2] == 0) return -1;
+ else if (special_flag[2] == 1) return 0;
+ else return 2;
+ } else {
+ if (special_flag[3] == 0) return -1;
+ else if (special_flag[3] == 1) return 0;
+ else return 3;
+ }
}
}
return 0;
diff --git a/src/output.cpp b/src/output.cpp
index 859aaa5dd1133dc996d29b9d53714a57fbe433c6..7cb5f44db59683916b49fe1fcc25f3d169fac8f7 100644
--- a/src/output.cpp
+++ b/src/output.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -39,7 +39,7 @@ using namespace LAMMPS_NS;
#define DELTA 1
/* ----------------------------------------------------------------------
- initialize all output
+ initialize all output
------------------------------------------------------------------------- */
Output::Output(LAMMPS *lmp) : Pointers(lmp)
@@ -71,10 +71,10 @@ Output::Output(LAMMPS *lmp) : Pointers(lmp)
newarg[0] = (char *) "one";
thermo = new Thermo(lmp,1,newarg);
delete [] newarg;
-
+
thermo_every = 0;
var_thermo = NULL;
-
+
ndump = 0;
max_dump = 0;
every_dump = NULL;
@@ -92,7 +92,7 @@ Output::Output(LAMMPS *lmp) : Pointers(lmp)
}
/* ----------------------------------------------------------------------
- free all memory
+ free all memory
------------------------------------------------------------------------- */
Output::~Output()
@@ -136,9 +136,9 @@ void Output::init()
if (every_dump[i] == 0) {
ivar_dump[i] = input->variable->find(var_dump[i]);
if (ivar_dump[i] < 0)
- error->all(FLERR,"Variable name for dump every does not exist");
+ error->all(FLERR,"Variable name for dump every does not exist");
if (!input->variable->equalstyle(ivar_dump[i]))
- error->all(FLERR,"Variable for dump every is invalid style");
+ error->all(FLERR,"Variable for dump every is invalid style");
}
if (restart_flag_single && restart_every_single == 0) {
@@ -182,26 +182,26 @@ void Output::setup(int flag)
for (int idump = 0; idump < ndump; idump++) {
if (dump[idump]->clearstep) modify->clearstep_compute();
writeflag = 0;
- if (every_dump[idump] && ntimestep % every_dump[idump] == 0 &&
- last_dump[idump] != ntimestep) writeflag = 1;
+ if (every_dump[idump] && ntimestep % every_dump[idump] == 0 &&
+ last_dump[idump] != ntimestep) writeflag = 1;
if (last_dump[idump] < 0 && dump[idump]->first_flag == 1) writeflag = 1;
if (writeflag) {
- dump[idump]->write();
- last_dump[idump] = ntimestep;
+ dump[idump]->write();
+ last_dump[idump] = ntimestep;
}
if (every_dump[idump])
- next_dump[idump] =
- (ntimestep/every_dump[idump])*every_dump[idump] + every_dump[idump];
+ next_dump[idump] =
+ (ntimestep/every_dump[idump])*every_dump[idump] + every_dump[idump];
else {
- bigint nextdump = static_cast<bigint>
- (input->variable->compute_equal(ivar_dump[idump]));
- if (nextdump <= ntimestep)
- error->all(FLERR,"Dump every variable returned a bad timestep");
- next_dump[idump] = nextdump;
+ bigint nextdump = static_cast<bigint>
+ (input->variable->compute_equal(ivar_dump[idump]));
+ if (nextdump <= ntimestep)
+ error->all(FLERR,"Dump every variable returned a bad timestep");
+ next_dump[idump] = nextdump;
}
if (dump[idump]->clearstep) {
- if (writeflag) modify->addstep_compute(next_dump[idump]);
- else modify->addstep_compute_all(next_dump[idump]);
+ if (writeflag) modify->addstep_compute(next_dump[idump]);
+ else modify->addstep_compute_all(next_dump[idump]);
}
if (idump) next_dump_any = MIN(next_dump_any,next_dump[idump]);
else next_dump_any = next_dump[0];
@@ -216,28 +216,28 @@ void Output::setup(int flag)
if (restart_flag && update->restrict_output == 0) {
if (restart_flag_single) {
if (restart_every_single)
- next_restart_single =
- (ntimestep/restart_every_single)*restart_every_single +
- restart_every_single;
+ next_restart_single =
+ (ntimestep/restart_every_single)*restart_every_single +
+ restart_every_single;
else {
- bigint nextrestart = static_cast<bigint>
- (input->variable->compute_equal(ivar_restart_single));
- if (nextrestart <= ntimestep)
- error->all(FLERR,"Restart variable returned a bad timestep");
- next_restart_single = nextrestart;
+ bigint nextrestart = static_cast<bigint>
+ (input->variable->compute_equal(ivar_restart_single));
+ if (nextrestart <= ntimestep)
+ error->all(FLERR,"Restart variable returned a bad timestep");
+ next_restart_single = nextrestart;
}
} else next_restart_single = update->laststep + 1;
if (restart_flag_double) {
if (restart_every_double)
- next_restart_double =
- (ntimestep/restart_every_double)*restart_every_double +
- restart_every_double;
+ next_restart_double =
+ (ntimestep/restart_every_double)*restart_every_double +
+ restart_every_double;
else {
- bigint nextrestart = static_cast<bigint>
- (input->variable->compute_equal(ivar_restart_double));
- if (nextrestart <= ntimestep)
- error->all(FLERR,"Restart variable returned a bad timestep");
- next_restart_double = nextrestart;
+ bigint nextrestart = static_cast<bigint>
+ (input->variable->compute_equal(ivar_restart_double));
+ if (nextrestart <= ntimestep)
+ error->all(FLERR,"Restart variable returned a bad timestep");
+ next_restart_double = nextrestart;
}
} else next_restart_double = update->laststep + 1;
next_restart = MIN(next_restart_single,next_restart_double);
@@ -262,7 +262,7 @@ void Output::setup(int flag)
next_thermo = (ntimestep/thermo_every)*thermo_every + thermo_every;
next_thermo = MIN(next_thermo,update->laststep);
} else if (var_thermo) {
- next_thermo = static_cast<bigint>
+ next_thermo = static_cast<bigint>
(input->variable->compute_equal(ivar_thermo));
if (next_thermo <= ntimestep)
error->all(FLERR,"Thermo every variable returned a bad timestep");
@@ -289,21 +289,21 @@ void Output::write(bigint ntimestep)
// download data from GPU if necessary
if (next_dump_any == ntimestep) {
- if (lmp->cuda && !lmp->cuda->oncpu) lmp->cuda->downloadAll();
-
+ if (lmp->cuda && !lmp->cuda->oncpu) lmp->cuda->downloadAll();
+
for (int idump = 0; idump < ndump; idump++) {
if (next_dump[idump] == ntimestep && last_dump[idump] != ntimestep) {
if (dump[idump]->clearstep) modify->clearstep_compute();
- dump[idump]->write();
- last_dump[idump] = ntimestep;
- if (every_dump[idump]) next_dump[idump] += every_dump[idump];
- else {
- bigint nextdump = static_cast<bigint>
- (input->variable->compute_equal(ivar_dump[idump]));
- if (nextdump <= ntimestep)
- error->all(FLERR,"Dump every variable returned a bad timestep");
- next_dump[idump] = nextdump;
- }
+ dump[idump]->write();
+ last_dump[idump] = ntimestep;
+ if (every_dump[idump]) next_dump[idump] += every_dump[idump];
+ else {
+ bigint nextdump = static_cast<bigint>
+ (input->variable->compute_equal(ivar_dump[idump]));
+ if (nextdump <= ntimestep)
+ error->all(FLERR,"Dump every variable returned a bad timestep");
+ next_dump[idump] = nextdump;
+ }
if (dump[idump]->clearstep) modify->addstep_compute(next_dump[idump]);
}
if (idump) next_dump_any = MIN(next_dump_any,next_dump[idump]);
@@ -316,8 +316,8 @@ void Output::write(bigint ntimestep)
// download data from GPU if necessary
if (next_restart == ntimestep && last_restart != ntimestep) {
- if (lmp->cuda && !lmp->cuda->oncpu) lmp->cuda->downloadAll();
-
+ if (lmp->cuda && !lmp->cuda->oncpu) lmp->cuda->downloadAll();
+
if (next_restart_single == ntimestep) {
char *file = new char[strlen(restart1) + 16];
char *ptr = strchr(restart1,'*');
@@ -328,28 +328,28 @@ void Output::write(bigint ntimestep)
delete [] file;
if (restart_every_single) next_restart_single += restart_every_single;
else {
- bigint nextrestart = static_cast<bigint>
- (input->variable->compute_equal(ivar_restart_single));
- if (nextrestart <= ntimestep)
- error->all(FLERR,"Restart variable returned a bad timestep");
- next_restart_single = nextrestart;
+ bigint nextrestart = static_cast<bigint>
+ (input->variable->compute_equal(ivar_restart_single));
+ if (nextrestart <= ntimestep)
+ error->all(FLERR,"Restart variable returned a bad timestep");
+ next_restart_single = nextrestart;
}
}
if (next_restart_double == ntimestep) {
if (restart_toggle == 0) {
- restart->write(restart2a);
- restart_toggle = 1;
+ restart->write(restart2a);
+ restart_toggle = 1;
} else {
- restart->write(restart2b);
- restart_toggle = 0;
+ restart->write(restart2b);
+ restart_toggle = 0;
}
if (restart_every_double) next_restart_double += restart_every_double;
else {
- bigint nextrestart = static_cast<bigint>
- (input->variable->compute_equal(ivar_restart_double));
- if (nextrestart <= ntimestep)
- error->all(FLERR,"Restart variable returned a bad timestep");
- next_restart_double = nextrestart;
+ bigint nextrestart = static_cast<bigint>
+ (input->variable->compute_equal(ivar_restart_double));
+ if (nextrestart <= ntimestep)
+ error->all(FLERR,"Restart variable returned a bad timestep");
+ next_restart_double = nextrestart;
}
}
last_restart = ntimestep;
@@ -365,10 +365,10 @@ void Output::write(bigint ntimestep)
last_thermo = ntimestep;
if (thermo_every) next_thermo += thermo_every;
else if (var_thermo) {
- next_thermo = static_cast<bigint>
- (input->variable->compute_equal(ivar_thermo));
+ next_thermo = static_cast<bigint>
+ (input->variable->compute_equal(ivar_thermo));
if (next_thermo <= ntimestep)
- error->all(FLERR,"Thermo every variable returned a bad timestep");
+ error->all(FLERR,"Thermo every variable returned a bad timestep");
} else next_thermo = update->laststep;
next_thermo = MIN(next_thermo,update->laststep);
modify->addstep_compute(next_thermo);
@@ -423,7 +423,7 @@ void Output::write_restart(bigint ntimestep)
}
/* ----------------------------------------------------------------------
- add a Dump to list of Dumps
+ add a Dump to list of Dumps
------------------------------------------------------------------------- */
void Output::add_dump(int narg, char **arg)
@@ -433,7 +433,7 @@ void Output::add_dump(int narg, char **arg)
// error checks
for (int idump = 0; idump < ndump; idump++)
- if (strcmp(arg[0],dump[idump]->id) == 0)
+ if (strcmp(arg[0],dump[idump]->id) == 0)
error->all(FLERR,"Reuse of dump ID");
int igroup = group->find(arg[1]);
if (igroup == -1) error->all(FLERR,"Could not find dump group ID");
@@ -473,7 +473,7 @@ void Output::add_dump(int narg, char **arg)
}
/* ----------------------------------------------------------------------
- modify parameters of a Dump
+ modify parameters of a Dump
------------------------------------------------------------------------- */
void Output::modify_dump(int narg, char **arg)
@@ -491,7 +491,7 @@ void Output::modify_dump(int narg, char **arg)
}
/* ----------------------------------------------------------------------
- delete a Dump from list of Dumps
+ delete a Dump from list of Dumps
------------------------------------------------------------------------- */
void Output::delete_dump(char *id)
@@ -520,7 +520,7 @@ void Output::delete_dump(char *id)
}
/* ----------------------------------------------------------------------
- new Thermo style
+ new Thermo style
------------------------------------------------------------------------- */
void Output::create_thermo(int narg, char **arg)
@@ -529,14 +529,14 @@ void Output::create_thermo(int narg, char **arg)
// don't allow this so that dipole style can safely allocate inertia vector
- if (domain->box_exist == 0)
+ if (domain->box_exist == 0)
error->all(FLERR,"Thermo_style command before simulation box is defined");
// warn if previous thermo had been modified via thermo_modify command
if (thermo->modified && comm->me == 0)
error->warning(FLERR,"New thermo_style command, "
- "previous thermo_modify settings will be lost");
+ "previous thermo_modify settings will be lost");
// set thermo = NULL in case new Thermo throws an error
@@ -553,7 +553,7 @@ void Output::create_thermo(int narg, char **arg)
void Output::create_restart(int narg, char **arg)
{
if (narg < 1) error->all(FLERR,"Illegal restart command");
-
+
int every = 0;
int varflag = 0;
@@ -642,7 +642,7 @@ void Output::memory_usage()
if (comm->me == 0) {
if (screen)
fprintf(screen,"Memory usage per processor = %g Mbytes\n",mbytes);
- if (logfile)
+ if (logfile)
fprintf(logfile,"Memory usage per processor = %g Mbytes\n",mbytes);
}
}
diff --git a/src/output.h b/src/output.h
index 673ea085374bdea5b8e24c6f8215da64d603f22a..2511d42331fd88520f3e2407be0a42bb09783039 100644
--- a/src/output.h
+++ b/src/output.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/pack.h b/src/pack.h
index 5f032e68c74265266a323622a938835c0d219830..5db35117c55162ed2045ca37f1b2850a1c8922e3 100644
--- a/src/pack.h
+++ b/src/pack.h
@@ -5,21 +5,21 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-// loop counters for doing a pack/unpack
+// loop counters for doing a pack/unpack
struct pack_plan_3d {
- int nfast; // # of elements in fast index
- int nmid; // # of elements in mid index
- int nslow; // # of elements in slow index
- int nstride_line; // stride between successive mid indices
+ int nfast; // # of elements in fast index
+ int nmid; // # of elements in mid index
+ int nslow; // # of elements in slow index
+ int nstride_line; // stride between successive mid indices
int nstride_plane; // stride between successive slow indices
- int nqty; // # of values/element
+ int nqty; // # of values/element
};
@@ -44,13 +44,13 @@ struct pack_plan_3d {
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
- pack/unpack with array indices
+ pack/unpack with array indices
------------------------------------------------------------------------- */
#ifdef PACK_ARRAY
/* ----------------------------------------------------------------------
- pack from data -> buf
+ pack from data -> buf
------------------------------------------------------------------------- */
static void pack_3d(PACK_DATA *data, PACK_DATA *buf, struct pack_plan_3d *plan)
@@ -70,13 +70,13 @@ static void pack_3d(PACK_DATA *data, PACK_DATA *buf, struct pack_plan_3d *plan)
for (mid = 0; mid < nmid; mid++) {
out = plane + mid*nstride_line;
for (fast = 0; fast < nfast; fast++)
- buf[in++] = data[out++];
+ buf[in++] = data[out++];
}
}
}
/* ----------------------------------------------------------------------
- unpack from buf -> data
+ unpack from buf -> data
------------------------------------------------------------------------- */
static void unpack_3d(PACK_DATA *buf, PACK_DATA *data, struct pack_plan_3d *plan)
@@ -96,13 +96,13 @@ static void unpack_3d(PACK_DATA *buf, PACK_DATA *data, struct pack_plan_3d *plan
for (mid = 0; mid < nmid; mid++) {
in = plane + mid*nstride_line;
for (fast = 0; fast < nfast; fast++)
- data[in++] = buf[out++];
+ data[in++] = buf[out++];
}
}
}
/* ----------------------------------------------------------------------
- unpack from buf -> data, one axis permutation, 1 value/element
+ unpack from buf -> data, one axis permutation, 1 value/element
------------------------------------------------------------------------- */
static void unpack_3d_permute1_1(PACK_DATA *buf, PACK_DATA *data, struct pack_plan_3d *plan)
@@ -122,13 +122,13 @@ static void unpack_3d_permute1_1(PACK_DATA *buf, PACK_DATA *data, struct pack_pl
for (mid = 0; mid < nmid; mid++) {
in = plane + mid;
for (fast = 0; fast < nfast; fast++, in += nstride_plane)
- data[in] = buf[out++];
+ data[in] = buf[out++];
}
}
}
/* ----------------------------------------------------------------------
- unpack from buf -> data, one axis permutation, 2 values/element
+ unpack from buf -> data, one axis permutation, 2 values/element
------------------------------------------------------------------------- */
static void unpack_3d_permute1_2(PACK_DATA *buf, PACK_DATA *data, struct pack_plan_3d *plan)
@@ -148,15 +148,15 @@ static void unpack_3d_permute1_2(PACK_DATA *buf, PACK_DATA *data, struct pack_pl
for (mid = 0; mid < nmid; mid++) {
in = plane + 2*mid;
for (fast = 0; fast < nfast; fast++, in += nstride_plane) {
- data[in] = buf[out++];
- data[in+1] = buf[out++];
+ data[in] = buf[out++];
+ data[in+1] = buf[out++];
}
}
}
}
/* ----------------------------------------------------------------------
- unpack from buf -> data, one axis permutation, nqty values/element
+ unpack from buf -> data, one axis permutation, nqty values/element
------------------------------------------------------------------------- */
static void unpack_3d_permute1_n(PACK_DATA *buf, PACK_DATA *data, struct pack_plan_3d *plan)
@@ -178,15 +178,15 @@ static void unpack_3d_permute1_n(PACK_DATA *buf, PACK_DATA *data, struct pack_pl
for (mid = 0; mid < nmid; mid++) {
instart = plane + nqty*mid;
for (fast = 0; fast < nfast; fast++, instart += nstride_plane) {
- in = instart;
- for (iqty = 0; iqty < nqty; iqty++) data[in++] = buf[out++];
+ in = instart;
+ for (iqty = 0; iqty < nqty; iqty++) data[in++] = buf[out++];
}
}
}
}
/* ----------------------------------------------------------------------
- unpack from buf -> data, two axis permutation, 1 value/element
+ unpack from buf -> data, two axis permutation, 1 value/element
------------------------------------------------------------------------- */
static void unpack_3d_permute2_1(PACK_DATA *buf, PACK_DATA *data, struct pack_plan_3d *plan)
@@ -206,13 +206,13 @@ static void unpack_3d_permute2_1(PACK_DATA *buf, PACK_DATA *data, struct pack_pl
for (mid = 0; mid < nmid; mid++) {
in = slow + mid*nstride_plane;
for (fast = 0; fast < nfast; fast++, in += nstride_line)
- data[in] = buf[out++];
+ data[in] = buf[out++];
}
}
}
/* ----------------------------------------------------------------------
- unpack from buf -> data, two axis permutation, 2 values/element
+ unpack from buf -> data, two axis permutation, 2 values/element
------------------------------------------------------------------------- */
static void unpack_3d_permute2_2(PACK_DATA *buf, PACK_DATA *data, struct pack_plan_3d *plan)
@@ -232,15 +232,15 @@ static void unpack_3d_permute2_2(PACK_DATA *buf, PACK_DATA *data, struct pack_pl
for (mid = 0; mid < nmid; mid++) {
in = 2*slow + mid*nstride_plane;
for (fast = 0; fast < nfast; fast++, in += nstride_line) {
- data[in] = buf[out++];
- data[in+1] = buf[out++];
+ data[in] = buf[out++];
+ data[in+1] = buf[out++];
}
}
}
}
/* ----------------------------------------------------------------------
- unpack from buf -> data, two axis permutation, nqty values/element
+ unpack from buf -> data, two axis permutation, nqty values/element
------------------------------------------------------------------------- */
static void unpack_3d_permute2_n(PACK_DATA *buf, PACK_DATA *data, struct pack_plan_3d *plan)
@@ -261,8 +261,8 @@ static void unpack_3d_permute2_n(PACK_DATA *buf, PACK_DATA *data, struct pack_pl
for (mid = 0; mid < nmid; mid++) {
instart = nqty*slow + mid*nstride_plane;
for (fast = 0; fast < nfast; fast++, instart += nstride_line) {
- in = instart;
- for (iqty = 0; iqty < nqty; iqty++) data[in++] = buf[out++];
+ in = instart;
+ for (iqty = 0; iqty < nqty; iqty++) data[in++] = buf[out++];
}
}
}
@@ -271,13 +271,13 @@ static void unpack_3d_permute2_n(PACK_DATA *buf, PACK_DATA *data, struct pack_pl
#endif
/* ----------------------------------------------------------------------
- pack/unpack with pointers
+ pack/unpack with pointers
------------------------------------------------------------------------- */
#ifdef PACK_POINTER
/* ----------------------------------------------------------------------
- pack from data -> buf
+ pack from data -> buf
------------------------------------------------------------------------- */
static void pack_3d(PACK_DATA *data, PACK_DATA *buf, struct pack_plan_3d *plan)
@@ -300,13 +300,13 @@ static void pack_3d(PACK_DATA *data, PACK_DATA *buf, struct pack_plan_3d *plan)
begin = &(data[plane+mid*nstride_line]);
end = begin + nfast;
for (out = begin; out < end; out++)
- *(in++) = *out;
+ *(in++) = *out;
}
}
}
/* ----------------------------------------------------------------------
- unpack from buf -> data
+ unpack from buf -> data
------------------------------------------------------------------------- */
static void unpack_3d(PACK_DATA *buf, PACK_DATA *data, struct pack_plan_3d *plan)
@@ -329,13 +329,13 @@ static void unpack_3d(PACK_DATA *buf, PACK_DATA *data, struct pack_plan_3d *plan
begin = &(data[plane+mid*nstride_line]);
end = begin + nfast;
for (in = begin; in < end; in++)
- *in = *(out++);
+ *in = *(out++);
}
}
}
/* ----------------------------------------------------------------------
- unpack from buf -> data, one axis permutation, 1 value/element
+ unpack from buf -> data, one axis permutation, 1 value/element
------------------------------------------------------------------------- */
static void unpack_3d_permute1_1(PACK_DATA *buf, PACK_DATA *data, struct pack_plan_3d *plan)
@@ -358,13 +358,13 @@ static void unpack_3d_permute1_1(PACK_DATA *buf, PACK_DATA *data, struct pack_pl
begin = &(data[plane+mid]);
end = begin + nfast*nstride_plane;
for (in = begin; in < end; in += nstride_plane)
- *in = *(out++);
+ *in = *(out++);
}
}
}
/* ----------------------------------------------------------------------
- unpack from buf -> data, one axis permutation, 2 values/element
+ unpack from buf -> data, one axis permutation, 2 values/element
------------------------------------------------------------------------- */
static void unpack_3d_permute1_2(PACK_DATA *buf, PACK_DATA *data, struct pack_plan_3d *plan)
@@ -387,15 +387,15 @@ static void unpack_3d_permute1_2(PACK_DATA *buf, PACK_DATA *data, struct pack_pl
begin = &(data[plane+2*mid]);
end = begin + nfast*nstride_plane;
for (in = begin; in < end; in += nstride_plane) {
- *in = *(out++);
- *(in+1) = *(out++);
+ *in = *(out++);
+ *(in+1) = *(out++);
}
}
}
}
/* ----------------------------------------------------------------------
- unpack from buf -> data, one axis permutation, nqty values/element
+ unpack from buf -> data, one axis permutation, nqty values/element
------------------------------------------------------------------------- */
static void unpack_3d_permute1_n(PACK_DATA *buf, PACK_DATA *data, struct pack_plan_3d *plan)
@@ -419,15 +419,15 @@ static void unpack_3d_permute1_n(PACK_DATA *buf, PACK_DATA *data, struct pack_pl
begin = &(data[plane+nqty*mid]);
end = begin + nfast*nstride_plane;
for (instart = begin; instart < end; instart += nstride_plane) {
- in = instart;
- for (iqty = 0; iqty < nqty; iqty++) *(in++) = *(out++);
+ in = instart;
+ for (iqty = 0; iqty < nqty; iqty++) *(in++) = *(out++);
}
}
}
}
/* ----------------------------------------------------------------------
- unpack from buf -> data, two axis permutation, 1 value/element
+ unpack from buf -> data, two axis permutation, 1 value/element
------------------------------------------------------------------------- */
static void unpack_3d_permute2_1(PACK_DATA *buf, PACK_DATA *data, struct pack_plan_3d *plan)
@@ -449,13 +449,13 @@ static void unpack_3d_permute2_1(PACK_DATA *buf, PACK_DATA *data, struct pack_pl
begin = &(data[slow+mid*nstride_plane]);
end = begin + nfast*nstride_line;
for (in = begin; in < end; in += nstride_line)
- *in = *(out++);
+ *in = *(out++);
}
}
}
/* ----------------------------------------------------------------------
- unpack from buf -> data, two axis permutation, 2 values/element
+ unpack from buf -> data, two axis permutation, 2 values/element
------------------------------------------------------------------------- */
static void unpack_3d_permute2_2(PACK_DATA *buf, PACK_DATA *data, struct pack_plan_3d *plan)
@@ -477,15 +477,15 @@ static void unpack_3d_permute2_2(PACK_DATA *buf, PACK_DATA *data, struct pack_pl
begin = &(data[2*slow+mid*nstride_plane]);
end = begin + nfast*nstride_line;
for (in = begin; in < end; in += nstride_line) {
- *in = *(out++);
- *(in+1) = *(out++);
+ *in = *(out++);
+ *(in+1) = *(out++);
}
}
}
}
/* ----------------------------------------------------------------------
- unpack from buf -> data, two axis permutation, nqty values/element
+ unpack from buf -> data, two axis permutation, nqty values/element
------------------------------------------------------------------------- */
static void unpack_3d_permute2_n(PACK_DATA *buf, PACK_DATA *data, struct pack_plan_3d *plan)
@@ -508,8 +508,8 @@ static void unpack_3d_permute2_n(PACK_DATA *buf, PACK_DATA *data, struct pack_pl
begin = &(data[nqty*slow+mid*nstride_plane]);
end = begin + nfast*nstride_line;
for (instart = begin; instart < end; instart += nstride_line) {
- in = instart;
- for (iqty = 0; iqty < nqty; iqty++) *(in++) = *(out++);
+ in = instart;
+ for (iqty = 0; iqty < nqty; iqty++) *(in++) = *(out++);
}
}
}
@@ -518,15 +518,15 @@ static void unpack_3d_permute2_n(PACK_DATA *buf, PACK_DATA *data, struct pack_pl
#endif
/* ----------------------------------------------------------------------
- pack/unpack with pointers and memcpy function
+ pack/unpack with pointers and memcpy function
no memcpy version of unpack_permute routines,
- just use PACK_POINTER versions
+ just use PACK_POINTER versions
------------------------------------------------------------------------- */
#ifdef PACK_MEMCPY
/* ----------------------------------------------------------------------
- pack from data -> buf
+ pack from data -> buf
------------------------------------------------------------------------- */
static void pack_3d(PACK_DATA *data, PACK_DATA *buf, struct pack_plan_3d *plan)
@@ -555,7 +555,7 @@ static void pack_3d(PACK_DATA *data, PACK_DATA *buf, struct pack_plan_3d *plan)
}
/* ----------------------------------------------------------------------
- unpack from buf -> data
+ unpack from buf -> data
------------------------------------------------------------------------- */
static void unpack_3d(PACK_DATA *buf, PACK_DATA *data, struct pack_plan_3d *plan)
@@ -584,7 +584,7 @@ static void unpack_3d(PACK_DATA *buf, PACK_DATA *data, struct pack_plan_3d *plan
}
/* ----------------------------------------------------------------------
- unpack from buf -> data, one axis permutation, 1 value/element
+ unpack from buf -> data, one axis permutation, 1 value/element
------------------------------------------------------------------------- */
static void unpack_3d_permute1_1(PACK_DATA *buf, PACK_DATA *data, struct pack_plan_3d *plan)
@@ -607,13 +607,13 @@ static void unpack_3d_permute1_1(PACK_DATA *buf, PACK_DATA *data, struct pack_pl
begin = &(data[plane+mid]);
end = begin + nfast*nstride_plane;
for (in = begin; in < end; in += nstride_plane)
- *in = *(out++);
+ *in = *(out++);
}
}
}
/* ----------------------------------------------------------------------
- unpack from buf -> data, one axis permutation, 2 values/element
+ unpack from buf -> data, one axis permutation, 2 values/element
------------------------------------------------------------------------- */
static void unpack_3d_permute1_2(PACK_DATA *buf, PACK_DATA *data, struct pack_plan_3d *plan)
@@ -636,15 +636,15 @@ static void unpack_3d_permute1_2(PACK_DATA *buf, PACK_DATA *data, struct pack_pl
begin = &(data[plane+2*mid]);
end = begin + nfast*nstride_plane;
for (in = begin; in < end; in += nstride_plane) {
- *in = *(out++);
- *(in+1) = *(out++);
+ *in = *(out++);
+ *(in+1) = *(out++);
}
}
}
}
/* ----------------------------------------------------------------------
- unpack from buf -> data, one axis permutation, nqty values/element
+ unpack from buf -> data, one axis permutation, nqty values/element
------------------------------------------------------------------------- */
static void unpack_3d_permute1_n(PACK_DATA *buf, PACK_DATA *data, struct pack_plan_3d *plan)
@@ -668,15 +668,15 @@ static void unpack_3d_permute1_n(PACK_DATA *buf, PACK_DATA *data, struct pack_pl
begin = &(data[plane+nqty*mid]);
end = begin + nfast*nstride_plane;
for (instart = begin; instart < end; instart += nstride_plane) {
- in = instart;
- for (iqty = 0; iqty < nqty; iqty++) *(in++) = *(out++);
+ in = instart;
+ for (iqty = 0; iqty < nqty; iqty++) *(in++) = *(out++);
}
}
}
}
/* ----------------------------------------------------------------------
- unpack from buf -> data, two axis permutation, 1 value/element
+ unpack from buf -> data, two axis permutation, 1 value/element
------------------------------------------------------------------------- */
static void unpack_3d_permute2_1(PACK_DATA *buf, PACK_DATA *data, struct pack_plan_3d *plan)
@@ -698,13 +698,13 @@ static void unpack_3d_permute2_1(PACK_DATA *buf, PACK_DATA *data, struct pack_pl
begin = &(data[slow+mid*nstride_plane]);
end = begin + nfast*nstride_line;
for (in = begin; in < end; in += nstride_line)
- *in = *(out++);
+ *in = *(out++);
}
}
}
/* ----------------------------------------------------------------------
- unpack from buf -> data, two axis permutation, 2 values/element
+ unpack from buf -> data, two axis permutation, 2 values/element
------------------------------------------------------------------------- */
static void unpack_3d_permute2_2(PACK_DATA *buf, PACK_DATA *data, struct pack_plan_3d *plan)
@@ -726,15 +726,15 @@ static void unpack_3d_permute2_2(PACK_DATA *buf, PACK_DATA *data, struct pack_pl
begin = &(data[2*slow+mid*nstride_plane]);
end = begin + nfast*nstride_line;
for (in = begin; in < end; in += nstride_line) {
- *in = *(out++);
- *(in+1) = *(out++);
+ *in = *(out++);
+ *(in+1) = *(out++);
}
}
}
}
/* ----------------------------------------------------------------------
- unpack from buf -> data, two axis permutation, nqty values/element
+ unpack from buf -> data, two axis permutation, nqty values/element
------------------------------------------------------------------------- */
static void unpack_3d_permute2_n(PACK_DATA *buf, PACK_DATA *data, struct pack_plan_3d *plan)
@@ -757,8 +757,8 @@ static void unpack_3d_permute2_n(PACK_DATA *buf, PACK_DATA *data, struct pack_pl
begin = &(data[nqty*slow+mid*nstride_plane]);
end = begin + nfast*nstride_line;
for (instart = begin; instart < end; instart += nstride_line) {
- in = instart;
- for (iqty = 0; iqty < nqty; iqty++) *(in++) = *(out++);
+ in = instart;
+ for (iqty = 0; iqty < nqty; iqty++) *(in++) = *(out++);
}
}
}
diff --git a/src/pair.cpp b/src/pair.cpp
index 4cdc7a85425a8128dab3e1ebbf20c883eb4bfe84..96c6cc9feb08d15196d3dfd38eb8bdfccfd33be3 100644
--- a/src/pair.cpp
+++ b/src/pair.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -114,7 +114,7 @@ void Pair::modify_params(int narg, char **arg)
} else if (strcmp(arg[iarg],"table") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal pair_modify command");
ncoultablebits = atoi(arg[iarg+1]);
- if (ncoultablebits > sizeof(float)*CHAR_BIT)
+ if (ncoultablebits > sizeof(float)*CHAR_BIT)
error->all(FLERR,"Too many total bits for bitmapped lookup table");
iarg += 2;
} else if (strcmp(arg[iarg],"tabinner") == 0) {
@@ -176,12 +176,12 @@ void Pair::init()
cutsq[i][j] = cutsq[j][i] = cut*cut;
cutforce = MAX(cutforce,cut);
if (tail_flag) {
- etail += etail_ij;
- ptail += ptail_ij;
- if (i != j) {
- etail += etail_ij;
- ptail += ptail_ij;
- }
+ etail += etail_ij;
+ ptail += ptail_ij;
+ if (i != j) {
+ etail += etail_ij;
+ ptail += ptail_ij;
+ }
}
}
}
@@ -202,12 +202,12 @@ void Pair::reinit()
for (j = i; j <= atom->ntypes; j++) {
tmp = init_one(i,j);
if (tail_flag) {
- etail += etail_ij;
- ptail += ptail_ij;
- if (i != j) {
- etail += etail_ij;
- ptail += ptail_ij;
- }
+ etail += etail_ij;
+ ptail += ptail_ij;
+ if (i != j) {
+ etail += etail_ij;
+ ptail += ptail_ij;
+ }
}
}
}
@@ -372,27 +372,27 @@ void Pair::ev_unset()
------------------------------------------------------------------------- */
void Pair::ev_tally(int i, int j, int nlocal, int newton_pair,
- double evdwl, double ecoul, double fpair,
- double delx, double dely, double delz)
+ double evdwl, double ecoul, double fpair,
+ double delx, double dely, double delz)
{
double evdwlhalf,ecoulhalf,epairhalf,v[6];
if (eflag_either) {
if (eflag_global) {
if (newton_pair) {
- eng_vdwl += evdwl;
- eng_coul += ecoul;
+ eng_vdwl += evdwl;
+ eng_coul += ecoul;
} else {
- evdwlhalf = 0.5*evdwl;
- ecoulhalf = 0.5*ecoul;
- if (i < nlocal) {
- eng_vdwl += evdwlhalf;
- eng_coul += ecoulhalf;
- }
- if (j < nlocal) {
- eng_vdwl += evdwlhalf;
- eng_coul += ecoulhalf;
- }
+ evdwlhalf = 0.5*evdwl;
+ ecoulhalf = 0.5*ecoul;
+ if (i < nlocal) {
+ eng_vdwl += evdwlhalf;
+ eng_coul += ecoulhalf;
+ }
+ if (j < nlocal) {
+ eng_vdwl += evdwlhalf;
+ eng_coul += ecoulhalf;
+ }
}
}
if (eflag_atom) {
@@ -412,59 +412,59 @@ void Pair::ev_tally(int i, int j, int nlocal, int newton_pair,
if (vflag_global) {
if (newton_pair) {
- virial[0] += v[0];
- virial[1] += v[1];
- virial[2] += v[2];
- virial[3] += v[3];
- virial[4] += v[4];
- virial[5] += v[5];
+ virial[0] += v[0];
+ virial[1] += v[1];
+ virial[2] += v[2];
+ virial[3] += v[3];
+ virial[4] += v[4];
+ virial[5] += v[5];
} else {
- if (i < nlocal) {
- virial[0] += 0.5*v[0];
- virial[1] += 0.5*v[1];
- virial[2] += 0.5*v[2];
- virial[3] += 0.5*v[3];
- virial[4] += 0.5*v[4];
- virial[5] += 0.5*v[5];
- }
- if (j < nlocal) {
- virial[0] += 0.5*v[0];
- virial[1] += 0.5*v[1];
- virial[2] += 0.5*v[2];
- virial[3] += 0.5*v[3];
- virial[4] += 0.5*v[4];
- virial[5] += 0.5*v[5];
- }
+ if (i < nlocal) {
+ virial[0] += 0.5*v[0];
+ virial[1] += 0.5*v[1];
+ virial[2] += 0.5*v[2];
+ virial[3] += 0.5*v[3];
+ virial[4] += 0.5*v[4];
+ virial[5] += 0.5*v[5];
+ }
+ if (j < nlocal) {
+ virial[0] += 0.5*v[0];
+ virial[1] += 0.5*v[1];
+ virial[2] += 0.5*v[2];
+ virial[3] += 0.5*v[3];
+ virial[4] += 0.5*v[4];
+ virial[5] += 0.5*v[5];
+ }
}
}
if (vflag_atom) {
if (newton_pair || i < nlocal) {
- vatom[i][0] += 0.5*v[0];
- vatom[i][1] += 0.5*v[1];
- vatom[i][2] += 0.5*v[2];
- vatom[i][3] += 0.5*v[3];
- vatom[i][4] += 0.5*v[4];
- vatom[i][5] += 0.5*v[5];
+ vatom[i][0] += 0.5*v[0];
+ vatom[i][1] += 0.5*v[1];
+ vatom[i][2] += 0.5*v[2];
+ vatom[i][3] += 0.5*v[3];
+ vatom[i][4] += 0.5*v[4];
+ vatom[i][5] += 0.5*v[5];
}
if (newton_pair || j < nlocal) {
- vatom[j][0] += 0.5*v[0];
- vatom[j][1] += 0.5*v[1];
- vatom[j][2] += 0.5*v[2];
- vatom[j][3] += 0.5*v[3];
- vatom[j][4] += 0.5*v[4];
- vatom[j][5] += 0.5*v[5];
+ vatom[j][0] += 0.5*v[0];
+ vatom[j][1] += 0.5*v[1];
+ vatom[j][2] += 0.5*v[2];
+ vatom[j][3] += 0.5*v[3];
+ vatom[j][4] += 0.5*v[4];
+ vatom[j][5] += 0.5*v[5];
}
}
}
}
-/* ----------------------------------------------------------------------
+/* ----------------------------------------------------------------------
tally eng_vdwl and virial into global and per-atom accumulators
can use this version with full neighbor lists
------------------------------------------------------------------------- */
-void Pair::ev_tally_full(int i, double evdwl, double ecoul, double fpair,
+void Pair::ev_tally_full(int i, double evdwl, double ecoul, double fpair,
double delx, double dely, double delz)
{
double v[6];
@@ -511,28 +511,28 @@ void Pair::ev_tally_full(int i, double evdwl, double ecoul, double fpair,
------------------------------------------------------------------------- */
void Pair::ev_tally_xyz(int i, int j, int nlocal, int newton_pair,
- double evdwl, double ecoul,
- double fx, double fy, double fz,
- double delx, double dely, double delz)
+ double evdwl, double ecoul,
+ double fx, double fy, double fz,
+ double delx, double dely, double delz)
{
double evdwlhalf,ecoulhalf,epairhalf,v[6];
-
+
if (eflag_either) {
if (eflag_global) {
if (newton_pair) {
- eng_vdwl += evdwl;
- eng_coul += ecoul;
+ eng_vdwl += evdwl;
+ eng_coul += ecoul;
} else {
- evdwlhalf = 0.5*evdwl;
- ecoulhalf = 0.5*ecoul;
- if (i < nlocal) {
- eng_vdwl += evdwlhalf;
- eng_coul += ecoulhalf;
- }
- if (j < nlocal) {
- eng_vdwl += evdwlhalf;
- eng_coul += ecoulhalf;
- }
+ evdwlhalf = 0.5*evdwl;
+ ecoulhalf = 0.5*ecoul;
+ if (i < nlocal) {
+ eng_vdwl += evdwlhalf;
+ eng_coul += ecoulhalf;
+ }
+ if (j < nlocal) {
+ eng_vdwl += evdwlhalf;
+ eng_coul += ecoulhalf;
+ }
}
}
if (eflag_atom) {
@@ -552,48 +552,48 @@ void Pair::ev_tally_xyz(int i, int j, int nlocal, int newton_pair,
if (vflag_global) {
if (newton_pair) {
- virial[0] += v[0];
- virial[1] += v[1];
- virial[2] += v[2];
- virial[3] += v[3];
- virial[4] += v[4];
- virial[5] += v[5];
+ virial[0] += v[0];
+ virial[1] += v[1];
+ virial[2] += v[2];
+ virial[3] += v[3];
+ virial[4] += v[4];
+ virial[5] += v[5];
} else {
- if (i < nlocal) {
- virial[0] += 0.5*v[0];
- virial[1] += 0.5*v[1];
- virial[2] += 0.5*v[2];
- virial[3] += 0.5*v[3];
- virial[4] += 0.5*v[4];
- virial[5] += 0.5*v[5];
- }
- if (j < nlocal) {
- virial[0] += 0.5*v[0];
- virial[1] += 0.5*v[1];
- virial[2] += 0.5*v[2];
- virial[3] += 0.5*v[3];
- virial[4] += 0.5*v[4];
- virial[5] += 0.5*v[5];
- }
+ if (i < nlocal) {
+ virial[0] += 0.5*v[0];
+ virial[1] += 0.5*v[1];
+ virial[2] += 0.5*v[2];
+ virial[3] += 0.5*v[3];
+ virial[4] += 0.5*v[4];
+ virial[5] += 0.5*v[5];
+ }
+ if (j < nlocal) {
+ virial[0] += 0.5*v[0];
+ virial[1] += 0.5*v[1];
+ virial[2] += 0.5*v[2];
+ virial[3] += 0.5*v[3];
+ virial[4] += 0.5*v[4];
+ virial[5] += 0.5*v[5];
+ }
}
}
if (vflag_atom) {
if (newton_pair || i < nlocal) {
- vatom[i][0] += 0.5*v[0];
- vatom[i][1] += 0.5*v[1];
- vatom[i][2] += 0.5*v[2];
- vatom[i][3] += 0.5*v[3];
- vatom[i][4] += 0.5*v[4];
- vatom[i][5] += 0.5*v[5];
+ vatom[i][0] += 0.5*v[0];
+ vatom[i][1] += 0.5*v[1];
+ vatom[i][2] += 0.5*v[2];
+ vatom[i][3] += 0.5*v[3];
+ vatom[i][4] += 0.5*v[4];
+ vatom[i][5] += 0.5*v[5];
}
if (newton_pair || j < nlocal) {
- vatom[j][0] += 0.5*v[0];
- vatom[j][1] += 0.5*v[1];
- vatom[j][2] += 0.5*v[2];
- vatom[j][3] += 0.5*v[3];
- vatom[j][4] += 0.5*v[4];
- vatom[j][5] += 0.5*v[5];
+ vatom[j][0] += 0.5*v[0];
+ vatom[j][1] += 0.5*v[1];
+ vatom[j][2] += 0.5*v[2];
+ vatom[j][3] += 0.5*v[3];
+ vatom[j][4] += 0.5*v[4];
+ vatom[j][5] += 0.5*v[5];
}
}
}
@@ -606,11 +606,11 @@ void Pair::ev_tally_xyz(int i, int j, int nlocal, int newton_pair,
------------------------------------------------------------------------- */
void Pair::ev_tally_xyz_full(int i, double evdwl, double ecoul,
- double fx, double fy, double fz,
- double delx, double dely, double delz)
+ double fx, double fy, double fz,
+ double delx, double dely, double delz)
{
double evdwlhalf,ecoulhalf,epairhalf,v[6];
-
+
if (eflag_either) {
if (eflag_global) {
evdwlhalf = 0.5*evdwl;
@@ -640,7 +640,7 @@ void Pair::ev_tally_xyz_full(int i, double evdwl, double ecoul,
virial[4] += v[4];
virial[5] += v[5];
}
-
+
if (vflag_atom) {
vatom[i][0] += v[0];
vatom[i][1] += v[1];
@@ -659,7 +659,7 @@ void Pair::ev_tally_xyz_full(int i, double evdwl, double ecoul,
------------------------------------------------------------------------- */
void Pair::ev_tally3(int i, int j, int k, double evdwl, double ecoul,
- double *fj, double *fk, double *drji, double *drki)
+ double *fj, double *fk, double *drji, double *drki)
{
double epairthird,v[6];
@@ -683,7 +683,7 @@ void Pair::ev_tally3(int i, int j, int k, double evdwl, double ecoul,
v[3] = drji[0]*fj[1] + drki[0]*fk[1];
v[4] = drji[0]*fj[2] + drki[0]*fk[2];
v[5] = drji[1]*fj[2] + drki[1]*fk[2];
-
+
if (vflag_global) {
virial[0] += v[0];
virial[1] += v[1];
@@ -695,7 +695,7 @@ void Pair::ev_tally3(int i, int j, int k, double evdwl, double ecoul,
if (vflag_atom) {
vatom[i][0] += THIRD*v[0]; vatom[i][1] += THIRD*v[1];
- vatom[i][2] += THIRD*v[2]; vatom[i][3] += THIRD*v[3];
+ vatom[i][2] += THIRD*v[2]; vatom[i][3] += THIRD*v[3];
vatom[i][4] += THIRD*v[4]; vatom[i][5] += THIRD*v[5];
vatom[j][0] += THIRD*v[0]; vatom[j][1] += THIRD*v[1];
@@ -715,8 +715,8 @@ void Pair::ev_tally3(int i, int j, int k, double evdwl, double ecoul,
------------------------------------------------------------------------- */
void Pair::ev_tally4(int i, int j, int k, int m, double evdwl,
- double *fi, double *fj, double *fk,
- double *drim, double *drjm, double *drkm)
+ double *fi, double *fj, double *fk,
+ double *drim, double *drjm, double *drkm)
{
double epairfourth,v[6];
@@ -738,7 +738,7 @@ void Pair::ev_tally4(int i, int j, int k, int m, double evdwl,
v[3] = 0.25 * (drim[0]*fi[1] + drjm[0]*fj[1] + drkm[0]*fk[1]);
v[4] = 0.25 * (drim[0]*fi[2] + drjm[0]*fj[2] + drkm[0]*fk[2]);
v[5] = 0.25 * (drim[1]*fi[2] + drjm[1]*fj[2] + drkm[1]*fk[2]);
-
+
vatom[i][0] += v[0]; vatom[i][1] += v[1]; vatom[i][2] += v[2];
vatom[i][3] += v[3]; vatom[i][4] += v[4]; vatom[i][5] += v[5];
vatom[j][0] += v[0]; vatom[j][1] += v[1]; vatom[j][2] += v[2];
@@ -786,13 +786,13 @@ void Pair::ev_tally_list(int n, int *list, double ecoul, double *v)
v[4] /= n;
v[5] /= n;
for (i = 0; i < n; i++) {
- j = list[i];
- vatom[j][0] += v[0];
- vatom[j][1] += v[1];
- vatom[j][2] += v[2];
- vatom[j][3] += v[3];
- vatom[j][4] += v[4];
- vatom[j][5] += v[5];
+ j = list[i];
+ vatom[j][0] += v[0];
+ vatom[j][1] += v[1];
+ vatom[j][2] += v[2];
+ vatom[j][3] += v[3];
+ vatom[j][4] += v[4];
+ vatom[j][5] += v[5];
}
}
}
@@ -807,7 +807,7 @@ void Pair::ev_tally_list(int n, int *list, double ecoul, double *v)
void Pair::v_tally(int i, double *fi, double *deli)
{
double v[6];
-
+
v[0] = 0.5*deli[0]*fi[0];
v[1] = 0.5*deli[1]*fi[1];
v[2] = 0.5*deli[2]*fi[2];
@@ -828,7 +828,7 @@ void Pair::v_tally(int i, double *fi, double *deli)
void Pair::v_tally2(int i, int j, double fpair, double *drij)
{
double v[6];
-
+
v[0] = 0.5 * drij[0]*drij[0]*fpair;
v[1] = 0.5 * drij[1]*drij[1]*fpair;
v[2] = 0.5 * drij[2]*drij[2]*fpair;
@@ -848,10 +848,10 @@ void Pair::v_tally2(int i, int j, double fpair, double *drij)
------------------------------------------------------------------------- */
void Pair::v_tally3(int i, int j, int k,
- double *fi, double *fj, double *drik, double *drjk)
+ double *fi, double *fj, double *drik, double *drjk)
{
double v[6];
-
+
v[0] = THIRD * (drik[0]*fi[0] + drjk[0]*fj[0]);
v[1] = THIRD * (drik[1]*fi[1] + drjk[1]*fj[1]);
v[2] = THIRD * (drik[2]*fi[2] + drjk[2]*fj[2]);
@@ -873,8 +873,8 @@ void Pair::v_tally3(int i, int j, int k,
------------------------------------------------------------------------- */
void Pair::v_tally4(int i, int j, int k, int m,
- double *fi, double *fj, double *fk,
- double *drim, double *drjm, double *drkm)
+ double *fi, double *fj, double *fk,
+ double *drim, double *drjm, double *drkm)
{
double v[6];
@@ -901,8 +901,8 @@ void Pair::v_tally4(int i, int j, int k, int m,
------------------------------------------------------------------------- */
void Pair::v_tally_tensor(int i, int j, int nlocal, int newton_pair,
- double vxx, double vyy, double vzz,
- double vxy, double vxz, double vyz)
+ double vxx, double vyy, double vzz,
+ double vxy, double vxz, double vyz)
{
double v[6];
@@ -912,7 +912,7 @@ void Pair::v_tally_tensor(int i, int j, int nlocal, int newton_pair,
v[3] = vxy;
v[4] = vxz;
v[5] = vyz;
-
+
if (vflag_global) {
if (newton_pair) {
virial[0] += v[0];
@@ -923,20 +923,20 @@ void Pair::v_tally_tensor(int i, int j, int nlocal, int newton_pair,
virial[5] += v[5];
} else {
if (i < nlocal) {
- virial[0] += 0.5*v[0];
- virial[1] += 0.5*v[1];
- virial[2] += 0.5*v[2];
- virial[3] += 0.5*v[3];
- virial[4] += 0.5*v[4];
- virial[5] += 0.5*v[5];
+ virial[0] += 0.5*v[0];
+ virial[1] += 0.5*v[1];
+ virial[2] += 0.5*v[2];
+ virial[3] += 0.5*v[3];
+ virial[4] += 0.5*v[4];
+ virial[5] += 0.5*v[5];
}
if (j < nlocal) {
- virial[0] += 0.5*v[0];
- virial[1] += 0.5*v[1];
- virial[2] += 0.5*v[2];
- virial[3] += 0.5*v[3];
- virial[4] += 0.5*v[4];
- virial[5] += 0.5*v[5];
+ virial[0] += 0.5*v[0];
+ virial[1] += 0.5*v[1];
+ virial[2] += 0.5*v[2];
+ virial[3] += 0.5*v[3];
+ virial[4] += 0.5*v[4];
+ virial[5] += 0.5*v[5];
}
}
}
@@ -1017,7 +1017,7 @@ void Pair::virial_fdotr_compute()
void Pair::write_file(int narg, char **arg)
{
if (narg < 8) error->all(FLERR,"Illegal pair_write command");
- if (single_enable == 0)
+ if (single_enable == 0)
error->all(FLERR,"Pair style does not support pair_write");
// parse arguments
@@ -1050,10 +1050,10 @@ void Pair::write_file(int narg, char **arg)
fp = fopen(arg[6],"a");
if (fp == NULL) error->one(FLERR,"Cannot open pair_write file");
fprintf(fp,"# Pair potential %s for atom types %d %d: i,r,energy,force\n",
- force->pair_style,itype,jtype);
- if (style == RLINEAR)
+ force->pair_style,itype,jtype);
+ if (style == RLINEAR)
fprintf(fp,"\n%s\nN %d R %g %g\n\n",arg[7],n,inner,outer);
- if (style == RSQ)
+ if (style == RSQ)
fprintf(fp,"\n%s\nN %d RSQ %g %g\n\n",arg[7],n,inner,outer);
}
@@ -1097,7 +1097,7 @@ void Pair::write_file(int narg, char **arg)
n = ntable;
}
- double r,e,f,rsq;
+ double r,e,f,rsq;
union_int_float_t rsq_lookup;
for (int i = 0; i < n; i++) {
@@ -1130,7 +1130,7 @@ void Pair::write_file(int narg, char **arg)
double *tmp;
if (epair) epair->swap_eam(eamfp_hold,&tmp);
if (atom->q) atom->q = q_hold;
-
+
if (me == 0) fclose(fp);
}
@@ -1138,20 +1138,20 @@ void Pair::write_file(int narg, char **arg)
define bitmap parameters based on inner and outer cutoffs
------------------------------------------------------------------------- */
-void Pair::init_bitmap(double inner, double outer, int ntablebits,
+void Pair::init_bitmap(double inner, double outer, int ntablebits,
int &masklo, int &maskhi, int &nmask, int &nshiftbits)
{
if (sizeof(int) != sizeof(float))
error->all(FLERR,"Bitmapped lookup tables require int/float be same size");
-
- if (ntablebits > sizeof(float)*CHAR_BIT)
+
+ if (ntablebits > sizeof(float)*CHAR_BIT)
error->all(FLERR,"Too many total bits for bitmapped lookup table");
-
- if (inner >= outer)
+
+ if (inner >= outer)
error->warning(FLERR,"Table inner cutoff >= outer cutoff");
-
+
int nlowermin = 1;
- while (!((pow(double(2),(double)nlowermin) <= inner*inner) &&
+ while (!((pow(double(2),(double)nlowermin) <= inner*inner) &&
(pow(double(2),(double)nlowermin+1.0) > inner*inner))) {
if (pow(double(2),(double)nlowermin) <= inner*inner) nlowermin++;
else nlowermin--;
@@ -1160,15 +1160,15 @@ void Pair::init_bitmap(double inner, double outer, int ntablebits,
int nexpbits = 0;
double required_range = outer*outer / pow(double(2),(double)nlowermin);
double available_range = 2.0;
-
+
while (available_range < required_range) {
nexpbits++;
available_range = pow(double(2),pow(double(2),(double)nexpbits));
}
-
+
int nmantbits = ntablebits - nexpbits;
- if (nexpbits > sizeof(float)*CHAR_BIT - FLT_MANT_DIG)
+ if (nexpbits > sizeof(float)*CHAR_BIT - FLT_MANT_DIG)
error->all(FLERR,"Too many exponent bits for lookup table");
if (nmantbits+1 > FLT_MANT_DIG)
error->all(FLERR,"Too many mantissa bits for lookup table");
diff --git a/src/pair.h b/src/pair.h
index a2f77462878da8d668a9d75595d5a51390a3593a..2c67e9bdb069cb74ca846adc5d4f7377eb977578 100644
--- a/src/pair.h
+++ b/src/pair.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -63,7 +63,7 @@ class Pair : protected Pointers {
int single_extra; // number of extra single values calculated
double *svector; // vector of extra single quantities
-
+
class NeighList *list; // standard neighbor list used by most pairs
class NeighList *listhalf; // half list used by some pairs
class NeighList *listfull; // full list used by some pairs
@@ -92,14 +92,14 @@ class Pair : protected Pointers {
void v_tally(int, double *, double *);
void ev_tally(int, int, int, int, double, double, double,
- double, double, double);
+ double, double, double);
void ev_tally3(int, int, int, double, double,
- double *, double *, double *, double *);
+ double *, double *, double *, double *);
void v_tally3(int, int, int, double *, double *, double *, double *);
void v_tally4(int, int, int, int, double *, double *, double *,
- double *, double *, double *);
+ double *, double *, double *);
void ev_tally_xyz(int, int, int, int, double, double,
- double, double, double, double, double, double);
+ double, double, double, double, double, double);
// general child-class methods
@@ -109,7 +109,7 @@ class Pair : protected Pointers {
virtual void compute_outer(int, int) {}
virtual double single(int, int, int, int,
- double, double, double, double &) {return 0.0;}
+ double, double, double, double &) {return 0.0;}
virtual void settings(int, char **) = 0;
virtual void coeff(int, char **) = 0;
@@ -130,7 +130,7 @@ class Pair : protected Pointers {
virtual double memory_usage();
// specific child-class methods for certain Pair styles
-
+
virtual void *extract(const char *, int &) {return NULL;}
virtual void swap_eam(double *, double **) {}
virtual void reset_dt() {}
@@ -162,13 +162,13 @@ class Pair : protected Pointers {
void ev_unset();
void ev_tally_full(int, double, double, double, double, double, double);
void ev_tally_xyz_full(int, double, double,
- double, double, double, double, double, double);
+ double, double, double, double, double, double);
void ev_tally4(int, int, int, int, double,
- double *, double *, double *, double *, double *, double *);
+ double *, double *, double *, double *, double *, double *);
void ev_tally_list(int, int *, double, double *);
void v_tally2(int, int, double, double *);
void v_tally_tensor(int, int, int, int,
- double, double, double, double, double, double);
+ double, double, double, double, double, double);
void virial_fdotr_compute();
inline int sbmask(int j) {
diff --git a/src/pair_beck.cpp b/src/pair_beck.cpp
index d96cae416cd173ef7a5a91663a700a846539fad5..696fb6c79c709f9164eedbb1adb645f756682781 100644
--- a/src/pair_beck.cpp
+++ b/src/pair_beck.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -59,7 +59,7 @@ void PairBeck::compute(int eflag, int vflag)
double aaij,alphaij,betaij;
double term1,term1inv,term2,term3,term4,term5,term6;
int *ilist,*jlist,*numneigh,**firstneigh;
-
+
evdwl = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
@@ -70,12 +70,12 @@ void PairBeck::compute(int eflag, int vflag)
int nlocal = atom->nlocal;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
-
+
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@@ -97,10 +97,10 @@ void PairBeck::compute(int eflag, int vflag)
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
-
+
if (rsq < cutsq[itype][jtype]) {
r = sqrt(rsq);
- r5 = rsq*rsq*r;
+ r5 = rsq*rsq*r;
aaij = aa[itype][jtype];
alphaij = alpha[itype][jtype];
betaij = beta[itype][jtype];
@@ -108,31 +108,31 @@ void PairBeck::compute(int eflag, int vflag)
term2 = 1.0/pow(term1,5.0);
term3 = 21.672 + 30.0*aaij*aaij + 6.0*rsq;
term4 = alphaij + r5*betaij;
- term5 = alphaij + 6.0*r5*betaij;
+ term5 = alphaij + 6.0*r5*betaij;
rinv = 1.0/r;
- force_beck = AA[itype][jtype]*exp(-1.0*r*term4)*term5;
- force_beck -= BB[itype][jtype]*r*term2*term3;
-
- fpair = factor_lj*force_beck*rinv;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (eflag) {
+ force_beck = AA[itype][jtype]*exp(-1.0*r*term4)*term5;
+ force_beck -= BB[itype][jtype]*r*term2*term3;
+
+ fpair = factor_lj*force_beck*rinv;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (eflag) {
term6 = 1.0/pow(term1,3.0);
term1inv = 1.0/term1;
evdwl = AA[itype][jtype]*exp(-1.0*r*term4);
evdwl -= BB[itype][jtype]*term6*(1.0+(2.709+3.0*aaij*aaij)*term1inv);
- }
+ }
- if (evflag) ev_tally(i,j,nlocal,newton_pair,
- evdwl,0.0,fpair,delx,dely,delz);
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ evdwl,0.0,fpair,delx,dely,delz);
}
}
}
@@ -141,7 +141,7 @@ void PairBeck::compute(int eflag, int vflag)
}
/* ----------------------------------------------------------------------
- allocate all arrays
+ allocate all arrays
------------------------------------------------------------------------- */
void PairBeck::allocate()
@@ -165,7 +165,7 @@ void PairBeck::allocate()
}
/* ----------------------------------------------------------------------
- global settings
+ global settings
------------------------------------------------------------------------- */
void PairBeck::settings(int narg, char **arg)
@@ -180,9 +180,9 @@ void PairBeck::settings(int narg, char **arg)
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
- if (setflag[i][j]) {
- cut[i][j] = cut_global;
- }
+ if (setflag[i][j]) {
+ cut[i][j] = cut_global;
+ }
}
}
@@ -205,7 +205,7 @@ void PairBeck::coeff(int narg, char **arg)
double aa_one = atof(arg[4]);
double alpha_one = atof(arg[5]);
double beta_one = atof(arg[6]);
-
+
double cut_one = cut_global;
if (narg == 8) cut_one = atof(arg[7]);
@@ -245,7 +245,7 @@ double PairBeck::init_one(int i, int j)
}
/* ----------------------------------------------------------------------
- proc 0 writes to restart file
+ proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairBeck::write_restart(FILE *fp)
@@ -257,12 +257,12 @@ void PairBeck::write_restart(FILE *fp)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
- fwrite(&AA[i][j],sizeof(double),1,fp);
- fwrite(&BB[i][j],sizeof(double),1,fp);
- fwrite(&aa[i][j],sizeof(double),1,fp);
- fwrite(&alpha[i][j],sizeof(double),1,fp);
- fwrite(&beta[i][j],sizeof(double),1,fp);
- fwrite(&cut[i][j],sizeof(double),1,fp);
+ fwrite(&AA[i][j],sizeof(double),1,fp);
+ fwrite(&BB[i][j],sizeof(double),1,fp);
+ fwrite(&aa[i][j],sizeof(double),1,fp);
+ fwrite(&alpha[i][j],sizeof(double),1,fp);
+ fwrite(&beta[i][j],sizeof(double),1,fp);
+ fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
@@ -283,20 +283,20 @@ void PairBeck::read_restart(FILE *fp)
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
- if (me == 0) {
- fread(&AA[i][j],sizeof(double),1,fp);
- fread(&BB[i][j],sizeof(double),1,fp);
- fread(&aa[i][j],sizeof(double),1,fp);
- fread(&alpha[i][j],sizeof(double),1,fp);
- fread(&beta[i][j],sizeof(double),1,fp);
- fread(&cut[i][j],sizeof(double),1,fp);
- }
- MPI_Bcast(&AA[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&BB[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&aa[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&alpha[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&beta[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
+ if (me == 0) {
+ fread(&AA[i][j],sizeof(double),1,fp);
+ fread(&BB[i][j],sizeof(double),1,fp);
+ fread(&aa[i][j],sizeof(double),1,fp);
+ fread(&alpha[i][j],sizeof(double),1,fp);
+ fread(&beta[i][j],sizeof(double),1,fp);
+ fread(&cut[i][j],sizeof(double),1,fp);
+ }
+ MPI_Bcast(&AA[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&BB[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&aa[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&alpha[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&beta[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
@@ -328,10 +328,10 @@ void PairBeck::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairBeck::single(int i, int j, int itype, int jtype,
- double rsq,
- double factor_coul, double factor_lj,
- double &fforce)
+double PairBeck::single(int i, int j, int itype, int jtype,
+ double rsq,
+ double factor_coul, double factor_lj,
+ double &fforce)
{
double phi_beck,r,rinv;
double r5,force_beck;
diff --git a/src/pair_beck.h b/src/pair_beck.h
index 8790d67d95afd7ae82c37754e56225dd45204865..922dac7507131fb5f174535cdb366463c2b881cb 100644
--- a/src/pair_beck.h
+++ b/src/pair_beck.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/pair_born.cpp b/src/pair_born.cpp
index 68905a95d2229cae79e19e314c9eb094d621dd7e..08aa6a96db7cb7827944c925e83bc1077f76f7cd 100644
--- a/src/pair_born.cpp
+++ b/src/pair_born.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -82,7 +82,7 @@ void PairBorn::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@@ -106,31 +106,31 @@ void PairBorn::compute(int eflag, int vflag)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
- r = sqrt(rsq);
- rexp = exp((sigma[itype][jtype]-r)*rhoinv[itype][jtype]);
- forceborn = born1[itype][jtype]*r*rexp - born2[itype][jtype]*r6inv
- + born3[itype][jtype]*r2inv*r6inv;
- fpair = factor_lj*forceborn*r2inv;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (eflag) {
- evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv
- + d[itype][jtype]*r6inv*r2inv - offset[itype][jtype];
- evdwl *= factor_lj;
- }
-
- if (evflag) ev_tally(i,j,nlocal,newton_pair,
- evdwl,0.0,fpair,delx,dely,delz);
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
+ r = sqrt(rsq);
+ rexp = exp((sigma[itype][jtype]-r)*rhoinv[itype][jtype]);
+ forceborn = born1[itype][jtype]*r*rexp - born2[itype][jtype]*r6inv
+ + born3[itype][jtype]*r2inv*r6inv;
+ fpair = factor_lj*forceborn*r2inv;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (eflag) {
+ evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv
+ + d[itype][jtype]*r6inv*r2inv - offset[itype][jtype];
+ evdwl *= factor_lj;
+ }
+
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ evdwl,0.0,fpair,delx,dely,delz);
}
}
}
@@ -183,7 +183,7 @@ void PairBorn::settings(int narg, char **arg)
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
- if (setflag[i][j]) cut[i][j] = cut_global;
+ if (setflag[i][j]) cut[i][j] = cut_global;
}
}
@@ -238,8 +238,8 @@ double PairBorn::init_one(int i, int j)
rhoinv[i][j] = 1.0/rho[i][j];
born1[i][j] = a[i][j]/rho[i][j];
born2[i][j] = 6.0*c[i][j];
- born3[i][j] = 8.0*d[i][j];
-
+ born3[i][j] = 8.0*d[i][j];
+
if (offset_flag) {
double rexp = exp((sigma[i][j]-cut[i][j])*rhoinv[i][j]);
offset[i][j] = a[i][j]*rexp - c[i][j]/pow(cut[i][j],6.0) +
@@ -256,19 +256,19 @@ double PairBorn::init_one(int i, int j)
born3[j][i] = born3[i][j];
offset[j][i] = offset[i][j];
- // compute I,J contribution to long-range tail correction
- // count total # of atoms of type I and J via Allreduce
+ // compute I,J contribution to long-range tail correction
+ // count total # of atoms of type I and J via Allreduce
- if (tail_flag) {
- int *type = atom->type;
- int nlocal = atom->nlocal;
+ if (tail_flag) {
+ int *type = atom->type;
+ int nlocal = atom->nlocal;
- double count[2],all[2];
- count[0] = count[1] = 0.0;
- for (int k = 0; k < nlocal; k++) {
- if (type[k] == i) count[0] += 1.0;
- if (type[k] == j) count[1] += 1.0;
- }
+ double count[2],all[2];
+ count[0] = count[1] = 0.0;
+ for (int k = 0; k < nlocal; k++) {
+ if (type[k] == i) count[0] += 1.0;
+ if (type[k] == j) count[1] += 1.0;
+ }
MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world);
double rho1 = rho[i][j];
@@ -278,15 +278,15 @@ double PairBorn::init_one(int i, int j)
double rc2 = rc*rc;
double rc3 = rc2*rc;
double rc5 = rc3*rc2;
- etail_ij = 2.0*MY_PI*all[0]*all[1] *
- (a[i][j]*exp((sigma[i][j]-rc)/rho1)*rho1*
- (rc2 + 2.0*rho1*rc + 2.0*rho2) -
- c[i][j]/(3.0*rc3) + d[i][j]/(5.0*rc5));
- ptail_ij = (-1/3.0)*2.0*MY_PI*all[0]*all[1] *
- (-a[i][j]*exp((sigma[i][j]-rc)/rho1) *
- (rc3 + 3.0*rho1*rc2 + 6.0*rho2*rc + 6.0*rho3) +
- 2.0*c[i][j]/rc3 - 8.0*d[i][j]/(5.0*rc5));
- }
+ etail_ij = 2.0*MY_PI*all[0]*all[1] *
+ (a[i][j]*exp((sigma[i][j]-rc)/rho1)*rho1*
+ (rc2 + 2.0*rho1*rc + 2.0*rho2) -
+ c[i][j]/(3.0*rc3) + d[i][j]/(5.0*rc5));
+ ptail_ij = (-1/3.0)*2.0*MY_PI*all[0]*all[1] *
+ (-a[i][j]*exp((sigma[i][j]-rc)/rho1) *
+ (rc3 + 3.0*rho1*rc2 + 6.0*rho2*rc + 6.0*rho3) +
+ 2.0*c[i][j]/rc3 - 8.0*d[i][j]/(5.0*rc5));
+ }
return cut[i][j];
}
@@ -304,12 +304,12 @@ void PairBorn::write_restart(FILE *fp)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
- fwrite(&a[i][j],sizeof(double),1,fp);
- fwrite(&rho[i][j],sizeof(double),1,fp);
- fwrite(&sigma[i][j],sizeof(double),1,fp);
- fwrite(&c[i][j],sizeof(double),1,fp);
+ fwrite(&a[i][j],sizeof(double),1,fp);
+ fwrite(&rho[i][j],sizeof(double),1,fp);
+ fwrite(&sigma[i][j],sizeof(double),1,fp);
+ fwrite(&c[i][j],sizeof(double),1,fp);
fwrite(&d[i][j],sizeof(double),1,fp);
- fwrite(&cut[i][j],sizeof(double),1,fp);
+ fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
@@ -331,20 +331,20 @@ void PairBorn::read_restart(FILE *fp)
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
- if (me == 0) {
- fread(&a[i][j],sizeof(double),1,fp);
- fread(&rho[i][j],sizeof(double),1,fp);
- fread(&sigma[i][j],sizeof(double),1,fp);
- fread(&c[i][j],sizeof(double),1,fp);
+ if (me == 0) {
+ fread(&a[i][j],sizeof(double),1,fp);
+ fread(&rho[i][j],sizeof(double),1,fp);
+ fread(&sigma[i][j],sizeof(double),1,fp);
+ fread(&c[i][j],sizeof(double),1,fp);
fread(&d[i][j],sizeof(double),1,fp);
- fread(&cut[i][j],sizeof(double),1,fp);
- }
- MPI_Bcast(&a[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&rho[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&c[i][j],1,MPI_DOUBLE,0,world);
+ fread(&cut[i][j],sizeof(double),1,fp);
+ }
+ MPI_Bcast(&a[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&rho[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&c[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&d[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
@@ -379,8 +379,8 @@ void PairBorn::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairBorn::single(int i, int j, int itype, int jtype,
- double rsq, double factor_coul, double factor_lj,
- double &fforce)
+ double rsq, double factor_coul, double factor_lj,
+ double &fforce)
{
double r2inv,r6inv,r,rexp,forceborn,phiborn;
@@ -391,7 +391,7 @@ double PairBorn::single(int i, int j, int itype, int jtype,
forceborn = born1[itype][jtype]*r*rexp - born2[itype][jtype]*r6inv +
born3[itype][jtype]*r2inv*r6inv;
fforce = factor_lj*forceborn*r2inv;
-
+
phiborn = a[itype][jtype]*rexp - c[itype][jtype]*r6inv +
d[itype][jtype]*r2inv*r6inv - offset[itype][jtype];
return factor_lj*phiborn;
diff --git a/src/pair_born.h b/src/pair_born.h
index 566fdc7c447b855a0aa7cf247bab8d1defb8cacd..a37dd916501292ddf50edf2dbd561791cbfab786 100644
--- a/src/pair_born.h
+++ b/src/pair_born.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -45,7 +45,7 @@ class PairBorn : public Pair {
double **cut;
double **a,**rho,**sigma,**c, **d;
double **rhoinv,**born1,**born2,**born3,**offset;
-
+
void allocate();
};
diff --git a/src/pair_born_coul_wolf.cpp b/src/pair_born_coul_wolf.cpp
index db4a8849107c6d7287e8f1b3657198270fba20e3..7acb117b73124f8f48bc640cdda7768bb6b649ef 100644
--- a/src/pair_born_coul_wolf.cpp
+++ b/src/pair_born_coul_wolf.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -88,16 +88,16 @@ void PairBornCoulWolf::compute(int eflag, int vflag)
// self and shifted coulombic energy
- e_self = v_sh = 0.0;
+ e_self = v_sh = 0.0;
e_shift = erfc(alf*cut_coul)/cut_coul;
- f_shift = -(e_shift+ 2.0*alf/MY_PIS * exp(-alf*alf*cut_coul*cut_coul)) /
- cut_coul;
+ f_shift = -(e_shift+ 2.0*alf/MY_PIS * exp(-alf*alf*cut_coul*cut_coul)) /
+ cut_coul;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@@ -127,52 +127,52 @@ void PairBornCoulWolf::compute(int eflag, int vflag)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
+ r2inv = 1.0/rsq;
- if (rsq < cut_coulsq) {
- r = sqrt(rsq);
+ if (rsq < cut_coulsq) {
+ r = sqrt(rsq);
prefactor = qqrd2e*qtmp*q[j]/r;
- erfcc = erfc(alf*r);
+ erfcc = erfc(alf*r);
erfcd = exp(-alf*alf*r*r);
- v_sh = (erfcc - e_shift*r) * prefactor;
+ v_sh = (erfcc - e_shift*r) * prefactor;
dvdrr = (erfcc/rsq + 2.0*alf/MY_PIS * erfcd/r) + f_shift;
forcecoul = dvdrr*rsq*prefactor;
- if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
- } else forcecoul = 0.0;
+ if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
+ } else forcecoul = 0.0;
- if (rsq < cut_ljsq[itype][jtype]) {
- r6inv = r2inv*r2inv*r2inv;
+ if (rsq < cut_ljsq[itype][jtype]) {
+ r6inv = r2inv*r2inv*r2inv;
r = sqrt(rsq);
- rexp = exp((sigma[itype][jtype]-r)*rhoinv[itype][jtype]);
- forceborn = born1[itype][jtype]*r*rexp - born2[itype][jtype]*r6inv
- + born3[itype][jtype]*r2inv*r6inv;
- } else forceborn = 0.0;
-
- fpair = (forcecoul + factor_lj*forceborn) * r2inv;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (eflag) {
- if (rsq < cut_coulsq) {
- ecoul = v_sh;
- if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
- } else ecoul = 0.0;
- if (rsq < cut_ljsq[itype][jtype]) {
- evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv +
- d[itype][jtype]*r6inv*r2inv - offset[itype][jtype];
- evdwl *= factor_lj;
- } else evdwl = 0.0;
- }
-
- if (evflag) ev_tally(i,j,nlocal,newton_pair,
- evdwl,ecoul,fpair,delx,dely,delz);
+ rexp = exp((sigma[itype][jtype]-r)*rhoinv[itype][jtype]);
+ forceborn = born1[itype][jtype]*r*rexp - born2[itype][jtype]*r6inv
+ + born3[itype][jtype]*r2inv*r6inv;
+ } else forceborn = 0.0;
+
+ fpair = (forcecoul + factor_lj*forceborn) * r2inv;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (eflag) {
+ if (rsq < cut_coulsq) {
+ ecoul = v_sh;
+ if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
+ } else ecoul = 0.0;
+ if (rsq < cut_ljsq[itype][jtype]) {
+ evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv +
+ d[itype][jtype]*r6inv*r2inv - offset[itype][jtype];
+ evdwl *= factor_lj;
+ } else evdwl = 0.0;
+ }
+
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
@@ -227,7 +227,7 @@ void PairBornCoulWolf::settings(int narg, char **arg)
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
- if (setflag[i][j]) cut_lj[i][j] = cut_lj_global;
+ if (setflag[i][j]) cut_lj[i][j] = cut_lj_global;
}
}
@@ -237,7 +237,7 @@ void PairBornCoulWolf::settings(int narg, char **arg)
void PairBornCoulWolf::coeff(int narg, char **arg)
{
- if (narg < 7 || narg > 8)
+ if (narg < 7 || narg > 8)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
@@ -301,7 +301,7 @@ double PairBornCoulWolf::init_one(int i, int j)
born1[i][j] = a[i][j]/rho[i][j];
born2[i][j] = 6.0*c[i][j];
born3[i][j] = 8.0*d[i][j];
-
+
if (offset_flag) {
double rexp = exp(-cut_lj[i][j]/rho[i][j]);
offset[i][j] = a[i][j]*rexp - c[i][j]/pow(cut_lj[i][j],6.0)
@@ -335,12 +335,12 @@ void PairBornCoulWolf::write_restart(FILE *fp)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
- fwrite(&a[i][j],sizeof(double),1,fp);
- fwrite(&rho[i][j],sizeof(double),1,fp);
- fwrite(&sigma[i][j],sizeof(double),1,fp);
- fwrite(&c[i][j],sizeof(double),1,fp);
- fwrite(&d[i][j],sizeof(double),1,fp);
- fwrite(&cut_lj[i][j],sizeof(double),1,fp);
+ fwrite(&a[i][j],sizeof(double),1,fp);
+ fwrite(&rho[i][j],sizeof(double),1,fp);
+ fwrite(&sigma[i][j],sizeof(double),1,fp);
+ fwrite(&c[i][j],sizeof(double),1,fp);
+ fwrite(&d[i][j],sizeof(double),1,fp);
+ fwrite(&cut_lj[i][j],sizeof(double),1,fp);
}
}
}
@@ -362,20 +362,20 @@ void PairBornCoulWolf::read_restart(FILE *fp)
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
- if (me == 0) {
- fread(&a[i][j],sizeof(double),1,fp);
- fread(&rho[i][j],sizeof(double),1,fp);
- fread(&sigma[i][j],sizeof(double),1,fp);
- fread(&c[i][j],sizeof(double),1,fp);
- fread(&d[i][j],sizeof(double),1,fp);
- fread(&cut_lj[i][j],sizeof(double),1,fp);
- }
- MPI_Bcast(&a[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&rho[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&c[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&d[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world);
+ if (me == 0) {
+ fread(&a[i][j],sizeof(double),1,fp);
+ fread(&rho[i][j],sizeof(double),1,fp);
+ fread(&sigma[i][j],sizeof(double),1,fp);
+ fread(&c[i][j],sizeof(double),1,fp);
+ fread(&d[i][j],sizeof(double),1,fp);
+ fread(&cut_lj[i][j],sizeof(double),1,fp);
+ }
+ MPI_Bcast(&a[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&rho[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&c[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&d[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world);
}
}
}
@@ -418,23 +418,23 @@ void PairBornCoulWolf::read_restart_settings(FILE *fp)
------------------------------------------------------------------------- */
double PairBornCoulWolf::single(int i, int j, int itype, int jtype,
- double rsq,
- double factor_coul, double factor_lj,
- double &fforce)
+ double rsq,
+ double factor_coul, double factor_lj,
+ double &fforce)
{
double r2inv,r6inv,r,prefactor,rexp;
double forcecoul,forceborn,phicoul,phiborn;
- double e_shift,f_shift,dvdrr,erfcc,erfcd;
+ double e_shift,f_shift,dvdrr,erfcc,erfcd;
r2inv = 1.0/rsq;
e_shift = erfc(alf*cut_coul) / cut_coul;
- f_shift = -(e_shift+2*alf/MY_PIS * exp(-alf*alf*cut_coul*cut_coul)) /
- cut_coul;
-
+ f_shift = -(e_shift+2*alf/MY_PIS * exp(-alf*alf*cut_coul*cut_coul)) /
+ cut_coul;
+
if (rsq < cut_coulsq) {
r = sqrt(rsq);
prefactor = force->qqrd2e * atom->q[i]*atom->q[j]/r;
- erfcc = erfc(alf*r);
+ erfcc = erfc(alf*r);
erfcd = exp(-alf*alf*r*r);
dvdrr = (erfcc/rsq + 2.0*alf/MY_PIS * erfcd/r) + f_shift;
forcecoul = dvdrr*rsq*prefactor;
@@ -450,7 +450,7 @@ double PairBornCoulWolf::single(int i, int j, int itype, int jtype,
} else forceborn = 0.0;
fforce = (forcecoul + factor_lj*forceborn) * r2inv;
-
+
double eng = 0.0;
if (rsq < cut_coulsq) {
phicoul = prefactor * (erfcc-e_shift*r);
@@ -458,7 +458,7 @@ double PairBornCoulWolf::single(int i, int j, int itype, int jtype,
eng += phicoul;
}
if (rsq < cut_ljsq[itype][jtype]) {
- phiborn = a[itype][jtype]*rexp - c[itype][jtype]*r6inv
+ phiborn = a[itype][jtype]*rexp - c[itype][jtype]*r6inv
+ d[itype][jtype]*r2inv*r6inv - offset[itype][jtype];
eng += factor_lj*phiborn;
}
diff --git a/src/pair_born_coul_wolf.h b/src/pair_born_coul_wolf.h
index 1042e68800707e2282549b1243a86c1450ead3a6..3428432542474fe4c30582c655037bfbcd46e739 100644
--- a/src/pair_born_coul_wolf.h
+++ b/src/pair_born_coul_wolf.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -38,7 +38,7 @@ class PairBornCoulWolf : public Pair {
void write_restart_settings(FILE *);
void read_restart_settings(FILE *);
double single(int, int, int, int, double, double, double, double &);
-
+
protected:
double cut_lj_global,alf;
double **cut_lj,**cut_ljsq;
diff --git a/src/pair_buck.cpp b/src/pair_buck.cpp
index abd3d2dadab0fab6a9aef8b43964b9c0e7ac6198..4fba27257eb16f2f7782a99586fd72ecb3ae734d 100644
--- a/src/pair_buck.cpp
+++ b/src/pair_buck.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -75,7 +75,7 @@ void PairBuck::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@@ -99,30 +99,30 @@ void PairBuck::compute(int eflag, int vflag)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
- r = sqrt(rsq);
- rexp = exp(-r*rhoinv[itype][jtype]);
- forcebuck = buck1[itype][jtype]*r*rexp - buck2[itype][jtype]*r6inv;
- fpair = factor_lj*forcebuck*r2inv;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (eflag) {
- evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv -
- offset[itype][jtype];
- evdwl *= factor_lj;
- }
-
- if (evflag) ev_tally(i,j,nlocal,newton_pair,
- evdwl,0.0,fpair,delx,dely,delz);
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
+ r = sqrt(rsq);
+ rexp = exp(-r*rhoinv[itype][jtype]);
+ forcebuck = buck1[itype][jtype]*r*rexp - buck2[itype][jtype]*r6inv;
+ fpair = factor_lj*forcebuck*r2inv;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (eflag) {
+ evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv -
+ offset[itype][jtype];
+ evdwl *= factor_lj;
+ }
+
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ evdwl,0.0,fpair,delx,dely,delz);
}
}
}
@@ -172,7 +172,7 @@ void PairBuck::settings(int narg, char **arg)
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
- if (setflag[i][j]) cut[i][j] = cut_global;
+ if (setflag[i][j]) cut[i][j] = cut_global;
}
}
@@ -223,7 +223,7 @@ double PairBuck::init_one(int i, int j)
rhoinv[i][j] = 1.0/rho[i][j];
buck1[i][j] = a[i][j]/rho[i][j];
buck2[i][j] = 6.0*c[i][j];
-
+
if (offset_flag) {
double rexp = exp(-cut[i][j]/rho[i][j]);
offset[i][j] = a[i][j]*rexp - c[i][j]/pow(cut[i][j],6.0);
@@ -236,8 +236,8 @@ double PairBuck::init_one(int i, int j)
buck2[j][i] = buck2[i][j];
offset[j][i] = offset[i][j];
- // compute I,J contribution to long-range tail correction
- // count total # of atoms of type I and J via Allreduce
+ // compute I,J contribution to long-range tail correction
+ // count total # of atoms of type I and J via Allreduce
if (tail_flag) {
int *type = atom->type;
@@ -258,13 +258,13 @@ double PairBuck::init_one(int i, int j)
double rc2 = rc*rc;
double rc3 = rc2*rc;
etail_ij = 2.0*MY_PI*all[0]*all[1]*
- (a[i][j]*exp(-rc/rho1)*rho1*(rc2 + 2.0*rho1*rc + 2.0*rho2) -
+ (a[i][j]*exp(-rc/rho1)*rho1*(rc2 + 2.0*rho1*rc + 2.0*rho2) -
c[i][j]/(3.0*rc3));
ptail_ij = (-1/3.0)*2.0*MY_PI*all[0]*all[1]*
(-a[i][j]*exp(-rc/rho1)*
(rc3 + 3.0*rho1*rc2 + 6.0*rho2*rc + 6.0*rho3) + 2.0*c[i][j]/rc3);
}
-
+
return cut[i][j];
}
@@ -281,10 +281,10 @@ void PairBuck::write_restart(FILE *fp)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
- fwrite(&a[i][j],sizeof(double),1,fp);
- fwrite(&rho[i][j],sizeof(double),1,fp);
- fwrite(&c[i][j],sizeof(double),1,fp);
- fwrite(&cut[i][j],sizeof(double),1,fp);
+ fwrite(&a[i][j],sizeof(double),1,fp);
+ fwrite(&rho[i][j],sizeof(double),1,fp);
+ fwrite(&c[i][j],sizeof(double),1,fp);
+ fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
@@ -306,16 +306,16 @@ void PairBuck::read_restart(FILE *fp)
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
- if (me == 0) {
- fread(&a[i][j],sizeof(double),1,fp);
- fread(&rho[i][j],sizeof(double),1,fp);
- fread(&c[i][j],sizeof(double),1,fp);
- fread(&cut[i][j],sizeof(double),1,fp);
- }
- MPI_Bcast(&a[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&rho[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&c[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
+ if (me == 0) {
+ fread(&a[i][j],sizeof(double),1,fp);
+ fread(&rho[i][j],sizeof(double),1,fp);
+ fread(&c[i][j],sizeof(double),1,fp);
+ fread(&cut[i][j],sizeof(double),1,fp);
+ }
+ MPI_Bcast(&a[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&rho[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&c[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
@@ -350,8 +350,8 @@ void PairBuck::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairBuck::single(int i, int j, int itype, int jtype,
- double rsq, double factor_coul, double factor_lj,
- double &fforce)
+ double rsq, double factor_coul, double factor_lj,
+ double &fforce)
{
double r2inv,r6inv,r,rexp,forcebuck,phibuck;
@@ -361,7 +361,7 @@ double PairBuck::single(int i, int j, int itype, int jtype,
rexp = exp(-r*rhoinv[itype][jtype]);
forcebuck = buck1[itype][jtype]*r*rexp - buck2[itype][jtype]*r6inv;
fforce = factor_lj*forcebuck*r2inv;
-
+
phibuck = a[itype][jtype]*rexp - c[itype][jtype]*r6inv -
offset[itype][jtype];
return factor_lj*phibuck;
diff --git a/src/pair_buck.h b/src/pair_buck.h
index fe9034329cdd3bf84be283cc5357e91793a0b7df..8ed41fb28e7da5a24e0a8aa7ad13a4c6a9fa4b79 100644
--- a/src/pair_buck.h
+++ b/src/pair_buck.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/pair_buck_coul_cut.cpp b/src/pair_buck_coul_cut.cpp
index a2f0784a3d0ee5ce23b63002c661573b3f62976d..612539465b1679f96eab0b26ac253a06f59fec4f 100644
--- a/src/pair_buck_coul_cut.cpp
+++ b/src/pair_buck_coul_cut.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -85,7 +85,7 @@ void PairBuckCoulCut::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@@ -111,43 +111,43 @@ void PairBuckCoulCut::compute(int eflag, int vflag)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
+ r2inv = 1.0/rsq;
r = sqrt(rsq);
- if (rsq < cut_coulsq[itype][jtype])
- forcecoul = qqrd2e * qtmp*q[j]/r;
- else forcecoul = 0.0;
-
- if (rsq < cut_ljsq[itype][jtype]) {
- r6inv = r2inv*r2inv*r2inv;
- rexp = exp(-r*rhoinv[itype][jtype]);
- forcebuck = buck1[itype][jtype]*r*rexp - buck2[itype][jtype]*r6inv;
- } else forcebuck = 0.0;
-
- fpair = (factor_coul*forcecoul + factor_lj*forcebuck) * r2inv;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (eflag) {
- if (rsq < cut_coulsq[itype][jtype])
- ecoul = factor_coul * qqrd2e * qtmp*q[j]/r;
- else ecoul = 0.0;
- if (rsq < cut_ljsq[itype][jtype]) {
- evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv -
- offset[itype][jtype];
- evdwl *= factor_lj;
- } else evdwl = 0.0;
- }
-
- if (evflag) ev_tally(i,j,nlocal,newton_pair,
- evdwl,ecoul,fpair,delx,dely,delz);
+ if (rsq < cut_coulsq[itype][jtype])
+ forcecoul = qqrd2e * qtmp*q[j]/r;
+ else forcecoul = 0.0;
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ r6inv = r2inv*r2inv*r2inv;
+ rexp = exp(-r*rhoinv[itype][jtype]);
+ forcebuck = buck1[itype][jtype]*r*rexp - buck2[itype][jtype]*r6inv;
+ } else forcebuck = 0.0;
+
+ fpair = (factor_coul*forcecoul + factor_lj*forcebuck) * r2inv;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (eflag) {
+ if (rsq < cut_coulsq[itype][jtype])
+ ecoul = factor_coul * qqrd2e * qtmp*q[j]/r;
+ else ecoul = 0.0;
+ if (rsq < cut_ljsq[itype][jtype]) {
+ evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv -
+ offset[itype][jtype];
+ evdwl *= factor_lj;
+ } else evdwl = 0.0;
+ }
+
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
@@ -203,10 +203,10 @@ void PairBuckCoulCut::settings(int narg, char **arg)
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
- if (setflag[i][j]) {
- cut_lj[i][j] = cut_lj_global;
- cut_coul[i][j] = cut_coul_global;
- }
+ if (setflag[i][j]) {
+ cut_lj[i][j] = cut_lj_global;
+ cut_coul[i][j] = cut_coul_global;
+ }
}
}
@@ -276,7 +276,7 @@ double PairBuckCoulCut::init_one(int i, int j)
rhoinv[i][j] = 1.0/rho[i][j];
buck1[i][j] = a[i][j]/rho[i][j];
buck2[i][j] = 6.0*c[i][j];
-
+
if (offset_flag) {
double rexp = exp(-cut_lj[i][j]/rho[i][j]);
offset[i][j] = a[i][j]*rexp - c[i][j]/pow(cut_lj[i][j],6.0);
@@ -291,8 +291,8 @@ double PairBuckCoulCut::init_one(int i, int j)
buck2[j][i] = buck2[i][j];
offset[j][i] = offset[i][j];
- // compute I,J contribution to long-range tail correction
- // count total # of atoms of type I and J via Allreduce
+ // compute I,J contribution to long-range tail correction
+ // count total # of atoms of type I and J via Allreduce
if (tail_flag) {
int *type = atom->type;
@@ -313,13 +313,13 @@ double PairBuckCoulCut::init_one(int i, int j)
double rc2 = rc*rc;
double rc3 = rc2*rc;
etail_ij = 2.0*MY_PI*all[0]*all[1]*
- (a[i][j]*exp(-rc/rho1)*rho1*(rc2 + 2.0*rho1*rc + 2.0*rho2) -
+ (a[i][j]*exp(-rc/rho1)*rho1*(rc2 + 2.0*rho1*rc + 2.0*rho2) -
c[i][j]/(3.0*rc3));
ptail_ij = (-1/3.0)*2.0*MY_PI*all[0]*all[1]*
(-a[i][j]*exp(-rc/rho1)*
(rc3 + 3.0*rho1*rc2 + 6.0*rho2*rc + 6.0*rho3) + 2.0*c[i][j]/rc3);
}
-
+
return cut;
}
@@ -336,11 +336,11 @@ void PairBuckCoulCut::write_restart(FILE *fp)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
- fwrite(&a[i][j],sizeof(double),1,fp);
- fwrite(&rho[i][j],sizeof(double),1,fp);
- fwrite(&c[i][j],sizeof(double),1,fp);
- fwrite(&cut_lj[i][j],sizeof(double),1,fp);
- fwrite(&cut_coul[i][j],sizeof(double),1,fp);
+ fwrite(&a[i][j],sizeof(double),1,fp);
+ fwrite(&rho[i][j],sizeof(double),1,fp);
+ fwrite(&c[i][j],sizeof(double),1,fp);
+ fwrite(&cut_lj[i][j],sizeof(double),1,fp);
+ fwrite(&cut_coul[i][j],sizeof(double),1,fp);
}
}
}
@@ -362,18 +362,18 @@ void PairBuckCoulCut::read_restart(FILE *fp)
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
- if (me == 0) {
- fread(&a[i][j],sizeof(double),1,fp);
- fread(&rho[i][j],sizeof(double),1,fp);
- fread(&c[i][j],sizeof(double),1,fp);
- fread(&cut_lj[i][j],sizeof(double),1,fp);
- fread(&cut_coul[i][j],sizeof(double),1,fp);
- }
- MPI_Bcast(&a[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&rho[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&c[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&cut_coul[i][j],1,MPI_DOUBLE,0,world);
+ if (me == 0) {
+ fread(&a[i][j],sizeof(double),1,fp);
+ fread(&rho[i][j],sizeof(double),1,fp);
+ fread(&c[i][j],sizeof(double),1,fp);
+ fread(&cut_lj[i][j],sizeof(double),1,fp);
+ fread(&cut_coul[i][j],sizeof(double),1,fp);
+ }
+ MPI_Bcast(&a[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&rho[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&c[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut_coul[i][j],1,MPI_DOUBLE,0,world);
}
}
}
@@ -411,9 +411,9 @@ void PairBuckCoulCut::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairBuckCoulCut::single(int i, int j, int itype, int jtype,
- double rsq,
- double factor_coul, double factor_lj,
- double &fforce)
+ double rsq,
+ double factor_coul, double factor_lj,
+ double &fforce)
{
double r2inv,r6inv,r,rexp,forcecoul,forcebuck,phicoul,phibuck;
@@ -428,7 +428,7 @@ double PairBuckCoulCut::single(int i, int j, int itype, int jtype,
forcebuck = buck1[itype][jtype]*r*rexp - buck2[itype][jtype]*r6inv;
} else forcebuck = 0.0;
fforce = (factor_coul*forcecoul + factor_lj*forcebuck) * r2inv;
-
+
double eng = 0.0;
if (rsq < cut_coulsq[itype][jtype]) {
phicoul = force->qqrd2e * atom->q[i]*atom->q[j]*sqrt(r2inv);
diff --git a/src/pair_buck_coul_cut.h b/src/pair_buck_coul_cut.h
index d4db4f8cae34cb4c878e6205d89cf8d312ed9606..df2d407c7280b133a26c637c0a855ecbb14b3d13 100644
--- a/src/pair_buck_coul_cut.h
+++ b/src/pair_buck_coul_cut.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/pair_coul_cut.cpp b/src/pair_coul_cut.cpp
index 2fb10dabd66efb4cd6ea1e84480a2ceec304d2bd..4bca683b23b91ca9f0eda848278988bfb213b194 100644
--- a/src/pair_coul_cut.cpp
+++ b/src/pair_coul_cut.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -69,7 +69,7 @@ void PairCoulCut::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@@ -94,25 +94,25 @@ void PairCoulCut::compute(int eflag, int vflag)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- rinv = sqrt(r2inv);
- forcecoul = qqrd2e * scale[itype][jtype] * qtmp*q[j]*rinv;
- fpair = factor_coul*forcecoul * r2inv;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (eflag)
- ecoul = factor_coul * qqrd2e * scale[itype][jtype] * qtmp*q[j]*rinv;
-
- if (evflag) ev_tally(i,j,nlocal,newton_pair,
- 0.0,ecoul,fpair,delx,dely,delz);
+ r2inv = 1.0/rsq;
+ rinv = sqrt(r2inv);
+ forcecoul = qqrd2e * scale[itype][jtype] * qtmp*q[j]*rinv;
+ fpair = factor_coul*forcecoul * r2inv;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (eflag)
+ ecoul = factor_coul * qqrd2e * scale[itype][jtype] * qtmp*q[j]*rinv;
+
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ 0.0,ecoul,fpair,delx,dely,delz);
}
}
}
@@ -156,7 +156,7 @@ void PairCoulCut::settings(int narg, char **arg)
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
- if (setflag[i][j]) cut[i][j] = cut_global;
+ if (setflag[i][j]) cut[i][j] = cut_global;
}
}
@@ -248,8 +248,8 @@ void PairCoulCut::read_restart(FILE *fp)
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
- if (me == 0) fread(&cut[i][j],sizeof(double),1,fp);
- MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
+ if (me == 0) fread(&cut[i][j],sizeof(double),1,fp);
+ MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
@@ -284,8 +284,8 @@ void PairCoulCut::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairCoulCut::single(int i, int j, int itype, int jtype,
- double rsq, double factor_coul, double factor_lj,
- double &fforce)
+ double rsq, double factor_coul, double factor_lj,
+ double &fforce)
{
double r2inv,rinv,forcecoul,phicoul;
diff --git a/src/pair_coul_cut.h b/src/pair_coul_cut.h
index 6e3e1fdc85344435f05c8424d391440b61de608f..fbd76c4bb3c4a289c257b3c0e723880d502de56f 100644
--- a/src/pair_coul_cut.h
+++ b/src/pair_coul_cut.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/pair_coul_debye.cpp b/src/pair_coul_debye.cpp
index 2606a1f3cb09594dd735b89b9ae3669235a359f8..81d8a9e905dee9f960609c73bf4bd685ac0ef48c 100644
--- a/src/pair_coul_debye.cpp
+++ b/src/pair_coul_debye.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -56,7 +56,7 @@ void PairCoulDebye::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@@ -81,26 +81,26 @@ void PairCoulDebye::compute(int eflag, int vflag)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- r = sqrt(rsq);
- rinv = 1.0/r;
- screening = exp(-kappa*r);
- forcecoul = qqrd2e * qtmp*q[j] * screening * (kappa + rinv);
- fpair = factor_coul*forcecoul * r2inv;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (eflag) ecoul = factor_coul * qqrd2e * qtmp*q[j] * rinv * screening;
-
- if (evflag) ev_tally(i,j,nlocal,newton_pair,
- 0.0,ecoul,fpair,delx,dely,delz);
+ r2inv = 1.0/rsq;
+ r = sqrt(rsq);
+ rinv = 1.0/r;
+ screening = exp(-kappa*r);
+ forcecoul = qqrd2e * qtmp*q[j] * screening * (kappa + rinv);
+ fpair = factor_coul*forcecoul * r2inv;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (eflag) ecoul = factor_coul * qqrd2e * qtmp*q[j] * rinv * screening;
+
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ 0.0,ecoul,fpair,delx,dely,delz);
}
}
}
@@ -125,7 +125,7 @@ void PairCoulDebye::settings(int narg, char **arg)
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
- if (setflag[i][j]) cut[i][j] = cut_global;
+ if (setflag[i][j]) cut[i][j] = cut_global;
}
}
@@ -162,8 +162,8 @@ void PairCoulDebye::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairCoulDebye::single(int i, int j, int itype, int jtype,
- double rsq, double factor_coul, double factor_lj,
- double &fforce)
+ double rsq, double factor_coul, double factor_lj,
+ double &fforce)
{
double r2inv,r,rinv,forcecoul,phicoul,screening;
diff --git a/src/pair_coul_debye.h b/src/pair_coul_debye.h
index 33f2785b24c6c7f15d0671e62b91f8037acb9a2d..9e7cca67b64ac9304c8f208b53e477586089b3c4 100644
--- a/src/pair_coul_debye.h
+++ b/src/pair_coul_debye.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/pair_coul_wolf.cpp b/src/pair_coul_wolf.cpp
index a1382913c96e7037048817f4df391ee32f8c6f11..af9751fa11cdaf173c9554d09a4ca558462a48ad 100644
--- a/src/pair_coul_wolf.cpp
+++ b/src/pair_coul_wolf.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -74,16 +74,16 @@ void PairCoulWolf::compute(int eflag, int vflag)
// self and shifted coulombic energy
- e_self = v_sh = 0.0;
+ e_self = v_sh = 0.0;
e_shift = erfc(alf*cut_coul)/cut_coul;
- f_shift = -(e_shift+ 2.0*alf/MY_PIS * exp(-alf*alf*cut_coul*cut_coul)) /
- cut_coul;
+ f_shift = -(e_shift+ 2.0*alf/MY_PIS * exp(-alf*alf*cut_coul*cut_coul)) /
+ cut_coul;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@@ -112,38 +112,38 @@ void PairCoulWolf::compute(int eflag, int vflag)
jtype = type[j];
if (rsq < cut_coulsq) {
- r = sqrt(rsq);
- prefactor = qqrd2e*qtmp*q[j]/r;
- erfcc = erfc(alf*r);
- erfcd = exp(-alf*alf*r*r);
- v_sh = (erfcc - e_shift*r) * prefactor;
- dvdrr = (erfcc/rsq + 2.0*alf/MY_PIS * erfcd/r) + f_shift;
- forcecoul = dvdrr*rsq*prefactor;
- if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
- fpair = forcecoul / rsq;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (eflag) {
- if (rsq < cut_coulsq) {
- ecoul = v_sh;
- if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
- } else ecoul = 0.0;
- }
-
- if (evflag) ev_tally(i,j,nlocal,newton_pair,
- 0.0,ecoul,fpair,delx,dely,delz);
+ r = sqrt(rsq);
+ prefactor = qqrd2e*qtmp*q[j]/r;
+ erfcc = erfc(alf*r);
+ erfcd = exp(-alf*alf*r*r);
+ v_sh = (erfcc - e_shift*r) * prefactor;
+ dvdrr = (erfcc/rsq + 2.0*alf/MY_PIS * erfcd/r) + f_shift;
+ forcecoul = dvdrr*rsq*prefactor;
+ if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
+ fpair = forcecoul / rsq;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (eflag) {
+ if (rsq < cut_coulsq) {
+ ecoul = v_sh;
+ if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
+ } else ecoul = 0.0;
+ }
+
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ 0.0,ecoul,fpair,delx,dely,delz);
}
}
}
-
+
if (vflag_fdotr) virial_fdotr_compute();
}
@@ -179,7 +179,7 @@ void PairCoulWolf::settings(int narg, char **arg)
}
/* ----------------------------------------------------------------------
- set cutoffs for one or more type pairs, optional
+ set cutoffs for one or more type pairs, optional
------------------------------------------------------------------------- */
void PairCoulWolf::coeff(int narg, char **arg)
@@ -203,7 +203,7 @@ void PairCoulWolf::coeff(int narg, char **arg)
}
/* ----------------------------------------------------------------------
- init specific to this pair style
+ init specific to this pair style
------------------------------------------------------------------------- */
void PairCoulWolf::init_style()
@@ -291,29 +291,29 @@ void PairCoulWolf::read_restart_settings(FILE *fp)
only the pair part is calculated here
------------------------------------------------------------------------- */
-double PairCoulWolf::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
- double &fforce)
+double PairCoulWolf::single(int i, int j, int itype, int jtype, double rsq,
+ double factor_coul, double factor_lj,
+ double &fforce)
{
double r6inv,r,prefactor,rexp;
double forcecoul,forceborn,phicoul;
- double e_shift,f_shift,dvdrr,erfcc,erfcd;
+ double e_shift,f_shift,dvdrr,erfcc,erfcd;
e_shift = erfc(alf*cut_coul) / cut_coul;
- f_shift = -(e_shift+ 2.0*alf/MY_PIS * exp(-alf*alf*cut_coul*cut_coul)) /
- cut_coul;
-
+ f_shift = -(e_shift+ 2.0*alf/MY_PIS * exp(-alf*alf*cut_coul*cut_coul)) /
+ cut_coul;
+
if (rsq < cut_coulsq) {
r = sqrt(rsq);
prefactor = force->qqrd2e * atom->q[i]*atom->q[j]/r;
- erfcc = erfc(alf*r);
+ erfcc = erfc(alf*r);
erfcd = exp(-alf*alf*r*r);
dvdrr = (erfcc/rsq + 2.0*alf/MY_PIS * erfcd/r) + f_shift;
forcecoul = dvdrr*rsq*prefactor;
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
} else forcecoul = 0.0;
fforce = forcecoul / rsq;
-
+
double eng = 0.0;
if (rsq < cut_coulsq) {
phicoul = prefactor * (erfcc-e_shift*r);
diff --git a/src/pair_coul_wolf.h b/src/pair_coul_wolf.h
index d73602ca872bbbe97750cce53974b1b8cd6023dd..89391ffc776868f1274fcdd2a9776a889f816c47 100644
--- a/src/pair_coul_wolf.h
+++ b/src/pair_coul_wolf.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -40,7 +40,7 @@ class PairCoulWolf : public Pair {
double single(int, int, int, int, double, double, double, double &);
protected:
- double cut_coul,cut_coulsq,alf;
+ double cut_coul,cut_coulsq,alf;
void allocate();
};
diff --git a/src/pair_dpd.cpp b/src/pair_dpd.cpp
index 5c701a89e19288abf0360e687dafff3a0a9b8163..04f216ec850a4bf1eb77e2e8fd80330593ad2140 100644
--- a/src/pair_dpd.cpp
+++ b/src/pair_dpd.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -85,7 +85,7 @@ void PairDPD::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@@ -112,44 +112,44 @@ void PairDPD::compute(int eflag, int vflag)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r = sqrt(rsq);
- if (r < EPSILON) continue; // r can be 0.0 in DPD systems
- rinv = 1.0/r;
- delvx = vxtmp - v[j][0];
- delvy = vytmp - v[j][1];
- delvz = vztmp - v[j][2];
- dot = delx*delvx + dely*delvy + delz*delvz;
- wd = 1.0 - r/cut[itype][jtype];
- randnum = random->gaussian();
-
- // conservative force = a0 * wd
- // drag force = -gamma * wd^2 * (delx dot delv) / r
- // random force = sigma * wd * rnd * dtinvsqrt;
-
- fpair = a0[itype][jtype]*wd;
- fpair -= gamma[itype][jtype]*wd*wd*dot*rinv;
- fpair += sigma[itype][jtype]*wd*randnum*dtinvsqrt;
- fpair *= factor_dpd*rinv;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (eflag) {
+ r = sqrt(rsq);
+ if (r < EPSILON) continue; // r can be 0.0 in DPD systems
+ rinv = 1.0/r;
+ delvx = vxtmp - v[j][0];
+ delvy = vytmp - v[j][1];
+ delvz = vztmp - v[j][2];
+ dot = delx*delvx + dely*delvy + delz*delvz;
+ wd = 1.0 - r/cut[itype][jtype];
+ randnum = random->gaussian();
+
+ // conservative force = a0 * wd
+ // drag force = -gamma * wd^2 * (delx dot delv) / r
+ // random force = sigma * wd * rnd * dtinvsqrt;
+
+ fpair = a0[itype][jtype]*wd;
+ fpair -= gamma[itype][jtype]*wd*wd*dot*rinv;
+ fpair += sigma[itype][jtype]*wd*randnum*dtinvsqrt;
+ fpair *= factor_dpd*rinv;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (eflag) {
// unshifted eng of conservative term:
- // evdwl = -a0[itype][jtype]*r * (1.0-0.5*r/cut[itype][jtype]);
- // eng shifted to 0.0 at cutoff
- evdwl = 0.5*a0[itype][jtype]*cut[itype][jtype] * wd*wd;
- evdwl *= factor_dpd;
- }
-
- if (evflag) ev_tally(i,j,nlocal,newton_pair,
- evdwl,0.0,fpair,delx,dely,delz);
+ // evdwl = -a0[itype][jtype]*r * (1.0-0.5*r/cut[itype][jtype]);
+ // eng shifted to 0.0 at cutoff
+ evdwl = 0.5*a0[itype][jtype]*cut[itype][jtype] * wd*wd;
+ evdwl *= factor_dpd;
+ }
+
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ evdwl,0.0,fpair,delx,dely,delz);
}
}
}
@@ -158,7 +158,7 @@ void PairDPD::compute(int eflag, int vflag)
}
/* ----------------------------------------------------------------------
- allocate all arrays
+ allocate all arrays
------------------------------------------------------------------------- */
void PairDPD::allocate()
@@ -180,7 +180,7 @@ void PairDPD::allocate()
}
/* ----------------------------------------------------------------------
- global settings
+ global settings
------------------------------------------------------------------------- */
void PairDPD::settings(int narg, char **arg)
@@ -203,7 +203,7 @@ void PairDPD::settings(int narg, char **arg)
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
- if (setflag[i][j]) cut[i][j] = cut_global;
+ if (setflag[i][j]) cut[i][j] = cut_global;
}
}
@@ -267,7 +267,7 @@ double PairDPD::init_one(int i, int j)
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
sigma[i][j] = sqrt(2.0*force->boltz*temperature*gamma[i][j]);
-
+
cut[j][i] = cut[i][j];
a0[j][i] = a0[i][j];
gamma[j][i] = gamma[i][j];
@@ -289,9 +289,9 @@ void PairDPD::write_restart(FILE *fp)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
- fwrite(&a0[i][j],sizeof(double),1,fp);
- fwrite(&gamma[i][j],sizeof(double),1,fp);
- fwrite(&cut[i][j],sizeof(double),1,fp);
+ fwrite(&a0[i][j],sizeof(double),1,fp);
+ fwrite(&gamma[i][j],sizeof(double),1,fp);
+ fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
@@ -313,14 +313,14 @@ void PairDPD::read_restart(FILE *fp)
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
- if (me == 0) {
- fread(&a0[i][j],sizeof(double),1,fp);
- fread(&gamma[i][j],sizeof(double),1,fp);
- fread(&cut[i][j],sizeof(double),1,fp);
- }
- MPI_Bcast(&a0[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&gamma[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
+ if (me == 0) {
+ fread(&a0[i][j],sizeof(double),1,fp);
+ fread(&gamma[i][j],sizeof(double),1,fp);
+ fread(&cut[i][j],sizeof(double),1,fp);
+ }
+ MPI_Bcast(&a0[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&gamma[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
@@ -364,7 +364,7 @@ void PairDPD::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairDPD::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_dpd, double &fforce)
+ double factor_coul, double factor_dpd, double &fforce)
{
double r,rinv,wd,phi;
diff --git a/src/pair_dpd.h b/src/pair_dpd.h
index 9ee8ead873db036215a2d5fceba671109ed2d25b..0a6cf243fb0eb8e14bf16f768a6abc955bd4ed72 100644
--- a/src/pair_dpd.h
+++ b/src/pair_dpd.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/pair_dpd_tstat.cpp b/src/pair_dpd_tstat.cpp
index 4151ecc5b17bc524cd215fc65f324c317aee0927..4bcccede18b226f775ae060d4617f2a8d5e5a9bf 100644
--- a/src/pair_dpd_tstat.cpp
+++ b/src/pair_dpd_tstat.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -54,7 +54,7 @@ void PairDPDTstat::compute(int eflag, int vflag)
double boltz = force->boltz;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++)
- sigma[i][j] = sigma[j][i] = sqrt(2.0*boltz*temperature*gamma[i][j]);
+ sigma[i][j] = sigma[j][i] = sqrt(2.0*boltz*temperature*gamma[i][j]);
}
double **x = atom->x;
@@ -70,7 +70,7 @@ void PairDPDTstat::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@@ -97,34 +97,34 @@ void PairDPDTstat::compute(int eflag, int vflag)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r = sqrt(rsq);
- if (r < EPSILON) continue; // r can be 0.0 in DPD systems
- rinv = 1.0/r;
- delvx = vxtmp - v[j][0];
- delvy = vytmp - v[j][1];
- delvz = vztmp - v[j][2];
- dot = delx*delvx + dely*delvy + delz*delvz;
- wd = 1.0 - r/cut[itype][jtype];
- randnum = random->gaussian();
-
- // drag force = -gamma * wd^2 * (delx dot delv) / r
- // random force = sigma * wd * rnd * dtinvsqrt;
-
- fpair = -gamma[itype][jtype]*wd*wd*dot*rinv;
- fpair += sigma[itype][jtype]*wd*randnum*dtinvsqrt;
- fpair *= factor_dpd*rinv;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (evflag) ev_tally(i,j,nlocal,newton_pair,
- 0.0,0.0,fpair,delx,dely,delz);
+ r = sqrt(rsq);
+ if (r < EPSILON) continue; // r can be 0.0 in DPD systems
+ rinv = 1.0/r;
+ delvx = vxtmp - v[j][0];
+ delvy = vytmp - v[j][1];
+ delvz = vztmp - v[j][2];
+ dot = delx*delvx + dely*delvy + delz*delvz;
+ wd = 1.0 - r/cut[itype][jtype];
+ randnum = random->gaussian();
+
+ // drag force = -gamma * wd^2 * (delx dot delv) / r
+ // random force = sigma * wd * rnd * dtinvsqrt;
+
+ fpair = -gamma[itype][jtype]*wd*wd*dot*rinv;
+ fpair += sigma[itype][jtype]*wd*randnum*dtinvsqrt;
+ fpair *= factor_dpd*rinv;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ 0.0,0.0,fpair,delx,dely,delz);
}
}
}
@@ -133,7 +133,7 @@ void PairDPDTstat::compute(int eflag, int vflag)
}
/* ----------------------------------------------------------------------
- global settings
+ global settings
------------------------------------------------------------------------- */
void PairDPDTstat::settings(int narg, char **arg)
@@ -159,7 +159,7 @@ void PairDPDTstat::settings(int narg, char **arg)
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
- if (setflag[i][j]) cut[i][j] = cut_global;
+ if (setflag[i][j]) cut[i][j] = cut_global;
}
}
@@ -234,4 +234,3 @@ void PairDPDTstat::read_restart_settings(FILE *fp)
if (random) delete random;
random = new RanMars(lmp,seed + comm->me);
}
-
diff --git a/src/pair_dpd_tstat.h b/src/pair_dpd_tstat.h
index d4383c56bc9121b80fcd5e4d540ea293db8d21cc..86d2565027dfb48b4f59a1544f926e806444c29e 100644
--- a/src/pair_dpd_tstat.h
+++ b/src/pair_dpd_tstat.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/pair_gauss.cpp b/src/pair_gauss.cpp
index 820d1e8b7ea645cde8706037141f5fa8746cd408..81b03a8a2c7ca5fe4a405ff82642ebac248d590d 100644
--- a/src/pair_gauss.cpp
+++ b/src/pair_gauss.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -60,12 +60,12 @@ PairGauss::~PairGauss()
/* ---------------------------------------------------------------------- */
void PairGauss::compute(int eflag, int vflag)
-{
+{
int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double r,rsq,r2inv,forcelj;
int *ilist,*jlist,*numneigh,**firstneigh;
-
+
evdwl = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
@@ -76,7 +76,7 @@ void PairGauss::compute(int eflag, int vflag)
int *type = atom->type;
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
-
+
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
@@ -93,45 +93,45 @@ void PairGauss::compute(int eflag, int vflag)
jlist = firstneigh[i];
jnum = numneigh[i];
- for (jj = 0; jj < jnum; jj++) {
+ for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
-
+
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
-
+
// define a Gaussian well to be occupied if
- // the site it interacts with is within the force maximum
-
+ // the site it interacts with is within the force maximum
+
if (eflag_global && rsq < 0.5/b[itype][jtype]) occ++;
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- r = sqrt(rsq);
- forcelj = - 2.0*a[itype][jtype]*b[itype][jtype] * rsq *
- exp(-b[itype][jtype]*rsq);
- fpair = forcelj*r2inv;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (eflag)
- evdwl = -(a[itype][jtype]*exp(-b[itype][jtype]*rsq) -
- offset[itype][jtype]);
-
- if (evflag) ev_tally(i,j,nlocal,newton_pair,
- evdwl,0.0,fpair,delx,dely,delz);
+ r2inv = 1.0/rsq;
+ r = sqrt(rsq);
+ forcelj = - 2.0*a[itype][jtype]*b[itype][jtype] * rsq *
+ exp(-b[itype][jtype]*rsq);
+ fpair = forcelj*r2inv;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (eflag)
+ evdwl = -(a[itype][jtype]*exp(-b[itype][jtype]*rsq) -
+ offset[itype][jtype]);
+
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ evdwl,0.0,fpair,delx,dely,delz);
}
- }
+ }
}
if (eflag_global) pvector[0] = occ;
@@ -146,18 +146,18 @@ void PairGauss::allocate()
{
allocated = 1;
int n = atom->ntypes;
-
+
memory->create(setflag,n+1,n+1,"pair:setflag");
for (int i = 1; i <= n; i++)
for (int j = 1; j <= n; j++)
setflag[i][j] = 0;
-
+
memory->create(cutsq,n+1,n+1,"pair:cutsq");
-
+
memory->create(cut,n+1,n+1,"pair:cut_gauss");
memory->create(a,n+1,n+1,"pair:a");
memory->create(b,n+1,n+1,"pair:b");
- memory->create(offset,n+1,n+1,"pair:offset");
+ memory->create(offset,n+1,n+1,"pair:offset");
}
/* ----------------------------------------------------------------------
@@ -165,18 +165,18 @@ void PairGauss::allocate()
------------------------------------------------------------------------- */
void PairGauss::settings(int narg, char **arg)
-{
+{
if (narg != 1) error->all(FLERR,"Illegal pair_style command");
-
+
cut_global = atof(arg[0]);
// reset cutoffs that have been explicity set
-
+
if (allocated) {
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
- if (setflag[i][j]) cut[i][j] = cut_global;
+ if (setflag[i][j]) cut[i][j] = cut_global;
}
}
@@ -192,24 +192,24 @@ void PairGauss::coeff(int narg, char **arg)
int ilo, ihi, jlo, jhi;
force->bounds(arg[0],atom->ntypes,ilo,ihi);
force->bounds(arg[1],atom->ntypes,jlo,jhi);
-
+
double a_one = atof(arg[2]);
double b_one = atof(arg[3]);
double cut_one = cut_global;
if (narg == 5) cut_one = atof(arg[4]);
-
+
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j<=jhi; j++) {
- a[i][j] = a_one;
+ a[i][j] = a_one;
b[i][j] = b_one;
cut[i][j] = cut_one;
setflag[i][j] = 1;
count++ ;
}
}
-
+
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
@@ -220,15 +220,15 @@ void PairGauss::coeff(int narg, char **arg)
double PairGauss::init_one(int i, int j)
{
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
-
+
if (offset_flag) offset[i][j] = a[i][j]*exp(-b[i][j]*cut[i][j]*cut[i][j]);
else offset[i][j] = 0.0;
-
+
a[j][i] = a[i][j];
b[j][i] = b[i][j];
offset[j][i] = offset[i][j];
-
- return cut[i][j];
+
+ return cut[i][j];
}
/* ----------------------------------------------------------------------
@@ -244,9 +244,9 @@ void PairGauss::write_restart(FILE *fp)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
- fwrite(&a[i][j],sizeof(double),1,fp);
- fwrite(&b[i][j],sizeof(double),1,fp);
- fwrite(&cut[i][j],sizeof(double),1,fp);
+ fwrite(&a[i][j],sizeof(double),1,fp);
+ fwrite(&b[i][j],sizeof(double),1,fp);
+ fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
@@ -268,14 +268,14 @@ void PairGauss::read_restart(FILE *fp)
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
- if (me == 0) {
- fread(&a[i][j],sizeof(double),1,fp);
- fread(&b[i][j],sizeof(double),1,fp);
- fread(&cut[i][j],sizeof(double),1,fp);
- }
- MPI_Bcast(&a[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&b[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
+ if (me == 0) {
+ fread(&a[i][j],sizeof(double),1,fp);
+ fread(&b[i][j],sizeof(double),1,fp);
+ fread(&cut[i][j],sizeof(double),1,fp);
+ }
+ MPI_Bcast(&a[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&b[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
@@ -310,16 +310,16 @@ void PairGauss::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairGauss::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
- double &fforce)
+ double factor_coul, double factor_lj,
+ double &fforce)
{
double r2inv,forcelj,philj,r;
r = sqrt(rsq);
-
+
r2inv = 1.0/rsq;
philj = -(a[itype][jtype]*exp(-b[itype][jtype]*rsq) - offset[itype][jtype]);
-
+
forcelj = -2.0*a[itype][jtype]*b[itype][jtype]*rsq*exp(-b[itype][jtype]*rsq);
fforce = forcelj*r2inv;
return philj;
diff --git a/src/pair_gauss.h b/src/pair_gauss.h
index 115a8948bea7d0633cf4e0e211f3b7db50f0d8ec..d38c8a477e8aa198cdf203520e1e451de206528e 100644
--- a/src/pair_gauss.h
+++ b/src/pair_gauss.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -31,20 +31,20 @@ class PairGauss : public Pair {
virtual void compute(int,int);
void settings(int, char **);
void coeff(int, char **);
- double init_one(int, int);
+ double init_one(int, int);
void write_restart(FILE *);
void read_restart(FILE *);
void write_restart_settings(FILE *);
void read_restart_settings(FILE *);
double single(int, int, int, int, double, double, double, double &);
void *extract(const char *, int &);
-
- protected:
+
+ protected:
double cut_global;
double **cut;
double **a,**b;
double **offset;
-
+
void allocate();
};
diff --git a/src/pair_hybrid.cpp b/src/pair_hybrid.cpp
index 00e530d5a2d509b5967a6ed52e3820dd6c4479e9..4fdf8161b44fee39faccfd948cf5f47bf843ae70 100644
--- a/src/pair_hybrid.cpp
+++ b/src/pair_hybrid.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -82,12 +82,12 @@ void PairHybrid::compute(int eflag, int vflag)
// incoming vflag = 2, then
// reset vflag as if global component were 1
// necessary since one or more sub-styles cannot compute virial as F dot r
-
+
if (no_virial_fdotr_compute && vflag % 4 == 2) vflag = 1 + vflag/4 * 4;
if (eflag || vflag) ev_setup(eflag,vflag);
- else evflag = vflag_fdotr = eflag_global = vflag_global =
- eflag_atom = vflag_atom = 0;
+ else evflag = vflag_fdotr = eflag_global = vflag_global =
+ eflag_atom = vflag_atom = 0;
// check if global component of incoming vflag = 2
// if so, reset vflag passed to substyle as if it were 0
@@ -118,8 +118,8 @@ void PairHybrid::compute(int eflag, int vflag)
if (force->newton_pair) n += atom->nghost;
double **vatom_substyle = styles[m]->vatom;
for (i = 0; i < n; i++)
- for (j = 0; j < 6; j++)
- vatom[i][j] += vatom_substyle[i][j];
+ for (j = 0; j < 6; j++)
+ vatom[i][j] += vatom_substyle[i][j];
}
}
@@ -151,7 +151,7 @@ void PairHybrid::compute_outer(int eflag, int vflag)
}
/* ----------------------------------------------------------------------
- allocate all arrays
+ allocate all arrays
------------------------------------------------------------------------- */
void PairHybrid::allocate()
@@ -221,9 +221,9 @@ void PairHybrid::settings(int narg, char **arg)
iarg = 0;
nstyles = 0;
while (iarg < narg) {
- if (strcmp(arg[iarg],"hybrid") == 0)
+ if (strcmp(arg[iarg],"hybrid") == 0)
error->all(FLERR,"Pair style hybrid cannot have hybrid as an argument");
- if (strcmp(arg[iarg],"none") == 0)
+ if (strcmp(arg[iarg],"none") == 0)
error->all(FLERR,"Pair style hybrid cannot have none as an argument");
styles[nstyles] = force->new_pair(arg[iarg],lmp->suffix,dummy);
int n = strlen(arg[iarg]) + 1;
@@ -248,7 +248,7 @@ void PairHybrid::settings(int narg, char **arg)
for (int j = 0; j < nstyles; j++) {
if (strcmp(keywords[j],keywords[i]) == 0) count++;
if (j == i) multiple[i] = count;
- }
+ }
if (count == 1) multiple[i] = 0;
}
@@ -258,7 +258,7 @@ void PairHybrid::settings(int narg, char **arg)
if (styles[m]) comm_forward = MAX(comm_forward,styles[m]->comm_forward);
if (styles[m]) comm_reverse = MAX(comm_reverse,styles[m]->comm_reverse);
if (styles[m]) comm_reverse_off = MAX(comm_reverse_off,
- styles[m]->comm_reverse_off);
+ styles[m]->comm_reverse_off);
}
// single_enable = 1 if any sub-style is set
@@ -313,13 +313,13 @@ void PairHybrid::coeff(int narg, char **arg)
multflag = 0;
if (strcmp(arg[2],keywords[m]) == 0) {
if (multiple[m]) {
- multflag = 1;
- if (narg < 4) error->all(FLERR,"Incorrect args for pair coefficients");
- if (!isdigit(arg[3][0]))
- error->all(FLERR,"Incorrect args for pair coefficients");
- int index = atoi(arg[3]);
- if (index == multiple[m]) break;
- else continue;
+ multflag = 1;
+ if (narg < 4) error->all(FLERR,"Incorrect args for pair coefficients");
+ if (!isdigit(arg[3][0]))
+ error->all(FLERR,"Incorrect args for pair coefficients");
+ int index = atoi(arg[3]);
+ if (index == multiple[m]) break;
+ else continue;
} else break;
}
}
@@ -348,10 +348,10 @@ void PairHybrid::coeff(int narg, char **arg)
if (!none && styles[m]->one_coeff)
for (int i = 1; i <= atom->ntypes; i++)
for (int j = i; j <= atom->ntypes; j++)
- if (nmap[i][j] && map[i][j][0] == m) {
- setflag[i][j] = 0;
- nmap[i][j] = 0;
- }
+ if (nmap[i][j] && map[i][j][0] == m) {
+ setflag[i][j] = 0;
+ nmap[i][j] = 0;
+ }
// set setflag and which type pairs map to which sub-style
// if sub-style is none: set hybrid setflag, wipe out map
@@ -362,14 +362,14 @@ void PairHybrid::coeff(int narg, char **arg)
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
if (none) {
- setflag[i][j] = 1;
- nmap[i][j] = 0;
- count++;
+ setflag[i][j] = 1;
+ nmap[i][j] = 0;
+ count++;
} else if (styles[m]->setflag[i][j]) {
- setflag[i][j] = 1;
- nmap[i][j] = 1;
- map[i][j][0] = m;
- count++;
+ setflag[i][j] = 1;
+ nmap[i][j] = 1;
+ map[i][j][0] = m;
+ count++;
}
}
}
@@ -393,8 +393,8 @@ void PairHybrid::init_style()
used = 0;
for (itype = 1; itype <= ntypes; itype++)
for (jtype = itype; jtype <= ntypes; jtype++)
- for (m = 0; m < nmap[itype][jtype]; m++)
- if (map[itype][jtype][m] == istyle) used = 1;
+ for (m = 0; m < nmap[itype][jtype]; m++)
+ if (map[itype][jtype][m] == istyle) used = 1;
if (used == 0) error->all(FLERR,"Pair hybrid sub-style is not used");
}
@@ -428,23 +428,23 @@ void PairHybrid::init_style()
for (itype = 1; itype <= ntypes; itype++)
for (jtype = 1; jtype <= ntypes; jtype++)
- ijskip[itype][jtype] = 1;
+ ijskip[itype][jtype] = 1;
for (itype = 1; itype <= ntypes; itype++)
for (jtype = itype; jtype <= ntypes; jtype++) {
- for (m = 0; m < nmap[itype][jtype]; m++)
- if (map[itype][jtype][m] == istyle)
- ijskip[itype][jtype] = ijskip[jtype][itype] = 0;
- if (nmap[itype][jtype] == 0 &&
- nmap[itype][itype] == 1 && map[itype][itype][0] == istyle &&
- nmap[jtype][jtype] == 1 && map[jtype][jtype][0] == istyle)
- ijskip[itype][jtype] = ijskip[jtype][itype] = 0;
+ for (m = 0; m < nmap[itype][jtype]; m++)
+ if (map[itype][jtype][m] == istyle)
+ ijskip[itype][jtype] = ijskip[jtype][itype] = 0;
+ if (nmap[itype][jtype] == 0 &&
+ nmap[itype][itype] == 1 && map[itype][itype][0] == istyle &&
+ nmap[jtype][jtype] == 1 && map[jtype][jtype][0] == istyle)
+ ijskip[itype][jtype] = ijskip[jtype][itype] = 0;
}
for (itype = 1; itype <= ntypes; itype++) {
iskip[itype] = 1;
for (jtype = 1; jtype <= ntypes; jtype++)
- if (ijskip[itype][jtype] == 0) iskip[itype] = 0;
+ if (ijskip[itype][jtype] == 0) iskip[itype] = 0;
}
// if any skipping occurs
@@ -454,7 +454,7 @@ void PairHybrid::init_style()
skip = 0;
for (itype = 1; itype <= ntypes; itype++)
for (jtype = 1; jtype <= ntypes; jtype++)
- if (ijskip[itype][jtype] == 1) skip = 1;
+ if (ijskip[itype][jtype] == 1) skip = 1;
if (skip) {
neighbor->requests[i]->skip = 1;
@@ -504,11 +504,11 @@ double PairHybrid::init_one(int i, int j)
for (int k = 0; k < nmap[i][j]; k++) {
map[j][i][k] = map[i][j][k];
double cut = styles[map[i][j][k]]->init_one(i,j);
- styles[map[i][j][k]]->cutsq[i][j] =
+ styles[map[i][j][k]]->cutsq[i][j] =
styles[map[i][j][k]]->cutsq[j][i] = cut*cut;
if (styles[map[i][j][k]]->ghostneigh)
- cutghost[i][j] = cutghost[j][i] =
- MAX(cutghost[i][j],styles[map[i][j][k]]->cutghost[i][j]);
+ cutghost[i][j] = cutghost[j][i] =
+ MAX(cutghost[i][j],styles[map[i][j][k]]->cutghost[i][j]);
if (tail_flag) {
etail_ij += styles[map[i][j][k]]->etail_ij;
ptail_ij += styles[map[i][j][k]]->ptail_ij;
@@ -639,8 +639,8 @@ void PairHybrid::read_restart(FILE *fp)
------------------------------------------------------------------------- */
double PairHybrid::single(int i, int j, int itype, int jtype,
- double rsq, double factor_coul, double factor_lj,
- double &fforce)
+ double rsq, double factor_coul, double factor_lj,
+ double &fforce)
{
if (nmap[itype][jtype] == 0)
error->one(FLERR,"Invoked pair single on pair style none");
@@ -652,17 +652,17 @@ double PairHybrid::single(int i, int j, int itype, int jtype,
for (int m = 0; m < nmap[itype][jtype]; m++) {
if (rsq < styles[map[itype][jtype][m]]->cutsq[itype][jtype]) {
if (styles[map[itype][jtype][m]]->single_enable == 0)
- error->one(FLERR,"Pair hybrid sub-style does not support single call");
+ error->one(FLERR,"Pair hybrid sub-style does not support single call");
esum += styles[map[itype][jtype][m]]->
- single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fone);
+ single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fone);
fforce += fone;
// copy substyle extra values into hybrid's svector
if (single_extra && styles[map[itype][jtype][m]]->single_extra)
- for (m = 0; m < single_extra; m++)
- svector[m] = styles[map[itype][jtype][m]]->svector[m];
+ for (m = 0; m < single_extra; m++)
+ svector[m] = styles[map[itype][jtype][m]]->svector[m];
}
}
@@ -700,8 +700,8 @@ void *PairHybrid::extract(const char *str, int &dim)
double *p_newvalue = (double *) ptr;
double newvalue = *p_newvalue;
if (cutptr && newvalue != cutvalue)
- error->all(FLERR,
- "Coulomb cutoffs of pair hybrid sub-styles do not match");
+ error->all(FLERR,
+ "Coulomb cutoffs of pair hybrid sub-styles do not match");
cutptr = ptr;
cutvalue = newvalue;
} else if (ptr) return ptr;
diff --git a/src/pair_hybrid.h b/src/pair_hybrid.h
index 78cd09a9d00e434ffa496ca3ca296cb9e148119b..225869cb213e464a3dd237108d7f2efd1610cd03 100644
--- a/src/pair_hybrid.h
+++ b/src/pair_hybrid.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/pair_hybrid_overlay.cpp b/src/pair_hybrid_overlay.cpp
index ede18ef74806b43405a0d815312614415f93d787..327c395b228312696c26ffef990faf0950ca2af4 100644
--- a/src/pair_hybrid_overlay.cpp
+++ b/src/pair_hybrid_overlay.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -51,13 +51,13 @@ void PairHybridOverlay::coeff(int narg, char **arg)
multflag = 0;
if (strcmp(arg[2],keywords[m]) == 0) {
if (multiple[m]) {
- multflag = 1;
- if (narg < 4) error->all(FLERR,"Incorrect args for pair coefficients");
- if (!isdigit(arg[3][0]))
- error->all(FLERR,"Incorrect args for pair coefficients");
- int index = atoi(arg[3]);
- if (index == multiple[m]) break;
- else continue;
+ multflag = 1;
+ if (narg < 4) error->all(FLERR,"Incorrect args for pair coefficients");
+ if (!isdigit(arg[3][0]))
+ error->all(FLERR,"Incorrect args for pair coefficients");
+ int index = atoi(arg[3]);
+ if (index == multiple[m]) break;
+ else continue;
} else break;
}
}
@@ -89,16 +89,16 @@ void PairHybridOverlay::coeff(int narg, char **arg)
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
if (none) {
- setflag[i][j] = 1;
- nmap[i][j] = 0;
- count++;
+ setflag[i][j] = 1;
+ nmap[i][j] = 0;
+ count++;
} else if (styles[m]->setflag[i][j]) {
- int k;
- for (k = 0; k < nmap[i][j]; k++)
- if (map[i][j][k] == m) break;
- if (k == nmap[i][j]) map[i][j][nmap[i][j]++] = m;
- setflag[i][j] = 1;
- count++;
+ int k;
+ for (k = 0; k < nmap[i][j]; k++)
+ if (map[i][j][k] == m) break;
+ if (k == nmap[i][j]) map[i][j][nmap[i][j]++] = m;
+ setflag[i][j] = 1;
+ count++;
}
}
}
@@ -129,9 +129,9 @@ void PairHybridOverlay::modify_requests()
if (!neighbor->requests[j]->pair) continue;
jrq = neighbor->requests[j];
if (irq->same_kind(jrq) && irq->same_skip(jrq)) {
- irq->copy = 1;
- irq->otherlist = j;
- break;
+ irq->copy = 1;
+ irq->otherlist = j;
+ break;
}
}
}
diff --git a/src/pair_hybrid_overlay.h b/src/pair_hybrid_overlay.h
index a3da3254b8c01c75af10f4ace38926ab72b292bf..b79bd97a188804c000992d41aeb08a7b8cb31659 100644
--- a/src/pair_hybrid_overlay.h
+++ b/src/pair_hybrid_overlay.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/pair_lj96_cut.cpp b/src/pair_lj96_cut.cpp
index 0ccc343a4edac8437c9cca80e0df20fc9c6665d7..5fe152ab45f98bc66f1c5f114cd7f100acb0a502 100644
--- a/src/pair_lj96_cut.cpp
+++ b/src/pair_lj96_cut.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -86,7 +86,7 @@ void PairLJ96Cut::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@@ -110,29 +110,29 @@ void PairLJ96Cut::compute(int eflag, int vflag)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
- r3inv = sqrt(r6inv);
- forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
- fpair = factor_lj*forcelj*r2inv;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (eflag) {
- evdwl = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) -
- offset[itype][jtype];
- evdwl *= factor_lj;
- }
-
- if (evflag) ev_tally(i,j,nlocal,newton_pair,
- evdwl,0.0,fpair,delx,dely,delz);
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
+ r3inv = sqrt(r6inv);
+ forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
+ fpair = factor_lj*forcelj*r2inv;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (eflag) {
+ evdwl = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) -
+ offset[itype][jtype];
+ evdwl *= factor_lj;
+ }
+
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ evdwl,0.0,fpair,delx,dely,delz);
}
}
}
@@ -155,7 +155,7 @@ void PairLJ96Cut::compute_inner()
int nlocal = atom->nlocal;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
-
+
inum = listinner->inum;
ilist = listinner->ilist;
numneigh = listinner->numneigh;
@@ -163,11 +163,11 @@ void PairLJ96Cut::compute_inner()
double cut_out_on = cut_respa[0];
double cut_out_off = cut_respa[1];
-
+
double cut_out_diff = cut_out_off - cut_out_on;
double cut_out_on_sq = cut_out_on*cut_out_on;
double cut_out_off_sq = cut_out_off*cut_out_off;
-
+
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@@ -190,25 +190,25 @@ void PairLJ96Cut::compute_inner()
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cut_out_off_sq) {
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
- r3inv = sqrt(r6inv);
- jtype = type[j];
- forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
- fpair = factor_lj*forcelj*r2inv;
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
+ r3inv = sqrt(r6inv);
+ jtype = type[j];
+ forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
+ fpair = factor_lj*forcelj*r2inv;
if (rsq > cut_out_on_sq) {
- rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
- fpair *= 1.0 - rsw*rsw*(3.0 - 2.0*rsw);
- }
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
+ rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
+ fpair *= 1.0 - rsw*rsw*(3.0 - 2.0*rsw);
+ }
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
}
}
}
@@ -269,29 +269,29 @@ void PairLJ96Cut::compute_middle()
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cut_out_off_sq && rsq > cut_in_off_sq) {
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
- r3inv = sqrt(r6inv);
- jtype = type[j];
- forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
- fpair = factor_lj*forcelj*r2inv;
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
+ r3inv = sqrt(r6inv);
+ jtype = type[j];
+ forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
+ fpair = factor_lj*forcelj*r2inv;
if (rsq < cut_in_on_sq) {
- rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff;
- fpair *= rsw*rsw*(3.0 - 2.0*rsw);
- }
+ rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff;
+ fpair *= rsw*rsw*(3.0 - 2.0*rsw);
+ }
if (rsq > cut_out_on_sq) {
- rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
- fpair *= 1.0 + rsw*rsw*(2.0*rsw - 3.0);
- }
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
+ rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
+ fpair *= 1.0 + rsw*rsw*(2.0*rsw - 3.0);
+ }
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
}
}
}
@@ -352,56 +352,56 @@ void PairLJ96Cut::compute_outer(int eflag, int vflag)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- if (rsq > cut_in_off_sq) {
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
- r3inv = sqrt(r6inv);
- forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
- fpair = factor_lj*forcelj*r2inv;
+ if (rsq > cut_in_off_sq) {
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
+ r3inv = sqrt(r6inv);
+ forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
+ fpair = factor_lj*forcelj*r2inv;
if (rsq < cut_in_on_sq) {
- rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff;
- fpair *= rsw*rsw*(3.0 - 2.0*rsw);
- }
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
- }
-
- if (eflag) {
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
- r3inv = sqrt(r6inv);
- evdwl = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) -
- offset[itype][jtype];
- evdwl *= factor_lj;
- }
-
- if (vflag) {
- if (rsq <= cut_in_off_sq) {
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
- r3inv = sqrt(r6inv);
- forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
- fpair = factor_lj*forcelj*r2inv;
- } else if (rsq < cut_in_on_sq)
- fpair = factor_lj*forcelj*r2inv;
- }
-
- if (evflag) ev_tally(i,j,nlocal,newton_pair,
- evdwl,0.0,fpair,delx,dely,delz);
+ rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff;
+ fpair *= rsw*rsw*(3.0 - 2.0*rsw);
+ }
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+ }
+
+ if (eflag) {
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
+ r3inv = sqrt(r6inv);
+ evdwl = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) -
+ offset[itype][jtype];
+ evdwl *= factor_lj;
+ }
+
+ if (vflag) {
+ if (rsq <= cut_in_off_sq) {
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
+ r3inv = sqrt(r6inv);
+ forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
+ fpair = factor_lj*forcelj*r2inv;
+ } else if (rsq < cut_in_on_sq)
+ fpair = factor_lj*forcelj*r2inv;
+ }
+
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ evdwl,0.0,fpair,delx,dely,delz);
}
}
}
}
/* ----------------------------------------------------------------------
- allocate all arrays
+ allocate all arrays
------------------------------------------------------------------------- */
void PairLJ96Cut::allocate()
@@ -427,7 +427,7 @@ void PairLJ96Cut::allocate()
}
/* ----------------------------------------------------------------------
- global settings
+ global settings
------------------------------------------------------------------------- */
void PairLJ96Cut::settings(int narg, char **arg)
@@ -442,7 +442,7 @@ void PairLJ96Cut::settings(int narg, char **arg)
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
- if (setflag[i][j]) cut[i][j] = cut_global;
+ if (setflag[i][j]) cut[i][j] = cut_global;
}
}
@@ -452,7 +452,7 @@ void PairLJ96Cut::settings(int narg, char **arg)
void PairLJ96Cut::coeff(int narg, char **arg)
{
- if (narg < 4 || narg > 5)
+ if (narg < 4 || narg > 5)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
@@ -551,7 +551,7 @@ double PairLJ96Cut::init_one(int i, int j)
{
if (setflag[i][j] == 0) {
epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j],
- sigma[i][i],sigma[j][j]);
+ sigma[i][i],sigma[j][j]);
sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]);
cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
}
@@ -591,23 +591,23 @@ double PairLJ96Cut::init_one(int i, int j)
if (type[k] == j) count[1] += 1.0;
}
MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world);
-
+
double sig3 = sigma[i][j]*sigma[i][j]*sigma[i][j];
double sig6 = sig3*sig3;
double rc3 = cut[i][j]*cut[i][j]*cut[i][j];
double rc6 = rc3*rc3;
-
- etail_ij = 8.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
- sig6 * (sig3 - 2.0*rc3) / (6.0*rc6);
- ptail_ij = 8.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
- sig6 * (3.0*sig3 - 4.0*rc3) / (6.0*rc6);
- }
+
+ etail_ij = 8.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
+ sig6 * (sig3 - 2.0*rc3) / (6.0*rc6);
+ ptail_ij = 8.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
+ sig6 * (3.0*sig3 - 4.0*rc3) / (6.0*rc6);
+ }
return cut[i][j];
}
/* ----------------------------------------------------------------------
- proc 0 writes to restart file
+ proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairLJ96Cut::write_restart(FILE *fp)
@@ -619,9 +619,9 @@ void PairLJ96Cut::write_restart(FILE *fp)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
- fwrite(&epsilon[i][j],sizeof(double),1,fp);
- fwrite(&sigma[i][j],sizeof(double),1,fp);
- fwrite(&cut[i][j],sizeof(double),1,fp);
+ fwrite(&epsilon[i][j],sizeof(double),1,fp);
+ fwrite(&sigma[i][j],sizeof(double),1,fp);
+ fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
@@ -642,14 +642,14 @@ void PairLJ96Cut::read_restart(FILE *fp)
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
- if (me == 0) {
- fread(&epsilon[i][j],sizeof(double),1,fp);
- fread(&sigma[i][j],sizeof(double),1,fp);
- fread(&cut[i][j],sizeof(double),1,fp);
- }
- MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
+ if (me == 0) {
+ fread(&epsilon[i][j],sizeof(double),1,fp);
+ fread(&sigma[i][j],sizeof(double),1,fp);
+ fread(&cut[i][j],sizeof(double),1,fp);
+ }
+ MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
@@ -685,8 +685,8 @@ void PairLJ96Cut::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairLJ96Cut::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
- double &fforce)
+ double factor_coul, double factor_lj,
+ double &fforce)
{
double r2inv,r3inv,r6inv,forcelj,philj;
diff --git a/src/pair_lj96_cut.h b/src/pair_lj96_cut.h
index 4d2f619477f50368ce673875ce3c1137261712bd..56430cc5d73b2cdefd073b32eca8ce174f2e1dfe 100644
--- a/src/pair_lj96_cut.h
+++ b/src/pair_lj96_cut.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/pair_lj_cubic.cpp b/src/pair_lj_cubic.cpp
index df06f7deda78470b9abc935d8df95968ea1d4298..2fd224239dacc7c5adfdfba67f9c40d64ff82486 100644
--- a/src/pair_lj_cubic.cpp
+++ b/src/pair_lj_cubic.cpp
@@ -6,7 +6,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -81,7 +81,7 @@ void PairLJCubic::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@@ -105,38 +105,38 @@ void PairLJCubic::compute(int eflag, int vflag)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
+ r2inv = 1.0/rsq;
if (rsq <= cut_inner_sq[itype][jtype]) {
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- } else {
- r = sqrt(rsq);
- rmin = sigma[itype][jtype]*RT6TWO;
- t = (r - cut_inner[itype][jtype])/rmin;
- forcelj = epsilon[itype][jtype]*(-DPHIDS + A3*t*t/2.0)*r/rmin;
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ } else {
+ r = sqrt(rsq);
+ rmin = sigma[itype][jtype]*RT6TWO;
+ t = (r - cut_inner[itype][jtype])/rmin;
+ forcelj = epsilon[itype][jtype]*(-DPHIDS + A3*t*t/2.0)*r/rmin;
+ }
+ fpair = factor_lj*forcelj*r2inv;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
}
- fpair = factor_lj*forcelj*r2inv;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (eflag) {
+
+ if (eflag) {
if (rsq <= cut_inner_sq[itype][jtype])
- evdwl = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
- else
- evdwl = epsilon[itype][jtype]*
- (PHIS + DPHIDS*t - A3*t*t*t/6.0);
- evdwl *= factor_lj;
-
- if (evflag) ev_tally(i,j,nlocal,newton_pair,
- evdwl,0.0,fpair,delx,dely,delz);
- }
+ evdwl = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
+ else
+ evdwl = epsilon[itype][jtype]*
+ (PHIS + DPHIDS*t - A3*t*t*t/6.0);
+ evdwl *= factor_lj;
+
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ evdwl,0.0,fpair,delx,dely,delz);
+ }
}
}
}
@@ -185,7 +185,7 @@ void PairLJCubic::settings(int narg, char **arg)
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
- if (setflag[i][j]) cut[i][j] = 0.0;
+ if (setflag[i][j]) cut[i][j] = 0.0;
}
}
@@ -230,7 +230,7 @@ double PairLJCubic::init_one(int i, int j)
{
if (setflag[i][j] == 0) {
epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j],
- sigma[i][i],sigma[j][j]);
+ sigma[i][i],sigma[j][j]);
sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]);
cut_inner[i][j] = mix_distance(cut_inner[i][i],cut_inner[j][j]);
cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
@@ -265,10 +265,10 @@ void PairLJCubic::write_restart(FILE *fp)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
- fwrite(&epsilon[i][j],sizeof(double),1,fp);
- fwrite(&sigma[i][j],sizeof(double),1,fp);
- fwrite(&cut_inner[i][j],sizeof(double),1,fp);
- fwrite(&cut[i][j],sizeof(double),1,fp);
+ fwrite(&epsilon[i][j],sizeof(double),1,fp);
+ fwrite(&sigma[i][j],sizeof(double),1,fp);
+ fwrite(&cut_inner[i][j],sizeof(double),1,fp);
+ fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
@@ -289,16 +289,16 @@ void PairLJCubic::read_restart(FILE *fp)
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
- if (me == 0) {
- fread(&epsilon[i][j],sizeof(double),1,fp);
- fread(&sigma[i][j],sizeof(double),1,fp);
- fread(&cut_inner[i][j],sizeof(double),1,fp);
- fread(&cut[i][j],sizeof(double),1,fp);
- }
- MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&cut_inner[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
+ if (me == 0) {
+ fread(&epsilon[i][j],sizeof(double),1,fp);
+ fread(&sigma[i][j],sizeof(double),1,fp);
+ fread(&cut_inner[i][j],sizeof(double),1,fp);
+ fread(&cut[i][j],sizeof(double),1,fp);
+ }
+ MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut_inner[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
@@ -328,9 +328,9 @@ void PairLJCubic::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairLJCubic::single(int i, int j, int itype, int jtype,
- double rsq,
- double factor_coul, double factor_lj,
- double &fforce)
+ double rsq,
+ double factor_coul, double factor_lj,
+ double &fforce)
{
double r2inv,r6inv,forcelj,philj;
double r,t;
@@ -341,7 +341,7 @@ double PairLJCubic::single(int i, int j, int itype, int jtype,
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
} else {
- r = sqrt(rsq);
+ r = sqrt(rsq);
rmin = sigma[itype][jtype]*RT6TWO;
t = (r - cut_inner[itype][jtype])/rmin;
forcelj = epsilon[itype][jtype]*(-DPHIDS + A3*t*t/2.0)*r/rmin;
diff --git a/src/pair_lj_cubic.h b/src/pair_lj_cubic.h
index 0b90f25ff5749eede2f6700ecbd2fa993fd039f0..cdb311c41b91e0ed09be80a6a1379658c0ed2ead 100644
--- a/src/pair_lj_cubic.h
+++ b/src/pair_lj_cubic.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -50,14 +50,14 @@ class PairLJCubic : public Pair {
namespace PairLJCubicConstants {
// LJ quantities scaled by epsilon and rmin = sigma*2^1/6
-
+
static const double RT6TWO = 1.1224621; // 2^1/6
static const double SS = 1.1086834; // inflection point (13/7)^1/6
static const double PHIS = -0.7869823; // energy at s
static const double DPHIDS = 2.6899009; // gradient at s
static const double A3 = 27.93357; // cubic coefficient
static const double SM = 1.5475375; // cubic cutoff = s*67/48
-
+
}
}
diff --git a/src/pair_lj_cut.cpp b/src/pair_lj_cut.cpp
index 69add0d110f2194260b9659b1a514df96ed0eac6..29d0531ca797e14ec48da960d4610acd2f94f282 100644
--- a/src/pair_lj_cut.cpp
+++ b/src/pair_lj_cut.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -86,7 +86,7 @@ void PairLJCut::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@@ -110,28 +110,28 @@ void PairLJCut::compute(int eflag, int vflag)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- fpair = factor_lj*forcelj*r2inv;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (eflag) {
- evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
- offset[itype][jtype];
- evdwl *= factor_lj;
- }
-
- if (evflag) ev_tally(i,j,nlocal,newton_pair,
- evdwl,0.0,fpair,delx,dely,delz);
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ fpair = factor_lj*forcelj*r2inv;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (eflag) {
+ evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
+ offset[itype][jtype];
+ evdwl *= factor_lj;
+ }
+
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ evdwl,0.0,fpair,delx,dely,delz);
}
}
}
@@ -154,7 +154,7 @@ void PairLJCut::compute_inner()
int nlocal = atom->nlocal;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
-
+
inum = listinner->inum;
ilist = listinner->ilist;
numneigh = listinner->numneigh;
@@ -162,11 +162,11 @@ void PairLJCut::compute_inner()
double cut_out_on = cut_respa[0];
double cut_out_off = cut_respa[1];
-
+
double cut_out_diff = cut_out_off - cut_out_on;
double cut_out_on_sq = cut_out_on*cut_out_on;
double cut_out_off_sq = cut_out_off*cut_out_off;
-
+
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@@ -189,24 +189,24 @@ void PairLJCut::compute_inner()
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cut_out_off_sq) {
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
- jtype = type[j];
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- fpair = factor_lj*forcelj*r2inv;
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
+ jtype = type[j];
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ fpair = factor_lj*forcelj*r2inv;
if (rsq > cut_out_on_sq) {
- rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
- fpair *= 1.0 - rsw*rsw*(3.0 - 2.0*rsw);
- }
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
+ rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
+ fpair *= 1.0 - rsw*rsw*(3.0 - 2.0*rsw);
+ }
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
}
}
}
@@ -267,28 +267,28 @@ void PairLJCut::compute_middle()
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cut_out_off_sq && rsq > cut_in_off_sq) {
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
- jtype = type[j];
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- fpair = factor_lj*forcelj*r2inv;
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
+ jtype = type[j];
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ fpair = factor_lj*forcelj*r2inv;
if (rsq < cut_in_on_sq) {
- rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff;
- fpair *= rsw*rsw*(3.0 - 2.0*rsw);
- }
+ rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff;
+ fpair *= rsw*rsw*(3.0 - 2.0*rsw);
+ }
if (rsq > cut_out_on_sq) {
- rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
- fpair *= 1.0 + rsw*rsw*(2.0*rsw - 3.0);
- }
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
+ rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
+ fpair *= 1.0 + rsw*rsw*(2.0*rsw - 3.0);
+ }
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
}
}
}
@@ -349,53 +349,53 @@ void PairLJCut::compute_outer(int eflag, int vflag)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- if (rsq > cut_in_off_sq) {
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- fpair = factor_lj*forcelj*r2inv;
+ if (rsq > cut_in_off_sq) {
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ fpair = factor_lj*forcelj*r2inv;
if (rsq < cut_in_on_sq) {
- rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff;
- fpair *= rsw*rsw*(3.0 - 2.0*rsw);
- }
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
- }
-
- if (eflag) {
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
- evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
- offset[itype][jtype];
- evdwl *= factor_lj;
- }
-
- if (vflag) {
- if (rsq <= cut_in_off_sq) {
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- fpair = factor_lj*forcelj*r2inv;
- } else if (rsq < cut_in_on_sq)
- fpair = factor_lj*forcelj*r2inv;
- }
-
- if (evflag) ev_tally(i,j,nlocal,newton_pair,
- evdwl,0.0,fpair,delx,dely,delz);
+ rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff;
+ fpair *= rsw*rsw*(3.0 - 2.0*rsw);
+ }
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+ }
+
+ if (eflag) {
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
+ evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
+ offset[itype][jtype];
+ evdwl *= factor_lj;
+ }
+
+ if (vflag) {
+ if (rsq <= cut_in_off_sq) {
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ fpair = factor_lj*forcelj*r2inv;
+ } else if (rsq < cut_in_on_sq)
+ fpair = factor_lj*forcelj*r2inv;
+ }
+
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ evdwl,0.0,fpair,delx,dely,delz);
}
}
}
}
/* ----------------------------------------------------------------------
- allocate all arrays
+ allocate all arrays
------------------------------------------------------------------------- */
void PairLJCut::allocate()
@@ -421,7 +421,7 @@ void PairLJCut::allocate()
}
/* ----------------------------------------------------------------------
- global settings
+ global settings
------------------------------------------------------------------------- */
void PairLJCut::settings(int narg, char **arg)
@@ -431,12 +431,12 @@ void PairLJCut::settings(int narg, char **arg)
cut_global = force->numeric(arg[0]);
// reset cutoffs that have been explicitly set
-
+
if (allocated) {
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
- if (setflag[i][j]) cut[i][j] = cut_global;
+ if (setflag[i][j]) cut[i][j] = cut_global;
}
}
@@ -446,7 +446,7 @@ void PairLJCut::settings(int narg, char **arg)
void PairLJCut::coeff(int narg, char **arg)
{
- if (narg < 4 || narg > 5)
+ if (narg < 4 || narg > 5)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
@@ -545,7 +545,7 @@ double PairLJCut::init_one(int i, int j)
{
if (setflag[i][j] == 0) {
epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j],
- sigma[i][i],sigma[j][j]);
+ sigma[i][i],sigma[j][j]);
sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]);
cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
}
@@ -585,23 +585,23 @@ double PairLJCut::init_one(int i, int j)
if (type[k] == j) count[1] += 1.0;
}
MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world);
-
+
double sig2 = sigma[i][j]*sigma[i][j];
double sig6 = sig2*sig2*sig2;
double rc3 = cut[i][j]*cut[i][j]*cut[i][j];
double rc6 = rc3*rc3;
double rc9 = rc3*rc6;
- etail_ij = 8.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
- sig6 * (sig6 - 3.0*rc6) / (9.0*rc9);
- ptail_ij = 16.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
- sig6 * (2.0*sig6 - 3.0*rc6) / (9.0*rc9);
- }
+ etail_ij = 8.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
+ sig6 * (sig6 - 3.0*rc6) / (9.0*rc9);
+ ptail_ij = 16.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
+ sig6 * (2.0*sig6 - 3.0*rc6) / (9.0*rc9);
+ }
return cut[i][j];
}
/* ----------------------------------------------------------------------
- proc 0 writes to restart file
+ proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairLJCut::write_restart(FILE *fp)
@@ -613,9 +613,9 @@ void PairLJCut::write_restart(FILE *fp)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
- fwrite(&epsilon[i][j],sizeof(double),1,fp);
- fwrite(&sigma[i][j],sizeof(double),1,fp);
- fwrite(&cut[i][j],sizeof(double),1,fp);
+ fwrite(&epsilon[i][j],sizeof(double),1,fp);
+ fwrite(&sigma[i][j],sizeof(double),1,fp);
+ fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
@@ -636,14 +636,14 @@ void PairLJCut::read_restart(FILE *fp)
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
- if (me == 0) {
- fread(&epsilon[i][j],sizeof(double),1,fp);
- fread(&sigma[i][j],sizeof(double),1,fp);
- fread(&cut[i][j],sizeof(double),1,fp);
- }
- MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
+ if (me == 0) {
+ fread(&epsilon[i][j],sizeof(double),1,fp);
+ fread(&sigma[i][j],sizeof(double),1,fp);
+ fread(&cut[i][j],sizeof(double),1,fp);
+ }
+ MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
@@ -679,8 +679,8 @@ void PairLJCut::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairLJCut::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
- double &fforce)
+ double factor_coul, double factor_lj,
+ double &fforce)
{
double r2inv,r6inv,forcelj,philj;
diff --git a/src/pair_lj_cut.h b/src/pair_lj_cut.h
index 8eb4a4867ec207a4fc6e61e232dea5e1d22bb8cd..97a121296513aa0731280fc64d5137db7d093e44 100644
--- a/src/pair_lj_cut.h
+++ b/src/pair_lj_cut.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/pair_lj_cut_coul_cut.cpp b/src/pair_lj_cut_coul_cut.cpp
index c6973b258029c4b3f19f3d23ade932456b481139..50ee7dc99fbb790743a9158098505bfd971e42bb 100644
--- a/src/pair_lj_cut_coul_cut.cpp
+++ b/src/pair_lj_cut_coul_cut.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -81,7 +81,7 @@ void PairLJCutCoulCut::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@@ -107,41 +107,41 @@ void PairLJCutCoulCut::compute(int eflag, int vflag)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
-
- if (rsq < cut_coulsq[itype][jtype])
- forcecoul = qqrd2e * qtmp*q[j]*sqrt(r2inv);
- else forcecoul = 0.0;
-
- if (rsq < cut_ljsq[itype][jtype]) {
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- } else forcelj = 0.0;
-
- fpair = (factor_coul*forcecoul + factor_lj*forcelj) * r2inv;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (eflag) {
- if (rsq < cut_coulsq[itype][jtype])
- ecoul = factor_coul * qqrd2e * qtmp*q[j]*sqrt(r2inv);
- else ecoul = 0.0;
- if (rsq < cut_ljsq[itype][jtype]) {
- evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
- offset[itype][jtype];
- evdwl *= factor_lj;
- } else evdwl = 0.0;
- }
-
- if (evflag) ev_tally(i,j,nlocal,newton_pair,
- evdwl,ecoul,fpair,delx,dely,delz);
+ r2inv = 1.0/rsq;
+
+ if (rsq < cut_coulsq[itype][jtype])
+ forcecoul = qqrd2e * qtmp*q[j]*sqrt(r2inv);
+ else forcecoul = 0.0;
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ } else forcelj = 0.0;
+
+ fpair = (factor_coul*forcecoul + factor_lj*forcelj) * r2inv;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (eflag) {
+ if (rsq < cut_coulsq[itype][jtype])
+ ecoul = factor_coul * qqrd2e * qtmp*q[j]*sqrt(r2inv);
+ else ecoul = 0.0;
+ if (rsq < cut_ljsq[itype][jtype]) {
+ evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
+ offset[itype][jtype];
+ evdwl *= factor_lj;
+ } else evdwl = 0.0;
+ }
+
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
@@ -196,10 +196,10 @@ void PairLJCutCoulCut::settings(int narg, char **arg)
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
- if (setflag[i][j]) {
- cut_lj[i][j] = cut_lj_global;
- cut_coul[i][j] = cut_coul_global;
- }
+ if (setflag[i][j]) {
+ cut_lj[i][j] = cut_lj_global;
+ cut_coul[i][j] = cut_coul_global;
+ }
}
}
@@ -259,7 +259,7 @@ double PairLJCutCoulCut::init_one(int i, int j)
{
if (setflag[i][j] == 0) {
epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j],
- sigma[i][i],sigma[j][j]);
+ sigma[i][i],sigma[j][j]);
sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]);
cut_lj[i][j] = mix_distance(cut_lj[i][i],cut_lj[j][j]);
cut_coul[i][j] = mix_distance(cut_coul[i][i],cut_coul[j][j]);
@@ -273,12 +273,12 @@ double PairLJCutCoulCut::init_one(int i, int j)
lj2[i][j] = 24.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
-
+
if (offset_flag) {
double ratio = sigma[i][j] / cut_lj[i][j];
offset[i][j] = 4.0 * epsilon[i][j] * (pow(ratio,12.0) - pow(ratio,6.0));
} else offset[i][j] = 0.0;
-
+
cut_ljsq[j][i] = cut_ljsq[i][j];
cut_coulsq[j][i] = cut_coulsq[i][j];
lj1[j][i] = lj1[i][j];
@@ -301,17 +301,17 @@ double PairLJCutCoulCut::init_one(int i, int j)
if (type[k] == j) count[1] += 1.0;
}
MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world);
-
+
double sig2 = sigma[i][j]*sigma[i][j];
double sig6 = sig2*sig2*sig2;
double rc3 = cut_lj[i][j]*cut_lj[i][j]*cut_lj[i][j];
double rc6 = rc3*rc3;
double rc9 = rc3*rc6;
- etail_ij = 8.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
- sig6 * (sig6 - 3.0*rc6) / (9.0*rc9);
- ptail_ij = 16.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
- sig6 * (2.0*sig6 - 3.0*rc6) / (9.0*rc9);
- }
+ etail_ij = 8.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
+ sig6 * (sig6 - 3.0*rc6) / (9.0*rc9);
+ ptail_ij = 16.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
+ sig6 * (2.0*sig6 - 3.0*rc6) / (9.0*rc9);
+ }
return cut;
}
@@ -329,10 +329,10 @@ void PairLJCutCoulCut::write_restart(FILE *fp)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
- fwrite(&epsilon[i][j],sizeof(double),1,fp);
- fwrite(&sigma[i][j],sizeof(double),1,fp);
- fwrite(&cut_lj[i][j],sizeof(double),1,fp);
- fwrite(&cut_coul[i][j],sizeof(double),1,fp);
+ fwrite(&epsilon[i][j],sizeof(double),1,fp);
+ fwrite(&sigma[i][j],sizeof(double),1,fp);
+ fwrite(&cut_lj[i][j],sizeof(double),1,fp);
+ fwrite(&cut_coul[i][j],sizeof(double),1,fp);
}
}
}
@@ -353,16 +353,16 @@ void PairLJCutCoulCut::read_restart(FILE *fp)
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
- if (me == 0) {
- fread(&epsilon[i][j],sizeof(double),1,fp);
- fread(&sigma[i][j],sizeof(double),1,fp);
- fread(&cut_lj[i][j],sizeof(double),1,fp);
- fread(&cut_coul[i][j],sizeof(double),1,fp);
- }
- MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&cut_coul[i][j],1,MPI_DOUBLE,0,world);
+ if (me == 0) {
+ fread(&epsilon[i][j],sizeof(double),1,fp);
+ fread(&sigma[i][j],sizeof(double),1,fp);
+ fread(&cut_lj[i][j],sizeof(double),1,fp);
+ fread(&cut_coul[i][j],sizeof(double),1,fp);
+ }
+ MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut_coul[i][j],1,MPI_DOUBLE,0,world);
}
}
}
@@ -400,9 +400,9 @@ void PairLJCutCoulCut::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairLJCutCoulCut::single(int i, int j, int itype, int jtype,
- double rsq,
- double factor_coul, double factor_lj,
- double &fforce)
+ double rsq,
+ double factor_coul, double factor_lj,
+ double &fforce)
{
double r2inv,r6inv,forcecoul,forcelj,phicoul,philj;
diff --git a/src/pair_lj_cut_coul_cut.h b/src/pair_lj_cut_coul_cut.h
index 3746df9f91927bc8b9b559de3c6e3a84954ca212..28f4664df5176812c86b99b5b6079c927ff3c1a7 100644
--- a/src/pair_lj_cut_coul_cut.h
+++ b/src/pair_lj_cut_coul_cut.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/pair_lj_cut_coul_debye.cpp b/src/pair_lj_cut_coul_debye.cpp
index 023d86654273b8f24e37b4ef017c50ca7084a7ab..7a892ad7f73917eed194ef4a235f21f46be426e3 100644
--- a/src/pair_lj_cut_coul_debye.cpp
+++ b/src/pair_lj_cut_coul_debye.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -54,7 +54,7 @@ void PairLJCutCoulDebye::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@@ -80,44 +80,44 @@ void PairLJCutCoulDebye::compute(int eflag, int vflag)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
-
- if (rsq < cut_coulsq[itype][jtype]) {
- r = sqrt(rsq);
- rinv = 1.0/r;
- screening = exp(-kappa*r);
- forcecoul = qqrd2e * qtmp*q[j] * screening * (kappa + rinv);
- } else forcecoul = 0.0;
-
- if (rsq < cut_ljsq[itype][jtype]) {
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- } else forcelj = 0.0;
-
- fpair = (factor_coul*forcecoul + factor_lj*forcelj) * r2inv;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (eflag) {
- if (rsq < cut_coulsq[itype][jtype])
- ecoul = factor_coul * qqrd2e * qtmp*q[j] * rinv * screening;
- else ecoul = 0.0;
- if (rsq < cut_ljsq[itype][jtype]) {
- evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
- offset[itype][jtype];
- evdwl *= factor_lj;
- } else evdwl = 0.0;
- }
-
- if (evflag) ev_tally(i,j,nlocal,newton_pair,
- evdwl,ecoul,fpair,delx,dely,delz);
+ r2inv = 1.0/rsq;
+
+ if (rsq < cut_coulsq[itype][jtype]) {
+ r = sqrt(rsq);
+ rinv = 1.0/r;
+ screening = exp(-kappa*r);
+ forcecoul = qqrd2e * qtmp*q[j] * screening * (kappa + rinv);
+ } else forcecoul = 0.0;
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ } else forcelj = 0.0;
+
+ fpair = (factor_coul*forcecoul + factor_lj*forcelj) * r2inv;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (eflag) {
+ if (rsq < cut_coulsq[itype][jtype])
+ ecoul = factor_coul * qqrd2e * qtmp*q[j] * rinv * screening;
+ else ecoul = 0.0;
+ if (rsq < cut_ljsq[itype][jtype]) {
+ evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
+ offset[itype][jtype];
+ evdwl *= factor_lj;
+ } else evdwl = 0.0;
+ }
+
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
@@ -126,7 +126,7 @@ void PairLJCutCoulDebye::compute(int eflag, int vflag)
}
/* ----------------------------------------------------------------------
- global settings
+ global settings
------------------------------------------------------------------------- */
void PairLJCutCoulDebye::settings(int narg, char **arg)
@@ -144,10 +144,10 @@ void PairLJCutCoulDebye::settings(int narg, char **arg)
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
- if (setflag[i][j] == 1) {
- cut_lj[i][j] = cut_lj_global;
- cut_coul[i][j] = cut_coul_global;
- }
+ if (setflag[i][j] == 1) {
+ cut_lj[i][j] = cut_lj_global;
+ cut_coul[i][j] = cut_coul_global;
+ }
}
}
@@ -187,9 +187,9 @@ void PairLJCutCoulDebye::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairLJCutCoulDebye::single(int i, int j, int itype, int jtype,
- double rsq,
- double factor_coul, double factor_lj,
- double &fforce)
+ double rsq,
+ double factor_coul, double factor_lj,
+ double &fforce)
{
double r2inv,r6inv,r,rinv,screening,forcecoul,forcelj,phicoul,philj;
diff --git a/src/pair_lj_cut_coul_debye.h b/src/pair_lj_cut_coul_debye.h
index 073c1b5b02d451179a80e90e288de5fead3ba63a..4dd41080c798f75bc0064144d93834a141a0bde0 100644
--- a/src/pair_lj_cut_coul_debye.h
+++ b/src/pair_lj_cut_coul_debye.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/pair_lj_expand.cpp b/src/pair_lj_expand.cpp
index 10e69ba9779b960200b5663ceef5ec49ec9dbe6a..0cb2598cd2ec59f5b2caa63a4222149f336b4563 100644
--- a/src/pair_lj_expand.cpp
+++ b/src/pair_lj_expand.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -75,7 +75,7 @@ void PairLJExpand::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@@ -99,31 +99,31 @@ void PairLJExpand::compute(int eflag, int vflag)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r = sqrt(rsq);
- rshift = r - shift[itype][jtype];
- rshiftsq = rshift*rshift;
- r2inv = 1.0/rshiftsq;
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- fpair = factor_lj*forcelj/rshift/r;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (eflag) {
- evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
- offset[itype][jtype];
- evdwl *= factor_lj;
- }
-
- if (evflag) ev_tally(i,j,nlocal,newton_pair,
- evdwl,0.0,fpair,delx,dely,delz);
+ r = sqrt(rsq);
+ rshift = r - shift[itype][jtype];
+ rshiftsq = rshift*rshift;
+ r2inv = 1.0/rshiftsq;
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ fpair = factor_lj*forcelj/rshift/r;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (eflag) {
+ evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
+ offset[itype][jtype];
+ evdwl *= factor_lj;
+ }
+
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ evdwl,0.0,fpair,delx,dely,delz);
}
}
}
@@ -132,7 +132,7 @@ void PairLJExpand::compute(int eflag, int vflag)
}
/* ----------------------------------------------------------------------
- allocate all arrays
+ allocate all arrays
------------------------------------------------------------------------- */
void PairLJExpand::allocate()
@@ -159,7 +159,7 @@ void PairLJExpand::allocate()
}
/* ----------------------------------------------------------------------
- global settings
+ global settings
------------------------------------------------------------------------- */
void PairLJExpand::settings(int narg, char **arg)
@@ -174,7 +174,7 @@ void PairLJExpand::settings(int narg, char **arg)
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
- if (setflag[i][j]) cut[i][j] = cut_global;
+ if (setflag[i][j]) cut[i][j] = cut_global;
}
}
@@ -223,7 +223,7 @@ double PairLJExpand::init_one(int i, int j)
if (setflag[i][j] == 0) {
epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j],
- sigma[i][i],sigma[j][j]);
+ sigma[i][i],sigma[j][j]);
sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]);
cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
shift[i][j] = 0.5 * (shift[i][i] + shift[j][j]);
@@ -233,7 +233,7 @@ double PairLJExpand::init_one(int i, int j)
lj2[i][j] = 24.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
-
+
if (offset_flag) {
double ratio = sigma[i][j] / cut[i][j];
offset[i][j] = 4.0 * epsilon[i][j] * (pow(ratio,12.0) - pow(ratio,6.0));
@@ -274,16 +274,16 @@ double PairLJExpand::init_one(int i, int j)
double rc12 = rc11*shiftcut;
double shift2 = shift[i][j]*shift[i][j];
double shift3 = shift2*shift[i][j];
- etail_ij = 8.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
+ etail_ij = 8.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
sig6*((-1.0/(9.0*rc9) + shift[i][j]/(5.0*rc10) -
- shift2/(11.0*rc11))*sig6 +
- 1.0/(3.0*rc3) - shift[i][j]/(2.0*rc4) + shift2/(5.0*rc5));
- ptail_ij = 8.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
+ shift2/(11.0*rc11))*sig6 +
+ 1.0/(3.0*rc3) - shift[i][j]/(2.0*rc4) + shift2/(5.0*rc5));
+ ptail_ij = 8.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
sig6* ((-4.0/(3.0*rc9) + 18.0*shift[i][j]/(5.0*rc10) -
- 36.0*shift2/(11.0*rc11) + shift3/rc12)*sig6 +
- 2.0/rc3 - 9.0*shift[i][j]/(2.0*rc4) +
- 18.0*shift2/(5.0*rc5) - shift3/rc6)/3.0;
- }
+ 36.0*shift2/(11.0*rc11) + shift3/rc12)*sig6 +
+ 2.0/rc3 - 9.0*shift[i][j]/(2.0*rc4) +
+ 18.0*shift2/(5.0*rc5) - shift3/rc6)/3.0;
+ }
return cut[i][j] + shift[i][j];
}
@@ -301,10 +301,10 @@ void PairLJExpand::write_restart(FILE *fp)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
- fwrite(&epsilon[i][j],sizeof(double),1,fp);
- fwrite(&sigma[i][j],sizeof(double),1,fp);
- fwrite(&shift[i][j],sizeof(double),1,fp);
- fwrite(&cut[i][j],sizeof(double),1,fp);
+ fwrite(&epsilon[i][j],sizeof(double),1,fp);
+ fwrite(&sigma[i][j],sizeof(double),1,fp);
+ fwrite(&shift[i][j],sizeof(double),1,fp);
+ fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
@@ -326,16 +326,16 @@ void PairLJExpand::read_restart(FILE *fp)
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
- if (me == 0) {
- fread(&epsilon[i][j],sizeof(double),1,fp);
- fread(&sigma[i][j],sizeof(double),1,fp);
- fread(&shift[i][j],sizeof(double),1,fp);
- fread(&cut[i][j],sizeof(double),1,fp);
- }
- MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&shift[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
+ if (me == 0) {
+ fread(&epsilon[i][j],sizeof(double),1,fp);
+ fread(&sigma[i][j],sizeof(double),1,fp);
+ fread(&shift[i][j],sizeof(double),1,fp);
+ fread(&cut[i][j],sizeof(double),1,fp);
+ }
+ MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&shift[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
@@ -370,8 +370,8 @@ void PairLJExpand::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairLJExpand::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
- double &fforce)
+ double factor_coul, double factor_lj,
+ double &fforce)
{
double r,rshift,rshiftsq,r2inv,r6inv,forcelj,philj;
diff --git a/src/pair_lj_expand.h b/src/pair_lj_expand.h
index a0babd99dcf168249738df63355a194c311dd931..f132857e7e24923a5fd3d0a537b45006e6f42374 100644
--- a/src/pair_lj_expand.h
+++ b/src/pair_lj_expand.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/pair_lj_gromacs.cpp b/src/pair_lj_gromacs.cpp
index 5b43ff2acce5f81e201fabfc5aca68fc60ecc2ff..f62e2e879aaafb7b9c2a2dd5ab1b52e0130df6a8 100644
--- a/src/pair_lj_gromacs.cpp
+++ b/src/pair_lj_gromacs.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -84,7 +84,7 @@ void PairLJGromacs::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@@ -108,39 +108,39 @@ void PairLJGromacs::compute(int eflag, int vflag)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
if (rsq > cut_inner_sq[itype][jtype]) {
- r = sqrt(rsq);
- t = r - cut_inner[itype][jtype];
- fswitch = r*t*t*(ljsw1[itype][jtype] + ljsw2[itype][jtype]*t);
- forcelj += fswitch;
+ r = sqrt(rsq);
+ t = r - cut_inner[itype][jtype];
+ fswitch = r*t*t*(ljsw1[itype][jtype] + ljsw2[itype][jtype]*t);
+ forcelj += fswitch;
}
- fpair = factor_lj*forcelj*r2inv;
+ fpair = factor_lj*forcelj*r2inv;
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
- if (eflag) {
- evdwl = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
- evdwl += ljsw5[itype][jtype];
+ if (eflag) {
+ evdwl = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
+ evdwl += ljsw5[itype][jtype];
if (rsq > cut_inner_sq[itype][jtype]) {
eswitch = t*t*t*(ljsw3[itype][jtype] + ljsw4[itype][jtype]*t);
evdwl += eswitch;
}
- evdwl *= factor_lj;
- }
+ evdwl *= factor_lj;
+ }
- if (evflag) ev_tally(i,j,nlocal,newton_pair,
- evdwl,0.0,fpair,delx,dely,delz);
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ evdwl,0.0,fpair,delx,dely,delz);
}
}
}
@@ -200,10 +200,10 @@ void PairLJGromacs::settings(int narg, char **arg)
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
- if (setflag[i][j]) {
- cut_inner[i][j] = cut_inner_global;
- cut[i][j] = cut_global;
- }
+ if (setflag[i][j]) {
+ cut_inner[i][j] = cut_inner_global;
+ cut[i][j] = cut_global;
+ }
}
}
@@ -257,7 +257,7 @@ double PairLJGromacs::init_one(int i, int j)
{
if (setflag[i][j] == 0) {
epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j],
- sigma[i][i],sigma[j][j]);
+ sigma[i][i],sigma[j][j]);
sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]);
cut_inner[i][j] = mix_distance(cut_inner[i][i],cut_inner[j][j]);
cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
@@ -316,10 +316,10 @@ void PairLJGromacs::write_restart(FILE *fp)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
- fwrite(&epsilon[i][j],sizeof(double),1,fp);
- fwrite(&sigma[i][j],sizeof(double),1,fp);
- fwrite(&cut_inner[i][j],sizeof(double),1,fp);
- fwrite(&cut[i][j],sizeof(double),1,fp);
+ fwrite(&epsilon[i][j],sizeof(double),1,fp);
+ fwrite(&sigma[i][j],sizeof(double),1,fp);
+ fwrite(&cut_inner[i][j],sizeof(double),1,fp);
+ fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
@@ -340,16 +340,16 @@ void PairLJGromacs::read_restart(FILE *fp)
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
- if (me == 0) {
- fread(&epsilon[i][j],sizeof(double),1,fp);
- fread(&sigma[i][j],sizeof(double),1,fp);
- fread(&cut_inner[i][j],sizeof(double),1,fp);
- fread(&cut[i][j],sizeof(double),1,fp);
- }
- MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&cut_inner[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
+ if (me == 0) {
+ fread(&epsilon[i][j],sizeof(double),1,fp);
+ fread(&sigma[i][j],sizeof(double),1,fp);
+ fread(&cut_inner[i][j],sizeof(double),1,fp);
+ fread(&cut[i][j],sizeof(double),1,fp);
+ }
+ MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut_inner[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
@@ -388,9 +388,9 @@ void PairLJGromacs::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairLJGromacs::single(int i, int j, int itype, int jtype,
- double rsq,
- double factor_coul, double factor_lj,
- double &fforce)
+ double rsq,
+ double factor_coul, double factor_lj,
+ double &fforce)
{
double r2inv,r6inv,forcelj,philj;
double r,t,fswitch,phiswitch;
@@ -399,7 +399,7 @@ double PairLJGromacs::single(int i, int j, int itype, int jtype,
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
if (rsq > cut_inner_sq[itype][jtype]) {
- r = sqrt(rsq);
+ r = sqrt(rsq);
t = r - cut_inner[itype][jtype];
fswitch = r*t*t*(ljsw1[itype][jtype] + ljsw2[itype][jtype]*t);
forcelj += fswitch;
diff --git a/src/pair_lj_gromacs.h b/src/pair_lj_gromacs.h
index 3e61d7645095a5f25a74f518312698d37cef1aa3..9e3e55de7a877ea59aa9020f41d45865466adf25 100644
--- a/src/pair_lj_gromacs.h
+++ b/src/pair_lj_gromacs.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/pair_lj_gromacs_coul_gromacs.cpp b/src/pair_lj_gromacs_coul_gromacs.cpp
index af681aeab0210ba96e279b8ba9aacad558df5161..7f973708e3e13f2dd24d76228b8cdc29785bbeef 100644
--- a/src/pair_lj_gromacs_coul_gromacs.cpp
+++ b/src/pair_lj_gromacs_coul_gromacs.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -84,7 +84,7 @@ void PairLJGromacsCoulGromacs::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@@ -109,68 +109,68 @@ void PairLJGromacsCoulGromacs::compute(int eflag, int vflag)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cut_bothsq) {
- r2inv = 1.0/rsq;
+ r2inv = 1.0/rsq;
- // skip if qi or qj = 0.0 since this potential may be used as
- // coarse-grain model with many uncharged atoms
+ // skip if qi or qj = 0.0 since this potential may be used as
+ // coarse-grain model with many uncharged atoms
- if (rsq < cut_coulsq && qtmp != 0.0 && q[j] != 0.0) {
- forcecoul = qqrd2e * qtmp*q[j]*sqrt(r2inv);
+ if (rsq < cut_coulsq && qtmp != 0.0 && q[j] != 0.0) {
+ forcecoul = qqrd2e * qtmp*q[j]*sqrt(r2inv);
if (rsq > cut_coul_innersq) {
- r = sqrt(rsq);
- tc = r - cut_coul_inner;
+ r = sqrt(rsq);
+ tc = r - cut_coul_inner;
fswitchcoul = qqrd2e * qtmp*q[j]*r*tc*tc*(coulsw1 + coulsw2*tc);
forcecoul += fswitchcoul;
}
- } else forcecoul = 0.0;
+ } else forcecoul = 0.0;
- if (rsq < cut_ljsq) {
- r6inv = r2inv*r2inv*r2inv;
- jtype = type[j];
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ if (rsq < cut_ljsq) {
+ r6inv = r2inv*r2inv*r2inv;
+ jtype = type[j];
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
if (rsq > cut_lj_innersq) {
- r = sqrt(rsq);
- tlj = r - cut_lj_inner;
- fswitch = r*tlj*tlj*(ljsw1[itype][jtype] +
- ljsw2[itype][jtype]*tlj);
- forcelj += fswitch;
+ r = sqrt(rsq);
+ tlj = r - cut_lj_inner;
+ fswitch = r*tlj*tlj*(ljsw1[itype][jtype] +
+ ljsw2[itype][jtype]*tlj);
+ forcelj += fswitch;
}
- } else forcelj = 0.0;
-
- fpair = (factor_coul*forcecoul + factor_lj*forcelj) * r2inv;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (eflag) {
- if (rsq < cut_coulsq) {
- ecoul = qqrd2e * qtmp*q[j] * (sqrt(r2inv) - coulsw5);
+ } else forcelj = 0.0;
+
+ fpair = (factor_coul*forcecoul + factor_lj*forcelj) * r2inv;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (eflag) {
+ if (rsq < cut_coulsq) {
+ ecoul = qqrd2e * qtmp*q[j] * (sqrt(r2inv) - coulsw5);
if (rsq > cut_coul_innersq) {
ecoulswitch = tc*tc*tc * (coulsw3 + coulsw4*tc);
ecoul += qqrd2e*qtmp*q[j]*ecoulswitch;
}
- ecoul *= factor_coul;
- } else ecoul = 0.0;
- if (rsq < cut_ljsq) {
- evdwl = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
- evdwl += ljsw5[itype][jtype];
+ ecoul *= factor_coul;
+ } else ecoul = 0.0;
+ if (rsq < cut_ljsq) {
+ evdwl = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
+ evdwl += ljsw5[itype][jtype];
if (rsq > cut_lj_innersq) {
- eswitch = tlj*tlj*tlj *
- (ljsw3[itype][jtype] + ljsw4[itype][jtype]*tlj);
+ eswitch = tlj*tlj*tlj *
+ (ljsw3[itype][jtype] + ljsw4[itype][jtype]*tlj);
evdwl += eswitch;
}
- evdwl *= factor_lj;
- } else evdwl = 0.0;
- }
+ evdwl *= factor_lj;
+ } else evdwl = 0.0;
+ }
- if (evflag) ev_tally(i,j,nlocal,newton_pair,
- evdwl,ecoul,fpair,delx,dely,delz);
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
@@ -213,7 +213,7 @@ void PairLJGromacsCoulGromacs::allocate()
void PairLJGromacsCoulGromacs::settings(int narg, char **arg)
{
- if (narg != 2 && narg != 4)
+ if (narg != 2 && narg != 4)
error->all(FLERR,"Illegal pair_style command");
cut_lj_inner = force->numeric(arg[0]);
@@ -287,7 +287,7 @@ double PairLJGromacsCoulGromacs::init_one(int i, int j)
{
if (setflag[i][j] == 0) {
epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j],
- sigma[i][i],sigma[j][j]);
+ sigma[i][i],sigma[j][j]);
sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]);
}
@@ -355,8 +355,8 @@ void PairLJGromacsCoulGromacs::write_restart(FILE *fp)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
- fwrite(&epsilon[i][j],sizeof(double),1,fp);
- fwrite(&sigma[i][j],sizeof(double),1,fp);
+ fwrite(&epsilon[i][j],sizeof(double),1,fp);
+ fwrite(&sigma[i][j],sizeof(double),1,fp);
}
}
}
@@ -377,12 +377,12 @@ void PairLJGromacsCoulGromacs::read_restart(FILE *fp)
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
- if (me == 0) {
- fread(&epsilon[i][j],sizeof(double),1,fp);
- fread(&sigma[i][j],sizeof(double),1,fp);
- }
- MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
+ if (me == 0) {
+ fread(&epsilon[i][j],sizeof(double),1,fp);
+ fread(&sigma[i][j],sizeof(double),1,fp);
+ }
+ MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
}
}
}
@@ -426,21 +426,21 @@ void PairLJGromacsCoulGromacs::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairLJGromacsCoulGromacs::single(int i, int j, int itype, int jtype,
- double rsq,
- double factor_coul, double factor_lj,
- double &fforce)
+ double rsq,
+ double factor_coul, double factor_lj,
+ double &fforce)
{
double r2inv,r6inv,forcecoul,forcelj,phicoul,philj;
- double r,tlj,tc,fswitch,phiswitch,fswitchcoul,phiswitchcoul;
+ double r,tlj,tc,fswitch,phiswitch,fswitchcoul,phiswitchcoul;
r2inv = 1.0/rsq;
if (rsq < cut_coulsq) {
forcecoul = force->qqrd2e * atom->q[i]*atom->q[j]*sqrt(r2inv);
if (rsq > cut_coul_innersq) {
- r = sqrt(rsq);
+ r = sqrt(rsq);
tc = r - cut_coul_inner;
- fswitchcoul = force->qqrd2e *
- atom->q[i]*atom->q[j] * r*tc*tc * (coulsw1 + coulsw2*tc);
+ fswitchcoul = force->qqrd2e *
+ atom->q[i]*atom->q[j] * r*tc*tc * (coulsw1 + coulsw2*tc);
forcecoul += fswitchcoul;
}
} else forcecoul = 0.0;
@@ -449,7 +449,7 @@ double PairLJGromacsCoulGromacs::single(int i, int j, int itype, int jtype,
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
if (rsq > cut_lj_innersq) {
- r = sqrt(rsq);
+ r = sqrt(rsq);
tlj = r - cut_lj_inner;
fswitch = r*tlj*tlj*(ljsw1[itype][jtype] + ljsw2[itype][jtype]*tlj);
forcelj += fswitch;
@@ -463,7 +463,7 @@ double PairLJGromacsCoulGromacs::single(int i, int j, int itype, int jtype,
phicoul = force->qqrd2e * atom->q[i]*atom->q[j] * (sqrt(r2inv)-coulsw5);
if (rsq > cut_coul_innersq) {
phiswitchcoul = force->qqrd2e * atom->q[i]*atom->q[j] *
- tc*tc*tc * (coulsw3 + coulsw4*tc);
+ tc*tc*tc * (coulsw3 + coulsw4*tc);
phicoul += phiswitchcoul;
}
eng += factor_coul*phicoul;
@@ -473,8 +473,8 @@ double PairLJGromacsCoulGromacs::single(int i, int j, int itype, int jtype,
philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
philj += ljsw5[itype][jtype];
if (rsq > cut_lj_innersq) {
- phiswitch = tlj*tlj*tlj *
- (ljsw3[itype][jtype] + ljsw4[itype][jtype]*tlj);
+ phiswitch = tlj*tlj*tlj *
+ (ljsw3[itype][jtype] + ljsw4[itype][jtype]*tlj);
philj += phiswitch;
}
eng += factor_lj*philj;
diff --git a/src/pair_lj_gromacs_coul_gromacs.h b/src/pair_lj_gromacs_coul_gromacs.h
index bb6d28ba04b922990ff23a62644300b4e7185421..fb7d97bbb50a689d2efd178750ad16ad8b2f29ed 100644
--- a/src/pair_lj_gromacs_coul_gromacs.h
+++ b/src/pair_lj_gromacs_coul_gromacs.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/pair_lj_smooth.cpp b/src/pair_lj_smooth.cpp
index de1276991cacce9efd17f2424b9c41ffda43ee29..3465c3ca1958af4aa9f1a30a8b0630c7e881f3c9 100644
--- a/src/pair_lj_smooth.cpp
+++ b/src/pair_lj_smooth.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -67,7 +67,7 @@ void PairLJSmooth::compute(int eflag, int vflag)
double rsq,r2inv,r6inv,forcelj,factor_lj;
double r,t,tsq,fskin;
int *ilist,*jlist,*numneigh,**firstneigh;
-
+
evdwl = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
@@ -78,12 +78,12 @@ void PairLJSmooth::compute(int eflag, int vflag)
int nlocal = atom->nlocal;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
-
+
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@@ -105,45 +105,45 @@ void PairLJSmooth::compute(int eflag, int vflag)
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
-
+
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- if (rsq < cut_inner_sq[itype][jtype]) {
- r6inv = r2inv*r2inv*r2inv;
- forcelj = r6inv * (lj1[itype][jtype]*r6inv-lj2[itype][jtype]);
- } else {
- r = sqrt(rsq);
- t = r - cut_inner[itype][jtype];
- tsq = t*t;
- fskin = ljsw1[itype][jtype] + ljsw2[itype][jtype]*t +
- ljsw3[itype][jtype]*tsq + ljsw4[itype][jtype]*tsq*t;
- forcelj = fskin*r;
- }
-
- fpair = factor_lj*forcelj*r2inv;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (eflag) {
- if (rsq < cut_inner_sq[itype][jtype])
- evdwl = r6inv * (lj3[itype][jtype]*r6inv -
- lj4[itype][jtype]) - offset[itype][jtype];
- else
- evdwl = ljsw0[itype][jtype] - ljsw1[itype][jtype]*t -
- ljsw2[itype][jtype]*tsq/2.0 - ljsw3[itype][jtype]*tsq*t/3.0 -
- ljsw4[itype][jtype]*tsq*tsq/4.0 - offset[itype][jtype];
- evdwl *= factor_lj;
- }
-
- if (evflag) ev_tally(i,j,nlocal,newton_pair,
- evdwl,0.0,fpair,delx,dely,delz);
+ r2inv = 1.0/rsq;
+ if (rsq < cut_inner_sq[itype][jtype]) {
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv-lj2[itype][jtype]);
+ } else {
+ r = sqrt(rsq);
+ t = r - cut_inner[itype][jtype];
+ tsq = t*t;
+ fskin = ljsw1[itype][jtype] + ljsw2[itype][jtype]*t +
+ ljsw3[itype][jtype]*tsq + ljsw4[itype][jtype]*tsq*t;
+ forcelj = fskin*r;
+ }
+
+ fpair = factor_lj*forcelj*r2inv;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (eflag) {
+ if (rsq < cut_inner_sq[itype][jtype])
+ evdwl = r6inv * (lj3[itype][jtype]*r6inv -
+ lj4[itype][jtype]) - offset[itype][jtype];
+ else
+ evdwl = ljsw0[itype][jtype] - ljsw1[itype][jtype]*t -
+ ljsw2[itype][jtype]*tsq/2.0 - ljsw3[itype][jtype]*tsq*t/3.0 -
+ ljsw4[itype][jtype]*tsq*tsq/4.0 - offset[itype][jtype];
+ evdwl *= factor_lj;
+ }
+
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ evdwl,0.0,fpair,delx,dely,delz);
}
}
}
@@ -152,7 +152,7 @@ void PairLJSmooth::compute(int eflag, int vflag)
}
/* ----------------------------------------------------------------------
- allocate all arrays
+ allocate all arrays
------------------------------------------------------------------------- */
void PairLJSmooth::allocate()
@@ -185,7 +185,7 @@ void PairLJSmooth::allocate()
}
/* ----------------------------------------------------------------------
- global settings
+ global settings
------------------------------------------------------------------------- */
void PairLJSmooth::settings(int narg, char **arg)
@@ -204,10 +204,10 @@ void PairLJSmooth::settings(int narg, char **arg)
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
- if (setflag[i][j]) {
- cut_inner[i][j] = cut_inner_global;
- cut[i][j] = cut_global;
- }
+ if (setflag[i][j]) {
+ cut_inner[i][j] = cut_inner_global;
+ cut[i][j] = cut_global;
+ }
}
}
@@ -227,7 +227,7 @@ void PairLJSmooth::coeff(int narg, char **arg)
double epsilon_one = force->numeric(arg[2]);
double sigma_one = force->numeric(arg[3]);
-
+
double cut_inner_one = cut_inner_global;
double cut_one = cut_global;
if (narg == 6) {
@@ -261,7 +261,7 @@ double PairLJSmooth::init_one(int i, int j)
{
if (setflag[i][j] == 0) {
epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j],
- sigma[i][i],sigma[j][j]);
+ sigma[i][i],sigma[j][j]);
sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]);
cut_inner[i][j] = mix_distance(cut_inner[i][i],cut_inner[j][j]);
cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
@@ -286,7 +286,7 @@ double PairLJSmooth::init_one(int i, int j)
ljsw4[i][j] = -1.0/(3.0*tsq) * (ljsw2[i][j] + 2.0*ljsw3[i][j]*t);
if (offset_flag)
offset[i][j] = ljsw0[i][j] - ljsw1[i][j]*t - ljsw2[i][j]*tsq/2.0 -
- ljsw3[i][j]*tsq*t/3.0 - ljsw4[i][j]*tsq*tsq/4.0;
+ ljsw3[i][j]*tsq*t/3.0 - ljsw4[i][j]*tsq*tsq/4.0;
else offset[i][j] = 0.0;
} else {
ljsw0[i][j] = 0.0;
@@ -299,7 +299,7 @@ double PairLJSmooth::init_one(int i, int j)
offset[i][j] = 4.0 * epsilon[i][j] * (pow(ratio,12.0) - pow(ratio,6.0));
else offset[i][j] = 0.0;
}
-
+
cut_inner[j][i] = cut_inner[i][j];
cut_inner_sq[j][i] = cut_inner_sq[i][j];
lj1[j][i] = lj1[i][j];
@@ -317,7 +317,7 @@ double PairLJSmooth::init_one(int i, int j)
}
/* ----------------------------------------------------------------------
- proc 0 writes to restart file
+ proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairLJSmooth::write_restart(FILE *fp)
@@ -329,10 +329,10 @@ void PairLJSmooth::write_restart(FILE *fp)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
- fwrite(&epsilon[i][j],sizeof(double),1,fp);
- fwrite(&sigma[i][j],sizeof(double),1,fp);
- fwrite(&cut_inner[i][j],sizeof(double),1,fp);
- fwrite(&cut[i][j],sizeof(double),1,fp);
+ fwrite(&epsilon[i][j],sizeof(double),1,fp);
+ fwrite(&sigma[i][j],sizeof(double),1,fp);
+ fwrite(&cut_inner[i][j],sizeof(double),1,fp);
+ fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
@@ -353,16 +353,16 @@ void PairLJSmooth::read_restart(FILE *fp)
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
- if (me == 0) {
- fread(&epsilon[i][j],sizeof(double),1,fp);
- fread(&sigma[i][j],sizeof(double),1,fp);
- fread(&cut_inner[i][j],sizeof(double),1,fp);
- fread(&cut[i][j],sizeof(double),1,fp);
- }
- MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&cut_inner[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
+ if (me == 0) {
+ fread(&epsilon[i][j],sizeof(double),1,fp);
+ fread(&sigma[i][j],sizeof(double),1,fp);
+ fread(&cut_inner[i][j],sizeof(double),1,fp);
+ fread(&cut[i][j],sizeof(double),1,fp);
+ }
+ MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut_inner[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
@@ -401,8 +401,8 @@ void PairLJSmooth::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairLJSmooth::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
- double &fforce)
+ double factor_coul, double factor_lj,
+ double &fforce)
{
double r2inv,r6inv,forcelj,philj,r,t,tsq,fskin;
@@ -411,15 +411,15 @@ double PairLJSmooth::single(int i, int j, int itype, int jtype, double rsq,
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv-lj2[itype][jtype]);
} else {
- r = sqrt(rsq);
+ r = sqrt(rsq);
t = r - cut_inner[itype][jtype];
tsq = t*t;
- fskin = ljsw1[itype][jtype] + ljsw2[itype][jtype]*t +
- ljsw3[itype][jtype]*tsq + ljsw4[itype][jtype]*tsq*t;
+ fskin = ljsw1[itype][jtype] + ljsw2[itype][jtype]*t +
+ ljsw3[itype][jtype]*tsq + ljsw4[itype][jtype]*tsq*t;
forcelj = fskin*r;
}
fforce = factor_lj*forcelj*r2inv;
-
+
if (rsq < cut_inner_sq[itype][jtype])
philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]) -
offset[itype][jtype];
diff --git a/src/pair_lj_smooth.h b/src/pair_lj_smooth.h
index b81a1b79ff2634d6796beb18f602f82c60ae7a72..d68f3568d4e63fce1078a9b5bdc1d5c814da6b85 100644
--- a/src/pair_lj_smooth.h
+++ b/src/pair_lj_smooth.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/pair_lj_smooth_linear.cpp b/src/pair_lj_smooth_linear.cpp
index ed18f1296471c0fa840723c2a34f383984a1f2d7..7e8a8cab1b093e85e62fd9de40e9fbafd2a16523 100644
--- a/src/pair_lj_smooth_linear.cpp
+++ b/src/pair_lj_smooth_linear.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -60,7 +60,7 @@ void PairLJSmoothLinear::compute(int eflag, int vflag)
double rsq,r2inv,r6inv,forcelj,factor_lj;
double r,rinv;
int *ilist,*jlist,*numneigh,**firstneigh;
-
+
evdwl = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
@@ -72,12 +72,12 @@ void PairLJSmoothLinear::compute(int eflag, int vflag)
int nall = nlocal + atom->nghost;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
-
+
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@@ -99,34 +99,34 @@ void PairLJSmoothLinear::compute(int eflag, int vflag)
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
-
+
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- r6inv = r2inv*r2inv*r2inv;
+ r2inv = 1.0/rsq;
+ r6inv = r2inv*r2inv*r2inv;
rinv = sqrt(r2inv);
- forcelj = r6inv*(lj1[itype][jtype]*r6inv-lj2[itype][jtype]);
- forcelj = rinv*forcelj - dljcut[itype][jtype];
-
- fpair = factor_lj*forcelj*rinv;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (eflag) {
+ forcelj = r6inv*(lj1[itype][jtype]*r6inv-lj2[itype][jtype]);
+ forcelj = rinv*forcelj - dljcut[itype][jtype];
+
+ fpair = factor_lj*forcelj*rinv;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (eflag) {
r = sqrt(rsq);
- evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
+ evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
evdwl = evdwl - ljcut[itype][jtype]
- + (r-cut[itype][jtype])*dljcut[itype][jtype];
- }
+ + (r-cut[itype][jtype])*dljcut[itype][jtype];
+ }
- if (evflag) ev_tally(i,j,nlocal,newton_pair,
- evdwl,0.0,fpair,delx,dely,delz);
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ evdwl,0.0,fpair,delx,dely,delz);
}
}
}
@@ -135,7 +135,7 @@ void PairLJSmoothLinear::compute(int eflag, int vflag)
}
/* ----------------------------------------------------------------------
- allocate all arrays
+ allocate all arrays
------------------------------------------------------------------------- */
void PairLJSmoothLinear::allocate()
@@ -162,7 +162,7 @@ void PairLJSmoothLinear::allocate()
}
/* ----------------------------------------------------------------------
- global settings
+ global settings
------------------------------------------------------------------------- */
void PairLJSmoothLinear::settings(int narg, char **arg)
@@ -177,9 +177,9 @@ void PairLJSmoothLinear::settings(int narg, char **arg)
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
- if (setflag[i][j]) {
- cut[i][j] = cut_global;
- }
+ if (setflag[i][j]) {
+ cut[i][j] = cut_global;
+ }
}
}
@@ -199,7 +199,7 @@ void PairLJSmoothLinear::coeff(int narg, char **arg)
double epsilon_one = atof(arg[2]);
double sigma_one = atof(arg[3]);
-
+
double cut_one = cut_global;
if (narg == 5) {
cut_one = atof(arg[4]);
@@ -227,7 +227,7 @@ double PairLJSmoothLinear::init_one(int i, int j)
{
if (setflag[i][j] == 0) {
epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j],
- sigma[i][i],sigma[j][j]);
+ sigma[i][i],sigma[j][j]);
sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]);
cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
}
@@ -252,7 +252,7 @@ double PairLJSmoothLinear::init_one(int i, int j)
}
/* ----------------------------------------------------------------------
- proc 0 writes to restart file
+ proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairLJSmoothLinear::write_restart(FILE *fp)
@@ -264,9 +264,9 @@ void PairLJSmoothLinear::write_restart(FILE *fp)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
- fwrite(&epsilon[i][j],sizeof(double),1,fp);
- fwrite(&sigma[i][j],sizeof(double),1,fp);
- fwrite(&cut[i][j],sizeof(double),1,fp);
+ fwrite(&epsilon[i][j],sizeof(double),1,fp);
+ fwrite(&sigma[i][j],sizeof(double),1,fp);
+ fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
@@ -287,14 +287,14 @@ void PairLJSmoothLinear::read_restart(FILE *fp)
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
- if (me == 0) {
- fread(&epsilon[i][j],sizeof(double),1,fp);
- fread(&sigma[i][j],sizeof(double),1,fp);
- fread(&cut[i][j],sizeof(double),1,fp);
- }
- MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
+ if (me == 0) {
+ fread(&epsilon[i][j],sizeof(double),1,fp);
+ fread(&sigma[i][j],sizeof(double),1,fp);
+ fread(&cut[i][j],sizeof(double),1,fp);
+ }
+ MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
@@ -326,10 +326,10 @@ void PairLJSmoothLinear::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairLJSmoothLinear::single(int i, int j, int itype, int jtype,
- double rsq,
- double factor_coul, double factor_lj,
- double &fforce)
+double PairLJSmoothLinear::single(int i, int j, int itype, int jtype,
+ double rsq,
+ double factor_coul, double factor_lj,
+ double &fforce)
{
double r2inv,r6inv,forcelj,philj,r,rinv;
diff --git a/src/pair_lj_smooth_linear.h b/src/pair_lj_smooth_linear.h
index 43d9238a7711249138d059b4d8cd1ada7cbec29d..0e3376b7894abf73180fbfcb8fc640fba5162f39 100644
--- a/src/pair_lj_smooth_linear.h
+++ b/src/pair_lj_smooth_linear.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/pair_morse.cpp b/src/pair_morse.cpp
index d05235a978d3d6488e8c756e55cd14be86a64ee5..080f19fe5e413db9895c16092505951532eabcce 100644
--- a/src/pair_morse.cpp
+++ b/src/pair_morse.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -69,7 +69,7 @@ void PairMorse::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@@ -93,28 +93,28 @@ void PairMorse::compute(int eflag, int vflag)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r = sqrt(rsq);
- dr = r - r0[itype][jtype];
- dexp = exp(-alpha[itype][jtype] * dr);
- fpair = factor_lj * morse1[itype][jtype] * (dexp*dexp - dexp) / r;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (eflag) {
- evdwl = d0[itype][jtype] * (dexp*dexp - 2.0*dexp) -
- offset[itype][jtype];
- evdwl *= factor_lj;
- }
-
- if (evflag) ev_tally(i,j,nlocal,newton_pair,
- evdwl,0.0,fpair,delx,dely,delz);
+ r = sqrt(rsq);
+ dr = r - r0[itype][jtype];
+ dexp = exp(-alpha[itype][jtype] * dr);
+ fpair = factor_lj * morse1[itype][jtype] * (dexp*dexp - dexp) / r;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (eflag) {
+ evdwl = d0[itype][jtype] * (dexp*dexp - 2.0*dexp) -
+ offset[itype][jtype];
+ evdwl *= factor_lj;
+ }
+
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ evdwl,0.0,fpair,delx,dely,delz);
}
}
}
@@ -123,7 +123,7 @@ void PairMorse::compute(int eflag, int vflag)
}
/* ----------------------------------------------------------------------
- allocate all arrays
+ allocate all arrays
------------------------------------------------------------------------- */
void PairMorse::allocate()
@@ -147,7 +147,7 @@ void PairMorse::allocate()
}
/* ----------------------------------------------------------------------
- global settings
+ global settings
------------------------------------------------------------------------- */
void PairMorse::settings(int narg, char **arg)
@@ -162,7 +162,7 @@ void PairMorse::settings(int narg, char **arg)
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
- if (setflag[i][j]) cut[i][j] = cut_global;
+ if (setflag[i][j]) cut[i][j] = cut_global;
}
}
@@ -211,7 +211,7 @@ double PairMorse::init_one(int i, int j)
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
morse1[i][j] = 2.0*d0[i][j]*alpha[i][j];
-
+
if (offset_flag) {
double alpha_dr = -alpha[i][j] * (cut[i][j] - r0[i][j]);
offset[i][j] = d0[i][j] * (exp(2.0*alpha_dr) - 2.0*exp(alpha_dr));
@@ -239,10 +239,10 @@ void PairMorse::write_restart(FILE *fp)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
- fwrite(&d0[i][j],sizeof(double),1,fp);
- fwrite(&alpha[i][j],sizeof(double),1,fp);
- fwrite(&r0[i][j],sizeof(double),1,fp);
- fwrite(&cut[i][j],sizeof(double),1,fp);
+ fwrite(&d0[i][j],sizeof(double),1,fp);
+ fwrite(&alpha[i][j],sizeof(double),1,fp);
+ fwrite(&r0[i][j],sizeof(double),1,fp);
+ fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
@@ -264,16 +264,16 @@ void PairMorse::read_restart(FILE *fp)
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
- if (me == 0) {
- fread(&d0[i][j],sizeof(double),1,fp);
- fread(&alpha[i][j],sizeof(double),1,fp);
- fread(&r0[i][j],sizeof(double),1,fp);
- fread(&cut[i][j],sizeof(double),1,fp);
- }
- MPI_Bcast(&d0[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&alpha[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&r0[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
+ if (me == 0) {
+ fread(&d0[i][j],sizeof(double),1,fp);
+ fread(&alpha[i][j],sizeof(double),1,fp);
+ fread(&r0[i][j],sizeof(double),1,fp);
+ fread(&cut[i][j],sizeof(double),1,fp);
+ }
+ MPI_Bcast(&d0[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&alpha[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&r0[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
@@ -308,8 +308,8 @@ void PairMorse::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairMorse::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
- double &fforce)
+ double factor_coul, double factor_lj,
+ double &fforce)
{
double r,dr,dexp,phi;
@@ -317,7 +317,7 @@ double PairMorse::single(int i, int j, int itype, int jtype, double rsq,
dr = r - r0[itype][jtype];
dexp = exp(-alpha[itype][jtype] * dr);
fforce = factor_lj * morse1[itype][jtype] * (dexp*dexp - dexp) / r;
-
+
phi = d0[itype][jtype] * (dexp*dexp - 2.0*dexp) - offset[itype][jtype];
return factor_lj*phi;
}
diff --git a/src/pair_morse.h b/src/pair_morse.h
index 2110237b7dc5b5685f579f5241d8f7084271f000..fbc2df85098270b5b6fb32ff8e85d24d31de5832 100644
--- a/src/pair_morse.h
+++ b/src/pair_morse.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/pair_soft.cpp b/src/pair_soft.cpp
index fb2889ddfcad9ebfe4510a26c125ec095c53c101..c6d38c70554af40c12e15fc93e09db69bd9b249d 100644
--- a/src/pair_soft.cpp
+++ b/src/pair_soft.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -69,7 +69,7 @@ void PairSoft::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@@ -93,26 +93,26 @@ void PairSoft::compute(int eflag, int vflag)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r = sqrt(rsq);
- arg = MY_PI*r/cut[itype][jtype];
- if (r > 0.0) fpair = factor_lj * prefactor[itype][jtype] *
- sin(arg) * MY_PI/cut[itype][jtype]/r;
- else fpair = 0.0;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (eflag)
- evdwl = factor_lj * prefactor[itype][jtype] * (1.0+cos(arg));
-
- if (evflag) ev_tally(i,j,nlocal,newton_pair,
- evdwl,0.0,fpair,delx,dely,delz);
+ r = sqrt(rsq);
+ arg = MY_PI*r/cut[itype][jtype];
+ if (r > 0.0) fpair = factor_lj * prefactor[itype][jtype] *
+ sin(arg) * MY_PI/cut[itype][jtype]/r;
+ else fpair = 0.0;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (eflag)
+ evdwl = factor_lj * prefactor[itype][jtype] * (1.0+cos(arg));
+
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ evdwl,0.0,fpair,delx,dely,delz);
}
}
}
@@ -121,7 +121,7 @@ void PairSoft::compute(int eflag, int vflag)
}
/* ----------------------------------------------------------------------
- allocate all arrays
+ allocate all arrays
------------------------------------------------------------------------- */
void PairSoft::allocate()
@@ -141,7 +141,7 @@ void PairSoft::allocate()
}
/* ----------------------------------------------------------------------
- global settings
+ global settings
------------------------------------------------------------------------- */
void PairSoft::settings(int narg, char **arg)
@@ -156,7 +156,7 @@ void PairSoft::settings(int narg, char **arg)
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
- if (setflag[i][j]) cut[i][j] = cut_global;
+ if (setflag[i][j]) cut[i][j] = cut_global;
}
}
@@ -223,8 +223,8 @@ void PairSoft::write_restart(FILE *fp)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
- fwrite(&prefactor[i][j],sizeof(double),1,fp);
- fwrite(&cut[i][j],sizeof(double),1,fp);
+ fwrite(&prefactor[i][j],sizeof(double),1,fp);
+ fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
@@ -246,12 +246,12 @@ void PairSoft::read_restart(FILE *fp)
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
- if (me == 0) {
- fread(&prefactor[i][j],sizeof(double),1,fp);
- fread(&cut[i][j],sizeof(double),1,fp);
- }
- MPI_Bcast(&prefactor[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
+ if (me == 0) {
+ fread(&prefactor[i][j],sizeof(double),1,fp);
+ fread(&cut[i][j],sizeof(double),1,fp);
+ }
+ MPI_Bcast(&prefactor[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
@@ -283,16 +283,16 @@ void PairSoft::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairSoft::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
- double &fforce)
+ double factor_coul, double factor_lj,
+ double &fforce)
{
double r,arg,philj;
r = sqrt(rsq);
arg = MY_PI*r/cut[itype][jtype];
- fforce = factor_lj * prefactor[itype][jtype] *
+ fforce = factor_lj * prefactor[itype][jtype] *
sin(arg) * MY_PI/cut[itype][jtype]/r;
-
+
philj = prefactor[itype][jtype] * (1.0+cos(arg));
return factor_lj*philj;
}
diff --git a/src/pair_soft.h b/src/pair_soft.h
index c5927cefdabe51185e0b0b4be6643af1d428ab0c..9027c83c8e92c31dd73c4039a867887c6ff209ed 100644
--- a/src/pair_soft.h
+++ b/src/pair_soft.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/pair_table.cpp b/src/pair_table.cpp
index 4585f181422094e922085c13d74c1ecdf3676bea..17e9058b6fd67737e4ad79c29da5a97296da6fa1 100644
--- a/src/pair_table.cpp
+++ b/src/pair_table.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -64,7 +64,7 @@ void PairTable::compute(int eflag, int vflag)
double rsq,factor_lj,fraction,value,a,b;
int *ilist,*jlist,*numneigh,**firstneigh;
Table *tb;
-
+
union_int_float_t rsq_lookup;
int tlm1 = tablength - 1;
@@ -83,7 +83,7 @@ void PairTable::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@@ -105,66 +105,66 @@ void PairTable::compute(int eflag, int vflag)
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
-
+
if (rsq < cutsq[itype][jtype]) {
- tb = &tables[tabindex[itype][jtype]];
- if (rsq < tb->innersq)
- error->one(FLERR,"Pair distance < table inner cutoff");
-
- if (tabstyle == LOOKUP) {
- itable = static_cast<int> ((rsq - tb->innersq) * tb->invdelta);
- if (itable >= tlm1)
- error->one(FLERR,"Pair distance > table outer cutoff");
- fpair = factor_lj * tb->f[itable];
- } else if (tabstyle == LINEAR) {
- itable = static_cast<int> ((rsq - tb->innersq) * tb->invdelta);
- if (itable >= tlm1)
- error->one(FLERR,"Pair distance > table outer cutoff");
- fraction = (rsq - tb->rsq[itable]) * tb->invdelta;
- value = tb->f[itable] + fraction*tb->df[itable];
- fpair = factor_lj * value;
- } else if (tabstyle == SPLINE) {
- itable = static_cast<int> ((rsq - tb->innersq) * tb->invdelta);
- if (itable >= tlm1)
- error->one(FLERR,"Pair distance > table outer cutoff");
- b = (rsq - tb->rsq[itable]) * tb->invdelta;
- a = 1.0 - b;
- value = a * tb->f[itable] + b * tb->f[itable+1] +
- ((a*a*a-a)*tb->f2[itable] + (b*b*b-b)*tb->f2[itable+1]) *
+ tb = &tables[tabindex[itype][jtype]];
+ if (rsq < tb->innersq)
+ error->one(FLERR,"Pair distance < table inner cutoff");
+
+ if (tabstyle == LOOKUP) {
+ itable = static_cast<int> ((rsq - tb->innersq) * tb->invdelta);
+ if (itable >= tlm1)
+ error->one(FLERR,"Pair distance > table outer cutoff");
+ fpair = factor_lj * tb->f[itable];
+ } else if (tabstyle == LINEAR) {
+ itable = static_cast<int> ((rsq - tb->innersq) * tb->invdelta);
+ if (itable >= tlm1)
+ error->one(FLERR,"Pair distance > table outer cutoff");
+ fraction = (rsq - tb->rsq[itable]) * tb->invdelta;
+ value = tb->f[itable] + fraction*tb->df[itable];
+ fpair = factor_lj * value;
+ } else if (tabstyle == SPLINE) {
+ itable = static_cast<int> ((rsq - tb->innersq) * tb->invdelta);
+ if (itable >= tlm1)
+ error->one(FLERR,"Pair distance > table outer cutoff");
+ b = (rsq - tb->rsq[itable]) * tb->invdelta;
+ a = 1.0 - b;
+ value = a * tb->f[itable] + b * tb->f[itable+1] +
+ ((a*a*a-a)*tb->f2[itable] + (b*b*b-b)*tb->f2[itable+1]) *
tb->deltasq6;
- fpair = factor_lj * value;
- } else {
- rsq_lookup.f = rsq;
- itable = rsq_lookup.i & tb->nmask;
- itable >>= tb->nshiftbits;
- fraction = (rsq_lookup.f - tb->rsq[itable]) * tb->drsq[itable];
- value = tb->f[itable] + fraction*tb->df[itable];
- fpair = factor_lj * value;
- }
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (eflag) {
- if (tabstyle == LOOKUP)
- evdwl = tb->e[itable];
- else if (tabstyle == LINEAR || tabstyle == BITMAP)
- evdwl = tb->e[itable] + fraction*tb->de[itable];
- else
- evdwl = a * tb->e[itable] + b * tb->e[itable+1] +
- ((a*a*a-a)*tb->e2[itable] + (b*b*b-b)*tb->e2[itable+1]) *
- tb->deltasq6;
- evdwl *= factor_lj;
- }
-
- if (evflag) ev_tally(i,j,nlocal,newton_pair,
- evdwl,0.0,fpair,delx,dely,delz);
+ fpair = factor_lj * value;
+ } else {
+ rsq_lookup.f = rsq;
+ itable = rsq_lookup.i & tb->nmask;
+ itable >>= tb->nshiftbits;
+ fraction = (rsq_lookup.f - tb->rsq[itable]) * tb->drsq[itable];
+ value = tb->f[itable] + fraction*tb->df[itable];
+ fpair = factor_lj * value;
+ }
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (eflag) {
+ if (tabstyle == LOOKUP)
+ evdwl = tb->e[itable];
+ else if (tabstyle == LINEAR || tabstyle == BITMAP)
+ evdwl = tb->e[itable] + fraction*tb->de[itable];
+ else
+ evdwl = a * tb->e[itable] + b * tb->e[itable+1] +
+ ((a*a*a-a)*tb->e2[itable] + (b*b*b-b)*tb->e2[itable+1]) *
+ tb->deltasq6;
+ evdwl *= factor_lj;
+ }
+
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ evdwl,0.0,fpair,delx,dely,delz);
}
}
}
@@ -173,7 +173,7 @@ void PairTable::compute(int eflag, int vflag)
}
/* ----------------------------------------------------------------------
- allocate all arrays
+ allocate all arrays
------------------------------------------------------------------------- */
void PairTable::allocate()
@@ -191,7 +191,7 @@ void PairTable::allocate()
}
/* ----------------------------------------------------------------------
- global settings
+ global settings
------------------------------------------------------------------------- */
void PairTable::settings(int narg, char **arg)
@@ -237,10 +237,10 @@ void PairTable::coeff(int narg, char **arg)
int ilo,ihi,jlo,jhi;
force->bounds(arg[0],atom->ntypes,ilo,ihi);
force->bounds(arg[1],atom->ntypes,jlo,jhi);
-
+
int me;
MPI_Comm_rank(world,&me);
- tables = (Table *)
+ tables = (Table *)
memory->srealloc(tables,(ntables+1)*sizeof(Table),"pair:tables");
Table *tb = &tables[ntables];
null_table(tb);
@@ -276,9 +276,9 @@ void PairTable::coeff(int narg, char **arg)
// for tabstyle SPLINE, always need to build spline tables
tb->match = 0;
- if (tabstyle == LINEAR && tb->ninput == tablength &&
+ if (tabstyle == LINEAR && tb->ninput == tablength &&
tb->rflag == RSQ && tb->rhi == tb->cut) tb->match = 1;
- if (tabstyle == BITMAP && tb->ninput == 1 << tablength &&
+ if (tabstyle == BITMAP && tb->ninput == 1 << tablength &&
tb->rflag == BMP && tb->rhi == tb->cut) tb->match = 1;
if (tb->rflag == BMP && tb->match == 0)
error->all(FLERR,"Bitmapped table in file does not match requested table");
@@ -319,7 +319,7 @@ double PairTable::init_one(int i, int j)
/* ----------------------------------------------------------------------
read a table section from a tabulated potential file
only called by proc 0
- this function sets these values in Table:
+ this function sets these values in Table:
ninput,rfile,efile,ffile,rflag,rlo,rhi,fpflag,fplo,fphi,ntablebits
------------------------------------------------------------------------- */
@@ -386,8 +386,8 @@ void PairTable::read_table(Table *tb, char *file, char *keyword)
if (tb->rflag == RLINEAR)
rtmp = tb->rlo + (tb->rhi - tb->rlo)*i/(tb->ninput-1);
else if (tb->rflag == RSQ) {
- rtmp = tb->rlo*tb->rlo +
- (tb->rhi*tb->rhi - tb->rlo*tb->rlo)*i/(tb->ninput-1);
+ rtmp = tb->rlo*tb->rlo +
+ (tb->rhi*tb->rhi - tb->rlo*tb->rlo)*i/(tb->ninput-1);
rtmp = sqrt(rtmp);
} else if (tb->rflag == BMP) {
rsq_lookup.i = i << nshiftbits;
@@ -457,7 +457,7 @@ void PairTable::spline_table(Table *tb)
if (tb->fpflag == 0) {
tb->fplo = (tb->ffile[1] - tb->ffile[0]) / (tb->rfile[1] - tb->rfile[0]);
- tb->fphi = (tb->ffile[tb->ninput-1] - tb->ffile[tb->ninput-2]) /
+ tb->fphi = (tb->ffile[tb->ninput-1] - tb->ffile[tb->ninput-2]) /
(tb->rfile[tb->ninput-1] - tb->rfile[tb->ninput-2]);
}
@@ -477,14 +477,14 @@ void PairTable::param_extract(Table *tb, char *line)
tb->ninput = 0;
tb->rflag = NONE;
tb->fpflag = 0;
-
+
char *word = strtok(line," \t\n\r\f");
while (word) {
if (strcmp(word,"N") == 0) {
word = strtok(NULL," \t\n\r\f");
tb->ninput = atoi(word);
} else if (strcmp(word,"R") == 0 || strcmp(word,"RSQ") == 0 ||
- strcmp(word,"BITMAP") == 0) {
+ strcmp(word,"BITMAP") == 0) {
if (strcmp(word,"R") == 0) tb->rflag = RLINEAR;
else if (strcmp(word,"RSQ") == 0) tb->rflag = RSQ;
else if (strcmp(word,"BITMAP") == 0) tb->rflag = BMP;
@@ -568,14 +568,14 @@ void PairTable::compute_table(Table *tb)
r = sqrt(rsq);
tb->rsq[i] = rsq;
if (tb->match) {
- tb->e[i] = tb->efile[i];
- tb->f[i] = tb->ffile[i]/r;
+ tb->e[i] = tb->efile[i];
+ tb->f[i] = tb->ffile[i]/r;
} else {
- tb->e[i] = splint(tb->rfile,tb->efile,tb->e2file,tb->ninput,r);
- tb->f[i] = splint(tb->rfile,tb->ffile,tb->f2file,tb->ninput,r)/r;
+ tb->e[i] = splint(tb->rfile,tb->efile,tb->e2file,tb->ninput,r);
+ tb->f[i] = splint(tb->rfile,tb->ffile,tb->f2file,tb->ninput,r)/r;
}
}
-
+
for (int i = 0; i < tlm1; i++) {
tb->de[i] = tb->e[i+1] - tb->e[i];
tb->df[i] = tb->f[i+1] - tb->f[i];
@@ -605,11 +605,11 @@ void PairTable::compute_table(Table *tb)
r = sqrt(rsq);
tb->rsq[i] = rsq;
if (tb->match) {
- tb->e[i] = tb->efile[i];
- tb->f[i] = tb->ffile[i]/r;
+ tb->e[i] = tb->efile[i];
+ tb->f[i] = tb->ffile[i]/r;
} else {
- tb->e[i] = splint(tb->rfile,tb->efile,tb->e2file,tb->ninput,r);
- tb->f[i] = splint(tb->rfile,tb->ffile,tb->f2file,tb->ninput,r);
+ tb->e[i] = splint(tb->rfile,tb->efile,tb->e2file,tb->ninput,r);
+ tb->f[i] = splint(tb->rfile,tb->ffile,tb->f2file,tb->ninput,r);
}
}
@@ -634,7 +634,7 @@ void PairTable::compute_table(Table *tb)
double rsq1 = tb->innersq;
double rsq2 = rsq1 + secant_factor*tb->delta;
fp0 = (splint(tb->rfile,tb->ffile,tb->f2file,tb->ninput,sqrt(rsq2)) /
- sqrt(rsq2) - tb->f[0] / sqrt(rsq1)) / (secant_factor*tb->delta);
+ sqrt(rsq2) - tb->f[0] / sqrt(rsq1)) / (secant_factor*tb->delta);
}
if (tb->fpflag && tb->cut == tb->rfile[tb->ninput-1]) fpn =
@@ -642,9 +642,9 @@ void PairTable::compute_table(Table *tb)
else {
double rsq2 = tb->cut * tb->cut;
double rsq1 = rsq2 - secant_factor*tb->delta;
- fpn = (tb->f[tlm1] / sqrt(rsq2) -
- splint(tb->rfile,tb->ffile,tb->f2file,tb->ninput,sqrt(rsq1)) /
- sqrt(rsq1)) / (secant_factor*tb->delta);
+ fpn = (tb->f[tlm1] / sqrt(rsq2) -
+ splint(tb->rfile,tb->ffile,tb->f2file,tb->ninput,sqrt(rsq1)) /
+ sqrt(rsq1)) / (secant_factor*tb->delta);
}
for (int i = 0; i < tablength; i++) tb->f[i] /= sqrt(tb->rsq[i]);
@@ -663,7 +663,7 @@ void PairTable::compute_table(Table *tb)
// linear lookup tables of length ntable = 2^n
// stored value = value at lower edge of bin
-
+
init_bitmap(inner,tb->cut,tablength,masklo,maskhi,tb->nmask,tb->nshiftbits);
int ntable = 1 << tablength;
int ntablem1 = ntable - 1;
@@ -674,7 +674,7 @@ void PairTable::compute_table(Table *tb)
memory->create(tb->de,ntable,"pair:de");
memory->create(tb->df,ntable,"pair:df");
memory->create(tb->drsq,ntable,"pair:drsq");
-
+
union_int_float_t minrsq_lookup;
minrsq_lookup.i = 0 << tb->nshiftbits;
minrsq_lookup.i |= maskhi;
@@ -689,56 +689,56 @@ void PairTable::compute_table(Table *tb)
r = sqrtf(rsq_lookup.f);
tb->rsq[i] = rsq_lookup.f;
if (tb->match) {
- tb->e[i] = tb->efile[i];
- tb->f[i] = tb->ffile[i]/r;
+ tb->e[i] = tb->efile[i];
+ tb->f[i] = tb->ffile[i]/r;
} else {
- tb->e[i] = splint(tb->rfile,tb->efile,tb->e2file,tb->ninput,r);
- tb->f[i] = splint(tb->rfile,tb->ffile,tb->f2file,tb->ninput,r)/r;
+ tb->e[i] = splint(tb->rfile,tb->efile,tb->e2file,tb->ninput,r);
+ tb->f[i] = splint(tb->rfile,tb->ffile,tb->f2file,tb->ninput,r)/r;
}
minrsq_lookup.f = MIN(minrsq_lookup.f,rsq_lookup.f);
}
tb->innersq = minrsq_lookup.f;
-
+
for (int i = 0; i < ntablem1; i++) {
tb->de[i] = tb->e[i+1] - tb->e[i];
tb->df[i] = tb->f[i+1] - tb->f[i];
tb->drsq[i] = 1.0/(tb->rsq[i+1] - tb->rsq[i]);
- }
+ }
- // get the delta values for the last table entries
+ // get the delta values for the last table entries
// tables are connected periodically between 0 and ntablem1
-
+
tb->de[ntablem1] = tb->e[0] - tb->e[ntablem1];
tb->df[ntablem1] = tb->f[0] - tb->f[ntablem1];
tb->drsq[ntablem1] = 1.0/(tb->rsq[0] - tb->rsq[ntablem1]);
- // get the correct delta values at itablemax
+ // get the correct delta values at itablemax
// smallest r is in bin itablemin
// largest r is in bin itablemax, which is itablemin-1,
// or ntablem1 if itablemin=0
// deltas at itablemax only needed if corresponding rsq < cut*cut
- // if so, compute deltas between rsq and cut*cut
+ // if so, compute deltas between rsq and cut*cut
// if tb->match, data at cut*cut is unavailable, so we'll take
// deltas at itablemax-1 as a good approximation
-
+
double e_tmp,f_tmp;
int itablemin = minrsq_lookup.i & tb->nmask;
- itablemin >>= tb->nshiftbits;
- int itablemax = itablemin - 1;
- if (itablemin == 0) itablemax = ntablem1;
- int itablemaxm1 = itablemax - 1;
- if (itablemax == 0) itablemaxm1 = ntablem1;
+ itablemin >>= tb->nshiftbits;
+ int itablemax = itablemin - 1;
+ if (itablemin == 0) itablemax = ntablem1;
+ int itablemaxm1 = itablemax - 1;
+ if (itablemax == 0) itablemaxm1 = ntablem1;
rsq_lookup.i = itablemax << tb->nshiftbits;
- rsq_lookup.i |= maskhi;
+ rsq_lookup.i |= maskhi;
if (rsq_lookup.f < tb->cut*tb->cut) {
if (tb->match) {
tb->de[itablemax] = tb->de[itablemaxm1];
tb->df[itablemax] = tb->df[itablemaxm1];
tb->drsq[itablemax] = tb->drsq[itablemaxm1];
} else {
- rsq_lookup.f = tb->cut*tb->cut;
+ rsq_lookup.f = tb->cut*tb->cut;
r = sqrtf(rsq_lookup.f);
e_tmp = splint(tb->rfile,tb->efile,tb->e2file,tb->ninput,r);
f_tmp = splint(tb->rfile,tb->ffile,tb->f2file,tb->ninput,r)/r;
@@ -747,7 +747,7 @@ void PairTable::compute_table(Table *tb)
tb->drsq[itablemax] = 1.0/(rsq_lookup.f - tb->rsq[itablemax]);
}
}
- }
+ }
}
/* ----------------------------------------------------------------------
@@ -789,7 +789,7 @@ void PairTable::free_table(Table *tb)
------------------------------------------------------------------------- */
void PairTable::spline(double *x, double *y, int n,
- double yp1, double ypn, double *y2)
+ double yp1, double ypn, double *y2)
{
int i,k;
double p,qn,sig,un;
@@ -835,7 +835,7 @@ double PairTable::splint(double *xa, double *ya, double *y2a, int n, double x)
h = xa[khi]-xa[klo];
a = (xa[khi]-x) / h;
b = (x-xa[klo]) / h;
- y = a*ya[klo] + b*ya[khi] +
+ y = a*ya[klo] + b*ya[khi] +
((a*a*a-a)*y2a[klo] + (b*b*b-b)*y2a[khi]) * (h*h)/6.0;
return y;
}
@@ -886,8 +886,8 @@ void PairTable::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairTable::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
- double &fforce)
+ double factor_coul, double factor_lj,
+ double &fforce)
{
int itable;
double fraction,value,a,b,phi;
@@ -911,8 +911,8 @@ double PairTable::single(int i, int j, int itype, int jtype, double rsq,
if (itable >= tlm1) error->one(FLERR,"Pair distance > table outer cutoff");
b = (rsq - tb->rsq[itable]) * tb->invdelta;
a = 1.0 - b;
- value = a * tb->f[itable] + b * tb->f[itable+1] +
- ((a*a*a-a)*tb->f2[itable] + (b*b*b-b)*tb->f2[itable+1]) *
+ value = a * tb->f[itable] + b * tb->f[itable+1] +
+ ((a*a*a-a)*tb->f2[itable] + (b*b*b-b)*tb->f2[itable+1]) *
tb->deltasq6;
fforce = factor_lj * value;
} else {
@@ -930,7 +930,7 @@ double PairTable::single(int i, int j, int itype, int jtype, double rsq,
else if (tabstyle == LINEAR || tabstyle == BITMAP)
phi = tb->e[itable] + fraction*tb->de[itable];
else
- phi = a * tb->e[itable] + b * tb->e[itable+1] +
+ phi = a * tb->e[itable] + b * tb->e[itable+1] +
((a*a*a-a)*tb->e2[itable] + (b*b*b-b)*tb->e2[itable+1]) * tb->deltasq6;
return factor_lj*phi;
}
@@ -951,7 +951,7 @@ void *PairTable::extract(const char *str, int &dim)
for (int m = 1; m < ntables; m++)
if (tables[m].cut != cut_coul)
error->all(FLERR,
- "Pair table cutoffs must all be equal to use with KSpace");
+ "Pair table cutoffs must all be equal to use with KSpace");
dim = 0;
return &tables[0].cut;
}
diff --git a/src/pair_table.h b/src/pair_table.h
index ac5d28ec6c1f88bea021bfdbaa72e79b109054dc..09d81fb037b8e5f6827456b8face8e0101ccbada 100644
--- a/src/pair_table.h
+++ b/src/pair_table.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/pair_yukawa.cpp b/src/pair_yukawa.cpp
index f631fc44164994b5fcb8a4057e68b0d6b8158a1b..e7682dacb4ce2579108af13e8bffd1579656a3dc 100644
--- a/src/pair_yukawa.cpp
+++ b/src/pair_yukawa.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -66,7 +66,7 @@ void PairYukawa::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@@ -90,30 +90,30 @@ void PairYukawa::compute(int eflag, int vflag)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
- r = sqrt(rsq);
- rinv = 1.0/r;
- screening = exp(-kappa*r);
- forceyukawa = a[itype][jtype] * screening * (kappa + rinv);
-
- fpair = factor*forceyukawa * r2inv;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (eflag) {
- evdwl = a[itype][jtype] * screening * rinv - offset[itype][jtype];
- evdwl *= factor;
- }
-
- if (evflag) ev_tally(i,j,nlocal,newton_pair,
- evdwl,0.0,fpair,delx,dely,delz);
+ r2inv = 1.0/rsq;
+ r = sqrt(rsq);
+ rinv = 1.0/r;
+ screening = exp(-kappa*r);
+ forceyukawa = a[itype][jtype] * screening * (kappa + rinv);
+
+ fpair = factor*forceyukawa * r2inv;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (eflag) {
+ evdwl = a[itype][jtype] * screening * rinv - offset[itype][jtype];
+ evdwl *= factor;
+ }
+
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ evdwl,0.0,fpair,delx,dely,delz);
}
}
}
@@ -122,7 +122,7 @@ void PairYukawa::compute(int eflag, int vflag)
}
/* ----------------------------------------------------------------------
- allocate all arrays
+ allocate all arrays
------------------------------------------------------------------------- */
void PairYukawa::allocate()
@@ -144,7 +144,7 @@ void PairYukawa::allocate()
}
/* ----------------------------------------------------------------------
- global settings
+ global settings
------------------------------------------------------------------------- */
void PairYukawa::settings(int narg, char **arg)
@@ -160,7 +160,7 @@ void PairYukawa::settings(int narg, char **arg)
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
- if (setflag[i][j]) cut[i][j] = cut_global;
+ if (setflag[i][j]) cut[i][j] = cut_global;
}
}
@@ -170,7 +170,7 @@ void PairYukawa::settings(int narg, char **arg)
void PairYukawa::coeff(int narg, char **arg)
{
- if (narg < 3 || narg > 4)
+ if (narg < 3 || narg > 4)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
@@ -231,8 +231,8 @@ void PairYukawa::write_restart(FILE *fp)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
- fwrite(&a[i][j],sizeof(double),1,fp);
- fwrite(&cut[i][j],sizeof(double),1,fp);
+ fwrite(&a[i][j],sizeof(double),1,fp);
+ fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
@@ -254,12 +254,12 @@ void PairYukawa::read_restart(FILE *fp)
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
- if (me == 0) {
- fread(&a[i][j],sizeof(double),1,fp);
- fread(&cut[i][j],sizeof(double),1,fp);
- }
- MPI_Bcast(&a[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
+ if (me == 0) {
+ fread(&a[i][j],sizeof(double),1,fp);
+ fread(&cut[i][j],sizeof(double),1,fp);
+ }
+ MPI_Bcast(&a[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
@@ -297,8 +297,8 @@ void PairYukawa::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairYukawa::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
- double &fforce)
+ double factor_coul, double factor_lj,
+ double &fforce)
{
double r2inv,r,rinv,screening,forceyukawa,phi;
diff --git a/src/pair_yukawa.h b/src/pair_yukawa.h
index 2c07456c8f7f66683f0a48a9536cb497ba274b95..18b72790f5bb2e580a6493fce8f422e71ed85a15 100644
--- a/src/pair_yukawa.h
+++ b/src/pair_yukawa.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/pointers.h b/src/pointers.h
index 963561792fe6389a034c2178c643467ed07ab086..981b5ccd83e710c2151a8b86c52abc80eb34c242 100644
--- a/src/pointers.h
+++ b/src/pointers.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -36,7 +36,7 @@ namespace LAMMPS_NS {
class Pointers {
public:
- Pointers(LAMMPS *ptr) :
+ Pointers(LAMMPS *ptr) :
lmp(ptr),
memory(ptr->memory),
error(ptr->error),
diff --git a/src/procmap.cpp b/src/procmap.cpp
index b0bd120fa6710986203f42d608e87a340f0760a9..6703b08d25477d8dd87bb1fa4365e89b34217f11 100644
--- a/src/procmap.cpp
+++ b/src/procmap.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -40,8 +40,8 @@ ProcMap::ProcMap(LAMMPS *lmp) : Pointers(lmp) {}
------------------------------------------------------------------------- */
void ProcMap::onelevel_grid(int nprocs, int *user_procgrid, int *procgrid,
- int otherflag, int other_style,
- int *other_procgrid, int *other_coregrid)
+ int otherflag, int other_style,
+ int *other_procgrid, int *other_coregrid)
{
int **factors;
@@ -56,8 +56,8 @@ void ProcMap::onelevel_grid(int nprocs, int *user_procgrid, int *procgrid,
if (domain->dimension == 2) npossible = cull_2d(npossible,factors,3);
npossible = cull_user(npossible,factors,3,user_procgrid);
if (otherflag) npossible = cull_other(npossible,factors,3,
- other_style,other_procgrid,
- other_coregrid);
+ other_style,other_procgrid,
+ other_coregrid);
// user/other constraints make failure possible
@@ -78,15 +78,15 @@ void ProcMap::onelevel_grid(int nprocs, int *user_procgrid, int *procgrid,
------------------------------------------------------------------------- */
void ProcMap::twolevel_grid(int nprocs, int *user_procgrid, int *procgrid,
- int ncores, int *user_coregrid, int *coregrid,
- int otherflag, int other_style,
- int *other_procgrid, int *other_coregrid)
+ int ncores, int *user_coregrid, int *coregrid,
+ int otherflag, int other_style,
+ int *other_procgrid, int *other_coregrid)
{
int **nfactors,**cfactors,**factors;
- if (nprocs % ncores)
+ if (nprocs % ncores)
error->all(FLERR,"Processors twogrid requires proc count "
- "be a multiple of core count");
+ "be a multiple of core count");
// nfactors = list of all possible 3 factors of node count
// constrain by 2d
@@ -117,8 +117,8 @@ void ProcMap::twolevel_grid(int nprocs, int *user_procgrid, int *procgrid,
npossible = cull_user(npossible,factors,4,user_procgrid);
if (otherflag) npossible = cull_other(npossible,factors,4,
- other_style,other_procgrid,
- other_coregrid);
+ other_style,other_procgrid,
+ other_coregrid);
// user/other constraints make failure possible
@@ -147,7 +147,7 @@ void ProcMap::twolevel_grid(int nprocs, int *user_procgrid, int *procgrid,
------------------------------------------------------------------------- */
void ProcMap::numa_grid(int nprocs, int *user_procgrid, int *procgrid,
- int *numagrid)
+ int *numagrid)
{
// hardwire this for now
@@ -163,7 +163,7 @@ void ProcMap::numa_grid(int nprocs, int *user_procgrid, int *procgrid,
MPI_Allgather(node_name,MPI_MAX_PROCESSOR_NAME,MPI_CHAR,node_names,
MPI_MAX_PROCESSOR_NAME,MPI_CHAR,world);
std::string node_string = std::string(node_name);
-
+
// get number of procs per node
// NOTE: could do this without STL map
@@ -177,17 +177,17 @@ void ProcMap::numa_grid(int nprocs, int *user_procgrid, int *procgrid,
}
procs_per_node = name_map.begin()->second;
procs_per_numa = procs_per_node / numa_nodes;
-
+
delete [] node_names;
// error if any of these conditions met
-
+
if (nprocs % procs_per_numa || // total procs not a multiple of node
user_procgrid[0] > 1 || // user specified grid > 1 in any dim
user_procgrid[1] > 1 ||
user_procgrid[2] > 1)
error->all(FLERR,"Could not create numa grid of processors");
-
+
// user settings for the factorization per numa node
// currently not user settable
// if user specifies 1 for a proc grid dimension,
@@ -199,7 +199,7 @@ void ProcMap::numa_grid(int nprocs, int *user_procgrid, int *procgrid,
if (user_procgrid[0] == 1) user_numagrid[0] = 1;
if (user_procgrid[1] == 1) user_numagrid[1] = 1;
if (user_procgrid[2] == 1) user_numagrid[2] = 1;
-
+
// initial factorization within NUMA node
int **numafactors;
@@ -207,7 +207,7 @@ void ProcMap::numa_grid(int nprocs, int *user_procgrid, int *procgrid,
memory->create(numafactors,numapossible,3,"procmap:numafactors");
numapossible = factor(procs_per_numa,numafactors);
- if (domain->dimension == 2)
+ if (domain->dimension == 2)
numapossible = cull_2d(numapossible,numafactors,3);
numapossible = cull_user(numapossible,numafactors,3,user_numagrid);
@@ -232,7 +232,7 @@ void ProcMap::numa_grid(int nprocs, int *user_procgrid, int *procgrid,
memory->create(nodefactors,nodepossible,3,"procmap:nodefactors");
nodepossible = factor(node_count,nodefactors);
- if (domain->dimension == 2)
+ if (domain->dimension == 2)
nodepossible = cull_2d(nodepossible,nodefactors,3);
nodepossible = cull_user(nodepossible,nodefactors,3,user_nodegrid);
@@ -240,14 +240,14 @@ void ProcMap::numa_grid(int nprocs, int *user_procgrid, int *procgrid,
error->all(FLERR,"Could not create numa grid of processors");
best_factors(nodepossible,nodefactors,nodegrid,
- numagrid[0],numagrid[1],numagrid[2]);
-
+ numagrid[0],numagrid[1],numagrid[2]);
+
// repeat NUMA node factorization using subdomain sizes
// refines the factorization if the user specified the node layout
// NOTE: this will not re-enforce user-procgrid constraint will it?
best_factors(numapossible,numafactors,numagrid,
- nodegrid[0],nodegrid[1],nodegrid[2]);
+ nodegrid[0],nodegrid[1],nodegrid[2]);
memory->destroy(numafactors);
memory->destroy(nodefactors);
@@ -273,7 +273,7 @@ void ProcMap::numa_grid(int nprocs, int *user_procgrid, int *procgrid,
------------------------------------------------------------------------- */
void ProcMap::custom_grid(char *cfile, int nprocs,
- int *user_procgrid, int *procgrid)
+ int *user_procgrid, int *procgrid)
{
FILE *fp;
char line[MAXLINE];
@@ -286,7 +286,7 @@ void ProcMap::custom_grid(char *cfile, int nprocs,
if (fp == NULL) error->one(FLERR,"Cannot open custom file");
// skip header = blank and comment lines
-
+
char *ptr;
if (!fgets(line,MAXLINE,fp))
error->one(FLERR,"Unexpected end of custom file");
@@ -294,7 +294,7 @@ void ProcMap::custom_grid(char *cfile, int nprocs,
if (ptr = strchr(line,'#')) *ptr = '\0';
if (strspn(line," \t\n\r") != strlen(line)) break;
if (!fgets(line,MAXLINE,fp))
- error->one(FLERR,"Unexpected end of custom file");
+ error->one(FLERR,"Unexpected end of custom file");
}
}
@@ -320,9 +320,9 @@ void ProcMap::custom_grid(char *cfile, int nprocs,
if (me == 0) {
for (int i = 0; i < nprocs; i++) {
if (!fgets(line,MAXLINE,fp))
- error->one(FLERR,"Unexpected end of custom file");
+ error->one(FLERR,"Unexpected end of custom file");
sscanf(line,"%d %d %d %d",
- &cmap[i][0],&cmap[i][1],&cmap[i][2],&cmap[i][3]);
+ &cmap[i][0],&cmap[i][1],&cmap[i][2],&cmap[i][3]);
}
fclose(fp);
}
@@ -349,12 +349,12 @@ void ProcMap::custom_grid(char *cfile, int nprocs,
------------------------------------------------------------------------- */
void ProcMap::cart_map(int reorder, int *procgrid,
- int *myloc, int procneigh[3][2], int ***grid2proc)
+ int *myloc, int procneigh[3][2], int ***grid2proc)
{
int periods[3];
periods[0] = periods[1] = periods[2] = 1;
MPI_Comm cartesian;
-
+
MPI_Cart_create(world,3,procgrid,periods,reorder,&cartesian);
MPI_Cart_get(cartesian,3,procgrid,periods,myloc);
MPI_Cart_shift(cartesian,0,1,&procneigh[0][0],&procneigh[0][1]);
@@ -366,10 +366,10 @@ void ProcMap::cart_map(int reorder, int *procgrid,
for (i = 0; i < procgrid[0]; i++)
for (j = 0; j < procgrid[1]; j++)
for (k = 0; k < procgrid[2]; k++) {
- coords[0] = i; coords[1] = j; coords[2] = k;
- MPI_Cart_rank(cartesian,coords,&grid2proc[i][j][k]);
+ coords[0] = i; coords[1] = j; coords[2] = k;
+ MPI_Cart_rank(cartesian,coords,&grid2proc[i][j][k]);
}
-
+
MPI_Comm_free(&cartesian);
}
@@ -380,7 +380,7 @@ void ProcMap::cart_map(int reorder, int *procgrid,
------------------------------------------------------------------------- */
void ProcMap::cart_map(int reorder, int *procgrid, int ncores, int *coregrid,
- int *myloc, int procneigh[3][2], int ***grid2proc)
+ int *myloc, int procneigh[3][2], int ***grid2proc)
{
// setup NUMA params that numa_grid() sets up
@@ -405,7 +405,7 @@ void ProcMap::cart_map(int reorder, int *procgrid, int ncores, int *coregrid,
------------------------------------------------------------------------- */
void ProcMap::xyz_map(char *xyz, int *procgrid,
- int *myloc, int procneigh[3][2], int ***grid2proc)
+ int *myloc, int procneigh[3][2], int ***grid2proc)
{
int me;
MPI_Comm_rank(world,&me);
@@ -414,22 +414,22 @@ void ProcMap::xyz_map(char *xyz, int *procgrid,
for (i = 0; i < procgrid[0]; i++)
for (j = 0; j < procgrid[1]; j++)
for (k = 0; k < procgrid[2]; k++) {
- if (xyz[0] == 'x' && xyz[1] == 'y' && xyz[2] == 'z')
- grid2proc[i][j][k] = k*procgrid[1]*procgrid[0] + j*procgrid[0] + i;
- else if (xyz[0] == 'x' && xyz[1] == 'z' && xyz[2] == 'y')
- grid2proc[i][j][k] = j*procgrid[2]*procgrid[0] + k*procgrid[0] + i;
- else if (xyz[0] == 'y' && xyz[1] == 'x' && xyz[2] == 'z')
- grid2proc[i][j][k] = k*procgrid[0]*procgrid[1] + i*procgrid[1] + j;
- else if (xyz[0] == 'y' && xyz[1] == 'z' && xyz[2] == 'x')
- grid2proc[i][j][k] = i*procgrid[2]*procgrid[1] + k*procgrid[1] + j;
- else if (xyz[0] == 'z' && xyz[1] == 'x' && xyz[2] == 'y')
- grid2proc[i][j][k] = j*procgrid[0]*procgrid[2] + i*procgrid[2] + k;
- else if (xyz[0] == 'z' && xyz[1] == 'y' && xyz[2] == 'x')
- grid2proc[i][j][k] = i*procgrid[1]*procgrid[2] + j*procgrid[2] + k;
-
- if (grid2proc[i][j][k] == me) {
- myloc[0] = i; myloc[1] = j, myloc[2] = k;
- }
+ if (xyz[0] == 'x' && xyz[1] == 'y' && xyz[2] == 'z')
+ grid2proc[i][j][k] = k*procgrid[1]*procgrid[0] + j*procgrid[0] + i;
+ else if (xyz[0] == 'x' && xyz[1] == 'z' && xyz[2] == 'y')
+ grid2proc[i][j][k] = j*procgrid[2]*procgrid[0] + k*procgrid[0] + i;
+ else if (xyz[0] == 'y' && xyz[1] == 'x' && xyz[2] == 'z')
+ grid2proc[i][j][k] = k*procgrid[0]*procgrid[1] + i*procgrid[1] + j;
+ else if (xyz[0] == 'y' && xyz[1] == 'z' && xyz[2] == 'x')
+ grid2proc[i][j][k] = i*procgrid[2]*procgrid[1] + k*procgrid[1] + j;
+ else if (xyz[0] == 'z' && xyz[1] == 'x' && xyz[2] == 'y')
+ grid2proc[i][j][k] = j*procgrid[0]*procgrid[2] + i*procgrid[2] + k;
+ else if (xyz[0] == 'z' && xyz[1] == 'y' && xyz[2] == 'x')
+ grid2proc[i][j][k] = i*procgrid[1]*procgrid[2] + j*procgrid[2] + k;
+
+ if (grid2proc[i][j][k] == me) {
+ myloc[0] = i; myloc[1] = j, myloc[2] = k;
+ }
}
// proc IDs of neighbors
@@ -455,7 +455,7 @@ void ProcMap::xyz_map(char *xyz, int *procgrid,
------------------------------------------------------------------------- */
void ProcMap::xyz_map(char *xyz, int *procgrid, int ncores, int *coregrid,
- int *myloc, int procneigh[3][2], int ***grid2proc)
+ int *myloc, int procneigh[3][2], int ***grid2proc)
{
int me;
MPI_Comm_rank(world,&me);
@@ -468,41 +468,41 @@ void ProcMap::xyz_map(char *xyz, int *procgrid, int ncores, int *coregrid,
for (i = 0; i < procgrid[0]; i++)
for (j = 0; j < procgrid[1]; j++)
for (k = 0; k < procgrid[2]; k++) {
- inode = i/coregrid[0];
- jnode = j/coregrid[1];
- knode = k/coregrid[2];
- icore = i % coregrid[0];
- jcore = j % coregrid[1];
- kcore = k % coregrid[2];
-
- if (xyz[0] == 'x' && xyz[1] == 'y' && xyz[2] == 'z') {
- grid2proc[i][j][k] = ncores *
- (knode*nodegrid[1]*nodegrid[0] + jnode*nodegrid[0] + inode) +
- (kcore*coregrid[1]*coregrid[0] + jcore*coregrid[0] + icore);
- } else if (xyz[0] == 'x' && xyz[1] == 'z' && xyz[2] == 'y')
- grid2proc[i][j][k] = ncores *
- (jnode*nodegrid[2]*nodegrid[0] + knode*nodegrid[0] + inode) +
- (jcore*coregrid[2]*coregrid[0] + kcore*coregrid[0] + icore);
- else if (xyz[0] == 'y' && xyz[1] == 'x' && xyz[2] == 'z')
- grid2proc[i][j][k] = ncores *
- (knode*nodegrid[0]*nodegrid[1] + inode*nodegrid[1] + jnode) +
- (kcore*coregrid[0]*coregrid[1] + icore*coregrid[1] + jcore);
- else if (xyz[0] == 'y' && xyz[1] == 'z' && xyz[2] == 'x')
- grid2proc[i][j][k] = ncores *
- (inode*nodegrid[2]*nodegrid[1] + knode*nodegrid[1] + jnode) +
- (icore*coregrid[2]*coregrid[1] + kcore*coregrid[1] + jcore);
- else if (xyz[0] == 'z' && xyz[1] == 'x' && xyz[2] == 'y')
- grid2proc[i][j][k] = ncores *
- (jnode*nodegrid[0]*nodegrid[2] + inode*nodegrid[2] + knode) +
- (jcore*coregrid[0]*coregrid[2] + icore*coregrid[2] + kcore);
- else if (xyz[0] == 'z' && xyz[1] == 'y' && xyz[2] == 'x')
- grid2proc[i][j][k] = ncores *
- (inode*nodegrid[1]*nodegrid[2] + jnode*nodegrid[2] + knode) +
- (icore*coregrid[1]*coregrid[2] + jcore*coregrid[2] + kcore);
-
- if (grid2proc[i][j][k] == me) {
- myloc[0] = i; myloc[1] = j, myloc[2] = k;
- }
+ inode = i/coregrid[0];
+ jnode = j/coregrid[1];
+ knode = k/coregrid[2];
+ icore = i % coregrid[0];
+ jcore = j % coregrid[1];
+ kcore = k % coregrid[2];
+
+ if (xyz[0] == 'x' && xyz[1] == 'y' && xyz[2] == 'z') {
+ grid2proc[i][j][k] = ncores *
+ (knode*nodegrid[1]*nodegrid[0] + jnode*nodegrid[0] + inode) +
+ (kcore*coregrid[1]*coregrid[0] + jcore*coregrid[0] + icore);
+ } else if (xyz[0] == 'x' && xyz[1] == 'z' && xyz[2] == 'y')
+ grid2proc[i][j][k] = ncores *
+ (jnode*nodegrid[2]*nodegrid[0] + knode*nodegrid[0] + inode) +
+ (jcore*coregrid[2]*coregrid[0] + kcore*coregrid[0] + icore);
+ else if (xyz[0] == 'y' && xyz[1] == 'x' && xyz[2] == 'z')
+ grid2proc[i][j][k] = ncores *
+ (knode*nodegrid[0]*nodegrid[1] + inode*nodegrid[1] + jnode) +
+ (kcore*coregrid[0]*coregrid[1] + icore*coregrid[1] + jcore);
+ else if (xyz[0] == 'y' && xyz[1] == 'z' && xyz[2] == 'x')
+ grid2proc[i][j][k] = ncores *
+ (inode*nodegrid[2]*nodegrid[1] + knode*nodegrid[1] + jnode) +
+ (icore*coregrid[2]*coregrid[1] + kcore*coregrid[1] + jcore);
+ else if (xyz[0] == 'z' && xyz[1] == 'x' && xyz[2] == 'y')
+ grid2proc[i][j][k] = ncores *
+ (jnode*nodegrid[0]*nodegrid[2] + inode*nodegrid[2] + knode) +
+ (jcore*coregrid[0]*coregrid[2] + icore*coregrid[2] + kcore);
+ else if (xyz[0] == 'z' && xyz[1] == 'y' && xyz[2] == 'x')
+ grid2proc[i][j][k] = ncores *
+ (inode*nodegrid[1]*nodegrid[2] + jnode*nodegrid[2] + knode) +
+ (icore*coregrid[1]*coregrid[2] + jcore*coregrid[2] + kcore);
+
+ if (grid2proc[i][j][k] == me) {
+ myloc[0] = i; myloc[1] = j, myloc[2] = k;
+ }
}
// proc IDs of neighbors
@@ -526,28 +526,28 @@ void ProcMap::xyz_map(char *xyz, int *procgrid, int ncores, int *coregrid,
------------------------------------------------------------------------- */
void ProcMap::numa_map(int reorder, int *numagrid,
- int *myloc, int procneigh[3][2], int ***grid2proc)
+ int *myloc, int procneigh[3][2], int ***grid2proc)
{
// setup a per node communicator and find rank within
MPI_Comm node_comm;
- MPI_Comm_split(world,node_id,0,&node_comm);
+ MPI_Comm_split(world,node_id,0,&node_comm);
int node_rank;
MPI_Comm_rank(node_comm,&node_rank);
-
+
// setup a per numa communicator and find rank within
MPI_Comm numa_comm;
int local_numa = node_rank / procs_per_numa;
- MPI_Comm_split(node_comm,local_numa,0,&numa_comm);
+ MPI_Comm_split(node_comm,local_numa,0,&numa_comm);
int numa_rank;
MPI_Comm_rank(numa_comm,&numa_rank);
-
+
// setup a communicator with the rank 0 procs from each numa node
MPI_Comm numa_leaders;
MPI_Comm_split(world,numa_rank,0,&numa_leaders);
-
+
// use the MPI Cartesian routines to map the nodes to the grid
int periods[3];
@@ -557,11 +557,11 @@ void ProcMap::numa_map(int reorder, int *numagrid,
MPI_Cart_create(numa_leaders,3,nodegrid,periods,reorder,&cartesian);
MPI_Cart_get(cartesian,3,nodegrid,periods,myloc);
}
-
+
// broadcast numa node location in grid to other procs in numa node
MPI_Bcast(myloc,3,MPI_INT,0,numa_comm);
-
+
// compute my location within the node grid
int z_offset = numa_rank / (numagrid[0] * numagrid[1]);
@@ -570,7 +570,7 @@ void ProcMap::numa_map(int reorder, int *numagrid,
myloc[0] = myloc[0] * numagrid[0] + x_offset;
myloc[1] = myloc[1] * numagrid[1] + y_offset;
myloc[2] = myloc[2] * numagrid[2] + z_offset;
-
+
// allgather of myloc into gridi to fill grid2proc
int nprocs;
@@ -582,7 +582,7 @@ void ProcMap::numa_map(int reorder, int *numagrid,
for (int i = 0; i < nprocs; i++)
grid2proc[gridi[i][0]][gridi[i][1]][gridi[i][2]] = i;
memory->destroy(gridi);
-
+
// proc IDs of neighbors
int minus,plus;
@@ -611,7 +611,7 @@ void ProcMap::numa_map(int reorder, int *numagrid,
------------------------------------------------------------------------- */
void ProcMap::custom_map(int *procgrid,
- int *myloc, int procneigh[3][2], int ***grid2proc)
+ int *myloc, int procneigh[3][2], int ***grid2proc)
{
int me,nprocs;
MPI_Comm_rank(world,&me);
@@ -670,9 +670,9 @@ void ProcMap::output(char *file, int *procgrid, int ***grid2proc)
for (int i = 0; i < procgrid[0]; i++)
for (int j = 0; j < procgrid[1]; j++)
for (int k = 0; k < procgrid[2]; k++)
- if (grid2proc[i][j][k] == me) {
- ime = i; jme = j; kme = k;
- }
+ if (grid2proc[i][j][k] == me) {
+ ime = i; jme = j; kme = k;
+ }
// polled comm of grid mapping info from each proc to proc 0
@@ -695,16 +695,16 @@ void ProcMap::output(char *file, int *procgrid, int ***grid2proc)
if (me == 0) {
for (int iproc = 0; iproc < nprocs; iproc++) {
if (iproc) {
- MPI_Send(&tmp,0,MPI_INT,iproc,0,world);
- MPI_Recv(vec,6,MPI_INT,iproc,0,world,&status);
- MPI_Recv(procname,MPI_MAX_PROCESSOR_NAME+1,MPI_CHAR,
- iproc,0,world,&status);
+ MPI_Send(&tmp,0,MPI_INT,iproc,0,world);
+ MPI_Recv(vec,6,MPI_INT,iproc,0,world,&status);
+ MPI_Recv(procname,MPI_MAX_PROCESSOR_NAME+1,MPI_CHAR,
+ iproc,0,world,&status);
}
fprintf(fp,"%d %d %d: %d %d %d: %s\n",
- vec[0],vec[1],vec[2],vec[3],vec[4],vec[5],procname);
+ vec[0],vec[1],vec[2],vec[3],vec[4],vec[5],procname);
}
-
+
} else {
MPI_Recv(&tmp,0,MPI_INT,0,0,world,&status);
MPI_Send(vec,6,MPI_INT,0,0,world);
@@ -733,9 +733,9 @@ int ProcMap::factor(int n, int **factors)
for (j = 1; j <= nyz; j++) {
if (nyz % j) continue;
if (factors) {
- factors[m][0] = i;
- factors[m][1] = j;
- factors[m][2] = nyz/j;
+ factors[m][0] = i;
+ factors[m][1] = j;
+ factors[m][2] = nyz/j;
}
m++;
}
@@ -750,7 +750,7 @@ int ProcMap::factor(int n, int **factors)
------------------------------------------------------------------------- */
int ProcMap::combine_factors(int n1, int **factors1, int n2, int **factors2,
- int **factors)
+ int **factors)
{
int m = 0;
for (int i = 0; i < n1; i++)
@@ -806,9 +806,9 @@ int ProcMap::cull_user(int n, int **factors, int m, int *user_factors)
where Nx,Ny,Nz = node grid = procgrid/coregrid
------------------------------------------------------------------------- */
-int ProcMap::cull_other(int n, int **factors, int m,
- int other_style, int *other_procgrid,
- int *other_coregrid)
+int ProcMap::cull_other(int n, int **factors, int m,
+ int other_style, int *other_procgrid,
+ int *other_coregrid)
{
int i = 0;
while (i < n) {
@@ -818,8 +818,8 @@ int ProcMap::cull_other(int n, int **factors, int m,
if ((other_procgrid[1]/other_coregrid[1]) % factors[i][1]) flag = 1;
if ((other_procgrid[2]/other_coregrid[2]) % factors[i][2]) flag = 1;
if (flag) {
- for (int j = 0; j < m; j++) factors[i][j] = factors[n-1][j];
- n--;
+ for (int j = 0; j < m; j++) factors[i][j] = factors[n-1][j];
+ n--;
} else i++;
}
}
@@ -834,13 +834,13 @@ int ProcMap::cull_other(int n, int **factors, int m,
------------------------------------------------------------------------- */
int ProcMap::best_factors(int npossible, int **factors, int *best,
- const int sx, const int sy, const int sz)
+ const int sx, const int sy, const int sz)
{
// determine cross-sectional areas for orthogonal and triclinic boxes
// for triclinic, area = cross product of 2 edge vectors stored in h matrix
// area[3] = surface area 3 box faces divided by sx,sy,sz
// area[0] = xy, area[1] = xz, area[2] = yz
-
+
double area[3];
if (domain->triclinic == 0) {
area[0] = domain->xprd * domain->yprd / (sx*sy);
@@ -868,8 +868,8 @@ int ProcMap::best_factors(int npossible, int **factors, int *best,
double bestsurf = 2.0 * (area[0]+area[1]+area[2]);
for (int m = 0; m < npossible; m++) {
- surf = area[0]/factors[m][0]/factors[m][1] +
- area[1]/factors[m][0]/factors[m][2] +
+ surf = area[0]/factors[m][0]/factors[m][1] +
+ area[1]/factors[m][0]/factors[m][2] +
area[2]/factors[m][1]/factors[m][2];
if (surf < bestsurf) {
bestsurf = surf;
@@ -887,11 +887,10 @@ int ProcMap::best_factors(int npossible, int **factors, int *best,
minus,plus = indices of neighboring processors in a dimension
------------------------------------------------------------------------- */
-void ProcMap::grid_shift(int myloc, int nprocs, int &minus, int &plus)
+void ProcMap::grid_shift(int myloc, int nprocs, int &minus, int &plus)
{
minus = myloc - 1;
if (minus < 0) minus = nprocs - 1;
plus = myloc + 1;
if (plus == nprocs) plus = 0;
}
-
diff --git a/src/procmap.h b/src/procmap.h
index d8376040dfd067dabd39594b0ae8e153859347c2..c7e3c02fbc397e2c0e8d80de13d81a482845dea1 100644
--- a/src/procmap.h
+++ b/src/procmap.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -23,8 +23,8 @@ class ProcMap : protected Pointers {
ProcMap(class LAMMPS *);
~ProcMap() {}
void onelevel_grid(int, int *, int *, int, int, int *, int *);
- void twolevel_grid(int, int *, int *, int, int *, int *, int, int,
- int *, int *);
+ void twolevel_grid(int, int *, int *, int, int *, int *, int, int,
+ int *, int *);
void numa_grid(int, int *, int *, int *);
void custom_grid(char *, int, int *, int *);
void cart_map(int, int *, int *, int [3][2], int ***);
diff --git a/src/random_mars.cpp b/src/random_mars.cpp
index 0dd5990362a7fda0d3c9663a9977bf804999a9d6..387cf6a781f7e7c636f79724e71809aec6bd90dc 100644
--- a/src/random_mars.cpp
+++ b/src/random_mars.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -68,7 +68,7 @@ RanMars::~RanMars()
}
/* ----------------------------------------------------------------------
- uniform RN
+ uniform RN
------------------------------------------------------------------------- */
double RanMars::uniform()
@@ -88,7 +88,7 @@ double RanMars::uniform()
}
/* ----------------------------------------------------------------------
- gaussian RN
+ gaussian RN
------------------------------------------------------------------------- */
double RanMars::gaussian()
diff --git a/src/random_mars.h b/src/random_mars.h
index 6c183bcc5fbf75f4267e210a5b46b1fb2341f008..b31999f68cc540da4aa93d35a57bb1bb6ea539a5 100644
--- a/src/random_mars.h
+++ b/src/random_mars.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/random_park.cpp b/src/random_park.cpp
index bc46cde4f377696a503a039530b0cf7fea9bfab2..8e1c88a2462f1ce645297d7c591f737ff5dd0393 100644
--- a/src/random_park.cpp
+++ b/src/random_park.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -36,7 +36,7 @@ RanPark::RanPark(LAMMPS *lmp, int seed_init) : Pointers(lmp)
}
/* ----------------------------------------------------------------------
- uniform RN
+ uniform RN
------------------------------------------------------------------------- */
double RanPark::uniform()
@@ -49,7 +49,7 @@ double RanPark::uniform()
}
/* ----------------------------------------------------------------------
- gaussian RN
+ gaussian RN
------------------------------------------------------------------------- */
double RanPark::gaussian()
diff --git a/src/random_park.h b/src/random_park.h
index 7b17184983aed0b7b8c3b28f1e3c3a135fbcec02..d43fbe10be6975f59b620de8b9963bf0dc596d37 100644
--- a/src/random_park.h
+++ b/src/random_park.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/read_data.cpp b/src/read_data.cpp
index ded09669a0faffa1a86ddd4e88d9f970052fae60..23c423c706f5ad65e2e88aa95e29de85b83e6c0c 100644
--- a/src/read_data.cpp
+++ b/src/read_data.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -86,7 +86,7 @@ void ReadData::command(int narg, char **arg)
{
if (narg < 1) error->all(FLERR,"Illegal read_data command");
- if (domain->box_exist)
+ if (domain->box_exist)
error->all(FLERR,"Cannot read_data after simulation box is defined");
if (domain->dimension == 2 && domain->zperiodic == 0)
error->all(FLERR,"Cannot run 2d simulation with nonperiodic Z dimension");
@@ -102,17 +102,17 @@ void ReadData::command(int narg, char **arg)
while (iarg < narg) {
if (strcmp(arg[iarg],"fix") == 0) {
if (iarg+4 > narg)
- error->all(FLERR,"Illegal read_data command");
+ error->all(FLERR,"Illegal read_data command");
memory->grow(fix_index,nfix+1,"read_data:fix_index");
- fix_header = (char **)
- memory->srealloc(fix_header,(nfix+1)*sizeof(char *),
- "read_data:fix_header");
- fix_section = (char **)
- memory->srealloc(fix_section,(nfix+1)*sizeof(char *),
- "read_data:fix_section");
+ fix_header = (char **)
+ memory->srealloc(fix_header,(nfix+1)*sizeof(char *),
+ "read_data:fix_header");
+ fix_section = (char **)
+ memory->srealloc(fix_section,(nfix+1)*sizeof(char *),
+ "read_data:fix_section");
fix_index[nfix] = modify->find_fix(arg[iarg+1]);
- if (fix_index[nfix] < 0)
- error->all(FLERR,"Fix ID for Read_data does not exist");
+ if (fix_index[nfix] < 0)
+ error->all(FLERR,"Fix ID for Read_data does not exist");
int n = strlen(arg[iarg+2]) + 1;
fix_header[nfix] = new char[n];
strcpy(fix_header[nfix],arg[iarg+2]);
@@ -124,7 +124,7 @@ void ReadData::command(int narg, char **arg)
} else error->all(FLERR,"Illegal read_data command");
}
- // scan data file to determine max topology needed per atom
+ // scan data file to determine max topology needed per atom
// allocate initial topology arrays
if (atom->molecular) {
@@ -133,7 +133,7 @@ void ReadData::command(int narg, char **arg)
open(arg[0]);
header(0);
scan(atom->bond_per_atom,atom->angle_per_atom,
- atom->dihedral_per_atom,atom->improper_per_atom);
+ atom->dihedral_per_atom,atom->improper_per_atom);
if (compressed) pclose(fp);
else fclose(fp);
atom->bond_per_atom += atom->extra_bond_per_atom;
@@ -187,13 +187,13 @@ void ReadData::command(int narg, char **arg)
if (nfix) {
for (n = 0; n < nfix; n++)
- if (strstr(line,fix_section[n])) {
- bigint nlines =
- modify->fix[fix_index[n]]->read_data_skip_lines(keyword);
- fix(n,keyword,nlines);
- parse_keyword(0,1);
- break;
- }
+ if (strstr(line,fix_section[n])) {
+ bigint nlines =
+ modify->fix[fix_index[n]]->read_data_skip_lines(keyword);
+ fix(n,keyword,nlines);
+ parse_keyword(0,1);
+ break;
+ }
if (n < nfix) continue;
}
@@ -205,128 +205,128 @@ void ReadData::command(int narg, char **arg)
velocities();
} else if (strcmp(keyword,"Ellipsoids") == 0) {
- if (!avec_ellipsoid)
- error->all(FLERR,"Invalid data file section: Ellipsoids");
+ if (!avec_ellipsoid)
+ error->all(FLERR,"Invalid data file section: Ellipsoids");
if (atomflag == 0) error->all(FLERR,"Must read Atoms before Ellipsoids");
bonus(nellipsoids,(AtomVec *) avec_ellipsoid,"ellipsoids");
} else if (strcmp(keyword,"Lines") == 0) {
- if (!avec_line)
- error->all(FLERR,"Invalid data file section: Lines");
+ if (!avec_line)
+ error->all(FLERR,"Invalid data file section: Lines");
if (atomflag == 0) error->all(FLERR,"Must read Atoms before Lines");
bonus(nlines,(AtomVec *) avec_line,"lines");
} else if (strcmp(keyword,"Triangles") == 0) {
- if (!avec_tri)
- error->all(FLERR,"Invalid data file section: Triangles");
+ if (!avec_tri)
+ error->all(FLERR,"Invalid data file section: Triangles");
if (atomflag == 0) error->all(FLERR,"Must read Atoms before Triangles");
bonus(ntris,(AtomVec *) avec_tri,"triangles");
} else if (strcmp(keyword,"Bonds") == 0) {
- if (atom->avec->bonds_allow == 0)
- error->all(FLERR,"Invalid data file section: Bonds");
+ if (atom->avec->bonds_allow == 0)
+ error->all(FLERR,"Invalid data file section: Bonds");
if (atomflag == 0) error->all(FLERR,"Must read Atoms before Bonds");
bonds();
} else if (strcmp(keyword,"Angles") == 0) {
if (atom->avec->angles_allow == 0)
- error->all(FLERR,"Invalid data file section: Angles");
+ error->all(FLERR,"Invalid data file section: Angles");
if (atomflag == 0) error->all(FLERR,"Must read Atoms before Angles");
angles();
} else if (strcmp(keyword,"Dihedrals") == 0) {
if (atom->avec->dihedrals_allow == 0)
- error->all(FLERR,"Invalid data file section: Dihedrals");
+ error->all(FLERR,"Invalid data file section: Dihedrals");
if (atomflag == 0) error->all(FLERR,"Must read Atoms before Dihedrals");
dihedrals();
} else if (strcmp(keyword,"Impropers") == 0) {
- if (atom->avec->impropers_allow == 0)
- error->all(FLERR,"Invalid data file section: Impropers");
+ if (atom->avec->impropers_allow == 0)
+ error->all(FLERR,"Invalid data file section: Impropers");
if (atomflag == 0) error->all(FLERR,"Must read Atoms before Impropers");
impropers();
} else if (strcmp(keyword,"Masses") == 0) {
mass();
} else if (strcmp(keyword,"Pair Coeffs") == 0) {
- if (force->pair == NULL)
- error->all(FLERR,"Must define pair_style before Pair Coeffs");
+ if (force->pair == NULL)
+ error->all(FLERR,"Must define pair_style before Pair Coeffs");
paircoeffs();
} else if (strcmp(keyword,"Bond Coeffs") == 0) {
- if (atom->avec->bonds_allow == 0)
- error->all(FLERR,"Invalid data file section: Bond Coeffs");
- if (force->bond == NULL)
- error->all(FLERR,"Must define bond_style before Bond Coeffs");
+ if (atom->avec->bonds_allow == 0)
+ error->all(FLERR,"Invalid data file section: Bond Coeffs");
+ if (force->bond == NULL)
+ error->all(FLERR,"Must define bond_style before Bond Coeffs");
bondcoeffs();
} else if (strcmp(keyword,"Angle Coeffs") == 0) {
- if (atom->avec->angles_allow == 0)
- error->all(FLERR,"Invalid data file section: Angle Coeffs");
- if (force->angle == NULL)
- error->all(FLERR,"Must define angle_style before Angle Coeffs");
+ if (atom->avec->angles_allow == 0)
+ error->all(FLERR,"Invalid data file section: Angle Coeffs");
+ if (force->angle == NULL)
+ error->all(FLERR,"Must define angle_style before Angle Coeffs");
anglecoeffs(0);
} else if (strcmp(keyword,"Dihedral Coeffs") == 0) {
- if (atom->avec->dihedrals_allow == 0)
- error->all(FLERR,"Invalid data file section: Dihedral Coeffs");
- if (force->dihedral == NULL)
- error->all(FLERR,"Must define dihedral_style before Dihedral Coeffs");
+ if (atom->avec->dihedrals_allow == 0)
+ error->all(FLERR,"Invalid data file section: Dihedral Coeffs");
+ if (force->dihedral == NULL)
+ error->all(FLERR,"Must define dihedral_style before Dihedral Coeffs");
dihedralcoeffs(0);
} else if (strcmp(keyword,"Improper Coeffs") == 0) {
- if (atom->avec->impropers_allow == 0)
- error->all(FLERR,"Invalid data file section: Improper Coeffs");
- if (force->improper == NULL)
- error->all(FLERR,"Must define improper_style before Improper Coeffs");
+ if (atom->avec->impropers_allow == 0)
+ error->all(FLERR,"Invalid data file section: Improper Coeffs");
+ if (force->improper == NULL)
+ error->all(FLERR,"Must define improper_style before Improper Coeffs");
impropercoeffs(0);
} else if (strcmp(keyword,"BondBond Coeffs") == 0) {
- if (atom->avec->angles_allow == 0)
- error->all(FLERR,"Invalid data file section: BondBond Coeffs");
- if (force->angle == NULL)
- error->all(FLERR,"Must define angle_style before BondBond Coeffs");
+ if (atom->avec->angles_allow == 0)
+ error->all(FLERR,"Invalid data file section: BondBond Coeffs");
+ if (force->angle == NULL)
+ error->all(FLERR,"Must define angle_style before BondBond Coeffs");
anglecoeffs(1);
} else if (strcmp(keyword,"BondAngle Coeffs") == 0) {
- if (atom->avec->angles_allow == 0)
- error->all(FLERR,"Invalid data file section: BondAngle Coeffs");
- if (force->angle == NULL)
- error->all(FLERR,"Must define angle_style before BondAngle Coeffs");
+ if (atom->avec->angles_allow == 0)
+ error->all(FLERR,"Invalid data file section: BondAngle Coeffs");
+ if (force->angle == NULL)
+ error->all(FLERR,"Must define angle_style before BondAngle Coeffs");
anglecoeffs(2);
} else if (strcmp(keyword,"MiddleBondTorsion Coeffs") == 0) {
- if (atom->avec->dihedrals_allow == 0)
- error->all(FLERR,"Invalid data file section: MiddleBondTorsion Coeffs");
- if (force->dihedral == NULL)
- error->all(FLERR,
- "Must define dihedral_style before "
- "MiddleBondTorsion Coeffs");
+ if (atom->avec->dihedrals_allow == 0)
+ error->all(FLERR,"Invalid data file section: MiddleBondTorsion Coeffs");
+ if (force->dihedral == NULL)
+ error->all(FLERR,
+ "Must define dihedral_style before "
+ "MiddleBondTorsion Coeffs");
dihedralcoeffs(1);
} else if (strcmp(keyword,"EndBondTorsion Coeffs") == 0) {
- if (atom->avec->dihedrals_allow == 0)
- error->all(FLERR,"Invalid data file section: EndBondTorsion Coeffs");
- if (force->dihedral == NULL)
- error->all(FLERR,
- "Must define dihedral_style before EndBondTorsion Coeffs");
+ if (atom->avec->dihedrals_allow == 0)
+ error->all(FLERR,"Invalid data file section: EndBondTorsion Coeffs");
+ if (force->dihedral == NULL)
+ error->all(FLERR,
+ "Must define dihedral_style before EndBondTorsion Coeffs");
dihedralcoeffs(2);
} else if (strcmp(keyword,"AngleTorsion Coeffs") == 0) {
- if (atom->avec->dihedrals_allow == 0)
- error->all(FLERR,"Invalid data file section: AngleTorsion Coeffs");
- if (force->dihedral == NULL)
- error->all(FLERR,
- "Must define dihedral_style before AngleTorsion Coeffs");
+ if (atom->avec->dihedrals_allow == 0)
+ error->all(FLERR,"Invalid data file section: AngleTorsion Coeffs");
+ if (force->dihedral == NULL)
+ error->all(FLERR,
+ "Must define dihedral_style before AngleTorsion Coeffs");
dihedralcoeffs(3);
} else if (strcmp(keyword,"AngleAngleTorsion Coeffs") == 0) {
- if (atom->avec->dihedrals_allow == 0)
- error->all(FLERR,"Invalid data file section: AngleAngleTorsion Coeffs");
- if (force->dihedral == NULL)
- error->all(FLERR,
- "Must define dihedral_style before "
- "AngleAngleTorsion Coeffs");
+ if (atom->avec->dihedrals_allow == 0)
+ error->all(FLERR,"Invalid data file section: AngleAngleTorsion Coeffs");
+ if (force->dihedral == NULL)
+ error->all(FLERR,
+ "Must define dihedral_style before "
+ "AngleAngleTorsion Coeffs");
dihedralcoeffs(4);
} else if (strcmp(keyword,"BondBond13 Coeffs") == 0) {
- if (atom->avec->dihedrals_allow == 0)
- error->all(FLERR,"Invalid data file section: BondBond13 Coeffs");
- if (force->dihedral == NULL)
- error->all(FLERR,"Must define dihedral_style before BondBond13 Coeffs");
+ if (atom->avec->dihedrals_allow == 0)
+ error->all(FLERR,"Invalid data file section: BondBond13 Coeffs");
+ if (force->dihedral == NULL)
+ error->all(FLERR,"Must define dihedral_style before BondBond13 Coeffs");
dihedralcoeffs(5);
} else if (strcmp(keyword,"AngleAngle Coeffs") == 0) {
- if (atom->avec->impropers_allow == 0)
- error->all(FLERR,"Invalid data file section: AngleAngle Coeffs");
- if (force->improper == NULL)
- error->all(FLERR,"Must define improper_style before AngleAngle Coeffs");
+ if (atom->avec->impropers_allow == 0)
+ error->all(FLERR,"Invalid data file section: AngleAngle Coeffs");
+ if (force->improper == NULL)
+ error->all(FLERR,"Must define improper_style before AngleAngle Coeffs");
impropercoeffs(1);
} else {
@@ -344,10 +344,10 @@ void ReadData::command(int narg, char **arg)
if (compressed) pclose(fp);
else fclose(fp);
}
-
+
// error if natoms > 0 yet no atoms were read
- if (atom->natoms > 0 && atomflag == 0)
+ if (atom->natoms > 0 && atomflag == 0)
error->all(FLERR,"No atoms in data file");
// create bond topology now that system is defined
@@ -376,7 +376,7 @@ void ReadData::header(int flag)
// customize for new sections
- const char *section_keywords[NSECTIONS] =
+ const char *section_keywords[NSECTIONS] =
{"Atoms","Velocities","Ellipsoids","Lines","Triangles",
"Bonds","Angles","Dihedrals","Impropers",
"Masses","Pair Coeffs","Bond Coeffs","Angle Coeffs",
@@ -426,10 +426,10 @@ void ReadData::header(int flag)
if (nfix) {
for (n = 0; n < nfix; n++)
- if (strstr(line,fix_header[n])) {
- modify->fix[fix_index[n]]->read_data_header(line);
- break;
- }
+ if (strstr(line,fix_header[n])) {
+ modify->fix[fix_index[n]]->read_data_header(line);
+ break;
+ }
if (n < nfix) continue;
}
@@ -442,41 +442,41 @@ void ReadData::header(int flag)
else if (strstr(line,"ellipsoids")) {
if (!avec_ellipsoid && me == 0)
- error->one(FLERR,"No ellipsoids allowed with this atom style");
+ error->one(FLERR,"No ellipsoids allowed with this atom style");
sscanf(line,BIGINT_FORMAT,&nellipsoids);
} else if (strstr(line,"lines")) {
if (!avec_line && me == 0)
- error->one(FLERR,"No lines allowed with this atom style");
+ error->one(FLERR,"No lines allowed with this atom style");
sscanf(line,BIGINT_FORMAT,&nlines);
} else if (strstr(line,"triangles")) {
if (!avec_tri && me == 0)
- error->one(FLERR,"No triangles allowed with this atom style");
+ error->one(FLERR,"No triangles allowed with this atom style");
sscanf(line,BIGINT_FORMAT,&ntris);
}
else if (strstr(line,"bonds")) sscanf(line,BIGINT_FORMAT,&atom->nbonds);
else if (strstr(line,"angles")) sscanf(line,BIGINT_FORMAT,&atom->nangles);
else if (strstr(line,"dihedrals")) sscanf(line,BIGINT_FORMAT,
- &atom->ndihedrals);
+ &atom->ndihedrals);
else if (strstr(line,"impropers")) sscanf(line,BIGINT_FORMAT,
- &atom->nimpropers);
+ &atom->nimpropers);
else if (strstr(line,"atom types")) sscanf(line,"%d",&atom->ntypes);
else if (strstr(line,"bond types")) sscanf(line,"%d",&atom->nbondtypes);
else if (strstr(line,"angle types")) sscanf(line,"%d",&atom->nangletypes);
- else if (strstr(line,"dihedral types"))
+ else if (strstr(line,"dihedral types"))
sscanf(line,"%d",&atom->ndihedraltypes);
- else if (strstr(line,"improper types"))
+ else if (strstr(line,"improper types"))
sscanf(line,"%d",&atom->nimpropertypes);
else if (strstr(line,"extra bond per atom"))
sscanf(line,"%d",&atom->extra_bond_per_atom);
- else if (strstr(line,"xlo xhi"))
+ else if (strstr(line,"xlo xhi"))
sscanf(line,"%lg %lg",&domain->boxlo[0],&domain->boxhi[0]);
- else if (strstr(line,"ylo yhi"))
+ else if (strstr(line,"ylo yhi"))
sscanf(line,"%lg %lg",&domain->boxlo[1],&domain->boxhi[1]);
- else if (strstr(line,"zlo zhi"))
+ else if (strstr(line,"zlo zhi"))
sscanf(line,"%lg %lg",&domain->boxlo[2],&domain->boxhi[2]);
else if (strstr(line,"xy xz yz")) {
domain->triclinic = 1;
@@ -507,16 +507,16 @@ void ReadData::header(int flag)
// error check on consistency of header values
- if ((atom->nbonds || atom->nbondtypes) &&
+ if ((atom->nbonds || atom->nbondtypes) &&
atom->avec->bonds_allow == 0 && me == 0)
error->one(FLERR,"No bonds allowed with this atom style");
- if ((atom->nangles || atom->nangletypes) &&
+ if ((atom->nangles || atom->nangletypes) &&
atom->avec->angles_allow == 0 && me == 0)
error->one(FLERR,"No angles allowed with this atom style");
- if ((atom->ndihedrals || atom->ndihedraltypes) &&
+ if ((atom->ndihedrals || atom->ndihedraltypes) &&
atom->avec->dihedrals_allow == 0 && me == 0)
error->one(FLERR,"No dihedrals allowed with this atom style");
- if ((atom->nimpropers || atom->nimpropertypes) &&
+ if ((atom->nimpropers || atom->nimpropertypes) &&
atom->avec->impropers_allow == 0 && me == 0)
error->one(FLERR,"No impropers allowed with this atom style");
@@ -537,7 +537,7 @@ void ReadData::header(int flag)
void ReadData::atoms()
{
int i,m,nchunk;
-
+
bigint nread = 0;
bigint natoms = atom->natoms;
@@ -548,9 +548,9 @@ void ReadData::atoms()
char *eof;
m = 0;
for (i = 0; i < nchunk; i++) {
- eof = fgets(&buffer[m],MAXLINE,fp);
- if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
- m += strlen(&buffer[m]);
+ eof = fgets(&buffer[m],MAXLINE,fp);
+ if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
+ m += strlen(&buffer[m]);
}
m++;
}
@@ -571,14 +571,14 @@ void ReadData::atoms()
if (logfile) fprintf(logfile," " BIGINT_FORMAT " atoms\n",natoms);
}
- if (natoms != atom->natoms)
+ if (natoms != atom->natoms)
error->all(FLERR,"Did not assign all atoms correctly");
-
+
// if any atom ID < 0, error
// if all atom IDs = 0, tag_enable = 0
// if any atom ID > 0, error if any atom ID == 0
// not checking if atom IDs > natoms or are unique
-
+
int nlocal = atom->nlocal;
int *tag = atom->tag;
@@ -615,7 +615,7 @@ void ReadData::atoms()
/* ----------------------------------------------------------------------
read all velocities
- to find atoms, must build atom map if not a molecular system
+ to find atoms, must build atom map if not a molecular system
------------------------------------------------------------------------- */
void ReadData::velocities()
@@ -640,9 +640,9 @@ void ReadData::velocities()
char *eof;
m = 0;
for (i = 0; i < nchunk; i++) {
- eof = fgets(&buffer[m],MAXLINE,fp);
- if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
- m += strlen(&buffer[m]);
+ eof = fgets(&buffer[m],MAXLINE,fp);
+ if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
+ m += strlen(&buffer[m]);
}
m++;
}
@@ -666,7 +666,7 @@ void ReadData::velocities()
/* ----------------------------------------------------------------------
read all bonus data
- to find atoms, must build atom map if not a molecular system
+ to find atoms, must build atom map if not a molecular system
------------------------------------------------------------------------- */
void ReadData::bonus(bigint nbonus, AtomVec *ptr, const char *type)
@@ -691,9 +691,9 @@ void ReadData::bonus(bigint nbonus, AtomVec *ptr, const char *type)
char *eof;
m = 0;
for (i = 0; i < nchunk; i++) {
- eof = fgets(&buffer[m],MAXLINE,fp);
- if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
- m += strlen(&buffer[m]);
+ eof = fgets(&buffer[m],MAXLINE,fp);
+ if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
+ m += strlen(&buffer[m]);
}
m++;
}
@@ -730,9 +730,9 @@ void ReadData::bonds()
char *eof;
m = 0;
for (i = 0; i < nchunk; i++) {
- eof = fgets(&buffer[m],MAXLINE,fp);
- if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
- m += strlen(&buffer[m]);
+ eof = fgets(&buffer[m],MAXLINE,fp);
+ if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
+ m += strlen(&buffer[m]);
}
m++;
}
@@ -757,7 +757,7 @@ void ReadData::bonds()
if (screen) fprintf(screen," " BIGINT_FORMAT " bonds\n",sum/factor);
if (logfile) fprintf(logfile," " BIGINT_FORMAT " bonds\n",sum/factor);
}
- if (sum != factor*atom->nbonds)
+ if (sum != factor*atom->nbonds)
error->all(FLERR,"Bonds assigned incorrectly");
}
@@ -776,9 +776,9 @@ void ReadData::angles()
char *eof;
m = 0;
for (i = 0; i < nchunk; i++) {
- eof = fgets(&buffer[m],MAXLINE,fp);
- if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
- m += strlen(&buffer[m]);
+ eof = fgets(&buffer[m],MAXLINE,fp);
+ if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
+ m += strlen(&buffer[m]);
}
m++;
}
@@ -803,7 +803,7 @@ void ReadData::angles()
if (screen) fprintf(screen," " BIGINT_FORMAT " angles\n",sum/factor);
if (logfile) fprintf(logfile," " BIGINT_FORMAT " angles\n",sum/factor);
}
- if (sum != factor*atom->nangles)
+ if (sum != factor*atom->nangles)
error->all(FLERR,"Angles assigned incorrectly");
}
@@ -822,9 +822,9 @@ void ReadData::dihedrals()
char *eof;
m = 0;
for (i = 0; i < nchunk; i++) {
- eof = fgets(&buffer[m],MAXLINE,fp);
- if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
- m += strlen(&buffer[m]);
+ eof = fgets(&buffer[m],MAXLINE,fp);
+ if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
+ m += strlen(&buffer[m]);
}
m++;
}
@@ -849,7 +849,7 @@ void ReadData::dihedrals()
if (screen) fprintf(screen," " BIGINT_FORMAT " dihedrals\n",sum/factor);
if (logfile) fprintf(logfile," " BIGINT_FORMAT " dihedrals\n",sum/factor);
}
- if (sum != factor*atom->ndihedrals)
+ if (sum != factor*atom->ndihedrals)
error->all(FLERR,"Dihedrals assigned incorrectly");
}
@@ -868,9 +868,9 @@ void ReadData::impropers()
char *eof;
m = 0;
for (i = 0; i < nchunk; i++) {
- eof = fgets(&buffer[m],MAXLINE,fp);
- if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
- m += strlen(&buffer[m]);
+ eof = fgets(&buffer[m],MAXLINE,fp);
+ if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
+ m += strlen(&buffer[m]);
}
m++;
}
@@ -895,7 +895,7 @@ void ReadData::impropers()
if (screen) fprintf(screen," " BIGINT_FORMAT " impropers\n",sum/factor);
if (logfile) fprintf(logfile," " BIGINT_FORMAT " impropers\n",sum/factor);
}
- if (sum != factor*atom->nimpropers)
+ if (sum != factor*atom->nimpropers)
error->all(FLERR,"Impropers assigned incorrectly");
}
@@ -1109,9 +1109,9 @@ void ReadData::fix(int ifix, char *line, bigint nlines)
char *eof;
m = 0;
for (i = 0; i < nchunk; i++) {
- eof = fgets(&buffer[m],MAXLINE,fp);
- if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
- m += strlen(&buffer[m]);
+ eof = fgets(&buffer[m],MAXLINE,fp);
+ if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
+ m += strlen(&buffer[m]);
}
m++;
}
@@ -1124,11 +1124,11 @@ void ReadData::fix(int ifix, char *line, bigint nlines)
}
/* ----------------------------------------------------------------------
- proc 0 scans the data file for topology maximums
+ proc 0 scans the data file for topology maximums
------------------------------------------------------------------------- */
void ReadData::scan(int &bond_per_atom, int &angle_per_atom,
- int &dihedral_per_atom, int &improper_per_atom)
+ int &dihedral_per_atom, int &improper_per_atom)
{
int i,tmp1,tmp2,atom1,atom2,atom3,atom4;
char *eof;
@@ -1160,14 +1160,14 @@ void ReadData::scan(int &bond_per_atom, int &angle_per_atom,
if (nfix) {
for (i = 0; i < nfix; i++) {
- printf("LINE SECTION %s %s\n",line,fix_section[i]);
- if (strstr(line,fix_section[i])) {
- int n = modify->fix[fix_index[i]]->read_data_skip_lines(keyword);
- printf("NLINES SKIP %d\n",n);
- skip_lines(n);
- parse_keyword(0,0);
- break;
- }
+ printf("LINE SECTION %s %s\n",line,fix_section[i]);
+ if (strstr(line,fix_section[i])) {
+ int n = modify->fix[fix_index[i]]->read_data_skip_lines(keyword);
+ printf("NLINES SKIP %d\n",n);
+ skip_lines(n);
+ parse_keyword(0,0);
+ break;
+ }
}
if (i < nfix) continue;
}
@@ -1177,8 +1177,8 @@ void ReadData::scan(int &bond_per_atom, int &angle_per_atom,
else if (strcmp(keyword,"Velocities") == 0) skip_lines(natoms);
else if (strcmp(keyword,"Ellipsoids") == 0) {
- if (!avec_ellipsoid)
- error->one(FLERR,"Invalid data file section: Ellipsoids");
+ if (!avec_ellipsoid)
+ error->one(FLERR,"Invalid data file section: Ellipsoids");
ellipsoid_flag = 1;
skip_lines(nellipsoids);
} else if (strcmp(keyword,"Lines") == 0) {
@@ -1191,109 +1191,109 @@ void ReadData::scan(int &bond_per_atom, int &angle_per_atom,
skip_lines(ntris);
} else if (strcmp(keyword,"Pair Coeffs") == 0) {
- if (force->pair == NULL)
- error->one(FLERR,"Must define pair_style before Pair Coeffs");
+ if (force->pair == NULL)
+ error->one(FLERR,"Must define pair_style before Pair Coeffs");
skip_lines(atom->ntypes);
} else if (strcmp(keyword,"Bond Coeffs") == 0) {
- if (atom->avec->bonds_allow == 0)
- error->one(FLERR,"Invalid data file section: Bond Coeffs");
- if (force->bond == NULL)
- error->one(FLERR,"Must define bond_style before Bond Coeffs");
+ if (atom->avec->bonds_allow == 0)
+ error->one(FLERR,"Invalid data file section: Bond Coeffs");
+ if (force->bond == NULL)
+ error->one(FLERR,"Must define bond_style before Bond Coeffs");
skip_lines(atom->nbondtypes);
} else if (strcmp(keyword,"Angle Coeffs") == 0) {
- if (atom->avec->angles_allow == 0)
- error->one(FLERR,"Invalid data file section: Angle Coeffs");
- if (force->angle == NULL)
- error->one(FLERR,"Must define angle_style before Angle Coeffs");
+ if (atom->avec->angles_allow == 0)
+ error->one(FLERR,"Invalid data file section: Angle Coeffs");
+ if (force->angle == NULL)
+ error->one(FLERR,"Must define angle_style before Angle Coeffs");
skip_lines(atom->nangletypes);
} else if (strcmp(keyword,"Dihedral Coeffs") == 0) {
skip_lines(atom->ndihedraltypes);
- if (atom->avec->dihedrals_allow == 0)
- error->one(FLERR,"Invalid data file section: Dihedral Coeffs");
- if (force->dihedral == NULL)
- error->one(FLERR,"Must define dihedral_style before Dihedral Coeffs");
+ if (atom->avec->dihedrals_allow == 0)
+ error->one(FLERR,"Invalid data file section: Dihedral Coeffs");
+ if (force->dihedral == NULL)
+ error->one(FLERR,"Must define dihedral_style before Dihedral Coeffs");
} else if (strcmp(keyword,"Improper Coeffs") == 0) {
- if (atom->avec->impropers_allow == 0)
- error->one(FLERR,"Invalid data file section: Improper Coeffs");
- if (force->improper == NULL)
- error->one(FLERR,"Must define improper_style before Improper Coeffs");
+ if (atom->avec->impropers_allow == 0)
+ error->one(FLERR,"Invalid data file section: Improper Coeffs");
+ if (force->improper == NULL)
+ error->one(FLERR,"Must define improper_style before Improper Coeffs");
skip_lines(atom->nimpropertypes);
} else if (strcmp(keyword,"BondBond Coeffs") == 0) {
- if (atom->avec->angles_allow == 0)
- error->one(FLERR,"Invalid data file section: BondBond Coeffs");
- if (force->angle == NULL)
- error->one(FLERR,"Must define angle_style before BondBond Coeffs");
+ if (atom->avec->angles_allow == 0)
+ error->one(FLERR,"Invalid data file section: BondBond Coeffs");
+ if (force->angle == NULL)
+ error->one(FLERR,"Must define angle_style before BondBond Coeffs");
skip_lines(atom->nangletypes);
} else if (strcmp(keyword,"BondAngle Coeffs") == 0) {
- if (atom->avec->angles_allow == 0)
- error->one(FLERR,"Invalid data file section: BondAngle Coeffs");
- if (force->angle == NULL)
- error->one(FLERR,"Must define angle_style before BondAngle Coeffs");
+ if (atom->avec->angles_allow == 0)
+ error->one(FLERR,"Invalid data file section: BondAngle Coeffs");
+ if (force->angle == NULL)
+ error->one(FLERR,"Must define angle_style before BondAngle Coeffs");
skip_lines(atom->nangletypes);
} else if (strcmp(keyword,"MiddleBondTorsion Coeffs") == 0) {
- if (atom->avec->dihedrals_allow == 0)
- error->one(FLERR,"Invalid data file section: MiddleBondTorsion Coeffs");
- if (force->dihedral == NULL)
- error->one(FLERR,
- "Must define dihedral_style before "
- "MiddleBondTorsion Coeffs");
+ if (atom->avec->dihedrals_allow == 0)
+ error->one(FLERR,"Invalid data file section: MiddleBondTorsion Coeffs");
+ if (force->dihedral == NULL)
+ error->one(FLERR,
+ "Must define dihedral_style before "
+ "MiddleBondTorsion Coeffs");
skip_lines(atom->ndihedraltypes);
} else if (strcmp(keyword,"EndBondTorsion Coeffs") == 0) {
- if (atom->avec->dihedrals_allow == 0)
- error->one(FLERR,"Invalid data file section: EndBondTorsion Coeffs");
- if (force->dihedral == NULL)
- error->one(FLERR,
- "Must define dihedral_style before EndBondTorsion Coeffs");
+ if (atom->avec->dihedrals_allow == 0)
+ error->one(FLERR,"Invalid data file section: EndBondTorsion Coeffs");
+ if (force->dihedral == NULL)
+ error->one(FLERR,
+ "Must define dihedral_style before EndBondTorsion Coeffs");
skip_lines(atom->ndihedraltypes);
} else if (strcmp(keyword,"AngleTorsion Coeffs") == 0) {
- if (atom->avec->dihedrals_allow == 0)
- error->one(FLERR,"Invalid data file section: AngleTorsion Coeffs");
- if (force->dihedral == NULL)
- error->one(FLERR,
- "Must define dihedral_style before AngleTorsion Coeffs");
+ if (atom->avec->dihedrals_allow == 0)
+ error->one(FLERR,"Invalid data file section: AngleTorsion Coeffs");
+ if (force->dihedral == NULL)
+ error->one(FLERR,
+ "Must define dihedral_style before AngleTorsion Coeffs");
skip_lines(atom->ndihedraltypes);
} else if (strcmp(keyword,"AngleAngleTorsion Coeffs") == 0) {
- if (atom->avec->dihedrals_allow == 0)
- error->one(FLERR,"Invalid data file section: AngleAngleTorsion Coeffs");
- if (force->dihedral == NULL)
- error->one(FLERR,
- "Must define dihedral_style before "
- "AngleAngleTorsion Coeffs");
+ if (atom->avec->dihedrals_allow == 0)
+ error->one(FLERR,"Invalid data file section: AngleAngleTorsion Coeffs");
+ if (force->dihedral == NULL)
+ error->one(FLERR,
+ "Must define dihedral_style before "
+ "AngleAngleTorsion Coeffs");
skip_lines(atom->ndihedraltypes);
} else if (strcmp(keyword,"BondBond13 Coeffs") == 0) {
- if (atom->avec->dihedrals_allow == 0)
- error->one(FLERR,"Invalid data file section: BondBond13 Coeffs");
- if (force->dihedral == NULL)
- error->one(FLERR,"Must define dihedral_style before BondBond13 Coeffs");
+ if (atom->avec->dihedrals_allow == 0)
+ error->one(FLERR,"Invalid data file section: BondBond13 Coeffs");
+ if (force->dihedral == NULL)
+ error->one(FLERR,"Must define dihedral_style before BondBond13 Coeffs");
skip_lines(atom->ndihedraltypes);
} else if (strcmp(keyword,"AngleAngle Coeffs") == 0) {
- if (atom->avec->impropers_allow == 0)
- error->one(FLERR,"Invalid data file section: AngleAngle Coeffs");
- if (force->improper == NULL)
- error->one(FLERR,"Must define improper_style before AngleAngle Coeffs");
+ if (atom->avec->impropers_allow == 0)
+ error->one(FLERR,"Invalid data file section: AngleAngle Coeffs");
+ if (force->improper == NULL)
+ error->one(FLERR,"Must define improper_style before AngleAngle Coeffs");
skip_lines(atom->nimpropertypes);
} else if (strcmp(keyword,"Bonds") == 0) {
for (i = 1; i < cmax; i++) count[i] = 0;
if (force->newton_bond)
- for (i = 0; i < atom->nbonds; i++) {
- eof = fgets(line,MAXLINE,fp);
- if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
- sscanf(line,"%d %d %d %d",&tmp1,&tmp2,&atom1,&atom2);
- if (atom1 >= cmax) cmax = reallocate(&count,cmax,atom1);
- count[atom1]++;
- }
+ for (i = 0; i < atom->nbonds; i++) {
+ eof = fgets(line,MAXLINE,fp);
+ if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
+ sscanf(line,"%d %d %d %d",&tmp1,&tmp2,&atom1,&atom2);
+ if (atom1 >= cmax) cmax = reallocate(&count,cmax,atom1);
+ count[atom1]++;
+ }
else
- for (i = 0; i < atom->nbonds; i++) {
- eof = fgets(line,MAXLINE,fp);
- if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
- sscanf(line,"%d %d %d %d",&tmp1,&tmp2,&atom1,&atom2);
- int amax = MAX(atom1,atom2);
- if (amax >= cmax) cmax = reallocate(&count,cmax,amax);
- count[atom1]++;
- count[atom2]++;
- }
+ for (i = 0; i < atom->nbonds; i++) {
+ eof = fgets(line,MAXLINE,fp);
+ if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
+ sscanf(line,"%d %d %d %d",&tmp1,&tmp2,&atom1,&atom2);
+ int amax = MAX(atom1,atom2);
+ if (amax >= cmax) cmax = reallocate(&count,cmax,amax);
+ count[atom1]++;
+ count[atom2]++;
+ }
for (i = 1; i < cmax; i++) bond_per_atom = MAX(bond_per_atom,count[i]);
if (screen) fprintf(screen," %d = max bonds/atom\n",bond_per_atom);
if (logfile) fprintf(logfile," %d = max bonds/atom\n",bond_per_atom);
@@ -1301,25 +1301,25 @@ void ReadData::scan(int &bond_per_atom, int &angle_per_atom,
} else if (strcmp(keyword,"Angles") == 0) {
for (i = 1; i < cmax; i++) count[i] = 0;
if (force->newton_bond)
- for (i = 0; i < atom->nangles; i++) {
- eof = fgets(line,MAXLINE,fp);
- if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
- sscanf(line,"%d %d %d %d %d",&tmp1,&tmp2,&atom1,&atom2,&atom3);
- if (atom2 >= cmax) cmax = reallocate(&count,cmax,atom2);
- count[atom2]++;
- }
+ for (i = 0; i < atom->nangles; i++) {
+ eof = fgets(line,MAXLINE,fp);
+ if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
+ sscanf(line,"%d %d %d %d %d",&tmp1,&tmp2,&atom1,&atom2,&atom3);
+ if (atom2 >= cmax) cmax = reallocate(&count,cmax,atom2);
+ count[atom2]++;
+ }
else
- for (i = 0; i < atom->nangles; i++) {
- eof = fgets(line,MAXLINE,fp);
- if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
- sscanf(line,"%d %d %d %d %d",&tmp1,&tmp2,&atom1,&atom2,&atom3);
- int amax = MAX(atom1,atom2);
- amax = MAX(amax,atom3);
- if (amax >= cmax) cmax = reallocate(&count,cmax,amax);
- count[atom1]++;
- count[atom2]++;
- count[atom3]++;
- }
+ for (i = 0; i < atom->nangles; i++) {
+ eof = fgets(line,MAXLINE,fp);
+ if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
+ sscanf(line,"%d %d %d %d %d",&tmp1,&tmp2,&atom1,&atom2,&atom3);
+ int amax = MAX(atom1,atom2);
+ amax = MAX(amax,atom3);
+ if (amax >= cmax) cmax = reallocate(&count,cmax,amax);
+ count[atom1]++;
+ count[atom2]++;
+ count[atom3]++;
+ }
for (i = 1; i < cmax; i++) angle_per_atom = MAX(angle_per_atom,count[i]);
if (screen) fprintf(screen," %d = max angles/atom\n",angle_per_atom);
if (logfile) fprintf(logfile," %d = max angles/atom\n",angle_per_atom);
@@ -1327,68 +1327,68 @@ void ReadData::scan(int &bond_per_atom, int &angle_per_atom,
} else if (strcmp(keyword,"Dihedrals") == 0) {
for (i = 1; i < cmax; i++) count[i] = 0;
if (force->newton_bond)
- for (i = 0; i < atom->ndihedrals; i++) {
- eof = fgets(line,MAXLINE,fp);
- if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
- sscanf(line,"%d %d %d %d %d %d",
- &tmp1,&tmp2,&atom1,&atom2,&atom3,&atom4);
- if (atom2 >= cmax) cmax = reallocate(&count,cmax,atom2);
- count[atom2]++;
- }
+ for (i = 0; i < atom->ndihedrals; i++) {
+ eof = fgets(line,MAXLINE,fp);
+ if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
+ sscanf(line,"%d %d %d %d %d %d",
+ &tmp1,&tmp2,&atom1,&atom2,&atom3,&atom4);
+ if (atom2 >= cmax) cmax = reallocate(&count,cmax,atom2);
+ count[atom2]++;
+ }
else
- for (i = 0; i < atom->ndihedrals; i++) {
- eof = fgets(line,MAXLINE,fp);
- if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
- sscanf(line,"%d %d %d %d %d %d",
- &tmp1,&tmp2,&atom1,&atom2,&atom3,&atom4);
- int amax = MAX(atom1,atom2);
- amax = MAX(amax,atom3);
- amax = MAX(amax,atom4);
- if (amax >= cmax) cmax = reallocate(&count,cmax,amax);
- count[atom1]++;
- count[atom2]++;
- count[atom3]++;
- count[atom4]++;
- }
- for (i = 1; i < cmax; i++)
- dihedral_per_atom = MAX(dihedral_per_atom,count[i]);
- if (screen)
- fprintf(screen," %d = max dihedrals/atom\n",dihedral_per_atom);
- if (logfile)
- fprintf(logfile," %d = max dihedrals/atom\n",dihedral_per_atom);
+ for (i = 0; i < atom->ndihedrals; i++) {
+ eof = fgets(line,MAXLINE,fp);
+ if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
+ sscanf(line,"%d %d %d %d %d %d",
+ &tmp1,&tmp2,&atom1,&atom2,&atom3,&atom4);
+ int amax = MAX(atom1,atom2);
+ amax = MAX(amax,atom3);
+ amax = MAX(amax,atom4);
+ if (amax >= cmax) cmax = reallocate(&count,cmax,amax);
+ count[atom1]++;
+ count[atom2]++;
+ count[atom3]++;
+ count[atom4]++;
+ }
+ for (i = 1; i < cmax; i++)
+ dihedral_per_atom = MAX(dihedral_per_atom,count[i]);
+ if (screen)
+ fprintf(screen," %d = max dihedrals/atom\n",dihedral_per_atom);
+ if (logfile)
+ fprintf(logfile," %d = max dihedrals/atom\n",dihedral_per_atom);
} else if (strcmp(keyword,"Impropers") == 0) {
for (i = 1; i < cmax; i++) count[i] = 0;
if (force->newton_bond)
- for (i = 0; i < atom->nimpropers; i++) {
- eof = fgets(line,MAXLINE,fp);
- if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
- sscanf(line,"%d %d %d %d %d %d",
- &tmp1,&tmp2,&atom1,&atom2,&atom3,&atom4);
- if (atom2 >= cmax) cmax = reallocate(&count,cmax,atom2);
- count[atom2]++;
- }
+ for (i = 0; i < atom->nimpropers; i++) {
+ eof = fgets(line,MAXLINE,fp);
+ if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
+ sscanf(line,"%d %d %d %d %d %d",
+ &tmp1,&tmp2,&atom1,&atom2,&atom3,&atom4);
+ if (atom2 >= cmax) cmax = reallocate(&count,cmax,atom2);
+ count[atom2]++;
+ }
else
- for (i = 0; i < atom->nimpropers; i++) {
- eof = fgets(line,MAXLINE,fp);
- if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
- sscanf(line,"%d %d %d %d %d %d",
- &tmp1,&tmp2,&atom1,&atom2,&atom3,&atom4);
- int amax = MAX(atom1,atom2);
- amax = MAX(amax,atom3);
- amax = MAX(amax,atom4);
- if (amax >= cmax) cmax = reallocate(&count,cmax,amax);
- count[atom1]++;
- count[atom2]++;
- count[atom3]++;
- count[atom4]++;
- }
+ for (i = 0; i < atom->nimpropers; i++) {
+ eof = fgets(line,MAXLINE,fp);
+ if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
+ sscanf(line,"%d %d %d %d %d %d",
+ &tmp1,&tmp2,&atom1,&atom2,&atom3,&atom4);
+ int amax = MAX(atom1,atom2);
+ amax = MAX(amax,atom3);
+ amax = MAX(amax,atom4);
+ if (amax >= cmax) cmax = reallocate(&count,cmax,amax);
+ count[atom1]++;
+ count[atom2]++;
+ count[atom3]++;
+ count[atom4]++;
+ }
for (i = 1; i < cmax; i++)
- improper_per_atom = MAX(improper_per_atom,count[i]);
- if (screen)
- fprintf(screen," %d = max impropers/atom\n",improper_per_atom);
- if (logfile)
- fprintf(logfile," %d = max impropers/atom\n",improper_per_atom);
+ improper_per_atom = MAX(improper_per_atom,count[i]);
+ if (screen)
+ fprintf(screen," %d = max impropers/atom\n",improper_per_atom);
+ if (logfile)
+ fprintf(logfile," %d = max impropers/atom\n",improper_per_atom);
} else {
char str[128];
@@ -1408,7 +1408,7 @@ void ReadData::scan(int &bond_per_atom, int &angle_per_atom,
if ((atom->nbonds && !bond_per_atom) ||
(atom->nangles && !angle_per_atom) ||
(atom->ndihedrals && !dihedral_per_atom) ||
- (atom->nimpropers && !improper_per_atom))
+ (atom->nimpropers && !improper_per_atom))
error->one(FLERR,"Needed topology not in data file");
// customize for new sections
@@ -1513,8 +1513,8 @@ void ReadData::parse_keyword(int first, int flag)
int start = strspn(line," \t\n\r");
int stop = strlen(line) - 1;
- while (line[stop] == ' ' || line[stop] == '\t'
- || line[stop] == '\n' || line[stop] == '\r') stop--;
+ while (line[stop] == ' ' || line[stop] == '\t'
+ || line[stop] == '\n' || line[stop] == '\r') stop--;
line[stop+1] = '\0';
strcpy(keyword,&line[start]);
}
@@ -1550,8 +1550,8 @@ void ReadData::parse_coeffs(char *line, const char *addstr, int dupflag)
while (word) {
if (narg == maxarg) {
maxarg += DELTA;
- arg = (char **)
- memory->srealloc(arg,maxarg*sizeof(char *),"read_data:arg");
+ arg = (char **)
+ memory->srealloc(arg,maxarg*sizeof(char *),"read_data:arg");
}
if (addstr && narg == 1 && !islower(word[0])) arg[narg++] = (char *) addstr;
arg[narg++] = word;
diff --git a/src/read_data.h b/src/read_data.h
index f3edaf442388d5d74e101e65451322f45403bdba..169a4cd54ae9586622b621e52ff1a5ab3fdd08de 100644
--- a/src/read_data.h
+++ b/src/read_data.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/read_dump.cpp b/src/read_dump.cpp
index 1b1434c3b44d2c7ff6c9659ef9a10d20dab9779b..128902e76c8b4d199456d9c97f754a7930201e7a 100644
--- a/src/read_dump.cpp
+++ b/src/read_dump.cpp
@@ -12,7 +12,7 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
- Contributing author: Timothy Sirk (U Vermont)
+ Contributing author: Timothy Sirk (ARL)
------------------------------------------------------------------------- */
#include "lmptype.h"
@@ -45,6 +45,38 @@ ReadDump::ReadDump(LAMMPS *lmp) : Pointers(lmp)
{
MPI_Comm_rank(world,&me);
MPI_Comm_size(world,&nprocs);
+
+ dimension = domain->dimension;
+ triclinic = domain->triclinic;
+
+ nfiles = 0;
+ files = NULL;
+
+ nfield = 0;
+ fieldtype = NULL;
+ fieldlabel = NULL;
+ fields = NULL;
+ uflag = ucflag = ucflag_all = NULL;
+
+ reader = NULL;
+}
+
+/* ---------------------------------------------------------------------- */
+
+ReadDump::~ReadDump()
+{
+ for (int i = 0; i < nfiles; i++) delete [] files[i];
+ delete [] files;
+ for (int i = 0; i < nfield; i++) delete [] fieldlabel[i];
+ delete [] fieldlabel;
+ delete [] fieldtype;
+
+ memory->destroy(fields);
+ memory->destroy(uflag);
+ memory->destroy(ucflag);
+ memory->destroy(ucflag_all);
+
+ delete reader;
}
/* ---------------------------------------------------------------------- */
@@ -53,168 +85,200 @@ void ReadDump::command(int narg, char **arg)
{
if (narg < 2) error->all(FLERR,"Illegal read_dump command");
- nstep = ATOBIGINT(arg[1]);
+ store_files(1,&arg[0]);
+ bigint nstep = ATOBIGINT(arg[1]);
+ fields_and_keywords(narg-2,&arg[2]);
+ setup_reader();
- // per-field vectors
+ // find the snapshot and read/bcast/process header info
- int firstfield = 2;
- fieldtype = new int[narg];
- fieldlabel = new char*[narg];
+ if (me == 0 && screen) fprintf(screen,"Scanning dump file ...\n");
- // scan ahead to see if "add yes" keyword/value is used
- // requires extra "type" field from from dump file
- // add id and type fields as needed
+ bigint ntimestep = seek(nstep,1);
+ if (ntimestep < 0)
+ error->all(FLERR,"Dump file does not contain requested snapshot");
+ header(1);
- int iarg;
- for (iarg = firstfield; iarg < narg; iarg++)
- if (strcmp(arg[iarg],"add") == 0)
- if (iarg < narg-1 && strcmp(arg[iarg+1],"yes") == 0) break;
+ // reset timestep to nstep
- nfield = 0;
- fieldtype[nfield++] = ID;
- if (iarg < narg) fieldtype[nfield++] = TYPE;
+ update->reset_timestep(nstep);
- // parse fields
+ // counters
- iarg = firstfield;
- while (iarg < narg) {
- if (strcmp(arg[iarg],"x") == 0) fieldtype[nfield++] = X;
- else if (strcmp(arg[iarg],"y") == 0) fieldtype[nfield++] = Y;
- else if (strcmp(arg[iarg],"z") == 0) fieldtype[nfield++] = Z;
- else if (strcmp(arg[iarg],"vx") == 0) fieldtype[nfield++] = VX;
- else if (strcmp(arg[iarg],"vy") == 0) fieldtype[nfield++] = VY;
- else if (strcmp(arg[iarg],"vz") == 0) fieldtype[nfield++] = VZ;
- else if (strcmp(arg[iarg],"ix") == 0) fieldtype[nfield++] = IX;
- else if (strcmp(arg[iarg],"iy") == 0) fieldtype[nfield++] = IY;
- else if (strcmp(arg[iarg],"iz") == 0) fieldtype[nfield++] = IZ;
- else break;
- iarg++;
- }
+ // read in the snapshot and reset system
- dimension = domain->dimension;
- triclinic = domain->triclinic;
+ if (me == 0 && screen)
+ fprintf(screen,"Reading snapshot from dump file ...\n");
- if (fieldtype[nfield-1] == ID || fieldtype[nfield-1] == TYPE)
- error->all(FLERR,"Illegal read_dump command");
+ bigint natoms_prev = atom->natoms;
+ atoms();
- if (dimension == 2) {
- for (int i = 0; i < nfield; i++)
- if (fieldtype[i] == Z || fieldtype[i] == VZ || fieldtype[i] == IZ)
- error->all(FLERR,"Illegal read_dump command");
- }
+ // NOTE: this logic is not yet right
+ if (me == 0) close();
- for (int i = 0; i < nfield; i++)
- for (int j = i+1; j < nfield; j++)
- if (fieldtype[i] == fieldtype[j])
- error->all(FLERR,"Duplicate fields in read_dump command");
+ // print out stats
- // parse optional args
+ bigint npurge_all,nreplace_all,ntrim_all,nadd_all;
- boxflag = 1;
- replaceflag = 1;
- purgeflag = 0;
- trimflag = 0;
- addflag = 0;
- for (int i = 0; i < nfield; i++) fieldlabel[i] = NULL;
- scaledflag = UNSCALED;
- format = NATIVE;
+ bigint tmp;
+ tmp = npurge;
+ MPI_Allreduce(&tmp,&npurge_all,1,MPI_LMP_BIGINT,MPI_SUM,world);
+ tmp = nreplace;
+ MPI_Allreduce(&tmp,&nreplace_all,1,MPI_LMP_BIGINT,MPI_SUM,world);
+ tmp = ntrim;
+ MPI_Allreduce(&tmp,&ntrim_all,1,MPI_LMP_BIGINT,MPI_SUM,world);
+ tmp = nadd;
+ MPI_Allreduce(&tmp,&nadd_all,1,MPI_LMP_BIGINT,MPI_SUM,world);
- while (iarg < narg) {
- if (strcmp(arg[iarg],"box") == 0) {
- if (iarg+2 > narg) error->all(FLERR,"Illegal read_dump command");
- if (strcmp(arg[iarg+1],"yes") == 0) boxflag = 1;
- else if (strcmp(arg[iarg+1],"no") == 0) boxflag = 0;
- else error->all(FLERR,"Illegal read_dump command");
- iarg += 2;
- } else if (strcmp(arg[iarg],"replace") == 0) {
- if (iarg+2 > narg) error->all(FLERR,"Illegal read_dump command");
- if (strcmp(arg[iarg+1],"yes") == 0) replaceflag = 1;
- else if (strcmp(arg[iarg+1],"no") == 0) replaceflag = 0;
- else error->all(FLERR,"Illegal read_dump command");
- iarg += 2;
- } else if (strcmp(arg[iarg],"purge") == 0) {
- if (iarg+2 > narg) error->all(FLERR,"Illegal read_dump command");
- if (strcmp(arg[iarg+1],"yes") == 0) purgeflag = 1;
- else if (strcmp(arg[iarg+1],"no") == 0) purgeflag = 0;
- else error->all(FLERR,"Illegal read_dump command");
- iarg += 2;
- } else if (strcmp(arg[iarg],"trim") == 0) {
- if (iarg+2 > narg) error->all(FLERR,"Illegal read_dump command");
- if (strcmp(arg[iarg+1],"yes") == 0) trimflag = 1;
- else if (strcmp(arg[iarg+1],"no") == 0) trimflag = 0;
- else error->all(FLERR,"Illegal read_dump command");
- iarg += 2;
- } else if (strcmp(arg[iarg],"add") == 0) {
- if (iarg+2 > narg) error->all(FLERR,"Illegal read_dump command");
- if (strcmp(arg[iarg+1],"yes") == 0) addflag = 1;
- else if (strcmp(arg[iarg+1],"no") == 0) addflag = 0;
- else error->all(FLERR,"Illegal read_dump command");
- iarg += 2;
- } else if (strcmp(arg[iarg],"label") == 0) {
- if (iarg+3 > narg) error->all(FLERR,"Illegal read_dump command");
- int i;
- for (i = 0; i < nfield; i++)
- if (strcmp(arg[firstfield+i],arg[iarg+1]) == 0) break;
- if (i == nfield) error->all(FLERR,"Illegal read_dump command");
- fieldlabel[i] = arg[iarg+2];
- iarg += 3;
- } else if (strcmp(arg[iarg],"scaled") == 0) {
- if (iarg+2 > narg) error->all(FLERR,"Illegal read_dump command");
- if (strcmp(arg[iarg+1],"yes") == 0) scaledflag = SCALED;
- else if (strcmp(arg[iarg+1],"no") == 0) scaledflag = UNSCALED;
- else error->all(FLERR,"Illegal read_dump command");
- iarg += 2;
- } else if (strcmp(arg[iarg],"format") == 0) {
- if (iarg+2 > narg) error->all(FLERR,"Illegal read_dump command");
- if (strcmp(arg[iarg+1],"native") == 0) format = NATIVE;
- else error->all(FLERR,"Illegal read_dump command");
- iarg += 2;
- } else error->all(FLERR,"Illegal read_dump command");
+ domain->print_box(" ");
+
+ if (me == 0) {
+ if (screen) {
+ fprintf(screen," " BIGINT_FORMAT " atoms before read\n",natoms_prev);
+ fprintf(screen," " BIGINT_FORMAT " atoms in snapshot\n",nsnapatoms);
+ fprintf(screen," " BIGINT_FORMAT " atoms purged\n",npurge_all);
+ fprintf(screen," " BIGINT_FORMAT " atoms replaced\n",nreplace_all);
+ fprintf(screen," " BIGINT_FORMAT " atoms trimmed\n",ntrim_all);
+ fprintf(screen," " BIGINT_FORMAT " atoms added\n",nadd_all);
+ fprintf(screen," " BIGINT_FORMAT " atoms after read\n",atom->natoms);
+ }
+ if (logfile) {
+ fprintf(logfile," " BIGINT_FORMAT " atoms before read\n",natoms_prev);
+ fprintf(logfile," " BIGINT_FORMAT " atoms in snapshot\n",nsnapatoms);
+ fprintf(logfile," " BIGINT_FORMAT " atoms purged\n",npurge_all);
+ fprintf(logfile," " BIGINT_FORMAT " atoms replaced\n",nreplace_all);
+ fprintf(logfile," " BIGINT_FORMAT " atoms trimmed\n",ntrim_all);
+ fprintf(logfile," " BIGINT_FORMAT " atoms added\n",nadd_all);
+ fprintf(logfile," " BIGINT_FORMAT " atoms after read\n",atom->natoms);
+ }
}
+}
- if (purgeflag && (replaceflag || trimflag))
- error->all(FLERR,"If read_dump purges it cannot replace or trim");
+/* ---------------------------------------------------------------------- */
- // allocate snapshot field buffer
+void ReadDump::store_files(int nstr, char **str)
+{
+ nfiles = nstr;
+ files = new char*[nfiles];
- memory->create(fields,CHUNK,nfield,"read_dump:fields");
+ for (int i = 0; i < nfiles; i++) {
+ int n = strlen(str[i]) + 1;
+ files[i] = new char[n];
+ strcpy(files[i],str[i]);
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+void ReadDump::setup_reader()
+{
// create reader class
// could make this a parent class and customize with other readers
if (format == NATIVE) reader = new ReadDumpNative(lmp);
- // proc 0 opens dump file and scans to correct snapshot
- // after scan these values are set, so Bcast them:
- // nsnapatoms, box[3][3], scaled
- // NOTE: fieldlabel is just ptrs to input args in read_dump command
- // will not persist if want to use labels in rerun() command
+ // allocate snapshot field buffer
+
+ memory->create(fields,CHUNK,nfield,"read_dump:fields");
+}
+
+/* ----------------------------------------------------------------------
+ seek Nrequest timestep in one or more dump files
+ Nrequest can be a timestamp or -1 to match first step with exact = 0
+ if exact = 1, must find exactly Nrequest
+ if exact = 0, find first step >= Nrequest
+ return matching ntimestep or -1 if did not find a match
+------------------------------------------------------------------------- */
+
+bigint ReadDump::seek(bigint nrequest, int exact)
+{
+ int ifile,eofflag;
+ bigint ntimestep;
if (me == 0) {
- if (screen) fprintf(screen,"Scanning dump file ...\n");
- open(arg[0]);
- reader->init(fp);
- reader->scan(nstep,nfield,fieldtype,fieldlabel,scaledflag,
- nsnapatoms,box,scaled);
+ for (ifile = 0; ifile < nfiles; ifile++) {
+ ntimestep = -1;
+ open(files[ifile]);
+ reader->file(fp);
+ while (1) {
+ eofflag = reader->read_time(ntimestep);
+ if (eofflag) break;
+ if (ntimestep >= nrequest) break;
+ reader->skip();
+ }
+ if (ntimestep >= nrequest) break;
+ close();
+ }
+
+ currentfile = ifile;
+ if (ntimestep < nrequest) close();
+ if (ntimestep < nrequest) ntimestep = -1;
+ if (exact && ntimestep != nrequest) ntimestep = -1;
}
- MPI_Bcast(&nsnapatoms,1,MPI_LMP_BIGINT,0,world);
- MPI_Bcast(&box[0][0],9,MPI_DOUBLE,0,world);
- MPI_Bcast(&scaled,1,MPI_INT,0,world);
+ MPI_Bcast(&ntimestep,1,MPI_LMP_BIGINT,0,world);
+ return ntimestep;
+}
- // for scaled coords and triclinic box:
- // yindex,zindex = index of Y and Z fields
- // already known to exist because checked in scan()
- // needed for unscaling to absolute coords in xfield(), yfield(), zfield()
+/* ----------------------------------------------------------------------
+ find next matching snapshot in one or more dump files
+ Ncurrent = current timestep from last snapshot
+ Nstop = match no timestep bigger than Nstop
+ Nevery = only match timesteps that are a multiple of Nevery
+ Nskip = skip every this many timesteps
+ return matching ntimestep or -1 if did not find a match
+------------------------------------------------------------------------- */
- if (scaled == SCALED && triclinic) {
- for (int i = 0; i < nfield; i++) {
- if (fieldtype[i] == Y) yindex = i;
- if (fieldtype[i] == Z) zindex = i;
+bigint ReadDump::next(bigint ncurrent, bigint nstop, int nevery, int nskip)
+{
+ int ifile,eofflag;
+ bigint ntimestep;
+
+ // NOTE: this logic is not yet right
+
+ if (me == 0) {
+ for (ifile = currentfile; ifile < nfiles; ifile++) {
+ ntimestep = -1;
+ if (ifile != currentfile) open(files[ifile]);
+ reader->file(fp);
+ while (1) {
+ eofflag = reader->read_time(ntimestep);
+ if (eofflag) ntimestep = -1;
+ break;
+ }
+ if (ntimestep > ncurrent) break;
+ close();
}
+
+ currentfile = ifile;
}
- // make local copy of snapshot box params
+ MPI_Bcast(&ntimestep,1,MPI_LMP_BIGINT,0,world);
+ return ntimestep;
+}
+
+/* ----------------------------------------------------------------------
+ read and broadcast and store snapshot header info
+ set nsnapatoms = # of atoms in snapshot
+ set yindex,zindex
+------------------------------------------------------------------------- */
+
+void ReadDump::header(int fieldinfo)
+{
+ int triclinic_snap;
+ int fieldflag,xflag,yflag,zflag;
+
+ if (me == 0)
+ nsnapatoms = reader->read_header(box,triclinic_snap,
+ fieldinfo,nfield,fieldtype,fieldlabel,
+ scaledflag,fieldflag,xflag,yflag,zflag);
+
+ MPI_Bcast(&nsnapatoms,1,MPI_LMP_BIGINT,0,world);
+ MPI_Bcast(&triclinic_snap,1,MPI_INT,0,world);
+ MPI_Bcast(&box[0][0],9,MPI_DOUBLE,0,world);
+
+ // local copy of snapshot box parameters
+ // used in xfield,yfield,zfield when converting dump atom to absolute coords
xlo = box[0][0];
xhi = box[0][1];
@@ -225,56 +289,68 @@ void ReadDump::command(int narg, char **arg)
xprd = xhi - xlo;
yprd = yhi - ylo;
zprd = zhi - zlo;
- if (triclinic) {
+ if (triclinic_snap) {
xy = box[0][2];
xz = box[1][2];
yz = box[2][2];
}
- // reset timestep to nstep
+ // done if not checking fields
- char *tstr[1];
- char str[32];
- sprintf(str,BIGINT_FORMAT,nstep);
- tstr[0] = str;
- update->reset_timestep(1,tstr);
+ if (!fieldinfo) return;
- // reset simulation box from snapshot box parameters if requested
- // do it now, so if adding atoms, procs will have correct sub-domains
- // call domain->reset_box() later,
- // since can't shrink wrap until atom coords change and atoms are added
+ MPI_Bcast(&fieldflag,1,MPI_INT,0,world);
+ MPI_Bcast(&xflag,1,MPI_INT,0,world);
+ MPI_Bcast(&yflag,1,MPI_INT,0,world);
+ MPI_Bcast(&zflag,1,MPI_INT,0,world);
- if (boxflag) {
- domain->boxlo[0] = xlo;
- domain->boxhi[0] = xhi;
- domain->boxlo[1] = ylo;
- domain->boxhi[1] = yhi;
- if (dimension == 3) {
- domain->boxlo[2] = zlo;
- domain->boxhi[2] = zhi;
- }
- if (triclinic) {
- domain->xy = xy;
- if (dimension == 3) {
- domain->xz = xz;
- domain->yz = yz;
- }
- }
+ // error check on current vs new box and fields
- domain->set_initial_box();
- domain->set_global_box();
- comm->set_proc_grid();
- domain->set_local_box();
- }
+ if ((triclinic_snap && !triclinic) ||
+ (!triclinic_snap && triclinic))
+ error->one(FLERR,"Read_dump triclinic status does not match simulation");
- // read in the snapshot
+ // error check field and scaling info
- if (me == 0)
- if (screen) fprintf(screen,"Reading snapshot from dump file ...\n");
+ if (fieldflag < 0)
+ error->one(FLERR,"Read_dump field not found in dump file");
- // counters
+ // set overall scaling of coordinates
+ // error if x,y,z scaling are not the same
+
+ scaled = MAX(xflag,yflag);
+ scaled = MAX(zflag,scaled);
+ if ((xflag != UNSET && xflag != scaled) ||
+ (yflag != UNSET && yflag != scaled) ||
+ (zflag != UNSET && zflag != scaled))
+ error->one(FLERR,"Read_dump x,y,z fields do not have consistent scaling");
+
+ // scaled, triclinic coords require all 3 x,y,z fields, to perform unscaling
+ // set yindex,zindex = column index of Y and Z fields in fields array
+ // needed for unscaling to absolute coords in xfield(), yfield(), zfield()
+
+ if (scaled == SCALED && triclinic) {
+ int flag = 0;
+ if (xflag != scaled) flag = 1;
+ if (yflag != scaled) flag = 1;
+ if (dimension == 3 && zflag != scaled) flag = 1;
+ if (flag)
+ error->one(FLERR,"All read_dump x,y,z fields must be specified for "
+ "scaled, triclinic coords");
+
+ for (int i = 0; i < nfield; i++) {
+ if (fieldtype[i] == Y) yindex = i;
+ if (fieldtype[i] == Z) zindex = i;
+ }
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ReadDump::atoms()
+{
+ // initialize counters
- bigint natoms_prev = atom->natoms;
npurge = nreplace = ntrim = nadd = 0;
// if purgeflag set, delete all current atoms
@@ -300,12 +376,19 @@ void ReadDump::command(int narg, char **arg)
// uflag[i] = 1 for each owned atom appearing in dump
// ucflag = similar flag for each chunk atom, used in process_atoms()
+ // NOTE: this logic is sloppy
+
+ memory->destroy(uflag);
+ memory->destroy(ucflag);
+ memory->destroy(ucflag_all);
+ uflag = ucflag = ucflag_all = NULL;
+
int nlocal = atom->nlocal;
memory->create(uflag,nlocal,"read_dump:uflag");
for (int i = 0; i < nlocal; i++) uflag[i] = 0;
memory->create(ucflag,CHUNK,"read_dump:ucflag");
memory->create(ucflag_all,CHUNK,"read_dump:ucflag");
-
+
// read, broadcast, and process atoms from snapshot in chunks
addproc = -1;
@@ -314,7 +397,7 @@ void ReadDump::command(int narg, char **arg)
bigint nread = 0;
while (nread < nsnapatoms) {
nchunk = MIN(nsnapatoms-nread,CHUNK);
- if (me == 0) reader->read(nchunk,fields);
+ if (me == 0) reader->read_atoms(nchunk,nfield,fields);
MPI_Bcast(&fields[0][0],nchunk*nfield,MPI_DOUBLE,0,world);
process_atoms(nchunk);
nread += nchunk;
@@ -334,7 +417,7 @@ void ReadDump::command(int narg, char **arg)
// if trimflag set, delete atoms not replaced by snapshot atoms
if (trimflag) {
- delete_atoms(uflag);
+ delete_atoms();
bigint nblocal = atom->nlocal;
MPI_Allreduce(&nblocal,&atom->natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);
}
@@ -352,11 +435,29 @@ void ReadDump::command(int narg, char **arg)
atom->map_set();
}
- // close dump file
+ // overwrite simulation box with dump snapshot box if requested
- if (me == 0) {
- if (compressed) pclose(fp);
- else fclose(fp);
+ if (boxflag) {
+ domain->boxlo[0] = xlo;
+ domain->boxhi[0] = xhi;
+ domain->boxlo[1] = ylo;
+ domain->boxhi[1] = yhi;
+ if (dimension == 3) {
+ domain->boxlo[2] = zlo;
+ domain->boxhi[2] = zhi;
+ }
+ if (triclinic) {
+ domain->xy = xy;
+ if (dimension == 3) {
+ domain->xz = xz;
+ domain->yz = yz;
+ }
+ }
+
+ domain->set_initial_box();
+ domain->set_global_box();
+ comm->set_proc_grid();
+ domain->set_local_box();
}
// move atoms back inside simulation box and to new processors
@@ -375,55 +476,134 @@ void ReadDump::command(int narg, char **arg)
irregular->migrate_atoms();
delete irregular;
if (triclinic) domain->lamda2x(atom->nlocal);
+}
- domain->print_box(" ");
+/* ----------------------------------------------------------------------
+ process arg list for dump file fields and optional keywords
+------------------------------------------------------------------------- */
- // clean up
+void ReadDump::fields_and_keywords(int narg, char **arg)
+{
+ // per-field vectors, leave space for ID + TYPE
- delete reader;
- delete [] fieldtype;
- delete [] fieldlabel;
- memory->destroy(fields);
- memory->destroy(uflag);
- memory->destroy(ucflag);
- memory->destroy(ucflag_all);
+ fieldtype = new int[narg+2];
+ fieldlabel = new char*[narg+2];
- // print out stats
+ // add id and type fields as needed
+ // scan ahead to see if "add yes" keyword/value is used
+ // requires extra "type" field from from dump file
- bigint npurge_all,nreplace_all,ntrim_all,nadd_all;
+ int iarg;
+ for (iarg = 0; iarg < narg; iarg++)
+ if (strcmp(arg[iarg],"add") == 0)
+ if (iarg < narg-1 && strcmp(arg[iarg+1],"yes") == 0) break;
- bigint tmp;
- tmp = npurge;
- MPI_Allreduce(&tmp,&npurge_all,1,MPI_LMP_BIGINT,MPI_SUM,world);
- tmp = nreplace;
- MPI_Allreduce(&tmp,&nreplace_all,1,MPI_LMP_BIGINT,MPI_SUM,world);
- tmp = ntrim;
- MPI_Allreduce(&tmp,&ntrim_all,1,MPI_LMP_BIGINT,MPI_SUM,world);
- tmp = nadd;
- MPI_Allreduce(&tmp,&nadd_all,1,MPI_LMP_BIGINT,MPI_SUM,world);
+ nfield = 0;
+ fieldtype[nfield++] = ID;
+ if (iarg < narg) fieldtype[nfield++] = TYPE;
- if (me == 0) {
- if (screen) {
- fprintf(screen," " BIGINT_FORMAT " atoms before read\n",natoms_prev);
- fprintf(screen," " BIGINT_FORMAT " atoms in snapshot\n",nsnapatoms);
- fprintf(screen," " BIGINT_FORMAT " atoms purged\n",npurge_all);
- fprintf(screen," " BIGINT_FORMAT " atoms replaced\n",nreplace_all);
- fprintf(screen," " BIGINT_FORMAT " atoms trimmed\n",ntrim_all);
- fprintf(screen," " BIGINT_FORMAT " atoms added\n",nadd_all);
- fprintf(screen," " BIGINT_FORMAT " atoms after read\n",atom->natoms);
- }
- if (logfile) {
- fprintf(logfile," " BIGINT_FORMAT " atoms before read\n",natoms_prev);
- fprintf(logfile," " BIGINT_FORMAT " atoms in snapshot\n",nsnapatoms);
- fprintf(logfile," " BIGINT_FORMAT " atoms purged\n",npurge_all);
- fprintf(logfile," " BIGINT_FORMAT " atoms replaced\n",nreplace_all);
- fprintf(logfile," " BIGINT_FORMAT " atoms trimmed\n",ntrim_all);
- fprintf(logfile," " BIGINT_FORMAT " atoms added\n",nadd_all);
- fprintf(logfile," " BIGINT_FORMAT " atoms after read\n",atom->natoms);
- }
+ // parse fields
+
+ iarg = 0;
+ while (iarg < narg) {
+ if (strcmp(arg[iarg],"x") == 0) fieldtype[nfield++] = X;
+ else if (strcmp(arg[iarg],"y") == 0) fieldtype[nfield++] = Y;
+ else if (strcmp(arg[iarg],"z") == 0) fieldtype[nfield++] = Z;
+ else if (strcmp(arg[iarg],"vx") == 0) fieldtype[nfield++] = VX;
+ else if (strcmp(arg[iarg],"vy") == 0) fieldtype[nfield++] = VY;
+ else if (strcmp(arg[iarg],"vz") == 0) fieldtype[nfield++] = VZ;
+ else if (strcmp(arg[iarg],"ix") == 0) fieldtype[nfield++] = IX;
+ else if (strcmp(arg[iarg],"iy") == 0) fieldtype[nfield++] = IY;
+ else if (strcmp(arg[iarg],"iz") == 0) fieldtype[nfield++] = IZ;
+ else break;
+ iarg++;
}
-}
+ // check for no fields
+
+ if (fieldtype[nfield-1] == ID || fieldtype[nfield-1] == TYPE)
+ error->all(FLERR,"Illegal read_dump command");
+
+ if (dimension == 2) {
+ for (int i = 0; i < nfield; i++)
+ if (fieldtype[i] == Z || fieldtype[i] == VZ || fieldtype[i] == IZ)
+ error->all(FLERR,"Illegal read_dump command");
+ }
+
+ for (int i = 0; i < nfield; i++)
+ for (int j = i+1; j < nfield; j++)
+ if (fieldtype[i] == fieldtype[j])
+ error->all(FLERR,"Duplicate fields in read_dump command");
+
+ // parse optional args
+
+ boxflag = 1;
+ replaceflag = 1;
+ purgeflag = 0;
+ trimflag = 0;
+ addflag = 0;
+ for (int i = 0; i < nfield; i++) fieldlabel[i] = NULL;
+ scaledflag = UNSCALED;
+ format = NATIVE;
+
+ while (iarg < narg) {
+ if (strcmp(arg[iarg],"box") == 0) {
+ if (iarg+2 > narg) error->all(FLERR,"Illegal read_dump command");
+ if (strcmp(arg[iarg+1],"yes") == 0) boxflag = 1;
+ else if (strcmp(arg[iarg+1],"no") == 0) boxflag = 0;
+ else error->all(FLERR,"Illegal read_dump command");
+ iarg += 2;
+ } else if (strcmp(arg[iarg],"replace") == 0) {
+ if (iarg+2 > narg) error->all(FLERR,"Illegal read_dump command");
+ if (strcmp(arg[iarg+1],"yes") == 0) replaceflag = 1;
+ else if (strcmp(arg[iarg+1],"no") == 0) replaceflag = 0;
+ else error->all(FLERR,"Illegal read_dump command");
+ iarg += 2;
+ } else if (strcmp(arg[iarg],"purge") == 0) {
+ if (iarg+2 > narg) error->all(FLERR,"Illegal read_dump command");
+ if (strcmp(arg[iarg+1],"yes") == 0) purgeflag = 1;
+ else if (strcmp(arg[iarg+1],"no") == 0) purgeflag = 0;
+ else error->all(FLERR,"Illegal read_dump command");
+ iarg += 2;
+ } else if (strcmp(arg[iarg],"trim") == 0) {
+ if (iarg+2 > narg) error->all(FLERR,"Illegal read_dump command");
+ if (strcmp(arg[iarg+1],"yes") == 0) trimflag = 1;
+ else if (strcmp(arg[iarg+1],"no") == 0) trimflag = 0;
+ else error->all(FLERR,"Illegal read_dump command");
+ iarg += 2;
+ } else if (strcmp(arg[iarg],"add") == 0) {
+ if (iarg+2 > narg) error->all(FLERR,"Illegal read_dump command");
+ if (strcmp(arg[iarg+1],"yes") == 0) addflag = 1;
+ else if (strcmp(arg[iarg+1],"no") == 0) addflag = 0;
+ else error->all(FLERR,"Illegal read_dump command");
+ iarg += 2;
+ } else if (strcmp(arg[iarg],"label") == 0) {
+ if (iarg+3 > narg) error->all(FLERR,"Illegal read_dump command");
+ int i;
+ for (i = 0; i < nfield; i++)
+ if (fieldlabel[i] && strcmp(arg[iarg+1],fieldlabel[i]) == 0) break;
+ if (i == nfield) error->all(FLERR,"Illegal read_dump command");
+ int n = strlen(arg[iarg+2]) + 1;
+ fieldlabel[i] = new char[n];
+ strcpy(fieldlabel[i],arg[iarg+2]);
+ iarg += 3;
+ } else if (strcmp(arg[iarg],"scaled") == 0) {
+ if (iarg+2 > narg) error->all(FLERR,"Illegal read_dump command");
+ if (strcmp(arg[iarg+1],"yes") == 0) scaledflag = SCALED;
+ else if (strcmp(arg[iarg+1],"no") == 0) scaledflag = UNSCALED;
+ else error->all(FLERR,"Illegal read_dump command");
+ iarg += 2;
+ } else if (strcmp(arg[iarg],"format") == 0) {
+ if (iarg+2 > narg) error->all(FLERR,"Illegal read_dump command");
+ if (strcmp(arg[iarg+1],"native") == 0) format = NATIVE;
+ else error->all(FLERR,"Illegal read_dump command");
+ iarg += 2;
+ } else error->all(FLERR,"Illegal read_dump command");
+ }
+
+ if (purgeflag && (replaceflag || trimflag))
+ error->all(FLERR,"If read_dump purges it cannot replace or trim");
+}
/* ----------------------------------------------------------------------
process each of N atoms in chunk read from dump file
@@ -462,48 +642,48 @@ void ReadDump::process_atoms(int n)
nreplace++;
// current image flags
-
+
xbox = (image[m] & 1023) - 512;
ybox = (image[m] >> 10 & 1023) - 512;
zbox = (image[m] >> 20) - 512;
-
+
// overwrite atom attributes with field info
// start from field 1 since 0 = id, 1 will be skipped if type
-
+
for (ifield = 1; ifield < nfield; ifield++) {
- switch (fieldtype[ifield]) {
- case X:
- x[m][0] = xfield(i,ifield);
- break;
- case Y:
- x[m][1] = yfield(i,ifield);
- break;
- case Z:
- x[m][2] = zfield(i,ifield);
- break;
- case VX:
- v[m][0] = fields[i][ifield];
- break;
- case VY:
- v[m][1] = fields[i][ifield];
- break;
- case VZ:
- v[m][2] = fields[i][ifield];
- break;
- case IX:
- xbox = static_cast<int> (fields[i][ifield]);
- break;
- case IY:
- ybox = static_cast<int> (fields[i][ifield]);
- break;
- case IZ:
- zbox = static_cast<int> (fields[i][ifield]);
- break;
- }
+ switch (fieldtype[ifield]) {
+ case X:
+ x[m][0] = xfield(i,ifield);
+ break;
+ case Y:
+ x[m][1] = yfield(i,ifield);
+ break;
+ case Z:
+ x[m][2] = zfield(i,ifield);
+ break;
+ case VX:
+ v[m][0] = fields[i][ifield];
+ break;
+ case VY:
+ v[m][1] = fields[i][ifield];
+ break;
+ case VZ:
+ v[m][2] = fields[i][ifield];
+ break;
+ case IX:
+ xbox = static_cast<int> (fields[i][ifield]);
+ break;
+ case IY:
+ ybox = static_cast<int> (fields[i][ifield]);
+ break;
+ case IZ:
+ zbox = static_cast<int> (fields[i][ifield]);
+ break;
+ }
}
-
+
// replace image flag in case changed by ix,iy,iz fields
-
+
image[m] = (xbox << 20) | (ybox << 10) | zbox;
}
}
@@ -535,17 +715,17 @@ void ReadDump::process_atoms(int n)
for (ifield = 1; ifield < nfield; ifield++) {
switch (fieldtype[ifield]) {
case TYPE:
- itype = static_cast<int> (fields[i][ifield]);
- break;
+ itype = static_cast<int> (fields[i][ifield]);
+ break;
case X:
- one[0] = xfield(i,ifield);
- break;
+ one[0] = xfield(i,ifield);
+ break;
case Y:
- one[1] = yfield(i,ifield);
- break;
+ one[1] = yfield(i,ifield);
+ break;
case Z:
- one[2] = zfield(i,ifield);
- break;
+ one[2] = zfield(i,ifield);
+ break;
}
}
@@ -554,7 +734,7 @@ void ReadDump::process_atoms(int n)
atom->avec->create_atom(itype,one);
nadd++;
-
+
v = atom->v;
image = atom->image;
m = atom->nlocal;
@@ -567,27 +747,27 @@ void ReadDump::process_atoms(int n)
for (ifield = 1; ifield < nfield; ifield++) {
switch (fieldtype[ifield]) {
case VX:
- v[m][0] = fields[i][ifield];
- break;
+ v[m][0] = fields[i][ifield];
+ break;
case VY:
- v[m][1] = fields[i][ifield];
- break;
+ v[m][1] = fields[i][ifield];
+ break;
case VZ:
- v[m][2] = fields[i][ifield];
- break;
+ v[m][2] = fields[i][ifield];
+ break;
case IX:
- xbox = static_cast<int> (fields[i][ifield]);
- break;
+ xbox = static_cast<int> (fields[i][ifield]);
+ break;
case IY:
- ybox = static_cast<int> (fields[i][ifield]);
- break;
+ ybox = static_cast<int> (fields[i][ifield]);
+ break;
case IZ:
- zbox = static_cast<int> (fields[i][ifield]);
- break;
+ zbox = static_cast<int> (fields[i][ifield]);
+ break;
}
// replace image flag in case changed by ix,iy,iz fields
-
+
image[m] = (xbox << 20) | (ybox << 10) | zbox;
}
}
@@ -597,7 +777,7 @@ void ReadDump::process_atoms(int n)
delete atoms not flagged as replaced by dump atoms
------------------------------------------------------------------------- */
-void ReadDump::delete_atoms(int *uflag)
+void ReadDump::delete_atoms()
{
AtomVec *avec = atom->avec;
int nlocal = atom->nlocal;
@@ -625,7 +805,7 @@ double ReadDump::xfield(int i, int j)
{
if (scaled == UNSCALED) return fields[i][j];
else if (!triclinic) return fields[i][j]*xprd + xlo;
- else if (dimension == 2)
+ else if (dimension == 2)
return xprd*fields[i][j] + xy*fields[i][yindex] + xlo;
return xprd*fields[i][j] + xy*fields[i][yindex] + xz*fields[i][zindex] + xlo;
}
@@ -671,3 +851,14 @@ void ReadDump::open(char *file)
error->one(FLERR,str);
}
}
+
+/* ----------------------------------------------------------------------
+ close current dump file
+ only called by proc 0
+------------------------------------------------------------------------- */
+
+void ReadDump::close()
+{
+ if (compressed) pclose(fp);
+ else fclose(fp);
+}
diff --git a/src/read_dump.h b/src/read_dump.h
index 94f9f9bb8ba33535c81b65344e893a8239c60617..19e2323e76d21eb231a80c8db5900a39aa834297 100644
--- a/src/read_dump.h
+++ b/src/read_dump.h
@@ -30,17 +30,29 @@ namespace LAMMPS_NS {
class ReadDump : protected Pointers {
public:
ReadDump(class LAMMPS *);
- ~ReadDump() {}
+ ~ReadDump();
void command(int, char **);
+ void store_files(int, char **);
+ void setup_reader();
+ bigint seek(bigint, int);
+ void header(int);
+ bigint next(bigint, bigint, int, int);
+ void atoms();
+ void fields_and_keywords(int, char **);
+
private:
int me,nprocs;
FILE *fp;
+
int dimension;
int triclinic;
- bigint nstep; // timestep to find in dump file
- int boxflag; // use dump file box params
+ int nfiles; // # of dump files to process
+ char **files; // list of file names
+ int currentfile; // currently open file
+
+ int boxflag; // overwrite simulation with dump file box params
int replaceflag,addflag; // flags for processing dump snapshot atoms
int trimflag,purgeflag;
int scaledflag; // user setting for coordinate scaling
@@ -54,7 +66,7 @@ private:
double **fields; // per-atom field values
double box[3][3]; // dump file box parameters
- double xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz;
+ double xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz; // dump snapshot box params
double xprd,yprd,zprd;
bigint nsnapatoms; // # of atoms in dump file shapshot
@@ -69,13 +81,14 @@ private:
class ReadDumpNative *reader; // class that reads native dump file
void process_atoms(int);
- void delete_atoms(int *);
+ void delete_atoms();
double xfield(int, int);
double yfield(int, int);
double zfield(int, int);
void open(char *);
+ void close();
};
}
diff --git a/src/read_dump_native.cpp b/src/read_dump_native.cpp
index 8d0424a18d44a0965011995755f923e44a305224..695a680d3e9a6e3b1602b3e74902e4b5132e006e 100644
--- a/src/read_dump_native.cpp
+++ b/src/read_dump_native.cpp
@@ -15,7 +15,7 @@
#include "stdlib.h"
#include "read_dump_native.h"
#include "atom.h"
-#include "domain.h"
+#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
@@ -29,9 +29,6 @@ enum{UNSET,UNSCALED,SCALED};
ReadDumpNative::ReadDumpNative(LAMMPS *lmp) : Pointers(lmp)
{
- dimension = domain->dimension;
- triclinic = domain->triclinic;
-
line = new char[MAXLINE];
words = NULL;
fieldindex = NULL;
@@ -43,117 +40,132 @@ ReadDumpNative::~ReadDumpNative()
{
delete [] line;
delete [] words;
- delete [] fieldindex;
+ memory->destroy(fieldindex);
}
-/* ---------------------------------------------------------------------- */
+/* ----------------------------------------------------------------------
+ set file ptr
+ caller opens/closes dump files
+------------------------------------------------------------------------- */
-void ReadDumpNative::init(FILE *fpcaller)
+void ReadDumpNative::file(FILE *fpcaller)
{
fp = fpcaller;
}
/* ----------------------------------------------------------------------
- proc 0 scans dump file until reaching snapshot with timestamp = Nstep
- extract natoms and box bounds from snapshot
- set fieldindex for specified fields and overall scaled setting
- error check on current vs new box and fields
- NOTE: error checking should maybe be moved to parent
+ read and return time stamp from dump file
+ if first read reaches end-of-file, return 1 so caller can open next file
+ only called by proc 0
------------------------------------------------------------------------- */
-void ReadDumpNative::scan(bigint nstep,
- int nfield_caller, int *fieldtype,
- char **fieldlabel, int scaledflag,
- bigint &natoms, double box[3][3], int &scaled)
+int ReadDumpNative::read_time(bigint &ntimestep)
{
- int nchunk,triclinic_snap,s_index,u_index,su_index;
- bigint ntimestep,nremain;
- char *bc,*names;
-
- nfield = nfield_caller;
+ char *eof = fgets(line,MAXLINE,fp);
+ if (eof == NULL) return 1;
+ if (strstr(line,"ITEM: TIMESTEP") != line)
+ error->one(FLERR,"Dump file is incorrectly formatted");
read_lines(1);
+ sscanf(line,BIGINT_FORMAT,&ntimestep);
- while (1) {
- if (strstr(line,"ITEM: TIMESTEP") != line)
- error->one(FLERR,"Incorrectly formatted dump file");
- read_lines(1);
- sscanf(line,BIGINT_FORMAT,&ntimestep);
-
- if (ntimestep > nstep)
- error->one(FLERR,"Dump file does not contain requested snapshot");
+ return 0;
+}
- read_lines(2);
- sscanf(line,BIGINT_FORMAT,&natoms);
+/* ----------------------------------------------------------------------
+ skip snapshot from timestamp onward
+ only called by proc 0
+------------------------------------------------------------------------- */
- // skip snapshot
- // invoke read_lines() in chunks no larger than MAXSMALLINT
+void ReadDumpNative::skip()
+{
+ read_lines(2);
+ bigint natoms;
+ sscanf(line,BIGINT_FORMAT,&natoms);
- if (ntimestep < nstep) {
- read_lines(5);
+ read_lines(5);
- nremain = natoms;
- while (nremain) {
- nchunk = MIN(nremain,MAXSMALLINT);
- read_lines(nchunk);
- nremain -= nchunk;
- }
+ // invoke read_lines() in chunks no larger than MAXSMALLINT
- read_lines(1);
- } else break;
+ int nchunk;
+ bigint nremain = natoms;
+ while (nremain) {
+ nchunk = MIN(nremain,MAXSMALLINT);
+ read_lines(nchunk);
+ nremain -= nchunk;
}
+}
- // found correct snapshot
- // read box size and boundary conditions
+/* ----------------------------------------------------------------------
+ read remaining header info:
+ return natoms
+ box bounds, triclinic (inferred), fieldflag (1 if any fields not found),
+ xyz flag = UNSET (not a requested field), SCALED, UNSCALED
+ if fieldflag set:
+ match Nfield fields to per-atom column labels
+ allocate and set fieldindex = which column each field maps to
+ fieldtype = X,VX,IZ etc
+ fieldlabel = user-specified label or NULL if use fieldtype default
+ xyz flag = scaledflag if has fieldlabel name, else set by x,xs,xu,xsu
+ only called by proc 0
+------------------------------------------------------------------------- */
+
+bigint ReadDumpNative::read_header(double box[3][3], int &triclinic,
+ int fieldinfo, int nfield,
+ int *fieldtype, char **fieldlabel,
+ int scaledflag, int &fieldflag,
+ int &xflag, int &yflag, int &zflag)
+{
+ bigint natoms;
+ read_lines(2);
+ sscanf(line,BIGINT_FORMAT,&natoms);
- triclinic_snap = 0;
+ triclinic = 0;
box[0][2] = box[1][2] = box[2][2] = 0.0;
read_lines(1);
- bc = &line[strlen("ITEM: BOX BOUNDS ")];
- if (bc[0] == 'x') {
- triclinic_snap = 1;
- bc = &bc[9];
- }
-
- char boundstr[9];
- domain->boundary_string(boundstr);
- if (strstr(bc,boundstr) != bc)
- error->warning(FLERR,"Read_dump boundary flags do not match simulation");
-
+ if (line[strlen("ITEM: BOX BOUNDS ")] == 'x') triclinic = 1;
+
read_lines(1);
- if (!triclinic_snap) sscanf(line,"%lg %lg",&box[0][0],&box[0][1]);
+ if (!triclinic) sscanf(line,"%lg %lg",&box[0][0],&box[0][1]);
else sscanf(line,"%lg %lg %lg",&box[0][0],&box[0][1],&box[0][2]);
read_lines(1);
- if (!triclinic_snap) sscanf(line,"%lg %lg",&box[1][0],&box[1][1]);
+ if (!triclinic) sscanf(line,"%lg %lg",&box[1][0],&box[1][1]);
else sscanf(line,"%lg %lg %lg",&box[1][0],&box[1][1],&box[1][2]);
read_lines(1);
- if (!triclinic_snap) sscanf(line,"%lg %lg",&box[2][0],&box[2][1]);
+ if (!triclinic) sscanf(line,"%lg %lg",&box[2][0],&box[2][1]);
else sscanf(line,"%lg %lg %lg",&box[2][0],&box[2][1],&box[2][2]);
-
- // read ITEM: ATOMS line
- // labels = column labels
-
+
read_lines(1);
- names = &line[strlen("ITEM: ATOMS ")];
-
- nwords = atom->count_words(names);
+
+ // if no field info requested, just return
+
+ if (!fieldinfo) return natoms;
+
+ // exatract column labels and match to requested fields
+
+ char *labelline = &line[strlen("ITEM: ATOMS ")];
+
+ nwords = atom->count_words(labelline);
char **labels = new char*[nwords];
- labels[0] = strtok(names," \t\n\r\f");
- if (labels[0] == NULL)
- error->one(FLERR,"Incorrect atom format in dump file");
+ labels[0] = strtok(labelline," \t\n\r\f");
+ if (labels[0] == NULL) return 1;
for (int m = 1; m < nwords; m++) {
labels[m] = strtok(NULL," \t\n\r\f");
- if (labels[m] == NULL)
- error->one(FLERR,"Incorrect atom format in dump file");
+ if (labels[m] == NULL) return 1;
}
-
- // match each field with column
-
- fieldindex = new int[nfield];
- int xflag = UNSET;
- int yflag = UNSET;
- int zflag = UNSET;
-
+
+ // match each field with a column of per-atom data
+ // if fieldlabel set, match with explicit column
+ // else infer one or more column matches from fieldtype
+ // xyz flag set by scaledflag (if fieldlabel set) or column label
+
+ memory->create(fieldindex,nfield,"read_dump:fieldindex");
+
+ int s_index,u_index,su_index;
+ xflag = UNSET;
+ yflag = UNSET;
+ zflag = UNSET;
+
for (int i = 0; i < nfield; i++) {
if (fieldlabel[i]) {
fieldindex[i] = find_label(fieldlabel[i],nwords,labels);
@@ -161,81 +173,81 @@ void ReadDumpNative::scan(bigint nstep,
else if (fieldtype[i] == Y) yflag = scaledflag;
else if (fieldtype[i] == Z) zflag = scaledflag;
}
-
+
else if (fieldtype[i] == ID)
fieldindex[i] = find_label("id",nwords,labels);
else if (fieldtype[i] == TYPE)
fieldindex[i] = find_label("type",nwords,labels);
-
+
else if (fieldtype[i] == X) {
fieldindex[i] = find_label("x",nwords,labels);
xflag = UNSCALED;
if (fieldindex[i] < 0) {
- fieldindex[i] = nwords;
- s_index = find_label("xs",nwords,labels);
- u_index = find_label("xu",nwords,labels);
- su_index = find_label("xsu",nwords,labels);
- if (s_index >= 0 && s_index < fieldindex[i]) {
- fieldindex[i] = s_index;
- xflag = SCALED;
- }
- if (u_index >= 0 && u_index < fieldindex[i]) {
- fieldindex[i] = u_index;
- xflag = UNSCALED;
- }
- if (su_index >= 0 && su_index < fieldindex[i]) {
- fieldindex[i] = su_index;
- xflag = SCALED;
- }
+ fieldindex[i] = nwords;
+ s_index = find_label("xs",nwords,labels);
+ u_index = find_label("xu",nwords,labels);
+ su_index = find_label("xsu",nwords,labels);
+ if (s_index >= 0 && s_index < fieldindex[i]) {
+ fieldindex[i] = s_index;
+ xflag = SCALED;
+ }
+ if (u_index >= 0 && u_index < fieldindex[i]) {
+ fieldindex[i] = u_index;
+ xflag = UNSCALED;
+ }
+ if (su_index >= 0 && su_index < fieldindex[i]) {
+ fieldindex[i] = su_index;
+ xflag = SCALED;
+ }
}
if (fieldindex[i] == nwords) fieldindex[i] = -1;
-
+
} else if (fieldtype[i] == Y) {
fieldindex[i] = find_label("y",nwords,labels);
yflag = UNSCALED;
if (fieldindex[i] < 0) {
- fieldindex[i] = nwords;
- s_index = find_label("ys",nwords,labels);
- u_index = find_label("yu",nwords,labels);
- su_index = find_label("ysu",nwords,labels);
- if (s_index >= 0 && s_index < fieldindex[i]) {
- fieldindex[i] = s_index;
- yflag = SCALED;
- }
- if (u_index >= 0 && u_index < fieldindex[i]) {
- fieldindex[i] = u_index;
- yflag = UNSCALED;
- }
- if (su_index >= 0 && su_index < fieldindex[i]) {
- fieldindex[i] = su_index;
- yflag = SCALED;
- }
+ fieldindex[i] = nwords;
+ s_index = find_label("ys",nwords,labels);
+ u_index = find_label("yu",nwords,labels);
+ su_index = find_label("ysu",nwords,labels);
+ if (s_index >= 0 && s_index < fieldindex[i]) {
+ fieldindex[i] = s_index;
+ yflag = SCALED;
+ }
+ if (u_index >= 0 && u_index < fieldindex[i]) {
+ fieldindex[i] = u_index;
+ yflag = UNSCALED;
+ }
+ if (su_index >= 0 && su_index < fieldindex[i]) {
+ fieldindex[i] = su_index;
+ yflag = SCALED;
+ }
}
if (fieldindex[i] == nwords) fieldindex[i] = -1;
-
+
} else if (fieldtype[i] == Z) {
fieldindex[i] = find_label("z",nwords,labels);
zflag = UNSCALED;
if (fieldindex[i] < 0) {
- fieldindex[i] = nwords;
- s_index = find_label("zs",nwords,labels);
- u_index = find_label("zu",nwords,labels);
- su_index = find_label("zsu",nwords,labels);
- if (s_index >= 0 && s_index < fieldindex[i]) {
- fieldindex[i] = s_index;
- zflag = SCALED;
- }
- if (u_index >= 0 && u_index < fieldindex[i]) {
- fieldindex[i] = u_index;
- zflag = UNSCALED;
- }
- if (su_index >= 0 && su_index < fieldindex[i]) {
- fieldindex[i] = su_index;
- zflag = SCALED;
- }
+ fieldindex[i] = nwords;
+ s_index = find_label("zs",nwords,labels);
+ u_index = find_label("zu",nwords,labels);
+ su_index = find_label("zsu",nwords,labels);
+ if (s_index >= 0 && s_index < fieldindex[i]) {
+ fieldindex[i] = s_index;
+ zflag = SCALED;
+ }
+ if (u_index >= 0 && u_index < fieldindex[i]) {
+ fieldindex[i] = u_index;
+ zflag = UNSCALED;
+ }
+ if (su_index >= 0 && su_index < fieldindex[i]) {
+ fieldindex[i] = su_index;
+ zflag = SCALED;
+ }
}
if (fieldindex[i] == nwords) fieldindex[i] = -1;
-
+
} else if (fieldtype[i] == VX)
fieldindex[i] = find_label("vx",nwords,labels);
else if (fieldtype[i] == VY)
@@ -249,52 +261,30 @@ void ReadDumpNative::scan(bigint nstep,
else if (fieldtype[i] == IZ)
fieldindex[i] = find_label("iz",nwords,labels);
}
-
- // error checks
-
- if ((triclinic_snap && !triclinic) ||
- (!triclinic_snap && triclinic))
- error->one(FLERR,"Read_dump triclinic setting does not match simulation");
-
- for (int i = 0; i < nfield; i++)
- if (fieldindex[i] < 0)
- error->one(FLERR,"Read_dump field not found in dump file");
-
- // set overall scaling of coordinates
- // error if x,y,z scaling is not the same
-
- scaled = MAX(xflag,yflag);
- scaled = MAX(zflag,scaled);
- if ((xflag != UNSET && xflag != scaled) ||
- (yflag != UNSET && yflag != scaled) ||
- (zflag != UNSET && zflag != scaled))
- error->one(FLERR,"Read_dump x,y,z fields do not have consistent scaling");
-
- // scaled, triclinic coords require all 3 x,y,z fields to perform unscaling
-
- if (scaled == SCALED && triclinic) {
- int flag = 0;
- if (xflag != scaled) flag = 1;
- if (yflag != scaled) flag = 1;
- if (dimension == 3 && zflag != scaled) flag = 1;
- if (flag)
- error->one(FLERR,"All read_dump x,y,z fields must be specified for "
- "scaled, triclinic coords");
- }
-
+
delete [] labels;
-
- // create vector of word ptrs for future parsing of per-atom lines
-
+
+ // set fieldflag = 1 if any unfound fields
+
+ fieldflag = 0;
+ for (int i = 0; i < nfield; i++)
+ if (fieldindex[i] < 0) fieldflag = 1;
+
+ // create internal vector of word ptrs for future parsing of per-atom lines
+
words = new char*[nwords];
+
+ return natoms;
}
/* ----------------------------------------------------------------------
- proc 0 reads N atom lines from dump file
+ read N atom lines from dump file
stores appropriate values in fields array
+ return 0 if success, 1 if error
+ only called by proc 0
------------------------------------------------------------------------- */
-void ReadDumpNative::read(int n, double **fields)
+void ReadDumpNative::read_atoms(int n, int nfield, double **fields)
{
int i,m;
char *eof;
@@ -329,13 +319,15 @@ int ReadDumpNative::find_label(const char *label, int n, char **labels)
}
/* ----------------------------------------------------------------------
- proc 0 reads N lines from file
+ read N lines from dump file
only last one is saved in line
+ return NULL if end-of-file error, else non-NULL
+ only called by proc 0
------------------------------------------------------------------------- */
void ReadDumpNative::read_lines(int n)
{
char *eof;
for (int i = 0; i < n; i++) eof = fgets(line,MAXLINE,fp);
- if (eof == NULL) error->one(FLERR,"Unexpected end of dump file");
+ if (eof == NULL) error->all(FLERR,"Unexpected end of dump file");
}
diff --git a/src/read_dump_native.h b/src/read_dump_native.h
index 183710ebdfa758dbc32e7b1def531348ed8293ca..e7295c253527c6385fc345371874c9e5d66a4fab 100644
--- a/src/read_dump_native.h
+++ b/src/read_dump_native.h
@@ -26,21 +26,20 @@ class ReadDumpNative : protected Pointers {
ReadDumpNative(class LAMMPS *);
~ReadDumpNative();
- void init(FILE *);
- void scan(bigint, int, int *, char **, int, bigint &, double [3][3], int &);
- void read(int, double **);
+ void file(FILE *);
+ int read_time(bigint &);
+ void skip();
+ bigint read_header(double [3][3], int &, int, int, int *, char **,
+ int, int &, int &, int &, int &);
+ void read_atoms(int, int, double **);
private:
FILE *fp; // pointer to file opened by caller
char *line; // line read from dump file
- int dimension;
- int triclinic;
int nwords; // # of per-atom columns in dump file
- char **words; // ptrs to words in parsed per-atom line
-
- int nfield; // # of fields to extract for each atom
- int *fieldindex; // index into words for each field
+ char **words; // ptrs to values in parsed per-atom line
+ int *fieldindex; //
int find_label(const char *, int, char **);
void read_lines(int);
diff --git a/src/read_restart.cpp b/src/read_restart.cpp
index accb4b94583d31f0cdefa5d3fad03a763079a7ea..3afd4c42e21de2ba830e120b65e1c4b67af6ca99 100644
--- a/src/read_restart.cpp
+++ b/src/read_restart.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -71,7 +71,7 @@ void ReadRestart::command(int narg, char **arg)
{
if (narg != 1) error->all(FLERR,"Illegal read_restart command");
- if (domain->box_exist)
+ if (domain->box_exist)
error->all(FLERR,"Cannot read_restart after simulation box is defined");
MPI_Comm_rank(world,&me);
@@ -181,30 +181,30 @@ void ReadRestart::command(int narg, char **arg)
for (int iproc = 0; iproc < nprocs_file; iproc++) {
n = read_int();
if (n > maxbuf) {
- maxbuf = n;
- memory->destroy(buf);
- memory->create(buf,maxbuf,"read_restart:buf");
+ maxbuf = n;
+ memory->destroy(buf);
+ memory->create(buf,maxbuf,"read_restart:buf");
}
if (n > 0) {
- if (me == 0) nread_double(buf,n,fp);
- MPI_Bcast(buf,n,MPI_DOUBLE,0,world);
+ if (me == 0) nread_double(buf,n,fp);
+ MPI_Bcast(buf,n,MPI_DOUBLE,0,world);
}
m = 0;
while (m < n) {
- x = &buf[m+1];
- if (triclinic) {
- domain->x2lamda(x,lamda);
- coord = lamda;
- } else coord = x;
-
- if (coord[0] >= sublo[0] && coord[0] < subhi[0] &&
- coord[1] >= sublo[1] && coord[1] < subhi[1] &&
- coord[2] >= sublo[2] && coord[2] < subhi[2]) {
- m += avec->unpack_restart(&buf[m]);
- }
- else m += static_cast<int> (buf[m]);
+ x = &buf[m+1];
+ if (triclinic) {
+ domain->x2lamda(x,lamda);
+ coord = lamda;
+ } else coord = x;
+
+ if (coord[0] >= sublo[0] && coord[0] < subhi[0] &&
+ coord[1] >= sublo[1] && coord[1] < subhi[1] &&
+ coord[2] >= sublo[2] && coord[2] < subhi[2]) {
+ m += avec->unpack_restart(&buf[m]);
+ }
+ else m += static_cast<int> (buf[m]);
}
}
@@ -227,16 +227,16 @@ void ReadRestart::command(int narg, char **arg)
*ptr = '%';
fp = fopen(perproc,"rb");
if (fp == NULL) {
- char str[128];
- sprintf(str,"Cannot open restart file %s",perproc);
- error->one(FLERR,str);
+ char str[128];
+ sprintf(str,"Cannot open restart file %s",perproc);
+ error->one(FLERR,str);
}
nread_int(&n,1,fp);
if (n > maxbuf) {
- maxbuf = n;
- memory->destroy(buf);
- memory->create(buf,maxbuf,"read_restart:buf");
+ maxbuf = n;
+ memory->destroy(buf);
+ memory->create(buf,maxbuf,"read_restart:buf");
}
if (n > 0) nread_double(buf,n,fp);
@@ -288,8 +288,8 @@ void ReadRestart::command(int narg, char **arg)
double **atom_extra = atom->extra;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
- for (int j = 0; j < count[i]; j++)
- atom_extra[i][j] = extra[i][j];
+ for (int j = 0; j < count[i]; j++)
+ atom_extra[i][j] = extra[i][j];
modify->delete_fix("_read_restart");
}
}
@@ -310,7 +310,7 @@ void ReadRestart::command(int narg, char **arg)
if (logfile) fprintf(logfile," " BIGINT_FORMAT " atoms\n",natoms);
}
- if (natoms != atom->natoms)
+ if (natoms != atom->natoms)
error->all(FLERR,"Did not assign all atoms correctly");
if (me == 0) {
@@ -320,21 +320,21 @@ void ReadRestart::command(int narg, char **arg)
}
if (atom->nangles) {
if (screen) fprintf(screen," " BIGINT_FORMAT " angles\n",
- atom->nangles);
+ atom->nangles);
if (logfile) fprintf(logfile," " BIGINT_FORMAT " angles\n",
- atom->nangles);
+ atom->nangles);
}
if (atom->ndihedrals) {
if (screen) fprintf(screen," " BIGINT_FORMAT " dihedrals\n",
- atom->ndihedrals);
+ atom->ndihedrals);
if (logfile) fprintf(logfile," " BIGINT_FORMAT " dihedrals\n",
- atom->ndihedrals);
+ atom->ndihedrals);
}
if (atom->nimpropers) {
if (screen) fprintf(screen," " BIGINT_FORMAT " impropers\n",
- atom->nimpropers);
+ atom->nimpropers);
if (logfile) fprintf(logfile," " BIGINT_FORMAT " impropers\n",
- atom->nimpropers);
+ atom->nimpropers);
}
}
@@ -414,7 +414,7 @@ void ReadRestart::file_search(char *infile, char *outfile)
struct dirent *ep;
DIR *dp = opendir(dirname);
- if (dp == NULL)
+ if (dp == NULL)
error->one(FLERR,"Cannot open dir to search for restart file");
while (ep = readdir(dp)) {
if (strstr(ep->d_name,begin) != ep->d_name) continue;
@@ -448,7 +448,7 @@ void ReadRestart::file_search(char *infile, char *outfile)
}
/* ----------------------------------------------------------------------
- read header of restart file
+ read header of restart file
------------------------------------------------------------------------- */
void ReadRestart::header()
@@ -467,27 +467,27 @@ void ReadRestart::header()
if (flag == VERSION) {
char *version = read_char();
if (strcmp(version,universe->version) != 0 && me == 0) {
- error->warning(FLERR,
- "Restart file version does not match LAMMPS version");
- if (screen) fprintf(screen," restart file = %s, LAMMPS = %s\n",
- version,universe->version);
+ error->warning(FLERR,
+ "Restart file version does not match LAMMPS version");
+ if (screen) fprintf(screen," restart file = %s, LAMMPS = %s\n",
+ version,universe->version);
}
delete [] version;
-
+
// check lmptype.h sizes, error if different
} else if (flag == SMALLINT) {
int size = read_int();
if (size != sizeof(smallint))
- error->all(FLERR,"Smallint setting in lmptype.h is not compatible");
+ error->all(FLERR,"Smallint setting in lmptype.h is not compatible");
} else if (flag == TAGINT) {
int size = read_int();
if (size != sizeof(tagint))
- error->all(FLERR,"Tagint setting in lmptype.h is not compatible");
+ error->all(FLERR,"Tagint setting in lmptype.h is not compatible");
} else if (flag == BIGINT) {
int size = read_int();
if (size != sizeof(bigint))
- error->all(FLERR,"Bigint setting in lmptype.h is not compatible");
+ error->all(FLERR,"Bigint setting in lmptype.h is not compatible");
// reset unit_style only if different
// so that timestep,neighbor-skin are not changed
@@ -506,15 +506,15 @@ void ReadRestart::header()
int dimension = read_int();
domain->dimension = dimension;
if (domain->dimension == 2 && domain->zperiodic == 0)
- error->all(FLERR,
- "Cannot run 2d simulation with nonperiodic Z dimension");
+ error->all(FLERR,
+ "Cannot run 2d simulation with nonperiodic Z dimension");
// read nprocs from restart file, warn if different
} else if (flag == NPROCS) {
nprocs_file = read_int();
if (nprocs_file != comm->nprocs && me == 0)
- error->warning(FLERR,"Restart file used different # of processors");
+ error->warning(FLERR,"Restart file used different # of processors");
// don't set procgrid, warn if different
@@ -524,10 +524,10 @@ void ReadRestart::header()
py = read_int();
} else if (flag == PROCGRID_2) {
pz = read_int();
- if (comm->user_procgrid[0] != 0 &&
- (px != comm->user_procgrid[0] || py != comm->user_procgrid[1] ||
- pz != comm->user_procgrid[2]) && me == 0)
- error->warning(FLERR,"Restart file used different 3d processor grid");
+ if (comm->user_procgrid[0] != 0 &&
+ (px != comm->user_procgrid[0] || py != comm->user_procgrid[1] ||
+ pz != comm->user_procgrid[2]) && me == 0)
+ error->warning(FLERR,"Restart file used different 3d processor grid");
// don't set newton_pair, leave input script value unchanged
// set newton_bond from restart file
@@ -536,18 +536,18 @@ void ReadRestart::header()
} else if (flag == NEWTON_PAIR) {
int newton_pair_file = read_int();
if (force->newton_pair != 1) {
- if (newton_pair_file != force->newton_pair && me == 0)
- error->warning(FLERR,
- "Restart file used different newton pair setting, "
- "using input script value");
+ if (newton_pair_file != force->newton_pair && me == 0)
+ error->warning(FLERR,
+ "Restart file used different newton pair setting, "
+ "using input script value");
}
} else if (flag == NEWTON_BOND) {
int newton_bond_file = read_int();
if (force->newton_bond != 1) {
- if (newton_bond_file != force->newton_bond && me == 0)
- error->warning(FLERR,
- "Restart file used different newton bond setting, "
- "using restart file value");
+ if (newton_bond_file != force->newton_bond && me == 0)
+ error->warning(FLERR,
+ "Restart file used different newton bond setting, "
+ "using restart file value");
}
force->newton_bond = newton_bond_file;
if (force->newton_pair || force->newton_bond) force->newton = 1;
@@ -575,20 +575,20 @@ void ReadRestart::header()
} else if (flag == BOUNDARY_21) {
boundary[2][1] = read_int();
- if (domain->boundary[0][0] || domain->boundary[0][1] ||
- domain->boundary[1][0] || domain->boundary[1][1] ||
- domain->boundary[2][0] || domain->boundary[2][1]) {
- if (boundary[0][0] != domain->boundary[0][0] ||
- boundary[0][1] != domain->boundary[0][1] ||
- boundary[1][0] != domain->boundary[1][0] ||
- boundary[1][1] != domain->boundary[1][1] ||
- boundary[2][0] != domain->boundary[2][0] ||
- boundary[2][1] != domain->boundary[2][1]) {
- if (me == 0)
- error->warning(FLERR,
- "Restart file used different boundary settings, "
- "using restart file values");
- }
+ if (domain->boundary[0][0] || domain->boundary[0][1] ||
+ domain->boundary[1][0] || domain->boundary[1][1] ||
+ domain->boundary[2][0] || domain->boundary[2][1]) {
+ if (boundary[0][0] != domain->boundary[0][0] ||
+ boundary[0][1] != domain->boundary[0][1] ||
+ boundary[1][0] != domain->boundary[1][0] ||
+ boundary[1][1] != domain->boundary[1][1] ||
+ boundary[2][0] != domain->boundary[2][0] ||
+ boundary[2][1] != domain->boundary[2][1]) {
+ if (me == 0)
+ error->warning(FLERR,
+ "Restart file used different boundary settings, "
+ "using restart file values");
+ }
}
domain->boundary[0][0] = boundary[0][0];
@@ -601,14 +601,14 @@ void ReadRestart::header()
domain->periodicity[0] = domain->xperiodic = xperiodic;
domain->periodicity[1] = domain->yperiodic = yperiodic;
domain->periodicity[2] = domain->zperiodic = zperiodic;
-
+
domain->nonperiodic = 0;
if (xperiodic == 0 || yperiodic == 0 || zperiodic == 0) {
- domain->nonperiodic = 1;
- if (boundary[0][0] >= 2 || boundary[0][1] >= 2 ||
- boundary[1][0] >= 2 || boundary[1][1] >= 2 ||
- boundary[2][0] >= 2 || boundary[2][1] >= 2)
- domain->nonperiodic = 2;
+ domain->nonperiodic = 1;
+ if (boundary[0][0] >= 2 || boundary[0][1] >= 2 ||
+ boundary[1][0] >= 2 || boundary[1][1] >= 2 ||
+ boundary[2][0] >= 2 || boundary[2][1] >= 2)
+ domain->nonperiodic = 2;
}
// create new AtomVec class
@@ -621,9 +621,9 @@ void ReadRestart::header()
char **words = NULL;
if (strcmp(style,"hybrid") == 0) {
- nwords = read_int();
- words = new char*[nwords];
- for (int i = 0; i < nwords; i++) words[i] = read_char();
+ nwords = read_int();
+ words = new char*[nwords];
+ for (int i = 0; i < nwords; i++) words[i] = read_char();
}
atom->create_avec(style,nwords,words);
@@ -717,7 +717,7 @@ void ReadRestart::type_arrays()
delete [] mass;
} else error->all(FLERR,
- "Invalid flag in type arrays section of restart file");
+ "Invalid flag in type arrays section of restart file");
flag = read_int();
}
@@ -743,8 +743,8 @@ void ReadRestart::force_fields()
delete [] style;
if (force->pair->restartinfo) force->pair->read_restart(fp);
else {
- delete force->pair;
- force->pair = NULL;
+ delete force->pair;
+ force->pair = NULL;
}
} else if (flag == BOND) {
@@ -752,7 +752,7 @@ void ReadRestart::force_fields()
style = new char[n];
if (me == 0) nread_char(style,n,fp);
MPI_Bcast(style,n,MPI_CHAR,0,world);
-
+
force->create_bond(style);
delete [] style;
force->bond->read_restart(fp);
@@ -788,7 +788,7 @@ void ReadRestart::force_fields()
force->improper->read_restart(fp);
} else error->all(FLERR,
- "Invalid flag in force field section of restart file");
+ "Invalid flag in force field section of restart file");
flag = read_int();
}
diff --git a/src/read_restart.h b/src/read_restart.h
index c7186a771d8047f1d6ea02ca3050bce8ac8c47e8..d49189075cf31e71c3e3e30523476e03043bf226 100644
--- a/src/read_restart.h
+++ b/src/read_restart.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/region.cpp b/src/region.cpp
index d73ebd368aae406faa4d9297b55886013c0b1e85..9ce1d9fd2a264437ecba0a2df7cf3a6c324b32a1 100644
--- a/src/region.cpp
+++ b/src/region.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -116,7 +116,7 @@ int Region::match(double x, double y, double z)
before: inverse transform x,y,z (unmove, then unrotate)
after: forward transform contact point xs,yx,zs (rotate, then move),
then reset contact delx,dely,delz based on new contact point
- no need to do this if no rotation since delxyz doesn't change
+ no need to do this if no rotation since delxyz doesn't change
------------------------------------------------------------------------- */
int Region::surface(double x, double y, double z, double cutoff)
@@ -183,7 +183,7 @@ void Region::forward_transform(double &x, double &y, double &z)
theta = input->variable->compute_equal(tvar);
rotate(x,y,z,theta);
}
-
+
if (moveflag) {
if (update->ntimestep != laststep) {
if (xstr) dx = input->variable->compute_equal(xvar);
@@ -221,7 +221,7 @@ void Region::inverse_transform(double &x, double &y, double &z)
theta = input->variable->compute_equal(tvar);
rotate(x,y,z,-theta);
}
-
+
laststep = update->ntimestep;
}
@@ -248,7 +248,7 @@ void Region::rotate(double &x, double &y, double &z, double angle)
double sine = sin(angle);
double cosine = cos(angle);
- double x0dotr = x*runit[0] + y*runit[1] + z*runit[2];
+ double x0dotr = x*runit[0] + y*runit[1] + z*runit[2];
c[0] = x0dotr * runit[0];
c[1] = x0dotr * runit[1];
c[2] = x0dotr * runit[2];
@@ -301,33 +301,33 @@ void Region::options(int narg, char **arg)
} else if (strcmp(arg[iarg],"move") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal region command");
if (strcmp(arg[iarg+1],"NULL") != 0) {
- if (strstr(arg[iarg+1],"v_") != arg[iarg+1])
- error->all(FLERR,"Illegal region command");
- int n = strlen(&arg[iarg+1][2]) + 1;
- xstr = new char[n];
- strcpy(xstr,&arg[iarg+1][2]);
+ if (strstr(arg[iarg+1],"v_") != arg[iarg+1])
+ error->all(FLERR,"Illegal region command");
+ int n = strlen(&arg[iarg+1][2]) + 1;
+ xstr = new char[n];
+ strcpy(xstr,&arg[iarg+1][2]);
}
if (strcmp(arg[iarg+2],"NULL") != 0) {
- if (strstr(arg[iarg+2],"v_") != arg[iarg+2])
- error->all(FLERR,"Illegal region command");
- int n = strlen(&arg[iarg+2][2]) + 1;
- ystr = new char[n];
- strcpy(ystr,&arg[iarg+2][2]);
+ if (strstr(arg[iarg+2],"v_") != arg[iarg+2])
+ error->all(FLERR,"Illegal region command");
+ int n = strlen(&arg[iarg+2][2]) + 1;
+ ystr = new char[n];
+ strcpy(ystr,&arg[iarg+2][2]);
}
if (strcmp(arg[iarg+3],"NULL") != 0) {
- if (strstr(arg[iarg+3],"v_") != arg[iarg+3])
- error->all(FLERR,"Illegal region command");
- int n = strlen(&arg[iarg+3][2]) + 1;
- zstr = new char[n];
- strcpy(zstr,&arg[iarg+3][2]);
+ if (strstr(arg[iarg+3],"v_") != arg[iarg+3])
+ error->all(FLERR,"Illegal region command");
+ int n = strlen(&arg[iarg+3][2]) + 1;
+ zstr = new char[n];
+ strcpy(zstr,&arg[iarg+3][2]);
}
moveflag = 1;
iarg += 4;
} else if (strcmp(arg[iarg],"rotate") == 0) {
if (iarg+8 > narg) error->all(FLERR,"Illegal region command");
- if (strstr(arg[iarg+1],"v_") != arg[iarg+1])
- error->all(FLERR,"Illegal region command");
+ if (strstr(arg[iarg+1],"v_") != arg[iarg+1])
+ error->all(FLERR,"Illegal region command");
int n = strlen(&arg[iarg+1][2]) + 1;
tstr = new char[n];
strcpy(tstr,&arg[iarg+1][2]);
@@ -343,8 +343,8 @@ void Region::options(int narg, char **arg)
}
// error check
-
- if ((moveflag || rotateflag) &&
+
+ if ((moveflag || rotateflag) &&
(strcmp(style,"union") == 0 || strcmp(style,"intersect") == 0))
error->all(FLERR,"Region union or intersect cannot be dynamic");
@@ -370,7 +370,7 @@ void Region::options(int narg, char **arg)
if (rotateflag) {
double len = sqrt(axis[0]*axis[0] + axis[1]*axis[1] + axis[2]*axis[2]);
- if (len == 0.0)
+ if (len == 0.0)
error->all(FLERR,"Region cannot have 0 length rotation vector");
runit[0] = axis[0]/len;
runit[1] = axis[1]/len;
diff --git a/src/region.h b/src/region.h
index 7a61f9b7b1aeeba9b808d810cd7bbb8c35ccfe57..9b04bfd9c3df3c6b6e1b7d29adbfdbc60c46f347 100644
--- a/src/region.h
+++ b/src/region.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -37,7 +37,7 @@ class Region : protected Pointers {
};
Contact *contact; // list of contacts
int cmax; // max # of contacts possible with region
-
+
Region(class LAMMPS *, int, char **);
virtual ~Region();
void init();
diff --git a/src/region_block.cpp b/src/region_block.cpp
index 9a714f53210fb077c693e047174db3e61ad99fc6..3a295472f95086b1abecf33f9f3f906ec4e47fdc 100644
--- a/src/region_block.cpp
+++ b/src/region_block.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -26,9 +26,9 @@ using namespace LAMMPS_NS;
RegBlock::RegBlock(LAMMPS *lmp, int narg, char **arg) : Region(lmp, narg, arg)
{
options(narg-8,&arg[8]);
-
+
if (strcmp(arg[2],"INF") == 0 || strcmp(arg[2],"EDGE") == 0) {
- if (domain->box_exist == 0)
+ if (domain->box_exist == 0)
error->all(FLERR,"Cannot use region INF or EDGE when box does not exist");
if (strcmp(arg[2],"INF") == 0) xlo = -BIG;
else if (domain->triclinic == 0) xlo = domain->boxlo[0];
@@ -36,7 +36,7 @@ RegBlock::RegBlock(LAMMPS *lmp, int narg, char **arg) : Region(lmp, narg, arg)
} else xlo = xscale*atof(arg[2]);
if (strcmp(arg[3],"INF") == 0 || strcmp(arg[3],"EDGE") == 0) {
- if (domain->box_exist == 0)
+ if (domain->box_exist == 0)
error->all(FLERR,"Cannot use region INF or EDGE when box does not exist");
if (strcmp(arg[3],"INF") == 0) xhi = BIG;
else if (domain->triclinic == 0) xhi = domain->boxhi[0];
@@ -44,7 +44,7 @@ RegBlock::RegBlock(LAMMPS *lmp, int narg, char **arg) : Region(lmp, narg, arg)
} else xhi = xscale*atof(arg[3]);
if (strcmp(arg[4],"INF") == 0 || strcmp(arg[4],"EDGE") == 0) {
- if (domain->box_exist == 0)
+ if (domain->box_exist == 0)
error->all(FLERR,"Cannot use region INF or EDGE when box does not exist");
if (strcmp(arg[4],"INF") == 0) ylo = -BIG;
else if (domain->triclinic == 0) ylo = domain->boxlo[1];
@@ -52,7 +52,7 @@ RegBlock::RegBlock(LAMMPS *lmp, int narg, char **arg) : Region(lmp, narg, arg)
} else ylo = yscale*atof(arg[4]);
if (strcmp(arg[5],"INF") == 0 || strcmp(arg[5],"EDGE") == 0) {
- if (domain->box_exist == 0)
+ if (domain->box_exist == 0)
error->all(FLERR,"Cannot use region INF or EDGE when box does not exist");
if (strcmp(arg[5],"INF") == 0) yhi = BIG;
else if (domain->triclinic == 0) yhi = domain->boxhi[1];
@@ -60,7 +60,7 @@ RegBlock::RegBlock(LAMMPS *lmp, int narg, char **arg) : Region(lmp, narg, arg)
} else yhi = yscale*atof(arg[5]);
if (strcmp(arg[6],"INF") == 0 || strcmp(arg[6],"EDGE") == 0) {
- if (domain->box_exist == 0)
+ if (domain->box_exist == 0)
error->all(FLERR,"Cannot use region INF or EDGE when box does not exist");
if (strcmp(arg[6],"INF") == 0) zlo = -BIG;
else if (domain->triclinic == 0) zlo = domain->boxlo[2];
@@ -68,7 +68,7 @@ RegBlock::RegBlock(LAMMPS *lmp, int narg, char **arg) : Region(lmp, narg, arg)
} else zlo = zscale*atof(arg[6]);
if (strcmp(arg[7],"INF") == 0 || strcmp(arg[7],"EDGE") == 0) {
- if (domain->box_exist == 0)
+ if (domain->box_exist == 0)
error->all(FLERR,"Cannot use region INF or EDGE when box does not exist");
if (strcmp(arg[7],"INF") == 0) zhi = BIG;
else if (domain->triclinic == 0) zhi = domain->boxhi[2];
diff --git a/src/region_block.h b/src/region_block.h
index 111051a3e302cdb4928eff9f32de73e8c1a50dcf..1d1c065e6c69a7b4c032eae76f1524cbf8397830 100644
--- a/src/region_block.h
+++ b/src/region_block.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/region_cone.cpp b/src/region_cone.cpp
index adb409118ecb9aa1825f653c91882a3f66be3fae..f692839c8faab08a560dfba4689ed58f19509c04 100644
--- a/src/region_cone.cpp
+++ b/src/region_cone.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -33,7 +33,7 @@ RegCone::RegCone(LAMMPS *lmp, int narg, char **arg) :
{
options(narg-9,&arg[9]);
- if (strcmp(arg[2],"x") && strcmp(arg[2],"y") && strcmp(arg[2],"z"))
+ if (strcmp(arg[2],"x") && strcmp(arg[2],"y") && strcmp(arg[2],"z"))
error->all(FLERR,"Illegal region cylinder command");
axis = arg[2][0];
@@ -55,7 +55,7 @@ RegCone::RegCone(LAMMPS *lmp, int narg, char **arg) :
}
if (strcmp(arg[7],"INF") == 0 || strcmp(arg[7],"EDGE") == 0) {
- if (domain->box_exist == 0)
+ if (domain->box_exist == 0)
error->all(FLERR,"Cannot use region INF or EDGE when box does not exist");
if (axis == 'x') {
if (strcmp(arg[7],"INF") == 0) lo = -BIG;
@@ -79,7 +79,7 @@ RegCone::RegCone(LAMMPS *lmp, int narg, char **arg) :
}
if (strcmp(arg[8],"INF") == 0 || strcmp(arg[7],"EDGE") == 0) {
- if (domain->box_exist == 0)
+ if (domain->box_exist == 0)
error->all(FLERR,"Cannot use region INF or EDGE when box does not exist");
if (axis == 'x') {
if (strcmp(arg[8],"INF") == 0) hi = BIG;
@@ -218,7 +218,7 @@ int RegCone::surface_interior(double *x, double cutoff)
currentradius = radiuslo + (x[0]-lo)*(radiushi-radiuslo)/(hi-lo);
// x is exterior to cone
-
+
if (r > currentradius || x[0] < lo || x[0] > hi) return 0;
// x is interior to cone or on its surface
@@ -238,11 +238,11 @@ int RegCone::surface_interior(double *x, double cutoff)
delz = x[2] - xs[2];
dist = sqrt(delx*delx + dely*dely + delz*delz);
if (dist < cutoff) {
- contact[n].r = dist;
- contact[n].delx = delx;
- contact[n].dely = dely;
- contact[n].delz = delz;
- n++;
+ contact[n].r = dist;
+ contact[n].delx = delx;
+ contact[n].dely = dely;
+ contact[n].delz = delz;
+ n++;
}
}
@@ -268,7 +268,7 @@ int RegCone::surface_interior(double *x, double cutoff)
currentradius = radiuslo + (x[1]-lo)*(radiushi-radiuslo)/(hi-lo);
// y is exterior to cone
-
+
if (r > currentradius || x[1] < lo || x[1] > hi) return 0;
// y is interior to cone or on its surface
@@ -288,11 +288,11 @@ int RegCone::surface_interior(double *x, double cutoff)
delz = x[2] - xs[2];
dist = sqrt(delx*delx + dely*dely + delz*delz);
if (dist < cutoff) {
- contact[n].r = dist;
- contact[n].delx = delx;
- contact[n].dely = dely;
- contact[n].delz = delz;
- n++;
+ contact[n].r = dist;
+ contact[n].delx = delx;
+ contact[n].dely = dely;
+ contact[n].delz = delz;
+ n++;
}
}
@@ -318,7 +318,7 @@ int RegCone::surface_interior(double *x, double cutoff)
currentradius = radiuslo + (x[2]-lo)*(radiushi-radiuslo)/(hi-lo);
// z is exterior to cone
-
+
if (r > currentradius || x[2] < lo || x[2] > hi) return 0;
// z is interior to cone or on its surface
@@ -338,11 +338,11 @@ int RegCone::surface_interior(double *x, double cutoff)
delz = x[2] - xs[2];
dist = sqrt(delx*delx + dely*dely + delz*delz);
if (dist < cutoff) {
- contact[n].r = dist;
- contact[n].delx = delx;
- contact[n].dely = dely;
- contact[n].delz = delz;
- n++;
+ contact[n].r = dist;
+ contact[n].delx = delx;
+ contact[n].dely = dely;
+ contact[n].delz = delz;
+ n++;
}
}
@@ -385,8 +385,8 @@ int RegCone::surface_exterior(double *x, double cutoff)
// x is far enough from cone that there is no contact
// x is interior to cone
- if (r >= maxradius+cutoff ||
- x[0] <= lo-cutoff || x[0] >= hi+cutoff) return 0;
+ if (r >= maxradius+cutoff ||
+ x[0] <= lo-cutoff || x[0] >= hi+cutoff) return 0;
if (r < currentradius && x[0] > lo && x[0] < hi) return 0;
// x is exterior to cone or on its surface
@@ -430,8 +430,8 @@ int RegCone::surface_exterior(double *x, double cutoff)
// y is far enough from cone that there is no contact
// y is interior to cone
- if (r >= maxradius+cutoff ||
- x[1] <= lo-cutoff || x[1] >= hi+cutoff) return 0;
+ if (r >= maxradius+cutoff ||
+ x[1] <= lo-cutoff || x[1] >= hi+cutoff) return 0;
if (r < currentradius && x[1] > lo && x[1] < hi) return 0;
// y is exterior to cone or on its surface
@@ -475,8 +475,8 @@ int RegCone::surface_exterior(double *x, double cutoff)
// z is far enough from cone that there is no contact
// z is interior to cone
- if (r >= maxradius+cutoff ||
- x[2] <= lo-cutoff || x[2] >= hi+cutoff) return 0;
+ if (r >= maxradius+cutoff ||
+ x[2] <= lo-cutoff || x[2] >= hi+cutoff) return 0;
if (r < currentradius && x[2] > lo && x[2] < hi) return 0;
// z is exterior to cone or on its surface
@@ -522,8 +522,8 @@ int RegCone::surface_exterior(double *x, double cutoff)
else closest point is between A and B
------------------------------------------------------------------------- */
-void RegCone::point_on_line_segment(double *a, double *b,
- double *c, double *d)
+void RegCone::point_on_line_segment(double *a, double *b,
+ double *c, double *d)
{
double ba[3],ca[3];
diff --git a/src/region_cone.h b/src/region_cone.h
index 782ebf2b3ca1b05a00004c187e15da4ffb7abc2f..30f9c38fb77644d96a7d9f1d221e385bf233f9a7 100644
--- a/src/region_cone.h
+++ b/src/region_cone.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/region_cylinder.cpp b/src/region_cylinder.cpp
index 9aafb9ca87fc3fcfd58520f73a5e0f6fefe9bad6..d6d71ba9b9b449267481363f4e8f5ed2ac7cb852 100644
--- a/src/region_cylinder.cpp
+++ b/src/region_cylinder.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -29,7 +29,7 @@ RegCylinder::RegCylinder(LAMMPS *lmp, int narg, char **arg) :
{
options(narg-8,&arg[8]);
- if (strcmp(arg[2],"x") && strcmp(arg[2],"y") && strcmp(arg[2],"z"))
+ if (strcmp(arg[2],"x") && strcmp(arg[2],"y") && strcmp(arg[2],"z"))
error->all(FLERR,"Illegal region cylinder command");
axis = arg[2][0];
@@ -48,7 +48,7 @@ RegCylinder::RegCylinder(LAMMPS *lmp, int narg, char **arg) :
}
if (strcmp(arg[6],"INF") == 0 || strcmp(arg[6],"EDGE") == 0) {
- if (domain->box_exist == 0)
+ if (domain->box_exist == 0)
error->all(FLERR,"Cannot use region INF or EDGE when box does not exist");
if (axis == 'x') {
if (strcmp(arg[6],"INF") == 0) lo = -BIG;
@@ -72,7 +72,7 @@ RegCylinder::RegCylinder(LAMMPS *lmp, int narg, char **arg) :
}
if (strcmp(arg[7],"INF") == 0 || strcmp(arg[6],"EDGE") == 0) {
- if (domain->box_exist == 0)
+ if (domain->box_exist == 0)
error->all(FLERR,"Cannot use region INF or EDGE when box does not exist");
if (axis == 'x') {
if (strcmp(arg[7],"INF") == 0) hi = BIG;
@@ -195,7 +195,7 @@ int RegCylinder::surface_interior(double *x, double cutoff)
r = sqrt(del1*del1 + del2*del2);
// x is exterior to cylinder
-
+
if (r > radius || x[0] < lo || x[0] > hi) return 0;
// x is interior to cylinder or on its surface
@@ -229,7 +229,7 @@ int RegCylinder::surface_interior(double *x, double cutoff)
r = sqrt(del1*del1 + del2*del2);
// y is exterior to cylinder
-
+
if (r > radius || x[1] < lo || x[1] > hi) return 0;
// y is interior to cylinder or on its surface
@@ -263,7 +263,7 @@ int RegCylinder::surface_interior(double *x, double cutoff)
r = sqrt(del1*del1 + del2*del2);
// z is exterior to cylinder
-
+
if (r > radius || x[2] < lo || x[2] > hi) return 0;
// z is interior to cylinder or on its surface
diff --git a/src/region_cylinder.h b/src/region_cylinder.h
index 63de0f1aedd3782397e92ab058d33d3e569f30d8..93bb74aaff5e531f2ae0ff1bd7617932569ffa32 100644
--- a/src/region_cylinder.h
+++ b/src/region_cylinder.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/region_intersect.cpp b/src/region_intersect.cpp
index 5618b46b270adb78ac3acfcc94f52012688fc024..1d3d78d18670b2ee2aae2a00a27db794aebdb64b 100644
--- a/src/region_intersect.cpp
+++ b/src/region_intersect.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -56,13 +56,13 @@ RegIntersect::RegIntersect(LAMMPS *lmp, int narg, char **arg) :
for (int ilist = 0; ilist < nregion; ilist++) {
if (regions[list[ilist]]->bboxflag == 0) continue;
if (first) {
- extent_xlo = regions[list[ilist]]->extent_xlo;
- extent_ylo = regions[list[ilist]]->extent_ylo;
- extent_zlo = regions[list[ilist]]->extent_zlo;
- extent_xhi = regions[list[ilist]]->extent_xhi;
- extent_yhi = regions[list[ilist]]->extent_yhi;
- extent_zhi = regions[list[ilist]]->extent_zhi;
- first = 0;
+ extent_xlo = regions[list[ilist]]->extent_xlo;
+ extent_ylo = regions[list[ilist]]->extent_ylo;
+ extent_zlo = regions[list[ilist]]->extent_zlo;
+ extent_xhi = regions[list[ilist]]->extent_xhi;
+ extent_yhi = regions[list[ilist]]->extent_yhi;
+ extent_zhi = regions[list[ilist]]->extent_zhi;
+ first = 0;
}
extent_xlo = MAX(extent_xlo,regions[list[ilist]]->extent_xlo);
@@ -141,20 +141,20 @@ int RegIntersect::surface_interior(double *x, double cutoff)
ys = x[1] - regions[iregion]->contact[m].dely;
zs = x[2] - regions[iregion]->contact[m].delz;
for (jlist = 0; jlist < nregion; jlist++) {
- if (jlist == ilist) continue;
- jregion = list[jlist];
- if (!regions[jregion]->match(xs,ys,zs)) break;
+ if (jlist == ilist) continue;
+ jregion = list[jlist];
+ if (!regions[jregion]->match(xs,ys,zs)) break;
}
if (jlist == nregion) {
- contact[n].r = regions[iregion]->contact[m].r;
- contact[n].delx = regions[iregion]->contact[m].delx;
- contact[n].dely = regions[iregion]->contact[m].dely;
- contact[n].delz = regions[iregion]->contact[m].delz;
- n++;
+ contact[n].r = regions[iregion]->contact[m].r;
+ contact[n].delx = regions[iregion]->contact[m].delx;
+ contact[n].dely = regions[iregion]->contact[m].dely;
+ contact[n].delz = regions[iregion]->contact[m].delz;
+ n++;
}
}
}
-
+
return n;
}
@@ -186,22 +186,22 @@ int RegIntersect::surface_exterior(double *x, double cutoff)
ys = x[1] - regions[iregion]->contact[m].dely;
zs = x[2] - regions[iregion]->contact[m].delz;
for (jlist = 0; jlist < nregion; jlist++) {
- if (jlist == ilist) continue;
- jregion = list[jlist];
- if (regions[jregion]->match(xs,ys,zs)) break;
+ if (jlist == ilist) continue;
+ jregion = list[jlist];
+ if (regions[jregion]->match(xs,ys,zs)) break;
}
if (jlist == nregion) {
- contact[n].r = regions[iregion]->contact[m].r;
- contact[n].delx = regions[iregion]->contact[m].delx;
- contact[n].dely = regions[iregion]->contact[m].dely;
- contact[n].delz = regions[iregion]->contact[m].delz;
- n++;
+ contact[n].r = regions[iregion]->contact[m].r;
+ contact[n].delx = regions[iregion]->contact[m].delx;
+ contact[n].dely = regions[iregion]->contact[m].dely;
+ contact[n].delz = regions[iregion]->contact[m].delz;
+ n++;
}
}
}
for (ilist = 0; ilist < nregion; ilist++)
regions[list[ilist]]->interior ^= 1;
-
+
return n;
}
diff --git a/src/region_intersect.h b/src/region_intersect.h
index c5ad1a0b0d1746eadad9a18b486db6dd42c91d87..a8bd460f34796a2a24e406f38d25af884eb1a379 100644
--- a/src/region_intersect.h
+++ b/src/region_intersect.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/region_plane.cpp b/src/region_plane.cpp
index aa2827422dbc19a785101a4e9ba454c6836bf0c8..2a7955332767f863816506b739da5c95658575f3 100644
--- a/src/region_plane.cpp
+++ b/src/region_plane.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/region_plane.h b/src/region_plane.h
index 8443a4c55e22e8367c56c753da5d8a0246c30363..a3445f2aaf128634969d5bbe86cc218c289144ec 100644
--- a/src/region_plane.h
+++ b/src/region_plane.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/region_prism.cpp b/src/region_prism.cpp
index 72f40987cdbb36c731686d7aed75521ba7a34822..041865c632a027541b122d4d15135517d6ad3f81 100644
--- a/src/region_prism.cpp
+++ b/src/region_prism.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -34,42 +34,42 @@ RegPrism::RegPrism(LAMMPS *lmp, int narg, char **arg) : Region(lmp, narg, arg)
options(narg-11,&arg[11]);
if (strcmp(arg[2],"INF") == 0 || strcmp(arg[2],"EDGE") == 0) {
- if (domain->box_exist == 0)
+ if (domain->box_exist == 0)
error->all(FLERR,"Cannot use region INF or EDGE when box does not exist");
if (strcmp(arg[2],"INF") == 0) xlo = -BIG;
else xlo = domain->boxlo[0];
} else xlo = xscale*atof(arg[2]);
if (strcmp(arg[3],"INF") == 0 || strcmp(arg[3],"EDGE") == 0) {
- if (domain->box_exist == 0)
+ if (domain->box_exist == 0)
error->all(FLERR,"Cannot use region INF or EDGE when box does not exist");
if (strcmp(arg[3],"INF") == 0) xhi = BIG;
else xhi = domain->boxhi[0];
} else xhi = xscale*atof(arg[3]);
if (strcmp(arg[4],"INF") == 0 || strcmp(arg[4],"EDGE") == 0) {
- if (domain->box_exist == 0)
+ if (domain->box_exist == 0)
error->all(FLERR,"Cannot use region INF or EDGE when box does not exist");
if (strcmp(arg[4],"INF") == 0) ylo = -BIG;
else ylo = domain->boxlo[1];
} else ylo = yscale*atof(arg[4]);
if (strcmp(arg[5],"INF") == 0 || strcmp(arg[5],"EDGE") == 0) {
- if (domain->box_exist == 0)
+ if (domain->box_exist == 0)
error->all(FLERR,"Cannot use region INF or EDGE when box does not exist");
if (strcmp(arg[5],"INF") == 0) yhi = BIG;
else yhi = domain->boxhi[1];
} else yhi = yscale*atof(arg[5]);
if (strcmp(arg[6],"INF") == 0 || strcmp(arg[6],"EDGE") == 0) {
- if (domain->box_exist == 0)
+ if (domain->box_exist == 0)
error->all(FLERR,"Cannot use region INF or EDGE when box does not exist");
if (strcmp(arg[6],"INF") == 0) zlo = -BIG;
else zlo = domain->boxlo[2];
} else zlo = zscale*atof(arg[6]);
if (strcmp(arg[7],"INF") == 0 || strcmp(arg[7],"EDGE") == 0) {
- if (domain->box_exist == 0)
+ if (domain->box_exist == 0)
error->all(FLERR,"Cannot use region INF or EDGE when box does not exist");
if (strcmp(arg[7],"INF") == 0) zhi = BIG;
else zhi = domain->boxhi[2];
@@ -102,14 +102,14 @@ RegPrism::RegPrism(LAMMPS *lmp, int narg, char **arg) : Region(lmp, narg, arg)
error->all(FLERR,"Illegal region prism command");
// extent of prism
-
+
if (interior) {
bboxflag = 1;
extent_xlo = MIN(xlo,xlo+xy);
extent_xlo = MIN(extent_xlo,extent_xlo+xz);
extent_ylo = MIN(ylo,ylo+yz);
extent_zlo = zlo;
-
+
extent_xhi = MAX(xhi,xhi+xy);
extent_xhi = MAX(extent_xhi,extent_xhi+xz);
extent_yhi = MAX(yhi,yhi+yz);
@@ -266,7 +266,7 @@ int RegPrism::surface_interior(double *x, double cutoff)
for (i = 0; i < 6; i++) {
if (i % 2) corner = chi;
else corner = clo;
- dot = (x[0]-corner[0])*face[i][0] + (x[1]-corner[1])*face[i][1] +
+ dot = (x[0]-corner[0])*face[i][0] + (x[1]-corner[1])*face[i][1] +
(x[2]-corner[2])*face[i][2];
if (dot < 0.0) return 0;
}
@@ -278,7 +278,7 @@ int RegPrism::surface_interior(double *x, double cutoff)
for (int i = 0; i < 6; i++) {
if (i % 2) corner = chi;
else corner = clo;
- dot = (x[0]-corner[0])*face[i][0] + (x[1]-corner[1])*face[i][1] +
+ dot = (x[0]-corner[0])*face[i][0] + (x[1]-corner[1])*face[i][1] +
(x[2]-corner[2])*face[i][2];
if (dot < cutoff) {
contact[n].r = dot;
@@ -310,7 +310,7 @@ int RegPrism::surface_exterior(double *x, double cutoff)
for (i = 0; i < 6; i++) {
if (i % 2) corner = chi;
else corner = clo;
- dot = (x[0]-corner[0])*face[i][0] + (x[1]-corner[1])*face[i][1] +
+ dot = (x[0]-corner[0])*face[i][0] + (x[1]-corner[1])*face[i][1] +
(x[2]-corner[2])*face[i][2];
if (dot <= -cutoff) return 0;
}
@@ -320,7 +320,7 @@ int RegPrism::surface_exterior(double *x, double cutoff)
for (i = 0; i < 6; i++) {
if (i % 2) corner = chi;
else corner = clo;
- dot = (x[0]-corner[0])*face[i][0] + (x[1]-corner[1])*face[i][1] +
+ dot = (x[0]-corner[0])*face[i][0] + (x[1]-corner[1])*face[i][1] +
(x[2]-corner[2])*face[i][2];
if (dot <= 0.0) break;
}
@@ -364,8 +364,8 @@ void RegPrism::find_nearest(double *x, double &xp, double &yp, double &zp)
i = tri[itri][0];
j = tri[itri][1];
k = tri[itri][2];
- dot = (x[0]-corners[i][0])*face[iface][0] +
- (x[1]-corners[i][1])*face[iface][1] +
+ dot = (x[0]-corners[i][0])*face[iface][0] +
+ (x[1]-corners[i][1])*face[iface][1] +
(x[2]-corners[i][2])*face[iface][2];
xproj[0] = x[0] - dot*face[iface][0];
xproj[1] = x[1] - dot*face[iface][1];
@@ -381,7 +381,7 @@ void RegPrism::find_nearest(double *x, double &xp, double &yp, double &zp)
distsq = closest(x,xline,nearest,distsq);
}
}
-
+
xp = nearest[0];
yp = nearest[1];
zp = nearest[2];
@@ -397,7 +397,7 @@ void RegPrism::find_nearest(double *x, double &xp, double &yp, double &zp)
------------------------------------------------------------------------- */
int RegPrism::inside_tri(double *x, double *v1, double *v2, double *v3,
- double *norm)
+ double *norm)
{
double edge[3],pvec[3],xproduct[3];
@@ -428,8 +428,8 @@ int RegPrism::inside_tri(double *x, double *v1, double *v2, double *v3,
else closest point is between A and B
------------------------------------------------------------------------- */
-void RegPrism::point_on_line_segment(double *a, double *b,
- double *c, double *d)
+void RegPrism::point_on_line_segment(double *a, double *b,
+ double *c, double *d)
{
double ba[3],ca[3];
diff --git a/src/region_prism.h b/src/region_prism.h
index 01f813c5fce25b35c7614e4f041045945b8676f2..b4ceb0e9b65ec493b7ac0490f4c3bbffff5bef87 100644
--- a/src/region_prism.h
+++ b/src/region_prism.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/region_sphere.cpp b/src/region_sphere.cpp
index 80446b55a81e2ba2157ed41135ce8104ed8172c3..e90704dd742dc4ad9400ebb1f041595d59db6a49 100644
--- a/src/region_sphere.cpp
+++ b/src/region_sphere.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/region_sphere.h b/src/region_sphere.h
index 53bbafd44a68582256f4c036e22539aa7ae6d364..73556d07c327d9669d7074257e1d15295073277c 100644
--- a/src/region_sphere.h
+++ b/src/region_sphere.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/region_union.cpp b/src/region_union.cpp
index ff566087efa9de199ed2779e2d571ecb3871cf0d..ca1e693f37bc69db548b5257c893891ea04b112e 100644
--- a/src/region_union.cpp
+++ b/src/region_union.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -133,20 +133,20 @@ int RegUnion::surface_interior(double *x, double cutoff)
ys = x[1] - regions[iregion]->contact[m].dely;
zs = x[2] - regions[iregion]->contact[m].delz;
for (jlist = 0; jlist < nregion; jlist++) {
- if (jlist == ilist) continue;
- jregion = list[jlist];
- if (regions[jregion]->match(xs,ys,zs)) break;
+ if (jlist == ilist) continue;
+ jregion = list[jlist];
+ if (regions[jregion]->match(xs,ys,zs)) break;
}
if (jlist == nregion) {
- contact[n].r = regions[iregion]->contact[m].r;
- contact[n].delx = regions[iregion]->contact[m].delx;
- contact[n].dely = regions[iregion]->contact[m].dely;
- contact[n].delz = regions[iregion]->contact[m].delz;
- n++;
+ contact[n].r = regions[iregion]->contact[m].r;
+ contact[n].delx = regions[iregion]->contact[m].delx;
+ contact[n].dely = regions[iregion]->contact[m].dely;
+ contact[n].delz = regions[iregion]->contact[m].delz;
+ n++;
}
}
}
-
+
return n;
}
@@ -178,22 +178,22 @@ int RegUnion::surface_exterior(double *x, double cutoff)
ys = x[1] - regions[iregion]->contact[m].dely;
zs = x[2] - regions[iregion]->contact[m].delz;
for (jlist = 0; jlist < nregion; jlist++) {
- if (jlist == ilist) continue;
- jregion = list[jlist];
- if (!regions[jregion]->match(xs,ys,zs)) break;
+ if (jlist == ilist) continue;
+ jregion = list[jlist];
+ if (!regions[jregion]->match(xs,ys,zs)) break;
}
if (jlist == nregion) {
- contact[n].r = regions[iregion]->contact[m].r;
- contact[n].delx = regions[iregion]->contact[m].delx;
- contact[n].dely = regions[iregion]->contact[m].dely;
- contact[n].delz = regions[iregion]->contact[m].delz;
- n++;
+ contact[n].r = regions[iregion]->contact[m].r;
+ contact[n].delx = regions[iregion]->contact[m].delx;
+ contact[n].dely = regions[iregion]->contact[m].dely;
+ contact[n].delz = regions[iregion]->contact[m].delz;
+ n++;
}
}
}
for (ilist = 0; ilist < nregion; ilist++)
regions[list[ilist]]->interior ^= 1;
-
+
return n;
}
diff --git a/src/region_union.h b/src/region_union.h
index aace98bfc4eb15cd2429d99302f72799fef5e73a..44d99375c983957eb41c2d8b9c6bd2311643adc7 100644
--- a/src/region_union.h
+++ b/src/region_union.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/replicate.cpp b/src/replicate.cpp
index d430be744d06448a2ab6d1a6829fbd6896ecb33c..90101668b05cde0ff7f91522e5b9611f25bfac2a 100644
--- a/src/replicate.cpp
+++ b/src/replicate.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -57,13 +57,13 @@ void Replicate::command(int narg, char **arg)
// error and warning checks
- if (nx <= 0 || ny <= 0 || nz <= 0)
+ if (nx <= 0 || ny <= 0 || nz <= 0)
error->all(FLERR,"Illegal replicate command");
if (domain->dimension == 2 && nz != 1)
error->all(FLERR,"Cannot replicate 2d simulation in z dimension");
- if ((nx > 1 && domain->xperiodic == 0) ||
+ if ((nx > 1 && domain->xperiodic == 0) ||
(ny > 1 && domain->yperiodic == 0) ||
- (nz > 1 && domain->zperiodic == 0)) {
+ (nz > 1 && domain->zperiodic == 0)) {
if (comm->me == 0)
error->warning(FLERR,"Replicating in a non-periodic dimension");
}
@@ -137,9 +137,9 @@ void Replicate::command(int narg, char **arg)
atom->tag[i] = 0;
if (nrep*old->natoms < 0 || nrep*old->natoms > MAXBIGINT ||
- nrep*old->nbonds < 0 || nrep*old->nbonds > MAXBIGINT ||
- nrep*old->nangles < 0 || nrep*old->nangles > MAXBIGINT ||
- nrep*old->ndihedrals < 0 || nrep*old->ndihedrals > MAXBIGINT ||
+ nrep*old->nbonds < 0 || nrep*old->nbonds > MAXBIGINT ||
+ nrep*old->nangles < 0 || nrep*old->nangles > MAXBIGINT ||
+ nrep*old->ndihedrals < 0 || nrep*old->ndihedrals > MAXBIGINT ||
nrep*old->nimpropers < 0 || nrep*old->nimpropers > MAXBIGINT)
error->all(FLERR,"Replicated system is too big");
@@ -156,7 +156,7 @@ void Replicate::command(int narg, char **arg)
atom->nangletypes = old->nangletypes;
atom->ndihedraltypes = old->ndihedraltypes;
atom->nimpropertypes = old->nimpropertypes;
-
+
atom->bond_per_atom = old->bond_per_atom;
atom->angle_per_atom = old->angle_per_atom;
atom->dihedral_per_atom = old->dihedral_per_atom;
@@ -270,77 +270,77 @@ void Replicate::command(int narg, char **arg)
for (ix = 0; ix < nx; ix++) {
for (iy = 0; iy < ny; iy++) {
- for (iz = 0; iz < nz; iz++) {
-
- // while loop over one proc's atom list
-
- m = 0;
- while (m < n) {
- image = (512 << 20) | (512 << 10) | 512;
- if (triclinic == 0) {
- x[0] = buf[m+1] + ix*old_xprd;
- x[1] = buf[m+2] + iy*old_yprd;
- x[2] = buf[m+3] + iz*old_zprd;
- } else {
- x[0] = buf[m+1] + ix*old_xprd + iy*old_xy + iz*old_xz;
- x[1] = buf[m+2] + iy*old_yprd + iz*old_yz;
- x[2] = buf[m+3] + iz*old_zprd;
- }
- domain->remap(x,image);
- if (triclinic) {
- domain->x2lamda(x,lamda);
- coord = lamda;
- } else coord = x;
-
- if (coord[0] >= sublo[0] && coord[0] < subhi[0] &&
- coord[1] >= sublo[1] && coord[1] < subhi[1] &&
- coord[2] >= sublo[2] && coord[2] < subhi[2]) {
-
- m += avec->unpack_restart(&buf[m]);
-
- i = atom->nlocal - 1;
- if (tag_enable)
- atom_offset = iz*ny*nx*maxtag + iy*nx*maxtag + ix*maxtag;
- else atom_offset = 0;
- mol_offset = iz*ny*nx*maxmol + iy*nx*maxmol + ix*maxmol;
-
- atom->x[i][0] = x[0];
- atom->x[i][1] = x[1];
- atom->x[i][2] = x[2];
-
- atom->tag[i] += atom_offset;
- atom->image[i] = image;
-
- if (atom->molecular) {
- if (atom->molecule[i] > 0)
- atom->molecule[i] += mol_offset;
- if (atom->avec->bonds_allow)
- for (j = 0; j < atom->num_bond[i]; j++)
- atom->bond_atom[i][j] += atom_offset;
- if (atom->avec->angles_allow)
- for (j = 0; j < atom->num_angle[i]; j++) {
- atom->angle_atom1[i][j] += atom_offset;
- atom->angle_atom2[i][j] += atom_offset;
- atom->angle_atom3[i][j] += atom_offset;
- }
- if (atom->avec->dihedrals_allow)
- for (j = 0; j < atom->num_dihedral[i]; j++) {
- atom->dihedral_atom1[i][j] += atom_offset;
- atom->dihedral_atom2[i][j] += atom_offset;
- atom->dihedral_atom3[i][j] += atom_offset;
- atom->dihedral_atom4[i][j] += atom_offset;
- }
- if (atom->avec->impropers_allow)
- for (j = 0; j < atom->num_improper[i]; j++) {
- atom->improper_atom1[i][j] += atom_offset;
- atom->improper_atom2[i][j] += atom_offset;
- atom->improper_atom3[i][j] += atom_offset;
- atom->improper_atom4[i][j] += atom_offset;
- }
- }
- } else m += static_cast<int> (buf[m]);
- }
- }
+ for (iz = 0; iz < nz; iz++) {
+
+ // while loop over one proc's atom list
+
+ m = 0;
+ while (m < n) {
+ image = (512 << 20) | (512 << 10) | 512;
+ if (triclinic == 0) {
+ x[0] = buf[m+1] + ix*old_xprd;
+ x[1] = buf[m+2] + iy*old_yprd;
+ x[2] = buf[m+3] + iz*old_zprd;
+ } else {
+ x[0] = buf[m+1] + ix*old_xprd + iy*old_xy + iz*old_xz;
+ x[1] = buf[m+2] + iy*old_yprd + iz*old_yz;
+ x[2] = buf[m+3] + iz*old_zprd;
+ }
+ domain->remap(x,image);
+ if (triclinic) {
+ domain->x2lamda(x,lamda);
+ coord = lamda;
+ } else coord = x;
+
+ if (coord[0] >= sublo[0] && coord[0] < subhi[0] &&
+ coord[1] >= sublo[1] && coord[1] < subhi[1] &&
+ coord[2] >= sublo[2] && coord[2] < subhi[2]) {
+
+ m += avec->unpack_restart(&buf[m]);
+
+ i = atom->nlocal - 1;
+ if (tag_enable)
+ atom_offset = iz*ny*nx*maxtag + iy*nx*maxtag + ix*maxtag;
+ else atom_offset = 0;
+ mol_offset = iz*ny*nx*maxmol + iy*nx*maxmol + ix*maxmol;
+
+ atom->x[i][0] = x[0];
+ atom->x[i][1] = x[1];
+ atom->x[i][2] = x[2];
+
+ atom->tag[i] += atom_offset;
+ atom->image[i] = image;
+
+ if (atom->molecular) {
+ if (atom->molecule[i] > 0)
+ atom->molecule[i] += mol_offset;
+ if (atom->avec->bonds_allow)
+ for (j = 0; j < atom->num_bond[i]; j++)
+ atom->bond_atom[i][j] += atom_offset;
+ if (atom->avec->angles_allow)
+ for (j = 0; j < atom->num_angle[i]; j++) {
+ atom->angle_atom1[i][j] += atom_offset;
+ atom->angle_atom2[i][j] += atom_offset;
+ atom->angle_atom3[i][j] += atom_offset;
+ }
+ if (atom->avec->dihedrals_allow)
+ for (j = 0; j < atom->num_dihedral[i]; j++) {
+ atom->dihedral_atom1[i][j] += atom_offset;
+ atom->dihedral_atom2[i][j] += atom_offset;
+ atom->dihedral_atom3[i][j] += atom_offset;
+ atom->dihedral_atom4[i][j] += atom_offset;
+ }
+ if (atom->avec->impropers_allow)
+ for (j = 0; j < atom->num_improper[i]; j++) {
+ atom->improper_atom1[i][j] += atom_offset;
+ atom->improper_atom2[i][j] += atom_offset;
+ atom->improper_atom3[i][j] += atom_offset;
+ atom->improper_atom4[i][j] += atom_offset;
+ }
+ }
+ } else m += static_cast<int> (buf[m]);
+ }
+ }
}
}
}
@@ -363,7 +363,7 @@ void Replicate::command(int narg, char **arg)
if (natoms != atom->natoms)
error->all(FLERR,"Replicate did not assign all atoms correctly");
-
+
if (me == 0) {
if (atom->nbonds) {
if (screen) fprintf(screen," " BIGINT_FORMAT " bonds\n",atom->nbonds);
@@ -371,21 +371,21 @@ void Replicate::command(int narg, char **arg)
}
if (atom->nangles) {
if (screen) fprintf(screen," " BIGINT_FORMAT " angles\n",
- atom->nangles);
+ atom->nangles);
if (logfile) fprintf(logfile," " BIGINT_FORMAT " angles\n",
- atom->nangles);
+ atom->nangles);
}
if (atom->ndihedrals) {
if (screen) fprintf(screen," " BIGINT_FORMAT " dihedrals\n",
- atom->ndihedrals);
+ atom->ndihedrals);
if (logfile) fprintf(logfile," " BIGINT_FORMAT " dihedrals\n",
- atom->ndihedrals);
+ atom->ndihedrals);
}
if (atom->nimpropers) {
if (screen) fprintf(screen," " BIGINT_FORMAT " impropers\n",
- atom->nimpropers);
+ atom->nimpropers);
if (logfile) fprintf(logfile," " BIGINT_FORMAT " impropers\n",
- atom->nimpropers);
+ atom->nimpropers);
}
}
diff --git a/src/replicate.h b/src/replicate.h
index 5c8f8eb967af5da3e7ed43ed6c38078e593e0dc7..79350cdfb34bd1b57dd531eeff8252134f523f38 100644
--- a/src/replicate.h
+++ b/src/replicate.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/respa.cpp b/src/respa.cpp
index aedfa03027ce3956cc2f399cb3e42d3f83f2c0fa..51be81ebe8339aaaff979b54be2dbda6de8daca6 100644
--- a/src/respa.cpp
+++ b/src/respa.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -112,13 +112,13 @@ Respa::Respa(LAMMPS *lmp, int narg, char **arg) : Integrate(lmp, narg, arg)
// cannot specify both pair and inner/middle/outer
- if (level_pair >= 0 &&
+ if (level_pair >= 0 &&
(level_inner >= 0 || level_middle >= 0 || level_outer >= 0))
error->all(FLERR,"Cannot set both respa pair and inner/middle/outer");
// if either inner and outer is specified, then both must be
- if ((level_inner >= 0 && level_outer == -1) ||
+ if ((level_inner >= 0 && level_outer == -1) ||
(level_outer >= 0 && level_inner == -1))
error->all(FLERR,"Must set both respa inner and outer");
@@ -148,39 +148,39 @@ Respa::Respa(LAMMPS *lmp, int narg, char **arg) : Integrate(lmp, narg, arg)
if (screen) {
fprintf(screen,"Respa levels:\n");
for (int i = 0; i < nlevels; i++) {
- fprintf(screen," %d =",i);
- if (level_bond == i) fprintf(screen," bond");
- if (level_angle == i) fprintf(screen," angle");
- if (level_dihedral == i) fprintf(screen," dihedral");
- if (level_improper == i) fprintf(screen," improper");
- if (level_pair == i) fprintf(screen," pair");
- if (level_inner == i) fprintf(screen," pair-inner");
- if (level_middle == i) fprintf(screen," pair-middle");
- if (level_outer == i) fprintf(screen," pair-outer");
- if (level_kspace == i) fprintf(screen," kspace");
- fprintf(screen,"\n");
+ fprintf(screen," %d =",i);
+ if (level_bond == i) fprintf(screen," bond");
+ if (level_angle == i) fprintf(screen," angle");
+ if (level_dihedral == i) fprintf(screen," dihedral");
+ if (level_improper == i) fprintf(screen," improper");
+ if (level_pair == i) fprintf(screen," pair");
+ if (level_inner == i) fprintf(screen," pair-inner");
+ if (level_middle == i) fprintf(screen," pair-middle");
+ if (level_outer == i) fprintf(screen," pair-outer");
+ if (level_kspace == i) fprintf(screen," kspace");
+ fprintf(screen,"\n");
}
}
if (logfile) {
fprintf(logfile,"Respa levels:\n");
for (int i = 0; i < nlevels; i++) {
- fprintf(logfile," %d =",i);
- if (level_bond == i) fprintf(logfile," bond");
- if (level_angle == i) fprintf(logfile," angle");
- if (level_dihedral == i) fprintf(logfile," dihedral");
- if (level_improper == i) fprintf(logfile," improper");
- if (level_pair == i) fprintf(logfile," pair");
- if (level_inner == i) fprintf(logfile," pair-inner");
- if (level_middle == i) fprintf(logfile," pair-middle");
- if (level_outer == i) fprintf(logfile," pair-outer");
- if (level_kspace == i) fprintf(logfile," kspace");
- fprintf(logfile,"\n");
+ fprintf(logfile," %d =",i);
+ if (level_bond == i) fprintf(logfile," bond");
+ if (level_angle == i) fprintf(logfile," angle");
+ if (level_dihedral == i) fprintf(logfile," dihedral");
+ if (level_improper == i) fprintf(logfile," improper");
+ if (level_pair == i) fprintf(logfile," pair");
+ if (level_inner == i) fprintf(logfile," pair-inner");
+ if (level_middle == i) fprintf(logfile," pair-middle");
+ if (level_outer == i) fprintf(logfile," pair-outer");
+ if (level_kspace == i) fprintf(logfile," kspace");
+ fprintf(logfile,"\n");
}
}
}
// check that levels are in correct order
-
+
if (level_angle < level_bond || level_dihedral < level_angle ||
level_improper < level_dihedral)
error->all(FLERR,"Invalid order of forces within respa levels");
@@ -190,12 +190,12 @@ Respa::Respa(LAMMPS *lmp, int narg, char **arg) : Integrate(lmp, narg, arg)
}
if (level_pair == -1 && level_middle == -1) {
if (level_inner < level_improper || level_outer < level_inner ||
- level_kspace != level_outer)
+ level_kspace != level_outer)
error->all(FLERR,"Invalid order of forces within respa levels");
}
if (level_pair == -1 && level_middle >= 0) {
if (level_inner < level_improper || level_middle < level_inner ||
- level_outer < level_inner || level_kspace != level_outer)
+ level_outer < level_inner || level_kspace != level_outer)
error->all(FLERR,"Invalid order of forces within respa levels");
}
@@ -204,9 +204,9 @@ Respa::Respa(LAMMPS *lmp, int narg, char **arg) : Integrate(lmp, narg, arg)
int flag = 0;
for (int i = 0; i < nlevels; i++)
if (level_bond != i && level_angle != i && level_dihedral != i &&
- level_improper != i && level_pair != i && level_inner != i &&
- level_middle != i && level_outer != i && level_kspace != i) flag = 1;
- if (flag && comm->me == 0)
+ level_improper != i && level_pair != i && level_inner != i &&
+ level_middle != i && level_outer != i && level_kspace != i) flag = 1;
+ if (flag && comm->me == 0)
error->warning(FLERR,"One or more respa levels compute no forces");
// check cutoff consistency if inner/middle/outer are enabled
@@ -294,7 +294,7 @@ void Respa::init()
// step[] = timestep for each level
step[nlevels-1] = update->dt;
- for (int ilevel = nlevels-2; ilevel >= 0; ilevel--)
+ for (int ilevel = nlevels-2; ilevel >= 0; ilevel--)
step[ilevel] = step[ilevel+1]/loop[ilevel];
// set newton flag for each level
@@ -302,14 +302,14 @@ void Respa::init()
for (int ilevel = 0; ilevel < nlevels; ilevel++) {
newton[ilevel] = 0;
if (force->newton_bond) {
- if (level_bond == ilevel || level_angle == ilevel ||
- level_dihedral == ilevel || level_improper == ilevel)
- newton[ilevel] = 1;
+ if (level_bond == ilevel || level_angle == ilevel ||
+ level_dihedral == ilevel || level_improper == ilevel)
+ newton[ilevel] = 1;
}
if (force->newton_pair) {
- if (level_pair == ilevel || level_inner == ilevel ||
- level_middle == ilevel || level_outer == ilevel)
- newton[ilevel] = 1;
+ if (level_pair == ilevel || level_inner == ilevel ||
+ level_middle == ilevel || level_outer == ilevel)
+ newton[ilevel] = 1;
}
}
@@ -355,11 +355,11 @@ void Respa::setup()
modify->setup_pre_force_respa(vflag,ilevel);
if (level_bond == ilevel && force->bond)
force->bond->compute(eflag,vflag);
- if (level_angle == ilevel && force->angle)
+ if (level_angle == ilevel && force->angle)
force->angle->compute(eflag,vflag);
- if (level_dihedral == ilevel && force->dihedral)
+ if (level_dihedral == ilevel && force->dihedral)
force->dihedral->compute(eflag,vflag);
- if (level_improper == ilevel && force->improper)
+ if (level_improper == ilevel && force->improper)
force->improper->compute(eflag,vflag);
if (level_pair == ilevel && pair_compute_flag)
force->pair->compute(eflag,vflag);
@@ -376,7 +376,7 @@ void Respa::setup()
if (newton[ilevel]) comm->reverse_comm();
copy_f_flevel(ilevel);
}
-
+
modify->setup(vflag);
sum_flevel_f();
output->setup(1);
@@ -419,11 +419,11 @@ void Respa::setup_minimal(int flag)
modify->setup_pre_force_respa(vflag,ilevel);
if (level_bond == ilevel && force->bond)
force->bond->compute(eflag,vflag);
- if (level_angle == ilevel && force->angle)
+ if (level_angle == ilevel && force->angle)
force->angle->compute(eflag,vflag);
- if (level_dihedral == ilevel && force->dihedral)
+ if (level_dihedral == ilevel && force->dihedral)
force->dihedral->compute(eflag,vflag);
- if (level_improper == ilevel && force->improper)
+ if (level_improper == ilevel && force->improper)
force->improper->compute(eflag,vflag);
if (level_pair == ilevel && pair_compute_flag)
force->pair->compute(eflag,vflag);
@@ -440,7 +440,7 @@ void Respa::setup_minimal(int flag)
if (newton[ilevel]) comm->reverse_comm();
copy_f_flevel(ilevel);
}
-
+
modify->setup(vflag);
sum_flevel_f();
update->setupflag = 0;
@@ -487,7 +487,7 @@ void Respa::cleanup()
void Respa::reset_dt()
{
step[nlevels-1] = update->dt;
- for (int ilevel = nlevels-2; ilevel >= 0; ilevel--)
+ for (int ilevel = nlevels-2; ilevel >= 0; ilevel--)
step[ilevel] = step[ilevel+1]/loop[ilevel];
}
@@ -512,24 +512,24 @@ void Respa::recurse(int ilevel)
if (ilevel == nlevels-1) {
int nflag = neighbor->decide();
if (nflag) {
- if (modify->n_pre_exchange) modify->pre_exchange();
- if (triclinic) domain->x2lamda(atom->nlocal);
- domain->pbc();
- if (domain->box_change) {
- domain->reset_box();
- comm->setup();
- if (neighbor->style) neighbor->setup_bins();
- }
- timer->stamp();
- comm->exchange();
- if (atom->sortfreq > 0 &&
- update->ntimestep >= atom->nextsort) atom->sort();
- comm->borders();
- if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
- timer->stamp(TIME_COMM);
- if (modify->n_pre_neighbor) modify->pre_neighbor();
- neighbor->build();
- timer->stamp(TIME_NEIGHBOR);
+ if (modify->n_pre_exchange) modify->pre_exchange();
+ if (triclinic) domain->x2lamda(atom->nlocal);
+ domain->pbc();
+ if (domain->box_change) {
+ domain->reset_box();
+ comm->setup();
+ if (neighbor->style) neighbor->setup_bins();
+ }
+ timer->stamp();
+ comm->exchange();
+ if (atom->sortfreq > 0 &&
+ update->ntimestep >= atom->nextsort) atom->sort();
+ comm->borders();
+ if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
+ timer->stamp(TIME_COMM);
+ if (modify->n_pre_neighbor) modify->pre_neighbor();
+ neighbor->build();
+ timer->stamp(TIME_NEIGHBOR);
}
} else if (ilevel == 0) {
@@ -584,7 +584,7 @@ void Respa::recurse(int ilevel)
comm->reverse_comm();
timer->stamp(TIME_COMM);
}
-
+
if (modify->n_post_force_respa)
modify->post_force_respa(vflag,ilevel,iloop);
modify->final_integrate_respa(ilevel,iloop);
@@ -636,7 +636,7 @@ void Respa::force_clear(int newtonflag)
double *de = atom->de;
for (i = 0; i < nall; i++) de[i] = 0.0;
}
-
+
if (rho_flag) {
double *drho = atom->drho;
for (i = 0; i < nall; i++) drho[i] = 0.0;
diff --git a/src/respa.h b/src/respa.h
index 126a56cfc0c7ed393283dc4182c1f4fbf22f5522..e54bd2a669012ba52ddde429d8cabb5aa33e452f 100644
--- a/src/respa.h
+++ b/src/respa.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/run.cpp b/src/run.cpp
index 6ec64fe174c0fc1a6ba5a8d9dca27d350cfee9fc..781001ae9f29957847e383705eb47e965838b43b 100644
--- a/src/run.cpp
+++ b/src/run.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -54,7 +54,7 @@ void Run::command(int narg, char **arg)
int nevery = 0;
int ncommands = 0;
int first,last;
-
+
int iarg = 1;
while (iarg < narg) {
if (strcmp(arg[iarg],"upto") == 0) {
@@ -101,7 +101,7 @@ void Run::command(int narg, char **arg)
}
// set nsteps as integer, using upto value if specified
-
+
int nsteps;
if (!uptoflag) {
if (nsteps_input < 0 || nsteps_input > MAXSMALLINT)
@@ -195,7 +195,7 @@ void Run::command(int narg, char **arg)
update->firststep = update->ntimestep;
update->laststep = update->ntimestep + nsteps;
if (update->laststep < 0 || update->laststep > MAXBIGINT)
- error->all(FLERR,"Too many timesteps");
+ error->all(FLERR,"Too many timesteps");
if (startflag) update->beginstep = start;
else update->beginstep = update->firststep;
@@ -203,8 +203,8 @@ void Run::command(int narg, char **arg)
else update->endstep = update->laststep;
if (preflag || iter == 0) {
- lmp->init();
- update->integrate->setup();
+ lmp->init();
+ update->integrate->setup();
} else output->setup(0);
timer->init();
@@ -222,9 +222,9 @@ void Run::command(int narg, char **arg)
// since a command may invoke computes via variables
if (ncommands) {
- modify->clearstep_compute();
- for (int i = 0; i < ncommands; i++) input->one(commands[i]);
- modify->addstep_compute(update->ntimestep + nevery);
+ modify->clearstep_compute();
+ for (int i = 0; i < ncommands; i++) input->one(commands[i]);
+ modify->addstep_compute(update->ntimestep + nevery);
}
nleft -= nsteps;
diff --git a/src/run.h b/src/run.h
index 8d2b8ad0ebe729c561136fbac9fed0a2773fbde0..00a24d499998f9a8933d501d95308263a9ecae8d 100644
--- a/src/run.h
+++ b/src/run.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/set.cpp b/src/set.cpp
index 4b2d7f0b04a4cf9bea3120d7b8e01c3bd78c0833..eaa34538bafcd1800bd813eb006471d8f3ca63a7 100644
--- a/src/set.cpp
+++ b/src/set.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -79,12 +79,12 @@ void Set::command(int narg, char **arg)
while (iarg < narg) {
count = 0;
origarg = iarg;
-
+
if (strcmp(arg[iarg],"type") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
ivalue = atoi(arg[iarg+1]);
if (ivalue <= 0 || ivalue > atom->ntypes)
- error->all(FLERR,"Invalid value in set command");
+ error->all(FLERR,"Invalid value in set command");
set(TYPE);
iarg += 2;
} else if (strcmp(arg[iarg],"type/fraction") == 0) {
@@ -93,18 +93,18 @@ void Set::command(int narg, char **arg)
fraction = atof(arg[iarg+2]);
ivalue = atoi(arg[iarg+3]);
if (newtype <= 0 || newtype > atom->ntypes)
- error->all(FLERR,"Invalid value in set command");
- if (fraction < 0.0 || fraction > 1.0)
- error->all(FLERR,"Invalid value in set command");
- if (ivalue <= 0)
- error->all(FLERR,"Invalid random number seed in set command");
+ error->all(FLERR,"Invalid value in set command");
+ if (fraction < 0.0 || fraction > 1.0)
+ error->all(FLERR,"Invalid value in set command");
+ if (ivalue <= 0)
+ error->all(FLERR,"Invalid random number seed in set command");
setrandom(TYPE_FRACTION);
iarg += 4;
} else if (strcmp(arg[iarg],"mol") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
ivalue = atoi(arg[iarg+1]);
if (!atom->molecule_flag)
- error->all(FLERR,"Cannot set this attribute for this atom style");
+ error->all(FLERR,"Cannot set this attribute for this atom style");
set(MOLECULE);
iarg += 2;
} else if (strcmp(arg[iarg],"x") == 0) {
@@ -126,14 +126,14 @@ void Set::command(int narg, char **arg)
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
dvalue = atof(arg[iarg+1]);
if (!atom->q_flag)
- error->all(FLERR,"Cannot set this attribute for this atom style");
+ error->all(FLERR,"Cannot set this attribute for this atom style");
set(CHARGE);
iarg += 2;
} else if (strcmp(arg[iarg],"mass") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
dvalue = atof(arg[iarg+1]);
if (!atom->rmass_flag)
- error->all(FLERR,"Cannot set this attribute for this atom style");
+ error->all(FLERR,"Cannot set this attribute for this atom style");
if (dvalue <= 0.0) error->all(FLERR,"Invalid mass in set command");
set(MASS);
iarg += 2;
@@ -143,12 +143,12 @@ void Set::command(int narg, char **arg)
yvalue = atof(arg[iarg+2]);
zvalue = atof(arg[iarg+3]);
if (!atom->ellipsoid_flag)
- error->all(FLERR,"Cannot set this attribute for this atom style");
+ error->all(FLERR,"Cannot set this attribute for this atom style");
if (xvalue < 0.0 || yvalue < 0.0 || zvalue < 0.0)
- error->all(FLERR,"Invalid shape in set command");
+ error->all(FLERR,"Invalid shape in set command");
if (xvalue > 0.0 || yvalue > 0.0 || zvalue > 0.0) {
- if (xvalue == 0.0 || yvalue == 0.0 || zvalue == 0.0)
- error->one(FLERR,"Invalid shape in set command");
+ if (xvalue == 0.0 || yvalue == 0.0 || zvalue == 0.0)
+ error->one(FLERR,"Invalid shape in set command");
}
set(SHAPE);
iarg += 4;
@@ -174,7 +174,7 @@ void Set::command(int narg, char **arg)
yvalue = atof(arg[iarg+2]);
zvalue = atof(arg[iarg+3]);
if (!atom->mu_flag)
- error->all(FLERR,"Cannot set this attribute for this atom style");
+ error->all(FLERR,"Cannot set this attribute for this atom style");
set(DIPOLE);
iarg += 4;
} else if (strcmp(arg[iarg],"dipole/random") == 0) {
@@ -182,11 +182,11 @@ void Set::command(int narg, char **arg)
ivalue = atoi(arg[iarg+1]);
dvalue = atof(arg[iarg+2]);
if (!atom->mu_flag)
- error->all(FLERR,"Cannot set this attribute for this atom style");
- if (ivalue <= 0)
- error->all(FLERR,"Invalid random number seed in set command");
- if (dvalue <= 0.0)
- error->all(FLERR,"Invalid dipole length in set command");
+ error->all(FLERR,"Cannot set this attribute for this atom style");
+ if (ivalue <= 0)
+ error->all(FLERR,"Invalid random number seed in set command");
+ if (dvalue <= 0.0)
+ error->all(FLERR,"Invalid dipole length in set command");
setrandom(DIPOLE_RANDOM);
iarg += 3;
} else if (strcmp(arg[iarg],"quat") == 0) {
@@ -196,16 +196,16 @@ void Set::command(int narg, char **arg)
zvalue = atof(arg[iarg+3]);
wvalue = atof(arg[iarg+4]);
if (!atom->ellipsoid_flag && !atom->tri_flag)
- error->all(FLERR,"Cannot set this attribute for this atom style");
+ error->all(FLERR,"Cannot set this attribute for this atom style");
set(QUAT);
iarg += 5;
} else if (strcmp(arg[iarg],"quat/random") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
ivalue = atoi(arg[iarg+1]);
if (!atom->ellipsoid_flag && !atom->tri_flag)
- error->all(FLERR,"Cannot set this attribute for this atom style");
- if (ivalue <= 0)
- error->all(FLERR,"Invalid random number seed in set command");
+ error->all(FLERR,"Cannot set this attribute for this atom style");
+ if (ivalue <= 0)
+ error->all(FLERR,"Invalid random number seed in set command");
setrandom(QUAT_RANDOM);
iarg += 2;
} else if (strcmp(arg[iarg],"theta") == 0) {
@@ -251,96 +251,96 @@ void Set::command(int narg, char **arg)
if (iarg+4 > narg) error->all(FLERR,"Illegal set command");
ximageflag = yimageflag = zimageflag = 0;
if (strcmp(arg[iarg+1],"NULL") != 0) {
- ximageflag = 1;
- ximage = atoi(arg[iarg+1]);
+ ximageflag = 1;
+ ximage = atoi(arg[iarg+1]);
}
if (strcmp(arg[iarg+2],"NULL") != 0) {
- yimageflag = 1;
- yimage = atoi(arg[iarg+2]);
+ yimageflag = 1;
+ yimage = atoi(arg[iarg+2]);
}
if (strcmp(arg[iarg+3],"NULL") != 0) {
- zimageflag = 1;
- zimage = atoi(arg[iarg+3]);
+ zimageflag = 1;
+ zimage = atoi(arg[iarg+3]);
}
- if (ximageflag && ximage && !domain->xperiodic)
- error->all(FLERR,
- "Cannot set non-zero image flag for non-periodic dimension");
- if (yimageflag && yimage && !domain->yperiodic)
- error->all(FLERR,
- "Cannot set non-zero image flag for non-periodic dimension");
- if (zimageflag && zimage && !domain->zperiodic)
- error->all(FLERR,
- "Cannot set non-zero image flag for non-periodic dimension");
+ if (ximageflag && ximage && !domain->xperiodic)
+ error->all(FLERR,
+ "Cannot set non-zero image flag for non-periodic dimension");
+ if (yimageflag && yimage && !domain->yperiodic)
+ error->all(FLERR,
+ "Cannot set non-zero image flag for non-periodic dimension");
+ if (zimageflag && zimage && !domain->zperiodic)
+ error->all(FLERR,
+ "Cannot set non-zero image flag for non-periodic dimension");
set(IMAGE);
iarg += 4;
} else if (strcmp(arg[iarg],"bond") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
ivalue = atoi(arg[iarg+1]);
if (atom->avec->bonds_allow == 0)
- error->all(FLERR,"Cannot set this attribute for this atom style");
+ error->all(FLERR,"Cannot set this attribute for this atom style");
if (ivalue <= 0 || ivalue > atom->nbondtypes)
- error->all(FLERR,"Invalid value in set command");
+ error->all(FLERR,"Invalid value in set command");
topology(BOND);
iarg += 2;
} else if (strcmp(arg[iarg],"angle") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
ivalue = atoi(arg[iarg+1]);
if (atom->avec->angles_allow == 0)
- error->all(FLERR,"Cannot set this attribute for this atom style");
+ error->all(FLERR,"Cannot set this attribute for this atom style");
if (ivalue <= 0 || ivalue > atom->nangletypes)
- error->all(FLERR,"Invalid value in set command");
+ error->all(FLERR,"Invalid value in set command");
topology(ANGLE);
iarg += 2;
} else if (strcmp(arg[iarg],"dihedral") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
ivalue = atoi(arg[iarg+1]);
if (atom->avec->dihedrals_allow == 0)
- error->all(FLERR,"Cannot set this attribute for this atom style");
+ error->all(FLERR,"Cannot set this attribute for this atom style");
if (ivalue <= 0 || ivalue > atom->ndihedraltypes)
- error->all(FLERR,"Invalid value in set command");
+ error->all(FLERR,"Invalid value in set command");
topology(DIHEDRAL);
iarg += 2;
} else if (strcmp(arg[iarg],"improper") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
ivalue = atoi(arg[iarg+1]);
if (atom->avec->impropers_allow == 0)
- error->all(FLERR,"Cannot set this attribute for this atom style");
+ error->all(FLERR,"Cannot set this attribute for this atom style");
if (ivalue <= 0 || ivalue > atom->nimpropertypes)
- error->all(FLERR,"Invalid value in set command");
+ error->all(FLERR,"Invalid value in set command");
topology(IMPROPER);
iarg += 2;
} else if (strcmp(arg[iarg],"meso_e") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
dvalue = atof(arg[iarg+1]);
if (!atom->e_flag)
- error->all(FLERR,"Cannot set this attribute for this atom style");
+ error->all(FLERR,"Cannot set this attribute for this atom style");
set(MESO_E);
iarg += 2;
} else if (strcmp(arg[iarg],"meso_cv") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
dvalue = atof(arg[iarg+1]);
if (!atom->cv_flag)
- error->all(FLERR,"Cannot set this attribute for this atom style");
+ error->all(FLERR,"Cannot set this attribute for this atom style");
set(MESO_CV);
iarg += 2;
} else if (strcmp(arg[iarg],"meso_rho") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
dvalue = atof(arg[iarg+1]);
if (!atom->rho_flag)
- error->all(FLERR,"Cannot set meso_rho for this atom style");
+ error->all(FLERR,"Cannot set meso_rho for this atom style");
set(MESO_RHO);
iarg += 2;
- } else error->all(FLERR,"Illegal set command");
+ } else error->all(FLERR,"Illegal set command");
// statistics
MPI_Allreduce(&count,&allcount,1,MPI_INT,MPI_SUM,world);
-
+
if (comm->me == 0) {
if (screen) fprintf(screen," %d settings made for %s\n",
- allcount,arg[origarg]);
+ allcount,arg[origarg]);
if (logfile) fprintf(logfile," %d settings made for %s\n",
- allcount,arg[origarg]);
+ allcount,arg[origarg]);
}
}
@@ -407,7 +407,7 @@ void Set::selection(int n)
double **x = atom->x;
for (int i = 0; i < n; i++)
if (domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2]))
- select[i] = 1;
+ select[i] = 1;
else select[i] = 0;
}
}
@@ -418,7 +418,7 @@ void Set::selection(int n)
void Set::set(int keyword)
{
- AtomVecEllipsoid *avec_ellipsoid =
+ AtomVecEllipsoid *avec_ellipsoid =
(AtomVecEllipsoid *) atom->style_match("ellipsoid");
AtomVecLine *avec_line = (AtomVecLine *) atom->style_match("line");
AtomVecTri *avec_tri = (AtomVecTri *) atom->style_match("tri");
@@ -466,29 +466,29 @@ void Set::set(int keyword)
else if (keyword == DENSITY) {
if (atom->radius_flag && atom->radius[i] > 0.0)
- atom->rmass[i] = 4.0*MY_PI/3.0 *
- atom->radius[i]*atom->radius[i]*atom->radius[i] * dvalue;
+ atom->rmass[i] = 4.0*MY_PI/3.0 *
+ atom->radius[i]*atom->radius[i]*atom->radius[i] * dvalue;
else if (atom->ellipsoid_flag && atom->ellipsoid[i] >= 0) {
- double *shape = avec_ellipsoid->bonus[atom->ellipsoid[i]].shape;
- atom->rmass[i] = 4.0*MY_PI/3.0 * shape[0]*shape[1]*shape[2] * dvalue;
+ double *shape = avec_ellipsoid->bonus[atom->ellipsoid[i]].shape;
+ atom->rmass[i] = 4.0*MY_PI/3.0 * shape[0]*shape[1]*shape[2] * dvalue;
} else if (atom->line_flag && atom->line[i] >= 0) {
- double length = avec_line->bonus[atom->line[i]].length;
- atom->rmass[i] = length * dvalue;
+ double length = avec_line->bonus[atom->line[i]].length;
+ atom->rmass[i] = length * dvalue;
} else if (atom->tri_flag && atom->tri[i] >= 0) {
- double *c1 = avec_tri->bonus[atom->tri[i]].c1;
- double *c2 = avec_tri->bonus[atom->tri[i]].c2;
- double *c3 = avec_tri->bonus[atom->tri[i]].c3;
- double c2mc1[2],c3mc1[3];
- MathExtra::sub3(c2,c1,c2mc1);
- MathExtra::sub3(c3,c1,c3mc1);
- double norm[3];
- MathExtra::cross3(c2mc1,c3mc1,norm);
- double area = 0.5 * MathExtra::len3(norm);
- atom->rmass[i] = area * dvalue;
+ double *c1 = avec_tri->bonus[atom->tri[i]].c1;
+ double *c2 = avec_tri->bonus[atom->tri[i]].c2;
+ double *c3 = avec_tri->bonus[atom->tri[i]].c3;
+ double c2mc1[2],c3mc1[3];
+ MathExtra::sub3(c2,c1,c2mc1);
+ MathExtra::sub3(c3,c1,c3mc1);
+ double norm[3];
+ MathExtra::cross3(c2mc1,c3mc1,norm);
+ double area = 0.5 * MathExtra::len3(norm);
+ atom->rmass[i] = area * dvalue;
} else atom->rmass[i] = dvalue;
// reset any or all of 3 image flags
-
+
} else if (keyword == IMAGE) {
int xbox = (atom->image[i] & 1023) - 512;
int ybox = (atom->image[i] >> 10 & 1023) - 512;
@@ -497,28 +497,28 @@ void Set::set(int keyword)
if (yimageflag) ybox = yimage;
if (zimageflag) zbox = zimage;
atom->image[i] = ((zbox + 512 & 1023) << 20) |
- ((ybox + 512 & 1023) << 10) | (xbox + 512 & 1023);
-
+ ((ybox + 512 & 1023) << 10) | (xbox + 512 & 1023);
+
// set dipole moment
-
+
} else if (keyword == DIPOLE) {
double **mu = atom->mu;
mu[i][0] = xvalue;
mu[i][1] = yvalue;
mu[i][2] = zvalue;
- mu[i][3] = sqrt(mu[i][0]*mu[i][0] + mu[i][1]*mu[i][1] +
- mu[i][2]*mu[i][2]);
-
+ mu[i][3] = sqrt(mu[i][0]*mu[i][0] + mu[i][1]*mu[i][1] +
+ mu[i][2]*mu[i][2]);
+
// set quaternion orientation of ellipsoid or tri particle
} else if (keyword == QUAT) {
double *quat;
if (avec_ellipsoid && atom->ellipsoid[i] >= 0)
- quat = avec_ellipsoid->bonus[atom->ellipsoid[i]].quat;
+ quat = avec_ellipsoid->bonus[atom->ellipsoid[i]].quat;
else if (avec_tri && atom->tri[i] >= 0)
- quat = avec_tri->bonus[atom->tri[i]].quat;
+ quat = avec_tri->bonus[atom->tri[i]].quat;
else
- error->one(FLERR,"Cannot set quaternion for atom that has none");
+ error->one(FLERR,"Cannot set quaternion for atom that has none");
double theta2 = MY_PI2 * wvalue/180.0;
double sintheta2 = sin(theta2);
@@ -532,7 +532,7 @@ void Set::set(int keyword)
} else if (keyword == THETA) {
if (atom->line[i] < 0)
- error->one(FLERR,"Cannot set theta for atom that is not a line");
+ error->one(FLERR,"Cannot set theta for atom that is not a line");
avec_line->bonus[atom->line[i]].theta = dvalue;
// set angmom of ellipsoidal or tri particle
@@ -557,7 +557,7 @@ void Set::setrandom(int keyword)
{
int i;
- AtomVecEllipsoid *avec_ellipsoid =
+ AtomVecEllipsoid *avec_ellipsoid =
(AtomVecEllipsoid *) atom->style_match("ellipsoid");
AtomVecLine *avec_line = (AtomVecLine *) atom->style_match("line");
AtomVecTri *avec_tri = (AtomVecTri *) atom->style_match("tri");
@@ -574,9 +574,9 @@ void Set::setrandom(int keyword)
for (i = 0; i < nlocal; i++)
if (select[i]) {
- random->reset(seed,x[i]);
- if (random->uniform() > fraction) continue;
- atom->type[i] = newtype;
+ random->reset(seed,x[i]);
+ if (random->uniform() > fraction) continue;
+ atom->type[i] = newtype;
count++;
}
@@ -591,34 +591,34 @@ void Set::setrandom(int keyword)
if (domain->dimension == 3) {
for (i = 0; i < nlocal; i++)
- if (select[i]) {
- random->reset(seed,x[i]);
- mu[i][0] = random->uniform() - 0.5;
- mu[i][1] = random->uniform() - 0.5;
- mu[i][2] = random->uniform() - 0.5;
- msq = mu[i][0]*mu[i][0] + mu[i][1]*mu[i][1] + mu[i][2]*mu[i][2];
- scale = dvalue/sqrt(msq);
- mu[i][0] *= scale;
- mu[i][1] *= scale;
- mu[i][2] *= scale;
- mu[i][3] = dvalue;
- count++;
- }
+ if (select[i]) {
+ random->reset(seed,x[i]);
+ mu[i][0] = random->uniform() - 0.5;
+ mu[i][1] = random->uniform() - 0.5;
+ mu[i][2] = random->uniform() - 0.5;
+ msq = mu[i][0]*mu[i][0] + mu[i][1]*mu[i][1] + mu[i][2]*mu[i][2];
+ scale = dvalue/sqrt(msq);
+ mu[i][0] *= scale;
+ mu[i][1] *= scale;
+ mu[i][2] *= scale;
+ mu[i][3] = dvalue;
+ count++;
+ }
} else {
for (i = 0; i < nlocal; i++)
- if (select[i]) {
- random->reset(seed,x[i]);
- mu[i][0] = random->uniform() - 0.5;
- mu[i][1] = random->uniform() - 0.5;
- mu[i][2] = 0.0;
- msq = mu[i][0]*mu[i][0] + mu[i][1]*mu[i][1];
- scale = dvalue/sqrt(msq);
- mu[i][0] *= scale;
- mu[i][1] *= scale;
- mu[i][3] = dvalue;
- count++;
- }
+ if (select[i]) {
+ random->reset(seed,x[i]);
+ mu[i][0] = random->uniform() - 0.5;
+ mu[i][1] = random->uniform() - 0.5;
+ mu[i][2] = 0.0;
+ msq = mu[i][0]*mu[i][0] + mu[i][1]*mu[i][1];
+ scale = dvalue/sqrt(msq);
+ mu[i][0] *= scale;
+ mu[i][1] *= scale;
+ mu[i][3] = dvalue;
+ count++;
+ }
}
// set quaternions to random orientations in 3d or 2d
@@ -632,44 +632,44 @@ void Set::setrandom(int keyword)
if (domain->dimension == 3) {
double s,t1,t2,theta1,theta2;
for (i = 0; i < nlocal; i++)
- if (select[i]) {
- if (avec_ellipsoid && atom->ellipsoid[i] >= 0)
- quat = avec_ellipsoid->bonus[atom->ellipsoid[i]].quat;
- else if (avec_tri && atom->tri[i] >= 0)
- quat = avec_tri->bonus[atom->tri[i]].quat;
- else
- error->one(FLERR,"Cannot set quaternion for atom that has none");
-
- random->reset(seed,x[i]);
- s = random->uniform();
- t1 = sqrt(1.0-s);
- t2 = sqrt(s);
- theta1 = 2.0*MY_PI*random->uniform();
- theta2 = 2.0*MY_PI*random->uniform();
- quat[0] = cos(theta2)*t2;
- quat[1] = sin(theta1)*t1;
- quat[2] = cos(theta1)*t1;
- quat[3] = sin(theta2)*t2;
- count++;
- }
+ if (select[i]) {
+ if (avec_ellipsoid && atom->ellipsoid[i] >= 0)
+ quat = avec_ellipsoid->bonus[atom->ellipsoid[i]].quat;
+ else if (avec_tri && atom->tri[i] >= 0)
+ quat = avec_tri->bonus[atom->tri[i]].quat;
+ else
+ error->one(FLERR,"Cannot set quaternion for atom that has none");
+
+ random->reset(seed,x[i]);
+ s = random->uniform();
+ t1 = sqrt(1.0-s);
+ t2 = sqrt(s);
+ theta1 = 2.0*MY_PI*random->uniform();
+ theta2 = 2.0*MY_PI*random->uniform();
+ quat[0] = cos(theta2)*t2;
+ quat[1] = sin(theta1)*t1;
+ quat[2] = cos(theta1)*t1;
+ quat[3] = sin(theta2)*t2;
+ count++;
+ }
} else {
double theta2;
for (i = 0; i < nlocal; i++)
- if (select[i]) {
- if (avec_ellipsoid && atom->ellipsoid[i] >= 0)
- quat = avec_ellipsoid->bonus[atom->ellipsoid[i]].quat;
- else
- error->one(FLERR,"Cannot set quaternion for atom that has none");
-
- random->reset(seed,x[i]);
- theta2 = MY_PI*random->uniform();
- quat[0] = cos(theta2);
- quat[1] = 0.0;
- quat[2] = 0.0;
- quat[3] = sin(theta2);
- count++;
- }
+ if (select[i]) {
+ if (avec_ellipsoid && atom->ellipsoid[i] >= 0)
+ quat = avec_ellipsoid->bonus[atom->ellipsoid[i]].quat;
+ else
+ error->one(FLERR,"Cannot set quaternion for atom that has none");
+
+ random->reset(seed,x[i]);
+ theta2 = MY_PI*random->uniform();
+ quat[0] = cos(theta2);
+ quat[1] = 0.0;
+ quat[2] = 0.0;
+ quat[3] = sin(theta2);
+ count++;
+ }
}
}
@@ -686,7 +686,7 @@ void Set::topology(int keyword)
// enforce PBC before in case atoms are outside box
// init entire system since comm->exchange is done
// comm::init needs neighbor::init needs pair::init needs kspace::init, etc
-
+
if (comm->me == 0 && screen) fprintf(screen," system init for set ...\n");
lmp->init();
@@ -708,12 +708,12 @@ void Set::topology(int keyword)
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
for (m = 0; m < atom->num_bond[i]; m++) {
- atom1 = atom->map(atom->bond_atom[i][m]);
- if (atom1 == -1) error->one(FLERR,"Bond atom missing in set command");
- if (select[i] && select[atom1]) {
- atom->bond_type[i][m] = ivalue;
- count++;
- }
+ atom1 = atom->map(atom->bond_atom[i][m]);
+ if (atom1 == -1) error->one(FLERR,"Bond atom missing in set command");
+ if (select[i] && select[atom1]) {
+ atom->bond_type[i][m] = ivalue;
+ count++;
+ }
}
}
@@ -723,15 +723,15 @@ void Set::topology(int keyword)
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
for (m = 0; m < atom->num_angle[i]; m++) {
- atom1 = atom->map(atom->angle_atom1[i][m]);
- atom2 = atom->map(atom->angle_atom2[i][m]);
- atom3 = atom->map(atom->angle_atom3[i][m]);
- if (atom1 == -1 || atom2 == -1 || atom3 == -1)
- error->one(FLERR,"Angle atom missing in set command");
- if (select[atom1] && select[atom2] && select[atom3]) {
- atom->angle_type[i][m] = ivalue;
- count++;
- }
+ atom1 = atom->map(atom->angle_atom1[i][m]);
+ atom2 = atom->map(atom->angle_atom2[i][m]);
+ atom3 = atom->map(atom->angle_atom3[i][m]);
+ if (atom1 == -1 || atom2 == -1 || atom3 == -1)
+ error->one(FLERR,"Angle atom missing in set command");
+ if (select[atom1] && select[atom2] && select[atom3]) {
+ atom->angle_type[i][m] = ivalue;
+ count++;
+ }
}
}
@@ -741,16 +741,16 @@ void Set::topology(int keyword)
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
for (m = 0; m < atom->num_dihedral[i]; m++) {
- atom1 = atom->map(atom->dihedral_atom1[i][m]);
- atom2 = atom->map(atom->dihedral_atom2[i][m]);
- atom3 = atom->map(atom->dihedral_atom3[i][m]);
- atom4 = atom->map(atom->dihedral_atom4[i][m]);
- if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1)
- error->one(FLERR,"Dihedral atom missing in set command");
- if (select[atom1] && select[atom2] && select[atom3] && select[atom4]) {
- atom->dihedral_type[i][m] = ivalue;
- count++;
- }
+ atom1 = atom->map(atom->dihedral_atom1[i][m]);
+ atom2 = atom->map(atom->dihedral_atom2[i][m]);
+ atom3 = atom->map(atom->dihedral_atom3[i][m]);
+ atom4 = atom->map(atom->dihedral_atom4[i][m]);
+ if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1)
+ error->one(FLERR,"Dihedral atom missing in set command");
+ if (select[atom1] && select[atom2] && select[atom3] && select[atom4]) {
+ atom->dihedral_type[i][m] = ivalue;
+ count++;
+ }
}
}
@@ -760,16 +760,16 @@ void Set::topology(int keyword)
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
for (m = 0; m < atom->num_improper[i]; m++) {
- atom1 = atom->map(atom->improper_atom1[i][m]);
- atom2 = atom->map(atom->improper_atom2[i][m]);
- atom3 = atom->map(atom->improper_atom3[i][m]);
- atom4 = atom->map(atom->improper_atom4[i][m]);
- if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1)
- error->one(FLERR,"Improper atom missing in set command");
- if (select[atom1] && select[atom2] && select[atom3] && select[atom4]) {
- atom->improper_type[i][m] = ivalue;
- count++;
- }
+ atom1 = atom->map(atom->improper_atom1[i][m]);
+ atom2 = atom->map(atom->improper_atom2[i][m]);
+ atom3 = atom->map(atom->improper_atom3[i][m]);
+ atom4 = atom->map(atom->improper_atom4[i][m]);
+ if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1)
+ error->one(FLERR,"Improper atom missing in set command");
+ if (select[atom1] && select[atom2] && select[atom3] && select[atom4]) {
+ atom->improper_type[i][m] = ivalue;
+ count++;
+ }
}
}
}
diff --git a/src/set.h b/src/set.h
index b1951b452312a5baf7d595258558b0b4191d78e6..abbbeeceeb73d33627add08e1b13afd416b1e721 100644
--- a/src/set.h
+++ b/src/set.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/special.cpp b/src/special.cpp
index 189b2374fb7e088ca87680fc6ea31e17f978004c..195d5188a02cc7ddffef25e2be4651321c4c9b55 100644
--- a/src/special.cpp
+++ b/src/special.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -44,7 +44,7 @@ Special::~Special()
/* ----------------------------------------------------------------------
create 1-2, 1-3, 1-4 lists of topology neighbors
store in onetwo, onethree, onefour for each atom
- store 3 counters in nspecial[i]
+ store 3 counters in nspecial[i]
------------------------------------------------------------------------- */
void Special::build()
@@ -70,7 +70,7 @@ void Special::build()
// setup ring of procs
int next = me + 1;
- int prev = me -1;
+ int prev = me -1;
if (next == nprocs) next = 0;
if (prev < 0) prev = nprocs - 1;
@@ -110,7 +110,7 @@ void Special::build()
size = 0;
for (i = 0; i < nlocal; i++)
for (j = 0; j < num_bond[i]; j++)
- buf[size++] = bond_atom[i][j];
+ buf[size++] = bond_atom[i][j];
// cycle buffer around ring of procs back to self
// when receive buffer, scan tags for atoms I own
@@ -119,15 +119,15 @@ void Special::build()
messtag = 1;
for (loop = 0; loop < nprocs; loop++) {
for (i = 0; i < size; i++) {
- m = atom->map(buf[i]);
- if (m >= 0 && m < nlocal) nspecial[m][0]++;
+ m = atom->map(buf[i]);
+ if (m >= 0 && m < nlocal) nspecial[m][0]++;
}
if (me != next) {
- MPI_Irecv(bufcopy,nbufmax,MPI_INT,prev,messtag,world,&request);
- MPI_Send(buf,size,MPI_INT,next,messtag,world);
- MPI_Wait(&request,&status);
- MPI_Get_count(&status,MPI_INT,&size);
- for (j = 0; j < size; j++) buf[j] = bufcopy[j];
+ MPI_Irecv(bufcopy,nbufmax,MPI_INT,prev,messtag,world,&request);
+ MPI_Send(buf,size,MPI_INT,next,messtag,world);
+ MPI_Wait(&request,&status);
+ MPI_Get_count(&status,MPI_INT,&size);
+ for (j = 0; j < size; j++) buf[j] = bufcopy[j];
}
}
@@ -182,8 +182,8 @@ void Special::build()
size = 0;
for (i = 0; i < nlocal; i++)
for (j = 0; j < num_bond[i]; j++) {
- buf[size++] = tag[i];
- buf[size++] = bond_atom[i][j];
+ buf[size++] = tag[i];
+ buf[size++] = bond_atom[i][j];
}
// cycle buffer around ring of procs back to self
@@ -193,15 +193,15 @@ void Special::build()
messtag = 2;
for (loop = 0; loop < nprocs; loop++) {
for (i = 1; i < size; i += 2) {
- m = atom->map(buf[i]);
- if (m >= 0 && m < nlocal) onetwo[m][count[m]++] = buf[i-1];
+ m = atom->map(buf[i]);
+ if (m >= 0 && m < nlocal) onetwo[m][count[m]++] = buf[i-1];
}
if (me != next) {
- MPI_Irecv(bufcopy,nbufmax,MPI_INT,prev,messtag,world,&request);
- MPI_Send(buf,size,MPI_INT,next,messtag,world);
- MPI_Wait(&request,&status);
- MPI_Get_count(&status,MPI_INT,&size);
- for (j = 0; j < size; j++) buf[j] = bufcopy[j];
+ MPI_Irecv(bufcopy,nbufmax,MPI_INT,prev,messtag,world,&request);
+ MPI_Send(buf,size,MPI_INT,next,messtag,world);
+ MPI_Wait(&request,&status);
+ MPI_Get_count(&status,MPI_INT,&size);
+ for (j = 0; j < size; j++) buf[j] = bufcopy[j];
}
}
@@ -259,8 +259,8 @@ void Special::build()
n = buf[i];
num12 = buf[i+1];
for (j = 0; j < num12; j++) {
- m = atom->map(buf[i+2+j]);
- if (m >= 0 && m < nlocal) n += nspecial[m][0] - 1;
+ m = atom->map(buf[i+2+j]);
+ if (m >= 0 && m < nlocal) n += nspecial[m][0] - 1;
}
buf[i] = n;
i += 2 + num12;
@@ -346,11 +346,11 @@ void Special::build()
num13 = buf[i+2];
n = buf[i+3];
for (j = 0; j < num12; j++) {
- m = atom->map(buf[i+4+j]);
- if (m >= 0 && m < nlocal)
- for (k = 0; k < nspecial[m][0]; k++)
- if (onetwo[m][k] != original)
- buf[i+4+num12+(n++)] = onetwo[m][k];
+ m = atom->map(buf[i+4+j]);
+ if (m >= 0 && m < nlocal)
+ for (k = 0; k < nspecial[m][0]; k++)
+ if (onetwo[m][k] != original)
+ buf[i+4+num12+(n++)] = onetwo[m][k];
}
buf[i+3] = n;
i += 4 + num12 + num13;
@@ -373,7 +373,7 @@ void Special::build()
if (buf[j+3] != nspecial[i][1])
error->one(FLERR,"1-3 bond count is inconsistent");
j += 4 + nspecial[i][0];
- for (k = 0; k < nspecial[i][1]; k++)
+ for (k = 0; k < nspecial[i][1]; k++)
onethree[i][k] = buf[j++];
}
@@ -426,8 +426,8 @@ void Special::build()
n = buf[i];
num13 = buf[i+1];
for (j = 0; j < num13; j++) {
- m = atom->map(buf[i+2+j]);
- if (m >= 0 && m < nlocal) n += nspecial[m][0];
+ m = atom->map(buf[i+2+j]);
+ if (m >= 0 && m < nlocal) n += nspecial[m][0];
}
buf[i] = n;
i += 2 + num13;
@@ -473,7 +473,7 @@ void Special::build()
// info for each atom = 3 scalars + list of 1-3 neighs + list of 1-4 neighs
nbuf = 0;
- for (i = 0; i < nlocal; i++)
+ for (i = 0; i < nlocal; i++)
nbuf += 3 + nspecial[i][1] + nspecial[i][2];
MPI_Allreduce(&nbuf,&nbufmax,1,MPI_INT,MPI_MAX,world);
@@ -510,10 +510,10 @@ void Special::build()
num14 = buf[i+1];
n = buf[i+2];
for (j = 0; j < num13; j++) {
- m = atom->map(buf[i+3+j]);
- if (m >= 0 && m < nlocal)
- for (k = 0; k < nspecial[m][0]; k++)
- buf[i+3+num13+(n++)] = onetwo[m][k];
+ m = atom->map(buf[i+3+j]);
+ if (m >= 0 && m < nlocal)
+ for (k = 0; k < nspecial[m][0]; k++)
+ buf[i+3+num13+(n++)] = onetwo[m][k];
}
buf[i+2] = n;
i += 3 + num13 + num14;
@@ -536,7 +536,7 @@ void Special::build()
if (buf[j+2] != nspecial[i][2])
error->one(FLERR,"1-4 bond count is inconsistent");
j += 3 + nspecial[i][1];
- for (k = 0; k < nspecial[i][2]; k++)
+ for (k = 0; k < nspecial[i][2]; k++)
onefour[i][k] = buf[j++];
}
@@ -551,7 +551,7 @@ void Special::build()
/* ----------------------------------------------------------------------
concatenate onetwo, onethree, onefour into master atom->special list
remove duplicates
- convert nspecial[0], nspecial[1], nspecial[2] into cumulative counters
+ convert nspecial[0], nspecial[1], nspecial[2] into cumulative counters
------------------------------------------------------------------------- */
void Special::combine()
@@ -589,22 +589,22 @@ void Special::combine()
for (j = 0; j < nspecial[i][0]; j++) {
m = onetwo[i][j];
if (atom->map(m) < 0) {
- unique++;
- atom->map_one(m,0);
+ unique++;
+ atom->map_one(m,0);
}
}
for (j = 0; j < nspecial[i][1]; j++) {
m = onethree[i][j];
if (atom->map(m) < 0) {
- unique++;
- atom->map_one(m,0);
+ unique++;
+ atom->map_one(m,0);
}
}
for (j = 0; j < nspecial[i][2]; j++) {
m = onefour[i][j];
if (atom->map(m) < 0) {
- unique++;
- atom->map_one(m,0);
+ unique++;
+ atom->map_one(m,0);
}
}
@@ -657,8 +657,8 @@ void Special::combine()
for (j = 0; j < nspecial[i][0]; j++) {
m = onetwo[i][j];
if (atom->map(m) < 0) {
- special[i][unique++] = m;
- atom->map_one(m,0);
+ special[i][unique++] = m;
+ atom->map_one(m,0);
}
}
nspecial[i][0] = unique;
@@ -666,8 +666,8 @@ void Special::combine()
for (j = 0; j < nspecial[i][1]; j++) {
m = onethree[i][j];
if (atom->map(m) < 0) {
- special[i][unique++] = m;
- atom->map_one(m,0);
+ special[i][unique++] = m;
+ atom->map_one(m,0);
}
}
nspecial[i][1] = unique;
@@ -675,8 +675,8 @@ void Special::combine()
for (j = 0; j < nspecial[i][2]; j++) {
m = onefour[i][j];
if (atom->map(m) < 0) {
- special[i][unique++] = m;
- atom->map_one(m,0);
+ special[i][unique++] = m;
+ atom->map_one(m,0);
}
}
nspecial[i][2] = unique;
@@ -702,7 +702,7 @@ void Special::angle_trim()
int i,j,m,n,iglobal,jglobal,ilocal,jlocal;
MPI_Request request;
MPI_Status status;
-
+
int *num_angle = atom->num_angle;
int *num_dihedral = atom->num_dihedral;
int **angle_atom1 = atom->angle_atom1;
@@ -720,19 +720,19 @@ void Special::angle_trim()
double onethreecount = 0.0;
for (i = 0; i < nlocal; i++)
onethreecount += nspecial[i][1] - nspecial[i][0];
-
+
double allcount;
MPI_Allreduce(&onethreecount,&allcount,1,MPI_DOUBLE,MPI_SUM,world);
-
+
if (me == 0) {
if (screen)
fprintf(screen,
- " %g = # of 1-3 neighbors before angle trim\n",allcount);
+ " %g = # of 1-3 neighbors before angle trim\n",allcount);
if (logfile)
fprintf(logfile,
- " %g = # of 1-3 neighbors before angle trim\n",allcount);
+ " %g = # of 1-3 neighbors before angle trim\n",allcount);
}
-
+
// if angles or dihedrals are defined,
// flag each 1-3 neigh if it appears in an angle or dihedral
@@ -745,7 +745,7 @@ void Special::angle_trim()
maxcount = MAX(maxcount,nspecial[i][1]-nspecial[i][0]);
int **dflag;
memory->create(dflag,nlocal,maxcount,"special::dflag");
-
+
for (i = 0; i < nlocal; i++) {
n = nspecial[i][1] - nspecial[i][0];
for (j = 0; j < n; j++) dflag[i][j] = 0;
@@ -754,31 +754,31 @@ void Special::angle_trim()
// nbufmax = largest buffer needed to hold info from any proc
// info for each atom = list of 1,3 atoms in each angle stored by atom
// and list of 1,3 and 2,4 atoms in each dihedral stored by atom
-
+
int nbuf = 0;
for (i = 0; i < nlocal; i++) nbuf += 2*num_angle[i] + 2*2*num_dihedral[i];
-
+
int nbufmax;
MPI_Allreduce(&nbuf,&nbufmax,1,MPI_INT,MPI_MAX,world);
-
+
int *buf = new int[nbufmax];
int *bufcopy = new int[nbufmax];
-
+
// fill buffer with list of 1,3 atoms in each angle
// and with list of 1,3 and 2,4 atoms in each dihedral
int size = 0;
for (i = 0; i < nlocal; i++)
for (j = 0; j < num_angle[i]; j++) {
- buf[size++] = angle_atom1[i][j];
- buf[size++] = angle_atom3[i][j];
+ buf[size++] = angle_atom1[i][j];
+ buf[size++] = angle_atom3[i][j];
}
for (i = 0; i < nlocal; i++)
for (j = 0; j < num_dihedral[i]; j++) {
- buf[size++] = dihedral_atom1[i][j];
- buf[size++] = dihedral_atom3[i][j];
- buf[size++] = dihedral_atom2[i][j];
- buf[size++] = dihedral_atom4[i][j];
+ buf[size++] = dihedral_atom1[i][j];
+ buf[size++] = dihedral_atom3[i][j];
+ buf[size++] = dihedral_atom2[i][j];
+ buf[size++] = dihedral_atom4[i][j];
}
// cycle buffer around ring of procs back to self
@@ -786,7 +786,7 @@ void Special::angle_trim()
// when find one, scan its 1-3 neigh list and mark I,J as in an angle
int next = me + 1;
- int prev = me -1;
+ int prev = me -1;
if (next == nprocs) next = 0;
if (prev < 0) prev = nprocs - 1;
@@ -794,48 +794,48 @@ void Special::angle_trim()
for (int loop = 0; loop < nprocs; loop++) {
i = 0;
while (i < size) {
- iglobal = buf[i];
- jglobal = buf[i+1];
- ilocal = atom->map(iglobal);
- jlocal = atom->map(jglobal);
- if (ilocal >= 0 && ilocal < nlocal)
- for (m = nspecial[ilocal][0]; m < nspecial[ilocal][1]; m++)
- if (jglobal == special[ilocal][m]) {
- dflag[ilocal][m-nspecial[ilocal][0]] = 1;
- break;
- }
- if (jlocal >= 0 && jlocal < nlocal)
- for (m = nspecial[jlocal][0]; m < nspecial[jlocal][1]; m++)
- if (iglobal == special[jlocal][m]) {
- dflag[jlocal][m-nspecial[jlocal][0]] = 1;
- break;
- }
- i += 2;
+ iglobal = buf[i];
+ jglobal = buf[i+1];
+ ilocal = atom->map(iglobal);
+ jlocal = atom->map(jglobal);
+ if (ilocal >= 0 && ilocal < nlocal)
+ for (m = nspecial[ilocal][0]; m < nspecial[ilocal][1]; m++)
+ if (jglobal == special[ilocal][m]) {
+ dflag[ilocal][m-nspecial[ilocal][0]] = 1;
+ break;
+ }
+ if (jlocal >= 0 && jlocal < nlocal)
+ for (m = nspecial[jlocal][0]; m < nspecial[jlocal][1]; m++)
+ if (iglobal == special[jlocal][m]) {
+ dflag[jlocal][m-nspecial[jlocal][0]] = 1;
+ break;
+ }
+ i += 2;
}
if (me != next) {
- MPI_Irecv(bufcopy,nbufmax,MPI_INT,prev,messtag,world,&request);
- MPI_Send(buf,size,MPI_INT,next,messtag,world);
- MPI_Wait(&request,&status);
- MPI_Get_count(&status,MPI_INT,&size);
- for (j = 0; j < size; j++) buf[j] = bufcopy[j];
+ MPI_Irecv(bufcopy,nbufmax,MPI_INT,prev,messtag,world,&request);
+ MPI_Send(buf,size,MPI_INT,next,messtag,world);
+ MPI_Wait(&request,&status);
+ MPI_Get_count(&status,MPI_INT,&size);
+ for (j = 0; j < size; j++) buf[j] = bufcopy[j];
}
}
-
+
// delete 1-3 neighbors if they are not flagged in dflag
// preserve 1-4 neighbors
-
+
int offset;
for (i = 0; i < nlocal; i++) {
offset = m = nspecial[i][0];
for (j = nspecial[i][0]; j < nspecial[i][1]; j++)
- if (dflag[i][j-offset]) special[i][m++] = special[i][j];
+ if (dflag[i][j-offset]) special[i][m++] = special[i][j];
offset = m;
for (j = nspecial[i][1]; j < nspecial[i][2]; j++)
- special[i][m++] = special[i][j];
+ special[i][m++] = special[i][j];
nspecial[i][1] = offset;
nspecial[i][2] = m;
}
-
+
// clean up
memory->destroy(dflag);
@@ -849,7 +849,7 @@ void Special::angle_trim()
for (i = 0; i < nlocal; i++) {
m = nspecial[i][0];
for (j = nspecial[i][1]; j < nspecial[i][2]; j++)
- special[i][m++] = special[i][j];
+ special[i][m++] = special[i][j];
nspecial[i][1] = nspecial[i][0];
nspecial[i][2] = m;
}
@@ -860,17 +860,17 @@ void Special::angle_trim()
onethreecount = 0.0;
for (i = 0; i < nlocal; i++)
onethreecount += nspecial[i][1] - nspecial[i][0];
-
+
MPI_Allreduce(&onethreecount,&allcount,1,MPI_DOUBLE,MPI_SUM,world);
if (me == 0) {
if (screen)
fprintf(screen,
- " %g = # of 1-3 neighbors after angle trim\n",allcount);
+ " %g = # of 1-3 neighbors after angle trim\n",allcount);
if (logfile)
fprintf(logfile,
- " %g = # of 1-3 neighbors after angle trim\n",allcount);
- }
+ " %g = # of 1-3 neighbors after angle trim\n",allcount);
+ }
}
/* ----------------------------------------------------------------------
@@ -903,10 +903,10 @@ void Special::dihedral_trim()
if (me == 0) {
if (screen)
fprintf(screen,
- " %g = # of 1-4 neighbors before dihedral trim\n",allcount);
+ " %g = # of 1-4 neighbors before dihedral trim\n",allcount);
if (logfile)
fprintf(logfile,
- " %g = # of 1-4 neighbors before dihedral trim\n",allcount);
+ " %g = # of 1-4 neighbors before dihedral trim\n",allcount);
}
// if dihedrals are defined, flag each 1-4 neigh if it appears in a dihedral
@@ -943,8 +943,8 @@ void Special::dihedral_trim()
int size = 0;
for (i = 0; i < nlocal; i++)
for (j = 0; j < num_dihedral[i]; j++) {
- buf[size++] = dihedral_atom1[i][j];
- buf[size++] = dihedral_atom4[i][j];
+ buf[size++] = dihedral_atom1[i][j];
+ buf[size++] = dihedral_atom4[i][j];
}
// cycle buffer around ring of procs back to self
@@ -952,7 +952,7 @@ void Special::dihedral_trim()
// when find one, scan its 1-4 neigh list and mark I,J as in a dihedral
int next = me + 1;
- int prev = me -1;
+ int prev = me -1;
if (next == nprocs) next = 0;
if (prev < 0) prev = nprocs - 1;
@@ -960,43 +960,43 @@ void Special::dihedral_trim()
for (int loop = 0; loop < nprocs; loop++) {
i = 0;
while (i < size) {
- iglobal = buf[i];
- jglobal = buf[i+1];
- ilocal = atom->map(iglobal);
- jlocal = atom->map(jglobal);
- if (ilocal >= 0 && ilocal < nlocal)
- for (m = nspecial[ilocal][1]; m < nspecial[ilocal][2]; m++)
- if (jglobal == special[ilocal][m]) {
- dflag[ilocal][m-nspecial[ilocal][1]] = 1;
- break;
- }
- if (jlocal >= 0 && jlocal < nlocal)
- for (m = nspecial[jlocal][1]; m < nspecial[jlocal][2]; m++)
- if (iglobal == special[jlocal][m]) {
- dflag[jlocal][m-nspecial[jlocal][1]] = 1;
- break;
- }
- i += 2;
+ iglobal = buf[i];
+ jglobal = buf[i+1];
+ ilocal = atom->map(iglobal);
+ jlocal = atom->map(jglobal);
+ if (ilocal >= 0 && ilocal < nlocal)
+ for (m = nspecial[ilocal][1]; m < nspecial[ilocal][2]; m++)
+ if (jglobal == special[ilocal][m]) {
+ dflag[ilocal][m-nspecial[ilocal][1]] = 1;
+ break;
+ }
+ if (jlocal >= 0 && jlocal < nlocal)
+ for (m = nspecial[jlocal][1]; m < nspecial[jlocal][2]; m++)
+ if (iglobal == special[jlocal][m]) {
+ dflag[jlocal][m-nspecial[jlocal][1]] = 1;
+ break;
+ }
+ i += 2;
}
if (me != next) {
- MPI_Irecv(bufcopy,nbufmax,MPI_INT,prev,messtag,world,&request);
- MPI_Send(buf,size,MPI_INT,next,messtag,world);
- MPI_Wait(&request,&status);
- MPI_Get_count(&status,MPI_INT,&size);
- for (j = 0; j < size; j++) buf[j] = bufcopy[j];
+ MPI_Irecv(bufcopy,nbufmax,MPI_INT,prev,messtag,world,&request);
+ MPI_Send(buf,size,MPI_INT,next,messtag,world);
+ MPI_Wait(&request,&status);
+ MPI_Get_count(&status,MPI_INT,&size);
+ for (j = 0; j < size; j++) buf[j] = bufcopy[j];
}
}
// delete 1-4 neighbors if they are not flagged in dflag
-
+
int offset;
for (i = 0; i < nlocal; i++) {
offset = m = nspecial[i][1];
for (j = nspecial[i][1]; j < nspecial[i][2]; j++)
- if (dflag[i][j-offset]) special[i][m++] = special[i][j];
+ if (dflag[i][j-offset]) special[i][m++] = special[i][j];
nspecial[i][2] = m;
}
-
+
// clean up
memory->destroy(dflag);
@@ -1018,9 +1018,9 @@ void Special::dihedral_trim()
if (me == 0) {
if (screen)
fprintf(screen,
- " %g = # of 1-4 neighbors after dihedral trim\n",allcount);
+ " %g = # of 1-4 neighbors after dihedral trim\n",allcount);
if (logfile)
fprintf(logfile,
- " %g = # of 1-4 neighbors after dihedral trim\n",allcount);
+ " %g = # of 1-4 neighbors after dihedral trim\n",allcount);
}
}
diff --git a/src/special.h b/src/special.h
index b269f01fe686e6067f4b4dc95429b15a1c0c99c0..b550f1ac47b34ec122753077633aeba52ee6552d 100644
--- a/src/special.h
+++ b/src/special.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/suffix.h b/src/suffix.h
index 9dd105ed53ff3badbe6930cf401d422016ff1b18..2a150ed5efa142d62ce6453b92f26ea267bf5aa2 100644
--- a/src/suffix.h
+++ b/src/suffix.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/thermo.cpp b/src/thermo.cpp
index 9167cd89281111a76aa52182e2f93d4727d5fef3..36501c15030aced3c9d7fcea0245893124691483 100644
--- a/src/thermo.cpp
+++ b/src/thermo.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -248,7 +248,7 @@ void Thermo::init()
int ivariable;
for (i = 0; i < nvariable; i++) {
ivariable = input->variable->find(id_variable[i]);
- if (ivariable < 0)
+ if (ivariable < 0)
error->all(FLERR,"Could not find thermo variable name");
variables[i] = ivariable;
}
@@ -271,7 +271,7 @@ void Thermo::header()
for (int i = 0; i < nfield; i++)
loc += sprintf(&line[loc],"%s ",keyword[i]);
sprintf(&line[loc],"\n");
-
+
if (me == 0) {
if (screen) fprintf(screen,line);
if (logfile) fprintf(logfile,line);
@@ -299,18 +299,18 @@ void Thermo::compute(int flag)
for (i = 0; i < ncompute; i++)
if (compute_which[i] == SCALAR) {
if (!(computes[i]->invoked_flag & INVOKED_SCALAR)) {
- computes[i]->compute_scalar();
- computes[i]->invoked_flag |= INVOKED_SCALAR;
+ computes[i]->compute_scalar();
+ computes[i]->invoked_flag |= INVOKED_SCALAR;
}
} else if (compute_which[i] == VECTOR) {
if (!(computes[i]->invoked_flag & INVOKED_VECTOR)) {
- computes[i]->compute_vector();
- computes[i]->invoked_flag |= INVOKED_VECTOR;
+ computes[i]->compute_vector();
+ computes[i]->invoked_flag |= INVOKED_VECTOR;
}
} else if (compute_which[i] == ARRAY) {
if (!(computes[i]->invoked_flag & INVOKED_ARRAY)) {
- computes[i]->compute_array();
- computes[i]->invoked_flag |= INVOKED_ARRAY;
+ computes[i]->compute_array();
+ computes[i]->invoked_flag |= INVOKED_ARRAY;
}
}
@@ -330,7 +330,7 @@ void Thermo::compute(int flag)
(this->*vfunc[ifield])();
if (vtype[ifield] == FLOAT)
loc += sprintf(&line[loc],format[ifield],dvalue);
- else if (vtype[ifield] == INT)
+ else if (vtype[ifield] == INT)
loc += sprintf(&line[loc],format[ifield],ivalue);
else if (vtype[ifield] == BIGINT) {
loc += sprintf(&line[loc],format[ifield],bivalue);
@@ -362,7 +362,7 @@ bigint Thermo::lost_check()
bigint ntotal;
bigint nblocal = atom->nlocal;
MPI_Allreduce(&nblocal,&ntotal,1,MPI_LMP_BIGINT,MPI_SUM,world);
- if (ntotal < 0 || ntotal > MAXBIGINT)
+ if (ntotal < 0 || ntotal > MAXBIGINT)
error->all(FLERR,"Too many total atoms");
if (ntotal == atom->natoms) return ntotal;
@@ -380,8 +380,8 @@ bigint Thermo::lost_check()
if (lostflag == ERROR) {
char str[64];
sprintf(str,
- "Lost atoms: original " BIGINT_FORMAT " current " BIGINT_FORMAT,
- atom->natoms,ntotal);
+ "Lost atoms: original " BIGINT_FORMAT " current " BIGINT_FORMAT,
+ atom->natoms,ntotal);
error->all(FLERR,str);
}
@@ -389,8 +389,8 @@ bigint Thermo::lost_check()
char str[64];
sprintf(str,
- "Lost atoms: original " BIGINT_FORMAT " current " BIGINT_FORMAT,
- atom->natoms,ntotal);
+ "Lost atoms: original " BIGINT_FORMAT " current " BIGINT_FORMAT,
+ atom->natoms,ntotal);
if (me == 0) error->warning(FLERR,str,0);
// reset total atom count
@@ -415,10 +415,10 @@ void Thermo::modify_params(int narg, char **arg)
if (strcmp(arg[iarg],"every") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal thermo_modify command");
if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) {
- delete [] output->var_thermo;
- int n = strlen(&arg[iarg+1][2]) + 1;
- output->var_thermo = new char[n];
- strcpy(output->var_thermo,&arg[iarg+1][2]);
+ delete [] output->var_thermo;
+ int n = strlen(&arg[iarg+1][2]) + 1;
+ output->var_thermo = new char[n];
+ strcpy(output->var_thermo,&arg[iarg+1][2]);
} else error->all(FLERR,"Illegal thermo_modify command");
output->thermo_every = 0;
iarg += 2;
@@ -431,28 +431,28 @@ void Thermo::modify_params(int narg, char **arg)
strcpy(id_compute[index_temp],arg[iarg+1]);
int icompute = modify->find_compute(arg[iarg+1]);
- if (icompute < 0)
- error->all(FLERR,"Could not find thermo_modify temperature ID");
+ if (icompute < 0)
+ error->all(FLERR,"Could not find thermo_modify temperature ID");
temperature = modify->compute[icompute];
if (temperature->tempflag == 0)
- error->all(FLERR,"Thermo_modify temperature ID does not "
- "compute temperature");
+ error->all(FLERR,"Thermo_modify temperature ID does not "
+ "compute temperature");
if (temperature->igroup != 0 && comm->me == 0)
- error->warning(FLERR,
- "Temperature for thermo pressure is not for group all");
+ error->warning(FLERR,
+ "Temperature for thermo pressure is not for group all");
// reset id_temp of pressure to new temperature ID
// either pressure currently being used by thermo or "thermo_press"
if (index_press_scalar >= 0) {
- icompute = modify->find_compute(id_compute[index_press_scalar]);
- if (icompute < 0) error->all(FLERR,
- "Pressure ID for thermo does not exist");
+ icompute = modify->find_compute(id_compute[index_press_scalar]);
+ if (icompute < 0) error->all(FLERR,
+ "Pressure ID for thermo does not exist");
} else if (index_press_vector >= 0) {
- icompute = modify->find_compute(id_compute[index_press_vector]);
- if (icompute < 0) error->all(FLERR,
- "Pressure ID for thermo does not exist");
+ icompute = modify->find_compute(id_compute[index_press_vector]);
+ if (icompute < 0) error->all(FLERR,
+ "Pressure ID for thermo does not exist");
} else icompute = modify->find_compute((char *) "thermo_press");
modify->compute[icompute]->reset_extra_compute_fix(arg[iarg+1]);
@@ -462,28 +462,28 @@ void Thermo::modify_params(int narg, char **arg)
} else if (strcmp(arg[iarg],"press") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal thermo_modify command");
if (index_press_scalar < 0 && index_press_vector < 0)
- error->all(FLERR,"Thermo style does not use press");
+ error->all(FLERR,"Thermo style does not use press");
if (index_press_scalar >= 0) {
- delete [] id_compute[index_press_scalar];
- int n = strlen(arg[iarg+1]) + 1;
- id_compute[index_press_scalar] = new char[n];
- strcpy(id_compute[index_press_scalar],arg[iarg+1]);
+ delete [] id_compute[index_press_scalar];
+ int n = strlen(arg[iarg+1]) + 1;
+ id_compute[index_press_scalar] = new char[n];
+ strcpy(id_compute[index_press_scalar],arg[iarg+1]);
}
if (index_press_vector >= 0) {
- delete [] id_compute[index_press_vector];
- int n = strlen(arg[iarg+1]) + 1;
- id_compute[index_press_vector] = new char[n];
- strcpy(id_compute[index_press_vector],arg[iarg+1]);
+ delete [] id_compute[index_press_vector];
+ int n = strlen(arg[iarg+1]) + 1;
+ id_compute[index_press_vector] = new char[n];
+ strcpy(id_compute[index_press_vector],arg[iarg+1]);
}
int icompute = modify->find_compute(arg[iarg+1]);
if (icompute < 0) error->all(FLERR,
- "Could not find thermo_modify pressure ID");
+ "Could not find thermo_modify pressure ID");
pressure = modify->compute[icompute];
if (pressure->pressflag == 0)
- error->all(FLERR,"Thermo_modify pressure ID does not compute pressure");
+ error->all(FLERR,"Thermo_modify pressure ID does not compute pressure");
iarg += 2;
@@ -520,34 +520,34 @@ void Thermo::modify_params(int narg, char **arg)
} else if (strcmp(arg[iarg],"format") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal thermo_modify command");
if (strcmp(arg[iarg+1],"int") == 0) {
- if (format_int_user) delete [] format_int_user;
- int n = strlen(arg[iarg+2]) + 1;
- format_int_user = new char[n];
- strcpy(format_int_user,arg[iarg+2]);
- if (format_bigint_user) delete [] format_bigint_user;
- n = strlen(format_int_user) + 3;
- format_bigint_user = new char[n];
- char *ptr = strchr(format_int_user,'d');
- if (ptr == NULL)
- error->all(FLERR,
- "Thermo_modify int format does not contain d character");
- *ptr = '\0';
- sprintf(format_bigint_user,"%s%s%s",format_int_user,
- BIGINT_FORMAT,ptr+1);
- *ptr = 'd';
+ if (format_int_user) delete [] format_int_user;
+ int n = strlen(arg[iarg+2]) + 1;
+ format_int_user = new char[n];
+ strcpy(format_int_user,arg[iarg+2]);
+ if (format_bigint_user) delete [] format_bigint_user;
+ n = strlen(format_int_user) + 3;
+ format_bigint_user = new char[n];
+ char *ptr = strchr(format_int_user,'d');
+ if (ptr == NULL)
+ error->all(FLERR,
+ "Thermo_modify int format does not contain d character");
+ *ptr = '\0';
+ sprintf(format_bigint_user,"%s%s%s",format_int_user,
+ BIGINT_FORMAT,ptr+1);
+ *ptr = 'd';
} else if (strcmp(arg[iarg+1],"float") == 0) {
- if (format_float_user) delete [] format_float_user;
- int n = strlen(arg[iarg+2]) + 1;
- format_float_user = new char[n];
- strcpy(format_float_user,arg[iarg+2]);
+ if (format_float_user) delete [] format_float_user;
+ int n = strlen(arg[iarg+2]) + 1;
+ format_float_user = new char[n];
+ strcpy(format_float_user,arg[iarg+2]);
} else {
- int i = atoi(arg[iarg+1]) - 1;
- if (i < 0 || i >= nfield_initial)
- error->all(FLERR,"Illegal thermo_modify command");
- if (format_user[i]) delete [] format_user[i];
- int n = strlen(arg[iarg+2]) + 1;
- format_user[i] = new char[n];
- strcpy(format_user[i],arg[iarg+2]);
+ int i = atoi(arg[iarg+1]) - 1;
+ if (i < 0 || i >= nfield_initial)
+ error->all(FLERR,"Illegal thermo_modify command");
+ if (format_user[i]) delete [] format_user[i];
+ int n = strlen(arg[iarg+2]) + 1;
+ format_user[i] = new char[n];
+ strcpy(format_user[i],arg[iarg+2]);
}
iarg += 3;
@@ -745,16 +745,16 @@ void Thermo::parse_fields(char *str)
addfield("Yz",&Thermo::compute_yz,FLOAT);
} else if (strcmp(word,"xlat") == 0) {
- if (domain->lattice == NULL)
- error->all(FLERR,"Thermo keyword requires lattice be defined");
+ if (domain->lattice == NULL)
+ error->all(FLERR,"Thermo keyword requires lattice be defined");
addfield("Xlat",&Thermo::compute_xlat,FLOAT);
} else if (strcmp(word,"ylat") == 0) {
- if (domain->lattice == NULL)
- error->all(FLERR,"Thermo keyword requires lattice be defined");
+ if (domain->lattice == NULL)
+ error->all(FLERR,"Thermo keyword requires lattice be defined");
addfield("Ylat",&Thermo::compute_ylat,FLOAT);
} else if (strcmp(word,"zlat") == 0) {
- if (domain->lattice == NULL)
- error->all(FLERR,"Thermo keyword requires lattice be defined");
+ if (domain->lattice == NULL)
+ error->all(FLERR,"Thermo keyword requires lattice be defined");
addfield("Zlat",&Thermo::compute_zlat,FLOAT);
} else if (strcmp(word,"pxx") == 0) {
@@ -799,7 +799,7 @@ void Thermo::parse_fields(char *str)
// copy = at most 8 chars of ID to pass to addfield
} else if ((strncmp(word,"c_",2) == 0) || (strncmp(word,"f_",2) == 0) ||
- (strncmp(word,"v_",2) == 0)) {
+ (strncmp(word,"v_",2) == 0)) {
int n = strlen(word);
char *id = new char[n];
@@ -814,74 +814,74 @@ void Thermo::parse_fields(char *str)
char *ptr = strchr(id,'[');
if (ptr == NULL) argindex1[nfield] = 0;
else {
- *ptr = '\0';
- argindex1[nfield] = input->variable->int_between_brackets(ptr);
- ptr++;
- if (*ptr == '[') {
- argindex2[nfield] = input->variable->int_between_brackets(ptr);
- ptr++;
- } else argindex2[nfield] = 0;
+ *ptr = '\0';
+ argindex1[nfield] = input->variable->int_between_brackets(ptr);
+ ptr++;
+ if (*ptr == '[') {
+ argindex2[nfield] = input->variable->int_between_brackets(ptr);
+ ptr++;
+ } else argindex2[nfield] = 0;
}
if (word[0] == 'c') {
- n = modify->find_compute(id);
- if (n < 0) error->all(FLERR,"Could not find thermo custom compute ID");
- if (argindex1[nfield] == 0 && modify->compute[n]->scalar_flag == 0)
- error->all(FLERR,"Thermo compute does not compute scalar");
- if (argindex1[nfield] > 0 && argindex2[nfield] == 0) {
- if (modify->compute[n]->vector_flag == 0)
- error->all(FLERR,"Thermo compute does not compute vector");
- if (argindex1[nfield] > modify->compute[n]->size_vector)
- error->all(FLERR,"Thermo compute vector is accessed out-of-range");
- }
- if (argindex1[nfield] > 0 && argindex2[nfield] > 0) {
- if (modify->compute[n]->array_flag == 0)
- error->all(FLERR,"Thermo compute does not compute array");
- if (argindex1[nfield] > modify->compute[n]->size_array_rows ||
- argindex2[nfield] > modify->compute[n]->size_array_cols)
- error->all(FLERR,"Thermo compute array is accessed out-of-range");
- }
-
- if (argindex1[nfield] == 0)
- field2index[nfield] = add_compute(id,SCALAR);
- else if (argindex2[nfield] == 0)
- field2index[nfield] = add_compute(id,VECTOR);
- else
- field2index[nfield] = add_compute(id,ARRAY);
- addfield(copy,&Thermo::compute_compute,FLOAT);
+ n = modify->find_compute(id);
+ if (n < 0) error->all(FLERR,"Could not find thermo custom compute ID");
+ if (argindex1[nfield] == 0 && modify->compute[n]->scalar_flag == 0)
+ error->all(FLERR,"Thermo compute does not compute scalar");
+ if (argindex1[nfield] > 0 && argindex2[nfield] == 0) {
+ if (modify->compute[n]->vector_flag == 0)
+ error->all(FLERR,"Thermo compute does not compute vector");
+ if (argindex1[nfield] > modify->compute[n]->size_vector)
+ error->all(FLERR,"Thermo compute vector is accessed out-of-range");
+ }
+ if (argindex1[nfield] > 0 && argindex2[nfield] > 0) {
+ if (modify->compute[n]->array_flag == 0)
+ error->all(FLERR,"Thermo compute does not compute array");
+ if (argindex1[nfield] > modify->compute[n]->size_array_rows ||
+ argindex2[nfield] > modify->compute[n]->size_array_cols)
+ error->all(FLERR,"Thermo compute array is accessed out-of-range");
+ }
+
+ if (argindex1[nfield] == 0)
+ field2index[nfield] = add_compute(id,SCALAR);
+ else if (argindex2[nfield] == 0)
+ field2index[nfield] = add_compute(id,VECTOR);
+ else
+ field2index[nfield] = add_compute(id,ARRAY);
+ addfield(copy,&Thermo::compute_compute,FLOAT);
} else if (word[0] == 'f') {
- n = modify->find_fix(id);
- if (n < 0) error->all(FLERR,"Could not find thermo custom fix ID");
- if (argindex1[nfield] == 0 && modify->fix[n]->scalar_flag == 0)
- error->all(FLERR,"Thermo fix does not compute scalar");
- if (argindex1[nfield] > 0 && argindex2[nfield] == 0) {
- if (modify->fix[n]->vector_flag == 0)
- error->all(FLERR,"Thermo fix does not compute vector");
- if (argindex1[nfield] > modify->fix[n]->size_vector)
- error->all(FLERR,"Thermo fix vector is accessed out-of-range");
- }
- if (argindex1[nfield] > 0 && argindex2[nfield] > 0) {
- if (modify->fix[n]->array_flag == 0)
- error->all(FLERR,"Thermo fix does not compute array");
- if (argindex1[nfield] > modify->fix[n]->size_array_rows ||
- argindex2[nfield] > modify->fix[n]->size_array_cols)
- error->all(FLERR,"Thermo fix array is accessed out-of-range");
- }
-
- field2index[nfield] = add_fix(id);
- addfield(copy,&Thermo::compute_fix,FLOAT);
+ n = modify->find_fix(id);
+ if (n < 0) error->all(FLERR,"Could not find thermo custom fix ID");
+ if (argindex1[nfield] == 0 && modify->fix[n]->scalar_flag == 0)
+ error->all(FLERR,"Thermo fix does not compute scalar");
+ if (argindex1[nfield] > 0 && argindex2[nfield] == 0) {
+ if (modify->fix[n]->vector_flag == 0)
+ error->all(FLERR,"Thermo fix does not compute vector");
+ if (argindex1[nfield] > modify->fix[n]->size_vector)
+ error->all(FLERR,"Thermo fix vector is accessed out-of-range");
+ }
+ if (argindex1[nfield] > 0 && argindex2[nfield] > 0) {
+ if (modify->fix[n]->array_flag == 0)
+ error->all(FLERR,"Thermo fix does not compute array");
+ if (argindex1[nfield] > modify->fix[n]->size_array_rows ||
+ argindex2[nfield] > modify->fix[n]->size_array_cols)
+ error->all(FLERR,"Thermo fix array is accessed out-of-range");
+ }
+
+ field2index[nfield] = add_fix(id);
+ addfield(copy,&Thermo::compute_fix,FLOAT);
} else if (word[0] == 'v') {
- n = input->variable->find(id);
- if (n < 0) error->all(FLERR,"Could not find thermo custom variable name");
- if (input->variable->equalstyle(n) == 0)
- error->all(FLERR,"Thermo custom variable is not equal-style variable");
- if (argindex1[nfield])
- error->all(FLERR,"Thermo custom variable cannot be indexed");
-
- field2index[nfield] = add_variable(id);
- addfield(copy,&Thermo::compute_variable,FLOAT);
+ n = input->variable->find(id);
+ if (n < 0) error->all(FLERR,"Could not find thermo custom variable name");
+ if (input->variable->equalstyle(n) == 0)
+ error->all(FLERR,"Thermo custom variable is not equal-style variable");
+ if (argindex1[nfield])
+ error->all(FLERR,"Thermo custom variable cannot be indexed");
+
+ field2index[nfield] = add_variable(id);
+ addfield(copy,&Thermo::compute_variable,FLOAT);
}
delete [] id;
@@ -914,8 +914,8 @@ int Thermo::add_compute(const char *id, int which)
{
int icompute;
for (icompute = 0; icompute < ncompute; icompute++)
- if ((strcmp(id,id_compute[icompute]) == 0) &&
- which == compute_which[icompute]) break;
+ if ((strcmp(id,id_compute[icompute]) == 0) &&
+ which == compute_which[icompute]) break;
if (icompute < ncompute) return icompute;
int n = strlen(id) + 1;
@@ -967,7 +967,7 @@ int Thermo::evaluate_keyword(char *word, double *answer)
// if inbetween runs and needed compute is not current, error
// if in middle of run and needed compute is not current, invoke it
// for keywords that use pe indirectly (evdwl, ebond, etc):
- // check if energy was tallied on this timestep and set pe->invoked_flag
+ // check if energy was tallied on this timestep and set pe->invoked_flag
// this will trigger next timestep for energy tallying via addstep()
if (strcmp(word,"step") == 0) {
@@ -975,13 +975,13 @@ int Thermo::evaluate_keyword(char *word, double *answer)
dvalue = bivalue;
} else if (strcmp(word,"elapsed") == 0) {
- if (update->whichflag == 0)
+ if (update->whichflag == 0)
error->all(FLERR,"This variable thermo keyword cannot be used between runs");
compute_elapsed();
dvalue = bivalue;
} else if (strcmp(word,"elaplong") == 0) {
- if (update->whichflag == 0)
+ if (update->whichflag == 0)
error->all(FLERR,"This variable thermo keyword cannot be used between runs");
compute_elapsed_long();
dvalue = bivalue;
@@ -990,17 +990,17 @@ int Thermo::evaluate_keyword(char *word, double *answer)
compute_dt();
} else if (strcmp(word,"cpu") == 0) {
- if (update->whichflag == 0)
+ if (update->whichflag == 0)
error->all(FLERR,"This variable thermo keyword cannot be used between runs");
compute_cpu();
} else if (strcmp(word,"tpcpu") == 0) {
- if (update->whichflag == 0)
+ if (update->whichflag == 0)
error->all(FLERR,"This variable thermo keyword cannot be used between runs");
compute_tpcpu();
} else if (strcmp(word,"spcpu") == 0) {
- if (update->whichflag == 0)
+ if (update->whichflag == 0)
error->all(FLERR,"This variable thermo keyword cannot be used between runs");
compute_spcpu();
@@ -1011,25 +1011,25 @@ int Thermo::evaluate_keyword(char *word, double *answer)
} else if (strcmp(word,"temp") == 0) {
if (!temperature)
error->all(FLERR,"Thermo keyword in variable requires "
- "thermo to use/init temp");
+ "thermo to use/init temp");
if (update->whichflag == 0) {
if (temperature->invoked_scalar != update->ntimestep)
- error->all(FLERR,"Compute used in variable thermo keyword between runs "
- "is not current");
+ error->all(FLERR,"Compute used in variable thermo keyword between runs "
+ "is not current");
} else if (!(temperature->invoked_flag & INVOKED_SCALAR)) {
temperature->compute_scalar();
temperature->invoked_flag |= INVOKED_SCALAR;
}
compute_temp();
-
+
} else if (strcmp(word,"press") == 0) {
if (!pressure)
error->all(FLERR,"Thermo keyword in variable requires "
- "thermo to use/init press");
+ "thermo to use/init press");
if (update->whichflag == 0) {
if (pressure->invoked_scalar != update->ntimestep)
- error->all(FLERR,"Compute used in variable thermo keyword between runs "
- "is not current");
+ error->all(FLERR,"Compute used in variable thermo keyword between runs "
+ "is not current");
} else if (!(pressure->invoked_flag & INVOKED_SCALAR)) {
pressure->compute_scalar();
pressure->invoked_flag |= INVOKED_SCALAR;
@@ -1041,8 +1041,8 @@ int Thermo::evaluate_keyword(char *word, double *answer)
error->all(FLERR,"Thermo keyword in variable requires thermo to use/init pe");
if (update->whichflag == 0) {
if (pe->invoked_scalar != update->ntimestep)
- error->all(FLERR,"Compute used in variable thermo keyword between runs "
- "is not current");
+ error->all(FLERR,"Compute used in variable thermo keyword between runs "
+ "is not current");
} else if (!(pe->invoked_flag & INVOKED_SCALAR)) {
pe->compute_scalar();
pe->invoked_flag |= INVOKED_SCALAR;
@@ -1052,11 +1052,11 @@ int Thermo::evaluate_keyword(char *word, double *answer)
} else if (strcmp(word,"ke") == 0) {
if (!temperature)
error->all(FLERR,"Thermo keyword in variable requires "
- "thermo to use/init temp");
+ "thermo to use/init temp");
if (update->whichflag == 0) {
if (temperature->invoked_scalar != update->ntimestep)
- error->all(FLERR,"Compute used in variable thermo keyword between runs "
- "is not current");
+ error->all(FLERR,"Compute used in variable thermo keyword between runs "
+ "is not current");
} else if (!(temperature->invoked_flag & INVOKED_SCALAR)) {
temperature->compute_scalar();
temperature->invoked_flag |= INVOKED_SCALAR;
@@ -1068,19 +1068,19 @@ int Thermo::evaluate_keyword(char *word, double *answer)
error->all(FLERR,"Thermo keyword in variable requires thermo to use/init pe");
if (update->whichflag == 0) {
if (pe->invoked_scalar != update->ntimestep)
- error->all(FLERR,"Compute used in variable thermo keyword between runs "
- "is not current");
+ error->all(FLERR,"Compute used in variable thermo keyword between runs "
+ "is not current");
} else if (!(pe->invoked_flag & INVOKED_SCALAR)) {
pe->compute_scalar();
pe->invoked_flag |= INVOKED_SCALAR;
}
if (!temperature)
error->all(FLERR,"Thermo keyword in variable requires "
- "thermo to use/init temp");
+ "thermo to use/init temp");
if (update->whichflag == 0) {
if (temperature->invoked_scalar != update->ntimestep)
- error->all(FLERR,"Compute used in variable thermo keyword between runs "
- "is not current");
+ error->all(FLERR,"Compute used in variable thermo keyword between runs "
+ "is not current");
} else if (!(temperature->invoked_flag & INVOKED_SCALAR)) {
temperature->compute_scalar();
temperature->invoked_flag |= INVOKED_SCALAR;
@@ -1092,30 +1092,30 @@ int Thermo::evaluate_keyword(char *word, double *answer)
error->all(FLERR,"Thermo keyword in variable requires thermo to use/init pe");
if (update->whichflag == 0) {
if (pe->invoked_scalar != update->ntimestep)
- error->all(FLERR,"Compute used in variable thermo keyword between runs "
- "is not current");
+ error->all(FLERR,"Compute used in variable thermo keyword between runs "
+ "is not current");
} else if (!(pe->invoked_flag & INVOKED_SCALAR)) {
pe->compute_scalar();
pe->invoked_flag |= INVOKED_SCALAR;
}
if (!temperature)
error->all(FLERR,"Thermo keyword in variable requires "
- "thermo to use/init temp");
+ "thermo to use/init temp");
if (update->whichflag == 0) {
if (temperature->invoked_scalar != update->ntimestep)
- error->all(FLERR,"Compute used in variable thermo keyword between runs "
- "is not current");
+ error->all(FLERR,"Compute used in variable thermo keyword between runs "
+ "is not current");
} else if (!(temperature->invoked_flag & INVOKED_SCALAR)) {
temperature->compute_scalar();
temperature->invoked_flag |= INVOKED_SCALAR;
}
if (!pressure)
error->all(FLERR,"Thermo keyword in variable requires "
- "thermo to use/init press");
+ "thermo to use/init press");
if (update->whichflag == 0) {
if (pressure->invoked_scalar != update->ntimestep)
- error->all(FLERR,"Compute used in variable thermo keyword between runs "
- "is not current");
+ error->all(FLERR,"Compute used in variable thermo keyword between runs "
+ "is not current");
} else if (!(pressure->invoked_flag & INVOKED_SCALAR)) {
pressure->compute_scalar();
pressure->invoked_flag |= INVOKED_SCALAR;
@@ -1219,26 +1219,26 @@ int Thermo::evaluate_keyword(char *word, double *answer)
else if (strcmp(word,"yz") == 0) compute_yz();
else if (strcmp(word,"xlat") == 0) {
- if (domain->lattice == NULL)
+ if (domain->lattice == NULL)
error->all(FLERR,"Thermo keyword in variable requires lattice be defined");
compute_xlat();
} else if (strcmp(word,"ylat") == 0) {
- if (domain->lattice == NULL)
+ if (domain->lattice == NULL)
error->all(FLERR,"Thermo keyword in variable requires lattice be defined");
- compute_ylat();
+ compute_ylat();
} else if (strcmp(word,"zlat") == 0) {
- if (domain->lattice == NULL)
+ if (domain->lattice == NULL)
error->all(FLERR,"Thermo keyword in variable requires lattice be defined");
compute_zlat();
} else if (strcmp(word,"pxx") == 0) {
if (!pressure)
error->all(FLERR,"Thermo keyword in variable requires "
- "thermo to use/init press");
+ "thermo to use/init press");
if (update->whichflag == 0) {
if (pressure->invoked_vector != update->ntimestep)
- error->all(FLERR,"Compute used in variable thermo keyword between runs "
- "is not current");
+ error->all(FLERR,"Compute used in variable thermo keyword between runs "
+ "is not current");
} else if (!(pressure->invoked_flag & INVOKED_VECTOR)) {
pressure->compute_vector();
pressure->invoked_flag |= INVOKED_VECTOR;
@@ -1248,11 +1248,11 @@ int Thermo::evaluate_keyword(char *word, double *answer)
} else if (strcmp(word,"pyy") == 0) {
if (!pressure)
error->all(FLERR,"Thermo keyword in variable requires "
- "thermo to use/init press");
+ "thermo to use/init press");
if (update->whichflag == 0) {
if (pressure->invoked_vector != update->ntimestep)
- error->all(FLERR,"Compute used in variable thermo keyword between runs "
- "is not current");
+ error->all(FLERR,"Compute used in variable thermo keyword between runs "
+ "is not current");
} else if (!(pressure->invoked_flag & INVOKED_VECTOR)) {
pressure->compute_vector();
pressure->invoked_flag |= INVOKED_VECTOR;
@@ -1262,11 +1262,11 @@ int Thermo::evaluate_keyword(char *word, double *answer)
} else if (strcmp(word,"pzz") == 0) {
if (!pressure)
error->all(FLERR,"Thermo keyword in variable requires "
- "thermo to use/init press");
+ "thermo to use/init press");
if (update->whichflag == 0) {
if (pressure->invoked_vector != update->ntimestep)
- error->all(FLERR,"Compute used in variable thermo keyword between runs "
- "is not current");
+ error->all(FLERR,"Compute used in variable thermo keyword between runs "
+ "is not current");
} else if (!(pressure->invoked_flag & INVOKED_VECTOR)) {
pressure->compute_vector();
pressure->invoked_flag |= INVOKED_VECTOR;
@@ -1276,11 +1276,11 @@ int Thermo::evaluate_keyword(char *word, double *answer)
} else if (strcmp(word,"pxy") == 0) {
if (!pressure)
error->all(FLERR,"Thermo keyword in variable requires "
- "thermo to use/init press");
+ "thermo to use/init press");
if (update->whichflag == 0) {
if (pressure->invoked_vector != update->ntimestep)
- error->all(FLERR,"Compute used in variable thermo keyword between runs "
- "is not current");
+ error->all(FLERR,"Compute used in variable thermo keyword between runs "
+ "is not current");
} else if (!(pressure->invoked_flag & INVOKED_VECTOR)) {
pressure->compute_vector();
pressure->invoked_flag |= INVOKED_VECTOR;
@@ -1290,11 +1290,11 @@ int Thermo::evaluate_keyword(char *word, double *answer)
} else if (strcmp(word,"pxz") == 0) {
if (!pressure)
error->all(FLERR,"Thermo keyword in variable requires "
- "thermo to use/init press");
+ "thermo to use/init press");
if (update->whichflag == 0) {
if (pressure->invoked_vector != update->ntimestep)
- error->all(FLERR,"Compute used in variable thermo keyword between runs "
- "is not current");
+ error->all(FLERR,"Compute used in variable thermo keyword between runs "
+ "is not current");
} else if (!(pressure->invoked_flag & INVOKED_VECTOR)) {
pressure->compute_vector();
pressure->invoked_flag |= INVOKED_VECTOR;
@@ -1304,11 +1304,11 @@ int Thermo::evaluate_keyword(char *word, double *answer)
} else if (strcmp(word,"pyz") == 0) {
if (!pressure)
error->all(FLERR,"Thermo keyword in variable requires "
- "thermo to use/init press");
+ "thermo to use/init press");
if (update->whichflag == 0) {
if (pressure->invoked_vector != update->ntimestep)
- error->all(FLERR,"Compute used in variable thermo keyword between runs "
- "is not current");
+ error->all(FLERR,"Compute used in variable thermo keyword between runs "
+ "is not current");
} else if (!(pressure->invoked_flag & INVOKED_VECTOR)) {
pressure->compute_vector();
pressure->invoked_flag |= INVOKED_VECTOR;
@@ -1900,7 +1900,7 @@ void Thermo::compute_cellalpha()
double cosalpha = (h[5]*h[4]+h[1]*h[3])/
sqrt((h[1]*h[1]+h[5]*h[5])*(h[2]*h[2]+h[3]*h[3]+h[4]*h[4]));
dvalue = acos(cosalpha)*180.0/MY_PI;
- }
+ }
}
/* ---------------------------------------------------------------------- */
diff --git a/src/thermo.h b/src/thermo.h
index ceac5be9cb1a7bb0c15ab6484416f0378fd232a8..ca920758d2cde13e7cbb5b3126cc29018255ad1e 100644
--- a/src/thermo.h
+++ b/src/thermo.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/timer.cpp b/src/timer.cpp
index eb38d5d2496239e9c0fa0dab858d9286e228050c..329de00d605091f2e24064e4af18bbeee5acc113 100644
--- a/src/timer.cpp
+++ b/src/timer.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/timer.h b/src/timer.h
index 95851dfd23dd9673db746e2e536ffbbe7bcfb4f5..1c421cb631832f0331041b4e136a10ce3edd5c07 100644
--- a/src/timer.h
+++ b/src/timer.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/universe.cpp b/src/universe.cpp
index b9d88ca70060ac6f2e4a798deeeafde38026d685..62048c55a96cdbf6c6b3dc3bc1d021eac2b4b321 100644
--- a/src/universe.cpp
+++ b/src/universe.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -78,9 +78,9 @@ void Universe::reorder(char *style, char *arg)
if (strcmp(style,"nth") == 0) {
int n = atoi(arg);
- if (n <= 0)
+ if (n <= 0)
error->universe_all(FLERR,"Invalid -reorder N value");
- if (nprocs % n)
+ if (nprocs % n)
error->universe_all(FLERR,"Nprocs not a multiple of N for -reorder");
for (int i = 0; i < nprocs; i++) {
if (i < (n-1)*nprocs/n) uni2orig[i] = i/(n-1) * n + (i % (n-1));
@@ -97,12 +97,12 @@ void Universe::reorder(char *style, char *arg)
char *ptr;
if (!fgets(line,MAXLINE,fp))
- error->one(FLERR,"Unexpected end of -reorder file");
+ error->one(FLERR,"Unexpected end of -reorder file");
while (1) {
- if (ptr = strchr(line,'#')) *ptr = '\0';
- if (strspn(line," \t\n\r") != strlen(line)) break;
- if (!fgets(line,MAXLINE,fp))
- error->one(FLERR,"Unexpected end of -reorder file");
+ if (ptr = strchr(line,'#')) *ptr = '\0';
+ if (strspn(line," \t\n\r") != strlen(line)) break;
+ if (!fgets(line,MAXLINE,fp))
+ error->one(FLERR,"Unexpected end of -reorder file");
}
// read nprocs lines
@@ -111,24 +111,24 @@ void Universe::reorder(char *style, char *arg)
int me_orig,me_new;
sscanf(line,"%d %d",&me_orig,&me_new);
if (me_orig < 0 || me_orig >= nprocs ||
- me_new < 0 || me_new >= nprocs)
- error->one(FLERR,"Invalid entry in -reorder file");
+ me_new < 0 || me_new >= nprocs)
+ error->one(FLERR,"Invalid entry in -reorder file");
uni2orig[me_new] = me_orig;
for (int i = 1; i < nprocs; i++) {
- if (!fgets(line,MAXLINE,fp))
- error->one(FLERR,"Unexpected end of -reorder file");
- sscanf(line,"%d %d",&me_orig,&me_new);
- if (me_orig < 0 || me_orig >= nprocs ||
- me_new < 0 || me_new >= nprocs)
- error->one(FLERR,"Invalid entry in -reorder file");
- uni2orig[me_new] = me_orig;
+ if (!fgets(line,MAXLINE,fp))
+ error->one(FLERR,"Unexpected end of -reorder file");
+ sscanf(line,"%d %d",&me_orig,&me_new);
+ if (me_orig < 0 || me_orig >= nprocs ||
+ me_new < 0 || me_new >= nprocs)
+ error->one(FLERR,"Invalid entry in -reorder file");
+ uni2orig[me_new] = me_orig;
}
fclose(fp);
}
// bcast uni2org from proc 0 to all other universe procs
-
+
MPI_Bcast(uni2orig,nprocs,MPI_INT,0,uorig);
} else error->universe_all(FLERR,"Invalid command-line argument");
diff --git a/src/universe.h b/src/universe.h
index 7d831d0b0bfe075cf950024fe61de86f46ce2337..b9978596680c6dc6bbc7224ba2111bd09b41e71f 100644
--- a/src/universe.h
+++ b/src/universe.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -36,7 +36,7 @@ class Universe : protected Pointers {
int *root_proc; // root proc in each world
MPI_Comm uorig; // original communicator passed to LAMMPS instance
- int *uni2orig; // proc I in universe uworld is
+ int *uni2orig; // proc I in universe uworld is
// proc uni2orig[I] in original communicator
Universe(class LAMMPS *, MPI_Comm);
diff --git a/src/update.cpp b/src/update.cpp
index d1f084f91fe19a437f43c9618bbd35b3f10f9218..5135214b68c0cf1a8fbb1ad47fb7ae0a7952628c 100644
--- a/src/update.cpp
+++ b/src/update.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -116,7 +116,7 @@ void Update::set_units(const char *style)
// physical constants from:
// http://physics.nist.gov/cuu/Constants/Table/allascii.txt
// using thermochemical calorie = 4.184 J
-
+
if (strcmp(style,"lj") == 0) {
force->boltz = 1.0;
force->hplanck = 0.18292026; // using LJ parameters for argon
@@ -137,7 +137,7 @@ void Update::set_units(const char *style)
dt = 0.005;
neighbor->skin = 0.3;
-
+
} else if (strcmp(style,"real") == 0) {
force->boltz = 0.0019872067;
force->hplanck = 95.306976368;
@@ -146,7 +146,7 @@ void Update::set_units(const char *style)
force->mv2d = 1.0 / 0.602214179;
force->nktv2p = 68568.415;
force->qqr2e = 332.06371;
- force->qe2f = 23.060549;
+ force->qe2f = 23.060549;
force->vxmu2f = 1.4393264316e4;
force->xxt2kmu = 0.1;
force->e_mass = 1.0/1836.1527556560675;
@@ -223,15 +223,15 @@ void Update::set_units(const char *style)
neighbor->skin = 0.1;
} else if (strcmp(style,"electron") == 0) {
- force->boltz = 3.16681534e-6;
+ force->boltz = 3.16681534e-6;
force->hplanck = 0.1519829846;
- force->mvv2e = 1.06657236;
- force->ftm2v = 0.937582899;
- force->mv2d = 1.0;
- force->nktv2p = 2.94210108e13;
- force->qqr2e = 1.0;
- force->qe2f = 1.94469051e-10;
- force->vxmu2f = 3.39893149e1;
+ force->mvv2e = 1.06657236;
+ force->ftm2v = 0.937582899;
+ force->mv2d = 1.0;
+ force->nktv2p = 2.94210108e13;
+ force->qqr2e = 1.0;
+ force->qe2f = 1.94469051e-10;
+ force->vxmu2f = 3.39893149e1;
force->xxt2kmu = 3.13796367e-2;
force->e_mass = 0.0; // not yet set
force->hhmrr2e = 0.0;
@@ -242,7 +242,7 @@ void Update::set_units(const char *style)
dt = 0.001;
neighbor->skin = 2.0;
-
+
} else error->all(FLERR,"Illegal units command");
delete [] unit_style;
@@ -281,7 +281,7 @@ void Update::create_integrate(int narg, char **arg, char *suffix)
------------------------------------------------------------------------- */
void Update::new_integrate(char *style, int narg, char **arg,
- char *suffix, int &sflag)
+ char *suffix, int &sflag)
{
int success = 0;
@@ -370,16 +370,16 @@ void Update::reset_timestep(bigint newstep)
for (int i = 0; i < output->ndump; i++)
if (output->last_dump[i] >= 0)
error->all(FLERR,
- "Cannot reset timestep with dump file already written to");
+ "Cannot reset timestep with dump file already written to");
if (output->restart && output->last_restart >= 0)
error->all(FLERR,
- "Cannot reset timestep with restart file already written");
+ "Cannot reset timestep with restart file already written");
for (int i = 0; i < modify->nfix; i++)
if (modify->fix[i]->time_depend)
error->all(FLERR,
- "Cannot reset timestep with a time-dependent fix defined");
+ "Cannot reset timestep with a time-dependent fix defined");
for (int i = 0; i < domain->nregion; i++)
if (domain->regions[i]->dynamic_check())
diff --git a/src/update.h b/src/update.h
index 9f9e1388c3dbb9c1953fd600eda97a0fcdac1fe5..954e9357a2512e3094b92a77e849ed58c66847e0 100644
--- a/src/update.h
+++ b/src/update.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/variable.cpp b/src/variable.cpp
index 1f50a3af366e5c7a1161f18507375bc183036203..82b32765044e56a9f41aaf9efc494b885859a08c 100644
--- a/src/variable.cpp
+++ b/src/variable.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -157,18 +157,18 @@ void Variable::set(int narg, char **arg)
nlast = atoi(arg[2]);
if (nlast <= 0) error->all(FLERR,"Illegal variable command");
if (narg == 4 && strcmp(arg[3],"pad") == 0) {
- char digits[12];
- sprintf(digits,"%d",nlast);
- pad[nvar] = strlen(digits);
+ char digits[12];
+ sprintf(digits,"%d",nlast);
+ pad[nvar] = strlen(digits);
} else pad[nvar] = 0;
} else if (narg == 4 || (narg == 5 && strcmp(arg[4],"pad") == 0)) {
nfirst = atoi(arg[2]);
nlast = atoi(arg[3]);
if (nfirst > nlast || nlast <= 0) error->all(FLERR,"Illegal variable command");
if (narg == 5 && strcmp(arg[4],"pad") == 0) {
- char digits[12];
- sprintf(digits,"%d",nlast);
- pad[nvar] = strlen(digits);
+ char digits[12];
+ sprintf(digits,"%d",nlast);
+ pad[nvar] = strlen(digits);
} else pad[nvar] = 0;
} else error->all(FLERR,"Illegal variable command");
num[nvar] = nlast;
@@ -212,7 +212,7 @@ void Variable::set(int narg, char **arg)
copy(num[nvar],&arg[2],data[nvar]);
} else if (strcmp(arg[1],"uloop") == 0) {
if (narg < 3 || narg > 4 || (narg == 4 && strcmp(arg[3],"pad") != 0))
- error->all(FLERR,"Illegal variable command");
+ error->all(FLERR,"Illegal variable command");
if (find(arg[0]) >= 0) return;
if (nvar == maxvar) extend();
style[nvar] = ULOOP;
@@ -220,9 +220,9 @@ void Variable::set(int narg, char **arg)
data[nvar] = new char*[1];
data[nvar][0] = NULL;
if (narg == 4) {
- char digits[12];
- sprintf(digits,"%d",num[nvar]);
- pad[nvar] = strlen(digits);
+ char digits[12];
+ sprintf(digits,"%d",num[nvar]);
+ pad[nvar] = strlen(digits);
} else pad[nvar] = 0;
}
@@ -237,9 +237,9 @@ void Variable::set(int narg, char **arg)
}
for (int jvar = 0; jvar < nvar; jvar++)
- if (num[jvar] && (style[jvar] == UNIVERSE || style[jvar] == ULOOP) &&
- num[nvar] != num[jvar])
- error->all(FLERR,"All universe/uloop variables must have same # of values");
+ if (num[jvar] && (style[jvar] == UNIVERSE || style[jvar] == ULOOP) &&
+ num[nvar] != num[jvar])
+ error->all(FLERR,"All universe/uloop variables must have same # of values");
// STRING
// remove pre-existing var if also style STRING (allows it to be reset)
@@ -250,7 +250,7 @@ void Variable::set(int narg, char **arg)
if (narg != 3) error->all(FLERR,"Illegal variable command");
if (find(arg[0]) >= 0) {
if (style[find(arg[0])] != STRING)
- error->all(FLERR,"Cannot redefine variable as a different style");
+ error->all(FLERR,"Cannot redefine variable as a different style");
remove(find(arg[0]));
}
if (nvar == maxvar) extend();
@@ -260,7 +260,7 @@ void Variable::set(int narg, char **arg)
pad[nvar] = 0;
data[nvar] = new char*[num[nvar]];
copy(1,&arg[2],data[nvar]);
-
+
// EQUAL
// remove pre-existing var if also style EQUAL (allows it to be reset)
// num = 2, which = 1st value
@@ -270,7 +270,7 @@ void Variable::set(int narg, char **arg)
if (narg != 3) error->all(FLERR,"Illegal variable command");
if (find(arg[0]) >= 0) {
if (style[find(arg[0])] != EQUAL)
- error->all(FLERR,"Cannot redefine variable as a different style");
+ error->all(FLERR,"Cannot redefine variable as a different style");
remove(find(arg[0]));
}
if (nvar == maxvar) extend();
@@ -281,7 +281,7 @@ void Variable::set(int narg, char **arg)
data[nvar] = new char*[num[nvar]];
copy(1,&arg[2],data[nvar]);
data[nvar][1] = NULL;
-
+
// ATOM
// remove pre-existing var if also style ATOM (allows it to be reset)
// num = 1, which = 1st value
@@ -291,7 +291,7 @@ void Variable::set(int narg, char **arg)
if (narg != 3) error->all(FLERR,"Illegal variable command");
if (find(arg[0]) >= 0) {
if (style[find(arg[0])] != ATOM)
- error->all(FLERR,"Cannot redefine variable as a different style");
+ error->all(FLERR,"Cannot redefine variable as a different style");
remove(find(arg[0]));
}
if (nvar == maxvar) extend();
@@ -301,7 +301,7 @@ void Variable::set(int narg, char **arg)
pad[nvar] = 0;
data[nvar] = new char*[num[nvar]];
copy(1,&arg[2],data[nvar]);
-
+
} else error->all(FLERR,"Illegal variable command");
// set name of variable
@@ -315,7 +315,7 @@ void Variable::set(int narg, char **arg)
for (int i = 0; i < n-1; i++)
if (!isalnum(names[nvar][i]) && names[nvar][i] != '_')
error->all(FLERR,"Variable name must be alphanumeric or "
- "underscore characters");
+ "underscore characters");
nvar++;
}
@@ -374,8 +374,8 @@ int Variable::next(int narg, char **arg)
ivar = find(arg[iarg]);
which[ivar]++;
if (which[ivar] >= num[ivar]) {
- flag = 1;
- remove(ivar);
+ flag = 1;
+ remove(ivar);
}
}
@@ -388,8 +388,8 @@ int Variable::next(int narg, char **arg)
int nextindex;
if (me == 0) {
while (1) {
- if (!rename("tmp.lammps.variable","tmp.lammps.variable.lock")) break;
- usleep(100000);
+ if (!rename("tmp.lammps.variable","tmp.lammps.variable.lock")) break;
+ usleep(100000);
}
FILE *fp = fopen("tmp.lammps.variable.lock","r");
fscanf(fp,"%d",&nextindex);
@@ -399,13 +399,13 @@ int Variable::next(int narg, char **arg)
fclose(fp);
rename("tmp.lammps.variable.lock","tmp.lammps.variable");
if (universe->uscreen)
- fprintf(universe->uscreen,
- "Increment via next: value %d on partition %d\n",
- nextindex+1,universe->iworld);
+ fprintf(universe->uscreen,
+ "Increment via next: value %d on partition %d\n",
+ nextindex+1,universe->iworld);
if (universe->ulogfile)
- fprintf(universe->ulogfile,
- "Increment via next: value %d on partition %d\n",
- nextindex+1,universe->iworld);
+ fprintf(universe->ulogfile,
+ "Increment via next: value %d on partition %d\n",
+ nextindex+1,universe->iworld);
}
MPI_Bcast(&nextindex,1,MPI_INT,0,world);
@@ -413,8 +413,8 @@ int Variable::next(int narg, char **arg)
ivar = find(arg[iarg]);
which[ivar] = nextindex;
if (which[ivar] >= num[ivar]) {
- flag = 1;
- remove(ivar);
+ flag = 1;
+ remove(ivar);
}
}
}
@@ -438,7 +438,7 @@ char *Variable::retrieve(char *name)
if (which[ivar] >= num[ivar]) return NULL;
char *str;
- if (style[ivar] == INDEX || style[ivar] == WORLD ||
+ if (style[ivar] == INDEX || style[ivar] == WORLD ||
style[ivar] == UNIVERSE || style[ivar] == STRING) {
str = data[ivar][which[ivar]];
} else if (style[ivar] == LOOP || style[ivar] == ULOOP) {
@@ -485,7 +485,7 @@ double Variable::compute_equal(int ivar)
------------------------------------------------------------------------- */
void Variable::compute_atom(int ivar, int igroup,
- double *result, int stride, int sumflag)
+ double *result, int stride, int sumflag)
{
Tree *tree;
double tmp = evaluate(data[ivar][0],&tree);
@@ -518,7 +518,7 @@ void Variable::compute_atom(int ivar, int igroup,
search for name in list of variables names
return index or -1 if not found
------------------------------------------------------------------------- */
-
+
int Variable::find(char *name)
{
for (int i = 0; i < nvar; i++)
@@ -529,7 +529,7 @@ int Variable::find(char *name)
/* ----------------------------------------------------------------------
return 1 if variable is EQUAL style, 0 if not
------------------------------------------------------------------------- */
-
+
int Variable::equalstyle(int ivar)
{
if (style[ivar] == EQUAL) return 1;
@@ -539,7 +539,7 @@ int Variable::equalstyle(int ivar)
/* ----------------------------------------------------------------------
return 1 if variable is ATOM style, 0 if not
------------------------------------------------------------------------- */
-
+
int Variable::atomstyle(int ivar)
{
if (style[ivar] == ATOM) return 1;
@@ -549,7 +549,7 @@ int Variable::atomstyle(int ivar)
/* ----------------------------------------------------------------------
remove Nth variable from list and compact list
------------------------------------------------------------------------- */
-
+
void Variable::remove(int n)
{
delete [] names[n];
@@ -581,14 +581,14 @@ void Variable::extend()
memory->grow(num,maxvar,"var:num");
memory->grow(which,maxvar,"var:which");
memory->grow(pad,maxvar,"var:pad");
- data = (char ***)
+ data = (char ***)
memory->srealloc(data,maxvar*sizeof(char **),"var:data");
}
/* ----------------------------------------------------------------------
copy narg strings from **from to **to, and allocate space for them
------------------------------------------------------------------------- */
-
+
void Variable::copy(int narg, char **from, char **to)
{
int n;
@@ -608,7 +608,7 @@ void Variable::copy(int narg, char **from, char **to)
math operation = (),-x,x+y,x-y,x*y,x/y,x^y,
x==y,x!=y,x<y,x<=y,x>y,x>=y,x&&y,x||y,
sqrt(x),exp(x),ln(x),log(x),
- sin(x),cos(x),tan(x),asin(x),atan2(y,x),...
+ sin(x),cos(x),tan(x),asin(x),atan2(y,x),...
group function = count(group), mass(group), xcm(group,x), ...
special function = sum(x),min(x), ...
atom value = x[i], y[i], vx[i], ...
@@ -662,9 +662,9 @@ double Variable::evaluate(char *str, Tree **tree)
// evaluate contents and push on stack
if (tree) {
- Tree *newtree;
- evaluate(contents,&newtree);
- treestack[ntreestack++] = newtree;
+ Tree *newtree;
+ evaluate(contents,&newtree);
+ treestack[ntreestack++] = newtree;
} else argstack[nargstack++] = evaluate(contents,NULL);
delete [] contents;
@@ -682,9 +682,9 @@ double Variable::evaluate(char *str, Tree **tree)
int istart = i;
while (isdigit(str[i]) || str[i] == '.') i++;
if (str[i] == 'e' || str[i] == 'E') {
- i++;
- if (str[i] == '+' || str[i] == '-') i++;
- while (isdigit(str[i])) i++;
+ i++;
+ if (str[i] == '+' || str[i] == '-') i++;
+ while (isdigit(str[i])) i++;
}
int istop = i - 1;
@@ -695,10 +695,10 @@ double Variable::evaluate(char *str, Tree **tree)
if (tree) {
Tree *newtree = new Tree();
- newtree->type = VALUE;
- newtree->value = atof(number);
- newtree->left = newtree->middle = newtree->right = NULL;
- treestack[ntreestack++] = newtree;
+ newtree->type = VALUE;
+ newtree->value = atof(number);
+ newtree->left = newtree->middle = newtree->right = NULL;
+ treestack[ntreestack++] = newtree;
} else argstack[nargstack++] = atof(number);
delete [] number;
@@ -729,438 +729,438 @@ double Variable::evaluate(char *str, Tree **tree)
// ----------------
if (strncmp(word,"c_",2) == 0) {
- if (domain->box_exist == 0)
- error->all(FLERR,"Variable evaluation before simulation box is defined");
-
- n = strlen(word) - 2 + 1;
- char *id = new char[n];
- strcpy(id,&word[2]);
-
- int icompute = modify->find_compute(id);
- if (icompute < 0) error->all(FLERR,"Invalid compute ID in variable formula");
- Compute *compute = modify->compute[icompute];
- delete [] id;
-
- // parse zero or one or two trailing brackets
- // point i beyond last bracket
- // nbracket = # of bracket pairs
- // index1,index2 = int inside each bracket pair
-
- int nbracket,index1,index2;
- if (str[i] != '[') nbracket = 0;
- else {
- nbracket = 1;
- ptr = &str[i];
- index1 = int_between_brackets(ptr);
- i = ptr-str+1;
- if (str[i] == '[') {
- nbracket = 2;
- ptr = &str[i];
- index2 = int_between_brackets(ptr);
- i = ptr-str+1;
- }
- }
+ if (domain->box_exist == 0)
+ error->all(FLERR,"Variable evaluation before simulation box is defined");
+
+ n = strlen(word) - 2 + 1;
+ char *id = new char[n];
+ strcpy(id,&word[2]);
+
+ int icompute = modify->find_compute(id);
+ if (icompute < 0) error->all(FLERR,"Invalid compute ID in variable formula");
+ Compute *compute = modify->compute[icompute];
+ delete [] id;
+
+ // parse zero or one or two trailing brackets
+ // point i beyond last bracket
+ // nbracket = # of bracket pairs
+ // index1,index2 = int inside each bracket pair
+
+ int nbracket,index1,index2;
+ if (str[i] != '[') nbracket = 0;
+ else {
+ nbracket = 1;
+ ptr = &str[i];
+ index1 = int_between_brackets(ptr);
+ i = ptr-str+1;
+ if (str[i] == '[') {
+ nbracket = 2;
+ ptr = &str[i];
+ index2 = int_between_brackets(ptr);
+ i = ptr-str+1;
+ }
+ }
// c_ID = scalar from global scalar
- if (nbracket == 0 && compute->scalar_flag) {
-
- if (update->whichflag == 0) {
- if (compute->invoked_scalar != update->ntimestep)
- error->all(FLERR,"Compute used in variable between runs "
- "is not current");
- } else if (!(compute->invoked_flag & INVOKED_SCALAR)) {
- compute->compute_scalar();
- compute->invoked_flag |= INVOKED_SCALAR;
- }
-
- value1 = compute->scalar;
- if (tree) {
- Tree *newtree = new Tree();
- newtree->type = VALUE;
- newtree->value = value1;
- newtree->left = newtree->middle = newtree->right = NULL;
- treestack[ntreestack++] = newtree;
- } else argstack[nargstack++] = value1;
+ if (nbracket == 0 && compute->scalar_flag) {
+
+ if (update->whichflag == 0) {
+ if (compute->invoked_scalar != update->ntimestep)
+ error->all(FLERR,"Compute used in variable between runs "
+ "is not current");
+ } else if (!(compute->invoked_flag & INVOKED_SCALAR)) {
+ compute->compute_scalar();
+ compute->invoked_flag |= INVOKED_SCALAR;
+ }
+
+ value1 = compute->scalar;
+ if (tree) {
+ Tree *newtree = new Tree();
+ newtree->type = VALUE;
+ newtree->value = value1;
+ newtree->left = newtree->middle = newtree->right = NULL;
+ treestack[ntreestack++] = newtree;
+ } else argstack[nargstack++] = value1;
// c_ID[i] = scalar from global vector
- } else if (nbracket == 1 && compute->vector_flag) {
-
- if (index1 > compute->size_vector)
- error->all(FLERR,"Variable formula compute vector "
- "is accessed out-of-range");
- if (update->whichflag == 0) {
- if (compute->invoked_vector != update->ntimestep)
- error->all(FLERR,"Compute used in variable between runs "
- "is not current");
- } else if (!(compute->invoked_flag & INVOKED_VECTOR)) {
- compute->compute_vector();
- compute->invoked_flag |= INVOKED_VECTOR;
- }
-
- value1 = compute->vector[index1-1];
- if (tree) {
- Tree *newtree = new Tree();
- newtree->type = VALUE;
- newtree->value = value1;
- newtree->left = newtree->middle = newtree->right = NULL;
- treestack[ntreestack++] = newtree;
- } else argstack[nargstack++] = value1;
+ } else if (nbracket == 1 && compute->vector_flag) {
+
+ if (index1 > compute->size_vector)
+ error->all(FLERR,"Variable formula compute vector "
+ "is accessed out-of-range");
+ if (update->whichflag == 0) {
+ if (compute->invoked_vector != update->ntimestep)
+ error->all(FLERR,"Compute used in variable between runs "
+ "is not current");
+ } else if (!(compute->invoked_flag & INVOKED_VECTOR)) {
+ compute->compute_vector();
+ compute->invoked_flag |= INVOKED_VECTOR;
+ }
+
+ value1 = compute->vector[index1-1];
+ if (tree) {
+ Tree *newtree = new Tree();
+ newtree->type = VALUE;
+ newtree->value = value1;
+ newtree->left = newtree->middle = newtree->right = NULL;
+ treestack[ntreestack++] = newtree;
+ } else argstack[nargstack++] = value1;
// c_ID[i][j] = scalar from global array
- } else if (nbracket == 2 && compute->array_flag) {
-
- if (index1 > compute->size_array_rows)
- error->all(FLERR,"Variable formula compute array "
- "is accessed out-of-range");
- if (index2 > compute->size_array_cols)
- error->all(FLERR,"Variable formula compute array "
- "is accessed out-of-range");
- if (update->whichflag == 0) {
- if (compute->invoked_array != update->ntimestep)
- error->all(FLERR,"Compute used in variable between runs "
- "is not current");
- } else if (!(compute->invoked_flag & INVOKED_ARRAY)) {
- compute->compute_array();
- compute->invoked_flag |= INVOKED_ARRAY;
- }
-
- value1 = compute->array[index1-1][index2-1];
- if (tree) {
- Tree *newtree = new Tree();
- newtree->type = VALUE;
- newtree->value = value1;
- newtree->left = newtree->middle = newtree->right = NULL;
- treestack[ntreestack++] = newtree;
- } else argstack[nargstack++] = value1;
+ } else if (nbracket == 2 && compute->array_flag) {
+
+ if (index1 > compute->size_array_rows)
+ error->all(FLERR,"Variable formula compute array "
+ "is accessed out-of-range");
+ if (index2 > compute->size_array_cols)
+ error->all(FLERR,"Variable formula compute array "
+ "is accessed out-of-range");
+ if (update->whichflag == 0) {
+ if (compute->invoked_array != update->ntimestep)
+ error->all(FLERR,"Compute used in variable between runs "
+ "is not current");
+ } else if (!(compute->invoked_flag & INVOKED_ARRAY)) {
+ compute->compute_array();
+ compute->invoked_flag |= INVOKED_ARRAY;
+ }
+
+ value1 = compute->array[index1-1][index2-1];
+ if (tree) {
+ Tree *newtree = new Tree();
+ newtree->type = VALUE;
+ newtree->value = value1;
+ newtree->left = newtree->middle = newtree->right = NULL;
+ treestack[ntreestack++] = newtree;
+ } else argstack[nargstack++] = value1;
// c_ID[i] = scalar from per-atom vector
- } else if (nbracket == 1 && compute->peratom_flag &&
- compute->size_peratom_cols == 0) {
+ } else if (nbracket == 1 && compute->peratom_flag &&
+ compute->size_peratom_cols == 0) {
- if (update->whichflag == 0) {
- if (compute->invoked_peratom != update->ntimestep)
- error->all(FLERR,"Compute used in variable between runs "
- "is not current");
- } else if (!(compute->invoked_flag & INVOKED_PERATOM)) {
- compute->compute_peratom();
- compute->invoked_flag |= INVOKED_PERATOM;
- }
+ if (update->whichflag == 0) {
+ if (compute->invoked_peratom != update->ntimestep)
+ error->all(FLERR,"Compute used in variable between runs "
+ "is not current");
+ } else if (!(compute->invoked_flag & INVOKED_PERATOM)) {
+ compute->compute_peratom();
+ compute->invoked_flag |= INVOKED_PERATOM;
+ }
- peratom2global(1,NULL,compute->vector_atom,1,index1,
- tree,treestack,ntreestack,argstack,nargstack);
+ peratom2global(1,NULL,compute->vector_atom,1,index1,
+ tree,treestack,ntreestack,argstack,nargstack);
// c_ID[i][j] = scalar from per-atom array
- } else if (nbracket == 2 && compute->peratom_flag &&
- compute->size_peratom_cols > 0) {
-
- if (index2 > compute->size_peratom_cols)
- error->all(FLERR,"Variable formula compute array "
- "is accessed out-of-range");
- if (update->whichflag == 0) {
- if (compute->invoked_peratom != update->ntimestep)
- error->all(FLERR,"Compute used in variable between runs "
- "is not current");
- } else if (!(compute->invoked_flag & INVOKED_PERATOM)) {
- compute->compute_peratom();
- compute->invoked_flag |= INVOKED_PERATOM;
- }
-
- peratom2global(1,NULL,&compute->array_atom[0][index2-1],
- compute->size_peratom_cols,index1,
- tree,treestack,ntreestack,argstack,nargstack);
+ } else if (nbracket == 2 && compute->peratom_flag &&
+ compute->size_peratom_cols > 0) {
+
+ if (index2 > compute->size_peratom_cols)
+ error->all(FLERR,"Variable formula compute array "
+ "is accessed out-of-range");
+ if (update->whichflag == 0) {
+ if (compute->invoked_peratom != update->ntimestep)
+ error->all(FLERR,"Compute used in variable between runs "
+ "is not current");
+ } else if (!(compute->invoked_flag & INVOKED_PERATOM)) {
+ compute->compute_peratom();
+ compute->invoked_flag |= INVOKED_PERATOM;
+ }
+
+ peratom2global(1,NULL,&compute->array_atom[0][index2-1],
+ compute->size_peratom_cols,index1,
+ tree,treestack,ntreestack,argstack,nargstack);
// c_ID = vector from per-atom vector
- } else if (nbracket == 0 && compute->peratom_flag &&
- compute->size_peratom_cols == 0) {
-
- if (tree == NULL)
- error->all(FLERR,
- "Per-atom compute in equal-style variable formula");
- if (update->whichflag == 0) {
- if (compute->invoked_peratom != update->ntimestep)
- error->all(FLERR,"Compute used in variable between runs "
- "is not current");
- } else if (!(compute->invoked_flag & INVOKED_PERATOM)) {
- compute->compute_peratom();
- compute->invoked_flag |= INVOKED_PERATOM;
- }
-
- Tree *newtree = new Tree();
- newtree->type = ATOMARRAY;
- newtree->array = compute->vector_atom;
- newtree->nstride = 1;
- newtree->left = newtree->middle = newtree->right = NULL;
- treestack[ntreestack++] = newtree;
+ } else if (nbracket == 0 && compute->peratom_flag &&
+ compute->size_peratom_cols == 0) {
+
+ if (tree == NULL)
+ error->all(FLERR,
+ "Per-atom compute in equal-style variable formula");
+ if (update->whichflag == 0) {
+ if (compute->invoked_peratom != update->ntimestep)
+ error->all(FLERR,"Compute used in variable between runs "
+ "is not current");
+ } else if (!(compute->invoked_flag & INVOKED_PERATOM)) {
+ compute->compute_peratom();
+ compute->invoked_flag |= INVOKED_PERATOM;
+ }
+
+ Tree *newtree = new Tree();
+ newtree->type = ATOMARRAY;
+ newtree->array = compute->vector_atom;
+ newtree->nstride = 1;
+ newtree->left = newtree->middle = newtree->right = NULL;
+ treestack[ntreestack++] = newtree;
// c_ID[i] = vector from per-atom array
- } else if (nbracket == 1 && compute->peratom_flag &&
- compute->size_peratom_cols > 0) {
-
- if (tree == NULL)
- error->all(FLERR,
- "Per-atom compute in equal-style variable formula");
- if (index1 > compute->size_peratom_cols)
- error->all(FLERR,"Variable formula compute array "
- "is accessed out-of-range");
- if (update->whichflag == 0) {
- if (compute->invoked_peratom != update->ntimestep)
- error->all(FLERR,"Compute used in variable between runs "
- "is not current");
- } else if (!(compute->invoked_flag & INVOKED_PERATOM)) {
- compute->compute_peratom();
- compute->invoked_flag |= INVOKED_PERATOM;
- }
-
- Tree *newtree = new Tree();
- newtree->type = ATOMARRAY;
- newtree->array = &compute->array_atom[0][index1-1];
- newtree->nstride = compute->size_peratom_cols;
- newtree->left = newtree->middle = newtree->right = NULL;
- treestack[ntreestack++] = newtree;
-
- } else error->all(FLERR,"Mismatched compute in variable formula");
+ } else if (nbracket == 1 && compute->peratom_flag &&
+ compute->size_peratom_cols > 0) {
+
+ if (tree == NULL)
+ error->all(FLERR,
+ "Per-atom compute in equal-style variable formula");
+ if (index1 > compute->size_peratom_cols)
+ error->all(FLERR,"Variable formula compute array "
+ "is accessed out-of-range");
+ if (update->whichflag == 0) {
+ if (compute->invoked_peratom != update->ntimestep)
+ error->all(FLERR,"Compute used in variable between runs "
+ "is not current");
+ } else if (!(compute->invoked_flag & INVOKED_PERATOM)) {
+ compute->compute_peratom();
+ compute->invoked_flag |= INVOKED_PERATOM;
+ }
+
+ Tree *newtree = new Tree();
+ newtree->type = ATOMARRAY;
+ newtree->array = &compute->array_atom[0][index1-1];
+ newtree->nstride = compute->size_peratom_cols;
+ newtree->left = newtree->middle = newtree->right = NULL;
+ treestack[ntreestack++] = newtree;
+
+ } else error->all(FLERR,"Mismatched compute in variable formula");
// ----------------
// fix
// ----------------
} else if (strncmp(word,"f_",2) == 0) {
- if (domain->box_exist == 0)
- error->all(FLERR,
- "Variable evaluation before simulation box is defined");
-
- n = strlen(word) - 2 + 1;
- char *id = new char[n];
- strcpy(id,&word[2]);
-
- int ifix = modify->find_fix(id);
- if (ifix < 0) error->all(FLERR,"Invalid fix ID in variable formula");
- Fix *fix = modify->fix[ifix];
- delete [] id;
-
- // parse zero or one or two trailing brackets
- // point i beyond last bracket
- // nbracket = # of bracket pairs
- // index1,index2 = int inside each bracket pair
-
- int nbracket,index1,index2;
- if (str[i] != '[') nbracket = 0;
- else {
- nbracket = 1;
- ptr = &str[i];
- index1 = int_between_brackets(ptr);
- i = ptr-str+1;
- if (str[i] == '[') {
- nbracket = 2;
- ptr = &str[i];
- index2 = int_between_brackets(ptr);
- i = ptr-str+1;
- }
- }
+ if (domain->box_exist == 0)
+ error->all(FLERR,
+ "Variable evaluation before simulation box is defined");
+
+ n = strlen(word) - 2 + 1;
+ char *id = new char[n];
+ strcpy(id,&word[2]);
+
+ int ifix = modify->find_fix(id);
+ if (ifix < 0) error->all(FLERR,"Invalid fix ID in variable formula");
+ Fix *fix = modify->fix[ifix];
+ delete [] id;
+
+ // parse zero or one or two trailing brackets
+ // point i beyond last bracket
+ // nbracket = # of bracket pairs
+ // index1,index2 = int inside each bracket pair
+
+ int nbracket,index1,index2;
+ if (str[i] != '[') nbracket = 0;
+ else {
+ nbracket = 1;
+ ptr = &str[i];
+ index1 = int_between_brackets(ptr);
+ i = ptr-str+1;
+ if (str[i] == '[') {
+ nbracket = 2;
+ ptr = &str[i];
+ index2 = int_between_brackets(ptr);
+ i = ptr-str+1;
+ }
+ }
// f_ID = scalar from global scalar
- if (nbracket == 0 && fix->scalar_flag) {
+ if (nbracket == 0 && fix->scalar_flag) {
- if (update->whichflag > 0 && update->ntimestep % fix->global_freq)
- error->all(FLERR,"Fix in variable not computed at compatible time");
+ if (update->whichflag > 0 && update->ntimestep % fix->global_freq)
+ error->all(FLERR,"Fix in variable not computed at compatible time");
- value1 = fix->compute_scalar();
- if (tree) {
- Tree *newtree = new Tree();
- newtree->type = VALUE;
- newtree->value = value1;
- newtree->left = newtree->middle = newtree->right = NULL;
- treestack[ntreestack++] = newtree;
- } else argstack[nargstack++] = value1;
+ value1 = fix->compute_scalar();
+ if (tree) {
+ Tree *newtree = new Tree();
+ newtree->type = VALUE;
+ newtree->value = value1;
+ newtree->left = newtree->middle = newtree->right = NULL;
+ treestack[ntreestack++] = newtree;
+ } else argstack[nargstack++] = value1;
// f_ID[i] = scalar from global vector
- } else if (nbracket == 1 && fix->vector_flag) {
+ } else if (nbracket == 1 && fix->vector_flag) {
- if (index1 > fix->size_vector)
- error->all(FLERR,
- "Variable formula fix vector is accessed out-of-range");
- if (update->whichflag > 0 && update->ntimestep % fix->global_freq)
- error->all(FLERR,"Fix in variable not computed at compatible time");
+ if (index1 > fix->size_vector)
+ error->all(FLERR,
+ "Variable formula fix vector is accessed out-of-range");
+ if (update->whichflag > 0 && update->ntimestep % fix->global_freq)
+ error->all(FLERR,"Fix in variable not computed at compatible time");
- value1 = fix->compute_vector(index1-1);
- if (tree) {
- Tree *newtree = new Tree();
- newtree->type = VALUE;
- newtree->value = value1;
- newtree->left = newtree->middle = newtree->right = NULL;
- treestack[ntreestack++] = newtree;
- } else argstack[nargstack++] = value1;
+ value1 = fix->compute_vector(index1-1);
+ if (tree) {
+ Tree *newtree = new Tree();
+ newtree->type = VALUE;
+ newtree->value = value1;
+ newtree->left = newtree->middle = newtree->right = NULL;
+ treestack[ntreestack++] = newtree;
+ } else argstack[nargstack++] = value1;
// f_ID[i][j] = scalar from global array
- } else if (nbracket == 2 && fix->array_flag) {
-
- if (index1 > fix->size_array_rows)
- error->all(FLERR,
- "Variable formula fix array is accessed out-of-range");
- if (index2 > fix->size_array_cols)
- error->all(FLERR,
- "Variable formula fix array is accessed out-of-range");
- if (update->whichflag > 0 && update->ntimestep % fix->global_freq)
- error->all(FLERR,"Fix in variable not computed at compatible time");
-
- value1 = fix->compute_array(index1-1,index2-1);
- if (tree) {
- Tree *newtree = new Tree();
- newtree->type = VALUE;
- newtree->value = value1;
- newtree->left = newtree->middle = newtree->right = NULL;
- treestack[ntreestack++] = newtree;
- } else argstack[nargstack++] = value1;
+ } else if (nbracket == 2 && fix->array_flag) {
+
+ if (index1 > fix->size_array_rows)
+ error->all(FLERR,
+ "Variable formula fix array is accessed out-of-range");
+ if (index2 > fix->size_array_cols)
+ error->all(FLERR,
+ "Variable formula fix array is accessed out-of-range");
+ if (update->whichflag > 0 && update->ntimestep % fix->global_freq)
+ error->all(FLERR,"Fix in variable not computed at compatible time");
+
+ value1 = fix->compute_array(index1-1,index2-1);
+ if (tree) {
+ Tree *newtree = new Tree();
+ newtree->type = VALUE;
+ newtree->value = value1;
+ newtree->left = newtree->middle = newtree->right = NULL;
+ treestack[ntreestack++] = newtree;
+ } else argstack[nargstack++] = value1;
// f_ID[i] = scalar from per-atom vector
- } else if (nbracket == 1 && fix->peratom_flag &&
- fix->size_peratom_cols == 0) {
+ } else if (nbracket == 1 && fix->peratom_flag &&
+ fix->size_peratom_cols == 0) {
- if (update->whichflag > 0 &&
- update->ntimestep % fix->peratom_freq)
- error->all(FLERR,
- "Fix in variable not computed at compatible time");
+ if (update->whichflag > 0 &&
+ update->ntimestep % fix->peratom_freq)
+ error->all(FLERR,
+ "Fix in variable not computed at compatible time");
- peratom2global(1,NULL,fix->vector_atom,1,index1,
- tree,treestack,ntreestack,argstack,nargstack);
+ peratom2global(1,NULL,fix->vector_atom,1,index1,
+ tree,treestack,ntreestack,argstack,nargstack);
// f_ID[i][j] = scalar from per-atom array
- } else if (nbracket == 2 && fix->peratom_flag &&
- fix->size_peratom_cols > 0) {
+ } else if (nbracket == 2 && fix->peratom_flag &&
+ fix->size_peratom_cols > 0) {
- if (index2 > fix->size_peratom_cols)
- error->all(FLERR,
- "Variable formula fix array is accessed out-of-range");
- if (update->whichflag > 0 &&
- update->ntimestep % fix->peratom_freq)
- error->all(FLERR,"Fix in variable not computed at compatible time");
+ if (index2 > fix->size_peratom_cols)
+ error->all(FLERR,
+ "Variable formula fix array is accessed out-of-range");
+ if (update->whichflag > 0 &&
+ update->ntimestep % fix->peratom_freq)
+ error->all(FLERR,"Fix in variable not computed at compatible time");
- peratom2global(1,NULL,&fix->array_atom[0][index2-1],
- fix->size_peratom_cols,index1,
- tree,treestack,ntreestack,argstack,nargstack);
+ peratom2global(1,NULL,&fix->array_atom[0][index2-1],
+ fix->size_peratom_cols,index1,
+ tree,treestack,ntreestack,argstack,nargstack);
// f_ID = vector from per-atom vector
- } else if (nbracket == 0 && fix->peratom_flag &&
- fix->size_peratom_cols == 0) {
+ } else if (nbracket == 0 && fix->peratom_flag &&
+ fix->size_peratom_cols == 0) {
- if (tree == NULL)
- error->all(FLERR,"Per-atom fix in equal-style variable formula");
- if (update->whichflag > 0 &&
- update->ntimestep % fix->peratom_freq)
- error->all(FLERR,"Fix in variable not computed at compatible time");
+ if (tree == NULL)
+ error->all(FLERR,"Per-atom fix in equal-style variable formula");
+ if (update->whichflag > 0 &&
+ update->ntimestep % fix->peratom_freq)
+ error->all(FLERR,"Fix in variable not computed at compatible time");
- Tree *newtree = new Tree();
- newtree->type = ATOMARRAY;
- newtree->array = fix->vector_atom;
- newtree->nstride = 1;
- newtree->left = newtree->middle = newtree->right = NULL;
- treestack[ntreestack++] = newtree;
+ Tree *newtree = new Tree();
+ newtree->type = ATOMARRAY;
+ newtree->array = fix->vector_atom;
+ newtree->nstride = 1;
+ newtree->left = newtree->middle = newtree->right = NULL;
+ treestack[ntreestack++] = newtree;
// f_ID[i] = vector from per-atom array
- } else if (nbracket == 1 && fix->peratom_flag &&
- fix->size_peratom_cols > 0) {
+ } else if (nbracket == 1 && fix->peratom_flag &&
+ fix->size_peratom_cols > 0) {
- if (tree == NULL)
- error->all(FLERR,"Per-atom fix in equal-style variable formula");
- if (index1 > fix->size_peratom_cols)
- error->all(FLERR,
- "Variable formula fix array is accessed out-of-range");
- if (update->whichflag > 0 &&
- update->ntimestep % fix->peratom_freq)
- error->all(FLERR,"Fix in variable not computed at compatible time");
+ if (tree == NULL)
+ error->all(FLERR,"Per-atom fix in equal-style variable formula");
+ if (index1 > fix->size_peratom_cols)
+ error->all(FLERR,
+ "Variable formula fix array is accessed out-of-range");
+ if (update->whichflag > 0 &&
+ update->ntimestep % fix->peratom_freq)
+ error->all(FLERR,"Fix in variable not computed at compatible time");
- Tree *newtree = new Tree();
- newtree->type = ATOMARRAY;
- newtree->array = &fix->array_atom[0][index1-1];
- newtree->nstride = fix->size_peratom_cols;
- newtree->left = newtree->middle = newtree->right = NULL;
- treestack[ntreestack++] = newtree;
+ Tree *newtree = new Tree();
+ newtree->type = ATOMARRAY;
+ newtree->array = &fix->array_atom[0][index1-1];
+ newtree->nstride = fix->size_peratom_cols;
+ newtree->left = newtree->middle = newtree->right = NULL;
+ treestack[ntreestack++] = newtree;
- } else error->all(FLERR,"Mismatched fix in variable formula");
+ } else error->all(FLERR,"Mismatched fix in variable formula");
// ----------------
// variable
// ----------------
} else if (strncmp(word,"v_",2) == 0) {
- n = strlen(word) - 2 + 1;
- char *id = new char[n];
- strcpy(id,&word[2]);
-
- int ivar = find(id);
- if (ivar < 0)
- error->all(FLERR,"Invalid variable name in variable formula");
-
- // parse zero or one trailing brackets
- // point i beyond last bracket
- // nbracket = # of bracket pairs
- // index = int inside bracket
-
- int nbracket,index;
- if (str[i] != '[') nbracket = 0;
- else {
- nbracket = 1;
- ptr = &str[i];
- index = int_between_brackets(ptr);
- i = ptr-str+1;
- }
+ n = strlen(word) - 2 + 1;
+ char *id = new char[n];
+ strcpy(id,&word[2]);
+
+ int ivar = find(id);
+ if (ivar < 0)
+ error->all(FLERR,"Invalid variable name in variable formula");
+
+ // parse zero or one trailing brackets
+ // point i beyond last bracket
+ // nbracket = # of bracket pairs
+ // index = int inside bracket
+
+ int nbracket,index;
+ if (str[i] != '[') nbracket = 0;
+ else {
+ nbracket = 1;
+ ptr = &str[i];
+ index = int_between_brackets(ptr);
+ i = ptr-str+1;
+ }
// v_name = scalar from non atom-style global scalar
- if (nbracket == 0 && style[ivar] != ATOM) {
+ if (nbracket == 0 && style[ivar] != ATOM) {
- char *var = retrieve(id);
- if (var == NULL)
- error->all(FLERR,"Invalid variable evaluation in variable formula");
- if (tree) {
- Tree *newtree = new Tree();
- newtree->type = VALUE;
- newtree->value = atof(var);
- newtree->left = newtree->middle = newtree->right = NULL;
- treestack[ntreestack++] = newtree;
- } else argstack[nargstack++] = atof(var);
+ char *var = retrieve(id);
+ if (var == NULL)
+ error->all(FLERR,"Invalid variable evaluation in variable formula");
+ if (tree) {
+ Tree *newtree = new Tree();
+ newtree->type = VALUE;
+ newtree->value = atof(var);
+ newtree->left = newtree->middle = newtree->right = NULL;
+ treestack[ntreestack++] = newtree;
+ } else argstack[nargstack++] = atof(var);
// v_name = vector from atom-style per-atom vector
- } else if (nbracket == 0 && style[ivar] == ATOM) {
+ } else if (nbracket == 0 && style[ivar] == ATOM) {
- if (tree == NULL)
- error->all(FLERR,
- "Atom-style variable in equal-style variable formula");
- Tree *newtree;
- evaluate(data[ivar][0],&newtree);
- treestack[ntreestack++] = newtree;
+ if (tree == NULL)
+ error->all(FLERR,
+ "Atom-style variable in equal-style variable formula");
+ Tree *newtree;
+ evaluate(data[ivar][0],&newtree);
+ treestack[ntreestack++] = newtree;
// v_name[N] = scalar from atom-style per-atom vector
- // compute the per-atom variable in result
- // use peratom2global to extract single value from result
+ // compute the per-atom variable in result
+ // use peratom2global to extract single value from result
- } else if (nbracket && style[ivar] == ATOM) {
+ } else if (nbracket && style[ivar] == ATOM) {
- double *result;
- memory->create(result,atom->nlocal,"variable:result");
- compute_atom(ivar,0,result,1,0);
- peratom2global(1,NULL,result,1,index,
- tree,treestack,ntreestack,argstack,nargstack);
- memory->destroy(result);
+ double *result;
+ memory->create(result,atom->nlocal,"variable:result");
+ compute_atom(ivar,0,result,1,0);
+ peratom2global(1,NULL,result,1,index,
+ tree,treestack,ntreestack,argstack,nargstack);
+ memory->destroy(result);
- } else error->all(FLERR,"Mismatched variable in variable formula");
+ } else error->all(FLERR,"Mismatched variable in variable formula");
- delete [] id;
+ delete [] id;
// ----------------
// math/group/special function or atom value/vector or
@@ -1169,86 +1169,86 @@ double Variable::evaluate(char *str, Tree **tree)
} else {
- // ----------------
- // math or group or special function
- // ----------------
-
- if (str[i] == '(') {
- char *contents;
- i = find_matching_paren(str,i,contents);
- i++;
-
- if (math_function(word,contents,tree,
- treestack,ntreestack,argstack,nargstack));
- else if (group_function(word,contents,tree,
- treestack,ntreestack,argstack,nargstack));
- else if (special_function(word,contents,tree,
- treestack,ntreestack,argstack,nargstack));
- else error->all(FLERR,"Invalid math/group/special function "
- "in variable formula");
- delete [] contents;
-
- // ----------------
- // atom value
- // ----------------
-
- } else if (str[i] == '[') {
- if (domain->box_exist == 0)
- error->all(FLERR,
- "Variable evaluation before simulation box is defined");
-
- ptr = &str[i];
- int id = int_between_brackets(ptr);
- i = ptr-str+1;
-
- peratom2global(0,word,NULL,0,id,
- tree,treestack,ntreestack,argstack,nargstack);
-
- // ----------------
- // atom vector
- // ----------------
-
- } else if (is_atom_vector(word)) {
- if (domain->box_exist == 0)
- error->all(FLERR,
- "Variable evaluation before simulation box is defined");
-
- atom_vector(word,tree,treestack,ntreestack);
-
- // ----------------
- // constant
- // ----------------
-
- } else if (is_constant(word)) {
- value1 = constant(word);
- if (tree) {
- Tree *newtree = new Tree();
- newtree->type = VALUE;
- newtree->value = value1;
- newtree->left = newtree->middle = newtree->right = NULL;
- treestack[ntreestack++] = newtree;
- } else argstack[nargstack++] = value1;
-
- // ----------------
- // thermo keyword
- // ----------------
-
- } else {
- if (domain->box_exist == 0)
- error->all(FLERR,
- "Variable evaluation before simulation box is defined");
-
- int flag = output->thermo->evaluate_keyword(word,&value1);
- if (flag)
- error->all(FLERR,"Invalid thermo keyword in variable formula");
- if (tree) {
- Tree *newtree = new Tree();
- newtree->type = VALUE;
- newtree->value = value1;
- newtree->left = newtree->middle = newtree->right = NULL;
- treestack[ntreestack++] = newtree;
- } else argstack[nargstack++] = value1;
- }
+ // ----------------
+ // math or group or special function
+ // ----------------
+
+ if (str[i] == '(') {
+ char *contents;
+ i = find_matching_paren(str,i,contents);
+ i++;
+
+ if (math_function(word,contents,tree,
+ treestack,ntreestack,argstack,nargstack));
+ else if (group_function(word,contents,tree,
+ treestack,ntreestack,argstack,nargstack));
+ else if (special_function(word,contents,tree,
+ treestack,ntreestack,argstack,nargstack));
+ else error->all(FLERR,"Invalid math/group/special function "
+ "in variable formula");
+ delete [] contents;
+
+ // ----------------
+ // atom value
+ // ----------------
+
+ } else if (str[i] == '[') {
+ if (domain->box_exist == 0)
+ error->all(FLERR,
+ "Variable evaluation before simulation box is defined");
+
+ ptr = &str[i];
+ int id = int_between_brackets(ptr);
+ i = ptr-str+1;
+
+ peratom2global(0,word,NULL,0,id,
+ tree,treestack,ntreestack,argstack,nargstack);
+
+ // ----------------
+ // atom vector
+ // ----------------
+
+ } else if (is_atom_vector(word)) {
+ if (domain->box_exist == 0)
+ error->all(FLERR,
+ "Variable evaluation before simulation box is defined");
+
+ atom_vector(word,tree,treestack,ntreestack);
+
+ // ----------------
+ // constant
+ // ----------------
+
+ } else if (is_constant(word)) {
+ value1 = constant(word);
+ if (tree) {
+ Tree *newtree = new Tree();
+ newtree->type = VALUE;
+ newtree->value = value1;
+ newtree->left = newtree->middle = newtree->right = NULL;
+ treestack[ntreestack++] = newtree;
+ } else argstack[nargstack++] = value1;
+
+ // ----------------
+ // thermo keyword
+ // ----------------
+
+ } else {
+ if (domain->box_exist == 0)
+ error->all(FLERR,
+ "Variable evaluation before simulation box is defined");
+
+ int flag = output->thermo->evaluate_keyword(word,&value1);
+ if (flag)
+ error->all(FLERR,"Invalid thermo keyword in variable formula");
+ if (tree) {
+ Tree *newtree = new Tree();
+ newtree->type = VALUE;
+ newtree->value = value1;
+ newtree->left = newtree->middle = newtree->right = NULL;
+ treestack[ntreestack++] = newtree;
+ } else argstack[nargstack++] = value1;
+ }
}
delete [] word;
@@ -1264,48 +1264,48 @@ double Variable::evaluate(char *str, Tree **tree)
else if (onechar == '/') op = DIVIDE;
else if (onechar == '^') op = CARAT;
else if (onechar == '=') {
- if (str[i+1] != '=')
- error->all(FLERR,"Invalid syntax in variable formula");
- op = EQ;
- i++;
+ if (str[i+1] != '=')
+ error->all(FLERR,"Invalid syntax in variable formula");
+ op = EQ;
+ i++;
} else if (onechar == '!') {
- if (str[i+1] == '=') {
- op = NE;
- i++;
- } else op = NOT;
+ if (str[i+1] == '=') {
+ op = NE;
+ i++;
+ } else op = NOT;
} else if (onechar == '<') {
- if (str[i+1] != '=') op = LT;
- else {
- op = LE;
- i++;
- }
+ if (str[i+1] != '=') op = LT;
+ else {
+ op = LE;
+ i++;
+ }
} else if (onechar == '>') {
- if (str[i+1] != '=') op = GT;
- else {
- op = GE;
- i++;
- }
+ if (str[i+1] != '=') op = GT;
+ else {
+ op = GE;
+ i++;
+ }
} else if (onechar == '&') {
- if (str[i+1] != '&')
- error->all(FLERR,"Invalid syntax in variable formula");
- op = AND;
- i++;
+ if (str[i+1] != '&')
+ error->all(FLERR,"Invalid syntax in variable formula");
+ op = AND;
+ i++;
} else if (onechar == '|') {
- if (str[i+1] != '|')
- error->all(FLERR,"Invalid syntax in variable formula");
- op = OR;
- i++;
+ if (str[i+1] != '|')
+ error->all(FLERR,"Invalid syntax in variable formula");
+ op = OR;
+ i++;
} else op = DONE;
i++;
if (op == SUBTRACT && expect == ARG) {
- opstack[nopstack++] = UNARY;
- continue;
+ opstack[nopstack++] = UNARY;
+ continue;
}
if (op == NOT && expect == ARG) {
- opstack[nopstack++] = op;
- continue;
+ opstack[nopstack++] = op;
+ continue;
}
if (expect == ARG) error->all(FLERR,"Invalid syntax in variable formula");
@@ -1315,71 +1315,71 @@ double Variable::evaluate(char *str, Tree **tree)
// before pushing current op onto stack
while (nopstack && precedence[opstack[nopstack-1]] >= precedence[op]) {
- opprevious = opstack[--nopstack];
-
- if (tree) {
- Tree *newtree = new Tree();
- newtree->type = opprevious;
- if (opprevious == UNARY) {
- newtree->left = treestack[--ntreestack];
- newtree->middle = newtree->right = NULL;
- } else {
- newtree->right = treestack[--ntreestack];
- newtree->middle = NULL;
- newtree->left = treestack[--ntreestack];
- }
- treestack[ntreestack++] = newtree;
-
- } else {
- value2 = argstack[--nargstack];
- if (opprevious != UNARY && opprevious != NOT)
- value1 = argstack[--nargstack];
-
- if (opprevious == ADD)
- argstack[nargstack++] = value1 + value2;
- else if (opprevious == SUBTRACT)
- argstack[nargstack++] = value1 - value2;
- else if (opprevious == MULTIPLY)
- argstack[nargstack++] = value1 * value2;
- else if (opprevious == DIVIDE) {
- if (value2 == 0.0)
- error->all(FLERR,"Divide by 0 in variable formula");
- argstack[nargstack++] = value1 / value2;
- } else if (opprevious == CARAT) {
- if (value2 == 0.0)
- error->all(FLERR,"Power by 0 in variable formula");
- argstack[nargstack++] = pow(value1,value2);
- } else if (opprevious == UNARY) {
- argstack[nargstack++] = -value2;
- } else if (opprevious == NOT) {
- if (value2 == 0.0) argstack[nargstack++] = 1.0;
- else argstack[nargstack++] = 0.0;
- } else if (opprevious == EQ) {
- if (value1 == value2) argstack[nargstack++] = 1.0;
- else argstack[nargstack++] = 0.0;
- } else if (opprevious == NE) {
- if (value1 != value2) argstack[nargstack++] = 1.0;
- else argstack[nargstack++] = 0.0;
- } else if (opprevious == LT) {
- if (value1 < value2) argstack[nargstack++] = 1.0;
- else argstack[nargstack++] = 0.0;
- } else if (opprevious == LE) {
- if (value1 <= value2) argstack[nargstack++] = 1.0;
- else argstack[nargstack++] = 0.0;
- } else if (opprevious == GT) {
- if (value1 > value2) argstack[nargstack++] = 1.0;
- else argstack[nargstack++] = 0.0;
- } else if (opprevious == GE) {
- if (value1 >= value2) argstack[nargstack++] = 1.0;
- else argstack[nargstack++] = 0.0;
- } else if (opprevious == AND) {
- if (value1 != 0.0 && value2 != 0.0) argstack[nargstack++] = 1.0;
- else argstack[nargstack++] = 0.0;
- } else if (opprevious == OR) {
- if (value1 != 0.0 || value2 != 0.0) argstack[nargstack++] = 1.0;
- else argstack[nargstack++] = 0.0;
- }
- }
+ opprevious = opstack[--nopstack];
+
+ if (tree) {
+ Tree *newtree = new Tree();
+ newtree->type = opprevious;
+ if (opprevious == UNARY) {
+ newtree->left = treestack[--ntreestack];
+ newtree->middle = newtree->right = NULL;
+ } else {
+ newtree->right = treestack[--ntreestack];
+ newtree->middle = NULL;
+ newtree->left = treestack[--ntreestack];
+ }
+ treestack[ntreestack++] = newtree;
+
+ } else {
+ value2 = argstack[--nargstack];
+ if (opprevious != UNARY && opprevious != NOT)
+ value1 = argstack[--nargstack];
+
+ if (opprevious == ADD)
+ argstack[nargstack++] = value1 + value2;
+ else if (opprevious == SUBTRACT)
+ argstack[nargstack++] = value1 - value2;
+ else if (opprevious == MULTIPLY)
+ argstack[nargstack++] = value1 * value2;
+ else if (opprevious == DIVIDE) {
+ if (value2 == 0.0)
+ error->all(FLERR,"Divide by 0 in variable formula");
+ argstack[nargstack++] = value1 / value2;
+ } else if (opprevious == CARAT) {
+ if (value2 == 0.0)
+ error->all(FLERR,"Power by 0 in variable formula");
+ argstack[nargstack++] = pow(value1,value2);
+ } else if (opprevious == UNARY) {
+ argstack[nargstack++] = -value2;
+ } else if (opprevious == NOT) {
+ if (value2 == 0.0) argstack[nargstack++] = 1.0;
+ else argstack[nargstack++] = 0.0;
+ } else if (opprevious == EQ) {
+ if (value1 == value2) argstack[nargstack++] = 1.0;
+ else argstack[nargstack++] = 0.0;
+ } else if (opprevious == NE) {
+ if (value1 != value2) argstack[nargstack++] = 1.0;
+ else argstack[nargstack++] = 0.0;
+ } else if (opprevious == LT) {
+ if (value1 < value2) argstack[nargstack++] = 1.0;
+ else argstack[nargstack++] = 0.0;
+ } else if (opprevious == LE) {
+ if (value1 <= value2) argstack[nargstack++] = 1.0;
+ else argstack[nargstack++] = 0.0;
+ } else if (opprevious == GT) {
+ if (value1 > value2) argstack[nargstack++] = 1.0;
+ else argstack[nargstack++] = 0.0;
+ } else if (opprevious == GE) {
+ if (value1 >= value2) argstack[nargstack++] = 1.0;
+ else argstack[nargstack++] = 0.0;
+ } else if (opprevious == AND) {
+ if (value1 != 0.0 && value2 != 0.0) argstack[nargstack++] = 1.0;
+ else argstack[nargstack++] = 0.0;
+ } else if (opprevious == OR) {
+ if (value1 != 0.0 || value2 != 0.0) argstack[nargstack++] = 1.0;
+ else argstack[nargstack++] = 0.0;
+ }
+ }
}
// if end-of-string, break out of entire formula evaluation loop
@@ -1579,7 +1579,7 @@ double Variable::collapse_tree(Tree *tree)
arg1 = collapse_tree(tree->left);
if (tree->left->type != VALUE) return 0.0;
tree->type = VALUE;
- if (arg1 < 0.0)
+ if (arg1 < 0.0)
error->one(FLERR,"Sqrt of negative value in variable formula");
tree->value = sqrt(arg1);
return tree->value;
@@ -1597,7 +1597,7 @@ double Variable::collapse_tree(Tree *tree)
arg1 = collapse_tree(tree->left);
if (tree->left->type != VALUE) return 0.0;
tree->type = VALUE;
- if (arg1 <= 0.0)
+ if (arg1 <= 0.0)
error->one(FLERR,"Log of zero/negative value in variable formula");
tree->value = log(arg1);
return tree->value;
@@ -1607,7 +1607,7 @@ double Variable::collapse_tree(Tree *tree)
arg1 = collapse_tree(tree->left);
if (tree->left->type != VALUE) return 0.0;
tree->type = VALUE;
- if (arg1 <= 0.0)
+ if (arg1 <= 0.0)
error->one(FLERR,"Log of zero/negative value in variable formula");
tree->value = log10(arg1);
return tree->value;
@@ -1681,8 +1681,8 @@ double Variable::collapse_tree(Tree *tree)
collapse_tree(tree->middle);
if (randomatom == NULL) {
int seed = static_cast<int> (collapse_tree(tree->right));
- if (seed <= 0)
- error->one(FLERR,"Invalid math function in variable formula");
+ if (seed <= 0)
+ error->one(FLERR,"Invalid math function in variable formula");
randomatom = new RanMars(lmp,seed+me);
}
return 0.0;
@@ -1691,12 +1691,12 @@ double Variable::collapse_tree(Tree *tree)
if (tree->type == NORMAL) {
collapse_tree(tree->left);
double sigma = collapse_tree(tree->middle);
- if (sigma < 0.0)
+ if (sigma < 0.0)
error->one(FLERR,"Invalid math function in variable formula");
if (randomatom == NULL) {
int seed = static_cast<int> (collapse_tree(tree->right));
- if (seed <= 0)
- error->one(FLERR,"Invalid math function in variable formula");
+ if (seed <= 0)
+ error->one(FLERR,"Invalid math function in variable formula");
randomatom = new RanMars(lmp,seed+me);
}
return 0.0;
@@ -1756,7 +1756,7 @@ double Variable::collapse_tree(Tree *tree)
int ivalue2 = static_cast<int> (collapse_tree(tree->middle));
int ivalue3 = static_cast<int> (collapse_tree(tree->right));
if (tree->left->type != VALUE || tree->middle->type != VALUE ||
- tree->right->type != VALUE) return 0.0;
+ tree->right->type != VALUE) return 0.0;
tree->type = VALUE;
if (ivalue1 <= 0 || ivalue2 <= 0 || ivalue3 <= 0 || ivalue2 >= ivalue3)
error->one(FLERR,"Invalid math function in variable formula");
@@ -1776,7 +1776,7 @@ double Variable::collapse_tree(Tree *tree)
int ivalue2 = static_cast<int> (collapse_tree(tree->middle));
int ivalue3 = static_cast<int> (collapse_tree(tree->right));
if (tree->left->type != VALUE || tree->middle->type != VALUE ||
- tree->right->type != VALUE) return 0.0;
+ tree->right->type != VALUE) return 0.0;
tree->type = VALUE;
if (ivalue1 < 0 || ivalue2 < 0 || ivalue3 <= 0 || ivalue1 > ivalue2)
error->one(FLERR,"Invalid math function in variable formula");
@@ -1804,9 +1804,9 @@ double Variable::collapse_tree(Tree *tree)
double arg2 = collapse_tree(tree->middle);
double arg3 = collapse_tree(tree->right);
if (tree->left->type != VALUE || tree->middle->type != VALUE ||
- tree->right->type != VALUE) return 0.0;
+ tree->right->type != VALUE) return 0.0;
tree->type = VALUE;
- if (arg3 == 0.0)
+ if (arg3 == 0.0)
error->one(FLERR,"Invalid math function in variable formula");
double delta = update->ntimestep - update->beginstep;
double omega = 2.0*MY_PI/arg3;
@@ -1819,9 +1819,9 @@ double Variable::collapse_tree(Tree *tree)
double arg2 = collapse_tree(tree->middle);
double arg3 = collapse_tree(tree->right);
if (tree->left->type != VALUE || tree->middle->type != VALUE ||
- tree->right->type != VALUE) return 0.0;
+ tree->right->type != VALUE) return 0.0;
tree->type = VALUE;
- if (arg3 == 0.0)
+ if (arg3 == 0.0)
error->one(FLERR,"Invalid math function in variable formula");
double delta = update->ntimestep - update->beginstep;
double omega = 2.0*MY_PI/arg3;
@@ -1917,7 +1917,7 @@ double Variable::eval_tree(Tree *tree, int i)
if (tree->type == SQRT) {
arg1 = eval_tree(tree->left,i);
- if (arg1 < 0.0)
+ if (arg1 < 0.0)
error->one(FLERR,"Sqrt of negative value in variable formula");
return sqrt(arg1);
}
@@ -1925,13 +1925,13 @@ double Variable::eval_tree(Tree *tree, int i)
return exp(eval_tree(tree->left,i));
if (tree->type == LN) {
arg1 = eval_tree(tree->left,i);
- if (arg1 <= 0.0)
+ if (arg1 <= 0.0)
error->one(FLERR,"Log of zero/negative value in variable formula");
return log(arg1);
}
if (tree->type == LOG) {
arg1 = eval_tree(tree->left,i);
- if (arg1 <= 0.0)
+ if (arg1 <= 0.0)
error->one(FLERR,"Log of zero/negative value in variable formula");
return log10(arg1);
}
@@ -1965,8 +1965,8 @@ double Variable::eval_tree(Tree *tree, int i)
double upper = eval_tree(tree->middle,i);
if (randomatom == NULL) {
int seed = static_cast<int> (eval_tree(tree->right,i));
- if (seed <= 0)
- error->one(FLERR,"Invalid math function in variable formula");
+ if (seed <= 0)
+ error->one(FLERR,"Invalid math function in variable formula");
randomatom = new RanMars(lmp,seed+me);
}
return randomatom->uniform()*(upper-lower)+lower;
@@ -1974,12 +1974,12 @@ double Variable::eval_tree(Tree *tree, int i)
if (tree->type == NORMAL) {
double mu = eval_tree(tree->left,i);
double sigma = eval_tree(tree->middle,i);
- if (sigma < 0.0)
+ if (sigma < 0.0)
error->one(FLERR,"Invalid math function in variable formula");
if (randomatom == NULL) {
int seed = static_cast<int> (eval_tree(tree->right,i));
if (seed <= 0)
- error->one(FLERR,"Invalid math function in variable formula");
+ error->one(FLERR,"Invalid math function in variable formula");
randomatom = new RanMars(lmp,seed+me);
}
return mu + sigma*randomatom->gaussian();
@@ -2057,7 +2057,7 @@ double Variable::eval_tree(Tree *tree, int i)
arg1 = eval_tree(tree->left,i);
arg2 = eval_tree(tree->middle,i);
arg3 = eval_tree(tree->right,i);
- if (arg3 == 0.0)
+ if (arg3 == 0.0)
error->one(FLERR,"Invalid math function in variable formula");
double delta = update->ntimestep - update->beginstep;
double omega = 2.0*MY_PI/arg3;
@@ -2069,7 +2069,7 @@ double Variable::eval_tree(Tree *tree, int i)
arg1 = eval_tree(tree->left,i);
arg2 = eval_tree(tree->middle,i);
arg3 = eval_tree(tree->right,i);
- if (arg3 == 0.0)
+ if (arg3 == 0.0)
error->one(FLERR,"Invalid math function in variable formula");
double delta = update->ntimestep - update->beginstep;
double omega = 2.0*MY_PI/arg3;
@@ -2084,16 +2084,16 @@ double Variable::eval_tree(Tree *tree, int i)
if (tree->type == RMASK) {
if (domain->regions[tree->ivalue1]->inside(atom->x[i][0],
- atom->x[i][1],
- atom->x[i][2])) return 1.0;
+ atom->x[i][1],
+ atom->x[i][2])) return 1.0;
else return 0.0;
}
if (tree->type == GRMASK) {
if ((atom->mask[i] & tree->ivalue1) &&
- (domain->regions[tree->ivalue2]->inside(atom->x[i][0],
- atom->x[i][1],
- atom->x[i][2]))) return 1.0;
+ (domain->regions[tree->ivalue2]->inside(atom->x[i][0],
+ atom->x[i][1],
+ atom->x[i][2]))) return 1.0;
else return 0.0;
}
@@ -2153,7 +2153,7 @@ int Variable::int_between_brackets(char *&ptr)
char *start = ++ptr;
while (*ptr && *ptr != ']') {
- if (!isdigit(*ptr))
+ if (!isdigit(*ptr))
error->all(FLERR,"Non digit character between brackets in variable");
ptr++;
}
@@ -2165,7 +2165,7 @@ int Variable::int_between_brackets(char *&ptr)
int index = atoi(start);
*ptr = ']';
- if (index == 0)
+ if (index == 0)
error->all(FLERR,"Index between variable brackets must be positive");
return index;
}
@@ -2184,21 +2184,21 @@ int Variable::int_between_brackets(char *&ptr)
------------------------------------------------------------------------- */
int Variable::math_function(char *word, char *contents, Tree **tree,
- Tree **treestack, int &ntreestack,
- double *argstack, int &nargstack)
+ Tree **treestack, int &ntreestack,
+ double *argstack, int &nargstack)
{
// word not a match to any math function
- if (strcmp(word,"sqrt") && strcmp(word,"exp") &&
+ if (strcmp(word,"sqrt") && strcmp(word,"exp") &&
strcmp(word,"ln") && strcmp(word,"log") &&
strcmp(word,"sin") && strcmp(word,"cos") &&
strcmp(word,"tan") && strcmp(word,"asin") &&
- strcmp(word,"acos") && strcmp(word,"atan") &&
- strcmp(word,"atan2") && strcmp(word,"random") &&
- strcmp(word,"normal") && strcmp(word,"ceil") &&
+ strcmp(word,"acos") && strcmp(word,"atan") &&
+ strcmp(word,"atan2") && strcmp(word,"random") &&
+ strcmp(word,"normal") && strcmp(word,"ceil") &&
strcmp(word,"floor") && strcmp(word,"round") &&
strcmp(word,"ramp") && strcmp(word,"stagger") &&
- strcmp(word,"logfreq") && strcmp(word,"stride") &&
+ strcmp(word,"logfreq") && strcmp(word,"stride") &&
strcmp(word,"vdisplace") &&
strcmp(word,"swiggle") && strcmp(word,"cwiggle"))
return 0;
@@ -2234,7 +2234,7 @@ int Variable::math_function(char *word, char *contents, Tree **tree,
} else arg3 = NULL;
// evaluate args
-
+
Tree *newtree;
double tmp,value1,value2,value3;
@@ -2272,135 +2272,135 @@ int Variable::math_function(char *word, char *contents, Tree **tree,
value3 = evaluate(arg3,NULL);
}
}
-
+
if (strcmp(word,"sqrt") == 0) {
if (narg != 1)
error->all(FLERR,"Invalid math function in variable formula");
if (tree) newtree->type = SQRT;
else {
- if (value1 < 0.0)
- error->all(FLERR,"Sqrt of negative value in variable formula");
+ if (value1 < 0.0)
+ error->all(FLERR,"Sqrt of negative value in variable formula");
argstack[nargstack++] = sqrt(value1);
}
} else if (strcmp(word,"exp") == 0) {
- if (narg != 1)
+ if (narg != 1)
error->all(FLERR,"Invalid math function in variable formula");
if (tree) newtree->type = EXP;
else argstack[nargstack++] = exp(value1);
} else if (strcmp(word,"ln") == 0) {
- if (narg != 1)
+ if (narg != 1)
error->all(FLERR,"Invalid math function in variable formula");
if (tree) newtree->type = LN;
else {
- if (value1 <= 0.0)
- error->all(FLERR,"Log of zero/negative value in variable formula");
+ if (value1 <= 0.0)
+ error->all(FLERR,"Log of zero/negative value in variable formula");
argstack[nargstack++] = log(value1);
}
} else if (strcmp(word,"log") == 0) {
- if (narg != 1)
+ if (narg != 1)
error->all(FLERR,"Invalid math function in variable formula");
if (tree) newtree->type = LOG;
else {
- if (value1 <= 0.0)
- error->all(FLERR,"Log of zero/negative value in variable formula");
+ if (value1 <= 0.0)
+ error->all(FLERR,"Log of zero/negative value in variable formula");
argstack[nargstack++] = log10(value1);
}
} else if (strcmp(word,"sin") == 0) {
- if (narg != 1)
+ if (narg != 1)
error->all(FLERR,"Invalid math function in variable formula");
if (tree) newtree->type = SIN;
else argstack[nargstack++] = sin(value1);
} else if (strcmp(word,"cos") == 0) {
- if (narg != 1)
+ if (narg != 1)
error->all(FLERR,"Invalid math function in variable formula");
if (tree) newtree->type = COS;
else argstack[nargstack++] = cos(value1);
} else if (strcmp(word,"tan") == 0) {
- if (narg != 1)
+ if (narg != 1)
error->all(FLERR,"Invalid math function in variable formula");
if (tree) newtree->type = TAN;
else argstack[nargstack++] = tan(value1);
} else if (strcmp(word,"asin") == 0) {
- if (narg != 1)
+ if (narg != 1)
error->all(FLERR,"Invalid math function in variable formula");
if (tree) newtree->type = ASIN;
else {
- if (value1 < -1.0 || value1 > 1.0)
- error->all(FLERR,"Arcsin of invalid value in variable formula");
+ if (value1 < -1.0 || value1 > 1.0)
+ error->all(FLERR,"Arcsin of invalid value in variable formula");
argstack[nargstack++] = asin(value1);
}
} else if (strcmp(word,"acos") == 0) {
- if (narg != 1)
+ if (narg != 1)
error->all(FLERR,"Invalid math function in variable formula");
if (tree) newtree->type = ACOS;
else {
- if (value1 < -1.0 || value1 > 1.0)
- error->all(FLERR,"Arccos of invalid value in variable formula");
+ if (value1 < -1.0 || value1 > 1.0)
+ error->all(FLERR,"Arccos of invalid value in variable formula");
argstack[nargstack++] = acos(value1);
}
} else if (strcmp(word,"atan") == 0) {
- if (narg != 1)
+ if (narg != 1)
error->all(FLERR,"Invalid math function in variable formula");
if (tree) newtree->type = ATAN;
else argstack[nargstack++] = atan(value1);
} else if (strcmp(word,"atan2") == 0) {
- if (narg != 2)
+ if (narg != 2)
error->all(FLERR,"Invalid math function in variable formula");
if (tree) newtree->type = ATAN2;
else argstack[nargstack++] = atan2(value1,value2);
} else if (strcmp(word,"random") == 0) {
- if (narg != 3)
+ if (narg != 3)
error->all(FLERR,"Invalid math function in variable formula");
if (tree) newtree->type = RANDOM;
else {
if (randomequal == NULL) {
- int seed = static_cast<int> (value3);
- if (seed <= 0)
- error->all(FLERR,"Invalid math function in variable formula");
- randomequal = new RanMars(lmp,seed);
+ int seed = static_cast<int> (value3);
+ if (seed <= 0)
+ error->all(FLERR,"Invalid math function in variable formula");
+ randomequal = new RanMars(lmp,seed);
}
argstack[nargstack++] = randomequal->uniform()*(value2-value1) + value1;
}
} else if (strcmp(word,"normal") == 0) {
- if (narg != 3)
+ if (narg != 3)
error->all(FLERR,"Invalid math function in variable formula");
if (tree) newtree->type = NORMAL;
else {
- if (value2 < 0.0)
- error->all(FLERR,"Invalid math function in variable formula");
+ if (value2 < 0.0)
+ error->all(FLERR,"Invalid math function in variable formula");
if (randomequal == NULL) {
- int seed = static_cast<int> (value3);
- if (seed <= 0)
- error->all(FLERR,"Invalid math function in variable formula");
- randomequal = new RanMars(lmp,seed);
+ int seed = static_cast<int> (value3);
+ if (seed <= 0)
+ error->all(FLERR,"Invalid math function in variable formula");
+ randomequal = new RanMars(lmp,seed);
}
argstack[nargstack++] = value1 + value2*randomequal->gaussian();
}
} else if (strcmp(word,"ceil") == 0) {
- if (narg != 1)
+ if (narg != 1)
error->all(FLERR,"Invalid math function in variable formula");
if (tree) newtree->type = CEIL;
else argstack[nargstack++] = ceil(value1);
} else if (strcmp(word,"floor") == 0) {
- if (narg != 1)
+ if (narg != 1)
error->all(FLERR,"Invalid math function in variable formula");
if (tree) newtree->type = FLOOR;
else argstack[nargstack++] = floor(value1);
} else if (strcmp(word,"round") == 0) {
- if (narg != 1)
+ if (narg != 1)
error->all(FLERR,"Invalid math function in variable formula");
if (tree) newtree->type = ROUND;
else argstack[nargstack++] = MYROUND(value1);
} else if (strcmp(word,"ramp") == 0) {
- if (narg != 2)
+ if (narg != 2)
error->all(FLERR,"Invalid math function in variable formula");
if (update->whichflag == 0)
error->all(FLERR,"Cannot use ramp in variable formula between runs");
@@ -2413,14 +2413,14 @@ int Variable::math_function(char *word, char *contents, Tree **tree,
}
} else if (strcmp(word,"stagger") == 0) {
- if (narg != 2)
+ if (narg != 2)
error->all(FLERR,"Invalid math function in variable formula");
if (tree) newtree->type = STAGGER;
else {
int ivalue1 = static_cast<int> (value1);
int ivalue2 = static_cast<int> (value2);
if (ivalue1 <= 0 || ivalue2 <= 0 || ivalue1 <= ivalue2)
- error->all(FLERR,"Invalid math function in variable formula");
+ error->all(FLERR,"Invalid math function in variable formula");
int lower = update->ntimestep/ivalue1 * ivalue1;
int delta = update->ntimestep - lower;
double value;
@@ -2438,21 +2438,21 @@ int Variable::math_function(char *word, char *contents, Tree **tree,
int ivalue2 = static_cast<int> (value2);
int ivalue3 = static_cast<int> (value3);
if (ivalue1 <= 0 || ivalue2 <= 0 || ivalue3 <= 0 || ivalue2 >= ivalue3)
- error->all(FLERR,"Invalid math function in variable formula");
+ error->all(FLERR,"Invalid math function in variable formula");
double value;
if (update->ntimestep < ivalue1) value = ivalue1;
else {
- int lower = ivalue1;
- while (update->ntimestep >= ivalue3*lower) lower *= ivalue3;
- int multiple = update->ntimestep/lower;
- if (multiple < ivalue2) value = (multiple+1)*lower;
- else value = lower*ivalue3;
+ int lower = ivalue1;
+ while (update->ntimestep >= ivalue3*lower) lower *= ivalue3;
+ int multiple = update->ntimestep/lower;
+ if (multiple < ivalue2) value = (multiple+1)*lower;
+ else value = lower*ivalue3;
}
argstack[nargstack++] = value;
}
} else if (strcmp(word,"stride") == 0) {
- if (narg != 3)
+ if (narg != 3)
error->all(FLERR,"Invalid math function in variable formula");
if (tree) newtree->type = STRIDE;
else {
@@ -2460,19 +2460,19 @@ int Variable::math_function(char *word, char *contents, Tree **tree,
int ivalue2 = static_cast<int> (value2);
int ivalue3 = static_cast<int> (value3);
if (ivalue1 < 0 || ivalue2 < 0 || ivalue3 <= 0 || ivalue1 > ivalue2)
- error->one(FLERR,"Invalid math function in variable formula");
+ error->one(FLERR,"Invalid math function in variable formula");
double value;
if (update->ntimestep < ivalue1) value = ivalue1;
else if (update->ntimestep < ivalue2) {
- int offset = update->ntimestep - ivalue1;
- value = ivalue1 + (offset/ivalue3)*ivalue3 + ivalue3;
- if (value > ivalue2) value = 9.0e18;
+ int offset = update->ntimestep - ivalue1;
+ value = ivalue1 + (offset/ivalue3)*ivalue3 + ivalue3;
+ if (value > ivalue2) value = 9.0e18;
} else value = 9.0e18;
argstack[nargstack++] = value;
}
-
+
} else if (strcmp(word,"vdisplace") == 0) {
- if (narg != 2)
+ if (narg != 2)
error->all(FLERR,"Invalid math function in variable formula");
if (update->whichflag == 0)
error->all(FLERR,"Cannot use vdisplace in variable formula between runs");
@@ -2484,14 +2484,14 @@ int Variable::math_function(char *word, char *contents, Tree **tree,
}
} else if (strcmp(word,"swiggle") == 0) {
- if (narg != 3)
+ if (narg != 3)
error->all(FLERR,"Invalid math function in variable formula");
if (update->whichflag == 0)
error->all(FLERR,"Cannot use swiggle in variable formula between runs");
if (tree) newtree->type = CWIGGLE;
else {
if (value3 == 0.0)
- error->all(FLERR,"Invalid math function in variable formula");
+ error->all(FLERR,"Invalid math function in variable formula");
double delta = update->ntimestep - update->beginstep;
double omega = 2.0*MY_PI/value3;
double value = value1 + value2*sin(omega*delta*update->dt);
@@ -2499,14 +2499,14 @@ int Variable::math_function(char *word, char *contents, Tree **tree,
}
} else if (strcmp(word,"cwiggle") == 0) {
- if (narg != 3)
+ if (narg != 3)
error->all(FLERR,"Invalid math function in variable formula");
if (update->whichflag == 0)
error->all(FLERR,"Cannot use cwiggle in variable formula between runs");
if (tree) newtree->type = CWIGGLE;
else {
if (value3 == 0.0)
- error->all(FLERR,"Invalid math function in variable formula");
+ error->all(FLERR,"Invalid math function in variable formula");
double delta = update->ntimestep - update->beginstep;
double omega = 2.0*MY_PI/value3;
double value = value1 + value2*(1.0-cos(omega*delta*update->dt));
@@ -2535,17 +2535,17 @@ int Variable::math_function(char *word, char *contents, Tree **tree,
------------------------------------------------------------------------- */
int Variable::group_function(char *word, char *contents, Tree **tree,
- Tree **treestack, int &ntreestack,
- double *argstack, int &nargstack)
+ Tree **treestack, int &ntreestack,
+ double *argstack, int &nargstack)
{
// word not a match to any group function
- if (strcmp(word,"count") && strcmp(word,"mass") &&
+ if (strcmp(word,"count") && strcmp(word,"mass") &&
strcmp(word,"charge") && strcmp(word,"xcm") &&
strcmp(word,"vcm") && strcmp(word,"fcm") &&
strcmp(word,"bound") && strcmp(word,"gyration") &&
strcmp(word,"ke") && strcmp(word,"angmom") &&
- strcmp(word,"torque") && strcmp(word,"inertia") &&
+ strcmp(word,"torque") && strcmp(word,"inertia") &&
strcmp(word,"omega"))
return 0;
@@ -2757,7 +2757,7 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
else if (strcmp(arg2,"z") == 0) value = omega[2];
else error->all(FLERR,"Invalid group function in variable formula");
}
-
+
delete [] arg1;
delete [] arg2;
delete [] arg3;
@@ -2796,8 +2796,8 @@ int Variable::region_function(char *id)
------------------------------------------------------------------------- */
int Variable::special_function(char *word, char *contents, Tree **tree,
- Tree **treestack, int &ntreestack,
- double *argstack, int &nargstack)
+ Tree **treestack, int &ntreestack,
+ double *argstack, int &nargstack)
{
// word not a match to any special function
@@ -2848,9 +2848,9 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
else if (strcmp(word,"max") == 0) method = XMAX;
else if (strcmp(word,"ave") == 0) method = AVE;
else if (strcmp(word,"trap") == 0) method = TRAP;
-
+
if (narg != 1) error->all(FLERR,"Invalid special function in variable formula");
-
+
Compute *compute = NULL;
Fix *fix = NULL;
int index,nvec,nstride;
@@ -2858,113 +2858,113 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
if (strstr(arg1,"c_") == arg1) {
ptr1 = strchr(arg1,'[');
if (ptr1) {
- ptr2 = ptr1;
- index = int_between_brackets(ptr2);
- *ptr1 = '\0';
+ ptr2 = ptr1;
+ index = int_between_brackets(ptr2);
+ *ptr1 = '\0';
} else index = 0;
int icompute = modify->find_compute(&arg1[2]);
if (icompute < 0) error->all(FLERR,"Invalid compute ID in variable formula");
compute = modify->compute[icompute];
if (index == 0 && compute->vector_flag) {
- if (update->whichflag == 0) {
- if (compute->invoked_vector != update->ntimestep)
- error->all(FLERR,"Compute used in variable between runs is not current");
- } else if (!(compute->invoked_flag & INVOKED_VECTOR)) {
- compute->compute_vector();
- compute->invoked_flag |= INVOKED_VECTOR;
- }
- nvec = compute->size_vector;
- nstride = 1;
+ if (update->whichflag == 0) {
+ if (compute->invoked_vector != update->ntimestep)
+ error->all(FLERR,"Compute used in variable between runs is not current");
+ } else if (!(compute->invoked_flag & INVOKED_VECTOR)) {
+ compute->compute_vector();
+ compute->invoked_flag |= INVOKED_VECTOR;
+ }
+ nvec = compute->size_vector;
+ nstride = 1;
} else if (index && compute->array_flag) {
- if (index > compute->size_array_cols)
- error->all(FLERR,"Variable formula compute array "
- "is accessed out-of-range");
- if (update->whichflag == 0) {
- if (compute->invoked_array != update->ntimestep)
- error->all(FLERR,"Compute used in variable between runs is not current");
- } else if (!(compute->invoked_flag & INVOKED_ARRAY)) {
- compute->compute_array();
- compute->invoked_flag |= INVOKED_ARRAY;
- }
- nvec = compute->size_array_rows;
- nstride = compute->size_array_cols;
+ if (index > compute->size_array_cols)
+ error->all(FLERR,"Variable formula compute array "
+ "is accessed out-of-range");
+ if (update->whichflag == 0) {
+ if (compute->invoked_array != update->ntimestep)
+ error->all(FLERR,"Compute used in variable between runs is not current");
+ } else if (!(compute->invoked_flag & INVOKED_ARRAY)) {
+ compute->compute_array();
+ compute->invoked_flag |= INVOKED_ARRAY;
+ }
+ nvec = compute->size_array_rows;
+ nstride = compute->size_array_cols;
} else error->all(FLERR,"Mismatched compute in variable formula");
-
+
} else if (strstr(arg1,"f_") == arg1) {
ptr1 = strchr(arg1,'[');
if (ptr1) {
- ptr2 = ptr1;
- index = int_between_brackets(ptr2);
- *ptr1 = '\0';
+ ptr2 = ptr1;
+ index = int_between_brackets(ptr2);
+ *ptr1 = '\0';
} else index = 0;
-
+
int ifix = modify->find_fix(&arg1[2]);
if (ifix < 0) error->all(FLERR,"Invalid fix ID in variable formula");
fix = modify->fix[ifix];
if (index == 0 && fix->vector_flag) {
- if (update->whichflag > 0 && update->ntimestep % fix->global_freq)
- error->all(FLERR,"Fix in variable not computed at compatible time");
- nvec = fix->size_vector;
- nstride = 1;
+ if (update->whichflag > 0 && update->ntimestep % fix->global_freq)
+ error->all(FLERR,"Fix in variable not computed at compatible time");
+ nvec = fix->size_vector;
+ nstride = 1;
} else if (index && fix->array_flag) {
- if (index > fix->size_array_cols)
- error->all(FLERR,"Variable formula fix array is accessed out-of-range");
- if (update->whichflag > 0 && update->ntimestep % fix->global_freq)
- error->all(FLERR,"Fix in variable not computed at compatible time");
- nvec = fix->size_array_rows;
- nstride = fix->size_array_cols;
+ if (index > fix->size_array_cols)
+ error->all(FLERR,"Variable formula fix array is accessed out-of-range");
+ if (update->whichflag > 0 && update->ntimestep % fix->global_freq)
+ error->all(FLERR,"Fix in variable not computed at compatible time");
+ nvec = fix->size_array_rows;
+ nstride = fix->size_array_cols;
} else error->all(FLERR,"Mismatched fix in variable formula");
-
+
} else error->all(FLERR,"Invalid special function in variable formula");
-
+
double value = 0.0;
if (method == XMIN) value = BIG;
if (method == XMAX) value = -BIG;
-
+
if (compute) {
double *vec;
if (index) vec = &compute->array[0][index-1];
- else vec = compute->vector;
-
+ else vec = compute->vector;
+
int j = 0;
for (int i = 0; i < nvec; i++) {
- if (method == SUM) value += vec[j];
- else if (method == XMIN) value = MIN(value,vec[j]);
- else if (method == XMAX) value = MAX(value,vec[j]);
- else if (method == AVE) value += vec[j];
- else if (method == TRAP) {
- if (i > 0 && i < nvec-1) value += vec[j];
- else value += 0.5*vec[j];
- }
- j += nstride;
+ if (method == SUM) value += vec[j];
+ else if (method == XMIN) value = MIN(value,vec[j]);
+ else if (method == XMAX) value = MAX(value,vec[j]);
+ else if (method == AVE) value += vec[j];
+ else if (method == TRAP) {
+ if (i > 0 && i < nvec-1) value += vec[j];
+ else value += 0.5*vec[j];
+ }
+ j += nstride;
}
}
-
+
if (fix) {
double one;
for (int i = 0; i < nvec; i++) {
- if (index) one = fix->compute_array(i,index-1);
- else one = fix->compute_vector(i);
- if (method == SUM) value += one;
- else if (method == XMIN) value = MIN(value,one);
- else if (method == XMAX) value = MAX(value,one);
- else if (method == AVE) value += one;
- else if (method == TRAP) {
- if (i > 1 && i < nvec) value += one;
- else value += 0.5*one;
- }
+ if (index) one = fix->compute_array(i,index-1);
+ else one = fix->compute_vector(i);
+ if (method == SUM) value += one;
+ else if (method == XMIN) value = MIN(value,one);
+ else if (method == XMAX) value = MAX(value,one);
+ else if (method == AVE) value += one;
+ else if (method == TRAP) {
+ if (i > 1 && i < nvec) value += one;
+ else value += 0.5*one;
+ }
}
}
-
+
if (method == AVE) value /= nvec;
-
+
delete [] arg1;
delete [] arg2;
delete [] arg3;
-
+
// save value in tree or on argstack
-
+
if (tree) {
Tree *newtree = new Tree();
newtree->type = VALUE;
@@ -2983,7 +2983,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
int igroup = group->find(arg1);
if (igroup == -1)
error->all(FLERR,"Group ID in variable formula does not exist");
-
+
Tree *newtree = new Tree();
newtree->type = GMASK;
newtree->ivalue1 = group->bitmask[igroup];
@@ -2996,7 +2996,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
if (narg != 1) error->all(FLERR,"Invalid special function in variable formula");
int iregion = region_function(arg1);
-
+
Tree *newtree = new Tree();
newtree->type = RMASK;
newtree->ivalue1 = iregion;
@@ -3012,7 +3012,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
if (igroup == -1)
error->all(FLERR,"Group ID in variable formula does not exist");
int iregion = region_function(arg2);
-
+
Tree *newtree = new Tree();
newtree->type = RMASK;
newtree->ivalue1 = group->bitmask[igroup];
@@ -3035,9 +3035,9 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
------------------------------------------------------------------------- */
void Variable::peratom2global(int flag, char *word,
- double *vector, int nstride, int id,
- Tree **tree, Tree **treestack, int &ntreestack,
- double *argstack, int &nargstack)
+ double *vector, int nstride, int id,
+ Tree **tree, Tree **treestack, int &ntreestack,
+ double *argstack, int &nargstack)
{
if (atom->map_style == 0)
error->all(FLERR,"Indexed per-atom vector in variable formula without atom map");
@@ -3049,8 +3049,8 @@ void Variable::peratom2global(int flag, char *word,
if (flag == 0) {
if (strcmp(word,"mass") == 0) {
- if (atom->rmass) mine = atom->rmass[index];
- else mine = atom->mass[atom->type[index]];
+ if (atom->rmass) mine = atom->rmass[index];
+ else mine = atom->mass[atom->type[index]];
}
else if (strcmp(word,"type") == 0) mine = atom->type[index];
else if (strcmp(word,"x") == 0) mine = atom->x[index][0];
@@ -3062,16 +3062,16 @@ void Variable::peratom2global(int flag, char *word,
else if (strcmp(word,"fx") == 0) mine = atom->f[index][0];
else if (strcmp(word,"fy") == 0) mine = atom->f[index][1];
else if (strcmp(word,"fz") == 0) mine = atom->f[index][2];
-
+
else error->one(FLERR,"Invalid atom vector in variable formula");
} else mine = vector[index*nstride];
-
+
} else mine = 0.0;
double value;
MPI_Allreduce(&mine,&value,1,MPI_DOUBLE,MPI_SUM,world);
-
+
if (tree) {
Tree *newtree = new Tree();
newtree->type = VALUE;
@@ -3113,7 +3113,7 @@ int Variable::is_atom_vector(char *word)
------------------------------------------------------------------------- */
void Variable::atom_vector(char *word, Tree **tree,
- Tree **treestack, int &ntreestack)
+ Tree **treestack, int &ntreestack)
{
if (tree == NULL)
error->all(FLERR,"Atom vector in equal-style variable formula");
@@ -3123,7 +3123,7 @@ void Variable::atom_vector(char *word, Tree **tree,
newtree->nstride = 3;
newtree->left = newtree->middle = newtree->right = NULL;
treestack[ntreestack++] = newtree;
-
+
if (strcmp(word,"mass") == 0) {
if (atom->rmass) {
newtree->nstride = 1;
@@ -3215,7 +3215,7 @@ char *Variable::find_next_comma(char *str)
{
int level = 0;
for (char *p = str; *p; ++p) {
- if ('(' == *p) level++;
+ if ('(' == *p) level++;
else if (')' == *p) level--;
else if (',' == *p && !level) return p;
}
@@ -3259,151 +3259,151 @@ double Variable::evaluate_boolean(char *str)
while (1) {
onechar = str[i];
-
+
// whitespace: just skip
-
+
if (isspace(onechar)) i++;
-
+
// ----------------
// parentheses: recursively evaluate contents of parens
// ----------------
-
+
else if (onechar == '(') {
if (expect == OP) error->all(FLERR,"Invalid Boolean syntax in if command");
expect = OP;
-
+
char *contents;
i = find_matching_paren(str,i,contents);
i++;
-
+
// evaluate contents and push on stack
-
+
argstack[nargstack++] = evaluate_boolean(contents);
-
+
delete [] contents;
-
+
// ----------------
// number: push value onto stack
// ----------------
-
+
} else if (isdigit(onechar) || onechar == '.' || onechar == '-') {
if (expect == OP) error->all(FLERR,"Invalid Boolean syntax in if command");
expect = OP;
-
+
// istop = end of number, including scientific notation
-
+
int istart = i++;
while (isdigit(str[i]) || str[i] == '.') i++;
if (str[i] == 'e' || str[i] == 'E') {
- i++;
- if (str[i] == '+' || str[i] == '-') i++;
- while (isdigit(str[i])) i++;
+ i++;
+ if (str[i] == '+' || str[i] == '-') i++;
+ while (isdigit(str[i])) i++;
}
int istop = i - 1;
-
+
int n = istop - istart + 1;
char *number = new char[n+1];
strncpy(number,&str[istart],n);
number[n] = '\0';
-
+
argstack[nargstack++] = atof(number);
-
+
delete [] number;
-
+
// ----------------
// Boolean operator, including end-of-string
// ----------------
-
+
} else if (strchr("<>=!&|\0",onechar)) {
if (onechar == '=') {
- if (str[i+1] != '=')
- error->all(FLERR,"Invalid Boolean syntax in if command");
- op = EQ;
- i++;
+ if (str[i+1] != '=')
+ error->all(FLERR,"Invalid Boolean syntax in if command");
+ op = EQ;
+ i++;
} else if (onechar == '!') {
- if (str[i+1] == '=') {
- op = NE;
- i++;
- } else op = NOT;
+ if (str[i+1] == '=') {
+ op = NE;
+ i++;
+ } else op = NOT;
} else if (onechar == '<') {
- if (str[i+1] != '=') op = LT;
- else {
- op = LE;
- i++;
- }
+ if (str[i+1] != '=') op = LT;
+ else {
+ op = LE;
+ i++;
+ }
} else if (onechar == '>') {
- if (str[i+1] != '=') op = GT;
- else {
- op = GE;
- i++;
- }
+ if (str[i+1] != '=') op = GT;
+ else {
+ op = GE;
+ i++;
+ }
} else if (onechar == '&') {
- if (str[i+1] != '&')
- error->all(FLERR,"Invalid Boolean syntax in if command");
- op = AND;
- i++;
+ if (str[i+1] != '&')
+ error->all(FLERR,"Invalid Boolean syntax in if command");
+ op = AND;
+ i++;
} else if (onechar == '|') {
- if (str[i+1] != '|')
- error->all(FLERR,"Invalid Boolean syntax in if command");
- op = OR;
- i++;
+ if (str[i+1] != '|')
+ error->all(FLERR,"Invalid Boolean syntax in if command");
+ op = OR;
+ i++;
} else op = DONE;
-
+
i++;
-
+
if (op == NOT && expect == ARG) {
- opstack[nopstack++] = op;
- continue;
+ opstack[nopstack++] = op;
+ continue;
}
if (expect == ARG) error->all(FLERR,"Invalid Boolean syntax in if command");
expect = ARG;
-
+
// evaluate stack as deep as possible while respecting precedence
// before pushing current op onto stack
while (nopstack && precedence[opstack[nopstack-1]] >= precedence[op]) {
- opprevious = opstack[--nopstack];
-
- value2 = argstack[--nargstack];
- if (opprevious != NOT) value1 = argstack[--nargstack];
-
- if (opprevious == NOT) {
- if (value2 == 0.0) argstack[nargstack++] = 1.0;
- else argstack[nargstack++] = 0.0;
- } else if (opprevious == EQ) {
- if (value1 == value2) argstack[nargstack++] = 1.0;
- else argstack[nargstack++] = 0.0;
- } else if (opprevious == NE) {
- if (value1 != value2) argstack[nargstack++] = 1.0;
- else argstack[nargstack++] = 0.0;
- } else if (opprevious == LT) {
- if (value1 < value2) argstack[nargstack++] = 1.0;
- else argstack[nargstack++] = 0.0;
- } else if (opprevious == LE) {
- if (value1 <= value2) argstack[nargstack++] = 1.0;
- else argstack[nargstack++] = 0.0;
- } else if (opprevious == GT) {
- if (value1 > value2) argstack[nargstack++] = 1.0;
- else argstack[nargstack++] = 0.0;
- } else if (opprevious == GE) {
- if (value1 >= value2) argstack[nargstack++] = 1.0;
- else argstack[nargstack++] = 0.0;
- } else if (opprevious == AND) {
- if (value1 != 0.0 && value2 != 0.0) argstack[nargstack++] = 1.0;
- else argstack[nargstack++] = 0.0;
- } else if (opprevious == OR) {
- if (value1 != 0.0 || value2 != 0.0) argstack[nargstack++] = 1.0;
- else argstack[nargstack++] = 0.0;
- }
+ opprevious = opstack[--nopstack];
+
+ value2 = argstack[--nargstack];
+ if (opprevious != NOT) value1 = argstack[--nargstack];
+
+ if (opprevious == NOT) {
+ if (value2 == 0.0) argstack[nargstack++] = 1.0;
+ else argstack[nargstack++] = 0.0;
+ } else if (opprevious == EQ) {
+ if (value1 == value2) argstack[nargstack++] = 1.0;
+ else argstack[nargstack++] = 0.0;
+ } else if (opprevious == NE) {
+ if (value1 != value2) argstack[nargstack++] = 1.0;
+ else argstack[nargstack++] = 0.0;
+ } else if (opprevious == LT) {
+ if (value1 < value2) argstack[nargstack++] = 1.0;
+ else argstack[nargstack++] = 0.0;
+ } else if (opprevious == LE) {
+ if (value1 <= value2) argstack[nargstack++] = 1.0;
+ else argstack[nargstack++] = 0.0;
+ } else if (opprevious == GT) {
+ if (value1 > value2) argstack[nargstack++] = 1.0;
+ else argstack[nargstack++] = 0.0;
+ } else if (opprevious == GE) {
+ if (value1 >= value2) argstack[nargstack++] = 1.0;
+ else argstack[nargstack++] = 0.0;
+ } else if (opprevious == AND) {
+ if (value1 != 0.0 && value2 != 0.0) argstack[nargstack++] = 1.0;
+ else argstack[nargstack++] = 0.0;
+ } else if (opprevious == OR) {
+ if (value1 != 0.0 || value2 != 0.0) argstack[nargstack++] = 1.0;
+ else argstack[nargstack++] = 0.0;
+ }
}
-
+
// if end-of-string, break out of entire formula evaluation loop
-
+
if (op == DONE) break;
-
+
// push current operation onto stack
-
+
opstack[nopstack++] = op;
} else error->all(FLERR,"Invalid Boolean syntax in if command");
diff --git a/src/variable.h b/src/variable.h
index dac393966856120ed7fa2fdb35bc3729dbcbf903..407fd17b3c205a2a3da47f6e66f35259cedcbbfd 100644
--- a/src/variable.h
+++ b/src/variable.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -72,10 +72,10 @@ class Variable : protected Pointers {
int math_function(char *, char *, Tree **, Tree **, int &, double *, int &);
int group_function(char *, char *, Tree **, Tree **, int &, double *, int &);
int region_function(char *);
- int special_function(char *, char *, Tree **, Tree **,
- int &, double *, int &);
+ int special_function(char *, char *, Tree **, Tree **,
+ int &, double *, int &);
void peratom2global(int, char *, double *, int, int,
- Tree **, Tree **, int &, double *, int &);
+ Tree **, Tree **, int &, double *, int &);
int is_atom_vector(char *);
void atom_vector(char *, Tree **, Tree **, int &);
int is_constant(char *);
diff --git a/src/velocity.cpp b/src/velocity.cpp
index eb46bc0f6b86ddafbe5de122b12793d9f0eb4dad..fa3712bbbd3af99c6f31dfea254bfb9a22ab89a9 100644
--- a/src/velocity.cpp
+++ b/src/velocity.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -53,7 +53,7 @@ void Velocity::command(int narg, char **arg)
{
if (narg < 2) error->all(FLERR,"Illegal velocity command");
- if (domain->box_exist == 0)
+ if (domain->box_exist == 0)
error->all(FLERR,"Velocity command before simulation box is defined");
if (atom->natoms == 0)
error->all(FLERR,"Velocity command with no atoms existing");
@@ -194,7 +194,7 @@ void Velocity::create(double t_desired, int seed)
int m;
double vx,vy,vz,factor;
RanPark *random;
-
+
if (loop_flag == ALL) {
// create an atom map if one doesn't exist already
@@ -213,9 +213,11 @@ void Velocity::create(double t_desired, int seed)
if (atom->natoms > MAXSMALLINT)
error->all(FLERR,"Too big a problem to use velocity create loop all");
if (atom->tag_enable == 0)
- error->all(FLERR,"Cannot use velocity create loop all unless atoms have IDs");
+ error->all(FLERR,
+ "Cannot use velocity create loop all unless atoms have IDs");
if (atom->tag_consecutive() == 0)
- error->all(FLERR,"Atom IDs must be consecutive for velocity create loop all");
+ error->all(FLERR,
+ "Atom IDs must be consecutive for velocity create loop all");
// loop over all atoms in system
// generate RNGs for all atoms, only assign to ones I own
@@ -226,24 +228,24 @@ void Velocity::create(double t_desired, int seed)
for (i = 1; i <= natoms; i++) {
if (dist_flag == 0) {
- vx = random->uniform();
- vy = random->uniform();
- vz = random->uniform();
+ vx = random->uniform();
+ vy = random->uniform();
+ vz = random->uniform();
} else {
- vx = random->gaussian();
- vy = random->gaussian();
- vz = random->gaussian();
+ vx = random->gaussian();
+ vy = random->gaussian();
+ vz = random->gaussian();
}
m = atom->map(i);
if (m >= 0 && m < nlocal) {
- if (mask[m] & groupbit) {
- if (rmass) factor = 1.0/sqrt(rmass[m]);
- else factor = 1.0/sqrt(mass[type[m]]);
- v[m][0] = vx * factor;
- v[m][1] = vy * factor;
- if (dimension == 3) v[m][2] = vz * factor;
- else v[m][2] = 0.0;
- }
+ if (mask[m] & groupbit) {
+ if (rmass) factor = 1.0/sqrt(rmass[m]);
+ else factor = 1.0/sqrt(mass[type[m]]);
+ v[m][0] = vx * factor;
+ v[m][1] = vy * factor;
+ if (dimension == 3) v[m][2] = vz * factor;
+ else v[m][2] = 0.0;
+ }
}
}
@@ -260,47 +262,47 @@ void Velocity::create(double t_desired, int seed)
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
- if (dist_flag == 0) {
- vx = random->uniform();
- vy = random->uniform();
- vz = random->uniform();
- } else {
- vx = random->gaussian();
- vy = random->gaussian();
- vz = random->gaussian();
- }
- if (rmass) factor = 1.0/sqrt(rmass[i]);
- else factor = 1.0/sqrt(mass[type[i]]);
- v[i][0] = vx * factor;
- v[i][1] = vy * factor;
- if (dimension == 3) v[i][2] = vz * factor;
- else v[i][2] = 0.0;
+ if (dist_flag == 0) {
+ vx = random->uniform();
+ vy = random->uniform();
+ vz = random->uniform();
+ } else {
+ vx = random->gaussian();
+ vy = random->gaussian();
+ vz = random->gaussian();
+ }
+ if (rmass) factor = 1.0/sqrt(rmass[i]);
+ else factor = 1.0/sqrt(mass[type[i]]);
+ v[i][0] = vx * factor;
+ v[i][1] = vy * factor;
+ if (dimension == 3) v[i][2] = vz * factor;
+ else v[i][2] = 0.0;
}
}
} else if (loop_flag == GEOM) {
random = new RanPark(lmp,1);
double **x = atom->x;
-
+
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
- random->reset(seed,x[i]);
- if (dist_flag == 0) {
- vx = random->uniform();
- vy = random->uniform();
- vz = random->uniform();
- } else {
- vx = random->gaussian();
- vy = random->gaussian();
- vz = random->gaussian();
- }
-
- if (rmass) factor = 1.0/sqrt(rmass[i]);
- else factor = 1.0/sqrt(mass[type[i]]);
- v[i][0] = vx * factor;
- v[i][1] = vy * factor;
- if (dimension == 3) v[i][2] = vz * factor;
- else v[i][2] = 0.0;
+ random->reset(seed,x[i]);
+ if (dist_flag == 0) {
+ vx = random->uniform();
+ vy = random->uniform();
+ vz = random->uniform();
+ } else {
+ vx = random->gaussian();
+ vy = random->gaussian();
+ vz = random->gaussian();
+ }
+
+ if (rmass) factor = 1.0/sqrt(rmass[i]);
+ else factor = 1.0/sqrt(mass[type[i]]);
+ v[i][0] = vx * factor;
+ v[i][1] = vy * factor;
+ if (dimension == 3) v[i][2] = vz * factor;
+ else v[i][2] = 0.0;
}
}
}
@@ -315,14 +317,14 @@ void Velocity::create(double t_desired, int seed)
double t = temperature->compute_scalar();
rescale(t,t_desired);
- // if sum_flag set, add back in previous velocities
+ // if sum_flag set, add back in previous velocities
if (sum_flag) {
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
- v[i][0] += vhold[i][0];
- v[i][1] += vhold[i][1];
- v[i][2] += vhold[i][2];
+ v[i][0] += vhold[i][0];
+ v[i][1] += vhold[i][1];
+ v[i][2] += vhold[i][2];
}
}
}
@@ -397,21 +399,24 @@ void Velocity::set(int narg, char **arg)
if (xstr) {
xvar = input->variable->find(xstr);
- if (xvar < 0) error->all(FLERR,"Variable name for velocity set does not exist");
+ if (xvar < 0)
+ error->all(FLERR,"Variable name for velocity set does not exist");
if (input->variable->equalstyle(xvar)) xstyle = EQUAL;
else if (input->variable->atomstyle(xvar)) xstyle = ATOM;
else error->all(FLERR,"Variable for velocity set is invalid style");
}
if (ystr) {
yvar = input->variable->find(ystr);
- if (yvar < 0) error->all(FLERR,"Variable name for velocity set does not exist");
+ if (yvar < 0)
+ error->all(FLERR,"Variable name for velocity set does not exist");
if (input->variable->equalstyle(yvar)) ystyle = EQUAL;
else if (input->variable->atomstyle(yvar)) ystyle = ATOM;
else error->all(FLERR,"Variable for velocity set is invalid style");
}
if (zstr) {
zvar = input->variable->find(zstr);
- if (zvar < 0) error->all(FLERR,"Variable name for velocity set does not exist");
+ if (zvar < 0)
+ error->all(FLERR,"Variable name for velocity set does not exist");
if (input->variable->equalstyle(zvar)) zstyle = EQUAL;
else if (input->variable->atomstyle(zvar)) zstyle = ATOM;
else error->all(FLERR,"Variable for velocity set is invalid style");
@@ -446,15 +451,15 @@ void Velocity::set(int narg, char **arg)
if (varflag == CONSTANT) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
- if (sum_flag == 0) {
- if (xstyle) v[i][0] = vx;
- if (ystyle) v[i][1] = vy;
- if (zstyle) v[i][2] = vz;
- } else {
- if (xstyle) v[i][0] += vx;
- if (ystyle) v[i][1] += vy;
- if (zstyle) v[i][2] += vz;
- }
+ if (sum_flag == 0) {
+ if (xstyle) v[i][0] = vx;
+ if (ystyle) v[i][1] = vy;
+ if (zstyle) v[i][2] = vz;
+ } else {
+ if (xstyle) v[i][0] += vx;
+ if (ystyle) v[i][1] += vy;
+ if (zstyle) v[i][2] += vz;
+ }
}
}
@@ -473,21 +478,21 @@ void Velocity::set(int narg, char **arg)
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- if (sum_flag == 0) {
- if (xstyle == ATOM) v[i][0] = vfield[i][0];
- else if (xstyle) v[i][0] = vx;
- if (ystyle == ATOM) v[i][1] = vfield[i][1];
- else if (ystyle) v[i][1] = vy;
- if (zstyle == ATOM) v[i][2] = vfield[i][2];
- else if (zstyle) v[i][2] = vz;
- } else {
- if (xstyle == ATOM) v[i][0] += vfield[i][0];
- else if (xstyle) v[i][0] += vx;
- if (ystyle == ATOM) v[i][1] += vfield[i][1];
- else if (ystyle) v[i][1] += vy;
- if (zstyle == ATOM) v[i][2] += vfield[i][2];
- else if (zstyle) v[i][2] += vz;
- }
+ if (sum_flag == 0) {
+ if (xstyle == ATOM) v[i][0] = vfield[i][0];
+ else if (xstyle) v[i][0] = vx;
+ if (ystyle == ATOM) v[i][1] = vfield[i][1];
+ else if (ystyle) v[i][1] = vy;
+ if (zstyle == ATOM) v[i][2] = vfield[i][2];
+ else if (zstyle) v[i][2] = vz;
+ } else {
+ if (xstyle == ATOM) v[i][0] += vfield[i][0];
+ else if (xstyle) v[i][0] += vx;
+ if (ystyle == ATOM) v[i][1] += vfield[i][1];
+ else if (ystyle) v[i][1] += vy;
+ if (zstyle == ATOM) v[i][2] += vfield[i][2];
+ else if (zstyle) v[i][2] += vz;
+ }
}
}
@@ -500,7 +505,7 @@ void Velocity::set(int narg, char **arg)
}
/* ----------------------------------------------------------------------
- rescale velocities of a group after computing its temperature
+ rescale velocities of a group after computing its temperature
------------------------------------------------------------------------- */
void Velocity::scale(int narg, char **arg)
@@ -538,7 +543,7 @@ void Velocity::scale(int narg, char **arg)
}
/* ----------------------------------------------------------------------
- apply a ramped set of velocities
+ apply a ramped set of velocities
------------------------------------------------------------------------- */
void Velocity::ramp(int narg, char **arg)
@@ -563,7 +568,7 @@ void Velocity::ramp(int narg, char **arg)
else if (strcmp(arg[0],"vz") == 0) v_dim = 2;
else error->all(FLERR,"Illegal velocity command");
- if (v_dim == 2 && domain->dimension == 2)
+ if (v_dim == 2 && domain->dimension == 2)
error->all(FLERR,"Velocity ramp in z for a 2d problem");
double v_lo,v_hi;
@@ -598,7 +603,7 @@ void Velocity::ramp(int narg, char **arg)
// vramp = ramped velocity component for v_dim
// add or set based on sum_flag
-
+
double **x = atom->x;
double **v = atom->v;
int *mask = atom->mask;
@@ -629,7 +634,7 @@ void Velocity::zero(int narg, char **arg)
}
/* ----------------------------------------------------------------------
- rescale velocities of group atoms to t_new from t_old
+ rescale velocities of group atoms to t_new from t_old
------------------------------------------------------------------------- */
void Velocity::rescale(double t_old, double t_new)
@@ -712,13 +717,13 @@ void Velocity::zero_rotation()
int *mask = atom->mask;
int *image = atom->image;
int nlocal = atom->nlocal;
-
+
int xbox,ybox,zbox;
double dx,dy,dz;
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
-
+
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
xbox = (image[i] & 1023) - 512;
@@ -734,7 +739,7 @@ void Velocity::zero_rotation()
}
/* ----------------------------------------------------------------------
- parse optional parameters at end of velocity input line
+ parse optional parameters at end of velocity input line
------------------------------------------------------------------------- */
void Velocity::options(int narg, char **arg)
@@ -771,12 +776,13 @@ void Velocity::options(int narg, char **arg)
if (iarg+2 > narg) error->all(FLERR,"Illegal velocity command");
int icompute;
for (icompute = 0; icompute < modify->ncompute; icompute++)
- if (strcmp(arg[iarg+1],modify->compute[icompute]->id) == 0) break;
- if (icompute == modify->ncompute)
- error->all(FLERR,"Could not find velocity temperature ID");
+ if (strcmp(arg[iarg+1],modify->compute[icompute]->id) == 0) break;
+ if (icompute == modify->ncompute)
+ error->all(FLERR,"Could not find velocity temperature ID");
temperature = modify->compute[icompute];
if (temperature->tempflag == 0)
- error->all(FLERR,"Velocity temperature ID does not compute temperature");
+ error->all(FLERR,
+ "Velocity temperature ID does not compute temperature");
iarg += 2;
} else if (strcmp(arg[iarg],"loop") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal velocity command");
diff --git a/src/velocity.h b/src/velocity.h
index c6404339462d76785c6a938c89e51f50b30dfb38..7d249d16d5a9eab451fceb5adc339519e9b325f5 100644
--- a/src/velocity.h
+++ b/src/velocity.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/verlet.cpp b/src/verlet.cpp
index 51902811739615de2f41d99cb056d5608f94076c..6ed4f40b0cbef6e62818291bf8a951512118f62c 100644
--- a/src/verlet.cpp
+++ b/src/verlet.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -240,9 +240,9 @@ void Verlet::run(int n)
if (triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
if (domain->box_change) {
- domain->reset_box();
- comm->setup();
- if (neighbor->style) neighbor->setup_bins();
+ domain->reset_box();
+ comm->setup();
+ if (neighbor->style) neighbor->setup_bins();
}
timer->stamp();
comm->exchange();
@@ -354,13 +354,13 @@ void Verlet::force_clear()
f[i][1] = 0.0;
f[i][2] = 0.0;
}
-
+
if (torqueflag) {
double **torque = atom->torque;
for (i = 0; i < nall; i++) {
- torque[i][0] = 0.0;
- torque[i][1] = 0.0;
- torque[i][2] = 0.0;
+ torque[i][0] = 0.0;
+ torque[i][1] = 0.0;
+ torque[i][2] = 0.0;
}
}
@@ -383,33 +383,33 @@ void Verlet::force_clear()
nall = atom->nlocal + atom->nghost;
for (i = atom->nlocal; i < nall; i++) {
- f[i][0] = 0.0;
- f[i][1] = 0.0;
- f[i][2] = 0.0;
+ f[i][0] = 0.0;
+ f[i][1] = 0.0;
+ f[i][2] = 0.0;
}
-
+
if (torqueflag) {
- double **torque = atom->torque;
- for (i = atom->nlocal; i < nall; i++) {
- torque[i][0] = 0.0;
- torque[i][1] = 0.0;
- torque[i][2] = 0.0;
- }
+ double **torque = atom->torque;
+ for (i = atom->nlocal; i < nall; i++) {
+ torque[i][0] = 0.0;
+ torque[i][1] = 0.0;
+ torque[i][2] = 0.0;
+ }
}
if (erforceflag) {
- double *erforce = atom->erforce;
- for (i = atom->nlocal; i < nall; i++) erforce[i] = 0.0;
+ double *erforce = atom->erforce;
+ for (i = atom->nlocal; i < nall; i++) erforce[i] = 0.0;
}
if (e_flag) {
- double *de = atom->de;
- for (i = 0; i < nall; i++) de[i] = 0.0;
+ double *de = atom->de;
+ for (i = 0; i < nall; i++) de[i] = 0.0;
}
if (rho_flag) {
- double *drho = atom->drho;
- for (i = 0; i < nall; i++) drho[i] = 0.0;
+ double *drho = atom->drho;
+ for (i = 0; i < nall; i++) drho[i] = 0.0;
}
}
}
diff --git a/src/verlet.h b/src/verlet.h
index 9dbcf32723dd01ffe3c65d1aa50697000c0631bf..1f3bb1767b9d5ac51764c33a84624c4731e25da8 100644
--- a/src/verlet.h
+++ b/src/verlet.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/write_restart.cpp b/src/write_restart.cpp
index 6dcec7659f6a0732b343fa9ed84ee7bead85f2b2..1471a8ba16787e09b200e0830a53025c44726b2c 100644
--- a/src/write_restart.cpp
+++ b/src/write_restart.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -131,7 +131,7 @@ void WriteRestart::write(char *file)
bigint nblocal = atom->nlocal;
MPI_Allreduce(&nblocal,&natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);
- if (natoms != atom->natoms && output->thermo->lostflag == ERROR)
+ if (natoms != atom->natoms && output->thermo->lostflag == ERROR)
error->all(FLERR,"Atom count is inconsistent, cannot write restart file");
// check if filename contains "%"
@@ -218,19 +218,19 @@ void WriteRestart::write(char *file)
if (triclinic) domain->x2lamda(x,x);
if (xperiodic) {
- if (x[0] < lo[0]) x[0] += period[0];
- if (x[0] >= hi[0]) x[0] -= period[0];
- x[0] = MAX(x[0],lo[0]);
+ if (x[0] < lo[0]) x[0] += period[0];
+ if (x[0] >= hi[0]) x[0] -= period[0];
+ x[0] = MAX(x[0],lo[0]);
}
if (yperiodic) {
- if (x[1] < lo[1]) x[1] += period[1];
- if (x[1] >= hi[1]) x[1] -= period[1];
- x[1] = MAX(x[1],lo[1]);
+ if (x[1] < lo[1]) x[1] += period[1];
+ if (x[1] >= hi[1]) x[1] -= period[1];
+ x[1] = MAX(x[1],lo[1]);
}
if (zperiodic) {
- if (x[2] < lo[2]) x[2] += period[2];
- if (x[2] >= hi[2]) x[2] -= period[2];
- x[2] = MAX(x[2],lo[2]);
+ if (x[2] < lo[2]) x[2] += period[2];
+ if (x[2] >= hi[2]) x[2] -= period[2];
+ x[2] = MAX(x[2],lo[2]);
}
if (triclinic) domain->lamda2x(x,x);
@@ -252,15 +252,15 @@ void WriteRestart::write(char *file)
if (me == 0) {
for (int iproc = 0; iproc < nprocs; iproc++) {
- if (iproc) {
- MPI_Irecv(buf,max_size,MPI_DOUBLE,iproc,0,world,&request);
- MPI_Send(&tmp,0,MPI_INT,iproc,0,world);
- MPI_Wait(&request,&status);
- MPI_Get_count(&status,MPI_DOUBLE,&recv_size);
- } else recv_size = send_size;
-
- fwrite(&recv_size,sizeof(int),1,fp);
- fwrite(buf,sizeof(double),recv_size,fp);
+ if (iproc) {
+ MPI_Irecv(buf,max_size,MPI_DOUBLE,iproc,0,world,&request);
+ MPI_Send(&tmp,0,MPI_INT,iproc,0,world);
+ MPI_Wait(&request,&status);
+ MPI_Get_count(&status,MPI_DOUBLE,&recv_size);
+ } else recv_size = send_size;
+
+ fwrite(&recv_size,sizeof(int),1,fp);
+ fwrite(buf,sizeof(double),recv_size,fp);
}
fclose(fp);
@@ -288,12 +288,12 @@ void WriteRestart::write(char *file)
fwrite(buf,sizeof(double),send_size,fp);
fclose(fp);
}
-
+
memory->destroy(buf);
}
/* ----------------------------------------------------------------------
- proc 0 writes out problem description
+ proc 0 writes out problem description
------------------------------------------------------------------------- */
void WriteRestart::header()
@@ -452,7 +452,7 @@ void WriteRestart::force_fields()
}
/* ----------------------------------------------------------------------
- write a flag and an int into restart file
+ write a flag and an int into restart file
------------------------------------------------------------------------- */
void WriteRestart::write_int(int flag, int value)
@@ -462,7 +462,7 @@ void WriteRestart::write_int(int flag, int value)
}
/* ----------------------------------------------------------------------
- write a flag and a double into restart file
+ write a flag and a double into restart file
------------------------------------------------------------------------- */
void WriteRestart::write_double(int flag, double value)
@@ -472,7 +472,7 @@ void WriteRestart::write_double(int flag, double value)
}
/* ----------------------------------------------------------------------
- write a flag and a char str into restart file
+ write a flag and a char str into restart file
------------------------------------------------------------------------- */
void WriteRestart::write_char(int flag, char *value)
@@ -484,7 +484,7 @@ void WriteRestart::write_char(int flag, char *value)
}
/* ----------------------------------------------------------------------
- write a flag and a bigint into restart file
+ write a flag and a bigint into restart file
------------------------------------------------------------------------- */
void WriteRestart::write_bigint(int flag, bigint value)
diff --git a/src/write_restart.h b/src/write_restart.h
index d473141895cdf6b992bd483e5eb62690c64b07a3..812c756283c480ae36494d3dc5c227f46c8374c8 100644
--- a/src/write_restart.h
+++ b/src/write_restart.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.