diff --git a/src/BODY/body_rounded_polygon.cpp b/src/BODY/body_rounded_polygon.cpp
index 00a09c912d8982e959de8c1ab46ff719fcfe39f6..d352c789d79d8cf803ae3fe60b090593e75ed8fc 100644
--- a/src/BODY/body_rounded_polygon.cpp
+++ b/src/BODY/body_rounded_polygon.cpp
@@ -170,7 +170,7 @@ void BodyRoundedPolygon::data_body(int ibonus, int ninteger, int ndouble,
// nentries = number of double entries to be read from Body section:
// 6 for inertia + 3*nsub for vertex coords + 1 for rounded radius
- int nentries = 6 + 3*nsub + 1;
+ int nentries = 6 + 3*nsub + 1;
if (ndouble != nentries)
error->one(FLERR,"Incorrect # of floating-point values in "
"Bodies section of data file");
@@ -279,7 +279,7 @@ void BodyRoundedPolygon::data_body(int ibonus, int ninteger, int ndouble,
bonus->dvalue[k] = 0;
*(&bonus->dvalue[k]+1) = 1;
k += 2;
- }
+ }
erad = sqrt(erad2);
bonus->dvalue[k] = erad;
@@ -341,7 +341,7 @@ double BodyRoundedPolygon::radius_body(int /*ninteger*/, int ndouble,
double maxrad = 0.0;
double delta[3];
- int offset = 6;
+ int offset = 6;
for (int i = 0; i < nsub; i++) {
delta[0] = dfile[offset];
delta[1] = dfile[offset+1];
@@ -350,9 +350,9 @@ double BodyRoundedPolygon::radius_body(int /*ninteger*/, int ndouble,
onerad = MathExtra::len3(delta);
maxrad = MAX(maxrad,onerad);
}
-
+
// add in radius of rounded corners
-
+
return maxrad + 0.5*dfile[offset];
}
@@ -401,7 +401,7 @@ int BodyRoundedPolygon::image(int ibonus, double flag1, double /*flag2*/,
AtomVecBody::Bonus *bonus = &avec->bonus[ibonus];
int n = bonus->ivalue[0];
-
+
if (n == 1) {
for (int i = 0; i < n; i++) {
imflag[i] = SPHERE;
@@ -418,7 +418,7 @@ int BodyRoundedPolygon::image(int ibonus, double flag1, double /*flag2*/,
}
} else {
-
+
// first end pt of each line
for (int i = 0; i < n; i++) {
@@ -436,7 +436,7 @@ int BodyRoundedPolygon::image(int ibonus, double flag1, double /*flag2*/,
}
// second end pt of each line
-
+
for (int i = 0; i < n; i++) {
j = i+1;
if (j == n) j = 0;
diff --git a/src/BODY/body_rounded_polyhedron.cpp b/src/BODY/body_rounded_polyhedron.cpp
index 0e2ebbed8307e90341247be332e1d9a90f0219d6..99a380a932ef50b90010c29c778707a4b3cb81f8 100644
--- a/src/BODY/body_rounded_polyhedron.cpp
+++ b/src/BODY/body_rounded_polyhedron.cpp
@@ -132,7 +132,7 @@ double BodyRoundedPolyhedron::enclosing_radius(struct AtomVecBody::Bonus *bonus)
int nvertices = bonus->ivalue[0];
if (nvertices == 1 || nvertices == 2)
return *(bonus->dvalue+3*nsub(bonus)+2);
- return *(bonus->dvalue+3*nsub(bonus) + 2*nedges(bonus) +
+ return *(bonus->dvalue+3*nsub(bonus) + 2*nedges(bonus) +
MAX_FACE_SIZE*nfaces(bonus));
}
@@ -143,7 +143,7 @@ double BodyRoundedPolyhedron::rounded_radius(struct AtomVecBody::Bonus *bonus)
int nvertices = bonus->ivalue[0];
if (nvertices == 1 || nvertices == 2)
return *(bonus->dvalue+3*nsub(bonus)+2+1);
- return *(bonus->dvalue+3*nsub(bonus) + 2*nedges(bonus) +
+ return *(bonus->dvalue+3*nsub(bonus) + 2*nedges(bonus) +
MAX_FACE_SIZE*nfaces(bonus)+1);
}
@@ -207,7 +207,7 @@ void BodyRoundedPolyhedron::data_body(int ibonus, int ninteger, int ndouble,
// nsub == 1 || nsub == 2 || nsub == 3:
// 6 for inertia + 3*nsub for vertex coords + 1 for rounded radius
// nsub > 3:
- // 6 for inertia + 3*nsub for vertex coords + 2*nsub for edges +
+ // 6 for inertia + 3*nsub for vertex coords + 2*nsub for edges +
// 3*nfaces + 1 for rounded radius
int nedges,nentries;
@@ -327,7 +327,7 @@ void BodyRoundedPolyhedron::data_body(int ibonus, int ninteger, int ndouble,
bonus->dvalue[k] = 0;
*(&bonus->dvalue[k]+1) = 1;
k += 2;
- }
+ }
erad = sqrt(erad2);
bonus->dvalue[k] = erad;
@@ -407,7 +407,7 @@ double BodyRoundedPolyhedron::radius_body(int /*ninteger*/, int ndouble,
double maxrad = 0.0;
double delta[3];
- int offset = 6;
+ int offset = 6;
for (int i = 0; i < nsub; i++) {
delta[0] = dfile[offset];
delta[1] = dfile[offset+1];
@@ -420,7 +420,7 @@ double BodyRoundedPolyhedron::radius_body(int /*ninteger*/, int ndouble,
if (nsub > 2) offset += (2*nedges+MAX_FACE_SIZE*nfac);
// add in radius of rounded corners
-
+
return maxrad + 0.5*dfile[offset];
}
diff --git a/src/BODY/fix_wall_body_polygon.cpp b/src/BODY/fix_wall_body_polygon.cpp
index 3f8c08b6bdfae307512aae97d1b88be821a4b433..0c9bd3e74183abd1437c603e5e5dfe7dce38ecf9 100644
--- a/src/BODY/fix_wall_body_polygon.cpp
+++ b/src/BODY/fix_wall_body_polygon.cpp
@@ -263,7 +263,7 @@ void FixWallBodyPolygon::post_force(int /*vflag*/)
}
ndiscrete = nedge = 0;
- for (i = 0; i < nlocal; i++)
+ for (i = 0; i < nlocal; i++)
dnum[i] = ednum[i] = 0;
for (i = 0; i < nlocal; i++) {
@@ -675,7 +675,7 @@ void FixWallBodyPolygon::contact_forces(Contact& contact, double j_a,
AtomVecBody::Bonus *bonus;
ibody = contact.ibody;
-
+
// compute the velocity of the vertex in the space-fixed frame
ibonus = atom->body[ibody];
diff --git a/src/BODY/fix_wall_body_polyhedron.cpp b/src/BODY/fix_wall_body_polyhedron.cpp
index 9504e256b497b45a9266a4680be2d5c8a4c7d9a4..295608a444f0ff1d363b8cd1168b6ad42c7569d4 100644
--- a/src/BODY/fix_wall_body_polyhedron.cpp
+++ b/src/BODY/fix_wall_body_polyhedron.cpp
@@ -102,7 +102,7 @@ FixWallBodyPolyhedron::FixWallBodyPolyhedron(LAMMPS *lmp, int narg, char **arg)
if (strcmp(arg[iarg+2],"NULL") == 0) hi = BIG;
else hi = force->numeric(FLERR,arg[iarg+2]);
iarg += 3;
- }
+ }
// check for trailing keyword/values
@@ -274,7 +274,7 @@ void FixWallBodyPolyhedron::post_force(int /*vflag*/)
}
ndiscrete = nedge = nface = 0;
- for (i = 0; i < nlocal; i++)
+ for (i = 0; i < nlocal; i++)
dnum[i] = ednum[i] = facnum[i] = 0;
for (i = 0; i < nlocal; i++) {
@@ -320,7 +320,7 @@ void FixWallBodyPolyhedron::post_force(int /*vflag*/)
wall_pos = whi;
side = ZHI;
}
- }
+ }
rsq = dx*dx + dy*dy + dz*dz;
if (rsq > radius[i]*radius[i]) continue;
@@ -502,7 +502,7 @@ int FixWallBodyPolyhedron::sphere_against_wall(int i, double wall_pos,
hi[0] = x[i][0];
hi[1] = x[i][1];
hi[2] = wall_pos;
- }
+ }
distance(hi, x[i], d);
@@ -536,7 +536,7 @@ int FixWallBodyPolyhedron::sphere_against_wall(int i, double wall_pos,
Output:
contact_list = list of contacts between i and the wall
num_contacts = number of contacts between i's vertices and the wall
- Return:
+ Return:
number of contacts of the edge to the wall (0, 1 or 2)
---------------------------------------------------------------------- */
@@ -578,7 +578,7 @@ int FixWallBodyPolyhedron::edge_against_wall(int i, double wall_pos,
------------------------------------------------------------------------- */
int FixWallBodyPolyhedron::compute_distance_to_wall(int ibody, int edge_index,
- double *xmi, double rounded_radius_i, double wall_pos,
+ double *xmi, double rounded_radius_i, double wall_pos,
int /*side*/, double* vwall, int &contact)
{
int mode,ifirst,iefirst,npi1,npi2;
@@ -623,7 +623,7 @@ int FixWallBodyPolyhedron::compute_distance_to_wall(int ibody, int edge_index,
hi[0] = xpi1[0];
hi[1] = xpi1[1];
hi[2] = wall_pos;
- }
+ }
distance(hi, xpi1, d1);
@@ -658,7 +658,7 @@ int FixWallBodyPolyhedron::compute_distance_to_wall(int ibody, int edge_index,
hi[0] = xpi2[0];
hi[1] = xpi2[1];
hi[2] = wall_pos;
- }
+ }
distance(hi, xpi2, d2);
@@ -790,7 +790,7 @@ void FixWallBodyPolyhedron::contact_forces(Contact& contact, double j_a,
AtomVecBody::Bonus *bonus;
ibody = contact.ibody;
-
+
// compute the velocity of the vertex in the space-fixed frame
ibonus = atom->body[ibody];
diff --git a/src/BODY/fix_wall_body_polyhedron.h b/src/BODY/fix_wall_body_polyhedron.h
index ff7b7ca7cfd0806de2d5f4fcd16c79b48c980954..7479f79e23c8833cd67ad77282a584155ca17305 100644
--- a/src/BODY/fix_wall_body_polyhedron.h
+++ b/src/BODY/fix_wall_body_polyhedron.h
@@ -90,7 +90,7 @@ class FixWallBodyPolyhedron : public Fix {
double rounded_radius_i, double wall_pos, int side,
double* vwall, int &contact);
double contact_separation(const Contact& c1, const Contact& c2);
- void contact_forces(int ibody, double j_a, double *xi, double *xj,
+ void contact_forces(int ibody, double j_a, double *xi, double *xj,
double delx, double dely, double delz,
double fx, double fy, double fz, double** x, double** v,
double** angmom, double** f, double** torque, double* vwall);
diff --git a/src/BODY/pair_body_rounded_polygon.cpp b/src/BODY/pair_body_rounded_polygon.cpp
index 90408177726a33191129fefc791e30f3e60fe1f0..b6dcab29ae18194b4591161d430c62adc84747fe 100644
--- a/src/BODY/pair_body_rounded_polygon.cpp
+++ b/src/BODY/pair_body_rounded_polygon.cpp
@@ -275,9 +275,9 @@ void PairBodyRoundedPolygon::compute(int eflag, int vflag)
// scale the force at both contacts
- contact_forces(contact_list[m], j_a, x, v, angmom, f, torque,
+ contact_forces(contact_list[m], j_a, x, v, angmom, f, torque,
evdwl, facc);
- contact_forces(contact_list[n], j_a, x, v, angmom, f, torque,
+ contact_forces(contact_list[n], j_a, x, v, angmom, f, torque,
evdwl, facc);
done = 1;
@@ -288,15 +288,15 @@ void PairBodyRoundedPolygon::compute(int eflag, int vflag)
"xv = %f %f %f; xe = %f %f %f\n",
m, contact_list[m].vertex, contact_list[m].ibody,
contact_list[m].edge, contact_list[m].jbody,
- contact_list[m].xv[0], contact_list[m].xv[1],
- contact_list[m].xv[2], contact_list[m].xe[0],
+ contact_list[m].xv[0], contact_list[m].xv[1],
+ contact_list[m].xv[2], contact_list[m].xe[0],
contact_list[m].xe[1], contact_list[m].xe[2]);
printf(" %d: vertex %d of body %d and edge %d of body %d; "
"xv = %f %f %f; xe = %f %f %f\n",
n, contact_list[n].vertex, contact_list[n].ibody,
contact_list[n].edge, contact_list[n].jbody,
- contact_list[n].xv[0], contact_list[n].xv[1],
- contact_list[n].xv[2], contact_list[n].xe[0],
+ contact_list[n].xv[0], contact_list[n].xv[1],
+ contact_list[n].xv[2], contact_list[n].xe[0],
contact_list[n].xe[1], contact_list[n].xe[2]);
#endif
@@ -420,7 +420,7 @@ void PairBodyRoundedPolygon::coeff(int narg, char **arg)
void PairBodyRoundedPolygon::init_style()
{
avec = (AtomVecBody *) atom->style_match("body");
- if (!avec)
+ if (!avec)
error->all(FLERR,"Pair body/rounded/polygon requires atom style body");
if (strcmp(avec->bptr->style,"rounded/polygon") != 0)
error->all(FLERR,"Pair body/rounded/polygon requires "
@@ -501,7 +501,7 @@ void PairBodyRoundedPolygon::init_style()
if (dnum[i] == 0) body2space(i);
eradi = enclosing_radius[i];
if (eradi > merad[itype]) merad[itype] = eradi;
- } else
+ } else
merad[itype] = 0;
}
@@ -669,7 +669,7 @@ void PairBodyRoundedPolygon::sphere_against_sphere(int i, int j,
f[i][0] += fx;
f[i][1] += fy;
f[i][2] += fz;
-
+
if (newton_pair || j < nlocal) {
f[j][0] -= fx;
f[j][1] -= fy;
@@ -860,7 +860,7 @@ int PairBodyRoundedPolygon::vertex_against_edge(int i, int j,
#ifdef _CONVEX_POLYGON
// done with the edges from body j,
- // given that vertex ni interacts with only one vertex
+ // given that vertex ni interacts with only one vertex
// from one edge of body j
break;
#endif
@@ -1124,7 +1124,7 @@ int PairBodyRoundedPolygon::compute_distance_to_vertex(int ibody,
mode = EDGE;
if (d < contact_dist + EPSILON)
contact = 1;
-
+
} else { // t < 0 || t > 1: closer to either vertices of the edge
if (t < 0) {
diff --git a/src/BODY/pair_body_rounded_polyhedron.cpp b/src/BODY/pair_body_rounded_polyhedron.cpp
index eea2aa37249e011bab1a5122282c4b3511f48f5d..1a4653ce535c6533fb2c5f15db7624a5112a385b 100644
--- a/src/BODY/pair_body_rounded_polyhedron.cpp
+++ b/src/BODY/pair_body_rounded_polyhedron.cpp
@@ -283,7 +283,7 @@ void PairBodyRoundedPolyhedron::compute(int eflag, int vflag)
// check interaction between i's edges and j' faces
#ifdef _POLYHEDRON_DEBUG
printf("INTERACTION between edges of %d vs. faces of %d:\n", i, j);
- #endif
+ #endif
interact = edge_against_face(i, j, itype, jtype, x, contact_list,
num_contacts, evdwl, facc);
@@ -297,7 +297,7 @@ void PairBodyRoundedPolyhedron::compute(int eflag, int vflag)
// check interaction between i's edges and j' edges
#ifdef _POLYHEDRON_DEBUG
printf("INTERACTION between edges of %d vs. edges of %d:\n", i, j);
- #endif
+ #endif
interact = edge_against_edge(i, j, itype, jtype, x, contact_list,
num_contacts, evdwl, facc);
@@ -478,7 +478,7 @@ void PairBodyRoundedPolyhedron::init_style()
if (dnum[i] == 0) body2space(i);
eradi = enclosing_radius[i];
if (eradi > merad[itype]) merad[itype] = eradi;
- } else
+ } else
merad[itype] = 0;
}
@@ -630,7 +630,7 @@ void PairBodyRoundedPolyhedron::sphere_against_sphere(int ibody, int jbody,
vr3 = v[ibody][2] - v[jbody][2];
// normal component
-
+
rsqinv = 1.0/rsq;
vnnr = vr1*delx + vr2*dely + vr3*delz;
vn1 = delx*vnnr * rsqinv;
@@ -664,7 +664,7 @@ void PairBodyRoundedPolyhedron::sphere_against_sphere(int ibody, int jbody,
f[ibody][0] += fx;
f[ibody][1] += fy;
f[ibody][2] += fz;
-
+
if (newton_pair || jbody < nlocal) {
f[jbody][0] -= fx;
f[jbody][1] -= fy;
@@ -797,7 +797,7 @@ void PairBodyRoundedPolyhedron::sphere_against_edge(int ibody, int jbody,
fn[1] = -c_n * vn2;
fn[2] = -c_n * vn3;
- // tangential friction term at contact,
+ // tangential friction term at contact,
// excluding the tangential deformation term
ft[0] = -c_t * vt1;
@@ -873,7 +873,7 @@ void PairBodyRoundedPolyhedron::sphere_against_face(int ibody, int jbody,
xi3[2] = x[ibody][2] + discrete[ifirst+npi3][2];
// find the normal unit vector of the face
-
+
MathExtra::sub3(xi2, xi1, ui);
MathExtra::sub3(xi3, xi1, vi);
MathExtra::cross3(ui, vi, n);
@@ -1076,7 +1076,7 @@ int PairBodyRoundedPolyhedron::edge_against_face(int ibody, int jbody,
itype, jtype, cut_inner,
contact_list, num_contacts,
energy, facc);
- }
+ }
} // end for looping through the edges of body i
@@ -1171,7 +1171,7 @@ int PairBodyRoundedPolyhedron::interaction_edge_to_edge(int ibody,
printf(" edge npi1 = %d (%f %f %f); npi2 = %d (%f %f %f) vs."
" edge npj1 = %d (%f %f %f); npj2 = %d (%f %f %f): "
"t1 = %f; t2 = %f; r = %f; dot = %f\n",
- npi1, xi1[0], xi1[1], xi1[2], npi2, xi2[0], xi2[1], xi2[2],
+ npi1, xi1[0], xi1[1], xi1[2], npi2, xi2[0], xi2[1], xi2[2],
npj1, xpj1[0], xpj1[1], xpj1[2], npj2, xpj2[0], xpj2[1], xpj2[2],
t1, t2, r, dot);
#endif
@@ -1276,7 +1276,7 @@ int PairBodyRoundedPolyhedron::interaction_face_to_edge(int ibody,
xi3[2] = xmi[2] + discrete[ifirst+npi3][2];
// find the normal unit vector of the face, ensure it point outward of the body
-
+
MathExtra::sub3(xi2, xi1, ui);
MathExtra::sub3(xi3, xi1, vi);
MathExtra::cross3(ui, vi, n);
@@ -1305,7 +1305,7 @@ int PairBodyRoundedPolyhedron::interaction_face_to_edge(int ibody,
xpj2[1] = xmj[1] + discrete[jfirst+npj2][1];
xpj2[2] = xmj[2] + discrete[jfirst+npj2][2];
- // no interaction if two ends of the edge
+ // no interaction if two ends of the edge
// are on the same side with the COM wrt the face
if (opposite_sides(n, xi1, xmi, xpj1) == 0 &&
@@ -1340,9 +1340,9 @@ int PairBodyRoundedPolyhedron::interaction_face_to_edge(int ibody,
int jflag = 1;
#ifdef _POLYHEDRON_DEBUG
- if (interact == EF_SAME_SIDE_OF_FACE)
+ if (interact == EF_SAME_SIDE_OF_FACE)
printf(" - same side of face\n");
- else if (interact == EF_PARALLEL)
+ else if (interact == EF_PARALLEL)
printf(" - parallel\n");
printf(" face: xi1 (%f %f %f) xi2 (%f %f %f) xi3 (%f %f %f)\n",
xi1[0], xi1[1], xi1[2], xi2[0], xi2[1], xi2[2], xi3[0], xi3[1], xi3[2]);
@@ -1387,9 +1387,9 @@ int PairBodyRoundedPolyhedron::interaction_face_to_edge(int ibody,
} else {
num_outside++;
}
- }
+ }
- // xpj2 is in the interaction zone
+ // xpj2 is in the interaction zone
// and its projection on the face is inside the triangle
// compute vertex-face interaction and accumulate force/torque to both bodies
@@ -1401,7 +1401,7 @@ int PairBodyRoundedPolyhedron::interaction_face_to_edge(int ibody,
jflag, energy, facc);
#ifdef _POLYHEDRON_DEBUG
printf(" - compute pair force between vertex %d from edge %d of body %d "
- "with face %d of body %d: d2 = %f\n",
+ "with face %d of body %d: d2 = %f\n",
npj2, edge_index, jbody, face_index, ibody, d2);
#endif
@@ -1448,7 +1448,7 @@ int PairBodyRoundedPolyhedron::interaction_face_to_edge(int ibody,
// compute interaction between the edge with the three edges of the face
#ifdef _POLYHEDRON_DEBUG
- printf(" - intersect outside triangle\n");
+ printf(" - intersect outside triangle\n");
printf(" - compute pair force between edge %d of body %d "
"with face %d of body %d\n", edge_index, jbody, face_index, ibody);
printf(" face: xi1 (%f %f %f) xi2 (%f %f %f) xi3 (%f %f %f)\n",
@@ -1693,7 +1693,7 @@ void PairBodyRoundedPolyhedron::rescale_cohesive_forces(double** x,
xc[0] /= (double)num_unique_contacts;
xc[1] /= (double)num_unique_contacts;
xc[2] /= (double)num_unique_contacts;
-
+
contact_area = 0.0;
for (int m = 0; m < num_contacts; m++) {
if (contact_list[m].unique == 0) continue;
@@ -1847,12 +1847,12 @@ int PairBodyRoundedPolyhedron::edge_face_intersect(double* x1, double* x2,
if (t < 0 || t > 1) {
interact = EF_SAME_SIDE_OF_FACE;
} else {
- if (inside == 1)
+ if (inside == 1)
interact = EF_INTERSECT_INSIDE;
else
interact = EF_INTERSECT_OUTSIDE;
}
-
+
return interact;
}
@@ -1998,7 +1998,7 @@ void PairBodyRoundedPolyhedron::project_pt_plane(const double* q,
q_proj[2] = q[2] + n[2] * t;
// check if the projection point is inside the triangle
- // exclude the edges and vertices
+ // exclude the edges and vertices
// edge-sphere and sphere-sphere interactions are handled separately
inside = 0;
@@ -2022,7 +2022,7 @@ void PairBodyRoundedPolyhedron::project_pt_line(const double* q,
MathExtra::sub3(xi2, xi1, u);
MathExtra::norm3(u);
MathExtra::sub3(q, xi1, v);
-
+
s = MathExtra::dot3(u, v);
h[0] = xi1[0] + s * u[0];
h[1] = xi1[1] + s * u[1];
@@ -2039,13 +2039,13 @@ void PairBodyRoundedPolyhedron::project_pt_line(const double* q,
t = (h[2] - xi1[2])/(xi2[2] - xi1[2]);
}
-/* ----------------------------------------------------------------------
+/* ----------------------------------------------------------------------
compute the shortest distance between two edges (line segments)
x1, x2: two endpoints of the first edge
x3, x4: two endpoints of the second edge
- h1: the end point of the shortest segment perpendicular to both edges
+ h1: the end point of the shortest segment perpendicular to both edges
on the line (x1;x2)
- h2: the end point of the shortest segment perpendicular to both edges
+ h2: the end point of the shortest segment perpendicular to both edges
on the line (x3;x4)
t1: fraction of h1 in the segment (x1,x2)
t2: fraction of h2 in the segment (x3,x4)
@@ -2080,7 +2080,7 @@ void PairBodyRoundedPolyhedron::distance_bt_edges(const double* x1,
double s1,s2,x13[3],x23[3],x13h[3];
double t13,t23,t31,t41,x31[3],x41[3];
t13=t23=t31=t41=0.0;
-
+
MathExtra::sub3(x1,x3,x13); // x13 = x1 - x3
MathExtra::sub3(x2,x3,x23); // x23 = x2 - x3
@@ -2089,7 +2089,7 @@ void PairBodyRoundedPolyhedron::distance_bt_edges(const double* x1,
x13h[1] = x13[1] - s1*v[1];
x13h[2] = x13[2] - s1*v[2];
r = MathExtra::len3(x13h);
-
+
// x13 is the projection of x1 on x3-x4
x13[0] = x3[0] + s1*v[0];
@@ -2102,7 +2102,7 @@ void PairBodyRoundedPolyhedron::distance_bt_edges(const double* x1,
x23[0] = x3[0] + s2*v[0];
x23[1] = x3[1] + s2*v[1];
x23[2] = x3[2] + s2*v[2];
-
+
// find the fraction of the projection points on the edges
if (fabs(x4[0] - x3[0]) > 0)
@@ -2177,8 +2177,8 @@ void PairBodyRoundedPolyhedron::distance_bt_edges(const double* x1,
h1[0] = (x1[0]+x2[0])/2;
h1[1] = (x1[1]+x2[1])/2;
h1[2] = (x1[2]+x2[2])/2;
- h2[0] = (x13[0]+x23[0])/2;
- h2[1] = (x13[1]+x23[1])/2;
+ h2[0] = (x13[0]+x23[0])/2;
+ h2[1] = (x13[1]+x23[1])/2;
h2[2] = (x13[2]+x23[2])/2;
t1 = 0.5;
t2 = (t13+t23)/2;
@@ -2216,8 +2216,8 @@ void PairBodyRoundedPolyhedron::distance_bt_edges(const double* x1,
h1[0] = (x31[0]+x41[0])/2;
h1[1] = (x31[1]+x41[1])/2;
h1[2] = (x31[2]+x41[2])/2;
- h2[0] = (x3[0]+x4[0])/2;
- h2[1] = (x3[1]+x4[1])/2;
+ h2[0] = (x3[0]+x4[0])/2;
+ h2[1] = (x3[1]+x4[1])/2;
h2[2] = (x3[2]+x4[2])/2;
t1 = (t31+t41)/2;
t2 = 0.5;
@@ -2225,7 +2225,7 @@ void PairBodyRoundedPolyhedron::distance_bt_edges(const double* x1,
n2++;
}
}
- }
+ }
// if n1 == 0 and n2 == 0 at this point,
// which means no overlapping segments bt two parallel edges,
@@ -2233,10 +2233,10 @@ void PairBodyRoundedPolyhedron::distance_bt_edges(const double* x1,
return;
- }
+ }
// find the vector n perpendicular to both edges
-
+
MathExtra::cross3(u, v, n);
MathExtra::norm3(n);
@@ -2326,7 +2326,7 @@ double PairBodyRoundedPolyhedron::contact_separation(const Contact& c1,
find the number of unique contacts
------------------------------------------------------------------------- */
-void PairBodyRoundedPolyhedron::find_unique_contacts(Contact* contact_list,
+void PairBodyRoundedPolyhedron::find_unique_contacts(Contact* contact_list,
int& num_contacts)
{
int n = num_contacts;
diff --git a/src/BODY/pair_body_rounded_polyhedron.h b/src/BODY/pair_body_rounded_polyhedron.h
index 71c04ff9665aa0b24b7e7f4069cc4f4f4766bf4d..369f394c504b573aa82641905e5a865f98a922be 100644
--- a/src/BODY/pair_body_rounded_polyhedron.h
+++ b/src/BODY/pair_body_rounded_polyhedron.h
@@ -155,13 +155,13 @@ class PairBodyRoundedPolyhedron : public Pair {
int& inside_a, int& inside_b);
// helper functions
int opposite_sides(double* n, double* x0, double* a, double* b);
- void project_pt_plane(const double* q, const double* p,
+ void project_pt_plane(const double* q, const double* p,
const double* n, double* q_proj, double &d);
- void project_pt_plane(const double* q, const double* x1, const double* x2,
+ void project_pt_plane(const double* q, const double* x1, const double* x2,
const double* x3, double* q_proj, double &d, int& inside);
void project_pt_line(const double* q, const double* xi1, const double* xi2,
double* h, double& d, double& t);
- void inside_polygon(int ibody, int face_index, double* xmi,
+ void inside_polygon(int ibody, int face_index, double* xmi,
const double* q1, const double* q2, int& inside1, int& inside2);
void distance_bt_edges(const double* x1, const double* x2,
diff --git a/src/KOKKOS/atom_vec_sphere_kokkos.cpp b/src/KOKKOS/atom_vec_sphere_kokkos.cpp
index 3dfbc5efdca0f6fe2c9ba87600396971439684d6..f05e8d09df5d832f59f9fdbffaca127df29c8117 100644
--- a/src/KOKKOS/atom_vec_sphere_kokkos.cpp
+++ b/src/KOKKOS/atom_vec_sphere_kokkos.cpp
@@ -792,7 +792,7 @@ int AtomVecSphereKokkos::pack_comm_self(
const int &n, const DAT::tdual_int_2d &list, const int &iswap,
const int nfirst, const int &pbc_flag, const int* const pbc) {
// Fallback to AtomVecKokkos if radvary == 0
- if (radvary == 0)
+ if (radvary == 0)
return AtomVecKokkos::pack_comm_self(n,list,iswap,nfirst,pbc_flag,pbc);
if(commKK->forward_comm_on_host) {
sync(Host,X_MASK|RADIUS_MASK|RMASS_MASK);
@@ -1462,7 +1462,7 @@ struct AtomVecSphereKokkos_PackBorder {
const int maxsend = (buf.extent(0)*buf.extent(1))/elements;
_buf = typename ArrayTypes<DeviceType>::t_xfloat_2d_um(buf.data(),maxsend,elements);
}
-
+
KOKKOS_INLINE_FUNCTION
void operator() (const int& i) const {
const int j = _list(_iswap,i);
diff --git a/src/KOKKOS/comm_kokkos.cpp b/src/KOKKOS/comm_kokkos.cpp
index f40156aabcec16b85fe396b70e54c08164a3921f..1d31c0718058d0e564b393f90045b7246df65300 100644
--- a/src/KOKKOS/comm_kokkos.cpp
+++ b/src/KOKKOS/comm_kokkos.cpp
@@ -210,7 +210,7 @@ void CommKokkos::forward_comm_device(int dummy)
space,X_MASK);
}
} else if (ghost_velocity) {
- if (size_forward_recv[iswap]) {
+ if (size_forward_recv[iswap]) {
MPI_Irecv(k_buf_recv.view<DeviceType>().data(),
size_forward_recv[iswap],MPI_DOUBLE,
recvproc[iswap],0,world,&request);
diff --git a/src/KOKKOS/fix_freeze_kokkos.cpp b/src/KOKKOS/fix_freeze_kokkos.cpp
index b87ec86f8f5c28ab4afe97a0c2e4d2cb9f0d1507..ccf7c7ff85bf5f501491916d3778a67e6fc654ce 100644
--- a/src/KOKKOS/fix_freeze_kokkos.cpp
+++ b/src/KOKKOS/fix_freeze_kokkos.cpp
@@ -75,7 +75,7 @@ void FixFreezeKokkos<DeviceType>::post_force(int vflag)
OriginalForce original;
Kokkos::parallel_reduce(nlocal, *this, original);
copymode = 0;
-
+
foriginal[0] = original.values[0];
foriginal[1] = original.values[1];
foriginal[2] = original.values[2];
diff --git a/src/KOKKOS/fix_freeze_kokkos.h b/src/KOKKOS/fix_freeze_kokkos.h
index 193e0119958ec44422342a17a9ff8a22855287e0..3b5bc8e437862d378408b161795952103551c4d5 100644
--- a/src/KOKKOS/fix_freeze_kokkos.h
+++ b/src/KOKKOS/fix_freeze_kokkos.h
@@ -26,7 +26,7 @@ FixStyle(freeze/kk/host,FixFreezeKokkos<LMPHostType>)
#include "kokkos_type.h"
namespace LAMMPS_NS {
-
+
template<class DeviceType>
class FixFreezeKokkos : public FixFreeze {
public:
@@ -66,7 +66,7 @@ class FixFreezeKokkos : public FixFreeze {
KOKKOS_INLINE_FUNCTION
void operator()(const int i, OriginalForce &original) const;
-
+
private:
typename ArrayTypes<DeviceType>::t_f_array f;
typename ArrayTypes<DeviceType>::t_f_array torque;
diff --git a/src/KOKKOS/fix_gravity_kokkos.h b/src/KOKKOS/fix_gravity_kokkos.h
index cc487a0e2dd317f4ee69f344ecc26bdb0eb423e5..9aa9ef803f75e8eb3c3f4e6bdb5db383f17028b6 100644
--- a/src/KOKKOS/fix_gravity_kokkos.h
+++ b/src/KOKKOS/fix_gravity_kokkos.h
@@ -50,7 +50,7 @@ class FixGravityKokkos : public FixGravity {
typename ArrayTypes<DeviceType>::t_int_1d type;
typename ArrayTypes<DeviceType>::t_int_1d mask;
};
-
+
} // namespace LAMMPS_NS
#endif // LMP_FIX_GRAVITY_KOKKOS_H
diff --git a/src/KOKKOS/fix_neigh_history_kokkos.cpp b/src/KOKKOS/fix_neigh_history_kokkos.cpp
index d481c20818f1362ae0894b1fb00d2b014699d5cb..ea0bd138f4f959dee327cadc4ec82ea503dbafcf 100644
--- a/src/KOKKOS/fix_neigh_history_kokkos.cpp
+++ b/src/KOKKOS/fix_neigh_history_kokkos.cpp
@@ -77,7 +77,7 @@ template <class DeviceType>
void FixNeighHistoryKokkos<DeviceType>::pre_exchange()
{
copymode = 1;
-
+
h_resize() = 1;
while (h_resize() > 0) {
FixNeighHistoryKokkosZeroPartnerCountFunctor<DeviceType> zero(this);
@@ -156,7 +156,7 @@ template <class DeviceType>
void FixNeighHistoryKokkos<DeviceType>::post_neighbor()
{
tag = atomKK->k_tag.view<DeviceType>();
-
+
int inum = pair->list->inum;
NeighListKokkos<DeviceType>* k_list = static_cast<NeighListKokkos<DeviceType>*>(pair->list);
d_numneigh = k_list->d_numneigh;
@@ -179,7 +179,7 @@ void FixNeighHistoryKokkos<DeviceType>::post_neighbor()
}
copymode = 1;
-
+
FixNeighHistoryKokkosPostNeighborFunctor<DeviceType> f(this);
Kokkos::parallel_for(inum,f);
@@ -251,7 +251,7 @@ void FixNeighHistoryKokkos<DeviceType>::grow_arrays(int nmax)
k_npartner.template sync<LMPHostType>(); // force reallocation on host
k_partner.template sync<LMPHostType>();
k_valuepartner.template sync<LMPHostType>();
-
+
memoryKK->grow_kokkos(k_npartner,npartner,nmax,"neighbor_history:npartner");
memoryKK->grow_kokkos(k_partner,partner,nmax,maxpartner,"neighbor_history:partner");
memoryKK->grow_kokkos(k_valuepartner,valuepartner,nmax,dnum*maxpartner,"neighbor_history:valuepartner");
diff --git a/src/KOKKOS/fix_neigh_history_kokkos.h b/src/KOKKOS/fix_neigh_history_kokkos.h
index d5bb1c3971d5dbea19cca627e0314ae1c4b5cb35..ba594a567fe18cf0c4ff447206b993275779b6c0 100644
--- a/src/KOKKOS/fix_neigh_history_kokkos.h
+++ b/src/KOKKOS/fix_neigh_history_kokkos.h
@@ -61,11 +61,11 @@ class FixNeighHistoryKokkos : public FixNeighHistory {
typename ArrayTypes<DeviceType>::t_neighbors_2d d_neighbors;
typename ArrayTypes<DeviceType>::t_int_1d_randomread d_ilist;
typename ArrayTypes<DeviceType>::t_int_1d_randomread d_numneigh;
-
+
typename ArrayTypes<DeviceType>::t_tagint_1d tag;
typename ArrayTypes<DeviceType>::t_int_1d d_npartner;
typename ArrayTypes<DeviceType>::t_tagint_2d d_partner;
- typename ArrayTypes<DeviceType>::t_float_2d d_valuepartner;
+ typename ArrayTypes<DeviceType>::t_float_2d d_valuepartner;
typename ArrayTypes<DeviceType>::t_int_scalar d_resize;
typename ArrayTypes<LMPHostType>::t_int_scalar h_resize;
diff --git a/src/KOKKOS/fix_nve_sphere_kokkos.cpp b/src/KOKKOS/fix_nve_sphere_kokkos.cpp
index d636f56b20747656a50b6f12ec529d4e37724ef0..9c408d0630a93f4119db6edcdef5d38ee0cb75fa 100644
--- a/src/KOKKOS/fix_nve_sphere_kokkos.cpp
+++ b/src/KOKKOS/fix_nve_sphere_kokkos.cpp
@@ -75,7 +75,7 @@ void FixNVESphereKokkos<DeviceType>::initial_integrate(int vflag)
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
- FixNVESphereKokkosInitialIntegrateFunctor<DeviceType> f(this);
+ FixNVESphereKokkosInitialIntegrateFunctor<DeviceType> f(this);
Kokkos::parallel_for(nlocal,f);
}
@@ -95,7 +95,7 @@ void FixNVESphereKokkos<DeviceType>::initial_integrate_item(const int i) const
x(i,0) += dtv * v(i,0);
x(i,1) += dtv * v(i,1);
x(i,2) += dtv * v(i,2);
-
+
const double dtirotate = dtfrotate / (radius(i)*radius(i)*rmass(i));
omega(i,0) += dtirotate * torque(i,0);
omega(i,1) += dtirotate * torque(i,1);
@@ -139,7 +139,7 @@ void FixNVESphereKokkos<DeviceType>::final_integrate_item(const int i) const
v(i,0) += dtfm * f(i,0);
v(i,1) += dtfm * f(i,1);
v(i,2) += dtfm * f(i,2);
-
+
const double dtirotate = dtfrotate / (radius(i)*radius(i)*rmass(i));
omega(i,0) += dtirotate * torque(i,0);
omega(i,1) += dtirotate * torque(i,1);
diff --git a/src/KOKKOS/fix_nve_sphere_kokkos.h b/src/KOKKOS/fix_nve_sphere_kokkos.h
index 382e530319f85ec52945dc90ea25bf47fe7f1b7f..87a1835eb765a08c58b0c820973ce768c0071d9b 100644
--- a/src/KOKKOS/fix_nve_sphere_kokkos.h
+++ b/src/KOKKOS/fix_nve_sphere_kokkos.h
@@ -26,7 +26,7 @@ FixStyle(nve/sphere/kk/host,FixNVESphereKokkos<LMPHostType>)
#include "kokkos_type.h"
namespace LAMMPS_NS {
-
+
template<class DeviceType>
class FixNVESphereKokkos : public FixNVESphere {
public:
@@ -36,7 +36,7 @@ class FixNVESphereKokkos : public FixNVESphere {
void init();
void initial_integrate(int);
void final_integrate();
-
+
KOKKOS_INLINE_FUNCTION
void initial_integrate_item(const int i) const;
KOKKOS_INLINE_FUNCTION
diff --git a/src/KOKKOS/kokkos.h b/src/KOKKOS/kokkos.h
index e1e17a425a3c3e99fff4f615cfa958431e0448ea..cd429d5c1cb343924c16347a7c9dc44002ef34ff 100644
--- a/src/KOKKOS/kokkos.h
+++ b/src/KOKKOS/kokkos.h
@@ -46,10 +46,10 @@ class KokkosLMP : protected Pointers {
int need_dup()
{
int value = 0;
-
+
if (neighflag == HALFTHREAD)
value = NeedDup<HALFTHREAD,DeviceType>::value;
-
+
return value;
}
diff --git a/src/KOKKOS/pair_gran_hooke_history_kokkos.cpp b/src/KOKKOS/pair_gran_hooke_history_kokkos.cpp
index cd8beed583a4f29e3990a5723bed0e17cb243bca..09e6c709a464d29ff2da4d123bf1f1424b2cbf54 100644
--- a/src/KOKKOS/pair_gran_hooke_history_kokkos.cpp
+++ b/src/KOKKOS/pair_gran_hooke_history_kokkos.cpp
@@ -331,7 +331,7 @@ void PairGranHookeHistoryKokkos<DeviceType>::operator()(TagPairGranHookeHistoryC
const LMP_FLOAT imass = rmass[i];
const LMP_FLOAT irad = radius[i];
const int jnum = d_numneigh_touch[i];
-
+
F_FLOAT fx_i = 0.0;
F_FLOAT fy_i = 0.0;
F_FLOAT fz_i = 0.0;
@@ -343,7 +343,7 @@ void PairGranHookeHistoryKokkos<DeviceType>::operator()(TagPairGranHookeHistoryC
for (int jj = 0; jj < jnum; jj++) {
const int m = d_neighbors_touch(i, jj);
const int j = d_neighbors(i, m) & NEIGHMASK;
-
+
const X_FLOAT delx = xtmp - x(j,0);
const X_FLOAT dely = ytmp - x(j,1);
const X_FLOAT delz = ztmp - x(j,2);
@@ -363,16 +363,16 @@ void PairGranHookeHistoryKokkos<DeviceType>::operator()(TagPairGranHookeHistoryC
V_FLOAT vr1 = v(i,0) - v(j,0);
V_FLOAT vr2 = v(i,1) - v(j,1);
V_FLOAT vr3 = v(i,2) - v(j,2);
-
+
// normal component
V_FLOAT vnnr = vr1*delx + vr2*dely + vr3*delz;
V_FLOAT vn1 = delx*vnnr * rsqinv;
V_FLOAT vn2 = dely*vnnr * rsqinv;
V_FLOAT vn3 = delz*vnnr * rsqinv;
-
+
// tangential component
-
+
V_FLOAT vt1 = vr1 - vn1;
V_FLOAT vt2 = vr2 - vn2;
V_FLOAT vt3 = vr3 - vn3;
@@ -467,7 +467,7 @@ void PairGranHookeHistoryKokkos<DeviceType>::operator()(TagPairGranHookeHistoryC
torquex_i -= irad*tor1;
torquey_i -= irad*tor2;
torquez_i -= irad*tor3;
-
+
if (NEWTON_PAIR || j < nlocal) {
a_f(j,0) -= fx;
a_f(j,1) -= fy;
@@ -550,7 +550,7 @@ void PairGranHookeHistoryKokkos<DeviceType>::ev_tally_xyz_atom(EV_FLOAT &ev, int
F_FLOAT fx, F_FLOAT fy, F_FLOAT fz,
X_FLOAT delx, X_FLOAT dely, X_FLOAT delz) const
{
- Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > v_vatom = k_vatom.view<DeviceType>();
+ Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > v_vatom = k_vatom.view<DeviceType>();
F_FLOAT v[6];
diff --git a/src/KOKKOS/pair_gran_hooke_history_kokkos.h b/src/KOKKOS/pair_gran_hooke_history_kokkos.h
index 822b9203a46ee5945c01eec2e353ca67be42385b..8d1778e09189a167f54e5126a470d25e27a6d07e 100644
--- a/src/KOKKOS/pair_gran_hooke_history_kokkos.h
+++ b/src/KOKKOS/pair_gran_hooke_history_kokkos.h
@@ -30,7 +30,7 @@ namespace LAMMPS_NS {
template <class DeviceType>
class FixNeighHistoryKokkos;
-
+
template<int NEIGHFLAG, int NEWTON_PAIR, int EVFLAG, int SHEARUPDATE>
struct TagPairGranHookeHistoryCompute {};
@@ -68,7 +68,7 @@ class PairGranHookeHistoryKokkos : public PairGranHookeHistory {
void ev_tally_xyz_atom(EV_FLOAT &ev, int i, int j,
F_FLOAT fx, F_FLOAT fy, F_FLOAT fz,
X_FLOAT delx, X_FLOAT dely, X_FLOAT delz) const;
-
+
protected:
typename AT::t_x_array_randomread x;
typename AT::t_x_array c_x;
@@ -96,7 +96,7 @@ class PairGranHookeHistoryKokkos : public PairGranHookeHistory {
typename AT::t_neighbors_2d d_neighbors_touch;
typename AT::t_int_1d d_numneigh_touch;
-
+
int newton_pair;
double special_lj[4];
diff --git a/src/KOKKOS/pair_reaxc_kokkos.cpp b/src/KOKKOS/pair_reaxc_kokkos.cpp
index 46ecddfd83849f0f0b6fcfcfa2d5aa301faa1758..fc4298bf6dbe7ad68a43d1e551a5cb5d139e556e 100644
--- a/src/KOKKOS/pair_reaxc_kokkos.cpp
+++ b/src/KOKKOS/pair_reaxc_kokkos.cpp
@@ -854,7 +854,7 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
//dup_Cdbo = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterDuplicated>(d_Cdbo);
//dup_Cdbopi = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterDuplicated>(d_Cdbopi);
//dup_Cdbopi2 = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterDuplicated>(d_Cdbopi2);
- } else {
+ } else {
ndup_CdDelta = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterNonDuplicated>(d_CdDelta);
//ndup_Cdbo = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterNonDuplicated>(d_Cdbo);
//ndup_Cdbopi = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterNonDuplicated>(d_Cdbopi);
diff --git a/src/KSPACE/ewald.cpp b/src/KSPACE/ewald.cpp
index a24e3e123db7e38baab99999c062710e0a6bb681..283c672bad90a6ea892cbb790e4ff6c2738c4c81 100644
--- a/src/KSPACE/ewald.cpp
+++ b/src/KSPACE/ewald.cpp
@@ -72,7 +72,7 @@ void Ewald::settings(int narg, char **arg)
if (narg != 1) error->all(FLERR,"Illegal kspace_style ewald command");
accuracy_relative = fabs(force->numeric(FLERR,arg[0]));
-}
+}
/* ----------------------------------------------------------------------
free all memory
diff --git a/src/LATTE/fix_latte.cpp b/src/LATTE/fix_latte.cpp
index a89be57beda1419af68bad20e494bfa6d26a3bf9..d1a96d32c67a72f6cd8437ba8395253974248cbe 100644
--- a/src/LATTE/fix_latte.cpp
+++ b/src/LATTE/fix_latte.cpp
@@ -299,7 +299,7 @@ void FixLatte::post_force(int vflag)
if (coulomb) forces = &flatte[0][0];
else forces = &atom->f[0][0];
int maxiter = -1;
-
+
latte(flags,&natoms,coords,type,&ntypes,mass,boxlo,boxhi,&domain->xy,
&domain->xz,&domain->yz,forces,&maxiter,&latte_energy,
&atom->v[0][0],&update->dt,virial,&newsystem,&latteerror);
diff --git a/src/MANYBODY/pair_atm.cpp b/src/MANYBODY/pair_atm.cpp
index a6e52faeba2428c41681d4ee060aa4dd0d4ea088..e3be72443e5dd8d876bc4fa350c19b1565369f21 100644
--- a/src/MANYBODY/pair_atm.cpp
+++ b/src/MANYBODY/pair_atm.cpp
@@ -272,7 +272,7 @@ double PairATM::init_one(int i, int j)
int ntypes = atom->ntypes;
for (int k = j; k <= ntypes; k++)
- nu[i][k][j] = nu[j][i][k] = nu[j][k][i] = nu[k][i][j] = nu[k][j][i] =
+ nu[i][k][j] = nu[j][i][k] = nu[j][k][i] = nu[k][i][j] = nu[k][j][i] =
nu[i][j][k];
return cut_global;
@@ -290,8 +290,8 @@ void PairATM::write_restart(FILE *fp)
for (i = 1; i <= atom->ntypes; i++) {
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
- if (setflag[i][j])
- for (k = j; k <= atom->ntypes; k++)
+ if (setflag[i][j])
+ for (k = j; k <= atom->ntypes; k++)
fwrite(&nu[i][j][k],sizeof(double),1,fp);
}
}
@@ -361,12 +361,12 @@ void PairATM::interaction_ddd(double nu, double r6,
rrk = rjk[0]*rik[0] + rjk[1]*rik[1] + rjk[2]*rik[2];
rrr = 5.0*rri*rrj*rrk;
for (int i = 0; i < 3; i++) {
- fj[i] = rrj*(rrk - rri)*rik[i] -
- (rrk*rri - rjk2*rik2 + rrr/rij2) * rij[i] +
+ fj[i] = rrj*(rrk - rri)*rik[i] -
+ (rrk*rri - rjk2*rik2 + rrr/rij2) * rij[i] +
(rrk*rri - rik2*rij2 + rrr/rjk2) * rjk[i];
fj[i] *= 3.0*r5inv;
- fk[i] = rrk*(rri + rrj)*rij[i] +
- (rri*rrj + rik2*rij2 - rrr/rjk2) * rjk[i] +
+ fk[i] = rrk*(rri + rrj)*rij[i] +
+ (rri*rrj + rik2*rij2 - rrr/rjk2) * rjk[i] +
(rri*rrj + rij2*rjk2 - rrr/rik2) * rik[i];
fk[i] *= 3.0*r5inv;
}
diff --git a/src/MANYBODY/pair_atm.h b/src/MANYBODY/pair_atm.h
index 70883a81c76fa62fd05ae6aa4d1d1df9572da845..8a9d38ec3b0fd9b20c0f263d4275027c3484175a 100644
--- a/src/MANYBODY/pair_atm.h
+++ b/src/MANYBODY/pair_atm.h
@@ -43,7 +43,7 @@ class PairATM : public Pair {
double ***nu;
void allocate();
- void interaction_ddd(double, double, double, double, double, double *,
+ void interaction_ddd(double, double, double, double, double, double *,
double *, double *, double *, double *, int, double &);
};
diff --git a/src/MANYBODY/pair_gw.cpp b/src/MANYBODY/pair_gw.cpp
index f2d3b67eb055e20701104afc645211d068912e0f..7649090a99221238f8edc4f5370e543ac6f16912 100644
--- a/src/MANYBODY/pair_gw.cpp
+++ b/src/MANYBODY/pair_gw.cpp
@@ -521,7 +521,7 @@ void PairGW::setup_params()
for (m = 0; m < nparams; m++) {
if (i == params[m].ielement && j == params[m].jelement &&
k == params[m].kelement) {
- if (n >= 0)
+ if (n >= 0)
error->all(FLERR,"Potential file has duplicate entry");
n = m;
}
diff --git a/src/MESSAGE/fix_client_md.cpp b/src/MESSAGE/fix_client_md.cpp
index aca5cd41f9184c947e102c6dc21b33d9e5e2d135..9c1bfcc7967a2fe256d7942c2c0d207dbbd08290 100644
--- a/src/MESSAGE/fix_client_md.cpp
+++ b/src/MESSAGE/fix_client_md.cpp
@@ -40,11 +40,11 @@ enum{FORCES=1,ENERGY,PRESSURE,ERROR};
FixClientMD::FixClientMD(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
- if (lmp->clientserver != 1)
+ if (lmp->clientserver != 1)
error->all(FLERR,"Fix client/md requires LAMMPS be running as a client");
if (!atom->map_style) error->all(FLERR,"Fix client/md requires atom map");
- if (sizeof(tagint) != 4)
+ if (sizeof(tagint) != 4)
error->all(FLERR,"Fix client/md requires 4-byte atom IDs");
if (strcmp(update->unit_style,"real") == 0) units = REAL;
@@ -306,7 +306,7 @@ void FixClientMD::receive_fev(int vflag)
}
eng = econvert * cs->unpack_double(ENERGY);
-
+
if (vflag) {
double *v = (double *) cs->unpack(PRESSURE);
diff --git a/src/MESSAGE/message.cpp b/src/MESSAGE/message.cpp
index 329ce1fbd9e46fec5e0fd5665659f794431d0065..e9bff7d38ab510759f5dc97869e824afbd97f0df 100644
--- a/src/MESSAGE/message.cpp
+++ b/src/MESSAGE/message.cpp
@@ -51,13 +51,13 @@ void Message::command(int narg, char **arg)
strcmp(arg[2],"mpi/two") == 0) {
if (narg != 4) error->all(FLERR,"Illegal message command");
lmp->cslib = new CSlib(clientserver-1,arg[2],arg[3],&world);
-
+
} else if (strcmp(arg[2],"mpi/one") == 0) {
if (narg != 3) error->all(FLERR,"Illegal message command");
- if (!lmp->cscomm)
+ if (!lmp->cscomm)
error->all(FLERR,"Message mpi/one mode, but -mpi cmdline arg not used");
lmp->cslib = new CSlib(clientserver-1,arg[2],&lmp->cscomm,&world);
-
+
} else error->all(FLERR,"Illegal message command");
// perform initial handshake between client and server
@@ -75,16 +75,16 @@ void Message::command(int narg, char **arg)
int *fieldID,*fieldtype,*fieldlen;
int msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
if (msgID != 0) error->one(FLERR,"Bad initial client/server handshake");
-
+
} else {
int nfield;
int *fieldID,*fieldtype,*fieldlen;
int msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
if (msgID != 0) error->one(FLERR,"Bad initial client/server handshake");
char *pstr = cs->unpack_string(1);
- if (strcmp(pstr,arg[1]) != 0)
+ if (strcmp(pstr,arg[1]) != 0)
error->one(FLERR,"Mismatch in client/server protocol");
-
+
cs->send(0,0);
}
}
diff --git a/src/MESSAGE/server_mc.cpp b/src/MESSAGE/server_mc.cpp
index 8a7344e86b6930483c5079e413372b578dff994c..8e9a2979126de10caf6da538d9fafcbad28c37af 100644
--- a/src/MESSAGE/server_mc.cpp
+++ b/src/MESSAGE/server_mc.cpp
@@ -128,7 +128,7 @@ void ServerMC::loop()
update->nsteps = nsteps;
update->firststep = update->ntimestep;
update->laststep = update->ntimestep + nsteps;
-
+
update->integrate->setup(1);
update->integrate->run(nsteps);
diff --git a/src/MESSAGE/server_md.cpp b/src/MESSAGE/server_md.cpp
index aa771b7d4654b05469dd62b5d42e486532455323..8debd3a98791c8c3e65668f7f0add542f158cb01 100644
--- a/src/MESSAGE/server_md.cpp
+++ b/src/MESSAGE/server_md.cpp
@@ -100,7 +100,7 @@ void ServerMD::loop()
if (msgID < 0) break;
// SETUP receive at beginning of each run
- // required fields: DIM, PERIODICTY, ORIGIN, BOX,
+ // required fields: DIM, PERIODICTY, ORIGIN, BOX,
// NATOMS, NTYPES, TYPES, COORDS
// optional fields: others in enum above
@@ -152,7 +152,7 @@ void ServerMD::loop()
} else error->all(FLERR,"Server md setup field unknown");
}
- if (dim == 0 || !periodicity || !origin || !box ||
+ if (dim == 0 || !periodicity || !origin || !box ||
natoms < 0 || ntypes < 0 || !types || !coords)
error->all(FLERR,"Required server md setup field not received");
@@ -164,8 +164,8 @@ void ServerMD::loop()
// reset box, global and local
// reset proc decomposition
-
- if ((box[3] != 0.0 || box[6] != 0.0 || box[7] != 0.0) &&
+
+ if ((box[3] != 0.0 || box[6] != 0.0 || box[7] != 0.0) &&
domain->triclinic == 0)
error->all(FLERR,"Server md is not initialized for a triclinic box");
@@ -194,7 +194,7 @@ void ServerMD::loop()
int ntotal;
MPI_Allreduce(&atom->nlocal,&ntotal,1,MPI_INT,MPI_SUM,world);
- if (ntotal != natoms)
+ if (ntotal != natoms)
error->all(FLERR,"Server md atom count does not match client");
atom->map_init();
@@ -247,7 +247,7 @@ void ServerMD::loop()
// reset global/local box like FixDeform at end_of_step()
if (origin && box) {
- if ((box[3] != 0.0 || box[6] != 0.0 || box[7] != 0.0) &&
+ if ((box[3] != 0.0 || box[6] != 0.0 || box[7] != 0.0) &&
domain->triclinic == 0)
error->all(FLERR,"Server md is not initialized for a triclinic box");
box_change(origin,box);
@@ -348,7 +348,7 @@ void ServerMD::send_fev(int msgID)
CSlib *cs = (CSlib *) lmp->cslib;
cs->send(msgID,3);
-
+
double *forces = NULL;
if (atom->nlocal) {
if (units != REAL) forces = &atom->f[0][0];
@@ -370,7 +370,7 @@ void ServerMD::send_fev(int msgID)
MPI_Allreduce(&eng,&engall,1,MPI_DOUBLE,MPI_SUM,world);
engall *= econvert;
cs->pack_double(ENERGY,engall);
-
+
double v[6],vall[6];
for (int i = 0; i < 6; i++)
v[i] = force->pair->virial[i];
diff --git a/src/POEMS/fix_poems.cpp b/src/POEMS/fix_poems.cpp
index a01878bffd23d5e59224eac7d5eb310dd6912024..41cfcede345357b2d9745f5365a39f1112df01eb 100644
--- a/src/POEMS/fix_poems.cpp
+++ b/src/POEMS/fix_poems.cpp
@@ -366,7 +366,7 @@ void FixPOEMS::init()
int pflag = 0;
for (i = 0; i < modify->nfix; i++) {
if (strcmp(modify->fix[i]->style,"poems") == 0) pflag = 1;
- if (pflag && (modify->fmask[i] & POST_FORCE) &&
+ if (pflag && (modify->fmask[i] & POST_FORCE) &&
!modify->fix[i]->rigid_flag) {
char str[128];
snprintf(str,128,"Fix %s alters forces after fix poems",modify->fix[i]->id);
diff --git a/src/REPLICA/fix_hyper_global.cpp b/src/REPLICA/fix_hyper_global.cpp
index d119083a3bdd020af9f6c9493a8e9efd8656a703..d235b06dc02f30e6f6c9dafeb137d714872feb31 100644
--- a/src/REPLICA/fix_hyper_global.cpp
+++ b/src/REPLICA/fix_hyper_global.cpp
@@ -44,7 +44,7 @@ using namespace FixConst;
FixHyperGlobal::FixHyperGlobal(LAMMPS *lmp, int narg, char **arg) :
FixHyper(lmp, narg, arg), blist(NULL), xold(NULL), tagold(NULL)
{
- if (atom->map_style == 0)
+ if (atom->map_style == 0)
error->all(FLERR,"Fix hyper/global command requires atom map");
if (narg != 7) error->all(FLERR,"Illegal fix hyper/global command");
@@ -392,7 +392,7 @@ void FixHyperGlobal::grow_bond()
maxbond += DELTA;
if (maxbond < 0 || maxbond > MAXSMALLINT)
error->one(FLERR,"Fix hyper/local per-processor bond count is too big");
- blist = (OneBond *)
+ blist = (OneBond *)
memory->srealloc(blist,maxbond*sizeof(OneBond),"hyper/local:blist");
}
@@ -429,7 +429,7 @@ double FixHyperGlobal::compute_vector(int i)
// i = 7 = max bond length during this run
// i = 8 = cummulative hyper time since fix created
- // i = 9 = cummulative # of event timesteps since fix created
+ // i = 9 = cummulative # of event timesteps since fix created
// i = 10 = cummulative # of atoms in events since fix created
if (i == 0) return outvec[1];
@@ -478,7 +478,7 @@ double FixHyperGlobal::query(int i)
{
if (i == 1) return compute_vector(8); // cummulative hyper time
if (i == 2) return compute_vector(9); // nevent
- if (i == 3) return compute_vector(10); // nevent_atom
+ if (i == 3) return compute_vector(10); // nevent_atom
if (i == 4) return compute_vector(4); // ave bonds/atom
if (i == 5) return compute_vector(6); // maxdrift
if (i == 6) return compute_vector(7); // maxbondlen
diff --git a/src/REPLICA/fix_hyper_local.cpp b/src/REPLICA/fix_hyper_local.cpp
index d4fa08f261bd64250f3d6ac5a444571605e314b2..25dd3d72af533724de4022f4de85b6a18b310f8f 100644
--- a/src/REPLICA/fix_hyper_local.cpp
+++ b/src/REPLICA/fix_hyper_local.cpp
@@ -54,7 +54,7 @@ FixHyperLocal::FixHyperLocal(LAMMPS *lmp, int narg, char **arg) :
// local index vs global ID in same variable
// maybe need to declare them all tagint, not int
- if (atom->map_style == 0)
+ if (atom->map_style == 0)
error->all(FLERR,"Fix hyper/local command requires atom map");
if (sizeof(tagint) != sizeof(int))
@@ -81,7 +81,7 @@ FixHyperLocal::FixHyperLocal(LAMMPS *lmp, int narg, char **arg) :
alpha_user = force->numeric(FLERR,arg[8]);
boosttarget = force->numeric(FLERR,arg[9]);
- if (cutbond < 0.0 || qfactor < 0.0 || vmax < 0.0 ||
+ if (cutbond < 0.0 || qfactor < 0.0 || vmax < 0.0 ||
tequil <= 0.0 || dcut <= 0.0 || alpha_user <= 0.0 || boosttarget < 1.0)
error->all(FLERR,"Illegal fix hyper/local command");
@@ -107,7 +107,7 @@ FixHyperLocal::FixHyperLocal(LAMMPS *lmp, int narg, char **arg) :
histo_count = force->inumeric(FLERR,arg[iarg+2]);
histo_delta = force->numeric(FLERR,arg[iarg+3]);
histo_print = force->inumeric(FLERR,arg[iarg+4]);
- if (histo_every <= 0 || histo_count % 2 ||
+ if (histo_every <= 0 || histo_count % 2 ||
histo_delta <= 0.0 || histo_print <= 0)
error->all(FLERR,"Illegal fix hyper/local command");
iarg += 5;
@@ -276,16 +276,16 @@ void FixHyperLocal::init()
// warn if no drift distance added to cutghost
if (firstflag) {
- double cutghost;
- if (force->pair)
+ double cutghost;
+ if (force->pair)
cutghost = MAX(force->pair->cutforce+neighbor->skin,comm->cutghostuser);
- else
+ else
cutghost = comm->cutghostuser;
-
- if (cutghost < dcut)
+
+ if (cutghost < dcut)
error->all(FLERR,"Fix hyper/local bond cutoff exceeds ghost atom range - "
"use comm_modify cutoff command");
- if (cutghost < dcut+cutbond/2.0 && me == 0)
+ if (cutghost < dcut+cutbond/2.0 && me == 0)
error->warning(FLERR,"Fix hyper/local ghost atom range "
"may not allow for atom drift between events");
}
@@ -371,8 +371,8 @@ void FixHyperLocal::pre_neighbor()
missing_coeff += bonds[i][m].boostcoeff;
if (lostbond != IGNORE) {
char str[128];
- sprintf(str,"Fix hyper/local bond info missing for bond "
- TAGINT_FORMAT "," TAGINT_FORMAT
+ sprintf(str,"Fix hyper/local bond info missing for bond "
+ TAGINT_FORMAT "," TAGINT_FORMAT
" with coeff %g at step " BIGINT_FORMAT,
atom->tag[i],bonds[i][m].jtag,bonds[i][m].boostcoeff,
update->ntimestep);
@@ -520,7 +520,7 @@ void FixHyperLocal::pre_reverse(int /* eflag */, int /* vflag */)
i = old2now[iold];
emax = maxstrain[i];
-
+
for (jj = 0; jj < jnum; jj++) {
jold = jlist[jj];
j = old2now[jold];
@@ -722,13 +722,13 @@ void FixHyperLocal::pre_reverse(int /* eflag */, int /* vflag */)
if (me == 0) {
if (screen) {
fprintf(screen,"Histogram of bias coeffs:\n");
- for (i = 0; i < histo_count+2; i++)
+ for (i = 0; i < histo_count+2; i++)
fprintf(screen," %g",1.0*allhisto[i]/total);
fprintf(screen,"\n");
}
if (logfile) {
fprintf(logfile,"Histogram of bias coeffs:\n");
- for (i = 0; i < histo_count+2; i++)
+ for (i = 0; i < histo_count+2; i++)
fprintf(logfile," %g",1.0*allhisto[i]/total);
fprintf(logfile,"\n");
}
@@ -790,7 +790,7 @@ void FixHyperLocal::pre_reverse(int /* eflag */, int /* vflag */)
if (checkcoeff && update->ntimestep % checkcoeff_every == 0) {
int jb,jbonds;
-
+
for (i = 0; i < nlocal; i++) {
nbond = numbond[i];
for (m = 0; m < nbond; m++) {
@@ -802,9 +802,9 @@ void FixHyperLocal::pre_reverse(int /* eflag */, int /* vflag */)
jbonds = numbond[j];
for (jb = 0; jb < jbonds; jb++)
if (bonds[j][jb].jtag == itag) break;
- if (jb == jbonds)
+ if (jb == jbonds)
error->one(FLERR,"Fix hyper/local could not find duplicate bond");
- if (bonds[i][m].boostcoeff != bonds[j][jb].boostcoeff)
+ if (bonds[i][m].boostcoeff != bonds[j][jb].boostcoeff)
checkcoeff_count++;
}
}
@@ -885,7 +885,7 @@ void FixHyperLocal::build_bond_list(int natom)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
while (1) {
bonds = (OneBond **) memory->create(bonds,nmax,maxbondperatom,
"hyper/local:bonds");
@@ -941,7 +941,7 @@ void FixHyperLocal::build_bond_list(int natom)
nbond++;
continue;
}
-
+
bonds[i][nbond].r0 = sqrt(rsq);
bonds[i][nbond].jtag = tag[j];
bonds[i][nbond].j = j;
@@ -998,7 +998,7 @@ void FixHyperLocal::build_bond_list(int natom)
/* ---------------------------------------------------------------------- */
-int FixHyperLocal::pack_forward_comm(int n, int *list, double *buf,
+int FixHyperLocal::pack_forward_comm(int n, int *list, double *buf,
int /* pbc_flag */, int * /* pbc */)
{
int i,j,m;
@@ -1233,7 +1233,7 @@ double FixHyperLocal::compute_vector(int i)
// i = 9 = average bias potential for all bonds during this run
// i = 10 = max bias potential for any bond during this run
// i = 11 = min bias potential for any bond during this run
- // i = 12 = max dist from my box of any ghost atom with
+ // i = 12 = max dist from my box of any ghost atom with
// maxstain < qfactor during this run
// i = 13 = max dist from my box of any ghost atom with
// any maxstrain during this run
@@ -1245,7 +1245,7 @@ double FixHyperLocal::compute_vector(int i)
// i = 18 = count of non-matching bias coefficients found during this run
// i = 19 = cummulative hyper time
- // i = 20 = cummulative # of event timesteps since fix created
+ // i = 20 = cummulative # of event timesteps since fix created
// i = 21 = cummulative # of atoms in events since fix created
// i = 22 = cummulative # of new bonds formed since fix created
@@ -1394,7 +1394,7 @@ double FixHyperLocal::query(int i)
{
if (i == 1) return compute_vector(19); // cummulative hyper time
if (i == 2) return compute_vector(20); // nevent
- if (i == 3) return compute_vector(21); // nevent_atom
+ if (i == 3) return compute_vector(21); // nevent_atom
if (i == 4) return compute_vector(3); // ave bonds/atom
if (i == 5) return compute_vector(6); // maxdrift
if (i == 6) return compute_vector(7); // maxbondlen
diff --git a/src/REPLICA/fix_hyper_local.h b/src/REPLICA/fix_hyper_local.h
index 967101837e4ea065b40eb6699ffeb3734c93840f..147e3ef1efa47856deb6851b8cd9a4c2a39e1a27 100644
--- a/src/REPLICA/fix_hyper_local.h
+++ b/src/REPLICA/fix_hyper_local.h
@@ -82,7 +82,7 @@ class FixHyperLocal : public FixHyper {
double allboost; // sum of boostcoeff on all bonds on this step
int nnewbond; // running tally of number of new bonds created
- int maxbondperatom; // max # of bonds any atom ever has
+ int maxbondperatom; // max # of bonds any atom ever has
int commflag; // flag for communication mode
int nevent; // # of events that trigger bond rebuild
int nevent_atom; // # of atoms that experienced an event
@@ -115,7 +115,7 @@ class FixHyperLocal : public FixHyper {
double **xold; // coords of owned+ghost atoms when bonds created
tagint *tagold; // global IDs of owned+ghost atoms when b created
-
+
int maxold; // allocated size of old2now
int maxbond; // allocated size of bonds
int old_nall; // nlocal+nghost when old2now was last setup
diff --git a/src/REPLICA/hyper.cpp b/src/REPLICA/hyper.cpp
index 89409d63fcd995a961b5ff09073f2cfb2f312818..22940de221596d3f8967782130e9e73b7f334185 100644
--- a/src/REPLICA/hyper.cpp
+++ b/src/REPLICA/hyper.cpp
@@ -40,7 +40,7 @@ enum{NOHYPER,GLOBAL,LOCAL};
/* ---------------------------------------------------------------------- */
-Hyper::Hyper(LAMMPS *lmp) :
+Hyper::Hyper(LAMMPS *lmp) :
Pointers(lmp), dumplist(NULL)
{}
@@ -73,7 +73,7 @@ void Hyper::command(int narg, char **arg)
// total # of timesteps must be multiple of t_event
- if (t_event <= 0)
+ if (t_event <= 0)
error->all(FLERR,"Invalid t_event in hyper command");
if (nsteps % t_event)
error->all(FLERR,"Hyper nsteps must be multiple of t_event");
@@ -209,7 +209,7 @@ void Hyper::command(int narg, char **arg)
dynamics(t_event,time_dynamics);
fix_event->store_state_quench();
quench(0);
-
+
ecount = compute_event->all_events();
if (ecount) {
@@ -226,7 +226,7 @@ void Hyper::command(int narg, char **arg)
fix_event->store_event();
if (hyperenable) fix_hyper->build_bond_list(ecount);
}
-
+
fix_event->restore_state_quench();
istep = update->ntimestep - update->beginstep;
}
@@ -519,7 +519,7 @@ void Hyper::options(int narg, char **arg)
if (iarg+2 > narg) error->all(FLERR,"Illegal hyper command");
dumpflag = 1;
int idump = output->find_dump(arg[iarg+1]);
- if (idump < 0)
+ if (idump < 0)
error->all(FLERR,"Dump ID in hyper command does not exist");
memory->grow(dumplist,ndump+1,"hyper:dumplist");
dumplist[ndump++] = idump;
diff --git a/src/RIGID/fix_ehex.h b/src/RIGID/fix_ehex.h
index b606330f11ae1b75e2e7836354de02806ac559ee..e29ddac1352bc4119aca6b6ad1e92481b829c6c0 100644
--- a/src/RIGID/fix_ehex.h
+++ b/src/RIGID/fix_ehex.h
@@ -75,7 +75,7 @@ class FixEHEX : public Fix {
/* ERROR/WARNING messages:
-E: Illegal fix ehex command: wrong number of parameters
+E: Illegal fix ehex command: wrong number of parameters
UNDOCUMENTED
@@ -87,11 +87,11 @@ E: Region ID for fix ehex does not exist
Self-explanatory.
-E: Illegal fix ehex keyword
+E: Illegal fix ehex keyword
UNDOCUMENTED
-E: You can only use the keyword 'com' together with the keyword 'constrain'
+E: You can only use the keyword 'com' together with the keyword 'constrain'
UNDOCUMENTED
diff --git a/src/RIGID/fix_rattle.h b/src/RIGID/fix_rattle.h
index a0405bbdcc6c052955418af76ad846cfaa8ba568..48edaef37981a0df5d437f394f722eb825028545 100644
--- a/src/RIGID/fix_rattle.h
+++ b/src/RIGID/fix_rattle.h
@@ -79,7 +79,7 @@ class FixRattle : public FixShake {
/* ERROR/WARNING messages:
-W: Fix rattle should come after all other integration fixes
+W: Fix rattle should come after all other integration fixes
UNDOCUMENTED
@@ -88,15 +88,15 @@ E: Rattle determinant = 0.0
The determinant of the matrix being solved for a single cluster
specified by the fix rattle command is numerically invalid.
-E: Rattle failed
+E: Rattle failed
UNDOCUMENTED
-E: Coordinate constraints are not satisfied up to desired tolerance
+E: Coordinate constraints are not satisfied up to desired tolerance
UNDOCUMENTED
-E: Velocity constraints are not satisfied up to desired tolerance
+E: Velocity constraints are not satisfied up to desired tolerance
UNDOCUMENTED
diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp
index 39c49ca1c4bfc32c78b6a1edce01bb1284d9a870..8fa43b89ce0b4e6746d02d2b6355c9542147ed19 100644
--- a/src/RIGID/fix_rigid.cpp
+++ b/src/RIGID/fix_rigid.cpp
@@ -174,7 +174,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
MPI_Allreduce(&vmin,&minval,1,MPI_INT,MPI_MIN,world);
molecule = new tagint[nlocal];
for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit)
+ if (mask[i] & groupbit)
molecule[i] = (tagint)((tagint)value[i] - minval + 1);
delete[] value;
} else error->all(FLERR,"Unsupported fix rigid custom property");
@@ -727,7 +727,7 @@ void FixRigid::init()
int rflag = 0;
for (i = 0; i < modify->nfix; i++) {
if (modify->fix[i]->rigid_flag) rflag = 1;
- if (rflag && (modify->fmask[i] & POST_FORCE) &&
+ if (rflag && (modify->fmask[i] & POST_FORCE) &&
!modify->fix[i]->rigid_flag) {
char str[128];
snprintf(str,128,"Fix %s alters forces after fix rigid",modify->fix[i]->id);
@@ -2639,7 +2639,7 @@ int FixRigid::modify_param(int narg, char **arg)
else error->all(FLERR,"Illegal fix_modify command");
// reset fix mask
- // must do here and not in init,
+ // must do here and not in init,
// since modify.cpp::init() uses fix masks before calling fix::init()
for (int i = 0; i < modify->nfix; i++)
diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp
index 44e1870e0a97a2b14201a83bc72bd1939027413c..fb185d7702bce23a75c448160876aa8406976a85 100644
--- a/src/RIGID/fix_rigid_small.cpp
+++ b/src/RIGID/fix_rigid_small.cpp
@@ -566,7 +566,7 @@ void FixRigidSmall::init()
int rflag = 0;
for (i = 0; i < modify->nfix; i++) {
if (modify->fix[i]->rigid_flag) rflag = 1;
- if (rflag && (modify->fmask[i] & POST_FORCE) &&
+ if (rflag && (modify->fmask[i] & POST_FORCE) &&
!modify->fix[i]->rigid_flag) {
char str[128];
snprintf(str,128,"Fix %s alters forces after fix rigid",modify->fix[i]->id);
@@ -3430,7 +3430,7 @@ int FixRigidSmall::modify_param(int narg, char **arg)
else error->all(FLERR,"Illegal fix_modify command");
// reset fix mask
- // must do here and not in init,
+ // must do here and not in init,
// since modify.cpp::init() uses fix masks before calling fix::init()
for (int i = 0; i < modify->nfix; i++)
diff --git a/src/SPIN/pair_spin_dmi.cpp b/src/SPIN/pair_spin_dmi.cpp
index 6f8114042e83370ad8fe66dddee1f82c74226fc0..18682fdb9f91869f6dc0c8369b0b2451560b2e79 100644
--- a/src/SPIN/pair_spin_dmi.cpp
+++ b/src/SPIN/pair_spin_dmi.cpp
@@ -414,7 +414,7 @@ void PairSpinDmi::compute_dmi(int i, int j, double eij[3], double fmi[3], double
compute the mechanical force due to the dmi interaction between atom i and atom j
------------------------------------------------------------------------- */
-void PairSpinDmi::compute_dmi_mech(int i, int j, double rsq, double /*eij*/[3],
+void PairSpinDmi::compute_dmi_mech(int i, int j, double rsq, double /*eij*/[3],
double fi[3], double spi[3], double spj[3])
{
int *type = atom->type;
diff --git a/src/SPIN/pair_spin_exchange.cpp b/src/SPIN/pair_spin_exchange.cpp
index 72a4c0d7de4f52b514a4f4e187bd359a5c4be503..8cd9d33abded41835e8761ff6320416451741901 100644
--- a/src/SPIN/pair_spin_exchange.cpp
+++ b/src/SPIN/pair_spin_exchange.cpp
@@ -134,7 +134,7 @@ void PairSpinExchange::coeff(int narg, char **arg)
count++;
}
}
-
+
if (count == 0) error->all(FLERR,"Incorrect args in pair_style command");
}
@@ -395,7 +395,7 @@ void PairSpinExchange::compute_exchange(int i, int j, double rsq, double fmi[3],
compute the mechanical force due to the exchange interaction between atom i and atom j
------------------------------------------------------------------------- */
-void PairSpinExchange::compute_exchange_mech(int i, int j, double rsq, double eij[3],
+void PairSpinExchange::compute_exchange_mech(int i, int j, double rsq, double eij[3],
double fi[3], double spi[3], double spj[3])
{
int *type = atom->type;
diff --git a/src/USER-INTEL/fix_intel.cpp b/src/USER-INTEL/fix_intel.cpp
index b3055907293918b8e94b51857dab724af89e3be5..67bf33e7518c0ed219e3213dfe40c48def43eb80 100644
--- a/src/USER-INTEL/fix_intel.cpp
+++ b/src/USER-INTEL/fix_intel.cpp
@@ -456,7 +456,7 @@ void FixIntel::pair_init_check(const bool cdmessage)
" exclusions with Intel");
}
#endif
-
+
int need_tag = 0;
if (atom->molecular) need_tag = 1;
diff --git a/src/USER-INTEL/fix_intel.h b/src/USER-INTEL/fix_intel.h
index a01ed18bfed97af04a1d5c69c54e7ce30f80fe1b..3810b57355b26e3f680386a6db7c4ea206df0f18 100644
--- a/src/USER-INTEL/fix_intel.h
+++ b/src/USER-INTEL/fix_intel.h
@@ -83,7 +83,7 @@ class FixIntel : public Fix {
}
inline void set_reduce_flag() { if (_nthreads > 1) _need_reduce = 1; }
inline int lrt() {
- if (force->kspace_match("pppm/intel", 0) && update->whichflag == 1)
+ if (force->kspace_match("pppm/intel", 0) && update->whichflag == 1)
return _lrt;
else return 0;
}
@@ -104,7 +104,7 @@ class FixIntel : public Fix {
int _pair_intel_count, _pair_hybrid_flag;
// These should be removed in subsequent update w/ simpler hybrid arch
int _pair_hybrid_zero, _hybrid_nonpair, _zero_master;
-
+
public:
inline int* get_overflow_flag() { return _overflow_flag; }
inline int* get_off_overflow_flag() { return _off_overflow_flag; }
@@ -215,7 +215,7 @@ class FixIntel : public Fix {
_alignvar(double _stopwatch_offload_pair[1],64);
void _sync_main_arrays(const int prereverse);
-
+
template <class ft>
void reduce_results(ft * _noalias const f_in);
@@ -512,13 +512,13 @@ issues. Please use 14.0.1.106 or 15.1.133 or later.
E: Currently, cannot offload more than one intel style with hybrid.
-Currently, when using offload, hybrid pair styles can only use the intel
+Currently, when using offload, hybrid pair styles can only use the intel
suffix for one of the pair styles.
E: Cannot yet use hybrid styles with Intel offload.
The hybrid pair style configuration is not yet supported when using offload
-within the Intel package. Support is limited to hybrid/overlay or a hybrid
+within the Intel package. Support is limited to hybrid/overlay or a hybrid
style that does not require a skip list.
W: Leaving a core/node free can improve performance for offload
@@ -564,7 +564,7 @@ atoms throughout the simulation.
E: Intel package requires fdotr virial with newton on.
This error can occur with a hybrid pair style that mixes styles that are
-incompatible with the newton pair setting turned on. Try turning the
+incompatible with the newton pair setting turned on. Try turning the
newton pair setting off.
E: Add -DLMP_INTEL_NBOR_COMPAT to build for special_bond exclusions with Intel
diff --git a/src/USER-INTEL/intel_buffers.cpp b/src/USER-INTEL/intel_buffers.cpp
index b7026f90b762793124c42a4c474db8e09b3756a9..c0995b6a9c9e9ac9de50d3905595d6ea2d958299 100644
--- a/src/USER-INTEL/intel_buffers.cpp
+++ b/src/USER-INTEL/intel_buffers.cpp
@@ -255,7 +255,7 @@ void IntelBuffers<flt_t, acc_t>::free_list_local()
#endif
lmp->memory->destroy(cnumneigh);
}
-
+
#ifdef _LMP_INTEL_OFFLOAD
if (_off_map_ilist != NULL) {
const int * ilist = _off_map_ilist;
@@ -295,7 +295,7 @@ void IntelBuffers<flt_t, acc_t>::grow_data3(NeighList *list,
{
const int size = list->get_maxlocal();
int list_num;
- for (list_num = 0; list_num < _n_list_ptrs; list_num++)
+ for (list_num = 0; list_num < _n_list_ptrs; list_num++)
if (_neigh_list_ptrs[list_num].list_ptr == (void*)list) break;
if (list_num == _n_list_ptrs) {
if (_n_list_ptrs == _max_list_ptrs) {
diff --git a/src/USER-INTEL/intel_preprocess.h b/src/USER-INTEL/intel_preprocess.h
index 178a20c6e13396c0e2b9c00ab3814f7aa6a6e8d5..2515e47c52499e3f0db259b8c2e9c5905551c187 100644
--- a/src/USER-INTEL/intel_preprocess.h
+++ b/src/USER-INTEL/intel_preprocess.h
@@ -146,7 +146,7 @@ enum {TIME_PACK, TIME_HOST_NEIGHBOR, TIME_HOST_PAIR, TIME_OFFLOAD_NEIGHBOR,
}
#else
-
+
#define IP_PRE_edge_align(n, esize) \
#endif
diff --git a/src/USER-INTEL/npair_full_bin_ghost_intel.cpp b/src/USER-INTEL/npair_full_bin_ghost_intel.cpp
index 5149b26f2f82019149589a2c307f58fbcdbc82cd..db4b0c50a42da3e8c37f63321b3b9304621abdc2 100644
--- a/src/USER-INTEL/npair_full_bin_ghost_intel.cpp
+++ b/src/USER-INTEL/npair_full_bin_ghost_intel.cpp
@@ -482,7 +482,7 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list,
#endif
}
}
-
+
#ifndef _LMP_INTEL_OFFLOAD
if (exclude) {
int alln = n;
@@ -515,7 +515,7 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list,
}
}
#endif
-
+
int ns = n - maxnbors;
int alln = n;
atombin[i] = ns;
diff --git a/src/USER-INTEL/npair_halffull_newton_intel.cpp b/src/USER-INTEL/npair_halffull_newton_intel.cpp
index 93a1a9792392a6ffd89f6fe8e9e41a0d65f836f7..8248f2257ae4f9df7c7d04ff6892071437d5d512 100644
--- a/src/USER-INTEL/npair_halffull_newton_intel.cpp
+++ b/src/USER-INTEL/npair_halffull_newton_intel.cpp
@@ -61,7 +61,7 @@ void NPairHalffullNewtonIntel::build_t(NeighList *list,
const int * _noalias const numneigh_full = list->listfull->numneigh;
const int ** _noalias const firstneigh_full =
(const int ** const)list->listfull->firstneigh;
-
+
#if defined(_OPENMP)
#pragma omp parallel
#endif
@@ -148,7 +148,7 @@ void NPairHalffullNewtonIntel::build_t3(NeighList *list, int *numhalf)
const int * _noalias const numneigh_full = numhalf;
const int ** _noalias const firstneigh_full =
(const int ** const)list->listfull->firstneigh;
-
+
int packthreads = 1;
if (comm->nthreads > INTEL_HTHREADS) packthreads = comm->nthreads;
diff --git a/src/USER-INTEL/npair_intel.cpp b/src/USER-INTEL/npair_intel.cpp
index a1c0785d4c4191312f769a577c2104e5060114ec..e20c437cb7d58007166ec4815d77be8c3647f6ef 100644
--- a/src/USER-INTEL/npair_intel.cpp
+++ b/src/USER-INTEL/npair_intel.cpp
@@ -72,7 +72,7 @@ void NPairIntel::copy_cutsq_info(IntelBuffers<flt_t,acc_t> *buffers) {
if (cutneighghostsq)
use_ghost_cut = 1;
buffers->set_ntypes(tp1, use_ghost_cut);
-
+
flt_t **cutneighsqb = buffers->get_cutneighsq();
for (int i = 1; i <= atom->ntypes; i++)
for (int j = 1; j <= atom->ntypes; j++)
@@ -116,7 +116,7 @@ void NPairIntel::bin_newton(const int offload, NeighList *list,
#ifdef _LMP_INTEL_OFFLOAD
if (offload_noghost && offload) nall_t = atom->nlocal;
#endif
-
+
const int pack_width = _fix->nbor_pack_width();
const ATOM_T * _noalias const x = buffers->get_x();
@@ -146,7 +146,7 @@ void NPairIntel::bin_newton(const int offload, NeighList *list,
int ** _noalias const firstneigh = list->firstneigh;
int * _noalias const numneigh = list->numneigh;
int * _noalias const cnumneigh = buffers->cnumneigh();
-
+
const int nstencil = this->nstencil;
const int * _noalias const stencil = this->stencil;
const flt_t * _noalias const cutneighsq = buffers->get_cutneighsq()[0];
@@ -204,7 +204,7 @@ void NPairIntel::bin_newton(const int offload, NeighList *list,
}
}
const int special_bound = sb;
-
+
#ifdef _LMP_INTEL_OFFLOAD
const int * _noalias const binhead = this->binhead;
const int * _noalias const bins = this->bins;
@@ -547,7 +547,7 @@ void NPairIntel::bin_newton(const int offload, NeighList *list,
j = -j - 1;
} else
ofind_special(which, special, nspecial, i, tag[j]);
-
+
if (which) {
j = j ^ (which << SBBITS);
if (which < special_bound) addme = 0;
@@ -562,7 +562,7 @@ void NPairIntel::bin_newton(const int offload, NeighList *list,
if (THREE) {
alln = n2;
n2 = pack_offset + maxnbors;
-
+
#if defined(LMP_SIMD_COMPILER)
#pragma vector aligned
#ifdef LMP_INTEL_NBOR_COMPAT
@@ -592,7 +592,7 @@ void NPairIntel::bin_newton(const int offload, NeighList *list,
}
}
}
-
+
#ifndef _LMP_INTEL_OFFLOAD
if (exclude) {
neighptr2 = neighptr;
@@ -643,7 +643,7 @@ void NPairIntel::bin_newton(const int offload, NeighList *list,
n += pack_width;
}
#endif
-
+
for (int u = pack_offset + maxnbors; u < n2; u++) {
#ifdef LMP_INTEL_3BODY_FAST
neighptr[n] = neighptr2[u];
diff --git a/src/USER-INTEL/npair_intel.h b/src/USER-INTEL/npair_intel.h
index e47687abea10424a5e052afdfd6b81b949e0574e..6d4e01462f5684c28daf3ccfc7a13aae056884a9 100644
--- a/src/USER-INTEL/npair_intel.h
+++ b/src/USER-INTEL/npair_intel.h
@@ -76,7 +76,7 @@ class NPairIntel : public NPair {
NPairIntel(class LAMMPS *);
~NPairIntel();
virtual void copy_neighbor_info();
-
+
#ifdef _LMP_INTEL_OFFLOAD
void grow_stencil();
#endif
@@ -86,7 +86,7 @@ class NPairIntel : public NPair {
template <class flt_t, class acc_t>
void copy_cutsq_info(IntelBuffers<flt_t,acc_t> *);
-
+
template <class flt_t, class acc_t, int, int, int, int, int>
void bin_newton(const int, NeighList *, IntelBuffers<flt_t,acc_t> *,
const int, const int, const int offload_end = 0);
diff --git a/src/USER-INTEL/npair_skip_intel.cpp b/src/USER-INTEL/npair_skip_intel.cpp
index 3d2463a0b978d883c66a4c364427668b1b7a1719..fa202d5da1ab604fa26c725ab14c1eae6e037b59 100644
--- a/src/USER-INTEL/npair_skip_intel.cpp
+++ b/src/USER-INTEL/npair_skip_intel.cpp
@@ -109,7 +109,7 @@ void NPairSkipIntel::build_t(NeighList *list, int *numhalf, int *cnumneigh,
int my_inum = ifrom;
_inum_starts[tid] = ifrom;
-
+
// loop over parent full list
for (int ii = ifrom; ii < ito; ii++) {
const int i = ilist_skip[ii];
@@ -131,7 +131,7 @@ void NPairSkipIntel::build_t(NeighList *list, int *numhalf, int *cnumneigh,
const int j = joriginal & NEIGHMASK;
if (!ijskip[itype][type[j]]) neighptr[n++] = joriginal;
}
- numhalf[my_inum] = n;
+ numhalf[my_inum] = n;
for (int jj = jnumhalf; jj < jnum; jj++) {
const int joriginal = jlist[jj];
diff --git a/src/USER-INTEL/npair_skip_intel.h b/src/USER-INTEL/npair_skip_intel.h
index e3277708d5c4188ebeef2197a18270ae561bacef..6bb3dfa5d05d648286f02779f6ed71c293db4ee1 100644
--- a/src/USER-INTEL/npair_skip_intel.h
+++ b/src/USER-INTEL/npair_skip_intel.h
@@ -46,7 +46,7 @@ class NPairSkipIntel : public NPair {
~NPairSkipIntel();
virtual void copy_neighbor_info();
void build(class NeighList *);
-
+
protected:
FixIntel *_fix;
int *_inum_starts, *_inum_counts, *_full_props;
diff --git a/src/USER-INTEL/pair_airebo_intel.h b/src/USER-INTEL/pair_airebo_intel.h
index 8a319536de119f6f02ac2a42b90f493e1c389f33..95e054fc0fbc372bbe98e361970a621adad92456 100644
--- a/src/USER-INTEL/pair_airebo_intel.h
+++ b/src/USER-INTEL/pair_airebo_intel.h
@@ -110,7 +110,7 @@ path and name are correct.
E: Cannot yet use airebo/intel with hybrid.
Pair style airebo/intel cannot currently be used as part of a hybrid
-pair style (with the exception of hybrid/overlay).
+pair style (with the exception of hybrid/overlay).
*/
diff --git a/src/USER-INTEL/pair_buck_coul_cut_intel.cpp b/src/USER-INTEL/pair_buck_coul_cut_intel.cpp
index 3954d559e1472b6fe808cb2fa28c683e28140a6f..f82f4c1c7aee4f41def4313c0bb5bcd3c84a81db 100644
--- a/src/USER-INTEL/pair_buck_coul_cut_intel.cpp
+++ b/src/USER-INTEL/pair_buck_coul_cut_intel.cpp
@@ -204,7 +204,7 @@ void PairBuckCoulCutIntel::eval(const int offload, const int vflag,
acc_t oevdwl, oecoul, ov0, ov1, ov2, ov3, ov4, ov5;
if (EFLAG || vflag)
oevdwl = oecoul = ov0 = ov1 = ov2 = ov3 = ov4 = ov5 = (acc_t)0;
- if (NEWTON_PAIR == 0 && inum != nlocal)
+ if (NEWTON_PAIR == 0 && inum != nlocal)
memset(f_start, 0, f_stride * sizeof(FORCE_T));
// loop over neighbors of my atoms
diff --git a/src/USER-INTEL/pair_dpd_intel.cpp b/src/USER-INTEL/pair_dpd_intel.cpp
index 9baa64e8e05984afd58aa55115d6ca2c2b911dac..5d67a60c4badb129dcbedceb6bb88f2d9ab7bffb 100644
--- a/src/USER-INTEL/pair_dpd_intel.cpp
+++ b/src/USER-INTEL/pair_dpd_intel.cpp
@@ -521,7 +521,7 @@ void PairDPDIntel::pack_force_const(ForceConst<flt_t> &fc,
}
}
if (mytypes > 1 || atom->molecular) _onetype = 0;
-
+
for (int i = 0; i < 4; i++) {
fc.special_lj[i] = force->special_lj[i];
fc.special_lj[0] = 1.0;
diff --git a/src/USER-INTEL/pppm_intel.cpp b/src/USER-INTEL/pppm_intel.cpp
index f3fa8dd15db9ec59bfe6e4d6a90b98976ee6d3c8..59455bcf52604cc5c5ffea73e6c22a571232f29b 100644
--- a/src/USER-INTEL/pppm_intel.cpp
+++ b/src/USER-INTEL/pppm_intel.cpp
@@ -586,7 +586,7 @@ void PPPMIntel::fieldforce_ik(IntelBuffers<flt_t,acc_t> *buffers)
if (force->newton_pair) zl += atom->nghost;
memset(f, 0, zl * sizeof(FORCE_T));
}
-
+
#if defined(_OPENMP)
#pragma omp parallel default(none) \
shared(nlocal, nthr) if(!_use_lrt)
@@ -737,7 +737,7 @@ void PPPMIntel::fieldforce_ad(IntelBuffers<flt_t,acc_t> *buffers)
if (force->newton_pair) zl += atom->nghost;
memset(f, 0, zl * sizeof(FORCE_T));
}
-
+
#if defined(_OPENMP)
#pragma omp parallel default(none) \
shared(nlocal, nthr) if(!_use_lrt)
diff --git a/src/USER-MEAMC/meam_impl.cpp b/src/USER-MEAMC/meam_impl.cpp
index d4a47a4f48fc428243183d1527cf413af4e183ce..b099ead8d5b3677a1f543577bad33e9e51d8c20c 100644
--- a/src/USER-MEAMC/meam_impl.cpp
+++ b/src/USER-MEAMC/meam_impl.cpp
@@ -34,12 +34,12 @@ MEAM::MEAM(Memory* mem)
maxneigh = 0;
scrfcn = dscrfcn = fcpair = NULL;
-
+
neltypes = 0;
for (int i = 0; i < maxelt; i++) {
- Omega_meam[i] = Z_meam[i] = A_meam[i] = rho0_meam[i] = beta0_meam[i] =
- beta1_meam[i]= beta2_meam[i] = beta3_meam[i] =
- t0_meam[i] = t1_meam[i] = t2_meam[i] = t3_meam[i] =
+ Omega_meam[i] = Z_meam[i] = A_meam[i] = rho0_meam[i] = beta0_meam[i] =
+ beta1_meam[i]= beta2_meam[i] = beta3_meam[i] =
+ t0_meam[i] = t1_meam[i] = t2_meam[i] = t3_meam[i] =
rho_ref_meam[i] = ibar_meam[i] = ielt_meam[i] = 0.0;
for (int j = 0; j < maxelt; j++) {
lattce_meam[i][j] = FCC;
diff --git a/src/USER-MISC/compute_stress_mop.h b/src/USER-MISC/compute_stress_mop.h
index 2047d1d54fe05770996022335a4267b9791d251d..07bb7741488559805870d5bc0e89d2cf330cd667 100644
--- a/src/USER-MISC/compute_stress_mop.h
+++ b/src/USER-MISC/compute_stress_mop.h
@@ -56,47 +56,47 @@ namespace LAMMPS_NS {
#endif
/* ERROR/WARNING messages:
-
+
E: Illegal ... command
-
+
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
-
+
E: Compute stress/mop incompatible with simulation dimension
-
+
Compute stress/mop only works with 3D simulations.
-
+
E: Compute stress/mop incompatible with triclinic simulation box
-
+
Self-explanatory.
-
+
E: Compute stress/mop requires a fixed simulation box
-
+
Compute stress/mop is not compatible with any change of volume or shape
or boundary conditions of the simulation box.
-
+
E: No pair style is defined for compute stress/mop
-
+
Self-explanatory. Compute stress/mop requires the definition of a pair style.
-
+
E: Pair style does not support compute stress/mop
-
+
The pair style does not have a single() function, so it can
not be invoked by compute stress/mop.
-
+
W: compute stress/mop does not account for bond potentials
-
+
W: compute stress/mop does not account for angle potentials
-
+
W: compute stress/mop does not account for dihedral potentials
-
+
W: compute stress/mop does not account for improper potentials
-
+
W: compute stress/mop does not account for kspace contributions
-
+
Compute stress/mop only accounts for pairwise additive interactions for
the computation of local stress tensor components.
-
+
*/
diff --git a/src/USER-MISC/compute_stress_mop_profile.h b/src/USER-MISC/compute_stress_mop_profile.h
index 0ab774f3db387bb3f2b3809bce4a9776767115c7..d86237b0bd3aaee224a1b80d10f12c19b3735bea 100644
--- a/src/USER-MISC/compute_stress_mop_profile.h
+++ b/src/USER-MISC/compute_stress_mop_profile.h
@@ -70,43 +70,43 @@ namespace LAMMPS_NS {
command-line option when running LAMMPS to see the offending line.
E: Compute stress/mop/profile incompatible with simulation dimension
-
+
Compute stress/mop/profile only works with 3D simulations.
-
+
E: Compute stress/mop/profile incompatible with triclinic simulation box
-
+
Self-explanatory.
-
+
E: Compute stress/mop/profile requires a fixed simulation box
-
+
Compute stress/mop/profile is not compatible with any change of volume or shape
or boundary conditions of the simulation box.
-
+
E: No pair style is defined for compute stress/mop/profile
-
+
Self-explanatory. Compute stress/mop/profile requires the definition of a pair style.
-
+
E: Pair style does not support compute stress/mop/profile
-
+
The pair style does not have a single() function, so it can
not be invoked by compute stress/mop/profile.
-
+
E: Origin of bins for compute stress/mop/profile is out of bounds
-
+
Self-explanatory.
-
+
W: compute stress/mop/profile does not account for bond potentials
-
+
W: compute stress/mop/profile does not account for angle potentials
-
+
W: compute stress/mop/profile does not account for dihedral potentials
-
+
W: compute stress/mop/profile does not account for improper potentials
-
+
W: compute stress/mop/profile does not account for kspace contributions
-
+
Compute stress/mop/profile only accounts for pairwise additive interactions for
the computation of local stress tensor components.
-
+
*/
diff --git a/src/USER-MISC/dihedral_table_cut.cpp b/src/USER-MISC/dihedral_table_cut.cpp
index 7345bcdad164c2df0cd598c8606b8f26cf1fc511..963364d289c6ee9f03634e26282b07d69e4142d1 100644
--- a/src/USER-MISC/dihedral_table_cut.cpp
+++ b/src/USER-MISC/dihedral_table_cut.cpp
@@ -454,7 +454,7 @@ DihedralTableCut::~DihedralTableCut()
void DihedralTableCut::compute(int eflag, int vflag)
{
-
+
int i1,i2,i3,i4,i,j,k,n,type;
double edihedral;
double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm;
@@ -704,12 +704,12 @@ void DihedralTableCut::compute(int eflag, int vflag)
double gptt = 0;
if ( acos(costh12) > aat_theta0_1[type]) {
- gt *= 1-da1*da1/dtheta/dtheta;
+ gt *= 1-da1*da1/dtheta/dtheta;
gpt = -aat_k[type]*2*da1/dtheta/dtheta;
}
if ( acos(costh23) > aat_theta0_1[type]) {
- gtt *= 1-da2*da2/dtheta/dtheta;
+ gtt *= 1-da2*da2/dtheta/dtheta;
gptt = -aat_k[type]*2*da2/dtheta/dtheta;
}
@@ -717,7 +717,7 @@ void DihedralTableCut::compute(int eflag, int vflag)
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
- fabcd[i][j] -= - gt*gtt*fpphi*dphidr[i][j]
+ fabcd[i][j] -= - gt*gtt*fpphi*dphidr[i][j]
- gt*gptt*fphi*dthetadr[1][i][j] + gpt*gtt*fphi*dthetadr[0][i][j];
// apply force to each of 4 atoms
diff --git a/src/USER-MISC/pair_kolmogorov_crespi_z.cpp b/src/USER-MISC/pair_kolmogorov_crespi_z.cpp
index 75edd42102ed3abdd83bce4723ae5a970c1bc77b..e9583032fe28195a4f85be9957219c77893756ad 100644
--- a/src/USER-MISC/pair_kolmogorov_crespi_z.cpp
+++ b/src/USER-MISC/pair_kolmogorov_crespi_z.cpp
@@ -85,7 +85,7 @@ void PairKolmogorovCrespiZ::compute(int eflag, int vflag)
double rsq,r,rhosq,exp1,exp2,r6,r8;
double frho,sumC,sumC2,sumCff,fsum,rdsq;
int *ilist,*jlist,*numneigh,**firstneigh;
-
+
evdwl = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
@@ -121,7 +121,7 @@ void PairKolmogorovCrespiZ::compute(int eflag, int vflag)
// rho^2 = r^2 - (n,r) = r^2 - z^2
rhosq = delx*delx + dely*dely;
rsq = rhosq + delz*delz;
-
+
if (rsq < cutsq[itype][jtype]) {
int iparam_ij = elem2param[map[itype]][map[jtype]];
@@ -137,7 +137,7 @@ void PairKolmogorovCrespiZ::compute(int eflag, int vflag)
exp2 = exp(-rdsq);
// note that f(rho_ij) equals f(rho_ji) as normals are all along z
- sumC = p.C0+p.C2*rdsq+p.C4*rdsq*rdsq;
+ sumC = p.C0+p.C2*rdsq+p.C4*rdsq*rdsq;
sumC2 = (2*p.C2+4*p.C4*rdsq)*p.delta2inv;
frho = exp2*sumC;
sumCff = p.C + 2*frho;
@@ -221,9 +221,9 @@ void PairKolmogorovCrespiZ::settings(int narg, char **arg)
void PairKolmogorovCrespiZ::coeff(int narg, char **arg)
{
- int i,j,n;
+ int i,j,n;
- if (narg != 3 + atom->ntypes)
+ if (narg != 3 + atom->ntypes)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
@@ -262,7 +262,7 @@ void PairKolmogorovCrespiZ::coeff(int narg, char **arg)
read_file(arg[2]);
-
+
double cut_one = cut_global;
int count = 0;
@@ -407,7 +407,7 @@ void PairKolmogorovCrespiZ::read_file(char *filename)
params[nparams].S = atof(words[10]);
// energies in meV further scaled by S
- double meV = 1.0e-3*params[nparams].S;
+ double meV = 1.0e-3*params[nparams].S;
params[nparams].C *= meV;
params[nparams].A *= meV;
params[nparams].C0 *= meV;
diff --git a/src/USER-MISC/pair_lj_mdf.cpp b/src/USER-MISC/pair_lj_mdf.cpp
index e6f174e811f36db214e6644d792bd70af94c229b..4cd21b1dbe51c2275c2f5ea000f1369437d5b337 100644
--- a/src/USER-MISC/pair_lj_mdf.cpp
+++ b/src/USER-MISC/pair_lj_mdf.cpp
@@ -82,7 +82,7 @@ void PairLJMDF::compute(int eflag, int vflag)
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
-
+
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
@@ -109,7 +109,7 @@ void PairLJMDF::compute(int eflag, int vflag)
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
if (rsq > cut_inner_sq[itype][jtype]) {
- philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
+ philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
rr = sqrt(rsq);
dp = (cut[itype][jtype] - cut_inner[itype][jtype]);
diff --git a/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp b/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp
index dd39002fe4e654f8cd79ce7e9b889ae28f9e5cef..1fc4644420801f7699e5d4b801a67363af2d51ad 100644
--- a/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp
+++ b/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp
@@ -142,7 +142,7 @@ void PairBuck6dCoulGaussDSF::compute(int eflag, int vflag)
term3 = term2*term2;
term4 = 1.0/(1.0 + term2);
term5 = 1.0/(1.0 + 2.0*term2 + term3);
- forcebuck6d = buck6d1[itype][jtype]*buck6d2[itype][jtype]*r*rexp;
+ forcebuck6d = buck6d1[itype][jtype]*buck6d2[itype][jtype]*r*rexp;
forcebuck6d -= term1*(6.0*term4 - term5*14.0*term2);
ebuck6d = buck6d1[itype][jtype]*rexp - term1*term4;
@@ -150,11 +150,11 @@ void PairBuck6dCoulGaussDSF::compute(int eflag, int vflag)
if (rsq > rsmooth_sq[itype][jtype]) {
rcu = r*rsq;
rqu = rsq*rsq;
- sme = c5[itype][jtype]*rqu*r + c4[itype][jtype]*rqu + c3[itype][jtype]*rcu +
+ sme = c5[itype][jtype]*rqu*r + c4[itype][jtype]*rqu + c3[itype][jtype]*rcu +
c2[itype][jtype]*rsq + c1[itype][jtype]*r + c0[itype][jtype];
- smf = 5.0*c5[itype][jtype]*rqu + 4.0*c4[itype][jtype]*rcu +
+ smf = 5.0*c5[itype][jtype]*rqu + 4.0*c4[itype][jtype]*rcu +
3.0*c3[itype][jtype]*rsq + 2.0*c2[itype][jtype]*r + c1[itype][jtype];
- // forcebuck6d is -dE/dr*r
+ // forcebuck6d is -dE/dr*r
forcebuck6d = forcebuck6d*sme - ebuck6d*smf*r; //RS was here: changed this from +E*smf to -E*smf*r
ebuck6d *= sme;
}
@@ -167,10 +167,10 @@ void PairBuck6dCoulGaussDSF::compute(int eflag, int vflag)
arg = alpha_ij[itype][jtype]*r;
erfcd = MathSpecial::expmsq(arg);
erfcc = 1 - (MathSpecial::my_erfcx(arg) * erfcd);
-
- forcecoul = prefactor * ((erfcc/r) - (2.0/MY_PIS*alpha_ij[itype][jtype]*erfcd) +
+
+ forcecoul = prefactor * ((erfcc/r) - (2.0/MY_PIS*alpha_ij[itype][jtype]*erfcd) +
r*f_shift_ij[itype][jtype]) * r;
-
+
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
} else forcecoul = 0.0;
@@ -191,7 +191,7 @@ void PairBuck6dCoulGaussDSF::compute(int eflag, int vflag)
} else evdwl = 0.0;
if (rsq < cut_coulsq) {
- ecoul = prefactor * (erfcc - r*e_shift_ij[itype][jtype] -
+ ecoul = prefactor * (erfcc - r*e_shift_ij[itype][jtype] -
rsq*f_shift_ij[itype][jtype]);
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
} else ecoul = 0.0;
@@ -317,7 +317,7 @@ void PairBuck6dCoulGaussDSF::init_style()
neighbor->request(this,instance_me);
- cut_coulsq = cut_coul * cut_coul;
+ cut_coulsq = cut_coul * cut_coul;
}
/* ----------------------------------------------------------------------
@@ -330,7 +330,7 @@ double PairBuck6dCoulGaussDSF::init_one(int i, int j)
double cut = MAX(cut_lj[i][j],cut_coul);
cut_ljsq[i][j] = cut_lj[i][j] * cut_lj[i][j];
-
+
//calculation of smoothing coefficients c0-c5
c0[i][j] = c1[i][j] = c2[i][j] = c3[i][j] = c4[i][j] = c5[i][j] = 0.0;
rsmooth_sq[i][j] = cut_ljsq[i][j];
@@ -347,7 +347,7 @@ double PairBuck6dCoulGaussDSF::init_one(int i, int j)
c5[i][j] = -6.0/denom;
rsmooth_sq[i][j] = rsm_sq;
}
-
+
// if offset_flag, shift is only invoked if there is not already smoothing
if (offset_flag && vdwl_smooth >= 1.0) {
double term1 = buck6d3[i][j]/pow(cut_lj[i][j],6.0);
@@ -355,12 +355,12 @@ double PairBuck6dCoulGaussDSF::init_one(int i, int j)
double rexp = exp(-cut_lj[i][j]*buck6d2[i][j]);
offset[i][j] = buck6d1[i][j]*rexp - term1*term4;
} else offset[i][j] = 0.0;
-
+
double erfcd_c = exp(-alpha_ij[i][j]*alpha_ij[i][j]*cut_coul*cut_coul);
double erfcc_c = erf(alpha_ij[i][j]*cut_coul);
f_shift_ij[i][j] = -erfcc_c/cut_coulsq + 2.0/MY_PIS*alpha_ij[i][j]*erfcd_c/cut_coul;
e_shift_ij[i][j] = erfcc_c/cut_coul - f_shift_ij[i][j]*cut_coul;
-
+
cut_ljsq[j][i] = cut_ljsq[i][j];
alpha_ij[j][i] = alpha_ij[i][j];
f_shift_ij[j][i] = f_shift_ij[i][j];
@@ -520,18 +520,18 @@ double PairBuck6dCoulGaussDSF::single(int i, int j, int itype, int jtype, double
term3 = term2*term2;
term4 = 1.0/(1.0 + term2);
term5 = 1.0/(1.0 + 2.0*term2 + term3);
- forcebuck6d = buck6d1[itype][jtype]*buck6d2[itype][jtype]*r*rexp;
+ forcebuck6d = buck6d1[itype][jtype]*buck6d2[itype][jtype]*r*rexp;
forcebuck6d -= term1*(6.0*term4 - term5*14.0*term2);
ebuck6d = buck6d1[itype][jtype]*rexp - term1*term4;
// smoothing term
if (rsq > rsmooth_sq[itype][jtype]) {
rcu = r*rsq;
rqu = rsq*rsq;
- sme = c5[itype][jtype]*rqu*r + c4[itype][jtype]*rqu + c3[itype][jtype]*rcu +
+ sme = c5[itype][jtype]*rqu*r + c4[itype][jtype]*rqu + c3[itype][jtype]*rcu +
c2[itype][jtype]*rsq + c1[itype][jtype]*r + c0[itype][jtype];
- smf = 5.0*c5[itype][jtype]*rqu + 4.0*c4[itype][jtype]*rcu +
+ smf = 5.0*c5[itype][jtype]*rqu + 4.0*c4[itype][jtype]*rcu +
3.0*c3[itype][jtype]*rsq + 2.0*c2[itype][jtype]*r + c1[itype][jtype];
- // forcebuck6d is -dE/dr*r
+ // forcebuck6d is -dE/dr*r
forcebuck6d = forcebuck6d*sme - ebuck6d*smf*r; //RS was here: changed this from +E*smf to -E*smf*r
ebuck6d *= sme;
}
@@ -542,7 +542,7 @@ double PairBuck6dCoulGaussDSF::single(int i, int j, int itype, int jtype, double
arg = alpha_ij[itype][jtype]*r;
erfcd = MathSpecial::expmsq(arg);
erfcc = 1 - (MathSpecial::my_erfcx(arg) * erfcd);
- forcecoul = prefactor * ((erfcc/r) - (2.0/MY_PIS*alpha_ij[itype][jtype]*erfcd) +
+ forcecoul = prefactor * ((erfcc/r) - (2.0/MY_PIS*alpha_ij[itype][jtype]*erfcd) +
r*f_shift_ij[itype][jtype]) * r;
} else forcecoul = 0.0;
@@ -555,7 +555,7 @@ double PairBuck6dCoulGaussDSF::single(int i, int j, int itype, int jtype, double
}
if (rsq < cut_coulsq) {
- phicoul = prefactor * (erfcc - r*e_shift_ij[itype][jtype] -
+ phicoul = prefactor * (erfcc - r*e_shift_ij[itype][jtype] -
rsq*f_shift_ij[itype][jtype]);
eng += phicoul;
}
diff --git a/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp b/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp
index ffeb6fa9578e7931d5904eda066ce790b4459984..1ca42d864e7abc53c1b73c4403db82f5582c96b6 100644
--- a/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp
+++ b/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp
@@ -144,17 +144,17 @@ void PairBuck6dCoulGaussLong::compute(int eflag, int vflag)
term3 = term2*term2;
term4 = 1.0/(1.0 + term2);
term5 = 1.0/(1.0 + 2.0*term2 + term3);
- forcebuck6d = buck6d1[itype][jtype]*buck6d2[itype][jtype]*r*rexp;
+ forcebuck6d = buck6d1[itype][jtype]*buck6d2[itype][jtype]*r*rexp;
forcebuck6d -= term1*(6.0*term4 - term5*14.0*term2);
ebuck6d = buck6d1[itype][jtype]*rexp - term1*term4;
-
+
// smoothing term
if (rsq > rsmooth_sq[itype][jtype]) {
rcu = r*rsq;
rqu = rsq*rsq;
- sme = c5[itype][jtype]*rqu*r + c4[itype][jtype]*rqu + c3[itype][jtype]*rcu +
+ sme = c5[itype][jtype]*rqu*r + c4[itype][jtype]*rqu + c3[itype][jtype]*rcu +
c2[itype][jtype]*rsq + c1[itype][jtype]*r + c0[itype][jtype];
- smf = 5.0*c5[itype][jtype]*rqu + 4.0*c4[itype][jtype]*rcu +
+ smf = 5.0*c5[itype][jtype]*rqu + 4.0*c4[itype][jtype]*rcu +
3.0*c3[itype][jtype]*rsq + 2.0*c2[itype][jtype]*r + c1[itype][jtype];
// forcebuck6d is -dE/dr*r
forcebuck6d = forcebuck6d*sme - ebuck6d*smf*r;
@@ -172,15 +172,15 @@ void PairBuck6dCoulGaussLong::compute(int eflag, int vflag)
arg = alpha_ij[itype][jtype]*r;
expa = MathSpecial::expmsq(arg);
erfa = 1 - (MathSpecial::my_erfcx(arg) * expa);
-
+
prefactor = qqrd2e*qtmp*q[j]/r;
falpha = erfa - EWALD_F*arg*expa;
forcecoul = prefactor * (falpha - erf + EWALD_F*grij*expm2);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor*falpha;
-
+
// (q*q/r) * (gauss(alpha_ij) - gauss(alpha_long)
ealpha = prefactor * (erfa-erf);
- // smoothing term - NOTE: ingnored in special_bonds correction
+ // smoothing term - NOTE: ingnored in special_bonds correction
// since likely rsmooth_sq_c >> d(special)
if (rsq > rsmooth_sq_c) {
rcu = r*rsq;
@@ -191,7 +191,7 @@ void PairBuck6dCoulGaussLong::compute(int eflag, int vflag)
ealpha *= sme;
}
} else forcecoul = 0.0;
-
+
fpair = (forcecoul + factor_lj*forcebuck6d) * r2inv;
f[i][0] += delx*fpair;
@@ -340,8 +340,8 @@ void PairBuck6dCoulGaussLong::init_style()
neighbor->request(this,instance_me);
- cut_coulsq = cut_coul * cut_coul;
-
+ cut_coulsq = cut_coul * cut_coul;
+
//calculation of smoothing coefficients c0_c-c5_c for coulomb smoothing
c0_c = c1_c = c2_c = c3_c = c4_c = c5_c = 0.0;
rsmooth_sq_c = cut_coulsq;
@@ -370,7 +370,7 @@ double PairBuck6dCoulGaussLong::init_one(int i, int j)
double cut = MAX(cut_lj[i][j],cut_coul);
cut_ljsq[i][j] = cut_lj[i][j] * cut_lj[i][j];
-
+
//calculation of smoothing coefficients c0-c5
c0[i][j] = c1[i][j] = c2[i][j] = c3[i][j] = c4[i][j] = c5[i][j] = 0.0;
rsmooth_sq[i][j] = cut_ljsq[i][j];
@@ -395,7 +395,7 @@ double PairBuck6dCoulGaussLong::init_one(int i, int j)
double rexp = exp(-cut_lj[i][j]*buck6d2[i][j]);
offset[i][j] = buck6d1[i][j]*rexp - term1*term4;
} else offset[i][j] = 0.0;
-
+
cut_ljsq[j][i] = cut_ljsq[i][j];
alpha_ij[j][i] = alpha_ij[i][j];
buck6d1[j][i] = buck6d1[i][j];
@@ -557,18 +557,18 @@ double PairBuck6dCoulGaussLong::single(int i, int j, int itype, int jtype, doubl
term3 = term2*term2;
term4 = 1.0/(1.0 + term2);
term5 = 1.0/(1.0 + 2.0*term2 + term3);
- forcebuck6d = buck6d1[itype][jtype]*buck6d2[itype][jtype]*r*rexp;
+ forcebuck6d = buck6d1[itype][jtype]*buck6d2[itype][jtype]*r*rexp;
forcebuck6d -= term1*(6.0*term4 - term5*14.0*term2);
ebuck6d = buck6d1[itype][jtype]*rexp - term1*term4;
// smoothing term
if (rsq > rsmooth_sq[itype][jtype]) {
rcu = r*rsq;
rqu = rsq*rsq;
- sme = c5[itype][jtype]*rqu*r + c4[itype][jtype]*rqu + c3[itype][jtype]*rcu +
+ sme = c5[itype][jtype]*rqu*r + c4[itype][jtype]*rqu + c3[itype][jtype]*rcu +
c2[itype][jtype]*rsq + c1[itype][jtype]*r + c0[itype][jtype];
- smf = 5.0*c5[itype][jtype]*rqu + 4.0*c4[itype][jtype]*rcu +
+ smf = 5.0*c5[itype][jtype]*rqu + 4.0*c4[itype][jtype]*rcu +
3.0*c3[itype][jtype]*rsq + 2.0*c2[itype][jtype]*r + c1[itype][jtype];
- // forcebuck6d is -dE/dr*r
+ // forcebuck6d is -dE/dr*r
forcebuck6d = forcebuck6d*sme - ebuck6d*smf*r; //RS was here: changed this from +E*smf to -E*smf*r
ebuck6d *= sme;
}
@@ -584,12 +584,12 @@ double PairBuck6dCoulGaussLong::single(int i, int j, int itype, int jtype, doubl
arg = alpha_ij[itype][jtype]*r;
expa = MathSpecial::expmsq(arg);
erfa = 1 - (MathSpecial::my_erfcx(arg) * expa);
-
+
prefactor = force->qqrd2e * atom->q[i] * atom->q[j] / r;
falpha = erfa - EWALD_F*arg*expa;
forcecoul = prefactor * (falpha - erf + EWALD_F*grij*expm2);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor*falpha;
-
+
ealpha = prefactor * (erfa-erf);
// smoothing term
if (rsq > rsmooth_sq_c) {
diff --git a/src/USER-PTM/ptm_polar.cpp b/src/USER-PTM/ptm_polar.cpp
index d75424e11fcedfab056aa29fd1641f41966b9d23..d5dca957be1f3101641a88910ff2f98c9e02fafe 100644
--- a/src/USER-PTM/ptm_polar.cpp
+++ b/src/USER-PTM/ptm_polar.cpp
@@ -1,5 +1,5 @@
/*******************************************************************************
- * -/_|:|_|_\-
+ * -/_|:|_|_\-
*
* This code is a modification of D.L. Theobald's QCP rotation code.
* It has been adapted to calculate the polar decomposition of a 3x3 matrix
@@ -14,7 +14,7 @@
* USA
*
* dtheobald@brandeis.edu
- *
+ *
* Pu Liu
* Johnson & Johnson Pharmaceutical Research and Development, L.L.C.
* 665 Stockton Drive
@@ -22,7 +22,7 @@
* USA
*
* pliu24@its.jnj.com
- *
+ *
*
* If you use this QCP rotation calculation method in a publication, please
* reference:
@@ -33,7 +33,7 @@
* Acta Crystallographica A 61(4):478-480.
*
* Pu Liu, Dmitris K. Agrafiotis, and Douglas L. Theobald (2009)
- * "Fast determination of the optimal rotational matrix for macromolecular
+ * "Fast determination of the optimal rotational matrix for macromolecular
* superpositions."
* Journal of Computational Chemistry 31(7):1561-1563.
*
@@ -63,7 +63,7 @@
* DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
* THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
- * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*
* Source: started anew.
*
@@ -82,7 +82,7 @@
*
* 2016/05/29 QCP method adapted for polar decomposition of a 3x3 matrix,
* for use in Polyhedral Template Matching.
- *
+ *
******************************************************************************/
#include <cmath>
@@ -327,7 +327,7 @@ void InnerProduct(double *A, int num, const double (*coords1)[3], double (*coord
A[6] += z1 * x2;
A[7] += z1 * y2;
- A[8] += z1 * z2;
+ A[8] += z1 * z2;
}
}
diff --git a/src/USER-SCAFACOS/scafacos.cpp b/src/USER-SCAFACOS/scafacos.cpp
index 482a5586c7e78c03928a5764398bc34bf5f4c725..8d2b69deee137bacae9bf67e68389d28b87fda2d 100644
--- a/src/USER-SCAFACOS/scafacos.cpp
+++ b/src/USER-SCAFACOS/scafacos.cpp
@@ -65,10 +65,10 @@ void Scafacos::settings(int narg, char **arg)
if (strcmp(method,"fmm") == 0) {
tolerance_type = FCS_TOLERANCE_TYPE_ENERGY;
fmm_tuning_flag = 0;
- } else if (strcmp(method,"p3m") == 0 ||
- strcmp(method,"p2nfft") == 0 ||
+ } else if (strcmp(method,"p3m") == 0 ||
+ strcmp(method,"p2nfft") == 0 ||
strcmp(method,"ewald") == 0) {
- tolerance_type = FCS_TOLERANCE_TYPE_FIELD;
+ tolerance_type = FCS_TOLERANCE_TYPE_FIELD;
} else if (strcmp(method,"direct") == 0) {
; // direct summation has no tolerance type
} else {
@@ -100,7 +100,7 @@ void Scafacos::init()
if (logfile && me == 0) fprintf(logfile,
"Setting up ScaFaCoS with solver %s ...\n",method);
- if (!atom->q_flag)
+ if (!atom->q_flag)
error->all(FLERR,"Kspace style requires atom attribute q");
if (domain->dimension == 2)
@@ -112,7 +112,7 @@ void Scafacos::init()
if (atom->natoms > INT_MAX && sizeof(int) != 8)
error->all(FLERR,"Scafacos atom count exceeds 2B");
- if (atom->molecular > 0)
+ if (atom->molecular > 0)
error->all(FLERR,
"Cannot use Scafacos with molecular charged systems yet");
@@ -140,7 +140,7 @@ void Scafacos::init()
}
double **x = atom->x;
- double *q = atom->q;
+ double *q = atom->q;
int nlocal = atom->nlocal;
if (strcmp(method,"fmm") == 0)
@@ -164,7 +164,7 @@ void Scafacos::init()
result = fcs_tune((FCS)fcs,nlocal,&x[0][0],q);
check_result((void*)&result);
- // more useful here, since the parameters should be tuned now
+ // more useful here, since the parameters should be tuned now
if (me == 0) fcs_print_parameters((FCS)fcs);
}
@@ -194,12 +194,12 @@ void Scafacos::compute(int eflag, int vflag)
}
if (eflag || vflag) ev_setup(eflag,vflag);
- else
+ else
{
eflag_atom = 0;
vflag_global = 0;
}
-
+
// grow xpbc, epot, efield if necessary
if (nlocal > maxatom || maxatom == 0) {
@@ -270,7 +270,7 @@ void Scafacos::compute(int eflag, int vflag)
f[i][1] += qone * efield[i][1];
f[i][2] += qone * efield[i][2];
myeng += 0.5 * qone * epot[i];
- }
+ }
if (eflag_atom) {
for (int i = 0; i < nlocal; i++)
@@ -296,50 +296,50 @@ int Scafacos::modify_param(int narg, char **arg)
if (narg < 3) error->all(FLERR,
"Illegal kspace_modify command (tolerance)");
if (strcmp(arg[2],"energy") == 0)
- tolerance_type = FCS_TOLERANCE_TYPE_ENERGY;
+ tolerance_type = FCS_TOLERANCE_TYPE_ENERGY;
else if (strcmp(arg[2],"energy_rel") == 0)
- tolerance_type = FCS_TOLERANCE_TYPE_ENERGY_REL;
+ tolerance_type = FCS_TOLERANCE_TYPE_ENERGY_REL;
else if (strcmp(arg[2],"field") == 0)
- tolerance_type = FCS_TOLERANCE_TYPE_FIELD;
+ tolerance_type = FCS_TOLERANCE_TYPE_FIELD;
else if (strcmp(arg[2],"field_rel") == 0)
- tolerance_type = FCS_TOLERANCE_TYPE_FIELD_REL;
+ tolerance_type = FCS_TOLERANCE_TYPE_FIELD_REL;
else if (strcmp(arg[2],"potential") == 0)
- tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL;
+ tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL;
else if (strcmp(arg[2],"potential_rel") == 0)
- tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL_REL;
+ tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL_REL;
else error->all(FLERR,
"Illegal kspace_modify command (tolerance argument)");
// check if method is compatatible to chosen tolerance type
if(
(
- strcmp(method,"fmm") == 0 &&
- (
- tolerance_type != FCS_TOLERANCE_TYPE_ENERGY &&
+ strcmp(method,"fmm") == 0 &&
+ (
+ tolerance_type != FCS_TOLERANCE_TYPE_ENERGY &&
tolerance_type != FCS_TOLERANCE_TYPE_ENERGY_REL
- )
- ) ||
+ )
+ ) ||
(
- strcmp(method,"p2nfft") == 0 &&
- (
- tolerance_type != FCS_TOLERANCE_TYPE_FIELD &&
+ strcmp(method,"p2nfft") == 0 &&
+ (
+ tolerance_type != FCS_TOLERANCE_TYPE_FIELD &&
tolerance_type != FCS_TOLERANCE_TYPE_POTENTIAL
- )
+ )
) ||
(
- strcmp(method,"p3m") == 0 &&
- (
- tolerance_type != FCS_TOLERANCE_TYPE_FIELD
- )
+ strcmp(method,"p3m") == 0 &&
+ (
+ tolerance_type != FCS_TOLERANCE_TYPE_FIELD
+ )
) ||
(
- strcmp(method,"ewald") == 0 &&
- (
- tolerance_type != FCS_TOLERANCE_TYPE_FIELD
+ strcmp(method,"ewald") == 0 &&
+ (
+ tolerance_type != FCS_TOLERANCE_TYPE_FIELD
)
- )
+ )
)
error->all(FLERR,"Illegal kspace_modify command \
- (invalid tolerance / method combination)");
+ (invalid tolerance / method combination)");
return 3;
}
@@ -375,7 +375,7 @@ double Scafacos::memory_usage()
}
/* ----------------------------------------------------------------------
- setup of ScaFaCoS handle with common parameters
+ setup of ScaFaCoS handle with common parameters
------------------------------------------------------------------------- */
void Scafacos::setup_handle()
@@ -443,7 +443,7 @@ bool Scafacos::box_has_changed()
int *periodicity = domain->periodicity;
double *prd = domain->prd;
- bool changed =
+ bool changed =
(periodicity[0] != old_periodicity[0]) ||
(periodicity[1] != old_periodicity[1]) ||
(periodicity[2] != old_periodicity[2]) ||
@@ -462,14 +462,14 @@ bool Scafacos::box_has_changed()
check ScaFaCoS result for error condition
------------------------------------------------------------------------- */
-void Scafacos::check_result(void* result_p)
+void Scafacos::check_result(void* result_p)
{
FCSResult result = *(FCSResult*)result_p;
if (!result) return;
std::stringstream ss;
- ss << "ScaFaCoS: " << fcs_result_get_function(result) << "\n"
+ ss << "ScaFaCoS: " << fcs_result_get_function(result) << "\n"
<< fcs_result_get_message(result) << "\n";
fcs_result_destroy(result);
std::string err_msg = ss.str();
@@ -477,4 +477,4 @@ void Scafacos::check_result(void* result_p)
error->one(FLERR,str);
}
-
+
diff --git a/src/USER-SDPD/fix_meso_move.cpp b/src/USER-SDPD/fix_meso_move.cpp
index 4e591c90881166c4fdeaf6afc0ed4beace1d91f2..85b08a2af7833df21b0cf7e4be1007e97ece435a 100644
--- a/src/USER-SDPD/fix_meso_move.cpp
+++ b/src/USER-SDPD/fix_meso_move.cpp
@@ -360,7 +360,7 @@ void FixMesoMove::init () {
}
void FixMesoMove::setup_pre_force (int /*vflag*/) {
- // set vest equal to v
+ // set vest equal to v
double **v = atom->v;
double **vest = atom->vest;
int *mask = atom->mask;
diff --git a/src/USER-SDPD/fix_rigid_meso.cpp b/src/USER-SDPD/fix_rigid_meso.cpp
index 4889acd0de76d5349f59c128461b825569965634..49c9ca86146e420ee814288f92b90e344fa1b279 100644
--- a/src/USER-SDPD/fix_rigid_meso.cpp
+++ b/src/USER-SDPD/fix_rigid_meso.cpp
@@ -20,7 +20,7 @@
/* ----------------------------------------------------------------------
Contributing author:
Morteza Jalalvand (IASBS) jalalvand.m AT gmail.com
-
+
This is an extension of fix/rigid/nve to SPH/SDPD particles
You can see the original copyright notice of fix/rigid authors above
Note that the Kamberaj paper was related to the nvt variant
@@ -53,10 +53,10 @@ FixRigid (lmp, narg, arg) {
if ((atom->e_flag != 1) || (atom->rho_flag != 1))
error->all (FLERR, "fix rigid/meso command requires atom_style with"
" both energy and density");
-
+
if (langflag || tstat_flag)
error->all (FLERR,"Can not use thermostat with fix rigid/meso");
-
+
if (pstat_flag)
error->all (FLERR,"Can not use barostat with fix rigid/meso");
@@ -277,11 +277,11 @@ void FixRigidMeso::set_xv () {
for (int i = 0; i < nlocal; i++) {
if (body[i] < 0) continue;
-
+
// half-step update of particle internal energy and density
e[i] += dtf * de[i];
rho[i] += dtf * drho[i];
-
+
ibody = body[i];
xbox = (xcmimage[i] & IMGMASK) - IMGMAX;
@@ -301,7 +301,7 @@ void FixRigidMeso::set_xv () {
x2 = x[i][2] + zbox*zprd;
}
}
-
+
v0 = v[i][0];
v1 = v[i][1];
v2 = v[i][2];
@@ -319,7 +319,7 @@ void FixRigidMeso::set_xv () {
vcm[ibody][1];
v[i][2] = omega[ibody][0]*x[i][1] - omega[ibody][1]*x[i][0] +
vcm[ibody][2];
-
+
vest[i][0] = 2*v[i][0] - v0;
vest[i][1] = 2*v[i][1] - v1;
vest[i][2] = 2*v[i][2] - v2;
@@ -406,11 +406,11 @@ void FixRigidMeso::set_v () {
for (int i = 0; i < nlocal; i++) {
if (body[i] < 0) continue;
-
+
// half-step update of particle internal energy and density
e[i] += dtf * de[i];
rho[i] += dtf * drho[i];
-
+
const int ibody = body[i];
MathExtra::matvec (ex_space[ibody],ey_space[ibody],
diff --git a/src/USER-SDPD/pair_sdpd_taitwater_isothermal.cpp b/src/USER-SDPD/pair_sdpd_taitwater_isothermal.cpp
index 0350843eb76177804b7cba5a3add4ab7fcbc6368..7cfc950eff072e21956554bcd29bcb6adaffbf65 100644
--- a/src/USER-SDPD/pair_sdpd_taitwater_isothermal.cpp
+++ b/src/USER-SDPD/pair_sdpd_taitwater_isothermal.cpp
@@ -14,7 +14,7 @@
/* ----------------------------------------------------------------------
Contributing author:
Morteza Jalalvand (IASBS) jalalvand.m AT gmail.com
-
+
references: Espanol and Revenga, Phys Rev E 67, 026705 (2003)
------------------------------------------------------------------------- */
@@ -169,7 +169,7 @@ void PairSDPDTaitwaterIsothermal::compute (int eflag, int vflag) {
wiener[0][0] = gaussian (generator);
wiener[1][1] = gaussian (generator);
wiener[2][2] = gaussian (generator);
-
+
wiener[0][1] = wiener[1][0] = sqrt_2_inv * gaussian (generator);
wiener[0][2] = wiener[2][0] = sqrt_2_inv * gaussian (generator);
wiener[1][2] = wiener[2][1] = sqrt_2_inv * gaussian (generator);
@@ -177,18 +177,18 @@ void PairSDPDTaitwaterIsothermal::compute (int eflag, int vflag) {
wiener[0][0] = random->gaussian ();
wiener[1][1] = random->gaussian ();
wiener[2][2] = random->gaussian ();
-
+
wiener[0][1] = wiener[1][0] = sqrt_2_inv * random->gaussian ();
wiener[0][2] = wiener[2][0] = sqrt_2_inv * random->gaussian ();
wiener[1][2] = wiener[2][1] = sqrt_2_inv * random->gaussian ();
#endif
-
+
prefactor = sqrt (-4. * kBoltzmann*temperature * fvisc * dtinv) / r;
-
+
f_random[0] = prefactor * (wiener[0][0]*delx + wiener[0][1]*dely + wiener[0][2]*delz);
f_random[1] = prefactor * (wiener[1][0]*delx + wiener[1][1]*dely + wiener[1][2]*delz);
f_random[2] = prefactor * (wiener[2][0]*delx + wiener[2][1]*dely + wiener[2][2]*delz);
-
+
f[i][0] += delx * fpair + (velx + delx * delVdotDelR / rsq) * fvisc + f_random[0];
f[i][1] += dely * fpair + (vely + dely * delVdotDelR / rsq) * fvisc + f_random[1];
f[i][2] += delz * fpair + (velz + delz * delVdotDelR / rsq) * fvisc + f_random[2];
@@ -241,13 +241,13 @@ void PairSDPDTaitwaterIsothermal::settings (int narg, char **arg) {
if (narg != 2 && narg != 3)
error->all (FLERR, "Illegal number of arguments for "
"pair_style sdpd/taitwater/morris/isothermal");
-
+
temperature = force->numeric (FLERR, arg[0]);
viscosity = force->numeric (FLERR, arg[1]);
-
+
if (temperature <= 0) error->all (FLERR, "Temperature must be positive");
if (viscosity <= 0) error->all (FLERR, "Viscosity must be positive");
-
+
// seed is immune to underflow/overflow because it is unsigned
seed = comm->nprocs + comm->me + atom->nlocal;
if (narg == 3) seed += force->inumeric (FLERR, arg[2]);
@@ -266,7 +266,7 @@ void PairSDPDTaitwaterIsothermal::coeff (int narg, char **arg) {
if (narg != 5)
error->all (FLERR, "Incorrect args for pair_style "
"sph/taitwater/morris coefficients");
-
+
if (!allocated) allocate();
int ilo, ihi, jlo, jhi;
@@ -277,7 +277,7 @@ void PairSDPDTaitwaterIsothermal::coeff (int narg, char **arg) {
double soundspeed_one = force->numeric (FLERR,arg[3]);
double cut_one = force->numeric (FLERR,arg[4]);
double B_one = soundspeed_one * soundspeed_one * rho0_one / 7.0;
-
+
if (rho0_one <= 0) error->all (FLERR, "Density must be positive");
if (soundspeed_one <= 0) error->all (FLERR, "Sound speed must be positive");
if (cut_one <= 0) error->all (FLERR, "Cutoff must be positive");
@@ -304,7 +304,7 @@ void PairSDPDTaitwaterIsothermal::coeff (int narg, char **arg) {
------------------------------------------------------------------------- */
double PairSDPDTaitwaterIsothermal::init_one (int i, int j) {
- if (setflag[i][j] == 0)
+ if (setflag[i][j] == 0)
error->all(FLERR,"Not all pair sph/taitwater/morris coeffs are set");
cut[j][i] = cut[i][j];
diff --git a/src/USER-UEF/uef_utils.cpp b/src/USER-UEF/uef_utils.cpp
index a2e6cb291e0cb4c7b4ff48e9d1d181d0b7f65e4a..75d4ee889503afdb6595a75a45cba44e012ba0f1 100644
--- a/src/USER-UEF/uef_utils.cpp
+++ b/src/USER-UEF/uef_utils.cpp
@@ -150,7 +150,7 @@ void UEFBox::step_deform(const double ex, const double ey)
theta[0] +=winv[0][0]*ex + winv[0][1]*ey;
theta[1] +=winv[1][0]*ex + winv[1][1]*ey;
- // deformation of the box. reduce() needs to be called regularly or
+ // deformation of the box. reduce() needs to be called regularly or
// calculation will become unstable
double eps[3];
@@ -169,7 +169,7 @@ void UEFBox::step_deform(const double ex, const double ey)
------------------------------------------------------------------------- */
bool UEFBox::reduce()
{
- // determine how many times to apply the automorphisms and find new theta
+ // determine how many times to apply the automorphisms and find new theta
// values
int f1 = round(theta[0]);
@@ -184,7 +184,7 @@ bool UEFBox::reduce()
for (int j=0;j<3;j++)
r0[k][j]=r[k][j];
- // this modifies the old change basis matrix to handle the case where the
+ // this modifies the old change basis matrix to handle the case where the
// automorphism transforms the box but the reduced basis doesn't change
// (r0 should still equal r at the end)
@@ -417,7 +417,7 @@ void make_unique(double b[3][3], int r[3][3], int ri[3][3])
if (fabs(b[0][0]) < fabs(b[0][1])) {
col_swap(b,0,1);
col_swap(r,0,1);
- col_swap(ri,0,1);
+ col_swap(ri,0,1);
}
if (fabs(b[0][0]) < fabs(b[0][2])) {
col_swap(b,0,2);
@@ -433,7 +433,7 @@ void make_unique(double b[3][3], int r[3][3], int ri[3][3])
if (b[0][0] < 0) {
neg_col(b,0);
neg_col(r,0);
- neg_col(ri,0);
+ neg_col(ri,0);
}
if (b[1][1] < 0) {
neg_col(b,1);
@@ -442,8 +442,8 @@ void make_unique(double b[3][3], int r[3][3], int ri[3][3])
}
if (det(b) < 0) {
neg_col(b,2);
- neg_col(r,2);
- neg_col(ri,2);
+ neg_col(r,2);
+ neg_col(ri,2);
}
}
}}