diff --git a/src/ASPHERE/pair_line_lj.cpp b/src/ASPHERE/pair_line_lj.cpp
index fc92ed4dc1b98565d64d3fffd328651b8fb40e69..83a6f4ea8c998ccef44ac408d3d7b523dc9be061 100644
--- a/src/ASPHERE/pair_line_lj.cpp
+++ b/src/ASPHERE/pair_line_lj.cpp
@@ -450,7 +450,7 @@ void PairLineLJ::discretize(int i, double size)
double length = bonus[atom->line[i]].length;
double theta = bonus[atom->line[i]].theta;
int n = static_cast<int> (length/size) + 1;
-
+
dnum[i] = n;
dfirst[i] = ndiscrete;
diff --git a/src/BODY/compute_body_local.cpp b/src/BODY/compute_body_local.cpp
index 46122435a372031ad5ab09dde05433f2da4e8771..e72dd59b25fb214cd6ae536333f2367dfdc1b3c4 100644
--- a/src/BODY/compute_body_local.cpp
+++ b/src/BODY/compute_body_local.cpp
@@ -62,7 +62,7 @@ ComputeBodyLocal::ComputeBodyLocal(LAMMPS *lmp, int narg, char **arg) :
int indexmax = bptr->noutcol();
for (int i = 0; i < nvalues; i++) {
- if (which[i] == INDEX && (index[i] < 0 || index[i] >= indexmax))
+ if (which[i] == INDEX && (index[i] < 0 || index[i] >= indexmax))
error->all(FLERR,"Invalid index in compute body/local command");
}
@@ -93,7 +93,7 @@ void ComputeBodyLocal::init()
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
- if (mask[i] & groupbit)
+ if (mask[i] & groupbit)
if (body[i] < 0) nonbody = 1;
int flag;
diff --git a/src/CLASS2/dihedral_class2.cpp b/src/CLASS2/dihedral_class2.cpp
index b985a862d2bd19be78c060b60c1731b99ea46c0b..b79f574829e3c40d3e4f4f2abdbe56a462d22612 100644
--- a/src/CLASS2/dihedral_class2.cpp
+++ b/src/CLASS2/dihedral_class2.cpp
@@ -664,7 +664,7 @@ void DihedralClass2::coeff(int narg, char **arg)
}
} else if (strcmp(arg[1],"ebt") == 0) {
- if (narg != 10)
+ if (narg != 10)
error->all(FLERR,"Incorrect args for dihedral coefficients");
double f1_1_one = force->numeric(FLERR,arg[2]);
@@ -690,7 +690,7 @@ void DihedralClass2::coeff(int narg, char **arg)
}
} else if (strcmp(arg[1],"at") == 0) {
- if (narg != 10)
+ if (narg != 10)
error->all(FLERR,"Incorrect args for dihedral coefficients");
double f1_1_one = force->numeric(FLERR,arg[2]);
diff --git a/src/GPU/pair_ufm_gpu.cpp b/src/GPU/pair_ufm_gpu.cpp
index 88f2c2d3ad47709b7397652a525a961beff38e6e..ad66c3871fa5a2a03820ce60e344f1c222294655 100644
--- a/src/GPU/pair_ufm_gpu.cpp
+++ b/src/GPU/pair_ufm_gpu.cpp
@@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
-
+
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
-
+
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
diff --git a/src/GPU/pair_vashishta_gpu.cpp b/src/GPU/pair_vashishta_gpu.cpp
index 19e0799671a9a05e2b722d32d2f33319f08e35d1..7d21aaa581763d7da631cebf1dbb42cfbce8f098 100644
--- a/src/GPU/pair_vashishta_gpu.cpp
+++ b/src/GPU/pair_vashishta_gpu.cpp
@@ -44,7 +44,7 @@ int vashishta_gpu_init(const int ntypes, const int inum, const int nall, const i
const double* gamma, const double* eta,
const double* lam1inv, const double* lam4inv,
const double* zizj, const double* mbigd,
- const double* dvrc, const double* big6w,
+ const double* dvrc, const double* big6w,
const double* heta, const double* bigh,
const double* bigw, const double* c0,
const double* costheta, const double* bigb,
@@ -133,7 +133,7 @@ void PairVashishtaGPU::allocate()
PairVashishta::allocate();
}
int n = atom->ntypes;
-
+
memory->create(cutghost,n+1,n+1,"pair:cutghost");
gpu_allocated = true;
}
@@ -162,7 +162,7 @@ void PairVashishtaGPU::init_style()
dvrc = big6w = heta = bigh = NULL;
bigw = c0 = costheta = bigb = NULL;
big2b = bigc = NULL;
-
+
memory->create(cutsq,nparams,"pair:cutsq");
memory->create(r0,nparams,"pair:r0");
memory->create(gamma,nparams,"pair:gamma");
@@ -204,8 +204,8 @@ void PairVashishtaGPU::init_style()
}
int success = vashishta_gpu_init(atom->ntypes+1, atom->nlocal, atom->nlocal+atom->nghost, 500,
cell_size, gpu_mode, screen, map, nelements,
- elem2param, nparams, cutsq, r0, gamma, eta, lam1inv,
- lam4inv, zizj, mbigd, dvrc, big6w, heta, bigh, bigw,
+ elem2param, nparams, cutsq, r0, gamma, eta, lam1inv,
+ lam4inv, zizj, mbigd, dvrc, big6w, heta, bigh, bigw,
c0, costheta, bigb, big2b, bigc);
memory->destroy(cutsq);
memory->destroy(r0);
diff --git a/src/GPU/pppm_gpu.cpp b/src/GPU/pppm_gpu.cpp
index 99f61a7fc953f4cb4b5e5f7a75d34cee44e44faf..b2b529f7ef1183494439c23c0c932ee11105bd2e 100644
--- a/src/GPU/pppm_gpu.cpp
+++ b/src/GPU/pppm_gpu.cpp
@@ -775,7 +775,7 @@ void PPPMGPU::compute_group_group(int groupbit_A, int groupbit_B, int AA_flag)
// extend size of per-atom arrays if necessary
// part2grid needs to be allocated
-
+
if (atom->nmax > nmax || part2grid == NULL) {
memory->destroy(part2grid);
nmax = atom->nmax;
diff --git a/src/KOKKOS/angle_class2_kokkos.cpp b/src/KOKKOS/angle_class2_kokkos.cpp
index 108b4f48f225827228fe1a5667edbd7a7c8ad6aa..670cfa152d44ac7fe3b8e1e121d42354bf1bcd8b 100644
--- a/src/KOKKOS/angle_class2_kokkos.cpp
+++ b/src/KOKKOS/angle_class2_kokkos.cpp
@@ -83,7 +83,7 @@ void AngleClass2Kokkos<DeviceType>::compute(int eflag_in, int vflag_in)
//atomKK->sync(execution_space,datamask_read);
//if (eflag || vflag) atomKK->modified(execution_space,datamask_modify);
//else atomKK->modified(execution_space,F_MASK);
-
+
k_theta0.template sync<DeviceType>();
k_k2.template sync<DeviceType>();
k_k3.template sync<DeviceType>();
@@ -222,7 +222,7 @@ void AngleClass2Kokkos<DeviceType>::operator()(TagAngleClass2Compute<NEWTON_BOND
if (eflag) eangle = d_k2[type]*dtheta2 + d_k3[type]*dtheta3 + d_k4[type]*dtheta4;
// force & energy for bond-bond term
-
+
const F_FLOAT dr1 = r1 - d_bb_r1[type];
const F_FLOAT dr2 = r2 - d_bb_r2[type];
const F_FLOAT tk1 = d_bb_k[type] * dr1;
diff --git a/src/KOKKOS/atom_vec_dpd_kokkos.cpp b/src/KOKKOS/atom_vec_dpd_kokkos.cpp
index 8f453f1e0d04d6a13e46b687df3b330480c915ac..ca1779d0eeb7807e84d17461631b9bafeee7d0a5 100644
--- a/src/KOKKOS/atom_vec_dpd_kokkos.cpp
+++ b/src/KOKKOS/atom_vec_dpd_kokkos.cpp
@@ -368,7 +368,7 @@ struct AtomVecDPDKokkos_PackCommSelf {
_dpdTheta(dpdTheta.view<DeviceType>()),
_uCond(uCond.view<DeviceType>()),
_uMech(uMech.view<DeviceType>()),
- _uChem(uChem.view<DeviceType>()),
+ _uChem(uChem.view<DeviceType>()),
_nfirst(nfirst),_list(list.view<DeviceType>()),_iswap(iswap),
_xprd(xprd),_yprd(yprd),_zprd(zprd),
_xy(xy),_xz(xz),_yz(yz) {
@@ -397,7 +397,7 @@ struct AtomVecDPDKokkos_PackCommSelf {
_dpdTheta(i+_nfirst) = _dpdTheta(j);
_uCond(i+_nfirst) = _uCond(j);
_uMech(i+_nfirst) = _uMech(j);
- _uChem(i+_nfirst) = _uChem(j);
+ _uChem(i+_nfirst) = _uChem(j);
}
};
@@ -656,7 +656,7 @@ int AtomVecDPDKokkos::pack_comm_vel(int n, int *list, double *buf,
buf[m++] = h_dpdTheta(j);
buf[m++] = h_uCond(j);
buf[m++] = h_uMech(j);
- buf[m++] = h_uChem(j);
+ buf[m++] = h_uChem(j);
}
}
}
diff --git a/src/KOKKOS/comm_kokkos.cpp b/src/KOKKOS/comm_kokkos.cpp
index e8eb8b2b825dc710b6b8bb95b07931ed028c74b5..b41849197be85d30188cbce317fadea4608008f4 100644
--- a/src/KOKKOS/comm_kokkos.cpp
+++ b/src/KOKKOS/comm_kokkos.cpp
@@ -292,7 +292,7 @@ void CommKokkos::reverse_comm_device()
MPI_Request request;
AtomVecKokkos *avec = (AtomVecKokkos *) atom->avec;
double *buf;
-
+
// exchange data with another proc
// if other proc is self, just copy
// if comm_f_only set, exchange or copy directly from f, don't pack
@@ -309,7 +309,7 @@ void CommKokkos::reverse_comm_device()
if (size_reverse_send[iswap]) {
buf = atomKK->k_f.view<DeviceType>().ptr_on_device() +
firstrecv[iswap]*atomKK->k_f.view<DeviceType>().dimension_1();
-
+
MPI_Send(buf,size_reverse_send[iswap],MPI_DOUBLE,
recvproc[iswap],0,world);
}
@@ -718,7 +718,7 @@ void CommKokkos::borders()
exchange_comm_classic = true;
}
}
-
+
if (!exchange_comm_classic) {
if (exchange_comm_on_host) borders_device<LMPHostType>();
else borders_device<LMPDeviceType>();
diff --git a/src/KOKKOS/dihedral_class2_kokkos.cpp b/src/KOKKOS/dihedral_class2_kokkos.cpp
index d32ea4a4611089808f31faf7756967f6572e0f94..85013ddd9b753281b454508e22649c78e1d2557e 100644
--- a/src/KOKKOS/dihedral_class2_kokkos.cpp
+++ b/src/KOKKOS/dihedral_class2_kokkos.cpp
@@ -87,7 +87,7 @@ void DihedralClass2Kokkos<DeviceType>::compute(int eflag_in, int vflag_in)
//atomKK->sync(execution_space,datamask_read);
k_k1.template sync<DeviceType>();
- k_k2.template sync<DeviceType>();
+ k_k2.template sync<DeviceType>();
k_k3.template sync<DeviceType>();
k_phi1.template sync<DeviceType>();
k_phi2.template sync<DeviceType>();
@@ -95,7 +95,7 @@ void DihedralClass2Kokkos<DeviceType>::compute(int eflag_in, int vflag_in)
k_mbt_f1.template sync<DeviceType>();
k_mbt_f2.template sync<DeviceType>();
k_mbt_f3.template sync<DeviceType>();
- k_mbt_r0.template sync<DeviceType>();
+ k_mbt_r0.template sync<DeviceType>();
k_ebt_f1_1.template sync<DeviceType>();
k_ebt_f2_1.template sync<DeviceType>();
k_ebt_f3_1.template sync<DeviceType>();
@@ -108,21 +108,21 @@ void DihedralClass2Kokkos<DeviceType>::compute(int eflag_in, int vflag_in)
k_at_f2_1.template sync<DeviceType>();
k_at_f3_1.template sync<DeviceType>();
k_at_f1_2.template sync<DeviceType>();
- k_at_f2_2.template sync<DeviceType>();
- k_at_f3_2.template sync<DeviceType>();
+ k_at_f2_2.template sync<DeviceType>();
+ k_at_f3_2.template sync<DeviceType>();
k_at_theta0_1.template sync<DeviceType>();
k_at_theta0_2.template sync<DeviceType>();
k_aat_k.template sync<DeviceType>();
k_aat_theta0_1.template sync<DeviceType>();
k_aat_theta0_2.template sync<DeviceType>();
- k_bb13t_k.template sync<DeviceType>();
+ k_bb13t_k.template sync<DeviceType>();
k_bb13t_r10.template sync<DeviceType>();
- k_bb13t_r30.template sync<DeviceType>();
- k_setflag_d.template sync<DeviceType>();
+ k_bb13t_r30.template sync<DeviceType>();
+ k_setflag_d.template sync<DeviceType>();
k_setflag_mbt.template sync<DeviceType>();
k_setflag_ebt.template sync<DeviceType>();
- k_setflag_at.template sync<DeviceType>();
- k_setflag_aat.template sync<DeviceType>();
+ k_setflag_at.template sync<DeviceType>();
+ k_setflag_aat.template sync<DeviceType>();
k_setflag_bb13t.template sync<DeviceType>();
//if (eflag || vflag) atomKK->modified(execution_space,datamask_modify);
@@ -229,7 +229,7 @@ void DihedralClass2Kokkos<DeviceType>::operator()(TagDihedralClass2Compute<NEWTO
const F_FLOAT vb3z = x(i4,2) - x(i3,2);
// distance: c0 calculation
-
+
const F_FLOAT r1mag2 = vb1x*vb1x + vb1y*vb1y + vb1z*vb1z;
const F_FLOAT r1 = sqrt(r1mag2);
const F_FLOAT r2mag2 = vb2x*vb2x + vb2y*vb2y + vb2z*vb2z;
@@ -247,7 +247,7 @@ void DihedralClass2Kokkos<DeviceType>::operator()(TagDihedralClass2Compute<NEWTO
const F_FLOAT c0 = (vb1x*vb3x + vb1y*vb3y + vb1z*vb3z) * rb1*rb3;
// 1st and 2nd angle
-
+
const F_FLOAT r12c1 = rb1*rb2;
const F_FLOAT r12c2 = rb2*rb3;
const F_FLOAT costh12 = (vb1x*vb2x + vb1y*vb2y + vb1z*vb2z) * r12c1;
@@ -393,7 +393,7 @@ void DihedralClass2Kokkos<DeviceType>::operator()(TagDihedralClass2Compute<NEWTO
// set up d(theta)/d(r) array
// dthetadr(i,j,k) = angle i, atom j, coordinate k
-
+
F_FLOAT dthetadr[2][4][3];
for (int i = 0; i < 2; i++)
@@ -593,9 +593,9 @@ void DihedralClass2Kokkos<DeviceType>::operator()(TagDihedralClass2Compute<NEWTO
fabcd[3][1] += tk1 * vb3y;
fabcd[3][2] += tk1 * vb3z;
}
-
+
F_FLOAT f1[3],f2[3],f3[3],f4[3];
-
+
for (int i = 0; i < 3; i++) {
f1[i] = fabcd[0][i];
f2[i] = fabcd[1][i];
@@ -781,8 +781,8 @@ void DihedralClass2Kokkos<DeviceType>::coeff(int narg, char **arg)
k_setflag_bb13t.h_view[i] = setflag_bb13t[i];
}
- k_k1.template modify<LMPHostType>();
- k_k2.template modify<LMPHostType>();
+ k_k1.template modify<LMPHostType>();
+ k_k2.template modify<LMPHostType>();
k_k3.template modify<LMPHostType>();
k_phi1.template modify<LMPHostType>();
k_phi2.template modify<LMPHostType>();
@@ -790,7 +790,7 @@ void DihedralClass2Kokkos<DeviceType>::coeff(int narg, char **arg)
k_mbt_f1.template modify<LMPHostType>();
k_mbt_f2.template modify<LMPHostType>();
k_mbt_f3.template modify<LMPHostType>();
- k_mbt_r0.template modify<LMPHostType>();
+ k_mbt_r0.template modify<LMPHostType>();
k_ebt_f1_1.template modify<LMPHostType>();
k_ebt_f2_1.template modify<LMPHostType>();
k_ebt_f3_1.template modify<LMPHostType>();
@@ -803,21 +803,21 @@ void DihedralClass2Kokkos<DeviceType>::coeff(int narg, char **arg)
k_at_f2_1.template modify<LMPHostType>();
k_at_f3_1.template modify<LMPHostType>();
k_at_f1_2.template modify<LMPHostType>();
- k_at_f2_2.template modify<LMPHostType>();
- k_at_f3_2.template modify<LMPHostType>();
+ k_at_f2_2.template modify<LMPHostType>();
+ k_at_f3_2.template modify<LMPHostType>();
k_at_theta0_1.template modify<LMPHostType>();
k_at_theta0_2.template modify<LMPHostType>();
k_aat_k.template modify<LMPHostType>();
k_aat_theta0_1.template modify<LMPHostType>();
k_aat_theta0_2.template modify<LMPHostType>();
- k_bb13t_k.template modify<LMPHostType>();
+ k_bb13t_k.template modify<LMPHostType>();
k_bb13t_r10.template modify<LMPHostType>();
- k_bb13t_r30.template modify<LMPHostType>();
- k_setflag_d.template modify<LMPHostType>();
+ k_bb13t_r30.template modify<LMPHostType>();
+ k_setflag_d.template modify<LMPHostType>();
k_setflag_mbt.template modify<LMPHostType>();
k_setflag_ebt.template modify<LMPHostType>();
- k_setflag_at.template modify<LMPHostType>();
- k_setflag_aat.template modify<LMPHostType>();
+ k_setflag_at.template modify<LMPHostType>();
+ k_setflag_aat.template modify<LMPHostType>();
k_setflag_bb13t.template modify<LMPHostType>();
}
diff --git a/src/KOKKOS/fix_momentum_kokkos.cpp b/src/KOKKOS/fix_momentum_kokkos.cpp
index 8dc4a1555152872fd5b2b6342b04559653a1fd48..9ffe67a46ba7615efd9255f6a95500bcbe69af6e 100644
--- a/src/KOKKOS/fix_momentum_kokkos.cpp
+++ b/src/KOKKOS/fix_momentum_kokkos.cpp
@@ -116,7 +116,7 @@ void FixMomentumKokkos<DeviceType>::end_of_step()
// adjust velocities by vcm to zero linear momentum
// only adjust a component if flag is set
-
+
auto xflag2 = xflag;
auto yflag2 = yflag;
auto zflag2 = zflag;
diff --git a/src/KOKKOS/fix_qeq_reax_kokkos.cpp b/src/KOKKOS/fix_qeq_reax_kokkos.cpp
index 95e9fc9dead468a4a6c796cfcc610dc8fab44236..ca2525d4f0783f14851fe4c9c69b5fbd57fac32e 100644
--- a/src/KOKKOS/fix_qeq_reax_kokkos.cpp
+++ b/src/KOKKOS/fix_qeq_reax_kokkos.cpp
@@ -93,13 +93,13 @@ void FixQEqReaxKokkos<DeviceType>::init()
neighflag = lmp->kokkos->neighflag_qeq;
int irequest = neighbor->nrequest - 1;
-
+
neighbor->requests[irequest]->
kokkos_host = Kokkos::Impl::is_same<DeviceType,LMPHostType>::value &&
!Kokkos::Impl::is_same<DeviceType,LMPDeviceType>::value;
neighbor->requests[irequest]->
kokkos_device = Kokkos::Impl::is_same<DeviceType,LMPDeviceType>::value;
-
+
if (neighflag == FULL) {
neighbor->requests[irequest]->fix = 1;
neighbor->requests[irequest]->pair = 0;
diff --git a/src/KOKKOS/fix_rx_kokkos.cpp b/src/KOKKOS/fix_rx_kokkos.cpp
index 61290ece33dfb72c50dc787542e4cea50fe5a077..0319c79cb35b8a1ecfddae39ecb7d7fec68f3258 100644
--- a/src/KOKKOS/fix_rx_kokkos.cpp
+++ b/src/KOKKOS/fix_rx_kokkos.cpp
@@ -152,7 +152,7 @@ void FixRxKokkos<DeviceType>::init()
!Kokkos::Impl::is_same<DeviceType,LMPDeviceType>::value;
neighbor->requests[irequest]->
kokkos_device = Kokkos::Impl::is_same<DeviceType,LMPDeviceType>::value;
-
+
if (neighflag == FULL) {
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->half = 0;
@@ -1493,10 +1493,10 @@ void FixRxKokkos<DeviceType>::solve_reactions(const int vflag, const bool isPreF
// ...
// Local references to the atomKK objects.
- //typename ArrayTypes<DeviceType>::t_efloat_1d d_dpdTheta = atomKK->k_dpdTheta.view<DeviceType>();
+ //typename ArrayTypes<DeviceType>::t_efloat_1d d_dpdTheta = atomKK->k_dpdTheta.view<DeviceType>();
//typename ArrayTypes<DeviceType>::t_float_2d d_dvector = atomKK->k_dvector.view<DeviceType>();
//typename ArrayTypes<DeviceType>::t_int_1d d_mask = atomKK->k_mask.view<DeviceType>();
- this->d_dpdTheta = atomKK->k_dpdTheta.view<DeviceType>();
+ this->d_dpdTheta = atomKK->k_dpdTheta.view<DeviceType>();
this->d_dvector = atomKK->k_dvector.view<DeviceType>();
this->d_mask = atomKK->k_mask.view<DeviceType>();
@@ -1920,7 +1920,7 @@ void FixRxKokkos<DeviceType>::operator()(Tag_FixRxKokkos_firstPairOperator<WT_FL
double i_sumWeights = 0.0;
const int i = d_ilist(ii);
-
+
const double xtmp = d_x(i,0);
const double ytmp = d_x(i,1);
const double ztmp = d_x(i,2);
@@ -2000,10 +2000,10 @@ void FixRxKokkos<DeviceType>::computeLocalTemperature()
{
//typename ArrayTypes<DeviceType>::t_x_array_randomread d_x = atomKK->k_x.view<DeviceType>();
//typename ArrayTypes<DeviceType>::t_int_1d_randomread d_type = atomKK->k_type.view<DeviceType>();
- //typename ArrayTypes<DeviceType>::t_efloat_1d d_dpdTheta = atomKK->k_dpdTheta.view<DeviceType>();
+ //typename ArrayTypes<DeviceType>::t_efloat_1d d_dpdTheta = atomKK->k_dpdTheta.view<DeviceType>();
d_x = atomKK->k_x.view<DeviceType>();
d_type = atomKK->k_type.view<DeviceType>();
- d_dpdTheta = atomKK->k_dpdTheta.view<DeviceType>();
+ d_dpdTheta = atomKK->k_dpdTheta.view<DeviceType>();
atomKK->sync(execution_space, X_MASK | TYPE_MASK | DPDTHETA_MASK );
@@ -2096,7 +2096,7 @@ void FixRxKokkos<DeviceType>::computeLocalTemperature()
double i_sumWeights = 0.0;
const int i = d_ilist(ii);
-
+
const double xtmp = d_x(i,0);
const double ytmp = d_x(i,1);
const double ztmp = d_x(i,2);
diff --git a/src/KOKKOS/improper_class2_kokkos.cpp b/src/KOKKOS/improper_class2_kokkos.cpp
index d2d465a250f1ff97bfd4668fe26eec489f62f850..2171305a9ce0599858dfcbc502de9700061aa6bb 100644
--- a/src/KOKKOS/improper_class2_kokkos.cpp
+++ b/src/KOKKOS/improper_class2_kokkos.cpp
@@ -252,7 +252,7 @@ void ImproperClass2Kokkos<DeviceType>::operator()(TagImproperClass2Compute<NEWTO
delr[2][2] = x(i4,2) - x(i2,2);
// bond lengths and associated values
-
+
for (i = 0; i < 3; i++) {
rmag2[i] = delr[i][0]*delr[i][0] + delr[i][1]*delr[i][1] + delr[i][2]*delr[i][2];
rmag[i] = sqrt(rmag2[i]);
diff --git a/src/KOKKOS/kokkos.cpp b/src/KOKKOS/kokkos.cpp
index 5a742233534403a48b99ca12eae8f8873583401f..5f81078afdfb97f62404d9574f464afd3c8ab764 100644
--- a/src/KOKKOS/kokkos.cpp
+++ b/src/KOKKOS/kokkos.cpp
@@ -176,7 +176,7 @@ void KokkosLMP::accelerator(int narg, char **arg)
else if (strcmp(arg[iarg+1],"half") == 0) {
if (num_threads > 1 || ngpu > 0)
neighflag = HALFTHREAD;
- else
+ else
neighflag = HALF;
} else if (strcmp(arg[iarg+1],"n2") == 0) neighflag = N2;
else error->all(FLERR,"Illegal package kokkos command");
@@ -188,7 +188,7 @@ void KokkosLMP::accelerator(int narg, char **arg)
else if (strcmp(arg[iarg+1],"half") == 0) {
if (num_threads > 1 || ngpu > 0)
neighflag_qeq = HALFTHREAD;
- else
+ else
neighflag_qeq = HALF;
} else if (strcmp(arg[iarg+1],"n2") == 0) neighflag_qeq = N2;
else error->all(FLERR,"Illegal package kokkos command");
diff --git a/src/KOKKOS/neighbor_kokkos.cpp b/src/KOKKOS/neighbor_kokkos.cpp
index 8d36add10bd6a10d8d861cd0cff5a27cef5fd1f3..ea90a182709160fc80e50a53b364463eb6f4783f 100644
--- a/src/KOKKOS/neighbor_kokkos.cpp
+++ b/src/KOKKOS/neighbor_kokkos.cpp
@@ -386,7 +386,7 @@ void NeighborKokkos::build_topology() {
k_improperlist = neighbond_device.k_improperlist;
// Transfer topology neighbor lists to Host for non-Kokkos styles
-
+
if (force->bond && force->bond->execution_space == Host)
k_bondlist.sync<LMPHostType>();
if (force->angle && force->angle->execution_space == Host)
diff --git a/src/KOKKOS/pair_eam_kokkos.cpp b/src/KOKKOS/pair_eam_kokkos.cpp
index 0aa43b26b2112f6970bae5562b506b4cabe6718d..ffa65acb87db22116d32361ea1c049ae38c69e0a 100644
--- a/src/KOKKOS/pair_eam_kokkos.cpp
+++ b/src/KOKKOS/pair_eam_kokkos.cpp
@@ -534,11 +534,11 @@ void PairEAMKokkos<DeviceType>::operator()(TagPairEAMKernelA<NEIGHFLAG,NEWTON_PA
p -= m;
p = MIN(p,1.0);
const int d_type2rhor_ji = d_type2rhor(jtype,itype);
- rhotmp += ((d_rhor_spline(d_type2rhor_ji,m,3)*p + d_rhor_spline(d_type2rhor_ji,m,4))*p +
+ rhotmp += ((d_rhor_spline(d_type2rhor_ji,m,3)*p + d_rhor_spline(d_type2rhor_ji,m,4))*p +
d_rhor_spline(d_type2rhor_ji,m,5))*p + d_rhor_spline(d_type2rhor_ji,m,6);
if (NEWTON_PAIR || j < nlocal) {
const int d_type2rhor_ij = d_type2rhor(itype,jtype);
- rho[j] += ((d_rhor_spline(d_type2rhor_ij,m,3)*p + d_rhor_spline(d_type2rhor_ij,m,4))*p +
+ rho[j] += ((d_rhor_spline(d_type2rhor_ij,m,3)*p + d_rhor_spline(d_type2rhor_ij,m,4))*p +
d_rhor_spline(d_type2rhor_ij,m,5))*p + d_rhor_spline(d_type2rhor_ij,m,6);
}
}
@@ -570,7 +570,7 @@ void PairEAMKokkos<DeviceType>::operator()(TagPairEAMKernelB<EFLAG>, const int &
const int d_type2frho_i = d_type2frho[itype];
d_fp[i] = (d_frho_spline(d_type2frho_i,m,0)*p + d_frho_spline(d_type2frho_i,m,1))*p + d_frho_spline(d_type2frho_i,m,2);
if (EFLAG) {
- F_FLOAT phi = ((d_frho_spline(d_type2frho_i,m,3)*p + d_frho_spline(d_type2frho_i,m,4))*p +
+ F_FLOAT phi = ((d_frho_spline(d_type2frho_i,m,3)*p + d_frho_spline(d_type2frho_i,m,4))*p +
d_frho_spline(d_type2frho_i,m,5))*p + d_frho_spline(d_type2frho_i,m,6);
if (d_rho[i] > rhomax) phi += d_fp[i] * (d_rho[i]-rhomax);
if (eflag_global) ev.evdwl += phi;
@@ -625,7 +625,7 @@ void PairEAMKokkos<DeviceType>::operator()(TagPairEAMKernelAB<EFLAG>, const int
p -= m;
p = MIN(p,1.0);
const int d_type2rhor_ji = d_type2rhor(jtype,itype);
- rhotmp += ((d_rhor_spline(d_type2rhor_ji,m,3)*p + d_rhor_spline(d_type2rhor_ji,m,4))*p +
+ rhotmp += ((d_rhor_spline(d_type2rhor_ji,m,3)*p + d_rhor_spline(d_type2rhor_ji,m,4))*p +
d_rhor_spline(d_type2rhor_ji,m,5))*p + d_rhor_spline(d_type2rhor_ji,m,6);
}
@@ -645,7 +645,7 @@ void PairEAMKokkos<DeviceType>::operator()(TagPairEAMKernelAB<EFLAG>, const int
const int d_type2frho_i = d_type2frho[itype];
d_fp[i] = (d_frho_spline(d_type2frho_i,m,0)*p + d_frho_spline(d_type2frho_i,m,1))*p + d_frho_spline(d_type2frho_i,m,2);
if (EFLAG) {
- F_FLOAT phi = ((d_frho_spline(d_type2frho_i,m,3)*p + d_frho_spline(d_type2frho_i,m,4))*p +
+ F_FLOAT phi = ((d_frho_spline(d_type2frho_i,m,3)*p + d_frho_spline(d_type2frho_i,m,4))*p +
d_frho_spline(d_type2frho_i,m,5))*p + d_frho_spline(d_type2frho_i,m,6);
if (d_rho[i] > rhomax) phi += d_fp[i] * (d_rho[i]-rhomax);
if (eflag_global) ev.evdwl += phi;
@@ -718,12 +718,12 @@ void PairEAMKokkos<DeviceType>::operator()(TagPairEAMKernelC<NEIGHFLAG,NEWTON_PA
const F_FLOAT rhoip = (d_rhor_spline(d_type2rhor_ij,m,0)*p + d_rhor_spline(d_type2rhor_ij,m,1))*p +
d_rhor_spline(d_type2rhor_ij,m,2);
const int d_type2rhor_ji = d_type2rhor(jtype,itype);
- const F_FLOAT rhojp = (d_rhor_spline(d_type2rhor_ji,m,0)*p + d_rhor_spline(d_type2rhor_ji,m,1))*p +
+ const F_FLOAT rhojp = (d_rhor_spline(d_type2rhor_ji,m,0)*p + d_rhor_spline(d_type2rhor_ji,m,1))*p +
d_rhor_spline(d_type2rhor_ji,m,2);
const int d_type2z2r_ij = d_type2z2r(itype,jtype);
- const F_FLOAT z2p = (d_z2r_spline(d_type2z2r_ij,m,0)*p + d_z2r_spline(d_type2z2r_ij,m,1))*p +
+ const F_FLOAT z2p = (d_z2r_spline(d_type2z2r_ij,m,0)*p + d_z2r_spline(d_type2z2r_ij,m,1))*p +
d_z2r_spline(d_type2z2r_ij,m,2);
- const F_FLOAT z2 = ((d_z2r_spline(d_type2z2r_ij,m,3)*p + d_z2r_spline(d_type2z2r_ij,m,4))*p +
+ const F_FLOAT z2 = ((d_z2r_spline(d_type2z2r_ij,m,3)*p + d_z2r_spline(d_type2z2r_ij,m,4))*p +
d_z2r_spline(d_type2z2r_ij,m,5))*p + d_z2r_spline(d_type2z2r_ij,m,6);
const F_FLOAT recip = 1.0/r;
diff --git a/src/KOKKOS/pair_exp6_rx_kokkos.cpp b/src/KOKKOS/pair_exp6_rx_kokkos.cpp
index a09a1d27e34c544c15c79de45ff28ee6a2650e54..5f8e724a60a9a6828a0bdfbab9e7cfcaedbff4be 100644
--- a/src/KOKKOS/pair_exp6_rx_kokkos.cpp
+++ b/src/KOKKOS/pair_exp6_rx_kokkos.cpp
@@ -771,7 +771,7 @@ void PairExp6rxKokkos<DeviceType>::operator()(TagPairExp6rxCompute<NEIGHFLAG,NEW
evdwl = evdwlOld;
if (EVFLAG)
ev.evdwl += (((NEIGHFLAG==HALF || NEIGHFLAG==HALFTHREAD) && (NEWTON_PAIR||(j<nlocal)))?1.0:0.5)*evdwl;
- //if (vflag_either || eflag_atom)
+ //if (vflag_either || eflag_atom)
if (EVFLAG) this->template ev_tally<NEIGHFLAG,NEWTON_PAIR>(ev,i,j,evdwl,fpair,delx,dely,delz);
}
}
@@ -1142,7 +1142,7 @@ void PairExp6rxKokkos<DeviceType>::operator()(TagPairExp6rxComputeNoAtomics<NEIG
evdwl = evdwlOld;
if (EVFLAG)
ev.evdwl += (((NEIGHFLAG==HALF || NEIGHFLAG==HALFTHREAD) && (NEWTON_PAIR||(j<nlocal)))?1.0:0.5)*evdwl;
- //if (vflag_either || eflag_atom)
+ //if (vflag_either || eflag_atom)
if (EVFLAG) this->template ev_tally<NEIGHFLAG,NEWTON_PAIR>(ev,i,j,evdwl,fpair,delx,dely,delz);
}
}
@@ -1588,7 +1588,7 @@ void PairExp6rxKokkos<DeviceType>::vectorized_operator(const int &ii, EV_FLOAT&
double evdwl = evdwlOld_j[jlane];
if (EVFLAG)
ev.evdwl += (((NEIGHFLAG==HALF || NEIGHFLAG==HALFTHREAD) && (NEWTON_PAIR||(j<nlocal)))?1.0:0.5)*evdwl;
- //if (vflag_either || eflag_atom)
+ //if (vflag_either || eflag_atom)
if (EVFLAG) this->template ev_tally<NEIGHFLAG,NEWTON_PAIR>(ev,i,j,evdwl,fpair_j[jlane],delx_j[jlane],dely_j[jlane],delz_j[jlane]);
}
}
@@ -1678,7 +1678,7 @@ template<class DeviceType>
void PairExp6rxKokkos<DeviceType>::coeff(int narg, char **arg)
{
PairExp6rx::coeff(narg,arg);
-
+
if (scalingFlag == POLYNOMIAL)
for (int i = 0; i < 6; i++) {
s_coeffAlpha[i] = coeffAlpha[i];
@@ -2117,7 +2117,7 @@ void partition_range( const int begin, const int end, int &thread_begin, int &th
#ifndef KOKKOS_HAVE_CUDA
template<class DeviceType>
template<class ArrayT>
-void PairExp6rxKokkos<DeviceType>::getMixingWeightsVect(const int np_total, int errorFlag,
+void PairExp6rxKokkos<DeviceType>::getMixingWeightsVect(const int np_total, int errorFlag,
ArrayT &epsilon1, ArrayT &alpha1, ArrayT &rm1, ArrayT &mixWtSite1, ArrayT &epsilon2, ArrayT &alpha2, ArrayT &rm2, ArrayT &mixWtSite2, ArrayT &epsilon1_old, ArrayT &alpha1_old, ArrayT &rm1_old, ArrayT &mixWtSite1old, ArrayT &epsilon2_old, ArrayT &alpha2_old, ArrayT &rm2_old, ArrayT &mixWtSite2old) const
{
ArrayT epsilon = PairExp6ParamDataVect.epsilon ;
diff --git a/src/KOKKOS/pair_morse_kokkos.cpp b/src/KOKKOS/pair_morse_kokkos.cpp
index 5768d7e42cedba7cbdfb16bec74a765af657b837..dd555b6eb9cf937be79a1377096a4687b026ca92 100644
--- a/src/KOKKOS/pair_morse_kokkos.cpp
+++ b/src/KOKKOS/pair_morse_kokkos.cpp
@@ -167,7 +167,7 @@ compute_fpair(const F_FLOAT& rsq, const int& i, const int&j, const int& itype, c
const F_FLOAT d0 = STACKPARAMS ? m_params[itype][jtype].d0 : params(itype,jtype).d0;
const F_FLOAT aa = STACKPARAMS ? m_params[itype][jtype].alpha : params(itype,jtype).alpha;
const F_FLOAT dr = rr - r0;
-
+
// U = d0 * [ exp( -2*a*(x-r0)) - 2*exp(-a*(x-r0)) ]
// f = -2*a*d0*[ -exp( -2*a*(x-r0) ) + exp( -a*(x-r0) ) ] * grad(r)
// = +2*a*d0*[ exp( -2*a*(x-r0) ) - exp( -a*(x-r0) ) ] * grad(r)
@@ -189,7 +189,7 @@ compute_evdwl(const F_FLOAT& rsq, const int& i, const int&j, const int& itype, c
const F_FLOAT d0 = STACKPARAMS ? m_params[itype][jtype].d0 : params(itype,jtype).d0;
const F_FLOAT aa = STACKPARAMS ? m_params[itype][jtype].alpha : params(itype,jtype).alpha;
const F_FLOAT dr = rr - r0;
-
+
// U = d0 * [ exp( -2*a*(x-r0)) - 2*exp(-a*(x-r0)) ]
// f = -2*a*d0*[ -exp( -2*a*(x-r0) ) + exp( -a*(x-r0) ) ] * grad(r)
// = +2*a*d0*[ exp( -2*a*(x-r0) ) - exp( -a*(x-r0) ) ] * grad(r)
@@ -286,7 +286,7 @@ double PairMorseKokkos<DeviceType>::init_one(int i, int j)
k_params.h_view(i,j).offset = offset[i][j];
k_params.h_view(i,j).cutsq = cutone*cutone;
k_params.h_view(j,i) = k_params.h_view(i,j);
-
+
if(i<MAX_TYPES_STACKPARAMS+1 && j<MAX_TYPES_STACKPARAMS+1) {
m_params[i][j] = m_params[j][i] = k_params.h_view(i,j);
m_cutsq[j][i] = m_cutsq[i][j] = cutone*cutone;
diff --git a/src/KOKKOS/pair_reaxc_kokkos.cpp b/src/KOKKOS/pair_reaxc_kokkos.cpp
index 232ed5a1b93872def211ccb5f93193b0fffb28f7..7a72a24e3b434d1f93fbef6d65ef5730c67569fd 100644
--- a/src/KOKKOS/pair_reaxc_kokkos.cpp
+++ b/src/KOKKOS/pair_reaxc_kokkos.cpp
@@ -391,14 +391,14 @@ void PairReaxCKokkos<DeviceType>::init_md()
typename LR_lookup_table_kk<DeviceType>::tdual_cubic_spline_coef_1d k_CEvd = typename LR_lookup_table_kk<DeviceType>::tdual_cubic_spline_coef_1d("lookup:LR[i,j].CEvd",n);
typename LR_lookup_table_kk<DeviceType>::tdual_cubic_spline_coef_1d k_ele = typename LR_lookup_table_kk<DeviceType>::tdual_cubic_spline_coef_1d("lookup:LR[i,j].ele",n);
typename LR_lookup_table_kk<DeviceType>::tdual_cubic_spline_coef_1d k_CEclmb = typename LR_lookup_table_kk<DeviceType>::tdual_cubic_spline_coef_1d("lookup:LR[i,j].CEclmb",n);
-
+
k_LR.h_view(i,j).d_y = k_y.template view<DeviceType>();
k_LR.h_view(i,j).d_H = k_H.template view<DeviceType>();
k_LR.h_view(i,j).d_vdW = k_vdW.template view<DeviceType>();
k_LR.h_view(i,j).d_CEvd = k_CEvd.template view<DeviceType>();
k_LR.h_view(i,j).d_ele = k_ele.template view<DeviceType>();
k_LR.h_view(i,j).d_CEclmb = k_CEclmb.template view<DeviceType>();
-
+
for (int k = 0; k < n; k++) {
k_y.h_view(k) = LR[i][j].y[k];
k_H.h_view(k) = LR[i][j].H[k];
@@ -407,14 +407,14 @@ void PairReaxCKokkos<DeviceType>::init_md()
k_ele.h_view(k) = LR[i][j].ele[k];
k_CEclmb.h_view(k) = LR[i][j].CEclmb[k];
}
-
+
k_y.template modify<LMPHostType>();
k_H.template modify<LMPHostType>();
k_vdW.template modify<LMPHostType>();
k_CEvd.template modify<LMPHostType>();
k_ele.template modify<LMPHostType>();
k_CEclmb.template modify<LMPHostType>();
-
+
k_y.template sync<DeviceType>();
k_H.template sync<DeviceType>();
k_vdW.template sync<DeviceType>();
@@ -3191,15 +3191,15 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeHydrogen<NEIGHFLAG,E
for (int d = 0; d < 3; d++) fi_tmp[d] = CEhb2 * dcos_theta_di[d];
for (int d = 0; d < 3; d++) fj_tmp[d] = CEhb2 * dcos_theta_dj[d];
for (int d = 0; d < 3; d++) fk_tmp[d] = CEhb2 * dcos_theta_dk[d];
-
+
// dr terms
for (int d = 0; d < 3; d++) fi_tmp[d] -= CEhb3/rik * delik[d];
for (int d = 0; d < 3; d++) fk_tmp[d] += CEhb3/rik * delik[d];
-
+
for (int d = 0; d < 3; d++) fitmp[d] -= fi_tmp[d];
for (int d = 0; d < 3; d++) a_f(j,d) -= fj_tmp[d];
for (int d = 0; d < 3; d++) a_f(k,d) -= fk_tmp[d];
-
+
for (int d = 0; d < 3; d++) delki[d] = -1.0 * delik[d];
for (int d = 0; d < 3; d++) delji[d] = -1.0 * delij[d];
if (eflag_atom) this->template e_tally<NEIGHFLAG>(ev,i,j,e_hb);
@@ -4153,9 +4153,9 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxFindBondSpecies, const int
j &= NEIGHMASK;
if (j < i) continue;
const int j_index = jj - j_start;
-
+
double bo_tmp = d_BO(i,j_index);
-
+
if (bo_tmp >= 0.10 ) { // Why is this a hardcoded value?
k_tmpid.view<DeviceType>()(i,nj) = j;
k_tmpbo.view<DeviceType>()(i,nj) = bo_tmp;
diff --git a/src/KOKKOS/pair_vashishta_kokkos.cpp b/src/KOKKOS/pair_vashishta_kokkos.cpp
index 670df650be56ece2f0e3b6528a76138806963986..5611aa132bb825e970304a323e4798ab093fc095 100644
--- a/src/KOKKOS/pair_vashishta_kokkos.cpp
+++ b/src/KOKKOS/pair_vashishta_kokkos.cpp
@@ -128,7 +128,7 @@ void PairVashishtaKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (d_numneigh_short_2body.dimension_0()!=ignum) {
d_numneigh_short_2body = Kokkos::View<int*,DeviceType>("Vashishta::numneighs_short_2body",ignum);
}
-
+
if ((d_neighbors_short_3body.dimension_1() != max_neighs) ||
(d_neighbors_short_3body.dimension_0() != ignum)) {
d_neighbors_short_3body = Kokkos::View<int**,DeviceType>("Vashishta::neighbors_short_3body",ignum,max_neighs);
@@ -212,7 +212,7 @@ void PairVashishtaKokkos<DeviceType>::operator()(TagPairVashishtaComputeShortNei
j &= NEIGHMASK;
const int jtype = d_map[type[j]];
const int ijparam = d_elem2param(itype,jtype,jtype);
-
+
const X_FLOAT delx = xtmp - x(j,0);
const X_FLOAT dely = ytmp - x(j,1);
const X_FLOAT delz = ztmp - x(j,2);
@@ -283,7 +283,7 @@ void PairVashishtaKokkos<DeviceType>::operator()(TagPairVashishtaComputeHalf<NEI
const F_FLOAT rsq = delx*delx + dely*dely + delz*delz;
const int ijparam = d_elem2param(itype,jtype,jtype);
-
+
twobody(d_params[ijparam],rsq,fpair,eflag,evdwl);
fxtmpi += delx*fpair;
@@ -310,7 +310,7 @@ void PairVashishtaKokkos<DeviceType>::operator()(TagPairVashishtaComputeHalf<NEI
delr1[1] = x(j,1) - ytmp;
delr1[2] = x(j,2) - ztmp;
const F_FLOAT rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2];
-
+
F_FLOAT fxtmpj = 0.0;
F_FLOAT fytmpj = 0.0;
F_FLOAT fztmpj = 0.0;
diff --git a/src/KOKKOS/pppm_kokkos.cpp b/src/KOKKOS/pppm_kokkos.cpp
index 03de42c68ca1d387784210e911d5cfe2f97c652d..a28e462044ac7a4f1b674b620c7c3102a846c9aa 100644
--- a/src/KOKKOS/pppm_kokkos.cpp
+++ b/src/KOKKOS/pppm_kokkos.cpp
@@ -162,7 +162,7 @@ PPPMKokkos<DeviceType>::~PPPMKokkos()
if (peratom_allocate_flag) deallocate_peratom();
//memory->destroy(part2grid);
//memory->destroy(acons);
-
+
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->destroy_kokkos(k_vatom,vatom);
eatom = NULL;
diff --git a/src/KOKKOS/rand_pool_wrap_kokkos.cpp b/src/KOKKOS/rand_pool_wrap_kokkos.cpp
index c11764640be2f1ed4056e13a0466e47b92177357..39b91f160016fd8f10cdeb9276aacb46a81aa935 100644
--- a/src/KOKKOS/rand_pool_wrap_kokkos.cpp
+++ b/src/KOKKOS/rand_pool_wrap_kokkos.cpp
@@ -40,7 +40,7 @@ void RandPoolWrap::destroy()
if (random_thr) {
for (int i=1; i < nthreads; ++i)
delete random_thr[i];
-
+
delete[] random_thr;
random_thr = NULL;
}
@@ -52,10 +52,10 @@ void RandPoolWrap::init(RanMars* random, int seed)
if (random_thr) {
for (int i=1; i < this->nthreads; ++i)
delete random_thr[i];
-
+
delete[] random_thr;
}
-
+
// allocate pool of RNGs
// generate a random number generator instance for
// all threads != 0. make sure we use unique seeds.
diff --git a/src/KSPACE/ewald.cpp b/src/KSPACE/ewald.cpp
index c7d242031f6d527455bbd2e78d0cdb761831ee98..766520172b46e0c5103c7821bad3dc70c612ff3a 100644
--- a/src/KSPACE/ewald.cpp
+++ b/src/KSPACE/ewald.cpp
@@ -53,7 +53,7 @@ Ewald::Ewald(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg),
ewaldflag = 1;
group_group_enable = 1;
-
+
accuracy_relative = fabs(force->numeric(FLERR,arg[0]));
kmax = 0;
diff --git a/src/KSPACE/fft3d.cpp b/src/KSPACE/fft3d.cpp
index a332f435e19feeb805b572067f7d37b249a50e51..2a0d85bac655ff24000fb8755c4b531a47358763 100644
--- a/src/KSPACE/fft3d.cpp
+++ b/src/KSPACE/fft3d.cpp
@@ -87,7 +87,7 @@ void fft_3d(FFT_DATA *in, FFT_DATA *out, int flag, struct fft_plan_3d *plan)
if (plan->pre_plan) {
if (plan->pre_target == 0) copy = out;
else copy = plan->copy;
- remap_3d((FFT_SCALAR *) in, (FFT_SCALAR *) copy,
+ remap_3d((FFT_SCALAR *) in, (FFT_SCALAR *) copy,
(FFT_SCALAR *) plan->scratch, plan->pre_plan);
data = copy;
}
@@ -129,7 +129,7 @@ void fft_3d(FFT_DATA *in, FFT_DATA *out, int flag, struct fft_plan_3d *plan)
if (plan->mid1_target == 0) copy = out;
else copy = plan->copy;
- remap_3d((FFT_SCALAR *) data, (FFT_SCALAR *) copy,
+ remap_3d((FFT_SCALAR *) data, (FFT_SCALAR *) copy,
(FFT_SCALAR *) plan->scratch, plan->mid1_plan);
data = copy;
@@ -168,7 +168,7 @@ void fft_3d(FFT_DATA *in, FFT_DATA *out, int flag, struct fft_plan_3d *plan)
if (plan->mid2_target == 0) copy = out;
else copy = plan->copy;
- remap_3d((FFT_SCALAR *) data, (FFT_SCALAR *) copy,
+ remap_3d((FFT_SCALAR *) data, (FFT_SCALAR *) copy,
(FFT_SCALAR *) plan->scratch, plan->mid2_plan);
data = copy;
@@ -206,7 +206,7 @@ void fft_3d(FFT_DATA *in, FFT_DATA *out, int flag, struct fft_plan_3d *plan)
// destination is always out
if (plan->post_plan)
- remap_3d((FFT_SCALAR *) data, (FFT_SCALAR *) out,
+ remap_3d((FFT_SCALAR *) data, (FFT_SCALAR *) out,
(FFT_SCALAR *) plan->scratch, plan->post_plan);
// scaling if required
@@ -414,7 +414,7 @@ struct fft_plan_3d *fft_3d_create_plan(
// configure plan memory pointers and allocate work space
// out_size = amount of memory given to FFT by user
- // first/second/third_size =
+ // first/second/third_size =
// amount of memory needed after pre,mid1,mid2 remaps
// copy_size = amount needed internally for extra copy of data
// scratch_size = amount needed internally for remap scratch space
@@ -484,27 +484,27 @@ struct fft_plan_3d *fft_3d_create_plan(
// and scaling normalization
#if defined(FFT_MKL)
- DftiCreateDescriptor( &(plan->handle_fast), FFT_MKL_PREC, DFTI_COMPLEX, 1,
+ DftiCreateDescriptor( &(plan->handle_fast), FFT_MKL_PREC, DFTI_COMPLEX, 1,
(MKL_LONG)nfast);
- DftiSetValue(plan->handle_fast, DFTI_NUMBER_OF_TRANSFORMS,
+ DftiSetValue(plan->handle_fast, DFTI_NUMBER_OF_TRANSFORMS,
(MKL_LONG)plan->total1/nfast);
DftiSetValue(plan->handle_fast, DFTI_PLACEMENT,DFTI_INPLACE);
DftiSetValue(plan->handle_fast, DFTI_INPUT_DISTANCE, (MKL_LONG)nfast);
DftiSetValue(plan->handle_fast, DFTI_OUTPUT_DISTANCE, (MKL_LONG)nfast);
DftiCommitDescriptor(plan->handle_fast);
- DftiCreateDescriptor( &(plan->handle_mid), FFT_MKL_PREC, DFTI_COMPLEX, 1,
+ DftiCreateDescriptor( &(plan->handle_mid), FFT_MKL_PREC, DFTI_COMPLEX, 1,
(MKL_LONG)nmid);
- DftiSetValue(plan->handle_mid, DFTI_NUMBER_OF_TRANSFORMS,
+ DftiSetValue(plan->handle_mid, DFTI_NUMBER_OF_TRANSFORMS,
(MKL_LONG)plan->total2/nmid);
DftiSetValue(plan->handle_mid, DFTI_PLACEMENT,DFTI_INPLACE);
DftiSetValue(plan->handle_mid, DFTI_INPUT_DISTANCE, (MKL_LONG)nmid);
DftiSetValue(plan->handle_mid, DFTI_OUTPUT_DISTANCE, (MKL_LONG)nmid);
DftiCommitDescriptor(plan->handle_mid);
- DftiCreateDescriptor( &(plan->handle_slow), FFT_MKL_PREC, DFTI_COMPLEX, 1,
+ DftiCreateDescriptor( &(plan->handle_slow), FFT_MKL_PREC, DFTI_COMPLEX, 1,
(MKL_LONG)nslow);
- DftiSetValue(plan->handle_slow, DFTI_NUMBER_OF_TRANSFORMS,
+ DftiSetValue(plan->handle_slow, DFTI_NUMBER_OF_TRANSFORMS,
(MKL_LONG)plan->total3/nslow);
DftiSetValue(plan->handle_slow, DFTI_PLACEMENT,DFTI_INPLACE);
DftiSetValue(plan->handle_slow, DFTI_INPUT_DISTANCE, (MKL_LONG)nslow);
diff --git a/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp b/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp
index 1fb83db28c5a23bab3af3275ce8ceb56ec841e46..4a37ddb81fa29989b06eb0934637ed77cf7931ff 100644
--- a/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp
+++ b/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp
@@ -13,8 +13,8 @@
/* ----------------------------------------------------------------------
Contributing author: Paul Crozier (SNL)
- The lj-fsw sections (force-switched) were provided by
- Robert Meissner and Lucio Colombi Ciacchi of
+ The lj-fsw sections (force-switched) were provided by
+ Robert Meissner and Lucio Colombi Ciacchi of
Bremen University, Bremen, Germany, with
additional assistance from Robert A. Latour, Clemson University
------------------------------------------------------------------------- */
@@ -229,15 +229,15 @@ void PairLJCharmmfswCoulLong::compute(int eflag, int vflag)
r = sqrt(rsq);
rinv = 1.0/r;
r3inv = rinv*rinv*rinv;
- evdwl12 = lj3[itype][jtype]*cut_lj6*denom_lj12 *
+ evdwl12 = lj3[itype][jtype]*cut_lj6*denom_lj12 *
(r6inv - cut_lj6inv)*(r6inv - cut_lj6inv);
- evdwl6 = -lj4[itype][jtype]*cut_lj3*denom_lj6 *
+ evdwl6 = -lj4[itype][jtype]*cut_lj3*denom_lj6 *
(r3inv - cut_lj3inv)*(r3inv - cut_lj3inv);;
evdwl = evdwl12 + evdwl6;
} else {
- evdwl12 = r6inv*lj3[itype][jtype]*r6inv -
+ evdwl12 = r6inv*lj3[itype][jtype]*r6inv -
lj3[itype][jtype]*cut_lj_inner6inv*cut_lj6inv;
- evdwl6 = -lj4[itype][jtype]*r6inv +
+ evdwl6 = -lj4[itype][jtype]*r6inv +
lj4[itype][jtype]*cut_lj_inner3inv*cut_lj3inv;
evdwl = evdwl12 + evdwl6;
}
@@ -589,15 +589,15 @@ void PairLJCharmmfswCoulLong::compute_outer(int eflag, int vflag)
if (rsq > cut_lj_innersq) {
rinv = 1.0/r;
r3inv = rinv*rinv*rinv;
- evdwl12 = lj3[itype][jtype]*cut_lj6*denom_lj12 *
+ evdwl12 = lj3[itype][jtype]*cut_lj6*denom_lj12 *
(r6inv - cut_lj6inv)*(r6inv - cut_lj6inv);
- evdwl6 = -lj4[itype][jtype]*cut_lj3*denom_lj6 *
+ evdwl6 = -lj4[itype][jtype]*cut_lj3*denom_lj6 *
(r3inv - cut_lj3inv)*(r3inv - cut_lj3inv);;
evdwl = evdwl12 + evdwl6;
} else {
- evdwl12 = r6inv*lj3[itype][jtype]*r6inv -
+ evdwl12 = r6inv*lj3[itype][jtype]*r6inv -
lj3[itype][jtype]*cut_lj_inner6inv*cut_lj6inv;
- evdwl6 = -lj4[itype][jtype]*r6inv +
+ evdwl6 = -lj4[itype][jtype]*r6inv +
lj4[itype][jtype]*cut_lj_inner3inv*cut_lj3inv;
evdwl = evdwl12 + evdwl6;
}
@@ -1042,15 +1042,15 @@ double PairLJCharmmfswCoulLong::single(int i, int j, int itype, int jtype,
if (rsq < cut_ljsq) {
if (rsq > cut_lj_innersq) {
- philj12 = lj3[itype][jtype]*cut_lj6*denom_lj12 *
+ philj12 = lj3[itype][jtype]*cut_lj6*denom_lj12 *
(r6inv - cut_lj6inv)*(r6inv - cut_lj6inv);
- philj6 = -lj4[itype][jtype]*cut_lj3*denom_lj6 *
+ philj6 = -lj4[itype][jtype]*cut_lj3*denom_lj6 *
(r3inv - cut_lj3inv)*(r3inv - cut_lj3inv);;
philj = philj12 + philj6;
} else {
- philj12 = r6inv*lj3[itype][jtype]*r6inv -
+ philj12 = r6inv*lj3[itype][jtype]*r6inv -
lj3[itype][jtype]*cut_lj_inner6inv*cut_lj6inv;
- philj6 = -lj4[itype][jtype]*r6inv +
+ philj6 = -lj4[itype][jtype]*r6inv +
lj4[itype][jtype]*cut_lj_inner3inv*cut_lj3inv;
philj = philj12 + philj6;
}
diff --git a/src/KSPACE/pair_lj_long_coul_long.cpp b/src/KSPACE/pair_lj_long_coul_long.cpp
index 61b69011f1ac5ae04ca191bd0423f5a4296d7e27..cb9c379f9cc49bc0f3b067c145956e507ee58706 100644
--- a/src/KSPACE/pair_lj_long_coul_long.cpp
+++ b/src/KSPACE/pair_lj_long_coul_long.cpp
@@ -254,14 +254,14 @@ void PairLJLongCoulLong::init_style()
if (force->kspace->neighrequest_flag) {
int irequest;
int respa = 0;
-
+
if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;
}
-
+
irequest = neighbor->request(this,instance_me);
-
+
if (respa >= 1) {
neighbor->requests[irequest]->respaouter = 1;
neighbor->requests[irequest]->respainner = 1;
diff --git a/src/KSPACE/pppm.cpp b/src/KSPACE/pppm.cpp
index 53ab2e5a9d72159e116e2cd02bba223552a558ca..bc82dce5320a7e8ea87d75dc6d29b18a86561263 100644
--- a/src/KSPACE/pppm.cpp
+++ b/src/KSPACE/pppm.cpp
@@ -64,7 +64,7 @@ enum{FORWARD_IK,FORWARD_AD,FORWARD_IK_PERATOM,FORWARD_AD_PERATOM};
/* ---------------------------------------------------------------------- */
-PPPM::PPPM(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg),
+PPPM::PPPM(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg),
factors(NULL), density_brick(NULL), vdx_brick(NULL), vdy_brick(NULL), vdz_brick(NULL),
u_brick(NULL), v0_brick(NULL), v1_brick(NULL), v2_brick(NULL), v3_brick(NULL),
v4_brick(NULL), v5_brick(NULL), greensfn(NULL), vg(NULL), fkx(NULL), fky(NULL),
diff --git a/src/KSPACE/pppm_cg.cpp b/src/KSPACE/pppm_cg.cpp
index 8076f0f058239bfce9dcb88367d58647f25d4e84..9489224e03031b8c279e05a5365a3ad9a58bb572 100644
--- a/src/KSPACE/pppm_cg.cpp
+++ b/src/KSPACE/pppm_cg.cpp
@@ -48,7 +48,7 @@ enum{FORWARD_IK,FORWARD_AD,FORWARD_IK_PERATOM,FORWARD_AD_PERATOM};
/* ---------------------------------------------------------------------- */
-PPPMCG::PPPMCG(LAMMPS *lmp, int narg, char **arg) : PPPM(lmp, narg, arg),
+PPPMCG::PPPMCG(LAMMPS *lmp, int narg, char **arg) : PPPM(lmp, narg, arg),
is_charged(NULL)
{
if ((narg < 1) || (narg > 2))
diff --git a/src/KSPACE/pppm_disp.cpp b/src/KSPACE/pppm_disp.cpp
index 821cfd06d57b11328046fc7e84650389509223ca..3e764cc3e7f6f3104f2d0a0722a4e72b5399ebe5 100644
--- a/src/KSPACE/pppm_disp.cpp
+++ b/src/KSPACE/pppm_disp.cpp
@@ -65,46 +65,46 @@ enum{FORWARD_IK, FORWARD_AD, FORWARD_IK_PERATOM, FORWARD_AD_PERATOM,
/* ---------------------------------------------------------------------- */
PPPMDisp::PPPMDisp(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg),
- factors(NULL), csumi(NULL), cii(NULL), B(NULL), density_brick(NULL), vdx_brick(NULL),
- vdy_brick(NULL), vdz_brick(NULL), density_fft(NULL), u_brick(NULL), v0_brick(NULL),
- v1_brick(NULL), v2_brick(NULL), v3_brick(NULL), v4_brick(NULL), v5_brick(NULL),
- density_brick_g(NULL), vdx_brick_g(NULL), vdy_brick_g(NULL), vdz_brick_g(NULL),
- density_fft_g(NULL), u_brick_g(NULL), v0_brick_g(NULL), v1_brick_g(NULL), v2_brick_g(NULL),
- v3_brick_g(NULL), v4_brick_g(NULL), v5_brick_g(NULL), density_brick_a0(NULL),
- vdx_brick_a0(NULL), vdy_brick_a0(NULL), vdz_brick_a0(NULL), density_fft_a0(NULL),
- u_brick_a0(NULL), v0_brick_a0(NULL), v1_brick_a0(NULL), v2_brick_a0(NULL),
- v3_brick_a0(NULL), v4_brick_a0(NULL), v5_brick_a0(NULL), density_brick_a1(NULL),
- vdx_brick_a1(NULL), vdy_brick_a1(NULL), vdz_brick_a1(NULL), density_fft_a1(NULL),
- u_brick_a1(NULL), v0_brick_a1(NULL), v1_brick_a1(NULL), v2_brick_a1(NULL),
- v3_brick_a1(NULL), v4_brick_a1(NULL), v5_brick_a1(NULL), density_brick_a2(NULL),
- vdx_brick_a2(NULL), vdy_brick_a2(NULL), vdz_brick_a2(NULL), density_fft_a2(NULL),
- u_brick_a2(NULL), v0_brick_a2(NULL), v1_brick_a2(NULL), v2_brick_a2(NULL),
- v3_brick_a2(NULL), v4_brick_a2(NULL), v5_brick_a2(NULL), density_brick_a3(NULL),
- vdx_brick_a3(NULL), vdy_brick_a3(NULL), vdz_brick_a3(NULL), density_fft_a3(NULL),
- u_brick_a3(NULL), v0_brick_a3(NULL), v1_brick_a3(NULL), v2_brick_a3(NULL),
- v3_brick_a3(NULL), v4_brick_a3(NULL), v5_brick_a3(NULL), density_brick_a4(NULL),
- vdx_brick_a4(NULL), vdy_brick_a4(NULL), vdz_brick_a4(NULL), density_fft_a4(NULL),
- u_brick_a4(NULL), v0_brick_a4(NULL), v1_brick_a4(NULL), v2_brick_a4(NULL),
- v3_brick_a4(NULL), v4_brick_a4(NULL), v5_brick_a4(NULL), density_brick_a5(NULL),
- vdx_brick_a5(NULL), vdy_brick_a5(NULL), vdz_brick_a5(NULL), density_fft_a5(NULL),
- u_brick_a5(NULL), v0_brick_a5(NULL), v1_brick_a5(NULL), v2_brick_a5(NULL),
- v3_brick_a5(NULL), v4_brick_a5(NULL), v5_brick_a5(NULL), density_brick_a6(NULL),
- vdx_brick_a6(NULL), vdy_brick_a6(NULL), vdz_brick_a6(NULL), density_fft_a6(NULL),
- u_brick_a6(NULL), v0_brick_a6(NULL), v1_brick_a6(NULL), v2_brick_a6(NULL),
- v3_brick_a6(NULL), v4_brick_a6(NULL), v5_brick_a6(NULL), density_brick_none(NULL),
- vdx_brick_none(NULL), vdy_brick_none(NULL), vdz_brick_none(NULL),
- density_fft_none(NULL), u_brick_none(NULL), v0_brick_none(NULL), v1_brick_none(NULL),
- v2_brick_none(NULL), v3_brick_none(NULL), v4_brick_none(NULL), v5_brick_none(NULL),
- greensfn(NULL), vg(NULL), vg2(NULL), greensfn_6(NULL), vg_6(NULL), vg2_6(NULL),
- fkx(NULL), fky(NULL), fkz(NULL), fkx2(NULL), fky2(NULL), fkz2(NULL), fkx_6(NULL),
- fky_6(NULL), fkz_6(NULL), fkx2_6(NULL), fky2_6(NULL), fkz2_6(NULL), gf_b(NULL),
- gf_b_6(NULL), sf_precoeff1(NULL), sf_precoeff2(NULL), sf_precoeff3(NULL),
- sf_precoeff4(NULL), sf_precoeff5(NULL), sf_precoeff6(NULL), sf_precoeff1_6(NULL),
- sf_precoeff2_6(NULL), sf_precoeff3_6(NULL), sf_precoeff4_6(NULL), sf_precoeff5_6(NULL),
- sf_precoeff6_6(NULL), rho1d(NULL), rho_coeff(NULL), drho1d(NULL), drho_coeff(NULL),
+ factors(NULL), csumi(NULL), cii(NULL), B(NULL), density_brick(NULL), vdx_brick(NULL),
+ vdy_brick(NULL), vdz_brick(NULL), density_fft(NULL), u_brick(NULL), v0_brick(NULL),
+ v1_brick(NULL), v2_brick(NULL), v3_brick(NULL), v4_brick(NULL), v5_brick(NULL),
+ density_brick_g(NULL), vdx_brick_g(NULL), vdy_brick_g(NULL), vdz_brick_g(NULL),
+ density_fft_g(NULL), u_brick_g(NULL), v0_brick_g(NULL), v1_brick_g(NULL), v2_brick_g(NULL),
+ v3_brick_g(NULL), v4_brick_g(NULL), v5_brick_g(NULL), density_brick_a0(NULL),
+ vdx_brick_a0(NULL), vdy_brick_a0(NULL), vdz_brick_a0(NULL), density_fft_a0(NULL),
+ u_brick_a0(NULL), v0_brick_a0(NULL), v1_brick_a0(NULL), v2_brick_a0(NULL),
+ v3_brick_a0(NULL), v4_brick_a0(NULL), v5_brick_a0(NULL), density_brick_a1(NULL),
+ vdx_brick_a1(NULL), vdy_brick_a1(NULL), vdz_brick_a1(NULL), density_fft_a1(NULL),
+ u_brick_a1(NULL), v0_brick_a1(NULL), v1_brick_a1(NULL), v2_brick_a1(NULL),
+ v3_brick_a1(NULL), v4_brick_a1(NULL), v5_brick_a1(NULL), density_brick_a2(NULL),
+ vdx_brick_a2(NULL), vdy_brick_a2(NULL), vdz_brick_a2(NULL), density_fft_a2(NULL),
+ u_brick_a2(NULL), v0_brick_a2(NULL), v1_brick_a2(NULL), v2_brick_a2(NULL),
+ v3_brick_a2(NULL), v4_brick_a2(NULL), v5_brick_a2(NULL), density_brick_a3(NULL),
+ vdx_brick_a3(NULL), vdy_brick_a3(NULL), vdz_brick_a3(NULL), density_fft_a3(NULL),
+ u_brick_a3(NULL), v0_brick_a3(NULL), v1_brick_a3(NULL), v2_brick_a3(NULL),
+ v3_brick_a3(NULL), v4_brick_a3(NULL), v5_brick_a3(NULL), density_brick_a4(NULL),
+ vdx_brick_a4(NULL), vdy_brick_a4(NULL), vdz_brick_a4(NULL), density_fft_a4(NULL),
+ u_brick_a4(NULL), v0_brick_a4(NULL), v1_brick_a4(NULL), v2_brick_a4(NULL),
+ v3_brick_a4(NULL), v4_brick_a4(NULL), v5_brick_a4(NULL), density_brick_a5(NULL),
+ vdx_brick_a5(NULL), vdy_brick_a5(NULL), vdz_brick_a5(NULL), density_fft_a5(NULL),
+ u_brick_a5(NULL), v0_brick_a5(NULL), v1_brick_a5(NULL), v2_brick_a5(NULL),
+ v3_brick_a5(NULL), v4_brick_a5(NULL), v5_brick_a5(NULL), density_brick_a6(NULL),
+ vdx_brick_a6(NULL), vdy_brick_a6(NULL), vdz_brick_a6(NULL), density_fft_a6(NULL),
+ u_brick_a6(NULL), v0_brick_a6(NULL), v1_brick_a6(NULL), v2_brick_a6(NULL),
+ v3_brick_a6(NULL), v4_brick_a6(NULL), v5_brick_a6(NULL), density_brick_none(NULL),
+ vdx_brick_none(NULL), vdy_brick_none(NULL), vdz_brick_none(NULL),
+ density_fft_none(NULL), u_brick_none(NULL), v0_brick_none(NULL), v1_brick_none(NULL),
+ v2_brick_none(NULL), v3_brick_none(NULL), v4_brick_none(NULL), v5_brick_none(NULL),
+ greensfn(NULL), vg(NULL), vg2(NULL), greensfn_6(NULL), vg_6(NULL), vg2_6(NULL),
+ fkx(NULL), fky(NULL), fkz(NULL), fkx2(NULL), fky2(NULL), fkz2(NULL), fkx_6(NULL),
+ fky_6(NULL), fkz_6(NULL), fkx2_6(NULL), fky2_6(NULL), fkz2_6(NULL), gf_b(NULL),
+ gf_b_6(NULL), sf_precoeff1(NULL), sf_precoeff2(NULL), sf_precoeff3(NULL),
+ sf_precoeff4(NULL), sf_precoeff5(NULL), sf_precoeff6(NULL), sf_precoeff1_6(NULL),
+ sf_precoeff2_6(NULL), sf_precoeff3_6(NULL), sf_precoeff4_6(NULL), sf_precoeff5_6(NULL),
+ sf_precoeff6_6(NULL), rho1d(NULL), rho_coeff(NULL), drho1d(NULL), drho_coeff(NULL),
rho1d_6(NULL), rho_coeff_6(NULL), drho1d_6(NULL), drho_coeff_6(NULL), work1(NULL),
- work2(NULL), work1_6(NULL), work2_6(NULL), fft1(NULL), fft2(NULL), fft1_6(NULL),
- fft2_6(NULL), remap(NULL), remap_6(NULL), cg(NULL), cg_peratom(NULL), cg_6(NULL),
+ work2(NULL), work1_6(NULL), work2_6(NULL), fft1(NULL), fft2(NULL), fft1_6(NULL),
+ fft2_6(NULL), remap(NULL), remap_6(NULL), cg(NULL), cg_peratom(NULL), cg_6(NULL),
cg_peratom_6(NULL), part2grid(NULL), part2grid_6(NULL), boxlo(NULL)
{
if (narg < 1) error->all(FLERR,"Illegal kspace_style pppm/disp command");
diff --git a/src/KSPACE/pppm_stagger.cpp b/src/KSPACE/pppm_stagger.cpp
index 88a559605f1a5d0d77e905ed14224fe2a50360a4..49c84e58c0b4f36c8be56d758fa2759a0c478c2b 100644
--- a/src/KSPACE/pppm_stagger.cpp
+++ b/src/KSPACE/pppm_stagger.cpp
@@ -52,7 +52,7 @@ enum{FORWARD_IK,FORWARD_AD,FORWARD_IK_PERATOM,FORWARD_AD_PERATOM};
/* ---------------------------------------------------------------------- */
PPPMStagger::PPPMStagger(LAMMPS *lmp, int narg, char **arg) :
- PPPM(lmp, narg, arg),
+ PPPM(lmp, narg, arg),
gf_b2(NULL)
{
if (narg < 1) error->all(FLERR,"Illegal kspace_style pppm/stagger command");
diff --git a/src/MANYBODY/pair_airebo.cpp b/src/MANYBODY/pair_airebo.cpp
index 5a56b0cd59849642a59fc7ad3d0f10eeaa4795fc..fd5691fecbc508cb7456e7885cac98db39f3a184 100644
--- a/src/MANYBODY/pair_airebo.cpp
+++ b/src/MANYBODY/pair_airebo.cpp
@@ -2085,7 +2085,7 @@ double PairAIREBO::bondorder(int i, int j, double rij[3],
/* ----------------------------------------------------------------------
Bij* function
--------------------------------------------------------------------------
+-------------------------------------------------------------------------
This function calculates S(t_b(b_ij*)) as specified in the AIREBO paper.
To do so, it needs to compute b_ij*, i.e. the bondorder given that the
@@ -2291,7 +2291,7 @@ double PairAIREBO::bondorderLJ(int i, int j, double rij_mod[3], double rijmag_mo
cos321 = MAX(cos321,-1.0);
sin321 = sqrt(1.0 - cos321*cos321);
if ((sin321 > TOL) && (r21mag > TOL)) { // XXX was sin321 != 0.0
- w21 = Sp(r21mag,rcmin[itype][ktype],rcmaxp[itype][ktype],dw21);
+ w21 = Sp(r21mag,rcmin[itype][ktype],rcmaxp[itype][ktype],dw21);
tspjik = Sp2(cos321,thmin,thmax,dtsjik);
REBO_neighs_j = REBO_firstneigh[j];
@@ -2471,7 +2471,7 @@ double PairAIREBO::bondorderLJ(int i, int j, double rij_mod[3], double rijmag_mo
(rijmag*rjlmag);
cosijl = MIN(cosijl,1.0);
cosijl = MAX(cosijl,-1.0);
-
+
dcosijldri[0] = (-rjl[0]/(rijmag*rjlmag)) -
(cosijl*rij[0]/(rijmag*rijmag));
dcosijldri[1] = (-rjl[1]/(rijmag*rjlmag)) -
@@ -2501,7 +2501,7 @@ double PairAIREBO::bondorderLJ(int i, int j, double rij_mod[3], double rijmag_mo
fl[0] = -tmp2*dcosijldrl[0];
fl[1] = -tmp2*dcosijldrl[1];
fl[2] = -tmp2*dcosijldrl[2];
-
+
tmp2 = VA*.5*(tmp*wjl*g*exp(lamdaijl)*4.0*kronecker(jtype,1));
fj[0] += tmp2*(rjl[0]/rjlmag);
fj[1] += tmp2*(rjl[1]/rjlmag);
diff --git a/src/MANYBODY/pair_polymorphic.cpp b/src/MANYBODY/pair_polymorphic.cpp
index 110fc0a44de987ba09446d279045810eb85c36c9..9ceceed076825d4d81c4a90c85c9a40969a8def1 100644
--- a/src/MANYBODY/pair_polymorphic.cpp
+++ b/src/MANYBODY/pair_polymorphic.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -86,17 +86,17 @@ PairPolymorphic::~PairPolymorphic()
memory->destroy(setflag);
memory->destroy(cutsq);
delete [] map;
- delete [] firstneighV;
- delete [] firstneighW;
+ delete [] firstneighV;
+ delete [] firstneighW;
delete [] firstneighW1;
- delete [] delxV;
- delete [] delyV;
- delete [] delzV;
- delete [] drV;
- delete [] delxW;
- delete [] delyW;
- delete [] delzW;
- delete [] drW;
+ delete [] delxV;
+ delete [] delyV;
+ delete [] delzV;
+ delete [] drV;
+ delete [] delxW;
+ delete [] delyW;
+ delete [] delzW;
+ delete [] drW;
}
}
@@ -272,7 +272,7 @@ void PairPolymorphic::compute(int eflag, int vflag)
for (kk = 0; kk <= numneighW; kk++) {
k = firstneighW[kk];
ktype = map[type[k]];
-
+
iparam_kk = elem2param[ktype][ktype];
PairParameters & q = pairParameters[iparam_kk];
@@ -312,7 +312,7 @@ void PairPolymorphic::compute(int eflag, int vflag)
f[k][0] -= delr2[0]*fpair;
f[k][1] -= delr2[1]*fpair;
f[k][2] -= delr2[2]*fpair;
-
+
if (vflag_atom) v_tally2(i, k, -fpair, delr2);
}
}
@@ -340,7 +340,7 @@ void PairPolymorphic::compute(int eflag, int vflag)
k = firstneighW[kk];
if (j == k) continue;
ktype = map[type[k]];
- iparam_ijk = elem3param[jtype][itype][ktype];
+ iparam_ijk = elem3param[jtype][itype][ktype];
TripletParameters & trip = tripletParameters[iparam_ijk];
if ((trip.G)->get_vmax() <= epsilon) continue;
@@ -361,7 +361,7 @@ void PairPolymorphic::compute(int eflag, int vflag)
(q.W)->value(r2,wfac,1,fpair,0);
(q.P)->value(r1-(p.xi)*r2,pfac,1,fpair,0);
(trip.G)->value(costheta,gfac,1,fpair,0);
-
+
zeta_ij += wfac*pfac*gfac;
}
@@ -372,14 +372,14 @@ void PairPolymorphic::compute(int eflag, int vflag)
fpair = -0.5*bij*fa_d / r1;
prefactor = 0.5* fa * bij_d;
if (eflag) evdwl = -0.5*bij*fa;
-
+
f[i][0] += delr1[0]*fpair;
f[i][1] += delr1[1]*fpair;
f[i][2] += delr1[2]*fpair;
f[j][0] -= delr1[0]*fpair;
f[j][1] -= delr1[1]*fpair;
f[j][2] -= delr1[2]*fpair;
-
+
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,0.0,-fpair,-delr1[0],-delr1[1],-delr1[2]);
@@ -399,9 +399,9 @@ void PairPolymorphic::compute(int eflag, int vflag)
iparam_ik = elem2param[itype][ktype];
PairParameters & q = pairParameters[iparam_ik];
-
+
attractive(&q,&trip,prefactor,r1,r2,delr1,delr2,fi,fj,fk);
-
+
f[i][0] += fi[0];
f[i][1] += fi[1];
f[i][2] += fi[2];
@@ -411,7 +411,7 @@ void PairPolymorphic::compute(int eflag, int vflag)
f[k][0] += fk[0];
f[k][1] += fk[1];
f[k][2] += fk[2];
-
+
if (vflag_atom) v_tally3(i,j,k,fj,fk,delr1,delr2);
}
}
@@ -447,7 +447,7 @@ void PairPolymorphic::allocate()
}
/* ----------------------------------------------------------------------
- global settings
+ global settings
------------------------------------------------------------------------- */
void PairPolymorphic::settings(int narg, char **arg)
@@ -507,7 +507,7 @@ void PairPolymorphic::coeff(int narg, char **arg)
}
// read potential file and initialize potential parameters
-
+
read_file(arg[2]);
setup_params();
@@ -606,7 +606,7 @@ void PairPolymorphic::read_file(char *file)
for (j = 0; j < nelements; j++) {
if (strcmp(ptr,elements[j]) == 0) break;
}
- if (j == nelements)
+ if (j == nelements)
error->all(FLERR,"Element not defined in potential file");
match[i] = j;
}
@@ -762,7 +762,7 @@ void PairPolymorphic::setup_params()
}
// map atom triplet to parameter index
-
+
n = 0;
for (i = 0; i < nelements; i++)
for (j = 0; j < nelements; j++)
@@ -771,12 +771,12 @@ void PairPolymorphic::setup_params()
n++;
}
-// for debugging, call write_tables() to check the tabular functions
+// for debugging, call write_tables() to check the tabular functions
// if (comm->me == 0) {
// write_tables(51);
// errorX->all(FLERR,"Test potential tables");
// }
-}
+}
/* ----------------------------------------------------------------------
attractive term
@@ -792,7 +792,7 @@ void PairPolymorphic::attractive(PairParameters *p, TripletParameters *trip,
rijinv = 1.0/rij;
vec3_scale(rijinv,delrij,rij_hat);
-
+
rikinv = 1.0/rik;
vec3_scale(rikinv,delrik,rik_hat);
@@ -871,12 +871,12 @@ void PairPolymorphic::costheta_d(double *rij_hat, double rij,
* values can be several to a line
* only called by proc 0
* ------------------------------------------------------------------------- */
-
+
void PairPolymorphic::grab(FILE *fp, int n, double *list)
{
char *ptr;
char line[MAXLINE];
-
+
int i = 0;
while (i < n) {
fgets(line,MAXLINE,fp);
@@ -886,7 +886,7 @@ void PairPolymorphic::grab(FILE *fp, int n, double *list)
list[i++] = atof(ptr);
}
}
-
+
/* ---------------------------------------------------------------------- */
void PairPolymorphic::write_tables(int npts)
diff --git a/src/MANYBODY/pair_rebo.cpp b/src/MANYBODY/pair_rebo.cpp
index 1cec1aef40a027da4961929df882e74eadedb339..37948f3038757ae1d22504a794fb9dc614b567e5 100644
--- a/src/MANYBODY/pair_rebo.cpp
+++ b/src/MANYBODY/pair_rebo.cpp
@@ -33,6 +33,6 @@ void PairREBO::settings(int narg, char **arg)
// this one parameter for C-C interactions is different in REBO vs AIREBO
// see Favata, Micheletti, Ryu, Pugno, Comp Phys Comm (2016)
-
+
PCCf_2_0 = 0.0;
}
diff --git a/src/MANYBODY/pair_vashishta.cpp b/src/MANYBODY/pair_vashishta.cpp
index 9f2ed03945febc1f873b51c91d99a599216c974f..bc594d9b4daf614bc0bc3afe835bb86bd0dfcd82 100644
--- a/src/MANYBODY/pair_vashishta.cpp
+++ b/src/MANYBODY/pair_vashishta.cpp
@@ -65,7 +65,7 @@ PairVashishta::PairVashishta(LAMMPS *lmp) : Pair(lmp)
PairVashishta::~PairVashishta()
{
if (copymode) return;
-
+
if (elements)
for (int i = 0; i < nelements; i++) delete [] elements[i];
delete [] elements;
diff --git a/src/MANYBODY/pair_vashishta_table.cpp b/src/MANYBODY/pair_vashishta_table.cpp
index c58f1286d8c741c9f77c2cf22ea3168b0e8fdb9d..18e77946e85264d6433471e19846ee4a280e897a 100644
--- a/src/MANYBODY/pair_vashishta_table.cpp
+++ b/src/MANYBODY/pair_vashishta_table.cpp
@@ -200,7 +200,7 @@ void PairVashishtaTable::compute(int eflag, int vflag)
/* ---------------------------------------------------------------------- */
-void PairVashishtaTable::twobody_table(const Param ¶m, double rsq,
+void PairVashishtaTable::twobody_table(const Param ¶m, double rsq,
double &fforce, int eflag, double &eng)
{
// use analytic form if rsq is inside inner cutoff
@@ -212,15 +212,15 @@ void PairVashishtaTable::twobody_table(const Param ¶m, double rsq,
}
// double -> int will only keep the 0.xxxx part
-
+
const int tableIndex = (rsq - tabinnersq)*oneOverDeltaR2;
const double fraction = (rsq - tabinnersq)*oneOverDeltaR2 - tableIndex;
-
+
// force/energy are linearly interpolated between two adjacent values
double force0 = forceTable[param.ielement][param.jelement][tableIndex];
double force1 = forceTable[param.ielement][param.jelement][tableIndex+1];
- fforce = (1.0 - fraction)*force0 + fraction*force1;
+ fforce = (1.0 - fraction)*force0 + fraction*force1;
if (evflag) {
double energy0 = potentialTable[param.ielement][param.jelement][tableIndex];
diff --git a/src/MC/fix_atom_swap.cpp b/src/MC/fix_atom_swap.cpp
index 669afb5d48c966659ad9da22fcfdc3b0f119df2f..100600c0daeb2c169b6ed0a9ed66243315603e1e 100644
--- a/src/MC/fix_atom_swap.cpp
+++ b/src/MC/fix_atom_swap.cpp
@@ -57,9 +57,9 @@ using namespace MathConst;
FixAtomSwap::FixAtomSwap(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg),
- idregion(NULL), type_list(NULL), mu(NULL), qtype(NULL),
- sqrt_mass_ratio(NULL), local_swap_iatom_list(NULL),
- local_swap_jatom_list(NULL), local_swap_atom_list(NULL),
+ idregion(NULL), type_list(NULL), mu(NULL), qtype(NULL),
+ sqrt_mass_ratio(NULL), local_swap_iatom_list(NULL),
+ local_swap_jatom_list(NULL), local_swap_atom_list(NULL),
random_equal(NULL), random_unequal(NULL), c_pe(NULL)
{
if (narg < 10) error->all(FLERR,"Illegal fix atom/swap command");
@@ -72,7 +72,7 @@ FixAtomSwap::FixAtomSwap(LAMMPS *lmp, int narg, char **arg) :
extvector = 0;
restart_global = 1;
time_depend = 1;
-
+
// required args
nevery = force->inumeric(FLERR,arg[3]);
diff --git a/src/MC/fix_tfmc.cpp b/src/MC/fix_tfmc.cpp
index 46a93914a790b4f033b8840c696173335f051d3a..60ded5fd4470edab95493552700d820111323b9c 100644
--- a/src/MC/fix_tfmc.cpp
+++ b/src/MC/fix_tfmc.cpp
@@ -235,7 +235,7 @@ void FixTFMC::initial_integrate(int vflag)
xcm_dall[1] /= masstotal;
xcm_dall[2] /= masstotal;
} else xcm_dall[0] = xcm_dall[1] = xcm_dall[2] = 0.0;
-
+
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (xflag) x[i][0] -= xcm_dall[0];
diff --git a/src/MISC/dump_xtc.cpp b/src/MISC/dump_xtc.cpp
index 6a89312bcf66a262a0649d767db3173b45d1b571..674e480f9e697fd0b2049d208fa79094e2b99ff8 100644
--- a/src/MISC/dump_xtc.cpp
+++ b/src/MISC/dump_xtc.cpp
@@ -53,7 +53,7 @@ int xdr3dfcoord(XDR *, float *, int *, float *);
/* ---------------------------------------------------------------------- */
-DumpXTC::DumpXTC(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg),
+DumpXTC::DumpXTC(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg),
coords(NULL)
{
if (narg != 5) error->all(FLERR,"Illegal dump xtc command");
diff --git a/src/MISC/fix_gld.cpp b/src/MISC/fix_gld.cpp
index a515ade91ffb1dae02ca4a7f3bb51efe7c42e524..90579388cc9cb953d6447d40cf2a95ea6514ef45 100644
--- a/src/MISC/fix_gld.cpp
+++ b/src/MISC/fix_gld.cpp
@@ -43,7 +43,7 @@ using namespace FixConst;
------------------------------------------------------------------------- */
FixGLD::FixGLD(LAMMPS *lmp, int narg, char **arg) :
- Fix(lmp, narg, arg),
+ Fix(lmp, narg, arg),
step_respa(NULL), prony_c(NULL), prony_tau(NULL), s_gld(NULL), random(NULL)
{
int narg_min = 8;
diff --git a/src/MISC/fix_orient_bcc.cpp b/src/MISC/fix_orient_bcc.cpp
index 87bdc55535b842549582d7ca362af62eba436bd3..1f4a588913373360df64d8e572305f8e370d654f 100644
--- a/src/MISC/fix_orient_bcc.cpp
+++ b/src/MISC/fix_orient_bcc.cpp
@@ -14,7 +14,7 @@
/* ----------------------------------------------------------------------
Contributing authors: Koenraad Janssens and David Olmsted (SNL)
Modification for bcc provided by: Tegar Wicaksono (UBC)
- For a tutorial, please see "Order parameters of crystals in LAMMPS"
+ For a tutorial, please see "Order parameters of crystals in LAMMPS"
(https://dx.doi.org/10.6084/m9.figshare.1488628.v1
------------------------------------------------------------------------- */
@@ -57,7 +57,7 @@ static const char cite_fix_orient_bcc[] =
/* ---------------------------------------------------------------------- */
FixOrientBCC::FixOrientBCC(LAMMPS *lmp, int narg, char **arg) :
- Fix(lmp, narg, arg),
+ Fix(lmp, narg, arg),
xifilename(NULL), chifilename(NULL), order(NULL), nbr(NULL), sort(NULL), list(NULL)
{
if (lmp->citeme) lmp->citeme->add(cite_fix_orient_bcc);
diff --git a/src/MISC/fix_orient_fcc.cpp b/src/MISC/fix_orient_fcc.cpp
index 401a99177ba92be692ad9a51854cb377feb36e34..6743132cfa2e0f1d862626e4b4a1de040f9d45b7 100644
--- a/src/MISC/fix_orient_fcc.cpp
+++ b/src/MISC/fix_orient_fcc.cpp
@@ -55,7 +55,7 @@ static const char cite_fix_orient_fcc[] =
FixOrientFCC::FixOrientFCC(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg),
- xifilename(NULL), chifilename(NULL), order(NULL), nbr(NULL),
+ xifilename(NULL), chifilename(NULL), order(NULL), nbr(NULL),
sort(NULL), list(NULL)
{
if (lmp->citeme) lmp->citeme->add(cite_fix_orient_fcc);
diff --git a/src/MISC/fix_ttm.cpp b/src/MISC/fix_ttm.cpp
index 00e7803f8a6c372abdbb86084492733a6549ba2c..bb13b166fbcf4ceb7ea645a55e709067e5c2c075 100644
--- a/src/MISC/fix_ttm.cpp
+++ b/src/MISC/fix_ttm.cpp
@@ -40,11 +40,11 @@ using namespace FixConst;
/* ---------------------------------------------------------------------- */
FixTTM::FixTTM(LAMMPS *lmp, int narg, char **arg) :
- Fix(lmp, narg, arg),
- random(NULL), fp(NULL), fpr(NULL), nsum(NULL), nsum_all(NULL),
- T_initial_set(NULL), gfactor1(NULL), gfactor2(NULL), ratio(NULL),
- flangevin(NULL), T_electron(NULL), T_electron_old(NULL), sum_vsq(NULL),
- sum_mass_vsq(NULL), sum_vsq_all(NULL), sum_mass_vsq_all(NULL),
+ Fix(lmp, narg, arg),
+ random(NULL), fp(NULL), fpr(NULL), nsum(NULL), nsum_all(NULL),
+ T_initial_set(NULL), gfactor1(NULL), gfactor2(NULL), ratio(NULL),
+ flangevin(NULL), T_electron(NULL), T_electron_old(NULL), sum_vsq(NULL),
+ sum_mass_vsq(NULL), sum_vsq_all(NULL), sum_mass_vsq_all(NULL),
net_energy_transfer(NULL), net_energy_transfer_all(NULL)
{
if (narg < 15) error->all(FLERR,"Illegal fix ttm command");
@@ -92,7 +92,7 @@ FixTTM::FixTTM(LAMMPS *lmp, int narg, char **arg) :
// error check
- if (seed <= 0)
+ if (seed <= 0)
error->all(FLERR,"Invalid random number seed in fix ttm command");
if (electronic_specific_heat <= 0.0)
error->all(FLERR,"Fix ttm electronic_specific_heat must be > 0.0");
@@ -348,7 +348,7 @@ void FixTTM::read_initial_electron_temperatures()
while (1) {
if (fgets(line,MAXLINE,fpr) == NULL) break;
sscanf(line,"%d %d %d %lg",&ixnode,&iynode,&iznode,&T_tmp);
- if (T_tmp < 0.0)
+ if (T_tmp < 0.0)
error->one(FLERR,"Fix ttm electron temperatures must be > 0.0");
T_electron[ixnode][iynode][iznode] = T_tmp;
T_initial_set[ixnode][iynode][iznode] = 1;
diff --git a/src/MOLECULE/dihedral_charmmfsw.cpp b/src/MOLECULE/dihedral_charmmfsw.cpp
index feb3e02bd42135ca5ac82b416d0043431dc7b1b5..d33db36fda302c9d01c88c9a3bcf23cc17322915 100644
--- a/src/MOLECULE/dihedral_charmmfsw.cpp
+++ b/src/MOLECULE/dihedral_charmmfsw.cpp
@@ -13,9 +13,9 @@
/* ----------------------------------------------------------------------
Contributing author: Paul Crozier (SNL)
- The force-shifted sections were provided by Robert Meissner
+ The force-shifted sections were provided by Robert Meissner
and Lucio Colombi Ciacchi of Bremen University, Bremen, Germany,
- with additional assistance from Robert A. Latour, Clemson University
+ with additional assistance from Robert A. Latour, Clemson University
------------------------------------------------------------------------- */
#include <mpi.h>
@@ -279,7 +279,7 @@ void DihedralCharmmfsw::compute(int eflag, int vflag)
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
- // modifying coul and LJ force and energies to apply
+ // modifying coul and LJ force and energies to apply
// force_shift and force_switch as in CHARMM pairwise
// LJ interactions between 1-4 atoms should usually be
// for r < cut_inner, so switching not applied
@@ -287,7 +287,7 @@ void DihedralCharmmfsw::compute(int eflag, int vflag)
r = sqrt(rsq);
if (implicit) forcecoul = qqrd2e * q[i1]*q[i4]*r2inv;
else if (dihedflag) forcecoul = qqrd2e * q[i1]*q[i4]*sqrt(r2inv);
- else forcecoul = qqrd2e * q[i1]*q[i4]*(sqrt(r2inv) -
+ else forcecoul = qqrd2e * q[i1]*q[i4]*(sqrt(r2inv) -
r*cut_coulinv14*cut_coulinv14);
forcelj = r6inv * (lj14_1[itype][jtype]*r6inv - lj14_2[itype][jtype]);
fpair = weight[type] * (forcelj+forcecoul)*r2inv;
@@ -295,11 +295,11 @@ void DihedralCharmmfsw::compute(int eflag, int vflag)
if (eflag) {
if (dihedflag) ecoul = weight[type] * forcecoul;
else ecoul = weight[type] * qqrd2e * q[i1]*q[i4] *
- (sqrt(r2inv) + r*cut_coulinv14*cut_coulinv14 -
+ (sqrt(r2inv) + r*cut_coulinv14*cut_coulinv14 -
2.0*cut_coulinv14);
- evdwl14_12 = r6inv*lj14_3[itype][jtype]*r6inv -
+ evdwl14_12 = r6inv*lj14_3[itype][jtype]*r6inv -
lj14_3[itype][jtype]*cut_lj_inner6inv*cut_lj6inv;
- evdwl14_6 = -lj14_4[itype][jtype]*r6inv +
+ evdwl14_6 = -lj14_4[itype][jtype]*r6inv +
lj14_4[itype][jtype]*cut_lj_inner3inv*cut_lj3inv;
evdwl = evdwl14_12 + evdwl14_6;
evdwl *= weight[type];
@@ -429,18 +429,18 @@ void DihedralCharmmfsw::init_style()
double *p_cutljinner = (double *) force->pair->extract("cut_lj_inner",itmp);
double *p_cutlj = (double *) force->pair->extract("cut_lj",itmp);
double *p_cutcoul = (double *) force->pair->extract("cut_coul",itmp);
-
- if (p_cutcoul == NULL || p_cutljinner == NULL ||
+
+ if (p_cutcoul == NULL || p_cutljinner == NULL ||
p_cutlj == NULL || p_dihedflag == NULL)
error->all(FLERR,"Dihedral charmmfsw is incompatible with Pair style");
-
+
dihedflag = *p_dihedflag;
cut_coul14 = *p_cutcoul;
cut_lj_inner14 = *p_cutljinner;
cut_lj14 = *p_cutlj;
cut_coulinv14 = 1/cut_coul14;
- cut_lj_inner3inv = (1/cut_lj_inner14) * (1/cut_lj_inner14) *
+ cut_lj_inner3inv = (1/cut_lj_inner14) * (1/cut_lj_inner14) *
(1/cut_lj_inner14);
cut_lj_inner6inv = cut_lj_inner3inv * cut_lj_inner3inv;
cut_lj3inv = (1/cut_lj14) * (1/cut_lj14) * (1/cut_lj14);
diff --git a/src/MOLECULE/fix_cmap.cpp b/src/MOLECULE/fix_cmap.cpp
index 56106cc3e0b26fb787c51bf5759ccebc2a255ab6..f4bc6c1ee645ee98fa9b77b680dc5c7fefe32b07 100644
--- a/src/MOLECULE/fix_cmap.cpp
+++ b/src/MOLECULE/fix_cmap.cpp
@@ -62,12 +62,12 @@ using namespace MathConst;
/* ---------------------------------------------------------------------- */
-FixCMAP::FixCMAP(LAMMPS *lmp, int narg, char **arg) :
+FixCMAP::FixCMAP(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg),
- crosstermlist(NULL), num_crossterm(NULL), crossterm_type(NULL),
- crossterm_atom1(NULL), crossterm_atom2(NULL), crossterm_atom3(NULL),
+ crosstermlist(NULL), num_crossterm(NULL), crossterm_type(NULL),
+ crossterm_atom1(NULL), crossterm_atom2(NULL), crossterm_atom3(NULL),
crossterm_atom4(NULL), crossterm_atom5(NULL),
- g_axis(NULL), cmapgrid(NULL), d1cmapgrid(NULL), d2cmapgrid(NULL),
+ g_axis(NULL), cmapgrid(NULL), d1cmapgrid(NULL), d2cmapgrid(NULL),
d12cmapgrid(NULL)
{
if (narg != 4) error->all(FLERR,"Illegal fix cmap command");
diff --git a/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp b/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp
index 7d69995fed8172d93b9462c1b85c8c05be450597..7da6d59d32f5ef2a1ae49b59226312968a6f080e 100644
--- a/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp
+++ b/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp
@@ -14,9 +14,9 @@
/* ----------------------------------------------------------------------
Contributing author: Paul Crozier (SNL)
The lj-fsw/coul-fsh (force-switched and force-shifted) sections
- were provided by Robert Meissner
+ were provided by Robert Meissner
and Lucio Colombi Ciacchi of Bremen University, Bremen, Germany,
- with additional assistance from Robert A. Latour, Clemson University
+ with additional assistance from Robert A. Latour, Clemson University
------------------------------------------------------------------------- */
#include <math.h>
@@ -37,7 +37,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-PairLJCharmmfswCoulCharmmfsh::PairLJCharmmfswCoulCharmmfsh(LAMMPS *lmp) :
+PairLJCharmmfswCoulCharmmfsh::PairLJCharmmfswCoulCharmmfsh(LAMMPS *lmp) :
Pair(lmp)
{
implicit = 0;
@@ -185,15 +185,15 @@ void PairLJCharmmfswCoulCharmmfsh::compute(int eflag, int vflag)
if (rsq > cut_lj_innersq) {
rinv = 1.0/r;
r3inv = rinv*rinv*rinv;
- evdwl12 = lj3[itype][jtype]*cut_lj6*denom_lj12 *
+ evdwl12 = lj3[itype][jtype]*cut_lj6*denom_lj12 *
(r6inv - cut_lj6inv)*(r6inv - cut_lj6inv);
- evdwl6 = -lj4[itype][jtype]*cut_lj3*denom_lj6 *
+ evdwl6 = -lj4[itype][jtype]*cut_lj3*denom_lj6 *
(r3inv - cut_lj3inv)*(r3inv - cut_lj3inv);;
evdwl = evdwl12 + evdwl6;
} else {
- evdwl12 = r6inv*lj3[itype][jtype]*r6inv -
+ evdwl12 = r6inv*lj3[itype][jtype]*r6inv -
lj3[itype][jtype]*cut_lj_inner6inv*cut_lj6inv;
- evdwl6 = -lj4[itype][jtype]*r6inv +
+ evdwl6 = -lj4[itype][jtype]*r6inv +
lj4[itype][jtype]*cut_lj_inner3inv*cut_lj3inv;
evdwl = evdwl12 + evdwl6;
}
@@ -248,7 +248,7 @@ void PairLJCharmmfswCoulCharmmfsh::allocate()
void PairLJCharmmfswCoulCharmmfsh::settings(int narg, char **arg)
{
- if (narg != 2 && narg != 3)
+ if (narg != 2 && narg != 3)
error->all(FLERR,"Illegal pair_style command");
cut_lj_inner = force->numeric(FLERR,arg[0]);
@@ -266,7 +266,7 @@ void PairLJCharmmfswCoulCharmmfsh::settings(int narg, char **arg)
void PairLJCharmmfswCoulCharmmfsh::coeff(int narg, char **arg)
{
- if (narg != 4 && narg != 6)
+ if (narg != 4 && narg != 6)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
@@ -331,7 +331,7 @@ void PairLJCharmmfswCoulCharmmfsh::init_style()
cut_coulinv = 1.0/cut_coul;
cut_bothsq = MAX(cut_ljsq,cut_coulsq);
- denom_lj = (cut_ljsq-cut_lj_innersq) * (cut_ljsq-cut_lj_innersq) *
+ denom_lj = (cut_ljsq-cut_lj_innersq) * (cut_ljsq-cut_lj_innersq) *
(cut_ljsq-cut_lj_innersq);
denom_lj12 = 1.0/(cut_lj6 - cut_lj_inner6);
denom_lj6 = 1.0/(cut_lj3 - cut_lj_inner3);
@@ -362,7 +362,7 @@ double PairLJCharmmfswCoulCharmmfsh::init_one(int i, int j)
lj14_2[i][j] = 24.0 * eps14[i][j] * pow(sigma14[i][j],6.0);
lj14_3[i][j] = 4.0 * eps14[i][j] * pow(sigma14[i][j],12.0);
lj14_4[i][j] = 4.0 * eps14[i][j] * pow(sigma14[i][j],6.0);
-
+
lj1[j][i] = lj1[i][j];
lj2[j][i] = lj2[i][j];
lj3[j][i] = lj3[i][j];
@@ -498,7 +498,7 @@ single(int i, int j, int itype, int jtype,
r = sqrt(rsq);
rinv = 1.0/r;
if (rsq < cut_coulsq) {
- forcecoul = force->qqrd2e * atom->q[i]*atom->q[j] *
+ forcecoul = force->qqrd2e * atom->q[i]*atom->q[j] *
(sqrt(r2inv) - r*cut_coulinv*cut_coulinv);
} else forcecoul = 0.0;
@@ -517,21 +517,21 @@ single(int i, int j, int itype, int jtype,
double eng = 0.0;
if (rsq < cut_coulsq) {
- phicoul = force->qqrd2e * atom->q[i]*atom->q[j] *
+ phicoul = force->qqrd2e * atom->q[i]*atom->q[j] *
(sqrt(r2inv) + cut_coulinv*cut_coulinv*r - 2.0*cut_coulinv);
eng += factor_coul*phicoul;
}
if (rsq < cut_ljsq) {
if (rsq > cut_lj_innersq) {
- philj12 = lj3[itype][jtype]*cut_lj6*denom_lj12 *
+ philj12 = lj3[itype][jtype]*cut_lj6*denom_lj12 *
(r6inv - cut_lj6inv)*(r6inv - cut_lj6inv);
- philj6 = -lj4[itype][jtype]*cut_lj3*denom_lj6 *
+ philj6 = -lj4[itype][jtype]*cut_lj3*denom_lj6 *
(r3inv - cut_lj3inv)*(r3inv - cut_lj3inv);;
philj = philj12 + philj6;
} else {
- philj12 = r6inv*lj3[itype][jtype]*r6inv -
+ philj12 = r6inv*lj3[itype][jtype]*r6inv -
lj3[itype][jtype]*cut_lj_inner6inv*cut_lj6inv;
- philj6 = -lj4[itype][jtype]*r6inv +
+ philj6 = -lj4[itype][jtype]*r6inv +
lj4[itype][jtype]*cut_lj_inner3inv*cut_lj3inv;
philj = philj12 + philj6;
}
diff --git a/src/POEMS/fix_poems.cpp b/src/POEMS/fix_poems.cpp
index effd06f477dfea0510e3c6aa45840a26d1593e28..7ff9e91af8127ad76b0b7e661a00cbe47f1fbce1 100644
--- a/src/POEMS/fix_poems.cpp
+++ b/src/POEMS/fix_poems.cpp
@@ -62,11 +62,11 @@ static const char cite_fix_poems[] =
------------------------------------------------------------------------- */
FixPOEMS::FixPOEMS(LAMMPS *lmp, int narg, char **arg) :
- Fix(lmp, narg, arg), step_respa(NULL), natom2body(NULL),
- atom2body(NULL), displace(NULL), nrigid(NULL), masstotal(NULL),
- xcm(NULL), vcm(NULL), fcm(NULL), inertia(NULL), ex_space(NULL),
- ey_space(NULL), ez_space(NULL), angmom(NULL), omega(NULL),
- torque(NULL), sum(NULL), all(NULL), jointbody(NULL),
+ Fix(lmp, narg, arg), step_respa(NULL), natom2body(NULL),
+ atom2body(NULL), displace(NULL), nrigid(NULL), masstotal(NULL),
+ xcm(NULL), vcm(NULL), fcm(NULL), inertia(NULL), ex_space(NULL),
+ ey_space(NULL), ez_space(NULL), angmom(NULL), omega(NULL),
+ torque(NULL), sum(NULL), all(NULL), jointbody(NULL),
xjoint(NULL), freelist(NULL), poems(NULL)
{
if (lmp->citeme) lmp->citeme->add(cite_fix_poems);
diff --git a/src/PYTHON/python_impl.cpp b/src/PYTHON/python_impl.cpp
index cd8e691782a621eb15bab027b1907c76c2a9ea55..9f018ad6029e4b30789037d3e05ff88912440dd6 100644
--- a/src/PYTHON/python_impl.cpp
+++ b/src/PYTHON/python_impl.cpp
@@ -345,7 +345,7 @@ void PythonImpl::invoke_function(int ifunc, char *result)
sprintf(result,"%.15g",PyFloat_AsDouble(pValue));
} else if (otype == STRING) {
char *pystr = PY_STRING_AS_STRING(pValue);
- if (pfuncs[ifunc].longstr)
+ if (pfuncs[ifunc].longstr)
strncpy(pfuncs[ifunc].longstr,pystr,pfuncs[ifunc].length_longstr);
else strncpy(result,pystr,VALUELENGTH-1);
}
@@ -478,7 +478,7 @@ int PythonImpl::create_entry(char *name)
else error->all(FLERR,"Invalid python command");
if (length_longstr) {
- if (pfuncs[ifunc].otype != STRING)
+ if (pfuncs[ifunc].otype != STRING)
error->all(FLERR,"Python command length keyword "
"cannot be used unless output is a string");
pfuncs[ifunc].length_longstr = length_longstr;
diff --git a/src/QEQ/fix_qeq.cpp b/src/QEQ/fix_qeq.cpp
index bc8a660066205e2ff3a24ac15232972038146f7b..afa2801831f0c677a979d4c49df7af2fe63bee75 100644
--- a/src/QEQ/fix_qeq.cpp
+++ b/src/QEQ/fix_qeq.cpp
@@ -46,10 +46,10 @@ using namespace FixConst;
/* ---------------------------------------------------------------------- */
FixQEq::FixQEq(LAMMPS *lmp, int narg, char **arg) :
- Fix(lmp, narg, arg), list(NULL), chi(NULL), eta(NULL),
- gamma(NULL), zeta(NULL), zcore(NULL), chizj(NULL), shld(NULL),
- s(NULL), t(NULL), s_hist(NULL), t_hist(NULL), Hdia_inv(NULL), b_s(NULL),
- b_t(NULL), p(NULL), q(NULL), r(NULL), d(NULL),
+ Fix(lmp, narg, arg), list(NULL), chi(NULL), eta(NULL),
+ gamma(NULL), zeta(NULL), zcore(NULL), chizj(NULL), shld(NULL),
+ s(NULL), t(NULL), s_hist(NULL), t_hist(NULL), Hdia_inv(NULL), b_s(NULL),
+ b_t(NULL), p(NULL), q(NULL), r(NULL), d(NULL),
qf(NULL), q1(NULL), q2(NULL), qv(NULL)
{
if (narg < 8) error->all(FLERR,"Illegal fix qeq command");
diff --git a/src/REPLICA/neb.cpp b/src/REPLICA/neb.cpp
index 1388a260ea71d4af72b43c0196e7e044e47cf92d..692f9361258a847e51775cb1f451e1f04895ce11 100644
--- a/src/REPLICA/neb.cpp
+++ b/src/REPLICA/neb.cpp
@@ -229,8 +229,8 @@ void NEB::run()
"RDN PEN\n");
}
}
-
- if (ulogfile) {
+
+ if (ulogfile) {
if (verbose) {
fprintf(ulogfile,"Step MaxReplicaForce MaxAtomForce "
"GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... "
@@ -657,15 +657,15 @@ void NEB::print_status()
if (verbose) {
fprintf(uscreen,"%12.5g %12.5g %12.5g %12.5g %12.5g %12.5g",
NAN,180-acos(all[0][5])*todeg,180-acos(all[0][6])*todeg,
- all[0][3],freplica[0],fmaxatomInRepl[0]);
+ all[0][3],freplica[0],fmaxatomInRepl[0]);
for (int i = 1; i < nreplica-1; i++)
fprintf(uscreen,"%12.5g %12.5g %12.5g %12.5g %12.5g %12.5g",
180-acos(all[i][4])*todeg,180-acos(all[i][5])*todeg,
180-acos(all[i][6])*todeg,all[i][3],freplica[i],
- fmaxatomInRepl[i]);
+ fmaxatomInRepl[i]);
fprintf(uscreen,"%12.5g %12.5g %12.5g %12.5g %12.5g %12.5g",
NAN,180-acos(all[nreplica-1][5])*todeg,NAN,all[nreplica-1][3],
- freplica[nreplica-1],fmaxatomInRepl[nreplica-1]);
+ freplica[nreplica-1],fmaxatomInRepl[nreplica-1]);
}
fprintf(uscreen,"\n");
}
@@ -681,15 +681,15 @@ void NEB::print_status()
if (verbose) {
fprintf(ulogfile,"%12.5g %12.5g %12.5g %12.5g %12.5g %12.5g",
NAN,180-acos(all[0][5])*todeg,180-acos(all[0][6])*todeg,
- all[0][3],freplica[0],fmaxatomInRepl[0]);
+ all[0][3],freplica[0],fmaxatomInRepl[0]);
for (int i = 1; i < nreplica-1; i++)
fprintf(ulogfile,"%12.5g %12.5g %12.5g %12.5g %12.5g %12.5g",
180-acos(all[i][4])*todeg,180-acos(all[i][5])*todeg,
180-acos(all[i][6])*todeg,all[i][3],freplica[i],
- fmaxatomInRepl[i]);
+ fmaxatomInRepl[i]);
fprintf(ulogfile,"%12.5g %12.5g %12.5g %12.5g %12.5g %12.5g",
NAN,180-acos(all[nreplica-1][5])*todeg,NAN,all[nreplica-1][3],
- freplica[nreplica-1],fmaxatomInRepl[nreplica-1]);
+ freplica[nreplica-1],fmaxatomInRepl[nreplica-1]);
}
fprintf(ulogfile,"\n");
fflush(ulogfile);
diff --git a/src/REPLICA/prd.cpp b/src/REPLICA/prd.cpp
index f7d369cee6a4b162a5fdecc040310f5f60c492b5..684277a698b265f778864f5290325dffb232c21a 100644
--- a/src/REPLICA/prd.cpp
+++ b/src/REPLICA/prd.cpp
@@ -118,7 +118,7 @@ void PRD::command(int narg, char **arg)
// comm mode for inter-replica exchange of coords
- if (nreplica == nprocs_universe && atom->sortfreq == 0)
+ if (nreplica == nprocs_universe && atom->sortfreq == 0)
cmode = SINGLE_PROC_DIRECT;
else if (nreplica == nprocs_universe) cmode = SINGLE_PROC_MAP;
else cmode = MULTI_PROC;
@@ -854,20 +854,20 @@ void PRD::replicate(int ireplica)
MPI_Gatherv(atom->x[0],3*atom->nlocal,MPI_DOUBLE,
xall[0],counts,displacements,MPI_DOUBLE,0,world);
}
-
+
if (me == 0) {
MPI_Bcast(tagall,natoms,MPI_LMP_TAGINT,ireplica,comm_replica);
MPI_Bcast(imageall,natoms,MPI_LMP_IMAGEINT,ireplica,comm_replica);
MPI_Bcast(xall[0],3*natoms,MPI_DOUBLE,ireplica,comm_replica);
}
-
+
MPI_Bcast(tagall,natoms,MPI_LMP_TAGINT,0,world);
MPI_Bcast(imageall,natoms,MPI_LMP_IMAGEINT,0,world);
MPI_Bcast(xall[0],3*natoms,MPI_DOUBLE,0,world);
-
+
double **x = atom->x;
int nlocal = atom->nlocal;
-
+
for (i = 0; i < natoms; i++) {
m = atom->map(tagall[i]);
if (m < 0 || m >= nlocal) continue;
diff --git a/src/RIGID/compute_rigid_local.cpp b/src/RIGID/compute_rigid_local.cpp
index 9b2f7c7da17e01e36bdc32bc4f8653a189c60957..deca01f2aea749fa9cc82c075659fba711f13807 100644
--- a/src/RIGID/compute_rigid_local.cpp
+++ b/src/RIGID/compute_rigid_local.cpp
@@ -33,7 +33,7 @@ enum{ID,MOL,MASS,X,Y,Z,XU,YU,ZU,VX,VY,VZ,FX,FY,FZ,IX,IY,IZ,
/* ---------------------------------------------------------------------- */
ComputeRigidLocal::ComputeRigidLocal(LAMMPS *lmp, int narg, char **arg) :
- Compute(lmp, narg, arg),
+ Compute(lmp, narg, arg),
rstyle(NULL), idrigid(NULL), fixrigid(NULL), vlocal(NULL), alocal(NULL)
{
if (narg < 5) error->all(FLERR,"Illegal compute rigid/local command");
@@ -194,11 +194,11 @@ int ComputeRigidLocal::compute_rigid(int flag)
ptr[n] = body->xcm[2];
break;
case XU:
- ptr[n] = body->xcm[0] +
+ ptr[n] = body->xcm[0] +
((body->image & IMGMASK) - IMGMAX) * xprd;
break;
case YU:
- ptr[n] = body->xcm[1] +
+ ptr[n] = body->xcm[1] +
((body->image >> IMGBITS & IMGMASK) - IMGMAX) * yprd;
break;
case ZU:
diff --git a/src/RIGID/fix_ehex.cpp b/src/RIGID/fix_ehex.cpp
index 522076639b434a9675acdd54d3513e4e76d09970..61b76b513f57f654268936711bfe535b2250b751 100644
--- a/src/RIGID/fix_ehex.cpp
+++ b/src/RIGID/fix_ehex.cpp
@@ -50,11 +50,11 @@ enum{CONSTANT,EQUAL,ATOM};
/* ---------------------------------------------------------------------- */
FixEHEX::FixEHEX(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
- idregion(NULL), x(NULL), f(NULL), v(NULL),
+ idregion(NULL), x(NULL), f(NULL), v(NULL),
mass(NULL), rmass(NULL), type(NULL), scalingmask(NULL)
{
MPI_Comm_rank(world, &me);
-
+
// check
if (narg < 4) error->all(FLERR,"Illegal fix ehex command: wrong number of parameters ");
@@ -75,7 +75,7 @@ FixEHEX::FixEHEX(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
// optional args
iregion = -1;
-
+
// NOTE: constraints are deactivated by default
constraints = 0;
@@ -85,7 +85,7 @@ FixEHEX::FixEHEX(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
cluster = 0;
// NOTE: hex = 1 means that no coordinate correction is applied in which case eHEX reduces to HEX
-
+
hex = 0;
int iarg = 5;
@@ -100,7 +100,7 @@ FixEHEX::FixEHEX(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
idregion = new char[n];
strcpy(idregion,arg[iarg+1]);
iarg += 2;
- }
+ }
// apply constraints (shake/rattle) at the end of the timestep
@@ -115,7 +115,7 @@ FixEHEX::FixEHEX(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
cluster = 1;
iarg += 1;
}
-
+
// don't apply a coordinate correction if this keyword is specified
else if (strcmp(arg[iarg], "hex") == 0) {
@@ -124,11 +124,11 @@ FixEHEX::FixEHEX(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
}
else
error->all(FLERR, "Illegal fix ehex keyword ");
- }
+ }
// check options
- if (cluster && !constraints)
+ if (cluster && !constraints)
error->all(FLERR, "You can only use the keyword 'com' together with the keyword 'constrain' ");
scale = 1.0;
@@ -183,26 +183,26 @@ void FixEHEX::init()
error->all(FLERR,"Fix ehex group has no atoms");
fshake = NULL;
- if (constraints) {
+ if (constraints) {
// check if constraining algorithm is used (FixRattle inherits from FixShake)
int cnt_shake = 0;
int id_shake;
- for (int i = 0; i < modify->nfix; i++) {
+ for (int i = 0; i < modify->nfix; i++) {
if (strcmp("rattle", modify->fix[i]->style) == 0 ||
strcmp("shake", modify->fix[i]->style) == 0) {
cnt_shake++;
id_shake = i;
}
- }
-
- if (cnt_shake > 1)
+ }
+
+ if (cnt_shake > 1)
error->all(FLERR,"Multiple instances of fix shake/rattle detected (not supported yet)");
else if (cnt_shake == 1) {
fshake = ((FixShake*) modify->fix[id_shake]);
}
- else if (cnt_shake == 0)
+ else if (cnt_shake == 0)
error->all(FLERR, "Fix ehex was configured with keyword constrain, but shake/rattle was not defined");
}
}
@@ -227,20 +227,20 @@ void FixEHEX::end_of_step() {
update_scalingmask();
- // rescale velocities
+ // rescale velocities
rescale();
// if required use shake/rattle to correct coordinates and velocities
- if (constraints && fshake)
+ if (constraints && fshake)
fshake->shake_end_of_step(0);
}
/* ----------------------------------------------------------------------
- Iterate over all atoms, rescale the velocities and apply coordinate
+ Iterate over all atoms, rescale the velocities and apply coordinate
corrections.
------------------------------------------------------------------------- */
@@ -254,17 +254,17 @@ void FixEHEX::rescale() {
dt = update->dt;
// calculate centre of mass properties
-
- com_properties(vcm, sfr, &sfvr, &Ke, &Kr, &masstotal);
+
+ com_properties(vcm, sfr, &sfvr, &Ke, &Kr, &masstotal);
// heat flux into the reservoir
F = heat_input * force->ftm2v * nevery;
-
+
// total mass
mr = masstotal;
-
+
// energy scaling factor
escale = 1. + (F*dt)/Kr;
@@ -292,7 +292,7 @@ void FixEHEX::rescale() {
// epsr_ik implements Eq. (20) in the paper
- eta_ik = mi * F/(2.*Kr) * (v[i][k] - vcm[k]);
+ eta_ik = mi * F/(2.*Kr) * (v[i][k] - vcm[k]);
epsr_ik = eta_ik / (mi*Kr) * (F/48. + sfvr/6.*force->ftm2v) - F/(12.*Kr) * (f[i][k]/mi - sfr[k]/mr)*force->ftm2v;
x[i][k] -= dt*dt*dt * epsr_ik;
@@ -328,8 +328,8 @@ double FixEHEX::memory_usage()
/* ----------------------------------------------------------------------
- Update the array scalingmask depending on which individual atoms
- will be rescaled or not.
+ Update the array scalingmask depending on which individual atoms
+ will be rescaled or not.
------------------------------------------------------------------------- */
void FixEHEX::update_scalingmask() {
@@ -349,14 +349,14 @@ void FixEHEX::update_scalingmask() {
// only rescale molecules whose center of mass if fully contained in the region
if (cluster) {
-
+
// loop over all clusters
for (int i=0; i < fshake->nlist; i++) {
- // cluster id
+ // cluster id
- m = fshake->list[i];
+ m = fshake->list[i];
// check if the centre of mass of the cluster is inside the region
// if region == NULL, just check the group information of all sites
@@ -368,7 +368,7 @@ void FixEHEX::update_scalingmask() {
else nsites = 0;
if (nsites == 0) {
- error->all(FLERR,"Internal error: shake_flag[m] has to be between 1 and 4 for m in nlist");
+ error->all(FLERR,"Internal error: shake_flag[m] has to be between 1 and 4 for m in nlist");
}
stat = check_cluster(fshake->shake_atom[m], nsites, region);
@@ -376,22 +376,22 @@ void FixEHEX::update_scalingmask() {
for (int l=0; l < nsites; l++) {
lid = atom->map(fshake->shake_atom[m][l]);
scalingmask[lid] = stat;
- }
+ }
}
// check atoms that do not belong to any cluster
for (int i=0; i<atom->nlocal; i++) {
- if (fshake->shake_flag[i] == 0)
+ if (fshake->shake_flag[i] == 0)
scalingmask[i] = rescale_atom(i,region);
}
- }
+ }
// no clusters, just individual sites (e.g. monatomic system or flexible molecules)
else {
- for (int i=0; i<atom->nlocal; i++)
+ for (int i=0; i<atom->nlocal; i++)
scalingmask[i] = rescale_atom(i,region);
}
@@ -411,7 +411,7 @@ bool FixEHEX::check_cluster(tagint *shake_atom, int n, Region * region) {
double **x = atom->x;
double * rmass = atom->rmass;
- double * mass = atom->mass;
+ double * mass = atom->mass;
int * type = atom->type;
int * mask = atom->mask;
double xcom[3], xtemp[3];
@@ -432,7 +432,7 @@ bool FixEHEX::check_cluster(tagint *shake_atom, int n, Region * region) {
// get local id
lid[i] = atom->map(shake_atom[i]);
-
+
// check if all sites of the cluster belong to the correct group
stat = stat && (mask[lid[i]] & groupbit);
@@ -444,21 +444,21 @@ bool FixEHEX::check_cluster(tagint *shake_atom, int n, Region * region) {
mi = (rmass) ? rmass[lid[i]] : mass[type[lid[i]]];
mcluster += mi;
- // accumulate centre of mass
+ // accumulate centre of mass
// NOTE: you can either use unwrapped coordinates or take site x[lid[0]] as reference,
// i.e. reconstruct the molecule around this site and calculate the com.
- for (int k=0; k<3; k++)
+ for (int k=0; k<3; k++)
xtemp[k] = x[lid[i]][k] - x[lid[0]][k];
-
+
// take into account pbc
-
+
domain->minimum_image(xtemp);
for (int k=0; k<3; k++)
xcom[k] += mi * (x[lid[0]][k] + xtemp[k]) ;
- }
- }
+ }
+ }
// check if centre of mass is inside the region (if specified)
@@ -472,17 +472,17 @@ bool FixEHEX::check_cluster(tagint *shake_atom, int n, Region * region) {
// divide by total mass
- for (int k=0; k<3; k++)
- xcom[k] = xcom[k]/mcluster;
-
+ for (int k=0; k<3; k++)
+ xcom[k] = xcom[k]/mcluster;
+
// apply periodic boundary conditions (centre of mass could be outside the box)
// and check if molecule is inside the region
domain->remap(xcom);
stat = stat && region->match(xcom[0], xcom[1], xcom[2]);
}
-
- return stat;
+
+ return stat;
}
@@ -536,7 +536,7 @@ void FixEHEX::com_properties(double * vr, double * sfr, double *sfvr, double *K,
double mi;
double l_buf[9];
double buf[9];
-
+
// calculate partial sums
l_vr[0] = l_vr[1] = l_vr[2] = 0;
@@ -546,8 +546,8 @@ void FixEHEX::com_properties(double * vr, double * sfr, double *sfvr, double *K,
l_K = 0;
for (int i = 0; i < nlocal; i++) {
- if (scalingmask[i]) {
-
+ if (scalingmask[i]) {
+
// check if reduced mass is used
mi = (rmass) ? rmass[i] : mass[type[i]];
@@ -555,7 +555,7 @@ void FixEHEX::com_properties(double * vr, double * sfr, double *sfvr, double *K,
// accumulate total mass
l_mr += mi;
-
+
// accumulate kinetic energy
l_K += mi/2. * (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]);
@@ -595,7 +595,7 @@ void FixEHEX::com_properties(double * vr, double * sfr, double *sfvr, double *K,
error->all(FLERR, "Fix ehex error mass of region is close to zero");
}
- // total kinetic energy of region
+ // total kinetic energy of region
*K = buf[3];
@@ -616,7 +616,7 @@ void FixEHEX::com_properties(double * vr, double * sfr, double *sfvr, double *K,
*Kr = *K - 0.5* (*mr) * (vr[0]*vr[0]+vr[1]*vr[1]+vr[2]*vr[2]);
// calculate sum_j f_j * (v_j - v_r) = sum_j f_j * v_j - v_r * sum_j f_j
-
+
*sfvr = buf[8] - (vr[0]*sfr[0] + vr[1]*sfr[1] + vr[2]*sfr[2]);
}
diff --git a/src/RIGID/fix_rattle.cpp b/src/RIGID/fix_rattle.cpp
index 359be6b885e2ae3085d6b1f68bde7ce349fffe9f..666561b462bb7011378e02e2d3bba776f723ff97 100644
--- a/src/RIGID/fix_rattle.cpp
+++ b/src/RIGID/fix_rattle.cpp
@@ -80,14 +80,14 @@ FixRattle::FixRattle(LAMMPS *lmp, int narg, char **arg) :
comm_mode = XSHAKE;
vflag_post_force = 0;
- verr_max = 0;
+ verr_max = 0;
derr_max = 0;
}
/* ---------------------------------------------------------------------- */
FixRattle::~FixRattle()
-{
+{
memory->destroy(vp);
@@ -116,11 +116,11 @@ int FixRattle::setmask()
{
int mask = 0;
mask |= PRE_NEIGHBOR;
- mask |= POST_FORCE;
+ mask |= POST_FORCE;
mask |= POST_FORCE_RESPA;
mask |= FINAL_INTEGRATE;
mask |= FINAL_INTEGRATE_RESPA;
- if (RATTLE_DEBUG) mask |= END_OF_STEP;
+ if (RATTLE_DEBUG) mask |= END_OF_STEP;
return mask;
}
@@ -176,10 +176,10 @@ void FixRattle::post_force(int vflag)
int m;
for (int i = 0; i < nlist; i++) {
m = list[i];
- if (shake_flag[m] == 2) vrattle2(m);
- else if (shake_flag[m] == 3) vrattle3(m);
- else if (shake_flag[m] == 4) vrattle4(m);
- else vrattle3angle(m);
+ if (shake_flag[m] == 2) vrattle2(m);
+ else if (shake_flag[m] == 3) vrattle3(m);
+ else if (shake_flag[m] == 4) vrattle4(m);
+ else vrattle3angle(m);
}
}
@@ -261,7 +261,7 @@ void FixRattle::vrattle3angle(int m)
domain->minimum_image(r02);
domain->minimum_image(r12);
- // v01,v02,v12 = velocity differences
+ // v01,v02,v12 = velocity differences
MathExtra::sub3(vp[i1],vp[i0],vp01);
MathExtra::sub3(vp[i2],vp[i0],vp02);
@@ -285,7 +285,7 @@ void FixRattle::vrattle3angle(int m)
a[0][1] = (imass[0] ) * MathExtra::dot3(r01,r02);
a[0][2] = (-imass[1] ) * MathExtra::dot3(r01,r12);
a[1][0] = a[0][1];
- a[1][1] = (imass[0] + imass[2]) * MathExtra::dot3(r02,r02);
+ a[1][1] = (imass[0] + imass[2]) * MathExtra::dot3(r02,r02);
a[1][2] = (imass[2] ) * MathExtra::dot3(r02,r12);
a[2][0] = a[0][2];
a[2][1] = a[1][2];
@@ -304,15 +304,15 @@ void FixRattle::vrattle3angle(int m)
// add corrections to the velocities if processor owns atom
if (i0 < nlocal) {
- for (int k=0; k<3; k++)
+ for (int k=0; k<3; k++)
v[i0][k] -= imass[0]* ( l[0] * r01[k] + l[1] * r02[k] );
- }
+ }
if (i1 < nlocal) {
- for (int k=0; k<3; k++)
+ for (int k=0; k<3; k++)
v[i1][k] -= imass[1] * ( -l[0] * r01[k] + l[2] * r12[k] );
}
if (i2 < nlocal) {
- for (int k=0; k<3; k++)
+ for (int k=0; k<3; k++)
v[i2][k] -= imass[2] * ( -l[1] * r02[k] - l[2] * r12[k] );
}
}
@@ -350,17 +350,17 @@ void FixRattle::vrattle2(int m)
// Lagrange multiplier: exact solution
- double l01 = - MathExtra::dot3(r01,vp01) /
+ double l01 = - MathExtra::dot3(r01,vp01) /
(MathExtra::dot3(r01,r01) * (imass[0] + imass[1]));
// add corrections to the velocities if the process owns this atom
if (i0 < nlocal) {
- for (int k=0; k<3; k++)
+ for (int k=0; k<3; k++)
v[i0][k] -= imass[0] * l01 * r01[k];
- }
+ }
if (i1 < nlocal) {
- for (int k=0; k<3; k++)
+ for (int k=0; k<3; k++)
v[i1][k] -= imass[1] * (-l01) * r01[k];
}
}
@@ -383,7 +383,7 @@ void FixRattle::vrattle3(int m)
MathExtra::sub3(x[i1],x[i0],r01);
MathExtra::sub3(x[i2],x[i0],r02);
-
+
domain->minimum_image(r01);
domain->minimum_image(r02);
@@ -421,15 +421,15 @@ void FixRattle::vrattle3(int m)
// add corrections to the velocities if the process owns this atom
if (i0 < nlocal) {
- for (int k=0; k<3; k++)
+ for (int k=0; k<3; k++)
v[i0][k] -= imass[0] * ( l[0] * r01[k] + l[1] * r02[k] );
- }
- if (i1 < nlocal)
+ }
+ if (i1 < nlocal)
for (int k=0; k<3; k++) {
v[i1][k] -= imass[1] * ( -l[0] * r01[k] );
}
if (i2 < nlocal) {
- for (int k=0; k<3; k++)
+ for (int k=0; k<3; k++)
v[i2][k] -= imass[2] * ( -l[1] * r02[k] );
}
}
@@ -504,26 +504,26 @@ void FixRattle::vrattle4(int m)
// add corrections to the velocities if the process owns this atom
if (i0 < nlocal) {
- for (int k=0; k<3; k++)
+ for (int k=0; k<3; k++)
v[i0][k] -= imass[0] * ( l[0] * r01[k] + l[1] * r02[k] + l[2] * r03[k]);
- }
+ }
if (i1 < nlocal) {
- for (int k=0; k<3; k++)
- v[i1][k] -= imass[1] * (-l[0] * r01[k]);
+ for (int k=0; k<3; k++)
+ v[i1][k] -= imass[1] * (-l[0] * r01[k]);
}
if (i2 < nlocal) {
- for (int k=0; k<3; k++)
+ for (int k=0; k<3; k++)
v[i2][k] -= imass[2] * ( -l[1] * r02[k]);
}
if (i3 < nlocal) {
- for (int k=0; k<3; k++)
- v[i3][k] -= imass[3] * ( -l[2] * r03[k]);
+ for (int k=0; k<3; k++)
+ v[i3][k] -= imass[3] * ( -l[2] * r03[k]);
}
}
/* ---------------------------------------------------------------------- */
-void FixRattle::solve2x2exactly(const double a[][2],
+void FixRattle::solve2x2exactly(const double a[][2],
const double c[], double l[])
{
double determ, determinv;
@@ -545,18 +545,18 @@ void FixRattle::solve2x2exactly(const double a[][2],
/* ---------------------------------------------------------------------- */
-void FixRattle::solve3x3exactly(const double a[][3],
+void FixRattle::solve3x3exactly(const double a[][3],
const double c[], double l[])
{
double ai[3][3];
double determ, determinv;
-
+
// calculate the determinant of the matrix
- determ = a[0][0]*a[1][1]*a[2][2] + a[0][1]*a[1][2]*a[2][0] +
- a[0][2]*a[1][0]*a[2][1] - a[0][0]*a[1][2]*a[2][1] -
+ determ = a[0][0]*a[1][1]*a[2][2] + a[0][1]*a[1][2]*a[2][0] +
+ a[0][2]*a[1][0]*a[2][1] - a[0][0]*a[1][2]*a[2][1] -
a[0][1]*a[1][0]*a[2][2] - a[0][2]*a[1][1]*a[2][0];
-
+
// check if matrix is actually invertible
if (determ == 0.0) error->one(FLERR,"Rattle determinant = 0.0");
@@ -565,7 +565,7 @@ void FixRattle::solve3x3exactly(const double a[][3],
determinv = 1.0/determ;
ai[0][0] = determinv * (a[1][1]*a[2][2] - a[1][2]*a[2][1]);
- ai[0][1] = -determinv * (a[0][1]*a[2][2] - a[0][2]*a[2][1]);
+ ai[0][1] = -determinv * (a[0][1]*a[2][2] - a[0][2]*a[2][1]);
ai[0][2] = determinv * (a[0][1]*a[1][2] - a[0][2]*a[1][1]);
ai[1][0] = -determinv * (a[1][0]*a[2][2] - a[1][2]*a[2][0]);
ai[1][1] = determinv * (a[0][0]*a[2][2] - a[0][2]*a[2][0]);
@@ -578,9 +578,9 @@ void FixRattle::solve3x3exactly(const double a[][3],
for (int i=0; i<3; i++) {
l[i] = 0;
- for (int j=0; j<3; j++)
+ for (int j=0; j<3; j++)
l[i] += ai[i][j] * c[j];
- }
+ }
}
/* ---------------------------------------------------------------------- */
@@ -686,7 +686,7 @@ int FixRattle::pack_forward_comm(int n, int *list, double *buf,
break;
}
return m;
-}
+}
/* ---------------------------------------------------------------------- */
@@ -739,7 +739,7 @@ void FixRattle::shake_end_of_step(int vflag) {
/* ----------------------------------------------------------------------
- Let shake calculate new constraining forces and correct the
+ Let shake calculate new constraining forces and correct the
coordinates. Nothing to do for rattle here.
------------------------------------------------------------------------- */
@@ -789,7 +789,7 @@ void FixRattle::correct_velocities() {
/* ----------------------------------------------------------------------
DEBUGGING methods
- The functions below allow you to check whether the
+ The functions below allow you to check whether the
coordinate and velocity constraints are satisfied at the
end of the timestep
only enabled if RATTLE_DEBUG is set to 1 at top of file
@@ -817,9 +817,9 @@ bool FixRattle::check_constraints(double **v, bool checkr, bool checkv)
int i=0;
while (i < nlist && ret) {
m = list[i];
- if (shake_flag[m] == 2) ret = check2(v,m,checkr,checkv);
- else if (shake_flag[m] == 3) ret = check3(v,m,checkr,checkv);
- else if (shake_flag[m] == 4) ret = check4(v,m,checkr,checkv);
+ if (shake_flag[m] == 2) ret = check2(v,m,checkr,checkv);
+ else if (shake_flag[m] == 3) ret = check3(v,m,checkr,checkv);
+ else if (shake_flag[m] == 4) ret = check4(v,m,checkr,checkv);
else ret = check3angle(v,m,checkr,checkv);
i++;
if (!RATTLE_RAISE_ERROR) ret = true;
@@ -835,7 +835,7 @@ bool FixRattle::check2(double **v, int m, bool checkr, bool checkv)
double r01[3],v01[3];
const double tol = tolerance;
double bond1 = bond_distance[shake_type[m][0]];
-
+
tagint i0 = atom->map(shake_atom[m][0]);
tagint i1 = atom->map(shake_atom[m][1]);
@@ -844,12 +844,12 @@ bool FixRattle::check2(double **v, int m, bool checkr, bool checkv)
MathExtra::sub3(v[i1],v[i0],v01);
stat = !(checkr && (fabs(sqrt(MathExtra::dot3(r01,r01)) - bond1) > tol));
- if (!stat)
+ if (!stat)
error->one(FLERR,"Coordinate constraints are not satisfied "
"up to desired tolerance ");
stat = !(checkv && (fabs(MathExtra::dot3(r01,v01)) > tol));
- if (!stat)
+ if (!stat)
error->one(FLERR,"Velocity constraints are not satisfied "
"up to desired tolerance ");
return stat;
@@ -865,14 +865,14 @@ bool FixRattle::check3(double **v, int m, bool checkr, bool checkv)
const double tol = tolerance;
double bond1 = bond_distance[shake_type[m][0]];
double bond2 = bond_distance[shake_type[m][1]];
-
+
i0 = atom->map(shake_atom[m][0]);
i1 = atom->map(shake_atom[m][1]);
i2 = atom->map(shake_atom[m][2]);
MathExtra::sub3(x[i1],x[i0],r01);
MathExtra::sub3(x[i2],x[i0],r02);
-
+
domain->minimum_image(r01);
domain->minimum_image(r02);
@@ -881,13 +881,13 @@ bool FixRattle::check3(double **v, int m, bool checkr, bool checkv)
stat = !(checkr && (fabs(sqrt(MathExtra::dot3(r01,r01)) - bond1) > tol ||
fabs(sqrt(MathExtra::dot3(r02,r02))-bond2) > tol));
- if (!stat)
+ if (!stat)
error->one(FLERR,"Coordinate constraints are not satisfied "
"up to desired tolerance ");
- stat = !(checkv && (fabs(MathExtra::dot3(r01,v01)) > tol ||
+ stat = !(checkv && (fabs(MathExtra::dot3(r01,v01)) > tol ||
fabs(MathExtra::dot3(r02,v02)) > tol));
- if (!stat)
+ if (!stat)
error->one(FLERR,"Velocity constraints are not satisfied "
"up to desired tolerance ");
return stat;
@@ -921,17 +921,17 @@ bool FixRattle::check4(double **v, int m, bool checkr, bool checkv)
MathExtra::sub3(v[i2],v[i0],v02);
MathExtra::sub3(v[i3],v[i0],v03);
- stat = !(checkr && (fabs(sqrt(MathExtra::dot3(r01,r01)) - bond1) > tol ||
- fabs(sqrt(MathExtra::dot3(r02,r02))-bond2) > tol ||
+ stat = !(checkr && (fabs(sqrt(MathExtra::dot3(r01,r01)) - bond1) > tol ||
+ fabs(sqrt(MathExtra::dot3(r02,r02))-bond2) > tol ||
fabs(sqrt(MathExtra::dot3(r03,r03))-bond3) > tol));
- if (!stat)
+ if (!stat)
error->one(FLERR,"Coordinate constraints are not satisfied "
"up to desired tolerance ");
- stat = !(checkv && (fabs(MathExtra::dot3(r01,v01)) > tol ||
- fabs(MathExtra::dot3(r02,v02)) > tol ||
+ stat = !(checkv && (fabs(MathExtra::dot3(r01,v01)) > tol ||
+ fabs(MathExtra::dot3(r02,v02)) > tol ||
fabs(MathExtra::dot3(r03,v03)) > tol));
- if (!stat)
+ if (!stat)
error->one(FLERR,"Velocity constraints are not satisfied "
"up to desired tolerance ");
return stat;
@@ -971,8 +971,8 @@ bool FixRattle::check3angle(double **v, int m, bool checkr, bool checkv)
double db12 = fabs(sqrt(MathExtra::dot3(r12,r12))-bond12);
- stat = !(checkr && (db1 > tol ||
- db2 > tol ||
+ stat = !(checkr && (db1 > tol ||
+ db2 > tol ||
db12 > tol));
if (derr_max < db1/bond1) derr_max = db1/bond1;
@@ -980,7 +980,7 @@ bool FixRattle::check3angle(double **v, int m, bool checkr, bool checkv)
if (derr_max < db12/bond12) derr_max = db12/bond12;
- if (!stat && RATTLE_RAISE_ERROR)
+ if (!stat && RATTLE_RAISE_ERROR)
error->one(FLERR,"Coordinate constraints are not satisfied "
"up to desired tolerance ");
@@ -993,12 +993,12 @@ bool FixRattle::check3angle(double **v, int m, bool checkr, bool checkv)
if (verr_max < dv12) verr_max = dv12;
- stat = !(checkv && (dv1 > tol ||
- dv2 > tol ||
+ stat = !(checkv && (dv1 > tol ||
+ dv2 > tol ||
dv12> tol));
- if (!stat && RATTLE_RAISE_ERROR)
+ if (!stat && RATTLE_RAISE_ERROR)
error->one(FLERR,"Velocity constraints are not satisfied "
"up to desired tolerance!");
diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp
index 630c89fe934d0384ec02012be40029eb7bdeaf87..e9f668dafdd4873d5c81f3ecd4275e0d470dd8a6 100644
--- a/src/RIGID/fix_rigid.cpp
+++ b/src/RIGID/fix_rigid.cpp
@@ -58,15 +58,15 @@ enum{ISO,ANISO,TRICLINIC};
/* ---------------------------------------------------------------------- */
FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
- Fix(lmp, narg, arg), step_respa(NULL),
- infile(NULL), nrigid(NULL), mol2body(NULL), body2mol(NULL),
- body(NULL), displace(NULL), masstotal(NULL), xcm(NULL),
- vcm(NULL), fcm(NULL), inertia(NULL), ex_space(NULL),
- ey_space(NULL), ez_space(NULL), angmom(NULL), omega(NULL),
- torque(NULL), quat(NULL), imagebody(NULL), fflag(NULL),
- tflag(NULL), langextra(NULL), sum(NULL), all(NULL),
- remapflag(NULL), xcmimage(NULL), eflags(NULL), orient(NULL),
- dorient(NULL), id_dilate(NULL), random(NULL), avec_ellipsoid(NULL),
+ Fix(lmp, narg, arg), step_respa(NULL),
+ infile(NULL), nrigid(NULL), mol2body(NULL), body2mol(NULL),
+ body(NULL), displace(NULL), masstotal(NULL), xcm(NULL),
+ vcm(NULL), fcm(NULL), inertia(NULL), ex_space(NULL),
+ ey_space(NULL), ez_space(NULL), angmom(NULL), omega(NULL),
+ torque(NULL), quat(NULL), imagebody(NULL), fflag(NULL),
+ tflag(NULL), langextra(NULL), sum(NULL), all(NULL),
+ remapflag(NULL), xcmimage(NULL), eflags(NULL), orient(NULL),
+ dorient(NULL), id_dilate(NULL), random(NULL), avec_ellipsoid(NULL),
avec_line(NULL), avec_tri(NULL)
{
int i,ibody;
@@ -966,7 +966,7 @@ void FixRigid::post_force(int vflag)
langextra[i][0] = gamma1*vcm[i][0] + gamma2*(random->uniform()-0.5);
langextra[i][1] = gamma1*vcm[i][1] + gamma2*(random->uniform()-0.5);
langextra[i][2] = gamma1*vcm[i][2] + gamma2*(random->uniform()-0.5);
-
+
gamma1 = -1.0 / t_period / ftm2v;
gamma2 = tsqrt * sqrt(24.0*boltz/t_period/dt/mvv2e) / ftm2v;
langextra[i][3] = inertia[i][0]*gamma1*omega[i][0] +
diff --git a/src/RIGID/fix_rigid_nh.cpp b/src/RIGID/fix_rigid_nh.cpp
index e67f3761353f0f3ae197d407dddc2c33890509c1..c6c926668868ff0f0b82a9dfee361da189df80a8 100644
--- a/src/RIGID/fix_rigid_nh.cpp
+++ b/src/RIGID/fix_rigid_nh.cpp
@@ -47,11 +47,11 @@ enum{ISO,ANISO,TRICLINIC}; // same as in FixRigid
/* ---------------------------------------------------------------------- */
FixRigidNH::FixRigidNH(LAMMPS *lmp, int narg, char **arg) :
- FixRigid(lmp, narg, arg), conjqm(NULL), w(NULL),
- wdti1(NULL), wdti2(NULL), wdti4(NULL), q_t(NULL), q_r(NULL),
- eta_t(NULL), eta_r(NULL), eta_dot_t(NULL), eta_dot_r(NULL),
- f_eta_t(NULL), f_eta_r(NULL), q_b(NULL), eta_b(NULL),
- eta_dot_b(NULL), f_eta_b(NULL), rfix(NULL), id_temp(NULL),
+ FixRigid(lmp, narg, arg), conjqm(NULL), w(NULL),
+ wdti1(NULL), wdti2(NULL), wdti4(NULL), q_t(NULL), q_r(NULL),
+ eta_t(NULL), eta_r(NULL), eta_dot_t(NULL), eta_dot_r(NULL),
+ f_eta_t(NULL), f_eta_r(NULL), q_b(NULL), eta_b(NULL),
+ eta_dot_b(NULL), f_eta_b(NULL), rfix(NULL), id_temp(NULL),
id_press(NULL), temperature(NULL), pressure(NULL)
{
// error checks: could be moved up to FixRigid
diff --git a/src/RIGID/fix_rigid_nh_small.cpp b/src/RIGID/fix_rigid_nh_small.cpp
index 199c04bd9c483938c2d90463f5ee0737dce7f64f..71f7075339c8050f8955af48a38d340b4723124a 100644
--- a/src/RIGID/fix_rigid_nh_small.cpp
+++ b/src/RIGID/fix_rigid_nh_small.cpp
@@ -50,11 +50,11 @@ enum{FULL_BODY,INITIAL,FINAL,FORCE_TORQUE,VCM_ANGMOM,XCM_MASS,ITENSOR,DOF};
/* ---------------------------------------------------------------------- */
FixRigidNHSmall::FixRigidNHSmall(LAMMPS *lmp, int narg, char **arg) :
- FixRigidSmall(lmp, narg, arg), w(NULL), wdti1(NULL),
- wdti2(NULL), wdti4(NULL), q_t(NULL), q_r(NULL), eta_t(NULL),
- eta_r(NULL), eta_dot_t(NULL), eta_dot_r(NULL), f_eta_t(NULL),
- f_eta_r(NULL), q_b(NULL), eta_b(NULL), eta_dot_b(NULL),
- f_eta_b(NULL), rfix(NULL), id_temp(NULL), id_press(NULL),
+ FixRigidSmall(lmp, narg, arg), w(NULL), wdti1(NULL),
+ wdti2(NULL), wdti4(NULL), q_t(NULL), q_r(NULL), eta_t(NULL),
+ eta_r(NULL), eta_dot_t(NULL), eta_dot_r(NULL), f_eta_t(NULL),
+ f_eta_r(NULL), q_b(NULL), eta_b(NULL), eta_dot_b(NULL),
+ f_eta_b(NULL), rfix(NULL), id_temp(NULL), id_press(NULL),
temperature(NULL), pressure(NULL)
{
// error checks
@@ -322,7 +322,7 @@ void FixRigidNHSmall::setup(int vflag)
{
FixRigidSmall::setup(vflag);
compute_dof();
-
+
double mbody[3];
akin_t = akin_r = 0.0;
for (int ibody = 0; ibody < nlocal_body; ibody++) {
diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp
index 6eb2a2cc23cf7ac8e6dddd40a4e4bb24cbe2e2bd..0cdec74fe86d3af2a675fd759badf913d2f95f3f 100644
--- a/src/RIGID/fix_rigid_small.cpp
+++ b/src/RIGID/fix_rigid_small.cpp
@@ -65,7 +65,7 @@ enum{FULL_BODY,INITIAL,FINAL,FORCE_TORQUE,VCM_ANGMOM,XCM_MASS,ITENSOR,DOF};
/* ---------------------------------------------------------------------- */
FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
- Fix(lmp, narg, arg), step_respa(NULL),
+ Fix(lmp, narg, arg), step_respa(NULL),
infile(NULL), body(NULL), bodyown(NULL), bodytag(NULL), atom2body(NULL),
xcmimage(NULL), displace(NULL), eflags(NULL), orient(NULL), dorient(NULL),
avec_ellipsoid(NULL), avec_line(NULL), avec_tri(NULL), counts(NULL),
@@ -138,7 +138,7 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
MPI_Allreduce(&vmin,&minval,1,MPI_INT,MPI_MIN,world);
for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit)
+ if (mask[i] & groupbit)
bodyid[i] = (tagint)(value[i] - minval + 1);
else bodyid[i] = 0;
@@ -801,14 +801,14 @@ void FixRigidSmall::post_force(int vflag)
vcm = body[ibody].vcm;
omega = body[ibody].omega;
inertia = body[ibody].inertia;
-
+
gamma1 = -body[ibody].mass / t_period / ftm2v;
gamma2 = sqrt(body[ibody].mass) * tsqrt *
sqrt(24.0*boltz/t_period/dt/mvv2e) / ftm2v;
langextra[ibody][0] = gamma1*vcm[0] + gamma2*(random->uniform()-0.5);
langextra[ibody][1] = gamma1*vcm[1] + gamma2*(random->uniform()-0.5);
langextra[ibody][2] = gamma1*vcm[2] + gamma2*(random->uniform()-0.5);
-
+
gamma1 = -1.0 / t_period / ftm2v;
gamma2 = tsqrt * sqrt(24.0*boltz/t_period/dt/mvv2e) / ftm2v;
langextra[ibody][3] = inertia[0]*gamma1*omega[0] +
diff --git a/src/RIGID/fix_shake.cpp b/src/RIGID/fix_shake.cpp
index c624fe2fe8d981a41dfeeaece2a3f118f2f2982f..35c8d7a91741432f04dd22ea46f3fa6939bd31c4 100644
--- a/src/RIGID/fix_shake.cpp
+++ b/src/RIGID/fix_shake.cpp
@@ -45,15 +45,15 @@ using namespace MathConst;
/* ---------------------------------------------------------------------- */
FixShake::FixShake(LAMMPS *lmp, int narg, char **arg) :
- Fix(lmp, narg, arg), bond_flag(NULL), angle_flag(NULL),
- type_flag(NULL), mass_list(NULL), bond_distance(NULL), angle_distance(NULL),
- loop_respa(NULL), step_respa(NULL), x(NULL), v(NULL), f(NULL), ftmp(NULL),
- vtmp(NULL), mass(NULL), rmass(NULL), type(NULL), shake_flag(NULL),
- shake_atom(NULL), shake_type(NULL), xshake(NULL), nshake(NULL),
- list(NULL), b_count(NULL), b_count_all(NULL), b_ave(NULL), b_max(NULL),
- b_min(NULL), b_ave_all(NULL), b_max_all(NULL), b_min_all(NULL),
- a_count(NULL), a_count_all(NULL), a_ave(NULL), a_max(NULL), a_min(NULL),
- a_ave_all(NULL), a_max_all(NULL), a_min_all(NULL), atommols(NULL),
+ Fix(lmp, narg, arg), bond_flag(NULL), angle_flag(NULL),
+ type_flag(NULL), mass_list(NULL), bond_distance(NULL), angle_distance(NULL),
+ loop_respa(NULL), step_respa(NULL), x(NULL), v(NULL), f(NULL), ftmp(NULL),
+ vtmp(NULL), mass(NULL), rmass(NULL), type(NULL), shake_flag(NULL),
+ shake_atom(NULL), shake_type(NULL), xshake(NULL), nshake(NULL),
+ list(NULL), b_count(NULL), b_count_all(NULL), b_ave(NULL), b_max(NULL),
+ b_min(NULL), b_ave_all(NULL), b_max_all(NULL), b_min_all(NULL),
+ a_count(NULL), a_count_all(NULL), a_ave(NULL), a_max(NULL), a_min(NULL),
+ a_ave_all(NULL), a_max_all(NULL), a_min_all(NULL), atommols(NULL),
onemols(NULL)
{
MPI_Comm_rank(world,&me);
@@ -78,7 +78,7 @@ FixShake::FixShake(LAMMPS *lmp, int narg, char **arg) :
shake_type = NULL;
xshake = NULL;
- ftmp = NULL;
+ ftmp = NULL;
vtmp = NULL;
grow_arrays(atom->nmax);
@@ -447,7 +447,7 @@ void FixShake::setup(int vflag)
// set respa to 0 if verlet is used and to 1 otherwise
- if (strstr(update->integrate_style,"verlet"))
+ if (strstr(update->integrate_style,"verlet"))
respa = 0;
else
respa = 1;
@@ -515,7 +515,7 @@ void FixShake::pre_neighbor()
atom2 = atom->map(shake_atom[i][1]);
if (atom1 == -1 || atom2 == -1) {
char str[128];
- sprintf(str,"Shake atoms " TAGINT_FORMAT " " TAGINT_FORMAT
+ sprintf(str,"Shake atoms " TAGINT_FORMAT " " TAGINT_FORMAT
" missing on proc %d at step " BIGINT_FORMAT,
shake_atom[i][0],shake_atom[i][1],me,update->ntimestep);
error->one(FLERR,str);
@@ -527,7 +527,7 @@ void FixShake::pre_neighbor()
atom3 = atom->map(shake_atom[i][2]);
if (atom1 == -1 || atom2 == -1 || atom3 == -1) {
char str[128];
- sprintf(str,"Shake atoms "
+ sprintf(str,"Shake atoms "
TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT
" missing on proc %d at step " BIGINT_FORMAT,
shake_atom[i][0],shake_atom[i][1],shake_atom[i][2],
@@ -542,8 +542,8 @@ void FixShake::pre_neighbor()
atom4 = atom->map(shake_atom[i][3]);
if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
char str[128];
- sprintf(str,"Shake atoms "
- TAGINT_FORMAT " " TAGINT_FORMAT " "
+ sprintf(str,"Shake atoms "
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT
" missing on proc %d at step " BIGINT_FORMAT,
shake_atom[i][0],shake_atom[i][1],
@@ -586,7 +586,7 @@ void FixShake::post_force(int vflag)
else if (shake_flag[m] == 4) shake4(m);
else shake3angle(m);
}
-
+
// store vflag for coordinate_constraints_end_of_step()
vflag_post_force = vflag;
@@ -685,7 +685,7 @@ void FixShake::find_clusters()
tagint tagprev;
double massone;
tagint *buf;
-
+
if (me == 0 && screen) {
if (!rattle) fprintf(screen,"Finding SHAKE clusters ...\n");
else fprintf(screen,"Finding RATTLE clusters ...\n");
@@ -700,7 +700,7 @@ void FixShake::find_clusters()
double *rmass = atom->rmass;
int **nspecial = atom->nspecial;
tagint **special = atom->special;
-
+
int *molindex = atom->molindex;
int *molatom = atom->molatom;
@@ -969,7 +969,7 @@ void FixShake::find_clusters()
comm->ring(size,sizeof(tagint),buf,2,ring_nshake,buf,(void *)this);
// store partner info returned to me
-
+
m = 0;
while (m < size) {
i = atom->map(buf[m]);
@@ -2333,7 +2333,7 @@ int FixShake::bondtype_findset(int i, tagint n1, tagint n2, int setflag)
tagint *batom = atommols[imol]->bond_atom[iatom];
btype = atommols[imol]->bond_type[iatom];
nbonds = atommols[imol]->num_bond[iatom];
-
+
for (m = 0; m < nbonds; m++) {
if (n1 == tag[i] && n2 == batom[m]+tagprev) break;
if (n1 == batom[m]+tagprev && n2 == tag[i]) break;
@@ -2390,7 +2390,7 @@ int FixShake::angletype_findset(int i, tagint n1, tagint n2, int setflag)
tagint *aatom3 = atommols[imol]->angle_atom3[iatom];
atype = atommols[imol]->angle_type[iatom];
nangles = atommols[imol]->num_angle[iatom];
-
+
for (m = 0; m < nangles; m++) {
if (n1 == aatom1[m]+tagprev && n2 == aatom3[m]+tagprev) break;
if (n1 == aatom3[m]+tagprev && n2 == aatom1[m]+tagprev) break;
@@ -2504,7 +2504,7 @@ void FixShake::update_arrays(int i, int atom_offset)
shake_atom[i][0] += atom_offset;
shake_atom[i][1] += atom_offset;
shake_atom[i][2] += atom_offset;
- } else if (flag == 2) {
+ } else if (flag == 2) {
shake_atom[i][0] += atom_offset;
shake_atom[i][1] += atom_offset;
} else if (flag == 3) {
@@ -2650,7 +2650,7 @@ int FixShake::unpack_exchange(int nlocal, double *buf)
/* ---------------------------------------------------------------------- */
-int FixShake::pack_forward_comm(int n, int *list, double *buf,
+int FixShake::pack_forward_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
@@ -2766,10 +2766,10 @@ void FixShake::correct_velocities() {}
change coordinates
------------------------------------------------------------------------- */
-void FixShake::correct_coordinates(int vflag) {
-
- // save current forces and velocities so that you
- // initialise them to zero such that FixShake::unconstrained_coordinate_update has no effect
+void FixShake::correct_coordinates(int vflag) {
+
+ // save current forces and velocities so that you
+ // initialise them to zero such that FixShake::unconstrained_coordinate_update has no effect
for (int j=0; j<nlocal; j++) {
for (int k=0; k<3; k++) {
@@ -2793,24 +2793,24 @@ void FixShake::correct_coordinates(int vflag) {
FixShake::post_force(vflag);
// integrate coordiantes: x' = xnp1 + dt^2/2m_i * f, where f is the constraining force
- // NOTE: After this command, the coordinates geometry of the molecules will be correct!
-
- double dtfmsq;
- if (rmass) {
- for (int i = 0; i < nlocal; i++) {
- dtfmsq = dtfsq/ rmass[i];
- x[i][0] = x[i][0] + dtfmsq*f[i][0];
- x[i][1] = x[i][1] + dtfmsq*f[i][1];
- x[i][2] = x[i][2] + dtfmsq*f[i][2];
- }
- }
- else {
- for (int i = 0; i < nlocal; i++) {
- dtfmsq = dtfsq / mass[type[i]];
- x[i][0] = x[i][0] + dtfmsq*f[i][0];
- x[i][1] = x[i][1] + dtfmsq*f[i][1];
- x[i][2] = x[i][2] + dtfmsq*f[i][2];
- }
+ // NOTE: After this command, the coordinates geometry of the molecules will be correct!
+
+ double dtfmsq;
+ if (rmass) {
+ for (int i = 0; i < nlocal; i++) {
+ dtfmsq = dtfsq/ rmass[i];
+ x[i][0] = x[i][0] + dtfmsq*f[i][0];
+ x[i][1] = x[i][1] + dtfmsq*f[i][1];
+ x[i][2] = x[i][2] + dtfmsq*f[i][2];
+ }
+ }
+ else {
+ for (int i = 0; i < nlocal; i++) {
+ dtfmsq = dtfsq / mass[type[i]];
+ x[i][0] = x[i][0] + dtfmsq*f[i][0];
+ x[i][1] = x[i][1] + dtfmsq*f[i][1];
+ x[i][2] = x[i][2] + dtfmsq*f[i][2];
+ }
}
// copy forces and velocities back
@@ -2825,8 +2825,8 @@ void FixShake::correct_coordinates(int vflag) {
if (!rattle) dtfsq = update->dt * update->dt * force->ftm2v;
// communicate changes
- // NOTE: for compatibility xshake is temporarily set to x, such that pack/unpack_forward
- // can be used for communicating the coordinates.
+ // NOTE: for compatibility xshake is temporarily set to x, such that pack/unpack_forward
+ // can be used for communicating the coordinates.
double **xtmp = xshake;
xshake = x;
diff --git a/src/SHOCK/fix_append_atoms.cpp b/src/SHOCK/fix_append_atoms.cpp
index 13aca77ca314d6b8bd41a510848420eb709f998e..80be74bee1634a0665c0a08fffde6b1197cd885e 100644
--- a/src/SHOCK/fix_append_atoms.cpp
+++ b/src/SHOCK/fix_append_atoms.cpp
@@ -37,7 +37,7 @@ enum{LAYOUT_UNIFORM,LAYOUT_NONUNIFORM,LAYOUT_TILED}; // several files
/* ---------------------------------------------------------------------- */
FixAppendAtoms::FixAppendAtoms(LAMMPS *lmp, int narg, char **arg) :
- Fix(lmp, narg, arg), randomx(NULL), randomt(NULL), basistype(NULL),
+ Fix(lmp, narg, arg), randomx(NULL), randomt(NULL), basistype(NULL),
spatialid(NULL), gfactor1(NULL), gfactor2(NULL)
{
force_reneighbor = 1;
diff --git a/src/SNAP/compute_sna_atom.cpp b/src/SNAP/compute_sna_atom.cpp
index 75b08f08bf3fd605c021abbaf9fe659d1d4d3eb8..4b114d9ce777714ee305311398421979b99f69b7 100644
--- a/src/SNAP/compute_sna_atom.cpp
+++ b/src/SNAP/compute_sna_atom.cpp
@@ -30,7 +30,7 @@
using namespace LAMMPS_NS;
ComputeSNAAtom::ComputeSNAAtom(LAMMPS *lmp, int narg, char **arg) :
- Compute(lmp, narg, arg), cutsq(NULL), list(NULL), sna(NULL),
+ Compute(lmp, narg, arg), cutsq(NULL), list(NULL), sna(NULL),
radelem(NULL), wjelem(NULL)
{
double rmin0, rfac0;
@@ -277,7 +277,7 @@ void ComputeSNAAtom::compute_peratom()
double bi = snaptr[tid]->bvec[icoeff];
// upper-triangular elements of quadratic matrix
-
+
for (int jcoeff = icoeff; jcoeff < ncoeff; jcoeff++)
sna[i][ncount++] = bi*snaptr[tid]->bvec[jcoeff];
}
diff --git a/src/SNAP/compute_snad_atom.cpp b/src/SNAP/compute_snad_atom.cpp
index 0f522edf82af2db32535b68e6c88d160f7905466..54a6ce761248c3ee6fcb2c4ab14fce16e5520e00 100644
--- a/src/SNAP/compute_snad_atom.cpp
+++ b/src/SNAP/compute_snad_atom.cpp
@@ -30,7 +30,7 @@
using namespace LAMMPS_NS;
ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) :
- Compute(lmp, narg, arg), cutsq(NULL), list(NULL), snad(NULL),
+ Compute(lmp, narg, arg), cutsq(NULL), list(NULL), snad(NULL),
radelem(NULL), wjelem(NULL)
{
double rfac0, rmin0;
@@ -50,9 +50,9 @@ ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) :
switchflag = 1;
bzeroflag = 1;
quadraticflag = 0;
-
+
// process required arguments
-
+
memory->create(radelem,ntypes+1,"sna/atom:radelem"); // offset by 1 to match up with types
memory->create(wjelem,ntypes+1,"sna/atom:wjelem");
rcutfac = atof(arg[3]);
@@ -288,7 +288,7 @@ void ComputeSNADAtom::compute_peratom()
snaptr[tid]->compute_bi();
snaptr[tid]->copy_bi2bvec();
}
-
+
for (int jj = 0; jj < ninside; jj++) {
const int j = snaptr[tid]->inside[jj];
snaptr[tid]->compute_duidrj(snaptr[tid]->rij[jj],
@@ -322,7 +322,7 @@ void ComputeSNADAtom::compute_peratom()
double biz = snaptr[tid]->dbvec[icoeff][2];
// upper-triangular elements of quadratic matrix
-
+
for (int jcoeff = icoeff; jcoeff < ncoeff; jcoeff++) {
double dbxtmp = bi*snaptr[tid]->dbvec[jcoeff][0]
+ bix*snaptr[tid]->bvec[jcoeff];
diff --git a/src/SNAP/compute_snav_atom.cpp b/src/SNAP/compute_snav_atom.cpp
index f284ddab0be06e174535c9efc2ecac242cb17b13..0278be5a97414f8dd9fb9ba681edd33255ecfbed 100644
--- a/src/SNAP/compute_snav_atom.cpp
+++ b/src/SNAP/compute_snav_atom.cpp
@@ -52,7 +52,7 @@ ComputeSNAVAtom::ComputeSNAVAtom(LAMMPS *lmp, int narg, char **arg) :
quadraticflag = 0;
// process required arguments
-
+
memory->create(radelem,ntypes+1,"sna/atom:radelem"); // offset by 1 to match up with types
memory->create(wjelem,ntypes+1,"sna/atom:wjelem");
rcutfac = atof(arg[3]);
@@ -332,7 +332,7 @@ void ComputeSNAVAtom::compute_peratom()
double biz = snaptr[tid]->dbvec[icoeff][2];
// upper-triangular elements of quadratic matrix
-
+
for (int jcoeff = icoeff; jcoeff < ncoeff; jcoeff++) {
double dbxtmp = bi*snaptr[tid]->dbvec[jcoeff][0]
+ bix*snaptr[tid]->bvec[jcoeff];
diff --git a/src/SNAP/pair_snap.cpp b/src/SNAP/pair_snap.cpp
index 3de5d0c6c807b35639b0cf7375cbe58e0a42ef4e..377235685cd0f052d2f51ab01967a63f6679707c 100644
--- a/src/SNAP/pair_snap.cpp
+++ b/src/SNAP/pair_snap.cpp
@@ -262,7 +262,7 @@ void PairSNAP::compute_regular(int eflag, int vflag)
fij[2] = 0.0;
// linear contributions
-
+
for (int k = 1; k <= ncoeff; k++) {
double bgb = coeffi[k];
fij[0] += bgb*snaptr->dbvec[k-1][0];
@@ -271,7 +271,7 @@ void PairSNAP::compute_regular(int eflag, int vflag)
}
// quadratic contributions
-
+
if (quadraticflag) {
int k = ncoeff+1;
for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
@@ -302,7 +302,7 @@ void PairSNAP::compute_regular(int eflag, int vflag)
f[j][2] -= fij[2];
// tally per-atom virial contribution
-
+
if (vflag)
ev_tally_xyz(i,j,nlocal,newton_pair,0.0,0.0,
fij[0],fij[1],fij[2],
@@ -321,7 +321,7 @@ void PairSNAP::compute_regular(int eflag, int vflag)
snaptr->compute_bi();
snaptr->copy_bi2bvec();
}
-
+
// E = beta.B + 0.5*B^t.alpha.B
// coeff[k] = beta[k-1] or
// coeff[k] = alpha_ii or
@@ -632,7 +632,7 @@ void PairSNAP::compute_optimized(int eflag, int vflag)
}
// quadratic contributions
-
+
if (quadraticflag) {
int k = ncoeff+1;
for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
@@ -694,12 +694,12 @@ void PairSNAP::compute_optimized(int eflag, int vflag)
// coeff[k] = alpha_ij = alpha_ji, j != i
// linear contributions
-
+
for (int k = 1; k <= ncoeff; k++)
evdwl += coeffi[k]*sna[tid]->bvec[k-1];
// quadratic contributions
-
+
if (quadraticflag) {
int k = ncoeff+1;
for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
@@ -710,7 +710,7 @@ void PairSNAP::compute_optimized(int eflag, int vflag)
}
}
}
-
+
#if defined(_OPENMP)
#pragma omp critical
#endif
@@ -1465,8 +1465,8 @@ void PairSNAP::coeff(int narg, char **arg)
// ncoeffall should be (ncoeff+2)*(ncoeff+1)/2
// so, ncoeff = floor(sqrt(2*ncoeffall))-1
-
- ncoeff = sqrt(2*ncoeffall)-1;
+
+ ncoeff = sqrt(2*ncoeffall)-1;
ncoeffq = (ncoeff*(ncoeff+1))/2;
int ntmp = 1+ncoeff+ncoeffq;
if (ntmp != ncoeffall) {
@@ -1632,7 +1632,7 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
int nelemfile = atoi(words[0]);
ncoeffall = atoi(words[1]);
-
+
// Set up element lists
memory->create(radelem,nelements,"pair:radelem");
@@ -1748,7 +1748,7 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
switchflag = 1;
bzeroflag = 1;
quadraticflag = 0;
-
+
// open SNAP parameter file on proc 0
FILE *fpparam;
diff --git a/src/SNAP/sna.cpp b/src/SNAP/sna.cpp
index 21470876d4a6ff363f7b04f71dd4f083fb453c17..16c382cc4ce34949e463d4b1bb8fae52512290ee 100644
--- a/src/SNAP/sna.cpp
+++ b/src/SNAP/sna.cpp
@@ -118,7 +118,7 @@ SNA::SNA(LAMMPS* lmp, double rfac0_in,
double rmin0_in, int switch_flag_in, int bzero_flag_in) : Pointers(lmp)
{
wself = 1.0;
-
+
use_shared_arrays = use_shared_arrays_in;
rfac0 = rfac0_in;
rmin0 = rmin0_in;
@@ -148,7 +148,7 @@ SNA::SNA(LAMMPS* lmp, double rfac0_in,
for(int j = 0; j <= twojmax; j++)
bzero[j] = www*(j+1);
}
-
+
#ifdef TIMING_INFO
timers = new double[20];
for(int i = 0; i < 20; i++) timers[i] = 0;
@@ -158,7 +158,7 @@ SNA::SNA(LAMMPS* lmp, double rfac0_in,
build_indexlist();
-
+
}
/* ---------------------------------------------------------------------- */
@@ -1524,7 +1524,7 @@ void SNA::create_twojmax_arrays()
memory->create(bzero, jdim,"sna:bzero");
else
bzero = NULL;
-
+
if(!use_shared_arrays) {
memory->create(uarraytot_r, jdim, jdim, jdim,
diff --git a/src/SRD/fix_srd.cpp b/src/SRD/fix_srd.cpp
index c1c83ce59a7dd0f3ba9eef7a4fd9e7e8d96b2714..81ef2024203c0b858500466ecaab0500e828c955 100644
--- a/src/SRD/fix_srd.cpp
+++ b/src/SRD/fix_srd.cpp
@@ -80,11 +80,11 @@ static const char cite_fix_srd[] =
/* ---------------------------------------------------------------------- */
FixSRD::FixSRD(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
- wallfix(NULL), wallwhich(NULL), xwall(NULL), xwallhold(NULL),
- vwall(NULL), fwall(NULL), avec_ellipsoid(NULL), avec_line(NULL),
- avec_tri(NULL), random(NULL), randomshift(NULL), flocal(NULL),
- tlocal(NULL), biglist(NULL), binhead(NULL), binnext(NULL), sbuf1(NULL),
- sbuf2(NULL), rbuf1(NULL), rbuf2(NULL), nbinbig(NULL), binbig(NULL),
+ wallfix(NULL), wallwhich(NULL), xwall(NULL), xwallhold(NULL),
+ vwall(NULL), fwall(NULL), avec_ellipsoid(NULL), avec_line(NULL),
+ avec_tri(NULL), random(NULL), randomshift(NULL), flocal(NULL),
+ tlocal(NULL), biglist(NULL), binhead(NULL), binnext(NULL), sbuf1(NULL),
+ sbuf2(NULL), rbuf1(NULL), rbuf2(NULL), nbinbig(NULL), binbig(NULL),
binsrd(NULL), stencil(NULL)
{
if (lmp->citeme) lmp->citeme->add(cite_fix_srd);
diff --git a/src/USER-CGDNA/bond_oxdna2_fene.cpp b/src/USER-CGDNA/bond_oxdna2_fene.cpp
index 5faff07c06522bfe88cf2f29ca493ee814cdd817..b2e1afb073d5af6a71a61428a2b64249d4af3166 100644
--- a/src/USER-CGDNA/bond_oxdna2_fene.cpp
+++ b/src/USER-CGDNA/bond_oxdna2_fene.cpp
@@ -42,8 +42,8 @@ void BondOxdna2Fene::compute_interaction_sites(double e1[3],
{
double d_cs_x=-0.34, d_cs_y=+0.3408;
- r[0] = d_cs_x*e1[0] + d_cs_y*e2[0];
- r[1] = d_cs_x*e1[1] + d_cs_y*e2[1];
- r[2] = d_cs_x*e1[2] + d_cs_y*e2[2];
+ r[0] = d_cs_x*e1[0] + d_cs_y*e2[0];
+ r[1] = d_cs_x*e1[1] + d_cs_y*e2[1];
+ r[2] = d_cs_x*e1[2] + d_cs_y*e2[2];
}
diff --git a/src/USER-CGDNA/bond_oxdna_fene.cpp b/src/USER-CGDNA/bond_oxdna_fene.cpp
index dcb171d545fa43439593fb2047de11bc2a242a19..e5d3a3e45242d29b21ba2c5683082d82f0e98f08 100644
--- a/src/USER-CGDNA/bond_oxdna_fene.cpp
+++ b/src/USER-CGDNA/bond_oxdna_fene.cpp
@@ -60,9 +60,9 @@ void BondOxdnaFene::compute_interaction_sites(double e1[3],
{
double d_cs=-0.4;
- r[0] = d_cs*e1[0];
- r[1] = d_cs*e1[1];
- r[2] = d_cs*e1[2];
+ r[0] = d_cs*e1[0];
+ r[1] = d_cs*e1[1];
+ r[2] = d_cs*e1[2];
}
diff --git a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp
index 9d10fe1614bc78d54cc6a88b88bd96a823cd5f91..8312d92bc06f788c8c87d76bb063fd6ad4ef1e67 100644
--- a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp
+++ b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp
@@ -855,7 +855,7 @@ void PairOxdna2Coaxstk::read_restart(FILE *fp)
fread(&dtheta_cxst1_ast[i][j],sizeof(double),1,fp);
fread(&b_cxst1[i][j],sizeof(double),1,fp);
fread(&dtheta_cxst1_c[i][j],sizeof(double),1,fp);
-
+
fread(&a_cxst4[i][j],sizeof(double),1,fp);
fread(&theta_cxst4_0[i][j],sizeof(double),1,fp);
fread(&dtheta_cxst4_ast[i][j],sizeof(double),1,fp);
diff --git a/src/USER-CGDNA/pair_oxdna2_dh.cpp b/src/USER-CGDNA/pair_oxdna2_dh.cpp
index 73072f4c0eae9fdb61875387129faa52d3a9998f..48914239251e282239e8510a4355b31148e05dae 100644
--- a/src/USER-CGDNA/pair_oxdna2_dh.cpp
+++ b/src/USER-CGDNA/pair_oxdna2_dh.cpp
@@ -168,7 +168,7 @@ void PairOxdna2Dh::compute(int eflag, int vflag)
if (r <= cut_dh_ast[atype][btype]) {
- fpair = qeff_dh_pf[atype][btype] * exp(-kappa_dh[atype][btype] * r) *
+ fpair = qeff_dh_pf[atype][btype] * exp(-kappa_dh[atype][btype] * r) *
(kappa_dh[atype][btype] + rinv) * rinv * rinv;
if (eflag) {
@@ -186,7 +186,7 @@ void PairOxdna2Dh::compute(int eflag, int vflag)
}
- // knock out nearest-neighbour interaction between adjacent backbone sites
+ // knock out nearest-neighbour interaction between adjacent backbone sites
fpair *= factor_lj;
evdwl *= factor_lj;
@@ -298,31 +298,31 @@ void PairOxdna2Dh::coeff(int narg, char **arg)
// Debye length and inverse Debye length
/*
- NOTE:
- The numerical factor is the Debye length in s.u.
- lambda(T = 300 K = 0.1) =
+ NOTE:
+ The numerical factor is the Debye length in s.u.
+ lambda(T = 300 K = 0.1) =
sqrt(eps_0 * eps_r * k_B * T/(2 * N_A * e^2 * 1000 mol/m^3))
* 1/oxDNA_energy_unit
(see B. Snodin et al., J. Chem. Phys. 142, 234901 (2015).)
- We use
+ We use
eps_0 = vacuum permittivity = 8.854187817e-12 F/m
eps_r = relative permittivity of water = 80
k_B = Boltzmann constant = 1.3806485279e-23 J/K
T = absolute temperature = 300 K
N_A = Avogadro constant = 6.02214085774e23 / mol
e = elementary charge = 1.6021766208e-19 C
- oxDNA_length_unit = 8.518e-10 m
+ oxDNA_length_unit = 8.518e-10 m
*/
lambda_dh_one = 0.3616455075438555*sqrt(T/0.1/rhos_dh_one);
kappa_dh_one = 1.0/lambda_dh_one;
-
+
// prefactor in DH interaction containing qeff^2
/*
- NOTE:
- The numerical factor is
+ NOTE:
+ The numerical factor is
qeff_dh_pf = e^2/(4 * pi * eps_0 * eps_r)
* 1/(oxDNA_energy_unit * oxDNA_length_unit)
(see B. Snodin et al., J. Chem. Phys. 142, 234901 (2015).)
@@ -335,14 +335,14 @@ void PairOxdna2Dh::coeff(int narg, char **arg)
// smoothing parameters - determined through continuity and differentiability
- cut_dh_ast_one = 3.0*lambda_dh_one;
+ cut_dh_ast_one = 3.0*lambda_dh_one;
b_dh_one = -(exp(-cut_dh_ast_one/lambda_dh_one) * qeff_dh_pf_one * qeff_dh_pf_one *
(cut_dh_ast_one + lambda_dh_one) * (cut_dh_ast_one + lambda_dh_one))/
- (-4.0 * cut_dh_ast_one * cut_dh_ast_one * cut_dh_ast_one *
+ (-4.0 * cut_dh_ast_one * cut_dh_ast_one * cut_dh_ast_one *
lambda_dh_one * lambda_dh_one * qeff_dh_pf_one);
- cut_dh_c_one = cut_dh_ast_one * (qeff_dh_pf_one*cut_dh_ast_one +
+ cut_dh_c_one = cut_dh_ast_one * (qeff_dh_pf_one*cut_dh_ast_one +
3.0*qeff_dh_pf_one * lambda_dh_one)/
(qeff_dh_pf_one * (cut_dh_ast_one+lambda_dh_one));
@@ -517,7 +517,7 @@ void PairOxdna2Dh::write_data(FILE *fp)
%g %g\
%g %g %g\
\n",i,
- kappa_dh[i][i],qeff_dh_pf[i][i],
+ kappa_dh[i][i],qeff_dh_pf[i][i],
b_dh[i][i],cut_dh_ast[i][i],cut_dh_c[i][i]);
}
@@ -533,7 +533,7 @@ void PairOxdna2Dh::write_data_all(FILE *fp)
%g %g\
%g %g %g\
\n",i,j,
- kappa_dh[i][j],qeff_dh_pf[i][j],
+ kappa_dh[i][j],qeff_dh_pf[i][j],
b_dh[i][j],cut_dh_ast[i][j],cut_dh_c[i][j]);
}
diff --git a/src/USER-CGDNA/pair_oxdna_hbond.cpp b/src/USER-CGDNA/pair_oxdna_hbond.cpp
index 99f490f3fb10f293e9b36f3b11e1cf4a8297c077..1caf320ef1b0105cc336cfa8c2125203bb4c3337 100644
--- a/src/USER-CGDNA/pair_oxdna_hbond.cpp
+++ b/src/USER-CGDNA/pair_oxdna_hbond.cpp
@@ -40,7 +40,7 @@ using namespace MFOxdna;
// sequence-specific base-pairing strength
// A:0 C:1 G:2 T:3, 5'- (i,j) -3'
-static const double alpha[4][4] =
+static const double alpha[4][4] =
{{1.00000,1.00000,1.00000,0.82915},
{1.00000,1.00000,1.15413,1.00000},
{1.00000,1.15413,1.00000,1.00000},
diff --git a/src/USER-DIFFRACTION/fix_saed_vtk.cpp b/src/USER-DIFFRACTION/fix_saed_vtk.cpp
index 064a40ae25ebf3d926b61274747bbf7a7a21e049..dfa63f630ad5537b7700a25b330d9e17af1d1185 100644
--- a/src/USER-DIFFRACTION/fix_saed_vtk.cpp
+++ b/src/USER-DIFFRACTION/fix_saed_vtk.cpp
@@ -44,7 +44,7 @@ enum{FIRST,MULTI};
/* ---------------------------------------------------------------------- */
FixSAEDVTK::FixSAEDVTK(LAMMPS *lmp, int narg, char **arg) :
- Fix(lmp, narg, arg), ids(NULL), fp(NULL), vector(NULL),
+ Fix(lmp, narg, arg), ids(NULL), fp(NULL), vector(NULL),
vector_total(NULL), vector_list(NULL), compute_saed(NULL), filename(NULL)
{
if (narg < 7) error->all(FLERR,"Illegal fix saed/vtk command");
diff --git a/src/USER-DRUDE/fix_langevin_drude.cpp b/src/USER-DRUDE/fix_langevin_drude.cpp
index 319516aa7db0603898db6d41a0627e0b3345bf50..d04adb022327de0e3822f47b246e37c73d870513 100644
--- a/src/USER-DRUDE/fix_langevin_drude.cpp
+++ b/src/USER-DRUDE/fix_langevin_drude.cpp
@@ -46,7 +46,7 @@ FixLangevinDrude::FixLangevinDrude(LAMMPS *lmp, int narg, char **arg) :
nevery = 1;
global_freq = nevery;
comm_reverse = 3;
-
+
// core temperature
tstr_core = NULL;
if (strstr(arg[3],"v_") == arg[3]) {
diff --git a/src/USER-INTEL/dihedral_fourier_intel.cpp b/src/USER-INTEL/dihedral_fourier_intel.cpp
index 17a33b6f658a6d606872e5b9fc20b46b3d39b2c2..c46617bbc253ac9ac2bf3290d5a047ff456c0b95 100644
--- a/src/USER-INTEL/dihedral_fourier_intel.cpp
+++ b/src/USER-INTEL/dihedral_fourier_intel.cpp
@@ -236,7 +236,7 @@ void DihedralFourierIntel::eval(const int vflag,
flt_t deng;
flt_t df = (flt_t)0.0;
if (EFLAG) deng = (flt_t)0.0;
-
+
for (int j = 0; j < nterms[type]; j++) {
const flt_t tcos_shift = fc.bp[j][type].cos_shift;
const flt_t tsin_shift = fc.bp[j][type].sin_shift;
@@ -257,7 +257,7 @@ void DihedralFourierIntel::eval(const int vflag,
df1 = df1*tcos_shift - ddf1*tsin_shift;
df1 *= -m;
p += (flt_t)1.0;
-
+
if (m == 0) {
p = (flt_t)1.0 + tcos_shift;
df1 = (flt_t)0.0;
diff --git a/src/USER-INTEL/intel_buffers.cpp b/src/USER-INTEL/intel_buffers.cpp
index 1ef078821e704042d0c0af4d1a075a1dc4db17aa..8948abe1725ebe2547301591748523f021d81c5f 100644
--- a/src/USER-INTEL/intel_buffers.cpp
+++ b/src/USER-INTEL/intel_buffers.cpp
@@ -569,7 +569,7 @@ void IntelBuffers<flt_t, acc_t>::fdotr_reduce(const int nall,
/* ---------------------------------------------------------------------- */
template <class flt_t, class acc_t>
-void IntelBuffers<flt_t, acc_t>::set_ntypes(const int ntypes,
+void IntelBuffers<flt_t, acc_t>::set_ntypes(const int ntypes,
const int use_ghost_cut)
{
if (ntypes != _ntypes) {
@@ -593,7 +593,7 @@ void IntelBuffers<flt_t, acc_t>::set_ntypes(const int ntypes,
if (ntypes > 0) {
lmp->memory->create(_cutneighsq, ntypes, ntypes, "_cutneighsq");
if (use_ghost_cut)
- lmp->memory->create(_cutneighghostsq, ntypes, ntypes,
+ lmp->memory->create(_cutneighghostsq, ntypes, ntypes,
"_cutneighghostsq");
#ifdef _LMP_INTEL_OFFLOAD
flt_t * cutneighsqo = _cutneighsq[0];
diff --git a/src/USER-INTEL/npair_full_bin_ghost_intel.cpp b/src/USER-INTEL/npair_full_bin_ghost_intel.cpp
index 574855e4682c323c36a277033ee9bba5c8b6125e..24d5076c34192a45e538c0435c8693e102a9f4f5 100644
--- a/src/USER-INTEL/npair_full_bin_ghost_intel.cpp
+++ b/src/USER-INTEL/npair_full_bin_ghost_intel.cpp
@@ -67,8 +67,8 @@ void NPairFullBinGhostIntel::build(NeighList *list)
/* ---------------------------------------------------------------------- */
template<class flt_t, class acc_t>
-void NPairFullBinGhostIntel::fbi(NeighList * list,
- IntelBuffers<flt_t,acc_t> * buffers)
+void NPairFullBinGhostIntel::fbi(NeighList * list,
+ IntelBuffers<flt_t,acc_t> * buffers)
{
const int nlocal = atom->nlocal;
const int nall = atom->nlocal + atom->nghost;
@@ -106,7 +106,7 @@ void NPairFullBinGhostIntel::fbi(NeighList * list,
/* ---------------------------------------------------------------------- */
template<class flt_t, class acc_t, int need_ic>
-void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list,
+void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list,
IntelBuffers<flt_t,acc_t> * buffers,
const int pstart, const int pend) {
if (pend-pstart == 0) return;
@@ -146,7 +146,7 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list,
const int nstencil = this->nstencil;
const int * _noalias const stencil = this->stencil;
const flt_t * _noalias const cutneighsq = buffers->get_cutneighsq()[0];
- const flt_t * _noalias const cutneighghostsq =
+ const flt_t * _noalias const cutneighghostsq =
buffers->get_cutneighghostsq()[0];
const int ntypes = atom->ntypes + 1;
const int nlocal = atom->nlocal;
@@ -162,8 +162,8 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list,
int moltemplate;
if (molecular == 2) moltemplate = 1;
else moltemplate = 0;
- if (moltemplate)
- error->all(FLERR,
+ if (moltemplate)
+ error->all(FLERR,
"Can't use moltemplate with npair style full/bin/ghost/intel.");
int tnum;
@@ -511,7 +511,7 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list,
if (molecular) {
int ito_m = ito;
- if (ito >= nlocal) ito_m = nlocal;
+ if (ito >= nlocal) ito_m = nlocal;
for (int i = ifrom; i < ito_m; ++i) {
int * _noalias jlist = firstneigh + cnumneigh[i];
const int jnum = numneigh[i];
diff --git a/src/USER-INTEL/pair_airebo_intel.cpp b/src/USER-INTEL/pair_airebo_intel.cpp
index 0499d2ad629746d9a8413281ea92c452e968e22e..43e0bb7eedc9e64888d3e3ebbd5d4ecfab5ccc68 100644
--- a/src/USER-INTEL/pair_airebo_intel.cpp
+++ b/src/USER-INTEL/pair_airebo_intel.cpp
@@ -264,11 +264,11 @@ PairAIREBOIntelParam<flt_t,acc_t> PairAIREBOIntel::get_param()
#undef B
for (int i = 0; i < 5; i++) fc.gDom[i] = fc.gCdom[i];
for (int i = 0; i < 4; i++) fc.gDom[5+i] = fc.gHdom[i];
- for (int i = 0; i < 4; i++) for (int j = 0; j < 6; j++)
+ for (int i = 0; i < 4; i++) for (int j = 0; j < 6; j++)
fc.gVal[6*i+j] = fc.gC1[i][j];
- for (int i = 0; i < 4; i++) for (int j = 0; j < 6; j++)
+ for (int i = 0; i < 4; i++) for (int j = 0; j < 6; j++)
fc.gVal[4*6+6*i+j] = fc.gC2[i][j];
- for (int i = 0; i < 3; i++) for (int j = 0; j < 6; j++)
+ for (int i = 0; i < 3; i++) for (int j = 0; j < 6; j++)
fc.gVal[8*6+6*i+j] = fc.gH[i][j];
return fc;
@@ -739,7 +739,7 @@ inline flt_t gSpline(KernelArgsAIREBOT<flt_t,acc_t> * ka, int itype, flt_t cos,
}
template<typename flt_t>
-inline flt_t eval_poly_bi(int n, flt_t * coeffs, flt_t x, flt_t y,
+inline flt_t eval_poly_bi(int n, flt_t * coeffs, flt_t x, flt_t y,
flt_t * deriv) {
flt_t dy;
flt_t vy = eval_poly_lin(n, &coeffs[n * (n - 1)], y, &dy);
@@ -758,7 +758,7 @@ inline flt_t eval_poly_bi(int n, flt_t * coeffs, flt_t x, flt_t y,
}
template<typename flt_t>
-inline flt_t eval_poly_tri(int n, flt_t * coeffs, flt_t x, flt_t y, flt_t z,
+inline flt_t eval_poly_tri(int n, flt_t * coeffs, flt_t x, flt_t y, flt_t z,
flt_t * deriv) {
flt_t dyz[2];
flt_t vyz = eval_poly_bi(n, &coeffs[n * n * (n - 1)], y, z, &dyz[0]);
@@ -780,12 +780,12 @@ inline flt_t eval_poly_tri(int n, flt_t * coeffs, flt_t x, flt_t y, flt_t z,
}
template<typename flt_t, typename acc_t>
-inline flt_t PijSpline(KernelArgsAIREBOT<flt_t,acc_t> * ka, int itype,
+inline flt_t PijSpline(KernelArgsAIREBOT<flt_t,acc_t> * ka, int itype,
int jtype, flt_t NC, flt_t NH, flt_t * dN) {
dN[0] = 0.0;
dN[1] = 0.0;
if (itype == HYDROGEN) return 0;
- flt_t *pCJdom = jtype == CARBON ? &ka->params.pCCdom[0][0] :
+ flt_t *pCJdom = jtype == CARBON ? &ka->params.pCCdom[0][0] :
&ka->params.pCHdom[0][0];
NC = fmax_nonan(pCJdom[0], fmin_nonan(pCJdom[1], NC));
NH = fmax_nonan(pCJdom[2], fmin_nonan(pCJdom[3], NH));
@@ -804,7 +804,7 @@ inline flt_t PijSpline(KernelArgsAIREBOT<flt_t,acc_t> * ka, int itype,
}
template<typename flt_t, typename acc_t>
-inline flt_t TijSpline(KernelArgsAIREBOT<flt_t,acc_t> * ka, flt_t Nij,
+inline flt_t TijSpline(KernelArgsAIREBOT<flt_t,acc_t> * ka, flt_t Nij,
flt_t Nji, flt_t Nijconj, acc_t * dN3) {
flt_t * Tijdom = &ka->params.Tijdom[0][0];
Nij = fmax_nonan(Tijdom[0], fmin_nonan(Tijdom[1], Nij));
@@ -813,7 +813,7 @@ inline flt_t TijSpline(KernelArgsAIREBOT<flt_t,acc_t> * ka, flt_t Nij,
int nij = floor(Nij);
int nji = floor(Nji);
int nijconj = floor(Nijconj);
- if (fabs(Nij - nij) < TOL && fabs(Nji - nji) <
+ if (fabs(Nij - nij) < TOL && fabs(Nji - nji) <
TOL && fabs(Nijconj - nijconj) < TOL) {
dN3[0] = ka->params.Tdfdx[nij][nji][nijconj];
dN3[1] = ka->params.Tdfdy[nij][nji][nijconj];
@@ -823,12 +823,12 @@ inline flt_t TijSpline(KernelArgsAIREBOT<flt_t,acc_t> * ka, flt_t Nij,
if (Nij == Tijdom[1]) nij -= 1;
if (Nji == Tijdom[3]) nji -= 1;
if (Nijconj == Tijdom[5]) nijconj -= 1;
- return eval_poly_tri<acc_t>(4, &ka->params.Tijc[nij][nji][nijconj][0], Nij,
+ return eval_poly_tri<acc_t>(4, &ka->params.Tijc[nij][nji][nijconj][0], Nij,
Nji, Nijconj, dN3);
}
template<typename flt_t, typename acc_t>
-inline flt_t piRCSpline(KernelArgsAIREBOT<flt_t,acc_t> * ka, int itype,
+inline flt_t piRCSpline(KernelArgsAIREBOT<flt_t,acc_t> * ka, int itype,
int jtype, flt_t Nij, flt_t Nji, flt_t Nijconj, acc_t * dN3) {
const int HH = 2;
const int CH = 1;
@@ -838,7 +838,7 @@ inline flt_t piRCSpline(KernelArgsAIREBOT<flt_t,acc_t> * ka, int itype,
ka->params.b : ka->params.c)
flt_t * piIJdom = &piRCSelect(piHHdom, piCHdom, piCCdom)[0][0];
if (select == HH) {
- if (Nij < piIJdom[0] || Nij > piIJdom[1] || Nji < piIJdom[2] ||
+ if (Nij < piIJdom[0] || Nij > piIJdom[1] || Nji < piIJdom[2] ||
Nji > piIJdom[3] || Nijconj < piIJdom[4] || Nijconj > piIJdom[5]) {
Nij = 0;
Nji = 0;
@@ -851,7 +851,7 @@ inline flt_t piRCSpline(KernelArgsAIREBOT<flt_t,acc_t> * ka, int itype,
int nij = floor(Nij);
int nji = floor(Nji);
int nijconj = floor(Nijconj);
- if (fabs(Nij - nij) < TOL && fabs(Nji - nji) <
+ if (fabs(Nij - nij) < TOL && fabs(Nji - nji) <
TOL && fabs(Nijconj - nijconj) < TOL) {
dN3[0] = piRCSelect(piHHdfdx, piCHdfdx, piCCdfdx)[nij][nji][nijconj];
dN3[1] = piRCSelect(piHHdfdy, piCHdfdy, piCCdfdy)[nij][nji][nijconj];
@@ -861,8 +861,8 @@ inline flt_t piRCSpline(KernelArgsAIREBOT<flt_t,acc_t> * ka, int itype,
if (Nij == piIJdom[1]) nij -= 1;
if (Nji == piIJdom[3]) nji -= 1;
if (Nijconj == piIJdom[5]) nijconj -= 1;
- return eval_poly_tri<acc_t>(4,
- &piRCSelect(piHH, piCH, piCC)[nij][nji][nijconj][0], Nij, Nji, Nijconj,
+ return eval_poly_tri<acc_t>(4,
+ &piRCSelect(piHH, piCH, piCC)[nij][nji][nijconj][0], Nij, Nji, Nijconj,
dN3);
#undef piRCSelect
}
@@ -872,8 +872,8 @@ inline flt_t piRCSpline(KernelArgsAIREBOT<flt_t,acc_t> * ka, int itype,
* in the original lammps code.
*/
template<typename flt_t, typename acc_t>
-inline flt_t frebo_pij(KernelArgsAIREBOT<flt_t,acc_t> * ka, int i, int j,
- flt_t rijx, flt_t rijy, flt_t rijz, flt_t rijmag, flt_t wij, flt_t VA,
+inline flt_t frebo_pij(KernelArgsAIREBOT<flt_t,acc_t> * ka, int i, int j,
+ flt_t rijx, flt_t rijy, flt_t rijz, flt_t rijmag, flt_t wij, flt_t VA,
flt_t * sum_N, acc_t fij[3]) {
ResultForceT<acc_t> * result_f = ka->result_f;
AtomAIREBOT<flt_t> * x = ka->x;
@@ -921,7 +921,7 @@ inline flt_t frebo_pij(KernelArgsAIREBOT<flt_t,acc_t> * ka, int i, int j,
flt_t dwik;
flt_t wik = Sp(rikmag, rcminik, rcmaxik, &dwik);
flt_t Nki = nC[k] + nH[k] - wik;
- flt_t cosjik = (rijx * rikx + rijy * riky + rijz * rikz) /
+ flt_t cosjik = (rijx * rikx + rijy * riky + rijz * rikz) /
(rijmag * rikmag);
cosjik = fmin_nonan<flt_t>(1, fmax_nonan<flt_t>(-1, cosjik));
flt_t dgdc, dgdN;
@@ -1029,7 +1029,7 @@ inline flt_t frebo_pij(KernelArgsAIREBOT<flt_t,acc_t> * ka, int i, int j,
}
template<typename flt_t, typename acc_t>
-inline flt_t frebo_pi_rc(KernelArgsAIREBOT<flt_t,acc_t> * ka, int itype,
+inline flt_t frebo_pi_rc(KernelArgsAIREBOT<flt_t,acc_t> * ka, int itype,
int jtype, flt_t Nij, flt_t Nji, flt_t Nijconj, flt_t * dN3) {
acc_t dN3tmp[3] = {0};
flt_t ret = piRCSpline(ka, itype, jtype, Nij, Nji, Nijconj, dN3tmp);
@@ -1040,7 +1040,7 @@ inline flt_t frebo_pi_rc(KernelArgsAIREBOT<flt_t,acc_t> * ka, int itype,
}
template<typename flt_t, typename acc_t>
-inline flt_t frebo_Tij(KernelArgsAIREBOT<flt_t,acc_t> * ka, int itype,
+inline flt_t frebo_Tij(KernelArgsAIREBOT<flt_t,acc_t> * ka, int itype,
int jtype, flt_t Nij, flt_t Nji, flt_t Nijconj, flt_t * dN3) {
dN3[0] = 0;
dN3[1] = 0;
@@ -1088,7 +1088,7 @@ inline flt_t frebo_sum_omega(KernelArgsAIREBOT<flt_t,acc_t> * ka, int i, int j,
flt_t r21y = x[a2].y - x[a1].y;
flt_t r21z = x[a2].z - x[a1].z;
flt_t r21mag = overloaded::sqrt(r21x * r21x + r21y * r21y + r21z * r21z);
- flt_t cos321 = (r23x * r21x + r23y * r21y + r23z * r21z) /
+ flt_t cos321 = (r23x * r21x + r23y * r21y + r23z * r21z) /
(r23mag * r21mag);
cos321 = fmin_nonan<flt_t>(1, fmax_nonan<flt_t>(-1, cos321));
flt_t sin321 = overloaded::sqrt(1 - cos321 * cos321);
@@ -1131,7 +1131,7 @@ inline flt_t frebo_sum_omega(KernelArgsAIREBOT<flt_t,acc_t> * ka, int i, int j,
flt_t r34y = x[a3].y - x[a4].y;
flt_t r34z = x[a3].z - x[a4].z;
flt_t r34mag = overloaded::sqrt(r34x * r34x + r34y * r34y + r34z * r34z);
- flt_t cos234 = (r32x * r34x + r32y * r34y + r32z * r34z) /
+ flt_t cos234 = (r32x * r34x + r32y * r34y + r32z * r34z) /
(r23mag * r34mag);
cos234 = fmin_nonan<flt_t>(1, fmax_nonan<flt_t>(-1, cos234));
flt_t sin234 = overloaded::sqrt(1 - cos234 * cos234);
@@ -1298,7 +1298,7 @@ inline flt_t frebo_sum_omega(KernelArgsAIREBOT<flt_t,acc_t> * ka, int i, int j,
* Occurs four times in each bondorder and bondorderLJ.
*/
template<typename flt_t, typename acc_t>
-inline void frebo_N_spline_force(KernelArgsAIREBOT<flt_t,acc_t> * ka, int i,
+inline void frebo_N_spline_force(KernelArgsAIREBOT<flt_t,acc_t> * ka, int i,
int j, flt_t VA, flt_t dN, flt_t dNconj, flt_t Nconj) {
int * map = ka->map;
AtomAIREBOT<flt_t> * x = ka->x;
@@ -1386,7 +1386,7 @@ struct LennardJonesPathAIREBOT {
*/
template<typename flt_t, typename acc_t>
inline flt_t ref_lennard_jones_test_path_single(
- KernelArgsAIREBOT<flt_t,acc_t> * ka, flt_t best, int num, int * idxs,
+ KernelArgsAIREBOT<flt_t,acc_t> * ka, flt_t best, int num, int * idxs,
LennardJonesPathAIREBOT<flt_t> * path) {
LennardJonesPathAIREBOT<flt_t> result;
AtomAIREBOT<flt_t> * x = ka->x;
@@ -1404,7 +1404,7 @@ inline flt_t ref_lennard_jones_test_path_single(
int type1 = map[x[a1].w];
if (rsq >= ka->params.rcmaxsq[type0][type1]) return best;
flt_t r = overloaded::sqrt(rsq);
- flt_t dw, w = Sp<flt_t>(r, ka->params.rcmin[type0][type1],
+ flt_t dw, w = Sp<flt_t>(r, ka->params.rcmin[type0][type1],
ka->params.rcmax[type0][type1], &dw);
if (w == 0) return best;
combined *= w;
@@ -1429,8 +1429,8 @@ inline flt_t ref_lennard_jones_test_path_single(
* loop.
*/
template<typename flt_t, typename acc_t>
-inline flt_t ref_lennard_jones_test_path(KernelArgsAIREBOT<flt_t,acc_t> * ka,
- int i, int j, flt_t rij, flt_t rcmax,
+inline flt_t ref_lennard_jones_test_path(KernelArgsAIREBOT<flt_t,acc_t> * ka,
+ int i, int j, flt_t rij, flt_t rcmax,
LennardJonesPathAIREBOT<flt_t> * path) {
int idxs[4];
idxs[0] = i;
@@ -1463,7 +1463,7 @@ inline flt_t ref_lennard_jones_test_path(KernelArgsAIREBOT<flt_t,acc_t> * ka,
* Conducts the force update due to C_ij, given the active path.
*/
template<typename flt_t, typename acc_t>
-inline void ref_lennard_jones_force_path(KernelArgsAIREBOT<flt_t,acc_t> * ka,
+inline void ref_lennard_jones_force_path(KernelArgsAIREBOT<flt_t,acc_t> * ka,
flt_t dC, LennardJonesPathAIREBOT<flt_t> * path) {
AtomAIREBOT<flt_t> * x = ka->x;
ResultForceT<acc_t> * result_f = ka->result_f;
@@ -1485,7 +1485,7 @@ inline void ref_lennard_jones_force_path(KernelArgsAIREBOT<flt_t,acc_t> * ka,
* Calculate the bondorderLJ term.
*/
template<typename flt_t, typename acc_t>
-inline flt_t ref_lennard_jones_bondorder(KernelArgsAIREBOT<flt_t,acc_t> * ka,
+inline flt_t ref_lennard_jones_bondorder(KernelArgsAIREBOT<flt_t,acc_t> * ka,
int i, int j, flt_t VA, acc_t fij[3]) {
AtomAIREBOT<flt_t> * x = ka->x;
int * map = ka->map;
@@ -1511,57 +1511,57 @@ inline flt_t ref_lennard_jones_bondorder(KernelArgsAIREBOT<flt_t,acc_t> * ka,
flt_t Nji = ka->nH[j] + ka->nC[j] - wij;
flt_t NconjtmpI;
acc_t fijc[3] = {0}, fjic[3] = {0};
- flt_t pij = frebo_pij<flt_t,acc_t>(ka, i, j, delx * scale, dely * scale,
+ flt_t pij = frebo_pij<flt_t,acc_t>(ka, i, j, delx * scale, dely * scale,
delz * scale, the_r, wij, 0.0, &NconjtmpI, fijc);
flt_t NconjtmpJ;
- flt_t pji = frebo_pij<flt_t,acc_t>(ka, j, i, -delx * scale, -dely * scale,
+ flt_t pji = frebo_pij<flt_t,acc_t>(ka, j, i, -delx * scale, -dely * scale,
-delz * scale, the_r, wij, 0.0, &NconjtmpJ, fjic);
flt_t Nijconj = 1.0 + (NconjtmpI * NconjtmpI) + (NconjtmpJ * NconjtmpJ);
flt_t dN3_pi_rc[3];
- flt_t pi_rc = frebo_pi_rc<flt_t,acc_t>(ka, itype, jtype, Nij, Nji, Nijconj,
+ flt_t pi_rc = frebo_pi_rc<flt_t,acc_t>(ka, itype, jtype, Nij, Nji, Nijconj,
dN3_pi_rc);
flt_t dN3_Tij[3];
- flt_t Tij = frebo_Tij<flt_t,acc_t>(ka, itype, jtype, Nij, Nji, Nijconj,
+ flt_t Tij = frebo_Tij<flt_t,acc_t>(ka, itype, jtype, Nij, Nji, Nijconj,
dN3_Tij);
flt_t sum_omega = 0;
if (fabs(Tij) > TOL) {
- sum_omega = frebo_sum_omega<flt_t,acc_t>(ka, i, j, delx * scale, dely *
- scale, delz * scale, the_r, 0.0,
+ sum_omega = frebo_sum_omega<flt_t,acc_t>(ka, i, j, delx * scale, dely *
+ scale, delz * scale, the_r, 0.0,
fijc);
}
flt_t pi_dh = Tij * sum_omega;
flt_t bij = 0.5 * (pij + pji) + pi_rc + pi_dh;
flt_t dStb;
- flt_t Stb = Sp2<flt_t>(bij, ka->params.bLJmin[itype][jtype],
+ flt_t Stb = Sp2<flt_t>(bij, ka->params.bLJmin[itype][jtype],
ka->params.bLJmax[itype][jtype], &dStb);
if (dStb != 0) {
- flt_t pij_reverse = frebo_pij<flt_t,acc_t>(ka, i, j, delx * scale,
+ flt_t pij_reverse = frebo_pij<flt_t,acc_t>(ka, i, j, delx * scale,
dely * scale, delz * scale, the_r, wij, VA * dStb, &NconjtmpI, fijc);
- flt_t pji_reverse = frebo_pij<flt_t,acc_t>(ka, j, i, -delx * scale,
+ flt_t pji_reverse = frebo_pij<flt_t,acc_t>(ka, j, i, -delx * scale,
-dely * scale, -delz * scale, the_r, wij, VA * dStb, &NconjtmpJ, fjic);
fijc[0] -= fjic[0];
fijc[1] -= fjic[1];
fijc[2] -= fjic[2];
- frebo_N_spline_force<flt_t,acc_t>(ka, i, j, VA * dStb, dN3_pi_rc[0],
+ frebo_N_spline_force<flt_t,acc_t>(ka, i, j, VA * dStb, dN3_pi_rc[0],
dN3_pi_rc[2], NconjtmpI);
- frebo_N_spline_force<flt_t,acc_t>(ka, j, i, VA * dStb, dN3_pi_rc[1],
+ frebo_N_spline_force<flt_t,acc_t>(ka, j, i, VA * dStb, dN3_pi_rc[1],
dN3_pi_rc[2], NconjtmpJ);
if (fabs(Tij) > TOL) {
- flt_t sum_omega_reverse = frebo_sum_omega<flt_t,acc_t>(ka, i, j,
+ flt_t sum_omega_reverse = frebo_sum_omega<flt_t,acc_t>(ka, i, j,
delx * scale, dely * scale, delz * scale, the_r, VA * dStb * Tij, fijc);
- frebo_N_spline_force(ka, i, j, VA * dStb * sum_omega, dN3_Tij[0],
+ frebo_N_spline_force(ka, i, j, VA * dStb * sum_omega, dN3_Tij[0],
dN3_Tij[2], NconjtmpI);
- frebo_N_spline_force(ka, j, i, VA * dStb * sum_omega, dN3_Tij[1],
+ frebo_N_spline_force(ka, j, i, VA * dStb * sum_omega, dN3_Tij[1],
dN3_Tij[2], NconjtmpJ);
}
assert(fij[0] == 0);
assert(fij[1] == 0);
assert(fij[2] == 0);
- fij[0] = scale * (fijc[0] - (delx * delx * fijc[0] + dely * delx *
+ fij[0] = scale * (fijc[0] - (delx * delx * fijc[0] + dely * delx *
fijc[1] + delz * delx * fijc[2]) / rsq);
- fij[1] = scale * (fijc[1] - (delx * dely * fijc[0] + dely * dely *
+ fij[1] = scale * (fijc[1] - (delx * dely * fijc[0] + dely * dely *
fijc[1] + delz * dely * fijc[2]) / rsq);
- fij[2] = scale * (fijc[2] - (delx * delz * fijc[0] + dely * delz *
+ fij[2] = scale * (fijc[2] - (delx * delz * fijc[0] + dely * delz *
fijc[1] + delz * delz * fijc[2]) / rsq);
}
return Stb;
@@ -1952,7 +1952,7 @@ void ref_torsion(KernelArgsAIREBOT<flt_t,acc_t> * ka) {
* inlined.
*/
template<typename flt_t, typename acc_t>
-void ref_frebo_single_interaction(KernelArgsAIREBOT<flt_t,acc_t> * ka, int i,
+void ref_frebo_single_interaction(KernelArgsAIREBOT<flt_t,acc_t> * ka, int i,
int j) {
AtomAIREBOT<flt_t> * x = ka->x;
int * map = ka->map;
@@ -2000,11 +2000,11 @@ void ref_frebo_single_interaction(KernelArgsAIREBOT<flt_t,acc_t> * ka, int i,
flt_t Nij = ka->nH[i] + ka->nC[i] - wij;
flt_t Nji = ka->nH[j] + ka->nC[j] - wij;
flt_t NconjtmpI;
- flt_t pij = frebo_pij(ka, i, j, delx, dely, delz, rij, wij, VA, &NconjtmpI,
+ flt_t pij = frebo_pij(ka, i, j, delx, dely, delz, rij, wij, VA, &NconjtmpI,
fij);
flt_t NconjtmpJ;
acc_t fji[3] = {0};
- flt_t pji = frebo_pij(ka, j, i, -delx, -dely, -delz, rij, wij, VA,
+ flt_t pji = frebo_pij(ka, j, i, -delx, -dely, -delz, rij, wij, VA,
&NconjtmpJ, fji);
fij[0] -= fji[0]; fij[1] -= fji[1]; fij[2] -= fji[2];
flt_t Nijconj = 1.0 + (NconjtmpI * NconjtmpI) + (NconjtmpJ * NconjtmpJ);
@@ -2080,7 +2080,7 @@ void ref_frebo(KernelArgsAIREBOT<flt_t,acc_t> * ka, int torflag) {
}
template<typename flt_t, typename acc_t>
-void ref_lennard_jones_single_interaction(KernelArgsAIREBOT<flt_t,acc_t> * ka,
+void ref_lennard_jones_single_interaction(KernelArgsAIREBOT<flt_t,acc_t> * ka,
int i, int j, int morseflag) {
AtomAIREBOT<flt_t> * x = ka->x;
int * map = ka->map;
@@ -2101,7 +2101,7 @@ void ref_lennard_jones_single_interaction(KernelArgsAIREBOT<flt_t,acc_t> * ka,
flt_t cij = 1.0;
if (rij < ka->params.cut3rebo) {
#pragma noinline
- cij = ref_lennard_jones_test_path<flt_t,acc_t>(ka, i, j, rij,
+ cij = ref_lennard_jones_test_path<flt_t,acc_t>(ka, i, j, rij,
ka->params.rcmax[itype][jtype], &testpath);
}
if (cij == 0) {
@@ -2119,24 +2119,24 @@ void ref_lennard_jones_single_interaction(KernelArgsAIREBOT<flt_t,acc_t> * ka,
flt_t vdw, dvdw;
if (morseflag) {
const flt_t exr = exp(-rij * ka->params.lj4[itype][jtype]);
- vdw = ka->params.lj1[itype][jtype] * exr *
+ vdw = ka->params.lj1[itype][jtype] * exr *
(ka->params.lj2[itype][jtype]*exr - 2);
- dvdw = ka->params.lj3[itype][jtype] * exr *
+ dvdw = ka->params.lj3[itype][jtype] * exr *
(1 - ka->params.lj2[itype][jtype]*exr);
} else {
flt_t r2inv = 1 / rsq;
flt_t r6inv = r2inv * r2inv * r2inv;
- vdw = r6inv * (ka->params.lj3[itype][jtype]*r6inv -
+ vdw = r6inv * (ka->params.lj3[itype][jtype]*r6inv -
ka->params.lj4[itype][jtype]);
- dvdw = -r6inv * (ka->params.lj1[itype][jtype]*r6inv -
+ dvdw = -r6inv * (ka->params.lj1[itype][jtype]*r6inv -
ka->params.lj2[itype][jtype]) / rij;
}
flt_t VLJ = vdw * slw;
flt_t dVLJ = dvdw * slw + vdw * dslw;
- flt_t dStr, Str = Sp2<flt_t>(rij, ka->params.rcLJmin[itype][jtype],
+ flt_t dStr, Str = Sp2<flt_t>(rij, ka->params.rcLJmin[itype][jtype],
ka->params.rcLJmax[itype][jtype], &dStr);
flt_t VA = Str * cij * VLJ;
flt_t Stb = 0;
@@ -2158,7 +2158,7 @@ void ref_lennard_jones_single_interaction(KernelArgsAIREBOT<flt_t,acc_t> * ka,
if (cij < 1) {
#pragma noinline
- ref_lennard_jones_force_path(ka, Str * Stb * VLJ + (1 - Str) * VLJ,
+ ref_lennard_jones_force_path(ka, Str * Stb * VLJ + (1 - Str) * VLJ,
&testpath);
}
}
@@ -2200,7 +2200,7 @@ typedef typename intr_types<flt_t, acc_t>::bvec bvec;
VEC_INLINE inline
static void aut_loadatoms_vec(
AtomAIREBOT<flt_t> * atoms, ivec j_vec,
- fvec *x, fvec * y, fvec * z, bvec * type_mask, int * map, ivec map_i,
+ fvec *x, fvec * y, fvec * z, bvec * type_mask, int * map, ivec map_i,
ivec c_1
) {
const ivec c_4 = ivec::set1(4);
@@ -2329,10 +2329,10 @@ static void aut_rebo_neigh(KernelArgsAIREBOT<flt_t,acc_t> * ka) {
ka->neigh_rebo.offset[i] = offset;
- int jnum = ka->rebuild_flag ? ka->neigh_lmp.num[i] :
+ int jnum = ka->rebuild_flag ? ka->neigh_lmp.num[i] :
ka->neigh_rebo.num_half[i];
- int * neighs = ka->rebuild_flag ?
- &ka->neigh_lmp.entries[ka->neigh_lmp.offset[i]] :
+ int * neighs = ka->rebuild_flag ?
+ &ka->neigh_lmp.entries[ka->neigh_lmp.offset[i]] :
&ka->neigh_rebo.entries[ka->neigh_rebo.offset[i]+jnum];
int * skin_target = &ka->neigh_rebo.entries[offset+ka->num_neighs_per_atom];
int n = 0;
@@ -2355,7 +2355,7 @@ static void aut_rebo_neigh(KernelArgsAIREBOT<flt_t,acc_t> * ka) {
fvec delz = z_i - z_j;
fvec rsq = delx * delx + dely * dely + delz * delz;
if (ka->rebuild_flag) {
- fvec rcmaxskinsq = fvec::mask_blend(jtype_mask, rcmaxskinsq0,
+ fvec rcmaxskinsq = fvec::mask_blend(jtype_mask, rcmaxskinsq0,
rcmaxskinsq1);
bvec c_mask = fvec::mask_cmplt(j_mask, rsq, rcmaxskinsq);
ivec::mask_compressstore(c_mask, &skin_target[n_skin], ji);
@@ -2392,7 +2392,7 @@ static void aut_rebo_neigh(KernelArgsAIREBOT<flt_t,acc_t> * ka) {
}
-static fvec aut_eval_poly_lin_pd_2(int n, flt_t * vals, ivec idx, fvec x,
+static fvec aut_eval_poly_lin_pd_2(int n, flt_t * vals, ivec idx, fvec x,
fvec * deriv) {
fvec c_1 = fvec::set1(1);
fvec x_i = c_1;
@@ -2412,8 +2412,8 @@ static fvec aut_eval_poly_lin_pd_2(int n, flt_t * vals, ivec idx, fvec x,
return result;
}
-static fvec aut_mask_gSpline_pd_2(KernelArgsAIREBOT<flt_t,acc_t> * ka,
- bvec active_mask, int itype, fvec cosjik,
+static fvec aut_mask_gSpline_pd_2(KernelArgsAIREBOT<flt_t,acc_t> * ka,
+ bvec active_mask, int itype, fvec cosjik,
fvec Nij, fvec *dgdc, fvec *dgdN) {
int i;
flt_t * gDom = NULL;
@@ -2430,7 +2430,7 @@ static fvec aut_mask_gSpline_pd_2(KernelArgsAIREBOT<flt_t,acc_t> * ka,
gDom = &ka->params.gHdom[0];
offs = ivec::set1(8 * 6);
}
- cosjik = fvec::max(fvec::set1(gDom[0]), fvec::min(fvec::set1(gDom[nDom]),
+ cosjik = fvec::max(fvec::set1(gDom[0]), fvec::min(fvec::set1(gDom[nDom]),
cosjik));
ivec index6 = ivec::setzero();
for (i = 0; i < nDom; i++) {
@@ -2438,7 +2438,7 @@ static fvec aut_mask_gSpline_pd_2(KernelArgsAIREBOT<flt_t,acc_t> * ka,
bvec cosle = fvec::cmple(cosjik, fvec::set1(gDom[i+1]));
index6 = ivec::mask_blend(cosge & cosle, index6, ivec::set1(6*i));
}
- fvec g = aut_eval_poly_lin_pd_2(6, &ka->params.gVal[0], offs + index6,
+ fvec g = aut_eval_poly_lin_pd_2(6, &ka->params.gVal[0], offs + index6,
cosjik, dgdc);
*dgdN = fvec::setzero();
if (itype == 0) {
@@ -2447,7 +2447,7 @@ static fvec aut_mask_gSpline_pd_2(KernelArgsAIREBOT<flt_t,acc_t> * ka,
bvec Nmask = Ngt & Nlt;
if (bvec::test_any_set(Nmask)) {
fvec dg1;
- fvec g1 = aut_eval_poly_lin_pd_2(6, &ka->params.gVal[0], index6, cosjik,
+ fvec g1 = aut_eval_poly_lin_pd_2(6, &ka->params.gVal[0], index6, cosjik,
&dg1);
fvec dS;
fvec cut = aut_Sp_deriv(Nij, NCmin, NCmax, &dS);
@@ -2459,7 +2459,7 @@ static fvec aut_mask_gSpline_pd_2(KernelArgsAIREBOT<flt_t,acc_t> * ka,
return g;
}
-static fvec aut_PijSpline(KernelArgsAIREBOT<flt_t,acc_t> * ka, int itype,
+static fvec aut_PijSpline(KernelArgsAIREBOT<flt_t,acc_t> * ka, int itype,
int jtype, fvec NijC, fvec NijH, fvec *dN2) {
flt_t ret[fvec::VL] __attribute__((aligned(64)));
flt_t dN20[fvec::VL] __attribute__((aligned(64)));
@@ -2579,10 +2579,10 @@ static fvec aut_frebo_pij_pd_2(
fvec sum_pij = fvec::setzero();
fvec sum_dpij_dN = fvec::setzero();
fvec dN2[2];
- ivec offseti = ivec::mask_gather(ivec::setzero(), bvec::full(), vi,
+ ivec offseti = ivec::mask_gather(ivec::setzero(), bvec::full(), vi,
ka->neigh_rebo.offset, sizeof(int));
int buf_len = 0;
- ivec knum = ivec::mask_gather(ivec::setzero(), bvec::full(), vi,
+ ivec knum = ivec::mask_gather(ivec::setzero(), bvec::full(), vi,
ka->neigh_rebo.num, sizeof(int));
ivec kk = ivec::setzero();
bvec active_mask = ivec::cmplt(kk, knum);
@@ -2612,7 +2612,7 @@ static fvec aut_frebo_pij_pd_2(
*sum_N = fvec::setzero();
{
while (bvec::test_any_set(active_mask)) {
- ivec k = ivec::mask_gather(ivec::setzero(), active_mask, kk + offseti,
+ ivec k = ivec::mask_gather(ivec::setzero(), active_mask, kk + offseti,
ka->neigh_rebo.entries, sizeof(int));
bvec excluded_mask = ivec::cmpeq(k, vj) & active_mask;
if (bvec::test_any_set(excluded_mask)) {
@@ -2622,35 +2622,35 @@ static fvec aut_frebo_pij_pd_2(
}
fvec x_k, y_k, z_k;
bvec ktype_mask;
- aut_loadatoms_vec(x, k, &x_k, &y_k, &z_k, &ktype_mask, ka->map, map_i,
+ aut_loadatoms_vec(x, k, &x_k, &y_k, &z_k, &ktype_mask, ka->map, map_i,
c_i1);
fvec rikx = x_i - x_k;
fvec riky = y_i - y_k;
fvec rikz = z_i - z_k;
fvec rikmag = fvec::sqrt(rikx * rikx + riky * riky + rikz * rikz);
fvec rho_k = fvec::mask_blend(ktype_mask, rho_k0, rho_k1);
- fvec lamdajik = c_4 * factor_itype * ( rho_k - rikmag - ( rho_j -
+ fvec lamdajik = c_4 * factor_itype * ( rho_k - rikmag - ( rho_j -
rijmag));
fvec ex_lam = fvec::exp(lamdajik);
fvec rcmax = fvec::mask_blend(ktype_mask, rcmax0, rcmax1);
fvec rcmin = fvec::mask_blend(ktype_mask, rcmin0, rcmin1);
fvec dwik;
fvec wik = aut_Sp_deriv(rikmag, rcmin, rcmax, &dwik);
- fvec Nki = fvec::gather(k, nC, sizeof(flt_t)) +
+ fvec Nki = fvec::gather(k, nC, sizeof(flt_t)) +
fvec::gather(k, nH, sizeof(flt_t)) - wik;
- fvec cosjik = (rijx * rikx + rijy * riky + rijz * rikz) /
+ fvec cosjik = (rijx * rikx + rijy * riky + rijz * rikz) /
( rijmag * rikmag);
cosjik = fvec::min(c_1, fvec::max(c_m1, cosjik));
fvec dgdc, dgdN;
- fvec g = aut_mask_gSpline_pd_2(ka, active_mask, itype, cosjik, Nij,
+ fvec g = aut_mask_gSpline_pd_2(ka, active_mask, itype, cosjik, Nij,
&dgdc, &dgdN);
sum_pij = fvec::mask_add(sum_pij, active_mask, sum_pij, wik * g * ex_lam);
- sum_dpij_dN = fvec::mask_add(sum_dpij_dN, active_mask, sum_dpij_dN,
+ sum_dpij_dN = fvec::mask_add(sum_dpij_dN, active_mask, sum_dpij_dN,
wik * ex_lam * dgdN);
fvec dcutN;
fvec cutN = aut_Sp_deriv(Nki, Nmin, Nmax, &dcutN);
- *sum_N = fvec::mask_add(*sum_N, active_mask, *sum_N,
- fvec::mask_blend(ktype_mask, c_1,
+ *sum_N = fvec::mask_add(*sum_N, active_mask, *sum_N,
+ fvec::mask_blend(ktype_mask, c_1,
fvec::setzero()) * wik * cutN);
if (buf_len == BUF_CAP) goto exceed_buffer;
data->rikx_buf[buf_len] = rikx;
@@ -2804,7 +2804,7 @@ static fvec aut_frebo_pij_pd_2(
* the respective neighbors.
*/
static void aut_frebo_data_writeback(
- KernelArgsAIREBOT<flt_t,acc_t> * _noalias ka,
+ KernelArgsAIREBOT<flt_t,acc_t> * _noalias ka,
struct aut_frebo_data * _noalias data) {
ResultForceT<acc_t> * _noalias result_f = ka->result_f;
flt_t fk_x_buf[fvec::VL] __attribute__((aligned(64)));
@@ -2833,8 +2833,8 @@ static void aut_frebo_data_writeback(
}
static void aut_frebo_N_spline_force(
- KernelArgsAIREBOT<flt_t,acc_t> * _noalias ka,
- struct aut_frebo_data * _noalias data, int itype, int jtype, ivec vi,
+ KernelArgsAIREBOT<flt_t,acc_t> * _noalias ka,
+ struct aut_frebo_data * _noalias data, int itype, int jtype, ivec vi,
ivec vj, fvec VA, fvec dN, fvec dNconj, fvec Nconj) {
ivec c_i1 = ivec::set1(1);
fvec c_2 = fvec::set1(2);
@@ -2956,14 +2956,14 @@ static void aut_frebo_N_spline_force(
}
static fvec aut_frebo_pi_rc_pd(KernelArgsAIREBOT<flt_t,acc_t> * ka, int itype,
- int jtype, fvec Nij, fvec Nji, fvec Nijconj,
+ int jtype, fvec Nij, fvec Nji, fvec Nijconj,
fvec * dN3) {
flt_t ret[fvec::VL] __attribute__((aligned(64)));
flt_t dN3ret[3][fvec::VL] __attribute__((aligned(64)));
int i;
for (i = 0; i < fvec::VL; i++) {
flt_t dN3tmp[3];
- ret[i] = frebo_pi_rc(ka, itype, jtype, fvec::at(Nij, i), fvec::at(Nji, i),
+ ret[i] = frebo_pi_rc(ka, itype, jtype, fvec::at(Nij, i), fvec::at(Nji, i),
fvec::at(Nijconj, i), &dN3tmp[0]);
dN3ret[0][i] = dN3tmp[0];
dN3ret[1][i] = dN3tmp[1];
@@ -2975,15 +2975,15 @@ static fvec aut_frebo_pi_rc_pd(KernelArgsAIREBOT<flt_t,acc_t> * ka, int itype,
return fvec::load(&ret[0]);
}
-static fvec aut_frebo_Tij(KernelArgsAIREBOT<flt_t,acc_t> * ka, int itype,
- int jtype, fvec Nij, fvec Nji, fvec Nijconj,
+static fvec aut_frebo_Tij(KernelArgsAIREBOT<flt_t,acc_t> * ka, int itype,
+ int jtype, fvec Nij, fvec Nji, fvec Nijconj,
fvec * dN3) {
flt_t ret[fvec::VL] __attribute__((aligned(64)));
flt_t dN3ret[3][fvec::VL] __attribute__((aligned(64)));
int i;
for (i = 0; i < fvec::VL; i++) {
flt_t dN3tmp[3];
- ret[i] = frebo_Tij(ka, itype, jtype, fvec::at(Nij, i), fvec::at(Nji, i),
+ ret[i] = frebo_Tij(ka, itype, jtype, fvec::at(Nij, i), fvec::at(Nji, i),
fvec::at(Nijconj, i), &dN3tmp[0]);
dN3ret[0][i] = dN3tmp[0];
dN3ret[1][i] = dN3tmp[1];
@@ -3030,9 +3030,9 @@ static fvec aut_frebo_sum_omega(
fvec sin321 = fvec::sqrt(c_1 - cos321 * cos321);
bvec mask_outer = fvec::cmpneq(fvec::setzero(), sin321) & mask_start;
// add "continue"
- fvec sink2i = fvec::mask_recip(fvec::undefined(), mask_outer,
+ fvec sink2i = fvec::mask_recip(fvec::undefined(), mask_outer,
sin321 * sin321);
- fvec rik2i = fvec::mask_recip(fvec::undefined(), mask_outer,
+ fvec rik2i = fvec::mask_recip(fvec::undefined(), mask_outer,
r21mag * r21mag);
fvec rr = r23mag * r23mag - r21mag * r21mag;
fvec r31x = r21x - r23x;
@@ -3041,9 +3041,9 @@ static fvec aut_frebo_sum_omega(
fvec r31mag2 = r31x * r31x + r31y * r31y + r31z * r31z;
fvec rijrik = c_2 * r23mag * r21mag;
fvec r21mag2 = r21mag * r21mag;
- fvec dctik = fvec::mask_div(fvec::undefined(), mask_outer, r31mag2 - rr,
+ fvec dctik = fvec::mask_div(fvec::undefined(), mask_outer, r31mag2 - rr,
rijrik * r21mag2);
- fvec dctij = fvec::mask_div(fvec::undefined(), mask_outer, r31mag2 + rr,
+ fvec dctij = fvec::mask_div(fvec::undefined(), mask_outer, r31mag2 + rr,
rijrik * r23mag * r23mag);
fvec dctjk = fvec::mask_div(fvec::undefined(), mask_outer, c_m2, rijrik);
fvec dw21 = i_data->dwik_buf[buf_idx_i];
@@ -3056,25 +3056,25 @@ static fvec aut_frebo_sum_omega(
// check l == k in second loop.
// l == a4 == buf_idx_j
ivec l = j_data->k_buf[buf_idx_j];
- bvec mask_inner_0 = ivec::mask_cmpneq(mask_outer, k, l) &
+ bvec mask_inner_0 = ivec::mask_cmpneq(mask_outer, k, l) &
j_data->mask_buf[buf_idx_j];
// add "continue"
fvec r34x = j_data->rikx_buf[buf_idx_j];
fvec r34y = j_data->riky_buf[buf_idx_j];
fvec r34z = j_data->rikz_buf[buf_idx_j];
fvec r34mag = j_data->rikmag_buf[buf_idx_j];
- fvec cos234 = fvec::mask_div(fvec::undefined(), mask_inner_0,
- r32x * r34x + r32y * r34y + r32z * r34z,
+ fvec cos234 = fvec::mask_div(fvec::undefined(), mask_inner_0,
+ r32x * r34x + r32y * r34y + r32z * r34z,
r23mag * r34mag);
cos234 = fvec::min(c_1, fvec::max(c_m1, cos234));
- fvec sin234 = fvec::mask_sqrt(fvec::undefined(), mask_inner_0,
+ fvec sin234 = fvec::mask_sqrt(fvec::undefined(), mask_inner_0,
c_1 - cos234 * cos234);
- bvec mask_inner_1 = fvec::mask_cmpneq(mask_inner_0, sin234,
+ bvec mask_inner_1 = fvec::mask_cmpneq(mask_inner_0, sin234,
fvec::setzero());
// add "continue"
- fvec sinl2i = fvec::mask_recip(fvec::undefined(), mask_inner_1,
+ fvec sinl2i = fvec::mask_recip(fvec::undefined(), mask_inner_1,
sin234 * sin234);
- fvec rjl2i = fvec::mask_recip(fvec::undefined(), mask_inner_1,
+ fvec rjl2i = fvec::mask_recip(fvec::undefined(), mask_inner_1,
r34mag * r34mag);
fvec dw34 = j_data->dwik_buf[buf_idx_j];
fvec w34 = j_data->wik_buf[buf_idx_j];
@@ -3085,11 +3085,11 @@ static fvec aut_frebo_sum_omega(
fvec r242 = r24x * r24x + r24y * r24y + r24z * r24z;
fvec rijrjl = c_2 * r23mag * r34mag;
fvec rjl2 = r34mag * r34mag;
- fvec dctjl = fvec::mask_div(fvec::undefined(), mask_inner_1, r242 - rr,
+ fvec dctjl = fvec::mask_div(fvec::undefined(), mask_inner_1, r242 - rr,
rijrjl * rjl2);
- fvec dctji = fvec::mask_div(fvec::undefined(), mask_inner_1, r242 + rr,
+ fvec dctji = fvec::mask_div(fvec::undefined(), mask_inner_1, r242 + rr,
rijrjl * r23mag * r23mag);
- fvec dctil = fvec::mask_div(fvec::undefined(), mask_inner_1, c_m2,
+ fvec dctil = fvec::mask_div(fvec::undefined(), mask_inner_1, c_m2,
rijrjl);
fvec dtsijl;
fvec tspijl = aut_Sp2_deriv(cos234, thmin, thmax, &dtsijl);
@@ -3106,19 +3106,19 @@ static fvec aut_frebo_sum_omega(
fvec cwnum = cross321x * cross234x + cross321y * cross234y + cross321z *
cross234z;
fvec cwnom = r21mag * r34mag * r23mag * r23mag * sin321 * sin234;
- fvec om1234 = fvec::mask_div(fvec::undefined(), mask_inner_1, cwnum,
+ fvec om1234 = fvec::mask_div(fvec::undefined(), mask_inner_1, cwnum,
cwnom);
fvec cw = om1234;
fvec sum_omega_contrib = (c_1 - om1234 * om1234) * w21 * w34 *
(c_1 - tspjik) * ( c_1 - tspijl);
- sum_omega = fvec::mask_add(sum_omega, mask_inner_1, sum_omega,
+ sum_omega = fvec::mask_add(sum_omega, mask_inner_1, sum_omega,
sum_omega_contrib);
fvec dt1dik = rik2i - dctik * sink2i * cos321;
fvec dt1djk = fvec::setzero() - dctjk * sink2i * cos321;
fvec dt1djl = rjl2i - dctjl * sinl2i * cos234;
fvec dt1dil = fvec::setzero() - dctil * sinl2i * cos234;
- fvec dt1dij = fvec::mask_div(fvec::undefined(), mask_inner_1, c_2,
- r23mag * r23mag) -
+ fvec dt1dij = fvec::mask_div(fvec::undefined(), mask_inner_1, c_2,
+ r23mag * r23mag) -
dctij * sink2i * cos321 - dctji * sinl2i * cos234;
fvec dt2dikx = r23y * cross234z - r23z * cross234y;
@@ -3136,7 +3136,7 @@ static fvec aut_frebo_sum_omega(
fvec dt2dijz = r21y * cross234x + r34x * cross321y -
( r34y * cross321x + r21x * cross234y);
- fvec aa = prefactor * c_2 * fvec::mask_div(fvec::undefined(),
+ fvec aa = prefactor * c_2 * fvec::mask_div(fvec::undefined(),
mask_inner_1, cw, cwnom) *
w21 * w34 * (c_1 - tspjik) * ( c_1 - tspijl);
fvec aaa1 = (fvec::setzero() - prefactor) * (c_1 - om1234 * om1234) *
@@ -3145,7 +3145,7 @@ static fvec aut_frebo_sum_omega(
w21 * w34;
fvec at2 = aa * cwnum;
- fvec fcijpc = aaa2 * dtsjik * dctij * (c_1 - tspijl) + aaa2 * dtsijl *
+ fvec fcijpc = aaa2 * dtsjik * dctij * (c_1 - tspijl) + aaa2 * dtsijl *
dctji * (c_1 - tspjik) - dt1dij * at2;
fvec fcikpc = aaa2 * dtsjik * dctik * (c_1 - tspijl) - dt1dik * at2;
fvec fcjlpc = aaa2 * dtsijl * dctjl * (c_1 - tspjik) - dt1djl * at2;
@@ -3192,8 +3192,8 @@ static fvec aut_frebo_sum_omega(
fij[2] = fvec::mask_add(fij[2], mask_inner_1, fij[2],
F23z + F24z - F31z);
- fvec tmp20 = VA * (c_1 - om1234 * om1234) * (c_1 - tspjik) *
- (c_1 - tspijl) * dw21 * w34 * fvec::mask_recip(fvec::undefined(),
+ fvec tmp20 = VA * (c_1 - om1234 * om1234) * (c_1 - tspjik) *
+ (c_1 - tspijl) * dw21 * w34 * fvec::mask_recip(fvec::undefined(),
mask_inner_1, r21mag);
f2x = f2x - tmp20 * r21x;
f2y = f2y - tmp20 * r21y;
@@ -3202,8 +3202,8 @@ static fvec aut_frebo_sum_omega(
f1y = f1y + tmp20 * r21y;
f1z = f1z + tmp20 * r21z;
- fvec tmp21 = VA * (c_1 - om1234 * om1234) * (c_1 - tspjik) *
- (c_1 - tspijl) * w21 * dw34 * fvec::mask_recip(fvec::undefined(),
+ fvec tmp21 = VA * (c_1 - om1234 * om1234) * (c_1 - tspjik) *
+ (c_1 - tspijl) * w21 * dw34 * fvec::mask_recip(fvec::undefined(),
mask_inner_1, r34mag);
f3x = f3x - tmp21 * r34x;
f3y = f3y - tmp21 * r34y;
@@ -3213,35 +3213,35 @@ static fvec aut_frebo_sum_omega(
f4z = f4z + tmp21 * r34z;
// 1 == buf_idx_i, 2 == i, 3 == j, 4 == buf_idx_j
- i_data->force_k_x_buf[buf_idx_i] =
- fvec::mask_add(i_data->force_k_x_buf[buf_idx_i],
+ i_data->force_k_x_buf[buf_idx_i] =
+ fvec::mask_add(i_data->force_k_x_buf[buf_idx_i],
mask_inner_1, i_data->force_k_x_buf[buf_idx_i], f1x);
- i_data->force_k_y_buf[buf_idx_i] =
- fvec::mask_add(i_data->force_k_y_buf[buf_idx_i], mask_inner_1,
+ i_data->force_k_y_buf[buf_idx_i] =
+ fvec::mask_add(i_data->force_k_y_buf[buf_idx_i], mask_inner_1,
i_data->force_k_y_buf[buf_idx_i], f1y);
- i_data->force_k_z_buf[buf_idx_i] =
- fvec::mask_add(i_data->force_k_z_buf[buf_idx_i], mask_inner_1,
+ i_data->force_k_z_buf[buf_idx_i] =
+ fvec::mask_add(i_data->force_k_z_buf[buf_idx_i], mask_inner_1,
i_data->force_k_z_buf[buf_idx_i], f1z);
- i_data->force_i_x =
+ i_data->force_i_x =
fvec::mask_add(i_data->force_i_x, mask_inner_1, i_data->force_i_x, f2x);
- i_data->force_i_y =
+ i_data->force_i_y =
fvec::mask_add(i_data->force_i_y, mask_inner_1, i_data->force_i_y, f2y);
- i_data->force_i_z =
+ i_data->force_i_z =
fvec::mask_add(i_data->force_i_z, mask_inner_1, i_data->force_i_z, f2z);
- j_data->force_i_x =
+ j_data->force_i_x =
fvec::mask_add(j_data->force_i_x, mask_inner_1, j_data->force_i_x, f3x);
- j_data->force_i_y =
+ j_data->force_i_y =
fvec::mask_add(j_data->force_i_y, mask_inner_1, j_data->force_i_y, f3y);
- j_data->force_i_z =
+ j_data->force_i_z =
fvec::mask_add(j_data->force_i_z, mask_inner_1, j_data->force_i_z, f3z);
- j_data->force_k_x_buf[buf_idx_j] =
- fvec::mask_add(j_data->force_k_x_buf[buf_idx_j], mask_inner_1,
+ j_data->force_k_x_buf[buf_idx_j] =
+ fvec::mask_add(j_data->force_k_x_buf[buf_idx_j], mask_inner_1,
j_data->force_k_x_buf[buf_idx_j], f4x);
- j_data->force_k_y_buf[buf_idx_j] =
- fvec::mask_add(j_data->force_k_y_buf[buf_idx_j], mask_inner_1,
+ j_data->force_k_y_buf[buf_idx_j] =
+ fvec::mask_add(j_data->force_k_y_buf[buf_idx_j], mask_inner_1,
j_data->force_k_y_buf[buf_idx_j], f4y);
- j_data->force_k_z_buf[buf_idx_j] =
- fvec::mask_add(j_data->force_k_z_buf[buf_idx_j], mask_inner_1,
+ j_data->force_k_z_buf[buf_idx_j] =
+ fvec::mask_add(j_data->force_k_z_buf[buf_idx_j], mask_inner_1,
j_data->force_k_z_buf[buf_idx_j], f4z);
}
}
@@ -3277,7 +3277,7 @@ static fvec aut_frebo_pi_dh(
}
/*
- We can reuse the aut_frebo_data buffers here to do this calculation very
+ We can reuse the aut_frebo_data buffers here to do this calculation very
cheaply.
*/
static void aut_torsion_vec(
@@ -3350,7 +3350,7 @@ static void aut_torsion_vec(
ivec k = i_data->k_buf[buf_idx_i];
for (int buf_idx_j = 0; buf_idx_j < j_data->buf_len; buf_idx_j++) {
ivec l = j_data->k_buf[buf_idx_j];
- bvec mask_inner_0 = ivec::mask_cmpneq(mask_start, k, l) &
+ bvec mask_inner_0 = ivec::mask_cmpneq(mask_start, k, l) &
j_data->mask_buf[buf_idx_j];
if (! bvec::test_any_set(mask_inner_0)) continue;
fvec del34x = j_data->rikx_buf[buf_idx_j];
@@ -3379,16 +3379,16 @@ static void aut_torsion_vec(
fvec cross321x = del32y * del21z - del32z * del21y;
fvec cross321y = del32z * del21x - del32x * del21z;
fvec cross321z = del32x * del21y - del32y * del21x;
- fvec cross321mag = fvec::sqrt(cross321x * cross321x +
- cross321y * cross321y +
+ fvec cross321mag = fvec::sqrt(cross321x * cross321x +
+ cross321y * cross321y +
cross321z * cross321z);
fvec cross234x = del23y * del34z - del23z * del34y;
fvec cross234y = del23z * del34x - del23x * del34z;
fvec cross234z = del23x * del34y - del23y * del34x;
- fvec cross234mag = fvec::sqrt(cross234x * cross234x +
- cross234y * cross234y +
+ fvec cross234mag = fvec::sqrt(cross234x * cross234x +
+ cross234y * cross234y +
cross234z * cross234z);
- fvec cwnum = cross321x * cross234x + cross321y * cross234y +
+ fvec cwnum = cross321x * cross234x + cross321y * cross234y +
cross321z * cross234z;
fvec cwnom = r21 * r34 * r32 * r32 * sin321 * sin234;
fvec cw = cwnum / cwnom;
@@ -3513,7 +3513,7 @@ static void aut_torsion_vec(
// coordination forces
- fvec fpair = Vtors * dw21 * w23 * w34 * (c_1_0 - tspjik) *
+ fvec fpair = Vtors * dw21 * w23 * w34 * (c_1_0 - tspjik) *
(c_1_0 - tspijl) / r21;
fix = fix - del21x * fpair;
fiy = fiy - del21y * fpair;
@@ -3568,7 +3568,7 @@ static void aut_torsion_vec(
fky = fky - fpair * deljky;
fkz = fkz - fpair * deljkz;
- fcpc = fvec::setzero() - Vtors * w21 * w23 * w34 * (c_1_0 - tspjik) *
+ fcpc = fvec::setzero() - Vtors * w21 * w23 * w34 * (c_1_0 - tspjik) *
dtsijl;
fpair = fcpc * dcjdji / rij;
fix = fix + fpair * del23x;
@@ -3596,35 +3596,35 @@ static void aut_torsion_vec(
// sum per-atom forces into atom force array
- i_data->force_i_x = fvec::mask_add(i_data->force_i_x, mask_inner_0,
+ i_data->force_i_x = fvec::mask_add(i_data->force_i_x, mask_inner_0,
i_data->force_i_x, fix);
- i_data->force_i_y = fvec::mask_add(i_data->force_i_y, mask_inner_0,
+ i_data->force_i_y = fvec::mask_add(i_data->force_i_y, mask_inner_0,
i_data->force_i_y, fiy);
- i_data->force_i_z = fvec::mask_add(i_data->force_i_z, mask_inner_0,
+ i_data->force_i_z = fvec::mask_add(i_data->force_i_z, mask_inner_0,
i_data->force_i_z, fiz);
- i_data->force_j_x = fvec::mask_add(i_data->force_j_x, mask_inner_0,
+ i_data->force_j_x = fvec::mask_add(i_data->force_j_x, mask_inner_0,
i_data->force_j_x, fjx);
- i_data->force_j_y = fvec::mask_add(i_data->force_j_y, mask_inner_0,
+ i_data->force_j_y = fvec::mask_add(i_data->force_j_y, mask_inner_0,
i_data->force_j_y, fjy);
- i_data->force_j_z = fvec::mask_add(i_data->force_j_z, mask_inner_0,
+ i_data->force_j_z = fvec::mask_add(i_data->force_j_z, mask_inner_0,
i_data->force_j_z, fjz);
- i_data->force_k_x_buf[buf_idx_i] =
- fvec::mask_add(i_data->force_k_x_buf[buf_idx_i], mask_inner_0,
+ i_data->force_k_x_buf[buf_idx_i] =
+ fvec::mask_add(i_data->force_k_x_buf[buf_idx_i], mask_inner_0,
i_data->force_k_x_buf[buf_idx_i], fkx);
- i_data->force_k_y_buf[buf_idx_i] =
- fvec::mask_add(i_data->force_k_y_buf[buf_idx_i], mask_inner_0,
+ i_data->force_k_y_buf[buf_idx_i] =
+ fvec::mask_add(i_data->force_k_y_buf[buf_idx_i], mask_inner_0,
i_data->force_k_y_buf[buf_idx_i], fky);
- i_data->force_k_z_buf[buf_idx_i] =
- fvec::mask_add(i_data->force_k_z_buf[buf_idx_i], mask_inner_0,
+ i_data->force_k_z_buf[buf_idx_i] =
+ fvec::mask_add(i_data->force_k_z_buf[buf_idx_i], mask_inner_0,
i_data->force_k_z_buf[buf_idx_i], fkz);
- j_data->force_k_x_buf[buf_idx_j] =
- fvec::mask_add(j_data->force_k_x_buf[buf_idx_j], mask_inner_0,
+ j_data->force_k_x_buf[buf_idx_j] =
+ fvec::mask_add(j_data->force_k_x_buf[buf_idx_j], mask_inner_0,
j_data->force_k_x_buf[buf_idx_j], flx);
- j_data->force_k_y_buf[buf_idx_j] =
- fvec::mask_add(j_data->force_k_y_buf[buf_idx_j], mask_inner_0,
+ j_data->force_k_y_buf[buf_idx_j] =
+ fvec::mask_add(j_data->force_k_y_buf[buf_idx_j], mask_inner_0,
j_data->force_k_y_buf[buf_idx_j], fly);
- j_data->force_k_z_buf[buf_idx_j] =
- fvec::mask_add(j_data->force_k_z_buf[buf_idx_j], mask_inner_0,
+ j_data->force_k_z_buf[buf_idx_j] =
+ fvec::mask_add(j_data->force_k_z_buf[buf_idx_j], mask_inner_0,
j_data->force_k_z_buf[buf_idx_j], flz);
}
}
@@ -3632,11 +3632,11 @@ static void aut_torsion_vec(
/*
* Processes VL elements of the same type itype/jtype for REBO and TORSION
- * interactions. This allows us to reuse the aut_frebo_data buffes in the
+ * interactions. This allows us to reuse the aut_frebo_data buffes in the
* torsion calculaltion.
*/
-static void aut_frebo_batch_of_kind(KernelArgsAIREBOT<flt_t,acc_t> * ka,
- int torflag, int itype, int jtype,
+static void aut_frebo_batch_of_kind(KernelArgsAIREBOT<flt_t,acc_t> * ka,
+ int torflag, int itype, int jtype,
int * i_buf, int * j_buf) {
{ // jump-scope for exceed_limits
AtomAIREBOT<flt_t> * x = ka->x;
@@ -3757,11 +3757,11 @@ static void aut_frebo_batch_of_kind(KernelArgsAIREBOT<flt_t,acc_t> * ka,
fvec Nijconj = c_1_0 + NconjtmpI * NconjtmpI + NconjtmpJ * NconjtmpJ;
fvec dN3[3];
fvec pi_rc = aut_frebo_pi_rc_pd(ka, itype, jtype, Nij, Nji, Nijconj, dN3);
- aut_frebo_N_spline_force(ka, &i_data, itype, jtype, vi, vj, VA, dN3[0],
+ aut_frebo_N_spline_force(ka, &i_data, itype, jtype, vi, vj, VA, dN3[0],
dN3[2], NconjtmpI);
- aut_frebo_N_spline_force(ka, &j_data, jtype, itype, vj, vi, VA, dN3[1],
+ aut_frebo_N_spline_force(ka, &j_data, jtype, itype, vj, vi, VA, dN3[1],
dN3[2], NconjtmpJ);
- fvec pi_dh = aut_frebo_pi_dh(ka, &i_data, &j_data, itype, jtype, vi, vj,
+ fvec pi_dh = aut_frebo_pi_dh(ka, &i_data, &j_data, itype, jtype, vi, vj,
delx, dely, delz, rij, VA, Nij, Nji, Nijconj,
NconjtmpI, NconjtmpJ, fij);
@@ -3835,13 +3835,13 @@ exceed_limits:
int i = i_buf[l];
int j = j_buf[l];
ref_frebo_single_interaction(ka, i, j);
- if (torflag && itype == 0 && jtype == 0)
+ if (torflag && itype == 0 && jtype == 0)
ref_torsion_single_interaction(ka, i, j);
}
}
/*
- Orders the interactions by itype and jtype and passes chunks to the above
+ Orders the interactions by itype and jtype and passes chunks to the above
method.
*/
static void aut_frebo(KernelArgsAIREBOT<flt_t,acc_t> * ka, int torflag) {
@@ -3894,7 +3894,7 @@ static void aut_frebo(KernelArgsAIREBOT<flt_t,acc_t> * ka, int torflag) {
int i = i_buf[itype][jtype][l];
int j = j_buf[itype][jtype][l];
ref_frebo_single_interaction(ka, i, j);
- if (torflag && itype == 0 && jtype == 0)
+ if (torflag && itype == 0 && jtype == 0)
ref_torsion_single_interaction(ka, i, j);
}
}
@@ -3904,7 +3904,7 @@ static void aut_frebo(KernelArgsAIREBOT<flt_t,acc_t> * ka, int torflag) {
/*
* Apply paths in scalar fashion, not crucial for performance.
*/
-static void aut_airebo_lj_force_path(KernelArgsAIREBOT<flt_t,acc_t> * ka,
+static void aut_airebo_lj_force_path(KernelArgsAIREBOT<flt_t,acc_t> * ka,
bvec mask, fvec dC, LennardJonesPathAIREBOT<flt_t> path[fvec::VL]) {
for (int i = 0; i < fvec::VL; i++) {
if (bvec::test_at(mask, i)) {
@@ -3948,11 +3948,11 @@ static ivec aut_airebo_lj_tap_hash_fn_vec(ivec val, ivec attempt) {
}
/*
- * Enter all those (potential) neighbors of i (including 2nd and 3rd degree)
- * into the hash-map. There is no good way to vectorize this, and it does not
+ * Enter all those (potential) neighbors of i (including 2nd and 3rd degree)
+ * into the hash-map. There is no good way to vectorize this, and it does not
* seem time-critical.
*/
-static bool aut_airebo_lj_test_all_paths(KernelArgsAIREBOT<flt_t,acc_t> * ka,
+static bool aut_airebo_lj_test_all_paths(KernelArgsAIREBOT<flt_t,acc_t> * ka,
int i, struct aut_airebo_lj_test_path_result_data * result) {
AtomAIREBOT<flt_t> * x = ka->x;
int * map = ka->map;
@@ -3982,7 +3982,7 @@ static bool aut_airebo_lj_test_all_paths(KernelArgsAIREBOT<flt_t,acc_t> * ka,
int attempt = 0;
int start_hash_slot = aut_lj_tap_hash_fn(j, attempt);
int hash_slot = start_hash_slot;
- while (result->i[hash_slot] == i && result->j[hash_slot] != j &&
+ while (result->i[hash_slot] == i && result->j[hash_slot] != j &&
attempt < OPT_TEST_PATH_SIZE) {
hash_slot = aut_lj_tap_hash_fn(j, ++attempt);
}
@@ -3995,7 +3995,7 @@ static bool aut_airebo_lj_test_all_paths(KernelArgsAIREBOT<flt_t,acc_t> * ka,
if (wj != 1.0) {
if (path_insert_pos >= OPT_TEST_PATH_ITEMS) goto exceed_limits;
result->testpath_idx[hash_slot] = path_insert_pos;
- LennardJonesPathAIREBOT<flt_t> *path =
+ LennardJonesPathAIREBOT<flt_t> *path =
&result->testpath[path_insert_pos++];
path->num = 2;
path->del[0].x = dijx;
@@ -4027,7 +4027,7 @@ static bool aut_airebo_lj_test_all_paths(KernelArgsAIREBOT<flt_t,acc_t> * ka,
int attempt = 0;
int start_hash_slot = aut_lj_tap_hash_fn(k, attempt);
int hash_slot = start_hash_slot;
- while (result->i[hash_slot] == i && result->j[hash_slot] != k &&
+ while (result->i[hash_slot] == i && result->j[hash_slot] != k &&
attempt < OPT_TEST_PATH_SIZE) {
hash_slot = aut_lj_tap_hash_fn(k, ++attempt);
}
@@ -4040,7 +4040,7 @@ static bool aut_airebo_lj_test_all_paths(KernelArgsAIREBOT<flt_t,acc_t> * ka,
if (wj * wk != 1.0) {
if (path_insert_pos >= OPT_TEST_PATH_ITEMS) goto exceed_limits;
result->testpath_idx[hash_slot] = path_insert_pos;
- LennardJonesPathAIREBOT<flt_t> *path =
+ LennardJonesPathAIREBOT<flt_t> *path =
&result->testpath[path_insert_pos++];
path->num = 3;
path->del[0].x = dijx;
@@ -4080,7 +4080,7 @@ static bool aut_airebo_lj_test_all_paths(KernelArgsAIREBOT<flt_t,acc_t> * ka,
int attempt = 0;
int start_hash_slot = aut_lj_tap_hash_fn(l, attempt);
int hash_slot = start_hash_slot;
- while (result->i[hash_slot] == i && result->j[hash_slot] != l &&
+ while (result->i[hash_slot] == i && result->j[hash_slot] != l &&
attempt < OPT_TEST_PATH_SIZE) {
hash_slot = aut_lj_tap_hash_fn(l, ++attempt);
}
@@ -4093,7 +4093,7 @@ static bool aut_airebo_lj_test_all_paths(KernelArgsAIREBOT<flt_t,acc_t> * ka,
if (wj * wk * wl != 1.0) {
if (path_insert_pos >= OPT_TEST_PATH_ITEMS) goto exceed_limits;
result->testpath_idx[hash_slot] = path_insert_pos;
- LennardJonesPathAIREBOT<flt_t> *path =
+ LennardJonesPathAIREBOT<flt_t> *path =
&result->testpath[path_insert_pos++];
path->num = 4;
path->del[0].x = dijx;
@@ -4134,9 +4134,9 @@ exceed_limits:
/*
* Attempt to look up an element in the hash-map.
*/
-static fvec aut_airebo_lj_tap_test_path(KernelArgsAIREBOT<flt_t,acc_t> * ka,
+static fvec aut_airebo_lj_tap_test_path(KernelArgsAIREBOT<flt_t,acc_t> * ka,
struct aut_airebo_lj_test_path_result_data * test_path_result,
- bvec need_search, ivec i_bc, ivec j,
+ bvec need_search, ivec i_bc, ivec j,
LennardJonesPathAIREBOT<flt_t> path[fvec::VL]
) {
const ivec c_i1 = ivec::set1(1);
@@ -4173,13 +4173,13 @@ static fvec aut_airebo_lj_tap_test_path(KernelArgsAIREBOT<flt_t,acc_t> * ka,
found_items = ivec::mask_cmpeq(correct_i, lookup_j, j);
another_attempt = correct_i & ~ found_items;
}
- cij = fvec::mask_gather(cij, found_items, hash_slot,
+ cij = fvec::mask_gather(cij, found_items, hash_slot,
&test_path_result->cij[0], sizeof(flt_t));
bvec need_testpath = fvec::mask_cmplt(found_items, fvec::setzero(), cij);
if (bvec::test_any_set(need_testpath)) {
for (int i = 0; i < fvec::VL; i++) {
if (bvec::test_at(need_testpath, i)) {
- int testpath_idx =
+ int testpath_idx =
test_path_result->testpath_idx[ivec::at(hash_slot, i)];
path[i] = test_path_result->testpath[testpath_idx];
}
@@ -4303,8 +4303,8 @@ static void aut_lj_with_bo(
fvec scale = the_r / rij;
fvec NconjtmpI;
- fvec pij = aut_frebo_pij_pd_2(ka, &i_data, itype, jtype, vi, vj,
- delx * scale, dely * scale, delz * scale,
+ fvec pij = aut_frebo_pij_pd_2(ka, &i_data, itype, jtype, vi, vj,
+ delx * scale, dely * scale, delz * scale,
the_r, wij, VA, &NconjtmpI, fij);
if (i_data.buf_len < 0) goto exceed_limits;
@@ -4313,8 +4313,8 @@ static void aut_lj_with_bo(
fvec rjix = fvec::setzero() - delx;
fvec rjiy = fvec::setzero() - dely;
fvec rjiz = fvec::setzero() - delz;
- fvec pji = aut_frebo_pij_pd_2(ka, &j_data, jtype, itype, vj, vi,
- rjix * scale, rjiy * scale, rjiz * scale,
+ fvec pji = aut_frebo_pij_pd_2(ka, &j_data, jtype, itype, vj, vi,
+ rjix * scale, rjiy * scale, rjiz * scale,
the_r, wij, VA, &NconjtmpJ, fji);
fij[0] = fij[0] - fji[0];
fij[1] = fij[1] - fji[1];
@@ -4375,23 +4375,23 @@ static void aut_lj_with_bo(
fijc[0] = dStb * fij[0];
fijc[1] = dStb * fij[1];
fijc[2] = dStb * fij[2];
- fij[0] = scale * (fijc[0] - (delx * delx * fijc[0] + dely * delx *
+ fij[0] = scale * (fijc[0] - (delx * delx * fijc[0] + dely * delx *
fijc[1] + delz * delx * fijc[2]) / rsq);
- fij[1] = scale * (fijc[1] - (delx * dely * fijc[0] + dely * dely *
+ fij[1] = scale * (fijc[1] - (delx * dely * fijc[0] + dely * dely *
fijc[1] + delz * dely * fijc[2]) / rsq);
- fij[2] = scale * (fijc[2] - (delx * delz * fijc[0] + dely * delz *
+ fij[2] = scale * (fijc[2] - (delx * delz * fijc[0] + dely * delz *
fijc[1] + delz * delz * fijc[2]) / rsq);
- aut_frebo_N_spline_force(ka, &i_data, itype, jtype, vi, vj, dStb * VA,
+ aut_frebo_N_spline_force(ka, &i_data, itype, jtype, vi, vj, dStb * VA,
dN3[0], dN3[2], NconjtmpI);
- aut_frebo_N_spline_force(ka, &j_data, jtype, itype, vj, vi, dStb * VA,
+ aut_frebo_N_spline_force(ka, &j_data, jtype, itype, vj, vi, dStb * VA,
dN3[1], dN3[2], NconjtmpJ);
if (bvec::test_any_set(TijgtTOLmask)) {
- aut_frebo_N_spline_force(ka, &i_data, itype, jtype, vi, vj,
- dStb * VA * sum_omega, dN3_dh[0], dN3_dh[2],
+ aut_frebo_N_spline_force(ka, &i_data, itype, jtype, vi, vj,
+ dStb * VA * sum_omega, dN3_dh[0], dN3_dh[2],
NconjtmpI);
- aut_frebo_N_spline_force(ka, &j_data, jtype, itype, vj, vi,
- dStb * VA * sum_omega, dN3_dh[1], dN3_dh[2],
+ aut_frebo_N_spline_force(ka, &j_data, jtype, itype, vj, vi,
+ dStb * VA * sum_omega, dN3_dh[1], dN3_dh[2],
NconjtmpJ);
}
@@ -4474,7 +4474,7 @@ static void aut_lj_with_bo(
}
exceed_limits:
for (int l = 0; l < fvec::VL; l++) {
- ref_lennard_jones_single_interaction(ka, ivec::at(i, l), ivec::at(j, l),
+ ref_lennard_jones_single_interaction(ka, ivec::at(i, l), ivec::at(j, l),
MORSEFLAG);
}
return;
@@ -4588,9 +4588,9 @@ static void aut_lennard_jones(KernelArgsAIREBOT<flt_t,acc_t> * ka) {
if (jj + (fvec::VL - 1) >= jnum) mask_0 = bvec::only(jnum - jj);
j = ivec::maskz_loadu(mask_0, &neighs[jj]);
fvec x_j, y_j, z_j;
- aut_loadatoms_vec(x, j, &x_j, &y_j, &z_j, &jtype_mask, map, map_i,
+ aut_loadatoms_vec(x, j, &x_j, &y_j, &z_j, &jtype_mask, map, map_i,
c_i1);
- fvec::gather_prefetch0(ivec::mullo(c_i4,
+ fvec::gather_prefetch0(ivec::mullo(c_i4,
ivec::maskz_loadu(bvec::full(), &neighs[jj + fvec::VL])), x);
_mm_prefetch((const char*)&neighs[jj + 2 * fvec::VL], _MM_HINT_T0);
delx = x_i - x_j;
@@ -4675,7 +4675,7 @@ static void aut_lennard_jones(KernelArgsAIREBOT<flt_t,acc_t> * ka) {
if (bvec::test_any_set(need_search)) {
fvec p_rcmax = fvec::mask_blend(jtype_mask, p_rcmax0, p_rcmax1);
#pragma noinline
- cij = aut_airebo_lj_tap_test_path(ka, &test_path_result, need_search,
+ cij = aut_airebo_lj_tap_test_path(ka, &test_path_result, need_search,
i_bc, j, testpath);
}
current_mask = fvec::mask_cmplt(current_mask, c_0_0, cij);
@@ -4734,13 +4734,13 @@ static void aut_lennard_jones(KernelArgsAIREBOT<flt_t,acc_t> * ka) {
ivec itmp = ivec::masku_compress(need_bo_with_jtype, ivec::set1(i));
fvec cijtmp = fvec::masku_compress(need_bo_with_jtype, cij);
bvec insert_mask = bvec::after(num_bo[itype][jtype]);
- i_bo[itype][jtype] = ivec::mask_expand(i_bo[itype][jtype],
+ i_bo[itype][jtype] = ivec::mask_expand(i_bo[itype][jtype],
insert_mask, itmp);
- j_bo[itype][jtype] = ivec::mask_expand(j_bo[itype][jtype],
+ j_bo[itype][jtype] = ivec::mask_expand(j_bo[itype][jtype],
insert_mask, jtmp);
- cij_bo[itype][jtype] = fvec::mask_expand(cij_bo[itype][jtype],
+ cij_bo[itype][jtype] = fvec::mask_expand(cij_bo[itype][jtype],
insert_mask, cijtmp);
- bvec need_path_force_with_jtype = need_bo_with_jtype &
+ bvec need_path_force_with_jtype = need_bo_with_jtype &
need_path_force;
int testpath_end = fvec::VL;
if (bvec::test_any_set(need_path_force_with_jtype)) {
@@ -4758,16 +4758,16 @@ static void aut_lennard_jones(KernelArgsAIREBOT<flt_t,acc_t> * ka) {
}
}
}
- num_bo[itype][jtype] = num_bo[itype][jtype] +
+ num_bo[itype][jtype] = num_bo[itype][jtype] +
bvec::popcnt(need_bo_with_jtype);
if (num_bo[itype][jtype] >= fvec::VL) {
#pragma noinline
- aut_lj_with_bo<MORSEFLAG>(ka, itype, jtype, i_bo[itype][jtype],
+ aut_lj_with_bo<MORSEFLAG>(ka, itype, jtype, i_bo[itype][jtype],
j_bo[itype][jtype], cij_bo[itype][jtype],
testpath_bo[itype][jtype]);
num_bo[itype][jtype] -= fvec::VL;
- insert_mask = bvec::onlyafter(num_bo[itype][jtype],
- bvec::popcnt(need_bo_with_jtype) -
+ insert_mask = bvec::onlyafter(num_bo[itype][jtype],
+ bvec::popcnt(need_bo_with_jtype) -
num_bo[itype][jtype]);
i_bo[itype][jtype] = ivec::masku_compress(insert_mask, itmp);
j_bo[itype][jtype] = ivec::masku_compress(insert_mask, jtmp);
@@ -4797,30 +4797,30 @@ static void aut_lennard_jones(KernelArgsAIREBOT<flt_t,acc_t> * ka) {
fvec fix = fpair * delx + fij[0];
fvec fiy = fpair * dely + fij[1];
fvec fiz = fpair * delz + fij[2];
- result_f_i_x = fvec::mask_add(result_f_i_x, current_mask, result_f_i_x,
+ result_f_i_x = fvec::mask_add(result_f_i_x, current_mask, result_f_i_x,
fix);
- result_f_i_y = fvec::mask_add(result_f_i_y, current_mask, result_f_i_y,
+ result_f_i_y = fvec::mask_add(result_f_i_y, current_mask, result_f_i_y,
fiy);
- result_f_i_z = fvec::mask_add(result_f_i_z, current_mask, result_f_i_z,
+ result_f_i_z = fvec::mask_add(result_f_i_z, current_mask, result_f_i_z,
fiz);
result_eng = fvec::mask_add(result_eng, current_mask, result_eng, evdwl);
ivec j_dbl_idx = ivec::mullo(j, c_i4);
- avec fjx = avec::mask_gather(avec::undefined(), current_mask, j_dbl_idx,
+ avec fjx = avec::mask_gather(avec::undefined(), current_mask, j_dbl_idx,
&ka->result_f[0].x, sizeof(acc_t));
- avec fjy = avec::mask_gather(avec::undefined(), current_mask, j_dbl_idx,
+ avec fjy = avec::mask_gather(avec::undefined(), current_mask, j_dbl_idx,
&ka->result_f[0].y, sizeof(acc_t));
- avec fjz = avec::mask_gather(avec::undefined(), current_mask, j_dbl_idx,
+ avec fjz = avec::mask_gather(avec::undefined(), current_mask, j_dbl_idx,
&ka->result_f[0].z, sizeof(acc_t));
fjx = fjx - fix;
fjy = fjy - fiy;
fjz = fjz - fiz;
- avec::mask_i32loscatter(&ka->result_f[0].x, current_mask, j_dbl_idx, fjx,
+ avec::mask_i32loscatter(&ka->result_f[0].x, current_mask, j_dbl_idx, fjx,
sizeof(acc_t));
- avec::mask_i32loscatter(&ka->result_f[0].y, current_mask, j_dbl_idx, fjy,
+ avec::mask_i32loscatter(&ka->result_f[0].y, current_mask, j_dbl_idx, fjy,
sizeof(acc_t));
- avec::mask_i32loscatter(&ka->result_f[0].z, current_mask, j_dbl_idx, fjz,
+ avec::mask_i32loscatter(&ka->result_f[0].z, current_mask, j_dbl_idx, fjz,
sizeof(acc_t));
if (bvec::test_any_set(need_path_force)) {
diff --git a/src/USER-INTEL/pair_airebo_morse_intel.cpp b/src/USER-INTEL/pair_airebo_morse_intel.cpp
index 9c0f3b8ed0f4089acb2556aac48e0f2ecd473243..21de29e1a7a27a9c2cea8c28ded8872e0fcc57a5 100644
--- a/src/USER-INTEL/pair_airebo_morse_intel.cpp
+++ b/src/USER-INTEL/pair_airebo_morse_intel.cpp
@@ -22,7 +22,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-PairAIREBOMorseIntel::PairAIREBOMorseIntel(LAMMPS *lmp)
+PairAIREBOMorseIntel::PairAIREBOMorseIntel(LAMMPS *lmp)
: PairAIREBOIntel(lmp) {}
/* ----------------------------------------------------------------------
diff --git a/src/USER-INTEL/pair_dpd_intel.cpp b/src/USER-INTEL/pair_dpd_intel.cpp
index 889e1a1da2b95121fc5441e994290765623e4ab1..60361cac7953c17db45cde6683948499fb23dba2 100644
--- a/src/USER-INTEL/pair_dpd_intel.cpp
+++ b/src/USER-INTEL/pair_dpd_intel.cpp
@@ -266,10 +266,10 @@ void PairDPDIntel::eval(const int offload, const int vflag,
if (rngi + jnum > rng_size) {
#ifdef LMP_USE_MKL_RNG
if (sizeof(flt_t) == sizeof(float))
- vsRngGaussian(VSL_RNG_METHOD_GAUSSIAN_ICDF, *my_random, rngi,
+ vsRngGaussian(VSL_RNG_METHOD_GAUSSIAN_ICDF, *my_random, rngi,
(float*)my_rand_buffer, (float)0.0, (float)1.0 );
else
- vdRngGaussian(VSL_RNG_METHOD_GAUSSIAN_ICDF, *my_random, rngi,
+ vdRngGaussian(VSL_RNG_METHOD_GAUSSIAN_ICDF, *my_random, rngi,
(double*)my_rand_buffer, 0.0, 1.0 );
#else
for (int jj = 0; jj < rngi; jj++)
@@ -440,7 +440,7 @@ void PairDPDIntel::settings(int narg, char **arg) {
#pragma omp parallel
{
int tid = omp_get_thread_num();
- vslNewStream(&random_thread[tid], LMP_MKL_RNG,
+ vslNewStream(&random_thread[tid], LMP_MKL_RNG,
seed + comm->me + comm->nprocs * tid );
}
#endif
@@ -557,7 +557,7 @@ void PairDPDIntel::ForceConst<flt_t>::set_ntypes(const int ntypes,
if (ntypes > 0) {
_cop = cop;
memory->create(param,ntypes,ntypes,"fc.param");
- memory->create(rand_buffer_thread, nthreads, max_nbors,
+ memory->create(rand_buffer_thread, nthreads, max_nbors,
"fc.rand_buffer_thread");
memory->create(rngi,nthreads,"fc.param");
for (int i = 0; i < nthreads; i++) rngi[i] = max_nbors;
@@ -595,7 +595,7 @@ void PairDPDIntel::read_restart_settings(FILE *fp)
#pragma omp parallel
{
int tid = omp_get_thread_num();
- vslNewStream(&random_thread[tid], LMP_MKL_RNG,
+ vslNewStream(&random_thread[tid], LMP_MKL_RNG,
seed + comm->me + comm->nprocs * tid );
}
#endif
diff --git a/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp b/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp
index 05ffa2d50eecb8074b57d13efbe28d1edbc5bd84..b36e594f54e8ddb81a28ff0ea96671c99ba12ad1 100644
--- a/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp
+++ b/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp
@@ -303,7 +303,7 @@ void PairLJCharmmCoulCharmmIntel::eval(const int offload, const int vflag,
const flt_t ccr = cut_coulsq - rsq;
const flt_t switch1 = ccr * ccr * inv_denom_coul *
(cut_coulsq + (flt_t)2.0 * rsq - (flt_t)3.0 * cut_coul_innersq);
- forcecoul *= switch1;
+ forcecoul *= switch1;
}
#ifdef INTEL_VMASK
diff --git a/src/USER-INTEL/pair_rebo_intel.cpp b/src/USER-INTEL/pair_rebo_intel.cpp
index 006830a5fa41e004a31bf2a92e8fad2a55703c63..bc7197000bf3e8f94ee067c57f6f1310e2e440a8 100644
--- a/src/USER-INTEL/pair_rebo_intel.cpp
+++ b/src/USER-INTEL/pair_rebo_intel.cpp
@@ -37,6 +37,6 @@ void PairREBOIntel::settings(int narg, char **arg)
//
// this one parameter for C-C interactions is different in REBO vs AIREBO
// see Favata, Micheletti, Ryu, Pugno, Comp Phys Comm (2016)
-
+
PCCf_2_0 = 0.0;
}
diff --git a/src/USER-INTEL/pppm_intel.cpp b/src/USER-INTEL/pppm_intel.cpp
index e187216b62dae2c392ef97ee55f908b513d8eb1b..1fd267be51900d9c61d1112fb648f52491101ee6 100644
--- a/src/USER-INTEL/pppm_intel.cpp
+++ b/src/USER-INTEL/pppm_intel.cpp
@@ -1027,8 +1027,8 @@ void PPPMIntel::allocate()
Create 3D-offset allocation with extra padding for vector writes
------------------------------------------------------------------------- */
-FFT_SCALAR *** PPPMIntel::create3d_offset(FFT_SCALAR ***&array, int n1lo,
- int n1hi, int n2lo, int n2hi,
+FFT_SCALAR *** PPPMIntel::create3d_offset(FFT_SCALAR ***&array, int n1lo,
+ int n1hi, int n2lo, int n2hi,
int n3lo, int n3hi,
const char *name)
{
@@ -1036,7 +1036,7 @@ FFT_SCALAR *** PPPMIntel::create3d_offset(FFT_SCALAR ***&array, int n1lo,
int n2 = n2hi - n2lo + 1;
int n3 = n3hi - n3lo + 1;
- bigint nbytes = ((bigint) sizeof(FFT_SCALAR)) * n1*n2*n3 +
+ bigint nbytes = ((bigint) sizeof(FFT_SCALAR)) * n1*n2*n3 +
INTEL_P3M_ALIGNED_MAXORDER*2;
FFT_SCALAR *data = (FFT_SCALAR *) memory->smalloc(nbytes,name);
nbytes = ((bigint) sizeof(FFT_SCALAR *)) * n1*n2;
diff --git a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp b/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp
index 5d32ef777d475a4bf0ee1551c68c97f99763876b..a8ce87ef111256b4eeb4c5bfa3c50c56c5ade443 100644
--- a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp
+++ b/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp
@@ -280,9 +280,9 @@ void FixNVEManifoldRattle::init()
void FixNVEManifoldRattle::update_var_params()
{
-
+
double *ptr_params = ptr_m->params;
-
+
for( int i = 0; i < nvars; ++i ){
if( is_var[i] ){
tvars[i] = input->variable->find(tstrs[i]);
@@ -293,7 +293,7 @@ void FixNVEManifoldRattle::update_var_params()
if( input->variable->equalstyle(tvars[i]) ){
tstyle[i] = EQUAL;
double new_val = input->variable->compute_equal(tvars[i]);
-
+
ptr_params[i] = new_val;
}else{
error->all(FLERR,
diff --git a/src/USER-MEAMC/pair_meamc.cpp b/src/USER-MEAMC/pair_meamc.cpp
index e35c54352e5375b71ba34d569377808b9abdad8e..7608e42631ce88625bb6e7302fd00c30590d803a 100644
--- a/src/USER-MEAMC/pair_meamc.cpp
+++ b/src/USER-MEAMC/pair_meamc.cpp
@@ -121,7 +121,7 @@ void PairMEAMC::compute(int eflag, int vflag)
n = 0;
for (ii = 0; ii < inum_half; ii++) n += numneigh_half[ilist_half[ii]];
-
+
meam_inst->meam_dens_setup(atom->nmax, nall, n);
double **x = atom->x;
diff --git a/src/USER-MESO/atom_vec_edpd.cpp b/src/USER-MESO/atom_vec_edpd.cpp
index 385e8fd426d36ccf183b56cb71fa0725cebb1a2a..c8f1421512f5e74211e5e768f0cc89e9a6f58f61 100644
--- a/src/USER-MESO/atom_vec_edpd.cpp
+++ b/src/USER-MESO/atom_vec_edpd.cpp
@@ -41,7 +41,7 @@ AtomVecEDPD::AtomVecEDPD(LAMMPS *lmp) : AtomVec(lmp)
size_forward = 3 + 5; // edpd_temp + vest[4]
size_reverse = 3 + 1; // edpd_flux
size_border = 6 + 6; // edpd_temp + edpd_cv + vest[4]
- size_velocity = 3;
+ size_velocity = 3;
size_data_atom = 5 + 2; // we read id + type + edpd_temp + edpd_cv + xyz[3]
size_data_vel = 4;
xcol_data = 5;
@@ -90,7 +90,7 @@ void AtomVecEDPD::grow_reset()
tag = atom->tag; type = atom->type;
mask = atom->mask; image = atom->image;
x = atom->x; v = atom->v; f = atom->f;
- edpd_cv = atom->cv; edpd_temp = atom->edpd_temp; edpd_flux = atom->edpd_flux;
+ edpd_cv = atom->cv; edpd_temp = atom->edpd_temp; edpd_flux = atom->edpd_flux;
vest = atom->vest;
}
@@ -150,7 +150,7 @@ int AtomVecEDPD::pack_comm(int n, int *list, double *buf,
buf[m++] = vest[j][0];
buf[m++] = vest[j][1];
buf[m++] = vest[j][2];
- buf[m++] = vest[j][3];
+ buf[m++] = vest[j][3];
}
} else {
if (domain->triclinic == 0) {
@@ -271,7 +271,7 @@ void AtomVecEDPD::unpack_comm(int n, int first, double *buf)
vest[i][0] = buf[m++];
vest[i][1] = buf[m++];
vest[i][2] = buf[m++];
- vest[i][3] = buf[m++];
+ vest[i][3] = buf[m++];
}
}
@@ -354,7 +354,7 @@ int AtomVecEDPD::pack_border(int n, int *list, double *buf,
buf[m++] = vest[j][0];
buf[m++] = vest[j][1];
buf[m++] = vest[j][2];
- buf[m++] = vest[j][3];
+ buf[m++] = vest[j][3];
}
} else {
if (domain->triclinic == 0) {
@@ -663,7 +663,7 @@ int AtomVecEDPD::pack_restart(int i, double *buf)
buf[m++] = vest[i][0];
buf[m++] = vest[i][1];
buf[m++] = vest[i][2];
- buf[m++] = vest[i][3];
+ buf[m++] = vest[i][3];
if (atom->nextra_restart)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
@@ -697,14 +697,14 @@ int AtomVecEDPD::unpack_restart(double *buf)
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
-
+
edpd_temp[nlocal] = buf[m++];
edpd_cv[nlocal]= buf[m++];
vest[nlocal][0] = buf[m++];
vest[nlocal][1] = buf[m++];
vest[nlocal][2] = buf[m++];
vest[nlocal][3] = buf[m++];
-
+
double **extra = atom->extra;
if (atom->nextra_store) {
int size = static_cast<int> (buf[0]) - m;
diff --git a/src/USER-MESO/atom_vec_mdpd.cpp b/src/USER-MESO/atom_vec_mdpd.cpp
index 0d2350a645c260f8d0e81abad6c55263edf6bf15..1d81bd2c39a0693d0becbf634800d1db32ec899f 100644
--- a/src/USER-MESO/atom_vec_mdpd.cpp
+++ b/src/USER-MESO/atom_vec_mdpd.cpp
@@ -527,7 +527,7 @@ int AtomVecMDPD::pack_border_vel(int n, int *list, double *buf, int pbc_flag,
} else {
buf[m++] = v[j][0];
buf[m++] = v[j][1];
- buf[m++] = v[j][2];
+ buf[m++] = v[j][2];
buf[m++] = rho[j];
buf[m++] = vest[j][0];
buf[m++] = vest[j][1];
diff --git a/src/USER-MESO/atom_vec_tdpd.cpp b/src/USER-MESO/atom_vec_tdpd.cpp
index 34f2b1a0310992142445a90f447b8155078a3427..6733e3e4df51b3d1dddf7ee0691ba771929754f8 100644
--- a/src/USER-MESO/atom_vec_tdpd.cpp
+++ b/src/USER-MESO/atom_vec_tdpd.cpp
@@ -46,9 +46,9 @@ AtomVecTDPD::AtomVecTDPD(LAMMPS *lmp) : AtomVec(lmp)
size_forward = 3 + cc_species + 3; //vest[3]
size_reverse = 3 + cc_species;
size_border = 6 + cc_species + 3; //vest[3]
- size_velocity = 3;
+ size_velocity = 3;
// for data_atom, we read id + type + xyz[3] + cc[i] where i=1,cc_species
- size_data_atom = 5 + cc_species;
+ size_data_atom = 5 + cc_species;
size_data_vel = 4;
xcol_data = 3;
@@ -73,7 +73,7 @@ void AtomVecTDPD::process_args(int narg, char **arg)
size_forward = 3 + cc_species + 3;
size_reverse = 3 + cc_species;
size_border = 6 + cc_species + 3;
- size_data_atom = 5 + cc_species;
+ size_data_atom = 5 + cc_species;
}
/* ----------------------------------------------------------------------
@@ -171,7 +171,7 @@ int AtomVecTDPD::pack_comm(int n, int *list, double *buf,
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
-
+
for(k = 0; k < cc_species; k++)
buf[m++] = cc[j][k];
@@ -194,7 +194,7 @@ int AtomVecTDPD::pack_comm(int n, int *list, double *buf,
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
-
+
for(k = 0; k < cc_species; k++)
buf[m++] = cc[j][k];
@@ -224,7 +224,7 @@ int AtomVecTDPD::pack_comm_vel(int n, int *list, double *buf,
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
-
+
for(k = 0; k < cc_species; k++)
buf[m++] = cc[j][k];
@@ -328,7 +328,7 @@ void AtomVecTDPD::unpack_comm_vel(int n, int first, double *buf)
v[i][2] = buf[m++];
for(int k = 0; k < cc_species; k++)
cc[i][k] = buf[m++];
-
+
vest[i][0] = buf[m++];
vest[i][1] = buf[m++];
vest[i][2] = buf[m++];
@@ -415,7 +415,7 @@ int AtomVecTDPD::pack_border(int n, int *list, double *buf,
buf[m++] = ubuf(mask[j]).d;
for(int k = 0; k < cc_species; k++)
buf[m++] = cc[j][k];
-
+
buf[m++] = vest[j][0];
buf[m++] = vest[j][1];
buf[m++] = vest[j][2];
diff --git a/src/USER-MESO/fix_edpd_source.cpp b/src/USER-MESO/fix_edpd_source.cpp
index 3ee7e8e2911d92667ebc24ff475f5d6b3a976c22..fb8fecdcdf470c3beb7edde514b2e2c187088b8e 100644
--- a/src/USER-MESO/fix_edpd_source.cpp
+++ b/src/USER-MESO/fix_edpd_source.cpp
@@ -33,11 +33,11 @@ using namespace FixConst;
FixEDPDSource::FixEDPDSource(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
- if (strcmp(style,"edpd/source") != 0 && narg < 4)
+ if (strcmp(style,"edpd/source") != 0 && narg < 4)
error->all(FLERR,"Illegal fix edpd/source command");
int iarg = 3;
-
+
if (strcmp(arg[iarg],"sphere") == 0) option = 0;
else if (strcmp(arg[iarg],"cuboid") == 0) option = 1;
else error->all(FLERR,"Illegal fix edpd/source command");
@@ -55,10 +55,10 @@ FixEDPDSource::FixEDPDSource(LAMMPS *lmp, int narg, char **arg) :
if (narg != 11 ) error->all(FLERR,"Illegal fix edpd/edpd command (7 args for cuboid)");
center[0] = force->numeric(FLERR,arg[iarg++]);
center[1] = force->numeric(FLERR,arg[iarg++]);
- center[2] = force->numeric(FLERR,arg[iarg++]);
+ center[2] = force->numeric(FLERR,arg[iarg++]);
dLx = force->numeric(FLERR,arg[iarg++]);
dLy = force->numeric(FLERR,arg[iarg++]);
- dLz = force->numeric(FLERR,arg[iarg++]);
+ dLz = force->numeric(FLERR,arg[iarg++]);
value = force->numeric(FLERR,arg[iarg++]);
}
else error->all(FLERR,"Illegal fix edpd/source command");
diff --git a/src/USER-MESO/fix_mvv_dpd.cpp b/src/USER-MESO/fix_mvv_dpd.cpp
index 299f453ea7c308c28d489662c00a8d716da3c881..c1c4f203f1cc0547fd87b4c46d7b822b0308e435 100644
--- a/src/USER-MESO/fix_mvv_dpd.cpp
+++ b/src/USER-MESO/fix_mvv_dpd.cpp
@@ -12,8 +12,8 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
- This is a time integrator for position and velocity (x and v) using the
- modified velocity-Verlet (MVV) algorithm.
+ This is a time integrator for position and velocity (x and v) using the
+ modified velocity-Verlet (MVV) algorithm.
Setting verlet = 0.5 recovers the standard velocity-Verlet algorithm.
Contributing author: Zhen Li (Brown University)
@@ -90,7 +90,7 @@ void FixMvvDPD::initial_integrate(int vflag)
if (mask[i] & groupbit) {
if (rmass) dtfm = dtf / rmass[i];
else dtfm = dtf / mass[type[i]];
-
+
vest[i][0] = v[i][0] + dtfm * f[i][0];
vest[i][1] = v[i][1] + dtfm * f[i][1];
vest[i][2] = v[i][2] + dtfm * f[i][2];
diff --git a/src/USER-MESO/fix_mvv_edpd.cpp b/src/USER-MESO/fix_mvv_edpd.cpp
index fe801d6d36cf80ae85ed71acee7f1940169f1c5b..12c8bbcafbbe0cb9e465ffc5cc9b5c50474023ea 100644
--- a/src/USER-MESO/fix_mvv_edpd.cpp
+++ b/src/USER-MESO/fix_mvv_edpd.cpp
@@ -12,8 +12,8 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
- This is a time integrator for position, velocity and temperature (x,
- v and edpd_T) using the modified velocity-Verlet (MVV) algorithm.
+ This is a time integrator for position, velocity and temperature (x,
+ v and edpd_T) using the modified velocity-Verlet (MVV) algorithm.
Setting verlet = 0.5 recovers the standard velocity-Verlet algorithm.
Contributing author: Zhen Li (Brown University)
@@ -21,11 +21,11 @@
Please cite the related publication:
Z. Li, Y.-H. Tang, H. Lei, B. Caswell and G.E. Karniadakis. "Energy-
- conserving dissipative particle dynamics with temperature-dependent
+ conserving dissipative particle dynamics with temperature-dependent
properties". Journal of Computational Physics, 2014, 265: 113-127.
-
+
Z. Li, Y.-H. Tang , X. Li and G.E. Karniadakis. "Mesoscale modeling of
- phase transition dynamics of thermoresponsive polymers". Chemical
+ phase transition dynamics of thermoresponsive polymers". Chemical
Communications, 2015, 51: 11038-11040.
------------------------------------------------------------------------- */
@@ -101,7 +101,7 @@ void FixMvvEDPD::initial_integrate(int vflag)
if (mask[i] & groupbit) {
if (rmass) dtfm = dtf / rmass[i];
else dtfm = dtf / mass[type[i]];
-
+
dtT = 0.5 * dtv / edpd_cv[i];
vest[i][0] = v[i][0] + dtfm * f[i][0];
diff --git a/src/USER-MESO/fix_mvv_tdpd.cpp b/src/USER-MESO/fix_mvv_tdpd.cpp
index 382ce9033abee6be19caf3be59e4895d0c8ab61f..58832e084654f8b938350f0819389c0876bf067d 100644
--- a/src/USER-MESO/fix_mvv_tdpd.cpp
+++ b/src/USER-MESO/fix_mvv_tdpd.cpp
@@ -12,15 +12,15 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
- This is a time integrator for position, velocity and concentration (x,
- v and cc) using the modified velocity-Verlet (MVV) algorithm.
+ This is a time integrator for position, velocity and concentration (x,
+ v and cc) using the modified velocity-Verlet (MVV) algorithm.
Setting verlet = 0.5 recovers the standard velocity-Verlet algorithm.
Contributing author: Zhen Li (Brown University)
Email: zhen_li@brown.edu
Please cite the related publication:
- Z. Li, A. Yazdani, A. Tartakovsky and G.E. Karniadakis. "Transport
+ Z. Li, A. Yazdani, A. Tartakovsky and G.E. Karniadakis. "Transport
dissipative particle dynamics model for mesoscopic advection-diffusion
-reaction problems". The Journal of Chemical Physics, 2015, 143: 014101.
------------------------------------------------------------------------- */
@@ -98,7 +98,7 @@ void FixMvvTDPD::initial_integrate(int vflag)
if (mask[i] & groupbit) {
if (rmass) dtfm = dtf / rmass[i];
else dtfm = dtf / mass[type[i]];
-
+
vest[i][0] = v[i][0] + dtfm * f[i][0];
vest[i][1] = v[i][1] + dtfm * f[i][1];
vest[i][2] = v[i][2] + dtfm * f[i][2];
diff --git a/src/USER-MESO/fix_tdpd_source.cpp b/src/USER-MESO/fix_tdpd_source.cpp
index 3dfeba47878ca7c9afbc26df1f5f5ab68d73b3df..c58dff76be3915b8a5c313cf6e144cf351715bd5 100644
--- a/src/USER-MESO/fix_tdpd_source.cpp
+++ b/src/USER-MESO/fix_tdpd_source.cpp
@@ -33,12 +33,12 @@ using namespace FixConst;
FixTDPDSource::FixTDPDSource(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
- if (strcmp(style,"tdpd/source") != 0 && narg < 4)
+ if (strcmp(style,"tdpd/source") != 0 && narg < 4)
error->all(FLERR,"Illegal fix tdpd/source command");
int iarg = 3;
cc_index = force->inumeric(FLERR,arg[iarg++]);
-
+
if (strcmp(arg[iarg],"sphere") == 0) option = 0;
else if (strcmp(arg[iarg],"cuboid") == 0) option = 1;
else error->all(FLERR,"Illegal fix tdpd/source command");
@@ -56,10 +56,10 @@ FixTDPDSource::FixTDPDSource(LAMMPS *lmp, int narg, char **arg) :
if (narg != 12 ) error->all(FLERR,"Illegal fix tdpd/edpd command (7 args for cuboid)");
center[0] = force->numeric(FLERR,arg[iarg++]);
center[1] = force->numeric(FLERR,arg[iarg++]);
- center[2] = force->numeric(FLERR,arg[iarg++]);
+ center[2] = force->numeric(FLERR,arg[iarg++]);
dLx = force->numeric(FLERR,arg[iarg++]);
dLy = force->numeric(FLERR,arg[iarg++]);
- dLz = force->numeric(FLERR,arg[iarg++]);
+ dLz = force->numeric(FLERR,arg[iarg++]);
value = force->numeric(FLERR,arg[iarg++]);
}
else error->all(FLERR,"Illegal fix tdpd/source command");
diff --git a/src/USER-MESO/pair_edpd.cpp b/src/USER-MESO/pair_edpd.cpp
index c1c100db43ce71395c5cc5cea16fc5b93acc979d..64d29cb65df27be31a658d5a4aeb5241090b9acf 100644
--- a/src/USER-MESO/pair_edpd.cpp
+++ b/src/USER-MESO/pair_edpd.cpp
@@ -65,7 +65,7 @@ static const char cite_pair_edpd[] =
PairEDPD::PairEDPD(LAMMPS *lmp) : Pair(lmp)
{
- if (lmp->citeme) lmp->citeme->add(cite_pair_edpd);
+ if (lmp->citeme) lmp->citeme->add(cite_pair_edpd);
writedata = 1;
random = NULL;
randomT = NULL;
@@ -116,7 +116,7 @@ void PairEDPD::compute(int eflag, int vflag)
int newton_pair = force->newton_pair;
double dtinvsqrt = 1.0/sqrt(update->dt);
double kboltz = 1.0;
-
+
int inum = list->inum;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
@@ -166,12 +166,12 @@ void PairEDPD::compute(int eflag, int vflag)
double power_d = power[itype][jtype];
if(power_flag){
- double factor = 1.0;
+ double factor = 1.0;
for(int k = 0; k < 4; k++)
factor += sc[itype][jtype][k]*T_pow[k];
power_d *= factor;
}
-
+
power_d = MAX(0.01,power_d);
double wc = 1.0 - r/cut[itype][jtype];
wc = MAX(0.0,MIN(1.0,wc));
@@ -198,9 +198,9 @@ void PairEDPD::compute(int eflag, int vflag)
wrT = pow(wrT, 0.5*powerT[itype][jtype]);
double randnumT = randomT->gaussian();
randnumT = MAX(-5.0,MIN(randnum,5.0));
-
+
double kappaT = kappa[itype][jtype];
- if(kappa_flag) {
+ if(kappa_flag) {
double factor = 1.0;
for(int k = 0; k < 4; k++)
factor += kc[itype][jtype][k]*T_pow[k];
@@ -209,7 +209,7 @@ void PairEDPD::compute(int eflag, int vflag)
double kij = cv[i]*cv[j]*kappaT * T_ij*T_ij;
double alphaij = sqrt(2.0*kboltz*kij);
-
+
dQc = kij * wrT*wrT * ( T[j] - T[i] )/(T[i]*T[j]);
dQd = wr*wr*( GammaIJ * vijeij*vijeij - SigmaIJ*SigmaIJ/mass[itype] ) - SigmaIJ * wr *vijeij *randnum;
dQd /= (cv[i]+cv[j]);
@@ -217,7 +217,7 @@ void PairEDPD::compute(int eflag, int vflag)
Q[i] += (dQc + dQd + dQr );
}
//-----------------------------------------------------------
-
+
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
@@ -247,7 +247,7 @@ void PairEDPD::allocate()
int i,j;
allocated = 1;
int n = atom->ntypes;
-
+
memory->create(setflag,n+1,n+1,"pair:setflag");
for (i = 1; i <= n; i++)
for (j = i; j <= n; j++)
@@ -285,8 +285,8 @@ void PairEDPD::settings(int narg, char **arg)
}
delete random;
random = new RanMars(lmp,(seed + comm->me) % 900000000);
- randomT = new RanMars(lmp,(2*seed + comm->me) % 900000000);
-
+ randomT = new RanMars(lmp,(2*seed + comm->me) % 900000000);
+
// reset cutoffs that have been explicitly set
if (allocated) {
@@ -341,7 +341,7 @@ void PairEDPD::coeff(int narg, char **arg)
memory->create(kc,n+1,n+1,4,"pair:kc");
} else error->all(FLERR,"Illegal pair edpd coefficients");
}
-
+
int count = 0;
for (int i = ilo; i <= ihi; i++)
for (int j = MAX(jlo,i); j <= jhi; j++) {
@@ -352,15 +352,15 @@ void PairEDPD::coeff(int narg, char **arg)
kappa[i][j] = kappa_one;
powerT[i][j]= powerT_one;
cutT[i][j] = cutT_one;
-
- if(power_flag)
+
+ if(power_flag)
for (int k = 0; k < 4; k++)
sc[i][j][k] = sc_one[k];
if(kappa_flag)
for (int k = 0; k < 4; k++)
kc[i][j][k] = kc_one[k];
-
+
setflag[i][j] = 1;
count++;
}
@@ -401,7 +401,7 @@ double PairEDPD::init_one(int i, int j)
power[j][i] = power[i][j];
kappa[j][i] = kappa[i][j];
powerT[j][i]= powerT[i][j];
-
+
if(power_flag)
for (int k = 0; k < 4; k++)
sc[j][i][k] = sc[i][j][k];
@@ -409,7 +409,7 @@ double PairEDPD::init_one(int i, int j)
if(kappa_flag)
for (int k = 0; k < 4; k++)
kc[j][i][k] = kc[i][j][k];
-
+
return cut[i][j];
}
@@ -435,7 +435,7 @@ void PairEDPD::write_restart(FILE *fp)
if(power_flag)
for (int k = 0; k < 4; k++)
fwrite(&sc[i][j][k],sizeof(double),1,fp);
-
+
if(kappa_flag)
for (int k = 0; k < 4; k++)
fwrite(&kc[i][j][k],sizeof(double),1,fp);
@@ -470,7 +470,7 @@ void PairEDPD::read_restart(FILE *fp)
if(power_flag)
for (int k = 0; k < 4; k++)
fread(&sc[i][j][k],sizeof(double),1,fp);
-
+
if(kappa_flag)
for (int k = 0; k < 4; k++)
fread(&kc[i][j][k],sizeof(double),1,fp);
@@ -480,12 +480,12 @@ void PairEDPD::read_restart(FILE *fp)
MPI_Bcast(&power[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&kappa[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&powerT[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&powerT[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cutT[i][j],1,MPI_DOUBLE,0,world);
if(power_flag)
for (int k = 0; k < 4; k++)
MPI_Bcast(&sc[i][j][k],1,MPI_DOUBLE,0,world);
-
+
if(kappa_flag)
for (int k = 0; k < 4; k++)
MPI_Bcast(&kc[i][j][k],1,MPI_DOUBLE,0,world);
diff --git a/src/USER-MESO/pair_mdpd.cpp b/src/USER-MESO/pair_mdpd.cpp
index ba72304ddb61ac34a3f4561c5786b48aae340f67..1b8cd45be98d06900975243bf4aad62eaf2791f7 100644
--- a/src/USER-MESO/pair_mdpd.cpp
+++ b/src/USER-MESO/pair_mdpd.cpp
@@ -53,7 +53,7 @@ static const char cite_pair_mdpd[] =
PairMDPD::PairMDPD(LAMMPS *lmp) : Pair(lmp)
{
if (lmp->citeme) lmp->citeme->add(cite_pair_mdpd);
-
+
writedata = 1;
random = NULL;
}
@@ -139,7 +139,7 @@ void PairMDPD::compute(int eflag, int vflag)
delvy = vytmp - v[j][1];
delvz = vztmp - v[j][2];
dot = delx*delvx + dely*delvy + delz*delvz;
-
+
wc = 1.0 - r/cut[itype][jtype];
wc_r = 1.0 - r/cut_r[itype][jtype];
wc_r = MAX(wc_r,0.0);
diff --git a/src/USER-MESO/pair_mdpd_rhosum.cpp b/src/USER-MESO/pair_mdpd_rhosum.cpp
index d2a4ad33d84c3860032348e4651d93ae50481125..ecfc9d5c00eb3d4f7ba4c86848d631b0805262f4 100644
--- a/src/USER-MESO/pair_mdpd_rhosum.cpp
+++ b/src/USER-MESO/pair_mdpd_rhosum.cpp
@@ -12,10 +12,10 @@
------------------------------------------------------------------------- */
/*-----------------------------------------------------------------------
- This is a Child Class PairMDPD for taking care of density summation
+ This is a Child Class PairMDPD for taking care of density summation
before the force calculation.
The code uses 3D Lucy kernel, it can be modified for other kernels.
-
+
Contributing author: Zhen Li (Brown University)
------------------------------------------------------------------------- */
@@ -125,7 +125,7 @@ void PairMDPDRhoSum::compute(int eflag, int vflag) {
wf = 2.0889086280811262819e0 / (h * h * h);
rho[i] = 0;
}
-
+
// add density at each atom via kernel function overlap
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
diff --git a/src/USER-MESO/pair_tdpd.cpp b/src/USER-MESO/pair_tdpd.cpp
index 42904d2b5a168a5148fe4bd74fad73b436f5a5d6..71dbaaba83e23bbe91f1404fb0422599adbb6851 100644
--- a/src/USER-MESO/pair_tdpd.cpp
+++ b/src/USER-MESO/pair_tdpd.cpp
@@ -176,7 +176,7 @@ void PairTDPD::compute(int eflag, int vflag)
}
}
//-----------------------------------------------------------
-
+
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
@@ -205,7 +205,7 @@ void PairTDPD::allocate()
int i,j;
allocated = 1;
int n = atom->ntypes;
-
+
memory->create(setflag,n+1,n+1,"pair:setflag");
for (i = 1; i <= n; i++)
for (j = i; j <= n; j++)
@@ -220,7 +220,7 @@ void PairTDPD::allocate()
memory->create(sigma,n+1,n+1,"pair:sigma");
memory->create(power,n+1,n+1,"pair:power");
memory->create(kappa,n+1,n+1,cc_species,"pair:kappa");
- memory->create(epsilon,n+1,n+1,cc_species,"pair:epsilon");
+ memory->create(epsilon,n+1,n+1,cc_species,"pair:epsilon");
memory->create(powercc,n+1,n+1,cc_species,"pair:powercc");
for (i = 0; i <= atom->ntypes; i++)
diff --git a/src/USER-MISC/angle_dipole.cpp b/src/USER-MISC/angle_dipole.cpp
index e393b3717bfd7e031a2c6620762c3aeed9928e2f..1e8c0e18fb1ba99594e9ac19231364540dad6a6c 100644
--- a/src/USER-MISC/angle_dipole.cpp
+++ b/src/USER-MISC/angle_dipole.cpp
@@ -97,14 +97,14 @@ void AngleDipole::compute(int eflag, int vflag)
delTx = tangle * (dely*mu[iDip][2] - delz*mu[iDip][1]);
delTy = tangle * (delz*mu[iDip][0] - delx*mu[iDip][2]);
delTz = tangle * (delx*mu[iDip][1] - dely*mu[iDip][0]);
-
+
torque[iDip][0] += delTx;
torque[iDip][1] += delTy;
torque[iDip][2] += delTz;
-
+
// Force couple that counterbalances dipolar torque
fx = dely*delTz - delz*delTy; // direction (fi): - r x (-T)
- fy = delz*delTx - delx*delTz;
+ fy = delz*delTx - delx*delTz;
fz = delx*delTy - dely*delTx;
fmod = sqrt(delTx*delTx + delTy*delTy + delTz*delTz) / r; // magnitude
@@ -117,11 +117,11 @@ void AngleDipole::compute(int eflag, int vflag)
fj[0] = -fi[0];
fj[1] = -fi[1];
fj[2] = -fi[2];
-
+
f[iDip][0] += fj[0];
f[iDip][1] += fj[1];
f[iDip][2] += fj[2];
-
+
f[iRef][0] += fi[0];
f[iRef][1] += fi[1];
f[iRef][2] += fi[2];
diff --git a/src/USER-MISC/dihedral_fourier.cpp b/src/USER-MISC/dihedral_fourier.cpp
index 403f63341afcc679adfa3cbc4699b6fd7970042b..fff10fde11b3c10b4c69294e9b0579869ff807a3 100644
--- a/src/USER-MISC/dihedral_fourier.cpp
+++ b/src/USER-MISC/dihedral_fourier.cpp
@@ -38,7 +38,7 @@ using namespace MathConst;
/* ---------------------------------------------------------------------- */
-DihedralFourier::DihedralFourier(LAMMPS *lmp) : Dihedral(lmp)
+DihedralFourier::DihedralFourier(LAMMPS *lmp) : Dihedral(lmp)
{
writedata = 1;
}
diff --git a/src/USER-MISC/dihedral_nharmonic.cpp b/src/USER-MISC/dihedral_nharmonic.cpp
index 8958340bb611adad706f6abd86ccfe7dcb9aad80..abb5904b6af55773b43a505263a457c2e92c0a6b 100644
--- a/src/USER-MISC/dihedral_nharmonic.cpp
+++ b/src/USER-MISC/dihedral_nharmonic.cpp
@@ -277,7 +277,7 @@ void DihedralNHarmonic::coeff(int narg, char **arg)
if (narg < 4 ) error->all(FLERR,"Incorrect args for dihedral coefficients");
int n = force->inumeric(FLERR,arg[1]);
- if (narg != n + 2)
+ if (narg != n + 2)
error->all(FLERR,"Incorrect args for dihedral coefficients");
if (!allocated) allocate();
diff --git a/src/USER-MISC/dihedral_spherical.cpp b/src/USER-MISC/dihedral_spherical.cpp
index c3345453c9a9e76668bc593ab28debf31faf608f..77fa885b7a44bf7ecf87d64f504f1da08ef35916 100644
--- a/src/USER-MISC/dihedral_spherical.cpp
+++ b/src/USER-MISC/dihedral_spherical.cpp
@@ -13,7 +13,7 @@
/* ----------------------------------------------------------------------
Contributing author: Andrew Jewett (Caltech)
- [ using code borrowed from Loukas D. Peristeras (Scienomics SARL)
+ [ using code borrowed from Loukas D. Peristeras (Scienomics SARL)
and Paul Crozier (SNL) ]
------------------------------------------------------------------------- */
@@ -168,9 +168,9 @@ void DihedralSpherical::compute(int eflag, int vflag)
//
// proj12on23 proj34on23
// ---------> ----------->
- //
- //
- //
+ //
+ //
+ //
// x[i2] x[i3]
// . __@----------vb23-------->@ .
// /|\ /| \ |
@@ -364,9 +364,9 @@ void DihedralSpherical::compute(int eflag, int vflag)
//where d=0,1,2 corresponds to x,y,z (g_dim==3)
double L12sqr = dot3(vb12, vb12);
- double L12 = sqrt(L12sqr);
+ double L12 = sqrt(L12sqr);
double L34sqr = dot3(vb34, vb34);
- double L34 = sqrt(L34sqr);
+ double L34 = sqrt(L34sqr);
double inv_L12sqr = 0.0;
double inv_L12 = 0.0;
double inv_L34sqr = 0.0;
@@ -400,7 +400,7 @@ void DihedralSpherical::compute(int eflag, int vflag)
* . . proj23on34
* . .
* . .
- * x[i2] . _./ x[i3]
+ * x[i2] . _./ x[i3]
* __@----------vb23-------->@
* /| / \ \
* / theta1 theta2 \
@@ -469,7 +469,7 @@ void DihedralSpherical::compute(int eflag, int vflag)
double m_du_dphi = 0.0; // m_du_dphi = -du / d phi
u = CalcGeneralizedForces(type,
- phi, theta1, theta2,
+ phi, theta1, theta2,
&m_du_dth1, &m_du_dth2, &m_du_dphi);
if (eflag) edihedral = u;
@@ -600,7 +600,7 @@ CalcGeneralizedForces(int type,
energy += Ccoeff[i][j] * (phi_offset[i][j] - cp) *
(theta1_offset[i][j] - ct1) *
(theta2_offset[i][j] - ct2);
-
+
// Forces:
*m_du_dphi += -Ccoeff[i][j] * sp * phi_mult[i][j] *
(theta1_offset[i][j] - ct1) *
@@ -609,11 +609,11 @@ CalcGeneralizedForces(int type,
*m_du_dth1 += -Ccoeff[i][j] * (phi_offset[i][j] - cp) *
st1 * theta1_mult[i][j] *
(theta2_offset[i][j] - ct2);
-
+
*m_du_dth2 += -Ccoeff[i][j] * (phi_offset[i][j] - cp) *
(theta1_offset[i][j] - ct1) *
st2 * theta2_mult[i][j];
-
+
// Things to consider later:
// To speed up the computation, one could try to simplify the expansion:
@@ -622,13 +622,13 @@ CalcGeneralizedForces(int type,
// cos(L*theta2), sin(L*theta2), and
// cos(M*phi), sin(M*phi)
// Also: For integer K,L,M, the trig functions cos(M*phi) and sin(M*phi)
- // can be calculated more efficiently using polynomials of
+ // can be calculated more efficiently using polynomials of
// cos(phi) and sin(phi)
} //for (int j = 0; j < nterms[i]; j++) {
return energy;
-
+
} //CalcGeneralizedForces()
@@ -869,7 +869,7 @@ void DihedralSpherical::write_data(FILE *fp)
// double theta2 = acos(ct2);
//
// double u = CalcGeneralizedForces(type,
-// phi, theta1, theta2,
+// phi, theta1, theta2,
// &m_du_dth1, &m_du_dth2, &m_du_dphi);
// return u;
//}
diff --git a/src/USER-MISC/fix_ipi.cpp b/src/USER-MISC/fix_ipi.cpp
index 8326ef6667b9c70df103d5c4eca9ab7927c0490d..bacce679019beca073158a3f6a215134b2d0dfaa 100644
--- a/src/USER-MISC/fix_ipi.cpp
+++ b/src/USER-MISC/fix_ipi.cpp
@@ -219,7 +219,7 @@ FixIPI::FixIPI(LAMMPS *lmp, int narg, char **arg) :
// create instance of Irregular class
irregular = new Irregular(lmp);
-
+
// yet, we have not assigned a socket
socketflag = 0;
}
diff --git a/src/USER-MISC/fix_ttm_mod.cpp b/src/USER-MISC/fix_ttm_mod.cpp
index d2fc6ac9012bdcc3b02b29d9e1d03e7e4775e509..b7261b85d4103a63cbdf186f7d1d16d32b59c4ed 100644
--- a/src/USER-MISC/fix_ttm_mod.cpp
+++ b/src/USER-MISC/fix_ttm_mod.cpp
@@ -95,7 +95,7 @@ FixTTMMod::FixTTMMod(LAMMPS *lmp, int narg, char **arg) :
nznodes = force->inumeric(FLERR,arg[7]);
if (nxnodes <= 0 || nynodes <= 0 || nznodes <= 0)
error->all(FLERR,"Fix ttm/mod number of nodes must be > 0");
-
+
FILE *fpr = force->open_potential(arg[8]);
if (fpr == NULL) {
char str[128];
diff --git a/src/USER-MISC/pair_edip.cpp b/src/USER-MISC/pair_edip.cpp
index bd58b746b8ca1aa672bbef6c5b4ca70f2e1a730e..5f83af7f497809fd18c686dbcd6fc38fde7a098f 100644
--- a/src/USER-MISC/pair_edip.cpp
+++ b/src/USER-MISC/pair_edip.cpp
@@ -800,7 +800,7 @@ void PairEDIP::coeff(int narg, char **arg)
if (nelements != 1)
error->all(FLERR,"Pair style edip only supports single element potentials");
-
+
// read potential file and initialize potential parameters
read_file(arg[2]);
diff --git a/src/USER-MISC/pair_momb.cpp b/src/USER-MISC/pair_momb.cpp
index 98339bf60a6998aa72ef17f2b6c3cbcd663cbb5c..b69b8b86ccd066359667a8a161319ddd7bcb7919 100644
--- a/src/USER-MISC/pair_momb.cpp
+++ b/src/USER-MISC/pair_momb.cpp
@@ -12,7 +12,7 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
- Contributing authors: Kristen Fichthorn, Tonnam Balankura,
+ Contributing authors: Kristen Fichthorn, Tonnam Balankura,
Ya Zhou (Penn State University)
------------------------------------------------------------------------- */
@@ -255,7 +255,7 @@ double PairMomb::init_one(int i, int j)
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
morse1[i][j] = 2.0*d0[i][j]*alpha[i][j];
-
+
if (offset_flag) {
double alpha_dr = -alpha[i][j] * (cut[i][j] - r0[i][j]);
offset[i][j] = d0[i][j] * (exp(2.0*alpha_dr) - 2.0*exp(alpha_dr));
diff --git a/src/USER-MISC/pair_morse_smooth_linear.cpp b/src/USER-MISC/pair_morse_smooth_linear.cpp
index 0035338cd91af0b0c09eb59052ab9da8c8941794..37a880762079eb71885fa4c1286812c923abf997 100644
--- a/src/USER-MISC/pair_morse_smooth_linear.cpp
+++ b/src/USER-MISC/pair_morse_smooth_linear.cpp
@@ -223,7 +223,7 @@ double PairMorseSmoothLinear::init_one(int i, int j)
morse1[i][j] = 2.0*d0[i][j]*alpha[i][j];
double alpha_dr = -alpha[i][j] * (cut[i][j] - r0[i][j]);
-
+
offset[i][j] = d0[i][j] * (exp(2.0*alpha_dr) - 2.0*exp(alpha_dr));
der_at_cutoff[i][j] = -2.0*alpha[i][j]*d0[i][j] * (exp(2.0*alpha_dr) - exp(alpha_dr));
diff --git a/src/USER-MOFFF/angle_class2_p6.cpp b/src/USER-MOFFF/angle_class2_p6.cpp
index aba117ca9017201f97a457788fa424e8b2b62fcc..d173669771f4fbbdadd1b87732ccf2c5acc9cb61 100644
--- a/src/USER-MOFFF/angle_class2_p6.cpp
+++ b/src/USER-MOFFF/angle_class2_p6.cpp
@@ -135,7 +135,7 @@ void AngleClass2P6::compute(int eflag, int vflag)
dtheta6 = dtheta5*dtheta;
de_angle = 2.0*k2[type]*dtheta + 3.0*k3[type]*dtheta2 +
- 4.0*k4[type]*dtheta3 + 5.0*k5[type]*dtheta4 +
+ 4.0*k4[type]*dtheta3 + 5.0*k5[type]*dtheta4 +
6.0*k6[type]*dtheta5;
a = -de_angle*s;
diff --git a/src/USER-MOFFF/angle_cosine_buck6d.cpp b/src/USER-MOFFF/angle_cosine_buck6d.cpp
index 3f8df52887f45a80b1ca697bbcec863dc7f3e1fe..493807dbdca9f34a3eca831403b4e81e2ae5f521 100644
--- a/src/USER-MOFFF/angle_cosine_buck6d.cpp
+++ b/src/USER-MOFFF/angle_cosine_buck6d.cpp
@@ -71,7 +71,7 @@ void AngleCosineBuck6d::compute(int eflag, int vflag)
eangle = evdwl = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = 0;
-
+
// insure pair->ev_tally() will use 1-3 virial contribution
if (vflag_global == 2)
@@ -120,7 +120,7 @@ void AngleCosineBuck6d::compute(int eflag, int vflag)
s = sqrt(1.0 - c*c);
if (s < SMALL) s = SMALL;
s = 1.0/s;
-
+
// force & energy
// explicit lj-contribution
@@ -135,7 +135,7 @@ void AngleCosineBuck6d::compute(int eflag, int vflag)
if (rsq3 < cut_ljsq[itype][jtype]) {
r3 = sqrt(rsq3);
- r32inv = 1.0/rsq3;
+ r32inv = 1.0/rsq3;
r36inv = r32inv*r32inv*r32inv;
r314inv = r36inv*r36inv*r32inv;
rexp = exp(-r3*buck6d2[itype][jtype]);
@@ -144,7 +144,7 @@ void AngleCosineBuck6d::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]*r3*rexp;
+ forcebuck6d = buck6d1[itype][jtype]*buck6d2[itype][jtype]*r3*rexp;
forcebuck6d -= term1*(6.0*term4 - term5*14.0*term2);
ebuck6d = buck6d1[itype][jtype]*rexp - term1*term4;
@@ -152,14 +152,14 @@ void AngleCosineBuck6d::compute(int eflag, int vflag)
if (rsq3 > rsmooth_sq[itype][jtype]) {
rcu = r3*rsq3;
rqu = rsq3*rsq3;
- sme = c5[itype][jtype]*rqu*r3 + c4[itype][jtype]*rqu + c3[itype][jtype]*rcu +
+ sme = c5[itype][jtype]*rqu*r3 + c4[itype][jtype]*rqu + c3[itype][jtype]*rcu +
c2[itype][jtype]*rsq3 + c1[itype][jtype]*r3 + 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]*rsq3 + 2.0*c2[itype][jtype]*r3 + c1[itype][jtype];
forcebuck6d = forcebuck6d*sme + ebuck6d*smf;
ebuck6d *= sme;
}
- } else forcebuck6d = 0.0;
+ } else forcebuck6d = 0.0;
// add forces of additional LJ interaction
@@ -185,8 +185,8 @@ void AngleCosineBuck6d::compute(int eflag, int vflag)
//update pair energy and velocities
if (evflag) force->pair->ev_tally(i1,i3,nlocal,newton_pair,
- evdwl,0.0,fpair,delx3,dely3,delz3);
-
+ evdwl,0.0,fpair,delx3,dely3,delz3);
+
tk = multiplicity[type]*acos(c)-th0[type];
if (eflag) eangle = k[type]*(1.0+cos(tk));
diff --git a/src/USER-MOFFF/improper_inversion_harmonic.cpp b/src/USER-MOFFF/improper_inversion_harmonic.cpp
index 9e8a419eacb4b9ccb961a56e629c041ec1eb53a5..3a7c0272aa31f21706f315646f29208ce3f6a148 100644
--- a/src/USER-MOFFF/improper_inversion_harmonic.cpp
+++ b/src/USER-MOFFF/improper_inversion_harmonic.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -44,7 +44,7 @@ using namespace MathConst;
ImproperInversionHarmonic::ImproperInversionHarmonic(LAMMPS *lmp) : Improper(lmp)
{
- writedata = 1;
+ writedata = 1;
}
/* ---------------------------------------------------------------------- */
@@ -79,7 +79,7 @@ void ImproperInversionHarmonic::compute(int eflag, int vflag)
i3 = improperlist[n][2];
i4 = improperlist[n][3];
type = improperlist[n][4];
-
+
// 1st bond - IJ
vb1x = x[i2][0] - x[i1][0];
@@ -103,16 +103,16 @@ void ImproperInversionHarmonic::compute(int eflag, int vflag)
vb3z = x[i4][2] - x[i1][2];
rrvb3 = 1.0/sqrt(vb3x*vb3x+vb3y*vb3y+vb3z*vb3z);
rr2vb3 = rrvb3*rrvb3;
-
+
// compute all three inversion angles
invang(i1,i2,i3,i4, type,evflag,eflag,
- vb3x, vb3y, vb3z, rrvb3, rr2vb3,
+ vb3x, vb3y, vb3z, rrvb3, rr2vb3,
vb2x, vb2y, vb2z, rrvb2, rr2vb2,
vb1x, vb1y, vb1z, rrvb1, rr2vb1);
invang(i1,i3,i4,i2, type,evflag,eflag,
vb1x, vb1y, vb1z, rrvb1, rr2vb1,
vb3x, vb3y, vb3z, rrvb3, rr2vb3,
- vb2x, vb2y, vb2z, rrvb2, rr2vb2);
+ vb2x, vb2y, vb2z, rrvb2, rr2vb2);
invang(i1,i4,i2,i3, type,evflag,eflag,
vb2x, vb2y, vb2z, rrvb2, rr2vb2,
vb1x, vb1y, vb1z, rrvb1, rr2vb1,
@@ -127,11 +127,11 @@ void ImproperInversionHarmonic::compute(int eflag, int vflag)
void ImproperInversionHarmonic::invang(const int &i1,const int &i2,
const int &i3,const int &i4,
const int &type,const int &evflag,const int &eflag,
- const double &vb1x, const double &vb1y, const double &vb1z,
+ const double &vb1x, const double &vb1y, const double &vb1z,
const double &rrvb1, const double &rr2vb1,
- const double &vb2x, const double &vb2y, const double &vb2z,
+ const double &vb2x, const double &vb2y, const double &vb2z,
const double &rrvb2, const double &rr2vb2,
- const double &vb3x, const double &vb3y, const double &vb3z,
+ const double &vb3x, const double &vb3y, const double &vb3z,
const double &rrvb3, const double &rr2vb3)
{
double eimproper,f1[3],f2[3],f3[3],f4[3];
@@ -145,8 +145,8 @@ void ImproperInversionHarmonic::invang(const int &i1,const int &i2,
int newton_bond = force->newton_bond;
eimproper = 0.0;
-
- // scalar products of IJ*IK and IJ*IL
+
+ // scalar products of IJ*IK and IJ*IL
rjk=vb3x*vb2x+vb3y*vb2y+vb3z*vb2z;
rjl=vb1x*vb3x+vb1y*vb3y+vb1z*vb3z;
@@ -159,7 +159,7 @@ void ImproperInversionHarmonic::invang(const int &i1,const int &i2,
upy=upy*upn;
upz=upz*upn;
rup=vb3x*upx+vb3y*upy+vb3z*upz;
-
+
// unit-vector: IK-IL
umx=vb2x*rrvb2-vb1x*rrvb1;
umy=vb2y*rrvb2-vb1y*rrvb1;
@@ -195,29 +195,29 @@ void ImproperInversionHarmonic::invang(const int &i1,const int &i2,
rupupn = rup*upn;
rumumn = rum*umn;
- // force contributions of angle
- f2[0]=gomega*(-cosomega*vb3x*rr2vb3+rrvb3*(rup*upx+rum*umx)/wwr);
+ // force contributions of angle
+ f2[0]=gomega*(-cosomega*vb3x*rr2vb3+rrvb3*(rup*upx+rum*umx)/wwr);
f2[1]=gomega*(-cosomega*vb3y*rr2vb3+rrvb3*(rup*upy+rum*umy)/wwr);
f2[2]=gomega*(-cosomega*vb3z*rr2vb3+rrvb3*(rup*upz+rum*umz)/wwr);
- f3[0]=gomega*rrvb3*(rupupn*rrvb2*(vb3x-rup*upx-rucb*vb2x*rr2vb2) +
+ f3[0]=gomega*rrvb3*(rupupn*rrvb2*(vb3x-rup*upx-rucb*vb2x*rr2vb2) +
rumumn*rrvb2*(vb3x-rum*umx-rvcb*vb2x*rr2vb2))/wwr;
- f3[1]=gomega*rrvb3*(rupupn*rrvb2*(vb3y-rup*upy-rucb*vb2y*rr2vb2) +
+ f3[1]=gomega*rrvb3*(rupupn*rrvb2*(vb3y-rup*upy-rucb*vb2y*rr2vb2) +
rumumn*rrvb2*(vb3y-rum*umy-rvcb*vb2y*rr2vb2))/wwr;
- f3[2]=gomega*rrvb3*(rupupn*rrvb2*(vb3z-rup*upz-rucb*vb2z*rr2vb2) +
+ f3[2]=gomega*rrvb3*(rupupn*rrvb2*(vb3z-rup*upz-rucb*vb2z*rr2vb2) +
rumumn*rrvb2*(vb3z-rum*umz-rvcb*vb2z*rr2vb2))/wwr;
- f4[0]=gomega*rrvb3*(rupupn*rrvb1*(vb3x-rup*upx-rudb*vb1x*rr2vb1) -
+ f4[0]=gomega*rrvb3*(rupupn*rrvb1*(vb3x-rup*upx-rudb*vb1x*rr2vb1) -
rumumn*rrvb1*(vb3x-rum*umx-rvdb*vb1x*rr2vb1))/wwr;
- f4[1]=gomega*rrvb3*(rupupn*rrvb1*(vb3y-rup*upy-rudb*vb1y*rr2vb1) -
+ f4[1]=gomega*rrvb3*(rupupn*rrvb1*(vb3y-rup*upy-rudb*vb1y*rr2vb1) -
rumumn*rrvb1*(vb3y-rum*umy-rvdb*vb1y*rr2vb1))/wwr;
- f4[2]=gomega*rrvb3*(rupupn*rrvb1*(vb3z-rup*upz-rudb*vb1z*rr2vb1) -
+ f4[2]=gomega*rrvb3*(rupupn*rrvb1*(vb3z-rup*upz-rudb*vb1z*rr2vb1) -
rumumn*rrvb1*(vb3z-rum*umz-rvdb*vb1z*rr2vb1))/wwr;
f1[0] = -(f2[0] + f3[0] + f4[0]);
f1[1] = -(f2[1] + f3[1] + f4[1]);
f1[2] = -(f2[2] + f3[2] + f4[2]);
-
+
if (newton_bond || i1 < nlocal) {
f[i1][0] += f1[0];
f[i1][1] += f1[1];
@@ -241,10 +241,10 @@ void ImproperInversionHarmonic::invang(const int &i1,const int &i2,
f[i4][1] += f4[1];
f[i4][2] += f4[2];
}
-
+
double rb1x, rb1y, rb1z, rb2x, rb2y, rb2z, rb3x, rb3y, rb3z;
if (evflag)
-
+
rb3x = vb1x - vb2x;
rb3y = vb1y - vb2y;
rb3z = vb1z - vb2z;
@@ -299,7 +299,7 @@ void ImproperInversionHarmonic::coeff(int narg, char **arg)
}
/* ----------------------------------------------------------------------
- proc 0 writes out coeffs to restart file
+ proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void ImproperInversionHarmonic::write_restart(FILE *fp)
@@ -309,7 +309,7 @@ void ImproperInversionHarmonic::write_restart(FILE *fp)
}
/* ----------------------------------------------------------------------
- proc 0 reads coeffs from restart file, bcasts them
+ proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void ImproperInversionHarmonic::read_restart(FILE *fp)
diff --git a/src/USER-OMP/angle_dipole_omp.cpp b/src/USER-OMP/angle_dipole_omp.cpp
index 2fa6fff0ef9c58cb3e1b5d509abf92c68d7570be..ee2af539183d514a7c38b8273e8bf12dbbde64f9 100644
--- a/src/USER-OMP/angle_dipole_omp.cpp
+++ b/src/USER-OMP/angle_dipole_omp.cpp
@@ -126,7 +126,7 @@ void AngleDipoleOMP::eval(int nfrom, int nto, ThrData * const thr)
torque[iDip][0] += delTx;
torque[iDip][1] += delTy;
torque[iDip][2] += delTz;
-
+
// Force couple that counterbalances dipolar torque
fx = dely*delTz - delz*delTy; // direction (fi): - r x (-T)
fy = delz*delTx - delx*delTz;
diff --git a/src/USER-OMP/fix_neigh_history_omp.cpp b/src/USER-OMP/fix_neigh_history_omp.cpp
index 21aed6c7c04665555727e1b89b45ecdf67732a64..a7ee18257f30ba43e90a137fa67808ba8940304d 100644
--- a/src/USER-OMP/fix_neigh_history_omp.cpp
+++ b/src/USER-OMP/fix_neigh_history_omp.cpp
@@ -129,7 +129,7 @@ void FixNeighHistoryOMP::pre_exchange_onesided()
allflags = firstflag[i];
for (jj = 0; jj < jnum; jj++)
- if (allflags[jj])
+ if (allflags[jj])
if ((i >= lfrom) && (i < lto)) npartner[i]++;
}
@@ -256,7 +256,7 @@ void FixNeighHistoryOMP::pre_exchange_newton()
}
}
}
-#if defined(_OPENMP)
+#if defined(_OPENMP)
#pragma omp barrier
{;}
@@ -330,7 +330,7 @@ void FixNeighHistoryOMP::pre_exchange_newton()
}
}
}
-#if defined(_OPENMP)
+#if defined(_OPENMP)
#pragma omp barrier
{;}
@@ -516,9 +516,9 @@ void FixNeighHistoryOMP::post_neighbor()
memory->sfree(firstflag);
memory->sfree(firstvalue);
maxatom = nall;
- firstflag = (int **)
+ firstflag = (int **)
memory->smalloc(maxatom*sizeof(int *),"neighbor_history:firstflag");
- firstvalue = (double **)
+ firstvalue = (double **)
memory->smalloc(maxatom*sizeof(double *),"neighbor_history:firstvalue");
}
@@ -576,7 +576,7 @@ void FixNeighHistoryOMP::post_neighbor()
rflag = sbmask(j);
j &= NEIGHMASK;
jlist[jj] = j;
-
+
// rflag = 1 if r < radsum in npair_size() method
// preserve neigh history info if tag[j] is in old-neigh partner list
// this test could be more geometrically precise for two sphere/line/tri
diff --git a/src/USER-OMP/pair_airebo_omp.cpp b/src/USER-OMP/pair_airebo_omp.cpp
index 73529847f27f266e85316ea64f6b0be99c5acd98..3e8f6d6df3ba242bc5d47249d8563bdc5136e03b 100644
--- a/src/USER-OMP/pair_airebo_omp.cpp
+++ b/src/USER-OMP/pair_airebo_omp.cpp
@@ -1846,7 +1846,7 @@ double PairAIREBOOMP::bondorder_thr(int i, int j, double rij[3], double rijmag,
/* ----------------------------------------------------------------------
Bij* function
--------------------------------------------------------------------------
+-------------------------------------------------------------------------
This function calculates S(t_b(b_ij*)) as specified in the AIREBO paper.
To do so, it needs to compute b_ij*, i.e. the bondorder given that the
@@ -2045,7 +2045,7 @@ double PairAIREBOOMP::bondorderLJ_thr(int i, int j, double rij_mod[3], double ri
cos321 = MAX(cos321,-1.0);
sin321 = sqrt(1.0 - cos321*cos321);
if ((sin321 > TOL) && (r21mag > TOL)) { // XXX was sin321 != 0.0
- w21 = Sp(r21mag,rcmin[itype][ktype],rcmaxp[itype][ktype],dw21);
+ w21 = Sp(r21mag,rcmin[itype][ktype],rcmaxp[itype][ktype],dw21);
tspjik = Sp2(cos321,thmin,thmax,dtsjik);
REBO_neighs_j = REBO_firstneigh[j];
@@ -2225,7 +2225,7 @@ double PairAIREBOOMP::bondorderLJ_thr(int i, int j, double rij_mod[3], double ri
(rijmag*rjlmag);
cosijl = MIN(cosijl,1.0);
cosijl = MAX(cosijl,-1.0);
-
+
dcosijldri[0] = (-rjl[0]/(rijmag*rjlmag)) -
(cosijl*rij[0]/(rijmag*rijmag));
dcosijldri[1] = (-rjl[1]/(rijmag*rjlmag)) -
@@ -2255,7 +2255,7 @@ double PairAIREBOOMP::bondorderLJ_thr(int i, int j, double rij_mod[3], double ri
fl[0] = -tmp2*dcosijldrl[0];
fl[1] = -tmp2*dcosijldrl[1];
fl[2] = -tmp2*dcosijldrl[2];
-
+
tmp2 = VA*.5*(tmp*wjl*g*exp(lamdaijl)*4.0*kronecker(jtype,1));
fj[0] += tmp2*(rjl[0]/rjlmag);
fj[1] += tmp2*(rjl[1]/rjlmag);
diff --git a/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp b/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp
index 60445d2d865a32eff8c5e5a3a6f6a7c25e480477..7689d2783bdd2573cfd6693fd9ddbf04709fc827 100644
--- a/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp
+++ b/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp
@@ -1139,7 +1139,7 @@ void PairLJLongTIP4PLongOMP::eval_inner(int iifrom, int iito, ThrData * const th
ytmp = x[i].y;
ztmp = x[i].z;
itype = type[i];
-
+
// if atom I = water O, set x1 = offset charge site
// else x1 = x of atom I
// NOTE: to make this part thread safe, we need to
@@ -1634,7 +1634,7 @@ void PairLJLongTIP4PLongOMP::eval_outer(int iifrom, int iito, ThrData * const th
const double qqrd2e = force->qqrd2e;
const double cut_coulsqplus = (cut_coul+2.0*qdist)*(cut_coul+2.0*qdist);
const int vflag = vflag_atom || vflag_global;
-
+
int i,j,ii,jj,jnum,itype,jtype;
int n,vlist[6];
int key;
diff --git a/src/USER-OMP/reaxc_bond_orders_omp.cpp b/src/USER-OMP/reaxc_bond_orders_omp.cpp
index e0b08fa49e4b6a7643eef1effedbcf3b40b39bbb..8b78a3aa55c0de49456b0141ee2ed466d167e460 100644
--- a/src/USER-OMP/reaxc_bond_orders_omp.cpp
+++ b/src/USER-OMP/reaxc_bond_orders_omp.cpp
@@ -1,12 +1,12 @@
/*----------------------------------------------------------------------
PuReMD - Purdue ReaxFF Molecular Dynamics Program
Website: https://www.cs.purdue.edu/puremd
-
+
Copyright (2010) Purdue University
-
- Contributing authors:
+
+ Contributing authors:
H. M. Aktulga, J. Fogarty, S. Pandit, A. Grama
- Corresponding author:
+ Corresponding author:
Hasan Metin Aktulga, Michigan State University, hma@cse.msu.edu
Please cite the related publication:
@@ -468,7 +468,7 @@ void BOOMP( reax_system *system, control_params *control, simulation_data *data,
#if defined(_OPENMP)
#pragma omp barrier
#endif
-
+
/* Corrected Bond Order calculations */
#if defined(_OPENMP)
#pragma omp for schedule(guided)
@@ -496,23 +496,23 @@ void BOOMP( reax_system *system, control_params *control, simulation_data *data,
bo_ij->C1dbo = 1.000000;
bo_ij->C2dbo = 0.000000;
bo_ij->C3dbo = 0.000000;
-
+
bo_ij->C1dbopi = 1.000000;
bo_ij->C2dbopi = 0.000000;
bo_ij->C3dbopi = 0.000000;
bo_ij->C4dbopi = 0.000000;
-
+
bo_ij->C1dbopi2 = 1.000000;
bo_ij->C2dbopi2 = 0.000000;
bo_ij->C3dbopi2 = 0.000000;
bo_ij->C4dbopi2 = 0.000000;
-
+
}
else {
val_j = system->reax_param.sbp[type_j].valency;
Deltap_j = workspace->Deltap[j];
Deltap_boc_j = workspace->Deltap_boc[j];
-
+
/* on page 1 */
if( twbp->ovc >= 0.001 ) {
/* Correction for overcoordination */
@@ -520,12 +520,12 @@ void BOOMP( reax_system *system, control_params *control, simulation_data *data,
exp_p2i = exp( -p_boc2 * Deltap_i );
exp_p1j = exp( -p_boc1 * Deltap_j );
exp_p2j = exp( -p_boc2 * Deltap_j );
-
+
f2 = exp_p1i + exp_p1j;
f3 = -1.0 / p_boc2 * log( 0.5 * ( exp_p2i + exp_p2j ) );
f1 = 0.5 * ( ( val_i + f2 )/( val_i + f2 + f3 ) +
( val_j + f2 )/( val_j + f2 + f3 ) );
-
+
/* Now come the derivates */
/* Bond Order pages 5-7, derivative of f1 */
temp = f2 + f3;
@@ -535,7 +535,7 @@ void BOOMP( reax_system *system, control_params *control, simulation_data *data,
1.0 / SQR( u1_ji ));
Cf1B_ij = -0.5 * (( u1_ij - f3 ) / SQR( u1_ij ) +
( u1_ji - f3 ) / SQR( u1_ji ));
-
+
Cf1_ij = 0.50 * ( -p_boc1 * exp_p1i / u1_ij -
((val_i+f2) / SQR(u1_ij)) *
( -p_boc1 * exp_p1i +
@@ -544,8 +544,8 @@ void BOOMP( reax_system *system, control_params *control, simulation_data *data,
((val_j+f2) / SQR(u1_ji)) *
( -p_boc1 * exp_p1i +
exp_p2i / ( exp_p2i + exp_p2j ) ));
-
-
+
+
Cf1_ji = -Cf1A_ij * p_boc1 * exp_p1j +
Cf1B_ij * exp_p2j / ( exp_p2i + exp_p2j );
}
@@ -561,11 +561,11 @@ void BOOMP( reax_system *system, control_params *control, simulation_data *data,
Deltap_boc_i) * twbp->p_boc3 + twbp->p_boc5);
exp_f5 =exp(-(twbp->p_boc4 * SQR( bo_ij->BO ) -
Deltap_boc_j) * twbp->p_boc3 + twbp->p_boc5);
-
+
f4 = 1. / (1. + exp_f4);
f5 = 1. / (1. + exp_f5);
f4f5 = f4 * f5;
-
+
/* Bond Order pages 8-9, derivative of f4 and f5 */
Cf45_ij = -f4 * exp_f4;
Cf45_ji = -f5 * exp_f5;
@@ -574,7 +574,7 @@ void BOOMP( reax_system *system, control_params *control, simulation_data *data,
f4 = f5 = f4f5 = 1.0;
Cf45_ij = Cf45_ji = 0.0;
}
-
+
/* Bond Order page 10, derivative of total bond order */
A0_ij = f1 * f4f5;
A1_ij = -2 * twbp->p_boc3 * twbp->p_boc4 * bo_ij->BO *
@@ -583,28 +583,28 @@ void BOOMP( reax_system *system, control_params *control, simulation_data *data,
A2_ji = Cf1_ji / f1 + twbp->p_boc3 * Cf45_ji;
A3_ij = A2_ij + Cf1_ij / f1;
A3_ji = A2_ji + Cf1_ji / f1;
-
+
/* find corrected bond orders and their derivative coef */
bo_ij->BO = bo_ij->BO * A0_ij;
bo_ij->BO_pi = bo_ij->BO_pi * A0_ij *f1;
bo_ij->BO_pi2= bo_ij->BO_pi2* A0_ij *f1;
bo_ij->BO_s = bo_ij->BO - ( bo_ij->BO_pi + bo_ij->BO_pi2 );
-
+
bo_ij->C1dbo = A0_ij + bo_ij->BO * A1_ij;
bo_ij->C2dbo = bo_ij->BO * A2_ij;
bo_ij->C3dbo = bo_ij->BO * A2_ji;
-
+
bo_ij->C1dbopi = f1*f1*f4*f5;
bo_ij->C2dbopi = bo_ij->BO_pi * A1_ij;
bo_ij->C3dbopi = bo_ij->BO_pi * A3_ij;
bo_ij->C4dbopi = bo_ij->BO_pi * A3_ji;
-
+
bo_ij->C1dbopi2 = f1*f1*f4*f5;
bo_ij->C2dbopi2 = bo_ij->BO_pi2 * A1_ij;
bo_ij->C3dbopi2 = bo_ij->BO_pi2 * A3_ij;
bo_ij->C4dbopi2 = bo_ij->BO_pi2 * A3_ji;
}
-
+
/* neglect bonds that are < 1e-10 */
if( bo_ij->BO < 1e-10 )
bo_ij->BO = 0.0;
@@ -614,7 +614,7 @@ void BOOMP( reax_system *system, control_params *control, simulation_data *data,
bo_ij->BO_pi = 0.0;
if( bo_ij->BO_pi2 < 1e-10 )
bo_ij->BO_pi2 = 0.0;
-
+
workspace->total_bond_order[i] += bo_ij->BO; //now keeps total_BO
}
// else {
@@ -626,7 +626,7 @@ void BOOMP( reax_system *system, control_params *control, simulation_data *data,
// bo_ij->BO_s = bo_ji->BO_s;
// bo_ij->BO_pi = bo_ji->BO_pi;
// bo_ij->BO_pi2 = bo_ji->BO_pi2;
-
+
// workspace->total_bond_order[i] += bo_ij->BO;// now keeps total_BO
// }
}
@@ -659,14 +659,14 @@ void BOOMP( reax_system *system, control_params *control, simulation_data *data,
/* We only need to update bond orders from bo_ji
everything else is set in uncorrected_bo calculations */
sym_index = bonds->select.bond_list[pj].sym_index;
-
+
bo_ij = &( bonds->select.bond_list[pj].bo_data );
bo_ji = &(bonds->select.bond_list[ sym_index ].bo_data);
bo_ij->BO = bo_ji->BO;
bo_ij->BO_s = bo_ji->BO_s;
bo_ij->BO_pi = bo_ji->BO_pi;
bo_ij->BO_pi2 = bo_ji->BO_pi2;
-
+
workspace->total_bond_order[i] += bo_ij->BO;// now keeps total_BO
}
}
diff --git a/src/USER-OMP/reaxc_bonds_omp.cpp b/src/USER-OMP/reaxc_bonds_omp.cpp
index bc038e2aa188f6e7460a1387f3ea4fd44c55f9cf..0ccb4d8f99969e62ba8757c27f2c8389e94cea16 100644
--- a/src/USER-OMP/reaxc_bonds_omp.cpp
+++ b/src/USER-OMP/reaxc_bonds_omp.cpp
@@ -1,12 +1,12 @@
/*----------------------------------------------------------------------
PuReMD - Purdue ReaxFF Molecular Dynamics Program
Website: https://www.cs.purdue.edu/puremd
-
+
Copyright (2010) Purdue University
-
- Contributing authors:
+
+ Contributing authors:
H. M. Aktulga, J. Fogarty, S. Pandit, A. Grama
- Corresponding author:
+ Corresponding author:
Hasan Metin Aktulga, Michigan State University, hma@cse.msu.edu
Please cite the related publication:
@@ -73,7 +73,7 @@ void BondsOMP( reax_system *system, control_params *control,
single_body_parameters *sbp_i, *sbp_j;
two_body_parameters *twbp;
bond_order_data *bo_ij;
-
+
#if defined(_OPENMP)
int tid = omp_get_thread_num();
#else
@@ -151,22 +151,22 @@ void BondsOMP( reax_system *system, control_params *control,
exphub1 = exp(-gp3 * (workspace->total_bond_order[j]-bo_ij->BO));
exphuov = exp(gp4 * (workspace->Delta[i] + workspace->Delta[j]));
hulpov = 1.0 / (1.0 + 25.0 * exphuov);
-
+
estriph = gp10 * exphu * hulpov * (exphua1 + exphub1);
total_Ebond += estriph;
-
+
decobdbo = gp10 * exphu * hulpov * (exphua1 + exphub1) *
( gp3 - 2.0 * gp7 * (bo_ij->BO-2.50) );
decobdboua = -gp10 * exphu * hulpov *
(gp3*exphua1 + 25.0*gp4*exphuov*hulpov*(exphua1+exphub1));
decobdboub = -gp10 * exphu * hulpov *
(gp3*exphub1 + 25.0*gp4*exphuov*hulpov*(exphua1+exphub1));
-
+
/* tally into per-atom energy */
if (system->pair_ptr->evflag)
pair_reax_ptr->ev_tally_thr_proxy(system->pair_ptr, i, j, natoms, 1,
estriph, 0.0, 0.0, 0.0, 0.0, 0.0, thr);
-
+
bo_ij->Cdbo += decobdbo;
workspace->CdDelta[i] += decobdboua;
workspace->CdDeltaReduction[reductionOffset+j] += decobdboub;
diff --git a/src/USER-OMP/reaxc_forces_omp.cpp b/src/USER-OMP/reaxc_forces_omp.cpp
index f02c527d9f4fecdd3858770919b444f5377120d5..01e58c4fd30d10c561d68b4d4a4881e382ccbe42 100644
--- a/src/USER-OMP/reaxc_forces_omp.cpp
+++ b/src/USER-OMP/reaxc_forces_omp.cpp
@@ -1,12 +1,12 @@
/*----------------------------------------------------------------------
PuReMD - Purdue ReaxFF Molecular Dynamics Program
Website: https://www.cs.purdue.edu/puremd
-
+
Copyright (2010) Purdue University
-
- Contributing authors:
+
+ Contributing authors:
H. M. Aktulga, J. Fogarty, S. Pandit, A. Grama
- Corresponding author:
+ Corresponding author:
Hasan Metin Aktulga, Michigan State University, hma@cse.msu.edu
Please cite the related publication:
@@ -407,9 +407,9 @@ void Init_Forces_noQEq_OMP( reax_system *system, control_params *control,
// btop_i++;
// Set_End_Index(i, btop_i, bonds);
// }
-
+
// }
-
+
// Trying to minimize time spent in critical section by moving initial part of BOp()
// outside of critical section.
@@ -423,26 +423,26 @@ void Init_Forces_noQEq_OMP( reax_system *system, control_params *control,
BO_s = (1.0 + bo_cut) * exp( C12 );
}
else BO_s = C12 = 0.0;
-
+
if( sbp_i->r_pi > 0.0 && sbp_j->r_pi > 0.0 ) {
C34 = twbp->p_bo3 * pow( nbr_pj->d / twbp->r_p, twbp->p_bo4 );
BO_pi = exp( C34 );
}
else BO_pi = C34 = 0.0;
-
+
if( sbp_i->r_pi_pi > 0.0 && sbp_j->r_pi_pi > 0.0 ) {
C56 = twbp->p_bo5 * pow( nbr_pj->d / twbp->r_pp, twbp->p_bo6 );
BO_pi2= exp( C56 );
}
else BO_pi2 = C56 = 0.0;
-
+
/* Initially BO values are the uncorrected ones, page 1 */
BO = BO_s + BO_pi + BO_pi2;
// End top portion of BOp()
-
+
if(BO >= bo_cut) {
int btop_j;
-
+
// Update indices in critical section
#if defined(_OPENMP)
#pragma omp critical
@@ -453,28 +453,28 @@ void Init_Forces_noQEq_OMP( reax_system *system, control_params *control,
Set_End_Index( j, btop_j+1, bonds );
Set_End_Index( i, btop_i+1, bonds );
} // omp critical
-
+
// Finish remaining BOp() work
BOp_OMP(workspace, bonds, bo_cut,
i , btop_i, nbr_pj, sbp_i, sbp_j, twbp, btop_j,
C12, C34, C56, BO, BO_s, BO_pi, BO_pi2);
-
+
bond_data * ibond = &(bonds->select.bond_list[btop_i]);
bond_order_data * bo_ij = &(ibond->bo_data);
-
+
bond_data * jbond = &(bonds->select.bond_list[btop_j]);
bond_order_data * bo_ji = &(jbond->bo_data);
-
+
workspace->total_bond_order[i] += bo_ij->BO;
tmp_bond_order[reductionOffset + j] += bo_ji->BO;
-
+
rvec_Add(workspace->dDeltap_self[i], bo_ij->dBOp);
rvec_Add(tmp_ddelta[reductionOffset + j], bo_ji->dBOp);
-
+
btop_i++;
num_bonds++;
} // if(BO>=bo_cut)
-
+
} // if(cutoff)
} // for(pj)
@@ -518,7 +518,7 @@ void Init_Forces_noQEq_OMP( reax_system *system, control_params *control,
if (ihb == 1 || ihb == 2) {
start_i = Start_Index(i, far_nbrs);
end_i = End_Index(i, far_nbrs);
-
+
for (pj = start_i; pj < end_i; ++pj) {
nbr_pj = &( far_nbrs->select.far_nbr_list[pj] );
j = nbr_pj->nbr;
@@ -531,10 +531,10 @@ void Init_Forces_noQEq_OMP( reax_system *system, control_params *control,
if (nbr_pj->d <= control->hbond_cut) {
int iflag = 0;
int jflag = 0;
-
+
if(ihb==1 && jhb==2) iflag = 1;
else if(j<system->n && ihb == 2 && jhb == 1) jflag = 1;
-
+
if(iflag || jflag) {
if(iflag) {
ihb_top = End_Index(atom_i->Hindex, hbonds);
@@ -553,7 +553,7 @@ void Init_Forces_noQEq_OMP( reax_system *system, control_params *control,
hbonds->select.hbond_list[jhb_top].scl = -1;
hbonds->select.hbond_list[jhb_top].ptr = nbr_pj;
}
-
+
num_hbonds++;
} // if(iflag || jflag)
diff --git a/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp b/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp
index 062436a703b4bb8c4276f7c1db03ba26418bdde7..4c0a4c269e7d8e0fab9ab2ec1aa9d43dd30e3743 100644
--- a/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp
+++ b/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp
@@ -1,12 +1,12 @@
/*----------------------------------------------------------------------
PuReMD - Purdue ReaxFF Molecular Dynamics Program
Website: https://www.cs.purdue.edu/puremd
-
+
Copyright (2010) Purdue University
-
- Contributing authors:
+
+ Contributing authors:
H. M. Aktulga, J. Fogarty, S. Pandit, A. Grama
- Corresponding author:
+ Corresponding author:
Hasan Metin Aktulga, Michigan State University, hma@cse.msu.edu
Please cite the related publication:
diff --git a/src/USER-OMP/reaxc_init_md_omp.cpp b/src/USER-OMP/reaxc_init_md_omp.cpp
index c0e4a45eaa3e3c9c0f82362886c14503e6e85094..68d39d4f801a9187cbf0ed6818b15ba99b71834e 100644
--- a/src/USER-OMP/reaxc_init_md_omp.cpp
+++ b/src/USER-OMP/reaxc_init_md_omp.cpp
@@ -1,12 +1,12 @@
/*----------------------------------------------------------------------
PuReMD - Purdue ReaxFF Molecular Dynamics Program
Website: https://www.cs.purdue.edu/puremd
-
+
Copyright (2010) Purdue University
-
- Contributing authors:
+
+ Contributing authors:
H. M. Aktulga, J. Fogarty, S. Pandit, A. Grama
- Corresponding author:
+ Corresponding author:
Hasan Metin Aktulga, Michigan State University, hma@cse.msu.edu
Please cite the related publication:
diff --git a/src/USER-OMP/reaxc_multi_body_omp.cpp b/src/USER-OMP/reaxc_multi_body_omp.cpp
index 4653ada714856c5aab080f0d4666761e8f53d9b3..fc4982ca9fc71fbc2b7bcd33ad00449d34aa5ce2 100644
--- a/src/USER-OMP/reaxc_multi_body_omp.cpp
+++ b/src/USER-OMP/reaxc_multi_body_omp.cpp
@@ -1,12 +1,12 @@
/*----------------------------------------------------------------------
PuReMD - Purdue ReaxFF Molecular Dynamics Program
Website: https://www.cs.purdue.edu/puremd
-
+
Copyright (2010) Purdue University
-
- Contributing authors:
+
+ Contributing authors:
H. M. Aktulga, J. Fogarty, S. Pandit, A. Grama
- Corresponding author:
+ Corresponding author:
Hasan Metin Aktulga, Michigan State University, hma@cse.msu.edu
Please cite the related publication:
@@ -144,16 +144,16 @@ void Atom_EnergyOMP( reax_system *system, control_params *control,
bo_ij = &( bonds->select.bond_list[pj].bo_data );
Di = workspace->Delta[i];
vov3 = bo_ij->BO - Di - 0.040*pow(Di, 4.);
-
+
if( vov3 > 3. ) {
total_Elp += e_lph = p_lp3 * SQR(vov3-3.0);
deahu2dbo = 2.*p_lp3*(vov3 - 3.);
deahu2dsbo = 2.*p_lp3*(vov3 - 3.)*(-1. - 0.16*pow(Di, 3.));
-
+
bo_ij->Cdbo += deahu2dbo;
workspace->CdDelta[i] += deahu2dsbo;
-
+
/* tally into per-atom energy */
if( system->pair_ptr->evflag)
pair_reax_ptr->ev_tally_thr_proxy(system->pair_ptr, i, j, system->n, 1,
diff --git a/src/USER-OMP/reaxc_nonbonded_omp.cpp b/src/USER-OMP/reaxc_nonbonded_omp.cpp
index 504dfbe685b1c08c3adfd77b06d9c85bfa62a063..552783e41cc6f4e4cd12e208d0a568e6238f54ce 100644
--- a/src/USER-OMP/reaxc_nonbonded_omp.cpp
+++ b/src/USER-OMP/reaxc_nonbonded_omp.cpp
@@ -1,12 +1,12 @@
/*----------------------------------------------------------------------
PuReMD - Purdue ReaxFF Molecular Dynamics Program
Website: https://www.cs.purdue.edu/puremd
-
+
Copyright (2010) Purdue University
-
- Contributing authors:
+
+ Contributing authors:
H. M. Aktulga, J. Fogarty, S. Pandit, A. Grama
- Corresponding author:
+ Corresponding author:
Hasan Metin Aktulga, Michigan State University, hma@cse.msu.edu
Please cite the related publication:
@@ -121,11 +121,11 @@ void vdW_Coulomb_Energy_OMP( reax_system *system, control_params *control,
}
if (flag) {
-
+
r_ij = nbr_pj->d;
twbp = &(system->reax_param.tbp[ system->my_atoms[i].type ]
[ system->my_atoms[j].type ]);
-
+
/* Calculate Taper and its derivative */
// Tap = nbr_pj->Tap; -- precomputed during compte_H
Tap = workspace->Tap[7] * r_ij + workspace->Tap[6];
@@ -135,27 +135,27 @@ void vdW_Coulomb_Energy_OMP( reax_system *system, control_params *control,
Tap = Tap * r_ij + workspace->Tap[2];
Tap = Tap * r_ij + workspace->Tap[1];
Tap = Tap * r_ij + workspace->Tap[0];
-
+
dTap = 7*workspace->Tap[7] * r_ij + 6*workspace->Tap[6];
dTap = dTap * r_ij + 5*workspace->Tap[5];
dTap = dTap * r_ij + 4*workspace->Tap[4];
dTap = dTap * r_ij + 3*workspace->Tap[3];
dTap = dTap * r_ij + 2*workspace->Tap[2];
dTap += workspace->Tap[1]/r_ij;
-
+
/*vdWaals Calculations*/
if(system->reax_param.gp.vdw_type==1 || system->reax_param.gp.vdw_type==3)
{ // shielding
powr_vdW1 = pow(r_ij, p_vdW1);
powgi_vdW1 = pow( 1.0 / twbp->gamma_w, p_vdW1);
-
+
fn13 = pow( powr_vdW1 + powgi_vdW1, p_vdW1i );
exp1 = exp( twbp->alpha * (1.0 - fn13 / twbp->r_vdW) );
exp2 = exp( 0.5 * twbp->alpha * (1.0 - fn13 / twbp->r_vdW) );
-
+
e_vdW = twbp->D * (exp1 - 2.0 * exp2);
total_EvdW += Tap * e_vdW;
-
+
dfn13 = pow( powr_vdW1 + powgi_vdW1, p_vdW1i - 1.0) *
pow(r_ij, p_vdW1 - 2.0);
@@ -165,48 +165,48 @@ void vdW_Coulomb_Energy_OMP( reax_system *system, control_params *control,
else{ // no shielding
exp1 = exp( twbp->alpha * (1.0 - r_ij / twbp->r_vdW) );
exp2 = exp( 0.5 * twbp->alpha * (1.0 - r_ij / twbp->r_vdW) );
-
+
e_vdW = twbp->D * (exp1 - 2.0 * exp2);
total_EvdW += Tap * e_vdW;
-
+
CEvd = dTap * e_vdW -
Tap * twbp->D * (twbp->alpha / twbp->r_vdW) * (exp1 - exp2) / r_ij;
}
-
+
if(system->reax_param.gp.vdw_type==2 || system->reax_param.gp.vdw_type==3)
{ // innner wall
e_core = twbp->ecore * exp(twbp->acore * (1.0-(r_ij/twbp->rcore)));
total_EvdW += Tap * e_core;
-
+
de_core = -(twbp->acore/twbp->rcore) * e_core;
CEvd += dTap * e_core + Tap * de_core / r_ij;
-
+
// lg correction, only if lgvdw is yes
if (control->lgflag) {
r_ij5 = pow( r_ij, 5.0 );
r_ij6 = pow( r_ij, 6.0 );
re6 = pow( twbp->lgre, 6.0 );
-
+
e_lg = -(twbp->lgcij/( r_ij6 + re6 ));
total_EvdW += Tap * e_lg;
-
+
de_lg = -6.0 * e_lg * r_ij5 / ( r_ij6 + re6 ) ;
CEvd += dTap * e_lg + Tap * de_lg / r_ij;
}
-
+
}
-
+
/*Coulomb Calculations*/
dr3gamij_1 = ( r_ij * r_ij * r_ij + twbp->gamma );
dr3gamij_3 = pow( dr3gamij_1 , 0.33333333333333 );
-
+
tmp = Tap / dr3gamij_3;
total_Eele += e_ele =
C_ele * system->my_atoms[i].q * system->my_atoms[j].q * tmp;
-
+
CEclmb = C_ele * system->my_atoms[i].q * system->my_atoms[j].q *
( dTap - Tap * r_ij / dr3gamij_1 ) / dr3gamij_3;
-
+
/* tally into per-atom energy */
if( system->pair_ptr->evflag || system->pair_ptr->vflag_atom) {
pe_vdw = Tap * (e_vdW + e_core + e_lg);
@@ -217,7 +217,7 @@ void vdW_Coulomb_Energy_OMP( reax_system *system, control_params *control,
1, pe_vdw, e_ele, f_tmp,
delij[0], delij[1], delij[2], thr);
}
-
+
if( control->virial == 0 ) {
rvec_ScaledAdd( workspace->f[i], -(CEvd + CEclmb), nbr_pj->dvec );
rvec_ScaledAdd( workspace->forceReduction[reductionOffset+j],
@@ -226,13 +226,13 @@ void vdW_Coulomb_Energy_OMP( reax_system *system, control_params *control,
else { /* NPT, iNPT or sNPT */
/* for pressure coupling, terms not related to bond order
derivatives are added directly into pressure vector/tensor */
-
+
rvec_Scale( temp, CEvd + CEclmb, nbr_pj->dvec );
rvec_ScaledAdd( workspace->f[reductionOffset+i], -1., temp );
rvec_Add( workspace->forceReduction[reductionOffset+j], temp);
-
+
rvec_iMultiply( ext_press, nbr_pj->rel_box, temp );
-
+
rvec_Add( workspace->my_ext_pressReduction[tid], ext_press );
}
}
@@ -320,35 +320,35 @@ void Tabulated_vdW_Coulomb_Energy_OMP(reax_system *system,control_params *contro
}
if (flag) {
-
+
r_ij = nbr_pj->d;
tmin = MIN( type_i, type_j );
tmax = MAX( type_i, type_j );
t = &( LR[tmin][tmax] );
-
+
/* Cubic Spline Interpolation */
r = (int)(r_ij * t->inv_dx);
if( r == 0 ) ++r;
base = (double)(r+1) * t->dx;
dif = r_ij - base;
-
+
e_vdW = ((t->vdW[r].d*dif + t->vdW[r].c)*dif + t->vdW[r].b)*dif +
t->vdW[r].a;
-
+
e_ele = ((t->ele[r].d*dif + t->ele[r].c)*dif + t->ele[r].b)*dif +
t->ele[r].a;
e_ele *= system->my_atoms[i].q * system->my_atoms[j].q;
-
+
total_EvdW += e_vdW;
total_Eele += e_ele;
-
+
CEvd = ((t->CEvd[r].d*dif + t->CEvd[r].c)*dif + t->CEvd[r].b)*dif +
t->CEvd[r].a;
-
+
CEclmb = ((t->CEclmb[r].d*dif+t->CEclmb[r].c)*dif+t->CEclmb[r].b)*dif +
t->CEclmb[r].a;
CEclmb *= system->my_atoms[i].q * system->my_atoms[j].q;
-
+
/* tally into per-atom energy */
if( system->pair_ptr->evflag || system->pair_ptr->vflag_atom) {
rvec_ScaledSum( delij, 1., system->my_atoms[i].x,
@@ -357,7 +357,7 @@ void Tabulated_vdW_Coulomb_Energy_OMP(reax_system *system,control_params *contro
pair_reax_ptr->ev_tally_thr_proxy(system->pair_ptr, i, j, natoms, 1, e_vdW, e_ele,
f_tmp, delij[0], delij[1], delij[2], thr);
}
-
+
if( control->virial == 0 ) {
rvec_ScaledAdd( workspace->f[i], -(CEvd + CEclmb), nbr_pj->dvec );
rvec_ScaledAdd( workspace->forceReduction[froffset+j],
@@ -367,10 +367,10 @@ void Tabulated_vdW_Coulomb_Energy_OMP(reax_system *system,control_params *contro
/* for pressure coupling, terms not related to bond order derivatives
are added directly into pressure vector/tensor */
rvec_Scale( temp, CEvd + CEclmb, nbr_pj->dvec );
-
+
rvec_ScaledAdd( workspace->f[i], -1., temp );
rvec_Add( workspace->forceReduction[froffset+j], temp );
-
+
rvec_iMultiply( ext_press, nbr_pj->rel_box, temp );
rvec_Add( workspace->my_ext_pressReduction[tid], ext_press );
}
diff --git a/src/USER-OMP/reaxc_torsion_angles_omp.cpp b/src/USER-OMP/reaxc_torsion_angles_omp.cpp
index ed9ae6c21ef55bb029f0d37a933e13a69f509b5b..94a06bf1f9e0e260bf4e87dd293a45fea8eb5cd0 100644
--- a/src/USER-OMP/reaxc_torsion_angles_omp.cpp
+++ b/src/USER-OMP/reaxc_torsion_angles_omp.cpp
@@ -1,12 +1,12 @@
/*----------------------------------------------------------------------
PuReMD - Purdue ReaxFF Molecular Dynamics Program
Website: https://www.cs.purdue.edu/puremd
-
+
Copyright (2010) Purdue University
-
- Contributing authors:
+
+ Contributing authors:
H. M. Aktulga, J. Fogarty, S. Pandit, A. Grama
- Corresponding author:
+ Corresponding author:
Hasan Metin Aktulga, Michigan State University, hma@cse.msu.edu
Please cite the related publication:
@@ -159,7 +159,7 @@ void Torsion_AnglesOMP( reax_system *system, control_params *control,
if (system->my_atoms[j].orig_id < system->my_atoms[k].orig_id &&
bo_jk->BO > control->thb_cut/*0*/ && Num_Entries(pk, thb_intrs)) {
pj = pbond_jk->sym_index; // pj points to j on k's list
-
+
/* do the same check as above:
are there any 3-body interactions involving k&j
where k is the central atom */
@@ -167,27 +167,27 @@ void Torsion_AnglesOMP( reax_system *system, control_params *control,
type_k = system->my_atoms[k].type;
Delta_k = workspace->Delta_boc[k];
r_jk = pbond_jk->d;
-
+
start_pk = Start_Index(pk, thb_intrs );
end_pk = End_Index(pk, thb_intrs );
start_pj = Start_Index(pj, thb_intrs );
end_pj = End_Index(pj, thb_intrs );
-
+
exp_tor2_jk = exp( -p_tor2 * BOA_jk );
exp_cot2_jk = exp( -p_cot2 * SQR(BOA_jk - 1.5) );
exp_tor3_DjDk = exp( -p_tor3 * (Delta_j + Delta_k) );
exp_tor4_DjDk = exp( p_tor4 * (Delta_j + Delta_k) );
exp_tor34_inv = 1.0 / (1.0 + exp_tor3_DjDk + exp_tor4_DjDk);
f11_DjDk = (2.0 + exp_tor3_DjDk) * exp_tor34_inv;
-
-
+
+
/* pick i up from j-k interaction where j is the central atom */
for (pi = start_pk; pi < end_pk; ++pi) {
p_ijk = &( thb_intrs->select.three_body_list[pi] );
pij = p_ijk->pthb; // pij is pointer to i on j's bond_list
pbond_ij = &( bonds->select.bond_list[pij] );
bo_ij = &( pbond_ij->bo_data );
-
+
if (bo_ij->BO > control->thb_cut/*0*/) {
i = p_ijk->thb;
type_i = system->my_atoms[i].type;
@@ -232,7 +232,7 @@ void Torsion_AnglesOMP( reax_system *system, control_params *control,
r_kl = pbond_kl->d;
BOA_kl = bo_kl->BO - control->thb_cut;
-
+
theta_jkl = p_jkl->theta;
sin_jkl = sin( theta_jkl );
cos_jkl = cos( theta_jkl );
@@ -242,12 +242,12 @@ void Torsion_AnglesOMP( reax_system *system, control_params *control,
else if( sin_jkl <= 0 && sin_jkl >= -MIN_SINE )
tan_jkl_i = cos_jkl / -MIN_SINE;
else tan_jkl_i = cos_jkl /sin_jkl;
-
+
rvec_ScaledSum( dvec_li, 1., system->my_atoms[i].x,
-1., system->my_atoms[l].x );
r_li = rvec_Norm( dvec_li );
-
-
+
+
/* omega and its derivative */
omega = Calculate_Omega( pbond_ij->dvec, r_ij,
pbond_jk->dvec, r_jk,
@@ -262,7 +262,7 @@ void Torsion_AnglesOMP( reax_system *system, control_params *control,
cos2omega = cos( 2. * omega );
cos3omega = cos( 3. * omega );
/* end omega calculations */
-
+
/* torsion energy */
exp_tor1 = exp( fbp->p_tor1 *
SQR(2.0 - bo_jk->BO_pi - f11_DjDk) );
@@ -367,35 +367,35 @@ void Torsion_AnglesOMP( reax_system *system, control_params *control,
}
else {
ivec_Sum(rel_box_jl, pbond_jk->rel_box, pbond_kl->rel_box);
-
+
/* dcos_theta_ijk */
rvec_Scale( force, CEtors7 + CEconj4, p_ijk->dcos_dk );
rvec_Add( workspace->forceReduction[reductionOffset+i], force );
rvec_iMultiply( ext_press, pbond_ij->rel_box, force );
rvec_Add( workspace->my_ext_pressReduction[tid], ext_press );
-
+
rvec_ScaledAdd( workspace->f[j],
CEtors7 + CEconj4, p_ijk->dcos_dj );
-
+
rvec_Scale( force, CEtors7 + CEconj4, p_ijk->dcos_di );
rvec_Add( workspace->forceReduction[reductionOffset+k], force );
rvec_iMultiply( ext_press, pbond_jk->rel_box, force );
rvec_Add( workspace->my_ext_pressReduction[tid], ext_press );
-
+
/* dcos_theta_jkl */
rvec_ScaledAdd( workspace->f[j],
CEtors8 + CEconj5, p_jkl->dcos_di );
-
+
rvec_Scale( force, CEtors8 + CEconj5, p_jkl->dcos_dj );
rvec_Add( workspace->forceReduction[reductionOffset+k], force );
rvec_iMultiply( ext_press, pbond_jk->rel_box, force );
rvec_Add( workspace->my_ext_pressReduction[tid], ext_press );
-
+
rvec_Scale( force, CEtors8 + CEconj5, p_jkl->dcos_dk );
rvec_Add( workspace->forceReduction[reductionOffset+l], force );
rvec_iMultiply( ext_press, rel_box_jl, force );
rvec_Add( workspace->my_ext_pressReduction[tid], ext_press );
-
+
/* dcos_omega */
rvec_Scale( force, CEtors9 + CEconj6, dcos_omega_di );
rvec_Add( workspace->forceReduction[reductionOffset+i], force );
@@ -418,7 +418,7 @@ void Torsion_AnglesOMP( reax_system *system, control_params *control,
/* tally into per-atom virials */
if( system->pair_ptr->vflag_atom || system->pair_ptr->evflag) {
-
+
// acquire vectors
rvec_ScaledSum( delil, 1., system->my_atoms[l].x,
-1., system->my_atoms[i].x );
@@ -430,19 +430,19 @@ void Torsion_AnglesOMP( reax_system *system, control_params *control,
rvec_Scale( fi_tmp, CEtors7 + CEconj4, p_ijk->dcos_dk );
rvec_Scale( fj_tmp, CEtors7 + CEconj4, p_ijk->dcos_dj );
rvec_Scale( fk_tmp, CEtors7 + CEconj4, p_ijk->dcos_di );
-
+
// dcos_theta_jkl
rvec_ScaledAdd( fj_tmp, CEtors8 + CEconj5, p_jkl->dcos_di );
rvec_ScaledAdd( fk_tmp, CEtors8 + CEconj5, p_jkl->dcos_dj );
-
+
// dcos_omega
rvec_ScaledAdd( fi_tmp, CEtors9 + CEconj6, dcos_omega_di );
rvec_ScaledAdd( fj_tmp, CEtors9 + CEconj6, dcos_omega_dj );
rvec_ScaledAdd( fk_tmp, CEtors9 + CEconj6, dcos_omega_dk );
-
+
// tally
eng_tmp = e_tor + e_con;
-
+
if (system->pair_ptr->evflag)
pair_reax_ptr->ev_tally_thr_proxy(system->pair_ptr, j, k, system->n, 1,
eng_tmp, 0.0, 0.0, 0.0, 0.0, 0.0, thr);
@@ -452,7 +452,7 @@ void Torsion_AnglesOMP( reax_system *system, control_params *control,
system->pair_ptr->v_tally4(i, j, k, l, fi_tmp, fj_tmp, fk_tmp,
delil, deljl, delkl );
}
-
+
} // pl check ends
} // pl loop ends
} // pi check ends
diff --git a/src/USER-OMP/reaxc_valence_angles_omp.cpp b/src/USER-OMP/reaxc_valence_angles_omp.cpp
index 5366a84878d63573b80a7145caaad05f8df6d821..6765c091b93070c75831454aa8e0197aaca62390 100644
--- a/src/USER-OMP/reaxc_valence_angles_omp.cpp
+++ b/src/USER-OMP/reaxc_valence_angles_omp.cpp
@@ -1,12 +1,12 @@
/*----------------------------------------------------------------------
PuReMD - Purdue ReaxFF Molecular Dynamics Program
Website: https://www.cs.purdue.edu/puremd
-
+
Copyright (2010) Purdue University
-
- Contributing authors:
+
+ Contributing authors:
H. M. Aktulga, J. Fogarty, S. Pandit, A. Grama
- Corresponding author:
+ Corresponding author:
Hasan Metin Aktulga, Michigan State University, hma@cse.msu.edu
Please cite the related publication:
@@ -198,21 +198,21 @@ void Valence_AnglesOMP( reax_system *system, control_params *control,
BOA_ij = bo_ij->BO - control->thb_cut;
if (BOA_ij > 0.0) {
- i = pbond_ij->nbr;
-
+ i = pbond_ij->nbr;
+
/* first copy 3-body intrs from previously computed ones where i>k.
in the second for-loop below,
we compute only new 3-body intrs where i < k */
for (pk = start_j; pk < pi; ++pk) {
start_pk = Start_Index( pk, thb_intrs );
end_pk = End_Index( pk, thb_intrs );
-
+
for (t = start_pk; t < end_pk; ++t)
if (thb_intrs->select.three_body_list[t].thb == i) {
p_ijk = &(thb_intrs->select.three_body_list[my_offset] );
p_ijk->thb = bonds->select.bond_list[pk].nbr;
-
+
++my_offset;
break;
}
@@ -227,7 +227,7 @@ void Valence_AnglesOMP( reax_system *system, control_params *control,
p_ijk = &( thb_intrs->select.three_body_list[my_offset] );
p_ijk->thb = k;
-
+
++my_offset; // add this to the list of 3-body interactions
} // for(pk)
} // if()
@@ -345,34 +345,34 @@ void Valence_AnglesOMP( reax_system *system, control_params *control,
if (BOA_ij > 0.0) {
i = pbond_ij->nbr;
type_i = system->my_atoms[i].type;
-
-
+
+
/* first copy 3-body intrs from previously computed ones where i>k.
in the second for-loop below,
we compute only new 3-body intrs where i < k */
for (pk = start_j; pk < pi; ++pk) {
start_pk = Start_Index( pk, thb_intrs );
end_pk = End_Index( pk, thb_intrs );
-
+
for (t = start_pk; t < end_pk; ++t)
if (thb_intrs->select.three_body_list[t].thb == i) {
p_ijk = &(thb_intrs->select.three_body_list[my_offset] );
p_kji = &(thb_intrs->select.three_body_list[t]);
-
+
p_ijk->thb = bonds->select.bond_list[pk].nbr;
p_ijk->pthb = pk;
p_ijk->theta = p_kji->theta;
rvec_Copy( p_ijk->dcos_di, p_kji->dcos_dk );
rvec_Copy( p_ijk->dcos_dj, p_kji->dcos_dj );
rvec_Copy( p_ijk->dcos_dk, p_kji->dcos_di );
-
+
++my_offset;
++num_thb_intrs;
break;
}
} // for(pk)
-
-
+
+
/* and this is the second for loop mentioned above */
for (pk = pi+1; pk < end_j; ++pk) {
pbond_jk = &(bonds->select.bond_list[pk]);
@@ -381,15 +381,15 @@ void Valence_AnglesOMP( reax_system *system, control_params *control,
k = pbond_jk->nbr;
type_k = system->my_atoms[k].type;
p_ijk = &( thb_intrs->select.three_body_list[my_offset] );
-
+
// Fix by Sudhir
// if (BOA_jk <= 0) continue;
if (j >= system->n && i >= system->n && k >= system->n) continue;
-
+
Calculate_Theta( pbond_ij->dvec, pbond_ij->d,
pbond_jk->dvec, pbond_jk->d,
&theta, &cos_theta );
-
+
Calculate_dCos_ThetaOMP( pbond_ij->dvec, pbond_ij->d,
pbond_jk->dvec, pbond_jk->d,
&(p_ijk->dcos_di), &(p_ijk->dcos_dj),
@@ -397,66 +397,66 @@ void Valence_AnglesOMP( reax_system *system, control_params *control,
p_ijk->thb = k;
p_ijk->pthb = pk;
p_ijk->theta = theta;
-
+
sin_theta = sin( theta );
if( sin_theta < 1.0e-5 )
sin_theta = 1.0e-5;
-
+
++my_offset; // add this to the list of 3-body interactions
++num_thb_intrs;
-
+
if ((j < system->n) && (BOA_jk > 0.0) &&
(bo_ij->BO > control->thb_cut) &&
(bo_jk->BO > control->thb_cut) &&
(bo_ij->BO * bo_jk->BO > control->thb_cutsq)) {
thbh = &( system->reax_param.thbp[ type_i ][ type_j ][ type_k ] );
-
+
for (cnt = 0; cnt < thbh->cnt; ++cnt) {
-
+
if( fabs(thbh->prm[cnt].p_val1) > 0.001 ) {
thbp = &( thbh->prm[cnt] );
-
+
/* ANGLE ENERGY */
p_val1 = thbp->p_val1;
p_val2 = thbp->p_val2;
p_val4 = thbp->p_val4;
p_val7 = thbp->p_val7;
theta_00 = thbp->theta_00;
-
+
exp3ij = exp( -p_val3 * pow( BOA_ij, p_val4 ) );
f7_ij = 1.0 - exp3ij;
Cf7ij = p_val3 * p_val4 * pow( BOA_ij, p_val4 - 1.0 ) * exp3ij;
-
+
exp3jk = exp( -p_val3 * pow( BOA_jk, p_val4 ) );
f7_jk = 1.0 - exp3jk;
Cf7jk = p_val3 * p_val4 * pow( BOA_jk, p_val4 - 1.0 ) * exp3jk;
-
+
expval7 = exp( -p_val7 * workspace->Delta_boc[j] );
trm8 = 1.0 + expval6 + expval7;
f8_Dj = p_val5 - ( (p_val5 - 1.0) * (2.0 + expval6) / trm8 );
Cf8j = ( (1.0 - p_val5) / SQR(trm8) ) *
( p_val6 * expval6 * trm8 -
(2.0 + expval6) * ( p_val6*expval6 - p_val7*expval7 ) );
-
+
theta_0 = 180.0 - theta_00 * (1.0 -
exp(-p_val10 * (2.0 - SBO2)));
theta_0 = DEG2RAD( theta_0 );
-
+
expval2theta = exp( -p_val2 * SQR(theta_0 - theta) );
if (p_val1 >= 0)
expval12theta = p_val1 * (1.0 - expval2theta);
else // To avoid linear Me-H-Me angles (6/6/06)
expval12theta = p_val1 * -expval2theta;
-
+
CEval1 = Cf7ij * f7_jk * f8_Dj * expval12theta;
CEval2 = Cf7jk * f7_ij * f8_Dj * expval12theta;
CEval3 = Cf8j * f7_ij * f7_jk * expval12theta;
CEval4 = -2.0 * p_val1 * p_val2 * f7_ij * f7_jk * f8_Dj *
expval2theta * (theta_0 - theta);
-
+
Ctheta_0 = p_val10 * DEG2RAD(theta_00) *
exp( -p_val10 * (2.0 - SBO2) );
-
+
CEval5 = -CEval4 * Ctheta_0 * CSBO2;
CEval6 = CEval5 * dSBO1;
CEval7 = CEval5 * dSBO2;
@@ -465,8 +465,8 @@ void Valence_AnglesOMP( reax_system *system, control_params *control,
total_Eang += e_ang =
f7_ij * f7_jk * f8_Dj * expval12theta;
/* END ANGLE ENERGY*/
-
-
+
+
/* PENALTY ENERGY */
p_pen1 = thbp->p_pen1;
p_pen2 = system->reax_param.gp.l[19];
@@ -486,20 +486,20 @@ void Valence_AnglesOMP( reax_system *system, control_params *control,
total_Epen += e_pen =
p_pen1 * f9_Dj * exp_pen2ij * exp_pen2jk;
-
+
CEpen1 = e_pen * Cf9j / f9_Dj;
temp = -2.0 * p_pen2 * e_pen;
CEpen2 = temp * (BOA_ij - 2.0);
CEpen3 = temp * (BOA_jk - 2.0);
/* END PENALTY ENERGY */
-
-
+
+
/* COALITION ENERGY */
p_coa1 = thbp->p_coa1;
p_coa2 = system->reax_param.gp.l[2];
p_coa3 = system->reax_param.gp.l[38];
p_coa4 = system->reax_param.gp.l[30];
-
+
exp_coa2 = exp( p_coa2 * workspace->Delta_val[j] );
total_Ecoa += e_coa =
p_coa1 / (1. + exp_coa2) *
@@ -507,7 +507,7 @@ void Valence_AnglesOMP( reax_system *system, control_params *control,
exp( -p_coa3 * SQR(workspace->total_bond_order[k]-BOA_jk) ) *
exp( -p_coa4 * SQR(BOA_ij - 1.5) ) *
exp( -p_coa4 * SQR(BOA_jk - 1.5) );
-
+
CEcoa1 = -2 * p_coa4 * (BOA_ij - 1.5) * e_coa;
CEcoa2 = -2 * p_coa4 * (BOA_jk - 1.5) * e_coa;
CEcoa3 = -p_coa2 * exp_coa2 * e_coa / (1 + exp_coa2);
@@ -516,15 +516,15 @@ void Valence_AnglesOMP( reax_system *system, control_params *control,
CEcoa5 = -2 * p_coa3 *
(workspace->total_bond_order[k]-BOA_jk) * e_coa;
/* END COALITION ENERGY */
-
-
+
+
/* FORCES */
bo_ij->Cdbo += (CEval1 + CEpen2 + (CEcoa1 - CEcoa4));
bo_jk->Cdbo += (CEval2 + CEpen3 + (CEcoa2 - CEcoa5));
workspace->CdDelta[j] += ((CEval3 + CEval7) + CEpen1 + CEcoa3);
workspace->CdDeltaReduction[reductionOffset+i] += CEcoa4;
workspace->CdDeltaReduction[reductionOffset+k] += CEcoa5;
-
+
for (t = start_j; t < end_j; ++t) {
pbond_jt = &( bonds->select.bond_list[t] );
bo_jt = &(pbond_jt->bo_data);
@@ -536,7 +536,7 @@ void Valence_AnglesOMP( reax_system *system, control_params *control,
bo_jt->Cdbopi += CEval5;
bo_jt->Cdbopi2 += CEval5;
}
-
+
if( control->virial == 0 ) {
rvec_ScaledAdd( workspace->f[j], CEval8, p_ijk->dcos_dj );
rvec_ScaledAdd( workspace->forceReduction[reductionOffset+i],
@@ -549,34 +549,34 @@ void Valence_AnglesOMP( reax_system *system, control_params *control,
added directly into forces and pressure vector/tensor */
rvec_Scale( force, CEval8, p_ijk->dcos_di );
rvec_Add( workspace->forceReduction[reductionOffset+i], force );
-
+
rvec_iMultiply( ext_press, pbond_ij->rel_box, force );
rvec_Add( workspace->my_ext_pressReduction[tid], ext_press );
-
+
rvec_ScaledAdd( workspace->f[j], CEval8, p_ijk->dcos_dj );
-
+
rvec_Scale( force, CEval8, p_ijk->dcos_dk );
rvec_Add( workspace->forceReduction[reductionOffset+k], force );
rvec_iMultiply( ext_press, pbond_jk->rel_box, force );
rvec_Add( workspace->my_ext_pressReduction[tid], ext_press );
}
-
+
/* tally into per-atom virials */
if( system->pair_ptr->vflag_atom || system->pair_ptr->evflag) {
-
+
/* Acquire vectors */
rvec_ScaledSum( delij, 1., system->my_atoms[i].x,
-1., system->my_atoms[j].x );
rvec_ScaledSum( delkj, 1., system->my_atoms[k].x,
-1., system->my_atoms[j].x );
-
+
rvec_Scale( fi_tmp, -CEval8, p_ijk->dcos_di );
rvec_Scale( fj_tmp, -CEval8, p_ijk->dcos_dj );
rvec_Scale( fk_tmp, -CEval8, p_ijk->dcos_dk );
-
+
eng_tmp = e_ang + e_pen + e_coa;
-
+
if( system->pair_ptr->evflag)
pair_reax_ptr->ev_tally_thr_proxy(system->pair_ptr, j, j, system->N, 1,
eng_tmp, 0.0, 0.0, 0.0, 0.0, 0.0, thr);
diff --git a/src/USER-PHONON/fix_phonon.cpp b/src/USER-PHONON/fix_phonon.cpp
index e4ff1dd31c815cb372b8b555b59cd5c6c90eb240..a0fa614eca8eba0dec0d404c2c5dbb75ec65d965 100644
--- a/src/USER-PHONON/fix_phonon.cpp
+++ b/src/USER-PHONON/fix_phonon.cpp
@@ -66,7 +66,7 @@ FixPhonon::FixPhonon(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
MPI_Comm_rank(world,&me);
MPI_Comm_size(world,&nprocs);
-
+
if (narg < 8) error->all(FLERR,"Illegal fix phonon command: number of arguments < 8");
nevery = force->inumeric(FLERR, arg[3]); // Calculate this fix every n steps!
@@ -87,7 +87,7 @@ FixPhonon::FixPhonon(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
strcpy(prefix, arg[7]);
logfile = new char[n+4];
sprintf(logfile,"%s.log",prefix);
-
+
int sdim = sysdim = domain->dimension;
int iarg = 8;
nasr = 20;
@@ -167,10 +167,10 @@ FixPhonon::FixPhonon(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
memory->create(RIloc,ngroup,(sysdim+1),"fix_phonon:RIloc");
memory->create(RIall,ngroup,(sysdim+1),"fix_phonon:RIall");
memory->create(Rsort,ngroup, sysdim, "fix_phonon:Rsort");
-
+
memory->create(Rnow, MAX(1,mynpt),fft_dim,"fix_phonon:Rnow");
memory->create(Rsum, MAX(1,mynpt),fft_dim,"fix_phonon:Rsum");
-
+
memory->create(basis,nucell, sysdim, "fix_phonon:basis");
// because of hermit, only nearly half of q points are stored
@@ -218,7 +218,7 @@ FixPhonon::FixPhonon(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
fflush(flog);
}
surf2tag.clear();
-
+
// default temperature is from thermo
TempSum = new double[sysdim];
id_temp = new char[12];
@@ -270,7 +270,7 @@ FixPhonon::~FixPhonon()
// destroy FFT
delete fft;
memory->sfree(fft_data);
-
+
// clear map info
tag2surf.clear();
surf2tag.clear();
@@ -348,7 +348,7 @@ void FixPhonon::end_of_step()
idx = tag2surf[itag];
domain->unmap(x[i], image[i], xcur);
-
+
for (idim = 0; idim < sysdim; ++idim) RIloc[nfind][idim] = xcur[idim];
RIloc[nfind++][sysdim] = static_cast<double>(idx);
}
@@ -542,13 +542,13 @@ void FixPhonon::readmap()
for (int i = 0; i < atom->nlocal; ++i){
if (atom->mask[i] & groupbit) tag_loc[nfind++] = atom->tag[i];
}
-
+
// gather IDs on local proc
displs[0] = 0;
for (int i = 0; i < nprocs; ++i) recvcnts[i] = 0;
MPI_Allgather(&nfind,1,MPI_INT,recvcnts,1,MPI_INT,world);
for (int i = 1; i < nprocs; ++i) displs[i] = displs[i-1] + recvcnts[i-1];
-
+
MPI_Allgatherv(tag_loc,nfind,MPI_LMP_TAGINT,tag_all,recvcnts,displs,MPI_LMP_TAGINT,world);
for (int i = 0; i < ngroup; ++i){
itag = tag_all[i];
@@ -569,24 +569,24 @@ void FixPhonon::readmap()
error->all(FLERR,line);
}
- if (fgets(line,MAXLINE,fp) == NULL)
+ if (fgets(line,MAXLINE,fp) == NULL)
error->all(FLERR,"Error while reading header of mapping file!");
nx = force->inumeric(FLERR, strtok(line, " \n\t\r\f"));
ny = force->inumeric(FLERR, strtok(NULL, " \n\t\r\f"));
nz = force->inumeric(FLERR, strtok(NULL, " \n\t\r\f"));
nucell = force->inumeric(FLERR, strtok(NULL, " \n\t\r\f"));
ntotal = nx*ny*nz;
- if (ntotal*nucell != ngroup)
+ if (ntotal*nucell != ngroup)
error->all(FLERR,"FFT mesh and number of atoms in group mismatch!");
-
+
// second line of mapfile is comment
- if (fgets(line,MAXLINE,fp) == NULL)
+ if (fgets(line,MAXLINE,fp) == NULL)
error->all(FLERR,"Error while reading comment of mapping file!");
int ix, iy, iz, iu;
// the remaining lines carry the mapping info
for (int i = 0; i < ngroup; ++i){
- if (fgets(line,MAXLINE,fp) == NULL) {info = 1; break;}
+ if (fgets(line,MAXLINE,fp) == NULL) {info = 1; break;}
ix = force->inumeric(FLERR, strtok(line, " \n\t\r\f"));
iy = force->inumeric(FLERR, strtok(NULL, " \n\t\r\f"));
iz = force->inumeric(FLERR, strtok(NULL, " \n\t\r\f"));
@@ -594,7 +594,7 @@ void FixPhonon::readmap()
itag = force->inumeric(FLERR, strtok(NULL, " \n\t\r\f"));
// check if index is in correct range
- if (ix < 0 || ix >= nx || iy < 0 || iy >= ny ||
+ if (ix < 0 || ix >= nx || iy < 0 || iy >= ny ||
iz < 0 || iz >= nz || iu < 0 || iu >= nucell) {info = 2; break;}
// 1 <= itag <= natoms
if (itag < 1 || itag > static_cast<tagint>(atom->natoms)) {info = 3; break;}
@@ -604,11 +604,11 @@ void FixPhonon::readmap()
}
fclose(fp);
- if (tag2surf.size() != surf2tag.size() ||
+ if (tag2surf.size() != surf2tag.size() ||
tag2surf.size() != static_cast<std::size_t>(ngroup) )
error->all(FLERR,"The mapping is incomplete!");
if (info) error->all(FLERR,"Error while reading mapping file!");
-
+
// check the correctness of mapping
int *mask = atom->mask;
tagint *tag = atom->tag;
@@ -618,7 +618,7 @@ void FixPhonon::readmap()
if (mask[i] & groupbit){
itag = tag[i];
idx = tag2surf[itag];
- if (itag != surf2tag[idx])
+ if (itag != surf2tag[idx])
error->one(FLERR,"The mapping info read is incorrect!");
}
}
@@ -677,7 +677,7 @@ void FixPhonon::postprocess( )
TempAve += TempSum[idim] * TempFac;
}
TempAve /= sysdim*boltz;
-
+
for (idq = 0; idq < mynq; ++idq){
GaussJordan(fft_dim, Phi_q[idq]);
ndim =0;
@@ -690,7 +690,7 @@ void FixPhonon::postprocess( )
for (int i = 0; i < nprocs; ++i) recvcnts[i] = fft_cnts[i]*fft_dim*2;
for (int i = 1; i < nprocs; ++i) displs[i] = displs[i-1] + recvcnts[i-1];
MPI_Gatherv(Phi_q[0],mynq*fft_dim2*2,MPI_DOUBLE,Phi_all[0],recvcnts,displs,MPI_DOUBLE,0,world);
-
+
// to collect all basis info and averaged it on root
double basis_root[fft_dim];
if (fft_dim > sysdim) MPI_Reduce(&basis[1][0], &basis_root[sysdim], fft_dim-sysdim, MPI_DOUBLE, MPI_SUM, 0, world);
@@ -709,7 +709,7 @@ void FixPhonon::postprocess( )
basevec[7] = hsum[3] * inv_neval / double(nz);
basevec[6] = hsum[4] * inv_neval / double(nz);
basevec[3] = hsum[5] * inv_neval / double(ny);
-
+
// write binary file, in fact, it is the force constants matrix that is written
// Enforcement of ASR and the conversion of dynamical matrix is done in the postprocessing code
char fname[MAXLINE];
@@ -824,7 +824,7 @@ void FixPhonon::GaussJordan(int n, std::complex<double> *Mat)
indxc[i] = icol;
idr = icol*n+icol;
if (Mat[idr] == std::complex<double>(0.,0.)) error->one(FLERR,"Singular matrix in complex GaussJordan!");
-
+
pivinv = 1./ Mat[idr];
Mat[idr] = std::complex<double>(1.,0.);
idr = icol*n;
@@ -883,7 +883,7 @@ void FixPhonon::EnforceASR()
}
}
}
-
+
// symmetrize
for (int k = 0; k < nucell; ++k)
for (int kp = k; kp < nucell; ++kp){
diff --git a/src/USER-REAXC/pair_reaxc.cpp b/src/USER-REAXC/pair_reaxc.cpp
index 6081563e18359262e3388469cc813ad94a4be450..7f77d875bc8cea1c45a613c6a1f87bc68222de6f 100644
--- a/src/USER-REAXC/pair_reaxc.cpp
+++ b/src/USER-REAXC/pair_reaxc.cpp
@@ -391,7 +391,7 @@ void PairReaxC::init_style( )
if ((cutmax < 2.0*control->bond_cut) && (comm->me == 0))
error->warning(FLERR,"Total cutoff < 2*bond cutoff. May need to use an "
"increased neighbor list skin.");
-
+
for( int i = 0; i < LIST_N; ++i )
lists[i].allocated = 0;
diff --git a/src/USER-SMD/atom_vec_smd.cpp b/src/USER-SMD/atom_vec_smd.cpp
index 84fbfd93efb384983aa71048e5443d5bacc52349..ca38ca7ab5d1b2c6bde35c9468a7cdbcbabac6cb 100644
--- a/src/USER-SMD/atom_vec_smd.cpp
+++ b/src/USER-SMD/atom_vec_smd.cpp
@@ -1143,7 +1143,7 @@ void AtomVecSMD::pack_data(double **buf) {
buf[i][7] = x[i][0];
buf[i][8] = x[i][1];
buf[i][9] = x[i][2];
-
+
buf[i][10] = x0[i][0];
buf[i][11] = x0[i][1];
buf[i][12] = x0[i][2];
diff --git a/src/VORONOI/compute_voronoi_atom.cpp b/src/VORONOI/compute_voronoi_atom.cpp
index cd7d73392d5a6e963130b428f7e4be52ee45dc30..d55db85ef8624501183cecc238fa9c9ae598e8e8 100644
--- a/src/VORONOI/compute_voronoi_atom.cpp
+++ b/src/VORONOI/compute_voronoi_atom.cpp
@@ -42,9 +42,9 @@ using namespace voro;
/* ---------------------------------------------------------------------- */
ComputeVoronoi::ComputeVoronoi(LAMMPS *lmp, int narg, char **arg) :
- Compute(lmp, narg, arg), con_mono(NULL), con_poly(NULL),
- radstr(NULL), voro(NULL), edge(NULL), sendvector(NULL),
- rfield(NULL), tags(NULL), occvec(NULL), sendocc(NULL),
+ Compute(lmp, narg, arg), con_mono(NULL), con_poly(NULL),
+ radstr(NULL), voro(NULL), edge(NULL), sendvector(NULL),
+ rfield(NULL), tags(NULL), occvec(NULL), sendocc(NULL),
lroot(NULL), lnext(NULL), faces(NULL)
{
int sgroup;
@@ -608,7 +608,7 @@ void ComputeVoronoi::processCell(voronoicell_neighbor &c, int i)
nfaces++;
}
}
-
+
} else if (i < atom->nlocal) voro[i][0] = voro[i][1] = 0.0;
}
diff --git a/src/atom.cpp b/src/atom.cpp
index aeb3c1303e01818687701a605feeadc18e63c1bf..ae36a8884b84e5093c98dbd4aabfde2079277ef5 100644
--- a/src/atom.cpp
+++ b/src/atom.cpp
@@ -1384,7 +1384,7 @@ void Atom::data_bodies(int n, char *buf, AtomVecBody *avec_body,
ninteger = force->inumeric(FLERR,strtok(NULL," \t\n\r\f"));
ndouble = force->inumeric(FLERR,strtok(NULL," \t\n\r\f"));
-
+
if ((m = map(tagdata)) >= 0) {
if (ninteger > maxint) {
delete [] ivalues;
@@ -1396,14 +1396,14 @@ void Atom::data_bodies(int n, char *buf, AtomVecBody *avec_body,
maxdouble = ndouble;
dvalues = new double[maxdouble];
}
-
+
for (j = 0; j < ninteger; j++)
ivalues[j] = force->inumeric(FLERR,strtok(NULL," \t\n\r\f"));
for (j = 0; j < ndouble; j++)
dvalues[j] = force->numeric(FLERR,strtok(NULL," \t\n\r\f"));
-
+
avec_body->data_body(m,ninteger,ndouble,ivalues,dvalues);
-
+
} else {
nvalues = ninteger + ndouble; // number of values to skip
for (j = 0; j < nvalues; j++)
@@ -1540,7 +1540,7 @@ void Atom::check_mass(const char *file, int line)
if (mass == NULL) return;
if (rmass_flag) return;
for (int itype = 1; itype <= ntypes; itype++)
- if (mass_setflag[itype] == 0)
+ if (mass_setflag[itype] == 0)
error->all(file,line,"Not all per-type masses are set");
}
@@ -1676,7 +1676,7 @@ void Atom::add_molecule_atom(Molecule *onemol, int iatom,
onemol->ibodyparams,onemol->dbodyparams);
onemol->avec_body->set_quat(ilocal,onemol->quat_external);
}
-
+
if (molecular != 1) return;
// add bond topology info
diff --git a/src/atom_vec_line.cpp b/src/atom_vec_line.cpp
index 3451285370284972a7a5416ed3e0f2b5d0cc9316..ec278562f9ea702abeeeb0b595cfef36487f2ac4 100644
--- a/src/atom_vec_line.cpp
+++ b/src/atom_vec_line.cpp
@@ -1183,7 +1183,7 @@ void AtomVecLine::pack_data(double **buf)
buf[i][2] = ubuf(type[i]).d;
if (line[i] < 0) buf[i][3] = ubuf(0).d;
else buf[i][3] = ubuf(1).d;
- if (line[i] < 0)
+ if (line[i] < 0)
buf[i][4] = rmass[i] / (4.0*MY_PI/3.0 * radius[i]*radius[i]*radius[i]);
else buf[i][4] = rmass[i]/bonus[line[i]].length;
buf[i][5] = x[i][0];
diff --git a/src/balance.cpp b/src/balance.cpp
index 8f994466ad8e18cd30658f92108ff6648fade083..99d88c638338e2cd745d81b063f51027965bbf74 100644
--- a/src/balance.cpp
+++ b/src/balance.cpp
@@ -12,7 +12,7 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
- Contributing authors, for weighted balancing:
+ Contributing authors, for weighted balancing:
Axel Kohlmeyer (Temple U), Iain Bethune (EPCC)
------------------------------------------------------------------------- */
@@ -291,7 +291,7 @@ void Balance::command(int narg, char **arg)
#endif
int niter = 0;
-
+
// perform load-balance
// style XYZ = explicit setting of cutting planes of logical 3d grid
@@ -661,7 +661,7 @@ int *Balance::bisection(int sortflag)
rcb->compute(dim,atom->nlocal,atom->x,weight,shrinklo,shrinkhi);
} else rcb->compute(dim,atom->nlocal,atom->x,NULL,shrinklo,shrinkhi);
}
-
+
rcb->invert(sortflag);
// reset RCB lo/hi bounding box to full simulation box as needed
diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp
index 06227b7a84cfeb2e7e230218778a4b60fca411cb..992d988f902d553f1093341bcf17f61a963a030d 100644
--- a/src/comm_brick.cpp
+++ b/src/comm_brick.cpp
@@ -51,13 +51,13 @@ enum{LAYOUT_UNIFORM,LAYOUT_NONUNIFORM,LAYOUT_TILED}; // several files
/* ---------------------------------------------------------------------- */
-CommBrick::CommBrick(LAMMPS *lmp) :
+CommBrick::CommBrick(LAMMPS *lmp) :
Comm(lmp),
- sendnum(NULL), recvnum(NULL), sendproc(NULL), recvproc(NULL),
+ sendnum(NULL), recvnum(NULL), sendproc(NULL), recvproc(NULL),
size_forward_recv(NULL),
- size_reverse_send(NULL), size_reverse_recv(NULL),
+ size_reverse_send(NULL), size_reverse_recv(NULL),
slablo(NULL), slabhi(NULL), multilo(NULL), multihi(NULL),
- cutghostmulti(NULL), pbc_flag(NULL), pbc(NULL), firstrecv(NULL),
+ cutghostmulti(NULL), pbc_flag(NULL), pbc(NULL), firstrecv(NULL),
sendlist(NULL), maxsendlist(NULL), buf_send(NULL), buf_recv(NULL)
{
style = 0;
diff --git a/src/compute.cpp b/src/compute.cpp
index 00a3984aab3c668b776216e12b8dd7871b1d96de..467faf9fe1e0e258fd4fb22b3a0c1e7fe9b902d2 100644
--- a/src/compute.cpp
+++ b/src/compute.cpp
@@ -38,7 +38,7 @@ int Compute::instance_total = 0;
/* ---------------------------------------------------------------------- */
-Compute::Compute(LAMMPS *lmp, int narg, char **arg) :
+Compute::Compute(LAMMPS *lmp, int narg, char **arg) :
Pointers(lmp),
id(NULL), style(NULL),
vector(NULL), array(NULL), vector_atom(NULL),
@@ -46,7 +46,7 @@ Compute::Compute(LAMMPS *lmp, int narg, char **arg) :
tlist(NULL), vbiasall(NULL)
{
instance_me = instance_total++;
-
+
if (narg < 3) error->all(FLERR,"Illegal compute command");
// compute ID, group, and style
@@ -98,7 +98,7 @@ Compute::Compute(LAMMPS *lmp, int narg, char **arg) :
// setup list of timesteps
ntime = maxtime = 0;
-
+
// data masks
execution_space = Host;
@@ -129,12 +129,12 @@ void Compute::modify_params(int narg, char **arg)
while (iarg < narg) {
// added more specific keywords in Mar17
// at some point, remove generic extra and dynamic
- if (strcmp(arg[iarg],"extra") == 0 ||
+ if (strcmp(arg[iarg],"extra") == 0 ||
strcmp(arg[iarg],"extra/dof") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal compute_modify command");
extra_dof = force->numeric(FLERR,arg[iarg+1]);
iarg += 2;
- } else if (strcmp(arg[iarg],"dynamic") == 0 ||
+ } else if (strcmp(arg[iarg],"dynamic") == 0 ||
strcmp(arg[iarg],"dynamic/dof") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal compute_modify command");
if (strcmp(arg[iarg+1],"no") == 0) dynamic_user = 0;
diff --git a/src/compute_angle.cpp b/src/compute_angle.cpp
index a9fe0f817e1ecf078d6de8de95db6f46ff9519e8..8546350ecd9afc69398cf9d91b73c03172060843 100644
--- a/src/compute_angle.cpp
+++ b/src/compute_angle.cpp
@@ -40,7 +40,7 @@ ComputeAngle::ComputeAngle(LAMMPS *lmp, int narg, char **arg) :
if (!angle)
error->all(FLERR,"Angle style for compute angle command is not hybrid");
size_vector = nsub = angle->nstyles;
-
+
emine = new double[nsub];
vector = new double[nsub];
}
@@ -62,7 +62,7 @@ void ComputeAngle::init()
angle = (AngleHybrid *) force->angle_match("hybrid");
if (!angle)
error->all(FLERR,"Angle style for compute angle command is not hybrid");
- if (angle->nstyles != nsub)
+ if (angle->nstyles != nsub)
error->all(FLERR,"Angle style for compute angle command has changed");
}
diff --git a/src/compute_bond.cpp b/src/compute_bond.cpp
index 29869713e72237f0ebd5e2574ff882e2084ee1dd..29d7ce0ecec42556db00830cd80573ceb171adbf 100644
--- a/src/compute_bond.cpp
+++ b/src/compute_bond.cpp
@@ -40,7 +40,7 @@ ComputeBond::ComputeBond(LAMMPS *lmp, int narg, char **arg) :
if (!bond)
error->all(FLERR,"Bond style for compute bond command is not hybrid");
size_vector = nsub = bond->nstyles;
-
+
emine = new double[nsub];
vector = new double[nsub];
}
@@ -62,7 +62,7 @@ void ComputeBond::init()
bond = (BondHybrid *) force->bond_match("hybrid");
if (!bond)
error->all(FLERR,"Bond style for compute bond command is not hybrid");
- if (bond->nstyles != nsub)
+ if (bond->nstyles != nsub)
error->all(FLERR,"Bond style for compute bond command has changed");
}
diff --git a/src/compute_bond_local.cpp b/src/compute_bond_local.cpp
index e145ad373d7aeafaa42b83c6f19245f7c9abd5d8..b7e84d0a29f64e0844931f0a095f406eb2efb07c 100644
--- a/src/compute_bond_local.cpp
+++ b/src/compute_bond_local.cpp
@@ -216,14 +216,14 @@ int ComputeBondLocal::compute_bonds(int flag)
dz = x[atom1][2] - x[atom2][2];
domain->minimum_image(dx,dy,dz);
rsq = dx*dx + dy*dy + dz*dz;
-
+
if (btype == 0) {
engpot = fbond = 0.0;
engvib = engrot = engtrans = omegasq = vvib = 0.0;
} else {
if (singleflag) engpot = bond->single(btype,rsq,atom1,atom2,fbond);
-
+
if (velflag) {
if (rmass) {
mass1 = rmass[atom1];
@@ -241,51 +241,51 @@ int ComputeBondLocal::compute_bonds(int flag)
vcm[0] = (mass1*v[atom1][0] + mass2*v[atom2][0]) * invmasstotal;
vcm[1] = (mass1*v[atom1][1] + mass2*v[atom2][1]) * invmasstotal;
vcm[2] = (mass1*v[atom1][2] + mass2*v[atom2][2]) * invmasstotal;
-
+
engtrans = 0.5 * masstotal * MathExtra::lensq3(vcm);
-
+
// r12 = unit bond vector from atom1 to atom2
-
+
MathExtra::sub3(x[atom2],x[atom1],r12);
MathExtra::norm3(r12);
-
+
// delr = vector from COM to each atom
// delv = velocity of each atom relative to COM
-
+
MathExtra::sub3(x[atom1],xcm,delr1);
MathExtra::sub3(x[atom2],xcm,delr2);
MathExtra::sub3(v[atom1],vcm,delv1);
MathExtra::sub3(v[atom2],vcm,delv2);
-
+
// vpar = component of delv parallel to bond vector
-
+
vpar1 = MathExtra::dot3(delv1,r12);
vpar2 = MathExtra::dot3(delv2,r12);
engvib = 0.5 * (mass1*vpar1*vpar1 + mass2*vpar2*vpar2);
-
+
// vvib = relative velocity of 2 atoms along bond direction
// vvib < 0 for 2 atoms moving towards each other
// vvib > 0 for 2 atoms moving apart
-
+
vvib = vpar2 - vpar1;
-
+
// vrotsq = tangential speed squared of atom1 only
// omegasq = omega squared, and is the same for atom1 and atom2
-
- inertia = mass1*MathExtra::lensq3(delr1) +
+
+ inertia = mass1*MathExtra::lensq3(delr1) +
mass2*MathExtra::lensq3(delr2);
vrotsq = MathExtra::lensq3(delv1) - vpar1*vpar1;
omegasq = vrotsq / MathExtra::lensq3(delr1);
-
+
engrot = 0.5 * inertia * omegasq;
-
+
// sanity check: engtotal = engtrans + engvib + engrot
-
- //engtot = 0.5 * (mass1*MathExtra::lensq3(v[atom1]) +
+
+ //engtot = 0.5 * (mass1*MathExtra::lensq3(v[atom1]) +
// mass2*MathExtra::lensq3(v[atom2]));
//if (fabs(engtot-engtrans-engvib-engrot) > EPSILON)
// error->one(FLERR,"Sanity check on 3 energy components failed");
-
+
// scale energies by units
mvv2e = force->mvv2e;
diff --git a/src/compute_centro_atom.cpp b/src/compute_centro_atom.cpp
index c76b569462aa3e4bbd6a03a38c5df9d0b46fb8c7..089c57798008527c99b5046565fce975492c0e41 100644
--- a/src/compute_centro_atom.cpp
+++ b/src/compute_centro_atom.cpp
@@ -207,7 +207,7 @@ void ComputeCentroAtom::compute_peratom()
// check whether to include local crystal symmetry axes
if (!axes_flag) {
-
+
// if not nnn neighbors, centro = 0.0
if (n < nnn) {
@@ -234,9 +234,9 @@ void ComputeCentroAtom::compute_peratom()
}
}
-
+
} else {
-
+
// calculate local crystal symmetry axes
// rsq1, rsq2 are two smallest values of R^2
@@ -248,7 +248,7 @@ void ComputeCentroAtom::compute_peratom()
double* r1 = &array_atom[i][1];
double* r2 = &array_atom[i][4];
double* r3 = &array_atom[i][7];
-
+
if (n < nnn) {
centro[i] = 0.0;
MathExtra::zero3(r1);
@@ -272,7 +272,7 @@ void ComputeCentroAtom::compute_peratom()
delz = x[jj][2] + x[kk][2] - 2.0*ztmp;
double rsq = delx*delx + dely*dely + delz*delz;
pairs[n++] = rsq;
-
+
if (rsq < rsq2) {
if (rsq < rsq1) {
rsq2 = rsq1;
diff --git a/src/compute_chunk_atom.cpp b/src/compute_chunk_atom.cpp
index 4463e48fa8fe4e55b4b270292fe7c92b48cadaca..b1453a2a119902e110e9260888f2c9467acc064c 100644
--- a/src/compute_chunk_atom.cpp
+++ b/src/compute_chunk_atom.cpp
@@ -322,7 +322,7 @@ ComputeChunkAtom::ComputeChunkAtom(LAMMPS *lmp, int narg, char **arg) :
(dim[0] == dim[1] || dim[1] == dim[2] || dim[0] == dim[2]))
error->all(FLERR,"Illegal compute chunk/atom command");
if (which == BINSPHERE) {
- if (domain->dimension == 2 && sorigin_user[2] != 0.0)
+ if (domain->dimension == 2 && sorigin_user[2] != 0.0)
error->all(FLERR,"Compute chunk/atom sphere z origin must be 0.0 for 2d");
if (sradmin_user < 0.0 || sradmin_user >= sradmax_user || nsbin < 1)
error->all(FLERR,"Illegal compute chunk/atom command");
@@ -330,7 +330,7 @@ ComputeChunkAtom::ComputeChunkAtom(LAMMPS *lmp, int narg, char **arg) :
if (which == BINCYLINDER) {
if (delta[0] <= 0.0)
error->all(FLERR,"Illegal compute chunk/atom command");
- if (domain->dimension == 2 && dim[0] != 2)
+ if (domain->dimension == 2 && dim[0] != 2)
error->all(FLERR,"Compute chunk/atom cylinder axis must be z for 2d");
if (cradmin_user < 0.0 || cradmin_user >= cradmax_user || ncbin < 1)
error->all(FLERR,"Illegal compute chunk/atom command");
@@ -401,7 +401,7 @@ ComputeChunkAtom::ComputeChunkAtom(LAMMPS *lmp, int narg, char **arg) :
if (binflag) {
double scale;
- if (which == BIN1D || which == BIN2D || which == BIN3D ||
+ if (which == BIN1D || which == BIN2D || which == BIN3D ||
which == BINCYLINDER) {
if (which == BIN1D || which == BINCYLINDER) ndim = 1;
if (which == BIN2D) ndim = 2;
@@ -1305,9 +1305,9 @@ int ComputeChunkAtom::setup_sphere_bins()
int flag = 0;
if (periodicity[0] && sradmax > prd_half[0]) flag = 1;
if (periodicity[1] && sradmax > prd_half[1]) flag = 1;
- if (domain->dimension == 3 &&
+ if (domain->dimension == 3 &&
periodicity[2] && sradmax > prd_half[2]) flag = 1;
- if (flag)
+ if (flag)
error->all(FLERR,"Compute chunk/atom bin/sphere radius "
"is too large for periodic box");
}
@@ -1370,7 +1370,7 @@ int ComputeChunkAtom::setup_cylinder_bins()
int flag = 0;
if (periodicity[cdim1] && sradmax > prd_half[cdim1]) flag = 1;
if (periodicity[cdim2] && sradmax > prd_half[cdim2]) flag = 1;
- if (flag)
+ if (flag)
error->all(FLERR,"Compute chunk/atom bin/cylinder radius "
"is too large for periodic box");
}
diff --git a/src/compute_dihedral.cpp b/src/compute_dihedral.cpp
index bbd7fe20384e6b83dbd4585a62264365571f78a0..2afcb5e321ae655cee5c3af02a46a6543ca715e0 100644
--- a/src/compute_dihedral.cpp
+++ b/src/compute_dihedral.cpp
@@ -41,7 +41,7 @@ ComputeDihedral::ComputeDihedral(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,
"Dihedral style for compute dihedral command is not hybrid");
size_vector = nsub = dihedral->nstyles;
-
+
emine = new double[nsub];
vector = new double[nsub];
}
@@ -64,7 +64,7 @@ void ComputeDihedral::init()
if (!dihedral)
error->all(FLERR,
"Dihedral style for compute dihedral command is not hybrid");
- if (dihedral->nstyles != nsub)
+ if (dihedral->nstyles != nsub)
error->all(FLERR,"Dihedral style for compute dihedral command has changed");
}
diff --git a/src/compute_dipole_chunk.cpp b/src/compute_dipole_chunk.cpp
index 45389ee61418a425f082e8bb80ec6438a2f8f322..b4beacb9849a792e97e1acd6d44fce5992ef7609 100644
--- a/src/compute_dipole_chunk.cpp
+++ b/src/compute_dipole_chunk.cpp
@@ -29,13 +29,13 @@ enum { MASSCENTER, GEOMCENTER };
/* ---------------------------------------------------------------------- */
-ComputeDipoleChunk::ComputeDipoleChunk(LAMMPS *lmp, int narg, char **arg) :
+ComputeDipoleChunk::ComputeDipoleChunk(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg),
- idchunk(NULL), massproc(NULL), masstotal(NULL), chrgproc(NULL),
+ idchunk(NULL), massproc(NULL), masstotal(NULL), chrgproc(NULL),
chrgtotal(NULL), com(NULL),
comall(NULL), dipole(NULL), dipoleall(NULL)
{
- if ((narg != 4) && (narg != 5))
+ if ((narg != 4) && (narg != 5))
error->all(FLERR,"Illegal compute dipole/chunk command");
array_flag = 1;
@@ -57,7 +57,7 @@ ComputeDipoleChunk::ComputeDipoleChunk(LAMMPS *lmp, int narg, char **arg) :
else if (strcmp(arg[4],"mass") == 0) usecenter = MASSCENTER;
else error->all(FLERR,"Illegal compute dipole/chunk command");
}
-
+
init();
// chunk-based data
diff --git a/src/compute_global_atom.cpp b/src/compute_global_atom.cpp
index b786043a34f21d11b64bfe902f069322452ae936..6cd79f919c9ac27cef83b1edb69b20594ab29c37 100644
--- a/src/compute_global_atom.cpp
+++ b/src/compute_global_atom.cpp
@@ -59,11 +59,11 @@ ComputeGlobalAtom::ComputeGlobalAtom(LAMMPS *lmp, int narg, char **arg) :
if (arg[iarg][0] == 'c') whichref = COMPUTE;
else if (arg[iarg][0] == 'f') whichref = FIX;
else if (arg[iarg][0] == 'v') whichref = VARIABLE;
-
+
int n = strlen(arg[iarg]);
char *suffix = new char[n];
strcpy(suffix,&arg[iarg][2]);
-
+
char *ptr = strchr(suffix,'[');
if (ptr) {
if (suffix[strlen(suffix)-1] != ']')
@@ -71,7 +71,7 @@ ComputeGlobalAtom::ComputeGlobalAtom(LAMMPS *lmp, int narg, char **arg) :
indexref = atoi(ptr+1);
*ptr = '\0';
} else indexref = 0;
-
+
n = strlen(suffix) + 1;
idref = new char[n];
strcpy(idref,suffix);
@@ -157,7 +157,7 @@ ComputeGlobalAtom::ComputeGlobalAtom(LAMMPS *lmp, int narg, char **arg) :
if (indexref && indexref > modify->compute[icompute]->size_peratom_cols)
error->all(FLERR,
"Compute global/atom compute array is accessed out-of-range");
-
+
} else if (whichref == FIX) {
int ifix = modify->find_fix(idref);
if (ifix < 0)
@@ -286,7 +286,7 @@ void ComputeGlobalAtom::init()
error->all(FLERR,"Variable name for compute global/atom does not exist");
ref2index = ivariable;
}
-
+
for (int m = 0; m < nvalues; m++) {
if (which[m] == COMPUTE) {
int icompute = modify->find_compute(ids[m]);
@@ -332,17 +332,17 @@ void ComputeGlobalAtom::compute_peratom()
memory->create(array_atom,nmax,nvalues,"global/atom:array_atom");
}
}
-
+
// setup current peratom indices
// integer indices are rounded down from double values
// indices are decremented from 1 to N -> 0 to N-1
int *mask = atom->mask;
int nlocal = atom->nlocal;
-
+
if (whichref == COMPUTE) {
Compute *compute = modify->compute[ref2index];
-
+
if (!(compute->invoked_flag & INVOKED_PERATOM)) {
compute->compute_peratom();
compute->invoked_flag |= INVOKED_PERATOM;
@@ -351,42 +351,42 @@ void ComputeGlobalAtom::compute_peratom()
if (indexref == 0) {
double *compute_vector = compute->vector_atom;
for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit)
+ if (mask[i] & groupbit)
indices[i] = static_cast<int> (compute_vector[i]) - 1;
} else {
double **compute_array = compute->array_atom;
int im1 = indexref - 1;
for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit)
+ if (mask[i] & groupbit)
indices[i] = static_cast<int> (compute_array[i][im1]) - 1;
}
-
+
} else if (whichref == FIX) {
if (update->ntimestep % modify->fix[ref2index]->peratom_freq)
error->all(FLERR,"Fix used in compute global/atom not "
"computed at compatible time");
Fix *fix = modify->fix[ref2index];
-
+
if (indexref == 0) {
double *fix_vector = fix->vector_atom;
for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit)
+ if (mask[i] & groupbit)
indices[i] = static_cast<int> (fix_vector[i]) - 1;
} else {
double **fix_array = fix->array_atom;
int im1 = indexref - 1;
for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit)
+ if (mask[i] & groupbit)
indices[i] = static_cast<int> (fix_array[i][im1]) - 1;
}
-
+
} else if (whichref == VARIABLE) {
if (atom->nmax > nmax) {
nmax = atom->nmax;
memory->destroy(varatom);
memory->create(varatom,nmax,"global/atom:varatom");
}
-
+
input->variable->compute_atom(ref2index,igroup,varatom,1,0);
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
@@ -410,7 +410,7 @@ void ComputeGlobalAtom::compute_peratom()
compute->compute_vector();
compute->invoked_flag |= INVOKED_VECTOR;
}
-
+
source = compute->vector;
vmax = compute->size_vector;
@@ -468,7 +468,7 @@ void ComputeGlobalAtom::compute_peratom()
compute->compute_array();
compute->invoked_flag |= INVOKED_ARRAY;
}
-
+
double **compute_array = compute->array;
vmax = compute->size_array_rows;
diff --git a/src/compute_group_group.cpp b/src/compute_group_group.cpp
index d0c6c92e576541a38715fe0a613aa1c7424188d8..51c978cb530017af17c9cffaf4ca6217551608c8 100644
--- a/src/compute_group_group.cpp
+++ b/src/compute_group_group.cpp
@@ -259,7 +259,7 @@ void ComputeGroupGroup::pair_contribution()
// skip if atom J is not in either group
- if (!(mask[j] & groupbit || mask[j] & jgroupbit)) continue;
+ if (!(mask[j] & groupbit || mask[j] & jgroupbit)) continue;
// skip if atoms I,J are only in the same group
@@ -267,8 +267,8 @@ void ComputeGroupGroup::pair_contribution()
int ji_flag = 0;
if (mask[i] & groupbit && mask[j] & jgroupbit) ij_flag = 1;
if (mask[j] & groupbit && mask[i] & jgroupbit) ji_flag = 1;
- if (!ij_flag && !ji_flag) continue;
-
+ if (!ij_flag && !ji_flag) continue;
+
// skip if molecule IDs of atoms I,J do not satisfy molflag setting
if (molflag != OFF) {
diff --git a/src/compute_gyration.cpp b/src/compute_gyration.cpp
index 7f06df91036357ac12157970ffac7f79596d2471..0877efa4d9214201442da4463d0c7f0bde1375ac 100644
--- a/src/compute_gyration.cpp
+++ b/src/compute_gyration.cpp
@@ -109,7 +109,7 @@ void ComputeGyration::compute_vector()
}
MPI_Allreduce(rg,vector,6,MPI_DOUBLE,MPI_SUM,world);
- if (masstotal > 0.0)
+ if (masstotal > 0.0)
for (int i = 0; i < 6; i++)
vector[i] /= masstotal;
}
diff --git a/src/compute_gyration_chunk.cpp b/src/compute_gyration_chunk.cpp
index ddec1315a2ddb4edc05ba739d55f278ea94a9879..efb26c9ad2721f006da6ee4896baa313b7755453 100644
--- a/src/compute_gyration_chunk.cpp
+++ b/src/compute_gyration_chunk.cpp
@@ -28,7 +28,7 @@ using namespace LAMMPS_NS;
ComputeGyrationChunk::ComputeGyrationChunk(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg),
- idchunk(NULL), massproc(NULL), masstotal(NULL), com(NULL), comall(NULL),
+ idchunk(NULL), massproc(NULL), masstotal(NULL), com(NULL), comall(NULL),
rg(NULL), rgall(NULL), rgt(NULL), rgtall(NULL)
{
if (narg < 4) error->all(FLERR,"Illegal compute gyration/chunk command");
diff --git a/src/compute_hexorder_atom.cpp b/src/compute_hexorder_atom.cpp
index 04421dca3efbb8c5e74a6cade90ab5cba1c79369..44525e67a2e9f2d5e7f0443d4574db2b1386f40f 100644
--- a/src/compute_hexorder_atom.cpp
+++ b/src/compute_hexorder_atom.cpp
@@ -65,7 +65,7 @@ ComputeHexOrderAtom::ComputeHexOrderAtom(LAMMPS *lmp, int narg, char **arg) :
iarg += 2;
} else if (strcmp(arg[iarg],"nnn") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal compute hexorder/atom command");
- if (strcmp(arg[iarg+1],"NULL") == 0)
+ if (strcmp(arg[iarg+1],"NULL") == 0)
nnn = 0;
else {
nnn = force->numeric(FLERR,arg[iarg+1]);
@@ -179,7 +179,7 @@ void ComputeHexOrderAtom::compute_peratom()
ztmp = x[i][2];
jlist = firstneigh[i];
jnum = numneigh[i];
-
+
// insure distsq and nearest arrays are long enough
if (jnum > maxneigh) {
@@ -225,11 +225,11 @@ void ComputeHexOrderAtom::compute_peratom()
double usum = 0.0;
double vsum = 0.0;
-
+
for (jj = 0; jj < ncount; jj++) {
j = nearest[jj];
j &= NEIGHMASK;
-
+
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
double u, v;
@@ -339,8 +339,8 @@ void ComputeHexOrderAtom::select2(int k, int n, double *arr, int *iarr)
double ComputeHexOrderAtom::memory_usage()
{
double bytes = ncol*nmax * sizeof(double);
- bytes += maxneigh * sizeof(double);
- bytes += maxneigh * sizeof(int);
+ bytes += maxneigh * sizeof(double);
+ bytes += maxneigh * sizeof(int);
return bytes;
}
diff --git a/src/compute_improper.cpp b/src/compute_improper.cpp
index 32c5811af13ff272be9829a8656b5553f9074821..60d22d0d70d938d8718f62eb6e5a21d875afb37b 100644
--- a/src/compute_improper.cpp
+++ b/src/compute_improper.cpp
@@ -41,7 +41,7 @@ ComputeImproper::ComputeImproper(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,
"Improper style for compute improper command is not hybrid");
size_vector = nsub = improper->nstyles;
-
+
emine = new double[nsub];
vector = new double[nsub];
}
@@ -64,7 +64,7 @@ void ComputeImproper::init()
if (!improper)
error->all(FLERR,
"Improper style for compute improper command is not hybrid");
- if (improper->nstyles != nsub)
+ if (improper->nstyles != nsub)
error->all(FLERR,"Improper style for compute improper command has changed");
}
diff --git a/src/compute_omega_chunk.cpp b/src/compute_omega_chunk.cpp
index f2a83949641fdce2f380eea3583d9f61690819f0..d89c57889e2ce515fca42ec070ef898eda1786c6 100644
--- a/src/compute_omega_chunk.cpp
+++ b/src/compute_omega_chunk.cpp
@@ -207,8 +207,8 @@ void ComputeOmegaChunk::compute_array()
// determinant = triple product of rows of inertia matrix
iall = &inertiaall[m][0];
- determinant = iall[0] * (iall[1]*iall[2] - iall[4]*iall[4]) +
- iall[3] * (iall[4]*iall[5] - iall[3]*iall[2]) +
+ determinant = iall[0] * (iall[1]*iall[2] - iall[4]*iall[4]) +
+ iall[3] * (iall[4]*iall[5] - iall[3]*iall[2]) +
iall[5] * (iall[3]*iall[4] - iall[1]*iall[5]);
ione[0][0] = iall[0];
@@ -238,7 +238,7 @@ void ComputeOmegaChunk::compute_array()
for (i = 0; i < 3; i++)
for (j = 0; j < 3; j++)
inverse[i][j] *= invdeterminant;
-
+
mall = &angmomall[m][0];
omega[m][0] = inverse[0][0]*mall[0] + inverse[0][1]*mall[1] +
inverse[0][2]*mall[2];
@@ -268,16 +268,16 @@ void ComputeOmegaChunk::compute_array()
// enforce 3 evectors as a right-handed coordinate system
// flip 3rd vector if needed
-
+
MathExtra::cross3(ex,ey,cross);
if (MathExtra::dot3(cross,ez) < 0.0) MathExtra::negate3(ez);
// if any principal moment < scaled EPSILON, set to 0.0
-
+
double max;
max = MAX(idiag[0],idiag[1]);
max = MAX(max,idiag[2]);
-
+
if (idiag[0] < EPSILON*max) idiag[0] = 0.0;
if (idiag[1] < EPSILON*max) idiag[1] = 0.0;
if (idiag[2] < EPSILON*max) idiag[2] = 0.0;
diff --git a/src/compute_orientorder_atom.cpp b/src/compute_orientorder_atom.cpp
index b443d56bf82b3fd7a8d4f50b58181ecb49e922e4..4fc9ab060b39eda652f027023d1864535c6b3355 100644
--- a/src/compute_orientorder_atom.cpp
+++ b/src/compute_orientorder_atom.cpp
@@ -74,7 +74,7 @@ ComputeOrientOrderAtom::ComputeOrientOrderAtom(LAMMPS *lmp, int narg, char **arg
int iarg = 3;
while (iarg < narg) {
if (strcmp(arg[iarg],"nnn") == 0) {
- if (iarg+2 > narg)
+ if (iarg+2 > narg)
error->all(FLERR,"Illegal compute orientorder/atom command");
if (strcmp(arg[iarg+1],"NULL") == 0) {
nnn = 0;
@@ -93,7 +93,7 @@ ComputeOrientOrderAtom::ComputeOrientOrderAtom(LAMMPS *lmp, int narg, char **arg
memory->destroy(qlist);
memory->create(qlist,nqlist,"orientorder/atom:qlist");
iarg += 2;
- if (iarg+nqlist > narg)
+ if (iarg+nqlist > narg)
error->all(FLERR,"Illegal compute orientorder/atom command");
qmax = 0;
for (int iw = 0; iw < nqlist; iw++) {
@@ -501,7 +501,7 @@ double ComputeOrientOrderAtom::dist(const double r[])
Y_l^m (theta, phi) = prefactor(l, m, cos(theta)) * exp(i*m*phi)
------------------------------------------------------------------------- */
-double ComputeOrientOrderAtom::polar_prefactor(int l, int m, double costheta)
+double ComputeOrientOrderAtom::polar_prefactor(int l, int m, double costheta)
{
const int mabs = abs(m);
@@ -521,7 +521,7 @@ double ComputeOrientOrderAtom::polar_prefactor(int l, int m, double costheta)
associated legendre polynomial
------------------------------------------------------------------------- */
-double ComputeOrientOrderAtom::associated_legendre(int l, int m, double x)
+double ComputeOrientOrderAtom::associated_legendre(int l, int m, double x)
{
if (l < m) return 0.0;
diff --git a/src/compute_pair_local.cpp b/src/compute_pair_local.cpp
index adac486bef34567c9245813bf7712dcd18fa1883..1d28ae8b769ebcbc7ea427fa9b5008e986a03fc2 100644
--- a/src/compute_pair_local.cpp
+++ b/src/compute_pair_local.cpp
@@ -76,7 +76,7 @@ ComputePairLocal::ComputePairLocal(LAMMPS *lmp, int narg, char **arg) :
while (iarg < narg) {
if (strcmp(arg[iarg],"cutoff") == 0) {
- if (iarg+2 > narg)
+ if (iarg+2 > narg)
error->all(FLERR,"Illegal compute pair/local command");
if (strcmp(arg[iarg+1],"type") == 0) cutstyle = TYPE;
else if (strcmp(arg[iarg+1],"radius") == 0) cutstyle = RADIUS;
diff --git a/src/compute_pe_atom.cpp b/src/compute_pe_atom.cpp
index f83c91b94cd7e71397a0090c8ba81b9ca9df4e37..c324a8eff7d4740b723c96559f0a69bf9dc92ed4 100644
--- a/src/compute_pe_atom.cpp
+++ b/src/compute_pe_atom.cpp
@@ -153,7 +153,7 @@ void ComputePEAtom::compute_peratom()
// add in per-atom contributions from relevant fixes
// always only for owned atoms, not ghost
- if (fixflag && modify->n_thermo_energy_atom)
+ if (fixflag && modify->n_thermo_energy_atom)
modify->thermo_energy_atom(nlocal,energy);
// communicate ghost energy between neighbor procs
diff --git a/src/compute_property_local.cpp b/src/compute_property_local.cpp
index 27b31979c9885e797314c09ec23bef5fc4c45bd7..e38817b4ea8085a22f3dda409d9be22d272a4a7a 100644
--- a/src/compute_property_local.cpp
+++ b/src/compute_property_local.cpp
@@ -222,7 +222,7 @@ ComputePropertyLocal::ComputePropertyLocal(LAMMPS *lmp, int narg, char **arg) :
while (iarg < narg) {
if (strcmp(arg[iarg],"cutoff") == 0) {
- if (iarg+2 > narg)
+ if (iarg+2 > narg)
error->all(FLERR,"Illegal compute property/local command");
if (strcmp(arg[iarg+1],"type") == 0) cutstyle = TYPE;
else if (strcmp(arg[iarg+1],"radius") == 0) cutstyle = RADIUS;
diff --git a/src/compute_reduce.cpp b/src/compute_reduce.cpp
index 41a810757155755657dbe2b22e41644c339e9b7b..91379e9ba6dca5169c052530c71b53b032a869c7 100644
--- a/src/compute_reduce.cpp
+++ b/src/compute_reduce.cpp
@@ -44,8 +44,8 @@ enum{PERATOM,LOCAL};
ComputeReduce::ComputeReduce(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg),
- nvalues(0), which(NULL), argindex(NULL), flavor(NULL),
- value2index(NULL), ids(NULL), onevec(NULL), replace(NULL), indices(NULL),
+ nvalues(0), which(NULL), argindex(NULL), flavor(NULL),
+ value2index(NULL), ids(NULL), onevec(NULL), replace(NULL), indices(NULL),
owner(NULL), idregion(NULL), varatom(NULL)
{
int iarg = 0;
diff --git a/src/compute_slice.cpp b/src/compute_slice.cpp
index aa2c1067c48cb1c1e5f08723a2eaa7a935a00936..23bed054ace3815a9a9cb19770ec17369e55b954 100644
--- a/src/compute_slice.cpp
+++ b/src/compute_slice.cpp
@@ -343,7 +343,7 @@ void ComputeSlice::extract_one(int m, double *vec, int stride)
} else if (which[m] == VARIABLE) {
double *varvec;
int nvec = input->variable->compute_vector(value2index[m],&varvec);
- if (nvec < nstop)
+ if (nvec < nstop)
error->all(FLERR,"Compute slice variable is not long enough");
j = 0;
for (i = nstart; i < nstop; i += nskip) {
diff --git a/src/compute_temp_chunk.cpp b/src/compute_temp_chunk.cpp
index 7de894d3679f39e1bcbc387c4a76709fcd090750..1cc98c4ee83c9d63d3027b96271f74233573117f 100644
--- a/src/compute_temp_chunk.cpp
+++ b/src/compute_temp_chunk.cpp
@@ -30,7 +30,7 @@ enum{TEMP,KECOM,INTERNAL};
ComputeTempChunk::ComputeTempChunk(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg),
- which(NULL), idchunk(NULL), id_bias(NULL), sum(NULL), sumall(NULL), count(NULL),
+ which(NULL), idchunk(NULL), id_bias(NULL), sum(NULL), sumall(NULL), count(NULL),
countall(NULL), massproc(NULL), masstotal(NULL), vcm(NULL), vcmall(NULL)
{
if (narg < 4) error->all(FLERR,"Illegal compute temp/chunk command");
@@ -131,7 +131,7 @@ ComputeTempChunk::ComputeTempChunk(LAMMPS *lmp, int narg, char **arg) :
nchunk = 1;
maxchunk = 0;
-
+
if (nvalues) {
array_flag = 1;
size_array_cols = nvalues;
diff --git a/src/create_atoms.cpp b/src/create_atoms.cpp
index 992049a81f0d73d8182e393d2d1a2ac4343c6d35..6caa4157ce89e5b7b241415e0a357d111358eaf0 100644
--- a/src/create_atoms.cpp
+++ b/src/create_atoms.cpp
@@ -365,7 +365,7 @@ void CreateAtoms::command(int narg, char **arg)
else add_lattice();
// init per-atom fix/compute/variable values for created atoms
-
+
atom->data_fix_compute_variable(nlocal_previous,atom->nlocal);
// set new total # of atoms and error check
diff --git a/src/create_bonds.cpp b/src/create_bonds.cpp
index 48f12406b6ea06cb4fda7a20ed90fd4b85ef8bf0..f19458772086dd9831f517e9d22011780d2b3088 100644
--- a/src/create_bonds.cpp
+++ b/src/create_bonds.cpp
@@ -329,7 +329,7 @@ void CreateBonds::single_bond()
int allcount;
MPI_Allreduce(&count,&allcount,1,MPI_INT,MPI_SUM,world);
- if (allcount != 2)
+ if (allcount != 2)
error->all(FLERR,"Create_bonds single/bond atoms do not exist");
// create bond once or 2x if newton_bond set
@@ -373,7 +373,7 @@ void CreateBonds::single_angle()
int allcount;
MPI_Allreduce(&count,&allcount,1,MPI_INT,MPI_SUM,world);
- if (allcount != 3)
+ if (allcount != 3)
error->all(FLERR,"Create_bonds single/angle atoms do not exist");
// create angle once or 3x if newton_bond set
@@ -434,7 +434,7 @@ void CreateBonds::single_dihedral()
int allcount;
MPI_Allreduce(&count,&allcount,1,MPI_INT,MPI_SUM,world);
- if (allcount != 4)
+ if (allcount != 4)
error->all(FLERR,"Create_bonds single/dihedral atoms do not exist");
// create bond once or 4x if newton_bond set
diff --git a/src/displace_atoms.cpp b/src/displace_atoms.cpp
index a9aa5cf8558aa2c620d9e5ce99ab882d7eb7af4b..66988d467339c4d56a3b6d93ed136ab700473d23 100644
--- a/src/displace_atoms.cpp
+++ b/src/displace_atoms.cpp
@@ -260,8 +260,8 @@ void DisplaceAtoms::command(int narg, char **arg)
if (ellipsoid_flag || tri_flag || body_flag) quat_flag = 1;
// AtomVec pointers to retrieve per-atom storage of extra quantities
-
- AtomVecEllipsoid *avec_ellipsoid =
+
+ AtomVecEllipsoid *avec_ellipsoid =
(AtomVecEllipsoid *) atom->style_match("ellipsoid");
AtomVecLine *avec_line = (AtomVecLine *) atom->style_match("line");
AtomVecTri *avec_tri = (AtomVecTri *) atom->style_match("tri");
@@ -304,14 +304,14 @@ void DisplaceAtoms::command(int narg, char **arg)
if (dim == 3) x[i][2] = point[2] + c[2] + disp[2];
// theta for lines
-
+
if (theta_flag && line[i] >= 0.0) {
theta_new = fmod(avec_line->bonus[line[i]].theta+angle,MY_2PI);
avec_line->bonus[atom->line[i]].theta = theta_new;
}
-
+
// quats for ellipsoids, tris, and bodies
-
+
if (quat_flag) {
quat = NULL;
if (ellipsoid_flag && ellipsoid[i] >= 0)
diff --git a/src/domain.cpp b/src/domain.cpp
index 8522046434a9687b063c1c364d81bd6391548d68..c4dcf20b6423dc48d98c28243dbec9f97738b3ec 100644
--- a/src/domain.cpp
+++ b/src/domain.cpp
@@ -636,7 +636,7 @@ int Domain::inside(double* x)
x[1] < lo[1] || x[1] >= hi[1] ||
x[2] < lo[2] || x[2] >= hi[2]) return 0;
else return 1;
-
+
} else {
lo = boxlo_lamda;
hi = boxhi_lamda;
@@ -647,7 +647,7 @@ int Domain::inside(double* x)
lamda[1] < lo[1] || lamda[1] >= hi[1] ||
lamda[2] < lo[2] || lamda[2] >= hi[2]) return 0;
else return 1;
-
+
}
}
@@ -1617,7 +1617,7 @@ void Domain::image_flip(int m, int n, int p)
return 1 if this proc owns atom with coords x, else return 0
x is returned remapped into periodic box
if image flag is passed, flag is updated via remap(x,image)
- if image = NULL is passed, no update with remap(x)
+ if image = NULL is passed, no update with remap(x)
if shrinkexceed, atom can be outside shrinkwrap boundaries
called from create_atoms() in library.cpp
------------------------------------------------------------------------- */
@@ -1626,7 +1626,7 @@ int Domain::ownatom(int id, double *x, imageint *image, int shrinkexceed)
{
double lamda[3];
double *coord,*blo,*bhi,*slo,*shi;
-
+
if (image) remap(x,*image);
else remap(x);
@@ -1653,7 +1653,7 @@ int Domain::ownatom(int id, double *x, imageint *image, int shrinkexceed)
coord[1] >= slo[1] && coord[1] < shi[1] &&
coord[2] >= slo[2] && coord[2] < shi[2]) return 1;
- // check if atom did not return 1 only b/c it was
+ // check if atom did not return 1 only b/c it was
// outside a shrink-wrapped boundary
if (shrinkexceed) {
diff --git a/src/dump_custom.cpp b/src/dump_custom.cpp
index 84ada95975bf3d24d3e34547bf899e0a510aab82..9892387cbebb3490fa2020ed3b64d80b4eece324 100644
--- a/src/dump_custom.cpp
+++ b/src/dump_custom.cpp
@@ -1025,12 +1025,12 @@ int DumpCustom::count()
} else if (thresh_op[ithresh] == XOR) {
if (lastflag) {
for (i = 0; i < nlocal; i++, ptr += nstride)
- if (choose[i] && (*ptr == 0.0 && values[i] == 0.0) ||
+ if (choose[i] && (*ptr == 0.0 && values[i] == 0.0) ||
(*ptr != 0.0 && values[i] != 0.0))
choose[i] = 0;
} else {
for (i = 0; i < nlocal; i++, ptr += nstride)
- if (choose[i] && (*ptr == 0.0 && value == 0.0) ||
+ if (choose[i] && (*ptr == 0.0 && value == 0.0) ||
(*ptr != 0.0 && value != 0.0))
choose[i] = 0;
}
@@ -1704,7 +1704,7 @@ int DumpCustom::modify_param(int narg, char **arg)
memory->grow(thresh_op,(nthresh+1),"dump:thresh_op");
memory->grow(thresh_value,(nthresh+1),"dump:thresh_value");
memory->grow(thresh_last,(nthresh+1),"dump:thresh_last");
-
+
// set attribute type of threshold
// customize by adding to if statement
@@ -1949,7 +1949,7 @@ int DumpCustom::modify_param(int narg, char **arg)
thresh_value[nthresh] = force->numeric(FLERR,arg[3]);
thresh_last[nthresh] = -1;
} else {
- thresh_fix = (FixStore **)
+ thresh_fix = (FixStore **)
memory->srealloc(thresh_fix,(nthreshlast+1)*sizeof(FixStore *),
"dump:thresh_fix");
thresh_fixID = (char **)
diff --git a/src/dump_image.cpp b/src/dump_image.cpp
index 0e5f57be6bcdb46a99bce387f9b43b8221523f28..9ca6ad34e90fa88c99d317bd36c755325fd72949 100644
--- a/src/dump_image.cpp
+++ b/src/dump_image.cpp
@@ -49,11 +49,11 @@ enum{NO,YES};
/* ---------------------------------------------------------------------- */
DumpImage::DumpImage(LAMMPS *lmp, int narg, char **arg) :
- DumpCustom(lmp, narg, arg), thetastr(NULL), phistr(NULL), cxstr(NULL),
- cystr(NULL), czstr(NULL), upxstr(NULL), upystr(NULL), upzstr(NULL),
- zoomstr(NULL), perspstr(NULL), diamtype(NULL), diamelement(NULL),
- bdiamtype(NULL), colortype(NULL), colorelement(NULL), bcolortype(NULL),
- avec_line(NULL), avec_tri(NULL), avec_body(NULL), fixptr(NULL), image(NULL),
+ DumpCustom(lmp, narg, arg), thetastr(NULL), phistr(NULL), cxstr(NULL),
+ cystr(NULL), czstr(NULL), upxstr(NULL), upystr(NULL), upzstr(NULL),
+ zoomstr(NULL), perspstr(NULL), diamtype(NULL), diamelement(NULL),
+ bdiamtype(NULL), colortype(NULL), colorelement(NULL), bcolortype(NULL),
+ avec_line(NULL), avec_tri(NULL), avec_body(NULL), fixptr(NULL), image(NULL),
chooseghost(NULL), bufcopy(NULL)
{
if (binary || multiproc) error->all(FLERR,"Invalid dump image filename");
@@ -376,17 +376,17 @@ DumpImage::DumpImage(LAMMPS *lmp, int narg, char **arg) :
if (lineflag) {
avec_line = (AtomVecLine *) atom->style_match("line");
- if (!avec_line)
+ if (!avec_line)
error->all(FLERR,"Dump image line requires atom style line");
}
if (triflag) {
avec_tri = (AtomVecTri *) atom->style_match("tri");
- if (!avec_tri)
+ if (!avec_tri)
error->all(FLERR,"Dump image tri requires atom style tri");
}
if (bodyflag) {
avec_body = (AtomVecBody *) atom->style_match("body");
- if (!avec_body)
+ if (!avec_body)
error->all(FLERR,"Dump image body yes requires atom style body");
}
diff --git a/src/dump_local.cpp b/src/dump_local.cpp
index a3e62907a6941b78a8aa9751e906d1eb054685f9..ca8b1822a2611dfffae2fc6c6579f8995c434617 100644
--- a/src/dump_local.cpp
+++ b/src/dump_local.cpp
@@ -38,8 +38,8 @@ enum{INT,DOUBLE};
DumpLocal::DumpLocal(LAMMPS *lmp, int narg, char **arg) :
Dump(lmp, narg, arg),
- label(NULL), vtype(NULL), vformat(NULL), columns(NULL), field2index(NULL),
- argindex(NULL), id_compute(NULL), compute(NULL), id_fix(NULL), fix(NULL),
+ label(NULL), vtype(NULL), vformat(NULL), columns(NULL), field2index(NULL),
+ argindex(NULL), id_compute(NULL), compute(NULL), id_fix(NULL), fix(NULL),
pack_choice(NULL)
{
if (narg == 5) error->all(FLERR,"No dump local arguments specified");
diff --git a/src/fix_adapt.cpp b/src/fix_adapt.cpp
index e34f2dcf55b608dab765d76c66fe22bf56408c1b..10b09f4a7f56d5d14c49489eba9a0eb343ceebc9 100644
--- a/src/fix_adapt.cpp
+++ b/src/fix_adapt.cpp
@@ -389,7 +389,7 @@ void FixAdapt::init()
} else if (ad->which == BOND){
ad->bond = NULL;
anybond = 1;
-
+
int n = strlen(ad->bstyle) + 1;
char *bstyle = new char[n];
strcpy(bstyle,ad->bstyle);
@@ -408,7 +408,7 @@ void FixAdapt::init()
error->all(FLERR,"Fix adapt bond style does not exist");
void *ptr = ad->bond->extract(ad->bparam,ad->bdim);
-
+
if (ptr == NULL)
error->all(FLERR,"Fix adapt bond style param not supported");
@@ -421,7 +421,7 @@ void FixAdapt::init()
error->all(FLERR,"Fix adapt does not support bond_style hybrid");
delete [] bstyle;
-
+
} else if (ad->which == KSPACE) {
if (force->kspace == NULL)
error->all(FLERR,"Fix adapt kspace style does not exist");
@@ -449,12 +449,12 @@ void FixAdapt::init()
ad->array_orig[i][j] = ad->array[i][j];
} else if (ad->which == PAIR && ad->pdim == 0){
ad->scalar_orig = *ad->scalar;
-
+
} else if (ad->which == BOND && ad->bdim == 1){
for (i = ad->ilo; i <= ad->ihi; ++i )
ad->vector_orig[i] = ad->vector[i];
}
-
+
}
// fixes that store initial per-atom values
@@ -547,7 +547,7 @@ void FixAdapt::change_settings()
}
// set bond type array values:
-
+
} else if (ad->which == BOND) {
if (ad->bdim == 1){
if (scaleflag)
@@ -557,7 +557,7 @@ void FixAdapt::change_settings()
for (i = ad->ilo; i <= ad->ihi; ++i )
ad->vector[i] = value;
}
-
+
// set kspace scale factor
} else if (ad->which == KSPACE) {
@@ -657,7 +657,7 @@ void FixAdapt::restore_settings()
for (int i = ad->ilo; i <= ad->ihi; i++)
ad->vector[i] = ad->vector_orig[i];
}
-
+
} else if (ad->which == KSPACE) {
*kspace_scale = 1.0;
diff --git a/src/fix_ave_atom.cpp b/src/fix_ave_atom.cpp
index 3d8e40ac17bc1c8553b093e136a87e601aa6768a..c4222f6fcd056dde4816de1629394ec2e03f0b21 100644
--- a/src/fix_ave_atom.cpp
+++ b/src/fix_ave_atom.cpp
@@ -36,7 +36,7 @@ enum{X,V,F,COMPUTE,FIX,VARIABLE};
FixAveAtom::FixAveAtom(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg),
- nvalues(0), which(NULL), argindex(NULL), value2index(NULL),
+ nvalues(0), which(NULL), argindex(NULL), value2index(NULL),
ids(NULL), array(NULL)
{
if (narg < 7) error->all(FLERR,"Illegal fix ave/atom command");
diff --git a/src/fix_ave_chunk.cpp b/src/fix_ave_chunk.cpp
index 5b57c7a1f8639ed1f2834bb98b047a9b1d33c625..8558e8695c10d3e04a5ef218aee8bc32e499b657 100644
--- a/src/fix_ave_chunk.cpp
+++ b/src/fix_ave_chunk.cpp
@@ -793,7 +793,7 @@ void FixAveChunk::end_of_step()
// if normflag = SAMPLE, one = value/count, accumulate one to many
// count is MPI summed here, value is MPI summed below across samples
// exception is TEMPERATURE: normalize by DOF
- // exception is DENSITY_NUMBER:
+ // exception is DENSITY_NUMBER:
// normalize by bin volume, not by atom count
// exception is DENSITY_MASS:
// scale by mv2d, normalize by bin volume, not by atom count
@@ -868,11 +868,11 @@ void FixAveChunk::end_of_step()
// time average across samples
// if normflag = ALL, final is total value / total count
// exception is TEMPERATURE: normalize by DOF for total count
- // exception is DENSITY_NUMBER:
+ // exception is DENSITY_NUMBER:
// normalize by final bin_volume and repeat, not by total count
// exception is DENSITY_MASS:
// scale by mv2d, normalize by bin volume and repeat, not by total count
- // exception is scaleflag == NOSCALE:
+ // exception is scaleflag == NOSCALE:
// normalize by repeat, not by total count
// check last so other options can take precedence
// if normflag = SAMPLE, final is sum of ave / repeat
diff --git a/src/fix_ave_histo.cpp b/src/fix_ave_histo.cpp
index b4516a0fd29f6149370acede868c089c793f59ff..e104512479f07ed93af3dcadc866de7cf557cb70 100644
--- a/src/fix_ave_histo.cpp
+++ b/src/fix_ave_histo.cpp
@@ -46,7 +46,7 @@ enum{IGNORE,END,EXTRA};
FixAveHisto::FixAveHisto(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg),
- nvalues(0), which(NULL), argindex(NULL), value2index(NULL), ids(NULL), fp(NULL), stats_list(NULL),
+ nvalues(0), which(NULL), argindex(NULL), value2index(NULL), ids(NULL), fp(NULL), stats_list(NULL),
bin(NULL), bin_total(NULL), bin_all(NULL), bin_list(NULL), coord(NULL), vector(NULL)
{
if (narg < 10) error->all(FLERR,"Illegal fix ave/histo command");
@@ -396,7 +396,7 @@ FixAveHisto::FixAveHisto(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,"Variable name for fix ave/histo does not exist");
if (argindex[i] == 0 && input->variable->vectorstyle(ivariable) == 0)
error->all(FLERR,"Fix ave/histo variable is not vector-style variable");
- if (argindex[i])
+ if (argindex[i])
error->all(FLERR,"Fix ave/histo variable cannot be indexed");
} else if (which[i] == VARIABLE && kind == PERATOM) {
@@ -405,7 +405,7 @@ FixAveHisto::FixAveHisto(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,"Variable name for fix ave/histo does not exist");
if (argindex[i] == 0 && input->variable->atomstyle(ivariable) == 0)
error->all(FLERR,"Fix ave/histo variable is not atom-style variable");
- if (argindex[i])
+ if (argindex[i])
error->all(FLERR,"Fix ave/histo variable cannot be indexed");
}
}
diff --git a/src/fix_ave_time.cpp b/src/fix_ave_time.cpp
index 56a2458aad322d1f1d56d2c4da1631643cee62c9..5de32c7faea287cb391f2520dacd7b5aedbc0eec 100644
--- a/src/fix_ave_time.cpp
+++ b/src/fix_ave_time.cpp
@@ -43,9 +43,9 @@ enum{SCALAR,VECTOR};
FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg),
- nvalues(0), which(NULL), argindex(NULL), value2index(NULL),
+ nvalues(0), which(NULL), argindex(NULL), value2index(NULL),
offcol(NULL), varlen(NULL), ids(NULL),
- fp(NULL), offlist(NULL), format(NULL), format_user(NULL),
+ fp(NULL), offlist(NULL), format(NULL), format_user(NULL),
vector(NULL), vector_total(NULL), vector_list(NULL),
column(NULL), array(NULL), array_total(NULL), array_list(NULL)
{
@@ -115,7 +115,7 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
argindex[i] = atoi(ptr+1);
*ptr = '\0';
} else argindex[i] = 0;
-
+
n = strlen(suffix) + 1;
ids[i] = new char[n];
strcpy(ids[i],suffix);
@@ -809,7 +809,7 @@ void FixAveTime::invoke_vector(bigint ntimestep)
} else if (which[j] == VARIABLE) {
double *varvec;
int nvec = input->variable->compute_vector(m,&varvec);
- if (nvec != nrows)
+ if (nvec != nrows)
error->all(FLERR,"Fix ave/time vector-style variable changed length");
for (i = 0; i < nrows; i++)
column[i] = varvec[i];
@@ -938,7 +938,7 @@ int FixAveTime::column_length(int dynamic)
else lengthone = modify->fix[ifix]->size_array_rows;
} else if (which[i] == VARIABLE) {
// variables are always varlen = 1, so dynamic
- }
+ }
if (length == 0) length = lengthone;
else if (lengthone != length)
error->all(FLERR,"Fix ave/time columns are inconsistent lengths");
diff --git a/src/fix_balance.cpp b/src/fix_balance.cpp
index 7e0aa681bbfb942f1c81304be9f497aabc2d6702..9f29400d9a5291590c5f7ed83e9a6d90b26b33b1 100644
--- a/src/fix_balance.cpp
+++ b/src/fix_balance.cpp
@@ -115,7 +115,7 @@ FixBalance::FixBalance(LAMMPS *lmp, int narg, char **arg) :
if (nevery) force_reneighbor = 1;
lastbalance = -1;
-
+
// compute initial outputs
itercount = 0;
diff --git a/src/fix_controller.cpp b/src/fix_controller.cpp
index ee3e97c942869822400ad38a40fe6a0bbb847c53..e283b1c19257b36758c4c685369fb03ae4fc8b26 100644
--- a/src/fix_controller.cpp
+++ b/src/fix_controller.cpp
@@ -32,7 +32,7 @@ enum{COMPUTE,FIX,VARIABLE};
/* ---------------------------------------------------------------------- */
-FixController::FixController(LAMMPS *lmp, int narg, char **arg) :
+FixController::FixController(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg),
pvID(NULL), cvID(NULL)
{
@@ -64,7 +64,7 @@ FixController::FixController(LAMMPS *lmp, int narg, char **arg) :
int n = strlen(arg[iarg]);
char *suffix = new char[n];
strcpy(suffix,&arg[iarg][2]);
-
+
char *ptr = strchr(suffix,'[');
if (ptr) {
if (suffix[strlen(suffix)-1] != ']')
@@ -72,7 +72,7 @@ FixController::FixController(LAMMPS *lmp, int narg, char **arg) :
pvindex = atoi(ptr+1);
*ptr = '\0';
} else pvindex = 0;
-
+
n = strlen(suffix) + 1;
pvID = new char[n];
strcpy(pvID,suffix);
@@ -161,10 +161,10 @@ void FixController::init()
{
if (pvwhich == COMPUTE) {
int icompute = modify->find_compute(pvID);
- if (icompute < 0)
+ if (icompute < 0)
error->all(FLERR,"Compute ID for fix controller does not exist");
pcompute = modify->compute[icompute];
-
+
} else if (pvwhich == FIX) {
int ifix = modify->find_fix(pvID);
if (ifix < 0) error->all(FLERR,"Fix ID for fix controller does not exist");
@@ -172,7 +172,7 @@ void FixController::init()
} else if (pvwhich == VARIABLE) {
pvar = input->variable->find(pvID);
- if (pvar < 0)
+ if (pvar < 0)
error->all(FLERR,"Variable name for fix controller does not exist");
}
@@ -214,13 +214,13 @@ void FixController::end_of_step()
}
// access fix field, guaranteed to be ready
-
+
} else if (pvwhich == FIX) {
if (pvindex == 0) current = pfix->compute_scalar();
else current = pfix->compute_vector(pvindex-1);
-
+
// evaluate equal-style variable
-
+
} else if (pvwhich == VARIABLE) {
current = input->variable->compute_equal(pvar);
}
@@ -232,7 +232,7 @@ void FixController::end_of_step()
// note: this deviates from standard notation, which is
// cv = kp*err +ki*sumerr +kd*deltaerr
// the difference is in the sign and the time integral
-
+
err = current - setpoint;
if (firsttime) {
diff --git a/src/fix_halt.cpp b/src/fix_halt.cpp
index bf6060779951b5244ac0b3ad0ebbb511e8a03ae8..48d0f5da25ae55b9de9683980e41126cfb930ae4 100644
--- a/src/fix_halt.cpp
+++ b/src/fix_halt.cpp
@@ -175,7 +175,7 @@ void FixHalt::end_of_step()
} else if (operation == NEQ) {
if (attvalue == value) return;
} else if (operation == XOR) {
- if ((attvalue == 0.0 && value == 0.0) ||
+ if ((attvalue == 0.0 && value == 0.0) ||
(attvalue != 0.0 && value != 0.0)) return;
}
@@ -251,7 +251,7 @@ double FixHalt::tlimit()
if (cpu < value) {
bigint elapsed = update->ntimestep - update->firststep;
- bigint final = update->firststep +
+ bigint final = update->firststep +
static_cast<bigint> (tratio*value/cpu * elapsed);
nextstep = (final/nevery)*nevery + nevery;
if (nextstep == update->ntimestep) nextstep += nevery;
diff --git a/src/fix_langevin.cpp b/src/fix_langevin.cpp
index 7afc18b33c170b3e8d7d39ee28d10b545f86b85e..22993530010c9b0a016bb04e67006d6232e111e1 100644
--- a/src/fix_langevin.cpp
+++ b/src/fix_langevin.cpp
@@ -149,7 +149,7 @@ FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) :
energy = 0.0;
// flangevin is unallocated until first call to setup()
- // compute_scalar checks for this and returns 0.0
+ // compute_scalar checks for this and returns 0.0
// if flangevin_allocated is not set
flangevin = NULL;
diff --git a/src/fix_move.cpp b/src/fix_move.cpp
index d3c4b12e3d1163a00eb90034172d4258d31841d6..a32c80c1e9e7d29fa5d098c086171a1cbb40ab3b 100644
--- a/src/fix_move.cpp
+++ b/src/fix_move.cpp
@@ -48,9 +48,9 @@ enum{EQUAL,ATOM};
FixMove::FixMove(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg),
- xvarstr(NULL), yvarstr(NULL), zvarstr(NULL), vxvarstr(NULL),
+ xvarstr(NULL), yvarstr(NULL), zvarstr(NULL), vxvarstr(NULL),
vyvarstr(NULL), vzvarstr(NULL),
- xoriginal(NULL), toriginal(NULL), qoriginal(NULL),
+ xoriginal(NULL), toriginal(NULL), qoriginal(NULL),
displace(NULL), velocity(NULL)
{
if (narg < 4) error->all(FLERR,"Illegal fix move command");
@@ -69,7 +69,7 @@ FixMove::FixMove(LAMMPS *lmp, int narg, char **arg) :
// parse args
int iarg;
-
+
if (strcmp(arg[3],"linear") == 0) {
if (narg < 7) error->all(FLERR,"Illegal fix move command");
iarg = 7;
@@ -237,7 +237,7 @@ FixMove::FixMove(LAMMPS *lmp, int narg, char **arg) :
// set flags for extra attributes particles may store
// relevant extra attributes = omega, angmom, theta, quat
-
+
omega_flag = atom->omega_flag;
angmom_flag = atom->angmom_flag;
@@ -253,7 +253,7 @@ FixMove::FixMove(LAMMPS *lmp, int narg, char **arg) :
extra_flag = 0;
if (omega_flag || angmom_flag || theta_flag || quat_flag) extra_flag = 1;
-
+
// perform initial allocation of atom-based array
// register with Atom class
@@ -313,7 +313,7 @@ FixMove::FixMove(LAMMPS *lmp, int narg, char **arg) :
qoriginal[i][1] = quat[1];
qoriginal[i][2] = quat[2];
qoriginal[i][3] = quat[3];
- } else qoriginal[i][0] = qoriginal[i][1] =
+ } else qoriginal[i][0] = qoriginal[i][1] =
qoriginal[i][2] = qoriginal[i][3] = 0.0;
}
}
@@ -664,17 +664,17 @@ void FixMove::initial_integrate(int vflag)
}
// angmom for ellipsoids, tris, and bodies
-
+
if (angmom_flag) {
quat = inertia = NULL;
if (ellipsoid_flag && ellipsoid[i] >= 0) {
quat = avec_ellipsoid->bonus[ellipsoid[i]].quat;
shape = avec_ellipsoid->bonus[ellipsoid[i]].shape;
- inertia_ellipsoid[0] =
+ inertia_ellipsoid[0] =
INERTIA*rmass[i] * (shape[1]*shape[1]+shape[2]*shape[2]);
- inertia_ellipsoid[1] =
+ inertia_ellipsoid[1] =
INERTIA*rmass[i] * (shape[0]*shape[0]+shape[2]*shape[2]);
- inertia_ellipsoid[2] =
+ inertia_ellipsoid[2] =
INERTIA*rmass[i] * (shape[0]*shape[0]+shape[1]*shape[1]);
inertia = inertia_ellipsoid;
} else if (tri_flag && tri[i] >= 0) {
@@ -694,14 +694,14 @@ void FixMove::initial_integrate(int vflag)
}
// theta for lines
-
+
if (theta_flag && line[i] >= 0.0) {
theta_new = fmod(toriginal[i]+arg,MY_2PI);
avec_line->bonus[atom->line[i]].theta = theta_new;
}
-
+
// quats for ellipsoids, tris, and bodies
-
+
if (quat_flag) {
quat = NULL;
if (ellipsoid_flag && ellipsoid[i] >= 0)
@@ -1108,20 +1108,20 @@ void FixMove::set_arrays(int i)
xoriginal[i][0] = point[0] + c[0] + disp[0];
xoriginal[i][1] = point[1] + c[1] + disp[1];
xoriginal[i][2] = point[2] + c[2] + disp[2];
-
+
// set theta and quat extra attributes affected by rotation
if (extra_flag) {
// theta for lines
-
+
if (theta_flag && line[i] >= 0.0) {
theta = avec_line->bonus[atom->line[i]].theta;
toriginal[i] = theta - 0.0; // NOTE: edit this line
}
-
+
// quats for ellipsoids, tris, and bodies
-
+
if (quat_flag) {
quat = NULL;
if (ellipsoid_flag && ellipsoid[i] >= 0)
diff --git a/src/fix_nh.cpp b/src/fix_nh.cpp
index f95bde95d06fff004d53988eef5f9da7e2ffe6e3..e4500b19ca09c189f867b1e11819cd7af7e407bd 100644
--- a/src/fix_nh.cpp
+++ b/src/fix_nh.cpp
@@ -50,7 +50,7 @@ enum{ISO,ANISO,TRICLINIC};
NVT,NPH,NPT integrators for improved Nose-Hoover equations of motion
---------------------------------------------------------------------- */
-FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) :
+FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg),
rfix(NULL), id_dilate(NULL), irregular(NULL), id_temp(NULL), id_press(NULL),
eta(NULL), eta_dot(NULL), eta_dotdot(NULL),
@@ -348,7 +348,7 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) :
fixedpoint[2] = force->numeric(FLERR,arg[iarg+3]);
iarg += 4;
- // disc keyword is also parsed in fix/nh/sphere
+ // disc keyword is also parsed in fix/nh/sphere
} else if (strcmp(arg[iarg],"disc") == 0) {
iarg++;
diff --git a/src/fix_nh_sphere.cpp b/src/fix_nh_sphere.cpp
index 28de5490d4e3f3590b0b7bfb7d69786836069da5..cc59e4a1016eef159e0b4e04f21dc9f21bfa111c 100644
--- a/src/fix_nh_sphere.cpp
+++ b/src/fix_nh_sphere.cpp
@@ -39,8 +39,8 @@ FixNHSphere::FixNHSphere(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,"Fix nvt/nph/npt sphere requires atom style sphere");
// inertia = moment of inertia prefactor for sphere or disc
-
- inertia = 0.4;
+
+ inertia = 0.4;
int iarg = 3;
while (iarg < narg) {
@@ -69,7 +69,7 @@ void FixNHSphere::init()
if (mask[i] & groupbit)
if (radius[i] == 0.0)
error->one(FLERR,"Fix nvt/npt/nph/sphere require extended particles");
-
+
FixNH::init();
}
@@ -120,7 +120,7 @@ void FixNHSphere::nve_x()
FixNH::nve_x();
// update mu for dipoles
-
+
if (dipole_flag) {
double **mu = atom->mu;
double **omega = atom->omega;
@@ -130,7 +130,7 @@ void FixNHSphere::nve_x()
// d_mu/dt = omega cross mu
// renormalize mu to dipole length
double msq,scale,g[3];
-
+
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (mu[i][3] > 0.0) {
@@ -148,21 +148,21 @@ void FixNHSphere::nve_x()
vector w, w_temp, a;
matrix Q, Q_temp, R;
double scale,s2,inv_len_mu;
-
+
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit && mu[i][3] > 0.0) {
-
+
// Construct Q from dipole:
// Q is the rotation matrix from space frame to body frame
// i.e. v_b = Q.v_s
-
+
// Define mu to lie along the z axis in the body frame
// We take the unit dipole to avoid getting a scaling matrix
inv_len_mu = 1.0/mu[i][3];
a[0] = mu[i][0]*inv_len_mu;
a[1] = mu[i][1]*inv_len_mu;
a[2] = mu[i][2]*inv_len_mu;
-
+
// v = a x [0 0 1] - cross product of mu in space and body frames
// s = |v|
// c = a.[0 0 1] = a[2]
@@ -171,11 +171,11 @@ void FixNHSphere::nve_x()
// -v[1] v[0] 0 ]
// then
// Q = I + vx + vx^2 * (1-c)/s^2
-
+
s2 = a[0]*a[0] + a[1]*a[1];
if (s2 != 0.0){ // i.e. the vectors are not parallel
scale = (1.0 - a[2])/s2;
-
+
Q[0][0] = 1.0 - scale*a[0]*a[0]; Q[0][1] = -scale*a[0]*a[1]; Q[0][2] = -a[0];
Q[1][0] = -scale*a[0]*a[1]; Q[1][1] = 1.0 - scale*a[1]*a[1]; Q[1][2] = -a[1];
Q[2][0] = a[0]; Q[2][1] = a[1]; Q[2][2] = 1.0 - scale*(a[0]*a[0] + a[1]*a[1]);
@@ -184,62 +184,62 @@ void FixNHSphere::nve_x()
Q[1][0] = 0.0; Q[1][1] = 1.0/a[2]; Q[1][2] = 0.0;
Q[2][0] = 0.0; Q[2][1] = 0.0; Q[2][2] = 1.0/a[2];
}
-
+
// Local copy of this particle's angular velocity (in space frame)
w[0] = omega[i][0]; w[1] = omega[i][1]; w[2] = omega[i][2];
-
+
// Transform omega into body frame: w_temp= Q.w
matvec(Q,w,w_temp);
-
+
// Construct rotation R1
BuildRxMatrix(R, dtf/force->ftm2v*w_temp[0]);
-
+
// Apply R1 to w: w = R.w_temp
matvec(R,w_temp,w);
-
+
// Apply R1 to Q: Q_temp = R^T.Q
transpose_times3(R,Q,Q_temp);
-
+
// Construct rotation R2
BuildRyMatrix(R, dtf/force->ftm2v*w[1]);
-
+
// Apply R2 to w: w_temp = R.w
matvec(R,w,w_temp);
-
+
// Apply R2 to Q: Q = R^T.Q_temp
transpose_times3(R,Q_temp,Q);
-
+
// Construct rotation R3
BuildRzMatrix(R, 2.0*dtf/force->ftm2v*w_temp[2]);
-
+
// Apply R3 to w: w = R.w_temp
matvec(R,w_temp,w);
-
+
// Apply R3 to Q: Q_temp = R^T.Q
transpose_times3(R,Q,Q_temp);
-
+
// Construct rotation R4
BuildRyMatrix(R, dtf/force->ftm2v*w[1]);
-
+
// Apply R4 to w: w_temp = R.w
matvec(R,w,w_temp);
-
+
// Apply R4 to Q: Q = R^T.Q_temp
transpose_times3(R,Q_temp,Q);
-
+
// Construct rotation R5
BuildRxMatrix(R, dtf/force->ftm2v*w_temp[0]);
-
+
// Apply R5 to w: w = R.w_temp
matvec(R,w_temp,w);
-
+
// Apply R5 to Q: Q_temp = R^T.Q
transpose_times3(R,Q,Q_temp);
-
+
// Transform w back into space frame w_temp = Q^T.w
transpose_matvec(Q_temp,w,w_temp);
omega[i][0] = w_temp[0]; omega[i][1] = w_temp[1]; omega[i][2] = w_temp[2];
-
+
// Set dipole according to updated Q: mu = Q^T.[0 0 1] * |mu|
mu[i][0] = Q_temp[2][0] * mu[i][3];
mu[i][1] = Q_temp[2][1] * mu[i][3];
diff --git a/src/fix_nve_sphere.cpp b/src/fix_nve_sphere.cpp
index 7ffd92e23214de2eb782c91f0c9048a4fd1fbde4..daf89871ab60a459f339959d2bf5abb4dce22d99 100644
--- a/src/fix_nve_sphere.cpp
+++ b/src/fix_nve_sphere.cpp
@@ -46,7 +46,7 @@ FixNVESphere::FixNVESphere(LAMMPS *lmp, int narg, char **arg) :
extra = NONE;
dlm = NODLM;
- inertia = 0.4;
+ inertia = 0.4;
int iarg = 3;
while (iarg < narg) {
@@ -58,11 +58,11 @@ FixNVESphere::FixNVESphere(LAMMPS *lmp, int narg, char **arg) :
dlm = DLM;
} else error->all(FLERR,"Illegal fix nve/sphere command");
iarg += 2;
- }
+ }
else if (strcmp(arg[iarg],"disc")==0) {
inertia = 0.5;
if (domain->dimension != 2)
- error->all(FLERR,"Fix nve/sphere disc requires 2d simulation");
+ error->all(FLERR,"Fix nve/sphere disc requires 2d simulation");
iarg++;
}
else error->all(FLERR,"Illegal fix nve/sphere command");
@@ -138,9 +138,9 @@ void FixNVESphere::initial_integrate(int vflag)
omega[i][2] += dtirotate * torque[i][2];
}
}
-
+
// update mu for dipoles
-
+
if (extra == DIPOLE) {
double **mu = atom->mu;
if (dlm == NODLM) {
@@ -166,11 +166,11 @@ void FixNVESphere::initial_integrate(int vflag)
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit && mu[i][3] > 0.0) {
-
+
// Construct Q from dipole:
// Q is the rotation matrix from space frame to body frame
// i.e. v_b = Q.v_s
-
+
// define mu to lie along the z axis in the body frame
// take the unit dipole to avoid getting a scaling matrix
@@ -178,7 +178,7 @@ void FixNVESphere::initial_integrate(int vflag)
a[0] = mu[i][0]*inv_len_mu;
a[1] = mu[i][1]*inv_len_mu;
a[2] = mu[i][2]*inv_len_mu;
-
+
// v = a x [0 0 1] - cross product of mu in space and body frames
// s = |v|
// c = a.[0 0 1] = a[2]
@@ -187,12 +187,12 @@ void FixNVESphere::initial_integrate(int vflag)
// -v[1] v[0] 0 ]
// then
// Q = I + vx + vx^2 * (1-c)/s^2
-
+
s2 = a[0]*a[0] + a[1]*a[1];
if (s2 != 0.0){ // i.e. the vectors are not parallel
scale = (1.0 - a[2])/s2;
-
- Q[0][0] = 1.0 - scale*a[0]*a[0];
+
+ Q[0][0] = 1.0 - scale*a[0]*a[0];
Q[0][1] = -scale*a[0]*a[1];
Q[0][2] = -a[0];
Q[1][0] = -scale*a[0]*a[1];
@@ -206,64 +206,64 @@ void FixNVESphere::initial_integrate(int vflag)
Q[1][0] = 0.0; Q[1][1] = 1.0/a[2]; Q[1][2] = 0.0;
Q[2][0] = 0.0; Q[2][1] = 0.0; Q[2][2] = 1.0/a[2];
}
-
+
// Local copy of this particle's angular velocity (in space frame)
w[0] = omega[i][0]; w[1] = omega[i][1]; w[2] = omega[i][2];
-
+
// Transform omega into body frame: w_temp= Q.w
matvec(Q,w,w_temp);
-
+
// Construct rotation R1
BuildRxMatrix(R, dtf/force->ftm2v*w_temp[0]);
-
+
// Apply R1 to w: w = R.w_temp
matvec(R,w_temp,w);
-
+
// Apply R1 to Q: Q_temp = R^T.Q
transpose_times3(R,Q,Q_temp);
-
+
// Construct rotation R2
BuildRyMatrix(R, dtf/force->ftm2v*w[1]);
-
+
// Apply R2 to w: w_temp = R.w
matvec(R,w,w_temp);
-
+
// Apply R2 to Q: Q = R^T.Q_temp
transpose_times3(R,Q_temp,Q);
-
+
// Construct rotation R3
BuildRzMatrix(R, 2.0*dtf/force->ftm2v*w_temp[2]);
-
+
// Apply R3 to w: w = R.w_temp
matvec(R,w_temp,w);
-
+
// Apply R3 to Q: Q_temp = R^T.Q
transpose_times3(R,Q,Q_temp);
-
+
// Construct rotation R4
BuildRyMatrix(R, dtf/force->ftm2v*w[1]);
-
+
// Apply R4 to w: w_temp = R.w
matvec(R,w,w_temp);
-
+
// Apply R4 to Q: Q = R^T.Q_temp
transpose_times3(R,Q_temp,Q);
-
+
// Construct rotation R5
BuildRxMatrix(R, dtf/force->ftm2v*w_temp[0]);
-
+
// Apply R5 to w: w = R.w_temp
matvec(R,w_temp,w);
-
+
// Apply R5 to Q: Q_temp = R^T.Q
transpose_times3(R,Q,Q_temp);
-
+
// Transform w back into space frame w_temp = Q^T.w
transpose_matvec(Q_temp,w,w_temp);
- omega[i][0] = w_temp[0];
+ omega[i][0] = w_temp[0];
omega[i][1] = w_temp[1];
omega[i][2] = w_temp[2];
-
+
// Set dipole according to updated Q: mu = Q^T.[0 0 1] * |mu|
mu[i][0] = Q_temp[2][0] * mu[i][3];
mu[i][1] = Q_temp[2][1] * mu[i][3];
@@ -309,8 +309,8 @@ void FixNVESphere::final_integrate()
omega[i][0] += dtirotate * torque[i][0];
omega[i][1] += dtirotate * torque[i][1];
omega[i][2] += dtirotate * torque[i][2];
- rke += (omega[i][0]*omega[i][0] + omega[i][1]*omega[i][1] +
+ rke += (omega[i][0]*omega[i][0] + omega[i][1]*omega[i][1] +
omega[i][2]*omega[i][2])*radius[i]*radius[i]*rmass[i];
}
-
+
}
diff --git a/src/fix_restrain.cpp b/src/fix_restrain.cpp
index f276be76af9074456f2369f4063525e4c22665c3..af11136d78d666851d4f446dac505ed526409632 100644
--- a/src/fix_restrain.cpp
+++ b/src/fix_restrain.cpp
@@ -45,7 +45,7 @@ enum{BOND,ANGLE,DIHEDRAL};
FixRestrain::FixRestrain(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg),
- rstyle(NULL), ids(NULL), kstart(NULL), kstop(NULL), target(NULL),
+ rstyle(NULL), ids(NULL), kstart(NULL), kstop(NULL), target(NULL),
cos_target(NULL), sin_target(NULL)
{
if (narg < 4) error->all(FLERR,"Illegal fix restrain command");
@@ -59,7 +59,7 @@ FixRestrain::FixRestrain(LAMMPS *lmp, int narg, char **arg) :
// parse args
nrestrain = maxrestrain = 0;
-
+
int iarg = 3;
while (iarg < narg) {
if (nrestrain == maxrestrain) {
diff --git a/src/fix_store.cpp b/src/fix_store.cpp
index 84e94fc2b7807c3fc3c1a8938e8d6ce370885d30..3738629820e45e146b6ba569b7c2f459e815351c 100644
--- a/src/fix_store.cpp
+++ b/src/fix_store.cpp
@@ -42,7 +42,7 @@ vstore(NULL), astore(NULL), rbuf(NULL)
disable = 0;
nvalues = vecflag = 0;
- flavor = UNKNOWN;
+ flavor = UNKNOWN;
if (strcmp(arg[3],"global") == 0) flavor = GLOBAL;
else if (strcmp(arg[3],"peratom") == 0) flavor = PERATOM;
diff --git a/src/fix_store_state.cpp b/src/fix_store_state.cpp
index 36f5c6a92ee4c91cf0566301625d2dc5da77647f..2f2ba3feff7ffbcf7deea48f91568e8cdc846874 100644
--- a/src/fix_store_state.cpp
+++ b/src/fix_store_state.cpp
@@ -38,7 +38,7 @@ enum{KEYWORD,COMPUTE,FIX,VARIABLE,DNAME,INAME};
FixStoreState::FixStoreState(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg),
- nvalues(0), which(NULL), argindex(NULL), value2index(NULL),
+ nvalues(0), which(NULL), argindex(NULL), value2index(NULL),
ids(NULL), values(NULL),
vbuf(NULL), pack_choice(NULL)
{
@@ -1026,7 +1026,7 @@ void FixStoreState::pack_xsu(int n)
double invxprd = 1.0/domain->xprd;
for (int i = 0; i < nlocal; i++) {
- if (mask[i] & groupbit)
+ if (mask[i] & groupbit)
vbuf[n] = (x[i][0]-boxxlo)*invxprd + ((image[i] & IMGMASK) - IMGMAX);
else vbuf[n] = 0.0;
n += nvalues;
@@ -1046,8 +1046,8 @@ void FixStoreState::pack_ysu(int n)
double invyprd = 1.0/domain->yprd;
for (int i = 0; i < nlocal; i++) {
- if (mask[i] & groupbit)
- vbuf[n] = (x[i][1]-boxylo)*invyprd +
+ if (mask[i] & groupbit)
+ vbuf[n] = (x[i][1]-boxylo)*invyprd +
(image[i] >> IMGBITS & IMGMASK) - IMGMAX;
else vbuf[n] = 0.0;
n += nvalues;
@@ -1067,7 +1067,7 @@ void FixStoreState::pack_zsu(int n)
double invzprd = 1.0/domain->zprd;
for (int i = 0; i < nlocal; i++) {
- if (mask[i] & groupbit)
+ if (mask[i] & groupbit)
vbuf[n] = (x[i][2]-boxzlo)*invzprd + (image[i] >> IMG2BITS) - IMGMAX;
else vbuf[n] = 0.0;
n += nvalues;
@@ -1087,7 +1087,7 @@ void FixStoreState::pack_xsu_triclinic(int n)
double *h_inv = domain->h_inv;
for (int i = 0; i < nlocal; i++) {
- if (mask[i] & groupbit)
+ if (mask[i] & groupbit)
vbuf[n] = h_inv[0]*(x[i][0]-boxlo[0]) + h_inv[5]*(x[i][1]-boxlo[1]) +
h_inv[4]*(x[i][2]-boxlo[2]) + (image[i] & IMGMASK) - IMGMAX;
else vbuf[n] = 0.0;
@@ -1108,7 +1108,7 @@ void FixStoreState::pack_ysu_triclinic(int n)
double *h_inv = domain->h_inv;
for (int i = 0; i < nlocal; i++) {
- if (mask[i] & groupbit)
+ if (mask[i] & groupbit)
vbuf[n] = h_inv[1]*(x[i][1]-boxlo[1]) + h_inv[3]*(x[i][2]-boxlo[2]) +
(image[i] >> IMGBITS & IMGMASK) - IMGMAX;
else vbuf[n] = 0.0;
@@ -1129,7 +1129,7 @@ void FixStoreState::pack_zsu_triclinic(int n)
double *h_inv = domain->h_inv;
for (int i = 0; i < nlocal; i++) {
- if (mask[i] & groupbit)
+ if (mask[i] & groupbit)
vbuf[n] = h_inv[2]*(x[i][2]-boxlo[2]) + (image[i] >> IMG2BITS) - IMGMAX;
else vbuf[n] = 0.0;
n += nvalues;
@@ -1160,7 +1160,7 @@ void FixStoreState::pack_iy(int n)
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
- if (mask[i] & groupbit)
+ if (mask[i] & groupbit)
vbuf[n] = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
else vbuf[n] = 0.0;
n += nvalues;
diff --git a/src/fix_vector.cpp b/src/fix_vector.cpp
index 07841d5ba7420a3cf58c50691d29de1627761085..4847926aaf60e6cb20060712a76a3e0e075b513c 100644
--- a/src/fix_vector.cpp
+++ b/src/fix_vector.cpp
@@ -296,7 +296,7 @@ void FixVector::end_of_step()
// evaluate equal-style or vector-style variable
} else if (which[i] == VARIABLE) {
- if (argindex[i] == 0)
+ if (argindex[i] == 0)
result[i] = input->variable->compute_equal(m);
else {
double *varvec;
diff --git a/src/group.cpp b/src/group.cpp
index 93c9c12bcf8df5618cae05075181ba396787ae18..72224dcf25b58c186b544f9135e93ca4082aa847 100644
--- a/src/group.cpp
+++ b/src/group.cpp
@@ -1690,18 +1690,18 @@ void Group::omega(double *angmom, double inertia[3][3], double *w)
if (determinant > EPSILON) {
inverse[0][0] = inertia[1][1]*inertia[2][2] - inertia[1][2]*inertia[2][1];
- inverse[0][1] = -(inertia[0][1]*inertia[2][2] -
+ inverse[0][1] = -(inertia[0][1]*inertia[2][2] -
inertia[0][2]*inertia[2][1]);
inverse[0][2] = inertia[0][1]*inertia[1][2] - inertia[0][2]*inertia[1][1];
- inverse[1][0] = -(inertia[1][0]*inertia[2][2] -
+ inverse[1][0] = -(inertia[1][0]*inertia[2][2] -
inertia[1][2]*inertia[2][0]);
inverse[1][1] = inertia[0][0]*inertia[2][2] - inertia[0][2]*inertia[2][0];
- inverse[1][2] = -(inertia[0][0]*inertia[1][2] -
+ inverse[1][2] = -(inertia[0][0]*inertia[1][2] -
inertia[0][2]*inertia[1][0]);
inverse[2][0] = inertia[1][0]*inertia[2][1] - inertia[1][1]*inertia[2][0];
- inverse[2][1] = -(inertia[0][0]*inertia[2][1] -
+ inverse[2][1] = -(inertia[0][0]*inertia[2][1] -
inertia[0][1]*inertia[2][0]);
inverse[2][2] = inertia[0][0]*inertia[1][1] - inertia[0][1]*inertia[1][0];
@@ -1735,25 +1735,25 @@ void Group::omega(double *angmom, double inertia[3][3], double *w)
ez[0] = evectors[0][2];
ez[1] = evectors[1][2];
ez[2] = evectors[2][2];
-
+
// enforce 3 evectors as a right-handed coordinate system
// flip 3rd vector if needed
-
+
MathExtra::cross3(ex,ey,cross);
if (MathExtra::dot3(cross,ez) < 0.0) MathExtra::negate3(ez);
-
+
// if any principal moment < scaled EPSILON, set to 0.0
-
+
double max;
max = MAX(idiag[0],idiag[1]);
max = MAX(max,idiag[2]);
-
+
if (idiag[0] < EPSILON*max) idiag[0] = 0.0;
if (idiag[1] < EPSILON*max) idiag[1] = 0.0;
if (idiag[2] < EPSILON*max) idiag[2] = 0.0;
-
+
// calculate omega using diagonalized inertia matrix
-
+
MathExtra::angmom_to_omega(angmom,ex,ey,ez,idiag,w);
}
}
diff --git a/src/imbalance_neigh.cpp b/src/imbalance_neigh.cpp
index 9246e083c73d941eb6827f4879e21ace84623702..2a55754da8205cd7421aa9705d0f47b9c104a585 100644
--- a/src/imbalance_neigh.cpp
+++ b/src/imbalance_neigh.cpp
@@ -53,7 +53,7 @@ void ImbalanceNeigh::compute(double *weight)
// find suitable neighbor list
// can only use certain conventional neighbor lists
// NOTE: why not full list, if half does not exist?
-
+
for (req = 0; req < neighbor->old_nrequest; ++req) {
if (neighbor->old_requests[req]->half &&
neighbor->old_requests[req]->skip == 0 &&
diff --git a/src/imbalance_store.cpp b/src/imbalance_store.cpp
index 26dd47fb1bbdbe3d76155ac47e030cd7f414202c..2903f8497ea29ed6940db945c0195f58ddf4f097 100644
--- a/src/imbalance_store.cpp
+++ b/src/imbalance_store.cpp
@@ -49,14 +49,14 @@ void ImbalanceStore::compute(double *weight)
{
int dflag = 0;
int idx = atom->find_custom(name,dflag);
-
+
// property does not exist
-
+
if (idx < 0 || dflag != 1) return;
-
+
double *prop = atom->dvector[idx];
const int nlocal = atom->nlocal;
-
+
for (int i = 0; i < nlocal; ++i)
prop[i] = weight[i];
}
diff --git a/src/imbalance_time.cpp b/src/imbalance_time.cpp
index 4450390e76f37376678779b2a45bd7b389b801b8..a5fe538b8f70f2de226c11d93b6c61c6659638b6 100644
--- a/src/imbalance_time.cpp
+++ b/src/imbalance_time.cpp
@@ -97,9 +97,9 @@ void ImbalanceTime::compute(double *weight)
}
for (int i = 0; i < nlocal; i++) weight[i] *= localwt;
-
+
// record time up to this point
-
+
last += cost;
}
diff --git a/src/info.cpp b/src/info.cpp
index c8cf25d871d2a23bbdabef9139819cb09124c282..e1103c0530b8638d3505ec9a13b50023d280bad9 100644
--- a/src/info.cpp
+++ b/src/info.cpp
@@ -305,7 +305,7 @@ void Info::command(int narg, char **arg)
ut.sysname, ut.release, ut.machine);
#endif
}
-
+
if (flags & MEMORY) {
fprintf(out,"\nMemory allocation information (MPI rank 0):\n\n");
diff --git a/src/input.cpp b/src/input.cpp
index 3d458c1ea4b3d1c1c9ec7574bac5779114b1271e..a0691f78a49c119ad65ce1b16f777e472f8b9d7e 100644
--- a/src/input.cpp
+++ b/src/input.cpp
@@ -644,16 +644,16 @@ int Input::expand_args(int narg, char **arg, int mode, char **&earg)
} else if (mode == 1 && modify->compute[icompute]->array_flag) {
nmax = modify->compute[icompute]->size_array_cols;
expandflag = 1;
- } else if (modify->compute[icompute]->peratom_flag &&
+ } else if (modify->compute[icompute]->peratom_flag &&
modify->compute[icompute]->size_peratom_cols) {
nmax = modify->compute[icompute]->size_peratom_cols;
expandflag = 1;
- } else if (modify->compute[icompute]->local_flag &&
+ } else if (modify->compute[icompute]->local_flag &&
modify->compute[icompute]->size_local_cols) {
nmax = modify->compute[icompute]->size_local_cols;
expandflag = 1;
}
- }
+ }
} else if (arg[iarg][0] == 'f') {
*ptr1 = '\0';
ifix = modify->find_fix(&arg[iarg][2]);
@@ -668,11 +668,11 @@ int Input::expand_args(int narg, char **arg, int mode, char **&earg)
} else if (mode == 1 && modify->fix[ifix]->array_flag) {
nmax = modify->fix[ifix]->size_array_cols;
expandflag = 1;
- } else if (modify->fix[ifix]->peratom_flag &&
+ } else if (modify->fix[ifix]->peratom_flag &&
modify->fix[ifix]->size_peratom_cols) {
nmax = modify->fix[ifix]->size_peratom_cols;
expandflag = 1;
- } else if (modify->fix[ifix]->local_flag &&
+ } else if (modify->fix[ifix]->local_flag &&
modify->fix[ifix]->size_local_cols) {
nmax = modify->fix[ifix]->size_local_cols;
expandflag = 1;
@@ -691,7 +691,7 @@ int Input::expand_args(int narg, char **arg, int mode, char **&earg)
*ptr2 = ']';
if (newarg+nhi-nlo+1 > maxarg) {
maxarg += nhi-nlo+1;
- earg = (char **)
+ earg = (char **)
memory->srealloc(earg,maxarg*sizeof(char *),"input:earg");
}
for (index = nlo; index <= nhi; index++) {
@@ -706,7 +706,7 @@ int Input::expand_args(int narg, char **arg, int mode, char **&earg)
} else {
if (newarg == maxarg) {
maxarg++;
- earg = (char **)
+ earg = (char **)
memory->srealloc(earg,maxarg*sizeof(char *),"input:earg");
}
n = strlen(arg[iarg]) + 1;
diff --git a/src/library.cpp b/src/library.cpp
index b30c6e9595de5a6817dc92e1cc415c83bebd2888..6001cf3f8eafba07ab7af03e06115601d265fb1e 100644
--- a/src/library.cpp
+++ b/src/library.cpp
@@ -268,7 +268,7 @@ void lammps_commands_list(void *ptr, int ncmd, char **cmds)
/* ----------------------------------------------------------------------
process multiple input commands in single long str, separated by newlines
- single command can span multiple lines via continuation characters
+ single command can span multiple lines via continuation characters
multi-line commands enabled by triple quotes will not work
------------------------------------------------------------------------- */
@@ -449,7 +449,7 @@ void lammps_extract_box(void *ptr, double *boxlo, double *boxhi,
periodicity[0] = domain->periodicity[0];
periodicity[1] = domain->periodicity[1];
periodicity[2] = domain->periodicity[2];
-
+
*box_change = domain->box_change;
}
@@ -791,7 +791,7 @@ void lammps_gather_atoms(void *ptr, char *name,
// error if tags are not defined or not consecutive
int flag = 0;
- if (lmp->atom->tag_enable == 0 || lmp->atom->tag_consecutive() == 0)
+ if (lmp->atom->tag_enable == 0 || lmp->atom->tag_consecutive() == 0)
flag = 1;
if (lmp->atom->natoms > MAXSMALLINT) flag = 1;
if (flag) {
@@ -845,7 +845,7 @@ void lammps_gather_atoms(void *ptr, char *name,
for (j = 0; j < count; j++)
copy[offset++] = array[i][j];
}
-
+
MPI_Allreduce(copy,data,count*natoms,MPI_INT,MPI_SUM,lmp->world);
lmp->memory->destroy(copy);
@@ -900,7 +900,7 @@ void lammps_scatter_atoms(void *ptr, char *name,
// error if tags are not defined or not consecutive or no atom map
int flag = 0;
- if (lmp->atom->tag_enable == 0 || lmp->atom->tag_consecutive() == 0)
+ if (lmp->atom->tag_enable == 0 || lmp->atom->tag_consecutive() == 0)
flag = 1;
if (lmp->atom->natoms > MAXSMALLINT) flag = 1;
if (lmp->atom->map_style == 0) flag = 1;
@@ -1031,7 +1031,7 @@ void lammps_create_atoms(void *ptr, int n, tagint *id, int *type,
bigint natoms_prev = atom->natoms;
int nlocal_prev = nlocal;
double xdata[3];
-
+
for (int i = 0; i < n; i++) {
xdata[0] = x[3*i];
xdata[1] = x[3*i+1];
@@ -1039,7 +1039,7 @@ void lammps_create_atoms(void *ptr, int n, tagint *id, int *type,
imageint * img = image ? &image[i] : NULL;
tagint tag = id ? id[i] : -1;
if (!domain->ownatom(tag, xdata, img, shrinkexceed)) continue;
-
+
atom->avec->create_atom(type[i],xdata);
if (id) atom->tag[nlocal] = id[i];
else atom->tag[nlocal] = i+1;
@@ -1071,7 +1071,7 @@ void lammps_create_atoms(void *ptr, int n, tagint *id, int *type,
}
// warn if new natoms is not correct
-
+
if (lmp->atom->natoms != natoms_prev + n) {
char str[128];
sprintf(str,"Library warning in lammps_create_atoms, "
diff --git a/src/math_extra.cpp b/src/math_extra.cpp
index de61c8901c4846982189c442131495e9161211a5..d1700a3070cb6cc546e7e39ed0c1c10a5ad2a9f7 100644
--- a/src/math_extra.cpp
+++ b/src/math_extra.cpp
@@ -616,7 +616,7 @@ void BuildRxMatrix(double R[3][3], const double angle)
const double angleSq = angle * angle;
const double cosAngle = (1.0 - angleSq * 0.25) / (1.0 + angleSq * 0.25);
const double sinAngle = angle / (1.0 + angleSq * 0.25);
-
+
R[0][0] = 1.0; R[0][1] = 0.0; R[0][2] = 0.0;
R[1][0] = 0.0; R[1][1] = cosAngle; R[1][2] = -sinAngle;
R[2][0] = 0.0; R[2][1] = sinAngle; R[2][2] = cosAngle;
@@ -631,7 +631,7 @@ void BuildRyMatrix(double R[3][3], const double angle)
const double angleSq = angle * angle;
const double cosAngle = (1.0 - angleSq * 0.25) / (1.0 + angleSq * 0.25);
const double sinAngle = angle / (1.0 + angleSq * 0.25);
-
+
R[0][0] = cosAngle; R[0][1] = 0.0; R[0][2] = sinAngle;
R[1][0] = 0.0; R[1][1] = 1.0; R[1][2] = 0.0;
R[2][0] = -sinAngle; R[2][1] = 0.0; R[2][2] = cosAngle;
@@ -646,7 +646,7 @@ void BuildRzMatrix(double R[3][3], const double angle)
const double angleSq = angle * angle;
const double cosAngle = (1.0 - angleSq * 0.25) / (1.0 + angleSq * 0.25);
const double sinAngle = angle / (1.0 + angleSq * 0.25);
-
+
R[0][0] = cosAngle; R[0][1] = -sinAngle; R[0][2] = 0.0;
R[1][0] = sinAngle; R[1][1] = cosAngle; R[1][2] = 0.0;
R[2][0] = 0.0; R[2][1] = 0.0; R[2][2] = 1.0;
diff --git a/src/neigh_list.cpp b/src/neigh_list.cpp
index 93f4b13bf2c3359db2d0a22037e0218b960fe9c4..2851bae14fa4fec3d1dfe233465c6d03bb002acb 100644
--- a/src/neigh_list.cpp
+++ b/src/neigh_list.cpp
@@ -134,7 +134,7 @@ NeighList::~NeighList()
void NeighList::post_constructor(NeighRequest *nq)
{
// copy request settings used by list itself
-
+
occasional = nq->occasional;
ghost = nq->ghost;
ssa = nq->ssa;
diff --git a/src/neighbor.cpp b/src/neighbor.cpp
index 82017c8525beb0dbe8322b9de469078ab9d6ce95..31dddd9f15eb39964967a9308feee577fe1162a5 100644
--- a/src/neighbor.cpp
+++ b/src/neighbor.cpp
@@ -199,7 +199,7 @@ Neighbor::~Neighbor()
delete [] slist;
delete [] plist;
- for (int i = 0; i < nrequest; i++)
+ for (int i = 0; i < nrequest; i++)
if (requests[i]) delete requests[i];
memory->sfree(requests);
for (int i = 0; i < old_nrequest; i++)
@@ -527,7 +527,7 @@ void Neighbor::init_styles()
#undef NBinStyle
#undef NBIN_CLASS
- binclass = new BinCreator[nbclass];
+ binclass = new BinCreator[nbclass];
binnames = new char*[nbclass];
binmasks = new int[nbclass];
nbclass = 0;
@@ -551,7 +551,7 @@ void Neighbor::init_styles()
#undef NStencilStyle
#undef NSTENCIL_CLASS
- stencilclass = new StencilCreator[nsclass];
+ stencilclass = new StencilCreator[nsclass];
stencilnames = new char*[nsclass];
stencilmasks = new int[nsclass];
nsclass = 0;
@@ -575,7 +575,7 @@ void Neighbor::init_styles()
#undef NPairStyle
#undef NPAIR_CLASS
- pairclass = new PairCreator[npclass];
+ pairclass = new PairCreator[npclass];
pairnames = new char*[npclass];
pairmasks = new int[npclass];
npclass = 0;
@@ -669,7 +669,7 @@ int Neighbor::init_pair()
// (5) copy = convert as many lists as possible to copy lists
// order of morph methods matters:
// (3) after (2), b/c it adjusts lists created by (2)
- // (4) after (2) and (3),
+ // (4) after (2) and (3),
// b/c (2) may create new full lists, (3) may change them
// (5) last, after all lists are finalized, so all possible copies found
@@ -680,13 +680,13 @@ int Neighbor::init_pair()
morph_granular(); // this method can change flags set by requestor
morph_halffull();
morph_copy();
-
+
// create new lists, one per request including added requests
// wait to allocate initial pages until copy lists are detected
// NOTE: can I allocate now, instead of down below?
nlist = nrequest;
-
+
lists = new NeighList*[nrequest];
neigh_bin = new NBin*[nrequest];
neigh_stencil = new NStencil*[nrequest];
@@ -697,11 +697,11 @@ int Neighbor::init_pair()
// only for original requests, not ones added by Neighbor class
for (i = 0; i < nrequest; i++) {
- if (requests[i]->kokkos_host || requests[i]->kokkos_device)
+ if (requests[i]->kokkos_host || requests[i]->kokkos_device)
create_kokkos_list(i);
else lists[i] = new NeighList(lmp);
lists[i]->index = i;
-
+
if (requests[i]->pair && i < nrequest_original) {
Pair *pair = (Pair *) requests[i]->requestor;
pair->init_list(requests[i]->id,lists[i]);
@@ -721,22 +721,22 @@ int Neighbor::init_pair()
lists[i]->post_constructor(requests[i]);
// assign Bin,Stencil,Pair style to each list
-
+
int flag;
for (i = 0; i < nrequest; i++) {
flag = choose_bin(requests[i]);
lists[i]->bin_method = flag;
- if (flag < 0)
+ if (flag < 0)
error->all(FLERR,"Requested neighbor bin option does not exist");
flag = choose_stencil(requests[i]);
lists[i]->stencil_method = flag;
- if (flag < 0)
+ if (flag < 0)
error->all(FLERR,"Requested neighbor stencil method does not exist");
flag = choose_pair(requests[i]);
lists[i]->pair_method = flag;
- if (flag < 0)
+ if (flag < 0)
error->all(FLERR,"Requested neighbor pair method does not exist");
}
@@ -821,18 +821,18 @@ int Neighbor::init_pair()
}
// allocate initial pages for each list, except if copy flag set
-
+
for (i = 0; i < nlist; i++) {
if (lists[i]->copy) continue;
lists[i]->setup_pages(pgsize,oneatom);
}
// first-time allocation of per-atom data for lists that are built and store
- // lists that do not store: copy
+ // lists that do not store: copy
// use atom->nmax for both grow() args
// i.e. grow first time to expanded size to avoid future reallocs
// also Kokkos list initialization
-
+
int maxatom = atom->nmax;
for (i = 0; i < nlist; i++)
if (neigh_pair[i] && !lists[i]->copy) lists[i]->grow(maxatom,maxatom);
@@ -841,7 +841,7 @@ int Neighbor::init_pair()
// perpetual = non-occasional, re-built at every reneighboring
// slist = indices of perpetual NStencil classes
// perpetual = used by any perpetual NPair class
-
+
delete [] slist;
delete [] plist;
nstencil_perpetual = npair_perpetual = 0;
@@ -852,11 +852,11 @@ int Neighbor::init_pair()
if (lists[i]->occasional == 0 && lists[i]->pair_method)
plist[npair_perpetual++] = i;
}
-
+
for (i = 0; i < nstencil; i++) {
flag = 0;
for (j = 0; j < npair_perpetual; j++)
- if (lists[plist[j]]->stencil_method == neigh_stencil[i]->istyle)
+ if (lists[plist[j]]->stencil_method == neigh_stencil[i]->istyle)
flag = 1;
if (flag) slist[nstencil_perpetual++] = i;
}
@@ -913,7 +913,7 @@ int Neighbor::init_pair()
void Neighbor::morph_unique()
{
NeighRequest *irq;
-
+
for (int i = 0; i < nrequest; i++) {
irq = requests[i];
@@ -955,7 +955,7 @@ void Neighbor::morph_skip()
for (j = 0; j < nrequest; j++) {
if (i == j) continue;
jrq = requests[j];
-
+
// can only skip from a perpetual non-skip list
if (jrq->occasional) continue;
@@ -970,7 +970,7 @@ void Neighbor::morph_skip()
// IJ newton = 1 for newton on, 2 for newton off
inewton = irq->newton;
- if (inewton == 0) inewton = force->newton_pair ? 1 : 2;
+ if (inewton == 0) inewton = force->newton_pair ? 1 : 2;
jnewton = jrq->newton;
if (jnewton == 0) jnewton = force->newton_pair ? 1 : 2;
if (inewton != jnewton) continue;
@@ -1151,7 +1151,7 @@ void Neighbor::morph_halffull()
break;
}
-
+
// if matching list exists, point to it
if (j < nrequest) {
@@ -1170,7 +1170,7 @@ void Neighbor::morph_copy()
{
int i,j,inewton,jnewton;
NeighRequest *irq,*jrq;
-
+
for (i = 0; i < nrequest; i++) {
irq = requests[i];
@@ -1205,7 +1205,7 @@ void Neighbor::morph_copy()
// IJ newton = 1 for newton on, 2 for newton off
inewton = irq->newton;
- if (inewton == 0) inewton = force->newton_pair ? 1 : 2;
+ if (inewton == 0) inewton = force->newton_pair ? 1 : 2;
jnewton = jrq->newton;
if (jnewton == 0) jnewton = force->newton_pair ? 1 : 2;
if (inewton != jnewton) continue;
@@ -1343,11 +1343,11 @@ void Neighbor::init_topology()
else bondwhich = ALL;
if (!neigh_bond || bondwhich != old_bondwhich) {
delete neigh_bond;
- if (bondwhich == ALL)
+ if (bondwhich == ALL)
neigh_bond = new NTopoBondAll(lmp);
- else if (bondwhich == PARTIAL)
+ else if (bondwhich == PARTIAL)
neigh_bond = new NTopoBondPartial(lmp);
- else if (bondwhich == TEMPLATE)
+ else if (bondwhich == TEMPLATE)
neigh_bond = new NTopoBondTemplate(lmp);
}
}
@@ -1359,11 +1359,11 @@ void Neighbor::init_topology()
else anglewhich = ALL;
if (!neigh_angle || anglewhich != old_anglewhich) {
delete neigh_angle;
- if (anglewhich == ALL)
+ if (anglewhich == ALL)
neigh_angle = new NTopoAngleAll(lmp);
- else if (anglewhich == PARTIAL)
+ else if (anglewhich == PARTIAL)
neigh_angle = new NTopoAnglePartial(lmp);
- else if (anglewhich == TEMPLATE)
+ else if (anglewhich == TEMPLATE)
neigh_angle = new NTopoAngleTemplate(lmp);
}
}
@@ -1375,11 +1375,11 @@ void Neighbor::init_topology()
else dihedralwhich = ALL;
if (!neigh_dihedral || dihedralwhich != old_dihedralwhich) {
delete neigh_dihedral;
- if (dihedralwhich == ALL)
+ if (dihedralwhich == ALL)
neigh_dihedral = new NTopoDihedralAll(lmp);
- else if (dihedralwhich == PARTIAL)
+ else if (dihedralwhich == PARTIAL)
neigh_dihedral = new NTopoDihedralPartial(lmp);
- else if (dihedralwhich == TEMPLATE)
+ else if (dihedralwhich == TEMPLATE)
neigh_dihedral = new NTopoDihedralTemplate(lmp);
}
}
@@ -1391,11 +1391,11 @@ void Neighbor::init_topology()
else improperwhich = ALL;
if (!neigh_improper || improperwhich != old_improperwhich) {
delete neigh_improper;
- if (improperwhich == ALL)
+ if (improperwhich == ALL)
neigh_improper = new NTopoImproperAll(lmp);
- else if (improperwhich == PARTIAL)
+ else if (improperwhich == PARTIAL)
neigh_improper = new NTopoImproperPartial(lmp);
- else if (improperwhich == TEMPLATE)
+ else if (improperwhich == TEMPLATE)
neigh_improper = new NTopoImproperTemplate(lmp);
}
}
@@ -1449,7 +1449,7 @@ void Neighbor::print_pairwise_info()
fprintf(out," binsize = %g, bins = %g %g %g\n",binsize,
ceil(bbox[0]/binsize), ceil(bbox[1]/binsize),
ceil(bbox[2]/binsize));
-
+
fprintf(out," %d neighbor lists, "
"perpetual/occasional/extra = %d %d %d\n",
nlist,nperpetual,noccasional,nextra);
@@ -1478,7 +1478,7 @@ void Neighbor::print_pairwise_info()
if (rq->copy)
fprintf(out,", copy from (%d)",rq->copylist+1);
- else if (rq->halffull)
+ else if (rq->halffull)
fprintf(out,", half/full from (%d)",rq->halffulllist+1);
else if (rq->skip)
fprintf(out,", skip from (%d)",rq->skiplist+1);
@@ -1496,7 +1496,7 @@ void Neighbor::print_pairwise_info()
else fprintf(out,", newton off");
} else if (rq->newton == 1) fprintf(out,", newton on");
else if (rq->newton == 2) fprintf(out,", newton off");
-
+
if (rq->ghost) fprintf(out,", ghost");
if (rq->size) fprintf(out,", size");
if (rq->history) fprintf(out,", history");
@@ -1516,17 +1516,17 @@ void Neighbor::print_pairwise_info()
fprintf(out," ");
if (lists[i]->pair_method == 0) fprintf(out,"pair build: none\n");
else fprintf(out,"pair build: %s\n",pairnames[lists[i]->pair_method-1]);
-
+
fprintf(out," ");
if (lists[i]->stencil_method == 0) fprintf(out,"stencil: none\n");
else fprintf(out,"stencil: %s\n",
stencilnames[lists[i]->stencil_method-1]);
-
+
fprintf(out," ");
if (lists[i]->bin_method == 0) fprintf(out,"bin: none\n");
else fprintf(out,"bin: %s\n",binnames[lists[i]->bin_method-1]);
}
-
+
/*
fprintf(out," %d stencil methods\n",nstencil);
for (i = 0; i < nstencil; i++)
@@ -1540,7 +1540,7 @@ void Neighbor::print_pairwise_info()
}
}
}
-
+
/* ----------------------------------------------------------------------
make copy of current requests and Neighbor params
used to compare to when next run occurs
@@ -1663,7 +1663,7 @@ int Neighbor::choose_stencil(NeighRequest *rq)
// mask & NS_NEWTOFF,mask & NS_GHOST,mask & NS_SSA);
// exactly one of half or full is set and must match
-
+
if (rq->half) {
if (!(mask & NS_HALF)) continue;
} else if (rq->full) {
@@ -1678,7 +1678,7 @@ int Neighbor::choose_stencil(NeighRequest *rq)
if (!(mask & NS_NEWTOFF)) continue;
}
- // require match of these request flags and mask bits
+ // require match of these request flags and mask bits
// (!A != !B) is effectively a logical xor
if (!rq->ghost != !(mask & NS_GHOST)) continue;
@@ -1701,7 +1701,7 @@ int Neighbor::choose_stencil(NeighRequest *rq)
}
// domain triclinic flag is on or off and must match
-
+
if (triclinic) {
if (!(mask & NS_TRI)) continue;
} else if (!triclinic) {
@@ -1741,7 +1741,7 @@ int Neighbor::choose_pair(NeighRequest *rq)
else if (rq->newton == 2) newtflag = 0;
int molecular = atom->molecular;
-
+
//printf("PAIR RQ FLAGS: hf %d %d n %d g %d sz %d gos %d r %d b %d o %d i %d "
// "kk %d %d ss %d dn %d sk %d cp %d hf %d oo %d\n",
// rq->half,rq->full,rq->newton,rq->ghost,rq->size,
@@ -1795,7 +1795,7 @@ int Neighbor::choose_pair(NeighRequest *rq)
if (mask & NP_MOLONLY) continue;
}
- // require match of these request flags and mask bits
+ // require match of these request flags and mask bits
// (!A != !B) is effectively a logical xor
if (!rq->ghost != !(mask & NP_GHOST)) continue;
@@ -1809,7 +1809,7 @@ int Neighbor::choose_pair(NeighRequest *rq)
if (!rq->kokkos_device != !(mask & NP_KOKKOS_DEVICE)) continue;
if (!rq->kokkos_host != !(mask & NP_KOKKOS_HOST)) continue;
if (!rq->ssa != !(mask & NP_SSA)) continue;
-
+
if (!rq->skip != !(mask & NP_SKIP)) continue;
if (!rq->halffull != !(mask & NP_HALF_FULL)) continue;
@@ -2129,7 +2129,7 @@ void Neighbor::build_one(class NeighList *mylist, int preflag)
// build_one() should never be invoked on a perpetual list
- if (!mylist->occasional)
+ if (!mylist->occasional)
error->all(FLERR,"Neighbor build one invoked on perpetual list");
// no need to build if already built since last re-neighbor
@@ -2147,7 +2147,7 @@ void Neighbor::build_one(class NeighList *mylist, int preflag)
// if this is copy list and parent is occasional list,
// or this is halffull and parent is occasional list,
- // insure parent is current
+ // insure parent is current
if (mylist->listcopy && mylist->listcopy->occasional)
build_one(mylist->listcopy,preflag);
@@ -2325,7 +2325,7 @@ void Neighbor::modify_params(int narg, char **arg)
ex_mol_intra[nex_mol] = 0;
nex_mol++;
iarg += 3;
-
+
} else if (strcmp(arg[iarg+1],"none") == 0) {
nex_type = nex_group = nex_mol = 0;
iarg += 2;
@@ -2348,9 +2348,9 @@ void Neighbor::exclusion_group_group_delete(int group1, int group2)
break;
mlast = m;
- if (mlast == nex_group)
+ if (mlast == nex_group)
error->all(FLERR,"Unable to find group-group exclusion");
-
+
for (m = mlast+1; m < nex_group; m++) {
ex1_group[m-1] = ex1_group[m];
ex2_group[m-1] = ex2_group[m];
diff --git a/src/npair_half_size_bin_newtoff.cpp b/src/npair_half_size_bin_newtoff.cpp
index d575f3eb1f572ceccb4bdbb59a624db44130da22..6cd97c71d13383cb34a1c7a7ba21d1cef2461293 100644
--- a/src/npair_half_size_bin_newtoff.cpp
+++ b/src/npair_half_size_bin_newtoff.cpp
@@ -79,14 +79,14 @@ void NPairHalfSizeBinNewtoff::build(NeighList *list)
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
if (j <= i) continue;
if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
-
+
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
radsum = radi + radius[j];
cutsq = (radsum+skin) * (radsum+skin);
-
+
if (rsq <= cutsq) {
if (history && rsq < radsum*radsum)
neighptr[n++] = j ^ mask_history;
diff --git a/src/npair_half_size_bin_newton.cpp b/src/npair_half_size_bin_newton.cpp
index da29cb2029aecc4e0db37e3d4aa1ee44a3f77c6d..c0ed03816625f3bc91de2b43c4fe472e8895b36a 100644
--- a/src/npair_half_size_bin_newton.cpp
+++ b/src/npair_half_size_bin_newton.cpp
@@ -91,9 +91,9 @@ void NPairHalfSizeBinNewton::build(NeighList *list)
cutsq = (radsum+skin) * (radsum+skin);
if (rsq <= cutsq) {
- if (history && rsq < radsum*radsum)
+ if (history && rsq < radsum*radsum)
neighptr[n++] = j ^ mask_history;
- else
+ else
neighptr[n++] = j;
}
}
@@ -113,7 +113,7 @@ void NPairHalfSizeBinNewton::build(NeighList *list)
cutsq = (radsum+skin) * (radsum+skin);
if (rsq <= cutsq) {
- if (history && rsq < radsum*radsum)
+ if (history && rsq < radsum*radsum)
neighptr[n++] = j ^ mask_history;
else
neighptr[n++] = j;
diff --git a/src/ntopo_dihedral_partial.cpp b/src/ntopo_dihedral_partial.cpp
index abfc30ba311524a3a73e01d04057d462fcaa49e5..603c81e68c674487f48fdd241c93516e9cc47439 100644
--- a/src/ntopo_dihedral_partial.cpp
+++ b/src/ntopo_dihedral_partial.cpp
@@ -28,7 +28,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-NTopoDihedralPartial::NTopoDihedralPartial(LAMMPS *lmp) :
+NTopoDihedralPartial::NTopoDihedralPartial(LAMMPS *lmp) :
NTopo(lmp)
{
allocate_dihedral();
diff --git a/src/ntopo_dihedral_template.cpp b/src/ntopo_dihedral_template.cpp
index 8ef60de2372ac239f8791b61b208b0adb16d428b..38d319fb9643b6ed5c18cb185f2eea22fbffed5a 100644
--- a/src/ntopo_dihedral_template.cpp
+++ b/src/ntopo_dihedral_template.cpp
@@ -30,7 +30,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-NTopoDihedralTemplate::NTopoDihedralTemplate(LAMMPS *lmp) :
+NTopoDihedralTemplate::NTopoDihedralTemplate(LAMMPS *lmp) :
NTopo(lmp)
{
allocate_dihedral();
diff --git a/src/ntopo_improper_partial.cpp b/src/ntopo_improper_partial.cpp
index f8f06cf41b367c2bda97c3df8a6f564ca230bc2c..072a2aa76790d0f762e070c8034dc78e0b73607c 100644
--- a/src/ntopo_improper_partial.cpp
+++ b/src/ntopo_improper_partial.cpp
@@ -28,7 +28,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-NTopoImproperPartial::NTopoImproperPartial(LAMMPS *lmp) :
+NTopoImproperPartial::NTopoImproperPartial(LAMMPS *lmp) :
NTopo(lmp)
{
allocate_improper();
diff --git a/src/ntopo_improper_template.cpp b/src/ntopo_improper_template.cpp
index 4662e3693f53625fad2464cee0b4e2893129fcae..cb15a077d5a30e928cbd35fc20fdac0ce1322a84 100644
--- a/src/ntopo_improper_template.cpp
+++ b/src/ntopo_improper_template.cpp
@@ -30,7 +30,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-NTopoImproperTemplate::NTopoImproperTemplate(LAMMPS *lmp) :
+NTopoImproperTemplate::NTopoImproperTemplate(LAMMPS *lmp) :
NTopo(lmp)
{
allocate_improper();
diff --git a/src/pair_buck.cpp b/src/pair_buck.cpp
index ac7ac0aeb504901fe1e89246b6b9e65cb11b872b..8cbf97a6badc13f8bd22c20d85e6175626f897e7 100644
--- a/src/pair_buck.cpp
+++ b/src/pair_buck.cpp
@@ -187,7 +187,7 @@ void PairBuck::settings(int narg, char **arg)
void PairBuck::coeff(int narg, char **arg)
{
- if (narg < 5 || narg > 6)
+ if (narg < 5 || narg > 6)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
diff --git a/src/pair_morse.cpp b/src/pair_morse.cpp
index 5f906420653530a824ea38541056af259e157e13..0e40fc75512277a36b3ef83c3bc5c299134090d7 100644
--- a/src/pair_morse.cpp
+++ b/src/pair_morse.cpp
@@ -176,7 +176,7 @@ void PairMorse::settings(int narg, char **arg)
void PairMorse::coeff(int narg, char **arg)
{
- if (narg < 5 || narg > 6)
+ if (narg < 5 || narg > 6)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
diff --git a/src/pair_morse.h b/src/pair_morse.h
index e7fb9a8cd514acee390e85a655b58c1b8886e743..881fd6650e257779662e9f3bdb66a6d6b8df3ebb 100644
--- a/src/pair_morse.h
+++ b/src/pair_morse.h
@@ -29,7 +29,7 @@ class PairMorse : public Pair {
PairMorse(class LAMMPS *);
virtual ~PairMorse();
virtual void compute(int, int);
-
+
void settings(int, char **);
void coeff(int, char **);
double init_one(int, int);
diff --git a/src/pair_table.cpp b/src/pair_table.cpp
index 782fb43f9a352b529fb37bb9b1cea286dceeb861..0ee4effb0190b989d966689293d6fbd07d875e62 100644
--- a/src/pair_table.cpp
+++ b/src/pair_table.cpp
@@ -113,7 +113,7 @@ void PairTable::compute(int eflag, int vflag)
if (rsq < cutsq[itype][jtype]) {
tb = &tables[tabindex[itype][jtype]];
if (rsq < tb->innersq) {
- sprintf(estr,"Pair distance < table inner cutoff: "
+ sprintf(estr,"Pair distance < table inner cutoff: "
"ijtype %d %d dist %g",itype,jtype,sqrt(rsq));
error->one(FLERR,estr);
}
@@ -121,7 +121,7 @@ void PairTable::compute(int eflag, int vflag)
if (tabstyle == LOOKUP) {
itable = static_cast<int> ((rsq - tb->innersq) * tb->invdelta);
if (itable >= tlm1) {
- sprintf(estr,"Pair distance > table outer cutoff: "
+ sprintf(estr,"Pair distance > table outer cutoff: "
"ijtype %d %d dist %g",itype,jtype,sqrt(rsq));
error->one(FLERR,estr);
}
@@ -129,7 +129,7 @@ void PairTable::compute(int eflag, int vflag)
} else if (tabstyle == LINEAR) {
itable = static_cast<int> ((rsq - tb->innersq) * tb->invdelta);
if (itable >= tlm1) {
- sprintf(estr,"Pair distance > table outer cutoff: "
+ sprintf(estr,"Pair distance > table outer cutoff: "
"ijtype %d %d dist %g",itype,jtype,sqrt(rsq));
error->one(FLERR,estr);
}
@@ -139,7 +139,7 @@ void PairTable::compute(int eflag, int vflag)
} else if (tabstyle == SPLINE) {
itable = static_cast<int> ((rsq - tb->innersq) * tb->invdelta);
if (itable >= tlm1) {
- sprintf(estr,"Pair distance > table outer cutoff: "
+ sprintf(estr,"Pair distance > table outer cutoff: "
"ijtype %d %d dist %g",itype,jtype,sqrt(rsq));
error->one(FLERR,estr);
}
diff --git a/src/pair_ufm.cpp b/src/pair_ufm.cpp
index 6462c0e79745f20c2f8f3fd1bae6adc9fa6f8168..e036e2cdd96cfbf0472c6b61a0c736bda90ede6f 100644
--- a/src/pair_ufm.cpp
+++ b/src/pair_ufm.cpp
@@ -2,17 +2,17 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
-
+
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
-
+
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* -----------------------------------------------------------------------
- Contributing author:
+ Contributing author:
Rodolfo Paula Leite (Unicamp/Brazil) - pl.rodolfo@gmail.com
Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br
------------------------------------------------------------------------- */
@@ -233,7 +233,7 @@ double PairUFM::init_one(int i, int j)
sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]);
cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
}
-
+
uf1[i][j] = 2.0 * epsilon[i][j] / pow(sigma[i][j],2.0);
uf2[i][j] = 1.0 / pow(sigma[i][j],2.0);
uf3[i][j] = epsilon[i][j];
diff --git a/src/read_data.cpp b/src/read_data.cpp
index bc588051aff866ba70f57f9e4a8fbd3401d8b859..4b84016744c9d462fbe564f8c71d0f57e561fa8b 100644
--- a/src/read_data.cpp
+++ b/src/read_data.cpp
@@ -757,7 +757,7 @@ void ReadData::command(int narg, char **arg)
}
// init per-atom fix/compute/variable values for created atoms
-
+
atom->data_fix_compute_variable(nlocal_previous,atom->nlocal);
// assign atoms added by this data file to specified group
@@ -886,7 +886,7 @@ void ReadData::command(int narg, char **arg)
}
// restore old styles, when reading with nocoeff flag given
-
+
if (coeffflag == 0) {
if (force->pair) delete force->pair;
force->pair = saved_pair;
@@ -1650,7 +1650,7 @@ void ReadData::bodies(int firstpass)
m += strlen(&buffer[m]);
onebody++;
}
- if (nword > ninteger)
+ if (nword > ninteger)
error->one(FLERR,"Too many values in body lines in data file");
nword = 0;
@@ -1664,7 +1664,7 @@ void ReadData::bodies(int firstpass)
m += strlen(&buffer[m]);
onebody++;
}
- if (nword > ndouble)
+ if (nword > ndouble)
error->one(FLERR,"Too many values in body lines in data file");
if (onebody+1 > MAXBODY)
diff --git a/src/read_dump.cpp b/src/read_dump.cpp
index 2a566cba4e0b56651facf50993e555bf843efda2..f11f0f20eb265fdabeefc07de2eb966c8000ef7e 100644
--- a/src/read_dump.cpp
+++ b/src/read_dump.cpp
@@ -607,7 +607,7 @@ int ReadDump::fields_and_keywords(int narg, char **arg)
if (dimension == 2) {
for (int i = 0; i < nfield; i++)
- if (fieldtype[i] == Z || fieldtype[i] == VZ ||
+ if (fieldtype[i] == Z || fieldtype[i] == VZ ||
fieldtype[i] == IZ || fieldtype[i] == FZ)
error->all(FLERR,"Illegal read_dump command");
}
@@ -923,7 +923,7 @@ void ReadDump::process_atoms(int n)
}
// init per-atom fix/compute/variable values for created atoms
-
+
atom->data_fix_compute_variable(nlocal_previous,atom->nlocal);
}
diff --git a/src/region.cpp b/src/region.cpp
index da814746ad24ef686a7224e9df7ecad8570a0bd0..047c43ce4b0aa1b6a3e5eb0abc8701e769bd6c52 100644
--- a/src/region.cpp
+++ b/src/region.cpp
@@ -28,9 +28,9 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-Region::Region(LAMMPS *lmp, int narg, char **arg) :
+Region::Region(LAMMPS *lmp, int narg, char **arg) :
Pointers(lmp),
- id(NULL), style(NULL), contact(NULL), list(NULL),
+ id(NULL), style(NULL), contact(NULL), list(NULL),
xstr(NULL), ystr(NULL), zstr(NULL), tstr(NULL)
{
int n = strlen(arg[0]) + 1;
diff --git a/src/region_intersect.cpp b/src/region_intersect.cpp
index fbbbb575b28cf7656aaef34b43344bb8d284214c..4fb84dda5999f047a115d1fcb26c1acbe6bc6619 100644
--- a/src/region_intersect.cpp
+++ b/src/region_intersect.cpp
@@ -26,7 +26,7 @@ RegIntersect::RegIntersect(LAMMPS *lmp, int narg, char **arg) :
Region(lmp, narg, arg), idsub(NULL)
{
nregion = 0;
-
+
if (narg < 5) error->all(FLERR,"Illegal region command");
int n = force->inumeric(FLERR,arg[2]);
if (n < 2) error->all(FLERR,"Illegal region command");
diff --git a/src/respa.cpp b/src/respa.cpp
index 18630c06d6fe8c525716cebd9bf5d689406dfe86..7080a739484de0c772463b72963c501b8312dc52 100644
--- a/src/respa.cpp
+++ b/src/respa.cpp
@@ -44,9 +44,9 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-Respa::Respa(LAMMPS *lmp, int narg, char **arg) :
+Respa::Respa(LAMMPS *lmp, int narg, char **arg) :
Integrate(lmp, narg, arg),
- step(NULL), loop(NULL), hybrid_level(NULL), hybrid_compute(NULL),
+ step(NULL), loop(NULL), hybrid_level(NULL), hybrid_compute(NULL),
newton(NULL), fix_respa(NULL)
{
nhybrid_styles = 0;
diff --git a/src/set.cpp b/src/set.cpp
index 0565dafb7d62f2507381d1a2260a29d383592539..77cae4cb0972c25604610199903406d99f3bdf14 100644
--- a/src/set.cpp
+++ b/src/set.cpp
@@ -525,7 +525,7 @@ void Set::command(int narg, char **arg)
if (comm->me == 0) {
if (screen) {
- if (strcmp(arg[origarg],"cc") == 0)
+ if (strcmp(arg[origarg],"cc") == 0)
fprintf(screen," %d settings made for %s index %s\n",
allcount,arg[origarg],arg[origarg+1]);
else
@@ -533,7 +533,7 @@ void Set::command(int narg, char **arg)
allcount,arg[origarg]);
}
if (logfile) {
- if (strcmp(arg[origarg],"cc") == 0)
+ if (strcmp(arg[origarg],"cc") == 0)
fprintf(logfile," %d settings made for %s index %s\n",
allcount,arg[origarg],arg[origarg+1]);
else
@@ -724,7 +724,7 @@ void Set::set(int keyword)
else if (keyword == EDPD_CV) atom->edpd_cv[i] = dvalue;
else if (keyword == CC) atom->cc[i][cc_index-1] = dvalue;
- else if (keyword == SMD_MASS_DENSITY) {
+ else if (keyword == SMD_MASS_DENSITY) {
// set mass from volume and supplied mass density
atom->rmass[i] = atom->vfrac[i] * dvalue;
}
@@ -780,18 +780,18 @@ void Set::set(int keyword)
else if (keyword == DENSITY) {
if (dvalue <= 0.0) error->one(FLERR,"Invalid density in set command");
if (atom->radius_flag && atom->radius[i] > 0.0)
- if (discflag)
+ if (discflag)
atom->rmass[i] = MY_PI*atom->radius[i]*atom->radius[i] * dvalue;
- else
- atom->rmass[i] = 4.0*MY_PI/3.0 *
+ else
+ atom->rmass[i] = 4.0*MY_PI/3.0 *
atom->radius[i]*atom->radius[i]*atom->radius[i] * dvalue;
else if (atom->ellipsoid_flag && atom->ellipsoid[i] >= 0) {
double *shape = avec_ellipsoid->bonus[atom->ellipsoid[i]].shape;
// enable 2d ellipse (versus 3d ellipsoid) when time integration
// options (fix nve/asphere, fix nh/asphere) are also implemented
- // if (discflag)
+ // if (discflag)
// atom->rmass[i] = MY_PI*shape[0]*shape[1] * dvalue;
- // else
+ // else
atom->rmass[i] = 4.0*MY_PI/3.0 * shape[0]*shape[1]*shape[2] * dvalue;
} else if (atom->line_flag && atom->line[i] >= 0) {
double length = avec_line->bonus[atom->line[i]].length;
@@ -823,7 +823,7 @@ void Set::set(int keyword)
// set quaternion orientation of ellipsoid or tri or body particle
// enforce quat rotation vector in z dir for 2d systems
-
+
else if (keyword == QUAT) {
double *quat;
if (avec_ellipsoid && atom->ellipsoid[i] >= 0)
@@ -837,7 +837,7 @@ void Set::set(int keyword)
if (domain->dimension == 2 && (xvalue != 0.0 || yvalue != 0.0))
error->one(FLERR,"Cannot set quaternion with xy components "
"for 2d system");
-
+
double theta2 = MY_PI2 * wvalue/180.0;
double sintheta2 = sin(theta2);
quat[0] = cos(theta2);
diff --git a/src/thermo.cpp b/src/thermo.cpp
index d4f7c5cc9e1434e86e8efb45dbcb7c0015ef8a25..211ace5232b3b89f3a64ad4a0a102628e4990383 100644
--- a/src/thermo.cpp
+++ b/src/thermo.cpp
@@ -55,7 +55,7 @@ using namespace MathConst;
// customize a new keyword by adding to this list:
-// step, elapsed, elaplong, dt, time, cpu, tpcpu, spcpu, cpuremain,
+// step, elapsed, elaplong, dt, time, cpu, tpcpu, spcpu, cpuremain,
// part, timeremain
// atoms, temp, press, pe, ke, etotal, enthalpy
// evdwl, ecoul, epair, ebond, eangle, edihed, eimp, emol, elong, etail
@@ -197,7 +197,7 @@ Thermo::~Thermo()
deallocate();
// format strings
-
+
delete [] format_line_user;
delete [] format_float_user;
delete [] format_int_user;
@@ -1091,7 +1091,7 @@ int Thermo::evaluate_keyword(char *word, double *answer)
// this will trigger next timestep for energy tallying via addstep()
// this means keywords that use pe (pe, etotal, enthalpy)
// need to always invoke it even if invoked_flag is set,
- // because evdwl/etc may have set invoked_flag w/out
+ // because evdwl/etc may have set invoked_flag w/out
// actually invoking pe->compute_scalar()
if (strcmp(word,"step") == 0) {
@@ -1571,7 +1571,7 @@ void Thermo::compute_variable()
dvalue = input->variable->compute_equal(variables[field2index[ifield]]);
else {
double *varvec;
- int nvec =
+ int nvec =
input->variable->compute_vector(variables[field2index[ifield]],&varvec);
if (nvec < iarg) dvalue = 0.0;
else dvalue = varvec[iarg-1];
diff --git a/src/variable.cpp b/src/variable.cpp
index 744762dcd49ba75aac586947e04a9d8d0a2f39b3..34dc33da39a084d46fef21a6727b04ec5d341095 100644
--- a/src/variable.cpp
+++ b/src/variable.cpp
@@ -590,7 +590,7 @@ int Variable::next(int narg, char **arg)
int istyle = style[find(arg[0])];
if (istyle == STRING || istyle == EQUAL || istyle == WORLD ||
- istyle == GETENV || istyle == ATOM || istyle == VECTOR ||
+ istyle == GETENV || istyle == ATOM || istyle == VECTOR ||
istyle == FORMAT || istyle == PYTHON || istyle == INTERNAL)
error->all(FLERR,"Invalid variable style with next command");
@@ -890,7 +890,7 @@ char *Variable::retrieve(char *name)
str = data[ivar][0];
} else if (style[ivar] == ATOM || style[ivar] == ATOMFILE ||
style[ivar] == VECTOR) return NULL;
-
+
eval_in_progress[ivar] = 0;
return str;
@@ -1279,7 +1279,7 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
print_var_error(FLERR,"Variable evaluation before "
"simulation box is defined",ivar);
- // uppercase used to force access of
+ // uppercase used to force access of
// global vector vs global scalar, and global array vs global vector
int lowercase = 1;
@@ -1396,7 +1396,7 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
} else argstack[nargstack++] = value1;
// c_ID = vector from global vector, lowercase or uppercase
-
+
} else if (nbracket == 0 && compute->vector_flag) {
if (tree == NULL)
@@ -1405,7 +1405,7 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
if (treetype == ATOM)
print_var_error(FLERR,"Compute global vector in "
"atom-style variable formula",ivar);
- if (compute->size_vector == 0)
+ if (compute->size_vector == 0)
print_var_error(FLERR,"Variable formula compute "
"vector is zero length",ivar);
if (update->whichflag == 0) {
@@ -1428,7 +1428,7 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
treestack[ntreestack++] = newtree;
// c_ID[i] = vector from global array, lowercase or uppercase
-
+
} else if (nbracket == 1 && compute->array_flag) {
if (tree == NULL)
@@ -1437,7 +1437,7 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
if (treetype == ATOM)
print_var_error(FLERR,"Compute global vector in "
"atom-style variable formula",ivar);
- if (compute->size_array_rows == 0)
+ if (compute->size_array_rows == 0)
print_var_error(FLERR,"Variable formula compute array "
"is zero length",ivar);
if (update->whichflag == 0) {
@@ -1576,7 +1576,7 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
if (domain->box_exist == 0)
print_var_error(FLERR,"Variable evaluation before simulation box is defined",ivar);
- // uppercase used to force access of
+ // uppercase used to force access of
// global vector vs global scalar, and global array vs global vector
int lowercase = 1;
@@ -1683,7 +1683,7 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
print_var_error(FLERR,"Fix global vector in ""equal-style variable formula",ivar);
if (treetype == ATOM)
print_var_error(FLERR,"Fix global vector in ""atom-style variable formula",ivar);
- if (fix->size_vector == 0)
+ if (fix->size_vector == 0)
print_var_error(FLERR,"Variable formula fix vector is zero length",ivar);
int nvec = fix->size_vector;
@@ -1863,7 +1863,7 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
// v_name = scalar from non atom/atomfile & non vector-style variable
// access value via retrieve()
- } else if (nbracket == 0 && style[ivar] != ATOM &&
+ } else if (nbracket == 0 && style[ivar] != ATOM &&
style[ivar] != ATOMFILE && style[ivar] != VECTOR) {
char *var = retrieve(word+2);
@@ -2216,7 +2216,7 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
if (value1 != 0.0 || value2 != 0.0) argstack[nargstack++] = 1.0;
else argstack[nargstack++] = 0.0;
} else if (opprevious == XOR) {
- if ((value1 == 0.0 && value2 != 0.0) ||
+ if ((value1 == 0.0 && value2 != 0.0) ||
(value1 != 0.0 && value2 == 0.0)) argstack[nargstack++] = 1.0;
else argstack[nargstack++] = 0.0;
}
@@ -2862,7 +2862,7 @@ double Variable::eval_tree(Tree *tree, int i)
else return 0.0;
}
if (tree->type == XOR) {
- if ((eval_tree(tree->first,i) == 0.0 && eval_tree(tree->second,i) != 0.0)
+ if ((eval_tree(tree->first,i) == 0.0 && eval_tree(tree->second,i) != 0.0)
||
(eval_tree(tree->first,i) != 0.0 && eval_tree(tree->second,i) == 0.0))
return 1.0;
@@ -3128,7 +3128,7 @@ int Variable::size_tree_vector(Tree *tree)
if (tree->second) nsize = compare_tree_vector(nsize,
size_tree_vector(tree->second));
if (tree->nextra) {
- for (int i = 0; i < tree->nextra; i++)
+ for (int i = 0; i < tree->nextra; i++)
nsize = compare_tree_vector(nsize,size_tree_vector(tree->extra[i]));
}
return nsize;
@@ -4037,15 +4037,15 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
*ptr1 = '\0';
} else index = 0;
- if (index)
+ if (index)
print_var_error(FLERR,"Invalid special function in variable formula",ivar);
ivar = find(&args[0][2]);
- if (ivar < 0)
+ if (ivar < 0)
print_var_error(FLERR,"Invalid special function in variable formula",ivar);
- if (style[ivar] != VECTOR)
+ if (style[ivar] != VECTOR)
print_var_error(FLERR,"Mis-matched special function variable "
"in variable formula",ivar);
- if (eval_in_progress[ivar])
+ if (eval_in_progress[ivar])
print_var_error(FLERR,"Variable has circular dependency",ivar);
double *vec;