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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14139 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2015-10-21 19:39:28 +00:00
parent abe4c06219
commit 8a10c55a3b
20 changed files with 38 additions and 21 deletions
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1
src/CORESHELL/pair_lj_cut_coul_long_cs.cpp
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@ -556,6 +556,7 @@ void PairLJCutCoulLongCS::compute_outer(int eflag, int vflag)
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
} else if (rsq <= cut_in_on_sq)
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
fpair = (forcecoul + factor_lj*forcelj) * r2inv;

1
src/KSPACE/fix_tune_kspace.cpp
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@ -212,6 +212,7 @@ void FixTuneKspace::store_old_kspace_settings()
old_differentiation_flag = force->kspace->differentiation_flag;
old_slabflag = force->kspace->slabflag;
old_slab_volfactor = force->kspace->slab_volfactor;
delete[] old_kspace_style;
}
/* ----------------------------------------------------------------------

8
src/KSPACE/msm.cpp
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@ -1712,7 +1712,7 @@ void MSM::direct(int n)
egridn[icz][icy][icx] += esum;
if (vflag_atom) {
if (vflag_atom && !scalar_pressure_flag) {
v0gridn[icz][icy][icx] += v0sum;
v1gridn[icz][icy][icx] += v1sum;
v2gridn[icz][icy][icx] += v2sum;
@ -2075,7 +2075,7 @@ void MSM::direct_top(int n)
egridn[icz][icy][icx] += esum;
if (vflag_atom) {
if (vflag_atom && !scalar_pressure_flag) {
v0gridn[icz][icy][icx] += v0sum;
v1gridn[icz][icy][icx] += v1sum;
v2gridn[icz][icy][icx] += v2sum;
@ -2912,7 +2912,7 @@ void MSM::compute_phis_and_dphis(const double &dx, const double &dy,
inline double MSM::compute_phi(const double &xi)
{
double phi;
double phi = 0.0;
double abs_xi = fabs(xi);
double xi2 = xi*xi;
@ -2991,7 +2991,7 @@ inline double MSM::compute_phi(const double &xi)
inline double MSM::compute_dphi(const double &xi)
{
double dphi;
double dphi = 0.0;
double abs_xi = fabs(xi);
if (order == 4) {

2
src/KSPACE/pair_born_coul_msm.cpp
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@ -126,9 +126,9 @@ void PairBornCoulMSM::compute(int eflag, int vflag)
if (rsq < cutsq[itype][jtype]) {
r2inv = 1.0/rsq;
r = sqrt(rsq);
if (rsq < cut_coulsq) {
r = sqrt(rsq);
prefactor = qqrd2e * qtmp*q[j]/r;
egamma = 1.0 - (r/cut_coul)*force->kspace->gamma(r/cut_coul);
fgamma = 1.0 + (rsq/cut_coulsq)*force->kspace->dgamma(r/cut_coul);

2
src/KSPACE/pair_buck_coul_msm.cpp
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@ -123,9 +123,9 @@ void PairBuckCoulMSM::compute(int eflag, int vflag)
if (rsq < cutsq[itype][jtype]) {
r2inv = 1.0/rsq;
r = sqrt(rsq);
if (rsq < cut_coulsq) {
r = sqrt(rsq);
prefactor = qqrd2e * qtmp*q[j]/r;
egamma = 1.0 - (r/cut_coul)*force->kspace->gamma(r/cut_coul);
fgamma = 1.0 + (rsq/cut_coulsq)*force->kspace->dgamma(r/cut_coul);

1
src/KSPACE/pair_lj_charmm_coul_long.cpp
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@ -597,6 +597,7 @@ void PairLJCharmmCoulLong::compute_outer(int eflag, int vflag)
forcelj = forcelj*switch1 + philj*switch2;
}
} else if (rsq <= cut_in_on_sq) {
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *

1
src/KSPACE/pair_lj_charmm_coul_msm.cpp
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@ -437,6 +437,7 @@ void PairLJCharmmCoulMSM::compute_outer(int eflag, int vflag)
forcelj = forcelj*switch1 + philj*switch2;
}
} else if (rsq <= cut_in_on_sq) {
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *

1
src/KSPACE/pair_lj_cut_coul_long.cpp
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@ -551,6 +551,7 @@ void PairLJCutCoulLong::compute_outer(int eflag, int vflag)
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
} else if (rsq <= cut_in_on_sq)
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
fpair = (forcecoul + factor_lj*forcelj) * r2inv;

1
src/KSPACE/pair_lj_cut_coul_msm.cpp
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@ -404,6 +404,7 @@ void PairLJCutCoulMSM::compute_outer(int eflag, int vflag)
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
} else if (rsq <= cut_in_on_sq)
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
fpair = (forcecoul + factor_lj*forcelj) * r2inv;

2
src/KSPACE/pppm_disp.cpp
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@ -3543,7 +3543,7 @@ void PPPMDisp::set_init_g6()
double acc_rspace = accuracy;
if (accuracy_real_6 > 0) acc_rspace = accuracy_real_6;
g_ewald_6 = 1.0/cutoff_lj;
g_ewald_old = g_ewald_6 = 1.0/cutoff_lj;
df_real = lj_rspace_error() - acc_rspace;
int counter = 0;
if (df_real > 0) {

2
src/REPLICA/fix_neb.cpp
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@ -138,7 +138,7 @@ void FixNEB::min_post_force(int vflag)
// veng = PE of this replica
// vprev,vnext = PEs of adjacent replicas
veng = pe->compute_scalar();
vprev = vnext = veng = pe->compute_scalar();
if (ireplica < nreplica-1) MPI_Send(&veng,1,MPI_DOUBLE,procnext,0,uworld);
if (ireplica > 0) MPI_Recv(&vprev,1,MPI_DOUBLE,procprev,0,uworld,MPI_STATUS_IGNORE);

2
src/SHOCK/fix_append_atoms.cpp
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@ -50,6 +50,7 @@ FixAppendAtoms::FixAppendAtoms(LAMMPS *lmp, int narg, char **arg) :
scaleflag = 1;
spatflag=0;
spatialid = NULL;
xloflag = xhiflag = yloflag = yhiflag = zloflag = zhiflag = 0;
tempflag = 0;
@ -210,6 +211,7 @@ FixAppendAtoms::~FixAppendAtoms()
delete [] basistype;
if (ranflag) delete randomx;
if (spatflag) delete[] spatialid;
if (tempflag) {
delete randomt;
delete [] gfactor1;

11
src/USER-DRUDE/pair_thole.cpp
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@ -392,21 +392,18 @@ double PairThole::single(int i, int j, int itype, int jtype,
}
r2inv = 1.0/rsq;
fforce = phicoul = 0.0;
if (rsq < cutsq[itype][jtype]) {
rinv = sqrt(r2inv);
r = sqrt(rsq);
asr = ascreen[itype][jtype] * r;
exp_asr = exp(-asr);
dcoul = force->qqrd2e * qi * qj * rinv;
dcoul = force->qqrd2e * qi * qj * scale[itype][jtype] * rinv;
factor_f = 0.5*(2. + (exp_asr * (-2. - asr * (2. + asr)))) - factor_coul;
forcecoul += factor_f * dcoul;
fforce = factor_f * dcoul * r2inv;
factor_e = 0.5*(2. - (exp_asr * (2. + asr))) - factor_coul;
} else forcecoul= 0.0;
fforce = factor_f*forcecoul * r2inv;
if (rsq < cutsq[itype][jtype]) {
phicoul = factor_e * dcoul;
} else phicoul = 0.0;
}
return phicoul;
}

2
src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp
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@ -565,6 +565,8 @@ void PairLJCharmmCoulLongSoft::compute_outer(int eflag, int vflag)
forcelj = forcelj*switch1 + philj*switch2;
}
} else if (rsq <= cut_in_on_sq) {
r4sig6 = rsq*rsq / lj2[itype][jtype];
denlj = lj3[itype][jtype] + rsq*r4sig6;
forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
(48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj));
if (rsq > cut_lj_innersq) {

2
src/USER-FEP/pair_lj_cut_coul_long_soft.cpp
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@ -516,6 +516,8 @@ void PairLJCutCoulLongSoft::compute_outer(int eflag, int vflag)
forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
(48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj));
} else if (rsq < cut_in_on_sq) {
r4sig6 = rsq*rsq / lj2[itype][jtype];
denlj = lj3[itype][jtype] + rsq*r4sig6;
forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
(48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj));
}

1
src/USER-FEP/pair_lj_cut_soft.cpp
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@ -393,6 +393,7 @@ void PairLJCutSoft::compute_outer(int eflag, int vflag)
}
if (eflag) {
denlj = lj3[itype][jtype] + rsq*r4sig6;
evdwl = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
(1.0/(denlj*denlj) - 1.0/denlj) - offset[itype][jtype];
evdwl *= factor_lj;

9
src/USER-MISC/fix_smd.cpp
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@ -210,6 +210,10 @@ void FixSMD::smd_tether()
fy = k_smd*dy*dr/r;
fz = k_smd*dz*dr/r;
pmf += (fx*xn + fy*yn + fz*zn) * v_smd * update->dt;
} else {
fx = 0.0;
fy = 0.0;
fz = 0.0;
}
} else {
r_old = r;
@ -306,8 +310,11 @@ void FixSMD::smd_couple()
fy = k_smd*dy*dr/r;
fz = k_smd*dz*dr/r;
pmf += (fx*xn + fy*yn + fz*zn) * fsign * v_smd * update->dt;
} else {
fx = 0.0;
fy = 0.0;
fz = 0.0;
}
} else {
dx = xcm2[0] - xcm[0];
dy = xcm2[1] - xcm[1];

1
src/USER-MISC/pair_srp.cpp
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@ -153,6 +153,7 @@ void PairSRP::compute(int eflag, int vflag)
double wd, lever0, lever1, evdwl, fpair;
double fxlever0, fylever0, fzlever0, fxlever1, fylever1, fzlever1;
double fx, fy, fz;
evdwl = 0.0;
// mapping global to local for atoms inside bond particles
// exclude 1-2 neighs if requested

8
src/compute_bond_local.cpp
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@ -172,11 +172,9 @@ int ComputeBondLocal::compute_bonds(int flag)
domain->minimum_image(delx,dely,delz);
rsq = delx*delx + dely*dely + delz*delz;
if (singleflag) {
if (btype > 0)
eng = bond->single(btype,rsq,atom1,atom2,fbond);
else eng = fbond = 0.0;
}
if (singleflag && (btype > 0))
eng = bond->single(btype,rsq,atom1,atom2,fbond);
else eng = fbond = 0.0;
if (nvalues == 1) ptr = &vector[m];
else ptr = array[m];

1
src/compute_pair_local.cpp
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@ -221,6 +221,7 @@ int ComputePairLocal::compute_pairs(int flag)
if (flag) {
if (singleflag)
eng = pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
else eng = fpair = 0.0;
if (nvalues == 1) ptr = &vector[m];
else ptr = array[m];