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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5896 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2011-04-05 19:10:43 +00:00
parent eecbb7e1e5
commit eb7d288360
97 changed files with 537 additions and 788 deletions
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9
src/ASPHERE/pair_gayberne.cpp
View File

@ -91,7 +91,6 @@ void PairGayBerne::compute(int eflag, int vflag)
double **tor = atom->torque;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
@ -119,12 +118,8 @@ void PairGayBerne::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_lj = 1.0;
else {
factor_lj = special_lj[j/nall];
j %= nall;
}
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
// r12 = center to center vector

9
src/ASPHERE/pair_resquared.cpp
View File

@ -96,7 +96,6 @@ void PairRESquared::compute(int eflag, int vflag)
double **tor = atom->torque;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
@ -120,12 +119,8 @@ void PairRESquared::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_lj = 1.0;
else {
factor_lj = special_lj[j/nall];
j %= nall;
}
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
// r12 = center to center vector

9
src/CLASS2/pair_lj_class2.cpp
View File

@ -67,7 +67,6 @@ void PairLJClass2::compute(int eflag, int vflag)
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
@ -89,12 +88,8 @@ void PairLJClass2::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_lj = 1.0;
else {
factor_lj = special_lj[j/nall];
j %= nall;
}
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];

11
src/CLASS2/pair_lj_class2_coul_cut.cpp
View File

@ -73,7 +73,6 @@ void PairLJClass2CoulCut::compute(int eflag, int vflag)
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
@ -98,13 +97,9 @@ void PairLJClass2CoulCut::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_coul = factor_lj = 1.0;
else {
factor_coul = special_coul[j/nall];
factor_lj = special_lj[j/nall];
j %= nall;
}
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];

11
src/CLASS2/pair_lj_class2_coul_long.cpp
View File

@ -82,7 +82,6 @@ void PairLJClass2CoulLong::compute(int eflag, int vflag)
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
@ -107,13 +106,9 @@ void PairLJClass2CoulLong::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_coul = factor_lj = 1.0;
else {
factor_coul = special_coul[j/nall];
factor_lj = special_lj[j/nall];
j %= nall;
}
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];

9
src/COLLOID/pair_colloid.cpp
View File

@ -84,7 +84,6 @@ void PairColloid::compute(int eflag, int vflag)
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
@ -106,12 +105,8 @@ void PairColloid::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_lj = 1.0;
else {
factor_lj = special_lj[j/nall];
j %= nall;
}
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];

2
src/COLLOID/pair_lubricate.cpp
View File

@ -117,6 +117,8 @@ void PairLubricate::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];

9
src/COLLOID/pair_yukawa_colloid.cpp
View File

@ -51,7 +51,6 @@ void PairYukawaColloid::compute(int eflag, int vflag)
double **shape = atom->shape;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_coul = force->special_coul;
int newton_pair = force->newton_pair;
@ -74,12 +73,8 @@ void PairYukawaColloid::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_coul = 1.0;
else {
factor_coul = special_coul[j/nall];
j %= nall;
}
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];

11
src/DIPOLE/pair_dipole_cut.cpp
View File

@ -81,7 +81,6 @@ void PairDipoleCut::compute(int eflag, int vflag)
int *type = atom->type;
double *dipole = atom->dipole;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
@ -106,13 +105,9 @@ void PairDipoleCut::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_coul = factor_lj = 1.0;
else {
factor_coul = special_coul[j/nall];
factor_lj = special_lj[j/nall];
j = j % nall;
}
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];

18
src/GPU/pair_gayberne_gpu.cpp
View File

@ -210,7 +210,6 @@ void PairGayBerneGPU::cpu_compute(int start, int eflag, int vflag)
double **tor = atom->torque;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_lj = force->special_lj;
inum = list->inum;
@ -237,12 +236,8 @@ void PairGayBerneGPU::cpu_compute(int start, int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_lj = 1.0;
else {
factor_lj = special_lj[j/nall];
j %= nall;
}
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
// r12 = center to center vector
@ -336,7 +331,6 @@ void PairGayBerneGPU::cpu_compute(int *nbors, int start, int eflag, int vflag)
double **tor = atom->torque;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int stride = nlocal-start;
double *special_lj = force->special_lj;
@ -360,12 +354,8 @@ void PairGayBerneGPU::cpu_compute(int *nbors, int start, int eflag, int vflag)
for ( ; nbor < nbor_end; nbor += stride) {
j = *nbor;
if (j < nall) factor_lj = 1.0;
else {
factor_lj = special_lj[j/nall];
j %= nall;
}
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
// r12 = center to center vector

18
src/GPU/pair_lj96_cut_gpu.cpp
View File

@ -188,7 +188,6 @@ void PairLJ96CutGPU::cpu_compute(int start, int eflag, int vflag) {
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_lj = force->special_lj;
inum = list->inum;
@ -209,12 +208,8 @@ void PairLJ96CutGPU::cpu_compute(int start, int eflag, int vflag) {
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_lj = 1.0;
else {
factor_lj = special_lj[j/nall];
j %= nall;
}
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
@ -250,7 +245,6 @@ void PairLJ96CutGPU::cpu_compute(int start, int eflag, int vflag) {
void PairLJ96CutGPU::cpu_compute(int *nbors, int start, int eflag, int vflag) {
int i,j,itype,jtype;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int stride = nlocal-start;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,r2inv,r3inv,r6inv,forcelj,factor_lj;
@ -274,12 +268,8 @@ void PairLJ96CutGPU::cpu_compute(int *nbors, int start, int eflag, int vflag) {
for (; nbor<nbor_end; nbor+=stride) {
j = *nbor;
if (j < nall) factor_lj = 1.0;
else {
factor_lj = special_lj[j/nall];
j %= nall;
}
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];

22
src/GPU/pair_lj_charmm_coul_long_gpu.cpp
View File

@ -231,7 +231,6 @@ void PairLJCharmmCoulLongGPU::cpu_compute(int start, int eflag, int vflag)
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
double qqrd2e = force->qqrd2e;
@ -255,13 +254,9 @@ void PairLJCharmmCoulLongGPU::cpu_compute(int start, int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_coul = factor_lj = 1.0;
else {
factor_coul = special_coul[j/nall];
factor_lj = special_lj[j/nall];
j %= nall;
}
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
@ -365,7 +360,6 @@ void PairLJCharmmCoulLongGPU::cpu_compute(int *nbors, int start, int eflag,
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int stride = nlocal - start;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
@ -386,13 +380,9 @@ void PairLJCharmmCoulLongGPU::cpu_compute(int *nbors, int start, int eflag,
for (; nbor<nbor_end; nbor+=stride) {
j = *nbor;
if (j < nall) factor_coul = factor_lj = 1.0;
else {
factor_coul = special_coul[j/nall];
factor_lj = special_lj[j/nall];
j %= nall;
}
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];

22
src/GPU/pair_lj_cut_coul_cut_gpu.cpp
View File

@ -196,7 +196,6 @@ void PairLJCutCoulCutGPU::cpu_compute(int start, int eflag, int vflag)
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
@ -221,13 +220,9 @@ void PairLJCutCoulCutGPU::cpu_compute(int start, int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_coul = factor_lj = 1.0;
else {
factor_coul = special_coul[j/nall];
factor_lj = special_lj[j/nall];
j %= nall;
}
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
@ -286,7 +281,6 @@ void PairLJCutCoulCutGPU::cpu_compute(int *nbors, int start, int eflag,
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int stride = nlocal-start;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
@ -307,13 +301,9 @@ void PairLJCutCoulCutGPU::cpu_compute(int *nbors, int start, int eflag,
for (; nbor<nbor_end; nbor+=stride) {
j = *nbor;
if (j < nall) factor_coul = factor_lj = 1.0;
else {
factor_coul = special_coul[j/nall];
factor_lj = special_lj[j/nall];
j %= nall;
}
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];

22
src/GPU/pair_lj_cut_coul_long_gpu.cpp
View File

@ -224,7 +224,6 @@ void PairLJCutCoulLongGPU::cpu_compute(int start, int eflag, int vflag)
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
double qqrd2e = force->qqrd2e;
@ -248,13 +247,9 @@ void PairLJCutCoulLongGPU::cpu_compute(int start, int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_coul = factor_lj = 1.0;
else {
factor_coul = special_coul[j/nall];
factor_lj = special_lj[j/nall];
j %= nall;
}
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
@ -345,7 +340,6 @@ void PairLJCutCoulLongGPU::cpu_compute(int *nbors, int start, int eflag,
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int stride = nlocal-start;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
@ -366,13 +360,9 @@ void PairLJCutCoulLongGPU::cpu_compute(int *nbors, int start, int eflag,
for (; nbor<nbor_end; nbor+=stride) {
j = *nbor;
if (j < nall) factor_coul = factor_lj = 1.0;
else {
factor_coul = special_coul[j/nall];
factor_lj = special_lj[j/nall];
j %= nall;
}
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];

18
src/GPU/pair_lj_cut_gpu.cpp
View File

@ -188,7 +188,6 @@ void PairLJCutGPU::cpu_compute(int start, int eflag, int vflag) {
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_lj = force->special_lj;
inum = list->inum;
@ -209,12 +208,8 @@ void PairLJCutGPU::cpu_compute(int start, int eflag, int vflag) {
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_lj = 1.0;
else {
factor_lj = special_lj[j/nall];
j %= nall;
}
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
@ -249,7 +244,6 @@ void PairLJCutGPU::cpu_compute(int start, int eflag, int vflag) {
void PairLJCutGPU::cpu_compute(int *nbors, int start, int eflag, int vflag) {
int i,j,itype,jtype;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int stride = nlocal-start;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,r2inv,r6inv,forcelj,factor_lj;
@ -273,12 +267,8 @@ void PairLJCutGPU::cpu_compute(int *nbors, int start, int eflag, int vflag) {
for (; nbor<nbor_end; nbor+=stride) {
j = *nbor;
if (j < nall) factor_lj = 1.0;
else {
factor_lj = special_lj[j/nall];
j %= nall;
}
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];

1
src/GRANULAR/pair_gran_hertz_history.cpp
View File

@ -93,6 +93,7 @@ void PairGranHertzHistory::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];

1
src/GRANULAR/pair_gran_hooke.cpp
View File

@ -84,6 +84,7 @@ void PairGranHooke::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];

1
src/GRANULAR/pair_gran_hooke_history.cpp
View File

@ -127,6 +127,7 @@ void PairGranHookeHistory::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];

11
src/KSPACE/pair_born_coul_long.cpp
View File

@ -89,7 +89,6 @@ void PairBornCoulLong::compute(int eflag, int vflag)
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
@ -114,13 +113,9 @@ void PairBornCoulLong::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_coul = factor_lj = 1.0;
else {
factor_coul = special_coul[j/nall];
factor_lj = special_lj[j/nall];
j %= nall;
}
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];

11
src/KSPACE/pair_buck_coul_long.cpp
View File

@ -82,7 +82,6 @@ void PairBuckCoulLong::compute(int eflag, int vflag)
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
@ -107,13 +106,9 @@ void PairBuckCoulLong::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_coul = factor_lj = 1.0;
else {
factor_coul = special_coul[j/nall];
factor_lj = special_lj[j/nall];
j %= nall;
}
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];

9
src/KSPACE/pair_coul_long.cpp
View File

@ -86,7 +86,6 @@ void PairCoulLong::compute(int eflag, int vflag)
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_coul = force->special_coul;
int newton_pair = force->newton_pair;
double qqrd2e = force->qqrd2e;
@ -110,12 +109,8 @@ void PairCoulLong::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_coul = 1.0;
else {
factor_coul = special_coul[j/nall];
j %= nall;
}
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];

44
src/KSPACE/pair_lj_charmm_coul_long.cpp
View File

@ -104,7 +104,6 @@ void PairLJCharmmCoulLong::compute(int eflag, int vflag)
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
@ -129,13 +128,9 @@ void PairLJCharmmCoulLong::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_coul = factor_lj = 1.0;
else {
factor_coul = special_coul[j/nall];
factor_lj = special_lj[j/nall];
j %= nall;
}
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
@ -242,7 +237,6 @@ void PairLJCharmmCoulLong::compute_inner()
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
@ -274,13 +268,9 @@ void PairLJCharmmCoulLong::compute_inner()
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_coul = factor_lj = 1.0;
else {
factor_coul = special_coul[j/nall];
factor_lj = special_lj[j/nall];
j %= nall;
}
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
@ -332,7 +322,6 @@ void PairLJCharmmCoulLong::compute_middle()
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
@ -370,14 +359,10 @@ void PairLJCharmmCoulLong::compute_middle()
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
if (j < nall) factor_coul = factor_lj = 1.0;
else {
factor_coul = special_coul[j/nall];
factor_lj = special_lj[j/nall];
j %= nall;
}
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
@ -446,7 +431,6 @@ void PairLJCharmmCoulLong::compute_outer(int eflag, int vflag)
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
@ -478,13 +462,9 @@ void PairLJCharmmCoulLong::compute_outer(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_coul = factor_lj = 1.0;
else {
factor_coul = special_coul[j/nall];
factor_lj = special_lj[j/nall];
j %= nall;
}
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];

48
src/KSPACE/pair_lj_cut_coul_long.cpp
View File

@ -79,7 +79,7 @@ PairLJCutCoulLong::~PairLJCutCoulLong()
void PairLJCutCoulLong::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype,itable;
int i,ii,j,jj,inum,jnum,itype,jtype,itable;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
double fraction,table;
double r,r2inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj;
@ -96,7 +96,6 @@ void PairLJCutCoulLong::compute(int eflag, int vflag)
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
@ -106,7 +105,7 @@ void PairLJCutCoulLong::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@ -121,13 +120,9 @@ void PairLJCutCoulLong::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_coul = factor_lj = 1.0;
else {
factor_coul = special_coul[j/nall];
factor_lj = special_lj[j/nall];
j %= nall;
}
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
@ -222,7 +217,6 @@ void PairLJCutCoulLong::compute_inner()
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
@ -254,13 +248,9 @@ void PairLJCutCoulLong::compute_inner()
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_coul = factor_lj = 1.0;
else {
factor_coul = special_coul[j/nall];
factor_lj = special_lj[j/nall];
j %= nall;
}
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
@ -312,7 +302,6 @@ void PairLJCutCoulLong::compute_middle()
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
@ -349,13 +338,9 @@ void PairLJCutCoulLong::compute_middle()
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_coul = factor_lj = 1.0;
else {
factor_coul = special_coul[j/nall];
factor_lj = special_lj[j/nall];
j %= nall;
}
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
@ -418,7 +403,6 @@ void PairLJCutCoulLong::compute_outer(int eflag, int vflag)
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
@ -450,13 +434,9 @@ void PairLJCutCoulLong::compute_outer(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_coul = factor_lj = 1.0;
else {
factor_coul = special_coul[j/nall];
factor_lj = special_lj[j/nall];
j %= nall;
}
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];

11
src/KSPACE/pair_lj_cut_coul_long_tip4p.cpp
View File

@ -88,7 +88,6 @@ void PairLJCutCoulLongTIP4P::compute(int eflag, int vflag)
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
@ -117,13 +116,9 @@ void PairLJCutCoulLongTIP4P::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_coul = factor_lj = 1.0;
else {
factor_coul = special_coul[j/nall];
factor_lj = special_lj[j/nall];
j %= nall;
}
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];

2
src/MANYBODY/pair_airebo.cpp
View File

@ -351,6 +351,7 @@ void PairAIREBO::REBO_neigh()
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
jtype = map[type[j]];
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
@ -534,6 +535,7 @@ void PairAIREBO::FLJ(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
jtag = tag[j];
if (itag > jtag) {

7
src/MANYBODY/pair_comb.cpp
View File

@ -182,6 +182,7 @@ void PairComb::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
jtag = tag[j];
if (itag > jtag) {
@ -261,6 +262,7 @@ void PairComb::compute(int eflag, int vflag)
if (cor_flag) {
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
jtype = map[type[j]];
iparam_ij = elem2param[itype][jtype][jtype];
@ -281,6 +283,7 @@ void PairComb::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
jtype = map[type[j]];
iparam_ij = elem2param[itype][jtype][jtype];
@ -303,6 +306,7 @@ void PairComb::compute(int eflag, int vflag)
for (kk = 0; kk < jnum; kk++) {
if (jj == kk) continue;
k = jlist[kk];
k &= NEIGHMASK;
ktype = map[type[k]];
iparam_ijk = elem2param[itype][jtype][ktype];
@ -347,6 +351,7 @@ void PairComb::compute(int eflag, int vflag)
for (kk = 0; kk < jnum; kk++) {
if (jj == kk) continue;
k = jlist[kk];
k &= NEIGHMASK;
ktype = map[type[k]];
iparam_ijk = elem2param[itype][jtype][ktype];
@ -1678,6 +1683,7 @@ double PairComb::yasu_char(double *qf_fix, int &igroup)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
jtype = map[type[j]];
jq = q[j];
@ -1719,6 +1725,7 @@ double PairComb::yasu_char(double *qf_fix, int &igroup)
for (kk = 0; kk < jnum; kk++) {
if (jj == kk) continue;
k = jlist[kk];
k &= NEIGHMASK;
ktype = map[type[k]];
iparam_ijk = elem2param[itype][jtype][ktype];

2
src/MANYBODY/pair_eam.cpp
View File

@ -177,6 +177,7 @@ void PairEAM::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
@ -242,6 +243,7 @@ void PairEAM::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];

3
src/MANYBODY/pair_eim.cpp
View File

@ -166,6 +166,7 @@ void PairEIM::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
jtype = type[j];
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
@ -205,6 +206,7 @@ void PairEIM::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
jtype = type[j];
delx = xtmp - x[j][0];
@ -259,6 +261,7 @@ void PairEIM::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
jtype = type[j];
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];

3
src/MANYBODY/pair_sw.cpp
View File

@ -113,6 +113,7 @@ void PairSW::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
jtag = tag[j];
if (itag > jtag) {
@ -152,6 +153,7 @@ void PairSW::compute(int eflag, int vflag)
for (jj = 0; jj < jnumm1; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
jtype = map[type[j]];
ijparam = elem2param[itype][jtype][jtype];
delr1[0] = x[j][0] - xtmp;
@ -162,6 +164,7 @@ void PairSW::compute(int eflag, int vflag)
for (kk = jj+1; kk < jnum; kk++) {
k = jlist[kk];
k &= NEIGHMASK;
ktype = map[type[k]];
ikparam = elem2param[itype][ktype][ktype];
ijkparam = elem2param[itype][jtype][ktype];

4
src/MANYBODY/pair_tersoff.cpp
View File

@ -116,6 +116,7 @@ void PairTersoff::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
jtag = tag[j];
if (itag > jtag) {
@ -156,6 +157,7 @@ void PairTersoff::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
jtype = map[type[j]];
iparam_ij = elem2param[itype][jtype][jtype];
@ -172,6 +174,7 @@ void PairTersoff::compute(int eflag, int vflag)
for (kk = 0; kk < jnum; kk++) {
if (jj == kk) continue;
k = jlist[kk];
k &= NEIGHMASK;
ktype = map[type[k]];
iparam_ijk = elem2param[itype][jtype][ktype];
@ -203,6 +206,7 @@ void PairTersoff::compute(int eflag, int vflag)
for (kk = 0; kk < jnum; kk++) {
if (jj == kk) continue;
k = jlist[kk];
k &= NEIGHMASK;
ktype = map[type[k]];
iparam_ijk = elem2param[itype][jtype][ktype];

29
src/MEAM/pair_meam.cpp
View File

@ -180,6 +180,14 @@ void PairMEAM::compute(int eflag, int vflag)
numneigh_full = listfull->numneigh;
firstneigh_full = listfull->firstneigh;
// strip neighbor lists of any special bond flags before using with MEAM
// necessary before doing neigh_f2c and neigh_c2f conversions each step
if (neighbor->ago == 0) {
neigh_strip(inum_half,ilist_half,numneigh_half,firstneigh_half);
neigh_strip(inum_half,ilist_half,numneigh_full,firstneigh_full);
}
// check size of scrfcn based on half neighbor list
int nlocal = atom->nlocal;
@ -887,6 +895,27 @@ double PairMEAM::memory_usage()
return bytes;
}
/* ----------------------------------------------------------------------
strip special bond flags from neighbor list entries
are not used with MEAM
need to do here so Fortran lib doesn't see them
done once per reneighbor so that neigh_f2c and neigh_c2f don't see them
------------------------------------------------------------------------- */
void PairMEAM::neigh_strip(int inum, int *ilist,
int *numneigh, int **firstneigh)
{
int i,j,ii,jnum;
int *jlist;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
jlist = firstneigh[i];
jnum = numneigh[i];
for (j = 0; j < jnum; j++) jlist[j] &= NEIGHMASK;
}
}
/* ----------------------------------------------------------------------
toggle neighbor list indices between zero- and one-based values
needed for access by MEAM Fortran library

1
src/MEAM/pair_meam.h
View File

@ -94,6 +94,7 @@ class PairMEAM : public Pair {
void allocate();
void read_files(char *, char *);
void neigh_strip(int, int *, int *, int **);
void neigh_f2c(int, int *, int *, int **);
void neigh_c2f(int, int *, int *, int **);
};

1
src/MOLECULE/fix_bond_create.cpp
View File

@ -328,6 +328,7 @@ void FixBondCreate::post_integrate()
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
if (!(mask[j] & groupbit)) continue;
jtype = type[j];

1
src/MOLECULE/fix_bond_swap.cpp
View File

@ -241,6 +241,7 @@ void FixBondSwap::pre_neighbor()
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
if (j >= nlocal) continue;
if ((mask[j] & groupbit) == 0) continue;
if (molecule[i] != molecule[j]) continue;

9
src/MOLECULE/pair_hbond_dreiding_lj.cpp
View File

@ -98,7 +98,6 @@ void PairHbondDreidingLJ::compute(int eflag, int vflag)
int *type = atom->type;
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_lj = force->special_lj;
inum = list->inum;
@ -123,11 +122,9 @@ void PairHbondDreidingLJ::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_hb = 1.0;
else {
factor_hb = special_lj[j/nall];
j %= nall;
}
factor_hb = special_lj[sbmask(j)];
j &= NEIGHMASK;
jtype = type[j];
if (!acceptor[jtype]) continue;

9
src/MOLECULE/pair_hbond_dreiding_morse.cpp
View File

@ -66,7 +66,6 @@ void PairHbondDreidingMorse::compute(int eflag, int vflag)
int *type = atom->type;
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_lj = force->special_lj;
inum = list->inum;
@ -91,11 +90,9 @@ void PairHbondDreidingMorse::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_hb = 1.0;
else {
factor_hb = special_lj[j/nall];
j %= nall;
}
factor_hb = special_lj[sbmask(j)];
j &= NEIGHMASK;
jtype = type[j];
if (!acceptor[jtype]) continue;

11
src/MOLECULE/pair_lj_charmm_coul_charmm.cpp
View File

@ -85,7 +85,6 @@ void PairLJCharmmCoulCharmm::compute(int eflag, int vflag)
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
@ -110,13 +109,9 @@ void PairLJCharmmCoulCharmm::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_coul = factor_lj = 1.0;
else {
factor_coul = special_coul[j/nall];
factor_lj = special_lj[j/nall];
j %= nall;
}
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];

11
src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.cpp
View File

@ -47,7 +47,6 @@ void PairLJCharmmCoulCharmmImplicit::compute(int eflag, int vflag)
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
@ -72,13 +71,9 @@ void PairLJCharmmCoulCharmmImplicit::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_coul = factor_lj = 1.0;
else {
factor_coul = special_coul[j/nall];
factor_lj = special_lj[j/nall];
j %= nall;
}
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];

10
src/OPT/pair_lj_charmm_coul_long_opt.h
View File

@ -82,7 +82,6 @@ void PairLJCharmmCoulLongOpt::eval()
double* __restrict__ q = atom->q;
int* __restrict__ type = atom->type;
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
double* __restrict__ special_coul = force->special_coul;
double* __restrict__ special_lj = force->special_lj;
double qqrd2e = force->qqrd2e;
@ -134,7 +133,7 @@ void PairLJCharmmCoulLongOpt::eval()
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) {
if (j <= NEIGHMASK) {
double delx = xtmp - xx[j].x;
double dely = ytmp - xx[j].y;
double delz = ztmp - xx[j].z;
@ -220,9 +219,10 @@ void PairLJCharmmCoulLongOpt::eval()
}
} else {
factor_coul = special_coul[j/nall];
factor_lj = special_lj[j/nall];
j %= nall;
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
double delx = xtmp - xx[j].x;
double dely = ytmp - xx[j].y;
double delz = ztmp - xx[j].z;

7
src/OPT/pair_lj_cut_opt.h
View File

@ -61,7 +61,6 @@ void PairLJCutOpt::eval()
double** __restrict__ f = atom->f;
int* __restrict__ type = atom->type;
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
double* __restrict__ special_lj = force->special_lj;
inum = list->inum;
@ -109,7 +108,7 @@ void PairLJCutOpt::eval()
j = jlist[jj];
double factor_lj;
if (j < nall) {
if (j <= NEIGHMASK) {
double delx = xtmp - xx[j].x;
double dely = ytmp - xx[j].y;
double delz = ztmp - xx[j].z;
@ -142,8 +141,8 @@ void PairLJCutOpt::eval()
}
} else {
factor_lj = special_lj[j/nall];
j = j % nall;
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
double delx = xtmp - xx[j].x;
double dely = ytmp - xx[j].y;

7
src/OPT/pair_morse_opt.h
View File

@ -62,7 +62,6 @@ void PairMorseOpt::eval()
double** __restrict__ f = atom->f;
int* __restrict__ type = atom->type;
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
double* __restrict__ special_lj = force->special_lj;
inum = list->inum;
@ -110,7 +109,7 @@ void PairMorseOpt::eval()
j = jlist[jj];
double factor_lj;
if (j < nall) {
if (j <= NEIGHMASK) {
double delx = xtmp - xx[j].x;
double dely = ytmp - xx[j].y;
double delz = ztmp - xx[j].z;
@ -141,8 +140,8 @@ void PairMorseOpt::eval()
}
} else {
factor_lj = special_lj[j/nall];
j = j % nall;
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
double delx = xtmp - xx[j].x;
double dely = ytmp - xx[j].y;

2
src/PERI/fix_peri_neigh.cpp
View File

@ -177,6 +177,7 @@ void FixPeriNeigh::setup(int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
@ -224,6 +225,7 @@ void FixPeriNeigh::setup(int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];

3
src/PERI/pair_peri_lps.cpp
View File

@ -119,7 +119,6 @@ void PairPeriLPS::compute(int eflag, int vflag)
// short-range forces
int nall = atom->nlocal + atom->nghost;
int newton_pair = force->newton_pair;
int periodic = domain->xperiodic || domain->yperiodic || domain->zperiodic;
@ -147,7 +146,7 @@ void PairPeriLPS::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j %= nall;
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];

3
src/PERI/pair_peri_pmb.cpp
View File

@ -111,7 +111,6 @@ void PairPeriPMB::compute(int eflag, int vflag)
// short-range forces
int nall = atom->nlocal + atom->nghost;
int newton_pair = force->newton_pair;
int periodic = (domain->xperiodic || domain->yperiodic || domain->zperiodic);
@ -137,7 +136,7 @@ void PairPeriPMB::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j %= nall;
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];

12
src/REAX/pair_reax.cpp
View File

@ -309,9 +309,7 @@ void PairREAX::write_reax_vlist()
int nvpair, nvlself, nvpairmax;
int nbond;
int inum,jnum;
int *ilist;
int *jlist;
int *numneigh,**firstneigh;
int *ilist,*jlist,*numneigh,**firstneigh;
double delr2;
double delx, dely, delz;
double rtmp[3];
@ -343,6 +341,8 @@ void PairREAX::write_reax_vlist()
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
xjtmp = x[j][0];
yjtmp = x[j][1];
zjtmp = x[j][2];
@ -755,9 +755,7 @@ void PairREAX::compute_charge(double &energy_charge_equilibration)
double sw;
double rtmp[3];
int inum,jnum;
int *ilist;
int *jlist;
int *numneigh,**firstneigh;
int *ilist,*jlist,*numneigh,**firstneigh;
double **x = atom->x;
double *q = atom->q;
@ -811,6 +809,8 @@ void PairREAX::compute_charge(double &energy_charge_equilibration)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
xjtmp = x[j][0];
yjtmp = x[j][1];
zjtmp = x[j][2];

3
src/USER-ACKLAND/compute_ackland_atom.cpp
View File

@ -126,7 +126,6 @@ void ComputeAcklandAtom::compute_peratom()
double **x = atom->x;
int *mask = atom->mask;
int nall = atom->nlocal + atom->nghost;
double cutsq = force->pair->cutforce * force->pair->cutforce;
for (ii = 0; ii < inum; ii++) {
@ -159,7 +158,7 @@ void ComputeAcklandAtom::compute_peratom()
n = 0;
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j >= nall) j %= nall;
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];

3
src/USER-CD-EAM/pair_cdeam.cpp
View File

@ -136,6 +136,7 @@ void PairCDEAM::compute(int eflag, int vflag)
for(jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
@ -225,6 +226,7 @@ void PairCDEAM::compute(int eflag, int vflag)
for(jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
jtype = type[j];
if(itype == jtype) continue;
@ -304,6 +306,7 @@ void PairCDEAM::compute(int eflag, int vflag)
for(jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];

2
src/USER-CG-CMM/pair_cmm_common.cpp
View File

@ -474,5 +474,3 @@ double PairCMMCommon::eval_single(int coul_type, int i, int j, int itype, int jt
fforce = factor_lj*lj_force + factor_coul*coul_force;
return factor_lj*lj_erg + factor_coul*coul_erg;
}
/* ------------------------------------------------------------------------ */

56
src/USER-CG-CMM/pair_cmm_common.h
View File

@ -185,10 +185,10 @@ namespace LAMMPS_NS {
const double * const q = atom->q;
const int * const type = atom->type;
const int nlocal = atom->nlocal;
const int nall = nlocal + atom->nghost;
const double * const special_lj = force->special_lj;
const double * const special_coul = force->special_coul;
const double qqrd2e = force->qqrd2e;
double factor_lj,factor_coul;
const int inum = list->inum;
const int * const ilist = list->ilist;
@ -211,15 +211,9 @@ namespace LAMMPS_NS {
for (jj = 0; jj < jnum; jj++) {
int j2 = jlist[jj];
double factor_lj = 1.0;
double factor_coul = 1.0;
if (j2 >= nall) {
factor_lj = special_lj[j2/nall];
if (COUL_TYPE != CG_COUL_NONE) factor_coul=special_coul[j2/nall];
j2 %= nall;
}
const int j = j2;
factor_lj = special_lj[sbmask(j2)];
factor_coul = special_coul[sbmask(j2)];
const int j = j2 & NEIGHMASK;
const double delx = xtmp - x[j][0];
const double dely = ytmp - x[j][1];
@ -323,10 +317,10 @@ namespace LAMMPS_NS {
const double * const q = atom->q;
const int * const type = atom->type;
const int nlocal = atom->nlocal;
const int nall = nlocal + atom->nghost;
const double * const special_lj = force->special_lj;
const double * const special_coul = force->special_coul;
const double qqrd2e = force->qqrd2e;
double factor_lj,factor_coul;
const int inum = listinner->inum;
const int * const ilist = listinner->ilist;
@ -355,15 +349,9 @@ namespace LAMMPS_NS {
for (jj = 0; jj < jnum; jj++) {
int j2 = jlist[jj];
double factor_lj = 1.0;
double factor_coul = 1.0;
if (j2 >= nall) {
factor_lj = special_lj[j2/nall];
if (COUL_TYPE != CG_COUL_NONE) factor_coul=special_coul[j2/nall];
j2 %= nall;
}
const int j = j2;
factor_lj = special_lj[sbmask(j2)];
factor_coul = special_coul[sbmask(j2)];
const int j = j2 & NEIGHMASK;
const double delx = xtmp - x[j][0];
const double dely = ytmp - x[j][1];
@ -427,10 +415,10 @@ namespace LAMMPS_NS {
const double * const q = atom->q;
const int * const type = atom->type;
const int nlocal = atom->nlocal;
const int nall = nlocal + atom->nghost;
const double * const special_lj = force->special_lj;
const double * const special_coul = force->special_coul;
const double qqrd2e = force->qqrd2e;
double factor_lj,factor_coul;
const int inum = listmiddle->inum;
const int * const ilist = listmiddle->ilist;
@ -464,15 +452,9 @@ namespace LAMMPS_NS {
for (jj = 0; jj < jnum; jj++) {
int j2 = jlist[jj];
double factor_lj = 1.0;
double factor_coul = 1.0;
if (j2 >= nall) {
factor_lj = special_lj[j2/nall];
if (COUL_TYPE != CG_COUL_NONE) factor_coul=special_coul[j2/nall];
j2 %= nall;
}
const int j = j2;
factor_lj = special_lj[sbmask(j2)];
factor_coul = special_coul[sbmask(j2)];
const int j = j2 & NEIGHMASK;
const double delx = xtmp - x[j][0];
const double dely = ytmp - x[j][1];
@ -545,10 +527,10 @@ namespace LAMMPS_NS {
const double * const q = atom->q;
const int * const type = atom->type;
const int nlocal = atom->nlocal;
const int nall = nlocal + atom->nghost;
const double * const special_lj = force->special_lj;
const double * const special_coul = force->special_coul;
const double qqrd2e = force->qqrd2e;
double factor_lj,factor_coul;
const int inum = listouter->inum;
const int * const ilist = listouter->ilist;
@ -577,15 +559,9 @@ namespace LAMMPS_NS {
for (jj = 0; jj < jnum; jj++) {
int j2 = jlist[jj];
double factor_lj = 1.0;
double factor_coul = 1.0;
if (j2 >= nall) {
factor_lj = special_lj[j2/nall];
if (COUL_TYPE != CG_COUL_NONE) factor_coul=special_coul[j2/nall];
j2 %= nall;
}
const int j = j2;
factor_lj = special_lj[sbmask(j2)];
factor_coul = special_coul[sbmask(j2)];
const int j = j2 & NEIGHMASK;
const double delx = xtmp - x[j][0];
const double dely = ytmp - x[j][1];

1
src/USER-EFF/pair_eff_cut.cpp
View File

@ -169,6 +169,7 @@ void PairEffCut::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];

54
src/USER-EWALDN/pair_buck_coul.cpp
View File

@ -453,7 +453,6 @@ void PairBuckCoul::compute(int eflag, int vflag)
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
@ -480,8 +479,9 @@ void PairBuckCoul::compute(int eflag, int vflag)
jneighn = (jneigh = list->firstneigh[i])+list->numneigh[i];
for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
if ((j = *jneigh) < nall) ni = -1;
else { ni = j/nall; j %= nall; } // special index
j = *jneigh;
ni = sbmask(j);
j &= NEIGHMASK;
{ register double *xj = x0+(j+(j<<1));
d[0] = xi[0] - xj[0]; // pair vector
@ -496,7 +496,7 @@ void PairBuckCoul::compute(int eflag, int vflag)
if (!ncoultablebits || rsq <= tabinnersq) { // series real space
register double x = g_ewald*r;
register double s = qri*q[j], t = 1.0/(1.0+EWALD_P*x);
if (ni < 0) {
if (ni == 0) {
s *= g_ewald*exp(-x*x);
force_coul = (t *= ((((t*A5+A4)*t+A3)*t+A2)*t+A1)*s/x)+EWALD_F*s;
if (eflag) ecoul = t;
@ -513,7 +513,7 @@ void PairBuckCoul::compute(int eflag, int vflag)
t.f = rsq;
register const int k = (t.i & ncoulmask) >> ncoulshiftbits;
register double f = (rsq-rtable[k])*drtable[k], qiqj = qi*q[j];
if (ni < 0) {
if (ni == 0) {
force_coul = qiqj*(ftable[k]+f*dftable[k]);
if (eflag) ecoul = qiqj*(etable[k]+f*detable[k]);
}
@ -532,7 +532,7 @@ void PairBuckCoul::compute(int eflag, int vflag)
if (order6) { // long-range
register double x2 = g2*rsq, a2 = 1.0/x2;
x2 = a2*exp(-x2)*buckci[typej];
if (ni < 0) {
if (ni == 0) {
force_buck =
r*expr*buck1i[typej]-g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq;
if (eflag) evdwl = expr*buckai[typej]-g6*((a2+1.0)*a2+0.5)*x2;
@ -546,7 +546,7 @@ void PairBuckCoul::compute(int eflag, int vflag)
}
}
else { // cut
if (ni < 0) {
if (ni == 0) {
force_buck = r*expr*buck1i[typej]-rn*buck2i[typej];
if (eflag) evdwl = expr*buckai[typej] -
rn*buckci[typej]-offseti[typej];
@ -591,7 +591,6 @@ void PairBuckCoul::compute_inner()
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *x0 = atom->x[0], *f0 = atom->f[0], *fi = f0, *q = atom->q;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
@ -621,8 +620,9 @@ void PairBuckCoul::compute_inner()
jneighn = (jneigh = listinner->firstneigh[i])+listinner->numneigh[i];
for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
if ((j = *jneigh) < nall) ni = -1;
else { ni = j/nall; j %= nall; }
j = *jneigh;
ni = sbmask(j);
j &= NEIGHMASK;
{ register double *xj = x0+(j+(j<<1));
d[0] = xi[0] - xj[0]; // pair vector
@ -634,13 +634,13 @@ void PairBuckCoul::compute_inner()
r = sqrt(rsq);
if (order1 && (rsq < cut_coulsq)) // coulombic
force_coul = ni<0 ?
force_coul = ni == 0 ?
qri*q[j]/r : qri*q[j]/r*special_coul[ni];
if (rsq < cut_bucksqi[typej = type[j]]) { // buckingham
register double rn = r2inv*r2inv*r2inv,
expr = exp(-r*rhoinvi[typej]);
force_buck = ni<0 ?
force_buck = ni == 0 ?
(r*expr*buck1i[typej]-rn*buck2i[typej]) :
(r*expr*buck1i[typej]-rn*buck2i[typej])*special_lj[ni];
}
@ -676,7 +676,6 @@ void PairBuckCoul::compute_middle()
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *x0 = atom->x[0], *f0 = atom->f[0], *fi = f0, *q = atom->q;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
@ -711,8 +710,9 @@ void PairBuckCoul::compute_middle()
jneighn = (jneigh = listmiddle->firstneigh[i])+listmiddle->numneigh[i];
for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
if ((j = *jneigh) < nall) ni = -1;
else { ni = j/nall; j %= nall; }
j = *jneigh;
ni = sbmask(j);
j &= NEIGHMASK;
{ register double *xj = x0+(j+(j<<1));
d[0] = xi[0] - xj[0]; // pair vector
@ -725,13 +725,13 @@ void PairBuckCoul::compute_middle()
r = sqrt(rsq);
if (order1 && (rsq < cut_coulsq)) // coulombic
force_coul = ni<0 ?
force_coul = ni == 0 ?
qri*q[j]/r : qri*q[j]/r*special_coul[ni];
if (rsq < cut_bucksqi[typej = type[j]]) { // buckingham
register double rn = r2inv*r2inv*r2inv,
expr = exp(-r*rhoinvi[typej]);
force_buck = ni<0 ?
force_buck = ni == 0 ?
(r*expr*buck1i[typej]-rn*buck2i[typej]) :
(r*expr*buck1i[typej]-rn*buck2i[typej])*special_lj[ni];
}
@ -777,7 +777,6 @@ void PairBuckCoul::compute_outer(int eflag, int vflag)
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
@ -812,8 +811,9 @@ void PairBuckCoul::compute_outer(int eflag, int vflag)
jneighn = (jneigh = listouter->firstneigh[i])+listouter->numneigh[i];
for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
if ((j = *jneigh) < nall) ni = -1;
else { ni = j/nall; j %= nall; } // special index
j = *jneigh;
ni = sbmask(j);
j &= NEIGHMASK;
{ register double *xj = x0+(j+(j<<1));
d[0] = xi[0] - xj[0]; // pair vector
@ -833,9 +833,9 @@ void PairBuckCoul::compute_outer(int eflag, int vflag)
if (!ncoultablebits || rsq <= tabinnersq) { // series real space
register double s = qri*q[j];
if (respa_flag) // correct for respa
respa_coul = ni<0 ? frespa*s/r : frespa*s/r*special_coul[ni];
respa_coul = ni == 0 ? frespa*s/r : frespa*s/r*special_coul[ni];
register double x = g_ewald*r, t = 1.0/(1.0+EWALD_P*x);
if (ni < 0) {
if (ni == 0) {
s *= g_ewald*exp(-x*x);
force_coul = (t *= ((((t*A5+A4)*t+A3)*t+A2)*t+A1)*s/x)+EWALD_F*s;
if (eflag) ecoul = t;
@ -847,14 +847,14 @@ void PairBuckCoul::compute_outer(int eflag, int vflag)
}
} // table real space
else {
if (respa_flag) respa_coul = ni<0 ? // correct for respa
if (respa_flag) respa_coul = ni == 0 ? // correct for respa
frespa*qri*q[j]/r :
frespa*qri*q[j]/r*special_coul[ni];
register union_int_float_t t;
t.f = rsq;
register const int k = (t.i & ncoulmask) >> ncoulshiftbits;
register double f = (rsq-rtable[k])*drtable[k], qiqj = qi*q[j];
if (ni < 0) {
if (ni == 0) {
force_coul = qiqj*(ftable[k]+f*dftable[k]);
if (eflag) ecoul = qiqj*(etable[k]+f*detable[k]);
}
@ -870,13 +870,13 @@ void PairBuckCoul::compute_outer(int eflag, int vflag)
if (rsq < cut_bucksqi[typej]) { // buckingham
register double rn = r2inv*r2inv*r2inv,
expr = exp(-r*rhoinvi[typej]);
if (respa_flag) respa_buck = ni<0 ? // correct for respa
if (respa_flag) respa_buck = ni == 0 ? // correct for respa
frespa*(r*expr*buck1i[typej]-rn*buck2i[typej]) :
frespa*(r*expr*buck1i[typej]-rn*buck2i[typej])*special_lj[ni];
if (order6) { // long-range form
register double x2 = g2*rsq, a2 = 1.0/x2;
x2 = a2*exp(-x2)*buckci[typej];
if (ni < 0) {
if (ni == 0) {
force_buck =
r*expr*buck1i[typej]-g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq;
if (eflag) evdwl = expr*buckai[typej]-g6*((a2+1.0)*a2+0.5)*x2;
@ -890,7 +890,7 @@ void PairBuckCoul::compute_outer(int eflag, int vflag)
}
}
else { // cut form
if (ni < 0) {
if (ni == 0) {
force_buck = r*expr*buck1i[typej]-rn*buck2i[typej];
if (eflag)
evdwl = expr*buckai[typej]-rn*buckci[typej]-offseti[typej];

56
src/USER-EWALDN/pair_lj_coul.cpp
View File

@ -459,7 +459,6 @@ void PairLJCoul::compute(int eflag, int vflag)
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
@ -484,8 +483,9 @@ void PairLJCoul::compute(int eflag, int vflag)
jneighn = (jneigh = list->firstneigh[i])+list->numneigh[i];
for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
if ((j = *jneigh) < nall) ni = -1;
else { ni = j/nall; j %= nall; } // special index
j = *jneigh;
ni = sbmask(j);
j &= NEIGHMASK;
{ register double *xj = x0+(j+(j<<1));
d[0] = xi[0] - xj[0]; // pair vector
@ -499,7 +499,7 @@ void PairLJCoul::compute(int eflag, int vflag)
if (!ncoultablebits || rsq <= tabinnersq) { // series real space
register double r = sqrt(rsq), x = g_ewald*r;
register double s = qri*q[j], t = 1.0/(1.0+EWALD_P*x);
if (ni < 0) {
if (ni == 0) {
s *= g_ewald*exp(-x*x);
force_coul = (t *= ((((t*A5+A4)*t+A3)*t+A2)*t+A1)*s/x)+EWALD_F*s;
if (eflag) ecoul = t;
@ -515,7 +515,7 @@ void PairLJCoul::compute(int eflag, int vflag)
t.f = rsq;
register const int k = (t.i & ncoulmask)>>ncoulshiftbits;
register double f = (rsq-rtable[k])*drtable[k], qiqj = qi*q[j];
if (ni < 0) {
if (ni == 0) {
force_coul = qiqj*(ftable[k]+f*dftable[k]);
if (eflag) ecoul = qiqj*(etable[k]+f*detable[k]);
}
@ -533,7 +533,7 @@ void PairLJCoul::compute(int eflag, int vflag)
register double rn = r2inv*r2inv*r2inv;
register double x2 = g2*rsq, a2 = 1.0/x2;
x2 = a2*exp(-x2)*lj4i[typej];
if (ni < 0) {
if (ni == 0) {
force_lj =
(rn*=rn)*lj1i[typej]-g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq;
if (eflag)
@ -549,7 +549,7 @@ void PairLJCoul::compute(int eflag, int vflag)
}
else { // cut lj
register double rn = r2inv*r2inv*r2inv;
if (ni < 0) {
if (ni == 0) {
force_lj = rn*(rn*lj1i[typej]-lj2i[typej]);
if (eflag) evdwl = rn*(rn*lj3i[typej]-lj4i[typej])-offseti[typej];
}
@ -593,7 +593,6 @@ void PairLJCoul::compute_inner()
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *x0 = atom->x[0], *f0 = atom->f[0], *fi = f0, *q = atom->q;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
@ -623,8 +622,9 @@ void PairLJCoul::compute_inner()
jneighn = (jneigh = list->firstneigh[i])+list->numneigh[i];
for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
if ((j = *jneigh) < nall) ni = -1;
else { ni = j/nall; j %= nall; }
j = *jneigh;
ni = sbmask(j);
j &= NEIGHMASK;
{ register double *xj = x0+(j+(j<<1));
d[0] = xi[0] - xj[0]; // pair vector
@ -635,12 +635,12 @@ void PairLJCoul::compute_inner()
r2inv = 1.0/rsq;
if (order1 && (rsq < cut_coulsq)) // coulombic
force_coul = ni<0 ?
force_coul = ni == 0 ?
qri*q[j]*sqrt(r2inv) : qri*q[j]*sqrt(r2inv)*special_coul[ni];
if (rsq < cut_ljsqi[typej = type[j]]) { // lennard-jones
register double rn = r2inv*r2inv*r2inv;
force_lj = ni<0 ?
force_lj = ni == 0 ?
rn*(rn*lj1i[typej]-lj2i[typej]) :
rn*(rn*lj1i[typej]-lj2i[typej])*special_lj[ni];
}
@ -676,7 +676,6 @@ void PairLJCoul::compute_middle()
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *x0 = atom->x[0], *f0 = atom->f[0], *fi = f0, *q = atom->q;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
@ -711,8 +710,9 @@ void PairLJCoul::compute_middle()
jneighn = (jneigh = list->firstneigh[i])+list->numneigh[i];
for (; jneigh<jneighn; ++jneigh) {
if ((j = *jneigh) < nall) ni = -1;
else { ni = j/nall; j %= nall; }
j = *jneigh;
ni = sbmask(j);
j &= NEIGHMASK;
{ register double *xj = x0+(j+(j<<1));
d[0] = xi[0] - xj[0]; // pair vector
@ -724,12 +724,12 @@ void PairLJCoul::compute_middle()
r2inv = 1.0/rsq;
if (order1 && (rsq < cut_coulsq)) // coulombic
force_coul = ni<0 ?
force_coul = ni == 0 ?
qri*q[j]*sqrt(r2inv) : qri*q[j]*sqrt(r2inv)*special_coul[ni];
if (rsq < cut_ljsqi[typej = type[j]]) { // lennard-jones
register double rn = r2inv*r2inv*r2inv;
force_lj = ni<0 ?
force_lj = ni == 0 ?
rn*(rn*lj1i[typej]-lj2i[typej]) :
rn*(rn*lj1i[typej]-lj2i[typej])*special_lj[ni];
}
@ -775,7 +775,6 @@ void PairLJCoul::compute_outer(int eflag, int vflag)
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
@ -808,9 +807,10 @@ void PairLJCoul::compute_outer(int eflag, int vflag)
jneighn = (jneigh = list->firstneigh[i])+list->numneigh[i];
for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
if ((j = *jneigh) < nall) ni = -1;
else { ni = j/nall; j %= nall; } // special index
j = *jneigh;
ni = sbmask(j);
j &= NEIGHMASK;
{ register double *xj = x0+(j+(j<<1));
d[0] = xi[0] - xj[0]; // pair vector
d[1] = xi[1] - xj[1];
@ -828,9 +828,9 @@ void PairLJCoul::compute_outer(int eflag, int vflag)
if (!ncoultablebits || rsq <= tabinnersq) { // series real space
register double r = sqrt(rsq), s = qri*q[j];
if (respa_flag) // correct for respa
respa_coul = ni<0 ? frespa*s/r : frespa*s/r*special_coul[ni];
respa_coul = ni == 0 ? frespa*s/r : frespa*s/r*special_coul[ni];
register double x = g_ewald*r, t = 1.0/(1.0+EWALD_P*x);
if (ni < 0) {
if (ni == 0) {
s *= g_ewald*exp(-x*x);
force_coul = (t *= ((((t*A5+A4)*t+A3)*t+A2)*t+A1)*s/x)+EWALD_F*s;
if (eflag) ecoul = t;
@ -842,14 +842,14 @@ void PairLJCoul::compute_outer(int eflag, int vflag)
}
} // table real space
else {
if (respa_flag) respa_coul = ni<0 ? // correct for respa
if (respa_flag) respa_coul = ni == 0 ? // correct for respa
frespa*qri*q[j]/sqrt(rsq) :
frespa*qri*q[j]/sqrt(rsq)*special_coul[ni];
register union_int_float_t t;
t.f = rsq;
register const int k = (t.i & ncoulmask) >> ncoulshiftbits;
register double f = (rsq-rtable[k])*drtable[k], qiqj = qi*q[j];
if (ni < 0) {
if (ni == 0) {
force_coul = qiqj*(ftable[k]+f*dftable[k]);
if (eflag) ecoul = qiqj*(etable[k]+f*detable[k]);
}
@ -864,13 +864,13 @@ void PairLJCoul::compute_outer(int eflag, int vflag)
if (rsq < cut_ljsqi[typej]) { // lennard-jones
register double rn = r2inv*r2inv*r2inv;
if (respa_flag) respa_lj = ni<0 ? // correct for respa
if (respa_flag) respa_lj = ni == 0 ? // correct for respa
frespa*rn*(rn*lj1i[typej]-lj2i[typej]) :
frespa*rn*(rn*lj1i[typej]-lj2i[typej])*special_lj[ni];
if (order6) { // long-range form
register double x2 = g2*rsq, a2 = 1.0/x2;
x2 = a2*exp(-x2)*lj4i[typej];
if (ni < 0) {
if (ni == 0) {
force_lj =
(rn*=rn)*lj1i[typej]-g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq;
if (eflag) evdwl = rn*lj3i[typej]-g6*((a2+1.0)*a2+0.5)*x2;
@ -884,7 +884,7 @@ void PairLJCoul::compute_outer(int eflag, int vflag)
}
}
else { // cut form
if (ni < 0) {
if (ni == 0) {
force_lj = rn*(rn*lj1i[typej]-lj2i[typej]);
if (eflag) evdwl = rn*(rn*lj3i[typej]-lj4i[typej])-offseti[typej];
}

6
src/USER-REAXC/pair_reax_c.cpp
View File

@ -561,6 +561,7 @@ int PairReaxC::estimate_reax_lists()
for( itr_j = 0; itr_j < numneigh[i]; ++itr_j ){
j = jlist[itr_j];
j &= NEIGHMASK;
get_distance( x[j], x[i], &d_sqr, &dvec );
dist[j] = sqrt(d_sqr);
@ -571,6 +572,7 @@ int PairReaxC::estimate_reax_lists()
// compute the nbrs among ghost atoms
for( itr_j = 0; itr_j < numneigh[i]; ++itr_j ){
j = jlist[itr_j];
j &= NEIGHMASK;
if( j >= nlocal && !marked[j] &&
dist[j] <= (control->vlist_cut - control->bond_cut) ){
@ -579,6 +581,7 @@ int PairReaxC::estimate_reax_lists()
for( itr_g = 0; itr_g < numneigh[i]; ++itr_g ){
g = jlist[itr_g];
g &= NEIGHMASK;
if( g >= nlocal && !marked[g] ){
get_distance( x[g], x[j], &g_d_sqr, &g_dvec );
@ -649,6 +652,7 @@ int PairReaxC::write_reax_lists()
for( itr_j = 0; itr_j < numneigh[i]; ++itr_j ){
j = jlist[itr_j];
j &= NEIGHMASK;
get_distance( x[j], x[i], &d_sqr, &dvec );
dist[j] = sqrt( d_sqr );
@ -662,6 +666,7 @@ int PairReaxC::write_reax_lists()
// compute the nbrs among ghost atoms
for( itr_j = 0; itr_j < numneigh[i]; ++itr_j ){
j = jlist[itr_j];
j &= NEIGHMASK;
if( j >= nlocal && !marked[j] &&
dist[j] <= (control->vlist_cut - control->bond_cut) ){
@ -670,6 +675,7 @@ int PairReaxC::write_reax_lists()
for( itr_g = 0; itr_g < numneigh[i]; ++itr_g ){
g = jlist[itr_g];
g &= NEIGHMASK;
if( g >= nlocal && !marked[g] ){
get_distance( x[g], x[j], &g_d_sqr, &g_dvec );

4
src/compute.h
View File

@ -121,6 +121,10 @@ class Compute : protected Pointers {
int *molmap; // convert molecule ID to local index
int molecules_in_group(int &, int &);
inline int sbmask(int j) {
return j >> SBBITS & 3;
}
};
}

2
src/compute_centro_atom.cpp
View File

@ -163,7 +163,7 @@ void ComputeCentroAtom::compute_peratom()
n = 0;
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j >= nall) j %= nall;
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];

2
src/compute_cluster_atom.cpp
View File

@ -162,7 +162,7 @@ void ComputeClusterAtom::compute_peratom()
n = 0;
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j >= nall) j %= nall;
j &= NEIGHMASK;
if (!(mask[j] & groupbit)) continue;
if (clusterID[i] == clusterID[j]) continue;

3
src/compute_cna_atom.cpp
View File

@ -168,6 +168,8 @@ void ComputeCNAAtom::compute_peratom()
n = 0;
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
@ -247,6 +249,7 @@ void ComputeCNAAtom::compute_peratom()
n = 0;
for (kk = 0; kk < jnum; kk++) {
k = jlist[kk];
k &= NEIGHMASK;
if (k == j) continue;
delx = xtmp - x[k][0];

2
src/compute_coord_atom.cpp
View File

@ -132,7 +132,7 @@ void ComputeCoordAtom::compute_peratom()
n = 0;
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j >= nall) j %= nall;
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];

10
src/compute_group_group.cpp
View File

@ -165,13 +165,9 @@ void ComputeGroupGroup::interact()
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_coul = factor_lj = 1.0;
else {
factor_coul = special_coul[j/nall];
factor_lj = special_lj[j/nall];
j %= nall;
}
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
if (!(mask[j] & othergroupbit)) continue;

10
src/compute_pair_local.cpp
View File

@ -169,13 +169,9 @@ int ComputePairLocal::compute_pairs(int flag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_coul = factor_lj = 1.0;
else {
factor_coul = special_coul[j/nall];
factor_lj = special_lj[j/nall];
j %= nall;
}
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
if (!(mask[j] & groupbit)) continue;
if (newton_pair == 0 && j >= nlocal) continue;

10
src/compute_property_local.cpp
View File

@ -322,13 +322,9 @@ int ComputePropertyLocal::count_pairs(int allflag, int forceflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_coul = factor_lj = 1.0;
else {
factor_coul = special_coul[j/nall];
factor_lj = special_lj[j/nall];
j %= nall;
}
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
if (!(mask[j] & groupbit)) continue;
if (newton_pair == 0 && j >= nlocal) continue;

16
src/compute_rdf.cpp
View File

@ -178,6 +178,7 @@ void ComputeRDF::compute_array()
int i,j,m,ii,jj,inum,jnum,itype,jtype,ipair,jpair,ibin,ihisto;
double xtmp,ytmp,ztmp,delx,dely,delz,r;
int *ilist,*jlist,*numneigh,**firstneigh;
double factor_lj,factor_coul;
invoked_array = update->ntimestep;
@ -199,8 +200,6 @@ void ComputeRDF::compute_array()
// tally the RDF
// both atom i and j must be in fix group
// itype,jtype must have been specified by user
// weighting factor must be != 0.0 for this pair
// could be 0 and still be in neigh list for long-range Coulombics
// consider I,J as one interaction even if neighbor pair is stored on 2 procs
// tally I,J pair each time I is central atom, and each time J is central
@ -226,12 +225,15 @@ void ComputeRDF::compute_array()
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
if (j >= nall) {
if (special_coul[j/nall] == 0.0 && special_lj[j/nall] == 0.0)
continue;
j %= nall;
}
// if both weighting factors are 0, skip this pair
// could be 0 and still be in neigh list for long-range Coulombics
// want consistency with non-charged pairs which wouldn't be in list
if (factor_lj == 0.0 && factor_coul == 0.0) continue;
if (!(mask[j] & groupbit)) continue;
jtype = type[j];

11
src/delete_atoms.cpp
View File

@ -251,6 +251,7 @@ void DeleteAtoms::delete_overlap(int narg, char **arg)
int i,j,ii,jj,inum,jnum;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *ilist,*jlist,*numneigh,**firstneigh;
double factor_lj,factor_coul;
inum = list->inum;
ilist = list->ilist;
@ -267,15 +268,15 @@ void DeleteAtoms::delete_overlap(int narg, char **arg)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
// if weighting factors are 0, skip this pair
// if both weighting factors are 0, skip this pair
// could be 0 and still be in neigh list for long-range Coulombics
// want consistency with non-charged pairs which wouldn't be in list
if (j >= nall) {
if (special_coul[j/nall] == 0.0 && special_lj[j/nall] == 0.0) continue;
j %= nall;
}
if (factor_lj == 0.0 && factor_coul == 0.0) continue;
// only consider deletion if I,J distance < cutoff

4
src/delete_atoms.h
View File

@ -38,6 +38,10 @@ class DeleteAtoms : protected Pointers {
void delete_overlap(int, char **);
void delete_porosity(int, char **);
void options(int, char **);
inline int sbmask(int j) {
return j >> SBBITS & 3;
}
};
}

1
src/fix_orient_fcc.cpp
View File

@ -289,6 +289,7 @@ void FixOrientFCC::post_force(int vflag)
nsort = 0;
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
count++;
dx = x[i][0] - x[j][0];

1
src/fix_shear_history.cpp
View File

@ -136,6 +136,7 @@ void FixShearHistory::pre_exchange()
if (touch[jj]) {
shear = &allshear[3*jj];
j = jlist[jj];
j &= NEIGHMASK;
if (npartner[i] < MAXTOUCH) {
m = npartner[i];
partner[i][m] = tag[j];

1
src/force.cpp
View File

@ -47,6 +47,7 @@ Force::Force(LAMMPS *lmp) : Pointers(lmp)
{
newton = newton_pair = newton_bond = 1;
special_lj[0] = special_coul[0] = 1.0;
special_lj[1] = special_lj[2] = special_lj[3] = 0.0;
special_coul[1] = special_coul[2] = special_coul[3] = 0.0;
special_angle = special_dihedral = 0;

6
src/lmptype.h
View File

@ -41,6 +41,12 @@
namespace LAMMPS_NS {
// reserve 2 hi bits in molecular system neigh list for special bonds flag
// max local + ghost atoms per processor = 2^30 - 1
#define SBBITS 30
#define NEIGHMASK 0x3FFFFFFF
// default settings
// 32-bit smallint and tagint, 64-bit bigint

35
src/neigh_derive.cpp
View File

@ -27,7 +27,7 @@ using namespace LAMMPS_NS;
void Neighbor::half_from_full_no_newton(NeighList *list)
{
int i,j,ii,jj,n,jnum;
int i,j,ii,jj,n,jnum,joriginal;
int *neighptr,*jlist;
int *ilist = list->ilist;
@ -63,8 +63,9 @@ void Neighbor::half_from_full_no_newton(NeighList *list)
jnum = numneigh_full[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j > i) neighptr[n++] = j;
joriginal = jlist[jj];
j = joriginal & NEIGHMASK;
if (j > i) neighptr[n++] = joriginal;
}
ilist[inum++] = i;
@ -93,7 +94,6 @@ void Neighbor::half_from_full_newton(NeighList *list)
double **x = atom->x;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
@ -132,11 +132,11 @@ void Neighbor::half_from_full_newton(NeighList *list)
jnum = numneigh_full[i];
for (jj = 0; jj < jnum; jj++) {
j = joriginal = jlist[jj];
joriginal = jlist[jj];
j = joriginal & NEIGHMASK;
if (j < nlocal) {
if (i > j) continue;
} else {
if (j >= nall) j %= nall;
if (x[j][2] < ztmp) continue;
if (x[j][2] == ztmp) {
if (x[j][1] < ytmp) continue;
@ -171,7 +171,6 @@ void Neighbor::skip_from(NeighList *list)
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
@ -214,8 +213,8 @@ void Neighbor::skip_from(NeighList *list)
jnum = numneigh_skip[i];
for (jj = 0; jj < jnum; jj++) {
j = joriginal = jlist[jj];
if (j >= nall) j %= nall;
joriginal = jlist[jj];
j = joriginal & NEIGHMASK;
if (ijskip[itype][type[j]]) continue;
neighptr[n++] = joriginal;
}
@ -252,7 +251,6 @@ void Neighbor::skip_from_granular(NeighList *list)
double *shearptr,*shearptr_skip;
int *type = atom->type;
int nall = atom->nlocal + atom->nghost;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
@ -311,8 +309,8 @@ void Neighbor::skip_from_granular(NeighList *list)
jnum = numneigh_skip[i];
for (jj = 0; jj < jnum; jj++) {
j = joriginal = jlist[jj];
if (j >= nall) j %= nall;
joriginal = jlist[jj];
j = joriginal & NEIGHMASK;
if (ijskip[itype][type[j]]) continue;
neighptr[n] = joriginal;
touchptr[n++] = touchptr_skip[jj];
@ -346,7 +344,6 @@ void Neighbor::skip_from_respa(NeighList *list)
int *neighptr,*jlist,*neighptr_inner,*neighptr_middle;
int *type = atom->type;
int nall = atom->nlocal + atom->nghost;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
@ -431,8 +428,8 @@ void Neighbor::skip_from_respa(NeighList *list)
jnum = numneigh_skip[i];
for (jj = 0; jj < jnum; jj++) {
j = joriginal = jlist[jj];
if (j >= nall) j %= nall;
joriginal = jlist[jj];
j = joriginal & NEIGHMASK;
if (ijskip[itype][type[j]]) continue;
neighptr[n++] = joriginal;
}
@ -443,8 +440,8 @@ void Neighbor::skip_from_respa(NeighList *list)
jnum = numneigh_inner_skip[i];
for (jj = 0; jj < jnum; jj++) {
j = joriginal = jlist[jj];
if (j >= nall) j %= nall;
joriginal = jlist[jj];
j = joriginal & NEIGHMASK;
if (ijskip[itype][type[j]]) continue;
neighptr_inner[n_inner++] = joriginal;
}
@ -456,8 +453,8 @@ void Neighbor::skip_from_respa(NeighList *list)
jnum = numneigh_middle_skip[i];
for (jj = 0; jj < jnum; jj++) {
j = joriginal = jlist[jj];
if (j >= nall) j %= nall;
joriginal = jlist[jj];
j = joriginal & NEIGHMASK;
if (ijskip[itype][type[j]]) continue;
neighptr_middle[n_middle++] = joriginal;
}

58
src/neigh_full.cpp
View File

@ -87,10 +87,10 @@ void Neighbor::full_nsq(NeighList *list)
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) which = find_special(special[i],nspecial[i],tag[j]);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
}
}
@ -171,10 +171,10 @@ void Neighbor::full_nsq_ghost(NeighList *list)
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) which = find_special(special[i],nspecial[i],tag[j]);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
}
}
} else {
@ -188,10 +188,10 @@ void Neighbor::full_nsq_ghost(NeighList *list)
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighghostsq[itype][jtype]) {
if (molecular) which = find_special(special[i],nspecial[i],tag[j]);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
}
}
}
@ -232,7 +232,6 @@ void Neighbor::full_bin(NeighList *list)
int *mask = atom->mask;
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int molecular = atom->molecular;
if (includegroup) nlocal = atom->nfirst;
@ -283,10 +282,10 @@ void Neighbor::full_bin(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) which = find_special(special[i],nspecial[i],tag[j]);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
}
}
}
@ -381,10 +380,10 @@ void Neighbor::full_bin_ghost(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) which = find_special(special[i],nspecial[i],tag[j]);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
}
}
}
@ -410,10 +409,10 @@ void Neighbor::full_bin_ghost(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighghostsq[itype][jtype]) {
if (molecular) which = find_special(special[i],nspecial[i],tag[j]);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
}
}
}
@ -459,7 +458,6 @@ void Neighbor::full_multi(NeighList *list)
int *mask = atom->mask;
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int molecular = atom->molecular;
if (includegroup) nlocal = atom->nfirst;
@ -514,10 +512,10 @@ void Neighbor::full_multi(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) which = find_special(special[i],nspecial[i],tag[j]);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
}
}
}

39
src/neigh_half_bin.cpp
View File

@ -46,7 +46,6 @@ void Neighbor::half_bin_no_newton(NeighList *list)
int *mask = atom->mask;
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
if (includegroup) nlocal = atom->nfirst;
int molecular = atom->molecular;
@ -97,10 +96,10 @@ void Neighbor::half_bin_no_newton(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) which = find_special(special[i],nspecial[i],tag[j]);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
}
}
}
@ -143,9 +142,8 @@ void Neighbor::half_bin_newton(NeighList *list)
int *mask = atom->mask;
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int molecular = atom->molecular;
if (includegroup) nlocal = atom->nfirst;
int molecular = atom->molecular;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
@ -196,10 +194,10 @@ void Neighbor::half_bin_newton(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) which = find_special(special[i],nspecial[i],tag[j]);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
}
}
@ -217,10 +215,10 @@ void Neighbor::half_bin_newton(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) which = find_special(special[i],nspecial[i],tag[j]);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
}
}
}
@ -263,9 +261,8 @@ void Neighbor::half_bin_newton_tri(NeighList *list)
int *mask = atom->mask;
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int molecular = atom->molecular;
if (includegroup) nlocal = atom->nfirst;
int molecular = atom->molecular;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
@ -321,10 +318,10 @@ void Neighbor::half_bin_newton_tri(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) which = find_special(special[i],nspecial[i],tag[j]);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
}
}
}

35
src/neigh_half_multi.cpp
View File

@ -48,7 +48,6 @@ void Neighbor::half_multi_no_newton(NeighList *list)
int *mask = atom->mask;
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int molecular = atom->molecular;
if (includegroup) nlocal = atom->nfirst;
@ -105,10 +104,10 @@ void Neighbor::half_multi_no_newton(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) which = find_special(special[i],nspecial[i],tag[j]);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
}
}
}
@ -153,7 +152,6 @@ void Neighbor::half_multi_newton(NeighList *list)
int *mask = atom->mask;
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int molecular = atom->molecular;
if (includegroup) nlocal = atom->nfirst;
@ -207,10 +205,10 @@ void Neighbor::half_multi_newton(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) which = find_special(special[i],nspecial[i],tag[j]);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
}
}
@ -235,10 +233,10 @@ void Neighbor::half_multi_newton(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) which = find_special(special[i],nspecial[i],tag[j]);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
}
}
}
@ -283,7 +281,6 @@ void Neighbor::half_multi_newton_tri(NeighList *list)
int *mask = atom->mask;
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int molecular = atom->molecular;
if (includegroup) nlocal = atom->nfirst;
@ -349,10 +346,10 @@ void Neighbor::half_multi_newton_tri(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) which = find_special(special[i],nspecial[i],tag[j]);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
}
}
}

16
src/neigh_half_nsq.cpp
View File

@ -87,10 +87,10 @@ void Neighbor::half_nsq_no_newton(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) which = find_special(special[i],nspecial[i],tag[j]);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
}
}
@ -191,10 +191,10 @@ void Neighbor::half_nsq_newton(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) which = find_special(special[i],nspecial[i],tag[j]);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
}
}

84
src/neigh_respa.cpp
View File

@ -128,19 +128,20 @@ void Neighbor::respa_nsq_no_newton(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) which = find_special(special[i],nspecial[i],tag[j]);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
if (rsq < cut_inner_sq) {
if (which == 0) neighptr_inner[n_inner++] = j;
else if (which > 0) neighptr_inner[n_inner++] = which*nall + j;
else if (which > 0) neighptr_inner[n_inner++] = j ^ (which << SBBITS);
}
if (respamiddle && rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
if (which == 0) neighptr_middle[n_middle++] = j;
else if (which > 0) neighptr_middle[n_middle++] = which*nall + j;
else if (which > 0)
neighptr_middle[n_middle++] = j ^ (which << SBBITS);
}
}
}
@ -303,20 +304,21 @@ void Neighbor::respa_nsq_newton(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) which = find_special(special[i],nspecial[i],tag[j]);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
if (rsq < cut_inner_sq) {
if (which == 0) neighptr_inner[n_inner++] = j;
else if (which > 0) neighptr_inner[n_inner++] = which*nall + j;
else if (which > 0) neighptr_inner[n_inner++] = j ^ (which << SBBITS);
}
if (respamiddle &&
rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
if (which == 0) neighptr_middle[n_middle++] = j;
else if (which > 0) neighptr_middle[n_middle++] = which*nall + j;
else if (which > 0)
neighptr_middle[n_middle++] = j ^ (which << SBBITS);
}
}
}
@ -381,7 +383,6 @@ void Neighbor::respa_bin_no_newton(NeighList *list)
int *mask = atom->mask;
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int molecular = atom->molecular;
if (includegroup) nlocal = atom->nfirst;
@ -471,20 +472,22 @@ void Neighbor::respa_bin_no_newton(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) which = find_special(special[i],nspecial[i],tag[j]);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
if (rsq < cut_inner_sq) {
if (which == 0) neighptr_inner[n_inner++] = j;
else if (which > 0) neighptr_inner[n_inner++] = which*nall + j;
else if (which > 0)
neighptr_inner[n_inner++] = j ^ (which << SBBITS);
}
if (respamiddle &&
rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
if (which == 0) neighptr_middle[n_middle++] = j;
else if (which > 0) neighptr_middle[n_middle++] = which*nall + j;
else if (which > 0)
neighptr_middle[n_middle++] = j ^ (which << SBBITS);
}
}
}
@ -549,7 +552,6 @@ void Neighbor::respa_bin_newton(NeighList *list)
int *mask = atom->mask;
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int molecular = atom->molecular;
if (includegroup) nlocal = atom->nfirst;
@ -642,20 +644,21 @@ void Neighbor::respa_bin_newton(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) which = find_special(special[i],nspecial[i],tag[j]);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
if (rsq < cut_inner_sq) {
if (which == 0) neighptr_inner[n_inner++] = j;
else if (which > 0) neighptr_inner[n_inner++] = which*nall + j;
else if (which > 0) neighptr_inner[n_inner++] = j ^ (which << SBBITS);
}
if (respamiddle &&
rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
if (which == 0) neighptr_middle[n_middle++] = j;
else if (which > 0) neighptr_middle[n_middle++] = which*nall + j;
else if (which > 0)
neighptr_middle[n_middle++] = j ^ (which << SBBITS);
}
}
}
@ -674,20 +677,22 @@ void Neighbor::respa_bin_newton(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) which = find_special(special[i],nspecial[i],tag[j]);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
if (rsq < cut_inner_sq) {
if (which == 0) neighptr_inner[n_inner++] = j;
else if (which > 0) neighptr_inner[n_inner++] = which*nall + j;
else if (which > 0)
neighptr_inner[n_inner++] = j ^ (which << SBBITS);
}
if (respamiddle &&
rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
if (which == 0) neighptr_middle[n_middle++] = j;
else if (which > 0) neighptr_middle[n_middle++] = which*nall + j;
else if (which > 0)
neighptr_middle[n_middle++] = j ^ (which << SBBITS);
}
}
}
@ -752,7 +757,6 @@ void Neighbor::respa_bin_newton_tri(NeighList *list)
int *mask = atom->mask;
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int molecular = atom->molecular;
if (includegroup) nlocal = atom->nfirst;
@ -850,20 +854,22 @@ void Neighbor::respa_bin_newton_tri(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) which = find_special(special[i],nspecial[i],tag[j]);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
if (rsq < cut_inner_sq) {
if (which == 0) neighptr_inner[n_inner++] = j;
else if (which > 0) neighptr_inner[n_inner++] = which*nall + j;
else if (which > 0)
neighptr_inner[n_inner++] = j ^ (which << SBBITS);
}
if (respamiddle &&
rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
if (which == 0) neighptr_middle[n_middle++] = j;
else if (which > 0) neighptr_middle[n_middle++] = which*nall + j;
else if (which > 0)
neighptr_middle[n_middle++] = j ^ (which << SBBITS);
}
}
}

14
src/neighbor.cpp
View File

@ -1172,13 +1172,10 @@ void Neighbor::build()
memory->create(bins,maxbin,"bins");
}
// check that pairwise lists with special bond weighting will not overflow
// check that neighbor list with special bond flags will not overflow
if (atom->molecular && maxwt && nblist) {
bigint max = maxwt * static_cast<bigint> (atom->nlocal + atom->nghost);
if (max > MAXSMALLINT)
error->one("Weighted neighbor list values are too big");
}
if (atom->nlocal+atom->nghost > NEIGHMASK)
error->one("Too many local+ghost atoms for neighbor list");
// invoke building of pair and molecular neighbor lists
// only for pairwise lists with buildflag set
@ -1218,6 +1215,11 @@ void Neighbor::build_one(int i)
memory->create(bins,maxbin,"bins");
}
// check that neighbor list with special bond flags will not overflow
if (atom->nlocal+atom->nghost > NEIGHMASK)
error->one("Too many local+ghost atoms for neighbor list");
// when occasional list built, LAMMPS can crash if atoms have moved too far
// why is this?, give warning if this is the case
// no easy workaround b/c all neighbor lists really need to be rebuilt

66
src/neighbor.h
View File

@ -165,39 +165,6 @@ class Neighbor : protected Pointers {
void choose_build(int, class NeighRequest *);
void choose_stencil(int, class NeighRequest *);
// find_special: determine if atom j is in special list of atom i
// if it is not, return 0
// if it is and special flag is 0 (both coeffs are 0.0), return -1
// if it is and special flag is 1 (both coeffs are 1.0), return 0
// if it is and special flag is 2 (otherwise), return 1,2,3
// for which neighbor it is (and which coeff it maps to)
inline int find_special(const int *list, const int *nspecial,
const int tag) const {
const int n1 = nspecial[0];
const int n2 = nspecial[1];
const int n3 = nspecial[2];
for (int i = 0; i < n3; i++) {
if (list[i] == tag) {
if (i < n1) {
if (special_flag[1] == 0) return -1;
else if (special_flag[1] == 1) return 0;
else return 1;
} else if (i < n2) {
if (special_flag[2] == 0) return -1;
else if (special_flag[2] == 1) return 0;
else return 2;
} else {
if (special_flag[3] == 0) return -1;
else if (special_flag[3] == 1) return 0;
else return 3;
}
}
}
return 0;
};
// pairwise build functions
typedef void (Neighbor::*PairPtr)(class NeighList *);
@ -284,6 +251,39 @@ class Neighbor : protected Pointers {
BondPtr improper_build; // ptr to improper list functions
void improper_all(); // improper list with all impropers
void improper_partial(); // exclude certain impropers
// find_special: determine if atom j is in special list of atom i
// if it is not, return 0
// if it is and special flag is 0 (both coeffs are 0.0), return -1
// if it is and special flag is 1 (both coeffs are 1.0), return 0
// if it is and special flag is 2 (otherwise), return 1,2,3
// for which neighbor it is (and which coeff it maps to)
inline int find_special(const int *list, const int *nspecial,
const int tag) const {
const int n1 = nspecial[0];
const int n2 = nspecial[1];
const int n3 = nspecial[2];
for (int i = 0; i < n3; i++) {
if (list[i] == tag) {
if (i < n1) {
if (special_flag[1] == 0) return -1;
else if (special_flag[1] == 1) return 0;
else return 1;
} else if (i < n2) {
if (special_flag[2] == 0) return -1;
else if (special_flag[2] == 1) return 0;
else return 2;
} else {
if (special_flag[3] == 0) return -1;
else if (special_flag[3] == 1) return 0;
else return 3;
}
}
}
return 0;
};
};
}

4
src/pair.h
View File

@ -147,6 +147,10 @@ class Pair : protected Pointers {
void v_tally_tensor(int, int, int, int,
double, double, double, double, double, double);
void virial_compute();
inline int sbmask(int j) {
return j >> SBBITS & 3;
}
};
}

9
src/pair_born.cpp
View File

@ -76,7 +76,6 @@ void PairBorn::compute(int eflag, int vflag)
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
@ -98,12 +97,8 @@ void PairBorn::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_lj = 1.0;
else {
factor_lj = special_lj[j/nall];
j %= nall;
}
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];

9
src/pair_buck.cpp
View File

@ -69,7 +69,6 @@ void PairBuck::compute(int eflag, int vflag)
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
@ -91,12 +90,8 @@ void PairBuck::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_lj = 1.0;
else {
factor_lj = special_lj[j/nall];
j %= nall;
}
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];

11
src/pair_buck_coul_cut.cpp
View File

@ -77,7 +77,6 @@ void PairBuckCoulCut::compute(int eflag, int vflag)
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
@ -102,13 +101,9 @@ void PairBuckCoulCut::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_coul = factor_lj = 1.0;
else {
factor_coul = special_coul[j/nall];
factor_lj = special_lj[j/nall];
j %= nall;
}
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];

9
src/pair_coul_cut.cpp
View File

@ -64,7 +64,6 @@ void PairCoulCut::compute(int eflag, int vflag)
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_coul = force->special_coul;
int newton_pair = force->newton_pair;
double qqrd2e = force->qqrd2e;
@ -88,12 +87,8 @@ void PairCoulCut::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_coul = 1.0;
else {
factor_coul = special_coul[j/nall];
j %= nall;
}
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];

9
src/pair_coul_debye.cpp
View File

@ -51,7 +51,6 @@ void PairCoulDebye::compute(int eflag, int vflag)
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_coul = force->special_coul;
int newton_pair = force->newton_pair;
double qqrd2e = force->qqrd2e;
@ -75,12 +74,8 @@ void PairCoulDebye::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_coul = 1.0;
else {
factor_coul = special_coul[j/nall];
j %= nall;
}
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];

9
src/pair_dpd.cpp
View File

@ -80,7 +80,6 @@ void PairDPD::compute(int eflag, int vflag)
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
double dtinvsqrt = 1.0/sqrt(update->dt);
@ -106,12 +105,8 @@ void PairDPD::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_dpd = 1.0;
else {
factor_dpd = special_lj[j/nall];
j %= nall;
}
factor_dpd = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];

9
src/pair_dpd_tstat.cpp
View File

@ -65,7 +65,6 @@ void PairDPDTstat::compute(int eflag, int vflag)
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
double dtinvsqrt = 1.0/sqrt(update->dt);
@ -91,12 +90,8 @@ void PairDPDTstat::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_dpd = 1.0;
else {
factor_dpd = special_lj[j/nall];
j %= nall;
}
factor_dpd = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];

2
src/pair_gauss.cpp
View File

@ -78,7 +78,6 @@ void PairGauss::compute(int eflag, int vflag)
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int newton_pair = force->newton_pair;
inum = list->inum;
@ -99,6 +98,7 @@ void PairGauss::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];

37
src/pair_lj96_cut.cpp
View File

@ -80,11 +80,9 @@ void PairLJ96Cut::compute(int eflag, int vflag)
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
@ -103,12 +101,8 @@ void PairLJ96Cut::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_lj = 1.0;
else {
factor_lj = special_lj[j/nall];
j %= nall;
}
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
@ -160,7 +154,6 @@ void PairLJ96Cut::compute_inner()
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
@ -189,12 +182,8 @@ void PairLJ96Cut::compute_inner()
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_lj = 1.0;
else {
factor_lj = special_lj[j/nall];
j %= nall;
}
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
@ -239,7 +228,6 @@ void PairLJ96Cut::compute_middle()
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
@ -273,12 +261,8 @@ void PairLJ96Cut::compute_middle()
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_lj = 1.0;
else {
factor_lj = special_lj[j/nall];
j %= nall;
}
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
@ -331,7 +315,6 @@ void PairLJ96Cut::compute_outer(int eflag, int vflag)
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
@ -360,12 +343,8 @@ void PairLJ96Cut::compute_outer(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_lj = 1.0;
else {
factor_lj = special_lj[j/nall];
j %= nall;
}
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];

36
src/pair_lj_cut.cpp
View File

@ -80,7 +80,6 @@ void PairLJCut::compute(int eflag, int vflag)
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
@ -102,12 +101,8 @@ void PairLJCut::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_lj = 1.0;
else {
factor_lj = special_lj[j/nall];
j %= nall;
}
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
@ -158,7 +153,6 @@ void PairLJCut::compute_inner()
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
@ -187,12 +181,8 @@ void PairLJCut::compute_inner()
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_lj = 1.0;
else {
factor_lj = special_lj[j/nall];
j %= nall;
}
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
@ -236,7 +226,6 @@ void PairLJCut::compute_middle()
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
@ -270,12 +259,8 @@ void PairLJCut::compute_middle()
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_lj = 1.0;
else {
factor_lj = special_lj[j/nall];
j %= nall;
}
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
@ -327,7 +312,6 @@ void PairLJCut::compute_outer(int eflag, int vflag)
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
@ -356,12 +340,8 @@ void PairLJCut::compute_outer(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_lj = 1.0;
else {
factor_lj = special_lj[j/nall];
j %= nall;
}
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];

11
src/pair_lj_cut_coul_cut.cpp
View File

@ -73,7 +73,6 @@ void PairLJCutCoulCut::compute(int eflag, int vflag)
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
@ -98,13 +97,9 @@ void PairLJCutCoulCut::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_coul = factor_lj = 1.0;
else {
factor_coul = special_coul[j/nall];
factor_lj = special_lj[j/nall];
j %= nall;
}
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];

11
src/pair_lj_cut_coul_debye.cpp
View File

@ -45,7 +45,6 @@ void PairLJCutCoulDebye::compute(int eflag, int vflag)
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
@ -70,13 +69,9 @@ void PairLJCutCoulDebye::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_coul = factor_lj = 1.0;
else {
factor_coul = special_coul[j/nall];
factor_lj = special_lj[j/nall];
j %= nall;
}
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];

9
src/pair_lj_expand.cpp
View File

@ -69,7 +69,6 @@ void PairLJExpand::compute(int eflag, int vflag)
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
@ -91,12 +90,8 @@ void PairLJExpand::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_lj = 1.0;
else {
factor_lj = special_lj[j/nall];
j %= nall;
}
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];

9
src/pair_lj_gromacs.cpp
View File

@ -80,7 +80,6 @@ void PairLJGromacs::compute(int eflag, int vflag)
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
@ -102,12 +101,8 @@ void PairLJGromacs::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_lj = 1.0;
else {
factor_lj = special_lj[j/nall];
j %= nall;
}
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];

11
src/pair_lj_gromacs_coul_gromacs.cpp
View File

@ -78,7 +78,6 @@ void PairLJGromacsCoulGromacs::compute(int eflag, int vflag)
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
@ -103,13 +102,9 @@ void PairLJGromacsCoulGromacs::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_coul = factor_lj = 1.0;
else {
factor_coul = special_coul[j/nall];
factor_lj = special_lj[j/nall];
j %= nall;
}
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];

9
src/pair_lj_smooth.cpp
View File

@ -79,7 +79,6 @@ void PairLJSmooth::compute(int eflag, int vflag)
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
@ -101,13 +100,9 @@ void PairLJSmooth::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
if (j < nall) factor_lj = 1.0;
else {
factor_lj = special_lj[j/nall];
j %= nall;
}
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];

9
src/pair_morse.cpp
View File

@ -65,7 +65,6 @@ void PairMorse::compute(int eflag, int vflag)
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
@ -87,12 +86,8 @@ void PairMorse::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_lj = 1.0;
else {
factor_lj = special_lj[j/nall];
j %= nall;
}
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];

9
src/pair_soft.cpp
View File

@ -66,7 +66,6 @@ void PairSoft::compute(int eflag, int vflag)
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
@ -88,12 +87,8 @@ void PairSoft::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_lj = 1.0;
else {
factor_lj = special_lj[j/nall];
j %= nall;
}
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];

9
src/pair_table.cpp
View File

@ -86,7 +86,6 @@ void PairTable::compute(int eflag, int vflag)
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
@ -108,13 +107,9 @@ void PairTable::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
if (j < nall) factor_lj = 1.0;
else {
factor_lj = special_lj[j/nall];
j %= nall;
}
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];

9
src/pair_yukawa.cpp
View File

@ -61,7 +61,6 @@ void PairYukawa::compute(int eflag, int vflag)
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_coul = force->special_coul;
int newton_pair = force->newton_pair;
@ -83,12 +82,8 @@ void PairYukawa::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_coul = 1.0;
else {
factor_coul = special_coul[j/nall];
j %= nall;
}
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];