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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11407 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2014-01-30 22:12:56 +00:00
parent d4552ec92e
commit 170ff252db
5 changed files with 497 additions and 146 deletions
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150
src/USER-OMP/neigh_full_omp.cpp
View File

@ -15,6 +15,8 @@
#include "neighbor_omp.h"
#include "neigh_list.h"
#include "atom.h"
#include "atom_vec.h"
#include "molecule.h"
#include "comm.h"
#include "domain.h"
#include "group.h"
@ -32,6 +34,8 @@ void Neighbor::full_nsq_omp(NeighList *list)
{
const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
const int bitmask = (includegroup) ? group->bitmask[includegroup] : 0;
const int molecular = atom->molecular;
const int moltemplate = (molecular == 2) ? 1 : 0;
NEIGH_OMP_INIT;
#if defined(_OPENMP)
@ -39,20 +43,23 @@ void Neighbor::full_nsq_omp(NeighList *list)
#endif
NEIGH_OMP_SETUP(nlocal);
int i,j,n,itype,jtype,which;
int i,j,n,itype,jtype,which,imol,iatom;
tagint tagprev;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr;
tagint **special = atom->special;
int **nspecial = atom->nspecial;
tagint *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
tagint *tag = atom->tag;
tagint *molecule = atom->molecule;
tagint **special = atom->special;
int **nspecial = atom->nspecial;
int nall = atom->nlocal + atom->nghost;
int molecular = atom->molecular;
int *molindex = atom->molindex;
int *molatom = atom->molatom;
Molecule **onemols = atom->avec->onemols;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
@ -73,6 +80,11 @@ void Neighbor::full_nsq_omp(NeighList *list)
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
if (moltemplate) {
imol = molindex[i];
iatom = molatom[i];
tagprev = tag[i] - iatom - 1;
}
// loop over all atoms, owned and ghost
// skip i = j
@ -89,7 +101,13 @@ void Neighbor::full_nsq_omp(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]);
if (!moltemplate)
which = find_special(special[i],nspecial[i],tag[j]);
else if (imol >=0)
which = find_special(onemols[imol]->special[iatom],
onemols[imol]->nspecial[iatom],
tag[j]-tagprev);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;
@ -120,6 +138,8 @@ void Neighbor::full_nsq_ghost_omp(NeighList *list)
{
const int nlocal = atom->nlocal;
const int nall = nlocal + atom->nghost;
const int molecular = atom->molecular;
const int moltemplate = (molecular == 2) ? 1 : 0;
NEIGH_OMP_INIT;
#if defined(_OPENMP)
@ -127,19 +147,22 @@ void Neighbor::full_nsq_ghost_omp(NeighList *list)
#endif
NEIGH_OMP_SETUP(nall);
int i,j,n,itype,jtype,which;
int i,j,n,itype,jtype,which,imol,iatom;
tagint tagprev;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr;
tagint **special = atom->special;
int **nspecial = atom->nspecial;
tagint *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
tagint *tag = atom->tag;
tagint *molecule = atom->molecule;
int molecular = atom->molecular;
tagint **special = atom->special;
int **nspecial = atom->nspecial;
int *molindex = atom->molindex;
int *molatom = atom->molatom;
Molecule **onemols = atom->avec->onemols;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
@ -160,6 +183,11 @@ void Neighbor::full_nsq_ghost_omp(NeighList *list)
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
if (moltemplate) {
imol = molindex[i];
iatom = molatom[i];
tagprev = tag[i] - iatom - 1;
}
// loop over all atoms, owned and ghost
// skip i = j
@ -177,7 +205,13 @@ void Neighbor::full_nsq_ghost_omp(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]);
if (!moltemplate)
which = find_special(special[i],nspecial[i],tag[j]);
else if (imol >=0)
which = find_special(onemols[imol]->special[iatom],
onemols[imol]->nspecial[iatom],
tag[j]-tagprev);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;
@ -224,6 +258,8 @@ void Neighbor::full_bin_omp(NeighList *list)
bin_atoms();
const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
const int molecular = atom->molecular;
const int moltemplate = (molecular == 2) ? 1 : 0;
NEIGH_OMP_INIT;
#if defined(_OPENMP)
@ -231,19 +267,21 @@ void Neighbor::full_bin_omp(NeighList *list)
#endif
NEIGH_OMP_SETUP(nlocal);
int i,j,k,n,itype,jtype,ibin,which;
int i,j,k,n,itype,jtype,ibin,which,imol,iatom;
tagint tagprev;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr;
tagint **special = atom->special;
int **nspecial = atom->nspecial;
tagint *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
tagint *tag = atom->tag;
tagint *molecule = atom->molecule;
int molecular = atom->molecular;
tagint **special = atom->special;
int **nspecial = atom->nspecial;
int *molindex = atom->molindex;
int *molatom = atom->molatom;
Molecule **onemols = atom->avec->onemols;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
@ -266,6 +304,11 @@ void Neighbor::full_bin_omp(NeighList *list)
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
if (moltemplate) {
imol = molindex[i];
iatom = molatom[i];
tagprev = tag[i] - iatom - 1;
}
// loop over all atoms in surrounding bins in stencil including self
// skip i = j
@ -286,7 +329,13 @@ void Neighbor::full_bin_omp(NeighList *list)
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (!moltemplate)
which = find_special(special[i],nspecial[i],tag[j]);
else if (imol >=0)
which = find_special(onemols[imol]->special[iatom],
onemols[imol]->nspecial[iatom],
tag[j]-tagprev);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;
@ -322,6 +371,8 @@ void Neighbor::full_bin_ghost_omp(NeighList *list)
const int nlocal = atom->nlocal;
const int nall = nlocal + atom->nghost;
const int molecular = atom->molecular;
const int moltemplate = (molecular == 2) ? 1 : 0;
NEIGH_OMP_INIT;
#if defined(_OPENMP)
@ -329,20 +380,23 @@ void Neighbor::full_bin_ghost_omp(NeighList *list)
#endif
NEIGH_OMP_SETUP(nall);
int i,j,k,n,itype,jtype,ibin,which;
int i,j,k,n,itype,jtype,ibin,which,imol,iatom;
tagint tagprev;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int xbin,ybin,zbin,xbin2,ybin2,zbin2;
int *neighptr;
tagint **special = atom->special;
int **nspecial = atom->nspecial;
tagint *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
tagint *tag = atom->tag;
tagint *molecule = atom->molecule;
int molecular = atom->molecular;
tagint **special = atom->special;
int **nspecial = atom->nspecial;
int *molindex = atom->molindex;
int *molatom = atom->molatom;
Molecule **onemols = atom->avec->onemols;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
@ -366,6 +420,11 @@ void Neighbor::full_bin_ghost_omp(NeighList *list)
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
if (moltemplate) {
imol = molindex[i];
iatom = molatom[i];
tagprev = tag[i] - iatom - 1;
}
// loop over all atoms in surrounding bins in stencil including self
// when i is a ghost atom, must check if stencil bin is out of bounds
@ -388,7 +447,13 @@ void Neighbor::full_bin_ghost_omp(NeighList *list)
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (!moltemplate)
which = find_special(special[i],nspecial[i],tag[j]);
else if (imol >=0)
which = find_special(onemols[imol]->special[iatom],
onemols[imol]->nspecial[iatom],
tag[j]-tagprev);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;
@ -448,6 +513,8 @@ void Neighbor::full_multi_omp(NeighList *list)
bin_atoms();
const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
const int molecular = atom->molecular;
const int moltemplate = (molecular == 2) ? 1 : 0;
NEIGH_OMP_INIT;
#if defined(_OPENMP)
@ -455,22 +522,25 @@ void Neighbor::full_multi_omp(NeighList *list)
#endif
NEIGH_OMP_SETUP(nlocal);
int i,j,k,n,itype,jtype,ibin,which,ns;
int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom;
tagint tagprev;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr,*s;
double *cutsq,*distsq;
// loop over each atom, storing neighbors
tagint **special = atom->special;
int **nspecial = atom->nspecial;
tagint *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
tagint *tag = atom->tag;
tagint *molecule = atom->molecule;
int molecular = atom->molecular;
tagint **special = atom->special;
int **nspecial = atom->nspecial;
int *molindex = atom->molindex;
int *molatom = atom->molatom;
Molecule **onemols = atom->avec->onemols;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
@ -492,6 +562,11 @@ void Neighbor::full_multi_omp(NeighList *list)
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
if (moltemplate) {
imol = molindex[i];
iatom = molatom[i];
tagprev = tag[i] - iatom - 1;
}
// loop over all atoms in other bins in stencil, including self
// skip if i,j neighbor cutoff is less than bin distance
@ -517,6 +592,13 @@ void Neighbor::full_multi_omp(NeighList *list)
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) {
if (!moltemplate)
which = find_special(special[i],nspecial[i],tag[j]);
else if (imol >=0)
which = find_special(onemols[imol]->special[iatom],
onemols[imol]->nspecial[iatom],
tag[j]-tagprev);
else which = 0;
which = find_special(special[i],nspecial[i],tag[j]);
if (which == 0) neighptr[n++] = j;
else if (domain->minimum_image_check(delx,dely,delz))

138
src/USER-OMP/neigh_half_bin_omp.cpp
View File

@ -15,6 +15,8 @@
#include "neighbor_omp.h"
#include "neigh_list.h"
#include "atom.h"
#include "atom_vec.h"
#include "molecule.h"
#include "comm.h"
#include "domain.h"
#include "my_page.h"
@ -36,6 +38,8 @@ void Neighbor::half_bin_no_newton_omp(NeighList *list)
bin_atoms();
const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
const int molecular = atom->molecular;
const int moltemplate = (molecular == 2) ? 1 : 0;
NEIGH_OMP_INIT;
#if defined(_OPENMP)
@ -43,21 +47,24 @@ void Neighbor::half_bin_no_newton_omp(NeighList *list)
#endif
NEIGH_OMP_SETUP(nlocal);
int i,j,k,n,itype,jtype,ibin,which;
int i,j,k,n,itype,jtype,ibin,which,imol,iatom;
tagint tagprev;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr;
// loop over each atom, storing neighbors
tagint **special = atom->special;
int **nspecial = atom->nspecial;
tagint *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
tagint *tag = atom->tag;
tagint *molecule = atom->molecule;
int molecular = atom->molecular;
tagint **special = atom->special;
int **nspecial = atom->nspecial;
int *molindex = atom->molindex;
int *molatom = atom->molatom;
Molecule **onemols = atom->avec->onemols;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
@ -78,6 +85,11 @@ void Neighbor::half_bin_no_newton_omp(NeighList *list)
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
if (moltemplate) {
imol = molindex[i];
iatom = molatom[i];
tagprev = tag[i] - iatom - 1;
}
// loop over all atoms in other bins in stencil including self
// only store pair if i < j
@ -100,7 +112,13 @@ void Neighbor::half_bin_no_newton_omp(NeighList *list)
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (!moltemplate)
which = find_special(special[i],nspecial[i],tag[j]);
else if (imol >=0)
which = find_special(onemols[imol]->special[iatom],
onemols[imol]->nspecial[iatom],
tag[j]-tagprev);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;
@ -132,8 +150,14 @@ void Neighbor::half_bin_no_newton_omp(NeighList *list)
void Neighbor::half_bin_no_newton_ghost_omp(NeighList *list)
{
// bin local & ghost atoms
bin_atoms();
const int nlocal = atom->nlocal;
const int nall = nlocal + atom->nghost;
const int molecular = atom->molecular;
const int moltemplate = (molecular == 2) ? 1 : 0;
NEIGH_OMP_INIT;
#if defined(_OPENMP)
@ -141,26 +165,25 @@ void Neighbor::half_bin_no_newton_ghost_omp(NeighList *list)
#endif
NEIGH_OMP_SETUP(nall);
int i,j,k,n,itype,jtype,ibin,which;
int i,j,k,n,itype,jtype,ibin,which,imol,iatom;
tagint tagprev;
int xbin,ybin,zbin,xbin2,ybin2,zbin2;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr;
// bin local & ghost atoms
bin_atoms();
// loop over each atom, storing neighbors
tagint **special = atom->special;
int **nspecial = atom->nspecial;
tagint *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
tagint *tag = atom->tag;
tagint *molecule = atom->molecule;
int molecular = atom->molecular;
tagint **special = atom->special;
int **nspecial = atom->nspecial;
int *molindex = atom->molindex;
int *molatom = atom->molatom;
Molecule **onemols = atom->avec->onemols;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
@ -182,6 +205,11 @@ void Neighbor::half_bin_no_newton_ghost_omp(NeighList *list)
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
if (moltemplate) {
imol = molindex[i];
iatom = molatom[i];
tagprev = tag[i] - iatom - 1;
}
// loop over all atoms in other bins in stencil including self
// when i is a ghost atom, must check if stencil bin is out of bounds
@ -208,7 +236,13 @@ void Neighbor::half_bin_no_newton_ghost_omp(NeighList *list)
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (!moltemplate)
which = find_special(special[i],nspecial[i],tag[j]);
else if (imol >=0)
which = find_special(onemols[imol]->special[iatom],
onemols[imol]->nspecial[iatom],
tag[j]-tagprev);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;
@ -268,6 +302,8 @@ void Neighbor::half_bin_newton_omp(NeighList *list)
bin_atoms();
const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
const int molecular = atom->molecular;
const int moltemplate = (molecular == 2) ? 1 : 0;
NEIGH_OMP_INIT;
#if defined(_OPENMP)
@ -275,21 +311,24 @@ void Neighbor::half_bin_newton_omp(NeighList *list)
#endif
NEIGH_OMP_SETUP(nlocal);
int i,j,k,n,itype,jtype,ibin,which;
int i,j,k,n,itype,jtype,ibin,which,imol,iatom;
tagint tagprev;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr;
// loop over each atom, storing neighbors
tagint **special = atom->special;
int **nspecial = atom->nspecial;
tagint *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
tagint *tag = atom->tag;
tagint *molecule = atom->molecule;
int molecular = atom->molecular;
tagint **special = atom->special;
int **nspecial = atom->nspecial;
int *molindex = atom->molindex;
int *molatom = atom->molatom;
Molecule **onemols = atom->avec->onemols;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
@ -310,6 +349,11 @@ void Neighbor::half_bin_newton_omp(NeighList *list)
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
if (moltemplate) {
imol = molindex[i];
iatom = molatom[i];
tagprev = tag[i] - iatom - 1;
}
// loop over rest of atoms in i's bin, ghosts are at end of linked list
// if j is owned atom, store it, since j is beyond i in linked list
@ -334,7 +378,13 @@ void Neighbor::half_bin_newton_omp(NeighList *list)
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (!moltemplate)
which = find_special(special[i],nspecial[i],tag[j]);
else if (imol >=0)
which = find_special(onemols[imol]->special[iatom],
onemols[imol]->nspecial[iatom],
tag[j]-tagprev);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;
@ -359,7 +409,13 @@ void Neighbor::half_bin_newton_omp(NeighList *list)
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (!moltemplate)
which = find_special(special[i],nspecial[i],tag[j]);
else if (imol >=0)
which = find_special(onemols[imol]->special[iatom],
onemols[imol]->nspecial[iatom],
tag[j]-tagprev);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;
@ -394,6 +450,8 @@ void Neighbor::half_bin_newton_tri_omp(NeighList *list)
bin_atoms();
const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
const int molecular = atom->molecular;
const int moltemplate = (molecular == 2) ? 1 : 0;
NEIGH_OMP_INIT;
#if defined(_OPENMP)
@ -401,21 +459,24 @@ void Neighbor::half_bin_newton_tri_omp(NeighList *list)
#endif
NEIGH_OMP_SETUP(nlocal);
int i,j,k,n,itype,jtype,ibin,which;
int i,j,k,n,itype,jtype,ibin,which,imol,iatom;
tagint tagprev;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr;
// loop over each atom, storing neighbors
tagint **special = atom->special;
int **nspecial = atom->nspecial;
tagint *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
tagint *tag = atom->tag;
tagint *molecule = atom->molecule;
int molecular = atom->molecular;
tagint **special = atom->special;
int **nspecial = atom->nspecial;
int *molindex = atom->molindex;
int *molatom = atom->molatom;
Molecule **onemols = atom->avec->onemols;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
@ -436,6 +497,11 @@ void Neighbor::half_bin_newton_tri_omp(NeighList *list)
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
if (moltemplate) {
imol = molindex[i];
iatom = molatom[i];
tagprev = tag[i] - iatom - 1;
}
// loop over all atoms in bins in stencil
// pairs for atoms j "below" i are excluded
@ -465,7 +531,13 @@ void Neighbor::half_bin_newton_tri_omp(NeighList *list)
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (!moltemplate)
which = find_special(special[i],nspecial[i],tag[j]);
else if (imol >=0)
which = find_special(onemols[imol]->special[iatom],
onemols[imol]->nspecial[iatom],
tag[j]-tagprev);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;

100
src/USER-OMP/neigh_half_multi_omp.cpp
View File

@ -15,6 +15,8 @@
#include "neighbor_omp.h"
#include "neigh_list.h"
#include "atom.h"
#include "atom_vec.h"
#include "molecule.h"
#include "comm.h"
#include "domain.h"
#include "my_page.h"
@ -37,6 +39,8 @@ void Neighbor::half_multi_no_newton_omp(NeighList *list)
bin_atoms();
const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
const int molecular = atom->molecular;
const int moltemplate = (molecular == 2) ? 1 : 0;
NEIGH_OMP_INIT;
#if defined(_OPENMP)
@ -44,22 +48,25 @@ void Neighbor::half_multi_no_newton_omp(NeighList *list)
#endif
NEIGH_OMP_SETUP(nlocal);
int i,j,k,n,itype,jtype,ibin,which,ns;
int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom;
tagint tagprev;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr,*s;
double *cutsq,*distsq;
// loop over each atom, storing neighbors
tagint **special = atom->special;
int **nspecial = atom->nspecial;
tagint *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
tagint *tag = atom->tag;
tagint *molecule = atom->molecule;
int molecular = atom->molecular;
tagint **special = atom->special;
int **nspecial = atom->nspecial;
int *molindex = atom->molindex;
int *molatom = atom->molatom;
Molecule **onemols = atom->avec->onemols;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
@ -81,6 +88,11 @@ void Neighbor::half_multi_no_newton_omp(NeighList *list)
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
if (moltemplate) {
imol = molindex[i];
iatom = molatom[i];
tagprev = tag[i] - iatom - 1;
}
// loop over all atoms in other bins in stencil including self
// only store pair if i < j
@ -108,7 +120,13 @@ void Neighbor::half_multi_no_newton_omp(NeighList *list)
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (!moltemplate)
which = find_special(special[i],nspecial[i],tag[j]);
else if (imol >=0)
which = find_special(onemols[imol]->special[iatom],
onemols[imol]->nspecial[iatom],
tag[j]-tagprev);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;
@ -143,6 +161,8 @@ void Neighbor::half_multi_newton_omp(NeighList *list)
bin_atoms();
const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
const int molecular = atom->molecular;
const int moltemplate = (molecular == 2) ? 1 : 0;
NEIGH_OMP_INIT;
#if defined(_OPENMP)
@ -150,22 +170,25 @@ void Neighbor::half_multi_newton_omp(NeighList *list)
#endif
NEIGH_OMP_SETUP(nlocal);
int i,j,k,n,itype,jtype,ibin,which,ns;
int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom;
tagint tagprev;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr,*s;
double *cutsq,*distsq;
// loop over each atom, storing neighbors
tagint **special = atom->special;
int **nspecial = atom->nspecial;
tagint *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
tagint *tag = atom->tag;
tagint *molecule = atom->molecule;
int molecular = atom->molecular;
tagint **special = atom->special;
int **nspecial = atom->nspecial;
int *molindex = atom->molindex;
int *molatom = atom->molatom;
Molecule **onemols = atom->avec->onemols;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
@ -187,6 +210,11 @@ void Neighbor::half_multi_newton_omp(NeighList *list)
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
if (moltemplate) {
imol = molindex[i];
iatom = molatom[i];
tagprev = tag[i] - iatom - 1;
}
// loop over rest of atoms in i's bin, ghosts are at end of linked list
// if j is owned atom, store it, since j is beyond i in linked list
@ -211,7 +239,13 @@ void Neighbor::half_multi_newton_omp(NeighList *list)
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (!moltemplate)
which = find_special(special[i],nspecial[i],tag[j]);
else if (imol >=0)
which = find_special(onemols[imol]->special[iatom],
onemols[imol]->nspecial[iatom],
tag[j]-tagprev);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;
@ -242,7 +276,13 @@ void Neighbor::half_multi_newton_omp(NeighList *list)
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (!moltemplate)
which = find_special(special[i],nspecial[i],tag[j]);
else if (imol >=0)
which = find_special(onemols[imol]->special[iatom],
onemols[imol]->nspecial[iatom],
tag[j]-tagprev);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;
@ -277,6 +317,8 @@ void Neighbor::half_multi_newton_tri_omp(NeighList *list)
bin_atoms();
const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
const int molecular = atom->molecular;
const int moltemplate = (molecular == 2) ? 1 : 0;
NEIGH_OMP_INIT;
#if defined(_OPENMP)
@ -284,22 +326,25 @@ void Neighbor::half_multi_newton_tri_omp(NeighList *list)
#endif
NEIGH_OMP_SETUP(nlocal);
int i,j,k,n,itype,jtype,ibin,which,ns;
int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom;
tagint tagprev;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr,*s;
double *cutsq,*distsq;
// loop over each atom, storing neighbors
tagint **special = atom->special;
int **nspecial = atom->nspecial;
tagint *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
tagint *tag = atom->tag;
tagint *molecule = atom->molecule;
int molecular = atom->molecular;
tagint **special = atom->special;
int **nspecial = atom->nspecial;
int *molindex = atom->molindex;
int *molatom = atom->molatom;
Molecule **onemols = atom->avec->onemols;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
@ -321,6 +366,11 @@ void Neighbor::half_multi_newton_tri_omp(NeighList *list)
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
if (moltemplate) {
imol = molindex[i];
iatom = molatom[i];
tagprev = tag[i] - iatom - 1;
}
// loop over all atoms in bins, including self, in stencil
// skip if i,j neighbor cutoff is less than bin distance
@ -357,7 +407,13 @@ void Neighbor::half_multi_newton_tri_omp(NeighList *list)
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (!moltemplate)
which = find_special(special[i],nspecial[i],tag[j]);
else if (imol >=0)
which = find_special(onemols[imol]->special[iatom],
onemols[imol]->nspecial[iatom],
tag[j]-tagprev);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;

93
src/USER-OMP/neigh_half_nsq_omp.cpp
View File

@ -15,6 +15,8 @@
#include "neighbor_omp.h"
#include "neigh_list.h"
#include "atom.h"
#include "atom_vec.h"
#include "molecule.h"
#include "comm.h"
#include "domain.h"
#include "group.h"
@ -34,6 +36,8 @@ void Neighbor::half_nsq_no_newton_omp(NeighList *list)
const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
const int bitmask = (includegroup) ? group->bitmask[includegroup] : 0;
const int nall = atom->nlocal + atom->nghost;
const int molecular = atom->molecular;
const int moltemplate = (molecular == 2) ? 1 : 0;
NEIGH_OMP_INIT;
#if defined(_OPENMP)
@ -41,19 +45,22 @@ void Neighbor::half_nsq_no_newton_omp(NeighList *list)
#endif
NEIGH_OMP_SETUP(nlocal);
int i,j,n,itype,jtype,which;
int i,j,n,itype,jtype,which,imol,iatom;
tagint tagprev;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr;
tagint **special = atom->special;
int **nspecial = atom->nspecial;
tagint *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
tagint *tag = atom->tag;
tagint *molecule = atom->molecule;
int molecular = atom->molecular;
tagint **special = atom->special;
int **nspecial = atom->nspecial;
int *molindex = atom->molindex;
int *molatom = atom->molatom;
Molecule **onemols = atom->avec->onemols;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
@ -74,6 +81,11 @@ void Neighbor::half_nsq_no_newton_omp(NeighList *list)
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
if (moltemplate) {
imol = molindex[i];
iatom = molatom[i];
tagprev = tag[i] - iatom - 1;
}
// loop over remaining atoms, owned and ghost
// only store pair if i < j
@ -90,7 +102,13 @@ void Neighbor::half_nsq_no_newton_omp(NeighList *list)
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (!moltemplate)
which = find_special(special[i],nspecial[i],tag[j]);
else if (imol >=0)
which = find_special(onemols[imol]->special[iatom],
onemols[imol]->nspecial[iatom],
tag[j]-tagprev);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;
@ -123,6 +141,8 @@ void Neighbor::half_nsq_no_newton_ghost_omp(NeighList *list)
const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
const int bitmask = (includegroup) ? group->bitmask[includegroup] : 0;
const int nall = nlocal + atom->nghost;
const int molecular = atom->molecular;
const int moltemplate = (molecular == 2) ? 1 : 0;
NEIGH_OMP_INIT;
#if defined(_OPENMP)
@ -130,19 +150,22 @@ void Neighbor::half_nsq_no_newton_ghost_omp(NeighList *list)
#endif
NEIGH_OMP_SETUP(nall);
int i,j,n,itype,jtype,which;
int i,j,n,itype,jtype,which,imol,iatom;
tagint tagprev;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr;
tagint **special = atom->special;
int **nspecial = atom->nspecial;
tagint *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
tagint *tag = atom->tag;
tagint *molecule = atom->molecule;
int molecular = atom->molecular;
tagint **special = atom->special;
int **nspecial = atom->nspecial;
int *molindex = atom->molindex;
int *molatom = atom->molatom;
Molecule **onemols = atom->avec->onemols;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
@ -163,6 +186,11 @@ void Neighbor::half_nsq_no_newton_ghost_omp(NeighList *list)
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
if (moltemplate) {
imol = molindex[i];
iatom = molatom[i];
tagprev = tag[i] - iatom - 1;
}
// loop over remaining atoms, owned and ghost
// only store pair if i < j
@ -184,7 +212,13 @@ void Neighbor::half_nsq_no_newton_ghost_omp(NeighList *list)
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (!moltemplate)
which = find_special(special[i],nspecial[i],tag[j]);
else if (imol >=0)
which = find_special(onemols[imol]->special[iatom],
onemols[imol]->nspecial[iatom],
tag[j]-tagprev);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;
@ -230,6 +264,8 @@ void Neighbor::half_nsq_newton_omp(NeighList *list)
{
const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
const int bitmask = (includegroup) ? group->bitmask[includegroup] : 0;
const int molecular = atom->molecular;
const int moltemplate = (molecular == 2) ? 1 : 0;
NEIGH_OMP_INIT;
#if defined(_OPENMP)
@ -237,22 +273,26 @@ void Neighbor::half_nsq_newton_omp(NeighList *list)
#endif
NEIGH_OMP_SETUP(nlocal);
int i,j,n,itype,jtype,itag,jtag,which;
int i,j,n,itype,jtype,itag,jtag,which,imol,iatom;
tagint tagprev;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr;
// loop over each atom, storing neighbors
tagint **special = atom->special;
int **nspecial = atom->nspecial;
tagint *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
tagint *tag = atom->tag;
tagint *molecule = atom->molecule;
tagint **special = atom->special;
int **nspecial = atom->nspecial;
int *molindex = atom->molindex;
int *molatom = atom->molatom;
Molecule **onemols = atom->avec->onemols;
int nall = atom->nlocal + atom->nghost;
int molecular = atom->molecular;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
@ -272,6 +312,11 @@ void Neighbor::half_nsq_newton_omp(NeighList *list)
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
if (moltemplate) {
imol = molindex[i];
iatom = molatom[i];
tagprev = tag[i] - iatom - 1;
}
// loop over remaining atoms, owned and ghost
// itag = jtag is possible for long cutoffs that include images of self
@ -304,7 +349,13 @@ void Neighbor::half_nsq_newton_omp(NeighList *list)
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (!moltemplate)
which = find_special(special[i],nspecial[i],tag[j]);
else if (imol >=0)
which = find_special(onemols[imol]->special[iatom],
onemols[imol]->nspecial[iatom],
tag[j]-tagprev);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;

162
src/USER-OMP/neigh_respa_omp.cpp
View File

@ -15,6 +15,8 @@
#include "neighbor_omp.h"
#include "neigh_list.h"
#include "atom.h"
#include "atom_vec.h"
#include "molecule.h"
#include "comm.h"
#include "domain.h"
#include "group.h"
@ -34,6 +36,8 @@ void Neighbor::respa_nsq_no_newton_omp(NeighList *list)
{
const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
const int bitmask = (includegroup) ? group->bitmask[includegroup] : 0;
const int molecular = atom->molecular;
const int moltemplate = (molecular == 2) ? 1 : 0;
NEIGH_OMP_INIT;
@ -46,22 +50,26 @@ void Neighbor::respa_nsq_no_newton_omp(NeighList *list)
#endif
NEIGH_OMP_SETUP(nlocal);
int i,j,n,itype,jtype,n_inner,n_middle;
int i,j,n,itype,jtype,n_inner,n_middle,imol,iatom;
tagint tagprev;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr,*neighptr_inner,*neighptr_middle;
// loop over each atom, storing neighbors
tagint **special = atom->special;
int **nspecial = atom->nspecial;
tagint *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
tagint *tag = atom->tag;
tagint *molecule = atom->molecule;
tagint **special = atom->special;
int **nspecial = atom->nspecial;
int *molindex = atom->molindex;
int *molatom = atom->molatom;
Molecule **onemols = atom->avec->onemols;
int nall = atom->nlocal + atom->nghost;
int molecular = atom->molecular;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
@ -107,6 +115,11 @@ void Neighbor::respa_nsq_no_newton_omp(NeighList *list)
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
if (moltemplate) {
imol = molindex[i];
iatom = molatom[i];
tagprev = tag[i] - iatom - 1;
}
// loop over remaining atoms, owned and ghost
@ -122,7 +135,13 @@ void Neighbor::respa_nsq_no_newton_omp(NeighList *list)
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (!moltemplate)
which = find_special(special[i],nspecial[i],tag[j]);
else if (imol >=0)
which = find_special(onemols[imol]->special[iatom],
onemols[imol]->nspecial[iatom],
tag[j]-tagprev);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (minchange = domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;
@ -185,6 +204,8 @@ void Neighbor::respa_nsq_newton_omp(NeighList *list)
{
const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
const int bitmask = (includegroup) ? group->bitmask[includegroup] : 0;
const int molecular = atom->molecular;
const int moltemplate = (molecular == 2) ? 1 : 0;
NEIGH_OMP_INIT;
@ -197,22 +218,26 @@ void Neighbor::respa_nsq_newton_omp(NeighList *list)
#endif
NEIGH_OMP_SETUP(nlocal);
int i,j,n,itype,jtype,itag,jtag,n_inner,n_middle;
int i,j,n,itype,jtype,itag,jtag,n_inner,n_middle,imol,iatom;
tagint tagprev;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr,*neighptr_inner,*neighptr_middle;
// loop over each atom, storing neighbors
tagint **special = atom->special;
int **nspecial = atom->nspecial;
tagint *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
tagint *tag = atom->tag;
tagint *molecule = atom->molecule;
tagint **special = atom->special;
int **nspecial = atom->nspecial;
int *molindex = atom->molindex;
int *molatom = atom->molatom;
Molecule **onemols = atom->avec->onemols;
int nall = atom->nlocal + atom->nghost;
int molecular = atom->molecular;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
@ -259,6 +284,11 @@ void Neighbor::respa_nsq_newton_omp(NeighList *list)
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
if (moltemplate) {
imol = molindex[i];
iatom = molatom[i];
tagprev = tag[i] - iatom - 1;
}
// loop over remaining atoms, owned and ghost
@ -290,7 +320,13 @@ void Neighbor::respa_nsq_newton_omp(NeighList *list)
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (!moltemplate)
which = find_special(special[i],nspecial[i],tag[j]);
else if (imol >=0)
which = find_special(onemols[imol]->special[iatom],
onemols[imol]->nspecial[iatom],
tag[j]-tagprev);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (minchange = domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;
@ -357,6 +393,8 @@ void Neighbor::respa_bin_no_newton_omp(NeighList *list)
bin_atoms();
const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
const int molecular = atom->molecular;
const int moltemplate = (molecular == 2) ? 1 : 0;
NEIGH_OMP_INIT;
@ -369,21 +407,24 @@ void Neighbor::respa_bin_no_newton_omp(NeighList *list)
#endif
NEIGH_OMP_SETUP(nlocal);
int i,j,k,n,itype,jtype,ibin,n_inner,n_middle;
int i,j,k,n,itype,jtype,ibin,n_inner,n_middle,imol,iatom;
tagint tagprev;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr,*neighptr_inner,*neighptr_middle;
// loop over each atom, storing neighbors
tagint **special = atom->special;
int **nspecial = atom->nspecial;
tagint *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
tagint *tag = atom->tag;
tagint *molecule = atom->molecule;
int molecular = atom->molecular;
tagint **special = atom->special;
int **nspecial = atom->nspecial;
int *molindex = atom->molindex;
int *molatom = atom->molatom;
Molecule **onemols = atom->avec->onemols;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
@ -432,6 +473,11 @@ void Neighbor::respa_bin_no_newton_omp(NeighList *list)
ytmp = x[i][1];
ztmp = x[i][2];
ibin = coord2bin(x[i]);
if (moltemplate) {
imol = molindex[i];
iatom = molatom[i];
tagprev = tag[i] - iatom - 1;
}
// loop over all atoms in surrounding bins in stencil including self
// only store pair if i < j
@ -452,7 +498,13 @@ void Neighbor::respa_bin_no_newton_omp(NeighList *list)
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (!moltemplate)
which = find_special(special[i],nspecial[i],tag[j]);
else if (imol >=0)
which = find_special(onemols[imol]->special[iatom],
onemols[imol]->nspecial[iatom],
tag[j]-tagprev);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (minchange = domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;
@ -520,6 +572,8 @@ void Neighbor::respa_bin_newton_omp(NeighList *list)
bin_atoms();
const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
const int molecular = atom->molecular;
const int moltemplate = (molecular == 2) ? 1 : 0;
NEIGH_OMP_INIT;
@ -532,21 +586,24 @@ void Neighbor::respa_bin_newton_omp(NeighList *list)
#endif
NEIGH_OMP_SETUP(nlocal);
int i,j,k,n,itype,jtype,ibin,n_inner,n_middle;
int i,j,k,n,itype,jtype,ibin,n_inner,n_middle,imol,iatom;
tagint tagprev;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr,*neighptr_inner,*neighptr_middle;
// loop over each atom, storing neighbors
tagint **special = atom->special;
int **nspecial = atom->nspecial;
tagint *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
tagint *tag = atom->tag;
tagint *molecule = atom->molecule;
int molecular = atom->molecular;
tagint **special = atom->special;
int **nspecial = atom->nspecial;
int *molindex = atom->molindex;
int *molatom = atom->molatom;
Molecule **onemols = atom->avec->onemols;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
@ -594,6 +651,11 @@ void Neighbor::respa_bin_newton_omp(NeighList *list)
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
if (moltemplate) {
imol = molindex[i];
iatom = molatom[i];
tagprev = tag[i] - iatom - 1;
}
// loop over rest of atoms in i's bin, ghosts are at end of linked list
// if j is owned atom, store it, since j is beyond i in linked list
@ -618,7 +680,13 @@ void Neighbor::respa_bin_newton_omp(NeighList *list)
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (!moltemplate)
which = find_special(special[i],nspecial[i],tag[j]);
else if (imol >=0)
which = find_special(onemols[imol]->special[iatom],
onemols[imol]->nspecial[iatom],
tag[j]-tagprev);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (minchange = domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;
@ -656,7 +724,13 @@ void Neighbor::respa_bin_newton_omp(NeighList *list)
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (!moltemplate)
which = find_special(special[i],nspecial[i],tag[j]);
else if (imol >=0)
which = find_special(onemols[imol]->special[iatom],
onemols[imol]->nspecial[iatom],
tag[j]-tagprev);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (minchange = domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;
@ -724,6 +798,8 @@ void Neighbor::respa_bin_newton_tri_omp(NeighList *list)
bin_atoms();
const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
const int molecular = atom->molecular;
const int moltemplate = (molecular == 2) ? 1 : 0;
NEIGH_OMP_INIT;
@ -736,21 +812,24 @@ void Neighbor::respa_bin_newton_tri_omp(NeighList *list)
#endif
NEIGH_OMP_SETUP(nlocal);
int i,j,k,n,itype,jtype,ibin,n_inner,n_middle;
int i,j,k,n,itype,jtype,ibin,n_inner,n_middle,imol,iatom;
tagint tagprev;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr,*neighptr_inner,*neighptr_middle;
// loop over each atom, storing neighbors
tagint **special = atom->special;
int **nspecial = atom->nspecial;
tagint *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
tagint *tag = atom->tag;
tagint *molecule = atom->molecule;
int molecular = atom->molecular;
tagint **special = atom->special;
int **nspecial = atom->nspecial;
int *molindex = atom->molindex;
int *molatom = atom->molatom;
Molecule **onemols = atom->avec->onemols;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
@ -798,6 +877,11 @@ void Neighbor::respa_bin_newton_tri_omp(NeighList *list)
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
if (moltemplate) {
imol = molindex[i];
iatom = molatom[i];
tagprev = tag[i] - iatom - 1;
}
// loop over all atoms in bins in stencil
// pairs for atoms j "below" i are excluded
@ -827,7 +911,13 @@ void Neighbor::respa_bin_newton_tri_omp(NeighList *list)
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (!moltemplate)
which = find_special(special[i],nspecial[i],tag[j]);
else if (imol >=0)
which = find_special(onemols[imol]->special[iatom],
onemols[imol]->nspecial[iatom],
tag[j]-tagprev);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (minchange = domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;