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Sun, May 26, 05:13
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rLAMMPS lammps
neigh_respa_omp.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "neighbor.h"
#include "neighbor_omp.h"
#include "neigh_list.h"
#include "atom.h"
#include "comm.h"
#include "domain.h"
#include "group.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ----------------------------------------------------------------------
multiple respa lists
N^2 / 2 search for neighbor pairs with partial Newton's 3rd law
pair added to list if atoms i and j are both owned and i < j
pair added if j is ghost (also stored by proc owning j)
------------------------------------------------------------------------- */
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;
NEIGH_OMP_INIT;
NeighList *listinner = list->listinner;
if (nthreads > listinner->maxpage)
listinner->add_pages(nthreads - listinner->maxpage);
NeighList *listmiddle;
const int respamiddle = list->respamiddle;
if (respamiddle) {
listmiddle = list->listmiddle;
if (nthreads > listmiddle->maxpage)
listmiddle->add_pages(nthreads - listmiddle->maxpage);
}
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(list,listinner,listmiddle)
#endif
NEIGH_OMP_SETUP(nlocal);
int i,j,n,itype,jtype,n_inner,n_middle;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr,*neighptr_inner,*neighptr_middle;
// loop over each atom, storing neighbors
int **special = atom->special;
int **nspecial = atom->nspecial;
int *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
int nall = atom->nlocal + atom->nghost;
int molecular = atom->molecular;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
int *ilist_inner = listinner->ilist;
int *numneigh_inner = listinner->numneigh;
int **firstneigh_inner = listinner->firstneigh;
int *ilist_middle,*numneigh_middle,**firstneigh_middle;
if (respamiddle) {
ilist_middle = listmiddle->ilist;
numneigh_middle = listmiddle->numneigh;
firstneigh_middle = listmiddle->firstneigh;
}
int npage = tid;
int npnt = 0;
int npage_inner = tid;
int npnt_inner = 0;
int npage_middle = tid;
int npnt_middle = 0;
int which = 0;
int minchange = 0;
for (i = ifrom; i < ito; i++) {
#if defined(_OPENMP)
#pragma omp critical
#endif
if (pgsize - npnt < oneatom) {
npnt = 0;
npage += nthreads;
if (npage == list->maxpage) list->add_pages(nthreads);
}
neighptr = &(list->pages[npage][npnt]);
n = 0;
#if defined(_OPENMP)
#pragma omp critical
#endif
if (pgsize - npnt_inner < oneatom) {
npnt_inner = 0;
npage_inner += nthreads;
if (npage_inner == listinner->maxpage) listinner->add_pages(nthreads);
}
neighptr_inner = &(listinner->pages[npage_inner][npnt_inner]);
n_inner = 0;
#if defined(_OPENMP)
#pragma omp critical
#endif
if (respamiddle) {
if (pgsize - npnt_middle < oneatom) {
npnt_middle = 0;
npage_middle += nthreads;
if (npage_middle == listmiddle->maxpage) listmiddle->add_pages(nthreads);
}
neighptr_middle = &(listmiddle->pages[npage_middle][npnt_middle]);
n_middle = 0;
}
itype = type[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
// loop over remaining atoms, owned and ghost
for (j = i+1; j < nall; j++) {
if (includegroup && !(mask[j] & bitmask)) continue;
jtype = type[j];
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (which == 0) neighptr[n++] = j;
else if (minchange = domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;
else 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 (minchange) neighptr_inner[n_inner++] = 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 (minchange) neighptr_middle[n_middle++] = j;
else if (which > 0)
neighptr_middle[n_middle++] = j ^ (which << SBBITS);
}
}
}
ilist[i] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
npnt += n;
if (n > oneatom)
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
ilist_inner[i] = i;
firstneigh_inner[i] = neighptr_inner;
numneigh_inner[i] = n_inner;
npnt_inner += n_inner;
if (n_inner > oneatom)
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
if (respamiddle) {
ilist_middle[i] = i;
firstneigh_middle[i] = neighptr_middle;
numneigh_middle[i] = n_middle;
npnt_middle += n_middle;
if (n_middle > oneatom)
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
}
NEIGH_OMP_CLOSE;
list->inum = nlocal;
listinner->inum = nlocal;
if (respamiddle) listmiddle->inum = nlocal;
}
/* ----------------------------------------------------------------------
multiple respa lists
N^2 / 2 search for neighbor pairs with full Newton's 3rd law
pair added to list if atoms i and j are both owned and i < j
if j is ghost only me or other proc adds pair
decision based on itag,jtag tests
------------------------------------------------------------------------- */
void Neighbor::respa_nsq_newton_omp(NeighList *list)
{
const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
const int bitmask = (includegroup) ? group->bitmask[includegroup] : 0;
NEIGH_OMP_INIT;
NeighList *listinner = list->listinner;
if (nthreads > listinner->maxpage)
listinner->add_pages(nthreads - listinner->maxpage);
NeighList *listmiddle;
const int respamiddle = list->respamiddle;
if (respamiddle) {
listmiddle = list->listmiddle;
if (nthreads > listmiddle->maxpage)
listmiddle->add_pages(nthreads - listmiddle->maxpage);
}
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(list,listinner,listmiddle)
#endif
NEIGH_OMP_SETUP(nlocal);
int i,j,n,itype,jtype,itag,jtag,n_inner,n_middle;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr,*neighptr_inner,*neighptr_middle;
// loop over each atom, storing neighbors
int **special = atom->special;
int **nspecial = atom->nspecial;
int *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
int nall = atom->nlocal + atom->nghost;
int molecular = atom->molecular;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
int *ilist_inner = listinner->ilist;
int *numneigh_inner = listinner->numneigh;
int **firstneigh_inner = listinner->firstneigh;
int *ilist_middle,*numneigh_middle,**firstneigh_middle;
if (respamiddle) {
ilist_middle = listmiddle->ilist;
numneigh_middle = listmiddle->numneigh;
firstneigh_middle = listmiddle->firstneigh;
}
int npage = tid;
int npnt = 0;
int npage_inner = tid;
int npnt_inner = 0;
int npage_middle = tid;
int npnt_middle = 0;
int which = 0;
int minchange = 0;
for (i = ifrom; i < ito; i++) {
#if defined(_OPENMP)
#pragma omp critical
#endif
if (pgsize - npnt < oneatom) {
npnt = 0;
npage += nthreads;
if (npage == list->maxpage) list->add_pages(nthreads);
}
neighptr = &(list->pages[npage][npnt]);
n = 0;
#if defined(_OPENMP)
#pragma omp critical
#endif
if (pgsize - npnt_inner < oneatom) {
npnt_inner = 0;
npage_inner += nthreads;
if (npage_inner == listinner->maxpage) listinner->add_pages(nthreads);
}
neighptr_inner = &(listinner->pages[npage_inner][npnt_inner]);
n_inner = 0;
#if defined(_OPENMP)
#pragma omp critical
#endif
if (respamiddle) {
if (pgsize - npnt_middle < oneatom) {
npnt_middle = 0;
npage_middle += nthreads;
if (npage_middle == listmiddle->maxpage) listmiddle->add_pages(nthreads);
}
neighptr_middle = &(listmiddle->pages[npage_middle][npnt_middle]);
n_middle = 0;
}
itag = tag[i];
itype = type[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
// loop over remaining atoms, owned and ghost
for (j = i+1; j < nall; j++) {
if (includegroup && !(mask[j] & bitmask)) continue;
if (j >= nlocal) {
jtag = tag[j];
if (itag > jtag) {
if ((itag+jtag) % 2 == 0) continue;
} else if (itag < jtag) {
if ((itag+jtag) % 2 == 1) continue;
} else {
if (x[j][2] < ztmp) continue;
if (x[j][2] == ztmp) {
if (x[j][1] < ytmp) continue;
if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
}
}
}
jtype = type[j];
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (which == 0) neighptr[n++] = j;
else if (minchange = domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;
else 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 (minchange) neighptr_inner[n_inner++] = 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 (minchange) neighptr_middle[n_middle++] = j;
else if (which > 0)
neighptr_middle[n_middle++] = j ^ (which << SBBITS);
}
}
}
ilist[i] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
npnt += n;
if (n > oneatom)
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
ilist_inner[i] = i;
firstneigh_inner[i] = neighptr_inner;
numneigh_inner[i] = n_inner;
npnt_inner += n_inner;
if (n_inner > oneatom)
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
if (respamiddle) {
ilist_middle[i] = i;
firstneigh_middle[i] = neighptr_middle;
numneigh_middle[i] = n_middle;
npnt_middle += n_middle;
if (n_middle > oneatom)
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
}
NEIGH_OMP_CLOSE;
list->inum = nlocal;
listinner->inum = nlocal;
if (respamiddle) listmiddle->inum = nlocal;
}
/* ----------------------------------------------------------------------
multiple respa lists
binned neighbor list construction with partial Newton's 3rd law
each owned atom i checks own bin and surrounding bins in non-Newton stencil
pair stored once if i,j are both owned and i < j
pair stored by me if j is ghost (also stored by proc owning j)
------------------------------------------------------------------------- */
void Neighbor::respa_bin_no_newton_omp(NeighList *list)
{
// bin local & ghost atoms
bin_atoms();
const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
NEIGH_OMP_INIT;
NeighList *listinner = list->listinner;
if (nthreads > listinner->maxpage)
listinner->add_pages(nthreads - listinner->maxpage);
NeighList *listmiddle;
const int respamiddle = list->respamiddle;
if (respamiddle) {
listmiddle = list->listmiddle;
if (nthreads > listmiddle->maxpage)
listmiddle->add_pages(nthreads - listmiddle->maxpage);
}
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(list,listinner,listmiddle)
#endif
NEIGH_OMP_SETUP(nlocal);
int i,j,k,n,itype,jtype,ibin,n_inner,n_middle;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr,*neighptr_inner,*neighptr_middle;
// loop over each atom, storing neighbors
int **special = atom->special;
int **nspecial = atom->nspecial;
int *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
int molecular = atom->molecular;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
int nstencil = list->nstencil;
int *stencil = list->stencil;
int *ilist_inner = listinner->ilist;
int *numneigh_inner = listinner->numneigh;
int **firstneigh_inner = listinner->firstneigh;
int *ilist_middle,*numneigh_middle,**firstneigh_middle;
if (respamiddle) {
ilist_middle = listmiddle->ilist;
numneigh_middle = listmiddle->numneigh;
firstneigh_middle = listmiddle->firstneigh;
}
int npage = tid;
int npnt = 0;
int npage_inner = tid;
int npnt_inner = 0;
int npage_middle = tid;
int npnt_middle = 0;
int which = 0;
int minchange = 0;
for (i = ifrom; i < ito; i++) {
#if defined(_OPENMP)
#pragma omp critical
#endif
if (pgsize - npnt < oneatom) {
npnt = 0;
npage += nthreads;
if (npage == list->maxpage) list->add_pages(nthreads);
}
neighptr = &(list->pages[npage][npnt]);
n = 0;
#if defined(_OPENMP)
#pragma omp critical
#endif
if (pgsize - npnt_inner < oneatom) {
npnt_inner = 0;
npage_inner += nthreads;
if (npage_inner == listinner->maxpage) listinner->add_pages(nthreads);
}
neighptr_inner = &(listinner->pages[npage_inner][npnt_inner]);
n_inner = 0;
#if defined(_OPENMP)
#pragma omp critical
#endif
if (respamiddle) {
if (pgsize - npnt_middle < oneatom) {
npnt_middle = 0;
npage_middle += nthreads;
if (npage_middle == listmiddle->maxpage) listmiddle->add_pages(nthreads);
}
neighptr_middle = &(listmiddle->pages[npage_middle][npnt_middle]);
n_middle = 0;
}
itype = type[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
ibin = coord2bin(x[i]);
// loop over all atoms in surrounding bins in stencil including self
// only store pair if i < j
// stores own/own pairs only once
// stores own/ghost pairs on both procs
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
if (j <= i) continue;
jtype = type[j];
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (which == 0) neighptr[n++] = j;
else if (minchange = domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;
else 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 (minchange) neighptr_inner[n_inner++] = 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 (minchange) neighptr_middle[n_middle++] = j;
else if (which > 0)
neighptr_middle[n_middle++] = j ^ (which << SBBITS);
}
}
}
}
ilist[i] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
npnt += n;
if (n > oneatom)
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
ilist_inner[i] = i;
firstneigh_inner[i] = neighptr_inner;
numneigh_inner[i] = n_inner;
npnt_inner += n_inner;
if (n_inner > oneatom)
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
if (respamiddle) {
ilist_middle[i] = i;
firstneigh_middle[i] = neighptr_middle;
numneigh_middle[i] = n_middle;
npnt_middle += n_middle;
if (n_middle > oneatom)
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
}
NEIGH_OMP_CLOSE;
list->inum = nlocal;
listinner->inum = nlocal;
if (respamiddle) listmiddle->inum = nlocal;
}
/* ----------------------------------------------------------------------
multiple respa lists
binned neighbor list construction with full Newton's 3rd law
each owned atom i checks its own bin and other bins in Newton stencil
every pair stored exactly once by some processor
------------------------------------------------------------------------- */
void Neighbor::respa_bin_newton_omp(NeighList *list)
{
// bin local & ghost atoms
bin_atoms();
const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
NEIGH_OMP_INIT;
NeighList *listinner = list->listinner;
if (nthreads > listinner->maxpage)
listinner->add_pages(nthreads - listinner->maxpage);
NeighList *listmiddle;
const int respamiddle = list->respamiddle;
if (respamiddle) {
listmiddle = list->listmiddle;
if (nthreads > listmiddle->maxpage)
listmiddle->add_pages(nthreads - listmiddle->maxpage);
}
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(list,listinner,listmiddle)
#endif
NEIGH_OMP_SETUP(nlocal);
int i,j,k,n,itype,jtype,ibin,n_inner,n_middle;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr,*neighptr_inner,*neighptr_middle;
// loop over each atom, storing neighbors
int **special = atom->special;
int **nspecial = atom->nspecial;
int *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
int molecular = atom->molecular;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
int nstencil = list->nstencil;
int *stencil = list->stencil;
int *ilist_inner = listinner->ilist;
int *numneigh_inner = listinner->numneigh;
int **firstneigh_inner = listinner->firstneigh;
int *ilist_middle,*numneigh_middle,**firstneigh_middle;
if (respamiddle) {
ilist_middle = listmiddle->ilist;
numneigh_middle = listmiddle->numneigh;
firstneigh_middle = listmiddle->firstneigh;
}
int npage = tid;
int npnt = 0;
int npage_inner = tid;
int npnt_inner = 0;
int npage_middle = tid;
int npnt_middle = 0;
int which = 0;
int minchange = 0;
for (i = ifrom; i < ito; i++) {
#if defined(_OPENMP)
#pragma omp critical
#endif
if (pgsize - npnt < oneatom) {
npnt = 0;
npage += nthreads;
if (npage == list->maxpage) list->add_pages(nthreads);
}
neighptr = &(list->pages[npage][npnt]);
n = 0;
#if defined(_OPENMP)
#pragma omp critical
#endif
if (pgsize - npnt_inner < oneatom) {
npnt_inner = 0;
npage_inner += nthreads;
if (npage_inner == listinner->maxpage) listinner->add_pages(nthreads);
}
neighptr_inner = &(listinner->pages[npage_inner][npnt_inner]);
n_inner = 0;
#if defined(_OPENMP)
#pragma omp critical
#endif
if (respamiddle) {
if (pgsize - npnt_middle < oneatom) {
npnt_middle = 0;
npage_middle += nthreads;
if (npage_middle == listmiddle->maxpage) listmiddle->add_pages(nthreads);
}
neighptr_middle = &(listmiddle->pages[npage_middle][npnt_middle]);
n_middle = 0;
}
itype = type[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
// 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
// if j is ghost, only store if j coords are "above and to the right" of i
for (j = bins[i]; j >= 0; j = bins[j]) {
if (j >= nlocal) {
if (x[j][2] < ztmp) continue;
if (x[j][2] == ztmp) {
if (x[j][1] < ytmp) continue;
if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
}
}
jtype = type[j];
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (which == 0) neighptr[n++] = j;
else if (minchange = domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;
else 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 (minchange) neighptr_inner[n_inner++] = 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 (minchange) neighptr_middle[n_middle++] = j;
else if (which > 0)
neighptr_middle[n_middle++] = j ^ (which << SBBITS);
}
}
}
// loop over all atoms in other bins in stencil, store every pair
ibin = coord2bin(x[i]);
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
jtype = type[j];
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (which == 0) neighptr[n++] = j;
else if (minchange = domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;
else 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 (minchange) neighptr_inner[n_inner++] = 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 (minchange) neighptr_middle[n_middle++] = j;
else if (which > 0)
neighptr_middle[n_middle++] = j ^ (which << SBBITS);
}
}
}
}
ilist[i] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
npnt += n;
if (n > oneatom)
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
ilist_inner[i] = i;
firstneigh_inner[i] = neighptr_inner;
numneigh_inner[i] = n_inner;
npnt_inner += n_inner;
if (n_inner > oneatom)
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
if (respamiddle) {
ilist_middle[i] = i;
firstneigh_middle[i] = neighptr_middle;
numneigh_middle[i] = n_middle;
npnt_middle += n_middle;
if (n_middle > oneatom)
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
}
NEIGH_OMP_CLOSE;
list->inum = nlocal;
listinner->inum = nlocal;
if (respamiddle) listmiddle->inum = nlocal;
}
/* ----------------------------------------------------------------------
multiple respa lists
binned neighbor list construction with Newton's 3rd law for triclinic
each owned atom i checks its own bin and other bins in triclinic stencil
every pair stored exactly once by some processor
------------------------------------------------------------------------- */
void Neighbor::respa_bin_newton_tri_omp(NeighList *list)
{
// bin local & ghost atoms
bin_atoms();
const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
NEIGH_OMP_INIT;
NeighList *listinner = list->listinner;
if (nthreads > listinner->maxpage)
listinner->add_pages(nthreads - listinner->maxpage);
NeighList *listmiddle;
const int respamiddle = list->respamiddle;
if (respamiddle) {
listmiddle = list->listmiddle;
if (nthreads > listmiddle->maxpage)
listmiddle->add_pages(nthreads - listmiddle->maxpage);
}
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(list,listinner,listmiddle)
#endif
NEIGH_OMP_SETUP(nlocal);
int i,j,k,n,itype,jtype,ibin,n_inner,n_middle;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr,*neighptr_inner,*neighptr_middle;
// loop over each atom, storing neighbors
int **special = atom->special;
int **nspecial = atom->nspecial;
int *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
int molecular = atom->molecular;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
int nstencil = list->nstencil;
int *stencil = list->stencil;
int *ilist_inner = listinner->ilist;
int *numneigh_inner = listinner->numneigh;
int **firstneigh_inner = listinner->firstneigh;
int *ilist_middle,*numneigh_middle,**firstneigh_middle;
if (respamiddle) {
ilist_middle = listmiddle->ilist;
numneigh_middle = listmiddle->numneigh;
firstneigh_middle = listmiddle->firstneigh;
}
int npage = tid;
int npnt = 0;
int npage_inner = tid;
int npnt_inner = 0;
int npage_middle = tid;
int npnt_middle = 0;
int which = 0;
int minchange = 0;
for (i = ifrom; i < ito; i++) {
#if defined(_OPENMP)
#pragma omp critical
#endif
if (pgsize - npnt < oneatom) {
npnt = 0;
npage += nthreads;
if (npage == list->maxpage) list->add_pages(nthreads);
}
neighptr = &(list->pages[npage][npnt]);
n = 0;
#if defined(_OPENMP)
#pragma omp critical
#endif
if (pgsize - npnt_inner < oneatom) {
npnt_inner = 0;
npage_inner += nthreads;
if (npage_inner == listinner->maxpage) listinner->add_pages(nthreads);
}
neighptr_inner = &(listinner->pages[npage_inner][npnt_inner]);
n_inner = 0;
#if defined(_OPENMP)
#pragma omp critical
#endif
if (respamiddle) {
if (pgsize - npnt_middle < oneatom) {
npnt_middle = 0;
npage_middle += nthreads;
if (npage_middle == listmiddle->maxpage) listmiddle->add_pages(nthreads);
}
neighptr_middle = &(listmiddle->pages[npage_middle][npnt_middle]);
n_middle = 0;
}
itype = type[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
// loop over all atoms in bins in stencil
// pairs for atoms j "below" i are excluded
// below = lower z or (equal z and lower y) or (equal zy and lower x)
// (equal zyx and j <= i)
// latter excludes self-self interaction but allows superposed atoms
ibin = coord2bin(x[i]);
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
if (x[j][2] < ztmp) continue;
if (x[j][2] == ztmp) {
if (x[j][1] < ytmp) continue;
if (x[j][1] == ytmp) {
if (x[j][0] < xtmp) continue;
if (x[j][0] == xtmp && j <= i) continue;
}
}
jtype = type[j];
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (which == 0) neighptr[n++] = j;
else if (minchange = domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;
else 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 (minchange) neighptr_inner[n_inner++] = 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 (minchange) neighptr_middle[n_middle++] = j;
else if (which > 0)
neighptr_middle[n_middle++] = j ^ (which << SBBITS);
}
}
}
}
ilist[i] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
npnt += n;
if (n > oneatom)
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
ilist_inner[i] = i;
firstneigh_inner[i] = neighptr_inner;
numneigh_inner[i] = n_inner;
npnt_inner += n_inner;
if (n_inner > oneatom)
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
if (respamiddle) {
ilist_middle[i] = i;
firstneigh_middle[i] = neighptr_middle;
numneigh_middle[i] = n_middle;
npnt_middle += n_middle;
if (n_middle > oneatom)
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
}
NEIGH_OMP_CLOSE;
list->inum = nlocal;
listinner->inum = nlocal;
if (respamiddle) listmiddle->inum = nlocal;
}
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