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multi-thread one more neighbor list build type

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This commit is contained in:
Axel Kohlmeyer
2011-10-02 14:46:12 -04:00
parent 0023fb24ad
commit afe2a11219
1 changed files with 55 additions and 34 deletions
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89
src/neigh_half_nsq.cpp
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@ -14,9 +14,14 @@
#include "neighbor.h"
#include "neigh_list.h"
#include "atom.h"
#include "comm.h"
#include "group.h"
#include "error.h"
#if defined(_OPENMP)
#include <omp.h>
#endif
using namespace LAMMPS_NS;
/* ----------------------------------------------------------------------
@ -27,7 +32,17 @@ using namespace LAMMPS_NS;
void Neighbor::half_nsq_no_newton(NeighList *list)
{
int i,j,n,itype,jtype,which,bitmask;
const int nthreads = comm->nthreads;
const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
const int bitmask = (includegroup) ? group->bitmask[includegroup] : 0;
NEIGH_OMP_INIT;
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(list)
#endif
NEIGH_OMP_SETUP(nlocal);
int i,j,n,itype,jtype,which;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr;
@ -41,32 +56,30 @@ void Neighbor::half_nsq_no_newton(NeighList *list)
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int nall = atom->nlocal + atom->nghost;
int molecular = atom->molecular;
if (includegroup) {
nlocal = atom->nfirst;
bitmask = group->bitmask[includegroup];
}
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
int **pages = list->pages;
int inum = 0;
int npage = 0;
int npage = tid;
int npnt = 0;
for (i = 0; i < nlocal; i++) {
for (i = ifrom; i < ito; i++) {
if (pgsize - npnt < oneatom) {
npnt = 0;
npage++;
if (npage == list->maxpage) pages = list->add_pages();
npage += nthreads;
// only one thread at a time may check whether we
// need new neighbor list pages and then add to them.
#if defined(_OPENMP)
#pragma omp critical
#endif
if (npage >= list->maxpage) list->add_pages(nthreads);
}
neighptr = &pages[npage][npnt];
neighptr = &(list->pages[npage][npnt]);
n = 0;
itype = type[i];
@ -94,15 +107,15 @@ void Neighbor::half_nsq_no_newton(NeighList *list)
}
}
ilist[inum++] = i;
ilist[i] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
npnt += n;
if (n > oneatom || npnt >= pgsize)
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one or page");
}
list->inum = inum;
NEIGH_OMP_CLOSE;
list->inum = nlocal;
}
/* ----------------------------------------------------------------------
@ -113,7 +126,17 @@ void Neighbor::half_nsq_no_newton(NeighList *list)
void Neighbor::half_nsq_newton(NeighList *list)
{
int i,j,n,itype,jtype,itag,jtag,which,bitmask;
const int nthreads = comm->nthreads;
const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
const int bitmask = (includegroup) ? group->bitmask[includegroup] : 0;
NEIGH_OMP_INIT;
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(list)
#endif
NEIGH_OMP_SETUP(nlocal);
int i,j,n,itype,jtype,itag,jtag,which;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr;
@ -127,32 +150,30 @@ void Neighbor::half_nsq_newton(NeighList *list)
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int nall = atom->nlocal + atom->nghost;
int molecular = atom->molecular;
if (includegroup) {
nlocal = atom->nfirst;
bitmask = group->bitmask[includegroup];
}
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
int **pages = list->pages;
int inum = 0;
int npage = 0;
int npage = tid;
int npnt = 0;
for (i = 0; i < nlocal; i++) {
for (i = ifrom; i < ito; i++) {
if (pgsize - npnt < oneatom) {
npnt = 0;
npage++;
if (npage == list->maxpage) pages = list->add_pages();
npage += nthreads;
// only one thread at a time may check whether we
// need new neighbor list pages and then add to them.
#if defined(_OPENMP)
#pragma omp critical
#endif
if (npage >= list->maxpage) list->add_pages(nthreads);
}
neighptr = &pages[npage][npnt];
neighptr = &(list->pages[npage][npnt]);
n = 0;
itag = tag[i];
@ -198,13 +219,13 @@ void Neighbor::half_nsq_newton(NeighList *list)
}
}
ilist[inum++] = i;
ilist[i] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
npnt += n;
if (n > oneatom || npnt >= pgsize)
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one or page");
}
list->inum = inum;
NEIGH_OMP_CLOSE;
list->inum = nlocal;
}