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npair_full_bin_atomonly_omp.cpp
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Fri, Nov 8, 02:57

npair_full_bin_atomonly_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 "npair_full_bin_atomonly_omp.h"
#include "npair_omp.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "atom.h"
#include "atom_vec.h"
#include "domain.h"
#include "my_page.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace NeighConst;
/* ---------------------------------------------------------------------- */
NPairFullBinAtomonlyOmp::NPairFullBinAtomonlyOmp(LAMMPS *lmp) : NPair(lmp) {}
/* ----------------------------------------------------------------------
binned neighbor list construction for all neighbors
every neighbor pair appears in list of both atoms i and j
------------------------------------------------------------------------- */
void NPairFullBinAtomonlyOmp::build(NeighList *list)
{
const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
NPAIR_OMP_INIT;
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(list)
#endif
NPAIR_OMP_SETUP(nlocal);
int i,j,k,n,itype,jtype,ibin;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr;
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
tagint *molecule = atom->molecule;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
// each thread has its own page allocator
MyPage<int> &ipage = list->ipage[tid];
ipage.reset();
// loop over owned atoms, storing neighbors
for (i = ifrom; i < ito; i++) {
n = 0;
neighptr = ipage.vget();
itype = type[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
// loop over all atoms in surrounding bins in stencil including self
// skip i = j
ibin = atom2bin[i];
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
if (i == j) 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]) neighptr[n++] = j;
}
}
ilist[i] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
ipage.vgot(n);
if (ipage.status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
NPAIR_OMP_CLOSE;
list->inum = nlocal;
list->gnum = 0;
}

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