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npair_half_size_bin_newtoff_omp.cpp
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Wed, Jul 31, 18:23

npair_half_size_bin_newtoff_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 <string.h>
#include "npair_half_size_bin_newtoff_omp.h"
#include "npair_omp.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "atom.h"
#include "atom_vec.h"
#include "molecule.h"
#include "domain.h"
#include "fix_shear_history.h"
#include "my_page.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
NPairHalfSizeBinNewtoffOmp::NPairHalfSizeBinNewtoffOmp(LAMMPS *lmp) :
NPair(lmp) {}
/* ----------------------------------------------------------------------
size particles
binned neighbor list construction with partial Newton's 3rd law
shear history must be accounted for when a neighbor pair is added
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 NPairHalfSizeBinNewtoffOmp::build(NeighList *list)
{
const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
FixShearHistory * const fix_history = list->fix_history;
NeighList * listgranhistory = list->listgranhistory;
NPAIR_OMP_INIT;
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(list,listgranhistory)
#endif
NPAIR_OMP_SETUP(nlocal);
int i,j,k,m,n,nn,ibin,dnum,dnumbytes;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
double radi,radsum,cutsq;
int *neighptr,*touchptr;
double *shearptr;
MyPage<int> *ipage_touch;
MyPage<double> *dpage_shear;
int *npartner;
tagint **partner;
double **shearpartner;
int **firsttouch;
double **firstshear;
// loop over each atom, storing neighbors
double **x = atom->x;
double *radius = atom->radius;
tagint *tag = atom->tag;
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();
if (fix_history) {
npartner = fix_history->npartner;
partner = fix_history->partner;
shearpartner = fix_history->shearpartner;
firsttouch = listgranhistory->firstneigh;
firstshear = listgranhistory->firstdouble;
ipage_touch = listgranhistory->ipage+tid;
dpage_shear = listgranhistory->dpage+tid;
dnum = listgranhistory->dnum;
dnumbytes = dnum * sizeof(double);
ipage_touch->reset();
dpage_shear->reset();
}
for (i = ifrom; i < ito; i++) {
n = 0;
neighptr = ipage.vget();
if (fix_history) {
nn = 0;
touchptr = ipage_touch->vget();
shearptr = dpage_shear->vget();
}
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
radi = radius[i];
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;
if (exclude && exclusion(i,j,type[i],type[j],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;
radsum = radi + radius[j];
cutsq = (radsum+skin) * (radsum+skin);
if (rsq <= cutsq) {
neighptr[n] = j;
if (fix_history) {
if (rsq < radsum*radsum) {
for (m = 0; m < npartner[i]; m++)
if (partner[i][m] == tag[j]) break;
if (m < npartner[i]) {
touchptr[n] = 1;
memcpy(&shearptr[nn],&shearpartner[i][dnum*m],dnumbytes);
nn += dnum;
} else {
touchptr[n] = 0;
memcpy(&shearptr[nn],zeroes,dnumbytes);
nn += dnum;
}
} else {
touchptr[n] = 0;
memcpy(&shearptr[nn],zeroes,dnumbytes);
nn += dnum;
}
}
n++;
}
}
}
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");
if (fix_history) {
firsttouch[i] = touchptr;
firstshear[i] = shearptr;
ipage_touch->vgot(n);
dpage_shear->vgot(nn);
}
}
NPAIR_OMP_CLOSE;
list->inum = nlocal;
}

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