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npair_half_bin_newtoff_ghost.cpp
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Mon, Oct 14, 08:11

npair_half_bin_newtoff_ghost.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_half_bin_newtoff_ghost.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "atom.h"
#include "atom_vec.h"
#include "molecule.h"
#include "domain.h"
#include "my_page.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
NPairHalfBinNewtoffGhost::NPairHalfBinNewtoffGhost(LAMMPS *lmp) : NPair(lmp) {}
/* ----------------------------------------------------------------------
binned neighbor list construction with partial Newton's 3rd law
include neighbors of ghost atoms, but no "special neighbors" for ghosts
owned and ghost atoms check own bin and other bins in stencil
pair stored once if i,j are both owned and i < j
pair stored by me if i owned and j ghost (also stored by proc owning j)
pair stored once if i,j are both ghost and i < j
------------------------------------------------------------------------- */
void NPairHalfBinNewtoffGhost::build(NeighList *list)
{
int i,j,k,n,itype,jtype,ibin,which,imol,iatom,moltemplate;
tagint tagprev;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int xbin,ybin,zbin,xbin2,ybin2,zbin2;
int *neighptr;
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 nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
if (includegroup) nlocal = atom->nfirst;
int *molindex = atom->molindex;
int *molatom = atom->molatom;
Molecule **onemols = atom->avec->onemols;
if (molecular == 2) moltemplate = 1;
else moltemplate = 0;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
MyPage<int> *ipage = list->ipage;
int inum = 0;
ipage->reset();
for (i = 0; i < nall; i++) {
n = 0;
neighptr = ipage->vget();
itype = type[i];
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
// only store pair if i < j
// stores own/own pairs only once
// stores own/ghost pairs with owned atom only, on both procs
// stores ghost/ghost pairs only once
// no molecular test when i = ghost atom
if (i < nlocal) {
ibin = coord2bin(x[i]);
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) {
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;
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
}
}
}
} else {
ibin = coord2bin(x[i],xbin,ybin,zbin);
for (k = 0; k < nstencil; k++) {
xbin2 = xbin + stencilxyz[k][0];
ybin2 = ybin + stencilxyz[k][1];
zbin2 = zbin + stencilxyz[k][2];
if (xbin2 < 0 || xbin2 >= mbinx ||
ybin2 < 0 || ybin2 >= mbiny ||
zbin2 < 0 || zbin2 >= mbinz) continue;
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 <= cutneighghostsq[itype][jtype]) neighptr[n++] = j;
}
}
}
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
ipage->vgot(n);
if (ipage->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
list->inum = atom->nlocal;
list->gnum = inum - atom->nlocal;
}

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