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sjplimp
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "neighbor.h"
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#include "neigh_list.h"
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#include "atom.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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/* ----------------------------------------------------------------------
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binned neighbor list construction with partial Newton's 3rd law
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each owned atom i checks own bin and other bins in stencil
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pair stored once if i,j are both owned and i < j
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pair stored by me if j is ghost (also stored by proc owning j)
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------------------------------------------------------------------------- */
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void Neighbor::half_bin_no_newton(NeighList *list)
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{
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int i,j,k,n,itype,jtype,ibin,which;
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double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
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int *neighptr;
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// bin local & ghost atoms
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bin_atoms();
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// loop over each atom, storing neighbors
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double **x = atom->x;
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int *type = atom->type;
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int *mask = atom->mask;
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int *molecule = atom->molecule;
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int nlocal = atom->nlocal;
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int nall = atom->nlocal + atom->nghost;
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int molecular = atom->molecular;
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int *ilist = list->ilist;
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int *numneigh = list->numneigh;
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int **firstneigh = list->firstneigh;
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int **pages = list->pages;
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int nstencil = list->nstencil;
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int *stencil = list->stencil;
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int inum = 0;
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int npage = 0;
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int npnt = 0;
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for (i = 0; i < nlocal; i++) {
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if (pgsize - npnt < oneatom) {
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npnt = 0;
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npage++;
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if (npage == list->maxpage) pages = list->add_pages();
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}
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neighptr = &pages[npage][npnt];
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n = 0;
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itype = type[i];
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xtmp = x[i][0];
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ytmp = x[i][1];
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ztmp = x[i][2];
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// loop over all atoms in other bins in stencil including self
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// only store pair if i < j
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// stores own/own pairs only once
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// stores own/ghost pairs on both procs
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ibin = coord2bin(x[i]);
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for (k = 0; k < nstencil; k++) {
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for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
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if (j <= i) continue;
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jtype = type[j];
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if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
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delx = xtmp - x[j][0];
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dely = ytmp - x[j][1];
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delz = ztmp - x[j][2];
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rsq = delx*delx + dely*dely + delz*delz;
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if (rsq <= cutneighsq[itype][jtype]) {
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if (molecular) which = find_special(i,j);
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else which = 0;
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if (which == 0) neighptr[n++] = j;
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else if (which > 0) neighptr[n++] = which*nall + j;
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}
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}
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}
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ilist[inum] = i;
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firstneigh[i] = neighptr;
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numneigh[i] = n;
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inum++;
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npnt += n;
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if (npnt >= pgsize)
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error->one("Neighbor list overflow, boost neigh_modify one or page");
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}
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list->inum = inum;
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}
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/* ----------------------------------------------------------------------
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binned neighbor list construction with full Newton's 3rd law
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each owned atom i checks its own bin and other bins in Newton stencil
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every pair stored exactly once by some processor
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------------------------------------------------------------------------- */
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void Neighbor::half_bin_newton(NeighList *list)
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{
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int i,j,k,n,itype,jtype,ibin,which;
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double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
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int *neighptr;
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// bin local & ghost atoms
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bin_atoms();
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// loop over each atom, storing neighbors
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double **x = atom->x;
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int *type = atom->type;
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int *mask = atom->mask;
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int *molecule = atom->molecule;
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int nlocal = atom->nlocal;
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int nall = atom->nlocal + atom->nghost;
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int molecular = atom->molecular;
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int *ilist = list->ilist;
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int *numneigh = list->numneigh;
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int **firstneigh = list->firstneigh;
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int **pages = list->pages;
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int skip = list->skip;
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int nstencil = list->nstencil;
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int *stencil = list->stencil;
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int inum = 0;
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int npage = 0;
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int npnt = 0;
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for (i = 0; i < nlocal; i++) {
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if (pgsize - npnt < oneatom) {
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npnt = 0;
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npage++;
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if (npage == list->maxpage) pages = list->add_pages();
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}
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neighptr = &pages[npage][npnt];
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n = 0;
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itype = type[i];
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xtmp = x[i][0];
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ytmp = x[i][1];
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ztmp = x[i][2];
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// loop over rest of atoms in i's bin, ghosts are at end of linked list
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// if j is owned atom, store it, since j is beyond i in linked list
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// if j is ghost, only store if j coords are "above and to the right" of i
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for (j = bins[i]; j >= 0; j = bins[j]) {
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if (j >= nlocal) {
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if (x[j][2] < ztmp) continue;
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if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
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if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
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}
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jtype = type[j];
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if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
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delx = xtmp - x[j][0];
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dely = ytmp - x[j][1];
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delz = ztmp - x[j][2];
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rsq = delx*delx + dely*dely + delz*delz;
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if (rsq <= cutneighsq[itype][jtype]) {
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if (molecular) which = find_special(i,j);
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else which = 0;
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if (which == 0) neighptr[n++] = j;
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else if (which > 0) neighptr[n++] = which*nall + j;
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}
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}
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// loop over all atoms in other bins in stencil, store every pair
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ibin = coord2bin(x[i]);
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for (k = 0; k < nstencil; k++) {
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for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
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jtype = type[j];
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if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
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delx = xtmp - x[j][0];
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dely = ytmp - x[j][1];
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delz = ztmp - x[j][2];
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rsq = delx*delx + dely*dely + delz*delz;
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if (rsq <= cutneighsq[itype][jtype]) {
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if (molecular) which = find_special(i,j);
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else which = 0;
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if (which == 0) neighptr[n++] = j;
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else if (which > 0) neighptr[n++] = which*nall + j;
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}
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}
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}
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ilist[inum] = i;
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firstneigh[i] = neighptr;
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numneigh[i] = n;
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inum++;
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npnt += n;
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if (npnt >= pgsize)
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error->one("Neighbor list overflow, boost neigh_modify one or page");
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}
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list->inum = inum;
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}
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/* ----------------------------------------------------------------------
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binned neighbor list construction with Newton's 3rd law for triclinic
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each owned atom i checks its own bin and other bins in triclinic stencil
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every pair stored exactly once by some processor
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------------------------------------------------------------------------- */
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void Neighbor::half_bin_newton_tri(NeighList *list)
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{
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int i,j,k,n,itype,jtype,ibin,which;
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double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
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int *neighptr;
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// bin local & ghost atoms
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bin_atoms();
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// loop over each atom, storing neighbors
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double **x = atom->x;
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int *type = atom->type;
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int *mask = atom->mask;
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int *molecule = atom->molecule;
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int nlocal = atom->nlocal;
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int nall = atom->nlocal + atom->nghost;
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int molecular = atom->molecular;
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int *ilist = list->ilist;
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int *numneigh = list->numneigh;
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int **firstneigh = list->firstneigh;
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int **pages = list->pages;
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int nstencil = list->nstencil;
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int *stencil = list->stencil;
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int inum = 0;
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int npage = 0;
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int npnt = 0;
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for (i = 0; i < nlocal; i++) {
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if (pgsize - npnt < oneatom) {
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npnt = 0;
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npage++;
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if (npage == list->maxpage) pages = list->add_pages();
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}
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neighptr = &pages[npage][npnt];
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n = 0;
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itype = type[i];
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xtmp = x[i][0];
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ytmp = x[i][1];
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ztmp = x[i][2];
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// loop over all atoms in bins in stencil
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// pairs for atoms j "below" i are excluded
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// below = lower z or (equal z and lower y) or (equal zy and <= x)
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// this excludes self-self interaction
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ibin = coord2bin(x[i]);
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for (k = 0; k < nstencil; k++) {
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for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
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if (x[j][2] < ztmp) continue;
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if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
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if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] <= xtmp) continue;
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jtype = type[j];
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if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
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delx = xtmp - x[j][0];
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dely = ytmp - x[j][1];
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delz = ztmp - x[j][2];
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rsq = delx*delx + dely*dely + delz*delz;
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if (rsq <= cutneighsq[itype][jtype]) {
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if (molecular) which = find_special(i,j);
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else which = 0;
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if (which == 0) neighptr[n++] = j;
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else if (which > 0) neighptr[n++] = which*nall + j;
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}
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}
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}
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ilist[inum] = i;
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firstneigh[i] = neighptr;
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numneigh[i] = n;
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inum++;
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npnt += n;
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if (npnt >= pgsize)
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error->one("Neighbor list overflow, boost neigh_modify one or page");
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}
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list->inum = inum;
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}
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