127 lines
3.7 KiB
C++
127 lines
3.7 KiB
C++
/* ----------------------------------------------------------------------
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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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es 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 <string.h>
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#include "npair_half_size_multi2_newtoff.h"
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#include "neigh_list.h"
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#include "atom.h"
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#include "atom_vec.h"
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#include "my_page.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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NPairHalfSizeMulti2Newtoff::NPairHalfSizeMulti2Newtoff(LAMMPS *lmp) : NPair(lmp) {}
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/* ----------------------------------------------------------------------
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REWRITE
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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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multi-type stencil is itype dependent and is distance checked
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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 NPairHalfSizeMulti2Newtoff::build(NeighList *list)
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{
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int i,j,k,n,itype,jtype,ktype,ibin,kbin,ns;
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double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
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double radi,radsum,cutdistsq;
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int *neighptr,*s;
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int js;
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double **x = atom->x;
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double *radius = atom->radius;
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int *type = atom->type;
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int *mask = atom->mask;
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tagint *molecule = atom->molecule;
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int nlocal = atom->nlocal;
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if (includegroup) nlocal = atom->nfirst;
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int history = list->history;
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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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MyPage<int> *ipage = list->ipage;
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int mask_history = 3 << SBBITS;
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int inum = 0;
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ipage->reset();
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for (i = 0; i < nlocal; i++) {
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n = 0;
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neighptr = ipage->vget();
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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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radi = radius[i];
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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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// skip if i,j neighbor cutoff is less than bin distance
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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 = atom2bin_multi2[itype][i];
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for (ktype = 1; ktype <= atom->ntypes; ktype++) {
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if (itype == ktype) {
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kbin = ibin;
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} else {
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// Locate i in ktype bin
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kbin = coord2bin(x[i], ktype);
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}
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s = stencil_multi2[itype][ktype];
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ns = nstencil_multi2[itype][ktype];
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for (k = 0; k < ns; k++) {
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js = binhead_multi2[ktype][kbin + s[k]];
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for (j = js; j >=0; j = bins_multi2[ktype][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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radsum = radi + radius[j];
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cutdistsq = (radsum+skin) * (radsum+skin);
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if (rsq <= cutdistsq) {
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if (history && rsq < radsum*radsum)
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neighptr[n++] = j ^ mask_history;
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else
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neighptr[n++] = j;
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}
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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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ipage->vgot(n);
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if (ipage->status())
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error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
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}
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list->inum = inum;
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}
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