93 lines
2.6 KiB
C++
93 lines
2.6 KiB
C++
/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://www.lammps.org/, Sandia National Laboratories
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LAMMPS development team: developers@lammps.org
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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 "npair_full_bin_atomonly.h"
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#include "atom.h"
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#include "error.h"
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#include "my_page.h"
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#include "neigh_list.h"
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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NPairFullBinAtomonly::NPairFullBinAtomonly(LAMMPS *lmp) : NPair(lmp) {}
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/* ----------------------------------------------------------------------
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binned neighbor list construction for all neighbors
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every neighbor pair appears in list of both atoms i and j
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------------------------------------------------------------------------- */
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void NPairFullBinAtomonly::build(NeighList *list)
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{
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int i, j, k, n, itype, jtype, ibin;
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double xtmp, ytmp, ztmp, delx, dely, delz, rsq;
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int *neighptr;
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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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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 *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 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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// loop over all atoms in surrounding bins in stencil including self
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// skip i = j
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ibin = atom2bin[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 (i == j) 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]) neighptr[n++] = j;
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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()) 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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list->gnum = 0;
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}
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