132 lines
3.7 KiB
C++
132 lines
3.7 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_nsq.h"
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#include "atom.h"
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#include "atom_vec.h"
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#include "domain.h"
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#include "error.h"
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#include "group.h"
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#include "molecule.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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NPairFullNsq::NPairFullNsq(LAMMPS *lmp) : NPair(lmp) {}
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/* ----------------------------------------------------------------------
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N^2 search 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 NPairFullNsq::build(NeighList *list)
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{
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int i, j, n, itype, jtype, which, bitmask, imol, iatom, moltemplate;
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tagint tagprev;
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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 *tag = atom->tag;
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tagint *molecule = atom->molecule;
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tagint **special = atom->special;
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int **nspecial = atom->nspecial;
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int nlocal = atom->nlocal;
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int nall = nlocal + atom->nghost;
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if (includegroup) {
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nlocal = atom->nfirst;
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bitmask = group->bitmask[includegroup];
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}
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int *molindex = atom->molindex;
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int *molatom = atom->molatom;
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Molecule **onemols = atom->avec->onemols;
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if (molecular == Atom::TEMPLATE)
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moltemplate = 1;
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else
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moltemplate = 0;
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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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if (moltemplate) {
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imol = molindex[i];
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iatom = molatom[i];
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tagprev = tag[i] - iatom - 1;
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}
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// loop over all atoms, owned and ghost
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// skip i = j
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for (j = 0; j < nall; j++) {
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if (includegroup && !(mask[j] & bitmask)) continue;
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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]) {
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if (molecular != Atom::ATOMIC) {
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if (!moltemplate) {
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which = find_special(special[i], nspecial[i], tag[j]);
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} else if (imol >= 0) {
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const auto mol = onemols[imol];
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which = find_special(mol->special[iatom], mol->nspecial[iatom], tag[j] - tagprev);
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} else {
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which = 0;
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}
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if (which == 0)
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neighptr[n++] = j;
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else if (domain->minimum_image_check(delx, dely, delz))
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neighptr[n++] = j;
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else if (which > 0)
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neighptr[n++] = j ^ (which << SBBITS);
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} else
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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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