forked from lijiext/lammps
104 lines
2.9 KiB
C++
104 lines
2.9 KiB
C++
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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 "npair_skip.h"
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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 "atom_vec.h"
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#include "molecule.h"
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#include "domain.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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NPairSkip::NPairSkip(LAMMPS *lmp) : NPair(lmp) {}
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/* ----------------------------------------------------------------------
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build skip list for subset of types from parent list
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iskip and ijskip flag which atom types and type pairs to skip
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this is for half and full lists
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if ghost, also store neighbors of ghost atoms & set inum,gnum correctly
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------------------------------------------------------------------------- */
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void NPairSkip::build(NeighList *list)
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{
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int i,j,ii,jj,n,itype,jnum,joriginal;
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int *neighptr,*jlist;
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int *type = atom->type;
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int nlocal = atom->nlocal;
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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 *ilist_skip = list->listskip->ilist;
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int *numneigh_skip = list->listskip->numneigh;
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int **firstneigh_skip = list->listskip->firstneigh;
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int num_skip = list->listskip->inum;
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if (list->ghost) num_skip += list->listskip->gnum;
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int *iskip = list->iskip;
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int **ijskip = list->ijskip;
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int inum = 0;
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ipage->reset();
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// loop over atoms in other list
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// skip I atom entirely if iskip is set for type[I]
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// skip I,J pair if ijskip is set for type[I],type[J]
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for (ii = 0; ii < num_skip; ii++) {
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i = ilist_skip[ii];
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itype = type[i];
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if (iskip[itype]) continue;
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n = 0;
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neighptr = ipage->vget();
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// loop over parent non-skip list
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jlist = firstneigh_skip[i];
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jnum = numneigh_skip[i];
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for (jj = 0; jj < jnum; jj++) {
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joriginal = jlist[jj];
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j = joriginal & NEIGHMASK;
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if (ijskip[itype][type[j]]) continue;
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neighptr[n++] = joriginal;
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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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if (list->ghost) {
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int num = 0;
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for (i = 0; i < inum; i++)
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if (ilist[i] < nlocal) num++;
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else break;
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list->inum = num;
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list->gnum = inum - num;
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}
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}
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