102 lines
3.0 KiB
C++
102 lines
3.0 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_halffull_newtoff_trim.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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NPairHalffullNewtoffTrim::NPairHalffullNewtoffTrim(LAMMPS *lmp) : NPair(lmp) {}
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/* ----------------------------------------------------------------------
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build half list from full list
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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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works if full list is a skip list
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works for owned (non-ghost) list, also for ghost list
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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 NPairHalffullNewtoffTrim::build(NeighList *list)
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{
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int i, j, ii, jj, n, jnum, joriginal;
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int *neighptr, *jlist;
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double xtmp, ytmp, ztmp;
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double delx, dely, delz, rsq;
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double **x = atom->x;
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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_full = list->listfull->ilist;
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int *numneigh_full = list->listfull->numneigh;
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int **firstneigh_full = list->listfull->firstneigh;
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int inum_full = list->listfull->inum;
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if (list->ghost) inum_full += list->listfull->gnum;
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int inum = 0;
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ipage->reset();
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double cutsq_custom = cutoff_custom * cutoff_custom;
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// loop over atoms in full list
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for (ii = 0; ii < inum_full; ii++) {
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n = 0;
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neighptr = ipage->vget();
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// loop over parent full list
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i = ilist_full[ii];
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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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jlist = firstneigh_full[i];
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jnum = numneigh_full[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 (j > i) {
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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 > cutsq_custom) continue;
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neighptr[n++] = joriginal;
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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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if (list->ghost) list->gnum = list->listfull->gnum;
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}
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