141 lines
4.4 KiB
C++
141 lines
4.4 KiB
C++
// clang-format off
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/* ----------------------------------------------------------------------
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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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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_half_size_multi_newton_tri.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 "neighbor.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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NPairHalfSizeMultiNewtonTri::NPairHalfSizeMultiNewtonTri(LAMMPS *lmp) : NPair(lmp) {}
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/* ----------------------------------------------------------------------
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size particles
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binned neighbor list construction with Newton's 3rd law for triclinic
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multi stencil is icollection-jcollection dependent
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each owned atom i checks its own bin and other bins in triclinic stencil
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every pair stored exactly once by some processor
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------------------------------------------------------------------------- */
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void NPairHalfSizeMultiNewtonTri::build(NeighList *list)
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{
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int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,ns,js;
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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 *collection = neighbor->collection;
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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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icollection = collection[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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ibin = atom2bin[i];
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// loop through stencils for all collections
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for (jcollection = 0; jcollection < ncollections; jcollection++) {
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// if same collection use own bin
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if (icollection == jcollection) jbin = ibin;
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else jbin = coord2bin(x[i], jcollection);
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// loop over all atoms in bins in stencil
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// stencil is empty if i larger than j
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// stencil is half if i same size as j
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// stencil is full if i smaller than j
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// if half: pairs for atoms j "below" i are excluded
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// below = lower z or (equal z and lower y) or (equal zy and lower x)
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// (equal zyx and j <= i)
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// latter excludes self-self interaction but allows superposed atoms
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s = stencil_multi[icollection][jcollection];
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ns = nstencil_multi[icollection][jcollection];
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for (k = 0; k < ns; k++) {
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js = binhead_multi[jcollection][jbin + s[k]];
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for (j = js; j >= 0; j = bins[j]) {
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// if same size (same collection), use half stencil
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if (cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){
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if (x[j][2] < ztmp) continue;
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if (x[j][2] == ztmp) {
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if (x[j][1] < ytmp) continue;
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if (x[j][1] == ytmp) {
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if (x[j][0] < xtmp) continue;
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if (x[j][0] == xtmp && j <= i) continue;
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}
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}
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}
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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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