148 lines
4.5 KiB
C++
148 lines
4.5 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_bin_newton_tri.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 "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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NPairHalfSizeBinNewtonTri::NPairHalfSizeBinNewtonTri(LAMMPS *lmp) :
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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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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 NPairHalfSizeBinNewtonTri::build(NeighList *list)
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{
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int i,j,jh,k,n,ibin,which,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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double radi,radsum,cutsq;
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int *neighptr;
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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 *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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if (includegroup) nlocal = atom->nfirst;
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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) moltemplate = 1;
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else moltemplate = 0;
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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 = 1 << HISTBITS;
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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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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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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 in bins in stencil
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// 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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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 (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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if (exclude && exclusion(i,j,type[i],type[j],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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cutsq = (radsum+skin) * (radsum+skin);
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if (rsq <= cutsq) {
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jh = j;
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if (history && rsq < radsum*radsum)
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jh = jh ^ mask_history;
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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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which = find_special(onemols[imol]->special[iatom],
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onemols[imol]->nspecial[iatom],
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tag[j]-tagprev);
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else which = 0;
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if (which == 0) neighptr[n++] = jh;
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else if (domain->minimum_image_check(delx,dely,delz))
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neighptr[n++] = jh;
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else if (which > 0) neighptr[n++] = jh ^ (which << SBBITS);
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} else neighptr[n++] = jh;
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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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