261 lines
8.3 KiB
C++
261 lines
8.3 KiB
C++
/* ----------------------------------------------------------------------
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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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/* ----------------------------------------------------------------------
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Contributing authors:
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James Larentzos and Timothy I. Mattox (Engility Corporation)
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------------------------------------------------------------------------- */
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#include "npair_half_bin_newton_ssa.h"
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#include "neighbor.h"
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#include "nstencil_ssa.h"
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#include "nbin_ssa.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 "group.h"
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#include "memory.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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// allocate space for static class variable
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// prototype for non-class function
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static int *ssaAIRptr;
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static int cmp_ssaAIR(const void *, const void *);
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/* ---------------------------------------------------------------------- */
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NPairHalfBinNewtonSSA::NPairHalfBinNewtonSSA(LAMMPS *lmp) : NPair(lmp) {}
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/* ----------------------------------------------------------------------
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binned neighbor list construction with full Newton's 3rd law
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for use by Shardlow Spliting Algorithm
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each owned atom i checks its own bin and other bins in Newton stencil
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every pair stored exactly once by some processor
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------------------------------------------------------------------------- */
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void NPairHalfBinNewtonSSA::build(NeighList *list)
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{
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int i,j,k,n,itype,jtype,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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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) nlocal = atom->nfirst;
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int *ssaAIR = atom->ssaAIR;
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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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int molecular = atom->molecular;
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if (molecular == 2) moltemplate = 1;
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else 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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NStencilSSA *ns_ssa = dynamic_cast<NStencilSSA*>(ns);
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if (!ns_ssa) error->one(FLERR, "NStencil wasn't a NStencilSSA object");
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int nstencil_half = ns_ssa->nstencil_half;
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int nstencil_full = ns_ssa->nstencil;
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NBinSSA *nb_ssa = dynamic_cast<NBinSSA*>(nb);
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if (!nb_ssa) error->one(FLERR, "NBin wasn't a NBinSSA object");
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int *bins_ssa = nb_ssa->bins_ssa;
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int *binhead_ssa = nb_ssa->binhead_ssa;
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int *gbinhead_ssa = nb_ssa->gbinhead_ssa;
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int inum = 0;
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ipage->reset();
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// loop over owned atoms, storing half of the neighbors
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for (i = 0; i < nlocal; i++) {
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int AIRct[8] = { 0 };
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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 rest of local atoms in i's bin
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// just store them, since j is beyond i in linked list
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for (j = bins_ssa[i]; j >= 0; j = bins_ssa[j]) {
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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) {
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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++] = 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) neighptr[n++] = j ^ (which << SBBITS);
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} else neighptr[n++] = j;
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}
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}
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ibin = coord2bin(x[i]);
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// loop over all local atoms in other bins in "half" stencil
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for (k = 0; k < nstencil_half; k++) {
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for (j = binhead_ssa[ibin+stencil[k]]; j >= 0;
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j = bins_ssa[j]) {
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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) {
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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++] = 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) neighptr[n++] = j ^ (which << SBBITS);
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} else neighptr[n++] = j;
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}
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}
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}
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AIRct[0] = n;
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// loop over AIR ghost atoms in all bins in "full" stencil
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// Note: the non-AIR ghost atoms have already been filtered out
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// That is a significant time savings because of the "full" stencil
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// Note2: only non-pure locals can have ghosts as neighbors
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if (ssaAIR[i] == 1) for (k = 0; k < nstencil_full; k++) {
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for (j = gbinhead_ssa[ibin+stencil[k]]; j >= 0;
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j = bins_ssa[j]) {
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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) {
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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) {
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neighptr[n++] = j;
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++(AIRct[ssaAIR[j] - 1]);
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} else if (domain->minimum_image_check(delx,dely,delz)) {
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neighptr[n++] = j;
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++(AIRct[ssaAIR[j] - 1]);
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} else if (which > 0) {
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neighptr[n++] = j ^ (which << SBBITS);
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++(AIRct[ssaAIR[j] - 1]);
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}
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} else {
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neighptr[n++] = j;
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++(AIRct[ssaAIR[j] - 1]);
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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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// sort the ghosts in the neighbor list by their ssaAIR number
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ssaAIRptr = atom->ssaAIR;
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qsort(&(neighptr[AIRct[0]]), n - AIRct[0], sizeof(int), cmp_ssaAIR);
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// do a prefix sum on the counts to turn them into indexes
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list->ndxAIR_ssa[i][0] = AIRct[0];
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for (int ndx = 1; ndx < 8; ++ndx) {
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list->ndxAIR_ssa[i][ndx] = AIRct[ndx] + list->ndxAIR_ssa[i][ndx - 1];
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}
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}
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list->inum = inum;
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}
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/* ----------------------------------------------------------------------
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comparison function invoked by qsort()
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accesses static class member ssaAIRptr, set before call to qsort()
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------------------------------------------------------------------------- */
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static int cmp_ssaAIR(const void *iptr, const void *jptr)
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{
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int i = *((int *) iptr);
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int j = *((int *) jptr);
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if (ssaAIRptr[i] < ssaAIRptr[j]) return -1;
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if (ssaAIRptr[i] > ssaAIRptr[j]) return 1;
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return 0;
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}
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