forked from lijiext/lammps
591 lines
17 KiB
C++
591 lines
17 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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#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 "group.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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/* ----------------------------------------------------------------------
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N^2 search for all neighbors
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every neighbor pair appears in list of both atoms i and j
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------------------------------------------------------------------------- */
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void Neighbor::full_nsq(NeighList *list)
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{
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int i,j,n,itype,jtype,which,bitmask,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) {
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nlocal = atom->nfirst;
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bitmask = group->bitmask[includegroup];
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}
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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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int inum = 0;
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ipage->reset();
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// loop over owned atoms, storing neighbors
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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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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 all atoms, owned and ghost
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// skip i = j
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for (j = 0; j < nall; j++) {
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if (includegroup && !(mask[j] & bitmask)) continue;
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if (i == j) continue;
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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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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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list->gnum = 0;
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}
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/* ----------------------------------------------------------------------
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N^2 search for all neighbors
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include neighbors of ghost atoms, but no "special neighbors" for ghosts
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every neighbor pair appears in list of both atoms i and j
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------------------------------------------------------------------------- */
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void Neighbor::full_nsq_ghost(NeighList *list)
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{
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int i,j,n,itype,jtype,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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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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int inum = 0;
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ipage->reset();
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// loop over owned & ghost atoms, storing neighbors
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for (i = 0; i < nall; 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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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 all atoms, owned and ghost
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// skip i = j
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// no molecular test when i = ghost atom
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if (i < nlocal) {
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for (j = 0; j < nall; j++) {
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if (i == j) continue;
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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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} else {
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for (j = 0; j < nall; j++) {
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if (i == j) continue;
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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 <= cutneighghostsq[itype][jtype]) neighptr[n++] = j;
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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 = atom->nlocal;
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list->gnum = inum - atom->nlocal;
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}
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/* ----------------------------------------------------------------------
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binned neighbor list construction for all neighbors
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every neighbor pair appears in list of both atoms i and j
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------------------------------------------------------------------------- */
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void Neighbor::full_bin(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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// bin owned & ghost atoms
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if (binatomflag) bin_atoms();
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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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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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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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int nstencil = list->nstencil;
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int *stencil = list->stencil;
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MyPage<int> *ipage = list->ipage;
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int inum = 0;
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ipage->reset();
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// loop over owned atoms, storing neighbors
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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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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 all atoms in surrounding bins in stencil including self
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// skip i = j
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ibin = coord2bin(x[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 (i == j) continue;
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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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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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list->gnum = 0;
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}
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/* ----------------------------------------------------------------------
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binned neighbor list construction for all neighbors
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include neighbors of ghost atoms, but no "special neighbors" for ghosts
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every neighbor pair appears in list of both atoms i and j
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------------------------------------------------------------------------- */
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void Neighbor::full_bin_ghost(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 xbin,ybin,zbin,xbin2,ybin2,zbin2;
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int *neighptr;
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// bin owned & ghost atoms
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if (binatomflag) bin_atoms();
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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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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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int nstencil = list->nstencil;
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int *stencil = list->stencil;
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int **stencilxyz = list->stencilxyz;
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MyPage<int> *ipage = list->ipage;
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int inum = 0;
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ipage->reset();
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// loop over owned & ghost atoms, storing neighbors
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for (i = 0; i < nall; 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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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 all atoms in surrounding bins in stencil including self
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// when i is a ghost atom, must check if stencil bin is out of bounds
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// skip i = j
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// no molecular test when i = ghost atom
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if (i < nlocal) {
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ibin = coord2bin(x[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 (i == j) continue;
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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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} else {
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ibin = coord2bin(x[i],xbin,ybin,zbin);
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for (k = 0; k < nstencil; k++) {
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xbin2 = xbin + stencilxyz[k][0];
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ybin2 = ybin + stencilxyz[k][1];
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zbin2 = zbin + stencilxyz[k][2];
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if (xbin2 < 0 || xbin2 >= mbinx ||
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ybin2 < 0 || ybin2 >= mbiny ||
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zbin2 < 0 || zbin2 >= mbinz) continue;
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for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
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if (i == j) continue;
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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 <= cutneighghostsq[itype][jtype]) neighptr[n++] = j;
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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 = atom->nlocal;
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list->gnum = inum - atom->nlocal;
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}
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/* ----------------------------------------------------------------------
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binned neighbor list construction for all neighbors
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multi-type stencil is itype dependent and is distance checked
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every neighbor pair appears in list of both atoms i and j
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------------------------------------------------------------------------- */
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void Neighbor::full_multi(NeighList *list)
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{
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int i,j,k,n,itype,jtype,ibin,which,ns,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,*s;
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double *cutsq,*distsq;
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// bin local & ghost atoms
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if (binatomflag) bin_atoms();
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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;
|
|
tagint **special = atom->special;
|
|
int **nspecial = atom->nspecial;
|
|
int nlocal = atom->nlocal;
|
|
if (includegroup) nlocal = atom->nfirst;
|
|
|
|
int *molindex = atom->molindex;
|
|
int *molatom = atom->molatom;
|
|
Molecule **onemols = atom->avec->onemols;
|
|
int molecular = atom->molecular;
|
|
if (molecular == 2) moltemplate = 1;
|
|
else moltemplate = 0;
|
|
|
|
int *ilist = list->ilist;
|
|
int *numneigh = list->numneigh;
|
|
int **firstneigh = list->firstneigh;
|
|
int *nstencil_multi = list->nstencil_multi;
|
|
int **stencil_multi = list->stencil_multi;
|
|
double **distsq_multi = list->distsq_multi;
|
|
MyPage<int> *ipage = list->ipage;
|
|
|
|
int inum = 0;
|
|
ipage->reset();
|
|
|
|
// loop over each atom, storing neighbors
|
|
|
|
for (i = 0; i < nlocal; i++) {
|
|
n = 0;
|
|
neighptr = ipage->vget();
|
|
|
|
itype = type[i];
|
|
xtmp = x[i][0];
|
|
ytmp = x[i][1];
|
|
ztmp = x[i][2];
|
|
if (moltemplate) {
|
|
imol = molindex[i];
|
|
iatom = molatom[i];
|
|
tagprev = tag[i] - iatom - 1;
|
|
}
|
|
|
|
// loop over all atoms in other bins in stencil, including self
|
|
// skip if i,j neighbor cutoff is less than bin distance
|
|
// skip i = j
|
|
|
|
ibin = coord2bin(x[i]);
|
|
s = stencil_multi[itype];
|
|
distsq = distsq_multi[itype];
|
|
cutsq = cutneighsq[itype];
|
|
ns = nstencil_multi[itype];
|
|
for (k = 0; k < ns; k++) {
|
|
for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
|
|
jtype = type[j];
|
|
if (cutsq[jtype] < distsq[k]) continue;
|
|
if (i == j) continue;
|
|
|
|
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
|
|
|
delx = xtmp - x[j][0];
|
|
dely = ytmp - x[j][1];
|
|
delz = ztmp - x[j][2];
|
|
rsq = delx*delx + dely*dely + delz*delz;
|
|
|
|
if (rsq <= cutneighsq[itype][jtype]) {
|
|
if (molecular) {
|
|
if (!moltemplate)
|
|
which = find_special(special[i],nspecial[i],tag[j]);
|
|
else if (imol >= 0)
|
|
which = find_special(onemols[imol]->special[iatom],
|
|
onemols[imol]->nspecial[iatom],
|
|
tag[j]-tagprev);
|
|
else which = 0;
|
|
if (which == 0) neighptr[n++] = j;
|
|
else if (domain->minimum_image_check(delx,dely,delz))
|
|
neighptr[n++] = j;
|
|
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
|
|
} else neighptr[n++] = j;
|
|
}
|
|
}
|
|
}
|
|
|
|
ilist[inum++] = i;
|
|
firstneigh[i] = neighptr;
|
|
numneigh[i] = n;
|
|
ipage->vgot(n);
|
|
if (ipage->status())
|
|
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
|
|
}
|
|
|
|
list->inum = inum;
|
|
list->gnum = 0;
|
|
}
|