830 lines
23 KiB
C++
830 lines
23 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 "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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multiple respa lists
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N^2 / 2 search for neighbor pairs with partial Newton's 3rd law
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pair added to list if atoms i and j are both owned and i < j
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pair added if j is ghost (also stored by proc owning j)
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------------------------------------------------------------------------- */
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void Neighbor::respa_nsq_no_newton(NeighList *list)
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{
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int i,j,n,itype,jtype,which,n_inner,n_middle,bitmask;
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double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
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int *neighptr,*neighptr_inner,*neighptr_middle;
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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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int *molecule = atom->molecule;
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int nlocal = atom->nlocal;
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int nall = nlocal + atom->nghost;
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int molecular = atom->molecular;
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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 *ilist = list->ilist;
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int *numneigh = list->numneigh;
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int **firstneigh = list->firstneigh;
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int **pages = list->pages;
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NeighList *listinner = list->listinner;
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int *numneigh_inner = listinner->numneigh;
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int **firstneigh_inner = listinner->firstneigh;
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int **pages_inner = listinner->pages;
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NeighList *listmiddle;
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int *numneigh_middle,**firstneigh_middle,**pages_middle;
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int respamiddle = list->respamiddle;
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if (respamiddle) {
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listmiddle = list->listmiddle;
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numneigh_middle = listmiddle->numneigh;
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firstneigh_middle = listmiddle->firstneigh;
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pages_middle = listmiddle->pages;
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}
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int inum = 0;
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int npage = 0;
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int npnt = 0;
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int npage_inner = 0;
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int npnt_inner = 0;
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int npage_middle = 0;
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int npnt_middle = 0;
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for (i = 0; i < nlocal; i++) {
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if (pgsize - npnt < oneatom) {
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npnt = 0;
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npage++;
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if (npage == list->maxpage) pages = list->add_pages();
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}
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neighptr = &pages[npage][npnt];
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n = 0;
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if (pgsize - npnt_inner < oneatom) {
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npnt_inner = 0;
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npage_inner++;
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if (npage_inner == listinner->maxpage)
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pages_inner = listinner->add_pages();
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}
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neighptr_inner = &pages_inner[npage_inner][npnt_inner];
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n_inner = 0;
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if (respamiddle) {
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if (pgsize - npnt_middle < oneatom) {
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npnt_middle = 0;
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npage_middle++;
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if (npage_middle == listmiddle->maxpage)
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pages_middle = listmiddle->add_pages();
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}
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neighptr_middle = &pages_middle[npage_middle][npnt_middle];
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n_middle = 0;
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}
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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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// loop over remaining atoms, owned and ghost
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for (j = i+1; j < nall; j++) {
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if (includegroup && !(mask[j] & bitmask)) 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) which = find_special(i,j);
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else which = 0;
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if (which == 0) neighptr[n++] = j;
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else if (which > 0) neighptr[n++] = which*nall + j;
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if (rsq < cut_inner_sq) {
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if (which == 0) neighptr_inner[n_inner++] = j;
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else if (which > 0) neighptr_inner[n_inner++] = which*nall + j;
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}
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if (respamiddle && rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
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if (which == 0) neighptr_middle[n_middle++] = j;
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else if (which > 0) neighptr_middle[n_middle++] = which*nall + 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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npnt += n;
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if (npnt >= pgsize)
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error->one("Neighbor list overflow, boost neigh_modify one or page");
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firstneigh_inner[i] = neighptr_inner;
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numneigh_inner[i] = n_inner;
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npnt_inner += n_inner;
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if (npnt_inner >= pgsize)
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error->one("Neighbor list overflow, boost neigh_modify one or page");
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if (respamiddle) {
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firstneigh_middle[i] = neighptr_middle;
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numneigh_middle[i] = n_middle;
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npnt_middle += n_middle;
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if (npnt_middle >= pgsize)
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error->one("Neighbor list overflow, boost neigh_modify one or page");
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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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multiple respa lists
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N^2 / 2 search for neighbor pairs with full Newton's 3rd law
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pair added to list if atoms i and j are both owned and i < j
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if j is ghost only me or other proc adds pair
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decision based on itag,jtag tests
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------------------------------------------------------------------------- */
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void Neighbor::respa_nsq_newton(NeighList *list)
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{
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int i,j,n,itype,jtype,itag,jtag,which,n_inner,n_middle,bitmask;
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double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
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int *neighptr,*neighptr_inner,*neighptr_middle;
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double **x = atom->x;
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int *tag = atom->tag;
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int *type = atom->type;
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int *mask = atom->mask;
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int *molecule = atom->molecule;
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int nlocal = atom->nlocal;
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int nall = nlocal + atom->nghost;
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int molecular = atom->molecular;
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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 *ilist = list->ilist;
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int *numneigh = list->numneigh;
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int **firstneigh = list->firstneigh;
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int **pages = list->pages;
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NeighList *listinner = list->listinner;
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int *numneigh_inner = listinner->numneigh;
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int **firstneigh_inner = listinner->firstneigh;
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int **pages_inner = listinner->pages;
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NeighList *listmiddle;
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int *numneigh_middle,**firstneigh_middle,**pages_middle;
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int respamiddle = list->respamiddle;
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if (respamiddle) {
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listmiddle = list->listmiddle;
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numneigh_middle = listmiddle->numneigh;
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firstneigh_middle = listmiddle->firstneigh;
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pages_middle = listmiddle->pages;
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}
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int inum = 0;
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int npage = 0;
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int npnt = 0;
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int npage_inner = 0;
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int npnt_inner = 0;
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int npage_middle = 0;
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int npnt_middle = 0;
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for (i = 0; i < nlocal; i++) {
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if (pgsize - npnt < oneatom) {
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npnt = 0;
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npage++;
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if (npage == list->maxpage) pages = list->add_pages();
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}
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neighptr = &pages[npage][npnt];
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n = 0;
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if (pgsize - npnt_inner < oneatom) {
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npnt_inner = 0;
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npage_inner++;
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if (npage_inner == listinner->maxpage)
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pages_inner = listinner->add_pages();
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}
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neighptr_inner = &pages_inner[npage_inner][npnt_inner];
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n_inner = 0;
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if (respamiddle) {
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if (pgsize - npnt_middle < oneatom) {
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npnt_middle = 0;
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npage_middle++;
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if (npage_middle == listmiddle->maxpage)
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pages_middle = listmiddle->add_pages();
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}
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neighptr_middle = &pages_middle[npage_middle][npnt_middle];
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n_middle = 0;
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}
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itag = tag[i];
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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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// loop over remaining atoms, owned and ghost
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for (j = i+1; j < nall; j++) {
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if (includegroup && !(mask[j] & bitmask)) continue;
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if (j >= nlocal) {
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jtag = tag[j];
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if (itag > jtag) {
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if ((itag+jtag) % 2 == 0) continue;
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} else if (itag < jtag) {
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if ((itag+jtag) % 2 == 1) continue;
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} else {
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if (x[j][2] < ztmp) continue;
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else if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
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else if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp)
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continue;
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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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if (rsq <= cutneighsq[itype][jtype]) {
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if (molecular) which = find_special(i,j);
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else which = 0;
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if (which == 0) neighptr[n++] = j;
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else if (which > 0) neighptr[n++] = which*nall + j;
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if (rsq < cut_inner_sq) {
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if (which == 0) neighptr_inner[n_inner++] = j;
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else if (which > 0) neighptr_inner[n_inner++] = which*nall + j;
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}
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if (respamiddle &&
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rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
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if (which == 0) neighptr_middle[n_middle++] = j;
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else if (which > 0) neighptr_middle[n_middle++] = which*nall + 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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npnt += n;
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if (npnt >= pgsize)
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error->one("Neighbor list overflow, boost neigh_modify one or page");
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firstneigh_inner[i] = neighptr_inner;
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numneigh_inner[i] = n_inner;
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npnt_inner += n_inner;
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if (npnt_inner >= pgsize)
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error->one("Neighbor list overflow, boost neigh_modify one or page");
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if (respamiddle) {
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firstneigh_middle[i] = neighptr_middle;
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numneigh_middle[i] = n_middle;
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npnt_middle += n_middle;
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if (npnt_middle >= pgsize)
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error->one("Neighbor list overflow, boost neigh_modify one or page");
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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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multiple respa lists
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binned neighbor list construction with partial Newton's 3rd law
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each owned atom i checks own bin and surrounding bins in non-Newton stencil
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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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------------------------------------------------------------------------- */
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void Neighbor::respa_bin_no_newton(NeighList *list)
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{
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int i,j,k,n,itype,jtype,ibin,which,n_inner,n_middle;
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double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
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int *neighptr,*neighptr_inner,*neighptr_middle;
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// bin local & ghost atoms
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bin_atoms();
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// loop over each atom, storing neighbors
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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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int *molecule = atom->molecule;
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int nlocal = atom->nlocal;
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int nall = nlocal + atom->nghost;
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int molecular = atom->molecular;
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if (includegroup) nlocal = atom->nfirst;
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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 **pages = list->pages;
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int nstencil = list->nstencil;
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int *stencil = list->stencil;
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NeighList *listinner = list->listinner;
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int *numneigh_inner = listinner->numneigh;
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int **firstneigh_inner = listinner->firstneigh;
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int **pages_inner = listinner->pages;
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NeighList *listmiddle;
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int *numneigh_middle,**firstneigh_middle,**pages_middle;
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int respamiddle = list->respamiddle;
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if (respamiddle) {
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listmiddle = list->listmiddle;
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numneigh_middle = listmiddle->numneigh;
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firstneigh_middle = listmiddle->firstneigh;
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pages_middle = listmiddle->pages;
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}
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int inum = 0;
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int npage = 0;
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int npnt = 0;
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int npage_inner = 0;
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int npnt_inner = 0;
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int npage_middle = 0;
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int npnt_middle = 0;
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for (i = 0; i < nlocal; i++) {
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if (pgsize - npnt < oneatom) {
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npnt = 0;
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npage++;
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if (npage == list->maxpage) pages = list->add_pages();
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}
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neighptr = &pages[npage][npnt];
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n = 0;
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if (pgsize - npnt_inner < oneatom) {
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npnt_inner = 0;
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npage_inner++;
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if (npage_inner == listinner->maxpage)
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pages_inner = listinner->add_pages();
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}
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neighptr_inner = &pages_inner[npage_inner][npnt_inner];
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n_inner = 0;
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if (respamiddle) {
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if (pgsize - npnt_middle < oneatom) {
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npnt_middle = 0;
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npage_middle++;
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if (npage_middle == listmiddle->maxpage)
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pages_middle = listmiddle->add_pages();
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}
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neighptr_middle = &pages_middle[npage_middle][npnt_middle];
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n_middle = 0;
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}
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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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ibin = coord2bin(x[i]);
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// loop over all atoms in surrounding bins in stencil including self
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// only store pair if i < j
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// stores own/own pairs only once
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// stores own/ghost pairs on both procs
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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 (j <= i) 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) which = find_special(i,j);
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else which = 0;
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if (which == 0) neighptr[n++] = j;
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else if (which > 0) neighptr[n++] = which*nall + j;
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if (rsq < cut_inner_sq) {
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if (which == 0) neighptr_inner[n_inner++] = j;
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else if (which > 0) neighptr_inner[n_inner++] = which*nall + j;
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}
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if (respamiddle &&
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rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
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if (which == 0) neighptr_middle[n_middle++] = j;
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else if (which > 0) neighptr_middle[n_middle++] = which*nall + 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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npnt += n;
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if (npnt >= pgsize)
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error->one("Neighbor list overflow, boost neigh_modify one or page");
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firstneigh_inner[i] = neighptr_inner;
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numneigh_inner[i] = n_inner;
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npnt_inner += n_inner;
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if (npnt_inner >= pgsize)
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error->one("Neighbor list overflow, boost neigh_modify one or page");
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if (respamiddle) {
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firstneigh_middle[i] = neighptr_middle;
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numneigh_middle[i] = n_middle;
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npnt_middle += n_middle;
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if (npnt_middle >= pgsize)
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error->one("Neighbor list overflow, boost neigh_modify one or page");
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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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multiple respa lists
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binned neighbor list construction with full Newton's 3rd law
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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 Neighbor::respa_bin_newton(NeighList *list)
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{
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int i,j,k,n,itype,jtype,ibin,which,n_inner,n_middle;
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double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
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int *neighptr,*neighptr_inner,*neighptr_middle;
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|
|
|
// bin local & ghost atoms
|
|
|
|
bin_atoms();
|
|
|
|
// loop over each atom, storing neighbors
|
|
|
|
double **x = atom->x;
|
|
int *type = atom->type;
|
|
int *mask = atom->mask;
|
|
int *molecule = atom->molecule;
|
|
int nlocal = atom->nlocal;
|
|
int nall = nlocal + atom->nghost;
|
|
int molecular = atom->molecular;
|
|
if (includegroup) nlocal = atom->nfirst;
|
|
|
|
int *ilist = list->ilist;
|
|
int *numneigh = list->numneigh;
|
|
int **firstneigh = list->firstneigh;
|
|
int **pages = list->pages;
|
|
int nstencil = list->nstencil;
|
|
int *stencil = list->stencil;
|
|
|
|
NeighList *listinner = list->listinner;
|
|
int *numneigh_inner = listinner->numneigh;
|
|
int **firstneigh_inner = listinner->firstneigh;
|
|
int **pages_inner = listinner->pages;
|
|
|
|
NeighList *listmiddle;
|
|
int *numneigh_middle,**firstneigh_middle,**pages_middle;
|
|
int respamiddle = list->respamiddle;
|
|
if (respamiddle) {
|
|
listmiddle = list->listmiddle;
|
|
numneigh_middle = listmiddle->numneigh;
|
|
firstneigh_middle = listmiddle->firstneigh;
|
|
pages_middle = listmiddle->pages;
|
|
}
|
|
|
|
int inum = 0;
|
|
int npage = 0;
|
|
int npnt = 0;
|
|
int npage_inner = 0;
|
|
int npnt_inner = 0;
|
|
int npage_middle = 0;
|
|
int npnt_middle = 0;
|
|
|
|
for (i = 0; i < nlocal; i++) {
|
|
|
|
if (pgsize - npnt < oneatom) {
|
|
npnt = 0;
|
|
npage++;
|
|
if (npage == list->maxpage) pages = list->add_pages();
|
|
}
|
|
neighptr = &pages[npage][npnt];
|
|
n = 0;
|
|
|
|
if (pgsize - npnt_inner < oneatom) {
|
|
npnt_inner = 0;
|
|
npage_inner++;
|
|
if (npage_inner == listinner->maxpage)
|
|
pages_inner = listinner->add_pages();
|
|
}
|
|
neighptr_inner = &pages_inner[npage_inner][npnt_inner];
|
|
n_inner = 0;
|
|
|
|
if (respamiddle) {
|
|
if (pgsize - npnt_middle < oneatom) {
|
|
npnt_middle = 0;
|
|
npage_middle++;
|
|
if (npage_middle == listmiddle->maxpage)
|
|
pages_middle = listmiddle->add_pages();
|
|
}
|
|
neighptr_middle = &pages_middle[npage_middle][npnt_middle];
|
|
n_middle = 0;
|
|
}
|
|
|
|
itype = type[i];
|
|
xtmp = x[i][0];
|
|
ytmp = x[i][1];
|
|
ztmp = x[i][2];
|
|
|
|
// loop over rest of atoms in i's bin, ghosts are at end of linked list
|
|
// if j is owned atom, store it, since j is beyond i in linked list
|
|
// if j is ghost, only store if j coords are "above and to the right" of i
|
|
|
|
for (j = bins[i]; j >= 0; j = bins[j]) {
|
|
if (j >= nlocal) {
|
|
if (x[j][2] < ztmp) continue;
|
|
if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
|
|
if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
|
|
}
|
|
|
|
jtype = type[j];
|
|
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) which = find_special(i,j);
|
|
else which = 0;
|
|
if (which == 0) neighptr[n++] = j;
|
|
else if (which > 0) neighptr[n++] = which*nall + j;
|
|
|
|
if (rsq < cut_inner_sq) {
|
|
if (which == 0) neighptr_inner[n_inner++] = j;
|
|
else if (which > 0) neighptr_inner[n_inner++] = which*nall + j;
|
|
}
|
|
|
|
if (respamiddle &&
|
|
rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
|
|
if (which == 0) neighptr_middle[n_middle++] = j;
|
|
else if (which > 0) neighptr_middle[n_middle++] = which*nall + j;
|
|
}
|
|
}
|
|
}
|
|
|
|
// loop over all atoms in other bins in stencil, store every pair
|
|
|
|
ibin = coord2bin(x[i]);
|
|
for (k = 0; k < nstencil; k++) {
|
|
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
|
|
jtype = type[j];
|
|
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) which = find_special(i,j);
|
|
else which = 0;
|
|
if (which == 0) neighptr[n++] = j;
|
|
else if (which > 0) neighptr[n++] = which*nall + j;
|
|
|
|
if (rsq < cut_inner_sq) {
|
|
if (which == 0) neighptr_inner[n_inner++] = j;
|
|
else if (which > 0) neighptr_inner[n_inner++] = which*nall + j;
|
|
}
|
|
|
|
if (respamiddle &&
|
|
rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
|
|
if (which == 0) neighptr_middle[n_middle++] = j;
|
|
else if (which > 0) neighptr_middle[n_middle++] = which*nall + j;
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
ilist[inum++] = i;
|
|
firstneigh[i] = neighptr;
|
|
numneigh[i] = n;
|
|
npnt += n;
|
|
if (npnt >= pgsize)
|
|
error->one("Neighbor list overflow, boost neigh_modify one or page");
|
|
|
|
firstneigh_inner[i] = neighptr_inner;
|
|
numneigh_inner[i] = n_inner;
|
|
npnt_inner += n_inner;
|
|
if (npnt_inner >= pgsize)
|
|
error->one("Neighbor list overflow, boost neigh_modify one or page");
|
|
|
|
if (respamiddle) {
|
|
firstneigh_middle[i] = neighptr_middle;
|
|
numneigh_middle[i] = n_middle;
|
|
npnt_middle += n_middle;
|
|
if (npnt_middle >= pgsize)
|
|
error->one("Neighbor list overflow, boost neigh_modify one or page");
|
|
}
|
|
}
|
|
|
|
list->inum = inum;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
multiple respa lists
|
|
binned neighbor list construction with Newton's 3rd law for triclinic
|
|
each owned atom i checks its own bin and other bins in triclinic stencil
|
|
every pair stored exactly once by some processor
|
|
------------------------------------------------------------------------- */
|
|
|
|
void Neighbor::respa_bin_newton_tri(NeighList *list)
|
|
{
|
|
int i,j,k,n,itype,jtype,ibin,which,n_inner,n_middle;
|
|
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
|
|
int *neighptr,*neighptr_inner,*neighptr_middle;
|
|
|
|
// bin local & ghost atoms
|
|
|
|
bin_atoms();
|
|
|
|
// loop over each atom, storing neighbors
|
|
|
|
double **x = atom->x;
|
|
int *type = atom->type;
|
|
int *mask = atom->mask;
|
|
int *molecule = atom->molecule;
|
|
int nlocal = atom->nlocal;
|
|
int nall = nlocal + atom->nghost;
|
|
int molecular = atom->molecular;
|
|
if (includegroup) nlocal = atom->nfirst;
|
|
|
|
int *ilist = list->ilist;
|
|
int *numneigh = list->numneigh;
|
|
int **firstneigh = list->firstneigh;
|
|
int **pages = list->pages;
|
|
int nstencil = list->nstencil;
|
|
int *stencil = list->stencil;
|
|
|
|
NeighList *listinner = list->listinner;
|
|
int *numneigh_inner = listinner->numneigh;
|
|
int **firstneigh_inner = listinner->firstneigh;
|
|
int **pages_inner = listinner->pages;
|
|
|
|
NeighList *listmiddle;
|
|
int *numneigh_middle,**firstneigh_middle,**pages_middle;
|
|
int respamiddle = list->respamiddle;
|
|
if (respamiddle) {
|
|
listmiddle = list->listmiddle;
|
|
numneigh_middle = listmiddle->numneigh;
|
|
firstneigh_middle = listmiddle->firstneigh;
|
|
pages_middle = listmiddle->pages;
|
|
}
|
|
|
|
int inum = 0;
|
|
int npage = 0;
|
|
int npnt = 0;
|
|
int npage_inner = 0;
|
|
int npnt_inner = 0;
|
|
int npage_middle = 0;
|
|
int npnt_middle = 0;
|
|
|
|
for (i = 0; i < nlocal; i++) {
|
|
|
|
if (pgsize - npnt < oneatom) {
|
|
npnt = 0;
|
|
npage++;
|
|
if (npage == list->maxpage) pages = list->add_pages();
|
|
}
|
|
neighptr = &pages[npage][npnt];
|
|
n = 0;
|
|
|
|
if (pgsize - npnt_inner < oneatom) {
|
|
npnt_inner = 0;
|
|
npage_inner++;
|
|
if (npage_inner == listinner->maxpage)
|
|
pages_inner = listinner->add_pages();
|
|
}
|
|
neighptr_inner = &pages_inner[npage_inner][npnt_inner];
|
|
n_inner = 0;
|
|
|
|
if (respamiddle) {
|
|
if (pgsize - npnt_middle < oneatom) {
|
|
npnt_middle = 0;
|
|
npage_middle++;
|
|
if (npage_middle == listmiddle->maxpage)
|
|
pages_middle = listmiddle->add_pages();
|
|
}
|
|
neighptr_middle = &pages_middle[npage_middle][npnt_middle];
|
|
n_middle = 0;
|
|
}
|
|
|
|
itype = type[i];
|
|
xtmp = x[i][0];
|
|
ytmp = x[i][1];
|
|
ztmp = x[i][2];
|
|
|
|
// loop over all atoms in bins in stencil
|
|
// pairs for atoms j "below" i are excluded
|
|
// below = lower z or (equal z and lower y) or (equal zy and <= x)
|
|
// this excludes self-self interaction
|
|
|
|
ibin = coord2bin(x[i]);
|
|
for (k = 0; k < nstencil; k++) {
|
|
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
|
|
if (x[j][2] < ztmp) continue;
|
|
if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
|
|
if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] <= xtmp) continue;
|
|
|
|
jtype = type[j];
|
|
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) which = find_special(i,j);
|
|
else which = 0;
|
|
if (which == 0) neighptr[n++] = j;
|
|
else if (which > 0) neighptr[n++] = which*nall + j;
|
|
|
|
if (rsq < cut_inner_sq) {
|
|
if (which == 0) neighptr_inner[n_inner++] = j;
|
|
else if (which > 0) neighptr_inner[n_inner++] = which*nall + j;
|
|
}
|
|
|
|
if (respamiddle &&
|
|
rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
|
|
if (which == 0) neighptr_middle[n_middle++] = j;
|
|
else if (which > 0) neighptr_middle[n_middle++] = which*nall + j;
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
ilist[inum++] = i;
|
|
firstneigh[i] = neighptr;
|
|
numneigh[i] = n;
|
|
npnt += n;
|
|
if (npnt >= pgsize)
|
|
error->one("Neighbor list overflow, boost neigh_modify one or page");
|
|
|
|
firstneigh_inner[i] = neighptr_inner;
|
|
numneigh_inner[i] = n_inner;
|
|
npnt_inner += n_inner;
|
|
if (npnt_inner >= pgsize)
|
|
error->one("Neighbor list overflow, boost neigh_modify one or page");
|
|
|
|
if (respamiddle) {
|
|
firstneigh_middle[i] = neighptr_middle;
|
|
numneigh_middle[i] = n_middle;
|
|
npnt_middle += n_middle;
|
|
if (npnt_middle >= pgsize)
|
|
error->one("Neighbor list overflow, boost neigh_modify one or page");
|
|
}
|
|
}
|
|
|
|
list->inum = inum;
|
|
}
|