440 lines
14 KiB
C++
440 lines
14 KiB
C++
/* ----------------------------------------------------------------------
|
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
|
http://lammps.sandia.gov, Sandia National Laboratories
|
|
Steve Plimpton, sjplimp@sandia.gov
|
|
|
|
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
|
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
|
certain rights in this software. This software is distributed under
|
|
the GNU General Public License.
|
|
|
|
See the README file in the top-level LAMMPS directory.
|
|
------------------------------------------------------------------------- */
|
|
|
|
/* ----------------------------------------------------------------------
|
|
Contributing authors:
|
|
James Larentzos and Timothy I. Mattox (Engility Corporation)
|
|
------------------------------------------------------------------------- */
|
|
|
|
#include "neighbor.h"
|
|
#include "neigh_list.h"
|
|
#include "neigh_request.h"
|
|
#include "atom.h"
|
|
#include "atom_vec.h"
|
|
#include "molecule.h"
|
|
#include "domain.h"
|
|
#include "group.h"
|
|
#include "memory.h"
|
|
#include "error.h"
|
|
#include "update.h"
|
|
|
|
using namespace LAMMPS_NS;
|
|
|
|
/* ----------------------------------------------------------------------
|
|
routines to create a stencil = list of bin offsets
|
|
stencil = bins whose closest corner to central bin is within cutoff
|
|
sx,sy,sz = bin bounds = furthest the stencil could possibly extend
|
|
3d creates xyz stencil, 2d creates xy stencil
|
|
for half list with newton on:
|
|
stencil is bins to the "upper right" of central bin
|
|
stencil does not include self
|
|
------------------------------------------------------------------------- */
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void Neighbor::stencil_half_bin_2d_ssa(NeighList *list,
|
|
int sx, int sy, int sz)
|
|
{
|
|
int i,j;
|
|
int *stencil = list->stencil;
|
|
int nstencil = 0;
|
|
|
|
for (j = 0; j <= sy; j++)
|
|
for (i = -sx; i <= sx; i++)
|
|
if (j > 0 || (j == 0 && i > 0))
|
|
if (bin_distance(i,j,0) < cutneighmaxsq)
|
|
stencil[nstencil++] = j*mbinx + i;
|
|
|
|
list->nstencil = nstencil;
|
|
|
|
// Now include additional bins for AIR ghosts only
|
|
for (j = -sy; j <= 0; j++)
|
|
for (i = -sx; i <= sx; i++) {
|
|
if (j == 0 && i > 0) continue;
|
|
if (bin_distance(i,j,0) < cutneighmaxsq)
|
|
stencil[nstencil++] = j*mbinx + i;
|
|
}
|
|
|
|
while (nstencil < list->maxstencil) {
|
|
stencil[nstencil++] = INT_MAX;
|
|
}
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void Neighbor::stencil_half_bin_3d_ssa(NeighList *list,
|
|
int sx, int sy, int sz)
|
|
{
|
|
int i,j,k;
|
|
int *stencil = list->stencil;
|
|
int nstencil = 0;
|
|
|
|
for (k = 0; k <= sz; k++)
|
|
for (j = -sy; j <= sy; j++)
|
|
for (i = -sx; i <= sx; i++)
|
|
if (k > 0 || j > 0 || (j == 0 && i > 0))
|
|
if (bin_distance(i,j,k) < cutneighmaxsq)
|
|
stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i;
|
|
|
|
list->nstencil = nstencil;
|
|
|
|
// Now include additional bins for AIR ghosts only
|
|
for (k = -sz; k < 0; k++)
|
|
for (j = -sy; j <= sy; j++)
|
|
for (i = -sx; i <= sx; i++)
|
|
if (bin_distance(i,j,k) < cutneighmaxsq)
|
|
stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i;
|
|
k = 0; // skip already included bins at k == 0
|
|
for (j = -sy; j <= 0; j++)
|
|
for (i = -sx; i <= sx; i++) {
|
|
if (j == 0 && i > 0) continue;
|
|
if (bin_distance(i,j,k) < cutneighmaxsq)
|
|
stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i;
|
|
}
|
|
|
|
while (nstencil < list->maxstencil) {
|
|
stencil[nstencil++] = INT_MAX;
|
|
}
|
|
}
|
|
|
|
// space for static variable ssaAIRptr so it
|
|
// can be used in qsort's compair function "cmp_ssaAIR()"
|
|
static int *ssaAIRptr;
|
|
|
|
static int cmp_ssaAIR(const void *iptr, const void *jptr)
|
|
{
|
|
int i = *((int *) iptr);
|
|
int j = *((int *) jptr);
|
|
if (ssaAIRptr[i] < ssaAIRptr[j]) return -1;
|
|
if (ssaAIRptr[i] > ssaAIRptr[j]) return 1;
|
|
return 0;
|
|
}
|
|
|
|
|
|
/* ----------------------------------------------------------------------
|
|
build half list from full list for use by Shardlow Spliting Algorithm
|
|
pair stored once if i,j are both owned and i < j
|
|
if j is ghost, only store if j coords are "above and to the right" of i
|
|
works if full list is a skip list
|
|
------------------------------------------------------------------------- */
|
|
|
|
void Neighbor::half_from_full_newton_ssa(NeighList *list)
|
|
{
|
|
int i,j,ii,jj,n,jnum,joriginal;
|
|
int *neighptr,*jlist;
|
|
|
|
int nlocal = atom->nlocal;
|
|
int *ssaAIR = atom->ssaAIR;
|
|
|
|
int *ilist = list->ilist;
|
|
int *numneigh = list->numneigh;
|
|
int **firstneigh = list->firstneigh;
|
|
MyPage<int> *ipage = list->ipage;
|
|
|
|
int *ilist_full = list->listfull->ilist;
|
|
int *numneigh_full = list->listfull->numneigh;
|
|
int **firstneigh_full = list->listfull->firstneigh;
|
|
int inum_full = list->listfull->inum;
|
|
|
|
int inum = 0;
|
|
ipage->reset();
|
|
|
|
// loop over parent full list
|
|
|
|
for (ii = 0; ii < inum_full; ii++) {
|
|
int AIRct[8] = { 0 };
|
|
n = 0;
|
|
neighptr = ipage->vget();
|
|
|
|
i = ilist_full[ii];
|
|
|
|
// loop over full neighbor list
|
|
|
|
jlist = firstneigh_full[i];
|
|
jnum = numneigh_full[i];
|
|
|
|
for (jj = 0; jj < jnum; jj++) {
|
|
joriginal = jlist[jj];
|
|
j = joriginal & NEIGHMASK;
|
|
if (j < nlocal) {
|
|
if (i > j) continue;
|
|
++(AIRct[0]);
|
|
} else {
|
|
if (ssaAIR[j] < 2) continue; // skip ghost atoms not in AIR
|
|
++(AIRct[ssaAIR[j] - 1]);
|
|
}
|
|
neighptr[n++] = joriginal;
|
|
}
|
|
|
|
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");
|
|
|
|
// sort the locals+ghosts in the neighbor list by their ssaAIR number
|
|
ssaAIRptr = atom->ssaAIR;
|
|
qsort(&(neighptr[0]), n, sizeof(int), cmp_ssaAIR);
|
|
|
|
// Do a prefix sum on the counts to turn them into indexes.
|
|
list->ndxAIR_ssa[i][0] = AIRct[0];
|
|
for (int ndx = 1; ndx < 8; ++ndx) {
|
|
list->ndxAIR_ssa[i][ndx] = AIRct[ndx] + list->ndxAIR_ssa[i][ndx - 1];
|
|
}
|
|
}
|
|
|
|
list->inum = inum;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
for Shardlow Spliting Algorithm:
|
|
binned neighbor list construction with full Newton's 3rd law
|
|
each owned atom i checks its own bin and other bins in Newton stencil
|
|
every pair stored exactly once by some processor
|
|
------------------------------------------------------------------------- */
|
|
|
|
void Neighbor::half_bin_newton_ssa(NeighList *list)
|
|
{
|
|
int i,j,k,n,itype,jtype,ibin,which,imol,iatom,moltemplate;
|
|
tagint tagprev;
|
|
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
|
|
int *neighptr;
|
|
|
|
double **x = atom->x;
|
|
int *type = atom->type;
|
|
int *mask = atom->mask;
|
|
tagint *tag = atom->tag;
|
|
tagint *molecule = atom->molecule;
|
|
tagint **special = atom->special;
|
|
int **nspecial = atom->nspecial;
|
|
int nlocal = atom->nlocal;
|
|
int nall = nlocal + atom->nghost;
|
|
if (includegroup) nlocal = atom->nfirst;
|
|
int *ssaAIR = atom->ssaAIR;
|
|
|
|
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 = list->nstencil;
|
|
int maxstencil = list->maxstencil;
|
|
int *stencil = list->stencil;
|
|
MyPage<int> *ipage = list->ipage;
|
|
|
|
int inum = 0;
|
|
|
|
if (binatomflag) { /* only false in Neighbor::build_one */
|
|
/* ----------------------------------------------------------------------
|
|
bin owned and ghost atoms for use by Shardlow Splitting Algorithm
|
|
exclude ghost atoms that are not in the Active Interaction Regions (AIR)
|
|
------------------------------------------------------------------------- */
|
|
|
|
if (mbins > list->maxhead_ssa) {
|
|
list->maxhead_ssa = mbins;
|
|
memory->destroy(list->gbinhead_ssa);
|
|
memory->destroy(list->binhead_ssa);
|
|
memory->create(list->binhead_ssa,list->maxhead_ssa,"binhead_ssa");
|
|
memory->create(list->gbinhead_ssa,list->maxhead_ssa,"gbinhead_ssa");
|
|
}
|
|
for (i = 0; i < mbins; i++) {
|
|
list->gbinhead_ssa[i] = -1;
|
|
list->binhead_ssa[i] = -1;
|
|
}
|
|
|
|
if (maxbin > list->maxbin_ssa) {
|
|
list->maxbin_ssa = maxbin;
|
|
memory->destroy(list->bins_ssa);
|
|
memory->create(list->bins_ssa,list->maxbin_ssa,"bins_ssa");
|
|
}
|
|
|
|
// bin in reverse order so linked list will be in forward order
|
|
|
|
if (includegroup) {
|
|
int bitmask = group->bitmask[includegroup];
|
|
int nowned = atom->nlocal; // NOTE: nlocal was set to atom->nfirst above
|
|
for (i = nall-1; i >= nowned; i--) {
|
|
if (ssaAIR[i] < 2) continue; // skip ghost atoms not in AIR
|
|
if (mask[i] & bitmask) {
|
|
ibin = coord2bin(x[i]);
|
|
list->bins_ssa[i] = list->gbinhead_ssa[ibin];
|
|
list->gbinhead_ssa[ibin] = i;
|
|
}
|
|
}
|
|
} else {
|
|
for (i = nall-1; i >= nlocal; i--) {
|
|
if (ssaAIR[i] < 2) continue; // skip ghost atoms not in AIR
|
|
ibin = coord2bin(x[i]);
|
|
list->bins_ssa[i] = list->gbinhead_ssa[ibin];
|
|
list->gbinhead_ssa[ibin] = i;
|
|
}
|
|
}
|
|
for (i = nlocal-1; i >= 0; i--) {
|
|
ibin = coord2bin(x[i]);
|
|
list->bins_ssa[i] = list->binhead_ssa[ibin];
|
|
list->binhead_ssa[ibin] = i;
|
|
}
|
|
} /* else reuse previous binning. See Neighbor::build_one comment. */
|
|
|
|
ipage->reset();
|
|
|
|
// loop over owned atoms, storing half of the neighbors
|
|
|
|
for (i = 0; i < nlocal; i++) {
|
|
int AIRct[8] = { 0 };
|
|
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 rest of local atoms in i's bin
|
|
// just store them, since j is beyond i in linked list
|
|
|
|
for (j = list->bins_ssa[i]; j >= 0; j = list->bins_ssa[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) {
|
|
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;
|
|
}
|
|
}
|
|
|
|
ibin = coord2bin(x[i]);
|
|
|
|
// loop over all local atoms in other bins in "half" stencil
|
|
for (k = 0; k < nstencil; k++) {
|
|
for (j = list->binhead_ssa[ibin+stencil[k]]; j >= 0; j = list->bins_ssa[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) {
|
|
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;
|
|
}
|
|
}
|
|
}
|
|
AIRct[0] = n;
|
|
|
|
// loop over AIR ghost atoms in all bins in "full" stencil
|
|
// Note: the non-AIR ghost atoms have already been filtered out
|
|
// That is a significant time savings because of the "full" stencil
|
|
// Note2: only non-pure locals can have ghosts as neighbors
|
|
if (ssaAIR[i] == 1) for (k = 0; k < maxstencil; k++) {
|
|
if (stencil[k] > mbins) break; /* Check if ghost stencil bins are exhausted */
|
|
for (j = list->gbinhead_ssa[ibin+stencil[k]]; j >= 0; j = list->bins_ssa[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) {
|
|
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;
|
|
++(AIRct[ssaAIR[j] - 1]);
|
|
} else if (domain->minimum_image_check(delx,dely,delz)) {
|
|
neighptr[n++] = j;
|
|
++(AIRct[ssaAIR[j] - 1]);
|
|
} else if (which > 0) {
|
|
neighptr[n++] = j ^ (which << SBBITS);
|
|
++(AIRct[ssaAIR[j] - 1]);
|
|
}
|
|
} else {
|
|
neighptr[n++] = j;
|
|
++(AIRct[ssaAIR[j] - 1]);
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
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");
|
|
|
|
// sort the ghosts in the neighbor list by their ssaAIR number
|
|
ssaAIRptr = atom->ssaAIR;
|
|
qsort(&(neighptr[AIRct[0]]), n - AIRct[0], sizeof(int), cmp_ssaAIR);
|
|
|
|
// Do a prefix sum on the counts to turn them into indexes.
|
|
list->ndxAIR_ssa[i][0] = AIRct[0];
|
|
for (int ndx = 1; ndx < 8; ++ndx) {
|
|
list->ndxAIR_ssa[i][ndx] = AIRct[ndx] + list->ndxAIR_ssa[i][ndx - 1];
|
|
}
|
|
}
|
|
|
|
list->inum = inum;
|
|
}
|