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lammps/src/neigh_shardlow.cpp
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/* ----------------------------------------------------------------------
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;
/* ----------------------------------------------------------------------
convert atom coords into the ssa active interaction region number
------------------------------------------------------------------------- */
int Neighbor::coord2ssa_airnum(double *x)
{
int ix, iy, iz;
ix = iy = iz = 0;
if (x[2] < domain->sublo[2]) iz = -1;
if (x[2] > domain->subhi[2]) iz = 1;
if (x[1] < domain->sublo[1]) iy = -1;
if (x[1] > domain->subhi[1]) iy = 1;
if (x[0] < domain->sublo[0]) ix = -1;
if (x[0] > domain->subhi[0]) ix = 1;
if(iz < 0) return 0;
if(iz == 0){
if( iy<0 ) return 0; // bottom left/middle/right
if( (iy==0) && (ix<0) ) return 0; // left atoms
if( (iy==0) && (ix==0) ) return 1; // Locally owned atoms
if( (iy==0) && (ix>0) ) return 3; // Right atoms
if( (iy>0) && (ix==0) ) return 2; // Top-middle atoms
if( (iy>0) && (ix!=0) ) return 4; // Top-right and top-left atoms
} else if(iz > 0) {
if((ix==0) && (iy==0)) return 5; // Back atoms
if((ix==0) && (iy!=0)) return 6; // Top-back and bottom-back atoms
if((ix!=0) && (iy==0)) return 7; // Left-back and right-back atoms
if((ix!=0) && (iy!=0)) return 8; // Back corner atoms
}
return 0;
}
/* ----------------------------------------------------------------------
* assign owned and ghost atoms their ssa active interaction region numbers
* Called in the pre_neighbor and setup_pre_neighbor fix stages
------------------------------------------------------------------------- */
void Neighbor::assign_ssa_airnums()
{
int i,ibin;
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
if (nall > len_ssa_airnum) {
len_ssa_airnum = nall;
memory->destroy(ssa_airnum);
memory->create(ssa_airnum,len_ssa_airnum,"ssa_airnum");
}
// bin in reverse order so linked list will be in forward order
if (includegroup) {
int bitmask = group->bitmask[includegroup];
for (i = nall-1; i >= nlocal; i--) {
if (mask[i] & bitmask) {
ibin = coord2ssa_airnum(x[i]);
} else {
ibin = 0;
}
ssa_airnum[i] = ibin;
}
// All the local excluded atoms are in the zero airnum
ibin = 0;
for (i = atom->nlocal-1; i >= atom->nfirst; i--) {
ssa_airnum[i] = ibin;
}
} else {
for (i = nall-1; i >= nlocal; i--) {
ibin = coord2ssa_airnum(x[i]);
ssa_airnum[i] = ibin;
}
}
// All the local included atoms are in the same airnum (#1)
if (i >= 0) {
ibin = coord2ssa_airnum(x[i]);
do {
ssa_airnum[i] = ibin;
} while (--i >= 0);
}
}
/* ----------------------------------------------------------------------
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;
}
}
/* ----------------------------------------------------------------------
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 *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++) {
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;
} else {
if (ssa_airnum[j] <= 0) continue;
}
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");
}
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;
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;
/* ----------------------------------------------------------------------
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 > maxhead_ssa) {
maxhead_ssa = mbins;
memory->destroy(gbinhead_ssa);
memory->destroy(binhead_ssa);
memory->create(binhead_ssa,maxhead_ssa,"binhead_ssa");
memory->create(gbinhead_ssa,maxhead_ssa,"gbinhead_ssa");
}
for (i = 0; i < mbins; i++) {
gbinhead_ssa[i] = -1;
binhead_ssa[i] = -1;
}
if (maxbin > maxbin_ssa) {
maxbin_ssa = maxbin;
memory->destroy(bins_ssa);
memory->create(bins_ssa,maxbin_ssa,"bins_ssa");
}
// bin in reverse order so linked list will be in forward order
if (includegroup) {
int bitmask = group->bitmask[includegroup];
for (i = nall-1; i >= nlocal; i--) {
if (ssa_airnum[i] <= 0) continue; // skip ghost atoms not in AIR
if (mask[i] & bitmask) {
ibin = coord2bin(x[i]);
bins_ssa[i] = gbinhead_ssa[ibin];
gbinhead_ssa[ibin] = i;
}
}
nlocal = atom->nfirst; // This is important for the code that follows!
} else {
for (i = nall-1; i >= nlocal; i--) {
if (ssa_airnum[i] <= 0) continue; // skip ghost atoms not in AIR
ibin = coord2bin(x[i]);
bins_ssa[i] = gbinhead_ssa[ibin];
gbinhead_ssa[ibin] = i;
}
}
for (i = nlocal-1; i >= 0; i--) {
ibin = coord2bin(x[i]);
bins_ssa[i] = binhead_ssa[ibin];
binhead_ssa[ibin] = i;
}
ipage->reset();
// loop over owned atoms, storing half of the 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 rest of local atoms in i's bin
// just store them, since j is beyond i in linked list
for (j = bins_ssa[i]; j >= 0; j = 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 = binhead_ssa[ibin+stencil[k]]; j >= 0; j = 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;
}
}
}
// loop over AIR ghost atoms in all bins in "full" stencil
// Note: the non-AIR ghost atoms have already been filtered out
for (k = 0; k < maxstencil; k++) {
if (stencil[k] > mbins) break; /* Check if ghost stencil bins are exhausted */
for (j = gbinhead_ssa[ibin+stencil[k]]; j >= 0; j = 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;
}
}
}
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;
}
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