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lammps/src/npair_half_bin_newton_ssa.cpp
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npair_half_bin_newton_ssa.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 "npair_half_bin_newton_ssa.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "atom.h"
#include "atom_vec.h"
#include "molecule.h"
#include "domain.h"
#include "group.h"
#include "memory.h"
#include "my_page.h"
#include "error.h"
using namespace LAMMPS_NS;
// allocate space for static class variable
// prototype for non-class function
static int *ssaAIRptr;
static int cmp_ssaAIR(const void *, const void *);
/* ---------------------------------------------------------------------- */
NPairHalfBinNewtonSSA::NPairHalfBinNewtonSSA(LAMMPS *lmp) : NPair(lmp) {}
/* ----------------------------------------------------------------------
binned neighbor list construction with full Newton's 3rd law
for use by Shardlow Spliting Algorithm
each owned atom i checks its own bin and other bins in Newton stencil
every pair stored exactly once by some processor
------------------------------------------------------------------------- */
void NPairHalfBinNewtonSSA::build(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;
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)
// NOTE to Tim: this binatomflag no longer exists
// the logic up higher assures that binning has been done
// before this build() method is called
// maybe this code below needs to be in a new NBinShardlow class?
// this class also inherits NPair::nb from its parent
// which points to the NBin class that did the binning
// there are last_step variables stored there which indicate
// the last time binning was done
// the basic question is what data is created/stored by SSA binning
// and in what class should it live?
// if it is created by the binning operation, then I think
// it should be in a new NBinShardlow class
if (true /* binatomflag */) { // only false in Neighbor::build_one
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 (nall > list->maxbin_ssa) {
list->maxbin_ssa = nall;
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 < nstencil_ssa; k++) {
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;
}
/* ----------------------------------------------------------------------
comparison function invoked by qsort()
accesses static class member ssaAIRptr, set before call to qsort()
------------------------------------------------------------------------- */
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;
}
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