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npair_half_bin_newton_ssa.cpp
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Thu, Jul 4, 15:53

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 "nstencil_ssa.h"
#include "nbin_ssa.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;
/* ---------------------------------------------------------------------- */
NPairHalfBinNewtonSSA::NPairHalfBinNewtonSSA(LAMMPS *lmp) : NPair(lmp)
{
ssa_maxPhaseCt = 0;
ssa_maxPhaseLen = 0;
ssa_phaseCt = 0;
ssa_phaseLen = NULL;
ssa_itemLoc = NULL;
ssa_itemLen = NULL;
}
/* ---------------------------------------------------------------------- */
NPairHalfBinNewtonSSA::~NPairHalfBinNewtonSSA()
{
ssa_maxPhaseCt = 0;
ssa_maxPhaseLen = 0;
ssa_phaseCt = 0;
memory->destroy(ssa_phaseLen);
memory->destroy(ssa_itemLoc);
memory->destroy(ssa_itemLen);
}
/* ----------------------------------------------------------------------
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;
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;
MyPage<int> *ipage = list->ipage;
NStencilSSA *ns_ssa = dynamic_cast<NStencilSSA*>(ns);
if (!ns_ssa) error->one(FLERR, "NStencil wasn't a NStencilSSA object");
int *nstencil_ssa = &(ns_ssa->nstencil_ssa[0]);
int nstencil_full = ns_ssa->nstencil;
NBinSSA *nb_ssa = dynamic_cast<NBinSSA*>(nb);
if (!nb_ssa) error->one(FLERR, "NBin wasn't a NBinSSA object");
int *bins = nb_ssa->bins;
int *binhead = nb_ssa->binhead;
int *gairhead_ssa = &(nb_ssa->gairhead_ssa[0]);
int inum = 0;
int gnum = 0;
int xbin,ybin,zbin,xbin2,ybin2,zbin2;
int **stencilxyz = ns_ssa->stencilxyz;
int lbinxlo = nb_ssa->lbinxlo;
int lbinxhi = nb_ssa->lbinxhi;
int lbinylo = nb_ssa->lbinylo;
int lbinyhi = nb_ssa->lbinyhi;
int lbinzlo = nb_ssa->lbinzlo;
int lbinzhi = nb_ssa->lbinzhi;
int sx1 = ns_ssa->sx + 1;
int sy1 = ns_ssa->sy + 1;
int sz1 = ns_ssa->sz + 1;
ssa_phaseCt = sz1*sy1*sx1;
xbin = (lbinxhi - lbinxlo + sx1 - 1) / sx1 + 1;
ybin = (lbinyhi - lbinylo + sy1 - 1) / sy1 + 1;
zbin = (lbinzhi - lbinzlo + sz1 - 1) / sz1 + 1;
int phaseLenEstimate = xbin*ybin*zbin;
if (ssa_phaseCt > ssa_maxPhaseCt) {
ssa_maxPhaseCt = ssa_phaseCt;
ssa_maxPhaseLen = 0;
memory->destroy(ssa_phaseLen);
memory->destroy(ssa_itemLoc);
memory->destroy(ssa_itemLen);
memory->create(ssa_phaseLen,ssa_maxPhaseCt,"NPairHalfBinNewtonSSA:ssa_phaseLen");
}
if (phaseLenEstimate > ssa_maxPhaseLen) {
ssa_maxPhaseLen = phaseLenEstimate;
memory->destroy(ssa_itemLoc);
memory->destroy(ssa_itemLen);
memory->create(ssa_itemLoc,ssa_maxPhaseCt,ssa_maxPhaseLen,"NPairHalfBinNewtonSSA:ssa_itemLoc");
memory->create(ssa_itemLen,ssa_maxPhaseCt,ssa_maxPhaseLen,"NPairHalfBinNewtonSSA:ssa_itemLen");
}
ipage->reset();
int workPhase = 0;
// loop over bins with local atoms, storing half of the neighbors
for (int zoff = ns_ssa->sz; zoff >= 0; --zoff) {
for (int yoff = ns_ssa->sy; yoff >= 0; --yoff) {
for (int xoff = ns_ssa->sx; xoff >= 0; --xoff) {
int workItem = 0;
for (zbin = lbinzlo + zoff; zbin < lbinzhi; zbin += sz1) {
for (ybin = lbinylo + yoff - ns_ssa->sy; ybin < lbinyhi; ybin += sy1) {
for (xbin = lbinxlo + xoff - ns_ssa->sx; xbin < lbinxhi; xbin += sx1) {
if (workItem >= phaseLenEstimate) error->one(FLERR,"phaseLenEstimate was too small");
ssa_itemLoc[workPhase][workItem] = inum; // record where workItem starts in ilist
for (int subphase = 0; subphase < 4; subphase++) {
int s_ybin = ybin + ((subphase & 0x2) ? ns_ssa->sy : 0);
int s_xbin = xbin + ((subphase & 0x1) ? ns_ssa->sx : 0);
int ibin, ct;
if ((s_ybin < lbinylo) || (s_ybin >= lbinyhi)) continue;
if ((s_xbin < lbinxlo) || (s_xbin >= lbinxhi)) continue;
ibin = zbin*nb_ssa->mbiny*nb_ssa->mbinx
+ s_ybin*nb_ssa->mbinx
+ s_xbin;
for (i = binhead[ibin]; i >= 0; i = bins[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 local atoms in the current stencil "subphase"
for (k = nstencil_ssa[subphase]; k < nstencil_ssa[subphase+1]; k++) {
const int jbin = ibin+stencil[k];
if (jbin != ibin) j = binhead[jbin];
else j = bins[i]; // same bin as i, so start just past i in the bin
for (; 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) {
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;
}
}
}
if (n > 0) {
firstneigh[inum] = neighptr;
numneigh[inum] = n;
ilist[inum++] = i;
}
ipage->vgot(n);
if (ipage->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
}
// record where workItem ends in ilist
ssa_itemLen[workPhase][workItem] = inum - ssa_itemLoc[workPhase][workItem];
if (ssa_itemLen[workPhase][workItem] > 0) workItem++;
}
}
}
// record where workPhase ends
ssa_phaseLen[workPhase++] = workItem;
}
}
}
if (ssa_phaseCt != workPhase) error->one(FLERR,"ssa_phaseCt was wrong");
list->AIRct_ssa[0] = list->inum = inum;
// loop over AIR ghost atoms, storing their local neighbors
// since these are ghosts, must check if stencil bin is out of bounds
for (int airnum = 1; airnum <= 7; airnum++) {
int locAIRct = 0;
for (i = gairhead_ssa[airnum]; i >= 0; i = bins[i]) {
n = 0;
neighptr = ipage->vget();
itype = type[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
ibin = coord2bin(x[i],xbin,ybin,zbin);
// 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 < nstencil_full; k++) {
xbin2 = xbin + stencilxyz[k][0];
ybin2 = ybin + stencilxyz[k][1];
zbin2 = zbin + stencilxyz[k][2];
// Skip it if this bin is outside the extent of local bins
if (xbin2 < lbinxlo || xbin2 >= lbinxhi ||
ybin2 < lbinylo || ybin2 >= lbinyhi ||
zbin2 < lbinzlo || zbin2 >= lbinzhi) continue;
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) {
if (!moltemplate)
which = find_special(special[j],nspecial[j],tag[i]);
else {
int jmol = molindex[j];
if (jmol >= 0) {
int jatom = molatom[j];
which = find_special(onemols[jmol]->special[jatom],
onemols[jmol]->nspecial[jatom],
tag[i] - (tag[j] - jatom - 1));
} 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;
}
}
}
if (n > 0) {
firstneigh[inum + gnum] = neighptr;
numneigh[inum + gnum] = n;
ilist[inum + (gnum++)] = i;
++locAIRct;
}
ipage->vgot(n);
if (ipage->status())
error->one(FLERR,"Neighbor (ghost) list overflow, boost neigh_modify one");
}
list->AIRct_ssa[airnum] = locAIRct;
}
list->gnum = gnum;
}

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