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lammps/src/neigh_half_multi.cpp
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neigh_half_multi.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.
------------------------------------------------------------------------- */
#include "neighbor.h"
#include "neigh_list.h"
#include "atom.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ----------------------------------------------------------------------
binned neighbor list construction with partial Newton's 3rd law
each owned atom i checks own bin and other bins in stencil
multi-type stencil is itype dependent and is distance checked
pair stored once if i,j are both owned and i < j
pair stored by me if j is ghost (also stored by proc owning j)
------------------------------------------------------------------------- */
void Neighbor::half_multi_no_newton(NeighList *list)
{
int i,j,k,n,itype,jtype,ibin,which,ns;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr,*s;
double *cutsq,*distsq;
// bin local & ghost atoms
bin_atoms();
// loop over each atom, storing neighbors
int **special = atom->special;
int **nspecial = atom->nspecial;
int *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
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_multi = list->nstencil_multi;
int **stencil_multi = list->stencil_multi;
double **distsq_multi = list->distsq_multi;
int inum = 0;
int npage = 0;
int npnt = 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;
itype = type[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
// loop over all atoms in other bins in stencil including self
// only store pair if i < j
// skip if i,j neighbor cutoff is less than bin distance
// stores own/own pairs only once
// stores own/ghost pairs on both procs
ibin = coord2bin(x[i]);
s = stencil_multi[itype];
distsq = distsq_multi[itype];
cutsq = cutneighsq[itype];
ns = nstencil_multi[itype];
for (k = 0; k < ns; k++) {
for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
if (j <= i) continue;
jtype = type[j];
if (cutsq[jtype] < distsq[k]) continue;
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(special[i],nspecial[i],tag[j]);
if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
}
}
}
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
npnt += n;
if (n > oneatom)
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
list->inum = inum;
}
/* ----------------------------------------------------------------------
binned neighbor list construction with full Newton's 3rd law
each owned atom i checks its own bin and other bins in Newton stencil
multi-type stencil is itype dependent and is distance checked
every pair stored exactly once by some processor
------------------------------------------------------------------------- */
void Neighbor::half_multi_newton(NeighList *list)
{
int i,j,k,n,itype,jtype,ibin,which,ns;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr,*s;
double *cutsq,*distsq;
// bin local & ghost atoms
bin_atoms();
// loop over each atom, storing neighbors
int **special = atom->special;
int **nspecial = atom->nspecial;
int *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
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_multi = list->nstencil_multi;
int **stencil_multi = list->stencil_multi;
double **distsq_multi = list->distsq_multi;
int inum = 0;
int npage = 0;
int npnt = 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;
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) {
if (x[j][1] < ytmp) continue;
if (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(special[i],nspecial[i],tag[j]);
if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
}
}
// loop over all atoms in other bins in stencil, store every pair
// skip if i,j neighbor cutoff is less than bin distance
ibin = coord2bin(x[i]);
s = stencil_multi[itype];
distsq = distsq_multi[itype];
cutsq = cutneighsq[itype];
ns = nstencil_multi[itype];
for (k = 0; k < ns; k++) {
for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
jtype = type[j];
if (cutsq[jtype] < distsq[k]) continue;
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(special[i],nspecial[i],tag[j]);
if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
}
}
}
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
npnt += n;
if (n > oneatom)
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
list->inum = inum;
}
/* ----------------------------------------------------------------------
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
multi-type stencil is itype dependent and is distance checked
every pair stored exactly once by some processor
------------------------------------------------------------------------- */
void Neighbor::half_multi_newton_tri(NeighList *list)
{
int i,j,k,n,itype,jtype,ibin,which,ns;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr,*s;
double *cutsq,*distsq;
// bin local & ghost atoms
bin_atoms();
// loop over each atom, storing neighbors
int **special = atom->special;
int **nspecial = atom->nspecial;
int *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
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_multi = list->nstencil_multi;
int **stencil_multi = list->stencil_multi;
double **distsq_multi = list->distsq_multi;
int inum = 0;
int npage = 0;
int npnt = 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;
itype = type[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
// loop over all atoms in bins, including self, in stencil
// skip if i,j neighbor cutoff is less than bin distance
// bins below self are excluded from stencil
// pairs for atoms j "below" i are excluded
// below = lower z or (equal z and lower y) or (equal zy and lower x)
// (equal zyx and j <= i)
// latter excludes self-self interaction but allows superposed atoms
ibin = coord2bin(x[i]);
s = stencil_multi[itype];
distsq = distsq_multi[itype];
cutsq = cutneighsq[itype];
ns = nstencil_multi[itype];
for (k = 0; k < ns; k++) {
for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
jtype = type[j];
if (cutsq[jtype] < distsq[k]) continue;
if (x[j][2] < ztmp) continue;
if (x[j][2] == ztmp) {
if (x[j][1] < ytmp) continue;
if (x[j][1] == ytmp) {
if (x[j][0] < xtmp) continue;
if (x[j][0] == xtmp && j <= i) continue;
}
}
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(special[i],nspecial[i],tag[j]);
if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
}
}
}
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
npnt += n;
if (n > oneatom)
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
list->inum = inum;
}
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