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lammps/src/neigh_half.cpp
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neigh_half.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 "atom.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ----------------------------------------------------------------------
N^2 / 2 search for neighbor pairs with partial Newton's 3rd law
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_nsq_no_newton()
{
int i,j,n,itype,jtype,which;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr;
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
int molecular = atom->molecular;
int npage = 0;
int npnt = 0;
for (i = 0; i < nlocal; i++) {
if (pgsize - npnt < oneatom) {
npnt = 0;
npage++;
if (npage == maxpage) add_pages(npage);
}
neighptr = &pages[npage][npnt];
n = 0;
itype = type[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
// loop over remaining atoms, owned and ghost
for (j = i+1; j < nall; j++) {
if (exclude && exclusion(i,j,type,mask,molecule)) continue;
jtype = type[j];
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(i,j);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
}
}
firstneigh[i] = neighptr;
numneigh[i] = n;
npnt += n;
if (npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
}
}
/* ----------------------------------------------------------------------
N^2 / 2 search for neighbor pairs with full Newton's 3rd law
every pair stored exactly once by some processor
decision on ghost atoms based on itag,jtag tests
------------------------------------------------------------------------- */
void Neighbor::half_nsq_newton()
{
int i,j,n,itype,jtype,itag,jtag,which;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr;
double **x = atom->x;
int *tag = atom->tag;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
int molecular = atom->molecular;
int npage = 0;
int npnt = 0;
for (i = 0; i < nlocal; i++) {
if (pgsize - npnt < oneatom) {
npnt = 0;
npage++;
if (npage == maxpage) add_pages(npage);
}
neighptr = &pages[npage][npnt];
n = 0;
itag = tag[i];
itype = type[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
// loop over remaining atoms, owned and ghost
// itag = jtag is possible for long cutoffs that include images of self
for (j = i+1; j < nall; j++) {
if (j >= nlocal) {
jtag = tag[j];
if (itag > jtag) {
if ((itag+jtag) % 2 == 0) continue;
} else if (itag < jtag) {
if ((itag+jtag) % 2 == 1) continue;
} else {
if (x[j][2] < ztmp) continue;
else if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
else if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp)
continue;
}
}
if (exclude && exclusion(i,j,type,mask,molecule)) continue;
jtype = type[j];
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(i,j);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
}
}
firstneigh[i] = neighptr;
numneigh[i] = n;
npnt += n;
if (npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
}
}
/* ----------------------------------------------------------------------
binned neighbor list construction with partial Newton's 3rd law
each owned atom i checks own bin and surrounding bins in non-Newton stencil
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_bin_no_newton()
{
int i,j,k,n,itype,jtype,ibin,which;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr;
// bin local & ghost atoms
bin_atoms();
// loop over each atom, storing neighbors
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
int molecular = atom->molecular;
int npage = 0;
int npnt = 0;
for (i = 0; i < nlocal; i++) {
if (pgsize - npnt < oneatom) {
npnt = 0;
npage++;
if (npage == maxpage) add_pages(npage);
}
neighptr = &pages[npage][npnt];
n = 0;
itype = type[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
ibin = coord2bin(x[i]);
// loop over all atoms in surrounding bins in stencil including self
// only store pair if i < j
// stores own/own pairs only once
// stores own/ghost pairs on both procs
for (k = 0; k < nstencil; k++) {
j = binhead[ibin+stencil[k]];
while (j >= 0) {
if (j <= i) {
j = bins[j];
continue;
}
if (exclude && exclusion(i,j,type,mask,molecule)) {
j = bins[j];
continue;
}
jtype = type[j];
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(i,j);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
}
j = bins[j];
}
}
firstneigh[i] = neighptr;
numneigh[i] = n;
npnt += n;
if (npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
}
}
/* ----------------------------------------------------------------------
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()
{
int i,j,k,n,itype,jtype,ibin,which;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr;
// bin local & ghost atoms
bin_atoms();
// loop over each atom, storing neighbors
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
int molecular = atom->molecular;
int npage = 0;
int npnt = 0;
for (i = 0; i < nlocal; i++) {
if (pgsize - npnt < oneatom) {
npnt = 0;
npage++;
if (npage == maxpage) add_pages(npage);
}
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
j = bins[i];
while (j >= 0) {
if (j >= nlocal) {
if ((x[j][2] < ztmp) || (x[j][2] == ztmp && x[j][1] < ytmp) ||
(x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp)) {
j = bins[j];
continue;
}
}
if (exclude && exclusion(i,j,type,mask,molecule)) {
j = bins[j];
continue;
}
jtype = type[j];
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(i,j);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
}
j = bins[j];
}
// loop over all atoms in other bins in stencil, store every pair
ibin = coord2bin(x[i]);
for (k = 0; k < nstencil; k++) {
j = binhead[ibin+stencil[k]];
while (j >= 0) {
if (exclude && exclusion(i,j,type,mask,molecule)) {
j = bins[j];
continue;
}
jtype = type[j];
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(i,j);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
}
j = bins[j];
}
}
firstneigh[i] = neighptr;
numneigh[i] = n;
npnt += n;
if (npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
}
}
/* ----------------------------------------------------------------------
build half list from full list
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_full_no_newton()
{
int i,j,k,n,nfull;
int *neighptr,*neighs;
int nlocal = atom->nlocal;
int npage = 0;
int npnt = 0;
for (i = 0; i < nlocal; i++) {
if (pgsize - npnt < oneatom) {
npnt = 0;
npage++;
if (npage == maxpage) add_pages(npage);
}
neighptr = &pages[npage][npnt];
n = 0;
// loop over full neighbor list
neighs = firstneigh_full[i];
nfull = numneigh_full[i];
for (k = 0; k < nfull; k++) {
j = neighs[k];
if (j > i) neighptr[n++] = j;
}
firstneigh[i] = neighptr;
numneigh[i] = n;
npnt += n;
if (npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
}
}
/* ----------------------------------------------------------------------
build half list from full list
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_full_newton()
{
int i,j,k,n,nfull;
int *neighptr,*neighs;
double xtmp,ytmp,ztmp;
double **x = atom->x;
int nlocal = atom->nlocal;
int npage = 0;
int npnt = 0;
for (i = 0; i < nlocal; i++) {
if (pgsize - npnt < oneatom) {
npnt = 0;
npage++;
if (npage == maxpage) add_pages(npage);
}
neighptr = &pages[npage][npnt];
n = 0;
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
// loop over full neighbor list
neighs = firstneigh_full[i];
nfull = numneigh_full[i];
for (k = 0; k < nfull; k++) {
j = neighs[k];
if (j < nlocal) {
if (i > j) continue;
} else {
if ((x[j][2] < ztmp) || (x[j][2] == ztmp && x[j][1] < ytmp) ||
(x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp)) {
j = bins[j];
continue;
}
}
neighptr[n++] = j;
}
firstneigh[i] = neighptr;
numneigh[i] = n;
npnt += n;
if (npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
}
}
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