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lammps/src/neigh_stencil.cpp
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neigh_stencil.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"
using namespace LAMMPS_NS;
/* ----------------------------------------------------------------------
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 off:
stencil is all surrounding bins including self
regardless of triclinic
for half list with newton on:
stencil is bins to the "upper right" of central bin
stencil does not include self
for half list with triclinic:
stencil is all bins in z-plane of self and above, but not below
in 2d is all bins in y-plane of self and above, but not below
stencil includes self
for full list:
stencil is all surrounding bins including self
regardless of newton on/off or triclinic
for multi:
create one stencil for each atom type
stencil is same bin bounds as newton on/off, triclinic, half/full
cutoff is not cutneighmaxsq, but max cutoff for that atom type
------------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
void Neighbor::stencil_half_bin_2d_no_newton(NeighList *list,
int sx, int sy, int sz)
{
int i,j;
int *stencil = list->stencil;
int nstencil = 0;
for (j = -sy; j <= sy; j++)
for (i = -sx; i <= sx; i++)
if (bin_distance(i,j,0) < cutneighmaxsq)
stencil[nstencil++] = j*mbinx + i;
list->nstencil = nstencil;
}
/* ---------------------------------------------------------------------- */
void Neighbor::stencil_half_ghost_bin_2d_no_newton(NeighList *list,
int sx, int sy, int sz)
{
int *stencil = list->stencil;
int **stencilxyz = list->stencilxyz;
int nstencil = 0;
for (int j = -sy; j <= sy; j++)
for (int i = -sx; i <= sx; i++)
if (bin_distance(i,j,0) < cutneighmaxsq) {
stencilxyz[nstencil][0] = i;
stencilxyz[nstencil][1] = j;
stencilxyz[nstencil][2] = 0;
stencil[nstencil++] = j*mbinx + i;
}
list->nstencil = nstencil;
}
/* ---------------------------------------------------------------------- */
void Neighbor::stencil_half_bin_3d_no_newton(NeighList *list,
int sx, int sy, int sz)
{
int i,j,k;
int *stencil = list->stencil;
int nstencil = 0;
for (k = -sz; k <= sz; 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;
list->nstencil = nstencil;
}
/* ---------------------------------------------------------------------- */
void Neighbor::stencil_half_ghost_bin_3d_no_newton(NeighList *list,
int sx, int sy, int sz)
{
int i,j,k;
int *stencil = list->stencil;
int **stencilxyz = list->stencilxyz;
int nstencil = 0;
for (k = -sz; k <= sz; k++)
for (j = -sy; j <= sy; j++)
for (i = -sx; i <= sx; i++)
if (bin_distance(i,j,k) < cutneighmaxsq) {
stencilxyz[nstencil][0] = i;
stencilxyz[nstencil][1] = j;
stencilxyz[nstencil][2] = k;
stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i;
}
list->nstencil = nstencil;
}
/* ---------------------------------------------------------------------- */
void Neighbor::stencil_half_bin_2d_newton(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;
}
/* ---------------------------------------------------------------------- */
void Neighbor::stencil_half_bin_3d_newton(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;
}
/* ---------------------------------------------------------------------- */
void Neighbor::stencil_half_bin_2d_newton_tri(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 (bin_distance(i,j,0) < cutneighmaxsq)
stencil[nstencil++] = j*mbinx + i;
list->nstencil = nstencil;
}
/* ---------------------------------------------------------------------- */
void Neighbor::stencil_half_bin_3d_newton_tri(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 (bin_distance(i,j,k) < cutneighmaxsq)
stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i;
list->nstencil = nstencil;
}
/* ---------------------------------------------------------------------- */
void Neighbor::stencil_half_multi_2d_no_newton(NeighList *list,
int sx, int sy, int sz)
{
int i,j,n;
double rsq,typesq;
int *s;
double *distsq;
int *nstencil_multi = list->nstencil_multi;
int **stencil_multi = list->stencil_multi;
double **distsq_multi = list->distsq_multi;
int ntypes = atom->ntypes;
for (int itype = 1; itype <= ntypes; itype++) {
typesq = cuttypesq[itype];
s = stencil_multi[itype];
distsq = distsq_multi[itype];
n = 0;
for (j = -sy; j <= sy; j++)
for (i = -sx; i <= sx; i++) {
rsq = bin_distance(i,j,0);
if (rsq < typesq) {
distsq[n] = rsq;
s[n++] = j*mbinx + i;
}
}
nstencil_multi[itype] = n;
}
}
/* ---------------------------------------------------------------------- */
void Neighbor::stencil_half_multi_3d_no_newton(NeighList *list,
int sx, int sy, int sz)
{
int i,j,k,n;
double rsq,typesq;
int *s;
double *distsq;
int *nstencil_multi = list->nstencil_multi;
int **stencil_multi = list->stencil_multi;
double **distsq_multi = list->distsq_multi;
int ntypes = atom->ntypes;
for (int itype = 1; itype <= ntypes; itype++) {
typesq = cuttypesq[itype];
s = stencil_multi[itype];
distsq = distsq_multi[itype];
n = 0;
for (k = -sz; k <= sz; k++)
for (j = -sy; j <= sy; j++)
for (i = -sx; i <= sx; i++) {
rsq = bin_distance(i,j,k);
if (rsq < typesq) {
distsq[n] = rsq;
s[n++] = k*mbiny*mbinx + j*mbinx + i;
}
}
nstencil_multi[itype] = n;
}
}
/* ---------------------------------------------------------------------- */
void Neighbor::stencil_half_multi_2d_newton(NeighList *list,
int sx, int sy, int sz)
{
int i,j,n;
double rsq,typesq;
int *s;
double *distsq;
int *nstencil_multi = list->nstencil_multi;
int **stencil_multi = list->stencil_multi;
double **distsq_multi = list->distsq_multi;
int ntypes = atom->ntypes;
for (int itype = 1; itype <= ntypes; itype++) {
typesq = cuttypesq[itype];
s = stencil_multi[itype];
distsq = distsq_multi[itype];
n = 0;
for (j = 0; j <= sy; j++)
for (i = -sx; i <= sx; i++)
if (j > 0 || (j == 0 && i > 0)) {
rsq = bin_distance(i,j,0);
if (rsq < typesq) {
distsq[n] = rsq;
s[n++] = j*mbinx + i;
}
}
nstencil_multi[itype] = n;
}
}
/* ---------------------------------------------------------------------- */
void Neighbor::stencil_half_multi_3d_newton(NeighList *list,
int sx, int sy, int sz)
{
int i,j,k,n;
double rsq,typesq;
int *s;
double *distsq;
int *nstencil_multi = list->nstencil_multi;
int **stencil_multi = list->stencil_multi;
double **distsq_multi = list->distsq_multi;
int ntypes = atom->ntypes;
for (int itype = 1; itype <= ntypes; itype++) {
typesq = cuttypesq[itype];
s = stencil_multi[itype];
distsq = distsq_multi[itype];
n = 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)) {
rsq = bin_distance(i,j,k);
if (rsq < typesq) {
distsq[n] = rsq;
s[n++] = k*mbiny*mbinx + j*mbinx + i;
}
}
nstencil_multi[itype] = n;
}
}
/* ---------------------------------------------------------------------- */
void Neighbor::stencil_half_multi_2d_newton_tri(NeighList *list,
int sx, int sy, int sz)
{
int i,j,n;
double rsq,typesq;
int *s;
double *distsq;
int *nstencil_multi = list->nstencil_multi;
int **stencil_multi = list->stencil_multi;
double **distsq_multi = list->distsq_multi;
int ntypes = atom->ntypes;
for (int itype = 1; itype <= ntypes; itype++) {
typesq = cuttypesq[itype];
s = stencil_multi[itype];
distsq = distsq_multi[itype];
n = 0;
for (j = 0; j <= sy; j++)
for (i = -sx; i <= sx; i++) {
rsq = bin_distance(i,j,0);
if (rsq < typesq) {
distsq[n] = rsq;
s[n++] = j*mbinx + i;
}
}
nstencil_multi[itype] = n;
}
}
/* ---------------------------------------------------------------------- */
void Neighbor::stencil_half_multi_3d_newton_tri(NeighList *list,
int sx, int sy, int sz)
{
int i,j,k,n;
double rsq,typesq;
int *s;
double *distsq;
int *nstencil_multi = list->nstencil_multi;
int **stencil_multi = list->stencil_multi;
double **distsq_multi = list->distsq_multi;
int ntypes = atom->ntypes;
for (int itype = 1; itype <= ntypes; itype++) {
typesq = cuttypesq[itype];
s = stencil_multi[itype];
distsq = distsq_multi[itype];
n = 0;
for (k = 0; k <= sz; k++)
for (j = -sy; j <= sy; j++)
for (i = -sx; i <= sx; i++) {
rsq = bin_distance(i,j,k);
if (rsq < typesq) {
distsq[n] = rsq;
s[n++] = k*mbiny*mbinx + j*mbinx + i;
}
}
nstencil_multi[itype] = n;
}
}
/* ---------------------------------------------------------------------- */
void Neighbor::stencil_full_bin_2d(NeighList *list,
int sx, int sy, int sz)
{
int i,j;
int *stencil = list->stencil;
int nstencil = 0;
for (j = -sy; j <= sy; j++)
for (i = -sx; i <= sx; i++)
if (bin_distance(i,j,0) < cutneighmaxsq)
stencil[nstencil++] = j*mbinx + i;
list->nstencil = nstencil;
}
/* ---------------------------------------------------------------------- */
void Neighbor::stencil_full_ghost_bin_2d(NeighList *list,
int sx, int sy, int sz)
{
int i,j;
int *stencil = list->stencil;
int **stencilxyz = list->stencilxyz;
int nstencil = 0;
for (j = -sy; j <= sy; j++)
for (i = -sx; i <= sx; i++)
if (bin_distance(i,j,0) < cutneighmaxsq) {
stencilxyz[nstencil][0] = i;
stencilxyz[nstencil][1] = j;
stencilxyz[nstencil][2] = 0;
stencil[nstencil++] = j*mbinx + i;
}
list->nstencil = nstencil;
}
/* ---------------------------------------------------------------------- */
void Neighbor::stencil_full_bin_3d(NeighList *list,
int sx, int sy, int sz)
{
int i,j,k;
int *stencil = list->stencil;
int nstencil = 0;
for (k = -sz; k <= sz; 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;
list->nstencil = nstencil;
}
/* ---------------------------------------------------------------------- */
void Neighbor::stencil_full_ghost_bin_3d(NeighList *list,
int sx, int sy, int sz)
{
int i,j,k;
int *stencil = list->stencil;
int **stencilxyz = list->stencilxyz;
int nstencil = 0;
for (k = -sz; k <= sz; k++)
for (j = -sy; j <= sy; j++)
for (i = -sx; i <= sx; i++)
if (bin_distance(i,j,k) < cutneighmaxsq) {
stencilxyz[nstencil][0] = i;
stencilxyz[nstencil][1] = j;
stencilxyz[nstencil][2] = k;
stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i;
}
list->nstencil = nstencil;
}
/* ---------------------------------------------------------------------- */
void Neighbor::stencil_full_multi_2d(NeighList *list,
int sx, int sy, int sz)
{
int i,j,n;
double rsq,typesq;
int *s;
double *distsq;
int *nstencil_multi = list->nstencil_multi;
int **stencil_multi = list->stencil_multi;
double **distsq_multi = list->distsq_multi;
int ntypes = atom->ntypes;
for (int itype = 1; itype <= ntypes; itype++) {
typesq = cuttypesq[itype];
s = stencil_multi[itype];
distsq = distsq_multi[itype];
n = 0;
for (j = -sy; j <= sy; j++)
for (i = -sx; i <= sx; i++) {
rsq = bin_distance(i,j,0);
if (rsq < typesq) {
distsq[n] = rsq;
s[n++] = j*mbinx + i;
}
}
nstencil_multi[itype] = n;
}
}
/* ---------------------------------------------------------------------- */
void Neighbor::stencil_full_multi_3d(NeighList *list,
int sx, int sy, int sz)
{
int i,j,k,n;
double rsq,typesq;
int *s;
double *distsq;
int *nstencil_multi = list->nstencil_multi;
int **stencil_multi = list->stencil_multi;
double **distsq_multi = list->distsq_multi;
int ntypes = atom->ntypes;
for (int itype = 1; itype <= ntypes; itype++) {
typesq = cuttypesq[itype];
s = stencil_multi[itype];
distsq = distsq_multi[itype];
n = 0;
for (k = -sz; k <= sz; k++)
for (j = -sy; j <= sy; j++)
for (i = -sx; i <= sx; i++) {
rsq = bin_distance(i,j,k);
if (rsq < typesq) {
distsq[n] = rsq;
s[n++] = k*mbiny*mbinx + j*mbinx + i;
}
}
nstencil_multi[itype] = n;
}
}
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