539 lines
15 KiB
C++
539 lines
15 KiB
C++
/* ----------------------------------------------------------------------
|
|
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
|
|
stencil includes 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 i,j,k;
|
|
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_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;
|
|
}
|
|
}
|