git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@438 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
461
src/neigh_stencil.cpp
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461
src/neigh_stencil.cpp
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@ -0,0 +1,461 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "neighbor.h"
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#include "atom.h"
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#include "memory.h"
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using namespace LAMMPS_NS;
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enum{NSQ,BIN,MULTI}; // also in neighbor.cpp
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/* ----------------------------------------------------------------------
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routines to create a stencil = list of bin offsets
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stencil = bins whose closest corner to central bin is within cutoff
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sx,sy,sz = bin bounds = furthest the stencil could possibly extend
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3d creates xyz stencil, 2d creates xy stencil
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for half neigh list with partial Newton:
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stencil is all surrounding bins
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stencil includes self
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for half neigh list with full Newton:
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stencil is bins to the "upper right" of central bin
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stencil does not include self
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for half neigh list with triclinic:
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stencil is all bins in z-plane of self and above, but not below
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in 2d is all bins in y-plane of self and above, but not below
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stencil includes self
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for full neigh list:
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stencil is all surrounding bins including self
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regardless of newton on/off or triclinic
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for multi:
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create one stencil for each atom type
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stencil is same bin bounds as newton on/off, triclinic, half/full
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cutoff is not cutneighmaxsq, but max cutoff for that atom type
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------------------------------------------------------------------------- */
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/* ---------------------------------------------------------------------- */
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void Neighbor::stencil_allocate(int sx, int sy, int sz)
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{
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int i;
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int nmax = (2*sz+1) * (2*sy+1) * (2*sx+1);
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if (half) {
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if (style == BIN) {
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if (nmax > maxstencil) {
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maxstencil = nmax;
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memory->sfree(stencil);
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stencil = (int *) memory->smalloc(nmax*sizeof(int),"neigh:stencil");
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}
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} else {
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int n = atom->ntypes;
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if (nstencil_multi == NULL) {
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maxstencil_multi = 0;
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nstencil_multi = new int[n+1];
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stencil_multi = new int*[n+1];
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distsq_multi = new double*[n+1];
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for (i = 1; i <= n; i++) {
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nstencil_multi[i] = 0;
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stencil_multi[i] = NULL;
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distsq_multi[i] = NULL;
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}
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}
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if (nmax > maxstencil_multi) {
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maxstencil_multi = nmax;
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for (int i = 1; i <= n; i++) {
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memory->sfree(stencil_multi[i]);
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memory->sfree(distsq_multi[i]);
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stencil_multi[i] = (int *)
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memory->smalloc(nmax*sizeof(int),"neigh:stencil_multi");
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distsq_multi[i] = (double *) memory->smalloc(nmax*sizeof(double),
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"neigh:distsq_multi");
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}
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}
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}
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}
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if (full) {
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if (style == BIN) {
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if (nmax > maxstencil_full) {
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maxstencil_full = nmax;
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memory->sfree(stencil_full);
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stencil_full = (int *) memory->smalloc(nmax*sizeof(int),
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"neigh:stencil_full");
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}
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} else {
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int n = atom->ntypes;
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if (nstencil_full_multi == NULL) {
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maxstencil_full_multi = 0;
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nstencil_full_multi = new int[n+1];
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stencil_full_multi = new int*[n+1];
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distsq_full_multi = new double*[n+1];
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for (i = 1; i <= n; i++) {
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nstencil_full_multi[i] = 0;
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stencil_full_multi[i] = NULL;
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distsq_full_multi[i] = NULL;
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}
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}
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if (nmax > maxstencil_full_multi) {
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maxstencil_full_multi = nmax;
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for (int i = 1; i <= n; i++) {
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memory->sfree(stencil_full_multi[i]);
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memory->sfree(distsq_full_multi[i]);
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stencil_full_multi[i] = (int *)
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memory->smalloc(nmax*sizeof(int),"neigh:stencil_full_multi");
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distsq_full_multi[i] =
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(double *) memory->smalloc(nmax*sizeof(double),
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"neigh:distsq_full_multi");
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}
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}
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}
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}
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}
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/* ---------------------------------------------------------------------- */
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void Neighbor::stencil_none(int sx, int sy, int sz) {}
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/* ---------------------------------------------------------------------- */
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void Neighbor::stencil_half_3d_no_newton(int sx, int sy, int sz)
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{
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int i,j,k;
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nstencil = 0;
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for (k = -sz; k <= sz; k++)
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for (j = -sy; j <= sy; j++)
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for (i = -sx; i <= sx; i++)
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if (bin_distance(i,j,k) < cutneighmaxsq)
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stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i;
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}
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/* ---------------------------------------------------------------------- */
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void Neighbor::stencil_half_3d_no_newton_multi(int sx, int sy, int sz)
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{
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int i,j,k,n;
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double rsq,typesq;
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int *s;
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double *distsq;
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int ntypes = atom->ntypes;
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for (int itype = 1; itype <= ntypes; itype++) {
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typesq = cuttypesq[itype];
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s = stencil_multi[itype];
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distsq = distsq_multi[itype];
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n = 0;
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for (k = -sz; k <= sz; k++)
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for (j = -sy; j <= sy; j++)
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for (i = -sx; i <= sx; i++) {
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rsq = bin_distance(i,j,k);
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if (rsq < typesq) {
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distsq[n] = rsq;
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s[n++] = k*mbiny*mbinx + j*mbinx + i;
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}
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}
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nstencil_multi[itype] = n;
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}
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}
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/* ---------------------------------------------------------------------- */
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void Neighbor::stencil_half_3d_newton(int sx, int sy, int sz)
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{
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int i,j,k;
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nstencil = 0;
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for (k = 0; k <= sz; k++)
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for (j = -sy; j <= sy; j++)
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for (i = -sx; i <= sx; i++)
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if (k > 0 || j > 0 || (j == 0 && i > 0))
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if (bin_distance(i,j,k) < cutneighmaxsq)
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stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i;
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}
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/* ---------------------------------------------------------------------- */
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void Neighbor::stencil_half_3d_newton_multi(int sx, int sy, int sz)
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{
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int i,j,k,n;
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double rsq,typesq;
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int *s;
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double *distsq;
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int ntypes = atom->ntypes;
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for (int itype = 1; itype <= ntypes; itype++) {
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typesq = cuttypesq[itype];
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s = stencil_multi[itype];
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distsq = distsq_multi[itype];
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n = 0;
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for (k = 0; k <= sz; k++)
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for (j = -sy; j <= sy; j++)
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for (i = -sx; i <= sx; i++)
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if (k > 0 || j > 0 || (j == 0 && i > 0)) {
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rsq = bin_distance(i,j,k);
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if (rsq < typesq) {
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distsq[n] = rsq;
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s[n++] = k*mbiny*mbinx + j*mbinx + i;
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}
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}
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nstencil_multi[itype] = n;
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}
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}
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/* ---------------------------------------------------------------------- */
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void Neighbor::stencil_half_3d_newton_tri(int sx, int sy, int sz)
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{
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int i,j,k;
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nstencil = 0;
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for (k = 0; k <= sz; k++)
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for (j = -sy; j <= sy; j++)
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for (i = -sx; i <= sx; i++)
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if (bin_distance(i,j,k) < cutneighmaxsq)
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stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i;
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}
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/* ---------------------------------------------------------------------- */
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void Neighbor::stencil_half_3d_newton_multi_tri(int sx, int sy, int sz)
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{
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int i,j,k,n;
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double rsq,typesq;
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int *s;
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double *distsq;
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int ntypes = atom->ntypes;
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for (int itype = 1; itype <= ntypes; itype++) {
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typesq = cuttypesq[itype];
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s = stencil_multi[itype];
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distsq = distsq_multi[itype];
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n = 0;
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for (k = 0; k <= sz; k++)
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for (j = -sy; j <= sy; j++)
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for (i = -sx; i <= sx; i++) {
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rsq = bin_distance(i,j,k);
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if (rsq < typesq) {
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distsq[n] = rsq;
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s[n++] = k*mbiny*mbinx + j*mbinx + i;
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}
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}
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nstencil_multi[itype] = n;
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}
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}
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/* ---------------------------------------------------------------------- */
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void Neighbor::stencil_half_2d_no_newton(int sx, int sy, int sz)
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{
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int i,j;
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nstencil = 0;
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for (j = -sy; j <= sy; j++)
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for (i = -sx; i <= sx; i++)
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if (bin_distance(i,j,0) < cutneighmaxsq)
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stencil[nstencil++] = j*mbinx + i;
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}
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/* ---------------------------------------------------------------------- */
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void Neighbor::stencil_half_2d_no_newton_multi(int sx, int sy, int sz)
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{
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int i,j,n;
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double rsq,typesq;
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int *s;
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double *distsq;
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int ntypes = atom->ntypes;
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for (int itype = 1; itype <= ntypes; itype++) {
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typesq = cuttypesq[itype];
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s = stencil_multi[itype];
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distsq = distsq_multi[itype];
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n = 0;
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for (j = -sy; j <= sy; j++)
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for (i = -sx; i <= sx; i++) {
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rsq = bin_distance(i,j,0);
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if (rsq < typesq) {
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distsq[n] = rsq;
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s[n++] = j*mbinx + i;
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}
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}
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nstencil_multi[itype] = n;
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}
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}
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/* ---------------------------------------------------------------------- */
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void Neighbor::stencil_half_2d_newton(int sx, int sy, int sz)
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{
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int i,j;
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nstencil = 0;
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for (j = 0; j <= sy; j++)
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for (i = -sx; i <= sx; i++)
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if (j > 0 || (j == 0 && i > 0))
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if (bin_distance(i,j,0) < cutneighmaxsq)
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stencil[nstencil++] = j*mbinx + i;
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}
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/* ---------------------------------------------------------------------- */
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void Neighbor::stencil_half_2d_newton_multi(int sx, int sy, int sz)
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{
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int i,j,n;
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double rsq,typesq;
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int *s;
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double *distsq;
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int ntypes = atom->ntypes;
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for (int itype = 1; itype <= ntypes; itype++) {
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typesq = cuttypesq[itype];
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s = stencil_multi[itype];
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distsq = distsq_multi[itype];
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n = 0;
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for (j = 0; j <= sy; j++)
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for (i = -sx; i <= sx; i++)
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if (j > 0 || (j == 0 && i > 0)) {
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rsq = bin_distance(i,j,0);
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if (rsq < typesq) {
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distsq[n] = rsq;
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s[n++] = j*mbinx + i;
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}
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}
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nstencil_multi[itype] = n;
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}
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}
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/* ---------------------------------------------------------------------- */
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void Neighbor::stencil_half_2d_newton_tri(int sx, int sy, int sz)
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{
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int i,j;
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nstencil = 0;
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for (j = 0; j <= sy; j++)
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for (i = -sx; i <= sx; i++)
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if (bin_distance(i,j,0) < cutneighmaxsq)
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stencil[nstencil++] = j*mbinx + i;
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}
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/* ---------------------------------------------------------------------- */
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void Neighbor::stencil_half_2d_newton_multi_tri(int sx, int sy, int sz)
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{
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int i,j,n;
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double rsq,typesq;
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int *s;
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double *distsq;
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int ntypes = atom->ntypes;
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for (int itype = 1; itype <= ntypes; itype++) {
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typesq = cuttypesq[itype];
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s = stencil_multi[itype];
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distsq = distsq_multi[itype];
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n = 0;
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for (j = 0; j <= sy; j++)
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for (i = -sx; i <= sx; i++) {
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rsq = bin_distance(i,j,0);
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if (rsq < typesq) {
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distsq[n] = rsq;
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s[n++] = j*mbinx + i;
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}
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}
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nstencil_multi[itype] = n;
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}
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}
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/* ---------------------------------------------------------------------- */
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void Neighbor::stencil_full_3d(int sx, int sy, int sz)
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{
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int i,j,k;
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nstencil_full = 0;
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for (k = -sz; k <= sz; k++)
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for (j = -sy; j <= sy; j++)
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for (i = -sx; i <= sx; i++)
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if (bin_distance(i,j,k) < cutneighmaxsq)
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stencil_full[nstencil_full++] = k*mbiny*mbinx + j*mbinx + i;
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}
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/* ---------------------------------------------------------------------- */
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void Neighbor::stencil_full_3d_multi(int sx, int sy, int sz)
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{
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int i,j,k,n;
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double rsq,typesq;
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int *s;
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double *distsq;
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int ntypes = atom->ntypes;
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for (int itype = 1; itype <= ntypes; itype++) {
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typesq = cuttypesq[itype];
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s = stencil_full_multi[itype];
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distsq = distsq_full_multi[itype];
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n = 0;
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for (k = -sz; k <= sz; k++)
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for (j = -sy; j <= sy; j++)
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for (i = -sx; i <= sx; i++) {
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rsq = bin_distance(i,j,k);
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if (rsq < typesq) {
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distsq[n] = rsq;
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s[n++] = k*mbiny*mbinx + j*mbinx + i;
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}
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}
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nstencil_full_multi[itype] = n;
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}
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}
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/* ---------------------------------------------------------------------- */
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void Neighbor::stencil_full_2d(int sx, int sy, int sz)
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{
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int i,j;
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nstencil_full = 0;
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for (j = -sy; j <= sy; j++)
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for (i = -sx; i <= sx; i++)
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if (bin_distance(i,j,0) < cutneighmaxsq)
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stencil_full[nstencil_full++] = j*mbinx + i;
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}
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/* ---------------------------------------------------------------------- */
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void Neighbor::stencil_full_2d_multi(int sx, int sy, int sz)
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{
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int i,j,n;
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double rsq,typesq;
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int *s;
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double *distsq;
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int ntypes = atom->ntypes;
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for (int itype = 1; itype <= ntypes; itype++) {
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typesq = cuttypesq[itype];
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s = stencil_full_multi[itype];
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distsq = distsq_full_multi[itype];
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n = 0;
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for (j = -sy; j <= sy; j++)
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for (i = -sx; i <= sx; i++) {
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rsq = bin_distance(i,j,0);
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if (rsq < typesq) {
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distsq[n] = rsq;
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s[n++] = j*mbinx + i;
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}
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}
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nstencil_full_multi[itype] = n;
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}
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}
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