forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14533 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
parent
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commit
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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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/* ----------------------------------------------------------------------
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Contributing authors:
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James Larentzos and Timothy I. Mattox (Engility Corporation)
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------------------------------------------------------------------------- */
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#include "neighbor.h"
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#include "neigh_list.h"
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#include "neigh_request.h"
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#include "atom.h"
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#include "atom_vec.h"
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#include "molecule.h"
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#include "domain.h"
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#include "group.h"
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#include "memory.h"
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#include "error.h"
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#include "update.h"
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using namespace LAMMPS_NS;
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/* ----------------------------------------------------------------------
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convert atom coords into the ssa active interaction region number
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------------------------------------------------------------------------- */
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int Neighbor::coord2ssa_airnum(double *x)
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{
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int ix, iy, iz;
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ix = iy = iz = 0;
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if (x[2] < domain->sublo[2]) iz = -1;
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if (x[2] > domain->subhi[2]) iz = 1;
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if (x[1] < domain->sublo[1]) iy = -1;
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if (x[1] > domain->subhi[1]) iy = 1;
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if (x[0] < domain->sublo[0]) ix = -1;
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if (x[0] > domain->subhi[0]) ix = 1;
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if(iz < 0) return 0;
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if(iz == 0){
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if( iy<0 ) return 0; // bottom left/middle/right
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if( (iy==0) && (ix<0) ) return 0; // left atoms
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if( (iy==0) && (ix==0) ) return 1; // Locally owned atoms
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if( (iy==0) && (ix>0) ) return 3; // Right atoms
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if( (iy>0) && (ix==0) ) return 2; // Top-middle atoms
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if( (iy>0) && (ix!=0) ) return 4; // Top-right and top-left atoms
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} else if(iz > 0) {
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if((ix==0) && (iy==0)) return 5; // Back atoms
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if((ix==0) && (iy!=0)) return 6; // Top-back and bottom-back atoms
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if((ix!=0) && (iy==0)) return 7; // Left-back and right-back atoms
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if((ix!=0) && (iy!=0)) return 8; // Back corner atoms
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}
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return 0;
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}
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/* ----------------------------------------------------------------------
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* assign owned and ghost atoms their ssa active interaction region numbers
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* Called in the pre_neighbor and setup_pre_neighbor fix stages
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------------------------------------------------------------------------- */
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void Neighbor::assign_ssa_airnums()
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{
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int i,ibin;
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double **x = atom->x;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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int nall = nlocal + atom->nghost;
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if (nall > len_ssa_airnum) {
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len_ssa_airnum = nall;
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memory->destroy(ssa_airnum);
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memory->create(ssa_airnum,len_ssa_airnum,"ssa_airnum");
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}
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// bin in reverse order so linked list will be in forward order
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if (includegroup) {
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int bitmask = group->bitmask[includegroup];
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for (i = nall-1; i >= nlocal; i--) {
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if (mask[i] & bitmask) {
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ibin = coord2ssa_airnum(x[i]);
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} else {
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ibin = 0;
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}
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ssa_airnum[i] = ibin;
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}
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// All the local excluded atoms are in the zero airnum
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ibin = 0;
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for (i = atom->nlocal-1; i >= atom->nfirst; i--) {
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ssa_airnum[i] = ibin;
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}
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} else {
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for (i = nall-1; i >= nlocal; i--) {
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ibin = coord2ssa_airnum(x[i]);
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ssa_airnum[i] = ibin;
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}
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}
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// All the local included atoms are in the same airnum (#1)
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if (i >= 0) {
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ibin = coord2ssa_airnum(x[i]);
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do {
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ssa_airnum[i] = ibin;
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} while (--i >= 0);
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}
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}
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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 list with newton on:
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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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------------------------------------------------------------------------- */
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/* ---------------------------------------------------------------------- */
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void Neighbor::stencil_half_bin_2d_ssa(NeighList *list,
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int sx, int sy, int sz)
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{
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int i,j;
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int *stencil = list->stencil;
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int 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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list->nstencil = nstencil;
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// Now include additional bins for AIR ghosts only
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for (j = -sy; j <= 0; j++)
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for (i = -sx; i <= sx; i++) {
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if (j == 0 && i > 0) continue;
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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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while (nstencil < list->maxstencil) {
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stencil[nstencil++] = INT_MAX;
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}
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}
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/* ---------------------------------------------------------------------- */
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void Neighbor::stencil_half_bin_3d_ssa(NeighList *list,
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int sx, int sy, int sz)
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{
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int i,j,k;
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int *stencil = list->stencil;
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int 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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list->nstencil = nstencil;
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// Now include additional bins for AIR ghosts only
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for (k = -sz; k < 0; 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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k = 0; // skip already included bins at k == 0
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for (j = -sy; j <= 0; j++)
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for (i = -sx; i <= sx; i++) {
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if (j == 0 && i > 0) continue;
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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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while (nstencil < list->maxstencil) {
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stencil[nstencil++] = INT_MAX;
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}
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}
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/* ----------------------------------------------------------------------
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build half list from full list for use by Shardlow Spliting Algorithm
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pair stored once if i,j are both owned and i < j
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if j is ghost, only store if j coords are "above and to the right" of i
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works if full list is a skip list
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------------------------------------------------------------------------- */
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void Neighbor::half_from_full_newton_ssa(NeighList *list)
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{
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int i,j,ii,jj,n,jnum,joriginal;
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int *neighptr,*jlist;
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int nlocal = atom->nlocal;
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int *ilist = list->ilist;
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int *numneigh = list->numneigh;
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int **firstneigh = list->firstneigh;
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MyPage<int> *ipage = list->ipage;
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int *ilist_full = list->listfull->ilist;
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int *numneigh_full = list->listfull->numneigh;
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int **firstneigh_full = list->listfull->firstneigh;
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int inum_full = list->listfull->inum;
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int inum = 0;
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ipage->reset();
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// loop over parent full list
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for (ii = 0; ii < inum_full; ii++) {
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n = 0;
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neighptr = ipage->vget();
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i = ilist_full[ii];
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// loop over full neighbor list
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jlist = firstneigh_full[i];
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jnum = numneigh_full[i];
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for (jj = 0; jj < jnum; jj++) {
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joriginal = jlist[jj];
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j = joriginal & NEIGHMASK;
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if (j < nlocal) {
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if (i > j) continue;
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} else {
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if (ssa_airnum[j] <= 0) continue;
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}
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neighptr[n++] = joriginal;
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}
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ilist[inum++] = i;
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firstneigh[i] = neighptr;
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numneigh[i] = n;
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ipage->vgot(n);
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if (ipage->status())
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error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
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}
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list->inum = inum;
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}
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/* ----------------------------------------------------------------------
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for Shardlow Spliting Algorithm:
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binned neighbor list construction with full Newton's 3rd law
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each owned atom i checks its own bin and other bins in Newton stencil
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every pair stored exactly once by some processor
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------------------------------------------------------------------------- */
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void Neighbor::half_bin_newton_ssa(NeighList *list)
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{
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int i,j,k,n,itype,jtype,ibin,which,imol,iatom,moltemplate;
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tagint tagprev;
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double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
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int *neighptr;
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double **x = atom->x;
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int *type = atom->type;
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int *mask = atom->mask;
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tagint *tag = atom->tag;
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tagint *molecule = atom->molecule;
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tagint **special = atom->special;
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int **nspecial = atom->nspecial;
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int nlocal = atom->nlocal;
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int nall = nlocal + atom->nghost;
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int *molindex = atom->molindex;
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int *molatom = atom->molatom;
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Molecule **onemols = atom->avec->onemols;
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int molecular = atom->molecular;
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if (molecular == 2) moltemplate = 1;
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else moltemplate = 0;
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int *ilist = list->ilist;
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int *numneigh = list->numneigh;
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int **firstneigh = list->firstneigh;
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int nstencil = list->nstencil;
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int maxstencil = list->maxstencil;
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int *stencil = list->stencil;
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MyPage<int> *ipage = list->ipage;
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int inum = 0;
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/* ----------------------------------------------------------------------
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bin owned and ghost atoms for use by Shardlow Splitting Algorithm
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exclude ghost atoms that are not in the Active Interaction Regions (AIR)
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------------------------------------------------------------------------- */
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if (mbins > maxhead_ssa) {
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maxhead_ssa = mbins;
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memory->destroy(gbinhead_ssa);
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memory->destroy(binhead_ssa);
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memory->create(binhead_ssa,maxhead_ssa,"binhead_ssa");
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memory->create(gbinhead_ssa,maxhead_ssa,"gbinhead_ssa");
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}
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for (i = 0; i < mbins; i++) {
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gbinhead_ssa[i] = -1;
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binhead_ssa[i] = -1;
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}
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if (maxbin > maxbin_ssa) {
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maxbin_ssa = maxbin;
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memory->destroy(bins_ssa);
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memory->create(bins_ssa,maxbin_ssa,"bins_ssa");
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}
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// bin in reverse order so linked list will be in forward order
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if (includegroup) {
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int bitmask = group->bitmask[includegroup];
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for (i = nall-1; i >= nlocal; i--) {
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if (ssa_airnum[i] <= 0) continue; // skip ghost atoms not in AIR
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if (mask[i] & bitmask) {
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ibin = coord2bin(x[i]);
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bins_ssa[i] = gbinhead_ssa[ibin];
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gbinhead_ssa[ibin] = i;
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}
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}
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nlocal = atom->nfirst; // This is important for the code that follows!
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} else {
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for (i = nall-1; i >= nlocal; i--) {
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if (ssa_airnum[i] <= 0) continue; // skip ghost atoms not in AIR
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ibin = coord2bin(x[i]);
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bins_ssa[i] = gbinhead_ssa[ibin];
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gbinhead_ssa[ibin] = i;
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}
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}
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for (i = nlocal-1; i >= 0; i--) {
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ibin = coord2bin(x[i]);
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bins_ssa[i] = binhead_ssa[ibin];
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binhead_ssa[ibin] = i;
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}
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ipage->reset();
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// loop over owned atoms, storing half of the neighbors
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for (i = 0; i < nlocal; i++) {
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n = 0;
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neighptr = ipage->vget();
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itype = type[i];
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xtmp = x[i][0];
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ytmp = x[i][1];
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ztmp = x[i][2];
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if (moltemplate) {
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imol = molindex[i];
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iatom = molatom[i];
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tagprev = tag[i] - iatom - 1;
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}
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// loop over rest of local atoms in i's bin
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// just store them, since j is beyond i in linked list
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for (j = bins_ssa[i]; j >= 0; j = bins_ssa[j]) {
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jtype = type[j];
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if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
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delx = xtmp - x[j][0];
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dely = ytmp - x[j][1];
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delz = ztmp - x[j][2];
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rsq = delx*delx + dely*dely + delz*delz;
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if (rsq <= cutneighsq[itype][jtype]) {
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if (molecular) {
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if (!moltemplate)
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which = find_special(special[i],nspecial[i],tag[j]);
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else if (imol >= 0)
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which = find_special(onemols[imol]->special[iatom],
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onemols[imol]->nspecial[iatom],
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tag[j]-tagprev);
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else which = 0;
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if (which == 0) neighptr[n++] = j;
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else if (domain->minimum_image_check(delx,dely,delz))
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neighptr[n++] = j;
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else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
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} else neighptr[n++] = j;
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}
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}
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ibin = coord2bin(x[i]);
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// loop over all local atoms in other bins in "half" stencil
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for (k = 0; k < nstencil; k++) {
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for (j = binhead_ssa[ibin+stencil[k]]; j >= 0; j = bins_ssa[j]) {
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jtype = type[j];
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if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
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delx = xtmp - x[j][0];
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dely = ytmp - x[j][1];
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delz = ztmp - x[j][2];
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rsq = delx*delx + dely*dely + delz*delz;
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if (rsq <= cutneighsq[itype][jtype]) {
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if (molecular) {
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if (!moltemplate)
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which = find_special(special[i],nspecial[i],tag[j]);
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else if (imol >= 0)
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which = find_special(onemols[imol]->special[iatom],
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onemols[imol]->nspecial[iatom],
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tag[j]-tagprev);
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else which = 0;
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if (which == 0) neighptr[n++] = j;
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else if (domain->minimum_image_check(delx,dely,delz))
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neighptr[n++] = j;
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else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
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} else neighptr[n++] = j;
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}
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}
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}
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// loop over AIR ghost atoms in all bins in "full" stencil
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// Note: the non-AIR ghost atoms have already been filtered out
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for (k = 0; k < maxstencil; k++) {
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if (stencil[k] > mbins) break; /* Check if ghost stencil bins are exhausted */
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for (j = gbinhead_ssa[ibin+stencil[k]]; j >= 0; j = bins_ssa[j]) {
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jtype = type[j];
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if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
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delx = xtmp - x[j][0];
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dely = ytmp - x[j][1];
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delz = ztmp - x[j][2];
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rsq = delx*delx + dely*dely + delz*delz;
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if (rsq <= cutneighsq[itype][jtype]) {
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if (molecular) {
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if (!moltemplate)
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which = find_special(special[i],nspecial[i],tag[j]);
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else if (imol >= 0)
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which = find_special(onemols[imol]->special[iatom],
|
||||
onemols[imol]->nspecial[iatom],
|
||||
tag[j]-tagprev);
|
||||
else which = 0;
|
||||
if (which == 0) neighptr[n++] = j;
|
||||
else if (domain->minimum_image_check(delx,dely,delz))
|
||||
neighptr[n++] = j;
|
||||
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
|
||||
} else neighptr[n++] = j;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
ilist[inum++] = i;
|
||||
firstneigh[i] = neighptr;
|
||||
numneigh[i] = n;
|
||||
ipage->vgot(n);
|
||||
if (ipage->status())
|
||||
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
|
||||
}
|
||||
|
||||
list->inum = inum;
|
||||
}
|
||||
|
|
@ -162,7 +162,6 @@ Neighbor::Neighbor(LAMMPS *lmp) : Pointers(lmp)
|
|||
improperlist = NULL;
|
||||
|
||||
copymode = 0;
|
||||
last_binning_timestep = -1;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
|
@ -2015,11 +2014,6 @@ void Neighbor::bin_atoms()
|
|||
{
|
||||
int i,ibin;
|
||||
|
||||
// NOTE: added for USER-DPD, why do we need this?
|
||||
|
||||
//if (last_binning_timestep == update->ntimestep) return;
|
||||
//last_binning_timestep = update->ntimestep;
|
||||
|
||||
for (i = 0; i < mbins; i++) binhead[i] = -1;
|
||||
|
||||
// bin in reverse order so linked list will be in forward order
|
||||
|
|
|
|||
|
|
@ -71,7 +71,7 @@ class Neighbor : protected Pointers {
|
|||
|
||||
int cluster_check; // 1 if check bond/angle/etc satisfies minimg
|
||||
|
||||
// USER-DPD package - better to make this private?
|
||||
// USER-DPD package
|
||||
|
||||
int *ssa_airnum; // AIR number of each atom for SSA in USER-DPD
|
||||
|
||||
|
|
@ -121,7 +121,6 @@ class Neighbor : protected Pointers {
|
|||
|
||||
int binatomflag; // bin atoms or not when build neigh list
|
||||
// turned off by build_one()
|
||||
bigint last_binning_timestep; // last step neighbor binning was done
|
||||
|
||||
int nbinx,nbiny,nbinz; // # of global bins
|
||||
int *bins; // ptr to next atom in each bin
|
||||
|
|
@ -180,7 +179,12 @@ class Neighbor : protected Pointers {
|
|||
|
||||
// USER-DPD package
|
||||
|
||||
int len_ssa_airnum; // length of ssa_airnum array
|
||||
int len_ssa_airnum; // length of ssa_airnum array
|
||||
int *bins_ssa; // ptr to next atom in each bin used by SSA
|
||||
int maxbin_ssa; // size of bins array used by SSA
|
||||
int *binhead_ssa; // ptr to 1st atom in each bin used by SSA
|
||||
int *gbinhead_ssa; // ptr to 1st ghost atom in each bin used by SSA
|
||||
int maxhead_ssa; // size of binhead array used by SSA
|
||||
|
||||
// methods
|
||||
|
||||
|
|
@ -320,13 +324,13 @@ class Neighbor : protected Pointers {
|
|||
|
||||
// SSA neighboring for USER-DPD
|
||||
|
||||
//int coord2ssa_airnum(double *); // map atom coord to an AIR number
|
||||
//void assign_ssa_airnums(); // set ssa_airnum values
|
||||
int coord2ssa_airnum(double *); // map atom coord to an AIR number
|
||||
void assign_ssa_airnums(); // set ssa_airnum values
|
||||
|
||||
void half_bin_newton_ssa(NeighList *) {}
|
||||
void half_from_full_newton_ssa(class NeighList *) {}
|
||||
void stencil_half_bin_2d_ssa(class NeighList *, int, int, int) {}
|
||||
void stencil_half_bin_3d_ssa(class NeighList *, int, int, int) {}
|
||||
void half_bin_newton_ssa(NeighList *);
|
||||
void half_from_full_newton_ssa(class NeighList *);
|
||||
void stencil_half_bin_2d_ssa(class NeighList *, int, int, int);
|
||||
void stencil_half_bin_3d_ssa(class NeighList *, int, int, int);
|
||||
|
||||
// find_special: determine if atom j is in special list of atom i
|
||||
// if it is not, return 0
|
||||
|
|
|
|||
Loading…
Reference in New Issue