new neighbor list changes
This commit is contained in:
Steve Plimpton
258
src/npair.cpp
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258
src/npair.cpp
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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 <math.h>
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#include "npair.h"
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#include "neighbor.h"
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#include "nbin.h"
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#include "nstencil.h"
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#include "atom.h"
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#include "update.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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NPair::NPair(LAMMPS *lmp) : Pointers(lmp)
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{
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last_build = -1;
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last_copy_bin_setup = last_copy_bin = last_copy_stencil = -1;
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molecular = atom->molecular;
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}
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/* ----------------------------------------------------------------------
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copy needed info from Neighbor class to this build class
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------------------------------------------------------------------------- */
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void NPair::copy_neighbor_info()
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{
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// general params
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includegroup = neighbor->includegroup;
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exclude = neighbor->exclude;
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skin = neighbor->skin;
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cutneighsq = neighbor->cutneighsq;
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cutneighghostsq = neighbor->cutneighghostsq;
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cut_inner_sq = neighbor->cut_inner_sq;
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cut_middle_sq = neighbor->cut_middle_sq;
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cut_middle_inside_sq = neighbor->cut_middle_inside_sq;
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zeroes = neighbor->zeroes;
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bboxlo = neighbor->bboxlo;
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bboxhi = neighbor->bboxhi;
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// exclusion info
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nex_type = neighbor->nex_type;
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ex1_type = neighbor->ex1_type;
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ex2_type = neighbor->ex2_type;
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ex_type = neighbor->ex_type;
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nex_group = neighbor->nex_group;
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ex1_group = neighbor->ex1_group;
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ex2_group = neighbor->ex2_group;
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ex1_bit = neighbor->ex1_bit;
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ex2_bit = neighbor->ex2_bit;
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nex_mol = neighbor->nex_mol;
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ex_mol_group = neighbor->ex_mol_group;
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ex_mol_bit = neighbor->ex_mol_bit;
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// special info
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special_flag = neighbor->special_flag;
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}
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/* ----------------------------------------------------------------------
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copy bin geometry info from NBin class to this build class
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------------------------------------------------------------------------- */
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void NPair::copy_bin_setup_info()
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{
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nbinx = nb->nbinx;
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nbiny = nb->nbiny;
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nbinz = nb->nbinz;
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mbins = nb->mbins;
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mbinx = nb->mbinx;
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mbiny = nb->mbiny;
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mbinz = nb->mbinz;
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mbinxlo = nb->mbinxlo;
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mbinylo = nb->mbinylo;
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mbinzlo = nb->mbinzlo;
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bininvx = nb->bininvx;
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bininvy = nb->bininvy;
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bininvz = nb->bininvz;
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}
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/* ----------------------------------------------------------------------
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copy per-atom and per-bin vectors from NBin class to this build class
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------------------------------------------------------------------------- */
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void NPair::copy_bin_info()
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{
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bins = nb->bins;
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binhead = nb->binhead;
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}
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/* ----------------------------------------------------------------------
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copy needed info from NStencil class to this build class
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------------------------------------------------------------------------- */
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void NPair::copy_stencil_info()
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{
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nstencil = ns->nstencil;
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nstencil_ssa = ns->nstencil_ssa;
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stencil = ns->stencil;
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stencilxyz = ns->stencilxyz;
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nstencil_multi = ns->nstencil_multi;
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stencil_multi = ns->stencil_multi;
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distsq_multi = ns->distsq_multi;
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}
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/* ----------------------------------------------------------------------
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copy needed info from NStencil class to this build class
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------------------------------------------------------------------------- */
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void NPair::build_setup()
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{
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if (nb && last_copy_bin_setup < nb->last_setup) {
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copy_bin_setup_info();
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last_copy_bin_setup = update->ntimestep;
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}
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if (nb && last_copy_bin < nb->last_bin_memory) {
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copy_bin_info();
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last_copy_bin = update->ntimestep;
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}
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if (ns && last_copy_stencil < ns->last_create) {
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copy_stencil_info();
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last_copy_stencil = update->ntimestep;
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}
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last_build = update->ntimestep;
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}
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/* ----------------------------------------------------------------------
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test if atom pair i,j is excluded from neighbor list
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due to type, group, molecule settings from neigh_modify command
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return 1 if should be excluded, 0 if included
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------------------------------------------------------------------------- */
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int NPair::exclusion(int i, int j, int itype, int jtype,
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int *mask, tagint *molecule) const {
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int m;
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if (nex_type && ex_type[itype][jtype]) return 1;
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if (nex_group) {
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for (m = 0; m < nex_group; m++) {
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if (mask[i] & ex1_bit[m] && mask[j] & ex2_bit[m]) return 1;
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if (mask[i] & ex2_bit[m] && mask[j] & ex1_bit[m]) return 1;
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}
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}
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if (nex_mol) {
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for (m = 0; m < nex_mol; m++)
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if (mask[i] & ex_mol_bit[m] && mask[j] & ex_mol_bit[m] &&
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molecule[i] == molecule[j]) return 1;
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}
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return 0;
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}
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/* ----------------------------------------------------------------------
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convert atom coords into local bin #
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for orthogonal, only ghost atoms will have coord >= bboxhi or coord < bboxlo
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take special care to insure ghosts are in correct bins even w/ roundoff
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hi ghost atoms = nbin,nbin+1,etc
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owned atoms = 0 to nbin-1
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lo ghost atoms = -1,-2,etc
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this is necessary so that both procs on either side of PBC
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treat a pair of atoms straddling the PBC in a consistent way
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for triclinic, doesn't matter since stencil & neigh list built differently
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------------------------------------------------------------------------- */
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int NPair::coord2bin(double *x)
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{
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int ix,iy,iz;
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if (!ISFINITE(x[0]) || !ISFINITE(x[1]) || !ISFINITE(x[2]))
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error->one(FLERR,"Non-numeric positions - simulation unstable");
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if (x[0] >= bboxhi[0])
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ix = static_cast<int> ((x[0]-bboxhi[0])*bininvx) + nbinx;
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else if (x[0] >= bboxlo[0]) {
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ix = static_cast<int> ((x[0]-bboxlo[0])*bininvx);
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ix = MIN(ix,nbinx-1);
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} else
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ix = static_cast<int> ((x[0]-bboxlo[0])*bininvx) - 1;
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if (x[1] >= bboxhi[1])
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iy = static_cast<int> ((x[1]-bboxhi[1])*bininvy) + nbiny;
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else if (x[1] >= bboxlo[1]) {
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iy = static_cast<int> ((x[1]-bboxlo[1])*bininvy);
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iy = MIN(iy,nbiny-1);
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} else
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iy = static_cast<int> ((x[1]-bboxlo[1])*bininvy) - 1;
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if (x[2] >= bboxhi[2])
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iz = static_cast<int> ((x[2]-bboxhi[2])*bininvz) + nbinz;
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else if (x[2] >= bboxlo[2]) {
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iz = static_cast<int> ((x[2]-bboxlo[2])*bininvz);
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iz = MIN(iz,nbinz-1);
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} else
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iz = static_cast<int> ((x[2]-bboxlo[2])*bininvz) - 1;
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return (iz-mbinzlo)*mbiny*mbinx + (iy-mbinylo)*mbinx + (ix-mbinxlo);
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}
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/* ----------------------------------------------------------------------
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same as coord2bin, but also return ix,iy,iz offsets in each dim
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------------------------------------------------------------------------- */
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int NPair::coord2bin(double *x, int &ix, int &iy, int &iz)
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{
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if (!ISFINITE(x[0]) || !ISFINITE(x[1]) || !ISFINITE(x[2]))
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error->one(FLERR,"Non-numeric positions - simulation unstable");
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if (x[0] >= bboxhi[0])
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ix = static_cast<int> ((x[0]-bboxhi[0])*bininvx) + nbinx;
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else if (x[0] >= bboxlo[0]) {
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ix = static_cast<int> ((x[0]-bboxlo[0])*bininvx);
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ix = MIN(ix,nbinx-1);
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} else
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ix = static_cast<int> ((x[0]-bboxlo[0])*bininvx) - 1;
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if (x[1] >= bboxhi[1])
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iy = static_cast<int> ((x[1]-bboxhi[1])*bininvy) + nbiny;
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else if (x[1] >= bboxlo[1]) {
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iy = static_cast<int> ((x[1]-bboxlo[1])*bininvy);
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iy = MIN(iy,nbiny-1);
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} else
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iy = static_cast<int> ((x[1]-bboxlo[1])*bininvy) - 1;
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if (x[2] >= bboxhi[2])
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iz = static_cast<int> ((x[2]-bboxhi[2])*bininvz) + nbinz;
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else if (x[2] >= bboxlo[2]) {
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iz = static_cast<int> ((x[2]-bboxlo[2])*bininvz);
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iz = MIN(iz,nbinz-1);
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} else
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iz = static_cast<int> ((x[2]-bboxlo[2])*bininvz) - 1;
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ix -= mbinxlo;
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iy -= mbinylo;
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iz -= mbinzlo;
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return iz*mbiny*mbinx + iy*mbinx + ix;
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}
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