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lammps/src/npair.cpp
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npair.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include <math.h>
#include "npair.h"
#include "neighbor.h"
#include "nbin.h"
#include "nstencil.h"
#include "atom.h"
#include "update.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
NPair::NPair(LAMMPS *lmp) : Pointers(lmp)
{
last_build = -1;
last_copy_bin_setup = last_copy_bin = last_copy_stencil = -1;
molecular = atom->molecular;
}
/* ----------------------------------------------------------------------
copy needed info from Neighbor class to this build class
------------------------------------------------------------------------- */
void NPair::copy_neighbor_info()
{
// general params
includegroup = neighbor->includegroup;
exclude = neighbor->exclude;
skin = neighbor->skin;
cutneighsq = neighbor->cutneighsq;
cutneighghostsq = neighbor->cutneighghostsq;
cut_inner_sq = neighbor->cut_inner_sq;
cut_middle_sq = neighbor->cut_middle_sq;
cut_middle_inside_sq = neighbor->cut_middle_inside_sq;
zeroes = neighbor->zeroes;
bboxlo = neighbor->bboxlo;
bboxhi = neighbor->bboxhi;
// exclusion info
nex_type = neighbor->nex_type;
ex1_type = neighbor->ex1_type;
ex2_type = neighbor->ex2_type;
ex_type = neighbor->ex_type;
nex_group = neighbor->nex_group;
ex1_group = neighbor->ex1_group;
ex2_group = neighbor->ex2_group;
ex1_bit = neighbor->ex1_bit;
ex2_bit = neighbor->ex2_bit;
nex_mol = neighbor->nex_mol;
ex_mol_group = neighbor->ex_mol_group;
ex_mol_bit = neighbor->ex_mol_bit;
// special info
special_flag = neighbor->special_flag;
}
/* ----------------------------------------------------------------------
copy bin geometry info from NBin class to this build class
------------------------------------------------------------------------- */
void NPair::copy_bin_setup_info()
{
nbinx = nb->nbinx;
nbiny = nb->nbiny;
nbinz = nb->nbinz;
mbins = nb->mbins;
mbinx = nb->mbinx;
mbiny = nb->mbiny;
mbinz = nb->mbinz;
mbinxlo = nb->mbinxlo;
mbinylo = nb->mbinylo;
mbinzlo = nb->mbinzlo;
bininvx = nb->bininvx;
bininvy = nb->bininvy;
bininvz = nb->bininvz;
}
/* ----------------------------------------------------------------------
copy per-atom and per-bin vectors from NBin class to this build class
------------------------------------------------------------------------- */
void NPair::copy_bin_info()
{
bins = nb->bins;
binhead = nb->binhead;
}
/* ----------------------------------------------------------------------
copy needed info from NStencil class to this build class
------------------------------------------------------------------------- */
void NPair::copy_stencil_info()
{
nstencil = ns->nstencil;
stencil = ns->stencil;
stencilxyz = ns->stencilxyz;
nstencil_multi = ns->nstencil_multi;
stencil_multi = ns->stencil_multi;
distsq_multi = ns->distsq_multi;
}
/* ----------------------------------------------------------------------
copy needed info from NStencil class to this build class
------------------------------------------------------------------------- */
void NPair::build_setup()
{
if (nb && last_copy_bin_setup < nb->last_setup) {
copy_bin_setup_info();
last_copy_bin_setup = update->ntimestep;
}
if (nb && last_copy_bin < nb->last_bin_memory) {
copy_bin_info();
last_copy_bin = update->ntimestep;
}
if (ns && last_copy_stencil < ns->last_create) {
copy_stencil_info();
last_copy_stencil = update->ntimestep;
}
last_build = update->ntimestep;
}
/* ----------------------------------------------------------------------
test if atom pair i,j is excluded from neighbor list
due to type, group, molecule settings from neigh_modify command
return 1 if should be excluded, 0 if included
------------------------------------------------------------------------- */
int NPair::exclusion(int i, int j, int itype, int jtype,
int *mask, tagint *molecule) const {
int m;
if (nex_type && ex_type[itype][jtype]) return 1;
if (nex_group) {
for (m = 0; m < nex_group; m++) {
if (mask[i] & ex1_bit[m] && mask[j] & ex2_bit[m]) return 1;
if (mask[i] & ex2_bit[m] && mask[j] & ex1_bit[m]) return 1;
}
}
if (nex_mol) {
for (m = 0; m < nex_mol; m++)
if (mask[i] & ex_mol_bit[m] && mask[j] & ex_mol_bit[m] &&
molecule[i] == molecule[j]) return 1;
}
return 0;
}
/* ----------------------------------------------------------------------
convert atom coords into local bin #
for orthogonal, only ghost atoms will have coord >= bboxhi or coord < bboxlo
take special care to insure ghosts are in correct bins even w/ roundoff
hi ghost atoms = nbin,nbin+1,etc
owned atoms = 0 to nbin-1
lo ghost atoms = -1,-2,etc
this is necessary so that both procs on either side of PBC
treat a pair of atoms straddling the PBC in a consistent way
for triclinic, doesn't matter since stencil & neigh list built differently
------------------------------------------------------------------------- */
int NPair::coord2bin(double *x)
{
int ix,iy,iz;
if (!ISFINITE(x[0]) || !ISFINITE(x[1]) || !ISFINITE(x[2]))
error->one(FLERR,"Non-numeric positions - simulation unstable");
if (x[0] >= bboxhi[0])
ix = static_cast<int> ((x[0]-bboxhi[0])*bininvx) + nbinx;
else if (x[0] >= bboxlo[0]) {
ix = static_cast<int> ((x[0]-bboxlo[0])*bininvx);
ix = MIN(ix,nbinx-1);
} else
ix = static_cast<int> ((x[0]-bboxlo[0])*bininvx) - 1;
if (x[1] >= bboxhi[1])
iy = static_cast<int> ((x[1]-bboxhi[1])*bininvy) + nbiny;
else if (x[1] >= bboxlo[1]) {
iy = static_cast<int> ((x[1]-bboxlo[1])*bininvy);
iy = MIN(iy,nbiny-1);
} else
iy = static_cast<int> ((x[1]-bboxlo[1])*bininvy) - 1;
if (x[2] >= bboxhi[2])
iz = static_cast<int> ((x[2]-bboxhi[2])*bininvz) + nbinz;
else if (x[2] >= bboxlo[2]) {
iz = static_cast<int> ((x[2]-bboxlo[2])*bininvz);
iz = MIN(iz,nbinz-1);
} else
iz = static_cast<int> ((x[2]-bboxlo[2])*bininvz) - 1;
return (iz-mbinzlo)*mbiny*mbinx + (iy-mbinylo)*mbinx + (ix-mbinxlo);
}
/* ----------------------------------------------------------------------
same as coord2bin, but also return ix,iy,iz offsets in each dim
------------------------------------------------------------------------- */
int NPair::coord2bin(double *x, int &ix, int &iy, int &iz)
{
if (!ISFINITE(x[0]) || !ISFINITE(x[1]) || !ISFINITE(x[2]))
error->one(FLERR,"Non-numeric positions - simulation unstable");
if (x[0] >= bboxhi[0])
ix = static_cast<int> ((x[0]-bboxhi[0])*bininvx) + nbinx;
else if (x[0] >= bboxlo[0]) {
ix = static_cast<int> ((x[0]-bboxlo[0])*bininvx);
ix = MIN(ix,nbinx-1);
} else
ix = static_cast<int> ((x[0]-bboxlo[0])*bininvx) - 1;
if (x[1] >= bboxhi[1])
iy = static_cast<int> ((x[1]-bboxhi[1])*bininvy) + nbiny;
else if (x[1] >= bboxlo[1]) {
iy = static_cast<int> ((x[1]-bboxlo[1])*bininvy);
iy = MIN(iy,nbiny-1);
} else
iy = static_cast<int> ((x[1]-bboxlo[1])*bininvy) - 1;
if (x[2] >= bboxhi[2])
iz = static_cast<int> ((x[2]-bboxhi[2])*bininvz) + nbinz;
else if (x[2] >= bboxlo[2]) {
iz = static_cast<int> ((x[2]-bboxlo[2])*bininvz);
iz = MIN(iz,nbinz-1);
} else
iz = static_cast<int> ((x[2]-bboxlo[2])*bininvz) - 1;
ix -= mbinxlo;
iy -= mbinylo;
iz -= mbinzlo;
return iz*mbiny*mbinx + iy*mbinx + ix;
}
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