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nbin.cpp
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Mon, Nov 18, 08:17

nbin.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 "nbin.h"
#include "neighbor.h"
#include "neigh_request.h"
#include "domain.h"
#include "update.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
NBin::NBin(LAMMPS *lmp) : Pointers(lmp)
{
last_bin = -1;
maxbin = maxatom = 0;
binhead = NULL;
bins = NULL;
// geometry settings
dimension = domain->dimension;
triclinic = domain->triclinic;
}
/* ---------------------------------------------------------------------- */
NBin::~NBin()
{
memory->destroy(binhead);
memory->destroy(bins);
}
/* ---------------------------------------------------------------------- */
void NBin::post_constructor(NeighRequest *nrq)
{
cutoff_custom = 0.0;
if (nrq->cut) cutoff_custom = nrq->cutoff;
}
/* ----------------------------------------------------------------------
copy needed info from Neighbor class
------------------------------------------------------------------------- */
void NBin::copy_neighbor_info()
{
includegroup = neighbor->includegroup;
cutneighmin = neighbor->cutneighmin;
cutneighmax = neighbor->cutneighmax;
binsizeflag = neighbor->binsizeflag;
binsize_user = neighbor->binsize_user;
bboxlo = neighbor->bboxlo;
bboxhi = neighbor->bboxhi;
// overwrite Neighbor cutoff with custom value set by requestor
// only works for style = BIN (checked by Neighbor class)
if (cutoff_custom > 0.0) cutneighmax = cutoff_custom;
}
/* ----------------------------------------------------------------------
setup for bin_atoms()
------------------------------------------------------------------------- */
void NBin::bin_atoms_setup(int nall)
{
// binhead = per-bin vector, mbins in length
// add 1 bin for USER-INTEL package
if (mbins > maxbin) {
maxbin = mbins;
memory->destroy(binhead);
memory->create(binhead,maxbin,"neigh:binhead");
}
// bins = per-atom vector
if (nall > maxatom) {
maxatom = nall;
memory->destroy(bins);
memory->create(bins,maxatom,"neigh:bins");
}
}
/* ----------------------------------------------------------------------
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 NBin::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);
}
/* ---------------------------------------------------------------------- */
bigint NBin::memory_usage()
{
bigint bytes = 0;
bytes += maxbin*sizeof(int);
bytes += maxatom*sizeof(int);
return bytes;
}

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