Homec4science
Diffusion lammps (lammm-devel) Browse

lammps/src/USER-DPD/nbin_ssa.cpp
88a882b4575dlammm-devel

Last Change
Raw File

nbin_ssa.cpp
View Options

/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors:
James Larentzos (ARL) and Timothy I. Mattox (Engility Corporation)
------------------------------------------------------------------------- */
#include "nbin_ssa.h"
#include "atom.h"
#include "update.h"
#include "group.h"
#include "domain.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
NBinSSA::NBinSSA(LAMMPS *lmp) : NBinStandard(lmp)
{
for (int i = 0; i < 8; i++) {
gairhead_ssa[i] = -1;
}
}
NBinSSA::~NBinSSA()
{
}
/* ----------------------------------------------------------------------
bin owned and ghost atoms for the Shardlow Splitting Algorithm (SSA)
local atoms are in distinct bins (binhead[]) from the ghosts
ghost atoms are "binned" in gairhead_ssa[] instead
ghosts which are not in an Active Interaction Region (AIR) are skipped
------------------------------------------------------------------------- */
void NBinSSA::bin_atoms()
{
int i,ibin;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
if (includegroup) nlocal = atom->nfirst;
double **x = atom->x;
int *mask = atom->mask;
int xbin,ybin,zbin;
last_bin = update->ntimestep;
bboxlo_[0] = bboxlo[0]; bboxlo_[1] = bboxlo[1]; bboxlo_[2] = bboxlo[2];
bboxhi_[0] = bboxhi[0]; bboxhi_[1] = bboxhi[1]; bboxhi_[2] = bboxhi[2];
for (i = 0; i < 8; i++) {
gairhead_ssa[i] = -1;
}
for (i = 0; i < mbins; i++) {
binhead[i] = -1;
}
// bin in reverse order so linked list will be in forward order
if (includegroup) {
int bitmask = group->bitmask[includegroup];
int nowned = atom->nlocal; // NOTE: nlocal was set to atom->nfirst above
for (i = nall-1; i >= nowned; i--) {
ibin = coord2ssaAIR(x[i]);
if (ibin < 1) continue; // skip ghost atoms not in AIR
if (mask[i] & bitmask) {
bins[i] = gairhead_ssa[ibin];
gairhead_ssa[ibin] = i;
}
}
} else {
for (i = nall-1; i >= nlocal; i--) {
ibin = coord2ssaAIR(x[i]);
if (ibin < 1) continue; // skip ghost atoms not in AIR
bins[i] = gairhead_ssa[ibin];
gairhead_ssa[ibin] = i;
}
}
for (i = nlocal-1; i >= 0; i--) {
ibin = coord2bin(x[i][0], x[i][1], x[i][2], xbin, ybin, zbin);
// Find the bounding box of the local atoms in the bins
if (xbin < lbinxlo) lbinxlo = xbin;
if (xbin >= lbinxhi) lbinxhi = xbin + 1;
if (ybin < lbinylo) lbinylo = ybin;
if (ybin >= lbinyhi) lbinyhi = ybin + 1;
if (zbin < lbinzlo) lbinzlo = zbin;
if (zbin >= lbinzhi) lbinzhi = zbin + 1;
bins[i] = binhead[ibin];
binhead[ibin] = i;
}
}
/* ---------------------------------------------------------------------- */
void NBinSSA::bin_atoms_setup(int nall)
{
NBinStandard::bin_atoms_setup(nall); // Setup the parent class's data too
// Clear the local bin extent bounding box.
lbinxlo = mbinx - 1; // Safe to = stencil->sx + 1
lbinylo = mbiny - 1; // Safe to = stencil->sy + 1
lbinzlo = mbinz - 1; // Safe to = stencil->sz + 1
lbinxhi = 0; // Safe to = mbinx - stencil->sx - 1
lbinyhi = 0; // Safe to = mbiny - stencil->sy - 1
lbinzhi = 0; // Safe to = mbinz - stencil->sz - 1
}
/* ---------------------------------------------------------------------- */
bigint NBinSSA::memory_usage()
{
bigint bytes = NBinStandard::memory_usage(); // Count the parent's usage too
return bytes;
}
/* ----------------------------------------------------------------------
convert atom coords into the ssa active interaction region number
------------------------------------------------------------------------- */
int NBinSSA::coord2ssaAIR(const double *x)
{
int ix, iy, iz;
ix = iy = iz = 0;
if (x[2] < domain->sublo[2]) iz = -1;
if (x[2] >= domain->subhi[2]) iz = 1;
if (x[1] < domain->sublo[1]) iy = -1;
if (x[1] >= domain->subhi[1]) iy = 1;
if (x[0] < domain->sublo[0]) ix = -1;
if (x[0] >= domain->subhi[0]) ix = 1;
if(iz < 0){
return -1;
} else if(iz == 0){
if( iy<0 ) return -1; // bottom left/middle/right
if( (iy==0) && (ix<0) ) return -1; // left atoms
if( (iy==0) && (ix==0) ) return 0; // Locally owned atoms
if( (iy==0) && (ix>0) ) return 2; // Right atoms
if( (iy>0) && (ix==0) ) return 1; // Top-middle atoms
if( (iy>0) && (ix!=0) ) return 3; // Top-right and top-left atoms
} else { // iz > 0
if((ix==0) && (iy==0)) return 4; // Back atoms
if((ix==0) && (iy!=0)) return 5; // Top-back and bottom-back atoms
if((ix!=0) && (iy==0)) return 6; // Left-back and right-back atoms
if((ix!=0) && (iy!=0)) return 7; // Back corner atoms
}
return -2;
}
c4science · Help