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lammps/src/neigh_list.cpp
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neigh_list.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 "neigh_list.h"
#include "atom.h"
#include "comm.h"
#include "neighbor.h"
#include "neigh_request.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define PGDELTA 1
enum{NSQ,BIN,MULTI}; // also in neighbor.cpp
/* ---------------------------------------------------------------------- */
NeighList::NeighList(LAMMPS *lmp, int size) : Pointers(lmp)
{
maxlocal = 0;
pgsize = size;
ilist = NULL;
numneigh = NULL;
firstneigh = NULL;
firstdouble = NULL;
maxpage = 0;
pages = NULL;
dpages = NULL;
dnum = 0;
iskip = NULL;
ijskip = NULL;
listgranhistory = NULL;
fix_history = NULL;
respamiddle = 0;
listinner = NULL;
listmiddle = NULL;
listfull = NULL;
listcopy = NULL;
listskip = NULL;
maxstencil = 0;
stencil = NULL;
maxstencil_multi = 0;
nstencil_multi = NULL;
stencil_multi = NULL;
distsq_multi = NULL;
}
/* ---------------------------------------------------------------------- */
NeighList::~NeighList()
{
if (!listcopy) {
memory->sfree(ilist);
memory->sfree(numneigh);
memory->sfree(firstneigh);
memory->sfree(firstdouble);
for (int i = 0; i < maxpage; i++) memory->sfree(pages[i]);
memory->sfree(pages);
if (dnum) {
for (int i = 0; i < maxpage; i++) memory->sfree(dpages[i]);
memory->sfree(dpages);
}
}
delete [] iskip;
memory->destroy_2d_int_array(ijskip);
if (maxstencil) memory->sfree(stencil);
if (maxstencil_multi) {
for (int i = 1; i <= atom->ntypes; i++) {
memory->sfree(stencil_multi[i]);
memory->sfree(distsq_multi[i]);
}
delete [] nstencil_multi;
delete [] stencil_multi;
delete [] distsq_multi;
}
}
/* ----------------------------------------------------------------------
grow atom arrays to allow for nmax atoms
triggered by more atoms on a processor
------------------------------------------------------------------------- */
void NeighList::grow(int nmax)
{
// skip if grow not needed
if (nmax <= maxlocal) return;
maxlocal = nmax;
memory->sfree(ilist);
memory->sfree(numneigh);
memory->sfree(firstneigh);
ilist = (int *)
memory->smalloc(maxlocal*sizeof(int),"neighlist:ilist");
numneigh = (int *)
memory->smalloc(maxlocal*sizeof(int),"neighlist:numneigh");
firstneigh = (int **)
memory->smalloc(maxlocal*sizeof(int *),"neighlist:firstneigh");
if (dnum)
firstdouble = (double **)
memory->smalloc(maxlocal*sizeof(double *),"neighlist:firstdouble");
}
/* ----------------------------------------------------------------------
insure stencils are large enough for smax bins
style = BIN or MULTI
------------------------------------------------------------------------- */
void NeighList::stencil_allocate(int smax, int style)
{
int i;
if (style == BIN) {
if (smax > maxstencil) {
maxstencil = smax;
memory->sfree(stencil);
stencil = (int *) memory->smalloc(smax*sizeof(int),"neighlist:stencil");
}
} else {
int n = atom->ntypes;
if (maxstencil_multi == 0) {
nstencil_multi = new int[n+1];
stencil_multi = new int*[n+1];
distsq_multi = new double*[n+1];
for (i = 1; i <= n; i++) {
nstencil_multi[i] = 0;
stencil_multi[i] = NULL;
distsq_multi[i] = NULL;
}
}
if (smax > maxstencil_multi) {
maxstencil_multi = smax;
for (i = 1; i <= n; i++) {
memory->sfree(stencil_multi[i]);
memory->sfree(distsq_multi[i]);
stencil_multi[i] = (int *)
memory->smalloc(smax*sizeof(int),"neighlist:stencil_multi");
distsq_multi[i] = (double *) memory->smalloc(smax*sizeof(double),
"neighlist:distsq_multi");
}
}
}
}
/* ----------------------------------------------------------------------
add PGDELTA pages to neighbor list
------------------------------------------------------------------------- */
int **NeighList::add_pages()
{
int npage = maxpage;
maxpage += PGDELTA;
pages = (int **)
memory->srealloc(pages,maxpage*sizeof(int *),"neighlist:pages");
for (int i = npage; i < maxpage; i++)
pages[i] = (int *) memory->smalloc(pgsize*sizeof(int),
"neighlist:pages[i]");
if (dnum) {
dpages = (double **)
memory->srealloc(dpages,maxpage*sizeof(double *),"neighlist:dpages");
for (int i = npage; i < maxpage; i++)
dpages[i] = (double *) memory->smalloc(dnum*pgsize*sizeof(double),
"neighlist:dpages[i]");
}
return pages;
}
/* ----------------------------------------------------------------------
copy skip info from request rq into list's iskip,ijskip
------------------------------------------------------------------------- */
void NeighList::copy_skip_info(int *rq_iskip, int **rq_ijskip)
{
int ntypes = atom->ntypes;
iskip = new int[ntypes+1];
ijskip = memory->create_2d_int_array(ntypes+1,ntypes+1,
"neigh_list:ijskip");
int i,j;
for (i = 1; i <= ntypes; i++) iskip[i] = rq_iskip[i];
for (i = 1; i <= ntypes; i++)
for (j = 1; j <= ntypes; j++)
ijskip[i][j] = rq_ijskip[i][j];
}
/* ----------------------------------------------------------------------
print attributes of this list and associated request
------------------------------------------------------------------------- */
void NeighList::print_attributes()
{
if (comm->me != 0) return;
NeighRequest *rq = neighbor->requests[index];
printf("Neighbor list/request %d:\n",index);
printf(" %d = build flag\n",buildflag);
printf(" %d = grow flag\n",growflag);
printf(" %d = stencil flag\n",stencilflag);
printf("\n");
printf(" %d = pair\n",rq->pair);
printf(" %d = fix\n",rq->fix);
printf(" %d = compute\n",rq->compute);
printf(" %d = command\n",rq->command);
printf("\n");
printf(" %d = half\n",rq->half);
printf(" %d = full\n",rq->full);
printf(" %d = gran\n",rq->gran);
printf(" %d = granhistory\n",rq->granhistory);
printf(" %d = respainner\n",rq->respainner);
printf(" %d = respamiddle\n",rq->respamiddle);
printf(" %d = respaouter\n",rq->respaouter);
printf(" %d = half_from_full\n",rq->half_from_full);
printf("\n");
printf(" %d = occasional\n",rq->occasional);
printf(" %d = dnum\n",rq->dnum);
printf(" %d = copy\n",rq->copy);
printf(" %d = skip\n",rq->skip);
printf(" %d = otherlist\n",rq->otherlist);
printf(" %p = listskip\n",listskip);
printf("\n");
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
if growflag = 0, maxlocal & maxpage will also be 0
if stencilflag = 0, maxstencil * maxstencil_multi will also be 0
------------------------------------------------------------------------- */
double NeighList::memory_usage()
{
double bytes = 0.0;
bytes += 2 * maxlocal * sizeof(int);
bytes += maxlocal * sizeof(int *);
bytes += maxpage*pgsize * sizeof(int);
if (dnum) {
bytes += maxlocal * sizeof(double *);
bytes += dnum * maxpage*pgsize * sizeof(double);
}
if (maxstencil) bytes += maxstencil * sizeof(int);
if (maxstencil_multi) {
bytes += atom->ntypes * maxstencil_multi * sizeof(int);
bytes += atom->ntypes * maxstencil_multi * sizeof(double);
}
return bytes;
}
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