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neigh_list.cpp
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Sun, May 5, 22:07
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rLAMMPS lammps
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 "update.h"
#include "pair.h"
#include "neighbor.h"
#include "neigh_request.h"
#include "my_page.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define PGDELTA 1
enum{NSQ,BIN,MULTI}; // also in Neighbor
/* ---------------------------------------------------------------------- */
NeighList::NeighList(LAMMPS *lmp) : Pointers(lmp)
{
// initializations
maxatom = 0;
inum = gnum = 0;
ilist = NULL;
numneigh = NULL;
firstneigh = NULL;
// defaults, but may be reset by post_constructor()
occasional = 0;
ghost = 0;
ssa = 0;
history = 0;
respaouter = 0;
respamiddle = 0;
respainner = 0;
copy = 0;
copymode = 0;
// ptrs
iskip = NULL;
ijskip = NULL;
listcopy = NULL;
listskip = NULL;
listfull = NULL;
fix_bond = NULL;
ipage = NULL;
// extra rRESPA lists
inum_inner = gnum_inner = 0;
ilist_inner = NULL;
numneigh_inner = NULL;
firstneigh_inner = NULL;
inum_middle = gnum_middle = 0;
ilist_middle = NULL;
numneigh_middle = NULL;
firstneigh_middle = NULL;
ipage_inner = NULL;
ipage_middle = NULL;
// Kokkos package
kokkos = 0;
execution_space = Host;
// USER-DPD package
for (int i = 0; i < 8; i++) AIRct_ssa[i] = 0;
np = NULL;
}
/* ---------------------------------------------------------------------- */
NeighList::~NeighList()
{
if (copymode) return;
if (!copy) {
memory->destroy(ilist);
memory->destroy(numneigh);
memory->sfree(firstneigh);
delete [] ipage;
}
if (respainner) {
memory->destroy(ilist_inner);
memory->destroy(numneigh_inner);
memory->sfree(firstneigh_inner);
delete [] ipage_inner;
}
if (respamiddle) {
memory->destroy(ilist_middle);
memory->destroy(numneigh_middle);
memory->sfree(firstneigh_middle);
delete [] ipage_middle;
}
delete [] iskip;
memory->destroy(ijskip);
}
/* ----------------------------------------------------------------------
adjust settings to match corresponding NeighRequest
cannot do this in constructor b/c not all NeighLists are allocated yet
copy -> set listcopy for list to copy from
skip -> set listskip for list to skip from, create copy of itype,ijtype
halffull -> set listfull for full list to derive from
respaouter -> set all 3 outer/middle/inner flags
bond -> set fix_bond to Fix that made the request
------------------------------------------------------------------------- */
void NeighList::post_constructor(NeighRequest *nq)
{
// copy request settings used by list itself
occasional = nq->occasional;
ghost = nq->ghost;
ssa = nq->ssa;
history = nq->history;
respaouter = nq->respaouter;
respamiddle = nq->respamiddle;
respainner = nq->respainner;
copy = nq->copy;
if (nq->copy)
listcopy = neighbor->lists[nq->copylist];
if (nq->skip) {
listskip = neighbor->lists[nq->skiplist];
int ntypes = atom->ntypes;
iskip = new int[ntypes+1];
memory->create(ijskip,ntypes+1,ntypes+1,"neigh_list:ijskip");
int i,j;
for (i = 1; i <= ntypes; i++) iskip[i] = nq->iskip[i];
for (i = 1; i <= ntypes; i++)
for (j = 1; j <= ntypes; j++)
ijskip[i][j] = nq->ijskip[i][j];
}
if (nq->halffull)
listfull = neighbor->lists[nq->halffulllist];
if (nq->bond) fix_bond = (Fix *) nq->requestor;
}
/* ---------------------------------------------------------------------- */
void NeighList::setup_pages(int pgsize_caller, int oneatom_caller)
{
pgsize = pgsize_caller;
oneatom = oneatom_caller;
int nmypage = comm->nthreads;
ipage = new MyPage<int>[nmypage];
for (int i = 0; i < nmypage; i++)
ipage[i].init(oneatom,pgsize,PGDELTA);
if (respainner) {
ipage_inner = new MyPage<int>[nmypage];
for (int i = 0; i < nmypage; i++)
ipage_inner[i].init(oneatom,pgsize,PGDELTA);
}
if (respamiddle) {
ipage_middle = new MyPage<int>[nmypage];
for (int i = 0; i < nmypage; i++)
ipage_middle[i].init(oneatom,pgsize,PGDELTA);
}
}
/* ----------------------------------------------------------------------
grow per-atom data to allow for nlocal/nall atoms
triggered by neighbor list build
not called if a copy list
------------------------------------------------------------------------- */
void NeighList::grow(int nlocal, int nall)
{
// skip if data structs are already big enough
if (ssa) {
if ((nlocal * 3) + nall <= maxatom) return;
} else if (ghost) {
if (nall <= maxatom) return;
} else {
if (nlocal <= maxatom) return;
}
if (ssa) maxatom = (nlocal * 3) + nall;
else maxatom = atom->nmax;
memory->destroy(ilist);
memory->destroy(numneigh);
memory->sfree(firstneigh);
memory->create(ilist,maxatom,"neighlist:ilist");
memory->create(numneigh,maxatom,"neighlist:numneigh");
firstneigh = (int **) memory->smalloc(maxatom*sizeof(int *),
"neighlist:firstneigh");
if (respainner) {
memory->destroy(ilist_inner);
memory->destroy(numneigh_inner);
memory->sfree(firstneigh_inner);
memory->create(ilist_inner,maxatom,"neighlist:ilist_inner");
memory->create(numneigh_inner,maxatom,"neighlist:numneigh_inner");
firstneigh_inner = (int **) memory->smalloc(maxatom*sizeof(int *),
"neighlist:firstneigh_inner");
}
if (respamiddle) {
memory->destroy(ilist_middle);
memory->destroy(numneigh_middle);
memory->sfree(firstneigh_middle);
memory->create(ilist_middle,maxatom,"neighlist:ilist_middle");
memory->create(numneigh_middle,maxatom,"neighlist:numneigh_middle");
firstneigh_middle = (int **) memory->smalloc(maxatom*sizeof(int *),
"neighlist:firstneigh_middle");
}
}
/* ----------------------------------------------------------------------
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(" %p = requestor ptr (instance %d id %d)\n",
rq->requestor,rq->requestor_instance,rq->id);
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(" %d = neigh\n",rq->neigh);
printf("\n");
printf(" %d = half\n",rq->half);
printf(" %d = full\n",rq->full);
printf("\n");
printf(" %d = occasional\n",occasional);
printf(" %d = newton\n",rq->newton);
printf(" %d = ghost flag\n",ghost);
printf(" %d = size\n",rq->size);
printf(" %d = history\n",rq->history);
printf(" %d = granonesided\n",rq->granonesided);
printf(" %d = respaouter\n",rq->respaouter);
printf(" %d = respamiddle\n",rq->respamiddle);
printf(" %d = respainner\n",rq->respainner);
printf(" %d = bond\n",rq->bond);
printf(" %d = omp\n",rq->omp);
printf(" %d = intel\n",rq->intel);
printf(" %d = kokkos host\n",rq->kokkos_host);
printf(" %d = kokkos device\n",rq->kokkos_device);
printf(" %d = ssa flag\n",ssa);
printf("\n");
printf(" %d = skip flag\n",rq->skip);
printf(" %d = off2on\n",rq->off2on);
printf(" %d = copy flag\n",rq->copy);
printf(" %d = half/full\n",rq->halffull);
printf("\n");
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
if growflag = 0, maxatom & maxpage will also be 0
if stencilflag = 0, maxstencil * maxstencil_multi will also be 0
------------------------------------------------------------------------- */
bigint NeighList::memory_usage()
{
bigint bytes = 0;
bytes += memory->usage(ilist,maxatom);
bytes += memory->usage(numneigh,maxatom);
bytes += maxatom * sizeof(int *);
int nmypage = comm->nthreads;
if (ipage) {
for (int i = 0; i < nmypage; i++)
bytes += ipage[i].size();
}
if (respainner) {
bytes += memory->usage(ilist_inner,maxatom);
bytes += memory->usage(numneigh_inner,maxatom);
bytes += maxatom * sizeof(int *);
if (ipage_inner) {
for (int i = 0; i < nmypage; i++)
bytes += ipage_inner[i].size();
}
}
if (respamiddle) {
bytes += memory->usage(ilist_middle,maxatom);
bytes += memory->usage(numneigh_middle,maxatom);
bytes += maxatom * sizeof(int *);
if (ipage_middle) {
for (int i = 0; i < nmypage; i++)
bytes += ipage_middle[i].size();
}
}
return bytes;
}
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