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npair_skip_respa.cpp
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Wed, May 22, 13:08

npair_skip_respa.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 "npair_skip_respa.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "atom.h"
#include "atom_vec.h"
#include "molecule.h"
#include "domain.h"
#include "my_page.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
NPairSkipRespa::NPairSkipRespa(LAMMPS *lmp) : NPair(lmp) {}
/* ----------------------------------------------------------------------
build skip list for subset of types from parent list
iskip and ijskip flag which atom types and type pairs to skip
this is for respa lists, copy the inner/middle values from parent
------------------------------------------------------------------------- */
void NPairSkipRespa::build(NeighList *list)
{
int i,j,ii,jj,n,itype,jnum,joriginal,n_inner,n_middle;
int *neighptr,*jlist,*neighptr_inner,*neighptr_middle;
int *type = atom->type;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
MyPage<int> *ipage = list->ipage;
int *ilist_skip = list->listskip->ilist;
int *numneigh_skip = list->listskip->numneigh;
int **firstneigh_skip = list->listskip->firstneigh;
int inum_skip = list->listskip->inum;
int *iskip = list->iskip;
int **ijskip = list->ijskip;
int *ilist_inner = list->ilist_inner;
int *numneigh_inner = list->numneigh_inner;
int **firstneigh_inner = list->firstneigh_inner;
MyPage<int> *ipage_inner = list->ipage_inner;
int *numneigh_inner_skip = list->listskip->numneigh_inner;
int **firstneigh_inner_skip = list->listskip->firstneigh_inner;
int *ilist_middle,*numneigh_middle,**firstneigh_middle;
MyPage<int> *ipage_middle;
int *numneigh_middle_skip,**firstneigh_middle_skip;
int respamiddle = list->respamiddle;
if (respamiddle) {
ilist_middle = list->ilist_middle;
numneigh_middle = list->numneigh_middle;
firstneigh_middle = list->firstneigh_middle;
ipage_middle = list->ipage_middle;
numneigh_middle_skip = list->listskip->numneigh_middle;
firstneigh_middle_skip = list->listskip->firstneigh_middle;
}
int inum = 0;
ipage->reset();
ipage_inner->reset();
if (respamiddle) ipage_middle->reset();
// loop over atoms in other list
// skip I atom entirely if iskip is set for type[I]
// skip I,J pair if ijskip is set for type[I],type[J]
for (ii = 0; ii < inum_skip; ii++) {
i = ilist_skip[ii];
itype = type[i];
if (iskip[itype]) continue;
n = n_inner = 0;
neighptr = ipage->vget();
neighptr_inner = ipage_inner->vget();
if (respamiddle) {
n_middle = 0;
neighptr_middle = ipage_middle->vget();
}
// loop over parent outer rRESPA list
jlist = firstneigh_skip[i];
jnum = numneigh_skip[i];
for (jj = 0; jj < jnum; jj++) {
joriginal = jlist[jj];
j = joriginal & NEIGHMASK;
if (ijskip[itype][type[j]]) continue;
neighptr[n++] = joriginal;
}
// loop over parent inner rRESPA list
jlist = firstneigh_inner_skip[i];
jnum = numneigh_inner_skip[i];
for (jj = 0; jj < jnum; jj++) {
joriginal = jlist[jj];
j = joriginal & NEIGHMASK;
if (ijskip[itype][type[j]]) continue;
neighptr_inner[n_inner++] = joriginal;
}
// loop over parent middle rRESPA list
if (respamiddle) {
jlist = firstneigh_middle_skip[i];
jnum = numneigh_middle_skip[i];
for (jj = 0; jj < jnum; jj++) {
joriginal = jlist[jj];
j = joriginal & NEIGHMASK;
if (ijskip[itype][type[j]]) continue;
neighptr_middle[n_middle++] = joriginal;
}
}
ilist[inum] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
ipage->vgot(n);
if (ipage->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
ilist_inner[inum] = i;
firstneigh_inner[i] = neighptr_inner;
numneigh_inner[i] = n_inner;
ipage_inner->vgot(n);
if (ipage_inner->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
if (respamiddle) {
ilist_middle[inum] = i;
firstneigh_middle[i] = neighptr_middle;
numneigh_middle[i] = n_middle;
ipage_middle->vgot(n);
if (ipage_middle->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
inum++;
}
list->inum = inum;
list->inum_inner = inum;
if (respamiddle) list->inum_middle = inum;
}

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