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lammps/src/npair_skip_size_off2on_oneside.cpp
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npair_skip_size_off2on_oneside.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 <string.h>
#include "npair_skip_size_off2on_oneside.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "atom.h"
#include "atom_vec.h"
#include "molecule.h"
#include "domain.h"
#include "fix_shear_history.h"
#include "my_page.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
NPairSkipSizeOff2onOneside::NPairSkipSizeOff2onOneside(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
parent non-skip list used newton off and was not onesided,
this skip list is newton on and onesided
if list requests it, preserve shear history via fix shear/history
------------------------------------------------------------------------- */
void NPairSkipSizeOff2onOneside::build(NeighList *list)
{
int i,j,ii,jj,m,n,nn,itype,jnum,joriginal,flip,dnum,dnumbytes,tmp;
tagint jtag;
int *surf,*jlist;
int *npartner;
tagint **partner;
double **shearpartner;
int **firsttouch;
double **firstshear;
MyPage<int> *ipage_touch;
MyPage<double> *dpage_shear;
NeighList *listhistory;
tagint *tag = atom->tag;
int *type = atom->type;
int nlocal = atom->nlocal;
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;
if (domain->dimension == 2) surf = atom->line;
else surf = atom->tri;
FixShearHistory *fix_history = (FixShearHistory *) list->fix_history;
if (fix_history) {
fix_history->nlocal_neigh = nlocal;
fix_history->nall_neigh = nlocal + atom->nghost;
npartner = fix_history->npartner;
partner = fix_history->partner;
shearpartner = fix_history->shearpartner;
listhistory = list->listhistory;
firsttouch = listhistory->firstneigh;
firstshear = listhistory->firstdouble;
ipage_touch = listhistory->ipage;
dpage_shear = listhistory->dpage;
dnum = listhistory->dnum;
dnumbytes = dnum * sizeof(double);
}
int inum = 0;
ipage->reset();
if (fix_history) {
ipage_touch->reset();
dpage_shear->reset();
}
// two loops over parent list required, one to count, one to store
// because onesided constraint means pair I,J may be stored with I or J
// so don't know in advance how much space to alloc for each atom's neighs
// first loop over atoms in other list to count neighbors
// 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 (i = 0; i < nlocal; i++) numneigh[i] = 0;
for (ii = 0; ii < inum_skip; ii++) {
i = ilist_skip[ii];
itype = type[i];
if (iskip[itype]) continue;
n = 0;
// loop over parent non-skip size 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;
// flip I,J if necessary to satisfy onesided constraint
// do not keep if I is now ghost
if (surf[i] >= 0) {
if (j >= nlocal) continue;
tmp = i;
i = j;
j = tmp;
flip = 1;
} else flip = 0;
numneigh[i]++;
if (flip) i = j;
}
}
// allocate all per-atom neigh list chunks, including history
for (i = 0; i < nlocal; i++) {
if (numneigh[i] == 0) continue;
n = numneigh[i];
firstneigh[i] = ipage->get(n);
if (ipage->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
if (fix_history) {
firsttouch[i] = ipage_touch->get(n);
firstshear[i] = dpage_shear->get(dnum*n);
}
}
// second loop over atoms in other list to store neighbors
// 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 (i = 0; i < nlocal; i++) numneigh[i] = 0;
for (ii = 0; ii < inum_skip; ii++) {
i = ilist_skip[ii];
itype = type[i];
if (iskip[itype]) continue;
// loop over parent non-skip size list and optionally its history info
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;
// flip I,J if necessary to satisfy onesided constraint
// do not keep if I is now ghost
if (surf[i] >= 0) {
if (j >= nlocal) continue;
tmp = i;
i = j;
j = tmp;
flip = 1;
} else flip = 0;
// store j in neigh list, not joriginal, like other neigh methods
// OK, b/c there is no special list flagging for surfs
firstneigh[i][numneigh[i]] = j;
// no numeric test for current touch
// just use FSH partner list to infer it
// would require complex calculation for surfs
if (fix_history) {
jtag = tag[j];
n = numneigh[i];
nn = dnum*n;
for (m = 0; m < npartner[i]; m++)
if (partner[i][m] == jtag) break;
if (m < npartner[i]) {
firsttouch[i][n] = 1;
memcpy(&firstshear[i][nn],&shearpartner[i][dnum*m],dnumbytes);
} else {
firsttouch[i][n] = 0;
memcpy(&firstshear[i][nn],zeroes,dnumbytes);
}
}
numneigh[i]++;
if (flip) i = j;
}
// only add atom I to ilist if it has neighbors
// fix shear/history allows for this in pre_exchange_onesided()
if (numneigh[i]) ilist[inum++] = i;
}
list->inum = inum;
}
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