249 lines
7.9 KiB
C++
249 lines
7.9 KiB
C++
// clang-format off
|
|
/* ----------------------------------------------------------------------
|
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
|
https://www.lammps.org/, Sandia National Laboratories
|
|
LAMMPS development team: developers@lammps.org
|
|
|
|
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_respa_nsq.h"
|
|
|
|
#include "atom.h"
|
|
#include "atom_vec.h"
|
|
#include "domain.h"
|
|
#include "error.h"
|
|
#include "force.h"
|
|
#include "group.h"
|
|
#include "molecule.h"
|
|
#include "my_page.h"
|
|
#include "neigh_list.h"
|
|
|
|
#include <cmath>
|
|
|
|
using namespace LAMMPS_NS;
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
template<int NEWTON, int TRI>
|
|
NPairRespaNsq<NEWTON, TRI>::NPairRespaNsq(LAMMPS *lmp) : NPair(lmp) {}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
multiple respa lists
|
|
Newtoff
|
|
N^2 / 2 search for neighbor pairs with partial Newton's 3rd law
|
|
pair added to list if atoms i and j are both owned and i < j
|
|
pair added if j is ghost (also stored by proc owning j)
|
|
Newton
|
|
N^2 / 2 search for neighbor pairs with full Newton's 3rd law
|
|
pair added to list if atoms i and j are both owned and i < j
|
|
if j is ghost only me or other proc adds pair
|
|
decision based on itag,jtag tests
|
|
use itag/jtag comparision to eliminate half the interactions
|
|
itag = jtag is possible for long cutoffs that include images of self
|
|
Newton + Triclinic:
|
|
for triclinic, must use delta to eliminate half the I/J interactions
|
|
cannot use I/J exact coord comparision as for orthog
|
|
b/c transforming orthog -> lambda -> orthog for ghost atoms
|
|
with an added PBC offset can shift all 3 coords by epsilon
|
|
|
|
------------------------------------------------------------------------- */
|
|
|
|
template<int NEWTON, int TRI>
|
|
void NPairRespaNsq<NEWTON, TRI>::build(NeighList *list)
|
|
{
|
|
int i, j, n, itype, jtype, n_inner, n_middle, bitmask, imol, iatom, moltemplate;
|
|
tagint itag, jtag, tagprev;
|
|
double xtmp, ytmp, ztmp, delx, dely, delz, rsq;
|
|
int *neighptr, *neighptr_inner, *neighptr_middle;
|
|
|
|
const double delta = 0.01 * force->angstrom;
|
|
|
|
double **x = atom->x;
|
|
int *type = atom->type;
|
|
int *mask = atom->mask;
|
|
tagint *tag = atom->tag;
|
|
tagint *molecule = atom->molecule;
|
|
tagint **special = atom->special;
|
|
int **nspecial = atom->nspecial;
|
|
int nlocal = atom->nlocal;
|
|
int nall = nlocal + atom->nghost;
|
|
if (includegroup) {
|
|
nlocal = atom->nfirst;
|
|
bitmask = group->bitmask[includegroup];
|
|
}
|
|
|
|
int *molindex = atom->molindex;
|
|
int *molatom = atom->molatom;
|
|
Molecule **onemols = atom->avec->onemols;
|
|
if (molecular == Atom::TEMPLATE) moltemplate = 1;
|
|
else moltemplate = 0;
|
|
|
|
int *ilist = list->ilist;
|
|
int *numneigh = list->numneigh;
|
|
int **firstneigh = list->firstneigh;
|
|
MyPage<int> *ipage = list->ipage;
|
|
|
|
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 *ilist_middle, *numneigh_middle, **firstneigh_middle;
|
|
MyPage<int> *ipage_middle;
|
|
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;
|
|
}
|
|
|
|
int inum = 0;
|
|
int which = 0;
|
|
int minchange = 0;
|
|
ipage->reset();
|
|
ipage_inner->reset();
|
|
if (respamiddle) ipage_middle->reset();
|
|
|
|
for (i = 0; i < nlocal; i++) {
|
|
n = n_inner = 0;
|
|
neighptr = ipage->vget();
|
|
neighptr_inner = ipage_inner->vget();
|
|
if (respamiddle) {
|
|
n_middle = 0;
|
|
neighptr_middle = ipage_middle->vget();
|
|
}
|
|
|
|
itype = type[i];
|
|
itag = tag[i];
|
|
xtmp = x[i][0];
|
|
ytmp = x[i][1];
|
|
ztmp = x[i][2];
|
|
if (moltemplate) {
|
|
imol = molindex[i];
|
|
iatom = molatom[i];
|
|
tagprev = tag[i] - iatom - 1;
|
|
}
|
|
|
|
// loop over remaining atoms, owned and ghost
|
|
// use itag/jtap comparision to eliminate half the interactions
|
|
// itag = jtag is possible for long cutoffs that include images of self
|
|
// for triclinic, must use delta to eliminate half the I/J interactions
|
|
// cannot use I/J exact coord comparision as for orthog
|
|
// b/c transforming orthog -> lambda -> orthog for ghost atoms
|
|
// with an added PBC offset can shift all 3 coords by epsilon
|
|
|
|
for (j = i + 1; j < nall; j++) {
|
|
if (includegroup && !(mask[j] & bitmask)) continue;
|
|
|
|
if (NEWTON) {
|
|
if (j >= nlocal) {
|
|
jtag = tag[j];
|
|
if (itag > jtag) {
|
|
if ((itag + jtag) % 2 == 0) continue;
|
|
} else if (itag < jtag) {
|
|
if ((itag + jtag) % 2 == 1) continue;
|
|
} else if (TRI) {
|
|
if (fabs(x[j][2] - ztmp) > delta) {
|
|
if (x[j][2] < ztmp) continue;
|
|
} else if (fabs(x[j][1] - ytmp) > delta) {
|
|
if (x[j][1] < ytmp) continue;
|
|
} else {
|
|
if (x[j][0] < xtmp) continue;
|
|
}
|
|
} else {
|
|
if (x[j][2] < ztmp) continue;
|
|
if (x[j][2] == ztmp) {
|
|
if (x[j][1] < ytmp) continue;
|
|
if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
jtype = type[j];
|
|
if (exclude && exclusion(i, j, itype, jtype, mask, molecule)) continue;
|
|
|
|
delx = xtmp - x[j][0];
|
|
dely = ytmp - x[j][1];
|
|
delz = ztmp - x[j][2];
|
|
rsq = delx * delx + dely * dely + delz * delz;
|
|
|
|
if (rsq <= cutneighsq[itype][jtype]) {
|
|
if (molecular != Atom::ATOMIC) {
|
|
if (!moltemplate)
|
|
which = find_special(special[i], nspecial[i], tag[j]);
|
|
else if (imol >= 0)
|
|
which = find_special(onemols[imol]->special[iatom], onemols[imol]->nspecial[iatom],
|
|
tag[j] - tagprev);
|
|
else
|
|
which = 0;
|
|
if (which == 0)
|
|
neighptr[n++] = j;
|
|
else if ((minchange = domain->minimum_image_check(delx, dely, delz)))
|
|
neighptr[n++] = j;
|
|
else if (which > 0)
|
|
neighptr[n++] = j ^ (which << SBBITS);
|
|
} else
|
|
neighptr[n++] = j;
|
|
|
|
if (rsq < cut_inner_sq) {
|
|
if (which == 0)
|
|
neighptr_inner[n_inner++] = j;
|
|
else if (minchange)
|
|
neighptr_inner[n_inner++] = j;
|
|
else if (which > 0)
|
|
neighptr_inner[n_inner++] = j ^ (which << SBBITS);
|
|
}
|
|
|
|
if (respamiddle && (rsq < cut_middle_sq) && (rsq > cut_middle_inside_sq)) {
|
|
if (which == 0)
|
|
neighptr_middle[n_middle++] = j;
|
|
else if (minchange)
|
|
neighptr_middle[n_middle++] = j;
|
|
else if (which > 0)
|
|
neighptr_middle[n_middle++] = j ^ (which << SBBITS);
|
|
}
|
|
}
|
|
}
|
|
|
|
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_inner);
|
|
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_middle);
|
|
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;
|
|
}
|
|
|
|
namespace LAMMPS_NS {
|
|
template class NPairRespaNsq<0,0>;
|
|
template class NPairRespaNsq<1,0>;
|
|
template class NPairRespaNsq<1,1>;
|
|
}
|