Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F120163011
npair_half_respa_nsq_newtoff.cpp
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Wed, Jul 2, 09:27
Size
5 KB
Mime Type
text/x-c
Expires
Fri, Jul 4, 09:27 (2 d)
Engine
blob
Format
Raw Data
Handle
27150142
Attached To
rLAMMPS lammps
npair_half_respa_nsq_newtoff.cpp
View Options
/* ----------------------------------------------------------------------
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_half_respa_nsq_newtoff.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "atom.h"
#include "atom_vec.h"
#include "group.h"
#include "molecule.h"
#include "domain.h"
#include "my_page.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
NPairHalfRespaNsqNewtoff::NPairHalfRespaNsqNewtoff(LAMMPS *lmp) : NPair(lmp) {}
/* ----------------------------------------------------------------------
multiple respa lists
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)
------------------------------------------------------------------------- */
void NPairHalfRespaNsqNewtoff::build(NeighList *list)
{
int i,j,n,itype,jtype,n_inner,n_middle,bitmask,imol,iatom,moltemplate;
tagint tagprev;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr,*neighptr_inner,*neighptr_middle;
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 == 2) 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];
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
for (j = i+1; j < nall; j++) {
if (includegroup && !(mask[j] & bitmask)) 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) {
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;
}
Event Timeline
Log In to Comment