lammps-sys 0.6.0

Generates bindings to LAMMPS' C interface (with optional builds from source)
Documentation 
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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 "neigh_list.h"
#include "atom.h"
#include "atom_vec.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;
}