/* ----------------------------------------------------------------------
   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.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;

/* ---------------------------------------------------------------------- */

NPairSkip::NPairSkip(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 half and full lists
   if ghost, also store neighbors of ghost atoms & set inum,gnum correctly
------------------------------------------------------------------------- */

void NPairSkip::build(NeighList *list)
{
  int i,j,ii,jj,n,itype,jnum,joriginal;
  int *neighptr,*jlist;

  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 num_skip = list->listskip->inum;
  if (list->ghost) num_skip += list->listskip->gnum;

  int *iskip = list->iskip;
  int **ijskip = list->ijskip;

  int inum = 0;
  ipage->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 < num_skip; ii++) {
    i = ilist_skip[ii];
    itype = type[i];
    if (iskip[itype]) continue;

    n = 0;
    neighptr = ipage->vget();

    // loop over parent non-skip 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;
    }

    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");
  }

  list->inum = inum;
  if (list->ghost) {
    int num = 0;
    for (i = 0; i < inum; i++)
      if (ilist[i] < nlocal) num++;
      else break;
    list->inum = num;
    list->gnum = inum - num;
  }
}