// clang-format off
/* ----------------------------------------------------------------------
   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
   https://www.lammps.org/, 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_full_bin_atomonly_omp.h"

#include "atom.h"
#include "error.h"
#include "my_page.h"
#include "neigh_list.h"
#include "npair_omp.h"

#include "omp_compat.h"

using namespace LAMMPS_NS;

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

NPairFullBinAtomonlyOmp::NPairFullBinAtomonlyOmp(LAMMPS *lmp) : NPair(lmp) {}

/* ----------------------------------------------------------------------
   binned neighbor list construction for all neighbors
   every neighbor pair appears in list of both atoms i and j
------------------------------------------------------------------------- */

void NPairFullBinAtomonlyOmp::build(NeighList *list)
{
  const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;

  NPAIR_OMP_INIT;
#if defined(_OPENMP)
#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(list)
#endif
  NPAIR_OMP_SETUP(nlocal);

  int i,j,k,n,itype,jtype,ibin;
  double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
  int *neighptr;

  double **x = atom->x;
  int *type = atom->type;
  int *mask = atom->mask;
  tagint *molecule = atom->molecule;

  int *ilist = list->ilist;
  int *numneigh = list->numneigh;
  int **firstneigh = list->firstneigh;

  // each thread has its own page allocator
  MyPage<int> &ipage = list->ipage[tid];
  ipage.reset();

  // loop over owned atoms, storing neighbors

  for (i = ifrom; i < ito; i++) {

    n = 0;
    neighptr = ipage.vget();

    itype = type[i];
    xtmp = x[i][0];
    ytmp = x[i][1];
    ztmp = x[i][2];

    // loop over all atoms in surrounding bins in stencil including self
    // skip i = j

    ibin = atom2bin[i];

    for (k = 0; k < nstencil; k++) {
      for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
        if (i == j) 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]) neighptr[n++] = j;
      }
    }

    ilist[i] = i;
    firstneigh[i] = neighptr;
    numneigh[i] = n;
    ipage.vgot(n);
    if (ipage.status())
      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
  }
  NPAIR_OMP_CLOSE;
  list->inum = nlocal;
  list->gnum = 0;
}
