// 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_half_size_bin_newton.h"

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

using namespace LAMMPS_NS;

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

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

/* ----------------------------------------------------------------------
   size particles
   binned neighbor list construction with full Newton's 3rd law
   each owned atom i checks its own bin and other bins in Newton stencil
   every pair stored exactly once by some processor
------------------------------------------------------------------------- */

void NPairHalfSizeBinNewton::build(NeighList *list)
{
  int i,j,k,n,ibin;
  double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
  double radi,radsum,cutsq;
  int *neighptr;

  double **x = atom->x;
  double *radius = atom->radius;
  int *type = atom->type;
  int *mask = atom->mask;
  tagint *molecule = atom->molecule;
  int nlocal = atom->nlocal;
  if (includegroup) nlocal = atom->nfirst;

  int history = list->history;
  int *ilist = list->ilist;
  int *numneigh = list->numneigh;
  int **firstneigh = list->firstneigh;
  MyPage<int> *ipage = list->ipage;

  int mask_history = 3 << SBBITS;

  int inum = 0;
  ipage->reset();

  for (i = 0; i < nlocal; i++) {
    n = 0;
    neighptr = ipage->vget();

    xtmp = x[i][0];
    ytmp = x[i][1];
    ztmp = x[i][2];
    radi = radius[i];

    // loop over rest of atoms in i's bin, ghosts are at end of linked list
    // if j is owned atom, store it, since j is beyond i in linked list
    // if j is ghost, only store if j coords are "above and to the right" of i

    for (j = bins[i]; j >= 0; j = bins[j]) {
      if (j >= nlocal) {
        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;
        }
      }

      if (exclude && exclusion(i,j,type[i],type[j],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;
      radsum = radi + radius[j];
      cutsq = (radsum+skin) * (radsum+skin);

      if (rsq <= cutsq) {
        if (history && rsq < radsum*radsum)
          neighptr[n++] = j ^ mask_history;
        else
          neighptr[n++] = j;
      }
    }

    // loop over all atoms in other bins in stencil, store every pair

    ibin = atom2bin[i];
    for (k = 0; k < nstencil; k++) {
      for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
        if (exclude && exclusion(i,j,type[i],type[j],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;
        radsum = radi + radius[j];
        cutsq = (radsum+skin) * (radsum+skin);

        if (rsq <= cutsq) {
          if (history && rsq < radsum*radsum)
            neighptr[n++] = j ^ mask_history;
          else
            neighptr[n++] = j;
        }
      }
    }

    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;
}
