// 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_multi_newton.h"

#include "atom.h"
#include "atom_vec.h"
#include "domain.h"
#include "error.h"
#include "molecule.h"
#include "my_page.h"
#include "neighbor.h"
#include "neigh_list.h"

using namespace LAMMPS_NS;

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

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

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

void NPairHalfMultiNewton::build(NeighList *list)
{
  int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,which,ns,imol,iatom,moltemplate;
  tagint tagprev;
  double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
  int *neighptr,*s;
  int js;

  int *collection = neighbor->collection;
  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;
  if (includegroup) nlocal = atom->nfirst;

  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 inum = 0;
  ipage->reset();

  for (i = 0; i < nlocal; i++) {
    n = 0;
    neighptr = ipage->vget();
    itype = type[i];
    icollection = collection[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;
    }

    ibin = atom2bin[i];

    // loop through stencils for all collections
    for (jcollection = 0; jcollection < ncollections; jcollection++) {

      // if same collection use own bin
      if(icollection == jcollection) jbin = ibin;
          else jbin = coord2bin(x[i], jcollection);

      // if same size: uses half stencil so check central bin
      if(cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){

        if (icollection == jcollection) js = bins[i];
        else js = binhead_multi[jcollection][jbin];

        // if same collection,
        //   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

        // if different collections,
        //   if j is owned atom, store it if j > i
        //   if j is ghost, only store if j coords are "above and to the right" of i

            for (j = js; j >= 0; j = bins[j]) {
          if((icollection != jcollection) && (j < i)) continue;

              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;
                }
              }

          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 (domain->minimum_image_check(delx,dely,delz))
                    neighptr[n++] = j;
                  else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
                } else neighptr[n++] = j;
              }
            }
      }

      // for all collections, loop over all atoms in other bins in stencil, store every pair
      // stencil is empty if i larger than j
      // stencil is half if i same size as j
      // stencil is full if i smaller than j

          s = stencil_multi[icollection][jcollection];
          ns = nstencil_multi[icollection][jcollection];

          for (k = 0; k < ns; k++) {
            js = binhead_multi[jcollection][jbin + s[k]];
            for (j = js; j >= 0; j = bins[j]) {

          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 != Atom::ATOMIC) {
                    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 (domain->minimum_image_check(delx,dely,delz))
                      neighptr[n++] = j;
                    else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
                } 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;
}