/* ----------------------------------------------------------------------
   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
   https://www.lammps.org/, Sandia National Laboratories
   LAMMPS development team: developers@lammps.org

   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_bin.h"

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

#include <cmath>

using namespace LAMMPS_NS;
using namespace NeighConst;

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

template<int HALF, int NEWTON, int TRI, int SIZE, int ATOMONLY>
NPairBin<HALF, NEWTON, TRI, SIZE, ATOMONLY>::NPairBin(LAMMPS *lmp) : NPair(lmp) {}

/* ----------------------------------------------------------------------
   Full:
     binned neighbor list construction for all neighbors
     every neighbor pair appears in list of both atoms i and j
   Half + Newtoff:
     binned neighbor list construction with partial Newton's 3rd law
     each owned atom i checks own bin and other bins in stencil
     pair stored once if i,j are both owned and i < j
     pair stored by me if j is ghost (also stored by proc owning j)
   Half + Newton:
     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
------------------------------------------------------------------------- */

template<int HALF, int NEWTON, int TRI, int SIZE, int ATOMONLY>
void NPairBin<HALF, NEWTON, TRI, SIZE, ATOMONLY>::build(NeighList *list)
{
  int i, j, jh, k, n, itype, jtype, ibin, bin_start, which, imol, iatom, moltemplate;
  tagint itag, jtag, tagprev;
  double xtmp, ytmp, ztmp, delx, dely, delz, rsq, radsum,cut,cutsq;
  int *neighptr;

  const double delta = 0.01 * force->angstrom;

  double **x = atom->x;
  double *radius = atom->radius;
  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 (!ATOMONLY) {
    if (molecular == Atom::TEMPLATE)
      moltemplate = 1;
    else
      moltemplate = 0;
  }

  int history = list->history;
  int mask_history = 1 << HISTBITS;

  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();

    itag = tag[i];
    itype = type[i];
    xtmp = x[i][0];
    ytmp = x[i][1];
    ztmp = x[i][2];
    if (!ATOMONLY) {
      if (moltemplate) {
        imol = molindex[i];
        iatom = molatom[i];
        tagprev = tag[i] - iatom - 1;
      }
    }

    ibin = atom2bin[i];

    for (k = 0; k < nstencil; k++) {
      bin_start = binhead[ibin + stencil[k]];
      if (HALF && NEWTON && (!TRI)) {
        if (k == 0) {
          // Half neighbor list, newton on, orthonormal
          // loop over rest of atoms in i's bin, ghosts are at end of linked list
          bin_start = bins[i];
        }
      }

      for (j = bin_start; j >= 0; j = bins[j]) {
        if (!HALF) {
          // Full neighbor list
          // only skip i = j
          if (i == j) continue;
        } else if (!NEWTON) {
          // Half neighbor list, newton off
          // only store pair if i < j
          // stores own/own pairs only once
          // stores own/ghost pairs on both procs
          if (j <= i) continue;
        } else if (TRI) {
          // for triclinic, bin stencil is full in all 3 dims
          // must use itag/jtag to eliminate half the I/J interactions
          // cannot use I/J exact coord comparision
          //   b/c transforming orthog -> lambda -> orthog for ghost atoms
          //   with an added PBC offset can shift all 3 coords by epsilon
          if (j <= i) continue;
          if (j >= nlocal) {
            jtag = tag[j];
            if (itag > jtag) {
              if ((itag + jtag) % 2 == 0) continue;
            } else if (itag < jtag) {
              if ((itag + jtag) % 2 == 1) continue;
            } else {
              if (fabs(x[j][2] - ztmp) > delta) {
                if (x[j][2] < ztmp) continue;
              } else if (fabs(x[j][1] - ytmp) > delta) {
                if (x[j][1] < ytmp) continue;
              } else {
                if (x[j][0] < xtmp) continue;
              }
            }
          }
        } else {
          // Half neighbor list, newton on, orthonormal
          // store every pair for every bin in stencil, except for i's bin

          if (k == 0) {
            // 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 (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 (SIZE) {
          radsum = radius[i] + radius[j];
          cut = radsum + skin;
          cutsq = cut * cut;

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

              if (molecular != Atom::ATOMIC) {
                if (!moltemplate)
                  which = find_special(special[i], nspecial[i], tag[j]);
                else if ((imol >= 0) && onemols[imol]->special)
                  which = find_special(onemols[imol]->special[iatom],
                                       onemols[imol]->nspecial[iatom], tag[j] - tagprev);
                else
                  which = 0;
                if (which == 0)
                  neighptr[n++] = jh;
                else if (domain->minimum_image_check(delx, dely, delz))
                  neighptr[n++] = jh;
                else if (which > 0)
                  neighptr[n++] = jh ^ (which << SBBITS);
              } else
                neighptr[n++] = jh;
            }
          }
        } else {
          if (ATOMONLY) {
            if (rsq <= cutneighsq[itype][jtype]) neighptr[n++] = j;
          } else {
            if (rsq <= cutneighsq[itype][jtype]) {
              if (molecular != Atom::ATOMIC) {
                if (!moltemplate)
                  which = find_special(special[i], nspecial[i], tag[j]);
                else if ((imol >= 0) && onemols[imol]->special)
                  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, Error::NOLASTLINE, "Neighbor list overflow, boost neigh_modify one" + utils::errorurl(36));
  }

  list->inum = inum;
  if (!HALF) list->gnum = 0;
}

namespace LAMMPS_NS {
template class NPairBin<0,1,0,0,0>;
template class NPairBin<1,0,0,0,0>;
template class NPairBin<1,1,0,0,0>;
template class NPairBin<1,1,1,0,0>;
template class NPairBin<0,1,0,1,0>;
template class NPairBin<1,0,0,1,0>;
template class NPairBin<1,1,0,1,0>;
template class NPairBin<1,1,1,1,0>;
template class NPairBin<0,1,0,0,1>;
template class NPairBin<1,0,0,0,1>;
template class NPairBin<1,1,0,0,1>;
template class NPairBin<1,1,1,0,1>;
template class NPairBin<0,1,0,1,1>;
template class NPairBin<1,0,0,1,1>;
template class NPairBin<1,1,0,1,1>;
template class NPairBin<1,1,1,1,1>;
}
