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

   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 "neighbor.h"

#include "neigh_list.h"

#include "atom.h"

#include "error.h"

using namespace LAMMPS_NS;

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

   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)

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

void Neighbor::half_bin_no_newton(NeighList *list)

{

  int i,j,k,n,itype,jtype,ibin,which;

  double xtmp,ytmp,ztmp,delx,dely,delz,rsq;

  int *neighptr;

  // bin local & ghost atoms

  bin_atoms();

  // loop over each atom, storing neighbors

  double **x = atom->x;

  int *type = atom->type;

  int *mask = atom->mask;

  int *molecule = atom->molecule;

  int nlocal = atom->nlocal;

  int nall = atom->nlocal + atom->nghost;

  int molecular = atom->molecular;

  int *ilist = list->ilist;

  int *numneigh = list->numneigh;

  int **firstneigh = list->firstneigh;

  int **pages = list->pages;

  int nstencil = list->nstencil;

  int *stencil = list->stencil;

  int inum = 0;

  int npage = 0;

  int npnt = 0;

  for (i = 0; i < nlocal; i++) {

    if (pgsize - npnt < oneatom) {

      npnt = 0;

      npage++;

      if (npage == list->maxpage) pages = list->add_pages();

    }

    neighptr = &pages[npage][npnt];

    n = 0;

    itype = type[i];

    xtmp = x[i][0];

    ytmp = x[i][1];

    ztmp = x[i][2];

    // loop over all atoms in other bins in stencil including self

    // only store pair if i < j

    // stores own/own pairs only once

    // stores own/ghost pairs on both procs

    ibin = coord2bin(x[i]);

    for (k = 0; k < nstencil; k++) {

      for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {

	if (j <= i) 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) which = find_special(i,j);

	  else which = 0;

	  if (which == 0) neighptr[n++] = j;

	  else if (which > 0) neighptr[n++] = which*nall + j;

	}

      }

    }

    ilist[inum] = i;

    firstneigh[i] = neighptr;

    numneigh[i] = n;

    inum++;

    npnt += n;

    if (npnt >= pgsize)

      error->one("Neighbor list overflow, boost neigh_modify one or page");

  }

  list->inum = inum;

}

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

   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 Neighbor::half_bin_newton(NeighList *list)

{

  int i,j,k,n,itype,jtype,ibin,which;

  double xtmp,ytmp,ztmp,delx,dely,delz,rsq;

  int *neighptr;

  // bin local & ghost atoms

  bin_atoms();

  // loop over each atom, storing neighbors

  double **x = atom->x;

  int *type = atom->type;

  int *mask = atom->mask;

  int *molecule = atom->molecule;

  int nlocal = atom->nlocal;

  int nall = atom->nlocal + atom->nghost;

  int molecular = atom->molecular;

  int *ilist = list->ilist;

  int *numneigh = list->numneigh;

  int **firstneigh = list->firstneigh;

  int **pages = list->pages;

  int skip = list->skip;

  int nstencil = list->nstencil;

  int *stencil = list->stencil;

  int inum = 0;

  int npage = 0;

  int npnt = 0;

  for (i = 0; i < nlocal; i++) {

    if (pgsize - npnt < oneatom) {

      npnt = 0;

      npage++;

      if (npage == list->maxpage) pages = list->add_pages();

    }

    neighptr = &pages[npage][npnt];

    n = 0;

    itype = type[i];

    xtmp = x[i][0];

    ytmp = x[i][1];

    ztmp = x[i][2];

    // 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 && x[j][1] < ytmp) continue;

	if (x[j][2] == ztmp && 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) which = find_special(i,j);

	else which = 0;

	if (which == 0) neighptr[n++] = j;

	else if (which > 0) neighptr[n++] = which*nall + j;

      }

    }

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

    ibin = coord2bin(x[i]);

    for (k = 0; k < nstencil; k++) {

      for (j = binhead[ibin+stencil[k]]; 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) which = find_special(i,j);

	  else which = 0;

	  if (which == 0) neighptr[n++] = j;

	  else if (which > 0) neighptr[n++] = which*nall + j;

	}

      }

    }

    ilist[inum] = i;

    firstneigh[i] = neighptr;

    numneigh[i] = n;

    inum++;

    npnt += n;

    if (npnt >= pgsize)

      error->one("Neighbor list overflow, boost neigh_modify one or page");

  }

  list->inum = inum;

}

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

   binned neighbor list construction with Newton's 3rd law for triclinic

   each owned atom i checks its own bin and other bins in triclinic stencil

   every pair stored exactly once by some processor

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

void Neighbor::half_bin_newton_tri(NeighList *list)

{

  int i,j,k,n,itype,jtype,ibin,which;

  double xtmp,ytmp,ztmp,delx,dely,delz,rsq;

  int *neighptr;

  // bin local & ghost atoms

  bin_atoms();

  // loop over each atom, storing neighbors

  double **x = atom->x;

  int *type = atom->type;

  int *mask = atom->mask;

  int *molecule = atom->molecule;

  int nlocal = atom->nlocal;

  int nall = atom->nlocal + atom->nghost;

  int molecular = atom->molecular;

  int *ilist = list->ilist;

  int *numneigh = list->numneigh;

  int **firstneigh = list->firstneigh;

  int **pages = list->pages;

  int nstencil = list->nstencil;

  int *stencil = list->stencil;

  int inum = 0;

  int npage = 0;

  int npnt = 0;

  for (i = 0; i < nlocal; i++) {

    if (pgsize - npnt < oneatom) {

      npnt = 0;

      npage++;

      if (npage == list->maxpage) pages = list->add_pages();

    }

    neighptr = &pages[npage][npnt];

    n = 0;

    itype = type[i];

    xtmp = x[i][0];

    ytmp = x[i][1];

    ztmp = x[i][2];

    // loop over all atoms in bins in stencil

    // pairs for atoms j "below" i are excluded

    // below = lower z or (equal z and lower y) or (equal zy and <= x)

    // this excludes self-self interaction

    ibin = coord2bin(x[i]);

    for (k = 0; k < nstencil; k++) {

      for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {

	if (x[j][2] < ztmp) continue;

	if (x[j][2] == ztmp && x[j][1] < ytmp) continue;

	if (x[j][2] == ztmp && 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) which = find_special(i,j);

	  else which = 0;

	  if (which == 0) neighptr[n++] = j;

	  else if (which > 0) neighptr[n++] = which*nall + j;

	}

      }

    }

    ilist[inum] = i;

    firstneigh[i] = neighptr;

    numneigh[i] = n;

    inum++;

    npnt += n;

    if (npnt >= pgsize)

      error->one("Neighbor list overflow, boost neigh_modify one or page");

  }

  list->inum = inum;

}