/* ----------------------------------------------------------------------
   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 "domain.h"
#include "group.h"
#include "my_page.h"
#include "error.h"

using namespace LAMMPS_NS;

/* ----------------------------------------------------------------------
   multiple respa lists
   N^2 / 2 search for neighbor pairs with partial Newton's 3rd law
   pair added to list if atoms i and j are both owned and i < j
   pair added if j is ghost (also stored by proc owning j)
------------------------------------------------------------------------- */

void Neighbor::respa_nsq_no_newton(NeighList *list)
{
  int i,j,n,itype,jtype,n_inner,n_middle,bitmask;
  double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
  int *neighptr,*neighptr_inner,*neighptr_middle;

  // loop over each atom, storing neighbors

  int **special = atom->special;
  int **nspecial = atom->nspecial;
  int *tag = atom->tag;

  double **x = atom->x;
  int *type = atom->type;
  int *mask = atom->mask;
  int *molecule = atom->molecule;
  int nlocal = atom->nlocal;
  int nall = nlocal + atom->nghost;
  int molecular = atom->molecular;
  if (includegroup) {
    nlocal = atom->nfirst;
    bitmask = group->bitmask[includegroup];
  }

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

  NeighList *listinner = list->listinner;
  int *ilist_inner = listinner->ilist;
  int *numneigh_inner = listinner->numneigh;
  int **firstneigh_inner = listinner->firstneigh;
  MyPage<int> *ipage_inner = listinner->ipage;

  NeighList *listmiddle;
  int *ilist_middle,*numneigh_middle,**firstneigh_middle;
  MyPage<int> *ipage_middle;
  int respamiddle = list->respamiddle;
  if (respamiddle) {
    listmiddle = list->listmiddle;
    ilist_middle = listmiddle->ilist;
    numneigh_middle = listmiddle->numneigh;
    firstneigh_middle = listmiddle->firstneigh;
    ipage_middle = listmiddle->ipage;
  }

  int inum = 0;
  int which = 0;
  int minchange = 0;
  ipage->reset();
  ipage_inner->reset();
  if (respamiddle) ipage_middle->reset();

  for (i = 0; i < nlocal; i++) {
    n = n_inner = 0;
    neighptr = ipage->vget();
    neighptr_inner = ipage_inner->vget();
    if (respamiddle) {
      n_middle = 0;
      neighptr_middle = ipage_middle->vget();
    }

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

    // loop over remaining atoms, owned and ghost

    for (j = i+1; j < nall; j++) {
      if (includegroup && !(mask[j] & bitmask)) 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(special[i],nspecial[i],tag[j]);
          if (which == 0) neighptr[n++] = j;
          else if (minchange = domain->minimum_image_check(delx,dely,delz))
            neighptr[n++] = j;
          else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
        } else neighptr[n++] = j;

        if (rsq < cut_inner_sq) {
          if (which == 0) neighptr_inner[n_inner++] = j;
          else if (minchange) neighptr_inner[n_inner++] = j;
          else if (which > 0) neighptr_inner[n_inner++] = j ^ (which << SBBITS);
        }

        if (respamiddle && rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
          if (which == 0) neighptr_middle[n_middle++] = j;
          else if (minchange) neighptr_middle[n_middle++] = j;
          else if (which > 0)
            neighptr_middle[n_middle++] = j ^ (which << SBBITS);
        }
      }
    }

    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");

    ilist_inner[inum] = i;
    firstneigh_inner[i] = neighptr_inner;
    numneigh_inner[i] = n_inner;
    ipage_inner->vgot(n_inner);
    if (ipage_inner->status())
      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");

    if (respamiddle) {
      ilist_middle[inum] = i;
      firstneigh_middle[i] = neighptr_middle;
      numneigh_middle[i] = n_middle;
      ipage_middle->vgot(n_middle);
      if (ipage_middle->status())
        error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
    }

    inum++;
  }

  list->inum = inum;
  listinner->inum = inum;
  if (respamiddle) listmiddle->inum = inum;
}

/* ----------------------------------------------------------------------
   multiple respa lists
   N^2 / 2 search for neighbor pairs with full Newton's 3rd law
   pair added to list if atoms i and j are both owned and i < j
   if j is ghost only me or other proc adds pair
   decision based on itag,jtag tests
------------------------------------------------------------------------- */

void Neighbor::respa_nsq_newton(NeighList *list)
{
  int i,j,n,itype,jtype,itag,jtag,n_inner,n_middle,bitmask;
  double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
  int *neighptr,*neighptr_inner,*neighptr_middle;

  // loop over each atom, storing neighbors

  int **special = atom->special;
  int **nspecial = atom->nspecial;
  int *tag = atom->tag;

  double **x = atom->x;
  int *type = atom->type;
  int *mask = atom->mask;
  int *molecule = atom->molecule;
  int nlocal = atom->nlocal;
  int nall = nlocal + atom->nghost;
  int molecular = atom->molecular;
  if (includegroup) {
    nlocal = atom->nfirst;
    bitmask = group->bitmask[includegroup];
  }

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

  NeighList *listinner = list->listinner;
  int *ilist_inner = listinner->ilist;
  int *numneigh_inner = listinner->numneigh;
  int **firstneigh_inner = listinner->firstneigh;
  MyPage<int> *ipage_inner = listinner->ipage;

  NeighList *listmiddle;
  int *ilist_middle,*numneigh_middle,**firstneigh_middle;
  MyPage<int> *ipage_middle;
  int respamiddle = list->respamiddle;
  if (respamiddle) {
    listmiddle = list->listmiddle;
    ilist_middle = listmiddle->ilist;
    numneigh_middle = listmiddle->numneigh;
    firstneigh_middle = listmiddle->firstneigh;
    ipage_middle = listmiddle->ipage;
  }

  int inum = 0;
  int which = 0;
  int minchange = 0;
  ipage->reset();
  ipage_inner->reset();
  if (respamiddle) ipage_middle->reset();

  for (i = 0; i < nlocal; i++) {
    n = n_inner = 0;
    neighptr = ipage->vget();
    neighptr_inner = ipage_inner->vget();
    if (respamiddle) {
      n_middle = 0;
      neighptr_middle = ipage_middle->vget();
    }

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

    // loop over remaining atoms, owned and ghost

    for (j = i+1; j < nall; j++) {
      if (includegroup && !(mask[j] & bitmask)) 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 (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) {
          which = find_special(special[i],nspecial[i],tag[j]);
          if (which == 0) neighptr[n++] = j;
          else if (minchange = domain->minimum_image_check(delx,dely,delz))
            neighptr[n++] = j;
          else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
        } else neighptr[n++] = j;

        if (rsq < cut_inner_sq) {
          if (which == 0) neighptr_inner[n_inner++] = j;
          else if (minchange) neighptr_inner[n_inner++] = j;
          else if (which > 0) neighptr_inner[n_inner++] = j ^ (which << SBBITS);
        }

        if (respamiddle &&
            rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
          if (which == 0) neighptr_middle[n_middle++] = j;
          else if (minchange) neighptr_middle[n_middle++] = j;
          else if (which > 0)
            neighptr_middle[n_middle++] = j ^ (which << SBBITS);
        }
      }
    }

    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");

    ilist_inner[inum] = i;
    firstneigh_inner[i] = neighptr_inner;
    numneigh_inner[i] = n_inner;
    ipage_inner->vgot(n_inner);
    if (ipage_inner->status())
      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");

    if (respamiddle) {
      ilist_middle[inum] = i;
      firstneigh_middle[i] = neighptr_middle;
      numneigh_middle[i] = n_middle;
      ipage_middle->vgot(n_middle);
      if (ipage_middle->status())
        error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
    }

    inum++;
  }

  list->inum = inum;
  listinner->inum = inum;
  if (respamiddle) listmiddle->inum = inum;
}

/* ----------------------------------------------------------------------
   multiple respa lists
   binned neighbor list construction with partial Newton's 3rd law
   each owned atom i checks own bin and surrounding bins in non-Newton 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::respa_bin_no_newton(NeighList *list)
{
  int i,j,k,n,itype,jtype,ibin,n_inner,n_middle;
  double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
  int *neighptr,*neighptr_inner,*neighptr_middle;

  // bin local & ghost atoms

  bin_atoms();

  // loop over each atom, storing neighbors

  int **special = atom->special;
  int **nspecial = atom->nspecial;
  int *tag = atom->tag;

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

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

  NeighList *listinner = list->listinner;
  int *ilist_inner = listinner->ilist;
  int *numneigh_inner = listinner->numneigh;
  int **firstneigh_inner = listinner->firstneigh;
  MyPage<int> *ipage_inner = listinner->ipage;

  NeighList *listmiddle;
  int *ilist_middle,*numneigh_middle,**firstneigh_middle;
  MyPage<int> *ipage_middle;
  int respamiddle = list->respamiddle;
  if (respamiddle) {
    listmiddle = list->listmiddle;
    ilist_middle = listmiddle->ilist;
    numneigh_middle = listmiddle->numneigh;
    firstneigh_middle = listmiddle->firstneigh;
    ipage_middle = listmiddle->ipage;
  }

  int inum = 0;
  int which = 0;
  int minchange = 0;
  ipage->reset();
  ipage_inner->reset();
  if (respamiddle) ipage_middle->reset();

  for (i = 0; i < nlocal; i++) {
    n = n_inner = 0;
    neighptr = ipage->vget();
    neighptr_inner = ipage_inner->vget();
    if (respamiddle) {
      n_middle = 0;
      neighptr_middle = ipage_middle->vget();
    }

    itype = type[i];
    xtmp = x[i][0];
    ytmp = x[i][1];
    ztmp = x[i][2];
    ibin = coord2bin(x[i]);

    // loop over all atoms in surrounding bins in stencil including self
    // only store pair if i < j
    // stores own/own pairs only once
    // stores own/ghost pairs on both procs

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

          if (rsq < cut_inner_sq) {
            if (which == 0) neighptr_inner[n_inner++] = j;
            else if (minchange) neighptr_inner[n_inner++] = j;
            else if (which > 0)
              neighptr_inner[n_inner++] = j ^ (which << SBBITS);
          }

          if (respamiddle &&
              rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
            if (which == 0) neighptr_middle[n_middle++] = j;
            else if (minchange) neighptr_middle[n_middle++] = j;
            else if (which > 0)
              neighptr_middle[n_middle++] = j ^ (which << SBBITS);
          }
        }
      }
    }

    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");

    ilist_inner[inum] = i;
    firstneigh_inner[i] = neighptr_inner;
    numneigh_inner[i] = n_inner;
    ipage_inner->vgot(n_inner);
    if (ipage_inner->status())
      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");

    if (respamiddle) {
      ilist_middle[inum] = i;
      firstneigh_middle[i] = neighptr_middle;
      numneigh_middle[i] = n_middle;
      ipage_middle->vgot(n_middle);
      if (ipage_middle->status())
        error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
    }

    inum++;
  }

  list->inum = inum;
  listinner->inum = inum;
  if (respamiddle) listmiddle->inum = inum;
}

/* ----------------------------------------------------------------------
   multiple respa lists
   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::respa_bin_newton(NeighList *list)
{
  int i,j,k,n,itype,jtype,ibin,n_inner,n_middle;
  double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
  int *neighptr,*neighptr_inner,*neighptr_middle;

  // bin local & ghost atoms

  bin_atoms();

  // loop over each atom, storing neighbors

  int **special = atom->special;
  int **nspecial = atom->nspecial;
  int *tag = atom->tag;

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

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

  NeighList *listinner = list->listinner;
  int *ilist_inner = listinner->ilist;
  int *numneigh_inner = listinner->numneigh;
  int **firstneigh_inner = listinner->firstneigh;
  MyPage<int> *ipage_inner = listinner->ipage;

  NeighList *listmiddle;
  int *ilist_middle,*numneigh_middle,**firstneigh_middle;
  MyPage<int> *ipage_middle;
  int respamiddle = list->respamiddle;
  if (respamiddle) {
    listmiddle = list->listmiddle;
    ilist_middle = listmiddle->ilist;
    numneigh_middle = listmiddle->numneigh;
    firstneigh_middle = listmiddle->firstneigh;
    ipage_middle = listmiddle->ipage;
  }

  int inum = 0;
  int which = 0;
  int minchange = 0;
  ipage->reset();
  ipage_inner->reset();
  if (respamiddle) ipage_middle->reset();

  for (i = 0; i < nlocal; i++) {
    n = n_inner = 0;
    neighptr = ipage->vget();
    neighptr_inner = ipage_inner->vget();
    if (respamiddle) {
      n_middle = 0;
      neighptr_middle = ipage_middle->vget();
    }

    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) {
          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) {
          which = find_special(special[i],nspecial[i],tag[j]);
          if (which == 0) neighptr[n++] = j;
          else if (minchange = domain->minimum_image_check(delx,dely,delz))
            neighptr[n++] = j;
          else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
        } else neighptr[n++] = j;

        if (rsq < cut_inner_sq) {
          if (which == 0) neighptr_inner[n_inner++] = j;
          else if (minchange) neighptr_inner[n_inner++] = j;
          else if (which > 0) neighptr_inner[n_inner++] = j ^ (which << SBBITS);
        }

        if (respamiddle &&
            rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
          if (which == 0) neighptr_middle[n_middle++] = j;
          else if (minchange) neighptr_middle[n_middle++] = j;
          else if (which > 0)
            neighptr_middle[n_middle++] = j ^ (which << SBBITS);
        }
      }
    }

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

          if (rsq < cut_inner_sq) {
            if (which == 0) neighptr_inner[n_inner++] = j;
            else if (minchange) neighptr_inner[n_inner++] = j;
            else if (which > 0)
              neighptr_inner[n_inner++] = j ^ (which << SBBITS);
          }

          if (respamiddle &&
              rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
            if (which == 0) neighptr_middle[n_middle++] = j;
            else if (minchange) neighptr_middle[n_middle++] = j;
            else if (which > 0)
              neighptr_middle[n_middle++] = j ^ (which << SBBITS);
          }
        }
      }
    }

    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");

    ilist_inner[inum] = i;
    firstneigh_inner[i] = neighptr_inner;
    numneigh_inner[i] = n_inner;
    ipage_inner->vgot(n_inner);
    if (ipage_inner->status())
      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");

    if (respamiddle) {
      ilist_middle[inum] = i;
      firstneigh_middle[i] = neighptr_middle;
      numneigh_middle[i] = n_middle;
      ipage_middle->vgot(n_middle);
      if (ipage_middle->status())
        error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
    }

    inum++;
  }

  list->inum = inum;
  listinner->inum = inum;
  if (respamiddle) listmiddle->inum = inum;
}

/* ----------------------------------------------------------------------
   multiple respa lists
   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::respa_bin_newton_tri(NeighList *list)
{
  int i,j,k,n,itype,jtype,ibin,n_inner,n_middle;
  double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
  int *neighptr,*neighptr_inner,*neighptr_middle;

  // bin local & ghost atoms

  bin_atoms();

  // loop over each atom, storing neighbors

  int **special = atom->special;
  int **nspecial = atom->nspecial;
  int *tag = atom->tag;

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

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

  NeighList *listinner = list->listinner;
  int *ilist_inner = listinner->ilist;
  int *numneigh_inner = listinner->numneigh;
  int **firstneigh_inner = listinner->firstneigh;
  MyPage<int> *ipage_inner = listinner->ipage;

  NeighList *listmiddle;
  int *ilist_middle,*numneigh_middle,**firstneigh_middle;
  MyPage<int> *ipage_middle;
  int respamiddle = list->respamiddle;
  if (respamiddle) {
    listmiddle = list->listmiddle;
    ilist_middle = listmiddle->ilist;
    numneigh_middle = listmiddle->numneigh;
    firstneigh_middle = listmiddle->firstneigh;
    ipage_middle = listmiddle->ipage;
  }

  int inum = 0;
  int which = 0;
  int minchange = 0;
  ipage->reset();
  ipage_inner->reset();
  if (respamiddle) ipage_middle->reset();

  for (i = 0; i < nlocal; i++) {
    n = n_inner = 0;
    neighptr = ipage->vget();
    neighptr_inner = ipage_inner->vget();
    if (respamiddle) {
      n_middle = 0;
      neighptr_middle = ipage_middle->vget();
    }

    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 lower x)
    //         (equal zyx and j <= i)
    // latter excludes self-self interaction but allows superposed atoms

    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) {
          if (x[j][1] < ytmp) continue;
          if (x[j][1] == ytmp) {
            if (x[j][0] < xtmp) continue;
            if (x[j][0] == xtmp && 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(special[i],nspecial[i],tag[j]);
            if (which == 0) neighptr[n++] = j;
            else if (minchange = domain->minimum_image_check(delx,dely,delz))
              neighptr[n++] = j;
            else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
          } else neighptr[n++] = j;

          if (rsq < cut_inner_sq) {
            if (which == 0) neighptr_inner[n_inner++] = j;
            else if (minchange) neighptr_inner[n_inner++] = j;
            else if (which > 0)
              neighptr_inner[n_inner++] = j ^ (which << SBBITS);
          }

          if (respamiddle &&
              rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
            if (which == 0) neighptr_middle[n_middle++] = j;
            else if (minchange) neighptr_middle[n_middle++] = j;
            else if (which > 0)
              neighptr_middle[n_middle++] = j ^ (which << SBBITS);
          }
        }
      }
    }

    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");

    ilist_inner[inum] = i;
    firstneigh_inner[i] = neighptr_inner;
    numneigh_inner[i] = n_inner;
    ipage_inner->vgot(n_inner);
    if (ipage_inner->status())
      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");

    if (respamiddle) {
      ilist_middle[inum] = i;
      firstneigh_middle[i] = neighptr_middle;
      numneigh_middle[i] = n_middle;
      ipage_middle->vgot(n_middle);
      if (ipage_middle->status())
        error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
    }

    inum++;
  }

  list->inum = inum;
  listinner->inum = inum;
  if (respamiddle) listmiddle->inum = inum;
}
