lammps/src/npair_bin_ghost.cpp

// clang-format off
/* ----------------------------------------------------------------------
   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_ghost.h"

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

using namespace LAMMPS_NS;
using namespace NeighConst;

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

template<int HALF>
NPairBinGhost<HALF>::NPairBinGhost(LAMMPS *lmp) : NPair(lmp) {}

/* ----------------------------------------------------------------------
   Full:
     binned neighbor list construction for all neighbors
     include neighbors of ghost atoms, but no "special neighbors" for ghosts
     every neighbor pair appears in list of both atoms i and j
   Half + Newtoff:
     binned neighbor list construction with partial Newton's 3rd law
     include neighbors of ghost atoms, but no "special neighbors" for ghosts
     owned and ghost atoms check own bin and other bins in stencil
     pair stored once if i,j are both owned and i < j
     pair stored by me if i owned and j ghost (also stored by proc owning j)
     pair stored once if i,j are both ghost and i < j
------------------------------------------------------------------------- */

template<int HALF>
void NPairBinGhost<HALF>::build(NeighList *list)
{
  int i, j, k, n, itype, jtype, ibin, bin_start, which, imol, iatom, moltemplate;
  tagint tagprev;
  double xtmp, ytmp, ztmp, delx, dely, delz, rsq;
  int xbin, ybin, zbin, xbin2, ybin2, zbin2;
  int *neighptr;

  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;
  int nall = nlocal + atom->nghost;
  if (includegroup) nlocal = atom->nfirst;

  int *molindex = atom->molindex;
  int *molatom = atom->molatom;
  Molecule **onemols = atom->avec->onemols;
  if (molecular == Atom::TEMPLATE)
    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();

  // loop over owned & ghost atoms, storing neighbors
  for (i = 0; i < nall; i++) {
    n = 0;
    neighptr = ipage->vget();

    itype = type[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;
    }

    if (i < nlocal) {
      ibin = atom2bin[i];

      // loop over all atoms in surrounding bins in stencil including self
      // when i is a ghost atom, must check if stencil bin is out of bounds
      // no molecular test when i = ghost atom
      for (k = 0; k < nstencil; k++) {
        bin_start = binhead[ibin + stencil[k]];
        for (j = bin_start; j >= 0; j = bins[j]) {
          if (HALF) {
            // Half neighbor list, newton off
            // only store pair if i < j
            // stores own/own pairs only once
            // stores own/ghost pairs on both procs
            // stores ghost/ghost pairs only once
            if (j <= i) continue;
          } else {
            // Full neighbor list
            // only skip i = j
            if (i == j) 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 != 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;
          }
        }
      }
    } else {
      ibin = coord2bin(x[i], xbin, ybin, zbin);
      for (k = 0; k < nstencil; k++) {
        xbin2 = xbin + stencilxyz[k][0];
        ybin2 = ybin + stencilxyz[k][1];
        zbin2 = zbin + stencilxyz[k][2];
        if (xbin2 < 0 || xbin2 >= mbinx ||
            ybin2 < 0 || ybin2 >= mbiny ||
            zbin2 < 0 || zbin2 >= mbinz) continue;
        for (j = binhead[ibin + stencil[k]]; j >= 0; j = bins[j]) {
          if (HALF) {
            if (j <= i) continue;
          } else {
            if (i == j) 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 <= cutneighghostsq[itype][jtype]) 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 = atom->nlocal;
  list->gnum = inum - atom->nlocal;
}

namespace LAMMPS_NS {
template class NPairBinGhost<0>;
template class NPairBinGhost<1>;
}