lammps/src/compute_cluster_atom.cpp

/* ----------------------------------------------------------------------
   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 "compute_cluster_atom.h"

#include "atom.h"
#include "comm.h"
#include "error.h"
#include "force.h"
#include "memory.h"
#include "modify.h"
#include "neigh_list.h"
#include "neighbor.h"
#include "pair.h"
#include "update.h"

#include <cmath>

using namespace LAMMPS_NS;

static constexpr int MAXLOOP = 100;
/* ---------------------------------------------------------------------- */

ComputeClusterAtom::ComputeClusterAtom(LAMMPS *lmp, int narg, char **arg) :
    Compute(lmp, narg, arg), clusterID(nullptr)
{
  if (narg != 4) error->all(FLERR, "Illegal compute cluster/atom command");

  double cutoff = utils::numeric(FLERR, arg[3], false, lmp);
  cutsq = cutoff * cutoff;

  peratom_flag = 1;
  size_peratom_cols = 0;
  comm_forward = 1;

  nmax = 0;
}

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

ComputeClusterAtom::~ComputeClusterAtom()
{
  memory->destroy(clusterID);
}

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

void ComputeClusterAtom::init()
{
  if (atom->tag_enable == 0)
    error->all(FLERR, "Cannot use compute cluster/atom unless atoms have IDs");
  if (force->pair == nullptr)
    error->all(FLERR, "Compute cluster/atom requires a pair style to be defined");
  if (sqrt(cutsq) > force->pair->cutforce)
    error->all(FLERR, "Compute cluster/atom cutoff is longer than pairwise cutoff");

  // need an occasional full neighbor list
  // full required so that pair of atoms on 2 procs both set their clusterID

  neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_OCCASIONAL);

  if (modify->get_compute_by_style(style).size() > 1)
    if (comm->me == 0) error->warning(FLERR, "More than one compute {}", style);
}

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

void ComputeClusterAtom::init_list(int /*id*/, NeighList *ptr)
{
  list = ptr;
}

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

void ComputeClusterAtom::compute_peratom()
{
  int i, j, ii, jj, inum, jnum;
  double xtmp, ytmp, ztmp, delx, dely, delz, rsq;
  int *ilist, *jlist, *numneigh, **firstneigh;

  invoked_peratom = update->ntimestep;

  // grow clusterID array if necessary

  if (atom->nmax > nmax) {
    memory->destroy(clusterID);
    nmax = atom->nmax;
    memory->create(clusterID, nmax, "cluster/atom:clusterID");
    vector_atom = clusterID;
  }

  // communicate coords for ghost atoms if box can change, e.g. fix deform
  // this ensures ghost atom coords are current

  comm->forward_comm();

  // invoke full neighbor list (will copy or build if necessary)
  // on the first step of a run, set preflag to one in neighbor->build_one(...)

  if (update->firststep == update->ntimestep)
    neighbor->build_one(list, 1);
  else
    neighbor->build_one(list);

  inum = list->inum;
  ilist = list->ilist;
  numneigh = list->numneigh;
  firstneigh = list->firstneigh;

  // every atom starts in its own cluster, with clusterID = atomID

  tagint *tag = atom->tag;
  int *mask = atom->mask;

  for (ii = 0; ii < inum; ii++) {
    i = ilist[ii];
    if (mask[i] & groupbit)
      clusterID[i] = tag[i];
    else
      clusterID[i] = 0;
  }

  // loop until no more changes on any proc:
  // acquire clusterIDs of ghost atoms
  // loop over my atoms, checking distance to neighbors
  // if both atoms are in cluster, assign lowest clusterID to both
  // iterate until no changes in my atoms
  // then check if any proc made changes

  double **x = atom->x;

  int change, done, anychange;

  int counter = 0;
  // stop after MAXLOOP iterations
  while (counter < MAXLOOP) {
    comm->forward_comm(this);
    ++counter;
    change = 0;
    while (true) {
      done = 1;
      for (ii = 0; ii < inum; ii++) {
        i = ilist[ii];
        if (!(mask[i] & groupbit)) continue;

        xtmp = x[i][0];
        ytmp = x[i][1];
        ztmp = x[i][2];
        jlist = firstneigh[i];
        jnum = numneigh[i];

        for (jj = 0; jj < jnum; jj++) {
          j = jlist[jj];
          j &= NEIGHMASK;
          if (!(mask[j] & groupbit)) continue;
          if (clusterID[i] == clusterID[j]) 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 < cutsq) {
            clusterID[i] = clusterID[j] = MIN(clusterID[i], clusterID[j]);
            done = 0;
          }
        }
      }
      if (!done) change = 1;
      if (done) break;
    }

    // stop if all procs are done

    MPI_Allreduce(&change, &anychange, 1, MPI_INT, MPI_MAX, world);
    if (!anychange) break;
  }
  if ((comm->me == 0) && (counter >= MAXLOOP))
    error->warning(FLERR, "Compute cluster/atom did not converge after {} iterations", MAXLOOP);
}

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

int ComputeClusterAtom::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/,
                                          int * /*pbc*/)
{
  int i, j, m;

  m = 0;
  for (i = 0; i < n; i++) {
    j = list[i];
    buf[m++] = clusterID[j];
  }

  return m;
}

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

void ComputeClusterAtom::unpack_forward_comm(int n, int first, double *buf)
{
  int i, m, last;

  m = 0;
  last = first + n;
  for (i = first; i < last; i++) clusterID[i] = buf[m++];
}

/* ----------------------------------------------------------------------
   memory usage of local atom-based array
------------------------------------------------------------------------- */

double ComputeClusterAtom::memory_usage()
{
  double bytes = (double) nmax * sizeof(double);
  return bytes;
}