lammps/src/compute_cluster_atom.cpp

/* ----------------------------------------------------------------------
   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 "math.h"
#include "string.h"
#include "stdlib.h"
#include "compute_cluster_atom.h"
#include "atom.h"
#include "update.h"
#include "modify.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "force.h"
#include "pair.h"
#include "comm.h"
#include "memory.h"
#include "error.h"

using namespace LAMMPS_NS;

#define MIN(A,B) ((A) < (B)) ? (A) : (B)
#define MAX(A,B) ((A) > (B)) ? (A) : (B)

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

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

  double cutoff = atof(arg[3]);
  cutsq = cutoff*cutoff;

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

  nmax = 0;
  clusterID = NULL;
}

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

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

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

void ComputeClusterAtom::init()
{
  if (atom->tag_enable == 0)
    error->all("Cannot use compute cluster/atom unless atoms have IDs");
  if (force->pair == NULL) 
    error->all("Compute cluster/atom requires a pair style be defined");
  if (sqrt(cutsq) > force->pair->cutforce) 
    error->all("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

  int irequest = neighbor->request((void *) this);
  neighbor->requests[irequest]->pair = 0;
  neighbor->requests[irequest]->compute = 1;
  neighbor->requests[irequest]->half = 0;
  neighbor->requests[irequest]->full = 1;
  neighbor->requests[irequest]->occasional = 1;

  int count = 0;
  for (int i = 0; i < modify->ncompute; i++)
    if (strcmp(modify->compute[i]->style,"cluster/atom") == 0) count++;
  if (count > 1 && comm->me == 0)
    error->warning("More than one compute cluster/atom");
}

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

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

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

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

  invoked_peratom = update->ntimestep;

  // grow clusterID array if necessary

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

  // invoke full neighbor list (will copy or build if necessary)

  neighbor->build_one(list->index);

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

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

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

  int change,done,anychange;

  while (1) {
    comm->forward_comm_compute(this);

    change = 0;
    while (1) {
      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];
	
	n = 0;
	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;
  }
}

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

int ComputeClusterAtom::pack_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 1;
}

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

void ComputeClusterAtom::unpack_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 = nmax * sizeof(double);
  return bytes;
}