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compute_aggregate_atom.cpp
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Fri, Jun 21, 21:37

compute_aggregate_atom.cpp
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/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
#include <string.h>
#include "compute_aggregate_atom.h"
#include "atom.h"
#include "atom_vec.h"
#include "update.h"
#include "modify.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "pair.h"
#include "force.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
#include "group.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeAggregateAtom::ComputeAggregateAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg),
aggregateID(NULL)
{
if (narg != 4) error->all(FLERR,"Illegal compute aggregate/atom command");
double cutoff = force->numeric(FLERR,arg[3]);
cutsq = cutoff*cutoff;
if (atom->avec->bonds_allow == 0)
error->all(FLERR,"Compute aggregate/atom used when bonds are not allowed");
peratom_flag = 1;
size_peratom_cols = 0;
comm_forward = 1;
nmax = 0;
}
/* ---------------------------------------------------------------------- */
ComputeAggregateAtom::~ComputeAggregateAtom()
{
memory->destroy(aggregateID);
}
/* ---------------------------------------------------------------------- */
void ComputeAggregateAtom::init()
{
if (atom->tag_enable == 0)
error->all(FLERR,"Cannot use compute aggregate/atom unless atoms have IDs");
if (force->bond == NULL)
error->all(FLERR,"Compute aggregate/atom requires a bond style to be defined");
if (force->pair == NULL)
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
int irequest = neighbor->request(this,instance_me);
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,"aggregate/atom") == 0) count++;
if (count > 1 && comm->me == 0)
error->warning(FLERR,"More than one compute aggregate/atom");
}
/* ---------------------------------------------------------------------- */
void ComputeAggregateAtom::init_list(int id, NeighList *ptr)
{
list = ptr;
}
/* ---------------------------------------------------------------------- */
void ComputeAggregateAtom::compute_peratom()
{
int i,j,k;
invoked_peratom = update->ntimestep;
// grow aggregateID array if necessary
if (atom->nmax > nmax) {
memory->destroy(aggregateID);
nmax = atom->nmax;
memory->create(aggregateID,nmax,"aggregate/atom:aggregateID");
vector_atom = aggregateID;
}
// invoke full neighbor list (will copy or build if necessary)
neighbor->build_one(list);
// if group is dynamic, insure ghost atom masks are current
if (group->dynamic[igroup]) {
commflag = 0;
comm->forward_comm_compute(this);
}
// each atom starts in its own aggregate,
int nlocal = atom->nlocal;
int inum = list->inum;
tagint *tag = atom->tag;
int *mask = atom->mask;
int *num_bond = atom->num_bond;
int **bond_type = atom->bond_type;
tagint **bond_atom = atom->bond_atom;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
double **x = atom->x;
for (i = 0; i < nlocal + atom->nghost; i++)
if (mask[i] & groupbit) aggregateID[i] = tag[i];
else aggregateID[i] = 0;
// loop until no more changes on any proc:
// acquire aggregateIDs of ghost atoms
// loop over my atoms, and check atoms bound to it
// if both atoms are in aggregate, assign lowest aggregateID to both
// then 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
commflag = 1;
int change,done,anychange;
while (1) {
comm->forward_comm_compute(this);
change = 0;
while (1) {
done = 1;
for (i = 0; i < nlocal; i++) {
if (!(mask[i] & groupbit)) continue;
for (j = 0; j < num_bond[i]; j++) {
if (bond_type[i][j] == 0) continue;
k = atom->map(bond_atom[i][j]);
if (k < 0) continue;
if (!(mask[k] & groupbit)) continue;
if (aggregateID[i] == aggregateID[k]) continue;
aggregateID[i] = aggregateID[k] = MIN(aggregateID[i],aggregateID[k]);
done = 0;
}
}
for (int ii = 0; ii < inum; ii++) {
i = ilist[ii];
if (!(mask[i] & groupbit)) continue;
const double xtmp = x[i][0];
const double ytmp = x[i][1];
const double ztmp = x[i][2];
int *jlist = firstneigh[i];
const int jnum = numneigh[i];
for (int jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
if (!(mask[j] & groupbit)) continue;
if (aggregateID[i] == aggregateID[j]) continue;
const double delx = xtmp - x[j][0];
const double dely = ytmp - x[j][1];
const double delz = ztmp - x[j][2];
const double rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cutsq) {
aggregateID[i] = aggregateID[j]
= MIN(aggregateID[i],aggregateID[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 ComputeAggregateAtom::pack_forward_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
m = 0;
if (commflag) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = aggregateID[j];
}
} else {
int *mask = atom->mask;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = ubuf(mask[j]).d;
}
}
return m;
}
/* ---------------------------------------------------------------------- */
void ComputeAggregateAtom::unpack_forward_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
if (commflag)
for (i = first; i < last; i++) aggregateID[i] = buf[m++];
else {
int *mask = atom->mask;
for (i = first; i < last; i++) mask[i] = (int) ubuf(buf[m++]).i;
}
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
double ComputeAggregateAtom::memory_usage()
{
double bytes = nmax * sizeof(double);
return bytes;
}

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