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compute_fragment_atom.cpp
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Sat, Jul 12, 10:40

compute_fragment_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_fragment_atom.h"
#include "atom.h"
#include "atom_vec.h"
#include "update.h"
#include "modify.h"
#include "neighbor.h"
#include "force.h"
#include "pair.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
#include "group.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeFragmentAtom::ComputeFragmentAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg),
fragmentID(NULL)
{
if (narg != 3) error->all(FLERR,"Illegal compute fragment/atom command");
if (atom->avec->bonds_allow == 0)
error->all(FLERR,"Compute fragment/atom used when bonds are not allowed");
peratom_flag = 1;
size_peratom_cols = 0;
comm_forward = 1;
nmax = 0;
}
/* ---------------------------------------------------------------------- */
ComputeFragmentAtom::~ComputeFragmentAtom()
{
memory->destroy(fragmentID);
}
/* ---------------------------------------------------------------------- */
void ComputeFragmentAtom::init()
{
if (atom->tag_enable == 0)
error->all(FLERR,"Cannot use compute fragment/atom unless atoms have IDs");
if (force->bond == NULL)
error->all(FLERR,"Compute fragment/atom requires a bond style to be defined");
int count = 0;
for (int i = 0; i < modify->ncompute; i++)
if (strcmp(modify->compute[i]->style,"fragment/atom") == 0) count++;
if (count > 1 && comm->me == 0)
error->warning(FLERR,"More than one compute fragment/atom");
}
/* ---------------------------------------------------------------------- */
void ComputeFragmentAtom::compute_peratom()
{
int i,j,k;
invoked_peratom = update->ntimestep;
// grow fragmentID array if necessary
if (atom->nmax > nmax) {
memory->destroy(fragmentID);
nmax = atom->nmax;
memory->create(fragmentID,nmax,"fragment/atom:fragmentID");
vector_atom = fragmentID;
}
int nbondlist = neighbor->nbondlist;
int **bondlist = neighbor->bondlist;
// if group is dynamic, insure ghost atom masks are current
if (group->dynamic[igroup]) {
commflag = 0;
comm->forward_comm_compute(this);
}
// every bond starts in its own fragment,
// with fragmentID = MIN(b1atomID,b2atomID)
// only bonds wholly contained in the group are considered
tagint *tag = atom->tag;
int *mask = atom->mask;
for (i = 0; i < nbondlist; i++) {
const int b1 = bondlist[i][0];
const int b2 = bondlist[i][1];
if ((mask[b1] & groupbit) && (mask[b2] & groupbit))
fragmentID[b1] = fragmentID[b2] = MIN(tag[b1],tag[b2]);
else fragmentID[b1] = fragmentID[b2] = 0;
}
// loop until no more changes on any proc:
// acquire fragmentIDs of ghost atoms
// loop over my atoms, and check atoms bound to it
// if both atoms are in fragment, assign lowest fragmentID to both
// iterate until no changes in my atoms
// then check if any proc made changes
commflag = 1;
int nlocal = atom->nlocal;
int *num_bond = atom->num_bond;
tagint **bond_atom = atom->bond_atom;
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++) {
k = bond_atom[i][j];
if (!(mask[k] & groupbit)) continue;
if (fragmentID[i] == fragmentID[k]) continue;
fragmentID[i] = fragmentID[k] = MIN(fragmentID[i],fragmentID[k]);
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 ComputeFragmentAtom::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++] = fragmentID[j];
}
} else {
int *mask = atom->mask;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = ubuf(mask[j]).d;
}
}
return m;
}
/* ---------------------------------------------------------------------- */
void ComputeFragmentAtom::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++) fragmentID[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 ComputeFragmentAtom::memory_usage()
{
double bytes = nmax * sizeof(double);
return bytes;
}

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