git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5769 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
225
src/compute_cluster_atom.cpp
Normal file
225
src/compute_cluster_atom.cpp
Normal file
@ -0,0 +1,225 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
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->sfree(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->sfree(clusterID);
|
||||
nmax = atom->nmax;
|
||||
clusterID = (double *)
|
||||
memory->smalloc(nmax*sizeof(double),"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];
|
||||
if (j >= nall) j %= nall;
|
||||
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;
|
||||
}
|
||||
Reference in New Issue
Block a user