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compute_msd_chunk.cpp
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Tue, Nov 12, 08:52

compute_msd_chunk.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.
------------------------------------------------------------------------- */
#include <string.h>
#include "compute_msd_chunk.h"
#include "atom.h"
#include "group.h"
#include "update.h"
#include "modify.h"
#include "compute_chunk_atom.h"
#include "domain.h"
#include "fix_store.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeMSDChunk::ComputeMSDChunk(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg),
idchunk(NULL), id_fix(NULL), massproc(NULL), masstotal(NULL), com(NULL), comall(NULL), msd(NULL)
{
if (narg != 4) error->all(FLERR,"Illegal compute msd/chunk command");
array_flag = 1;
size_array_cols = 4;
size_array_rows = 0;
size_array_rows_variable = 1;
extarray = 0;
// ID of compute chunk/atom
int n = strlen(arg[3]) + 1;
idchunk = new char[n];
strcpy(idchunk,arg[3]);
firstflag = 1;
init();
// create a new fix STORE style for reference positions
// id = compute-ID + COMPUTE_STORE, fix group = compute group
// do not know size of array at this point, just allocate 1x3 array
// fix creation must be done now so that a restart run can
// potentially re-populate the fix array (and change it to correct size)
// otherwise size reset and init will be done in setup()
n = strlen(id) + strlen("_COMPUTE_STORE") + 1;
id_fix = new char[n];
strcpy(id_fix,id);
strcat(id_fix,"_COMPUTE_STORE");
char **newarg = new char*[6];
newarg[0] = id_fix;
newarg[1] = group->names[igroup];
newarg[2] = (char *) "STORE";
newarg[3] = (char *) "global";
newarg[4] = (char *) "1";
newarg[5] = (char *) "1";
modify->add_fix(6,newarg);
fix = (FixStore *) modify->fix[modify->nfix-1];
delete [] newarg;
}
/* ---------------------------------------------------------------------- */
ComputeMSDChunk::~ComputeMSDChunk()
{
// check nfix in case all fixes have already been deleted
if (modify->nfix) modify->delete_fix(id_fix);
delete [] id_fix;
delete [] idchunk;
memory->destroy(massproc);
memory->destroy(masstotal);
memory->destroy(com);
memory->destroy(comall);
memory->destroy(msd);
}
/* ---------------------------------------------------------------------- */
void ComputeMSDChunk::init()
{
int icompute = modify->find_compute(idchunk);
if (icompute < 0)
error->all(FLERR,"Chunk/atom compute does not exist for compute msd/chunk");
cchunk = (ComputeChunkAtom *) modify->compute[icompute];
if (strcmp(cchunk->style,"chunk/atom") != 0)
error->all(FLERR,"Compute msd/chunk does not use chunk/atom compute");
// set fix which stores reference atom coords
// if firstflag, will be created in setup()
if (!firstflag) {
int ifix = modify->find_fix(id_fix);
if (ifix < 0) error->all(FLERR,"Could not find compute msd/chunk fix ID");
fix = (FixStore *) modify->fix[ifix];
}
}
/* ----------------------------------------------------------------------
compute initial COM for each chunk
only once on timestep compute is defined, when firstflag = 1
------------------------------------------------------------------------- */
void ComputeMSDChunk::setup()
{
if (!firstflag) return;
compute_array();
firstflag = 0;
// if fix->astore is already correct size, restart file set it up
// otherwise reset its size now and initialize to current COM
if (fix->nrow == nchunk && fix->ncol == 3) return;
fix->reset_global(nchunk,3);
double **cominit = fix->astore;
for (int i = 0; i < nchunk; i++) {
cominit[i][0] = comall[i][0];
cominit[i][1] = comall[i][1];
cominit[i][2] = comall[i][2];
msd[i][0] = msd[i][1] = msd[i][2] = msd[i][3] = 0.0;
}
}
/* ---------------------------------------------------------------------- */
void ComputeMSDChunk::compute_array()
{
int index;
double massone;
double unwrap[3];
invoked_array = update->ntimestep;
// compute chunk/atom assigns atoms to chunk IDs
// extract ichunk index vector from compute
// ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms
int n = cchunk->setup_chunks();
cchunk->compute_ichunk();
int *ichunk = cchunk->ichunk;
// first time call, allocate per-chunk arrays
// thereafter, require nchunk remain the same
if (firstflag) {
nchunk = n;
allocate();
size_array_rows = nchunk;
} else if (n != nchunk)
error->all(FLERR,"Compute msd/chunk nchunk is not static");
// zero local per-chunk values
for (int i = 0; i < nchunk; i++) {
massproc[i] = 0.0;
com[i][0] = com[i][1] = com[i][2] = 0.0;
}
// compute current COM for each chunk
double **x = atom->x;
int *mask = atom->mask;
int *type = atom->type;
imageint *image = atom->image;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
index = ichunk[i]-1;
if (index < 0) continue;
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
domain->unmap(x[i],image[i],unwrap);
massproc[index] += massone;
com[index][0] += unwrap[0] * massone;
com[index][1] += unwrap[1] * massone;
com[index][2] += unwrap[2] * massone;
}
MPI_Allreduce(massproc,masstotal,nchunk,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(&com[0][0],&comall[0][0],3*nchunk,MPI_DOUBLE,MPI_SUM,world);
for (int i = 0; i < nchunk; i++) {
if (masstotal[i] > 0.0) {
comall[i][0] /= masstotal[i];
comall[i][1] /= masstotal[i];
comall[i][2] /= masstotal[i];
}
}
// MSD is difference between current and initial COM
// cominit is initilialized by setup() when firstflag is set
if (firstflag) return;
double dx,dy,dz;
double **cominit = fix->astore;
for (int i = 0; i < nchunk; i++) {
dx = comall[i][0] - cominit[i][0];
dy = comall[i][1] - cominit[i][1];
dz = comall[i][2] - cominit[i][2];
msd[i][0] = dx*dx;
msd[i][1] = dy*dy;
msd[i][2] = dz*dz;
msd[i][3] = dx*dx + dy*dy + dz*dz;
}
}
/* ----------------------------------------------------------------------
lock methods: called by fix ave/time
these methods insure vector/array size is locked for Nfreq epoch
by passing lock info along to compute chunk/atom
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
increment lock counter
------------------------------------------------------------------------- */
void ComputeMSDChunk::lock_enable()
{
cchunk->lockcount++;
}
/* ----------------------------------------------------------------------
decrement lock counter in compute chunk/atom, it if still exists
------------------------------------------------------------------------- */
void ComputeMSDChunk::lock_disable()
{
int icompute = modify->find_compute(idchunk);
if (icompute >= 0) {
cchunk = (ComputeChunkAtom *) modify->compute[icompute];
cchunk->lockcount--;
}
}
/* ----------------------------------------------------------------------
calculate and return # of chunks = length of vector/array
------------------------------------------------------------------------- */
int ComputeMSDChunk::lock_length()
{
nchunk = cchunk->setup_chunks();
return nchunk;
}
/* ----------------------------------------------------------------------
set the lock from startstep to stopstep
------------------------------------------------------------------------- */
void ComputeMSDChunk::lock(Fix *fixptr, bigint startstep, bigint stopstep)
{
cchunk->lock(fixptr,startstep,stopstep);
}
/* ----------------------------------------------------------------------
unset the lock
------------------------------------------------------------------------- */
void ComputeMSDChunk::unlock(Fix *fixptr)
{
cchunk->unlock(fixptr);
}
/* ----------------------------------------------------------------------
one-time allocate of per-chunk arrays
------------------------------------------------------------------------- */
void ComputeMSDChunk::allocate()
{
memory->create(massproc,nchunk,"msd/chunk:massproc");
memory->create(masstotal,nchunk,"msd/chunk:masstotal");
memory->create(com,nchunk,3,"msd/chunk:com");
memory->create(comall,nchunk,3,"msd/chunk:comall");
memory->create(msd,nchunk,4,"msd/chunk:msd");
array = msd;
}
/* ----------------------------------------------------------------------
memory usage of local data
------------------------------------------------------------------------- */
double ComputeMSDChunk::memory_usage()
{
double bytes = (bigint) nchunk * 2 * sizeof(double);
bytes += (bigint) nchunk * 2*3 * sizeof(double);
bytes += (bigint) nchunk * 4 * sizeof(double);
return bytes;
}

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