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compute_property_chunk.cpp
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Tue, Jul 23, 01:00
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Thu, Jul 25, 01:00 (2 d)
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rLAMMPS lammps
compute_property_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_property_chunk.h"
#include "atom.h"
#include "update.h"
#include "modify.h"
#include "compute_chunk_atom.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputePropertyChunk::ComputePropertyChunk(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg < 5) error->all(FLERR,"Illegal compute property/chunk command");
// ID of compute chunk/atom
int n = strlen(arg[3]) + 1;
idchunk = new char[n];
strcpy(idchunk,arg[3]);
init();
// parse values
nvalues = narg - 4;
pack_choice = new FnPtrPack[nvalues];
countflag = 0;
int i;
for (int iarg = 4; iarg < narg; iarg++) {
i = iarg-4;
if (strcmp(arg[iarg],"count") == 0) {
pack_choice[i] = &ComputePropertyChunk::pack_count;
countflag = 1;
} else if (strcmp(arg[iarg],"id") == 0) {
if (!cchunk->compress)
error->all(FLERR,"Compute chunk/atom stores no IDs for "
"compute property/chunk");
pack_choice[i] = &ComputePropertyChunk::pack_id;
} else if (strcmp(arg[iarg],"coord1") == 0) {
if (cchunk->ncoord < 1)
error->all(FLERR,"Compute chunk/atom stores no coord1 for "
"compute property/chunk");
pack_choice[i] = &ComputePropertyChunk::pack_coord1;
} else if (strcmp(arg[iarg],"coord2") == 0) {
if (cchunk->ncoord < 2)
error->all(FLERR,"Compute chunk/atom stores no coord2 for "
"compute property/chunk");
pack_choice[i] = &ComputePropertyChunk::pack_coord2;
} else if (strcmp(arg[iarg],"coord3") == 0) {
if (cchunk->ncoord < 3)
error->all(FLERR,"Compute chunk/atom stores no coord3 for "
"compute property/chunk");
pack_choice[i] = &ComputePropertyChunk::pack_coord3;
} else error->all(FLERR,
"Invalid keyword in compute property/chunk command");
}
// initialization
nchunk = 1;
maxchunk = 0;
vector = NULL;
array = NULL;
count_one = count_all = NULL;
allocate();
if (nvalues == 1) {
vector_flag = 1;
size_vector = 0;
size_vector_variable = 1;
extvector = 0;
} else {
array_flag = 1;
size_array_cols = nvalues;
size_array_rows = 0;
size_array_rows_variable = 1;
extarray = 0;
}
}
/* ---------------------------------------------------------------------- */
ComputePropertyChunk::~ComputePropertyChunk()
{
delete [] idchunk;
delete [] pack_choice;
memory->destroy(vector);
memory->destroy(array);
memory->destroy(count_one);
memory->destroy(count_all);
}
/* ---------------------------------------------------------------------- */
void ComputePropertyChunk::init()
{
int icompute = modify->find_compute(idchunk);
if (icompute < 0)
error->all(FLERR,"Chunk/atom compute does not exist for "
"compute property/chunk");
cchunk = (ComputeChunkAtom *) modify->compute[icompute];
if (strcmp(cchunk->style,"chunk/atom") != 0)
error->all(FLERR,"Compute property/chunk does not use chunk/atom compute");
}
/* ---------------------------------------------------------------------- */
void ComputePropertyChunk::compute_vector()
{
invoked_vector = update->ntimestep;
// compute chunk/atom assigns atoms to chunk IDs
// if need count, extract ichunk index vector from compute
// ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms
nchunk = cchunk->setup_chunks();
if (nchunk > maxchunk) allocate();
if (nvalues == 1) size_vector = nchunk;
else size_array_rows = nchunk;
if (countflag) {
cchunk->compute_ichunk();
ichunk = cchunk->ichunk;
}
// fill vector
buf = vector;
(this->*pack_choice[0])(0);
}
/* ---------------------------------------------------------------------- */
void ComputePropertyChunk::compute_array()
{
invoked_array = update->ntimestep;
// compute chunk/atom assigns atoms to chunk IDs
// if need count, extract ichunk index vector from compute
// ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms
nchunk = cchunk->setup_chunks();
if (nchunk > maxchunk) allocate();
if (nvalues == 1) size_vector = nchunk;
else size_array_rows = nchunk;
if (countflag) {
cchunk->compute_ichunk();
ichunk = cchunk->ichunk;
}
// fill array
if (array) buf = &array[0][0];
for (int n = 0; n < nvalues; n++)
(this->*pack_choice[n])(n);
}
/* ----------------------------------------------------------------------
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 ComputePropertyChunk::lock_enable()
{
cchunk->lockcount++;
}
/* ----------------------------------------------------------------------
decrement lock counter in compute chunk/atom, it if still exists
------------------------------------------------------------------------- */
void ComputePropertyChunk::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 ComputePropertyChunk::lock_length()
{
nchunk = cchunk->setup_chunks();
return nchunk;
}
/* ----------------------------------------------------------------------
set the lock from startstep to stopstep
------------------------------------------------------------------------- */
void ComputePropertyChunk::lock(Fix *fixptr, bigint startstep, bigint stopstep)
{
cchunk->lock(fixptr,startstep,stopstep);
}
/* ----------------------------------------------------------------------
unset the lock
------------------------------------------------------------------------- */
void ComputePropertyChunk::unlock(Fix *fixptr)
{
cchunk->unlock(fixptr);
}
/* ----------------------------------------------------------------------
free and reallocate per-chunk arrays
------------------------------------------------------------------------- */
void ComputePropertyChunk::allocate()
{
memory->destroy(vector);
memory->destroy(array);
memory->destroy(count_one);
memory->destroy(count_all);
maxchunk = nchunk;
if (nvalues == 1) memory->create(vector,maxchunk,"property/chunk:vector");
else memory->create(array,maxchunk,nvalues,"property/chunk:array");
if (countflag) {
memory->create(count_one,maxchunk,"property/chunk:count_one");
memory->create(count_all,maxchunk,"property/chunk:count_all");
}
}
/* ----------------------------------------------------------------------
memory usage of local data
------------------------------------------------------------------------- */
double ComputePropertyChunk::memory_usage()
{
double bytes = (bigint) nchunk * nvalues * sizeof(double);
if (countflag) bytes += (bigint) nchunk * 2 * sizeof(int);
return bytes;
}
/* ----------------------------------------------------------------------
one method for every keyword compute property/chunk can output
the property is packed into buf starting at n with stride nvalues
customize a new keyword by adding a method
------------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
void ComputePropertyChunk::pack_count(int n)
{
int index;
for (int m = 0; m < nchunk; m++) count_one[m] = 0;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
index = ichunk[i]-1;
if (index < 0) continue;
count_one[index]++;
}
}
MPI_Allreduce(count_one,count_all,nchunk,MPI_INT,MPI_SUM,world);
for (int m = 0; m < nchunk; m++) {
buf[n] = count_all[m];
n += nvalues;
}
}
/* ---------------------------------------------------------------------- */
void ComputePropertyChunk::pack_id(int n)
{
int *origID = cchunk->chunkID;
for (int m = 0; m < nchunk; m++) {
buf[n] = origID[m];
n += nvalues;
}
}
/* ---------------------------------------------------------------------- */
void ComputePropertyChunk::pack_coord1(int n)
{
double **coord = cchunk->coord;
for (int m = 0; m < nchunk; m++) {
buf[n] = coord[m][0];
n += nvalues;
}
}
/* ---------------------------------------------------------------------- */
void ComputePropertyChunk::pack_coord2(int n)
{
double **coord = cchunk->coord;
for (int m = 0; m < nchunk; m++) {
buf[n] = coord[m][1];
n += nvalues;
}
}
/* ---------------------------------------------------------------------- */
void ComputePropertyChunk::pack_coord3(int n)
{
double **coord = cchunk->coord;
for (int m = 0; m < nchunk; m++) {
buf[n] = coord[m][2];
n += nvalues;
}
}
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