git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13098 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
335
src/compute_property_chunk.cpp
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335
src/compute_property_chunk.cpp
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "string.h"
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#include "compute_property_chunk.h"
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#include "atom.h"
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#include "update.h"
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#include "modify.h"
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#include "compute_chunk_atom.h"
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#include "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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ComputePropertyChunk::ComputePropertyChunk(LAMMPS *lmp, int narg, char **arg) :
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Compute(lmp, narg, arg)
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{
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if (narg < 5) error->all(FLERR,"Illegal compute property/chunk command");
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// ID of compute chunk/atom
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int n = strlen(arg[3]) + 1;
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idchunk = new char[n];
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strcpy(idchunk,arg[3]);
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init();
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// parse values
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nvalues = narg - 4;
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pack_choice = new FnPtrPack[nvalues];
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countflag = 0;
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int i;
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for (int iarg = 4; iarg < narg; iarg++) {
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i = iarg-4;
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if (strcmp(arg[iarg],"count") == 0) {
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pack_choice[i] = &ComputePropertyChunk::pack_count;
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countflag = 1;
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} else if (strcmp(arg[iarg],"id") == 0) {
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if (!cchunk->compress)
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error->all(FLERR,"Compute chunk/atom stores no IDs for "
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"compute property/chunk");
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pack_choice[i] = &ComputePropertyChunk::pack_id;
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} else if (strcmp(arg[iarg],"coord1") == 0) {
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if (cchunk->ncoord < 1)
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error->all(FLERR,"Compute chunk/atom stores no coord1 for "
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"compute property/chunk");
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pack_choice[i] = &ComputePropertyChunk::pack_coord1;
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} else if (strcmp(arg[iarg],"coord2") == 0) {
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if (cchunk->ncoord < 2)
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error->all(FLERR,"Compute chunk/atom stores no coord2 for "
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"compute property/chunk");
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pack_choice[i] = &ComputePropertyChunk::pack_coord2;
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} else if (strcmp(arg[iarg],"coord3") == 0) {
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if (cchunk->ncoord < 3)
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error->all(FLERR,"Compute chunk/atom stores no coord3 for "
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"compute property/chunk");
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pack_choice[i] = &ComputePropertyChunk::pack_coord3;
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} else error->all(FLERR,
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"Invalid keyword in compute property/chunk command");
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}
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// initialization
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nchunk = 1;
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maxchunk = 0;
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vector = NULL;
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array = NULL;
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count_one = count_all = NULL;
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allocate();
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if (nvalues == 1) {
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vector_flag = 1;
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size_vector = 0;
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size_vector_variable = 1;
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extvector = 0;
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} else {
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array_flag = 1;
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size_array_cols = nvalues;
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size_array_rows = 0;
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size_array_rows_variable = 1;
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extarray = 0;
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}
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}
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/* ---------------------------------------------------------------------- */
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ComputePropertyChunk::~ComputePropertyChunk()
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{
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delete [] idchunk;
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delete [] pack_choice;
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memory->destroy(vector);
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memory->destroy(array);
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memory->destroy(count_one);
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memory->destroy(count_all);
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}
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/* ---------------------------------------------------------------------- */
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void ComputePropertyChunk::init()
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{
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int icompute = modify->find_compute(idchunk);
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if (icompute < 0)
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error->all(FLERR,"Chunk/atom compute does not exist for "
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"compute property/chunk");
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cchunk = (ComputeChunkAtom *) modify->compute[icompute];
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if (strcmp(cchunk->style,"chunk/atom") != 0)
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error->all(FLERR,"Compute property/chunk does not use chunk/atom compute");
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}
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/* ---------------------------------------------------------------------- */
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void ComputePropertyChunk::compute_vector()
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{
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invoked_vector = update->ntimestep;
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// compute chunk/atom assigns atoms to chunk IDs
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// if need count, extract ichunk index vector from compute
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// ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms
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nchunk = cchunk->setup_chunks();
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if (nchunk > maxchunk) allocate();
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if (countflag) {
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cchunk->compute_ichunk();
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ichunk = cchunk->ichunk;
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}
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// fill vector
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buf = vector;
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(this->*pack_choice[0])(0);
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}
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/* ---------------------------------------------------------------------- */
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void ComputePropertyChunk::compute_array()
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{
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invoked_array = update->ntimestep;
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// compute chunk/atom assigns atoms to chunk IDs
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// if need count, extract ichunk index vector from compute
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// ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms
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nchunk = cchunk->setup_chunks();
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if (nchunk > maxchunk) allocate();
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if (countflag) {
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cchunk->compute_ichunk();
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ichunk = cchunk->ichunk;
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}
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// fill array
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if (array) buf = &array[0][0];
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for (int n = 0; n < nvalues; n++)
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(this->*pack_choice[n])(n);
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}
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/* ----------------------------------------------------------------------
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lock methods: called by fix ave/time
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these methods insure vector/array size is locked for Nfreq epoch
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by passing lock info along to compute chunk/atom
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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increment lock counter
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------------------------------------------------------------------------- */
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void ComputePropertyChunk::lock_enable()
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{
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cchunk->lockcount++;
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}
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/* ----------------------------------------------------------------------
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decrement lock counter in compute chunk/atom, it if still exists
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------------------------------------------------------------------------- */
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void ComputePropertyChunk::lock_disable()
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{
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int icompute = modify->find_compute(idchunk);
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if (icompute >= 0) {
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cchunk = (ComputeChunkAtom *) modify->compute[icompute];
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cchunk->lockcount--;
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}
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}
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/* ----------------------------------------------------------------------
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calculate and return # of chunks = length of vector/array
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------------------------------------------------------------------------- */
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int ComputePropertyChunk::lock_length()
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{
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nchunk = cchunk->setup_chunks();
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return nchunk;
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}
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/* ----------------------------------------------------------------------
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set the lock from startstep to stopstep
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------------------------------------------------------------------------- */
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void ComputePropertyChunk::lock(Fix *fixptr, bigint startstep, bigint stopstep)
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{
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cchunk->lock(fixptr,startstep,stopstep);
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}
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/* ----------------------------------------------------------------------
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unset the lock
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------------------------------------------------------------------------- */
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void ComputePropertyChunk::unlock(Fix *fixptr)
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{
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cchunk->unlock(fixptr);
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}
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/* ----------------------------------------------------------------------
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free and reallocate per-chunk arrays
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------------------------------------------------------------------------- */
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void ComputePropertyChunk::allocate()
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{
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memory->destroy(vector);
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memory->destroy(array);
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memory->destroy(count_one);
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memory->destroy(count_all);
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size_array_rows = maxchunk = nchunk;
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if (nvalues == 1) memory->create(vector,maxchunk,"property/chunk:vector");
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else memory->create(array,maxchunk,nvalues,"property/chunk:array");
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if (countflag) {
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memory->create(count_one,maxchunk,"property/chunk:count_one");
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memory->create(count_one,maxchunk,"property/chunk:count_all");
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}
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}
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/* ----------------------------------------------------------------------
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memory usage of local data
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------------------------------------------------------------------------- */
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double ComputePropertyChunk::memory_usage()
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{
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double bytes = (bigint) nchunk * nvalues * sizeof(double);
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if (countflag) bytes += (bigint) nchunk * 2 * sizeof(int);
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return bytes;
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}
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/* ----------------------------------------------------------------------
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one method for every keyword compute property/chunk can output
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the property is packed into buf starting at n with stride nvalues
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customize a new keyword by adding a method
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------------------------------------------------------------------------- */
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/* ---------------------------------------------------------------------- */
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void ComputePropertyChunk::pack_count(int n)
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{
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int index;
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for (int m = 0; m < nchunk; m++) count_one[m] = 0;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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index = ichunk[i]-1;
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if (index < 0) continue;
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count_one[index]++;
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}
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}
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MPI_Allreduce(count_one,count_all,nchunk,MPI_INT,MPI_SUM,world);
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for (int m = 0; m < nchunk; m++) {
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buf[n] = count_all[m];
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n += nvalues;
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}
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}
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/* ---------------------------------------------------------------------- */
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void ComputePropertyChunk::pack_id(int n)
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{
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int *origID = cchunk->chunkID;
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for (int m = 0; m < nchunk; m++) {
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buf[n] = origID[m];
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n += nvalues;
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}
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}
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/* ---------------------------------------------------------------------- */
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void ComputePropertyChunk::pack_coord1(int n)
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{
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double **coord = cchunk->coord;
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for (int m = 0; m < nchunk; m++) {
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buf[n] = coord[m][0];
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n += nvalues;
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}
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}
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/* ---------------------------------------------------------------------- */
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void ComputePropertyChunk::pack_coord2(int n)
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{
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double **coord = cchunk->coord;
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for (int m = 0; m < nchunk; m++) {
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buf[n] = coord[m][1];
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n += nvalues;
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}
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}
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/* ---------------------------------------------------------------------- */
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void ComputePropertyChunk::pack_coord3(int n)
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{
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double **coord = cchunk->coord;
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for (int m = 0; m < nchunk; m++) {
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buf[n] = coord[m][2];
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n += nvalues;
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}
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}
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