git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13098 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
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src/compute_msd_chunk.cpp
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261
src/compute_msd_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_msd_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 "domain.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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ComputeMSDChunk::ComputeMSDChunk(LAMMPS *lmp, int narg, char **arg) :
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Compute(lmp, narg, arg)
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{
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if (narg != 4) error->all(FLERR,"Illegal compute msd/chunk command");
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array_flag = 1;
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size_array_cols = 4;
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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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// ID of compute chunk/atom
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int n = strlen(arg[6]) + 1;
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idchunk = new char[n];
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strcpy(idchunk,arg[6]);
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init();
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massproc = masstotal = NULL;
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com = comall = cominit = NULL;
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msd = NULL;
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firstflag = 1;
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}
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/* ---------------------------------------------------------------------- */
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ComputeMSDChunk::~ComputeMSDChunk()
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{
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delete [] idchunk;
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memory->destroy(massproc);
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memory->destroy(masstotal);
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memory->destroy(com);
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memory->destroy(comall);
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memory->destroy(cominit);
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memory->destroy(msd);
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}
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/* ---------------------------------------------------------------------- */
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void ComputeMSDChunk::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 compute msd/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 msd/chunk does not use chunk/atom compute");
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}
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/* ----------------------------------------------------------------------
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compute initial COM for each chunk
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only once on timestep compute is defined, when firstflag = 1
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------------------------------------------------------------------------- */
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void ComputeMSDChunk::setup()
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{
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if (!firstflag) return;
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firstflag = 0;
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compute_array();
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for (int i = 0; i < nchunk; i++) {
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cominit[i][0] = comall[i][0];
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cominit[i][1] = comall[i][1];
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cominit[i][2] = comall[i][2];
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}
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}
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/* ---------------------------------------------------------------------- */
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void ComputeMSDChunk::compute_array()
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{
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int index;
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double massone;
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double unwrap[3];
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invoked_array = update->ntimestep;
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// compute chunk/atom assigns atoms to chunk IDs
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// 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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int n = cchunk->setup_chunks();
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cchunk->compute_ichunk();
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int *ichunk = cchunk->ichunk;
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// first time call, allocate per-chunk arrays
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// thereafter, require nchunk remain the same
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if (firstflag) allocate(n);
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else if (n != nchunk)
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error->all(FLERR,"Compute msd/chunk nchunk is not static");
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// zero local per-chunk values
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for (int i = 0; i < nchunk; i++) {
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massproc[i] = 0.0;
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com[i][0] = com[i][1] = com[i][2] = 0.0;
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}
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// compute current COM for each chunk
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double **x = atom->x;
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int *mask = atom->mask;
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int *type = atom->type;
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imageint *image = atom->image;
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double *mass = atom->mass;
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double *rmass = atom->rmass;
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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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if (rmass) massone = rmass[i];
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else massone = mass[type[i]];
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domain->unmap(x[i],image[i],unwrap);
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massproc[index] += massone;
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com[index][0] += unwrap[0] * massone;
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com[index][1] += unwrap[1] * massone;
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com[index][2] += unwrap[2] * massone;
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}
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MPI_Allreduce(massproc,masstotal,nchunk,MPI_DOUBLE,MPI_SUM,world);
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MPI_Allreduce(&com[0][0],&comall[0][0],3*nchunk,MPI_DOUBLE,MPI_SUM,world);
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for (int i = 0; i < nchunk; i++) {
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comall[i][0] /= masstotal[i];
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comall[i][1] /= masstotal[i];
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comall[i][2] /= masstotal[i];
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}
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// MSD is difference between current and initial COM
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// cominit does not yet exist when called from constructor
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if (firstflag) return;
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double dx,dy,dz;
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for (int i = 0; i < nchunk; i++) {
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dx = comall[i][0] - cominit[i][0];
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dy = comall[i][1] - cominit[i][1];
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dz = comall[i][2] - cominit[i][2];
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msd[i][0] = dx*dx;
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msd[i][1] = dy*dy;
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msd[i][2] = dz*dz;
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msd[i][3] = dx*dx + dy*dy + dz*dz;
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}
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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 ComputeMSDChunk::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 ComputeMSDChunk::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 ComputeMSDChunk::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 ComputeMSDChunk::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 ComputeMSDChunk::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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one-time allocate of per-chunk arrays
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------------------------------------------------------------------------- */
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void ComputeMSDChunk::allocate(int n)
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{
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size_array_rows = nchunk = n;
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memory->create(massproc,nchunk,"msd/chunk:massproc");
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memory->create(masstotal,nchunk,"msd/chunk:masstotal");
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memory->create(com,nchunk,3,"msd/chunk:com");
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memory->create(comall,nchunk,3,"msd/chunk:comall");
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memory->create(cominit,nchunk,3,"msd/chunk:cominit");
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memory->create(msd,nchunk,4,"msd/chunk:msd");
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array = msd;
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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 ComputeMSDChunk::memory_usage()
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{
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double bytes = (bigint) nchunk * 2 * sizeof(double);
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bytes += (bigint) nchunk * 3*3 * sizeof(double);
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bytes += (bigint) nchunk * 4 * sizeof(double);
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return bytes;
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}
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