git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13098 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
407
src/compute_temp_chunk.cpp
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407
src/compute_temp_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_temp_chunk.h"
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#include "atom.h"
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#include "update.h"
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#include "force.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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ComputeTempChunk::ComputeTempChunk(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 temp/chunk command");
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vector_flag = 1;
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size_vector = 1;
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size_vector_variable = 1;
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extvector = 0;
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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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biasflag = 0;
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init();
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// optional args
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comflag = 0;
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biasflag = 0;
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id_bias = NULL;
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adof = domain->dimension;
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cdof = 0.0;
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int iarg = 4;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"com") == 0) {
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if (iarg+2 > narg)
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error->all(FLERR,"Illegal compute temp/chunk command");
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if (strcmp(arg[iarg+1],"yes") == 0) comflag = 1;
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else if (strcmp(arg[iarg+1],"no") == 0) comflag = 0;
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else error->all(FLERR,"Illegal compute temp/chunk command");
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iarg += 2;
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} else if (strcmp(arg[iarg],"bias") == 0) {
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if (iarg+2 > narg)
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error->all(FLERR,"Illegal compute temp/chunk command");
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biasflag = 1;
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int n = strlen(arg[iarg+1]) + 1;
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id_bias = new char[n];
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strcpy(id_bias,arg[iarg+1]);
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iarg += 2;
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} else if (strcmp(arg[iarg],"adof") == 0) {
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if (iarg+2 > narg)
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error->all(FLERR,"Illegal compute temp/chunk command");
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adof = force->numeric(FLERR,arg[iarg+1]);
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iarg += 2;
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} else if (strcmp(arg[iarg],"cdof") == 0) {
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if (iarg+2 > narg)
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error->all(FLERR,"Illegal compute temp/chunk command");
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cdof = force->numeric(FLERR,arg[iarg+1]);
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iarg += 2;
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} else error->all(FLERR,"Illegal compute temp/chunk command");
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}
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if (comflag && biasflag)
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error->all(FLERR,"Cannot use both com and bias with compute temp/chunk");
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// error check on bias compute
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if (biasflag) {
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int i = modify->find_compute(id_bias);
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if (i < 0)
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error->all(FLERR,"Could not find compute ID for temperature bias");
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tbias = modify->compute[i];
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if (tbias->tempflag == 0)
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error->all(FLERR,"Bias compute does not calculate temperature");
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if (tbias->tempbias == 0)
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error->all(FLERR,"Bias compute does not calculate a velocity bias");
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}
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// chunk-based data
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nchunk = 1;
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maxchunk = 0;
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ke = keall = NULL;
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count = countall = NULL;
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massproc = masstotal = NULL;
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vcm = vcmall = NULL;
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allocate();
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}
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/* ---------------------------------------------------------------------- */
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ComputeTempChunk::~ComputeTempChunk()
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{
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delete [] idchunk;
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delete [] id_bias;
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memory->destroy(ke);
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memory->destroy(keall);
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memory->destroy(count);
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memory->destroy(countall);
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memory->destroy(massproc);
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memory->destroy(masstotal);
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memory->destroy(vcm);
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memory->destroy(vcmall);
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}
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/* ---------------------------------------------------------------------- */
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void ComputeTempChunk::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 temp/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 temp/chunk does not use chunk/atom compute");
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if (biasflag) {
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int i = modify->find_compute(id_bias);
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if (i < 0)
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error->all(FLERR,"Could not find compute ID for temperature bias");
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tbias = modify->compute[i];
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}
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}
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/* ---------------------------------------------------------------------- */
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void ComputeTempChunk::compute_vector()
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{
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int index;
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invoked_vector = 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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nchunk = cchunk->setup_chunks();
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cchunk->compute_ichunk();
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int *ichunk = cchunk->ichunk;
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if (nchunk > maxchunk) allocate();
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// calculate COM velocity for each chunk
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if (comflag) vcm_compute();
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// remove velocity bias
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if (biasflag) {
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if (tbias->invoked_scalar != update->ntimestep) tbias->compute_scalar();
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tbias->remove_bias_all();
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}
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// zero local per-chunk values
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for (int i = 0; i < nchunk; i++) {
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count[i] = 0;
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ke[i] = 0.0;
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}
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// compute temperature for each chunk
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// option for removing COM velocity
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double **v = atom->v;
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double *mass = atom->mass;
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double *rmass = atom->rmass;
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int *mask = atom->mask;
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int *type = atom->type;
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int nlocal = atom->nlocal;
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if (!comflag) {
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if (rmass) {
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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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ke[index] += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
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rmass[i];
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count[index]++;
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}
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} else {
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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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ke[index] += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
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mass[type[i]];
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count[index]++;
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}
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}
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} else {
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double vx,vy,vz;
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if (rmass) {
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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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vx = v[i][0] - vcmall[index][0];
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vy = v[i][1] - vcmall[index][1];
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vz = v[i][2] - vcmall[index][2];
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ke[index] += (vx*vx + vy*vy + vz*vz) * rmass[i];
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count[index]++;
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}
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} else {
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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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vx = v[i][0] - vcmall[index][0];
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vy = v[i][1] - vcmall[index][1];
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vz = v[i][2] - vcmall[index][2];
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ke[index] += (vx*vx + vy*vy + vz*vz) * mass[type[i]];
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count[index]++;
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}
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}
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}
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MPI_Allreduce(ke,keall,nchunk,MPI_DOUBLE,MPI_SUM,world);
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MPI_Allreduce(count,countall,nchunk,MPI_INT,MPI_SUM,world);
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// restore velocity bias
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if (biasflag) tbias->restore_bias_all();
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// normalize temperatures by per-chunk DOF
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double dof,tfactor;
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double mvv2e = force->mvv2e;
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double boltz = force->boltz;
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for (int i = 0; i < nchunk; i++) {
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dof = cdof + adof*countall[i];
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if (dof > 0.0) tfactor = mvv2e / (dof * boltz);
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else tfactor = 0.0;
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keall[i] *= tfactor;
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}
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}
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/* ----------------------------------------------------------------------
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calculate velocity of COM for each chunk
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------------------------------------------------------------------------- */
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void ComputeTempChunk::vcm_compute()
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{
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int index;
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double massone;
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int *ichunk = cchunk->ichunk;
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for (int i = 0; i < nchunk; i++) {
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vcm[i][0] = vcm[i][1] = vcm[i][2] = 0.0;
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massproc[i] = 0.0;
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}
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double **v = atom->v;
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int *mask = atom->mask;
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int *type = atom->type;
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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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vcm[index][0] += v[i][0] * massone;
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vcm[index][1] += v[i][1] * massone;
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vcm[index][2] += v[i][2] * massone;
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massproc[index] += massone;
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}
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MPI_Allreduce(&vcm[0][0],&vcmall[0][0],3*nchunk,MPI_DOUBLE,MPI_SUM,world);
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MPI_Allreduce(massproc,masstotal,nchunk,MPI_DOUBLE,MPI_SUM,world);
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for (int i = 0; i < nchunk; i++) {
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vcmall[i][0] /= masstotal[i];
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vcmall[i][1] /= masstotal[i];
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vcmall[i][2] /= masstotal[i];
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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 ComputeTempChunk::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 ComputeTempChunk::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 ComputeTempChunk::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 ComputeTempChunk::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 ComputeTempChunk::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 ComputeTempChunk::allocate()
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{
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memory->destroy(ke);
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memory->destroy(keall);
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memory->destroy(count);
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memory->destroy(countall);
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size_vector = maxchunk = nchunk;
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memory->create(ke,maxchunk,"temp/chunk:ke");
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memory->create(keall,maxchunk,"temp/chunk:keall");
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memory->create(count,maxchunk,"temp/chunk:count");
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memory->create(countall,maxchunk,"temp/chunk:countall");
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vector = keall;
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if (comflag) {
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memory->destroy(massproc);
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memory->destroy(masstotal);
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memory->destroy(vcm);
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memory->destroy(vcmall);
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memory->create(massproc,maxchunk,"vcm/chunk:massproc");
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memory->create(masstotal,maxchunk,"vcm/chunk:masstotal");
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memory->create(vcm,maxchunk,3,"vcm/chunk:vcm");
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memory->create(vcmall,maxchunk,3,"vcm/chunk:vcmall");
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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 ComputeTempChunk::memory_usage()
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{
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double bytes = (bigint) maxchunk * 2 * sizeof(double);
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bytes = (bigint) maxchunk * 2 * sizeof(int);
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if (comflag) {
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bytes += (bigint) maxchunk * 2 * sizeof(double);
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bytes += (bigint) maxchunk * 2*3 * sizeof(double);
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}
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return bytes;
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}
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