jianmu
/
lammps
forked from lijiext/lammps
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
lammps/src/compute_temp_chunk.cpp

409 lines
12 KiB
C++
Raw Blame History

/* ----------------------------------------------------------------------
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_temp_chunk.h"
#include "atom.h"
#include "update.h"
#include "force.h"
#include "modify.h"
#include "compute_chunk_atom.h"
#include "domain.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeTempChunk::ComputeTempChunk(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg < 4) error->all(FLERR,"Illegal compute temp/chunk command");
vector_flag = 1;
size_vector = 0;
size_vector_variable = 1;
extvector = 0;
// ID of compute chunk/atom
int n = strlen(arg[3]) + 1;
idchunk = new char[n];
strcpy(idchunk,arg[3]);
biasflag = 0;
init();
// optional args
comflag = 0;
biasflag = 0;
id_bias = NULL;
adof = domain->dimension;
cdof = 0.0;
int iarg = 4;
while (iarg < narg) {
if (strcmp(arg[iarg],"com") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal compute temp/chunk command");
if (strcmp(arg[iarg+1],"yes") == 0) comflag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) comflag = 0;
else error->all(FLERR,"Illegal compute temp/chunk command");
iarg += 2;
} else if (strcmp(arg[iarg],"bias") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal compute temp/chunk command");
biasflag = 1;
int n = strlen(arg[iarg+1]) + 1;
id_bias = new char[n];
strcpy(id_bias,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"adof") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal compute temp/chunk command");
adof = force->numeric(FLERR,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"cdof") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal compute temp/chunk command");
cdof = force->numeric(FLERR,arg[iarg+1]);
iarg += 2;
} else error->all(FLERR,"Illegal compute temp/chunk command");
}
if (comflag && biasflag)
error->all(FLERR,"Cannot use both com and bias with compute temp/chunk");
// error check on bias compute
if (biasflag) {
int i = modify->find_compute(id_bias);
if (i < 0)
error->all(FLERR,"Could not find compute ID for temperature bias");
tbias = modify->compute[i];
if (tbias->tempflag == 0)
error->all(FLERR,"Bias compute does not calculate temperature");
if (tbias->tempbias == 0)
error->all(FLERR,"Bias compute does not calculate a velocity bias");
}
// chunk-based data
nchunk = 1;
maxchunk = 0;
ke = keall = NULL;
count = countall = NULL;
massproc = masstotal = NULL;
vcm = vcmall = NULL;
allocate();
}
/* ---------------------------------------------------------------------- */
ComputeTempChunk::~ComputeTempChunk()
{
delete [] idchunk;
delete [] id_bias;
memory->destroy(ke);
memory->destroy(keall);
memory->destroy(count);
memory->destroy(countall);
memory->destroy(massproc);
memory->destroy(masstotal);
memory->destroy(vcm);
memory->destroy(vcmall);
}
/* ---------------------------------------------------------------------- */
void ComputeTempChunk::init()
{
int icompute = modify->find_compute(idchunk);
if (icompute < 0)
error->all(FLERR,"Chunk/atom compute does not exist for "
"compute temp/chunk");
cchunk = (ComputeChunkAtom *) modify->compute[icompute];
if (strcmp(cchunk->style,"chunk/atom") != 0)
error->all(FLERR,"Compute temp/chunk does not use chunk/atom compute");
if (biasflag) {
int i = modify->find_compute(id_bias);
if (i < 0)
error->all(FLERR,"Could not find compute ID for temperature bias");
tbias = modify->compute[i];
}
}
/* ---------------------------------------------------------------------- */
void ComputeTempChunk::compute_vector()
{
int index;
invoked_vector = 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
nchunk = cchunk->setup_chunks();
cchunk->compute_ichunk();
int *ichunk = cchunk->ichunk;
if (nchunk > maxchunk) allocate();
size_vector = nchunk;
// calculate COM velocity for each chunk
if (comflag) vcm_compute();
// remove velocity bias
if (biasflag) {
if (tbias->invoked_scalar != update->ntimestep) tbias->compute_scalar();
tbias->remove_bias_all();
}
// zero local per-chunk values
for (int i = 0; i < nchunk; i++) {
count[i] = 0;
ke[i] = 0.0;
}
// compute temperature for each chunk
// option for removing COM velocity
double **v = atom->v;
double *mass = atom->mass;
double *rmass = atom->rmass;
int *mask = atom->mask;
int *type = atom->type;
int nlocal = atom->nlocal;
if (!comflag) {
if (rmass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
index = ichunk[i]-1;
if (index < 0) continue;
ke[index] += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
rmass[i];
count[index]++;
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
index = ichunk[i]-1;
if (index < 0) continue;
ke[index] += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
mass[type[i]];
count[index]++;
}
}
} else {
double vx,vy,vz;
if (rmass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
index = ichunk[i]-1;
if (index < 0) continue;
vx = v[i][0] - vcmall[index][0];
vy = v[i][1] - vcmall[index][1];
vz = v[i][2] - vcmall[index][2];
ke[index] += (vx*vx + vy*vy + vz*vz) * rmass[i];
count[index]++;
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
index = ichunk[i]-1;
if (index < 0) continue;
vx = v[i][0] - vcmall[index][0];
vy = v[i][1] - vcmall[index][1];
vz = v[i][2] - vcmall[index][2];
ke[index] += (vx*vx + vy*vy + vz*vz) * mass[type[i]];
count[index]++;
}
}
}
MPI_Allreduce(ke,keall,nchunk,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(count,countall,nchunk,MPI_INT,MPI_SUM,world);
// restore velocity bias
if (biasflag) tbias->restore_bias_all();
// normalize temperatures by per-chunk DOF
double dof,tfactor;
double mvv2e = force->mvv2e;
double boltz = force->boltz;
for (int i = 0; i < nchunk; i++) {
dof = cdof + adof*countall[i];
if (dof > 0.0) tfactor = mvv2e / (dof * boltz);
else tfactor = 0.0;
keall[i] *= tfactor;
}
}
/* ----------------------------------------------------------------------
calculate velocity of COM for each chunk
------------------------------------------------------------------------- */
void ComputeTempChunk::vcm_compute()
{
int index;
double massone;
int *ichunk = cchunk->ichunk;
for (int i = 0; i < nchunk; i++) {
vcm[i][0] = vcm[i][1] = vcm[i][2] = 0.0;
massproc[i] = 0.0;
}
double **v = atom->v;
int *mask = atom->mask;
int *type = atom->type;
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]];
vcm[index][0] += v[i][0] * massone;
vcm[index][1] += v[i][1] * massone;
vcm[index][2] += v[i][2] * massone;
massproc[index] += massone;
}
MPI_Allreduce(&vcm[0][0],&vcmall[0][0],3*nchunk,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(massproc,masstotal,nchunk,MPI_DOUBLE,MPI_SUM,world);
for (int i = 0; i < nchunk; i++) {
vcmall[i][0] /= masstotal[i];
vcmall[i][1] /= masstotal[i];
vcmall[i][2] /= masstotal[i];
}
}
/* ----------------------------------------------------------------------
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 ComputeTempChunk::lock_enable()
{
cchunk->lockcount++;
}
/* ----------------------------------------------------------------------
decrement lock counter in compute chunk/atom, it if still exists
------------------------------------------------------------------------- */
void ComputeTempChunk::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 ComputeTempChunk::lock_length()
{
nchunk = cchunk->setup_chunks();
return nchunk;
}
/* ----------------------------------------------------------------------
set the lock from startstep to stopstep
------------------------------------------------------------------------- */
void ComputeTempChunk::lock(Fix *fixptr, bigint startstep, bigint stopstep)
{
cchunk->lock(fixptr,startstep,stopstep);
}
/* ----------------------------------------------------------------------
unset the lock
------------------------------------------------------------------------- */
void ComputeTempChunk::unlock(Fix *fixptr)
{
cchunk->unlock(fixptr);
}
/* ----------------------------------------------------------------------
free and reallocate per-chunk arrays
------------------------------------------------------------------------- */
void ComputeTempChunk::allocate()
{
memory->destroy(ke);
memory->destroy(keall);
memory->destroy(count);
memory->destroy(countall);
maxchunk = nchunk;
memory->create(ke,maxchunk,"temp/chunk:ke");
memory->create(keall,maxchunk,"temp/chunk:keall");
memory->create(count,maxchunk,"temp/chunk:count");
memory->create(countall,maxchunk,"temp/chunk:countall");
vector = keall;
if (comflag) {
memory->destroy(massproc);
memory->destroy(masstotal);
memory->destroy(vcm);
memory->destroy(vcmall);
memory->create(massproc,maxchunk,"vcm/chunk:massproc");
memory->create(masstotal,maxchunk,"vcm/chunk:masstotal");
memory->create(vcm,maxchunk,3,"vcm/chunk:vcm");
memory->create(vcmall,maxchunk,3,"vcm/chunk:vcmall");
}
}
/* ----------------------------------------------------------------------
memory usage of local data
------------------------------------------------------------------------- */
double ComputeTempChunk::memory_usage()
{
double bytes = (bigint) maxchunk * 2 * sizeof(double);
bytes = (bigint) maxchunk * 2 * sizeof(int);
if (comflag) {
bytes += (bigint) maxchunk * 2 * sizeof(double);
bytes += (bigint) maxchunk * 2*3 * sizeof(double);
}
return bytes;
}
Reference in New Issue View Git Blame Copy Permalink