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lammps/src/compute_gyration_chunk.cpp
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compute_gyration_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 <math.h>
#include <string.h>
#include "compute_gyration_chunk.h"
#include "atom.h"
#include "update.h"
#include "modify.h"
#include "compute_chunk_atom.h"
#include "domain.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeGyrationChunk::ComputeGyrationChunk(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg),
idchunk(NULL), massproc(NULL), masstotal(NULL), com(NULL), comall(NULL),
rg(NULL), rgall(NULL), rgt(NULL), rgtall(NULL)
{
if (narg < 4) error->all(FLERR,"Illegal compute gyration/chunk command");
// ID of compute chunk/atom
int n = strlen(arg[3]) + 1;
idchunk = new char[n];
strcpy(idchunk,arg[3]);
init();
// optional args
tensor = 0;
int iarg = 4;
while (iarg < narg) {
if (strcmp(arg[iarg],"tensor") == 0) {
tensor = 1;
iarg++;
} else error->all(FLERR,"Illegal compute gyration/chunk command");
}
if (tensor) {
array_flag = 1;
size_array_cols = 6;
size_array_rows = 0;
size_array_rows_variable = 1;
extarray = 0;
} else {
vector_flag = 1;
size_vector = 0;
size_vector_variable = 1;
extvector = 0;
}
// chunk-based data
nchunk = 1;
maxchunk = 0;
allocate();
}
/* ---------------------------------------------------------------------- */
ComputeGyrationChunk::~ComputeGyrationChunk()
{
delete [] idchunk;
memory->destroy(massproc);
memory->destroy(masstotal);
memory->destroy(com);
memory->destroy(comall);
memory->destroy(rg);
memory->destroy(rgall);
memory->destroy(rgt);
memory->destroy(rgtall);
}
/* ---------------------------------------------------------------------- */
void ComputeGyrationChunk::init()
{
int icompute = modify->find_compute(idchunk);
if (icompute < 0)
error->all(FLERR,"Chunk/atom compute does not exist for "
"compute gyration/chunk");
cchunk = (ComputeChunkAtom *) modify->compute[icompute];
if (strcmp(cchunk->style,"chunk/atom") != 0)
error->all(FLERR,"Compute gyration/chunk does not use chunk/atom compute");
}
/* ---------------------------------------------------------------------- */
void ComputeGyrationChunk::compute_vector()
{
int i,index;
double dx,dy,dz,massone;
double unwrap[3];
invoked_array = update->ntimestep;
com_chunk();
int *ichunk = cchunk->ichunk;
for (i = 0; i < nchunk; i++) rg[i] = 0.0;
// compute Rg for each chunk
double **x = atom->x;
int *mask = atom->mask;
int *type = atom->type;
imageint *image = atom->image;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
index = ichunk[i]-1;
if (index < 0) continue;
domain->unmap(x[i],image[i],unwrap);
dx = unwrap[0] - comall[index][0];
dy = unwrap[1] - comall[index][1];
dz = unwrap[2] - comall[index][2];
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
rg[index] += (dx*dx + dy*dy + dz*dz) * massone;
}
MPI_Allreduce(rg,rgall,nchunk,MPI_DOUBLE,MPI_SUM,world);
for (int i = 0; i < nchunk; i++)
if (masstotal[i] > 0.0)
rgall[i] = sqrt(rgall[i]/masstotal[i]);
}
/* ---------------------------------------------------------------------- */
void ComputeGyrationChunk::compute_array()
{
int i,j,index;
double dx,dy,dz,massone;
double unwrap[3];
invoked_array = update->ntimestep;
com_chunk();
int *ichunk = cchunk->ichunk;
for (i = 0; i < nchunk; i++)
for (j = 0; j < 6; j++) rgt[i][j] = 0.0;
double **x = atom->x;
int *mask = atom->mask;
int *type = atom->type;
imageint *image = atom->image;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
index = ichunk[i]-1;
if (index < 0) continue;
domain->unmap(x[i],image[i],unwrap);
dx = unwrap[0] - comall[index][0];
dy = unwrap[1] - comall[index][1];
dz = unwrap[2] - comall[index][2];
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
rgt[index][0] += dx*dx * massone;
rgt[index][1] += dy*dy * massone;
rgt[index][2] += dz*dz * massone;
rgt[index][3] += dx*dy * massone;
rgt[index][4] += dx*dz * massone;
rgt[index][5] += dy*dz * massone;
}
if (nchunk)
MPI_Allreduce(&rgt[0][0],&rgtall[0][0],nchunk*6,MPI_DOUBLE,MPI_SUM,world);
for (i = 0; i < nchunk; i++) {
if (masstotal[i] > 0.0) {
for (j = 0; j < 6; j++)
rgtall[i][j] = rgtall[i][j]/masstotal[i];
}
}
}
/* ----------------------------------------------------------------------
calculate per-chunk COM, used by both scalar and tensor
------------------------------------------------------------------------- */
void ComputeGyrationChunk::com_chunk()
{
int index;
double massone;
double unwrap[3];
// 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();
if (tensor) size_array_rows = nchunk;
else size_vector = nchunk;
// zero local per-chunk values
for (int i = 0; i < nchunk; i++) {
massproc[i] = 0.0;
com[i][0] = com[i][1] = com[i][2] = 0.0;
}
// compute COM for each chunk
double **x = atom->x;
int *mask = atom->mask;
int *type = atom->type;
imageint *image = atom->image;
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]];
domain->unmap(x[i],image[i],unwrap);
massproc[index] += massone;
com[index][0] += unwrap[0] * massone;
com[index][1] += unwrap[1] * massone;
com[index][2] += unwrap[2] * massone;
}
MPI_Allreduce(massproc,masstotal,nchunk,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(&com[0][0],&comall[0][0],3*nchunk,MPI_DOUBLE,MPI_SUM,world);
for (int i = 0; i < nchunk; i++) {
if (masstotal[i] > 0.0) {
comall[i][0] /= masstotal[i];
comall[i][1] /= masstotal[i];
comall[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 ComputeGyrationChunk::lock_enable()
{
cchunk->lockcount++;
}
/* ----------------------------------------------------------------------
decrement lock counter in compute chunk/atom, it if still exists
------------------------------------------------------------------------- */
void ComputeGyrationChunk::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 ComputeGyrationChunk::lock_length()
{
nchunk = cchunk->setup_chunks();
return nchunk;
}
/* ----------------------------------------------------------------------
set the lock from startstep to stopstep
------------------------------------------------------------------------- */
void ComputeGyrationChunk::lock(Fix *fixptr, bigint startstep, bigint stopstep)
{
cchunk->lock(fixptr,startstep,stopstep);
}
/* ----------------------------------------------------------------------
unset the lock
------------------------------------------------------------------------- */
void ComputeGyrationChunk::unlock(Fix *fixptr)
{
cchunk->unlock(fixptr);
}
/* ----------------------------------------------------------------------
free and reallocate per-chunk arrays
------------------------------------------------------------------------- */
void ComputeGyrationChunk::allocate()
{
memory->destroy(massproc);
memory->destroy(masstotal);
memory->destroy(com);
memory->destroy(comall);
memory->destroy(rg);
memory->destroy(rgall);
memory->destroy(rgt);
memory->destroy(rgtall);
maxchunk = nchunk;
memory->create(massproc,maxchunk,"gyration/chunk:massproc");
memory->create(masstotal,maxchunk,"gyration/chunk:masstotal");
memory->create(com,maxchunk,3,"gyration/chunk:com");
memory->create(comall,maxchunk,3,"gyration/chunk:comall");
if (tensor) {
memory->create(rgt,maxchunk,6,"gyration/chunk:rgt");
memory->create(rgtall,maxchunk,6,"gyration/chunk:rgtall");
array = rgtall;
} else {
memory->create(rg,maxchunk,"gyration/chunk:rg");
memory->create(rgall,maxchunk,"gyration/chunk:rgall");
vector = rgall;
}
}
/* ----------------------------------------------------------------------
memory usage of local data
------------------------------------------------------------------------- */
double ComputeGyrationChunk::memory_usage()
{
double bytes = (bigint) maxchunk * 2 * sizeof(double);
bytes += (bigint) maxchunk * 2*3 * sizeof(double);
if (tensor) bytes += (bigint) maxchunk * 2*6 * sizeof(double);
else bytes += (bigint) maxchunk * 2 * sizeof(double);
return bytes;
}
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