Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F71137059
compute_gyration_chunk.cpp
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Tue, Jul 9, 21:23
Size
10 KB
Mime Type
text/x-c
Expires
Thu, Jul 11, 21:23 (2 d)
Engine
blob
Format
Raw Data
Handle
18912592
Attached To
rLAMMPS lammps
compute_gyration_chunk.cpp
View Options
/* ----------------------------------------------------------------------
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;
}
Event Timeline
Log In to Comment