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lammps/src/compute_dipole_chunk.cpp
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compute_dipole_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 <string.h>
#include "compute_dipole_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"
#include "math_special.h"
using namespace LAMMPS_NS;
using namespace MathSpecial;
enum { MASSCENTER, GEOMCENTER };
/* ---------------------------------------------------------------------- */
ComputeDipoleChunk::ComputeDipoleChunk(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg),
idchunk(NULL), massproc(NULL), masstotal(NULL), chrgproc(NULL), chrgtotal(NULL), com(NULL),
comall(NULL), dipole(NULL), dipoleall(NULL)
{
if ((narg != 4) && (narg != 5)) error->all(FLERR,"Illegal compute dipole/chunk command");
array_flag = 1;
size_array_cols = 4;
size_array_rows = 0;
size_array_rows_variable = 1;
extarray = 0;
// ID of compute chunk/atom
int n = strlen(arg[3]) + 1;
idchunk = new char[n];
strcpy(idchunk,arg[3]);
usecenter = MASSCENTER;
if (narg == 5) {
if (strncmp(arg[4],"geom",4) == 0) usecenter = GEOMCENTER;
else if (strcmp(arg[4],"mass") == 0) usecenter = MASSCENTER;
else error->all(FLERR,"Illegal compute dipole/chunk command");
}
init();
// chunk-based data
nchunk = 1;
maxchunk = 0;
allocate();
}
/* ---------------------------------------------------------------------- */
ComputeDipoleChunk::~ComputeDipoleChunk()
{
delete [] idchunk;
memory->destroy(massproc);
memory->destroy(masstotal);
memory->destroy(chrgproc);
memory->destroy(chrgtotal);
memory->destroy(com);
memory->destroy(comall);
memory->destroy(dipole);
memory->destroy(dipoleall);
}
/* ---------------------------------------------------------------------- */
void ComputeDipoleChunk::init()
{
int icompute = modify->find_compute(idchunk);
if (icompute < 0)
error->all(FLERR,"Chunk/atom compute does not exist for "
"compute dipole/chunk");
cchunk = (ComputeChunkAtom *) modify->compute[icompute];
if (strcmp(cchunk->style,"chunk/atom") != 0)
error->all(FLERR,"Compute dipole/chunk does not use chunk/atom compute");
}
/* ---------------------------------------------------------------------- */
void ComputeDipoleChunk::compute_array()
{
int i,index;
double massone;
double unwrap[3];
invoked_array = 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_array_rows = nchunk;
// zero local per-chunk values
for (int i = 0; i < nchunk; i++) {
massproc[i] = chrgproc[i] = 0.0;
com[i][0] = com[i][1] = com[i][2] = 0.0;
dipole[i][0] = dipole[i][1] = dipole[i][2] = dipole[i][3] = 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;
double *q = atom->q;
double **mu = atom->mu;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
index = ichunk[i]-1;
if (index < 0) continue;
if (usecenter == MASSCENTER) {
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
} else massone = 1.0; // usecenter == GEOMCENTER
domain->unmap(x[i],image[i],unwrap);
massproc[index] += massone;
if (atom->q_flag) chrgproc[index] += atom->q[i];
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(chrgproc,chrgtotal,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];
}
}
// compute dipole for each chunk
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);
if (atom->q_flag) {
dipole[index][0] += q[i]*unwrap[0];
dipole[index][1] += q[i]*unwrap[1];
dipole[index][2] += q[i]*unwrap[2];
}
if (atom->mu_flag) {
dipole[index][0] += mu[i][0];
dipole[index][1] += mu[i][1];
dipole[index][2] += mu[i][2];
}
}
}
MPI_Allreduce(&dipole[0][0],&dipoleall[0][0],4*nchunk,
MPI_DOUBLE,MPI_SUM,world);
for (i = 0; i < nchunk; i++) {
// correct for position dependence with charged chunks
dipoleall[i][0] -= chrgtotal[i]*comall[i][0];
dipoleall[i][1] -= chrgtotal[i]*comall[i][1];
dipoleall[i][2] -= chrgtotal[i]*comall[i][2];
// compute total dipole moment
dipoleall[i][3] = sqrt(square(dipoleall[i][0])
+ square(dipoleall[i][1])
+ square(dipoleall[i][2]));
}
}
/* ----------------------------------------------------------------------
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 ComputeDipoleChunk::lock_enable()
{
cchunk->lockcount++;
}
/* ----------------------------------------------------------------------
decrement lock counter in compute chunk/atom, it if still exists
------------------------------------------------------------------------- */
void ComputeDipoleChunk::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 ComputeDipoleChunk::lock_length()
{
nchunk = cchunk->setup_chunks();
return nchunk;
}
/* ----------------------------------------------------------------------
set the lock from startstep to stopstep
------------------------------------------------------------------------- */
void ComputeDipoleChunk::lock(Fix *fixptr, bigint startstep, bigint stopstep)
{
cchunk->lock(fixptr,startstep,stopstep);
}
/* ----------------------------------------------------------------------
unset the lock
------------------------------------------------------------------------- */
void ComputeDipoleChunk::unlock(Fix *fixptr)
{
cchunk->unlock(fixptr);
}
/* ----------------------------------------------------------------------
free and reallocate per-chunk arrays
------------------------------------------------------------------------- */
void ComputeDipoleChunk::allocate()
{
memory->destroy(massproc);
memory->destroy(masstotal);
memory->destroy(chrgproc);
memory->destroy(chrgtotal);
memory->destroy(com);
memory->destroy(comall);
memory->destroy(dipole);
memory->destroy(dipoleall);
maxchunk = nchunk;
memory->create(massproc,maxchunk,"dipole/chunk:massproc");
memory->create(masstotal,maxchunk,"dipole/chunk:masstotal");
memory->create(chrgproc,maxchunk,"dipole/chunk:chrgproc");
memory->create(chrgtotal,maxchunk,"dipole/chunk:chrgtotal");
memory->create(com,maxchunk,3,"dipole/chunk:com");
memory->create(comall,maxchunk,3,"dipole/chunk:comall");
memory->create(dipole,maxchunk,4,"dipole/chunk:dipole");
memory->create(dipoleall,maxchunk,4,"dipole/chunk:dipoleall");
array = dipoleall;
}
/* ----------------------------------------------------------------------
memory usage of local data
------------------------------------------------------------------------- */
double ComputeDipoleChunk::memory_usage()
{
double bytes = (bigint) maxchunk * 2 * sizeof(double);
bytes += (bigint) maxchunk * 2*3 * sizeof(double);
bytes += (bigint) maxchunk * 2*4 * sizeof(double);
return bytes;
}
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