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lammps/src/compute_property_molecule.cpp
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compute_property_molecule.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_property_molecule.h"
#include "atom.h"
#include "update.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputePropertyMolecule::
ComputePropertyMolecule(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg < 4) error->all(FLERR,"Illegal compute property/molecule command");
if (atom->molecular == 0)
error->all(FLERR,"Compute property/molecule requires molecular atom style");
nvalues = narg - 3;
pack_choice = new FnPtrPack[nvalues];
int i;
for (int iarg = 3; iarg < narg; iarg++) {
i = iarg-3;
if (strcmp(arg[iarg],"mol") == 0)
pack_choice[i] = &ComputePropertyMolecule::pack_mol;
else if (strcmp(arg[iarg],"count") == 0)
pack_choice[i] = &ComputePropertyMolecule::pack_count;
else error->all(FLERR,
"Invalid keyword in compute property/molecule command");
}
// setup molecule-based data
nmolecules = molecules_in_group(idlo,idhi);
vector = NULL;
array = NULL;
if (nvalues == 1) {
memory->create(vector,nmolecules,"property/molecule:vector");
vector_flag = 1;
size_vector = nmolecules;
extvector = 0;
} else {
memory->create(array,nmolecules,nvalues,"property/molecule:array");
array_flag = 1;
size_array_rows = nmolecules;
size_array_cols = nvalues;
extarray = 0;
}
// fill vector or array with molecule values
if (nvalues == 1) {
buf = vector;
(this->*pack_choice[0])(0);
} else {
if (array) buf = &array[0][0];
for (int n = 0; n < nvalues; n++)
(this->*pack_choice[n])(n);
}
}
/* ---------------------------------------------------------------------- */
ComputePropertyMolecule::~ComputePropertyMolecule()
{
delete [] pack_choice;
memory->destroy(vector);
memory->destroy(array);
}
/* ---------------------------------------------------------------------- */
void ComputePropertyMolecule::init()
{
int ntmp = molecules_in_group(idlo,idhi);
if (ntmp != nmolecules)
error->all(FLERR,"Molecule count changed in compute property/molecule");
}
/* ---------------------------------------------------------------------- */
void ComputePropertyMolecule::compute_vector()
{
invoked_vector = update->ntimestep;
}
/* ---------------------------------------------------------------------- */
void ComputePropertyMolecule::compute_array()
{
invoked_array = update->ntimestep;
}
/* ----------------------------------------------------------------------
memory usage of local data
------------------------------------------------------------------------- */
double ComputePropertyMolecule::memory_usage()
{
double bytes = (bigint) nmolecules * nvalues * sizeof(double);
if (molmap) bytes += (idhi-idlo+1) * sizeof(int);
return bytes;
}
/* ----------------------------------------------------------------------
one method for every keyword compute property/molecule can output
the atom property is packed into buf starting at n with stride nvalues
customize a new keyword by adding a method
------------------------------------------------------------------------- */
void ComputePropertyMolecule::pack_mol(int n)
{
for (tagint m = idlo; m <= idhi; m++)
if (molmap == NULL || molmap[m-idlo] >= 0) {
buf[n] = m;
n += nvalues;
}
}
/* ---------------------------------------------------------------------- */
void ComputePropertyMolecule::pack_count(int n)
{
int i,m;
tagint imol;
int *count_one = new int[nmolecules];
for (m = 0; m < nmolecules; m++) count_one[m] = 0;
tagint *molecule = atom->molecule;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
imol = molecule[i];
if (molmap) imol = molmap[imol-idlo];
else imol--;
count_one[imol]++;
}
int *count_all = new int[nmolecules];
MPI_Allreduce(count_one,count_all,nmolecules,MPI_INT,MPI_SUM,world);
for (m = 0; m < nmolecules; m++)
if (molmap == NULL || molmap[m] >= 0) {
buf[n] = count_all[m];
n += nvalues;
}
delete [] count_one;
delete [] count_all;
}
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