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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12763 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2014-11-20 21:26:10 +00:00
parent f0259bd27e
commit 3d3a85df2b
2 changed files with 0 additions and 169 deletions
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106
src/compute_force_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 "compute_force_molecule.h"
#include "atom.h"
#include "update.h"
#include "domain.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeForceMolecule::ComputeForceMolecule(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 3) error->all(FLERR,"Illegal compute force/molecule command");
if (atom->molecular == 0)
error->all(FLERR,"Compute force/molecule requires molecular atom style");
array_flag = 1;
size_array_cols = 3;
extarray = 0;
// setup molecule-based data
nmolecules = molecules_in_group(idlo,idhi);
size_array_rows = nmolecules;
memory->create(force,nmolecules,3,"force/molecule:force");
memory->create(forceall,nmolecules,3,"force/molecule:forceall");
array = forceall;
}
/* ---------------------------------------------------------------------- */
ComputeForceMolecule::~ComputeForceMolecule()
{
memory->destroy(force);
memory->destroy(forceall);
}
/* ---------------------------------------------------------------------- */
void ComputeForceMolecule::init()
{
int ntmp = molecules_in_group(idlo,idhi);
if (ntmp != nmolecules)
error->all(FLERR,"Molecule count changed in compute force/molecule");
}
/* ---------------------------------------------------------------------- */
void ComputeForceMolecule::compute_array()
{
tagint imol;
double massone;
double unwrap[3];
invoked_array = update->ntimestep;
for (int i = 0; i < nmolecules; i++)
force[i][0] = force[i][1] = force[i][2] = 0.0;
double **f = atom->f;
int *mask = atom->mask;
tagint *molecule = atom->molecule;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
imol = molecule[i];
if (molmap) imol = molmap[imol-idlo];
else imol--;
force[imol][0] += f[i][0];
force[imol][1] += f[i][1];
force[imol][2] += f[i][2];
}
MPI_Allreduce(&force[0][0],&forceall[0][0],3*nmolecules,
MPI_DOUBLE,MPI_SUM,world);
}
/* ----------------------------------------------------------------------
memory usage of local data
------------------------------------------------------------------------- */
double ComputeForceMolecule::memory_usage()
{
double bytes = 0;
if (molmap) bytes += (idhi-idlo+1) * sizeof(int);
bytes += (bigint) nmolecules * 2*3 * sizeof(double);
return bytes;
}

63
src/compute_force_molecule.h
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/* -*- c++ -*- ----------------------------------------------------------
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.
------------------------------------------------------------------------- */
#ifdef COMPUTE_CLASS
ComputeStyle(force/molecule,ComputeForceMolecule)
#else
#ifndef LMP_COMPUTE_FORCE_MOLECULE_H
#define LMP_COMPUTE_FORCE_MOLECULE_H
#include "compute.h"
namespace LAMMPS_NS {
class ComputeForceMolecule : public Compute {
public:
ComputeForceMolecule(class LAMMPS *, int, char **);
~ComputeForceMolecule();
void init();
void compute_array();
double memory_usage();
private:
int nmolecules;
tagint idlo,idhi;
double **force,**forceall;
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Compute force/molecule requires molecular atom style
Self-explanatory.
E: Molecule count changed in compute force/molecule
Number of molecules must remain constant over time.
*/