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sjplimp
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "compute_force_molecule.h"
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#include "atom.h"
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#include "update.h"
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#include "domain.h"
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#include "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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ComputeForceMolecule::ComputeForceMolecule(LAMMPS *lmp, int narg, char **arg) :
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Compute(lmp, narg, arg)
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{
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if (narg != 3) error->all(FLERR,"Illegal compute force/molecule command");
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if (atom->molecular == 0)
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error->all(FLERR,"Compute force/molecule requires molecular atom style");
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array_flag = 1;
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size_array_cols = 3;
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extarray = 0;
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// setup molecule-based data
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nmolecules = molecules_in_group(idlo,idhi);
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size_array_rows = nmolecules;
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memory->create(force,nmolecules,3,"force/molecule:force");
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memory->create(forceall,nmolecules,3,"force/molecule:forceall");
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array = forceall;
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}
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/* ---------------------------------------------------------------------- */
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ComputeForceMolecule::~ComputeForceMolecule()
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{
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memory->destroy(force);
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memory->destroy(forceall);
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}
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/* ---------------------------------------------------------------------- */
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void ComputeForceMolecule::init()
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{
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int ntmp = molecules_in_group(idlo,idhi);
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if (ntmp != nmolecules)
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error->all(FLERR,"Molecule count changed in compute force/molecule");
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}
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/* ---------------------------------------------------------------------- */
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void ComputeForceMolecule::compute_array()
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{
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tagint imol;
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double massone;
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double unwrap[3];
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invoked_array = update->ntimestep;
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for (int i = 0; i < nmolecules; i++)
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force[i][0] = force[i][1] = force[i][2] = 0.0;
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double **f = atom->f;
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int *mask = atom->mask;
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tagint *molecule = atom->molecule;
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int nlocal = atom->nlocal;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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imol = molecule[i];
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if (molmap) imol = molmap[imol-idlo];
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else imol--;
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force[imol][0] += f[i][0];
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force[imol][1] += f[i][1];
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force[imol][2] += f[i][2];
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}
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MPI_Allreduce(&force[0][0],&forceall[0][0],3*nmolecules,
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MPI_DOUBLE,MPI_SUM,world);
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}
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/* ----------------------------------------------------------------------
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memory usage of local data
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------------------------------------------------------------------------- */
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double ComputeForceMolecule::memory_usage()
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{
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double bytes = 0;
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if (molmap) bytes += (idhi-idlo+1) * sizeof(int);
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bytes += (bigint) nmolecules * 2*3 * sizeof(double);
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return bytes;
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}
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/* -*- c++ -*- ----------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#ifdef COMPUTE_CLASS
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ComputeStyle(force/molecule,ComputeForceMolecule)
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#else
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#ifndef LMP_COMPUTE_FORCE_MOLECULE_H
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#define LMP_COMPUTE_FORCE_MOLECULE_H
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#include "compute.h"
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namespace LAMMPS_NS {
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class ComputeForceMolecule : public Compute {
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public:
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ComputeForceMolecule(class LAMMPS *, int, char **);
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~ComputeForceMolecule();
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void init();
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void compute_array();
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double memory_usage();
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private:
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int nmolecules;
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tagint idlo,idhi;
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double **force,**forceall;
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};
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}
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#endif
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#endif
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/* ERROR/WARNING messages:
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E: Illegal ... command
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Self-explanatory. Check the input script syntax and compare to the
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documentation for the command. You can use -echo screen as a
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command-line option when running LAMMPS to see the offending line.
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E: Compute force/molecule requires molecular atom style
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Self-explanatory.
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E: Molecule count changed in compute force/molecule
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Number of molecules must remain constant over time.
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*/
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@ -0,0 +1,147 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "compute_vcm_molecule.h"
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#include "atom.h"
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#include "update.h"
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#include "domain.h"
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#include "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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ComputeVCMMolecule::ComputeVCMMolecule(LAMMPS *lmp, int narg, char **arg) :
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Compute(lmp, narg, arg)
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{
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if (narg != 3) error->all(FLERR,"Illegal compute vcm/molecule command");
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if (atom->molecular == 0)
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error->all(FLERR,"Compute vcm/molecule requires molecular atom style");
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array_flag = 1;
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size_array_cols = 3;
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extarray = 0;
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// setup molecule-based data
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nmolecules = molecules_in_group(idlo,idhi);
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size_array_rows = nmolecules;
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memory->create(massproc,nmolecules,"vcm/molecule:massproc");
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memory->create(masstotal,nmolecules,"vcm/molecule:masstotal");
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memory->create(vcm,nmolecules,3,"vcm/molecule:vcm");
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memory->create(vcmall,nmolecules,3,"vcm/molecule:vcmall");
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array = vcmall;
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// compute masstotal for each molecule
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int *mask = atom->mask;
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tagint *molecule = atom->molecule;
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int *type = atom->type;
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double *mass = atom->mass;
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double *rmass = atom->rmass;
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int nlocal = atom->nlocal;
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tagint imol;
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double massone;
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for (int i = 0; i < nmolecules; i++) massproc[i] = 0.0;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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if (rmass) massone = rmass[i];
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else massone = mass[type[i]];
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imol = molecule[i];
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if (molmap) imol = molmap[imol-idlo];
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else imol--;
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massproc[imol] += massone;
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}
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MPI_Allreduce(massproc,masstotal,nmolecules,MPI_DOUBLE,MPI_SUM,world);
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}
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/* ---------------------------------------------------------------------- */
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ComputeVCMMolecule::~ComputeVCMMolecule()
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{
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memory->destroy(massproc);
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memory->destroy(masstotal);
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memory->destroy(vcm);
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memory->destroy(vcmall);
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}
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/* ---------------------------------------------------------------------- */
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void ComputeVCMMolecule::init()
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{
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int ntmp = molecules_in_group(idlo,idhi);
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if (ntmp != nmolecules)
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error->all(FLERR,"Molecule count changed in compute vcm/molecule");
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}
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/* ---------------------------------------------------------------------- */
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void ComputeVCMMolecule::compute_array()
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{
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tagint imol;
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double massone;
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double unwrap[3];
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invoked_array = update->ntimestep;
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for (int i = 0; i < nmolecules; i++)
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vcm[i][0] = vcm[i][1] = vcm[i][2] = 0.0;
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double **v = atom->v;
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int *mask = atom->mask;
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tagint *molecule = atom->molecule;
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int *type = atom->type;
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imageint *image = atom->image;
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double *mass = atom->mass;
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double *rmass = atom->rmass;
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int nlocal = atom->nlocal;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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if (rmass) massone = rmass[i];
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else massone = mass[type[i]];
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imol = molecule[i];
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if (molmap) imol = molmap[imol-idlo];
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else imol--;
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vcm[imol][0] += v[i][0] * massone;
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vcm[imol][1] += v[i][1] * massone;
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vcm[imol][2] += v[i][2] * massone;
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}
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MPI_Allreduce(&vcm[0][0],&vcmall[0][0],3*nmolecules,
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MPI_DOUBLE,MPI_SUM,world);
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for (int i = 0; i < nmolecules; i++) {
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vcmall[i][0] /= masstotal[i];
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vcmall[i][1] /= masstotal[i];
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vcmall[i][2] /= masstotal[i];
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}
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}
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/* ----------------------------------------------------------------------
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memory usage of local data
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------------------------------------------------------------------------- */
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double ComputeVCMMolecule::memory_usage()
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{
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double bytes = (bigint) nmolecules * 2 * sizeof(double);
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if (molmap) bytes += (idhi-idlo+1) * sizeof(int);
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bytes += (bigint) nmolecules * 2*3 * sizeof(double);
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return bytes;
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}
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@ -0,0 +1,64 @@
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/* -*- c++ -*- ----------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#ifdef COMPUTE_CLASS
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ComputeStyle(vcm/molecule,ComputeVCMMolecule)
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#else
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#ifndef LMP_COMPUTE_VCM_MOLECULE_H
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#define LMP_COMPUTE_VCM_MOLECULE_H
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#include "compute.h"
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namespace LAMMPS_NS {
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class ComputeVCMMolecule : public Compute {
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public:
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ComputeVCMMolecule(class LAMMPS *, int, char **);
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~ComputeVCMMolecule();
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void init();
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void compute_array();
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double memory_usage();
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private:
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int nmolecules;
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tagint idlo,idhi;
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double *massproc,*masstotal;
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double **vcm,**vcmall;
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};
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}
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#endif
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#endif
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/* ERROR/WARNING messages:
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E: Illegal ... command
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Self-explanatory. Check the input script syntax and compare to the
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documentation for the command. You can use -echo screen as a
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command-line option when running LAMMPS to see the offending line.
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E: Compute vcm/molecule requires molecular atom style
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Self-explanatory.
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E: Molecule count changed in compute vcm/molecule
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Number of molecules must remain constant over time.
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*/
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