/* ----------------------------------------------------------------------
   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 "compute_ke_molecule.h"
#include "atom.h"
#include "update.h"
#include "force.h"
#include "domain.h"
#include "memory.h"
#include "error.h"

using namespace LAMMPS_NS;

/* ---------------------------------------------------------------------- */

ComputeKEMolecule::ComputeKEMolecule(LAMMPS *lmp, int narg, char **arg) :
  Compute(lmp, narg, arg)
{
  if (narg != 3) error->all("Illegal compute ke/molecule command");

  if (atom->molecular == 0)
    error->all("Compute ke/molecule requires molecular atom style");

  vector_flag = 1;
  extvector = 0; 

  // setup molecule-based data

  nmolecules = molecules_in_group(idlo,idhi);
  size_vector = nmolecules;

  ke = (double *) memory->smalloc(nmolecules*sizeof(double),
                                     "ke/molecule:ke");
  keall = (double *) memory->smalloc(nmolecules*sizeof(double),
                                     "ke/molecule:keall");
  vector = keall;
}

/* ---------------------------------------------------------------------- */

ComputeKEMolecule::~ComputeKEMolecule()
{
  memory->sfree(ke);
  memory->sfree(keall);
}

/* ---------------------------------------------------------------------- */

void ComputeKEMolecule::init()
{
  int ntmp = molecules_in_group(idlo,idhi);
  if (ntmp != nmolecules)
    error->all("Molecule count changed in compute ke/molecule");
  pfactor = 0.5 * force->mvv2e;
}

/* ---------------------------------------------------------------------- */

void ComputeKEMolecule::compute_vector()
{
  int i,imol;
  double massone;
 
  invoked_array = update->ntimestep;

  int *mask = atom->mask;
  int *molecule = atom->molecule;
  int *type = atom->type;
  double **v = atom->v;
  double *rmass = atom->rmass;
  double *mass = atom->mass;
  int nlocal = atom->nlocal;

  for (i = 0; i < nmolecules; i++) ke[i] = 0.0;  

  for (int i = 0; i < nlocal; i++)
    if (mask[i] & groupbit) {
      imol = molecule[i];
      if (molmap) imol = molmap[imol-idlo];
      else imol--;
      if (rmass) massone = rmass[i];
      else massone = mass[type[i]];
      ke[imol] += massone * (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]);
    }

  MPI_Allreduce(ke,keall,nmolecules,MPI_DOUBLE,MPI_SUM,world);

  for (i = 0; i < nmolecules; i++) keall[i] = ke[i] * pfactor;
}