/* ----------------------------------------------------------------------
   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("Illegal compute property/molecule command");

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

  nvalues = narg - 3;
  if (nvalues == 1) size_array_cols = 0;

  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 error->all("Invalid keyword in compute property/molecule command");
  }

  // setup molecule-based data

  nmolecules = molecules_in_group(idlo,idhi);

  vector = NULL;
  array = NULL;

  if (nvalues == 1) {
    vector = (double *) memory->smalloc(nmolecules*sizeof(double),
					"property/molecule:vector");
    vector_flag = 1;
    size_vector = nmolecules;
    extvector = 0;
  } else {
    array = memory->create_2d_double_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->sfree(vector);
  memory->destroy_2d_double_array(array);
}

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

void ComputePropertyMolecule::init()
{
  int ntmp = molecules_in_group(idlo,idhi);
  if (ntmp != nmolecules)
    error->all("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 = 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 (int i = idlo; i <= idhi; i++)
    if (molmap[i-idlo] >= 0) {
      buf[n] = i;
      n += nvalues;
    }
}