/* ----------------------------------------------------------------------
   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 "stdio.h"
#include "string.h"
#include "fix_overdamp.h"
#include "atom.h"
#include "force.h"
#include "update.h"
#include "respa.h"
#include "error.h"
#include "math_extra.h"
#include "domain.h"

using namespace LAMMPS_NS;

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

FixOverdamp::FixOverdamp(LAMMPS *lmp, int narg, char **arg) :
  Fix(lmp, narg, arg)
{
  if (narg != 3) error->all("Illegal fix nve command");
}

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

int FixOverdamp::setmask()
{
  int mask = 0;
  mask |= INITIAL_INTEGRATE;
  mask |= FINAL_INTEGRATE;
  mask |= INITIAL_INTEGRATE_RESPA;
  mask |= FINAL_INTEGRATE_RESPA;
  return mask;
}

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

void FixOverdamp::init()
{
  dtv = update->dt;
  dtf = 0.5 * update->dt * force->ftm2v;
  dtq = 0.5 * update->dt;

}

/* ----------------------------------------------------------------------
   allow for both per-type and per-atom mass
------------------------------------------------------------------------- */

void FixOverdamp::initial_integrate()
{
}
/* ---------------------------------------------------------------------- */

void FixOverdamp::final_integrate()
{
  double dtfm;

  // update vthermal of only atoms in NVT group
  // lamda = 0-1 triclinic lamda coords
  // vstream = streaming velocity = Hrate*lamda + Hratelo
  // vthermal = thermal velocity = v - vstream
  // vdelu = Hrate*Hinv*vthermal

  double **x = atom->x;
  double **v = atom->v;
  double **f = atom->f;
  double *mass = atom->mass;
  int *type = atom->type;
  int *mask = atom->mask;
  int nlocal = atom->nlocal;

  double *h_rate = domain->h_rate;
  double *h_ratelo = domain->h_ratelo;
  double h_two[6],lamda[3],vstream[3],vthermal[3],vdelu[3];
  MathExtra::multiply_shape_shape(h_rate,domain->h_inv,h_two);

  for (int i = 0; i < nlocal; i++) {
    if (mask[i] & groupbit) {
      domain->x2lamda(x[i],lamda);
      vstream[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] + 
        h_rate[4]*lamda[2] + h_ratelo[0];
      vstream[1] = h_rate[1]*lamda[1] + h_rate[3]*lamda[2] + h_ratelo[1];
      vstream[2] = h_rate[2]*lamda[2] + h_ratelo[2];
      v[i][0] = vstream[0] + f[i][0];
      v[i][1] = vstream[1] + f[i][1];
      v[i][2] = vstream[2] + f[i][2];
      x[i][0] += dtv*v[i][0];
      x[i][1] += dtv*v[i][1];
      x[i][2] += dtv*v[i][2];

    }
  }
}

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

void FixOverdamp::reset_dt()
{
  dtv = update->dt;
  dtf = 0.5 * update->dt * force->ftm2v;
  dtq = 0.5 * update->dt;
}