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

   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 "stdlib.h"

#include "math.h"

#include "fix_npt_sphere.h"

#include "atom.h"

#include "atom_vec.h"

#include "force.h"

#include "compute.h"

#include "kspace.h"

#include "update.h"

#include "domain.h"

#include "error.h"

using namespace LAMMPS_NS;

#define INERTIA 0.4          // moment of inertia for sphere

enum{NOBIAS,BIAS};

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

FixNPTSphere::FixNPTSphere(LAMMPS *lmp, int narg, char **arg) :

  FixNPT(lmp, narg, arg)

{

  if (!atom->omega_flag || !atom->torque_flag)

    error->all("Fix nvt/sphere requires atom attributes omega, torque");

  dttype = new double[atom->ntypes+1];

}

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

FixNPTSphere::~FixNPTSphere()

{

  delete [] dttype;

}

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

void FixNPTSphere::init()

{

  FixNPT::init();

  dtfrotate = dtf / INERTIA;

  if (!atom->shape)

    error->all("Fix npt/sphere requires atom attribute shape");

  double *mass = atom->mass;

  double **shape = atom->shape;

  for (int i = 1; i <= atom->ntypes; i++) {

    if (shape[i][0] != shape[i][1] || shape[i][0] != shape[i][2])

      error->all("Fix npt/sphere requires spherical particle shapes");

    dttype[i] = dtfrotate / (0.25*shape[i][0]*shape[i][0]*mass[i]);

  }

}

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

   1st half of Verlet update 

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

void FixNPTSphere::initial_integrate(int vflag)

{

  int i;

  double dtfm,dtirotate;

  double delta = update->ntimestep - update->beginstep;

  delta /= update->endstep - update->beginstep;

  // update eta_dot

  t_target = t_start + delta * (t_stop-t_start);

  f_eta = t_freq*t_freq * (t_current/t_target - 1.0);

  eta_dot += f_eta*dthalf;

  eta_dot *= drag_factor;

  eta += dtv*eta_dot;

  // update omega_dot

  // for non-varying dims, p_freq is 0.0, so omega_dot doesn't change

  double f_omega,volume;

  if (dimension == 3) volume = domain->xprd*domain->yprd*domain->zprd;

  else volume = domain->xprd*domain->yprd;

  double denskt = atom->natoms*boltz*t_target / volume * nktv2p;

  for (i = 0; i < 3; i++) {

    p_target[i] = p_start[i] + delta * (p_stop[i]-p_start[i]);

    f_omega = p_freq[i]*p_freq[i] * (p_current[i]-p_target[i])/denskt;

    omega_dot[i] += f_omega*dthalf;

    omega_dot[i] *= drag_factor;

    omega[i] += dtv*omega_dot[i];

    factor[i] = exp(-dthalf*(eta_dot+omega_dot[i]));

    dilation[i] = exp(dthalf*omega_dot[i]);

  }

  factor_rotate = exp(-dthalf*eta_dot);

  // v update only for atoms in group

  double **x = atom->x;

  double **v = atom->v;

  double **f = atom->f;

  double **omega = atom->omega;

  double **torque = atom->torque;

  double *mass = atom->mass;

  int *type = atom->type;

  int *mask = atom->mask;

  int nlocal = atom->nlocal;

  if (igroup == atom->firstgroup) nlocal = atom->nfirst;

  if (which == NOBIAS) {

    for (i = 0; i < nlocal; i++) {

      if (mask[i] & groupbit) {

	dtfm = dtf / mass[type[i]];

	v[i][0] = v[i][0]*factor[0] + dtfm*f[i][0];

	v[i][1] = v[i][1]*factor[1] + dtfm*f[i][1];

	v[i][2] = v[i][2]*factor[2] + dtfm*f[i][2];

      }

    }

  } else if (which == BIAS) {

    for (i = 0; i < nlocal; i++) {

      if (mask[i] & groupbit) {

	temperature->remove_bias(i,v[i]);

	dtfm = dtf / mass[type[i]];

	v[i][0] = v[i][0]*factor[0] + dtfm*f[i][0];

	v[i][1] = v[i][1]*factor[1] + dtfm*f[i][1];

	v[i][2] = v[i][2]*factor[2] + dtfm*f[i][2];

	temperature->restore_bias(i,v[i]);

      }

    }

  }

  // remap simulation box and all owned atoms by 1/2 step

  remap(0);

  // x update by full step only for atoms in group

  for (i = 0; i < nlocal; i++) {

    if (mask[i] & groupbit) {

      x[i][0] += dtv * v[i][0];

      x[i][1] += dtv * v[i][1];

      x[i][2] += dtv * v[i][2];

    }

  }

  // update angular momentum by 1/2 step

  // update quaternion a full step via Richardson iteration

  // returns new normalized quaternion

  for (i = 0; i < nlocal; i++) {    

    if (mask[i] & groupbit) {

      dtirotate = dttype[type[i]];

      omega[i][0] = omega[i][0]*factor_rotate + dtirotate*torque[i][0];

      omega[i][1] = omega[i][1]*factor_rotate + dtirotate*torque[i][1];

      omega[i][2] = omega[i][2]*factor_rotate + dtirotate*torque[i][2];

    }

  }

  // remap simulation box and all owned atoms by 1/2 step

  // redo KSpace coeffs since volume has changed

  remap(0);

  if (kspace_flag) force->kspace->setup();

}

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

   2nd half of Verlet update 

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

void FixNPTSphere::final_integrate()

{

  int i,itype;

  double dtfm,dtirotate;

  // v update only for atoms in group

  double **v = atom->v;

  double **f = atom->f;

  double **omega = atom->omega;

  double **torque = atom->torque;

  double *mass = atom->mass;

  int *type = atom->type;

  int *mask = atom->mask;

  int nlocal = atom->nlocal;

  if (igroup == atom->firstgroup) nlocal = atom->nfirst;

  if (which == NOBIAS) {

    for (i = 0; i < nlocal; i++) {

      if (mask[i] & groupbit) {

	itype = type[i];

	dtfm = dtf / mass[itype];

	v[i][0] = (v[i][0] + dtfm*f[i][0]) * factor[0];

	v[i][1] = (v[i][1] + dtfm*f[i][1]) * factor[1];

	v[i][2] = (v[i][2] + dtfm*f[i][2]) * factor[2];

	dtirotate = dttype[itype];

	omega[i][0] = (omega[i][0] + dtirotate*torque[i][0]) * factor_rotate;

	omega[i][1] = (omega[i][1] + dtirotate*torque[i][1]) * factor_rotate;

	omega[i][2] = (omega[i][2] + dtirotate*torque[i][2]) * factor_rotate;

      }

    }

  } else if (which == BIAS) {

    for (i = 0; i < nlocal; i++) {

      if (mask[i] & groupbit) {

	itype = type[i];

	temperature->remove_bias(i,v[i]);

	dtfm = dtf / mass[itype];

	v[i][0] = (v[i][0] + dtfm*f[i][0]) * factor[0];

	v[i][1] = (v[i][1] + dtfm*f[i][1]) * factor[1];

	v[i][2] = (v[i][2] + dtfm*f[i][2]) * factor[2];

	temperature->restore_bias(i,v[i]);

	dtirotate = dttype[itype];

	omega[i][0] = (omega[i][0] + dtirotate*torque[i][0]) * factor_rotate;

	omega[i][1] = (omega[i][1] + dtirotate*torque[i][1]) * factor_rotate;

	omega[i][2] = (omega[i][2] + dtirotate*torque[i][2]) * factor_rotate;

      }

    }

  }

  // compute new T,P

  t_current = temperature->compute_scalar();

  if (press_couple == 0) {

    double tmp = pressure->compute_scalar();

  } else {

    temperature->compute_vector();

    pressure->compute_vector();

  }

  couple();

  // trigger virial computation on next timestep

  pressure->addstep(update->ntimestep+1);

  // update eta_dot

  f_eta = t_freq*t_freq * (t_current/t_target - 1.0);

  eta_dot += f_eta*dthalf;

  eta_dot *= drag_factor;

  // update omega_dot

  // for non-varying dims, p_freq is 0.0, so omega_dot doesn't change

  double f_omega,volume;

  if (dimension == 3) volume = domain->xprd*domain->yprd*domain->zprd;

  else volume = domain->xprd*domain->yprd;

  double denskt = atom->natoms*boltz*t_target / volume * nktv2p;

  for (i = 0; i < 3; i++) {

    f_omega = p_freq[i]*p_freq[i] * (p_current[i]-p_target[i])/denskt;

    omega_dot[i] += f_omega*dthalf;

    omega_dot[i] *= drag_factor;

  }

}

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

void FixNPTSphere::reset_dt()

{

  FixNPT::reset_dt();

  dtfrotate = dtf / INERTIA;

}

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

   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.

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

#ifndef FIX_NPT_SPHERE_H

#define FIX_NPT_SPHERE_H

#include "fix_npt.h"

namespace LAMMPS_NS {

class FixNPTSphere : public FixNPT {

 public:

  FixNPTSphere(class LAMMPS *, int, char **);

  ~FixNPTSphere();

  void init();

  void initial_integrate(int);

  void final_integrate();

  void reset_dt();

 private:

  double dtfrotate;

  double *dttype;

  double factor_rotate;

};

}

#endif

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

   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 "stdlib.h"

#include "math.h"

#include "fix_nvt_sphere.h"

#include "atom.h"

#include "atom_vec.h"

#include "force.h"

#include "comm.h"

#include "group.h"

#include "update.h"

#include "modify.h"

#include "compute.h"

#include "error.h"

using namespace LAMMPS_NS;

#define INERTIA 0.4          // moment of inertia for sphere

enum{NOBIAS,BIAS};

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

FixNVTSphere::FixNVTSphere(LAMMPS *lmp, int narg, char **arg) :

  FixNVT(lmp, narg, arg)

{

  if (!atom->omega_flag || !atom->torque_flag)

    error->all("Fix nvt/sphere requires atom attributes omega, torque");

  dttype = new double[atom->ntypes+1];

}

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

FixNVTSphere::~FixNVTSphere()

{

  delete [] dttype;

}

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

void FixNVTSphere::init()

{

  FixNVT::init();

  dtfrotate = dtf / INERTIA;

  if (!atom->shape)

    error->all("Fix nvt/sphere requires atom attribute shape");

  double *mass = atom->mass;

  double **shape = atom->shape;

  for (int i = 1; i <= atom->ntypes; i++) {

    if (shape[i][0] != shape[i][1] || shape[i][0] != shape[i][2])

      error->all("Fix nvt/sphere requires spherical particle shapes");

    dttype[i] = dtfrotate / (0.25*shape[i][0]*shape[i][0]*mass[i]);

  }

}

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

void FixNVTSphere::initial_integrate(int vflag)

{

  int itype;

  double dtfm,dtirotate;

  double delta = update->ntimestep - update->beginstep;

  delta /= update->endstep - update->beginstep;

  t_target = t_start + delta * (t_stop-t_start);

  // update eta_dot

  f_eta = t_freq*t_freq * (t_current/t_target - 1.0);

  eta_dot += f_eta*dthalf;

  eta_dot *= drag_factor;

  eta += dtv*eta_dot;

  factor = exp(-dthalf*eta_dot);

  // update v and x of only atoms in group

  double **x = atom->x;

  double **v = atom->v;

  double **f = atom->f;

  double **quat = atom->quat;

  double **omega = atom->omega;

  double **torque = atom->torque;

  double *mass = atom->mass;

  int *type = atom->type;

  int *mask = atom->mask;

  int nlocal = atom->nlocal;

  if (igroup == atom->firstgroup) nlocal = atom->nfirst;

  if (which == NOBIAS) {

    for (int i = 0; i < nlocal; i++) {

      if (mask[i] & groupbit) {

	itype = type[i];

	dtfm = dtf / mass[itype];

	v[i][0] = v[i][0]*factor + dtfm*f[i][0];

	v[i][1] = v[i][1]*factor + dtfm*f[i][1];

	v[i][2] = v[i][2]*factor + dtfm*f[i][2];

	x[i][0] += dtv * v[i][0];

	x[i][1] += dtv * v[i][1];

	x[i][2] += dtv * v[i][2];

	dtirotate = dttype[itype];

	omega[i][0] = omega[i][0]*factor + dtirotate*torque[i][0];

	omega[i][1] = omega[i][1]*factor + dtirotate*torque[i][1];

	omega[i][2] = omega[i][2]*factor + dtirotate*torque[i][2];

      }

    }

  } else if (which == BIAS) {

    for (int i = 0; i < nlocal; i++) {

      if (mask[i] & groupbit) {

	itype = type[i];

	temperature->remove_bias(i,v[i]);

	dtfm = dtf / mass[itype];

	v[i][0] = v[i][0]*factor + dtfm*f[i][0];

	v[i][1] = v[i][1]*factor + dtfm*f[i][1];

	v[i][2] = v[i][2]*factor + dtfm*f[i][2];

	temperature->restore_bias(i,v[i]);

	x[i][0] += dtv * v[i][0];

	x[i][1] += dtv * v[i][1];

	x[i][2] += dtv * v[i][2];

	dtirotate = dttype[itype];

	omega[i][0] = omega[i][0]*factor + dtirotate*torque[i][0];

	omega[i][1] = omega[i][1]*factor + dtirotate*torque[i][1];

	omega[i][2] = omega[i][2]*factor + dtirotate*torque[i][2];

      }

    }

  }

}

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

void FixNVTSphere::final_integrate()

{

  int itype;

  double dtfm,dtirotate;

  // update v of only atoms in group

  double **v = atom->v;

  double **f = atom->f;

  double **omega = atom->omega;

  double **torque = atom->torque;

  double *mass = atom->mass;

  int *type = atom->type;

  int *mask = atom->mask;

  int nlocal = atom->nlocal;

  if (igroup == atom->firstgroup) nlocal = atom->nfirst;

  if (which == NOBIAS) {

    for (int i = 0; i < nlocal; i++) {

      if (mask[i] & groupbit) {

	itype = type[i];

	dtfm = dtf / mass[itype] * factor;

	v[i][0] = v[i][0]*factor + dtfm*f[i][0];

	v[i][1] = v[i][1]*factor + dtfm*f[i][1];

	v[i][2] = v[i][2]*factor + dtfm*f[i][2];

	dtirotate = dttype[itype];

	omega[i][0] = (omega[i][0] + dtirotate*torque[i][0]) * factor;

	omega[i][1] = (omega[i][1] + dtirotate*torque[i][1]) * factor;

	omega[i][2] = (omega[i][2] + dtirotate*torque[i][2]) * factor;

      }

    }

  } else {

    for (int i = 0; i < nlocal; i++) {

      if (mask[i] & groupbit) {

	itype = type[i];

	temperature->remove_bias(i,v[i]);

	dtfm = dtf / mass[itype] * factor;

	v[i][0] = v[i][0]*factor + dtfm*f[i][0];

	v[i][1] = v[i][1]*factor + dtfm*f[i][1];

	v[i][2] = v[i][2]*factor + dtfm*f[i][2];

	temperature->restore_bias(i,v[i]);

	dtirotate = dttype[itype];

	omega[i][0] = (omega[i][0] + dtirotate*torque[i][0]) * factor;

	omega[i][1] = (omega[i][1] + dtirotate*torque[i][1]) * factor;

	omega[i][2] = (omega[i][2] + dtirotate*torque[i][2]) * factor;

      }

    }

  }

  // compute current T

  t_current = temperature->compute_scalar();

  // update eta_dot

  f_eta = t_freq*t_freq * (t_current/t_target - 1.0);

  eta_dot += f_eta*dthalf;

  eta_dot *= drag_factor;

}

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

void FixNVTSphere::reset_dt()

{

  FixNVT::reset_dt();

  dtfrotate = dtf / INERTIA;

}

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

   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.

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

#ifndef FIX_NVT_SPHERE_H

#define FIX_NVT_SPHERE_H

#include "fix_nvt.h"

namespace LAMMPS_NS {

class FixNVTSphere : public FixNVT {

 public:

  FixNVTSphere(class LAMMPS *, int, char **);

  ~FixNVTSphere();

  void init();

  void initial_integrate(int);

  void final_integrate();

  void reset_dt();

 private:

  double dtfrotate;

  double *dttype;

};

}

#endif