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

   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.

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

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

   Contributing author: Mike Brown (SNL)

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

#include "string.h"

#include "stdlib.h"

#include "math.h"

#include "fix_npt_asphere.h"

#include "math_extra.h"

#include "atom.h"

#include "force.h"

#include "compute.h"

#include "kspace.h"

#include "update.h"

#include "domain.h"

using namespace LAMMPS_NS;

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

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

  FixNPT(lmp, narg, arg)

{

  if (atom->quat == NULL || atom->angmom == NULL || atom->torque == NULL)

    error->all("Fix npt/asphere requires atom attributes "

	       "quat, angmom, torque");

}

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

void FixNPTASphere::init() 

{

  FixNPT::init();

  dtq = 0.5 * update->dt;

}

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

   1st half of Verlet update 

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

void FixNPTASphere::initial_integrate()

{

  int i;

  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;

  double denskt = (atom->natoms*boltz*t_target) / 

    (domain->xprd*domain->yprd*domain->zprd) * 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]);

  }

  ang_factor = exp(-dthalf*eta_dot);

  // v update only for atoms in NPT group

  double **x = atom->x;

  double **v = atom->v;

  double **f = atom->f;

  double **quat = atom->quat;

  double **angmom = atom->angmom;

  double **torque = atom->torque;

  double *mass = atom->mass;

  int *type = atom->type;

  int *mask = atom->mask;

  int nlocal = atom->nlocal;

  double dtfm;

  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];

    }

  }

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

  box_dilate(0);

  // x update by full step only for atoms in NPT 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) {

      angmom[i][0] = angmom[i][0] * ang_factor + dtf * torque[i][0];

      angmom[i][1] = angmom[i][1] * ang_factor + dtf * torque[i][1];

      angmom[i][2] = angmom[i][2] * ang_factor + dtf * torque[i][2];

      double inertia[3];

      calculate_inertia(atom->mass[type[i]],atom->shape[type[i]],inertia);

      richardson(quat[i],angmom[i],inertia);

    }

  }

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

  // redo KSpace coeffs since volume has changed

  box_dilate(0);

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

}

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

   2nd half of Verlet update 

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

void FixNPTASphere::final_integrate()

{

  int i;

  // v update only for atoms in NPT group

  double **v = atom->v;

  double **f = atom->f;

  double **angmom = atom->angmom;

  double **torque = atom->torque;

  double *mass = atom->mass;

  int *type = atom->type;

  int *mask = atom->mask;

  int nlocal = atom->nlocal;

  double dtfm;

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

    if (mask[i] & groupbit) {

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

      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];

      angmom[i][0] = (angmom[i][0] + dtf * torque[i][0]) * ang_factor;

      angmom[i][1] = (angmom[i][1] + dtf * torque[i][1]) * ang_factor;

      angmom[i][2] = (angmom[i][2] + dtf * torque[i][2]) * ang_factor;

    }

  }

  // compute new T,P

  t_current = temperature->compute_scalar();

  if (press_couple == 0) {

    if (ptemperature) double ptmp = ptemperature->compute_scalar();

    double tmp = pressure->compute_scalar();

  } else {

    temperature->compute_vector();

    if (ptemperature) ptemperature->compute_vector();

    pressure->compute_vector();

  }

  couple();

  // 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;

  double denskt = (atom->natoms*boltz*t_target) / 

    (domain->xprd*domain->yprd*domain->zprd) * 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;

  }

}

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

   Richardson iteration to update quaternion accurately

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

void FixNPTASphere::richardson(double *q, double *m, double *moments)

{

  // compute omega at 1/2 step from m at 1/2 step and q at 0

  double w[3];

  omega_from_mq(q,m,moments,w);

  // full update from dq/dt = 1/2 w q

  double wq[4];

  MathExtra::multiply_vec_quat(w,q,wq);

  double qfull[4];

  qfull[0] = q[0] + dtq * wq[0];

  qfull[1] = q[1] + dtq * wq[1];

  qfull[2] = q[2] + dtq * wq[2];

  qfull[3] = q[3] + dtq * wq[3];

  MathExtra::normalize4(qfull);

  // 1st half of update from dq/dt = 1/2 w q

  double qhalf[4];

  qhalf[0] = q[0] + 0.5*dtq * wq[0];

  qhalf[1] = q[1] + 0.5*dtq * wq[1];

  qhalf[2] = q[2] + 0.5*dtq * wq[2];

  qhalf[3] = q[3] + 0.5*dtq * wq[3];

  MathExtra::normalize4(qhalf);

  // re-compute omega at 1/2 step from m at 1/2 step and q at 1/2 step

  // recompute wq

  omega_from_mq(qhalf,m,moments,w);

  MathExtra::multiply_vec_quat(w,qhalf,wq);

  // 2nd half of update from dq/dt = 1/2 w q

  qhalf[0] += 0.5*dtq * wq[0];

  qhalf[1] += 0.5*dtq * wq[1];

  qhalf[2] += 0.5*dtq * wq[2];

  qhalf[3] += 0.5*dtq * wq[3];

  MathExtra::normalize4(qhalf);

  // corrected Richardson update

  q[0] = 2.0*qhalf[0] - qfull[0];

  q[1] = 2.0*qhalf[1] - qfull[1];

  q[2] = 2.0*qhalf[2] - qfull[2];

  q[3] = 2.0*qhalf[3] - qfull[3];

  MathExtra::normalize4(q);

}

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

   compute omega from angular momentum

   w = omega = angular velocity in space frame

   wbody = angular velocity in body frame

   project space-frame angular momentum onto body axes

     and divide by principal moments

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

void FixNPTASphere::omega_from_mq(double *q, double *m, double *inertia,

				  double *w)

{

  double rot[3][3];

  MathExtra::quat_to_mat(q,rot);

  double wbody[3];

  MathExtra::transpose_times_column3(rot,m,wbody);

  wbody[0] /= inertia[0];

  wbody[1] /= inertia[1];

  wbody[2] /= inertia[2];

  MathExtra::times_column3(rot,wbody,w);

}

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

   calculate the moment of inertia for an ellipsoid, from mass and radii

   shape = x,y,z radii in body frame

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

void FixNPTASphere::calculate_inertia(double mass, double *shape,

				      double *inertia)

{

  inertia[0] = mass*(shape[1]*shape[1]+shape[2]*shape[2])/5.0;

  inertia[1] = mass*(shape[0]*shape[0]+shape[2]*shape[2])/5.0;

  inertia[2] = mass*(shape[0]*shape[0]+shape[1]*shape[1])/5.0;

}

   See the README file in the top-level LAMMPS directory.

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

#ifndef FIX_VOL_RESCALE_H

#define FIX_VOL_RESCALE_H

#ifndef FIX_NPT_ASPHERE_H

#define FIX_NPT_ASPHERE_H

#include "fix.h"

#include "fix_npt.h"

namespace LAMMPS_NS {

class FixVolRescale : public Fix {

class FixNPTASphere : public FixNPT {

 public:

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

  ~FixVolRescale();

  int setmask();

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

  ~FixNPTASphere() {}

  void init();

  void end_of_step();

  void initial_integrate();

  void final_integrate();

 private:

  int xflag,yflag,zflag;

  double xlo_start,xlo_stop,xhi_start,xhi_stop;

  double ylo_start,ylo_stop,yhi_start,yhi_stop;

  double zlo_start,zlo_stop,zhi_start,zhi_stop;

  int kspace_flag;                 // 1 if KSpace invoked, 0 if not

  int nrigid;                      // number of rigid fixes

  int *rfix;                       // indices of rigid fixes

  double dtq;

  double ang_factor;

  void richardson(double *, double *, double *);

  void omega_from_mq(double *, double *, double *, double *);

  void calculate_inertia(double mass, double *shape, double *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.

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

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

   Contributing author: Mike Brown (SNL)

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

#include "string.h"

#include "stdlib.h"

#include "math.h"

#include "fix_nvt_asphere.h"

#include "math_extra.h"

#include "atom.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;

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

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

  FixNVT(lmp, narg, arg)

{

  if (atom->quat == NULL || atom->angmom == NULL || atom->torque == NULL)

    error->all("Fix nvt/asphere requires atom attributes "

	       "quat, angmom, torque");

}

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

void FixNVTASphere::init()

{

  FixNVT::init();

  dtq = 0.5 * update->dt;

}

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

void FixNVTASphere::initial_integrate()

{

  double dtfm;

  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 NVT group

  double **x = atom->x;

  double **v = atom->v;

  double **f = atom->f;

  double **quat = atom->quat;

  double **angmom = atom->angmom;

  double **torque = atom->torque;

  double *mass = atom->mass;

  int *type = atom->type;

  int *mask = atom->mask;

  int nlocal = atom->nlocal;

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

    if (mask[i] & groupbit) {

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

      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];

      // update angular momentum by 1/2 step

      // update quaternion a full step via Richardson iteration

      // returns new normalized quaternion

      angmom[i][0] = angmom[i][0] * factor + dtf * torque[i][0];

      angmom[i][1] = angmom[i][1] * factor + dtf * torque[i][1];

      angmom[i][2] = angmom[i][2] * factor + dtf * torque[i][2];

      double inertia[3];

      calculate_inertia(atom->mass[type[i]],atom->shape[type[i]],inertia);

      richardson(quat[i],angmom[i],inertia);

    }

  }

}

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

void FixNVTASphere::final_integrate()

{

  double dtfm;

  // update v of only atoms in NVT group

  double **v = atom->v;

  double **f = atom->f;

  double **angmom = atom->angmom;

  double **torque = atom->torque;

  double *mass = atom->mass;

  int *type = atom->type;

  int *mask = atom->mask;

  int nlocal = atom->nlocal;

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

    if (mask[i] & groupbit) {

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

      angmom[i][0] = angmom[i][0] * factor + dtf * torque[i][0];

      angmom[i][1] = angmom[i][1] * factor + dtf * torque[i][1];

      angmom[i][2] = angmom[i][2] * factor + dtf * torque[i][2];

    }

  }

  // 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;

}

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

   Richardson iteration to update quaternion accurately

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

void FixNVTASphere::richardson(double *q, double *m, double *moments)

{

  // compute omega at 1/2 step from m at 1/2 step and q at 0

  double w[3];

  omega_from_mq(q,m,moments,w);

  // full update from dq/dt = 1/2 w q

  double wq[4];

  MathExtra::multiply_vec_quat(w,q,wq);

  double qfull[4];

  qfull[0] = q[0] + dtq * wq[0];

  qfull[1] = q[1] + dtq * wq[1];

  qfull[2] = q[2] + dtq * wq[2];

  qfull[3] = q[3] + dtq * wq[3];

  MathExtra::normalize4(qfull);

  // 1st half of update from dq/dt = 1/2 w q

  double qhalf[4];

  qhalf[0] = q[0] + 0.5*dtq * wq[0];

  qhalf[1] = q[1] + 0.5*dtq * wq[1];

  qhalf[2] = q[2] + 0.5*dtq * wq[2];

  qhalf[3] = q[3] + 0.5*dtq * wq[3];

  MathExtra::normalize4(qhalf);

  // re-compute omega at 1/2 step from m at 1/2 step and q at 1/2 step

  // recompute wq

  omega_from_mq(qhalf,m,moments,w);

  MathExtra::multiply_vec_quat(w,qhalf,wq);

  // 2nd half of update from dq/dt = 1/2 w q

  qhalf[0] += 0.5*dtq * wq[0];

  qhalf[1] += 0.5*dtq * wq[1];

  qhalf[2] += 0.5*dtq * wq[2];

  qhalf[3] += 0.5*dtq * wq[3];

  MathExtra::normalize4(qhalf);

  // corrected Richardson update

  q[0] = 2.0*qhalf[0] - qfull[0];

  q[1] = 2.0*qhalf[1] - qfull[1];

  q[2] = 2.0*qhalf[2] - qfull[2];

  q[3] = 2.0*qhalf[3] - qfull[3];

  MathExtra::normalize4(q);

}

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

   compute omega from angular momentum

   w = omega = angular velocity in space frame

   wbody = angular velocity in body frame

   project space-frame angular momentum onto body axes

     and divide by principal moments

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

void FixNVTASphere::omega_from_mq(double *q, double *m, double *inertia,

				  double *w)

{

  double rot[3][3];

  MathExtra::quat_to_mat(q,rot);

  double wbody[3];

  MathExtra::transpose_times_column3(rot,m,wbody);

  wbody[0] /= inertia[0];

  wbody[1] /= inertia[1];

  wbody[2] /= inertia[2];

  MathExtra::times_column3(rot,wbody,w);

}

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

   calculate the moment of inertia for an ELLIPSOID, from mass and radii

   shape = x,y,z radii in body frame

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

void FixNVTASphere::calculate_inertia(double mass, double *shape,

				      double *inertia)

{

  inertia[0] = mass*(shape[1]*shape[1]+shape[2]*shape[2])/5.0;

  inertia[1] = mass*(shape[0]*shape[0]+shape[2]*shape[2])/5.0;

  inertia[2] = mass*(shape[0]*shape[0]+shape[1]*shape[1])/5.0;

}

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

   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_ASPHERE_H

#define FIX_NVT_ASPHERE_H

#include "fix_nvt.h"

namespace LAMMPS_NS {

class FixNVTASphere : public FixNVT {

 public:

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

  ~FixNVTASphere() {}

  void init();

  void initial_integrate();

  void final_integrate();

 private:

  double dtq;

  void richardson(double *, double *, double *);