/* ----------------------------------------------------------------------
   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)
{
  // error checks

  if (!atom->omega_flag || !atom->torque_flag)
    error->all("Fix npt/sphere requires atom attributes omega, torque");
  if (!atom->radius_flag && !atom->avec->shape_type)
    error->all("Fix npt/sphere requires atom attribute radius or shape");
}

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

void FixNPTSphere::init()
{
  int i,itype;

  // check that all particles are finite-size and spherical
  // no point particles allowed

  if (atom->radius_flag) {
    double *radius = atom->radius;
    int *mask = atom->mask;
    int nlocal = atom->nlocal;
    if (igroup == atom->firstgroup) nlocal = atom->nfirst;

    for (i = 0; i < nlocal; i++)
      if (mask[i] & groupbit) {
	if (radius[i] == 0.0)
	  error->one("Fix nvt/sphere requires extended particles");
      }

  } else {
    double **shape = atom->shape;
    int *type = atom->type;
    int *mask = atom->mask;
    int nlocal = atom->nlocal;
    if (igroup == atom->firstgroup) nlocal = atom->nfirst;

    for (i = 0; i < nlocal; i++)
      if (mask[i] & groupbit) {
	itype = type[i];
	if (shape[itype][0] == 0.0)
	  error->one("Fix nvt/sphere requires extended particles");
	if (shape[itype][0] != shape[itype][1] || 
	    shape[itype][0] != shape[itype][2])
	  error->one("Fix nvt/sphere requires spherical particle shapes");
      }
  }

  FixNPT::init();
}

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

void FixNPTSphere::initial_integrate(int vflag)
{
  int i,itype;
  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);

  // update v of atoms in group
  // for BIAS:
  //   calculate temperature since some computes require temp
  //   computed on current nlocal atoms to remove bias
  //   OK to not test returned v = 0, since factor is multiplied by v

  double **x = atom->x;
  double **v = atom->v;
  double **f = atom->f;
  double **omega = atom->omega;
  double **torque = atom->torque;
  double *radius = atom->radius;
  double *rmass = atom->rmass;
  double *mass = atom->mass;
  double **shape = atom->shape;
  int *type = atom->type;
  int *mask = atom->mask;
  int nlocal = atom->nlocal;
  if (igroup == atom->firstgroup) nlocal = atom->nfirst;

  if (rmass) {
    if (which == NOBIAS) {
      for (i = 0; i < nlocal; i++) {
	if (mask[i] & groupbit) {
	  dtfm = dtf / rmass[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 {
      double tmp = temperature->compute_scalar();
      for (i = 0; i < nlocal; i++) {
	if (mask[i] & groupbit) {
	  temperature->remove_bias(i,v[i]);
	  dtfm = dtf / rmass[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]);
	}
      }
    }

  } else {
    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 {
      double tmp = temperature->compute_scalar();
      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);

  // update x by full step 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];
    }
  }

  // set timestep here since dt may have changed or come via rRESPA

  double dtfrotate = dtf / INERTIA;

  // update omega for all particles
  // d_omega/dt = torque / inertia
  // 4 cases depending on radius vs shape and rmass vs mass

  if (radius) {
    if (rmass) {
      for (i = 0; i < nlocal; i++) {    
	if (mask[i] & groupbit) {
	  dtirotate = dtfrotate / (radius[i]*radius[i]*rmass[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];
	}
      }
    } else {
      for (i = 0; i < nlocal; i++) {    
	if (mask[i] & groupbit) {
	  dtirotate = dtfrotate / (radius[i]*radius[i]*mass[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];
	}
      }
    }

  } else {
    if (rmass) {
      for (i = 0; i < nlocal; i++) {    
	if (mask[i] & groupbit) {
	  itype = type[i];
	  dtirotate = dtfrotate / (shape[itype][0]*shape[itype][0]*rmass[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];
	}
      }
    } else {
      for (i = 0; i < nlocal; i++) {    
	if (mask[i] & groupbit) {
	  itype = type[i];
	  dtirotate = dtfrotate / 
	    (shape[itype][0]*shape[itype][0]*mass[itype]);
	  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();
}

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

void FixNPTSphere::final_integrate()
{
  int i,itype;
  double dtfm,dtirotate;

  double **v = atom->v;
  double **f = atom->f;
  double **omega = atom->omega;
  double **torque = atom->torque;
  double *radius = atom->radius;
  double *rmass = atom->rmass;
  double *mass = atom->mass;
  double **shape = atom->shape;
  int *type = atom->type;
  int *mask = atom->mask;
  int nlocal = atom->nlocal;
  if (igroup == atom->firstgroup) nlocal = atom->nfirst;

  // set timestep here since dt may have changed or come via rRESPA

  double dtfrotate = dtf / INERTIA;

  // update v,omega of atoms in group
  // d_omega/dt = torque / inertia
  // 8 cases depending on radius vs shape, rmass vs mass, bias vs nobias
  // for BIAS:
  //   calculate temperature since some computes require temp
  //   computed on current nlocal atoms to remove bias
  //   OK to not test returned v = 0, since factor is multiplied by v

  if (radius) {
    if (rmass) {
      if (which == NOBIAS) {
	for (i = 0; i < nlocal; i++) {
	  if (mask[i] & groupbit) {
	    dtfm = dtf / rmass[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];
	    
	    dtirotate = dtfrotate / (radius[i]*radius[i]*rmass[i]);
	    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 {
	double tmp = temperature->compute_scalar();
	for (i = 0; i < nlocal; i++) {
	  if (mask[i] & groupbit) {
	    temperature->remove_bias(i,v[i]);
	    dtfm = dtf / rmass[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];
	    temperature->restore_bias(i,v[i]);
	    
	    dtirotate = dtfrotate / (radius[i]*radius[i]*rmass[i]);
	    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 == 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 = dtfrotate / (radius[i]*radius[i]*mass[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 {
	for (i = 0; i < nlocal; i++) {
	  double tmp = temperature->compute_scalar();
	  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 = dtfrotate / (radius[i]*radius[i]*mass[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 (rmass) {
      if (which == NOBIAS) {
	for (i = 0; i < nlocal; i++) {
	  if (mask[i] & groupbit) {
	    itype = type[i];
	    dtfm = dtf / rmass[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];
	    
	    dtirotate = dtfrotate / (shape[itype][0]*shape[itype][0]*rmass[i]);
	    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 {
	double tmp = temperature->compute_scalar();
	for (i = 0; i < nlocal; i++) {
	  if (mask[i] & groupbit) {
	    itype = type[i];
	    temperature->remove_bias(i,v[i]);
	    dtfm = dtf / rmass[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];
	    temperature->restore_bias(i,v[i]);
	    
	    dtirotate = dtfrotate / (shape[itype][0]*shape[itype][0]*rmass[i]);
	    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 == 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 = dtfrotate / 
	      (shape[itype][0]*shape[itype][0]*mass[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 {
	double tmp = temperature->compute_scalar();
	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 = dtfrotate / 
	      (shape[itype][0]*shape[itype][0]*mass[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;
  }
}