lammps-sys 0.6.0

/* ----------------------------------------------------------------------
   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.
------------------------------------------------------------------------- */

#include "fix_nve_tri.h"
#include "math_extra.h"
#include "atom.h"
#include "atom_vec_tri.h"
#include "domain.h"
#include "error.h"

using namespace LAMMPS_NS;
using namespace FixConst;

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

FixNVETri::FixNVETri(LAMMPS *lmp, int narg, char **arg) :
  FixNVE(lmp, narg, arg)
{
  if (narg != 3) error->all(FLERR,"Illegal fix nve/tri command");

  time_integrate = 1;
}

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

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

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

void FixNVETri::init()
{
  // error checks

  avec = (AtomVecTri *) atom->style_match("tri");
  if (!avec) error->all(FLERR,"Fix nve/tri requires atom style tri");

  if (domain->dimension != 3)
    error->all(FLERR,"Fix nve/tri can only be used for 3d simulations");

  // check that all particles are triangles
  // no point particles allowed

  int *tri = atom->tri;
  int *mask = atom->mask;
  int nlocal = atom->nlocal;

  for (int i = 0; i < nlocal; i++)
    if (mask[i] & groupbit) {
      if (tri[i] < 0) error->one(FLERR,"Fix nve/tri requires tri particles");
    }

  FixNVE::init();
}

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

void FixNVETri::initial_integrate(int /*vflag*/)
{
  double dtfm;
  double omega[3];

  AtomVecTri::Bonus *bonus = avec->bonus;
  int *tri = atom->tri;
  double **x = atom->x;
  double **v = atom->v;
  double **f = atom->f;
  double **angmom = atom->angmom;
  double **torque = atom->torque;
  double *rmass = atom->rmass;
  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

  dtq = 0.5 * dtv;

  for (int i = 0; i < nlocal; i++)
    if (mask[i] & groupbit) {
      dtfm = dtf / rmass[i];
      v[i][0] += dtfm * f[i][0];
      v[i][1] += dtfm * f[i][1];
      v[i][2] += 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

      angmom[i][0] += dtf * torque[i][0];
      angmom[i][1] += dtf * torque[i][1];
      angmom[i][2] += dtf * torque[i][2];

      // compute omega at 1/2 step from angmom at 1/2 step and current q
      // update quaternion a full step via Richardson iteration
      // returns new normalized quaternion

      MathExtra::mq_to_omega(angmom[i],bonus[tri[i]].quat,
                             bonus[tri[i]].inertia,omega);
      MathExtra::richardson(bonus[tri[i]].quat,angmom[i],omega,
                            bonus[tri[i]].inertia,dtq);
    }
}

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

void FixNVETri::final_integrate()
{
  double dtfm;

  double **v = atom->v;
  double **f = atom->f;
  double **angmom = atom->angmom;
  double **torque = atom->torque;
  double *rmass = atom->rmass;
  int *mask = atom->mask;
  int nlocal = atom->nlocal;
  if (igroup == atom->firstgroup) nlocal = atom->nfirst;

  // update v,omega for all particles
  // d_omega/dt = torque / inertia

  for (int i = 0; i < nlocal; i++)
    if (mask[i] & groupbit) {
      dtfm = dtf / rmass[i];
      v[i][0] += dtfm * f[i][0];
      v[i][1] += dtfm * f[i][1];
      v[i][2] += dtfm * f[i][2];

      angmom[i][0] += dtf * torque[i][0];
      angmom[i][1] += dtf * torque[i][1];
      angmom[i][2] += dtf * torque[i][2];
    }
}