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_limit.h"
#include <mpi.h>
#include <cmath>
#include <cstring>
#include "atom.h"
#include "force.h"
#include "update.h"
#include "respa.h"
#include "modify.h"
#include "comm.h"
#include "error.h"
#include "utils.h"

using namespace LAMMPS_NS;
using namespace FixConst;

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

FixNVELimit::FixNVELimit(LAMMPS *lmp, int narg, char **arg) :
  Fix(lmp, narg, arg)
{
  if (narg != 4) error->all(FLERR,"Illegal fix nve/limit command");

  time_integrate = 1;
  scalar_flag = 1;
  global_freq = 1;
  extscalar = 1;
  dynamic_group_allow = 1;

  xlimit = force->numeric(FLERR,arg[3]);

  ncount = 0;
}

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

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

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

void FixNVELimit::init()
{
  dtv = update->dt;
  dtf = 0.5 * update->dt * force->ftm2v;
  vlimitsq = (xlimit/dtv) * (xlimit/dtv);
  ncount = 0;

  if (strstr(update->integrate_style,"respa"))
    step_respa = ((Respa *) update->integrate)->step;

  // warn if using fix shake, which will lead to invalid constraint forces

  for (int i = 0; i < modify->nfix; i++)
    if (utils::strmatch(modify->fix[i]->style,"^shake")
        || utils::strmatch(modify->fix[i]->style,"^rattle")) {
      if (comm->me == 0)
        error->warning(FLERR,"Should not use fix nve/limit with fix shake or fix rattle");
    }
}

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

void FixNVELimit::initial_integrate(int /*vflag*/)
{
  double dtfm,vsq,scale;

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

  if (rmass) {
    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];

        vsq = v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2];
        if (vsq > vlimitsq) {
          ncount++;
          scale = sqrt(vlimitsq/vsq);
          v[i][0] *= scale;
          v[i][1] *= scale;
          v[i][2] *= scale;
        }

        x[i][0] += dtv * v[i][0];
        x[i][1] += dtv * v[i][1];
        x[i][2] += dtv * v[i][2];
      }
    }

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

        vsq = v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2];
        if (vsq > vlimitsq) {
          ncount++;
          scale = sqrt(vlimitsq/vsq);
          v[i][0] *= scale;
          v[i][1] *= scale;
          v[i][2] *= scale;
        }

        x[i][0] += dtv * v[i][0];
        x[i][1] += dtv * v[i][1];
        x[i][2] += dtv * v[i][2];
      }
    }
  }
}

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

void FixNVELimit::final_integrate()
{
  double dtfm,vsq,scale;

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

  if (rmass) {
    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];

        vsq = v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2];
        if (vsq > vlimitsq) {
          ncount++;
          scale = sqrt(vlimitsq/vsq);
          v[i][0] *= scale;
          v[i][1] *= scale;
          v[i][2] *= scale;
        }
      }
    }

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

        vsq = v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2];
        if (vsq > vlimitsq) {
          ncount++;
          scale = sqrt(vlimitsq/vsq);
          v[i][0] *= scale;
          v[i][1] *= scale;
          v[i][2] *= scale;
        }
      }
    }
  }
}

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

void FixNVELimit::initial_integrate_respa(int vflag, int ilevel, int /*iloop*/)
{
  dtv = step_respa[ilevel];
  dtf = 0.5 * step_respa[ilevel] * force->ftm2v;

  if (ilevel == 0) initial_integrate(vflag);
  else final_integrate();
}

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

void FixNVELimit::final_integrate_respa(int ilevel, int /*iloop*/)
{
  dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
  final_integrate();
}

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

void FixNVELimit::reset_dt()
{
  dtv = update->dt;
  dtf = 0.5 * update->dt * force->ftm2v;
  vlimitsq = (xlimit/dtv) * (xlimit/dtv);
}

/* ----------------------------------------------------------------------
   energy of indenter interaction
------------------------------------------------------------------------- */

double FixNVELimit::compute_scalar()
{
  double one = ncount;
  double all;
  MPI_Allreduce(&one,&all,1,MPI_DOUBLE,MPI_SUM,world);
  return all;
}