Add files via upload

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

   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 <cmath>

#include "compute_gyration.h"

#include "update.h"

#include "atom.h"

#include "group.h"

#include "domain.h"

#include "error.h"

using namespace LAMMPS_NS;

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

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

  Compute(lmp, narg, arg)

{

  if (narg != 3) error->all(FLERR,"Illegal compute gyration command");

  scalar_flag = vector_flag = 1;

  size_vector = 6;

  extscalar = 0;

  extvector = 0;

  vector = new double[6];

}

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

ComputeGyration::~ComputeGyration()

{

  delete [] vector;

}

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

void ComputeGyration::init()

{

  masstotal = group->mass(igroup);

}

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

double ComputeGyration::compute_scalar()

{

  invoked_scalar = update->ntimestep;

  double xcm[3];

  if (group->dynamic[igroup]) masstotal = group->mass(igroup);

  group->xcm(igroup,masstotal,xcm);

  scalar = group->gyration(igroup,masstotal,xcm);

  return scalar;

}

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

   compute the radius-of-gyration tensor of group of atoms

   around center-of-mass cm

   must unwrap atoms to compute Rg tensor correctly

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

void ComputeGyration::compute_vector()

{

  invoked_vector = update->ntimestep;

  double xcm[3];

  group->xcm(igroup,masstotal,xcm);

  double **x = atom->x;

  int *mask = atom->mask;

  int *type = atom->type;

  imageint *image = atom->image;

  double *mass = atom->mass;

  double *rmass = atom->rmass;

  int nlocal = atom->nlocal;

  double dx,dy,dz,massone;

  double unwrap[3];

  double rg[6];

  rg[0] = rg[1] = rg[2] = rg[3] = rg[4] = rg[5] = 0.0;

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

    if (mask[i] & groupbit) {

      if (rmass) massone = rmass[i];

      else massone = mass[type[i]];

      domain->unmap(x[i],image[i],unwrap);

      dx = unwrap[0] - xcm[0];

      dy = unwrap[1] - xcm[1];

      dz = unwrap[2] - xcm[2];

      rg[0] += dx*dx * massone;

      rg[1] += dy*dy * massone;

      rg[2] += dz*dz * massone;

      rg[3] += dx*dy * massone;

      rg[4] += dx*dz * massone;

      rg[5] += dy*dz * massone;

    }

  MPI_Allreduce(rg,vector,6,MPI_DOUBLE,MPI_SUM,world);

  if (masstotal > 0.0)

    for (int i = 0; i < 6; i++)

      vector[i] /= masstotal;

}

/* -*- c++ -*- ----------------------------------------------------------

   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.

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

#ifdef COMPUTE_CLASS

ComputeStyle(gyration/shape,ComputeGyrationShape)

#else

#ifndef LMP_COMPUTE_GYRATION_SHAPE_H

#define LMP_COMPUTE_GYRATION_SHAPE_H

#include "compute.h"

namespace LAMMPS_NS {

class ComputeGyrationShape : public Compute {

 public:

  char *id_gyration;              // fields accessed by other classes

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

  ~ComputeGyrationShape();

  void init();

  void compute_vector();

 private:

  class Compute *c_gyration;

};

}

#endif

#endif

/* ERROR/WARNING messages:

E: Illegal ... command

Self-explanatory.  Check the input script syntax and compare to the

documentation for the command.  You can use -echo screen as a

command-line option when running LAMMPS to see the offending line.

*/