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fix_wiggle.cpp
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Fri, Aug 16, 19:00

fix_wiggle.cpp
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/* ----------------------------------------------------------------------
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 "math.h"
#include "string.h"
#include "stdlib.h"
#include "fix_wiggle.h"
#include "atom.h"
#include "update.h"
#include "respa.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
FixWiggle::FixWiggle(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg != 6) error->all("Illegal fix wiggle command");
// parse command-line args
if (strcmp(arg[3],"x") == 0) axis = 0;
else if (strcmp(arg[3],"y") == 0) axis = 1;
else if (strcmp(arg[3],"z") == 0) axis = 2;
else error->all("Illegal fix wiggle command");
amplitude = atof(arg[4]);
period = atof(arg[5]);
// perform initial allocation of atom-based array
// register with Atom class
original = NULL;
grow_arrays(atom->nmax);
atom->add_callback(0);
// oscillation parameters
double PI = 4.0 * atan(1.0);
omega = 2.0*PI / period;
time_origin = update->ntimestep;
// original = initial atom coord in wiggled direction
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) original[i] = x[i][axis];
else original[i] = 0.0;
}
/* ---------------------------------------------------------------------- */
FixWiggle::~FixWiggle()
{
// unregister callbacks to this fix from Atom class
atom->delete_callback(id,0);
// delete locally stored array
memory->sfree(original);
}
/* ---------------------------------------------------------------------- */
int FixWiggle::setmask()
{
int mask = 0;
mask |= POST_FORCE;
mask |= POST_FORCE_RESPA;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixWiggle::init()
{
dt = update->dt;
if (strcmp(update->integrate_style,"respa") == 0)
nlevels_respa = ((Respa *) update->integrate)->nlevels;
}
/* ---------------------------------------------------------------------- */
void FixWiggle::post_force(int vflag)
{
double arg = omega * (update->ntimestep - time_origin) * dt;
double cosine = cos(arg);
double sine = sin(arg);
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
x[i][axis] = original[i] + amplitude - amplitude*cosine;
v[i][axis] = dt * amplitude*omega*sine;
f[i][axis] = 0.0;
}
}
}
/* ---------------------------------------------------------------------- */
void FixWiggle::post_force_respa(int vflag, int ilevel, int iloop)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
int FixWiggle::memory_usage()
{
int bytes = atom->nmax * sizeof(double);
return bytes;
}
/* ----------------------------------------------------------------------
allocate local atom-based array
------------------------------------------------------------------------- */
void FixWiggle::grow_arrays(int nmax)
{
original = (double *)
memory->srealloc(original,nmax*sizeof(double),"wiggle:original");
}
/* ----------------------------------------------------------------------
copy values within local atom-based array
------------------------------------------------------------------------- */
void FixWiggle::copy_arrays(int i, int j)
{
original[j] = original[i];
}
/* ----------------------------------------------------------------------
pack values in local atom-based array for exchange with another proc
------------------------------------------------------------------------- */
int FixWiggle::pack_exchange(int i, double *buf)
{
buf[0] = original[i];
return 1;
}
/* ----------------------------------------------------------------------
unpack values in local atom-based array from exchange with another proc
------------------------------------------------------------------------- */
int FixWiggle::unpack_exchange(int nlocal, double *buf)
{
original[nlocal] = buf[0];
return 1;
}

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