176 lines
4.8 KiB
C++
176 lines
4.8 KiB
C++
/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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www.cs.sandia.gov/~sjplimp/lammps.html
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Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "math.h"
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#include "string.h"
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#include "stdlib.h"
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#include "fix_wiggle.h"
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#include "atom.h"
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#include "update.h"
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#include "respa.h"
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#include "memory.h"
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#include "error.h"
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/* ---------------------------------------------------------------------- */
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FixWiggle::FixWiggle(int narg, char **arg) : Fix(narg, arg)
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{
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if (narg != 6) error->all("Illegal fix wiggle command");
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// parse command-line args
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if (strcmp(arg[3],"x") == 0) axis = 0;
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else if (strcmp(arg[3],"y") == 0) axis = 1;
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else if (strcmp(arg[3],"z") == 0) axis = 2;
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else error->all("Illegal fix wiggle command");
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amplitude = atof(arg[4]);
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period = atof(arg[5]);
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// perform initial allocation of atom-based array
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// register with atom class
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original = NULL;
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grow_arrays(atom->nmax);
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atom->add_callback(0);
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// oscillation parameters
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double PI = 4.0 * atan(1.0);
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omega = 2.0*PI / period;
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time_origin = update->ntimestep;
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// original = initial atom coord in wiggled direction
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double **x = atom->x;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) original[i] = x[i][axis];
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else original[i] = 0.0;
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}
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/* ---------------------------------------------------------------------- */
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FixWiggle::~FixWiggle()
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{
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// if atom class still exists:
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// unregister this fix so atom class doesn't invoke it any more
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if (atom) atom->delete_callback(id,0);
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// delete locally stored array
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memory->sfree(original);
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}
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/* ---------------------------------------------------------------------- */
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int FixWiggle::setmask()
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{
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int mask = 0;
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mask |= POST_FORCE;
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mask |= POST_FORCE_RESPA;
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return mask;
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}
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/* ---------------------------------------------------------------------- */
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void FixWiggle::init()
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{
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dt = update->dt;
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if (strcmp(update->integrate_style,"respa") == 0)
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nlevels_respa = ((Respa *) update->integrate)->nlevels;
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}
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/* ---------------------------------------------------------------------- */
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void FixWiggle::post_force(int vflag)
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{
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double arg = omega * (update->ntimestep - time_origin) * dt;
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double cosine = cos(arg);
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double sine = sin(arg);
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double **x = atom->x;
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double **v = atom->v;
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double **f = atom->f;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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x[i][axis] = original[i] + amplitude - amplitude*cosine;
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v[i][axis] = dt * amplitude*omega*sine;
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f[i][axis] = 0.0;
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}
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}
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}
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/* ---------------------------------------------------------------------- */
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void FixWiggle::post_force_respa(int vflag, int ilevel, int iloop)
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{
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if (ilevel == nlevels_respa-1) post_force(vflag);
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}
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/* ----------------------------------------------------------------------
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memory usage of local atom-based array
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------------------------------------------------------------------------- */
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int FixWiggle::memory_usage()
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{
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int bytes = atom->nmax * sizeof(double);
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return bytes;
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}
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/* ----------------------------------------------------------------------
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allocate local atom-based array
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------------------------------------------------------------------------- */
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void FixWiggle::grow_arrays(int nmax)
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{
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original = (double *)
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memory->srealloc(original,nmax*sizeof(double),"wiggle:original");
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}
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/* ----------------------------------------------------------------------
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copy values within local atom-based array
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------------------------------------------------------------------------- */
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void FixWiggle::copy_arrays(int i, int j)
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{
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original[j] = original[i];
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}
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/* ----------------------------------------------------------------------
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pack values in local atom-based array for exchange with another proc
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------------------------------------------------------------------------- */
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int FixWiggle::pack_exchange(int i, double *buf)
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{
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buf[0] = original[i];
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return 1;
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}
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/* ----------------------------------------------------------------------
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unpack values in local atom-based array from exchange with another proc
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------------------------------------------------------------------------- */
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int FixWiggle::unpack_exchange(int nlocal, double *buf)
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{
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original[nlocal] = buf[0];
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return 1;
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}
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