Homec4science
Diffusion lammps (HEAD -> master) Browse

lammps/src/fix_spring_self.cpp
0cc1d090f44eHEAD -> master

Last Change
Raw File

fix_spring_self.cpp
View Options

/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Naveen Michaud-Agrawal (Johns Hopkins University)
------------------------------------------------------------------------- */
#include "stdlib.h"
#include "string.h"
#include "fix_spring_self.h"
#include "atom.h"
#include "update.h"
#include "domain.h"
#include "respa.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
FixSpringSelf::FixSpringSelf(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg != 4) error->all("Illegal fix spring/self command");
restart_peratom = 1;
scalar_flag = 1;
scalar_vector_freq = 1;
extscalar = 1;
k = atof(arg[3]);
if (k <= 0.0) error->all("Illegal fix spring/self command");
// perform initial allocation of atom-based array
// register with Atom class
xoriginal = NULL;
grow_arrays(atom->nmax);
atom->add_callback(0);
atom->add_callback(1);
// xoriginal = initial unwrapped positions of atoms
double **x = atom->x;
int *mask = atom->mask;
int *image = atom->image;
int nlocal = atom->nlocal;
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
int xbox,ybox,zbox;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
xbox = (image[i] & 1023) - 512;
ybox = (image[i] >> 10 & 1023) - 512;
zbox = (image[i] >> 20) - 512;
xoriginal[i][0] = x[i][0] + xbox*xprd;
xoriginal[i][1] = x[i][1] + ybox*yprd;
xoriginal[i][2] = x[i][2] + zbox*zprd;
} else xoriginal[i][0] = xoriginal[i][1] = xoriginal[i][2] = 0.0;
}
espring = 0.0;
}
/* ---------------------------------------------------------------------- */
FixSpringSelf::~FixSpringSelf()
{
// unregister callbacks to this fix from Atom class
atom->delete_callback(id,0);
atom->delete_callback(id,1);
// delete locally stored array
memory->destroy_2d_double_array(xoriginal);
}
/* ---------------------------------------------------------------------- */
int FixSpringSelf::setmask()
{
int mask = 0;
mask |= POST_FORCE;
mask |= THERMO_ENERGY;
mask |= POST_FORCE_RESPA;
mask |= MIN_POST_FORCE;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixSpringSelf::init()
{
if (strcmp(update->integrate_style,"respa") == 0)
nlevels_respa = ((Respa *) update->integrate)->nlevels;
}
/* ---------------------------------------------------------------------- */
void FixSpringSelf::setup(int vflag)
{
if (strcmp(update->integrate_style,"verlet") == 0)
post_force(vflag);
else {
((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
post_force_respa(vflag,nlevels_respa-1,0);
((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
}
}
/* ---------------------------------------------------------------------- */
void FixSpringSelf::min_setup(int vflag)
{
post_force(vflag);
}
/* ---------------------------------------------------------------------- */
void FixSpringSelf::post_force(int vflag)
{
double **x = atom->x;
double **f = atom->f;
int *mask = atom->mask;
int *image = atom->image;
int nlocal = atom->nlocal;
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
int xbox,ybox,zbox;
double dx,dy,dz;
espring = 0.0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
xbox = (image[i] & 1023) - 512;
ybox = (image[i] >> 10 & 1023) - 512;
zbox = (image[i] >> 20) - 512;
dx = x[i][0] + xbox*xprd - xoriginal[i][0];
dy = x[i][1] + ybox*yprd - xoriginal[i][1];
dz = x[i][2] + zbox*zprd - xoriginal[i][2];
f[i][0] -= k*dx;
f[i][1] -= k*dy;
f[i][2] -= k*dz;
espring += k * (dx*dx + dy*dy + dz*dz);
}
espring *= 0.5;
}
/* ---------------------------------------------------------------------- */
void FixSpringSelf::post_force_respa(int vflag, int ilevel, int iloop)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
}
/* ----------------------------------------------------------------------
energy of stretched springs
------------------------------------------------------------------------- */
double FixSpringSelf::compute_scalar()
{
double all;
MPI_Allreduce(&espring,&all,1,MPI_DOUBLE,MPI_SUM,world);
return all;
}
/* ---------------------------------------------------------------------- */
void FixSpringSelf::min_post_force(int vflag)
{
post_force(vflag);
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
double FixSpringSelf::memory_usage()
{
double bytes = atom->nmax*3 * sizeof(double);
return bytes;
}
/* ----------------------------------------------------------------------
allocate atom-based array
------------------------------------------------------------------------- */
void FixSpringSelf::grow_arrays(int nmax)
{
xoriginal =
memory->grow_2d_double_array(xoriginal,nmax,3,"fix_spring/self:xoriginal");
}
/* ----------------------------------------------------------------------
copy values within local atom-based array
------------------------------------------------------------------------- */
void FixSpringSelf::copy_arrays(int i, int j)
{
xoriginal[j][0] = xoriginal[i][0];
xoriginal[j][1] = xoriginal[i][1];
xoriginal[j][2] = xoriginal[i][2];
}
/* ----------------------------------------------------------------------
pack values in local atom-based array for exchange with another proc
------------------------------------------------------------------------- */
int FixSpringSelf::pack_exchange(int i, double *buf)
{
buf[0] = xoriginal[i][0];
buf[1] = xoriginal[i][1];
buf[2] = xoriginal[i][2];
return 3;
}
/* ----------------------------------------------------------------------
unpack values in local atom-based array from exchange with another proc
------------------------------------------------------------------------- */
int FixSpringSelf::unpack_exchange(int nlocal, double *buf)
{
xoriginal[nlocal][0] = buf[0];
xoriginal[nlocal][1] = buf[1];
xoriginal[nlocal][2] = buf[2];
return 3;
}
/* ----------------------------------------------------------------------
pack values in local atom-based arrays for restart file
------------------------------------------------------------------------- */
int FixSpringSelf::pack_restart(int i, double *buf)
{
buf[0] = 4;
buf[1] = xoriginal[i][0];
buf[2] = xoriginal[i][1];
buf[3] = xoriginal[i][2];
return 4;
}
/* ----------------------------------------------------------------------
unpack values from atom->extra array to restart the fix
------------------------------------------------------------------------- */
void FixSpringSelf::unpack_restart(int nlocal, int nth)
{
double **extra = atom->extra;
// skip to Nth set of extra values
int m = 0;
for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);
m++;
xoriginal[nlocal][0] = extra[nlocal][m++];
xoriginal[nlocal][1] = extra[nlocal][m++];
xoriginal[nlocal][2] = extra[nlocal][m++];
}
/* ----------------------------------------------------------------------
maxsize of any atom's restart data
------------------------------------------------------------------------- */
int FixSpringSelf::maxsize_restart()
{
return 4;
}
/* ----------------------------------------------------------------------
size of atom nlocal's restart data
------------------------------------------------------------------------- */
int FixSpringSelf::size_restart(int nlocal)
{
return 4;
}
c4science · Help