Homec4science
Diffusion lammps (lammm-master-deprecated) Browse

lammps/src/fix_spring_rg.cpp
284c1f2d04aclammm-master-deprecated

Last Change
Raw File

fix_spring_rg.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 U)
Paul Crozier (SNL)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdlib.h"
#include "string.h"
#include "fix_spring_rg.h"
#include "atom.h"
#include "update.h"
#include "group.h"
#include "respa.h"
#include "domain.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
FixSpringRG::FixSpringRG(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg != 5) error->all("Illegal fix spring/rg command");
k = atof(arg[3]);
rg0_flag = 0;
if (strcmp(arg[4],"NULL") == 0) rg0_flag = 1;
else rg0 = atof(arg[4]);
}
/* ---------------------------------------------------------------------- */
int FixSpringRG::setmask()
{
int mask = 0;
mask |= POST_FORCE;
mask |= POST_FORCE_RESPA;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixSpringRG::init()
{
masstotal = group->mass(igroup);
// if rg0 was specified as NULL, compute current Rg
// only occurs on 1st run
if (rg0_flag) {
double xcm[3];
group->xcm(igroup,masstotal,xcm);
rg0 = group->gyration(igroup,masstotal,xcm);
rg0_flag = 0;
}
if (strcmp(update->integrate_style,"respa") == 0)
nlevels_respa = ((Respa *) update->integrate)->nlevels;
}
/* ---------------------------------------------------------------------- */
void FixSpringRG::setup()
{
if (strcmp(update->integrate_style,"verlet") == 0)
post_force(1);
else {
((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
post_force_respa(1,nlevels_respa-1,0);
((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
}
}
/* ---------------------------------------------------------------------- */
void FixSpringRG::post_force(int vflag)
{
// compute current Rg and center-of-mass
double xcm[3];
group->xcm(igroup,masstotal,xcm);
double rg = group->gyration(igroup,masstotal,xcm);
// apply restoring force to atoms in group
// f = -k*(r-r0)*mass/masstotal
double dx,dy,dz,term1;
double **f = atom->f;
double **x = atom->x;
int *mask = atom->mask;
int *type = atom->type;
int *image = atom->image;
double *mass = atom->mass;
int nlocal = atom->nlocal;
double massfrac;
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) {
term1 = 2.0 * k * (1.0 - rg0/rg);
xbox = (image[i] & 1023) - 512;
ybox = (image[i] >> 10 & 1023) - 512;
zbox = (image[i] >> 20) - 512;
dx = (x[i][0] + xbox*xprd) - xcm[0];
dy = (x[i][1] + ybox*yprd) - xcm[1];
dz = (x[i][2] + zbox*zprd) - xcm[2];
massfrac = mass[type[i]]/masstotal;
f[i][0] -= term1*dx*massfrac;
f[i][1] -= term1*dy*massfrac;
f[i][2] -= term1*dz*massfrac;
}
}
/* ---------------------------------------------------------------------- */
void FixSpringRG::post_force_respa(int vflag, int ilevel, int iloop)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
}
c4science · Help