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fix_spring_pull.cpp
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Thu, Nov 7, 20:44

fix_spring_pull.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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Paul Crozier (SNL)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdlib.h"
#include "string.h"
#include "fix_spring_pull.h"
#include "atom.h"
#include "update.h"
#include "respa.h"
#include "domain.h"
#include "error.h"
#include "group.h"
using namespace LAMMPS_NS;
using namespace FixConst;
#define SMALL 1.0e-10
/* ---------------------------------------------------------------------- */
FixSpringPull::FixSpringPull(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg != 11) error->all(FLERR,"Illegal fix spring/pull command");
scalar_flag = 1;
vector_flag = 1;
size_vector = 8;
global_freq = 1;
extscalar = 1;
extvector = 1;
k_spring = atof(arg[3]);
xflag = yflag = zflag = 1;
if (strcmp(arg[4],"NULL") == 0) xflag = 0;
else xc = atof(arg[4]);
if (strcmp(arg[5],"NULL") == 0) yflag = 0;
else yc = atof(arg[5]);
if (strcmp(arg[6],"NULL") == 0) zflag = 0;
else zc = atof(arg[6]);
xv = atof(arg[7]);
yv = atof(arg[8]);
zv = atof(arg[9]);
r0 = atof(arg[10]);
if (r0 < 0) error->all(FLERR,"R0 < 0 for fix spring/pull command");
ftotal[0] = ftotal[1] = ftotal[2] = ftotal[3] = 0.0;
ftotal[4] = ftotal[5] = ftotal[6] = ftotal[7] = 0.0;
}
/* ---------------------------------------------------------------------- */
int FixSpringPull::setmask()
{
int mask = 0;
mask |= POST_FORCE;
mask |= THERMO_ENERGY;
mask |= POST_FORCE_RESPA;
mask |= MIN_POST_FORCE;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixSpringPull::init()
{
masstotal = group->mass(igroup);
if (strcmp(update->integrate_style,"respa") == 0)
nlevels_respa = ((Respa *) update->integrate)->nlevels;
}
/* ---------------------------------------------------------------------- */
void FixSpringPull::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 FixSpringPull::min_setup(int vflag)
{
post_force(vflag);
}
/* ---------------------------------------------------------------------- */
void FixSpringPull::post_force(int vflag)
{
double xcm[3];
group->xcm(igroup,masstotal,xcm);
// fx,fy,fz = components of k * (r-r0) / masstotal
double dx,dy,dz,fx,fy,fz,r,dr;
// move reference point by one time step.
xc += xv * update->dt;
yc += yv * update->dt;
zc += zv * update->dt;
domain->minimum_image(xc,yc,zc);
dx = xcm[0] - xc;
dy = xcm[1] - yc;
dz = xcm[2] - zc;
domain->minimum_image(dx,dy,dz);
if (!xflag) dx = 0.0;
if (!yflag) dy = 0.0;
if (!zflag) dz = 0.0;
r = sqrt(dx*dx + dy*dy + dz*dz);
r = MAX(r,SMALL);
dr = r - r0;
fx = k_spring*dx*dr/r;
fy = k_spring*dy*dr/r;
fz = k_spring*dz*dr/r;
ftotal[0] = -fx;
ftotal[1] = -fy;
ftotal[2] = -fz;
ftotal[3] = sqrt(fx*fx + fy*fy + fz*fz);
ftotal[4] = r;
ftotal[5] = xc;
ftotal[6] = yc;
ftotal[7] = zc;
if (dr < 0.0) ftotal[3] = -ftotal[3];
espring = 0.5*k_spring * dr*dr;
fx /= masstotal;
fy /= masstotal;
fz /= masstotal;
// apply restoring force to atoms in group
double **f = atom->f;
int *mask = atom->mask;
int *type = atom->type;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
double massone;
if (rmass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
massone = rmass[i];
f[i][0] -= fx*massone;
f[i][1] -= fy*massone;
f[i][2] -= fz*massone;
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
massone = mass[type[i]];
f[i][0] -= fx*massone;
f[i][1] -= fy*massone;
f[i][2] -= fz*massone;
}
}
}
/* ---------------------------------------------------------------------- */
void FixSpringPull::post_force_respa(int vflag, int ilevel, int iloop)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
}
/* ---------------------------------------------------------------------- */
void FixSpringPull::min_post_force(int vflag)
{
post_force(vflag);
}
/* ----------------------------------------------------------------------
energy of stretched spring
------------------------------------------------------------------------- */
double FixSpringPull::compute_scalar()
{
return espring;
}
/* ----------------------------------------------------------------------
return components of total spring force on fix group
------------------------------------------------------------------------- */
double FixSpringPull::compute_vector(int n)
{
return ftotal[n];
}

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