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fix_spring.cpp
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Tue, Aug 6, 12:13

fix_spring.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.h"
#include "atom.h"
#include "update.h"
#include "respa.h"
#include "domain.h"
#include "error.h"
#include "group.h"
using namespace LAMMPS_NS;
#define TETHER 0
#define COUPLE 1
/* ---------------------------------------------------------------------- */
FixSpring::FixSpring(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 9) error->all("Illegal fix spring command");
vector_flag = 1;
size_vector = 3;
scalar_vector_freq = 1;
extensive = 1;
if (strcmp(arg[3],"tether") == 0) {
if (narg != 9) error->all("Illegal fix spring command");
styleflag = TETHER;
k_spring = atof(arg[4]);
xflag = yflag = zflag = 1;
if (strcmp(arg[5],"NULL") == 0) xflag = 0;
else xc = atof(arg[5]);
if (strcmp(arg[6],"NULL") == 0) yflag = 0;
else yc = atof(arg[6]);
if (strcmp(arg[7],"NULL") == 0) zflag = 0;
else zc = atof(arg[7]);
r0 = atof(arg[8]);
if (r0 < 0) error->all("R0 < 0 for fix spring command");
} else if (strcmp(arg[3],"couple") == 0) {
if (narg != 10) error->all("Illegal fix spring command");
styleflag = COUPLE;
igroup2 = group->find(arg[4]);
if (igroup2 == -1)
error->all("Could not find fix spring couple group ID");
group2bit = group->bitmask[igroup2];
k_spring = atof(arg[5]);
xflag = yflag = zflag = 1;
if (strcmp(arg[6],"NULL") == 0) xflag = 0;
else xc = atof(arg[6]);
if (strcmp(arg[7],"NULL") == 0) yflag = 0;
else yc = atof(arg[7]);
if (strcmp(arg[8],"NULL") == 0) zflag = 0;
else zc = atof(arg[8]);
r0 = atof(arg[9]);
if (r0 < 0) error->all("R0 < 0 for fix spring command");
} else error->all("Illegal fix spring command");
}
/* ---------------------------------------------------------------------- */
int FixSpring::setmask()
{
int mask = 0;
mask |= POST_FORCE;
mask |= POST_FORCE_RESPA;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixSpring::init()
{
masstotal = group->mass(igroup);
if (styleflag == COUPLE) masstotal2 = group->mass(igroup2);
if (strcmp(update->integrate_style,"respa") == 0)
nlevels_respa = ((Respa *) update->integrate)->nlevels;
}
/* ---------------------------------------------------------------------- */
void FixSpring::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 FixSpring::post_force(int vflag)
{
if (styleflag == TETHER) spring_tether();
else spring_couple();
}
/* ---------------------------------------------------------------------- */
void FixSpring::spring_tether()
{
double xcm[3];
group->xcm(igroup,masstotal,xcm);
// fx,fy,fz = components of k * (r-r0)
double dx,dy,dz,fx,fy,fz,r,dr;
dx = xcm[0] - xc;
dy = xcm[1] - yc;
dz = xcm[2] - zc;
if (!xflag) dx = 0.0;
if (!yflag) dy = 0.0;
if (!zflag) dz = 0.0;
r = sqrt(dx*dx + dy*dy + dz*dz);
dr = r - r0;
fx = k_spring*dx*dr/r;
fy = k_spring*dy*dr/r;
fz = k_spring*dz*dr/r;
// apply restoring force to atoms in group
// f = -k*(r-r0)*mass/masstotal
double **f = atom->f;
int *mask = atom->mask;
int *type = atom->type;
double *mass = atom->mass;
int nlocal = atom->nlocal;
ftotal[0] = ftotal[1] = ftotal[2] = 0.0;
force_flag = 0;
double massfrac;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
massfrac = mass[type[i]]/masstotal;
fx *= massfrac;
fy *= massfrac;
fz *= massfrac;
f[i][0] -= fx;
f[i][1] -= fy;
f[i][2] -= fz;
ftotal[0] -= fx;
ftotal[1] -= fy;
ftotal[2] -= fz;
}
}
/* ---------------------------------------------------------------------- */
void FixSpring::spring_couple()
{
double xcm[3],xcm2[3];
group->xcm(igroup,masstotal,xcm);
group->xcm(igroup2,masstotal2,xcm2);
// fx,fy,fz = components of k * (r-r0)
double dx,dy,dz,fx,fy,fz,r,dr;
dx = xcm2[0] - xcm[0] - xc;
dy = xcm2[1] - xcm[1] - yc;
dz = xcm2[2] - xcm[2] - zc;
if (!xflag) dx = 0.0;
if (!yflag) dy = 0.0;
if (!zflag) dz = 0.0;
r = sqrt(dx*dx + dy*dy + dz*dz);
dr = r - r0;
fx = k_spring*dx*dr/r;
fy = k_spring*dy*dr/r;
fz = k_spring*dz*dr/r;
// apply restoring force to atoms in group
// f = -k*(r-r0)*mass/masstotal
double **f = atom->f;
int *mask = atom->mask;
int *type = atom->type;
double *mass = atom->mass;
int nlocal = atom->nlocal;
ftotal[0] = ftotal[1] = ftotal[2] = 0.0;
force_flag = 0;
double massfrac;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
massfrac = mass[type[i]]/masstotal;
f[i][0] += fx*massfrac;
f[i][1] += fy*massfrac;
f[i][2] += fz*massfrac;
ftotal[0] += fx*massfrac;
ftotal[1] += fy*massfrac;
ftotal[2] += fz*massfrac;
}
if (mask[i] & group2bit) {
massfrac = mass[type[i]]/masstotal2;
f[i][0] -= fx*massfrac;
f[i][1] -= fy*massfrac;
f[i][2] -= fz*massfrac;
}
}
}
/* ---------------------------------------------------------------------- */
void FixSpring::post_force_respa(int vflag, int ilevel, int iloop)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
}
/* ----------------------------------------------------------------------
return components of total spring force on fix group
------------------------------------------------------------------------- */
double FixSpring::compute_vector(int n)
{
// only sum across procs one time
if (force_flag == 0) {
MPI_Allreduce(ftotal,ftotal_all,3,MPI_DOUBLE,MPI_SUM,world);
force_flag = 1;
}
return ftotal_all[n];
}

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