Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F119698613
fix_nve_sphere.cpp
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Sat, Jun 28, 16:54
Size
7 KB
Mime Type
text/x-c
Expires
Mon, Jun 30, 16:54 (2 d)
Engine
blob
Format
Raw Data
Handle
27045941
Attached To
rLAMMPS lammps
fix_nve_sphere.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.
------------------------------------------------------------------------- */
#include "math.h"
#include "stdio.h"
#include "string.h"
#include "fix_nve_sphere.h"
#include "atom.h"
#include "atom_vec.h"
#include "update.h"
#include "respa.h"
#include "force.h"
#include "error.h"
using namespace LAMMPS_NS;
#define INERTIA 0.4 // moment of inertia for sphere
enum{NONE,DIPOLE};
/* ---------------------------------------------------------------------- */
FixNVESphere::FixNVESphere(LAMMPS *lmp, int narg, char **arg) :
FixNVE(lmp, narg, arg)
{
if (narg < 3) error->all("Illegal fix nve/sphere command");
time_integrate = 1;
// process extra keywords
extra = NONE;
int iarg = 3;
while (iarg < narg) {
if (strcmp(arg[iarg],"update") == 0) {
if (iarg+2 > narg) error->all("Illegal fix nve/sphere command");
if (strcmp(arg[iarg+1],"dipole") == 0) extra = DIPOLE;
else error->all("Illegal fix nve/sphere command");
iarg += 2;
} else error->all("Illegal fix nve/sphere command");
}
// error check
if (!atom->omega_flag || !atom->torque_flag)
error->all("Fix nve/sphere requires atom attributes omega, torque");
if (extra == DIPOLE && !atom->mu_flag)
error->all("Fix nve/sphere requires atom attribute mu");
dttype = new double[atom->ntypes+1];
}
/* ---------------------------------------------------------------------- */
FixNVESphere::~FixNVESphere()
{
delete [] dttype;
}
/* ---------------------------------------------------------------------- */
int FixNVESphere::setmask()
{
int mask = 0;
mask |= INITIAL_INTEGRATE;
mask |= FINAL_INTEGRATE;
mask |= INITIAL_INTEGRATE_RESPA;
mask |= FINAL_INTEGRATE_RESPA;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixNVESphere::init()
{
dtv = update->dt;
dtf = 0.5 * update->dt * force->ftm2v;
if (strcmp(update->integrate_style,"respa") == 0)
step_respa = ((Respa *) update->integrate)->step;
if (atom->mass && !atom->shape)
error->all("Fix nve/sphere requires atom attribute shape");
if (!atom->mass && (!atom->radius_flag || !atom->rmass_flag))
error->all("Fix nve/sphere requires atom attributes radius, rmass");
if (atom->mass) {
double **shape = atom->shape;
for (int i = 1; i <= atom->ntypes; i++)
if (shape[i][0] != shape[i][1] || shape[i][0] != shape[i][2])
error->all("Fix nve/sphere requires spherical particle shapes");
}
}
/* ---------------------------------------------------------------------- */
void FixNVESphere::initial_integrate(int vflag)
{
int itype;
double dtfm,dtirotate,msq,scale;
double g[3];
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
double **omega = atom->omega;
double **torque = atom->torque;
double *radius = atom->radius;
double *rmass = atom->rmass;
double *mass = atom->mass;
int *mask = atom->mask;
int *type = atom->type;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
// recompute timesteps since dt may have changed or come via rRESPA
dtfrotate = dtf / INERTIA;
if (mass) {
double **shape = atom->shape;
int ntypes = atom->ntypes;
for (int i = 1; i <= ntypes; i++)
dttype[i] = dtfrotate / (shape[i][0]*shape[i][0]*mass[i]);
}
// update v,x,omega for all particles
// d_omega/dt = torque / inertia
if (mass) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
itype = type[i];
dtfm = dtf / mass[itype];
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
x[i][0] += dtv * v[i][0];
x[i][1] += dtv * v[i][1];
x[i][2] += dtv * v[i][2];
dtirotate = dttype[itype];
omega[i][0] += dtirotate * torque[i][0];
omega[i][1] += dtirotate * torque[i][1];
omega[i][2] += dtirotate * torque[i][2];
}
}
} else {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtfm = dtf / rmass[i];
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
x[i][0] += dtv * v[i][0];
x[i][1] += dtv * v[i][1];
x[i][2] += dtv * v[i][2];
dtirotate = dtfrotate / (radius[i]*radius[i]*rmass[i]);
omega[i][0] += dtirotate * torque[i][0];
omega[i][1] += dtirotate * torque[i][1];
omega[i][2] += dtirotate * torque[i][2];
}
}
}
// update mu for dipoles
// d_mu/dt = omega cross mu
// renormalize mu to dipole length
if (extra == DIPOLE) {
double **mu = atom->mu;
double *dipole = atom->dipole;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (dipole[type[i]] > 0.0) {
g[0] = mu[i][0] + dtv * (omega[i][1]*mu[i][2]-omega[i][2]*mu[i][1]);
g[1] = mu[i][1] + dtv * (omega[i][2]*mu[i][0]-omega[i][0]*mu[i][2]);
g[2] = mu[i][2] + dtv * (omega[i][0]*mu[i][1]-omega[i][1]*mu[i][0]);
msq = g[0]*g[0] + g[1]*g[1] + g[2]*g[2];
scale = dipole[type[i]]/sqrt(msq);
mu[i][0] = g[0]*scale;
mu[i][1] = g[1]*scale;
mu[i][2] = g[2]*scale;
}
}
}
}
}
/* ---------------------------------------------------------------------- */
void FixNVESphere::final_integrate()
{
int itype;
double dtfm,dtirotate;
double **v = atom->v;
double **f = atom->f;
double **omega = atom->omega;
double **torque = atom->torque;
double *mass = atom->mass;
double *rmass = atom->rmass;
double *radius = atom->radius;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
// recompute timesteps since dt may have changed or come via rRESPA
dtfrotate = dtf / INERTIA;
if (mass) {
double **shape = atom->shape;
int ntypes = atom->ntypes;
for (int i = 1; i <= ntypes; i++)
dttype[i] = dtfrotate / (shape[i][0]*shape[i][0]*mass[i]);
}
if (mass) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
itype = type[i];
dtfm = dtf / mass[itype];
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
dtirotate = dttype[itype];
omega[i][0] += dtirotate * torque[i][0];
omega[i][1] += dtirotate * torque[i][1];
omega[i][2] += dtirotate * torque[i][2];
}
}
} else {
dtfrotate = dtf / INERTIA;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtfm = dtf / rmass[i];
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
dtirotate = dtfrotate / (radius[i]*radius[i]*rmass[i]);
omega[i][0] += dtirotate * torque[i][0];
omega[i][1] += dtirotate * torque[i][1];
omega[i][2] += dtirotate * torque[i][2];
}
}
}
}
Event Timeline
Log In to Comment