git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1608 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
276
src/fix_nve_sphere.cpp
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276
src/fix_nve_sphere.cpp
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "math.h"
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#include "stdio.h"
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#include "string.h"
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#include "fix_nve_sphere.h"
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#include "atom.h"
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#include "atom_vec.h"
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#include "update.h"
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#include "respa.h"
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#include "force.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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#define INERTIA 0.4 // moment of inertia for sphere
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enum{NONE,DIPOLE};
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/* ---------------------------------------------------------------------- */
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FixNVESphere::FixNVESphere(LAMMPS *lmp, int narg, char **arg) :
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Fix(lmp, narg, arg)
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{
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if (narg < 3) error->all("Illegal fix nve/sphere command");
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// process extra keywords
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extra = NONE;
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int iarg = 3;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"update") == 0) {
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if (iarg+2 > narg) error->all("Illegal fix nve/sphere command");
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if (strcmp(arg[iarg+1],"dipole") == 0) extra = DIPOLE;
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else error->all("Illegal fix nve/sphere command");
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iarg += 2;
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} else error->all("Illegal fix nve/sphere command");
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}
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// error check
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if (!atom->omega_flag || !atom->torque_flag)
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error->all("Fix nve/sphere requires atom attributes omega, torque");
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if (extra == DIPOLE && !atom->mu_flag)
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error->all("Fix nve/sphere requires atom attribute mu");
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dttype = new double[atom->ntypes+1];
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}
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/* ---------------------------------------------------------------------- */
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FixNVESphere::~FixNVESphere()
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{
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delete [] dttype;
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}
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/* ---------------------------------------------------------------------- */
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int FixNVESphere::setmask()
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{
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int mask = 0;
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mask |= INITIAL_INTEGRATE;
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mask |= FINAL_INTEGRATE;
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mask |= INITIAL_INTEGRATE_RESPA;
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mask |= FINAL_INTEGRATE_RESPA;
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return mask;
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}
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/* ---------------------------------------------------------------------- */
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void FixNVESphere::init()
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{
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dtv = update->dt;
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dtf = 0.5 * update->dt * force->ftm2v;
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dtfrotate = dtf / INERTIA;
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if (strcmp(update->integrate_style,"respa") == 0)
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step_respa = ((Respa *) update->integrate)->step;
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if (atom->mass && !atom->shape)
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error->all("Fix nve/sphere requires atom attribute shape");
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if (!atom->mass && (!atom->radius_flag || !atom->rmass_flag))
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error->all("Fix nve/sphere requires atom attributes radius, rmass");
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if (atom->mass) {
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double *mass = atom->mass;
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double **shape = atom->shape;
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for (int i = 1; i <= atom->ntypes; i++) {
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if (shape[i][0] != shape[i][1] || shape[i][0] != shape[i][2])
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error->all("Fix nve/sphere requires spherical particle shapes");
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dttype[i] = dtfrotate / (0.25*shape[i][0]*shape[i][0]*mass[i]);
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}
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}
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}
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/* ---------------------------------------------------------------------- */
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void FixNVESphere::initial_integrate(int vflag)
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{
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int itype;
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double dtfm,dtirotate,msq,scale;
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double g[3];
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double **x = atom->x;
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double **v = atom->v;
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double **f = atom->f;
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double **omega = atom->omega;
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double **torque = atom->torque;
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double *radius = atom->radius;
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double *rmass = atom->rmass;
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double *mass = atom->mass;
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int *mask = atom->mask;
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int *type = atom->type;
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int nlocal = atom->nlocal;
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if (igroup == atom->firstgroup) nlocal = atom->nfirst;
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// update v,x,omega for all particles
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// d_omega/dt = torque / inertia
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if (mass) {
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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itype = type[i];
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dtfm = dtf / mass[itype];
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v[i][0] += dtfm * f[i][0];
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v[i][1] += dtfm * f[i][1];
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v[i][2] += dtfm * f[i][2];
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x[i][0] += dtv * v[i][0];
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x[i][1] += dtv * v[i][1];
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x[i][2] += dtv * v[i][2];
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dtirotate = dttype[itype];
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omega[i][0] += dtirotate * torque[i][0];
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omega[i][1] += dtirotate * torque[i][1];
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omega[i][2] += dtirotate * torque[i][2];
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}
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}
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} else {
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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dtfm = dtf / rmass[i];
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v[i][0] += dtfm * f[i][0];
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v[i][1] += dtfm * f[i][1];
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v[i][2] += dtfm * f[i][2];
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x[i][0] += dtv * v[i][0];
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x[i][1] += dtv * v[i][1];
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x[i][2] += dtv * v[i][2];
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dtirotate = dtfrotate / (radius[i]*radius[i]*rmass[i]);
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omega[i][0] += dtirotate * torque[i][0];
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omega[i][1] += dtirotate * torque[i][1];
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omega[i][2] += dtirotate * torque[i][2];
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}
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}
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}
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// update mu for dipoles
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// d_mu/dt = omega cross mu
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// renormalize mu to dipole length
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if (extra == DIPOLE) {
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double **mu = atom->mu;
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double *dipole = atom->dipole;
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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if (dipole[type[i]] > 0.0) {
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g[0] = mu[i][0] + dtv * (omega[i][1]*mu[i][2]-omega[i][2]*mu[i][1]);
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g[1] = mu[i][1] + dtv * (omega[i][2]*mu[i][0]-omega[i][0]*mu[i][2]);
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g[2] = mu[i][2] + dtv * (omega[i][0]*mu[i][1]-omega[i][1]*mu[i][0]);
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msq = g[0]*g[0] + g[1]*g[1] + g[2]*g[2];
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scale = dipole[type[i]]/sqrt(msq);
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mu[i][0] = g[0]*scale;
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mu[i][1] = g[1]*scale;
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mu[i][2] = g[2]*scale;
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}
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}
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}
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}
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}
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/* ---------------------------------------------------------------------- */
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void FixNVESphere::final_integrate()
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{
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int itype;
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double dtfm,dtirotate;
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double **v = atom->v;
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double **f = atom->f;
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double **omega = atom->omega;
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double **torque = atom->torque;
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double *mass = atom->mass;
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double *rmass = atom->rmass;
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double *radius = atom->radius;
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int *type = atom->type;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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if (igroup == atom->firstgroup) nlocal = atom->nfirst;
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if (mass) {
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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itype = type[i];
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dtfm = dtf / mass[itype];
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v[i][0] += dtfm * f[i][0];
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v[i][1] += dtfm * f[i][1];
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v[i][2] += dtfm * f[i][2];
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dtirotate = dttype[itype];
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omega[i][0] += dtirotate * torque[i][0];
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omega[i][1] += dtirotate * torque[i][1];
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omega[i][2] += dtirotate * torque[i][2];
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}
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}
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} else {
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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dtfm = dtf / rmass[i];
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v[i][0] += dtfm * f[i][0];
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v[i][1] += dtfm * f[i][1];
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v[i][2] += dtfm * f[i][2];
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dtirotate = dtfrotate / (radius[i]*radius[i]*rmass[i]);
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omega[i][0] += dtirotate * torque[i][0];
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omega[i][1] += dtirotate * torque[i][1];
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omega[i][2] += dtirotate * torque[i][2];
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}
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}
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}
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}
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/* ---------------------------------------------------------------------- */
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void FixNVESphere::initial_integrate_respa(int vflag, int ilevel, int flag)
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{
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if (flag) return; // only used by NPT,NPH
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dtv = step_respa[ilevel];
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dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
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dtfrotate = dtf / INERTIA;
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if (ilevel == 0) initial_integrate(vflag);
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else final_integrate();
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}
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/* ---------------------------------------------------------------------- */
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void FixNVESphere::final_integrate_respa(int ilevel)
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{
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dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
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dtfrotate = dtf / INERTIA;
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final_integrate();
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}
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/* ---------------------------------------------------------------------- */
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void FixNVESphere::reset_dt()
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{
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dtv = update->dt;
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dtf = 0.5 * update->dt * force->ftm2v;
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dtfrotate = dtf / INERTIA;
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}
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