git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1660 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
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src/fix_nvt_sphere.cpp
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src/fix_nvt_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 "string.h"
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#include "stdlib.h"
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#include "math.h"
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#include "fix_nvt_sphere.h"
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#include "atom.h"
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#include "atom_vec.h"
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#include "force.h"
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#include "comm.h"
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#include "group.h"
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#include "update.h"
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#include "modify.h"
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#include "compute.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{NOBIAS,BIAS};
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/* ---------------------------------------------------------------------- */
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FixNVTSphere::FixNVTSphere(LAMMPS *lmp, int narg, char **arg) :
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FixNVT(lmp, narg, arg)
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{
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if (!atom->omega_flag || !atom->torque_flag)
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error->all("Fix nvt/sphere requires atom attributes omega, torque");
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dttype = new double[atom->ntypes+1];
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}
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/* ---------------------------------------------------------------------- */
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FixNVTSphere::~FixNVTSphere()
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{
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delete [] dttype;
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}
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/* ---------------------------------------------------------------------- */
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void FixNVTSphere::init()
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{
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FixNVT::init();
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dtfrotate = dtf / INERTIA;
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if (!atom->shape)
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error->all("Fix nvt/sphere requires atom attribute shape");
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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 nvt/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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void FixNVTSphere::initial_integrate(int vflag)
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{
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int itype;
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double dtfm,dtirotate;
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double delta = update->ntimestep - update->beginstep;
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delta /= update->endstep - update->beginstep;
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t_target = t_start + delta * (t_stop-t_start);
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// update eta_dot
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f_eta = t_freq*t_freq * (t_current/t_target - 1.0);
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eta_dot += f_eta*dthalf;
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eta_dot *= drag_factor;
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eta += dtv*eta_dot;
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factor = exp(-dthalf*eta_dot);
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// update v and x of only atoms in group
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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 **quat = atom->quat;
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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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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 (which == NOBIAS) {
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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] = v[i][0]*factor + dtfm*f[i][0];
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v[i][1] = v[i][1]*factor + dtfm*f[i][1];
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v[i][2] = v[i][2]*factor + 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] = omega[i][0]*factor + dtirotate*torque[i][0];
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omega[i][1] = omega[i][1]*factor + dtirotate*torque[i][1];
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omega[i][2] = omega[i][2]*factor + dtirotate*torque[i][2];
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}
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}
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} else if (which == BIAS) {
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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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temperature->remove_bias(i,v[i]);
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dtfm = dtf / mass[itype];
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v[i][0] = v[i][0]*factor + dtfm*f[i][0];
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v[i][1] = v[i][1]*factor + dtfm*f[i][1];
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v[i][2] = v[i][2]*factor + dtfm*f[i][2];
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temperature->restore_bias(i,v[i]);
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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] = omega[i][0]*factor + dtirotate*torque[i][0];
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omega[i][1] = omega[i][1]*factor + dtirotate*torque[i][1];
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omega[i][2] = omega[i][2]*factor + 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 FixNVTSphere::final_integrate()
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{
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int itype;
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double dtfm,dtirotate;
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// update v of only atoms in group
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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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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 (which == NOBIAS) {
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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] * factor;
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v[i][0] = v[i][0]*factor + dtfm*f[i][0];
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v[i][1] = v[i][1]*factor + dtfm*f[i][1];
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v[i][2] = v[i][2]*factor + dtfm*f[i][2];
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dtirotate = dttype[itype];
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omega[i][0] = (omega[i][0] + dtirotate*torque[i][0]) * factor;
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omega[i][1] = (omega[i][1] + dtirotate*torque[i][1]) * factor;
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omega[i][2] = (omega[i][2] + dtirotate*torque[i][2]) * factor;
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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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itype = type[i];
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temperature->remove_bias(i,v[i]);
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dtfm = dtf / mass[itype] * factor;
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v[i][0] = v[i][0]*factor + dtfm*f[i][0];
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v[i][1] = v[i][1]*factor + dtfm*f[i][1];
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v[i][2] = v[i][2]*factor + dtfm*f[i][2];
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temperature->restore_bias(i,v[i]);
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dtirotate = dttype[itype];
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omega[i][0] = (omega[i][0] + dtirotate*torque[i][0]) * factor;
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omega[i][1] = (omega[i][1] + dtirotate*torque[i][1]) * factor;
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omega[i][2] = (omega[i][2] + dtirotate*torque[i][2]) * factor;
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}
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}
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}
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// compute current T
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t_current = temperature->compute_scalar();
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// update eta_dot
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f_eta = t_freq*t_freq * (t_current/t_target - 1.0);
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eta_dot += f_eta*dthalf;
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eta_dot *= drag_factor;
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}
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/* ---------------------------------------------------------------------- */
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void FixNVTSphere::reset_dt()
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{
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FixNVT::reset_dt();
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dtfrotate = dtf / INERTIA;
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}
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