232 lines
6.8 KiB
C++
Executable File
232 lines
6.8 KiB
C++
Executable File
/* ----------------------------------------------------------------------
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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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/* ----------------------------------------------------------------------
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Contributing author: Mike Brown (SNL)
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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_asphere.h"
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#include "math_extra.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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/* ---------------------------------------------------------------------- */
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FixNVTASphere::FixNVTASphere(LAMMPS *lmp, int narg, char **arg) :
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FixNVT(lmp, narg, arg)
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{
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if (!atom->quat_flag || !atom->angmom_flag || !atom->torque_flag ||
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!atom->avec->shape_type)
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error->all("Fix nvt/asphere requires atom attributes "
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"quat, angmom, torque, shape");
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}
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/* ---------------------------------------------------------------------- */
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void FixNVTASphere::initial_integrate(int vflag)
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{
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double dtfm;
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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 NVT 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 **angmom = atom->angmom;
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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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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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dtfm = dtf / mass[type[i]];
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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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// update angular momentum by 1/2 step
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// update quaternion a full step via Richardson iteration
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// returns new normalized quaternion
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angmom[i][0] = angmom[i][0] * factor + dtf * torque[i][0];
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angmom[i][1] = angmom[i][1] * factor + dtf * torque[i][1];
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angmom[i][2] = angmom[i][2] * factor + dtf * torque[i][2];
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double inertia[3];
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calculate_inertia(atom->mass[type[i]],atom->shape[type[i]],inertia);
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richardson(quat[i],angmom[i],inertia);
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}
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}
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}
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/* ---------------------------------------------------------------------- */
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void FixNVTASphere::final_integrate()
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{
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double dtfm;
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// update v of only atoms in NVT group
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double **v = atom->v;
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double **f = atom->f;
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double **angmom = atom->angmom;
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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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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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dtfm = dtf / mass[type[i]] * 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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angmom[i][0] = angmom[i][0] * factor + dtf * torque[i][0];
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angmom[i][1] = angmom[i][1] * factor + dtf * torque[i][1];
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angmom[i][2] = angmom[i][2] * factor + dtf * torque[i][2];
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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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Richardson iteration to update quaternion accurately
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------------------------------------------------------------------------- */
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void FixNVTASphere::richardson(double *q, double *m, double *moments)
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{
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// compute omega at 1/2 step from m at 1/2 step and q at 0
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double w[3];
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omega_from_mq(q,m,moments,w);
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// full update from dq/dt = 1/2 w q
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double wq[4];
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MathExtra::multiply_vec_quat(w,q,wq);
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double qfull[4];
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qfull[0] = q[0] + dtq * wq[0];
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qfull[1] = q[1] + dtq * wq[1];
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qfull[2] = q[2] + dtq * wq[2];
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qfull[3] = q[3] + dtq * wq[3];
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MathExtra::normalize4(qfull);
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// 1st half of update from dq/dt = 1/2 w q
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double qhalf[4];
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qhalf[0] = q[0] + 0.5*dtq * wq[0];
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qhalf[1] = q[1] + 0.5*dtq * wq[1];
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qhalf[2] = q[2] + 0.5*dtq * wq[2];
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qhalf[3] = q[3] + 0.5*dtq * wq[3];
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MathExtra::normalize4(qhalf);
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// re-compute omega at 1/2 step from m at 1/2 step and q at 1/2 step
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// recompute wq
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omega_from_mq(qhalf,m,moments,w);
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MathExtra::multiply_vec_quat(w,qhalf,wq);
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// 2nd half of update from dq/dt = 1/2 w q
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qhalf[0] += 0.5*dtq * wq[0];
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qhalf[1] += 0.5*dtq * wq[1];
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qhalf[2] += 0.5*dtq * wq[2];
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qhalf[3] += 0.5*dtq * wq[3];
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MathExtra::normalize4(qhalf);
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// corrected Richardson update
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q[0] = 2.0*qhalf[0] - qfull[0];
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q[1] = 2.0*qhalf[1] - qfull[1];
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q[2] = 2.0*qhalf[2] - qfull[2];
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q[3] = 2.0*qhalf[3] - qfull[3];
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MathExtra::normalize4(q);
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}
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/* ----------------------------------------------------------------------
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compute omega from angular momentum
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w = omega = angular velocity in space frame
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wbody = angular velocity in body frame
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project space-frame angular momentum onto body axes
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and divide by principal moments
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------------------------------------------------------------------------- */
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void FixNVTASphere::omega_from_mq(double *q, double *m, double *inertia,
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double *w)
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{
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double rot[3][3];
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MathExtra::quat_to_mat(q,rot);
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double wbody[3];
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MathExtra::transpose_times_column3(rot,m,wbody);
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wbody[0] /= inertia[0];
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wbody[1] /= inertia[1];
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wbody[2] /= inertia[2];
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MathExtra::times_column3(rot,wbody,w);
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}
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/* ----------------------------------------------------------------------
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calculate the moment of inertia for an ELLIPSOID, from mass and radii
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shape = x,y,z radii in body frame
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------------------------------------------------------------------------- */
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void FixNVTASphere::calculate_inertia(double mass, double *shape,
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double *inertia)
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{
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inertia[0] = mass*(shape[1]*shape[1]+shape[2]*shape[2])/5.0;
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inertia[1] = mass*(shape[0]*shape[0]+shape[2]*shape[2])/5.0;
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inertia[2] = mass*(shape[0]*shape[0]+shape[1]*shape[1])/5.0;
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}
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