git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@622 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
236
src/ASPHERE/fix_nve_asphere.cpp
Executable file
236
src/ASPHERE/fix_nve_asphere.cpp
Executable file
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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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/* ----------------------------------------------------------------------
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Contributing author: Mike Brown (SNL)
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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_asphere.h"
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#include "math_extra.h"
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#include "atom.h"
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#include "force.h"
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#include "update.h"
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#include "memory.h"
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#include "error.h"
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#define TOLERANCE 1.0e-6
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#define EPSILON 1.0e-7
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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FixNVEASphere::FixNVEASphere(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/asphere command");
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if (atom->quat == NULL || atom->angmom == NULL || atom->torque == NULL)
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error->all("Fix nve/asphere requires atom attributes "
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"quat, angmom, torque");
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inertia =
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memory->create_2d_double_array(atom->ntypes+1,3,"fix_temp_sphere:inertia");
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}
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/* ---------------------------------------------------------------------- */
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FixNVEASphere::~FixNVEASphere()
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{
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memory->destroy_2d_double_array(inertia);
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}
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/* ---------------------------------------------------------------------- */
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int FixNVEASphere::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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return mask;
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}
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/* ---------------------------------------------------------------------- */
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void FixNVEASphere::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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dtq = 0.5 * update->dt;
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calculate_inertia();
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}
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/* ---------------------------------------------------------------------- */
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void FixNVEASphere::initial_integrate()
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{
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double dtfm;
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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 < atom->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] += 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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// 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] += dtf * torque[i][0];
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angmom[i][1] += dtf * torque[i][1];
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angmom[i][2] += dtf * torque[i][2];
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richardson(quat[i],angmom[i],inertia[type[i]]);
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}
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}
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/* ---------------------------------------------------------------------- */
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void FixNVEASphere::final_integrate()
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{
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double dtfm;
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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[atom->type[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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angmom[i][0] += dtf * torque[i][0];
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angmom[i][1] += dtf * torque[i][1];
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angmom[i][2] += dtf * torque[i][2];
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}
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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 FixNVEASphere::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 FixNVEASphere::omega_from_mq(double *q, double *m, double *moments,
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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] /= moments[0];
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wbody[1] /= moments[1];
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wbody[2] /= moments[2];
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MathExtra::times_column3(rot,wbody,w);
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}
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/* ----------------------------------------------------------------------
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principal moments of inertia for ellipsoids
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------------------------------------------------------------------------- */
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void FixNVEASphere::calculate_inertia()
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{
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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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inertia[i][0] = mass[i] *
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(shape[i][1]*shape[i][1]+shape[i][2]*shape[i][2]) / 5.0;
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inertia[i][1] = mass[i] *
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(shape[i][0]*shape[i][0]+shape[i][2]*shape[i][2]) / 5.0;
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inertia[i][2] = mass[i] *
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(shape[i][0]*shape[i][0]+shape[i][1]*shape[i][1]) / 5.0;
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}
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}
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