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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 "string.h"
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#include "stdlib.h"
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#include "math.h"
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#include "math_extra.h"
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#include "fix_nh_asphere.h"
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#include "atom.h"
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#include "atom_vec.h"
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#include "group.h"
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#include "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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enum{NOBIAS,BIAS};
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/* ---------------------------------------------------------------------- */
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FixNHAsphere::FixNHAsphere(LAMMPS *lmp, int narg, char **arg) :
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FixNH(lmp, narg, arg)
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{
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inertia =
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memory->create_2d_double_array(atom->ntypes+1,3,"fix_nvt_asphere:inertia");
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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/nph/npt asphere requires atom attributes "
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"quat, angmom, torque, shape");
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if (atom->radius_flag || atom->rmass_flag)
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error->all("Fix nvt/nph/npt asphere cannot be used with atom attributes "
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"diameter or rmass");
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}
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/* ---------------------------------------------------------------------- */
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FixNHAsphere::~FixNHAsphere()
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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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void FixNHAsphere::init()
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{
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// check that all particles are finite-size
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// no point particles allowed, spherical is OK
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double **shape = atom->shape;
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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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if (shape[type[i]][0] == 0.0)
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error->one("Fix nvt/nph/npt asphere requires extended particles");
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FixNH::init();
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calculate_inertia();
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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 FixNHAsphere::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 FixNHAsphere::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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principal moments of inertia for ellipsoids
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------------------------------------------------------------------------- */
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void FixNHAsphere::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] = 0.2*mass[i] *
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(shape[i][1]*shape[i][1]+shape[i][2]*shape[i][2]);
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inertia[i][1] = 0.2*mass[i] *
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(shape[i][0]*shape[i][0]+shape[i][2]*shape[i][2]);
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inertia[i][2] = 0.2*mass[i] *
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(shape[i][0]*shape[i][0]+shape[i][1]*shape[i][1]);
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}
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}
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/* ----------------------------------------------------------------------
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perform half-step update of velocities
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-----------------------------------------------------------------------*/
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void FixNHAsphere::nve_v()
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{
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// standard nhc_nve_v velocity update
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FixNH::nve_v();
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int *type = atom->type;
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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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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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// set timestep here since dt may have changed or come via rRESPA
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dtq = 0.5 * dtv;
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// update angular momentum by 1/2 step for all particles
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// update quaternion a full step via Richardson iteration
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// returns new normalized quaternion
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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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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/* ----------------------------------------------------------------------
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perform half-step temperature scaling of velocities
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-----------------------------------------------------------------------*/
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void FixNHAsphere::nh_v_temp()
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{
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// standard nhc_nh_v velocity update
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FixNH::nh_v_temp();
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double **angmom = atom->angmom;
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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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// set timestep here since dt may have changed or come via rRESPA
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double factor_rotate = exp(-dthalf*eta_dot[0]);
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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angmom[i][0] *= factor_rotate;
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angmom[i][1] *= factor_rotate;
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angmom[i][2] *= factor_rotate;
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}
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}
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}
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@ -0,0 +1,40 @@
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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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#ifndef LMP_FIX_NH_ASPHERE_H
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#define LMP_FIX_NH_ASPHERE_H
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#include "fix_nh.h"
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namespace LAMMPS_NS {
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class FixNHAsphere : public FixNH {
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public:
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FixNHAsphere(class LAMMPS *, int, char **);
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virtual ~FixNHAsphere();
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void init();
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protected:
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double dtq;
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double **inertia;
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void richardson(double *, double *, double *);
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void omega_from_mq(double *, double *, double *, double *);
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void calculate_inertia();
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void nve_v();
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void nh_v_temp();
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};
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}
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#endif
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