140 lines
4.0 KiB
C++
140 lines
4.0 KiB
C++
/* ----------------------------------------------------------------------
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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 "mpi.h"
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#include "compute_erotate_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 "update.h"
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#include "force.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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/* ---------------------------------------------------------------------- */
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ComputeERotateAsphere::
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ComputeERotateAsphere(LAMMPS *lmp, int narg, char **arg) :
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Compute(lmp, narg, arg)
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{
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if (narg != 3) error->all("Illegal compute erotate/asphere command");
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scalar_flag = 1;
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extscalar = 1;
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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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// error checks
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if (!atom->angmom_flag || !atom->quat_flag ||
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!atom->avec->shape_type)
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error->all("Compute erotate/asphere requires atom attributes "
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"angmom, quat, shape");
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if (atom->radius_flag || atom->rmass_flag)
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error->all("Compute erotate/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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ComputeERotateAsphere::~ComputeERotateAsphere()
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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 ComputeERotateAsphere::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("Compute erotate/asphere requires extended particles");
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pfactor = 0.5 * force->mvv2e;
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calculate_inertia();
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}
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/* ---------------------------------------------------------------------- */
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double ComputeERotateAsphere::compute_scalar()
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{
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int i,itype;
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invoked_scalar = update->ntimestep;
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double **quat = atom->quat;
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double **angmom = atom->angmom;
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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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// sum rotational energy for each particle
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// no point particles since divide by inertia
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double wbody[3];
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double rot[3][3];
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double erotate = 0.0;
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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itype = type[i];
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// wbody = angular velocity in body frame
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MathExtra::quat_to_mat(quat[i],rot);
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MathExtra::transpose_times_column3(rot,angmom[i],wbody);
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wbody[0] /= inertia[itype][0];
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wbody[1] /= inertia[itype][1];
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wbody[2] /= inertia[itype][2];
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erotate += inertia[itype][0]*wbody[0]*wbody[0]+
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inertia[itype][1]*wbody[1]*wbody[1]+
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inertia[itype][2]*wbody[2]*wbody[2];
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}
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MPI_Allreduce(&erotate,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
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scalar *= pfactor;
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return scalar;
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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 ComputeERotateAsphere::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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