git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@622 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
227
src/ASPHERE/compute_temp_asphere.cpp
Executable file
227
src/ASPHERE/compute_temp_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 "mpi.h"
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#include "compute_temp_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 "modify.h"
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#include "fix.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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/* ---------------------------------------------------------------------- */
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ComputeTempAsphere::ComputeTempAsphere(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 temp command");
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if (atom->quat == NULL || atom->angmom == NULL)
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error->all("Compute temp/asphere requires atom attributes quat, angmom");
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scalar_flag = vector_flag = 1;
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size_vector = 6;
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extensive = 0;
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tempflag = 1;
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vector = new double[6];
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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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ComputeTempAsphere::~ComputeTempAsphere()
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{
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delete [] vector;
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memory->destroy_2d_double_array(inertia);
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}
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/* ---------------------------------------------------------------------- */
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void ComputeTempAsphere::init()
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{
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fix_dof = 0;
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for (int i = 0; i < modify->nfix; i++)
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fix_dof += modify->fix[i]->dof(igroup);
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recount();
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calculate_inertia();
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}
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/* ---------------------------------------------------------------------- */
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void ComputeTempAsphere::recount()
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{
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double natoms = group->count(igroup);
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dof = force->dimension * natoms;
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dof -= extra_dof + fix_dof;
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// add rotational degrees of freedom
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// 0 for sphere, 2 for uniaxial, 3 for biaxial
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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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int itype;
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int rot_dof = 0;
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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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if (shape[itype][0] == shape[itype][1] &&
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shape[itype][1] == shape[itype][2]) continue;
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else if (shape[itype][0] == shape[itype][1] ||
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shape[itype][1] == shape[itype][2] ||
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shape[itype][0] == shape[itype][2]) rot_dof += 2;
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else rot_dof += 3;
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}
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int rot_total;
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MPI_Allreduce(&rot_dof,&rot_total,1,MPI_INT,MPI_SUM,world);
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dof += rot_total;
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if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz);
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else tfactor = 0.0;
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}
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/* ---------------------------------------------------------------------- */
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double ComputeTempAsphere::compute_scalar()
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{
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double **v = atom->v;
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double **quat = atom->quat;
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double **angmom = atom->angmom;
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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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int itype;
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double wbody[3];
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double rot[3][3];
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double t = 0.0;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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// translational kinetic energy
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itype = type[i];
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t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) * mass[itype];
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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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// rotational kinetic energy
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t += 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(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
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if (dynamic) recount();
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scalar *= tfactor;
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return scalar;
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}
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/* ---------------------------------------------------------------------- */
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void ComputeTempAsphere::compute_vector()
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{
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int i;
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double **v = atom->v;
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double **quat = atom->quat;
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double **angmom = atom->angmom;
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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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int itype;
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double wbody[3];
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double rot[3][3];
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double massone,t[6];
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for (i = 0; i < 6; i++) t[i] = 0.0;
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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// translational kinetic energy
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itype = type[i];
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massone = mass[itype];
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t[0] += massone * v[i][0]*v[i][0];
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t[1] += massone * v[i][1]*v[i][1];
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t[2] += massone * v[i][2]*v[i][2];
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t[3] += massone * v[i][0]*v[i][1];
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t[4] += massone * v[i][0]*v[i][2];
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t[5] += massone * v[i][1]*v[i][2];
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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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// rotational kinetic energy
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t[0] += inertia[itype][0]*wbody[0]*wbody[0];
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t[1] += inertia[itype][1]*wbody[1]*wbody[1];
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t[2] += inertia[itype][2]*wbody[2]*wbody[2];
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t[3] += inertia[itype][0]*wbody[0]*wbody[1];
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t[4] += inertia[itype][1]*wbody[0]*wbody[2];
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t[5] += inertia[itype][2]*wbody[1]*wbody[2];
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}
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MPI_Allreduce(t,vector,6,MPI_DOUBLE,MPI_SUM,world);
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for (i = 0; i < 6; i++) vector[i] *= force->mvv2e;
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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 ComputeTempAsphere::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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