312 lines
8.9 KiB
C++
Executable File
312 lines
8.9 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 "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 "atom_vec.h"
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#include "update.h"
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#include "force.h"
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#include "domain.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 && narg != 4)
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error->all("Illegal compute temp/asphere command");
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scalar_flag = vector_flag = 1;
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size_vector = 6;
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extscalar = 0;
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extvector = 1;
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tempflag = 1;
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tempbias = 0;
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id_bias = NULL;
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if (narg == 4) {
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tempbias = 1;
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int n = strlen(arg[3]) + 1;
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id_bias = new char[n];
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strcpy(id_bias,arg[3]);
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}
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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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// 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 temp/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 temp/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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ComputeTempAsphere::~ComputeTempAsphere()
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{
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delete [] id_bias;
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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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// 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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if (igroup == atom->firstgroup) nlocal = atom->nfirst;
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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("Compue temp/asphere requires extended particles");
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if (tempbias) {
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int i = modify->find_compute(id_bias);
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if (i < 0) error->all("Could not find compute ID for temperature bias");
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tbias = modify->compute[i];
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if (tbias->tempflag == 0)
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error->all("Bias compute does not calculate temperature");
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if (tbias->tempbias == 0)
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error->all("Bias compute does not calculate a velocity bias");
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if (tbias->igroup != igroup)
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error->all("Bias compute group does not match compute group");
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tbias->init();
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if (strcmp(tbias->style,"temp/region") == 0) tempbias = 2;
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else tempbias = 1;
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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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dof_compute();
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calculate_inertia();
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}
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/* ---------------------------------------------------------------------- */
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void ComputeTempAsphere::dof_compute()
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{
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// 6 dof for 3d, 3 dof for 2d
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// assume full rotation of extended particles
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// user can correct this via compute_modify if needed
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double natoms = group->count(igroup);
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if (domain->dimension == 3) dof = 6*natoms;
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else dof = 3*natoms;
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// additional adjustments to dof
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if (tempbias == 1) dof -= tbias->dof_remove(-1) * natoms;
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else if (tempbias == 2) {
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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int count = 0;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit)
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if (tbias->dof_remove(i)) count++;
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int count_all;
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MPI_Allreduce(&count,&count_all,1,MPI_INT,MPI_SUM,world);
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if (domain->dimension == 3) dof -= 6*count_all;
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else dof -= 3*count_all;
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}
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dof -= extra_dof + fix_dof;
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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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invoked_scalar = update->ntimestep;
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if (tempbias) {
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if (tbias->invoked_scalar != update->ntimestep) tbias->compute_scalar();
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tbias->remove_bias_all();
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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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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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double wbody[3];
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double rot[3][3];
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double t = 0.0;
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// sum translationals and rotational energy for each particle
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// no point particles since divide by inertia
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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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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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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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if (tempbias) tbias->restore_bias_all();
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MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
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if (dynamic || tempbias == 2) dof_compute();
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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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invoked_vector = update->ntimestep;
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if (tempbias) {
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if (tbias->invoked_vector != update->ntimestep) tbias->compute_vector();
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tbias->remove_bias_all();
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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 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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if (tempbias) tbias->restore_bias_all();
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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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/* ----------------------------------------------------------------------
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remove velocity bias from atom I to leave thermal velocity
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------------------------------------------------------------------------- */
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void ComputeTempAsphere::remove_bias(int i, double *v)
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{
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if (tbias) tbias->remove_bias(i,v);
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}
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/* ----------------------------------------------------------------------
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add back in velocity bias to atom I removed by remove_bias()
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assume remove_bias() was previously called
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------------------------------------------------------------------------- */
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void ComputeTempAsphere::restore_bias(int i, double *v)
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{
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if (tbias) tbias->restore_bias(i,v);
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}
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