427 lines
13 KiB
C++
427 lines
13 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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/* ----------------------------------------------------------------------
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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 <cstring>
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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_ellipsoid.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 "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{ROTATE,ALL};
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#define INERTIA 0.2 // moment of inertia prefactor for ellipsoid
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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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id_bias(NULL), tbias(NULL), avec(NULL)
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{
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if (narg < 3) error->all(FLERR,"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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mode = ALL;
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int iarg = 3;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"bias") == 0) {
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if (iarg+2 > narg)
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error->all(FLERR,"Illegal compute temp/asphere command");
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tempbias = 1;
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int n = strlen(arg[iarg+1]) + 1;
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id_bias = new char[n];
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strcpy(id_bias,arg[iarg+1]);
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iarg += 2;
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} else if (strcmp(arg[iarg],"dof") == 0) {
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if (iarg+2 > narg)
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error->all(FLERR,"Illegal compute temp/asphere command");
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if (strcmp(arg[iarg+1],"rotate") == 0) mode = ROTATE;
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else if (strcmp(arg[iarg+1],"all") == 0) mode = ALL;
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else error->all(FLERR,"Illegal compute temp/asphere command");
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iarg += 2;
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} else error->all(FLERR,"Illegal compute temp/asphere command");
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}
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// when computing only the rotational temperature,
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// do not remove DOFs for translation as set by default
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if (mode == ROTATE) extra_dof = 0;
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vector = new double[6];
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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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}
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/* ---------------------------------------------------------------------- */
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void ComputeTempAsphere::init()
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{
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// error check
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avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
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if (!avec)
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error->all(FLERR,"Compute temp/asphere requires atom style ellipsoid");
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// check that all particles are finite-size, no point particles allowed
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int *ellipsoid = atom->ellipsoid;
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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 (ellipsoid[i] < 0)
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error->one(FLERR,"Compute 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)
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error->all(FLERR,"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(FLERR,"Bias compute does not calculate temperature");
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if (tbias->tempbias == 0)
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error->all(FLERR,"Bias compute does not calculate a velocity bias");
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if (tbias->igroup != igroup)
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error->all(FLERR,"Bias compute group does not match compute group");
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if (strcmp(tbias->style,"temp/region") == 0) tempbias = 2;
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else tempbias = 1;
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// init and setup bias compute because
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// this compute's setup()->dof_compute() may be called first
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tbias->init();
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tbias->setup();
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}
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}
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/* ---------------------------------------------------------------------- */
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void ComputeTempAsphere::setup()
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{
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dynamic = 0;
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if (dynamic_user || group->dynamic[igroup]) dynamic = 1;
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dof_compute();
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}
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/* ---------------------------------------------------------------------- */
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void ComputeTempAsphere::dof_compute()
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{
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adjust_dof_fix();
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// 6 dof for 3d, 3 dof for 2d
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// which dof are included also depends on mode
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// assume full rotation of extended particles
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// user should correct this via compute_modify if needed
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natoms_temp = group->count(igroup);
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int nper;
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if (domain->dimension == 3) {
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if (mode == ALL) nper = 6;
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else nper = 3;
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} else {
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if (mode == ALL) nper = 3;
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else nper = 1;
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}
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dof = nper*natoms_temp;
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// additional adjustments to dof
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if (tempbias == 1) {
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if (mode == ALL) dof -= tbias->dof_remove(-1) * natoms_temp;
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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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tbias->dof_remove_pre();
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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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dof -= nper*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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AtomVecEllipsoid::Bonus *bonus = avec->bonus;
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double **v = atom->v;
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double **angmom = atom->angmom;
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double *rmass = atom->rmass;
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int *ellipsoid = atom->ellipsoid;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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double *shape,*quat;
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double wbody[3],inertia[3];
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double rot[3][3];
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// sum translational and rotational energy for each particle
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// no point particles since divide by inertia
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double t = 0.0;
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if (mode == ALL) {
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) * rmass[i];
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// principal moments of inertia
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shape = bonus[ellipsoid[i]].shape;
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quat = bonus[ellipsoid[i]].quat;
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inertia[0] = INERTIA*rmass[i] * (shape[1]*shape[1]+shape[2]*shape[2]);
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inertia[1] = INERTIA*rmass[i] * (shape[0]*shape[0]+shape[2]*shape[2]);
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inertia[2] = INERTIA*rmass[i] * (shape[0]*shape[0]+shape[1]*shape[1]);
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// wbody = angular velocity in body frame
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MathExtra::quat_to_mat(quat,rot);
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MathExtra::transpose_matvec(rot,angmom[i],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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t += inertia[0]*wbody[0]*wbody[0] +
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inertia[1]*wbody[1]*wbody[1] + inertia[2]*wbody[2]*wbody[2];
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}
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} else {
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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// principal moments of inertia
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shape = bonus[ellipsoid[i]].shape;
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quat = bonus[ellipsoid[i]].quat;
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inertia[0] = INERTIA*rmass[i] * (shape[1]*shape[1]+shape[2]*shape[2]);
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inertia[1] = INERTIA*rmass[i] * (shape[0]*shape[0]+shape[2]*shape[2]);
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inertia[2] = INERTIA*rmass[i] * (shape[0]*shape[0]+shape[1]*shape[1]);
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// wbody = angular velocity in body frame
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MathExtra::quat_to_mat(quat,rot);
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MathExtra::transpose_matvec(rot,angmom[i],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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t += inertia[0]*wbody[0]*wbody[0] +
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inertia[1]*wbody[1]*wbody[1] + inertia[2]*wbody[2]*wbody[2];
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}
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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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if (dof < 0.0 && natoms_temp > 0.0)
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error->all(FLERR,"Temperature compute degrees of freedom < 0");
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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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AtomVecEllipsoid::Bonus *bonus = avec->bonus;
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double **v = atom->v;
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double **angmom = atom->angmom;
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double *rmass = atom->rmass;
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int *ellipsoid = atom->ellipsoid;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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double *shape,*quat;
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double wbody[3],inertia[3],t[6];
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double rot[3][3];
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double massone;
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// sum translational and rotational energy for each particle
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// no point particles since divide by inertia
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for (i = 0; i < 6; i++) t[i] = 0.0;
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if (mode == ALL) {
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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massone = rmass[i];
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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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// principal moments of inertia
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shape = bonus[ellipsoid[i]].shape;
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quat = bonus[ellipsoid[i]].quat;
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inertia[0] = INERTIA*massone * (shape[1]*shape[1]+shape[2]*shape[2]);
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inertia[1] = INERTIA*massone * (shape[0]*shape[0]+shape[2]*shape[2]);
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inertia[2] = INERTIA*massone * (shape[0]*shape[0]+shape[1]*shape[1]);
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// wbody = angular velocity in body frame
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MathExtra::quat_to_mat(quat,rot);
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MathExtra::transpose_matvec(rot,angmom[i],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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// rotational kinetic energy
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t[0] += inertia[0]*wbody[0]*wbody[0];
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t[1] += inertia[1]*wbody[1]*wbody[1];
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t[2] += inertia[2]*wbody[2]*wbody[2];
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t[3] += inertia[0]*wbody[0]*wbody[1];
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t[4] += inertia[1]*wbody[0]*wbody[2];
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t[5] += inertia[2]*wbody[1]*wbody[2];
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}
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} else {
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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// principal moments of inertia
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shape = bonus[ellipsoid[i]].shape;
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quat = bonus[ellipsoid[i]].quat;
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massone = rmass[i];
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inertia[0] = INERTIA*massone * (shape[1]*shape[1]+shape[2]*shape[2]);
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inertia[1] = INERTIA*massone * (shape[0]*shape[0]+shape[2]*shape[2]);
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inertia[2] = INERTIA*massone * (shape[0]*shape[0]+shape[1]*shape[1]);
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// wbody = angular velocity in body frame
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MathExtra::quat_to_mat(quat,rot);
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MathExtra::transpose_matvec(rot,angmom[i],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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// rotational kinetic energy
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t[0] += inertia[0]*wbody[0]*wbody[0];
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t[1] += inertia[1]*wbody[1]*wbody[1];
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t[2] += inertia[2]*wbody[2]*wbody[2];
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t[3] += inertia[0]*wbody[0]*wbody[1];
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t[4] += inertia[1]*wbody[0]*wbody[2];
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t[5] += inertia[2]*wbody[1]*wbody[2];
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}
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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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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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remove velocity bias from atom I to leave thermal velocity
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------------------------------------------------------------------------- */
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void ComputeTempAsphere::remove_bias_thr(int i, double *v, double *b)
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{
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if (tbias) tbias->remove_bias_thr(i,v,b);
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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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/* ----------------------------------------------------------------------
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add back in velocity bias to atom I removed by remove_bias_thr()
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assume remove_bias_thr() was previously called with the same buffer b
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------------------------------------------------------------------------- */
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void ComputeTempAsphere::restore_bias_thr(int i, double *v, double *b)
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{
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if (tbias) tbias->restore_bias_thr(i,v,b);
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}
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