356 lines
10 KiB
C++
356 lines
10 KiB
C++
// clang-format off
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://www.lammps.org/, 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 "compute_temp_sphere.h"
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#include <cstring>
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#include "atom.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 "error.h"
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using namespace LAMMPS_NS;
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enum{ROTATE,ALL};
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#define INERTIA 0.4 // moment of inertia prefactor for sphere
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/* ---------------------------------------------------------------------- */
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ComputeTempSphere::ComputeTempSphere(LAMMPS *lmp, int narg, char **arg) :
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Compute(lmp, narg, arg),
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id_bias(nullptr)
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{
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if (narg < 3) error->all(FLERR,"Illegal compute temp/sphere 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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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/sphere command");
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tempbias = 1;
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id_bias = utils::strdup(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/sphere 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/sphere command");
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iarg += 2;
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} else error->all(FLERR,"Illegal compute temp/sphere 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[size_vector];
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// error checks
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if (!atom->sphere_flag)
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error->all(FLERR,"Compute temp/sphere requires atom style sphere");
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}
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/* ---------------------------------------------------------------------- */
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ComputeTempSphere::~ComputeTempSphere()
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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 ComputeTempSphere::init()
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{
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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 ComputeTempSphere::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 ComputeTempSphere::dof_compute()
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{
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int count,count_all;
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adjust_dof_fix();
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natoms_temp = group->count(igroup);
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// 6 or 3 dof for extended/point particles for 3d
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// 3 or 2 dof for extended/point particles 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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double *radius = atom->radius;
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const int *mask = atom->mask;
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const int nlocal = atom->nlocal;
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count = 0;
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if (domain->dimension == 3) {
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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if (radius[i] == 0.0) {
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if (mode == ALL) count += 3;
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} else {
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if (mode == ALL) count += 6;
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else count += 3;
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}
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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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if (radius[i] == 0.0) {
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if (mode == ALL) count += 2;
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} else {
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if (mode == ALL) count += 3;
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else count += 1;
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}
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}
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}
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MPI_Allreduce(&count,&count_all,1,MPI_INT,MPI_SUM,world);
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dof = count_all;
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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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tbias->dof_remove_pre();
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count = 0;
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if (domain->dimension == 3) {
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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)) {
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if (radius[i] == 0.0) {
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if (mode == ALL) count += 3;
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} else {
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if (mode == ALL) count += 6;
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else count += 3;
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}
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}
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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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if (tbias->dof_remove(i)) {
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if (radius[i] == 0.0) {
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if (mode == ALL) count += 2;
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} else {
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if (mode == ALL) count += 3;
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else count += 1;
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}
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}
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}
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}
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MPI_Allreduce(&count,&count_all,1,MPI_INT,MPI_SUM,world);
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dof -= 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 ComputeTempSphere::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 **omega = atom->omega;
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double *radius = atom->radius;
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double *rmass = atom->rmass;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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// point particles will not contribute rotation due to radius = 0
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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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t += (omega[i][0]*omega[i][0] + omega[i][1]*omega[i][1] +
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omega[i][2]*omega[i][2]) * INERTIA*rmass[i]*radius[i]*radius[i];
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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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t += (omega[i][0]*omega[i][0] + omega[i][1]*omega[i][1] +
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omega[i][2]*omega[i][2]) * INERTIA*rmass[i]*radius[i]*radius[i];
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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 ComputeTempSphere::compute_vector()
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{
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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 **omega = atom->omega;
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double *rmass = atom->rmass;
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double *radius = atom->radius;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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// point particles will not contribute rotation due to radius = 0
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double massone,inertiaone,t[6];
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for (auto &ti : t) ti = 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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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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inertiaone = INERTIA*rmass[i]*radius[i]*radius[i];
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t[0] += inertiaone * omega[i][0]*omega[i][0];
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t[1] += inertiaone * omega[i][1]*omega[i][1];
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t[2] += inertiaone * omega[i][2]*omega[i][2];
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t[3] += inertiaone * omega[i][0]*omega[i][1];
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t[4] += inertiaone * omega[i][0]*omega[i][2];
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t[5] += inertiaone * omega[i][1]*omega[i][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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inertiaone = INERTIA*rmass[i]*radius[i]*radius[i];
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t[0] += inertiaone * omega[i][0]*omega[i][0];
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t[1] += inertiaone * omega[i][1]*omega[i][1];
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t[2] += inertiaone * omega[i][2]*omega[i][2];
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t[3] += inertiaone * omega[i][0]*omega[i][1];
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t[4] += inertiaone * omega[i][0]*omega[i][2];
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t[5] += inertiaone * omega[i][1]*omega[i][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 (int 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 ComputeTempSphere::remove_bias(int i, double *v)
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{
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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 ComputeTempSphere::remove_bias_thr(int i, double *v, double *b)
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{
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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 ComputeTempSphere::restore_bias(int i, double *v)
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{
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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 ComputeTempSphere::restore_bias_thr(int i, double *v, double *b)
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{
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tbias->restore_bias_thr(i,v,b);
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}
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