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lammps-gran-kokkos/src/compute_temp_sphere.cpp
Stan Moore 2c738669ff compute_temp_sphere does not modify positions
2024-10-04 16:16:02 -06:00

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "compute_temp_sphere.h"
#include "atom.h"
#include "atom_masks.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "group.h"
#include "modify.h"
#include "update.h"
#include <cstring>
using namespace LAMMPS_NS;
enum { ROTATE, ALL };
static constexpr double INERTIA = 0.4; // moment of inertia prefactor for sphere
/* ---------------------------------------------------------------------- */
ComputeTempSphere::ComputeTempSphere(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg), id_bias(nullptr)
{
if (narg < 3) utils::missing_cmd_args(FLERR, "compute temp/sphere", error);
scalar_flag = vector_flag = 1;
size_vector = 6;
extscalar = 0;
extvector = 1;
tempflag = 1;
tempbias = 0;
mode = ALL;
int iarg = 3;
while (iarg < narg) {
if (strcmp(arg[iarg], "bias") == 0) {
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "compute temp/sphere bias", error);
tempbias = 1;
id_bias = utils::strdup(arg[iarg + 1]);
iarg += 2;
} else if (strcmp(arg[iarg], "dof") == 0) {
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "compute temp/sphere dof", error);
if (strcmp(arg[iarg + 1], "rotate") == 0)
mode = ROTATE;
else if (strcmp(arg[iarg + 1], "all") == 0)
mode = ALL;
else
error->all(FLERR, "Unknown compute temp/sphere dof keyword {}", arg[iarg + 1]);
iarg += 2;
} else
error->all(FLERR, "Unknown compute temp/sphere keyword {}", arg[iarg]);
}
// when computing only the rotational temperature,
// do not remove DOFs for translation as set by default
if (mode == ROTATE) extra_dof = 0;
vector = new double[size_vector];
// error checks
if (!atom->omega_flag) error->all(FLERR, "Compute temp/sphere requires atom attribute omega");
if (!atom->radius_flag) error->all(FLERR, "Compute temp/sphere requires atom attribute radius");
datamask_modify = ALL_MASK & ~X_MASK;
}
/* ---------------------------------------------------------------------- */
ComputeTempSphere::~ComputeTempSphere()
{
delete[] id_bias;
delete[] vector;
}
/* ---------------------------------------------------------------------- */
void ComputeTempSphere::init()
{
if (tempbias) {
tbias = modify->get_compute_by_id(id_bias);
if (!tbias) error->all(FLERR, "Could not find compute {} for temperature bias", id_bias);
if (tbias->tempflag == 0) error->all(FLERR, "Bias compute does not calculate temperature");
if (tbias->tempbias == 0) error->all(FLERR, "Bias compute does not calculate a velocity bias");
if (tbias->igroup != igroup)
error->all(FLERR, "Bias compute group does not match compute group");
if (strcmp(tbias->style, "temp/region") == 0)
tempbias = 2;
else
tempbias = 1;
// init and setup bias compute because
// this compute's setup()->dof_compute() may be called first
tbias->init();
tbias->setup();
}
}
/* ---------------------------------------------------------------------- */
void ComputeTempSphere::setup()
{
dynamic = 0;
if (dynamic_user || group->dynamic[igroup]) dynamic = 1;
dof_compute();
}
/* ---------------------------------------------------------------------- */
void ComputeTempSphere::dof_compute()
{
int count, count_all;
adjust_dof_fix();
natoms_temp = group->count(igroup);
// 6 or 3 dof for extended/point particles for 3d
// 3 or 2 dof for extended/point particles for 2d
// which dof are included also depends on mode
// assume full rotation of extended particles
// user should correct this via compute_modify if needed
double *radius = atom->radius;
const int *mask = atom->mask;
const int nlocal = atom->nlocal;
count = 0;
if (domain->dimension == 3) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (radius[i] == 0.0) {
if (mode == ALL) count += 3;
} else {
if (mode == ALL)
count += 6;
else
count += 3;
}
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (radius[i] == 0.0) {
if (mode == ALL) count += 2;
} else {
if (mode == ALL)
count += 3;
else
count += 1;
}
}
}
MPI_Allreduce(&count, &count_all, 1, MPI_INT, MPI_SUM, world);
dof = count_all;
// additional adjustments to dof
if (tempbias == 1) {
if (mode == ALL) dof -= tbias->dof_remove(-1) * natoms_temp;
} else if (tempbias == 2) {
tbias->dof_remove_pre();
count = 0;
if (domain->dimension == 3) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (tbias->dof_remove(i)) {
if (radius[i] == 0.0) {
if (mode == ALL) count += 3;
} else {
if (mode == ALL)
count += 6;
else
count += 3;
}
}
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (tbias->dof_remove(i)) {
if (radius[i] == 0.0) {
if (mode == ALL) count += 2;
} else {
if (mode == ALL)
count += 3;
else
count += 1;
}
}
}
}
MPI_Allreduce(&count, &count_all, 1, MPI_INT, MPI_SUM, world);
dof -= count_all;
}
dof -= extra_dof + fix_dof;
if (dof > 0)
tfactor = force->mvv2e / (dof * force->boltz);
else
tfactor = 0.0;
}
/* ---------------------------------------------------------------------- */
double ComputeTempSphere::compute_scalar()
{
invoked_scalar = update->ntimestep;
if (tempbias) {
if (tbias->invoked_scalar != update->ntimestep) tbias->compute_scalar();
tbias->remove_bias_all();
}
double **v = atom->v;
double **omega = atom->omega;
double *radius = atom->radius;
double *rmass = atom->rmass;
int *mask = atom->mask;
int nlocal = atom->nlocal;
// point particles will not contribute rotation due to radius = 0
double t = 0.0;
// clang-format off
if (mode == ALL) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) * rmass[i];
t += (omega[i][0]*omega[i][0] + omega[i][1]*omega[i][1] +
omega[i][2]*omega[i][2]) * INERTIA*rmass[i]*radius[i]*radius[i];
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
t += (omega[i][0]*omega[i][0] + omega[i][1]*omega[i][1] +
omega[i][2]*omega[i][2]) * INERTIA*rmass[i]*radius[i]*radius[i];
}
// clang-format on
if (tempbias) tbias->restore_bias_all();
MPI_Allreduce(&t, &scalar, 1, MPI_DOUBLE, MPI_SUM, world);
if (dynamic || tempbias == 2) dof_compute();
if (dof < 0.0 && natoms_temp > 0.0)
error->all(FLERR, "Temperature compute degrees of freedom < 0");
scalar *= tfactor;
return scalar;
}
/* ---------------------------------------------------------------------- */
void ComputeTempSphere::compute_vector()
{
invoked_vector = update->ntimestep;
if (tempbias) {
if (tbias->invoked_vector != update->ntimestep) tbias->compute_vector();
tbias->remove_bias_all();
}
double **v = atom->v;
double **omega = atom->omega;
double *rmass = atom->rmass;
double *radius = atom->radius;
int *mask = atom->mask;
int nlocal = atom->nlocal;
// point particles will not contribute rotation due to radius = 0
double massone, inertiaone, t[6];
for (auto &ti : t) ti = 0.0;
if (mode == ALL) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
massone = rmass[i];
t[0] += massone * v[i][0] * v[i][0];
t[1] += massone * v[i][1] * v[i][1];
t[2] += massone * v[i][2] * v[i][2];
t[3] += massone * v[i][0] * v[i][1];
t[4] += massone * v[i][0] * v[i][2];
t[5] += massone * v[i][1] * v[i][2];
inertiaone = INERTIA * rmass[i] * radius[i] * radius[i];
t[0] += inertiaone * omega[i][0] * omega[i][0];
t[1] += inertiaone * omega[i][1] * omega[i][1];
t[2] += inertiaone * omega[i][2] * omega[i][2];
t[3] += inertiaone * omega[i][0] * omega[i][1];
t[4] += inertiaone * omega[i][0] * omega[i][2];
t[5] += inertiaone * omega[i][1] * omega[i][2];
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
inertiaone = INERTIA * rmass[i] * radius[i] * radius[i];
t[0] += inertiaone * omega[i][0] * omega[i][0];
t[1] += inertiaone * omega[i][1] * omega[i][1];
t[2] += inertiaone * omega[i][2] * omega[i][2];
t[3] += inertiaone * omega[i][0] * omega[i][1];
t[4] += inertiaone * omega[i][0] * omega[i][2];
t[5] += inertiaone * omega[i][1] * omega[i][2];
}
}
if (tempbias) tbias->restore_bias_all();
MPI_Allreduce(t, vector, 6, MPI_DOUBLE, MPI_SUM, world);
for (int i = 0; i < 6; i++) vector[i] *= force->mvv2e;
}
/* ----------------------------------------------------------------------
remove velocity bias from atom I to leave thermal velocity
------------------------------------------------------------------------- */
void ComputeTempSphere::remove_bias(int i, double *v)
{
tbias->remove_bias(i, v);
}
/* ----------------------------------------------------------------------
remove velocity bias from atom I to leave thermal velocity
------------------------------------------------------------------------- */
void ComputeTempSphere::remove_bias_thr(int i, double *v, double *b)
{
tbias->remove_bias_thr(i, v, b);
}
/* ----------------------------------------------------------------------
add back in velocity bias to atom I removed by remove_bias()
assume remove_bias() was previously called
------------------------------------------------------------------------- */
void ComputeTempSphere::restore_bias(int i, double *v)
{
tbias->restore_bias(i, v);
}
/* ----------------------------------------------------------------------
add back in velocity bias to atom I removed by remove_bias_thr()
assume remove_bias_thr() was previously called with the same buffer b
------------------------------------------------------------------------- */
void ComputeTempSphere::restore_bias_thr(int i, double *v, double *b)
{
tbias->restore_bias_thr(i, v, b);
}
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