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lammps/src/fix_heat.cpp
Axel Kohlmeyer 69d9c5187e refactor group access, enable and apply clang-format
2022-04-15 15:29:43 -04:00

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Paul Crozier (SNL)
------------------------------------------------------------------------- */
#include "fix_heat.h"
#include "atom.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "group.h"
#include "input.h"
#include "memory.h"
#include "modify.h"
#include "region.h"
#include "update.h"
#include "variable.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace FixConst;
enum { CONSTANT, EQUAL, ATOM };
/* ---------------------------------------------------------------------- */
FixHeat::FixHeat(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg), idregion(nullptr), region(nullptr), hstr(nullptr), vheat(nullptr),
vscale(nullptr)
{
if (narg < 4) error->all(FLERR, "Illegal fix heat command");
scalar_flag = 1;
global_freq = 1;
extscalar = 0;
nevery = utils::inumeric(FLERR, arg[3], false, lmp);
if (nevery <= 0) error->all(FLERR, "Illegal fix heat command");
hstr = nullptr;
if (utils::strmatch(arg[4], "^v_")) {
hstr = utils::strdup(arg[4] + 2);
} else {
heat_input = utils::numeric(FLERR, arg[4], false, lmp);
hstyle = CONSTANT;
}
// optional args
int iarg = 5;
while (iarg < narg) {
if (strcmp(arg[iarg], "region") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Illegal fix heat command");
region = domain->get_region_by_id(arg[iarg + 1]);
if (!region) error->all(FLERR, "Region {} for fix heat does not exist", arg[iarg + 1]);
idregion = utils::strdup(arg[iarg + 1]);
iarg += 2;
} else
error->all(FLERR, "Illegal fix heat command");
}
scale = 1.0;
maxatom = 0;
}
/* ---------------------------------------------------------------------- */
FixHeat::~FixHeat()
{
delete[] hstr;
delete[] idregion;
memory->destroy(vheat);
memory->destroy(vscale);
}
/* ---------------------------------------------------------------------- */
int FixHeat::setmask()
{
int mask = 0;
mask |= END_OF_STEP;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixHeat::init()
{
// set index and check validity of region
if (idregion) {
region = domain->get_region_by_id(idregion);
if (!region) error->all(FLERR, "Region {} for fix heat does not exist", idregion);
}
// check variable
if (hstr) {
hvar = input->variable->find(hstr);
if (hvar < 0) error->all(FLERR, "Variable name for fix heat does not exist");
if (input->variable->equalstyle(hvar))
hstyle = EQUAL;
else if (input->variable->atomstyle(hvar))
hstyle = ATOM;
else
error->all(FLERR, "Variable for fix heat is invalid style");
}
// check for rigid bodies in region (done here for performance reasons)
if (region && modify->check_rigid_region_overlap(groupbit, region))
error->warning(FLERR, "Cannot apply fix heat to atoms in rigid bodies");
// cannot have 0 atoms in group
if (group->count(igroup) == 0) error->all(FLERR, "Fix heat group has no atoms");
masstotal = group->mass(igroup);
if (masstotal <= 0.0) error->all(FLERR, "Fix heat group has invalid mass");
}
/* ---------------------------------------------------------------------- */
void FixHeat::end_of_step()
{
int i;
double heat, ke, massone;
double vsub[3], vcm[3];
double **x = atom->x;
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int *type = atom->type;
double *mass = atom->mass;
double *rmass = atom->rmass;
// reallocate per-atom arrays if necessary
if (hstyle == ATOM && atom->nmax > maxatom) {
maxatom = atom->nmax;
memory->destroy(vheat);
memory->destroy(vscale);
memory->create(vheat, maxatom, "heat:vheat");
memory->create(vscale, maxatom, "heat:vscale");
}
// evaluate variable
if (hstyle != CONSTANT) {
modify->clearstep_compute();
if (hstyle == EQUAL)
heat_input = input->variable->compute_equal(hvar);
else
input->variable->compute_atom(hvar, igroup, vheat, 1, 0);
modify->addstep_compute(update->ntimestep + nevery);
}
// vcm = center-of-mass velocity of scaled atoms
if (region) {
masstotal = group->mass(igroup, region);
if (masstotal == 0.0) error->all(FLERR, "Fix heat group has no atoms");
ke = group->ke(igroup, region) * force->ftm2v;
group->vcm(igroup, masstotal, vcm, region);
} else {
ke = group->ke(igroup) * force->ftm2v;
group->vcm(igroup, masstotal, vcm);
}
double vcmsq = vcm[0] * vcm[0] + vcm[1] * vcm[1] + vcm[2] * vcm[2];
// add heat via scale factor on velocities for CONSTANT and EQUAL cases
// scale = velocity scale factor to accomplish eflux change in energy
// vsub = velocity subtracted from each atom to preserve momentum
// overall KE cannot go negative
if (region) region->prematch();
if (hstyle != ATOM) {
heat = heat_input * nevery * update->dt * force->ftm2v;
double escale = (ke + heat - 0.5 * vcmsq * masstotal) / (ke - 0.5 * vcmsq * masstotal);
if (escale < 0.0) error->all(FLERR, "Fix heat kinetic energy went negative");
scale = sqrt(escale);
vsub[0] = (scale - 1.0) * vcm[0];
vsub[1] = (scale - 1.0) * vcm[1];
vsub[2] = (scale - 1.0) * vcm[2];
if (region) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0], x[i][1], x[i][2])) {
v[i][0] = scale * v[i][0] - vsub[0];
v[i][1] = scale * v[i][1] - vsub[1];
v[i][2] = scale * v[i][2] - vsub[2];
}
} else {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
v[i][0] = scale * v[i][0] - vsub[0];
v[i][1] = scale * v[i][1] - vsub[1];
v[i][2] = scale * v[i][2] - vsub[2];
}
}
// add heat via per-atom scale factor on velocities for ATOM case
// vscale = velocity scale factor to accomplish eflux change in energy
// vsub = velocity subtracted from each atom to preserve momentum
// KE of an atom cannot go negative
} else {
vsub[0] = vsub[1] = vsub[2] = 0.0;
if (region) {
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit && region->match(x[i][0], x[i][1], x[i][2])) {
heat = vheat[i] * nevery * update->dt * force->ftm2v;
vscale[i] = (ke + heat - 0.5 * vcmsq * masstotal) / (ke - 0.5 * vcmsq * masstotal);
if (vscale[i] < 0.0)
error->all(FLERR, "Fix heat kinetic energy of an atom went negative");
scale = sqrt(vscale[i]);
if (rmass)
massone = rmass[i];
else
massone = mass[type[i]];
vsub[0] += (scale - 1.0) * v[i][0] * massone;
vsub[1] += (scale - 1.0) * v[i][1] * massone;
vsub[2] += (scale - 1.0) * v[i][2] * massone;
}
}
vsub[0] /= masstotal;
vsub[1] /= masstotal;
vsub[2] /= masstotal;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0], x[i][1], x[i][2])) {
scale = sqrt(vscale[i]);
v[i][0] = scale * v[i][0] - vsub[0];
v[i][1] = scale * v[i][1] - vsub[1];
v[i][2] = scale * v[i][2] - vsub[2];
}
} else {
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
heat = vheat[i] * nevery * update->dt * force->ftm2v;
vscale[i] = (ke + heat - 0.5 * vcmsq * masstotal) / (ke - 0.5 * vcmsq * masstotal);
if (vscale[i] < 0.0)
error->all(FLERR, "Fix heat kinetic energy of an atom went negative");
scale = sqrt(vscale[i]);
if (rmass)
massone = rmass[i];
else
massone = mass[type[i]];
vsub[0] += (scale - 1.0) * v[i][0] * massone;
vsub[1] += (scale - 1.0) * v[i][1] * massone;
vsub[2] += (scale - 1.0) * v[i][2] * massone;
}
}
vsub[0] /= masstotal;
vsub[1] /= masstotal;
vsub[2] /= masstotal;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
scale = sqrt(vscale[i]);
v[i][0] = scale * v[i][0] - vsub[0];
v[i][1] = scale * v[i][1] - vsub[1];
v[i][2] = scale * v[i][2] - vsub[2];
}
}
}
}
/* ---------------------------------------------------------------------- */
double FixHeat::compute_scalar()
{
double average_scale = scale;
if (hstyle == ATOM) {
if (!vscale) return 1.0;
double scale_sum = 0.0;
int ncount = 0;
int *mask = atom->mask;
double **x = atom->x;
int nlocal = atom->nlocal;
if (region) {
region->prematch();
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit && region->match(x[i][0], x[i][1], x[i][2])) {
scale_sum += sqrt(vscale[i]);
ncount++;
}
}
} else {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
scale_sum += sqrt(vscale[i]);
ncount++;
}
}
}
double scale_sum_all = 0.0;
int ncount_all = 0;
MPI_Allreduce(&scale_sum, &scale_sum_all, 1, MPI_DOUBLE, MPI_SUM, world);
MPI_Allreduce(&ncount, &ncount_all, 1, MPI_INT, MPI_SUM, world);
if (ncount_all == 0)
average_scale = 0.0;
else
average_scale = scale_sum_all / static_cast<double>(ncount_all);
}
return average_scale;
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double FixHeat::memory_usage()
{
double bytes = 0.0;
if (hstyle == ATOM) bytes = atom->nmax * 2 * sizeof(double);
return bytes;
}
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