124 lines
4.7 KiB
C++
124 lines
4.7 KiB
C++
/* ----------------------------------------------------------------------
|
|
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.
|
|
------------------------------------------------------------------------- */
|
|
|
|
/* ----------------------------------------------------------------------
|
|
Contributing authors: Ludwig Ahrens-Iwers (TUHH), Shern Tee (UQ), Robert Meißner (TUHH)
|
|
------------------------------------------------------------------------- */
|
|
|
|
#include "fix_electrode_thermo.h"
|
|
|
|
#include "atom.h"
|
|
#include "error.h"
|
|
#include "fix_electrode_conp.h"
|
|
#include "input.h"
|
|
#include "random_mars.h"
|
|
#include "update.h"
|
|
#include "variable.h"
|
|
|
|
#include <cmath>
|
|
|
|
using namespace LAMMPS_NS;
|
|
|
|
static constexpr int NUM_GROUPS = 2;
|
|
static constexpr double SMALL = 0.00001;
|
|
|
|
/* ----------------------------------------------------------------------- */
|
|
|
|
// 0 1 2 3 4
|
|
// fix fxupdate group1 electrode/thermo pot1 eta couple group2 pot2
|
|
FixElectrodeThermo::FixElectrodeThermo(LAMMPS *lmp, int narg, char **arg) :
|
|
FixElectrodeConp(lmp, narg, arg)
|
|
{
|
|
if (num_of_groups != NUM_GROUPS)
|
|
error->all(FLERR, "Number of electrodes != two in electrode/thermo");
|
|
if (group_psi_var_styles[0] != group_psi_var_styles[1])
|
|
error->all(FLERR, "Potentials in electrode/thermo must have same style");
|
|
if (algo != Algo::MATRIX_INV) error->all(FLERR, "Algorithm not allowed in electrode/thermo");
|
|
if (thermo_time < SMALL) error->all(FLERR, "Keyword temp not set or zero in electrode/thermo");
|
|
|
|
thermo_random = new RanMars(lmp, thermo_init);
|
|
if (group_psi_var_styles[0] == VarStyle::CONST)
|
|
delta_psi_0 = group_psi_const[1] - group_psi_const[0];
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------- */
|
|
|
|
FixElectrodeThermo::~FixElectrodeThermo()
|
|
{
|
|
delete thermo_random;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------- */
|
|
|
|
void FixElectrodeThermo::compute_macro_matrices()
|
|
{
|
|
FixElectrodeConp::compute_macro_matrices();
|
|
if (symm)
|
|
vac_cap = macro_capacitance[0][0];
|
|
else
|
|
vac_cap = (macro_capacitance[0][0] * macro_capacitance[1][1] -
|
|
macro_capacitance[0][1] * macro_capacitance[0][1]) /
|
|
(macro_capacitance[0][0] + macro_capacitance[1][1] + 2 * macro_capacitance[0][1]);
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------- */
|
|
|
|
void FixElectrodeThermo::pre_update()
|
|
{
|
|
// total electrode charges after last step, required for update psi
|
|
int const nlocal = atom->nlocal;
|
|
int *mask = atom->mask;
|
|
double *q = atom->q;
|
|
for (int g = 0; g < NUM_GROUPS; g++) {
|
|
group_q_old[g] = 0.;
|
|
for (int i = 0; i < nlocal; i++) {
|
|
if (mask[i] & group_bits[g]) { group_q_old[g] += q[i]; }
|
|
}
|
|
}
|
|
MPI_Allreduce(MPI_IN_PLACE, &group_q_old, NUM_GROUPS, MPI_DOUBLE, MPI_SUM, world);
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------- */
|
|
|
|
void FixElectrodeThermo::update_psi()
|
|
{
|
|
double const dt = update->dt;
|
|
|
|
// group_q_eff is charge that corresponds to potential after previous step
|
|
double const group_q_eff[NUM_GROUPS] = {group_q_old[0] - sb_charges[0],
|
|
(symm) ? 0. : group_q_old[1] - sb_charges[1]};
|
|
double const group_psi_old[NUM_GROUPS] = {
|
|
macro_elastance[0][0] * group_q_eff[0] + macro_elastance[0][1] * group_q_eff[1],
|
|
macro_elastance[1][0] * group_q_eff[0] + macro_elastance[1][1] * group_q_eff[1]};
|
|
double const delta_psi = group_psi_old[1] - group_psi_old[0];
|
|
|
|
// target potential difference from input parameters
|
|
if (group_psi_var_styles[0] == VarStyle::EQUAL) {
|
|
delta_psi_0 = input->variable->compute_equal(group_psi_var_ids[1]) -
|
|
input->variable->compute_equal(group_psi_var_ids[0]);
|
|
}
|
|
|
|
double delta_charge = 0.5 * (group_q_old[1] - group_q_old[0]) -
|
|
vac_cap * (delta_psi - delta_psi_0) * (1. - exp(-dt / thermo_time));
|
|
delta_charge += sqrt((thermo_temp * vac_cap) * (1. - exp(-2. * dt / thermo_time))) *
|
|
thermo_random->gaussian();
|
|
|
|
double const group_remainder_q[NUM_GROUPS] = {-delta_charge - sb_charges[0],
|
|
(symm) ? 0. : delta_charge - sb_charges[1]};
|
|
|
|
group_psi[0] =
|
|
macro_elastance[0][0] * group_remainder_q[0] + macro_elastance[0][1] * group_remainder_q[1];
|
|
group_psi[1] =
|
|
macro_elastance[1][0] * group_remainder_q[0] + macro_elastance[1][1] * group_remainder_q[1];
|
|
}
|