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