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IonFlow.cpp
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IonFlow.cpp
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//! @file IonFlow.cpp
// This file is part of Cantera. See License.txt in the top-level directory or
// at https://cantera.org/license.txt for license and copyright information.
#include "cantera/oneD/IonFlow.h"
#include "cantera/oneD/StFlow.h"
#include "cantera/base/ctml.h"
#include "cantera/transport/TransportBase.h"
#include "cantera/numerics/funcs.h"
#include "cantera/numerics/polyfit.h"
using namespace std;
namespace Cantera
{
IonFlow::IonFlow(IdealGasPhase* ph, size_t nsp, size_t points) :
StFlow(ph, nsp, points),
m_import_electron_transport(false),
m_stage(1),
m_kElectron(npos)
{
// make a local copy of species charge
for (size_t k = 0; k < m_nsp; k++) {
m_speciesCharge.push_back(m_thermo->charge(k));
}
// Find indices for charge of species
for (size_t k = 0; k < m_nsp; k++){
if (m_speciesCharge[k] != 0){
m_kCharge.push_back(k);
} else {
m_kNeutral.push_back(k);
}
}
// Find the index of electron
if (m_thermo->speciesIndex("E") != npos ) {
m_kElectron = m_thermo->speciesIndex("E");
}
// no bound for electric potential
setBounds(c_offset_E, -1.0e20, 1.0e20);
// Set tighter negative species limit on charged species to avoid
// instabilities. Tolerance on electrons is even tighter to account for the
// low "molecular" weight.
for (size_t k : m_kCharge) {
setBounds(c_offset_Y + k, -1e-14, 1.0);
}
setBounds(c_offset_Y + m_kElectron, -1e-18, 1.0);
m_refiner->setActive(c_offset_E, false);
m_mobility.resize(m_nsp*m_points);
m_do_electric_field.resize(m_points,false);
}
void IonFlow::resize(size_t components, size_t points){
StFlow::resize(components, points);
m_mobility.resize(m_nsp*m_points);
m_do_species.resize(m_nsp,true);
m_do_electric_field.resize(m_points,false);
}
void IonFlow::updateTransport(double* x, size_t j0, size_t j1)
{
StFlow::updateTransport(x,j0,j1);
for (size_t j = j0; j < j1; j++) {
setGasAtMidpoint(x,j);
m_trans->getMobilities(&m_mobility[j*m_nsp]);
if (m_import_electron_transport) {
size_t k = m_kElectron;
double tlog = log(m_thermo->temperature());
m_mobility[k+m_nsp*j] = poly5(tlog, m_mobi_e_fix.data());
m_diff[k+m_nsp*j] = poly5(tlog, m_diff_e_fix.data());
}
}
}
void IonFlow::updateDiffFluxes(const double* x, size_t j0, size_t j1)
{
if (m_stage == 1) {
frozenIonMethod(x,j0,j1);
}
if (m_stage == 2) {
electricFieldMethod(x,j0,j1);
}
}
void IonFlow::frozenIonMethod(const double* x, size_t j0, size_t j1)
{
for (size_t j = j0; j < j1; j++) {
double wtm = m_wtm[j];
double rho = density(j);
double dz = z(j+1) - z(j);
double sum = 0.0;
for (size_t k : m_kNeutral) {
m_flux(k,j) = m_wt[k]*(rho*m_diff[k+m_nsp*j]/wtm);
m_flux(k,j) *= (X(x,k,j) - X(x,k,j+1))/dz;
sum -= m_flux(k,j);
}
// correction flux to insure that \sum_k Y_k V_k = 0.
for (size_t k : m_kNeutral) {
m_flux(k,j) += sum*Y(x,k,j);
}
// flux for ions
// Set flux to zero to prevent some fast charged species (e.g. electron)
// to run away
for (size_t k : m_kCharge) {
m_flux(k,j) = 0;
}
}
}
void IonFlow::electricFieldMethod(const double* x, size_t j0, size_t j1)
{
for (size_t j = j0; j < j1; j++) {
double wtm = m_wtm[j];
double rho = density(j);
double dz = z(j+1) - z(j);
// mixture-average diffusion
double sum = 0.0;
for (size_t k = 0; k < m_nsp; k++) {
m_flux(k,j) = m_wt[k]*(rho*m_diff[k+m_nsp*j]/wtm);
m_flux(k,j) *= (X(x,k,j) - X(x,k,j+1))/dz;
sum -= m_flux(k,j);
}
// ambipolar diffusion
double E_ambi = E(x,j);
for (size_t k : m_kCharge) {
double Yav = 0.5 * (Y(x,k,j) + Y(x,k,j+1));
double drift = rho * Yav * E_ambi
* m_speciesCharge[k] * m_mobility[k+m_nsp*j];
m_flux(k,j) += drift;
}
// correction flux
double sum_flux = 0.0;
for (size_t k = 0; k < m_nsp; k++) {
sum_flux -= m_flux(k,j); // total net flux
}
double sum_ion = 0.0;
for (size_t k : m_kCharge) {
sum_ion += Y(x,k,j);
}
// The portion of correction for ions is taken off
for (size_t k : m_kNeutral) {
m_flux(k,j) += Y(x,k,j) / (1-sum_ion) * sum_flux;
}
}
}
void IonFlow::setSolvingStage(const size_t stage)
{
if (stage == 1 || stage == 2) {
m_stage = stage;
} else {
throw CanteraError("IonFlow::setSolvingStage",
"solution stage must be set to: "
"1) frozenIonMethod, "
"2) electricFieldEqnMethod");
}
}
void IonFlow::evalResidual(double* x, double* rsd, int* diag,
double rdt, size_t jmin, size_t jmax)
{
StFlow::evalResidual(x, rsd, diag, rdt, jmin, jmax);
if (m_stage != 2) {
return;
}
for (size_t j = jmin; j <= jmax; j++) {
if (j == 0) {
// enforcing the flux for charged species is difficult
// since charged species are also affected by electric
// force, so Neumann boundary condition is used.
for (size_t k : m_kCharge) {
rsd[index(c_offset_Y + k, 0)] = Y(x,k,0) - Y(x,k,1);
}
rsd[index(c_offset_E, j)] = E(x,0);
diag[index(c_offset_E, j)] = 0;
} else if (j == m_points - 1) {
rsd[index(c_offset_E, j)] = dEdz(x,j) - rho_e(x,j) / epsilon_0;
diag[index(c_offset_E, j)] = 0;
} else {
//-----------------------------------------------
// Electric field by Gauss's law
//
// dE/dz = e/eps_0 * sum(q_k*n_k)
//
// E = -dV/dz
//-----------------------------------------------
rsd[index(c_offset_E, j)] = dEdz(x,j) - rho_e(x,j) / epsilon_0;
diag[index(c_offset_E, j)] = 0;
}
}
}
void IonFlow::solveElectricField(size_t j)
{
bool changed = false;
if (j == npos) {
for (size_t i = 0; i < m_points; i++) {
if (!m_do_electric_field[i]) {
changed = true;
}
m_do_electric_field[i] = true;
}
} else {
if (!m_do_electric_field[j]) {
changed = true;
}
m_do_electric_field[j] = true;
}
m_refiner->setActive(c_offset_U, true);
m_refiner->setActive(c_offset_V, true);
m_refiner->setActive(c_offset_T, true);
m_refiner->setActive(c_offset_E, true);
if (changed) {
needJacUpdate();
}
}
void IonFlow::fixElectricField(size_t j)
{
bool changed = false;
if (j == npos) {
for (size_t i = 0; i < m_points; i++) {
if (m_do_electric_field[i]) {
changed = true;
}
m_do_electric_field[i] = false;
}
} else {
if (m_do_electric_field[j]) {
changed = true;
}
m_do_electric_field[j] = false;
}
m_refiner->setActive(c_offset_U, false);
m_refiner->setActive(c_offset_V, false);
m_refiner->setActive(c_offset_T, false);
m_refiner->setActive(c_offset_E, false);
if (changed) {
needJacUpdate();
}
}
void IonFlow::setElectronTransport(vector_fp& tfix, vector_fp& diff_e,
vector_fp& mobi_e)
{
m_import_electron_transport = true;
size_t degree = 5;
size_t n = tfix.size();
vector_fp tlog;
for (size_t i = 0; i < n; i++) {
tlog.push_back(log(tfix[i]));
}
vector_fp w(n, -1.0);
m_diff_e_fix.resize(degree + 1);
m_mobi_e_fix.resize(degree + 1);
polyfit(n, degree, tlog.data(), diff_e.data(), w.data(), m_diff_e_fix.data());
polyfit(n, degree, tlog.data(), mobi_e.data(), w.data(), m_mobi_e_fix.data());
}
void IonFlow::_finalize(const double* x)
{
StFlow::_finalize(x);
bool p = m_do_electric_field[0];
if (p) {
solveElectricField();
}
}
}