1116 lines
37 KiB
C++
1116 lines
37 KiB
C++
/**
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* @file InterfaceKinetics.cpp
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*/
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// Copyright 2002 California Institute of Technology
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#include "cantera/kinetics/InterfaceKinetics.h"
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#include "cantera/kinetics/EdgeKinetics.h"
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#include "cantera/kinetics/RateCoeffMgr.h"
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#include "cantera/kinetics/ImplicitSurfChem.h"
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#include "cantera/thermo/SurfPhase.h"
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#include <cstdio>
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using namespace std;
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namespace Cantera
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{
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InterfaceKinetics::InterfaceKinetics(thermo_t* thermo) :
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m_redo_rates(false),
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m_nirrev(0),
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m_nrev(0),
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m_surf(0),
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m_integrator(0),
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m_logp0(0.0),
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m_logc0(0.0),
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m_ROP_ok(false),
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m_temp(0.0),
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m_logtemp(0.0),
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m_finalized(false),
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m_has_coverage_dependence(false),
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m_has_electrochem_rxns(false),
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m_has_exchange_current_density_formulation(false),
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m_phaseExistsCheck(false),
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m_ioFlag(0)
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{
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if (thermo != 0) {
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addPhase(*thermo);
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}
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}
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InterfaceKinetics::~InterfaceKinetics()
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{
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delete m_integrator;
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}
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InterfaceKinetics::InterfaceKinetics(const InterfaceKinetics& right)
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{
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/*
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* Call the assignment operator
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*/
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operator=(right);
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}
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InterfaceKinetics& InterfaceKinetics::operator=(const InterfaceKinetics& right)
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{
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/*
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* Check for self assignment.
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*/
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if (this == &right) {
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return *this;
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}
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Kinetics::operator=(right);
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m_grt = right.m_grt;
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m_revindex = right.m_revindex;
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m_rates = right.m_rates;
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m_redo_rates = right.m_redo_rates;
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m_irrev = right.m_irrev;
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m_nirrev = right.m_nirrev;
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m_nrev = right.m_nrev;
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m_conc = right.m_conc;
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m_actConc = right.m_actConc;
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m_mu0 = right.m_mu0;
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m_mu = right.m_mu;
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m_mu0_Kc = right.m_mu0_Kc;
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m_phi = right.m_phi;
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m_pot = right.m_pot;
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deltaElectricEnergy_ = right.deltaElectricEnergy_;
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m_E = right.m_E;
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m_surf = right.m_surf; //DANGER - shallow copy
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m_integrator = right.m_integrator; //DANGER - shallow copy
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m_beta = right.m_beta;
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m_ctrxn = right.m_ctrxn;
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m_ctrxn_BVform = right.m_ctrxn_BVform;
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m_ctrxn_ecdf = right.m_ctrxn_ecdf;
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m_StandardConc = right.m_StandardConc;
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m_deltaG0 = right.m_deltaG0;
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m_deltaG = right.m_deltaG;
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m_ProdStanConcReac = right.m_ProdStanConcReac;
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m_logp0 = right.m_logp0;
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m_logc0 = right.m_logc0;
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m_ROP_ok = right.m_ROP_ok;
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m_temp = right.m_temp;
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m_logtemp = right.m_logtemp;
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m_finalized = right.m_finalized;
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m_has_coverage_dependence = right.m_has_coverage_dependence;
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m_has_electrochem_rxns = right.m_has_electrochem_rxns;
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m_has_exchange_current_density_formulation = right.m_has_exchange_current_density_formulation;
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m_phaseExistsCheck = right.m_phaseExistsCheck;
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m_phaseExists = right.m_phaseExists;
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m_phaseIsStable = right.m_phaseIsStable;
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m_rxnPhaseIsReactant = right.m_rxnPhaseIsReactant;
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m_rxnPhaseIsProduct = right.m_rxnPhaseIsProduct;
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m_ioFlag = right.m_ioFlag;
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return *this;
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}
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int InterfaceKinetics::type() const
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{
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return cInterfaceKinetics;
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}
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Kinetics* InterfaceKinetics::duplMyselfAsKinetics(const std::vector<thermo_t*> & tpVector) const
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{
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InterfaceKinetics* iK = new InterfaceKinetics(*this);
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iK->assignShallowPointers(tpVector);
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return iK;
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}
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void InterfaceKinetics::setElectricPotential(int n, doublereal V)
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{
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thermo(n).setElectricPotential(V);
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m_redo_rates = true;
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}
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void InterfaceKinetics::_update_rates_T()
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{
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// First task is update the electrical potentials from the Phases
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_update_rates_phi();
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if (m_has_coverage_dependence) {
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m_surf->getCoverages(DATA_PTR(m_actConc));
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m_rates.update_C(DATA_PTR(m_actConc));
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m_redo_rates = true;
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}
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// Go find the temperature from the surface
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doublereal T = thermo(surfacePhaseIndex()).temperature();
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m_redo_rates = true;
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if (T != m_temp || m_redo_rates) {
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m_logtemp = log(T);
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// Calculate the forward rate constant by calling m_rates and store it in m_rfn[]
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m_rates.update(T, m_logtemp, DATA_PTR(m_rfn));
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applyStickingCorrection(&m_rfn[0]);
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// If we need to do conversions between exchange current density formulation and regular formulation
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// (either way) do it here.
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if (m_has_exchange_current_density_formulation) {
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convertExchangeCurrentDensityFormulation(DATA_PTR(m_rfn));
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}
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if (m_has_electrochem_rxns) {
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applyVoltageKfwdCorrection(DATA_PTR(m_rfn));
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}
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m_temp = T;
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updateKc();
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m_ROP_ok = false;
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m_redo_rates = false;
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}
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}
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void InterfaceKinetics::_update_rates_phi()
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{
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// Store electric potentials for each phase in the array m_phi[].
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for (size_t n = 0; n < nPhases(); n++) {
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if (thermo(n).electricPotential() != m_phi[n]) {
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m_phi[n] = thermo(n).electricPotential();
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m_redo_rates = true;
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}
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}
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}
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// Updates the internal variables m_actConc and m_conc
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void InterfaceKinetics::_update_rates_C()
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{
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for (size_t n = 0; n < nPhases(); n++) {
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const ThermoPhase* tp = m_thermo[n];
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/*
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* We call the getActivityConcentrations function of each
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* ThermoPhase class that makes up this kinetics object to
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* obtain the generalized concentrations for species within that
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* class. This is collected in the vector m_conc. m_start[]
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* are integer indices for that vector denoting the start of the
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* species for each phase.
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*/
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tp->getActivityConcentrations(DATA_PTR(m_actConc) + m_start[n]);
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// Get regular concentrations too
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tp->getConcentrations(DATA_PTR(m_conc) + m_start[n]);
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}
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m_ROP_ok = false;
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}
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void InterfaceKinetics::getActivityConcentrations(doublereal* const conc)
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{
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_update_rates_C();
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copy(m_actConc.begin(), m_actConc.end(), conc);
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}
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void InterfaceKinetics::updateKc()
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{
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fill(m_rkcn.begin(), m_rkcn.end(), 0.0);
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if (m_nrev > 0) {
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/*
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* Get the vector of standard state electrochemical potentials for species in the Interfacial
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* kinetics object and store it in m_mu0[] and m_mu0_Kc[]
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*/
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updateMu0();
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doublereal rrt = 1.0 / (GasConstant * thermo(0).temperature());
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// compute Delta mu^0 for all reversible reactions
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getRevReactionDelta(DATA_PTR(m_mu0_Kc), DATA_PTR(m_rkcn));
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for (size_t i = 0; i < m_nrev; i++) {
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size_t irxn = m_revindex[i];
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if (irxn == npos || irxn >= nReactions()) {
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throw CanteraError("InterfaceKinetics", "illegal value: irxn = "+int2str(irxn));
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}
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// WARNING this may overflow HKM
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m_rkcn[irxn] = exp(m_rkcn[irxn]*rrt);
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}
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for (size_t i = 0; i != m_nirrev; ++i) {
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m_rkcn[ m_irrev[i] ] = 0.0;
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}
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}
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}
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void InterfaceKinetics::updateMu0()
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{
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// First task is update the electrical potentials from the Phases
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_update_rates_phi();
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updateExchangeCurrentQuantities();
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/*
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* Get the vector of standard state electrochemical potentials for species in the Interfacial
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* kinetics object and store it in m_mu0[] and in m_mu0_Kc[]
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*/
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size_t nsp, ik = 0;
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size_t np = nPhases();
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for (size_t n = 0; n < np; n++) {
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thermo(n).getStandardChemPotentials(DATA_PTR(m_mu0) + m_start[n]);
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nsp = thermo(n).nSpecies();
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for (size_t k = 0; k < nsp; k++) {
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m_mu0_Kc[ik] = m_mu0[ik] + Faraday * m_phi[n] * thermo(n).charge(k);
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m_mu0_Kc[ik] -= thermo(0).RT() * thermo(n).logStandardConc(k);
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ik++;
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}
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}
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}
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void InterfaceKinetics::checkPartialEquil()
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{
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// First task is update the electrical potentials from the Phases
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_update_rates_phi();
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vector_fp dmu(nTotalSpecies(), 0.0);
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vector_fp rmu(std::max<size_t>(nReactions(), 1), 0.0);
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if (m_nrev > 0) {
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cout << "T = " << thermo(0).temperature() << " " << thermo(0).RT() << endl;
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size_t nsp, ik=0;
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doublereal delta;
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for (size_t n = 0; n < nPhases(); n++) {
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thermo(n).getChemPotentials(DATA_PTR(dmu) + m_start[n]);
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nsp = thermo(n).nSpecies();
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for (size_t k = 0; k < nsp; k++) {
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delta = Faraday * m_phi[n] * thermo(n).charge(k);
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dmu[ik] += delta;
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ik++;
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}
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}
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// compute Delta mu^ for all reversible reactions
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getRevReactionDelta(DATA_PTR(dmu), DATA_PTR(rmu));
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updateROP();
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for (size_t i = 0; i < m_nrev; i++) {
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size_t irxn = m_revindex[i];
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writelog("Reaction {} {}\n",
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reactionString(irxn), rmu[irxn]/thermo(0).RT());
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writelogf("%12.6e %12.6e %12.6e %12.6e \n",
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m_ropf[irxn], m_ropr[irxn], m_ropnet[irxn],
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m_ropnet[irxn]/(m_ropf[irxn] + m_ropr[irxn]));
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}
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}
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}
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void InterfaceKinetics::getEquilibriumConstants(doublereal* kc)
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{
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updateMu0();
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doublereal rrt = 1.0 / (GasConstant * thermo(0).temperature());
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std::fill(kc, kc + nReactions(), 0.0);
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getReactionDelta(DATA_PTR(m_mu0_Kc), kc);
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for (size_t i = 0; i < nReactions(); i++) {
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kc[i] = exp(-kc[i]*rrt);
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}
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}
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void InterfaceKinetics::updateExchangeCurrentQuantities()
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{
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/*
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* Calculate:
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* - m_StandardConc[]
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* - m_ProdStandConcReac[]
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* - m_deltaG0[]
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* - m_mu0[]
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*/
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/*
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* First collect vectors of the standard Gibbs free energies of the
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* species and the standard concentrations
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* - m_mu0
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* - m_StandardConc
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*/
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size_t ik = 0;
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for (size_t n = 0; n < nPhases(); n++) {
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thermo(n).getStandardChemPotentials(DATA_PTR(m_mu0) + m_start[n]);
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size_t nsp = thermo(n).nSpecies();
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for (size_t k = 0; k < nsp; k++) {
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m_StandardConc[ik] = thermo(n).standardConcentration(k);
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ik++;
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}
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}
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getReactionDelta(DATA_PTR(m_mu0), DATA_PTR(m_deltaG0));
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// Calculate the product of the standard concentrations of the reactants
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for (size_t i = 0; i < nReactions(); i++) {
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m_ProdStanConcReac[i] = 1.0;
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}
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m_reactantStoich.multiply(DATA_PTR(m_StandardConc), DATA_PTR(m_ProdStanConcReac));
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}
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void InterfaceKinetics::applyVoltageKfwdCorrection(doublereal* const kf)
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{
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// Compute the electrical potential energy of each species
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size_t ik = 0;
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for (size_t n = 0; n < nPhases(); n++) {
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size_t nsp = thermo(n).nSpecies();
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for (size_t k = 0; k < nsp; k++) {
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m_pot[ik] = Faraday * thermo(n).charge(k) * m_phi[n];
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ik++;
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}
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}
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// Compute the change in electrical potential energy for each
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// reaction. This will only be non-zero if a potential
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// difference is present.
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getReactionDelta(DATA_PTR(m_pot), DATA_PTR(deltaElectricEnergy_));
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// Modify the reaction rates. Only modify those with a
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// non-zero activation energy. Below we decrease the
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// activation energy below zero but in some debug modes
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// we print out a warning message about this.
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/*
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* NOTE, there is some discussion about this point.
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* Should we decrease the activation energy below zero?
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* I don't think this has been decided in any definitive way.
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* The treatment below is numerically more stable, however.
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*/
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doublereal eamod;
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for (size_t i = 0; i < m_beta.size(); i++) {
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size_t irxn = m_ctrxn[i];
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// If we calculate the BV form directly, we don't add the voltage correction to the
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// forward reaction rate constants.
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if (m_ctrxn_BVform[i] == 0) {
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eamod = m_beta[i] * deltaElectricEnergy_[irxn];
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if (eamod != 0.0) {
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kf[irxn] *= exp(-eamod/thermo(0).RT());
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}
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}
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}
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}
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void InterfaceKinetics::convertExchangeCurrentDensityFormulation(doublereal* const kfwd)
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{
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updateExchangeCurrentQuantities();
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// Loop over all reactions which are defined to have a voltage transfer coefficient that
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// affects the activity energy for the reaction
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for (size_t i = 0; i < m_ctrxn.size(); i++) {
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size_t irxn = m_ctrxn[i];
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// Determine whether the reaction rate constant is in an exchange current density formulation format.
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int iECDFormulation = m_ctrxn_ecdf[i];
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if (iECDFormulation) {
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// If the BV form is to be converted into the normal form then we go through this process.
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// If it isn't to be converted, then we don't go through this process.
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//
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// We need to have the straight chemical reaction rate constant to come out of this calculation.
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if (m_ctrxn_BVform[i] == 0) {
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// Calculate the term and modify the forward reaction
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double tmp = exp(- m_beta[i] * m_deltaG0[irxn] / thermo(0).RT());
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double tmp2 = m_ProdStanConcReac[irxn];
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tmp *= 1.0 / tmp2 / Faraday;
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kfwd[irxn] *= tmp;
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}
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// If BVform is nonzero we don't need to do anything.
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} else {
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// kfwd[] is the chemical reaction rate constant
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//
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// If we are to calculate the BV form directly, then we will do the reverse.
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// We will calculate the exchange current density formulation here and
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// substitute it.
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if (m_ctrxn_BVform[i] != 0) {
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// Calculate the term and modify the forward reaction rate constant so that
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// it's in the exchange current density formulation format
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double tmp = exp(m_beta[i] * m_deltaG0[irxn] * thermo(0).RT());
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double tmp2 = m_ProdStanConcReac[irxn];
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tmp *= Faraday * tmp2;
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kfwd[irxn] *= tmp;
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}
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}
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}
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}
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void InterfaceKinetics::getFwdRateConstants(doublereal* kfwd)
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{
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updateROP();
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// copy rate coefficients into kfwd
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copy(m_rfn.begin(), m_rfn.end(), kfwd);
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// multiply by perturbation factor
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multiply_each(kfwd, kfwd + nReactions(), m_perturb.begin());
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}
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void InterfaceKinetics::getRevRateConstants(doublereal* krev, bool doIrreversible)
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{
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getFwdRateConstants(krev);
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if (doIrreversible) {
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getEquilibriumConstants(&m_ropnet[0]);
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for (size_t i = 0; i < nReactions(); i++) {
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krev[i] /= m_ropnet[i];
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}
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} else {
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multiply_each(krev, krev + nReactions(), m_rkcn.begin());
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}
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}
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void InterfaceKinetics::updateROP()
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{
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// evaluate rate constants and equilibrium constants at temperature and phi (electric potential)
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_update_rates_T();
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// get updated activities (rates updated below)
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_update_rates_C();
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if (m_ROP_ok) {
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return;
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}
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// Copy the reaction rate coefficients, m_rfn, into m_ropf
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copy(m_rfn.begin(), m_rfn.end(), m_ropf.begin());
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// Multiply by the perturbation factor
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multiply_each(m_ropf.begin(), m_ropf.end(), m_perturb.begin());
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// Copy the forward rate constants to the reverse rate constants
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copy(m_ropf.begin(), m_ropf.end(), m_ropr.begin());
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// For reverse rates computed from thermochemistry, multiply
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// the forward rates copied into m_ropr by the reciprocals of
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// the equilibrium constants
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multiply_each(m_ropr.begin(), m_ropr.end(), m_rkcn.begin());
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// multiply ropf by the activity concentration reaction orders to obtain
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// the forward rates of progress.
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m_reactantStoich.multiply(DATA_PTR(m_actConc), DATA_PTR(m_ropf));
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// For reversible reactions, multiply ropr by the activity concentration products
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m_revProductStoich.multiply(DATA_PTR(m_actConc), DATA_PTR(m_ropr));
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|
|
// Fix up these calculations for cases where the above formalism doesn't hold
|
|
double OCV = 0.0;
|
|
for (size_t jrxn = 0; jrxn != nReactions(); ++jrxn) {
|
|
if (reactionType(jrxn) == BUTLERVOLMER_RXN) {
|
|
// OK, the reaction rate constant contains the current density rate constant calculation
|
|
// the rxnstoich calculation contained the dependence of the current density on the activity concentrations
|
|
// We finish up with the ROP calculation
|
|
//
|
|
// Calculate the overpotential of the reaction
|
|
double nStoichElectrons=1;
|
|
getDeltaGibbs(0);
|
|
if (nStoichElectrons != 0.0) {
|
|
OCV = m_deltaG[jrxn]/Faraday/ nStoichElectrons;
|
|
}
|
|
}
|
|
}
|
|
|
|
for (size_t j = 0; j != nReactions(); ++j) {
|
|
m_ropnet[j] = m_ropf[j] - m_ropr[j];
|
|
}
|
|
|
|
/*
|
|
* For reactions involving multiple phases, we must check that the phase
|
|
* being consumed actually exists. This is particularly important for
|
|
* phases that are stoichiometric phases containing one species with a unity activity
|
|
*/
|
|
if (m_phaseExistsCheck) {
|
|
for (size_t j = 0; j != nReactions(); ++j) {
|
|
if ((m_ropr[j] > m_ropf[j]) && (m_ropr[j] > 0.0)) {
|
|
for (size_t p = 0; p < nPhases(); p++) {
|
|
if (m_rxnPhaseIsProduct[j][p] && !m_phaseExists[p]) {
|
|
m_ropnet[j] = 0.0;
|
|
m_ropr[j] = m_ropf[j];
|
|
if (m_ropf[j] > 0.0) {
|
|
for (size_t rp = 0; rp < nPhases(); rp++) {
|
|
if (m_rxnPhaseIsReactant[j][rp] && !m_phaseExists[rp]) {
|
|
m_ropnet[j] = 0.0;
|
|
m_ropr[j] = m_ropf[j] = 0.0;
|
|
}
|
|
}
|
|
}
|
|
}
|
|
if (m_rxnPhaseIsReactant[j][p] && !m_phaseIsStable[p]) {
|
|
m_ropnet[j] = 0.0;
|
|
m_ropr[j] = m_ropf[j];
|
|
}
|
|
}
|
|
} else if ((m_ropf[j] > m_ropr[j]) && (m_ropf[j] > 0.0)) {
|
|
for (size_t p = 0; p < nPhases(); p++) {
|
|
if (m_rxnPhaseIsReactant[j][p] && !m_phaseExists[p]) {
|
|
m_ropnet[j] = 0.0;
|
|
m_ropf[j] = m_ropr[j];
|
|
if (m_ropf[j] > 0.0) {
|
|
for (size_t rp = 0; rp < nPhases(); rp++) {
|
|
if (m_rxnPhaseIsProduct[j][rp] && !m_phaseExists[rp]) {
|
|
m_ropnet[j] = 0.0;
|
|
m_ropf[j] = m_ropr[j] = 0.0;
|
|
}
|
|
}
|
|
}
|
|
}
|
|
if (m_rxnPhaseIsProduct[j][p] && !m_phaseIsStable[p]) {
|
|
m_ropnet[j] = 0.0;
|
|
m_ropf[j] = m_ropr[j];
|
|
}
|
|
}
|
|
}
|
|
}
|
|
}
|
|
m_ROP_ok = true;
|
|
}
|
|
|
|
void InterfaceKinetics::getDeltaGibbs(doublereal* deltaG)
|
|
{
|
|
/*
|
|
* Get the chemical potentials of the species in the all of the phases used in the
|
|
* kinetics mechanism
|
|
*/
|
|
for (size_t n = 0; n < nPhases(); n++) {
|
|
m_thermo[n]->getChemPotentials(DATA_PTR(m_mu) + m_start[n]);
|
|
}
|
|
|
|
// Use the stoichiometric manager to find deltaG for each reaction.
|
|
getReactionDelta(DATA_PTR(m_mu), DATA_PTR(m_deltaG));
|
|
if (deltaG != 0 && (DATA_PTR(m_deltaG) != deltaG)) {
|
|
for (size_t j = 0; j < nReactions(); ++j) {
|
|
deltaG[j] = m_deltaG[j];
|
|
}
|
|
}
|
|
}
|
|
|
|
void InterfaceKinetics::getDeltaElectrochemPotentials(doublereal* deltaM)
|
|
{
|
|
/*
|
|
* Get the chemical potentials of the species
|
|
*/
|
|
size_t np = nPhases();
|
|
for (size_t n = 0; n < np; n++) {
|
|
thermo(n).getElectrochemPotentials(DATA_PTR(m_grt) + m_start[n]);
|
|
}
|
|
/*
|
|
* Use the stoichiometric manager to find deltaG for each
|
|
* reaction.
|
|
*/
|
|
getReactionDelta(DATA_PTR(m_grt), deltaM);
|
|
}
|
|
|
|
void InterfaceKinetics::getDeltaEnthalpy(doublereal* deltaH)
|
|
{
|
|
/*
|
|
* Get the partial molar enthalpy of all species
|
|
*/
|
|
for (size_t n = 0; n < nPhases(); n++) {
|
|
thermo(n).getPartialMolarEnthalpies(DATA_PTR(m_grt) + m_start[n]);
|
|
}
|
|
/*
|
|
* Use the stoichiometric manager to find deltaG for each
|
|
* reaction.
|
|
*/
|
|
getReactionDelta(DATA_PTR(m_grt), deltaH);
|
|
}
|
|
|
|
void InterfaceKinetics::getDeltaEntropy(doublereal* deltaS)
|
|
{
|
|
/*
|
|
* Get the partial molar entropy of all species in all of
|
|
* the phases
|
|
*/
|
|
for (size_t n = 0; n < nPhases(); n++) {
|
|
thermo(n).getPartialMolarEntropies(DATA_PTR(m_grt) + m_start[n]);
|
|
}
|
|
/*
|
|
* Use the stoichiometric manager to find deltaS for each
|
|
* reaction.
|
|
*/
|
|
getReactionDelta(DATA_PTR(m_grt), deltaS);
|
|
}
|
|
|
|
void InterfaceKinetics::getDeltaSSGibbs(doublereal* deltaGSS)
|
|
{
|
|
/*
|
|
* Get the standard state chemical potentials of the species.
|
|
* This is the array of chemical potentials at unit activity
|
|
* We define these here as the chemical potentials of the pure
|
|
* species at the temperature and pressure of the solution.
|
|
*/
|
|
for (size_t n = 0; n < nPhases(); n++) {
|
|
thermo(n).getStandardChemPotentials(DATA_PTR(m_mu0) + m_start[n]);
|
|
}
|
|
/*
|
|
* Use the stoichiometric manager to find deltaG for each
|
|
* reaction.
|
|
*/
|
|
getReactionDelta(DATA_PTR(m_mu0), deltaGSS);
|
|
}
|
|
|
|
void InterfaceKinetics::getDeltaSSEnthalpy(doublereal* deltaH)
|
|
{
|
|
/*
|
|
* Get the standard state enthalpies of the species.
|
|
* This is the array of chemical potentials at unit activity
|
|
* We define these here as the enthalpies of the pure
|
|
* species at the temperature and pressure of the solution.
|
|
*/
|
|
for (size_t n = 0; n < nPhases(); n++) {
|
|
thermo(n).getEnthalpy_RT(DATA_PTR(m_grt) + m_start[n]);
|
|
}
|
|
for (size_t k = 0; k < m_kk; k++) {
|
|
m_grt[k] *= thermo(0).RT();
|
|
}
|
|
/*
|
|
* Use the stoichiometric manager to find deltaG for each
|
|
* reaction.
|
|
*/
|
|
getReactionDelta(DATA_PTR(m_grt), deltaH);
|
|
}
|
|
|
|
void InterfaceKinetics::getDeltaSSEntropy(doublereal* deltaS)
|
|
{
|
|
/*
|
|
* Get the standard state entropy of the species.
|
|
* We define these here as the entropies of the pure
|
|
* species at the temperature and pressure of the solution.
|
|
*/
|
|
for (size_t n = 0; n < nPhases(); n++) {
|
|
thermo(n).getEntropy_R(DATA_PTR(m_grt) + m_start[n]);
|
|
}
|
|
for (size_t k = 0; k < m_kk; k++) {
|
|
m_grt[k] *= GasConstant;
|
|
}
|
|
/*
|
|
* Use the stoichiometric manager to find deltaS for each
|
|
* reaction.
|
|
*/
|
|
getReactionDelta(DATA_PTR(m_grt), deltaS);
|
|
}
|
|
|
|
bool InterfaceKinetics::addReaction(shared_ptr<Reaction> r_base)
|
|
{
|
|
size_t i = nReactions();
|
|
bool added = Kinetics::addReaction(r_base);
|
|
if (!added) {
|
|
return false;
|
|
}
|
|
|
|
InterfaceReaction& r = dynamic_cast<InterfaceReaction&>(*r_base);
|
|
SurfaceArrhenius rate = buildSurfaceArrhenius(i, r);
|
|
m_rates.install(i, rate);
|
|
|
|
// Turn on the global flag indicating surface coverage dependence
|
|
if (!r.coverage_deps.empty()) {
|
|
m_has_coverage_dependence = true;
|
|
}
|
|
|
|
// Store activation energy
|
|
m_E.push_back(rate.activationEnergy_R());
|
|
|
|
ElectrochemicalReaction* re = dynamic_cast<ElectrochemicalReaction*>(&r);
|
|
if (re) {
|
|
m_has_electrochem_rxns = true;
|
|
m_beta.push_back(re->beta);
|
|
m_ctrxn.push_back(i);
|
|
if (re->exchange_current_density_formulation) {
|
|
m_has_exchange_current_density_formulation = true;
|
|
m_ctrxn_ecdf.push_back(1);
|
|
} else {
|
|
m_ctrxn_ecdf.push_back(0);
|
|
}
|
|
m_ctrxn_resistivity_.push_back(re->film_resistivity);
|
|
|
|
if (r.reaction_type == BUTLERVOLMER_NOACTIVITYCOEFFS_RXN ||
|
|
r.reaction_type == BUTLERVOLMER_RXN ||
|
|
r.reaction_type == SURFACEAFFINITY_RXN ||
|
|
r.reaction_type == GLOBAL_RXN) {
|
|
// Specify alternative forms of the electrochemical reaction
|
|
if (r.reaction_type == BUTLERVOLMER_RXN) {
|
|
m_ctrxn_BVform.push_back(1);
|
|
} else if (r.reaction_type == BUTLERVOLMER_NOACTIVITYCOEFFS_RXN) {
|
|
m_ctrxn_BVform.push_back(2);
|
|
} else {
|
|
// set the default to be the normal forward / reverse calculation method
|
|
m_ctrxn_BVform.push_back(0);
|
|
}
|
|
if (!r.orders.empty()) {
|
|
vector_fp orders(nTotalSpecies(), 0.0);
|
|
for (const auto& order : r.orders) {
|
|
orders[kineticsSpeciesIndex(order.first)] = order.second;
|
|
}
|
|
}
|
|
} else {
|
|
m_ctrxn_BVform.push_back(0);
|
|
if (re->film_resistivity > 0.0) {
|
|
throw CanteraError("InterfaceKinetics::addReaction()",
|
|
"film resistivity set for elementary reaction");
|
|
}
|
|
}
|
|
}
|
|
|
|
if (r.reversible) {
|
|
m_revindex.push_back(i);
|
|
m_nrev++;
|
|
} else {
|
|
m_irrev.push_back(i);
|
|
m_nirrev++;
|
|
}
|
|
|
|
m_rxnPhaseIsReactant.push_back(std::vector<bool>(nPhases(), false));
|
|
m_rxnPhaseIsProduct.push_back(std::vector<bool>(nPhases(), false));
|
|
|
|
for (const auto& sp : r.reactants) {
|
|
size_t k = kineticsSpeciesIndex(sp.first);
|
|
size_t p = speciesPhaseIndex(k);
|
|
m_rxnPhaseIsReactant[i][p] = true;
|
|
}
|
|
for (const auto& sp : r.products) {
|
|
size_t k = kineticsSpeciesIndex(sp.first);
|
|
size_t p = speciesPhaseIndex(k);
|
|
m_rxnPhaseIsProduct[i][p] = true;
|
|
}
|
|
return true;
|
|
}
|
|
|
|
void InterfaceKinetics::modifyReaction(size_t i, shared_ptr<Reaction> r_base)
|
|
{
|
|
Kinetics::modifyReaction(i, r_base);
|
|
InterfaceReaction& r = dynamic_cast<InterfaceReaction&>(*r_base);
|
|
SurfaceArrhenius rate = buildSurfaceArrhenius(npos, r);
|
|
m_rates.replace(i, rate);
|
|
|
|
// Invalidate cached data
|
|
m_redo_rates = true;
|
|
m_temp += 0.1;
|
|
}
|
|
|
|
SurfaceArrhenius InterfaceKinetics::buildSurfaceArrhenius(
|
|
size_t i, InterfaceReaction& r)
|
|
{
|
|
double A_rate = r.rate.preExponentialFactor();
|
|
double b_rate = r.rate.temperatureExponent();
|
|
|
|
if (r.is_sticking_coefficient) {
|
|
// Identify the interface phase
|
|
size_t iInterface = npos;
|
|
size_t min_dim = 4;
|
|
for (size_t n = 0; n < nPhases(); n++) {
|
|
if (thermo(n).nDim() < min_dim) {
|
|
iInterface = n;
|
|
min_dim = thermo(n).nDim();
|
|
}
|
|
}
|
|
|
|
b_rate += 0.5;
|
|
std::string sticking_species = r.sticking_species;
|
|
if (sticking_species == "") {
|
|
// Identify the sticking species if not explicitly given
|
|
bool foundStick = false;
|
|
for (const auto& sp : r.reactants) {
|
|
size_t iPhase = speciesPhaseIndex(kineticsSpeciesIndex(sp.first));
|
|
if (iPhase != iInterface) {
|
|
// Non-interface species. There should be exactly one of these
|
|
if (foundStick) {
|
|
throw CanteraError("InterfaceKinetics::addReaction",
|
|
"Multiple non-interface species found"
|
|
"in sticking reaction: '" + r.equation() + "'");
|
|
}
|
|
foundStick = true;
|
|
sticking_species = sp.first;
|
|
}
|
|
}
|
|
if (!foundStick) {
|
|
throw CanteraError("InterfaceKinetics::addReaction",
|
|
"No non-interface species found"
|
|
"in sticking reaction: '" + r.equation() + "'");
|
|
}
|
|
}
|
|
|
|
double surface_order = 0.0;
|
|
// Adjust the A-factor
|
|
for (const auto& sp : r.reactants) {
|
|
size_t iPhase = speciesPhaseIndex(kineticsSpeciesIndex(sp.first));
|
|
const ThermoPhase& p = thermo(iPhase);
|
|
const ThermoPhase& surf = thermo(surfacePhaseIndex());
|
|
size_t k = p.speciesIndex(sp.first);
|
|
if (sp.first == sticking_species) {
|
|
A_rate *= sqrt(GasConstant/(2*Pi*p.molecularWeight(k)));
|
|
} else {
|
|
// Non-sticking species. Convert from coverages used in the
|
|
// sticking probability expression to the concentration units
|
|
// used in the mass action rate expression. For surface phases,
|
|
// the dependence on the site density is incorporated when the
|
|
// rate constant is evaluated, since we don't assume that the
|
|
// site density is known at this time.
|
|
double order = getValue(r.orders, sp.first, sp.second);
|
|
if (&p == &surf) {
|
|
A_rate *= pow(p.size(k), order);
|
|
surface_order += order;
|
|
} else {
|
|
A_rate *= pow(p.standardConcentration(k), -order);
|
|
}
|
|
}
|
|
}
|
|
if (i != npos) {
|
|
m_sticking_orders.push_back(make_pair(i, surface_order));
|
|
}
|
|
}
|
|
|
|
SurfaceArrhenius rate(A_rate, b_rate, r.rate.activationEnergy_R());
|
|
|
|
// Set up coverage dependencies
|
|
for (const auto& sp : r.coverage_deps) {
|
|
size_t k = thermo(reactionPhaseIndex()).speciesIndex(sp.first);
|
|
rate.addCoverageDependence(k, sp.second.a, sp.second.m, sp.second.E);
|
|
}
|
|
return rate;
|
|
}
|
|
|
|
void InterfaceKinetics::setIOFlag(int ioFlag)
|
|
{
|
|
m_ioFlag = ioFlag;
|
|
if (m_integrator) {
|
|
m_integrator->setIOFlag(ioFlag);
|
|
}
|
|
}
|
|
|
|
void InterfaceKinetics::addPhase(thermo_t& thermo)
|
|
{
|
|
Kinetics::addPhase(thermo);
|
|
m_phaseExists.push_back(true);
|
|
m_phaseIsStable.push_back(true);
|
|
}
|
|
|
|
void InterfaceKinetics::init()
|
|
{
|
|
m_kk = 0;
|
|
for (size_t n = 0; n < nPhases(); n++) {
|
|
m_kk += thermo(n).nSpecies();
|
|
}
|
|
m_actConc.resize(m_kk);
|
|
m_conc.resize(m_kk);
|
|
m_mu0.resize(m_kk);
|
|
m_mu.resize(m_kk);
|
|
m_mu0_Kc.resize(m_kk);
|
|
m_grt.resize(m_kk);
|
|
m_pot.resize(m_kk, 0.0);
|
|
m_phi.resize(nPhases(), 0.0);
|
|
}
|
|
|
|
void InterfaceKinetics::finalize()
|
|
{
|
|
Kinetics::finalize();
|
|
size_t safe_reaction_size = std::max<size_t>(nReactions(), 1);
|
|
deltaElectricEnergy_.resize(safe_reaction_size);
|
|
size_t ks = reactionPhaseIndex();
|
|
if (ks == npos) throw CanteraError("InterfaceKinetics::finalize",
|
|
"no surface phase is present.");
|
|
|
|
// Check to see that the interface routine has a dimension of 2
|
|
m_surf = (SurfPhase*)&thermo(ks);
|
|
if (m_surf->nDim() != 2) {
|
|
throw CanteraError("InterfaceKinetics::finalize",
|
|
"expected interface dimension = 2, but got dimension = "
|
|
+int2str(m_surf->nDim()));
|
|
}
|
|
m_StandardConc.resize(m_kk, 0.0);
|
|
m_deltaG0.resize(safe_reaction_size, 0.0);
|
|
m_deltaG.resize(safe_reaction_size, 0.0);
|
|
m_ProdStanConcReac.resize(safe_reaction_size, 0.0);
|
|
|
|
if (m_thermo.size() != m_phaseExists.size()) {
|
|
throw CanteraError("InterfaceKinetics::finalize", "internal error");
|
|
}
|
|
|
|
// Guarantee that these arrays can be converted to double* even in the
|
|
// special case where there are no reactions defined.
|
|
if (!nReactions()) {
|
|
m_perturb.resize(1, 1.0);
|
|
m_ropf.resize(1, 0.0);
|
|
m_ropr.resize(1, 0.0);
|
|
m_ropnet.resize(1, 0.0);
|
|
m_rkcn.resize(1, 0.0);
|
|
}
|
|
m_finalized = true;
|
|
}
|
|
|
|
doublereal InterfaceKinetics::electrochem_beta(size_t irxn) const
|
|
{
|
|
for (size_t i = 0; i < m_ctrxn.size(); i++) {
|
|
if (m_ctrxn[i] == irxn) {
|
|
return m_beta[i];
|
|
}
|
|
}
|
|
return 0.0;
|
|
}
|
|
|
|
bool InterfaceKinetics::ready() const
|
|
{
|
|
return m_finalized;
|
|
}
|
|
|
|
void InterfaceKinetics::advanceCoverages(doublereal tstep)
|
|
{
|
|
if (m_integrator == 0) {
|
|
vector<InterfaceKinetics*> k;
|
|
k.push_back(this);
|
|
m_integrator = new ImplicitSurfChem(k);
|
|
m_integrator->initialize();
|
|
}
|
|
m_integrator->integrate(0.0, tstep);
|
|
delete m_integrator;
|
|
m_integrator = 0;
|
|
}
|
|
|
|
void InterfaceKinetics::solvePseudoSteadyStateProblem(
|
|
int ifuncOverride, doublereal timeScaleOverride)
|
|
{
|
|
// create our own solver object
|
|
if (m_integrator == 0) {
|
|
vector<InterfaceKinetics*> k;
|
|
k.push_back(this);
|
|
m_integrator = new ImplicitSurfChem(k);
|
|
m_integrator->initialize();
|
|
}
|
|
m_integrator->setIOFlag(m_ioFlag);
|
|
/*
|
|
* New direct method to go here
|
|
*/
|
|
m_integrator->solvePseudoSteadyStateProblem(ifuncOverride, timeScaleOverride);
|
|
}
|
|
|
|
void InterfaceKinetics::setPhaseExistence(const size_t iphase, const int exists)
|
|
{
|
|
if (iphase >= m_thermo.size()) {
|
|
throw CanteraError("InterfaceKinetics:setPhaseExistence", "out of bounds");
|
|
}
|
|
if (exists) {
|
|
if (!m_phaseExists[iphase]) {
|
|
m_phaseExistsCheck--;
|
|
m_phaseExistsCheck = std::max(m_phaseExistsCheck, 0);
|
|
m_phaseExists[iphase] = true;
|
|
}
|
|
m_phaseIsStable[iphase] = true;
|
|
} else {
|
|
if (m_phaseExists[iphase]) {
|
|
m_phaseExistsCheck++;
|
|
m_phaseExists[iphase] = false;
|
|
}
|
|
m_phaseIsStable[iphase] = false;
|
|
}
|
|
}
|
|
|
|
int InterfaceKinetics::phaseExistence(const size_t iphase) const
|
|
{
|
|
if (iphase >= m_thermo.size()) {
|
|
throw CanteraError("InterfaceKinetics:phaseExistence()", "out of bounds");
|
|
}
|
|
return m_phaseExists[iphase];
|
|
}
|
|
|
|
int InterfaceKinetics::phaseStability(const size_t iphase) const
|
|
{
|
|
if (iphase >= m_thermo.size()) {
|
|
throw CanteraError("InterfaceKinetics:phaseStability()", "out of bounds");
|
|
}
|
|
return m_phaseIsStable[iphase];
|
|
}
|
|
|
|
void InterfaceKinetics::setPhaseStability(const size_t iphase, const int isStable)
|
|
{
|
|
if (iphase >= m_thermo.size()) {
|
|
throw CanteraError("InterfaceKinetics:setPhaseStability", "out of bounds");
|
|
}
|
|
if (isStable) {
|
|
m_phaseIsStable[iphase] = true;
|
|
} else {
|
|
m_phaseIsStable[iphase] = false;
|
|
}
|
|
}
|
|
|
|
void InterfaceKinetics::determineFwdOrdersBV(ElectrochemicalReaction& r, vector_fp& fwdFullOrders)
|
|
{
|
|
// Start out with the full ROP orders vector.
|
|
// This vector will have the BV exchange current density orders in it.
|
|
fwdFullOrders.assign(nTotalSpecies(), 0.0);
|
|
for (const auto& order : r.orders) {
|
|
fwdFullOrders[kineticsSpeciesIndex(order.first)] = order.second;
|
|
}
|
|
|
|
// forward and reverse beta values
|
|
double betaf = r.beta;
|
|
|
|
// Loop over the reactants doing away with the BV terms.
|
|
// This should leave the reactant terms only, even if they are non-mass action.
|
|
for (const auto& sp : r.reactants) {
|
|
size_t k = kineticsSpeciesIndex(sp.first);
|
|
fwdFullOrders[k] += betaf * sp.second;
|
|
// just to make sure roundoff doesn't leave a term that should be zero (haven't checked this out yet)
|
|
if (abs(fwdFullOrders[k]) < 0.00001) {
|
|
fwdFullOrders[k] = 0.0;
|
|
}
|
|
}
|
|
|
|
// Loop over the products doing away with the BV terms.
|
|
// This should leave the reactant terms only, even if they are non-mass action.
|
|
for (const auto& sp : r.products) {
|
|
size_t k = kineticsSpeciesIndex(sp.first);
|
|
fwdFullOrders[k] -= betaf * sp.second;
|
|
// just to make sure roundoff doesn't leave a term that should be zero (haven't checked this out yet)
|
|
if (abs(fwdFullOrders[k]) < 0.00001) {
|
|
fwdFullOrders[k] = 0.0;
|
|
}
|
|
}
|
|
}
|
|
|
|
void InterfaceKinetics::applyStickingCorrection(double* kf)
|
|
{
|
|
if (m_sticking_orders.empty()) {
|
|
return;
|
|
}
|
|
|
|
static const int cacheId = m_cache.getId();
|
|
CachedArray cached = m_cache.getArray(cacheId);
|
|
vector_fp& factors = cached.value;
|
|
|
|
SurfPhase& surf = dynamic_cast<SurfPhase&>(thermo(reactionPhaseIndex()));
|
|
double n0 = surf.siteDensity();
|
|
if (!cached.validate(n0)) {
|
|
factors.resize(m_sticking_orders.size());
|
|
for (size_t n = 0; n < m_sticking_orders.size(); n++) {
|
|
factors[n] = pow(n0, -m_sticking_orders[n].second);
|
|
}
|
|
}
|
|
|
|
for (size_t n = 0; n < m_sticking_orders.size(); n++) {
|
|
kf[m_sticking_orders[n].first] *= factors[n];
|
|
}
|
|
}
|
|
|
|
|
|
void EdgeKinetics::finalize()
|
|
{
|
|
// Note we can't call the Interface::finalize() routine because we need to check for a dimension of 1 below.
|
|
// Therefore, we have to malloc room in arrays that would normally be
|
|
// handled by the InterfaceKinetics::finalize() call.
|
|
Kinetics::finalize();
|
|
|
|
size_t safe_reaction_size = std::max<size_t>(nReactions(), 1);
|
|
deltaElectricEnergy_.resize(safe_reaction_size);
|
|
size_t ks = reactionPhaseIndex();
|
|
if (ks == npos) throw CanteraError("EdgeKinetics::finalize",
|
|
"no surface phase is present.");
|
|
|
|
// Check to see edge phase has a dimension of 1
|
|
m_surf = (SurfPhase*)&thermo(ks);
|
|
if (m_surf->nDim() != 1) {
|
|
throw CanteraError("EdgeKinetics::finalize",
|
|
"expected interface dimension = 1, but got dimension = "
|
|
+int2str(m_surf->nDim()));
|
|
}
|
|
m_StandardConc.resize(m_kk, 0.0);
|
|
m_deltaG0.resize(safe_reaction_size, 0.0);
|
|
m_deltaG.resize(safe_reaction_size, 0.0);
|
|
|
|
m_ProdStanConcReac.resize(safe_reaction_size, 0.0);
|
|
|
|
if (m_thermo.size() != m_phaseExists.size()) {
|
|
throw CanteraError("InterfaceKinetics::finalize", "internal error");
|
|
}
|
|
|
|
// Guarantee that these arrays can be converted to double* even in the
|
|
// special case where there are no reactions defined.
|
|
if (!nReactions()) {
|
|
m_perturb.resize(1, 1.0);
|
|
m_ropf.resize(1, 0.0);
|
|
m_ropr.resize(1, 0.0);
|
|
m_ropnet.resize(1, 0.0);
|
|
m_rkcn.resize(1, 0.0);
|
|
}
|
|
m_finalized = true;
|
|
}
|
|
|
|
}
|