b84f19c439
Formerly getExchangeCurrentQuantities() is now updateExchangeCurrentQuantities(). This method updates things like m_StandardConc for computing reaction rates. Formerly applyExchangeCurrentDensityFormulation() is now convertExchangeCurrentDensityFormulation(). This method converts rate expressions from A/m2 to kmol/m2/s.
1150 lines
36 KiB
C++
1150 lines
36 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/ReactionData.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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Kinetics(),
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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_beta(0),
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m_ctrxn(0),
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m_ctrxn_ecdf(0),
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m_StandardConc(0),
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m_deltaG0(0),
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m_ProdStanConcReac(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_phaseExists(0),
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m_phaseIsStable(0),
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m_rxnPhaseIsReactant(0),
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m_rxnPhaseIsProduct(0),
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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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Kinetics(),
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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_beta(0),
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m_ctrxn(0),
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m_ctrxn_ecdf(0),
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m_StandardConc(0),
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m_deltaG0(0),
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m_ProdStanConcReac(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_phaseExists(0),
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m_phaseIsStable(0),
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m_rxnPhaseIsReactant(0),
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m_rxnPhaseIsProduct(0),
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m_ioFlag(0)
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{
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/*
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* Call the assignment operator
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*/
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*this = 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_index = right.m_index;
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m_irrev = right.m_irrev;
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m_rxnstoich = right.m_rxnstoich;
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m_nirrev = right.m_nirrev;
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m_nrev = right.m_nrev;
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m_rrxn = right.m_rrxn;
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m_prxn = right.m_prxn;
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m_rxneqn = right.m_rxneqn;
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m_conc = right.m_conc;
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m_mu0 = right.m_mu0;
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m_phi = right.m_phi;
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m_pot = right.m_pot;
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m_rwork = right.m_rwork;
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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_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_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_ropf = right.m_ropf;
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m_ropr = right.m_ropr;
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m_ropnet = right.m_ropnet;
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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_rfn = right.m_rfn;
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m_rkcn = right.m_rkcn;
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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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_update_rates_phi();
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if (m_has_coverage_dependence) {
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m_surf->getCoverages(DATA_PTR(m_conc));
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m_rates.update_C(DATA_PTR(m_conc));
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m_redo_rates = true;
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}
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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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m_rates.update(T, m_logtemp, DATA_PTR(m_rfn));
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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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applyButlerVolmerCorrection(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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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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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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/*
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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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thermo(n).getActivityConcentrations(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_conc.begin(), m_conc.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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//static vector_fp mu(nTotalSpecies());
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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[]
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*/
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size_t nsp, ik = 0;
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doublereal rt = GasConstant*thermo(0).temperature();
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doublereal rrt = 1.0 / rt;
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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[ik] -= rt * thermo(n).logStandardConc(k);
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m_mu0[ik] += Faraday * m_phi[n] * thermo(n).charge(k);
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ik++;
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}
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}
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// compute Delta mu^0 for all reversible reactions
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m_rxnstoich.getRevReactionDelta(m_ii, DATA_PTR(m_mu0), 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",
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"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::checkPartialEquil()
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{
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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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doublereal rt = GasConstant*thermo(0).temperature();
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cout << "T = " << thermo(0).temperature() << " " << rt << endl;
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size_t nsp, ik=0;
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//doublereal rt = GasConstant*thermo(0).temperature();
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// doublereal rrt = 1.0/rt;
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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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//cout << thermo(n).speciesName(k) << " " << (delta+dmu[ik])/rt << " " << dmu[ik]/rt << endl;
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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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m_rxnstoich.getRevReactionDelta(m_ii, 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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cout << "Reaction " << reactionString(irxn)
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<< " " << rmu[irxn]/rt << endl;
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printf("%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::getFwdRatesOfProgress(doublereal* fwdROP)
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{
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updateROP();
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std::copy(m_ropf.begin(), m_ropf.end(), fwdROP);
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}
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void InterfaceKinetics::getRevRatesOfProgress(doublereal* revROP)
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{
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updateROP();
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std::copy(m_ropr.begin(), m_ropr.end(), revROP);
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}
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void InterfaceKinetics::getNetRatesOfProgress(doublereal* netROP)
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{
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updateROP();
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std::copy(m_ropnet.begin(), m_ropnet.end(), netROP);
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}
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void InterfaceKinetics::getEquilibriumConstants(doublereal* kc)
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{
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size_t ik=0;
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doublereal rt = GasConstant*thermo(0).temperature();
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doublereal rrt = 1.0/rt;
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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_mu0[ik] -= rt*thermo(n).logStandardConc(k);
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m_mu0[ik] += Faraday * m_phi[n] * thermo(n).charge(k);
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ik++;
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}
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}
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fill(kc, kc + m_ii, 0.0);
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m_rxnstoich.getReactionDelta(m_ii, DATA_PTR(m_mu0), kc);
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for (size_t i = 0; i < m_ii; i++) {
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kc[i] = exp(-kc[i]*rrt);
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}
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}
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/** values needed to convert from exchange current density to surface reaction rate.
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*/
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void InterfaceKinetics::updateExchangeCurrentQuantities()
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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_logStandardConc
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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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m_rxnstoich.getReactionDelta(m_ii, DATA_PTR(m_mu0), DATA_PTR(m_deltaG0));
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for (size_t i = 0; i < m_ii; i++) {
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m_ProdStanConcReac[i] = 1.0;
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}
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m_rxnstoich.multiplyReactants(DATA_PTR(m_StandardConc), DATA_PTR(m_ProdStanConcReac));
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}
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void InterfaceKinetics::getCreationRates(doublereal* cdot)
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{
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updateROP();
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m_rxnstoich.getCreationRates(m_kk, &m_ropf[0], &m_ropr[0], cdot);
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}
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void InterfaceKinetics::getDestructionRates(doublereal* ddot)
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{
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updateROP();
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m_rxnstoich.getDestructionRates(m_kk, &m_ropf[0], &m_ropr[0], ddot);
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}
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void InterfaceKinetics::getNetProductionRates(doublereal* net)
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{
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updateROP();
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m_rxnstoich.getNetProductionRates(m_kk, &m_ropnet[0], net);
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}
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void InterfaceKinetics::applyButlerVolmerCorrection(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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m_rxnstoich.getReactionDelta(m_ii, DATA_PTR(m_pot), DATA_PTR(m_rwork));
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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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#ifdef DEBUG_KIN_MODE
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doublereal ea;
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#endif
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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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eamod = m_beta[i]*m_rwork[irxn];
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// if (eamod != 0.0 && m_E[irxn] != 0.0) {
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if (eamod != 0.0) {
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#ifdef DEBUG_KIN_MODE
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ea = GasConstant * m_E[irxn];
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if (eamod + ea < 0.0) {
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writelog("Warning: act energy mod too large!\n");
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writelog(" Delta phi = "+fp2str(m_rwork[irxn]/Faraday)+"\n");
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writelog(" Delta Ea = "+fp2str(eamod)+"\n");
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writelog(" Ea = "+fp2str(ea)+"\n");
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for (n = 0; n < np; n++) {
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writelog("Phase "+int2str(n)+": phi = "
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+fp2str(m_phi[n])+"\n");
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}
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}
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#endif
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doublereal rt = GasConstant*thermo(0).temperature();
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doublereal rrt = 1.0/rt;
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kf[irxn] *= exp(-eamod*rrt);
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}
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}
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}
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/**
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* For a reaction rate that was given in units of Amps/m2 (exchange current
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* density formulation with iECDFormulation == true), convert the rate to
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* kmoles/m2/s.
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* RENAMED THIS METHOD from "apply" to "convert"
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*/
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void InterfaceKinetics::convertExchangeCurrentDensityFormulation(doublereal* const kfwd)
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{
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updateExchangeCurrentQuantities();
|
|
doublereal rt = GasConstant*thermo(0).temperature();
|
|
doublereal rrt = 1.0/rt;
|
|
for (size_t i = 0; i < m_ctrxn.size(); i++) {
|
|
size_t irxn = m_ctrxn[i];
|
|
int iECDFormulation = m_ctrxn_ecdf[i];
|
|
if (iECDFormulation) {
|
|
double tmp = exp(- m_beta[i] * m_deltaG0[irxn] * rrt);
|
|
double tmp2 = m_ProdStanConcReac[irxn];
|
|
tmp *= 1.0 / tmp2 / Faraday;
|
|
kfwd[irxn] *= tmp;
|
|
}
|
|
}
|
|
}
|
|
|
|
void InterfaceKinetics::getFwdRateConstants(doublereal* kfwd)
|
|
{
|
|
|
|
updateROP();
|
|
|
|
// copy rate coefficients into kfwd
|
|
copy(m_rfn.begin(), m_rfn.end(), kfwd);
|
|
|
|
// multiply by perturbation factor
|
|
multiply_each(kfwd, kfwd + nReactions(), m_perturb.begin());
|
|
|
|
}
|
|
|
|
void InterfaceKinetics::getRevRateConstants(doublereal* krev, bool doIrreversible)
|
|
{
|
|
getFwdRateConstants(krev);
|
|
if (doIrreversible) {
|
|
getEquilibriumConstants(&m_ropnet[0]);
|
|
for (size_t i = 0; i < m_ii; i++) {
|
|
krev[i] /= m_ropnet[i];
|
|
}
|
|
} else {
|
|
multiply_each(krev, krev + nReactions(), m_rkcn.begin());
|
|
}
|
|
}
|
|
|
|
void InterfaceKinetics::updateROP()
|
|
{
|
|
// evaluate rate and equilibrium constants at temperature and phi (electric potential)
|
|
_update_rates_T();
|
|
// get updated activities (rates updated below)
|
|
_update_rates_C();
|
|
|
|
if (m_ROP_ok) {
|
|
return;
|
|
}
|
|
|
|
// copy rate coefficients into ropf
|
|
copy(m_rfn.begin(), m_rfn.end(), m_ropf.begin());
|
|
|
|
// multiply by perturbation factor
|
|
multiply_each(m_ropf.begin(), m_ropf.end(), m_perturb.begin());
|
|
|
|
// copy the forward rates to the reverse rates
|
|
copy(m_ropf.begin(), m_ropf.end(), m_ropr.begin());
|
|
|
|
// for reverse rates computed from thermochemistry, multiply
|
|
// the forward rates copied into m_ropr by the reciprocals of
|
|
// the equilibrium constants
|
|
multiply_each(m_ropr.begin(), m_ropr.end(), m_rkcn.begin());
|
|
|
|
// multiply ropf by concentration products
|
|
m_rxnstoich.multiplyReactants(DATA_PTR(m_conc), DATA_PTR(m_ropf));
|
|
//m_reactantStoich.multiply(m_conc.begin(), ropf.begin());
|
|
|
|
// for reversible reactions, multiply ropr by concentration
|
|
// products
|
|
m_rxnstoich.multiplyRevProducts(DATA_PTR(m_conc),
|
|
DATA_PTR(m_ropr));
|
|
//m_revProductStoich.multiply(m_conc.begin(), ropr.begin());
|
|
|
|
// do global reactions
|
|
//m_globalReactantStoich.power(m_conc.begin(), ropf.begin());
|
|
|
|
for (size_t j = 0; j != m_ii; ++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 != m_ii; ++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]) {
|
|
if (! 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]) {
|
|
if (! m_phaseExists[rp]) {
|
|
m_ropnet[j] = 0.0;
|
|
m_ropr[j] = m_ropf[j] = 0.0;
|
|
}
|
|
}
|
|
}
|
|
}
|
|
}
|
|
}
|
|
if (m_rxnPhaseIsReactant[j][p]) {
|
|
if (! 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]) {
|
|
if (! 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]) {
|
|
if (! m_phaseExists[rp]) {
|
|
m_ropnet[j] = 0.0;
|
|
m_ropf[j] = m_ropr[j] = 0.0;
|
|
}
|
|
}
|
|
}
|
|
}
|
|
}
|
|
}
|
|
if (m_rxnPhaseIsProduct[j][p]) {
|
|
if (! 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
|
|
* ideal gas solution.
|
|
*/
|
|
for (size_t n = 0; n < nPhases(); n++) {
|
|
thermo(n).getChemPotentials(DATA_PTR(m_grt) + m_start[n]);
|
|
}
|
|
//for (n = 0; n < m_grt.size(); n++) {
|
|
// cout << n << "G_RT = " << m_grt[n] << endl;
|
|
//}
|
|
|
|
/*
|
|
* Use the stoichiometric manager to find deltaG for each
|
|
* reaction.
|
|
*/
|
|
m_rxnstoich.getReactionDelta(m_ii, DATA_PTR(m_grt), deltaG);
|
|
}
|
|
|
|
void InterfaceKinetics::getDeltaElectrochemPotentials(doublereal* deltaM)
|
|
{
|
|
/*
|
|
* Get the chemical potentials of the species in the
|
|
* ideal gas solution.
|
|
*/
|
|
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.
|
|
*/
|
|
m_rxnstoich.getReactionDelta(m_ii, DATA_PTR(m_grt), deltaM);
|
|
}
|
|
|
|
void InterfaceKinetics::getDeltaEnthalpy(doublereal* deltaH)
|
|
{
|
|
/*
|
|
* Get the partial molar enthalpy of all species in the
|
|
* ideal gas.
|
|
*/
|
|
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.
|
|
*/
|
|
m_rxnstoich.getReactionDelta(m_ii, 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.
|
|
*/
|
|
m_rxnstoich.getReactionDelta(m_ii, DATA_PTR(m_grt), deltaS);
|
|
}
|
|
|
|
void InterfaceKinetics::getDeltaSSGibbs(doublereal* deltaG)
|
|
{
|
|
/*
|
|
* 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_grt) + m_start[n]);
|
|
}
|
|
/*
|
|
* Use the stoichiometric manager to find deltaG for each
|
|
* reaction.
|
|
*/
|
|
m_rxnstoich.getReactionDelta(m_ii, DATA_PTR(m_grt), deltaG);
|
|
}
|
|
|
|
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]);
|
|
}
|
|
doublereal RT = thermo().temperature() * GasConstant;
|
|
for (size_t k = 0; k < m_kk; k++) {
|
|
m_grt[k] *= RT;
|
|
}
|
|
/*
|
|
* Use the stoichiometric manager to find deltaG for each
|
|
* reaction.
|
|
*/
|
|
m_rxnstoich.getReactionDelta(m_ii, 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]);
|
|
}
|
|
doublereal R = GasConstant;
|
|
for (size_t k = 0; k < m_kk; k++) {
|
|
m_grt[k] *= R;
|
|
}
|
|
/*
|
|
* Use the stoichiometric manager to find deltaS for each
|
|
* reaction.
|
|
*/
|
|
m_rxnstoich.getReactionDelta(m_ii, DATA_PTR(m_grt), deltaS);
|
|
}
|
|
|
|
void InterfaceKinetics::addReaction(ReactionData& r)
|
|
{
|
|
/*
|
|
* Install the rate coefficient for the current reaction
|
|
* in the appropriate data structure.
|
|
*/
|
|
addElementaryReaction(r);
|
|
/*
|
|
* Add the reactants and products for m_ropnet;the current reaction
|
|
* to the various stoichiometric coefficient arrays.
|
|
*/
|
|
installReagents(r);
|
|
/*
|
|
* Save the reaction and product groups, which are
|
|
* part of the ReactionData class, in this class.
|
|
* They aren't used for anything but reaction path
|
|
* analysis.
|
|
*/
|
|
//installGroups(reactionNumber(), r.rgroups, r.pgroups);
|
|
/*
|
|
* Increase the internal number of reactions, m_ii, by one.
|
|
* increase the size of m_perturb by one as well.
|
|
*/
|
|
incrementRxnCount();
|
|
m_rxneqn.push_back(r.equation);
|
|
|
|
m_rxnPhaseIsReactant.push_back(std::vector<bool>(nPhases(), false));
|
|
m_rxnPhaseIsProduct.push_back(std::vector<bool>(nPhases(), false));
|
|
|
|
size_t i = m_ii - 1;
|
|
const std::vector<size_t>& vr = reactants(i);
|
|
for (size_t ik = 0; ik < vr.size(); ik++) {
|
|
size_t k = vr[ik];
|
|
size_t p = speciesPhaseIndex(k);
|
|
m_rxnPhaseIsReactant[i][p] = true;
|
|
}
|
|
const std::vector<size_t>& vp = products(i);
|
|
for (size_t ik = 0; ik < vp.size(); ik++) {
|
|
size_t k = vp[ik];
|
|
size_t p = speciesPhaseIndex(k);
|
|
m_rxnPhaseIsProduct[i][p] = true;
|
|
}
|
|
}
|
|
|
|
void InterfaceKinetics::addElementaryReaction(ReactionData& r)
|
|
{
|
|
// install rate coeff calculator
|
|
vector_fp& rp = r.rateCoeffParameters;
|
|
size_t ncov = r.cov.size();
|
|
if (ncov > 3) {
|
|
m_has_coverage_dependence = true;
|
|
}
|
|
for (size_t m = 0; m < ncov; m++) {
|
|
rp.push_back(r.cov[m]);
|
|
}
|
|
|
|
/*
|
|
* Temporarily change the reaction rate coefficient type to surface arrhenius.
|
|
* This is what is expected. We'll handle exchange current types below by hand.
|
|
*/
|
|
int reactionRateCoeffType_orig = r.rateCoeffType;
|
|
if (r.rateCoeffType == EXCHANGE_CURRENT_REACTION_RATECOEFF_TYPE) {
|
|
r.rateCoeffType = SURF_ARRHENIUS_REACTION_RATECOEFF_TYPE;
|
|
}
|
|
if (r.rateCoeffType == ARRHENIUS_REACTION_RATECOEFF_TYPE) {
|
|
r.rateCoeffType = SURF_ARRHENIUS_REACTION_RATECOEFF_TYPE;
|
|
}
|
|
/*
|
|
* Install the reaction rate into the vector of reactions handled by this class
|
|
*/
|
|
size_t iloc = m_rates.install(reactionNumber(), r);
|
|
|
|
/*
|
|
* Change the reaction rate coefficient type back to its original value
|
|
*/
|
|
r.rateCoeffType = reactionRateCoeffType_orig;
|
|
|
|
// store activation energy
|
|
m_E.push_back(r.rateCoeffParameters[2]);
|
|
|
|
if (r.beta > 0.0) {
|
|
m_has_electrochem_rxns = true;
|
|
m_beta.push_back(r.beta);
|
|
m_ctrxn.push_back(reactionNumber());
|
|
if (r.rateCoeffType == EXCHANGE_CURRENT_REACTION_RATECOEFF_TYPE) {
|
|
m_has_exchange_current_density_formulation = true;
|
|
m_ctrxn_ecdf.push_back(1);
|
|
} else {
|
|
m_ctrxn_ecdf.push_back(0);
|
|
}
|
|
}
|
|
|
|
// add constant term to rate coeff value vector
|
|
m_rfn.push_back(r.rateCoeffParameters[0]);
|
|
registerReaction(reactionNumber(), ELEMENTARY_RXN, iloc);
|
|
}
|
|
|
|
void InterfaceKinetics::setIOFlag(int ioFlag)
|
|
{
|
|
m_ioFlag = ioFlag;
|
|
if (m_integrator) {
|
|
m_integrator->setIOFlag(ioFlag);
|
|
}
|
|
}
|
|
|
|
// void InterfaceKinetics::
|
|
// addGlobalReaction(const ReactionData& r) {
|
|
|
|
// int iloc;
|
|
// // install rate coeff calculator
|
|
// vector_fp rp = r.rateCoeffParameters;
|
|
// int ncov = r.cov.size();
|
|
// for (int m = 0; m < ncov; m++) rp.push_back(r.cov[m]);
|
|
// iloc = m_rates.install( reactionNumber(),
|
|
// r.rateCoeffType, rp.size(),
|
|
// rp.begin() );
|
|
// // store activation energy
|
|
// m_E.push_back(r.rateCoeffParameters[2]);
|
|
// // add constant term to rate coeff value vector
|
|
// m_rfn.push_back(r.rateCoeffParameters[0]);
|
|
|
|
// int nr = r.order.size();
|
|
// vector_fp ordr(nr);
|
|
// for (int n = 0; n < nr; n++) {
|
|
// ordr[n] = r.order[n] - r.rstoich[n];
|
|
// }
|
|
// m_globalReactantStoich.add( reactionNumber(),
|
|
// r.reactants, ordr);
|
|
|
|
// registerReaction( reactionNumber(), GLOBAL_RXN, iloc);
|
|
// }
|
|
|
|
void InterfaceKinetics::installReagents(const ReactionData& r)
|
|
{
|
|
|
|
size_t n, ns, m;
|
|
doublereal nsFlt;
|
|
/*
|
|
* extend temporary storage by one for this rxn.
|
|
*/
|
|
m_ropf.push_back(0.0);
|
|
m_ropr.push_back(0.0);
|
|
m_ropnet.push_back(0.0);
|
|
m_rkcn.push_back(0.0);
|
|
|
|
/*
|
|
* Obtain the current reaction index for the reaction that we
|
|
* are adding. The first reaction is labeled 0.
|
|
*/
|
|
size_t rnum = reactionNumber();
|
|
|
|
// vectors rk and pk are lists of species numbers, with
|
|
// repeated entries for species with stoichiometric
|
|
// coefficients > 1. This allows the reaction to be defined
|
|
// with unity reaction order for each reactant, and so the
|
|
// faster method 'multiply' can be used to compute the rate of
|
|
// progress instead of 'power'.
|
|
|
|
std::vector<size_t> rk;
|
|
size_t nr = r.reactants.size();
|
|
for (n = 0; n < nr; n++) {
|
|
nsFlt = r.rstoich[n];
|
|
ns = (size_t) nsFlt;
|
|
if ((doublereal) ns != nsFlt) {
|
|
if (ns < 1) {
|
|
ns = 1;
|
|
}
|
|
}
|
|
/*
|
|
* Add to m_rrxn. m_rrxn is a vector of maps. m_rrxn has a length
|
|
* equal to the total number of species for each species, there
|
|
* exists a map, with the reaction number being the key, and the
|
|
* reactant stoichiometric coefficient being the value.
|
|
*/
|
|
m_rrxn[r.reactants[n]][rnum] = nsFlt;
|
|
for (m = 0; m < ns; m++) {
|
|
rk.push_back(r.reactants[n]);
|
|
}
|
|
}
|
|
/*
|
|
* Now that we have rk[], we add it into the vector<vector_int> m_reactants
|
|
* in the rnum index spot. Thus m_reactants[rnum] yields a vector
|
|
* of reactants for the rnum'th reaction
|
|
*/
|
|
m_reactants.push_back(rk);
|
|
std::vector<size_t> pk;
|
|
size_t np = r.products.size();
|
|
for (n = 0; n < np; n++) {
|
|
nsFlt = r.pstoich[n];
|
|
ns = (size_t) nsFlt;
|
|
if ((doublereal) ns != nsFlt) {
|
|
if (ns < 1) {
|
|
ns = 1;
|
|
}
|
|
}
|
|
/*
|
|
* Add to m_prxn. m_prxn is a vector of maps. m_prxn has a length
|
|
* equal to the total number of species for each species, there
|
|
* exists a map, with the reaction number being the key, and the
|
|
* product stoichiometric coefficient being the value.
|
|
*/
|
|
m_prxn[r.products[n]][rnum] = nsFlt;
|
|
for (m = 0; m < ns; m++) {
|
|
pk.push_back(r.products[n]);
|
|
}
|
|
}
|
|
/*
|
|
* Now that we have pk[], we add it into the vector<vector_int> m_products
|
|
* in the rnum index spot. Thus m_products[rnum] yields a vector
|
|
* of products for the rnum'th reaction
|
|
*/
|
|
m_products.push_back(pk);
|
|
/*
|
|
* Add this reaction to the stoichiometric coefficient manager. This
|
|
* calculates rates of species production from reaction rates of
|
|
* progress.
|
|
*/
|
|
m_rxnstoich.add(reactionNumber(), r);
|
|
/*
|
|
* register reaction in lists of reversible and irreversible rxns.
|
|
*/
|
|
if (r.reversible) {
|
|
m_revindex.push_back(reactionNumber());
|
|
m_nrev++;
|
|
} else {
|
|
m_irrev.push_back(reactionNumber());
|
|
m_nirrev++;
|
|
}
|
|
}
|
|
|
|
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_rrxn.resize(m_kk);
|
|
m_prxn.resize(m_kk);
|
|
m_conc.resize(m_kk);
|
|
m_mu0.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);
|
|
m_rwork.resize(safe_reaction_size);
|
|
size_t ks = reactionPhaseIndex();
|
|
if (ks == npos) throw CanteraError("InterfaceKinetics::finalize",
|
|
"no surface phase is present.");
|
|
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_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 (!m_ii) {
|
|
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--;
|
|
if (m_phaseExistsCheck < 0) {
|
|
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 EdgeKinetics::finalize()
|
|
{
|
|
m_rwork.resize(std::max<size_t>(nReactions(), 1));
|
|
size_t ks = reactionPhaseIndex();
|
|
if (ks == npos) throw CanteraError("EdgeKinetics::finalize",
|
|
"no edge phase is present.");
|
|
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()));
|
|
|
|
// Guarantee that these arrays can be converted to double* even in the
|
|
// special case where there are no reactions defined.
|
|
if (!m_ii) {
|
|
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;
|
|
}
|
|
|
|
}
|