43c1d33f67
equilibrium constants for reactions with fractional stoichiometric coefficients. The member data m_dn[] was being calculated incorrectly for theses cases and then used in the calculation of the equilibrium constant. m_dn[] now correctly evaluates the difference in rxn order between the reactants and products for fraction coefficient reactions.
834 lines
26 KiB
C++
834 lines
26 KiB
C++
/**
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* @file InterfaceKinetics.cpp
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*
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*/
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// Copyright 2002 California Institute of Technology
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// turn off warnings under Windows
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#ifdef WIN32
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#pragma warning(disable:4786)
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#pragma warning(disable:4503)
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#endif
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#include "InterfaceKinetics.h"
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#include "SurfPhase.h"
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#include "ReactionData.h"
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#include "RateCoeffMgr.h"
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#include "ImplicitSurfChem.h"
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namespace Cantera {
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//////////////////////////////////////////////////////////////////
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/**
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* Construct an empty InterfaceKinetics reaction mechanism.
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* @param thermo This is an optional parameter that may be
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* used to initialize the inherited Kinetics class with
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* one ThermoPhase class object -> in other words it's
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* useful for initialization of homogeneous kinetics
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* mechanisms.
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*/
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InterfaceKinetics::
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InterfaceKinetics(thermo_t* thermo) :
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Kinetics(),
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m_kk(0),
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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_finalized(false),
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m_has_coverage_dependence(false)
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{
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if (thermo != 0) addPhase(*thermo);
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m_kdata = new InterfaceKineticsData;
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m_kdata->m_temp = 0.0;
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}
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/**
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* Destructor
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*/
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InterfaceKinetics::
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~InterfaceKinetics(){
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delete m_kdata;
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delete m_integrator;
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}
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/**
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* Update properties that depend on temperature
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*
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*/
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void InterfaceKinetics::
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_update_rates_T() {
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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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if (T != m_kdata->m_temp || m_redo_rates) {
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m_kdata->m_logtemp = log(T);
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m_rates.update(T, m_kdata->m_logtemp, DATA_PTR(m_kdata->m_rfn));
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applyButlerVolmerCorrection(DATA_PTR(m_kdata->m_rfn));
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m_kdata->m_temp = T;
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updateKc();
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m_kdata->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::
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_update_rates_phi() {
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int np = nPhases();
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for (int n = 0; n < np; 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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/**
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* Update properties that depend on concentrations. This method
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* fills out the array of generalized concentrations by calling
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* method getActivityConcentrations for each phase, which classes
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* representing phases should overload to return the appropriate
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* quantities.
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*/
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void InterfaceKinetics::
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_update_rates_C() {
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int n;
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int np = nPhases();
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for (n = 0; n < np; 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 indecises 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_kdata->m_ROP_ok = false;
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}
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/**
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* Update the equilibrium constants in molar units for all
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* reversible reactions. Irreversible reactions have their
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* equilibrium constant set to zero.
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*/
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void InterfaceKinetics::updateKc() {
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int i, irxn;
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vector_fp& m_rkc = m_kdata->m_rkcn;
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fill(m_rkc.begin(), m_rkc.end(), 0.0);
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//static vector_fp mu(nTotalSpecies());
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if (m_nrev > 0) {
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int n, nsp, k, 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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int np = nPhases();
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for (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 (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_reactantStoich.decrementReactions(m_mu0.begin(), m_rkc.begin());
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//m_revProductStoich.incrementReactions(m_mu0.begin(), m_rkc.begin());
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m_rxnstoich.getRevReactionDelta(m_ii, DATA_PTR(m_mu0),
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DATA_PTR(m_rkc));
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for (i = 0; i < m_nrev; i++) {
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irxn = m_revindex[i];
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if (irxn < 0 || irxn >= nReactions()) {
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throw CanteraError("InterfaceKinetics","illegal value: irxn = "+int2str(irxn));
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}
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m_rkc[irxn] = exp(m_rkc[irxn]*rrt);
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}
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for (i = 0; i != m_nirrev; ++i) {
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m_rkc[ 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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int i, irxn;
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vector_fp dmu(nTotalSpecies(), 0.0);
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vector_fp rmu(nReactions(), 0.0);
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vector_fp frop(nReactions(), 0.0);
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vector_fp rrop(nReactions(), 0.0);
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vector_fp netrop(nReactions(), 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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int n, nsp, k, 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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int np = nPhases();
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doublereal delta;
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for (n = 0; n < np; 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 (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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getFwdRatesOfProgress(DATA_PTR(frop));
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getRevRatesOfProgress(DATA_PTR(rrop));
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getNetRatesOfProgress(DATA_PTR(netrop));
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for (i = 0; i < m_nrev; i++) {
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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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frop[irxn], rrop[irxn], netrop[irxn],
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netrop[irxn]/(frop[irxn] + rrop[irxn]));
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}
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}
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}
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/**
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* Get the equilibrium constants of all reactions, whether
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* reversible or not.
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*/
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void InterfaceKinetics::getEquilibriumConstants(doublereal* kc) {
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int i;
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int n, nsp, k, 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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int np = nPhases();
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for (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 (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_reactantStoich.decrementReactions(m_mu0.begin(), kc);
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//m_revProductStoich.incrementReactions(m_mu0.begin(), kc);
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//m_irrevProductStoich.incrementReactions(m_mu0.begin(), kc);
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m_rxnstoich.getReactionDelta(m_ii, DATA_PTR(m_mu0), kc);
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for (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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/**
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* For reactions that transfer charge across a potential difference,
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* the activation energies are modified by the potential difference.
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* (see, for example, ...). This method applies this correction.
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*/
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void InterfaceKinetics::applyButlerVolmerCorrection(doublereal* kf) {
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int i;
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int n, nsp, k, 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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int np = nPhases();
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// compute the electrical potential energy of each species
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for (n = 0; n < np; n++) {
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nsp = thermo(n).nSpecies();
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for (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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//fill(m_rwork.begin(), m_rwork.begin() + m_ii, 0.0);
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//m_reactantStoich.decrementReactions(m_pot.begin(), m_rwork.begin());
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//m_revProductStoich.incrementReactions(m_pot.begin(), m_rwork.begin());
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//m_irrevProductStoich.incrementReactions(m_pot.begin(), m_rwork.begin());
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m_rxnstoich.getReactionDelta(m_ii, DATA_PTR(m_pot),
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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, and do not decrease the
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// activation energy below zero.
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doublereal ea, eamod;
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for (i = 0; i < m_ii; i++) {
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eamod = 0.5*m_rwork[i];
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if (eamod != 0.0 && m_E[i] != 0.0) {
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ea = GasConstant * m_E[i];
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if (eamod + ea < 0.0) {
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eamod = -ea;
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writelog("warning: modified E < 0.\n");
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}
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kf[i] *= exp(-eamod*rrt);
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// if (kf[i] == 0.0) {
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// for (n = 0; n < np; n++) {
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// cout << "phi " << n << " " << thermo(n).electricPotential() << " " << m_phi[n] << endl;
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// }
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// cout << "Zero rate coeff." << endl;
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// cout << "eamod = " << eamod << " " << eamod*rrt << endl;
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// cout << eamod/Faraday << endl;
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// }
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}
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}
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}
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/**
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* Update the rates of progress of the reactions in the reaciton
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* mechanism. This routine operates on internal data.
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*/
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void InterfaceKinetics::getFwdRateConstants(doublereal* kfwd) {
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_update_rates_T();
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_update_rates_C();
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const vector_fp& rf = m_kdata->m_rfn;
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// copy rate coefficients into kfwd
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copy(rf.begin(), rf.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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/**
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* Update the rates of progress of the reactions in the reaciton
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* mechanism. This routine operates on internal data.
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*/
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void InterfaceKinetics::getRevRateConstants(doublereal* krev, bool doIrreversible) {
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getFwdRateConstants(krev);
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if (doIrreversible) {
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doublereal *tmpKc = DATA_PTR(m_kdata->m_ropnet);
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getEquilibriumConstants(tmpKc);
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for (int i = 0; i < m_ii; i++) {
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krev[i] /= tmpKc[i];
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}
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}
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else {
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const vector_fp& rkc = m_kdata->m_rkcn;
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multiply_each(krev, krev + nReactions(), rkc.begin());
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}
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}
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void InterfaceKinetics::getActivationEnergies(doublereal *E) {
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copy(m_E.begin(), m_E.end(), E);
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}
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/**
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* Update the rates of progress of the reactions in the reaciton
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* mechanism. This routine operates on internal data.
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*/
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void InterfaceKinetics::updateROP() {
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_update_rates_T();
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_update_rates_C();
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if (m_kdata->m_ROP_ok) return;
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const vector_fp& rf = m_kdata->m_rfn;
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const vector_fp& m_rkc = m_kdata->m_rkcn;
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array_fp& ropf = m_kdata->m_ropf;
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array_fp& ropr = m_kdata->m_ropr;
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array_fp& ropnet = m_kdata->m_ropnet;
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// copy rate coefficients into ropf
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copy(rf.begin(), rf.end(), ropf.begin());
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// multiply by perturbation factor
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multiply_each(ropf.begin(), ropf.end(), m_perturb.begin());
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// copy the forward rates to the reverse rates
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copy(ropf.begin(), ropf.end(), 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(ropr.begin(), ropr.end(), m_rkc.begin());
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// multiply ropf by concentration products
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m_rxnstoich.multiplyReactants(DATA_PTR(m_conc), DATA_PTR(ropf));
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//m_reactantStoich.multiply(m_conc.begin(), ropf.begin());
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// for reversible reactions, multiply ropr by concentration
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// products
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m_rxnstoich.multiplyRevProducts(DATA_PTR(m_conc),
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DATA_PTR(ropr));
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//m_revProductStoich.multiply(m_conc.begin(), ropr.begin());
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// do global reactions
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//m_globalReactantStoich.power(m_conc.begin(), ropf.begin());
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for (int j = 0; j != m_ii; ++j) {
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ropnet[j] = ropf[j] - ropr[j];
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}
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m_kdata->m_ROP_ok = true;
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}
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/**
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*
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* getDeltaGibbs():
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*
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* Return the vector of values for the reaction gibbs free energy
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* change
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* These values depend upon the concentration
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* of the ideal gas.
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*
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* units = J kmol-1
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*/
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void InterfaceKinetics::getDeltaGibbs(doublereal* deltaG) {
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/*
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* Get the chemical potentials of the species in the
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* ideal gas solution.
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*/
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int np = nPhases();
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int n;
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for (n = 0; n < np; n++) {
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thermo(n).getChemPotentials(DATA_PTR(m_grt) + m_start[n]);
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}
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/*
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* Use the stoichiometric manager to find deltaG for each
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* reaction.
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*/
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m_rxnstoich.getReactionDelta(m_ii, DATA_PTR(m_grt), deltaG);
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}
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/**
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*
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* getDeltaEnthalpy():
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*
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* Return the vector of values for the reactions change in
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* enthalpy.
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* These values depend upon the concentration
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* of the solution.
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*
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* units = J kmol-1
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*/
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void InterfaceKinetics::getDeltaEnthalpy(doublereal* deltaH) {
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/*
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* Get the partial molar enthalpy of all species in the
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* ideal gas.
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*/
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int np = nPhases();
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int n;
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for (n = 0; n < np; n++) {
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thermo(n).getPartialMolarEnthalpies(DATA_PTR(m_grt) + m_start[n]);
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}
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/*
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* Use the stoichiometric manager to find deltaG for each
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* reaction.
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*/
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m_rxnstoich.getReactionDelta(m_ii, DATA_PTR(m_grt), deltaH);
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}
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/************************************************************************
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*
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* getDeltaEntropy():
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*
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* Return the vector of values for the reactions change in
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* entropy.
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* These values depend upon the concentration
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* of the solution.
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*
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* units = J kmol-1 Kelvin-1
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*/
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void InterfaceKinetics::getDeltaEntropy( doublereal* deltaS) {
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/*
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* Get the partial molar entropy of all species in the
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* solid solution.
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*/
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int np = nPhases();
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int n;
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for (n = 0; n < np; n++) {
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thermo(n).getPartialMolarEntropies(DATA_PTR(m_grt) + m_start[n]);
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}
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/*
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* Use the stoichiometric manager to find deltaS for each
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* reaction.
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*/
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m_rxnstoich.getReactionDelta(m_ii, DATA_PTR(m_grt), deltaS);
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}
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/**
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*
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* getDeltaSSGibbs():
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*
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* Return the vector of values for the reaction
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* standard state gibbs free energy change.
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* These values don't depend upon the concentration
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* of the solution.
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*
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* units = J kmol-1
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*/
|
|
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.
|
|
*/
|
|
int np = nPhases();
|
|
int n;
|
|
for (n = 0; n < np; 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);
|
|
}
|
|
|
|
/**
|
|
*
|
|
* getDeltaSSEnthalpy():
|
|
*
|
|
* Return the vector of values for the change in the
|
|
* standard state enthalpies of reaction.
|
|
* These values don't depend upon the concentration
|
|
* of the solution.
|
|
*
|
|
* units = J kmol-1
|
|
*/
|
|
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.
|
|
*/
|
|
int np = nPhases();
|
|
int n;
|
|
for (n = 0; n < np; n++) {
|
|
thermo(n).getEnthalpy_RT(DATA_PTR(m_grt) + m_start[n]);
|
|
}
|
|
doublereal RT = thermo().temperature() * GasConstant;
|
|
for (int 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);
|
|
}
|
|
|
|
/*********************************************************************
|
|
*
|
|
* getDeltaSSEntropy():
|
|
*
|
|
* Return the vector of values for the change in the
|
|
* standard state entropies for each reaction.
|
|
* These values don't depend upon the concentration
|
|
* of the solution.
|
|
*
|
|
* units = J kmol-1 Kelvin-1
|
|
*/
|
|
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.
|
|
*/
|
|
int np = nPhases();
|
|
int n;
|
|
for (n = 0; n < np; n++) {
|
|
thermo(n).getEntropy_R(DATA_PTR(m_grt) + m_start[n]);
|
|
}
|
|
doublereal R = GasConstant;
|
|
for (int 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);
|
|
}
|
|
|
|
|
|
/**
|
|
* Add a single reaction to the mechanism. This routine
|
|
* must be called after init() and before finalize().
|
|
* This function branches on the types of reactions allowed
|
|
* by the interfaceKinetics manager in order to install
|
|
* the reaction correctly in the manager.
|
|
* The manager allows the following reaction types
|
|
* Elementary
|
|
* Surface
|
|
* Global
|
|
* There is no difference between elementary and surface
|
|
* reactions.
|
|
*/
|
|
void InterfaceKinetics::
|
|
addReaction(const ReactionData& r) {
|
|
|
|
addElementaryReaction(r);
|
|
|
|
// operations common to all reaction types
|
|
installReagents( r );
|
|
//installGroups(reactionNumber(), r.rgroups, r.pgroups);
|
|
incrementRxnCount();
|
|
m_rxneqn.push_back(r.equation);
|
|
}
|
|
|
|
|
|
void InterfaceKinetics::
|
|
addElementaryReaction(const ReactionData& r) {
|
|
int iloc;
|
|
// install rate coeff calculator
|
|
vector_fp rp = r.rateCoeffParameters;
|
|
int ncov = r.cov.size();
|
|
if (ncov > 3) {
|
|
m_has_coverage_dependence = true;
|
|
}
|
|
for (int m = 0; m < ncov; m++) rp.push_back(r.cov[m]);
|
|
iloc = m_rates.install( reactionNumber(),
|
|
r.rateCoeffType, rp.size(),
|
|
DATA_PTR(rp) );
|
|
// store activation energy
|
|
m_E.push_back(r.rateCoeffParameters[2]);
|
|
// add constant term to rate coeff value vector
|
|
m_kdata->m_rfn.push_back(r.rateCoeffParameters[0]);
|
|
registerReaction( reactionNumber(), ELEMENTARY_RXN, iloc);
|
|
}
|
|
|
|
|
|
// 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_kdata->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) {
|
|
|
|
int n, ns, m;
|
|
doublereal nsFlt;
|
|
/*
|
|
* extend temporary storage by one for this rxn.
|
|
*/
|
|
m_kdata->m_ropf.push_back(0.0);
|
|
m_kdata->m_ropr.push_back(0.0);
|
|
m_kdata->m_ropnet.push_back(0.0);
|
|
m_kdata->m_rkcn.push_back(0.0);
|
|
|
|
/*
|
|
* Obtain the current reaction index for the reaction that we
|
|
* are adding. The first reaction is labeled 0.
|
|
*/
|
|
int 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'.
|
|
|
|
vector_int rk;
|
|
int nr = r.reactants.size();
|
|
for (n = 0; n < nr; n++) {
|
|
nsFlt = r.rstoich[n];
|
|
ns = (int) 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] = ns;
|
|
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);
|
|
|
|
vector_int pk;
|
|
int np = r.products.size();
|
|
for (n = 0; n < np; n++) {
|
|
nsFlt = r.pstoich[n];
|
|
ns = (int) 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] = ns;
|
|
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::installGroups(int irxn,
|
|
// const vector<grouplist_t>& r, const vector<grouplist_t>& p) {
|
|
// if (!r.empty()) {
|
|
// m_rgroups[reactionNumber()] = r;
|
|
// m_pgroups[reactionNumber()] = p;
|
|
// }
|
|
//}
|
|
|
|
/**
|
|
* Prepare the class for the addition of reactions. This function
|
|
* must be called after instantiation of the class, but before
|
|
* any reactions are actually added to the mechanism.
|
|
* This function calculates m_kk the number of species in all
|
|
* phases participating in the reaction mechanism. We don't know
|
|
* m_kk previously, before all phases have been added.
|
|
*/
|
|
void InterfaceKinetics::init() {
|
|
int n;
|
|
m_kk = 0;
|
|
int np = nPhases();
|
|
for (n = 0; n < np; 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(np, 0.0);
|
|
}
|
|
|
|
/**
|
|
* Finish adding reactions and prepare for use. This function
|
|
* must be called after all reactions are entered into the mechanism
|
|
* and before the mechanism is used to calculate reaction rates.
|
|
*
|
|
* Here, we resize work arrays based on the number of reactions,
|
|
* since we don't know this number up to now.
|
|
*/
|
|
void InterfaceKinetics::finalize() {
|
|
m_rwork.resize(nReactions());
|
|
int ks = surfacePhaseIndex();
|
|
if (ks < 0) throw CanteraError("InterfaceKinetics::finalize",
|
|
"no surface phase is present.");
|
|
m_surf = (SurfPhase*)&thermo(ks);
|
|
m_finalized = true;
|
|
}
|
|
|
|
|
|
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;
|
|
}
|
|
|
|
}
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|