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cantera/include/cantera/kinetics/InterfaceKinetics.h
Ray Speth 23642ded3c [Kinetics] Use current site density sticking reaction rate coefficient 
The conversion of sticking coefficients to Arrhenius expressions includes the
site density on the surface phase, which may not be set when the reaction is
being added to the Kinetics object. We now defer the calculation of this
dependency until the rate coefficient is being evaluated so that the current
value for the site density can be used.
2015-04-29 11:55:07 -04:00

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/**
* @file InterfaceKinetics.h
*
* @ingroup chemkinetics
*/
// Copyright 2001 California Institute of Technology
#ifndef CT_IFACEKINETICS_H
#define CT_IFACEKINETICS_H
#include "cantera/thermo/mix_defs.h"
#include "Kinetics.h"
#include "cantera/kinetics/RxnMolChange.h"
#include "Reaction.h"
#include "cantera/base/utilities.h"
#include "RateCoeffMgr.h"
namespace Cantera
{
// forward declarations
class SurfPhase;
class ImplicitSurfChem;
class RxnMolChange;
//! forward orders
class RxnOrders {
public:
//! constructors
RxnOrders() {}
RxnOrders(const RxnOrders &right);
~RxnOrders() {}
RxnOrders& operator=(const RxnOrders &right);
//! Fill in the structure with the array.
/*!
* @param[in] Size of length kinetic species. The entries the values of the orders
*/
int fill(const vector_fp& fullForwardOrders);
//! ID's of the kinetic species
std::vector<size_t> kinSpeciesIDs_;
//! Orders of the kinetic species
vector_fp kinSpeciesOrders_;
};
//! A kinetics manager for heterogeneous reaction mechanisms. The
//! reactions are assumed to occur at a 2D interface between two 3D phases.
/*!
* There are some important additions to the behavior of the kinetics class
* due to the presence of multiple phases and a heterogeneous interface. If
* a reactant phase doesn't exists, i.e., has a mole number of zero, a
* heterogeneous reaction can not proceed from reactants to products. Note it
* could perhaps proceed from products to reactants if all of the product
* phases exist.
*
* In order to make the determination of whether a phase exists or not
* actually involves the specification of additional information to the
* kinetics object., which heretofore has only had access to intrinsic field
* information about the phases (i.e., temperature pressure, and mole
* fraction).
*
* The extrinsic specification of whether a phase exists or not must be
* specified on top of the intrinsic calculation of the reaction rate. This
* class carries a set of booleans indicating whether a phase in the
* heterogeneous mechanism exists or not.
*
* Additionally, the class carries a set of booleans around indicating
* whether a product phase is stable or not. If a phase is not
* thermodynamically stable, it may be the case that a particular reaction in
* a heterogeneous mechanism will create a product species in the unstable
* phase. However, other reactions in the mechanism will destruct that
* species. This may cause oscillations in the formation of the unstable
* phase from time step to time step within a ODE solver, in practice. In
* order to avoid this situation, a set of booleans is tracked which sets the
* stability of a phase. If a phase is deemed to be unstable, then species in
* that phase will not be allowed to be birthed by the kinetics operator.
* Nonexistent phases are deemed to be unstable by default, but this can be
* changed.
*
* @ingroup chemkinetics
*/
class InterfaceKinetics : public Kinetics
{
public:
//! Constructor
/*!
* @param thermo The optional parameter may be used to initialize
* the object with one ThermoPhase object.
* HKM Note -> Since the interface kinetics
* object will probably require multiple thermophase
* objects, this is probably not a good idea
* to have this parameter.
*/
InterfaceKinetics(thermo_t* thermo = 0);
/// Destructor.
virtual ~InterfaceKinetics();
//! Copy Constructor
InterfaceKinetics(const InterfaceKinetics& right);
//! Assignment operator
InterfaceKinetics& operator=(const InterfaceKinetics& right);
virtual Kinetics* duplMyselfAsKinetics(const std::vector<thermo_t*> & tpVector) const;
virtual int type() const;
//! Set the electric potential in the nth phase
/*!
* @param n phase Index in this kinetics object.
* @param V Electric potential (volts)
*/
void setElectricPotential(int n, doublereal V);
//! @name Reaction Rates Of Progress
//! @{
//! Equilibrium constant for all reactions including the voltage term
/*!
* Kc = exp(deltaG/RT)
*
* where deltaG is the electrochemical potential difference between
* products minus reactants.
*/
virtual void getEquilibriumConstants(doublereal* kc);
/** values needed to convert from exchange current density to surface reaction rate.
*/
void updateExchangeCurrentQuantities();
//! Return the vector of values for the reaction gibbs free energy change.
/*!
* (virtual from Kinetics.h)
* These values depend upon the concentration of the solution.
*
* units = J kmol-1
*
* @param deltaG Output vector of deltaG's for reactions Length: m_ii.
* If 0, this updates the internally stored values only.
*/
virtual void getDeltaGibbs(doublereal* deltaG);
virtual void getDeltaElectrochemPotentials(doublereal* deltaM);
virtual void getDeltaEnthalpy(doublereal* deltaH);
virtual void getDeltaEntropy(doublereal* deltaS);
virtual void getDeltaSSGibbs(doublereal* deltaG);
virtual void getDeltaSSEnthalpy(doublereal* deltaH);
virtual void getDeltaSSEntropy(doublereal* deltaS);
//! @}
//! @name Reaction Mechanism Informational Query Routines
//! @{
virtual void getActivityConcentrations(doublereal* const conc);
//! Return the charge transfer rxn Beta parameter for the ith reaction
/*!
* Returns the beta parameter for a charge transfer reaction. This
* parameter is not important for non-charge transfer reactions.
* Note, the parameter defaults to zero. However, a value of 0.5
* should be supplied for every charge transfer reaction if
* no information is known, as a value of 0.5 pertains to a
* symmetric transition state. The value can vary between 0 to 1.
*
* @param irxn Reaction number in the kinetics mechanism
*
* @return Beta parameter. This defaults to zero, even for charge
* transfer reactions.
*/
doublereal electrochem_beta(size_t irxn) const;
virtual bool isReversible(size_t i) {
if (std::find(m_revindex.begin(), m_revindex.end(), i)
< m_revindex.end()) {
return true;
} else {
return false;
}
}
virtual void getFwdRateConstants(doublereal* kfwd);
virtual void getRevRateConstants(doublereal* krev,
bool doIrreversible = false);
//! @}
//! @name Reaction Mechanism Construction
//! @{
//! Add a phase to the kinetics manager object.
/*!
* This must be done before the function init() is called or
* before any reactions are input.
*
* This function calls Kinetics::addPhase(). It also sets the following
* fields:
*
* m_phaseExists[]
*
* @param thermo Reference to the ThermoPhase to be added.
*/
virtual void addPhase(thermo_t& thermo);
virtual void init();
virtual void addReaction(ReactionData& r);
virtual void addReaction(shared_ptr<Reaction> r);
virtual void finalize();
virtual bool ready() const;
//! @}
//! Internal routine that updates the Rates of Progress of the reactions
/*!
* This is actually the guts of the functionality of the object
*/
virtual void updateROP();
//! Update properties that depend on temperature
/*!
* Current objects that this function updates:
* m_kdata->m_logtemp
* m_kdata->m_rfn
* m_rates.
* updateKc();
*/
void _update_rates_T();
//! Update properties that depend on the electric potential
void _update_rates_phi();
//! Update properties that depend on the species mole fractions and/or
//! concentration,
/*!
* This method fills out the array of generalized concentrations by
* calling method getActivityConcentrations for each phase, which classes
* representing phases should overload to return the appropriate
* quantities.
*/
void _update_rates_C();
//! Advance the surface coverages in time
/*!
* This method carries out a time-accurate advancement of the
* surface coverages for a specified amount of time.
*
* \f[
* \dot {\theta}_k = \dot s_k (\sigma_k / s_0)
* \f]
*
* @param tstep Time value to advance the surface coverages
*/
void advanceCoverages(doublereal tstep);
//! Solve for the pseudo steady-state of the surface problem
/*!
* This is the same thing as the advanceCoverages() function,
* but at infinite times.
*
* Note, a direct solve is carried out under the hood here,
* to reduce the computational time.
*
* @param ifuncOverride One of the values defined in @ref solvesp_methods.
* The default is -1, which means that the program will decide.
* @param timeScaleOverride When a pseudo transient is
* selected this value can be used to override
* the default time scale for integration which
* is one.
* When SFLUX_TRANSIENT is used, this is equal to the
* time over which the equations are integrated.
* When SFLUX_INITIALIZE is used, this is equal to the
* time used in the initial transient algorithm,
* before the equation system is solved directly.
*/
void solvePseudoSteadyStateProblem(int ifuncOverride = -1,
doublereal timeScaleOverride = 1.0);
void setIOFlag(int ioFlag);
void checkPartialEquil();
//! Update the standard state chemical potentials and species equilibrium constant entries
/*!
* Virtual because it is overwritten when dealing with experimental open circuit voltage overrides
*/
virtual void updateMu0();
//! Number of reactions in the mechanism
/*!
* @deprecated This is a duplicate of Kinetics::nReactions()
*/
size_t reactionNumber() const {
warn_deprecated("InterfaceKinetics::reactionNumber",
"To be removed after Cantera 2.2. Duplicate of nReactions().");
return m_ii;
}
//! Update the equilibrium constants and stored electrochemical potentials
//! in molar units for all reversible reactions and for all species.
/*!
* Irreversible reactions have their equilibrium constant set
* to zero. For reactions involving charged species the equilibrium
* constant is adjusted according to the electrostatic potential.
*/
void updateKc();
//! Apply modifications for the forward reaction rate for interfacial charge transfer reactions
/*!
* For reactions that transfer charge across a potential difference,
* the activation energies are modified by the potential difference.
* (see, for example, ...). This method applies this correction.
*
* @param kfwd Vector of forward reaction rate constants on which to have
* the voltage correction applied
*/
void applyVoltageKfwdCorrection(doublereal* const kfwd);
//! When an electrode reaction rate is optionally specified in terms of its
//! exchange current density, adjust kfwd to the standard reaction rate constant form and units.
//! When the BV reaction types are used, keep the exchange current density form.
/*!
* For a reaction rate constant that was given in units of Amps/m2 (exchange current
* density formulation with iECDFormulation == true), convert the rate to
* kmoles/m2/s.
*
* For a reaction rate constant that was given in units of kmol/m2/sec when the
* reaction type is a butler-volmer form, convert it to exchange current density
* form (amps/m2).
*
* @param kfwd Vector of forward reaction rate constants, given in either
* normal form or in exchange current density form.
*/
void convertExchangeCurrentDensityFormulation(doublereal* const kfwd);
//! Set the existence of a phase in the reaction object
/*!
* Tell the kinetics object whether a phase in the object exists. This is
* actually an extrinsic specification that must be carried out on top of
* the intrinsic calculation of the reaction rate. The routine will also
* flip the IsStable boolean within the kinetics object as well.
*
* @param iphase Index of the phase. This is the order within the
* internal thermo vector object
* @param exists Boolean indicating whether the phase exists or not
*/
void setPhaseExistence(const size_t iphase, const int exists);
//! Set the stability of a phase in the reaction object
/*!
* Tell the kinetics object whether a phase in the object is stable.
* Species in an unstable phase will not be allowed to have a positive
* rate of formation from this kinetics object. This is actually an
* extrinsic specification that must be carried out on top of the
* intrinsic calculation of the reaction rate.
*
* While conceptually not needed since kinetics is consistent with thermo
* when taken as a whole, in practice it has found to be very useful to
* turn off the creation of phases which shouldn't be forming. Typically
* this can reduce the oscillations in phase formation and destruction
* which are observed.
*
* @param iphase Index of the phase. This is the order within the
* internal thermo vector object
* @param isStable Flag indicating whether the phase is stable or not
*/
void setPhaseStability(const size_t iphase, const int isStable);
//! Gets the phase existence int for the ith phase
/*!
* @param iphase Phase Id
* @return The int specifying whether the kinetics object thinks the phase
* exists or not. If it exists, then species in that phase can be
* a reactant in reactions.
*/
int phaseExistence(const size_t iphase) const;
//! Gets the phase stability int for the ith phase
/*!
* @param iphase Phase Id
* @return The int specifying whether the kinetics object thinks the phase
* is stable with nonzero mole numbers. If it stable, then the
* kinetics object will allow for rates of production of of
* species in that phase that are positive.
*/
int phaseStability(const size_t iphase) const;
virtual void determineFwdOrdersBV(ReactionData& rdata, vector_fp& fwdFullorders);
virtual void determineFwdOrdersBV(ElectrochemicalReaction& r, vector_fp& fwdFullorders);
protected:
void addElementaryReaction(InterfaceReaction& rdata);
void addGlobalReaction(InterfaceReaction& r);
//! Temporary work vector of length m_kk
vector_fp m_grt;
//! List of reactions numbers which are reversible reactions
/*!
* This is a vector of reaction numbers. Each reaction in the list is
* reversible. Length = number of reversible reactions
*/
std::vector<size_t> m_revindex;
//! Templated class containing the vector of reactions for this interface
/*!
* The templated class is described in RateCoeffMgr.h
* The class SurfaceArrhenius is described in RxnRates.h
*/
Rate1<SurfaceArrhenius> m_rates;
bool m_redo_rates;
//! Vector of irreversible reaction numbers
/*!
* vector containing the reaction numbers of irreversible reactions.
*/
std::vector<size_t> m_irrev;
//! Number of irreversible reactions in the mechanism
size_t m_nirrev;
//! Number of reversible reactions in the mechanism
size_t m_nrev;
public:
//! Vector of additional information about each reaction
/*!
* This vector contains information about the phase mole change for each reaction,
* for example.
*/
std::vector<RxnMolChange*> rmcVector;
protected:
//! Array of concentrations for each species in the kinetics mechanism
/*!
* An array of generalized concentrations \f$ C_k \f$ that are defined
* such that \f$ a_k = C_k / C^0_k, \f$ where \f$ C^0_k \f$ is a standard
* concentration/ These generalized concentrations are used by this
* kinetics manager class to compute the forward and reverse rates of
* elementary reactions. The "units" for the concentrations of each phase
* depend upon the implementation of kinetics within that phase. The order
* of the species within the vector is based on the order of listed
* ThermoPhase objects in the class, and the order of the species within
* each ThermoPhase class.
*/
vector_fp m_conc;
//! Array of activity concentrations for each species in the kinetics object
/*!
* An array of activity concentrations \f$ Ca_k \f$ that are defined
* such that \f$ a_k = Ca_k / C^0_k, \f$ where \f$ C^0_k \f$ is a standard
* concentration. These activity concentrations are used by this
* kinetics manager class to compute the forward and reverse rates of
* elementary reactions. The "units" for the concentrations of each phase
* depend upon the implementation of kinetics within that phase. The order
* of the species within the vector is based on the order of listed
* ThermoPhase objects in the class, and the order of the species within
* each ThermoPhase class.
*/
vector_fp m_actConc;
//! Vector of standard state chemical potentials for all species
/*!
* This vector contains a temporary vector of standard state chemical
* potentials for all of the species in the kinetics object
*
* Length = m_kk. Units = J/kmol.
*/
vector_fp m_mu0;
//! Vector of chemical potentials for all species
/*!
* This vector contains a vector of chemical potentials for all of the species in the kinetics object
*
* Length = m_kk. Units = J/kmol.
*/
vector_fp m_mu;
//! Vector of standard state electrochemical potentials modified by
//! a standard concentration term.
/*!
* This vector contains a temporary vector of standard state electrochemical
* potentials + RTln(Cs) for all of the species in the kinetics object
*
* In order to get the units correct for the concentration equilibrium
* constant, each species needs to have an
* RT ln(Cs) added to its contribution to the equilibrium constant
* Cs is the standard concentration for the species. Frequently, for
* solid species, Cs is equal to 1. However, for gases Cs is P/RT.
*
* Length = m_kk. Units = J/kmol.
*/
vector_fp m_mu0_Kc;
//! Vector of phase electric potentials
/*!
* Temporary vector containing the potential of each phase in the kinetics
* object.
*
* length = number of phases. Units = Volts.
*/
vector_fp m_phi;
//! Vector of potential energies due to Voltages
/*!
* Length is the number of species in kinetics mech. It's
* used to store the potential energy due to the voltage.
*/
vector_fp m_pot;
//! Storage for the net electric energy change due to reaction.
/*!
* Length is number of reactions. It's used to store the
* net electric potential energy change due to the reaction.
*
* deltaElectricEnergy_[jrxn] = sum_i ( F V_i z_i nu_ij)
*/
vector_fp deltaElectricEnergy_;
//! Vector of raw activation energies for the reactions
/*!
* Units are in Kelvin.
* Length is number of reactions.
*/
vector_fp m_E;
//! Pointer to the single surface phase
SurfPhase* m_surf;
//! Pointer to the Implicit surface chemistry object
/*!
* Note this object is owned by this InterfaceKinetics object. It may only
* be used to solve this single InterfaceKinetics object's surface
* problem uncoupled from other surface phases.
*/
ImplicitSurfChem* m_integrator;
//! Electrochemical transfer coefficient for the forward direction
/*!
* Electrochemical transfer coefficient for all reactions that have transfer reactions
* the reaction is given by m_ctrxn[i]
*/
vector_fp m_beta;
//! Vector of reaction indexes specifying the id of the current transfer
//! reactions in the mechanism
/*!
* Vector of reaction indices which involve current transfers. This provides
* an index into the m_beta and m_ctrxn_BVform array.
*
* irxn = m_ctrxn[i]
*/
std::vector<size_t> m_ctrxn;
//! Vector of Reactions which follow the butler volmer methodology for specifying the
//! exchange current density first. Then, the other forms are specified based on this form.
/*!
* Length is equal to the number of reactions with charge transfer coefficients, m_ctrxn[]
*
* m_ctrxn_BVform[i] = 0; This means that the irxn reaction is calculated via the standard forward
* and reverse reaction rates
* m_ctrxn_BVform[i] = 1; This means that the irxn reaction is calculated via the BV format
* directly.
* m_ctrxn_BVform[i] = 2; this means that the irxn reaction is calculated via the BV format
* directly, using concentrations instead of activity concentrations.
*/
std::vector<size_t> m_ctrxn_BVform;
//! Vector of booleans indicating whether the charge transfer reaction rate constant
//! is described by an exchange current density rate constant expression
/*!
* Length is equal to the number of reactions with charge transfer coefficients, m_ctrxn[]
*
* m_ctrxn_ecdf[irxn] = 0 This means that the rate coefficient calculator will calculate
* the rate constant as a chemical forward rate constant, a standard format.
* m_ctrxn_ecdf[irxn] = 1 this means that the rate coefficient calculator will calculate
* the rate constant as an exchange current density rate constant expression.
*/
vector_int m_ctrxn_ecdf;
//! Vector of booleans indicating whether the charge transfer reaction rate constant
//! is described by an exchange current density rate constant expression
/*!
* Length is equal to the number of reactions with charge transfer coefficients, m_ctrxn[]
*
* Some reactions have zero in this list, those that don't need special treatment.
*/
std::vector<RxnOrders*> m_ctrxn_ROPOrdersList_;
//! Reaction Orders for the case where the forwards rate of progress is being calculated.
/*!
* Length is equal to the number of reactions with charge transfer coefficients, m_ctrxn[]
*
* Some reactions have zero in this list, indicating that the calculation isn't necessary.
*/
std::vector<RxnOrders*> m_ctrxn_FwdOrdersList_;
vector_fp m_ctrxn_resistivity_;
//! Vector of standard concentrations
/*!
* Length number of kinetic species
* units depend on the definition of the standard concentration within each phase
*/
vector_fp m_StandardConc;
//! Vector of delta G^0, the standard state gibbs free energies for each reaction
/*!
* Length is the number of reactions
* units are Joule kmol-1
*/
vector_fp m_deltaG0;
//! Vector of deltaG[] of reaction, the delta gibbs free energies for each reaction
/*!
* Length is the number of reactions
* units are Joule kmol-1
*/
vector_fp m_deltaG;
//! Vector of the products of the standard concentrations of the reactants
/*!
* Units vary wrt what the units of the standard concentrations are
* Length = number of reactions.
*/
vector_fp m_ProdStanConcReac;
doublereal m_logp0;
doublereal m_logc0;
bool m_ROP_ok;
//! Current temperature of the data
doublereal m_temp;
//! Current log of the temperature
doublereal m_logtemp;
//! Boolean indicating whether mechanism has been finalized
bool m_finalized;
//! Boolean flag indicating whether any reaction in the mechanism
//! has a coverage dependent forward reaction rate
/*!
* If this is true, then the coverage dependence is multiplied into
* the forward reaction rates constant
*/
bool m_has_coverage_dependence;
//! Boolean flag indicating whether any reaction in the mechanism
//! has a beta electrochemical parameter.
/*!
* If this is true, the Butler-Volmer correction is applied
* to the forward reaction rate for those reactions.
*
* fac = exp ( - beta * (delta_phi))
*/
bool m_has_electrochem_rxns;
//! Boolean flag indicating whether any reaction in the mechanism
//! is described by an exchange current density expression
/*!
* If this is true, the standard state gibbs free energy of the reaction
* and the product of the reactant standard concentrations must be
* precalculated in order to calculate the rate constant.
*/
bool m_has_exchange_current_density_formulation;
//! Int flag to indicate that some phases in the kinetics mechanism are
//! non-existent.
/*!
* We change the ROP vectors to make sure that non-existent phases are
* treated correctly in the kinetics operator. The value of this is equal
* to the number of phases which don't exist.
*/
int m_phaseExistsCheck;
//! Vector of booleans indicating whether phases exist or not
/*!
* Vector of booleans indicating whether a phase exists or not. We use
* this to set the ROP's so that unphysical things don't happen.
* For example, a reaction can't go in the forwards direction if a
* phase in which a reactant is present doesn't exist. Because InterfaceKinetics
* deals with intrinsic quantities only normally, nowhere else is this extrinsic
* concept introduced except here.
*
* length = number of phases in the object. By default all phases exist.
*/
std::vector<bool> m_phaseExists;
//! Vector of int indicating whether phases are stable or not
/*!
* Vector of booleans indicating whether a phase is stable or not under
* the current conditions. We use this to set the ROP's so that
* unphysical things don't happen.
*
* length = number of phases in the object. By default all phases are stable.
*/
std::vector<int> m_phaseIsStable;
//! Vector of vector of booleans indicating whether a phase participates in a
//! reaction as a reactant
/*!
* m_rxnPhaseIsReactant[j][p] indicates whether a species in phase p
* participates in reaction j as a reactant.
*/
std::vector<std::vector<bool> > m_rxnPhaseIsReactant;
//! Vector of vector of booleans indicating whether a phase participates in a
//! reaction as a product
/*!
* m_rxnPhaseIsReactant[j][p] indicates whether a species in phase p
* participates in reaction j as a product.
*/
std::vector<std::vector<bool> > m_rxnPhaseIsProduct;
//! Pairs of (reaction index, total order) for sticking reactions, which are
//! needed to compute the dependency of the rate constant on the site
//! density.
std::vector<std::pair<size_t, double> > m_sticking_orders;
void applyStickingCorrection(double* kf);
int m_ioFlag;
};
}
#endif
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