Cantera  2.2.1
ElectrodeKinetics Class Reference

A kinetics manager for heterogeneous reaction mechanisms. More...

#include <ElectrodeKinetics.h>

Inheritance diagram for ElectrodeKinetics:
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Collaboration diagram for ElectrodeKinetics:
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## Public Member Functions

ElectrodeKinetics (thermo_t *thermo=0)
Constructor. More...

virtual ~ElectrodeKinetics ()
Destructor. More...

ElectrodeKinetics (const ElectrodeKinetics &right)
Copy Constructor. More...

ElectrodeKineticsoperator= (const ElectrodeKinetics &right)
Assignment operator. More...

virtual KineticsduplMyselfAsKinetics (const std::vector< thermo_t * > &tpVector) const
Duplication function. More...

virtual int type () const
Identifies the kinetics manager type. More...

void identifyMetalPhase ()
Identify the metal phase and the electrons species. More...

virtual void updateROP ()
Internal routine that updates the Rates of Progress of the reactions. More...

virtual void determineFwdOrdersBV (ReactionData &rdata, std::vector< doublereal > &fwdFullorders)

double calcForwardROP_BV (size_t irxn, size_t iBeta, double ioc, double nStoich, double nu, doublereal ioNet)

double calcForwardROP_BV_NoAct (size_t irxn, size_t iBeta, double ioc, double nStoich, double nu, doublereal ioNet)

bool getExchangeCurrentDensityFormulation (size_t irxn, doublereal &nStoich, doublereal &OCV, doublereal &io, doublereal &overPotential, doublereal &beta, doublereal &resistance)

double openCircuitVoltage (size_t irxn)
Calculate the open circuit voltage of a given reaction. More...

double calcCurrentDensity (double nu, double nStoich, double io, double beta, double temp, doublereal resistivity=0.0) const

double solveCurrentRes (doublereal nu, doublereal nStoich, doublereal ioc, doublereal beta, doublereal temp, doublereal resistivity=0.0, int iprob=0) const

virtual void init ()
Prepare the class for the addition of reactions. More...

virtual void finalize ()
Finish adding reactions and prepare for use. More...

Public Member Functions inherited from InterfaceKinetics
InterfaceKinetics (thermo_t *thermo=0)
Constructor. More...

virtual ~InterfaceKinetics ()
Destructor. More...

InterfaceKinetics (const InterfaceKinetics &right)
Copy Constructor. More...

InterfaceKineticsoperator= (const InterfaceKinetics &right)
Assignment operator. More...

void setElectricPotential (int n, doublereal V)
Set the electric potential in the nth phase. More...

void _update_rates_T ()
Update properties that depend on temperature. More...

void _update_rates_phi ()
Update properties that depend on the electric potential. More...

void _update_rates_C ()
Update properties that depend on the species mole fractions and/or concentration,. More...

Advance the surface coverages in time. More...

void solvePseudoSteadyStateProblem (int ifuncOverride=-1, doublereal timeScaleOverride=1.0)
Solve for the pseudo steady-state of the surface problem. More...

void setIOFlag (int ioFlag)

void checkPartialEquil ()

virtual void updateMu0 ()
Update the standard state chemical potentials and species equilibrium constant entries. More...

size_t reactionNumber () const
Number of reactions in the mechanism. More...

void updateKc ()
Update the equilibrium constants and stored electrochemical potentials in molar units for all reversible reactions and for all species. More...

void applyVoltageKfwdCorrection (doublereal *const kfwd)
Apply modifications for the forward reaction rate for interfacial charge transfer reactions. More...

void convertExchangeCurrentDensityFormulation (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. More...

void setPhaseExistence (const size_t iphase, const int exists)
Set the existence of a phase in the reaction object. More...

void setPhaseStability (const size_t iphase, const int isStable)
Set the stability of a phase in the reaction object. More...

int phaseExistence (const size_t iphase) const
Gets the phase existence int for the ith phase. More...

int phaseStability (const size_t iphase) const
Gets the phase stability int for the ith phase. More...

virtual void determineFwdOrdersBV (ElectrochemicalReaction &r, vector_fp &fwdFullorders)

virtual void getEquilibriumConstants (doublereal *kc)
Equilibrium constant for all reactions including the voltage term. More...

void updateExchangeCurrentQuantities ()
values needed to convert from exchange current density to surface reaction rate. More...

virtual void getDeltaGibbs (doublereal *deltaG)
Return the vector of values for the reaction Gibbs free energy change. More...

virtual void getDeltaElectrochemPotentials (doublereal *deltaM)
Return the vector of values for the reaction electrochemical free energy change. More...

virtual void getDeltaEnthalpy (doublereal *deltaH)
Return the vector of values for the reactions change in enthalpy. More...

virtual void getDeltaEntropy (doublereal *deltaS)
Return the vector of values for the reactions change in entropy. More...

virtual void getDeltaSSGibbs (doublereal *deltaG)
Return the vector of values for the reaction standard state Gibbs free energy change. More...

virtual void getDeltaSSEnthalpy (doublereal *deltaH)
Return the vector of values for the change in the standard state enthalpies of reaction. More...

virtual void getDeltaSSEntropy (doublereal *deltaS)
Return the vector of values for the change in the standard state entropies for each reaction. More...

virtual void getActivityConcentrations (doublereal *const conc)
Get the vector of activity concentrations used in the kinetics object. More...

doublereal electrochem_beta (size_t irxn) const
Return the charge transfer rxn Beta parameter for the ith reaction. More...

virtual bool isReversible (size_t i)
True if reaction i has been declared to be reversible. More...

virtual void getFwdRateConstants (doublereal *kfwd)
Return the forward rate constants. More...

virtual void getRevRateConstants (doublereal *krev, bool doIrreversible=false)
Return the reverse rate constants. More...

Add a phase to the kinetics manager object. More...

Add a single reaction to the mechanism. More...

virtual bool addReaction (shared_ptr< Reaction > r)
Add a single reaction to the mechanism. More...

virtual void modifyReaction (size_t i, shared_ptr< Reaction > rNew)
Modify the rate expression associated with a reaction. More...

Returns true if the kinetics manager has been properly initialized and finalized. More...

Public Member Functions inherited from Kinetics
void incrementRxnCount ()
Increment the number of reactions in the mechanism by one. More...

virtual std::pair< size_t, size_t > checkDuplicates (bool throw_err=true) const
Check for duplicate reactions. More...

void selectPhase (const doublereal *data, const thermo_t *phase, doublereal *phase_data)

Kinetics ()
Default constructor. More...

virtual ~Kinetics ()
Destructor. More...

Kinetics (const Kinetics &)
Copy Constructor for the Kinetics object. More...

Kineticsoperator= (const Kinetics &right)
Assignment operator. More...

virtual void assignShallowPointers (const std::vector< thermo_t * > &tpVector)
Reassign the pointers within the Kinetics object. More...

size_t nReactions () const
Number of reactions in the reaction mechanism. More...

void checkReactionIndex (size_t m) const
Check that the specified reaction index is in range Throws an exception if i is greater than nReactions() More...

void checkReactionArraySize (size_t ii) const
Check that an array size is at least nReactions() Throws an exception if ii is less than nReactions(). More...

void checkSpeciesIndex (size_t k) const
Check that the specified species index is in range Throws an exception if k is greater than nSpecies()-1. More...

void checkSpeciesArraySize (size_t mm) const
Check that an array size is at least nSpecies() Throws an exception if kk is less than nSpecies(). More...

size_t nPhases () const
The number of phases participating in the reaction mechanism. More...

void checkPhaseIndex (size_t m) const
Check that the specified phase index is in range Throws an exception if m is greater than nPhases() More...

void checkPhaseArraySize (size_t mm) const
Check that an array size is at least nPhases() Throws an exception if mm is less than nPhases(). More...

size_t phaseIndex (const std::string &ph)
Return the phase index of a phase in the list of phases defined within the object. More...

size_t surfacePhaseIndex ()
This returns the integer index of the phase which has ThermoPhase type cSurf. More...

size_t reactionPhaseIndex ()
Phase where the reactions occur. More...

thermo_tthermo (size_t n=0)
This method returns a reference to the nth ThermoPhase object defined in this kinetics mechanism. More...

const thermo_tthermo (size_t n=0) const

size_t nTotalSpecies () const
The total number of species in all phases participating in the kinetics mechanism. More...

size_t kineticsSpeciesIndex (size_t k, size_t n) const
The location of species k of phase n in species arrays. More...

std::string kineticsSpeciesName (size_t k) const
Return the name of the kth species in the kinetics manager. More...

size_t kineticsSpeciesIndex (const std::string &nm) const
This routine will look up a species number based on the input std::string nm. More...

size_t kineticsSpeciesIndex (const std::string &nm, const std::string &ph) const
This routine will look up a species number based on the input std::string nm. More...

thermo_tspeciesPhase (const std::string &nm)
This function looks up the name of a species and returns a reference to the ThermoPhase object of the phase where the species resides. More...

thermo_tspeciesPhase (size_t k)
This function takes as an argument the kineticsSpecies index (i.e., the list index in the list of species in the kinetics manager) and returns the species' owning ThermoPhase object. More...

size_t speciesPhaseIndex (size_t k)
This function takes as an argument the kineticsSpecies index (i.e., the list index in the list of species in the kinetics manager) and returns the index of the phase owning the species. More...

virtual void getFwdRatesOfProgress (doublereal *fwdROP)
Return the forward rates of progress of the reactions. More...

virtual void getRevRatesOfProgress (doublereal *revROP)
Return the Reverse rates of progress of the reactions. More...

virtual void getNetRatesOfProgress (doublereal *netROP)
Net rates of progress. More...

virtual void getReactionDelta (const doublereal *property, doublereal *deltaProperty)
Change in species properties. More...

virtual void getRevReactionDelta (const doublereal *g, doublereal *dg)
Given an array of species properties 'g', return in array 'dg' the change in this quantity in the reversible reactions. More...

virtual void getCreationRates (doublereal *cdot)
Species creation rates [kmol/m^3/s or kmol/m^2/s]. More...

virtual void getDestructionRates (doublereal *ddot)
Species destruction rates [kmol/m^3/s or kmol/m^2/s]. More...

virtual void getNetProductionRates (doublereal *wdot)
Species net production rates [kmol/m^3/s or kmol/m^2/s]. More...

virtual double reactantStoichCoeff (size_t k, size_t i) const
Stoichiometric coefficient of species k as a reactant in reaction i. More...

virtual double productStoichCoeff (size_t k, size_t i) const
Stoichiometric coefficient of species k as a product in reaction i. More...

virtual doublereal reactantOrder (size_t k, size_t i) const
Reactant order of species k in reaction i. More...

virtual doublereal productOrder (int k, int i) const
product Order of species k in reaction i. More...

virtual const std::vector
< size_t > &
reactants (size_t i) const
Returns a read-only reference to the vector of reactant index numbers for reaction i. More...

virtual const std::vector
< size_t > &
products (size_t i) const
Returns a read-only reference to the vector of product index numbers for reaction i. More...

virtual int reactionType (size_t i) const
Flag specifying the type of reaction. More...

const std::string & reactionString (size_t i) const
Return a string representing the reaction. More...

const std::string & reactantString (size_t i) const
Returns a string containing the reactants side of the reaction equation. More...

const std::string & productString (size_t i) const
Returns a string containing the products side of the reaction equation. More...

shared_ptr< Reactionreaction (size_t i)
Return the Reaction object for reaction i. More...

void skipUndeclaredSpecies (bool skip)
Determine behavior when adding a new reaction that contains species not defined in any of the phases associated with this kinetics manager. More...

void skipUndeclaredThirdBodies (bool skip)
Determine behavior when adding a new reaction that contains third-body efficiencies for species not defined in any of the phases associated with this kinetics manager. More...

virtual void installReagents (const ReactionData &r)

virtual void installGroups (size_t irxn, const std::vector< grouplist_t > &r, const std::vector< grouplist_t > &p)

virtual const std::vector
< grouplist_t > &
reactantGroups (size_t i)

virtual const std::vector
< grouplist_t > &
productGroups (size_t i)

doublereal multiplier (size_t i) const
The current value of the multiplier for reaction i. More...

virtual void setMultiplier (size_t i, doublereal f)
Set the multiplier for reaction i to f. More...

## Public Attributes

std::vector< RxnMolChange * > rmcVector

## Protected Attributes

size_t metalPhaseIndex_
Index of the metal phase in the list of phases for this kinetics object. This is the electron phase. More...

size_t solnPhaseIndex_
Index of the solution phase in the list of phases for this surface. More...

size_t kElectronIndex_
Index of the electrons species in the list of species for this surface kinetics, if none set it to -1. More...

Protected Attributes inherited from InterfaceKinetics
vector_fp m_grt
Temporary work vector of length m_kk. More...

std::vector< size_t > m_revindex
List of reactions numbers which are reversible reactions. More...

Rate1< SurfaceArrheniusm_rates
Templated class containing the vector of reactions for this interface. More...

bool m_redo_rates

std::vector< size_t > m_irrev
Vector of irreversible reaction numbers. More...

size_t m_nirrev
Number of irreversible reactions in the mechanism. More...

size_t m_nrev
Number of reversible reactions in the mechanism. More...

vector_fp m_conc
Array of concentrations for each species in the kinetics mechanism. More...

vector_fp m_actConc
Array of activity concentrations for each species in the kinetics object. More...

vector_fp m_mu0
Vector of standard state chemical potentials for all species. More...

vector_fp m_mu
Vector of chemical potentials for all species. More...

vector_fp m_mu0_Kc
Vector of standard state electrochemical potentials modified by a standard concentration term. More...

vector_fp m_phi
Vector of phase electric potentials. More...

vector_fp m_pot
Vector of potential energies due to Voltages. More...

vector_fp deltaElectricEnergy_
Storage for the net electric energy change due to reaction. More...

vector_fp m_E
Vector of raw activation energies for the reactions. More...

SurfPhasem_surf
Pointer to the single surface phase. More...

ImplicitSurfChemm_integrator
Pointer to the Implicit surface chemistry object. More...

vector_fp m_beta
Electrochemical transfer coefficient for the forward direction. More...

std::vector< size_t > m_ctrxn
Vector of reaction indexes specifying the id of the current transfer reactions in the mechanism. More...

std::vector< size_t > m_ctrxn_BVform
Vector of Reactions which follow the Butler-Volmer methodology for specifying the exchange current density first. More...

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. More...

std::vector< RxnOrders * > m_ctrxn_ROPOrdersList_
Vector of booleans indicating whether the charge transfer reaction rate constant is described by an exchange current density rate constant expression. More...

std::vector< RxnOrders * > m_ctrxn_FwdOrdersList_
Reaction Orders for the case where the forwards rate of progress is being calculated. More...

vector_fp m_ctrxn_resistivity_

vector_fp m_StandardConc
Vector of standard concentrations. More...

vector_fp m_deltaG0
Vector of delta G^0, the standard state Gibbs free energies for each reaction. More...

vector_fp m_deltaG
Vector of deltaG[] of reaction, the delta Gibbs free energies for each reaction. More...

vector_fp m_ProdStanConcReac
Vector of the products of the standard concentrations of the reactants. More...

doublereal m_logp0

doublereal m_logc0

bool m_ROP_ok

doublereal m_temp
Current temperature of the data. More...

doublereal m_logtemp
Current log of the temperature. More...

bool m_finalized
Boolean indicating whether mechanism has been finalized. More...

bool m_has_coverage_dependence
Boolean flag indicating whether any reaction in the mechanism has a coverage dependent forward reaction rate. More...

bool m_has_electrochem_rxns
Boolean flag indicating whether any reaction in the mechanism has a beta electrochemical parameter. More...

bool m_has_exchange_current_density_formulation
Boolean flag indicating whether any reaction in the mechanism is described by an exchange current density expression. More...

int m_phaseExistsCheck
Int flag to indicate that some phases in the kinetics mechanism are non-existent. More...

std::vector< bool > m_phaseExists
Vector of booleans indicating whether phases exist or not. More...

std::vector< int > m_phaseIsStable
Vector of int indicating whether phases are stable or not. More...

std::vector< std::vector< bool > > m_rxnPhaseIsReactant
Vector of vector of booleans indicating whether a phase participates in a reaction as a reactant. More...

std::vector< std::vector< bool > > m_rxnPhaseIsProduct
Vector of vector of booleans indicating whether a phase participates in a reaction as a product. More...

std::vector< std::pair< size_t,
double > >
m_sticking_orders
Pairs of (reaction index, total order) for sticking reactions, which are needed to compute the dependency of the rate constant on the site density. More...

int m_ioFlag

Protected Attributes inherited from Kinetics
ValueCache m_cache
Cache for saved calculations within each Kinetics object. More...

size_t m_ii
Number of reactions in the mechanism. More...

size_t m_kk
The number of species in all of the phases that participate in this kinetics mechanism. More...

vector_fp m_perturb
Vector of perturbation factors for each reaction's rate of progress vector. More...

std::vector< shared_ptr
< Reaction > >
m_reactions
Vector of Reaction objects represented by this Kinetics manager. More...

std::vector< std::vector
< size_t > >
m_reactants
This is a vector of vectors containing the reactants for each reaction. More...

std::vector< std::vector
< size_t > >
m_products
This is a vector of vectors containing the products for each reaction. More...

std::vector< std::map< size_t,
doublereal > >
m_rrxn
m_rrxn is a vector of maps, containing the reactant stoichiometric coefficient information More...

std::vector< std::map< size_t,
doublereal > >
m_prxn
m_prxn is a vector of maps, containing the reactant stoichiometric coefficient information More...

std::vector< int > m_rxntype

std::vector< thermo_t * > m_thermo
m_thermo is a vector of pointers to ThermoPhase objects that are involved with this kinetics operator More...

std::vector< size_t > m_start
m_start is a vector of integers specifying the beginning position for the species vector for the n'th phase in the kinetics class. More...

std::map< std::string, size_t > m_phaseindex
Mapping of the phase id, i.e., the id attribute in the XML phase element to the position of the phase within the kinetics object. More...

size_t m_surfphase
Index in the list of phases of the one surface phase. More...

size_t m_rxnphase
Phase Index where reactions are assumed to be taking place. More...

size_t m_mindim
number of spatial dimensions of lowest-dimensional phase. More...

std::vector< std::string > m_rxneqn
Representation of each reaction equation. More...

std::vector< std::string > m_reactantStrings
Representation of the reactant side of each reaction equation. More...

std::vector< std::string > m_productStrings
Representation of the product side of each reaction equation. More...

vector_fp m_rfn
Forward rate constant for each reaction. More...

vector_fp m_rkcn
Reciprocal of the equilibrium constant in concentration units. More...

vector_fp m_ropf
Forward rate-of-progress for each reaction. More...

vector_fp m_ropr
Reverse rate-of-progress for each reaction. More...

vector_fp m_ropnet
Net rate-of-progress for each reaction. More...

bool m_skipUndeclaredSpecies

bool m_skipUndeclaredThirdBodies

StoichManagerN m_reactantStoich
Stoichiometry manager for the reactants for each reaction. More...

StoichManagerN m_revProductStoich
Stoichiometry manager for the products of reversible reactions. More...

StoichManagerN m_irrevProductStoich
Stoichiometry manager for the products of irreversible reactions. More...

Protected Member Functions inherited from InterfaceKinetics
SurfaceArrhenius buildSurfaceArrhenius (size_t i, InterfaceReaction &r)
Build a SurfaceArrhenius object from a Reaction, taking into account the possible sticking coefficient form and coverage dependencies. More...

void applyStickingCorrection (double *kf)

Protected Member Functions inherited from Kinetics
double checkDuplicateStoich (std::map< int, double > &r1, std::map< int, double > &r2) const
Check whether r1 and r2 represent duplicate stoichiometries This function returns a ratio if two reactions are duplicates of one another, and 0.0 otherwise. More...

void checkReactionBalance (const Reaction &R)
Check that the specified reaction is balanced (same number of atoms for each element in the reactants and products). More...

## Detailed Description

A kinetics manager for heterogeneous reaction mechanisms.

The reactions are assumed to occur at a 2D interface between two 3D phases.

This class is a slight addition to the InterfaceKinetics class, adding several concepts. First we explicitly identify the electrode and solution phases. We will also assume that there is an electron phase.

Deprecated:
Unfinished implementation to be removed after Cantera 2.2.

Definition at line 32 of file ElectrodeKinetics.h.

## Constructor & Destructor Documentation

 ElectrodeKinetics ( thermo_t * thermo = 0 )

Constructor.

Parameters
 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.

Definition at line 17 of file ElectrodeKinetics.cpp.

References Cantera::warn_deprecated().

 ~ElectrodeKinetics ( )
virtual

Destructor.

Definition at line 27 of file ElectrodeKinetics.cpp.

References ElectrodeKinetics::rmcVector.

 ElectrodeKinetics ( const ElectrodeKinetics & right )

Copy Constructor.

Definition at line 34 of file ElectrodeKinetics.cpp.

References ElectrodeKinetics::operator=().

## Member Function Documentation

 ElectrodeKinetics & operator= ( const ElectrodeKinetics & right )

Assignment operator.

Definition at line 44 of file ElectrodeKinetics.cpp.

Referenced by ElectrodeKinetics::ElectrodeKinetics().

 Kinetics * duplMyselfAsKinetics ( const std::vector< thermo_t * > & tpVector ) const
virtual

Duplication function.

Parameters
 tpVector Vector of ThermoPhase pointers. These are shallow pointers to the ThermoPhase objects that will comprise the phases for the new object.
Returns
Returns the duplicated object as the base class Kinetics object.

Reimplemented from InterfaceKinetics.

Definition at line 77 of file ElectrodeKinetics.cpp.

 int type ( ) const
virtual

Identifies the kinetics manager type.

Each class derived from Kinetics should overload this method to return a unique integer. Standard values are defined in file mix_defs.h.

Reimplemented from InterfaceKinetics.

Definition at line 72 of file ElectrodeKinetics.cpp.

 void identifyMetalPhase ( )

Identify the metal phase and the electrons species.

We fill in the internal variables, metalPhaseIndex_ and kElectronIndex_ here

Definition at line 85 of file ElectrodeKinetics.cpp.

Referenced by ElectrodeKinetics::init().

 void updateROP ( )
virtual
 double openCircuitVoltage ( size_t irxn )

Calculate the open circuit voltage of a given reaction.

If the reaction has no electron transport, then return 0.0

Parameters
 irxn Reaction id

Definition at line 725 of file ElectrodeKinetics.cpp.

 void init ( )
virtual

Prepare the class for the addition of reactions.

(virtual from Kinetics) We determine the metal phase and solution phase here

Reimplemented from InterfaceKinetics.

Definition at line 888 of file ElectrodeKinetics.cpp.

References ElectrodeKinetics::identifyMetalPhase(), and InterfaceKinetics::init().

 void finalize ( )
virtual

Finish adding reactions and prepare for use.

This method is called by importKinetics() after all reactions have been entered into the mechanism and before the mechanism is used to calculate reaction rates. The base class method does nothing, but derived classes may use this to perform any initialization (allocating arrays, etc.) that must be done after the reactions are entered.

Reimplemented from InterfaceKinetics.

Definition at line 894 of file ElectrodeKinetics.cpp.

## Member Data Documentation

 std::vector rmcVector

This vector contains information about the phase mole change for each reaction, for example.

Definition at line 116 of file ElectrodeKinetics.h.

 size_t metalPhaseIndex_
protected

Index of the metal phase in the list of phases for this kinetics object. This is the electron phase.

Definition at line 120 of file ElectrodeKinetics.h.

 size_t solnPhaseIndex_
protected

Index of the solution phase in the list of phases for this surface.

Definition at line 123 of file ElectrodeKinetics.h.

 size_t kElectronIndex_
protected

Index of the electrons species in the list of species for this surface kinetics, if none set it to -1.

Definition at line 126 of file ElectrodeKinetics.h.

Referenced by ElectrodeKinetics::identifyMetalPhase(), and ElectrodeKinetics::operator=().

The documentation for this class was generated from the following files: