Cantera
2.4.0
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A kinetics manager for heterogeneous reaction mechanisms. More...
#include <InterfaceKinetics.h>
Classes | |
struct | StickData |
Values used for converting sticking coefficients into rate constants. More... | |
Public Member Functions | |
InterfaceKinetics (thermo_t *thermo=0) | |
Constructor. More... | |
virtual std::string | kineticsType () const |
Identifies the Kinetics manager type. More... | |
void | setElectricPotential (int n, doublereal V) |
Set the electric potential in the nth phase. More... | |
virtual void | updateROP () |
Internal routine that updates the Rates of Progress of the reactions. 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... | |
void | advanceCoverages (doublereal tstep) |
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) |
virtual void | updateMu0 () |
Update the standard state chemical potentials and species equilibrium constant entries. 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) |
Reaction Rates Of Progress | |
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... | |
Reaction Mechanism Informational Query Routines | |
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... | |
double | effectivePreExponentialFactor (size_t irxn) |
Return effective preexponent for the specified reaction. More... | |
double | effectiveActivationEnergy_R (size_t irxn) |
Return effective activation energy for the specified reaction. More... | |
double | effectiveTemperatureExponent (size_t irxn) |
Return effective temperature exponent for the specified reaction. More... | |
Reaction Mechanism Construction | |
virtual void | addPhase (thermo_t &thermo) |
Add a phase to the kinetics manager object. More... | |
virtual void | init () |
Prepare the class for the addition of reactions, after all phases have been added. More... | |
virtual void | resizeSpecies () |
Resize arrays with sizes that depend on the total number of species. 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... | |
Public Member Functions inherited from Kinetics | |
virtual std::pair< size_t, size_t > | checkDuplicates (bool throw_err=true) const |
Check for unmarked duplicate reactions and unmatched marked duplicates. More... | |
void | selectPhase (const doublereal *data, const thermo_t *phase, doublereal *phase_data) |
Kinetics () | |
Default constructor. More... | |
virtual | ~Kinetics () |
Kinetics (const Kinetics &)=delete | |
Kinetics objects are not copyable or assignable. More... | |
Kinetics & | operator= (const Kinetics &)=delete |
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_t & | thermo (size_t n=0) |
This method returns a reference to the nth ThermoPhase object defined in this kinetics mechanism. More... | |
const thermo_t & | thermo (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_t & | speciesPhase (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_t & | speciesPhase (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 int | reactionType (size_t i) const |
Flag specifying the type of reaction. More... | |
std::string | reactionString (size_t i) const |
Return a string representing the reaction. More... | |
std::string | reactantString (size_t i) const |
Returns a string containing the reactants side of the reaction equation. More... | |
std::string | productString (size_t i) const |
Returns a string containing the products side of the reaction equation. More... | |
shared_ptr< Reaction > | reaction (size_t i) |
Return the Reaction object for reaction i. More... | |
shared_ptr< const Reaction > | reaction (size_t i) const |
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... | |
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... | |
virtual void | invalidateCache () |
Protected Member Functions | |
SurfaceArrhenius | buildSurfaceArrhenius (size_t i, InterfaceReaction &r, bool replace) |
Build a SurfaceArrhenius object from a Reaction, taking into account the possible sticking coefficient form and coverage dependencies. More... | |
void | applyStickingCorrection (double T, 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... | |
Protected Attributes | |
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< SurfaceArrhenius > | m_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... | |
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... | |
SurfPhase * | m_surf |
Pointer to the single surface phase. More... | |
ImplicitSurfChem * | m_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 charge 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... | |
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... | |
bool | m_ROP_ok |
doublereal | m_temp |
Current temperature of the data. More... | |
doublereal | m_logtemp |
Current log of the temperature. 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... | |
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< StickData > | m_stickingData |
Data for sticking reactions. More... | |
int | m_ioFlag |
size_t | m_nDim |
Number of dimensions of reacting phase (2 for InterfaceKinetics, 1 for EdgeKinetics) More... | |
Protected Attributes inherited from Kinetics | |
ValueCache | m_cache |
Cache for saved calculations within each Kinetics object. 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< 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... | |
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... | |
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.
Definition at line 58 of file InterfaceKinetics.h.
InterfaceKinetics | ( | thermo_t * | thermo = 0 | ) |
Constructor.
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 20 of file InterfaceKinetics.cpp.
References InterfaceKinetics::addPhase(), and Kinetics::thermo().
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inlinevirtual |
Identifies the Kinetics manager type.
Each class derived from Kinetics should override this method to return a meaningful identifier.
Reimplemented from Kinetics.
Reimplemented in EdgeKinetics.
Definition at line 73 of file InterfaceKinetics.h.
void setElectricPotential | ( | int | n, |
doublereal | V | ||
) |
Set the electric potential in the nth phase.
n | phase Index in this kinetics object. |
V | Electric potential (volts) |
Definition at line 44 of file InterfaceKinetics.cpp.
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Equilibrium constant for all reactions including the voltage term.
Kc = exp(deltaG/RT)
where deltaG is the electrochemical potential difference between products minus reactants.
Reimplemented from Kinetics.
Definition at line 168 of file InterfaceKinetics.cpp.
References Kinetics::getReactionDelta(), InterfaceKinetics::m_mu0_Kc, Kinetics::nReactions(), ThermoPhase::RT(), Kinetics::thermo(), and InterfaceKinetics::updateMu0().
Referenced by InterfaceKinetics::getRevRateConstants().
void updateExchangeCurrentQuantities | ( | ) |
values needed to convert from exchange current density to surface reaction rate.
Definition at line 179 of file InterfaceKinetics.cpp.
References Kinetics::getReactionDelta(), ThermoPhase::getStandardChemPotentials(), InterfaceKinetics::m_deltaG0, InterfaceKinetics::m_mu0, InterfaceKinetics::m_ProdStanConcReac, Kinetics::m_reactantStoich, InterfaceKinetics::m_StandardConc, Kinetics::m_start, Kinetics::nPhases(), Kinetics::nReactions(), Phase::nSpecies(), ThermoPhase::standardConcentration(), and Kinetics::thermo().
Referenced by InterfaceKinetics::convertExchangeCurrentDensityFormulation(), and InterfaceKinetics::updateMu0().
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virtual |
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
deltaG | Output vector of deltaG's for reactions Length: nReactions(). |
Reimplemented from Kinetics.
Definition at line 403 of file InterfaceKinetics.cpp.
References Kinetics::getReactionDelta(), InterfaceKinetics::m_deltaG, InterfaceKinetics::m_mu, Kinetics::m_start, Kinetics::m_thermo, Kinetics::nPhases(), and Kinetics::nReactions().
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Return the vector of values for the reaction electrochemical free energy change.
These values depend upon the concentration of the solution and the voltage of the phases
units = J kmol-1
deltaM | Output vector of deltaM's for reactions Length: nReactions(). |
Reimplemented from Kinetics.
Definition at line 420 of file InterfaceKinetics.cpp.
References ThermoPhase::getElectrochemPotentials(), Kinetics::getReactionDelta(), InterfaceKinetics::m_grt, Kinetics::m_start, Kinetics::nPhases(), and Kinetics::thermo().
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virtual |
Return the vector of values for the reactions change in enthalpy.
These values depend upon the concentration of the solution.
units = J kmol-1
deltaH | Output vector of deltaH's for reactions Length: nReactions(). |
Reimplemented from Kinetics.
Definition at line 431 of file InterfaceKinetics.cpp.
References ThermoPhase::getPartialMolarEnthalpies(), Kinetics::getReactionDelta(), InterfaceKinetics::m_grt, Kinetics::m_start, Kinetics::nPhases(), and Kinetics::thermo().
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virtual |
Return the vector of values for the reactions change in entropy.
These values depend upon the concentration of the solution.
units = J kmol-1 Kelvin-1
deltaS | Output vector of deltaS's for reactions Length: nReactions(). |
Reimplemented from Kinetics.
Definition at line 442 of file InterfaceKinetics.cpp.
References ThermoPhase::getPartialMolarEntropies(), Kinetics::getReactionDelta(), InterfaceKinetics::m_grt, Kinetics::m_start, Kinetics::nPhases(), and Kinetics::thermo().
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virtual |
Return the vector of values for the reaction standard state Gibbs free energy change.
These values don't depend upon the concentration of the solution.
units = J kmol-1
deltaG | Output vector of ss deltaG's for reactions Length: nReactions(). |
Reimplemented from Kinetics.
Definition at line 453 of file InterfaceKinetics.cpp.
References Kinetics::getReactionDelta(), ThermoPhase::getStandardChemPotentials(), InterfaceKinetics::m_mu0, Kinetics::m_start, Kinetics::nPhases(), and Kinetics::thermo().
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virtual |
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
deltaH | Output vector of ss deltaH's for reactions Length: nReactions(). |
Reimplemented from Kinetics.
Definition at line 467 of file InterfaceKinetics.cpp.
References ThermoPhase::getEnthalpy_RT(), Kinetics::getReactionDelta(), InterfaceKinetics::m_grt, Kinetics::m_kk, Kinetics::m_start, Kinetics::nPhases(), ThermoPhase::RT(), and Kinetics::thermo().
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virtual |
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
deltaS | Output vector of ss deltaS's for reactions Length: nReactions(). |
Reimplemented from Kinetics.
Definition at line 484 of file InterfaceKinetics.cpp.
References Cantera::GasConstant, ThermoPhase::getEntropy_R(), Kinetics::getReactionDelta(), InterfaceKinetics::m_grt, Kinetics::m_kk, Kinetics::m_start, Kinetics::nPhases(), and Kinetics::thermo().
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virtual |
Get the vector of activity concentrations used in the kinetics object.
[out] | conc | Vector of activity concentrations. Length is equal to the number of species in the kinetics object |
Reimplemented from Kinetics.
Definition at line 115 of file InterfaceKinetics.cpp.
References InterfaceKinetics::_update_rates_C(), and InterfaceKinetics::m_actConc.
doublereal electrochem_beta | ( | size_t | irxn | ) | const |
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.
irxn | Reaction number in the kinetics mechanism |
Definition at line 763 of file InterfaceKinetics.cpp.
References InterfaceKinetics::m_beta, and InterfaceKinetics::m_ctrxn.
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inlinevirtual |
True if reaction i has been declared to be reversible.
If isReversible(i) is false, then the reverse rate of progress for reaction i is always zero.
i | reaction index |
Reimplemented from Kinetics.
Definition at line 132 of file InterfaceKinetics.h.
References InterfaceKinetics::m_revindex.
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virtual |
Return the forward rate constants.
The computed values include all temperature-dependent, pressure-dependent, and third body contributions. Length is the number of reactions. Units are a combination of kmol, m^3 and s, that depend on the rate expression for the reaction.
kfwd | Output vector containing the forward reaction rate constants. Length: nReactions(). |
Reimplemented from Kinetics.
Definition at line 291 of file InterfaceKinetics.cpp.
References Kinetics::m_perturb, Kinetics::m_rfn, Cantera::multiply_each(), Kinetics::nReactions(), and InterfaceKinetics::updateROP().
Referenced by InterfaceKinetics::getRevRateConstants().
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virtual |
Return the reverse rate constants.
The computed values include all temperature-dependent, pressure-dependent, and third body contributions. Length is the number of reactions. Units are a combination of kmol, m^3 and s, that depend on the rate expression for the reaction. Note, this routine will return rate constants for irreversible reactions if the default for doIrreversible
is overridden.
krev | Output vector of reverse rate constants |
doIrreversible | boolean indicating whether irreversible reactions should be included. |
Reimplemented from Kinetics.
Definition at line 302 of file InterfaceKinetics.cpp.
References InterfaceKinetics::getEquilibriumConstants(), InterfaceKinetics::getFwdRateConstants(), Kinetics::m_rkcn, Kinetics::m_ropnet, Cantera::multiply_each(), and Kinetics::nReactions().
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inline |
Return effective preexponent for the specified reaction.
Returns effective preexponent, accounting for surface coverage dependencies.
irxn | Reaction number in the kinetics mechanism |
Definition at line 153 of file InterfaceKinetics.h.
References InterfaceKinetics::m_rates.
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inline |
Return effective activation energy for the specified reaction.
Returns effective activation energy, accounting for surface coverage dependencies.
irxn | Reaction number in the kinetics mechanism |
Definition at line 165 of file InterfaceKinetics.h.
References InterfaceKinetics::m_rates.
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Return effective temperature exponent for the specified reaction.
Returns effective temperature exponenty, accounting for surface coverage dependencies. Current parameterization in SurfaceArrhenius does not change this parameter with the change in surface coverages.
irxn | Reaction number in the kinetics mechanism |
Definition at line 178 of file InterfaceKinetics.h.
References InterfaceKinetics::m_rates.
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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[]
thermo | Reference to the ThermoPhase to be added. |
Reimplemented from Kinetics.
Definition at line 722 of file InterfaceKinetics.cpp.
References Kinetics::addPhase(), InterfaceKinetics::m_phaseExists, InterfaceKinetics::m_phaseIsStable, and Kinetics::thermo().
Referenced by InterfaceKinetics::InterfaceKinetics().
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Prepare the class for the addition of reactions, after all phases have been added.
This method is called automatically when the first reaction is added. It needs to be called directly only in the degenerate case where there are no reactions. The base class method does nothing, but derived classes may use this to perform any initialization (allocating arrays, etc.) that requires knowing the phases.
Reimplemented from Kinetics.
Definition at line 729 of file InterfaceKinetics.cpp.
References InterfaceKinetics::m_nDim, InterfaceKinetics::m_surf, Phase::nDim(), Cantera::npos, Kinetics::reactionPhaseIndex(), and Kinetics::thermo().
Referenced by InterfaceKinetics::addReaction().
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Resize arrays with sizes that depend on the total number of species.
Automatically called before adding each Reaction and Phase.
Reimplemented from Kinetics.
Definition at line 744 of file InterfaceKinetics.cpp.
References InterfaceKinetics::m_actConc, InterfaceKinetics::m_conc, InterfaceKinetics::m_grt, Kinetics::m_kk, InterfaceKinetics::m_mu, InterfaceKinetics::m_mu0, InterfaceKinetics::m_mu0_Kc, InterfaceKinetics::m_phi, InterfaceKinetics::m_pot, InterfaceKinetics::m_StandardConc, Kinetics::nPhases(), Kinetics::nReactions(), and Kinetics::resizeSpecies().
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Add a single reaction to the mechanism.
Derived classes should call the base class method in addition to handling their own specialized behavior.
r | Pointer to the Reaction object to be added. |
true
if the reaction is added or false
if it was skipped Reimplemented from Kinetics.
Definition at line 500 of file InterfaceKinetics.cpp.
References Kinetics::addReaction(), ElectrochemicalReaction::beta, InterfaceKinetics::buildSurfaceArrhenius(), Cantera::BUTLERVOLMER_NOACTIVITYCOEFFS_RXN, Cantera::BUTLERVOLMER_RXN, InterfaceReaction::coverage_deps, InterfaceKinetics::deltaElectricEnergy_, ElectrochemicalReaction::film_resistivity, Cantera::GLOBAL_RXN, InterfaceKinetics::init(), Kinetics::kineticsSpeciesIndex(), InterfaceKinetics::m_beta, InterfaceKinetics::m_ctrxn, InterfaceKinetics::m_ctrxn_BVform, InterfaceKinetics::m_ctrxn_ecdf, InterfaceKinetics::m_deltaG, InterfaceKinetics::m_deltaG0, InterfaceKinetics::m_has_coverage_dependence, InterfaceKinetics::m_has_electrochem_rxns, InterfaceKinetics::m_has_exchange_current_density_formulation, InterfaceKinetics::m_irrev, InterfaceKinetics::m_ProdStanConcReac, InterfaceKinetics::m_rates, InterfaceKinetics::m_revindex, InterfaceKinetics::m_rxnPhaseIsProduct, InterfaceKinetics::m_rxnPhaseIsReactant, InterfaceKinetics::m_surf, Kinetics::nPhases(), Cantera::npos, Kinetics::nReactions(), Kinetics::nTotalSpecies(), Reaction::orders, Reaction::products, Reaction::reactants, Reaction::reaction_type, Reaction::reversible, SurfPhase::size(), Phase::speciesIndex(), Kinetics::speciesPhaseIndex(), and Cantera::SURFACEAFFINITY_RXN.
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Modify the rate expression associated with a reaction.
The stoichiometric equation, type of the reaction, reaction orders, third body efficiencies, reversibility, etc. must be unchanged.
i | Index of the reaction to be modified |
rNew | Reaction with the new rate expressions |
Reimplemented from Kinetics.
Definition at line 610 of file InterfaceKinetics.cpp.
References InterfaceKinetics::buildSurfaceArrhenius(), InterfaceKinetics::m_rates, InterfaceKinetics::m_temp, and Kinetics::modifyReaction().
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Internal routine that updates the Rates of Progress of the reactions.
This is actually the guts of the functionality of the object
Reimplemented from Kinetics.
Definition at line 315 of file InterfaceKinetics.cpp.
References InterfaceKinetics::_update_rates_C(), InterfaceKinetics::_update_rates_T(), InterfaceKinetics::m_actConc, Kinetics::m_perturb, InterfaceKinetics::m_phaseExists, InterfaceKinetics::m_phaseExistsCheck, InterfaceKinetics::m_phaseIsStable, Kinetics::m_reactantStoich, Kinetics::m_revProductStoich, Kinetics::m_rfn, Kinetics::m_rkcn, Kinetics::m_ropf, Kinetics::m_ropnet, Kinetics::m_ropr, InterfaceKinetics::m_rxnPhaseIsProduct, InterfaceKinetics::m_rxnPhaseIsReactant, Cantera::multiply_each(), Kinetics::nPhases(), and Kinetics::nReactions().
Referenced by InterfaceKinetics::getFwdRateConstants().
void _update_rates_T | ( | ) |
Update properties that depend on temperature.
Current objects that this function updates: m_kdata->m_logtemp m_kdata->m_rfn m_rates. updateKc();
Definition at line 50 of file InterfaceKinetics.cpp.
References InterfaceKinetics::_update_rates_phi(), SurfPhase::getCoverages(), InterfaceKinetics::m_actConc, InterfaceKinetics::m_has_coverage_dependence, InterfaceKinetics::m_rates, and InterfaceKinetics::m_surf.
Referenced by InterfaceKinetics::updateROP().
void _update_rates_phi | ( | ) |
Update properties that depend on the electric potential.
Definition at line 85 of file InterfaceKinetics.cpp.
References ThermoPhase::electricPotential(), InterfaceKinetics::m_phi, Kinetics::nPhases(), and Kinetics::thermo().
Referenced by InterfaceKinetics::_update_rates_T(), and InterfaceKinetics::updateMu0().
void _update_rates_C | ( | ) |
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.
Definition at line 96 of file InterfaceKinetics.cpp.
References ThermoPhase::getActivityConcentrations(), Phase::getConcentrations(), InterfaceKinetics::m_actConc, InterfaceKinetics::m_conc, Kinetics::m_start, Kinetics::m_thermo, and Kinetics::nPhases().
Referenced by InterfaceKinetics::getActivityConcentrations(), and InterfaceKinetics::updateROP().
void advanceCoverages | ( | doublereal | tstep | ) |
Advance the surface coverages in time.
This method carries out a time-accurate advancement of the surface coverages for a specified amount of time.
\[ \dot {\theta}_k = \dot s_k (\sigma_k / s_0) \]
tstep | Time value to advance the surface coverages |
Definition at line 773 of file InterfaceKinetics.cpp.
References ImplicitSurfChem::initialize(), ImplicitSurfChem::integrate(), and InterfaceKinetics::m_integrator.
void solvePseudoSteadyStateProblem | ( | int | ifuncOverride = -1 , |
doublereal | timeScaleOverride = 1.0 |
||
) |
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.
ifuncOverride | One of the values defined in Surface Problem Solver Methods. The default is -1, which means that the program will decide. |
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. |
Definition at line 785 of file InterfaceKinetics.cpp.
References ImplicitSurfChem::initialize(), InterfaceKinetics::m_integrator, and ImplicitSurfChem::solvePseudoSteadyStateProblem().
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Update the standard state chemical potentials and species equilibrium constant entries.
Virtual because it is overridden when dealing with experimental open circuit voltage overrides
Definition at line 151 of file InterfaceKinetics.cpp.
References InterfaceKinetics::_update_rates_phi(), Phase::charge(), ThermoPhase::getStandardChemPotentials(), ThermoPhase::logStandardConc(), InterfaceKinetics::m_mu0, InterfaceKinetics::m_mu0_Kc, InterfaceKinetics::m_phi, Kinetics::m_start, Kinetics::nPhases(), Phase::nSpecies(), ThermoPhase::RT(), Kinetics::thermo(), and InterfaceKinetics::updateExchangeCurrentQuantities().
Referenced by InterfaceKinetics::getEquilibriumConstants(), and InterfaceKinetics::updateKc().
void updateKc | ( | ) |
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.
Definition at line 121 of file InterfaceKinetics.cpp.
References Kinetics::getRevReactionDelta(), InterfaceKinetics::m_irrev, InterfaceKinetics::m_mu0_Kc, InterfaceKinetics::m_revindex, Kinetics::m_rkcn, Cantera::npos, Kinetics::nReactions(), ThermoPhase::RT(), Kinetics::thermo(), and InterfaceKinetics::updateMu0().
void applyVoltageKfwdCorrection | ( | doublereal *const | kfwd | ) |
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.
kfwd | Vector of forward reaction rate constants on which to have the voltage correction applied |
Definition at line 211 of file InterfaceKinetics.cpp.
References Phase::charge(), InterfaceKinetics::deltaElectricEnergy_, Kinetics::getReactionDelta(), InterfaceKinetics::m_beta, InterfaceKinetics::m_ctrxn, InterfaceKinetics::m_ctrxn_BVform, InterfaceKinetics::m_phi, InterfaceKinetics::m_pot, Kinetics::nPhases(), Phase::nSpecies(), and Kinetics::thermo().
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.
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).
kfwd | Vector of forward reaction rate constants, given in either normal form or in exchange current density form. |
Definition at line 248 of file InterfaceKinetics.cpp.
References InterfaceKinetics::m_beta, InterfaceKinetics::m_ctrxn, InterfaceKinetics::m_ctrxn_BVform, InterfaceKinetics::m_ctrxn_ecdf, InterfaceKinetics::m_deltaG0, InterfaceKinetics::m_ProdStanConcReac, Kinetics::thermo(), and InterfaceKinetics::updateExchangeCurrentQuantities().
void setPhaseExistence | ( | const size_t | iphase, |
const int | exists | ||
) |
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.
iphase | Index of the phase. This is the order within the internal thermo vector object |
exists | Boolean indicating whether the phase exists or not |
Definition at line 799 of file InterfaceKinetics.cpp.
References InterfaceKinetics::m_phaseExists, InterfaceKinetics::m_phaseExistsCheck, InterfaceKinetics::m_phaseIsStable, and Kinetics::m_thermo.
void setPhaseStability | ( | const size_t | iphase, |
const int | isStable | ||
) |
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.
iphase | Index of the phase. This is the order within the internal thermo vector object |
isStable | Flag indicating whether the phase is stable or not |
Definition at line 836 of file InterfaceKinetics.cpp.
References InterfaceKinetics::m_phaseIsStable, and Kinetics::m_thermo.
int phaseExistence | ( | const size_t | iphase | ) | const |
Gets the phase existence int for the ith phase.
iphase | Phase Id |
Definition at line 820 of file InterfaceKinetics.cpp.
References InterfaceKinetics::m_phaseExists, and Kinetics::m_thermo.
int phaseStability | ( | const size_t | iphase | ) | const |
Gets the phase stability int for the ith phase.
iphase | Phase Id |
Definition at line 828 of file InterfaceKinetics.cpp.
References InterfaceKinetics::m_phaseIsStable, and Kinetics::m_thermo.
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Build a SurfaceArrhenius object from a Reaction, taking into account the possible sticking coefficient form and coverage dependencies.
i | Reaction number |
r | Reaction object containing rate coefficient parameters |
replace | True if replacing an existing reaction |
Definition at line 622 of file InterfaceKinetics.cpp.
References Arrhenius::activationEnergy_R(), InterfaceReaction::coverage_deps, Reaction::equation(), Cantera::GasConstant, Cantera::getValue(), InterfaceReaction::is_sticking_coefficient, Kinetics::kineticsSpeciesIndex(), InterfaceKinetics::m_stickingData, InterfaceKinetics::m_surf, Phase::molecularWeight(), Kinetics::multiplier(), Phase::nDim(), Kinetics::nPhases(), Cantera::npos, Reaction::orders, Cantera::Pi, Arrhenius::preExponentialFactor(), Reaction::reactants, Kinetics::reactionPhaseIndex(), SurfPhase::size(), Phase::speciesIndex(), Kinetics::speciesPhaseIndex(), ThermoPhase::standardConcentration(), InterfaceReaction::sticking_species, Arrhenius::temperatureExponent(), Kinetics::thermo(), and InterfaceReaction::use_motz_wise_correction.
Referenced by InterfaceKinetics::addReaction(), and InterfaceKinetics::modifyReaction().
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Temporary work vector of length m_kk.
Definition at line 381 of file InterfaceKinetics.h.
Referenced by InterfaceKinetics::getDeltaElectrochemPotentials(), InterfaceKinetics::getDeltaEnthalpy(), InterfaceKinetics::getDeltaEntropy(), InterfaceKinetics::getDeltaSSEnthalpy(), InterfaceKinetics::getDeltaSSEntropy(), and InterfaceKinetics::resizeSpecies().
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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
Definition at line 388 of file InterfaceKinetics.h.
Referenced by InterfaceKinetics::addReaction(), InterfaceKinetics::isReversible(), and InterfaceKinetics::updateKc().
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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
Definition at line 395 of file InterfaceKinetics.h.
Referenced by InterfaceKinetics::_update_rates_T(), InterfaceKinetics::addReaction(), InterfaceKinetics::effectiveActivationEnergy_R(), InterfaceKinetics::effectivePreExponentialFactor(), InterfaceKinetics::effectiveTemperatureExponent(), and InterfaceKinetics::modifyReaction().
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Vector of irreversible reaction numbers.
vector containing the reaction numbers of irreversible reactions.
Definition at line 403 of file InterfaceKinetics.h.
Referenced by InterfaceKinetics::addReaction(), and InterfaceKinetics::updateKc().
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Array of concentrations for each species in the kinetics mechanism.
An array of generalized concentrations \( C_k \) that are defined such that \( a_k = C_k / C^0_k, \) where \( C^0_k \) 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.
Definition at line 417 of file InterfaceKinetics.h.
Referenced by InterfaceKinetics::_update_rates_C(), and InterfaceKinetics::resizeSpecies().
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Array of activity concentrations for each species in the kinetics object.
An array of activity concentrations \( Ca_k \) that are defined such that \( a_k = Ca_k / C^0_k, \) where \( C^0_k \) 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.
Definition at line 431 of file InterfaceKinetics.h.
Referenced by InterfaceKinetics::_update_rates_C(), InterfaceKinetics::_update_rates_T(), InterfaceKinetics::getActivityConcentrations(), InterfaceKinetics::resizeSpecies(), and InterfaceKinetics::updateROP().
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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.
Definition at line 440 of file InterfaceKinetics.h.
Referenced by InterfaceKinetics::getDeltaSSGibbs(), InterfaceKinetics::resizeSpecies(), InterfaceKinetics::updateExchangeCurrentQuantities(), and InterfaceKinetics::updateMu0().
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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.
Definition at line 449 of file InterfaceKinetics.h.
Referenced by InterfaceKinetics::getDeltaGibbs(), and InterfaceKinetics::resizeSpecies().
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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.
Definition at line 463 of file InterfaceKinetics.h.
Referenced by InterfaceKinetics::getEquilibriumConstants(), InterfaceKinetics::resizeSpecies(), InterfaceKinetics::updateKc(), and InterfaceKinetics::updateMu0().
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Vector of phase electric potentials.
Temporary vector containing the potential of each phase in the kinetics object. length = number of phases. Units = Volts.
Definition at line 470 of file InterfaceKinetics.h.
Referenced by InterfaceKinetics::_update_rates_phi(), InterfaceKinetics::applyVoltageKfwdCorrection(), InterfaceKinetics::resizeSpecies(), and InterfaceKinetics::updateMu0().
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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.
Definition at line 477 of file InterfaceKinetics.h.
Referenced by InterfaceKinetics::applyVoltageKfwdCorrection(), and InterfaceKinetics::resizeSpecies().
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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)
Definition at line 486 of file InterfaceKinetics.h.
Referenced by InterfaceKinetics::addReaction(), and InterfaceKinetics::applyVoltageKfwdCorrection().
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Pointer to the single surface phase.
Definition at line 489 of file InterfaceKinetics.h.
Referenced by InterfaceKinetics::_update_rates_T(), InterfaceKinetics::addReaction(), InterfaceKinetics::buildSurfaceArrhenius(), and InterfaceKinetics::init().
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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.
Definition at line 497 of file InterfaceKinetics.h.
Referenced by InterfaceKinetics::advanceCoverages(), and InterfaceKinetics::solvePseudoSteadyStateProblem().
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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]
Definition at line 504 of file InterfaceKinetics.h.
Referenced by InterfaceKinetics::addReaction(), InterfaceKinetics::applyVoltageKfwdCorrection(), InterfaceKinetics::convertExchangeCurrentDensityFormulation(), and InterfaceKinetics::electrochem_beta().
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Vector of reaction indexes specifying the id of the charge transfer reactions in the mechanism.
Vector of reaction indices which involve charge transfers. This provides an index into the m_beta and m_ctrxn_BVform array.
irxn = m_ctrxn[i]
Definition at line 514 of file InterfaceKinetics.h.
Referenced by InterfaceKinetics::addReaction(), InterfaceKinetics::applyVoltageKfwdCorrection(), InterfaceKinetics::convertExchangeCurrentDensityFormulation(), and InterfaceKinetics::electrochem_beta().
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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.
Definition at line 528 of file InterfaceKinetics.h.
Referenced by InterfaceKinetics::addReaction(), InterfaceKinetics::applyVoltageKfwdCorrection(), and InterfaceKinetics::convertExchangeCurrentDensityFormulation().
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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.
Definition at line 540 of file InterfaceKinetics.h.
Referenced by InterfaceKinetics::addReaction(), and InterfaceKinetics::convertExchangeCurrentDensityFormulation().
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Vector of standard concentrations.
Length number of kinetic species units depend on the definition of the standard concentration within each phase
Definition at line 547 of file InterfaceKinetics.h.
Referenced by InterfaceKinetics::resizeSpecies(), and InterfaceKinetics::updateExchangeCurrentQuantities().
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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
Definition at line 554 of file InterfaceKinetics.h.
Referenced by InterfaceKinetics::addReaction(), InterfaceKinetics::convertExchangeCurrentDensityFormulation(), and InterfaceKinetics::updateExchangeCurrentQuantities().
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Vector of deltaG[] of reaction, the delta Gibbs free energies for each reaction.
Length is the number of reactions units are Joule kmol-1
Definition at line 561 of file InterfaceKinetics.h.
Referenced by InterfaceKinetics::addReaction(), and InterfaceKinetics::getDeltaGibbs().
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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.
Definition at line 568 of file InterfaceKinetics.h.
Referenced by InterfaceKinetics::addReaction(), InterfaceKinetics::convertExchangeCurrentDensityFormulation(), and InterfaceKinetics::updateExchangeCurrentQuantities().
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Current temperature of the data.
Definition at line 573 of file InterfaceKinetics.h.
Referenced by InterfaceKinetics::modifyReaction().
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Current log of the temperature.
Definition at line 576 of file InterfaceKinetics.h.
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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
Definition at line 584 of file InterfaceKinetics.h.
Referenced by InterfaceKinetics::_update_rates_T(), and InterfaceKinetics::addReaction().
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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))
Definition at line 594 of file InterfaceKinetics.h.
Referenced by InterfaceKinetics::addReaction().
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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.
Definition at line 603 of file InterfaceKinetics.h.
Referenced by InterfaceKinetics::addReaction().
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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.
Definition at line 612 of file InterfaceKinetics.h.
Referenced by InterfaceKinetics::setPhaseExistence(), and InterfaceKinetics::updateROP().
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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.
Definition at line 625 of file InterfaceKinetics.h.
Referenced by InterfaceKinetics::addPhase(), InterfaceKinetics::phaseExistence(), InterfaceKinetics::setPhaseExistence(), and InterfaceKinetics::updateROP().
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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.
Definition at line 635 of file InterfaceKinetics.h.
Referenced by InterfaceKinetics::addPhase(), InterfaceKinetics::phaseStability(), InterfaceKinetics::setPhaseExistence(), InterfaceKinetics::setPhaseStability(), and InterfaceKinetics::updateROP().
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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.
Definition at line 643 of file InterfaceKinetics.h.
Referenced by InterfaceKinetics::addReaction(), and InterfaceKinetics::updateROP().
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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.
Definition at line 651 of file InterfaceKinetics.h.
Referenced by InterfaceKinetics::addReaction(), and InterfaceKinetics::updateROP().
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Data for sticking reactions.
Definition at line 662 of file InterfaceKinetics.h.
Referenced by InterfaceKinetics::buildSurfaceArrhenius().
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Number of dimensions of reacting phase (2 for InterfaceKinetics, 1 for EdgeKinetics)
Definition at line 670 of file InterfaceKinetics.h.
Referenced by EdgeKinetics::EdgeKinetics(), and InterfaceKinetics::init().