Heterogeneous reactions at one-dimensional interfaces between multiple adjacent two-dimensional surfaces. More...
#include <EdgeKinetics.h>
Inheritance diagram for EdgeKinetics:
Collaboration diagram for EdgeKinetics:
Public Member Functions | |
| EdgeKinetics () | |
| Constructor. More... | |
| virtual std::string | kineticsType () const |
| Identifies the Kinetics manager type. More... | |
 Public Member Functions inherited from InterfaceKinetics | |
| InterfaceKinetics (thermo_t *thermo=0) | |
| Constructor. 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, double rtol=1.e-7, double atol=1.e-14, double maxStepSize=0, size_t maxSteps=20000, size_t maxErrTestFails=7) |
| 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) |
| 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... | |
| 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... | |
| 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 | |
| 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) const |
| Return the phase index of a phase in the list of phases defined within the object. More... | |
| size_t | surfacePhaseIndex () const |
| This returns the integer index of the phase which has ThermoPhase type cSurf. More... | |
| size_t | reactionPhaseIndex () const |
| 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... | |
| const thermo_t & | speciesPhase (const std::string &nm) const |
| 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) const |
| 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... | |
| bool | skipUndeclaredSpecies () const |
| 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... | |
| bool | skipUndeclaredThirdBodies () const |
| 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 () |
| 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) |
| virtual void | setRoot (std::shared_ptr< Solution > root) |
| Set root Solution holding all phase information. More... | |
Additional Inherited Members | |
| Protected Member Functions inherited from InterfaceKinetics | |
| 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 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< 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 | |
| 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... | |
| 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 name 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 |
| std::weak_ptr< Solution > | m_root |
| reference to Solution More... | |
| ValueCache | m_cache |
| Cache for saved calculations within each Kinetics object. More... | |
Detailed Description
Heterogeneous reactions at one-dimensional interfaces between multiple adjacent two-dimensional surfaces.
Definition at line 22 of file EdgeKinetics.h.
Constructor & Destructor Documentation
◆ EdgeKinetics()
|
inline |
Member Function Documentation
◆ kineticsType()
|
inlinevirtual |
Identifies the Kinetics manager type.
Each class derived from Kinetics should override this method to return a meaningful identifier.
Reimplemented from InterfaceKinetics.
Definition at line 30 of file EdgeKinetics.h.
The documentation for this class was generated from the following file:
