Cantera 2.6.0

Public Member Functions | List of all members
EdgeKinetics Class Reference

Heterogeneous reactions at one-dimensional interfaces between multiple adjacent two-dimensional surfaces. More...

`#include <EdgeKinetics.h>`

Inheritance diagram for EdgeKinetics:
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Collaboration diagram for EdgeKinetics:
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## Public Member Functions
| EdgeKinetics ()
| Constructor. More...
virtual std::string | kineticsType () const
| Identifies the Kinetics manager type. More...
Public Member Functions inherited from InterfaceKinetics
| InterfaceKinetics (ThermoPhase *thermo=0)
| Constructor. More...
virtual void | resizeReactions ()
| Finalize Kinetics object and associated objects. 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, 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 | 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 (ThermoPhase &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, bool resize=true)
| 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 double *data, const ThermoPhase *phase, double *phase_data)
virtual void | setRoot (std::shared_ptr< Solution > root)
| Set root Solution holding all phase information. More...
virtual double | reactionEnthalpy (const Composition &reactants, const Composition &products)
| Calculate the reaction enthalpy of a reaction which has not necessarily been added into the Kinetics object. More...
| 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...
ThermoPhase & | thermo (size_t n=0)
| This method returns a reference to the nth ThermoPhase object defined in this kinetics mechanism. More...
const ThermoPhase & | 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...
ThermoPhase & | 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 ThermoPhase & | speciesPhase (const std::string &nm) const
ThermoPhase & | speciesPhase (size_t k)
| This function takes as an argument the kineticsSpecies index (that is, 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 (that is, 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 double *property, double *deltaProperty) const
| Change in species properties. More...
virtual void | getRevReactionDelta (const double *g, double *dg) const
| Given an array of species properties 'g', return in array 'dg' the change in this quantity in the reversible reactions. More...
virtual void | getThirdBodyConcentrations (double *concm)
| Return a vector of values of effective concentrations of third-body collision partners of any reaction. More...
virtual const vector_fp & | thirdBodyConcentrations () const
| Provide direct access to current third-body concentration values. 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 void | getDerivativeSettings (AnyMap &settings) const
| Retrieve derivative settings. More...
virtual void | setDerivativeSettings (const AnyMap &settings)
| Set/modify derivative settings. More...
virtual void | getFwdRateConstants_ddT (double *dkfwd)
| Calculate derivatives for forward rate constants with respect to temperature at constant pressure, molar concentration and mole fractions. More...
virtual void | getFwdRateConstants_ddP (double *dkfwd)
| Calculate derivatives for forward rate constants with respect to pressure at constant temperature, molar concentration and mole fractions. More...
virtual void | getFwdRateConstants_ddC (double *dkfwd)
| Calculate derivatives for forward rate constants with respect to molar concentration at constant temperature, pressure and mole fractions. More...
virtual void | getFwdRatesOfProgress_ddT (double *drop)
| Calculate derivatives for forward rates-of-progress with respect to temperature at constant pressure, molar concentration and mole fractions. More...
virtual void | getFwdRatesOfProgress_ddP (double *drop)
| Calculate derivatives for forward rates-of-progress with respect to pressure at constant temperature, molar concentration and mole fractions. More...
virtual void | getFwdRatesOfProgress_ddC (double *drop)
| Calculate derivatives for forward rates-of-progress with respect to molar concentration at constant temperature, pressure and mole fractions. More...
virtual Eigen::SparseMatrix< double > | fwdRatesOfProgress_ddX ()
| Calculate derivatives for forward rates-of-progress with respect to species mole fractions at constant temperature, pressure and molar concentration. More...
virtual void | getRevRatesOfProgress_ddT (double *drop)
| Calculate derivatives for reverse rates-of-progress with respect to temperature at constant pressure, molar concentration and mole fractions. More...
virtual void | getRevRatesOfProgress_ddP (double *drop)
| Calculate derivatives for reverse rates-of-progress with respect to pressure at constant temperature, molar concentration and mole fractions. More...
virtual void | getRevRatesOfProgress_ddC (double *drop)
| Calculate derivatives for reverse rates-of-progress with respect to molar concentration at constant temperature, pressure and mole fractions. More...
virtual Eigen::SparseMatrix< double > | revRatesOfProgress_ddX ()
| Calculate derivatives for reverse rates-of-progress with respect to species mole fractions at constant temperature, pressure and molar concentration. More...
virtual void | getNetRatesOfProgress_ddT (double *drop)
| Calculate derivatives for net rates-of-progress with respect to temperature at constant pressure, molar concentration and mole fractions. More...
virtual void | getNetRatesOfProgress_ddP (double *drop)
| Calculate derivatives for net rates-of-progress with respect to pressure at constant temperature, molar concentration and mole fractions. More...
virtual void | getNetRatesOfProgress_ddC (double *drop)
| Calculate derivatives for net rates-of-progress with respect to molar concentration at constant temperature, pressure and mole fractions. More...
virtual Eigen::SparseMatrix< double > | netRatesOfProgress_ddX ()
| Calculate derivatives for net rates-of-progress with respect to species mole fractions at constant temperature, pressure and molar concentration. More...
void | getCreationRates_ddT (double *dwdot)
| Calculate derivatives for species creation rates with respect to temperature at constant pressure, molar concentration and mole fractions. More...
void | getCreationRates_ddP (double *dwdot)
| Calculate derivatives for species creation rates with respect to pressure at constant temperature, molar concentration and mole fractions. More...
void | getCreationRates_ddC (double *dwdot)
| Calculate derivatives for species creation rates with respect to molar concentration at constant temperature, pressure and mole fractions. More...
Eigen::SparseMatrix< double > | creationRates_ddX ()
| Calculate derivatives for species creation rates with respect to species mole fractions at constant temperature, pressure and molar concentration. More...
void | getDestructionRates_ddT (double *dwdot)
| Calculate derivatives for species destruction rates with respect to temperature at constant pressure, molar concentration and mole fractions. More...
void | getDestructionRates_ddP (double *dwdot)
| Calculate derivatives for species destruction rates with respect to pressure at constant temperature, molar concentration and mole fractions. More...
void | getDestructionRates_ddC (double *dwdot)
| Calculate derivatives for species destruction rates with respect to molar concentration at constant temperature, pressure and mole fractions. More...
Eigen::SparseMatrix< double > | destructionRates_ddX ()
| Calculate derivatives for species destruction rates with respect to species mole fractions at constant temperature, pressure and molar concentration. More...
void | getNetProductionRates_ddT (double *dwdot)
| Calculate derivatives for species net production rates with respect to temperature at constant pressure, molar concentration and mole fractions. More...
void | getNetProductionRates_ddP (double *dwdot)
| Calculate derivatives for species net production rates with respect to pressure at constant temperature, molar concentration and mole fractions. More...
void | getNetProductionRates_ddC (double *dwdot)
| Calculate derivatives for species net production rates with respect to molar concentration at constant temperature, pressure and mole fractions. More...
Eigen::SparseMatrix< double > | netProductionRates_ddX ()
| Calculate derivatives for species net production rates with respect to species mole fractions at constant temperature, pressure and molar concentration. More...
virtual double | reactantStoichCoeff (size_t k, size_t i) const
| Stoichiometric coefficient of species k as a reactant in reaction i. More...
Eigen::SparseMatrix< double > | reactantStoichCoeffs () const
| Stoichiometric coefficient matrix for reactants. More...
virtual double | productStoichCoeff (size_t k, size_t i) const
| Stoichiometric coefficient of species k as a product in reaction i. More...
Eigen::SparseMatrix< double > | productStoichCoeffs () const
| Stoichiometric coefficient matrix for products. More...
Eigen::SparseMatrix< double > | revProductStoichCoeffs () const
| Stoichiometric coefficient matrix for products of reversible reactions. 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...
virtual std::string | reactionTypeStr (size_t i) const
| String 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...
AnyMap | parameters ()
| Return the parameters for a phase definition which are needed to reconstruct an identical object using the newKinetics function. 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 ()

## Additional Inherited Members
Protected Member Functions inherited from InterfaceKinetics
SurfaceArrhenius | buildSurfaceArrhenius (size_t i, InterfaceReaction2 &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
virtual void | updateROP ()
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< unique_ptr< MultiRateBase > > | m_interfaceRates
| Vector of rate handlers for interface reactions. More...
std::map< std::string, size_t > | m_interfaceTypes
| Rate handler mapping. More...
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...
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...
bool | m_ready
| Boolean indicating whether Kinetics object is fully configured. 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< ThermoPhase * > | 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_delta_gibbs0
| Delta G^0 for all reactions. 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...
vector_fp | m_dH
| The enthalpy change for each reaction to calculate Blowers-Masel rates. More...
vector_fp | m_rbuf
| Buffer used for storage of intermediate reaction-specific results. More...
bool | m_skipUndeclaredSpecies
bool | m_skipUndeclaredThirdBodies
std::weak_ptr< Solution > | m_root
| reference to Solution More...
StoichManagerN | m_reactantStoich
| Stoichiometry manager for the reactants for each reaction. More...
StoichManagerN | m_productStoich
| Stoichiometry manager for the products for each reaction. More...
StoichManagerN | m_revProductStoich
| Stoichiometry manager for the products of reversible reactions. More...
Eigen::SparseMatrix< double > | m_stoichMatrix
| Net stoichiometry (products - reactants) 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()

EdgeKinetics | ( |  | ) |
| inline

Constructor.

Definition at line 26 of file EdgeKinetics.h.

References InterfaceKinetics::m_nDim.

## Member Function Documentation

## ◆ kineticsType()

virtual std::string kineticsType | ( |  | ) | const
| inline virtual

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:

- EdgeKinetics.h