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Public Member Functions | Protected Attributes | List of all members
InterfaceKinetics Class Reference
Chemical Kinetics » Kinetics Managers

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

`#include <InterfaceKinetics.h>`

Inheritance diagram for InterfaceKinetics:
[legend]

## Detailed Description

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, that is, 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 (for example, 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 55 of file InterfaceKinetics.h.

## Public Member Functions
| InterfaceKinetics ()=default
| Constructor.
| InterfaceKinetics (ThermoPhase *thermo)
| Constructor.
void | resizeReactions () override
| Finalize Kinetics object and associated objects.
string | kineticsType () const override
| Identifies the Kinetics manager type.
void | setElectricPotential (int n, double V)
| Set the electric potential in the nth phase.
void | updateROP () override
| Internal routine that updates the Rates of Progress of the reactions.
void | _update_rates_T ()
| Update properties that depend on temperature.
void | _update_rates_phi ()
| Update properties that depend on the electric potential.
void | _update_rates_C ()
| Update properties that depend on the species mole fractions and/or concentration,.
void | advanceCoverages (double 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.
void | solvePseudoSteadyStateProblem (int ifuncOverride=-1, double timeScaleOverride=1.0)
| Solve for the pseudo steady-state of the surface problem.
void | setIOFlag (int ioFlag)
virtual void | updateMu0 ()
| Update the standard state chemical potentials and species equilibrium constant entries.
void | updateKc ()
| Update the equilibrium constants and stored electrochemical potentials in molar units for all reversible reactions and for all species.
void | setPhaseExistence (const size_t iphase, const int exists)
| Set the existence of a phase in the reaction object.
void | setPhaseStability (const size_t iphase, const int isStable)
| Set the stability of a phase in the reaction object.
int | phaseExistence (const size_t iphase) const
| Gets the phase existence int for the ith phase.
int | phaseStability (const size_t iphase) const
| Gets the phase stability int for the ith phase.
double | interfaceCurrent (const size_t iphase)
| Gets the interface current for the ith phase.
void | setDerivativeSettings (const AnyMap &settings) override
| Set/modify derivative settings.
void | getDerivativeSettings (AnyMap &settings) const override
| Retrieve derivative settings.
Eigen::SparseMatrix< double > | fwdRatesOfProgress_ddCi () override
| Calculate derivatives for forward rates-of-progress with respect to species concentration at constant temperature, pressure and remaining species concentrations.
Eigen::SparseMatrix< double > | revRatesOfProgress_ddCi () override
| Calculate derivatives for forward rates-of-progress with respect to species concentration at constant temperature, pressure and remaining species concentrations.
Eigen::SparseMatrix< double > | netRatesOfProgress_ddCi () override
| Calculate derivatives for net rates-of-progress with respect to species concentration at constant temperature, pressure, and remaining species concentrations.
Reaction Rates Of Progress
void | getEquilibriumConstants (double *kc) override
| Equilibrium constant for all reactions including the voltage term.
void | getDeltaGibbs (double *deltaG) override
| Return the vector of values for the reaction Gibbs free energy change.
void | getDeltaElectrochemPotentials (double *deltaM) override
| Return the vector of values for the reaction electrochemical free energy change.
void | getDeltaEnthalpy (double *deltaH) override
| Return the vector of values for the reactions change in enthalpy.
void | getDeltaEntropy (double *deltaS) override
| Return the vector of values for the reactions change in entropy.
void | getDeltaSSGibbs (double *deltaG) override
| Return the vector of values for the reaction standard state Gibbs free energy change.
void | getDeltaSSEnthalpy (double *deltaH) override
| Return the vector of values for the change in the standard state enthalpies of reaction.
void | getDeltaSSEntropy (double *deltaS) override
| Return the vector of values for the change in the standard state entropies for each reaction.
Reaction Mechanism Informational Query Routines
void | getActivityConcentrations (double *const conc) override
| Get the vector of activity concentrations used in the kinetics object.
bool | isReversible (size_t i) override
| True if reaction i has been declared to be reversible.
void | getFwdRateConstants (double *kfwd) override
| Return the forward rate constants.
void | getRevRateConstants (double *krev, bool doIrreversible=false) override
| Return the reverse rate constants.
Reaction Mechanism Construction
void | addThermo (shared_ptr< ThermoPhase > thermo) override
| Add a thermo phase to the kinetics manager object.
void | addPhase (ThermoPhase &thermo) override
void | init () override
| Prepare the class for the addition of reactions, after all phases have been added.
void | resizeSpecies () override
| Resize arrays with sizes that depend on the total number of species.
bool | addReaction (shared_ptr< Reaction > r, bool resize=true) override
| Add a single reaction to the mechanism.
void | modifyReaction (size_t i, shared_ptr< Reaction > rNew) override
| Modify the rate expression associated with a reaction.
void | setMultiplier (size_t i, double f) override
| Set the multiplier for reaction i to f.
Public Member Functions inherited from Kinetics
virtual pair< size_t, size_t > | checkDuplicates (bool throw_err=true) const
| Check for unmarked duplicate reactions and unmatched marked duplicates.
void | selectPhase (const double *data, const ThermoPhase *phase, double *phase_data)
| Takes as input an array of properties for all species in the mechanism and copies those values belonging to a particular phase to the output array.
virtual void | setRoot (shared_ptr< Solution > root)
| Set root Solution holding all phase information.
shared_ptr< Solution > | root () const
| Get the Solution object containing this Kinetics object and associated ThermoPhase objects.
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.
| Kinetics ()=default
| Default constructor.
| Kinetics (const Kinetics &)=delete
| Kinetics objects are not copyable or assignable.
Kinetics & | operator= (const Kinetics &)=delete
size_t | nReactions () const
| Number of reactions in the reaction mechanism.
void | checkReactionIndex (size_t m) const
| Check that the specified reaction index is in range Throws an exception if i is greater than nReactions()
void | checkReactionArraySize (size_t ii) const
| Check that an array size is at least nReactions() Throws an exception if ii is less than nReactions().
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.
void | checkSpeciesArraySize (size_t mm) const
| Check that an array size is at least nSpecies() Throws an exception if kk is less than nSpecies().
size_t | nPhases () const
| The number of phases participating in the reaction mechanism.
void | checkPhaseIndex (size_t m) const
| Check that the specified phase index is in range Throws an exception if m is greater than nPhases()
void | checkPhaseArraySize (size_t mm) const
| Check that an array size is at least nPhases() Throws an exception if mm is less than nPhases().
size_t | phaseIndex (const string &ph) const
| Return the phase index of a phase in the list of phases defined within the object.
size_t | surfacePhaseIndex () const
| This returns the integer index of the phase which has ThermoPhase type cSurf.
size_t | reactionPhaseIndex () const
| Phase where the reactions occur.
shared_ptr< ThermoPhase > | reactionPhase () const
| Return pointer to phase where the reactions occur.
ThermoPhase & | thermo (size_t n=0)
| This method returns a reference to the nth ThermoPhase object defined in this kinetics mechanism.
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.
size_t | kineticsSpeciesIndex (size_t k, size_t n) const
| The location of species k of phase n in species arrays.
string | kineticsSpeciesName (size_t k) const
| Return the name of the kth species in the kinetics manager.
size_t | kineticsSpeciesIndex (const string &nm) const
| This routine will look up a species number based on the input string nm.
size_t | kineticsSpeciesIndex (const string &nm, const string &ph) const
| This routine will look up a species number based on the input string nm.
ThermoPhase & | speciesPhase (const 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.
const ThermoPhase & | speciesPhase (const 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.
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.
virtual void | getFwdRatesOfProgress (double *fwdROP)
| Return the forward rates of progress of the reactions.
virtual void | getRevRatesOfProgress (double *revROP)
| Return the Reverse rates of progress of the reactions.
virtual void | getNetRatesOfProgress (double *netROP)
| Net rates of progress.
virtual void | getReactionDelta (const double *property, double *deltaProperty) const
| Change in species properties.
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.
virtual void | getThirdBodyConcentrations (double *concm)
| Return a vector of values of effective concentrations of third-body collision partners of any reaction.
virtual const vector< double > & | thirdBodyConcentrations () const
| Provide direct access to current third-body concentration values.
virtual void | getCreationRates (double *cdot)
| Species creation rates [kmol/m^3/s or kmol/m^2/s].
virtual void | getDestructionRates (double *ddot)
| Species destruction rates [kmol/m^3/s or kmol/m^2/s].
virtual void | getNetProductionRates (double *wdot)
| Species net production rates [kmol/m^3/s or kmol/m^2/s].
virtual void | getFwdRateConstants_ddT (double *dkfwd)
| Calculate derivatives for forward rate constants with respect to temperature at constant pressure, molar concentration and mole fractions.
virtual void | getFwdRateConstants_ddP (double *dkfwd)
| Calculate derivatives for forward rate constants with respect to pressure at constant temperature, molar concentration and mole fractions.
virtual void | getFwdRateConstants_ddC (double *dkfwd)
| Calculate derivatives for forward rate constants with respect to molar concentration at constant temperature, pressure and mole fractions.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
void | getCreationRates_ddT (double *dwdot)
| Calculate derivatives for species creation rates with respect to temperature at constant pressure, molar concentration and mole fractions.
void | getCreationRates_ddP (double *dwdot)
| Calculate derivatives for species creation rates with respect to pressure at constant temperature, molar concentration and mole fractions.
void | getCreationRates_ddC (double *dwdot)
| Calculate derivatives for species creation rates with respect to molar concentration at constant temperature, pressure and mole fractions.
Eigen::SparseMatrix< double > | creationRates_ddX ()
| Calculate derivatives for species creation rates with respect to species mole fractions at constant temperature, pressure and molar concentration.
Eigen::SparseMatrix< double > | creationRates_ddCi ()
| Calculate derivatives for species creation rates with respect to species concentration at constant temperature, pressure, and concentration of all other species.
void | getDestructionRates_ddT (double *dwdot)
| Calculate derivatives for species destruction rates with respect to temperature at constant pressure, molar concentration and mole fractions.
void | getDestructionRates_ddP (double *dwdot)
| Calculate derivatives for species destruction rates with respect to pressure at constant temperature, molar concentration and mole fractions.
void | getDestructionRates_ddC (double *dwdot)
| Calculate derivatives for species destruction rates with respect to molar concentration at constant temperature, pressure and mole fractions.
Eigen::SparseMatrix< double > | destructionRates_ddX ()
| Calculate derivatives for species destruction rates with respect to species mole fractions at constant temperature, pressure and molar concentration.
Eigen::SparseMatrix< double > | destructionRates_ddCi ()
| Calculate derivatives for species destruction rates with respect to species concentration at constant temperature, pressure, and concentration of all other species.
void | getNetProductionRates_ddT (double *dwdot)
| Calculate derivatives for species net production rates with respect to temperature at constant pressure, molar concentration and mole fractions.
void | getNetProductionRates_ddP (double *dwdot)
| Calculate derivatives for species net production rates with respect to pressure at constant temperature, molar concentration and mole fractions.
void | getNetProductionRates_ddC (double *dwdot)
| Calculate derivatives for species net production rates with respect to molar concentration at constant temperature, pressure and mole fractions.
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.
Eigen::SparseMatrix< double > | netProductionRates_ddCi ()
| Calculate derivatives for species net production rates with respect to species concentration at constant temperature, pressure, and concentration of all other species.
virtual double | reactantStoichCoeff (size_t k, size_t i) const
| Stoichiometric coefficient of species k as a reactant in reaction i.
Eigen::SparseMatrix< double > | reactantStoichCoeffs () const
| Stoichiometric coefficient matrix for reactants.
virtual double | productStoichCoeff (size_t k, size_t i) const
| Stoichiometric coefficient of species k as a product in reaction i.
Eigen::SparseMatrix< double > | productStoichCoeffs () const
| Stoichiometric coefficient matrix for products.
Eigen::SparseMatrix< double > | revProductStoichCoeffs () const
| Stoichiometric coefficient matrix for products of reversible reactions.
virtual double | reactantOrder (size_t k, size_t i) const
| Reactant order of species k in reaction i.
virtual double | productOrder (int k, int i) const
| product Order of species k in reaction i.
virtual string | reactionType (size_t i) const
| String specifying the type of reaction.
virtual string | reactionTypeStr (size_t i) const
| String specifying the type of reaction.
string | reactionString (size_t i) const
| Return a string representing the reaction.
string | reactantString (size_t i) const
| Returns a string containing the reactants side of the reaction equation.
string | productString (size_t i) const
| Returns a string containing the products side of the reaction equation.
AnyMap | parameters ()
| Return the parameters for a phase definition which are needed to reconstruct an identical object using the newKinetics function.
shared_ptr< Reaction > | reaction (size_t i)
| Return the Reaction object for reaction i.
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.
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.
bool | skipUndeclaredThirdBodies () const
double | multiplier (size_t i) const
| The current value of the multiplier for reaction i.
virtual void | invalidateCache ()

## Protected Member Functions
Internal service methods
Note These methods are for internal use, and seek to avoid code duplication while evaluating terms used for rate constants, rates of progress, and their derivatives.
void | applyEquilibriumConstants (double *rop)
| Multiply rate with inverse equilibrium constant.
Eigen::SparseMatrix< double > | calculateCompositionDerivatives (StoichManagerN &stoich, const vector< double > &in)
| Process mole fraction derivative.
void | assertDerivativesValid (const string &name)
| Helper function ensuring that all rate derivatives can be calculated.
Protected Member Functions inherited from Kinetics
double | checkDuplicateStoich (map< int, double > &r1, 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.

## Protected Attributes
vector< double > | m_grt
| Temporary work vector of length m_kk.
vector< size_t > | m_revindex
| List of reactions numbers which are reversible reactions.
bool | m_redo_rates = false
vector< unique_ptr< MultiRateBase > > | m_interfaceRates
| Vector of rate handlers for interface reactions.
map< string, size_t > | m_interfaceTypes
| Rate handler mapping.
vector< size_t > | m_irrev
| Vector of irreversible reaction numbers.
vector< double > | m_conc
| Array of concentrations for each species in the kinetics mechanism.
vector< double > | m_actConc
| Array of activity concentrations for each species in the kinetics object.
vector< double > | m_mu0
| Vector of standard state chemical potentials for all species.
vector< double > | m_mu
| Vector of chemical potentials for all species.
vector< double > | m_mu0_Kc
| Vector of standard state electrochemical potentials modified by a standard concentration term.
vector< double > | m_phi
| Vector of phase electric potentials.
SurfPhase * | m_surf = nullptr
| Pointer to the single surface phase.
ImplicitSurfChem * | m_integrator = nullptr
| Pointer to the Implicit surface chemistry object.
bool | m_ROP_ok = false
double | m_temp = 0.0
| Current temperature of the data.
int | m_phaseExistsCheck = false
| Int flag to indicate that some phases in the kinetics mechanism are non-existent.
vector< bool > | m_phaseExists
| Vector of booleans indicating whether phases exist or not.
vector< int > | m_phaseIsStable
| Vector of int indicating whether phases are stable or not.
vector< vector< bool > > | m_rxnPhaseIsReactant
| Vector of vector of booleans indicating whether a phase participates in a reaction as a reactant.
vector< vector< bool > > | m_rxnPhaseIsProduct
| Vector of vector of booleans indicating whether a phase participates in a reaction as a product.
int | m_ioFlag = 0
size_t | m_nDim = 2
| Number of dimensions of reacting phase (2 for InterfaceKinetics, 1 for EdgeKinetics)
vector< double > | m_rbuf0
| Buffers for partial rop results with length nReactions()
vector< double > | m_rbuf1
bool | m_jac_skip_coverage_dependence = false
| A flag used to neglect rate coefficient coverage dependence in derivative formation.
bool | m_jac_skip_electrochemistry = false
| A flag used to neglect electrochemical contributions in derivative formation.
double | m_jac_rtol_delta = 1e-8
| Relative tolerance used in developing numerical portions of specific derivatives.
bool | m_has_electrochemistry = false
| A flag stating if the object uses electrochemistry.
bool | m_has_coverage_dependence = false
| A flag stating if the object has coverage dependent rates.
Protected Attributes inherited from Kinetics
ValueCache | m_cache
| Cache for saved calculations within each Kinetics object.
bool | m_ready = false
| Boolean indicating whether Kinetics object is fully configured.
size_t | m_kk = 0
| The number of species in all of the phases that participate in this kinetics mechanism.
vector< double > | m_perturb
| Vector of perturbation factors for each reaction's rate of progress vector.
vector< shared_ptr< Reaction > > | m_reactions
| Vector of Reaction objects represented by this Kinetics manager.
vector< ThermoPhase * > | m_thermo
| m_thermo is a vector of pointers to ThermoPhase objects that are involved with this kinetics operator
vector< shared_ptr< ThermoPhase > > | m_sharedThermo
| vector of shared pointers,
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.
map< string, size_t > | m_phaseindex
| Mapping of the phase name to the position of the phase within the kinetics object.
size_t | m_surfphase = npos
| Index in the list of phases of the one surface phase.
size_t | m_rxnphase = npos
| Phase Index where reactions are assumed to be taking place.
size_t | m_mindim = 4
| number of spatial dimensions of lowest-dimensional phase.
vector< double > | m_rfn
| Forward rate constant for each reaction.
vector< double > | m_delta_gibbs0
| Delta G^0 for all reactions.
vector< double > | m_rkcn
| Reciprocal of the equilibrium constant in concentration units.
vector< double > | m_ropf
| Forward rate-of-progress for each reaction.
vector< double > | m_ropr
| Reverse rate-of-progress for each reaction.
vector< double > | m_ropnet
| Net rate-of-progress for each reaction.
vector< double > | m_dH
| The enthalpy change for each reaction to calculate Blowers-Masel rates.
vector< double > | m_rbuf
| Buffer used for storage of intermediate reaction-specific results.
bool | m_skipUndeclaredSpecies = false
| See skipUndeclaredSpecies()
bool | m_skipUndeclaredThirdBodies = false
| See skipUndeclaredThirdBodies()
bool | m_hasUndeclaredThirdBodies = false
| Flag indicating whether reactions include undeclared third bodies.
std::weak_ptr< Solution > | m_root
| reference to Solution
StoichManagerN | m_reactantStoich
| Stoichiometry manager for the reactants for each reaction.
StoichManagerN | m_productStoich
| Stoichiometry manager for the products for each reaction.
StoichManagerN | m_revProductStoich
| Stoichiometry manager for the products of reversible reactions.
Eigen::SparseMatrix< double > | m_stoichMatrix
| Net stoichiometry (products - reactants)

## Constructor & Destructor Documentation

## ◆ InterfaceKinetics() [1/2]

InterfaceKinetics | ( |  | ) |
| default

Constructor.

## ◆ InterfaceKinetics() [2/2]

InterfaceKinetics | ( | ThermoPhase * | thermo | ) |

Constructor.

Parameters

  thermo | The 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.

Deprecated:
  To be removed after Cantera 3.0; code base only uses default.

Definition at line 17 of file InterfaceKinetics.cpp.

## ◆ ~InterfaceKinetics()

~InterfaceKinetics | ( |  | ) |
| override

Definition at line 25 of file InterfaceKinetics.cpp.

## Member Function Documentation

## ◆ resizeReactions()

void resizeReactions | ( |  | ) |
| override virtual

Finalize Kinetics object and associated objects.

Reimplemented from Kinetics.

Definition at line 30 of file InterfaceKinetics.cpp.

## ◆ kineticsType()

string kineticsType | ( |  | ) | const
| inline override virtual

Identifies the Kinetics manager type.

Each class derived from Kinetics should override this method to return a meaningful identifier.

Since
  Starting in Cantera 3.0, the name returned by this method corresponds to the canonical name used in the YAML input format.

Reimplemented from Kinetics.

Definition at line 76 of file InterfaceKinetics.h.

## ◆ setElectricPotential()

void setElectricPotential | ( | int | n,
|  | double | V
| ) |  |

Set the electric potential in the nth phase.

Parameters

  n | phase Index in this kinetics object.
  V | Electric potential (volts)

Definition at line 46 of file InterfaceKinetics.cpp.

## ◆ getEquilibriumConstants()

void getEquilibriumConstants | ( | double * | kc | ) |
| override virtual

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 175 of file InterfaceKinetics.cpp.

## ◆ getDeltaGibbs()

void getDeltaGibbs | ( | double * | deltaG | ) |
| override 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

Parameters

  deltaG | Output vector of deltaG's for reactions Length: nReactions().

Reimplemented from Kinetics.

Definition at line 292 of file InterfaceKinetics.cpp.

## ◆ getDeltaElectrochemPotentials()

void getDeltaElectrochemPotentials | ( | double * | deltaM | ) |
| override virtual

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

Parameters

  deltaM | Output vector of deltaM's for reactions Length: nReactions().

Reimplemented from Kinetics.

Definition at line 309 of file InterfaceKinetics.cpp.

## ◆ getDeltaEnthalpy()

void getDeltaEnthalpy | ( | double * | deltaH | ) |
| override 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

Parameters

  deltaH | Output vector of deltaH's for reactions Length: nReactions().

Reimplemented from Kinetics.

Definition at line 320 of file InterfaceKinetics.cpp.

## ◆ getDeltaEntropy()

void getDeltaEntropy | ( | double * | deltaS | ) |
| override 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

Parameters

  deltaS | Output vector of deltaS's for reactions Length: nReactions().

Reimplemented from Kinetics.

Definition at line 331 of file InterfaceKinetics.cpp.

## ◆ getDeltaSSGibbs()

void getDeltaSSGibbs | ( | double * | deltaG | ) |
| override 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

Parameters

  deltaG | Output vector of ss deltaG's for reactions Length: nReactions().

Reimplemented from Kinetics.

Definition at line 342 of file InterfaceKinetics.cpp.

## ◆ getDeltaSSEnthalpy()

void getDeltaSSEnthalpy | ( | double * | deltaH | ) |
| override 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

Parameters

  deltaH | Output vector of ss deltaH's for reactions Length: nReactions().

Reimplemented from Kinetics.

Definition at line 356 of file InterfaceKinetics.cpp.

## ◆ getDeltaSSEntropy()

void getDeltaSSEntropy | ( | double * | deltaS | ) |
| override 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

Parameters

  deltaS | Output vector of ss deltaS's for reactions Length: nReactions().

Reimplemented from Kinetics.

Definition at line 373 of file InterfaceKinetics.cpp.

## ◆ getActivityConcentrations()

void getActivityConcentrations | ( | double *const | conc | ) |
| override virtual

Get the vector of activity concentrations used in the kinetics object.

Parameters

  [out] | conc | Vector of activity concentrations. Length is equal to the number of species in the kinetics object

Reimplemented from Kinetics.

Definition at line 119 of file InterfaceKinetics.cpp.

## ◆ isReversible()

bool isReversible | ( | size_t | i | ) |
| inline override virtual

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.

Parameters

  i | reaction index

Reimplemented from Kinetics.

Definition at line 115 of file InterfaceKinetics.h.

## ◆ getFwdRateConstants()

void getFwdRateConstants | ( | double * | kfwd | ) |
| override virtual

Return the forward rate constants.

The computed values include all temperature-dependent and pressure-dependent contributions. By default, third-body concentrations are only considered if they are part of the reaction rate definition; for a legacy implementation that includes third-body concentrations see Cantera::use_legacy_rate_constants(). 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.

Parameters

  kfwd | Output vector containing the forward reaction rate constants. Length: nReactions().

Reimplemented from Kinetics.

Definition at line 186 of file InterfaceKinetics.cpp.

## ◆ getRevRateConstants()

void getRevRateConstants | ( | double * | krev,
|  | bool | doIrreversible = `false`
| ) |  |
| override virtual

Return the reverse rate constants.

The computed values include all temperature-dependent and pressure-dependent contributions. By default, third-body concentrations are only considered if they are part of the reaction rate definition; for a legacy implementation that includes third-body concentrations see Cantera::use_legacy_rate_constants(). 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.

Parameters

  krev | Output vector of reverse rate constants
  doIrreversible | boolean indicating whether irreversible reactions should be included.

Reimplemented from Kinetics.

Definition at line 195 of file InterfaceKinetics.cpp.

## ◆ addThermo()

void addThermo | ( | shared_ptr< ThermoPhase > | thermo | ) |
| override virtual

Add a thermo phase to the kinetics manager object.

This must be done before the function init() is called or before any reactions are input. The lowest dimensional phase, where reactions occur, must be added first.

This function calls Kinetics::addPhase(). It also sets the following fields:

       m_phaseExists[]

Parameters

  thermo | Reference to the ThermoPhase to be added.

Reimplemented from Kinetics.

Definition at line 496 of file InterfaceKinetics.cpp.

## ◆ addPhase()

void addPhase | ( | ThermoPhase & | thermo | ) |
| override virtual

See also
  InterfaceKinetics::addThermo(shared_ptr<ThermoPhase>)

Reimplemented from Kinetics.

Definition at line 503 of file InterfaceKinetics.cpp.

## ◆ init()

void init | ( |  | ) |
| override virtual

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 510 of file InterfaceKinetics.cpp.

## ◆ resizeSpecies()

void resizeSpecies | ( |  | ) |
| override virtual

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 527 of file InterfaceKinetics.cpp.

## ◆ addReaction()

bool addReaction | ( | shared_ptr< Reaction > | r,
|  | bool | resize = `true`
| ) |  |
| override virtual

Add a single reaction to the mechanism.

Derived classes should call the base class method in addition to handling their own specialized behavior.

Parameters

  r | Pointer to the Reaction object to be added.
  resize | If `true`, resizeReactions is called after reaction is added.

Returns
  `true` if the reaction is added or `false` if it was skipped

Reimplemented from Kinetics.

Definition at line 389 of file InterfaceKinetics.cpp.

## ◆ modifyReaction()

void modifyReaction | ( | size_t | i,
|  | shared_ptr< Reaction > | rNew
| ) |  |
| override virtual

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.

Parameters

  i | Index of the reaction to be modified
  rNew | Reaction with the new rate expressions

Reimplemented from Kinetics.

Definition at line 455 of file InterfaceKinetics.cpp.

## ◆ setMultiplier()

void setMultiplier | ( | size_t | i,
|  | double | f
| ) |  |
| override virtual

Set the multiplier for reaction i to f.

Parameters

  i | index of the reaction
  f | value of the multiplier.

Reimplemented from Kinetics.

Definition at line 482 of file InterfaceKinetics.cpp.

## ◆ updateROP()

void updateROP | ( |  | ) |
| override virtual

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 210 of file InterfaceKinetics.cpp.

## ◆ _update_rates_T()

void _update_rates_T | ( |  | ) |

Update properties that depend on temperature.

Current objects that this function updates: m_kdata->m_rfn updateKc();

Definition at line 52 of file InterfaceKinetics.cpp.

## ◆ _update_rates_phi()

void _update_rates_phi | ( |  | ) |

Update properties that depend on the electric potential.

Definition at line 89 of file InterfaceKinetics.cpp.

## ◆ _update_rates_C()

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 100 of file InterfaceKinetics.cpp.

## ◆ advanceCoverages()

void advanceCoverages | ( | double | 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.

This method carries out a time-accurate advancement of the surface coverages for a specified amount of time.

\[ \dot {\theta}_k = \dot s_k (\sigma_k / s_0) \]

Parameters

  tstep | Time value to advance the surface coverages
  rtol | The relative tolerance for the integrator
  atol | The absolute tolerance for the integrator
  maxStepSize | The maximum step-size the integrator is allowed to take. If zero, this option is disabled.
  maxSteps | The maximum number of time-steps the integrator can take. If not supplied, uses the default value in CVodeIntegrator (20000).
  maxErrTestFails | the maximum permissible number of error test failures If not supplied, uses the default value in CVODES (7).

Definition at line 544 of file InterfaceKinetics.cpp.

## ◆ solvePseudoSteadyStateProblem()

void solvePseudoSteadyStateProblem | ( | int | ifuncOverride = `-1`,
|  | double | 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.

Parameters

  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 560 of file InterfaceKinetics.cpp.

## ◆ setIOFlag()

void setIOFlag | ( | int | ioFlag | ) |

Definition at line 488 of file InterfaceKinetics.cpp.

## ◆ updateMu0()

void updateMu0 | ( |  | ) |
| virtual

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 156 of file InterfaceKinetics.cpp.

## ◆ 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 125 of file InterfaceKinetics.cpp.

## ◆ setPhaseExistence()

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.

Parameters

  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 574 of file InterfaceKinetics.cpp.

## ◆ setPhaseStability()

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.

Parameters

  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 605 of file InterfaceKinetics.cpp.

## ◆ phaseExistence()

int phaseExistence | ( | const size_t | iphase | ) | const

Gets the phase existence int for the ith phase.

Parameters

  iphase | Phase Id

Returns
  The int specifying whether the kinetics object thinks the phase exists or not. If it exists, then species in that phase can be a reactant in reactions.

Definition at line 593 of file InterfaceKinetics.cpp.

## ◆ phaseStability()

int phaseStability | ( | const size_t | iphase | ) | const

Gets the phase stability int for the ith phase.

Parameters

  iphase | Phase Id

Returns
  The int specifying whether the kinetics object thinks the phase is stable with nonzero mole numbers. If it stable, then the kinetics object will allow for rates of production of of species in that phase that are positive.

Definition at line 599 of file InterfaceKinetics.cpp.

## ◆ interfaceCurrent()

double interfaceCurrent | ( | const size_t | iphase | ) |

Gets the interface current for the ith phase.

Parameters

  iphase | Phase Id

Returns
  The double specifying the interface current. The interface current is useful when charge transfer reactions occur at an interface. It is defined here as the net positive charge entering the phase specified by the Phase Id. (Units: A/m^2 for a surface reaction, A/m for an edge reaction).

Definition at line 615 of file InterfaceKinetics.cpp.

## ◆ setDerivativeSettings()

void setDerivativeSettings | ( | const AnyMap & | settings | ) |
| override virtual

Set/modify derivative settings.

Parameters

  settings | AnyMap containing settings determining derivative evaluation.

Reimplemented from Kinetics.

Definition at line 668 of file InterfaceKinetics.cpp.

## ◆ getDerivativeSettings()

void getDerivativeSettings | ( | AnyMap & | settings | ) | const
| override virtual

Retrieve derivative settings.

Parameters

  settings | AnyMap containing settings determining derivative evaluation.

Reimplemented from Kinetics.

Definition at line 684 of file InterfaceKinetics.cpp.

## ◆ fwdRatesOfProgress_ddCi()

Eigen::SparseMatrix< double > fwdRatesOfProgress_ddCi | ( |  | ) |
| override virtual

Calculate derivatives for forward rates-of-progress with respect to species concentration at constant temperature, pressure and remaining species concentrations.

The method returns a matrix with nReactions() rows and nTotalSpecies() columns. For a derivative with respect to \( c_i \), all other \( c_j \) are held constant.

Warning
  This method is an experimental part of the Cantera API and may be changed or removed without notice.

Since
  New in Cantera 3.0.

Reimplemented from Kinetics.

Definition at line 632 of file InterfaceKinetics.cpp.

## ◆ revRatesOfProgress_ddCi()

Eigen::SparseMatrix< double > revRatesOfProgress_ddCi | ( |  | ) |
| override virtual

Calculate derivatives for forward rates-of-progress with respect to species concentration at constant temperature, pressure and remaining species concentrations.

The method returns a matrix with nReactions() rows and nTotalSpecies() columns. For a derivative with respect to \( c_i \), all other \( c_j \) are held constant.

Warning
  This method is an experimental part of the Cantera API and may be changed or removed without notice.

Since
  New in Cantera 3.0.

Reimplemented from Kinetics.

Definition at line 642 of file InterfaceKinetics.cpp.

## ◆ netRatesOfProgress_ddCi()

Eigen::SparseMatrix< double > netRatesOfProgress_ddCi | ( |  | ) |
| override virtual

Calculate derivatives for net rates-of-progress with respect to species concentration at constant temperature, pressure, and remaining species concentrations.

The method returns a matrix with nReactions() rows and nTotalSpecies() columns. For a derivative with respect to \( c_i \), all other \( c_j \) are held constant.

Warning
  This method is an experimental part of the Cantera API and may be changed or removed without notice.

Since
  New in Cantera 3.0.

Reimplemented from Kinetics.

Definition at line 653 of file InterfaceKinetics.cpp.

## ◆ applyEquilibriumConstants()

void applyEquilibriumConstants | ( | double * | rop | ) |
| protected

Multiply rate with inverse equilibrium constant.

Definition at line 709 of file InterfaceKinetics.cpp.

## ◆ calculateCompositionDerivatives()

Eigen::SparseMatrix< double > calculateCompositionDerivatives | ( | StoichManagerN & | stoich,
|  | const vector< double > & | in
| ) |  |
| protected

Process mole fraction derivative.

Parameters

  stoich | stoichiometry manager
  in | rate expression used for the derivative calculation

Returns
  a sparse matrix of derivative contributions for each reaction of dimensions nTotalReactions by nTotalSpecies

Definition at line 691 of file InterfaceKinetics.cpp.

## ◆ assertDerivativesValid()

void assertDerivativesValid | ( | const string & | name | ) |
| protected

Helper function ensuring that all rate derivatives can be calculated.

Parameters

  name | method name used for error output

Exceptions

  CanteraError | if coverage dependence or electrochemical reactions are included

Definition at line 700 of file InterfaceKinetics.cpp.

## Member Data Documentation

## ◆ m_grt

vector<double> m_grt
| protected

Temporary work vector of length m_kk.

Definition at line 343 of file InterfaceKinetics.h.

## ◆ m_revindex

vector<size_t> m_revindex
| protected

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 350 of file InterfaceKinetics.h.

## ◆ m_redo_rates

bool m_redo_rates = false
| protected

Definition at line 352 of file InterfaceKinetics.h.

## ◆ m_interfaceRates

vector<unique_ptr<MultiRateBase> > m_interfaceRates
| protected

Vector of rate handlers for interface reactions.

Definition at line 355 of file InterfaceKinetics.h.

## ◆ m_interfaceTypes

map<string, size_t> m_interfaceTypes
| protected

Rate handler mapping.

Definition at line 356 of file InterfaceKinetics.h.

## ◆ m_irrev

vector<size_t> m_irrev
| protected

Vector of irreversible reaction numbers.

vector containing the reaction numbers of irreversible reactions.

Definition at line 362 of file InterfaceKinetics.h.

## ◆ m_conc

vector<double> m_conc
| protected

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 376 of file InterfaceKinetics.h.

## ◆ m_actConc

vector<double> m_actConc
| protected

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 390 of file InterfaceKinetics.h.

## ◆ m_mu0

vector<double> m_mu0
| protected

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 399 of file InterfaceKinetics.h.

## ◆ m_mu

vector<double> m_mu
| protected

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 408 of file InterfaceKinetics.h.

## ◆ m_mu0_Kc

vector<double> m_mu0_Kc
| protected

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 422 of file InterfaceKinetics.h.

## ◆ m_phi

vector<double> m_phi
| protected

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 429 of file InterfaceKinetics.h.

## ◆ m_surf

SurfPhase* m_surf = nullptr
| protected

Pointer to the single surface phase.

Definition at line 432 of file InterfaceKinetics.h.

## ◆ m_integrator

ImplicitSurfChem* m_integrator = nullptr
| protected

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 440 of file InterfaceKinetics.h.

## ◆ m_ROP_ok

bool m_ROP_ok = false
| protected

Definition at line 442 of file InterfaceKinetics.h.

## ◆ m_temp

double m_temp = 0.0
| protected

Current temperature of the data.

Definition at line 445 of file InterfaceKinetics.h.

## ◆ m_phaseExistsCheck

int m_phaseExistsCheck = false
| protected

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 454 of file InterfaceKinetics.h.

## ◆ m_phaseExists

vector<bool> m_phaseExists
| protected

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 467 of file InterfaceKinetics.h.

## ◆ m_phaseIsStable

vector<int> m_phaseIsStable
| protected

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 477 of file InterfaceKinetics.h.

## ◆ m_rxnPhaseIsReactant

vector<vector<bool> > m_rxnPhaseIsReactant
| protected

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 485 of file InterfaceKinetics.h.

## ◆ m_rxnPhaseIsProduct

vector<vector<bool> > m_rxnPhaseIsProduct
| protected

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 493 of file InterfaceKinetics.h.

## ◆ m_ioFlag

int m_ioFlag = 0
| protected

Definition at line 495 of file InterfaceKinetics.h.

## ◆ m_nDim

size_t m_nDim = 2
| protected

Number of dimensions of reacting phase (2 for InterfaceKinetics, 1 for EdgeKinetics)

Definition at line 499 of file InterfaceKinetics.h.

## ◆ m_rbuf0

vector<double> m_rbuf0
| protected

Buffers for partial rop results with length nReactions()

Definition at line 502 of file InterfaceKinetics.h.

## ◆ m_rbuf1

vector<double> m_rbuf1
| protected

Definition at line 503 of file InterfaceKinetics.h.

## ◆ m_jac_skip_coverage_dependence

bool m_jac_skip_coverage_dependence = false
| protected

A flag used to neglect rate coefficient coverage dependence in derivative formation.

Definition at line 507 of file InterfaceKinetics.h.

## ◆ m_jac_skip_electrochemistry

bool m_jac_skip_electrochemistry = false
| protected

A flag used to neglect electrochemical contributions in derivative formation.

Definition at line 509 of file InterfaceKinetics.h.

## ◆ m_jac_rtol_delta

double m_jac_rtol_delta = 1e-8
| protected

Relative tolerance used in developing numerical portions of specific derivatives.

Definition at line 511 of file InterfaceKinetics.h.

## ◆ m_has_electrochemistry

bool m_has_electrochemistry = false
| protected

A flag stating if the object uses electrochemistry.

Definition at line 513 of file InterfaceKinetics.h.

## ◆ m_has_coverage_dependence

bool m_has_coverage_dependence = false
| protected

A flag stating if the object has coverage dependent rates.

Definition at line 515 of file InterfaceKinetics.h.

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

- InterfaceKinetics.h
- InterfaceKinetics.cpp