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

#include <InterfaceKinetics.h>

Inheritance diagram for InterfaceKinetics:

Collaboration diagram for InterfaceKinetics:

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

virtual	~InterfaceKinetics ()
	Destructor.

	InterfaceKinetics (const InterfaceKinetics &right)
	Copy Constructor for the Kinetics object.

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

virtual Kinetics *	duplMyselfAsKinetics (const std::vector< thermo_t * > &tpVector) const
	Duplication routine for objects which inherit from Kinetics.

virtual int	ID () const
	Return the ID of the kinetics object.

virtual int	type () const
	Return the type of the kinetics object.

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

void	incrementRxnCount ()
	Increment the number of reactions in the mechanism by one.

void	selectPhase (const doublereal data, const thermo_t phase, doublereal *phase_data)
	Extract from array `data` the portion pertaining to phase `phase`.

Reaction Rates Of Progress
virtual void	getFwdRatesOfProgress (doublereal *fwdROP)
	Return the forward rates of progress for each reaction.

virtual void	getRevRatesOfProgress (doublereal *revROP)
	Return the reverse rates of progress for each reaction.

virtual void	getNetRatesOfProgress (doublereal *netROP)
	Return the net rates of progress for each reaction.

virtual void	getEquilibriumConstants (doublereal *kc)
	Get the equilibrium constants of all reactions, whether the reaction is reversible or not.

void	getExchangeCurrentQuantities ()

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

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

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

virtual void	getDeltaEntropy (doublereal *deltaS)
	Return the vector of values for the change in entropy due to each reaction.

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

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

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

Species Production Rates
virtual void	getCreationRates (doublereal *cdot)
	Returns the Species creation rates [kmol/m^2/s].

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

virtual void	getNetProductionRates (doublereal *net)
	Return the species net production rates [kmol/m^2/s].

Reaction Mechanism Informational Query Routines
virtual doublereal	reactantStoichCoeff (size_t k, size_t i) const
	Stoichiometric coefficient of species k as a reactant in reaction i.

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

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

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

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

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

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

virtual void	getFwdRateConstants (doublereal *kfwd)
	Update the rates of progress of the reactions in the reaction mechanism.

virtual void	getRevRateConstants (doublereal *krev, bool doIrreversible=false)
	Update the rates of progress of the reactions in the reaction mechanism.

virtual void	getActivationEnergies (doublereal *E)
	Return the activation energies in Kelvin.

Constructors and General Information about Mechanism
virtual void	assignShallowPointers (const std::vector< thermo_t * > &tpVector)
	Reassign the shallow pointers within the FKinetics object.

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().

Information/Lookup Functions about Phases and Species
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 (std::string ph)
	Return the phase index of a phase in the list of phases defined within the object.

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

size_t	reactionPhaseIndex ()
	Phase where the reactions occur.

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

const thermo_t &	thermo (size_t n=0) const

thermo_t &	phase (size_t n=0)
	This method returns a reference to the nth ThermoPhase defined in this kinetics mechanism.

const thermo_t &	phase (size_t n=0) const
	This method returns a reference to the nth ThermoPhase defined in this kinetics mechanism.

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

size_t	start (size_t n)
	Returns the starting index of the species in the nth phase associated with the reaction mechanism.

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

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

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.

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

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

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.

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

Reaction Rates Of Progress
virtual void	getReactionDelta (const doublereal property, doublereal deltaProperty)
	Change in species properties.

Reaction Mechanism Informational Query Routines
virtual doublereal	reactantOrder (size_t k, size_t i) const
	Reactant order of species k in reaction i.

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

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

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

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

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

Altering Reaction Rates
These methods alter reaction rates. They are designed primarily for carrying out sensitivity analysis, but may be used for any purpose requiring dynamic alteration of rate constants. For each reaction, a real-valued multiplier may be defined that multiplies the reaction rate coefficient. The multiplier may be set to zero to completely remove a reaction from the mechanism.
doublereal	multiplier (size_t i) const
	The current value of the multiplier for reaction i.

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

Protected Attributes
size_t	m_ii
	Number of reactions in the mechanism.

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

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

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

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

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

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.

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

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

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

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

Reaction Mechanism Construction
vector_fp	m_grt
	Temporary work vector of length m_kk.

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

Rate1< SurfaceArrhenius >	m_rates
	Templated class containing the vector of reactions for this interface.

bool	m_redo_rates

std::map< size_t, std::pair < int, size_t > >	m_index
	Vector of information about reactions in the mechanism.

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

ReactionStoichMgr	m_rxnstoich
	Stoichiometric manager for the reaction mechanism.

size_t	m_nirrev
	Number of irreversible reactions in the mechanism.

size_t	m_nrev
	Number of reversible reactions in the mechanism.

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

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

std::vector< std::string >	m_rxneqn
	String expression for each rxn.

InterfaceKineticsData *	m_kdata
	Temporary data storage used in calculating the rates of of reactions.

vector_fp	m_conc
	an array of generalized concentrations for each species

vector_fp	m_mu0
	Vector of standard state chemical potentials.

vector_fp	m_phi
	Vector of phase electric potentials.

vector_fp	m_pot
	Vector of potential energies due to Voltages.

vector_fp	m_rwork
	Vector temporary.

vector_fp	m_E
	Vector of raw activation energies for the reactions.

SurfPhase *	m_surf
	Pointer to the single surface phase.

ImplicitSurfChem *	m_integrator
	Pointer to the Implicit surface chemistry object.

vector_fp	m_beta

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

vector_int	m_ctrxn_ecdf
	Vector of booleans indicating whether the charge transfer reaction may be described by an exchange current density expression.

vector_fp	m_StandardConc

vector_fp	m_deltaG0

vector_fp	m_ProdStanConcReac

bool	m_finalized
	boolean indicating whether mechanism has been finalized

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

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

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

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

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

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

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

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

std::vector< int >	m_phaseIsIntermediate
	Vector of ints indicating whether zeroed phase is an intermediate for the formation of another phase.

int	m_numIntermediatePhases

std::vector< doublereal >	m_rxnRateFactorPhaseIntermediates
	Reaction rate reduction factor for intermediates.

std::vector< doublereal >	m_speciesTmpP
	Work vector having length number of species.

std::vector< doublereal >	m_speciesTmpD

int	m_ioFlag

virtual void	addPhase (thermo_t &thermo)
	Add a phase to the kinetics manager object.

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

virtual void	addReaction (ReactionData &r)
	Add a single reaction to the mechanism.

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

virtual bool	ready () const
	Returns true if the kinetics manager has been properly initialized and finalized.

void	updateROP ()
	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 (doublereal tstep)
	Advance the surface coverages in time.

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

void	setIOFlag (int ioFlag)

void	checkPartialEquil ()

size_t	reactionNumber () const

void	addElementaryReaction (ReactionData &r)

void	addGlobalReaction (const ReactionData &r)

void	installReagents (const ReactionData &r)

void	updateKc ()
	Update the equilibrium constants in molar units for all reversible reactions.

void	registerReaction (size_t rxnNumber, int type, size_t loc)
	Write values into m_index.

void	applyButlerVolmerCorrection (doublereal *const kf)
	Apply corrections for interfacial charge transfer reactions.

void	applyExchangeCurrentDensityFormulation (doublereal *const kfwd)
	When an electrode reaction rate is optionally specified in terms of its exchange current density, extra vectors need to be precalculated.

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

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

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

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

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, i.e., has a mole number of zero, a heterogeneous reaction can not proceed from reactants to products. Note it could perhaps proceed from products to reactants if all of the product phases exist.

In order to make the determination of whether a phase exists or not actually involves the specification of additional information to the kinetics object., which heretofore has only had access to intrinsic field information about the phases (i.e., temperature pressure, and mole fraction).

The extrinsic specification of whether a phase exists or not must be specified on top of the intrinsic calculation of the reaction rate. This routine carries a set of booleans indicating whether a phase in the heterogeneous mechanism exists or not.

Additionally, the routine 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 104 of file InterfaceKinetics.h.

Constructor & Destructor Documentation

InterfaceKinetics ( thermo_t * thermo = 0 )

Constructor.

Parameters

thermo The optional parameter may be used to initialize the object with one ThermoPhase object. HKM Note -> Since the interface kinetics object will probably require multiple thermophase objects, this is probably not a good idea to have this parameter.

Definition at line 71 of file InterfaceKinetics.cpp.

References InterfaceKinetics::addPhase(), InterfaceKinetics::m_kdata, and InterfaceKineticsData::m_temp.

Referenced by InterfaceKinetics::duplMyselfAsKinetics().

~InterfaceKinetics ( )

virtual

Destructor.

Definition at line 105 of file InterfaceKinetics.cpp.

References Kinetics::m_ii, InterfaceKinetics::m_integrator, InterfaceKinetics::m_kdata, InterfaceKinetics::m_rxnPhaseIsProduct, and InterfaceKinetics::m_rxnPhaseIsReactant.

InterfaceKinetics ( const InterfaceKinetics & right )

Copy Constructor for the Kinetics object.

Currently, this is not fully implemented. If called it will throw an exception.

Definition at line 122 of file InterfaceKinetics.cpp.

References InterfaceKinetics::m_kdata, InterfaceKineticsData::m_temp, and InterfaceKinetics::operator=().

Member Function Documentation

InterfaceKinetics & operator= ( const InterfaceKinetics & right )

Assignment operator.

This is NOT a virtual function.

Parameters

right Reference to Kinetics object to be copied into the current one.

Definition at line 162 of file InterfaceKinetics.cpp.

Referenced by InterfaceKinetics::InterfaceKinetics(), and Interface::operator=().

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

virtual

Duplication routine for objects which inherit from Kinetics.

This virtual routine can be used to duplicate Kinetics objects inherited from Kinetics even if the application only has a pointer to Kinetics to work with.

These routines are basically wrappers around the derived copy constructor.

Parameters

tpVector Vector of shallow pointers to ThermoPhase objects. this is the m_thermo vector within this object

Reimplemented from Kinetics.

Reimplemented in EdgeKinetics.

Definition at line 253 of file InterfaceKinetics.cpp.

References Kinetics::assignShallowPointers(), and InterfaceKinetics::InterfaceKinetics().

int ID ( ) const

virtual

Return the ID of the kinetics object.

Deprecated:: use type() instead

Reimplemented from Kinetics.

Reimplemented in EdgeKinetics.

Definition at line 231 of file InterfaceKinetics.cpp.

int type ( ) const

virtual

Return the type of the kinetics object.

Reimplemented from Kinetics.

Reimplemented in EdgeKinetics.

Definition at line 236 of file InterfaceKinetics.cpp.

Referenced by InterfaceKinetics::registerReaction().

void setElectricPotential	(	int	n,
		doublereal	V
	)

Set the electric potential in the nth phase.

Parameters

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

Definition at line 265 of file InterfaceKinetics.cpp.

References ThermoPhase::setElectricPotential(), and Kinetics::thermo().

virtual void getFwdRatesOfProgress ( doublereal * fwdROP )

inlinevirtual

Return the forward rates of progress for each reaction.

Parameters

fwdROP vector of rates of progress. length = number of reactions, Units are kmol m-2 s-1.

Reimplemented from Kinetics.

Definition at line 181 of file InterfaceKinetics.h.

References InterfaceKinetics::m_kdata, and InterfaceKinetics::updateROP().

virtual void getRevRatesOfProgress ( doublereal * revROP )

inlinevirtual

Return the reverse rates of progress for each reaction.

Parameters

revROP vector of rates of progress. length = number of reactions, Units are kmol m-2 s-1.

Reimplemented from Kinetics.

Definition at line 191 of file InterfaceKinetics.h.

References InterfaceKinetics::m_kdata, and InterfaceKinetics::updateROP().

virtual void getNetRatesOfProgress ( doublereal * netROP )

inlinevirtual

Return the net rates of progress for each reaction.

Parameters

netROP vector of rates of progress. length = number of reactions, Units are kmol m-2 s-1.

Reimplemented from Kinetics.

Definition at line 201 of file InterfaceKinetics.h.

References InterfaceKinetics::m_kdata, and InterfaceKinetics::updateROP().

void getEquilibriumConstants ( doublereal * kc )

virtual

Get the equilibrium constants of all reactions, whether the reaction is reversible or not.

Get the equilibrium constants of all reactions, whether reversible or not.

Parameters

kc	Returns the concentration equation constant for the reaction. Length is the number of reactions

Reimplemented from Kinetics.

Definition at line 449 of file InterfaceKinetics.cpp.

References Phase::charge(), DATA_PTR, Cantera::GasConstant, ReactionStoichMgr::getReactionDelta(), ThermoPhase::getStandardChemPotentials(), ThermoPhase::logStandardConc(), Kinetics::m_ii, InterfaceKinetics::m_mu0, InterfaceKinetics::m_phi, InterfaceKinetics::m_rxnstoich, Kinetics::m_start, Kinetics::nPhases(), Phase::nSpecies(), Phase::temperature(), and Kinetics::thermo().

Referenced by InterfaceKinetics::getRevRateConstants().

void getDeltaGibbs ( doublereal * deltaG )

virtual

Return the vector of values for the reaction gibbs free energy change.

These values depend upon the concentration of the solution.

units = J kmol-1

Parameters

deltaG Output vector of deltaG's for reactions Length: m_ii.

Reimplemented from Kinetics.

Definition at line 841 of file InterfaceKinetics.cpp.

References DATA_PTR, ThermoPhase::getChemPotentials(), ReactionStoichMgr::getReactionDelta(), InterfaceKinetics::m_grt, InterfaceKinetics::m_rxnstoich, Kinetics::m_start, Kinetics::nPhases(), and Kinetics::thermo().

void getDeltaElectrochemPotentials ( doublereal * deltaM )

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: m_ii.

Reimplemented from Kinetics.

Definition at line 871 of file InterfaceKinetics.cpp.

References DATA_PTR, ThermoPhase::getElectrochemPotentials(), ReactionStoichMgr::getReactionDelta(), InterfaceKinetics::m_grt, InterfaceKinetics::m_rxnstoich, Kinetics::m_start, Kinetics::nPhases(), and Kinetics::thermo().

void getDeltaEnthalpy ( doublereal * deltaH )

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

Reimplemented from Kinetics.

Definition at line 899 of file InterfaceKinetics.cpp.

References DATA_PTR, ThermoPhase::getPartialMolarEnthalpies(), ReactionStoichMgr::getReactionDelta(), InterfaceKinetics::m_grt, InterfaceKinetics::m_rxnstoich, Kinetics::m_start, Kinetics::nPhases(), and Kinetics::thermo().

void getDeltaEntropy ( doublereal * deltaS )

virtual

Return the vector of values for the change in entropy due to each reaction.

These values depend upon the concentration of the solution.

units = J kmol-1 Kelvin-1

Parameters

deltaS vector of Enthalpy changes Length = m_ii, number of reactions

Reimplemented from Kinetics.

Definition at line 928 of file InterfaceKinetics.cpp.

References DATA_PTR, ThermoPhase::getPartialMolarEntropies(), ReactionStoichMgr::getReactionDelta(), InterfaceKinetics::m_grt, InterfaceKinetics::m_rxnstoich, Kinetics::m_start, Kinetics::nPhases(), and Kinetics::thermo().

void getDeltaSSGibbs ( doublereal * deltaG )

virtual

Return the vector of values for the reaction standard state gibbs free energy change.

getDeltaSSGibbs():

These values don't depend upon the concentration of the solution.

Parameters

deltaG vector of rxn SS free energy changes units = J kmol-1

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

Reimplemented from Kinetics.

Definition at line 955 of file InterfaceKinetics.cpp.

References DATA_PTR, ReactionStoichMgr::getReactionDelta(), ThermoPhase::getStandardChemPotentials(), InterfaceKinetics::m_grt, InterfaceKinetics::m_rxnstoich, Kinetics::m_start, Kinetics::nPhases(), and Kinetics::thermo().

void getDeltaSSEnthalpy ( doublereal * deltaH )

virtual

Return the vector of values for the change in the standard state enthalpies of reaction.

getDeltaSSEnthalpy():

These values don't depend upon the concentration of the solution.

Parameters

deltaH vector of rxn SS enthalpy changes units = J kmol-1

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

Reimplemented from Kinetics.

Definition at line 984 of file InterfaceKinetics.cpp.

References DATA_PTR, Cantera::GasConstant, ThermoPhase::getEnthalpy_RT(), ReactionStoichMgr::getReactionDelta(), InterfaceKinetics::m_grt, Kinetics::m_kk, InterfaceKinetics::m_rxnstoich, Kinetics::m_start, Kinetics::nPhases(), Phase::temperature(), and Kinetics::thermo().

void getDeltaSSEntropy ( doublereal * deltaS )

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.

Parameters

deltaS vector of rxn SS entropy changes units = J kmol-1 Kelvin-1

Reimplemented from Kinetics.

Definition at line 1017 of file InterfaceKinetics.cpp.

References DATA_PTR, Cantera::GasConstant, ThermoPhase::getEntropy_R(), ReactionStoichMgr::getReactionDelta(), InterfaceKinetics::m_grt, Kinetics::m_kk, InterfaceKinetics::m_rxnstoich, Kinetics::m_start, Kinetics::nPhases(), and Kinetics::thermo().

void getCreationRates ( doublereal * cdot )

virtual

Returns the Species creation rates [kmol/m^2/s].

Return the species creation rates in array cdot, which must be dimensioned at least as large as the total number of species in all phases of the kinetics model

Parameters

cdot	Vector containing creation rates. length = m_kk. units = kmol/m^2/s

Reimplemented from Kinetics.

Definition at line 513 of file InterfaceKinetics.cpp.

References ReactionStoichMgr::getCreationRates(), InterfaceKinetics::m_kdata, Kinetics::m_kk, InterfaceKinetics::m_rxnstoich, and InterfaceKinetics::updateROP().

void getDestructionRates ( doublereal * ddot )

virtual

Return the Species destruction rates [kmol/m^2/s].

Return the species destruction rates in array ddot, which must be dimensioned at least as large as the total number of species in all phases of the kinetics model

Parameters

ddot	Vector containing destruction rates. length = m_kk. units = kmol/m^2/s

Reimplemented from Kinetics.

Definition at line 526 of file InterfaceKinetics.cpp.

References ReactionStoichMgr::getDestructionRates(), InterfaceKinetics::m_kdata, Kinetics::m_kk, InterfaceKinetics::m_rxnstoich, and InterfaceKinetics::updateROP().

void getNetProductionRates ( doublereal * net )

virtual

Return the species net production rates [kmol/m^2/s].

Species net production rates [kmol/m^2/s]. Return the species net production rates (creation - destruction) in array wdot, which must be dimensioned at least as large as the total number of species in all phases of the kinetics model

Parameters

net	Vector of species production rates. units kmol m-d s-1, where d is dimension.

Reimplemented from Kinetics.

Definition at line 544 of file InterfaceKinetics.cpp.

References ReactionStoichMgr::getNetProductionRates(), InterfaceKinetics::m_kdata, Kinetics::m_kk, InterfaceKinetics::m_rxnstoich, and InterfaceKinetics::updateROP().

Referenced by solveSP::calc_t(), ReactingSurf1D::eval(), solveSP::fun_eval(), solveProb::print_header(), and solveProb::printIteration().

virtual doublereal reactantStoichCoeff	(	size_t	k,
		size_t	i
	)		const

inlinevirtual

Stoichiometric coefficient of species k as a reactant in reaction i.

Reimplemented from Kinetics.

Definition at line 353 of file InterfaceKinetics.h.

References InterfaceKinetics::m_rrxn.

virtual doublereal productStoichCoeff	(	size_t	k,
		size_t	i
	)		const

inlinevirtual

Stoichiometric coefficient of species k as a product in reaction i.

Reimplemented from Kinetics.

Definition at line 361 of file InterfaceKinetics.h.

References InterfaceKinetics::m_prxn.

virtual int reactionType ( size_t i ) const

inlinevirtual

Flag specifying the type of reaction.

The legal values and their meaning are specific to the particular kinetics manager.

Reimplemented from Kinetics.

Definition at line 370 of file InterfaceKinetics.h.

References InterfaceKinetics::m_index.

void getActivityConcentrations ( doublereal *const conc )

virtual

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

Parameters

conc	(output) Vector of activity concentrations. Length is equal to the number of species in the kinetics object

Reimplemented from Kinetics.

Definition at line 348 of file InterfaceKinetics.cpp.

References InterfaceKinetics::_update_rates_C(), and InterfaceKinetics::m_conc.

doublereal electrochem_beta ( size_t irxn ) const

Return the charge transfer rxn Beta parameter for the ith reaction.

Returns the beta parameter for a charge transfer reaction. This parameter is not important for non-charge transfer reactions. Note, the parameter defaults to zero. However, a value of 0.5 should be supplied for every charge transfer reaction if no information is known, as a value of 0.5 pertains to a symmetric transition state. The value can vary between 0 to 1.

Parameters

irxn	Reaction number in the kinetics mechanism

Returns: Beta parameter. This defaults to zero, even for charge transfer reactions.

Definition at line 1363 of file InterfaceKinetics.cpp.

References InterfaceKinetics::m_ctrxn.

virtual bool isReversible ( size_t i )

inlinevirtual

True if reaction i has been declared to be reversible.

If isReversible(i) is false, then the reverse rate of progress for reaction i is always zero.

Reimplemented from Kinetics.

Definition at line 404 of file InterfaceKinetics.h.

References InterfaceKinetics::m_revindex.

virtual std::string reactionString ( size_t i ) const

inlinevirtual

Return a string representing the reaction.

Reimplemented from Kinetics.

Definition at line 416 of file InterfaceKinetics.h.

References InterfaceKinetics::m_rxneqn.

void getFwdRateConstants ( doublereal * kfwd )

virtual

Update the rates of progress of the reactions in the reaction mechanism.

This routine operates on internal data.

Reimplemented from Kinetics.

Definition at line 641 of file InterfaceKinetics.cpp.

References InterfaceKinetics::m_kdata, Kinetics::m_perturb, Cantera::multiply_each(), Kinetics::nReactions(), and InterfaceKinetics::updateROP().

Referenced by InterfaceKinetics::getRevRateConstants().

void getRevRateConstants	(	doublereal *	krev,
		bool	doIrreversible = `false`
	)

virtual

Update the rates of progress of the reactions in the reaction mechanism.

This routine operates on internal data.

Reimplemented from Kinetics.

Definition at line 661 of file InterfaceKinetics.cpp.

References DATA_PTR, InterfaceKinetics::getEquilibriumConstants(), InterfaceKinetics::getFwdRateConstants(), Kinetics::m_ii, InterfaceKinetics::m_kdata, Cantera::multiply_each(), and Kinetics::nReactions().

void getActivationEnergies ( doublereal * E )

virtual

Return the activation energies in Kelvin.

length is the number of reactions

Parameters

E	Ouptut vector of activation energies. Length: m_ii.

Reimplemented from Kinetics.

Definition at line 677 of file InterfaceKinetics.cpp.

References InterfaceKinetics::m_E.

void addPhase ( thermo_t & thermo )

virtual

Add a phase to the kinetics manager object.

This must be done before the function init() is called or before any reactions are input.

This function calls the Kinetics operator addPhase. It also sets the following functions

   m_phaseExists[]

Parameters

thermo Reference to the ThermoPhase to be added.

Reimplemented from Kinetics.

Definition at line 1294 of file InterfaceKinetics.cpp.

References Kinetics::addPhase(), InterfaceKinetics::m_phaseExists, and InterfaceKinetics::m_phaseIsStable.

Referenced by InterfaceKinetics::InterfaceKinetics().

void init ( )

virtual

Prepare the class for the addition of reactions.

This function must be called after instantiation of the class, but before any reactions are actually added to the mechanism. This function calculates m_kk the number of species in all phases participating in the reaction mechanism. We don't know m_kk previously, before all phases have been added.

Reimplemented from Kinetics.

Definition at line 1309 of file InterfaceKinetics.cpp.

References InterfaceKinetics::m_conc, InterfaceKinetics::m_grt, Kinetics::m_kk, InterfaceKinetics::m_mu0, InterfaceKinetics::m_phi, InterfaceKinetics::m_pot, InterfaceKinetics::m_prxn, InterfaceKinetics::m_rrxn, Kinetics::nPhases(), Phase::nSpecies(), and Kinetics::thermo().

void addReaction ( ReactionData & r )

virtual

Add a single reaction to the mechanism.

Parameters

r	Reference to a ReactionData object containing all of the info needed to describe the reaction.

This routine must be called after init() and before finalize(). This function branches on the types of reactions allowed by the interfaceKinetics manager in order to install the reaction correctly in the manager. The manager allows the following reaction types Elementary Surface Global There is no difference between elementary and surface reactions.

Reimplemented from Kinetics.

Definition at line 1052 of file InterfaceKinetics.cpp.

References Kinetics::incrementRxnCount(), InterfaceKinetics::m_rxneqn, InterfaceKinetics::m_rxnPhaseIsProduct, InterfaceKinetics::m_rxnPhaseIsReactant, Kinetics::nPhases(), Kinetics::products(), Kinetics::reactants(), and Kinetics::speciesPhaseIndex().

void finalize ( )

virtual

Finish adding reactions and prepare for use.

This function must be called after all reactions are entered into the mechanism and before the mechanism is used to calculate reaction rates.

Here, we resize work arrays based on the number of reactions, since we don't know this number up to now.

Reimplemented from Kinetics.

Reimplemented in EdgeKinetics.

Definition at line 1332 of file InterfaceKinetics.cpp.

References Kinetics::finalize(), Cantera::int2str(), InterfaceKinetics::m_finalized, Kinetics::m_kk, Kinetics::m_perturb, InterfaceKinetics::m_phaseExists, InterfaceKinetics::m_rwork, InterfaceKinetics::m_surf, Kinetics::m_thermo, Phase::nDim(), Cantera::npos, Kinetics::nReactions(), Kinetics::reactionPhaseIndex(), and Kinetics::thermo().

bool ready ( ) const

virtual

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

Reimplemented from Kinetics.

Reimplemented in Interface.

Definition at line 1374 of file InterfaceKinetics.cpp.

References InterfaceKinetics::m_finalized.

void updateROP ( )

Internal routine that updates the Rates of Progress of the reactions.

Update the rates of progress of the reactions in the reaction mechanism.

This is actually the guts of the functionality of the object

This routine operates on internal data.

Definition at line 686 of file InterfaceKinetics.cpp.

Referenced by InterfaceKinetics::getCreationRates(), InterfaceKinetics::getDestructionRates(), InterfaceKinetics::getFwdRateConstants(), InterfaceKinetics::getFwdRatesOfProgress(), InterfaceKinetics::getNetProductionRates(), InterfaceKinetics::getNetRatesOfProgress(), and InterfaceKinetics::getRevRatesOfProgress().

void _update_rates_T ( )

Update properties that depend on temperature.

This is called to update all of the properties that depend on temperature

Current objects that this function updates m_kdata->m_logtemp m_kdata->m_rfn m_rates. updateKc();

Definition at line 281 of file InterfaceKinetics.cpp.

Referenced by InterfaceKinetics::updateROP().

void _update_rates_phi ( )

Update properties that depend on the electric potential.

This is called to update all of the properties that depend on potential

Definition at line 307 of file InterfaceKinetics.cpp.

References ThermoPhase::electricPotential(), InterfaceKinetics::m_phi, Kinetics::nPhases(), and Kinetics::thermo().

Referenced by InterfaceKinetics::_update_rates_T().

void _update_rates_C ( )

Update properties that depend on the species mole fractions and/or concentration.

Update properties that depend on concentrations.

This is called to update all of the properties that depend on 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 326 of file InterfaceKinetics.cpp.

References DATA_PTR, ThermoPhase::getActivityConcentrations(), InterfaceKinetics::m_conc, InterfaceKinetics::m_kdata, Kinetics::m_start, Kinetics::nPhases(), and Kinetics::thermo().

Referenced by InterfaceKinetics::getActivityConcentrations(), and InterfaceKinetics::updateROP().

void advanceCoverages ( doublereal tstep )

Advance the surface coverages in time.

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

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

Parameters

tstep Time value to advance the surface coverages

Definition at line 1384 of file InterfaceKinetics.cpp.

References ImplicitSurfChem::initialize(), ImplicitSurfChem::integrate(), and InterfaceKinetics::m_integrator.

void solvePseudoSteadyStateProblem	(	int	ifuncOverride = `-1`,
		doublereal	timeScaleOverride = `1.0`
	)

Solve for the pseudo steady-state of the surface problem.

Solve for the 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	4 values are possible 1 SFLUX_INITIALIZE 2 SFLUX_RESIDUAL 3 SFLUX_JACOBIAN 4 SFLUX_TRANSIENT 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 1410 of file InterfaceKinetics.cpp.

References ImplicitSurfChem::initialize(), InterfaceKinetics::m_integrator, and ImplicitSurfChem::solvePseudoSteadyStateProblem().

void updateKc ( )

Update the equilibrium constants in molar units for all reversible reactions.

Irreversible reactions have their equilibrium constant set to zero.

Definition at line 360 of file InterfaceKinetics.cpp.

Referenced by InterfaceKinetics::_update_rates_T().

void registerReaction	(	size_t	rxnNumber,
		int	type,
		size_t	loc
	)

inline

Write values into m_index.

Parameters

rxnNumber	reaction number
type	reaction type
loc	location ??

Definition at line 572 of file InterfaceKinetics.h.

References InterfaceKinetics::m_index, and InterfaceKinetics::type().

void applyButlerVolmerCorrection ( doublereal *const kf )

Apply corrections for interfacial charge transfer reactions.

For reactions that transfer charge across a potential difference, the activation energies are modified by the potential difference. (see, for example, ...). This method applies this correction.

Parameters

kf	Vector of forward reaction rate constants on which to have the correction applied

Definition at line 562 of file InterfaceKinetics.cpp.

References Phase::charge(), DATA_PTR, Cantera::fp2str(), Cantera::GasConstant, ReactionStoichMgr::getReactionDelta(), Cantera::int2str(), InterfaceKinetics::m_ctrxn, InterfaceKinetics::m_E, InterfaceKinetics::m_phi, InterfaceKinetics::m_pot, InterfaceKinetics::m_rwork, InterfaceKinetics::m_rxnstoich, Kinetics::nPhases(), Phase::nSpecies(), Phase::temperature(), Kinetics::thermo(), and Cantera::writelog().

Referenced by InterfaceKinetics::_update_rates_T().

void applyExchangeCurrentDensityFormulation ( doublereal *const kfwd )

When an electrode reaction rate is optionally specified in terms of its exchange current density, extra vectors need to be precalculated.

Definition at line 618 of file InterfaceKinetics.cpp.

References Cantera::GasConstant, InterfaceKinetics::m_ctrxn, InterfaceKinetics::m_ctrxn_ecdf, Phase::temperature(), and Kinetics::thermo().

Referenced by InterfaceKinetics::_update_rates_T().

void setPhaseExistence	(	const size_t	iphase,
		const bool	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 1427 of file InterfaceKinetics.cpp.

References InterfaceKinetics::m_phaseExists, InterfaceKinetics::m_phaseExistsCheck, InterfaceKinetics::m_phaseIsStable, and Kinetics::m_thermo.

void setPhaseStability	(	const int	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 1480 of file InterfaceKinetics.cpp.

References InterfaceKinetics::m_phaseIsStable, and Kinetics::m_thermo.

int phaseExistence ( const int iphase ) const

Gets the phase existence int for the ith phase.

Parameters

iphase Phase Id

Returns: 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 1454 of file InterfaceKinetics.cpp.

References InterfaceKinetics::m_phaseExists, and Kinetics::m_thermo.

int phaseStability ( const int iphase ) const

Gets the phase stability int for the ith phase.

Parameters

iphase Phase Id

Returns: 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 1471 of file InterfaceKinetics.cpp.

References InterfaceKinetics::m_phaseIsStable, and Kinetics::m_thermo.

void assignShallowPointers ( const std::vector< thermo_t * > & tpVector )

virtualinherited

Reassign the shallow pointers within the FKinetics object.

This type or routine is absolute necessary because the Kinetics object doesn't own the ThermoPhase objects. After a duplication, we need to point to different ThermoPhase objects.

We check that the ThermoPhase objects are aligned in the same order and have the following identical properties to the ones that they are replacing. id() eosType() nSpecies()

Parameters

tpVector Vector of shallow pointers to ThermoPhase objects. this is the m_thermo vector within this object

Definition at line 179 of file Kinetics.cpp.

References ThermoPhase::eosType(), Phase::id(), Kinetics::m_thermo, and Phase::nSpecies().

Referenced by EdgeKinetics::duplMyselfAsKinetics(), AqueousKinetics::duplMyselfAsKinetics(), GasKinetics::duplMyselfAsKinetics(), InterfaceKinetics::duplMyselfAsKinetics(), and Kinetics::duplMyselfAsKinetics().

size_t nReactions ( ) const

inlineinherited

Number of reactions in the reaction mechanism.

Definition at line 209 of file Kinetics.h.

References Kinetics::m_ii.

Referenced by EdgeKinetics::finalize(), InterfaceKinetics::finalize(), InterfaceKinetics::getFwdRateConstants(), InterfaceKinetics::getRevRateConstants(), and InterfaceKinetics::updateKc().

void checkReactionIndex ( size_t m ) const

inherited

Check that the specified reaction index is in range Throws an exception if i is greater than nReactions()

Definition at line 136 of file Kinetics.cpp.

References Kinetics::m_ii.

void checkReactionArraySize ( size_t ii ) const

inherited

Check that an array size is at least nReactions() Throws an exception if ii is less than nReactions().

Used before calls which take an array pointer.

Definition at line 143 of file Kinetics.cpp.

References Kinetics::m_ii.

void checkSpeciesIndex ( size_t k ) const

inherited

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

Definition at line 164 of file Kinetics.cpp.

References Kinetics::m_kk.

void checkSpeciesArraySize ( size_t mm ) const

inherited

Check that an array size is at least nSpecies() Throws an exception if kk is less than nSpecies().

Used before calls which take an array pointer.

Definition at line 171 of file Kinetics.cpp.

References Kinetics::m_kk.

size_t nPhases ( ) const

inlineinherited

The number of phases participating in the reaction mechanism.

For a homogeneous reaction mechanism, this will always return 1, but for a heterogeneous mechanism it will return the total number of phases in the mechanism.

Definition at line 244 of file Kinetics.h.

References Kinetics::m_thermo.

void checkPhaseIndex ( size_t m ) const

inherited

Check that the specified phase index is in range Throws an exception if m is greater than nPhases()

Definition at line 150 of file Kinetics.cpp.

References Kinetics::nPhases().

void checkPhaseArraySize ( size_t mm ) const

inherited

Check that an array size is at least nPhases() Throws an exception if mm is less than nPhases().

Used before calls which take an array pointer.

Definition at line 157 of file Kinetics.cpp.

References Kinetics::nPhases().

size_t phaseIndex ( std::string ph )

inlineinherited

Return the phase index of a phase in the list of phases defined within the object.

Parameters

ph	std::string name of the phase

If a -1 is returned, then the phase is not defined in the Kinetics object.

Definition at line 266 of file Kinetics.h.

References Kinetics::m_phaseindex, and Cantera::npos.

Referenced by Cantera::importKinetics().

size_t surfacePhaseIndex ( )

inlineinherited

This returns the integer index of the phase which has ThermoPhase type cSurf.

For heterogeneous mechanisms, this identifies the one surface phase. For homogeneous mechanisms, this returns -1.

Definition at line 280 of file Kinetics.h.

References Kinetics::m_surfphase.

Referenced by InterfaceKinetics::_update_rates_T(), solveSP::calc_t(), solveSP::fun_eval(), Cantera::getRateCoefficient(), solveProb::print_header(), and solveSP::solveSP().

size_t reactionPhaseIndex ( )

inlineinherited

Phase where the reactions occur.

For heterogeneous mechanisms, one of the phases in the list of phases represents the 2D interface or 1D edge at which the reactions take place. This method returns the index of the phase with the smallest spatial dimension (1, 2, or 3) among the list of phases. If there is more than one, the index of the first one is returned. For homogeneous mechanisms, the value 0 is returned.

Definition at line 294 of file Kinetics.h.

References Kinetics::m_rxnphase.

Referenced by EdgeKinetics::finalize(), and InterfaceKinetics::finalize().

thermo_t& thermo ( size_t n = 0 )

inlineinherited

This method returns a reference to the nth ThermoPhase object defined in this kinetics mechanism.

It is typically used so that member functions of the ThermoPhase object may be called. For homogeneous mechanisms, there is only one object, and this method can be called without an argument to access it.

Parameters

n	Index of the ThermoPhase being sought.

Definition at line 309 of file Kinetics.h.

References Kinetics::m_thermo.

thermo_t& phase ( size_t n = 0 )

inlineinherited

This method returns a reference to the nth ThermoPhase defined in this kinetics mechanism.

It is typically used so that member functions of the ThermoPhase may be called.

Deprecated:: This method is redundant.

Parameters

n	Index of the ThermoPhase being sought.

Definition at line 324 of file Kinetics.h.

References Cantera::deprecatedMethod(), and Kinetics::m_thermo.

const thermo_t& phase ( size_t n = 0 ) const

inlineinherited

This method returns a reference to the nth ThermoPhase defined in this kinetics mechanism.

It is typically used so that member functions of the ThermoPhase may be called.

Deprecated:: This method is redundant.

Parameters

n	Index of the ThermoPhase being sought.

Definition at line 336 of file Kinetics.h.

References Cantera::deprecatedMethod(), and Kinetics::m_thermo.

size_t nTotalSpecies ( ) const

inlineinherited

The total number of species in all phases participating in the kinetics mechanism.

This is useful to dimension arrays for use in calls to methods that return the species production rates, for example.

Definition at line 347 of file Kinetics.h.

References Kinetics::nPhases(), Phase::nSpecies(), and Kinetics::thermo().

Referenced by ReactingSurf1D::init(), and rxninfo::installReaction().

size_t start ( size_t n )

inlineinherited

Returns the starting index of the species in the nth phase associated with the reaction mechanism.

Parameters

n	Return the index of first species in the nth phase associated with the reaction mechanism.

Definition at line 363 of file Kinetics.h.

References Cantera::deprecatedMethod(), and Kinetics::m_start.

size_t kineticsSpeciesIndex	(	size_t	k,
		size_t	n
	)		const

inlineinherited

The location of species k of phase n in species arrays.

Kinetics manager classes return species production rates in flat arrays, with the species of each phases following one another, in the order the phases were added. This method is useful to find the value for a particular species of a particular phase in arrays returned from methods like getCreationRates that return an array of species-specific quantities.

Example: suppose a heterogeneous mechanism involves three phases. The first contains 12 species, the second 26, and the third 3. Then species arrays must have size at least 41, and positions 0 - 11 are the values for the species in the first phase, positions 12 - 37 are the values for the species in the second phase, etc. Then kineticsSpeciesIndex(7, 0) = 7, kineticsSpeciesIndex(4, 1) = 16, and kineticsSpeciesIndex(2, 2) = 40.

Parameters

k	species index
n	phase index for the species

Definition at line 391 of file Kinetics.h.

References Kinetics::m_start.

Referenced by solveSP::calc_t(), Cantera::checkRxnElementBalance(), ReactingSurf1D::eval(), solveSP::fun_eval(), Cantera::getEfficiencies(), Cantera::getReagents(), Cantera::getStick(), Kinetics::kineticsSpeciesIndex(), solveSP::solveSP(), and solveSP::updateMFKinSpecies().

size_t kineticsSpeciesIndex ( const std::string & nm ) const

inherited

This routine will look up a species number based on the input std::string nm.

The lookup of species will occur for all phases listed in the kinetics object.

return

If a match is found, the position in the species list is returned.
If no match is found, the value -1 is returned.

Parameters

nm	Input string name of the species

Definition at line 263 of file Kinetics.cpp.

References Phase::id(), Kinetics::m_start, Kinetics::m_thermo, Cantera::npos, Phase::speciesIndex(), and Kinetics::thermo().

size_t kineticsSpeciesIndex	(	const std::string &	nm,
		const std::string &	ph
	)		const

inherited

This routine will look up a species number based on the input std::string nm.

The lookup of species will occur in the specified phase of the object, or all phases if ph is "<any>".

return

If a match is found, the position in the species list is returned.
If no match is found, the value npos (-1) is returned.

Parameters

nm	Input string name of the species
ph	Input string name of the phase.

Definition at line 288 of file Kinetics.cpp.

References Phase::id(), Kinetics::kineticsSpeciesIndex(), Kinetics::m_start, Kinetics::m_thermo, Cantera::npos, Phase::speciesIndex(), and Kinetics::thermo().

string kineticsSpeciesName ( size_t k ) const

inherited

Return the std::string name of the kth species in the kinetics manager.

kineticsSpeciesName():

k is an integer from 0 to ktot - 1, where ktot is the number of species in the kinetics manager, which is the sum of the number of species in all phases participating in the kinetics manager. If k is out of bounds, the std::string "<unknown>" is returned.

Parameters

k	species index

Return the string name of the kth species in the kinetics manager. k is an integer from 0 to ktot - 1, where ktot is the number of species in the kinetics manager, which is the sum of the number of species in all phases participating in the kinetics manager. If k is out of bounds, the string "<unknown>" is returned.

Definition at line 242 of file Kinetics.cpp.

References Kinetics::m_start, Cantera::npos, Phase::speciesName(), and Kinetics::thermo().

Referenced by Cantera::getStick(), solveSP::printFinal(), solveProb::printIteration(), and solveSP::printIteration().

thermo_t & speciesPhase ( std::string nm )

inherited

This function looks up the std::string name of a species and returns a reference to the ThermoPhase object of the phase where the species resides.

This function looks up the string name of a species and returns a reference to the ThermoPhase object of the phase where the species resides.

Will throw an error if the species std::string doesn't match.

Parameters

nm	String containing the name of the species.

Will throw an error if the species string doesn't match.

Definition at line 315 of file Kinetics.cpp.

References Kinetics::m_thermo, Cantera::npos, Phase::speciesIndex(), and Kinetics::thermo().

Referenced by Cantera::checkRxnElementBalance(), Cantera::getStick(), and rxninfo::installReaction().

thermo_t& speciesPhase ( size_t k )

inlineinherited

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.

Parameters

k	Species index

Definition at line 454 of file Kinetics.h.

References Kinetics::speciesPhaseIndex(), and Kinetics::thermo().

size_t speciesPhaseIndex ( size_t k )

inherited

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.

Parameters

k	Species index

Definition at line 337 of file Kinetics.cpp.

References Cantera::int2str(), Kinetics::m_start, and Cantera::npos.

Referenced by InterfaceKinetics::addReaction(), Cantera::checkRxnElementBalance(), Cantera::getStick(), and Kinetics::speciesPhase().

virtual void getReactionDelta	(	const doublereal *	property,
		doublereal *	deltaProperty
	)

inlinevirtualinherited

Change in species properties.

Given an array of molar species property values \( z_k, k = 1, \dots, K \), return the array of reaction values

\[ \Delta Z_i = \sum_k \nu_{k,i} z_k, i = 1, \dots, I. \]

For example, if this method is called with the array of standard-state molar Gibbs free energies for the species, then the values returned in array deltaProperty would be the standard-state Gibbs free energies of reaction for each reaction.

Parameters

property	Input vector of property value. Length: m_kk.
deltaProperty	Output vector of deltaRxn. Length: m_ii.

Definition at line 547 of file Kinetics.h.

References Kinetics::err().

virtual doublereal reactantOrder	(	size_t	k,
		size_t	i
	)		const

inlinevirtualinherited

Reactant order of species k in reaction i.

This is the nominal order of the activity concentration in determining the forward rate of progress of the reaction

Parameters

k	kinetic species index
i	reaction index

Definition at line 735 of file Kinetics.h.

References Kinetics::err().

virtual doublereal productOrder	(	int	k,
		int	i
	)		const

inlinevirtualinherited

product Order of species k in reaction i.

This is the nominal order of the activity concentration of species k in determining the reverse rate of progress of the reaction i

For irreversible reactions, this will all be zero.

Parameters

k	kinetic species index
i	reaction index

Definition at line 750 of file Kinetics.h.

References Kinetics::err().

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

inlinevirtualinherited

Returns a read-only reference to the vector of reactant index numbers for reaction i.

Parameters

i	reaction index

Definition at line 770 of file Kinetics.h.

References Kinetics::m_reactants.

Referenced by InterfaceKinetics::addReaction(), and rxninfo::installReaction().

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

inlinevirtualinherited

Returns a read-only reference to the vector of product index numbers for reaction i.

Parameters

i	reaction index

Definition at line 780 of file Kinetics.h.

References Kinetics::m_products.

Referenced by InterfaceKinetics::addReaction(), and rxninfo::installReaction().

doublereal multiplier ( size_t i ) const

inlineinherited

The current value of the multiplier for reaction i.

Parameters

i	index of the reaction

Definition at line 953 of file Kinetics.h.

References Kinetics::m_perturb.

void setMultiplier	(	size_t	i,
		doublereal	f
	)

inlineinherited

Set the multiplier for reaction i to f.

Parameters

i	index of the reaction
f	value of the multiplier.

Definition at line 962 of file Kinetics.h.

References Kinetics::m_perturb.

void incrementRxnCount ( )

inlineinherited

Increment the number of reactions in the mechanism by one.

Todo:: Should be protected?

Definition at line 972 of file Kinetics.h.

References Kinetics::m_ii, and Kinetics::m_perturb.

Referenced by AqueousKinetics::addReaction(), GasKinetics::addReaction(), and InterfaceKinetics::addReaction().

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

inherited

Extract from array data the portion pertaining to phase phase.

Takes as input an array of properties for all species in the mechanism and copies those values beloning to a particular phase to the output array.

Parameters

data	data
phase	phase
phase_data	phase_data
data	Input data array.
phase	Pointer to one of the phase objects participating in this reaction mechanism
phase_data	Output array where the values for the the specified phase are to be written.

Definition at line 217 of file Kinetics.cpp.

References Kinetics::m_start, Kinetics::m_thermo, Kinetics::nPhases(), and Phase::nSpecies().

Member Data Documentation

vector_fp m_grt

protected

Temporary work vector of length m_kk.

Definition at line 647 of file InterfaceKinetics.h.

Referenced by InterfaceKinetics::getDeltaElectrochemPotentials(), InterfaceKinetics::getDeltaEnthalpy(), InterfaceKinetics::getDeltaEntropy(), InterfaceKinetics::getDeltaGibbs(), InterfaceKinetics::getDeltaSSEnthalpy(), InterfaceKinetics::getDeltaSSEntropy(), InterfaceKinetics::getDeltaSSGibbs(), InterfaceKinetics::init(), and InterfaceKinetics::operator=().

std::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 655 of file InterfaceKinetics.h.

Referenced by InterfaceKinetics::isReversible(), InterfaceKinetics::operator=(), and InterfaceKinetics::updateKc().

Rate1<SurfaceArrhenius> m_rates

protected

Templated class containing the vector of reactions for this interface.

The templated class is described in RateCoeffMgr.h The class SurfaceArrhenius is described in RxnRates.h

Definition at line 662 of file InterfaceKinetics.h.

Referenced by InterfaceKinetics::_update_rates_T(), and InterfaceKinetics::operator=().

std::map<size_t, std::pair<int, size_t> > m_index

mutableprotected

Vector of information about reactions in the mechanism.

The key is the reaction index (0 < i < m_ii). The first pair is the reactionType of the reaction. The second pair is ...

Definition at line 673 of file InterfaceKinetics.h.

Referenced by InterfaceKinetics::operator=(), InterfaceKinetics::reactionType(), and InterfaceKinetics::registerReaction().

std::vector<size_t> m_irrev

protected

Vector of irreversible reaction numbers.

vector containing the reaction numbers of irreversible reactions.

Definition at line 680 of file InterfaceKinetics.h.

Referenced by InterfaceKinetics::operator=(), and InterfaceKinetics::updateKc().

ReactionStoichMgr m_rxnstoich

protected

Stoichiometric manager for the reaction mechanism.

This is the manager for the kinetics mechanism that handles turning reaction extents into species production rates and also handles turning thermo properties into reaction thermo properties.

Definition at line 689 of file InterfaceKinetics.h.

size_t m_nirrev

protected

Number of irreversible reactions in the mechanism.

Definition at line 692 of file InterfaceKinetics.h.

Referenced by InterfaceKinetics::operator=(), and InterfaceKinetics::updateKc().

size_t m_nrev

protected

Number of reversible reactions in the mechanism.

Definition at line 695 of file InterfaceKinetics.h.

Referenced by InterfaceKinetics::operator=(), and InterfaceKinetics::updateKc().

std::vector<std::map<size_t, doublereal> > m_rrxn

mutableprotected

m_rrxn is a vector of maps, containing the reactant stoichiometric coefficient information

m_rrxn has a length equal to the total number of species in the kinetics object. For each species, there exists a map, with the reaction number being the key, and the reactant stoichiometric coefficient for the species being the value. HKM -> mutable because search sometimes creates extra entries. To be fixed in future...

Definition at line 709 of file InterfaceKinetics.h.

Referenced by InterfaceKinetics::init(), InterfaceKinetics::operator=(), and InterfaceKinetics::reactantStoichCoeff().

std::vector<std::map<size_t, doublereal> > m_prxn

mutableprotected

m_prxn is a vector of maps, containing the reactant stoichiometric coefficient information

m_prxn is a vector of maps. m_prxn has a length equal to the total number of species in the kinetics object. For each species, there exists a map, with the reaction number being the key, and the product stoichiometric coefficient for the species being the value.

Definition at line 720 of file InterfaceKinetics.h.

Referenced by InterfaceKinetics::init(), InterfaceKinetics::operator=(), and InterfaceKinetics::productStoichCoeff().

std::vector<std::string> m_rxneqn

protected

String expression for each rxn.

Vector of strings of length m_ii, the number of reactions, containing the string expressions for each reaction (e.g., reactants <=> product1 + product2)

Definition at line 729 of file InterfaceKinetics.h.

Referenced by InterfaceKinetics::addReaction(), InterfaceKinetics::operator=(), and InterfaceKinetics::reactionString().

InterfaceKineticsData* m_kdata

protected

Temporary data storage used in calculating the rates of of reactions.

Definition at line 735 of file InterfaceKinetics.h.

vector_fp m_conc

protected

an array of generalized concentrations for each species

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 751 of file InterfaceKinetics.h.

Referenced by InterfaceKinetics::_update_rates_C(), InterfaceKinetics::_update_rates_T(), InterfaceKinetics::getActivityConcentrations(), InterfaceKinetics::init(), InterfaceKinetics::operator=(), and InterfaceKinetics::updateROP().

vector_fp m_mu0

protected

Vector of standard state chemical potentials.

This vector contains a temporary vector of standard state chemical potentials for all of the species in the kinetics object

Length = m_k units = J/kmol

Definition at line 762 of file InterfaceKinetics.h.

Referenced by InterfaceKinetics::getEquilibriumConstants(), InterfaceKinetics::init(), InterfaceKinetics::operator=(), and InterfaceKinetics::updateKc().

vector_fp 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 772 of file InterfaceKinetics.h.

Referenced by InterfaceKinetics::_update_rates_phi(), InterfaceKinetics::applyButlerVolmerCorrection(), InterfaceKinetics::getEquilibriumConstants(), InterfaceKinetics::init(), InterfaceKinetics::operator=(), and InterfaceKinetics::updateKc().

vector_fp m_pot

protected

Vector of potential energies due to Voltages.

Length is the number of species in kinetics mech. It's used to store the potential energy due to the voltage.

Definition at line 779 of file InterfaceKinetics.h.

Referenced by InterfaceKinetics::applyButlerVolmerCorrection(), InterfaceKinetics::init(), and InterfaceKinetics::operator=().

vector_fp m_rwork

protected

Vector temporary.

Length is number of reactions. It's used to store the voltage contribution to the activation energy.

Definition at line 786 of file InterfaceKinetics.h.

Referenced by InterfaceKinetics::applyButlerVolmerCorrection(), EdgeKinetics::finalize(), InterfaceKinetics::finalize(), and InterfaceKinetics::operator=().

vector_fp m_E

protected

Vector of raw activation energies for the reactions.

units are in Kelvin Length is number of reactions.

Definition at line 793 of file InterfaceKinetics.h.

Referenced by InterfaceKinetics::applyButlerVolmerCorrection(), InterfaceKinetics::getActivationEnergies(), and InterfaceKinetics::operator=().

SurfPhase* m_surf

protected

Pointer to the single surface phase.

Definition at line 796 of file InterfaceKinetics.h.

Referenced by InterfaceKinetics::_update_rates_T(), EdgeKinetics::finalize(), InterfaceKinetics::finalize(), and InterfaceKinetics::operator=().

ImplicitSurfChem* m_integrator

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 objects's surface problem uncoupled from other surface phases.

Definition at line 805 of file InterfaceKinetics.h.

Referenced by InterfaceKinetics::advanceCoverages(), InterfaceKinetics::operator=(), InterfaceKinetics::solvePseudoSteadyStateProblem(), and InterfaceKinetics::~InterfaceKinetics().

std::vector<size_t> m_ctrxn

protected

Vector of reaction indexes specifying the id of the current transfer reactions in the mechanism.

Vector of reaction indices which involve current transfers. This provides an index into the m_beta array.

  irxn = m_ctrxn[i]

Definition at line 817 of file InterfaceKinetics.h.

Referenced by InterfaceKinetics::applyButlerVolmerCorrection(), InterfaceKinetics::applyExchangeCurrentDensityFormulation(), InterfaceKinetics::electrochem_beta(), and InterfaceKinetics::operator=().

vector_int m_ctrxn_ecdf

protected

Vector of booleans indicating whether the charge transfer reaction may be described by an exchange current density expression.

Definition at line 821 of file InterfaceKinetics.h.

Referenced by InterfaceKinetics::applyExchangeCurrentDensityFormulation(), and InterfaceKinetics::operator=().

bool m_finalized

protected

boolean indicating whether mechanism has been finalized

Definition at line 830 of file InterfaceKinetics.h.

Referenced by EdgeKinetics::finalize(), InterfaceKinetics::finalize(), InterfaceKinetics::operator=(), and InterfaceKinetics::ready().

bool m_has_coverage_dependence

protected

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

If this is true, then the coverage dependence is multiplied into the forward reaction rates constant

Definition at line 838 of file InterfaceKinetics.h.

Referenced by InterfaceKinetics::_update_rates_T(), and InterfaceKinetics::operator=().

bool m_has_electrochem_rxns

protected

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

If this is true, the Butler-Volmer correction is applied to the forward reaction rate for those reactions.

fac = exp ( - beta * (delta_phi))

Definition at line 848 of file InterfaceKinetics.h.

Referenced by InterfaceKinetics::_update_rates_T(), and InterfaceKinetics::operator=().

bool m_has_exchange_current_density_formulation

protected

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

If this is true, the standard state gibbs free energy of the reaction and the product of the reactant standard concentrations must be precalculated in order to calculate the rate constant.

Definition at line 857 of file InterfaceKinetics.h.

Referenced by InterfaceKinetics::_update_rates_T(), and InterfaceKinetics::operator=().

int m_phaseExistsCheck

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 866 of file InterfaceKinetics.h.

Referenced by InterfaceKinetics::operator=(), InterfaceKinetics::setPhaseExistence(), and InterfaceKinetics::updateROP().

std::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

length = number of phases in the object By default all phases exist.

Definition at line 876 of file InterfaceKinetics.h.

Referenced by InterfaceKinetics::addPhase(), InterfaceKinetics::finalize(), InterfaceKinetics::operator=(), InterfaceKinetics::phaseExistence(), InterfaceKinetics::setPhaseExistence(), and InterfaceKinetics::updateROP().

std::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 887 of file InterfaceKinetics.h.

Referenced by InterfaceKinetics::addPhase(), InterfaceKinetics::operator=(), InterfaceKinetics::phaseStability(), InterfaceKinetics::setPhaseExistence(), InterfaceKinetics::setPhaseStability(), and InterfaceKinetics::updateROP().

std::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 895 of file InterfaceKinetics.h.

Referenced by InterfaceKinetics::addReaction(), InterfaceKinetics::operator=(), InterfaceKinetics::updateROP(), and InterfaceKinetics::~InterfaceKinetics().

std::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 903 of file InterfaceKinetics.h.

Referenced by InterfaceKinetics::addReaction(), InterfaceKinetics::operator=(), InterfaceKinetics::updateROP(), and InterfaceKinetics::~InterfaceKinetics().

std::vector<int> m_phaseIsIntermediate

protected

Vector of ints indicating whether zeroed phase is an intermediate for the formation of another phase.

If a phase is zeroed out but it is an intermediate, then the phase can be formed whether it is stable or not, but the destruction rate of species in that phase can't exceed the formation rate for species in that phase.

length = number of phases in the object By default all phases are not intermediates

Definition at line 917 of file InterfaceKinetics.h.

std::vector<doublereal> m_rxnRateFactorPhaseIntermediates

protected

Reaction rate reduction factor for intermediates.

Individual reaction rates are reduced to accommodate the requirements of intermediate zero phases.

length = number of reactions in the object By default all phases are not intermediates

Definition at line 928 of file InterfaceKinetics.h.

std::vector<doublereal> m_speciesTmpP

protected

Work vector having length number of species.

Definition at line 931 of file InterfaceKinetics.h.

size_t m_ii

protectedinherited

Number of reactions in the mechanism.

Definition at line 1000 of file Kinetics.h.

Referenced by Kinetics::checkReactionArraySize(), Kinetics::checkReactionIndex(), AqueousKinetics::finalize(), GasKinetics::finalize(), AqueousKinetics::getDeltaEnthalpy(), GasKinetics::getDeltaEnthalpy(), AqueousKinetics::getDeltaEntropy(), GasKinetics::getDeltaEntropy(), AqueousKinetics::getDeltaGibbs(), GasKinetics::getDeltaGibbs(), AqueousKinetics::getDeltaSSEnthalpy(), GasKinetics::getDeltaSSEnthalpy(), AqueousKinetics::getDeltaSSEntropy(), GasKinetics::getDeltaSSEntropy(), AqueousKinetics::getDeltaSSGibbs(), GasKinetics::getDeltaSSGibbs(), AqueousKinetics::getEquilibriumConstants(), GasKinetics::getEquilibriumConstants(), InterfaceKinetics::getEquilibriumConstants(), AqueousKinetics::getFwdRateConstants(), GasKinetics::getFwdRateConstants(), AqueousKinetics::getRevRateConstants(), GasKinetics::getRevRateConstants(), InterfaceKinetics::getRevRateConstants(), Kinetics::incrementRxnCount(), Kinetics::nReactions(), InterfaceKinetics::operator=(), Kinetics::operator=(), AqueousKinetics::updateKc(), GasKinetics::updateKc(), InterfaceKinetics::updateKc(), InterfaceKinetics::updateROP(), and InterfaceKinetics::~InterfaceKinetics().

size_t m_kk

protectedinherited

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

Definition at line 1004 of file Kinetics.h.

Referenced by Kinetics::checkSpeciesArraySize(), Kinetics::checkSpeciesIndex(), InterfaceKinetics::finalize(), Kinetics::finalize(), AqueousKinetics::getCreationRates(), GasKinetics::getCreationRates(), InterfaceKinetics::getCreationRates(), AqueousKinetics::getDeltaSSEnthalpy(), GasKinetics::getDeltaSSEnthalpy(), InterfaceKinetics::getDeltaSSEnthalpy(), AqueousKinetics::getDeltaSSEntropy(), GasKinetics::getDeltaSSEntropy(), InterfaceKinetics::getDeltaSSEntropy(), AqueousKinetics::getDestructionRates(), GasKinetics::getDestructionRates(), InterfaceKinetics::getDestructionRates(), AqueousKinetics::getNetProductionRates(), GasKinetics::getNetProductionRates(), InterfaceKinetics::getNetProductionRates(), AqueousKinetics::init(), GasKinetics::init(), InterfaceKinetics::init(), and Kinetics::operator=().

vector_fp m_perturb

protectedinherited

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

It is initialized to one.

Definition at line 1009 of file Kinetics.h.

Referenced by EdgeKinetics::finalize(), AqueousKinetics::finalize(), GasKinetics::finalize(), InterfaceKinetics::finalize(), AqueousKinetics::getFwdRateConstants(), GasKinetics::getFwdRateConstants(), InterfaceKinetics::getFwdRateConstants(), Kinetics::incrementRxnCount(), Kinetics::multiplier(), Kinetics::operator=(), Kinetics::setMultiplier(), and InterfaceKinetics::updateROP().

std::vector<std::vector<size_t> > m_reactants

protectedinherited

This is a vector of vectors containing the reactants for each reaction.

The outer vector is over the number of reactions, m_ii. The inner vector is a list of species indices. If the stoichiometric coefficient for a reactant is greater than one, then the reactant is listed contiguously in the vector a number of times equal to its stoichiometric coefficient. NOTE: These vectors will be wrong if there are real stoichiometric coefficients in the expression.

Definition at line 1022 of file Kinetics.h.

Referenced by Kinetics::operator=(), and Kinetics::reactants().

std::vector<std::vector<size_t> > m_products

protectedinherited

This is a vector of vectors containing the products for each reaction.

The outer vector is over the number of reactions, m_ii. The inner vector is a list of species indices. If the stoichiometric coefficient for a product is greater than one, then the reactant is listed contiguously in the vector a number of times equal to its stoichiometric coefficient. NOTE: These vectors will be wrong if there are real stoichiometric coefficients in the expression.

Definition at line 1035 of file Kinetics.h.

Referenced by Kinetics::operator=(), and Kinetics::products().

std::vector<thermo_t*> m_thermo

protectedinherited

m_thermo is a vector of pointers to ThermoPhase objects that are involved with this kinetics operator

For homogeneous kinetics applications, this vector will only have one entry. For interfacial reactions, this vector will consist of multiple entries; some of them will be surface phases, and the other ones will be bulk phases. The order that the objects are listed determines the order in which the species comprising each phase are listed in the source term vector, originating from the reaction mechanism.

Note that this kinetics object doesn't own these ThermoPhase objects and is not responsible for creating or deleting them.

Definition at line 1052 of file Kinetics.h.

Referenced by Kinetics::addPhase(), Kinetics::assignShallowPointers(), InterfaceKinetics::finalize(), Kinetics::finalize(), GRI_30_Kinetics::gri30_updateKc(), Kinetics::kineticsSpeciesIndex(), Kinetics::nPhases(), Kinetics::operator=(), Kinetics::phase(), InterfaceKinetics::phaseExistence(), InterfaceKinetics::phaseStability(), Kinetics::selectPhase(), InterfaceKinetics::setPhaseExistence(), InterfaceKinetics::setPhaseStability(), Kinetics::speciesPhase(), and Kinetics::thermo().

std::vector<size_t> m_start

protectedinherited

m_start is a vector of integers specifying the beginning position for the species vector for the n'th phase in the kinetics class.

Definition at line 1059 of file Kinetics.h.

std::map<std::string, size_t> m_phaseindex

protectedinherited

Mapping of the phase id, i.e., the id attribute in the xml phase element to the position of the phase within the kinetics object.

Positions start with the value of 1. The member function, phaseIndex() decrements by one before returning the index value, so that missing phases return -1.

Definition at line 1069 of file Kinetics.h.

Referenced by Kinetics::addPhase(), Kinetics::operator=(), and Kinetics::phaseIndex().

size_t m_surfphase

protectedinherited

Index in the list of phases of the one surface phase.

Definition at line 1075 of file Kinetics.h.

Referenced by Kinetics::addPhase(), Kinetics::operator=(), and Kinetics::surfacePhaseIndex().

size_t m_rxnphase

protectedinherited

Phase Index where reactions are assumed to be taking place.

We calculate this by assuming that the phase with the lowest dimensionality is the phase where reactions are taking place