Kinetics manager for elementary aqueous-phase chemistry. More...

#include <AqueousKinetics.h>

Inheritance diagram for AqueousKinetics:

Collaboration diagram for AqueousKinetics:

Public Member Functions
	AqueousKinetics (thermo_t *thermo=0)
	Constructor. Creates an empty reaction mechanism. More...

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

virtual int	type () const
	Identifies the kinetics manager type. More...

virtual std::string	kineticsType () const
	Identifies the Kinetics manager type. More...

virtual void	getEquilibriumConstants (doublereal *kc)
	Return a vector of Equilibrium constants. More...

virtual void	getFwdRateConstants (doublereal *kfwd)
	Return the forward rate constants. More...

void	updateROP ()

void	_update_rates_T ()
	Update temperature-dependent portions of reaction rates. More...

void	_update_rates_C ()
	Update properties that depend on concentrations. More...

void	updateKc ()
	Update the equilibrium constants in molar units. More...

virtual bool	addReaction (shared_ptr< Reaction > r)
	Add a single reaction to the mechanism. More...

virtual void	modifyReaction (size_t i, shared_ptr< Reaction > rNew)
	Modify the rate expression associated with a reaction. More...

Public Member Functions inherited from BulkKinetics
	BulkKinetics (thermo_t *thermo=0)

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

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

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

virtual void	getDeltaEntropy (doublereal *deltaS)
	Return the vector of values for the reactions change in entropy. More...

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

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

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

virtual void	getRevRateConstants (doublereal *krev, bool doIrreversible=false)
	Return the reverse rate constants. More...

virtual void	resizeSpecies ()
	Resize arrays with sizes that depend on the total number of species. More...

virtual void	setMultiplier (size_t i, double f)
	Set the multiplier for reaction i to f. More...

virtual void	invalidateCache ()

Public Member Functions inherited from Kinetics
virtual bool	ready () const
	Returns true if the kinetics manager has been properly initialized and finalized. More...

virtual std::pair< size_t, size_t >	checkDuplicates (bool throw_err=true) const
	Check for duplicate reactions. More...

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

	Kinetics ()
	Default constructor. More...

virtual	~Kinetics ()

	Kinetics (const Kinetics &)

Kinetics &	operator= (const Kinetics &right)

virtual void	assignShallowPointers (const std::vector< thermo_t *> &tpVector)
	Reassign the pointers within the Kinetics object. More...

size_t	nReactions () const
	Number of reactions in the reaction mechanism. More...

void	checkReactionIndex (size_t m) const
	Check that the specified reaction index is in range Throws an exception if i is greater than nReactions() More...

void	checkReactionArraySize (size_t ii) const
	Check that an array size is at least nReactions() Throws an exception if ii is less than nReactions(). More...

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

void	checkSpeciesArraySize (size_t mm) const
	Check that an array size is at least nSpecies() Throws an exception if kk is less than nSpecies(). More...

size_t	nPhases () const
	The number of phases participating in the reaction mechanism. More...

void	checkPhaseIndex (size_t m) const
	Check that the specified phase index is in range Throws an exception if m is greater than nPhases() More...

void	checkPhaseArraySize (size_t mm) const
	Check that an array size is at least nPhases() Throws an exception if mm is less than nPhases(). More...

size_t	phaseIndex (const std::string &ph)
	Return the phase index of a phase in the list of phases defined within the object. More...

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

size_t	reactionPhaseIndex ()
	Phase where the reactions occur. More...

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

const thermo_t &	thermo (size_t n=0) const

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

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

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

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

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

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

thermo_t &	speciesPhase (size_t k)
	This function takes as an argument the kineticsSpecies index (i.e., the list index in the list of species in the kinetics manager) and returns the species' owning ThermoPhase object. More...

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

virtual void	getFwdRatesOfProgress (doublereal *fwdROP)
	Return the forward rates of progress of the reactions. More...

virtual void	getRevRatesOfProgress (doublereal *revROP)
	Return the Reverse rates of progress of the reactions. More...

virtual void	getNetRatesOfProgress (doublereal *netROP)
	Net rates of progress. More...

virtual void	getReactionDelta (const doublereal property, doublereal deltaProperty)
	Change in species properties. More...

virtual void	getRevReactionDelta (const doublereal g, doublereal dg)
	Given an array of species properties 'g', return in array 'dg' the change in this quantity in the reversible reactions. More...

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

virtual void	getCreationRates (doublereal *cdot)
	Species creation rates [kmol/m^3/s or kmol/m^2/s]. More...

virtual void	getDestructionRates (doublereal *ddot)
	Species destruction rates [kmol/m^3/s or kmol/m^2/s]. More...

virtual void	getNetProductionRates (doublereal *wdot)
	Species net production rates [kmol/m^3/s or kmol/m^2/s]. More...

virtual double	reactantStoichCoeff (size_t k, size_t i) const
	Stoichiometric coefficient of species k as a reactant in reaction i. More...

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

virtual doublereal	reactantOrder (size_t k, size_t i) const
	Reactant order of species k in reaction i. More...

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

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

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

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

std::string	reactantString (size_t i) const
	Returns a string containing the reactants side of the reaction equation. More...

std::string	productString (size_t i) const
	Returns a string containing the products side of the reaction equation. More...

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

virtual void	init ()
	Prepare the class for the addition of reactions, after all phases have been added. More...

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

shared_ptr< Reaction >	reaction (size_t i)
	Return the Reaction object for reaction i. More...

shared_ptr< const Reaction >	reaction (size_t i) const

void	skipUndeclaredSpecies (bool skip)
	Determine behavior when adding a new reaction that contains species not defined in any of the phases associated with this kinetics manager. More...

void	skipUndeclaredThirdBodies (bool skip)
	Determine behavior when adding a new reaction that contains third-body efficiencies for species not defined in any of the phases associated with this kinetics manager. More...

doublereal	multiplier (size_t i) const
	The current value of the multiplier for reaction i. More...

Additional Inherited Members
Protected Member Functions inherited from BulkKinetics
virtual void	addElementaryReaction (ElementaryReaction &r)

virtual void	modifyElementaryReaction (size_t i, ElementaryReaction &rNew)

Protected Member Functions inherited from Kinetics
double	checkDuplicateStoich (std::map< int, double > &r1, std::map< int, double > &r2) const
	Check whether `r1` and `r2` represent duplicate stoichiometries This function returns a ratio if two reactions are duplicates of one another, and 0.0 otherwise. More...

void	checkReactionBalance (const Reaction &R)
	Check that the specified reaction is balanced (same number of atoms for each element in the reactants and products). More...

Protected Attributes inherited from BulkKinetics
Rate1< Arrhenius >	m_rates

std::vector< size_t >	m_revindex
	Indices of reversible reactions. More...

std::vector< size_t >	m_irrev
	Indices of irreversible reactions. More...

vector_fp	m_dn
	Difference between the global reactants order and the global products order. More...

vector_fp	m_conc

vector_fp	m_grt

bool	m_ROP_ok

doublereal	m_temp

Protected Attributes inherited from Kinetics
ValueCache	m_cache
	Cache for saved calculations within each Kinetics object. More...

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

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

std::vector< shared_ptr< Reaction > >	m_reactions
	Vector of Reaction objects represented by this Kinetics manager. More...

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

std::vector< size_t >	m_start
	m_start is a vector of integers specifying the beginning position for the species vector for the n'th phase in the kinetics class. More...

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

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

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

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

vector_fp	m_rfn
	Forward rate constant for each reaction. More...

vector_fp	m_rkcn
	Reciprocal of the equilibrium constant in concentration units. More...

vector_fp	m_ropf
	Forward rate-of-progress for each reaction. More...

vector_fp	m_ropr
	Reverse rate-of-progress for each reaction. More...

vector_fp	m_ropnet
	Net rate-of-progress for each reaction. More...

bool	m_skipUndeclaredSpecies

bool	m_skipUndeclaredThirdBodies

StoichManagerN	m_reactantStoich
	Stoichiometry manager for the reactants for each reaction. More...

StoichManagerN	m_revProductStoich
	Stoichiometry manager for the products of reversible reactions. More...

StoichManagerN	m_irrevProductStoich
	Stoichiometry manager for the products of irreversible reactions. More...

Detailed Description

Kinetics manager for elementary aqueous-phase chemistry.

This kinetics manager implements standard mass-action reaction rate expressions for liquids

Attention: This class currently does not have any test cases or examples. Its implementation may be incomplete, and future changes to Cantera may unexpectedly cause this class to stop working. If you use this class, please consider contributing examples or test cases. In the absence of new tests or examples, this class may be deprecated and removed in a future version of Cantera. See https://github.com/Cantera/cantera/issues/267 for additional information.

Definition at line 31 of file AqueousKinetics.h.

Constructor & Destructor Documentation

◆ AqueousKinetics()

AqueousKinetics ( thermo_t * thermo = 0 )

Constructor. Creates an empty reaction mechanism.

Definition at line 18 of file AqueousKinetics.cpp.

Referenced by AqueousKinetics::duplMyselfAsKinetics().

Member Function Documentation

◆ duplMyselfAsKinetics()

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 BulkKinetics.

Definition at line 23 of file AqueousKinetics.cpp.

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

◆ type()

virtual int type ( ) const

inlinevirtual

Identifies the kinetics manager type.

Each class derived from Kinetics should overload this method to return a unique integer. Standard values are defined in file mix_defs.h.

Deprecated:: Use kineticsType() instead. To be removed after Cantera 2.3.

Reimplemented from Kinetics.

Definition at line 50 of file AqueousKinetics.h.

References Cantera::warn_deprecated().

◆ kineticsType()

virtual std::string kineticsType ( ) const

inlinevirtual

Identifies the Kinetics manager type.

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

Reimplemented from Kinetics.

Definition at line 56 of file AqueousKinetics.h.

◆ getEquilibriumConstants()

void getEquilibriumConstants ( doublereal * kc )

virtual

Return a vector of Equilibrium constants.

Return the equilibrium constants of the reactions in concentration units in array kc, which must be dimensioned at least as large as the total number of reactions.

\[ Kc_i = exp [ \Delta G_{ss,i} ] prod(Cs_k) exp(\sum_k \nu_{k,i} F \phi_n) ] \]

Parameters

kc	Output vector containing the equilibrium constants. Length: nReactions().

Reimplemented from Kinetics.

Definition at line 69 of file AqueousKinetics.cpp.

References AqueousKinetics::_update_rates_T(), Cantera::GasConstant, Kinetics::getReactionDelta(), ThermoPhase::getStandardChemPotentials(), ThermoPhase::logStandardConc(), Kinetics::m_rkcn, Kinetics::nReactions(), Phase::nSpecies(), ThermoPhase::RT(), and Kinetics::thermo().

◆ getFwdRateConstants()

void getFwdRateConstants ( doublereal * kfwd )

virtual

Return the forward rate constants.

length is the number of reactions. units depends on many issues.

Parameters

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

Reimplemented from Kinetics.

Definition at line 128 of file AqueousKinetics.cpp.

References AqueousKinetics::_update_rates_C(), AqueousKinetics::_update_rates_T(), Kinetics::m_perturb, Kinetics::m_rfn, Kinetics::m_ropf, Cantera::multiply_each(), and Kinetics::nReactions().

◆ _update_rates_T()

void _update_rates_T ( )

Update temperature-dependent portions of reaction rates.

Definition at line 30 of file AqueousKinetics.cpp.

Referenced by AqueousKinetics::getEquilibriumConstants(), and AqueousKinetics::getFwdRateConstants().

◆ _update_rates_C()

void _update_rates_C ( )

Update properties that depend on concentrations.

Definition at line 40 of file AqueousKinetics.cpp.

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

Referenced by AqueousKinetics::getFwdRateConstants().

◆ updateKc()

void updateKc ( )

Update the equilibrium constants in molar units.

Definition at line 46 of file AqueousKinetics.cpp.

References Cantera::GasConstant, Kinetics::getRevReactionDelta(), ThermoPhase::getStandardChemPotentials(), ThermoPhase::logStandardConc(), BulkKinetics::m_irrev, BulkKinetics::m_revindex, Kinetics::m_rkcn, Phase::nSpecies(), ThermoPhase::RT(), and Kinetics::thermo().

◆ addReaction()

bool addReaction ( shared_ptr< Reaction > r )

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.

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

Reimplemented from BulkKinetics.

Definition at line 144 of file AqueousKinetics.cpp.

References BulkKinetics::addReaction(), and Cantera::ELEMENTARY_RXN.

◆ modifyReaction()

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

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 159 of file AqueousKinetics.cpp.

References Kinetics::modifyReaction().

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

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ AqueousKinetics()

Member Function Documentation

◆ duplMyselfAsKinetics()

◆ type()

◆ kineticsType()

◆ getEquilibriumConstants()

◆ getFwdRateConstants()

◆ _update_rates_T()

◆ _update_rates_C()

◆ updateKc()

◆ addReaction()

◆ modifyReaction()