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

#include <AqueousKinetics.h>

Inheritance diagram for AqueousKinetics:

Collaboration diagram for AqueousKinetics:

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

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

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

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

	AqueousKinetics (const AqueousKinetics &right)

AqueousKinetics &	operator= (const AqueousKinetics &right)

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

Reaction Rates Of Progress
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	getEquilibriumConstants (doublereal *kc)
	Return a vector of Equilibrium constants. 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...

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

Reaction Mechanism Informational Query Routines
virtual int	reactionType (size_t i) const
	Flag specifying the type of reaction. More...

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

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

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

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

Reaction Mechanism Setup Routines
virtual void	init ()
	Prepare the class for the addition of reactions. More...

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

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

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

virtual void	update_T ()

virtual void	update_C ()

void	updateROP ()

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

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

void	_update_rates_T ()

void	_update_rates_C ()

Public Member Functions inherited from Kinetics
void	incrementRxnCount ()
	Increment the number of reactions in the mechanism by one. More...

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

	Kinetics ()
	Default constructor. More...

virtual	~Kinetics ()
	Destructor. More...

	Kinetics (const Kinetics &)
	Copy Constructor for the Kinetics object. More...

Kinetics &	operator= (const Kinetics &right)
	Assignment operator. More...

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

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

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. More...

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

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

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

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

Protected Attributes
size_t	m_nfall

Rate1< Arrhenius >	m_rates

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

std::vector< size_t >	m_irrev

ReactionStoichMgr	m_rxnstoich

std::vector< size_t >	m_fwdOrder

size_t	m_nirrev

size_t	m_nrev

std::map< size_t, std::vector < grouplist_t > >	m_rgroups

std::map< size_t, std::vector < grouplist_t > >	m_pgroups

std::vector< int >	m_rxntype

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

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

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

std::vector< size_t >	m_revindex

std::vector< std::string >	m_rxneqn

vector_fp	m_conc

vector_fp	m_grt

Aqueous kinetics data
vector_fp	m_ropf

vector_fp	m_ropr

vector_fp	m_ropnet

bool	m_ROP_ok

doublereal	m_temp

vector_fp	m_rfn

vector_fp	m_rkcn

Protected Attributes inherited from Kinetics
size_t	m_ii
	Number of reactions in the mechanism. 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< std::vector < size_t > >	m_reactants
	This is a vector of vectors containing the reactants for each reaction. More...

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

Private Member Functions
size_t	reactionNumber ()

void	addElementaryReaction (ReactionData &r)

void	installReagents (const ReactionData &r)

void	installGroups (size_t irxn, const std::vector< grouplist_t > &r, const std::vector< grouplist_t > &p)

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

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

Private Attributes
std::vector< std::map< int, doublereal > >	m_stoich

bool	m_finalized

Detailed Description

Kinetics manager for elementary aqueous-phase chemistry.

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

Concentration

Deprecated:: Not actually implemented

Definition at line 40 of file AqueousKinetics.h.

Constructor & Destructor Documentation

AqueousKinetics ( thermo_t * thermo = 0 )

Constructor. Creates an empty reaction mechanism.

Definition at line 24 of file AqueousKinetics.cpp.

References Kinetics::addPhase(), and Cantera::warn_deprecated().

Referenced by AqueousKinetics::duplMyselfAsKinetics().

Member Function Documentation

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.

Definition at line 98 of file AqueousKinetics.cpp.

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

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.

Reimplemented from Kinetics.

Definition at line 69 of file AqueousKinetics.h.

virtual doublereal reactantStoichCoeff	(	size_t	k,
		size_t	i
	)		const

inlinevirtual

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

Parameters

k	kinetic species index
i	reaction index

Reimplemented from Kinetics.

Definition at line 73 of file AqueousKinetics.h.

virtual doublereal productStoichCoeff	(	size_t	k,
		size_t	i
	)		const

inlinevirtual

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

Parameters

k	kinetic species index
i	reaction index

Reimplemented from Kinetics.

Definition at line 77 of file AqueousKinetics.h.

virtual void getFwdRatesOfProgress ( doublereal * fwdROP )

inlinevirtual

Return the forward rates of progress of the reactions.

Forward rates of progress. Return the forward rates of progress in array fwdROP, which must be dimensioned at least as large as the total number of reactions.

Parameters

fwdROP Output vector containing forward rates of progress of the reactions. Length: m_ii.

Reimplemented from Kinetics.

Definition at line 83 of file AqueousKinetics.h.

virtual void getRevRatesOfProgress ( doublereal * revROP )

inlinevirtual

Return the Reverse rates of progress of the reactions.

Return the reverse rates of progress in array revROP, which must be dimensioned at least as large as the total number of reactions.

Parameters

revROP Output vector containing reverse rates of progress of the reactions. Length: m_ii.

Reimplemented from Kinetics.

Definition at line 88 of file AqueousKinetics.h.

virtual void getNetRatesOfProgress ( doublereal * netROP )

inlinevirtual

Net rates of progress.

Return the net (forward - reverse) rates of progress in array netROP, which must be dimensioned at least as large as the total number of reactions.

Parameters

netROP Output vector of the net ROP. Length: m_ii.

Reimplemented from Kinetics.

Definition at line 93 of file AqueousKinetics.h.

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.

Parameters

kc	Output vector containing the equilibrium constants. Length: m_ii.

Reimplemented from Kinetics.

Definition at line 156 of file AqueousKinetics.cpp.

References AqueousKinetics::_update_rates_T(), Cantera::GasConstant, ReactionStoichMgr::getReactionDelta(), ThermoPhase::getStandardChemPotentials(), ThermoPhase::logStandardConc(), Kinetics::m_ii, Phase::nSpecies(), Phase::temperature(), and Kinetics::thermo().

Referenced by AqueousKinetics::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 181 of file AqueousKinetics.cpp.

References ThermoPhase::getChemPotentials(), ReactionStoichMgr::getReactionDelta(), Kinetics::m_ii, 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

Parameters

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

Reimplemented from Kinetics.

Definition at line 195 of file AqueousKinetics.cpp.

References ThermoPhase::getPartialMolarEnthalpies(), ReactionStoichMgr::getReactionDelta(), Kinetics::m_ii, and Kinetics::thermo().

void getDeltaEntropy ( doublereal * deltaS )

virtual

Return the vector of values for the reactions change in entropy.

These values depend upon the concentration of the solution.

units = J kmol-1 Kelvin-1

Parameters

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

Reimplemented from Kinetics.

Definition at line 209 of file AqueousKinetics.cpp.

References ThermoPhase::getPartialMolarEntropies(), ReactionStoichMgr::getReactionDelta(), Kinetics::m_ii, and Kinetics::thermo().

void getDeltaSSGibbs ( doublereal * deltaG )

virtual

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

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

units = J kmol-1

Parameters

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

Reimplemented from Kinetics.

Definition at line 223 of file AqueousKinetics.cpp.

References ReactionStoichMgr::getReactionDelta(), ThermoPhase::getStandardChemPotentials(), Kinetics::m_ii, and Kinetics::thermo().

void getDeltaSSEnthalpy ( doublereal * deltaH )

virtual

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

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

units = J kmol-1

Parameters

deltaH Output vector of ss deltaH's for reactions Length: m_ii.

Reimplemented from Kinetics.

Definition at line 239 of file AqueousKinetics.cpp.

References Cantera::GasConstant, ThermoPhase::getEnthalpy_RT(), ReactionStoichMgr::getReactionDelta(), Kinetics::m_ii, Kinetics::m_kk, 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.

units = J kmol-1 Kelvin-1

Parameters

deltaS Output vector of ss deltaS's for reactions Length: m_ii.

Reimplemented from Kinetics.

Definition at line 259 of file AqueousKinetics.cpp.

References Cantera::GasConstant, ThermoPhase::getEntropy_R(), ReactionStoichMgr::getReactionDelta(), Kinetics::m_ii, Kinetics::m_kk, and Kinetics::thermo().

virtual void getNetProductionRates ( doublereal * wdot )

inlinevirtual

Species net production rates [kmol/m^3/s or 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.

See Also: nTotalSpecies.

Parameters

wdot	Output vector of net production rates. Length: m_kk.

Reimplemented from Kinetics.

Definition at line 112 of file AqueousKinetics.h.

References ReactionStoichMgr::getNetProductionRates(), and Kinetics::m_kk.

virtual void getCreationRates ( doublereal * cdot )

inlinevirtual

Species creation rates [kmol/m^3/s or 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.

See Also: nTotalSpecies.

Parameters

cdot	Output vector of creation rates. Length: m_kk.

Reimplemented from Kinetics.

Definition at line 117 of file AqueousKinetics.h.

References ReactionStoichMgr::getCreationRates(), and Kinetics::m_kk.

virtual void getDestructionRates ( doublereal * ddot )

inlinevirtual

Species destruction rates [kmol/m^3/s or 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.

See Also: nTotalSpecies.

Parameters

ddot	Output vector of destruction rates. Length: m_kk.

Reimplemented from Kinetics.

Definition at line 122 of file AqueousKinetics.h.

References ReactionStoichMgr::getDestructionRates(), and Kinetics::m_kk.

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.

Parameters

i	reaction index

Reimplemented from Kinetics.

Definition at line 131 of file AqueousKinetics.h.

virtual std::string reactionString ( size_t i ) const

inlinevirtual

Return a string representing the reaction.

Parameters

i	reaction index

Reimplemented from Kinetics.

Definition at line 135 of file AqueousKinetics.h.

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.

Parameters

i	reaction index

Reimplemented from Kinetics.

Definition at line 139 of file AqueousKinetics.h.

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: m_ii.

Reimplemented from Kinetics.

Definition at line 318 of file AqueousKinetics.cpp.

References AqueousKinetics::_update_rates_C(), AqueousKinetics::_update_rates_T(), Kinetics::m_ii, Kinetics::m_perturb, and Cantera::multiply_each().

Referenced by AqueousKinetics::getRevRateConstants().

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

virtual

Return the reverse rate constants.

length is the number of reactions. units depends on many issues. Note, this routine will return rate constants for irreversible reactions if the default for doIrreversible is overridden.

Parameters

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

Reimplemented from Kinetics.

Definition at line 335 of file AqueousKinetics.cpp.

References AqueousKinetics::getEquilibriumConstants(), AqueousKinetics::getFwdRateConstants(), and Kinetics::m_ii.

void init ( )

virtual

Prepare the class for the addition of reactions.

This method is called by importKinetics() after all phases have been added but before any reactions have been. The base class method does nothing, but derived classes may use this to perform any initialization (allocating arrays, etc.) that requires knowing the phases and species, but before any reactions are added.

Reimplemented from Kinetics.

Definition at line 465 of file AqueousKinetics.cpp.

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

void addReaction ( ReactionData & r )

virtual

Add a single reaction to the mechanism.

This routine must be called after init() and before finalize().

Parameters

r	Reference to the ReactionData object for the reaction to be added.

Reimplemented from Kinetics.

Definition at line 359 of file AqueousKinetics.cpp.

References Cantera::ELEMENTARY_RXN, ReactionData::equation, Kinetics::incrementRxnCount(), ReactionData::pgroups, ReactionData::reactionType, and ReactionData::rgroups.

void finalize ( )

virtual

Finish adding reactions and prepare for use.

This method is called by importKinetics() after all reactions have been entered into the mechanism and before the mechanism is used to calculate reaction rates. The base class method does nothing, but derived classes may use this to perform any initialization (allocating arrays, etc.) that must be done after the reactions are entered.

Reimplemented from Kinetics.

Definition at line 474 of file AqueousKinetics.cpp.

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

bool ready ( ) const

virtual

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

Reimplemented from Kinetics.

Definition at line 491 of file AqueousKinetics.cpp.

void _update_rates_T ( )

Update temperature-dependent portions of reaction rates and falloff functions.

Definition at line 111 of file AqueousKinetics.cpp.

References Phase::temperature(), Kinetics::thermo(), and AqueousKinetics::updateKc().