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

#include <AqueousKinetics.h>

Inheritance diagram for AqueousKinetics:

Collaboration diagram for AqueousKinetics:

Public Member Functions
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`.

Constructors and General Information
	AqueousKinetics (thermo_t *thermo=0)
	Constructor.

	AqueousKinetics (const AqueousKinetics &right)

AqueousKinetics &	operator= (const AqueousKinetics &right)

virtual	~AqueousKinetics ()
	Destructor.

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

virtual int	ID () const

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

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.

Reaction Rates Of Progress
virtual void	getFwdRatesOfProgress (doublereal *fwdROP)
	Forward rates of progress.

virtual void	getRevRatesOfProgress (doublereal *revROP)
	Reverse rates of progress.

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

virtual void	getEquilibriumConstants (doublereal *kc)
	Equilibrium constants.

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

virtual void	getDeltaEnthalpy (doublereal *deltaH)
	Return the array of values for the reaction enthalpy change.

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

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

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

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

Species Production Rates
virtual void	getNetProductionRates (doublereal *net)
	Return the species net production rates.

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

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

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

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

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

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

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

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

virtual void	addReaction (ReactionData &r)
	Add a 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.

virtual void	update_T ()
	Update temperature-dependent portions of reaction rates and falloff functions.

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 ()
	Update properties that depend on concentrations.

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.

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

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

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.

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

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

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_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.

std::vector< size_t >	m_revindex

std::vector< std::string >	m_rxneqn

vector_fp	m_conc

vector_fp	m_grt

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.

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

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.

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

Definition at line 47 of file AqueousKinetics.h.

Constructor & Destructor Documentation

AqueousKinetics ( thermo_t * thermo = 0 )

Constructor.

Construct an empty reaction mechanism.

Definition at line 28 of file AqueousKinetics.cpp.

References Kinetics::addPhase().

Referenced by AqueousKinetics::duplMyselfAsKinetics().

~AqueousKinetics ( )

virtual

Destructor.

Definition at line 54 of file AqueousKinetics.cpp.

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 104 of file AqueousKinetics.cpp.

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

virtual int ID ( ) const

inlinevirtual

Deprecated:: use type() instead

Reimplemented from Kinetics.

Definition at line 83 of file AqueousKinetics.h.

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 86 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 90 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 94 of file AqueousKinetics.h.

virtual void getFwdRatesOfProgress ( doublereal * fwdROP )

inlinevirtual

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.

Reimplemented from Kinetics.

Definition at line 109 of file AqueousKinetics.h.

virtual void getRevRatesOfProgress ( doublereal * revROP )

inlinevirtual

Reverse rates of progress.

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

Reimplemented from Kinetics.

Definition at line 120 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.

Reimplemented from Kinetics.

Definition at line 131 of file AqueousKinetics.h.

void getEquilibriumConstants ( doublereal * kc )

virtual

Equilibrium constants.

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

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.

Reimplemented from Kinetics.

Definition at line 179 of file AqueousKinetics.cpp.

References 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 array of values for the reaction gibbs free energy change.

getDeltaGibbs():

These values depend on the species concentrations.

units = J kmol-1

Return the vector of values for the reaction gibbs free energy change These values depend upon the concentration of the ideal gas.

units = J kmol-1

Reimplemented from Kinetics.

Definition at line 215 of file AqueousKinetics.cpp.

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

void getDeltaEnthalpy ( doublereal * deltaH )

virtual

Return the array of values for the reaction enthalpy change.

getDeltaEnthalpy():

These values depend upon the species concentrations.

units = J kmol-1

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 240 of file AqueousKinetics.cpp.

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

void getDeltaEntropy ( doublereal * deltaS )

virtual

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

These values depend upon the concentration of the solution.

units = J kmol-1 Kelvin-1

Reimplemented from Kinetics.

Definition at line 265 of file AqueousKinetics.cpp.

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

void getDeltaSSGibbs ( doublereal * deltaG )

virtual

Return the array of values for the reaction standard state Gibbs free energy change.

getDeltaSSGibbs():

These values do not depend on the species concentrations.

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 290 of file AqueousKinetics.cpp.

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

void getDeltaSSEnthalpy ( doublereal * deltaH )

virtual

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

getDeltaSSEnthalpy():

These values do not depend upon the concentration of the solution.

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 317 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 array of values for the change in the standard state entropies for each reaction.

These values do not depend upon the concentration of the solution.

units = J kmol-1 Kelvin-1

Reimplemented from Kinetics.

Definition at line 348 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 * net )

inlinevirtual

Return the species net production rates.

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

Parameters

net	Array of species production rates. units kmol m-3 s-1

Reimplemented from Kinetics.

Definition at line 218 of file AqueousKinetics.h.

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

virtual void getCreationRates ( doublereal * cdot )

inlinevirtual

Species creation rates [kmol/m^3].

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

Reimplemented from Kinetics.

Definition at line 234 of file AqueousKinetics.h.

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

virtual void getDestructionRates ( doublereal * ddot )

inlinevirtual

Species destruction rates [kmol/m^3].

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

Reimplemented from Kinetics.

Definition at line 246 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.

Reimplemented from Kinetics.

Definition at line 262 of file AqueousKinetics.h.

virtual std::string reactionString ( size_t i ) const

inlinevirtual

Return a std::string representing the reaction.

Parameters

i	reaction index

Reimplemented from Kinetics.

Definition at line 266 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.

Reimplemented from Kinetics.

Definition at line 275 of file AqueousKinetics.h.

void getFwdRateConstants ( doublereal * kfwd )

virtual

Return the forward rate constants.

getFwdRateConstants():

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

Update the rate of progress for the reactions. This key routine makes sure that the rate of progress vectors located in the solid kinetics data class are up to date.

Reimplemented from Kinetics.

Definition at line 417 of file AqueousKinetics.cpp.

References AqueousKinetics::_update_rates_C(), 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.

getRevRateConstants():

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.

Return a vector of the reverse reaction 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.

Reimplemented from Kinetics.

Definition at line 445 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 function 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 584 of file AqueousKinetics.cpp.

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

void addReaction ( ReactionData & r )

virtual

Add a reaction to the mechanism.

Reimplemented from Kinetics.

Definition at line 469 of file AqueousKinetics.cpp.

References Cantera::ELEMENTARY_RXN, and Kinetics::incrementRxnCount().

void finalize ( )

virtual

Finish adding reactions and prepare for use.

This method is called by function 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 593 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 610 of file AqueousKinetics.cpp.

void update_T ( )

virtual

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

Definition at line 117 of file AqueousKinetics.cpp.

void _update_rates_C ( )

Update properties that depend on concentrations.

Currently only the enhanced collision partner concentrations are updated here.

Definition at line 139 of file AqueousKinetics.cpp.

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

Referenced by AqueousKinetics::getFwdRateConstants().

void updateKc ( )

private

Update the equilibrium constants in molar units.

Definition at line 149 of file AqueousKinetics.cpp.

References Cantera::GasConstant, ReactionStoichMgr::getRevReactionDelta(), ThermoPhase::getStandardChemPotentials(), ThermoPhase::logStandardConc(), Kinetics::m_ii, Phase::nSpecies(), Phase::temperature(), and Kinetics::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 void getDeltaElectrochemPotentials ( doublereal * deltaM )

inlinevirtualinherited

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 in InterfaceKinetics.

Definition at line 575 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 void getActivityConcentrations ( doublereal *const conc )

inlinevirtualinherited

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 in InterfaceKinetics.

Definition at line 760 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().

virtual void getActivationEnergies ( doublereal * E )

inlinevirtualinherited

Return the activation energies in Kelvin.

length is the number of reactions

Parameters

E	Ouptut vector of activation energies. Length: m_ii.

Reimplemented in InterfaceKinetics.

Definition at line 859 of file Kinetics.h.

References Kinetics::err().

void addPhase ( thermo_t & thermo )

virtualinherited

Add a phase to the kinetics manager object.

This must be done before the function init() is called or before any reactions are input. The following fields are updated: m_start -> vector of integers, containing the starting position of the species for each phase in the kinetics mechanism. m_surfphase -> index of the surface phase. m_thermo -> vector of pointers to ThermoPhase phases that participate in the kinetics mechanism. m_phaseindex -> map containing the std::string id of each ThermoPhase phase as a key and the index of the phase within the kinetics manager object as the value.

Parameters

thermo Reference to the ThermoPhase to be added.

Reimplemented in InterfaceKinetics.

Definition at line 365 of file Kinetics.cpp.

References Cantera::cEdge, Cantera::cSurf, ThermoPhase::eosType(), Kinetics::m_mindim, Kinetics::m_phaseindex, Kinetics::m_rxnphase, Kinetics::m_start, Kinetics::m_surfphase, Kinetics::m_thermo, Phase::nDim(), Kinetics::nPhases(), and Kinetics::type().

Referenced by InterfaceKinetics::addPhase(), AqueousKinetics::AqueousKinetics(), GasKinetics::GasKinetics(), and Cantera::importKinetics().

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_dn

protected

Difference between the input global reactants order and the input global products order.

Changed to a double to account for the fact that we can have real-valued stoichiometries.

Definition at line 367 of file AqueousKinetics.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