Partial specialization of Kinetics for chemistry in a single bulk phase. More...

#include <BulkKinetics.h>

Inheritance diagram for BulkKinetics:

Collaboration diagram for BulkKinetics:

Public Member Functions
	BulkKinetics (thermo_t *thermo=0)

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

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

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

virtual void	init ()
	Prepare the class for the addition of reactions. 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	setMultiplier (size_t i, double f)
	Set the multiplier for reaction i to f. More...

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

virtual int	type () const
	Identifies the kinetics manager type. 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	getEquilibriumConstants (doublereal *kc)
	Return a vector of Equilibrium constants. 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 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 int	reactionType (size_t i) const
	Flag specifying the type of reaction. More...

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

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

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

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

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

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

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

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...

virtual void	installReagents (const ReactionData &r)

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

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

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

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

Protected Member Functions
virtual void	addElementaryReaction (ReactionData &r)

virtual void	addElementaryReaction (ElementaryReaction &r)

virtual void	modifyElementaryReaction (size_t i, ElementaryReaction &rNew)

Protected Member Functions inherited from Kinetics
virtual void	updateROP ()

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
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

bool	m_finalized

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

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< shared_ptr < Reaction > >	m_reactions
	Vector of Reaction objects represented by this Kinetics manager. 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< std::map< size_t, doublereal > >	m_rrxn
	m_rrxn is a vector of maps, containing the reactant stoichiometric coefficient information More...

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

std::vector< int >	m_rxntype

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...

std::vector< std::string >	m_rxneqn
	Representation of each reaction equation. More...

std::vector< std::string >	m_reactantStrings
	Representation of the reactant side of each reaction equation. More...

std::vector< std::string >	m_productStrings
	Representation of the product side of each reaction equation. 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

Partial specialization of Kinetics for chemistry in a single bulk phase.

Definition at line 18 of file BulkKinetics.h.

Member Function Documentation

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

virtual

Duplication routine for objects which inherit from Kinetics.

This function can be used to duplicate objects derived 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 pointers to ThermoPhase objects. this is the m_thermo vector within this object

Reimplemented from Kinetics.

Reimplemented in AqueousKinetics, and GasKinetics.

Definition at line 18 of file BulkKinetics.cpp.

References Kinetics::assignShallowPointers().

bool isReversible ( size_t i )

virtual

True if reaction i has been declared to be reversible.

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

Parameters

i	reaction index

Reimplemented from Kinetics.

Definition at line 25 of file BulkKinetics.cpp.

References BulkKinetics::m_revindex.

void getDeltaGibbs ( doublereal * deltaG )

virtual

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

(virtual from Kinetics.h) These values depend upon the concentration of the solution.

units = J kmol-1

Parameters

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

Reimplemented from Kinetics.

Definition at line 35 of file BulkKinetics.cpp.

References ThermoPhase::getChemPotentials(), Kinetics::getReactionDelta(), 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 43 of file BulkKinetics.cpp.

References ThermoPhase::getPartialMolarEnthalpies(), Kinetics::getReactionDelta(), 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 51 of file BulkKinetics.cpp.

References ThermoPhase::getPartialMolarEntropies(), Kinetics::getReactionDelta(), 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 59 of file BulkKinetics.cpp.

References Kinetics::getReactionDelta(), ThermoPhase::getStandardChemPotentials(), 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 70 of file BulkKinetics.cpp.

References Cantera::GasConstant, ThermoPhase::getEnthalpy_RT(), Kinetics::getReactionDelta(), 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 82 of file BulkKinetics.cpp.

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

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 96 of file BulkKinetics.cpp.

References Kinetics::getEquilibriumConstants(), Kinetics::getFwdRateConstants(), Kinetics::m_ii, Kinetics::m_rkcn, and Kinetics::m_ropnet.

void addReaction ( ReactionData & r )

virtual

Add a single reaction to the mechanism.

This routine must be called after init() and before finalize(). Derived classes should call the base class method in addition to handling their own specialized behavior.

Parameters

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

Reimplemented from Kinetics.

Reimplemented in AqueousKinetics, and GasKinetics.

Definition at line 118 of file BulkKinetics.cpp.

References Kinetics::addReaction(), BulkKinetics::m_dn, BulkKinetics::m_irrev, BulkKinetics::m_revindex, Kinetics::nReactions(), ReactionData::pstoich, ReactionData::reversible, and ReactionData::rstoich.

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

Reimplemented in AqueousKinetics, and GasKinetics.

Definition at line 131 of file BulkKinetics.cpp.

References Kinetics::addReaction(), BulkKinetics::m_dn, BulkKinetics::m_irrev, BulkKinetics::m_revindex, and Kinetics::nReactions().

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.

Reimplemented in GasKinetics.

Definition at line 174 of file BulkKinetics.cpp.

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

Referenced by GasKinetics::init().

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.

Reimplemented in GasKinetics.

Definition at line 183 of file BulkKinetics.cpp.

References Kinetics::m_ii, Kinetics::m_perturb, Kinetics::m_rkcn, Kinetics::m_ropf, Kinetics::m_ropnet, and Kinetics::m_ropr.

Referenced by GasKinetics::finalize().

bool ready ( ) const

virtual

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

Reimplemented from Kinetics.

Reimplemented in GasKinetics, and IdealGasMix.

Definition at line 198 of file BulkKinetics.cpp.