Public interface for kinetics managers. More...

#include <Kinetics.h>

Inheritance diagram for Kinetics:

Collaboration diagram for Kinetics:

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

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

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

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

Constructors and General Information about Mechanism
	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 Kinetics *	duplMyselfAsKinetics (const std::vector< thermo_t * > &tpVector) const
	Duplication routine for objects which inherit from Kinetics. 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...

Information/Lookup Functions about Phases and Species
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...

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

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

Reaction Mechanism Informational Query Routines
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...

virtual bool	isReversible (size_t i)
	True if reaction i has been declared to be reversible. 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	getRevRateConstants (doublereal *krev, bool doIrreversible=false)
	Return the reverse rate constants. More...

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

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

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

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

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

Protected Member Functions
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
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

Stoichiometry management
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...

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

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

Detailed Description

Public interface for kinetics managers.

This class serves as a base class to derive 'kinetics managers', which are classes that manage homogeneous chemistry within one phase, or heterogeneous chemistry at one interface. The virtual methods of this class are meant to be overloaded in subclasses. The non-virtual methods perform generic functions and are implemented in Kinetics. They should not be overloaded. Only those methods required by a subclass need to be overloaded; the rest will throw exceptions if called.

When the nomenclature "kinetics species index" is used below, this means that the species index ranges over all species in all phases handled by the kinetics manager.

Definition at line 128 of file Kinetics.h.

Constructor & Destructor Documentation

Kinetics ( )

Default constructor.

Definition at line 19 of file Kinetics.cpp.

Referenced by Kinetics::duplMyselfAsKinetics().

~Kinetics ( )

virtual

Destructor.

Definition at line 31 of file Kinetics.cpp.

Kinetics ( const Kinetics & right )

Copy Constructor for the Kinetics object.

Definition at line 33 of file Kinetics.cpp.

Member Function Documentation

Kinetics & operator= ( const Kinetics & right )

Assignment operator.

Parameters

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

Definition at line 41 of file Kinetics.cpp.

References Kinetics::m_ii, Kinetics::m_irrevProductStoich, Kinetics::m_kk, Kinetics::m_mindim, Kinetics::m_perturb, Kinetics::m_phaseindex, Kinetics::m_products, Kinetics::m_productStrings, Kinetics::m_prxn, Kinetics::m_reactants, Kinetics::m_reactantStoich, Kinetics::m_reactantStrings, Kinetics::m_reactions, Kinetics::m_revProductStoich, Kinetics::m_rfn, Kinetics::m_rkcn, Kinetics::m_ropf, Kinetics::m_ropnet, Kinetics::m_ropr, Kinetics::m_rrxn, Kinetics::m_rxneqn, Kinetics::m_rxnphase, Kinetics::m_skipUndeclaredSpecies, Kinetics::m_start, Kinetics::m_surfphase, and Kinetics::m_thermo.

Referenced by InterfaceKinetics::operator=().

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 in InterfaceKinetics, ElectrodeKinetics, AqueousKinetics, EdgeKinetics, GasKinetics, and BulkKinetics.

Definition at line 85 of file Kinetics.cpp.

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

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

virtual

Reassign the pointers within the Kinetics object.

This type or routine is 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:

Parameters

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

Definition at line 140 of file Kinetics.cpp.

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

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

int type ( ) const

virtual

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 in InterfaceKinetics, ElectrodeKinetics, EdgeKinetics, AqueousKinetics, and GasKinetics.

Definition at line 93 of file Kinetics.cpp.

Referenced by Kinetics::addPhase().

size_t nReactions ( ) const

inline

Number of reactions in the reaction mechanism.

Definition at line 193 of file Kinetics.h.

References Kinetics::m_ii.

Referenced by BulkKinetics::addReaction(), InterfaceKinetics::addReaction(), Kinetics::addReaction(), Reactor::addSensitivityReaction(), ExtraGlobalRxn::ExtraGlobalRxn(), InterfaceKinetics::getFwdRateConstants(), InterfaceKinetics::getRevRateConstants(), RxnMolChange::RxnMolChange(), and InterfaceKinetics::updateKc().

void checkReactionIndex ( size_t m ) const

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

Definition at line 98 of file Kinetics.cpp.

References Kinetics::m_ii.

Referenced by Kinetics::modifyReaction(), and Kinetics::reaction().

void checkReactionArraySize ( size_t ii ) const

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 105 of file Kinetics.cpp.

References Kinetics::m_ii.

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.

Definition at line 126 of file Kinetics.cpp.

References Kinetics::m_kk.

void checkSpeciesArraySize ( size_t mm ) const

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 133 of file Kinetics.cpp.

References Kinetics::m_kk.

size_t nPhases ( ) const

inline

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 225 of file Kinetics.h.

References Kinetics::m_thermo.

void checkPhaseIndex ( size_t m ) const

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

Definition at line 112 of file Kinetics.cpp.

References Kinetics::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().

Used before calls which take an array pointer.

Definition at line 119 of file Kinetics.cpp.

References Kinetics::nPhases().

size_t phaseIndex ( const std::string & ph )

inline

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 247 of file Kinetics.h.

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

Referenced by Cantera::importKinetics().

size_t surfacePhaseIndex ( )

inline

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 260 of file Kinetics.h.

References Kinetics::m_surfphase.

Referenced by InterfaceKinetics::_update_rates_T(), InterfaceKinetics::buildSurfaceArrhenius(), solveSP::calc_t(), Reactor::evalSurfaces(), solveSP::fun_eval(), Cantera::getRateCoefficient(), solveProb::print_header(), Wall::setKinetics(), and solveSP::solveSP().

size_t reactionPhaseIndex ( )

inline

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 272 of file Kinetics.h.

References Kinetics::m_rxnphase.

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

thermo_t& thermo ( size_t n = 0 )

inline

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 285 of file Kinetics.h.

References Kinetics::m_thermo.

size_t nTotalSpecies ( ) const

inline

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 297 of file Kinetics.h.

References Kinetics::m_kk.

Referenced by InterfaceKinetics::addReaction(), Kinetics::checkDuplicates(), ExtraGlobalRxn::ExtraGlobalRxn(), ReactingSurf1D::init(), and RxnMolChange::RxnMolChange().

size_t kineticsSpeciesIndex	(	size_t	k,
		size_t	n
	)		const

inline

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 323 of file Kinetics.h.

References Kinetics::m_start.

Referenced by InterfaceKinetics::addReaction(), Kinetics::addReaction(), InterfaceKinetics::buildSurfaceArrhenius(), solveSP::calc_t(), Kinetics::checkDuplicates(), Cantera::checkRxnElementBalance(), ReactingSurf1D::eval(), Reactor::evalSurfaces(), solveSP::fun_eval(), Cantera::getEfficiencies(), Cantera::getReagents(), Cantera::getStick(), Kinetics::kineticsSpeciesIndex(), RxnMolChange::RxnMolChange(), solveSP::solveSP(), and solveSP::updateMFKinSpecies().

string kineticsSpeciesName ( size_t k ) const

Return the 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.

Parameters

k	species index

Definition at line 359 of file Kinetics.cpp.

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

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

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

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 369 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

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 382 of file Kinetics.cpp.

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

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.

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

Parameters

nm	String containing the name of the species.

Definition at line 402 of file Kinetics.cpp.

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

Referenced by Kinetics::checkReactionBalance(), Cantera::checkRxnElementBalance(), Cantera::getStick(), and ElectrodeKinetics::updateROP().

thermo_t& speciesPhase ( size_t k )

inline

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 382 of file Kinetics.h.

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

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.

Parameters

k	Species index

Definition at line 417 of file Kinetics.cpp.

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

Referenced by InterfaceKinetics::addReaction(), InterfaceKinetics::buildSurfaceArrhenius(), Cantera::checkRxnElementBalance(), Cantera::getStick(), RxnMolChange::RxnMolChange(), Kinetics::speciesPhase(), and ElectrodeKinetics::updateROP().

void getFwdRatesOfProgress ( doublereal * fwdROP )

virtual

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.

Definition at line 438 of file Kinetics.cpp.

References Kinetics::m_ropf.

void getRevRatesOfProgress ( doublereal * revROP )

virtual

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.

Definition at line 444 of file Kinetics.cpp.

References Kinetics::m_ropr.

void getNetRatesOfProgress ( doublereal * netROP )

virtual

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.

Definition at line 450 of file Kinetics.cpp.

References Kinetics::m_ropnet.

virtual void getEquilibriumConstants ( doublereal * kc )

inlinevirtual

Return a vector of Equilibrium constants.

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

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

Parameters

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

Reimplemented in InterfaceKinetics, GasKinetics, and AqueousKinetics.

Definition at line 442 of file Kinetics.h.

Referenced by BulkKinetics::getRevRateConstants().

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

virtual

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 456 of file Kinetics.cpp.

References Kinetics::m_ii, Kinetics::m_irrevProductStoich, Kinetics::m_reactantStoich, and Kinetics::m_revProductStoich.

Referenced by InterfaceKinetics::applyVoltageKfwdCorrection(), InterfaceKinetics::getDeltaElectrochemPotentials(), BulkKinetics::getDeltaEnthalpy(), InterfaceKinetics::getDeltaEnthalpy(), BulkKinetics::getDeltaEntropy(), InterfaceKinetics::getDeltaEntropy(), BulkKinetics::getDeltaGibbs(), InterfaceKinetics::getDeltaGibbs(), BulkKinetics::getDeltaSSEnthalpy(), InterfaceKinetics::getDeltaSSEnthalpy(), BulkKinetics::getDeltaSSEntropy(), InterfaceKinetics::getDeltaSSEntropy(), BulkKinetics::getDeltaSSGibbs(), InterfaceKinetics::getDeltaSSGibbs(), AqueousKinetics::getEquilibriumConstants(), GasKinetics::getEquilibriumConstants(), InterfaceKinetics::getEquilibriumConstants(), and InterfaceKinetics::updateExchangeCurrentQuantities().

void getRevReactionDelta	(	const doublereal *	g,
		doublereal *	dg
	)

virtual

Given an array of species properties 'g', return in array 'dg' the change in this quantity in the reversible reactions.

Array 'g' must have a length at least as great as the number of species, and array 'dg' must have a length as great as the total number of reactions. This method only computes 'dg' for the reversible reactions, and the entries of 'dg' for the irreversible reactions are unaltered. This is primarily designed for use in calculating reverse rate coefficients from thermochemistry for reversible reactions.

Definition at line 466 of file Kinetics.cpp.

References Kinetics::m_ii, Kinetics::m_reactantStoich, and Kinetics::m_revProductStoich.

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

virtual void getDeltaGibbs ( doublereal * deltaG )

inlinevirtual

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 in InterfaceKinetics, and BulkKinetics.

Definition at line 486 of file Kinetics.h.

virtual void getDeltaElectrochemPotentials ( doublereal * deltaM )

inlinevirtual

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 500 of file Kinetics.h.

virtual void getDeltaEnthalpy ( doublereal * deltaH )

inlinevirtual

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 in InterfaceKinetics, and BulkKinetics.

Definition at line 512 of file Kinetics.h.

virtual void getDeltaEntropy ( doublereal * deltaS )

inlinevirtual

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 in InterfaceKinetics, and BulkKinetics.

Definition at line 524 of file Kinetics.h.

virtual void getDeltaSSGibbs ( doublereal * deltaG )

inlinevirtual

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 in InterfaceKinetics, and BulkKinetics.

Definition at line 537 of file Kinetics.h.

virtual void getDeltaSSEnthalpy ( doublereal * deltaH )

inlinevirtual

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 in InterfaceKinetics, and BulkKinetics.

Definition at line 550 of file Kinetics.h.

virtual void getDeltaSSEntropy ( doublereal * deltaS )

inlinevirtual

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 in InterfaceKinetics, and BulkKinetics.

Definition at line 563 of file Kinetics.h.

void getCreationRates ( doublereal * cdot )

virtual

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.

Definition at line 475 of file Kinetics.cpp.

References Kinetics::m_irrevProductStoich, Kinetics::m_kk, Kinetics::m_reactantStoich, Kinetics::m_revProductStoich, Kinetics::m_ropf, and Kinetics::m_ropr.

void getDestructionRates ( doublereal * ddot )

virtual

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.

Definition at line 490 of file Kinetics.cpp.

References Kinetics::m_kk, Kinetics::m_reactantStoich, Kinetics::m_revProductStoich, Kinetics::m_ropf, and Kinetics::m_ropr.

void getNetProductionRates ( doublereal * wdot )

virtual

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.

Definition at line 501 of file Kinetics.cpp.

References Kinetics::m_irrevProductStoich, Kinetics::m_kk, Kinetics::m_reactantStoich, Kinetics::m_revProductStoich, and Kinetics::m_ropnet.

Referenced by solveSP::calc_t(), ReactingSurf1D::eval(), FlowReactor::evalEqs(), Reactor::evalEqs(), Reactor::evalSurfaces(), solveSP::fun_eval(), StFlow::getWdot(), solveProb::print_header(), and solveProb::printIteration().

double reactantStoichCoeff	(	size_t	k,
		size_t	i
	)		const

virtual

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

Parameters

k	kinetic species index
i	reaction index

Definition at line 428 of file Kinetics.cpp.

References Cantera::getValue(), and Kinetics::m_rrxn.

Referenced by RxnMolChange::RxnMolChange().

double productStoichCoeff	(	size_t	k,
		size_t	i
	)		const

virtual

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

Parameters

k	kinetic species index
i	reaction index

Definition at line 433 of file Kinetics.cpp.

References Cantera::getValue(), and Kinetics::m_prxn.

Referenced by RxnMolChange::RxnMolChange().

virtual doublereal reactantOrder	(	size_t	k,
		size_t	i
	)		const

inlinevirtual

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 626 of file Kinetics.h.

virtual doublereal productOrder	(	int	k,
		int	i
	)		const

inlinevirtual

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 640 of file Kinetics.h.

virtual void getActivityConcentrations ( doublereal *const conc )

inlinevirtual

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

Parameters

[out] conc Vector of activity concentrations. Length is equal to the number of species in the kinetics object

Reimplemented in InterfaceKinetics.

Definition at line 649 of file Kinetics.h.

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

inlinevirtual

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

Parameters

i	reaction index

Deprecated:: To be removed after Cantera 2.2.

Definition at line 660 of file Kinetics.h.

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

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

inlinevirtual

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

Parameters

i	reaction index

Deprecated:: To be removed after Cantera 2.2.

Definition at line 673 of file Kinetics.h.

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

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

Definition at line 686 of file Kinetics.h.

Referenced by InterfaceKinetics::addReaction(), ElectrodeKinetics::updateROP(), and InterfaceKinetics::updateROP().

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 in InterfaceKinetics, and BulkKinetics.

Definition at line 697 of file Kinetics.h.

const std::string& reactionString ( size_t i ) const

inline

Return a string representing the reaction.

Parameters

i	reaction index

Definition at line 706 of file Kinetics.h.

References Kinetics::m_rxneqn.

Referenced by Reactor::addSensitivityReaction().

const std::string& reactantString ( size_t i ) const

inline

Returns a string containing the reactants side of the reaction equation.

Definition at line 711 of file Kinetics.h.

References Kinetics::m_reactantStrings.

const std::string& productString ( size_t i ) const

inline

Returns a string containing the products side of the reaction equation.

Definition at line 716 of file Kinetics.h.

References Kinetics::m_productStrings.

virtual void getFwdRateConstants ( doublereal * kfwd )

inlinevirtual

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 in InterfaceKinetics, GasKinetics, and AqueousKinetics.

Definition at line 728 of file Kinetics.h.

Referenced by BulkKinetics::getRevRateConstants().

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

inlinevirtual

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 in InterfaceKinetics, and BulkKinetics.

Definition at line 743 of file Kinetics.h.

void addPhase ( thermo_t & thermo )

virtual

Add a phase to the kinetics manager object.

This must be done before the function init() is called or before any reactions are input. 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 513 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(), and Cantera::importKinetics().

virtual void init ( )

inlinevirtual

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 in InterfaceKinetics, ElectrodeKinetics, GasKinetics, and BulkKinetics.

Definition at line 778 of file Kinetics.h.

Referenced by Cantera::importKinetics().

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 in InterfaceKinetics, ElectrodeKinetics, GasKinetics, EdgeKinetics, and BulkKinetics.

Definition at line 548 of file Kinetics.cpp.

References Kinetics::m_kk, Kinetics::m_thermo, and Kinetics::nPhases().

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

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 in InterfaceKinetics, AqueousKinetics, GasKinetics, and BulkKinetics.

Definition at line 557 of file Kinetics.cpp.

References ReactionData::equation, ReactionData::forwardFullOrder_, Kinetics::incrementRxnCount(), Kinetics::m_ii, Kinetics::m_irrevProductStoich, Kinetics::m_products, Kinetics::m_productStrings, Kinetics::m_prxn, Kinetics::m_reactants, Kinetics::m_reactantStoich, Kinetics::m_reactantStrings, Kinetics::m_revProductStoich, Kinetics::m_rfn, Kinetics::m_rkcn, Kinetics::m_ropf, Kinetics::m_ropnet, Kinetics::m_ropr, Kinetics::m_rrxn, Kinetics::m_rxneqn, Kinetics::nReactions(), ReactionData::pgroups, ReactionData::porder, ReactionData::products, ReactionData::productString, ReactionData::pstoich, ReactionData::reactants, ReactionData::reactantString, ReactionData::reactionType, ReactionData::reversible, ReactionData::rgroups, ReactionData::rorder, and ReactionData::rstoich.

Referenced by BulkKinetics::addReaction(), InterfaceKinetics::addReaction(), and Cantera::installReactionArrays().

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 in InterfaceKinetics, AqueousKinetics, GasKinetics, and BulkKinetics.

Definition at line 656 of file Kinetics.cpp.

References Kinetics::checkReactionBalance(), Kinetics::incrementRxnCount(), Kinetics::kineticsSpeciesIndex(), Kinetics::m_irrevProductStoich, Kinetics::m_products, Kinetics::m_productStrings, Kinetics::m_prxn, Kinetics::m_reactants, Kinetics::m_reactantStoich, Kinetics::m_reactantStrings, Kinetics::m_reactions, Kinetics::m_revProductStoich, Kinetics::m_rfn, Kinetics::m_rkcn, Kinetics::m_ropf, Kinetics::m_ropnet, Kinetics::m_ropr, Kinetics::m_rrxn, Kinetics::m_rxneqn, Kinetics::m_skipUndeclaredSpecies, Cantera::npos, and Kinetics::nReactions().

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

virtual

Modify the rate expression associated with a reaction.

The stoichiometric equation, type of the reaction, reaction orders, third body efficiencies, reversibility, etc. must be unchanged.

Parameters

i	Index of the reaction to be modified
rNew	Reaction with the new rate expressions

Reimplemented in InterfaceKinetics, AqueousKinetics, and GasKinetics.

Definition at line 773 of file Kinetics.cpp.

References Kinetics::checkReactionIndex(), Cantera::int2str(), and Kinetics::m_reactions.

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

shared_ptr< Reaction > reaction ( size_t i )

Return the Reaction object for reaction i.

Definition at line 797 of file Kinetics.cpp.

References Kinetics::checkReactionIndex(), and Kinetics::m_reactions.

void skipUndeclaredSpecies ( bool skip )

inline

Determine behavior when adding a new reaction that contains species not defined in any of the phases associated with this kinetics manager.

If set to true, the reaction will silently be ignored. If false, (the default) an exception will be raised.

Definition at line 829 of file Kinetics.h.

References Kinetics::m_skipUndeclaredSpecies.

Referenced by Cantera::installReactionArrays().

void skipUndeclaredThirdBodies ( bool skip )

inline

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.

If set to true, the given third-body efficiency will be ignored. If false, (the default) an exception will be raised.

Definition at line 838 of file Kinetics.h.

References Kinetics::m_skipUndeclaredThirdBodies.

Referenced by Cantera::installReactionArrays().

virtual void installReagents ( const ReactionData & r )

inlinevirtual

Deprecated:: To be removed after Cantera 2.2. No longer called as part of addReaction.

Definition at line 844 of file Kinetics.h.

doublereal multiplier ( size_t i ) const

inline

The current value of the multiplier for reaction i.

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.

Parameters

i	index of the reaction

Definition at line 875 of file Kinetics.h.

References Kinetics::m_perturb.

Referenced by Reactor::applySensitivity(), FlowReactor::evalEqs(), and Reactor::resetSensitivity().

virtual void setMultiplier	(	size_t	i,
		doublereal	f
	)

inlinevirtual

Set the multiplier for reaction i to f.

Parameters

i	index of the reaction
f	value of the multiplier.

Reimplemented in BulkKinetics.

Definition at line 884 of file Kinetics.h.

References Kinetics::m_perturb.

Referenced by Reactor::applySensitivity(), FlowReactor::evalEqs(), Reactor::resetSensitivity(), and BulkKinetics::setMultiplier().

void incrementRxnCount ( )

inline

Increment the number of reactions in the mechanism by one.

Todo:: Should be protected?

Definition at line 894 of file Kinetics.h.

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

Referenced by Kinetics::addReaction().

virtual bool ready ( ) const

inlinevirtual

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

Reimplemented in InterfaceKinetics, Interface, GasKinetics, IdealGasMix, BulkKinetics, and Edge.

Definition at line 903 of file Kinetics.h.

std::pair< size_t, size_t > checkDuplicates ( bool throw_err = true ) const

virtual

Check for duplicate reactions.

If throw_err is true, then an exception will be thrown if any unmarked duplicate reactions are found. Otherwise, the indices of the first pair of duplicate reactions found will be returned. If no duplicate reactions are found, returns (npos, npos).

Definition at line 168 of file Kinetics.cpp.

References Kinetics::checkDuplicateStoich(), Cantera::CHEMACT_RXN, Reaction::duplicate, ThirdBody::efficiency(), Reaction::equation(), Cantera::FALLOFF_RXN, Cantera::int2str(), Kinetics::kineticsSpeciesIndex(), Kinetics::kineticsSpeciesName(), Kinetics::m_reactions, Cantera::npos, Kinetics::nTotalSpecies(), Reaction::products, Reaction::reactants, Reaction::reaction_type, Reaction::reversible, and Cantera::THREE_BODY_RXN.

Referenced by Cantera::installReactionArrays().

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

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

Parameters

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 345 of file Kinetics.cpp.

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

void checkReactionBalance ( const Reaction & R )

protected

Check that the specified reaction is balanced (same number of atoms for each element in the reactants and products).

Raises an exception if the reaction is not balanced.

Definition at line 298 of file Kinetics.cpp.

References Phase::elementName(), Reaction::equation(), Cantera::fp2str(), Phase::nAtoms(), Phase::nElements(), Reaction::products, Reaction::reactants, Phase::speciesIndex(), and Kinetics::speciesPhase().

Referenced by Kinetics::addReaction().

Member Data Documentation

ValueCache m_cache

protected

Cache for saved calculations within each Kinetics object.

Definition at line 931 of file Kinetics.h.

StoichManagerN m_reactantStoich

protected

Stoichiometry manager for the reactants for each reaction.

These objects and functions handle turning reaction extents into species production rates and also handle turning thermo properties into reaction thermo properties.

Definition at line 968 of file Kinetics.h.

Referenced by Kinetics::addReaction(), Kinetics::getCreationRates(), Kinetics::getDestructionRates(), Kinetics::getNetProductionRates(), Kinetics::getReactionDelta(), Kinetics::getRevReactionDelta(), Kinetics::operator=(), InterfaceKinetics::updateExchangeCurrentQuantities(), ElectrodeKinetics::updateROP(), and InterfaceKinetics::updateROP().

StoichManagerN m_revProductStoich

protected

Stoichiometry manager for the products of reversible reactions.

Definition at line 971 of file Kinetics.h.

Referenced by Kinetics::addReaction(), Kinetics::getCreationRates(), Kinetics::getDestructionRates(), Kinetics::getNetProductionRates(), Kinetics::getReactionDelta(), Kinetics::getRevReactionDelta(), Kinetics::operator=(), ElectrodeKinetics::updateROP(), and InterfaceKinetics::updateROP().

StoichManagerN m_irrevProductStoich

protected

Stoichiometry manager for the products of irreversible reactions.

Definition at line 974 of file Kinetics.h.

Referenced by Kinetics::addReaction(), Kinetics::getCreationRates(), Kinetics::getNetProductionRates(), Kinetics::getReactionDelta(), and Kinetics::operator=().

size_t m_ii

protected

Number of reactions in the mechanism.

Definition at line 978 of file Kinetics.h.

Referenced by InterfaceKinetics::addReaction(), Kinetics::addReaction(), Kinetics::checkReactionArraySize(), Kinetics::checkReactionIndex(), BulkKinetics::finalize(), EdgeKinetics::finalize(), ElectrodeKinetics::finalize(), InterfaceKinetics::finalize(), InterfaceKinetics::getDeltaGibbs(), AqueousKinetics::getEquilibriumConstants(), GasKinetics::getEquilibriumConstants(), InterfaceKinetics::getEquilibriumConstants(), AqueousKinetics::getFwdRateConstants(), GasKinetics::getFwdRateConstants(), Kinetics::getReactionDelta(), BulkKinetics::getRevRateConstants(), InterfaceKinetics::getRevRateConstants(), Kinetics::getRevReactionDelta(), Kinetics::incrementRxnCount(), Kinetics::nReactions(), ElectrodeKinetics::operator=(), Kinetics::operator=(), InterfaceKinetics::reactionNumber(), InterfaceKinetics::updateExchangeCurrentQuantities(), ElectrodeKinetics::updateROP(), and InterfaceKinetics::updateROP().

size_t m_kk

protected

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

Definition at line 982 of file Kinetics.h.

Referenced by InterfaceKinetics::addReaction(), Kinetics::checkSpeciesArraySize(), Kinetics::checkSpeciesIndex(), EdgeKinetics::finalize(), InterfaceKinetics::finalize(), Kinetics::finalize(), Kinetics::getCreationRates(), BulkKinetics::getDeltaSSEnthalpy(), InterfaceKinetics::getDeltaSSEnthalpy(), BulkKinetics::getDeltaSSEntropy(), InterfaceKinetics::getDeltaSSEntropy(), Kinetics::getDestructionRates(), Kinetics::getNetProductionRates(), BulkKinetics::init(), InterfaceKinetics::init(), Kinetics::nTotalSpecies(), and Kinetics::operator=().

vector_fp m_perturb

protected

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

It is initialized to one.

Definition at line 986 of file Kinetics.h.

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

std::vector<shared_ptr<Reaction> > m_reactions

protected

Vector of Reaction objects represented by this Kinetics manager.

Definition at line 989 of file Kinetics.h.

Referenced by Kinetics::addReaction(), Kinetics::checkDuplicates(), Kinetics::modifyReaction(), Kinetics::operator=(), and Kinetics::reaction().

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

protected

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.

Deprecated:: To be removed after Cantera 2.2.

Definition at line 1003 of file Kinetics.h.

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

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

protected

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.

Deprecated:: To be removed after Cantera 2.2.

Definition at line 1017 of file Kinetics.h.

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

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

protected

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

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

Definition at line 1027 of file Kinetics.h.

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

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

protected

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

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

Definition at line 1037 of file Kinetics.h.

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

std::vector<thermo_t*> m_thermo

protected

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 1056 of file Kinetics.h.

Referenced by InterfaceKinetics::_update_rates_C(), Kinetics::addPhase(), Kinetics::assignShallowPointers(), EdgeKinetics::finalize(), InterfaceKinetics::finalize(), Kinetics::finalize(), InterfaceKinetics::getDeltaGibbs(), ElectrodeKinetics::identifyMetalPhase(), Kinetics::kineticsSpeciesIndex(), Kinetics::nPhases(), Kinetics::operator=(), InterfaceKinetics::phaseExistence(), InterfaceKinetics::phaseStability(), Kinetics::selectPhase(), InterfaceKinetics::setPhaseExistence(), InterfaceKinetics::setPhaseStability(), Kinetics::speciesPhase(), and Kinetics::thermo().

std::vector<size_t> m_start

protected

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 1063 of file Kinetics.h.

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

protected

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 1073 of file Kinetics.h.

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

size_t m_surfphase

protected

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

Definition at line 1076 of file Kinetics.h.

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

size_t m_rxnphase

protected

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.

Definition at line 1083 of file Kinetics.h.