Kinetics Class Reference

Public interface for kinetics managers. More...

#include <Kinetics.h>

Inheritance 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...
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	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 doublereal	reactantStoichCoeff (size_t k, size_t i) const
	Stoichiometric coefficient of species k as a reactant in reaction i. More...
virtual doublereal	productStoichCoeff (size_t k, size_t i) const
	Stoichiometric coefficient of species k as a product in reaction i. More...
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...
virtual std::string	reactionString (size_t i) const
	Return a string representing the reaction. 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...
virtual void	getActivationEnergies (doublereal *E)
	Return the activation energies in Kelvin. 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 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...
void	setMultiplier (size_t i, doublereal f)
	Set the multiplier for reaction i to f. More...

Protected Attributes
size_t	m_ii
	Number of reactions in the mechanism. More...
size_t	m_kk
	The number of species in all of the phases that participate in this kinetics mechanism. More...
vector_fp	m_perturb
	Vector of perturbation factors for each reaction's rate of progress vector. More...
std::vector< std::vector < size_t > >	m_reactants
	This is a vector of vectors containing the reactants for each reaction. More...
std::vector< std::vector < size_t > >	m_products
	This is a vector of vectors containing the products for each reaction. More...
std::vector< thermo_t * >	m_thermo
	m_thermo is a vector of pointers to ThermoPhase objects that are involved with this kinetics operator More...
std::vector< size_t >	m_start
	m_start is a vector of integers specifying the beginning position for the species vector for the n'th phase in the kinetics class. More...
std::map< std::string, size_t >	m_phaseindex
	Mapping of the phase id, i.e., the id attribute in the xml phase element to the position of the phase within the kinetics object. More...
size_t	m_surfphase
	Index in the list of phases of the one surface phase. More...
size_t	m_rxnphase
	Phase Index where reactions are assumed to be taking place. More...
size_t	m_mindim
	number of spatial dimensions of lowest-dimensional phase. More...

Private Member Functions
void	err (const std::string &m) const
	Function indicating that a function inherited from the base class hasn't had a definition assigned to it. More...

Private Attributes
std::vector< grouplist_t >	m_dummygroups
	Vector of group lists. More...

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 131 of file Kinetics.h.

Constructor & Destructor Documentation

Kinetics

(

)

Default constructor.

Definition at line 23 of file Kinetics.cpp.

Referenced by Kinetics::duplMyselfAsKinetics().

~Kinetics ( )

virtual

Destructor.

Definition at line 39 of file Kinetics.cpp.

Kinetics

(

const Kinetics &

right

)

Copy Constructor for the Kinetics object.

Definition at line 41 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 62 of file Kinetics.cpp.

References Kinetics::m_dummygroups, Kinetics::m_ii, Kinetics::m_kk, Kinetics::m_mindim, Kinetics::m_perturb, Kinetics::m_phaseindex, Kinetics::m_products, Kinetics::m_reactants, Kinetics::m_rxnphase, Kinetics::m_start, Kinetics::m_surfphase, and Kinetics::m_thermo.

Referenced by GasKinetics::operator=(), and 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, AqueousKinetics, GasKinetics, and EdgeKinetics.

Definition at line 89 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:

• ThermoPhase::id()
• ThermoPhase::eosType()
• ThermoPhase::nSpecies()

Parameters

tpVector

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

Definition at line 144 of file Kinetics.cpp.

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

Referenced by EdgeKinetics::duplMyselfAsKinetics(), GasKinetics::duplMyselfAsKinetics(), AqueousKinetics::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, AqueousKinetics, GasKinetics, EdgeKinetics, and GRI_30_Kinetics.

Definition at line 97 of file Kinetics.cpp.

Referenced by Kinetics::addPhase().

size_t nReactions ( ) const

inline

Number of reactions in the reaction mechanism.

Definition at line 196 of file Kinetics.h.

References Kinetics::m_ii.

Referenced by Reactor::addSensitivityReaction(), EdgeKinetics::finalize(), InterfaceKinetics::finalize(), InterfaceKinetics::getFwdRateConstants(), InterfaceKinetics::getRevRateConstants(), 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 102 of file Kinetics.cpp.

References Kinetics::m_ii.

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 109 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 130 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 137 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 228 of file Kinetics.h.

References Kinetics::m_thermo.

Referenced by InterfaceKinetics::_update_rates_C(), InterfaceKinetics::_update_rates_phi(), Kinetics::addPhase(), InterfaceKinetics::addReaction(), InterfaceKinetics::applyButlerVolmerCorrection(), Kinetics::checkPhaseArraySize(), Kinetics::checkPhaseIndex(), Kinetics::finalize(), InterfaceKinetics::getDeltaElectrochemPotentials(), InterfaceKinetics::getDeltaEnthalpy(), InterfaceKinetics::getDeltaEntropy(), InterfaceKinetics::getDeltaGibbs(), InterfaceKinetics::getDeltaSSEnthalpy(), InterfaceKinetics::getDeltaSSEntropy(), InterfaceKinetics::getDeltaSSGibbs(), InterfaceKinetics::getEquilibriumConstants(), ImplicitSurfChem::ImplicitSurfChem(), InterfaceKinetics::init(), Kinetics::nTotalSpecies(), solveProb::print_header(), Kinetics::selectPhase(), InterfaceKinetics::updateKc(), solveSP::updateMFKinSpecies(), and InterfaceKinetics::updateROP().

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 116 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 123 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 250 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 263 of file Kinetics.h.

References Kinetics::m_surfphase.

Referenced by InterfaceKinetics::_update_rates_T(), solveSP::calc_t(), ConstPressureReactor::evalEqs(), IdealGasReactor::evalEqs(), IdealGasConstPressureReactor::evalEqs(), Reactor::evalEqs(), 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 275 of file Kinetics.h.

References Kinetics::m_rxnphase.

Referenced by 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 288 of file Kinetics.h.

References Kinetics::m_thermo.

Referenced by AqueousKinetics::_update_rates_C(), InterfaceKinetics::_update_rates_C(), InterfaceKinetics::_update_rates_phi(), AqueousKinetics::_update_rates_T(), InterfaceKinetics::_update_rates_T(), InterfaceKinetics::applyButlerVolmerCorrection(), InterfaceKinetics::applyExchangeCurrentDensityFormulation(), solveSP::calc_t(), EdgeKinetics::finalize(), InterfaceKinetics::finalize(), InterfaceKinetics::getDeltaElectrochemPotentials(), GasKinetics::getDeltaEnthalpy(), AqueousKinetics::getDeltaEnthalpy(), InterfaceKinetics::getDeltaEnthalpy(), GasKinetics::getDeltaEntropy(), AqueousKinetics::getDeltaEntropy(), InterfaceKinetics::getDeltaEntropy(), GasKinetics::getDeltaGibbs(), AqueousKinetics::getDeltaGibbs(), InterfaceKinetics::getDeltaGibbs(), GasKinetics::getDeltaSSEnthalpy(), AqueousKinetics::getDeltaSSEnthalpy(), InterfaceKinetics::getDeltaSSEnthalpy(), GasKinetics::getDeltaSSEntropy(), AqueousKinetics::getDeltaSSEntropy(), InterfaceKinetics::getDeltaSSEntropy(), GasKinetics::getDeltaSSGibbs(), AqueousKinetics::getDeltaSSGibbs(), InterfaceKinetics::getDeltaSSGibbs(), Cantera::getEfficiencies(), GasKinetics::getEquilibriumConstants(), AqueousKinetics::getEquilibriumConstants(), InterfaceKinetics::getEquilibriumConstants(), Cantera::getRateCoefficient(), Cantera::getStick(), ImplicitSurfChem::ImplicitSurfChem(), GasKinetics::init(), AqueousKinetics::init(), InterfaceKinetics::init(), ConstPressureReactor::initialize(), Reactor::initialize(), Kinetics::kineticsSpeciesIndex(), Kinetics::kineticsSpeciesName(), Kinetics::nTotalSpecies(), solveProb::print_header(), InterfaceKinetics::setElectricPotential(), Wall::setKinetics(), ImplicitSurfChem::solvePseudoSteadyStateProblem(), solveSP::solveSP(), Kinetics::speciesPhase(), GasKinetics::update_rates_C(), GasKinetics::update_rates_T(), GasKinetics::updateKc(), AqueousKinetics::updateKc(), InterfaceKinetics::updateKc(), and solveSP::updateMFKinSpecies().

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 300 of file Kinetics.h.

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

Referenced by ReactingSurf1D::init(), and rxninfo::installReaction().

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 331 of file Kinetics.h.

References Kinetics::m_start.

Referenced by solveSP::calc_t(), Cantera::checkRxnElementBalance(), ReactingSurf1D::eval(), ConstPressureReactor::evalEqs(), IdealGasReactor::evalEqs(), IdealGasConstPressureReactor::evalEqs(), Reactor::evalEqs(), solveSP::fun_eval(), Cantera::getEfficiencies(), Cantera::getReagents(), Cantera::getStick(), Kinetics::kineticsSpeciesIndex(), 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 186 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().

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 196 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 209 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 229 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 )

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 390 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 244 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 getFwdRatesOfProgress ( doublereal *  fwdROP )

inlinevirtual

Return the forward rates of progress of the reactions.

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

Parameters

fwdROP

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

Reimplemented in InterfaceKinetics, AqueousKinetics, and GasKinetics.

Definition at line 416 of file Kinetics.h.

References Kinetics::err().

virtual void getRevRatesOfProgress ( doublereal *  revROP )

inlinevirtual

Return the Reverse rates of progress of the reactions.

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

Parameters

revROP

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

Reimplemented in InterfaceKinetics, AqueousKinetics, and GasKinetics.

Definition at line 428 of file Kinetics.h.

References Kinetics::err().

virtual void getNetRatesOfProgress ( doublereal *  netROP )

inlinevirtual

Net rates of progress.

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

Parameters

netROP

Output vector of the net ROP. Length: m_ii.

Reimplemented in InterfaceKinetics, AqueousKinetics, and GasKinetics.

Definition at line 439 of file Kinetics.h.

References Kinetics::err().

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.

Parameters

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

Reimplemented in InterfaceKinetics, AqueousKinetics, and GasKinetics.

Definition at line 452 of file Kinetics.h.

References Kinetics::err().

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

inlinevirtual

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 472 of file Kinetics.h.

References Kinetics::err().

virtual void getDeltaGibbs ( doublereal *  deltaG )

inlinevirtual

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

These values depend upon the concentration of the solution.

units = J kmol-1

Parameters

deltaG

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

Reimplemented in InterfaceKinetics, AqueousKinetics, and GasKinetics.

Definition at line 485 of file Kinetics.h.

References Kinetics::err().

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 499 of file Kinetics.h.

References Kinetics::err().

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, AqueousKinetics, and GasKinetics.

Definition at line 511 of file Kinetics.h.

References Kinetics::err().

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, AqueousKinetics, and GasKinetics.

Definition at line 523 of file Kinetics.h.

References Kinetics::err().

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, AqueousKinetics, and GasKinetics.

Definition at line 536 of file Kinetics.h.

References Kinetics::err().

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, AqueousKinetics, and GasKinetics.

Definition at line 549 of file Kinetics.h.

References Kinetics::err().

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, AqueousKinetics, and GasKinetics.

Definition at line 562 of file Kinetics.h.

References Kinetics::err().

virtual void getCreationRates ( doublereal *  cdot )

inlinevirtual

Species creation rates [kmol/m^3/s or kmol/m^2/s].

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

See Also

nTotalSpecies.

Parameters

cdot	Output vector of creation rates. Length: m_kk.

Reimplemented in InterfaceKinetics, AqueousKinetics, and GasKinetics.

Definition at line 577 of file Kinetics.h.

References Kinetics::err().

virtual void getDestructionRates ( doublereal *  ddot )

inlinevirtual

Species destruction rates [kmol/m^3/s or kmol/m^2/s].

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

See Also

nTotalSpecies.

Parameters

ddot	Output vector of destruction rates. Length: m_kk.

Reimplemented in InterfaceKinetics, AqueousKinetics, and GasKinetics.

Definition at line 588 of file Kinetics.h.

References Kinetics::err().

virtual void getNetProductionRates ( doublereal *  wdot )

inlinevirtual

Species net production rates [kmol/m^3/s or kmol/m^2/s].

Return the species net production rates (creation - destruction) in array wdot, which must be dimensioned at least as large as the total number of species.

See Also

nTotalSpecies.

Parameters

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

Reimplemented in InterfaceKinetics, AqueousKinetics, GasKinetics, and GRI_30_Kinetics.

Definition at line 600 of file Kinetics.h.

References Kinetics::err().

Referenced by FlowReactor::evalEqs(), ConstPressureReactor::evalEqs(), IdealGasReactor::evalEqs(), IdealGasConstPressureReactor::evalEqs(), Reactor::evalEqs(), and StFlow::getWdot().

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 in InterfaceKinetics, AqueousKinetics, and GasKinetics.

Definition at line 614 of file Kinetics.h.

References Kinetics::err().

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 in InterfaceKinetics, AqueousKinetics, and GasKinetics.

Definition at line 625 of file Kinetics.h.

References Kinetics::err().

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 638 of file Kinetics.h.

References Kinetics::err().

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 653 of file Kinetics.h.

References Kinetics::err().

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 663 of file Kinetics.h.

References Kinetics::err().

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

Definition at line 673 of file Kinetics.h.

References Kinetics::m_reactants.

Referenced by InterfaceKinetics::addReaction().

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

Definition at line 683 of file Kinetics.h.

References Kinetics::m_products.

Referenced by InterfaceKinetics::addReaction().

virtual int reactionType ( size_t  i ) const

inlinevirtual

Flag specifying the type of reaction.

The legal values and their meaning are specific to the particular kinetics manager.

Parameters

i	reaction index

Reimplemented in InterfaceKinetics, AqueousKinetics, and GasKinetics.

Definition at line 694 of file Kinetics.h.

References Kinetics::err().

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, AqueousKinetics, and GasKinetics.

Definition at line 706 of file Kinetics.h.

References Kinetics::err().

virtual std::string reactionString ( size_t  i ) const

inlinevirtual

Return a string representing the reaction.

Parameters

i	reaction index

Reimplemented in InterfaceKinetics, AqueousKinetics, and GasKinetics.

Definition at line 716 of file Kinetics.h.

References Kinetics::err().

Referenced by Reactor::addSensitivityReaction().

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, AqueousKinetics, and GasKinetics.

Definition at line 729 of file Kinetics.h.

References Kinetics::err().

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, AqueousKinetics, and GasKinetics.

Definition at line 744 of file Kinetics.h.

References Kinetics::err().

virtual void getActivationEnergies ( doublereal *  E )

inlinevirtual

Return the activation energies in Kelvin.

length is the number of reactions

Parameters

E	Ouptut vector of activation energies. Length: m_ii.

Deprecated:

To be removed in Cantera 2.2.

Reimplemented in InterfaceKinetics.

Definition at line 757 of file Kinetics.h.

References Kinetics::err().

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 255 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().

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, AqueousKinetics, and GasKinetics.

Definition at line 791 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, AqueousKinetics, GasKinetics, and EdgeKinetics.

Definition at line 290 of file Kinetics.cpp.

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

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

virtual void addReaction ( ReactionData &  r )

inlinevirtual

Add a single reaction to the mechanism.

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

Parameters

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

Reimplemented in InterfaceKinetics, AqueousKinetics, and GasKinetics.

Definition at line 810 of file Kinetics.h.

References Kinetics::err().

Referenced by rxninfo::installReaction().

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 840 of file Kinetics.h.

References Kinetics::m_perturb.

Referenced by FlowReactor::evalEqs(), ConstPressureReactor::evalEqs(), IdealGasConstPressureReactor::evalEqs(), and Reactor::evalEqs().

void setMultiplier ( size_t  i, doublereal  f  )

inline

Set the multiplier for reaction i to f.

Parameters

i	index of the reaction
f	value of the multiplier.

Definition at line 849 of file Kinetics.h.

References Kinetics::m_perturb.

Referenced by FlowReactor::evalEqs(), ConstPressureReactor::evalEqs(), and Reactor::evalEqs().

void incrementRxnCount ( )

inline

Increment the number of reactions in the mechanism by one.

Todo:

Should be protected?

Definition at line 859 of file Kinetics.h.

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

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

virtual bool ready ( ) const

inlinevirtual

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

Reimplemented in InterfaceKinetics, AqueousKinetics, GasKinetics, Interface, and GRI30.

Definition at line 868 of file Kinetics.h.

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 172 of file Kinetics.cpp.

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

void err ( const std::string &  m ) const

private

Function indicating that a function inherited from the base class hasn't had a definition assigned to it.

Parameters

m	String message

Definition at line 299 of file Kinetics.cpp.

Referenced by Kinetics::addReaction(), Kinetics::getActivationEnergies(), Kinetics::getActivityConcentrations(), Kinetics::getCreationRates(), Kinetics::getDeltaElectrochemPotentials(), Kinetics::getDeltaEnthalpy(), Kinetics::getDeltaEntropy(), Kinetics::getDeltaGibbs(), Kinetics::getDeltaSSEnthalpy(), Kinetics::getDeltaSSEntropy(), Kinetics::getDeltaSSGibbs(), Kinetics::getDestructionRates(), Kinetics::getEquilibriumConstants(), Kinetics::getFwdRateConstants(), Kinetics::getFwdRatesOfProgress(), Kinetics::getNetProductionRates(), Kinetics::getNetRatesOfProgress(), Kinetics::getReactionDelta(), Kinetics::getRevRateConstants(), Kinetics::getRevRatesOfProgress(), Kinetics::isReversible(), Kinetics::productOrder(), Kinetics::productStoichCoeff(), Kinetics::reactantOrder(), Kinetics::reactantStoichCoeff(), Kinetics::reactionString(), and Kinetics::reactionType().

Member Data Documentation

size_t m_ii

protected

Number of reactions in the mechanism.

Definition at line 887 of file Kinetics.h.

Referenced by Kinetics::checkReactionArraySize(), Kinetics::checkReactionIndex(), GasKinetics::finalize(), AqueousKinetics::finalize(), GasKinetics::getDeltaEnthalpy(), AqueousKinetics::getDeltaEnthalpy(), GasKinetics::getDeltaEntropy(), AqueousKinetics::getDeltaEntropy(), GasKinetics::getDeltaGibbs(), AqueousKinetics::getDeltaGibbs(), GasKinetics::getDeltaSSEnthalpy(), AqueousKinetics::getDeltaSSEnthalpy(), GasKinetics::getDeltaSSEntropy(), AqueousKinetics::getDeltaSSEntropy(), GasKinetics::getDeltaSSGibbs(), AqueousKinetics::getDeltaSSGibbs(), GasKinetics::getEquilibriumConstants(), AqueousKinetics::getEquilibriumConstants(), InterfaceKinetics::getEquilibriumConstants(), GasKinetics::getFwdRateConstants(), AqueousKinetics::getFwdRateConstants(), GasKinetics::getRevRateConstants(), AqueousKinetics::getRevRateConstants(), InterfaceKinetics::getRevRateConstants(), Kinetics::incrementRxnCount(), Kinetics::nReactions(), Kinetics::operator=(), GasKinetics::updateKc(), AqueousKinetics::updateKc(), InterfaceKinetics::updateKc(), 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 891 of file Kinetics.h.

Referenced by Kinetics::checkSpeciesArraySize(), Kinetics::checkSpeciesIndex(), InterfaceKinetics::finalize(), Kinetics::finalize(), GasKinetics::getCreationRates(), AqueousKinetics::getCreationRates(), InterfaceKinetics::getCreationRates(), GasKinetics::getDeltaSSEnthalpy(), AqueousKinetics::getDeltaSSEnthalpy(), InterfaceKinetics::getDeltaSSEnthalpy(), GasKinetics::getDeltaSSEntropy(), AqueousKinetics::getDeltaSSEntropy(), InterfaceKinetics::getDeltaSSEntropy(), GasKinetics::getDestructionRates(), AqueousKinetics::getDestructionRates(), InterfaceKinetics::getDestructionRates(), GasKinetics::getNetProductionRates(), AqueousKinetics::getNetProductionRates(), InterfaceKinetics::getNetProductionRates(), GRI_30_Kinetics::gri30_updateKc(), GasKinetics::init(), AqueousKinetics::init(), InterfaceKinetics::init(), 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 895 of file Kinetics.h.

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

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.

Definition at line 908 of file Kinetics.h.

Referenced by 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.

Definition at line 921 of file Kinetics.h.

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

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 938 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=(), 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 945 of file Kinetics.h.

Referenced by InterfaceKinetics::_update_rates_C(), Kinetics::addPhase(), InterfaceKinetics::getDeltaElectrochemPotentials(), InterfaceKinetics::getDeltaEnthalpy(), InterfaceKinetics::getDeltaEntropy(), InterfaceKinetics::getDeltaGibbs(), InterfaceKinetics::getDeltaSSEnthalpy(), InterfaceKinetics::getDeltaSSEntropy(), InterfaceKinetics::getDeltaSSGibbs(), InterfaceKinetics::getEquilibriumConstants(), Kinetics::kineticsSpeciesIndex(), Kinetics::kineticsSpeciesName(), Kinetics::operator=(), Kinetics::selectPhase(), Kinetics::speciesPhaseIndex(), and InterfaceKinetics::updateKc().

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 955 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 958 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 965 of file Kinetics.h.

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

size_t m_mindim

protected

number of spatial dimensions of lowest-dimensional phase.

Definition at line 968 of file Kinetics.h.

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

std::vector<grouplist_t> m_dummygroups

private

Vector of group lists.

Definition at line 972 of file Kinetics.h.

Referenced by Kinetics::operator=().

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

• Kinetics.h
• Kinetics.cpp