Abstract base class which stores data about a reaction and its rate parameterization so that it can be added to a Kinetics object. More...

#include <Reaction.h>

Inheritance diagram for Reaction:

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Collaboration diagram for Reaction:

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Public Member Functions
	Reaction (const Composition &reactants, const Composition &products, shared_ptr< ReactionRate > rate={})

	Reaction (const AnyMap &node, const Kinetics &kin)
	Construct a Reaction and it's corresponding ReactionRate based on AnyMap (YAML) input. More...

	Reaction (int type)

	Reaction (int type, const Composition &reactants, const Composition &products)

virtual std::string	reactantString () const
	The reactant side of the chemical equation for this reaction. More...

virtual std::string	productString () const
	The product side of the chemical equation for this reaction. More...

std::string	equation () const
	The chemical equation for this reaction. More...

virtual void	setEquation (const std::string &equation, const Kinetics *kin=0)
	Set the reactants and products based on the reaction equation. More...

virtual std::string	type () const
	The type of reaction. More...

virtual void	calculateRateCoeffUnits (const Kinetics &kin)
	Calculate the units of the rate constant. More...

UnitStack	calculateRateCoeffUnits3 (const Kinetics &kin)
	Calculate the units of the rate constant. More...

virtual void	validate ()
	Ensure that the rate constant and other parameters for this reaction are valid. More...

virtual void	validate (Kinetics &kin)
	Perform validation checks that need access to a complete Kinetics objects, for. More...

AnyMap	parameters (bool withInput=true) const
	Return the parameters such that an identical Reaction could be reconstructed using the newReaction() function. More...

virtual void	setParameters (const AnyMap &node, const Kinetics &kin)
	Set up reaction based on AnyMap node More...

bool	valid () const
	Get validity flag of reaction. More...

void	setValid (bool valid)
	Set validity flag of reaction. More...

void	checkBalance (const Kinetics &kin) const
	Check that the specified reaction is balanced (same number of atoms for each element in the reactants and products). More...

bool	checkSpecies (const Kinetics &kin) const
	Verify that all species involved in the reaction are defined in the Kinetics object. More...

bool	usesElectrochemistry (const Kinetics &kin) const
	Check whether reaction uses electrochemistry. More...

shared_ptr< ReactionRate >	rate ()
	Get reaction rate pointer. More...

void	setRate (shared_ptr< ReactionRate > rate)
	Set reaction rate pointer. More...

shared_ptr< ThirdBody >	thirdBody ()
	Get pointer to third-body. More...

bool	usesLegacy () const
	Indicate whether object uses legacy framework. More...

Public Attributes
int	reaction_type
	Type of the reaction. More...

Composition	reactants
	Reactant species and stoichiometric coefficients. More...

Composition	products
	Product species and stoichiometric coefficients. More...

Composition	orders
	Forward reaction order with respect to specific species. More...

std::string	id
	An identification string for the reaction, used in some filtering operations. More...

bool	reversible
	True if the current reaction is reversible. False otherwise. More...

bool	duplicate
	True if the current reaction is marked as duplicate. More...

bool	allow_nonreactant_orders
	True if reaction orders can be specified for non-reactant species. More...

bool	allow_negative_orders
	True if negative reaction orders are allowed. Default is `false`. More...

AnyMap	input
	Input data used for specific models. More...

Units	rate_units
	The units of the rate constant. More...

Protected Member Functions
virtual void	getParameters (AnyMap &reactionNode) const
	Store the parameters of a Reaction needed to reconstruct an identical object using the newReaction(AnyMap&, Kinetics&) function. More...

virtual std::pair< std::vector< std::string >, bool >	undeclaredThirdBodies (const Kinetics &kin) const

Protected Attributes
bool	m_valid
	Flag indicating whether reaction is set up correctly. More...

shared_ptr< ReactionRate >	m_rate
	Reaction rate used by generic reactions. More...

shared_ptr< ThirdBody >	m_third_body
	Relative efficiencies of third-body species in enhancing the reaction rate (if applicable) More...

Detailed Description

Abstract base class which stores data about a reaction and its rate parameterization so that it can be added to a Kinetics object.

Definition at line 32 of file Reaction.h.

Constructor & Destructor Documentation

◆ Reaction() [1/5]

Reaction ( )

Definition at line 31 of file Reaction.cpp.

◆ Reaction() [2/5]

Reaction	(	const Composition &	reactants,
		const Composition &	products,
		shared_ptr< ReactionRate >	rate = `{}`
	)

Definition at line 42 of file Reaction.cpp.

◆ Reaction() [3/5]

Reaction	(	const AnyMap &	node,
		const Kinetics &	kin
	)

Construct a Reaction and it's corresponding ReactionRate based on AnyMap (YAML) input.

Definition at line 58 of file Reaction.cpp.

References Reaction::calculateRateCoeffUnits3(), AnyMap::hasKey(), Phase::nDim(), Cantera::newReactionRate(), Kinetics::nPhases(), Kinetics::reactionPhaseIndex(), Reaction::setParameters(), Reaction::setRate(), Kinetics::thermo(), and Reaction::type().

◆ Reaction() [4/5]

Reaction ( int type )

explicit

Deprecated:: To be removed after Cantera 2.6.

Definition at line 93 of file Reaction.cpp.

◆ Reaction() [5/5]

Reaction	(	int	type,
		const Composition &	reactants,
		const Composition &	products
	)

Deprecated:: To be removed after Cantera 2.6.

Definition at line 107 of file Reaction.cpp.

◆ ~Reaction()

virtual ~Reaction ( )

inlinevirtual

Definition at line 48 of file Reaction.h.

Member Function Documentation

◆ reactantString()

std::string reactantString ( ) const

virtual

The reactant side of the chemical equation for this reaction.

Reimplemented in ThreeBodyReaction2, FalloffReaction2, ThreeBodyReaction3, and FalloffReaction3.

Definition at line 266 of file Reaction.cpp.

References Reaction::reactants.

Referenced by Reaction::equation(), ThreeBodyReaction2::reactantString(), FalloffReaction2::reactantString(), ThreeBodyReaction3::reactantString(), and FalloffReaction3::reactantString().

◆ productString()

std::string productString ( ) const

virtual

The product side of the chemical equation for this reaction.

Reimplemented in ThreeBodyReaction2, FalloffReaction2, ThreeBodyReaction3, and FalloffReaction3.

Definition at line 281 of file Reaction.cpp.

References Reaction::products.

Referenced by Reaction::equation(), ThreeBodyReaction2::productString(), FalloffReaction2::productString(), ThreeBodyReaction3::productString(), and FalloffReaction3::productString().

◆ equation()

std::string equation ( ) const

The chemical equation for this reaction.

Definition at line 296 of file Reaction.cpp.

References Reaction::productString(), Reaction::reactantString(), and Reaction::reversible.

Referenced by InterfaceKinetics::buildSurfaceArrhenius(), Reaction::checkBalance(), Reaction::checkSpecies(), Reaction::getParameters(), StickingCoverage::setContext(), FalloffReaction3::setEquation(), Reaction::setEquation(), ThreeBodyReaction3::setEquation(), ElementaryReaction2::validate(), FalloffReaction2::validate(), PlogReaction2::validate(), and Reaction::validate().

◆ setEquation()

void setEquation	(	const std::string &	equation,
		const Kinetics *	kin = `0`
	)

virtual

Set the reactants and products based on the reaction equation.

If a Kinetics object is provided, it is used to check that all reactants and products exist.

Reimplemented in FalloffReaction3, and ThreeBodyReaction3.

Definition at line 305 of file Reaction.cpp.

References Reaction::equation(), Reaction::input, and Cantera::parseReactionEquation().

Referenced by FalloffReaction3::setEquation(), ThreeBodyReaction3::setEquation(), and Reaction::setParameters().

◆ type()

std::string type ( ) const

virtual

The type of reaction.

Reimplemented in ElementaryReaction2, ThreeBodyReaction2, FalloffReaction2, ChemicallyActivatedReaction2, PlogReaction2, ChebyshevReaction2, InterfaceReaction2, ThreeBodyReaction3, FalloffReaction3, and CustomFunc1Reaction.

Definition at line 310 of file Reaction.cpp.

Referenced by Reaction::getParameters(), Reaction::Reaction(), and ElementaryReaction2::validate().

◆ calculateRateCoeffUnits()

void calculateRateCoeffUnits ( const Kinetics & kin )

virtual

Calculate the units of the rate constant.

These are determined by the units of the standard concentration of the reactant species' phases and the phase where the reaction occurs. Sets the value of rate_units.

Reimplemented in ThreeBodyReaction2, FalloffReaction2, ChemicallyActivatedReaction2, and InterfaceReaction2.

Definition at line 315 of file Reaction.cpp.

References Reaction::orders, Units::pow(), Reaction::rate_units, Reaction::reactants, Kinetics::reactionPhaseIndex(), Kinetics::speciesPhase(), ThermoPhase::standardConcentrationUnits(), Kinetics::thermo(), and Reaction::valid().

Referenced by ThreeBodyReaction2::calculateRateCoeffUnits(), FalloffReaction2::calculateRateCoeffUnits(), ChemicallyActivatedReaction2::calculateRateCoeffUnits(), and InterfaceReaction2::calculateRateCoeffUnits().

◆ calculateRateCoeffUnits3()

UnitStack calculateRateCoeffUnits3 ( const Kinetics & kin )

Calculate the units of the rate constant.

These are determined by the units of the standard concentration of the reactant species' phases and the phase where the reaction occurs. Sets the value of rate_units.

Definition at line 345 of file Reaction.cpp.

References Reaction::m_third_body, Reaction::orders, Reaction::rate_units, Reaction::reactants, Kinetics::reactionPhaseIndex(), Kinetics::speciesPhase(), Kinetics::thermo(), and Reaction::valid().

Referenced by Reaction::Reaction().

◆ validate() [1/2]

void validate ( )

virtual

Ensure that the rate constant and other parameters for this reaction are valid.

Reimplemented in ElementaryReaction2, ElementaryReaction2, FalloffReaction2, FalloffReaction2, PlogReaction2, PlogReaction2, and InterfaceReaction2.

Definition at line 124 of file Reaction.cpp.

References Reaction::allow_negative_orders, Reaction::allow_nonreactant_orders, Reaction::equation(), Reaction::input, Reaction::m_rate, Reaction::orders, Reaction::reactants, Reaction::reversible, and Reaction::usesLegacy().

Referenced by ElementaryReaction2::validate(), FalloffReaction2::validate(), and PlogReaction2::validate().

◆ validate() [2/2]

virtual void validate ( Kinetics & kin )

inlinevirtual

Perform validation checks that need access to a complete Kinetics objects, for.

Reimplemented in ElementaryReaction2, FalloffReaction2, PlogReaction2, InterfaceReaction2, and InterfaceReaction2.

Definition at line 82 of file Reaction.h.

References Reaction::equation(), and Reaction::m_rate.

◆ parameters()

AnyMap parameters ( bool withInput = true ) const

Return the parameters such that an identical Reaction could be reconstructed using the newReaction() function.

Behavior specific to derived classes is handled by the getParameters() method.

Parameters

withInput If true, include additional input data fields associated with the object, such as user-defined fields from a YAML input file, as contained in the input attribute.

Definition at line 162 of file Reaction.cpp.

References AnyMap::addOrderingRules(), Reaction::getParameters(), Reaction::input, and AnyMap::update().

◆ setParameters()

void setParameters	(	const AnyMap &	node,
		const Kinetics &	kin
	)

virtual

Set up reaction based on AnyMap node

Reimplemented in ThreeBodyReaction3, and FalloffReaction3.

Definition at line 216 of file Reaction.cpp.

References Reaction::allow_negative_orders, Reaction::allow_nonreactant_orders, AnyMap::copyMetadata(), Reaction::duplicate, AnyMap::empty(), AnyMap::getBool(), AnyMap::getString(), AnyMap::hasKey(), Reaction::input, Kinetics::kineticsSpeciesIndex(), Cantera::npos, Reaction::orders, Reaction::setEquation(), and Reaction::setValid().

Referenced by Reaction::Reaction(), ThreeBodyReaction3::setParameters(), and FalloffReaction3::setParameters().

◆ valid()

bool valid ( ) const

inline

Get validity flag of reaction.

Definition at line 100 of file Reaction.h.

References Reaction::m_valid.

Referenced by Reaction::calculateRateCoeffUnits(), Reaction::calculateRateCoeffUnits3(), and Reaction::setValid().

◆ setValid()

void setValid ( bool valid )

inline

Set validity flag of reaction.

Definition at line 105 of file Reaction.h.

References Reaction::m_valid, and Reaction::valid().

Referenced by Reaction::setParameters().

◆ checkBalance()

void checkBalance ( const Kinetics & kin ) const

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. Used by checkSpecies.

Parameters

kin	Kinetics object

Definition at line 409 of file Reaction.cpp.

References Phase::elementName(), Reaction::equation(), Reaction::input, Phase::nAtoms(), Phase::nDim(), Phase::nElements(), Cantera::npos, Reaction::products, Reaction::reactants, Kinetics::reactionPhaseIndex(), Phase::speciesIndex(), Kinetics::speciesPhase(), Kinetics::surfacePhaseIndex(), and Kinetics::thermo().

Referenced by Reaction::checkSpecies().

◆ checkSpecies()

bool checkSpecies ( const Kinetics & kin ) const

Verify that all species involved in the reaction are defined in the Kinetics object.

The function returns true if all species are found, and raises an exception unless the kinetics object is configured to skip undeclared species, in which case false is returned.

Parameters

kin	Kinetics object

Definition at line 479 of file Reaction.cpp.

References Reaction::checkBalance(), Reaction::equation(), AnyMap::hasKey(), Reaction::input, Reaction::orders, Reaction::products, Reaction::reactants, Kinetics::skipUndeclaredSpecies(), Kinetics::skipUndeclaredThirdBodies(), and Reaction::undeclaredThirdBodies().

◆ usesElectrochemistry()

bool usesElectrochemistry ( const Kinetics & kin ) const

Check whether reaction uses electrochemistry.

Parameters

kin	Kinetics object

Definition at line 540 of file Reaction.cpp.

References Phase::charge(), Kinetics::kineticsSpeciesIndex(), Kinetics::nPhases(), Reaction::products, Reaction::reactants, Phase::speciesIndex(), Kinetics::speciesPhaseIndex(), and Kinetics::thermo().

Referenced by InterfaceRateBase::setContext().

◆ rate()

shared_ptr< ReactionRate > rate ( )

inline

Get reaction rate pointer.

Definition at line 171 of file Reaction.h.

References Reaction::m_rate.

Referenced by Reaction::setRate().

◆ setRate()

void setRate ( shared_ptr< ReactionRate > rate )

Set reaction rate pointer.

Definition at line 243 of file Reaction.cpp.

References Reaction::input, Reaction::m_rate, Reaction::products, Reaction::rate(), Reaction::reactants, and Cantera::warn_deprecated().

Referenced by Reaction::Reaction().

◆ thirdBody()

shared_ptr< ThirdBody > thirdBody ( )

inline

Get pointer to third-body.

Definition at line 179 of file Reaction.h.

References Reaction::m_third_body.

◆ usesLegacy()

bool usesLegacy ( ) const

inline

Indicate whether object uses legacy framework.

Definition at line 184 of file Reaction.h.

References Reaction::m_rate.

Referenced by Reaction::validate().

◆ getParameters()

void getParameters ( AnyMap & reactionNode ) const

protectedvirtual

Store the parameters of a Reaction needed to reconstruct an identical object using the newReaction(AnyMap&, Kinetics&) function.

Does not include user-defined fields available in the input map.

Reimplemented in ElementaryReaction2, ThreeBodyReaction2, FalloffReaction2, ChemicallyActivatedReaction2, PlogReaction2, ChebyshevReaction2, InterfaceReaction2, ElectrochemicalReaction2, ThreeBodyReaction3, and FalloffReaction3.

Definition at line 184 of file Reaction.cpp.

References Reaction::allow_negative_orders, Reaction::allow_nonreactant_orders, Reaction::duplicate, Reaction::equation(), AnyMap::erase(), AnyMap::hasKey(), Reaction::m_rate, Reaction::orders, Reaction::type(), and AnyMap::update().

Referenced by ElementaryReaction2::getParameters(), FalloffReaction2::getParameters(), PlogReaction2::getParameters(), ChebyshevReaction2::getParameters(), ThreeBodyReaction3::getParameters(), FalloffReaction3::getParameters(), and Reaction::parameters().

◆ undeclaredThirdBodies()

std::pair< std::vector< std::string >, bool > undeclaredThirdBodies ( const Kinetics & kin ) const

protectedvirtual

Helper function returning vector of undeclared third body species and a boolean expression indicating whether the third body is specified. The function is used by the checkSpecies method and only needed as long as there is no unified approach to handle third body collision partners.

Parameters

kin	Kinetics object

Reimplemented in ThreeBodyReaction2, and FalloffReaction2.

Definition at line 398 of file Reaction.cpp.

References Reaction::m_third_body.

Referenced by Reaction::checkSpecies().

Member Data Documentation

◆ reaction_type

int reaction_type

Type of the reaction.

The valid types are listed in the file, reaction_defs.h, with constants ending in RXN.

Deprecated:: To be removed in Cantera 2.6. Superseded by Reaction::type().

Definition at line 132 of file Reaction.h.

◆ reactants

Composition reactants

Reactant species and stoichiometric coefficients.

Definition at line 135 of file Reaction.h.

Referenced by InterfaceKinetics::buildSurfaceArrhenius(), Reaction::calculateRateCoeffUnits(), ThreeBodyReaction2::calculateRateCoeffUnits(), Reaction::calculateRateCoeffUnits3(), Reaction::checkBalance(), Reaction::checkSpecies(), Reaction::reactantString(), InterfaceRateBase::setContext(), StickingCoverage::setContext(), BlowersMaselRate::setContext(), FalloffReaction3::setEquation(), ThreeBodyReaction3::setEquation(), Reaction::setRate(), Reaction::usesElectrochemistry(), and Reaction::validate().

◆ products

Composition products

Product species and stoichiometric coefficients.

Definition at line 138 of file Reaction.h.

Referenced by ThreeBodyReaction2::calculateRateCoeffUnits(), Reaction::checkBalance(), Reaction::checkSpecies(), Reaction::productString(), InterfaceRateBase::setContext(), BlowersMaselRate::setContext(), FalloffReaction3::setEquation(), ThreeBodyReaction3::setEquation(), Reaction::setRate(), and Reaction::usesElectrochemistry().

◆ orders

Composition orders

Forward reaction order with respect to specific species.

By default, mass-action kinetics is assumed, with the reaction order equal to each reactant's stoichiometric coefficient.

Definition at line 143 of file Reaction.h.

Referenced by InterfaceKinetics::buildSurfaceArrhenius(), Reaction::calculateRateCoeffUnits(), Reaction::calculateRateCoeffUnits3(), Reaction::checkSpecies(), Reaction::getParameters(), StickingCoverage::setContext(), Reaction::setParameters(), and Reaction::validate().

◆ id

std::string id

An identification string for the reaction, used in some filtering operations.

Definition at line 147 of file Reaction.h.

◆ reversible

bool reversible

True if the current reaction is reversible. False otherwise.

Definition at line 150 of file Reaction.h.

Referenced by Reaction::equation(), TwoTempPlasmaRate::setContext(), and Reaction::validate().

◆ duplicate

bool duplicate

True if the current reaction is marked as duplicate.

Definition at line 153 of file Reaction.h.

Referenced by Reaction::getParameters(), and Reaction::setParameters().

◆ allow_nonreactant_orders

bool allow_nonreactant_orders

True if reaction orders can be specified for non-reactant species.

Default is false.

Definition at line 157 of file Reaction.h.

Referenced by Reaction::getParameters(), Reaction::setParameters(), and Reaction::validate().

◆ allow_negative_orders

bool allow_negative_orders

True if negative reaction orders are allowed. Default is false.

Definition at line 160 of file Reaction.h.

Referenced by Reaction::getParameters(), Reaction::setParameters(), and Reaction::validate().

◆ input

AnyMap input

Input data used for specific models.

Definition at line 163 of file Reaction.h.

Referenced by InterfaceKinetics::buildSurfaceArrhenius(), InterfaceReaction2::calculateRateCoeffUnits(), Reaction::checkBalance(), Reaction::checkSpecies(), Reaction::parameters(), StickingCoverage::setContext(), TwoTempPlasmaRate::setContext(), FalloffReaction3::setEquation(), Reaction::setEquation(), ThreeBodyReaction3::setEquation(), Reaction::setParameters(), Reaction::setRate(), Reaction::validate(), ElementaryReaction2::validate(), and FalloffReaction2::validate().

◆ rate_units

Units rate_units

The units of the rate constant.

These are determined by the units of the standard concentration of the reactant species' phases of the phase where the reaction occurs.

Definition at line 168 of file Reaction.h.

Referenced by Reaction::calculateRateCoeffUnits(), ThreeBodyReaction2::calculateRateCoeffUnits(), FalloffReaction2::calculateRateCoeffUnits(), ChemicallyActivatedReaction2::calculateRateCoeffUnits(), InterfaceReaction2::calculateRateCoeffUnits(), Reaction::calculateRateCoeffUnits3(), ElementaryReaction2::getParameters(), FalloffReaction2::getParameters(), PlogReaction2::getParameters(), and ChebyshevReaction2::getParameters().

◆ m_valid

bool m_valid

protected

Flag indicating whether reaction is set up correctly.

Definition at line 195 of file Reaction.h.

Referenced by Reaction::setValid(), and Reaction::valid().

◆ m_rate

shared_ptr<ReactionRate> m_rate

protected

Reaction rate used by generic reactions.

Definition at line 206 of file Reaction.h.

Referenced by Reaction::getParameters(), Reaction::rate(), Reaction::setRate(), FalloffReaction3::type(), Reaction::usesLegacy(), and Reaction::validate().

◆ m_third_body

shared_ptr<ThirdBody> m_third_body

protected

Relative efficiencies of third-body species in enhancing the reaction rate (if applicable)

Definition at line 210 of file Reaction.h.

Referenced by Reaction::calculateRateCoeffUnits3(), ThreeBodyReaction3::getParameters(), FalloffReaction3::getParameters(), ThreeBodyReaction3::productString(), FalloffReaction3::productString(), ThreeBodyReaction3::reactantString(), FalloffReaction3::reactantString(), FalloffReaction3::setEquation(), ThreeBodyReaction3::setParameters(), FalloffReaction3::setParameters(), Reaction::thirdBody(), and Reaction::undeclaredThirdBodies().

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

Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ Reaction() [1/5]

◆ Reaction() [2/5]

◆ Reaction() [3/5]

◆ Reaction() [4/5]

◆ Reaction() [5/5]

◆ ~Reaction()

Member Function Documentation

◆ reactantString()

◆ productString()

◆ equation()

◆ setEquation()

◆ type()

◆ calculateRateCoeffUnits()

◆ calculateRateCoeffUnits3()

◆ validate() [1/2]

◆ validate() [2/2]

◆ parameters()

◆ setParameters()

◆ valid()

◆ setValid()

◆ checkBalance()

◆ checkSpecies()

◆ usesElectrochemistry()

◆ rate()

◆ setRate()

◆ thirdBody()

◆ usesLegacy()

◆ getParameters()

◆ undeclaredThirdBodies()

Member Data Documentation

◆ reaction_type

◆ reactants

◆ products

◆ orders

◆ id

◆ reversible

◆ duplicate

◆ allow_nonreactant_orders

◆ allow_negative_orders

◆ input

◆ rate_units

◆ m_valid

◆ m_rate

◆ m_third_body