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

#include <GasKinetics.h>

Inheritance diagram for GasKinetics:

Collaboration diagram for GasKinetics:

Public Member Functions
virtual void	resizeReactions ()
	Finalize Kinetics object and associated objects. More...

void	updateROP ()

virtual void	getDerivativeSettings (AnyMap &settings) const
	Retrieve derivative settings. More...

virtual void	setDerivativeSettings (const AnyMap &settings)
	Set/modify derivative settings. More...

virtual void	getFwdRateConstants_ddT (double *dkfwd)
	Calculate derivatives for forward rate constants with respect to temperature at constant pressure, molar concentration and mole fractions. More...

virtual void	getFwdRatesOfProgress_ddT (double *drop)
	Calculate derivatives for forward rates-of-progress with respect to temperature at constant pressure, molar concentration and mole fractions. More...

virtual void	getRevRatesOfProgress_ddT (double *drop)
	Calculate derivatives for reverse rates-of-progress with respect to temperature at constant pressure, molar concentration and mole fractions. More...

virtual void	getNetRatesOfProgress_ddT (double *drop)
	Calculate derivatives for net rates-of-progress with respect to temperature at constant pressure, molar concentration and mole fractions. More...

virtual void	getFwdRateConstants_ddP (double *dkfwd)
	Calculate derivatives for forward rate constants with respect to pressure at constant temperature, molar concentration and mole fractions. More...

virtual void	getFwdRatesOfProgress_ddP (double *drop)
	Calculate derivatives for forward rates-of-progress with respect to pressure at constant temperature, molar concentration and mole fractions. More...

virtual void	getRevRatesOfProgress_ddP (double *drop)
	Calculate derivatives for reverse rates-of-progress with respect to pressure at constant temperature, molar concentration and mole fractions. More...

virtual void	getNetRatesOfProgress_ddP (double *drop)
	Calculate derivatives for net rates-of-progress with respect to pressure at constant temperature, molar concentration and mole fractions. More...

virtual void	getFwdRateConstants_ddC (double *dkfwd)
	Calculate derivatives for forward rate constants with respect to molar concentration at constant temperature, pressure and mole fractions. More...

virtual void	getFwdRatesOfProgress_ddC (double *drop)
	Calculate derivatives for forward rates-of-progress with respect to molar concentration at constant temperature, pressure and mole fractions. More...

virtual void	getRevRatesOfProgress_ddC (double *drop)
	Calculate derivatives for reverse rates-of-progress with respect to molar concentration at constant temperature, pressure and mole fractions. More...

virtual void	getNetRatesOfProgress_ddC (double *drop)
	Calculate derivatives for net rates-of-progress with respect to molar concentration at constant temperature, pressure and mole fractions. More...

virtual Eigen::SparseMatrix< double >	fwdRatesOfProgress_ddX ()
	Calculate derivatives for forward rates-of-progress with respect to species mole fractions at constant temperature, pressure and molar concentration. More...

virtual Eigen::SparseMatrix< double >	revRatesOfProgress_ddX ()
	Calculate derivatives for reverse rates-of-progress with respect to species mole fractions at constant temperature, pressure and molar concentration. More...

virtual Eigen::SparseMatrix< double >	netRatesOfProgress_ddX ()
	Calculate derivatives for net rates-of-progress with respect to species mole fractions at constant temperature, pressure and molar concentration. More...

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

virtual void	update_rates_C ()
	Update properties that depend on concentrations. More...

Constructors and General Information
	GasKinetics (ThermoPhase *thermo=0)
	Constructor. More...

virtual std::string	kineticsType () const
	Identifies the Kinetics manager type. More...

virtual void	getThirdBodyConcentrations (double *concm)
	Return a vector of values of effective concentrations of third-body collision partners of any reaction. More...

virtual const vector_fp &	thirdBodyConcentrations () const
	Provide direct access to current third-body concentration values. More...

Reaction Rates Of Progress
virtual void	getEquilibriumConstants (doublereal *kc)
	Return a vector of Equilibrium constants. More...

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

Reaction Mechanism Setup Routines
virtual bool	addReaction (shared_ptr< Reaction > r, bool resize=true)
	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...

virtual void	invalidateCache ()

Public Member Functions inherited from BulkKinetics
	BulkKinetics (ThermoPhase *thermo=0)

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

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

virtual void	getDeltaEnthalpy (doublereal *deltaH)
	Return the vector of values for the reactions change in enthalpy. More...

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

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

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

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

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

virtual void	resizeSpecies ()
	Resize arrays with sizes that depend on the total number of species. More...

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

void	addThirdBody (shared_ptr< Reaction > r)

Public Member Functions inherited from Kinetics
virtual std::pair< size_t, size_t >	checkDuplicates (bool throw_err=true) const
	Check for unmarked duplicate reactions and unmatched marked duplicates. More...

void	selectPhase (const double data, const ThermoPhase phase, double *phase_data)

virtual void	setRoot (std::shared_ptr< Solution > root)
	Set root Solution holding all phase information. More...

virtual double	reactionEnthalpy (const Composition &reactants, const Composition &products)
	Calculate the reaction enthalpy of a reaction which has not necessarily been added into the Kinetics object. More...

	Kinetics ()
	Default constructor. More...

virtual	~Kinetics ()

	Kinetics (const Kinetics &)=delete
	Kinetics objects are not copyable or assignable. More...

Kinetics &	operator= (const Kinetics &)=delete

size_t	nReactions () const
	Number of reactions in the reaction mechanism. More...

void	checkReactionIndex (size_t m) const
	Check that the specified reaction index is in range Throws an exception if i is greater than nReactions() More...

void	checkReactionArraySize (size_t ii) const
	Check that an array size is at least nReactions() Throws an exception if ii is less than nReactions(). More...

void	checkSpeciesIndex (size_t k) const
	Check that the specified species index is in range Throws an exception if k is greater than nSpecies()-1. More...

void	checkSpeciesArraySize (size_t mm) const
	Check that an array size is at least nSpecies() Throws an exception if kk is less than nSpecies(). More...

size_t	nPhases () const
	The number of phases participating in the reaction mechanism. More...

void	checkPhaseIndex (size_t m) const
	Check that the specified phase index is in range Throws an exception if m is greater than nPhases() More...

void	checkPhaseArraySize (size_t mm) const
	Check that an array size is at least nPhases() Throws an exception if mm is less than nPhases(). More...

size_t	phaseIndex (const std::string &ph) const
	Return the phase index of a phase in the list of phases defined within the object. More...

size_t	surfacePhaseIndex () const
	This returns the integer index of the phase which has ThermoPhase type cSurf. More...

size_t	reactionPhaseIndex () const
	Phase where the reactions occur. More...

ThermoPhase &	thermo (size_t n=0)
	This method returns a reference to the nth ThermoPhase object defined in this kinetics mechanism. More...

const ThermoPhase &	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...

ThermoPhase &	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...

const ThermoPhase &	speciesPhase (const std::string &nm) const

ThermoPhase &	speciesPhase (size_t k)
	This function takes as an argument the kineticsSpecies index (that is, 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) const
	This function takes as an argument the kineticsSpecies index (that is, the list index in the list of species in the kinetics manager) and returns the index of the phase owning the species. More...

virtual void	getFwdRatesOfProgress (doublereal *fwdROP)
	Return the forward rates of progress of the reactions. More...

virtual void	getRevRatesOfProgress (doublereal *revROP)
	Return the Reverse rates of progress of the reactions. More...

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

virtual void	getReactionDelta (const double property, double deltaProperty) const
	Change in species properties. More...

virtual void	getRevReactionDelta (const double g, double dg) const
	Given an array of species properties 'g', return in array 'dg' the change in this quantity in the reversible reactions. More...

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

virtual void	getCreationRates (doublereal *cdot)
	Species creation rates [kmol/m^3/s or kmol/m^2/s]. More...

virtual void	getDestructionRates (doublereal *ddot)
	Species destruction rates [kmol/m^3/s or kmol/m^2/s]. More...

virtual void	getNetProductionRates (doublereal *wdot)
	Species net production rates [kmol/m^3/s or kmol/m^2/s]. More...

void	getCreationRates_ddT (double *dwdot)
	Calculate derivatives for species creation rates with respect to temperature at constant pressure, molar concentration and mole fractions. More...

void	getCreationRates_ddP (double *dwdot)
	Calculate derivatives for species creation rates with respect to pressure at constant temperature, molar concentration and mole fractions. More...

void	getCreationRates_ddC (double *dwdot)
	Calculate derivatives for species creation rates with respect to molar concentration at constant temperature, pressure and mole fractions. More...

Eigen::SparseMatrix< double >	creationRates_ddX ()
	Calculate derivatives for species creation rates with respect to species mole fractions at constant temperature, pressure and molar concentration. More...

void	getDestructionRates_ddT (double *dwdot)
	Calculate derivatives for species destruction rates with respect to temperature at constant pressure, molar concentration and mole fractions. More...

void	getDestructionRates_ddP (double *dwdot)
	Calculate derivatives for species destruction rates with respect to pressure at constant temperature, molar concentration and mole fractions. More...

void	getDestructionRates_ddC (double *dwdot)
	Calculate derivatives for species destruction rates with respect to molar concentration at constant temperature, pressure and mole fractions. More...

Eigen::SparseMatrix< double >	destructionRates_ddX ()
	Calculate derivatives for species destruction rates with respect to species mole fractions at constant temperature, pressure and molar concentration. More...

void	getNetProductionRates_ddT (double *dwdot)
	Calculate derivatives for species net production rates with respect to temperature at constant pressure, molar concentration and mole fractions. More...

void	getNetProductionRates_ddP (double *dwdot)
	Calculate derivatives for species net production rates with respect to pressure at constant temperature, molar concentration and mole fractions. More...

void	getNetProductionRates_ddC (double *dwdot)
	Calculate derivatives for species net production rates with respect to molar concentration at constant temperature, pressure and mole fractions. More...

Eigen::SparseMatrix< double >	netProductionRates_ddX ()
	Calculate derivatives for species net production rates with respect to species mole fractions at constant temperature, pressure and molar concentration. More...

virtual double	reactantStoichCoeff (size_t k, size_t i) const
	Stoichiometric coefficient of species k as a reactant in reaction i. More...

Eigen::SparseMatrix< double >	reactantStoichCoeffs () const
	Stoichiometric coefficient matrix for reactants. More...

virtual double	productStoichCoeff (size_t k, size_t i) const
	Stoichiometric coefficient of species k as a product in reaction i. More...

Eigen::SparseMatrix< double >	productStoichCoeffs () const
	Stoichiometric coefficient matrix for products. More...

Eigen::SparseMatrix< double >	revProductStoichCoeffs () const
	Stoichiometric coefficient matrix for products of reversible reactions. 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 int	reactionType (size_t i) const
	Flag specifying the type of reaction. More...

virtual std::string	reactionTypeStr (size_t i) const
	String specifying the type of reaction. More...

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

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

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

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

virtual void	init ()
	Prepare the class for the addition of reactions, after all phases have been added. More...

AnyMap	parameters ()
	Return the parameters for a phase definition which are needed to reconstruct an identical object using the newKinetics function. More...

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

shared_ptr< const Reaction >	reaction (size_t i) const

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...

bool	skipUndeclaredSpecies () const

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...

bool	skipUndeclaredThirdBodies () const

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

Protected Member Functions
void	processFalloffReactions (double *ropf)

void	addThreeBodyReaction (ThreeBodyReaction2 &r)

void	addFalloffReaction (FalloffReaction2 &r)

void	addPlogReaction (PlogReaction2 &r)

void	addChebyshevReaction (ChebyshevReaction2 &r)

void	modifyThreeBodyReaction (size_t i, ThreeBodyReaction2 &r)

void	modifyFalloffReaction (size_t i, FalloffReaction2 &r)

void	modifyPlogReaction (size_t i, PlogReaction2 &r)

void	modifyChebyshevReaction (size_t i, ChebyshevReaction2 &r)

void	updateKc ()
	Update the equilibrium constants in molar units. More...

Internal service methods
void	processFwdRateCoefficients (double *ropf)
	Calculate rate coefficients. More...

void	processThirdBodies (double *rop)
	Multiply rate with third-body collider concentrations. More...

void	processEquilibriumConstants (double *rop)
	Multiply rate with inverse equilibrium constant. More...

void	processEquilibriumConstants_ddT (double *drkcn)
	Multiply rate with scaled temperature derivatives of the inverse equilibrium constant. More...

void	process_ddT (const vector_fp &in, double *drop)
	Process temperature derivative. More...

void	process_ddP (const vector_fp &in, double *drop)
	Process pressure derivative. More...

void	process_ddC (StoichManagerN &stoich, const vector_fp &in, double *drop, bool mass_action=true)
	Process concentration (molar density) derivative. More...

Eigen::SparseMatrix< double >	process_ddX (StoichManagerN &stoich, const vector_fp &in)
	Process mole fraction derivative. More...

void	assertDerivativesValid (const std::string &name)
	Helper function ensuring that all rate derivatives can be calculated. More...

Protected Member Functions inherited from BulkKinetics
virtual void	addElementaryReaction (ElementaryReaction2 &r)

virtual void	modifyElementaryReaction (size_t i, ElementaryReaction2 &rNew)

Protected Member Functions inherited from Kinetics
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
std::vector< size_t >	m_fallindx
	Reaction index of each falloff reaction. More...

std::vector< size_t >	m_legacy
	Reaction index of each legacy reaction (old framework) More...

std::map< size_t, size_t >	m_rfallindx
	Map of reaction index to falloff reaction index (i.e indices in m_falloff_low_rates and m_falloff_high_rates) More...

Rate1< Arrhenius2 >	m_falloff_low_rates
	Rate expressions for falloff reactions at the low-pressure limit. More...

Rate1< Arrhenius2 >	m_falloff_high_rates
	Rate expressions for falloff reactions at the high-pressure limit. More...

FalloffMgr	m_falloffn

ThirdBodyCalc	m_3b_concm

ThirdBodyCalc	m_falloff_concm

Rate1< Plog >	m_plog_rates

Rate1< ChebyshevRate >	m_cheb_rates

vector_fp	m_rbuf0
	Buffers for partial rop results with length nReactions() More...

vector_fp	m_rbuf1

vector_fp	m_rbuf2

vector_fp	m_sbuf0

vector_fp	m_state

bool	m_jac_skip_third_bodies
	Derivative settings. More...

bool	m_jac_skip_falloff

double	m_jac_rtol_delta

Reaction rate data
doublereal	m_logStandConc

vector_fp	m_rfn_low

vector_fp	m_rfn_high

doublereal	m_pres
	Last pressure at which rates were evaluated. More...

vector_fp	falloff_work

vector_fp	concm_3b_values

vector_fp	concm_falloff_values

Protected Attributes inherited from BulkKinetics
std::vector< unique_ptr< MultiRateBase > >	m_bulk_rates
	Vector of rate handlers. More...

std::map< std::string, size_t >	m_bulk_types
	Mapping of rate handlers. More...

Rate1< Arrhenius2 >	m_rates

std::vector< size_t >	m_revindex
	Indices of reversible reactions. More...

std::vector< size_t >	m_irrev
	Indices of irreversible reactions. More...

vector_fp	m_dn
	Difference between the global reactants order and the global products order. More...

ThirdBodyCalc3	m_multi_concm
	used with MultiRate evaluator More...

vector_fp	m_concm
	Third body concentrations. More...

vector_fp	m_act_conc
	Activity concentrations, as calculated by ThermoPhase::getActivityConcentrations. More...

vector_fp	m_phys_conc
	Physical concentrations, as calculated by ThermoPhase::getConcentrations. More...

vector_fp	m_grt

bool	m_ROP_ok

doublereal	m_temp

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

bool	m_ready
	Boolean indicating whether Kinetics object is fully configured. 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< ThermoPhase * >	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 name 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...

vector_fp	m_rfn
	Forward rate constant for each reaction. More...

vector_fp	m_delta_gibbs0
	Delta G^0 for all reactions. 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...

vector_fp	m_dH
	The enthalpy change for each reaction to calculate Blowers-Masel rates. More...

vector_fp	m_rbuf
	Buffer used for storage of intermediate reaction-specific results. More...

bool	m_skipUndeclaredSpecies

bool	m_skipUndeclaredThirdBodies

std::weak_ptr< Solution >	m_root
	reference to Solution More...

StoichManagerN	m_reactantStoich
	Stoichiometry manager for the reactants for each reaction. More...

StoichManagerN	m_productStoich
	Stoichiometry manager for the products for each reaction. More...

StoichManagerN	m_revProductStoich
	Stoichiometry manager for the products of reversible reactions. More...

Eigen::SparseMatrix< double >	m_stoichMatrix
	Net stoichiometry (products - reactants) More...

Detailed Description

Kinetics manager for elementary gas-phase chemistry.

This kinetics manager implements standard mass-action reaction rate expressions for low-density gases.

Definition at line 25 of file GasKinetics.h.

Constructor & Destructor Documentation

◆ GasKinetics()

GasKinetics ( ThermoPhase * thermo = 0 )

Constructor.

Parameters

thermo Pointer to the gas ThermoPhase (optional)

Definition at line 15 of file GasKinetics.cpp.

References GasKinetics::setDerivativeSettings().

Member Function Documentation

◆ kineticsType()

virtual std::string kineticsType ( ) const

inlinevirtual

Identifies the Kinetics manager type.

Each class derived from Kinetics should override this method to return a meaningful identifier.

Reimplemented from Kinetics.

Definition at line 37 of file GasKinetics.h.

◆ getThirdBodyConcentrations()

void getThirdBodyConcentrations ( double * concm )

virtual

Return a vector of values of effective concentrations of third-body collision partners of any reaction.

Entries for reactions not involving third-body collision parters are not defined and set to not-a-number.

Parameters

concm Output vector of effective third-body concentrations. Length: nReactions().

Reimplemented from Kinetics.

Definition at line 34 of file GasKinetics.cpp.

References BulkKinetics::m_concm.

◆ thirdBodyConcentrations()

virtual const vector_fp & thirdBodyConcentrations ( ) const

inlinevirtual

Provide direct access to current third-body concentration values.

See also: getThirdBodyConcentrations.

Reimplemented from Kinetics.

Definition at line 42 of file GasKinetics.h.

References BulkKinetics::m_concm.

◆ getEquilibriumConstants()

void getEquilibriumConstants ( doublereal * kc )

virtual

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: nReactions().

Reimplemented from Kinetics.

Definition at line 188 of file GasKinetics.cpp.

References Kinetics::getReactionDelta(), BulkKinetics::m_dn, GasKinetics::m_rbuf0, Kinetics::nReactions(), ThermoPhase::RT(), Kinetics::thermo(), and GasKinetics::update_rates_T().

◆ getFwdRateConstants()

void getFwdRateConstants ( double * kfwd )

virtual

Return the forward rate constants.

The computed values include all temperature-dependent, pressure-dependent, and third body contributions. Length is the number of reactions. Units are a combination of kmol, m^3 and s, that depend on the rate expression for the reaction.

Parameters

kfwd	Output vector containing the forward reaction rate constants. Length: nReactions().

Deprecated:: Behavior to change after Cantera 2.6; for Cantera 2.6, rate constants of three-body reactions are multiplied with third-body concentrations (no change to legacy behavior). After Cantera 2.6, results will no longer include third-body concentrations and be consistent with conventional definitions (see Eq. 9.75 in Kee, Coltrin and Glarborg, 'Chemically Reacting Flow', Wiley Interscience, 2003). For new behavior, set 'Cantera::use_legacy_rate_constants(false)'.

Reimplemented from Kinetics.

Definition at line 254 of file GasKinetics.cpp.

References Cantera::legacy_rate_constants_used(), Kinetics::m_ropf, GasKinetics::processFwdRateCoefficients(), GasKinetics::processThirdBodies(), and Cantera::warn_deprecated().

◆ addReaction()

bool addReaction	(	shared_ptr< Reaction >	r,
		bool	resize = `true`
	)

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.
resize	If `true`, resizeReactions is called after reaction is added.

Returns: true if the reaction is added or false if it was skipped

Reimplemented from BulkKinetics.

Definition at line 574 of file GasKinetics.cpp.

References GasKinetics::addChebyshevReaction(), GasKinetics::addFalloffReaction(), GasKinetics::addPlogReaction(), BulkKinetics::addReaction(), GasKinetics::addThreeBodyReaction(), GasKinetics::m_legacy, and Kinetics::nReactions().

◆ modifyReaction()

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 from BulkKinetics.

Definition at line 662 of file GasKinetics.cpp.

References GasKinetics::modifyChebyshevReaction(), GasKinetics::modifyFalloffReaction(), GasKinetics::modifyPlogReaction(), BulkKinetics::modifyReaction(), and GasKinetics::modifyThreeBodyReaction().

◆ invalidateCache()

void invalidateCache ( )

virtual

Reimplemented from BulkKinetics.

Definition at line 716 of file GasKinetics.cpp.

◆ resizeReactions()

void resizeReactions ( )

virtual

Finalize Kinetics object and associated objects.

Reimplemented from BulkKinetics.

Definition at line 23 of file GasKinetics.cpp.

References GasKinetics::m_rbuf0, Kinetics::nReactions(), Kinetics::nTotalSpecies(), BulkKinetics::resizeReactions(), and Kinetics::thermo().

◆ updateROP()

void updateROP ( )

virtual

Reimplemented from Kinetics.

Definition at line 227 of file GasKinetics.cpp.

◆ getDerivativeSettings()

void getDerivativeSettings ( AnyMap & settings ) const

virtual

Retrieve derivative settings.

Derivatives are calculated with respect to temperature, pressure, molar concentrations and species mole fractions for forward/reverse/net rates of progress as well as creation/destruction and net production of species.

The following suffixes are used to indicate derivatives:

_ddT: derivative with respect to temperature (a vector)
_ddP: derivative with respect to pressure (a vector)
_ddC: derivative with respect to molar concentration (a vector)
_ddX: derivative with respect to species mole fractions (a matrix)

Settings for derivative evaluation are set by keyword/value pairs using the methods

See also: getDerivativeSettings and; setDerivativeSettings.

For GasKinetics, the following keyword/value pairs are supported:

skip-third-bodies (boolean) ... if false (default), third body concentrations are considered for the evaluation of jacobians
skip-falloff (boolean) ... if false (default), third-body effects on rate constants are considered for the evaluation of derivatives.
rtol-delta (double) ... relative tolerance used to perturb properties when calculating numerical derivatives. The default value is 1e-8.

Warning: The calculation of derivatives is an experimental part of the Cantera API and may be changed or removed without notice.

Parameters

settings AnyMap containing settings determining derivative evaluation.

Reimplemented from Kinetics.

Definition at line 273 of file GasKinetics.cpp.

References GasKinetics::m_jac_skip_third_bodies.

◆ setDerivativeSettings()

void setDerivativeSettings ( const AnyMap & settings )

virtual

Set/modify derivative settings.

Parameters

settings AnyMap containing settings determining derivative evaluation.

Reimplemented from Kinetics.

Definition at line 280 of file GasKinetics.cpp.

References AnyMap::empty(), AnyMap::getBool(), AnyMap::getDouble(), AnyMap::hasKey(), and GasKinetics::m_jac_skip_third_bodies.

Referenced by GasKinetics::GasKinetics().

◆ getFwdRateConstants_ddT()

void getFwdRateConstants_ddT ( double * dkfwd )

virtual

Calculate derivatives for forward rate constants with respect to temperature at constant pressure, molar concentration and mole fractions.

Parameters

[out] dkfwd Output vector of derivatives. Length: nReactions().

Reimplemented from Kinetics.

Definition at line 351 of file GasKinetics.cpp.

References GasKinetics::assertDerivativesValid(), Kinetics::m_rfn, and GasKinetics::process_ddT().

◆ getFwdRatesOfProgress_ddT()

void getFwdRatesOfProgress_ddT ( double * drop )

virtual

Calculate derivatives for forward rates-of-progress with respect to temperature at constant pressure, molar concentration and mole fractions.

Parameters

[out] drop Output vector of derivatives. Length: nReactions().

Reimplemented from Kinetics.

Definition at line 358 of file GasKinetics.cpp.

References GasKinetics::assertDerivativesValid(), Kinetics::m_ropf, and GasKinetics::process_ddT().

◆ getRevRatesOfProgress_ddT()

void getRevRatesOfProgress_ddT ( double * drop )

virtual

Calculate derivatives for reverse rates-of-progress with respect to temperature at constant pressure, molar concentration and mole fractions.

Parameters

[out] drop Output vector of derivatives. Length: nReactions().

Reimplemented from Kinetics.

Definition at line 365 of file GasKinetics.cpp.

References GasKinetics::assertDerivativesValid(), Kinetics::m_ropr, Kinetics::nReactions(), GasKinetics::process_ddT(), and GasKinetics::processEquilibriumConstants_ddT().

◆ getNetRatesOfProgress_ddT()

void getNetRatesOfProgress_ddT ( double * drop )

virtual

Calculate derivatives for net rates-of-progress with respect to temperature at constant pressure, molar concentration and mole fractions.

Parameters

[out] drop Output vector of derivatives. Length: nReactions().

Reimplemented from Kinetics.

Definition at line 379 of file GasKinetics.cpp.

References GasKinetics::assertDerivativesValid(), Kinetics::m_ropnet, Kinetics::m_ropr, Kinetics::nReactions(), GasKinetics::process_ddT(), and GasKinetics::processEquilibriumConstants_ddT().

◆ getFwdRateConstants_ddP()

void getFwdRateConstants_ddP ( double * dkfwd )

virtual

Calculate derivatives for forward rate constants with respect to pressure at constant temperature, molar concentration and mole fractions.

Parameters

[out] dkfwd Output vector of derivatives. Length: nReactions().

Reimplemented from Kinetics.

Definition at line 402 of file GasKinetics.cpp.

References GasKinetics::assertDerivativesValid(), Kinetics::m_rfn, and GasKinetics::process_ddP().

◆ getFwdRatesOfProgress_ddP()

void getFwdRatesOfProgress_ddP ( double * drop )

virtual

Calculate derivatives for forward rates-of-progress with respect to pressure at constant temperature, molar concentration and mole fractions.

Parameters

[out] drop Output vector of derivatives. Length: nReactions().

Reimplemented from Kinetics.

Definition at line 409 of file GasKinetics.cpp.

References GasKinetics::assertDerivativesValid(), Kinetics::m_ropf, and GasKinetics::process_ddP().

◆ getRevRatesOfProgress_ddP()

void getRevRatesOfProgress_ddP ( double * drop )

virtual

Calculate derivatives for reverse rates-of-progress with respect to pressure at constant temperature, molar concentration and mole fractions.

Parameters

[out] drop Output vector of derivatives. Length: nReactions().

Reimplemented from Kinetics.

Definition at line 416 of file GasKinetics.cpp.

References GasKinetics::assertDerivativesValid(), Kinetics::m_ropr, and GasKinetics::process_ddP().

◆ getNetRatesOfProgress_ddP()

void getNetRatesOfProgress_ddP ( double * drop )

virtual

Calculate derivatives for net rates-of-progress with respect to pressure at constant temperature, molar concentration and mole fractions.

Parameters

[out] drop Output vector of derivatives. Length: nReactions().

Reimplemented from Kinetics.

Definition at line 423 of file GasKinetics.cpp.

References GasKinetics::assertDerivativesValid(), Kinetics::m_ropnet, and GasKinetics::process_ddP().

◆ getFwdRateConstants_ddC()

void getFwdRateConstants_ddC ( double * dkfwd )

virtual

Calculate derivatives for forward rate constants with respect to molar concentration at constant temperature, pressure and mole fractions.

Parameters

[out] dkfwd Output vector of derivatives. Length: nReactions().

Warning: This method is an experimental part of the Cantera API and may be changed or removed without notice.

Reimplemented from Kinetics.

Definition at line 466 of file GasKinetics.cpp.

References GasKinetics::assertDerivativesValid(), Kinetics::m_reactantStoich, Kinetics::m_rfn, and GasKinetics::process_ddC().

◆ getFwdRatesOfProgress_ddC()

void getFwdRatesOfProgress_ddC ( double * drop )

virtual

Calculate derivatives for forward rates-of-progress with respect to molar concentration at constant temperature, pressure and mole fractions.

Parameters

[out] drop Output vector of derivatives. Length: nReactions().

Warning: This method is an experimental part of the Cantera API and may be changed or removed without notice.

Reimplemented from Kinetics.

Definition at line 473 of file GasKinetics.cpp.

References GasKinetics::assertDerivativesValid(), Kinetics::m_reactantStoich, Kinetics::m_ropf, and GasKinetics::process_ddC().

◆ getRevRatesOfProgress_ddC()

void getRevRatesOfProgress_ddC ( double * drop )

virtual

Calculate derivatives for reverse rates-of-progress with respect to molar concentration at constant temperature, pressure and mole fractions.

Parameters

[out] drop Output vector of derivatives. Length: nReactions().

Warning: This method is an experimental part of the Cantera API and may be changed or removed without notice.

Reimplemented from Kinetics.

Definition at line 480 of file GasKinetics.cpp.

References GasKinetics::assertDerivativesValid(), Kinetics::m_revProductStoich, Kinetics::m_ropr, and GasKinetics::process_ddC().

◆ getNetRatesOfProgress_ddC()

void getNetRatesOfProgress_ddC ( double * drop )

virtual

Calculate derivatives for net rates-of-progress with respect to molar concentration at constant temperature, pressure and mole fractions.

Parameters

[out] drop Output vector of derivatives. Length: nReactions().

Warning: This method is an experimental part of the Cantera API and may be changed or removed without notice.

Reimplemented from Kinetics.

Definition at line 487 of file GasKinetics.cpp.

References GasKinetics::assertDerivativesValid(), Kinetics::m_reactantStoich, Kinetics::m_revProductStoich, Kinetics::m_ropf, Kinetics::m_ropr, Kinetics::nReactions(), and GasKinetics::process_ddC().

◆ fwdRatesOfProgress_ddX()

Eigen::SparseMatrix< double > fwdRatesOfProgress_ddX ( )

virtual

Calculate derivatives for forward rates-of-progress with respect to species mole fractions at constant temperature, pressure and molar concentration.

The method returns a matrix with nReactions rows and nTotalSpecies columns. For a derivative with respect to \(X_i\), all other \(X_j\) are held constant, rather than enforcing \(\sum X_j = 1\).

Warning: This method is an experimental part of the Cantera API and may be changed or removed without notice.

Reimplemented from Kinetics.

Definition at line 539 of file GasKinetics.cpp.

References GasKinetics::assertDerivativesValid(), GasKinetics::m_rbuf0, Kinetics::m_reactantStoich, GasKinetics::process_ddX(), and GasKinetics::processFwdRateCoefficients().

◆ revRatesOfProgress_ddX()

Eigen::SparseMatrix< double > revRatesOfProgress_ddX ( )

virtual

Calculate derivatives for reverse rates-of-progress with respect to species mole fractions at constant temperature, pressure and molar concentration.

The method returns a matrix with nReactions rows and nTotalSpecies columns. For a derivative with respect to \(X_i\), all other \(X_j\) are held constant, rather than enforcing \(\sum X_j = 1\).

Warning: This method is an experimental part of the Cantera API and may be changed or removed without notice.

Reimplemented from Kinetics.

Definition at line 549 of file GasKinetics.cpp.

References GasKinetics::assertDerivativesValid(), GasKinetics::m_rbuf0, Kinetics::m_revProductStoich, GasKinetics::process_ddX(), GasKinetics::processEquilibriumConstants(), and GasKinetics::processFwdRateCoefficients().

◆ netRatesOfProgress_ddX()

Eigen::SparseMatrix< double > netRatesOfProgress_ddX ( )

virtual

Calculate derivatives for net rates-of-progress with respect to species mole fractions at constant temperature, pressure and molar concentration.

The method returns a matrix with nReactions rows and nTotalSpecies columns. For a derivative with respect to \(X_i\), all other \(X_j\) are held constant, rather than enforcing \(\sum X_j = 1\).

Warning: This method is an experimental part of the Cantera API and may be changed or removed without notice.

Reimplemented from Kinetics.

Definition at line 560 of file GasKinetics.cpp.

References GasKinetics::assertDerivativesValid(), GasKinetics::m_rbuf0, Kinetics::m_reactantStoich, Kinetics::m_revProductStoich, GasKinetics::process_ddX(), GasKinetics::processEquilibriumConstants(), and GasKinetics::processFwdRateCoefficients().

◆ update_rates_T()

void update_rates_T ( )

virtual

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

Definition at line 40 of file GasKinetics.cpp.

Referenced by GasKinetics::getEquilibriumConstants(), and GasKinetics::processFwdRateCoefficients().

◆ update_rates_C()

void update_rates_C ( )

virtual

Update properties that depend on concentrations.

Currently the enhanced collision partner concentrations are updated here, as well as the pressure-dependent portion of P-log and Chebyshev reactions.

Definition at line 91 of file GasKinetics.cpp.

References GasKinetics::concm_3b_values, GasKinetics::concm_falloff_values, ThirdBodyCalc::copy(), ThermoPhase::getActivityConcentrations(), Phase::getConcentrations(), GasKinetics::m_3b_concm, BulkKinetics::m_act_conc, GasKinetics::m_cheb_rates, BulkKinetics::m_concm, GasKinetics::m_falloff_concm, BulkKinetics::m_multi_concm, BulkKinetics::m_phys_conc, GasKinetics::m_plog_rates, Phase::molarDensity(), Kinetics::thermo(), and ThirdBodyCalc3::update().

Referenced by GasKinetics::processFwdRateCoefficients().

◆ processFwdRateCoefficients()

void processFwdRateCoefficients ( double * ropf )

protected

Calculate rate coefficients.

These methods are for

use, and seek to avoid code duplication while evaluating terms used for rate constants, rates of progress, and their derivatives.

Definition at line 148 of file GasKinetics.cpp.

References GasKinetics::m_falloff_high_rates, Kinetics::m_perturb, Kinetics::m_rfn, Kinetics::nReactions(), GasKinetics::processFalloffReactions(), GasKinetics::update_rates_C(), and GasKinetics::update_rates_T().

Referenced by GasKinetics::fwdRatesOfProgress_ddX(), GasKinetics::getFwdRateConstants(), GasKinetics::netRatesOfProgress_ddX(), and GasKinetics::revRatesOfProgress_ddX().

◆ processThirdBodies()

void processThirdBodies ( double * rop )

protected

Multiply rate with third-body collider concentrations.

Definition at line 166 of file GasKinetics.cpp.

References GasKinetics::concm_3b_values, GasKinetics::m_3b_concm, BulkKinetics::m_concm, BulkKinetics::m_multi_concm, and ThirdBodyCalc3::multiply().

Referenced by GasKinetics::getFwdRateConstants(), and GasKinetics::process_ddX().

◆ processEquilibriumConstants()

void processEquilibriumConstants ( double * rop )

protected

Multiply rate with inverse equilibrium constant.

Definition at line 179 of file GasKinetics.cpp.

References Kinetics::m_rkcn, and Kinetics::nReactions().

Referenced by GasKinetics::netRatesOfProgress_ddX(), and GasKinetics::revRatesOfProgress_ddX().

◆ processEquilibriumConstants_ddT()

void processEquilibriumConstants_ddT ( double * drkcn )

protected

Multiply rate with scaled temperature derivatives of the inverse equilibrium constant.

This (scaled) derivative is handled by a finite difference.

Definition at line 307 of file GasKinetics.cpp.

Referenced by GasKinetics::getNetRatesOfProgress_ddT(), and GasKinetics::getRevRatesOfProgress_ddT().

◆ process_ddT()

void process_ddT	(	const vector_fp &	in,
		double *	drop
	)

protected

Process temperature derivative.

Parameters

in	rate expression used for the derivative calculation
drop	pointer to output buffer

Definition at line 342 of file GasKinetics.cpp.

References BulkKinetics::m_bulk_rates, and Kinetics::m_rfn.

Referenced by GasKinetics::getFwdRateConstants_ddT(), GasKinetics::getFwdRatesOfProgress_ddT(), GasKinetics::getNetRatesOfProgress_ddT(), and GasKinetics::getRevRatesOfProgress_ddT().

◆ process_ddP()

void process_ddP	(	const vector_fp &	in,
		double *	drop
	)

protected

Process pressure derivative.

Parameters

in	rate expression used for the derivative calculation
drop	pointer to output buffer

Definition at line 393 of file GasKinetics.cpp.

References BulkKinetics::m_bulk_rates, and Kinetics::m_rfn.

Referenced by GasKinetics::getFwdRateConstants_ddP(), GasKinetics::getFwdRatesOfProgress_ddP(), GasKinetics::getNetRatesOfProgress_ddP(), and GasKinetics::getRevRatesOfProgress_ddP().

◆ process_ddC()

void process_ddC	(	StoichManagerN &	stoich,
		const vector_fp &	in,
		double *	drop,
		bool	mass_action = `true`
	)

protected

Process concentration (molar density) derivative.

Parameters

stoich	stoichiometry manager
in	rate expression used for the derivative calculation
drop	pointer to output buffer
mass_action	boolean indicating whether law of mass action applies

Definition at line 430 of file GasKinetics.cpp.

References ThirdBodyCalc3::empty(), BulkKinetics::m_bulk_rates, BulkKinetics::m_concm, GasKinetics::m_jac_skip_third_bodies, BulkKinetics::m_multi_concm, Kinetics::m_rfn, Phase::molarDensity(), Kinetics::nReactions(), StoichManagerN::scale(), ThirdBodyCalc3::scale(), ThirdBodyCalc3::scaleM(), and Kinetics::thermo().