Specialization of Kinetics for chemistry in a single bulk phase. More...

#include <BulkKinetics.h>

Inheritance diagram for BulkKinetics:

Detailed Description

Specialization of Kinetics for chemistry in a single bulk phase.

Definition at line 20 of file BulkKinetics.h.

Public Member Functions
Constructors and General Information
string	kineticsType () const override
	Identifies the Kinetics manager type.

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

Reaction Mechanism Setup Routines
bool	addReaction (shared_ptr< Reaction > r, bool resize=true) override
	Add a single reaction to the mechanism.

void	addThirdBody (shared_ptr< Reaction > r)

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

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

void	resizeReactions () override
	Finalize Kinetics object and associated objects.

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

void	invalidateCache () override

Reaction rate constants, rates of progress, and thermodynamic properties
void	getFwdRateConstants (double *kfwd) override
	Return the forward rate constants.

void	getEquilibriumConstants (double *kc) override
	Return a vector of Equilibrium constants.

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

void	getDeltaGibbs (double *deltaG) override
	Return the vector of values for the reaction Gibbs free energy change.

void	getDeltaEnthalpy (double *deltaH) override
	Return the vector of values for the reactions change in enthalpy.

void	getDeltaEntropy (double *deltaS) override
	Return the vector of values for the reactions change in entropy.

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

void	getDeltaSSEnthalpy (double *deltaH) override
	Return the vector of values for the change in the standard state enthalpies of reaction.

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

Derivatives of rate constants and rates of progress
void	getDerivativeSettings (AnyMap &settings) const override
	Retrieve derivative settings.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Eigen::SparseMatrix< double >	fwdRatesOfProgress_ddCi () override
	Calculate derivatives for forward rates-of-progress with respect to species concentration at constant temperature, pressure and remaining species concentrations.

Eigen::SparseMatrix< double >	revRatesOfProgress_ddCi () override
	Calculate derivatives for forward rates-of-progress with respect to species concentration at constant temperature, pressure and remaining species concentrations.

Eigen::SparseMatrix< double >	netRatesOfProgress_ddCi () override
	Calculate derivatives for net rates-of-progress with respect to species concentration at constant temperature, pressure, and remaining species concentrations.

Rate calculation intermediate methods
void	updateROP () override

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

const vector< double > &	thirdBodyConcentrations () const override
	Provide direct access to current third-body concentration values.

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

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

shared_ptr< Solution >	root () const
	Get the Solution object containing this Kinetics object and associated ThermoPhase objects.

	Kinetics ()=default
	Default constructor.

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

Kinetics &	operator= (const Kinetics &)=delete

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

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

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

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.

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

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

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

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

size_t	reactionPhaseIndex () const
	Phase where the reactions occur.

shared_ptr< ThermoPhase >	reactionPhase () const
	Return pointer to phase where the reactions occur.

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

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.

size_t	kineticsSpeciesIndex (size_t k, size_t n) const
	The location of species k of phase n in species arrays.

string	kineticsSpeciesName (size_t k) const
	Return the name of the kth species in the kinetics manager.

size_t	kineticsSpeciesIndex (const string &nm) const
	This routine will look up a species number based on the input string nm.

ThermoPhase &	speciesPhase (const 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.

const ThermoPhase &	speciesPhase (const 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.

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.

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

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

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

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

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.

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

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

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

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

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

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

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

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

Eigen::SparseMatrix< double >	creationRates_ddCi ()
	Calculate derivatives for species creation rates with respect to species concentration at constant temperature, pressure, and concentration of all other species.

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

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

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

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

Eigen::SparseMatrix< double >	destructionRates_ddCi ()
	Calculate derivatives for species destruction rates with respect to species concentration at constant temperature, pressure, and concentration of all other species.

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

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

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

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.

Eigen::SparseMatrix< double >	netProductionRates_ddCi ()
	Calculate derivatives for species net production rates with respect to species concentration at constant temperature, pressure, and concentration of all other species.

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

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

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

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

Eigen::SparseMatrix< double >	revProductStoichCoeffs () const
	Stoichiometric coefficient matrix for products of reversible reactions.

virtual double	reactantOrder (size_t k, size_t i) const
	Reactant order of species k in reaction i.

virtual double	productOrder (int k, int i) const
	product Order of species k in reaction i.

virtual void	getActivityConcentrations (double *const conc)
	Get the vector of activity concentrations used in the kinetics object.

virtual void	addThermo (shared_ptr< ThermoPhase > thermo)
	Add a phase to the kinetics manager object.

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

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

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

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.

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.

bool	skipUndeclaredThirdBodies () const

void	setExplicitThirdBodyDuplicateHandling (const string &flag)
	Specify how to handle duplicate third body reactions where one reaction has an explicit third body and the other has the generic third body with a non-zero efficiency for the former third body.

string	explicitThirdBodyDuplicateHandling () const

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

Protected Member Functions
Internal service methods
Note These methods are for internal use, and seek to avoid code duplication while evaluating terms used for rate constants, rates of progress, and their derivatives.
void	processThirdBodies (double *rop)
	Multiply rate with third-body collider concentrations.

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

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

void	process_ddT (const vector< double > &in, double *drop)
	Process temperature derivative.

void	process_ddP (const vector< double > &in, double *drop)
	Process pressure derivative.

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

Eigen::SparseMatrix< double >	calculateCompositionDerivatives (StoichManagerN &stoich, const vector< double > &in, bool ddX=true)
	Process derivatives.

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

Protected Member Functions inherited from Kinetics
virtual void	updateROP ()

double	checkDuplicateStoich (map< int, double > &r1, 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.

Protected Attributes
vector< unique_ptr< MultiRateBase > >	m_bulk_rates
	Vector of rate handlers.

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

vector< size_t >	m_revindex
	Indices of reversible reactions.

vector< size_t >	m_irrev
	Indices of irreversible reactions.

vector< double >	m_dn
	Difference between the global reactants order and the global products order.

ThirdBodyCalc	m_multi_concm
	used with MultiRate evaluator

vector< double >	m_concm
	Third body concentrations.

vector< double >	m_act_conc
	Activity concentrations, as calculated by ThermoPhase::getActivityConcentrations.

vector< double >	m_phys_conc
	Physical concentrations, as calculated by ThermoPhase::getConcentrations.

bool	m_jac_skip_third_bodies
	Derivative settings.

bool	m_jac_skip_falloff

double	m_jac_rtol_delta

bool	m_ROP_ok = false

vector< double >	m_rbuf0
	Buffers for partial rop results with length nReactions()

vector< double >	m_rbuf1

vector< double >	m_rbuf2

vector< double >	m_kf0
	Forward rate constants without perturbation.

vector< double >	m_sbuf0

vector< double >	m_state

vector< double >	m_grt
	Standard chemical potentials for each species.

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

bool	m_ready = false
	Boolean indicating whether Kinetics object is fully configured.

size_t	m_kk = 0
	The number of species in all of the phases that participate in this kinetics mechanism.

vector< double >	m_perturb
	Vector of perturbation factors for each reaction's rate of progress vector.

vector< shared_ptr< Reaction > >	m_reactions
	Vector of Reaction objects represented by this Kinetics manager.

vector< shared_ptr< ThermoPhase > >	m_thermo
	m_thermo is a vector of pointers to ThermoPhase objects that are involved with this kinetics operator

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.

map< string, size_t >	m_phaseindex
	Mapping of the phase name to the position of the phase within the kinetics object.

size_t	m_mindim = 4
	number of spatial dimensions of lowest-dimensional phase.

vector< double >	m_rfn
	Forward rate constant for each reaction.

vector< double >	m_delta_gibbs0
	Delta G^0 for all reactions.

vector< double >	m_rkcn
	Reciprocal of the equilibrium constant in concentration units.

vector< double >	m_ropf
	Forward rate-of-progress for each reaction.

vector< double >	m_ropr
	Reverse rate-of-progress for each reaction.

vector< double >	m_ropnet
	Net rate-of-progress for each reaction.

vector< double >	m_dH
	The enthalpy change for each reaction to calculate Blowers-Masel rates.

vector< double >	m_rbuf
	Buffer used for storage of intermediate reaction-specific results.

bool	m_skipUndeclaredSpecies = false
	See skipUndeclaredSpecies()

bool	m_skipUndeclaredThirdBodies = false
	See skipUndeclaredThirdBodies()

bool	m_hasUndeclaredThirdBodies = false
	Flag indicating whether reactions include undeclared third bodies.

string	m_explicit_third_body_duplicates = "warn"

std::weak_ptr< Solution >	m_root
	reference to Solution

StoichManagerN	m_reactantStoich
	Stoichiometry manager for the reactants for each reaction.

StoichManagerN	m_productStoich
	Stoichiometry manager for the products for each reaction.

StoichManagerN	m_revProductStoich
	Stoichiometry manager for the products of reversible reactions.

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

Constructor & Destructor Documentation

◆ BulkKinetics()

BulkKinetics ( )

Definition at line 11 of file BulkKinetics.cpp.

Member Function Documentation

◆ kineticsType()

string kineticsType ( ) const

inlineoverridevirtual

Identifies the Kinetics manager type.

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

Since: Starting in Cantera 3.0, the name returned by this method corresponds to the canonical name used in the YAML input format.

Reimplemented from Kinetics.

Definition at line 27 of file BulkKinetics.h.

◆ isReversible()

bool isReversible ( size_t i )

overridevirtual

True if reaction i has been declared to be reversible.

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

Parameters

i	reaction index

Reimplemented from Kinetics.

Definition at line 15 of file BulkKinetics.cpp.

◆ addReaction()

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

overridevirtual

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 Kinetics.

Definition at line 19 of file BulkKinetics.cpp.

◆ addThirdBody()

void addThirdBody ( shared_ptr< Reaction > r )

Definition at line 73 of file BulkKinetics.cpp.

◆ modifyReaction()

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

overridevirtual

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 Kinetics.

Definition at line 93 of file BulkKinetics.cpp.

◆ resizeSpecies()

void resizeSpecies ( )

overridevirtual

Resize arrays with sizes that depend on the total number of species.

Automatically called before adding each Reaction and Phase.

Reimplemented from Kinetics.

Definition at line 118 of file BulkKinetics.cpp.

◆ resizeReactions()

void resizeReactions ( )

overridevirtual

Finalize Kinetics object and associated objects.

Reimplemented from Kinetics.

Definition at line 129 of file BulkKinetics.cpp.

◆ setMultiplier()

void setMultiplier	(	size_t	i,
		double	f
	)

overridevirtual

Set the multiplier for reaction i to f.

Parameters

i	index of the reaction
f	value of the multiplier.

Reimplemented from Kinetics.

Definition at line 147 of file BulkKinetics.cpp.

◆ invalidateCache()

void invalidateCache ( )

overridevirtual

Reimplemented from Kinetics.

Definition at line 153 of file BulkKinetics.cpp.

◆ getFwdRateConstants()

void getFwdRateConstants ( double * kfwd )

overridevirtual

Return the forward rate constants.

The computed values include all temperature-dependent and pressure-dependent contributions. By default, third-body concentrations are only considered if they are part of the reaction rate definition; for a legacy implementation that includes third-body concentrations see Cantera::use_legacy_rate_constants(). 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().

Reimplemented from Kinetics.

Definition at line 159 of file BulkKinetics.cpp.

◆ getEquilibriumConstants()

void getEquilibriumConstants ( double * kc )

overridevirtual

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 168 of file BulkKinetics.cpp.

◆ getRevRateConstants()

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

overridevirtual

Return the reverse rate constants.

The computed values include all temperature-dependent and pressure-dependent contributions. By default, third-body concentrations are only considered if they are part of the reaction rate definition; for a legacy implementation that includes third-body concentrations see Cantera::use_legacy_rate_constants(). 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. Note, this routine will return rate constants for irreversible reactions if the default for doIrreversible is overridden.

Parameters

krev	Output vector of reverse rate constants
doIrreversible	boolean indicating whether irreversible reactions should be included.

Reimplemented from Kinetics.

Definition at line 185 of file BulkKinetics.cpp.

◆ getDeltaGibbs()

void getDeltaGibbs ( double * deltaG )

overridevirtual

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

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

units = J kmol-1

Parameters

deltaG Output vector of deltaG's for reactions Length: nReactions().

Reimplemented from Kinetics.

Definition at line 204 of file BulkKinetics.cpp.

◆ getDeltaEnthalpy()

void getDeltaEnthalpy ( double * deltaH )

overridevirtual

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: nReactions().

Reimplemented from Kinetics.

Definition at line 212 of file BulkKinetics.cpp.

◆ getDeltaEntropy()

void getDeltaEntropy ( double * deltaS )

overridevirtual

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: nReactions().

Reimplemented from Kinetics.

Definition at line 220 of file BulkKinetics.cpp.

◆ getDeltaSSGibbs()

void getDeltaSSGibbs ( double * deltaG )

overridevirtual

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: nReactions().

Reimplemented from Kinetics.

Definition at line 228 of file BulkKinetics.cpp.

◆ getDeltaSSEnthalpy()

void getDeltaSSEnthalpy ( double * deltaH )

overridevirtual

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: nReactions().

Reimplemented from Kinetics.

Definition at line 239 of file BulkKinetics.cpp.

◆ getDeltaSSEntropy()

void getDeltaSSEntropy ( double * deltaS )

overridevirtual

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: nReactions().

Reimplemented from Kinetics.

Definition at line 250 of file BulkKinetics.cpp.

◆ getDerivativeSettings()

void getDerivativeSettings ( AnyMap & settings ) const

overridevirtual

Retrieve derivative settings.

Parameters

settings AnyMap containing settings determining derivative evaluation.

Reimplemented from Kinetics.

Definition at line 263 of file BulkKinetics.cpp.

◆ setDerivativeSettings()

void setDerivativeSettings ( const AnyMap & settings )

overridevirtual

Set/modify derivative settings.

Parameters

settings AnyMap containing settings determining derivative evaluation.

Reimplemented from Kinetics.

Definition at line 270 of file BulkKinetics.cpp.

◆ getFwdRateConstants_ddT()

void getFwdRateConstants_ddT ( double * dkfwd )

overridevirtual

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 284 of file BulkKinetics.cpp.

◆ getFwdRatesOfProgress_ddT()

void getFwdRatesOfProgress_ddT ( double * drop )

overridevirtual

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 291 of file BulkKinetics.cpp.

◆ getRevRatesOfProgress_ddT()

void getRevRatesOfProgress_ddT ( double * drop )

overridevirtual

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 298 of file BulkKinetics.cpp.

◆ getNetRatesOfProgress_ddT()

void getNetRatesOfProgress_ddT ( double * drop )

overridevirtual

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 312 of file BulkKinetics.cpp.

◆ getFwdRateConstants_ddP()

void getFwdRateConstants_ddP ( double * dkfwd )

overridevirtual

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 326 of file BulkKinetics.cpp.

◆ getFwdRatesOfProgress_ddP()

void getFwdRatesOfProgress_ddP ( double * drop )

overridevirtual

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 333 of file BulkKinetics.cpp.

◆ getRevRatesOfProgress_ddP()

void getRevRatesOfProgress_ddP ( double * drop )

overridevirtual

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 340 of file BulkKinetics.cpp.

◆ getNetRatesOfProgress_ddP()

void getNetRatesOfProgress_ddP ( double * drop )

overridevirtual

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 347 of file BulkKinetics.cpp.

◆ getFwdRateConstants_ddC()

void getFwdRateConstants_ddC ( double * dkfwd )

overridevirtual

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 354 of file BulkKinetics.cpp.

◆ getFwdRatesOfProgress_ddC()

void getFwdRatesOfProgress_ddC ( double * drop )

overridevirtual

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 361 of file BulkKinetics.cpp.

◆ getRevRatesOfProgress_ddC()

void getRevRatesOfProgress_ddC ( double * drop )

overridevirtual

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 368 of file BulkKinetics.cpp.

◆ getNetRatesOfProgress_ddC()

void getNetRatesOfProgress_ddC ( double * drop )

overridevirtual

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 375 of file BulkKinetics.cpp.

◆ fwdRatesOfProgress_ddX()

Eigen::SparseMatrix< double > fwdRatesOfProgress_ddX ( )

overridevirtual

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 387 of file BulkKinetics.cpp.

◆ revRatesOfProgress_ddX()

Eigen::SparseMatrix< double > revRatesOfProgress_ddX ( )

overridevirtual

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 397 of file BulkKinetics.cpp.

◆ netRatesOfProgress_ddX()

Eigen::SparseMatrix< double > netRatesOfProgress_ddX ( )

overridevirtual

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 408 of file BulkKinetics.cpp.

◆ fwdRatesOfProgress_ddCi()

Eigen::SparseMatrix< double > fwdRatesOfProgress_ddCi ( )

overridevirtual

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

The method returns a matrix with nReactions() rows and nTotalSpecies() columns. For a derivative with respect to \( c_i \), all other \( c_j \) are held constant.

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

Since: New in Cantera 3.0.

Reimplemented from Kinetics.

Definition at line 422 of file BulkKinetics.cpp.

◆ revRatesOfProgress_ddCi()

Eigen::SparseMatrix< double > revRatesOfProgress_ddCi ( )

overridevirtual

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

The method returns a matrix with nReactions() rows and nTotalSpecies() columns. For a derivative with respect to \( c_i \), all other \( c_j \) are held constant.

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

Since: New in Cantera 3.0.

Reimplemented from Kinetics.

Definition at line 432 of file BulkKinetics.cpp.

◆ netRatesOfProgress_ddCi()

Eigen::SparseMatrix< double > netRatesOfProgress_ddCi ( )

overridevirtual

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

The method returns a matrix with nReactions() rows and nTotalSpecies() columns. For a derivative with respect to \( c_i \), all other \( c_j \) are held constant.

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

Since: New in Cantera 3.0.

Reimplemented from Kinetics.

Definition at line 443 of file BulkKinetics.cpp.

◆ updateROP()

void updateROP ( )

overridevirtual

Reimplemented from Kinetics.

Definition at line 457 of file BulkKinetics.cpp.

◆ getThirdBodyConcentrations()

void getThirdBodyConcentrations ( double * concm )

overridevirtual

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

Entries for reactions not involving third-body collision partners 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 542 of file BulkKinetics.cpp.

◆ thirdBodyConcentrations()

const vector< double > & thirdBodyConcentrations ( ) const

inlineoverridevirtual

Provide direct access to current third-body concentration values.

See also: getThirdBodyConcentrations.

Reimplemented from Kinetics.

Definition at line 90 of file BulkKinetics.h.

◆ processThirdBodies()

void processThirdBodies ( double * rop )

protected

Multiply rate with third-body collider concentrations.

Definition at line 548 of file BulkKinetics.cpp.

◆ applyEquilibriumConstants()

void applyEquilibriumConstants ( double * rop )

protected

Multiply rate with inverse equilibrium constant.

Definition at line 556 of file BulkKinetics.cpp.

◆ applyEquilibriumConstants_ddT()

void applyEquilibriumConstants_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 565 of file BulkKinetics.cpp.

◆ process_ddT()

void process_ddT	(	const vector< double > &	in,
		double *	drop
	)

protected

Process temperature derivative.

Parameters

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

Definition at line 600 of file BulkKinetics.cpp.

◆ process_ddP()

void process_ddP	(	const vector< double > &	in,
		double *	drop
	)

protected

Process pressure derivative.

Parameters

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

Definition at line 609 of file BulkKinetics.cpp.

◆ process_ddC()

void process_ddC	(	StoichManagerN &	stoich,
		const vector< double > &	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 618 of file BulkKinetics.cpp.

◆ calculateCompositionDerivatives()

Eigen::SparseMatrix< double > calculateCompositionDerivatives	(	StoichManagerN &	stoich,
		const vector< double > &	in,
		bool	ddX = `true`
	)

protected

Process derivatives.

Parameters

stoich	stoichiometry manager
in	rate expression used for the derivative calculation
ddX	true: w.r.t mole fractions false: w.r.t species concentrations

Returns: a sparse matrix of derivative contributions for each reaction of dimensions nTotalReactions by nTotalSpecies

Definition at line 653 of file BulkKinetics.cpp.

◆ assertDerivativesValid()

void assertDerivativesValid ( const string & name )

protected

Helper function ensuring that all rate derivatives can be calculated.

Parameters

name	method name used for error output

Exceptions

CanteraError if ideal gas assumption does not hold

Definition at line 695 of file BulkKinetics.cpp.

Member Data Documentation

◆ m_bulk_rates

vector<unique_ptr<MultiRateBase> > m_bulk_rates

protected

Vector of rate handlers.

Definition at line 152 of file BulkKinetics.h.

◆ m_bulk_types

map<string, size_t> m_bulk_types

protected

Mapping of rate handlers.

Definition at line 153 of file BulkKinetics.h.

◆ m_revindex

vector<size_t> m_revindex

protected

Indices of reversible reactions.

Definition at line 155 of file BulkKinetics.h.

◆ m_irrev

vector<size_t> m_irrev

protected

Indices of irreversible reactions.

Definition at line 156 of file BulkKinetics.h.

◆ m_dn

vector<double> m_dn

protected

Difference between the global reactants order and the global products order.

Of type "double" to account for the fact that we can have real- valued stoichiometries.

Definition at line 161 of file BulkKinetics.h.

◆ m_multi_concm

ThirdBodyCalc m_multi_concm

protected

used with MultiRate evaluator

Definition at line 163 of file BulkKinetics.h.

◆ m_concm

vector<double> m_concm

protected

Third body concentrations.

Definition at line 166 of file BulkKinetics.h.

◆ m_act_conc

vector<double> m_act_conc

protected

Activity concentrations, as calculated by ThermoPhase::getActivityConcentrations.

Definition at line 169 of file BulkKinetics.h.

◆ m_phys_conc

vector<double> m_phys_conc

protected

Physical concentrations, as calculated by ThermoPhase::getConcentrations.

Definition at line 172 of file BulkKinetics.h.

◆ m_jac_skip_third_bodies

bool m_jac_skip_third_bodies

protected

Derivative settings.

Definition at line 175 of file BulkKinetics.h.

◆ m_jac_skip_falloff

bool m_jac_skip_falloff

protected

Definition at line 176 of file BulkKinetics.h.

◆ m_jac_rtol_delta

double m_jac_rtol_delta

protected

Definition at line 177 of file BulkKinetics.h.

◆ m_ROP_ok

bool m_ROP_ok = false

protected

Definition at line 179 of file BulkKinetics.h.

◆ m_rbuf0

vector<double> m_rbuf0

protected

Buffers for partial rop results with length nReactions()

Definition at line 182 of file BulkKinetics.h.

◆ m_rbuf1

vector<double> m_rbuf1

protected

Definition at line 183 of file BulkKinetics.h.

◆ m_rbuf2

vector<double> m_rbuf2

protected

Definition at line 184 of file BulkKinetics.h.

◆ m_kf0

vector<double> m_kf0

protected

Forward rate constants without perturbation.

Definition at line 185 of file BulkKinetics.h.

◆ m_sbuf0

vector<double> m_sbuf0

protected

Definition at line 186 of file BulkKinetics.h.

◆ m_state

vector<double> m_state

protected

Definition at line 187 of file BulkKinetics.h.

◆ m_grt

vector<double> m_grt

protected

Standard chemical potentials for each species.

Definition at line 188 of file BulkKinetics.h.

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

Detailed Description

Public Member Functions

Protected Member Functions

Protected Attributes

Constructor & Destructor Documentation

◆ BulkKinetics()

Member Function Documentation

◆ kineticsType()

◆ isReversible()

◆ addReaction()

◆ addThirdBody()

◆ modifyReaction()

◆ resizeSpecies()

◆ resizeReactions()

◆ setMultiplier()

◆ invalidateCache()

◆ getFwdRateConstants()

◆ getEquilibriumConstants()

◆ getRevRateConstants()

◆ getDeltaGibbs()

◆ getDeltaEnthalpy()

◆ getDeltaEntropy()

◆ getDeltaSSGibbs()

◆ getDeltaSSEnthalpy()

◆ getDeltaSSEntropy()

◆ getDerivativeSettings()

◆ setDerivativeSettings()

◆ getFwdRateConstants_ddT()

◆ getFwdRatesOfProgress_ddT()

◆ getRevRatesOfProgress_ddT()

◆ getNetRatesOfProgress_ddT()

◆ getFwdRateConstants_ddP()

◆ getFwdRatesOfProgress_ddP()

◆ getRevRatesOfProgress_ddP()

◆ getNetRatesOfProgress_ddP()

◆ getFwdRateConstants_ddC()

◆ getFwdRatesOfProgress_ddC()

◆ getRevRatesOfProgress_ddC()

◆ getNetRatesOfProgress_ddC()

◆ fwdRatesOfProgress_ddX()

◆ revRatesOfProgress_ddX()

◆ netRatesOfProgress_ddX()

◆ fwdRatesOfProgress_ddCi()

◆ revRatesOfProgress_ddCi()

◆ netRatesOfProgress_ddCi()

◆ updateROP()

◆ getThirdBodyConcentrations()

◆ thirdBodyConcentrations()

◆ processThirdBodies()

◆ applyEquilibriumConstants()

◆ applyEquilibriumConstants_ddT()

◆ process_ddT()

◆ process_ddP()

◆ process_ddC()

◆ calculateCompositionDerivatives()

◆ assertDerivativesValid()

Member Data Documentation

◆ m_bulk_rates

◆ m_bulk_types

◆ m_revindex

◆ m_irrev

◆ m_dn

◆ m_multi_concm

◆ m_concm

◆ m_act_conc

◆ m_phys_conc

◆ m_jac_skip_third_bodies

◆ m_jac_skip_falloff

◆ m_jac_rtol_delta

◆ m_ROP_ok

◆ m_rbuf0

◆ m_rbuf1

◆ m_rbuf2

◆ m_kf0

◆ m_sbuf0

◆ m_state

◆ m_grt