Public interface for kinetics managers. More...

#include <Kinetics.h>

Inheritance diagram for Kinetics:

Detailed Description

Public interface for kinetics managers.

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

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

Definition at line 124 of file Kinetics.h.

Public Member Functions
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.

Constructors and General Information about Mechanism
	Kinetics ()=default
	Default constructor.

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

Kinetics &	operator= (const Kinetics &)=delete

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

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

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().

Information/Lookup Functions about Phases and Species
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.

Reaction Rates Of Progress
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	getEquilibriumConstants (double *kc)
	Return a vector of Equilibrium constants.

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

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

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

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

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

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

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

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

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

Species Production Rates
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].


Routines to Calculate Kinetics Derivatives (Jacobians) Kinetics 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) `_ddCi`: derivative with respect to species concentrations (a matrix) Since New in Cantera 2.6 Warning The calculation of kinetics derivatives is an experimental part of the Cantera API and may be changed or removed without notice. Source term derivatives are based on a generic rate-of-progress expression for the \( i \)-th reaction \( R_i \), which is a function of temperature \( T \), pressure \( P \) and molar concentrations \( C_j \): \[ R_i = k_{f,i} C_M^{\nu_{M,i}} \prod_j C_j^{\nu_{ji}^\prime} - k_{r,i} C_M^{\nu_{M,i}} \prod_j C_j^{\nu_{ji}^{\prime\prime}} \] Forward/reverse rate expressions \( k_{f,i} \) and \( k_{r,i} \) are implemented by ReactionRate specializations; forward/reverse stoichiometric coefficients are \( \nu_{ji}^\prime \) and \( \nu_{ji}^{\prime\prime} \). Unless the reaction involves third-body colliders, \( \nu_{M,i} = 0 \). For three-body reactions, effective ThirdBody collider concentrations \( C_M \) are considered with \( \nu_{M,i} = 1 \). For more detailed information on relevant theory, see, for example, Perini, et al. [31] or Niemeyer, et al. [29], although specifics of Cantera's implementation may differ. Partial derivatives are obtained from the product rule, where resulting terms consider reaction rate derivatives, derivatives of the concentration product term, and, if applicable, third-body term derivatives. ReactionRate specializations may implement exact derivatives (example: ArrheniusRate::ddTScaledFromStruct) or approximate them numerically (examples: ReactionData::perturbTemperature, PlogData::perturbPressure, FalloffData::perturbThirdBodies). Derivatives of concentration and third-body terms are based on analytic expressions. Species creation and destruction rates are obtained by multiplying rate-of-progress vectors by stoichiometric coefficient matrices. As this is a linear operation, it is possible to calculate derivatives the same way. All derivatives are calculated for source terms while holding other properties constant, independent of whether equation of state or \( \sum X_k = 1 \) constraints are satisfied. Thus, derivatives deviate from Jacobians and numerical derivatives that implicitly enforce these constraints. Depending on application and equation of state, derivatives can nevertheless be used to obtain Jacobians, for example: The Jacobian of net production rates \( \dot{\omega}_{k,\mathrm{net}} \) with respect to temperature at constant pressure needs to consider changes of molar density \( C \) due to temperature \[ \left. \frac{\partial \dot{\omega}_{k,\mathrm{net}}}{\partial T} \right\|_{P=\mathrm{const}} = \frac{\partial \dot{\omega}_{k,\mathrm{net}}}{\partial T} + \frac{\partial \dot{\omega}_{k,\mathrm{net}}}{\partial C} \left. \frac{\partial C}{\partial T} \right\|_{P=\mathrm{const}} \] where for an ideal gas \( \partial C / \partial T = - C / T \). The remaining partial derivatives are obtained from getNetProductionRates_ddT() and getNetProductionRates_ddC(), respectively. The Jacobian of \( \dot{\omega}_{k,\mathrm{net}} \) with respect to temperature at constant volume needs to consider pressure changes due to temperature \[ \left. \frac{\partial \dot{\omega}_{k,\mathrm{net}}}{\partial T} \right\|_{V=\mathrm{const}} = \frac{\partial \dot{\omega}_{k,\mathrm{net}}}{\partial T} + \frac{\partial \dot{\omega}_{k,\mathrm{net}}}{\partial P} \left. \frac{\partial P}{\partial T} \right\|_{V=\mathrm{const}} \] where for an ideal gas \( \partial P / \partial T = P / T \). The remaining partial derivatives are obtained from getNetProductionRates_ddT() and getNetProductionRates_ddP(), respectively. Similar expressions can be derived for other derivatives and source terms. While some applications require exact derivatives, others can tolerate approximate derivatives that neglect terms to increase computational speed and/or improve Jacobian sparsity (example: AdaptivePreconditioner). Derivative evaluations settings are accessible by keyword/value pairs using the methods getDerivativeSettings() and setDerivativeSettings(). For BulkKinetics, 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. For InterfaceKinetics, the following keyword/value pairs are supported: `skip-coverage-dependence` (boolean): if `false` (default), rate constant coverage dependence is not considered when evaluating derivatives. `skip-electrochemistry` (boolean): if `false` (default), electrical charge is not considered in evaluating the derivatives and these reactions are treated as normal surface reactions. `rtol-delta` (double): relative tolerance used to perturb properties when calculating numerical derivatives. The default value is 1e-8.
virtual void	getDerivativeSettings (AnyMap &settings) const
	Retrieve derivative settings.

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

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

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

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

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.

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.

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.

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.

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

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.

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.

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.

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.

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

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.

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.

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.

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.

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

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.

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

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

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

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

Reaction Mechanism Construction
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.

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

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

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

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

Altering Reaction Rates
These methods alter reaction rates. They are designed primarily for carrying out sensitivity analysis, but may be used for any purpose requiring dynamic alteration of rate constants. For each reaction, a real-valued multiplier may be defined that multiplies the reaction rate coefficient. The multiplier may be set to zero to completely remove a reaction from the mechanism.
double	multiplier (size_t i) const
	The current value of the multiplier for reaction i.

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

virtual void	invalidateCache ()

Protected Member Functions
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
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.

std::weak_ptr< Solution >	m_root
	reference to Solution

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

◆ Kinetics() [1/2]

Kinetics ( )

default

Default constructor.

◆ Kinetics() [2/2]

Kinetics ( const Kinetics & )

delete

Kinetics objects are not copyable or assignable.

Member Function Documentation

◆ kineticsType()

virtual string kineticsType ( ) const

inlinevirtual

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 in BulkKinetics, EdgeKinetics, and InterfaceKinetics.

Definition at line 144 of file Kinetics.h.

◆ resizeReactions()

void resizeReactions ( )

virtual

Finalize Kinetics object and associated objects.

Reimplemented in BulkKinetics, and InterfaceKinetics.

Definition at line 35 of file Kinetics.cpp.

◆ nReactions()

size_t nReactions ( ) const

inline

Number of reactions in the reaction mechanism.

Definition at line 152 of file Kinetics.h.

◆ checkReactionIndex()

void checkReactionIndex ( size_t m ) const

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

Definition at line 27 of file Kinetics.cpp.

◆ checkReactionArraySize()

void checkReactionArraySize ( size_t ii ) const

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

Used before calls which take an array pointer.

Definition at line 54 of file Kinetics.cpp.

◆ checkSpeciesIndex()

void checkSpeciesIndex ( size_t k ) const

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

Definition at line 88 of file Kinetics.cpp.

◆ checkSpeciesArraySize()

void checkSpeciesArraySize ( size_t mm ) const

Check that an array size is at least nSpecies() Throws an exception if kk is less than nSpecies().

Used before calls which take an array pointer.

Definition at line 95 of file Kinetics.cpp.

◆ nPhases()

size_t nPhases ( ) const

inline

The number of phases participating in the reaction mechanism.

For a homogeneous reaction mechanism, this will always return 1, but for a heterogeneous mechanism it will return the total number of phases in the mechanism.

Definition at line 184 of file Kinetics.h.

◆ checkPhaseIndex()

void checkPhaseIndex ( size_t m ) const

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

Definition at line 62 of file Kinetics.cpp.

◆ checkPhaseArraySize()

void checkPhaseArraySize ( size_t mm ) const

Check that an array size is at least nPhases() Throws an exception if mm is less than nPhases().

Used before calls which take an array pointer.

Definition at line 69 of file Kinetics.cpp.

◆ phaseIndex()

size_t phaseIndex ( const string & ph ) const

inline

Return the phase index of a phase in the list of phases defined within the object.

Parameters

ph	string name of the phase

If a -1 is returned, then the phase is not defined in the Kinetics object.

Definition at line 206 of file Kinetics.h.

◆ reactionPhaseIndex()

size_t reactionPhaseIndex ( ) const

Phase where the reactions occur.

For heterogeneous mechanisms, one of the phases in the list of phases represents the 2D interface or 1D edge at which the reactions take place. This method returns the index of the phase with the smallest spatial dimension (1, 2, or 3) among the list of phases. If there is more than one, the index of the first one is returned. For homogeneous mechanisms, the value 0 is returned.

Deprecated:: Starting in Cantera 3.0, the reacting phase is always be the first phase in the InterfaceKinetics object. To be removed after Cantera 3.1.

Definition at line 76 of file Kinetics.cpp.

◆ reactionPhase()

shared_ptr< ThermoPhase > reactionPhase ( ) const

Return pointer to phase where the reactions occur.

Since: New in Cantera 3.0

Definition at line 83 of file Kinetics.cpp.

◆ thermo() [1/2]

ThermoPhase & thermo ( size_t n = 0 )

inline

This method returns a reference to the nth ThermoPhase object defined in this kinetics mechanism.

It is typically used so that member functions of the ThermoPhase object may be called. For homogeneous mechanisms, there is only one object, and this method can be called without an argument to access it.

Parameters

n	Index of the ThermoPhase being sought.

Definition at line 242 of file Kinetics.h.

◆ thermo() [2/2]

const ThermoPhase & thermo ( size_t n = 0 ) const

inline

Definition at line 245 of file Kinetics.h.

◆ nTotalSpecies()

size_t nTotalSpecies ( ) const

inline

The total number of species in all phases participating in the kinetics mechanism.

This is useful to dimension arrays for use in calls to methods that return the species production rates, for example.

Definition at line 254 of file Kinetics.h.

◆ kineticsSpeciesIndex() [1/2]

size_t kineticsSpeciesIndex	(	size_t	k,
		size_t	n
	)		const

inline

The location of species k of phase n in species arrays.

Kinetics manager classes return species production rates in flat arrays, with the species of each phases following one another, in the order the phases were added. This method is useful to find the value for a particular species of a particular phase in arrays returned from methods like getCreationRates that return an array of species-specific quantities.

Example: suppose a heterogeneous mechanism involves three phases. The first contains 12 species, the second 26, and the third 3. Then species arrays must have size at least 41, and positions 0 - 11 are the values for the species in the first phase, positions 12 - 37 are the values for the species in the second phase, etc. Then kineticsSpeciesIndex(7, 0) = 7, kineticsSpeciesIndex(4, 1) = 16, and kineticsSpeciesIndex(2, 2) = 40.

Parameters

k	species index
n	phase index for the species

Definition at line 276 of file Kinetics.h.

◆ kineticsSpeciesName()

string kineticsSpeciesName ( size_t k ) const

Return the name of the kth species in the kinetics manager.

k is an integer from 0 to ktot - 1, where ktot is the number of species in the kinetics manager, which is the sum of the number of species in all phases participating in the kinetics manager. If k is out of bounds, the string "<unknown>" is returned.

Parameters

k	species index

Definition at line 238 of file Kinetics.cpp.

◆ kineticsSpeciesIndex() [2/2]

size_t kineticsSpeciesIndex ( const string & nm ) const

This routine will look up a species number based on the input string nm.

The lookup of species will occur for all phases listed in the kinetics object.

return

If a match is found, the position in the species list is returned.
If no match is found, the value -1 is returned.

Parameters

nm	Input string name of the species

Definition at line 248 of file Kinetics.cpp.

◆ speciesPhase() [1/3]

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.

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

Parameters

nm	String containing the name of the species.

Definition at line 260 of file Kinetics.cpp.

◆ speciesPhase() [2/3]

const ThermoPhase & speciesPhase ( const string & nm ) const

Definition at line 271 of file Kinetics.cpp.

◆ speciesPhase() [3/3]

ThermoPhase & speciesPhase ( size_t k )

inline

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.

Parameters

k	Species index

Definition at line 321 of file Kinetics.h.

◆ speciesPhaseIndex()

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.

Parameters

k	Species index

Definition at line 281 of file Kinetics.cpp.

◆ getFwdRatesOfProgress()

void getFwdRatesOfProgress ( double * fwdROP )

virtual

Return the forward rates of progress of the reactions.

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

Parameters

fwdROP Output vector containing forward rates of progress of the reactions. Length: nReactions().

Definition at line 302 of file Kinetics.cpp.

◆ getRevRatesOfProgress()

void getRevRatesOfProgress ( double * revROP )

virtual

Return the Reverse rates of progress of the reactions.

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

Parameters

revROP Output vector containing reverse rates of progress of the reactions. Length: nReactions().

Definition at line 308 of file Kinetics.cpp.

◆ getNetRatesOfProgress()

void getNetRatesOfProgress ( double * netROP )

virtual

Net rates of progress.

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

Parameters

netROP Output vector of the net ROP. Length: nReactions().

Definition at line 314 of file Kinetics.cpp.

◆ getEquilibriumConstants()

virtual void getEquilibriumConstants ( double * kc )

inlinevirtual

Return a vector of Equilibrium constants.

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

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

Parameters

kc	Output vector containing the equilibrium constants. Length: nReactions().

Reimplemented in BulkKinetics, and InterfaceKinetics.

Definition at line 381 of file Kinetics.h.

◆ getReactionDelta()

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

virtual

Change in species properties.

Given an array of molar species property values \( z_k, k = 1, \dots, K \), return the array of reaction values

\[ \Delta Z_i = \sum_k \nu_{k,i} z_k, i = 1, \dots, I. \]

For example, if this method is called with the array of standard-state molar Gibbs free energies for the species, then the values returned in array deltaProperty would be the standard-state Gibbs free energies of reaction for each reaction.

Parameters

property	Input vector of property value. Length: m_kk.
deltaProperty	Output vector of deltaRxn. Length: nReactions().

Definition at line 320 of file Kinetics.cpp.

◆ getRevReactionDelta()

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

virtual

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

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

Definition at line 329 of file Kinetics.cpp.

◆ getDeltaGibbs()

virtual void getDeltaGibbs ( double * deltaG )

inlinevirtual

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

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

units = J kmol-1

Parameters

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

Reimplemented in BulkKinetics, and InterfaceKinetics.

Definition at line 423 of file Kinetics.h.

◆ getDeltaElectrochemPotentials()

virtual void getDeltaElectrochemPotentials ( double * deltaM )

inlinevirtual

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

These values depend upon the concentration of the solution and the voltage of the phases

units = J kmol-1

Parameters

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

Reimplemented in InterfaceKinetics.

Definition at line 438 of file Kinetics.h.

◆ getDeltaEnthalpy()

virtual void getDeltaEnthalpy ( double * deltaH )

inlinevirtual

Return the vector of values for the reactions change in enthalpy.

These values depend upon the concentration of the solution.

units = J kmol-1

Parameters

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

Reimplemented in BulkKinetics, and InterfaceKinetics.

Definition at line 451 of file Kinetics.h.

◆ getDeltaEntropy()

virtual void getDeltaEntropy ( double * deltaS )

inlinevirtual

Return the vector of values for the reactions change in entropy.

These values depend upon the concentration of the solution.

units = J kmol-1 Kelvin-1

Parameters

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

Reimplemented in BulkKinetics, and InterfaceKinetics.

Definition at line 464 of file Kinetics.h.

◆ getDeltaSSGibbs()

virtual void getDeltaSSGibbs ( double * deltaG )

inlinevirtual

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

These values don't depend upon the concentration of the solution.

units = J kmol-1

Parameters

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

Reimplemented in BulkKinetics, and InterfaceKinetics.

Definition at line 478 of file Kinetics.h.

◆ getDeltaSSEnthalpy()

virtual void getDeltaSSEnthalpy ( double * deltaH )

inlinevirtual

Return the vector of values for the change in the standard state enthalpies of reaction.

These values don't depend upon the concentration of the solution.

units = J kmol-1

Parameters

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

Reimplemented in BulkKinetics, and InterfaceKinetics.

Definition at line 492 of file Kinetics.h.

◆ getDeltaSSEntropy()

virtual void getDeltaSSEntropy ( double * deltaS )

inlinevirtual

Return the vector of values for the change in the standard state entropies for each reaction.

These values don't depend upon the concentration of the solution.

units = J kmol-1 Kelvin-1

Parameters

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

Reimplemented in BulkKinetics, and InterfaceKinetics.

Definition at line 506 of file Kinetics.h.

◆ getThirdBodyConcentrations()

virtual void getThirdBodyConcentrations ( double * concm )

inlinevirtual

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 in BulkKinetics.

Definition at line 518 of file Kinetics.h.

◆ thirdBodyConcentrations()

virtual const vector< double > & thirdBodyConcentrations ( ) const

inlinevirtual

Provide direct access to current third-body concentration values.

See also: getThirdBodyConcentrations.

Reimplemented in BulkKinetics.

Definition at line 528 of file Kinetics.h.

◆ getCreationRates()

void getCreationRates ( double * cdot )

virtual

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

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

See also: nTotalSpecies.

Parameters

cdot	Output vector of creation rates. Length: m_kk.

Definition at line 338 of file Kinetics.cpp.

◆ getDestructionRates()

void getDestructionRates ( double * ddot )

virtual

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

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

See also: nTotalSpecies.

Parameters

ddot	Output vector of destruction rates. Length: m_kk.

Definition at line 352 of file Kinetics.cpp.

◆ getNetProductionRates()

void getNetProductionRates ( double * wdot )

virtual

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

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

See also: nTotalSpecies.

Parameters

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

Definition at line 363 of file Kinetics.cpp.

◆ reactantStoichCoeff()

double reactantStoichCoeff	(	size_t	k,
		size_t	i
	)		const

virtual

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

Parameters

k	kinetic species index
i	reaction index

Definition at line 292 of file Kinetics.cpp.

◆ reactantStoichCoeffs()

Eigen::SparseMatrix< double > reactantStoichCoeffs ( ) const

inline

Stoichiometric coefficient matrix for reactants.

Definition at line 1140 of file Kinetics.h.

◆ productStoichCoeff()

double productStoichCoeff	(	size_t	k,
		size_t	i
	)		const

virtual

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

Parameters

k	kinetic species index
i	reaction index

Definition at line 297 of file Kinetics.cpp.

◆ productStoichCoeffs()

Eigen::SparseMatrix< double > productStoichCoeffs ( ) const

inline

Stoichiometric coefficient matrix for products.

Definition at line 1155 of file Kinetics.h.

◆ revProductStoichCoeffs()

Eigen::SparseMatrix< double > revProductStoichCoeffs ( ) const

inline

Stoichiometric coefficient matrix for products of reversible reactions.

Definition at line 1162 of file Kinetics.h.

◆ reactantOrder()

virtual double reactantOrder	(	size_t	k,
		size_t	i
	)		const

inlinevirtual

Reactant order of species k in reaction i.

This is the nominal order of the activity concentration in determining the forward rate of progress of the reaction

Parameters

k	kinetic species index
i	reaction index

Definition at line 1174 of file Kinetics.h.

◆ productOrder()

virtual double productOrder	(	int	k,
		int	i
	)		const

inlinevirtual

product Order of species k in reaction i.

This is the nominal order of the activity concentration of species k in determining the reverse rate of progress of the reaction i

For irreversible reactions, this will all be zero.

Parameters

k	kinetic species index
i	reaction index

Definition at line 1188 of file Kinetics.h.

◆ getActivityConcentrations()

virtual void getActivityConcentrations ( double *const conc )

inlinevirtual

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

Parameters

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

Reimplemented in InterfaceKinetics.

Definition at line 1197 of file Kinetics.h.

◆ isReversible()

virtual bool isReversible ( size_t i )

inlinevirtual

True if reaction i has been declared to be reversible.

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

Parameters

i	reaction index

Reimplemented in BulkKinetics, and InterfaceKinetics.

Definition at line 1208 of file Kinetics.h.

◆ getFwdRateConstants()

virtual void getFwdRateConstants ( double * kfwd )

inlinevirtual

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 in BulkKinetics, and InterfaceKinetics.

Definition at line 1225 of file Kinetics.h.

◆ getRevRateConstants()

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

inlinevirtual

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 in BulkKinetics, and InterfaceKinetics.

Definition at line 1245 of file Kinetics.h.

◆ addThermo()

void addThermo ( shared_ptr< ThermoPhase > thermo )

virtual

Add a phase to the kinetics manager object.

This must be done before the function init() is called or before any reactions are input. The following fields are updated:

m_start -> vector of integers, containing the starting position of the species for each phase in the kinetics mechanism.
m_thermo -> vector of pointers to ThermoPhase phases that participate in the kinetics mechanism.
m_phaseindex -> map containing the string id of each ThermoPhase phase as a key and the index of the phase within the kinetics manager object as the value.

Parameters

thermo Reference to the ThermoPhase to be added.

Since: New in Cantera 3.0. Replaces addPhase.

Reimplemented in InterfaceKinetics.

Definition at line 520 of file Kinetics.cpp.

◆ init()

virtual void init ( )

inlinevirtual

Prepare the class for the addition of reactions, after all phases have been added.

This method is called automatically when the first reaction is added. It needs to be called directly only in the degenerate case where there are no reactions. The base class method does nothing, but derived classes may use this to perform any initialization (allocating arrays, etc.) that requires knowing the phases.

Reimplemented in InterfaceKinetics.

Definition at line 1280 of file Kinetics.h.

◆ parameters()

AnyMap parameters ( )

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

This excludes the reaction definitions, which are handled separately.

Definition at line 537 of file Kinetics.cpp.

◆ resizeSpecies()

void resizeSpecies ( )

virtual

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

Automatically called before adding each Reaction and Phase.

Reimplemented in BulkKinetics, and InterfaceKinetics.

Definition at line 553 of file Kinetics.cpp.

◆ 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 in BulkKinetics, and InterfaceKinetics.

Definition at line 565 of file Kinetics.cpp.

◆ 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 in BulkKinetics, and InterfaceKinetics.

Definition at line 653 of file Kinetics.cpp.

◆ reaction() [1/2]

shared_ptr< Reaction > reaction ( size_t i )

Return the Reaction object for reaction i.

Changes to this object do not affect the Kinetics object until the modifyReaction function is called.

Definition at line 684 of file Kinetics.cpp.

◆ reaction() [2/2]

shared_ptr< const Reaction > reaction ( size_t i ) const

Definition at line 690 of file Kinetics.cpp.

◆ skipUndeclaredSpecies() [1/2]

void skipUndeclaredSpecies ( bool skip )

inline

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

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

Definition at line 1326 of file Kinetics.h.

◆ skipUndeclaredSpecies() [2/2]

bool skipUndeclaredSpecies ( ) const

inline

Definition at line 1329 of file Kinetics.h.

◆ skipUndeclaredThirdBodies() [1/2]

void skipUndeclaredThirdBodies ( bool skip )

inline

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

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

Definition at line 1338 of file Kinetics.h.

◆ skipUndeclaredThirdBodies() [2/2]

bool skipUndeclaredThirdBodies ( ) const

inline

Definition at line 1341 of file Kinetics.h.

◆ multiplier()

double multiplier ( size_t i ) const

inline

The current value of the multiplier for reaction i.

Parameters

i	index of the reaction

Definition at line 1360 of file Kinetics.h.

◆ setMultiplier()

virtual void setMultiplier	(	size_t	i,
		double	f
	)

inlinevirtual

Set the multiplier for reaction i to f.

Parameters

i	index of the reaction
f	value of the multiplier.

Reimplemented in BulkKinetics, and InterfaceKinetics.

Definition at line 1369 of file Kinetics.h.

◆ invalidateCache()

virtual void invalidateCache ( )

inlinevirtual

Definition at line 1373 of file Kinetics.h.

◆ checkDuplicates()

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

virtual

Check for unmarked duplicate reactions and unmatched marked duplicates.

If throw_err is true, then an exception will be thrown if either any unmarked duplicate reactions are found, or if any marked duplicate reactions do not have a matching duplicate reaction. If throw_err is false, the indices of the first pair of duplicate reactions found will be returned, or the index of the unmatched duplicate will be returned as both elements of the pair. If no unmarked duplicates or unmatched marked duplicate reactions are found, returns (npos, npos).

Definition at line 102 of file Kinetics.cpp.

◆ setRoot()

virtual void setRoot ( shared_ptr< Solution > root )

inlinevirtual

Set root Solution holding all phase information.

Definition at line 1391 of file Kinetics.h.

◆ root()

shared_ptr< Solution > root ( ) const

inline

Get the Solution object containing this Kinetics object and associated ThermoPhase objects.

Definition at line 1397 of file Kinetics.h.

◆ updateROP()

virtual void updateROP ( )

inlineprotectedvirtual

Reimplemented in InterfaceKinetics.

Definition at line 1406 of file Kinetics.h.

◆ checkDuplicateStoich()

double checkDuplicateStoich	(	map< int, double > &	r1,
		map< int, double > &	r2
	)		const

protected

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.

r1 and r2 are maps of species key to stoichiometric coefficient, one for each reaction, where the species key is 1+k for reactants and -1-k for products and k is the species index.

Returns: 0.0 if the stoichiometries are not multiples of one another Otherwise, it returns the ratio of the stoichiometric coefficients.

Definition at line 195 of file Kinetics.cpp.

Member Data Documentation

◆ m_cache

ValueCache m_cache

protected

Cache for saved calculations within each Kinetics object.

Definition at line 1403 of file Kinetics.h.

◆ m_reactantStoich

StoichManagerN m_reactantStoich

protected

Stoichiometry manager for the reactants for each reaction.

Definition at line 1431 of file Kinetics.h.

◆ m_productStoich

StoichManagerN m_productStoich

protected

Stoichiometry manager for the products for each reaction.

Definition at line 1434 of file Kinetics.h.

◆ m_revProductStoich

StoichManagerN m_revProductStoich

protected

Stoichiometry manager for the products of reversible reactions.

Definition at line 1437 of file Kinetics.h.

◆ m_stoichMatrix

Eigen::SparseMatrix<double> m_stoichMatrix

protected

Net stoichiometry (products - reactants)

Definition at line 1440 of file Kinetics.h.

◆ m_ready

bool m_ready = false

protected

Boolean indicating whether Kinetics object is fully configured.

Definition at line 1444 of file Kinetics.h.

◆ m_kk

size_t m_kk = 0

protected

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

Definition at line 1448 of file Kinetics.h.

◆ m_perturb

vector<double> m_perturb

protected

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

It is initialized to one.

Definition at line 1452 of file Kinetics.h.

◆ m_reactions

vector<shared_ptr<Reaction> > m_reactions

protected

Vector of Reaction objects represented by this Kinetics manager.

Definition at line 1455 of file Kinetics.h.

◆ m_thermo

vector<shared_ptr<ThermoPhase> > m_thermo

protected

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

For homogeneous kinetics applications, this vector will only have one entry. For interfacial reactions, this vector will consist of multiple entries; some of them will be surface phases, and the other ones will be bulk phases. The order that the objects are listed determines the order in which the species comprising each phase are listed in the source term vector, originating from the reaction mechanism.

Definition at line 1467 of file Kinetics.h.

◆ m_start

vector<size_t> m_start

protected

m_start is a vector of integers specifying the beginning position for the species vector for the n'th phase in the kinetics class.

Definition at line 1473 of file Kinetics.h.

◆ m_phaseindex

map<string, size_t> m_phaseindex

protected

Mapping of the phase name to the position of the phase within the kinetics object.

Positions start with the value of 1. The member function, phaseIndex() decrements by one before returning the index value, so that missing phases return -1.

Definition at line 1481 of file Kinetics.h.

◆ m_mindim

size_t m_mindim = 4

protected

number of spatial dimensions of lowest-dimensional phase.

Definition at line 1484 of file Kinetics.h.

◆ m_rfn

vector<double> m_rfn

protected

Forward rate constant for each reaction.

Definition at line 1487 of file Kinetics.h.

◆ m_delta_gibbs0

vector<double> m_delta_gibbs0

protected

Delta G^0 for all reactions.

Definition at line 1490 of file Kinetics.h.

◆ m_rkcn

vector<double> m_rkcn

protected

Reciprocal of the equilibrium constant in concentration units.

Definition at line 1493 of file Kinetics.h.

◆ m_ropf

vector<double> m_ropf

protected

Forward rate-of-progress for each reaction.

Definition at line 1496 of file Kinetics.h.

◆ m_ropr

vector<double> m_ropr

protected

Reverse rate-of-progress for each reaction.

Definition at line 1499 of file Kinetics.h.

◆ m_ropnet

vector<double> m_ropnet

protected

Net rate-of-progress for each reaction.

Definition at line 1502 of file Kinetics.h.

◆ m_dH

vector<double> m_dH

protected

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

Definition at line 1505 of file Kinetics.h.

◆ m_rbuf

vector<double> m_rbuf

protected

Buffer used for storage of intermediate reaction-specific results.

Definition at line 1508 of file Kinetics.h.

◆ m_skipUndeclaredSpecies

bool m_skipUndeclaredSpecies = false

protected

See skipUndeclaredSpecies()

Definition at line 1511 of file Kinetics.h.

◆ m_skipUndeclaredThirdBodies

bool m_skipUndeclaredThirdBodies = false

protected

See skipUndeclaredThirdBodies()

Definition at line 1514 of file Kinetics.h.

◆ m_hasUndeclaredThirdBodies

bool m_hasUndeclaredThirdBodies = false

protected

Flag indicating whether reactions include undeclared third bodies.

Definition at line 1517 of file Kinetics.h.

◆ m_root

std::weak_ptr<Solution> m_root

protected

reference to Solution

Definition at line 1520 of file Kinetics.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

◆ Kinetics() [1/2]

◆ Kinetics() [2/2]

Member Function Documentation

◆ kineticsType()

◆ resizeReactions()

◆ nReactions()

◆ checkReactionIndex()

◆ checkReactionArraySize()

◆ checkSpeciesIndex()

◆ checkSpeciesArraySize()

◆ nPhases()

◆ checkPhaseIndex()

◆ checkPhaseArraySize()

◆ phaseIndex()

◆ reactionPhaseIndex()

◆ reactionPhase()

◆ thermo() [1/2]

◆ thermo() [2/2]

◆ nTotalSpecies()

◆ kineticsSpeciesIndex() [1/2]

◆ kineticsSpeciesName()

◆ kineticsSpeciesIndex() [2/2]

◆ speciesPhase() [1/3]

◆ speciesPhase() [2/3]

◆ speciesPhase() [3/3]

◆ speciesPhaseIndex()

◆ getFwdRatesOfProgress()

◆ getRevRatesOfProgress()

◆ getNetRatesOfProgress()

◆ getEquilibriumConstants()

◆ getReactionDelta()

◆ getRevReactionDelta()

◆ getDeltaGibbs()

◆ getDeltaElectrochemPotentials()

◆ getDeltaEnthalpy()

◆ getDeltaEntropy()

◆ getDeltaSSGibbs()

◆ getDeltaSSEnthalpy()

◆ getDeltaSSEntropy()

◆ getThirdBodyConcentrations()

◆ thirdBodyConcentrations()

◆ getCreationRates()

◆ getDestructionRates()

◆ getNetProductionRates()

◆ reactantStoichCoeff()

◆ reactantStoichCoeffs()

◆ productStoichCoeff()

◆ productStoichCoeffs()

◆ revProductStoichCoeffs()

◆ reactantOrder()

◆ productOrder()

◆ getActivityConcentrations()

◆ isReversible()

◆ getFwdRateConstants()

◆ getRevRateConstants()

◆ addThermo()

◆ init()

◆ parameters()

◆ resizeSpecies()

◆ addReaction()

◆ modifyReaction()

◆ reaction() [1/2]

◆ reaction() [2/2]

◆ skipUndeclaredSpecies() [1/2]

◆ skipUndeclaredSpecies() [2/2]

◆ skipUndeclaredThirdBodies() [1/2]

◆ skipUndeclaredThirdBodies() [2/2]

◆ multiplier()

◆ setMultiplier()

◆ invalidateCache()

◆ checkDuplicates()

◆ setRoot()

◆ root()

◆ updateROP()

◆ checkDuplicateStoich()