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Kinetics Class Reference
Chemical Kinetics » Kinetics Managers

Public interface for kinetics managers. More...

`#include <Kinetics.h>`

Inheritance diagram for Kinetics:
[legend]

## 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 125 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.
void | selectPhase (const double *data, const ThermoPhase *phase, double *phase_data)
| Takes as input an array of properties for all species in the mechanism and copies those values belonging to a particular phase to the output array.
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.
virtual double | reactionEnthalpy (const Composition &reactants, const Composition &products)
| Calculate the reaction enthalpy of a reaction which has not necessarily been added into the Kinetics object.
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 | surfacePhaseIndex () const
| This returns the integer index of the phase which has ThermoPhase type cSurf.
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.
size_t | kineticsSpeciesIndex (const string &nm, const string &ph) 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. [perini2012] or Niemeyer, et al. [niemeyer2017], 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 string | reactionType (size_t i) const
| String specifying the type of reaction.
virtual string | reactionTypeStr (size_t i) const
| String specifying the type of reaction.
virtual bool | isReversible (size_t i)
| True if reaction i has been declared to be reversible.
string | reactionString (size_t i) const
| Return a string representing the reaction.
string | reactantString (size_t i) const
| Returns a string containing the reactants side of the reaction equation.
string | productString (size_t i) const
| Returns a string containing the products side of the reaction equation.
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 | addPhase (ThermoPhase &thermo)
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< ThermoPhase * > | m_thermo
| m_thermo is a vector of pointers to ThermoPhase objects that are involved with this kinetics operator
vector< shared_ptr< ThermoPhase > > | m_sharedThermo
| vector of shared pointers,
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_surfphase = npos
| Index in the list of phases of the one surface phase.
size_t | m_rxnphase = npos
| Phase Index where reactions are assumed to be taking place.
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
| inline virtual

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, GasKinetics, and InterfaceKinetics.

Definition at line 145 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 153 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 93 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 100 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 185 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 207 of file Kinetics.h.

## ◆ surfacePhaseIndex()

size_t surfacePhaseIndex | ( |  | ) | const

This returns the integer index of the phase which has ThermoPhase type cSurf.

For heterogeneous mechanisms, this identifies the one surface phase. For homogeneous mechanisms, this returns -1.

Deprecated:
  To be removed after Cantera 3.0. Use reactionPhaseIndex instead.

Definition at line 76 of file Kinetics.cpp.

## ◆ reactionPhaseIndex()

size_t reactionPhaseIndex | ( |  | ) | const
| inline

Phase where the reactions occur.

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

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

Definition at line 235 of file Kinetics.h.

## ◆ 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 254 of file Kinetics.h.

## ◆ thermo() [2/2]

const ThermoPhase & thermo | ( | size_t | n = `0` | ) | const
| inline

Definition at line 257 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 266 of file Kinetics.h.

## ◆ kineticsSpeciesIndex() [1/3]

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 288 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 258 of file Kinetics.cpp.

## ◆ kineticsSpeciesIndex() [2/3]

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 268 of file Kinetics.cpp.

## ◆ kineticsSpeciesIndex() [3/3]

size_t kineticsSpeciesIndex | ( | const string & | nm,
|  | const string & | ph
| ) |  | const

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

The lookup of species will occur in the specified phase of the object, or all phases if ph is "<any>".

return

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

Parameters

  nm | Input string name of the species
  ph | Input string name of the phase.

Deprecated:
  To be removed after Cantera 3.0. Species names should be unique across all phases.

Definition at line 280 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 302 of file Kinetics.cpp.

## ◆ speciesPhase() [2/3]

const ThermoPhase & speciesPhase | ( | const string & | nm | ) | const

Definition at line 313 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 350 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 323 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 374 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 380 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 386 of file Kinetics.cpp.

## ◆ getEquilibriumConstants()

virtual void getEquilibriumConstants | ( | double * | kc | ) |
| inline virtual

Return a vector of Equilibrium constants.

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

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

Parameters

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

Reimplemented in BulkKinetics, and InterfaceKinetics.

Definition at line 410 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 392 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 401 of file Kinetics.cpp.

## ◆ getDeltaGibbs()

virtual void getDeltaGibbs | ( | double * | deltaG | ) |
| inline virtual

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 452 of file Kinetics.h.

## ◆ getDeltaElectrochemPotentials()

virtual void getDeltaElectrochemPotentials | ( | double * | deltaM | ) |
| inline virtual

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 467 of file Kinetics.h.

## ◆ getDeltaEnthalpy()

virtual void getDeltaEnthalpy | ( | double * | deltaH | ) |
| inline virtual

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 480 of file Kinetics.h.

## ◆ getDeltaEntropy()

virtual void getDeltaEntropy | ( | double * | deltaS | ) |
| inline virtual

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 493 of file Kinetics.h.

## ◆ getDeltaSSGibbs()

virtual void getDeltaSSGibbs | ( | double * | deltaG | ) |
| inline virtual

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 507 of file Kinetics.h.

## ◆ getDeltaSSEnthalpy()

virtual void getDeltaSSEnthalpy | ( | double * | deltaH | ) |
| inline virtual

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 521 of file Kinetics.h.

## ◆ getDeltaSSEntropy()

virtual void getDeltaSSEntropy | ( | double * | deltaS | ) |
| inline virtual

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 535 of file Kinetics.h.

## ◆ getThirdBodyConcentrations()

virtual void getThirdBodyConcentrations | ( | double * | concm | ) |
| inline virtual

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

Entries for reactions not involving third-body collision 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 547 of file Kinetics.h.

## ◆ thirdBodyConcentrations()

virtual const vector< double > & thirdBodyConcentrations | ( |  | ) | const
| inline virtual

Provide direct access to current third-body concentration values.

See also
  getThirdBodyConcentrations.

Reimplemented in BulkKinetics.

Definition at line 557 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 410 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 424 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 435 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 334 of file Kinetics.cpp.

## ◆ reactantStoichCoeffs()

Eigen::SparseMatrix< double > reactantStoichCoeffs | ( |  | ) | const
| inline

Stoichiometric coefficient matrix for reactants.

Definition at line 1169 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 339 of file Kinetics.cpp.

## ◆ productStoichCoeffs()

Eigen::SparseMatrix< double > productStoichCoeffs | ( |  | ) | const
| inline

Stoichiometric coefficient matrix for products.

Definition at line 1184 of file Kinetics.h.

## ◆ revProductStoichCoeffs()

Eigen::SparseMatrix< double > revProductStoichCoeffs | ( |  | ) | const
| inline

Stoichiometric coefficient matrix for products of reversible reactions.

Definition at line 1191 of file Kinetics.h.

## ◆ reactantOrder()

virtual double reactantOrder | ( | size_t | k,
|  | size_t | i
| ) |  | const
| inline virtual

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 1203 of file Kinetics.h.

## ◆ productOrder()

virtual double productOrder | ( | int | k,
|  | int | i
| ) |  | const
| inline virtual

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 1217 of file Kinetics.h.

## ◆ getActivityConcentrations()

virtual void getActivityConcentrations | ( | double *const | conc | ) |
| inline virtual

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 1226 of file Kinetics.h.

## ◆ reactionType()

string reactionType | ( | size_t | i | ) | const
| virtual

String specifying the type of reaction.

Parameters

  i | reaction index

Since
  Method returned magic number prior to Cantera 3.0.

Deprecated:
  To be removed after Cantera 3.0. Replace with `kin->reaction(i)->type()`

Definition at line 344 of file Kinetics.cpp.

## ◆ reactionTypeStr()

string reactionTypeStr | ( | size_t | i | ) | const
| virtual

String specifying the type of reaction.

Parameters

  i | reaction index

Deprecated:
  To be removed after Cantera 3.0.

Definition at line 349 of file Kinetics.cpp.

## ◆ isReversible()

virtual bool isReversible | ( | size_t | i | ) |
| inline virtual

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 1255 of file Kinetics.h.

## ◆ reactionString()

string reactionString | ( | size_t | i | ) | const

Return a string representing the reaction.

Parameters

  i | reaction index

Deprecated:
  To be removed after Cantera 3.0. Replace with `kin->reaction(i)->equation()`.

Definition at line 354 of file Kinetics.cpp.

## ◆ reactantString()

string reactantString | ( | size_t | i | ) | const

Returns a string containing the reactants side of the reaction equation.

Deprecated:
  To be removed after Cantera 3.0. Replace with `kin->reaction(i)->reactantString()`

Definition at line 361 of file Kinetics.cpp.

## ◆ productString()

string productString | ( | size_t | i | ) | const

Returns a string containing the products side of the reaction equation.

Deprecated:
  To be removed after Cantera 3.0. Replace with `kin->reaction(i)->productString()`

Definition at line 368 of file Kinetics.cpp.

## ◆ getFwdRateConstants()

virtual void getFwdRateConstants | ( | double * | kfwd | ) |
| inline virtual

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 1291 of file Kinetics.h.

## ◆ getRevRateConstants()

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

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 1311 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_rxnphase -> index of the phase where reactions occur, which is the lowest- dimensional phase in the system, for example the surface in a surface 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 592 of file Kinetics.cpp.

## ◆ addPhase()

void addPhase | ( | ThermoPhase & | thermo | ) |
| virtual

See also
  Kinetics::addThermo(shared_ptr<ThermoPhase>)

Deprecated:
  To be removed after Cantera 3.0. Replaced by addThermo pointer.

Reimplemented in InterfaceKinetics.

Definition at line 616 of file Kinetics.cpp.

## ◆ init()

virtual void init | ( |  | ) |
| inline virtual

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 1354 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 637 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 653 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 665 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 753 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 784 of file Kinetics.cpp.

## ◆ reaction() [2/2]

shared_ptr< const Reaction > reaction | ( | size_t | i | ) | const

Definition at line 790 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 1400 of file Kinetics.h.

## ◆ skipUndeclaredSpecies() [2/2]

bool skipUndeclaredSpecies | ( |  | ) | const
| inline

Definition at line 1403 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 1412 of file Kinetics.h.

## ◆ skipUndeclaredThirdBodies() [2/2]

bool skipUndeclaredThirdBodies | ( |  | ) | const
| inline

Definition at line 1415 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 1434 of file Kinetics.h.

## ◆ setMultiplier()

virtual void setMultiplier | ( | size_t | i,
|  | double | f
| ) |  |
| inline virtual

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 1443 of file Kinetics.h.

## ◆ invalidateCache()

virtual void invalidateCache | ( |  | ) |
| inline virtual

Definition at line 1447 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 107 of file Kinetics.cpp.

## ◆ selectPhase()

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

Takes as input an array of properties for all species in the mechanism and copies those values belonging to a particular phase to the output array.

Parameters

  data | Input data array.
  phase | Pointer to one of the phase objects participating in this reaction mechanism
  phase_data | Output array where the values for the the specified phase are to be written.

Deprecated:
  Unused. To be removed after Cantera 3.0.

Definition at line 243 of file Kinetics.cpp.

## ◆ setRoot()

virtual void setRoot | ( | shared_ptr< Solution > | root | ) |
| inline virtual

Set root Solution holding all phase information.

Definition at line 1479 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 1485 of file Kinetics.h.

## ◆ reactionEnthalpy()

double reactionEnthalpy | ( | const Composition & | reactants,
|  | const Composition & | products
| ) |  |
| virtual

Calculate the reaction enthalpy of a reaction which has not necessarily been added into the Kinetics object.

Deprecated:
  To be removed after Cantera 3.0

Definition at line 796 of file Kinetics.cpp.

## ◆ updateROP()

virtual void updateROP | ( |  | ) |
| inline protected virtual

Reimplemented in InterfaceKinetics.

Definition at line 1500 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 200 of file Kinetics.cpp.

## Member Data Documentation

## ◆ m_cache

ValueCache m_cache
| protected

Cache for saved calculations within each Kinetics object.

Definition at line 1497 of file Kinetics.h.

## ◆ m_reactantStoich

StoichManagerN m_reactantStoich
| protected

Stoichiometry manager for the reactants for each reaction.

Definition at line 1525 of file Kinetics.h.

## ◆ m_productStoich

StoichManagerN m_productStoich
| protected

Stoichiometry manager for the products for each reaction.

Definition at line 1528 of file Kinetics.h.

## ◆ m_revProductStoich

StoichManagerN m_revProductStoich
| protected

Stoichiometry manager for the products of reversible reactions.

Definition at line 1531 of file Kinetics.h.

## ◆ m_stoichMatrix

Eigen::SparseMatrix<double> m_stoichMatrix
| protected

Net stoichiometry (products - reactants)

Definition at line 1534 of file Kinetics.h.

## ◆ m_ready

bool m_ready = false
| protected

Boolean indicating whether Kinetics object is fully configured.

Definition at line 1538 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 1542 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 1546 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 1549 of file Kinetics.h.

## ◆ m_thermo

vector<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.

Note that this kinetics object doesn't own these ThermoPhase objects and is not responsible for creating or deleting them.

Definition at line 1564 of file Kinetics.h.

## ◆ m_sharedThermo

vector<shared_ptr<ThermoPhase> > m_sharedThermo
| protected

vector of shared pointers,

See also
  m_thermo

Todo:
  replace m_thermo with shared version after Cantera 3.0

Definition at line 1568 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 1574 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 1582 of file Kinetics.h.

## ◆ m_surfphase

size_t m_surfphase = npos
| protected

Index in the list of phases of the one surface phase.

Deprecated:
  To be removed after Cantera 3.0.

Definition at line 1586 of file Kinetics.h.

## ◆ m_rxnphase

size_t m_rxnphase = npos
| protected

Phase Index where reactions are assumed to be taking place.

We calculate this by assuming that the phase with the lowest dimensionality is the phase where reactions are taking place.

Definition at line 1593 of file Kinetics.h.

## ◆ m_mindim

size_t m_mindim = 4
| protected

number of spatial dimensions of lowest-dimensional phase.

Definition at line 1596 of file Kinetics.h.

## ◆ m_rfn

vector<double> m_rfn
| protected

Forward rate constant for each reaction.

Definition at line 1599 of file Kinetics.h.

## ◆ m_delta_gibbs0

vector<double> m_delta_gibbs0
| protected

Delta G^0 for all reactions.

Definition at line 1602 of file Kinetics.h.

## ◆ m_rkcn

vector<double> m_rkcn
| protected

Reciprocal of the equilibrium constant in concentration units.

Definition at line 1605 of file Kinetics.h.

## ◆ m_ropf

vector<double> m_ropf
| protected

Forward rate-of-progress for each reaction.

Definition at line 1608 of file Kinetics.h.

## ◆ m_ropr

vector<double> m_ropr
| protected

Reverse rate-of-progress for each reaction.

Definition at line 1611 of file Kinetics.h.

## ◆ m_ropnet

vector<double> m_ropnet
| protected

Net rate-of-progress for each reaction.

Definition at line 1614 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 1617 of file Kinetics.h.

## ◆ m_rbuf

vector<double> m_rbuf
| protected

Buffer used for storage of intermediate reaction-specific results.

Definition at line 1620 of file Kinetics.h.

## ◆ m_skipUndeclaredSpecies

bool m_skipUndeclaredSpecies = false
| protected

See skipUndeclaredSpecies()

Definition at line 1623 of file Kinetics.h.

## ◆ m_skipUndeclaredThirdBodies

bool m_skipUndeclaredThirdBodies = false
| protected

See skipUndeclaredThirdBodies()

Definition at line 1626 of file Kinetics.h.

## ◆ m_hasUndeclaredThirdBodies

bool m_hasUndeclaredThirdBodies = false
| protected

Flag indicating whether reactions include undeclared third bodies.

Definition at line 1629 of file Kinetics.h.

## ◆ m_root

std::weak_ptr<Solution> m_root
| protected

reference to Solution

Definition at line 1632 of file Kinetics.h.

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

- Kinetics.h
- Kinetics.cpp