Cantera  2.4.0
Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
Kinetics Class Reference

Public interface for kinetics managers. More...

#include <Kinetics.h>

Inheritance diagram for Kinetics:
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Collaboration diagram for Kinetics:
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Public Member Functions

virtual std::pair< size_t, size_t > checkDuplicates (bool throw_err=true) const
 Check for unmarked duplicate reactions and unmatched marked duplicates. More...
 
void selectPhase (const doublereal *data, const thermo_t *phase, doublereal *phase_data)
 
Constructors and General Information about Mechanism
 Kinetics ()
 Default constructor. More...
 
virtual ~Kinetics ()
 
 Kinetics (const Kinetics &)=delete
 Kinetics objects are not copyable or assignable. More...
 
Kineticsoperator= (const Kinetics &)=delete
 
virtual std::string kineticsType () const
 Identifies the Kinetics manager type. More...
 
size_t nReactions () const
 Number of reactions in the reaction mechanism. More...
 
void checkReactionIndex (size_t m) const
 Check that the specified reaction index is in range Throws an exception if i is greater than nReactions() More...
 
void checkReactionArraySize (size_t ii) const
 Check that an array size is at least nReactions() Throws an exception if ii is less than nReactions(). More...
 
void checkSpeciesIndex (size_t k) const
 Check that the specified species index is in range Throws an exception if k is greater than nSpecies()-1. More...
 
void checkSpeciesArraySize (size_t mm) const
 Check that an array size is at least nSpecies() Throws an exception if kk is less than nSpecies(). More...
 
Information/Lookup Functions about Phases and Species
size_t nPhases () const
 The number of phases participating in the reaction mechanism. More...
 
void checkPhaseIndex (size_t m) const
 Check that the specified phase index is in range Throws an exception if m is greater than nPhases() More...
 
void checkPhaseArraySize (size_t mm) const
 Check that an array size is at least nPhases() Throws an exception if mm is less than nPhases(). More...
 
size_t phaseIndex (const std::string &ph)
 Return the phase index of a phase in the list of phases defined within the object. More...
 
size_t surfacePhaseIndex ()
 This returns the integer index of the phase which has ThermoPhase type cSurf. More...
 
size_t reactionPhaseIndex ()
 Phase where the reactions occur. More...
 
thermo_tthermo (size_t n=0)
 This method returns a reference to the nth ThermoPhase object defined in this kinetics mechanism. More...
 
const thermo_tthermo (size_t n=0) const
 
size_t nTotalSpecies () const
 The total number of species in all phases participating in the kinetics mechanism. More...
 
size_t kineticsSpeciesIndex (size_t k, size_t n) const
 The location of species k of phase n in species arrays. More...
 
std::string kineticsSpeciesName (size_t k) const
 Return the name of the kth species in the kinetics manager. More...
 
size_t kineticsSpeciesIndex (const std::string &nm) const
 This routine will look up a species number based on the input std::string nm. More...
 
size_t kineticsSpeciesIndex (const std::string &nm, const std::string &ph) const
 This routine will look up a species number based on the input std::string nm. More...
 
thermo_tspeciesPhase (const std::string &nm)
 This function looks up the name of a species and returns a reference to the ThermoPhase object of the phase where the species resides. More...
 
thermo_tspeciesPhase (size_t k)
 This function takes as an argument the kineticsSpecies index (i.e., the list index in the list of species in the kinetics manager) and returns the species' owning ThermoPhase object. More...
 
size_t speciesPhaseIndex (size_t k)
 This function takes as an argument the kineticsSpecies index (i.e., the list index in the list of species in the kinetics manager) and returns the index of the phase owning the species. More...
 
Reaction Rates Of Progress
virtual void getFwdRatesOfProgress (doublereal *fwdROP)
 Return the forward rates of progress of the reactions. More...
 
virtual void getRevRatesOfProgress (doublereal *revROP)
 Return the Reverse rates of progress of the reactions. More...
 
virtual void getNetRatesOfProgress (doublereal *netROP)
 Net rates of progress. More...
 
virtual void getEquilibriumConstants (doublereal *kc)
 Return a vector of Equilibrium constants. More...
 
virtual void getReactionDelta (const doublereal *property, doublereal *deltaProperty)
 Change in species properties. More...
 
virtual void getRevReactionDelta (const doublereal *g, doublereal *dg)
 Given an array of species properties 'g', return in array 'dg' the change in this quantity in the reversible reactions. More...
 
virtual void getDeltaGibbs (doublereal *deltaG)
 Return the vector of values for the reaction Gibbs free energy change. More...
 
virtual void getDeltaElectrochemPotentials (doublereal *deltaM)
 Return the vector of values for the reaction electrochemical free energy change. More...
 
virtual void getDeltaEnthalpy (doublereal *deltaH)
 Return the vector of values for the reactions change in enthalpy. More...
 
virtual void getDeltaEntropy (doublereal *deltaS)
 Return the vector of values for the reactions change in entropy. More...
 
virtual void getDeltaSSGibbs (doublereal *deltaG)
 Return the vector of values for the reaction standard state Gibbs free energy change. More...
 
virtual void getDeltaSSEnthalpy (doublereal *deltaH)
 Return the vector of values for the change in the standard state enthalpies of reaction. More...
 
virtual void getDeltaSSEntropy (doublereal *deltaS)
 Return the vector of values for the change in the standard state entropies for each reaction. More...
 
Species Production Rates
virtual void getCreationRates (doublereal *cdot)
 Species creation rates [kmol/m^3/s or kmol/m^2/s]. More...
 
virtual void getDestructionRates (doublereal *ddot)
 Species destruction rates [kmol/m^3/s or kmol/m^2/s]. More...
 
virtual void getNetProductionRates (doublereal *wdot)
 Species net production rates [kmol/m^3/s or kmol/m^2/s]. More...
 
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. More...
 
virtual double productStoichCoeff (size_t k, size_t i) const
 Stoichiometric coefficient of species k as a product in reaction i. More...
 
virtual doublereal reactantOrder (size_t k, size_t i) const
 Reactant order of species k in reaction i. More...
 
virtual doublereal productOrder (int k, int i) const
 product Order of species k in reaction i. More...
 
virtual void getActivityConcentrations (doublereal *const conc)
 Get the vector of activity concentrations used in the kinetics object. More...
 
virtual int reactionType (size_t i) const
 Flag specifying the type of reaction. More...
 
virtual bool isReversible (size_t i)
 True if reaction i has been declared to be reversible. More...
 
std::string reactionString (size_t i) const
 Return a string representing the reaction. More...
 
std::string reactantString (size_t i) const
 Returns a string containing the reactants side of the reaction equation. More...
 
std::string productString (size_t i) const
 Returns a string containing the products side of the reaction equation. More...
 
virtual void getFwdRateConstants (doublereal *kfwd)
 Return the forward rate constants. More...
 
virtual void getRevRateConstants (doublereal *krev, bool doIrreversible=false)
 Return the reverse rate constants. More...
 
Reaction Mechanism Construction
virtual void addPhase (thermo_t &thermo)
 Add a phase to the kinetics manager object. More...
 
virtual void init ()
 Prepare the class for the addition of reactions, after all phases have been added. More...
 
virtual void resizeSpecies ()
 Resize arrays with sizes that depend on the total number of species. More...
 
virtual bool addReaction (shared_ptr< Reaction > r)
 Add a single reaction to the mechanism. More...
 
virtual void modifyReaction (size_t i, shared_ptr< Reaction > rNew)
 Modify the rate expression associated with a reaction. More...
 
shared_ptr< Reactionreaction (size_t i)
 Return the Reaction object for reaction i. More...
 
shared_ptr< const Reactionreaction (size_t i) const
 
void skipUndeclaredSpecies (bool skip)
 Determine behavior when adding a new reaction that contains species not defined in any of the phases associated with this kinetics manager. More...
 
void skipUndeclaredThirdBodies (bool skip)
 Determine behavior when adding a new reaction that contains third-body efficiencies for species not defined in any of the phases associated with this kinetics manager. More...
 
Altering Reaction Rates
doublereal multiplier (size_t i) const
 The current value of the multiplier for reaction i. More...
 
virtual void setMultiplier (size_t i, doublereal f)
 Set the multiplier for reaction i to f. More...
 
virtual void invalidateCache ()
 

Protected Member Functions

virtual void updateROP ()
 
double checkDuplicateStoich (std::map< int, double > &r1, std::map< int, double > &r2) const
 Check whether r1 and r2 represent duplicate stoichiometries This function returns a ratio if two reactions are duplicates of one another, and 0.0 otherwise. More...
 
void checkReactionBalance (const Reaction &R)
 Check that the specified reaction is balanced (same number of atoms for each element in the reactants and products). More...
 

Protected Attributes

ValueCache m_cache
 Cache for saved calculations within each Kinetics object. More...
 
size_t m_kk
 The number of species in all of the phases that participate in this kinetics mechanism. More...
 
vector_fp m_perturb
 Vector of perturbation factors for each reaction's rate of progress vector. More...
 
std::vector< shared_ptr< Reaction > > m_reactions
 Vector of Reaction objects represented by this Kinetics manager. More...
 
std::vector< thermo_t * > m_thermo
 m_thermo is a vector of pointers to ThermoPhase objects that are involved with this kinetics operator More...
 
std::vector< size_t > m_start
 m_start is a vector of integers specifying the beginning position for the species vector for the n'th phase in the kinetics class. More...
 
std::map< std::string, size_t > m_phaseindex
 Mapping of the phase id, i.e., the id attribute in the XML phase element to the position of the phase within the kinetics object. More...
 
size_t m_surfphase
 Index in the list of phases of the one surface phase. More...
 
size_t m_rxnphase
 Phase Index where reactions are assumed to be taking place. More...
 
size_t m_mindim
 number of spatial dimensions of lowest-dimensional phase. More...
 
vector_fp m_rfn
 Forward rate constant for each reaction. More...
 
vector_fp m_rkcn
 Reciprocal of the equilibrium constant in concentration units. More...
 
vector_fp m_ropf
 Forward rate-of-progress for each reaction. More...
 
vector_fp m_ropr
 Reverse rate-of-progress for each reaction. More...
 
vector_fp m_ropnet
 Net rate-of-progress for each reaction. More...
 
bool m_skipUndeclaredSpecies
 
bool m_skipUndeclaredThirdBodies
 
Stoichiometry management
StoichManagerN m_reactantStoich
 Stoichiometry manager for the reactants for each reaction. More...
 
StoichManagerN m_revProductStoich
 Stoichiometry manager for the products of reversible reactions. More...
 
StoichManagerN m_irrevProductStoich
 Stoichiometry manager for the products of irreversible reactions. More...
 

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 110 of file Kinetics.h.

Constructor & Destructor Documentation

◆ Kinetics() [1/2]

Kinetics ( )

Default constructor.

Definition at line 21 of file Kinetics.cpp.

◆ Kinetics() [2/2]

Kinetics ( const Kinetics )
delete

Kinetics objects are not copyable or assignable.

Member Function Documentation

◆ kineticsType()

virtual std::string kineticsType ( ) const
inlinevirtual

Identifies the Kinetics manager type.

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

Reimplemented in InterfaceKinetics, AqueousKinetics, GasKinetics, and EdgeKinetics.

Definition at line 130 of file Kinetics.h.

Referenced by Kinetics::addPhase().

◆ nReactions()

size_t nReactions ( ) const
inline

◆ 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 34 of file Kinetics.cpp.

References Kinetics::nReactions().

Referenced by Kinetics::modifyReaction(), and Kinetics::reaction().

◆ 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 41 of file Kinetics.cpp.

References Kinetics::nReactions().

◆ 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 62 of file Kinetics.cpp.

References Kinetics::m_kk.

◆ 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 69 of file Kinetics.cpp.

References Kinetics::m_kk.

◆ nPhases()

size_t nPhases ( ) const
inline

◆ 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 48 of file Kinetics.cpp.

References Kinetics::nPhases().

◆ 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 55 of file Kinetics.cpp.

References Kinetics::nPhases().

◆ phaseIndex()

size_t phaseIndex ( const std::string &  ph)
inline

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

Parameters
phstd::string name of the phase

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

Definition at line 189 of file Kinetics.h.

References Kinetics::m_phaseindex, and Cantera::npos.

Referenced by Cantera::importKinetics().

◆ surfacePhaseIndex()

size_t surfacePhaseIndex ( )
inline

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.

Definition at line 202 of file Kinetics.h.

References Kinetics::m_surfphase.

Referenced by solveSP::calc_t(), and solveSP::fun_eval().

◆ reactionPhaseIndex()

size_t reactionPhaseIndex ( )
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.

Definition at line 214 of file Kinetics.h.

References Kinetics::m_rxnphase.

Referenced by InterfaceKinetics::buildSurfaceArrhenius(), and InterfaceKinetics::init().

◆ thermo()

thermo_t& 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
nIndex of the ThermoPhase being sought.

Definition at line 227 of file Kinetics.h.

References Kinetics::m_thermo.

Referenced by AqueousKinetics::_update_rates_C(), InterfaceKinetics::_update_rates_phi(), InterfaceKinetics::addPhase(), Kinetics::addPhase(), InterfaceKinetics::applyVoltageKfwdCorrection(), InterfaceKinetics::buildSurfaceArrhenius(), solveSP::calc_t(), InterfaceKinetics::convertExchangeCurrentDensityFormulation(), InterfaceKinetics::getDeltaElectrochemPotentials(), BulkKinetics::getDeltaEnthalpy(), InterfaceKinetics::getDeltaEnthalpy(), BulkKinetics::getDeltaEntropy(), InterfaceKinetics::getDeltaEntropy(), BulkKinetics::getDeltaGibbs(), BulkKinetics::getDeltaSSEnthalpy(), InterfaceKinetics::getDeltaSSEnthalpy(), BulkKinetics::getDeltaSSEntropy(), InterfaceKinetics::getDeltaSSEntropy(), BulkKinetics::getDeltaSSGibbs(), InterfaceKinetics::getDeltaSSGibbs(), AqueousKinetics::getEquilibriumConstants(), GasKinetics::getEquilibriumConstants(), InterfaceKinetics::getEquilibriumConstants(), GasKinetics::init(), InterfaceKinetics::init(), InterfaceKinetics::InterfaceKinetics(), Kinetics::kineticsSpeciesIndex(), Kinetics::kineticsSpeciesName(), Kinetics::speciesPhase(), GasKinetics::update_rates_C(), InterfaceKinetics::updateExchangeCurrentQuantities(), AqueousKinetics::updateKc(), GasKinetics::updateKc(), InterfaceKinetics::updateKc(), solveSP::updateMFKinSpecies(), and InterfaceKinetics::updateMu0().

◆ 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 239 of file Kinetics.h.

References Kinetics::m_kk.

Referenced by InterfaceKinetics::addReaction(), and ReactingSurf1D::init().

◆ 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
kspecies index
nphase index for the species

Definition at line 261 of file Kinetics.h.

References Kinetics::m_start.

Referenced by InterfaceKinetics::addReaction(), Kinetics::addReaction(), InterfaceKinetics::buildSurfaceArrhenius(), solveSP::calc_t(), Cantera::checkElectrochemReaction(), ReactingSurf1D::eval(), solveSP::fun_eval(), Kinetics::kineticsSpeciesIndex(), and solveSP::updateMFKinSpecies().

◆ 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
kspecies index

Definition at line 279 of file Kinetics.cpp.

References Kinetics::m_start, Cantera::npos, Phase::speciesName(), and Kinetics::thermo().

Referenced by Kinetics::productStoichCoeff(), and Kinetics::reactantStoichCoeff().

◆ kineticsSpeciesIndex() [2/3]

size_t kineticsSpeciesIndex ( const std::string &  nm) const

This routine will look up a species number based on the input std::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
nmInput string name of the species

Definition at line 289 of file Kinetics.cpp.

References Phase::id(), Kinetics::m_start, Kinetics::m_thermo, Cantera::npos, Phase::speciesIndex(), and Kinetics::thermo().

◆ kineticsSpeciesIndex() [3/3]

size_t kineticsSpeciesIndex ( const std::string &  nm,
const std::string &  ph 
) const

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

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
nmInput string name of the species
phInput string name of the phase.

Definition at line 302 of file Kinetics.cpp.

References Phase::id(), Kinetics::kineticsSpeciesIndex(), Kinetics::m_start, Kinetics::m_thermo, Cantera::npos, Phase::speciesIndex(), and Kinetics::thermo().

◆ speciesPhase() [1/2]

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

This function looks up the name of a species and returns a reference to the ThermoPhase object of the phase where the species resides.

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

Parameters
nmString containing the name of the species.

Definition at line 322 of file Kinetics.cpp.

References Kinetics::m_thermo, Cantera::npos, Phase::speciesIndex(), and Kinetics::thermo().

Referenced by Cantera::checkElectrochemReaction().

◆ speciesPhase() [2/2]

thermo_t& speciesPhase ( size_t  k)
inline

This function takes as an argument the kineticsSpecies index (i.e., the list index in the list of species in the kinetics manager) and returns the species' owning ThermoPhase object.

Parameters
kSpecies index

Definition at line 320 of file Kinetics.h.

References Kinetics::speciesPhaseIndex(), and Kinetics::thermo().

◆ speciesPhaseIndex()

size_t speciesPhaseIndex ( size_t  k)

This function takes as an argument the kineticsSpecies index (i.e., the list index in the list of species in the kinetics manager) and returns the index of the phase owning the species.

Parameters
kSpecies index

Definition at line 333 of file Kinetics.cpp.

References Kinetics::m_start, and Cantera::npos.

Referenced by InterfaceKinetics::addReaction(), InterfaceKinetics::buildSurfaceArrhenius(), and Kinetics::speciesPhase().

◆ getFwdRatesOfProgress()

void getFwdRatesOfProgress ( doublereal *  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
fwdROPOutput vector containing forward rates of progress of the reactions. Length: nReactions().

Definition at line 355 of file Kinetics.cpp.

References Kinetics::m_ropf.

◆ getRevRatesOfProgress()

void getRevRatesOfProgress ( doublereal *  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
revROPOutput vector containing reverse rates of progress of the reactions. Length: nReactions().

Definition at line 361 of file Kinetics.cpp.

References Kinetics::m_ropr.

◆ getNetRatesOfProgress()

void getNetRatesOfProgress ( doublereal *  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
netROPOutput vector of the net ROP. Length: nReactions().

Definition at line 367 of file Kinetics.cpp.

References Kinetics::m_ropnet.

◆ getEquilibriumConstants()

virtual void getEquilibriumConstants ( doublereal *  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
kcOutput vector containing the equilibrium constants. Length: nReactions().

Reimplemented in InterfaceKinetics, GasKinetics, and AqueousKinetics.

Definition at line 380 of file Kinetics.h.

Referenced by BulkKinetics::getRevRateConstants().

◆ getReactionDelta()

void getReactionDelta ( const doublereal *  property,
doublereal *  deltaProperty 
)
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
propertyInput vector of property value. Length: m_kk.
deltaPropertyOutput vector of deltaRxn. Length: nReactions().

Definition at line 373 of file Kinetics.cpp.

References Kinetics::m_irrevProductStoich, Kinetics::m_reactantStoich, Kinetics::m_revProductStoich, and Kinetics::nReactions().

Referenced by InterfaceKinetics::applyVoltageKfwdCorrection(), InterfaceKinetics::getDeltaElectrochemPotentials(), BulkKinetics::getDeltaEnthalpy(), InterfaceKinetics::getDeltaEnthalpy(), BulkKinetics::getDeltaEntropy(), InterfaceKinetics::getDeltaEntropy(), BulkKinetics::getDeltaGibbs(), InterfaceKinetics::getDeltaGibbs(), BulkKinetics::getDeltaSSEnthalpy(), InterfaceKinetics::getDeltaSSEnthalpy(), BulkKinetics::getDeltaSSEntropy(), InterfaceKinetics::getDeltaSSEntropy(), BulkKinetics::getDeltaSSGibbs(), InterfaceKinetics::getDeltaSSGibbs(), AqueousKinetics::getEquilibriumConstants(), GasKinetics::getEquilibriumConstants(), InterfaceKinetics::getEquilibriumConstants(), and InterfaceKinetics::updateExchangeCurrentQuantities().

◆ getRevReactionDelta()

void getRevReactionDelta ( const doublereal *  g,
doublereal *  dg 
)
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 383 of file Kinetics.cpp.

References Kinetics::m_reactantStoich, Kinetics::m_revProductStoich, and Kinetics::nReactions().

Referenced by AqueousKinetics::updateKc(), GasKinetics::updateKc(), and InterfaceKinetics::updateKc().

◆ getDeltaGibbs()

virtual void getDeltaGibbs ( doublereal *  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
deltaGOutput vector of deltaG's for reactions Length: nReactions().

Reimplemented in InterfaceKinetics, and BulkKinetics.

Definition at line 423 of file Kinetics.h.

◆ getDeltaElectrochemPotentials()

virtual void getDeltaElectrochemPotentials ( doublereal *  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
deltaMOutput vector of deltaM's for reactions Length: nReactions().

Reimplemented in InterfaceKinetics.

Definition at line 438 of file Kinetics.h.

◆ getDeltaEnthalpy()

virtual void getDeltaEnthalpy ( doublereal *  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
deltaHOutput vector of deltaH's for reactions Length: nReactions().

Reimplemented in InterfaceKinetics, and BulkKinetics.

Definition at line 451 of file Kinetics.h.

◆ getDeltaEntropy()

virtual void getDeltaEntropy ( doublereal *  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
deltaSOutput vector of deltaS's for reactions Length: nReactions().

Reimplemented in InterfaceKinetics, and BulkKinetics.

Definition at line 464 of file Kinetics.h.

◆ getDeltaSSGibbs()

virtual void getDeltaSSGibbs ( doublereal *  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
deltaGOutput vector of ss deltaG's for reactions Length: nReactions().

Reimplemented in InterfaceKinetics, and BulkKinetics.

Definition at line 478 of file Kinetics.h.

◆ getDeltaSSEnthalpy()

virtual void getDeltaSSEnthalpy ( doublereal *  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
deltaHOutput vector of ss deltaH's for reactions Length: nReactions().

Reimplemented in InterfaceKinetics, and BulkKinetics.

Definition at line 492 of file Kinetics.h.

◆ getDeltaSSEntropy()

virtual void getDeltaSSEntropy ( doublereal *  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
deltaSOutput vector of ss deltaS's for reactions Length: nReactions().

Reimplemented in InterfaceKinetics, and BulkKinetics.

Definition at line 506 of file Kinetics.h.

◆ getCreationRates()

void getCreationRates ( doublereal *  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
cdotOutput vector of creation rates. Length: m_kk.

Definition at line 392 of file Kinetics.cpp.

References Kinetics::m_irrevProductStoich, Kinetics::m_kk, Kinetics::m_reactantStoich, Kinetics::m_revProductStoich, Kinetics::m_ropf, and Kinetics::m_ropr.

◆ getDestructionRates()

void getDestructionRates ( doublereal *  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
ddotOutput vector of destruction rates. Length: m_kk.

Definition at line 407 of file Kinetics.cpp.

References Kinetics::m_kk, Kinetics::m_reactantStoich, Kinetics::m_revProductStoich, Kinetics::m_ropf, and Kinetics::m_ropr.

◆ getNetProductionRates()

void getNetProductionRates ( doublereal *  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
wdotOutput vector of net production rates. Length: m_kk.

Definition at line 418 of file Kinetics.cpp.

References Kinetics::m_irrevProductStoich, Kinetics::m_kk, Kinetics::m_reactantStoich, Kinetics::m_revProductStoich, and Kinetics::m_ropnet.

Referenced by solveSP::calc_t(), ReactingSurf1D::eval(), FlowReactor::evalEqs(), Reactor::evalEqs(), solveSP::fun_eval(), and StFlow::getWdot().

◆ reactantStoichCoeff()

double reactantStoichCoeff ( size_t  k,
size_t  i 
) const
virtual

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

Parameters
kkinetic species index
ireaction index

Definition at line 343 of file Kinetics.cpp.

References Cantera::getValue(), Kinetics::kineticsSpeciesName(), and Kinetics::m_reactions.

◆ productStoichCoeff()

double productStoichCoeff ( size_t  k,
size_t  i 
) const
virtual

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

Parameters
kkinetic species index
ireaction index

Definition at line 349 of file Kinetics.cpp.

References Cantera::getValue(), Kinetics::kineticsSpeciesName(), and Kinetics::m_reactions.

◆ reactantOrder()

virtual doublereal 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
kkinetic species index
ireaction index

Definition at line 569 of file Kinetics.h.

◆ productOrder()

virtual doublereal 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
kkinetic species index
ireaction index

Definition at line 583 of file Kinetics.h.

◆ getActivityConcentrations()

virtual void getActivityConcentrations ( doublereal *const  conc)
inlinevirtual

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

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

Reimplemented in InterfaceKinetics.

Definition at line 592 of file Kinetics.h.

◆ reactionType()

virtual int reactionType ( size_t  i) const
inlinevirtual

Flag specifying the type of reaction.

The legal values and their meaning are specific to the particular kinetics manager.

Parameters
ireaction index

Definition at line 602 of file Kinetics.h.

References Kinetics::m_reactions.

◆ 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
ireaction index

Reimplemented in InterfaceKinetics, and BulkKinetics.

Definition at line 613 of file Kinetics.h.

◆ reactionString()

std::string reactionString ( size_t  i) const
inline

Return a string representing the reaction.

Parameters
ireaction index

Definition at line 622 of file Kinetics.h.

References Kinetics::m_reactions.

Referenced by Reactor::addSensitivityReaction().

◆ reactantString()

std::string reactantString ( size_t  i) const
inline

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

Definition at line 627 of file Kinetics.h.

References Kinetics::m_reactions.

◆ productString()

std::string productString ( size_t  i) const
inline

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

Definition at line 632 of file Kinetics.h.

References Kinetics::m_reactions.

◆ getFwdRateConstants()

virtual void getFwdRateConstants ( doublereal *  kfwd)
inlinevirtual

Return the forward rate constants.

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

Parameters
kfwdOutput vector containing the forward reaction rate constants. Length: nReactions().

Reimplemented in InterfaceKinetics, GasKinetics, and AqueousKinetics.

Definition at line 647 of file Kinetics.h.

Referenced by BulkKinetics::getRevRateConstants().

◆ getRevRateConstants()

virtual void getRevRateConstants ( doublereal *  krev,
bool  doIrreversible = false 
)
inlinevirtual

Return the reverse rate constants.

The computed values include all temperature-dependent, pressure-dependent, and third body contributions. Length is the number of reactions. Units are a combination of kmol, m^3 and s, that depend on the rate expression for the reaction. Note, this routine will return rate constants for irreversible reactions if the default for doIrreversible is overridden.

Parameters
krevOutput vector of reverse rate constants
doIrreversibleboolean indicating whether irreversible reactions should be included.

Reimplemented in InterfaceKinetics, and BulkKinetics.

Definition at line 664 of file Kinetics.h.

◆ addPhase()

void addPhase ( thermo_t 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_surfphase -> index of the surface phase.
  • m_thermo -> vector of pointers to ThermoPhase phases that participate in the kinetics mechanism.
  • m_phaseindex -> map containing the std::string id of each ThermoPhase phase as a key and the index of the phase within the kinetics manager object as the value.
Parameters
thermoReference to the ThermoPhase to be added.

Reimplemented in InterfaceKinetics.

Definition at line 430 of file Kinetics.cpp.

References Kinetics::kineticsType(), Kinetics::m_mindim, Kinetics::m_phaseindex, Kinetics::m_rxnphase, Kinetics::m_surfphase, Kinetics::m_thermo, Phase::nDim(), Kinetics::nPhases(), Kinetics::resizeSpecies(), Kinetics::thermo(), and ThermoPhase::type().

Referenced by InterfaceKinetics::addPhase(), and Cantera::importKinetics().

◆ 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, and GasKinetics.

Definition at line 699 of file Kinetics.h.

Referenced by Kinetics::addReaction(), Cantera::importKinetics(), and GasKinetics::init().

◆ 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 InterfaceKinetics, and BulkKinetics.

Definition at line 449 of file Kinetics.cpp.

References Kinetics::m_kk, Kinetics::m_start, Kinetics::m_thermo, and Kinetics::nPhases().

Referenced by Kinetics::addPhase(), Kinetics::addReaction(), BulkKinetics::resizeSpecies(), and InterfaceKinetics::resizeSpecies().

◆ addReaction()

bool addReaction ( shared_ptr< Reaction r)
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
rPointer to the Reaction object to be added.
Returns
true if the reaction is added or false if it was skipped

Reimplemented in InterfaceKinetics, AqueousKinetics, GasKinetics, and BulkKinetics.

Definition at line 461 of file Kinetics.cpp.

References Kinetics::checkReactionBalance(), Kinetics::init(), Kinetics::kineticsSpeciesIndex(), Kinetics::m_irrevProductStoich, Kinetics::m_kk, Kinetics::m_perturb, Kinetics::m_reactantStoich, Kinetics::m_reactions, Kinetics::m_revProductStoich, Kinetics::m_rfn, Kinetics::m_rkcn, Kinetics::m_ropf, Kinetics::m_ropnet, Kinetics::m_ropr, Kinetics::m_skipUndeclaredSpecies, Cantera::npos, Kinetics::nReactions(), and Kinetics::resizeSpecies().

Referenced by BulkKinetics::addReaction(), InterfaceKinetics::addReaction(), and Cantera::installReactionArrays().

◆ 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
iIndex of the reaction to be modified
rNewReaction with the new rate expressions

Reimplemented in InterfaceKinetics, AqueousKinetics, and GasKinetics.

Definition at line 572 of file Kinetics.cpp.

References Kinetics::checkReactionIndex(), and Kinetics::m_reactions.

Referenced by GasKinetics::modifyReaction(), AqueousKinetics::modifyReaction(), and InterfaceKinetics::modifyReaction().

◆ reaction()

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 597 of file Kinetics.cpp.

References Kinetics::checkReactionIndex(), and Kinetics::m_reactions.

◆ skipUndeclaredSpecies()

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 739 of file Kinetics.h.

References Kinetics::m_skipUndeclaredSpecies.

Referenced by Cantera::installReactionArrays().

◆ skipUndeclaredThirdBodies()

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 748 of file Kinetics.h.

References Kinetics::m_skipUndeclaredThirdBodies.

Referenced by Cantera::installReactionArrays().

◆ multiplier()

doublereal multiplier ( size_t  i) const
inline

The current value of the multiplier for reaction i.

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.

Parameters
iindex of the reaction

Definition at line 768 of file Kinetics.h.

References Kinetics::m_perturb.

Referenced by Reactor::applySensitivity(), and InterfaceKinetics::buildSurfaceArrhenius().

◆ setMultiplier()

virtual void setMultiplier ( size_t  i,
doublereal  f 
)
inlinevirtual

Set the multiplier for reaction i to f.

Parameters
iindex of the reaction
fvalue of the multiplier.

Reimplemented in BulkKinetics.

Definition at line 777 of file Kinetics.h.

References Kinetics::m_perturb.

Referenced by Reactor::applySensitivity(), Reactor::resetSensitivity(), and BulkKinetics::setMultiplier().

◆ checkDuplicates()

std::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 76 of file Kinetics.cpp.

References Kinetics::m_reactions.

Referenced by Cantera::installReactionArrays().

◆ selectPhase()

void selectPhase ( const doublereal *  data,
const thermo_t phase,
doublereal *  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
dataInput data array.
phasePointer to one of the phase objects participating in this reaction mechanism
phase_dataOutput array where the values for the the specified phase are to be written.

Definition at line 265 of file Kinetics.cpp.

References Kinetics::m_start, Kinetics::m_thermo, Kinetics::nPhases(), and Phase::nSpecies().

◆ checkReactionBalance()

void checkReactionBalance ( const Reaction R)
protected

Check that the specified reaction is balanced (same number of atoms for each element in the reactants and products).

Raises an exception if the reaction is not balanced.

Definition at line 224 of file Kinetics.cpp.

Referenced by Kinetics::addReaction().

Member Data Documentation

◆ m_cache

ValueCache m_cache
protected

Cache for saved calculations within each Kinetics object.

Definition at line 812 of file Kinetics.h.

◆ m_reactantStoich

StoichManagerN m_reactantStoich
protected

Stoichiometry manager for the reactants for each reaction.

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

Definition at line 849 of file Kinetics.h.

Referenced by Kinetics::addReaction(), Kinetics::getCreationRates(), Kinetics::getDestructionRates(), Kinetics::getNetProductionRates(), Kinetics::getReactionDelta(), Kinetics::getRevReactionDelta(), InterfaceKinetics::updateExchangeCurrentQuantities(), and InterfaceKinetics::updateROP().

◆ m_revProductStoich

StoichManagerN m_revProductStoich
protected

◆ m_irrevProductStoich

StoichManagerN m_irrevProductStoich
protected

Stoichiometry manager for the products of irreversible reactions.

Definition at line 855 of file Kinetics.h.

Referenced by Kinetics::addReaction(), Kinetics::getCreationRates(), Kinetics::getNetProductionRates(), and Kinetics::getReactionDelta().

◆ m_kk

size_t m_kk
protected

◆ m_perturb

vector_fp m_perturb
protected

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

It is initialized to one.

Definition at line 864 of file Kinetics.h.

Referenced by Kinetics::addReaction(), AqueousKinetics::getFwdRateConstants(), GasKinetics::getFwdRateConstants(), InterfaceKinetics::getFwdRateConstants(), Kinetics::multiplier(), Kinetics::setMultiplier(), and InterfaceKinetics::updateROP().

◆ m_reactions

std::vector<shared_ptr<Reaction> > m_reactions
protected

◆ m_thermo

std::vector<thermo_t*> 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 882 of file Kinetics.h.

Referenced by InterfaceKinetics::_update_rates_C(), Kinetics::addPhase(), InterfaceKinetics::getDeltaGibbs(), Kinetics::kineticsSpeciesIndex(), Kinetics::nPhases(), InterfaceKinetics::phaseExistence(), InterfaceKinetics::phaseStability(), Kinetics::resizeSpecies(), Kinetics::selectPhase(), InterfaceKinetics::setPhaseExistence(), InterfaceKinetics::setPhaseStability(), Kinetics::speciesPhase(), and Kinetics::thermo().

◆ m_start

std::vector<size_t> m_start
protected

◆ m_phaseindex

std::map<std::string, size_t> m_phaseindex
protected

Mapping of the phase id, i.e., the id attribute in the XML phase element 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 896 of file Kinetics.h.

Referenced by Kinetics::addPhase(), and Kinetics::phaseIndex().

◆ m_surfphase

size_t m_surfphase
protected

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

Definition at line 899 of file Kinetics.h.

Referenced by Kinetics::addPhase(), and Kinetics::surfacePhaseIndex().

◆ m_rxnphase

size_t m_rxnphase
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 906 of file Kinetics.h.

Referenced by Kinetics::addPhase(), and Kinetics::reactionPhaseIndex().

◆ m_mindim

size_t m_mindim
protected

number of spatial dimensions of lowest-dimensional phase.

Definition at line 909 of file Kinetics.h.

Referenced by Kinetics::addPhase().

◆ m_rfn

vector_fp m_rfn
protected

◆ m_rkcn

vector_fp m_rkcn
protected

◆ m_ropf

vector_fp m_ropf
protected

◆ m_ropr

vector_fp m_ropr
protected

◆ m_ropnet

vector_fp m_ropnet
protected

◆ m_skipUndeclaredSpecies

bool m_skipUndeclaredSpecies
protected
See also
skipUndeclaredSpecies()

Definition at line 927 of file Kinetics.h.

Referenced by Kinetics::addReaction(), and Kinetics::skipUndeclaredSpecies().

◆ m_skipUndeclaredThirdBodies

bool m_skipUndeclaredThirdBodies
protected
See also
skipUndeclaredThirdBodies()

Definition at line 930 of file Kinetics.h.

Referenced by Kinetics::skipUndeclaredThirdBodies().


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