Cantera  2.3.0
Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
BulkKinetics Class Reference

Partial specialization of Kinetics for chemistry in a single bulk phase. More...

#include <BulkKinetics.h>

Inheritance diagram for BulkKinetics:
[legend]
Collaboration diagram for BulkKinetics:
[legend]

Public Member Functions

 BulkKinetics (thermo_t *thermo=0)
 
virtual KineticsduplMyselfAsKinetics (const std::vector< thermo_t *> &tpVector) const
 Duplication routine for objects which inherit from Kinetics. More...
 
virtual bool isReversible (size_t i)
 True if reaction i has been declared to be reversible. More...
 
virtual void getDeltaGibbs (doublereal *deltaG)
 Return the vector of values for the reaction Gibbs free energy change. More...
 
virtual void getDeltaEnthalpy (doublereal *deltaH)
 Return the vector of values for the reactions change in enthalpy. More...
 
virtual void getDeltaEntropy (doublereal *deltaS)
 Return the vector of values for the reactions change in entropy. More...
 
virtual void getDeltaSSGibbs (doublereal *deltaG)
 Return the vector of values for the reaction standard state Gibbs free energy change. More...
 
virtual void getDeltaSSEnthalpy (doublereal *deltaH)
 Return the vector of values for the change in the standard state enthalpies of reaction. More...
 
virtual void getDeltaSSEntropy (doublereal *deltaS)
 Return the vector of values for the change in the standard state entropies for each reaction. More...
 
virtual void getRevRateConstants (doublereal *krev, bool doIrreversible=false)
 Return the reverse rate constants. More...
 
virtual bool addReaction (shared_ptr< Reaction > r)
 Add a single reaction to the mechanism. More...
 
virtual void resizeSpecies ()
 Resize arrays with sizes that depend on the total number of species. More...
 
virtual void setMultiplier (size_t i, double f)
 Set the multiplier for reaction i to f. More...
 
virtual void invalidateCache ()
 
- Public Member Functions inherited from Kinetics
virtual bool ready () const
 Returns true if the kinetics manager has been properly initialized and finalized. More...
 
virtual std::pair< size_t, size_t > checkDuplicates (bool throw_err=true) const
 Check for duplicate reactions. More...
 
void selectPhase (const doublereal *data, const thermo_t *phase, doublereal *phase_data)
 
 Kinetics ()
 Default constructor. More...
 
virtual ~Kinetics ()
 
 Kinetics (const Kinetics &)
 
Kineticsoperator= (const Kinetics &right)
 
virtual void assignShallowPointers (const std::vector< thermo_t *> &tpVector)
 Reassign the pointers within the Kinetics object. More...
 
virtual int type () const
 Identifies the kinetics manager type. More...
 
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...
 
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...
 
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 getDeltaElectrochemPotentials (doublereal *deltaM)
 Return the vector of values for the reaction electrochemical free energy change. More...
 
virtual void getCreationRates (doublereal *cdot)
 Species creation rates [kmol/m^3/s or kmol/m^2/s]. More...
 
virtual void getDestructionRates (doublereal *ddot)
 Species destruction rates [kmol/m^3/s or kmol/m^2/s]. More...
 
virtual void getNetProductionRates (doublereal *wdot)
 Species net production rates [kmol/m^3/s or kmol/m^2/s]. More...
 
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...
 
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 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 finalize ()
 Finish adding reactions and prepare for use. 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...
 
doublereal multiplier (size_t i) const
 The current value of the multiplier for reaction i. More...
 

Protected Member Functions

virtual void addElementaryReaction (ElementaryReaction &r)
 
virtual void modifyElementaryReaction (size_t i, ElementaryReaction &rNew)
 
- Protected Member Functions inherited from Kinetics
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

Rate1< Arrheniusm_rates
 
std::vector< size_t > m_revindex
 Indices of reversible reactions. More...
 
std::vector< size_t > m_irrev
 Indices of irreversible reactions. More...
 
vector_fp m_dn
 Difference between the global reactants order and the global products order. More...
 
vector_fp m_conc
 
vector_fp m_grt
 
bool m_ROP_ok
 
doublereal m_temp
 
- Protected Attributes inherited from Kinetics
ValueCache m_cache
 Cache for saved calculations within each Kinetics object. More...
 
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
 
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

Partial specialization of Kinetics for chemistry in a single bulk phase.

Definition at line 21 of file BulkKinetics.h.

Member Function Documentation

◆ duplMyselfAsKinetics()

Kinetics * duplMyselfAsKinetics ( const std::vector< thermo_t *> &  tpVector) const
virtual

Duplication routine for objects which inherit from Kinetics.

This function can be used to duplicate objects derived from Kinetics even if the application only has a pointer to Kinetics to work with.

These routines are basically wrappers around the derived copy constructor.

Parameters
tpVectorVector of pointers to ThermoPhase objects. this is the m_thermo vector within this object
Deprecated:
To be removed after Cantera 2.3 for all classes derived from Kinetics.

Reimplemented from Kinetics.

Reimplemented in AqueousKinetics, and GasKinetics.

Definition at line 19 of file BulkKinetics.cpp.

References Kinetics::assignShallowPointers().

◆ isReversible()

bool isReversible ( size_t  i)
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
ireaction index

Reimplemented from Kinetics.

Definition at line 26 of file BulkKinetics.cpp.

References BulkKinetics::m_revindex.

◆ getDeltaGibbs()

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

Reimplemented from Kinetics.

Definition at line 30 of file BulkKinetics.cpp.

References ThermoPhase::getChemPotentials(), Kinetics::getReactionDelta(), and Kinetics::thermo().

◆ getDeltaEnthalpy()

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

Reimplemented from Kinetics.

Definition at line 38 of file BulkKinetics.cpp.

References ThermoPhase::getPartialMolarEnthalpies(), Kinetics::getReactionDelta(), and Kinetics::thermo().

◆ getDeltaEntropy()

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

Reimplemented from Kinetics.

Definition at line 46 of file BulkKinetics.cpp.

References ThermoPhase::getPartialMolarEntropies(), Kinetics::getReactionDelta(), and Kinetics::thermo().

◆ getDeltaSSGibbs()

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

Reimplemented from Kinetics.

Definition at line 54 of file BulkKinetics.cpp.

References Kinetics::getReactionDelta(), ThermoPhase::getStandardChemPotentials(), and Kinetics::thermo().

◆ getDeltaSSEnthalpy()

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

Reimplemented from Kinetics.

Definition at line 65 of file BulkKinetics.cpp.

References ThermoPhase::getEnthalpy_RT(), Kinetics::getReactionDelta(), Kinetics::m_kk, ThermoPhase::RT(), and Kinetics::thermo().

◆ getDeltaSSEntropy()

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

Reimplemented from Kinetics.

Definition at line 76 of file BulkKinetics.cpp.

References Cantera::GasConstant, ThermoPhase::getEntropy_R(), Kinetics::getReactionDelta(), Kinetics::m_kk, and Kinetics::thermo().

◆ getRevRateConstants()

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

Return the reverse rate constants.

length is the number of reactions. units depends on many issues. 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 from Kinetics.

Definition at line 89 of file BulkKinetics.cpp.

References Kinetics::getEquilibriumConstants(), Kinetics::getFwdRateConstants(), Kinetics::m_rkcn, Kinetics::m_ropnet, and Kinetics::nReactions().

◆ 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 from Kinetics.

Reimplemented in AqueousKinetics, and GasKinetics.

Definition at line 108 of file BulkKinetics.cpp.

References Kinetics::addReaction(), BulkKinetics::m_dn, BulkKinetics::m_irrev, BulkKinetics::m_revindex, and Kinetics::nReactions().

Referenced by GasKinetics::addReaction(), and AqueousKinetics::addReaction().

◆ 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 from Kinetics.

Definition at line 142 of file BulkKinetics.cpp.

References Kinetics::m_kk, and Kinetics::resizeSpecies().

◆ setMultiplier()

void setMultiplier ( size_t  i,
double  f 
)
virtual

Set the multiplier for reaction i to f.

Parameters
iindex of the reaction
fvalue of the multiplier.

Reimplemented from Kinetics.

Definition at line 149 of file BulkKinetics.cpp.

References Kinetics::setMultiplier().

Member Data Documentation

◆ m_revindex

std::vector<size_t> m_revindex
protected

Indices of reversible reactions.

Definition at line 51 of file BulkKinetics.h.

Referenced by BulkKinetics::addReaction(), BulkKinetics::isReversible(), AqueousKinetics::updateKc(), and GasKinetics::updateKc().

◆ m_irrev

std::vector<size_t> m_irrev
protected

Indices of irreversible reactions.

Definition at line 52 of file BulkKinetics.h.

Referenced by BulkKinetics::addReaction(), AqueousKinetics::updateKc(), and GasKinetics::updateKc().

◆ m_dn

vector_fp m_dn
protected

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

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

Definition at line 57 of file BulkKinetics.h.

Referenced by BulkKinetics::addReaction(), GasKinetics::getEquilibriumConstants(), and GasKinetics::updateKc().


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