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Cantera
2.2.1
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Cantera
2.2.1
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Kinetics manager for elementary aqueous-phase chemistry. More...
#include <AqueousKinetics.h>
Public Member Functions | |
| AqueousKinetics (thermo_t *thermo=0) | |
| Constructor. Creates an empty reaction mechanism. More... | |
| virtual Kinetics * | duplMyselfAsKinetics (const std::vector< thermo_t * > &tpVector) const |
| Duplication routine for objects which inherit from Kinetics. More... | |
| virtual int | type () const |
| Identifies the kinetics manager type. More... | |
| virtual void | getEquilibriumConstants (doublereal *kc) |
| Return a vector of Equilibrium constants. More... | |
| virtual void | getFwdRateConstants (doublereal *kfwd) |
| Return the forward rate constants. More... | |
| void | updateROP () |
| void | _update_rates_T () |
| Update temperature-dependent portions of reaction rates. More... | |
| void | _update_rates_C () |
| Update properties that depend on concentrations. More... | |
| void | updateKc () |
| Update the equilibrium constants in molar units. More... | |
| virtual void | addReaction (ReactionData &r) |
| Add a single reaction to the mechanism. 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... | |
 Public Member Functions inherited from BulkKinetics | |
| BulkKinetics (thermo_t *thermo=0) | |
| 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 void | init () |
| Prepare the class for the addition of reactions. More... | |
| virtual void | finalize () |
| Finish adding reactions and prepare for use. More... | |
| virtual bool | ready () const |
| Returns true if the kinetics manager has been properly initialized and finalized. More... | |
| virtual void | setMultiplier (size_t i, double f) |
| Set the multiplier for reaction i to f. More... | |
| Public Member Functions inherited from Kinetics | |
| void | incrementRxnCount () |
| Increment the number of reactions in the mechanism by one. 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 () |
| Destructor. More... | |
| Kinetics (const Kinetics &) | |
| Copy Constructor for the Kinetics object. More... | |
| Kinetics & | operator= (const Kinetics &right) |
| Assignment operator. More... | |
| virtual void | assignShallowPointers (const std::vector< thermo_t * > &tpVector) |
| Reassign the pointers within the Kinetics object. 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_t & | thermo (size_t n=0) |
| This method returns a reference to the nth ThermoPhase object defined in this kinetics mechanism. More... | |
| const thermo_t & | thermo (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_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. More... | |
| thermo_t & | speciesPhase (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 | 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 const std::vector < size_t > & | reactants (size_t i) const |
| Returns a read-only reference to the vector of reactant index numbers for reaction i. More... | |
| virtual const std::vector < size_t > & | products (size_t i) const |
| Returns a read-only reference to the vector of product index numbers for reaction i. More... | |
| virtual int | reactionType (size_t i) const |
| Flag specifying the type of reaction. More... | |
| const std::string & | reactionString (size_t i) const |
| Return a string representing the reaction. More... | |
| const std::string & | reactantString (size_t i) const |
| Returns a string containing the reactants side of the reaction equation. More... | |
| const std::string & | productString (size_t i) const |
| Returns a string containing the products side of the reaction equation. More... | |
| virtual void | addPhase (thermo_t &thermo) |
| Add a phase to the kinetics manager object. More... | |
| shared_ptr< Reaction > | reaction (size_t i) |
| Return the Reaction object for reaction i. More... | |
| 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... | |
| virtual void | installReagents (const ReactionData &r) |
| virtual void | installGroups (size_t irxn, const std::vector< grouplist_t > &r, const std::vector< grouplist_t > &p) |
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virtual const std::vector < grouplist_t > & | reactantGroups (size_t i) |
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virtual const std::vector < grouplist_t > & | productGroups (size_t i) |
| doublereal | multiplier (size_t i) const |
| The current value of the multiplier for reaction i. More... | |
Additional Inherited Members | |
| Protected Member Functions inherited from BulkKinetics | |
| virtual void | addElementaryReaction (ReactionData &r) |
| virtual void | addElementaryReaction (ElementaryReaction &r) |
| virtual void | modifyElementaryReaction (size_t i, ElementaryReaction &rNew) |
| Protected Member Functions inherited from Kinetics | |
| 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 inherited from BulkKinetics | |
| Rate1< Arrhenius > | m_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 |
| bool | m_finalized |
| Protected Attributes inherited from Kinetics | |
| ValueCache | m_cache |
| Cache for saved calculations within each Kinetics object. More... | |
| size_t | m_ii |
| Number of reactions in the mechanism. 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< std::vector < size_t > > | m_reactants |
| This is a vector of vectors containing the reactants for each reaction. More... | |
| std::vector< std::vector < size_t > > | m_products |
| This is a vector of vectors containing the products for each reaction. More... | |
| std::vector< std::map< size_t, doublereal > > | m_rrxn |
| m_rrxn is a vector of maps, containing the reactant stoichiometric coefficient information More... | |
| std::vector< std::map< size_t, doublereal > > | m_prxn |
| m_prxn is a vector of maps, containing the reactant stoichiometric coefficient information More... | |
| std::vector< int > | m_rxntype |
| 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... | |
| std::vector< std::string > | m_rxneqn |
| Representation of each reaction equation. More... | |
| std::vector< std::string > | m_reactantStrings |
| Representation of the reactant side of each reaction equation. More... | |
| std::vector< std::string > | m_productStrings |
| Representation of the product side of each reaction equation. 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... | |
Kinetics manager for elementary aqueous-phase chemistry.
This kinetics manager implements standard mass-action reaction rate expressions for liquids
Definition at line 22 of file AqueousKinetics.h.
| AqueousKinetics | ( | thermo_t * | thermo = 0 | ) |
Constructor. Creates an empty reaction mechanism.
Definition at line 22 of file AqueousKinetics.cpp.
Referenced by AqueousKinetics::duplMyselfAsKinetics().
Duplication routine for objects which inherit from Kinetics.
This virtual routine can be used to duplicate Kinetics objects inherited 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.
| tpVector | Vector of shallow pointers to ThermoPhase objects. this is the m_thermo vector within this object |
Reimplemented from BulkKinetics.
Definition at line 27 of file AqueousKinetics.cpp.
References AqueousKinetics::AqueousKinetics(), and Kinetics::assignShallowPointers().
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Identifies the kinetics manager type.
Each class derived from Kinetics should overload this method to return a unique integer. Standard values are defined in file mix_defs.h.
Reimplemented from Kinetics.
Definition at line 41 of file AqueousKinetics.h.
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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.
\[ Kc_i = exp [ \Delta G_{ss,i} ] prod(Cs_k) exp(\sum_k \nu_{k,i} F \phi_n) ] \]
| kc | Output vector containing the equilibrium constants. Length: m_ii. |
Reimplemented from Kinetics.
Definition at line 75 of file AqueousKinetics.cpp.
References AqueousKinetics::_update_rates_T(), Cantera::GasConstant, Kinetics::getReactionDelta(), ThermoPhase::getStandardChemPotentials(), ThermoPhase::logStandardConc(), Kinetics::m_ii, Kinetics::m_rkcn, Phase::nSpecies(), Phase::temperature(), and Kinetics::thermo().
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Return the forward rate constants.
length is the number of reactions. units depends on many issues.
| kfwd | Output vector containing the forward reaction rate constants. Length: m_ii. |
Reimplemented from Kinetics.
Definition at line 135 of file AqueousKinetics.cpp.
References AqueousKinetics::_update_rates_C(), AqueousKinetics::_update_rates_T(), Kinetics::m_ii, Kinetics::m_perturb, Kinetics::m_rfn, Kinetics::m_ropf, and Cantera::multiply_each().
| void _update_rates_T | ( | ) |
Update temperature-dependent portions of reaction rates.
Definition at line 34 of file AqueousKinetics.cpp.
References Kinetics::m_rfn, Phase::temperature(), Kinetics::thermo(), and AqueousKinetics::updateKc().
Referenced by AqueousKinetics::getEquilibriumConstants(), and AqueousKinetics::getFwdRateConstants().
| void _update_rates_C | ( | ) |
Update properties that depend on concentrations.
Definition at line 44 of file AqueousKinetics.cpp.
References ThermoPhase::getActivityConcentrations(), and Kinetics::thermo().
Referenced by AqueousKinetics::getFwdRateConstants().
| void updateKc | ( | ) |
Update the equilibrium constants in molar units.
Definition at line 50 of file AqueousKinetics.cpp.
References Cantera::GasConstant, Kinetics::getRevReactionDelta(), ThermoPhase::getStandardChemPotentials(), ThermoPhase::logStandardConc(), BulkKinetics::m_irrev, BulkKinetics::m_revindex, Kinetics::m_rkcn, Phase::nSpecies(), Phase::temperature(), and Kinetics::thermo().
Referenced by AqueousKinetics::_update_rates_T().
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Add a single reaction to the mechanism.
This routine must be called after init() and before finalize(). Derived classes should call the base class method in addition to handling their own specialized behavior.
| r | Reference to the ReactionData object for the reaction to be added. |
Reimplemented from BulkKinetics.
Definition at line 151 of file AqueousKinetics.cpp.
References BulkKinetics::addReaction(), Cantera::ELEMENTARY_RXN, and ReactionData::reactionType.
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virtual |
Add a single reaction to the mechanism.
Derived classes should call the base class method in addition to handling their own specialized behavior.
| r | Pointer to the Reaction object to be added. |
true if the reaction is added or false if it was skipped Reimplemented from BulkKinetics.
Definition at line 160 of file AqueousKinetics.cpp.
References BulkKinetics::addReaction(), Cantera::ELEMENTARY_RXN, and Cantera::int2str().
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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.
| i | Index of the reaction to be modified |
| rNew | Reaction with the new rate expressions |
Reimplemented from Kinetics.
Definition at line 175 of file AqueousKinetics.cpp.
References Kinetics::modifyReaction().
1.8.6