Cantera  2.1.2
Public Member Functions | Protected Attributes | Private Member Functions | Private Attributes | List of all members
Kinetics Class Reference

Public interface for kinetics managers. More...

#include <Kinetics.h>

Inheritance diagram for Kinetics:
[legend]

Public Member Functions

void incrementRxnCount ()
 Increment the number of reactions in the mechanism by one. More...
 
virtual bool ready () const
 Returns true if the kinetics manager has been properly initialized and finalized. 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 ()
 Destructor. More...
 
 Kinetics (const Kinetics &)
 Copy Constructor for the Kinetics object. More...
 
Kineticsoperator= (const Kinetics &right)
 Assignment operator. More...
 
virtual KineticsduplMyselfAsKinetics (const std::vector< thermo_t * > &tpVector) const
 Duplication routine for objects which inherit from Kinetics. More...
 
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...
 
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 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 doublereal reactantStoichCoeff (size_t k, size_t i) const
 Stoichiometric coefficient of species k as a reactant in reaction i. More...
 
virtual doublereal 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...
 
virtual bool isReversible (size_t i)
 True if reaction i has been declared to be reversible. More...
 
virtual std::string reactionString (size_t i) const
 Return a string representing the reaction. 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...
 
virtual void getActivationEnergies (doublereal *E)
 Return the activation energies in Kelvin. 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. More...
 
virtual void finalize ()
 Finish adding reactions and prepare for use. More...
 
virtual void addReaction (ReactionData &r)
 Add a single reaction to the mechanism. More...
 
virtual const std::vector
< grouplist_t > & 
reactantGroups (size_t i)
 
virtual const std::vector
< grouplist_t > & 
productGroups (size_t i)
 
Altering Reaction Rates
doublereal multiplier (size_t i) const
 The current value of the multiplier for reaction i. More...
 
void setMultiplier (size_t i, doublereal f)
 Set the multiplier for reaction i to f. More...
 

Protected Attributes

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< 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< 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...
 

Private Member Functions

void err (const std::string &m) const
 Function indicating that a function inherited from the base class hasn't had a definition assigned to it. More...
 

Private Attributes

std::vector< grouplist_tm_dummygroups
 Vector of group lists. 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 131 of file Kinetics.h.

Constructor & Destructor Documentation

Kinetics ( )

Default constructor.

Definition at line 23 of file Kinetics.cpp.

Referenced by Kinetics::duplMyselfAsKinetics().

~Kinetics ( )
virtual

Destructor.

Definition at line 39 of file Kinetics.cpp.

Kinetics ( const Kinetics right)

Copy Constructor for the Kinetics object.

Definition at line 41 of file Kinetics.cpp.

Member Function Documentation

Kinetics & operator= ( const Kinetics right)
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

Reimplemented in InterfaceKinetics, AqueousKinetics, GasKinetics, and EdgeKinetics.

Definition at line 89 of file Kinetics.cpp.

References Kinetics::assignShallowPointers(), and Kinetics::Kinetics().

void assignShallowPointers ( const std::vector< thermo_t * > &  tpVector)
virtual

Reassign the pointers within the Kinetics object.

This type or routine is necessary because the Kinetics object doesn't own the ThermoPhase objects. After a duplication, we need to point to different ThermoPhase objects.

We check that the ThermoPhase objects are aligned in the same order and have the following identical properties to the ones that they are replacing:

Parameters
tpVectorVector of pointers to ThermoPhase objects. this is the m_thermo vector within this object

Definition at line 144 of file Kinetics.cpp.

References ThermoPhase::eosType(), Phase::id(), Kinetics::m_thermo, and Phase::nSpecies().

Referenced by EdgeKinetics::duplMyselfAsKinetics(), GasKinetics::duplMyselfAsKinetics(), AqueousKinetics::duplMyselfAsKinetics(), InterfaceKinetics::duplMyselfAsKinetics(), and Kinetics::duplMyselfAsKinetics().

int type ( ) const
virtual

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 in InterfaceKinetics, AqueousKinetics, GasKinetics, EdgeKinetics, and GRI_30_Kinetics.

Definition at line 97 of file Kinetics.cpp.

Referenced by Kinetics::addPhase().

size_t nReactions ( ) const
inline
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 102 of file Kinetics.cpp.

References Kinetics::m_ii.

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 109 of file Kinetics.cpp.

References Kinetics::m_ii.

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 130 of file Kinetics.cpp.

References Kinetics::m_kk.

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 137 of file Kinetics.cpp.

References Kinetics::m_kk.

size_t nPhases ( ) const
inline
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 116 of file Kinetics.cpp.

References Kinetics::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().

Used before calls which take an array pointer.

Definition at line 123 of file Kinetics.cpp.

References Kinetics::nPhases().

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 250 of file Kinetics.h.

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

Referenced by Cantera::importKinetics().

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 263 of file Kinetics.h.

References Kinetics::m_surfphase.

Referenced by InterfaceKinetics::_update_rates_T(), solveSP::calc_t(), ConstPressureReactor::evalEqs(), IdealGasReactor::evalEqs(), IdealGasConstPressureReactor::evalEqs(), Reactor::evalEqs(), solveSP::fun_eval(), Cantera::getRateCoefficient(), solveProb::print_header(), Wall::setKinetics(), and solveSP::solveSP().

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 275 of file Kinetics.h.

References Kinetics::m_rxnphase.

Referenced by EdgeKinetics::finalize(), and InterfaceKinetics::finalize().

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 288 of file Kinetics.h.

References Kinetics::m_thermo.

Referenced by AqueousKinetics::_update_rates_C(), InterfaceKinetics::_update_rates_C(), InterfaceKinetics::_update_rates_phi(), AqueousKinetics::_update_rates_T(), InterfaceKinetics::_update_rates_T(), InterfaceKinetics::applyButlerVolmerCorrection(), InterfaceKinetics::applyExchangeCurrentDensityFormulation(), solveSP::calc_t(), EdgeKinetics::finalize(), InterfaceKinetics::finalize(), InterfaceKinetics::getDeltaElectrochemPotentials(), GasKinetics::getDeltaEnthalpy(), AqueousKinetics::getDeltaEnthalpy(), InterfaceKinetics::getDeltaEnthalpy(), GasKinetics::getDeltaEntropy(), AqueousKinetics::getDeltaEntropy(), InterfaceKinetics::getDeltaEntropy(), GasKinetics::getDeltaGibbs(), AqueousKinetics::getDeltaGibbs(), InterfaceKinetics::getDeltaGibbs(), GasKinetics::getDeltaSSEnthalpy(), AqueousKinetics::getDeltaSSEnthalpy(), InterfaceKinetics::getDeltaSSEnthalpy(), GasKinetics::getDeltaSSEntropy(), AqueousKinetics::getDeltaSSEntropy(), InterfaceKinetics::getDeltaSSEntropy(), GasKinetics::getDeltaSSGibbs(), AqueousKinetics::getDeltaSSGibbs(), InterfaceKinetics::getDeltaSSGibbs(), Cantera::getEfficiencies(), GasKinetics::getEquilibriumConstants(), AqueousKinetics::getEquilibriumConstants(), InterfaceKinetics::getEquilibriumConstants(), Cantera::getRateCoefficient(), Cantera::getStick(), ImplicitSurfChem::ImplicitSurfChem(), GasKinetics::init(), AqueousKinetics::init(), InterfaceKinetics::init(), ConstPressureReactor::initialize(), Reactor::initialize(), Kinetics::kineticsSpeciesIndex(), Kinetics::kineticsSpeciesName(), Kinetics::nTotalSpecies(), solveProb::print_header(), InterfaceKinetics::setElectricPotential(), Wall::setKinetics(), ImplicitSurfChem::solvePseudoSteadyStateProblem(), solveSP::solveSP(), Kinetics::speciesPhase(), GasKinetics::update_rates_C(), GasKinetics::update_rates_T(), GasKinetics::updateKc(), AqueousKinetics::updateKc(), InterfaceKinetics::updateKc(), and solveSP::updateMFKinSpecies().

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 300 of file Kinetics.h.

References Kinetics::nPhases(), Phase::nSpecies(), and Kinetics::thermo().

Referenced by ReactingSurf1D::init(), and rxninfo::installReaction().

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 331 of file Kinetics.h.

References Kinetics::m_start.

Referenced by solveSP::calc_t(), Cantera::checkRxnElementBalance(), ReactingSurf1D::eval(), ConstPressureReactor::evalEqs(), IdealGasReactor::evalEqs(), IdealGasConstPressureReactor::evalEqs(), Reactor::evalEqs(), solveSP::fun_eval(), Cantera::getEfficiencies(), Cantera::getReagents(), Cantera::getStick(), Kinetics::kineticsSpeciesIndex(), solveSP::solveSP(), and solveSP::updateMFKinSpecies().

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 186 of file Kinetics.cpp.

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

Referenced by Cantera::getStick(), solveSP::printFinal(), solveProb::printIteration(), and solveSP::printIteration().

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 196 of file Kinetics.cpp.

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

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 209 of file Kinetics.cpp.

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

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 229 of file Kinetics.cpp.

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

Referenced by Cantera::checkRxnElementBalance(), Cantera::getStick(), and rxninfo::installReaction().

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 390 of file Kinetics.h.

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

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 244 of file Kinetics.cpp.

References Cantera::int2str(), Kinetics::m_start, and Cantera::npos.

Referenced by InterfaceKinetics::addReaction(), Cantera::checkRxnElementBalance(), Cantera::getStick(), and Kinetics::speciesPhase().

virtual void getFwdRatesOfProgress ( doublereal *  fwdROP)
inlinevirtual

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: m_ii.

Reimplemented in InterfaceKinetics, AqueousKinetics, and GasKinetics.

Definition at line 416 of file Kinetics.h.

References Kinetics::err().

virtual void getRevRatesOfProgress ( doublereal *  revROP)
inlinevirtual

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: m_ii.

Reimplemented in InterfaceKinetics, AqueousKinetics, and GasKinetics.

Definition at line 428 of file Kinetics.h.

References Kinetics::err().

virtual void getNetRatesOfProgress ( doublereal *  netROP)
inlinevirtual

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: m_ii.

Reimplemented in InterfaceKinetics, AqueousKinetics, and GasKinetics.

Definition at line 439 of file Kinetics.h.

References Kinetics::err().

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.

Parameters
kcOutput vector containing the equilibrium constants. Length: m_ii.

Reimplemented in InterfaceKinetics, AqueousKinetics, and GasKinetics.

Definition at line 452 of file Kinetics.h.

References Kinetics::err().

virtual void getReactionDelta ( const doublereal *  property,
doublereal *  deltaProperty 
)
inlinevirtual

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: m_ii.

Definition at line 472 of file Kinetics.h.

References Kinetics::err().

virtual void getDeltaGibbs ( doublereal *  deltaG)
inlinevirtual

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

These values depend upon the concentration of the solution.

units = J kmol-1

Parameters
deltaGOutput vector of deltaG's for reactions Length: m_ii.

Reimplemented in InterfaceKinetics, AqueousKinetics, and GasKinetics.

Definition at line 485 of file Kinetics.h.

References Kinetics::err().

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: m_ii.

Reimplemented in InterfaceKinetics.

Definition at line 499 of file Kinetics.h.

References Kinetics::err().

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: m_ii.

Reimplemented in InterfaceKinetics, AqueousKinetics, and GasKinetics.

Definition at line 511 of file Kinetics.h.

References Kinetics::err().

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: m_ii.

Reimplemented in InterfaceKinetics, AqueousKinetics, and GasKinetics.

Definition at line 523 of file Kinetics.h.

References Kinetics::err().

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: m_ii.

Reimplemented in InterfaceKinetics, AqueousKinetics, and GasKinetics.

Definition at line 536 of file Kinetics.h.

References Kinetics::err().

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: m_ii.

Reimplemented in InterfaceKinetics, AqueousKinetics, and GasKinetics.

Definition at line 549 of file Kinetics.h.

References Kinetics::err().

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: m_ii.

Reimplemented in InterfaceKinetics, AqueousKinetics, and GasKinetics.

Definition at line 562 of file Kinetics.h.

References Kinetics::err().

virtual void getCreationRates ( doublereal *  cdot)
inlinevirtual

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.

Reimplemented in InterfaceKinetics, AqueousKinetics, and GasKinetics.

Definition at line 577 of file Kinetics.h.

References Kinetics::err().

virtual void getDestructionRates ( doublereal *  ddot)
inlinevirtual

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.

Reimplemented in InterfaceKinetics, AqueousKinetics, and GasKinetics.

Definition at line 588 of file Kinetics.h.

References Kinetics::err().

virtual void getNetProductionRates ( doublereal *  wdot)
inlinevirtual

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.

Reimplemented in InterfaceKinetics, AqueousKinetics, GasKinetics, and GRI_30_Kinetics.

Definition at line 600 of file Kinetics.h.

References Kinetics::err().

Referenced by FlowReactor::evalEqs(), ConstPressureReactor::evalEqs(), IdealGasReactor::evalEqs(), IdealGasConstPressureReactor::evalEqs(), Reactor::evalEqs(), and StFlow::getWdot().

virtual doublereal reactantStoichCoeff ( size_t  k,
size_t  i 
) const
inlinevirtual

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

Parameters
kkinetic species index
ireaction index

Reimplemented in InterfaceKinetics, AqueousKinetics, and GasKinetics.

Definition at line 614 of file Kinetics.h.

References Kinetics::err().

virtual doublereal productStoichCoeff ( size_t  k,
size_t  i 
) const
inlinevirtual

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

Parameters
kkinetic species index
ireaction index

Reimplemented in InterfaceKinetics, AqueousKinetics, and GasKinetics.

Definition at line 625 of file Kinetics.h.

References Kinetics::err().

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 638 of file Kinetics.h.

References Kinetics::err().

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 653 of file Kinetics.h.

References Kinetics::err().

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 663 of file Kinetics.h.

References Kinetics::err().

virtual const std::vector<size_t>& reactants ( size_t  i) const
inlinevirtual

Returns a read-only reference to the vector of reactant index numbers for reaction i.

Parameters
ireaction index

Definition at line 673 of file Kinetics.h.

References Kinetics::m_reactants.

Referenced by InterfaceKinetics::addReaction().

virtual const std::vector<size_t>& products ( size_t  i) const
inlinevirtual

Returns a read-only reference to the vector of product index numbers for reaction i.

Parameters
ireaction index

Definition at line 683 of file Kinetics.h.

References Kinetics::m_products.

Referenced by InterfaceKinetics::addReaction().

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

Reimplemented in InterfaceKinetics, AqueousKinetics, and GasKinetics.

Definition at line 694 of file Kinetics.h.

References Kinetics::err().

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, AqueousKinetics, and GasKinetics.

Definition at line 706 of file Kinetics.h.

References Kinetics::err().

virtual std::string reactionString ( size_t  i) const
inlinevirtual

Return a string representing the reaction.

Parameters
ireaction index

Reimplemented in InterfaceKinetics, AqueousKinetics, and GasKinetics.

Definition at line 716 of file Kinetics.h.

References Kinetics::err().

Referenced by Reactor::addSensitivityReaction().

virtual void getFwdRateConstants ( doublereal *  kfwd)
inlinevirtual

Return the forward rate constants.

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

Parameters
kfwdOutput vector containing the forward reaction rate constants. Length: m_ii.

Reimplemented in InterfaceKinetics, AqueousKinetics, and GasKinetics.

Definition at line 729 of file Kinetics.h.

References Kinetics::err().

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

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 in InterfaceKinetics, AqueousKinetics, and GasKinetics.

Definition at line 744 of file Kinetics.h.

References Kinetics::err().

virtual void getActivationEnergies ( doublereal *  E)
inlinevirtual

Return the activation energies in Kelvin.

length is the number of reactions

Parameters
EOuptut vector of activation energies. Length: m_ii.
Deprecated:
To be removed in Cantera 2.2.

Reimplemented in InterfaceKinetics.

Definition at line 757 of file Kinetics.h.

References Kinetics::err().

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 255 of file Kinetics.cpp.

References Cantera::cEdge, Cantera::cSurf, ThermoPhase::eosType(), Kinetics::m_mindim, Kinetics::m_phaseindex, Kinetics::m_rxnphase, Kinetics::m_start, Kinetics::m_surfphase, Kinetics::m_thermo, Phase::nDim(), Kinetics::nPhases(), and Kinetics::type().

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

virtual void init ( )
inlinevirtual

Prepare the class for the addition of reactions.

This method is called by importKinetics() after all phases have been added but before any reactions have been. The base class method does nothing, but derived classes may use this to perform any initialization (allocating arrays, etc.) that requires knowing the phases and species, but before any reactions are added.

Reimplemented in InterfaceKinetics, AqueousKinetics, and GasKinetics.

Definition at line 791 of file Kinetics.h.

Referenced by Cantera::importKinetics().

void finalize ( )
virtual

Finish adding reactions and prepare for use.

This method is called by importKinetics() after all reactions have been entered into the mechanism and before the mechanism is used to calculate reaction rates. The base class method does nothing, but derived classes may use this to perform any initialization (allocating arrays, etc.) that must be done after the reactions are entered.

Reimplemented in InterfaceKinetics, AqueousKinetics, GasKinetics, and EdgeKinetics.

Definition at line 290 of file Kinetics.cpp.

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

Referenced by InterfaceKinetics::finalize(), and Cantera::installReactionArrays().

virtual void addReaction ( ReactionData r)
inlinevirtual

Add a single reaction to the mechanism.

This routine must be called after init() and before finalize().

Parameters
rReference to the ReactionData object for the reaction to be added.

Reimplemented in InterfaceKinetics, AqueousKinetics, and GasKinetics.

Definition at line 810 of file Kinetics.h.

References Kinetics::err().

Referenced by rxninfo::installReaction().

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 840 of file Kinetics.h.

References Kinetics::m_perturb.

Referenced by FlowReactor::evalEqs(), ConstPressureReactor::evalEqs(), IdealGasConstPressureReactor::evalEqs(), and Reactor::evalEqs().

void setMultiplier ( size_t  i,
doublereal  f 
)
inline

Set the multiplier for reaction i to f.

Parameters
iindex of the reaction
fvalue of the multiplier.

Definition at line 849 of file Kinetics.h.

References Kinetics::m_perturb.

Referenced by FlowReactor::evalEqs(), ConstPressureReactor::evalEqs(), and Reactor::evalEqs().

void incrementRxnCount ( )
inline

Increment the number of reactions in the mechanism by one.

Todo:
Should be protected?

Definition at line 859 of file Kinetics.h.

References Kinetics::m_ii, and Kinetics::m_perturb.

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

virtual bool ready ( ) const
inlinevirtual

Returns true if the kinetics manager has been properly initialized and finalized.

Reimplemented in InterfaceKinetics, AqueousKinetics, GasKinetics, Interface, and GRI30.

Definition at line 868 of file Kinetics.h.

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 172 of file Kinetics.cpp.

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

void err ( const std::string &  m) const
private

Member Data Documentation

size_t m_ii
protected
size_t m_kk
protected
vector_fp m_perturb
protected
std::vector<std::vector<size_t> > m_reactants
protected

This is a vector of vectors containing the reactants for each reaction.

The outer vector is over the number of reactions, m_ii. The inner vector is a list of species indices. If the stoichiometric coefficient for a reactant is greater than one, then the reactant is listed contiguously in the vector a number of times equal to its stoichiometric coefficient. NOTE: These vectors will be wrong if there are real stoichiometric coefficients in the expression.

Definition at line 908 of file Kinetics.h.

Referenced by Kinetics::operator=(), and Kinetics::reactants().

std::vector<std::vector<size_t> > m_products
protected

This is a vector of vectors containing the products for each reaction.

The outer vector is over the number of reactions, m_ii. The inner vector is a list of species indices. If the stoichiometric coefficient for a product is greater than one, then the reactant is listed contiguously in the vector a number of times equal to its stoichiometric coefficient. NOTE: These vectors will be wrong if there are real stoichiometric coefficients in the expression.

Definition at line 921 of file Kinetics.h.

Referenced by Kinetics::operator=(), and Kinetics::products().

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 938 of file Kinetics.h.

Referenced by Kinetics::addPhase(), Kinetics::assignShallowPointers(), InterfaceKinetics::finalize(), Kinetics::finalize(), GRI_30_Kinetics::gri30_updateKc(), Kinetics::kineticsSpeciesIndex(), Kinetics::nPhases(), Kinetics::operator=(), InterfaceKinetics::phaseExistence(), InterfaceKinetics::phaseStability(), Kinetics::selectPhase(), InterfaceKinetics::setPhaseExistence(), InterfaceKinetics::setPhaseStability(), Kinetics::speciesPhase(), and Kinetics::thermo().

std::vector<size_t> m_start
protected
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 955 of file Kinetics.h.

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

size_t m_surfphase
protected

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

Definition at line 958 of file Kinetics.h.

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

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 965 of file Kinetics.h.

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

size_t m_mindim
protected

number of spatial dimensions of lowest-dimensional phase.

Definition at line 968 of file Kinetics.h.

Referenced by Kinetics::addPhase(), and Kinetics::operator=().

std::vector<grouplist_t> m_dummygroups
private

Vector of group lists.

Definition at line 972 of file Kinetics.h.

Referenced by Kinetics::operator=().


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