Cantera
2.0
|
Public interface for kinetics managers. More...
#include <Kinetics.h>
Public Member Functions | |
void | incrementRxnCount () |
Increment the number of reactions in the mechanism by one. | |
virtual bool | ready () const |
Returns true if the kinetics manager has been properly initialized and finalized. | |
void | selectPhase (const doublereal *data, const thermo_t *phase, doublereal *phase_data) |
Extract from array data the portion pertaining to phase phase . | |
Constructors and General Information about Mechanism | |
Kinetics () | |
Default constructor. | |
virtual | ~Kinetics () |
Destructor. | |
Kinetics (const Kinetics &) | |
Copy Constructor for the Kinetics object. | |
Kinetics & | operator= (const Kinetics &right) |
Assignment operator. | |
virtual Kinetics * | duplMyselfAsKinetics (const std::vector< thermo_t * > &tpVector) const |
Duplication routine for objects which inherit from Kinetics. | |
virtual void | assignShallowPointers (const std::vector< thermo_t * > &tpVector) |
Reassign the shallow pointers within the FKinetics object. | |
virtual int | ID () const |
Identifies the subclass of the Kinetics manager type. | |
virtual int | type () const |
Identifies the kinetics manager type. | |
size_t | nReactions () const |
Number of reactions in the reaction mechanism. | |
void | checkReactionIndex (size_t m) const |
Check that the specified reaction index is in range Throws an exception if i is greater than nReactions() | |
void | checkReactionArraySize (size_t ii) const |
Check that an array size is at least nReactions() Throws an exception if ii is less than nReactions(). | |
void | checkSpeciesIndex (size_t k) const |
Check that the specified species index is in range Throws an exception if k is greater than nSpecies()-1. | |
void | checkSpeciesArraySize (size_t mm) const |
Check that an array size is at least nSpecies() Throws an exception if kk is less than nSpecies(). | |
Information/Lookup Functions about Phases and Species | |
size_t | nPhases () const |
The number of phases participating in the reaction mechanism. | |
void | checkPhaseIndex (size_t m) const |
Check that the specified phase index is in range Throws an exception if m is greater than nPhases() | |
void | checkPhaseArraySize (size_t mm) const |
Check that an array size is at least nPhases() Throws an exception if mm is less than nPhases(). | |
size_t | phaseIndex (std::string ph) |
Return the phase index of a phase in the list of phases defined within the object. | |
size_t | surfacePhaseIndex () |
This returns the integer index of the phase which has ThermoPhase type cSurf. | |
size_t | reactionPhaseIndex () |
Phase where the reactions occur. | |
thermo_t & | thermo (size_t n=0) |
This method returns a reference to the nth ThermoPhase object defined in this kinetics mechanism. | |
const thermo_t & | thermo (size_t n=0) const |
thermo_t & | phase (size_t n=0) |
This method returns a reference to the nth ThermoPhase defined in this kinetics mechanism. | |
const thermo_t & | phase (size_t n=0) const |
This method returns a reference to the nth ThermoPhase defined in this kinetics mechanism. | |
size_t | nTotalSpecies () const |
The total number of species in all phases participating in the kinetics mechanism. | |
size_t | start (size_t n) |
Returns the starting index of the species in the nth phase associated with the reaction mechanism. | |
size_t | kineticsSpeciesIndex (size_t k, size_t n) const |
The location of species k of phase n in species arrays. | |
std::string | kineticsSpeciesName (size_t k) const |
Return the std::string name of the kth species in the kinetics manager. | |
size_t | kineticsSpeciesIndex (const std::string &nm) const |
This routine will look up a species number based on the input std::string nm. | |
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. | |
thermo_t & | speciesPhase (std::string nm) |
This function looks up the std::string name of a species and returns a reference to the ThermoPhase object of the phase where the species resides. | |
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. | |
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. | |
Reaction Rates Of Progress | |
virtual void | getFwdRatesOfProgress (doublereal *fwdROP) |
Return the forward rates of progress of the reactions. | |
virtual void | getRevRatesOfProgress (doublereal *revROP) |
Return the Reverse rates of progress of the reactions. | |
virtual void | getNetRatesOfProgress (doublereal *netROP) |
Net rates of progress. | |
virtual void | getEquilibriumConstants (doublereal *kc) |
Return a vector of Equilibrium constants. | |
virtual void | getReactionDelta (const doublereal *property, doublereal *deltaProperty) |
Change in species properties. | |
virtual void | getDeltaGibbs (doublereal *deltaG) |
Return the vector of values for the reaction gibbs free energy change. | |
virtual void | getDeltaElectrochemPotentials (doublereal *deltaM) |
Return the vector of values for the reaction electrochemical free energy change. | |
virtual void | getDeltaEnthalpy (doublereal *deltaH) |
Return the vector of values for the reactions change in enthalpy. | |
virtual void | getDeltaEntropy (doublereal *deltaS) |
Return the vector of values for the reactions change in entropy. | |
virtual void | getDeltaSSGibbs (doublereal *deltaG) |
Return the vector of values for the reaction standard state gibbs free energy change. | |
virtual void | getDeltaSSEnthalpy (doublereal *deltaH) |
Return the vector of values for the change in the standard state enthalpies of reaction. | |
virtual void | getDeltaSSEntropy (doublereal *deltaS) |
Return the vector of values for the change in the standard state entropies for each reaction. | |
Species Production Rates | |
virtual void | getCreationRates (doublereal *cdot) |
Species creation rates [kmol/m^3/s or kmol/m^2/s]. | |
virtual void | getDestructionRates (doublereal *ddot) |
Species destruction rates [kmol/m^3/s or kmol/m^2/s]. | |
virtual void | getNetProductionRates (doublereal *wdot) |
Species net production rates [kmol/m^3/s or kmol/m^2/s]. | |
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. | |
virtual doublereal | productStoichCoeff (size_t k, size_t i) const |
Stoichiometric coefficient of species k as a product in reaction i. | |
virtual doublereal | reactantOrder (size_t k, size_t i) const |
Reactant order of species k in reaction i. | |
virtual doublereal | productOrder (int k, int i) const |
product Order of species k in reaction i. | |
virtual void | getActivityConcentrations (doublereal *const conc) |
Get the vector of activity concentrations used in the kinetics object. | |
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. | |
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. | |
virtual int | reactionType (size_t i) const |
Flag specifying the type of reaction. | |
virtual bool | isReversible (size_t i) |
True if reaction i has been declared to be reversible. | |
virtual std::string | reactionString (size_t i) const |
Return a std::string representing the reaction. | |
virtual void | getFwdRateConstants (doublereal *kfwd) |
Return the forward rate constants. | |
virtual void | getRevRateConstants (doublereal *krev, bool doIrreversible=false) |
Return the reverse rate constants. | |
virtual void | getActivationEnergies (doublereal *E) |
Return the activation energies in Kelvin. | |
Reaction Mechanism Construction | |
virtual void | addPhase (thermo_t &thermo) |
Add a phase to the kinetics manager object. | |
virtual void | init () |
Prepare the class for the addition of reactions. | |
virtual void | finalize () |
Finish adding reactions and prepare for use. | |
virtual void | addReaction (ReactionData &r) |
Add a single reaction to the mechanism. | |
virtual const std::vector < grouplist_t > & | reactantGroups (size_t i) |
virtual const std::vector < grouplist_t > & | productGroups (size_t i) |
Altering Reaction Rates | |
These methods alter reaction rates. They are designed primarily for carrying out sensitivity analysis, but may be used for any purpose requiring dynamic alteration of rate constants. For each reaction, a real-valued multiplier may be defined that multiplies the reaction rate coefficient. The multiplier may be set to zero to completely remove a reaction from the mechanism. | |
doublereal | multiplier (size_t i) const |
The current value of the multiplier for reaction i. | |
void | setMultiplier (size_t i, doublereal f) |
Set the multiplier for reaction i to f. | |
Protected Attributes | |
size_t | m_ii |
Number of reactions in the mechanism. | |
size_t | m_kk |
The number of species in all of the phases that participate in this kinetics mechanism. | |
vector_fp | m_perturb |
Vector of perturbation factors for each reaction's rate of progress vector. | |
std::vector< std::vector < size_t > > | m_reactants |
This is a vector of vectors containing the reactants for each reaction. | |
std::vector< std::vector < size_t > > | m_products |
This is a vector of vectors containing the products for each reaction. | |
std::vector< thermo_t * > | m_thermo |
m_thermo is a vector of pointers to ThermoPhase objects that are involved with this kinetics operator | |
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. | |
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. | |
size_t | m_surfphase |
Index in the list of phases of the one surface phase. | |
size_t | m_rxnphase |
Phase Index where reactions are assumed to be taking place. | |
size_t | m_mindim |
number of spatial dimensions of lowest-dimensional phase. | |
Private Member Functions | |
void | err (std::string m) const |
Private function of the class Kinetics, indicating that a function inherited from the base class hasn't had a definition assigned to it. | |
Private Attributes | |
std::vector< grouplist_t > | m_dummygroups |
Vector of group lists. | |
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.
Kinetics | ( | ) |
Default constructor.
Definition at line 28 of file Kinetics.cpp.
Referenced by Kinetics::duplMyselfAsKinetics().
|
virtual |
Destructor.
Definition at line 44 of file Kinetics.cpp.
Copy Constructor for the Kinetics object.
Currently, this is not fully implemented. If called it will throw an exception.
Definition at line 52 of file Kinetics.cpp.
Assignment operator.
This is NOT a virtual function.
right | Reference to Kinetics object to be copied into the current one. |
Definition at line 80 of file Kinetics.cpp.
References Kinetics::m_dummygroups, Kinetics::m_ii, Kinetics::m_kk, Kinetics::m_mindim, Kinetics::m_perturb, Kinetics::m_phaseindex, Kinetics::m_products, Kinetics::m_reactants, Kinetics::m_rxnphase, Kinetics::m_start, Kinetics::m_surfphase, and Kinetics::m_thermo.
Referenced by GasKinetics::operator=(), and InterfaceKinetics::operator=().
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 in InterfaceKinetics, GasKinetics, AqueousKinetics, and EdgeKinetics.
Definition at line 118 of file Kinetics.cpp.
References Kinetics::assignShallowPointers(), and Kinetics::Kinetics().
|
virtual |
Reassign the shallow pointers within the FKinetics object.
This type or routine is absolute 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. id() eosType() nSpecies()
tpVector | Vector of shallow pointers to ThermoPhase objects. this is the m_thermo vector within this object |
Definition at line 179 of file Kinetics.cpp.
References ThermoPhase::eosType(), Phase::id(), Kinetics::m_thermo, and Phase::nSpecies().
Referenced by EdgeKinetics::duplMyselfAsKinetics(), AqueousKinetics::duplMyselfAsKinetics(), GasKinetics::duplMyselfAsKinetics(), InterfaceKinetics::duplMyselfAsKinetics(), and Kinetics::duplMyselfAsKinetics().
|
virtual |
Identifies the subclass of the Kinetics manager type.
These are listed in mix_defs.h.
Reimplemented in InterfaceKinetics, GasKinetics, AqueousKinetics, EdgeKinetics, and GRI_30_Kinetics.
Definition at line 126 of file Kinetics.cpp.
|
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, GasKinetics, AqueousKinetics, EdgeKinetics, and GRI_30_Kinetics.
Definition at line 131 of file Kinetics.cpp.
Referenced by Kinetics::addPhase().
|
inline |
Number of reactions in the reaction mechanism.
Definition at line 209 of file Kinetics.h.
References Kinetics::m_ii.
Referenced by EdgeKinetics::finalize(), InterfaceKinetics::finalize(), InterfaceKinetics::getFwdRateConstants(), InterfaceKinetics::getRevRateConstants(), and InterfaceKinetics::updateKc().
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 136 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 143 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 164 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 171 of file Kinetics.cpp.
References Kinetics::m_kk.
|
inline |
The number of phases participating in the reaction mechanism.
For a homogeneous reaction mechanism, this will always return 1, but for a heterogeneous mechanism it will return the total number of phases in the mechanism.
Definition at line 244 of file Kinetics.h.
References Kinetics::m_thermo.
Referenced by InterfaceKinetics::_update_rates_C(), InterfaceKinetics::_update_rates_phi(), Kinetics::addPhase(), InterfaceKinetics::addReaction(), InterfaceKinetics::applyButlerVolmerCorrection(), Kinetics::checkPhaseArraySize(), Kinetics::checkPhaseIndex(), Kinetics::finalize(), InterfaceKinetics::getDeltaElectrochemPotentials(), InterfaceKinetics::getDeltaEnthalpy(), InterfaceKinetics::getDeltaEntropy(), InterfaceKinetics::getDeltaGibbs(), InterfaceKinetics::getDeltaSSEnthalpy(), InterfaceKinetics::getDeltaSSEntropy(), InterfaceKinetics::getDeltaSSGibbs(), InterfaceKinetics::getEquilibriumConstants(), ImplicitSurfChem::ImplicitSurfChem(), InterfaceKinetics::init(), Kinetics::nTotalSpecies(), InterfaceKinetics::operator=(), solveProb::print_header(), Kinetics::selectPhase(), InterfaceKinetics::updateKc(), solveSP::updateMFKinSpecies(), and InterfaceKinetics::updateROP().
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 150 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 157 of file Kinetics.cpp.
References Kinetics::nPhases().
|
inline |
Return the phase index of a phase in the list of phases defined within the object.
ph | std::string name of the phase |
If a -1 is returned, then the phase is not defined in the Kinetics object.
Definition at line 266 of file Kinetics.h.
References Kinetics::m_phaseindex, and Cantera::npos.
Referenced by Cantera::importKinetics().
|
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 280 of file Kinetics.h.
References Kinetics::m_surfphase.
Referenced by InterfaceKinetics::_update_rates_T(), solveSP::calc_t(), solveSP::fun_eval(), Cantera::getRateCoefficient(), solveProb::print_header(), and solveSP::solveSP().
|
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 294 of file Kinetics.h.
References Kinetics::m_rxnphase.
Referenced by EdgeKinetics::finalize(), and InterfaceKinetics::finalize().
|
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.
n | Index of the ThermoPhase being sought. |
Definition at line 309 of file Kinetics.h.
References Kinetics::m_thermo.
Referenced by AqueousKinetics::_update_rates_C(), InterfaceKinetics::_update_rates_C(), InterfaceKinetics::_update_rates_phi(), InterfaceKinetics::_update_rates_T(), InterfaceKinetics::applyButlerVolmerCorrection(), InterfaceKinetics::applyExchangeCurrentDensityFormulation(), solveSP::calc_t(), EdgeKinetics::finalize(), InterfaceKinetics::finalize(), InterfaceKinetics::getDeltaElectrochemPotentials(), AqueousKinetics::getDeltaEnthalpy(), GasKinetics::getDeltaEnthalpy(), InterfaceKinetics::getDeltaEnthalpy(), AqueousKinetics::getDeltaEntropy(), GasKinetics::getDeltaEntropy(), InterfaceKinetics::getDeltaEntropy(), AqueousKinetics::getDeltaGibbs(), GasKinetics::getDeltaGibbs(), InterfaceKinetics::getDeltaGibbs(), AqueousKinetics::getDeltaSSEnthalpy(), GasKinetics::getDeltaSSEnthalpy(), InterfaceKinetics::getDeltaSSEnthalpy(), AqueousKinetics::getDeltaSSEntropy(), GasKinetics::getDeltaSSEntropy(), InterfaceKinetics::getDeltaSSEntropy(), AqueousKinetics::getDeltaSSGibbs(), GasKinetics::getDeltaSSGibbs(), InterfaceKinetics::getDeltaSSGibbs(), Cantera::getEfficiencies(), AqueousKinetics::getEquilibriumConstants(), GasKinetics::getEquilibriumConstants(), InterfaceKinetics::getEquilibriumConstants(), Cantera::getRateCoefficient(), Cantera::getStick(), ImplicitSurfChem::ImplicitSurfChem(), AqueousKinetics::init(), GasKinetics::init(), InterfaceKinetics::init(), ConstPressureReactor::initialize(), Reactor::initialize(), Kinetics::kineticsSpeciesIndex(), Kinetics::kineticsSpeciesName(), Kinetics::nTotalSpecies(), solveProb::print_header(), InterfaceKinetics::setElectricPotential(), ImplicitSurfChem::solvePseudoSteadyStateProblem(), solveSP::solveSP(), Kinetics::speciesPhase(), AqueousKinetics::updateKc(), GasKinetics::updateKc(), InterfaceKinetics::updateKc(), and solveSP::updateMFKinSpecies().
|
inline |
This method returns a reference to the nth ThermoPhase defined in this kinetics mechanism.
It is typically used so that member functions of the ThermoPhase may be called.
n | Index of the ThermoPhase being sought. |
Definition at line 324 of file Kinetics.h.
References Cantera::deprecatedMethod(), and Kinetics::m_thermo.
|
inline |
This method returns a reference to the nth ThermoPhase defined in this kinetics mechanism.
It is typically used so that member functions of the ThermoPhase may be called.
n | Index of the ThermoPhase being sought. |
Definition at line 336 of file Kinetics.h.
References Cantera::deprecatedMethod(), and Kinetics::m_thermo.
|
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 347 of file Kinetics.h.
References Kinetics::nPhases(), Phase::nSpecies(), and Kinetics::thermo().
Referenced by ReactingSurf1D::init(), and rxninfo::installReaction().
|
inline |
Returns the starting index of the species in the nth phase associated with the reaction mechanism.
n | Return the index of first species in the nth phase associated with the reaction mechanism. |
Definition at line 363 of file Kinetics.h.
References Cantera::deprecatedMethod(), and Kinetics::m_start.
|
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.
k | species index |
n | phase index for the species |
Definition at line 391 of file Kinetics.h.
References Kinetics::m_start.
Referenced by solveSP::calc_t(), Cantera::checkRxnElementBalance(), ReactingSurf1D::eval(), solveSP::fun_eval(), Cantera::getEfficiencies(), Cantera::getReagents(), Cantera::getStick(), Kinetics::kineticsSpeciesIndex(), solveSP::solveSP(), and solveSP::updateMFKinSpecies().
string kineticsSpeciesName | ( | size_t | k | ) | const |
Return the std::string 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 std::string "<unknown>" is returned.
k | species index |
Return the string 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.
Definition at line 242 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
nm | Input string name of the species |
Definition at line 263 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
nm | Input string name of the species |
ph | Input string name of the phase. |
Definition at line 288 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 | ( | std::string | nm | ) |
This function looks up the std::string name of a species and returns a reference to the ThermoPhase object of the phase where the species resides.
This function looks up the string 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 std::string doesn't match.
nm | String containing the name of the species. |
Will throw an error if the species string doesn't match.
Definition at line 315 of file Kinetics.cpp.
References Kinetics::m_thermo, Cantera::npos, Phase::speciesIndex(), and Kinetics::thermo().
Referenced by Cantera::checkRxnElementBalance(), Cantera::getStick(), and rxninfo::installReaction().
|
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.
k | Species index |
Definition at line 454 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.
k | Species index |
Definition at line 337 of file Kinetics.cpp.
References Cantera::int2str(), Kinetics::m_start, and Cantera::npos.
Referenced by InterfaceKinetics::addReaction(), Cantera::checkRxnElementBalance(), Cantera::getStick(), and Kinetics::speciesPhase().
|
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.
fwdROP | Output vector containing forward rates of progress of the reactions. Length: m_ii. |
Reimplemented in InterfaceKinetics, GasKinetics, and AqueousKinetics.
Definition at line 486 of file Kinetics.h.
References Kinetics::err().
|
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.
revROP | Output vector containing reverse rates of progress of the reactions. Length: m_ii. |
Reimplemented in InterfaceKinetics, GasKinetics, and AqueousKinetics.
Definition at line 499 of file Kinetics.h.
References Kinetics::err().
|
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.
netROP | Output vector of the net ROP. Length: m_ii. |
Reimplemented in InterfaceKinetics, GasKinetics, and AqueousKinetics.
Definition at line 511 of file Kinetics.h.
References Kinetics::err().
|
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 | Output vector containing the equilibrium constants. Length: m_ii. |
Reimplemented in InterfaceKinetics, GasKinetics, and AqueousKinetics.
Definition at line 527 of file Kinetics.h.
References Kinetics::err().
|
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.
property | Input vector of property value. Length: m_kk. |
deltaProperty | Output vector of deltaRxn. Length: m_ii. |
Definition at line 547 of file Kinetics.h.
References Kinetics::err().
|
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
deltaG | Output vector of deltaG's for reactions Length: m_ii. |
Reimplemented in InterfaceKinetics, GasKinetics, and AqueousKinetics.
Definition at line 561 of file Kinetics.h.
References Kinetics::err().
|
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
deltaM | Output vector of deltaM's for reactions Length: m_ii. |
Reimplemented in InterfaceKinetics.
Definition at line 575 of file Kinetics.h.
References Kinetics::err().
|
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
deltaH | Output vector of deltaH's for reactions Length: m_ii. |
Reimplemented in InterfaceKinetics, GasKinetics, and AqueousKinetics.
Definition at line 589 of file Kinetics.h.
References Kinetics::err().
|
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
deltaS | Output vector of deltaS's for reactions Length: m_ii. |
Reimplemented in InterfaceKinetics, GasKinetics, and AqueousKinetics.
Definition at line 603 of file Kinetics.h.
References Kinetics::err().
|
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
deltaG | Output vector of ss deltaG's for reactions Length: m_ii. |
Reimplemented in InterfaceKinetics, GasKinetics, and AqueousKinetics.
Definition at line 617 of file Kinetics.h.
References Kinetics::err().
|
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
deltaH | Output vector of ss deltaH's for reactions Length: m_ii. |
Reimplemented in InterfaceKinetics, GasKinetics, and AqueousKinetics.
Definition at line 631 of file Kinetics.h.
References Kinetics::err().
|
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
deltaS | Output vector of ss deltaS's for reactions Length: m_ii. |
Reimplemented in InterfaceKinetics, GasKinetics, and AqueousKinetics.
Definition at line 645 of file Kinetics.h.
References Kinetics::err().
|
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.
cdot | Output vector of creation rates. Length: m_kk. |
Reimplemented in InterfaceKinetics, GasKinetics, and AqueousKinetics.
Definition at line 665 of file Kinetics.h.
References Kinetics::err().
|
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.
ddot | Output vector of destruction rates. Length: m_kk. |
Reimplemented in InterfaceKinetics, GasKinetics, and AqueousKinetics.
Definition at line 678 of file Kinetics.h.
References Kinetics::err().
|
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.
wdot | Output vector of net production rates. Length: m_kk. |
Reimplemented in InterfaceKinetics, GasKinetics, AqueousKinetics, and GRI_30_Kinetics.
Definition at line 691 of file Kinetics.h.
References Kinetics::err().
Referenced by StFlow::getWdot().
|
inlinevirtual |
Stoichiometric coefficient of species k as a reactant in reaction i.
k | kinetic species index |
i | reaction index |
Reimplemented in InterfaceKinetics, GasKinetics, and AqueousKinetics.
Definition at line 710 of file Kinetics.h.
References Kinetics::err().
|
inlinevirtual |
Stoichiometric coefficient of species k as a product in reaction i.
k | kinetic species index |
i | reaction index |
Reimplemented in InterfaceKinetics, GasKinetics, and AqueousKinetics.
Definition at line 722 of file Kinetics.h.
References Kinetics::err().
|
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
k | kinetic species index |
i | reaction index |
Definition at line 735 of file Kinetics.h.
References Kinetics::err().
|
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.
k | kinetic species index |
i | reaction index |
Definition at line 750 of file Kinetics.h.
References Kinetics::err().
|
inlinevirtual |
Get the vector of activity concentrations used in the kinetics object.
conc | (output) Vector of activity concentrations. Length is equal to the number of species in the kinetics object |
Reimplemented in InterfaceKinetics.
Definition at line 760 of file Kinetics.h.
References Kinetics::err().
|
inlinevirtual |
Returns a read-only reference to the vector of reactant index numbers for reaction i.
i | reaction index |
Definition at line 770 of file Kinetics.h.
References Kinetics::m_reactants.
Referenced by InterfaceKinetics::addReaction(), and rxninfo::installReaction().
|
inlinevirtual |
Returns a read-only reference to the vector of product index numbers for reaction i.
i | reaction index |
Definition at line 780 of file Kinetics.h.
References Kinetics::m_products.
Referenced by InterfaceKinetics::addReaction(), and rxninfo::installReaction().
|
inlinevirtual |
Flag specifying the type of reaction.
The legal values and their meaning are specific to the particular kinetics manager.
i | reaction index |
Reimplemented in InterfaceKinetics, GasKinetics, and AqueousKinetics.
Definition at line 791 of file Kinetics.h.
References Kinetics::err().
|
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.
i | reaction index |
Reimplemented in InterfaceKinetics, GasKinetics, and AqueousKinetics.
Definition at line 803 of file Kinetics.h.
References Kinetics::err().
|
inlinevirtual |
Return a std::string representing the reaction.
i | reaction index |
Reimplemented in InterfaceKinetics, GasKinetics, and AqueousKinetics.
Definition at line 813 of file Kinetics.h.
References Kinetics::err().
|
inlinevirtual |
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 in InterfaceKinetics, GasKinetics, and AqueousKinetics.
Definition at line 828 of file Kinetics.h.
References Kinetics::err().
|
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.
krev | Output vector of reverse rate constants. |
doIrreversible | boolean indicating whether irreversible reactions should be included. |
Reimplemented in InterfaceKinetics, GasKinetics, and AqueousKinetics.
Definition at line 845 of file Kinetics.h.
References Kinetics::err().
|
inlinevirtual |
Return the activation energies in Kelvin.
length is the number of reactions
E | Ouptut vector of activation energies. Length: m_ii. |
Reimplemented in InterfaceKinetics.
Definition at line 859 of file Kinetics.h.
References Kinetics::err().
|
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.
thermo | Reference to the ThermoPhase to be added. |
Reimplemented in InterfaceKinetics.
Definition at line 365 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().
|
inlinevirtual |
Prepare the class for the addition of reactions.
This method is called by function 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, GasKinetics, and AqueousKinetics.
Definition at line 900 of file Kinetics.h.
Referenced by Cantera::importKinetics().
|
virtual |
Finish adding reactions and prepare for use.
This method is called by function 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, GasKinetics, AqueousKinetics, and EdgeKinetics.
Definition at line 401 of file Kinetics.cpp.
References Kinetics::m_kk, Kinetics::m_thermo, and Kinetics::nPhases().
Referenced by InterfaceKinetics::finalize(), and Cantera::installReactionArrays().
|
inlinevirtual |
Add a single reaction to the mechanism.
This routine must be called after init() and before finalize().
r | Reference to the ReactionData object for the reaction to be added. |
Reimplemented in InterfaceKinetics, GasKinetics, and AqueousKinetics.
Definition at line 920 of file Kinetics.h.
References Kinetics::err().
Referenced by rxninfo::installReaction().
|
inline |
The current value of the multiplier for reaction i.
i | index of the reaction |
Definition at line 953 of file Kinetics.h.
References Kinetics::m_perturb.
|
inline |
Set the multiplier for reaction i to f.
i | index of the reaction |
f | value of the multiplier. |
Definition at line 962 of file Kinetics.h.
References Kinetics::m_perturb.
|
inline |
Increment the number of reactions in the mechanism by one.
Definition at line 972 of file Kinetics.h.
References Kinetics::m_ii, and Kinetics::m_perturb.
Referenced by AqueousKinetics::addReaction(), GasKinetics::addReaction(), and InterfaceKinetics::addReaction().
|
inlinevirtual |
Returns true if the kinetics manager has been properly initialized and finalized.
Reimplemented in InterfaceKinetics, GasKinetics, AqueousKinetics, Interface, and GRI30.
Definition at line 981 of file Kinetics.h.
void selectPhase | ( | const doublereal * | data, |
const thermo_t * | phase, | ||
doublereal * | phase_data | ||
) |
Extract from array data
the portion pertaining to phase phase
.
Takes as input an array of properties for all species in the mechanism and copies those values beloning to a particular phase to the output array.
data | data |
phase | phase |
phase_data | phase_data |
data | Input data array. |
phase | Pointer to one of the phase objects participating in this reaction mechanism |
phase_data | Output array where the values for the the specified phase are to be written. |
Definition at line 217 of file Kinetics.cpp.
References Kinetics::m_start, Kinetics::m_thermo, Kinetics::nPhases(), and Phase::nSpecies().
|
private |
Private function of the class Kinetics, indicating that a function inherited from the base class hasn't had a definition assigned to it.
m | String message |
Definition at line 415 of file Kinetics.cpp.
Referenced by Kinetics::addReaction(), Kinetics::getActivationEnergies(), Kinetics::getActivityConcentrations(), Kinetics::getCreationRates(), Kinetics::getDeltaElectrochemPotentials(), Kinetics::getDeltaEnthalpy(), Kinetics::getDeltaEntropy(), Kinetics::getDeltaGibbs(), Kinetics::getDeltaSSEnthalpy(), Kinetics::getDeltaSSEntropy(), Kinetics::getDeltaSSGibbs(), Kinetics::getDestructionRates(), Kinetics::getEquilibriumConstants(), Kinetics::getFwdRateConstants(), Kinetics::getFwdRatesOfProgress(), Kinetics::getNetProductionRates(), Kinetics::getNetRatesOfProgress(), Kinetics::getReactionDelta(), Kinetics::getRevRateConstants(), Kinetics::getRevRatesOfProgress(), Kinetics::isReversible(), Kinetics::productOrder(), Kinetics::productStoichCoeff(), Kinetics::reactantOrder(), Kinetics::reactantStoichCoeff(), Kinetics::reactionString(), and Kinetics::reactionType().
|
protected |
Number of reactions in the mechanism.
Definition at line 1000 of file Kinetics.h.
Referenced by Kinetics::checkReactionArraySize(), Kinetics::checkReactionIndex(), AqueousKinetics::finalize(), GasKinetics::finalize(), AqueousKinetics::getDeltaEnthalpy(), GasKinetics::getDeltaEnthalpy(), AqueousKinetics::getDeltaEntropy(), GasKinetics::getDeltaEntropy(), AqueousKinetics::getDeltaGibbs(), GasKinetics::getDeltaGibbs(), AqueousKinetics::getDeltaSSEnthalpy(), GasKinetics::getDeltaSSEnthalpy(), AqueousKinetics::getDeltaSSEntropy(), GasKinetics::getDeltaSSEntropy(), AqueousKinetics::getDeltaSSGibbs(), GasKinetics::getDeltaSSGibbs(), AqueousKinetics::getEquilibriumConstants(), GasKinetics::getEquilibriumConstants(), InterfaceKinetics::getEquilibriumConstants(), AqueousKinetics::getFwdRateConstants(), GasKinetics::getFwdRateConstants(), AqueousKinetics::getRevRateConstants(), GasKinetics::getRevRateConstants(), InterfaceKinetics::getRevRateConstants(), Kinetics::incrementRxnCount(), Kinetics::nReactions(), InterfaceKinetics::operator=(), Kinetics::operator=(), AqueousKinetics::updateKc(), GasKinetics::updateKc(), InterfaceKinetics::updateKc(), InterfaceKinetics::updateROP(), and InterfaceKinetics::~InterfaceKinetics().
|
protected |
The number of species in all of the phases that participate in this kinetics mechanism.
Definition at line 1004 of file Kinetics.h.
Referenced by Kinetics::checkSpeciesArraySize(), Kinetics::checkSpeciesIndex(), InterfaceKinetics::finalize(), Kinetics::finalize(), AqueousKinetics::getCreationRates(), GasKinetics::getCreationRates(), InterfaceKinetics::getCreationRates(), AqueousKinetics::getDeltaSSEnthalpy(), GasKinetics::getDeltaSSEnthalpy(), InterfaceKinetics::getDeltaSSEnthalpy(), AqueousKinetics::getDeltaSSEntropy(), GasKinetics::getDeltaSSEntropy(), InterfaceKinetics::getDeltaSSEntropy(), AqueousKinetics::getDestructionRates(), GasKinetics::getDestructionRates(), InterfaceKinetics::getDestructionRates(), AqueousKinetics::getNetProductionRates(), GasKinetics::getNetProductionRates(), InterfaceKinetics::getNetProductionRates(), AqueousKinetics::init(), GasKinetics::init(), InterfaceKinetics::init(), and Kinetics::operator=().
|
protected |
Vector of perturbation factors for each reaction's rate of progress vector.
It is initialized to one.
Definition at line 1009 of file Kinetics.h.
Referenced by EdgeKinetics::finalize(), AqueousKinetics::finalize(), GasKinetics::finalize(), InterfaceKinetics::finalize(), AqueousKinetics::getFwdRateConstants(), GasKinetics::getFwdRateConstants(), InterfaceKinetics::getFwdRateConstants(), Kinetics::incrementRxnCount(), Kinetics::multiplier(), Kinetics::operator=(), Kinetics::setMultiplier(), and InterfaceKinetics::updateROP().
|
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 1022 of file Kinetics.h.
Referenced by Kinetics::operator=(), and Kinetics::reactants().
|
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 1035 of file Kinetics.h.
Referenced by Kinetics::operator=(), and Kinetics::products().
|
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 1052 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=(), Kinetics::phase(), InterfaceKinetics::phaseExistence(), InterfaceKinetics::phaseStability(), Kinetics::selectPhase(), InterfaceKinetics::setPhaseExistence(), InterfaceKinetics::setPhaseStability(), Kinetics::speciesPhase(), and Kinetics::thermo().
|
protected |
m_start is a vector of integers specifying the beginning position for the species vector for the n'th phase in the kinetics class.
Definition at line 1059 of file Kinetics.h.
Referenced by InterfaceKinetics::_update_rates_C(), Kinetics::addPhase(), InterfaceKinetics::getDeltaElectrochemPotentials(), InterfaceKinetics::getDeltaEnthalpy(), InterfaceKinetics::getDeltaEntropy(), InterfaceKinetics::getDeltaGibbs(), InterfaceKinetics::getDeltaSSEnthalpy(), InterfaceKinetics::getDeltaSSEntropy(), InterfaceKinetics::getDeltaSSGibbs(), InterfaceKinetics::getEquilibriumConstants(), Kinetics::kineticsSpeciesIndex(), Kinetics::kineticsSpeciesName(), Kinetics::operator=(), Kinetics::selectPhase(), Kinetics::speciesPhaseIndex(), Kinetics::start(), and InterfaceKinetics::updateKc().
|
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 1069 of file Kinetics.h.
Referenced by Kinetics::addPhase(), Kinetics::operator=(), and Kinetics::phaseIndex().
|
protected |
Index in the list of phases of the one surface phase.
Definition at line 1075 of file Kinetics.h.
Referenced by Kinetics::addPhase(), Kinetics::operator=(), and Kinetics::surfacePhaseIndex().
|
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 1083 of file Kinetics.h.
Referenced by Kinetics::addPhase(), Kinetics::operator=(), and Kinetics::reactionPhaseIndex().
|
protected |
number of spatial dimensions of lowest-dimensional phase.
Definition at line 1086 of file Kinetics.h.
Referenced by Kinetics::addPhase(), and Kinetics::operator=().
|
private |
Vector of group lists.
Definition at line 1091 of file Kinetics.h.
Referenced by Kinetics::operator=().