cantera/include/cantera/kinetics/InterfaceKinetics.h
2015-05-26 16:58:18 -04:00

732 lines
28 KiB
C++

/**
* @file InterfaceKinetics.h
*
* @ingroup chemkinetics
*/
// Copyright 2001 California Institute of Technology
#ifndef CT_IFACEKINETICS_H
#define CT_IFACEKINETICS_H
#include "cantera/thermo/mix_defs.h"
#include "Kinetics.h"
#include "cantera/kinetics/RxnMolChange.h"
#include "Reaction.h"
#include "cantera/base/utilities.h"
#include "RateCoeffMgr.h"
namespace Cantera
{
// forward declarations
class SurfPhase;
class ImplicitSurfChem;
class RxnMolChange;
//! forward orders
//! @deprecated Incomplete implementation to be removed after Cantera 2.2.
class RxnOrders {
public:
//! constructors
RxnOrders() {}
RxnOrders(const RxnOrders &right);
~RxnOrders() {}
RxnOrders& operator=(const RxnOrders &right);
//! Fill in the structure with the array.
/*!
* @param[in] Size of length kinetic species. The entries the values of the orders
*/
int fill(const vector_fp& fullForwardOrders);
//! ID's of the kinetic species
std::vector<size_t> kinSpeciesIDs_;
//! Orders of the kinetic species
vector_fp kinSpeciesOrders_;
};
//! A kinetics manager for heterogeneous reaction mechanisms. The
//! reactions are assumed to occur at a 2D interface between two 3D phases.
/*!
* There are some important additions to the behavior of the kinetics class
* due to the presence of multiple phases and a heterogeneous interface. If
* a reactant phase doesn't exists, i.e., has a mole number of zero, a
* heterogeneous reaction can not proceed from reactants to products. Note it
* could perhaps proceed from products to reactants if all of the product
* phases exist.
*
* In order to make the determination of whether a phase exists or not
* actually involves the specification of additional information to the
* kinetics object., which heretofore has only had access to intrinsic field
* information about the phases (i.e., temperature pressure, and mole
* fraction).
*
* The extrinsic specification of whether a phase exists or not must be
* specified on top of the intrinsic calculation of the reaction rate. This
* class carries a set of booleans indicating whether a phase in the
* heterogeneous mechanism exists or not.
*
* Additionally, the class carries a set of booleans around indicating
* whether a product phase is stable or not. If a phase is not
* thermodynamically stable, it may be the case that a particular reaction in
* a heterogeneous mechanism will create a product species in the unstable
* phase. However, other reactions in the mechanism will destruct that
* species. This may cause oscillations in the formation of the unstable
* phase from time step to time step within a ODE solver, in practice. In
* order to avoid this situation, a set of booleans is tracked which sets the
* stability of a phase. If a phase is deemed to be unstable, then species in
* that phase will not be allowed to be birthed by the kinetics operator.
* Nonexistent phases are deemed to be unstable by default, but this can be
* changed.
*
* @ingroup chemkinetics
*/
class InterfaceKinetics : public Kinetics
{
public:
//! Constructor
/*!
* @param thermo The optional parameter may be used to initialize
* the object with one ThermoPhase object.
* HKM Note -> Since the interface kinetics
* object will probably require multiple ThermoPhase
* objects, this is probably not a good idea
* to have this parameter.
*/
InterfaceKinetics(thermo_t* thermo = 0);
/// Destructor.
virtual ~InterfaceKinetics();
//! Copy Constructor
InterfaceKinetics(const InterfaceKinetics& right);
//! Assignment operator
InterfaceKinetics& operator=(const InterfaceKinetics& right);
virtual Kinetics* duplMyselfAsKinetics(const std::vector<thermo_t*> & tpVector) const;
virtual int type() const;
//! Set the electric potential in the nth phase
/*!
* @param n phase Index in this kinetics object.
* @param V Electric potential (volts)
*/
void setElectricPotential(int n, doublereal V);
//! @name Reaction Rates Of Progress
//! @{
//! Equilibrium constant for all reactions including the voltage term
/*!
* Kc = exp(deltaG/RT)
*
* where deltaG is the electrochemical potential difference between
* products minus reactants.
*/
virtual void getEquilibriumConstants(doublereal* kc);
/** values needed to convert from exchange current density to surface reaction rate.
*/
void updateExchangeCurrentQuantities();
//! Return the vector of values for the reaction Gibbs free energy change.
/*!
* (virtual from Kinetics.h)
* These values depend upon the concentration of the solution.
*
* units = J kmol-1
*
* @param deltaG Output vector of deltaG's for reactions Length: m_ii.
* If 0, this updates the internally stored values only.
*/
virtual void getDeltaGibbs(doublereal* deltaG);
virtual void getDeltaElectrochemPotentials(doublereal* deltaM);
virtual void getDeltaEnthalpy(doublereal* deltaH);
virtual void getDeltaEntropy(doublereal* deltaS);
virtual void getDeltaSSGibbs(doublereal* deltaG);
virtual void getDeltaSSEnthalpy(doublereal* deltaH);
virtual void getDeltaSSEntropy(doublereal* deltaS);
//! @}
//! @name Reaction Mechanism Informational Query Routines
//! @{
virtual void getActivityConcentrations(doublereal* const conc);
//! Return the charge transfer rxn Beta parameter for the ith reaction
/*!
* Returns the beta parameter for a charge transfer reaction. This
* parameter is not important for non-charge transfer reactions.
* Note, the parameter defaults to zero. However, a value of 0.5
* should be supplied for every charge transfer reaction if
* no information is known, as a value of 0.5 pertains to a
* symmetric transition state. The value can vary between 0 to 1.
*
* @param irxn Reaction number in the kinetics mechanism
*
* @return Beta parameter. This defaults to zero, even for charge
* transfer reactions.
*/
doublereal electrochem_beta(size_t irxn) const;
virtual bool isReversible(size_t i) {
if (std::find(m_revindex.begin(), m_revindex.end(), i)
< m_revindex.end()) {
return true;
} else {
return false;
}
}
virtual void getFwdRateConstants(doublereal* kfwd);
virtual void getRevRateConstants(doublereal* krev,
bool doIrreversible = false);
//! @}
//! @name Reaction Mechanism Construction
//! @{
//! Add a phase to the kinetics manager object.
/*!
* This must be done before the function init() is called or
* before any reactions are input.
*
* This function calls Kinetics::addPhase(). It also sets the following
* fields:
*
* m_phaseExists[]
*
* @param thermo Reference to the ThermoPhase to be added.
*/
virtual void addPhase(thermo_t& thermo);
virtual void init();
virtual void addReaction(ReactionData& r);
virtual bool addReaction(shared_ptr<Reaction> r);
virtual void modifyReaction(size_t i, shared_ptr<Reaction> rNew);
virtual void finalize();
virtual bool ready() const;
//! @}
//! Internal routine that updates the Rates of Progress of the reactions
/*!
* This is actually the guts of the functionality of the object
*/
virtual void updateROP();
//! Update properties that depend on temperature
/*!
* Current objects that this function updates:
* m_kdata->m_logtemp
* m_kdata->m_rfn
* m_rates.
* updateKc();
*/
void _update_rates_T();
//! Update properties that depend on the electric potential
void _update_rates_phi();
//! Update properties that depend on the species mole fractions and/or
//! concentration,
/*!
* This method fills out the array of generalized concentrations by
* calling method getActivityConcentrations for each phase, which classes
* representing phases should overload to return the appropriate
* quantities.
*/
void _update_rates_C();
//! Advance the surface coverages in time
/*!
* This method carries out a time-accurate advancement of the
* surface coverages for a specified amount of time.
*
* \f[
* \dot {\theta}_k = \dot s_k (\sigma_k / s_0)
* \f]
*
* @param tstep Time value to advance the surface coverages
*/
void advanceCoverages(doublereal tstep);
//! Solve for the pseudo steady-state of the surface problem
/*!
* This is the same thing as the advanceCoverages() function,
* but at infinite times.
*
* Note, a direct solve is carried out under the hood here,
* to reduce the computational time.
*
* @param ifuncOverride One of the values defined in @ref solvesp_methods.
* The default is -1, which means that the program will decide.
* @param timeScaleOverride When a pseudo transient is
* selected this value can be used to override
* the default time scale for integration which
* is one.
* When SFLUX_TRANSIENT is used, this is equal to the
* time over which the equations are integrated.
* When SFLUX_INITIALIZE is used, this is equal to the
* time used in the initial transient algorithm,
* before the equation system is solved directly.
*/
void solvePseudoSteadyStateProblem(int ifuncOverride = -1,
doublereal timeScaleOverride = 1.0);
void setIOFlag(int ioFlag);
void checkPartialEquil();
//! Update the standard state chemical potentials and species equilibrium constant entries
/*!
* Virtual because it is overwritten when dealing with experimental open circuit voltage overrides
*/
virtual void updateMu0();
//! Number of reactions in the mechanism
/*!
* @deprecated This is a duplicate of Kinetics::nReactions()
*/
size_t reactionNumber() const {
warn_deprecated("InterfaceKinetics::reactionNumber",
"To be removed after Cantera 2.2. Duplicate of nReactions().");
return m_ii;
}
//! Update the equilibrium constants and stored electrochemical potentials
//! in molar units for all reversible reactions and for all species.
/*!
* Irreversible reactions have their equilibrium constant set
* to zero. For reactions involving charged species the equilibrium
* constant is adjusted according to the electrostatic potential.
*/
void updateKc();
//! Apply modifications for the forward reaction rate for interfacial charge transfer reactions
/*!
* For reactions that transfer charge across a potential difference,
* the activation energies are modified by the potential difference.
* (see, for example, ...). This method applies this correction.
*
* @param kfwd Vector of forward reaction rate constants on which to have
* the voltage correction applied
*/
void applyVoltageKfwdCorrection(doublereal* const kfwd);
//! When an electrode reaction rate is optionally specified in terms of its
//! exchange current density, adjust kfwd to the standard reaction rate constant form and units.
//! When the BV reaction types are used, keep the exchange current density form.
/*!
* For a reaction rate constant that was given in units of Amps/m2 (exchange current
* density formulation with iECDFormulation == true), convert the rate to
* kmoles/m2/s.
*
* For a reaction rate constant that was given in units of kmol/m2/sec when the
* reaction type is a Butler-Volmer form, convert it to exchange current density
* form (amps/m2).
*
* @param kfwd Vector of forward reaction rate constants, given in either
* normal form or in exchange current density form.
*/
void convertExchangeCurrentDensityFormulation(doublereal* const kfwd);
//! Set the existence of a phase in the reaction object
/*!
* Tell the kinetics object whether a phase in the object exists. This is
* actually an extrinsic specification that must be carried out on top of
* the intrinsic calculation of the reaction rate. The routine will also
* flip the IsStable boolean within the kinetics object as well.
*
* @param iphase Index of the phase. This is the order within the
* internal thermo vector object
* @param exists Boolean indicating whether the phase exists or not
*/
void setPhaseExistence(const size_t iphase, const int exists);
//! Set the stability of a phase in the reaction object
/*!
* Tell the kinetics object whether a phase in the object is stable.
* Species in an unstable phase will not be allowed to have a positive
* rate of formation from this kinetics object. This is actually an
* extrinsic specification that must be carried out on top of the
* intrinsic calculation of the reaction rate.
*
* While conceptually not needed since kinetics is consistent with thermo
* when taken as a whole, in practice it has found to be very useful to
* turn off the creation of phases which shouldn't be forming. Typically
* this can reduce the oscillations in phase formation and destruction
* which are observed.
*
* @param iphase Index of the phase. This is the order within the
* internal thermo vector object
* @param isStable Flag indicating whether the phase is stable or not
*/
void setPhaseStability(const size_t iphase, const int isStable);
//! Gets the phase existence int for the ith phase
/*!
* @param iphase Phase Id
* @return The int specifying whether the kinetics object thinks the phase
* exists or not. If it exists, then species in that phase can be
* a reactant in reactions.
*/
int phaseExistence(const size_t iphase) const;
//! Gets the phase stability int for the ith phase
/*!
* @param iphase Phase Id
* @return The int specifying whether the kinetics object thinks the phase
* is stable with nonzero mole numbers. If it stable, then the
* kinetics object will allow for rates of production of of
* species in that phase that are positive.
*/
int phaseStability(const size_t iphase) const;
virtual void determineFwdOrdersBV(ReactionData& rdata, vector_fp& fwdFullorders);
virtual void determineFwdOrdersBV(ElectrochemicalReaction& r, vector_fp& fwdFullorders);
protected:
//! Build a SurfaceArrhenius object from a Reaction, taking into account
//! the possible sticking coefficient form and coverage dependencies
//! @param i Reaction number. Set to npos if this reaction is replacing
//! an existing rate constant.
//! @param r Reaction object containing rate coefficient parameters
SurfaceArrhenius buildSurfaceArrhenius(size_t i, InterfaceReaction& r);
//! Temporary work vector of length m_kk
vector_fp m_grt;
//! List of reactions numbers which are reversible reactions
/*!
* This is a vector of reaction numbers. Each reaction in the list is
* reversible. Length = number of reversible reactions
*/
std::vector<size_t> m_revindex;
//! Templated class containing the vector of reactions for this interface
/*!
* The templated class is described in RateCoeffMgr.h
* The class SurfaceArrhenius is described in RxnRates.h
*/
Rate1<SurfaceArrhenius> m_rates;
bool m_redo_rates;
//! Vector of irreversible reaction numbers
/*!
* vector containing the reaction numbers of irreversible reactions.
*/
std::vector<size_t> m_irrev;
//! Number of irreversible reactions in the mechanism
size_t m_nirrev;
//! Number of reversible reactions in the mechanism
size_t m_nrev;
//! Array of concentrations for each species in the kinetics mechanism
/*!
* An array of generalized concentrations \f$ C_k \f$ that are defined
* such that \f$ a_k = C_k / C^0_k, \f$ where \f$ C^0_k \f$ is a standard
* concentration/ These generalized concentrations are used by this
* kinetics manager class to compute the forward and reverse rates of
* elementary reactions. The "units" for the concentrations of each phase
* depend upon the implementation of kinetics within that phase. The order
* of the species within the vector is based on the order of listed
* ThermoPhase objects in the class, and the order of the species within
* each ThermoPhase class.
*/
vector_fp m_conc;
//! Array of activity concentrations for each species in the kinetics object
/*!
* An array of activity concentrations \f$ Ca_k \f$ that are defined
* such that \f$ a_k = Ca_k / C^0_k, \f$ where \f$ C^0_k \f$ is a standard
* concentration. These activity concentrations are used by this
* kinetics manager class to compute the forward and reverse rates of
* elementary reactions. The "units" for the concentrations of each phase
* depend upon the implementation of kinetics within that phase. The order
* of the species within the vector is based on the order of listed
* ThermoPhase objects in the class, and the order of the species within
* each ThermoPhase class.
*/
vector_fp m_actConc;
//! Vector of standard state chemical potentials for all species
/*!
* This vector contains a temporary vector of standard state chemical
* potentials for all of the species in the kinetics object
*
* Length = m_kk. Units = J/kmol.
*/
vector_fp m_mu0;
//! Vector of chemical potentials for all species
/*!
* This vector contains a vector of chemical potentials for all of the species in the kinetics object
*
* Length = m_kk. Units = J/kmol.
*/
vector_fp m_mu;
//! Vector of standard state electrochemical potentials modified by
//! a standard concentration term.
/*!
* This vector contains a temporary vector of standard state electrochemical
* potentials + RTln(Cs) for all of the species in the kinetics object
*
* In order to get the units correct for the concentration equilibrium
* constant, each species needs to have an
* RT ln(Cs) added to its contribution to the equilibrium constant
* Cs is the standard concentration for the species. Frequently, for
* solid species, Cs is equal to 1. However, for gases Cs is P/RT.
*
* Length = m_kk. Units = J/kmol.
*/
vector_fp m_mu0_Kc;
//! Vector of phase electric potentials
/*!
* Temporary vector containing the potential of each phase in the kinetics
* object.
*
* length = number of phases. Units = Volts.
*/
vector_fp m_phi;
//! Vector of potential energies due to Voltages
/*!
* Length is the number of species in kinetics mech. It's
* used to store the potential energy due to the voltage.
*/
vector_fp m_pot;
//! Storage for the net electric energy change due to reaction.
/*!
* Length is number of reactions. It's used to store the
* net electric potential energy change due to the reaction.
*
* deltaElectricEnergy_[jrxn] = sum_i ( F V_i z_i nu_ij)
*/
vector_fp deltaElectricEnergy_;
//! Vector of raw activation energies for the reactions
/*!
* Units are in Kelvin.
* Length is number of reactions.
*/
vector_fp m_E;
//! Pointer to the single surface phase
SurfPhase* m_surf;
//! Pointer to the Implicit surface chemistry object
/*!
* Note this object is owned by this InterfaceKinetics object. It may only
* be used to solve this single InterfaceKinetics object's surface
* problem uncoupled from other surface phases.
*/
ImplicitSurfChem* m_integrator;
//! Electrochemical transfer coefficient for the forward direction
/*!
* Electrochemical transfer coefficient for all reactions that have transfer reactions
* the reaction is given by m_ctrxn[i]
*/
vector_fp m_beta;
//! Vector of reaction indexes specifying the id of the current transfer
//! reactions in the mechanism
/*!
* Vector of reaction indices which involve current transfers. This provides
* an index into the m_beta and m_ctrxn_BVform array.
*
* irxn = m_ctrxn[i]
*/
std::vector<size_t> m_ctrxn;
//! Vector of Reactions which follow the Butler-Volmer methodology for specifying the
//! exchange current density first. Then, the other forms are specified based on this form.
/*!
* Length is equal to the number of reactions with charge transfer coefficients, m_ctrxn[]
*
* m_ctrxn_BVform[i] = 0; This means that the irxn reaction is calculated via the standard forward
* and reverse reaction rates
* m_ctrxn_BVform[i] = 1; This means that the irxn reaction is calculated via the BV format
* directly.
* m_ctrxn_BVform[i] = 2; this means that the irxn reaction is calculated via the BV format
* directly, using concentrations instead of activity concentrations.
*/
std::vector<size_t> m_ctrxn_BVform;
//! Vector of booleans indicating whether the charge transfer reaction rate constant
//! is described by an exchange current density rate constant expression
/*!
* Length is equal to the number of reactions with charge transfer coefficients, m_ctrxn[]
*
* m_ctrxn_ecdf[irxn] = 0 This means that the rate coefficient calculator will calculate
* the rate constant as a chemical forward rate constant, a standard format.
* m_ctrxn_ecdf[irxn] = 1 this means that the rate coefficient calculator will calculate
* the rate constant as an exchange current density rate constant expression.
*/
vector_int m_ctrxn_ecdf;
//! Vector of booleans indicating whether the charge transfer reaction rate constant
//! is described by an exchange current density rate constant expression
/*!
* Length is equal to the number of reactions with charge transfer coefficients, m_ctrxn[]
*
* Some reactions have zero in this list, those that don't need special treatment.
* @deprecated To be removed after Cantera 2.2.
*/
std::vector<RxnOrders*> m_ctrxn_ROPOrdersList_;
//! Reaction Orders for the case where the forwards rate of progress is being calculated.
/*!
* Length is equal to the number of reactions with charge transfer coefficients, m_ctrxn[]
*
* Some reactions have zero in this list, indicating that the calculation isn't necessary.
* @deprecated To be removed after Cantera 2.2.
*/
std::vector<RxnOrders*> m_ctrxn_FwdOrdersList_;
vector_fp m_ctrxn_resistivity_;
//! Vector of standard concentrations
/*!
* Length number of kinetic species
* units depend on the definition of the standard concentration within each phase
*/
vector_fp m_StandardConc;
//! Vector of delta G^0, the standard state Gibbs free energies for each reaction
/*!
* Length is the number of reactions
* units are Joule kmol-1
*/
vector_fp m_deltaG0;
//! Vector of deltaG[] of reaction, the delta Gibbs free energies for each reaction
/*!
* Length is the number of reactions
* units are Joule kmol-1
*/
vector_fp m_deltaG;
//! Vector of the products of the standard concentrations of the reactants
/*!
* Units vary wrt what the units of the standard concentrations are
* Length = number of reactions.
*/
vector_fp m_ProdStanConcReac;
doublereal m_logp0;
doublereal m_logc0;
bool m_ROP_ok;
//! Current temperature of the data
doublereal m_temp;
//! Current log of the temperature
doublereal m_logtemp;
//! Boolean indicating whether mechanism has been finalized
bool m_finalized;
//! Boolean flag indicating whether any reaction in the mechanism
//! has a coverage dependent forward reaction rate
/*!
* If this is true, then the coverage dependence is multiplied into
* the forward reaction rates constant
*/
bool m_has_coverage_dependence;
//! Boolean flag indicating whether any reaction in the mechanism
//! has a beta electrochemical parameter.
/*!
* If this is true, the Butler-Volmer correction is applied
* to the forward reaction rate for those reactions.
*
* fac = exp ( - beta * (delta_phi))
*/
bool m_has_electrochem_rxns;
//! Boolean flag indicating whether any reaction in the mechanism
//! is described by an exchange current density expression
/*!
* If this is true, the standard state Gibbs free energy of the reaction
* and the product of the reactant standard concentrations must be
* precalculated in order to calculate the rate constant.
*/
bool m_has_exchange_current_density_formulation;
//! Int flag to indicate that some phases in the kinetics mechanism are
//! non-existent.
/*!
* We change the ROP vectors to make sure that non-existent phases are
* treated correctly in the kinetics operator. The value of this is equal
* to the number of phases which don't exist.
*/
int m_phaseExistsCheck;
//! Vector of booleans indicating whether phases exist or not
/*!
* Vector of booleans indicating whether a phase exists or not. We use
* this to set the ROP's so that unphysical things don't happen.
* For example, a reaction can't go in the forwards direction if a
* phase in which a reactant is present doesn't exist. Because InterfaceKinetics
* deals with intrinsic quantities only normally, nowhere else is this extrinsic
* concept introduced except here.
*
* length = number of phases in the object. By default all phases exist.
*/
std::vector<bool> m_phaseExists;
//! Vector of int indicating whether phases are stable or not
/*!
* Vector of booleans indicating whether a phase is stable or not under
* the current conditions. We use this to set the ROP's so that
* unphysical things don't happen.
*
* length = number of phases in the object. By default all phases are stable.
*/
std::vector<int> m_phaseIsStable;
//! Vector of vector of booleans indicating whether a phase participates in a
//! reaction as a reactant
/*!
* m_rxnPhaseIsReactant[j][p] indicates whether a species in phase p
* participates in reaction j as a reactant.
*/
std::vector<std::vector<bool> > m_rxnPhaseIsReactant;
//! Vector of vector of booleans indicating whether a phase participates in a
//! reaction as a product
/*!
* m_rxnPhaseIsReactant[j][p] indicates whether a species in phase p
* participates in reaction j as a product.
*/
std::vector<std::vector<bool> > m_rxnPhaseIsProduct;
//! Pairs of (reaction index, total order) for sticking reactions, which are
//! needed to compute the dependency of the rate constant on the site
//! density.
std::vector<std::pair<size_t, double> > m_sticking_orders;
void applyStickingCorrection(double* kf);
int m_ioFlag;
};
}
#endif