InterfaceKinetics.h

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/**
 * @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/base/utilities.h"
#include "RateCoeffMgr.h"
#include "ReactionStoichMgr.h"

namespace Cantera
{

// forward references
class ReactionData;
class ThermoPhase;
class SurfPhase;
class ImplicitSurfChem;

//!  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 for the %Kinetics object.
    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
    //! @{

    virtual void getFwdRatesOfProgress(doublereal* fwdROP);
    virtual void getRevRatesOfProgress(doublereal* revROP);
    virtual void getNetRatesOfProgress(doublereal* netROP);

    virtual void getEquilibriumConstants(doublereal* kc);

    void getExchangeCurrentQuantities();

    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 Species Production Rates
    //! @{

    virtual void getCreationRates(doublereal* cdot);
    virtual void getDestructionRates(doublereal* ddot);
    virtual void getNetProductionRates(doublereal* net);

    //! @}
    //! @name Reaction Mechanism Informational Query Routines
    //! @{

    virtual doublereal reactantStoichCoeff(size_t k, size_t i) const {
        return m_rrxn[k][i];
    }

    virtual doublereal productStoichCoeff(size_t k, size_t i) const {
        return m_prxn[k][i];
    }

    virtual int reactionType(size_t i) const {
        return m_index[i].first;
    }

    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 std::string reactionString(size_t i) const {
        return m_rxneqn[i];
    }

    virtual void getFwdRateConstants(doublereal* kfwd);
    virtual void getRevRateConstants(doublereal* krev,
                                     bool doIrreversible = false);
    virtual void getActivationEnergies(doublereal* E);

    //! @}
    //! @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 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
     */
    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();

    size_t reactionNumber() const {
        return m_ii;
    }

    void addElementaryReaction(ReactionData& r);
    void addGlobalReaction(const ReactionData& r);
    void installReagents(const ReactionData& r);

    /**
     * Update the equilibrium constants in molar units for all reversible
     * reactions. 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();

    //! Write values into m_index
    /*!
     * @param rxnNumber reaction number
     * @param type      reaction type
     * @param loc       location ??
     */
    void registerReaction(size_t rxnNumber, int type, size_t loc) {
        m_index[rxnNumber] = std::pair<int, size_t>(type, loc);
    }

    //! Apply corrections 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 kf  Vector of forward reaction rate constants on which to have
     *            the correction applied
     */
    void applyButlerVolmerCorrection(doublereal* const kf);

    //! When an electrode reaction rate is optionally specified in terms of its
    //! exchange current density, extra vectors need to be precalculated
    void applyExchangeCurrentDensityFormulation(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;

protected:
    //! 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 information about reactions in the mechanism.
     * The key is the reaction index (0 < i < m_ii).
     * The first pair is the reactionType of the reaction.
     * The second pair is ...
     */
    mutable std::map<size_t, std::pair<int, size_t> > m_index;

    //! Vector of irreversible reaction numbers
    /*!
     * vector containing the reaction numbers of irreversible reactions.
     */
    std::vector<size_t> m_irrev;

    //! Stoichiometric manager for the reaction mechanism
    /*!
     *  This is the manager for the kinetics mechanism that handles turning
     *  reaction extents into species production rates and also handles
     *  turning thermo properties into reaction thermo properties.
     */
    ReactionStoichMgr m_rxnstoich;

    //! Number of irreversible reactions in the mechanism
    size_t m_nirrev;

    //! Number of reversible reactions in the mechanism
    size_t m_nrev;

    //!  m_rrxn is a vector of maps, containing the reactant
    //!  stoichiometric coefficient information
    /*!
     *  m_rrxn has a length equal to the total number of species in the
     *  kinetics object. For each species, there exists a map, with the
     *  reaction number being the key, and the reactant stoichiometric
     *  coefficient for the species being the value.
     *
     *  HKM -> mutable because search sometimes creates extra
     *         entries. To be fixed in future...
     */
    mutable std::vector<std::map<size_t, doublereal> >     m_rrxn;

    //!  m_prxn is a vector of maps, containing the reactant
    //!  stoichiometric coefficient information
    /**
     *  m_prxn is a vector of maps. m_prxn has a length equal to the total
     *  number of species in the kinetics object. For each species, there
     *  exists a map, with the reaction number being the key, and the product
     *  stoichiometric coefficient for the species being the value.
     */
    mutable std::vector<std::map<size_t, doublereal> >     m_prxn;

    //! String expression for each rxn
    /*!
     * Vector of strings of length m_ii, the number of
     * reactions, containing the string expressions for each reaction
     * (e.g., reactants <=> product1 + product2)
     */
    std::vector<std::string> m_rxneqn;

    //! an array of generalized concentrations for each species
    /*!
     * 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;

    //! Vector of standard state chemical potentials
    /*!
     * This vector contains a temporary vector of standard state chemical
     * potentials for all of the species in the kinetics object
     *
     * Length = m_k. Units = J/kmol.
     */
    vector_fp m_mu0;

    //! 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;

    //! Vector temporary
    /*!
     * Length is number of reactions. It's used to store the
     * voltage contribution to the activation energy.
     */
    vector_fp m_rwork;

    //! 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 objects's surface
     * problem uncoupled from other surface phases.
     */
    ImplicitSurfChem* m_integrator;

    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 array.
     *
     *        irxn = m_ctrxn[i]
     */
    std::vector<size_t> m_ctrxn;

    //! Vector of booleans indicating whether the charge transfer reaction may
    //! be described by an exchange current density expression
    vector_int m_ctrxn_ecdf;

    vector_fp m_StandardConc;
    vector_fp m_deltaG0;
    vector_fp m_ProdStanConcReac;

    doublereal m_logp0;
    doublereal m_logc0;
    vector_fp m_ropf;
    vector_fp m_ropr;
    vector_fp m_ropnet;

    bool m_ROP_ok;

    //! Current temperature of the data
    doublereal m_temp;
    //! Current log of the temperature
    doublereal m_logtemp;
    vector_fp m_rfn;
    vector_fp m_rkcn;

    //! 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
     *
     *  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;

    int m_ioFlag;
};
}

#endif