Kinetics.h

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/**
 * @file Kinetics.h
 *  Base class for kinetics managers and also contains the kineticsmgr
 *  module documentation (see \ref  kineticsmgr and class
 *  \link Cantera::Kinetics Kinetics\endlink).
 */

// This file is part of Cantera. See License.txt in the top-level directory or
// at http://www.cantera.org/license.txt for license and copyright information.

#ifndef CT_KINETICS_H
#define CT_KINETICS_H

#include "cantera/thermo/ThermoPhase.h"
#include "StoichManager.h"
#include "cantera/thermo/mix_defs.h"
#include "cantera/kinetics/Reaction.h"
#include "cantera/base/global.h"

namespace Cantera
{

/**
 * @defgroup chemkinetics Chemical Kinetics
 */

/// @defgroup kineticsmgr Kinetics Managers
/// @section kinmodman Models and Managers
///
/// A kinetics manager is a C++ class that implements a kinetics model; a
/// kinetics model is a set of mathematical equation describing how various
/// kinetic quantities are to be computed -- reaction rates, species production
/// rates, etc. Many different kinetics models might be defined to handle
/// different types of kinetic processes. For example, one kinetics model might
/// use expressions valid for elementary reactions in ideal gas mixtures. It
/// might, for example, require the reaction orders to be integral and equal to
/// the forward stoichiometric coefficients, require that each reaction be
/// reversible with a reverse rate satisfying detailed balance, include
/// pressure-dependent unimolecular reactions, etc. Another kinetics model might
/// be designed for heterogeneous chemistry at interfaces, and might allow
/// empirical reaction orders, coverage-dependent activation energies,
/// irreversible reactions, and include effects of potential differences across
/// the interface on reaction rates.
///
/// A kinetics manager implements a kinetics model. Since the model equations
/// may be complex and expensive to evaluate, a kinetics manager may adopt
/// various strategies to 'manage' the computation and evaluate the expressions
/// efficiently. For example, if there are rate coefficients or other quantities
/// that depend only on temperature, a manager class may choose to store these
/// quantities internally, and re-evaluate them only when the temperature has
/// actually changed. Or a manager designed for use with reaction mechanisms
/// with a few repeated activation energies might precompute the terms \f$
/// exp(-E/RT) \f$, instead of evaluating the exponential repeatedly for each
/// reaction. There are many other possible 'management styles', each of which
/// might be better suited to some reaction mechanisms than others.
///
/// But however a manager structures the internal computation, the tasks the
/// manager class must perform are, for the most part, the same. It must be able
/// to compute reaction rates, species production rates, equilibrium constants,
/// etc. Therefore, all kinetics manager classes should have a common set of
/// public methods, but differ in how they implement these methods.
///
/// A kinetics manager computes reaction rates of progress, species production
/// rates, equilibrium constants, and similar quantities for a reaction
/// mechanism. All kinetics manager classes derive from class Kinetics, which
/// defines a common public interface for all kinetics managers. Each derived
/// class overloads the virtual methods of Kinetics to implement a particular
/// kinetics model.
///
/// For example, class GasKinetics implements reaction rate expressions
/// appropriate for homogeneous reactions in ideal gas mixtures, and class
/// InterfaceKinetics implements expressions appropriate for heterogeneous
/// mechanisms at interfaces, including how to handle reactions involving
/// charged species of phases with different electric potentials --- something
/// that class GasKinetics doesn't deal with at all.
///
/// Many of the methods of class Kinetics write into arrays the values of some
/// quantity for each species, for example the net production rate. These
/// methods always write the results into flat arrays, ordered by phase in the
/// order the phase was added, and within a phase in the order the species were
/// added to the phase (which is the same ordering as in the input file).
/// Example: suppose a heterogeneous mechanism involves three phases -- a bulk
/// phase 'a', another bulk phase 'b', and the surface phase 'a:b' at the a/b
/// interface. Phase 'a' contains 12 species, phase 'b' contains 3, and at the
/// interface there are 5 adsorbed species defined in phase 'a:b'. Then methods
/// like getNetProductionRates(doublereal* net) will write and output array of
/// length 20, beginning at the location pointed to by 'net'. The first 12
/// values will be the net production rates for all 12 species of phase 'a'
/// (even if some do not participate in the reactions), the next 3 will be for
/// phase 'b', and finally the net production rates for the surface species will
/// occupy the last 5 locations.
/// @ingroup chemkinetics


//! 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.
 *
 *  @ingroup kineticsmgr
 */
class Kinetics
{
public:
    /**
     * @name Constructors and General Information about Mechanism
     */
    //@{

    /// Default constructor.
    Kinetics();

    virtual ~Kinetics();

    //! @deprecated Copy constructor to be removed after Cantera 2.3 for all
    //!     classes derived from Kinetics.
    Kinetics(const Kinetics&);
    //! @deprecated Assignment operator to be removed after Cantera 2.3 for all
    //!     classes derived from Kinetics.
    Kinetics& operator=(const Kinetics& right);

    //! Duplication routine for objects which inherit from Kinetics
    /*!
     *  This function can be used to duplicate objects derived from Kinetics
     *  even if the application only has a pointer to Kinetics to work with.
     *
     *  These routines are basically wrappers around the derived copy
     *  constructor.
     *
     * @param  tpVector Vector of pointers to ThermoPhase objects. this is the
     *                  #m_thermo vector within this object
     * @deprecated To be removed after Cantera 2.3 for all classes derived from
     *     Kinetics.
     */
    virtual Kinetics* duplMyselfAsKinetics(const std::vector<thermo_t*> & tpVector) const;

    //! Reassign the pointers within the Kinetics object
    /*!
     *  This type or routine is necessary because the Kinetics object doesn't
     *  own the ThermoPhase objects. After a duplication, we need to point to
     *  different ThermoPhase objects.
     *
     *  We check that the ThermoPhase objects are aligned in the same order and
     *  have the following identical properties to the ones that they are
     *  replacing:
     *
     *  - ThermoPhase::id()
     *  - ThermoPhase::type()
     *  - ThermoPhase::nSpecies()
     *
     *  @param tpVector Vector of pointers to ThermoPhase objects. this is the
     *         #m_thermo vector within this object
     * @deprecated To be removed after Cantera 2.3 for all classes derived from
     *     Kinetics.
     */
    virtual void assignShallowPointers(const std::vector<thermo_t*> & tpVector);

    //!  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.
     *   @deprecated Use kineticsType() instead. To be removed after Cantera
     *       2.3.
     */
    virtual int type() const;

    //! Identifies the Kinetics manager type.
    //! Each class derived from Kinetics should override this method to return
    //! a meaningful identifier.
    virtual std::string kineticsType() const {
        return "Kinetics";
    }

    //! Number of reactions in the reaction mechanism.
    size_t nReactions() const {
        return m_reactions.size();
    }

    //! Check that the specified reaction index is in range
    //! Throws an exception if i is greater than nReactions()
    void checkReactionIndex(size_t m) 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.
    void checkReactionArraySize(size_t ii) const;

    //! Check that the specified species index is in range
    //! Throws an exception if k is greater than nSpecies()-1
    void checkSpeciesIndex(size_t k) 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.
    void checkSpeciesArraySize(size_t mm) const;

    //@}
    //! @name Information/Lookup Functions about Phases and Species
    //@{

    /**
     * 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.
     */
    size_t nPhases() const {
        return m_thermo.size();
    }

    //! Check that the specified phase index is in range
    //! Throws an exception if m is greater than nPhases()
    void checkPhaseIndex(size_t m) 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.
    void checkPhaseArraySize(size_t mm) const;

    /**
     * Return the phase index of a phase in the list of phases defined within
     * the object.
     *
     *  @param ph std::string name of the phase
     *
     * If a -1 is returned, then the phase is not defined in the Kinetics
     * object.
     */
    size_t phaseIndex(const std::string& ph) {
        if (m_phaseindex.find(ph) == m_phaseindex.end()) {
            return npos;
        } else {
            return m_phaseindex[ph] - 1;
        }
    }

    /**
     * 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.
     */
    size_t surfacePhaseIndex() {
        return m_surfphase;
    }

    /**
     * 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.
     */
    size_t reactionPhaseIndex() {
        return m_rxnphase;
    }

    /**
     * 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.
     *
     * @param n Index of the ThermoPhase being sought.
     */
    thermo_t& thermo(size_t n=0) {
        return *m_thermo[n];
    }
    const thermo_t& thermo(size_t n=0) const {
        return *m_thermo[n];
    }

    /**
     * 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.
     */
    size_t nTotalSpecies() const {
        return m_kk;
    }

    /**
     * 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.
     *
     * @param k species index
     * @param n phase index for the species
     */
    size_t kineticsSpeciesIndex(size_t k, size_t n) const {
        return m_start[n] + k;
    }

    //! Return the name of the kth species in the kinetics manager.
    /*!
     *  k is an integer from 0 to ktot - 1, where ktot is the number of
     * species in the kinetics manager, which is the sum of the number of
     * species in all phases participating in the kinetics manager. If k is
     * out of bounds, the string "<unknown>" is returned.
     *
     * @param k species index
     */
    std::string kineticsSpeciesName(size_t k) const;

    /**
     * This routine will look up a species number based on the input
     * std::string nm. The lookup of species will occur for all phases
     * listed in the kinetics object.
     *
     *  return
     *   - If a match is found, the position in the species list is returned.
     *   - If no match is found, the value -1 is returned.
     *
     * @param nm   Input string name of the species
     */
    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 in the specified
     * phase of the object, or all phases if ph is "<any>".
     *
     *  return
     *   - If a match is found, the position in the species list is returned.
     *   - If no match is found, the value npos (-1) is returned.
     *
     * @param nm   Input string name of the species
     * @param ph   Input string name of the phase.
     */
    size_t kineticsSpeciesIndex(const std::string& nm,
                                const std::string& ph) const;

    /**
     * This function looks up the name of a species and returns a
     * reference to the ThermoPhase object of the phase where the species
     * resides. Will throw an error if the species doesn't match.
     *
     * @param nm   String containing the name of the species.
     */
    thermo_t& speciesPhase(const std::string& nm);

    /**
     * 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.
     *
     * @param k          Species index
     */
    thermo_t& speciesPhase(size_t k) {
        return thermo(speciesPhaseIndex(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.
     *
     * @param k          Species index
     */
    size_t speciesPhaseIndex(size_t k);

    //! @}
    //! @name Reaction Rates Of Progress
    //! @{

    //!  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.
     *
     * @param fwdROP  Output vector containing forward rates
     *                of progress of the reactions. Length: nReactions().
     */
    virtual void getFwdRatesOfProgress(doublereal* fwdROP);

    //!  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.
     *
     * @param revROP  Output vector containing reverse rates
     *                of progress of the reactions. Length: nReactions().
     */
    virtual void getRevRatesOfProgress(doublereal* revROP);

    /**
     * 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.
     *
     * @param netROP  Output vector of the net ROP. Length: nReactions().
     */
    virtual void getNetRatesOfProgress(doublereal* netROP);

    //! 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.
     *
     * \f[
     *       Kc_i = exp [ \Delta G_{ss,i} ] prod(Cs_k) exp(\sum_k \nu_{k,i} F \phi_n) ]
     * \f]
     *
     * @param kc   Output vector containing the equilibrium constants.
     *             Length: nReactions().
     */
    virtual void getEquilibriumConstants(doublereal* kc) {
        throw NotImplementedError("Kinetics::getEquilibriumConstants");
    }

    /**
     * Change in species properties. Given an array of molar species property
     * values \f$ z_k, k = 1, \dots, K \f$, return the array of reaction values
     * \f[
     *    \Delta Z_i = \sum_k \nu_{k,i} z_k, i = 1, \dots, I.
     * \f]
     * 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 \c deltaProperty would be the standard-state Gibbs free energies of
     * reaction for each reaction.
     *
     * @param property Input vector of property value. Length: m_kk.
     * @param deltaProperty Output vector of deltaRxn. Length: nReactions().
     */
    virtual void getReactionDelta(const doublereal* property,
                                  doublereal* deltaProperty);

    /**
     * Given an array of species properties 'g', return in array 'dg' the
     * change in this quantity in the reversible reactions. Array 'g' must
     * have a length at least as great as the number of species, and array
     * 'dg' must have a length as great as the total number of reactions.
     * This method only computes 'dg' for the reversible reactions, and the
     * entries of 'dg' for the irreversible reactions are unaltered. This is
     * primarily designed for use in calculating reverse rate coefficients
     * from thermochemistry for reversible reactions.
     */
    virtual void getRevReactionDelta(const doublereal* g, doublereal* dg);

    //! 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:
     *     nReactions().
     */
    virtual void getDeltaGibbs(doublereal* deltaG) {
        throw NotImplementedError("Kinetics::getDeltaGibbs");
    }

    //! 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
     *
     * @param deltaM  Output vector of deltaM's for reactions Length:
     *     nReactions().
     */
    virtual void getDeltaElectrochemPotentials(doublereal* deltaM) {
        throw NotImplementedError("Kinetics::getDeltaElectrochemPotentials");
    }

    /**
     * Return the vector of values for the reactions change in enthalpy.
     * These values depend upon the concentration of the solution.
     *
     *  units = J kmol-1
     *
     * @param deltaH  Output vector of deltaH's for reactions Length:
     *     nReactions().
     */
    virtual void getDeltaEnthalpy(doublereal* deltaH) {
        throw NotImplementedError("Kinetics::getDeltaEnthalpy");
    }

    /**
     * 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
     *
     * @param deltaS  Output vector of deltaS's for reactions Length:
     *     nReactions().
     */
    virtual void getDeltaEntropy(doublereal* deltaS) {
        throw NotImplementedError("Kinetics::getDeltaEntropy");
    }

    /**
     * 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
     *
     * @param deltaG  Output vector of ss deltaG's for reactions Length:
     *     nReactions().
     */
    virtual void getDeltaSSGibbs(doublereal* deltaG) {
        throw NotImplementedError("Kinetics::getDeltaSSGibbs");
    }

    /**
     * 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
     *
     * @param deltaH  Output vector of ss deltaH's for reactions Length:
     *     nReactions().
     */
    virtual void getDeltaSSEnthalpy(doublereal* deltaH) {
        throw NotImplementedError("Kinetics::getDeltaSSEnthalpy");
    }

    /**
     * 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
     *
     * @param deltaS  Output vector of ss deltaS's for reactions Length:
     *     nReactions().
     */
    virtual void getDeltaSSEntropy(doublereal* deltaS) {
        throw NotImplementedError("Kinetics::getDeltaSSEntropy");
    }

    //! @}
    //! @name Species Production Rates
    //! @{

    /**
     * Species creation rates [kmol/m^3/s or kmol/m^2/s]. Return the species
     * creation rates in array cdot, which must be dimensioned at least as
     * large as the total number of species in all phases. @see nTotalSpecies.
     *
     * @param cdot   Output vector of creation rates. Length: m_kk.
     */
    virtual void getCreationRates(doublereal* cdot);

    /**
     * Species destruction rates [kmol/m^3/s or kmol/m^2/s]. Return the species
     * destruction rates in array ddot, which must be dimensioned at least as
     * large as the total number of species. @see nTotalSpecies.
     *
     * @param ddot   Output vector of destruction rates. Length: m_kk.
     */
    virtual void getDestructionRates(doublereal* ddot);

    /**
     * Species net production rates [kmol/m^3/s or kmol/m^2/s]. Return the
     * species net production rates (creation - destruction) in array wdot,
     * which must be dimensioned at least as large as the total number of
     * species. @see nTotalSpecies.
     *
     * @param wdot   Output vector of net production rates. Length: m_kk.
     */
    virtual void getNetProductionRates(doublereal* wdot);

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

    /**
     * Stoichiometric coefficient of species k as a reactant in reaction i.
     *
     * @param k   kinetic species index
     * @param i   reaction index
     */
    virtual double reactantStoichCoeff(size_t k, size_t i) const;
    /**
     * Stoichiometric coefficient of species k as a product in reaction i.
     *
     * @param k   kinetic species index
     * @param i   reaction index
     */
    virtual double productStoichCoeff(size_t k, size_t i) const;

    //! 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
     *
     * @param k   kinetic species index
     * @param i   reaction index
     */
    virtual doublereal reactantOrder(size_t k, size_t i) const {
        throw NotImplementedError("Kinetics::reactantOrder");
    }

    //! 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.
     *
     * @param k   kinetic species index
     * @param i   reaction index
     */
    virtual doublereal productOrder(int k, int i) const {
        throw NotImplementedError("Kinetics::productOrder");
    }

    //! Get the vector of activity concentrations used in the kinetics object
    /*!
     *  @param[out] conc  Vector of activity concentrations. Length is equal
     *               to the number of species in the kinetics object
     */
    virtual void getActivityConcentrations(doublereal* const conc) {
        throw NotImplementedError("Kinetics::getActivityConcentrations");
    }

    /**
     * Flag specifying the type of reaction. The legal values and their meaning
     * are specific to the particular kinetics manager.
     *
     * @param i   reaction index
     */
    virtual int reactionType(size_t i) const {
        return m_reactions[i]->reaction_type;
    }

    /**
     * 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.
     *
     * @param i   reaction index
     */
    virtual bool isReversible(size_t i) {
        throw NotImplementedError("Kinetics::isReversible");
    }

    /**
     * Return a string representing the reaction.
     *
     * @param i   reaction index
     */
    std::string reactionString(size_t i) const {
        return m_reactions[i]->equation();
    }

    //! Returns a string containing the reactants side of the reaction equation.
    std::string reactantString(size_t i) const {
        return m_reactions[i]->reactantString();
    }

    //! Returns a string containing the products side of the reaction equation.
    std::string productString(size_t i) const {
        return m_reactions[i]->productString();
    }

    /**
     * Return the forward rate constants
     *
     * length is the number of reactions. units depends on many issues.
     *
     * @param kfwd    Output vector containing the forward reaction rate
     *                constants. Length: nReactions().
     */
    virtual void getFwdRateConstants(doublereal* kfwd) {
        throw NotImplementedError("Kinetics::getFwdRateConstants");
    }

    /**
     * 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.
     *
     * @param krev   Output vector of reverse rate constants.
     * @param doIrreversible boolean indicating whether irreversible reactions
     *                       should be included.
     */
    virtual void getRevRateConstants(doublereal* krev,
                                     bool doIrreversible = false) {
        throw NotImplementedError("Kinetics::getFwdRateConstants");
    }

    //! @}
    //! @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. 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.
     *
     * @param thermo    Reference to the ThermoPhase to be added.
     */
    virtual void addPhase(thermo_t& thermo);

    /**
     * Prepare the class for the addition of reactions, after all phases have
     * been added. This method is called automatically when the first reaction
     * is added. It needs to be called directly only in the degenerate case
     * where there are no reactions. The base class method does nothing, but
     * derived classes may use this to perform any initialization (allocating
     * arrays, etc.) that requires knowing the phases.
     */
    virtual void init() {}

    /**
     * Resize arrays with sizes that depend on the total number of species.
     * Automatically called before adding each Reaction and Phase.
     */
    virtual void resizeSpecies();

    /**
     * Finish adding reactions and prepare for use. This method is called by
     * importKinetics() after all reactions have been entered into the
     * mechanism and before the mechanism is used to calculate reaction rates.
     * The base class method does nothing, but derived classes may use this to
     * perform any initialization (allocating arrays, etc.) that must be done
     * after the reactions are entered.
     * @deprecated No longer needed. To be removed after Cantera 2.3.
     */
    virtual void finalize();

    /**
     * Add a single reaction to the mechanism. Derived classes should call the
     * base class method in addition to handling their own specialized behavior.
     *
     * @param r      Pointer to the Reaction object to be added.
     * @return `true` if the reaction is added or `false` if it was skipped
     */
    virtual bool addReaction(shared_ptr<Reaction> r);

    /**
     * Modify the rate expression associated with a reaction. The
     * stoichiometric equation, type of the reaction, reaction orders, third
     * body efficiencies, reversibility, etc. must be unchanged.
     *
     * @param i    Index of the reaction to be modified
     * @param rNew Reaction with the new rate expressions
     */
    virtual void modifyReaction(size_t i, shared_ptr<Reaction> rNew);

    /**
     * Return the Reaction object for reaction *i*.
     */
    shared_ptr<Reaction> reaction(size_t i);
    
    shared_ptr<const Reaction> reaction(size_t i) const;

    //! Determine behavior when adding a new reaction that contains species not
    //! defined in any of the phases associated with this kinetics manager. If
    //! set to true, the reaction will silently be ignored. If false, (the
    //! default) an exception will be raised.
    void skipUndeclaredSpecies(bool skip) {
        m_skipUndeclaredSpecies = skip;
    }

    //! Determine behavior when adding a new reaction that contains third-body
    //! efficiencies for species not defined in any of the phases associated
    //! with this kinetics manager. If set to true, the given third-body
    //! efficiency will be ignored. If false, (the default) an exception will be
    //! raised.
    void skipUndeclaredThirdBodies(bool skip) {
        m_skipUndeclaredThirdBodies = skip;
    }

    //@}
    //! @name 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.
     */
    //@{

    //! The current value of the multiplier for reaction i.
    /*!
     * @param i index of the reaction
     */
    doublereal multiplier(size_t i) const {
        return m_perturb[i];
    }

    //! Set the multiplier for reaction i to f.
    /*!
     *  @param i  index of the reaction
     *  @param f  value of the multiplier.
     */
    virtual void setMultiplier(size_t i, doublereal f) {
        m_perturb[i] = f;
    }

    virtual void invalidateCache() {};

    //@}

    /**
     * Returns true if the kinetics manager has been properly initialized and
     * finalized.
     * @deprecated Object is always ready. To be removed after Cantera 2.3.
     */
    virtual bool ready() const {
        warn_deprecated("Kinetics::ready",
            "Object is always ready. To be removed after Cantera 2.3.");
        return true;
    }

    //! Check for duplicate reactions.
    /**
     * If `throw_err` is true, then an exception will be thrown if any unmarked
     * duplicate reactions are found. Otherwise, the indices of the first pair
     * of duplicate reactions found will be returned. If no duplicate reactions
     * are found, returns `(npos, npos)`.
     */
    virtual std::pair<size_t, size_t> checkDuplicates(bool throw_err=true) const;

    /*!
     * Takes as input an array of properties for all species in the mechanism
     * and copies those values belonging to a particular phase to the output
     * array.
     * @param data Input data array.
     * @param phase Pointer to one of the phase objects participating in this
     *     reaction mechanism
     * @param phase_data Output array where the values for the the specified
     *     phase are to be written.
     */
    void selectPhase(const doublereal* data, const thermo_t* phase,
                     doublereal* phase_data);

protected:
    //! Cache for saved calculations within each Kinetics object.
    ValueCache m_cache;

    // Update internal rate-of-progress variables #m_ropf and #m_ropr.
    virtual void updateROP() {
        throw NotImplementedError("Kinetics::updateROP");
    }

    //! Check whether `r1` and `r2` represent duplicate stoichiometries
    //! This function returns a ratio if two reactions are duplicates of
    //! one another, and 0.0 otherwise.
    /*!
     *  `r1` and `r2` are maps of species key to stoichiometric coefficient, one
     *  for each reaction, where the species key is `1+k` for reactants and
     *  `-1-k` for products and `k` is the species index.
     *
     *  @return 0.0 if the stoichiometries are not multiples of one another
     *    Otherwise, it returns the ratio of the stoichiometric coefficients.
     *
     * @ingroup kineticsmgr
     */
    double checkDuplicateStoich(std::map<int, double>& r1,
                                std::map<int, double>& r2) const;

    //! Check that the specified reaction is balanced (same number of atoms for
    //! each element in the reactants and products). Raises an exception if the
    //! reaction is not balanced.
    void checkReactionBalance(const Reaction& R);

    //! @name Stoichiometry management
    /*!
     *  These objects and functions handle turning reaction extents into species
     *  production rates and also handle turning thermo properties into reaction
     *  thermo properties.
     */
    //@{

    //! Stoichiometry manager for the reactants for each reaction
    StoichManagerN m_reactantStoich;

    //! Stoichiometry manager for the products of reversible reactions
    StoichManagerN m_revProductStoich;

    //! Stoichiometry manager for the products of irreversible reactions
    StoichManagerN m_irrevProductStoich;
    //@}

    //! The number of species in all of the phases
    //! that participate in this kinetics mechanism.
    size_t m_kk;

    /// Vector of perturbation factors for each reaction's rate of
    /// progress vector. It is initialized to one.
    vector_fp m_perturb;

    //! Vector of Reaction objects represented by this Kinetics manager
    std::vector<shared_ptr<Reaction> > m_reactions;

    //! 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.
     */
    std::vector<thermo_t*> m_thermo;

    /**
     * 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::vector<size_t> m_start;

    /**
     * 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.
     */
    std::map<std::string, size_t> m_phaseindex;

    //! Index in the list of phases of the one surface phase.
    size_t m_surfphase;

    //! 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.
     */
    size_t m_rxnphase;

    //! number of spatial dimensions of lowest-dimensional phase.
    size_t m_mindim;

    //! Forward rate constant for each reaction
    vector_fp m_rfn;

    //! Reciprocal of the equilibrium constant in concentration units
    vector_fp m_rkcn;

    //! Forward rate-of-progress for each reaction
    vector_fp m_ropf;

    //! Reverse rate-of-progress for each reaction
    vector_fp m_ropr;

    //! Net rate-of-progress for each reaction
    vector_fp m_ropnet;

    //! @see skipUndeclaredSpecies()
    bool m_skipUndeclaredSpecies;

    //! @see skipUndeclaredThirdBodies()
    bool m_skipUndeclaredThirdBodies;
};

}

#endif