LatticePhase.h

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/**
 *  @file LatticePhase.h
 *  Header for a simple thermodynamics model of a bulk phase derived from ThermoPhase,
 *  assuming a lattice of solid atoms
 *  (see \ref thermoprops and class \link Cantera::LatticePhase LatticePhase\endlink).
 */

//  Copyright 2005 California Institute of Technology

#ifndef CT_LATTICE_H
#define CT_LATTICE_H

#include "cantera/base/config.h"

#include "cantera/base/ct_defs.h"
#include "mix_defs.h"
#include "ThermoPhase.h"
#include "SpeciesThermo.h"
#include "cantera/base/utilities.h"

namespace Cantera
{

//!  A simple thermodynamic model for a bulk phase,
//!  assuming a lattice of solid atoms
/*!
 *  The bulk consists of a matrix of equivalent sites whose molar density
 *  does not vary with temperature or pressure. The thermodynamics
 *  obeys the ideal solution laws. The phase and the pure species phases which
 * comprise the standard states of the species are assumed to have
 * zero volume expansivity and zero isothermal compressibility.
 *
 * The density of matrix sites is given by the variable \f$ C_o \f$,
 * which has SI units of kmol m-3.
 *
 *
 * <b> Specification of Species Standard %State Properties </b>
 *
 *  It is assumed that the reference state thermodynamics may be
 *  obtained by a pointer to a populated species thermodynamic property
 *  manager class (see ThermoPhase::m_spthermo). However, how to relate pressure
 *  changes to the reference state thermodynamics is within this class.
 *
 *  Pressure is defined as an independent variable in this phase. However, it has
 *  no effect on any quantities, as the molar concentration is a constant.
 *
 * The standard state enthalpy function is given by the following relation,
 * which has a weak dependence on the system pressure, \f$P\f$.
 *
 *       \f[
 *   \raggedright   h^o_k(T,P) =
 *                  h^{ref}_k(T) +  \left( \frac{P - P_{ref}}{C_o} \right)
 *       \f]
 *
 * For an incompressible substance, the molar internal energy is
 * independent of pressure. Since the thermodynamic properties
 * are specified by giving the standard-state enthalpy, the
 * term \f$ \frac{P_{ref}}{C_o} \f$ is subtracted from the specified reference molar
 * enthalpy to compute the standard state molar internal energy:
 *
 *       \f[
 *            u^o_k(T,P) = h^{ref}_k(T) - \frac{P_{ref}}{C_o}
 *       \f]
 *
 * The standard state heat capacity, internal energy, and entropy are independent
 * of pressure. The standard state gibbs free energy is obtained
 * from the enthalpy and entropy functions.
 *
 * The standard state molar volume is independent of temperature, pressure,
 * and species identity:
 *
 *       \f[
 *            V^o_k(T,P) = \frac{1.0}{C_o}
 *       \f]
 *
 *
 * <HR>
 * <H2> Specification of Solution Thermodynamic Properties </H2>
 * <HR>
 *
 * The activity of species \f$ k \f$ defined in the phase, \f$ a_k \f$, is
 * given by the ideal solution law:
 *
 *       \f[
 *            a_k = X_k ,
 *       \f]
 *
 * where \f$ X_k \f$ is the mole fraction of species <I>k</I>.
 * The chemical potential for species <I>k</I> is equal to
 *
 *       \f[
 *            \mu_k(T,P) = \mu^o_k(T, P) + R T \log(X_k)
 *       \f]
 *
 * The partial molar entropy for species <I>k</I> is given by the following relation,
 *
 *       \f[
 *            \tilde{s}_k(T,P) = s^o_k(T,P) - R \log(X_k) = s^{ref}_k(T) - R \log(X_k)
 *       \f]
 *
 * The partial molar enthalpy for species <I>k</I> is
 *
 *       \f[
 *            \tilde{h}_k(T,P) = h^o_k(T,P) = h^{ref}_k(T) + \left( \frac{P - P_{ref}}{C_o} \right)
 *       \f]
 *
 * The partial molar Internal Energy for species <I>k</I> is
 *
 *       \f[
 *            \tilde{u}_k(T,P) = u^o_k(T,P) = u^{ref}_k(T)
 *       \f]
 *
 * The partial molar Heat Capacity for species <I>k</I> is
 *
 *       \f[
 *            \tilde{Cp}_k(T,P) = Cp^o_k(T,P) = Cp^{ref}_k(T)
 *       \f]
 *
 * The partial molar volume is independent of temperature, pressure,
 * and species identity:
 *
 *       \f[
 *            \tilde{V}_k(T,P) =  V^o_k(T,P) = \frac{1.0}{C_o}
 *       \f]
 *
 *  It is assumed that the reference state thermodynamics may be
 *  obtained by a pointer to a populated species thermodynamic property
 *  manager class (see ThermoPhase::m_spthermo). How to relate pressure
 *  changes to the reference state thermodynamics is resolved at this level.
 *
 *  Pressure is defined as an independent variable in this phase. However, it only
 *  has a weak dependence on the enthalpy, and doesn't effect the molar
 *  concentration.
 *
 * <HR>
 * <H2> %Application within %Kinetics Managers </H2>
 * <HR>
 *
 *   \f$ C^a_k\f$ are defined such that \f$ C^a_k = a_k = X_k  \f$
 *   \f$ C^s_k \f$, the standard concentration, is
 *   defined to be equal to one. \f$ a_k \f$ are activities used in the
 *   thermodynamic functions.  These activity (or generalized)
 *   concentrations are used
 *   by kinetics manager classes to compute the forward and
 *   reverse rates of elementary reactions.
 *   The activity concentration,\f$  C^a_k \f$, is given by the following expression.
 *
 *       \f[
 *            C^a_k = C^s_k  X_k  =  X_k
 *       \f]
 *
 * The standard concentration for species <I>k</I> is identically one
 *
 *        \f[
 *            C^s_k =  C^s = 1.0
 *        \f]
 *
 * For example, a bulk-phase binary gas reaction between species j and k, producing
 * a new species l would have the
 * following equation for its rate of progress variable, \f$ R^1 \f$, which has
 * units of  kmol m-3 s-1.
 *
 *   \f[
 *    R^1 = k^1 C_j^a C_k^a =  k^1  X_j X_k
 *   \f]
 *
 *  The reverse rate constant can then be obtained from the law of microscopic reversibility
 *  and the equilibrium expression for the system.
 *
 *   \f[
 *         \frac{X_j X_k}{ X_l} = K_a^{o,1} = \exp(\frac{\mu^o_l - \mu^o_j - \mu^o_k}{R T} )
 *   \f]
 *
 *  \f$  K_a^{o,1} \f$ is the dimensionless form of the equilibrium constant, associated with
 *  the pressure dependent standard states \f$ \mu^o_l(T,P) \f$ and their associated activities,
 *  \f$ a_l \f$, repeated here:
 *
 *       \f[
 *            \mu_l(T,P) = \mu^o_l(T, P) + R T \log(a_l)
 *       \f]
 *
 *   The concentration equilibrium constant, \f$ K_c \f$, may be obtained by changing over
 *   to activity concentrations. When this is done:
 *
 *   \f[
 *         \frac{C^a_j C^a_k}{ C^a_l} = C^o K_a^{o,1} = K_c^1 =
 *             \exp(\frac{\mu^{o}_l - \mu^{o}_j - \mu^{o}_k}{R T} )
 *   \f]
 *
 *
 *    %Kinetics managers will calculate the concentration equilibrium constant, \f$ K_c \f$,
 *    using the second and third part of the above expression as a definition for the concentration
 *    equilibrium constant.
 *
 * <HR>
 * <H2> Instantiation of the Class </H2>
 * <HR>
 *
 *
 * The constructor for this phase is located in the default ThermoFactory
 * for %Cantera. A new %LatticePhase object may be created by the following code snippet:
 *
 * @code
 *    XML_Node *xc = get_XML_File("O_lattice_SiO2.xml");
 *    XML_Node * const xs = xc->findNameID("phase", "O_lattice_SiO2");
 *    ThermoPhase *tp = newPhase(*xs);
 *    LatticePhase *o_lattice = dynamic_cast <LatticPhase *>(tp);
 * @endcode
 *
 * or by the following constructor:
 *
 * @code
 *    XML_Node *xc = get_XML_File("O_lattice_SiO2.xml");
 *    XML_Node * const xs = xc->findNameID("phase", "O_lattice_SiO2");
 *    LatticePhase *o_lattice = new LatticePhase(*xs);
 * @endcode
 *
 *  The XML file used in this example is listed in the next section
 *
 * <HR>
 * <H2> XML Example </H2>
 * <HR>
 *
 *   An example of an XML Element named phase setting up a LatticePhase object named "O_lattice_SiO2"
 *   is given below.
 *
 * @verbatim
   <!--     phase O_lattice_SiO2      -->
   <phase dim="3" id="O_lattice_SiO2">
      <elementArray datasrc="elements.xml"> Si  H  He </elementArray>
      <speciesArray datasrc="#species_data">
              O_O  Vac_O
      </speciesArray>
      <reactionArray datasrc="#reaction_data"/>
      <thermo model="Lattice">
  <site_density> 73.159 </site_density>
  <vacancy_species>  Vac_O </vacancy_species>
</thermo>
      <kinetics model="BulkKinetics"/>
      <transport model="None"/>
    </phase>
    @endverbatim
 *
 *   The model attribute "Lattice" of the thermo XML element identifies the phase as
 *   being of the type handled by the LatticePhase object.
 *
 * @ingroup thermoprops
 *
 */
class LatticePhase : public ThermoPhase
{

public:

    //! Base Empty constructor
    LatticePhase();

    //! Copy Constructor
    /*!
     * @param right Object to be copied
     */
    LatticePhase(const LatticePhase& right);

    //! Assignment operator
    /*!
     * @param right Object to be copied
     */
    LatticePhase& operator=(const LatticePhase& right);

    //! Full constructor for a lattice phase
    /*!
     * @param inputFile String name of the input file
     * @param id        string id of the phase name
     */
    LatticePhase(std::string inputFile, std::string id = "");

    //! Full constructor for a water phase
    /*!
     * @param phaseRef  XML node referencing the lattice phase.
     * @param id        string id of the phase name
     */
    LatticePhase(XML_Node& phaseRef, std::string id = "");

    //! Destructor
    virtual ~LatticePhase();

    //! Duplication function
    /*!
     * This virtual function is used to create a duplicate of the
     * current phase. It's used to duplicate the phase when given
     * a ThermoPhase pointer to the phase.
     *
     * @return It returns a ThermoPhase pointer.
     */
    ThermoPhase* duplMyselfAsThermoPhase() const;

    //! Import and initialize a %LatticePhase phase specification from an XML tree into the current object.
    /*!
     * @param phaseNode  XML file containing the description of the phase
     *
     * @param idTarget   Optional parameter identifying the name of the
     *                   phase. If none is given, the first XML  phase element is used.
     */
    void constructPhaseXML(XML_Node& phaseNode, std::string idTarget);

    //! Initialization of a %LatticePhase phase using an xml file
    /*!
     *
     * This routine is a precursor to constructPhaseXML(XML_Node*)
     * routine, which does most of the work.
     *
     * @param inputFile XML file containing the description of the phase
     *
     * @param id        Optional parameter identifying the name of the
     *                  phase. If none is given, the first XML
     *                  phase element will be used.
     */
    void constructPhaseFile(std::string inputFile, std::string id);

    //! Equation of state flag. Returns the value cLattice
    virtual int eosType() const {
        return cLattice;
    }

    /**
     * @name Molar Thermodynamic Properties of the Solution ------------------------
     * @{
     */

    //! Return the Molar Enthalpy. Units: J/kmol.
    /*!
     * For an ideal solution,
     *
     *   \f[
     *    \hat h(T,P) = \sum_k X_k \hat h^0_k(T,P),
     *   \f]
     *
     * The standard-state pure-species Enthalpies
     * \f$ \hat h^0_k(T,P) \f$ are computed first by the species reference
     * state thermodynamic property manager and then a small pressure dependent term is
     * added in.
     *
     * \see SpeciesThermo
     */
    virtual doublereal enthalpy_mole() const;

    //! Molar internal energy of the solution. Units: J/kmol.
    /*!
     * For an ideal, constant partial molar volume solution mixture with
     * pure species phases which exhibit zero volume expansivity and
     * zero isothermal compressibility:
     *
     * \f[
     * \hat u(T,X) = \hat h(T,P,X) - p \hat V
     *         =  \sum_k X_k \hat h^0_k(T)  - P_{ref} (\sum_k{X_k \hat V^0_k})
     * \f]
     *
     * and is a function only of temperature.
     * The reference-state pure-species enthalpies
     * \f$ \hat h^0_k(T) \f$ are computed by the species thermodynamic
     * property manager.
     * @see SpeciesThermo
     */
    virtual doublereal intEnergy_mole() const;

    //! Molar entropy of the solution. Units: J/kmol/K
    /*!
     * For an ideal, constant partial molar volume solution mixture with
     * pure species phases which exhibit zero volume expansivity:
     *   \f[
     *       \hat s(T, P, X_k) = \sum_k X_k \hat s^0_k(T)  - \hat R  \sum_k X_k log(X_k)
     *   \f]
     * The reference-state pure-species entropies
     * \f$ \hat s^0_k(T,p_{ref}) \f$ are computed by the species thermodynamic
     * property manager. The pure species entropies are independent of
     * pressure since the volume expansivities are equal to zero.
     *
     * Units: J/kmol/K.
     *
     * @see SpeciesThermo
     */
    virtual doublereal entropy_mole() const;

    //! Molar gibbs free energy of the solution. Units: J/kmol.
    /*!
     * For an ideal, constant partial molar volume solution mixture with
     * pure species phases which exhibit zero volume expansivity:
     *  \f[
     *    \hat g(T, P) = \sum_k X_k \hat g^0_k(T,P) + \hat R T \sum_k X_k log(X_k)
     *  \f]
     * The reference-state pure-species gibbs free energies
     * \f$ \hat g^0_k(T) \f$ are computed by the species thermodynamic
     * property manager, while the standard state gibbs free energies
     * \f$ \hat g^0_k(T,P) \f$ are computed by the member function, gibbs_RT().
     *
     * @see SpeciesThermo
     */
    virtual doublereal gibbs_mole() const;

    //! Molar heat capacity at constant pressure of the solution.
    //! Units: J/kmol/K.
    /*!
     * For an ideal, constant partial molar volume solution mixture with
     * pure species phases which exhibit zero volume expansivity:
     *   \f[
     *    \hat c_p(T,P) = \sum_k X_k \hat c^0_{p,k}(T) .
     *   \f]
     * The heat capacity is independent of pressure.
     * The reference-state pure-species heat capacities
     * \f$ \hat c^0_{p,k}(T) \f$ are computed by the species thermodynamic
     * property manager.
     *
     * @see SpeciesThermo
     */
    virtual doublereal cp_mole() const;

    //! Molar heat capacity at constant volume of the solution.
    //! Units: J/kmol/K.
    /*!
     * For an ideal, constant partial molar volume solution mixture with
     * pure species phases which exhibit zero volume expansivity:
     *  \f[
     *     \hat c_v(T,P) = \hat c_p(T,P)
     *  \f]
     *
     * The two heat capacities are equal.
     */
    virtual doublereal cv_mole() const;

    //@}
    /// @name Mechanical Equation of State Properties ------------------------------------
    //@{
    /**
     *   In this equation of state implementation, the density is a
     *   function only of the mole fractions. Therefore, it can't be
     *   an independent variable. Instead, the pressure is used as the
     *   independent variable. Functions which try to set the thermodynamic
     *   state by calling setDensity() may cause an exception to be
     *   thrown.
     */
    //@{


    //! Pressure. Units: Pa.
    /*!
     * For this incompressible system, we return the internally stored
     * independent value of the pressure.
     */
    virtual doublereal pressure() const {
        return m_Pcurrent;
    }

    //! Set the internally stored pressure (Pa) at constant
    //! temperature and composition
    /*!
     *  This method sets the pressure within the object.
     * The mass density is not a function of pressure.
     *
     * @param p   Input Pressure (Pa)
     */
    virtual void setPressure(doublereal p);

    //! Calculate the density of the mixture using the partial
    //! molar volumes and mole fractions as input
    /*!
     * The formula for this is
     *
     * \f[
     *      \rho = \frac{\sum_k{X_k W_k}}{\sum_k{X_k V_k}}
     * \f]
     *
     * where \f$X_k\f$ are the mole fractions, \f$W_k\f$ are
     * the molecular weights, and \f$V_k\f$ are the pure species
     * molar volumes.
     *
     * Note, the basis behind this formula is that in an ideal
     * solution the partial molar volumes are equal to the pure
     * species molar volumes. We have additionally specified
     * in this class that the pure species molar volumes are
     * independent of temperature and pressure.
     *
     * NOTE: This is a non-virtual function, which is not a
     *       member of the ThermoPhase base class.
     */
    doublereal calcDensity();

    //! Set the mole fractions
    /*!
     * @param x  Input vector of mole fractions.
     *           Length: m_kk.
     */
    virtual void setMoleFractions(const doublereal* const x);

    //! Set the mole fractions, but don't normalize them to one.
    /*!
     * @param x  Input vector of mole fractions.
     *           Length: m_kk.
     */
    virtual void setMoleFractions_NoNorm(const doublereal* const x);

    //! Set the mass fractions, and normalize them to one.
    /*!
     * @param y  Input vector of mass fractions.
     *           Length: m_kk.
     */
    virtual void setMassFractions(const doublereal* const y);

    //! Set the mass fractions, but don't normalize them to one
    /*!
     * @param y  Input vector of mass fractions.
     *           Length: m_kk.
     */
    virtual void setMassFractions_NoNorm(const doublereal* const y);

    //! Set the concentration,
    /*!
     * @param c  Input vector of concentrations.
     *           Length: m_kk.
     */
    virtual void setConcentrations(const doublereal* const c);


    //@}
    /// @name Activities, Standard States,  and Activity Concentrations
    /**
     *
     * The activity \f$a_k\f$ of a species in solution is
     * related to the chemical potential by \f[ \mu_k = \mu_k^0(T)
     * + \hat R T \log a_k. \f] The quantity \f$\mu_k^0(T,P)\f$ is
     * the chemical potential at unit activity, which depends only
     * on temperature and the pressure.
     * Activity is assumed to be molality-based here.
     */
    //@{

    /**
     * This method returns 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
     * defined below.  These generalized concentrations are used
     * by kinetics manager classes to compute the forward and
     * reverse rates of elementary reactions.
     *
     * @param c Array of generalized concentrations. The
     *          units depend upon the implementation of the
     *          reaction rate expressions within the phase.
     */
    virtual void getActivityConcentrations(doublereal* c) const;

    //! Return the standard concentration for the kth species
    /*!
     * The standard concentration \f$ C^0_k \f$ used to normalize
     * the activity (i.e., generalized) concentration for use
     *
     * For the time being, we will use the concentration of pure
     * solvent for the the standard concentration of all species.
     * This has the effect of making mass-action reaction rates
     * based on the molality of species proportional to the
     * molality of the species.
     *
     * @param k Optional parameter indicating the species. The default
     *         is to assume this refers to species 0.
     * @return
     *   Returns the standard Concentration in units of
     *   m<SUP>3</SUP> kmol<SUP>-1</SUP>.
     *
     * @param k Species index
     */
    virtual doublereal standardConcentration(size_t k=0) const;

    //! Returns the natural logarithm of the standard
    //! concentration of the kth species
    /*!
     * @param k Species index
     */
    virtual doublereal logStandardConc(size_t k=0) const;

    //! Get the array of non-dimensional activity coefficients at
    //! the current solution temperature, pressure, and solution concentration.
    /*!
     *  For this phase, the activity coefficients are all equal to one.
     *
     * @param ac Output vector of activity coefficients. Length: m_kk.
     */
    virtual void getActivityCoefficients(doublereal* ac) const;

    //@}
    /// @name  Partial Molar Properties of the Solution
    ///
    //@{

    //! Get the species chemical potentials. Units: J/kmol.
    /*!
     * This function returns a vector of chemical potentials of the
     * species in solid solution at the current temperature, pressure
     * and mole fraction of the solid solution.
     *
     * @param mu  Output vector of species chemical
     *            potentials. Length: m_kk. Units: J/kmol
     */
    virtual void getChemPotentials(doublereal* mu) const;


    //@}
    /// @name  Partial Molar Properties of the Solution -----------------------------
    //@{


    /**
     * Returns an array of partial molar enthalpies for the species
     * in the mixture.
     * Units (J/kmol)
     * For this phase, the partial molar enthalpies are equal to the
     * pure species enthalpies
     *  \f[
     * \bar h_k(T,P) = \hat h^{ref}_k(T) + (P - P_{ref}) \hat V^0_k
     * \f]
     * The reference-state pure-species enthalpies, \f$ \hat h^{ref}_k(T) \f$,
     * at the reference pressure,\f$ P_{ref} \f$,
     * are computed by the species thermodynamic
     * property manager. They are polynomial functions of temperature.
     * @see SpeciesThermo
     *
     * @param hbar Output vector containing partial molar enthalpies.
     *             Length: m_kk.
     */
    virtual void getPartialMolarEnthalpies(doublereal* hbar) const;

    /**
     * Returns an array of partial molar entropies of the species in the
     * solution. Units: J/kmol/K.
     * For this phase, the partial molar entropies are equal to the
     * pure species entropies plus the ideal solution contribution.
     *  \f[
     * \bar s_k(T,P) =  \hat s^0_k(T) - R log(X_k)
     * \f]
     * The reference-state pure-species entropies,\f$ \hat s^{ref}_k(T) \f$,
     * at the reference pressure, \f$ P_{ref} \f$,  are computed by the
     * species thermodynamic
     * property manager. They are polynomial functions of temperature.
     * @see SpeciesThermo
     *
     * @param sbar Output vector containing partial molar entropies.
     *             Length: m_kk.
     */
    virtual void getPartialMolarEntropies(doublereal* sbar) const;

    /**
     * Returns an array of partial molar Heat Capacities at constant
     * pressure of the species in the
     * solution. Units: J/kmol/K.
     * For this phase, the partial molar heat capacities are equal
     * to the standard state heat capacities.
     *
     * @param cpbar  Output vector of partial heat capacities. Length: m_kk.
     */
    virtual void getPartialMolarCp(doublereal* cpbar) const;

    //! Return an array of partial molar volumes for the
    //! species in the mixture. Units: m^3/kmol.
    /*!
     *  @param vbar   Output vector of species partial molar volumes.
     *                Length = m_kk. units are m^3/kmol.
     */
    virtual void getPartialMolarVolumes(doublereal* vbar) const;


    //! Get the array of chemical potentials at unit activity for the
    //! species standard states at the current <I>T</I> and <I>P</I> of the solution.
    /*!
     * These are the standard state chemical potentials \f$ \mu^0_k(T,P)
     * \f$. The values are evaluated at the current
     * temperature and pressure of the solution
     *
     * @param mu  Output vector of chemical potentials.
     *            Length: m_kk.
     */
    virtual void getStandardChemPotentials(doublereal* mu) const;

    //! Get the Gibbs functions for the standard
    //! state of the species at the current <I>T</I> and <I>P</I> of the solution
    /*!
     * Units are Joules/kmol
     * @param gpure  Output vector of  standard state gibbs free energies
     *               Length: m_kk.
     */
    virtual void getPureGibbs(doublereal* gpure) const;


    //@}
    /// @name  Properties of the Standard State of the Species in the Solution
    //@{

    //! Get the nondimensional Enthalpy functions for the species standard states
    //! at their standard states at the current <I>T</I> and <I>P</I> of the solution.
    /*!
     *  A small pressure dependent term is added onto the reference state enthalpy
     *  to get the pressure dependence of this term.
     *
     *       \f[
     *          h^o_k(T,P) = h^{ref}_k(T) +  \left( \frac{P - P_{ref}}{C_o} \right)
     *       \f]
     *
     *  The reference state thermodynamics is
     *  obtained by a pointer to a populated species thermodynamic property
     *  manager class (see ThermoPhase::m_spthermo). How to relate pressure
     *  changes to the reference state thermodynamics is resolved at this level.
     *
     * @param hrt      Output vector of nondimensional standard state enthalpies.
     *                 Length: m_kk.
     */
    virtual void getEnthalpy_RT(doublereal* hrt) const;

    //! Get the array of nondimensional Entropy functions for the
    //! species standard states at the current <I>T</I> and <I>P</I> of the solution.
    /*!
     *  The entropy of the standard state is defined as independent of
     *  pressure here.
     *
     *       \f[
     *            s^o_k(T,P) = s^{ref}_k(T)
     *       \f]
     *
     *  The reference state thermodynamics is
     *  obtained by a pointer to a populated species thermodynamic property
     *  manager class (see ThermoPhase::m_spthermo). How to relate pressure
     *  changes to the reference state thermodynamics is resolved at this level.
     *
     * @param sr   Output vector of  nondimensional standard state entropies.
     *             Length: m_kk.
     */
    virtual void getEntropy_R(doublereal* sr) const;

    //! Get the nondimensional Gibbs functions for the species
    //! standard states at the current <I>T</I> and <I>P</I> of the solution.
    /*!
     *  The standard gibbs free energies are obtained from the enthalpy
     *  and entropy formulation.
     *
     *       \f[
     *            g^o_k(T,P) = h^{o}_k(T,P) - T s^{o}_k(T,P)
     *       \f]
     *
     * @param grt  Output vector of nondimensional standard state gibbs free energies
     *             Length: m_kk.
     */
    virtual void getGibbs_RT(doublereal* grt) const;

    //! Get the nondimensional Heat Capacities at constant
    //! pressure for the species standard states
    //! at the current <I>T</I> and <I>P</I> of the solution
    /*!
     *  The heat capacity of the standard state is independent of pressure
     *
     *       \f[
     *            Cp^o_k(T,P) = Cp^{ref}_k(T)
     *       \f]
     *
     *  The reference state thermodynamics is
     *  obtained by a pointer to a populated species thermodynamic property
     *  manager class (see ThermoPhase::m_spthermo). How to relate pressure
     *  changes to the reference state thermodynamics is resolved at this level.
     *
     * @param cpr   Output vector of nondimensional standard state heat capacities
     *              Length: m_kk.
     */
    virtual void getCp_R(doublereal* cpr) const;

    //!  Get the molar volumes of the species standard states at the current
    //!  <I>T</I> and <I>P</I> of the solution.
    /*!
     * units = m^3 / kmol
     *
     * @param vol     Output vector containing the standard state volumes.
     *                Length: m_kk.
     */
    virtual void getStandardVolumes(doublereal* vol) const;

    //@}
    /// @name Thermodynamic Values for the Species Reference States
    //@{

#ifdef H298MODIFY_CAPABILITY

    //! Modify the value of the 298 K Heat of Formation of one species in the phase (J kmol-1)
    /*!
     *   The 298K heat of formation is defined as the enthalpy change to create the standard state
     *   of the species from its constituent elements in their standard states at 298 K and 1 bar.
     *
     *   @param  k           Species k
     *   @param  Hf298New    Specify the new value of the Heat of Formation at 298K and 1 bar
     */
    virtual void modifyOneHf298SS(const int k, const doublereal Hf298New) {
        m_spthermo->modifyOneHf298(k, Hf298New);
        m_tlast += 0.0001234;
    }
#endif

    //! Returns the vector of nondimensional
    //!  Enthalpies of the reference state at the current temperature
    //!  of the solution and the reference pressure for the phase.
    /*!
     * @return       Output vector of nondimensional reference state
     *               Enthalpies of the species.
     *               Length: m_kk
     */
    const vector_fp& enthalpy_RT_ref() const;

    //! Returns a reference to the dimensionless reference state Gibbs free energy vector.
    /*!
     * This function is part of the layer that checks/recalculates the reference
     * state thermo functions.
     */
    const vector_fp& gibbs_RT_ref() const;

    //!  Returns the vector of nondimensional
    //!  Gibbs Free Energies of the reference state at the current temperature
    //!  of the solution and the reference pressure for the species.
    /*!
     * @param grt     Output vector containing the nondimensional reference state
     *                Gibbs Free energies.  Length: m_kk.
     */
    virtual void getGibbs_RT_ref(doublereal* grt) const;

    //!  Returns the vector of the gibbs function of the reference state at the current temperature
    //!  of the solution and the reference pressure for the species.
    /*!
     *  units = J/kmol
     *
     * @param g       Output vector containing the  reference state
     *                Gibbs Free energies.  Length: m_kk. Units: J/kmol.
     */
    virtual void getGibbs_ref(doublereal* g) const;

    //! Returns a reference to the dimensionless reference state Entropy vector.
    /*!
     * This function is part of the layer that checks/recalculates the reference
     * state thermo functions.
     */
    const vector_fp& entropy_R_ref() const;

    //! Returns a reference to the dimensionless reference state Heat Capacity vector.
    /*!
     * This function is part of the layer that checks/recalculates the reference
     * state thermo functions.
     */
    const vector_fp& cp_R_ref() const;

    //@}
    /// @name  Utilities for Initialization of the Object
    //@{

    //! Initialize the ThermoPhase object after all species have been set up
    /*!
     * @internal Initialize.
     *
     * This method performs any initialization required after all
     * species have been added. For example, it is used to
     * resize internal work arrays that must have an entry for
     * each species.
     * This method is called from ThermoPhase::initThermoXML(),
     * which is called from importPhase(),
     * just prior to returning from the function, importPhase().
     *
     * @see importCTML.cpp
     */
    virtual void initThermo();


    //! Import and initialize a ThermoPhase object using an XML tree.
    /*!
     *   Here we read extra information about the XML description
     *   of a phase. Regular information about elements and species
     *   and their reference state thermodynamic information
     *   have already been read at this point.
     *   For example, we do not need to call this function for
     *   ideal gas equations of state.
     *   This function is called from importPhase()
     *   after the elements and the
     *   species are initialized with default ideal solution
     *   level data.
     *
     * @param phaseNode This object must be the phase node of a
     *             complete XML tree
     *             description of the phase, including all of the
     *             species data. In other words while "phase" must
     *             point to an XML phase object, it must have
     *             sibling nodes "speciesData" that describe
     *             the species in the phase.
     * @param id   ID of the phase. If nonnull, a check is done
     *             to see if phaseNode is pointing to the phase
     *             with the correct id.
     */
    virtual void initThermoXML(XML_Node& phaseNode, std::string id);

    //! Set the equation of state parameters from the argument list
    /*!
     * @internal
     * Set equation of state parameters.
     *
     * @param n number of parameters. Must be one
     * @param c array of \a n coefficients
     *           c[0] = The bulk  lattice density (kmol m-3)
     */
    virtual void setParameters(int n, doublereal* const c);

    //! Get the equation of state parameters in a vector
    /*!
     * @internal
     *
     * @param n number of parameters
     * @param c array of \a n coefficients
     *
     *  For this phase:
     *       -  n = 1
     *       -  c[0] = molar density of phase [ kmol/m^3 ]
     */
    virtual void getParameters(int& n, doublereal* const c) const;

    //! Set equation of state parameter values from XML entries.
    /*!
     * This method is called by function importPhase() in
     * file importCTML.cpp when processing a phase definition in
     * an input file. It should be overloaded in subclasses to set
     * any parameters that are specific to that particular phase
     * model. Note, this method is called before the phase is
     * initialized with elements and/or species.
     *
     *  For this phase, the molar density of the phase is specified in this block,
     *  and is a required parameter.
     *
     * @param eosdata An XML_Node object corresponding to
     *                the "thermo" entry for this phase in the input file.
     *
     * eosdata points to the thermo block, and looks like this:
     *
     *   @verbatim
         <phase id="O_lattice_SiO2" >
           <thermo model="Lattice">
               <site_density units="kmol/m^3"> 73.159 </site_density>
           <vacancy_species> "O_vacancy"  </vacancy_species>
           </thermo>
         </phase>    @endverbatim
     *
     */
    virtual void setParametersFromXML(const XML_Node& eosdata);

    //@}

protected:


    //! Number of elements
    size_t m_mm;

    //! Minimum temperature for valid species standard state thermo props
    /*!
     * This is the minimum temperature at which all species have valid standard
     * state thermo props defined.
     */
    doublereal m_tmin;

    //! Maximum temperature for valid species standard state thermo props
    /*!
     * This is the maximum temperature at which all species have valid standard
     * state thermo props defined.
     */
    doublereal m_tmax;

    //! Reference state pressure
    doublereal m_Pref;


    //! The current pressure
    /*!
     * Since the density isn't a function of pressure, but only of the
     * mole fractions, we need to independently specify the pressure.
     * The density variable which is inherited as part of the State class,
     * m_dens, is always kept current whenever T, P, or X[] change.
     */
    doublereal m_Pcurrent;

    //! Current value of the temperature (Kelvin)
    mutable doublereal m_tlast;

    //! Reference state enthalpies / RT
    mutable vector_fp m_h0_RT;

    //! Temporary storage for the reference state heat capacities
    mutable vector_fp m_cp0_R;

    //! Temporary storage for the reference state gibbs energies
    mutable vector_fp m_g0_RT;

    //! Temporary storage for the reference state entropies at the current temperature
    mutable vector_fp m_s0_R;


    //! String name for the species which represents a vacency
    //! in the lattice
    /*!
     *  This string is currently unused
     */
    std::string m_vacancy;

    //! Vector of molar volumes for each species in the solution
    /**
     * Species molar volumes \f$ m^3 kmol^-1 \f$
     */
    vector_fp   m_speciesMolarVolume;

    //! Site Density of the lattice solid
    /*!
     *  Currently, this is imposed as a function of T, P or composition
     *
     *  units are kmol m-3
     */
    doublereal m_site_density;

    // doublereal m_molar_lattice_volume;

private:

    //! Update the species reference state thermodynamic functions
    /*!
     * The polynomials for the standard state functions are only
     * reevaluated if the temperature has changed.
     */
    void _updateThermo() const;
};
}

#endif