/**
 *  @file
 *
 */
/*
 * Copyright (2009) Sandia Corporation. Under the terms of
 * Contract DE-AC04-94AL85000 with Sandia Corporation, the
 * U.S. Government retains certain rights in this software.
 */
/*
 *  $Date: 2010-11-12 14:37:41 -0700 (Fri, 12 Nov 2010) $
 *  $Revision: 641 $
 */


#include "cantera/thermo/PhaseCombo_Interaction.h"
#include "cantera/thermo/ThermoFactory.h"
#include <iomanip>

using namespace std;

namespace Cantera
{

static  const double xxSmall = 1.0E-150;
//====================================================================================================================
/*
 * Default constructor.
 *
 * HKM - Checked for Transition
 */
PhaseCombo_Interaction::PhaseCombo_Interaction() :
    GibbsExcessVPSSTP(),
    numBinaryInteractions_(0),
    formMargules_(0),
    formTempModel_(0)
{
}
//====================================================================================================================
/*
 * Working constructors
 *
 *  The two constructors below are the normal way
 *  the phase initializes itself. They are shells that call\
 *  the routine initThermo(), with a reference to the
 *  XML database to get the info for the phase.
 *
 * HKM - Checked for Transition
 */
PhaseCombo_Interaction::PhaseCombo_Interaction(std::string inputFile, std::string id) :
    GibbsExcessVPSSTP(),
    numBinaryInteractions_(0),
    formMargules_(0),
    formTempModel_(0)
{
    constructPhaseFile(inputFile, id);
}
//====================================================================================================================
//
/*
 *
 * HKM - Checked for Transition
 */
PhaseCombo_Interaction::PhaseCombo_Interaction(XML_Node& phaseRoot, std::string id) :
    GibbsExcessVPSSTP(),
    numBinaryInteractions_(0),
    formMargules_(0),
    formTempModel_(0)
{
    constructPhaseXML(phaseRoot, id);
}

//====================================================================================================================
/*
 * Copy Constructor:
 *
 *  Note this stuff will not work until the underlying phase
 *  has a working copy constructor
 *
 * HKM - Checked for Transition
 */
PhaseCombo_Interaction::PhaseCombo_Interaction(const PhaseCombo_Interaction& b) :
    GibbsExcessVPSSTP()
{
    PhaseCombo_Interaction::operator=(b);
}
//====================================================================================================================
/*
 * operator=()
 *
 *  Note this stuff will not work until the underlying phase
 *  has a working assignment operator
 *
 * HKM - Checked for Transition
 */
PhaseCombo_Interaction& PhaseCombo_Interaction::
operator=(const PhaseCombo_Interaction& b)
{
    if (&b == this) {
        return *this;
    }

    GibbsExcessVPSSTP::operator=(b);

    numBinaryInteractions_      = b.numBinaryInteractions_ ;
    m_HE_b_ij                   = b.m_HE_b_ij;
    m_HE_c_ij                   = b.m_HE_c_ij;
    m_HE_d_ij                   = b.m_HE_d_ij;
    m_SE_b_ij                   = b.m_SE_b_ij;
    m_SE_c_ij                   = b.m_SE_c_ij;
    m_SE_d_ij                   = b.m_SE_d_ij;
    m_VHE_b_ij                  = b.m_VHE_b_ij;
    m_VHE_c_ij                  = b.m_VHE_c_ij;
    m_VHE_d_ij                  = b.m_VHE_d_ij;
    m_VSE_b_ij                  = b.m_VSE_b_ij;
    m_VSE_c_ij                  = b.m_VSE_c_ij;
    m_VSE_d_ij                  = b.m_VSE_d_ij;
    m_pSpecies_A_ij             = b.m_pSpecies_A_ij;
    m_pSpecies_B_ij             = b.m_pSpecies_B_ij;
    formMargules_               = b.formMargules_;
    formTempModel_              = b.formTempModel_;

    return *this;
}
//====================================================================================================================
/**
 *
 * ~PhaseCombo_Interaction():   (virtual)
 *
 * Destructor: does nothing:
 *
 * HKM - Checked for Transition
 */
PhaseCombo_Interaction::~PhaseCombo_Interaction()
{
}
//====================================================================================================================
/*
 * This routine duplicates the current object and returnsa pointer to ThermoPhase.
 *
 * HKM - Checked for Transition
 */
ThermoPhase*
PhaseCombo_Interaction::duplMyselfAsThermoPhase() const
{
    PhaseCombo_Interaction* mtp = new PhaseCombo_Interaction(*this);
    return (ThermoPhase*) mtp;
}
//====================================================================================================================
// Special constructor for a hard-coded problem
/*
 *
 *   LiKCl treating the PseudoBinary layer as passthrough.
 *   -> test to predict the eutectic and liquidus correctly.
 *
 */
PhaseCombo_Interaction::PhaseCombo_Interaction(int testProb)  :
    GibbsExcessVPSSTP(),
    numBinaryInteractions_(0),
    formMargules_(0),
    formTempModel_(0)
{


    constructPhaseFile("PhaseCombo_Interaction.xml", "");


    numBinaryInteractions_ = 1;

    m_HE_b_ij.resize(1);
    m_HE_c_ij.resize(1);
    m_HE_d_ij.resize(1);

    m_SE_b_ij.resize(1);
    m_SE_c_ij.resize(1);
    m_SE_d_ij.resize(1);

    m_VHE_b_ij.resize(1);
    m_VHE_c_ij.resize(1);
    m_VHE_d_ij.resize(1);

    m_VSE_b_ij.resize(1);
    m_VSE_c_ij.resize(1);
    m_VSE_d_ij.resize(1);

    m_pSpecies_A_ij.resize(1);
    m_pSpecies_B_ij.resize(1);



    m_HE_b_ij[0] = -17570E3;
    m_HE_c_ij[0] = -377.0E3;
    m_HE_d_ij[0] = 0.0;

    m_SE_b_ij[0] = -7.627E3;
    m_SE_c_ij[0] =  4.958E3;
    m_SE_d_ij[0] =  0.0;


    size_t iLiT = speciesIndex("LiTFe1S2(S)");
    if (iLiT == npos) {
        throw CanteraError("PhaseCombo_Interaction test1 constructor",
                           "Unable to find LiTFe1S2(S)");
    }
    m_pSpecies_A_ij[0] = iLiT;


    size_t iLi2 = speciesIndex("Li2Fe1S2(S)");
    if (iLi2 == npos) {
        throw CanteraError("PhaseCombo_Interaction test1 constructor",
                           "Unable to find Li2Fe1S2(S)");
    }
    m_pSpecies_B_ij[0] = iLi2;
    throw CanteraError("", "unimplemented");
}
//====================================================================================================================

/*
 *  -------------- Utilities -------------------------------
 */


// Equation of state type flag.
/*
 * The ThermoPhase base class returns
 * zero. Subclasses should define this to return a unique
 * non-zero value. Known constants defined for this purpose are
 * listed in mix_defs.h. The PhaseCombo_Interaction class also returns
 * zero, as it is a non-complete class.
 */
int PhaseCombo_Interaction::eosType() const
{
    return cPhaseCombo_Interaction;
}
//====================================================================================================================
/*
 *   Import, construct, and initialize a phase
 *   specification from an XML tree into the current object.
 *
 * This routine is a precursor to constructPhaseXML(XML_Node*)
 * routine, which does most of the work.
 *
 * @param infile 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.
 *
 * HKM - Checked for Transition
 */
void PhaseCombo_Interaction::constructPhaseFile(std::string inputFile, std::string id)
{

    if ((int) inputFile.size() == 0) {
        throw CanteraError("PhaseCombo_Interaction:constructPhaseFile",
                           "input file is null");
    }
    string path = findInputFile(inputFile);
    std::ifstream fin(path.c_str());
    if (!fin) {
        throw CanteraError("PhaseCombo_Interaction:constructPhaseFile",
                           "Could not open " +path+" for reading.");
    }
    /*
     * The phase object automatically constructs an XML object.
     * Use this object to store information.
     */
    XML_Node& phaseNode_XML = xml();
    XML_Node* fxml = new XML_Node();
    fxml->build(fin);
    XML_Node* fxml_phase = findXMLPhase(fxml, id);
    if (!fxml_phase) {
        throw CanteraError("PhaseCombo_Interaction:constructPhaseFile",
                           "ERROR: Can not find phase named " + id + " in file named " + inputFile);
    }
    fxml_phase->copy(&phaseNode_XML);
    constructPhaseXML(*fxml_phase, id);
    delete fxml;
}
//====================================================================================================================
/*
 *   Import, construct, and initialize a HMWSoln phase
 *   specification from an XML tree into the current object.
 *
 *   Most of the work is carried out by the cantera base
 *   routine, importPhase(). That routine imports all of the
 *   species and element data, including the standard states
 *   of the species.
 *
 *   Then, In this routine, we read the information
 *   particular to the specification of the activity
 *   coefficient model for the Pitzer parameterization.
 *
 *   We also read information about the molar volumes of the
 *   standard states if present in the XML file.
 *
 * @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.
 *
 * HKM - Checked for Transition
 */
void PhaseCombo_Interaction::constructPhaseXML(XML_Node& phaseNode, std::string id)
{
    string stemp;
    if ((int) id.size() > 0) {
        string idp = phaseNode.id();
        if (idp != id) {
            throw CanteraError("PhaseCombo_Interaction::constructPhaseXML",
                               "phasenode and Id are incompatible");
        }
    }

    /*
     * Find the Thermo XML node
     */
    if (!phaseNode.hasChild("thermo")) {
        throw CanteraError("PhaseCombo_Interaction::constructPhaseXML",
                           "no thermo XML node");
    }
    XML_Node& thermoNode = phaseNode.child("thermo");

    /*
     * Make sure that the thermo model is PhaseCombo_Interaction
     */
    stemp = thermoNode.attrib("model");
    string formString = lowercase(stemp);
    if (formString != "phasecombo_interaction") {
        throw CanteraError("PhaseCombo_Interaction::constructPhaseXML",
                           "model name isn't PhaseCombo_Interaction: " + formString);
    }

    /*
     * Call the Cantera importPhase() function. This will import
     * all of the species into the phase. This will also handle
     * all of the species standard states
     */
    bool m_ok = importPhase(phaseNode, this);
    if (!m_ok) {
        throw CanteraError("PhaseCombo_Interaction::constructPhaseXML","importPhase failed ");
    }
}
//====================================================================================================================
/*
 * ------------ Molar Thermodynamic Properties ----------------------
 */
//====================================================================================================================
/*
 * - Activities, Standard States, Activity Concentrations -----------
 */
//====================================================================================================================
// Get the array of non-dimensional molar-based activity coefficients at
// the current solution temperature, pressure, and solution concentration.
/*
 * @param ac Output vector of activity coefficients. Length: m_kk.
 */
void PhaseCombo_Interaction::getActivityCoefficients(doublereal* ac) const
{
    /*
     * Update the activity coefficients
     */
    s_update_lnActCoeff();

    /*
     * take the exp of the internally stored coefficients.
     */
    for (size_t k = 0; k < m_kk; k++) {
        ac[k] = exp(lnActCoeff_Scaled_[k]);
    }
}

/*
 * ------------ Partial Molar Properties of the Solution ------------
 */

//====================================================================================================================

void PhaseCombo_Interaction::getElectrochemPotentials(doublereal* mu) const
{
    getChemPotentials(mu);
    double ve = Faraday * electricPotential();
    for (size_t k = 0; k < m_kk; k++) {
        mu[k] += ve*charge(k);
    }
}

//====================================================================================================================
void PhaseCombo_Interaction::getChemPotentials(doublereal* mu) const
{
    doublereal xx;
    /*
     * First get the standard chemical potentials in
     * molar form.
     *  -> this requires updates of standard state as a function
     *     of T and P
     */
    getStandardChemPotentials(mu);
    /*
     * Update the activity coefficients
     */
    s_update_lnActCoeff();
    /*
     *
     */
    doublereal RT = GasConstant * temperature();
    for (size_t k = 0; k < m_kk; k++) {
        xx = std::max(moleFractions_[k], xxSmall);
        mu[k] += RT * (log(xx) + lnActCoeff_Scaled_[k]);
    }
}
//====================================================================================================================
// Molar enthalpy. Units: J/kmol.
doublereal PhaseCombo_Interaction::enthalpy_mole() const
{
    size_t kk = nSpecies();
    double h = 0;
    vector_fp hbar(kk);
    getPartialMolarEnthalpies(&hbar[0]);
    for (size_t i = 0; i < kk; i++) {
        h += moleFractions_[i]*hbar[i];
    }
    return h;
}
//====================================================================================================================
// Molar entropy. Units: J/kmol.
doublereal PhaseCombo_Interaction::entropy_mole() const
{
    size_t kk = nSpecies();
    double s = 0;
    vector_fp sbar(kk);
    getPartialMolarEntropies(&sbar[0]);
    for (size_t i = 0; i < kk; i++) {
        s += moleFractions_[i]*sbar[i];
    }
    return s;
}
//====================================================================================================================
// Molar heat capacity at constant pressure. Units: J/kmol/K.
doublereal PhaseCombo_Interaction::cp_mole() const
{
    size_t kk = nSpecies();
    double cp = 0;
    vector_fp cpbar(kk);
    getPartialMolarCp(&cpbar[0]);
    for (size_t i = 0; i < kk; i++) {
        cp += moleFractions_[i]*cpbar[i];
    }
    return cp;
}
//====================================================================================================================
// Molar heat capacity at constant volume. Units: J/kmol/K.
doublereal PhaseCombo_Interaction::cv_mole() const
{
    return cp_mole() - GasConstant;
}
//====================================================================================================================
// 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
 * standard state enthalpies modified by the derivative of the
 * molality-based activity coefficent wrt temperature
 *
 *  \f[
 * \bar h_k(T,P) = h^o_k(T,P) - R T^2 \frac{d \ln(\gamma_k)}{dT}
 * \f]
 *
 */
void PhaseCombo_Interaction::getPartialMolarEnthalpies(doublereal* hbar) const
{
    /*
     * Get the nondimensional standard state enthalpies
     */
    getEnthalpy_RT(hbar);
    /*
     * dimensionalize it.
     */
    double T = temperature();
    double RT = GasConstant * T;
    for (size_t k = 0; k < m_kk; k++) {
        hbar[k] *= RT;
    }
    /*
     * Update the activity coefficients, This also update the
     * internally stored molalities.
     */
    s_update_lnActCoeff();
    s_update_dlnActCoeff_dT();
    double RTT = RT * T;
    for (size_t k = 0; k < m_kk; k++) {
        hbar[k] -= RTT * dlnActCoeffdT_Scaled_[k];
    }
}
//====================================================================================================================
// Returns an array of partial molar heat capacities for the species in the mixture.
/*
 * Units (J/kmol)
 *
 * For this phase, the partial molar enthalpies are equal to the
 * standard state enthalpies modified by the derivative of the
 * activity coefficent wrt temperature
 *
 *  \f[
 * ??????????? \bar s_k(T,P) = s^o_k(T,P) - R T^2 \frac{d \ln(\gamma_k)}{dT}
 * \f]
 *
 */
void PhaseCombo_Interaction::getPartialMolarCp(doublereal* cpbar) const
{
    /*
     * Get the nondimensional standard state entropies
     */
    getCp_R(cpbar);
    double T = temperature();
    /*
     * Update the activity coefficients, This also update the
     * internally stored molalities.
     */
    s_update_lnActCoeff();
    s_update_dlnActCoeff_dT();

    for (size_t k = 0; k < m_kk; k++) {
        cpbar[k] -= 2 * T * dlnActCoeffdT_Scaled_[k] + T * T * d2lnActCoeffdT2_Scaled_[k];
    }
    /*
     * dimensionalize it.
     */
    for (size_t k = 0; k < m_kk; k++) {
        cpbar[k] *= GasConstant;
    }
}
//====================================================================================================================
// Returns an array of partial molar entropies for the species
// in the mixture.
/*
 * Units (J/kmol)
 *
 * For this phase, the partial molar enthalpies are equal to the
 * standard state enthalpies modified by the derivative of the
 * activity coefficent wrt temperature
 *
 *  \f[
 *         \bar s_k(T,P) = s^o_k(T,P) - R T^2 \frac{d \ln(\gamma_k)}{dT}
 * \f]
 *
 */
void PhaseCombo_Interaction::getPartialMolarEntropies(doublereal* sbar) const
{
    double xx;
    /*
     * Get the nondimensional standard state entropies
     */
    getEntropy_R(sbar);
    double T = temperature();
    /*
     * Update the activity coefficients, This also update the
     * internally stored molalities.
     */
    s_update_lnActCoeff();
    s_update_dlnActCoeff_dT();

    for (size_t k = 0; k < m_kk; k++) {
        xx = std::max(moleFractions_[k], xxSmall);
        sbar[k] += - lnActCoeff_Scaled_[k] - log(xx) - T * dlnActCoeffdT_Scaled_[k];
    }
    /*
     * dimensionalize it.
     */
    for (size_t k = 0; k < m_kk; k++) {
        sbar[k] *= GasConstant;
    }
}
//====================================================================================================================
/*
 * ------------ Partial Molar Properties of the Solution ------------
 */

// Return an array of partial molar volumes for the species in the mixture. Units: m^3/kmol.
/*
 *  Frequently, for this class of thermodynamics representations,
 *  the excess Volume due to mixing is zero. Here, we set it as
 *  a default. It may be overridden in derived classes.
 *
 *  @param vbar   Output vector of species partial molar volumes.
 *                Length = m_kk. units are m^3/kmol.
 */
void PhaseCombo_Interaction::getPartialMolarVolumes(doublereal* vbar) const
{
    int delAK, delBK;
    double XA, XB, g0, g1;
    double T = temperature();

    /*
     * Get the standard state values in m^3 kmol-1
     */
    getStandardVolumes(vbar);

    for (size_t iK = 0; iK < m_kk; iK++) {
        delAK = 0;
        delBK = 0;
        for (size_t i = 0; i <  numBinaryInteractions_; i++) {

            size_t iA =  m_pSpecies_A_ij[i];
            size_t iB =  m_pSpecies_B_ij[i];

            if (iA==iK) {
                delAK = 1;
            } else if (iB==iK) {
                delBK = 1;
            }

            XA = moleFractions_[iA];
            XB = moleFractions_[iB];

            g0 = (m_VHE_b_ij[i] - T * m_VSE_b_ij[i]);
            g1 = (m_VHE_c_ij[i] - T * m_VSE_c_ij[i]);

            vbar[iK] += XA*XB*(g0+g1*XB)+((delAK-XA)*XB+XA*(delBK-XB))*(g0+g1*XB)+XA*XB*(delBK-XB)*g1;
        }
    }
}
//====================================================================================================================
doublereal PhaseCombo_Interaction::err(std::string msg) const
{
    throw CanteraError("PhaseCombo_Interaction","Base class method "
                       +msg+" called. Equation of state type: "+int2str(eosType()));
    return 0;
}

//====================================================================================================================
/*
 * @internal Initialize. This method is provided to allow
 * subclasses to perform any initialization required after all
 * species have been added. For example, it might be used to
 * resize internal work arrays that must have an entry for
 * each species.  The base class implementation does nothing,
 * and subclasses that do not require initialization do not
 * need to overload this method.  When importing a CTML phase
 * description, this method is called just prior to returning
 * from function importPhase.
 *
 * @see importCTML.cpp
 */
void PhaseCombo_Interaction::initThermo()
{
    initLengths();
    GibbsExcessVPSSTP::initThermo();
}

//====================================================================================================================
//   Initialize lengths of local variables after all species have
//   been identified.
void  PhaseCombo_Interaction::initLengths()
{
    m_kk = nSpecies();
    dlnActCoeffdlnN_.resize(m_kk, m_kk);
}
//====================================================================================================================
/*
 * initThermoXML()                (virtual from ThermoPhase)
 *   Import and initialize a ThermoPhase object
 *
 * @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.
 */
void PhaseCombo_Interaction::initThermoXML(XML_Node& phaseNode, std::string id)
{
    string subname = "PhaseCombo_Interaction::initThermoXML";
    string stemp;

    /*
     * Check on the thermo field. Must have:
     * <thermo model="IdealSolidSolution" />
     */

    XML_Node& thermoNode = phaseNode.child("thermo");
    string mStringa = thermoNode.attrib("model");
    string mString = lowercase(mStringa);
    if (mString != "phasecombo_interaction") {
        throw CanteraError(subname.c_str(), "Unknown thermo model: " + mStringa);
    }


    /*
     * Go get all of the coefficients and factors in the
     * activityCoefficients XML block
     */
    /*
     * Go get all of the coefficients and factors in the
     * activityCoefficients XML block
     */
    XML_Node* acNodePtr = 0;
    if (thermoNode.hasChild("activityCoefficients")) {
        XML_Node& acNode = thermoNode.child("activityCoefficients");
        acNodePtr = &acNode;
        string mStringa = acNode.attrib("model");
        string mString = lowercase(mStringa);
        if (mString != "margules") {
            throw CanteraError(subname.c_str(),
                               "Unknown activity coefficient model: " + mStringa);
        }
        size_t n = acNodePtr->nChildren();
        for (size_t i = 0; i < n; i++) {
            XML_Node& xmlACChild = acNodePtr->child(i);
            stemp = xmlACChild.name();
            string nodeName = lowercase(stemp);
            /*
             * Process a binary salt field, or any of the other XML fields
             * that make up the Pitzer Database. Entries will be ignored
             * if any of the species in the entry isn't in the solution.
             */
            if (nodeName == "binaryneutralspeciesparameters") {
                readXMLBinarySpecies(xmlACChild);

            }
        }
    }

    /*
     * Go down the chain
     */
    GibbsExcessVPSSTP::initThermoXML(phaseNode, id);


}
//===================================================================================================================
// Update the activity coefficients
/*
 * This function will be called to update the internally stored
 * natural logarithm of the activity coefficients
 *
 *   he = X_A X_B(B + C X_B)
 *
 *  HKM - Checked for Transition
 */
void PhaseCombo_Interaction::s_update_lnActCoeff() const
{
    int delAK, delBK;
    doublereal XA, XB, g0 , g1;
    doublereal xx;
    doublereal T = temperature();
    doublereal RT = GasConstant*T;
    lnActCoeff_Scaled_.assign(m_kk, 0.0);

    for (size_t iK = 0; iK < m_kk; iK++) {
        /*
         *  We never sample the end of the mole fraction domains
         */
        xx = std::max(moleFractions_[iK], xxSmall);
        /*
         *  First wipe out the ideal solution mixing term
         */
        lnActCoeff_Scaled_[iK] = - log(xx);

        /*
         *  Then add in the Margules interaction terms. that's it!
         */
        for (size_t i = 0; i <  numBinaryInteractions_; i++) {
            size_t iA =  m_pSpecies_A_ij[i];
            size_t iB =  m_pSpecies_B_ij[i];
            delAK = 0;
            delBK = 0;
            if (iA==iK) {
                delAK = 1;
            } else if (iB==iK) {
                delBK = 1;
            }
            XA = moleFractions_[iA];
            XB = moleFractions_[iB];
            g0 = (m_HE_b_ij[i] - T * m_SE_b_ij[i]) / RT;
            g1 = (m_HE_c_ij[i] - T * m_SE_c_ij[i]) / RT;
            lnActCoeff_Scaled_[iK] += (delAK * XB + XA * delBK - XA * XB) * (g0 + g1 * XB) + XA * XB * (delBK - XB) * g1;
        }
    }
}
//===================================================================================================================
// Update the derivative of the log of the activity coefficients wrt T
/*
 * This function will be called to update the internally stored
 * natural logarithm of the activity coefficients
 *
 *   he = X_A X_B(B + C X_B)
 *
 *  HKM - Checked for Transition
 */
void PhaseCombo_Interaction::s_update_dlnActCoeff_dT() const
{
    int delAK, delBK;
    doublereal XA, XB, g0, g1;
    doublereal T = temperature();
    doublereal RTT = GasConstant*T*T;
    dlnActCoeffdT_Scaled_.assign(m_kk, 0.0);
    d2lnActCoeffdT2_Scaled_.assign(m_kk, 0.0);
    for (size_t iK = 0; iK < m_kk; iK++) {
        for (size_t i = 0; i <  numBinaryInteractions_; i++) {
            size_t iA =  m_pSpecies_A_ij[i];
            size_t iB =  m_pSpecies_B_ij[i];
            delAK = 0;
            delBK = 0;
            if (iA==iK) {
                delAK = 1;
            } else if (iB==iK) {
                delBK = 1;
            }
            XA = moleFractions_[iA];
            XB = moleFractions_[iB];
            g0 = -m_HE_b_ij[i] / RTT;
            g1 = -m_HE_c_ij[i] / RTT;
            double temp = (delAK * XB + XA * delBK - XA * XB) * (g0 + g1 * XB) + XA * XB * (delBK - XB) * g1;
            dlnActCoeffdT_Scaled_[iK] += temp;
            d2lnActCoeffdT2_Scaled_[iK] -= 2.0 * temp / T;
        }
    }
}
//====================================================================================================================
//
/*
 * HKM - Checked for Transition
 */
void PhaseCombo_Interaction::getdlnActCoeffdT(doublereal* dlnActCoeffdT) const
{
    s_update_dlnActCoeff_dT();
    for (size_t k = 0; k < m_kk; k++) {
        dlnActCoeffdT[k] = dlnActCoeffdT_Scaled_[k];
    }
}
//====================================================================================================================
//
/*
 * HKM - Checked for Transition
 */
void PhaseCombo_Interaction::getd2lnActCoeffdT2(doublereal* d2lnActCoeffdT2) const
{
    s_update_dlnActCoeff_dT();
    for (size_t k = 0; k < m_kk; k++) {
        d2lnActCoeffdT2[k] = d2lnActCoeffdT2_Scaled_[k];
    }
}
//====================================================================================================================

// Get the change in activity coefficients w.r.t. change in state (temp, mole fraction, etc.) along
// a line in parameter space or along a line in physical space
/*
 *
 * @param dTds           Input of temperature change along the path
 * @param dXds           Input vector of changes in mole fraction along the path. length = m_kk
 *                       Along the path length it must be the case that the mole fractions sum to one.
 * @param dlnActCoeffds  Output vector of the directional derivatives of the
 *                       log Activity Coefficients along the path. length = m_kk
 *  units are 1/units(s). if s is a physical coordinate then the units are 1/m.
 *
 * HKM - Checked for Transition
 */
void  PhaseCombo_Interaction::getdlnActCoeffds(const doublereal dTds, const doublereal* const dXds,
        doublereal* dlnActCoeffds) const
{
    int delAK, delBK;
    doublereal XA, XB, g0 , g1, dXA, dXB;
    doublereal T = temperature();
    doublereal RT = GasConstant*T;
    doublereal xx;

    //fvo_zero_dbl_1(dlnActCoeff, m_kk);
    s_update_dlnActCoeff_dT();

    for (size_t iK = 0; iK < m_kk; iK++) {
        /*
         *  We never sample the end of the mole fraction domains
         */
        xx = std::max(moleFractions_[iK], xxSmall);
        /*
         *  First wipe out the ideal solution mixing term
         */
        if (xx > xxSmall) {
            dlnActCoeffds[iK] += - 1.0 / xx;
        }

        for (size_t i = 0; i <  numBinaryInteractions_; i++) {
            size_t iA =  m_pSpecies_A_ij[i];
            size_t iB =  m_pSpecies_B_ij[i];

            delAK = 0;
            delBK = 0;

            if (iA==iK) {
                delAK = 1;
            } else if (iB==iK) {
                delBK = 1;
            }

            XA = moleFractions_[iA];
            XB = moleFractions_[iB];

            dXA = dXds[iA];
            dXB = dXds[iB];

            g0 = (m_HE_b_ij[i] - T * m_SE_b_ij[i]) / RT;
            g1 = (m_HE_c_ij[i] - T * m_SE_c_ij[i]) / RT;

            dlnActCoeffds[iK] += ((delBK-XB)*dXA + (delAK-XA)*dXB)*(g0+2*g1*XB) + (delBK-XB)*2*g1*XA*dXB
                                 + dlnActCoeffdT_Scaled_[iK]*dTds;
        }
    }
}
//====================================================================================================================
// Update the derivative of the log of the activity coefficients wrt the log of the corresponding species number density
/*
 * This function will be called to update the internally stored gradients of the
 * logarithm of the activity coefficients.  These are used in the determination
 * of the diffusion coefficients.
 *
 *   he = X_A X_B(B + C X_B)
 *
 *  This function only carries out the diagonal calculation
 *
 * HKM - Checked for Transition
 */
void PhaseCombo_Interaction::s_update_dlnActCoeff_dlnN_diag() const
{
    int delAK, delBK;
    doublereal XA, XB, XK, g0 , g1;
    doublereal T = temperature();
    doublereal RT = GasConstant*T;
    doublereal xx;

    dlnActCoeffdlnN_diag_.assign(m_kk, 0.0);

    for (size_t iK = 0; iK < m_kk; iK++) {

        XK = moleFractions_[iK];
        /*
         *  We never sample the end of the mole fraction domains
         */
        xx = std::max(moleFractions_[iK], xxSmall);
        /*
         *  First wipe out the ideal solution mixing term
         */
        // lnActCoeff_Scaled_[iK] = - log(xx);
        if (xx > xxSmall) {
            dlnActCoeffdlnN_diag_[iK] = - 1.0 + xx;
        }

        for (size_t i = 0; i <  numBinaryInteractions_; i++) {
            size_t iA =  m_pSpecies_A_ij[i];
            size_t iB =  m_pSpecies_B_ij[i];

            delAK = 0;
            delBK = 0;

            if (iA==iK) {
                delAK = 1;
            } else if (iB==iK) {
                delBK = 1;
            }

            XA = moleFractions_[iA];
            XB = moleFractions_[iB];

            g0 = (m_HE_b_ij[i] - T * m_SE_b_ij[i]) / RT;
            g1 = (m_HE_c_ij[i] - T * m_SE_c_ij[i]) / RT;

            dlnActCoeffdlnN_diag_[iK] += 2*(delBK-XB)*(g0*(delAK-XA)+g1*(2*(delAK-XA)*XB+XA*(delBK-XB)));
        }
        dlnActCoeffdlnN_diag_[iK] = XK*dlnActCoeffdlnN_diag_[iK];
    }

}
//====================================================================================================================
// Update the derivative of the log of the activity coefficients wrt ln N_k
/*
 * This function will be called to update the internally stored gradients of the
 * logarithm of the activity coefficients.  These are used in the determination
 * of the diffusion coefficients.
 *
 * HKM - Checked for Transition
 */
void PhaseCombo_Interaction::s_update_dlnActCoeff_dlnN() const
{
    doublereal delAK, delBK;
    double XA, XB, g0, g1, XM;
    double xx , delKM;
    double T = temperature();
    double RT = GasConstant*T;

    doublereal delAM, delBM;

    dlnActCoeffdlnN_.zero();

    /*
     *  Loop over the activity coefficient gamma_k
     */
    for (size_t iK = 0; iK < m_kk; iK++) {
        /*
         *  We never sample the end of the mole fraction domains
         */
        xx = std::max(moleFractions_[iK], xxSmall);

        for (size_t iM = 0; iM < m_kk; iM++) {
            XM = moleFractions_[iM];

            if (xx > xxSmall) {
                delKM = 0.0;
                if (iK == iM) {
                    delKM = 1.0;
                }
                // this gets multiplied by XM at the bottom
                dlnActCoeffdlnN_(iK,iM) += - delKM/XM + 1.0;
            }

            for (size_t i = 0; i <  numBinaryInteractions_; i++) {
                size_t iA =  m_pSpecies_A_ij[i];
                size_t iB =  m_pSpecies_B_ij[i];

                delAK = 0.0;
                delBK = 0.0;
                delAM = 0.0;
                delBM = 0.0;
                if (iA==iK) {
                    delAK = 1.0;
                } else if (iB==iK) {
                    delBK = 1.0;
                }
                if (iA==iM) {
                    delAM = 1.0;
                } else if (iB==iM) {
                    delBM = 1.0;
                }

                XA = moleFractions_[iA];
                XB = moleFractions_[iB];

                g0 = (m_HE_b_ij[i] - T * m_SE_b_ij[i]) / RT;
                g1 = (m_HE_c_ij[i] - T * m_SE_c_ij[i]) / RT;

                dlnActCoeffdlnN_(iK,iM) += g0*((delAM-XA)*(delBK-XB)+(delAK-XA)*(delBM-XB));
                dlnActCoeffdlnN_(iK,iM) += 2*g1*((delAM-XA)*(delBK-XB)*XB+(delAK-XA)*(delBM-XB)*XB+(delBM-XB)*(delBK-XB)*XA);

            }
            dlnActCoeffdlnN_(iK,iM) = XM * dlnActCoeffdlnN_(iK,iM);
        }
    }
}
//====================================================================================================================
void PhaseCombo_Interaction::s_update_dlnActCoeff_dlnX_diag() const
{
    doublereal XA, XB, g0 , g1;
    doublereal T = temperature();

    dlnActCoeffdlnX_diag_.assign(m_kk, 0.0);
    doublereal RT = GasConstant * T;

    for (size_t i = 0; i <  numBinaryInteractions_; i++) {
        size_t iA =  m_pSpecies_A_ij[i];
        size_t iB =  m_pSpecies_B_ij[i];

        XA = moleFractions_[iA];
        XB = moleFractions_[iB];

        g0 = (m_HE_b_ij[i] - T * m_SE_b_ij[i]) / RT;
        g1 = (m_HE_c_ij[i] - T * m_SE_c_ij[i]) / RT;

        dlnActCoeffdlnX_diag_[iA] += XA*XB*(2*g1*-2*g0-6*g1*XB);
        dlnActCoeffdlnX_diag_[iB] += XA*XB*(2*g1*-2*g0-6*g1*XB);
    }
    throw CanteraError("", "unimplemented");
}

//====================================================================================================================
//
/*
 * HKM - Checked for Transition
 */
void PhaseCombo_Interaction::getdlnActCoeffdlnN_diag(doublereal* dlnActCoeffdlnN_diag) const
{
    s_update_dlnActCoeff_dlnN_diag();
    for (size_t k = 0; k < m_kk; k++) {
        dlnActCoeffdlnN_diag[k] = dlnActCoeffdlnN_diag_[k];
    }
}
//====================================================================================================================
//
/*
 * HKM - Checked for Transition
 */
void PhaseCombo_Interaction::getdlnActCoeffdlnX_diag(doublereal* dlnActCoeffdlnX_diag) const
{
    s_update_dlnActCoeff_dlnX_diag();
    for (size_t k = 0; k < m_kk; k++) {
        dlnActCoeffdlnX_diag[k] = dlnActCoeffdlnX_diag_[k];
    }
}
//====================================================================================================================
//
/*
 * HKM - Checked for Transition
 */
void PhaseCombo_Interaction::getdlnActCoeffdlnN(const size_t ld, doublereal* dlnActCoeffdlnN)
{
    s_update_dlnActCoeff_dlnN();
    double* data =  & dlnActCoeffdlnN_(0,0);
    for (size_t k = 0; k < m_kk; k++) {
        for (size_t m = 0; m < m_kk; m++) {
            dlnActCoeffdlnN[ld * k + m] = data[m_kk * k + m];
        }
    }
}
//====================================================================================================================
//
/*
 * HKM - Checked for Transition
 */
void PhaseCombo_Interaction::resizeNumInteractions(const size_t num)
{
    numBinaryInteractions_ = num;
    m_HE_b_ij.resize(num, 0.0);
    m_HE_c_ij.resize(num, 0.0);
    m_HE_d_ij.resize(num, 0.0);
    m_SE_b_ij.resize(num, 0.0);
    m_SE_c_ij.resize(num, 0.0);
    m_SE_d_ij.resize(num, 0.0);
    m_VHE_b_ij.resize(num, 0.0);
    m_VHE_c_ij.resize(num, 0.0);
    m_VHE_d_ij.resize(num, 0.0);
    m_VSE_b_ij.resize(num, 0.0);
    m_VSE_c_ij.resize(num, 0.0);
    m_VSE_d_ij.resize(num, 0.0);

    m_pSpecies_A_ij.resize(num, -1);
    m_pSpecies_B_ij.resize(num, -1);
}
//====================================================================================================================

/*
 * Process an XML node called "binaryNeutralSpeciesParameters"
 * This node contains all of the parameters necessary to describe
 * the Margules Interaction for a single binary interaction
 * This function reads the XML file and writes the coefficients
 * it finds to an internal data structures.
 */
void PhaseCombo_Interaction::readXMLBinarySpecies(XML_Node& xmLBinarySpecies)
{
    string xname = xmLBinarySpecies.name();
    if (xname != "binaryNeutralSpeciesParameters") {
        throw CanteraError("PhaseCombo_Interaction::readXMLBinarySpecies",
                           "Incorrect name for processing this routine: " + xname);
    }
    double* charge = DATA_PTR(m_speciesCharge);
    string stemp;
    size_t nParamsFound;
    vector_fp vParams;
    string iName = xmLBinarySpecies.attrib("speciesA");
    if (iName == "") {
        throw CanteraError("PhaseCombo_Interaction::readXMLBinarySpecies", "no speciesA attrib");
    }
    string jName = xmLBinarySpecies.attrib("speciesB");
    if (jName == "") {
        throw CanteraError("PhaseCombo_Interaction::readXMLBinarySpecies", "no speciesB attrib");
    }
    /*
     * Find the index of the species in the current phase. It's not
     * an error to not find the species
     */
    size_t iSpecies = speciesIndex(iName);
    if (iSpecies == npos) {
        return;
    }
    string ispName = speciesName(iSpecies);
    if (charge[iSpecies] != 0) {
        throw CanteraError("PhaseCombo_Interaction::readXMLBinarySpecies", "speciesA charge problem");
    }
    size_t jSpecies = speciesIndex(jName);
    if (jSpecies == npos) {
        return;
    }
    string jspName = speciesName(jSpecies);
    if (charge[jSpecies] != 0) {
        throw CanteraError("PhaseCombo_Interaction::readXMLBinarySpecies", "speciesB charge problem");
    }

    resizeNumInteractions(numBinaryInteractions_ + 1);
    size_t iSpot = numBinaryInteractions_ - 1;
    m_pSpecies_A_ij[iSpot] = iSpecies;
    m_pSpecies_B_ij[iSpot] = jSpecies;

    size_t num = xmLBinarySpecies.nChildren();
    for (size_t iChild = 0; iChild < num; iChild++) {
        XML_Node& xmlChild = xmLBinarySpecies.child(iChild);
        stemp = xmlChild.name();
        string nodeName = lowercase(stemp);
        /*
         * Process the binary species interaction child elements
         */
        if (nodeName == "excessenthalpy") {
            /*
             * Get the string containing all of the values
             */
            ctml::getFloatArray(xmlChild, vParams, true, "toSI", "excessEnthalpy");
            nParamsFound = vParams.size();

            if (nParamsFound != 2) {
                throw CanteraError("PhaseCombo_Interaction::readXMLBinarySpecies::excessEnthalpy for " + ispName
                                   + "::" + jspName,
                                   "wrong number of params found");
            }
            m_HE_b_ij[iSpot] = vParams[0];
            m_HE_c_ij[iSpot] = vParams[1];
        }

        if (nodeName == "excessentropy") {
            /*
             * Get the string containing all of the values
             */
            ctml::getFloatArray(xmlChild, vParams, true, "toSI", "excessEntropy");
            nParamsFound = vParams.size();

            if (nParamsFound != 2) {
                throw CanteraError("PhaseCombo_Interaction::readXMLBinarySpecies::excessEntropy for " + ispName
                                   + "::" + jspName,
                                   "wrong number of params found");
            }
            m_SE_b_ij[iSpot] = vParams[0];
            m_SE_c_ij[iSpot] = vParams[1];
        }

        if (nodeName == "excessvolume_enthalpy") {
            /*
             * Get the string containing all of the values
             */
            ctml::getFloatArray(xmlChild, vParams, true, "toSI", "excessVolume_Enthalpy");
            nParamsFound = vParams.size();

            if (nParamsFound != 2) {
                throw CanteraError("PhaseCombo_Interaction::readXMLBinarySpecies::excessVolume_Enthalpy for " + ispName
                                   + "::" + jspName,
                                   "wrong number of params found");
            }
            m_VHE_b_ij[iSpot] = vParams[0];
            m_VHE_c_ij[iSpot] = vParams[1];
        }

        if (nodeName == "excessvolume_entropy") {
            /*
             * Get the string containing all of the values
             */
            ctml::getFloatArray(xmlChild, vParams, true, "toSI", "excessVolume_Entropy");
            nParamsFound = vParams.size();

            if (nParamsFound != 2) {
                throw CanteraError("PhaseCombo_Interaction::readXMLBinarySpecies::excessVolume_Entropy for " + ispName
                                   + "::" + jspName,
                                   "wrong number of params found");
            }
            m_VSE_b_ij[iSpot] = vParams[0];
            m_VSE_c_ij[iSpot] = vParams[1];
        }


    }
}
//====================================================================================================================
}
//======================================================================================================================