/**
 *  @file importCTML.cpp
 *
 *     This file contains routines which are global routines, i.e.,
 *     not part of any object. These routine take as input, ctml
 *     pointers to data, and pointers to Cantera objects. The purpose
 *     of these routines is to intialize the Cantera objects with data
 *     from the ctml tree structures.
 */

/* $Author$
 * $Revision$
 * $Date$
 */

// Copyright 2002  California Institute of Technology

#ifdef WIN32
#pragma warning(disable:4786)
#pragma warning(disable:4503)
#endif

#include "importCTML.h"
#include "mix_defs.h"
#include <time.h>

//   STL includes
#include <map>
#include <string>
#include <vector>
using namespace std;

//   Cantera includes
#include "speciesThermoTypes.h"
#include "ThermoPhase.h"
#include "SurfPhase.h"
#include "ThermoFactory.h"
#include "SpeciesThermoFactory.h"
#include "KineticsFactory.h"
#include "reaction_defs.h"
#include "ReactionData.h"
#include "global.h"
#include "stringUtils.h"

#include "xml.h"
#include "ctml.h"
using namespace ctml;

#include <stdio.h>

// these are all used to check for duplicate reactions
vector< map<int, doublereal> > _reactiondata;
vector<string> _eqn;
vector_int _dup, _nr, _typ;
vector<bool> _rev;


namespace Cantera {

    /*
     * First we define a coule of typedef's which will
     * be used throught this file
     */
    typedef const vector<XML_Node*>    nodeset_t;
    typedef XML_Node             node_t;

    const doublereal DefaultPref = 1.01325e5;   // one atm


    static void split(const string& src, string& file, string& id) { 
	string::size_type ipound = src.find('#');
        if (ipound != string::npos) {
            id = src.substr(ipound+1,src.size());
            file = src.substr(0,ipound);
        }
        else {
            id = "";
            file = src;
        }
    }

    /**
     * This routine will locate an XML node in either the input
     * XML tree or in another input file specified by the file
     * part of the file_ID string. Searches are based on the
     * ID attribute of the XML element only.
     *
     * @param file_ID This is a concatenation of two strings seperated
     *                by the "#" character. The string before the
     *                pound character is the file name of an xml
     *                file to carry out the search. The string after
     *                the # character is the ID attribute 
     *                of the xml element to search for. 
     *                The string is interpreted as a file string if
     *                no # character is in the string.
     *
     * @param root    If the file string is empty, searches for the
     *                xml element with matching ID attribute are
     *                carried out from this XML node.
     */
    XML_Node* get_XML_Node(const string& file_ID, XML_Node* root) {
        string fname, idstr;
        XML_Node *db, *doc;
        split(file_ID, fname, idstr);
        if (fname == "") {
            if (!root) throw CanteraError("get_XML_Node","no file name given. file_ID = "+file_ID);
            db = root->findID(idstr, 3);
        } else {
	  doc = get_XML_File(fname);
	  if (!doc) throw CanteraError("get_XML_Node", "get_XML_File failed trying to open "+fname);
	  db = doc->findID(idstr, 3);
          if (!db) throw CanteraError("get_XML_Node", "id tag "+idstr+" not found.");
        }
        return db;
    }

   /**
     * This routine will locate an XML node in either the input
     * XML tree or in another input file specified by the file
     * part of the file_ID string. Searches are based on the
     * XML element name and the ID attribute of the XML element.
     * An exact match of both is usually required. However, the
     * ID attribute may be set to "", in which case the first
     * xml element with the correct element name will be returned.
     *
     * @param nameTarget This is the XML element name to look for.
     *                   
     * @param file_ID This is a concatenation of two strings seperated
     *                by the "#" character. The string before the
     *                pound character is the file name of an xml
     *                file to carry out the search. The string after
     *                the # character is the ID attribute 
     *                of the xml element to search for. 
     *                The string is interpreted as a file string if
     *                no # character is in the string.
     *
     * @param root    If the file string is empty, searches for the
     *                xml element with matching ID attribute are
     *                carried out from this XML node.
     */
    XML_Node* get_XML_NameID(const string& nameTarget,
			     const string& file_ID, 
			     XML_Node* root) {
        string fname, idTarget;
        XML_Node *db, *doc;
        split(file_ID, fname, idTarget);
        if (fname == "") {
	  if (!root) return 0;
	  db = root->findNameID(nameTarget, idTarget);
        } else {
	  doc = get_XML_File(fname);
	  if (!doc) return 0;
	  db = doc->findNameID(nameTarget, idTarget);
        }
        return db;
    }

    /** 
     * Install a NASA polynomial thermodynamic property
     * parameterization for species k.
     */
    static void installNasaThermo(SpeciesThermo& sp, int k, const XML_Node& f0, 
			   const XML_Node& f1) {
        doublereal tmin0, tmax0, tmin1, tmax1, tmin, tmid, tmax;

        tmin0 = fpValue(f0["Tmin"]);
        tmax0 = fpValue(f0["Tmax"]);
        tmin1 = fpValue(f1["Tmin"]);
        tmax1 = fpValue(f1["Tmax"]);

        vector_fp c0, c1;
        if (fabs(tmax0 - tmin1) < 0.01) {
            tmin = tmin0;
            tmid = tmax0;
            tmax = tmax1;
            getFloatArray(f0.child("floatArray"), c0, false);
            getFloatArray(f1.child("floatArray"), c1, false);
        }
        else if (fabs(tmax1 - tmin0) < 0.01) {
            tmin = tmin1;
            tmid = tmax1;
            tmax = tmax0;
            getFloatArray(f1.child("floatArray"), c0, false);
            getFloatArray(f0.child("floatArray"), c1, false);
        }
        else {
            throw CanteraError("installNasaThermo",
			       "non-continuous temperature ranges.");
        }
        array_fp c(15);
        c[0] = tmid;
        doublereal p0 = OneAtm;
        c[1] = c0[5];
        c[2] = c0[6];
        copy(c0.begin(), c0.begin()+5, c.begin() + 3);
        c[8] = c1[5];
        c[9] = c1[6];
        copy(c1.begin(), c1.begin()+5, c.begin() + 10);
        sp.install(k, NASA, c.begin(), tmin, tmax, p0);
    }


    /** 
     * Install a Shomate polynomial thermodynamic property
     * parameterization for species k.
     */
    static void installShomateThermo(SpeciesThermo& sp, int k, const XML_Node& f) {
        doublereal tmin, tmid, tmax;
        tmin = fpValue(f["Tmin"]);
        tmid = fpValue(f["Tmid"]);
        tmax = fpValue(f["Tmax"]);

        vector<XML_Node*> fa;
        f.getChildren("floatArray",fa);
        vector_fp c0, c1;
        getFloatArray(*fa[0], c0, false);
        getFloatArray(*fa[1], c1, false);
        array_fp c(15);
        c[0] = tmid;
        doublereal p0 = OneAtm;
        if ((*fa[0])["title"] == "low") {
            copy(c0.begin(), c0.end(), c.begin() + 1);
            copy(c1.begin(), c1.end(), c.begin() + 8);
        }
        else {
            copy(c1.begin(), c1.end(), c.begin() + 1);
            copy(c0.begin(), c0.end(), c.begin() + 8);
        }
        sp.install(k, SHOMATE, c.begin(), tmin, tmax, p0);
    }


    /** 
     * Install a constant-cp thermodynamic property
     * parameterization for species k.
     */
    static void installSimpleThermo(SpeciesThermo& sp, int k, const XML_Node& f) {
        doublereal tmin, tmax;
        tmin = fpValue(f["Tmin"]);
        tmax = fpValue(f["Tmax"]);
        if (tmax == 0.0) tmax = 1.0e30;

        vector_fp c(4);
        c[0] = getFloat(f, "t0", "-");
        c[1] = getFloat(f, "h0", "-");
        c[2] = getFloat(f, "s0", "-");
        c[3] = getFloat(f, "cp0", "-");
        doublereal p0 = OneAtm;
        sp.install(k, SIMPLE, c.begin(), tmin, tmax, p0);
    }

    /**
     * Install a species into a ThermoPhase object, which defines
     * the phase thermodynamics and speciation.
     *
     *  This routine first gathers the information from the Species XML
     *  tree and calls addUniqueSpecies() to add it to the
     *  ThermoPhase object, p.
     *  This information consists of:
     *         ecomp[] = element composition of species.
     *         chgr    = electric charge of species
     *         name    = string name of species
     *         sz      = size of the species 
     *                 (option double used a lot in thermo)
     *
     *  Then, the routine processes the "thermo" XML element and
     *  calls underlying utility routines to read the XML elements
     *  containing the thermodynamic information for the reference
     *  state of the species. Failures or lack of information trigger
     *  an "UnknownSpeciesThermoModel" exception being thrown.
     */
    bool installSpecies(int k, const XML_Node& s, thermo_t& p, 
			SpeciesThermo& spthermo, int rule) {

	// get the composition of the species
	const XML_Node& a = s.child("atomArray");
	map<string,string> comp;
	getMap(a, comp);

	// check that all elements in the species
	// exist in 'p'. If rule != 0, quietly skip 
        // this species if some elements are undeclared;
        // otherwise, throw an exception
	map<string,string>::const_iterator _b = comp.begin();
	for (; _b != comp.end(); ++_b) {
	  if (p.elementIndex(_b->first) < 0) {
	    if (rule == 0) 
		throw CanteraError("installSpecies", 
                    "Species " + s["name"] + 
                    " contains undeclared element " + _b->first);
	    else
		return false;
	  }
	}

	int m, nel = p.nElements();
	vector_fp ecomp(nel, 0.0);            
	for (m = 0; m < nel; m++) {
	  ecomp[m] = atoi(comp[p.elementName(m)].c_str());
	}

	/*
	 * Define a map and get all of the floats in the
	 * current XML species block
	 */
	doublereal chrg = 0.0;
	if (s.hasChild("charge")) chrg = getFloat(s, "charge");
	doublereal sz = 1.0;
	if (s.hasChild("size")) sz = getFloat(s, "size");

	p.addUniqueSpecies(s["name"], ecomp.begin(), chrg, sz);

	// get thermo.  We currently only support single-range Shomate
        // and const_cp, and dual-range NASA
	if (!s.hasChild("thermo")) {
	  throw 
	    UnknownSpeciesThermoModel("installSpecies", s["name"], "missing");
	  
	}
	const XML_Node& thermo = s.child("thermo");
	const vector<XML_Node*>& tp = thermo.children();
	int nc = tp.size();
	if (nc == 1) {
	  const XML_Node& f = *tp[0];
	  if (f.name() == "Shomate") {
	    installShomateThermo(spthermo, k, f);
	  }
	  else if (f.name() == "const_cp") {
	    installSimpleThermo(spthermo, k, f);
	  }
	  else {
	    UnknownSpeciesThermoModel("installSpecies", s["name"], f.name());
	  }
	}
	else if (nc == 2) {
	  const XML_Node& f0 = *tp[0];
	  const XML_Node& f1 = *tp[1];
	  if (f0.name() == "NASA" && f1.name() == "NASA") {
	    installNasaThermo(spthermo, k, f0, f1);
	  } else {
	    UnknownSpeciesThermoModel("installSpecies", s["name"], 
				      f0.name() + f1.name());
	  }
	}
	else {
	    UnknownSpeciesThermoModel("installSpecies", s["name"], 
				      "multiple");
	}
	return true;
    }


    /**
     * Get the reactants or products of a reaction. The information
     * is returned in the spnum, stoich, and order vectors. The
     * length of the vectors is the number of different types of
     * reactants or products found for the reaction.
     *
     * Input
     * --------
     *  rxn -> xml node pointing to the reaction element
     *         in the xml tree.
     *  kin -> Reference to the kinetics object to install
     *         the information into.
     *  rp = 1 -> Go get the reactants for a reaction
     *      -1 -> Go get the products for a reaction
     *  default_phase = String name for the default phase
     *          to loop up species in.
     *  Output
     * -----------
     *  spnum = vector of species numbers found. 
     *          Length is number of reactants or products. 
     *  stoich = stoichiometric coefficient of the reactant or product
     *          Length is number of reactants or products. 
     *  order = Order of the reactant and product in the reaction
     *          rate expression
     *  rule = If we fail to find a species, we will throw an error
     *         if rule != 1. If rule = 1, we simply return false, 
     *         allowing the calling routine to skip this reaction
     *         and continue.
     */
    static bool getReagents(const XML_Node& rxn, kinetics_t& kin, int rp,
        string default_phase, 
        vector_int& spnum, vector_int& stoich, vector_fp& order,
        int rule) {

        string rptype;

	/*
	 * The id of reactants and products are kept in child elements
	 * of reaction, named "reactants" and "products". We search
	 * the xml tree for these children based on the value of rp,
	 * and store the xml element pointer here.
	 */
        if (rp == 1) rptype = "reactants";
        else rptype = "products";
        const XML_Node& rg = rxn.child(rptype);

	/*
	 * The species and stoichiometric coefficient for the species
	 * are stored as a colon seperated pair. Get all of these 
	 * pairs in the reactions/products object.
	 */
        vector<string> key, val;
        getPairs(rg, key, val);

        int ns = key.size();

	/*
	 * Loop over each of the pairs and process them
	 */
        int stch, isp;
        doublereal ord;
        string ph, sp;
        map<string, int> speciesMap;
        for (int n = 0; n < ns; n++) {
            sp = key[n]; // sp is the string name for species
            ph = "";
	    /*
	     * Search for the species in the kinetics object using the
	     * member function kineticsSpeciesIndex(). We will search
	     * for the species in all phases defined in the kinetics operator. 
	     */
            isp = kin.kineticsSpeciesIndex(sp,"<any>");
            if (isp < 0) {
                if (rule == 1) 
                    return false;
                else {
                    throw CanteraError("getReagents",
                        "Undeclared reactant or product species "+sp);
                    return false;
                }
            }

	    /*
	     * For each reagent, we store the the species number, isp
	     * the stoichiometric coefficient, val[n], and the order
	     * species in the reaction rate expression. We assume mass
	     * action kinetics here, but will modify this below for
	     * specified species.
	     */
            spnum.push_back(isp);
            stch = atoi(val[n].c_str());
            stoich.push_back(stch);
            ord = doublereal(stch);
            order.push_back(ord);
            /*
             * Needed to process reaction orders below.
             */
            speciesMap[sp] = order.size();
        }

        /*
         * Check to see if reactant reaction orders have been specified. 
         */
        if (rp == 1 && rxn.hasChild("order")) {
            vector<XML_Node*> ord;
            rxn.getChildren("order",ord);
            int norder = ord.size();
            int loc;
            doublereal forder;
            for (int nn = 0; nn < norder; nn++) {
                const XML_Node& oo = *ord[nn];
                string sp = oo["species"];
                loc = speciesMap[sp];
                if (loc == 0) 
                    throw CanteraError("getReagents",
                        "reaction order specified for non-reactant: "
                        +sp);
                forder = fpValue(oo());
                if (forder < 0.0) {
                    throw CanteraError("getReagents",
                        "reaction order must be non-negative");
                }
                // replace the forward stoichiometric coefficient
                // stored above in 'order' with the specified
                // reaction order
                order[loc-1] = forder;
            }
        }
        return true;
    }
    

    /**
     * getArrhenius() parses the xml element called Arrhenius. 
     * The Arrhenius expression is
     * \f[        k =  A T^(b) exp (-E_a / RT). \f]
     */
    static void getArrhenius(const XML_Node& node, int& highlow, 
        doublereal& A, doublereal& b, doublereal& E) {
        
        if (node["name"] == "k0") 
            highlow = 0;
        else highlow = 1;
	/*
	 * We parse the children for the A, b, and E conponents.
	 */
        A = getFloat(node, "A", "-");
        b = getFloat(node, "b");
        E = getFloat(node, "E", "actEnergy");
        E /= GasConstant;
    }                

    /**
     * getStick() processes the element called Stick that specifies
     * sticking coefficients.
     */
    static void getStick(const XML_Node& node, Kinetics& kin,
        ReactionData& r, doublereal& A, doublereal& b, doublereal& E) {
        int nr = r.reactants.size();
        int k, klocal, not_surf = 0;
        int np = 0;
        doublereal f = 1.0;
        doublereal order;

        string spname = node["species"];
        ThermoPhase& th = kin.speciesPhase(spname);
        int isp = th.speciesIndex(spname);
        double mw = th.molecularWeights()[isp];

        // loop over the reactants
        for (int n = 0; n < nr; n++) {
            k = r.reactants[n];
            order = r.order[n];    // stoich coeff

            // get the phase species k belongs to
            np = kin.speciesPhaseIndex(k);  
            const ThermoPhase& p = kin.thermo(np); 

            // get the local index of species k in this phase
            klocal = p.speciesIndex(kin.kineticsSpeciesName(k));

            // if it is a surface species, divide f by the standard
            // concentration for this species, in order to convert
            // from concentration units used in the law of mass action
            // to coverages used in the sticking probability
            // expression
            if (p.eosType() == cSurf) {
                f /= pow(p.standardConcentration(klocal), order);
            }   
            // otherwise, increment the counter of bulk species
            else 
                not_surf++;
        }
        if (not_surf != 1) {
            throw CanteraError("getStick",
                "reaction probabilities can only be used in "
                "reactions with exactly 1 bulk species.");
        }

        doublereal cbar = sqrt(8.0*GasConstant/(Pi*mw));
        A = 0.25 * getFloat(node, "A", "-") * cbar * f;
        b = getFloat(node, "b") + 0.5;
        E = getFloat(node, "E", "actEnergy");
        E /= GasConstant;
    }                

    static void getCoverageDependence(const node_t& node, 
        thermo_t& surfphase, ReactionData& rdata) {
        vector<XML_Node*> cov;
        node.getChildren("coverage", cov);
        int k, nc = cov.size();
        doublereal e;
        string spname;
        if (nc > 0) {
            for (int n = 0; n < nc; n++) {
                const XML_Node& cnode = *cov[n];
                spname = cnode["species"];
                k = surfphase.speciesIndex(spname);
                rdata.cov.push_back(doublereal(k));
                rdata.cov.push_back(getFloat(cnode, "a"));
                rdata.cov.push_back(getFloat(cnode, "m"));
                e = getFloat(cnode, "e", "actEnergy");
                rdata.cov.push_back(e/GasConstant);
            }
        }
    }

    /**
     * Get falloff parameters for a reaction.
     */
    static void getFalloff(const node_t& f, ReactionData& rdata) {
        string type = f["type"];
        vector<string> p;
        getStringArray(f,p);
        vector_fp c;
        int np = p.size();
        for (int n = 0; n < np; n++) {
            c.push_back(fpValue(p[n]));
        }
        if (type == "Troe") {
            if (np == 4) rdata.falloffType = TROE4_FALLOFF;
            else rdata.falloffType = TROE3_FALLOFF;
        }
        else if (type == "SRI") {
            if (np == 5) rdata.falloffType = SRI5_FALLOFF;
            else rdata.falloffType = SRI3_FALLOFF;
        }
        rdata.falloffParameters = c;
    }

    /**
     * Get the enhanced collision efficiencies. It is assumed that the
     * reaction mechanism is homogeneous, so that all species belong
     * to phase(0) of 'kin'.
     */
    static void getEfficiencies(const node_t& eff, kinetics_t& kin, ReactionData& rdata) {

        // set the default collision efficiency
        rdata.default_3b_eff = fpValue(eff["default"]);

        vector<string> key, val;
        getPairs(eff, key, val);
        int ne = key.size();
        string nm;
        string phse = kin.thermo(0).id();
        int n, k;
        for (n = 0; n < ne; n++) { // ; bb != ee; ++bb) {
            nm = key[n];// bb->first;
            k = kin.kineticsSpeciesIndex(nm, phse);
            rdata.thirdBodyEfficiencies[k] = fpValue(val[n]); // bb->second;
        }
    }

    /**
     * Extract the rate coefficient for a reaction from the xml node, kf.
     * kf should point to a XML element named "rateCoeff".
     * rdata is the partially filled ReactionData object for the reaction.
     * This function will fill in more fields in the ReactionData object.
     * 
     */
    static void getRateCoefficient(const node_t& kf, kinetics_t& kin, 
        ReactionData& rdata, int negA) {

        int nc = kf.nChildren();
        nodeset_t& kf_children = kf.children();
        vector_fp clow(3,0.0), chigh(3,0.0);
        //        int nr = nReacMolecules(rdata);
        for (int m = 0; m < nc; m++) {
            const node_t& c = *kf_children[m];
            string nm = c.name();
            int highlow=0;

            if (nm == "Arrhenius") {
                vector_fp coeff(3);
                if (c["type"] == "stick") {
                    getStick(c, kin, rdata, coeff[0], coeff[1], coeff[2]);
                    chigh = coeff;
                }
                else {
                    getArrhenius(c, highlow, coeff[0], coeff[1], coeff[2]);
                    if (highlow == 1 || rdata.reactionType == THREE_BODY_RXN 
                        || rdata.reactionType == ELEMENTARY_RXN) 
                        chigh = coeff;
                    else clow = coeff;
                }
                if (rdata.reactionType == SURFACE_RXN) {
                    getCoverageDependence(c, 
                        kin.thermo(kin.surfacePhaseIndex()), rdata);
                }

                if (coeff[0] <= 0.0 && negA == 0) {
                    throw CanteraError("getRateCoefficient", 
                        "negative or zero A coefficient for reaction "+int2str(rdata.number));
                }
            }
            else if (nm == "falloff") {
                getFalloff(c, rdata);
            }
            else if (nm == "efficiencies") {
                getEfficiencies(c, kin, rdata);
            }
        }
	/*
	 * Store the coefficients in the ReactionData object for return
	 * from this function.
	 */
        if (rdata.reactionType == CHEMACT_RXN) 
            rdata.rateCoeffParameters = clow;        
        else
            rdata.rateCoeffParameters = chigh;

        if (rdata.reactionType == FALLOFF_RXN)
            rdata.auxRateCoeffParameters = clow;
        else if (rdata.reactionType == CHEMACT_RXN) 
            rdata.auxRateCoeffParameters = chigh; 
    }


    /**
     * Create a new ThermoPhase object and initializes it according
     * to the XML tree database. 
     * This routine first looks up the identity of the model for the
     * solution thermodynamics in the model attribute of the thermo
     * child of the xml phase node. Then, it does a string lookup on
     * the model to figure out what ThermoPhase derived class is
     * assigned. It mallocs a new instance of that class, and then
     * calls importPhase() to populate that class with the correct
     * parameters from the XML tree.
     */
    ThermoPhase* newPhase(XML_Node& xmlphase) {
        const XML_Node& th = xmlphase.child("thermo");
        string model = th["model"];
        ThermoPhase* t = newThermoPhase(model);
        importPhase(xmlphase, t);
        return t;
    }


    /**
     * Set the thermodynamic state.
     */
    static void setState(const XML_Node& phase, ThermoPhase* th) {
        if (!phase.hasChild("state")) return;
        const XML_Node state = phase.child("state");
        doublereal t, p, rho;
        string comp = getString(state,"moleFractions");
        if (comp != "") 
            th->setMoleFractionsByName(comp);
        else {
            comp = getString(state,"massFractions");
            if (comp != "") 
                th->setMassFractionsByName(comp);
        }
        if (state.hasChild("temperature")) {
            t = getFloat(state, "temperature", "temperature");
            th->setTemperature(t);
        }
        if (state.hasChild("pressure")) {
            p = getFloat(state, "pressure", "pressure");
            th->setPressure(p);
        }
        if (state.hasChild("density")) {
            rho = getFloat(state, "density", "density");
            th->setDensity(rho);
        }
        if (th->eosType() == cSurf && state.hasChild("coverages")) {
            comp = getString(state,"coverages");
            SurfPhase* s = (SurfPhase*)th;
            s->setCoveragesByName(comp);
        }
    }
        
    /**
     * Import a phase specification.
     *   Here we read an XML description of the phase.
     *   We import descriptions of the elements that make up the
     *   species in a phase.
     *   We import information about the species, including their
     *   reference state thermodynamic polynomials. We then freeze
     *   the state of the species, and finally call initThermo()
     *   a member function of the ThermoPhase object to "finish"
     *   the description.
     *
     *
     * @param phase 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 th   Pointer to the ThermoPhase object which will
     *             handle the thermodynamics for this phase.
     *             We initialize part of the Thermophase object
     *             here, especially for those objects which are
     *             part of the Cantera Kernel.
     */
    bool importPhase(XML_Node& phase, ThermoPhase* th) {

        int subflag = -1;

        if (phase.name() != "phase") 
            throw CanteraError("importPhase",
                "Current const XML_Node is not a phase element.");

        th->setID(phase.id());                // set the phase id

        // Number of spatial dimensions. Defaults to 3 (bulk phase)
        if (phase.hasAttrib("dim")) {
            int idim = intValue(phase["dim"]);
            if (idim < 1 || idim > 3)
                throw CanteraError("importPhase",
                    "unphysical number of dimensions: "+phase["dim"]);
            th->setNDim(idim);
        }
        else
            th->setNDim(3);     // default

	/**
	 * Equation of State: We initialize the ThermoPhase objects that
	 * we know about here, with additional parameters obtained from 
	 * the xml tree. EOS's that we don't know about don't create an
	 * error condition.
	 */
        if (phase.hasChild("thermo")) {
            const XML_Node& eos = phase.child("thermo");
            if (eos["model"] == "Incompressible") {
                if (th->eosType() == cIncompressible) {
                    doublereal rho = getFloat(eos, "density", "-");
                    //doublereal rho = d["density"];
                    th->setParameters(1, &rho);
                }
                else {
                    throw CanteraError("importCTML",
                        "wrong equation of state type");
                }
            }
            else if (eos["model"] == "SolidCompound") {
                if (th->eosType() == cSolidCompound) {
                    doublereal rho = getFloat(eos, "density", "-");
                    th->setDensity(rho);
                }
                else {
                    throw CanteraError("importCTML",
                        "wrong equation of state type");
                }
            }
            else if (eos["model"] == "Surface") {
                if (th->eosType() == cSurf) {
                    doublereal n = getFloat(eos, "site_density", "-");
                    if (n <= 0.0) 
                        throw CanteraError("importCTML",
                            "missing or negative site density");
                    th->setParameters(1, &n);
                }
                else {
                    throw CanteraError("importCTML",
                        "wrong equation of state type");
                }
            }
            else if (eos["model"] == "PureFluid") {
                if (th->eosType() == cPureFluid) {
                    subflag = atoi(eos["fluid_type"].c_str());
                    //doublereal h0 = getFloat(eos, "h0", "-");
                    //doublereal s0 = getFloat(eos, "s0", "-");
                    if (subflag < 0) 
                        throw CanteraError("importCTML",
                            "missing fluid type flag");
                    //doublereal c[3];
                    //c[0] = doublereal(subflag);
                    //c[1] = h0;
                    //c[2] = s0;
                    //th->setParameters(3, c);
                }
                else {
                    throw CanteraError("importCTML",
                        "wrong equation of state type");
                }
            }
        }


        /*************************************************
         *  Add elements.
         ************************************************/


        // get the declared element names
        XML_Node& elements = phase.child("elementArray");
        vector<string> enames;
        getStringArray(elements, enames);
        
        // // element database defaults to elements.xml
        string element_database = "elements.xml";
        if (elements.hasAttrib("datasrc")) 
            element_database = elements["datasrc"];
        XML_Node* doc = get_XML_File(element_database);
        XML_Node* dbe = &doc->child("ctml/elementData");

        int nel = enames.size();
        int i;
        string enm;
        for (i = 0; i < nel; i++) {
            XML_Node* e = dbe->findByAttr("name",enames[i]);
            if (e) {
                th->addUniqueElement(*e);
            }
            else {
                throw CanteraError("importPhase","no data for element "
                    +enames[i]);
            }
        }


        /***************************************************************
         * Add the species. First get the speciesArray element, then 
         * the species database.
         ***************************************************************/

        XML_Node* db = 0;
        vector<XML_Node*> sparrays;
        phase.getChildren("speciesArray", sparrays);
        int jsp, nspa = sparrays.size();
        vector<XML_Node*> dbases;
        vector_int sprule(nspa,0);

        for (jsp = 0; jsp < nspa; jsp++) {

            const XML_Node& species = *sparrays[jsp];

            if (species.hasChild("skip")) {
                const XML_Node& sk = species.child("skip");
                string eskip = sk["element"];
                if (eskip == "undeclared") {
                    sprule[jsp] = 1;
                }
            }
            string fname, idstr;
            
            db = get_XML_Node(species["datasrc"], &phase.root());
            //db = find_XML(species["datasrc"], &phase.root(), species["idRef"],
            //     "","speciesData");
            dbases.push_back(db);
        }


        /*******************************************************
         * Set the species thermo manager.
         * Function 'newSpeciesThermoMgr' looks at the species
         * in the database to see what thermodynamic property
         * parameterizations are used, and selects a class
         * that can handle the parameterizations found.
         ******************************************************/

        delete &th->speciesThermo();
        SpeciesThermo* spth = newSpeciesThermoMgr(dbases);
        th->setSpeciesThermo(spth);
        SpeciesThermo& spthermo = th->speciesThermo();

        map<string,bool> declared;
        int k = 0;
        for (jsp = 0; jsp < nspa; jsp++) {

            const XML_Node& species = *sparrays[jsp]; 
            db = dbases[jsp];

            /*
             * Get the array of species name strings.
             */                          
            vector<string> spnames;
            getStringArray(species, spnames);
            int nsp = spnames.size();

            if (nsp == 1 && spnames[0] == "all") {
                vector<XML_Node*> allsp;
                db->getChildren("species",allsp);
                nsp = allsp.size();
                spnames.resize(nsp);
                for (int nn = 0; nn < nsp; nn++) {
		  spnames[nn] = (*allsp[nn])["name"];
		}
            }

            string name;
            for (i = 0; i < nsp; i++) {
                name = spnames[i];
            
                // Check that every species is only declared once
                if (declared[name]) {
                    throw CanteraError("importPhase",
                        "duplicate species: "+name);
                }
                declared[name] = true;

                /*
                 * Find the species in the database by name.
                 */
                XML_Node* s = db->findByAttr("name",spnames[i]);
                if (s) {
                    if (installSpecies(k, *s, *th, spthermo, sprule[jsp])) 
                        ++k;
                }
                else {
                    throw CanteraError("importPhase","no data for species "
                        +name);
                }
            }
        }
        th->freezeSpecies();
        th->initThermo();
        setState(phase, th);

        th->saveSpeciesData(db);

        if (th->eosType() == cPureFluid) {
            doublereal dsub = doublereal(subflag);
            th->setParameters(1, &dsub);
        }

        return true;
    }        

    /**
     * This function returns true if two reactions are duplicates of
     * one another, and false otherwise.  The input arguments are two
     * maps from species number to stoichiometric coefficient, one for
     * each reaction. The reactions are considered duplicates if their
     * stoichiometric coefficients have the same ratio for all
     * species.
     */
    static doublereal isDuplicateReaction(map<int, doublereal>& r1, map<int, doublereal>& r2) {
        
        map<int, doublereal>::const_iterator b = r1.begin(), e = r1.end();
        int k1 = b->first;
        doublereal ratio = 0.0;
        if (r1[k1] == 0.0 || r2[k1] == 0.0) goto next;
        ratio = r2[k1]/r1[k1];
        ++b;
        for (; b != e; ++b) {
            k1 = b->first;
            if (r1[k1] == 0.0 || r2[k1] == 0.0) goto next;
            if (fabs(r2[k1]/r1[k1] - ratio) > 1.e-8) 
                goto next;
        }
        return ratio;
next:
        ratio = 0.0;
        b = r1.begin();
        k1 = b->first;
        if (r1[k1] == 0.0 || r2[-k1] == 0.0) return 0.0;
        ratio = r2[-k1]/r1[k1];
        ++b;
        for (; b != e; ++b) {
            k1 = b->first;
            if (r1[k1] == 0.0 || r2[-k1] == 0.0) return 0.0;
            if (fabs(r2[-k1]/r1[k1] - ratio) > 1.e-8) 
                return 0.0;
        }
        return ratio;
    }


    /**
     *  Install an individual reaction into the kinetics mechanism
     *  object, k. The data for the reaction is in the xml_node
     *  r. In other words, r points directly to an ctml element named
     *  "reaction". i refers to the number id of the reaction
     *  in the kinetics object.
     * other input
     * ------------ 
     *  rule = Provides a rule for specifying how to handle reactions
     *         which involve missing species.
     */
    static bool installReaction(int i, const XML_Node& r, Kinetics* k, 
        string default_phase, int rule, bool check_for_duplicates) {

        Kinetics& kin = *k;
	/*
	 *  We use the ReactionData object to store initial values read
	 *  in from the xml data. Then, when we have collected everything
	 *  we add the reaction to the kinetics object, k, at the end
	 * of the routine.
	 */
        ReactionData rdata;
        rdata.reactionType = ELEMENTARY_RXN;
        vector_int reac, prod;
        string eqn, type;
        int nn, eqlen;
        vector_fp dummy;

        int dup = 0;
        if (r.hasAttrib("duplicate")) dup = 1;
        int negA = 0;
        if (r.hasAttrib("negative_A")) negA = 1;


 	/*
	 * This seemingly simple expression goes and finds the child element,
	 * "equation". Then it treats all of the contents of the "equation"
	 * as a string, and returns it the variable eqn. We post process
	 * the string to convert [ and ] characters into < and >, which cannot be
         * stored in an XML file.
	 */
        if (r.hasChild("equation"))
            eqn = r("equation");
        else
            eqn = "<no equation>";

        eqlen = eqn.size();
        for (nn = 0; nn < eqlen; nn++) {
            if (eqn[nn] == '[') eqn[nn] = '<';
            if (eqn[nn] == ']') eqn[nn] = '>';
        }

        bool ok;
        // get the reactants
        ok = getReagents(r, kin, 1, default_phase, rdata.reactants, 
            rdata.rstoich, rdata.order, rule);

        /*
	 * Get the products. We store the id of products in rdata.products
	 */
        ok = ok && getReagents(r, kin, -1, default_phase, rdata.products, 
            rdata.pstoich, dummy, rule);
        if (!ok) {
            return false;
        }

        rdata.reversible = false;
        string isrev = r["reversible"];
        if (isrev == "yes" || isrev == "true")
            rdata.reversible = true;

        string typ = r["type"];

        /*
         * If reaction orders are specified, then this reaction
         * does not follow mass-action kinetics, and is not 
         * an elementary reaction. So check that it is not reversible,
         * since computing the reverse rate from thermochemistry only
         * works for elementary reactions. Set the type to global,
         * so that kinetics managers will know to process the reaction
         * orders.
         */
        if (r.hasChild("order")) {
            if (rdata.reversible == true) 
                throw CanteraError("installReaction",
                    "reaction orders may only be given for "
                    "irreversible reactions");
            //typ = "global";
        }


	/*
	 * Seaarch the reaction element for the attribute "type".
	 * If found, then branch on the type, to fill in appropriate
	 * fields in rdata. 
	 */

        if (typ == "falloff") {
            rdata.reactionType = FALLOFF_RXN;
            rdata.falloffType = SIMPLE_FALLOFF;
        }
        else if (typ == "chemAct") {
            rdata.reactionType = CHEMACT_RXN;
            rdata.falloffType = SIMPLE_FALLOFF;
        }
        else if (typ == "threeBody") {
            rdata.reactionType = THREE_BODY_RXN;
        }
        else if (typ == "surface") {
            rdata.reactionType = SURFACE_RXN;
        }
        //else if (typ == "global") {
        //    rdata.reactionType = GLOBAL_RXN;
        //}
        else if (typ != "")
            throw CanteraError("installReaction",
                "Unknown reaction type: " + typ);

        /*
         * Look for undeclared duplicate reactions.
         */
        if (check_for_duplicates) {
            doublereal c = 0.0;
            
            map<int, doublereal> rxnstoich;
            rxnstoich.clear();
            int nr = rdata.reactants.size();
            for (nn = 0; nn < nr; nn++) {
                rxnstoich[-1 - rdata.reactants[nn]] -= rdata.rstoich[nn];
            }
            int np = rdata.products.size();
            for (nn = 0; nn < np; nn++) {
                rxnstoich[rdata.products[nn]+1] += rdata.pstoich[nn];
            }
            int nrxns = _reactiondata.size();
            for (nn = 0; nn < nrxns; nn++) {
                if ((int(rdata.reactants.size()) == _nr[nn]) 
                    && (rdata.reactionType == _typ[nn])) {
                    c = isDuplicateReaction(rxnstoich, _reactiondata[nn]);
                    if (c > 0.0 
                        || (c < 0.0 && rdata.reversible)
                        || (c < 0.0 && _rev[nn])) {
                        if ((!dup || !_dup[nn])) {
                            string msg = string("Undeclared duplicate reactions detected: \n")
                                         +"Reaction "+int2str(nn+1)+": "+_eqn[nn]
                                         +"\nReaction "+int2str(i+1)+": "+eqn+"\n";
                            _reactiondata.clear();
                            _eqn.clear();
                            _rev.clear();
                            _nr.clear();
                            _typ.clear();
                            _dup.clear();
                            throw CanteraError("installReaction",msg);
                        }
                    }
                }
            }
            _dup.push_back(dup);
            _rev.push_back(rdata.reversible);
            _eqn.push_back(eqn);
            _nr.push_back(rdata.reactants.size());
            _typ.push_back(rdata.reactionType);
            _reactiondata.push_back(rxnstoich);
        }
        
        rdata.equation = eqn;
        rdata.number = i;
        rdata.rxn_number = i;

            
        getRateCoefficient(r.child("rateCoeff"), kin, rdata, negA);
	/*
	 * Ok we have read everything in about the reaction. Add it
	 * to the kinetics object by calling the Kinetics member function,
	 * addReaction()
	 */
        kin.addReaction(rdata);
        return true;
    }

   /**
     *  Take information from the XML tree, p, about reactions
     *  and install them into the kinetics object, kin. 
     *  default_phase is the default phase to assume when
     *  looking up species.
     *
     *  At this point, p usually refers to the phase xml element.
     *  One of the children of this element is reactionArray,
     *  the element which determines where in the xml file to
     *  look up the reaction rate data pertaining to the phase.
     *
     *  On return, if reaction instantiation goes correctly, return true.
     *  If there is a problem, return false.
     */
    bool installReactionArrays(const XML_Node& p, Kinetics& kin, 
        string default_phase, bool check_for_duplicates) {

        _eqn.clear();
        _dup.clear();
        _nr.clear();
        _typ.clear();
        _reactiondata.clear();
        _rev.clear();

        vector<XML_Node*> rarrays;
        int itot = 0;
	/*
	 * Search the children of the phase element for the
	 * xml element named reactionArray. If we can't find it,
	 * then return signaling having not found any reactions.
	 * Apparently, we allow multiple reactionArray elements here
	 * Each one will be processed sequentially, with the
	 * end result being purely additive.
	 */
        p.getChildren("reactionArray",rarrays);
        int na = rarrays.size();
        if (na == 0) return false;
        for (int n = 0; n < na; n++) {
	  /*
	   * Go get a reference to the current xml element, 
	   * reactionArray. We will process this element now.
	   */
	  const XML_Node& rxns = *rarrays[n];
	  /*
	   * The reactionArray element has an attribute called,
	   * datasrc. The value of the attribute is the xml
	   * element comprising the top of the
	   * tree of reactions for the phase.
	   * Find this datasrc element starting with the root
	   * of the current xml node.
	   */
          const XML_Node* rdata = get_XML_Node(rxns["datasrc"], &rxns.root());
	  //const XML_Node* rdata = find_XML(rxns["datasrc"],&rxns.root(),
          //			     "","","reactionData");
	  /*
	   * If the reactionArray element has a child element named
	   * "skip", and if the attribute of skip called "species" has
	   * a value of "undeclared", we will set rxnrule = 1.
	   * rxnrule is passed to the routine that parses each individual
	   * reaction. I believe what this means is that the parser will
	   * skip all reactions containing an undefined species without
	   * throwing an error condition.
	   */
	  int rxnrule = 0;
	  if (rxns.hasChild("skip")) {
	    const XML_Node& sk = rxns.child("skip");
	    string sskip = sk["species"];
	    if (sskip == "undeclared") {
	      rxnrule = 1;
	    }
	  }
	  int i, nrxns = 0;
	  /*
	   * Search for child elements called include. We only include
	   * a reaction if it's tagged by one of the include fields.
	   * Or, we include all reactions if there are no include fields.
	   */
	  vector<XML_Node*> incl;
	  rxns.getChildren("include",incl);
	  int ninc = incl.size();

	  vector<XML_Node*> allrxns;
	  rdata->getChildren("reaction",allrxns);
	  nrxns = allrxns.size();
	  // if no 'include' directive, then include all reactions
	  if (ninc == 0) {
	    for (i = 0; i < nrxns; i++) {
	      const XML_Node* r = allrxns[i];
	      if (r) {
		if (installReaction(itot, *r, &kin, 
                        default_phase, rxnrule, check_for_duplicates)) ++itot;
	      }
	    }
	  }
	  else {
	    for (int nii = 0; nii < ninc; nii++) {
	      const XML_Node& ii = *incl[nii];
	      string imin = ii["min"];
	      string imax = ii["max"];
	      for (i = 0; i < nrxns; i++) {
		const XML_Node* r = allrxns[i];
		string rxid;
		if (r) {
		  rxid = (*r)["id"];
		  /*
		   * To decide whether the reaction is included or not
		   * we do a lexical min max and operation. This 
		   * sometimes has surprising results.
		   */
		  if ((rxid >= imin) && (rxid <= imax)) {
		    if (installReaction(itot, *r, &kin, 
                            default_phase, rxnrule, check_for_duplicates)) ++itot;
		  }
		}
	      }
	    }
	  }
        }

	/*
	 * Finalize the installation of the kinetics, now that we know
	 * the true number of reactions in the mechanism, itot.
	 */
        kin.finalize();
        //writer = 0;
        _eqn.clear();
        _dup.clear();
        _nr.clear();
        _typ.clear();
        _reactiondata.clear();
        return true;
    }


    /**
     * Import a reaction mechanism for a phase or an interface.
     *
     * @param phase This is an xml node containing a description
     *              of a phase. Within the phase is a XML element
     *              called reactionArray containing the location
     *              of the description of the reactions that make
     *              up the kinetics object. 
     *              Also within the phase is an XML element called
     *              phaseArray containing a listing of other phases
     *              that participate in the kinetics mechanism.
     *
     * @param th    This is a list of ThermoPhase pointers containing
     *              the phases that participate in the kinetics
     *              reactions. 
     *
     * @param k     This is a pointer to the kinetics manager class
     *              that will be initialized with a kinetics 
     *              mechanism.
     */
    bool importKinetics(const XML_Node& phase, vector<ThermoPhase*> th, 
        Kinetics* k) {

        Kinetics& kin = *k;

        // This phase will be the default one
        string default_phase = phase["id"];

        bool check_for_duplicates = false;
        if (phase.parent()->hasChild("validate")) {
            const XML_Node& d = phase.parent()->child("validate");
            if (d["reactions"] == "yes") check_for_duplicates = true;
        }

        // if other phases are involved in the reaction mechanism,
        // they must be listed in a 'phaseArray' child
        // element. Homogeneous mechanisms do not need to include a
        // phaseArray element.

        vector<string> phase_ids;
        if (phase.hasChild("phaseArray")) {
            const XML_Node& pa = phase.child("phaseArray");
            getStringArray(pa, phase_ids);
        }
        phase_ids.push_back(default_phase);
            
        int np = phase_ids.size();
        int nt = th.size();

        // for each referenced phase, attempt to find its id among those
        // phases specified. 
        bool phase_ok;

        string phase_id;
        string msg = "";
        for (int n = 0; n < np; n++) {
            phase_id = phase_ids[n];
            phase_ok = false;

            // loop over the supplied 'ThermoPhase' objects representing
            // phases, to find an object with the same id.
            for (int m = 0; m < nt; m++) {
                if (th[m]->id() == phase_id) {
                    phase_ok = true;

                    // if no phase with this id has been added to 
                    //the kinetics manager yet, then add this one
                    if (kin.phaseIndex(phase_id) < 0) {
                        kin.addPhase(*th[m]);
                    }
                }
                msg += " "+th[m]->id();
            }
            if (!phase_ok) {
                throw CanteraError("importKinetics",
                    "phase "+phase_id+" not found. Supplied phases are:"+msg);
            }
        }

        // allocates arrays, etc. Must be called after the phases have 
        // been added to 'kin', so that the number of species in each
        // phase is known.
        kin.init();

        // Install the reactions.
        return installReactionArrays(phase, kin, default_phase, check_for_duplicates);
     }

    /**
     * Build a single-phase  ThermoPhase object with associated kinetics
     * mechanism.
     */
    bool buildSolutionFromXML(XML_Node& root, string id, string nm, 
        ThermoPhase* th, Kinetics* k) {
        XML_Node* x;
        x = get_XML_Node(string("#")+id, &root); 
        //x = find_XML("", &root, id, "", nm);
        if (!x) return false;
	/*
	 * Fill in the ThermoPhase object by querying the
	 * const XML_Node tree located at x.
	 */
        importPhase(*x, th);
	/*
	 * Create a vector of ThermoPhase pointers of length 1
	 * having the current th ThermoPhase as the entry.
	 */
        vector<ThermoPhase*> phases(1);
        phases[0] = th;
	/*
	 * Fill in the kinetics object k, by querying the
	 * const XML_Node tree located by x. The source terms and
	 * eventually the source term vector will be constructed
	 * from the list of ThermoPhases in the vector, phases.
	 */
        importKinetics(*x, phases, k);

        return true;
    }
}