/*
 *  @file importCTML.cpp
 *     This file contains a bunch of 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 "GasKineticsWriter.h"

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

#include <stdio.h>

GasKineticsWriter* writer = 0;

vector< map<int, doublereal> > _reactiondata;
vector<string> _eqn;
vector_int _dup;
vector<bool> _rev;


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

    /// Number of reactant molecules
    //static int nReacMolecules(ReactionData& r) {
    //    return accumulate(r.rstoich.begin(), r.rstoich.end(), 0);
    //}

    const doublereal DefaultPref = 1.01325e5;   // one atm

    /** 
     * Install a NASA polynomial thermodynamic property
     * parameterization for species k.
     */
    static void installNasaThermo(SpeciesThermo& sp, int k, XML_Node& f0, 
			   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, 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, 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
     */
    static bool installSpecies(int k, XML_Node& s, thermo_t& p, 
			SpeciesThermo& spthermo, int rule) {

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

	// check that all elements in the species
	// exist in 'p'
	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
	XML_Node& thermo = s.child("thermo");
	vector<XML_Node*> tp = thermo.children();
	int nc = tp.size();
	if (nc == 1) {
	  XML_Node& f = *tp[0];
	  if (f.name() == "Shomate") {
	    installShomateThermo(spthermo, k, f);
	  }
	  else if (f.name() == "const_cp") {
	    installSimpleThermo(spthermo, k, f);
	  }
	  else 
	      throw CanteraError("importCTML",
				 "Unsupported species thermo parameterization"
				 " for species "+s["name"]+": "+f.name());
	}
	else if (nc == 2) {
	  XML_Node& f0 = *tp[0];
	  XML_Node& f1 = *tp[1];
	  if (f0.name() == "NASA" && f1.name() == "NASA") {
	    installNasaThermo(spthermo, k, f0, f1);
	  }
	}
	else 
	    throw CanteraError("importCTML",
			       "Multiple thermo parameterizations given for "
			       "species "+s["name"]);

	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.
     */
    static bool getReagents(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";
        XML_Node& rg = rxn.child(rptype);
	/*
	 * The species and stoichiometric coefficient for the species
	 * are storred 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;
        for (int n = 0; n < ns; n++) {
            sp = key[n]; // sp is the string name for species
            ph = ""; //snode["phase"];
	    /*
	     * 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.
	     */
            spnum.push_back(isp);
            stch = atoi(val[n].c_str());
            stoich.push_back(stch);
            ord = doublereal(stch);
            order.push_back(ord);
        }
        return true;
    }
    

    /**
     * getArrhenious() parses the xml element called Arrhenius. 
     * Arrhenius expression is
     *         k =  A T^(b) exp (-Ea / RT).
     */
    static void getArrhenius(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;
    }                

    void getStick(XML_Node& node, doublereal mw, Kinetics& kin,
        ReactionData& r, doublereal& A, doublereal& b, doublereal& E) {
        int nr = r.reactants.size();
        int k, klocal, ns, not_surf = 0;
        int np = 0;
        doublereal f = 1.0;
        for (int n = 0; n < nr; n++) {
            k = r.reactants[n];
            ns = r.rstoich[n];
            //const ThermoPhase& p =
            np = kin.speciesPhaseIndex(k);
            const ThermoPhase& p = kin.thermo(np);
            klocal = p.speciesIndex(kin.kineticsSpeciesName(k));
            if (p.eosType() == cSurf) {
                f /= pow(p.standardConcentration(klocal),ns);
            }   
            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;
    }                


    /**
     * Get falloff parameters for a reaction.
     */
    static void getFalloff(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(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(node_t& kf, kinetics_t& kin, 
        ReactionData& rdata, int negA) {

        int nc = kf.nChildren();
        const 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++) {
            node_t& c = *kf_children[m];
            string nm = c.name();
            int highlow=0;

            if (nm == "Arrhenius") {
                vector_fp coeff(3);
                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 (coeff[0] <= 0.0 && negA == 0) {
                    throw CanteraError("getRateCoefficient", 
                        "negative or zero A coefficient for reaction "+int2str(rdata.number));
                }
            }
            else if (nm == "Stick") {
                vector_fp coeff(3);
                string spname = c["species"];
                ThermoPhase& th = kin.speciesPhase(spname);
                int isp = th.speciesIndex(spname);
                double mw = th.molecularWeights()[isp];
                getStick(c, mw, kin, rdata, coeff[0], coeff[1], coeff[2]);
                if (coeff[0] <= 0.0 && negA == 0) {
                    throw CanteraError("getRateCoefficient", 
                        "negative or zero A coefficient for reaction "+int2str(rdata.number));
                }
                chigh = coeff;
            }

            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.
     */
    ThermoPhase* newPhase(XML_Node& xmlphase) {
        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(XML_Node& phase, ThermoPhase* th) {
        if (!phase.hasChild("state")) return;
        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) {

        if (phase.name() != "phase") 
            throw CanteraError("importPhase",
                "Current 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")) {
            XML_Node& eos = phase.child("thermo");
            if (eos["model"] == "Incompressible") {
                if (th->eosType() == cIncompressible) {
                    //map<string, doublereal> d;
                    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");
                }
            }
        }


        /*************************************************
         *  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* db = find_XML(element_database,&phase.root(),"","",
            "elementData");

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


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

        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++) {

            XML_Node& species = *sparrays[jsp]; // phase.child("speciesArray");

            if (species.hasChild("skip")) {
                XML_Node& sk = species.child("skip");
                string eskip = sk["element"];
                if (eskip == "undeclared") {
                    sprule[jsp] = 1;
                }
            }
            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++) {

            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);
        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 bool 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 = r2[k1]/r1[k1];
        if (r1[k1] == 0.0 || r2[k1] == 0.0) return false;
        ++b;
        for (; b != e; ++b) {
            k1 = b->first;
            if (r1[k1] == 0.0 || r2[k1] == 0.0) return false;
            if (fabs(r2[k1]/r1[k1] - ratio) > 1.e-8) return false;
        }
        return true;
    }


    /**
     *  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, 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;
        }

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

        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[rdata.reactants[nn]] -= rdata.rstoich[nn];
            }
            int np = rdata.products.size();
            for (nn = 0; nn < np; nn++) {
                rxnstoich[rdata.products[nn]] += rdata.pstoich[nn];
            }
            int nrxns = _reactiondata.size();
            for (nn = 0; nn < nrxns; 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();
                        _dup.clear();
                        throw CanteraError("installReaction",msg);
                    }
                }
            }
            _dup.push_back(dup);
            _rev.push_back(rdata.reversible);
            _eqn.push_back(eqn);
            _reactiondata.push_back(rxnstoich);
        }
        
        rdata.equation = eqn;
        rdata.reversible = false;
        rdata.number = i;
        rdata.rxn_number = i;
	/*
	 * Seaarch the reaction element for the attribute "type".
	 * If found, then branch on the type, to fill in appropriate
	 * fields in rdata. 
	 */
        string typ = r["type"];
        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 != "")
            throw CanteraError("installReaction",
                "Unknown reaction type: " + typ);
            
        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(XML_Node& p, Kinetics& kin, 
        string default_phase, bool check_for_duplicates) {

        _eqn.clear();
        _dup.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.
	   */
	  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.
	   */
	  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")) {
	    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++) {
	      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++) {
	      XML_Node& ii = *incl[nii];
	      string imin = ii["min"];
	      string imax = ii["max"];
	      for (i = 0; i < nrxns; i++) {
		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();
        _reactiondata.clear();
        return true;
    }


    /**
     * Import a reaction mechanism for a phase or an interface.
     */
    bool importKinetics(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")) {
            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")) {
            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;
        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]);
                    }
                }
            }
            if (!phase_ok) {
                throw CanteraError("importKinetics",
                    "phase "+phase_id+" not found.");
            }
        }

        // 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 solution.
     */
    bool buildSolutionFromXML(XML_Node& root, string id, string nm, 
        ThermoPhase* th, Kinetics* k) {
        XML_Node* x;
        x = find_XML("", &root, id, "", nm);
        if (!x) return false;
	/*
	 * Fill in the ThermoPhase object by querying the
	 * 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
	 * 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;
    }
}