ctml.cpp

Go to the documentation of this file.

/**
 * @file ctml.cpp
 * Definitions for functions to read and write CTML.
 *
 */

/*
 * $Revision: 374 $
 * $Date: 2010-01-12 16:27:32 -0500 (Tue, 12 Jan 2010) $
 */

// Copyright 2002  California Institute of Technology


// turn off warnings under Windows
#ifdef WIN32
#pragma warning(disable:4786)
#pragma warning(disable:4503)
#endif

#include "ctml.h"

//@{
#define CTML_VERSION_1_4_1
//@}

#include "global.h"
#include "stringUtils.h"

#include <cctype>
#include <cstring>
#include <cstdlib>


using namespace std;
using namespace Cantera;

namespace ctml {

  static doublereal fpValue(std::string val) {
    return atof(stripws(val).c_str());
  }

  //  This function adds a child node with the name, "bool", with a value
  //  consisting of a single bool
  /*
   *   This function will add a child node to the current XML node, with the
   *   name "bool". It will have a title attribute, and the body
   *   of the XML node will be filled out with a single bool
   *
   *  Example:
   *
   * Code snipet:
   *       @verbatum
     const XML_Node &node;
     std::string titleString = "doSpecialOp";
     bool value = true;
     addBool(node, titleString, value);
     @endverbatum
   *
   *  Creates the following the snippet in the XML file:
   *  @verbatum
     <parentNode>
       <bool title="doSpecialOp" type="optional">
          true
       <\integer>
     <\parentNode>
   @endverbatum
   *
   *   @param node          reference to the XML_Node object of the parent XML element
   *   @param titleString   String name of the title attribute
   *   @param value         Value - single bool
   *
   * @todo I don't think this is used. Figure out what is used for writing bools,
   *       and codify that.
   */
  void addBool(Cantera::XML_Node& node, const std::string &title, const bool val) {
    std::string v = (val ? "true" : "false");
    XML_Node& f = node.addChild("bool", v);
    f.addAttribute("title", title);
  }

  //  This function adds a child node with the name, "integer", with a value
  //  consisting of a single integer
  /*
   *   This function will add a child node to the current XML node, with the
   *   name "integer". It will have a title attribute, and the body
   *   of the XML node will be filled out with a single integer
   *
   *  Example:
   *
   * Code snipet:
   *       @verbatum
   const XML_Node &node;
   std::string titleString = "maxIterations";
   int  value = 1000;
   std::string typeString = "optional";
   std::string units = "";
   addInteger(node, titleString, value, typeString, units);
   @endverbatum
   *
   *  Creates the following the snippet in the XML file:
   *  @verbatum
   <parentNode>
   <integer title="maxIterations" type="optional">
   100
   <\integer>
   <\parentNode>
   @endverbatum
   *
   *   @param node          reference to the XML_Node object of the parent XML element
   *   @param titleString   String name of the title attribute
   *   @param value         Value - single integer
   *   @param unitsString   String name of the Units attribute. The default is to
   *                        have an empty string.
   *   @param typeString    String type. This is an optional parameter. The default
   *                        is to have an empty string.
   */
  void addInteger(Cantera::XML_Node& node, const std::string &title, const int val, 
                  const std::string units, const std::string type) {
    XML_Node& f = node.addChild("integer",val);
    f.addAttribute("title",title);
    if (type != "") f.addAttribute("type",type);
    if (units != "") f.addAttribute("units",units);
  } 

  //  This function adds a child node with the name, "intArray", with a value
  //  consisting of a comma separated list of integers
  /*
   *   This function will add a child node to the current XML node, with the
   *   name "intArray". It will have a title attribute, and the body
   *   of the XML node will be filled out with a comma separated list of
   *   integers
   *
   *  Example:
   *
   *       @verbatum
     const XML_Node &node;
     std::string titleString = "additionalCases";
     int  n = 3;
     int cases[3] = [3, 6, 10];
     std::string typeString = "optional";
     std::string units = "";
     addIntegerArray(node, titleString, n, &cases[0], typeString, units);
     @endverbatum 
   *
   *  Creates the following the snippet in the XML file:
   *  @verbatum
     <parentNode>
       <intArray title="additionalCases" type="optional">
          3, 6, 10
       <\intArray>
     <\parentNode>
   @endverbatum
   *
   *
   *   @param node          reference to the XML_Node object of the parent XML element
   *   @param titleString   String name of the title attribute
   *   @param n             Length of the integer vector.
   *   @param values        Pointer to a vector of integers
   *   @param unitsString   String name of the Units attribute. This is an optional 
   *                        parameter. The default is to
   *                        have an empty string.
   *   @param typeString    String type. This is an optional parameter. The default
   *                        is to have an empty string.
   *   @param minval        Minimum allowed value of the int. This is an optional
   *                        parameter. The default is the
   *                        special double, Cantera::Undef, which means to ignore the
   *                        entry.
   *   @param maxval        Maximum allowed value of the int. This is an optional
   *                        parameter. The default is the
   *                        special double, Cantera::Undef, which means to ignore the
   *                        entry.
   *
   * @todo I don't think this is used. Figure out what is used for writing integers,
   *       and codify that. unitsString shouldn't be here, since it's an int.
   *       typeString should be codified as to its usage.
   */
  void addIntegerArray(Cantera::XML_Node& node, const std::string &title, const int n,
                       const int* const vals, const std::string units, const std::string type,
                       const doublereal minval, const doublereal maxval) {
    std::string fmt = "%8d";
    int i;
    std::string v = "";
    for (i = 0; i < n; i++) {
      v += int2str(vals[i],fmt);
      if (i == n-1) v += "\n"; 
      else if (i > 0 && (i+1) % 3 == 0) v += ",\n";
      else v += ", ";
    }
    XML_Node& f = node.addChild("intArray",v);
    f.addAttribute("title",title);
    if (type != "") f.addAttribute("type",type);        
    f.addAttribute("size",n);
    if (units != "") f.addAttribute("units",units);
    if (minval != Undef) f.addAttribute("min",minval);
    if (maxval != Undef) f.addAttribute("max",maxval);
  }

  //  This function adds a child node with the name, "float", with a value
  //  consisting of a single floating point number
  /*
   *   This function will add a child node to the current XML node, with the
   *   name "float". It will have a title attribute, and the body
   *   of the XML node will be filled out with a single float
   *
   *  Example:
   *
   * Code snipet:
   *       @verbatum
   const XML_Node &node;
   std::string titleString = "activationEnergy";
   double  value = 50.3;
   doublereal maxval = 1.0E3;
   doublereal minval = 0.0;
   std::string typeString = "optional";
   std::string unitsString = "kcal/gmol";
   addFloat(node, titleString, value, unitsString, typeString, minval, maxval);
   @endverbatum
   *
   *  Creates the following the snippet in the XML file:
   *  @verbatum
   <parentNode>
   <float title="activationEnergy" type="optional" units="kcal/gmol" min="0.0" max="1.0E3">
   50.3
   <\float>
   <\parentNode>
   @endverbatum
   *
   *   @param node          reference to the XML_Node object of the parent XML element
   *   @param titleString   String name of the title attribute
   *   @param value         Value - single integer
   *   @param unitsString   String name of the Units attribute. The default is to
   *                        have an empty string.
   *   @param typeString    String type. This is an optional parameter. The default
   *                        is to have an empty string.
   *
   * @todo I don't think this is used. Figure out what is used for writing floats,
   *       and codify that. minval and maxval should be codified.
   *       typeString should be codified as to its usage.
   */
  void addFloat(Cantera::XML_Node& node, const std::string &title, 
                const doublereal val, const std::string units, 
                const std::string type, const doublereal minval, 
                const doublereal maxval) {
    string fmt = "%17.9E";
#ifdef CTML_VERSION_1_4
    XML_Node& f = node.addChild("float",val,fmt);
    f.addAttribute("title",title);
#else
    XML_Node& f = node.addChild(title,val,fmt); 
#endif
    if (type != "") f.addAttribute("type",type);
    if (units != "") f.addAttribute("units",units);
    if (minval != Undef) f.addAttribute("min",minval);
    if (maxval != Undef) f.addAttribute("max",maxval);
  }

  //  This function adds a child node with the name, "floatArray", with a value
  //  consisting of a comma separated list of floats
  /*
   *   This function will add a child node to the current XML node, with the
   *   name "floatArray". It will have a title attribute, and the body
   *   of the XML node will be filled out with a comma separated list of
   *   integers
   *
   *  Example:
   *
   * Code snipet:
   *       @verbatum
     const XML_Node &node;
     std::string titleString = "additionalTemperatures";
     int  n = 3;
     int Tcases[3] = [273.15, 298.15, 373.15];
     std::string typeString = "optional";
     std::string units = "Kelvin";
     addFloatArray(node, titleString, n, &cases[0], typeString, units);
     @endverbatum
   *
   *  Creates the following the snippet in the XML file:
   *  @verbatum
     <parentNode>
       <floatArray title="additionalTemperatures" type="optional" units="Kelvin">
          273.15, 298.15, 373.15
       <\floatArray>
     <\parentNode>
   @endverbatum
   *
   *   @param node          reference to the XML_Node object of the parent XML element
   *   @param titleString   String name of the title attribute
   *   @param n             Length of the doubles vector.
   *   @param values        Pointer to a vector of doubles
   *   @param unitsString   String name of the Units attribute. This is an optional 
   *                        parameter. The default is to
   *                        have an empty string.
   *   @param typeString    String type. This is an optional parameter. The default
   *                        is to have an empty string.
   *   @param minval        Minimum allowed value of the int. This is an optional
   *                        parameter. The default is the
   *                        special double, Cantera::Undef, which means to ignore the
   *                        entry.
   *   @param maxval        Maximum allowed value of the int. This is an optional
   *                        parameter. The default is the
   *                        special double, Cantera::Undef, which means to ignore the
   *                        entry.
   *
   * @todo I don't think this is used. Figure out what is used for writing integers,
   *       and codify that. unitsString shouldn't be here, since it's an int.
   *       typeString should be codified as to its usage.
   */
  void addFloatArray(Cantera::XML_Node& node, const std::string &title, const int n, 
                     const doublereal* const vals, const std::string units, 
                     const std::string type,
                     const doublereal minval, const doublereal maxval) {
    std::string fmt = "%17.9E";
    int i;
    std::string v = "";
    for (i = 0; i < n; i++) {
      v += fp2str(vals[i],fmt);
      if (i == n-1) v += "\n"; 
      else if (i > 0 && (i+1) % 3 == 0) v += ",\n";
      else v += ", ";
    }
    XML_Node& f = node.addChild("floatArray",v);
    f.addAttribute("title",title);
    if (type != "") f.addAttribute("type",type);        
    f.addAttribute("size",n);
    if (units != "") f.addAttribute("units",units);
    if (minval != Undef) f.addAttribute("min",minval);
    if (maxval != Undef) f.addAttribute("max",maxval);
  }

  //  This function adds a child node with the name string with a string value
  //  to the current node
  /* 
   *   This function will add a child node to the current XML node, with the
   *   name "string". It will have a title attribute, and the body
   *   of the XML node will be filled out with the valueString argument verbatim.
   *
   *  Example:  
   *
   * Code snipet:
   *       @verbatum
   const XML_Node &node;
   addString(XML_Node& node, std::string titleString, std::string valueString, 
   std::string typeString);
   @endverbatum
   *
   *  Creates the following the snippet in the XML file:
   *  @verbatum
   <string title="titleString" type="typeString">
   valueString
   <\string>
   @endverbatum
   *
   *   @param node          reference to the XML_Node object of the parent XML element
   *   @param valueString   Value string to be used in the new XML node.
   *   @param titleString   String name of the title attribute
   *   @param typeString    String type. This is an optional parameter.
   */
  void addString(Cantera::XML_Node& node, const std::string &titleString, 
                 const std::string &valueString, 
                 const std::string typeString) {
    XML_Node& f = node.addChild("string", valueString);
    f.addAttribute("title", titleString);
    if (typeString != "") f.addAttribute("type", typeString);        
  }

  XML_Node* getByTitle(const Cantera::XML_Node& node, const std::string &title) {
    XML_Node* s = node.findByAttr("title", title);
    if (!s) return 0;
    if (s->parent() == &node) {
      return s;
    }
    return 0;
  }

  //  This function reads a child node with the name string and returns
  //  its xml value as the return string
  /*
   *   If the child XML_node named "name" doesn't exist, the empty string is returned.
   *  
   * Code snipet:
   *       @verbatum
   const XML_Node &parent;
   string name = "vacency_species";
   string valueString = getChildValue(parent, name
   std::string typeString);
   @endverbatum
   *
   *  returns valueString = "O(V)"
   * 
   *  from the following the snippet in the XML file:
   *
   *  @verbatum
   <vacencySpecies>
   O(V)
   <\vancencySpecies>
   @endverbatum
   *
   *   @param parent   parent reference to the XML_Node object of the parent XML element
   *   @param name     Name of the childe XML_Node to read the value from.
   *
   *   @return         String value of the child XML_Node
   */
  std::string getChildValue(const Cantera::XML_Node& parent, const std::string &nameString) {
    if (!parent.hasChild(nameString)) return "";
    return parent(nameString);
  }

  //  This function reads a child node with the name, "string", with a specific
  //  title attribute named "titleString"
  /* 
   *   This function will read a child node to the current XML node, with the
   *   name "string". It must have a title attribute, named titleString, and the body
   *   of the XML node will be read into the valueString output argument.
   *
   *  Example:  
   *
   * Code snipet:
   *       @verbatum
   const XML_Node &node;
   getString(XML_Node& node, std::string titleString, std::string valueString, 
   std::string typeString);
   @endverbatum
   *
   *  Reads the following the snippet in the XML file:
   *  @verbatum
   <string title="titleString" type="typeString">
     valueString
   <\string>
   @endverbatum
   *
   *   @param node          reference to the XML_Node object of the parent XML element
   *   @param titleString   String name of the title attribute of the child node
   *   @param valueString   Value string that is found in the child node. output variable
   *   @param typeString    String type. This is an optional output variable
   */
  void getString(const Cantera::XML_Node& node, const std::string &titleString, std::string& valueString, 
                 std::string& typeString) {
    valueString = "";
    typeString = "";
    XML_Node* s = getByTitle(node, titleString);
    if (s) 
      if (s->name() == "string") {
        valueString = (*s).value();
        typeString = (*s)["type"];
        return;
      }
  }


  //  Get a vector of integer values from a child element. 
  /* 
   *  Returns a std::map containing a keyed values for child XML_Nodes
   *  of the current node with the name, "integer". 
   *  In the keyed mapping there will be a list of titles vs. values
   *  for all of the XML nodes. 
   *  The integer XML_nodes are expected to be in a particular form created
   *  by the function addInteger(). One value per XML_node is expected.
   *  
   *
   *  Example:  
   *
   * Code snipet:
   *       @verbatum
     const XML_Node &State_XMLNode;
     std::map<std::string, integer> v;
     getinteger(State_XMLNode, v);
   @endverbatum
   *
   *  reads the corresponding XML file:
   *
   *  @verbatum
   <state>
     <integer title="i1">   1  <\integer>
     <integer title="i2">   2  <\integer>
     <integer title="i3">   3  <\integer>
   <\state>
   @endverbatum
   *
   *  Will produce the mapping:
   *
   *         v["i1"] = 1
   *         v["i2"] = 2
   *         v["i3"] = 3
   *
   *
   *   @param node     Current XML node to get the values from
   *   @param v        Output map of the results.
   */
  void getIntegers(const Cantera::XML_Node& node,
                   std::map<std::string, int>& v) {
    std::vector<XML_Node*> f;
    node.getChildren("integer",f);
    int n = static_cast<int>(f.size());
    integer x, x0, x1;
    std::string typ, title, vmin, vmax;
    for (int i = 0; i < n; i++) {
      const XML_Node& fi = *(f[i]);
      x = atoi(fi().c_str());
      title = fi["title"];
      vmin = fi["min"];
      vmax = fi["max"];
      if (vmin != "")
        x0 = atoi(vmin.c_str());
      if (fi["max"] != "")
        x1 = atoi(vmax.c_str());
      v[title] = x;
    }
  }


  //  Get a vector of floating-point values from a child element. 
  /* 
   *  Returns a std::map containing a keyed values for child XML_Nodes
   *  of the current node with the name, "float". 
   *  In the keyed mapping there will be a list of titles vs. values
   *  for all of the XML nodes. 
   *  The float XML_nodes are expected to be in a particular form created
   *  by the function addFloat(). One value per XML_node is expected.
   *  
   *
   *  Example:  
   *
   * Code snipet:
   *       @verbatum
     const XML_Node &State_XMLNode;
     std::map<std::string,double> v;
     bool convert = true;
     getFloats(State_XMLNode, v, convert);
   @endverbatum
   *
   *  reads the corresponding XML file:
   *
   *  @verbatum
   <state>
     <float title="a1" units="m3">   32.4 <\float>
     <float title="a2" units="cm3">   1.  <\float>
     <float title="a3">             100.  <\float>
   <\state>
   @endverbatum
   *
   *  Will produce the mapping:
   *
   *         v["a1"] = 32.4
   *         v["a2"] = 1.0E-6
   *         v["a3"] = 100.
   *
   *
   *   @param node     Current XML node to get the values from
   *   @param v        Output map of the results.
   *   @param convert  Turn on conversion to SI units
   */
  void getFloats(const Cantera::XML_Node& node, std::map<std::string, double>& v,
                 const bool convert) {
    std::vector<XML_Node*> f;
    node.getChildren("float",f);
    int n = static_cast<int>(f.size());
    doublereal x, x0, x1, fctr;
    std::string typ, title, units, vmin, vmax;
    for (int i = 0; i < n; i++) {
      const XML_Node& fi = *(f[i]);
      x = atof(fi().c_str());
      x0 = Undef;
      x1 = Undef;
      typ = fi["type"];
      title = fi["title"];
      units = fi["units"];
      vmin = fi["min"];
      vmax = fi["max"];
      if (vmin != "") {
        x0 = atof(vmin.c_str());
        if (x < x0 - Tiny) {
          writelog("\nWarning: value "+fi()+" is below lower limit of "
                   +vmin+".\n");
        }
      }
      if (fi["max"] != "") {
        x1 = atof(vmax.c_str());
        if (x > x1 + Tiny) {
          writelog("\nWarning: value "+fi()+" is above upper limit of "
                   +vmax+".\n");
        }
      }
      fctr = (convert ? toSI(units) : 1.0); // toSI(typ,units);
      v[title] = fctr*x;
    }
  }


  //  Get a floating-point value from a child element. 
  /* 
   *  Returns a double value for the child named 'name' of element 'parent'. If
   *  'type' is supplied and matches a known unit type, unit
   *  conversion to SI will be done if the child element has an attribute
   *  'units'.
   *
   *  Note, it's an error for the child element not to exist.
   *
   *  Example:  
   *
   * Code snipet:
   *       @verbatum
   const XML_Node &State_XMLNode;
   doublereal pres = OneAtm;
   if (state_XMLNode.hasChild("pressure")) {
   pres = getFloat(State_XMLNode, "pressure", "toSI");
   }
   @endverbatum
   *
   *  reads the corresponding XML file:
   *  @verbatum
   <state>
   <pressure units="Pa"> 101325.0 </pressure>
   <\state>
   @endverbatum
   *
   *   @param parent reference to the XML_Node object of the parent XML element
   *   @param name   Name of the XML child element
   *   @param type   String type. Currently known types are "toSI" and "actEnergy",
   *                 and "" , for no conversion. The default value is ""
   *                 which implies that no conversion is allowed.
   */
  doublereal getFloat(const Cantera::XML_Node& parent,
                      const std::string &name,
                      const std::string type) {
    if (!parent.hasChild(name)) 
      throw CanteraError("getFloat (called from XML Node \"" +
                         parent.name() + "\"): ",
                         "no child XML element named \"" + name + "\" exists");
    const XML_Node& node = parent.child(name);
    return getFloatCurrent(node, type);
  }

  doublereal getFloatCurrent(const Cantera::XML_Node& node,
                             const std::string type) {
    doublereal x, x0, x1, fctr = 1.0;
    string units, vmin, vmax;
    x = atof(node().c_str());
    x0 = Undef;
    x1 = Undef;
    units = node["units"];
    vmin = node["min"];
    vmax = node["max"];
    if (vmin != "") {
      x0 = atof(vmin.c_str());
      if (x < x0 - Tiny) {
        writelog("\nWarning: value "+node()+" is below lower limit of "
                 +vmin+".\n");
      }
    }
    if (node["max"] != "") {
      x1 = atof(vmax.c_str());
      if (x > x1 + Tiny) {
        writelog("\nWarning: value "+node()+" is above upper limit of "
                 +vmax+".\n");
      }
    }
    // Note, most type's of converters default to toSI() type atm.
    // This may change and become more specific in the future.
    if (type == "actEnergy" && units != "") {
      fctr = actEnergyToSI(units);
    } else if (type == "toSI" && units != "") {
      fctr = toSI(units);
    } else if (type == "temperature" && units != "") {
      fctr = toSI(units);
    } else if (type == "density" && units != "") {
      fctr = toSI(units);
    } else if (type == "pressure" && units != "") {
      fctr = toSI(units);
    } else if (type != "" && units != "") {
      fctr = toSI(units);
#ifdef DEBUG_MODE
      writelog("\nWarning: conversion toSI() was done on node value "  + node.name() + 
               "but wasn't explicity requested. Type was \"" + type + "\"\n");
#endif
    }
    // Note, below currently produces a lot of output due to transport blocks.
    // This needs to be addressed.
#ifdef DEBUG_MODE_MORE
    else if (type == "" && units != "") {
      writelog("\nWarning: XML node "  + node.name() + 
               "has a units attribute, \"" + units + "\","
               "but no conversion was done because the getFloat() command didn't have a type\n");
    }
#endif
    return fctr*x;
  }

  
  bool getOptionalFloat(const Cantera::XML_Node& parent,
                        const std::string &name,
                        doublereal &fltRtn,
                        const std::string type) {
    if (parent.hasChild(name)) {
      fltRtn= getFloat(parent, name, type);
      return true;
    }
    return false;
  }

  //  Get an optional floating-point value from a child element. 
  /* 
   *  Returns a doublereal value for the child named 'name' of element 'parent'. If
   *  'type' is supplied and matches a known unit type, unit
   *  conversion to SI will be done if the child element has an attribute
   *  'units'.
   *
   * 
   *
   *  Example:  
   *
   * Code snipet:
   *       @verbatim
   const XML_Node &State_XMLNode;
   doublereal pres = OneAtm;
   bool exists = getOptionalFloat(State_XMLNode, "pressure", pres, "toSI");
   @endverbatim
   *
   *  reads the corresponding XML file:
   *  @verbatim
   <state>
     <pressure units="Pa"> 101325.0 </pressure>
   <\state>
   @endverbatim
   *
   *   @param parent reference to the XML_Node object of the parent XML element
   *   @param name   Name of the XML child element
   *   @param fltRtn Float Return. It will be overridden if the XML 
   *                 element exists.
   *   @param type   String type. Currently known types are "toSI"
   *                 and "actEnergy",
   *                 and "" , for no conversion. The default value is "",
   *                 which implies that no conversion is allowed.
   *
   * @return returns true if the child element named "name" exists
   */
  doublereal getFloatDefaultUnits(const Cantera::XML_Node& parent, std::string name,
                                  std::string defaultUnits, std::string type) {

    doublereal fctr = 1.0;
    if (defaultUnits == "") {
      throw CanteraError("getFloatDefaultUnits",
                         "need to supply an actual value of defaultUnits"); 
    }
    if (type == "actEnergy") {
      fctr = actEnergyToSI(defaultUnits);
    } else if (type == "toSI") {
      fctr = toSI(defaultUnits);
    } else if (defaultUnits == "temperature") {
      fctr = toSI(defaultUnits);
    } else if (type == "density") {
      fctr = toSI(defaultUnits);
    } else if (type == "pressure") {
      fctr = toSI(defaultUnits);
    } else {
      throw CanteraError("getFloatDefaultUnits",
                         "type of units must be supplied and understood");
    }
    doublereal val = getFloat(parent, name, type);
    val /= fctr;
    return val;
  }

  bool getOptionalModel(const Cantera::XML_Node& parent, const std::string nodeName,
                        std::string &modelName) {
   if (parent.hasChild(nodeName)) {
     const XML_Node& node = parent.child(nodeName);
     modelName = node["model"];
     return true;
   }
   return false;
  }

  //  Get an integer value from a child element. 
  /* 
   *  Returns an integer value for the child named 'name' of element 'parent'.
   *
   *  Note, it's an error for the child element not to exist.
   *
   *  Example:  
   *
   * Code snipet:
   *       @verbatum
   const XML_Node &State_XMLNode;
   int number = 1;
   if (state_XMLNode.hasChild("NumProcs")) {
   number = getInteger(State_XMLNode, "numProcs");
   }
   @endverbatum
   *
   *  reads the corresponding XML file:
   *  @verbatum
   <state>
   <numProcs> 10 <numProcs/>
   <\state>
   @endverbatum
   *
   *   @param parent reference to the XML_Node object of the parent XML element
   *   @param name   Name of the XML child element
   */
  int getInteger(const Cantera::XML_Node& parent, std::string name) {
    if (!parent.hasChild(name)) { 
      throw CanteraError("getInteger (called from XML Node \"" +
                         parent.name() + "\"): ",
                         "no child XML element named " + name);
    }
    const XML_Node& node = parent.child(name);
    int x, x0, x1;
    string units, vmin, vmax;
    x = atoi(node().c_str());
    x0 = -9999999;
    x1 =  9999999;
    vmin = node["min"];
    vmax = node["max"];
    if (vmin != "") {
      x0 = atoi(vmin.c_str());
      if (x < x0) {
        writelog("\nWarning: value "+node()+" is below lower limit of "
                 +vmin+".\n");
      }
    }
    if (node["max"] != "") {
      x1 = atoi(vmax.c_str());
      if (x > x1) {
        writelog("\nWarning: value "+node()+" is above upper limit of "
                 +vmax+".\n");
      }
    }
    return x;
  }

  //  This function reads the current node or a  child node of the current node
  //  with the default name, "floatArray", with a value field
  //  consisting of a comma separated list of floats
  /*
   *   This function will read either the current XML node or a  child node
   *   to the current XML node, with the
   *   name "floatArray". It will have a title attribute, and the body
   *   of the XML node will be filled out with a comma separated list of
   *   doublereals.
   *     Get an array of floats from the XML Node. The argument field
   *   is assumed to consist of an arbitrary number of comma
   *   separated floats, with an arbitrary amount of white space
   *   separating each field.
   *      If the node array has an units attribute field, then
   *   the units are used to convert the floats, iff convert is true.
   *
   *  Example:  
   *
   * Code snipet:
   *       @verbatum
     const XML_Node &State_XMLNode;
     vector_fp v;
     bool convert = true;
     unitsString = "";
     nodeName="floatArray";
     getFloatArray(State_XMLNode, v, convert, unitsString, nodeName);
   @endverbatum
   *
   *  reads the corresponding XML file:
   *
   *  @verbatum
   <state>
     <floatArray  units="m3">   32.4, 1, 100. <\floatArray>
   <\state>
   @endverbatum
   *
   *  Will produce the vector
   *
   *         v[0] = 32.4
   *         v[1] = 1.0
   *         v[2] = 100.
   *
   *
   *   @param  node         XML parent node of the floatArray
   *   @param  v            Output vector of floats containing the floatArray information.
   *   @param  convert      Conversion to SI is carried out if this boolean is
   *                        True. The default is true.
   *   @param  unitsString  String name of the type attribute. This is an optional 
   *                        parameter. The default is to have an empty string.
   *                        The only string that is recognized is actEnergy. 
   *                        Anything else has no effect. This affects what
   *                        units converter is used.
   *   @param  nodeName     XML Name of the XML node to read. 
   *                        The default value for the node name is floatArray
   *
   *   @return              Returns the number of floats read
   */
  int  getFloatArray(const Cantera::XML_Node& node, Cantera::vector_fp& v, 
                     const bool convert, const std::string unitsString,
                     const std::string nodeName) {
    string::size_type icom;
    string numstr;
    doublereal dtmp;
    string nn = node.name();
    const Cantera::XML_Node *readNode = &node;
    if (nn != nodeName) { 
      vector<Cantera::XML_Node *> ll;  
      node.getChildren(nodeName, ll);
      if (ll.size() == 0) {
        throw CanteraError("getFloatArray",
                           "wrong xml element type/name: was expecting "
                         + nodeName + "but accessed " + node.name());
      } else {
        readNode = ll[0];
      }
    }

    v.clear();
    doublereal vmin = Undef, vmax = Undef;

    doublereal funit = 1.0;
    /*
     * Get the attributes field, units, from the XML node
     */
    std::string units = (*readNode)["units"];
    if (units != "" && convert) {
      if (unitsString == "actEnergy" && units != "") {
        funit = actEnergyToSI(units);
      } else if (unitsString != "" && units != "") {
        funit = toSI(units);
      }
    }

    if ((*readNode)["min"] != "") 
      vmin = atofCheck((*readNode)["min"].c_str());
    if ((*readNode)["max"] != "") 
      vmax = atofCheck((*readNode)["max"].c_str());

    doublereal vv;
    std::string val = readNode->value();
    while (1 > 0) {
      icom = val.find(',');
      if (icom != string::npos) {
        numstr = val.substr(0,icom);
        val = val.substr(icom+1,val.size());
        dtmp = atofCheck(numstr.c_str());
        v.push_back(dtmp);
      }
      else {
        /*
         * This little bit of code is to allow for the
         * possibility of a comma being the last 
         * item in the value text. This was allowed in
         * previous versions of Cantera, even though it
         * would appear to be odd. So, we keep the
         * possibilty in for backwards compatibility.
         */
        int nlen = strlen(val.c_str());
        if (nlen > 0) {
          dtmp = atofCheck(val.c_str());
          v.push_back(dtmp);
        }
        break;
      }
      vv = v.back();
      if (vmin != Undef && vv < vmin - Tiny) {
        writelog("\nWarning: value "+fp2str(vv)+
                 " is below lower limit of " +fp2str(vmin)+".\n");
      }
      if (vmax != Undef && vv > vmax + Tiny) {
        writelog("\nWarning: value "+fp2str(vv)+
                 " is above upper limit of " +fp2str(vmin)+".\n");
      }
    }
    int nv = v.size();
    for (int n = 0; n < nv; n++) {
      v[n] *= funit;
    }
    return v.size();
  }

  // This routine is used to interpret the value portions of XML
  // elements that contain colon separated pairs.
  /*
   *  These are used, for example, in describing the element 
   *  composition of species.
   *
   *       <atomArray> H:4 C:1 <atomArray>
   *
   *  The string is first separated into a string vector according
   * to the location of white space. Then each string is again
   * separated into two parts according to the location of a
   * colon in the string. The first part of the string is
   * used as the key, while the second part of the string is
   * used as the value, in the return map.
   * It is an error to not find a colon in each string pair.
   *
   *  @param node Current node
   *  @param m    Output Map containing the pairs of values found
   *              in the XML Node
   */
  void getMap(const Cantera::XML_Node& node, std::map<std::string, std::string>& m) {
    std::vector<std::string> v;
    getStringArray(node, v);
    std::string key, val;
    int n = static_cast<int>(v.size());
    string::size_type icolon;
    for (int i = 0; i < n; i++) {
      icolon = v[i].find(":");
      if (icolon == string::npos) {
        throw CanteraError("getMap","missing colon in map entry ("
                           +v[i]+")");
      }
      key = v[i].substr(0,icolon);
      val = v[i].substr(icolon+1, v[i].size());
      m[key] = val;
    }
  }

  // This function interprets the value portion of an XML element
  // as a series of "Pairs" separated by white space.
  /*
   * Each pair consists of nonwhite-space characters.
   * The first ":" found in the pair string is used to separate
   * the string into two parts. The first part is called the "key"
   * The second part is called the "val".
   * String vectors of key[i] and val[i] are returned in the
   * argument list.
   * Warning: No spaces are allowed in each pair. Quotes get included as part
   *          of the string.
   *   Example: @verbatum
       <xmlNode> 
          red:112    blue:34
          green:banana
       </xmlNode> 
              @endverbatum
   * 
   * Returns:
   *          key       val
   *     0:   "red"     "112"
   *     1:   "blue"    "34"
   *     2:   "green"   "banana"
   *
   *
   *  @param node             XML Node 
   *  @param key              Vector of keys for each entry
   *  @param val              Vector of values for each entry
   *
   *  @return Returns the number of pairs found
   */
  int getPairs(const Cantera::XML_Node& node, std::vector<std::string>& key, 
                std::vector<std::string>& val) {
    vector<string> v;
    getStringArray(node, v);
    int n = static_cast<int>(v.size());
    string::size_type icolon;
    for (int i = 0; i < n; i++) {
      icolon = v[i].find(":");
      if (icolon == string::npos) {
        throw CanteraError("getPairs","Missing a colon in the Pair entry ("
                           +v[i]+")");
      }
      key.push_back(v[i].substr(0,icolon));
      val.push_back(v[i].substr(icolon+1, v[i].size()));
      //cout << "getPairs: " << key.back() << " " << val.back() << endl;
    }
    return n;
  }

  // This function interprets the value portion of an XML element
  // as a series of "Matrix ids and entries" separated by white space.
  /*
   * Each pair consists of nonwhite-space characters.
   * The first two ":" found in the pair string is used to separate
   * the string into three parts. The first part is called the first
   * key. The second part is the second key. Both parts must match
   * an entry in the keyString1 and keyString2, respectively,
   * in order to provide a location to
   * place the object in the matrix.
   * The third part is called the value. It is expected to be
   * a double. It is translated into a double and placed into the
   * correct location in the matrix.
   *
   * Warning: No spaces are allowed in each triplet. Quotes are part
   *          of the string.
   *   Example
   *         keyString = red, blue, black, green
   *    <xmlNode>
   *        red:green:112
   *        blue:black:3.3E-23
   *
   *    </xmlNode>
   *
   * Returns:
   *     retnValues(0, 3) = 112
   *     retnValues(1, 2) = 3.3E-23
   *
   *
   *  @param node          XML Node containing the information for the matrix
   *  @param keyStringRow  Key string for the row
   *  @param keyStringCol  Key string for the column entries
   *  @param returnValues  Return Matrix.
   *  @param convert       If this is true, and if the node has a units 
   *                       attribute, then conversion to si units is carried
   *                       out. Default is true.
   *  @param matrixSymmetric  If true entries are made so that the matrix
   *                       is always symmetric. Default is false.
   */
  void getMatrixValues(const Cantera::XML_Node& node,
                       const std::vector<std::string>& keyStringRow,
                       const std::vector<std::string>& keyStringCol,
                       Cantera::Array2D &retnValues, const bool convert,
                       const bool matrixSymmetric) {
    int szKey1 = keyStringRow.size();
    int szKey2 = keyStringCol.size();
    int nrow   = retnValues.nRows();
    int ncol   = retnValues.nColumns();
    if (szKey1 > nrow) {
      throw CanteraError("getMatrixValues", 
                         "size of key1 greater than numrows");
    }
    if (szKey2 > ncol) {
      throw CanteraError("getMatrixValues", 
                         "size of key2 greater than num cols");
    }
    if (matrixSymmetric) {
      if (nrow != ncol) {
        throw CanteraError("getMatrixValues", 
                           "nrow != ncol for a symmetric matrix");
      }
    }

    /*
     * Get the attributes field, units, from the XML node
     * and determine the conversion factor, funit.
     */
    doublereal funit = 1.0;
    string units = node["units"];
    if (units != "" && convert) {
      funit = toSI(units);
    }
        
    string key1;
    string key2;
    string rmm;
    string val;
    vector<string> v;
    getStringArray(node, v);
    int icol, irow;
    int n = static_cast<int>(v.size());
    string::size_type icolon;
    for (int i = 0; i < n; i++) {
      icolon = v[i].find(":");
      if (icolon == string::npos) {
        throw CanteraError("getMatrixValues","Missing two colons ("
                           +v[i]+")");
      }
      key1 = v[i].substr(0,icolon);
      rmm = v[i].substr(icolon+1, v[i].size());
      icolon = rmm.find(":");
      if (icolon == string::npos) {
        throw CanteraError("getMatrixValues","Missing one colon ("
                           +v[i]+")");
      }
      key2 = rmm.substr(0,icolon);
      val = rmm.substr(icolon+1, rmm.size());
      icol = -1;
      irow = -1;
      for (int j = 0; j < szKey1; j++) {
        if (key1 == keyStringRow[j]) {
          irow = j;
          break;
        }
      }
      if (irow == -1) {
        throw CanteraError("getMatrixValues","Row not matched by string: "
                           + key1);             
      }
      for (int j = 0; j < szKey2; j++) {
        if (key2 == keyStringCol[j]) {
          icol = j;
          break;
        }
      }
      if (icol == -1) {
        throw CanteraError("getMatrixValues","Col not matched by string: "
                           + key2);     
      }
      double dval = atofCheck(val.c_str());
      dval *= funit;
      /*
       * Finally, insert the value;
       */
      retnValues(irow, icol) = dval;
      if (matrixSymmetric) {
        retnValues(icol, irow) = dval;
      }
    }
  }

  // This function interprets the value portion of an XML element
  // as a string. It then separates the string up into tokens
  // according to the location of white space.
  /*
   * The separate tokens are returned in the string vector
   *
   * @param node   Node to get the value from
   * @param v      Output vector containing the string tokens 
   */
  void getStringArray(const Cantera::XML_Node& node, std::vector<std::string>& v) {
    std::string val = node.value();
    tokenizeString(val, v);
  }

  //  This function reads a child node with the default name, "floatArray", with a value
  //  consisting of a comma separated list of floats
  /*
   *   This function will read a child node to the current XML node, with the
   *   name "floatArray". It will have a title attribute, and the body
   *   of the XML node will be filled out with a comma separated list of
   *   doublereals.
   *     Get an array of floats from the XML Node. The argument field
   *   is assumed to consist of an arbitrary number of comma
   *   separated floats, with an arbitrary amount of white space
   *   separating each field.
   *      If the node array has an units attribute field, then
   *   the units are used to convert the floats, iff convert is true.
   *
   *  Example:  
   *
   * Code snipet:
   *       @verbatum
     const XML_Node &State_XMLNode;
     vector_fp v;
     bool convert = true;
     unitsString = "";
     nodeName="floatArray";
     getFloatArray(State_XMLNode, v, convert, unitsString, nodeName);
   @endverbatum
   *
   *  reads the corresponding XML file:
   *
   *  @verbatum
   <state>
     <floatArray  units="m3">   32.4, 1, 100. <\floatArray>
   <\state>
   @endverbatum
   *
   *  Will produce the vector
   *
   *         v[0] = 32.4
   *         v[1] = 1.0
   *         v[2] = 100.
   *
   *
   *   @param  node         XML parent node of the floatArray
   *   @param  v            Output vector of floats containing the floatArray information.
   *   @param  convert      Conversion to SI is carried out if this boolean is
   *                        True. The default is true.
   *   @param  typeString   String name of the type attribute. This is an optional 
   *                        parameter. The default is to have an empty string.
   *                        The only string that is recognized is actEnergy. 
   *                        Anything else has no effect. This affects what
   *                        units converter is used.
   *   @param  nodeName     XML Name of the XML node to read. 
   *                        The default value for the node name is floatArray
   */
  void getFunction(const Cantera::XML_Node& node, std::string& type, doublereal& xmin,
                   doublereal& xmax, Cantera::vector_fp& coeffs) {
    const XML_Node& c = node.child("floatArray");
    coeffs.clear();
    getFloatArray(c,coeffs);
    xmin = Cantera::Undef;
    xmin = Cantera::Undef;
    if (node["min"] != "") xmin = fpValue(node["min"]);
    if (node["max"] != "") xmax = fpValue(node["max"]);
    type = node["type"];
  }
}