Elements.cpp

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/**
 *  @file Elements.cpp
 *  This file contains a database of atomic weights.
 */

//  Copyright 2003  California Institute of Technology

#include "cantera/thermo/Elements.h"
#include "cantera/base/ctml.h"
#include "cantera/base/stringUtils.h"

using namespace std;

namespace Cantera
{

/*! Database for atomic molecular weights
 *  Values are taken from the 1989 Standard Atomic Weights, CRC
 *
 *  awTable[] is a static function with scope limited to this file.
 *  It can only be referenced via the LookupWtElements() function.
 *
 *  units = kg / kg-mol (or equivalently gm / gm-mol)
 *
 * This structure was picked because it's simple, compact, and extensible.
 */
struct awData {
    char name[4];         //!< Null Terminated name, First letter capitalized
    double atomicWeight;  //!< atomic weight in kg / kg-mol
};

/*!
 *  @var static struct awData aWTable[]
 *  \brief aWTable is a vector containing the atomic weights database.
 *
 *  The size of the table is given by the initial instantiation.
 */
static struct awData aWTable[] = {
    {"H",    1.00794},
    {"D",    2.0    },
    {"Tr",   3.0    },
    {"He",   4.002602},
    {"Li",   6.941  },
    {"Be",   9.012182},
    {"B",   10.811  },
    {"C",   12.011  },
    {"N",   14.00674},
    {"O",   15.9994 },
    {"F",   18.9984032},
    {"Ne",  20.1797 },
    {"Na",  22.98977},
    {"Mg",  24.3050 },
    {"Al",  26.98154},
    {"Si",  28.0855 },
    {"P",   30.97376},
    {"S",   32.066  },
    {"Cl",  35.4527 },
    {"Ar",  39.948  },
    {"K",   39.0983 },
    {"Ca",  40.078  },
    {"Sc",  44.95591},
    {"Ti",  47.88   },
    {"V",   50.9415 },
    {"Cr",  51.9961 },
    {"Mn",  54.9381 },
    {"Fe",  55.847  },
    {"Co",  58.9332 },
    {"Ni",  58.69   },
    {"Cu",  63.546  },
    {"Zn",  65.39   },
    {"Ga",  69.723  },
    {"Ge",  72.61   },
    {"As",  74.92159},
    {"Se",  78.96   },
    {"Br",  79.904  },
    {"Kr",  83.80   },
    {"Rb",  85.4678 },
    {"Sr",  87.62   },
    {"Y",   88.90585},
    {"Zr",  91.224  },
    {"Nb",  92.90638},
    {"Mo",  95.94   },
    {"Tc",  97.9072 },
    {"Ru", 101.07   },
    {"Rh", 102.9055 },
    {"Pd", 106.42   },
    {"Ag", 107.8682 },
    {"Cd", 112.411  },
    {"In", 114.82   },
    {"Sn", 118.710  },
    {"Sb", 121.75   },
    {"Te", 127.6    },
    {"I",  126.90447},
    {"Xe", 131.29   },
    {"Cs", 132.90543},
    {"Ba", 137.327  },
    {"La", 138.9055 },
    {"Ce", 140.115  },
    {"Pr", 140.90765},
    {"Nd", 144.24   },
    {"Pm", 144.9127 },
    {"Sm", 150.36   },
    {"Eu", 151.965  },
    {"Gd", 157.25   },
    {"Tb", 158.92534},
    {"Dy", 162.50   },
    {"Ho", 164.93032},
    {"Er", 167.26   },
    {"Tm", 168.93421},
    {"Yb", 173.04   },
    {"Lu", 174.967  },
    {"Hf", 178.49   },
    {"Ta", 180.9479 },
    {"W",  183.85   },
    {"Re", 186.207  },
    {"Os", 190.2    },
    {"Ir", 192.22   },
    {"Pt", 195.08   },
    {"Au", 196.96654},
    {"Hg", 200.59   },
    {"Ti", 204.3833 },
    {"Pb", 207.2    },
    {"Bi", 208.98037},
    {"Po", 208.9824 },
    {"At", 209.9871 },
    {"Rn", 222.0176 },
    {"Fr", 223.0197 },
    {"Ra", 226.0254 },
    {"Ac", 227.0279 },
    {"Th", 232.0381 },
    {"Pa", 231.03588},
    {"U",  238.0508 },
    {"Np", 237.0482 },
    {"Pu", 244.0482 }
};


//  Static function to look up an atomic weight
/*
 *   This static function looks up the argument string in the
 *   database above and returns the associated molecular weight.
 *   The data are from the periodic table.
 *
 *  Note: The idea behind this function is to provide a unified
 *        source for the element atomic weights. This helps to
 *        ensure that mass is conserved.
 *
 *  @param s  String, Only the first 3 characters are significant
 *
 *  @return
 *    Return value contains the atomic weight of the element
 *    If a match for the string is not found, a value of -1.0 is
 *    returned.
 *
 *  @exception CanteraError
 *    If a match is not found, a CanteraError is thrown as well
 */
doublereal Elements::LookupWtElements(const std::string& ename)
{
    int num = sizeof(aWTable) / sizeof(struct awData);
    string s3 = ename.substr(0,3);
    for (int i = 0; i < num; i++) {
        if (s3 == aWTable[i].name) {
            return aWTable[i].atomicWeight;
        }
    }
    throw CanteraError("LookupWtElements", "element not found");
    return -1.0;
}

doublereal LookupWtElements(const std::string& ename)
{
    int num = sizeof(aWTable) / sizeof(struct awData);
    string s3 = ename.substr(0,3);
    for (int i = 0; i < num; i++) {
        if (s3 == aWTable[i].name) {
            return aWTable[i].atomicWeight;
        }
    }
    throw CanteraError("LookupWtElements", "element not found");
    return -1.0;
}

//!  Exception class to indicate a fixed set of elements.
/*!
 *   This class is used to warn the user when the number of elements
 *   are changed after at least one species is defined.
 */
class ElementsFrozen : public CanteraError
{
public:
    //! Constructor for class
    /*!
     * @param func Function where the error occurred.
     */
    ElementsFrozen(string func)
        : CanteraError(func,
                       "elements cannot be added after species.") {}
};

/*
 *  Elements Class Constructor
 *    We initialize all internal variables to zero here.
 */
Elements::Elements() :
    m_mm(0),
    m_elementsFrozen(false),
    m_elem_type(0),
    numSubscribers(0)
{
    warn_deprecated("class Elements",
        "Functionality is now part of class Phase. "
        "To be removed after Cantera 2.2.");
}

/*
 * Elements Class Destructor
 *   If the number of subscribers is not zero, through an error.
 *   A logic problem has occurred.
 *
 *  @exception CanteraError
 */
Elements::~Elements()
{
    if (numSubscribers != 0) {
        throw CanteraError("~Elements", "numSubscribers not zero");
    }
}

Elements::Elements(const Elements& right) :
    m_mm(0),
    m_elementsFrozen(false),
    numSubscribers(0)
{
    *this = right;
}

Elements& Elements::operator=(const Elements& right)
{
    if (&right == this) {
        return *this;
    }

    m_mm             = right.m_mm;
    m_elementsFrozen = right.m_elementsFrozen;
    m_atomicWeights  = right.m_atomicWeights;
    m_atomicNumbers  = right.m_atomicNumbers;
    m_elementNames   = right.m_elementNames;
    m_entropy298     = right.m_entropy298;
    m_elem_type      = right.m_elem_type;
    numSubscribers = 0;

    return *this;
}



/*
 * freezeElements():
 *
 *   Set the freeze flag. This is a prerequesite to other
 *   activivities, i.e., this is done before species are defined.
 */
void Elements::freezeElements()
{
    m_elementsFrozen = true;
}

/*
 * elementIndex():
 *
 * Index of element named \c name. The index is an integer
 * assigned to each element in the order it was added,
 * beginning with 0 for the first element.  If \c name is not
 * the name of an element in the set, then the value -1 is
 * returned.
 *
 */
int Elements::elementIndex(const std::string& name) const
{
    for (int i = 0; i < m_mm; i++) {
        if (m_elementNames[i] == name) {
            return i;
        }
    }
    return -1;
}

/*
 *
 * Name of the element with index \c m.  @param m Element
 * index. If m < 0 or m >= nElements() an exception is thrown.
 */
string Elements::elementName(int m) const
{
    if (m < 0 || m >= nElements()) {
        throw CanteraError("Elements::elementName()", "out of bounds: " + int2str(m) + " " + int2str(nElements()));
    }
    return m_elementNames[m];
}


doublereal Elements::entropyElement298(int m) const
{
    AssertThrowMsg(m_entropy298[m] != ENTROPY298_UNKNOWN,
                   "Elements::entropy298",
                   "Entropy at 298 K of element is unknown");
    AssertTrace(m >= 0 && m < m_mm);
    return m_entropy298[m];
}
//====================================================================================================================
//! Return the element constraint type
/*!
 * Possible types include:
 *
 * CT_ELEM_TYPE_TURNEDOFF         -1
 * CT_ELEM_TYPE_ABSPOS           0
 * CT_ELEM_TYPE_ELECTRONCHARGE   1
 * CT_ELEM_TYPE_CHARGENEUTRALITY 2
 * CT_ELEM_TYPE_LATTICERATIO 3
 * CT_ELEM_TYPE_KINETICFROZEN 4
 * CT_ELEM_TYPE_SURFACECONSTRAINT 5
 * CT_ELEM_TYPE_OTHERCONSTRAINT  6
 *
 * The default is  CT_ELEM_TYPE_ABSPOS
 */
int Elements::elementType(int m) const
{
    return m_elem_type[m];
}
//====================================================================================================================
// Change the element type of the mth constraint
/*
 *  Reassigns an element type
 *
 *  @param m  Element index
 *  @param elem_type New elem type to be assigned
 *
 *  @return Returns the old element type
 */
int Elements::changeElementType(int m, int elem_type)
{
    int old =  m_elem_type[m];
    m_elem_type[m] = elem_type;
    return old;
}
//====================================================================================================================
/*
 *
 * Add an element to the current set of elements in the current object.
 * @param symbol  symbol string
 * @param weight  atomic weight in kg/kmol.
 *
 *  The default weight is a special value, which will cause the
 *  routine to look up the actual weight via a string lookup.
 *
 *  There are two interfaces to this routine. The XML interface
 *  looks up the required parameters for the regular interface
 *  and then calls the base routine.
 */
void Elements::addElement(const std::string& symbol, doublereal weight)
{
    if (weight == -12345.0) {
        weight = LookupWtElements(symbol);
        if (weight < 0.0) {
            throw ElementsFrozen("addElement");
        }
    }
    if (m_elementsFrozen) {
        throw ElementsFrozen("addElement");
        return;
    }
    m_atomicWeights.push_back(weight);
    m_elementNames.push_back(symbol);
    if (symbol == "E") {
        m_elem_type.push_back(CT_ELEM_TYPE_ELECTRONCHARGE);
    } else {
        m_elem_type.push_back(CT_ELEM_TYPE_ABSPOS);
    }

    m_mm++;
}
//===========================================================================================================
void Elements::addElement(const XML_Node& e)
{
    doublereal weight = fpValue(e["atomicWt"]);
    string symbol = e["name"];
    addElement(symbol, weight);
}
//===========================================================================================================
/*
 *  addUniqueElement():
 *
 * Add a unique element to the set. This routine will not allow
 * duplicate elements to be input.
 *
 * @param symbol  symbol string
 * @param weight  atomic weight in kg/kmol.
 *
 *
 *  The default weight is a special value, which will cause the
 *  routine to look up the actual weight via a string lookup.
 */
void Elements::addUniqueElement(const std::string& symbol, doublereal weight,
                                int atomicNumber_, doublereal entropy298,
                                int elem_type)
{
    if (weight == -12345.0) {
        weight =  LookupWtElements(symbol);
        if (weight < 0.0) {
            throw ElementsFrozen("addElement");
        }
    }
    /*
     * First decide if this element has been previously added
     * by conducting a string search. If it unique, add it to
     * the list.
     */
    int ifound = 0;
    int i = 0;
    for (vector<string>::const_iterator it = m_elementNames.begin();
            it < m_elementNames.end(); ++it, ++i) {
        if (*it == symbol) {
            ifound = 1;
            break;
        }
    }
    if (!ifound) {
        if (m_elementsFrozen) {
            throw ElementsFrozen("addElement");
            return;
        }
        m_atomicWeights.push_back(weight);
        m_elementNames.push_back(symbol);
        m_atomicNumbers.push_back(atomicNumber_);
        m_entropy298.push_back(entropy298);
        if (symbol == "E") {
            m_elem_type.push_back(CT_ELEM_TYPE_ELECTRONCHARGE);
        } else {
            m_elem_type.push_back(elem_type);
        }
        m_mm++;
    } else {
        if (m_atomicWeights[i] != weight) {
            throw CanteraError("AddUniqueElement",
                               "Duplicate Elements (" + symbol + ") have different weights");
        }
    }
}

/*
 * @todo call addUniqueElement(symbol, weight) instead of
 * addElement.
 */
void Elements::addUniqueElement(const XML_Node& e)
{
    doublereal weight = 0.0;
    if (e.hasAttrib("atomicWt")) {
        weight = fpValue(stripws(e["atomicWt"]));
    }
    int anum = 0;
    if (e.hasAttrib("atomicNumber")) {
        anum = atoi(stripws(e["atomicNumber"]).c_str());
    }
    string symbol = e["name"];
    doublereal entropy298 = ENTROPY298_UNKNOWN;
    if (e.hasChild("entropy298")) {
        XML_Node& e298Node = e.child("entropy298");
        if (e298Node.hasAttrib("value")) {
            entropy298 = fpValueCheck(stripws(e298Node["value"]));
        }
    }
    if (weight != 0.0) {
        addUniqueElement(symbol, weight, anum, entropy298);
    } else {
        addUniqueElement(symbol);
    }
}

// True if freezeElements has been called.
bool Elements::elementsFrozen() const
{
    return m_elementsFrozen;
}

/*
 * clear()
 *
 *   Remove all elements from the structure.
 */
void Elements::clear()
{
    m_mm = 0;
    m_atomicWeights.resize(0);
    m_elementNames.resize(0);
    m_entropy298.resize(0);
    m_elem_type.resize(0);
    m_elementsFrozen = false;
}

/*
 * ready():
 *
 * True if the elements have been frozen
 */
bool Elements::ready() const
{
    return m_elementsFrozen;
}


void Elements::addElementsFromXML(const XML_Node& phase)
{

    // get the declared element names
    if (! phase.hasChild("elementArray")) {
        throw CanteraError("Elements::addElementsFromXML",
                           "phase XML node doesn't have \"elementArray\" XML Node");
    }
    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("elementData");

    XML_Node& root = phase.root();
    XML_Node* local_db = 0;
    if (root.hasChild("elementData")) {
        local_db = &root.child("elementData");
    }

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

}

/*
 *  subscribe(), unsubscribe(), and reportSubscriptions():
 *
 *   Handles setting and reporting the number of subscriptions to this
 *   object.
 */
void Elements::subscribe()
{
    ++numSubscribers;
}
int Elements::unsubscribe()
{
    --numSubscribers;
    return numSubscribers;
}
int Elements::reportSubscriptions() const
{
    return numSubscribers;
}

/********************* GLOBAL STATIC SECTION **************************/
/*
 *  We keep track of a vector of pointers to element objects.
 *  Initially there are no Elements objects. Whenever one is created,
 *  the pointer to that object is added onto this list.
 */
vector<Elements*> Elements::Global_Elements_List;
/***********************************************************************/
}