Ejemplo n.º 1
0
void installElements(Phase& th, const XML_Node& phaseNode)
{
    // get the declared element names
    if (!phaseNode.hasChild("elementArray")) {
        throw CanteraError("installElements",
                           "phase XML node doesn't have \"elementArray\" XML Node");
    }
    XML_Node& elements = phaseNode.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 = phaseNode.root();
    XML_Node* local_db = 0;
    if (root.hasChild("elementData")) {
        local_db = &root.child("elementData");
    }

    for (size_t i = 0; i < enames.size(); i++) {
        // Find the element data
        XML_Node* e = 0;
        if (local_db) {
            e = local_db->findByAttr("name",enames[i]);
        }
        if (!e) {
            e = dbe->findByAttr("name",enames[i]);
        }
        if (!e) {
            throw CanteraError("addElementsFromXML","no data for element "
                               +enames[i]);
        }

        // Add the element
        doublereal weight = 0.0;
        if (e->hasAttrib("atomicWt")) {
            weight = fpValue(e->attrib("atomicWt"));
        }
        int anum = 0;
        if (e->hasAttrib("atomicNumber")) {
            anum = intValue(e->attrib("atomicNumber"));
        }
        string symbol = e->attrib("name");
        doublereal entropy298 = ENTROPY298_UNKNOWN;
        if (e->hasChild("entropy298")) {
            XML_Node& e298Node = e->child("entropy298");
            if (e298Node.hasAttrib("value")) {
                entropy298 = fpValueCheck(e298Node["value"]);
            }
        }
        th.addElement(symbol, weight, anum, entropy298);
    }
}
Ejemplo n.º 2
0
void Phase::addElement(const XML_Node& e)
{
    warn_deprecated("Phase::addElement(XML_Node&)",
                    "To be removed after Cantera 2.2.");
    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) {
        addElement(symbol, weight, anum, entropy298);
    } else {
        addElement(symbol);
    }
}
Ejemplo n.º 3
0
compositionMap parseCompString(const std::string& ss,
                               const std::vector<std::string>& names)
{
    compositionMap x;
    for (size_t k = 0; k < names.size(); k++) {
        x[names[k]] = 0.0;
    }

    size_t start = 0;
    size_t stop = 0;
    while (stop < ss.size()) {
        size_t colon = ss.find(':', start);
        if (colon == npos) {
            break;
        }
        size_t valstart = ss.find_first_not_of(" \t\n", colon+1);
        stop = ss.find_first_of(", ;\n\t", valstart);
        std::string name = stripws(ss.substr(start, colon-start));
        if (!names.empty() && x.find(name) == x.end()) {
            throw CanteraError("parseCompString",
                "unknown species '" + name + "'");
        }
        x[name] = fpValueCheck(ss.substr(valstart, stop-colon-1));
        start = ss.find_first_not_of(", ;\n\t", stop+1);
    }
    if (stop != npos && !stripws(ss.substr(stop)).empty()) {
        throw CanteraError("parseCompString", "Found non-key:value data "
            "in composition string: '" + ss.substr(stop) + "'");
    }
    return x;
}
Ejemplo n.º 4
0
void LatticeSolidPhase::setParametersFromXML(const XML_Node& eosdata)
{
    eosdata._require("model","LatticeSolid");
    XML_Node& la = eosdata.child("LatticeArray");
    std::vector<XML_Node*> lattices = la.getChildren("phase");
    size_t nl = lattices.size();
    m_nlattice = nl;
    for (size_t n = 0; n < nl; n++) {
        XML_Node& i = *lattices[n];
        m_lattice.push_back((LatticePhase*)newPhase(i));
    }
    std::vector<string> pnam;
    std::vector<string> pval;
    XML_Node& ls = eosdata.child("LatticeStoichiometry");
    int np = ctml::getPairs(ls, pnam, pval);
    theta_.resize(nl);
    for (int i = 0; i < np; i++) {
        double val = fpValueCheck(pval[i]);
        bool found = false;
        for (size_t j = 0; j < nl; j++) {
            ThermoPhase& tp = *(m_lattice[j]);
            string idj = tp.id();
            if (idj == pnam[i]) {
                theta_[j] = val;
                found = true;
                break;
            }
        }
        if (!found) {
            throw CanteraError("", "not found");
        }
    }

}
Ejemplo n.º 5
0
  /**
   * constructPDSSXML:
   *
   * Initialization of a PDSS_IonsFromNeutral object using an
   * xml file.
 
   * @param id  Optional parameter identifying the name of the
   *            phase. If none is given, the first XML
   *            phase element will be used.
   */
  void PDSS_IonsFromNeutral::constructPDSSXML(VPStandardStateTP *tp, int spindex, 
					      const XML_Node& speciesNode,
					      const XML_Node& phaseNode, std::string id) {
    const XML_Node *tn = speciesNode.findByName("thermo");
    if (!tn) {
      throw CanteraError("PDSS_IonsFromNeutral::constructPDSSXML",
                         "no thermo Node for species " + speciesNode.name());
    }
    std::string model = lowercase((*tn)["model"]);
    if (model != "ionfromneutral") {
      throw CanteraError("PDSS_IonsFromNeutral::constructPDSSXML",
                         "thermo model for species isn't IonsFromNeutral: "
                         + speciesNode.name());
    } 
    const XML_Node *nsm = tn->findByName("neutralSpeciesMultipliers");
    if (!nsm) {
      throw CanteraError("PDSS_IonsFromNeutral::constructPDSSXML",
                         "no Thermo::neutralSpeciesMultipliers Node for species " + speciesNode.name());
    }

    IonsFromNeutralVPSSTP *ionPhase = dynamic_cast<IonsFromNeutralVPSSTP *>(tp);
    if (!ionPhase) {
      throw CanteraError("PDSS_IonsFromNeutral::constructPDSSXML", "Dynamic cast failed");
    }
    neutralMoleculePhase_ = ionPhase->neutralMoleculePhase_;

    std::vector<std::string> key;
    std::vector<std::string> val;

    /*
     * 
     */
    numMult_ = ctml::getPairs(*nsm,  key, val);
    idNeutralMoleculeVec.resize(numMult_);
    factorVec.resize(numMult_);
    tmpNM.resize(neutralMoleculePhase_->nSpecies());

    for (int i = 0; i < numMult_; i++) {
      idNeutralMoleculeVec[i] = neutralMoleculePhase_->speciesIndex(key[i]);
      factorVec[i] =  fpValueCheck(val[i]);
    }
    specialSpecies_ = 0;
    const XML_Node *ss = tn->findByName("specialSpecies");
    if (ss) {
      specialSpecies_ = 1;
    }
   const XML_Node *sss = tn->findByName("secondSpecialSpecies");
    if (sss) {
      specialSpecies_ = 2;
    }
    add2RTln2_ = true;
    if (specialSpecies_ == 1) {
      add2RTln2_ = false;
    }
  
  }
Ejemplo n.º 6
0
doublereal strSItoDbl(const std::string& strSI)
{
    std::vector<std::string> v;
    tokenizeString(strSI, v);
    doublereal fp = 1.0;
    size_t n = v.size();
    if (n > 2 || n < 1) {
        throw CanteraError("strSItoDbl",
                           "number of tokens is too high");
    } else if (n == 2) {
        fp = toSI(v[1]);
    }
    doublereal val = fpValueCheck(v[0]);
    return val * fp;
}
Ejemplo n.º 7
0
int fillArrayFromString(const std::string& str,
                        doublereal* const a, const char delim)
{
    warn_deprecated("fillArrayFromString", "To be removed after Cantera 2.2.");
    std::string::size_type iloc;
    int count = 0;
    std::string num;
    std::string s = str;
    while (s.size() > 0) {
        iloc = s.find(delim);
        if (iloc > 0) {
            num = s.substr(0, iloc);
            s = s.substr(iloc+1,s.size());
        } else {
            num = s;
            s = "";
        }
        a[count] = fpValueCheck(num);
        count++;
    }
    return count;
}
Ejemplo n.º 8
0
compositionMap parseCompString(const std::string& ss,
                               const std::vector<std::string>& names)
{
    compositionMap x;
    for (size_t k = 0; k < names.size(); k++) {
        x[names[k]] = 0.0;
    }

    size_t start = 0;
    size_t stop = 0;
    size_t left = 0;
    while (stop < ss.size()) {
        size_t colon = ss.find(':', left);
        if (colon == npos) {
            break;
        }
        size_t valstart = ss.find_first_not_of(" \t\n", colon+1);
        stop = ss.find_first_of(", ;\n\t", valstart);
        std::string name = ba::trim_copy(ss.substr(start, colon-start));
        if (!names.empty() && x.find(name) == x.end()) {
            throw CanteraError("parseCompString",
                "unknown species '" + name + "'");
        }

        double value;
        try {
            value = fpValueCheck(ss.substr(valstart, stop-valstart));
        } catch (CanteraError&) {
            // If we have a key containing a colon, we expect this to fail. In
            // this case, take the current substring as part of the key and look
            // to the right of the next colon for the corresponding value.
            // Otherwise, this is an invalid composition string.
            std::string testname = ss.substr(start, stop-start);
            if (testname.find_first_of(" \n\t") != npos) {
                // Space, tab, and newline are never allowed in names
                throw;
            } else if (ss.substr(valstart, stop-valstart).find(':') != npos) {
                left = colon + 1;
                stop = 0; // Force another iteration of this loop
                continue;
            } else {
                throw;
            }
        }
        if (getValue(x, name, 0.0) != 0.0) {
            throw CanteraError("parseCompString",
                               "Duplicate key: '" + name + "'.");
        }

        x[name] = value;
        start = ss.find_first_not_of(", ;\n\t", stop+1);
        left = start;
    }
    if (left != start) {
        throw CanteraError("parseCompString", "Unable to parse key-value pair:"
            "\n'{}'", ss.substr(start, stop));
    }
    if (stop != npos && !ba::trim_copy(ss.substr(stop)).empty()) {
        throw CanteraError("parseCompString", "Found non-key:value data "
            "in composition string: '" + ss.substr(stop) + "'");
    }
    return x;
}
Ejemplo n.º 9
0
size_t Phase::addElement(const std::string& symbol, doublereal weight,
                         int atomic_number, doublereal entropy298,
                         int elem_type)
{
    // Look up the atomic weight if not given
    if (weight == 0.0) {
        try {
            weight = getElementWeight(symbol);
        } catch (CanteraError&) {
            // assume this is just a custom element with zero atomic weight
        }
    } else if (weight == -12345.0) {
        weight = getElementWeight(symbol);
    }

    // Try to look up the standard entropy if not given. Fail silently.
    if (entropy298 == ENTROPY298_UNKNOWN) {
        try {
            XML_Node* db = get_XML_File("elements.xml");
            XML_Node* elnode = db->findByAttr("name", symbol);
            if (elnode && elnode->hasChild("entropy298")) {
                entropy298 = fpValueCheck(elnode->child("entropy298")["value"]);
            }
        } catch (CanteraError&) {
        }
    }

    // Check for duplicates
    auto iter = find(m_elementNames.begin(), m_elementNames.end(), symbol);
    if (iter != m_elementNames.end()) {
        size_t m = iter - m_elementNames.begin();
        if (m_atomicWeights[m] != weight) {
            throw CanteraError("Phase::addElement",
                "Duplicate elements ({}) have different weights", symbol);
        } else {
            // Ignore attempt to add duplicate element with the same weight
            return m;
        }
    }

    // Add the new element
    m_atomicWeights.push_back(weight);
    m_elementNames.push_back(symbol);
    m_atomicNumbers.push_back(atomic_number);
    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++;

    // Update species compositions
    if (m_kk) {
        vector_fp old(m_speciesComp);
        m_speciesComp.resize(m_kk*m_mm, 0.0);
        for (size_t k = 0; k < m_kk; k++) {
            size_t m_old = m_mm - 1;
            for (size_t m = 0; m < m_old; m++) {
                m_speciesComp[k * m_mm + m] = old[k * (m_old) + m];
            }
            m_speciesComp[k * (m_mm) + (m_mm-1)] = 0.0;
        }
    }

    return m_mm-1;
}
Ejemplo n.º 10
0
void getMatrixValues(const XML_Node& node,
                     const std::vector<std::string>& keyStringRow,
                     const std::vector<std::string>& keyStringCol,
                     Array2D& retnValues, const bool convert,
                     const bool matrixSymmetric)
{
    if (keyStringRow.size() > retnValues.nRows()) {
        throw CanteraError("getMatrixValues",
                           "size of key1 greater than numrows");
    } else if (keyStringCol.size() > retnValues.nColumns()) {
        throw CanteraError("getMatrixValues",
                           "size of key2 greater than num cols");
    } else if (matrixSymmetric && retnValues.nRows() != retnValues.nColumns()) {
        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;
    if (convert && node["units"] != "") {
        funit = toSI(node["units"]);
    }

    vector<string> v;
    getStringArray(node, v);
    for (size_t i = 0; i < v.size(); i++) {
        size_t icolon = v[i].find(":");
        if (icolon == string::npos) {
            throw CanteraError("getMatrixValues","Missing two colons ("
                               +v[i]+")");
        }
        string key1 = v[i].substr(0,icolon);
        string rmm = v[i].substr(icolon+1, v[i].size());

        icolon = rmm.find(":");
        if (icolon == string::npos) {
            throw CanteraError("getMatrixValues","Missing one colon ("
                               +v[i]+")");
        }

        size_t irow = find(keyStringRow.begin(), keyStringRow.end(), key1)
                      - keyStringRow.begin();
        if (irow == keyStringRow.size()) {
            throw CanteraError("getMatrixValues","Row not matched by string: "
                               + key1);
        }

        string key2 = rmm.substr(0,icolon);
        size_t icol = find(keyStringCol.begin(), keyStringCol.end(), key2)
                      - keyStringCol.begin();
        if (icol == keyStringCol.size()) {
            throw CanteraError("getMatrixValues","Col not matched by string: "
                               + key2);
        }
        double dval = fpValueCheck(rmm.substr(icolon+1, rmm.size())) * funit;
        /*
         * Finally, insert the value;
         */
        retnValues(irow, icol) = dval;
        if (matrixSymmetric) {
            retnValues(icol, irow) = dval;
        }
    }
}
Ejemplo n.º 11
0
size_t getFloatArray(const XML_Node& node, std::vector<doublereal> & v,
                     const bool convert, const std::string& unitsString,
                     const std::string& nodeName)
{
    const XML_Node* readNode = &node;
    if (node.name() != nodeName) {
        vector<XML_Node*> ll = node.getChildren(nodeName);
        if (ll.size() == 0) {
            throw CanteraError("getFloatArray",
                               "wrong XML element type/name: was expecting "
                               + nodeName + "but accessed " + node.name());
        } else {
            readNode = ll[0];
            ll = readNode->getChildren("floatArray");
            if (ll.size() > 0) {
                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->attrib("units");
    if (units != "" && convert) {
        if (unitsString == "actEnergy" && units != "") {
            funit = actEnergyToSI(units);
        } else if (unitsString != "" && units != "") {
            funit = toSI(units);
        }
    }

    if (readNode->attrib("min") != "") {
        vmin = fpValueCheck(readNode->attrib("min"));
    }
    if (readNode->attrib("max") != "") {
        vmax = fpValueCheck(readNode->attrib("max"));
    }

    std::string val = readNode->value();
    while (true) {
        size_t icom = val.find(',');
        if (icom != string::npos) {
            string numstr = val.substr(0,icom);
            val = val.substr(icom+1,val.size());
            v.push_back(fpValueCheck(numstr));
        } 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
             * possibility in for backwards compatibility.
             */
            if (!val.empty()) {
                v.push_back(fpValueCheck(val));
            }
            break;
        }
        doublereal 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");
        }
    }
    for (size_t n = 0; n < v.size(); n++) {
        v[n] *= funit;
    }
    return v.size();
}
Ejemplo n.º 12
0
bool installSpecies(size_t k, const XML_Node& s, thermo_t& th,
                    SpeciesThermo* spthermo_ptr, int rule,
                    XML_Node* phaseNode_ptr,
                    VPSSMgr* vpss_ptr,
                    SpeciesThermoFactory* factory)
{
    std::string xname = s.name();
    if (xname != "species") {
        throw CanteraError("installSpecies",
                           "Unexpected XML name of species XML_Node: " + xname);
    }
    // get the composition of the species
    const XML_Node& a = s.child("atomArray");
    map<string,string> comp;
    getMap(a, comp);

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

    // construct a vector of atom numbers for each element in phase th. Elements
    // not declared in the species (i.e., not in map comp) will have zero
    // entries in the vector.
    size_t nel = th.nElements();
    vector_fp ecomp(nel, 0.0);
    for (size_t m = 0; m < nel; m++) {
        std::string& es = comp[th.elementName(m)];
        if (!es.empty()) {
            ecomp[m] = fpValueCheck(es);
        }
    }


    // get the species charge, if any. Note that the charge need
    // not be explicitly specified if special element 'E'
    // (electron) is one of the elements.
    doublereal chrg = 0.0;
    if (s.hasChild("charge")) {
        chrg = getFloat(s, "charge");
    }

    // get the species size, if any. (This is used by surface
    // phases to represent how many sites a species occupies.)
    doublereal sz = 1.0;
    if (s.hasChild("size")) {
        sz = getFloat(s, "size");
    }

    // add the species to phase th
    th.addUniqueSpecies(s["name"], &ecomp[0], chrg, sz);

    if (vpss_ptr) {
        VPStandardStateTP* vp_ptr = dynamic_cast<VPStandardStateTP*>(&th);
        factory->installVPThermoForSpecies(k, s, vp_ptr, phaseNode_ptr);
    } else {
        // install the thermo parameterization for this species into
        // the species thermo manager for phase th
        factory->installThermoForSpecies(k, s, &th, *spthermo_ptr, phaseNode_ptr);
    }

    return true;
}
Ejemplo n.º 13
0
bool installSpecies(size_t k, const XML_Node& s, thermo_t& th,
                    SpeciesThermo* spthermo_ptr, int rule,
                    XML_Node* phaseNode_ptr,
                    VPSSMgr* vpss_ptr,
                    SpeciesThermoFactory* factory)
{
    std::string xname = s.name();
    if (xname != "species") {
        throw CanteraError("installSpecies",
                           "Unexpected XML name of species XML_Node: " + xname);
    }

    if (rule) {
        th.ignoreUndefinedElements();
    }

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

    // construct a vector of atom numbers for each element in phase th. Elements
    // not declared in the species (i.e., not in map comp) will have zero
    // entries in the vector.
    size_t nel = th.nElements();
    vector_fp ecomp(nel, 0.0);
    compositionMap comp_map = parseCompString(a.value());
    for (size_t m = 0; m < nel; m++) {
        std::string& es = comp[th.elementName(m)];
        if (!es.empty()) {
            ecomp[m] = fpValueCheck(es);
        }
    }

    // get the species charge, if any. Note that the charge need
    // not be explicitly specified if special element 'E'
    // (electron) is one of the elements.
    doublereal chrg = 0.0;
    if (s.hasChild("charge")) {
        chrg = getFloat(s, "charge");
    }

    // get the species size, if any. (This is used by surface
    // phases to represent how many sites a species occupies.)
    doublereal sz = 1.0;
    if (s.hasChild("size")) {
        sz = getFloat(s, "size");
    }

    if (vpss_ptr) {
        th.addUniqueSpecies(s["name"], &ecomp[0], chrg, sz);
        VPStandardStateTP* vp_ptr = dynamic_cast<VPStandardStateTP*>(&th);
        vp_ptr->createInstallPDSS(k, s, phaseNode_ptr);
    } else {
        SpeciesThermoInterpType* st = newSpeciesThermoInterpType(s);
        Species sp(s["name"], comp_map, st, chrg, sz);

        // Read gas-phase transport data, if provided
        if (s.hasChild("transport") &&
                s.child("transport")["model"] == "gas_transport") {
            XML_Node& tr = s.child("transport");

            string geometry, dummy;
            getString(tr, "geometry", geometry, dummy);

            double diam = getFloat(tr, "LJ_diameter");
            double welldepth = getFloat(tr, "LJ_welldepth");

            double dipole = 0.0;
            getOptionalFloat(tr, "dipoleMoment", dipole);

            double polar = 0.0;
            getOptionalFloat(tr, "polarizability", polar);

            double rot = 0.0;
            getOptionalFloat(tr, "rotRelax", rot);
            double acentric = 0.0;
            getOptionalFloat(tr, "acentric_factor", acentric);

            GasTransportData* gastran = new GasTransportData;
            gastran->setCustomaryUnits(sp.name, geometry, diam, welldepth,
                                       dipole, polar, rot, acentric);
            sp.transport.reset(gastran);
            gastran->validate(sp);
        }
        th.addSpecies(sp);
    }

    return true;
}