Пример #1
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);
    }
}
Пример #2
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);
    }
}
Пример #3
0
  static void installAdsorbateThermoFromXML(std::string speciesName,
					    SpeciesThermo& sp, int k, 
					    const XML_Node& f) { 		
    vector_fp freqs;
    doublereal tmin, tmax, pref = OneAtm;
    int nfreq = 0;
    tmin = fpValue(f["Tmin"]);
    tmax = fpValue(f["Tmax"]);
    if (f.hasAttrib("P0")) {
      pref = fpValue(f["P0"]);
    }
    if (f.hasAttrib("Pref")) {
      pref = fpValue(f["Pref"]);
    }
    if (tmax == 0.0) tmax = 1.0e30;

    if (f.hasChild("floatArray")) {
      getFloatArray(f.child("floatArray"), freqs, false);
      nfreq = freqs.size(); 
    }
    for (int n = 0; n < nfreq; n++) {
      freqs[n] *= 3.0e10;
    }
    vector_fp coeffs(nfreq + 2);
    coeffs[0] = nfreq;
    coeffs[1] = getFloat(f, "binding_energy", "toSI");
    copy(freqs.begin(), freqs.end(), coeffs.begin() + 2);
    //posc = new Adsorbate(k, tmin, tmax, pref,  
    //    DATA_PTR(coeffs)); 
    (&sp)->install(speciesName, k, ADSORBATE, &coeffs[0], tmin, tmax, pref);
  }
Пример #4
0
  /*
   * @todo call addUniqueElement(symbol, weight) instead of
   * addElement.
   */
  void Elements::
  addUniqueElement(const XML_Node& e) {
    doublereal weight = 0.0;
    if (e.hasAttrib("atomicWt")) 
      weight = atof(stripws(e["atomicWt"]).c_str());
    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 = atofCheck(stripws(e298Node["value"]).c_str());
      }
    }
    if (weight != 0.0) {
      addUniqueElement(symbol, weight, anum, entropy298);
    } else {
      addUniqueElement(symbol);
    }
  }
Пример #5
0
void importPhase(XML_Node& phase, ThermoPhase* th)
{
    // Check the the supplied XML node in fact represents a phase.
    if (phase.name() != "phase") {
        throw CanteraError("importPhase",
                           "Current const XML_Node named, " + phase.name() +
                           ", is not a phase element.");
    }

    // In this section of code, we get the reference to the phase XML tree
    // within the ThermoPhase object. Then, we clear it and fill it with the
    // current information that we are about to use to construct the object. We
    // will then be able to resurrect the information later by calling xml().
    th->setXMLdata(phase);

    // set the id attribute of the phase to the 'id' attribute in the XML tree.
    th->setID(phase.id());
    th->setName(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",
                               "phase, " + th->id() +
                               ", has unphysical number of dimensions: " + phase["dim"]);
        }
        th->setNDim(idim);
    } else {
        th->setNDim(3); // default
    }

    // Set equation of state parameters. The parameters are specific to each
    // subclass of ThermoPhase, so this is done by method setParametersFromXML
    // in each subclass.
    const XML_Node& eos = phase.child("thermo");
    if (phase.hasChild("thermo")) {
        th->setParametersFromXML(eos);
    } else {
        throw CanteraError("importPhase",
                           " phase, " + th->id() +
                           ", XML_Node does not have a \"thermo\" XML_Node");
    }

    VPStandardStateTP* vpss_ptr = 0;
    int ssConvention = th->standardStateConvention();
    if (ssConvention == cSS_CONVENTION_VPSS) {
        vpss_ptr = dynamic_cast <VPStandardStateTP*>(th);
        if (vpss_ptr == 0) {
            throw CanteraError("importPhase",
                               "phase, " + th->id() + ", was VPSS, but dynamic cast failed");
        }
    }

    // Add the elements.
    if (ssConvention != cSS_CONVENTION_SLAVE) {
        installElements(*th, phase);
    }

    // Add the species.
    //
    // Species definitions may be imported from multiple sources. For each one,
    // a speciesArray element must be present.
    vector<XML_Node*> sparrays = phase.getChildren("speciesArray");
    if (ssConvention != cSS_CONVENTION_SLAVE && sparrays.empty()) {
        throw CanteraError("importPhase",
                           "phase, " + th->id() + ", has zero \"speciesArray\" XML nodes.\n"
                           + " There must be at least one speciesArray nodes "
                           "with one or more species");
    }
    vector<XML_Node*> dbases;
    vector_int sprule(sparrays.size(),0);

    // Default behavior when importing from CTI/XML is for undefined elements to
    // be treated as an error
    th->throwUndefinedElements();

    // loop over the speciesArray elements
    for (size_t jsp = 0; jsp < sparrays.size(); jsp++) {
        const XML_Node& speciesArray = *sparrays[jsp];

        // If the speciesArray element has a child element
        //
        //   <skip element="undeclared">
        //
        // then set sprule[jsp] to 1, so that any species with an undeclared
        // element will be quietly skipped when importing species. Additionally,
        // if the skip node has the following attribute:
        //
        // <skip species="duplicate">
        //
        // then duplicate species names will not cause Cantera to throw an
        // exception. Instead, the duplicate entry will be discarded.
        if (speciesArray.hasChild("skip")) {
            const XML_Node& sk = speciesArray.child("skip");
            string eskip = sk["element"];
            if (eskip == "undeclared") {
                sprule[jsp] = 1;
            }
            string dskip = sk["species"];
            if (dskip == "duplicate") {
                sprule[jsp] += 10;
            }
        }

        // Get a pointer to the node containing the species definitions for the
        // species declared in this speciesArray element. This may be in the
        // local file containing the phase element, or may be in another file.
        XML_Node* db = get_XML_Node(speciesArray["datasrc"], &phase.root());
        if (db == 0) {
            throw CanteraError("importPhase()",
                               " Can not find XML node for species database: "
                               + speciesArray["datasrc"]);
        }

        // add this node to the list of species database nodes.
        dbases.push_back(db);
    }

    // Now, collect all the species names and all the XML_Node * pointers for
    // those species in a single vector. This is where we decide what species
    // are to be included in the phase. The logic is complicated enough that we
    // put it in a separate routine.
    std::vector<XML_Node*> spDataNodeList;
    std::vector<std::string> spNamesList;
    vector_int spRuleList;
    formSpeciesXMLNodeList(spDataNodeList, spNamesList, spRuleList,
                           sparrays, dbases, sprule);

    size_t nsp = spDataNodeList.size();
    if (ssConvention == cSS_CONVENTION_SLAVE && nsp > 0) {
        throw CanteraError("importPhase()", "For Slave standard states, "
            "number of species must be zero: {}", nsp);
    }
    for (size_t k = 0; k < nsp; k++) {
        XML_Node* s = spDataNodeList[k];
        AssertTrace(s != 0);
        if (spRuleList[k]) {
           th->ignoreUndefinedElements();
        }
        th->addSpecies(newSpecies(*s));
        if (vpss_ptr) {
            const XML_Node* const ss = s->findByName("standardState");
            std::string ss_model = (ss) ? ss->attrib("model") : "ideal-gas";
            unique_ptr<PDSS> kPDSS(newPDSS(ss_model));
            kPDSS->setParametersFromXML(*s);
            vpss_ptr->installPDSS(k, std::move(kPDSS));
        }
        th->saveSpeciesData(k, s);
    }

    // Done adding species. Perform any required subclass-specific
    // initialization.
    th->initThermo();

    // Perform any required subclass-specific initialization that requires the
    // XML phase object
    std::string id = "";
    th->initThermoXML(phase, id);
}
Пример #6
0
bool importPhase(XML_Node& phase, ThermoPhase* th,
                 SpeciesThermoFactory* spfactory)
{
    // Check the the supplied XML node in fact represents a phase.
    if (phase.name() != "phase") {
        throw CanteraError("importPhase",
                           "Current const XML_Node named, " + phase.name() +
                           ", is not a phase element.");
    }

    /*
     * In this section of code, we get the reference to the
     * phase xml tree within the ThermoPhase object. Then,
     * we clear it and fill it with the current information that
     * we are about to use to construct the object. We will then
     * be able to resurrect the information later by calling xml().
     */
    th->setXMLdata(phase);

    // set the id attribute of the phase to the 'id' attribute in the XML tree.
    th->setID(phase.id());
    th->setName(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",
                               "phase, " + th->id() +
                               ", has unphysical number of dimensions: " + phase["dim"]);
        th->setNDim(idim);
    } else {
        th->setNDim(3);     // default
    }

    // Set equation of state parameters. The parameters are
    // specific to each subclass of ThermoPhase, so this is done
    // by method setParametersFromXML in each subclass.
    const XML_Node& eos = phase.child("thermo");
    if (phase.hasChild("thermo")) {
        th->setParametersFromXML(eos);
    } else {
        throw CanteraError("importPhase",
                           " phase, " + th->id() +
                           ", XML_Node does not have a \"thermo\" XML_Node");
    }

    VPStandardStateTP* vpss_ptr = 0;
    int ssConvention = th->standardStateConvention();
    if (ssConvention == cSS_CONVENTION_VPSS) {
        vpss_ptr = dynamic_cast <VPStandardStateTP*>(th);
        if (vpss_ptr == 0) {
            throw CanteraError("importPhase",
                               "phase, " + th->id() + ", was VPSS, but dynamic cast failed");
        }
    }

    // if no species thermo factory was supplied, use the default one.
    if (!spfactory) {
        spfactory = SpeciesThermoFactory::factory();
    }

    /***************************************************************
     * Add the elements.
     ***************************************************************/
    if (ssConvention != cSS_CONVENTION_SLAVE) {
        installElements(*th, phase);
    }

    /***************************************************************
     * Add the species.
     *
     * Species definitions may be imported from multiple
     * sources. For each one, a speciesArray element must be
     * present.
     ***************************************************************/
    vector<XML_Node*> sparrays;
    phase.getChildren("speciesArray", sparrays);
    if (ssConvention != cSS_CONVENTION_SLAVE) {
        if (sparrays.empty()) {
            throw CanteraError("importPhase",
                               "phase, " + th->id() + ", has zero \"speciesArray\" XML nodes.\n"
                               + " There must be at least one speciesArray nodes "
                               "with one or more species");
        }
    }
    vector<XML_Node*> dbases;
    vector_int sprule(sparrays.size(),0);

    // loop over the speciesArray elements
    for (size_t jsp = 0; jsp < sparrays.size(); jsp++) {

        const XML_Node& speciesArray = *sparrays[jsp];

        // If the speciesArray element has a child element
        //
        //   <skip element="undeclared">
        //
        // then set sprule[jsp] to 1, so that any species with an undeclared
        // element will be quietly skipped when importing species. Additionally,
        // if the skip node has the following attribute:
        //
        // <skip species="duplicate">
        //
        // then duplicate species names will not cause Cantera to throw an
        // exception. Instead, the duplicate entry will be discarded.
        if (speciesArray.hasChild("skip")) {
            const XML_Node& sk = speciesArray.child("skip");
            string eskip = sk["element"];
            if (eskip == "undeclared") {
                sprule[jsp] = 1;
            }
            string dskip = sk["species"];
            if (dskip == "duplicate") {
                sprule[jsp] += 10;
            }
        }

        // Get a pointer to the node containing the species
        // definitions for the species declared in this
        // speciesArray element. This may be in the local file
        // containing the phase element, or may be in another
        // file.
        XML_Node* db = get_XML_Node(speciesArray["datasrc"], &phase.root());
        if (db == 0) {
            throw CanteraError("importPhase()",
                               " Can not find XML node for species database: "
                               + speciesArray["datasrc"]);
        }

        // add this node to the list of species database nodes.
        dbases.push_back(db);
    }

    // Now, collect all the species names and all the XML_Node * pointers
    // for those species in a single vector. This is where we decide what
    // species are to be included in the phase.
    // The logic is complicated enough that we put it in a separate routine.
    std::vector<XML_Node*>  spDataNodeList;
    std::vector<std::string> spNamesList;
    std::vector<int> spRuleList;
    formSpeciesXMLNodeList(spDataNodeList, spNamesList, spRuleList,
                           sparrays, dbases, sprule);

    // Decide whether the the phase has a variable pressure ss or not
    SpeciesThermo* spth = 0;
    VPSSMgr* vp_spth = 0;
    if (ssConvention == cSS_CONVENTION_TEMPERATURE) {
        // Create a new 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.
        spth = newSpeciesThermoMgr(spDataNodeList);

        // install it in the phase object
        th->setSpeciesThermo(spth);
    } else if (ssConvention == cSS_CONVENTION_SLAVE) {
        /*
         * No species thermo manager for this type
         */
    } else if (ssConvention == cSS_CONVENTION_VPSS) {
        vp_spth = newVPSSMgr(vpss_ptr, &phase, spDataNodeList);
        vpss_ptr->setVPSSMgr(vp_spth);
        spth = vp_spth->SpeciesThermoMgr();
        th->setSpeciesThermo(spth);
    } else {
        throw CanteraError("importPhase()", "unknown convention");
    }


    size_t k = 0;

    size_t nsp = spDataNodeList.size();
    if (ssConvention == cSS_CONVENTION_SLAVE) {
        if (nsp > 0) {
            throw CanteraError("importPhase()", "For Slave standard states, number of species must be zero: "
                               + int2str(nsp));
        }
    }
    for (size_t i = 0; i < nsp; i++) {
        XML_Node* s = spDataNodeList[i];
        AssertTrace(s != 0);
        bool ok = installSpecies(k, *s, *th, spth, spRuleList[i],
                                 &phase, vp_spth, spfactory);
        if (ok) {
            th->saveSpeciesData(k, s);
            ++k;
        }
    }

    if (ssConvention == cSS_CONVENTION_SLAVE) {
        th->installSlavePhases(&phase);
    }

    // Done adding species. Perform any required subclass-specific
    // initialization.
    th->initThermo();

    // Perform any required subclass-specific initialization
    // that requires the XML phase object
    std::string id = "";
    th->initThermoXML(phase, id);

    return true;
}