/**
* constructPDSSXML:
*
* Initialization of a PDSS_ConstVol object using an
* xml file.
*
* This routine is a precursor to initThermo(XML_Node*)
* routine, which does most of the work.
*
* @param infile XML file containing the description of the
* phase
*
* @param id Optional parameter identifying the name of the
* phase. If none is given, the first XML
* phase element will be used.
*/
void PDSS_ConstVol::constructPDSSXML(VPStandardStateTP *tp, int spindex,
const XML_Node& speciesNode,
const XML_Node& phaseNode, bool spInstalled) {
PDSS::initThermo();
SpeciesThermo &sp = m_tp->speciesThermo();
m_p0 = sp.refPressure(m_spindex);
if (!spInstalled) {
throw CanteraError("PDSS_ConstVol::constructPDSSXML", "spInstalled false not handled");
}
const XML_Node *ss = speciesNode.findByName("standardState");
if (!ss) {
throw CanteraError("PDSS_ConstVol::constructPDSSXML",
"no standardState Node for species " + speciesNode.name());
}
std::string model = (*ss)["model"];
if (model != "constant_incompressible") {
throw CanteraError("PDSS_ConstVol::initThermoXML",
"standardState model for species isn't constant_incompressible: " + speciesNode.name());
}
m_constMolarVolume = getFloat(*ss, "molarVolume", "toSI");
std::string id = "";
// initThermoXML(phaseNode, id);
}
/**
* 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;
}
}
void LatticePhase::initThermoXML(XML_Node& phaseNode, const std::string& id_)
{
if (!id_.empty() && id_ != phaseNode.id()) {
throw CanteraError("LatticePhase::initThermoXML",
"ids don't match");
}
// Check on the thermo field. Must have:
// <thermo model="Lattice" />
if (phaseNode.hasChild("thermo")) {
XML_Node& thNode = phaseNode.child("thermo");
std::string mString = thNode.attrib("model");
if (lowercase(mString) != "lattice") {
throw CanteraError("LatticePhase::initThermoXML",
"Unknown thermo model: " + mString);
}
} else {
throw CanteraError("LatticePhase::initThermoXML",
"Unspecified thermo model");
}
// Now go get the molar volumes. use the default if not found
XML_Node& speciesList = phaseNode.child("speciesArray");
XML_Node* speciesDB = get_XML_NameID("speciesData", speciesList["datasrc"], &phaseNode.root());
for (size_t k = 0; k < m_kk; k++) {
m_speciesMolarVolume[k] = m_site_density;
XML_Node* s = speciesDB->findByAttr("name", speciesName(k));
if (!s) {
throw CanteraError(" LatticePhase::initThermoXML", "database problems");
}
XML_Node* ss = s->findByName("standardState");
if (ss && ss->findByName("molarVolume")) {
m_speciesMolarVolume[k] = getFloat(*ss, "molarVolume", "toSI");
}
}
// Call the base initThermo, which handles setting the initial state.
ThermoPhase::initThermoXML(phaseNode, id_);
}
/*
* constructPDSSXML:
*
* Initialization of a PDSS_SSVol object using an
* xml file.
*
* This routine is a precursor to initThermo(XML_Node*)
* routine, which does most of the work.
*
* @param infile XML file containing the description of the
* phase
*
* @param id Optional parameter identifying the name of the
* phase. If none is given, the first XML
* phase element will be used.
*/
void PDSS_SSVol::constructPDSSXML(VPStandardStateTP *tp, int spindex,
const XML_Node& speciesNode,
const XML_Node& phaseNode, bool spInstalled) {
PDSS::initThermo();
SpeciesThermo &sp = m_tp->speciesThermo();
m_p0 = sp.refPressure(m_spindex);
if (!spInstalled) {
throw CanteraError("PDSS_SSVol::constructPDSSXML", "spInstalled false not handled");
}
const XML_Node *ss = speciesNode.findByName("standardState");
if (!ss) {
throw CanteraError("PDSS_SSVol::constructPDSSXML",
"no standardState Node for species " + speciesNode.name());
}
std::string model = (*ss)["model"];
if (model == "constant_incompressible" || model == "constant") {
volumeModel_ = cSSVOLUME_CONSTANT;
m_constMolarVolume = ctml::getFloat(*ss, "molarVolume", "toSI");
} else if (model == "temperature_polynomial") {
volumeModel_ = cSSVOLUME_TPOLY;
int num = ctml::getFloatArray(*ss, TCoeff_, true, "toSI", "volumeTemperaturePolynomial");
if (num != 4) {
throw CanteraError("PDSS_SSVol::constructPDSSXML",
" Didn't get 4 density polynomial numbers for species " + speciesNode.name());
}
} else if (model == "density_temperature_polynomial") {
volumeModel_ = cSSVOLUME_DENSITY_TPOLY;
int num = ctml::getFloatArray(*ss, TCoeff_, true, "toSI", "densityTemperaturePolynomial");
if (num != 4) {
throw CanteraError("PDSS_SSVol::constructPDSSXML",
" Didn't get 4 density polynomial numbers for species " + speciesNode.name());
}
} else {
throw CanteraError("PDSS_SSVol::constructPDSSXML",
"standardState model for species isn't constant_incompressible: " + speciesNode.name());
}
std::string id = "";
}
void PDSS_ConstVol::constructPDSSXML(VPStandardStateTP* tp, size_t spindex,
const XML_Node& speciesNode,
const XML_Node& phaseNode, bool spInstalled)
{
PDSS::initThermo();
m_p0 = m_tp->speciesThermo().refPressure(m_spindex);
if (!spInstalled) {
throw CanteraError("PDSS_ConstVol::constructPDSSXML", "spInstalled false not handled");
}
const XML_Node* ss = speciesNode.findByName("standardState");
if (!ss) {
throw CanteraError("PDSS_ConstVol::constructPDSSXML",
"no standardState Node for species " + speciesNode.name());
}
if (ss->attrib("model") != "constant_incompressible") {
throw CanteraError("PDSS_ConstVol::initThermoXML",
"standardState model for species isn't constant_incompressible: " + speciesNode.name());
}
m_constMolarVolume = getFloat(*ss, "molarVolume", "toSI");
}
TransportFromScratch()
: sH2(new Species("H2", parseCompString("H:2")))
, sO2(new Species("O2", parseCompString("O:2")))
, sH2O(new Species("H2O", parseCompString("H:2 O:1")))
, tH2(new GasTransportData())
, tO2(new GasTransportData())
, tH2O(new GasTransportData())
{
sH2->thermo.reset(new NasaPoly2(200, 3500, 101325, h2_nasa_coeffs));
sO2->thermo.reset(new NasaPoly2(200, 3500, 101325, o2_nasa_coeffs));
sH2O->thermo.reset(new NasaPoly2(200, 3500, 101325, h2o_nasa_coeffs));
tH2->setCustomaryUnits("linear", 2.92, 38.0, 0.0, 0.79, 280.0);
tO2->setCustomaryUnits("linear", 3.46, 107.40, 0.0, 1.60, 3.80);
tH2O->setCustomaryUnits("nonlinear", 2.60, 572.4, 1.84, 0.0, 4.00);
sH2->transport = tH2;
sO2->transport = tO2;
sH2O->transport = tH2O;
std::string phase_def = "ideal_gas(name='test', elements='O H',"
"species='gri30: H2 O2 H2O')";
XML_Node* fxml = get_XML_from_string(phase_def);
ref.reset(newPhase(*fxml->findByName("phase")));
test.reset(new IdealGasPhase());
test->addElement("O");
test->addElement("H");
test->addSpecies(sH2);
test->addSpecies(sO2);
test->addSpecies(sH2O);
test->initThermo();
ref->setState_TPX(400, 5e5, "H2:0.5, O2:0.3, H2O:0.2");
test->setState_TPX(400, 5e5, "H2:0.5, O2:0.3, H2O:0.2");
}
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);
}
void IdealSolidSolnPhase::initThermoXML(XML_Node& phaseNode, const std::string& id_)
{
if (id_.size() > 0 && phaseNode.id() != id_) {
throw CanteraError("IdealSolidSolnPhase::initThermoXML",
"phasenode and Id are incompatible");
}
/*
* Check on the thermo field. Must have:
* <thermo model="IdealSolidSolution" />
*/
if (phaseNode.hasChild("thermo")) {
XML_Node& thNode = phaseNode.child("thermo");
string mString = thNode.attrib("model");
if (lowercase(mString) != "idealsolidsolution") {
throw CanteraError("IdealSolidSolnPhase::initThermoXML",
"Unknown thermo model: " + mString);
}
} else {
throw CanteraError("IdealSolidSolnPhase::initThermoXML",
"Unspecified thermo model");
}
/*
* Form of the standard concentrations. Must have one of:
*
* <standardConc model="unity" />
* <standardConc model="molar_volume" />
* <standardConc model="solvent_volume" />
*/
if (phaseNode.hasChild("standardConc")) {
XML_Node& scNode = phaseNode.child("standardConc");
string formStringa = scNode.attrib("model");
string formString = lowercase(formStringa);
if (formString == "unity") {
m_formGC = 0;
} else if (formString == "molar_volume") {
m_formGC = 1;
} else if (formString == "solvent_volume") {
m_formGC = 2;
} else {
throw CanteraError("IdealSolidSolnPhase::initThermoXML",
"Unknown standardConc model: " + formStringa);
}
} else {
throw CanteraError("IdealSolidSolnPhase::initThermoXML",
"Unspecified standardConc model");
}
/*
* Initialize all of the lengths now that we know how many species
* there are in the phase.
*/
initLengths();
/*
* Now go get the molar volumes
*/
XML_Node& speciesList = phaseNode.child("speciesArray");
XML_Node* speciesDB = get_XML_NameID("speciesData", speciesList["datasrc"],
&phaseNode.root());
for (size_t k = 0; k < m_kk; k++) {
XML_Node* s = speciesDB->findByAttr("name", speciesName(k));
XML_Node* ss = s->findByName("standardState");
m_speciesMolarVolume[k] = getFloat(*ss, "molarVolume", "toSI");
}
/*
* Call the base initThermo, which handles setting the initial
* state.
*/
ThermoPhase::initThermoXML(phaseNode, id_);
}
void setup(const std::string& elements="H C O N Ar") {
XML_Node* phase = get_XML_from_string(
"ideal_gas(elements='" + elements + "', species='gri30: CH C2H2')");
gas.reset(newPhase(*phase->findByName("phase")));
gas->setState_TPX(1000, 1e5, "C2H2:0.9, CH:0.1");
}