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);
}
}
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);
}
}
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);
}
/*
* @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);
}
}
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);
}
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;
}
