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);
}
}
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");
}
}
}
/*
* Import and initialize a ThermoPhase object
*
* param phaseNode This object must be the phase node of a
* complete XML tree
* description of the phase, including all of the
* species data. In other words while "phase" must
* point to an XML phase object, it must have
* sibling nodes "speciesData" that describe
* the species in the phase.
* param id ID of the phase. If nonnull, a check is done
* to see if phaseNode is pointing to the phase
* with the correct id.
*
* This routine initializes the lengths in the current object and
* then calls the parent routine.
*/
void IdealSolnGasVPSS::initThermoXML(XML_Node& phaseNode, std::string id) {
IdealSolnGasVPSS::initLengths();
if (phaseNode.hasChild("thermo")) {
XML_Node& thermoNode = phaseNode.child("thermo");
std::string model = thermoNode["model"];
if (model == "IdealGasVPSS") {
m_idealGas = 1;
} else if (model == "IdealSolnVPSS") {
m_idealGas = 0;
} else {
throw CanteraError("IdealSolnGasVPSS::initThermoXML",
"Unknown thermo model : " + 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")) {
if (m_idealGas) {
throw CanteraError("IdealSolnGasVPSS::initThermoXML",
"standardConc node for ideal gas");
}
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("initThermoXML",
"Unknown standardConc model: " + formStringa);
}
} else {
if (!m_idealGas) {
throw CanteraError("initThermoXML",
"Unspecified standardConc model");
}
}
VPStandardStateTP::initThermoXML(phaseNode, id);
}
void Phase::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;
ctml::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("ctml/elementData");
XML_Node& root = phase.root();
XML_Node* local_db = 0;
if (root.hasChild("ctml")) {
if (root.child("ctml").hasChild("elementData")) {
local_db = &root.child("ctml/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) {
//writelog("looking in local database.");
e = local_db->findByAttr("name",enames[i]);
//if (!e) writelog(enames[i]+" not found.");
}
if (!e) {
e = dbe->findByAttr("name",enames[i]);
}
if (e) {
addUniqueElement(*e);
} else {
throw CanteraError("addElementsFromXML","no data for element "
+enames[i]);
}
}
}
/*!
*
* @param spDataNodeList, This vector contains a list
* of species XML nodes that will be in the phase
*
* @todo Make sure that spDadta_node is species Data XML node by checking its name is speciesData
*/
static void getSpeciesThermoTypes(std::vector<XML_Node *> & spDataNodeList,
int& has_nasa, int& has_shomate, int& has_simple,
int &has_other) {
size_t ns = spDataNodeList.size();
for (size_t n = 0; n < ns; n++) {
XML_Node* spNode = spDataNodeList[n];
if (spNode->hasChild("standardState")) {
const XML_Node& ss = spNode->child("standardState");
string mname = ss["model"];
if (mname == "water" || mname == "waterIAPWS") {
has_other = 1;
continue;
}
}
if (spNode->hasChild("thermo")) {
const XML_Node& th = spNode->child("thermo");
if (th.hasChild("NASA")) {
has_nasa = 1;
} else if (th.hasChild("Shomate")) {
has_shomate = 1;
} else if (th.hasChild("MinEQ3")) {
has_shomate = 1;
} else if (th.hasChild("const_cp")) {
has_simple = 1;
} else if (th.hasChild("poly")) {
if (th.child("poly")["order"] == "1") has_simple = 1;
else throw CanteraError("newSpeciesThermo",
"poly with order > 1 not yet supported");
}
else if (th.hasChild("Mu0")) {
has_other = 1;
} else if (th.hasChild("NASA9")) {
has_other = 1;
} else if (th.hasChild("NASA9MULTITEMP")) {
has_other = 1;
} else if (th.hasChild("adsorbate")) {
has_other = 1;
} else {
has_other = 1;
//throw UnknownSpeciesThermoModel("getSpeciesThermoTypes:",
// spNode->attrib("name"), "missing");
}
} else {
throw CanteraError("getSpeciesThermoTypes:",
spNode->attrib("name") + " is missing the thermo XML node");
}
}
}
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);
}
SurfPhase::SurfPhase(std::string infile, std::string id) :
ThermoPhase(),
m_n0(0.0),
m_logn0(0.0),
m_tmin(0.0),
m_tmax(0.0),
m_press(OneAtm),
m_tlast(0.0)
{
XML_Node* root = get_XML_File(infile);
if (id == "-") id = "";
XML_Node* xphase = get_XML_NameID("phase", std::string("#")+id, root);
if (!xphase) {
throw CanteraError("SurfPhase::SurfPhase",
"Couldn't find phase name in file:" + id);
}
// Check the model name to ensure we have compatibility
const XML_Node& th = xphase->child("thermo");
string model = th["model"];
if (model != "Surface" && model != "Edge") {
throw CanteraError("SurfPhase::SurfPhase",
"thermo model attribute must be Surface or Edge");
}
importPhase(*xphase, this);
}
MetalSHEelectrons::MetalSHEelectrons(const std::string& infile, std::string id_) :
SingleSpeciesTP(),
xdef_(0)
{
XML_Node* root;
if (infile == "MetalSHEelectrons_default.xml") {
xdef_ = MetalSHEelectrons::makeDefaultXMLTree();
root = xdef_;
} else {
root = get_XML_File(infile);
}
if (id_ == "-") {
id_ = "";
}
XML_Node* xphase = get_XML_NameID("phase", std::string("#")+id_, root);
if (!xphase) {
throw CanteraError("MetalSHEelectrons::MetalSHEelectrons",
"Couldn't find phase name in file:" + id_);
}
// Check the model name to ensure we have compatibility
const XML_Node& th = xphase->child("thermo");
std::string model = th["model"];
if (model != "MetalSHEelectrons") {
throw CanteraError("MetalSHEelectrons::MetalSHEelectrons",
"thermo model attribute must be MetalSHEelectrons");
}
importPhase(*xphase, this);
}
/*********************************************************************
* Utility Functions
*********************************************************************/
void MaskellSolidSolnPhase::initThermoXML(XML_Node& phaseNode, const std::string& id_)
{
if (id_.size() > 0 && phaseNode.id() != id_) {
throw CanteraError("MaskellSolidSolnPhase::initThermoXML",
"phasenode and Id are incompatible");
}
/*
* Check on the thermo field. Must have:
* <thermo model="MaskellSolidSolution" />
*/
if (phaseNode.hasChild("thermo")) {
XML_Node& thNode = phaseNode.child("thermo");
std::string mString = thNode.attrib("model");
if (lowercase(mString) != "maskellsolidsolnphase") {
throw CanteraError("MaskellSolidSolnPhase::initThermoXML",
"Unknown thermo model: " + mString);
}
/*
* Parse the enthalpy of mixing constant
*/
if (thNode.hasChild("h_mix")) {
set_h_mix(fpValue(thNode.child("h_mix").value()));
} else {
throw CanteraError("MaskellSolidSolnPhase::initThermoXML",
"Mixing enthalpy parameter not specified.");
}
if (thNode.hasChild("product_species")) {
std::string product_species_name = thNode.child("product_species").value();
product_species_index = speciesIndex(product_species_name);
if (product_species_index == static_cast<int>(npos)) {
throw CanteraError("MaskellSolidSolnPhase::initThermoXML",
"Species " + product_species_name + " not found.");
}
if (product_species_index == 0) {
reactant_species_index = 1;
} else {
reactant_species_index = 0;
}
}
} else {
throw CanteraError("MaskellSolidSolnPhase::initThermoXML",
"Unspecified thermo model");
}
// Confirm that the phase only contains 2 species
if (m_kk != 2) {
throw CanteraError("MaskellSolidSolnPhase::initThermoXML",
"MaskellSolidSolution model requires exactly 2 species.");
}
/*
* Call the base initThermo, which handles setting the initial
* state.
*/
VPStandardStateTP::initThermoXML(phaseNode, id_);
}
void VPSSMgr_Water_HKFT::initThermoXML(XML_Node& phaseNode,
const std::string& id)
{
VPSSMgr::initThermoXML(phaseNode, id);
XML_Node& speciesList = phaseNode.child("speciesArray");
XML_Node* speciesDB = get_XML_NameID("speciesData", speciesList["datasrc"],
&phaseNode.root());
m_waterSS->setState_TP(300., OneAtm);
m_Vss[0] = (m_waterSS->density()) / m_vptp_ptr->molecularWeight(0);
for (size_t k = 1; k < m_kk; k++) {
string name = m_vptp_ptr->speciesName(k);
const XML_Node* s = speciesDB->findByAttr("name", name);
if (!s) {
throw CanteraError("VPSSMgr_Water_HKFT::initThermoXML",
"No species Node for species " + name);
}
const XML_Node* ss = s->findByName("standardState");
if (!ss) {
throw CanteraError("VPSSMgr_Water_HKFT::initThermoXML",
"No standardState Node for species " + name);
}
std::string model = lowercase(ss->attrib("model"));
if (model != "hkft") {
throw CanteraError("VPSSMgr_Water_HKFT::initThermoXML",
"Standard state model for a solute species isn't "
"the HKFT standard state model: " + name);
}
}
}
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
VPSSMgr_ConstVol::initThermoXML(XML_Node& phaseNode, std::string id) {
VPSSMgr::initThermoXML(phaseNode, id);
XML_Node& speciesList = phaseNode.child("speciesArray");
XML_Node* speciesDB = get_XML_NameID("speciesData", speciesList["datasrc"],
&phaseNode.root());
const vector<string>&sss = m_vptp_ptr->speciesNames();
for (int k = 0; k < m_kk; k++) {
const XML_Node* s = speciesDB->findByAttr("name", sss[k]);
if (!s) {
throw CanteraError("VPSSMgr_ConstVol::initThermoXML",
"no species Node for species " + sss[k]);
}
const XML_Node *ss = s->findByName("standardState");
if (!ss) {
throw CanteraError("VPSSMgr_ConstVol::initThermoXML",
"no standardState Node for species " + s->name());
}
std::string model = (*ss)["model"];
if (model != "constant_incompressible" && model != "constantVolume") {
throw CanteraError("VPSSMgr_ConstVol::initThermoXML",
"standardState model for species isn't constant_incompressible: " + s->name());
}
m_Vss[k] = getFloat(*ss, "molarVolume", "toSI");
}
}
void MineralEQ3::initThermoXML(XML_Node& phaseNode, const std::string& id_)
{
/*
* Find the Thermo XML node
*/
if (!phaseNode.hasChild("thermo")) {
throw CanteraError("HMWSoln::initThermoXML",
"no thermo XML node");
}
std::vector<const XML_Node*> xspecies = speciesData();
const XML_Node* xsp = xspecies[0];
XML_Node* aStandardState = 0;
if (xsp->hasChild("standardState")) {
aStandardState = &xsp->child("standardState");
} else {
throw CanteraError("MineralEQ3::initThermoXML",
"no standard state mode");
}
doublereal volVal = 0.0;
string smodel = (*aStandardState)["model"];
if (smodel != "constantVolume") {
throw CanteraError("MineralEQ3::initThermoXML",
"wrong standard state mode");
}
if (aStandardState->hasChild("V0_Pr_Tr")) {
XML_Node& aV = aStandardState->child("V0_Pr_Tr");
string Aunits = "";
double Afactor = toSI("cm3/gmol");
if (aV.hasAttrib("units")) {
Aunits = aV.attrib("units");
Afactor = toSI(Aunits);
}
volVal = ctml::getFloat(*aStandardState, "V0_Pr_Tr");
m_V0_pr_tr= volVal;
volVal *= Afactor;
m_speciesSize[0] = volVal;
} else {
throw CanteraError("MineralEQ3::initThermoXML",
"wrong standard state mode");
}
doublereal rho = molecularWeight(0) / volVal;
setDensity(rho);
const XML_Node& sThermo = xsp->child("thermo");
const XML_Node& MinEQ3node = sThermo.child("MinEQ3");
m_deltaG_formation_pr_tr =
ctml::getFloatDefaultUnits(MinEQ3node, "DG0_f_Pr_Tr", "cal/gmol", "actEnergy");
m_deltaH_formation_pr_tr =
ctml::getFloatDefaultUnits(MinEQ3node, "DH0_f_Pr_Tr", "cal/gmol", "actEnergy");
m_Entrop_pr_tr = ctml::getFloatDefaultUnits(MinEQ3node, "S0_Pr_Tr", "cal/gmol/K");
m_a = ctml::getFloatDefaultUnits(MinEQ3node, "a", "cal/gmol/K");
m_b = ctml::getFloatDefaultUnits(MinEQ3node, "b", "cal/gmol/K2");
m_c = ctml::getFloatDefaultUnits(MinEQ3node, "c", "cal-K/gmol");
convertDGFormation();
}
void ThermoPhase::initThermoXML(XML_Node& phaseNode, const std::string& id)
{
if (phaseNode.hasChild("state")) {
setStateFromXML(phaseNode.child("state"));
}
xMol_Ref.resize(m_kk);
getMoleFractions(&xMol_Ref[0]);
}
void IdealMolalSoln::initThermoXML(XML_Node& phaseNode, const std::string& id_)
{
MolalityVPSSTP::initThermoXML(phaseNode, id_);
if (id_.size() > 0 && phaseNode.id() != id_) {
throw CanteraError("IdealMolalSoln::initThermo",
"phasenode and Id are incompatible");
}
// Find the Thermo XML node
if (!phaseNode.hasChild("thermo")) {
throw CanteraError("IdealMolalSoln::initThermo",
"no thermo XML node");
}
XML_Node& thermoNode = phaseNode.child("thermo");
// Possible change the form of the standard concentrations
if (thermoNode.hasChild("standardConc")) {
XML_Node& scNode = thermoNode.child("standardConc");
setStandardConcentrationModel(scNode["model"]);
}
if (thermoNode.hasChild("activityCoefficients")) {
XML_Node& acNode = thermoNode.child("activityCoefficients");
std::string modelString = acNode.attrib("model");
if (modelString != "IdealMolalSoln") {
throw CanteraError("IdealMolalSoln::initThermoXML",
"unknown ActivityCoefficient model: " + modelString);
}
if (acNode.hasChild("idealMolalSolnCutoff")) {
XML_Node& ccNode = acNode.child("idealMolalSolnCutoff");
modelString = ccNode.attrib("model");
if (modelString != "") {
setCutoffModel(modelString);
if (ccNode.hasChild("gamma_o_limit")) {
IMS_gamma_o_min_ = getFloat(ccNode, "gamma_o_limit");
}
if (ccNode.hasChild("gamma_k_limit")) {
IMS_gamma_k_min_ = getFloat(ccNode, "gamma_k_limit");
}
if (ccNode.hasChild("X_o_cutoff")) {
IMS_X_o_cutoff_ = getFloat(ccNode, "X_o_cutoff");
}
if (ccNode.hasChild("c_0_param")) {
IMS_cCut_ = getFloat(ccNode, "c_0_param");
}
if (ccNode.hasChild("slope_f_limit")) {
IMS_slopefCut_ = getFloat(ccNode, "slope_f_limit");
}
if (ccNode.hasChild("slope_g_limit")) {
IMS_slopegCut_ = getFloat(ccNode, "slope_g_limit");
}
}
} else {
setCutoffModel("none");
}
}
}
void SpeciesThermoFactory::installThermoForSpecies
(size_t k, const XML_Node& speciesNode, ThermoPhase* th_ptr,
SpeciesThermo& spthermo, const XML_Node* phaseNode_ptr) const
{
shared_ptr<SpeciesThermoInterpType> stit(
newSpeciesThermoInterpType(speciesNode.child("thermo")));
stit->validate(speciesNode["name"]);
spthermo.install_STIT(k, stit);
}
bool getOptionalModel(const XML_Node& parent, const std::string& nodeName,
std::string& modelName)
{
if (parent.hasChild(nodeName)) {
modelName = parent.child(nodeName)["model"];
return true;
}
return false;
}
doublereal getFloat(const XML_Node& parent,
const std::string& name,
const std::string& type)
{
if (!parent.hasChild(name))
throw CanteraError("getFloat (called from XML Node \"" +
parent.name() + "\"): ",
"no child XML element named \"" + name + "\" exists");
const XML_Node& node = parent.child(name);
return getFloatCurrent(node, type);
}
void MixedSolventElectrolyte::initThermoXML(XML_Node& phaseNode, const std::string& id_)
{
if ((int) id_.size() > 0 && phaseNode.id() != id_) {
throw CanteraError("MixedSolventElectrolyte::initThermoXML",
"phasenode and Id are incompatible");
}
/*
* Check on the thermo field. Must have:
* <thermo model="MixedSolventElectrolyte" />
*/
if (!phaseNode.hasChild("thermo")) {
throw CanteraError("MixedSolventElectrolyte::initThermoXML",
"no thermo XML node");
}
XML_Node& thermoNode = phaseNode.child("thermo");
string mString = thermoNode.attrib("model");
if (lowercase(mString) != "mixedsolventelectrolyte") {
throw CanteraError("MixedSolventElectrolyte::initThermoXML",
"Unknown thermo model: " + mString);
}
/*
* Go get all of the coefficients and factors in the
* activityCoefficients XML block
*/
if (thermoNode.hasChild("activityCoefficients")) {
XML_Node& acNode = thermoNode.child("activityCoefficients");
mString = acNode.attrib("model");
if (lowercase(mString) != "margules") {
throw CanteraError("MixedSolventElectrolyte::initThermoXML",
"Unknown activity coefficient model: " + mString);
}
for (size_t i = 0; i < acNode.nChildren(); i++) {
XML_Node& xmlACChild = acNode.child(i);
/*
* Process a binary salt field, or any of the other XML fields
* that make up the Pitzer Database. Entries will be ignored
* if any of the species in the entry isn't in the solution.
*/
if (lowercase(xmlACChild.name()) == "binaryneutralspeciesparameters") {
readXMLBinarySpecies(xmlACChild);
}
}
}
/*
* Go down the chain
*/
MolarityIonicVPSSTP::initThermoXML(phaseNode, id_);
}
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_);
}
void TransportFactory::getSolidTransportData(const XML_Node& transportNode,
XML_Node& log,
const std::string phaseName,
SolidTransportData& trParam)
{
try {
size_t num = transportNode.nChildren();
for (size_t iChild = 0; iChild < num; iChild++) {
//tranTypeNode is a type of transport property like viscosity
XML_Node& tranTypeNode = transportNode.child(iChild);
std::string nodeName = tranTypeNode.name();
ThermoPhase* temp_thermo = trParam.thermo;
//tranTypeNode contains the interaction model
switch (m_tranPropMap[nodeName]) {
case TP_IONCONDUCTIVITY:
trParam.ionConductivity = newLTP(tranTypeNode, phaseName,
m_tranPropMap[nodeName],
temp_thermo);
break;
case TP_THERMALCOND:
trParam.thermalConductivity = newLTP(tranTypeNode, phaseName,
m_tranPropMap[nodeName],
temp_thermo);
break;
case TP_DEFECTDIFF:
trParam.defectDiffusivity = newLTP(tranTypeNode, phaseName,
m_tranPropMap[nodeName],
temp_thermo);
break;
case TP_DEFECTCONC:
trParam.defectActivity = newLTP(tranTypeNode, phaseName,
m_tranPropMap[nodeName],
temp_thermo);
break;
case TP_ELECTCOND:
trParam.electConductivity = newLTP(tranTypeNode, phaseName,
m_tranPropMap[nodeName],
temp_thermo);
break;
default:
throw CanteraError("getSolidTransportData","unknown transport property: " + nodeName);
}
}
} catch (CanteraError) {
showErrors(std::cout);
}
return;
}
StoichSubstanceSSTP::StoichSubstanceSSTP(XML_Node& xmlphase, const std::string& id_)
{
if (id_ != "" && id_ != xmlphase["id"]) {
throw CanteraError("StoichSubstanceSSTP::StoichSubstanceSSTP",
"id's don't match");
}
std::string model = xmlphase.child("thermo")["model"];
if (model != "StoichSubstance" && model != "StoichSubstanceSSTP") {
throw CanteraError("StoichSubstanceSSTP::StoichSubstanceSSTP",
"thermo model attribute must be StoichSubstance");
}
importPhase(xmlphase, this);
}
void StoichSubstanceSSTP::initThermoXML(XML_Node& phaseNode, std::string id) {
/*
* Find the Thermo XML node
*/
if (!phaseNode.hasChild("thermo")) {
throw CanteraError("StoichSubstanceSSTP::initThermoXML",
"no thermo XML node");
}
XML_Node &tnode = phaseNode.child("thermo");
double dens = getFloatDefaultUnits(tnode, "density", "kg/m3");
setDensity(dens);
SingleSpeciesTP::initThermoXML(phaseNode, id);
}
electrodeElectron::electrodeElectron(XML_Node& xmlphase, const std::string& id_) :
StoichSubstanceSSTP()
{
if (id_ != "" && id_ != xmlphase["id"]) {
throw CanteraError("electrodeElectron::electrodeElectron",
"id's don't match");
}
if (xmlphase.child("thermo")["model"] != "electrodeElectron") {
throw CanteraError("electrodeElectron::electrodeElectron",
"thermo model attribute must be electrodeElectron");
}
importPhase(xmlphase, this);
}
void LatticeSolidPhase::setParametersFromXML(const XML_Node& eosdata) {
eosdata._require("model","LatticeSolid");
XML_Node& la = eosdata.child("LatticeArray");
vector<XML_Node*> lattices;
la.getChildren("phase",lattices);
int n;
int nl = lattices.size();
m_nlattice = nl;
for (n = 0; n < nl; n++) {
XML_Node& i = *lattices[n];
m_lattice.push_back((LatticePhase*)newPhase(i));
}
}
void MineralEQ3::initThermoXML(XML_Node& phaseNode, const std::string& id_)
{
// Find the Thermo XML node
if (!phaseNode.hasChild("thermo")) {
throw CanteraError("HMWSoln::initThermoXML",
"no thermo XML node");
}
const XML_Node* xsp = speciesData()[0];
XML_Node* aStandardState = 0;
if (xsp->hasChild("standardState")) {
aStandardState = &xsp->child("standardState");
} else {
throw CanteraError("MineralEQ3::initThermoXML",
"no standard state mode");
}
doublereal volVal = 0.0;
if (aStandardState->attrib("model") != "constantVolume") {
throw CanteraError("MineralEQ3::initThermoXML",
"wrong standard state mode");
}
if (aStandardState->hasChild("V0_Pr_Tr")) {
XML_Node& aV = aStandardState->child("V0_Pr_Tr");
double Afactor = toSI("cm3/gmol");
if (aV.hasAttrib("units")) {
Afactor = toSI(aV.attrib("units"));
}
volVal = getFloat(*aStandardState, "V0_Pr_Tr");
m_V0_pr_tr= volVal;
volVal *= Afactor;
} else {
throw CanteraError("MineralEQ3::initThermoXML",
"wrong standard state mode");
}
setDensity(molecularWeight(0) / volVal);
const XML_Node& MinEQ3node = xsp->child("thermo").child("MinEQ3");
m_deltaG_formation_pr_tr =
getFloat(MinEQ3node, "DG0_f_Pr_Tr", "actEnergy") / actEnergyToSI("cal/gmol");
m_deltaH_formation_pr_tr =
getFloat(MinEQ3node, "DH0_f_Pr_Tr", "actEnergy") / actEnergyToSI("cal/gmol");
m_Entrop_pr_tr = getFloat(MinEQ3node, "S0_Pr_Tr", "toSI") / toSI("cal/gmol/K");
m_a = getFloat(MinEQ3node, "a", "toSI") / toSI("cal/gmol/K");
m_b = getFloat(MinEQ3node, "b", "toSI") / toSI("cal/gmol/K2");
m_c = getFloat(MinEQ3node, "c", "toSI") / toSI("cal-K/gmol");
convertDGFormation();
}
SurfPhase::SurfPhase(XML_Node& xmlphase) :
ThermoPhase(),
m_n0(0.0),
m_logn0(0.0),
m_press(OneAtm)
{
const XML_Node& th = xmlphase.child("thermo");
string model = th["model"];
if (model != "Surface" && model != "Edge") {
throw CanteraError("SurfPhase::SurfPhase",
"thermo model attribute must be Surface or Edge");
}
importPhase(xmlphase, this);
}
void MetalSHEelectrons::initThermoXML(XML_Node& phaseNode, const std::string& id_)
{
// Find the Thermo XML node
if (!phaseNode.hasChild("thermo")) {
throw CanteraError("MetalSHEelectrons::initThermoXML",
"no thermo XML node");
}
XML_Node& tnode = phaseNode.child("thermo");
doublereal dens = 2.65E3;
if (tnode.hasChild("density")) {
dens = getFloat(tnode, "density", "toSI");
}
setDensity(dens);
SingleSpeciesTP::initThermoXML(phaseNode, id_);
}
void StoichSubstance::initThermoXML(XML_Node& phaseNode, const std::string& id_)
{
// Find the Thermo XML node
if (!phaseNode.hasChild("thermo")) {
throw CanteraError("StoichSubstance::initThermoXML",
"no thermo XML node");
}
XML_Node& tnode = phaseNode.child("thermo");
std::string model = tnode["model"];
if (model != "StoichSubstance" && model != "StoichSubstanceSSTP") {
throw CanteraError("StoichSubstance::initThermoXML",
"thermo model attribute must be StoichSubstance");
}
double dens = getFloat(tnode, "density", "toSI");
setDensity(dens);
SingleSpeciesTP::initThermoXML(phaseNode, id_);
}
void MargulesVPSSTP::initThermoXML(XML_Node& phaseNode, const std::string& id_)
{
if ((int) id_.size() > 0) {
string idp = phaseNode.id();
if (idp != id_) {
throw CanteraError("MargulesVPSSTP::initThermoXML", "phasenode and Id are incompatible");
}
}
// Find the Thermo XML node
if (!phaseNode.hasChild("thermo")) {
throw CanteraError("MargulesVPSSTP::initThermoXML",
"no thermo XML node");
}
XML_Node& thermoNode = phaseNode.child("thermo");
// Make sure that the thermo model is Margules
if (!caseInsensitiveEquals(thermoNode["model"], "margules")) {
throw CanteraError("MargulesVPSSTP::initThermoXML",
"model name isn't Margules: " + thermoNode["model"]);
}
// Go get all of the coefficients and factors in the activityCoefficients
// XML block
if (thermoNode.hasChild("activityCoefficients")) {
XML_Node& acNode = thermoNode.child("activityCoefficients");
if (!caseInsensitiveEquals(acNode["model"], "margules")) {
throw CanteraError("MargulesVPSSTP::initThermoXML",
"Unknown activity coefficient model: " + acNode["model"]);
}
for (size_t i = 0; i < acNode.nChildren(); i++) {
XML_Node& xmlACChild = acNode.child(i);
// Process a binary salt field, or any of the other XML fields that
// make up the Pitzer Database. Entries will be ignored if any of
// the species in the entry isn't in the solution.
if (caseInsensitiveEquals(xmlACChild.name(), "binaryneutralspeciesparameters")) {
readXMLBinarySpecies(xmlACChild);
}
}
}
// Go down the chain
GibbsExcessVPSSTP::initThermoXML(phaseNode, id_);
}