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 getString(const XML_Node& node, const std::string& titleString, std::string& valueString,
std::string& typeString)
{
XML_Node* s = getByTitle(node, titleString);
if (s && s->name() == "string") {
valueString = s->value();
typeString = s->attrib("type");
} else {
valueString = "";
typeString = "";
}
}
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();
}
/*!
*
* @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");
}
}
}
void RedlichKisterVPSSTP::readXMLBinarySpecies(XML_Node& xmLBinarySpecies)
{
std::string xname = xmLBinarySpecies.name();
if (xname != "binaryNeutralSpeciesParameters") {
throw CanteraError("RedlichKisterVPSSTP::readXMLBinarySpecies",
"Incorrect name for processing this routine: " + xname);
}
size_t Npoly = 0;
vector_fp hParams, sParams;
std::string iName = xmLBinarySpecies.attrib("speciesA");
if (iName == "") {
throw CanteraError("RedlichKisterVPSSTP::readXMLBinarySpecies", "no speciesA attrib");
}
std::string jName = xmLBinarySpecies.attrib("speciesB");
if (jName == "") {
throw CanteraError("RedlichKisterVPSSTP::readXMLBinarySpecies", "no speciesB attrib");
}
/*
* Find the index of the species in the current phase. It's not
* an error to not find the species. This means that the interaction doesn't occur for the current
* implementation of the phase.
*/
size_t iSpecies = speciesIndex(iName);
if (iSpecies == npos) {
return;
}
string ispName = speciesName(iSpecies);
if (charge(iSpecies) != 0) {
throw CanteraError("RedlichKisterVPSSTP::readXMLBinarySpecies", "speciesA charge problem");
}
size_t jSpecies = speciesIndex(jName);
if (jSpecies == npos) {
return;
}
std::string jspName = speciesName(jSpecies);
if (charge(jSpecies) != 0) {
throw CanteraError("RedlichKisterVPSSTP::readXMLBinarySpecies", "speciesB charge problem");
}
/*
* Ok we have found a valid interaction
*/
numBinaryInteractions_++;
size_t iSpot = numBinaryInteractions_ - 1;
m_pSpecies_A_ij.resize(numBinaryInteractions_);
m_pSpecies_B_ij.resize(numBinaryInteractions_);
m_pSpecies_A_ij[iSpot] = iSpecies;
m_pSpecies_B_ij[iSpot] = jSpecies;
for (size_t iChild = 0; iChild < xmLBinarySpecies.nChildren(); iChild++) {
XML_Node& xmlChild = xmLBinarySpecies.child(iChild);
string nodeName = lowercase(xmlChild.name());
/*
* Process the binary species interaction child elements
*/
if (nodeName == "excessenthalpy") {
/*
* Get the string containing all of the values
*/
getFloatArray(xmlChild, hParams, true, "toSI", "excessEnthalpy");
Npoly = std::max(hParams.size(), Npoly);
}
if (nodeName == "excessentropy") {
/*
* Get the string containing all of the values
*/
getFloatArray(xmlChild, sParams, true, "toSI", "excessEntropy");
Npoly = std::max(sParams.size(), Npoly);
}
}
hParams.resize(Npoly, 0.0);
sParams.resize(Npoly, 0.0);
m_HE_m_ij.push_back(hParams);
m_SE_m_ij.push_back(sParams);
m_N_ij.push_back(Npoly);
resizeNumInteractions(numBinaryInteractions_);
}
/*
* Examine the types of species thermo parameterizations,
* and return a flag indicating the type of parameterization
* needed by the species.
*
* @param spData_node Species Data XML node. This node contains a list
* of species XML nodes underneath it.
*
* @todo Make sure that spDadta_node is species Data XML node by checking
* its name is speciesData
*/
static void getVPSSMgrTypes(std::vector<XML_Node *> & spDataNodeList,
int &has_nasa_idealGas,
int &has_nasa_constVol,
int& has_shomate_idealGas,
int& has_shomate_constVol,
int& has_simple_idealGas,
int& has_simple_constVol,
int &has_water,
int &has_tpx,
int &has_hptx,
int &has_other) {
XML_Node *ss_ptr = 0;
string ssModel = "idealGas";
size_t ns = spDataNodeList.size();
for (size_t n = 0; n < ns; n++) {
bool ifound = false;
XML_Node* spNode = spDataNodeList[n];
if (spNode->hasChild("standardState")) {
const XML_Node& ssN = spNode->child("standardState");
string mm = ssN["model"];
if (mm == "waterIAPWS" || mm == "waterPDSS") {
has_water++;
ifound = true;
}
if (mm == "HKFT") {
has_hptx++;
ifound = true;
}
}
if (!ifound) {
if (spNode->hasChild("thermo")) {
const XML_Node& th = spNode->child("thermo");
if (spNode->hasChild("standardState")) {
ss_ptr = &(spNode->child("standardState"));
ssModel = ss_ptr->attrib("model");
}
if (th.hasChild("NASA")) {
if (ssModel == "idealGas") {
has_nasa_idealGas++;
} else if (ssModel == "constant_incompressible" ||
ssModel == "constantVolume") {
has_nasa_constVol++;
} else {
throw UnknownVPSSMgrModel("getVPSSMgrTypes:",
spNode->attrib("name"));
}
ifound = true;
}
if (th.hasChild("Shomate")) {
if (ssModel == "idealGas") {
has_shomate_idealGas++;
} else if (ssModel == "constant_incompressible" ||
ssModel == "constantVolume") {
has_shomate_constVol++;
} else {
throw UnknownVPSSMgrModel("getVPSSMgrTypes:",
spNode->attrib("name"));
}
ifound = true;
}
if (th.hasChild("const_cp")){
if (ssModel == "idealGas") {
has_simple_idealGas++;
} else if (ssModel == "constant_incompressible" ||
ssModel == "constantVolume") {
has_simple_constVol++;
} else {
throw UnknownVPSSMgrModel("getVPSSMgrTypes:",
spNode->attrib("name"));
}
ifound = true;
}
if (th.hasChild("poly")) {
if (th.child("poly")["order"] == "1") {
has_simple_constVol = 1;
ifound = true;
} else throw CanteraError("newSpeciesThermo",
"poly with order > 1 not yet supported");
}
if (th.hasChild("Mu0")) {
has_other++;
ifound = true;
}
if (th.hasChild("NASA9")) {
has_other++;
ifound = true;
}
if (th.hasChild("NASA9MULTITEMP")) {
has_other++;
ifound = true;
}
if (th.hasChild("adsorbate")) {
has_other++;
ifound = true;
}
if (th.hasChild("HKFT")) {
has_hptx++;
ifound = true;
}
} else {
throw UnknownVPSSMgrModel("getVPSSMgrTypes:",
spNode->attrib("name"));
}
}
}
}
void MixedSolventElectrolyte::readXMLBinarySpecies(XML_Node& xmLBinarySpecies)
{
string xname = xmLBinarySpecies.name();
if (xname != "binaryNeutralSpeciesParameters") {
throw CanteraError("MixedSolventElectrolyte::readXMLBinarySpecies",
"Incorrect name for processing this routine: " + xname);
}
string stemp;
size_t nParamsFound;
vector_fp vParams;
string iName = xmLBinarySpecies.attrib("speciesA");
if (iName == "") {
throw CanteraError("MixedSolventElectrolyte::readXMLBinarySpecies", "no speciesA attrib");
}
string jName = xmLBinarySpecies.attrib("speciesB");
if (jName == "") {
throw CanteraError("MixedSolventElectrolyte::readXMLBinarySpecies", "no speciesB attrib");
}
/*
* Find the index of the species in the current phase. It's not
* an error to not find the species
*/
size_t iSpecies = speciesIndex(iName);
if (iSpecies == npos) {
return;
}
string ispName = speciesName(iSpecies);
if (charge(iSpecies) != 0) {
throw CanteraError("MixedSolventElectrolyte::readXMLBinarySpecies", "speciesA charge problem");
}
size_t jSpecies = speciesIndex(jName);
if (jSpecies == npos) {
return;
}
string jspName = speciesName(jSpecies);
if (charge(jSpecies) != 0) {
throw CanteraError("MixedSolventElectrolyte::readXMLBinarySpecies", "speciesB charge problem");
}
resizeNumInteractions(numBinaryInteractions_ + 1);
size_t iSpot = numBinaryInteractions_ - 1;
m_pSpecies_A_ij[iSpot] = iSpecies;
m_pSpecies_B_ij[iSpot] = jSpecies;
size_t num = xmLBinarySpecies.nChildren();
for (size_t iChild = 0; iChild < num; iChild++) {
XML_Node& xmlChild = xmLBinarySpecies.child(iChild);
stemp = xmlChild.name();
string nodeName = lowercase(stemp);
/*
* Process the binary species interaction child elements
*/
if (nodeName == "excessenthalpy") {
/*
* Get the string containing all of the values
*/
ctml::getFloatArray(xmlChild, vParams, true, "toSI", "excessEnthalpy");
nParamsFound = vParams.size();
if (nParamsFound != 2) {
throw CanteraError("MixedSolventElectrolyte::readXMLBinarySpecies::excessEnthalpy for " + ispName
+ "::" + jspName,
"wrong number of params found");
}
m_HE_b_ij[iSpot] = vParams[0];
m_HE_c_ij[iSpot] = vParams[1];
}
if (nodeName == "excessentropy") {
/*
* Get the string containing all of the values
*/
ctml::getFloatArray(xmlChild, vParams, true, "toSI", "excessEntropy");
nParamsFound = vParams.size();
if (nParamsFound != 2) {
throw CanteraError("MixedSolventElectrolyte::readXMLBinarySpecies::excessEntropy for " + ispName
+ "::" + jspName,
"wrong number of params found");
}
m_SE_b_ij[iSpot] = vParams[0];
m_SE_c_ij[iSpot] = vParams[1];
}
if (nodeName == "excessvolume_enthalpy") {
/*
* Get the string containing all of the values
*/
ctml::getFloatArray(xmlChild, vParams, true, "toSI", "excessVolume_Enthalpy");
nParamsFound = vParams.size();
if (nParamsFound != 2) {
throw CanteraError("MixedSolventElectrolyte::readXMLBinarySpecies::excessVolume_Enthalpy for " + ispName
+ "::" + jspName,
"wrong number of params found");
}
m_VHE_b_ij[iSpot] = vParams[0];
m_VHE_c_ij[iSpot] = vParams[1];
}
if (nodeName == "excessvolume_entropy") {
/*
* Get the string containing all of the values
*/
ctml::getFloatArray(xmlChild, vParams, true, "toSI", "excessVolume_Entropy");
nParamsFound = vParams.size();
if (nParamsFound != 2) {
throw CanteraError("MixedSolventElectrolyte::readXMLBinarySpecies::excessVolume_Entropy for " + ispName
+ "::" + jspName,
"wrong number of params found");
}
m_VSE_b_ij[iSpot] = vParams[0];
m_VSE_c_ij[iSpot] = vParams[1];
}
}
}
void MargulesVPSSTP::readXMLBinarySpecies(XML_Node& xmLBinarySpecies)
{
string xname = xmLBinarySpecies.name();
if (xname != "binaryNeutralSpeciesParameters") {
throw CanteraError("MargulesVPSSTP::readXMLBinarySpecies",
"Incorrect name for processing this routine: " + xname);
}
string aName = xmLBinarySpecies.attrib("speciesA");
if (aName == "") {
throw CanteraError("MargulesVPSSTP::readXMLBinarySpecies", "no speciesA attrib");
}
string bName = xmLBinarySpecies.attrib("speciesB");
if (bName == "") {
throw CanteraError("MargulesVPSSTP::readXMLBinarySpecies", "no speciesB attrib");
}
vector_fp vParams;
double h0 = 0.0;
double h1 = 0.0;
double s0 = 0.0;
double s1 = 0.0;
double vh0 = 0.0;
double vh1 = 0.0;
double vs0 = 0.0;
double vs1 = 0.0;
for (size_t iChild = 0; iChild < xmLBinarySpecies.nChildren(); iChild++) {
XML_Node& xmlChild = xmLBinarySpecies.child(iChild);
string nodeName = toLowerCopy(xmlChild.name());
// Process the binary species interaction parameters.
// They are in subblocks labeled:
// excessEnthalpy
// excessEntropy
// excessVolume_Enthalpy
// excessVolume_Entropy
// Other blocks are currently ignored.
// @TODO determine a policy about ignoring blocks that should or shouldn't be there.
if (nodeName == "excessenthalpy") {
// Get the string containing all of the values
getFloatArray(xmlChild, vParams, true, "toSI", "excessEnthalpy");
if (vParams.size() != 2) {
throw CanteraError("MargulesVPSSTP::readXMLBinarySpecies"
"excessEnthalpy for {} : {}: wrong number of params found."
" Need 2", aName, bName);
}
h0 = vParams[0];
h1 = vParams[1];
} else if (nodeName == "excessentropy") {
// Get the string containing all of the values
getFloatArray(xmlChild, vParams, true, "toSI", "excessEntropy");
if (vParams.size() != 2) {
throw CanteraError("MargulesVPSSTP::readXMLBinarySpecies"
"excessEntropy for {} : {}: wrong number of params found."
" Need 2", aName, bName);
}
s0 = vParams[0];
s1 = vParams[1];
} else if (nodeName == "excessvolume_enthalpy") {
// Get the string containing all of the values
getFloatArray(xmlChild, vParams, true, "toSI", "excessVolume_Enthalpy");
if (vParams.size() != 2) {
throw CanteraError("MargulesVPSSTP::readXMLBinarySpecies"
"excessVolume_Enthalpy for {} : {}: wrong number of params"
" found. Need 2", aName, bName);
}
vh0 = vParams[0];
vh1 = vParams[1];
} else if (nodeName == "excessvolume_entropy") {
// Get the string containing all of the values
getFloatArray(xmlChild, vParams, true, "toSI", "excessVolume_Entropy");
if (vParams.size() != 2) {
throw CanteraError("MargulesVPSSTP::readXMLBinarySpecies"
"excessVolume_Entropy for {} : {}: wrong number of params"
" found. Need 2", aName, bName);
}
vs0 = vParams[0];
vs1 = vParams[1];
}
}
addBinaryInteraction(aName, bName, h0, h1, s0, s1, vh0, vh1, vs0, vs1);
}
