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 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);
}
}
compositionMap parseCompString(const std::string& ss,
const std::vector<std::string>& names)
{
compositionMap x;
for (size_t k = 0; k < names.size(); k++) {
x[names[k]] = 0.0;
}
size_t start = 0;
size_t stop = 0;
while (stop < ss.size()) {
size_t colon = ss.find(':', start);
if (colon == npos) {
break;
}
size_t valstart = ss.find_first_not_of(" \t\n", colon+1);
stop = ss.find_first_of(", ;\n\t", valstart);
std::string name = stripws(ss.substr(start, colon-start));
if (!names.empty() && x.find(name) == x.end()) {
throw CanteraError("parseCompString",
"unknown species '" + name + "'");
}
x[name] = fpValueCheck(ss.substr(valstart, stop-colon-1));
start = ss.find_first_not_of(", ;\n\t", stop+1);
}
if (stop != npos && !stripws(ss.substr(stop)).empty()) {
throw CanteraError("parseCompString", "Found non-key:value data "
"in composition string: '" + ss.substr(stop) + "'");
}
return x;
}
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");
}
}
}
/**
* 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;
}
}
doublereal strSItoDbl(const std::string& strSI)
{
std::vector<std::string> v;
tokenizeString(strSI, v);
doublereal fp = 1.0;
size_t n = v.size();
if (n > 2 || n < 1) {
throw CanteraError("strSItoDbl",
"number of tokens is too high");
} else if (n == 2) {
fp = toSI(v[1]);
}
doublereal val = fpValueCheck(v[0]);
return val * fp;
}
int fillArrayFromString(const std::string& str,
doublereal* const a, const char delim)
{
warn_deprecated("fillArrayFromString", "To be removed after Cantera 2.2.");
std::string::size_type iloc;
int count = 0;
std::string num;
std::string s = str;
while (s.size() > 0) {
iloc = s.find(delim);
if (iloc > 0) {
num = s.substr(0, iloc);
s = s.substr(iloc+1,s.size());
} else {
num = s;
s = "";
}
a[count] = fpValueCheck(num);
count++;
}
return count;
}
compositionMap parseCompString(const std::string& ss,
const std::vector<std::string>& names)
{
compositionMap x;
for (size_t k = 0; k < names.size(); k++) {
x[names[k]] = 0.0;
}
size_t start = 0;
size_t stop = 0;
size_t left = 0;
while (stop < ss.size()) {
size_t colon = ss.find(':', left);
if (colon == npos) {
break;
}
size_t valstart = ss.find_first_not_of(" \t\n", colon+1);
stop = ss.find_first_of(", ;\n\t", valstart);
std::string name = ba::trim_copy(ss.substr(start, colon-start));
if (!names.empty() && x.find(name) == x.end()) {
throw CanteraError("parseCompString",
"unknown species '" + name + "'");
}
double value;
try {
value = fpValueCheck(ss.substr(valstart, stop-valstart));
} catch (CanteraError&) {
// If we have a key containing a colon, we expect this to fail. In
// this case, take the current substring as part of the key and look
// to the right of the next colon for the corresponding value.
// Otherwise, this is an invalid composition string.
std::string testname = ss.substr(start, stop-start);
if (testname.find_first_of(" \n\t") != npos) {
// Space, tab, and newline are never allowed in names
throw;
} else if (ss.substr(valstart, stop-valstart).find(':') != npos) {
left = colon + 1;
stop = 0; // Force another iteration of this loop
continue;
} else {
throw;
}
}
if (getValue(x, name, 0.0) != 0.0) {
throw CanteraError("parseCompString",
"Duplicate key: '" + name + "'.");
}
x[name] = value;
start = ss.find_first_not_of(", ;\n\t", stop+1);
left = start;
}
if (left != start) {
throw CanteraError("parseCompString", "Unable to parse key-value pair:"
"\n'{}'", ss.substr(start, stop));
}
if (stop != npos && !ba::trim_copy(ss.substr(stop)).empty()) {
throw CanteraError("parseCompString", "Found non-key:value data "
"in composition string: '" + ss.substr(stop) + "'");
}
return x;
}
size_t Phase::addElement(const std::string& symbol, doublereal weight,
int atomic_number, doublereal entropy298,
int elem_type)
{
// Look up the atomic weight if not given
if (weight == 0.0) {
try {
weight = getElementWeight(symbol);
} catch (CanteraError&) {
// assume this is just a custom element with zero atomic weight
}
} else if (weight == -12345.0) {
weight = getElementWeight(symbol);
}
// Try to look up the standard entropy if not given. Fail silently.
if (entropy298 == ENTROPY298_UNKNOWN) {
try {
XML_Node* db = get_XML_File("elements.xml");
XML_Node* elnode = db->findByAttr("name", symbol);
if (elnode && elnode->hasChild("entropy298")) {
entropy298 = fpValueCheck(elnode->child("entropy298")["value"]);
}
} catch (CanteraError&) {
}
}
// Check for duplicates
auto iter = find(m_elementNames.begin(), m_elementNames.end(), symbol);
if (iter != m_elementNames.end()) {
size_t m = iter - m_elementNames.begin();
if (m_atomicWeights[m] != weight) {
throw CanteraError("Phase::addElement",
"Duplicate elements ({}) have different weights", symbol);
} else {
// Ignore attempt to add duplicate element with the same weight
return m;
}
}
// Add the new element
m_atomicWeights.push_back(weight);
m_elementNames.push_back(symbol);
m_atomicNumbers.push_back(atomic_number);
m_entropy298.push_back(entropy298);
if (symbol == "E") {
m_elem_type.push_back(CT_ELEM_TYPE_ELECTRONCHARGE);
} else {
m_elem_type.push_back(elem_type);
}
m_mm++;
// Update species compositions
if (m_kk) {
vector_fp old(m_speciesComp);
m_speciesComp.resize(m_kk*m_mm, 0.0);
for (size_t k = 0; k < m_kk; k++) {
size_t m_old = m_mm - 1;
for (size_t m = 0; m < m_old; m++) {
m_speciesComp[k * m_mm + m] = old[k * (m_old) + m];
}
m_speciesComp[k * (m_mm) + (m_mm-1)] = 0.0;
}
}
return m_mm-1;
}
void getMatrixValues(const XML_Node& node,
const std::vector<std::string>& keyStringRow,
const std::vector<std::string>& keyStringCol,
Array2D& retnValues, const bool convert,
const bool matrixSymmetric)
{
if (keyStringRow.size() > retnValues.nRows()) {
throw CanteraError("getMatrixValues",
"size of key1 greater than numrows");
} else if (keyStringCol.size() > retnValues.nColumns()) {
throw CanteraError("getMatrixValues",
"size of key2 greater than num cols");
} else if (matrixSymmetric && retnValues.nRows() != retnValues.nColumns()) {
throw CanteraError("getMatrixValues",
"nrow != ncol for a symmetric matrix");
}
/*
* Get the attributes field, units, from the XML node
* and determine the conversion factor, funit.
*/
doublereal funit = 1.0;
if (convert && node["units"] != "") {
funit = toSI(node["units"]);
}
vector<string> v;
getStringArray(node, v);
for (size_t i = 0; i < v.size(); i++) {
size_t icolon = v[i].find(":");
if (icolon == string::npos) {
throw CanteraError("getMatrixValues","Missing two colons ("
+v[i]+")");
}
string key1 = v[i].substr(0,icolon);
string rmm = v[i].substr(icolon+1, v[i].size());
icolon = rmm.find(":");
if (icolon == string::npos) {
throw CanteraError("getMatrixValues","Missing one colon ("
+v[i]+")");
}
size_t irow = find(keyStringRow.begin(), keyStringRow.end(), key1)
- keyStringRow.begin();
if (irow == keyStringRow.size()) {
throw CanteraError("getMatrixValues","Row not matched by string: "
+ key1);
}
string key2 = rmm.substr(0,icolon);
size_t icol = find(keyStringCol.begin(), keyStringCol.end(), key2)
- keyStringCol.begin();
if (icol == keyStringCol.size()) {
throw CanteraError("getMatrixValues","Col not matched by string: "
+ key2);
}
double dval = fpValueCheck(rmm.substr(icolon+1, rmm.size())) * funit;
/*
* Finally, insert the value;
*/
retnValues(irow, icol) = dval;
if (matrixSymmetric) {
retnValues(icol, irow) = dval;
}
}
}
size_t getFloatArray(const XML_Node& node, std::vector<doublereal> & v,
const bool convert, const std::string& unitsString,
const std::string& nodeName)
{
const XML_Node* readNode = &node;
if (node.name() != nodeName) {
vector<XML_Node*> ll = node.getChildren(nodeName);
if (ll.size() == 0) {
throw CanteraError("getFloatArray",
"wrong XML element type/name: was expecting "
+ nodeName + "but accessed " + node.name());
} else {
readNode = ll[0];
ll = readNode->getChildren("floatArray");
if (ll.size() > 0) {
readNode = ll[0];
}
}
}
v.clear();
doublereal vmin = Undef, vmax = Undef;
doublereal funit = 1.0;
/*
* Get the attributes field, units, from the XML node
*/
std::string units = readNode->attrib("units");
if (units != "" && convert) {
if (unitsString == "actEnergy" && units != "") {
funit = actEnergyToSI(units);
} else if (unitsString != "" && units != "") {
funit = toSI(units);
}
}
if (readNode->attrib("min") != "") {
vmin = fpValueCheck(readNode->attrib("min"));
}
if (readNode->attrib("max") != "") {
vmax = fpValueCheck(readNode->attrib("max"));
}
std::string val = readNode->value();
while (true) {
size_t icom = val.find(',');
if (icom != string::npos) {
string numstr = val.substr(0,icom);
val = val.substr(icom+1,val.size());
v.push_back(fpValueCheck(numstr));
} else {
/*
* This little bit of code is to allow for the
* possibility of a comma being the last
* item in the value text. This was allowed in
* previous versions of Cantera, even though it
* would appear to be odd. So, we keep the
* possibility in for backwards compatibility.
*/
if (!val.empty()) {
v.push_back(fpValueCheck(val));
}
break;
}
doublereal vv = v.back();
if (vmin != Undef && vv < vmin - Tiny) {
writelog("\nWarning: value "+fp2str(vv)+
" is below lower limit of " +fp2str(vmin)+".\n");
}
if (vmax != Undef && vv > vmax + Tiny) {
writelog("\nWarning: value "+fp2str(vv)+
" is above upper limit of " +fp2str(vmin)+".\n");
}
}
for (size_t n = 0; n < v.size(); n++) {
v[n] *= funit;
}
return v.size();
}
bool installSpecies(size_t k, const XML_Node& s, thermo_t& th,
SpeciesThermo* spthermo_ptr, int rule,
XML_Node* phaseNode_ptr,
VPSSMgr* vpss_ptr,
SpeciesThermoFactory* factory)
{
std::string xname = s.name();
if (xname != "species") {
throw CanteraError("installSpecies",
"Unexpected XML name of species XML_Node: " + xname);
}
// get the composition of the species
const XML_Node& a = s.child("atomArray");
map<string,string> comp;
getMap(a, comp);
// check that all elements in the species exist in 'p'. If rule != 0,
// quietly skip this species if some elements are undeclared; otherwise,
// throw an exception
map<string,string>::const_iterator _b = comp.begin();
for (; _b != comp.end(); ++_b) {
if (th.elementIndex(_b->first) == npos) {
if (rule == 0) {
throw CanteraError("installSpecies",
"Species " + s["name"] +
" contains undeclared element " + _b->first);
} else {
return false;
}
}
}
// construct a vector of atom numbers for each element in phase th. Elements
// not declared in the species (i.e., not in map comp) will have zero
// entries in the vector.
size_t nel = th.nElements();
vector_fp ecomp(nel, 0.0);
for (size_t m = 0; m < nel; m++) {
std::string& es = comp[th.elementName(m)];
if (!es.empty()) {
ecomp[m] = fpValueCheck(es);
}
}
// get the species charge, if any. Note that the charge need
// not be explicitly specified if special element 'E'
// (electron) is one of the elements.
doublereal chrg = 0.0;
if (s.hasChild("charge")) {
chrg = getFloat(s, "charge");
}
// get the species size, if any. (This is used by surface
// phases to represent how many sites a species occupies.)
doublereal sz = 1.0;
if (s.hasChild("size")) {
sz = getFloat(s, "size");
}
// add the species to phase th
th.addUniqueSpecies(s["name"], &ecomp[0], chrg, sz);
if (vpss_ptr) {
VPStandardStateTP* vp_ptr = dynamic_cast<VPStandardStateTP*>(&th);
factory->installVPThermoForSpecies(k, s, vp_ptr, phaseNode_ptr);
} else {
// install the thermo parameterization for this species into
// the species thermo manager for phase th
factory->installThermoForSpecies(k, s, &th, *spthermo_ptr, phaseNode_ptr);
}
return true;
}
bool installSpecies(size_t k, const XML_Node& s, thermo_t& th,
SpeciesThermo* spthermo_ptr, int rule,
XML_Node* phaseNode_ptr,
VPSSMgr* vpss_ptr,
SpeciesThermoFactory* factory)
{
std::string xname = s.name();
if (xname != "species") {
throw CanteraError("installSpecies",
"Unexpected XML name of species XML_Node: " + xname);
}
if (rule) {
th.ignoreUndefinedElements();
}
// get the composition of the species
const XML_Node& a = s.child("atomArray");
map<string,string> comp;
getMap(a, comp);
// construct a vector of atom numbers for each element in phase th. Elements
// not declared in the species (i.e., not in map comp) will have zero
// entries in the vector.
size_t nel = th.nElements();
vector_fp ecomp(nel, 0.0);
compositionMap comp_map = parseCompString(a.value());
for (size_t m = 0; m < nel; m++) {
std::string& es = comp[th.elementName(m)];
if (!es.empty()) {
ecomp[m] = fpValueCheck(es);
}
}
// get the species charge, if any. Note that the charge need
// not be explicitly specified if special element 'E'
// (electron) is one of the elements.
doublereal chrg = 0.0;
if (s.hasChild("charge")) {
chrg = getFloat(s, "charge");
}
// get the species size, if any. (This is used by surface
// phases to represent how many sites a species occupies.)
doublereal sz = 1.0;
if (s.hasChild("size")) {
sz = getFloat(s, "size");
}
if (vpss_ptr) {
th.addUniqueSpecies(s["name"], &ecomp[0], chrg, sz);
VPStandardStateTP* vp_ptr = dynamic_cast<VPStandardStateTP*>(&th);
vp_ptr->createInstallPDSS(k, s, phaseNode_ptr);
} else {
SpeciesThermoInterpType* st = newSpeciesThermoInterpType(s);
Species sp(s["name"], comp_map, st, chrg, sz);
// Read gas-phase transport data, if provided
if (s.hasChild("transport") &&
s.child("transport")["model"] == "gas_transport") {
XML_Node& tr = s.child("transport");
string geometry, dummy;
getString(tr, "geometry", geometry, dummy);
double diam = getFloat(tr, "LJ_diameter");
double welldepth = getFloat(tr, "LJ_welldepth");
double dipole = 0.0;
getOptionalFloat(tr, "dipoleMoment", dipole);
double polar = 0.0;
getOptionalFloat(tr, "polarizability", polar);
double rot = 0.0;
getOptionalFloat(tr, "rotRelax", rot);
double acentric = 0.0;
getOptionalFloat(tr, "acentric_factor", acentric);
GasTransportData* gastran = new GasTransportData;
gastran->setCustomaryUnits(sp.name, geometry, diam, welldepth,
dipole, polar, rot, acentric);
sp.transport.reset(gastran);
gastran->validate(sp);
}
th.addSpecies(sp);
}
return true;
}