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;
}