void Phase::addSpecies(const std::string& name_, const doublereal* comp,
doublereal charge_, doublereal size_)
{
freezeElements();
m_speciesNames.push_back(name_);
m_speciesCharge.push_back(charge_);
m_speciesSize.push_back(size_);
size_t ne = nElements();
// Create a changeable copy of the element composition. We now change
// the charge potentially
vector_fp compNew(ne);
for (size_t m = 0; m < ne; m++) {
compNew[m] = comp[m];
}
double wt = 0.0;
const vector_fp& aw = atomicWeights();
if (charge_ != 0.0) {
size_t eindex = elementIndex("E");
if (eindex != npos) {
doublereal ecomp = compNew[eindex];
if (fabs(charge_ + ecomp) > 0.001) {
if (ecomp != 0.0) {
throw CanteraError("Phase::addSpecies",
"Input charge and element E compositions differ "
"for species " + name_);
} else {
// Just fix up the element E composition based on the input
// species charge
compNew[eindex] = -charge_;
}
}
} else {
addUniqueElementAfterFreeze("E", 0.000545, 0, 0.0,
CT_ELEM_TYPE_ELECTRONCHARGE);
ne = nElements();
eindex = elementIndex("E");
compNew.resize(ne);
compNew[ne - 1] = - charge_;
}
}
for (size_t m = 0; m < ne; m++) {
m_speciesComp.push_back(compNew[m]);
wt += compNew[m] * aw[m];
}
m_molwts.push_back(wt);
m_kk++;
}
bool Phase::addSpecies(shared_ptr<Species> spec) {
m_species[spec->name] = spec;
vector_fp comp(nElements());
for (const auto& elem : spec->composition) {
size_t m = elementIndex(elem.first);
if (m == npos) { // Element doesn't exist in this phase
switch (m_undefinedElementBehavior) {
case UndefElement::ignore:
return false;
case UndefElement::add:
addElement(elem.first);
comp.resize(nElements());
m = elementIndex(elem.first);
break;
case UndefElement::error:
default:
throw CanteraError("Phase::addSpecies",
"Species '{}' contains an undefined element '{}'.",
spec->name, elem.first);
}
}
comp[m] = elem.second;
}
m_speciesNames.push_back(spec->name);
m_speciesIndices[spec->name] = m_kk;
m_speciesCharge.push_back(spec->charge);
m_speciesSize.push_back(spec->size);
size_t ne = nElements();
double wt = 0.0;
const vector_fp& aw = atomicWeights();
if (spec->charge != 0.0) {
size_t eindex = elementIndex("E");
if (eindex != npos) {
doublereal ecomp = comp[eindex];
if (fabs(spec->charge + ecomp) > 0.001) {
if (ecomp != 0.0) {
throw CanteraError("Phase::addSpecies",
"Input charge and element E compositions differ "
"for species " + spec->name);
} else {
// Just fix up the element E composition based on the input
// species charge
comp[eindex] = -spec->charge;
}
}
} else {
addElement("E", 0.000545, 0, 0.0, CT_ELEM_TYPE_ELECTRONCHARGE);
ne = nElements();
eindex = elementIndex("E");
comp.resize(ne);
comp[ne - 1] = - spec->charge;
}
}
for (size_t m = 0; m < ne; m++) {
m_speciesComp.push_back(comp[m]);
wt += comp[m] * aw[m];
}
// Some surface phases may define species representing empty sites
// that have zero molecular weight. Give them a very small molecular
// weight to avoid dividing by zero.
wt = std::max(wt, Tiny);
m_molwts.push_back(wt);
m_rmolwts.push_back(1.0/wt);
m_kk++;
// Ensure that the Phase has a valid mass fraction vector that sums to
// one. We will assume that species 0 has a mass fraction of 1.0 and mass
// fraction of all other species is 0.0.
if (m_kk == 1) {
m_y.push_back(1.0);
m_ym.push_back(m_rmolwts[0]);
m_mmw = 1.0 / m_ym[0];
} else {
m_y.push_back(0.0);
m_ym.push_back(0.0);
}
invalidateCache();
return true;
}
