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docs(fourdst::composition-and-fourdst::atomic): update documentation

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This commit is contained in:
Emily Boudreaux
2025-11-08 06:42:41 -05:00
parent a790d21df9
commit 7a303b8d3a
9 changed files with 787 additions and 278 deletions
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65
src/composition/lib/composition.cpp
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@@ -196,7 +196,7 @@ namespace fourdst::composition {
void Composition::registerSpecies(
const atomic::Species &species
) {
) noexcept {
m_registeredSpecies.insert(species);
if (!m_molarAbundances.contains(species)) {
m_molarAbundances.emplace(species, 0.0);
@@ -205,13 +205,13 @@ namespace fourdst::composition {
void Composition::registerSpecies(
const std::vector<atomic::Species> &species
) {
) noexcept {
for (const auto& s : species) {
registerSpecies(s);
}
}
std::set<std::string> Composition::getRegisteredSymbols() const {
std::set<std::string> Composition::getRegisteredSymbols() const noexcept {
std::set<std::string> symbols;
for (const auto& species : m_registeredSpecies) {
symbols.insert(std::string(species.name()));
@@ -219,7 +219,7 @@ namespace fourdst::composition {
return symbols;
}
const std::set<atomic::Species> &Composition::getRegisteredSpecies() const {
const std::set<atomic::Species> &Composition::getRegisteredSpecies() const noexcept {
return m_registeredSpecies;
}
@@ -235,6 +235,9 @@ namespace fourdst::composition {
double Composition::getMassFraction(
const atomic::Species &species
) const {
if (!m_molarAbundances.contains(species)) {
throw_unregistered_symbol(getLogger(), std::string(species.name()));
}
std::map<atomic::Species, double> raw_mass;
double totalMass = 0;
for (const auto& [sp, y] : m_molarAbundances) {
@@ -245,7 +248,7 @@ namespace fourdst::composition {
return raw_mass.at(species) / totalMass;
}
std::unordered_map<atomic::Species, double> Composition::getMassFraction() const {
std::unordered_map<atomic::Species, double> Composition::getMassFraction() const noexcept {
std::unordered_map<atomic::Species, double> mass_fractions;
for (const auto &species: m_molarAbundances | std::views::keys) {
mass_fractions.emplace(species, getMassFraction(species));
@@ -257,7 +260,7 @@ namespace fourdst::composition {
double Composition::getNumberFraction(
const std::string& symbol
) const {
auto species = getSpecies(symbol);
const auto species = getSpecies(symbol);
if (!species) {
throw_unknown_symbol(getLogger(), symbol);
}
@@ -267,6 +270,9 @@ namespace fourdst::composition {
double Composition::getNumberFraction(
const atomic::Species &species
) const {
if (!m_molarAbundances.contains(species)) {
throw_unregistered_symbol(getLogger(), std::string(species.name()));
}
double total_moles_per_gram = 0.0;
for (const auto &y: m_molarAbundances | std::views::values) {
total_moles_per_gram += y;
@@ -274,7 +280,7 @@ namespace fourdst::composition {
return m_molarAbundances.at(species) / total_moles_per_gram;
}
std::unordered_map<atomic::Species, double> Composition::getNumberFraction() const {
std::unordered_map<atomic::Species, double> Composition::getNumberFraction() const noexcept {
std::unordered_map<atomic::Species, double> number_fractions;
for (const auto &species: m_molarAbundances | std::views::keys) {
number_fractions.emplace(species, getNumberFraction(species));
@@ -285,7 +291,7 @@ namespace fourdst::composition {
double Composition::getMolarAbundance(
const std::string &symbol
) const {
auto species = getSpecies(symbol);
const auto species = getSpecies(symbol);
if (!species) {
throw_unknown_symbol(getLogger(), symbol);
}
@@ -297,13 +303,12 @@ namespace fourdst::composition {
const atomic::Species &species
) const {
if (!m_molarAbundances.contains(species)) {
LOG_CRITICAL(getLogger(), "Species {} is not registered in the composition.", species.name());
throw exceptions::UnregisteredSymbolError("Species " + std::string(species.name()) + " is not registered in the composition.");
throw_unregistered_symbol(getLogger(), std::string(species.name()));
}
return m_molarAbundances.at(species);
}
double Composition::getMeanParticleMass() const {
double Composition::getMeanParticleMass() const noexcept {
std::vector<double> X = getMassFractionVector();
double sum = 0.0;
for (const auto& [species, x] : std::views::zip(m_registeredSpecies, X)) {
@@ -313,7 +318,7 @@ namespace fourdst::composition {
return 1.0 / sum;
}
double Composition::getElectronAbundance() const {
double Composition::getElectronAbundance() const noexcept {
double Ye = 0.0;
for (const auto& [species, y] : m_molarAbundances) {
Ye += species.z() * y;
@@ -323,7 +328,6 @@ namespace fourdst::composition {
CanonicalComposition Composition::getCanonicalComposition(
const bool harsh
) const {
using namespace fourdst::atomic;
@@ -358,20 +362,15 @@ namespace fourdst::composition {
// ReSharper disable once CppTooWideScopeInitStatement
const double Z = 1.0 - (canonicalComposition.X + canonicalComposition.Y);
if (std::abs(Z - canonicalComposition.Z) > 1e-6) {
if (!harsh) {
LOG_WARNING(getLogger(), "Validation composition Z (X-Y = {}) is different than canonical composition Z ({}) (∑a_i where a_i != H/He).", Z, canonicalComposition.Z);
}
else {
LOG_ERROR(getLogger(), "Validation composition Z (X-Y = {}) is different than canonical composition Z ({}) (∑a_i where a_i != H/He).", Z, canonicalComposition.Z);
throw std::runtime_error("Validation composition Z (X-Y = " + std::to_string(Z) + ") is different than canonical composition Z (" + std::to_string(canonicalComposition.Z) + ") (∑a_i where a_i != H/He).");
}
if (std::abs(Z - canonicalComposition.Z) > 1e-16) {
LOG_ERROR(getLogger(), "Validation composition Z (X-Y = {}) is different than canonical composition Z ({}) (∑a_i where a_i != H/He).", Z, canonicalComposition.Z);
throw exceptions::InvalidCompositionError("Validation composition Z (X-Y = " + std::to_string(Z) + ") is different than canonical composition Z (" + std::to_string(canonicalComposition.Z) + ") (∑a_i where a_i != H/He).");
}
m_cache.canonicalComp = canonicalComposition;
return canonicalComposition;
}
std::vector<double> Composition::getMassFractionVector() const {
std::vector<double> Composition::getMassFractionVector() const noexcept {
if (m_cache.massFractions.has_value()) {
return m_cache.massFractions.value(); // Short circuit if we have cached the mass fractions
}
@@ -393,7 +392,7 @@ namespace fourdst::composition {
}
std::vector<double> Composition::getNumberFractionVector() const {
std::vector<double> Composition::getNumberFractionVector() const noexcept {
if (m_cache.numberFractions.has_value()) {
return m_cache.numberFractions.value(); // Short circuit if we have cached the number fractions
}
@@ -414,7 +413,7 @@ namespace fourdst::composition {
return numberFractions;
}
std::vector<double> Composition::getMolarAbundanceVector() const {
std::vector<double> Composition::getMolarAbundanceVector() const noexcept {
if (m_cache.molarAbundances.has_value()) {
return m_cache.molarAbundances.value(); // Short circuit if we have cached the molar abundances
}
@@ -500,12 +499,16 @@ namespace fourdst::composition {
}
std::vector<atomic::Species> sortedSymbols = sortVectorBy(speciesVector, speciesMass);
if (index >= sortedSymbols.size()) {
LOG_ERROR(getLogger(), "Index {} is out of range for composition of size {}.", index, sortedSymbols.size());
throw std::out_of_range("Index " + std::to_string(index) + " is out of range for composition of size " + std::to_string(sortedSymbols.size()) + ".");
}
return sortedSymbols.at(index);
}
bool Composition::contains(
const atomic::Species &species
) const {
) const noexcept {
return m_registeredSpecies.contains(species);
}
@@ -519,7 +522,7 @@ namespace fourdst::composition {
return contains(species.value());
}
size_t Composition::size() const {
size_t Composition::size() const noexcept {
return m_registeredSpecies.size();
}
@@ -532,11 +535,7 @@ namespace fourdst::composition {
throw_unknown_symbol(getLogger(), symbol);
}
if (!m_registeredSpecies.contains(species.value())) {
throw_unregistered_symbol(getLogger(), symbol);
}
m_molarAbundances.at(species.value()) = molar_abundance;
setMolarAbundance(species.value(), molar_abundance);
}
void Composition::setMolarAbundance(
@@ -546,6 +545,10 @@ namespace fourdst::composition {
if (!m_registeredSpecies.contains(species)) {
throw_unregistered_symbol(getLogger(), std::string(species.name()));
}
if (molar_abundance < 0.0) {
LOG_ERROR(getLogger(), "Molar abundance must be non-negative for symbol {}. Currently it is {}.", species.name(), molar_abundance);
throw exceptions::InvalidCompositionError("Molar abundance must be non-negative, got " + std::to_string(molar_abundance) + " for symbol " + std::string(species.name()) + ".");
}
m_molarAbundances.at(species) = molar_abundance;
}