From 4f47dc97a8198aba049e5890a43058777afd0179 Mon Sep 17 00:00:00 2001 From: Emily Boudreaux Date: Mon, 16 Jun 2025 15:00:33 -0400 Subject: [PATCH] feat(eos): EOS now uses composition module EOS code updated to make use of composition module. This is part of the larger change to change all composition handling to use the composition module. Note that the current implimentation is a bit hacky since it simply copies back and forth to the alredy used HELMEOSInput and HELMEOSOutput structs. In furture this can be more tightly connected to avoid extra copies. --- src/composition/private/composition.cpp | 1018 ++++++++++++----------- src/composition/public/composition.h | 38 +- 2 files changed, 569 insertions(+), 487 deletions(-) diff --git a/src/composition/private/composition.cpp b/src/composition/private/composition.cpp index 6af4a88..9543836 100644 --- a/src/composition/private/composition.cpp +++ b/src/composition/private/composition.cpp @@ -25,6 +25,7 @@ #include #include #include +#include #include @@ -32,539 +33,600 @@ namespace serif::composition { -CompositionEntry::CompositionEntry() : m_symbol("H-1"), m_isotope(chemSpecies::species.at("H-1")), m_initialized(false) {} - -CompositionEntry::CompositionEntry(const std::string& symbol, bool massFracMode) : m_symbol(symbol), m_isotope(chemSpecies::species.at(symbol)), m_massFracMode(massFracMode) { - setSpecies(symbol); -} - -CompositionEntry::CompositionEntry(const CompositionEntry& entry) : - m_symbol(entry.m_symbol), - m_isotope(entry.m_isotope), - m_massFracMode(entry.m_massFracMode), - m_massFraction(entry.m_massFraction), - m_numberFraction(entry.m_numberFraction), - m_relAbundance(entry.m_relAbundance), - m_initialized(entry.m_initialized) {} - -void CompositionEntry::setSpecies(const std::string& symbol) { - if (m_initialized) { - throw std::runtime_error("Composition entry is already initialized."); + CompositionEntry::CompositionEntry() : m_symbol("H-1"), m_isotope(chemSpecies::species.at("H-1")), + m_initialized(false) { } - if (chemSpecies::species.count(symbol) == 0) { - throw std::runtime_error("Invalid symbol."); + + CompositionEntry::CompositionEntry(const std::string& symbol, const bool massFracMode) : m_symbol(symbol), m_isotope(chemSpecies::species.at(symbol)), m_massFracMode(massFracMode) { + setSpecies(symbol); } - m_symbol = symbol; - m_isotope = chemSpecies::species.at(symbol); - m_initialized = true; -} -std::string CompositionEntry::symbol() const { - return m_symbol; -} + CompositionEntry::CompositionEntry(const CompositionEntry& entry) : + m_symbol(entry.m_symbol), + m_isotope(entry.m_isotope), + m_massFracMode(entry.m_massFracMode), + m_massFraction(entry.m_massFraction), + m_numberFraction(entry.m_numberFraction), + m_relAbundance(entry.m_relAbundance), + m_initialized(entry.m_initialized) {} -double CompositionEntry::mass_fraction() const { - if (!m_massFracMode) { - throw std::runtime_error("Composition entry is in number fraction mode."); + void CompositionEntry::setSpecies(const std::string& symbol) { + if (m_initialized) { + throw std::runtime_error("Composition entry is already initialized."); + } + if (chemSpecies::species.count(symbol) == 0) { + throw std::runtime_error("Invalid symbol."); + } + m_symbol = symbol; + m_isotope = chemSpecies::species.at(symbol); + m_initialized = true; } - return m_massFraction; -} -double CompositionEntry::mass_fraction(double meanMolarMass) const { - if (m_massFracMode) { + std::string CompositionEntry::symbol() const { + return m_symbol; + } + + double CompositionEntry::mass_fraction() const { + if (!m_massFracMode) { + throw std::runtime_error("Composition entry is in number fraction mode."); + } return m_massFraction; } - return m_relAbundance / meanMolarMass; -} - -double CompositionEntry::number_fraction() const { - if (m_massFracMode) { - throw std::runtime_error("Composition entry is in mass fraction mode."); - } - return m_numberFraction; -} - -double CompositionEntry::number_fraction(double totalMoles) const { - if (m_massFracMode) { - return m_relAbundance / totalMoles; - } - return m_numberFraction; -} - -double CompositionEntry::rel_abundance() const { - return m_relAbundance; -} - -chemSpecies::Species CompositionEntry::isotope() const { - return m_isotope; -} - -void CompositionEntry::setMassFraction(double mass_fraction) { - if (!m_massFracMode) { - throw std::runtime_error("Composition entry is in number fraction mode."); - } - m_massFraction = mass_fraction; - m_relAbundance = m_massFraction / m_isotope.mass(); -} - -void CompositionEntry::setNumberFraction(double number_fraction) { - if (m_massFracMode) { - throw std::runtime_error("Composition entry is in mass fraction mode."); - } - m_numberFraction = number_fraction; - m_relAbundance = m_numberFraction * m_isotope.mass(); -} - -bool CompositionEntry::setMassFracMode(double meanParticleMass) { - if (m_massFracMode) { - return false; - } - m_massFracMode = true; - m_massFraction = m_relAbundance / meanParticleMass; - return true; -} - -bool CompositionEntry::setNumberFracMode(double specificNumberDensity) { - if (!m_massFracMode) { - return false; - } - m_massFracMode = false; - m_numberFraction = m_relAbundance / specificNumberDensity; - return true; -} - -bool CompositionEntry::getMassFracMode() const { - return m_massFracMode; -} - -Composition::Composition(const std::vector& symbols) { - for (const auto& symbol : symbols) { - registerSymbol(symbol); - } -} - -Composition::Composition(const std::set& symbols) { - for (const auto& symbol : symbols) { - registerSymbol(symbol); - } -} - -Composition::Composition(const std::vector& symbols, const std::vector& fractions, bool massFracMode) : m_massFracMode(massFracMode) { - if (symbols.size() != fractions.size()) { - LOG_ERROR(m_logger, "The number of symbols and fractions must be equal."); - throw std::runtime_error("The number of symbols and fractions must be equal."); - } - - validateComposition(fractions); - - for (const auto &symbol : symbols) { - registerSymbol(symbol); - } - - for (size_t i = 0; i < symbols.size(); ++i) { + double CompositionEntry::mass_fraction(double meanMolarMass) const { if (m_massFracMode) { - setMassFraction(symbols[i], fractions[i]); + return m_massFraction; + } + return m_relAbundance / meanMolarMass; + } + + + double CompositionEntry::number_fraction() const { + if (m_massFracMode) { + throw std::runtime_error("Composition entry is in mass fraction mode."); + } + return m_numberFraction; + } + + double CompositionEntry::number_fraction(double totalMoles) const { + if (m_massFracMode) { + return m_relAbundance / totalMoles; + } + return m_numberFraction; + } + + double CompositionEntry::rel_abundance() const { + return m_relAbundance; + } + + chemSpecies::Species CompositionEntry::isotope() const { + return m_isotope; + } + + void CompositionEntry::setMassFraction(double mass_fraction) { + if (!m_massFracMode) { + throw std::runtime_error("Composition entry is in number fraction mode."); + } + m_massFraction = mass_fraction; + m_relAbundance = m_massFraction / m_isotope.mass(); + } + + void CompositionEntry::setNumberFraction(double number_fraction) { + if (m_massFracMode) { + throw std::runtime_error("Composition entry is in mass fraction mode."); + } + m_numberFraction = number_fraction; + m_relAbundance = m_numberFraction * m_isotope.mass(); + } + + bool CompositionEntry::setMassFracMode(double meanParticleMass) { + if (m_massFracMode) { + return false; + } + m_massFracMode = true; + m_massFraction = m_relAbundance / meanParticleMass; + return true; + } + + bool CompositionEntry::setNumberFracMode(double specificNumberDensity) { + if (!m_massFracMode) { + return false; + } + m_massFracMode = false; + m_numberFraction = m_relAbundance / specificNumberDensity; + return true; + } + + bool CompositionEntry::getMassFracMode() const { + return m_massFracMode; + } + + Composition::Composition(const std::vector& symbols) { + for (const auto& symbol : symbols) { + registerSymbol(symbol); + } + } + + Composition::Composition(const std::set& symbols) { + for (const auto& symbol : symbols) { + registerSymbol(symbol); + } + } + + Composition::Composition(const std::vector& symbols, const std::vector& fractions, bool massFracMode) : m_massFracMode(massFracMode) { + if (symbols.size() != fractions.size()) { + LOG_ERROR(m_logger, "The number of symbols and fractions must be equal."); + throw std::runtime_error("The number of symbols and fractions must be equal."); + } + + validateComposition(fractions); + + for (const auto &symbol : symbols) { + registerSymbol(symbol); + } + + for (size_t i = 0; i < symbols.size(); ++i) { + if (m_massFracMode) { + setMassFraction(symbols[i], fractions[i]); + } else { + setNumberFraction(symbols[i], fractions[i]); + } + } + finalize(); + } + + Composition::Composition(const Composition &composition) { + m_finalized = composition.m_finalized; + m_specificNumberDensity = composition.m_specificNumberDensity; + m_meanParticleMass = composition.m_meanParticleMass; + m_massFracMode = composition.m_massFracMode; + m_registeredSymbols = composition.m_registeredSymbols; + m_compositions = composition.m_compositions; + } + + Composition& Composition::operator=(const Composition &other) { + if (this != &other) { + m_finalized = other.m_finalized; + m_specificNumberDensity = other.m_specificNumberDensity; + m_meanParticleMass = other.m_meanParticleMass; + m_massFracMode = other.m_massFracMode; + m_registeredSymbols = other.m_registeredSymbols; + m_compositions = other.m_compositions; + // note: m_config remains bound to the same singleton, so we skip it + } + return *this; + + } + + void Composition::registerSymbol(const std::string& symbol, bool massFracMode) { + if (!isValidSymbol(symbol)) { + LOG_ERROR(m_logger, "Invalid symbol: {}", symbol); + throw std::runtime_error("Invalid symbol."); + } + + // If no symbols have been registered allow mode to be set + if (m_registeredSymbols.size() == 0) { + m_massFracMode = massFracMode; } else { - setNumberFraction(symbols[i], fractions[i]); + if (m_massFracMode != massFracMode) { + LOG_ERROR(m_logger, "Composition is in mass fraction mode. Cannot register symbol in number fraction mode."); + throw std::runtime_error("Composition is in mass fraction mode. Cannot register symbol in number fraction mode."); + } } - } - finalize(); -} -void Composition::registerSymbol(const std::string& symbol, bool massFracMode) { - if (!isValidSymbol(symbol)) { - LOG_ERROR(m_logger, "Invalid symbol: {}", symbol); - throw std::runtime_error("Invalid symbol."); + if (m_registeredSymbols.find(symbol) != m_registeredSymbols.end()) { + LOG_WARNING(m_logger, "Symbol {} is already registered.", symbol); + return; + } + + m_registeredSymbols.insert(symbol); + CompositionEntry entry(symbol, m_massFracMode); + m_compositions[symbol] = entry; + LOG_INFO(m_logger, "Registered symbol: {}", symbol); } - // If no symbols have been registered allow mode to be set - if (m_registeredSymbols.size() == 0) { - m_massFracMode = massFracMode; - } else { - if (m_massFracMode != massFracMode) { - LOG_ERROR(m_logger, "Composition is in mass fraction mode. Cannot register symbol in number fraction mode."); - throw std::runtime_error("Composition is in mass fraction mode. Cannot register symbol in number fraction mode."); + void Composition::registerSymbol(const std::vector& symbols, bool massFracMode) { + for (const auto& symbol : symbols) { + registerSymbol(symbol, massFracMode); } } - if (m_registeredSymbols.find(symbol) != m_registeredSymbols.end()) { - LOG_WARNING(m_logger, "Symbol {} is already registered.", symbol); - return; + std::set Composition::getRegisteredSymbols() const { + return m_registeredSymbols; } - m_registeredSymbols.insert(symbol); - CompositionEntry entry(symbol, m_massFracMode); - m_compositions[symbol] = entry; - LOG_INFO(m_logger, "Registered symbol: {}", symbol); -} - -void Composition::registerSymbol(const std::vector& symbols, bool massFracMode) { - for (const auto& symbol : symbols) { - registerSymbol(symbol, massFracMode); - } -} - -std::set Composition::getRegisteredSymbols() const { - return m_registeredSymbols; -} - -void Composition::validateComposition(const std::vector& fractions) const { - if (!isValidComposition(fractions)) { - LOG_ERROR(m_logger, "Invalid composition."); - throw std::runtime_error("Invalid composition."); - } -} - -bool Composition::isValidComposition(const std::vector& fractions) const { - double sum = 0.0; - for (const auto& fraction : fractions) { - sum += fraction; - } - if (sum < 0.999999 || sum > 1.000001) { - LOG_ERROR(m_logger, "The sum of fractions must be equal to 1."); - return false; + void Composition::validateComposition(const std::vector& fractions) const { + if (!isValidComposition(fractions)) { + LOG_ERROR(m_logger, "Invalid composition."); + throw std::runtime_error("Invalid composition."); + } } - return true; -} - -bool Composition::isValidSymbol(const std::string& symbol) const { - return chemSpecies::species.count(symbol) > 0; -} - -double Composition::setMassFraction(const std::string& symbol, const double& mass_fraction) { - if (m_registeredSymbols.find(symbol) == m_registeredSymbols.end()) { - LOG_ERROR(m_logger, "Symbol {} is not registered.", symbol); - throw std::runtime_error("Symbol is not registered."); - } - - if (!m_massFracMode) { - LOG_ERROR(m_logger, "Composition is in number fraction mode."); - throw std::runtime_error("Composition is in number fraction mode."); - } - - if (mass_fraction < 0.0 || mass_fraction > 1.0) { - LOG_ERROR(m_logger, "Mass fraction must be between 0 and 1 for symbol {}. Currently it is {}.", symbol, mass_fraction); - throw std::runtime_error("Mass fraction must be between 0 and 1."); - } - - m_finalized = false; - double old_mass_fraction = m_compositions.at(symbol).mass_fraction(); - m_compositions.at(symbol).setMassFraction(mass_fraction); - - return old_mass_fraction; -} - -std::vector Composition::setMassFraction(const std::vector& symbols, const std::vector& mass_fractions) { - if (symbols.size() != mass_fractions.size()) { - LOG_ERROR(m_logger, "The number of symbols and mass fractions must be equal."); - throw std::runtime_error("The number of symbols and mass fractions must be equal."); - } - - std::vector old_mass_fractions; - old_mass_fractions.reserve(symbols.size()); - for (size_t i = 0; i < symbols.size(); ++i) { - old_mass_fractions.push_back(setMassFraction(symbols[i], mass_fractions[i])); - } - return old_mass_fractions; -} - -double Composition::setNumberFraction(const std::string& symbol, const double& number_fraction) { - if (m_registeredSymbols.find(symbol) == m_registeredSymbols.end()) { - LOG_ERROR(m_logger, "Symbol {} is not registered.", symbol); - throw std::runtime_error("Symbol is not registered."); - } - - if (m_massFracMode) { - LOG_ERROR(m_logger, "Composition is in mass fraction mode."); - throw std::runtime_error("Composition is in mass fraction mode."); - } - - if (number_fraction < 0.0 || number_fraction > 1.0) { - LOG_ERROR(m_logger, "Number fraction must be between 0 and 1 for symbol {}. Currently it is {}.", symbol, number_fraction); - throw std::runtime_error("Number fraction must be between 0 and 1."); - } - - m_finalized = false; - double old_number_fraction = m_compositions.at(symbol).number_fraction(); - m_compositions.at(symbol).setNumberFraction(number_fraction); - - return old_number_fraction; -} - -std::vector Composition::setNumberFraction(const std::vector& symbols, const std::vector& number_fractions) { - if (symbols.size() != number_fractions.size()) { - LOG_ERROR(m_logger, "The number of symbols and number fractions must be equal."); - throw std::runtime_error("The number of symbols and number fractions must be equal."); - } - - std::vector old_number_fractions; - old_number_fractions.reserve(symbols.size()); - for (size_t i = 0; i < symbols.size(); ++i) { - old_number_fractions.push_back(setNumberFraction(symbols[i], number_fractions[i])); - } - return old_number_fractions; -} - -bool Composition::finalize(bool norm) { - bool finalized = false; - if (m_massFracMode) { - finalized = finalizeMassFracMode(norm); - } else { - finalized = finalizeNumberFracMode(norm); - } - if (finalized) { - m_finalized = true; - } - return finalized; -} - -bool Composition::finalizeMassFracMode(bool norm) { - std::vector mass_fractions; - mass_fractions.reserve(m_compositions.size()); - for (const auto& [_, entry] : m_compositions) { - mass_fractions.push_back(entry.mass_fraction()); - } - if (norm) { + bool Composition::isValidComposition(const std::vector& fractions) const { double sum = 0.0; - for (const auto& mass_fraction : mass_fractions) { - sum += mass_fraction; + for (const auto& fraction : fractions) { + sum += fraction; } - for (int i = 0; i < mass_fractions.size(); ++i) { - mass_fractions[i] /= sum; - } - for (auto& [symbol, entry] : m_compositions) { - setMassFraction(symbol, entry.mass_fraction() / sum); + if (sum < 0.999999 || sum > 1.000001) { + LOG_ERROR(m_logger, "The sum of fractions must be equal to 1."); + return false; } + + return true; } - try { - validateComposition(mass_fractions); - } catch (const std::runtime_error& e) { - double massSum = 0.0; - for (const auto& [_, entry] : m_compositions) { - massSum += entry.mass_fraction(); + + bool Composition::isValidSymbol(const std::string& symbol) const { + return chemSpecies::species.count(symbol) > 0; + } + + double Composition::setMassFraction(const std::string& symbol, const double& mass_fraction) { + if (m_registeredSymbols.find(symbol) == m_registeredSymbols.end()) { + LOG_ERROR(m_logger, "Symbol {} is not registered.", symbol); + throw std::runtime_error("Symbol is not registered."); } - LOG_ERROR(m_logger, "Composition is invalid (Total mass {}).", massSum); + + if (!m_massFracMode) { + LOG_ERROR(m_logger, "Composition is in number fraction mode."); + throw std::runtime_error("Composition is in number fraction mode."); + } + + if (mass_fraction < 0.0 || mass_fraction > 1.0) { + LOG_ERROR(m_logger, "Mass fraction must be between 0 and 1 for symbol {}. Currently it is {}.", symbol, mass_fraction); + throw std::runtime_error("Mass fraction must be between 0 and 1."); + } + m_finalized = false; - return false; - } - for (const auto& [_, entry] : m_compositions) { - m_specificNumberDensity += entry.rel_abundance(); - } - m_meanParticleMass = 1.0/m_specificNumberDensity; - return true; -} + double old_mass_fraction = m_compositions.at(symbol).mass_fraction(); + m_compositions.at(symbol).setMassFraction(mass_fraction); -bool Composition::finalizeNumberFracMode(bool norm) { - std::vector number_fractions; - number_fractions.reserve(m_compositions.size()); - for (const auto& [_, entry] : m_compositions) { - number_fractions.push_back(entry.number_fraction()); + return old_mass_fraction; } - if (norm) { - double sum = 0.0; - for (const auto& number_fraction : number_fractions) { - sum += number_fraction; + + std::vector Composition::setMassFraction(const std::vector& symbols, const std::vector& mass_fractions) { + if (symbols.size() != mass_fractions.size()) { + LOG_ERROR(m_logger, "The number of symbols and mass fractions must be equal."); + throw std::runtime_error("The number of symbols and mass fractions must be equal."); } - for (auto& [symbol, entry] : m_compositions) { - setNumberFraction(symbol, entry.number_fraction() / sum); + + std::vector old_mass_fractions; + old_mass_fractions.reserve(symbols.size()); + for (size_t i = 0; i < symbols.size(); ++i) { + old_mass_fractions.push_back(setMassFraction(symbols[i], mass_fractions[i])); } + return old_mass_fractions; } - try { - validateComposition(number_fractions); - } catch (const std::runtime_error& e) { - double numberSum = 0.0; - for (const auto& [_, entry] : m_compositions) { - numberSum += entry.number_fraction(); + + double Composition::setNumberFraction(const std::string& symbol, const double& number_fraction) { + if (m_registeredSymbols.find(symbol) == m_registeredSymbols.end()) { + LOG_ERROR(m_logger, "Symbol {} is not registered.", symbol); + throw std::runtime_error("Symbol is not registered."); } - LOG_ERROR(m_logger, "Composition is invalid (Total number {}).", numberSum); + + if (m_massFracMode) { + LOG_ERROR(m_logger, "Composition is in mass fraction mode."); + throw std::runtime_error("Composition is in mass fraction mode."); + } + + if (number_fraction < 0.0 || number_fraction > 1.0) { + LOG_ERROR(m_logger, "Number fraction must be between 0 and 1 for symbol {}. Currently it is {}.", symbol, number_fraction); + throw std::runtime_error("Number fraction must be between 0 and 1."); + } + m_finalized = false; - return false; - } - for (const auto& [_, entry] : m_compositions) { - m_meanParticleMass += entry.rel_abundance(); - } - m_specificNumberDensity = 1.0/m_meanParticleMass; - return true; -} + double old_number_fraction = m_compositions.at(symbol).number_fraction(); + m_compositions.at(symbol).setNumberFraction(number_fraction); -Composition Composition::mix(const Composition& other, double fraction) const { - if (!m_finalized || !other.m_finalized) { - LOG_ERROR(m_logger, "Compositions have not both been finalized."); - throw std::runtime_error("Compositions have not been finalized (Consider running .finalize())."); + return old_number_fraction; } - if (fraction < 0.0 || fraction > 1.0) { - LOG_ERROR(m_logger, "Fraction must be between 0 and 1."); - throw std::runtime_error("Fraction must be between 0 and 1."); + std::vector Composition::setNumberFraction(const std::vector& symbols, const std::vector& number_fractions) { + if (symbols.size() != number_fractions.size()) { + LOG_ERROR(m_logger, "The number of symbols and number fractions must be equal."); + throw std::runtime_error("The number of symbols and number fractions must be equal."); + } + + std::vector old_number_fractions; + old_number_fractions.reserve(symbols.size()); + for (size_t i = 0; i < symbols.size(); ++i) { + old_number_fractions.push_back(setNumberFraction(symbols[i], number_fractions[i])); + } + return old_number_fractions; } - std::set mixedSymbols = other.getRegisteredSymbols(); - // Get the union of the two sets - mixedSymbols.insert(m_registeredSymbols.begin(), m_registeredSymbols.end()); - - Composition mixedComposition(mixedSymbols); - for (const auto& symbol : mixedSymbols) { - double thisMassFrac, otherMassFrac = 0.0; - - thisMassFrac = hasSymbol(symbol) ? getMassFraction(symbol) : 0.0; - otherMassFrac = other.hasSymbol(symbol) ? other.getMassFraction(symbol) : 0.0; - - double massFraction = fraction * thisMassFrac + otherMassFrac * (1-fraction); - mixedComposition.setMassFraction(symbol, massFraction); - } - mixedComposition.finalize(); - return mixedComposition; -} - -double Composition::getMassFraction(const std::string& symbol) const { - if (!m_finalized) { - LOG_ERROR(m_logger, "Composition has not been finalized."); - throw std::runtime_error("Composition has not been finalized (Consider running .finalize())."); - } - if (m_compositions.count(symbol) == 0) { - LOG_ERROR(m_logger, "Symbol {} is not in the composition.", symbol); - throw std::runtime_error("Symbol is not in the composition."); - } - if (m_massFracMode) { - return m_compositions.at(symbol).mass_fraction(); - } else { - return m_compositions.at(symbol).mass_fraction(m_meanParticleMass); - } -} - -std::unordered_map Composition::getMassFraction() const { - std::unordered_map mass_fractions; - for (const auto& [symbol, entry] : m_compositions) { - mass_fractions[symbol] = getMassFraction(symbol); - } - return mass_fractions; -} - - -double Composition::getNumberFraction(const std::string& symbol) const { - if (!m_finalized) { - LOG_ERROR(m_logger, "Composition has not been finalized."); - throw std::runtime_error("Composition has not been finalized (Consider running .finalize())."); - } - if (m_compositions.count(symbol) == 0) { - LOG_ERROR(m_logger, "Symbol {} is not in the composition.", symbol); - throw std::runtime_error("Symbol is not in the composition."); - } - if (!m_massFracMode) { - return m_compositions.at(symbol).number_fraction(); - } else { - return m_compositions.at(symbol).number_fraction(m_specificNumberDensity); - } -} - -std::unordered_map Composition::getNumberFraction() const { - std::unordered_map number_fractions; - for (const auto& [symbol, entry] : m_compositions) { - number_fractions[symbol] = getNumberFraction(symbol); - } - return number_fractions; -} - -std::pair Composition::getComposition(const std::string& symbol) const { - if (!m_finalized) { - LOG_ERROR(m_logger, "Composition has not been finalized."); - throw std::runtime_error("Composition has not been finalized (Consider running .finalize())."); - } - if (m_compositions.count(symbol) == 0) { - LOG_ERROR(m_logger, "Symbol {} is not in the composition.", symbol); - throw std::runtime_error("Symbol is not in the composition."); - } - return {m_compositions.at(symbol), {m_specificNumberDensity, m_meanParticleMass}}; -} - -std::pair, GlobalComposition> Composition::getComposition() const { - if (!m_finalized) { - LOG_ERROR(m_logger, "Composition has not been finalized."); - throw std::runtime_error("Composition has not been finalized (Consider running .finalize())."); - } - return {m_compositions, {m_specificNumberDensity, m_meanParticleMass}}; -} - -Composition Composition::subset(const std::vector& symbols, std::string method) const { - std::array methods = {"norm", "none"}; - - if (std::find(methods.begin(), methods.end(), method) == methods.end()) { - std::string errorMessage = "Invalid method: " + method + ". Valid methods are 'norm' and 'none'."; - LOG_ERROR(m_logger, "Invalid method: {}. Valid methods are norm and none.", method); - throw std::runtime_error(errorMessage); + bool Composition::finalize(bool norm) { + bool finalized = false; + if (m_massFracMode) { + finalized = finalizeMassFracMode(norm); + } else { + finalized = finalizeNumberFracMode(norm); + } + if (finalized) { + m_finalized = true; + } + return finalized; } - Composition subsetComposition; - for (const auto& symbol : symbols) { + bool Composition::finalizeMassFracMode(bool norm) { + std::vector mass_fractions; + mass_fractions.reserve(m_compositions.size()); + for (const auto& [_, entry] : m_compositions) { + mass_fractions.push_back(entry.mass_fraction()); + } + if (norm) { + double sum = 0.0; + for (const auto& mass_fraction : mass_fractions) { + sum += mass_fraction; + } + for (int i = 0; i < mass_fractions.size(); ++i) { + mass_fractions[i] /= sum; + } + for (auto& [symbol, entry] : m_compositions) { + setMassFraction(symbol, entry.mass_fraction() / sum); + } + } + try { + validateComposition(mass_fractions); + } catch (const std::runtime_error& e) { + double massSum = 0.0; + for (const auto& [_, entry] : m_compositions) { + massSum += entry.mass_fraction(); + } + LOG_ERROR(m_logger, "Composition is invalid (Total mass {}).", massSum); + m_finalized = false; + return false; + } + for (const auto& [_, entry] : m_compositions) { + m_specificNumberDensity += entry.rel_abundance(); + } + m_meanParticleMass = 1.0/m_specificNumberDensity; + return true; + } + + bool Composition::finalizeNumberFracMode(bool norm) { + std::vector number_fractions; + number_fractions.reserve(m_compositions.size()); + for (const auto& [_, entry] : m_compositions) { + number_fractions.push_back(entry.number_fraction()); + } + if (norm) { + double sum = 0.0; + for (const auto& number_fraction : number_fractions) { + sum += number_fraction; + } + for (auto& [symbol, entry] : m_compositions) { + setNumberFraction(symbol, entry.number_fraction() / sum); + } + } + try { + validateComposition(number_fractions); + } catch (const std::runtime_error& e) { + double numberSum = 0.0; + for (const auto& [_, entry] : m_compositions) { + numberSum += entry.number_fraction(); + } + LOG_ERROR(m_logger, "Composition is invalid (Total number {}).", numberSum); + m_finalized = false; + return false; + } + for (const auto& [_, entry] : m_compositions) { + m_meanParticleMass += entry.rel_abundance(); + } + m_specificNumberDensity = 1.0/m_meanParticleMass; + return true; + } + + Composition Composition::mix(const Composition& other, double fraction) const { + if (!m_finalized || !other.m_finalized) { + LOG_ERROR(m_logger, "Compositions have not both been finalized."); + throw std::runtime_error("Compositions have not been finalized (Consider running .finalize())."); + } + + if (fraction < 0.0 || fraction > 1.0) { + LOG_ERROR(m_logger, "Fraction must be between 0 and 1."); + throw std::runtime_error("Fraction must be between 0 and 1."); + } + + std::set mixedSymbols = other.getRegisteredSymbols(); + // Get the union of the two sets + mixedSymbols.insert(m_registeredSymbols.begin(), m_registeredSymbols.end()); + + Composition mixedComposition(mixedSymbols); + for (const auto& symbol : mixedSymbols) { + double thisMassFrac, otherMassFrac = 0.0; + + thisMassFrac = hasSymbol(symbol) ? getMassFraction(symbol) : 0.0; + otherMassFrac = other.hasSymbol(symbol) ? other.getMassFraction(symbol) : 0.0; + + double massFraction = fraction * thisMassFrac + otherMassFrac * (1-fraction); + mixedComposition.setMassFraction(symbol, massFraction); + } + mixedComposition.finalize(); + return mixedComposition; + } + + double Composition::getMassFraction(const std::string& symbol) const { + if (!m_finalized) { + LOG_ERROR(m_logger, "Composition has not been finalized."); + throw std::runtime_error("Composition has not been finalized (Consider running .finalize())."); + } if (m_compositions.count(symbol) == 0) { LOG_ERROR(m_logger, "Symbol {} is not in the composition.", symbol); throw std::runtime_error("Symbol is not in the composition."); + } + if (m_massFracMode) { + return m_compositions.at(symbol).mass_fraction(); } else { - subsetComposition.registerSymbol(symbol); - } - subsetComposition.setMassFraction(symbol, m_compositions.at(symbol).mass_fraction()); - } - if (method == "norm") { - bool isNorm = subsetComposition.finalize(true); - if (!isNorm) { - LOG_ERROR(m_logger, "Subset composition is invalid."); - throw std::runtime_error("Subset composition is invalid."); + return m_compositions.at(symbol).mass_fraction(m_meanParticleMass); } } - return subsetComposition; -} -void Composition::setCompositionMode(bool massFracMode) { - if (!m_finalized) { - LOG_ERROR(m_logger, "Composition has not been finalized. Mode cannot be set unless composition is finalized."); - throw std::runtime_error("Composition has not been finalized (Consider running .finalize()). The mode cannot be set unless the composition is finalized."); + std::unordered_map Composition::getMassFraction() const { + std::unordered_map mass_fractions; + for (const auto& [symbol, entry] : m_compositions) { + mass_fractions[symbol] = getMassFraction(symbol); + } + return mass_fractions; } - bool okay = true; - for (auto& [_, entry] : m_compositions) { - if (massFracMode) { - okay = entry.setMassFracMode(m_meanParticleMass); + + double Composition::getNumberFraction(const std::string& symbol) const { + if (!m_finalized) { + LOG_ERROR(m_logger, "Composition has not been finalized."); + throw std::runtime_error("Composition has not been finalized (Consider running .finalize())."); + } + if (m_compositions.count(symbol) == 0) { + LOG_ERROR(m_logger, "Symbol {} is not in the composition.", symbol); + throw std::runtime_error("Symbol is not in the composition."); + } + if (!m_massFracMode) { + return m_compositions.at(symbol).number_fraction(); } else { - okay = entry.setNumberFracMode(m_specificNumberDensity); - } - if (!okay) { - LOG_ERROR(m_logger, "Composition mode could not be set."); - throw std::runtime_error("Composition mode could not be set due to an unknown error."); + return m_compositions.at(symbol).number_fraction(m_specificNumberDensity); } } - m_massFracMode = massFracMode; -} -bool Composition::hasSymbol(const std::string& symbol) const { - return m_compositions.count(symbol) > 0; -} - -/// OVERLOADS - -Composition Composition::operator+(const Composition& other) const { - return mix(other, 0.5); -} - -std::ostream& operator<<(std::ostream& os, const GlobalComposition& comp) { - os << "Global Composition: \n"; - os << "\tSpecific Number Density: " << comp.specificNumberDensity << "\n"; - os << "\tMean Particle Mass: " << comp.meanParticleMass << "\n"; - return os; -} - -std::ostream& operator<<(std::ostream& os, const CompositionEntry& entry) { - os << "<" << entry.m_symbol << " : m_frac = " << entry.mass_fraction() << ">"; - return os; -} - -std::ostream& operator<<(std::ostream& os, const Composition& composition) { - os << "Composition: \n"; - for (const auto& [symbol, entry] : composition.m_compositions) { - os << entry << "\n"; + std::unordered_map Composition::getNumberFraction() const { + std::unordered_map number_fractions; + for (const auto& [symbol, entry] : m_compositions) { + number_fractions[symbol] = getNumberFraction(symbol); + } + return number_fractions; + } + + std::pair Composition::getComposition(const std::string& symbol) const { + if (!m_finalized) { + LOG_ERROR(m_logger, "Composition has not been finalized."); + throw std::runtime_error("Composition has not been finalized (Consider running .finalize())."); + } + if (m_compositions.count(symbol) == 0) { + LOG_ERROR(m_logger, "Symbol {} is not in the composition.", symbol); + throw std::runtime_error("Symbol is not in the composition."); + } + return {m_compositions.at(symbol), {m_specificNumberDensity, m_meanParticleMass}}; + } + + std::pair, GlobalComposition> Composition::getComposition() const { + if (!m_finalized) { + LOG_ERROR(m_logger, "Composition has not been finalized."); + throw std::runtime_error("Composition has not been finalized (Consider running .finalize())."); + } + return {m_compositions, {m_specificNumberDensity, m_meanParticleMass}}; + } + + double Composition::getMeanParticleMass() const { + if (!m_finalized) { + LOG_ERROR(m_logger, "Composition has not been finalized."); + throw std::runtime_error("Composition has not been finalized (Consider running .finalize())."); + } + return m_meanParticleMass; + } + + double Composition::getMeanAtomicNumber() const { + if (!m_finalized) { + LOG_ERROR(m_logger, "Composition must be finalized before getting the mean atomic mass number."); + throw std::runtime_error("Composition not finalized. Cannot retrieve mean atomic mass number."); + } + + double mean_A = 0.0; + + // Loop through all registered species in the composition. + for (const auto &val: m_compositions | std::views::values) { + const CompositionEntry& entry = val; + const chemSpecies::Species& species = entry.isotope(); + + const double mass_fraction = entry.mass_fraction(); + const double particle_mass_g = species.mass(); + const int mass_number = species.a(); + + // Avoid division by zero, though a valid species should have a positive mass. + if (particle_mass_g > 0) { + // Calculate the number fraction for this species. + const double number_fraction = (mass_fraction / particle_mass_g) * m_meanParticleMass; + mean_A += number_fraction * mass_number; + } + } + + return mean_A; + } + + Composition Composition::subset(const std::vector& symbols, std::string method) const { + std::array methods = {"norm", "none"}; + + if (std::find(methods.begin(), methods.end(), method) == methods.end()) { + std::string errorMessage = "Invalid method: " + method + ". Valid methods are 'norm' and 'none'."; + LOG_ERROR(m_logger, "Invalid method: {}. Valid methods are norm and none.", method); + throw std::runtime_error(errorMessage); + } + + Composition subsetComposition; + for (const auto& symbol : symbols) { + if (m_compositions.count(symbol) == 0) { + LOG_ERROR(m_logger, "Symbol {} is not in the composition.", symbol); + throw std::runtime_error("Symbol is not in the composition."); + } else { + subsetComposition.registerSymbol(symbol); + } + subsetComposition.setMassFraction(symbol, m_compositions.at(symbol).mass_fraction()); + } + if (method == "norm") { + bool isNorm = subsetComposition.finalize(true); + if (!isNorm) { + LOG_ERROR(m_logger, "Subset composition is invalid."); + throw std::runtime_error("Subset composition is invalid."); + } + } + return subsetComposition; + } + + void Composition::setCompositionMode(bool massFracMode) { + if (!m_finalized) { + LOG_ERROR(m_logger, "Composition has not been finalized. Mode cannot be set unless composition is finalized."); + throw std::runtime_error("Composition has not been finalized (Consider running .finalize()). The mode cannot be set unless the composition is finalized."); + } + + bool okay = true; + for (auto& [_, entry] : m_compositions) { + if (massFracMode) { + okay = entry.setMassFracMode(m_meanParticleMass); + } else { + okay = entry.setNumberFracMode(m_specificNumberDensity); + } + if (!okay) { + LOG_ERROR(m_logger, "Composition mode could not be set."); + throw std::runtime_error("Composition mode could not be set due to an unknown error."); + } + } + m_massFracMode = massFracMode; + } + + bool Composition::hasSymbol(const std::string& symbol) const { + return m_compositions.count(symbol) > 0; + } + + /// OVERLOADS + + Composition Composition::operator+(const Composition& other) const { + return mix(other, 0.5); + } + + std::ostream& operator<<(std::ostream& os, const GlobalComposition& comp) { + os << "Global Composition: \n"; + os << "\tSpecific Number Density: " << comp.specificNumberDensity << "\n"; + os << "\tMean Particle Mass: " << comp.meanParticleMass << "\n"; + return os; + } + + std::ostream& operator<<(std::ostream& os, const CompositionEntry& entry) { + os << "<" << entry.m_symbol << " : m_frac = " << entry.mass_fraction() << ">"; + return os; + } + + std::ostream& operator<<(std::ostream& os, const Composition& composition) { + os << "Composition: \n"; + for (const auto& [symbol, entry] : composition.m_compositions) { + os << entry << "\n"; + } + return os; } - return os; -} } // namespace serif::composition \ No newline at end of file diff --git a/src/composition/public/composition.h b/src/composition/public/composition.h index e61a5c6..457f96d 100644 --- a/src/composition/public/composition.h +++ b/src/composition/public/composition.h @@ -277,7 +277,7 @@ namespace serif::composition { * Composition comp(symbols); * @endcode */ - Composition(const std::vector& symbols); + explicit Composition(const std::vector& symbols); /** * @brief Constructs a Composition with the given symbols as a set. @@ -288,7 +288,7 @@ namespace serif::composition { * Composition comp(symbols); * @endcode */ - Composition(const std::set& symbols); + explicit Composition(const std::set& symbols); /** * @brief Constructs a Composition with the given symbols and mass fractions. @@ -304,6 +304,14 @@ namespace serif::composition { */ Composition(const std::vector& symbols, const std::vector& mass_fractions, bool massFracMode=true); + /** + * @brief Constructs a Composition from another Composition. + * @param composition The Composition to copy. + */ + Composition(const Composition& composition); + + Composition& operator=(Composition const& other); + /** * @brief Registers a new symbol. * @param symbol The symbol to register. @@ -333,7 +341,7 @@ namespace serif::composition { * @brief Gets the registered symbols. * @return A set of registered symbols. */ - std::set getRegisteredSymbols() const; + [[nodiscard]] std::set getRegisteredSymbols() const; /** * @brief Sets the mass fraction for a given symbol. @@ -390,40 +398,52 @@ namespace serif::composition { * @brief Gets the mass fractions of all compositions. * @return An unordered map of compositions with their mass fractions. */ - std::unordered_map getMassFraction() const; + [[nodiscard]] std::unordered_map getMassFraction() const; /** * @brief Gets the mass fraction for a given symbol. * @param symbol The symbol to get the mass fraction for. * @return The mass fraction for the given symbol. */ - double getMassFraction(const std::string& symbol) const; + [[nodiscard]] double getMassFraction(const std::string& symbol) const; /** * @brief Gets the number fraction for a given symbol. * @param symbol The symbol to get the number fraction for. * @return The number fraction for the given symbol. */ - double getNumberFraction(const std::string& symbol) const; + [[nodiscard]] double getNumberFraction(const std::string& symbol) const; /** * @brief Gets the number fractions of all compositions. * @return An unordered map of compositions with their number fractions. */ - std::unordered_map getNumberFraction() const; + [[nodiscard]] std::unordered_map getNumberFraction() const; /** * @brief Gets the composition entry and global composition for a given symbol. * @param symbol The symbol to get the composition for. * @return A pair containing the CompositionEntry and GlobalComposition for the given symbol. */ - std::pair getComposition(const std::string& symbol) const; + [[nodiscard]] std::pair getComposition(const std::string& symbol) const; /** * @brief Gets all composition entries and the global composition. * @return A pair containing an unordered map of CompositionEntries and the GlobalComposition. */ - std::pair, GlobalComposition> getComposition() const; + [[nodiscard]] std::pair, GlobalComposition> getComposition() const; + + /** + * @brief Compute the mean particle mass of the composition. + * @return Mean particle mass in g. + */ + [[nodiscard]] double getMeanParticleMass() const; + + /** + * @brief Compute the mean atomic mass number of the composition. + * @return Mean atomic mass number. + */ + [[nodiscard]] double getMeanAtomicNumber() const; /** * @brief Gets a subset of the composition.