570 lines
20 KiB
C++
570 lines
20 KiB
C++
/* ***********************************************************************
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//
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// Copyright (C) 2025 -- The 4D-STAR Collaboration
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// File Author: Emily Boudreaux
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// Last Modified: March 26, 2025
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//
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// 4DSSE is free software; you can use it and/or modify
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// it under the terms and restrictions the GNU General Library Public
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// License version 3 (GPLv3) as published by the Free Software Foundation.
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//
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// 4DSSE is distributed in the hope that it will be useful,
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// but WITHOUT ANY WARRANTY; without even the implied warranty of
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// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
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// See the GNU Library General Public License for more details.
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//
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// You should have received a copy of the GNU Library General Public License
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// along with this software; if not, write to the Free Software
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// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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//
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// *********************************************************************** */
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#include "composition.h"
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#include "quill/LogMacros.h"
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#include <stdexcept>
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#include <unordered_map>
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#include <vector>
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#include <array>
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#include <utility>
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#include "atomicSpecies.h"
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namespace serif::composition {
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CompositionEntry::CompositionEntry() : m_symbol("H-1"), m_isotope(chemSpecies::species.at("H-1")), m_initialized(false) {}
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CompositionEntry::CompositionEntry(const std::string& symbol, bool massFracMode) : m_symbol(symbol), m_isotope(chemSpecies::species.at(symbol)), m_massFracMode(massFracMode) {
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setSpecies(symbol);
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}
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CompositionEntry::CompositionEntry(const CompositionEntry& entry) :
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m_symbol(entry.m_symbol),
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m_isotope(entry.m_isotope),
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m_massFracMode(entry.m_massFracMode),
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m_massFraction(entry.m_massFraction),
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m_numberFraction(entry.m_numberFraction),
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m_relAbundance(entry.m_relAbundance),
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m_initialized(entry.m_initialized) {}
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void CompositionEntry::setSpecies(const std::string& symbol) {
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if (m_initialized) {
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throw std::runtime_error("Composition entry is already initialized.");
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}
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if (chemSpecies::species.count(symbol) == 0) {
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throw std::runtime_error("Invalid symbol.");
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}
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m_symbol = symbol;
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m_isotope = chemSpecies::species.at(symbol);
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m_initialized = true;
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}
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std::string CompositionEntry::symbol() const {
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return m_symbol;
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}
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double CompositionEntry::mass_fraction() const {
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if (!m_massFracMode) {
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throw std::runtime_error("Composition entry is in number fraction mode.");
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}
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return m_massFraction;
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}
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double CompositionEntry::mass_fraction(double meanMolarMass) const {
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if (m_massFracMode) {
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return m_massFraction;
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}
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return m_relAbundance / meanMolarMass;
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}
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double CompositionEntry::number_fraction() const {
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if (m_massFracMode) {
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throw std::runtime_error("Composition entry is in mass fraction mode.");
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}
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return m_numberFraction;
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}
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double CompositionEntry::number_fraction(double totalMoles) const {
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if (m_massFracMode) {
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return m_relAbundance / totalMoles;
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}
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return m_numberFraction;
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}
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double CompositionEntry::rel_abundance() const {
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return m_relAbundance;
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}
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chemSpecies::Species CompositionEntry::isotope() const {
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return m_isotope;
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}
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void CompositionEntry::setMassFraction(double mass_fraction) {
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if (!m_massFracMode) {
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throw std::runtime_error("Composition entry is in number fraction mode.");
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}
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m_massFraction = mass_fraction;
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m_relAbundance = m_massFraction / m_isotope.mass();
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}
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void CompositionEntry::setNumberFraction(double number_fraction) {
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if (m_massFracMode) {
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throw std::runtime_error("Composition entry is in mass fraction mode.");
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}
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m_numberFraction = number_fraction;
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m_relAbundance = m_numberFraction * m_isotope.mass();
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}
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bool CompositionEntry::setMassFracMode(double meanParticleMass) {
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if (m_massFracMode) {
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return false;
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}
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m_massFracMode = true;
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m_massFraction = m_relAbundance / meanParticleMass;
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return true;
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}
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bool CompositionEntry::setNumberFracMode(double specificNumberDensity) {
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if (!m_massFracMode) {
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return false;
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}
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m_massFracMode = false;
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m_numberFraction = m_relAbundance / specificNumberDensity;
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return true;
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}
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bool CompositionEntry::getMassFracMode() const {
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return m_massFracMode;
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}
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Composition::Composition(const std::vector<std::string>& symbols) {
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for (const auto& symbol : symbols) {
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registerSymbol(symbol);
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}
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}
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Composition::Composition(const std::set<std::string>& symbols) {
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for (const auto& symbol : symbols) {
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registerSymbol(symbol);
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}
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}
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Composition::Composition(const std::vector<std::string>& symbols, const std::vector<double>& fractions, bool massFracMode) : m_massFracMode(massFracMode) {
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if (symbols.size() != fractions.size()) {
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LOG_ERROR(m_logger, "The number of symbols and fractions must be equal.");
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throw std::runtime_error("The number of symbols and fractions must be equal.");
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}
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validateComposition(fractions);
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for (const auto &symbol : symbols) {
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registerSymbol(symbol);
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}
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for (size_t i = 0; i < symbols.size(); ++i) {
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if (m_massFracMode) {
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setMassFraction(symbols[i], fractions[i]);
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} else {
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setNumberFraction(symbols[i], fractions[i]);
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}
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}
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finalize();
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}
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void Composition::registerSymbol(const std::string& symbol, bool massFracMode) {
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if (!isValidSymbol(symbol)) {
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LOG_ERROR(m_logger, "Invalid symbol: {}", symbol);
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throw std::runtime_error("Invalid symbol.");
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}
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// If no symbols have been registered allow mode to be set
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if (m_registeredSymbols.size() == 0) {
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m_massFracMode = massFracMode;
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} else {
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if (m_massFracMode != massFracMode) {
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LOG_ERROR(m_logger, "Composition is in mass fraction mode. Cannot register symbol in number fraction mode.");
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throw std::runtime_error("Composition is in mass fraction mode. Cannot register symbol in number fraction mode.");
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}
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}
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if (m_registeredSymbols.find(symbol) != m_registeredSymbols.end()) {
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LOG_WARNING(m_logger, "Symbol {} is already registered.", symbol);
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return;
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}
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m_registeredSymbols.insert(symbol);
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CompositionEntry entry(symbol, m_massFracMode);
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m_compositions[symbol] = entry;
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LOG_INFO(m_logger, "Registered symbol: {}", symbol);
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}
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void Composition::registerSymbol(const std::vector<std::string>& symbols, bool massFracMode) {
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for (const auto& symbol : symbols) {
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registerSymbol(symbol, massFracMode);
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}
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}
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std::set<std::string> Composition::getRegisteredSymbols() const {
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return m_registeredSymbols;
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}
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void Composition::validateComposition(const std::vector<double>& fractions) const {
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if (!isValidComposition(fractions)) {
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LOG_ERROR(m_logger, "Invalid composition.");
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throw std::runtime_error("Invalid composition.");
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}
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}
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bool Composition::isValidComposition(const std::vector<double>& fractions) const {
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double sum = 0.0;
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for (const auto& fraction : fractions) {
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sum += fraction;
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}
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if (sum < 0.999999 || sum > 1.000001) {
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LOG_ERROR(m_logger, "The sum of fractions must be equal to 1.");
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return false;
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}
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return true;
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}
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bool Composition::isValidSymbol(const std::string& symbol) const {
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return chemSpecies::species.count(symbol) > 0;
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}
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double Composition::setMassFraction(const std::string& symbol, const double& mass_fraction) {
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if (m_registeredSymbols.find(symbol) == m_registeredSymbols.end()) {
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LOG_ERROR(m_logger, "Symbol {} is not registered.", symbol);
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throw std::runtime_error("Symbol is not registered.");
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}
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if (!m_massFracMode) {
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LOG_ERROR(m_logger, "Composition is in number fraction mode.");
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throw std::runtime_error("Composition is in number fraction mode.");
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}
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if (mass_fraction < 0.0 || mass_fraction > 1.0) {
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LOG_ERROR(m_logger, "Mass fraction must be between 0 and 1 for symbol {}. Currently it is {}.", symbol, mass_fraction);
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throw std::runtime_error("Mass fraction must be between 0 and 1.");
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}
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m_finalized = false;
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double old_mass_fraction = m_compositions.at(symbol).mass_fraction();
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m_compositions.at(symbol).setMassFraction(mass_fraction);
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return old_mass_fraction;
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}
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std::vector<double> Composition::setMassFraction(const std::vector<std::string>& symbols, const std::vector<double>& mass_fractions) {
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if (symbols.size() != mass_fractions.size()) {
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LOG_ERROR(m_logger, "The number of symbols and mass fractions must be equal.");
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throw std::runtime_error("The number of symbols and mass fractions must be equal.");
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}
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std::vector<double> old_mass_fractions;
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old_mass_fractions.reserve(symbols.size());
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for (size_t i = 0; i < symbols.size(); ++i) {
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old_mass_fractions.push_back(setMassFraction(symbols[i], mass_fractions[i]));
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}
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return old_mass_fractions;
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}
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double Composition::setNumberFraction(const std::string& symbol, const double& number_fraction) {
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if (m_registeredSymbols.find(symbol) == m_registeredSymbols.end()) {
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LOG_ERROR(m_logger, "Symbol {} is not registered.", symbol);
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throw std::runtime_error("Symbol is not registered.");
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}
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if (m_massFracMode) {
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LOG_ERROR(m_logger, "Composition is in mass fraction mode.");
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throw std::runtime_error("Composition is in mass fraction mode.");
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}
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if (number_fraction < 0.0 || number_fraction > 1.0) {
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LOG_ERROR(m_logger, "Number fraction must be between 0 and 1 for symbol {}. Currently it is {}.", symbol, number_fraction);
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throw std::runtime_error("Number fraction must be between 0 and 1.");
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}
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m_finalized = false;
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double old_number_fraction = m_compositions.at(symbol).number_fraction();
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m_compositions.at(symbol).setNumberFraction(number_fraction);
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return old_number_fraction;
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}
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std::vector<double> Composition::setNumberFraction(const std::vector<std::string>& symbols, const std::vector<double>& number_fractions) {
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if (symbols.size() != number_fractions.size()) {
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LOG_ERROR(m_logger, "The number of symbols and number fractions must be equal.");
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throw std::runtime_error("The number of symbols and number fractions must be equal.");
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}
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std::vector<double> old_number_fractions;
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old_number_fractions.reserve(symbols.size());
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for (size_t i = 0; i < symbols.size(); ++i) {
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old_number_fractions.push_back(setNumberFraction(symbols[i], number_fractions[i]));
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}
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return old_number_fractions;
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}
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bool Composition::finalize(bool norm) {
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bool finalized = false;
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if (m_massFracMode) {
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finalized = finalizeMassFracMode(norm);
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} else {
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finalized = finalizeNumberFracMode(norm);
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}
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if (finalized) {
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m_finalized = true;
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}
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return finalized;
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}
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bool Composition::finalizeMassFracMode(bool norm) {
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std::vector<double> mass_fractions;
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mass_fractions.reserve(m_compositions.size());
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for (const auto& [_, entry] : m_compositions) {
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mass_fractions.push_back(entry.mass_fraction());
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}
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if (norm) {
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double sum = 0.0;
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for (const auto& mass_fraction : mass_fractions) {
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sum += mass_fraction;
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}
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for (int i = 0; i < mass_fractions.size(); ++i) {
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mass_fractions[i] /= sum;
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}
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for (auto& [symbol, entry] : m_compositions) {
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setMassFraction(symbol, entry.mass_fraction() / sum);
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}
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}
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try {
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validateComposition(mass_fractions);
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} catch (const std::runtime_error& e) {
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double massSum = 0.0;
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for (const auto& [_, entry] : m_compositions) {
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massSum += entry.mass_fraction();
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}
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LOG_ERROR(m_logger, "Composition is invalid (Total mass {}).", massSum);
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m_finalized = false;
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return false;
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}
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for (const auto& [_, entry] : m_compositions) {
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m_specificNumberDensity += entry.rel_abundance();
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}
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m_meanParticleMass = 1.0/m_specificNumberDensity;
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return true;
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}
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bool Composition::finalizeNumberFracMode(bool norm) {
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std::vector<double> number_fractions;
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number_fractions.reserve(m_compositions.size());
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for (const auto& [_, entry] : m_compositions) {
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number_fractions.push_back(entry.number_fraction());
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}
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if (norm) {
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double sum = 0.0;
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for (const auto& number_fraction : number_fractions) {
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sum += number_fraction;
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}
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for (auto& [symbol, entry] : m_compositions) {
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setNumberFraction(symbol, entry.number_fraction() / sum);
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}
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}
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try {
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validateComposition(number_fractions);
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} catch (const std::runtime_error& e) {
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double numberSum = 0.0;
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for (const auto& [_, entry] : m_compositions) {
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numberSum += entry.number_fraction();
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}
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LOG_ERROR(m_logger, "Composition is invalid (Total number {}).", numberSum);
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m_finalized = false;
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return false;
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}
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for (const auto& [_, entry] : m_compositions) {
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m_meanParticleMass += entry.rel_abundance();
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}
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m_specificNumberDensity = 1.0/m_meanParticleMass;
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return true;
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}
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Composition Composition::mix(const Composition& other, double fraction) const {
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if (!m_finalized || !other.m_finalized) {
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LOG_ERROR(m_logger, "Compositions have not both been finalized.");
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throw std::runtime_error("Compositions have not been finalized (Consider running .finalize()).");
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}
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if (fraction < 0.0 || fraction > 1.0) {
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LOG_ERROR(m_logger, "Fraction must be between 0 and 1.");
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throw std::runtime_error("Fraction must be between 0 and 1.");
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}
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std::set<std::string> mixedSymbols = other.getRegisteredSymbols();
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// Get the union of the two sets
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mixedSymbols.insert(m_registeredSymbols.begin(), m_registeredSymbols.end());
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Composition mixedComposition(mixedSymbols);
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for (const auto& symbol : mixedSymbols) {
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double thisMassFrac, otherMassFrac = 0.0;
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thisMassFrac = hasSymbol(symbol) ? getMassFraction(symbol) : 0.0;
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otherMassFrac = other.hasSymbol(symbol) ? other.getMassFraction(symbol) : 0.0;
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double massFraction = fraction * thisMassFrac + otherMassFrac * (1-fraction);
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mixedComposition.setMassFraction(symbol, massFraction);
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}
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mixedComposition.finalize();
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return mixedComposition;
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}
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double Composition::getMassFraction(const std::string& symbol) const {
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if (!m_finalized) {
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LOG_ERROR(m_logger, "Composition has not been finalized.");
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throw std::runtime_error("Composition has not been finalized (Consider running .finalize()).");
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}
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if (m_compositions.count(symbol) == 0) {
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LOG_ERROR(m_logger, "Symbol {} is not in the composition.", symbol);
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throw std::runtime_error("Symbol is not in the composition.");
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}
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if (m_massFracMode) {
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return m_compositions.at(symbol).mass_fraction();
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} else {
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return m_compositions.at(symbol).mass_fraction(m_meanParticleMass);
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}
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}
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std::unordered_map<std::string, double> Composition::getMassFraction() const {
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std::unordered_map<std::string, double> mass_fractions;
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for (const auto& [symbol, entry] : m_compositions) {
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mass_fractions[symbol] = getMassFraction(symbol);
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}
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return mass_fractions;
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}
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double Composition::getNumberFraction(const std::string& symbol) const {
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if (!m_finalized) {
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LOG_ERROR(m_logger, "Composition has not been finalized.");
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throw std::runtime_error("Composition has not been finalized (Consider running .finalize()).");
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}
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if (m_compositions.count(symbol) == 0) {
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LOG_ERROR(m_logger, "Symbol {} is not in the composition.", symbol);
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throw std::runtime_error("Symbol is not in the composition.");
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}
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if (!m_massFracMode) {
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return m_compositions.at(symbol).number_fraction();
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} else {
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return m_compositions.at(symbol).number_fraction(m_specificNumberDensity);
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}
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}
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std::unordered_map<std::string, double> Composition::getNumberFraction() const {
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std::unordered_map<std::string, double> number_fractions;
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for (const auto& [symbol, entry] : m_compositions) {
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number_fractions[symbol] = getNumberFraction(symbol);
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}
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return number_fractions;
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}
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std::pair<CompositionEntry, GlobalComposition> Composition::getComposition(const std::string& symbol) const {
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if (!m_finalized) {
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LOG_ERROR(m_logger, "Composition has not been finalized.");
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throw std::runtime_error("Composition has not been finalized (Consider running .finalize()).");
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}
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if (m_compositions.count(symbol) == 0) {
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LOG_ERROR(m_logger, "Symbol {} is not in the composition.", symbol);
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throw std::runtime_error("Symbol is not in the composition.");
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}
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return {m_compositions.at(symbol), {m_specificNumberDensity, m_meanParticleMass}};
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}
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std::pair<std::unordered_map<std::string, CompositionEntry>, GlobalComposition> Composition::getComposition() const {
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if (!m_finalized) {
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LOG_ERROR(m_logger, "Composition has not been finalized.");
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throw std::runtime_error("Composition has not been finalized (Consider running .finalize()).");
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}
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return {m_compositions, {m_specificNumberDensity, m_meanParticleMass}};
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}
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|
|
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Composition Composition::subset(const std::vector<std::string>& symbols, std::string method) const {
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std::array<std::string, 2> methods = {"norm", "none"};
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|
|
|
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;
|
|
}
|
|
|
|
} // namespace serif::composition
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