SERiF/src/composition/private/composition.cpp

/* ***********************************************************************
//
//   Copyright (C) 2025 -- The 4D-STAR Collaboration
//   File Author: Emily Boudreaux
//   Last Modified: March 26, 2025
//
//   4DSSE is free software; you can use it and/or modify
//   it under the terms and restrictions the GNU General Library Public
//   License version 3 (GPLv3) as published by the Free Software Foundation.
//
//   4DSSE is distributed in the hope that it will be useful,
//   but WITHOUT ANY WARRANTY; without even the implied warranty of
//   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
//   See the GNU Library General Public License for more details.
//
//   You should have received a copy of the GNU Library General Public License
//   along with this software; if not, write to the Free Software
//   Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
//
// *********************************************************************** */
#include "composition.h"
#include "quill/LogMacros.h"

#include <stdexcept>
#include <unordered_map>
#include <vector>
#include <array>
#include <ranges>

#include <utility>

#include "atomicSpecies.h"

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, const 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.");
        }
        if (chemSpecies::species.count(symbol) == 0) {
            throw std::runtime_error("Invalid symbol.");
        }
        m_symbol = symbol;
        m_isotope = chemSpecies::species.at(symbol);
        m_initialized = true;
    }

    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;
    }

    double CompositionEntry::mass_fraction(double meanMolarMass) const {
        if (m_massFracMode) {
            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<std::string>& symbols) {
        for (const auto& symbol : symbols) {
            registerSymbol(symbol);
        }
    }

    Composition::Composition(const std::set<std::string>& symbols) {
        for (const auto& symbol : symbols) {
            registerSymbol(symbol);
        }
    }

    Composition::Composition(const std::vector<std::string>& symbols, const std::vector<double>& 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 {
            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.");
            }
        }

        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);
    }

    void Composition::registerSymbol(const std::vector<std::string>& symbols, bool massFracMode) {
        for (const auto& symbol : symbols) {
            registerSymbol(symbol, massFracMode);
        }
    }

    std::set<std::string> Composition::getRegisteredSymbols() const {
        return m_registeredSymbols;
    }

    void Composition::validateComposition(const std::vector<double>& fractions) const {
        if (!isValidComposition(fractions)) {
            LOG_ERROR(m_logger, "Invalid composition.");
            throw std::runtime_error("Invalid composition.");
        }
    }

    bool Composition::isValidComposition(const std::vector<double>& 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;
        }

        return true;
    }

    bool Composition::isValidSymbol(const std::string& symbol) {
        return chemSpecies::species.contains(symbol);
    }

    double Composition::setMassFraction(const std::string& symbol, const double& mass_fraction) {
        if (!m_registeredSymbols.contains(symbol)) {
            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;
        const double old_mass_fraction = m_compositions.at(symbol).mass_fraction();
        m_compositions.at(symbol).setMassFraction(mass_fraction);

        return old_mass_fraction;
    }

    std::vector<double> Composition::setMassFraction(const std::vector<std::string>& symbols, const std::vector<double>& 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<double> 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<double> Composition::setNumberFraction(const std::vector<std::string>& symbols, const std::vector<double>& 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<double> 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(const 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<double> 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 < static_cast<int>(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<double> 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<std::string> 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 otherMassFrac = 0.0;

            const double 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.contains(symbol)) {
            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<std::string, double> Composition::getMassFraction() const {
        std::unordered_map<std::string, double> mass_fractions;
        for (const auto &symbol: m_compositions | std::views::keys) {
            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.contains(symbol)) {
            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<std::string, double> Composition::getNumberFraction() const {
        std::unordered_map<std::string, double> number_fractions;
        for (const auto &symbol: m_compositions | std::views::keys) {
            number_fractions[symbol] = getNumberFraction(symbol);
        }
        return number_fractions;
    }

    std::pair<CompositionEntry, GlobalComposition> 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.contains(symbol)) {
            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<std::unordered_map<std::string, CompositionEntry>, 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 zSum = 0.0;

        // Loop through all registered species in the composition.
        for (const auto &val: m_compositions | std::views::values) {
            zSum += (val.mass_fraction() * val.m_isotope.z())/val.m_isotope.a();
        }

        const double mean_A = m_meanParticleMass * zSum;
        return mean_A;
    }

    Composition Composition::subset(const std::vector<std::string>& symbols, std::string method) const {
        const std::array<std::string, 2> methods = {"norm", "none"};

        if (std::ranges::find(methods, method) == methods.end()) {
            const 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.contains(symbol)) {
                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") {
            const 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(const 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 | std::views::values) {
            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;
    }

    CanonicalComposition Composition::getCanonicalComposition(bool harsh) 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()).");
        }
        CanonicalComposition canonicalComposition;
        const std::array<std::string, 7> canonicalH = {
            "H-1", "H-2", "H-3", "H-4", "H-5", "H-6", "H-7"
        };
        const std::array<std::string, 8> canonicalHe = {
            "He-3", "He-4", "He-5", "He-6", "He-7", "He-8", "He-9", "He-10"
        };
        for (const auto& symbol : canonicalH) {
            if (hasSymbol(symbol)) {
                canonicalComposition.X += getMassFraction(symbol);
            }
        }
        for (const auto& symbol : canonicalHe) {
            if (hasSymbol(symbol)) {
                canonicalComposition.Y += getMassFraction(symbol);
            }
        }

        for (const auto& symbol : getRegisteredSymbols()) {
            const bool isHSymbol = std::ranges::find(canonicalH, symbol) != std::end(canonicalH);
            const bool isHeSymbol = std::ranges::find(canonicalHe, symbol) != std::end(canonicalHe);

            if (isHSymbol || isHeSymbol) {
                continue; // Skip canonical H and He symbols
            }

            canonicalComposition.Z += getMassFraction(symbol);
        }

        const double Z = 1.0 - (canonicalComposition.X + canonicalComposition.Y);
        if (std::abs(Z - canonicalComposition.Z) > 1e-6) {
            if (!harsh) {
                LOG_WARNING(m_logger, "Validation composition Z (X-Y = {}) is different than canonical composition Z ({}) (∑a_i where a_i != H/He).", Z, canonicalComposition.Z);
            }
            else {
                LOG_ERROR(m_logger, "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).");
            }
        }
        return canonicalComposition;
    }

    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