615 lines
21 KiB
C++
615 lines
21 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: October 6, 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 "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 <ranges>
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#include <algorithm>
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#include <set>
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#include <string>
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#include <utility>
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#include "fourdst/atomic/atomicSpecies.h"
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#include "fourdst/atomic/species.h"
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#include "fourdst/composition/composition.h"
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#include "fourdst/composition/exceptions/exceptions_composition.h"
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namespace {
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template<typename A, typename B>
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std::vector<A> sortVectorBy(
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std::vector<A> toSort,
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const std::vector<B>& by
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) {
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std::vector<std::size_t> indices(by.size());
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for (size_t i = 0; i < indices.size(); i++) {
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indices[i] = i;
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}
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std::ranges::sort(indices, [&](size_t a, size_t b) {
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return by[a] < by[b];
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});
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std::vector<A> sorted;
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sorted.reserve(indices.size());
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for (const auto idx: indices) {
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sorted.push_back(toSort[idx]);
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}
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return sorted;
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}
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std::optional<fourdst::atomic::Species> getSpecies(const std::string& symbol) {
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if (!fourdst::atomic::species.contains(symbol)) {
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return std::nullopt;
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}
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return fourdst::atomic::species.at(symbol);
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}
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void throw_unknown_symbol(quill::Logger* logger, const std::string& symbol) {
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LOG_ERROR(logger, "Symbol {} is not a valid species symbol (not in the species database)", symbol);
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throw fourdst::composition::exceptions::UnknownSymbolError("Symbol " + symbol + " is not a valid species symbol (not in the species database)");
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}
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void throw_unregistered_symbol(quill::Logger* logger, const std::string& symbol) {
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LOG_ERROR(logger, "Symbol {} is not registered in the composition.", symbol);
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throw fourdst::composition::exceptions::UnregisteredSymbolError("Symbol " + symbol + " is not registered in the composition.");
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}
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}
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namespace fourdst::composition {
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Composition::Composition(
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const std::vector<std::string>& symbols
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) {
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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(
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const std::set<std::string>& symbols
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) {
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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(
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const std::vector<atomic::Species> &species
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) {
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for (const auto& s : species) {
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registerSpecies(s);
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}
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}
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Composition::Composition(
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const std::set<atomic::Species> &species
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) {
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for (const auto& s : species) {
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registerSpecies(s);
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}
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}
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Composition::Composition(
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const std::vector<std::string>& symbols,
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const std::vector<double>& molarAbundances
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) {
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if (symbols.size() != molarAbundances.size()) {
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LOG_CRITICAL(getLogger(), "The number of symbols and molarAbundances must be equal (got {} symbols and {} molarAbundances).", symbols.size(), molarAbundances.size());
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throw exceptions::InvalidCompositionError("The number of symbols and fractions must be equal. Got " + std::to_string(symbols.size()) + " symbols and " + std::to_string(molarAbundances.size()) + " fractions.");
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}
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for (const auto &[symbol, y] : std::views::zip(symbols, molarAbundances)) {
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registerSymbol(symbol);
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setMolarAbundance(symbol, y);
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}
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}
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Composition::Composition(
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const std::vector<atomic::Species> &species,
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const std::vector<double> &molarAbundances
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) {
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if (species.size() != molarAbundances.size()) {
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LOG_CRITICAL(getLogger(), "The number of species and molarAbundances must be equal (got {} species and {} molarAbundances).", species.size(), molarAbundances.size());
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throw exceptions::InvalidCompositionError("The number of species and fractions must be equal. Got " + std::to_string(species.size()) + " species and " + std::to_string(molarAbundances.size()) + " fractions.");
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}
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for (const auto& [s, y] : std::views::zip(species, molarAbundances)) {
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registerSpecies(s);
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setMolarAbundance(s, y);
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}
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}
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Composition::Composition(
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const std::set<std::string> &symbols,
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const std::vector<double> &molarAbundances
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) {
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if (symbols.size() != molarAbundances.size()) {
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LOG_CRITICAL(getLogger(), "The number of symbols and molarAbundances must be equal (got {} symbols and {} molarAbundances).", symbols.size(), molarAbundances.size());
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throw exceptions::InvalidCompositionError("The number of symbols and fractions must be equal. Got " + std::to_string(symbols.size()) + " symbols and " + std::to_string(molarAbundances.size()) + " fractions.");
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}
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for (const auto& [symbol, y] : std::views::zip(sortVectorBy<std::string>(std::vector<std::string>(symbols.begin(), symbols.end()), molarAbundances), molarAbundances)) {
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registerSymbol(symbol);
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setMolarAbundance(symbol, y);
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}
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}
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Composition::Composition(
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const Composition &composition
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) {
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m_registeredSpecies = composition.m_registeredSpecies;
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m_molarAbundances = composition.m_molarAbundances;
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}
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Composition& Composition::operator=(
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const Composition &other
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) {
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if (this != &other) {
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m_registeredSpecies = other.m_registeredSpecies;
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m_molarAbundances = other.m_molarAbundances;
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}
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return *this;
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}
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void Composition::registerSymbol(
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const std::string& symbol
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) {
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const auto result = getSpecies(symbol);
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if (!result) {
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throw_unknown_symbol(getLogger(), symbol);
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}
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registerSpecies(result.value());
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}
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void Composition::registerSymbol(
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const std::vector<std::string>& symbols
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) {
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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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void Composition::registerSpecies(
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const atomic::Species &species
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) noexcept {
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m_registeredSpecies.insert(species);
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if (!m_molarAbundances.contains(species)) {
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m_molarAbundances.emplace(species, 0.0);
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}
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}
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void Composition::registerSpecies(
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const std::vector<atomic::Species> &species
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) noexcept {
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for (const auto& s : species) {
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registerSpecies(s);
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}
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}
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std::set<std::string> Composition::getRegisteredSymbols() const noexcept {
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std::set<std::string> symbols;
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for (const auto& species : m_registeredSpecies) {
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symbols.insert(std::string(species.name()));
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}
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return symbols;
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}
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const std::set<atomic::Species> &Composition::getRegisteredSpecies() const noexcept {
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return m_registeredSpecies;
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}
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double Composition::getMassFraction(const std::string& symbol) const {
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const auto species = getSpecies(symbol);
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if (!species) {
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throw_unknown_symbol(getLogger(), symbol);
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}
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return getMassFraction(species.value());
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}
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double Composition::getMassFraction(
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const atomic::Species &species
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) const {
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if (!m_molarAbundances.contains(species)) {
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throw_unregistered_symbol(getLogger(), std::string(species.name()));
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}
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std::map<atomic::Species, double> raw_mass;
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double totalMass = 0;
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for (const auto& [sp, y] : m_molarAbundances) {
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const double contrib = y * sp.mass();
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totalMass += contrib;
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raw_mass.emplace(sp, contrib);
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}
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return raw_mass.at(species) / totalMass;
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}
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std::unordered_map<atomic::Species, double> Composition::getMassFraction() const noexcept {
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std::unordered_map<atomic::Species, double> mass_fractions;
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for (const auto &species: m_molarAbundances | std::views::keys) {
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mass_fractions.emplace(species, getMassFraction(species));
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}
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return mass_fractions;
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}
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double Composition::getNumberFraction(
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const std::string& symbol
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) const {
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const auto species = getSpecies(symbol);
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if (!species) {
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throw_unknown_symbol(getLogger(), symbol);
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}
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return getNumberFraction(species.value());
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}
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double Composition::getNumberFraction(
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const atomic::Species &species
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) const {
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if (!m_molarAbundances.contains(species)) {
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throw_unregistered_symbol(getLogger(), std::string(species.name()));
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}
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double total_moles_per_gram = 0.0;
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for (const auto &y: m_molarAbundances | std::views::values) {
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total_moles_per_gram += y;
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}
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return m_molarAbundances.at(species) / total_moles_per_gram;
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}
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std::unordered_map<atomic::Species, double> Composition::getNumberFraction() const noexcept {
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std::unordered_map<atomic::Species, double> number_fractions;
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for (const auto &species: m_molarAbundances | std::views::keys) {
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number_fractions.emplace(species, getNumberFraction(species));
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}
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return number_fractions;
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}
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double Composition::getMolarAbundance(
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const std::string &symbol
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) const {
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const auto species = getSpecies(symbol);
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if (!species) {
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throw_unknown_symbol(getLogger(), symbol);
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}
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return getMolarAbundance(species.value());
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}
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double Composition::getMolarAbundance(
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const atomic::Species &species
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) const {
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if (!m_molarAbundances.contains(species)) {
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throw_unregistered_symbol(getLogger(), std::string(species.name()));
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}
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return m_molarAbundances.at(species);
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}
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double Composition::getMeanParticleMass() const noexcept {
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std::vector<double> X = getMassFractionVector();
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double sum = 0.0;
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for (const auto& [species, x] : std::views::zip(m_registeredSpecies, X)) {
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sum += x/species.mass();
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}
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return 1.0 / sum;
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}
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double Composition::getElectronAbundance() const noexcept {
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double Ye = 0.0;
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for (const auto& [species, y] : m_molarAbundances) {
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Ye += species.z() * y;
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}
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return Ye;
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}
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CanonicalComposition Composition::getCanonicalComposition(
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) const {
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using namespace fourdst::atomic;
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if (m_cache.canonicalComp.has_value()) {
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return m_cache.canonicalComp.value(); // Short circuit if we have cached the canonical composition
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}
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CanonicalComposition canonicalComposition;
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const std::set<Species> canonicalH = {H_1, H_2, H_3, H_4, H_5, H_6, H_7};
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const std::set<Species> canonicalHe = {He_3, He_4, He_5, He_6, He_7, He_8, He_9, He_10};
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for (const auto& symbol : canonicalH) {
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if (contains(symbol)) {
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canonicalComposition.X += getMassFraction(symbol);
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}
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}
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for (const auto& symbol : canonicalHe) {
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if (contains(symbol)) {
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canonicalComposition.Y += getMassFraction(symbol);
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}
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}
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for (const auto& species : m_molarAbundances | std::views::keys) {
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const bool isHIsotope = canonicalH.contains(species);
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const bool isHeIsotope = canonicalHe.contains(species);
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if (isHIsotope || isHeIsotope) {
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continue; // Skip canonical H and He symbols
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}
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canonicalComposition.Z += getMassFraction(species);
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}
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// ReSharper disable once CppTooWideScopeInitStatement
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const double Z = 1.0 - (canonicalComposition.X + canonicalComposition.Y);
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if (std::abs(Z - canonicalComposition.Z) > 1e-16) {
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LOG_ERROR(getLogger(), "Validation composition Z (X-Y = {}) is different than canonical composition Z ({}) (∑a_i where a_i != H/He).", Z, canonicalComposition.Z);
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throw exceptions::InvalidCompositionError("Validation composition Z (X-Y = " + std::to_string(Z) + ") is different than canonical composition Z (" + std::to_string(canonicalComposition.Z) + ") (∑a_i where a_i != H/He).");
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}
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m_cache.canonicalComp = canonicalComposition;
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return canonicalComposition;
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}
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std::vector<double> Composition::getMassFractionVector() const noexcept {
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if (m_cache.massFractions.has_value()) {
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return m_cache.massFractions.value(); // Short circuit if we have cached the mass fractions
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}
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std::vector<double> massFractionVector;
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std::vector<double> speciesMass;
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massFractionVector.reserve(m_molarAbundances.size());
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speciesMass.reserve(m_molarAbundances.size());
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for (const auto &species: m_molarAbundances | std::views::keys) {
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massFractionVector.push_back(getMassFraction(species));
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speciesMass.push_back(species.mass());
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}
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std::vector<double> massFractions = sortVectorBy(massFractionVector, speciesMass);
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m_cache.massFractions = massFractions; // Cache the result
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return massFractions;
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}
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std::vector<double> Composition::getNumberFractionVector() const noexcept {
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if (m_cache.numberFractions.has_value()) {
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return m_cache.numberFractions.value(); // Short circuit if we have cached the number fractions
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}
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std::vector<double> numberFractionVector;
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std::vector<double> speciesMass;
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numberFractionVector.reserve(m_molarAbundances.size());
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speciesMass.reserve(m_molarAbundances.size());
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for (const auto &species: m_molarAbundances | std::views::keys) {
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numberFractionVector.push_back(getNumberFraction(species));
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speciesMass.push_back(species.mass());
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}
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std::vector<double> numberFractions = sortVectorBy(numberFractionVector, speciesMass);
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m_cache.numberFractions = numberFractions; // Cache the result
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return numberFractions;
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}
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std::vector<double> Composition::getMolarAbundanceVector() const noexcept {
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if (m_cache.molarAbundances.has_value()) {
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return m_cache.molarAbundances.value(); // Short circuit if we have cached the molar abundances
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}
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std::vector<double> molarAbundanceVector;
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std::vector<double> speciesMass;
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molarAbundanceVector.reserve(m_molarAbundances.size());
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speciesMass.reserve(m_molarAbundances.size());
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for (const auto &[species, y]: m_molarAbundances) {
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molarAbundanceVector.push_back(y);
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speciesMass.push_back(species.mass());
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}
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std::vector<double> molarAbundances = sortVectorBy(molarAbundanceVector, speciesMass);
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m_cache.molarAbundances = molarAbundances; // Cache the result
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return molarAbundances;
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}
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size_t Composition::getSpeciesIndex(
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const std::string &symbol
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) const {
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const auto species = getSpecies(symbol);
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if (!species) {
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throw_unknown_symbol(getLogger(), symbol);
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}
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return getSpeciesIndex(species.value());
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}
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size_t Composition::getSpeciesIndex(
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const atomic::Species &species
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) const {
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if (!m_registeredSpecies.contains(species)) {
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LOG_ERROR(getLogger(), "Species {} is not in the composition.", species.name());
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throw exceptions::UnregisteredSymbolError("Species " + std::string(species.name()) + " is not in the composition.");
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}
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if (m_cache.sortedSpecies.has_value()) {
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return std::distance(
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m_cache.sortedSpecies->begin(),
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std::ranges::find(
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m_cache.sortedSpecies.value().begin(),
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m_cache.sortedSpecies.value().end(),
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species
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)
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);
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}
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std::vector<atomic::Species> speciesVector;
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std::vector<double> speciesMass;
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speciesVector.reserve(m_molarAbundances.size());
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speciesMass.reserve(m_molarAbundances.size());
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for (const auto &s: m_registeredSpecies) {
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speciesVector.emplace_back(s);
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speciesMass.push_back(s.mass());
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}
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std::vector<atomic::Species> sortedSpecies = sortVectorBy(speciesVector, speciesMass);
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m_cache.sortedSpecies = sortedSpecies;
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return std::distance(sortedSpecies.begin(), std::ranges::find(sortedSpecies, species));
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}
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atomic::Species Composition::getSpeciesAtIndex(
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const size_t index
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) const {
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if (m_cache.sortedSpecies.has_value()) {
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return m_cache.sortedSpecies.value().at(index);
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}
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std::vector<atomic::Species> speciesVector;
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std::vector<double> speciesMass;
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speciesVector.reserve(m_molarAbundances.size());
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speciesMass.reserve(m_molarAbundances.size());
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for (const auto &species: m_registeredSpecies) {
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speciesVector.emplace_back(species);
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speciesMass.push_back(species.mass());
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}
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std::vector<atomic::Species> sortedSymbols = sortVectorBy(speciesVector, speciesMass);
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if (index >= sortedSymbols.size()) {
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LOG_ERROR(getLogger(), "Index {} is out of range for composition of size {}.", index, sortedSymbols.size());
|
|
throw std::out_of_range("Index " + std::to_string(index) + " is out of range for composition of size " + std::to_string(sortedSymbols.size()) + ".");
|
|
}
|
|
return sortedSymbols.at(index);
|
|
}
|
|
|
|
std::unique_ptr<CompositionAbstract> Composition::clone() const {
|
|
return std::make_unique<Composition>(*this);
|
|
}
|
|
|
|
bool Composition::contains(
|
|
const atomic::Species &species
|
|
) const noexcept {
|
|
return m_registeredSpecies.contains(species);
|
|
}
|
|
|
|
bool Composition::contains(
|
|
const std::string &symbol
|
|
) const {
|
|
const auto species = getSpecies(symbol);
|
|
if (!species) {
|
|
throw_unknown_symbol(getLogger(), symbol);
|
|
}
|
|
return contains(species.value());
|
|
}
|
|
|
|
size_t Composition::size() const noexcept {
|
|
return m_registeredSpecies.size();
|
|
}
|
|
|
|
void Composition::setMolarAbundance(
|
|
const std::string &symbol,
|
|
const double &molar_abundance
|
|
) {
|
|
const auto species = getSpecies(symbol);
|
|
if (!species) {
|
|
throw_unknown_symbol(getLogger(), symbol);
|
|
}
|
|
|
|
setMolarAbundance(species.value(), molar_abundance);
|
|
}
|
|
|
|
void Composition::setMolarAbundance(
|
|
const atomic::Species &species,
|
|
const double &molar_abundance
|
|
) {
|
|
if (!m_registeredSpecies.contains(species)) {
|
|
throw_unregistered_symbol(getLogger(), std::string(species.name()));
|
|
}
|
|
if (molar_abundance < 0.0) {
|
|
LOG_ERROR(getLogger(), "Molar abundance must be non-negative for symbol {}. Currently it is {}.", species.name(), molar_abundance);
|
|
throw exceptions::InvalidCompositionError("Molar abundance must be non-negative, got " + std::to_string(molar_abundance) + " for symbol " + std::string(species.name()) + ".");
|
|
}
|
|
m_molarAbundances.at(species) = molar_abundance;
|
|
}
|
|
|
|
void Composition::setMolarAbundance(
|
|
const std::vector<std::string> &symbols,
|
|
const std::vector<double> &molar_abundances
|
|
) {
|
|
for (const auto& [symbol, y] : std::views::zip(symbols, molar_abundances)) {
|
|
setMolarAbundance(symbol, y);
|
|
}
|
|
}
|
|
|
|
void Composition::setMolarAbundance(
|
|
const std::vector<atomic::Species> &species,
|
|
const std::vector<double> &molar_abundances
|
|
) {
|
|
for (const auto& [s, y] : std::views::zip(species, molar_abundances)) {
|
|
setMolarAbundance(s, y);
|
|
}
|
|
}
|
|
|
|
void Composition::setMolarAbundance(
|
|
const std::set<std::string> &symbols,
|
|
const std::vector<double> &molar_abundances
|
|
) {
|
|
for (const auto& [symbol, y] : std::views::zip(symbols, molar_abundances)) {
|
|
setMolarAbundance(symbol, y);
|
|
}
|
|
}
|
|
|
|
void Composition::setMolarAbundance(
|
|
const std::set<atomic::Species> &species,
|
|
const std::vector<double> &molar_abundances
|
|
) {
|
|
for (const auto& [s, y] : std::views::zip(species, molar_abundances)) {
|
|
setMolarAbundance(s, y);
|
|
}
|
|
}
|
|
|
|
/// OVERLOADS
|
|
|
|
std::ostream& operator<<(
|
|
std::ostream& os,
|
|
const Composition& composition
|
|
) {
|
|
os << "Composition(Mass Fractions => [";
|
|
size_t count = 0;
|
|
for (const auto &species : composition.m_registeredSpecies) {
|
|
os << species << ": " << composition.getMassFraction(species);
|
|
if (count < composition.size() - 1) {
|
|
os << ", ";
|
|
}
|
|
count++;
|
|
}
|
|
os << "])";
|
|
return os;
|
|
}
|
|
|
|
} // namespace fourdst::composition
|