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feat(composition): added composition class

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in order to get composition in a standardized way anywhere in the code we now have a composition class
This commit is contained in:
Emily Boudreaux
2025-03-24 12:58:30 -04:00
parent 4840b439df
commit 7c42201ddb
4 changed files with 368 additions and 36 deletions
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1
src/composition/meson.build
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@@ -11,6 +11,7 @@ dependencies = [
probe_dep,
config_dep,
quill_dep,
species_weight_dep
]
# Define the libcomposition library so it can be linked against by other parts of the build system

153
src/composition/private/composition.cpp Normal file
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@@ -0,0 +1,153 @@
#include "composition.h"
#include "quill/LogMacros.h"
#include <stdexcept>
#include "atomicSpecies.h"
using namespace composition;
Composition::Composition(const std::vector<std::string>& symbols) {
for (const auto& symbol : symbols) {
registerSymbol(symbol);
}
}
void Composition::validateComposition(const std::vector<double>& mass_fractions) const {
if (!isValidComposition(mass_fractions)) {
LOG_ERROR(m_logger, "Invalid composition.");
throw std::runtime_error("Invalid composition.");
}
}
bool Composition::isValidComposition(const std::vector<double>& mass_fractions) const {
double sum = 0.0;
for (const auto& mass_fraction : mass_fractions) {
sum += mass_fraction;
}
if (sum < 0.99999999 || sum > 1.000000001) {
LOG_ERROR(m_logger, "The sum of mass fractions must be equal to 1.");
return false;
}
return true;
}
Composition::Composition(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.");
}
validateComposition(mass_fractions);
finalize();
for (const auto &symbol : symbols) {
registerSymbol(symbol);
}
for (size_t i = 0; i < symbols.size(); ++i) {
setComposition(symbols[i], mass_fractions[i]);
}
}
void Composition::registerSymbol(const std::string& symbol) {
if (!isValidSymbol(symbol)) {
LOG_ERROR(m_logger, "Invalid symbol: {}", symbol);
throw std::runtime_error("Invalid symbol.");
}
if (m_registeredSymbols.find(symbol) != m_registeredSymbols.end()) {
LOG_WARNING(m_logger, "Symbol {} is already registered.", symbol);
return;
}
m_registeredSymbols.insert(symbol);
LOG_INFO(m_logger, "Registered symbol: {}", symbol);
}
bool Composition::isValidSymbol(const std::string& symbol) const {
return chemSpecies::species.count(symbol) > 0;
}
double Composition::setComposition(const std::string& symbol, const double& mass_fraction) {
m_finalized = false;
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 (mass_fraction < 0.0 || mass_fraction > 1.0) {
LOG_ERROR(m_logger, "Mass fraction must be between 0 and 1.");
throw std::runtime_error("Mass fraction must be between 0 and 1.");
}
double old_mass_fraction = 0.0;
if (m_compositions.find(symbol) != m_compositions.end()) {
old_mass_fraction = m_compositions[symbol].mass_fraction;
}
m_compositions[symbol] = {symbol, mass_fraction};
return old_mass_fraction;
}
std::vector<double> Composition::setComposition(const std::vector<std::string>& symbols, const std::vector<double>& mass_fractions) {
m_finalized = false;
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(setComposition(symbols[i], mass_fractions[i]));
}
return old_mass_fractions;
}
std::set<std::string> Composition::getRegisteredSymbols() const {
return m_registeredSymbols;
}
std::unordered_map<std::string, CompositionEntry> Composition::getCompositions() 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;
}
bool Composition::finalize() {
m_finalized = true;
std::vector<double> mass_fractions;
mass_fractions.reserve(m_compositions.size());
for (const auto& [_, entry] : m_compositions) {
mass_fractions.push_back(entry.mass_fraction);
}
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;
}
return true;
}
CompositionEntry Composition::getComposition(const std::string& symbol) const {
if (!m_finalized) {
LOG_ERROR(m_logger, "Composition has not been finalized.");
throw std::runtime_error("Composition has not been finalized (Consider running .finalize()).");
}
if (m_compositions.count(symbol) == 0) {
LOG_ERROR(m_logger, "Symbol {} is not in the composition.", symbol);
throw std::runtime_error("Symbol is not in the composition.");
}
return m_compositions.at(symbol);
}

36
src/composition/private/composition.h
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@@ -1,36 +0,0 @@
#ifndef COMPOSITION_H
#define COMPOSITION_H
#include <iomanip>
#include <iostream>
#include <string>
#include <unordered_map>
#include <vector>
#include "quill/LogMacros.h
#include "probe.h"
#include "config.h"
struct CompositionEntry {
std::string symbol;
std::string mass_fraction;
friend std::ostream& operator<<(std::ostream& os, const CompositionEntry& entry) {
os << std::setw(5) << "<" << entry.symbol << " : " << entry.mass_fraction << ">";
return os;
}
};
class Composition {
private:
Config& m_config = Config::getInstance();
Probe::LogManager& m_logManager = Probe::LogManager::getInstance();
quill::Logger* m_logger = logManager.getLogger('log');
std::vector<std::string> m_registeredSymbols;
std::unordered_map<std::string, CompositionEntry> m_compositions;
}
#endif // COMPOSITION_H

214
src/composition/public/composition.h Normal file
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@@ -0,0 +1,214 @@
#ifndef COMPOSITION_H
#define COMPOSITION_H
#include <iomanip>
#include <iostream>
#include <string>
#include <unordered_map>
#include <set>
#include "quill/LogMacros.h"
#include "probe.h"
#include "config.h"
#include "atomicSpecies.h"
namespace composition{
/**
* @brief Represents an entry in the composition with a symbol and mass fraction.
*/
struct CompositionEntry {
std::string symbol; ///< The chemical symbol of the element.
double mass_fraction; ///< The mass fraction of the element.
/**
* @brief Overloaded output stream operator for CompositionEntry.
* @param os The output stream.
* @param entry The CompositionEntry to output.
* @return The output stream.
*/
friend std::ostream& operator<<(std::ostream& os, const CompositionEntry& entry) {
os << "<" << entry.symbol << " : " << entry.mass_fraction << ">";
return os;
}
};
/**
* @brief Manages the composition of elements.
* @details The composition is a collection of elements with their respective mass fractions.
* The general purpose of this class is to provide a standardized interface for managing the composition of
* any part of 4DSSE. There are a few rules when using this class.
* - Only species in the atomicSpecies.h database can be used. There are 1000s (All species from AME2020) in there so it should not be a problem.
* - Before a mass fraction can be set with a particular instance of Composition, the symbol must be registered. (i.e. register He-3 before setting its mass fraction)
* - Before any composition information can be retrived (e.g. getComposition), the composition must be finalized (call to .finalize()). This checks if the total mass fraction sums to approximatly 1 (within 1 part in 10^8)
* - Any changes made to the composition after finalization will "unfinalize" the composition. This means that the composition must be finalized again before any information can be retrived.
* - The mass fraction of any individual species must be no more than 1 and no less than 0.
* - The only exception to the finalize rule is if the compositon was constructed with symbols and mass fractions at instantiation time. In this case, the composition is automatically finalized.
* however, this means that the composition passed to the constructor must be valid.
*
* @example Constructing a finalized composition with symbols and mass fractions:
* @code
* std::vector<std::string> symbols = {"H", "O"};
* std::vector<double> mass_fractions = {0.1, 0.9};
* Composition comp(symbols, mass_fractions);
* @endcode
* @example Constructing a composition with symbols and finalizing it later:
* @code
* std::vector<std::string> symbols = {"H", "O"};
* Composition comp(symbols);
* comp.setComposition("H", 0.1);
* comp.setComposition("O", 0.9);
* comp.finalize();
* @endcode
*/
class Composition {
private:
Config& m_config = Config::getInstance();
Probe::LogManager& m_logManager = Probe::LogManager::getInstance();
quill::Logger* m_logger = m_logManager.getLogger("log");
bool m_finalized = false;
std::set<std::string> m_registeredSymbols;
std::unordered_map<std::string, CompositionEntry> m_compositions;
/**
* @brief Checks if the given symbol is valid.
* @details A symbol is valid if it is in the atomic species database (species in atomicSpecies.h). These include all the isotopes from AME2020.
* @param symbol The symbol to check.
* @return True if the symbol is valid, false otherwise.
*/
bool isValidSymbol(const std::string& symbol) const;
/**
* @brief Checks if the given mass fractions are valid.
* @param mass_fractions The mass fractions to check.
* @return True if the mass fractions are valid, false otherwise.
*/
bool isValidComposition(const std::vector<double>& mass_fractions) const;
/**
* @brief Validates the given mass fractions.
* @param mass_fractions The mass fractions to validate.
* @throws std::invalid_argument if the mass fractions are invalid.
*/
void validateComposition(const std::vector<double>& mass_fractions) const;
public:
/**
* @brief Default constructor.
*/
Composition() = default;
/**
* @brief Default destructor.
*/
~Composition() = default;
/**
* @brief Finalizes the composition.
* @return True if the composition is successfully finalized, false otherwise.
*/
bool finalize();
/**
* @brief Constructs a Composition with the given symbols.
* @param symbols The symbols to initialize the composition with.
* @example
* @code
* std::vector<std::string> symbols = {"H", "O"};
* Composition comp(symbols);
* @endcode
*/
Composition(const std::vector<std::string>& symbols);
/**
* @brief Constructs a Composition with the given symbols and mass fractions.
* @param symbols The symbols to initialize the composition with.
* @param mass_fractions The mass fractions corresponding to the symbols.
* @example
* @code
* std::vector<std::string> symbols = {"H", "O"};
* std::vector<double> mass_fractions = {0.1, 0.9};
* Composition comp(symbols, mass_fractions);
* @endcode
*/
Composition(const std::vector<std::string>& symbols, const std::vector<double>& mass_fractions);
/**
* @brief Registers a new symbol.
* @param symbol The symbol to register.
* @example
* @code
* Composition comp;
* comp.registerSymbol("H");
* @endcode
*/
void registerSymbol(const std::string& symbol);
/**
* @brief Gets the registered symbols.
* @return A set of registered symbols.
*/
std::set<std::string> getRegisteredSymbols() const;
/**
* @brief Sets the composition for a given symbol.
* @param symbol The symbol to set the composition for.
* @param mass_fraction The mass fraction to set.
* @return The mass fraction that was set.
* @example
* @code
* Composition comp;
* comp.setComposition("H", 0.1);
* @endcode
*/
double setComposition(const std::string& symbol, const double& mass_fraction);
/**
* @brief Sets the composition for multiple symbols.
* @param symbols The symbols to set the composition for.
* @param mass_fractions The mass fractions corresponding to the symbols.
* @return A vector of mass fractions that were set.
* @example
* @code
* std::vector<std::string> symbols = {"H", "O"};
* std::vector<double> mass_fractions = {0.1, 0.9};
* Composition comp;
* comp.setComposition(symbols, mass_fractions);
* @endcode
*/
std::vector<double> setComposition(const std::vector<std::string>& symbols, const std::vector<double>& mass_fractions);
/**
* @brief Gets the compositions.
* @return An unordered map of compositions.
*/
std::unordered_map<std::string, CompositionEntry> getCompositions() const;
/**
* @brief Gets the composition for a given symbol.
* @param symbol The symbol to get the composition for.
* @return The CompositionEntry for the given symbol.
*/
CompositionEntry getComposition(const std::string& symbol) const;
/**
* @brief Overloaded output stream operator for Composition.
* @param os The output stream.
* @param composition The Composition to output.
* @return The output stream.
*/
friend 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;
}
};
};
#endif // COMPOSITION_H