feat(Standard-Compositions): Imported standard metal fractions from MESA

.gitignore

@@ -74,6 +74,7 @@ subprojects/libconstants/
 subprojects/liblogging/
 subprojects/.wraplock
 subprojects/tomlplusplus-*/
+subprojects/CLI11-*/
 
 qhull.wrap
 quill.wrap

build-config/CLI11/meson.build

@@ -0,0 +1,2 @@
+cli11_proj = subproject('cli11')
+cli11_dep = cli11_proj.get_variable('CLI11_dep')

build-config/meson.build

@@ -2,4 +2,5 @@ cmake = import('cmake')
 
 subdir('fourdst')
 subdir('xxHash')
+subdir('CLI11')
 

src/composition/include/fourdst/composition/io/standard_compositions.h

@@ -0,0 +1,158 @@
+#pragma once
+
+#include "fourdst/config/config.h"
+#include "fourdst/logging/logging.h"
+#include "fourdst/composition/composition.h"
+
+#include "quill/Logger.h"
+
+#include <string>
+#include <vector>
+
+namespace fourdst::composition::io  {
+    typedef std::vector<std::string> ParsedChemicalData;
+    struct CompositionData {
+        std::string comment_str;
+        double he_abundance;
+        bool requires_atomic_weight;
+        std::vector<std::string> elements;
+        std::vector<double> abundances;
+    };
+    struct IsotopicPercentage {
+        std::string comment_str;
+        std::vector<int> atomic_numbers;
+        std::vector<std::string> elements;
+        std::vector<int> mass_numbers;
+        std::vector<double> percentages;
+    };
+
+    enum class SolarCompositions {
+        AG89,
+        GN93,
+        GS98,
+        L03,
+        AGS05,
+        AGS09,
+        A09_Pryzbilla,
+        MB22_photospheric,
+        AAG21_photospheric,
+        L09
+    };
+
+    enum class IsotopicPercentages {
+        L03,
+        L09
+    };
+
+    inline std::unordered_map<SolarCompositions, std::string> SolarCompositions_to_string_map = {
+        {SolarCompositions::AG89, "AG89"},
+        {SolarCompositions::GN93, "GN93"},
+        {SolarCompositions::GS98, "GS98"},
+        {SolarCompositions::L03, "L03"},
+        {SolarCompositions::AGS05, "AGS05"},
+        {SolarCompositions::AGS09, "AGS09"},
+        {SolarCompositions::A09_Pryzbilla, "A09_Pryzbilla"},
+        {SolarCompositions::MB22_photospheric, "MB22_photospheric"},
+        {SolarCompositions::AAG21_photospheric, "AAG21_photospheric"},
+        {SolarCompositions::L09, "L09"}
+    };
+
+    inline std::unordered_map<IsotopicPercentages, std::string> IsotopicPercentages_to_string_map = {
+        {IsotopicPercentages::L03, "L03_data"},
+        {IsotopicPercentages::L09, "L09_data"}
+    };
+
+    /**
+     * @class ChemicalFileParser
+     * @brief An abstract base class for chemical file parsers.
+     *
+     * This class defines the interface for parsing fortran code files that contain
+     * nuclide fractions. Derived classes must implement the `parse`
+     * method to handle specific file formats.
+     */
+    class ChemicalFileParser {
+    private:
+
+    public:
+
+        /**
+         * @brief Parses a chemical file and returns the parsed data.
+         *
+         * This is a pure virtual function that must be implemented by derived
+         * classes. It takes a filename as input and returns a `ParsedChemicalData`
+         * struct containing the information extracted from the file.
+         *
+         * @param filename The path to the Chemical file to parse.
+         * @return A `ParsedChemicalData` struct containing the parsed reaction data.
+         *
+         * @throws std::runtime_error If the file cannot be opened or a parsing
+         * error occurs.
+         *
+         * @b Usage
+         * @code
+         * std::unique_ptr<ChemicalFileParser> parser = std::make_unique<SimpleReactionListFileParser>();
+         * try {
+         *     ParsedChemicalData data = parser->parse("my_reactions.txt");
+         *     for (const auto& reaction_name : data.reactionPENames) {
+         *         // ... process reaction name
+        const mfem::GridFunction& grav_potential_at_inf(FEM& fem, const Args& args, const mfem::GridFunction& rho, bool pho_warm) {
+
+}
+         *     }
+         * } catch (const std::runtime_error& e) {
+         *     // ... handle error
+         * }
+         * @endcode
+         */
+        [[nodiscard]] CompositionData parse_compositon_data(const std::vector<char>& data,const std::string& scheme) const ;
+        [[nodiscard]] IsotopicPercentage parse_isotopic_percentage(const std::vector<char>& data,const std::string& scheme) const ;
+    };
+
+
+}
+
+namespace fourdst::composition {
+    /**
+     * @brief Function to retrieve a standard solar composition record indexed by their canonical names including
+     *  - AG89
+     *  - GN93
+     *  - GS98
+     *  - L03
+     *  - AGS05
+     *  - AGS08
+     *  - A09_Pryzbilla
+     *  - MB22_photospheric
+     *  - AAG21_photospheric
+     *  - L09
+     *  Further, isotopic percentages can be selected as either
+     *  - L03
+     *  - L09
+     *
+     *  These data have been extracted from chem_def.f90 from MESA <version>
+     *
+     *  @note Composition names are case normalized; therefore, the inputs for metal fraction scheme and isotopic percentage scheme are case insensitive.
+     *
+     *  @param metal_fraction_scheme The name of the metal fraction scheme to use. Must be one of the following: AG89, GN93, GS98, L03, AGS05, AGS08, A09_Pryzbilla, MB22_photospheric, AAG21_photospheric, L09
+     *  @param isotopic_percentage_scheme The name of the isotopic percentage scheme to use. Must be one of the following: L03, L09
+     *  @param initial_z <poojan_documenent_here>
+     *  @param initial_y <poojan document here>
+     */
+    [[nodiscard]] Composition get_composition_record(const std::string& metal_fraction_scheme,
+                                                     const std::string& isotopic_percentage_scheme,
+                                                     double initial_z,
+                                                     double initial_y);
+
+    /**
+     * @brief Overload of the string based version of this function which accepts the enums Solar
+     * @param metal_fraction_scheme Enum corresponding to the standard solar composition to select
+     * @param isotopic_percentage_scheme Enum corresponding to the isotopic percentages prescription to select
+     * @param initial_z <poojan_document_here>
+     * @param initial_y <poojan_document_here>
+     * @return
+     */
+    [[nodiscard]] Composition get_composition_record(io::SolarCompositions metal_fraction_scheme,
+                                                     io::IsotopicPercentages isotopic_percentage_scheme,
+                                                     double initial_z,
+                                                     double initial_y);
+
+}