docs(docs): added doxygen html directory

src/network/include/gridfire/engine/views/engine_defined.h

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+#pragma once
+
+#include "engine_view_abstract.h"
+#include "../engine_abstract.h"
+
+#include "fourdst/config/config.h"
+#include "fourdst/logging/logging.h"
+
+#include "quill/Logger.h"
+
+#include <string>
+
+namespace gridfire{
+    class FileDefinedEngineView final: public DynamicEngine, public EngineView<DynamicEngine> {
+    public:
+        explicit FileDefinedEngineView(DynamicEngine& baseEngine, const std::string& fileName);
+
+        // --- EngineView Interface ---
+        const DynamicEngine& getBaseEngine() const override;
+
+        // --- Engine Interface ---
+        const std::vector<fourdst::atomic::Species>& getNetworkSpecies() const override;
+
+        // --- DynamicEngine Interface ---
+        StepDerivatives<double> calculateRHSAndEnergy(
+            const std::vector<double>& Y_defined,
+            const double T9,
+            const double rho
+        ) const override;
+        void generateJacobianMatrix(
+            const std::vector<double>& Y_defined,
+            const double T9,
+            const double rho
+        ) override;
+        double getJacobianMatrixEntry(
+            const int i_defined,
+            const int j_defined
+        ) const override;
+        void generateStoichiometryMatrix() override;
+        int getStoichiometryMatrixEntry(
+            const int speciesIndex_defined,
+            const int reactionIndex_defined
+        ) const override;
+        double calculateMolarReactionFlow(
+            const reaction::Reaction& reaction,
+            const std::vector<double>& Y_defined,
+            const double T9,
+            const double rho
+        ) const override;
+        const reaction::LogicalReactionSet& getNetworkReactions() const override;
+        std::unordered_map<fourdst::atomic::Species, double> getSpeciesTimescales(
+            const std::vector<double>& Y_defined,
+            const double T9,
+            const double rho
+        ) const override;
+    private:
+        using Config = fourdst::config::Config;
+        using LogManager = fourdst::logging::LogManager;
+        Config& m_config = Config::getInstance();
+        quill::Logger* m_logger = LogManager::getInstance().getLogger("log");
+
+        DynamicEngine& m_baseEngine;
+
+        std::vector<fourdst::atomic::Species> m_activeSpecies; ///< Active species in the defined engine.
+        reaction::LogicalReactionSet m_activeReactions; ///< Active reactions in the defined engine.
+
+        std::vector<size_t> m_speciesIndexMap; ///< Maps indices of active species to indices in the full network.
+        std::vector<size_t> m_reactionIndexMap; ///< Maps indices of active reactions to indices in the full network.
+    private:
+        void buildFromFile(const std::string& fileName);
+
+        /**
+         * @brief Constructs the species index map.
+         *
+         * @return A vector mapping culled species indices to full species indices.
+         *
+         * This method creates a map from the indices of the active species to the indices of the
+         * corresponding species in the full network.
+         *
+         * @see AdaptiveEngineView::update()
+         */
+        std::vector<size_t> constructSpeciesIndexMap() const;
+
+        /**
+         * @brief Constructs the reaction index map.
+         *
+         * @return A vector mapping culled reaction indices to full reaction indices.
+         *
+         * This method creates a map from the indices of the active reactions to the indices of the
+         * corresponding reactions in the full network.
+         *
+         * @see AdaptiveEngineView::update()
+         */
+        std::vector<size_t> constructReactionIndexMap() const;
+
+        /**
+         * @brief Maps a vector of culled abundances to a vector of full abundances.
+         *
+         * @param culled A vector of abundances for the active species.
+         * @return A vector of abundances for the full network, with the abundances of the active
+         *         species copied from the culled vector.
+         */
+        std::vector<double> mapCulledToFull(const std::vector<double>& culled) const;
+
+        /**
+         * @brief Maps a vector of full abundances to a vector of culled abundances.
+         *
+         * @param full A vector of abundances for the full network.
+         * @return A vector of abundances for the active species, with the abundances of the active
+         *         species copied from the full vector.
+         */
+        std::vector<double> mapFullToCulled(const std::vector<double>& full) const;
+
+        /**
+         * @brief Maps a culled species index to a full species index.
+         *
+         * @param culledSpeciesIndex The index of the species in the culled species list.
+         * @return The index of the corresponding species in the full network.
+         *
+         * @throws std::out_of_range If the culled index is out of bounds for the species index map.
+         */
+        size_t mapCulledToFullSpeciesIndex(size_t culledSpeciesIndex) const;
+
+        /**
+         * @brief Maps a culled reaction index to a full reaction index.
+         *
+         * @param culledReactionIndex The index of the reaction in the culled reaction list.
+         * @return The index of the corresponding reaction in the full network.
+         *
+         * @throws std::out_of_range If the culled index is out of bounds for the reaction index map.
+         */
+        size_t mapCulledToFullReactionIndex(size_t culledReactionIndex) const;
+
+    };
+}