docs(docs): added robust docs

src/network/include/gridfire/engine/engine_adaptive.h

@@ -0,0 +1,78 @@
+#pragma once
+#include "gridfire/engine/engine_abstract.h"
+#include "gridfire/engine/engine_view_abstract.h"
+
+#include "fourdst/composition/atomicSpecies.h"
+#include "fourdst/logging/logging.h"
+
+#include "quill/Logger.h"
+
+namespace gridfire {
+    class AdaptiveEngineView final : public DynamicEngine, public EngineView<DynamicEngine> {
+    public:
+        explicit AdaptiveEngineView(DynamicEngine& baseEngine);
+
+        void update(const NetIn& netIn);
+
+        const std::vector<fourdst::atomic::Species>& getNetworkSpecies() const override;
+        StepDerivatives<double> calculateRHSAndEnergy(
+            const std::vector<double> &Y,
+            const double T9,
+            const double rho
+        ) const override;
+
+        void generateJacobianMatrix(
+            const std::vector<double> &Y,
+            const double T9,
+            const double rho
+        ) override;
+        double getJacobianMatrixEntry(
+            const int i,
+            const int j
+        ) const override;
+
+        void generateStoichiometryMatrix() override;
+        int getStoichiometryMatrixEntry(
+            const int speciesIndex,
+            const int reactionIndex
+        ) const override;
+
+        double calculateMolarReactionFlow(
+            const reaction::Reaction &reaction,
+            const std::vector<double> &Y,
+            double T9,
+            double rho
+        ) const override;
+
+        const reaction::REACLIBLogicalReactionSet& getNetworkReactions() const override;
+        std::unordered_map<fourdst::atomic::Species, double> getSpeciesTimescales(
+            const std::vector<double> &Y,
+            double T9,
+            double rho
+        ) const override;
+
+        const DynamicEngine& getBaseEngine() const override { return m_baseEngine; }
+    private:
+        using Config = fourdst::config::Config;
+        using LogManager = fourdst::logging::LogManager;
+
+        DynamicEngine& m_baseEngine;
+
+        std::vector<fourdst::atomic::Species> m_activeSpecies;
+        reaction::REACLIBLogicalReactionSet m_activeReactions;
+
+        std::vector<size_t> m_speciesIndexMap;
+
+        bool m_isStale = true;
+
+        Config& m_config = Config::getInstance();
+        quill::Logger* m_logger = LogManager::getInstance().getLogger("log");
+    private:
+        std::vector<size_t> constructSpeciesIndexMap() const;
+    private:
+        struct ReactionFlow {
+            const reaction::Reaction* reactionPtr;
+            double flowRate;
+        };
+    };
+}

src/network/include/gridfire/engine/engine_culled.h

@@ -1,55 +0,0 @@
-#pragma once
-#include "gridfire/engine/engine_abstract.h"
-
-#include "fourdst/composition/atomicSpecies.h"
-
-namespace gridfire {
-    class CulledEngine final : public DynamicEngine {
-    public:
-        explicit CulledEngine(DynamicEngine& baseEngine);
-
-        const std::vector<fourdst::atomic::Species>& getNetworkSpecies() const override;
-        StepDerivatives<double> calculateRHSAndEnergy(
-            const std::vector<double> &Y,
-            double T9,
-            double rho
-        ) const override;
-
-        void generateJacobianMatrix(
-            const std::vector<double> &Y,
-            double T9,
-            double rho
-        ) override;
-        double getJacobianMatrixEntry(
-            int i,
-            int j
-        ) const override;
-
-        void generateStoichiometryMatrix() override;
-        int getStoichiometryMatrixEntry(
-            int speciesIndex,
-            int reactionIndex
-        ) const override;
-
-        double calculateMolarReactionFlow(
-            const reaction::Reaction &reaction,
-            const std::vector<double> &Y,
-            double T9,
-            double rho
-        ) const override;
-
-        const reaction::REACLIBLogicalReactionSet& getNetworkReactions() const override;
-        std::unordered_map<fourdst::atomic::Species, double> getSpeciesTimescales(
-            const std::vector<double> &Y,
-            double T9,
-            double rho
-        ) const override;
-    private:
-        DynamicEngine& m_baseEngine;
-        std::unordered_map<fourdst::atomic::Species, size_t> m_fullSpeciesToIndexMap;
-        std::vector<fourdst::atomic::Species> m_culledSpecies;
-    private:
-        std::unordered_map<fourdst::atomic::Species, size_t> populatedSpeciesToIndexMap;
-        std::vector<fourdst::atomic::Species> determineCullableSpecies;
-    };
-}

src/network/include/gridfire/engine/engine_view_abstract.h

@@ -0,0 +1,8 @@
+//
+// Created by Emily Boudreaux on 6/27/25.
+//
+
+#ifndef ENGINE_VIEW_ABSTRACT_H
+#define ENGINE_VIEW_ABSTRACT_H
+
+#endif //ENGINE_VIEW_ABSTRACT_H