engine_adaptive.h

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#pragma once
#include "gridfire/engine/engine_abstract.h"
#include "gridfire/engine/engine_view_abstract.h"
#include "gridfire/network.h"
 
#include "fourdst/composition/atomicSpecies.h"
#include "fourdst/config/config.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_culled,
            const double T9,
            const double rho
        ) const override;

        void generateJacobianMatrix(
            const std::vector<double> &Y_culled,
            const double T9,
            const double rho
        ) override;

        double getJacobianMatrixEntry(
            const int i_culled,
            const int j_culled
        ) const override;

        void generateStoichiometryMatrix() override;

        int getStoichiometryMatrixEntry(
            const int speciesIndex_culled,
            const int reactionIndex_culled
        ) const override;

        double calculateMolarReactionFlow(
            const reaction::Reaction &reaction,
            const std::vector<double> &Y_culled,
            double T9,
            double rho
        ) const override;

        const reaction::LogicalReactionSet& getNetworkReactions() const override;

        std::unordered_map<fourdst::atomic::Species, double> getSpeciesTimescales(
            const std::vector<double> &Y_culled,
            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;
        Config& m_config = Config::getInstance();
        quill::Logger* m_logger = LogManager::getInstance().getLogger("log");
 
        DynamicEngine& m_baseEngine;
 
        std::vector<fourdst::atomic::Species> m_activeSpecies;
        reaction::LogicalReactionSet m_activeReactions;
 
        std::vector<size_t> m_speciesIndexMap;
        std::vector<size_t> m_reactionIndexMap;
 
        bool m_isStale = true;
 
    private:
        std::vector<size_t> constructSpeciesIndexMap() const;

        std::vector<size_t> constructReactionIndexMap() const;

        std::vector<double> mapCulledToFull(const std::vector<double>& culled) const;

        std::vector<double> mapFullToCulled(const std::vector<double>& full) const;

        size_t mapCulledToFullSpeciesIndex(size_t culledSpeciesIndex) const;

        size_t mapCulledToFullReactionIndex(size_t culledReactionIndex) const;

        void validateState() const;
    private:
        struct ReactionFlow {
            const reaction::Reaction* reactionPtr;
            double flowRate;
        };
    };
}