reaction.h

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#pragma once
 
#include <string_view>
 
#include "fourdst/composition/atomicSpecies.h"
#include "fourdst/logging/logging.h"
#include "quill/Logger.h"
#include <unordered_map>
#include <vector>
#include <unordered_set>
 
 
#include "cppad/cppad.hpp"

namespace gridfire::reaction {
    struct RateCoefficientSet {
        double a0; 
        double a1; 
        double a2; 
        double a3; 
        double a4; 
        double a5; 
        double a6; 

        friend std::ostream& operator<<(std::ostream& os, const RateCoefficientSet& r) {
            os << "[" << r.a0 << ", " << r.a1 << ", " << r.a2 << ", "
               << r.a3 << ", " << r.a4 << ", " << r.a5 << ", " << r.a6 << "]";
            return os;
        }
    };

    class Reaction {
    public:
        virtual ~Reaction() = default;

        Reaction(
            const std::string_view id,
            const std::string_view peName,
            const int chapter,
            const std::vector<fourdst::atomic::Species> &reactants,
            const std::vector<fourdst::atomic::Species> &products,
            const double qValue,
            const std::string_view label,
            const RateCoefficientSet &sets,
            const bool reverse = false);

        [[nodiscard]] virtual double calculate_rate(const double T9) const;

        [[nodiscard]] virtual CppAD::AD<double> calculate_rate(const CppAD::AD<double> T9) const;

        [[nodiscard]] virtual std::string_view peName() const { return m_peName; }

        [[nodiscard]] int chapter() const { return m_chapter; }

        [[nodiscard]] std::string_view sourceLabel() const { return m_sourceLabel; }

        [[nodiscard]] const RateCoefficientSet& rateCoefficients() const { return m_rateCoefficients; }

        [[nodiscard]] bool contains(const fourdst::atomic::Species& species) const;

        [[nodiscard]] bool contains_reactant(const fourdst::atomic::Species& species) const;

        [[nodiscard]] bool contains_product(const fourdst::atomic::Species& species) const;

        [[nodiscard]] std::unordered_set<fourdst::atomic::Species> all_species() const;

        [[nodiscard]] std::unordered_set<fourdst::atomic::Species> reactant_species() const;

        [[nodiscard]] std::unordered_set<fourdst::atomic::Species> product_species() const;

        [[nodiscard]] size_t num_species() const;

        [[nodiscard]] int stoichiometry(const fourdst::atomic::Species& species) const;

        [[nodiscard]] std::unordered_map<fourdst::atomic::Species, int> stoichiometry() const;

        [[nodiscard]] std::string_view id() const { return m_id; }

        [[nodiscard]] double qValue() const { return m_qValue; }

        [[nodiscard]] const std::vector<fourdst::atomic::Species>& reactants() const { return m_reactants; }

        [[nodiscard]] const std::vector<fourdst::atomic::Species>& products() const { return m_products; }

        [[nodiscard]] bool is_reverse() const { return m_reverse; }

        [[nodiscard]] double excess_energy() const;

        bool operator==(const Reaction& other) const { return m_id == other.m_id; }

        bool operator!=(const Reaction& other) const { return !(*this == other); }

        [[nodiscard]] uint64_t hash(uint64_t seed = 0) const;
 
    protected:
        quill::Logger* m_logger = fourdst::logging::LogManager::getInstance().getLogger("log");
        std::string m_id; 
        std::string m_peName; 
        int m_chapter;    
        double m_qValue = 0.0; 
        std::vector<fourdst::atomic::Species> m_reactants; 
        std::vector<fourdst::atomic::Species> m_products; 
        std::string m_sourceLabel; 
        RateCoefficientSet m_rateCoefficients; 
        bool m_reverse = false; 
    private:
        template <typename T>
        [[nodiscard]] T calculate_rate(const T T9) const {
            const T T913 = CppAD::pow(T9, 1.0/3.0);
            const T T953 = CppAD::pow(T9, 5.0/3.0);
            const T logT9 = CppAD::log(T9);
            const T exponent = m_rateCoefficients.a0 +
                   m_rateCoefficients.a1 / T9 +
                   m_rateCoefficients.a2 / T913 +
                   m_rateCoefficients.a3 * T913 +
                   m_rateCoefficients.a4 * T9 +
                   m_rateCoefficients.a5 * T953 +
                   m_rateCoefficients.a6 * logT9;
            return CppAD::exp(exponent);
        }
    };

    class ReactionSet {
    public:
        explicit ReactionSet(std::vector<Reaction> reactions);

        ReactionSet(const ReactionSet& other);

        ReactionSet& operator=(const ReactionSet& other);

        virtual ~ReactionSet() = default;

        virtual void add_reaction(Reaction reaction);

        virtual void remove_reaction(const Reaction& reaction);

        [[nodiscard]] bool contains(const std::string_view& id) const;

        [[nodiscard]] bool contains(const Reaction& reaction) const;

        [[nodiscard]] virtual size_t size() const { return m_reactions.size(); }

        void clear();

        [[nodiscard]] bool contains_species(const fourdst::atomic::Species& species) const;

        [[nodiscard]] bool contains_reactant(const fourdst::atomic::Species& species) const;

        [[nodiscard]] bool contains_product(const fourdst::atomic::Species& species) const;

        [[nodiscard]] virtual const Reaction& operator[](size_t index) const;

        [[nodiscard]] const Reaction& operator[](const std::string_view& id) const;

        bool operator==(const ReactionSet& other) const;

        bool operator!=(const ReactionSet& other) const;

        [[nodiscard]] uint64_t hash(uint64_t seed = 0) const;

        auto begin() { return m_reactions.begin(); }
        [[nodiscard]] auto begin() const { return m_reactions.cbegin(); }
        auto end() { return m_reactions.end(); }
        [[nodiscard]] auto end() const { return m_reactions.cend(); }
    private:
        quill::Logger* m_logger = fourdst::logging::LogManager::getInstance().getLogger("log");
        std::vector<Reaction> m_reactions;
        std::string m_id;
        std::unordered_map<std::string, Reaction> m_reactionNameMap; 
 
    };
 

    class LogicalReaction final : public Reaction {
    public:
        explicit LogicalReaction(const std::vector<Reaction> &reactions);

        void add_reaction(const Reaction& reaction);

        [[nodiscard]] size_t size() const { return m_rates.size(); }

        [[nodiscard]] std::vector<std::string> sources() const { return m_sources; }

        [[nodiscard]] double calculate_rate(const double T9) const override;

        [[nodiscard]] CppAD::AD<double> calculate_rate(const CppAD::AD<double> T9) const override;

        auto begin() { return m_rates.begin(); }
        [[nodiscard]] auto begin() const { return m_rates.cbegin(); }
        auto end() { return m_rates.end(); }
        [[nodiscard]] auto end() const { return m_rates.cend(); }
 
    private:
        std::vector<std::string> m_sources; 
        std::vector<RateCoefficientSet> m_rates; 
 
    private:
        template <typename T>
        [[nodiscard]] T calculate_rate(const T T9) const {
            T sum = static_cast<T>(0.0);
            const T T913 = CppAD::pow(T9, 1.0/3.0);
            const T T953 = CppAD::pow(T9, 5.0/3.0);
            const T logT9 = CppAD::log(T9);
            // ReSharper disable once CppUseStructuredBinding
            for (const auto& rate : m_rates) {
                const T exponent = rate.a0 +
                       rate.a1 / T9 +
                       rate.a2 / T913 +
                       rate.a3 * T913 +
                       rate.a4 * T9 +
                       rate.a5 * T953 +
                       rate.a6 * logT9;
                sum += CppAD::exp(exponent);
            }
            return sum;
        }
    };

    class LogicalReactionSet final : public ReactionSet {
    public:
        LogicalReactionSet() = delete;

        explicit LogicalReactionSet(const ReactionSet& reactionSet);

        auto begin() { return m_reactions.begin(); }
        [[nodiscard]] auto begin() const { return m_reactions.cbegin(); }
        auto end() { return m_reactions.end(); }
        [[nodiscard]] auto end() const { return m_reactions.cend(); }

        [[nodiscard]] size_t size() const { return m_reactions.size(); }

        [[nodiscard]] const LogicalReaction& operator[](size_t index) const { return m_reactions[index]; }
    private:
        quill::Logger* m_logger = fourdst::logging::LogManager::getInstance().getLogger("log");
        std::vector<LogicalReaction> m_reactions;
        std::string m_id;
        std::unordered_map<std::string, LogicalReaction> m_reactionNameMap; 
    };
 
}