/**
 * \file
 * \copyright
 * Copyright (c) 2012-2021, OpenGeoSys Community (http://www.opengeosys.org)
 *            Distributed under a Modified BSD License.
 *              See accompanying file LICENSE.txt or
 *              http://www.opengeosys.org/project/license
 *
 */

#pragma once

#include <memory>

#include "ChemicalSolverInterface.h"
#include "PhreeqcIOData/Knobs.h"

namespace MeshLib
{
class Mesh;
}

namespace ChemistryLib
{
namespace PhreeqcIOData
{
struct ChemicalSystem;
struct ReactionRate;
struct Output;
struct SurfaceSite;
struct ExchangeSite;
struct Dump;
struct UserPunch;

class PhreeqcIO final : public ChemicalSolverInterface
{
public:
    PhreeqcIO(std::string const& project_file_name,
              std::string&& database,
              std::unique_ptr<ChemicalSystem>&& chemical_system,
              std::vector<ReactionRate>&& reaction_rates,
              std::vector<SurfaceSite>&& surface,
              std::vector<ExchangeSite>&& exchange,
              std::unique_ptr<UserPunch>&& user_punch,
              std::unique_ptr<Output>&& output,
              std::unique_ptr<Dump>&& dump,
              Knobs&& knobs);

    void initialize() override;

    void initializeChemicalSystemConcrete(
        std::vector<double> const& concentrations,
        GlobalIndexType const& chemical_system_id,
        MaterialPropertyLib::Medium const& medium,
        ParameterLib::SpatialPosition const& pos,
        double const t) override;

    void setChemicalSystemConcrete(
        std::vector<double> const& concentrations,
        GlobalIndexType const& chemical_system_id,
        MaterialPropertyLib::Medium const* medium,
        MaterialPropertyLib::VariableArray const& vars,
        ParameterLib::SpatialPosition const& pos, double const t,
        double const dt) override;

    void setAqueousSolutionsPrevFromDumpFile() override;

    void executeSpeciationCalculation(double const dt) override;

    std::vector<GlobalVector*> getIntPtProcessSolutions() const override;

    friend std::ostream& operator<<(std::ostream& os,
                                    PhreeqcIO const& phreeqc_io);

    friend std::istream& operator>>(std::istream& in, PhreeqcIO& phreeqc_io);

    void updateVolumeFractionPostReaction(
        GlobalIndexType const& chemical_system_id,
        MaterialPropertyLib::Medium const& medium,
        ParameterLib::SpatialPosition const& pos, double const porosity,
        double const t, double const dt) override;

    void updatePorosityPostReaction(GlobalIndexType const& chemical_system_id,
                                    MaterialPropertyLib::Medium const& medium,
                                    double& porosity) override;

    void computeSecondaryVariable(
        std::size_t const ele_id,
        std::vector<GlobalIndexType> const& chemical_system_indices) override;

    std::vector<std::string> const getComponentList() const override;

    std::string const _phreeqc_input_file;

private:
    void writeInputsToFile(double const dt);

    void callPhreeqc();

    void readOutputsFromFile();

    PhreeqcIO& operator<<(double const dt)
    {
        _dt = dt;
        return *this;
    }

    std::string const _database;
    std::unique_ptr<ChemicalSystem> _chemical_system;
    std::vector<ReactionRate> const _reaction_rates;
    std::vector<SurfaceSite> const _surface;
    std::vector<ExchangeSite> const _exchange;
    std::unique_ptr<UserPunch> _user_punch;
    std::unique_ptr<Output> const _output;
    std::unique_ptr<Dump> const _dump;
    Knobs const _knobs;
    double _dt = std::numeric_limits<double>::quiet_NaN();
    const int phreeqc_instance_id = 0;
    std::size_t _num_chemical_systems = -1;
};
}  // namespace PhreeqcIOData
}  // namespace ChemistryLib