/*
Implementation of two-fluid greyscale color lattice boltzmann model
 */
#include <stdio.h>
#include <stdlib.h>
#include <sys/stat.h>
#include <iostream>
#include <exception>
#include <stdexcept>
#include <fstream>

#include "common/Communication.h"
#include "analysis/GreyPhase.h"
#include "common/MPI.h"
#include "ProfilerApp.h"
#include "threadpool/thread_pool.h"

/**
 * \class ScaLBL_GreyscaleColorModel
 *
 * @details
 * The ScaLBL_GreyscaleColorModel class extends the standard color model incorporate transport
 * through sub-resolution "greyscale" regions.
 * Momentum transport equations are described by a D3Q19 scheme
 * Mass transport equations are described by D3Q7 scheme
 */

class ScaLBL_GreyscaleColorModel {
public:
    /**
    * \brief Constructor
    * @param RANK        processor rank 
    * @param NP        number of processors 
    * @param COMM        MPI communicator 
    */
    ScaLBL_GreyscaleColorModel(int RANK, int NP, const Utilities::MPI &COMM);
    ~ScaLBL_GreyscaleColorModel();

    // functions in they should be run
    /**
    * \brief Read simulation parameters
    * @param filename       input database file that includes "Color" section 
    */
    void ReadParams(string filename);

    /**
    * \brief Read simulation parameters
    * @param db0       input database that includes "Color" section 
    */
    void ReadParams(std::shared_ptr<Database> db0);

    /**
    * \brief Create domain data structures
    */
    void SetDomain();

    /**
    * \brief Read image data
    */
    void ReadInput();

    /**
    * \brief Create color model data structures
    */
    void Create();

    /**
    * \brief Initialize the simulation
    */
    void Initialize();

    /**
    * \brief Run the simulation
    */
    void Run();

    /**
    * \brief Debugging function to dump simulation state to disk
    */
    void WriteDebug();
    void WriteVisFiles();

    bool Restart, pBC;
    bool REVERSE_FLOW_DIRECTION;
    int timestep, timestepMax;
    int BoundaryCondition;
    double tauA, tauB, rhoA, rhoB, alpha, beta;
    double tauA_eff, tauB_eff;
    double Fx, Fy, Fz, flux;
    double din, dout, inletA, inletB, outletA, outletB;
    double GreyPorosity;
    bool
        RecoloringOff; //recoloring can be turn off for grey nodes if this is true
    //double W;//wetting strength paramter for capillary pressure penalty for grey nodes

    int Nx, Ny, Nz, N, Np;
    int rank, nprocx, nprocy, nprocz, nprocs;
    double Lx, Ly, Lz;

    std::shared_ptr<Domain> Dm;   // this domain is for analysis
    std::shared_ptr<Domain> Mask; // this domain is for lbm
    std::shared_ptr<ScaLBL_Communicator> ScaLBL_Comm;
    std::shared_ptr<ScaLBL_Communicator> ScaLBL_Comm_Regular;
    std::shared_ptr<GreyPhaseAnalysis> Averages;

    // input database
    std::shared_ptr<Database> db;
    std::shared_ptr<Database> domain_db;
    std::shared_ptr<Database> greyscaleColor_db;
    std::shared_ptr<Database> analysis_db;
    std::shared_ptr<Database> vis_db;

    IntArray Map;
    signed char *id;
    int *NeighborList;
    int *dvcMap;
    double *fq, *Aq, *Bq;
    double *Den, *Phi;
    //double *GreySolidPhi; //Model 2 & 3
    //double *GreySolidGrad;//Model 1 & 4
    double *GreySolidW;
    double *GreySn;
    double *GreySw;
    double *GreyKn;
    double *GreyKw;
    double *MobilityRatio;
    double *Velocity;
    double *Pressure;
    double *Porosity_dvc;
    double *Permeability_dvc;
    //double *Psi;

private:
    Utilities::MPI comm;

    int dist_mem_size;
    int neighborSize;
    // filenames
    char LocalRankString[8];
    char LocalRankFilename[40];
    char LocalRestartFile[40];

    //int rank,nprocs;
    void LoadParams(std::shared_ptr<Database> db0);

    /**
    * \brief Assign wetting affinity values 
    */
    void AssignComponentLabels();

    /**
    * \brief Assign wetting affinity values in greyscale regions
    */
    void AssignGreySolidLabels();
    /**
    * \brief Assign porosity and permeability in greyscale regions
    */
    void AssignGreyPoroPermLabels();
    /**
    * \brief Seed phase field
    */
    double SeedPhaseField(const double seed_water_in_oil);
};