/*
 * Ion transporte LB Model
 */
#ifndef ScaLBL_IonModel_INC
#define ScaLBL_IonModel_INC

#include <stdio.h>
#include <stdlib.h>
#include <sys/stat.h>
#include <iostream>
#include <exception>
#include <stdexcept>
#include <fstream>
#include <vector>

#include "common/ScaLBL.h"
#include "common/Communication.h"
#include "common/Membrane.h"
#include "common/MPI.h"
#include "analysis/Minkowski.h"
#include "ProfilerApp.h"

class ScaLBL_IonModel {
public:
    ScaLBL_IonModel(int RANK, int NP, const Utilities::MPI &COMM);
    ~ScaLBL_IonModel();

    // functions in they should be run
    void ReadParams(string filename, vector<int> &num_iter);
    void ReadParams(string filename);
    void ReadParams(std::shared_ptr<Database> db0);
    void SetDomain();
    void SetMembrane();
    void ReadInput();
    void Create();
    void Initialize();
    void Run(double *Velocity, double *ElectricField);
    void RunMembrane(double *Velocity, double *ElectricField, double *Psi);
    void getIonConcentration(DoubleArray &IonConcentration, const size_t ic);
    void getIonConcentration_debug(int timestep);
    void getIonFluxDiffusive(DoubleArray &IonFlux_x, DoubleArray &IonFlux_y,
                             DoubleArray &IonFlux_z, const size_t ic);
    void getIonFluxAdvective(DoubleArray &IonFlux_x, DoubleArray &IonFlux_y,
                             DoubleArray &IonFlux_z, const size_t ic);
    void getIonFluxElectrical(DoubleArray &IonFlux_x, DoubleArray &IonFlux_y,
                              DoubleArray &IonFlux_z, const size_t ic);
    void getIonFluxDiffusive_debug(int timestep);
    void getIonFluxAdvective_debug(int timestep);
    void getIonFluxElectrical_debug(int timestep);
    void DummyFluidVelocity();
    void DummyElectricField();
    void Checkpoint();
    double CalIonDenConvergence(vector<double> &ci_avg_previous);

    bool Restart;
    int timestep;
    vector<int> timestepMax;
    int BoundaryConditionSolid;
    double h; //domain resolution, unit [um/lu]
    double kb, electron_charge, T, Vt;
    double k2_inv;
    double tolerance;
    double fluidVelx_dummy, fluidVely_dummy, fluidVelz_dummy;
    double Ex_dummy, Ey_dummy, Ez_dummy;

    size_t number_ion_species;
    vector<int> BoundaryConditionInlet;
    vector<int> BoundaryConditionOutlet;
    vector<double> IonDiffusivity; //User input unit [m^2/sec]
    vector<int> IonValence;
    vector<double> IonConcentration; //unit [mol/m^3]
    vector<double> MembraneIonConcentration; //unit [mol/m^3]
    vector<double> ThresholdVoltage;
    vector<double> MassFractionIn;
    vector<double> MassFractionOut;
    vector<double> ThresholdMassFractionIn;
    vector<double> ThresholdMassFractionOut;
    vector<double> Cin; //inlet boundary value, can be either concentration [mol/m^3] or flux [mol/m^2/sec]
    vector<double> Cout; //outlet boundary value, can be either concentration [mol/m^3] or flux [mol/m^2/sec]
    vector<double> tau;
    vector<double> time_conv;

    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;
    // input databaseF
    std::shared_ptr<Database> db;
    std::shared_ptr<Database> domain_db;
    std::shared_ptr<Database> ion_db;

    IntArray Map;
    DoubleArray Distance;
    int *NeighborList;
    int *dvcMap;
    double *fq;
    double *Ci;
    double *ChargeDensity;
    double *IonSolid;
    double *FluidVelocityDummy;
    double *ElectricFieldDummy;
    double *FluxDiffusive;
    double *FluxAdvective;
    double *FluxElectrical;
    
    /* these support membrane capabilities      */
    bool USE_MEMBRANE;
    std::shared_ptr<Database> membrane_db;
    std::shared_ptr<Membrane> IonMembrane;
    DoubleArray MembraneDistance;
    int MembraneCount; // number of links the cross the membrane
    
private:
    Utilities::MPI comm;

    // filenames
    char LocalRankString[8];
    char LocalRankFilename[40];
    char LocalRestartFile[40];
    char OutputFilename[200];

    //int rank,nprocs;
    void LoadParams(std::shared_ptr<Database> db0);
    void AssignSolidBoundary(double *ion_solid);
    void AssignIonConcentration_FromFile(double *Ci,
                                         const vector<std::string> &File_ion,
                                         int ic);
    void AssignIonConcentrationMembrane( double *Ci, int ic);

    void IonConcentration_LB_to_Phys(DoubleArray &Den_reg);
    void IonFlux_LB_to_Phys(DoubleArray &Den_reg, const size_t ic);
};
#endif