MultiphysController {
    timestepMax = 20
    num_iter_Ion_List = 2
    analysis_interval  = 50
    tolerance = 1.0e-9
    visualization_interval = 100        // Frequency to write visualization data
    analysis_interval = 50    // Frequency to perform analysis
}
Stokes {
    tau = 1.0
    F = 0, 0, 0
    ElectricField = 0, 0, 0 //body electric field; user-input unit: [V/m]
    nu_phys = 0.889e-6      //fluid kinematic viscosity; user-input unit: [m^2/sec]
}
Ions {
    use_membrane = true
    Restart = false
    IonConcentrationFile = "cell_concentration_Na_40x40x40.raw", "double", "cell_concentration_Cl_40x40x40.raw", "double"
    temperature = 293.15 //unit [K]
    number_ion_species = 2  //number of ions
    tauList = 1.0, 1.0
    IonDiffusivityList = 1.0e-9, 1.0e-9 //user-input unit: [m^2/sec]
    IonValenceList = 1, -1 //valence charge of ions; dimensionless; positive/negative integer
    IonConcentrationList = 1.0e-6, 1.0e-6 //user-input unit: [mol/m^3]
    BC_Solid = 0 //solid boundary condition; 0=non-flux BC; 1=surface ion concentration
    //SolidLabels = 0 //solid labels for assigning solid boundary condition; ONLY for BC_Solid=1
    //SolidValues = 1.0e-5 // user-input surface ion concentration unit: [mol/m^2]; ONLY for BC_Solid=1
    FluidVelDummy = 0.0, 0.0, 0.0 // dummy fluid velocity for debugging
}
Poisson {
    lattice_scheme = "D3Q19"
    Restart = false
    epsilonR = 78.5 //fluid dielectric constant [dimensionless]
    BC_Inlet  = 0  // ->1: fixed electric potential; ->2: sine/cosine periodic electric potential
    BC_Outlet = 0  // ->1: fixed electric potential; ->2: sine/cosine periodic electric potential
    //--------------------------------------------------------------------------
    //--------------------------------------------------------------------------
    BC_Solid = 2 //solid boundary condition; 1=surface potential; 2=surface charge density
    SolidLabels = 0 //solid labels for assigning solid boundary condition
    SolidValues = 0 //if surface potential, unit=[V]; if surface charge density, unit=[C/m^2]
    WriteLog = true //write convergence log for LB-Poisson solver
    // ------------------------------- Testing Utilities ----------------------------------------
    // ONLY for code debugging; the followings test sine/cosine voltage BCs; disabled by default
    TestPeriodic = false
    TestPeriodicTime = 1.0 //unit:[sec]
    TestPeriodicTimeConv = 0.01 //unit:[sec]
    TestPeriodicSaveInterval = 0.2 //unit:[sec]
    //------------------------------ advanced setting ------------------------------------
    timestepMax = 100000 //max timestep for obtaining steady-state electrical potential
    analysis_interval  = 200 //timestep checking steady-state convergence
    tolerance = 1.0e-6  //stopping criterion for steady-state solution
    InitialValueLabels = 1, 2
    InitialValues = 0.0, 0.0

}
Domain {
    Filename = "cell_40x40x40.raw"
    nproc = 1, 1, 1     // Number of processors (Npx,Npy,Npz)
    n = 40, 40, 40      // Size of local domain (Nx,Ny,Nz)
    N = 40, 40, 40         // size of the input image
    voxel_length = 1.0   //resolution; user-input unit: [um]
    BC = 0              // Boundary condition type
    ReadType = "8bit"
    ReadValues  = 0, 1, 2
    WriteValues = 0, 1, 2
}
Analysis {
    analysis_interval = 100
    subphase_analysis_interval = 50    // Frequency to perform analysis
    restart_interval = 5000    // Frequency to write restart data
    restart_file = "Restart"    // Filename to use for restart file (will append rank)
    N_threads    = 4            // Number of threads to use
    load_balance = "independent" // Load balance method to use: "none", "default", "independent"
}
Visualization {
    save_electric_potential = true
    save_concentration = true
    save_velocity = true
}
Membrane {
    MembraneLabels = 2
    VoltageThreshold = 0.0, 0.0
    MassFractionIn = 0e-2, 5e-2
    MassFractionOut = 0e-2, 5e-2
    ThresholdMassFractionIn = 0e-2, 5e-2
    ThresholdMassFractionOut = 0e-2, 5e-2

}