add input files for simple bacteria

example/SingleCell/Bacterium.db

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+MultiphysController {
+    timestepMax = 1000
+    num_iter_Ion_List = 2
+    analysis_interval  = 100
+    tolerance = 1.0e-9
+    visualization_interval = 100        // Frequency to write visualization data
+}
+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 {
+    MembraneIonConcentrationList = 25.0e-3, 25.0e-3 //user-input unit: [mol/m^3]
+    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 = 100.0e-3, 100.0e-3 //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
+    BC_InletList = 0, 0
+    BC_OutletList = 0, 0
+    
+}
+Poisson {
+    lattice_scheme = "D3Q19"
+    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 = 4000 //max timestep for obtaining steady-state electrical potential
+    analysis_interval  = 25 //timestep checking steady-state convergence
+    tolerance = 1.0e-10  //stopping criterion for steady-state solution
+    InitialValueLabels = 1, 2
+    InitialValues = 0.0, 0.0
+    
+}
+Domain {
+    Filename = "Bacterium.swc"
+    nproc = 2, 1, 1     // Number of processors (Npx,Npy,Npz)
+    n = 50, 64, 64      // Size of local domain (Nx,Ny,Nz)
+    N = 100, 64, 64         // size of the input image
+    voxel_length = 0.01   //resolution; user-input unit: [um]
+    BC = 0              // Boundary condition type
+    ReadType = "swc"
+    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 = false
+}
+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
+}

example/SingleCell/Bacterium.swc

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+# id,type,x,y,z,r,pid
+1 1 0.20 0.32 0.32 0.15 -1
+2 1 0.25 0.32 0.32 0.16 1
+3 1 0.33 0.32 0.32 0.17 2
+4 1 0.50 0.32 0.32 0.18 3
+5 1 0.67 0.32 0.32 0.17 4
+6 1 0.75 0.32 0.32 0.16 5
+7 1 0.80 0.32 0.32 0.15 6