76 lines
3.9 KiB
Plaintext
76 lines
3.9 KiB
Plaintext
MultiphysController {
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timestepMax = 60
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num_iter_Ion_List = 2
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analysis_interval = 50
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tolerance = 1.0e-9
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visualization_interval = 100 // Frequency to write visualization data
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analysis_interval = 50 // Frequency to perform analysis
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}
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Stokes {
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tau = 1.0
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F = 0, 0, 0
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ElectricField = 0, 0, 0 //body electric field; user-input unit: [V/m]
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nu_phys = 0.889e-6 //fluid kinematic viscosity; user-input unit: [m^2/sec]
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}
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Ions {
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IonConcentrationFile = "cell_concentration_K_40x40x40.raw", "double", "cell_concentration_Na_40x40x40.raw", "double", "cell_concentration_Cl_40x40x40.raw", "double", "cell_concentration_HCO3_40x40x40.raw", "double", "cell_concentration_anion_40x40x40.raw", "double", "cell_concentration_cation_40x40x40.raw", "double"
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temperature = 293.15 //unit [K]
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number_ion_species = 6 //number of ions
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tauList = 1.0, 1.0, 1.0, 1.0, 1.0, 1.0
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IonDiffusivityList = 1.0e-9, 1.0e-9, 1.0e-9, 1.0e-9, 1.0e-9, 1.0e-9 //user-input unit: [m^2/sec]
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IonValenceList = 1, 1, -1, -1, 1, -1 //valence charge of ions; dimensionless; positive/negative integer
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IonConcentrationList = 1.0e-6, 1.0e-6, 1.0e-6, 1.0e-6, 1.0e-6, 1.0e-6 //user-input unit: [mol/m^3]
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BC_Solid = 0 //solid boundary condition; 0=non-flux BC; 1=surface ion concentration
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//SolidLabels = 0 //solid labels for assigning solid boundary condition; ONLY for BC_Solid=1
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//SolidValues = 1.0e-5 // user-input surface ion concentration unit: [mol/m^2]; ONLY for BC_Solid=1
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FluidVelDummy = 0.0, 0.0, 1.0e-2 // dummy fluid velocity for debugging
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}
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Poisson {
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epsilonR = 78.5 //fluid dielectric constant [dimensionless]
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BC_Inlet = 0 // ->1: fixed electric potential; ->2: sine/cosine periodic electric potential
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BC_Outlet = 0 // ->1: fixed electric potential; ->2: sine/cosine periodic electric potential
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//--------------------------------------------------------------------------
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//--------------------------------------------------------------------------
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BC_Solid = 2 //solid boundary condition; 1=surface potential; 2=surface charge density
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SolidLabels = 0 //solid labels for assigning solid boundary condition
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SolidValues = 0 //if surface potential, unit=[V]; if surface charge density, unit=[C/m^2]
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WriteLog = true //write convergence log for LB-Poisson solver
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// ------------------------------- Testing Utilities ----------------------------------------
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// ONLY for code debugging; the followings test sine/cosine voltage BCs; disabled by default
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TestPeriodic = false
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TestPeriodicTime = 1.0 //unit:[sec]
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TestPeriodicTimeConv = 0.01 //unit:[sec]
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TestPeriodicSaveInterval = 0.2 //unit:[sec]
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//------------------------------ advanced setting ------------------------------------
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timestepMax = 100000 //max timestep for obtaining steady-state electrical potential
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analysis_interval = 200 //timestep checking steady-state convergence
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tolerance = 1.0e-6 //stopping criterion for steady-state solution
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}
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Domain {
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Filename = "cell_40x40x40.raw"
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nproc = 1, 1, 1 // Number of processors (Npx,Npy,Npz)
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n = 40, 40, 40 // Size of local domain (Nx,Ny,Nz)
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N = 40, 40, 40 // size of the input image
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voxel_length = 1.0 //resolution; user-input unit: [um]
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BC = 0 // Boundary condition type
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ReadType = "8bit"
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ReadValues = 0, 1, 2
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WriteValues = 0, 1, 2
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}
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Analysis {
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analysis_interval = 100
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subphase_analysis_interval = 50 // Frequency to perform analysis
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restart_interval = 5000 // Frequency to write restart data
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restart_file = "Restart" // Filename to use for restart file (will append rank)
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N_threads = 4 // Number of threads to use
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load_balance = "independent" // Load balance method to use: "none", "default", "independent"
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}
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Visualization {
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save_electric_potential = true
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save_concentration = true
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save_velocity = true
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}
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Membrane {
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MembraneLabels = 2
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}
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