Merge branch 'test_poisson' of github.com:JamesEMcClure/LBPM-WIA into test_poisson
This commit is contained in:
James McClure
commit
cf3bc417ce
117
example/PlaneMembrane/plane_membrane.db
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117
example/PlaneMembrane/plane_membrane.db
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MultiphysController {
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timestepMax = 20000
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visualization_interval = 1000 // Frequency to write visualization data
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analysis_interval = 20 // Frequency to perform analysis
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}
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Stokes {
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epsilonR = 78.5 //fluid dielectric constant [dimensionless]
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tau = 1.0
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F = 0, 0, 0
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rho_phys = 998.2
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nu_phys = 1.003e-6 //fluid kinematic viscosity; user-input unit: [m^2/sec]
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BC = 3 // Pressure constant BC
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din = 1.0 // Inlet pressure
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dout = 1.0 // Outlet pressure
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UseElectroosmoticVelocityBC = true
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SolidLabels = 0, -1
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ZetaPotentialSolidList = -0.005, -0.03 // unit [v]
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}
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Ions {
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temperature = 310.15 //unit [K]
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//number_ion_species = 5 //number of ions
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//tauList = 1.0, 1.0, 1.0, 1.0, 1.0 // H+, OH-, Na+, Cl-, Fe3+
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//IonDiffusivityList = 9.3e-9, 5.3e-9, 1.3e-9, 2.0e-9, 0.604e-9 //user-input unit: [m^2/sec]
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//IonValenceList = 1, -1, 1, -1, 3 //valence charge of ions; dimensionless; positive/negative integer
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//IonConcentrationList = 1.0e-4, 1.0e-4, 100, 100, 0 //user-input unit: [mol/m^3]
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number_ion_species = 2 //number of ions
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//IonConcentrationFile = "Pseudo3D_plane_membrane_concentration_Na_z192_xy64.raw", "double", "Pseudo3D_plane_membrane_concentration_Na_z192_xy64.raw", "double"
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tauList = 1.0,1.0 // Na+, anion
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IonDiffusivityList = 1e-9,1e-9 //user-input unit: [m^2/sec]
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IonValenceList = 1,-1 //valence charge of ions; dimensionless; positive/negative integer
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IonConcentrationList = 145e-3,145e-3 //user-input unit: [mol/m^3]
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MembraneIonConcentrationList = 15e-3, 15e-3
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BC_InletList = 0,0 //boundary condition for inlet; 0=periodic; 1=ion concentration; 2=ion flux
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BC_OutletList = 0,0 //boundary condition for outlet; 0=periodic; 1=ion concentration; 2=ion flux
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InletValueList = 15e-3, 15e-3 //if ion concentration unit=[mol/m^3]; if flux (inward) unit=[mol/m^2/sec]
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OutletValueList = 145e-3, 145e-3 //if ion concentration unit=[mol/m^3]; if flux (inward) unit=[mol/m^2/sec]
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BC_Solid = 0 //solid boundary condition; 0=non-flux BC; 1=surface ion concentration
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//SolidLabels = 0 olid 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, 0.0 // dummy fluid velocity for debugging
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}
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Poisson {
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epsilonR = 80.4 //fluid dielectric constant [dimensionless]
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tau = 4.5
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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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InitialValueLabels = 1,2//a list of labels of fluid nodes
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InitialValues = 60.6e-3, 0 //unit: [V]
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//------- Boundary Voltage for BC = 1 (Inlet & Outlet) ---------------------
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Vin = 60.6e-3 //ONLY for BC_Inlet = 1; electrical potential at inlet
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Vout = 0 //ONLY for BC_Outlet = 1; electrical potential at outlet
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//--------------------------------------------------------------------------
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//------- Boundary Voltage for BC = 2 (Inlet & Outlet) ---------------------
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//Vin0 = 0.01 //(ONLY for BC_Inlet = 2); unit:[Volt]
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//freqIn = 1.0 //(ONLY for BC_Inlet = 2); unit:[Hz]
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//t0_In = 0.0 //(ONLY for BC_Inlet = 1); unit:[sec]
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//Vin_Type = 1 //(ONLY for BC_Inlet = 1); 1->sin(); 2->cos()
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//Vout0 = 0.01 //(ONLY for BC_Outlet = 1); unit:[Volt]
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//freqOut = 1.0 //(ONLY for BC_Outlet = 1); unit:[Hz]
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//t0_Out = 0.0 //(ONLY for BC_Outlet = 1); unit:[sec]
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//Vout_Type = 1 //(ONLY for BC_Outlet = 1); 1->sin(); 2->cos()
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//--------------------------------------------------------------------------
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BC_SolidList = 1 //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 = -0.001 //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 = 10000 //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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Membrane {
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MembraneLabels = 1
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VoltageThreshold = 100.0, 100.0
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MassFractionIn = 1,0
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MassFractionOut = 1,0
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ThresholdMassFractionIn = 1, 0
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ThresholdMassFractionOut = 1, 0
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}
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Domain {
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Filename = "Pseudo3D_double_plane_membrane_z192_xy64_InsideLabel1_OutsideLabel2.raw"
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nproc = 1, 1, 3 // Number of processors (Npx,Npy,Npz)
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n = 64, 64, 64 // Size of local domain (Nx,Ny,Nz)
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N = 64, 64, 192 // size of the input image
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voxel_length = 0.01 //resolution; user-input unit: [um]
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BC = 0 // Boundary condition type0
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ReadType = "8bit"
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ReadValues = 2, 1
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WriteValues = 2, 1
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//InletLayers = 0, 0, 1
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//OutletLayers = 0, 0, 1
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//InletLayersPhase = 1
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//OutletLayersPhase = 1
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//checkerSize = 3 // size of the checker to use
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}
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Analysis {
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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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#save_pressure = true
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save_8bit_raw = true
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}
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90
example/PlaneMembrane/plane_membrane.py
Executable file
90
example/PlaneMembrane/plane_membrane.py
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import numpy as np
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import math
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import matplotlib.pyplot as plt
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#physical constant
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k_B_const = 1.380649e-23 #[J/K]
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N_A_const = 6.02214076e23 #[1/mol]
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e_const = 1.602176634e-19 #[C]
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epsilon0_const = 8.85418782e-12 #[C/V/m]
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#other material property parameters
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epsilonr_water = 80.4
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T=310.15 #[K]
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#input ion concentration
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C_Na_in = 15e-3 #[mol/m^3]
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C_Na_out = 145e-3 #[mol/m^3]
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C_K_in = 150e-3 #[mol/m^3]
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C_K_out = 4e-3 #[mol/m^3]
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C_Cl_in = 10e-3 #[mol/m^3]
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C_Cl_out = 110e-3 #[mol/m^3]
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#calculating Debye length
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#For the definition of Debye lenght in electrolyte solution, see:
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#DOI:10.1016/j.cnsns.2014.03.005
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#Eq(42) in Yoshida etal., Coupled LB method for simulator electrokinetic flows
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prefactor= math.sqrt(epsilonr_water*epsilon0_const*k_B_const*T/2.0/N_A_const/e_const**2)
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debye_length_in = prefactor*np.sqrt(np.array([1.0/C_Na_in,1.0/C_K_in,1.0/C_Cl_in]))
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debye_length_out = prefactor*np.sqrt(np.array([1.0/C_Na_out,1.0/C_K_out,1.0/C_Cl_out]))
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print("Debye length inside membrane in [m]")
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print(debye_length_in)
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print("Debye length outside membrane in [m]")
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print(debye_length_out)
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#setup domain
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cube_length_z = 192
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cube_length_xy = 64
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#set LBPM domain resoluiton
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h=0.01 #[um]
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print("Image resolution = %.6g [um] (= %.6g [m])"%(h,h*1e-6))
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domain=2*np.ones((cube_length_z,cube_length_xy,cube_length_xy),dtype=np.int8)
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zgrid,ygrid,xgrid=np.meshgrid(np.arange(cube_length_z),np.arange(cube_length_xy),np.arange(cube_length_xy),indexing='ij')
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domain_centre=cube_length_xy/2
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make_bubble = np.logical_and(zgrid>=cube_length_z/4,zgrid<=cube_length_z*0.75)
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domain[make_bubble]=1
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##save domain
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file_name= "Pseudo3D_double_plane_membrane_z192_xy64_InsideLabel1_OutsideLabel2.raw"
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domain.tofile(file_name)
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print("save file: "+file_name)
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#debug plot
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#plt.figure(1)
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#plt.pcolormesh(domain[:,int(domain_centre),:])
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#plt.colorbar()
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#plt.axis("equal")
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#plt.show()
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##generate initial ion concentration - 3D
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#domain_Na = C_Na_out*np.ones_like(domain,dtype=np.float64)
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#domain_Na[make_bubble] = C_Na_in
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#domain_K = C_K_out*np.ones_like(domain,dtype=np.float64)
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#domain_K[make_bubble] = C_K_in
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#domain_Cl = C_Cl_out*np.ones_like(domain,dtype=np.float64)
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#domain_Cl[make_bubble] = C_Cl_in
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#
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#domain_Na.tofile("Pseudo3D_plane_membrane_concentration_Na_z192_xy64.raw")
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#domain_K.tofile("Pseudo3D_plane_membrane_concentration_K_z192_xy64.raw")
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#domain_Cl.tofile("Pseudo3D_plane_membrane_concentration_Cl_z192_xy64.raw")
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##debug plot
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#plt.figure(2)
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#plt.subplot(1,3,1)
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#plt.title("Na concentration")
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#plt.pcolormesh(domain_Na[:,int(bubble_centre),:])
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#plt.colorbar()
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#plt.axis("equal")
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#plt.subplot(1,3,2)
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#plt.title("K concentration")
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#plt.pcolormesh(domain_K[:,int(bubble_centre),:])
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#plt.colorbar()
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#plt.axis("equal")
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#plt.subplot(1,3,3)
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#plt.title("Cl concentration")
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#plt.pcolormesh(domain_Cl[:,int(bubble_centre),:])
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#plt.colorbar()
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#plt.axis("equal")
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#plt.show()
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