update docs for cell model

example/SingleCell/NaCl-cell.py

@@ -1,41 +1,38 @@
 import numpy as np
 import matplotlib.pylab as plt
 
-Nx = 64
-Ny = 64
-Nz = 64
-cx = Nx/2
-cy = Ny/2
-cz = Nz/2
-radius = 12
+D=np.ones((40,40,40),dtype="uint8")
 
-D=np.ones((Nx,Ny,Nz),dtype="uint8")
+cx = 20
+cy = 20
+cz = 20
+radius = 8
 
-for i in range(0, Nx):
-    for j in range (0, Ny):
-        for k in range (0,Nz):
+for i in range(0, 40):
+    for j in range (0, 40):
+        for k in range (0,40):
             dist = np.sqrt((i-cx)*(i-cx) + (j-cx)*(j-cx) + (k-cz)*(k-cz))
             if (dist < radius ) :
                 D[i,j,k] = 2
 
-D.tofile("cell_64x64x64.raw")
+D.tofile("cell_40x40x40.raw")
 
                 
-C1=np.zeros((Nx,Ny,Nz),dtype="double")
-C2=np.zeros((Nx,Ny,Nz),dtype="double")
+C1=np.zeros((40,40,40),dtype="double")
+C2=np.zeros((40,40,40),dtype="double")
 
-for i in range(0, Nx):
-    for j in range (0, Ny):
-        for k in range (0,Nz):
+for i in range(0, 40):
+    for j in range (0, 40):
+        for k in range (0,40):
             #outside the cell
             C1[i,j,k] = 125.0e-6  # Na
             C2[i,j,k] = 125.0e-6  # Cl
             dist = np.sqrt((i-cx)*(i-cx) + (j-cx)*(j-cx) + (k-cz)*(k-cz))
             # inside the cell
             if (dist < radius ) :
-                C1[i,j,k] = 110.0e-6
-                C2[i,j,k] = 110.0e-6
+                C1[i,j,k] = 5.0e-6
+                C2[i,j,k] = 5.0e-6
 
-C1.tofile("cell_concentration_Na_64x64x64.raw")
-C2.tofile("cell_concentration_Cl_64x64x64.raw")
+C1.tofile("cell_concentration_Na_40x40x40.raw")
+C2.tofile("cell_concentration_Cl_40x40x40.raw")
 

example/SingleCell/NaCl.db

@@ -1,9 +1,10 @@
 MultiphysController {
-    timestepMax = 2000
+    timestepMax = 20
     num_iter_Ion_List = 2
-    analysis_interval  = 40
+    analysis_interval  = 50
     tolerance = 1.0e-9
-    visualization_interval = 40        // Frequency to write visualization data
+    visualization_interval = 100        // Frequency to write visualization data
+    analysis_interval = 50    // Frequency to perform analysis
 }
 Stokes {
     tau = 1.0
@@ -12,7 +13,9 @@ Stokes {
     nu_phys = 0.889e-6      //fluid kinematic viscosity; user-input unit: [m^2/sec]
 }
 Ions {
-    IonConcentrationFile = "cell_concentration_Na_64x64x64.raw", "double", "cell_concentration_Cl_64x64x64.raw", "double"
+    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
@@ -25,6 +28,8 @@ Ions {
     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
@@ -41,16 +46,19 @@ Poisson {
     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
+    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_64x64x64.raw"
+    Filename = "cell_40x40x40.raw"
     nproc = 1, 1, 1     // Number of processors (Npx,Npy,Npz)
-    n = 64, 64, 64      // Size of local domain (Nx,Ny,Nz)
-    N = 64, 64, 64         // size of the input image
-    voxel_length = 0.1   //resolution; user-input unit: [um]
+    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
@@ -72,9 +80,9 @@ Visualization {
 Membrane {
     MembraneLabels = 2
     VoltageThreshold = 0.0, 0.0
-    MassFractionIn = 1e-2, 1e-8
-    MassFractionOut = 1e-2, 1e-8
-    ThresholdMassFractionIn = 1e-2, 1e-8
-    ThresholdMassFractionOut = 1e-2, 1e-8
+    MassFractionIn = 0e-2, 5e-2
+    MassFractionOut = 0e-2, 5e-2
+    ThresholdMassFractionIn = 0e-2, 5e-2
+    ThresholdMassFractionOut = 0e-2, 5e-2
 
 }