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update cell example

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This commit is contained in:
James McClure 2022-04-12 20:51:13 -04:00
parent 032a21a872
commit 8fd8799ff9
2 changed files with 34 additions and 31 deletions
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42
example/SingleCell/NaCl-cell.py
View File

@ -1,37 +1,41 @@
import numpy as np
import matplotlib.pylab as plt
D=np.ones((40,40,40),dtype="uint8")
Nx = 64
Ny = 64
Nz = 64
cx = Nx/2
cy = Ny/2
cz = Nz/2
radius = 12
cx = 20
cy = 20
cz = 20
D=np.ones((Nx,Ny,Nz),dtype="uint8")
for i in range(0, 40):
for j in range (0, 40):
for k in range (0,40):
for i in range(0, Nx):
for j in range (0, Ny):
for k in range (0,Nz):
dist = np.sqrt((i-cx)*(i-cx) + (j-cx)*(j-cx) + (k-cz)*(k-cz))
if (dist < 15.5 ) :
if (dist < radius ) :
D[i,j,k] = 2
D.tofile("cell_40x40x40.raw")
D.tofile("cell_64x64x64.raw")
C1=np.zeros((40,40,40),dtype="double")
C2=np.zeros((40,40,40),dtype="double")
C1=np.zeros((Nx,Ny,Nz),dtype="double")
C2=np.zeros((Nx,Ny,Nz),dtype="double")
for i in range(0, 40):
for j in range (0, 40):
for k in range (0,40):
for i in range(0, Nx):
for j in range (0, Ny):
for k in range (0,Nz):
#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 < 15.5 ) :
C1[i,j,k] = 5.0e-6
C2[i,j,k] = 5.0e-6
if (dist < radius ) :
C1[i,j,k] = 110.0e-6
C2[i,j,k] = 110.0e-6
C1.tofile("cell_concentration_Na_40x40x40.raw")
C2.tofile("cell_concentration_Cl_40x40x40.raw")
C1.tofile("cell_concentration_Na_64x64x64.raw")
C2.tofile("cell_concentration_Cl_64x64x64.raw")

23
example/SingleCell/NaCl.db
View File

@ -1,10 +1,9 @@
MultiphysController {
timestepMax = 200
timestepMax = 2000
num_iter_Ion_List = 2
analysis_interval = 50
analysis_interval = 40
tolerance = 1.0e-9
visualization_interval = 100 // Frequency to write visualization data
analysis_interval = 50 // Frequency to perform analysis
visualization_interval = 40 // Frequency to write visualization data
}
Stokes {
tau = 1.0
@ -13,7 +12,7 @@ Stokes {
nu_phys = 0.889e-6 //fluid kinematic viscosity; user-input unit: [m^2/sec]
}
Ions {
IonConcentrationFile = "cell_concentration_Na_40x40x40.raw", "double", "cell_concentration_Cl_40x40x40.raw", "double"
IonConcentrationFile = "cell_concentration_Na_64x64x64.raw", "double", "cell_concentration_Cl_64x64x64.raw", "double"
temperature = 293.15 //unit [K]
number_ion_species = 2 //number of ions
tauList = 1.0, 1.0
@ -42,16 +41,16 @@ Poisson {
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
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
}
Domain {
Filename = "cell_40x40x40.raw"
Filename = "cell_64x64x64.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]
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]
BC = 0 // Boundary condition type
ReadType = "8bit"
ReadValues = 0, 1, 2