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refining cell example

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This commit is contained in:
James McClure 2022-03-20 18:01:19 -04:00
parent 4927e54707
commit 286e779459
2 changed files with 53 additions and 16 deletions
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51
example/Bubble/CreateCell.py
View File

@ -19,18 +19,59 @@ D.tofile("cell_40x40x40.raw")
C1=np.zeros((40,40,40),dtype="double")
C2=np.zeros((40,40,40),dtype="double")
C3=np.zeros((40,40,40),dtype="double")
C4=np.zeros((40,40,40),dtype="double")
C5=np.zeros((40,40,40),dtype="double")
C6=np.zeros((40,40,40),dtype="double")
for i in range(0, 40):
for j in range (0, 40):
for k in range (0,40):
C1[i,j,k] = 4.0e-6
C2[i,j,k] = 150.0e-6
#outside the cell
C1[i,j,k] = 4.0e-6 # K
C2[i,j,k] = 150.0e-6 # Na
C3[i,j,k] = 116.0e-6 # Cl
C4[i,j,k] = 29.0e-6 # HC03
#C5[i,j,k] = 2.4e-6 # Ca
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] = 140.0e-6
C2[i,j,k] = 10.0e-6
C1[i,j,k] = 145.0e-6
C2[i,j,k] = 12.0e-6
C3[i,j,k] = 4.0e-6
C4[i,j,k] = 12.0e-6 # 12 mmol / L
#C5[i,j,k] = 0.10e-6 # 100 nmol / L
# add up the total charge to make sure it is zero
TotalCharge = 0
for i in range(0, 40):
for j in range (0, 40):
for k in range (0,40):
TotalCharge += C1[i,j,k] + C2[i,j,k] - C3[i,j,k] - C4[i,j,k]
TotalCharge /= (40*40*40)
print("Total charge " + str(TotalCharge))
for i in range(0, 40):
for j in range (0, 40):
for k in range (0,40):
if TotalCharge < 0 :
# need more cation
C5[i,j,k] = abs(TotalCharge)
C6[i,j,k] = 0.0
else :
# need more anion
C5[i,j,k] = 0.0
C6[i,j,k] = abs(TotalCharge)
C1.tofile("cell_concentration_K_40x40x40.raw")
C2.tofile("cell_concentration_Na_40x40x40.raw")
C3.tofile("cell_concentration_Cl_40x40x40.raw")
C4.tofile("cell_concentration_HCO3_40x40x40.raw")
C5.tofile("cell_concentration_cation_40x40x40.raw")
C6.tofile("cell_concentration_anion_40x40x40.raw")

18
example/Bubble/cell.db
View File

@ -1,5 +1,5 @@
MultiphysController {
timestepMax = 20
timestepMax = 40
num_iter_Ion_List = 2
analysis_interval = 50
tolerance = 1.0e-9
@ -13,17 +13,13 @@ Stokes {
nu_phys = 0.889e-6 //fluid kinematic viscosity; user-input unit: [m^2/sec]
}
Ions {
IonConcentrationFile = "cell_concentration_K_40x40x40.raw", "double", "cell_concentration_Na_40x40x40.raw", "double"
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"
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 = 1.0e-6, 1.0e-6 //user-input unit: [mol/m^3]
BC_InletList = 0, 0 //boundary condition for inlet; 0=periodic; 1=ion concentration; 2=ion flux
BC_OutletList = 0, 0 //boundary condition for outlet; 0=periodic; 1=ion concentration; 2=ion flux
InletValueList = 0, 0 //if ion concentration unit=[mol/m^3]; if flux (inward) unit=[mol/m^2/sec]
OutletValueList = 0, 0 //if ion concentration unit=[mol/m^3]; if flux (inward) unit=[mol/m^2/sec]
number_ion_species = 6 //number of ions
tauList = 1.0, 1.0, 1.0, 1.0, 1.0, 1.0
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]
IonValenceList = 1, 1, -1, -1, 1, -1 //valence charge of ions; dimensionless; positive/negative integer
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]
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