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2_phase_sim.py
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import os
import subprocess
import mplbm_utils as mplbm
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.pyplot import cm
def create_capillary_tubes(inputs):
nx = 175
ny = 175
nz = 50
x = np.arange(0,nx)
y = np.arange(0,ny)
domain = np.ones((nx, ny), dtype=np.uint8) # A slice to add tubes to
# Create tubes
tube_radii = np.array([3, 4, 5, 6, 11, 16, 21])
spacing = 5
for i in range(0, len(tube_radii)):
r = tube_radii[i]
cx = spacing + np.max(tube_radii)
cy = spacing*(i+1) + np.sum(tube_radii[0:i]*2) + r
tube_mask = (x[np.newaxis, :] - cx)**2 + (y[:, np.newaxis] - cy)**2 < r**2
domain[tube_mask] = 0 # if in the tube, set to 0 for empty space
# Get smaller slice for a more efficient geometry
domain = domain[:, 0:(spacing*2 + np.max(tube_radii)*2)]
# Extend to 3D
num_slices = nz
tubes = np.repeat(domain[np.newaxis,:, :], num_slices, axis=0)
tubes = tubes.transpose([1,2,0]) # Transpose to get aligned for Palabos properly
# plt.figure()
# plt.imshow(tubes[:,:,0])
# plt.colorbar()
# plt.show()
#
# import vedo as vd
# vp = vd.Plotter(axes=3, bg='w', bg2='w', size=(1200, 900), offscreen=False)
# # domain = vd.Volume(domain).isosurface(0.5)
# tubes3d = vd.Volume(tubes).isosurface(threshold=0.5)
# vp += tubes3d.c('orange')
# vp.show()
tubes.tofile(f"{inputs['input output']['input folder']}/capillary_tubes.raw")
nx = tubes.shape[2]
ny = tubes.shape[1]
nz = tubes.shape[0]
inputs['geometry']['geometry size']['Nx'] = nz
inputs['geometry']['geometry size']['Ny'] = ny
inputs['geometry']['geometry size']['Nz'] = nx
inputs['domain']['domain size']['nx'] = nx
inputs['domain']['domain size']['ny'] = ny
inputs['domain']['domain size']['nz'] = nz
mplbm.replace_line_in_file('input.yml', ' Nx', f' Nx: {nx}')
mplbm.replace_line_in_file('input.yml', ' Ny', f' Ny: {ny}')
mplbm.replace_line_in_file('input.yml', ' Nz', f' Nz: {nz}')
mplbm.replace_line_in_file('input.yml', ' nx', f' nx: {nx}')
mplbm.replace_line_in_file('input.yml', ' ny', f' ny: {ny}')
mplbm.replace_line_in_file('input.yml', ' nz', f' nz: {nz}')
return inputs
def run_2_phase_sim(inputs):
# Steps
# 1) create geom for palabos
# 2) create palabos input file
# 3) run 2-phase sim
if inputs['simulation type'] == '1-phase':
raise KeyError('Simulation type set to 1-phase...please change to 2-phase.')
sim_directory = inputs['input output']['simulation directory']
# 1) Create Palabos geometry
print('Creating efficient geometry for Palabos...')
mplbm.create_geom_for_palabos(inputs)
# 2) Create simulation input file
print('Creating input file...')
mplbm.create_palabos_input_file(inputs)
# 3) Run 2-phase simulation
print('Running 2-phase simulation...')
num_procs = inputs['simulation']['num procs']
input_dir = inputs['input output']['input folder']
simulation_command = f"mpirun -np {num_procs} ../../src/2-phase_LBM/ShanChen {input_dir}2_phase_sim_input.xml"
file = open(f'{sim_directory}/{input_dir}run_shanchen_sim.sh', 'w')
file.write(f'{simulation_command}')
file.close()
simulation_command_subproc = f'bash {sim_directory}/{input_dir}run_shanchen_sim.sh'
subprocess.run(simulation_command_subproc.split(' '))
return
def process_and_plot_results(inputs, run_name, line_color):
# Process data
mplbm.create_pressure_data_file(inputs)
# Load and plot data
sim_dir = inputs['input output']['simulation directory'] + '/'
output_dir = inputs['input output']['output folder']
Sw = np.loadtxt(f'{sim_dir + output_dir}data_Sw.txt')
Pc = np.loadtxt(f'{sim_dir + output_dir}data_Pc.txt')
# krw = np.loadtxt(f'{sim_dir + output_dir}data_krw.txt')
# krnw = np.loadtxt(f'{sim_dir + output_dir}data_krnw.txt')
mplbm.plot_capillary_pressure_data(Sw, Pc, Pc_label=f'{run_name}', line_color=line_color, line_style='--')
return
def young_laplace_equation(radii, sigma, theta_w, height):
# Calculate Young-Laplace solution
Pc = 2*sigma*np.cos(theta_w)/radii
total_volume = np.sum(radii**2 * np.pi) * height
Sw = radii**2*np.pi / total_volume
# Add entry pressure and saturation of 1
entry_pressure = np.min(Pc)
Pc = np.append(Pc, entry_pressure)
Sw = np.append(Sw, 1)
return Pc, Sw
input_file = 'input.yml'
inputs = mplbm.parse_input_file(input_file) # Parse inputs
inputs['input output']['simulation directory'] = os.getcwd() # Store current working directory
output_folders = np.array(['1e-2', '1e-3', '1e-4', '1e-5'])
sigma = 0.15
theta_w = np.radians(180 - 156.4)
tube_height = 1
tube_radii = np.array([3, 4, 5, 6, 11, 16, 21])
Pc_yl, Sw_yl = young_laplace_equation(tube_radii, sigma, theta_w, tube_height)
plt.figure()
color = iter(cm.turbo(np.linspace(0, 1, len(output_folders)+1)))
for i in range(len(output_folders)):
inputs['input output']['output folder'] = output_folders[i] + '/'
inputs = create_capillary_tubes(inputs)
inputs['simulation']['convergence'] = float(output_folders[i])
run_2_phase_sim(inputs) # Run 2 phase sim
mplbm.create_geom_for_rel_perm(inputs) # In order to get saturation files
process_and_plot_results(inputs, run_name=output_folders[i], line_color=next(color)) # Plot results
mplbm.plot_capillary_pressure_data(Sw_yl, Pc_yl, Pc_label='Young-Laplace', line_color=next(color))
plt.legend()
plt.savefig('young_laplace_validation.png', dpi=400)
# Plot performance data
sim_times = np.array([360.532, 1316.74, 4736.49, 12388.5])/60 # in minutes
plt.figure()
mplbm.plot_capillary_pressure_data(output_folders.astype('float'), sim_times) # Repurposing for formatting
plt.xlabel('Tolerance')
plt.ylabel('Simulation Time [min]')
plt.title(f"Young-Laplace Validation Performance:\n {inputs['simulation']['num procs']} cores", fontsize=18)
plt.xscale('log')
plt.xlim([np.min(output_folders.astype('float')),np.max(output_folders.astype('float'))])
plt.savefig('young_laplace_validation_performance.png', dpi=400)
plt.show()