From db88295a87a008ae19c669ef910c4f2a768c47a0 Mon Sep 17 00:00:00 2001
From: JanHab <Jan.Habscheid@web.de>
Date: Sat, 17 Aug 2024 15:58:27 +0200
Subject: [PATCH] Added comparison to classical Nernst-Planck/Poisson-Boltzmann
model
---
examples/PoissonBoltzmann.py | 198 +++++++++++++++++++++++++++++++++++
1 file changed, 198 insertions(+)
create mode 100644 examples/PoissonBoltzmann.py
diff --git a/examples/PoissonBoltzmann.py b/examples/PoissonBoltzmann.py
new file mode 100644
index 0000000..c3a428a
--- /dev/null
+++ b/examples/PoissonBoltzmann.py
@@ -0,0 +1,198 @@
+'''
+Jan Habscheid
+Jan.Habscheid@rwth-aachen.de
+'''
+
+# import the src file needed to solve the system of equations
+import sys
+import os
+
+# Add the src directory to the sys.path
+src_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), '..', 'src')
+sys.path.insert(0, src_path)
+
+from Eq04 import solve_System_4eq
+
+# Remove the src directory from sys.path after import
+del sys.path[0]
+
+# Further imports
+import matplotlib.pyplot as plt
+import numpy as np
+from scipy.interpolate import interp1d
+
+# Define the parameters and boundary conditions
+# Define Parameter
+phi_left = 10.0
+phi_right = 0.0
+p_right = 0.0
+y_A_R, y_C_R = 1/3, 1/3
+z_A, z_C = -1.0, 1.0
+number_cells = 1024*4
+K = 'incompressible'
+Lambda2 = 8.553e-6
+a2 = 7.5412e-4
+refinement_style = 'log'
+rtol = 1e-8
+
+
+# DGM calculations
+y_A_DGM_10, y_C_DGM_10, phi_DGM_10, p_DGM_10, x_DGM_10 = solve_System_4eq(phi_left, phi_right, p_right, z_A, z_C, y_A_R, y_C_R, K, Lambda2, a2, number_cells, PoissonBoltzmann=False, relax_param=0.05, refinement_style=refinement_style, return_type='Vector', max_iter=10_000, rtol=rtol)
+y_S_DGM_10 = 1 - y_A_DGM_10 - y_C_DGM_10
+
+# PB calculations
+y_A_PB_10, y_C_PB_10, phi_PB_10, p_PB_10, x_PB_10 = solve_System_4eq(phi_left, phi_right, p_right, z_A, z_C, y_A_R, y_C_R, K, Lambda2, a2, number_cells, PoissonBoltzmann=True, relax_param=0.05, refinement_style=refinement_style, return_type='Vector', max_iter=10_000, rtol=rtol)
+y_S_PB_10 = 1 - y_A_PB_10 - y_C_PB_10
+
+
+
+fig, ax1 = plt.subplots()
+markers = ['-', '-.', ':']
+# Plot electric potential
+color_phi = 'tab:blue'
+color_p = 'tab:red'
+ax1.set_xlabel('x [-]')
+ax1.set_ylabel('$\\varphi$ [-]')#, color=color)
+ax1.tick_params(axis='y')#, labelcolor=color)
+ax1.plot(x_DGM_10, phi_DGM_10, markers[0], color=color_phi)
+ax1.plot(x_PB_10, phi_PB_10, markers[1], color=color_phi)
+ax1.grid()
+ax1.set_ylim(0.0, np.max(phi_DGM_10))
+ax1.set_xlabel('$x$ [-]')
+ax1.set_ylabel('$\\varphi$ [-]')
+ax1.set_xlim(0,0.05)
+dummy = ax1.plot(2,1/3, markers[0], color='grey', label='DGM')
+dummy = ax1.plot(2,1/3, markers[1], color='grey', label='PB')
+ax1.legend()
+
+# Create a second y-axis
+ax2 = ax1.twinx()
+# Plot pressure
+color = 'tab:red'
+ax2.set_ylabel('$p$ [-]', color=color)
+ax2.plot(x_DGM_10, p_DGM_10, markers[0], color=color_p)
+ax2.plot(x_PB_10, p_PB_10, markers[1], color=color_p)
+ax2.grid()
+ax2.set_ylim(0.0, np.max(p_DGM_10))
+ax2.set_xlim(0,0.05)
+ax2.set_xlabel('$x$ [-]')
+ax2.set_ylabel('$p$ [-]')
+ax2.legend()
+ax2.tick_params(axis='y', labelcolor=color)
+
+ax1.grid()
+fig.tight_layout()
+fig.show()
+
+# Plot Concentrations
+plt.figure()
+markers = ['--', '-', ':']
+colors = ['tab:blue', 'tab:orange', 'tab:green']
+plt.plot(x_DGM_10, y_A_DGM_10, markers[0], color=colors[0])
+plt.plot(x_PB_10, y_A_PB_10, markers[0], color=colors[1])
+plt.plot(x_DGM_10, y_C_DGM_10, markers[1], color=colors[0])
+plt.plot(x_PB_10, y_C_PB_10, markers[1], color=colors[1])
+plt.plot(x_DGM_10, y_S_DGM_10, markers[2], color=colors[0])
+plt.plot(x_PB_10, y_S_PB_10, markers[2], color=colors[1])
+dummy, = plt.plot(10, 0.1, color='grey', linestyle=markers[0], label='$y_A$')
+dummy, = plt.plot(10, 0.1, color='grey', linestyle=markers[1], label='$y_C$')
+dummy, = plt.plot(10, 0.1, color='grey', linestyle=markers[2], label='$y_S$')
+dummy, = plt.plot(10, 0.1, color=colors[0], linestyle='-', label='DGM')
+dummy, = plt.plot(10, 0.1, color=colors[1], linestyle='-', label='PB')
+plt.legend()
+plt.xlim(0,0.05)
+plt.ylim(-0.02, 1.02)
+plt.grid()
+plt.xlabel('x [-]')
+plt.ylabel('$y_\\alpha$ [-]')
+plt.tight_layout()
+plt.show()
+
+
+
+# DGM convergence towards PB
+# Define Potential differences
+phi_left_vec = np.linspace(1,10,10)
+phi_left_vec = np.append(np.array([0.1, 0.2, 0.3, 0.5, 0.7]), phi_left_vec)
+# Storage for the results
+y_A_DGM, y_C_DGM, y_S_DGM, phi_DGM, p_DGM, x_DGM = [], [], [], [], [], []
+y_A_PB, y_C_PB, y_S_PB, phi_PB, p_PB, x_PB = [], [], [], [], [], []
+# Loop over the potential differences
+for phi_left_ in phi_left_vec:
+ # DGM model
+ y_A_DGM_, y_C_DGM_, phi_DGM_, p_DGM_, x_DGM_ = solve_System_4eq(phi_left_, phi_right, p_right, z_A, z_C, y_A_R, y_C_R, K, Lambda2, a2, number_cells, PoissonBoltzmann=False, x0=0, x1=1, refinement_style=refinement_style, return_type='Vector', max_iter=250_000, rtol=rtol, relax_param=0.05)
+ y_A_DGM.append(y_A_DGM_)
+ y_C_DGM.append(y_C_DGM_)
+ y_S_DGM.append(1 - y_A_DGM_ - y_C_DGM_)
+ phi_DGM.append(phi_DGM_)
+ p_DGM.append(p_DGM_)
+ x_DGM.append(x_DGM_)
+
+ # PB model
+ y_A_PB_, y_C_PB_, phi_PB_, p_PB_, x_PB_ = solve_System_4eq(phi_left_, phi_right, p_right, z_A, z_C, y_A_R, y_C_R, K, Lambda2, a2, number_cells, PoissonBoltzmann=True, x0=0, x1=1, refinement_style=refinement_style, return_type='Vector', max_iter=250_000, rtol=rtol, relax_param=0.05)
+ y_A_PB.append(y_A_PB_)
+ y_C_PB.append(y_C_PB_)
+ y_S_PB.append(1 - y_A_PB_ - y_C_PB_)
+ phi_PB.append(phi_PB_)
+ p_PB.append(p_PB_)
+ x_PB.append(x_PB_)
+
+# L2-error
+# Interpolate solution vector
+y_A_DGM_interp1d = [interp1d(x_DGM[i], y_A_DGM[i]) for i in range(len(phi_left_vec))]
+y_C_DGM_interp1d = [interp1d(x_DGM[i], y_C_DGM[i]) for i in range(len(phi_left_vec))]
+y_S_DGM_interp1d = [interp1d(x_DGM[i], y_S_DGM[i]) for i in range(len(phi_left_vec))]
+phi_DGM_interp1d = [interp1d(x_DGM[i], phi_DGM[i]) for i in range(len(phi_left_vec))]
+p_DGM_interp1d = [interp1d(x_DGM[i], p_DGM[i]) for i in range(len(phi_left_vec))]
+
+y_A_PB_interp1d = [interp1d(x_PB[i], y_A_PB[i]) for i in range(len(phi_left_vec))]
+y_C_PB_interp1d = [interp1d(x_PB[i], y_C_PB[i]) for i in range(len(phi_left_vec))]
+y_S_PB_interp1d = [interp1d(x_PB[i], y_S_PB[i]) for i in range(len(phi_left_vec))]
+phi_PB_interp1d = [interp1d(x_PB[i], phi_PB[i]) for i in range(len(phi_left_vec))]
+p_PB_interp1d = [interp1d(x_PB[i], p_PB[i]) for i in range(len(phi_left_vec))]
+
+# Calculate L2-error
+y_A_error_L2, y_C_error_L2, y_S_error_L2, phi_error_L2, p_error_L2 = [], [], [], [], []
+for i in range(len(phi_left_vec)):
+ y_A_error_L2.append(np.trapz((y_A_DGM_interp1d[i](x_DGM[i]) - y_A_PB_interp1d[i](x_DGM[i]))**2, x_DGM[i]))
+ y_C_error_L2.append(np.trapz((y_C_DGM_interp1d[i](x_DGM[i]) - y_C_PB_interp1d[i](x_DGM[i]))**2, x_DGM[i]))
+ y_S_error_L2.append(np.trapz((y_S_DGM_interp1d[i](x_DGM[i]) - y_S_PB_interp1d[i](x_DGM[i]))**2, x_DGM[i]))
+ phi_error_L2.append(np.trapz((phi_DGM_interp1d[i](x_DGM[i]) - phi_PB_interp1d[i](x_DGM[i]))**2, x_DGM[i]))
+ p_error_L2.append(np.trapz((p_DGM_interp1d[i](x_DGM[i]) - p_PB_interp1d[i](x_DGM[i]))**2, x_DGM[i]))
+
+
+# Log-log plot of L2-error
+plt.figure()
+plt.plot(phi_left_vec, y_A_error_L2, 'o-', label='$y_A$')
+plt.plot(phi_left_vec, y_C_error_L2, 'o-', label='$y_C$')
+plt.plot(phi_left_vec, y_S_error_L2, 'o-', label='$y_S$')
+plt.yscale('log')
+plt.legend()
+plt.xlabel('$\Delta \\varphi$')
+plt.ylabel('log($L_2$)')
+plt.grid()
+plt.tight_layout()
+plt.show()
+
+
+# Calculate infinity error
+y_A_error_inf, y_C_error_inf, y_S_error_inf, phi_error_inf, p_error_inf = [], [], [], [], []
+for i in range(len(phi_left_vec)):
+ y_A_error_inf.append(np.max(np.abs(y_A_DGM_interp1d[i](x_DGM[i]) - y_A_PB_interp1d[i](x_DGM[i]))))
+ y_C_error_inf.append(np.max(np.abs(y_C_DGM_interp1d[i](x_DGM[i]) - y_C_PB_interp1d[i](x_DGM[i]))))
+ y_S_error_inf.append(np.max(np.abs(y_S_DGM_interp1d[i](x_DGM[i]) - y_S_PB_interp1d[i](x_DGM[i]))))
+ phi_error_inf.append(np.max(np.abs(phi_DGM_interp1d[i](x_DGM[i]) - phi_PB_interp1d[i](x_DGM[i]))))
+ p_error_inf.append(np.max(np.abs(p_DGM_interp1d[i](x_DGM[i]) - p_PB_interp1d[i](x_DGM[i]))))
+
+# Log-log plot of infinity error
+plt.figure()
+plt.plot(phi_left_vec, y_A_error_inf, 'o-', label='$y_A$')
+plt.plot(phi_left_vec, y_C_error_inf, 'o-', label='$y_C$')
+plt.plot(phi_left_vec, y_S_error_inf, 'o-', label='$y_S$')
+plt.yscale('log')
+plt.legend()
+plt.xlabel('$\Delta \\varphi$')
+plt.ylabel('log($L_\infty$)')
+plt.grid()
+plt.tight_layout()
+plt.show()
--
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