diff --git a/README.md b/README.md
index 05c83c73c0974ada4bd55a343470532594afcf07..0067dace29cb3ac2028e1c91a5ced5e4d531a620 100644
--- a/README.md
+++ b/README.md
@@ -27,7 +27,7 @@ All the calculations were performed on a Linux machine. According to the documen
```
conda create --name fenicsx-env python=3.12.3 -y
conda activate fenicsx-env
-conda install -c conda-forge fenics-dolfinx=0.8.0 mpich=4.2.1 pyvista=0.43.10 matplotlib=3.8.4 numpy=1.26.4 scipy=1.14.0 -y
+conda install -c conda-forge fenics-dolfinx=0.8.0 mpich=4.2.1 pyvista=0.43.10 matplotlib=3.8.4 numpy=1.26.4 scipy=1.14.0 pytest==8.3.3 -y
```
### Alternative installation
@@ -45,6 +45,16 @@ docker compose build
docker compose run solver
```
+### Testing
+
+Use pytest with
+```
+python -m pytest
+```
+
+to verify that everything was installed correctly.
+
+
## Usage
Find the visualizations from the thesis and some extra calculations in the "examples" folder.
diff --git a/environment.yml b/environment.yml
index 4c54a3639c4b9d7a7ec0829c6ec66d6eb1ffced1..c5ec78808a6c5a0ade6b7d19e74f92688e4b3da8 100644
--- a/environment.yml
+++ b/environment.yml
@@ -1,320 +1,85 @@
-name: fenicsx
-channels:
- - conda-forge
- - defaults
-dependencies:
- - _libgcc_mutex=0.1=conda_forge
- - _openmp_mutex=4.5=2_gnu
- - aiohttp=3.9.5=py312h98912ed_0
- - aiosignal=1.3.1=pyhd8ed1ab_0
- - alsa-lib=1.2.12=h4ab18f5_0
- - aom=3.9.1=hac33072_0
- - asttokens=2.4.1=pyhd8ed1ab_0
- - attr=2.5.1=h166bdaf_1
- - attrs=23.2.0=pyh71513ae_0
- - binutils_impl_linux-64=2.40=ha1999f0_7
- - binutils_linux-64=2.40=hb3c18ed_9
- - blosc=1.21.5=hc2324a3_1
- - brotli=1.1.0=hd590300_1
- - brotli-bin=1.1.0=hd590300_1
- - brotli-python=1.1.0=py312h30efb56_1
- - bzip2=1.0.8=hd590300_5
- - c-ares=1.28.1=hd590300_0
- - c-blosc2=2.14.4=hb4ffafa_1
- - ca-certificates=2024.6.2=hbcca054_0
- - cairo=1.18.0=h3faef2a_0
- - certifi=2024.6.2=pyhd8ed1ab_0
- - cffi=1.16.0=py312hf06ca03_0
- - charset-normalizer=3.3.2=pyhd8ed1ab_0
- - comm=0.2.2=pyhd8ed1ab_0
- - contourpy=1.2.1=py312h8572e83_0
- - cycler=0.12.1=pyhd8ed1ab_0
- - dav1d=1.2.1=hd590300_0
- - dbus=1.13.6=h5008d03_3
- - debugpy=1.8.1=py312h30efb56_0
- - decorator=5.1.1=pyhd8ed1ab_0
- - double-conversion=3.3.0=h59595ed_0
- - eigen=3.4.0=h00ab1b0_0
- - exceptiongroup=1.2.0=pyhd8ed1ab_2
- - executing=2.0.1=pyhd8ed1ab_0
- - expat=2.6.2=h59595ed_0
- - fenics-basix=0.8.0=py312h2492b07_1
- - fenics-dolfinx=0.8.0=py312hb4760eb_103
- - fenics-ffcx=0.8.0=pyh4af843d_0
- - fenics-libbasix=0.8.0=h9187eef_1
- - fenics-libdolfinx=0.8.0=h714c792_103
- - fenics-ufcx=0.8.0=h22f594c_0
- - fenics-ufl=2024.1.0=pyhd8ed1ab_0
- - ffmpeg=6.1.1=gpl_he44c6f3_112
- - fftw=3.3.10=mpi_mpich_hbcf76dd_10
- - font-ttf-dejavu-sans-mono=2.37=hab24e00_0
- - font-ttf-inconsolata=3.000=h77eed37_0
- - font-ttf-source-code-pro=2.038=h77eed37_0
- - font-ttf-ubuntu=0.83=h77eed37_2
- - fontconfig=2.14.2=h14ed4e7_0
- - fonts-conda-ecosystem=1=0
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- - gcc_impl_linux-64=12.3.0=h58ffeeb_11
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- - glew=2.1.0=h9c3ff4c_2
- - glib=2.80.2=hf974151_0
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- - gst-plugins-base=1.24.4=h9ad1361_0
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- - harfbuzz=8.5.0=hfac3d4d_0
- - hdf4=4.2.15=h2a13503_7
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- - tzdata==2024.1
-prefix: /home/janha/anaconda3/envs/fenicsx
+aiohttp @ file:///home/conda/feedstock_root/build_artifacts/aiohttp_1713964820544/work
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+executing @ file:///home/conda/feedstock_root/build_artifacts/executing_1698579936712/work
+fenics-basix @ file:///home/conda/feedstock_root/build_artifacts/fenics-basix-meta_1716296365445/work/python
+fenics-dolfinx @ file:///home/conda/feedstock_root/build_artifacts/fenics-dolfinx-split_1715597584729/work/python
+fenics-ffcx @ file:///home/conda/feedstock_root/build_artifacts/fenics-ffcx-ufcx_1714058897751/work
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diff --git a/tests/test_ElectrolyticDiode.py b/tests/test_ElectrolyticDiode.py
new file mode 100644
index 0000000000000000000000000000000000000000..b6aedddf45dcf5bfd3ee0d01a285ee9c33421304
--- /dev/null
+++ b/tests/test_ElectrolyticDiode.py
@@ -0,0 +1,94 @@
+'''
+Tests the ElectrolyticDiode implementation in src.ElectrolyticDiode.py
+'''
+
+
+from src.ElectrolyticDiode import ElectrolyticDiode
+import numpy as np
+
+# Define parameter to use in the test
+phi_bias = 10
+g_phi = 350
+y_fixed = 0.01
+z_A = -1.0
+z_C = 1.0
+K = 'incompressible'
+Lambda2 = 8.553e-6
+a2 = 7.5412e-4
+number_cells = [20, 128]
+Lx = 0.02
+Ly = 0.1
+x0 = np.array([0, 0])
+x1 = np.array([Lx, Ly])
+refinement_style = 'uniform'
+solvation = 5
+PoissonBoltzmann = False
+rtol = 1e-3
+relax_param = 0.15 # 0.1
+max_iter = 15_000
+
+
+data_comparison = np.load('tests/TestData/ElectrolyticDiode.npz')
+
+def test_ForwardBias():
+ y_A_ForwardBias, y_C_ForwardBias, phi_ForwardBias, p_ForwardBias, x_ForwardBias = ElectrolyticDiode('ForwardBias', phi_bias, g_phi, z_A, z_C, y_fixed, y_fixed, K, Lambda2, a2, number_cells, solvation, PoissonBoltzmann, relax_param, Lx, Ly, rtol, max_iter, return_type='Vector')
+
+ # test grid generation with no refinement
+ assert np.allclose(data_comparison['x_ForwardBias'], x_ForwardBias,\
+ rtol=1e-15, atol=1e-15),\
+ 'ForwardBias grid not generated correctly'
+ # test solution vector
+ assert np.allclose(data_comparison['y_A_ForwardBias'], y_A_ForwardBias,\
+ rtol=1e-15, atol=1e-15),\
+ 'y_A_ForwardBias not calculated correctly'
+ assert np.allclose(data_comparison['y_C_ForwardBias'], y_C_ForwardBias,\
+ rtol=1e-15, atol=1e-15),\
+ 'y_C_ForwardBias not calculated correctly'
+ assert np.allclose(data_comparison['phi_ForwardBias'], phi_ForwardBias,\
+ rtol=1e-15, atol=1e-15),\
+ 'phi_ForwardBias not calculated correctly'
+ assert np.allclose(data_comparison['p_ForwardBias'], p_ForwardBias,\
+ rtol=1e-15, atol=1e-15),\
+ 'p_ForwardBias not calculated correctly'
+
+def test_NoBias():
+ y_A_NoBias, y_C_NoBias, phi_NoBias, p_NoBias, x_NoBias = ElectrolyticDiode('NoBias', phi_bias, g_phi, z_A, z_C, y_fixed, y_fixed, K, Lambda2, a2, number_cells, solvation, PoissonBoltzmann, relax_param, Lx, Ly, rtol, max_iter, return_type='Vector')
+
+ # test grid generation with no refinement
+ assert np.allclose(data_comparison['x_NoBias'], x_NoBias,\
+ rtol=1e-15, atol=1e-15),\
+ 'NoBias grid not generated correctly'
+ # test solution vector
+ assert np.allclose(data_comparison['y_A_NoBias'], y_A_NoBias,\
+ rtol=1e-15, atol=1e-15),\
+ 'y_A_NoBias not calculated correctly'
+ assert np.allclose(data_comparison['y_C_NoBias'], y_C_NoBias,\
+ rtol=1e-15, atol=1e-15),\
+ 'y_C_NoBias not calculated correctly'
+ assert np.allclose(data_comparison['phi_NoBias'], phi_NoBias,\
+ rtol=1e-15, atol=1e-15),\
+ 'phi_NoBias not calculated correctly'
+ assert np.allclose(data_comparison['p_NoBias'], p_NoBias,\
+ rtol=1e-15, atol=1e-15),\
+ 'p_NoBias not calculated correctly'
+
+def test_BackwardBias():
+ y_A_BackwardBias, y_C_BackwardBias, phi_BackwardBias, p_BackwardBias, x_BackwardBias = ElectrolyticDiode('BackwardBias', phi_bias, g_phi, z_A, z_C, y_fixed, y_fixed, K, Lambda2, a2, number_cells, solvation, PoissonBoltzmann, relax_param, Lx, Ly, rtol, max_iter, return_type='Vector')
+
+ # test grid generation with no refinement
+ assert np.allclose(data_comparison['x_BackwardBias'], x_BackwardBias,\
+ rtol=1e-15, atol=1e-15),\
+ 'BackwardBias grid not generated correctly'
+ # test solution vector
+ assert np.allclose(data_comparison['y_A_BackwardBias'], y_A_BackwardBias,\
+ rtol=1e-15, atol=1e-15),\
+ 'y_A_BackwardBias not calculated correctly'
+ assert np.allclose(data_comparison['y_C_BackwardBias'], y_C_BackwardBias,\
+ rtol=1e-15, atol=1e-15),\
+ 'y_C_BackwardBias not calculated correctly'
+ assert np.allclose(data_comparison['phi_BackwardBias'], phi_BackwardBias,\
+ rtol=1e-15, atol=1e-15),\
+ 'phi_BackwardBias not calculated correctly'
+ assert np.allclose(data_comparison['p_BackwardBias'], p_BackwardBias,\
+ rtol=1e-15, atol=1e-15),\
+ 'p_BackwardBias not calculated correctly'
\ No newline at end of file
diff --git a/tests/test_Eq02.py b/tests/test_Eq02.py
new file mode 100644
index 0000000000000000000000000000000000000000..6356f24d54da28be63be14f3f5af6ab7e70c69f2
--- /dev/null
+++ b/tests/test_Eq02.py
@@ -0,0 +1,94 @@
+'''
+Tests the Eq02 implementation in src.Eq02.py
+'''
+
+
+from src.Eq02 import solve_System_2eq
+import numpy as np
+
+# Define parameter to use in the test
+phi_left = 10.0
+phi_right = 0.0
+p_right = 0.0
+y_A_R = 0.01
+y_C_R = 0.01
+z_A = -1.0
+z_C = 1.0
+K = 'incompressible'
+Lambda2 = 8.553e-6
+a2 = 7.5412e-4
+solvation = 0
+number_cells = 128
+relax_param = .1
+rtol = 1e-4
+max_iter = 500
+
+data_comparison = np.load('tests/TestData/Eq02.npz')
+
+def test_standard():
+ y_A, y_C, phi, p, x = solve_System_2eq(phi_left, phi_right, p_right, z_A, z_C, y_A_R, y_C_R, K, Lambda2, a2, number_cells, solvation=solvation, relax_param=relax_param, x0=0, x1=1, refinement_style='uniform', return_type='Vector', max_iter=max_iter, rtol=rtol)
+
+ # test grid generation with no refinement
+ assert np.allclose(data_comparison['x'], x,\
+ rtol=1e-15, atol=1e-15),\
+ 'Uniform grid not generated correctly'
+ # test solution vector
+ assert np.allclose(data_comparison['y_A'], y_A,\
+ rtol=1e-15, atol=1e-15),\
+ 'y_A not calculated correctly'
+ assert np.allclose(data_comparison['y_C'], y_C,\
+ rtol=1e-15, atol=1e-15),\
+ 'y_C not calculated correctly'
+ assert np.allclose(data_comparison['phi'], phi,\
+ rtol=1e-15, atol=1e-15),\
+ 'phi not calculated correctly'
+ assert np.allclose(data_comparison['p'], p,\
+ rtol=1e-15, atol=1e-15),\
+ 'p not calculated correctly'
+
+
+def test_solvation():
+ solvation = 5
+ y_A_solvation, y_C_solvation, phi_solvation, p_solvation, x_solvation = solve_System_2eq(phi_left, phi_right, p_right, z_A, z_C, y_A_R, y_C_R, K, Lambda2, a2, number_cells, solvation=solvation, relax_param=relax_param, x0=0, x1=1, refinement_style='log', return_type='Vector', max_iter=max_iter, rtol=rtol)
+
+ # test grid generation with logarithmic refinement
+ assert np.allclose(data_comparison['x_solvation'], x_solvation,\
+ rtol=1e-15, atol=1e-15),\
+ 'log grid not generated correctly'
+ # test solution vector
+ assert np.allclose(data_comparison['y_A_solvation'], y_A_solvation,\
+ rtol=1e-15, atol=1e-15),\
+ 'y_A with solvation not calculated correctly'
+ assert np.allclose(data_comparison['y_C_solvation'], y_C_solvation,\
+ rtol=1e-15, atol=1e-15),\
+ 'y_C with solvation not calculated correctly'
+ assert np.allclose(data_comparison['phi_solvation'], phi_solvation,\
+ rtol=1e-15, atol=1e-15),\
+ 'phi with solvation not calculated correctly'
+ assert np.allclose(data_comparison['p_solvation'], p_solvation,\
+ rtol=1e-15, atol=1e-15),\
+ 'p with solvation not calculated correctly'
+
+def test_compressibility():
+ solvation = 0
+ K = 5_000
+ y_A_compressible, y_C_compressible, phi_compressible, p_compressible, x_compressible = solve_System_2eq(phi_left, phi_right, p_right, z_A, z_C, y_A_R, y_C_R, K, Lambda2, a2, number_cells, solvation=solvation, relax_param=relax_param, x0=0, x1=1, refinement_style='hard_log', return_type='Vector', max_iter=max_iter, rtol=rtol)
+
+ # test grid generation with hard-logarithmic refinement
+ assert np.allclose(data_comparison['x_compressible'], x_compressible,\
+ rtol=1e-15, atol=1e-15),\
+ 'hard-log grid not generated correctly'
+ # test solution vector
+ assert np.allclose(data_comparison['y_A_compressible'], y_A_compressible,\
+ rtol=1e-15, atol=1e-15),\
+ 'y_A with compressible not calculated correctly'
+ assert np.allclose(data_comparison['y_C_compressible'], y_C_compressible,\
+ rtol=1e-15, atol=1e-15),\
+ 'y_C with compressible not calculated correctly'
+ assert np.allclose(data_comparison['phi_compressible'], phi_compressible,\
+ rtol=1e-15, atol=1e-15),\
+ 'phi with compressible not calculated correctly'
+ assert np.allclose(data_comparison['p_compressible'], p_compressible,\
+ rtol=1e-15, atol=1e-15),\
+ 'p with compressible not calculated correctly'
+
\ No newline at end of file
diff --git a/tests/test_Eq04.py b/tests/test_Eq04.py
new file mode 100644
index 0000000000000000000000000000000000000000..0d2652e8c8313f206af14c0540b47ca5c469f1b4
--- /dev/null
+++ b/tests/test_Eq04.py
@@ -0,0 +1,93 @@
+'''
+Tests the Eq04 implementation in src.Eq04.py
+'''
+
+from src.Eq04 import solve_System_4eq
+import numpy as np
+
+# Define parameter to use in the test
+phi_left = 10.0
+phi_right = 0.0
+p_right = 0.0
+y_A_R = 0.01
+y_C_R = 0.01
+z_A = -1.0
+z_C = 1.0
+K = 'incompressible'
+Lambda2 = 8.553e-6
+a2 = 7.5412e-4
+solvation = 0
+number_cells = 128
+relax_param = .1
+rtol = 1e-4
+max_iter = 500
+
+data_comparison = np.load('tests/TestData/Eq04.npz')
+
+def test_standard():
+ y_A, y_C, phi, p, x = solve_System_4eq(phi_left, phi_right, p_right, z_A, z_C, y_A_R, y_C_R, K, Lambda2, a2, number_cells, solvation=solvation, relax_param=relax_param, x0=0, x1=1, refinement_style='uniform', return_type='Vector', max_iter=max_iter, rtol=rtol)
+
+ # test grid generation with no refinement
+ assert np.allclose(data_comparison['x'], x,\
+ rtol=1e-15, atol=1e-15),\
+ 'Uniform grid not generated correctly'
+ # test solution vector
+ assert np.allclose(data_comparison['y_A'], y_A,\
+ rtol=1e-15, atol=1e-15),\
+ 'y_A not calculated correctly'
+ assert np.allclose(data_comparison['y_C'], y_C,\
+ rtol=1e-15, atol=1e-15),\
+ 'y_C not calculated correctly'
+ assert np.allclose(data_comparison['phi'], phi,\
+ rtol=1e-15, atol=1e-15),\
+ 'phi not calculated correctly'
+ assert np.allclose(data_comparison['p'], p,\
+ rtol=1e-15, atol=1e-15),\
+ 'p not calculated correctly'
+
+
+def test_solvation():
+ solvation = 5
+ y_A_solvation, y_C_solvation, phi_solvation, p_solvation, x_solvation = solve_System_4eq(phi_left, phi_right, p_right, z_A, z_C, y_A_R, y_C_R, K, Lambda2, a2, number_cells, solvation=solvation, relax_param=relax_param, x0=0, x1=1, refinement_style='log', return_type='Vector', max_iter=max_iter, rtol=rtol)
+
+ # test grid generation with logarithmic refinement
+ assert np.allclose(data_comparison['x_solvation'], x_solvation,\
+ rtol=1e-15, atol=1e-15),\
+ 'log grid not generated correctly'
+ # test solution vector
+ assert np.allclose(data_comparison['y_A_solvation'], y_A_solvation,\
+ rtol=1e-15, atol=1e-15),\
+ 'y_A with solvation not calculated correctly'
+ assert np.allclose(data_comparison['y_C_solvation'], y_C_solvation,\
+ rtol=1e-15, atol=1e-15),\
+ 'y_C with solvation not calculated correctly'
+ assert np.allclose(data_comparison['phi_solvation'], phi_solvation,\
+ rtol=1e-15, atol=1e-15),\
+ 'phi with solvation not calculated correctly'
+ assert np.allclose(data_comparison['p_solvation'], p_solvation,\
+ rtol=1e-15, atol=1e-15),\
+ 'p with solvation not calculated correctly'
+
+def test_compressibility():
+ solvation = 0
+ K = 5_000
+ y_A_compressible, y_C_compressible, phi_compressible, p_compressible, x_compressible = solve_System_4eq(phi_left, phi_right, p_right, z_A, z_C, y_A_R, y_C_R, K, Lambda2, a2, number_cells, solvation=solvation, relax_param=relax_param, x0=0, x1=1, refinement_style='hard_log', return_type='Vector', max_iter=max_iter, rtol=rtol)
+
+ # test grid generation with hard-logarithmic refinement
+ assert np.allclose(data_comparison['x_compressible'], x_compressible,\
+ rtol=1e-15, atol=1e-15),\
+ 'hard-log grid not generated correctly'
+ # test solution vector
+ assert np.allclose(data_comparison['y_A_compressible'], y_A_compressible,\
+ rtol=1e-15, atol=1e-15),\
+ 'y_A with compressible not calculated correctly'
+ assert np.allclose(data_comparison['y_C_compressible'], y_C_compressible,\
+ rtol=1e-15, atol=1e-15),\
+ 'y_C with compressible not calculated correctly'
+ assert np.allclose(data_comparison['phi_compressible'], phi_compressible,\
+ rtol=1e-15, atol=1e-15),\
+ 'phi with compressible not calculated correctly'
+ assert np.allclose(data_comparison['p_compressible'], p_compressible,\
+ rtol=1e-15, atol=1e-15),\
+ 'p with compressible not calculated correctly'
+
\ No newline at end of file
diff --git a/tests/test_EqN.py b/tests/test_EqN.py
new file mode 100644
index 0000000000000000000000000000000000000000..bc68dfb8aa2a79026540993821494d150ae21dfe
--- /dev/null
+++ b/tests/test_EqN.py
@@ -0,0 +1,66 @@
+'''
+Tests the EqN implementation in src.EqN.py
+'''
+
+
+from src.EqN import solve_System_Neq
+import numpy as np
+
+# Define parameter to use in the test
+phi_left = 10.0
+phi_right = 0.0
+p_right = 0.0
+y_R = [3/6, 1/6, 1/6]
+z_alpha = [-1.0, 1.0, 2.0]
+K = 'incompressible'
+Lambda2 = 8.553e-6
+a2 = 7.5412e-4
+solvation = 0
+number_cells = 128
+relax_param = .1
+rtol = 1e-4
+max_iter = 500
+
+data_comparison = np.load('tests/TestData/EqN.npz')
+
+def test_1():
+ y_alpha, phi, p, x = solve_System_Neq(phi_left, phi_right, p_right, z_alpha, y_R, K, Lambda2, a2, number_cells, solvation=solvation, relax_param=relax_param, x0=0, x1=1, refinement_style='uniform', return_type='Vector', max_iter=max_iter, rtol=rtol)
+
+ # test grid generation with no refinement
+ assert np.allclose(data_comparison['x'], x,\
+ rtol=1e-15, atol=1e-15),\
+ 'Uniform grid not generated correctly'
+ # test solution vector
+ assert np.allclose(data_comparison['y_alpha'], y_alpha,\
+ rtol=1e-15, atol=1e-15),\
+ 'y_alpha not calculated correctly'
+ assert np.allclose(data_comparison['phi'], phi,\
+ rtol=1e-15, atol=1e-15),\
+ 'phi not calculated correctly'
+ assert np.allclose(data_comparison['p'], p,\
+ rtol=1e-15, atol=1e-15),\
+ 'p not calculated correctly'
+
+def test_2():
+ y_R = [1/23, 1/23, 1/23, 1/23, 10/23]
+ z_alpha = [-4.0, -3.0, -2.0, -1.0, 1.0]
+ relax_param = 0.01
+ max_iter = 10_000
+
+ y_alpha_2, phi_2, p_2, x_2 = solve_System_Neq(phi_left, phi_right, p_right, z_alpha, y_R, K, Lambda2, a2, number_cells, solvation=solvation, relax_param=relax_param, x0=0, x1=1, refinement_style='log', return_type='Vector', max_iter=max_iter, rtol=rtol)
+
+ # test grid generation with no refinement
+ assert np.allclose(data_comparison['x_2'], x_2,\
+ rtol=1e-15, atol=1e-15),\
+ 'Log grid not generated correctly'
+ # test solution vector
+ assert np.allclose(data_comparison['y_alpha_2'], y_alpha_2,\
+ rtol=1e-15, atol=1e-15),\
+ 'y_alpha_2 not calculated correctly'
+ assert np.allclose(data_comparison['phi_2'], phi_2,\
+ rtol=1e-15, atol=1e-15),\
+ 'phi_2 not calculated correctly'
+ assert np.allclose(data_comparison['p_2'], p_2,\
+ rtol=1e-15, atol=1e-15),\
+ 'p_2 not calculated correctly'
+
\ No newline at end of file
diff --git a/tests/test_Helper_DoubleLayerCapacity.py b/tests/test_Helper_DoubleLayerCapacity.py
new file mode 100644
index 0000000000000000000000000000000000000000..0f16e3ee275608c36cd1a18266d9538d15d8055c
--- /dev/null
+++ b/tests/test_Helper_DoubleLayerCapacity.py
@@ -0,0 +1,195 @@
+'''
+Tests the Helpfer functions implemented in src.Helper_DoubleLayerCapacity.py
+'''
+
+
+from src.Helper_DoubleLayerCapacity import Phi_pot_center, dx, C_dl, n, Q_num_, Q_num_dim, Q_DL_dimless_ana, Q_DL_dim_ana, C_DL_dimless_ana, C_DL_dim_ana
+from src.Eq04 import solve_System_4eq
+from src.Eq02 import solve_System_2eq
+import numpy as np
+
+# Define Parameter
+e0 = 1.602e-19 # [As]
+k = 1.381e-23 # [J/K]
+T = 293.75 # [K]
+epsilon0 = 8.85e-12 #[F/m]
+F = 9.65e+4 # [As/mol]
+NA = 6.022e+23 # [1/mol] - Avogadro constant
+nR_mol = 55
+nR_m = nR_mol * NA * 1/(1e-3)# [1/m^3]
+pR = 1.01325 * 1e+5 # [Pa]
+LR = 20e-9
+chi = 80 # [-]
+
+# Parameter and bcs for the electrolyte
+Lambda2 = (k*T*epsilon0*(1+chi))/(e0**2 * nR_m * (LR)**2)
+a2 = (pR)/(nR_m * k * T)
+K_incompresible = 'incompressible'
+K_compressible = 20_000
+kappa = 0
+Molarity = 0.01
+y_R = Molarity / nR_mol
+z_A, z_C = -1.0, 1.0
+phi_right = 0.0
+p_right = 0
+
+# Solver settings
+number_cells = 128
+relax_param = 0.03
+p_right = 0
+rtol = 1e-4 # ! Change back to 1e-8
+
+
+# phi^L domain
+Vol_start = 0.05 # ! Change back to 0
+Volt_end = 0.75
+n_Volts = 10#0
+
+phi_left_dim = np.linspace(Vol_start, Volt_end, n_Volts)
+phi_left = phi_left_dim * e0/(k*T)
+
+data_comparison = np.load('tests/TestData/DLKap.npz')
+
+
+
+# Incompressible tests
+def test_incompressible():
+ # Calculate the numerical solution
+ y_A_num, y_C_num, y_S_num, phi_num, p_num, x_num = [], [], [], [], [], []
+ for i, phi_bcs in enumerate(phi_left):
+ y_A_, y_C_, phi_, p_, x_ = solve_System_4eq(phi_bcs, phi_right, p_right, z_A, z_C, y_R, y_R, K_incompresible, Lambda2, a2, number_cells, solvation=kappa, refinement_style='hard_log', rtol=rtol, max_iter=2500, return_type='Vector', relax_param=relax_param)
+ y_S_ = 1 - y_A_ - y_C_
+ y_A_num.append(y_A_)
+ y_C_num.append(y_C_)
+ y_S_num.append(y_S_)
+ phi_num.append(phi_)
+ p_num.append(p_)
+ x_num.append(x_)
+
+ # Calculate the numerical charge and capacity with finite differences and numerical integration
+ Q_num = []
+ Q_num_dim_ = []
+ for j in range(len(phi_left)):
+ Q_num.append(Q_num_(y_A_num[j], y_C_num[j], n(p_num[j], K_incompresible), x_num[j]))
+ Q_num_dim_.append(Q_num_dim(y_A_num[j], y_C_num[j], n(p_num[j], K_incompresible), x_num[j], z_A, z_C, nR_m, e0, LR))
+ Q_num = np.array(Q_num)
+ Q_num_dim_ = np.array(Q_num_dim_)
+
+ dx_ = phi_left[1] - phi_left[0] # [1/V], Assumption: phi^L is uniformly distributed
+ C_dl_num = C_dl(Q_num, phi_left)
+
+ dx_dim = phi_left_dim[1] - phi_left_dim[0]
+ C_dl_num_dim_ = C_dl(Q_num_dim_, phi_left_dim)
+
+
+ # Calculate the analytical charge and capacity
+ Q_ana = Q_DL_dimless_ana(y_R, y_R, 1-2*y_R, z_A, z_C, phi_left, phi_right, p_right, K_incompresible, Lambda2, a2, kappa)
+ Q_ana_dim_ = Q_DL_dim_ana(y_R, y_R, 1-2*y_R, z_A, z_C, phi_left, phi_right, p_right, K_incompresible, Lambda2, a2, nR_m, e0, LR, kappa)
+ C_dl_ana = C_DL_dimless_ana(y_R, y_R, 1-2*y_R, z_A, z_C, Phi_pot_center(phi_left), phi_right, p_right, K_incompresible, Lambda2, a2, kappa)
+ C_dl_ana_dim = C_DL_dim_ana(y_R, y_R, 1-2*y_R, z_A, z_C, Phi_pot_center(phi_left), phi_right, p_right, K_incompresible, Lambda2, a2, nR_m, e0, LR, k, T, kappa)
+
+ # Test the numerical charge and capacity
+ assert np.allclose(data_comparison['Q_num'], Q_num,\
+ rtol=1e-15, atol=1e-15),\
+ 'Incompressible: Numerical charge not calculated correctly for dimensions'
+ assert np.allclose(data_comparison['Q_num_dim_'], Q_num_dim_,\
+ rtol=1e-15, atol=1e-15),\
+ 'Incompressible: Numerical charge not calculated correctly for dimensionless'
+ assert np.allclose(data_comparison['C_dl_num'], C_dl_num,\
+ rtol=1e-15, atol=1e-15),\
+ 'Incompressible: Numerical capacity not calculated correctly for dimensions'
+ assert np.allclose(data_comparison['C_dl_num_dim_'], C_dl_num_dim_,\
+ rtol=1e-15, atol=1e-15),\
+ 'Incompressible: Numerical capacity not calculated correctly for dimensionless'
+
+ # Test the analytical charge and capacity
+ assert np.allclose(data_comparison['Q_ana'], Q_ana,\
+ rtol=1e-15, atol=1e-15),\
+ 'Incompressible: Analytical charge not calculated correctly for dimensions'
+ assert np.allclose(data_comparison['Q_ana_dim_'], Q_ana_dim_,\
+ rtol=1e-15, atol=1e-15),\
+ 'Incompressible: Analytical charge not calculated correctly for dimensionless'
+ assert np.allclose(data_comparison['C_dl_ana'], C_dl_ana,\
+ rtol=1e-15, atol=1e-15),\
+ 'Incompressible: Analytical capacity not calculated correctly for dimensions'
+ assert np.allclose(data_comparison['C_dl_ana_dim'], C_dl_ana_dim,\
+ rtol=1e-15, atol=1e-15),\
+ 'Incompressible: Analytical capacity not calculated correctly for dimensionless'
+
+# Compressible tests
+def test_compressible():
+ # Calculate the numerical solution
+ y_A_num_compressible, y_C_num_compressible, y_S_num_compressible, phi_num_compressible, p_num_compressible, x_num_compressible = [], [], [], [], [], []
+ for i, phi_bcs in enumerate(phi_left):
+ y_A_, y_C_, phi_, p_, x_ = solve_System_4eq(phi_bcs, phi_right, p_right, z_A, z_C, y_R, y_R, K_compressible, Lambda2, a2, number_cells, solvation=kappa, refinement_style='hard_log', rtol=1e-4, max_iter=2500, return_type='Vector', relax_param=relax_param)
+ y_S_ = 1 - y_A_ - y_C_
+ y_A_num_compressible.append(y_A_)
+ y_C_num_compressible.append(y_C_)
+ y_S_num_compressible.append(y_S_)
+ phi_num_compressible.append(phi_)
+ p_num_compressible.append(p_)
+ x_num_compressible.append(x_)
+
+ # Calculate the numerical charge and capacity with finite differences and numerical integration
+ Q_num_compressible = []
+ Q_num_dim_compressible = []
+ for j in range(len(phi_left)):
+ Q_num_compressible.append(Q_num_(y_A_num_compressible[j], y_C_num_compressible[j], n(p_num_compressible[j], K_compressible), x_num_compressible[j]))
+ Q_num_dim_compressible.append(Q_num_dim(y_A_num_compressible[j], y_C_num_compressible[j], n(p_num_compressible[j], K_compressible), x_num_compressible[j], z_A, z_C, nR_m, e0, LR))
+ Q_num_compressible = np.array(Q_num_compressible)
+ Q_num_dim_compressible = np.array(Q_num_dim_compressible)
+
+ dx__compressible = phi_left[1] - phi_left[0] # [1/V], Assumption: phi^L is uniformly distributed
+ C_dl_num_compressible = C_dl(Q_num_compressible, phi_left)
+
+ dx_dim_compressible = phi_left_dim[1] - phi_left_dim[0]
+ C_dl_num_dim_compressible = C_dl(Q_num_dim_compressible, phi_left_dim)
+
+ # Calculate the analytical charge and capacity
+ Q_ana_compressible = Q_DL_dimless_ana(y_R, y_R, 1-2*y_R, z_A, z_C, phi_left, phi_right, p_right, K_compressible, Lambda2, a2, kappa)
+ Q_ana_dim__compressible = Q_DL_dim_ana(y_R, y_R, 1-2*y_R, z_A, z_C, phi_left, phi_right, p_right, K_compressible, Lambda2, a2, nR_m, e0, LR, kappa)
+ C_dl_ana_compressible = C_DL_dimless_ana(y_R, y_R, 1-2*y_R, z_A, z_C, Phi_pot_center(phi_left), phi_right, p_right, K_compressible, Lambda2, a2, kappa)
+ C_dl_ana_dim_compressible = C_DL_dim_ana(y_R, y_R, 1-2*y_R, z_A, z_C, Phi_pot_center(phi_left), phi_right, p_right, K_compressible, Lambda2, a2, nR_m, e0, LR, k, T, kappa)
+
+ # Test the numerical charge and capacity
+ assert np.allclose(data_comparison['Q_num_compressible'], Q_num_compressible,\
+ rtol=1e-15, atol=1e-15),\
+ 'Compressible: Numerical charge not calculated correctly for dimensions'
+ assert np.allclose(data_comparison['Q_num_dim_compressible'], Q_num_dim_compressible,\
+ rtol=1e-15, atol=1e-15),\
+ 'Compressible: Numerical charge not calculated correctly for dimensionless'
+ assert np.allclose(data_comparison['C_dl_num_compressible'], C_dl_num_compressible,\
+ rtol=1e-15, atol=1e-15),\
+ 'Compressible: Numerical capacity not calculated correctly for dimensions'
+ assert np.allclose(data_comparison['C_dl_num_dim_compressible'], C_dl_num_dim_compressible,\
+ rtol=1e-15, atol=1e-15),\
+ 'Compressible: Numerical capacity not calculated correctly for dimensionless'
+
+ # Test the analytical charge and capacity
+ assert np.allclose(data_comparison['Q_ana_compressible'], Q_ana_compressible,\
+ rtol=1e-15, atol=1e-15),\
+ 'Compressible: Analytical charge not calculated correctly for dimensions'
+ assert np.allclose(data_comparison['Q_ana_dim__compressible'], Q_ana_dim__compressible,\
+ rtol=1e-15, atol=1e-15),\
+ 'Compressible: Analytical charge not calculated correctly for dimensionless'
+ assert np.allclose(data_comparison['C_dl_ana_compressible'], C_dl_ana_compressible,\
+ rtol=1e-15, atol=1e-15),\
+ 'Compressible: Analytical capacity not calculated correctly for dimensions'
+ assert np.allclose(data_comparison['C_dl_ana_dim_compressible'], C_dl_ana_dim_compressible,\
+ rtol=1e-15, atol=1e-15),\
+ 'Compressible: Analytical capacity not calculated correctly for dimensionless'
+
+# Test the functions
+def test_Phi_pot_center():
+ assert np.allclose(Phi_pot_center(phi_left), data_comparison['Phi_pot_center'],\
+ rtol=1e-15, atol=1e-15),\
+ 'Phi_pot_center not calculated correctly'
+
+def test_dx():
+ assert np.allclose(dx(phi_left), data_comparison['dx'],\
+ rtol=1e-15, atol=1e-15),\
+ 'dx not calculated correctly'
+def test_n():
+ assert np.allclose(n(data_comparison['p_num_compressible'][0], K_compressible), data_comparison['n'], rtol=1e-15, atol=1e-15),\
+ 'n not calculated correctly'
+
\ No newline at end of file