.gitignore

+# Taken and adapted from: https://git.rwth-aachen.de/lamBOO/fenicsR13
+# ignore VSCode's helper files
+*.vscode
+*.ipynb_checkpoints
+# ignore python cache
+*__pycache__*
+*.__pycache__
+*test/__pycache__
+*fxdgm/__pycache__
+*examples/__pycache__
+*examples/ReproduableCode/__pycache__
+*.pytest_cache*
+# ignore Sphinx documentation output
+*docs/build
+# Ignore coverage files
+.coverage
+htmlcov
+# Ignore pip folder
+*egg-info/*
+# Ignore venv files
+venv
+# Ignore .eggs
+*.eggs
+*eggs*
+*.egg-info
+# Ignore build files
+build
+# Ignore lyx temp files
+*.lyx~
+*.lyx#
+# Ignore .DS_Store
+.DS_Store
\ No newline at end of file

.gitlab-ci.yml

+image: docker:20.10.16  # Define the Docker image
+
+stages:  # Define stages in the pipeline
+  - prepare
+  - build
+  - test
+  - deploy
+
+prepare:
+  stage: prepare
+  tags:
+    - docker
+  services:
+    - docker:20.10.16-dind
+  before_script:
+    - echo "$CI_REGISTRY_PASSWORD" | docker login $CI_REGISTRY -u $CI_REGISTRY_USER --password-stdin
+  script:
+    - docker pull $CI_REGISTRY_IMAGE:latest || true
+    - docker build
+      --cache-from $CI_REGISTRY_IMAGE:latest
+      --tag $CI_REGISTRY_IMAGE:latest .
+    - docker push $CI_REGISTRY_IMAGE:latest
+
+# Job to build documentation
+build-docs:
+  stage: build
+  dependencies:
+    - prepare
+  image:
+    name: $CI_REGISTRY_IMAGE:latest
+    entrypoint: [""]
+  tags:
+    - docker
+  script:
+    - sphinx-build docs/source docs/build  # Build the documentation
+  artifacts:
+    paths:
+      - docs/build  # Save the build output for later stages
+    expire_in: 12 month  # Optional: Set how long to keep the artifacts (default: 30 days)
+
+# Job to test the implementation
+test:
+  stage: test
+  dependencies:
+  - prepare
+  image:
+    name: $CI_REGISTRY_IMAGE:latest
+    entrypoint: [""]
+  tags:
+    - docker
+  script:
+    -  pytest --cov=fxdgm --cov-report=term --cov-report=html tests/ # Run the tests and store coverage 
+  artifacts:
+    paths:
+      - htmlcov # Save the coverage report
+    expire_in: 12 month  # Optional: Set how long to keep the artifacts (default: 30 days)
+  coverage: '/^TOTAL.*\s+(\d+\%)$/'
+
+  
+# Job to deploy documentation to GitLab Pages
+pages:
+  stage: deploy
+  dependencies:
+  - build-docs
+  - test
+  image:
+    name: $CI_REGISTRY_IMAGE:latest
+    entrypoint: [""]
+  tags:
+    - docker
+  script:
+    - mv docs/build public  # Move the build output to the "public" directory
+    - mv htmlcov public  # Move the coverage report to the "public" directory
+  artifacts:
+    paths:
+      - public  # Files in the "public" folder will be deployed to GitLab Pages
+  only:
+    - main  # Only deploy if the changes are in the default branch

.vscode/settings.json

-{
-    "cSpell.enableFiletypes": [
-        "!markdown",
-        "!python"
-    ],
-    "python.analysis.typeCheckingMode": "off"
-}
\ No newline at end of file

Dockerfile

+# Start with a base image that includes conda
+FROM continuumio/miniconda3:latest
+
+# Set environment variables
+ENV CONDA_DEFAULT_ENV=base
+ENV PATH /opt/conda/envs/${CONDA_DEFAULT_ENV}/bin:$PATH
+ENV HOME /root
+
+# Create the environment and install packages
+# FEniCSx backend + documentation and testing dependencies
+# sqlite for coverage, it necessary
+RUN conda install -n ${CONDA_DEFAULT_ENV} -c conda-forge fenics-dolfinx=0.8.0 mpich=4.2.1 pyvista=0.43.10 gcc=12.4.0 sphinx=7.3.7 myst-parser=4.0.0 sphinx-copybutton=0.5.2 sphinx-rtd-theme=3.0.1 pytest=8.3.3 pytest-cov=6.0.0 sqlite=3.41.2 -y
+
+WORKDIR /root
+
+ADD . /fxdgm
+RUN pip install --editable /fxdgm/.
+
+CMD ["bash"]

README.md

-# Reproducibility Repository for: Numerical Treatment of a Thermodynamically Consistent Electrolyte Model (B.Sc. Thesis - Jan Habscheid)
+# fxdgm
 
-## Thesis
+[![Pipeline Status](https://git.rwth-aachen.de/janhab/fxdgm/badges/main/pipeline.svg)](https://git.rwth-aachen.de/janhab/fxdgm/pipelines)
+[![Documentation](https://img.shields.io/badge/docs-latest-blue)](https://janhab.pages.rwth-aachen.de/fxdgm/)
+[![coverage report](https://git.rwth-aachen.de/JanHab/fxdgm/badges/main/coverage.svg)](https://janhab.pages.rwth-aachen.de/fxdgm/htmlcov)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13645296.svg)](https://doi.org/10.5281/zenodo.13645296)
+[![GitLab Version](https://img.shields.io/badge/version-1.0-blue.svg)](https://git.rwth-aachen.de/janhab/fxdgm/-/tags)
+[![License](https://img.shields.io/badge/license-GPLv3-blue)](https://git.rwth-aachen.de/janhab/fxdgm/-/blob/main/LICENSE?ref_type=heads)
 
-This repository contains the code to reproduce the results presented in the bachelor thesis: Numerical Treatment of a Thermodynamically Consistent Electrolyte Model
-Find the thesis at:
-    - Insert link to thesis
+*A nonlinear, mixed finite element solver for the DGM electrolyte model*
 
-### Abstract
+<img src="media/logo.svg" alt="Logo" width="200" />
 
-- Insert Abstract from thesis
+## Physical Background
+
+The system, which is solved, refers to the original work, [Overcoming the shortcomings of the Nernst–Planck model](https://doi.org/10.1039/C3CP44390F), from Wolfgang Dreyer, Clemens Guhlke and Rüdiger Müller in 2013.\
+This paper introduces a new, generalized Nernst-Planck model, which is thermodynamically consistent, as the classical Nernst-Planck model fails to predict the correct ion-concentrations close to the boundaries.
+The open-source package [FEniCSx](https://fenicsproject.org/) was used for the numerical implementation.
+
+## Main Features
+
+- Solving steady [DGM](https://doi.org/10.1039/C3CP44390F) model in dimensionless units
+  - for a ternary electrolyte (cations, anions, neutral solvent)
+  - for an electrolyte of N arbitrary species
+- Local mesh refinement for one-dimensional domains towards the electrode
+- [Testcases](https://git.rwth-aachen.de/JanHab/fxdgm/-/tree/main/tests?ref_type=heads) for the one-dimensional case or the two-dimensional electrolytic diode
+- Solutions for the [Double-Layer Capacity](https://git.rwth-aachen.de/JanHab/fxdgm/-/tree/main/examples/ReproducableCode/DoubleLayerCapacity?ref_type=heads), both numerical and analytical
+- [Numerical Convergence](https://git.rwth-aachen.de/JanHab/fxdgm/-/blob/main/examples/ReproducableCode/Convergence.py?ref_type=heads) with relaxation parameter for newtons method
+- Two-dimensional testcases for the example of the [electrolytic diode](https://git.rwth-aachen.de/JanHab/fxdgm/-/tree/main/examples/ReproducableCode/ElectrolyticDiode?ref_type=heads)
 
 ## Installation
 
-As a numerical solver, mainly FEniCSx was used and installed via conda.
-All the calculations were performed on a Linux machine. According to the documentation, everything should work well on macOS, but this was not tested. FEniCSx offers some beta versions for Windows support, but it is recommended to use WSL2 instead.
+Install the fxdgm package with pip to get all the implemented functions.
 
+``` bash
+pip install git+https://git.rwth-aachen.de/JanHab/fxdgm
 ```
-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
+
+For the backend, FEniCSx was used and installed via conda.
+The necessery dependencies can be installed with
+
+``` bash
+conda install -c conda-forge fenics-dolfinx=0.8.0 mpich=4.2.1 pyvista=0.43.10 gcc=12.4.0 -y
 ```
 
-### Alternative installation
+It is also possible to install the FEniCSx backend in a different manner. See the [FEniCSx documentation](https://fenicsproject.org/download/) for this.
+Although this installation method should work, it was not tested for the purpose of this package.
+
+### macOS installation using Docker
 
-Use the "environment.yml" file to install all necessary environments
+The docker installation method works for linux too. It was not tested on windows.
 
+``` bash
+docker compose build
+docker compose run solver
 ```
-conda env create -f environment.yml
+
+### Testing
+
+For testing clone the repository, install pytest and run the tests with
+
+``` bash
+pip install pytest==8.3.3
+python -m pytest
 ```
 
 ## Usage
 
-Find the visualizations from the thesis and some extra calculations in the "examples" folder. 
-In the subfolder "ReproducableCode" is the code, to execute the calculations with some first visualizations.
-The subfolder "Data" stores the data for all the simulations in a *.npz file, which can be read with numpy `np.load(file.npz)`.
-"Visualizations" creates the necessary figures from the thesis and stores them in *.svg format in "Figures".
-
-In "src" there are the generic FEniCSx implementations, that were used to calculate the examples.
+Find the package source code in [fxdgm](https://git.rwth-aachen.de/JanHab/fxdgm/-/tree/main/fxdgm?ref_type=heads).
+This implements the nonlinear electrolyte model.
 
+Furthermore, some physical examples are provided in the [examples](https://git.rwth-aachen.de/JanHab/fxdgm/-/tree/main/examples?ref_type=heads).
+In the subfolder [ReproducableCode](https://git.rwth-aachen.de/JanHab/fxdgm/-/tree/main/examples/ReproducableCode?ref_type=heads) is the code, to execute the calculations with some first visualizations.
+The subfolder [Data](https://git.rwth-aachen.de/JanHab/fxdgm/-/tree/main/examples/Data?ref_type=heads) stores the data for all the simulations in a *.npz file, which can be read with numpy `np.load(file.npz)`.
+[Visualizations](https://git.rwth-aachen.de/JanHab/fxdgm/-/tree/main/examples/Visualizations?ref_type=heads) creates the necessary figures from the thesis and stores them either in *.svg or *.pdf format in "Figures".
 
 ## Contact
 
-**Author**
+### Author
+
 - Jan Habscheid
-- Jan.Habscheid@rwth-aachen.de
+- [Jan.Habscheid@rwth-aachen.de](mailto:Jan.Habscheid@rwth-aachen.de)
 
-**Supervisor**
-- Dr. Lambert Theissen
-- ACoM - Applied and Computational Mathematics
-- RWTH Aachen University
-- theisen@acom.rwth-aachen.de
+### Supervisor
 
-**Supervisor**
+- Dr. Lambert Theisen
+  - ACoM - Applied and Computational Mathematics
+  - RWTH Aachen University
+  - [theisen@acom.rwth-aachen.de](mailto:theisen@acom.rwth-aachen.de)
 - Prof. Dr. Manuel Torrilhon
-- ACoM - Applied and Computational Mathematics
-- RWTH Aachen University
-- mt@acom.rwth-aachen.de
\ No newline at end of file
+  - ACoM - Applied and Computational Mathematics
+  - RWTH Aachen University
+  - [mt@acom.rwth-aachen.de](mailto:mt@acom.rwth-aachen.de)

docker-compose.yml

+services:
+  solver:
+    build:
+      context: .
+      dockerfile: Dockerfile
+    volumes:
+      - .:/root/solver
+    stdin_open: true  # Equivalent to -i for interactive mode
+    tty: true         # Equivalent to -t for a terminal interface
+    command: ["/bin/bash"]

docs/Makefile

+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/make.bat

+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/source/conf.py

+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = 'fxdgm'
+copyright = '2024, Jan Habscheid'
+author = 'Jan Habscheid'
+release = 'September, 2024'
+
+# Add fxdgm folder to path
+import os
+import sys
+sys.path.insert(0, os.path.abspath(os.path.join("..", "../fxdgm")))
+sys.path.insert(0, os.path.abspath('../fxdgm'))
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+              'sphinx.ext.napoleon',
+              'sphinx.ext.autodoc', 
+              'myst_parser',
+              'sphinx_copybutton',
+              'sphinx.ext.coverage',
+              'sphinx.ext.autosectionlabel',
+              ]
+
+templates_path = ['_templates']
+exclude_patterns = []
+
+source_suffix = {
+    '.rst': 'restructuredtext',
+    '.txt': 'markdown',
+    '.md': 'markdown',
+}
+
+autosummary_generate = False
+# autoclass_content = 'both'
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'sphinx_rtd_theme'
\ No newline at end of file

docs/source/example.rst

+Example
+=======
+
+|  In this example, we are going to solve the thermodynamically consistent electrolyte model for a incompressible, ternary electrolyte, as it is done in `https://git.rwth-aachen.de/JanHab/fxdgm/-/blob/main/examples/ReproducableCode/TernaryElectrolyte.py?ref_type=heads <https://git.rwth-aachen.de/JanHab/fxdgm/-/blob/main/examples/ReproducableCode/TernaryElectrolyte.py?ref_type=heads>`_.
+
+Install the package and necessary libraries
+-------------------------------------------
+
+.. code-block:: python
+
+    pip install git+https://git.rwth-aachen.de/JanHab/fxdgm
+    conda install -c conda-forge fenics-dolfinx=0.8.0 mpich=4.2.1 pyvista=0.43.10 gcc=12.4.0 -y
+
+Import the necessary libraries
+-------------------------------------------
+
+.. code-block:: python
+
+    from fxdgm import solve_System_4eq
+
+    import matplotlib.pyplot as plt
+    import numpy as np
+
+Define parameters and boundary conditions
+-----------------------------------------
+
+.. code-block:: python
+
+    phi_left = 8.0
+    phi_right = 0.0
+    p_right = 0.0
+    y_A_R = 1/3
+    y_C_R = 1/3
+    z_A = -1.0
+    z_C = 1.0
+    K = 'incompressible'
+    Lambda2 = 8.553e-6
+    a2 = 7.5412e-4
+
+Define mesh and solver settings
+-------------------------------
+
+.. code-block:: python
+
+    number_cells = 1024
+    refinement_style = 'log'
+    rtol = 1e-8
+
+Solve the system
+----------------
+
+.. code-block:: python
+
+    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, relax_param=0.05, x0=0, x1=1,    refinement_style='hard_log', return_type='Vector', max_iter=1_000, rtol=rtol)
+
+Visualize the results
+---------------------
+
+.. code-block:: python
+
+    plt.figure()
+    plt.plot(x, phi)
+    plt.xlabel('x [-]')
+    plt.ylabel('$\\varphi$  [-]')
+    plt.xlim(0,0.05)
+    plt.grid()
+    plt.show()
+
+    plt.figure()
+    plt.plot(x, p)
+    plt.xlabel('x [-]')
+    plt.ylabel('$p$ [-]')
+    plt.xlim(0,0.05)
+    plt.grid()
+    plt.show()
+
+    plt.figure()
+    plt.plot(x, y_A, label='$y_A$')
+    plt.plot(x, y_C, label='$y_C$')
+    plt.plot(x, 1 - y_A - y_C, label='$y_S$')
+    plt.xlabel('x [-]')
+    plt.ylabel('$y_\\alpha$ [-]')
+    plt.xlim(0,0.05)
+    plt.grid()
+    plt.legend()
+    plt.show()
+
+The electric potential
+^^^^^^^^^^^^^^^^^^^^^^^
+
+.. image:: Figures/TernaryPotential.svg
+    :width: 600px
+
+The pressure 
+^^^^^^^^^^^^^
+
+.. image:: Figures/TernaryPressure.svg
+    :width: 600px
+
+The atomic fractions
+^^^^^^^^^^^^^^^^^^^^^
+.. image:: Figures/TernaryConcentrations.svg
+    :width: 600px
\ No newline at end of file

docs/source/index.rst

+fxdgm
+=====
+
+.. image:: https://git.rwth-aachen.de/janhab/fxdgm/badges/main/pipeline.svg
+   :target: https://git.rwth-aachen.de/JanHab/fxdgm/pipelines
+.. image:: https://img.shields.io/badge/docs-latest-blue
+   :target: https://janhab.pages.rwth-aachen.de/fxdgm/
+.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.13645296.svg
+   :target: https://doi.org/10.5281/zenodo.13645296
+.. image:: https://img.shields.io/badge/version-1.0-blue.svg
+   :target: https://git.rwth-aachen.de/janhab/fxdgm/-/tags
+
+*A nonlinear, mixed finite element solver for the DGM electrolyte model*
+
+.. image:: ../../media/logo.svg
+   :width: 300px
+
+Physical Background
+===================
+
+| The system, which is solved, refers to the original work, `Overcoming the shortcomings of the Nernst–Planck model <https://doi.org/10.1039/C3CP44390F>`_, from Wolfgang Dreyer, Clemens Guhlke and Rüdiger Müller in 2013.
+| This paper introduces a new, generalized Nernst-Planck model, which is thermodynamically consistent, as the classical Nernst-Planck model fails to predict the correct ion-concentrations close to the boundaries.
+| The open-source package `FEniCSx <https://fenicsproject.org/>`_ was used for the numerical implementation.
+
+Main Features
+=============
+
+- Solving stationary `DGM <https://doi.org/10.1039/C3CP44390F>`_ model in dimensionless units
+
+   - for a ternary electrolyte (cations, anions, neutral solvent)
+
+   - for an electrolyte of N arbitrary species
+
+- Local mesh refinement for one-dimensional domains towards the electrode
+
+- `Testcases <https://git.rwth-aachen.de/JanHab/fxdgm/-/tree/main/tests?ref_type=heads>`_ for the one-dimensional case or the two-dimensional electrolytic diode
+
+- Solutions for the `Double-Layer Capacity <https://git.rwth-aachen.de/JanHab/fxdgm/-/tree/main/examples/ReproducableCode/DoubleLayerCapacity?ref_type=heads>`_, both numerical and analytical
+
+- `Numerical Convergence <https://git.rwth-aachen.de/JanHab/fxdgm/-/blob/main/examples/ReproducableCode/Convergence.py?ref_type=heads>`_ with relaxation parameter for newtons method
+
+- Two-dimensional testcases for the example of the `electrolytic diode <https://git.rwth-aachen.de/JanHab/fxdgm/-/tree/main/examples/ReproducableCode/ElectrolyticDiode?ref_type=heads>`_
+
+
+Installation
+============
+| Install the fxdgm package with pip to get all the implemented functions.
+
+.. code-block:: 
+   
+   pip install git+https://git.rwth-aachen.de/JanHab/fxdgm
+
+| For the backend, FEniCSx was used and installed via conda.
+| The necessary dependencies can be installed with
+
+.. code-block:: 
+
+   conda install -c conda-forge fenics-dolfinx=0.8.0 mpich=4.2.1 pyvista=0.43.10 gcc=12.4.0 -y
+
+| It is also possible to install the FEniCSx backend in a different manner. See the `FEniCSx documentation <https://fenicsproject.org/download/>`_ for this.
+| Although this installation method should work, it was not tested for the purpose of this package.
+
+macOS installation using Docker
+-------------------------------
+
+| The docker installation method works for linux too. It was not tested on windows.
+
+.. code-block::
+
+   docker compose build
+   docker compose run solver
+
+Testing
+=======
+
+| For testing clone the repository, install pytest and run the tests with
+
+.. code-block::
+
+   pip install pytest==8.3.3
+   python -m pytest
+
+
+Usage
+=====
+
+| Find the package source code in `fxdgm <https://git.rwth-aachen.de/JanHab/fxdgm/-/tree/main/fxdgm?ref_type=heads>`_
+| This implements the nonlinear electrolyte model.
+
+| Furthermore, some physical examples are provided in the `examples <https://git.rwth-aachen.de/JanHab/fxdgm/-/tree/main/examples?ref_type=heads>`_ folder.
+| In the subfolder `ReproducableCode <https://git.rwth-aachen.de/JanHab/fxdgm/-/tree/main/examples/ReproducableCode?ref_type=heads>`_ is the code, to execute the calculations with some first visualizations.
+| The subfolder `Data <https://git.rwth-aachen.de/JanHab/fxdgm/-/tree/main/examples/Data?ref_type=heads>`_ stores the data for all the simulations in a \*.npz file, which can be read with numpy `np.load(file.npz)`.
+| `visualizations <https://git.rwth-aachen.de/JanHab/fxdgm/-/tree/main/examples/Visualizations?ref_type=heads>`_ creates the necessary figures from the thesis and stores them either in \*.svg or \*.pdf format in "Figures".
+
+Contact
+=======
+**Author**
+
+- Jan Habscheid
+- Jan.Habscheid@rwth-aachen.de
+
+**Supervisor**
+
+- Dr. Lambert Theisen
+
+   - ACoM - Applied and Computational Mathematics
+   - RWTH Aachen University
+   - theisen@acom.rwth-aachen.de
+
+- Prof. Dr. Manuel Torrilhon
+
+   - ACoM - Applied and Computational Mathematics
+   - RWTH Aachen University
+   - mt@acom.rwth-aachen.de
+
+.. toctree::
+   src/oneD
+   src/ElectrolyticDiode
+   src/Miscellaneous
+   example
+   :maxdepth: 2
+   :caption: fxdgm
+   :hidden:
+

docs/source/src/ElectrolyticDiode.rst

+Electrolytic Diode
+===================
+
+.. warning::
+    If the Newton solver diverges for any of the solutions, you may try to reduce the relaxation parameter.
+
+.. autofunction:: ElectrolyticDiode.ElectrolyticDiode

docs/source/src/Miscellaneous.rst

+Miscellaneous
+=============
+
+.. autofunction:: RefinedMesh1D.create_refined_mesh
+    
+.. automodule:: Helper_DoubleLayerCapacity
+    :members:
+    :undoc-members:
+    :show-inheritance:
\ No newline at end of file

docs/source/src/oneD.rst

+1D Electrolyte
+==============
+
+.. warning::
+    If the Newton solver diverges for any of the solutions, you may try to reduce the relaxation parameter.
+
+.. autofunction:: Eq04.solve_System_4eq
+
+.. autofunction:: EqN.solve_System_Neq
+
+.. autofunction:: Eq02.solve_System_2eq
\ No newline at end of file