From 9faf64be3b223c5d5d1aa89e2de1124f38ed4c89 Mon Sep 17 00:00:00 2001
From: Thomas Roy <roy27@llnl.gov>
Date: Thu, 18 Apr 2024 13:41:21 -0700
Subject: [PATCH] Add index of examples

---
 docs/source/examples.rst        | 37 +++++++++++++++++++++++++++++++++
 docs/source/index.rst           |  1 +
 examples/gupta.py               |  4 ++--
 examples/simple_flow_battery.py |  4 ++--
 4 files changed, 42 insertions(+), 4 deletions(-)
 create mode 100644 docs/source/examples.rst

diff --git a/docs/source/examples.rst b/docs/source/examples.rst
new file mode 100644
index 0000000..ee02192
--- /dev/null
+++ b/docs/source/examples.rst
@@ -0,0 +1,37 @@
+Examples
+========
+
+Here is a brief overview of the examples in `echemfem/examples <https://github.com/LLNL/echemfem/tree/main/examples>`_.
+
+* **Planar flow reactor** with electroneutral Nernst-Planck. A Butler-Volmer expression is used for the redox reaction, and there are no homogeneous bulk reactions. A custom mesh is used with refinements close to the electrodes.
+    
+    * `2D case for binary electrolyte <https://github.com/LLNL/echemfem/tree/main/examples/bortels_twoion.py>`_ (:math:`\ce{CuSO4}`)
+    * `Nondimensional version of binary case <https://github.com/LLNL/echemfem/tree/main/examples/bortels_twoion_nondim.py>`_ 
+    * `2D case for three-ion electrolyte <https://github.com/LLNL/echemfem/tree/main/examples/bortels_threeion.py>`_ (:math:`\ce{CuSO4}` and :math:`\ce{H2SO4}`)
+    * `Nondimensional version of three ion case <https://github.com/LLNL/echemfem/tree/main/examples/bortels_threeion_nondim.py>`_ 
+    * `3D version of the three-ion case using custom preconditioners for a Discontinuous Galerkin (DG) scheme, and nondimensional <https://github.com/LLNL/echemfem/tree/main/examples/bortels_threeion_extruded_3D_nondim.py>`_ 
+
+* Simple 1D reaction-diffusion system for :math:`\ce{CO2}` electrolysis in :math:`\ce{KHCO3}`
+    
+    * `Simplified bicarbonate bulk reactions <https://github.com/LLNL/echemfem/tree/main/examples/gupta.py>`_
+    * `Full bicarbonate bulk reactions <https://github.com/LLNL/echemfem/tree/main/examples/carbonate.py>`_
+    * `Different implementation of the full bicarbonate bulk reactions <https://github.com/LLNL/echemfem/tree/main/examples/carbonate_homog_params.py>`_ (using the :doc:`homog_params <user_guide/homog_params>` interface)
+
+* 2D flow-past the electrode with advection-diffusion
+
+    * `Two species toy model with shear flow <https://github.com/LLNL/echemfem/tree/main/examples/tworxn.py>`_
+    * `CO2 electrolysis in bicarbonate with linear charge-transfer kinetics and shear flow <https://github.com/LLNL/echemfem/tree/main/examples/bicarb.py>`_
+    * `Two species toy model with irregular electrode with Navier-Stokes for the flow <https://github.com/LLNL/echemfem/tree/main/examples/tworxn_irregular.py>`_
+
+* 1D model for the :math:`\ce{CO2}` electrolysis in a copper catalyst layer of a gas diffusion electrode (GDE). The model uses electroneutral Nernst-Planck in a porous medium.
+
+    * `Using substitution of the electroneutrality equation to eliminate a species <https://github.com/LLNL/echemfem/tree/main/examples/catalyst_layer_Cu.py>`_
+    * `Solving the electroneutrality equation explicitly <https://github.com/LLNL/echemfem/tree/main/examples/catalyst_layer_Cu_full.py>`_
+
+* `A simple Vanadium flow battery using advection-diffusion-reaction, Poisson for the ionic potential with a predefinied conductivity and Navier-Stokes-Brinkman for the flow <https://github.com/LLNL/echemfem/tree/main/examples/simple_flow_battery.py>`_
+
+* `A symmetric cylindrical pore model for CO2 electrolysis using electroneutral Nernst-Planck and simplified bicarbonate bulk reactions <https://github.com/LLNL/echemfem/tree/main/examples/cylindrical_pore.py>`_
+
+* `A tandem flow-past the electrode system with an Ag catalyst placed in front of a Cu catalyst with electroneutral Nernst-Planck and Tafel kinetics <https://github.com/LLNL/echemfem/tree/main/examples/bicarb_Ag_Cu_tandem_example.py>`_
+
+* `Simple example for the BMCSL model for finite size ion effects <https://github.com/LLNL/echemfem/tree/main/examples/BMCSL.py>`_
diff --git a/docs/source/index.rst b/docs/source/index.rst
index e3040c1..c396b5a 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -24,6 +24,7 @@ Contents
 .. toctree::
    :titlesonly:
 
+   examples
    api
 
 Copyright and License
diff --git a/examples/gupta.py b/examples/gupta.py
index ca4bcdb..13320b5 100644
--- a/examples/gupta.py
+++ b/examples/gupta.py
@@ -4,8 +4,8 @@
 
 class GuptaSolver(EchemSolver):
     """
-    A 1D example of diffusion-reaction for CO2 electrolysis with bicarbonate bulk
-    reactions.
+    A 1D example of diffusion-reaction for CO2 electrolysis with simplified
+    bicarbonate bulk reactions.
 
     Steady-state version of example from
     Gupta, N., Gattrell, M. and MacDougall, B., 2006. Calculation for the
diff --git a/examples/simple_flow_battery.py b/examples/simple_flow_battery.py
index 482bc79..cd1e79e 100644
--- a/examples/simple_flow_battery.py
+++ b/examples/simple_flow_battery.py
@@ -5,8 +5,8 @@
 
 """
 A simple Vanadium flow battery using advection-diffusion-reaction, Poisson for
-the ionic potential with a predefinied conductivity and Stokes-Brinkman for the
-flow.
+the ionic potential with a predefinied conductivity and Navier-Stokes-Brinkman
+for the flow.
 
 Model taken from
 Lin, T.Y., Baker, S.E., Duoss, E.B. and Beck, V.A., 2022. Topology optimization