Issue 2111 custom transport efficiency (pybamm-team#3437)

* log transport efficiency * logsqrt_transport * adding linear transport efficiency * half_transport_effciency added * add tortuosity factor submodel * add multiple tortuosity models * add tortuosity factor to model examples * Update submodel options and add citations. Also change the solid phase volume fraction to be (1-porosity) rather than the active material volume fraction * Update notebook and index for docs, get rid of unnecessary Bruggeman file * Update docs * Forgot the new file * Update title underline and add well_posed tests * style: pre-commit fixes * Add some missing tests * Update the transport efficieny print_name and add a bit more to notebook * Split the models into separate classes * style: pre-commit fixes * Update docs and add citations * style: pre-commit fixes * Change docs to footcite * style: pre-commit fixes * Update pybamm/models/submodels/transport_efficiency/tortuosity_factor.py Co-authored-by: Ferran Brosa Planella <[email protected]> * style: pre-commit fixes * Remove image from notebook * remove .virtual_documents * Update syntax for style * style: pre-commit fixes * Update index.rst * Adjust reference to Shen and Chen * style: pre-commit fixes * Add footbibliography to rst files * style: pre-commit fixes * Update CHANGELOG.md * Update CHANGELOG.md Co-authored-by: Agriya Khetarpal <[email protected]> * Update CITATIONS.bib --------- Co-authored-by: Ferran Brosa Planella <[email protected]> Co-authored-by: Julia Wind <[email protected]> Co-authored-by: amirDahari1 <[email protected]> Co-authored-by: Tom.Maull <[email protected]> Co-authored-by: amirDahari1 <[email protected]> Co-authored-by: Julia Wind <[email protected]> Co-authored-by: Ruimin-S <[email protected]> Co-authored-by: Isaac Squires <[email protected]> Co-authored-by: Ruimin-S <[email protected]> Co-authored-by: isaacsquires <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Valentin Sulzer <[email protected]> Co-authored-by: Agriya Khetarpal <[email protected]>
js1tr3 · Aug 12, 2024 · f42b469 · f42b469
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diff --git a/docs/source/api/models/submodels/transport_efficiency/bruggeman.rst b/docs/source/api/models/submodels/transport_efficiency/bruggeman.rst
@@ -0,0 +1,7 @@
+Bruggeman Transport Efficiency Model
+====================================
+
+.. autoclass:: pybamm.transport_efficiency.Bruggeman
+  :members:
+
+.. footbibliography::
diff --git a/...ce/api/models/submodels/transport_efficiency/bruggeman_transport_efficiency.rst b/...ce/api/models/submodels/transport_efficiency/bruggeman_transport_efficiency.rst
diff --git a/docs/source/api/models/submodels/transport_efficiency/cation_exchange_membrane.rst b/docs/source/api/models/submodels/transport_efficiency/cation_exchange_membrane.rst
@@ -0,0 +1,7 @@
+Cation-Exchange Membrane Transport Efficiency Model
+===================================================
+
+.. autoclass:: pybamm.transport_efficiency.CationExchangeMembrane
+  :members:
+
+.. footbibliography::
diff --git a/docs/source/api/models/submodels/transport_efficiency/heterogeneous_catalyst.rst b/docs/source/api/models/submodels/transport_efficiency/heterogeneous_catalyst.rst
@@ -0,0 +1,7 @@
+Heterogeneous Catalyst Transport Efficiency Model
+=================================================
+
+.. autoclass:: pybamm.transport_efficiency.HeterogeneousCatalyst
+  :members:
+
+.. footbibliography::
diff --git a/docs/source/api/models/submodels/transport_efficiency/hyperbola_of_revolution.rst b/docs/source/api/models/submodels/transport_efficiency/hyperbola_of_revolution.rst
@@ -0,0 +1,7 @@
+Hyperbola of Revolution Transport Efficiency Model
+==================================================
+
+.. autoclass:: pybamm.transport_efficiency.HyperbolaOfRevolution
+  :members:
+
+.. footbibliography::
diff --git a/docs/source/api/models/submodels/transport_efficiency/index.rst b/docs/source/api/models/submodels/transport_efficiency/index.rst
@@ -1,8 +1,15 @@
-transport_efficiency
+Transport Efficiency
 ====================
 
 .. toctree::
   :maxdepth: 1
 
   base_transport_efficiency
-  bruggeman_transport_efficiency
+  bruggeman
+  cation_exchange_membrane
+  heterogeneous_catalyst
+  hyperbola_of_revolution
+  ordered_packing
+  overlapping_spheres
+  random_overlapping_cylinders
+  tortuosity_factor
diff --git a/docs/source/api/models/submodels/transport_efficiency/ordered_packing.rst b/docs/source/api/models/submodels/transport_efficiency/ordered_packing.rst
@@ -0,0 +1,7 @@
+Ordered Packing Transport Efficiency Model
+==========================================
+
+.. autoclass:: pybamm.transport_efficiency.OrderedPacking
+  :members:
+
+.. footbibliography::
diff --git a/docs/source/api/models/submodels/transport_efficiency/overlapping_spheres.rst b/docs/source/api/models/submodels/transport_efficiency/overlapping_spheres.rst
@@ -0,0 +1,7 @@
+Overlapping Spheres Transport Efficiency Model
+==============================================
+
+.. autoclass:: pybamm.transport_efficiency.OverlappingSpheres
+  :members:
+
+.. footbibliography::
diff --git a/...urce/api/models/submodels/transport_efficiency/random_overlapping_cylinders.rst b/...urce/api/models/submodels/transport_efficiency/random_overlapping_cylinders.rst
@@ -0,0 +1,7 @@
+Random Overlapping Cylinders Transport Efficiency Model
+=======================================================
+
+.. autoclass:: pybamm.transport_efficiency.RandomOverlappingCylinders
+  :members:
+
+.. footbibliography::
diff --git a/docs/source/api/models/submodels/transport_efficiency/tortuosity_factor.rst b/docs/source/api/models/submodels/transport_efficiency/tortuosity_factor.rst
@@ -0,0 +1,7 @@
+Tortuosity Factor Transport Efficiency Model
+============================================
+
+.. autoclass:: pybamm.transport_efficiency.TortuosityFactor
+  :members:
+
+.. footbibliography::
diff --git a/docs/source/examples/index.rst b/docs/source/examples/index.rst
@@ -72,6 +72,7 @@ The notebooks are organised into subfolders, and can be viewed in the galleries
     notebooks/models/submodel_cracking_DFN_or_SPM.ipynb
     notebooks/models/loss_of_active_materials.ipynb
     notebooks/models/thermal-models.ipynb
+    notebooks/models/tortuosity_models.ipynb
     notebooks/models/unsteady-heat-equation.ipynb
     notebooks/models/using-model-options_thermal-example.ipynb
     notebooks/models/using-submodels.ipynb

diff --git a/docs/source/examples/notebooks/models/latexify.ipynb b/docs/source/examples/notebooks/models/latexify.ipynb