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diff --git a/.buildinfo b/.buildinfo
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+# Sphinx build info version 1
+# This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 5323d8be09131c0fa917404abdc54afd
+tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/.nojekyll b/.nojekyll
diff --git a/_sources/acknowledgments.rst.txt b/_sources/acknowledgments.rst.txt
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+Acknowledgments
+=====
+
+This work was authored by the National Renewable Energy Laboratory (NREL), operated by Alliance for Sustainable Energy, LLC, for the U.S. Department of Energy (DOE) under Contract No. DE-AC36-08GO28308. This work was supported by funding from DOE Bioenergy Technologies Office (BETO) `CO2RUe consortium <https://www.energy.gov/eere/co2rue>`_. The research was performed using computational resources sponsored by the Department of Energy's Office of Energy Efficiency and Renewable Energy and located at the National Renewable Energy Laboratory. The views expressed in the article do not necessarily represent the views of the DOE or the U.S. Government. The U.S. Government retains and the publisher, by accepting the article for publication, acknowledges that the U.S. Government retains a nonexclusive, paid-up, irrevocable, worldwide license to publish or reproduce the published form of this work, or allow others to do so, for U.S. Government purposes.
+
+
diff --git a/_sources/contribute.rst.txt b/_sources/contribute.rst.txt
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+Contributing
+=====
+
+We welcome pull requests from anybody!
+
+Formatting
+------------
+
+Code formatting and import sorting are done automatically with ``black`` and ``isort``.
+
+You can automatically enforce the formatting guidelines with
+
+.. code-block:: console
+
+   pip install black isort
+   bash fixFormat.sh
+
+Spelling is checked but not automatically fixed using ``codespell``
+
+
+Test
+------------
+Please ensure your contribution passes the tests in ``tests``
+
+
diff --git a/_sources/index.rst.txt b/_sources/index.rst.txt
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+Bio Reactor Design (BiRD)
+===================================
+
+`BiRD` is a toolbox aimed a facilitating the numerical simulation of bioreactors with OpenFOAM.
+The purpose of `BiRD` is 
+
+1. to ensure reproducibility of numerical simulations of bioreactors.
+2. to create a suite of test cases that can be used to test different reactor configurations.
+3. to facilitate validation of multiphase flow models against several experimental campaigns.
+4. to facilitate optimization (geometry and operating conditions) of bioreactors. 
+
+It contains a python module ``bird`` that can be used to generate input files that may be read by OpenFOAM to generate meshes and cases. It can also be used to post process the output of OpenFOAM simulations.
+
+We also provide a solver ``birdmultiphaseEulerFoam`` that contains custom models added to the base OpenFOAM-v9. 
+
+
+.. note::
+
+   This project is under active development. We welcome community contributions and testing!
+
+
+.. toctree::
+   :hidden:
+
+   quickstart
+   meshing
+   preprocess
+   postprocess
+   contribute
+   references
+   acknowledgments
diff --git a/_sources/meshing.rst.txt b/_sources/meshing.rst.txt
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+Meshing
+=====
+
+
+.. _stir_tank:
+
+Generate stirred tank reactor mesh
+------------
+
+Generate a ``blockMeshDict`` with
+
+.. code-block:: console
+
+   inp=bird/meshing/stirred_tank_mesh_templates/base_tank/tank_par.yaml
+   out=bird/meshing/stirred_tank_case_templates/base/system/blockMeshDict
+
+   python applications/write_stirred_tank_mesh.py -i $inp -o $out
+
+Then activate openFoam environment and mesh with
+
+.. code-block:: console
+
+   blockMesh -dict system/blockMeshDict
+   stitchMesh -perfect -overwrite inside_to_hub inside_to_hub_copy
+   stitchMesh -perfect -overwrite hub_to_rotor hub_to_rotor_copy
+   transformPoints "rotate=((0 0 1)(0 1 0))"
+
+Visualize mesh in Paraview
+
+.. _fig:stirredtank:
+
+.. figure:: https://raw.githubusercontent.com/NREL/BioReactorDesign/main/assets/stirred_tank.png
+     :width: 70%
+     :align: center
+     :name: fig-str
+     :target: https://raw.githubusercontent.com/NREL/BioReactorDesign/main/assets/stirred_tank.png
+     :alt: Stirred-tank reactor
+
+Related tutorial
+^^^^^^^^^^^^^^^
+
+- ``tutorial_cases/stirred_tank``
+
+
+
+.. _block_cyl:
+
+Block cylindrical meshing
+------------
+
+Generates ``system/blockMeshDict``
+
+.. code-block:: console
+
+   root=`pwd`
+   caseFolder=bird/meshing/block_cyl_cases_templates/case
+   mesh_temp=bird/meshing/block_cyl_mesh_templates/sideSparger
+
+   python applications/write_block_cyl_mesh.py -i $mesh_temp/input.json -t $mesh_temp/topology.json -o $caseFolder/system
+
+Then activate openFoam environment and mesh with
+
+.. code-block:: console
+
+   cd $caseFolder
+   blockMesh
+   transformPoints "scale=(0.001 0.001 0.001)"
+   transformPoints "rotate=((0 0 1) (0 1 0))"
+   cd $root
+
+Visualize mesh in Paraview
+
+.. _fig:sidesparger:
+
+.. figure:: https://raw.githubusercontent.com/NREL/BioReactorDesign/main/assets/3dsparger.png
+     :width: 50%
+     :align: center
+     :name: fig-sidesparger
+     :target: https://raw.githubusercontent.com/NREL/BioReactorDesign/main/assets/3dsparger.png
+     :alt: Reactor with a side sparger
+
+How to change the dimensions or mesh refinement?
+^^^^^^^^^^^^^^^
+
+All dimensions and mesh are controlled by the input file ``input.json``.
+The input file can also be in ``.yaml`` format. The parser will decide the file format based on its extension.
+See ``bird/meshing/block_cyl_mesh_templates/baseColumn/`` for an example of ``.yaml``
+
+How to change the arrangement of concentric cylinders?
+^^^^^^^^^^^^^^^
+
+The block topology is controlled by the ``topology.json``
+We recomment always working with a schematic. Here is the schematic for this case
+
+.. figure:: https://raw.githubusercontent.com/NREL/BioReactorDesign/main/assets/schematic.png
+     :width: 50%
+     :align: center
+     :name: fig-schematic
+     :target: https://raw.githubusercontent.com/NREL/BioReactorDesign/main/assets/schematic.png
+     :alt: Side sparger schematic
+
+
+The purple blocks are walls (not meshed) and the white blocks are fluid blocks (meshed). The symmetry axis is indicated as a dashed line
+
+In the ``topology.json``, the purple blocks are defined as
+
+.. code-block:: json
+
+   "Walls": {
+                   "Support": [
+                               {"R": 0, "L": 3},
+                               {"R": 1, "L": 3}
+                              ],
+                   "Sparger": [
+                               {"R": 0, "L": 2},
+                               {"R": 1, "L": 2},
+                               {"R": 2, "L": 2}
+                              ]
+           }
+
+
+How to change boundaries?
+^^^^^^^^^^^^^^^
+
+Boundaries are defined with three types, ``top``, ``bottom`` and ``lateral``
+
+In the case of sparger walls shown below with the red lines
+
+.. figure:: https://raw.githubusercontent.com/NREL/BioReactorDesign/main/assets/schematicSpargerWalls.png
+     :width: 50%
+     :align: center
+     :name: fig-schematicwalls
+     :target: https://raw.githubusercontent.com/NREL/BioReactorDesign/main/assets/schematicSpargerWalls.png
+     :alt: Wall side sparger schematic
+
+
+the boundary is defined in the ``topology.json`` as
+
+.. code-block:: json
+
+   "Boundary": {
+                   "wall_sparger":[
+                              {"type": "bottom", "Rmin": 2, "Rmax": 2, "Lmin": 2, "Lmax": 3},
+                              {"type": "top", "Rmin": 0, "Rmax": 0, "Lmin": 1, "Lmax": 2},
+                              {"type": "top", "Rmin": 1, "Rmax": 1, "Lmin": 1, "Lmax": 2},
+                              {"type": "top", "Rmin": 2, "Rmax": 2, "Lmin": 1, "Lmax": 2}
+                            ],
+
+For the side sparger, the inlet is shown below with the red line
+
+.. figure:: https://raw.githubusercontent.com/NREL/BioReactorDesign/main/assets/schematicSpargerInlet.png
+     :width: 50%
+     :align: center
+     :name: fig-schematicinlet
+     :target: https://raw.githubusercontent.com/NREL/BioReactorDesign/main/assets/schematicSpargerInlet.png
+     :alt: Inlet side sparger schematic
+
+the boundary is defined in the ``topology.json`` as
+
+.. code-block:: json
+
+   "Boundary": {
+                   "inlet": [
+                              {"type": "lateral", "Rmin": 2, "Rmax": 3, "Lmin": 2, "Lmax": 2}
+                            ],
+
+
+
+Related tutorials
+^^^^^^^^^^^^^^^
+
+- ``tutorial_cases/side_sparger``
+- ``tutorial_cases/bubble_column_20L``
+
+
+Block rectangular meshing
+------------
+
+Generates ``system/blockMeshDict``
+
+.. code-block:: console
+
+   root=`pwd`
+   caseFolder=bird/meshing/block_rect_cases_templates/case
+   mesh_temp=bird/meshing/block_rect_mesh_templates/loopReactor
+
+   python applications/write_block_rect_mesh.py -i $mesh_temp/input.json -o $caseFolder/system
+
+Then activate openFoam environment and mesh with
+
+.. code-block:: console
+
+   cd $caseFolder
+   blockMesh
+   cd $root
+
+Visualize mesh in Paraview
+
+.. _fig:loop_reactor:
+
+.. figure:: https://raw.githubusercontent.com/NREL/BioReactorDesign/main/assets/loop_react.png
+     :width: 80%
+     :align: center
+     :name: fig-loopreactor
+     :target: https://raw.githubusercontent.com/NREL/BioReactorDesign/main/assets/loop_react.png
+     :alt: Loop reactor
+
+
+How to change the block rectangular geometry?
+^^^^^^^^^^^^^^^
+The geometry of the block cylindrical mesh is defined within a 3D domain (X,Y,Z). The blocks that represent the fluid domain are a subset of a block rectangular background domain. The fluid blocks are defined using the geometry corners. For the mesh shown above, the geometry corners are the red blocks shown below
+
+.. _fig:loop_reactor_schematic:
+
+.. figure:: https://raw.githubusercontent.com/NREL/BioReactorDesign/main/bird/meshing/block_rect_mesh_templates/loopReactor/loop_schematic.png
+     :width: 80%
+     :align: center
+     :name: fig-loopreactor-schematic
+     :target: https://raw.githubusercontent.com/NREL/BioReactorDesign/main/bird/meshing/block_rect_mesh_templates/loopReactor/loop_schematic.png
+     :alt: Loop reactor schematic
+
+
+The corners are defined in the ``input.json``
+
+.. code-block:: json
+
+   "Geometry": {
+           "Fluids": [
+                   [ [0,0,0], [9,0,0], [9,0,4], [0,0,4] ],
+                   [ [0,1,4], [0,4,4], [0,4,0], [0,1,0] ]
+           ]
+   }
+
+
+Related tutorials
+^^^^^^^^^^^^^^^
+- ``tutorial_cases/loop_reactor_mixing``
+- ``tutorial_cases/loop_reactor_reacting``
+
+
diff --git a/_sources/postprocess.rst.txt b/_sources/postprocess.rst.txt
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+Postprocess
+=====
+
+
+.. _early_pred:
+
+
+Perform early prediction
+------------
+
+
+.. code-block:: console
+
+   python applications/early_prediction.py -df bird/postprocess/data_early
+
+Generates
+
+.. container:: figures-early-pred
+
+   .. figure:: https://raw.githubusercontent.com/NREL/BioReactorDesign/main/assets/early_det.png
+      :width: 70%
+      :align: center
+      :alt: Determinisitc early prediction
+
+   .. figure:: https://raw.githubusercontent.com/NREL/BioReactorDesign/main/assets/early_uq.png
+      :width: 70%
+      :align: center
+      :alt: Uncertainty-aware early prediction     
+
+
+Plot conditional means
+------------
+
+.. code-block:: console
+
+   python applications/compute_conditional_mean.py -f bird/postprocess/data_conditional_mean -avg 2
+
+Generates (among others)
+
+.. container:: figures-cond-mean
+
+   .. figure:: https://raw.githubusercontent.com/NREL/BioReactorDesign/main/assets/gh_cond_mean.png
+      :width: 70%
+      :align: center
+      :alt: Height-conditional gas holdup
+
+   .. figure:: https://raw.githubusercontent.com/NREL/BioReactorDesign/main/assets/co2g_cond_mean.png
+      :width: 70%
+      :align: center
+      :alt: Height-conditional CO2 gas fraction
+
+
+
+
+