asalmgren · Oct 7, 2026 · Oct 7, 2026 · Oct 7, 2026 · Oct 7, 2026
diff --git a/.github/workflows/dependencies/documentation.sh b/.github/workflows/dependencies/documentation.sh
@@ -9,13 +9,8 @@ set -eu -o pipefail
 
 sudo apt-get update
 
+# The docs job only builds HTML with Sphinx; doxygen and LaTeX are not used.
 sudo apt-get install -y --no-install-recommends\
     build-essential \
-    pandoc \
-    doxygen \
-    texlive \
-    texlive-latex-extra \
-    texlive-lang-cjk \
-    tex-gyre \
-    latexmk
+    pandoc
 
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -6,7 +6,7 @@ on:
   pull_request:
 
 concurrency:
-  group: ${{ github.head_ref }}-docs
+  group: ${{ github.ref }}-${{ github.head_ref }}-docs
   cancel-in-progress: true
 
 jobs:
@@ -21,7 +21,7 @@ jobs:
           .github/workflows/dependencies/documentation.sh
           echo "Installing python packages for docs..."
           python3 -m pip install --upgrade pip
-          python3 -m pip install sphinx sphinx_rtd_theme breathe sphinxcontrib.bibtex docutils
+          python3 -m pip install sphinx sphinx_rtd_theme sphinxcontrib.bibtex docutils
 
       - name: Install and Build
         run: |

diff --git a/.gitignore b/.gitignore
@@ -7,5 +7,7 @@ plt?????
 d/
 f/
 o/
+tmp_build_dir/
+tmp_install_dir/
 chk?????.old*
 plt?????.old*
diff --git a/Docs/sphinx_documentation/Makefile b/Docs/sphinx_documentation/Makefile
@@ -16,9 +16,7 @@ help:
 .PHONY: help Makefile
 
 clean:
-	rm -rf build ../Doxygen/xml source/class source/file
-	rm -f source/classlist.rst source/filelist.rst
-	rm -rf source/*_files.rst
+	rm -rf build
 
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).

diff --git a/Docs/sphinx_documentation/make_api.py b/Docs/sphinx_documentation/make_api.py
diff --git a/Docs/sphinx_documentation/source/AlgorithmOptions.rst b/Docs/sphinx_documentation/source/AlgorithmOptions.rst
@@ -27,23 +27,27 @@ Note that Temperature is only non-conservative. For more details, see :ref:`sec:
 Advection
 ---------
 
-IAMR has the option to use a Method of Lines (MOL) or Godunov scheme to compute the advective terms.
+IAMR computes the advective terms with an unsplit Godunov scheme (piecewise linear or piecewise
+parabolic reconstruction) or with the Bell-Dawson-Shubin (BDS) scheme. The following must be
+preceded by "ns."
 
 +-------------------------+-------------------------------------------------------------------------+-------------+--------------+
 |                         | Description                                                             |   Type      | Default      |
 +=========================+=========================================================================+=============+==============+
-| ns.use_godunov          | If true, use Godunov, else use MOL.                                     |    bool     |   true       |
+| advection_scheme        | Godunov_PLM, Godunov_PPM or BDS.  Godunov_PPM and BDS are not           |   String    | Godunov_PLM  |
+|                         | available with embedded boundaries.                                     |             |              |
 +-------------------------+-------------------------------------------------------------------------+-------------+--------------+
 
+Note that the old ``ns.use_godunov`` key and the MOL scheme have been removed; setting either
+aborts the run.
 
-For problems without embedded boundaries, there are additional options when using the Godunov method. The following must
+
+For problems without embedded boundaries, there is an additional option for the Godunov method. The following must
 be preceded by "godunov."
 
 +-------------------------+-------------------------------------------------------------------------+-------------+--------------+
 |                         | Description                                                             |   Type      | Default      |
 +=========================+=========================================================================+=============+==============+
-| use_ppm                 | Use the Piecewise Parabolic Method to construct edge states             |    bool     |   false      |
-+-------------------------+-------------------------------------------------------------------------+-------------+--------------+
 | use_forces_in_trans     | Use external forcing terms in constructing transverse derivatives       |    bool     |   false      |
 +-------------------------+-------------------------------------------------------------------------+-------------+--------------+
 
@@ -60,3 +64,56 @@ The following must be preceded by "ns."
 +-------------------------+-----------------------------------------------------------------------+-------------+--------------+
 
 Note the default value of ``ns.be_cn_theta = 0.5`` corresponds to the Crank-Nicolson method.
+
+
+.. _sec:LES:
+
+Large Eddy Simulation
+---------------------
+
+IAMR can add a subgrid-scale eddy viscosity to the viscous terms.  The following must be
+preceded by "ns."
+
++-------------------------+-----------------------------------------------------------------------+-------------+--------------+
+|                         | Description                                                           |   Type      | Default      |
++=========================+=======================================================================+=============+==============+
+| do_LES                  | Add a subgrid-scale eddy viscosity to the molecular viscosity         |    Int      |   0          |
++-------------------------+-----------------------------------------------------------------------+-------------+--------------+
+| LES_model               | Which model to use: Smagorinsky or Sigma.  Any other value aborts.    |  String     | Smagorinsky  |
+|                         | Sigma is 3D only.                                                     |             |              |
++-------------------------+-----------------------------------------------------------------------+-------------+--------------+
+| smago_Cs_cst            | Model constant, used only when LES_model = Smagorinsky                |   Real      |   0.18       |
++-------------------------+-----------------------------------------------------------------------+-------------+--------------+
+| sigma_Cs_cst            | Model constant, used only when LES_model = Sigma                      |   Real      |   1.5        |
++-------------------------+-----------------------------------------------------------------------+-------------+--------------+
+| getLESVerbose           | Print the model and constant in use from the LES routine              |    Int      |   0          |
++-------------------------+-----------------------------------------------------------------------+-------------+--------------+
+
+Note that each model reads its own constant, so changing ``ns.smago_Cs_cst`` has no effect
+when ``ns.LES_model = Sigma``, and vice versa.  The Sigma model is described in
+Nicoud et al., *Using singular values to build a subgrid-scale model for large eddy
+simulations*, Phys. Fluids 23, 085106 (2011).
+
+
+.. _sec:EBOptions:
+
+Embedded Boundaries
+-------------------
+
+These apply to builds with ``USE_EB=TRUE``; see :ref:`sec:EB-basics` for how the geometry
+itself is constructed.  The following must be preceded by "ns."
+
++-------------------------+-----------------------------------------------------------------------+-------------+--------------+
+|                         | Description                                                           |   Type      | Default      |
++=========================+=======================================================================+=============+==============+
+| redistribution_type     | How the advective update of a small cut cell is redistributed to its  |  String     | StateRedist  |
+|                         | neighbours: StateRedist, FluxRedist or NoRedist.  Any other value     |             |              |
+|                         | aborts.                                                               |             |              |
++-------------------------+-----------------------------------------------------------------------+-------------+--------------+
+| refine_cutcells         | Tag every cut cell for refinement, so that the embedded boundary      |    Int      |   1          |
+|                         | never crosses a coarse/fine boundary.  Setting 0 allows a partially   |             |              |
+|                         | refined EB, which is still under development and issues a warning.    |             |              |
++-------------------------+-----------------------------------------------------------------------+-------------+--------------+
+
+Note that ``ns.advection_scheme = Godunov_PPM`` and ``BDS`` are not available with embedded
+boundaries.
diff --git a/Docs/sphinx_documentation/source/Contributing.rst b/Docs/sphinx_documentation/source/Contributing.rst
@@ -65,7 +65,7 @@ Make your own fork
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 First, setup your local git repo. To make your own fork of the main
-(`upstream`) repository, press the fork button on the `IAMR Github page <https://github.com/IAMR-Codes/IAMR>`_.
+(`upstream`) repository, press the fork button on the `IAMR Github page <https://github.com/AMReX-Fluids/IAMR>`_.
 
 Then, clone your fork on your local computer. If you plan on doing a lot of IAMR development,
 we recommend configuring your clone to use ssh access so you won't have to enter your Github
@@ -77,7 +77,7 @@ password every time, which you can do using these commands:
 
   # Then, navigate into your repo, add a new remote for the main IAMR repo, and fetch it:
   cd IAMR
-  git remote add upstream https://github.com/IAMR-Codes/IAMR
+  git remote add upstream https://github.com/AMReX-Fluids/IAMR
   git remote set-url --push upstream git@github.com:<myGithubUsername>/IAMR.git
   git fetch upstream
 
@@ -95,7 +95,7 @@ If you instead prefer to use HTTPS authentication, configure your local clone as
 
   # Navigate into your repo, add a new remote for the main IAMR repo, and fetch it
   cd IAMR
-  git remote add upstream https://github.com/IAMR-Codes/IAMR
+  git remote add upstream https://github.com/AMReX-Fluids/IAMR
   git remote set-url --push upstream https://github.com/<myGithubUsername>/IAMR.git
   git fetch upstream
 

diff --git a/Docs/sphinx_documentation/source/Introduction_Chapter.rst b/Docs/sphinx_documentation/source/Introduction_Chapter.rst
@@ -16,7 +16,7 @@ Key software and algorithmic features of IAMR include:
 
 * Fluid velocity, density and tracers are defined at cell centroids; pressure is defined at nodes.
 
-* Possible advection algorithms: a Method-Of-Lines (MOL) approach and a Godunov-method algorithm. Both use an intermediate MAC projection for face-centered advection velocities.
+* Possible advection algorithms: an unsplit Godunov method (piecewise linear or piecewise parabolic reconstruction) and the Bell-Dawson-Shubin (BDS) scheme. All use an intermediate MAC projection for face-centered advection velocities.
 
 * Incompressibility of the fluid is imposed through the use of an approximate projection at the end of the time step.