Updated formatting, wording, and moved Tutorial to Tutorials

NCAR · Jul 8, 2024 · 8be1a79 · 8be1a79
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diff --git a/docs/Tutorial/cases.rst → docs/Tutorials/cases.rst b/docs/Tutorial/cases.rst → docs/Tutorials/cases.rst
diff --git a/docs/Tutorial/cases/CANOPY.rst → docs/Tutorials/cases/CANOPY.rst b/docs/Tutorial/cases/CANOPY.rst → docs/Tutorials/cases/CANOPY.rst
diff --git a/docs/Tutorial/cases/CBL.rst → docs/Tutorials/cases/CBL.rst b/docs/Tutorial/cases/CBL.rst → docs/Tutorials/cases/CBL.rst
diff --git a/docs/Tutorial/cases/MBL.rst → docs/Tutorials/cases/MBL.rst b/docs/Tutorial/cases/MBL.rst → docs/Tutorials/cases/MBL.rst
@@ -49,7 +49,7 @@ Should be changed to replace the references to *4* with *1* as follows:
 
   #PBS -l select=1:ncpus=1:mpiprocs=1:ngpus=1:mem=100GB
 
-And, any values of *4* in the last line of the script (the *mpirun* line for Casper and the *mpiexec* line for Derecho) should be changed to *1*.
+And, any values of *4* in the last line of the script (the :code:`mpirun` line for Casper and the :code:`mpiexec` line for Derecho) should be changed to *1*.
 
 
 Visualize the output

diff --git a/docs/Tutorial/cases/NBL.rst → docs/Tutorials/cases/NBL.rst b/docs/Tutorial/cases/NBL.rst → docs/Tutorials/cases/NBL.rst
diff --git a/docs/Tutorial/cases/OFFSHORE.rst → docs/Tutorials/cases/OFFSHORE.rst b/docs/Tutorial/cases/OFFSHORE.rst → docs/Tutorials/cases/OFFSHORE.rst
@@ -48,7 +48,7 @@ Run FastEddy using the input parameters file **/tutorials/examples/Example06_OFF
   * Change :code:`Nt` from 360000 to 1
   * Change :code:`NtBatch` from 7500 to 1
 
-Then, run the Jupyter notebook to modify the initial condition as described. Then, run FastEddy for the :math:`4` h of the simulation by changing :code:`frqOutput`, :code:`Nt`, and :code:`NtBatch` back to their original values.
+Then, run the Jupyter notebook to modify the initial condition as described in the first paragraph. Then, run FastEddy for the :math:`4` h of the simulation by changing :code:`frqOutput`, :code:`Nt`, and :code:`NtBatch` back to their original values.
 
 See :ref:`run_fasteddy` for instructions on how to build and run FastEddy on NSF NCAR's High Performance Computing machines.
 

diff --git a/docs/Tutorial/cases/SBL.rst → docs/Tutorials/cases/SBL.rst b/docs/Tutorial/cases/SBL.rst → docs/Tutorials/cases/SBL.rst
diff --git a/docs/Tutorial/getting_started.rst → docs/Tutorials/getting_started.rst b/docs/Tutorial/getting_started.rst → docs/Tutorials/getting_started.rst
diff --git a/.../Tutorial/images/MEAN-PROF-convective.png → ...Tutorials/images/MEAN-PROF-convective.png b/.../Tutorial/images/MEAN-PROF-convective.png → ...Tutorials/images/MEAN-PROF-convective.png
diff --git a/docs/Tutorial/images/MEAN-PROF-neutral.png → docs/Tutorials/images/MEAN-PROF-neutral.png b/docs/Tutorial/images/MEAN-PROF-neutral.png → docs/Tutorials/images/MEAN-PROF-neutral.png
diff --git a/docs/Tutorial/images/MEAN-PROF-offshore.png → docs/Tutorials/images/MEAN-PROF-offshore.png b/docs/Tutorial/images/MEAN-PROF-offshore.png → docs/Tutorials/images/MEAN-PROF-offshore.png
diff --git a/docs/Tutorial/images/MEAN-PROF-stable.png → docs/Tutorials/images/MEAN-PROF-stable.png b/docs/Tutorial/images/MEAN-PROF-stable.png → docs/Tutorials/images/MEAN-PROF-stable.png
diff --git a/docs/Tutorial/images/PDF-offshore.png → docs/Tutorials/images/PDF-offshore.png b/docs/Tutorial/images/PDF-offshore.png → docs/Tutorials/images/PDF-offshore.png
diff --git a/docs/Tutorial/images/README.txt → docs/Tutorials/images/README.txt b/docs/Tutorial/images/README.txt → docs/Tutorials/images/README.txt
diff --git a/docs/Tutorial/images/TURB-PROF-canopy.png → docs/Tutorials/images/TURB-PROF-canopy.png b/docs/Tutorial/images/TURB-PROF-canopy.png → docs/Tutorials/images/TURB-PROF-canopy.png
diff --git a/.../Tutorial/images/TURB-PROF-convective.png → ...Tutorials/images/TURB-PROF-convective.png b/.../Tutorial/images/TURB-PROF-convective.png → ...Tutorials/images/TURB-PROF-convective.png
diff --git a/docs/Tutorial/images/TURB-PROF-neutral.png → docs/Tutorials/images/TURB-PROF-neutral.png b/docs/Tutorial/images/TURB-PROF-neutral.png → docs/Tutorials/images/TURB-PROF-neutral.png
diff --git a/docs/Tutorial/images/TURB-PROF-offshore.png → docs/Tutorials/images/TURB-PROF-offshore.png b/docs/Tutorial/images/TURB-PROF-offshore.png → docs/Tutorials/images/TURB-PROF-offshore.png
diff --git a/docs/Tutorial/images/TURB-PROF-stable.png → docs/Tutorials/images/TURB-PROF-stable.png b/docs/Tutorial/images/TURB-PROF-stable.png → docs/Tutorials/images/TURB-PROF-stable.png
diff --git a/...ial/images/TimeEvolution_cldthres0.01.png → ...als/images/TimeEvolution_cldthres0.01.png b/...ial/images/TimeEvolution_cldthres0.01.png → ...als/images/TimeEvolution_cldthres0.01.png
diff --git a/docs/Tutorial/images/UVWTHETA-XY-canopy.png → docs/Tutorials/images/UVWTHETA-XY-canopy.png b/docs/Tutorial/images/UVWTHETA-XY-canopy.png → docs/Tutorials/images/UVWTHETA-XY-canopy.png
diff --git a/...utorial/images/UVWTHETA-XY-convective.png → ...torials/images/UVWTHETA-XY-convective.png b/...utorial/images/UVWTHETA-XY-convective.png → ...torials/images/UVWTHETA-XY-convective.png
diff --git a/docs/Tutorial/images/UVWTHETA-XY-neutral.png → .../Tutorials/images/UVWTHETA-XY-neutral.png b/docs/Tutorial/images/UVWTHETA-XY-neutral.png → .../Tutorials/images/UVWTHETA-XY-neutral.png
diff --git a/.../Tutorial/images/UVWTHETA-XY-offshore.png → ...Tutorials/images/UVWTHETA-XY-offshore.png b/.../Tutorial/images/UVWTHETA-XY-offshore.png → ...Tutorials/images/UVWTHETA-XY-offshore.png
diff --git a/docs/Tutorial/images/UVWTHETA-XY-stable.png → docs/Tutorials/images/UVWTHETA-XY-stable.png b/docs/Tutorial/images/UVWTHETA-XY-stable.png → docs/Tutorials/images/UVWTHETA-XY-stable.png
diff --git a/docs/Tutorial/images/UVWTHETA-XZ-canopy.png → docs/Tutorials/images/UVWTHETA-XZ-canopy.png b/docs/Tutorial/images/UVWTHETA-XZ-canopy.png → docs/Tutorials/images/UVWTHETA-XZ-canopy.png
diff --git a/...utorial/images/UVWTHETA-XZ-convective.png → ...torials/images/UVWTHETA-XZ-convective.png b/...utorial/images/UVWTHETA-XZ-convective.png → ...torials/images/UVWTHETA-XZ-convective.png
diff --git a/docs/Tutorial/images/UVWTHETA-XZ-neutral.png → .../Tutorials/images/UVWTHETA-XZ-neutral.png b/docs/Tutorial/images/UVWTHETA-XZ-neutral.png → .../Tutorials/images/UVWTHETA-XZ-neutral.png
diff --git a/.../Tutorial/images/UVWTHETA-XZ-offshore.png → ...Tutorials/images/UVWTHETA-XZ-offshore.png b/.../Tutorial/images/UVWTHETA-XZ-offshore.png → ...Tutorials/images/UVWTHETA-XZ-offshore.png
diff --git a/docs/Tutorial/images/UVWTHETA-XZ-stable.png → docs/Tutorials/images/UVWTHETA-XZ-stable.png b/docs/Tutorial/images/UVWTHETA-XZ-stable.png → docs/Tutorials/images/UVWTHETA-XZ-stable.png
diff --git a/docs/Tutorial/images/VerticalProfiles.png → docs/Tutorials/images/VerticalProfiles.png b/docs/Tutorial/images/VerticalProfiles.png → docs/Tutorials/images/VerticalProfiles.png
diff --git a/.../Tutorial/images/VerticalProfilesTurb.png → ...Tutorials/images/VerticalProfilesTurb.png b/.../Tutorial/images/VerticalProfilesTurb.png → ...Tutorials/images/VerticalProfilesTurb.png
diff --git a/docs/Tutorial/index.rst → docs/Tutorials/index.rst b/docs/Tutorial/index.rst → docs/Tutorials/index.rst
@@ -1,6 +1,6 @@
-########
-Tutorial
-########
+#########
+Tutorials
+#########
 
 .. toctree::
    :titlesonly:

diff --git a/docs/Tutorial/questions.rst → docs/Tutorials/questions.rst b/docs/Tutorial/questions.rst → docs/Tutorials/questions.rst
diff --git a/docs/Tutorial/sensitivity.rst → docs/Tutorials/sensitivity.rst b/docs/Tutorial/sensitivity.rst → docs/Tutorials/sensitivity.rst
diff --git a/docs/_static/fasteddy_logo_large_vertical_2024_06.png b/docs/_static/fasteddy_logo_large_vertical_2024_06.png
diff --git a/docs/conf.py b/docs/conf.py
@@ -62,7 +62,7 @@
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
-#html_logo = os.path.join('_static','fasteddy_logo.png')
+html_logo = os.path.join('_static','fasteddy_logo_large_vertical_2024_06.png')
 
 # -- Intersphinx control -----------------------------------------------------
 intersphinx_mapping = {'numpy':("https://docs.scipy.org/doc/numpy/", None)}

diff --git a/docs/index.rst b/docs/index.rst
@@ -28,5 +28,5 @@ This DOI represents all versions and will always resolve to the latest one.
    release_notes.rst
    run_ncar_hpcs.rst
    downloads.rst
-   Tutorial/index
+   Tutorials/index
    publications.rst
diff --git a/docs/run_ncar_hpcs.rst b/docs/run_ncar_hpcs.rst
@@ -1,10 +1,10 @@
 .. _run_fasteddy:
 
-*********************************
-Running FastEddy on NSF NCAR HPCs
-*********************************
+*************************
+Running under NSF NCAR HPC
+**************************
 
-These instructions will help users get started using FastEddy on
+These instructions will help users get started running FastEddy on 
 `NSF NCAR's High Performance Computing (HPC) machines <https://ncar-hpc-docs.readthedocs.io/en/latest/>`_,
 `Derecho <https://arc.ucar.edu/knowledge_base/74317833>`_ and
 `Casper <https://arc.ucar.edu/knowledge_base/70549550>`_.
@@ -14,14 +14,14 @@ Compilation
 
 The Makefile-based build system included here assumes deployment on the NSF
 NCAR HPCs. FastEddy requires a C-compiler, MPI, and CUDA. Currently, the
-default modules loaded at login suffice on Casper, however the `cuda` module
-will need to be loaded on Derecho by running `module load cuda`.
+default modules loaded at login suffice on Casper, however the :code:`cuda` module
+will need to be loaded on Derecho by running :code:`module load cuda`.
 
 1. Download the source code from the `Releases <https://github.com/NCAR/FastEddy-model/releases>`_ page and unpack the release in the desired location or clone the `repository <https://github.com/NCAR/FastEddy-model>`_ in the desired location.
 3. Navigate to the **SRC/FEMAIN** directory.
-4. To build the FastEddy executable run `make` (optionally run `make clean` first if appropriate).
+4. To build the FastEddy executable run :code:`make` (optionally run :code:`make clean` first if appropriate).
 
-The `FastEddy` executable will be located in the **SRC/FEMAIN** directory. To
+The :code:`FastEddy` executable will be located in the **SRC/FEMAIN** directory. To
 build on other HPC systems with NVIDIA GPUs, check for availability of the aformentioned
 modules/dependencies. Successful compilation may require modifications to shell environment
 variable include or library paths, or alternatively minor adjustments to the include or library
@@ -31,7 +31,7 @@ Example PBS job script for Casper
 =================================
 
 Below is bash-based PBS job submission script for running the model on NSF NCAR's Casper machine.
-The FastEddy code will write its output to an `output` directory. Please create an output
+The FastEddy code will write its output to an **output** directory. Please create an output
 directory, if one does not already exist, in the same location as this script.
 
 Sample Script
@@ -40,8 +40,8 @@ Sample Script
 .. note::
 
    * Replace "<ProjectAccount>" below with a valid Project Account.
-   * Replace "<path to code location>" below with the location that contains the `FastEddy-model` directory from unpacking the release.
-   * Replace "<example .in filename>" below with the name of the example .in filename.  For example, Example01_NBL.in, Example02_CBL.in, etc.
+   * Replace "<path to code location>" below with the location that contains the **FastEddy-model** directory from unpacking the release.
+   * Replace "<example .in filename>" below with the name of the example .in filename.  For example, *Example01_NBL.in*, *Example02_CBL.in*, etc.
 
 .. code-block:: bash