Overset tut

.gitignore

@@ -1,3 +1,7 @@
 _build
 .DS_Store
-*.cgns
+.vscode/*
+make.bat
+
+
+*.gitignore

machAeroTutorials/index.rst

@@ -8,3 +8,4 @@
    aero_overview
    opt_overview
    airfoilopt_overview
+   overset_zoverview

machAeroTutorials/overset.bib

@@ -0,0 +1,19 @@
+ @misc{nasaM6sim, 
+    title={3D ONERA M6 Wing Validation for Turbulence Model Numerical Analysis}, 
+    url={https://turbmodels.larc.nasa.gov/onerawingnumerics_val.html}, 
+    journal={NASA}, 
+    publisher={NASA}
+} 
+
+@misc{nasaM6real, 
+    title={ONERA M6 Wing}, 
+    url={https://www.grc.nasa.gov/WWW/wind/valid/m6wing/m6wing.html}, 
+    journal={NASA}, 
+    publisher={NASA}
+}
+
+@misc{nasaM6SA,
+	title = {{3D} {ONERA} {M6} {Wing} {Validation} for {Turbulence} {Model} {Numerical} {Analysis} - {SA}-neg {Model} {Results}},
+	url = {https://turbmodels.larc.nasa.gov/onerawingnumerics_val_sa.html},
+	urldate = {2020-12-11},
+}

machAeroTutorials/overset_analysis.rst

@@ -0,0 +1,207 @@
+.. _overset_analysis:
+
+*******************************************************
+CFD Analysis
+*******************************************************
+
+Introduction
+============
+
+This part will help guide you through the analysis part. We will setup the run script and let ADflow compute the 
+solution. From :cite:`nasaM6real` and :cite:`nasaM6SA`
+we know the flow conditions:
+
++--------------------+---------+
+| AoA                | 3.06°   |
++--------------------+---------+
+| Mach               | 0.8395  |
++--------------------+---------+
+| Reynolds Number    | 11.71e6 |
++--------------------+---------+
+| Reynols Ref Lenght | 0.646m  |
++--------------------+---------+
+| Temperature        | 300° K  |
++--------------------+---------+
+
+I developed a convenience package for ADflow called 
+`adflow_util <https://github.com/DavidAnderegg/adflow_util>`_\. It allows to plot the ADflow state variables live in the console and 
+handles some annoying stuff like creating the ``output`` folder for ADflow automatically. It also makes it easy
+to sweep a variable, for example ``alpha``. I will use this utility here, but the regular python API, 
+that is detailed in other tutorials, would work aswell.
+
+For simplicity, I will only cover the Calculation on the ``L3`` mesh.
+
+
+Files
+=====
+Navigate to the directory ``overset/analysis`` in your tutorial folder and create an empty file called 
+``run_adflow_L3.py``. If you did not create the volume mesh on the previous page, you will also have to 
+copy the meshfile:
+::
+
+    $ cp tutorial/overset/analysis/ONERA_M6_L3.cgns .
+
+If you want to use ``adflow_util`` download and install it:
+::
+
+    $ pip install git+https://github.com/DavidAnderegg/adflow_util.git
+
+
+ADflow
+======
+
+Setup the Script
+----------------
+
+First we have to import ``adflow_util``:
+
+.. literalinclude:: ../tutorial/overset/analysis/run_adflow_L3.py
+   :start-after: # rst Imports (beg)
+   :end-before: # rst Imports (end)
+
+Then we define a variable for the level we want to use. This makes it easier to switch, if we want to:
+
+.. literalinclude:: ../tutorial/overset/analysis/run_adflow_L3.py
+   :start-after: # rst Level (beg)
+   :end-before: # rst Level (end)
+
+``adflow_util`` takes 3 different dictionaries as input. One sets some ``adflow_util``-specific options, 
+one sets the boundary conditions, as ``AeroProblem`` would and the last one is the regular ``Adflow`` options dict.
+Lets set the ``adflow_util`` options first:
+
+.. literalinclude:: ../tutorial/overset/analysis/run_adflow_L3.py
+   :start-after: # rst Options (beg)
+   :end-before: # rst Options (end)
+
+name
+  This sets the name for the analysis. It defines how the various output files are named.
+
+surfaceFamilyGroups
+  This defines how the various surface families should be assembled. The ``key`` sets the family name and 
+  the ``array`` defines the various surfaces the family is made off.
+
+All adflow_util options can be found `here <https://github.com/DavidAnderegg/adflow_util/blob/master/adflow_util/adflow_util.py#L52>`_\.
+
+Now we define the ``AeroProblem`` options:
+
+.. literalinclude:: ../tutorial/overset/analysis/run_adflow_L3.py
+   :start-after: # rst AeroOptions (beg)
+   :end-before: # rst AeroOptions (end)
+
+Here we set the various flow parameters. It is exactly the same as you would set in ``baseclasses.AeroProblem``.
+But we could, for example, set alpha as an array of variables. In that case, ``adflow_util`` would handle everything else 
+for us.
+
+Now, let's set the ``ADflow`` options:
+
+.. literalinclude:: ../tutorial/overset/analysis/run_adflow_L3.py
+   :start-after: # rst SolverOptions (beg)
+   :end-before: # rst SolverOptions (end)
+
+I want to point out a few things:
+
+outputsurfacefamily
+    We choose ``wall`` which we defined earlier as consisting of ``near_wing`` and ``near_tip``. This will
+    write out only the wing as our surface solution.
+
+zippersurfacefamily
+    This tells ADflow which surfaces it should use to construct the geometry on which the forces are integrated.
+
+surfacevariables & volumevariables
+    Here it is very important to add ``blank``. This way we know which cells we can hide in the postprocessor as
+    the 'blanked' cells still show up in the solution. 
+
+.. note:: To only view computed cells, add a filter to your post-processor in a way, that only cells where
+          ``blank`` is bigger than 0 are shown.
+
+And lastly, we plug everything into ``adflow_util``:
+
+.. literalinclude:: ../tutorial/overset/analysis/run_adflow_L3.py
+   :start-after: # rst Run (beg)
+   :end-before: # rst Run (end)
+
+
+Simply Run the Script
+---------------------
+To run the script, proceed as usual:
+::
+
+    $ python run_adflow_L3.py
+
+If you want to run in parallel, start it with mpi
+::
+
+    $ mpirun -np 4 python run_adflow_L3.py
+
+
+Plot the Iterations in realtime
+-------------------------------
+If you want to have a graphical representation of all the ADflow variables, ``adflow_util`` comes in handy aswell.
+It has an additional package called ``adflow_plot``. If you installed it using pip, you can simply start it this way:
+::
+
+    $ adflow_plot -i run_adflow_L3.py
+
+If you want to run in parallel:
+::
+
+    $ adflow_plot -i run_adflow_L3.py -np 4
+
+This is simply an overlay, which starts the adflow script in the background and parses it's ``stdout``. At startup
+you will see the regular adflow-ouput. But as soon as the calculation starts, you'll see a plot of ``resRho``:
+
+.. figure:: images/overset_analysis_adflow_plot.png
+    :width: 600
+    :align: center 
+
+    ``adflow_plot`` output.
+
+At the bottom is a console where you can define which variables you want to see. As terminals usually have a low
+number of 'pixels', it is also possible to show only a limited number of iterations. Simply type ``help`` or ``h`` 
+and hit ``Enter``. You will get a list of all available commands. To quit, simply type ``q`` and confirm with ``y``.
+
+Outputfiles
+-----------
+In addition to the expected volume and surface files from adflow, there will also be a file called ``ONERA_M6_L3.out``.
+It is from ``adflow_util`` and looks like this:
+::
+
+    ONERA_M6_L3
+
+    Aero Options
+    --------------  ---------------------
+    alpha           3.06
+    mach            0.8395
+    reynolds        11720000.0
+    reynoldsLength  0.646
+    T               300
+    xRef            0.0
+    areaRef         0.7575
+    chordRef        0.646
+    evalFuncs       cl, cd, cmy, cdp, cdv
+    --------------  ---------------------
+
+
+    RESULTS 
+            cd         cdp         cdv          cl          cmy    totalRes    iterTot
+    ----------  ----------  ----------  ----------  -----------  ----------  ---------
+    0.01879813  0.01326940  0.00552873  0.26064807  -0.18639411  0.00011945         82
+
+It gives us a nice summary of the input and output values. If we had a sweep variable defined, the multiple
+points would be listed here too.
+
+
+Results
+=======
+
+I ran ADflow with all meshes and plotted the results combined with results from :cite:`nasaM6SA`. As you can see,
+ADflow lies right in the middle:
+
+.. figure:: images/overset_grid_convergence.png
+    :width: 800
+    :align: center 
+
+    Grid Convergence of ADflow in comparision to various other solvers.
+
+
+