mdolab · ewu63 · Mar 22, 2021 · Nov 25, 2020 · Nov 25, 2020 · Nov 26, 2020
diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,5 @@
 _build
 .DS_Store
 *.cgns
+.vscode/*
+make.bat
diff --git a/machAeroTutorials/images/cubeplot.jpg b/machAeroTutorials/images/cubeplot.jpg
diff --git a/machAeroTutorials/images/overset_IHC.png b/machAeroTutorials/images/overset_IHC.png
diff --git a/machAeroTutorials/images/overset_Overview.jpg b/machAeroTutorials/images/overset_Overview.jpg
diff --git a/machAeroTutorials/images/overset_analysis_adflow_plot.png b/machAeroTutorials/images/overset_analysis_adflow_plot.png
diff --git a/machAeroTutorials/images/overset_bad_IHC.png b/machAeroTutorials/images/overset_bad_IHC.png
diff --git a/machAeroTutorials/images/overset_grid_convergence.png b/machAeroTutorials/images/overset_grid_convergence.png
diff --git a/machAeroTutorials/images/overset_guide_10.jpg b/machAeroTutorials/images/overset_guide_10.jpg
diff --git a/machAeroTutorials/images/overset_guide_11.jpg b/machAeroTutorials/images/overset_guide_11.jpg
diff --git a/machAeroTutorials/images/overset_guide_14.jpg b/machAeroTutorials/images/overset_guide_14.jpg
diff --git a/machAeroTutorials/images/overset_guide_15.jpg b/machAeroTutorials/images/overset_guide_15.jpg
diff --git a/machAeroTutorials/images/overset_guide_3.jpg b/machAeroTutorials/images/overset_guide_3.jpg
diff --git a/machAeroTutorials/images/overset_guide_4.jpg b/machAeroTutorials/images/overset_guide_4.jpg
diff --git a/machAeroTutorials/images/overset_guide_8.jpg b/machAeroTutorials/images/overset_guide_8.jpg
diff --git a/machAeroTutorials/images/overset_m6_mesh_fields.png b/machAeroTutorials/images/overset_m6_mesh_fields.png
diff --git a/machAeroTutorials/images/overset_orphan_debug.png b/machAeroTutorials/images/overset_orphan_debug.png
diff --git a/machAeroTutorials/images/overset_pointwise_after_import.png b/machAeroTutorials/images/overset_pointwise_after_import.png
diff --git a/machAeroTutorials/images/overset_pointwise_cut_database.png b/machAeroTutorials/images/overset_pointwise_cut_database.png
diff --git a/machAeroTutorials/images/overset_pointwise_dat1.png b/machAeroTutorials/images/overset_pointwise_dat1.png
diff --git a/machAeroTutorials/images/overset_pointwise_del_root.png b/machAeroTutorials/images/overset_pointwise_del_root.png
diff --git a/machAeroTutorials/images/overset_pointwise_export_near_tip.png b/machAeroTutorials/images/overset_pointwise_export_near_tip.png
diff --git a/machAeroTutorials/images/overset_pointwise_near_close_TE.png b/machAeroTutorials/images/overset_pointwise_near_close_TE.png
diff --git a/machAeroTutorials/images/overset_pointwise_near_del_break_points.png b/machAeroTutorials/images/overset_pointwise_near_del_break_points.png
diff --git a/machAeroTutorials/images/overset_pointwise_near_dimension_LETE.png b/machAeroTutorials/images/overset_pointwise_near_dimension_LETE.png
diff --git a/machAeroTutorials/images/overset_pointwise_near_init.png b/machAeroTutorials/images/overset_pointwise_near_init.png
diff --git a/machAeroTutorials/images/overset_pointwise_near_layer.png b/machAeroTutorials/images/overset_pointwise_near_layer.png
diff --git a/machAeroTutorials/images/overset_pointwise_near_spacing.png b/machAeroTutorials/images/overset_pointwise_near_spacing.png
diff --git a/machAeroTutorials/images/overset_pointwise_near_wing1.png b/machAeroTutorials/images/overset_pointwise_near_wing1.png
diff --git a/machAeroTutorials/images/overset_pointwise_orient_near_tip.png b/machAeroTutorials/images/overset_pointwise_orient_near_tip.png
diff --git a/machAeroTutorials/images/overset_pointwise_overview.png b/machAeroTutorials/images/overset_pointwise_overview.png
diff --git a/machAeroTutorials/images/overset_pointwise_tip_clean_LE_tip.png b/machAeroTutorials/images/overset_pointwise_tip_clean_LE_tip.png
diff --git a/machAeroTutorials/images/overset_pointwise_tip_clean_root.png b/machAeroTutorials/images/overset_pointwise_tip_clean_root.png
diff --git a/machAeroTutorials/images/overset_pointwise_tip_clean_tip.png b/machAeroTutorials/images/overset_pointwise_tip_clean_tip.png
diff --git a/machAeroTutorials/images/overset_pointwise_tip_examine.png b/machAeroTutorials/images/overset_pointwise_tip_examine.png
diff --git a/machAeroTutorials/images/overset_pointwise_tip_mesh_LE_tip.png b/machAeroTutorials/images/overset_pointwise_tip_mesh_LE_tip.png
diff --git a/machAeroTutorials/images/overset_pointwise_tip_project.png b/machAeroTutorials/images/overset_pointwise_tip_project.png
diff --git a/machAeroTutorials/images/overset_pointwise_tip_semi-circle.png b/machAeroTutorials/images/overset_pointwise_tip_semi-circle.png
diff --git a/machAeroTutorials/images/overset_pointwise_tip_solve.png b/machAeroTutorials/images/overset_pointwise_tip_solve.png
diff --git a/machAeroTutorials/images/overset_pointwise_tip_spacing.png b/machAeroTutorials/images/overset_pointwise_tip_spacing.png
diff --git a/machAeroTutorials/images/overset_pointwise_tip_split_le_con.png b/machAeroTutorials/images/overset_pointwise_tip_split_le_con.png
diff --git a/machAeroTutorials/images/overset_tip1.png b/machAeroTutorials/images/overset_tip1.png
diff --git a/machAeroTutorials/images/overset_tip2.png b/machAeroTutorials/images/overset_tip2.png
diff --git a/machAeroTutorials/images/overset_view-of-ONERA.jpg b/machAeroTutorials/images/overset_view-of-ONERA.jpg
diff --git a/machAeroTutorials/images/overset_vsp_add_wing.png b/machAeroTutorials/images/overset_vsp_add_wing.png
diff --git a/machAeroTutorials/images/overset_vsp_change_airfoil.png b/machAeroTutorials/images/overset_vsp_change_airfoil.png
diff --git a/machAeroTutorials/images/overset_vsp_export.png b/machAeroTutorials/images/overset_vsp_export.png
diff --git a/machAeroTutorials/images/overset_vsp_half_wing.png b/machAeroTutorials/images/overset_vsp_half_wing.png
diff --git a/machAeroTutorials/images/overset_vsp_overview.png b/machAeroTutorials/images/overset_vsp_overview.png
diff --git a/machAeroTutorials/images/overset_vsp_round_tip.png b/machAeroTutorials/images/overset_vsp_round_tip.png
diff --git a/machAeroTutorials/images/overset_vsp_wing_geo.png b/machAeroTutorials/images/overset_vsp_wing_geo.png
diff --git a/machAeroTutorials/images/overset_zipper.jpg b/machAeroTutorials/images/overset_zipper.jpg
diff --git a/machAeroTutorials/index.rst b/machAeroTutorials/index.rst
@@ -8,3 +8,4 @@
    aero_overview
    opt_overview
    airfoilopt_overview
+   overset_overview
diff --git a/machAeroTutorials/ney_overset_tips.txt b/machAeroTutorials/ney_overset_tips.txt
@@ -0,0 +1,117 @@
+Overset Tips
+============
+--------------------------------------------------------------------------------
+General
+--------------------------------------------------------------------------------
+    - all meshes should have same off-wall spacing
+    - intersecting meshes must have mating surfaces (no actual intersections)
+    - once you have a valid hole-cutting, decrease the 'nearwalldist' to the
+        minimum possible value
+    - each compute cell must have at least two donor cells in each orthogonal
+        direction and one cell in each diagonal direction otherwise, it will be
+        flagged as an orphan (see ASCII art below)
+
+                |---|---|---|---|---|   The compute cell in the center would
+                | B | B | D | B | B |   not be flagged as an orphan as long
+                |---|---|---|---|---|   as it maintains the stencil of donor
+                | B | D | D | D | B |   cells (marked with D) in 3D.
+                |---|---|---|---|---|
+                | D | D | C | D | D |   Key:
+                |---|---|---|---|---|       D (donor) - compute or interpolate
+                | B | D | D | D | B |       B (blanked) - blanked, flooded,
+                |---|---|---|---|---|           flood seed or explicitly blanked
+                | B | B | D | B | B |
+                |---|---|---|---|---|
+--------------------------------------------------------------------------------
+Collar meshes
+--------------------------------------------------------------------------------
+    - must be much finer mesh in comparison to overlapping meshes
+
+--------------------------------------------------------------------------------
+How Implicit Hole Cutting Works
+--------------------------------------------------------------------------------
+1) Determine Overlap of N Blocks
+    Create an N x N matrix that tells, for a given block, which other blocks
+    overlap it.
+
+*) Designate Flood Seeds
+    Any cell farther than 'nearwalldist' from a wall in its own block that
+    intersects a wall on another block will be flagged as a flood seed.
+
+m) Flooding
+    In a given block, any compute cells that interface with a flood seed or a
+    flooded cell are converted to flooded cells. The flood is only contained
+    by interpolate cells.
+
+n) Fringe Reduction
+    After the iterative portion of the algorithm is over, excess fringe cells
+    are converted to blanked cells if they do not influence any compute cells.
+
+iBlank Values
+ 1 : Compute
+ 0 : Blanked
+-1 : Fringe (interpolate)
+-2 : Flooded
+-3 : Flood seed
+-4 : Explicitly blanked (cutCallBack)
+
+--------------------------------------------------------------------------------
+Adjusting Implicit Hole Cutting Process
+--------------------------------------------------------------------------------
+There are two related flags in pyADflow to help with this:
+
+    'usezippermesh': False (default=True)
+        Sometimes if your mesh is flooding out, the zipper mesh will fail and
+        the mesh will not be written to file. This is basically impossible to
+        troubleshoot. This can be avoided by setting 'usezippermesh' to False.
+
+    'nrefine': 1 (default=10)
+        You can choose how many cycles to run the hole cutting algorithm. In
+        flood-out cases, you may want to stop after 1 cycle to see where a leak
+        is occurring.
+
+Within each hole cutting cycle, there is a flooding procedure which generally
+takes at least two iterations. If the mesh is flooding out, you can go into the
+Fortran code to limit the number of iterations in this cycle so that you can
+tell where the leak starts.
+
+    > Open adflow/src/overset/floodInteriorCells.F90
+
+    > Insert an additional if statement in the code after line 231.
+
+        231      loopIter = loopIter + 1
+        232
+        233      ! Choose number of flood cycles
+        234      if (loopIter == 2) then
+        235         exit parallelSyncLoop
+        236      end if
+        237
+        238   end do parallelSyncLoop
+
+    > Using 'loopIter == 2' will stop the cycle after one Flood Iteration.
+
+    > Don't forget to recompile the code. (make in hg/adflow)
+
+--------------------------------------------------------------------------------
+Viewing iBlanks in Tecplot
+--------------------------------------------------------------------------------
+1. One Tecplot zone per CGNS/zone solution
+2. Check "Load Cell-centered Directly" (default)
+3. Change Surfaces to "Exposed cell faces"
+4. Change Contour Type to "Primary value flood"
+5. Contour Levels
+    - Minimum = -3
+    - Maximum = 0
+    - N levels = 4
+6. Blanking
+
+--------------------------------------------------------------------------------
+Generating grid families for a grid convergence study
+--------------------------------------------------------------------------------
+Say we have a base grid with level = j.
+Another grid with level "i" should be generated such that:
+    - Number of cells: Ni = Nj / (2**dim)**(i-j)
+    - Number of nodes on an edge: add one to # of cells
+    - Growth ratio: ri = rj**(i+1-j)
+
+For more information, see https://www.grc.nasa.gov/www/wind/valid/tutorial/spatconv.html
diff --git a/machAeroTutorials/overset.bib b/machAeroTutorials/overset.bib
@@ -0,0 +1,19 @@
+ @misc{nasaM6sim,
+    title={{3D} {ONERA} {M6} {W}ing Validation for Turbulence Model Numerical Analysis},
+    url={https://turbmodels.larc.nasa.gov/onerawingnumerics_val.html},
+    journal={NASA},
+    publisher={NASA}
+}
+
+@misc{nasaM6real,
+    title={{ONERA} {M6} {W}ing},
+    url={https://www.grc.nasa.gov/WWW/wind/valid/m6wing/m6wing.html},
+    journal={NASA},
+    publisher={NASA}
+}
+
+@misc{nasaM6SA,
+	title = {{3D} {ONERA} {M6} {W}ing Validation for Turbulence Model Numerical Analysis - {SA}-neg Model Results},
+	url = {https://turbmodels.larc.nasa.gov/onerawingnumerics_val_sa.html},
+	urldate = {2020-12-11},
+}
diff --git a/machAeroTutorials/overset_analysis.rst b/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 |
++--------------------+---------+
+| Reynolds Ref Length| 0.646m  |
++--------------------+---------+
+| Temperature        | 300° K  |
++--------------------+---------+
+
+There is 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``. This utility will be used here, but the regular python API,
+that is detailed in other tutorials, would work as well.
+
+For simplicity, only the calculation on the ``L3`` mesh is covered. The other meshes might require slightly different ADflow options.
+
+
+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 mesh file:
+::
+
+    $ 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)
+
+Some things to note:
+
+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 as well.
+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``.
+
+Output files
+------------
+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
+=======
+
+For validation purposes, ADflow was run with all meshes and the results were plotted against various different solvers 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 comparison to various other solvers.
+
+
+