documentation updates

Author: wilfonba

docs/documentation/case.md

@@ -530,7 +530,6 @@ If `file_per_process` is true, then pre_process, simulation, and post_process mu
 
 - `probe_wrt` activates output of state variables at coordinates specified by `probe(i)%[x;y,z]`.
 
-
 ### 8. Acoustic Source {#acoustic-source}
 
 | Parameter                             | Type    | Description |
@@ -756,6 +755,22 @@ $$ a_{x[y,z]} = g_{x[y,z]} + k_{x[y,z]}\sin\left(w_{x[y,z]}t + p_{x[y,z]}\right)
 
 Positive accelerations are in the `x[y,z]` direction are in the positive `x[y,z]` direction by convention.
 
+### 14. Cylindrical Coordinates
+
+When `cyl_coord = 'T'` is set in 3D the following constraints must be met:
+
+- `bc_y%beg = -14` to enable to axis boundary condition
+
+- `bc_z%beg = bc_z%end = -1` to enable periodic boundary conditions in the azimuthal direction
+
+- `z_domain%beg = 0` to set the azithmuthal starting point to 0
+
+- `z_comain%end = 2*math.pi` to set the azithmuthal ending point to $2\pi$ (note, requires `import math` in the case file)
+
+When `cyl_coord = 'T'` is set in 2D the following constraints must be met:
+
+- `bc_y%beg = -2` to enable reflective boundary conditions
+
 ## Enumerations
 
 ### Boundary conditions

docs/documentation/visualization.md

@@ -1,18 +1,49 @@
 # Flow visualization
 
-Post-processed database in Silo-HDF5 format can be visualized and analyzed using VisIt.
-VisIt is an open-source interactive parallel visualization and graphical analysis tool for viewing scientific data.
+Post-processed database in Silo-HDF5 format can be visualized and analyzed using Paraview and VisIt.
+After the post-processing of simulation data (see section [Running](running.md#running-1)), a directory named `silo_hdf5` contains a silo-HDF5 database.
+Here, `silo_hdf5/` includes a directory named `root/` that contains index files for flow field data at each saved time step.
+
+### Visualizing with Paraview
+
+Paraview is an open source interactive parallel visualization and graphical analysis tool for viewing scientific data.
+Paraview 5.11.0 has been confirmed to work with the MFC databases for some parallel environments.
+Nevertheless, installation and configuration of Paraview can be environment-dependent and are left to the user.
+
+The user can launch Paraview and open the index files under `/silo_hdf5/root`.
+Once the database is loaded, flow field variables contained in the database can be added to the render view.
+Further information on using Paraview can be found in the [documentation](https://docs.paraview.org/en/latest/).
+The figure below shows the iso-contour of the liquid void fraction (`alpha`) in the database generated by the example case `3D_sphbubcollapse`.
+
+![](../res/paraview.png)
+
+*Iso-contour of the liquid void fraction (`alpha1`) in the database generated by example case `3D_sphbubcollapse`*
+
+### Visualizing data in cylindrical coordinates
+
+Visualizing data in cylindrical coordinates requires a coordinate transformation of the raw data in the database file.
+In Paraview, this coordinate transformation can be accomplished with the following steps:
+
+1. Apply a `clean to grid` filter to the raw data
+
+2. Apply a `calculator` filter to the cleaned data
+    - Set the calulators `attribute type` to point data
+    - Check the box for `Coordinate Results`
+    - Enter the formulat `coordsX*cos(coordsY)*iHat + coordsX*sin(coordsY)*jHat + coordsZ*kHat`
+    - click apply
+
+These steps will transform the raw data into cylindrical coordinates.
+For many cases, this step will require resizing of the render view window.
+
+## Visualizing with VisIt
+
+VisIt is an alternative open-source interactive parallel visualization and graphical analysis tool for viewing scientific data.
 Versions of VisIt after 2.6.0 have been confirmed to work with the MFC databases for some parallel environments.
 Nevertheless, installation and configuration of VisIt can be environment-dependent and are left to the user.
 Further remarks on parallel flow visualization, analysis, and processing of the MFC database using VisIt can also be found in [Coralic (2015)](references.md#Coralic15) and [Meng (2016)](references.md#Meng16).
 
-## Procedure
-
-After the post-processing of simulation data (see section [Running](running.md#running-1)), a directory named `silo_hdf5` contains a silo-HDF5 database.
-Here, `silo_hdf5/` includes a directory named `root/` that contains index files for flow field data at each saved time step.
 The user can launch VisIt and open the index files under `/silo_hdf5/root`.
 Once the database is loaded, flow field variables contained in the database can be added to the plot.
-
 The figure below shows the iso-contour of the liquid void fraction (`alpha1`) in the database generated by the example case `3D_sphbubcollapse`.
 For analysis and processing of the database using VisIt's capability, the user is encouraged to address [VisIt user manual](https://wci.llnl.gov/simulation/computer-codes/visit/manuals).