Update visualization.md

Author: sbryngelson

docs/documentation/visualization.md

@@ -1,18 +1,18 @@
 # Flow visualization
 
-Post-processed database in Silo-HDF5 format can be visualized and analyzed using Paraview and VisIt.
+A 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 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.
+Nevertheless, the 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/).
+Further information on Paraview can be found in its [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)
@@ -27,13 +27,13 @@ In Paraview, this coordinate transformation can be accomplished with the followi
 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
+    - Set the calculator `attribute type` to point data
     - Check the box for `Coordinate Results`
-    - Enter the formulat `coordsX*cos(coordsY)*iHat + coordsX*sin(coordsY)*jHat + coordsZ*kHat`
+    - Enter the formula `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.
+For many cases, this step will require resizing the render view window.
 
 ## Visualizing with VisIt
 
@@ -53,9 +53,9 @@ For analysis and processing of the database using VisIt's capability, the user i
 
 ## Serial data output
 
-If `parallel_io = F` then MFC will output the conservative variables to a directory `D/`. 
+If ``parallel_io = 'F'``, MFC will output the conservative variables to a directory `D/`. 
 If multiple cores are used ($\mathtt{ppn > 1}$), then a separate file is created for each core.
-If there is only one coordinate dimension (`n = 0` and `p = 0`), the primitive variables will also be written to `D/`.
+If only one coordinate dimension (`n = 0` and `p = 0`) exists, the primitive variables will also be written to `D/`.
 The file names correspond to the variables associated with each equation solved by MFC.
 They are written at every `t_step_save` time step.
 The conservative variables are
@@ -70,7 +70,7 @@ where $N_c$ are the number of components `num_fluids` and $N_d$ is the number of
 There are exceptions: if `model_eqns = 3`, then the six-equation model appends these variables with the internal energies of each component.
 If there are sub-grid bubbles `bubbles = T`, then the bubble variables are also written. 
 These depend on the bubble dynamics model used.
-If `polytropic = T`, then the conservative variables are appended by 
+If ``polytropic = 'T'``, then the conservative variables are appended by 
 
 $$ n\_b R\_1, n\_b {\\dot R}\_1, \dots, n\_b R\_{N\_b}, n\_b {\\dot R}\_{N\_b} $$
 
@@ -93,11 +93,11 @@ Place the file `paceParview.zip` in your scratch direction on Phoenix and unzip
 Enter the new directory `paceParaview` and run `tar -xvf ParaView-5.11.0-egl-MPI-Linux-Python3.9-x86_64.tar.gz` to decompress the compiled binary.
 Now that you have the binary on Phoenix, you must download Paraview 5.11 on your local machine.
 Paraview binaries can be downloaded [here](https://www.paraview.org/download/).
-Be sure to select `v5.11` from the version drop-down bar and install a `5.11.0` version of Paraview.
+Select `v5.11` from the version drop-down bar and install a `5.11.0` version of Paraview.
 
 ### Step 2: Customizing the script
 
-While all of the options for the bash script could be passed as command-line arguments, hardcoding certain unlikely-to-change options saves time.
+While all of the bash script's options could be passed as command-line arguments, hardcoding certain unlikely-to-change options saves time.
 The following is a list of required and suggested updates to make to `pace-paraview-server`.
 
 - (Optional) Update line 4 to customize the job name that will show up in the scheduler
@@ -111,7 +111,7 @@ Before running `pace-paraview-server` for the first time, you must update its pe
 Once this has been done, you can run `./pace-paraview-server` with the following options:
 
 - `--account` specifies the charge account for the job.
-If you updated line 51 of `pace-paraview-server` to reflect a default account, this option is optional, otherwise it is required.
+If you updated line 51 of `pace-paraview-server` to reflect a default account, this option is optional; otherwise, it is required.
 - `--nodes` specifies the number of nodes to request (default 1)
 - `--mem` specifies the memory per node to request (default is to request all memory)
 - `--gres` specifies the GPU resources to request.
@@ -136,7 +136,7 @@ Below is a slightly altered version of that dialogue:
     * `ssh -L 8722:<nodeIdentifier>:53723 <paceSystemIdentifier>`
 
 2) Once you have `Paraview5.11.0` on your machine, select `File -> Connect..` to open the remote connection dialogue box.
-* If you've already set up the pace connection, simply double-click the existing configuration.
+* Double-click the existing configuration if you've already set up the pace connection.
 * Click `Add Server` If you have not set up the PACE connection.
 This will create a new dialogue box where you can specify a configuration name and set the `Port` to `8722`.
 Once this is done, click `configure` and then `save` on the next dialogue box.