diff --git a/docs/documentation/visualization.md b/docs/documentation/visualization.md index 0dd1f295ae..644a53c707 100644 --- a/docs/documentation/visualization.md +++ b/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::53723 ` 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.