VisIt Basics

Setting Up and Running VisIt

VisIt is currently installed on clover and grass. Clover does not have modules installed, so a different setup process is required on each machine.

Clover

Since clover doesn't have the modules program installed on it, you will have to manually add the visit executable's directory to your search path:

1. Go to your home directory and open your .bashrc file.
2. Add the following line to your .bashrc:

   export PATH=/opt/visit2/bin:$PATH
   

3. Close your .bashrc file and enter the command source .bashrc to add the change to your environment.
4. Enter the command visit to start VisIt.

Grass

VisIt is installed as a module on grass, so the setup is much more straightforward. The steps for making it part of your default environment, however, are very similar:

1. Go to your home directory and open your .bashrc file.
2. Add the following line to your .bashrc:

   module load visit
   

3. Close your .bashrc file and enter the command source .bashrc to add the change to your environment.
4. Enter the command visit to start VisIt.

In either case, once you see a screen like the one below, you are ready to go.

Opening Files in Visit

Visit reads HDF5 files and can recognize them from the File open screen, provided they have the .hdf extension. If a collection of .hdf files with the same numbering convention exists in a directory, Visit will group them together and open them as a batch, which makes producing images and animations easier. The process is as follows:

1. Go to the directory containing the files you want to open. This is not strictly necessary, but will make your life easier in the long run.

2. Enter the visit command to start VisIt (see the instructions above to make VisIt part of your environment, if you have not already done so).

3. Click File->Open file... to bring up the File open screen.

3. Enter the directory path of the files in the Path field.

4. The grouped HDF5 files are listed as .hdf databases in the File open window, with the individual files under the group header. Select the group you want and make sure that the "Open as File Type" box is set to "Chombo".

Creating a Pseudocolor Plot

One of the most common and useful plots at our disposal is the pseudocolor plot, which presents the intensity of a scalar attribute as a color spectrum. In two dimensions, this is fairly straightforward; in three dimensions an additional slice operation (see below) is usually required to get any useful information.

To create a pseudocolor plot:

1. Open a Chombo file or group of Chombo files (see above).

2. Under Plots, click Add->Pseudocolor->fieldname.

3. Click the Draw button. This will draw a pseudocolor image in the VisIt window to the right of the control window. For high-resolution images, this may take several minutes.

If the Chombo file is one of a series, you can animate them by clicking the play buttons. You can advance or retreat a single frame by clicking the skip buttons.

3D Plots and the Slice Operator ==

Pseudocolor plots are opaque by default. This means that if you try to create a pseudocolor plot of a 3D dataset, you will get a large colored block. The boundary conditions of the dataset will be visible, but you will probably want to see some of the interior. This is where the slice operator comes in.

The slice operator creates a 2D plot by taking a planar slice of a 3D one. This is especially effective for problems with some kind of axial symmetry, where a cross section of a coordinate plane will give you a pretty good idea of what's going on throughout the simulation.

To obtain a slice of a 3D pseudocolor plot:

1. Create a 3D pseudocolor plot (see "Creating a Pseudocolor Plot" above).

2. Under Plots, select Operators->Slicing-Slice.

Making Movies in Visit

1. Once you have drawn your plot, press the Play button on the main screen. This will give you a preview of your animation.

2. Click File->Save Movie and follow the on-screen instructions. If saving frames as .png files, follow the next step to convert the images into a movie.

3. Type "convert -quality 100 file_name00*.png movie.gif" from the command line within the directory the movie stills are located. This command strings together the .png files into an animated .gif file called "movie.gif". The asterisk indicates "all files that begin with…". message