# Running Legolas

Once you cloned the repository and installed both Legolas and the Pylbo framework you are set to run your first problem. As an example here we will run one of the pre-implemented equilibria already present in the source code.

Navigate to a directory of your choosing where you want to place the configuration files and output, and call the setup script:

cd my_favourite_directory
setuplegolas.py


Follow the instructions, this script will do and ask you a couple of things:

1. It copies over a CMakeLists.txt file if not already present
2. Ask if you want to copy over pylbo_wrapper.py, you need this if you want to plot your results immediately after running. Answer yes
3. Ask if you want to copy over a parfile if none was found. Answer no
4. Ask if you want to copy over a default submodule template smod_user_defined.f08 if none was found. Answer no

Since we are running a pre-implemented equilibrium we do not need the smod_user_defined.f08 file, this one is only needed if you want to set up and run your own problem.

Next call the build script:

buildlegolas.sh


If everything went well you should have 5 items in your current working directory: a CMakeLists.txt file, a build folder, an output folder, the file pylbo_wrapper.py and the legolas executable.

It is NOT recommended to create custom build or run directories inside the main legolas folder. Keeping the repository clean ensures that you don’t run into merge conflicts when updating the code. Run the setup scripts in a separate directory and let them take care of linking.

## Creating the configuration file

Configuring Legolas is done through use of a “parfile”, where various options are passed in the form of Fortran namelists. For an overview of different possibilities you can take a look here. During setup we answered “no” when the script asked to copy over the parfile. For now, create a new file called my_setup.par in which you copy the following lines:

&gridlist
gridpoints = 50
/

&equilibriumlist
equilibrium_type = "rayleigh_taylor"
/

&savelist
write_eigenfunctions = .true.
show_results = .true.
/


## Running the code

Finally call legolas and supply the parfile you just created as argument:

./legolas -i my_setup.par


This will run a setup which defines Rayleigh-Taylor instabilities in a Cartesian geometry, the spectrum itself should correspond to case a in Section 13.2, p. 487 of MHD of Laboratory and Astrophysical Plasmas.

When the run is completed (this should take a few seconds) the code will immediately fire up the post-processing framework since we set show_results = .true. in the parfile. A few interactive figures will pop up, including the spectrum. Click on one of the eigenvalues in the figure and press Enter, this will draw the corresponding eigenfunctions. You can cycle through multiple eigenfunctions using the arrow keys, right-clicking a point unselects it and pressing the d key clears all selected points.

The legend shows the various continuum regions, which can also be interactively toggled by clicking on their legend entries. More information on the interface can be found here.

This covers the basics of running Legolas on a single equilibrium. You can take a look at the various pre-implemented equilibria and modify the equilibriumlist or paramlist accordingly to play around with different options.