QuaLiKiz-pythontools has moved to GitLab: https://gitlab.com/qualikiz-group/QuaLiKiz-pythontools

QuaLiKiz-pythontools

A collection of tools for QuaLiKiz in Python.

Purpose

This is a collection of Python modules to be used for working with QuaLiKiz, a quasi-linear gyrokinetic code. QuaLiKiz can be found on GitHub. This repository contains the source for the Python package qualikiz_tools. Use the qualikiz_tools CLI (Command Line Interface) to generate, run and analyze QuaLiKiz runs. For more advanced usage scenarios the modules themselves can be used in other python scripts. For example, the QuaLiKiz Neural Network training set was generated in this way.

Install

The recommended way to install qualikiz_tools is to use pip. Although installation is not strictly necessary to use the python modules, it is advised to install anyway for the full power of the CLI.

1. Clone the repository from GitHub.

   • If you want to install as submodule of QuaLiKiz (preferred)

       git clone [email protected]:QuaLiKiz-group/QuaLiKiz.git
     

     and then

     git submodule init
     git submodule update
     

   • If you want to install standalone, clone using (not recommended)

       git clone [email protected]:QuaLiKiz-group/QuaLiKiz-pythontools.git
     

2. (Recommended) Install xarray dependencies

    apt-get install netcdf-dev hdf5
    pip install netcdf4
   

3. Install qualikiz_tools. This fully installs it in developer mode

    pip install -e .[test]
   

Usage

Examples scripts can be found in qualikiz_tools/examples. A workflow example is given below:

1. Generate a template QuaLiKiz run directory using the CLI

    qualikiz_tools create example
    cd runs/example
   

2. Adjust the parameters.json to your liking (optional)

3. Generate the input binaries using the CLI

    qualikiz_tools input generate .
   

4. Submit the job. We assume the machine specific files exist. Use 'bash' if they do not, which assumes you can run an mpi program using mpirun

    qualikiz_tools launcher launch bash .
   

5. After the job is done, convert the output to netCDF.

    qualikiz_tools output to_netcdf .
   

6. Plot your netCDF file, for example:

    qualikiz_tools plot --flux ef .
   

FAQ

• How do I run the unit tests?

    python setup.py test
  

• How do I find out what each CLI command does?

    qualikiz_tools help
    qualikiz_tools <command> help