Downloading and running the recipes

Each recipe of the atomistic cookbook can be viewed online as an interactive HTML page, but can also be downloaded as a stand-alone .py script, or a .ipynb Jupyter notebook. To simplify setting up an environment that contains all the dependencies needed for each recipe, each recipe can be downloaded as an archive that contains the script and notebook versions, together with any necessary data file and an environment.yml file that you can use with conda to create a custom environment to run the example. If you have never used conda before, you may want to read this beginners guide.

# Deflate the downloaded archive of the recipe
unzip recipe.zip

# Pick a path where to create the environment and replace
# <recipe-env-path> with it - this creates a local folder
# to avoid cluttering the global conda folder
conda env create --prefix <recipe-env-path> --file environment.yml

Whenever you want to run the recipe you just need to activate the environment and run the recipe file.

The environment.yml contents should also help you set up your own conda or pip environment to run without having to enter the recipe-specific environment.

Given that many recipes contain post-processing and visualizations that are used to render the HTML page of the recipe, you may prefer to run the recipe as a Jupyter notebook. If you want to do so and have not installed the dependencies globally, you will also have to create a kernel that uses the environment. Assuming you have a functioning Jupyter installation globally, you should run

# Activate the environment
conda env activate --name <recipe-env-path>
pip install ipykernel # in case is not part of the environment

# Create the kernel definition
python -m ipykernel install --user --name recipei-env-path --display-name "Python (recipe)"

# You can launch Jupyter from outside the conda environment,
# unless you also need conda-installed executables. When you open
# the notebook, make sure you selected "Python (recipe_env)" as the
# kernel to run it
jupyter lab recipe.ipynb