Installation

Prerequisit packages

Since this code uses the MELTS code as provided by the Thermoengine package, this needs to be installed before LavAtmos may be used. We suggest to follow the instructions on the Thermoengine GitLab page on how to run a container image locally. Note: This involves installing Docker onto your system.

Cloning the repository

Once you have installed Thermoengine, clone the LavAtmos repository into the Thermoengine directory using:

git clone https://github.com/cvbuchem/LavAtmos

If you do not have GitHub installed you can also download a zip file containing the code by going to the Github page, clicking on the green “Code” button and then clicking “Download ZIP”.

Running LavAtmos using Singularity

If you are for some reason unable to install docker (you may not have root access to your system for example) it is also possible to run the Thermoengine docker image using Singularity. You can check if the application is already installed by typing:

singularity --help

If not, follow the instructions on their Read the Docs page.

You can then pull the Thermoengine docker as follows:

singularity pull docker://registry.gitlab.com/enki-portal/thermoengine:master

Note

If you get the following error:

FATAL:   While making image from oci registry: error fetching image to cache: while building SIF from layers: unable to create new build: while searching for mksquashfs: exec: "mksquashfs": executable file not found in $PATH

A potential fix is to enter the following bash commands into your terminal:

export PATH="/usr/sbin:$PATH"

This will create a .sif file which allow you to shell into the Thermoengine docker image (see the Singularity documentation for more information). In order to run LavAtmos, clone the repository using the instrunctions given above:. You can then use the following commands to run an example script:

singularity shell thermoengine_master.sif
cd '/path/to/LavAtmos'
python3 scripts/run_lavatmos_example2.py

You may then alter the example script to suit your needs.