Installation

To run the FEDM code, it is required to install the Docker. On Ubuntu/Debian Linux systems, this can be done using the official repository in the following way:

sudo apt update
sudo apt-get install \
    apt-transport-https \
    ca-certificates \
    curl \
    gnupg-agent \
    software-properties-common
curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add -
sudo apt-key fingerprint 0EBFCD88
sudo add-apt-repository \
   "deb [arch=amd64] https://download.docker.com/linux/ubuntu \
   $(lsb_release -cs) \
   stable"
sudo apt update
sudo apt-get install docker-ce docker-ce-cli containerd.io

After installing the Docker, the latest stable FEniCS image (FEniCS 2019.1.0) can be run using the following command in the terminal:

sudo docker run -ti \
    -v $(pwd):/home/fenics/shared \
    -v /tmp \
    ghcr.io/scientificcomputing/fenics-gmsh:2024-05-30

Note that repeating above described procedure always creates a new container, which may eventually exhaust the local storage. Therefore, it is suggested to restart the same container using

docker start my_container
docker attach my_container

The following steps will also let you run Docker as a non-root user:

sudo groupadd docker # create docker group if none exists
sudo usermod -aG docker $USER # Add self to docker group
# ... log out and log back in, or call `newgrp docker` ...
docker run -ti \
    -v $(pwd):/home/fenics/shared \
    -v /tmp \
    quay.io/fenicsproject/stable

Here, it is assumed that the FEDM code is located in the subdirectory fedm within the current directory. Now, switch to the shared volume mounted in the container to use FEDM:

cd shared/fedm

Alternatively, it is possible to install FEniCS using Conda

conda create -n fenicsproject -c conda-forge fenics
source activate fenicsproject

or installing it from binary files (availability depends on the Linux distribution).

The code directory has the following structure:

fedm
├── examples
│   ├── glow_discharge
│   ├── streamer_discharge
│   └── time_of_flight
├── fedm
│   ├── file_io.py
│   ├── functions.py
│   ├── __init__.py
│   ├── physical_constants.py
│   ├── __pycache__
│   └── utils.py
├── LICENSE
├── pyproject.toml
├── README.md
├── run_tests.sh
├── setup.cfg
├── setup.py
└── tests
    ├── integrated_tests
    └── unit_tests

FEDM can be installed within the Docker container using:

python3 -m pip install --user .

The directory Examples contains the code for the three case studies described in detail here. One can execute each example by running the following command in the corresponding directory (you may need to use sudo):

python3 fedm-name_of_example.py

or in parallel using MPI:

mpirun –np 8 python3 fedm-name_of_example.py