Supplementary code for the paper: Title of paper

This repository contains supplementary code for the paper

Finsberg, H., Dokken, J. 2022. Title of paper, Journal of ..., volume, page, url

Abstract

Provide the abstract of the paper

Getting started

We provide a pre-build Docker image which can be used to run the the code in this repository. First thing you need to do is in ensure that you have docker installed.

To start an interactive docker container you can execute the following command

docker run --rm -it ghcr.io/scientificcomputing/example-paper-fenics:latest

Data

Data is available in a dropbox folder. Use the script download_data.sh in the data folder to download the data.

The data folder should have the following structure after the data is downloaded.

├── README.md
├── data.tar
├── download_data.sh
└── mesh
    ├── heart01.msh
    └── heart02.msh

These meshes are originally taken from https://ora.ox.ac.uk/objects/uuid:951b086c-c4ba-41ef-b967-c2106d87ee06, but since the original data is about 26GB we decided to make a smaller dataset for this example.

Eventually when you publish a paper you could put this data on e.g Zenodo. That will make sure the data gets it's own DOI.

Scripts

All the scripts are located in the folder called code in the repository. Is is assumed that you run the script from within this folder.

Pre-processing

In order to reproduce the results you need to first run the pre-processing script

python3 pre_processing.py

This will convert the meshes from Gmsh to a dolfin format.

Fiber generation

The next step is to run the fiber generation. You can do this by running the script

python3 run_fiber_generation.py

This will create a new folder code/results containing files called microstructure_<heart_nr>.h5.

Postprocessing

The final step is to postprocess the results by running the script

python3 postprocess.py

This will generate a file for visualizing the fibers in the Paraview (inside code/results called fiber_<heart_nr>.xdmf). This script will also compare some features computed from the fibers with the results published in the (artificial) paper. If the results differ, then the program will raise an error.

Citation

@software{Lisa_My_Research_Software_2017,
  author = {Lisa, Mona and Bot, Hew},
  doi = {10.5281/zenodo.1234},
  month = {12},
  title = {{My Research Software}},
  url = {https://github.com/scientificcomputing/example-paper},
  version = {2.0.4},
  year = {2017}
}

Having issues

If you have any troubles please file and issue in the GitHub repository.

License

MIT