A software for solving problems in cardiac mechanics.
pulse is a software based on FEniCS that aims to solve problems in cardiac mechanics (but is easily extended to solve more general problems in continuum mechanics). pulse is a results of the author's PhD thesis, where most of the relevant background for the code can be found.
While FEniCS offers a general framework for solving PDEs, pulse specifically targets problems in continuum mechanics. Therefore, most of the code for applying compatible boundary conditions, formulating the governing equations, choosing appropriate spaces for the solutions and applying iterative strategies etc. are already implemented, so that the user can focus on the actual problem he/she wants to solve rather than implementing all the necessary code for formulating and solving the underlying equations.
pulse can be installed directly from PyPI
python3 -m pip install fenics-pulse
or you can install the most recent development version
python3 -m pip install git+https://github.com/finsberg/pulse.git
You can also install the package using conda
conda install -c conda-forge pulse
It is also possible to use Docker. There is a prebuilt docker image using the development version of FEniCS, python3.10 and pulse. You can get it by typing
docker pull ghcr.io/finsberg/pulse:latest
- FEniCS version 2019.1.0 or newer (older versions might work but is not tested against anymore)
Note that if you install FEniCS using anaconda then you will not get support for parallel HDF5 see e.g this issue.
Check out the demos in the demo folder. These demos are currently in jupyter notebook format.
If you want to run them as python files you can convert the notebooks to .py files using e.g jupytext
If you have a question about how to use the software you can ask a question or start a new discussion in the discussion section
Test are provided in the folder tests. You can run the test
with pytest
python3 -m pytest tests -vv
Documentation can be found at finsberg.github.io/pulse
You can create documentation yourselves by typing make html in the
root directory.
If you use pulse in your own research, please cite the JOSS paper
@article{pulse,
doi = {10.21105/joss.01539},
url = {https://doi.org/10.21105/joss.01539},
year = {2019},
month = {sept},
publisher = {The Open Journal},
volume = {4},
number = {41},
pages = {1539},
author = {Henrik Finsberg},
title = {pulse: A python package based on FEniCS for solving problems in cardiac mechanics},
journal = {The Journal of Open Source Software}
}
- If you encounter errors with
h5pytry to uninstall it (pip uninstall h5py) and then re-install it without installing any binary packages, i.e
python3 -m pip install h5py --no-binary=h5py
See CONTRIBUTING.md