pulse

A software for solving problems in cardiac mechanics.

Overview

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.

Installation instructions

Install with pip

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

Install with conda

You can also install the package using conda

conda install -c conda-forge pulse

Docker

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

Requirements

• 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.

Getting started

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

Automated test

Test are provided in the folder tests. You can run the test with pytest

python3 -m pytest tests -vv

Documentation

Documentation can be found at finsberg.github.io/pulse You can create documentation yourselves by typing make html in the root directory.

Citing

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}
}

Known issues

• If you encounter errors with h5py try 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

Contributing

See CONTRIBUTING.md