pulse

A software for solving problems in cardiac mechanics. The code in this repository used to be part of pulse-adjoint, but now works as a standalone mechanics solver without the need for dolfin-adjoint.

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

pip install fenics-pulse

or you can install the most recent development version

pip install git+https://github.com/finsberg/pulse.git

Install with conda

You can also install the package using conda

conda install -c finsberg pulse

pulse is also available on conda-forge

conda install -c conda-forge pulse

Docker

It is also possible to use Docker. There is a prebuilt docker image using FEniCS 2017.2, python3.6 and pulse. You can get it by typing

docker pull finsberg/pulse:latest

Requirements

• FEniCS version 2016 or newer

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.

Automated test

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

python -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

pip install h5py --no-binary=h5py