simcardems 2023.5.5

Simula Cardiac electromechanics solver

Simula Cardiac Electro-Mechanics Solver

simcardems is a FEniCS-based cardiac electro-mechanics solver and is developed as a part of the SimCardio Test project. The solver depends on pulse and cbcbeat.

Installation

See Installation instructions

Getting started

See the demos

Documentation

Documentation is hosted at http://computationalphysiology.github.io/simcardems.

Automated test

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

python3 -m pytest tests -vv

Contributing

See the contributing section

Citing

If you use simcardems in your research, please cite it as follows

@article{Finsberg2023,
  doi = {10.21105/joss.04753},
  url = {https://doi.org/10.21105/joss.04753},
  year = {2023},
  publisher = {The Open Journal},
  volume = {8},
  number = {81},
  pages = {4753},
  author = {Henrik Nicolay Topnes Finsberg and Ilsbeth Gerarda Maria van Herck and Cécile Daversin-Catty and Hermenegild Arevalo and Samuel Wall},
  title = {simcardems: A FEniCS-based cardiac electro-mechanics solver},
  journal = {Journal of Open Source Software}
 }

Known issues

• Issue with h5py, see https://github.com/ComputationalPhysiology/pulse#known-issues

Authors

• Henrik Finsberg ([e-mail])
• Ilsbeth van Herck ([e-mail])
• Cécile Daversin-Catty ([e-mail])