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simcardems2

Simcardems2 is the next version of Simula Cardiac Electro-Mechanics Solver (simcardems) and a part of the SimCardioTest project. The solver uses pulse and fenics-beat to solve mechanics and electrophysiology, respectively. Both libraries are based on FEniCS.

Install with Docker

Create a directory for simcardems2 on your local computer and clone the github repository:

mkdir simcardems2
cd simcardems2
gh repo clone ComputationalPhysiology/simcardems2

To run simcardems2 in a Docker container, you can use the following pre-built Docker image which includes the FEniCS library:

docker pull ghcr.io/scientificcomputing/fenics-gmsh:2024-05-30

Inside your simcardems2 directory on your local computer, create a Docker container, here called simcardems2, using the Docker image provided above:

docker run --name simcardems2 -v "$(pwd)":/shared -w /shared -it ghcr.io/scientificcomputing/fenics-gmsh:2024-05-30

The option -v mounts the current directory and its files to the new container.

Inside the Docker container, enter the simcardems2 folder and install simcardems2:

cd simcardems2/
python3 -m pip install -e .

Citing

If you use simcardems2, please cite the original version 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}
 }