https://github.com/computationalphysiology/simcardems2

https://github.com/computationalphysiology/simcardems2

Last synced: 7 days ago
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• Host: GitHub
• URL: https://github.com/computationalphysiology/simcardems2
• Owner: ComputationalPhysiology
• License: mit
• Created: 2024-05-21T14:06:20.000Z (9 months ago)
• Default Branch: main
• Last Pushed: 2024-10-17T17:16:57.000Z (4 months ago)
• Last Synced: 2024-10-18T00:34:57.262Z (4 months ago)
• Language: Python
• Size: 150 KB
• Stars: 0
• Watchers: 3
• Forks: 0
• Open Issues: 6
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# simcardems2

Simcardems2 is the next version of [Simula Cardiac Electro-Mechanics Solver (simcardems)](https://github.com/ComputationalPhysiology/simcardems) and a part of the [SimCardioTest](https://www.simcardiotest.eu/wordpress/) project. The solver uses [pulse](https://github.com/finsberg/pulse) and [fenics-beat](https://github.com/finsberg/fenics-beat) to solve mechanics and electrophysiology, respectively. Both libraries are based on [FEniCS](https://fenicsproject.org/).

## Install with Docker

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

```shell

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](https://github.com/scientificcomputing/packages/pkgs/container/fenics-gmsh) which includes the FEniCS library:

```shell

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:

```shell

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`:

```shell

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}

 }

```