Cardiac Benchmark Toolkit

This repository contains minimal set of scripts that allow you to reproduce the mesh as well as the fibers in the cardiac mechanics benchmark using dolfinx.

Installation

This library requires FEniCS already installed in your system.

Using Pip

Execute the following command in your local session, it will install the required dependencies:

pip3 install .

Using Docker

Docker (Recommended) Download docker. Run the following command to start a container with dolfinx preinstalled:

docker run --name dolfinx-stable -v $(pwd):/home/shared -w /home/shared -ti ghcr.io/fenics/dolfinx/dolfinx:nightly

In order to enter the shell, use:

docker exec -ti dolfin-stable /bin/bash -l

You can also use a image provided in folder docker.

Quickstart

Mesh Generation

Preliminaries

The mesh creation relies on h5py and meshio. Install them by executing the folling command:

pip3 install --no-binary=h5py h5py meshio

Generating mesh

The ellipsoid domain can be created with a characteristic element size (default is 0.005 [m]) using the script mesh_generation.py. It will create a folder structure ./results to stores xdmf as well as pvd formats for further usage.

To execute it, consider the following command:

cardiac_benchmark_toolkit/mesh_generation.py -size 0.007

It will create an ellipsoid mesh with characteristic element size of 0.007 [m]. You can use it in conjuntion with the ellipsoid_fiber_generation to create the fiber directions for your specific simulation (and benchmark).

Example cases at different element sizes can be seen below:

Fiber Generation

Preliminaries

Saving binary solutions require PetscBinaryIO, the module can be loaded using:

export PYTHONPATH=$PYTHONPATH:/usr/local/petsc/lib/petsc/bin/

if PETSc was installed in /usr/local/ (e.g. in the case of the docker image).

Generating fibers

This repository provides an ellispoid tagged mesh for reference purposes in the folder ./meshes. Use the mesh ./meshes/ellipsoid_0.005.xdmf, you can create the fibers as follows:

python3 cardiac_benchmark_toolkitx/fiber_generation.py ./meshes/ellipsoid_0.005.xdmf

If succesfull, the script will create fibers in xdmf, vtk and PETSc binaries files in a ./results/ folder.

Further options can be found with:

python3 cardiac_benchmark_toolkitx/fiber_generation.py --help