This repository contains basic scripts that allow you to reproduce the mesh as well as the fibers in the cardiac mechanics benchmark in dolfin (legacy).
For the dolfinx implementation of the tools, check here
Docker (Recommended) Run the following command to start a container with all the required dependencies:
docker run --name dolfin-stable -v $(pwd):/home/shared -w /home/shared -ti ghcr.io/scientificcomputing/fenics-gmsh:2023-04-21
In order to enter the shell, use:
docker exec -ti dolfin-stable /bin/bash -l
Note docker image is courtesy of Simula Lab.
If your system has already fenics
version 2019.1.0.post0
, you can install this package typing:
pip3 install .
To have an overview of the options available through this package, execute it your terminal
cardiac-benchmark-toolkit --help
It the installation was succesfull you should be prompted with the following:
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 create-ellipsoid --char-length 0.007
Its command details can be seen with:
cardiac-benchmark-toolkit create-ellipsoid --help
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).
Examples of mesh at two different element sizes can be seen below:
The biventricular domain is provided in the ./data/
including source files in vtk
, pvd
for fine and coarse sizes.
Example of a fine geometry is depicted below:
This repository provides a tagged ellipsoid geometry for reference purposes in the folder ./data/monoventricle_mesh/
.
Using the mesh ./monoventricle_mesh/ellipsoid_0.005.xdmf
, you can create the fibers as follows:
cardiac-benchamrk-toolkit create-fibers-for-ellipsoid-mesh ./monoventricle_mesh/ellipsoid_0.005.xdmf
If succesfull, the script will create fibers in xdmf
and vtk
files in a ./results/
folder.
Further options can be found with:
cardiac-benchmark-toolkit create-fibers-for-ellipsoid-mesh --help
Reference fibers created using the lifex
can be found in the subfolder in ./data/
as fiber_biv.vtk
. This repository includes options to
generate FEniCS-compatible h5
format for fiber directions.
To crate fibers for the fine mesh in P2, run in your shell:
cardiac-benchmark-toolkit create-biv-domain-from-mesh-and-fibers data/biv_mesh_and_fibers_fine_p2/ --element_degree 2
The command line above will create fiber, sheet and sheet-normal directions from the vtk
source files in ./data/biv_mesh_and_fibers_fine_p2
.
Depicted below are fiber (left) and sheet (right) directions created from this procedure.