Simulation code, meshes and associated data to reproduce numerical examples presented in "Mechanisms behind perivascular fluid flow", C. Daversin-Catty, V. Vinje, K-A. Mardal, and M.E. Rognes (2020)
The 2D axi and 3D simulations are performed using CFD models based on the FEniCS project.
The corresponding Python scripts can be run within the latest FEniCS Docker container with the last version of Scipy installed :
git clone https://github.com/cdaversin/mechanisms-behind-pvs-flow.git
docker run -it -v $(pwd)/mechanisms-behind-pvs-flow:/home/fenics/shared quay.io/fenicsproject/dev
sudo pip3 install scipy --upgrade
cd shared
The 2D axi model can be configured and run using the script 2Daxi/script_2D.py
cd 2Daxi
python3 script_2D.py
The 3D model can be configured and run using the script 3D/script_C0075.py
cd 3D
python3 script_C0075.py
The graphs presented in the paper can be reproduced using Jupyter notebook, running the corresponding scripts in a Web browser.
cd mechanisms-behind-pvs-flow/notebooks
jupyter-notebook
Note : The data files used in the notebooks are present in the repository by default, and are re-generated when running the models as described in the dedicated section
The generation of the 3D PVS mesh presented in the paper is performed using VMTK
on a clipped geometry from Aneurisk dataset (case id C0075).
The meshes in mechanisms-behind-pvs-flow/3D/C0075_fine to be used in our 3D model are generated using the
dedicated bash script
cd mechanisms-behind-pvs-flow/MeshGeneration
bash generate_meshes.sh
This mesh generation tool requires both VMTK and FEniCS.
Any questions regarding this repository can be posted as Issues.