UnitDirectional Project

This project involves simulations of uniaxial stress fibers in the y-direction, using FEniCS for solving boundary value problems in a 3D mesh. The project is structured to define and solve fiber contraction problems within different material domains, including gel, cytoplasm, and nucleus.

Project Structure

UnitDirectional/

├── 06092019_G1/

├── dolfin/
│ └── python/ │ └── setup.py

├── UnitDir.py

└── README.md

Dependencies

The project uses the following key dependencies:

• FEniCS (for solving PDEs)
• meshio (for mesh file handling)
• mshr (for mesh generation)

Make sure these are installed before running the project. Additionally, you can use the setup.py file in the dolfin/python/ directory to install the required packages for Texar.

Running the Project

1. Ensure all dependencies are installed by running:

pip install -r requirements.txt

2. Run the sumulation:

python UnitDir.py

3. Results will be saved as .pvd files in the result/ directory.

Mesh Files

The folder 06092019_G1/ contains pre-processed mesh files in .xdmf, .h5, and .msh formats. These are used for setting up the simulation in UnitDir.py.

Texar Installation

If you're working with Texar, ensure Python 3.6+ is installed and run the setup.py script in the dolfin/python/ folder.

Contributions

Feel free to contribute by opening an issue or creating a pull request. Make sure to follow the guidelines provided in the Texar repository.