Flexodeal Lite

Check the release notes to learn more about the new features of the latest version!

This is a reduced version of the Flexodeal library which has been structured to follow deal.II tutorial guidelines. It is intended to simulate the deformation of a block of muscle tissue (similar to a biopsy). The stress response has been simplified to include contributions from muscle fibres (Hill-type model) and the base material (hyperelastic, Yeoh).

Check out this cool video of a fully dynamic, fully active, isometric contraction!

This is a library written in C++ meant to be run in Linux and MacOS environments. Windows users can use this library via WSL (Windows Subsystem for Linux). A graphical interface is not yet available.

How to use it?

• Make sure you have properly set up deal.II v9.3 (or newer) and its dependencies. For more information, visit their website.
• Get the latest release here. Alternatively, you can clone the repository for bleeding edge updates: git clone https://github.com/sfu-nml/flexodeal-lite.git.
• Navigate to the Flexodeal folder using cd.
• Call CMake:
  • In release mode: cmake . -DCMAKE_BUILD_TYPE=Release -DDEAL_II_DIR=<path/to/deal.II>.
  • In debug mode: cmake . -DCMAKE_BUILD_TYPE=Debug -DDEAL_II_DIR=<path/to/deal.II>.
• Call make. A simple call to make should suffice.
• Run the code. This either achieved by calling make run or ./dynamic-muscle parameters.prm control_points_strain.dat control_points_activation.dat . A folder with the current timestamp will be created. This is where the results of your execution will be stored.

How long does it take to run?

In an Intel i5-9600K (3.70 GHz x 6) machine the code with its default settings (dynamic) takes about 4 minutes to complete 500 ms of simulation. In turn, the quasi-static code (set Type of simulation = quasi-static) takes only 18 seconds! That speaks volumes about the nonlinearity of the dynamic problem.

Latest line count (in main branch)

Wed 13 Nov 2024 03:21:06 PM PST

>> cloc --exclude-dir=.vscode --exclude-lang=JSON,XML,make .
    
    9 text files.
    9 unique files.                              
    7 files ignored.

github.com/AlDanial/cloc v 1.90  T=0.02 s (198.1 files/s, 340860.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C++                              1            710           1084           3282
Markdown                         1             14              0             34
CMake                            1              6             15             18
-------------------------------------------------------------------------------
SUM:                             3            730           1099           3334
-------------------------------------------------------------------------------