Flexodeal Lite

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!

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.
• Clone the repository using your SSH keys: git clone git@github.com:sfu-nml/flexodeal.git. Download the repository as a .zip if you do not want to track your changes or you do not have a GitHub account.
• 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 6 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

Wed May 15 21:37:28 PDT 2024

>> cloc --exclude-dir=2024* --exclude-lang=JSON,XML,make .
    
    18 text files.
    18 unique files.                              
    14 files ignored.

github.com/AlDanial/cloc v 1.74  T=0.05 s (105.1 files/s, 117705.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C++                              1            696           1081           3160
TeX                              1             84             56            255
Visual Basic                     1             35              0            148
Markdown                         1             14              0             33
CMake                            1              6             15             18
-------------------------------------------------------------------------------
SUM:                             5            835           1152           3614
-------------------------------------------------------------------------------