A 3D vertex model code
Author:
Tao Zhang @ Shanghai Jiao Tong University, zhangtao.scholar@sjtu.edu.cn
Jennifer Schwarz @ Syracuse University, jschwarz@physics.syr.edu
This code is based on Okuda 2013 paper: https://link.springer.com/article/10.1007/s10237-012-0430-7.
- The network topology satisfies the following conditions:
- Two edges never share two vertices simultaneously.
- Two polygonal faces never share two or more edges simultaneously.
- EXTRA RULE Two polyhedral cells never share two or more polygonal faces simultaneously
The scripts are in the folder "scripts" on the main branch.
Current version of the code works ONLY for bulk system with periodic boundary condition.
Should you receive any warning prompts, please reach out to us as we work towards making the code more robust for more general geometries, deformations, and energy functionals.
mkdir build
cd build
cmake ../
makeAssuming the working directory is build, first create a configuration file conf
touch conf
vim confThe conf file defines values of simulation parameters. See an example as below:
time -10000.0 1000000.0 0.005
dump vtk 500.0
log 50.0
s0 5.60
Lth 0.02
T 1.0e-04
kv 10.
box 8. 8. 8. p p p
Here time specifies start time, end time, timestep;
dump specifies the dumped file format (the .vtk file format is for visualization using paraview), the dumping time period;
log specifies the time period logging simulation information to screen;
s0 specifies the target cell area;
Lth specifies the threshold edge length to trigger reconnection;
T specifies the temperature;
kv specifies the strength of the volume elasticity;
box specifies the simulation box sizes and boundary conditions.
Use python script scripts/tvm/main.py to generate the initial configuration file sample.topo,
which contains the information of vertices' coordinates and the system topology. Please install pyvoro in advance.
pip install pyvoro-mmalahe
python ../scripts/tvm/main.pyRun tvm
./tvmCopyright 2021-2023 Tao Zhang