Rheology of Vertex Model (RheoVM)

Requirements

• Linux or OS X (code compiles on Windows 10/11 systems using WSL 2)
• A modern C++ compiler supporting C++11/14 standards
• CMake
• Boost libraries (algorithm, lexical cast, property tree)
• VTK library (version 7 or newer) - it is recommended to compile it from source
• Python 3.5 or newer
• Eigen library (version 3) - eigen.tuxfamily.org
• pybind11 - CMake will automatically download it

Compiling the code

• Create a build directory in the source tree
• From the build directory run cmake .. (ccmake .. for GUI) and set all necessary paths
• Run make

Running the code

• Once compiled, you will find a file called rheovm.so in the build directory.
• Make sure that you PYTHONPATH environment variable points to the build directory or move the rheovm.so file somewhere where Python can find it
• in the directory makeconf you will find tools that create the initial configurations
• in the directory runscripts you will find several examples of Python scripts used to run simulations
• in the directory analysis you will find examples of MATLAB scripts used to analyse results.

Contributors

• Rastko Sknepnek (University of Dundee) - RheoVM code and initial configuration builders
• Sijie Tong (Princeton University) - runs and analysis code