A toolbox for object-tracking simulation. This toolbox contains a collection of useful tools for different tasks involved in a particle-tracking type simulation.
At the base level the code relies on
FDPS contains the headers to the Framework for Developing Particle Simulator.
Trilinos contains an interface to the huge C++ project for distributed linear algebra and some other useful stuff.
Collision contains the routines for LCP based collision resolution algorithms, supporting both OpenMP and MPI through
Sylinder contains a parallel
SylinderSystem class for simulating rigid spherocylinders with overdamped dynamics. A geometric constraint optimization method is implemented to resolve collisions. Parallel IO is also supported for each geometric primitive through the XML-based vtk routines. This code is used in my publications:
- Yan, Wen, Huan Zhang, and Michael J. Shelley. 2019. “Computing Collision Stress in Assemblies of Active Spherocylinders: Applications of a Fast and Generic Geometric Method.” The Journal of Chemical Physics 150(6): 064109.
Util contains some utilities to facilitate the application, including an interface to linear algebra
Eigen, a parallel RNG interface to
TRNG, a command line parser
cmdparser (https://github.com/FlorianRappl/CmdParser), a timer.
New functions will be continuously added to this toolbox to facilitate quick development of HPC simulation code.
Run the script
Gendoc.sh to generate html document with doxygen in