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A toolbox for object-tracking simulation
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Collision
FDPS
MPI
Sylinder
Trilinos
Util
cmake
.clang-format
.gitignore
CMakeLists.txt
Doxyfile
Gendoc.sh
LICENSE
LinuxSetup.md
MacSetup-deprecated.md
README.md
StepByStep.md
do-cmake.sh

README.md

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SimToolBox

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 and Trilinos. The folder FDPS contains the headers to the Framework for Developing Particle Simulator. The folder Trilinos contains an interface to the huge C++ project for distributed linear algebra and some other useful stuff.

The folder Collision contains the routines for LCP based collision resolution algorithms, supporting both OpenMP and MPI through Trilinos.

The folder 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:

  1. 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.

The folder 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 doc/html/index.html.

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