BDSim is a 2D Brownian dynamics simulation software. Its primary purpose is the numerical analysis of topological defects, providing several programs for simulation, visualization and analysis. This project has been developed during research on topological defects in twodimensional Brownian systems at the physics department of Johannes-Gutenberg Universität Mainz.
A detailed introduction can be found in the wiki.
The following figure illustrates the organization of the software system:
- BDSim is the core component which performs the simulation of a twodimensional system of Brownian particles. It can measure different thermodynamic quantities and system states as well as extract topological defects.
- DTracker generates the trajectories according to the time evolution of the topological defects
- DTAnalyzer creates statistical analyses of the generated trajectories.
- BDRenderer is used to render video files of the simulated systems, visualizing different aspects like trajectories of the defects, the local bond orientational order parameter, the distribution of the topological charges among the system and several other characteristics.
There is also BDumper for converting the binary file formats used by BDSim into text based data.
In order to install BDSim several prerequisites must be met.
The following open source libraries must be installed on your system.
For every program:
For the components:
BDSim
- A modified 2D version of C. Rycroft's Voro++, provided in this repository
- Boost.SIMD by Numscale
DTracker
DTAnalyzer
BDRenderer
If all dependencies are present on your system, every component of the BDSim Software can be built using a C++11 compliant compiler. There is a standard CMake configuration file for each component, a detailed description how to set up such a configuration file is given in the wiki. Assuming that the standard CMake configuration is sufficient, the following steps are to be performed for each of the five folders which contain the corresponding components running:
- Create a build folder for an out-of-place build:
mkdir build - Run cmake from within that folder to generate the standard build files:
cd build && cmake .. - Run the build tool to compile the code:
make - Move the compiled executable , e.g. BDSim, into to top-folder which contains the necessary configuration files in subfolders.
mv BDSim ../
For production runs, call cmake with the -DCMAKE_BUILD_TYPE=Release flag. To speed up the make process, execute it in parallel. Beware that too many parallel builds may exceed your primary memory capacity.
Every program in this software package is a command line interface application which takes several arguments. Some of the programs need supplementary configuration files which must be located in a special subfolder of the one in which the program is run. Most of the programs take an input path and an output path as start-up parameters. Some output needs extra processing which can be done via simple scripts which are given in the supplementary materials folder. The user manual can be found in the wiki.