OpenBDS

Open-source Brownian Dynamics Simulator OBDS.

Implements a Brownian Dynamics Simulator BDS in modern FORTRAN and C. The higher level Object-Oriented Programming OOP code is written in FORTRAN and everything else is written in C.

This is a work in progress, contributions are welcomed.

Motivation

This is a project that I have wanted to develop since I was a student. Back then there was just time to write production-ready code in the least amount of time. The aim was to obtain results quickly even if the code was not clean or even commented so that others could use it for their research.

I am implementing this BDS code from scratch and in an entirely different way from what I have done in the propietary codebases that I have contributed.

My main motivation for doing this is to apply in FORTRAN what I have learned from working with Java, C/C++, and Python.

Compilation

Instructions to compile the source code with GNU Make. Some degree of familiarity with the command line is assumed.

Compilation requirements: GNU Make, GCC 10 (or higher), and a POSIX compliant Operative System OS. The code has been tested in GNU/Linux and Mac OS X. It might be possible to compile the source in Windows under Cygwin but have yet to test it myself.

You can compile the OBDS code by issuing the following commands on the terminal (at the top level of the repository):

make clean && make

It would be a great idea to edit make-inc, the one at the top level of the repository, especially if you want to enable compiler optimizations (for these are turned off by default) or use a different compiler.

The OBDS code has been successfully built with the GNU C and FORTRAN Compilers gcc and gfortran, the LLVM C Compiler clang, and the Intel C and FORTRAN Compilers icc and ifort in both GNU/Linux and Mac OS X.

Set Up the Execution Environment

Create the output directories that the OBDS app expects:

mkdir -p run/bds/data/params

mkdir -p run/bds/data/positions

mkdir -p run/render/frames

Note that these directories must be present in your current working directory.

Executing the OBDS app

To execute the OBDS app issue the following command on the terminal:

./api/clang/src/bds/fortran/OpenBDS.bin

If you prefer to execute the OBDS code from Python change your working directory via

cd api/clang/src/bds/python

and then execute the code with the Python 3 interpreter:

python3 OpenBDS.py

contrary to its FORTRAN counterpart this one prepares the execution environment for you.

Running OBDS tests

Minimal OBDS FORTRAN Test Code can be executed from the top level of the repository:

./api/clang/src/test/particles-sphere/fortran-test-particles-sphere.bin

The test just spawns the particles in the system box, tests the computation of the interparticle forces, the application of the periodic boundaries, among other things. It is not by any means a fully fledged BDS code, in fact, it only executes one step and exits.

OBDS Test Code can be executed from the top level of the repository:

./api/clang/src/test/particles-sphere/test-particles-sphere.bin

This test code can be used to perform Brownian Dynamics Simulations.

Initialization Run Video

Click on the image below to watch the video on youtube.

BDS Run Videos

Links to OBDS runs videos hosted on youtube: