Brownian motion simulator for co-culture systems by Julian Butcher
First, fetch the source files:
git clone git://github.com/dankolbman/brownian.git
cd brownian
The default fortran compiler is set to gfortran. If you are using a different
compiler, change FC= in the Makefile. Compiler flags can be set by editing
FCFLAGS=. Only optimization flags are used by default.
After configuring the Makefile, build the program:
cd src/
make
cd ../
The binary is now in bin/
Run it with bin/brownian from the project directory.
The python scripts in 'scripts/' require python 3 and matplotlib for plotting.
Some python scripts are provided to provide some basic plotting functionality and post-processing.
Useage: python circplot.py sysparam.dat pos1.dat pos2.dat ...
Plot a circular boundary simulation with the given position files.
Useage: python grplot.py sysparam.dat gr1.dat gr2.dat ...
Plot the radial distribution functions.
Many files will be generated in the directory where the executable was run from. Here are some of the data files generated:
- sysparam.dat - The system parameters used for the simulation
- config(1,2)(n).dat - The initial positions for species 1 or 2 for the nth run.
- gr(11,12,22)(n).dat - The radial distribution function for species 1, 2, or 1 and 2 for the nth run.
- fpos(1,2)(n) - The final positions for species 1 or 2 for the nth run.
- fgr(1,2)(n) - The final radial distribution for species 1 or 2 for the nth run
- msd(1,2) - The mean squared displacements for species 1 or 2
- msdave(1,2) - The average mean squared displacements over all iterations for species 1 or 2