dibakma/revreaddy

A particle based reaction-diffusion simulation with reversible integration scheme.

revreaddy v0.1

A particle based reaction-diffusion simulation with a reversible integrator, which obeys detailed balance.

This early version features:

• Brownian Dynamics integrator with Metropolis-Hastings correction
• NO reactions (not yet!)
• customizable particle types with different radii and diffusion constants
• two possible repulsion potentials, harmonic repulsion and Lennard-Jones interaction
• geometric building blocks implemented as single particle potentials, currently repulsive plane "wall"
• cubic periodic boundary conditions, can be switched off (not recommended)
• observables which are calculated on the fly and saved to binary (.hdf5/.h5) files or text files (.dat/.txt). These are acceptance, energy, mean-squared-displacement, probability density, radial distribution function, trajectory
• the current state of the simulation can be saved to a compact binary format with a single line and also loaded from file with a single line

revreaddy is mainly a python module which wraps the functionality of an underlying C++ software using cython.

Large parts are still undocumented and unittests are not up-to-date.