pylj

pylj runs molecular dynamics and Metropolis Monte Carlo simulations of atoms interacting through pair potentials, in two dimensions, and draws them as they run. It is a teaching code, written in Python and NumPy.

Installation

pip install pylj

pylj needs Python 3.11 or later. To watch the figures redraw you need a Jupyter notebook; start each notebook with %matplotlib inline. In a script, a viewer’s fig is a matplotlib figure that can be saved.

Contents

• Getting started: a model, a molecular dynamics run and a Monte Carlo run.

• Simulations: building a simulation, the configuration, the two step() methods, sampling and restarting.

• Custom potentials: the PairPotential interface and mixtures.

• Viewers and panes: the viewers, and writing a pane.

• Modules: every class, function and argument, with units.

• Changelog.

Citing pylj

McCluskey, A. R., Morgan, B. J., Edler, K. J., and Parker, S. C. (2018). pylj: A teaching tool for classical atomistic simulation. Journal of Open Source Education, 1(2), 19. https://doi.org/10.21105/jose.00019

pylj.__cite__() opens the paper in a browser. Development is on GitHub.