pylj

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

Installation

pip install --pre pylj

pylj 2.0 is a beta release, so pip needs --pre to install it. Without --pre, pip installs the previous release, 1.5.2.

pylj needs Python 3.12 or later.

Contents

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

• Building a simulation: initialise, the starting lattices, and the configuration.

• Running a simulation: molecular dynamics, Monte Carlo, restarting, and how long a run takes.

• Samples and the trajectory: what sample() records, and g(r), S(q) and the mean squared displacement.

• Pictures and animations: view() and animate().

• Custom potentials: the PairPotential interface and mixtures.

• Units: the units pylj takes and reports, and its constants.

• 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.