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pylj is an educational software to introduce students to classical atomistic simulation using
a Lennnard-Jones potential model (Jones 1924). pylj is written in Python (using Cython
for pairwise interactions) and uses Jupyter notebooks (Kluyver et al. 2016) and Matplotlib (Hunter 2007) for visualisation (see example below). It can be easily deployed in a
computer laboratory, and students interact with it without needing to use the command
line, as would be the case for other molecular dynamics packages like Gromacs(Berendsen,
Spoel, and Drunen 1995), LAMMPS (Plimpton 1995), or DLPOLY (Smith, Yong, and
Rodger 2002). We provide example notebooks in the repository, showing how to use pylj
to simulate a 2D gas system using either mo
Original languageEnglish
Article number19
JournalThe Journal of Open Source Education
Issue number2
Publication statusPublished - 16 Jul 2018


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