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pylj: A teaching tool for classical atomistic simulation

DOI: 10.21105/jose DOI Help

Authors: Andrew R. Mccluskey (University of Bath; Diamond Light Source) , Benjamin J. Morgan (University of Bath) , Karen J. Edler (University of Bath) , Stephen C. Parker (University of Bath)
Co-authored by industrial partner: No

Type: Journal Paper
Journal: Journal Of Open Source Education , VOL 1

State: Published (Approved)
Published: July 2018

Open Access Open Access

Abstract: 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 molecular dynamics or Monte-Carlo methods. A variety of other applications are possible.

Subject Areas: Information and Communication Technology

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