(py)LIon: A package for simulating trapped ion trajectories

Journal article

The (py)LIon package is a set of tools to simulate the classical trajectories of ensembles of ions in electrodynamic traps. Molecular dynamics simulations are performed using LAMMPS, an efficient and feature-rich program. (py)LIon has been validated by comparison with the analytic theory describing ion trap dynamics. Notable features include GPU-accelerated force calculations, and treating collections of ions as rigid bodies to enable investigations of the rotational dynamics of large, mesoscopic charged particles.

Programme summary

Program Title: (py)LIon

Program Files doi: http://dx.doi.org/10.17632/ywwd9nnxjh.1

Licencing provisions: MIT

Programming language: Matlab, Python

Subprograms used: LAMMPS

Nature of problem: Simulating the dynamics of ions and mesoscopic charged particles confined in an electrodynamic trap using molecular dynamics methods

Solution method: Provide a tested, feature-rich API to configure molecular dynamics calculations in LAMMPS

Unusual features: (py)LIon can treat collections of ions as rigid bodies to simulate larger objects confined in electrodynamic traps. GPU acceleration is provided through the LAMMPS package.

Authors: Bentine, E; Foot, CJ; Trypogeorgos, D

• Publication status: Published
• Peer review status: Peer reviewed
• Publisher: Elsevier
• Journal: Computer Physics Communications
• Volume: 253
• Article number: 107187
• Publication date: 2020-01-27
• Acceptance date: 2020-01-13
• DOI: 10.1016/j.cpc.2020.107187
• ISSN: 0010-4655
• Language: English
• Keywords: LAMMPS; FFR; molecular dynamics; ion traps