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

Year: 2020

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

Autors Affiliation: Univ Oxford, Dept Phys, Clarendon Lab, Pk Rd, Oxford OX1 3PU, England; Univ Trento, INO CNR BEC Ctr, I-38123 Povo, Italy; Univ Trento, Dipartimento Fis, I-38123 Povo, Italy.

Abstract: 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 gpu package. (C) 2020 Elsevier B.V. All rights reserved.

Journal/Review: COMPUTER PHYSICS COMMUNICATIONS

Volume: 253      Pages from: 107187-1  to: 107187-9

More Information: EB acknowledges support from a Doctoral Training Studentship funded by the EPSRC. The authors thank Tiffany Harte and Michal Hejduk for comments on the manuscript.
KeyWords: LAMMPS; Ion traps; Molecular dynamics
DOI: 10.1016/j.cpc.2020.107187

ImpactFactor: 4.390
Citations: 8
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