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

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. Program summary Program Title: (py)LIon Program Files doi: http://dx.doi.org/10.17632/ywwd9nnxjh.1 Licensing 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.