Simulating Trapped Ions with (py)LIon

The (py)LIon package was written by Bentine et al. to simulate the classical trajectories of ion ensembles in electrodynamic traps. This package outsources simulations to LAMMPS, an established classical molecular dynamics program. This research project attempts to recreate past experiments in ion trapping by using (py)LIon, as well as to debug the package. (py)LIon demonstrates success in some simulations with linear Paul traps: it accurately predicts the locations of each ion in a trapped ion chain; it accurately predicts the change in temperature of an ion system subjected to Langevin baths of different temperatures and damping times. Laser cooling can be simulated by using an effective damping force, but the (py)LIon package fails to simulate laser cooling experiments due to erroneous coding. After some debugging, laser cooling simulations become consistent with preexisting theory and experiments. With this update, (py)LIon successfully reproduces expected results for experiments involving sympathetic cooling between a Ca$^+$ ion and a NH3$^+$ ion. We hope to use this package in the future to simulate sympathetic cooling between Ytterbium isotopes.