Date of Award

August 2021

Document Type


Degree Name

Doctor of Philosophy (PhD)


Physics and Astronomy

Committee Member

Chad E Sosolik

Committee Member

Domnita C Marinescu

Committee Member

Joan P Marler

Committee Member

Jian He


Molecular dynamics simulations are a powerful tool for modelling and predicting various material and surface properties. The main drawback, however, is time-scaling as systems under consideration get larger, either requiring significant computational resources or reducing the statistical significance of produced results. Here I present a molecular dynamics package, SAFARI, which is specifically optimised for low and hyperthermal energies and produces a statistically significant number of trajectories to assist in the analysis of ion-surface scattering spectra.

SAFARI is optimised for low and hyperthermal energies, where the sequential binary collision approximation (SBCA) does not produce precise results. The original version of SAFARI was also very heavily optimised under the assumptions that the surfaces in study could be rectilinearly tiled perpendicular to the surface, and that the repeating distance of such tiling was on the order of a few angstroms. This resulted in the simulation being unusable for surfaces such as (111) faces which exhibit hexagonal symmetries. The rewrite and further improvements to SAFARI to account for these limitations is the topic of this dissertation.

The primary focus of the re-implementation was to support simulating scattering at more arbitrary surfaces, including different surface orientations and surfaces exhibiting large scale features. This required new algorithms for generating the surface for the scattering simulation. Also this required implementing new algorithms for identifying the nearby lattice sites for interaction, as the original algorithm did not scale well to the new lattice sizes. The new lattice generation algorithm allows for generating vicinal surfaces, which exhibit large step features. Support was also added for providing arbitrary surfaces via external input files; this can be used to simulate scattering off surfaces which cannot be generated using the built-in algorithm.

These improvements have allowed for the generation of larger simulated datasets for comparison with experimental results, and potentially allow for streamlining some of our experimental processes, where the simulations can be used to assist with sample alignment, which traditionally requires the use of a low energy electron diffraction (LEED) apparatus.

I also present some experimental work towards scattering at Au(001), specifically a sample preparation method. Also included is an analysis of use of 3D printed materials for use in ion optics, as well as an analysis of plasma generated by an electron beam impact ionisation source.



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