• Numerical stability: In what ranges of parameters are the results sensible?
• Phase diagrams: How the density combined with the temperature determines the solid-liquid transition and how does the liquid-gas continuum behave?
• Morse and/or Buckingham potential: How the results change with a different functional form than Lennard-Jones. This one would need a few lines of code, which we can help with if needed?
• Benchmarks: How fast different parts of the code run on specific computer hardware?
• Different crystal structures: What happens to the results when the initial conditions are in a different crystal packing or packing?
• Equations of state: How well equations of state hold when taking into account microscopic components of pressure?
• Thermodynamic properties: How free energy and entropy change between phases, based on the Widom test-particle method?
• Equilibration time: How long it takes for the potential energy to become stable given a time step length and a number of time steps?
• Collisons: How often are particles closer together than their particle size 𝜎�?
• Diffusion: How far do particles move during the simulation?
• Defects: What happens to the geometry of the cell when an atom is added to a non-FCC point or an atom is removed?

Write down your research question in your Jupyter Notebook. Feel free to be as creative as you like, you can always change your research question later. The suggestion to combine two topics is just a way to give you inspiration but you don’t need to stick to it if you don’t want to.

Also write down a research plan detailing all of the calculations and data analysis which will be needed.

Your Jupyter Notebook will be marked based on the following criteria:

• 10% Annotation of the algorithm: The pieces of code are supplemented by comments and/or Markdown to clarify what they do. You should demonstrate the link between theory and the code provided by filling in the sections that say [FILL IN]. These annotations are needed for the pristine version of the code that is supplied to you, so if you make significant changes to the program, you should still also include an annotation version of the code before any changes.
• 20% Theory background: The notebook introduces the theory behind Velocity Verlet Molecular Dynamics, Lennard-Jones potentials, and any other scientific topics relevant to your research topic.
• 25% Research topic: Your research topic (and research question) are introduced logically, with a proposed plan on what calculations and data analysis will be carried out.
• 25% Figures: Images are supplied which supplement the reported results and investigations. The figures are clear, used appropriately, and at least one figure depicts a Radial Distribution Function (RDF).
• 5% Activity log: Your principal activities for the practical are recorded and timestamped in an activity log.
• 15% Clarity of presentation: Your writing and formatting makes the contents of the Notebook easy to read and understand.