Feedback on Simplest_MD.ipynb

[joelaforet]

Hi @mrshirts ! I reviewed the first draft of Simplest_MD.ipynb via the reviewNB plugin. My comments are here. Let me know if you have any difficulty seeing them.

[aiwe2320]

Here are some of my comments. I wasn't able to see Joe's comments so there might be some duplication:

• Plot titles are somewhat inconsistent across the notebook. For example early plots are titled like "velocity versus time" when under the velocity verlet section they are titled with "v vs. time"
• A few empty markdown cells throughout the notebook that could be deleted
• I had issues rendering certain equations with "\Bigr{|}" in VSCode I think due to an issue with the LaTeX rendering built into VSCode (KaTeX). This caused problems in markdown cells where a vertical line to denote a derivative evaluated at a point (ex. dx/dt|t). I don't know how extensive of a problem this would be in distributing the notebook, but it could be good to resolve. Replacing "\Bigr{|}" with "\bigg|" worked as a solution for me. I can file a PR with this change if desired.
• For the first example, the nsteps and dt in the notebook currently conserve energy quite well, but the markdown text implies that you expect the simulation to clearly run away.
• Markdown cell following the animation under "Diagnosing and improving our simulation": Typo 'definintely' -> 'definitely'
• Markdown cell following the "energy versus time" graph under "Energy conservation and improving our approach": Same typo as above (definintely' -> 'definitely'), and "So, definintely not conservation of energy" as a statement could be clearer. "So energy is definitely not conserved..."
• When comparing results using taylor1 and taylor2 the plots are untitled and the axes are unlabeled. The velocity of taylor2 is mislabeled in the legend as "x_t2" instead of "v_t2"
• Double check the "Symplectic algorithms and lack of drift" markdown section for typos/grammar
• Under "Fluctuation behavior of symplectic integrators" the "Question" has a typo --> "...fluctuations around average change get smaller..."

[mrshirts]

@aiwe2320 Thanks! re: "For the first example, the nsteps and dt in the notebook currently conserve energy quite well, but the markdown text implies that you expect the simulation to clearly run away." yes, this is the "show what happens when you increase dt by a lot and it sort of starts conserving energy".