[JOSS] Example Usage

[RMeli]

I think the Jupyter Notebooks showcasing the functionality of the code are great! They are an extremely valuable addition which will facilitate the use and adoption of hoomd-tf. To make them even better, I'd suggest to add some text explaining a bit more what the notebook is about and guiding the user through the most complicated cells, if possible.

Running the notebooks with the latest version of the code (be8b299cc8c62add8fff2ff719713b41814cc6ff) I encountered the following problems:

• Coarse Grained Simulations:
  • RuntimeError: Corrupt GSD file: CG_tutorial/meth.gsd on cell # 4
  • Spurious ; at line charged = hoomd.group.all(); in cell # 4? [Looks like C++ muscle memory ;) ]
• EDS biasing using HTF:
  • nglview should be listed as optional dependency at the top of the notebook instead than before cell # 4?
  • ValueError: Found no dependence on positions or neighborsso forces cannot be computed
• Multidimensional EDS biasing:
  • ValueError: Found no dependence on positions or neighborsso forces cannot be computed on cell # 3
• Particles in Harmonic Well:
  • ValueError: Found no dependence on positions or neighborsso forces cannot be computed on cell # 2

I think the solution for the ValueError: Found no dependence on positions or neighborsso forces cannot be computed is the following (see https://github.com/ur-whitelab/hoomd-tf/pull/183#pullrequestreview-436907018 and PR #186 ):

-    force = graph.compute_forces(energy)
+    force = graph.compute_forces(energy, positions=True)

---

JOSS review

[whitead]

Thanks for pointing out these issues. Some of these notebooks are indeed out of date and not that descriptive. Hopefully I've addressed this in PR #198

[malramsay64]

Changes are great. LGTM