Mesh tutorial

[SchoeniPhlippsn]

Description

Add a mesh tutorial that describes how to create and include meshes in hoomd.

Checklist:

• I have reviewed the Contributor Guidelines.
• I agree with the terms of the HOOMD-blue Contributor Agreement.
• My name is on the list of authors.

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[joaander]

I would suggest moving these parameters down to the code blocks where they are used. At this point in the tutorial, the user has no idea what the parameters mean or what they are used for.

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[joaander]

Add a markdown block that says something to the effect of "Let's run a simulation with a spherical mesh. As shown in the previous section, use the Fibonacci sphere to initialize the mesh."

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[joaander]

This code also needs some explanation. It is not obvious to a new user that the vertices of the mesh will become particles in the simulation. I'm not sure if that full explanation belongs here. It may be better to put a whole paragraph at the beginning that outlines the plan to place the vertices as particles and apply potentials that are functions of the mesh.

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[joaander]

Creating a simulation is not a new concept for readers, but initializing the mesh object is. I would condense the "standard" initialization into one code block and preface it with a short description.

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[joaander]

MD integration is also not new to users - you can probably merge it with the section above.

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[joaander]

I'm not sure what this code block is trying to convey. The tether parameter looks to belong with the "mesh_bond_potential" code below. The rest of the code looks like it belongs in its own block with some explanation of how these values might be used to validate the tether parameter choices?

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[joaander]

This code block seems like it should be included in the previous section.

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[joaander]

I would rephrase the 2nd sentence: "Pass the mesh_obj to the neighborlist and set the "meshbond" exclusion to exclude WCA forces between vertices in the same triangle".

Also, does this really exclude all vertices in the same triangle? Or only those that form an edge?

Lastly, WCA has not previously been defined in the tutorials. You could replace "WCA" with "repulsive".

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[joaander]

The rest of the sections need some explanation to describe what the potential is, how it affects the simulation, and when a user might want to add it (or not).

For a more visual guide, you might want to run the simulation without any rigidity potentials first to show the user the flexible mesh. Then turn on the rigidity potentials (possibly one at a time) to show the resulting behavior.

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[joaander]

Does the volume need to be slowly changed here? What if you just abruptly set the new volume and run the simulation? I think Brownian would be able to absorb the energy, but maybe not. Taking out the custom action would make the tutorial easier for new users to understand.

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[joaander]

Thanks!

I pushed some spelling and formatting fixes directly to the branch. The first section of the tutorial is great, simple and to the point. I like the code examples in the second, but I think they could use a little more explanation and a little rearranging to more clearly teach the new concepts (detailed comments on each block in reviewNB).