mphowardlab / azplugins

A HOOMD-blue component for soft matter simulations.
BSD 3-Clause "New" or "Revised" License
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Refactor double well bond potential #75

Closed mphoward closed 1 month ago

mphoward commented 1 month ago

@clpetix Can you polish this one off with documentation when you get a chance?

clpetix commented 1 month ago

On it!

astatt commented 1 month ago

@clpetix I apologize for creating more work for you! After talking to my student (the user of this potential), I think it makes the most sense to define:

Then I suggest the following naming/documentation:

Then, in the documentation we can mention the equation for the location of the second minimum etc.

Does this sound good and makes sense? Feel free to ping me if you need input/help!

clpetix commented 1 month ago

We updated the unit tests to make sense. The new implementation means that the differences of r, r0, and r1 could all be shifted arbitrarily without messing with the energies or forces.

This should be ready for y'all to review @astatt @mphoward !