Feature/bond double well

mphowardlab / azplugins

A HOOMD-blue component for soft matter simulations.

BSD 3-Clause "New" or "Revised" License

21 stars 13 forks source link

Feature/bond double well #30

Closed astatt closed 4 years ago

astatt commented 4 years ago

This is a simple double well bond potential, intended to mimic mechanically (or thermally) active bonds, which can be in two states (usually corresponding to ring-opening/closing chemistry). The position of the two minima and the barrier height in between can be tuned. Unit tests are added and are passing, documentation is added.

mphoward commented 4 years ago

Thank you! I will take a look through this soon. I needed to reconfigure the CI platform after I transferred the repository (huge headache), but I think it's working now. I want this to be targeted onto develop rather than master, so I redirected the PR. Can you merge develop into this branch before I look at it?

astatt commented 4 years ago

Develop is merged into this branch. It appears that the CI platform is working as intended as well!

astatt commented 4 years ago

Wait until you review/approve until I have implemented a check for nonsensical potential parameters please.

[x] Implement python check for b != 0 (possibly also a != 0?)
[x] Add unit test for those checks

mphoward commented 4 years ago

Just wanted to check: I'm still holding off on reviewing this until you finish these two items?

astatt commented 4 years ago

Yes, give me a few days, sorry for the delay!

astatt commented 4 years ago

Thanks for the thorough review and finding all the small things. This should be ready to merge.