Function that calculates centers in a trajectory.

[gwenwhite]

This function calculates the centers of a trajectory and stores them into a new GSD file (called "centers.gsd" in this code specifically).
Side note: Will need to make the code account for the image if we want to use it for MSD calculations.

[jennyfothergill]

Nice work, @gwenwhite! This is a much needed addition!

I agree that accounting for the image will be nice. I think you could add the image like this: unwrap the particle positions, calculate the centers as they are unwrapped, then use freud.Box.get_images to get the image of the unwrapped center. I'm happy to help you with any questions you have about adding the image.

I've suggested some minor style changes in my review. I also noted some (I think unintentional?) changes to gsd_rdf (the function above your get_centers function). I am guessing these are maybe due to a merge conflict.

[codecov]

Codecov Report

Merging #15 (6caa880) into master (5052ab4) will increase coverage by 0.04%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master      #15      +/-   ##
==========================================
+ Coverage   99.50%   99.55%   +0.04%     
==========================================
  Files           5        5              
  Lines         203      224      +21     
==========================================
+ Hits          202      223      +21     
  Misses          1        1              

Impacted Files	Coverage Δ
cmeutils/structure.py	100.00% <100.00%> (ø)

[gwenwhite]

In regards to commit #db09303134eb4ac96c7b4fb2fbf67c3336c296e3 - Code has been tested on larger system. It worked successfully.

[erjank]

Overall this looks good. The get_centers function looks to save out a trajectory with mapped coordinates. There are some small improvements to think about down the line in test_get_centers, since right now the only sanity check is whether get_centers returns None. It's true, but it's not particularly helpful. An example, more helpful test, might be if the number of frames in the new trajectory is the same as the number of frames in the old trajectory, or if the number of centers is equal to the number of molecules. Nice work!