Update to GSD 3

[chrisjonesBSU]

This PR makes all the changes needed for updating to GSD 3.

[codecov]

Codecov Report

Merging #59 (ad77da4) into master (6b83bc5) will not change coverage.
The diff coverage is 92.30%.

Additional details and impacted files

@@           Coverage Diff           @@
##           master      #59   +/-   ##
=======================================
  Coverage   95.95%   95.95%           
=======================================
  Files           8        8           
  Lines         642      642           
=======================================
  Hits          616      616           
  Misses         26       26           

Files Changed	Coverage Δ
cmeutils/visualize.py	96.89% <ø> (ø)
cmeutils/gsd_utils.py	86.04% <80.00%> (ø)
cmeutils/dynamics.py	96.00% <100.00%> (ø)
cmeutils/structure.py	100.00% <100.00%> (ø)