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cmelab / polybinder

Initialization of thermoplastic polymer systems to simulate thermal welding
GNU General Public License v3.0
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Update to Hoomd V3 #72

Closed chrisjonesBSU closed 2 years ago

chrisjonesBSU commented 2 years ago

This PR updates everything to run on hoomd v3.

There are a couple issues that need to be resolved else where. One is a PR I'll make to hoomd, and another is fixing how hoomd is used/imported in cmeutils

codecov[bot] commented 2 years ago

Codecov Report

Merging #72 (6f72990) into master (79c2447) will increase coverage by 1.52%. The diff coverage is 93.44%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master      #72      +/-   ##
==========================================
+ Coverage   90.80%   92.33%   +1.52%     
==========================================
  Files           7        7              
  Lines         729      744      +15     
==========================================
+ Hits          662      687      +25     
+ Misses         67       57      -10
Impacted Files Coverage Δ
polybinder/system.py 92.28% <0.00%> (ø)
polybinder/simulate.py 91.42% <93.82%> (+3.36%) :arrow_up:
chrisjonesBSU commented 2 years ago

So far it's passing the unit test that does change to nlist to a Tree. Maybe it would be safer to copy to contest of the original nlist.exclusions to a new list and use that?