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Patches for element reading in lattice builder #1066

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CalCraven
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PR Summary:

This is a small patch to check for element information from the lattice reader. This is relevant if the user doesn't pass a compund dict of the form {name(STR): compound(mb.Compound)} to map the lattice points to a specific compound. In this case, the only information the populate function has is the key for each lattice point, which is a string. We can then use the ele package to check if that is supposed to be an element. Like always, if this is a coarse grained bead without element information, use an _NAME syntax to denote that, and no element information will be found.

Usage:

lattice = mb.Lattice(
             lattice_spacing=[0.5, 0.5, 1],
             angles=[90, 90, 120],
             lattice_points={"O": [[0, 0, 0]]},
 )
 cpd_lat = lattice.populate(x=1, y=1, z=1)
 for part in cpd_lat:
     assert part.element.name == "oxygen" # the oxygen is identified from the lattice_points dict.

PR Checklist


  • Includes appropriate unit test(s)
  • Appropriate docstring(s) are added/updated
  • Code is (approximately) PEP8 compliant
  • Issue(s) raised/addressed?

Closes #1065.

@CalCraven CalCraven self-assigned this Dec 5, 2022
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@daico007 daico007 left a comment

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LGTM!

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codecov bot commented Dec 5, 2022

Codecov Report

Base: 90.69% // Head: 90.71% // Increases project coverage by +0.02% 🎉

Coverage data is based on head (2b2b86a) compared to base (ee91caa).
Patch coverage: 100.00% of modified lines in pull request are covered.

Additional details and impacted files
@@            Coverage Diff             @@
##             main    #1066      +/-   ##
==========================================
+ Coverage   90.69%   90.71%   +0.02%     
==========================================
  Files          57       57              
  Lines        5500     5513      +13     
==========================================
+ Hits         4988     5001      +13     
  Misses        512      512              
Impacted Files Coverage Δ
mbuild/lattice.py 96.81% <100.00%> (+0.19%) ⬆️

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match=r"Element assumed from cif file to be Element: silicon, symbol: Si, atomic number: 14, mass: 28.085.",
):
lattice_cif = load_cif(file_or_path=get_fn("ETV_triclinic.cif"))
periodic_boxed_molecule = lattice_cif.populate(x=1, y=1, z=1)

Check notice

Code scanning / CodeQL

Unused local variable

Variable periodic_boxed_molecule is not used.
@daico007
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daico007 commented Dec 6, 2022

Failing tests come from the new energy minimization with Windows (py39). I might have overlooked this when merging the other PR, but I think we should just skip those test on windows run.

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LGTM

@daico007 daico007 merged commit 82977a2 into mosdef-hub:main Dec 6, 2022
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The lattice builder won't check for element information if loaded from CIF
3 participants