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Patches for element reading in lattice builder #1066
Patches for element reading in lattice builder #1066
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…lements form compound_dicts
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LGTM!
Codecov ReportAll modified and coverable lines are covered by tests ✅
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 ☔ View full report in Codecov by Sentry. |
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
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
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:
PR Checklist
Closes #1065.