Allow hasStatMech to assess atomic molecules #1513
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
goldmanm
added
Arkane
Status: Ready for Review
|
@goldmanm, the code looks good, strange that the tests failed. Could you rebase and push, so we'll give the tests a second trial? |
Previously, hasStatMech would return True for any molecule with one atom, even if the E0 parameter was None. This raises issues when creating pdep networks since E0 is necessary. At the same time, this method does not check E0 parameters even for polyatomic molecules. This commit reworks hasStatMech to differentiate between atomic molecules, which it only checks the E0 parameter, and polyatomic molecules, which it checks both E0 and the number of modes.
goldmanm
force-pushed
the
hasStatMech_for_atomic_molecules
branch
from
88630d6 to
ffd76ed
Compare
Codecov Report
@@ Coverage Diff @@
## master #1513 +/- ##
==========================================
+ Coverage 42.04% 42.08% +0.04%
==========================================
Files 165 165
Lines 27821 27823 +2
Branches 5667 5668 +1
==========================================
+ Hits 11697 11710 +13
+ Misses 15340 15328 -12
- Partials 784 785 +1
Continue to review full report at Codecov.
|
|
@alongd Seems like the tests passed this time. |
alongd
removed
the
Status: Ready for Review
5 tasks
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Previously, hasStatMech would return True for any molecule with one atom, even if the E0 parameter was None. This raises issues when creating pdep networks from NASA polynomials in arkane since E0 is necessary. At the same time, this method does not check E0 parameters even for polyatomic
molecules.
This commit reworks hasStatMech to differentiate between atomic molecules, which it only checks the E0 parameter, and polyatomic molecules, which it checks both E0 and the number of modes.
I have tested the arkane example methoxy, which deals with atomic hydrogen, and this commit results in no change in that result. This commit does result in a fix when the user inputs an atomic molecule into the arkane input file given its NASA polynomial.
Reviewer Tips
Look over the code and let me know if anything should be added/fixed/etc.