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Add LogError to raise LogError for unconverged gaussian log file #1766

Merged
merged 2 commits into from
Nov 6, 2019
Merged

Add LogError to raise LogError for unconverged gaussian log file #1766

merged 2 commits into from
Nov 6, 2019

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hwpang
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@hwpang hwpang commented Oct 12, 2019

Motivation or Problem

As suggested in #1739

Description of Changes

Add LogError to raise LogError for unconverged gaussian log file

testing

didn't test

@hwpang hwpang requested a review from alongd October 12, 2019 06:49
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codecov bot commented Oct 12, 2019 •
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Codecov Report

Merging #1766 into master will not change coverage.
The diff coverage is n/a.

Impacted file tree graph

@@           Coverage Diff           @@
##           master    #1766   +/-   ##
=======================================
  Coverage   42.74%   42.74%           
=======================================
  Files          81       81           
  Lines       21078    21078           
  Branches     5491     5491           
=======================================
  Hits         9010     9010           
+ Misses      11067    11054   -13     
- Partials     1001     1014   +13
Impacted Files Coverage Δ
arkane/kinetics.py 12.14% <0%> (ø) ⬆️
rmgpy/data/statmech.py 42.2% <0%> (ø) ⬆️
rmgpy/rmg/pdep.py 12.21% <0%> (ø) ⬆️
rmgpy/data/kinetics/database.py 50.61% <0%> (ø) ⬆️
rmgpy/data/kinetics/family.py 48.35% <0%> (ø) ⬆️
rmgpy/statmech/ndTorsions.py 59.78% <0%> (ø) ⬆️
rmgpy/yml.py 15.71% <0%> (ø) ⬆️
arkane/sensitivity.py 10% <0%> (ø) ⬆️
rmgpy/rmg/input.py 34% <0%> (ø) ⬆️

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@hwpang hwpang requested review from cgrambow and removed request for alongd October 15, 2019 20:46
alongd
alongd reviewed Oct 16, 2019
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Thanks for this fix, @hwpang !
Please add a unit test using an errored Gaussian log file.
While at it, let's raise a similar error in QChem and Molpro Logs. You can find some example crashed jobs here.
(@dranasinghe, could you add a similar line to Orca?)

arkane/gaussian.py Outdated
@@ -247,6 +247,9 @@ def load_conformer(self, symmetry=None, spin_multiplicity=0, optical_isomers=Non
# Read the next line in the file
line = f.readline()

if 'Error termination' in line:
raise LogError('Gaussian log file did not converge.')
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Please change the text to f'The Gaussian job in {self.path} did not converge.'

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alongd commented Oct 29, 2019

@hwpang, we'll soon modify log files in Arkane, would you like to merge this PR soon to avoid conflicts?

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hwpang commented Oct 30, 2019

@hwpang, we'll soon modify log files in Arkane, would you like to merge this PR soon to avoid conflicts?

Sorry for the slow response. I was really busy last week. I will address the above comments before this Friday.

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hwpang commented Nov 4, 2019

Thanks for this fix, @hwpang !
Please add a unit test using an errored Gaussian log file.
While at it, let's raise a similar error in QChem and Molpro Logs. You can find some example crashed jobs here.
(@dranasinghe, could you add a similar line to Orca?)

I've modified the error message and added a unit test for it.

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alongd commented Nov 4, 2019

Great, thanks!
Please rebase and squash the fix commits

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hwpang commented Nov 4, 2019

Great, thanks!
Please rebase and squash the fix commits

I've rebased and squashed the fix commit. Thanks for reviewing!

alongd
alongd reviewed Nov 5, 2019
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It all looks good, thanks. Just a minor request: Could you squash the test commit with the commit that added the unconverged Gaussian log file?

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hwpang commented Nov 5, 2019

It all looks good, thanks. Just a minor request: Could you squash the test commit with the commit that added the unconverged Gaussian log file?

These two commits were squashed as requested. Thanks!

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alongd commented Nov 6, 2019

Perfect! Rebase again?

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hwpang commented Nov 6, 2019

Perfect! Rebase again?

I rebased this branch. Thanks!

alongd
alongd approved these changes Nov 6, 2019
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Thanks!

@alongd alongd merged commit 1d4c5cc into master Nov 6, 2019
@alongd alongd deleted the addErrorLoadConformer branch November 6, 2019 03:26
@mliu49 mliu49 mentioned this pull request Nov 26, 2019
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@mliu49 mliu49 mentioned this pull request Dec 4, 2019
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@mliu49 mliu49 mentioned this pull request Dec 16, 2019
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@alongd alongd alongd approved these changes

@cgrambow cgrambow Awaiting requested review from cgrambow

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@hwpang @alongd