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Fix: numeric energy input for ARKANE #1811

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jeehyunatrmg
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Motivation or Problem

I wanted to manually put energy in Arkane input file since Arkane doesn't contain model chemistry that I used. However, Arkane assumed float type as 'path' and giving out the error.

Description of Changes

added lines that can recognize the float type before it assumes as the path

Testing

it worked in my laptop..?

Reviewer Tips

Actually, Jerry did this fix...

if not os.path.isfile(energy.path):
if not hasattr(energy, 'path'):
pass
elif not os.path.isfile(energy.path):
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I would suggest putting the check in the same statement: if hasattr(energy, 'path') and not os.path.isfile(energy.path)

Also, I'm not sure if Alon has opinions on use of hasattr vs checking isinstance(energy, Log).

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I think isinstance(energy, Log) is cleaner, and it should definitely be in the same statement.
@jeehyunatrmg, we can do it together tomorrow if you'd like, or simply go-ahead and make these fixes.

@goldmanm
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goldmanm commented Nov 6, 2019

I also worked on a similar issue, which is in the PR Arkane bugfixes #1810 . You can see the change at this commit:
cba4f3f

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codecov bot commented Nov 6, 2019

Codecov Report

Merging #1811 into master will decrease coverage by 10.15%.
The diff coverage is n/a.

Impacted file tree graph

@@             Coverage Diff             @@
##           master    #1811       +/-   ##
===========================================
- Coverage   42.74%   32.58%   -10.16%     
===========================================
  Files          81       98       +17     
  Lines       21078    27665     +6587     
  Branches     5491     7254     +1763     
===========================================
+ Hits         9010     9016        +6     
- Misses      11067    17640     +6573     
- Partials     1001     1009        +8
Impacted Files Coverage Δ
rmgpy/data/statmech.py 42.2% <0%> (ø) ⬆️
rmgpy/rmg/pdep.py 12.21% <0%> (ø) ⬆️
rmgpy/data/kinetics/family.py 48.35% <0%> (ø) ⬆️
rmgpy/yml.py 15.71% <0%> (ø) ⬆️
rmgpy/data/kinetics/database.py 50.61% <0%> (ø) ⬆️
rmgpy/rmg/input.py 34% <0%> (ø) ⬆️
rmgpy/statmech/ndTorsions.py 59.78% <0%> (ø) ⬆️
.../test_data/testing_database/forbiddenStructures.py 100% <0%> (ø)
rmgpy/molecule/molecule.py 0% <0%> (ø)
rmgpy/species.py 0% <0%> (ø)
... and 14 more

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@alongd
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alongd commented Nov 6, 2019

We can either use this PR or @goldmanm's commit. This PR could also be a good practice. Either way we should also add a test.

@amarkpayne
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What is the current status of this PR? Are we using the change here or are we using the commit from @goldmanm ?

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9509839 fixed this issue.

@goldmanm goldmanm closed this Nov 18, 2019
@jeehyunatrmg jeehyunatrmg deleted the jeehyun_110519 branch November 18, 2019 21:06
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5 participants