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Solving the 'Fragment' object has no attribute 'count_internal_rotors' error#2395

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xiaoruiDong merged 2 commits intomainfrom
frag_err
Mar 7, 2023
Merged

Solving the 'Fragment' object has no attribute 'count_internal_rotors' error#2395
xiaoruiDong merged 2 commits intomainfrom
frag_err

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@alongd
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@alongd alongd commented Mar 5, 2023

Motivation or Problem

Recently, RMG crashes often, for different chemistries, with the following trace:

  File "/home/alongd/Code/RMG-Py/rmg.py", line 118, in <module>
    main()
  File "/home/alongd/Code/RMG-Py/rmg.py", line 112, in main
    rmg.execute(**kwargs)
  File "/home/alongd/Code/RMG-Py/rmgpy/rmg/main.py", line 944, in execute
    self.reaction_model.enlarge(objectToEnlarge)
  File "/home/alongd/Code/RMG-Py/rmgpy/rmg/model.py", line 709, in enlarge
    self.update_unimolecular_reaction_networks()
  File "/home/alongd/Code/RMG-Py/rmgpy/rmg/model.py", line 1918, in update_unimolecular_reaction_networks
    network.update(self, self.pressure_dependence)
  File "/home/alongd/Code/RMG-Py/rmgpy/rmg/pdep.py", line 808, in update
    spec.generate_statmech()
  File "rmgpy/species.py", line 821, in rmgpy.species.Species.generate_statmech
  File "/home/alongd/Code/RMG-Py/rmgpy/data/statmech.py", line 679, in get_statmech_data
    statmech_model = self.get_statmech_data_from_groups(molecule, thermo_model)
  File "/home/alongd/Code/RMG-Py/rmgpy/data/statmech.py", line 713, in get_statmech_data_from_groups
    return self.groups['groups'].get_statmech_data(molecule, thermo_model)
  File "/home/alongd/Code/RMG-Py/rmgpy/data/statmech.py", line 384, in get_statmech_data
    num_rotors = molecule.count_internal_rotors()
AttributeError: 'Fragment' object has no attribute 'count_internal_rotors'

Description of Changes

Two methods, count_internal_rotors() and is_bond_in_cycle() were added to the Fragment class.

@alongd alongd requested a review from lily90502 March 5, 2023 07:45
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codecov bot commented Mar 5, 2023 •
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Codecov Report

Merging #2395 (d0f1e64) into main (c2b0944) will decrease coverage by 0.01%.
The diff coverage is 20.00%.

@@            Coverage Diff             @@
##             main    #2395      +/-   ##
==========================================
- Coverage   48.25%   48.24%   -0.01%     
==========================================
  Files         110      110              
  Lines       30616    30626      +10     
  Branches     7982     7986       +4     
==========================================
+ Hits        14774    14776       +2     
- Misses      14298    14305       +7     
- Partials     1544     1545       +1
Impacted Files Coverage Δ
rmgpy/molecule/fragment.py 73.11% <20.00%> (-0.53%) ⬇️
arkane/kinetics.py 12.24% <0.00%> (ø)

📣 We’re building smart automated test selection to slash your CI/CD build times. Learn more

lily90502
lily90502 previously approved these changes Mar 5, 2023
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Thank you for adding these functions. These two look okay to me!

@alongd
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alongd commented Mar 6, 2023

@lily90502, I rebased. Could you please re-approve and merge?

xiaoruiDong
xiaoruiDong approved these changes Mar 7, 2023
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Looks good! Thanks @alongd @lily90502

@xiaoruiDong xiaoruiDong merged commit 5149ade into main Mar 7, 2023
@xiaoruiDong xiaoruiDong deleted the frag_err branch March 7, 2023 21:05
@alongd alongd mentioned this pull request Mar 15, 2023
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@xiaoruiDong xiaoruiDong xiaoruiDong approved these changes

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@alongd @lily90502 @xiaoruiDong