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e85 job causes AttributeError: 'rmg.chem.Atom' object has no attribute 'breakBond' #10

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rwest opened this issue Nov 13, 2009 · 2 comments
Closed

e85 job causes AttributeError: 'rmg.chem.Atom' object has no attribute 'breakBond' #10

rwest opened this issue Nov 13, 2009 · 2 comments

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@rwest
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rwest commented Nov 13, 2009

This is with 16f8145 ::

RMG execution initiated at Thu Nov 12 17:58:48 2009

################################################################
#                                                              #
#              RMG - Reaction Mechanism Generator              #
#                    Python Version 0.0.1                      #
#                         14 May 2009                          #
#                                                              #
#                 http://rmg.sourceforge.net/                  #
#                                                              #
################################################################

Found 1 database
Traceback (most recent call last):
  File "rmg.py", line 149, in <module>
    rmg.main.execute( args[0], options )
  File "/Users/rwest/XCodeProjects/RMGpy/source/rmg/main.py", line 96, in execute
    reactionModel, coreSpecies, reactionSystems = io.readInputFile(inputFile)
  File "/Users/rwest/XCodeProjects/RMGpy/source/rmg/io.py", line 295, in readInputFile
    reaction.kineticsDatabase.load(database[2] + os.sep)
  File "/Users/rwest/XCodeProjects/RMGpy/source/rmg/reaction.py", line 1650, in load
    family.load(path)
  File "/Users/rwest/XCodeProjects/RMGpy/source/rmg/reaction.py", line 636, in load
    self.loadTemplate(tempstr)
  File "/Users/rwest/XCodeProjects/RMGpy/source/rmg/reaction.py", line 1156, in loadTemplate
    self.generateProductTemplate()
  File "/Users/rwest/XCodeProjects/RMGpy/source/rmg/reaction.py", line 1191, in generateProductTemplate
    productStructure = self.applyRecipe(reactantStructure, unique=False)
  File "/Users/rwest/XCodeProjects/RMGpy/source/rmg/reaction.py", line 1277, in applyRecipe
    if not self.recipe.applyForward(reactantStructure, unique):
  File "/Users/rwest/XCodeProjects/RMGpy/source/rmg/reaction.py", line 529, in applyForward
    return self.__apply(struct, True, unique)
  File "/Users/rwest/XCodeProjects/RMGpy/source/rmg/reaction.py", line 490, in __apply
    atom1.breakBond(struct.getBonds(atom1), unique)
AttributeError: 'rmg.chem.Atom' object has no attribute 'breakBond'
@jwallen
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jwallen commented Nov 13, 2009

Seems to work okay for me. That function (among others) is new to the master/cantera branches as of this week since I decided to merge in the CO-less database. This is going to sound silly, but did you rebuild the Cython modules?

@rwest
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rwest commented Nov 16, 2009

No, I didn't. Silly indeed!

rwest added a commit that referenced this issue Jun 6, 2023
@rwest
Fix typo in environment.yml
a9b7a3d 
This is a combination of 12 commits, as we tried everything under the sun to debug the CI.
But they all cancelled out when merged (apart from fixing a typo in a comment)

- This is the 1st commit message:
CI: trying to force ubuntu-20.04 instead of ubuntu-latest (temporary)
While we figure out what's happening, let's try an older ubuntu.
- This is commit message #2:
fixup! CI: trying to force ubuntu-20.04 instead of ubuntu-latest (temporary)
- This is the commit message #3:
Switch back to ubuntu-latest
But leave a 20.04 in the matrix build
- This is the commit message #4:
Trying libstdcxx-ng < 13 in Conda environment.
Trying to debug. If this works it should be put in docker file too.
Or, better, the real cause found and fixed.
- This is the commit message #5:
fix typo in env, undo ubuntu os changes, set gcc version in CI to 6
this system object of this version is being provided by gcc, and the
runners no longer come prepackaged with it since its old (?)
- This is the commit message #6:
it wasn't the gcc version
- This is the commit message #7:
it was the julia version, 1.9.0 is brokey
as reported at conda-forge/julia-feedstock#253
the latest release of julia (1.9.0) is brokey, don't use it (put !=1.9.0 in the environment file)
- This is the commit message #8:
make mac and ubuntu use the same cxx library
- This is the commit message #9:
but what if it was rdkit all along?
- This is the commit message #10:
Revert "but what if it was rdkit all along?" because it wasn't
- This is the commit message #11:
Revert "make mac and ubuntu use the same cxx library" cos it didn't work
- This is the commit message #12:
Revert "it was the julia version, 1.9.0 is brokey" but it wasn't
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@rwest @jwallen