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Fix chemkin file duplicate flags #1856

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Fix chemkin file duplicate flags #1856

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24acee3
Fix chemkin duplicate reaction detection.
rwest Dec 30, 2019
bf6cf62
Tweak logging message for writing chemkin surface files
rwest Dec 30, 2019
b2da66f
Don't UNMARK duplicate reactions so aggressively.
rwest Dec 30, 2019
55c3020
Fix unit tests for: Don't UNMARK duplicate reactions so aggressively.
rwest Dec 30, 2019
186a20e
Update unit test for new pytest framework
rwest Aug 10, 2023
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22 changes: 11 additions & 11 deletions rmgpy/chemkin.pyx
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Expand Up @@ -1969,22 +1969,22 @@ def mark_duplicate_reaction(test_reaction, reaction_list):
# duplicates of one another.
# RHW question: why can't TemplateReaction be duplicate of LibraryReaction, in Chemkin terms? I guess it shouldn't happen in RMG.
continue
same_dir_match = (reaction1.reactants == reaction2.reactants and reaction1.products == reaction2.products)
opposite_dir_match = (reaction1.products == reaction2.reactants and reaction1.reactants == reaction2.products)
same_dir_match = (sorted(reaction1.reactants) == sorted(reaction2.reactants) and sorted(reaction1.products) == sorted(reaction2.products))
opposite_dir_match = (sorted(reaction1.products) == sorted(reaction2.reactants) and sorted(reaction1.reactants) == sorted(reaction2.products))
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There may need to be an edit here to catch errors like
InputFileError thrown by Kinetics::checkDuplicates: Undeclared duplicate reactions detected: Reaction ####: A <=> A Reaction ####: 2 A <=> 2 B

that results when you use either the ck2cti or ck2yaml.

if (same_dir_match or opposite_dir_match) and (reaction1.specific_collider == reaction2.specific_collider):
if reaction1.duplicate and reaction2.duplicate:
if reaction1.kinetics.is_pressure_dependent() != reaction2.kinetics.is_pressure_dependent():
# Reactions with mixed pressure dependence do not need to be marked duplicate in Chemkin
logging.warning('Marked reaction {0} as not duplicate because of mixed pressure dependence '
'for saving to Chemkin file.'.format(reaction1))
reaction1.duplicate = False
reaction2.duplicate = False
logging.warning('Reaction {0} is marked as duplicate but for Chemkin file it '
'doesn\'t need to be because of mixed pressure dependence'
'.'.format(reaction1))
# But leave it alone in case it's a DUPLICATE of some _other_ reaction.
elif opposite_dir_match and not reaction1.reversible and not reaction2.reversible:
# Irreversible reactions in opposite directions do not need to be marked duplicate in Chemkin
logging.warning('Marked reaction {0} as not duplicate because they are irreversible '
'in opposite directions for saving to Chemkin file.'.format(reaction1))
reaction1.duplicate = False
reaction2.duplicate = False
logging.warning('Reaction {0} is marked as duplicate but for Chemkin file it '
'doesn\'t need to be because they are irreversible '
'in opposite directions.'.format(reaction1))
# But leave it alone in case it's a DUPLICATE of some _other_ reaction.
else:
if (reaction1.kinetics.is_pressure_dependent() == reaction2.kinetics.is_pressure_dependent()
and ((reaction1.reversible and reaction2.reversible)
Expand Down Expand Up @@ -2150,7 +2150,7 @@ def save_chemkin_file(path, species, reactions, verbose=True, check_for_duplicat
f.write('\n')
f.write('END\n\n')
f.close()
logging.info("Chemkin file contains {0} reactions.".format(_chemkin_reaction_count))
logging.info("Chemkin surface file contains {0} reactions.".format(_chemkin_reaction_count))
_chemkin_reaction_count = None


Expand Down
17 changes: 17 additions & 0 deletions test/rmgpy/chemkinTest.py
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Expand Up @@ -503,6 +503,21 @@ def test_mark_duplicate_reactions(self):

assert duplicate_flags == expected_flags

@pytest.mark.skip(reason="WIP")
def test_unmark_duplicate_reactions(self):
"""Test that we can properly REMOVE duplicate reaction flags for Chemkin."""

"""
We can't do this properly yet.
See https://github.com/ReactionMechanismGenerator/RMG-Py/pull/1856
"""
s1 = Species().from_smiles('CC')
s2 = Species().from_smiles('[CH3]')
s3 = Species().from_smiles('[OH]')
s4 = Species().from_smiles('C[CH2]')
s5 = Species().from_smiles('O')
s6 = Species().from_smiles('[H]')

# Try initializing with duplicate=True
reaction_list = [
Reaction(reactants=[s1], products=[s2, s2], duplicate=True, kinetics=Arrhenius()),
Expand Down Expand Up @@ -549,6 +564,8 @@ def test_mark_duplicate_reactions(self):
),
]

expected_flags = [True, True, False, False, True, True, False, False]

mark_duplicate_reactions(reaction_list)
duplicate_flags = [rxn.duplicate for rxn in reaction_list]

Expand Down