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KeyError: 'Node not found in database.' when importing GRI-Mech seed #36

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rwest opened this issue Jun 11, 2011 · 1 comment
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@rwest
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rwest commented Jun 11, 2011

A job with this:

# Data sources
database(
    '../RMG-database/input',
    thermoLibraries = ['primaryThermoLibrary'],
    reactionLibraries = ['Methylformate'],
    seedMechanisms = ['GRI-Mech3.0'],
)

fails with this:

Adding seed mechanism GRI-Mech3.0 to model core...
Traceback (most recent call last):
  File "rmg.py", line 673, in <module>
    execute(args)
  File "rmg.py", line 262, in execute
    reactionModel.addSeedMechanismToCore(database, seedMechanism, react=False)
  File "/Users/rwest/XCodeProjects/RMGpy/RMG-Py/rmgpy/rmg/model.py", line 1317, in addSeedMechanismToCore
    if spec.reactive: spec.generateThermoData(database)
  File "/Users/rwest/XCodeProjects/RMGpy/RMG-Py/rmgpy/rmg/model.py", line 93, in generateThermoData
    tdata = database.thermo.getThermoData(molecule)
  File "/Users/rwest/XCodeProjects/RMGpy/RMG-Py/rmgpy/data/thermo.py", line 518, in getThermoData
    thermoData = self.getThermoDataFromGroups(molecule)
  File "/Users/rwest/XCodeProjects/RMGpy/RMG-Py/rmgpy/data/thermo.py", line 629, in getThermoDataFromGroups
    thermoData = self.__addThermoData(thermoData, self.__getGroupThermoData(self.groups['radical'], saturatedStruct, {'*':atom}))
  File "/Users/rwest/XCodeProjects/RMGpy/RMG-Py/rmgpy/data/thermo.py", line 720, in __getGroupThermoData
    raise KeyError('Node not found in database.')
KeyError: 'Node not found in database.'
@rwest
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rwest commented Jun 11, 2011

The culprit was atomic [C] which requires a 4-radical correction (which is not in the radical database/tree). The answer was to add 'GRI-Mech3.0' to the thermoLibraries list. I have changed the error message to make problems like this easier to solve in commit 85d36ff and moved it to a more sensible place in commit aee7a6e .

@rwest rwest closed this as completed Jun 11, 2011
rwest added a commit to rwest/RMG-Py that referenced this issue Jul 9, 2018
Species that are found in a gas phase thermo library take their name
from the library, rather than having it be generated from a SMILES
or chemical formula, so they by default don't have an X in them.
We now add the X.
Closes ReactionMechanismGenerator#36
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