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Occasional CClib parsing error in QM using Mopac #134
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Trying to help issue #134. This is unlikely to fix anything, but should help debugging.
f31693b may help with the debugging, but I can't quite see why it would be failing this way, unless it's an i/o problem, eg. the file has not finished being written yet when you start to parse it. Are you running this on a networked file share, eg. from your home user space on a cluster? I wonder if there's a way to wait until a file is no longer open by any other process, before parsing it. |
Seeing this also, when importing mechanims. File "/home/goktekin.e/Code/RMG-Py/importChemkin.py", line 2162, in <module>
mm.main()
File "/home/goktekin.e/Code/RMG-Py/importChemkin.py", line 1484, in main
self.limitEnlarge(self.speciesDict_rmg[labelToProcess])
File "/home/goktekin.e/Code/RMG-Py/importChemkin.py", line 1317, in limitEnlarge
spec.generateThermoData(database, quantumMechanics=rm.quantumMechanics)
File "/home/goktekin.e/Code/RMG-Py/rmgpy/rmg/model.py", line 149, in generateThermoData
thermo0 = quantumMechanics.getThermoData(molecule) # returns None if it fails
File "/home/goktekin.e/Code/RMG-Py/rmgpy/qm/main.py", line 147, in getThermoData
thermo0 = qm_molecule_calculator.generateThermoData()
File "/home/goktekin.e/Code/RMG-Py/rmgpy/qm/molecule.py", line 221, in generateThermoData
self.qmData = self.generateQMData()
File "/home/goktekin.e/Code/RMG-Py/rmgpy/qm/mopac.py", line 216, in generateQMData
result = self.parse() # parsed in cclib
File "/home/goktekin.e/Code/RMG-Py/rmgpy/qm/mopac.py", line 146, in parse
qmData = CCLibData(cclibData, radicalNumber+1)
File "/home/goktekin.e/Code/RMG-Py/rmgpy/qm/qmdata.py", line 87, in __init__
raise e
AttributeError: 'ccData' object has no attribute 'rotcons' and File "/home/goktekin.e/Code/RMG-Py/importChemkin.py", line 2162, in <module>
mm.main()
File "/home/goktekin.e/Code/RMG-Py/importChemkin.py", line 1484, in main
self.limitEnlarge(self.speciesDict_rmg[labelToProcess])
File "/home/goktekin.e/Code/RMG-Py/importChemkin.py", line 1317, in limitEnlarge
spec.generateThermoData(database, quantumMechanics=rm.quantumMechanics)
File "/home/goktekin.e/Code/RMG-Py/rmgpy/rmg/model.py", line 130, in generateThermoData
tdata = database.thermo.estimateRadicalThermoViaHBI(molecule, quantumMechanics.getThermoData)
File "/home/goktekin.e/Code/RMG-Py/rmgpy/data/thermo.py", line 803, in estimateRadicalThermoViaHBI
thermoData = stableThermoEstimator(saturatedStruct)
File "/home/goktekin.e/Code/RMG-Py/rmgpy/qm/main.py", line 147, in getThermoData
thermo0 = qm_molecule_calculator.generateThermoData()
File "/home/goktekin.e/Code/RMG-Py/rmgpy/qm/molecule.py", line 221, in generateThermoData
self.qmData = self.generateQMData()
File "/home/goktekin.e/Code/RMG-Py/rmgpy/qm/mopac.py", line 216, in generateQMData
result = self.parse() # parsed in cclib
File "/home/goktekin.e/Code/RMG-Py/rmgpy/qm/mopac.py", line 144, in parse
cclibData = parser.parse()
File "/home/goktekin.e/Code/RMG-Py/external/cclib/parser/logfileparser.py", line 221, in parse
self.extract(inputfile, line)
File "/home/goktekin.e/Code/RMG-Py/external/cclib/parser/mopacparser.py", line 142, in extract
self.inputatoms.append(symbol2int(broken[1]))
File "/home/goktekin.e/Code/RMG-Py/external/cclib/parser/mopacparser.py", line 20, in symbol2int
return t.number[symbol]
KeyError: '143' This is also somewhat random and only when running on a networked file system (on an HPC cluster). |
It was working 6 months ago, I haven't checked it since then. While it is Murat |
Temporary solution to avoid attribute errors from cclib during parsing. See issue ReactionMechanismGenerator#134
Temporary solution to avoid attribute errors from cclib during parsing. See issue ReactionMechanismGenerator#134
Temporary solution to avoid attribute errors from cclib during parsing. See issue ReactionMechanismGenerator#134
Temporary solution to avoid attribute errors from cclib during parsing. See issue ReactionMechanismGenerator#134
Temporary solution to avoid attribute errors from cclib during parsing. See issue ReactionMechanismGenerator#134
Temporary solution to avoid attribute errors from cclib during parsing. See issue ReactionMechanismGenerator#134
Temporary solution to avoid attribute errors from cclib during parsing. See issue ReactionMechanismGenerator#134
Temporary solution to avoid attribute errors from cclib during parsing. See issue ReactionMechanismGenerator#134
Temporary solution to avoid attribute errors from cclib during parsing. See issue #134
Temporary solution to avoid attribute errors from cclib during parsing. See issue #134
Temporary solution to avoid attribute errors from cclib during parsing. See issue #134
Temporary solution to avoid attribute errors from cclib during parsing. See issue ReactionMechanismGenerator#134
Temporary solution to avoid attribute errors from cclib during parsing. See issue ReactionMechanismGenerator#134
Temporary solution to avoid attribute errors from cclib during parsing. See issue ReactionMechanismGenerator#134
Temporary solution to avoid attribute errors from cclib during parsing. See issue ReactionMechanismGenerator#134
Temporary solution to avoid attribute errors from cclib during parsing. See issue ReactionMechanismGenerator#134
Temporary solution to avoid attribute errors from cclib during parsing. See issue #134
This error has popped up a few times in my jobs, but is not easily reproducible.
Using the cclib parser on the output file of interest it works correctly, and when I rerun the job keeping the original QM files it also seems to run fine the second time around. However, I have seen this error come up in other jobs.
The best fix may be to rerun MOPAC through a second attempt?
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