{"action":"created","issue":{"url":"https://api.github.com/repos/ReactionMechanismGenerator/RMG-Py/issues/619","repository_url":"https://api.github.com/repos/ReactionMechanismGenerator/RMG-Py","labels_url":"https://api.github.com/repos/ReactionMechanismGenerator/RMG-Py/issues/619/labels{/name}","comments_url":"https://api.github.com/repos/ReactionMechanismGenerator/RMG-Py/issues/619/comments","events_url":"https://api.github.com/repos/ReactionMechanismGenerator/RMG-Py/issues/619/events","html_url":"https://github.com/ReactionMechanismGenerator/RMG-Py/issues/619","id":141851203,"number":619,"title":"KineticsError: Unable to calculate degeneracy in reaction family 1,2_Insertion_carbene","user":{"login":"DetlevCM","id":1845934,"avatar_url":"https://avatars.githubusercontent.com/u/1845934?v=3","gravatar_id":"","url":"https://api.github.com/users/DetlevCM","html_url":"https://github.com/DetlevCM","followers_url":"https://api.github.com/users/DetlevCM/followers","following_url":"https://api.github.com/users/DetlevCM/following{/other_user}","gists_url":"https://api.github.com/users/DetlevCM/gists{/gist_id}","starred_url":"https://api.github.com/users/DetlevCM/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/DetlevCM/subscriptions","organizations_url":"https://api.github.com/users/DetlevCM/orgs","repos_url":"https://api.github.com/users/DetlevCM/repos","events_url":"https://api.github.com/users/DetlevCM/events{/privacy}","received_events_url":"https://api.github.com/users/DetlevCM/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":9,"created_at":"2016-03-18T12:24:39Z","updated_at":"2016-03-22T09:11:55Z","closed_at":null,"body":"This error occurred on a forked build - so I then ran it on (an older) regular RMG-Py install and obtained the same error...\r\n\r\nAt the end of the mechanism, RMG just fails creating an unexpected biradical as well as phenol and a cresol...\r\n\r\n```\r\nError: <Molecule \"[CH2]\">\r\nError: <Molecule \"OC1C=CC=CC=1\">\r\nError: <Molecule \"CC1=CC=CC(O)=C1\">\r\nTraceback (most recent call last): \r\n  File \"/home/irsrvshare2/R10/L0277/DCM_RMG/VPYTH_uptd/RMG-Py/rmg.py\", line 165, in <module>\r\n    rmg.execute(inputFile, output_dir, **kwargs)\r\n  File \"/home/irsrvshare2/R10/L0277/DCM_RMG/VPYTH_uptd/RMG-Py/rmgpy/rmg/main.py\", line 541, in execute\r\n    bimolecularReact=self.bimolecularReact)\r\n  File \"/home/irsrvshare2/R10/L0277/DCM_RMG/VPYTH_uptd/RMG-Py/rmgpy/rmg/model.py\", line 748, in enlarge\r\n    self.processNewReactions(self.react(database, self.core.species[i]), self.core.species[i], None)\r\n  File \"/home/irsrvshare2/R10/L0277/DCM_RMG/VPYTH_uptd/RMG-Py/rmgpy/rmg/model.py\", line 649, in react\r\n    reactionList.extend(database.kinetics.generateReactionsFromFamilies([moleculeA], products=None, only_families=only_families))\r\n  File \"/home/irsrvshare2/R10/L0277/DCM_RMG/VPYTH_uptd/RMG-Py/rmgpy/data/kinetics/database.py\", line 419, in generateReactionsFromFamilies\r\n    reactionList.extend(family.generateReactions(reactants))\r\n  File \"/home/irsrvshare2/R10/L0277/DCM_RMG/VPYTH_uptd/RMG-Py/rmgpy/data/kinetics/family.py\", line 1244, in generateReactions\r\n    reactionList.extend(self.__generateReactions(reactants, forward=False))\r\n  File \"/home/irsrvshare2/R10/L0277/DCM_RMG/VPYTH_uptd/RMG-Py/rmgpy/data/kinetics/family.py\", line 1474, in __generateReactions\r\n    reaction.degeneracy = self.calculateDegeneracy(reaction)\r\n  File \"/home/irsrvshare2/R10/L0277/DCM_RMG/VPYTH_uptd/RMG-Py/rmgpy/data/kinetics/family.py\", line 1272, in calculateDegeneracy\r\n    'but generated {2}').format(reaction, self.label, len(reactions)))\r\nrmgpy.data.kinetics.common.KineticsError: Unable to calculate degeneracy for reaction <Molecule \"[CH2]\"> + <Molecule \"OC1C=CC=CC=1\"> <=> <Molecule \"CC1=CC=CC(O)=C1\"> in reaction family 1,2_Insertion_carbene. Expected 1 reaction but generated 2\r\n```\r\n\r\nOutput from the RMG job including error at the end\r\n[out.log.txt](https://github.com/ReactionMechanismGenerator/RMG-Py/files/179604/out.log.txt)\r\n\r\n(This could potentially be fixed in a newer build of RMG - and it may also be related to a similarly funny issue in RMG Java where two identical biradicals lead to an error termination.)"},"comment":{"url":"https://api.github.com/repos/ReactionMechanismGenerator/RMG-Py/issues/comments/199710324","html_url":"https://github.com/ReactionMechanismGenerator/RMG-Py/issues/619#issuecomment-199710324","issue_url":"https://api.github.com/repos/ReactionMechanismGenerator/RMG-Py/issues/619","id":199710324,"user":{"login":"DetlevCM","id":1845934,"avatar_url":"https://avatars.githubusercontent.com/u/1845934?v=3","gravatar_id":"","url":"https://api.github.com/users/DetlevCM","html_url":"https://github.com/DetlevCM","followers_url":"https://api.github.com/users/DetlevCM/followers","following_url":"https://api.github.com/users/DetlevCM/following{/other_user}","gists_url":"https://api.github.com/users/DetlevCM/gists{/gist_id}","starred_url":"https://api.github.com/users/DetlevCM/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/DetlevCM/subscriptions","organizations_url":"https://api.github.com/users/DetlevCM/orgs","repos_url":"https://api.github.com/users/DetlevCM/repos","events_url":"https://api.github.com/users/DetlevCM/events{/privacy}","received_events_url":"https://api.github.com/users/DetlevCM/received_events","type":"User","site_admin":false},"created_at":"2016-03-22T09:11:55Z","updated_at":"2016-03-22T09:11:55Z","body":"OK, so I switched off the carbene library as there is no literature evidence to suggest it would apply to my case in the liquid phase. (not dealing with ionic liquids or the relevant initiators)\r\n\r\nAnd I got an error again - which to me sounds very much like the issue you described. In fact, RMG reports that it expected 1 reaction and found two.\r\n\r\nThis is the error output (don't think the rest of the log is needed)\r\n\r\n`Adding species C=C1[CH]C([O])=CC=C1(49357) to model core\r\nGenerating thermodynamics for new species...\r\nGenerating kinetics for new reactions...\r\n\r\nSummary of Model Enlargement\r\n---------------------------------\r\nAdded 1 new core species\r\n    C=C1[CH]C([O])=CC=C1(49357)\r\nCreated 0 new edge species\r\nMoved 1 reactions from edge to core\r\n    C=C1[CH]C([O])=CC=C1(49357) <=> C=C1C=CC=C2OC12(40915)\r\nAdded 0 new core reactions\r\nCreated 0 new edge reactions\r\n\r\nAfter model enlargement:\r\n    The model core has 68 species and 183 reactions\r\n    The model edge has 53179 species and 105764 reactions\r\n\r\n\r\nError: Expecting one matching reverse reaction, not 2 in reaction family H_Abstraction for forward reaction <Molecule \"Cc1cccc(O)c1\"> + <Molecule \"[CH2]C1=CC=CC([O])=C1\"> <=> <Molecule \"CC1=CC=CC([O])=C1\"> + <Molecule \"[CH2]c1cccc(O)c1\">.\r\n\r\nError: There is likely a bug in the RMG-database kinetics reaction family involving a missing group, missing atomlabels, forbidden groups, etc.\r\nReactant\r\n1  C u0 p0 c0 {2,S} {9,S} {10,S} {11,S}\r\n2  C u0 p0 c0 {1,S} {4,B} {5,B}\r\n3  C u0 p0 c0 {4,B} {6,B} {8,S}\r\n4  C u0 p0 c0 {2,B} {3,B} {12,S}\r\n5  C u0 p0 c0 {2,B} {7,B} {15,S}\r\n6  C u0 p0 c0 {3,B} {7,B} {13,S}\r\n7  C u0 p0 c0 {5,B} {6,B} {14,S}\r\n8  O u0 p2 c0 {3,S} {16,S}\r\n9  H u0 p0 c0 {1,S}\r\n10 H u0 p0 c0 {1,S}\r\n11 H u0 p0 c0 {1,S}\r\n12 H u0 p0 c0 {4,S}\r\n13 H u0 p0 c0 {6,S}\r\n14 H u0 p0 c0 {7,S}\r\n15 H u0 p0 c0 {5,S}\r\n16 H u0 p0 c0 {8,S}\r\n\r\nReactant\r\nmultiplicity 3\r\n1  C u0 p0 c0 {2,S} {3,D} {7,S}\r\n2  C u0 p0 c0 {1,S} {4,D} {9,S}\r\n3  C u0 p0 c0 {1,D} {6,S} {10,S}\r\n4  C u0 p0 c0 {2,D} {5,S} {8,S}\r\n5  C u0 p0 c0 {4,S} {6,D} {12,S}\r\n6  C u0 p0 c0 {3,S} {5,D} {11,S}\r\n7  C u1 p0 c0 {1,S} {13,S} {14,S}\r\n8  O u1 p2 c0 {4,S}\r\n9  H u0 p0 c0 {2,S}\r\n10 H u0 p0 c0 {3,S}\r\n11 H u0 p0 c0 {6,S}\r\n12 H u0 p0 c0 {5,S}\r\n13 H u0 p0 c0 {7,S}\r\n14 H u0 p0 c0 {7,S}\r\n\r\nProduct\r\nmultiplicity 2\r\n1  C u0 p0 c0 {2,S} {8,S} {9,S} {10,S}\r\n2  C u0 p0 c0 {1,S} {3,S} {4,D}\r\n3  C u0 p0 c0 {2,S} {5,D} {11,S}\r\n4  C u0 p0 c0 {2,D} {6,S} {12,S}\r\n5  C u0 p0 c0 {3,D} {7,S} {13,S}\r\n6  C u0 p0 c0 {4,S} {7,D} {14,S}\r\n7  C u0 p0 c0 {5,S} {6,D} {15,S}\r\n8  H u0 p0 c0 {1,S}\r\n9  H u0 p0 c0 {1,S}\r\n10 H u0 p0 c0 {1,S}\r\n11 H u0 p0 c0 {3,S}\r\n12 H u0 p0 c0 {4,S}\r\n13 O u1 p2 c0 {5,S}\r\n14 H u0 p0 c0 {6,S}\r\n15 H u0 p0 c0 {7,S}\r\n\r\nProduct\r\nmultiplicity 2\r\n1  C u0 p0 c0 {3,B} {4,B} {7,S}\r\n2  C u0 p0 c0 {3,B} {5,B} {8,S}\r\n3  C u0 p0 c0 {1,B} {2,B} {9,S}\r\n4  C u0 p0 c0 {1,B} {6,B} {12,S}\r\n5  C u0 p0 c0 {2,B} {6,B} {10,S}\r\n6  C u0 p0 c0 {4,B} {5,B} {11,S}\r\n7  C u1 p0 c0 {1,S} {13,S} {14,S}\r\n8  O u0 p2 c0 {2,S} {15,S}\r\n9  H u0 p0 c0 {3,S}\r\n10 H u0 p0 c0 {5,S}\r\n11 H u0 p0 c0 {6,S}\r\n12 H u0 p0 c0 {4,S}\r\n13 H u0 p0 c0 {7,S}\r\n14 H u0 p0 c0 {7,S}\r\n15 H u0 p0 c0 {8,S}\r\n\r\nError: Debugging why no reaction was found...\r\nError: Checking whether the family's forbidden species have affected reaction generation...\r\nError: Still experiencing error: Expecting one matching reverse reaction, not 2 in reaction family H_Abstraction for forward reaction <Molecule \"Cc1cccc(O)c1\"> + <Molecule \"[CH2]C1=CC=CC([O])=C1\"> <=> <Molecule \"CC1=CC=CC([O])=C1\"> + <Molecule \"[CH2]c1cccc(O)c1\">.\r\n`\r\n\r\n[expected-1-reac-got-2.txt](https://github.com/ReactionMechanismGenerator/RMG-Py/files/183796/expected-1-reac-got-2.txt)\r\n\r\nIncidentally, RMG Java has an issue with the species called Reactant2 as well and fails, however only with a less informative Species = Species message. \r\n"}}